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  <row Id="1" PostTypeId="1" AcceptedAnswerId="59" CreationDate="2011-12-14T21:17:44.370" Score="25" ViewCount="7383" Body="&lt;p&gt;In prokaryotic translation, how critical for efficient translation is the location of the ribosome binding site, relative to the start codon?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ideally, it is supposed to be -7b away from the start. How about if it is -9 bases away or even more? Will this have an observable effect on translation?&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="338" LastEditDate="2012-02-20T17:42:02.997" LastActivityDate="2012-02-20T17:42:02.997" Title="What is the criticality of the ribosome binding site relative to the start codon in prokaryotic translation?" Tags="&lt;ribosome&gt;&lt;binding-sites&gt;&lt;translation&gt;&lt;synthetic-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="2" PostTypeId="1" AcceptedAnswerId="12" CreationDate="2011-12-14T21:17:48.270" Score="21" ViewCount="1432" Body="&lt;p&gt;Does anyone have any suggestions to prevent RNAse contamination when working with RNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tend to have issues with degradation regardless of whether I use DEPC treated / RNAse free water and filtered pipette tips.&lt;/p&gt;&#xA;" OwnerUserId="12" LastEditorUserId="338" LastEditDate="2012-02-16T11:10:57.530" LastActivityDate="2012-02-16T11:10:57.530" Title="How is RNAse contamination in RNA based experiments prevented?" Tags="&lt;rna&gt;&lt;biochemistry&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3" PostTypeId="1" AcceptedAnswerId="31" CreationDate="2011-12-14T21:17:50.423" Score="22" ViewCount="802" Body="&lt;p&gt;Tortora writes in &lt;em&gt;Principles of Anatomy and Physiology&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Lymphocytes may be as small as 6–9 μm in diameter or as large as 10–14 μm in diameter.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Those ranges are quite close to each others. Should the above be taken to mean that lymphocytes sizes are clustered in two groups, or is it just a way of saying that lymphocytes are 6-14 μm?&lt;/p&gt;&#xA;" OwnerDisplayName="user24" LastEditorUserId="66" LastEditDate="2012-01-22T10:34:58.940" LastActivityDate="2012-01-22T10:34:58.940" Title="Are lymphocyte sizes clustered in two groups?" Tags="&lt;immunology&gt;&lt;cell-biology&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4" PostTypeId="1" AcceptedAnswerId="105" CreationDate="2011-12-14T21:19:43.527" Score="28" ViewCount="20147" Body="&lt;p&gt;Various people in our lab will prepare a liter or so of LB, add kanamycin to 25-37 mg/L for selection, and store it at 4 °C for minipreps or other small cultures (where dosing straight LB with a 1000X stock is troublesome).  Some think using it after more than a week is dubious, but we routinely use kan plates that are 1-2 months old with no ill effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How long can LB with antibiotic such as kanamycin, chloramphenicol, or ampicillin be stored at 4 °C and maintain selection?&lt;/p&gt;&#xA;" OwnerUserId="25" LastEditorUserId="25" LastEditDate="2011-12-15T14:12:51.133" LastActivityDate="2018-10-03T13:40:21.967" Title="How long does antibiotic-dosed LB maintain good selection?" Tags="&lt;cell-culture&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5" PostTypeId="1" AcceptedAnswerId="24" CreationDate="2011-12-14T21:22:40.450" Score="19" ViewCount="2544" Body="&lt;p&gt;Are there any cases in which the splicing machinery constructs an mRNA in which the exons are not in the 5' -&gt; 3' genomic order? I'm interested any such cases, whether they involve constitutive or alternative splicing.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2011-12-14T21:56:20.140" LastActivityDate="2012-09-13T08:36:24.423" Title="Is exon order always preserved in splicing?" Tags="&lt;splicing&gt;&lt;mrna&gt;&lt;spliceosome&gt;&lt;introns&gt;&lt;exons&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="6" PostTypeId="1" AcceptedAnswerId="51" CreationDate="2011-12-14T21:23:42.183" Score="10" ViewCount="314" Body="&lt;p&gt;I'm interested in sequencing and analyzing the bound DNA, and minimizing the amount of unbound DNA that gets sequenced through digestion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When digesting protein-bound DNA, is &lt;em&gt;all&lt;/em&gt; of the unbound DNA digested? Is there a way to maximize the amount of unbound DNA that is digested?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="25" LastEditDate="2011-12-15T00:00:48.087" LastActivityDate="2012-04-06T17:19:23.543" Title="How can I avoid digesting protein-bound DNA?" Tags="&lt;dna&gt;&lt;biochemistry&gt;&lt;molecular-biology&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8" PostTypeId="1" AcceptedAnswerId="48" CreationDate="2011-12-14T21:26:00.387" Score="17" ViewCount="519" Body="&lt;p&gt;I'm looking for resources or any information about the formation of dendritic spines and synaptogenesis, especially in relation to how new connections are formed on a daily basis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the electrotonic signalling along the axons and through the spines cause new connections to be made based on some kind of spatial condition (maybe an electrical or chemical attraction), or is there some larger heuristic here?&lt;/p&gt;&#xA;" OwnerUserId="35" LastEditorUserId="36209" LastEditDate="2017-11-03T04:45:16.193" LastActivityDate="2017-11-03T04:45:16.193" Title="Under what conditions do dendritic spines form?" Tags="&lt;neuroscience&gt;&lt;synapses&gt;&lt;dendritic-spines&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9" PostTypeId="1" AcceptedAnswerId="36" CreationDate="2011-12-14T21:26:35.037" Score="28" ViewCount="12286" Body="&lt;p&gt;I shipped 10 µL of my vector miniprep to a collaborator in a 1.5 mL eppendorf parafilmed shut and stuffed into a 50 mL conical with some paper-towel padding.  However, something happened on the way and there was nothing (no liquid) in the tube when it arrived.  They didn't make any comments about the microcentrifuge tube popping open or broken parafilm, so nothing crazy happened but something did.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the most reliable way to ship plasmids?&lt;/p&gt;&#xA;" OwnerUserId="25" LastActivityDate="2013-01-14T14:55:40.767" Title="How should I ship plasmids?" Tags="&lt;plasmids&gt;" AnswerCount="6" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10" PostTypeId="1" AcceptedAnswerId="22" CreationDate="2011-12-14T21:29:09.537" Score="18" ViewCount="560" Body="&lt;p&gt;I noticed within example experiments in class that different reporter genes are chosen to be inserted near your gene of interest to prove whether or not the gene is being expressed. For example, you may insert the gene for fluorescence next to your gene of interest so you know if it is transcribed or not by whether the organism's cells are fluorescent and to what degree they are fluorescing at.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have noticed in some experiments that have multiple versions that in one case they use the fluorescent gene and in the next a different gene (for example lactose). Both portions of the experiment use almost the exact same steps so why would they not choose the same reporter gene?&lt;/p&gt;&#xA;" OwnerUserId="19" LastEditorUserId="444" LastEditDate="2012-04-19T13:25:19.893" LastActivityDate="2013-12-16T05:21:04.960" Title="What is the reason behind choosing the reporter gene when experimenting on your gene of interest?" Tags="&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;experimental-design&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11" PostTypeId="1" AcceptedAnswerId="60" CreationDate="2011-12-14T21:30:09.820" Score="23" ViewCount="4088" Body="&lt;p&gt;According to the endosymbiont theory, mitochondria and chloroplasts originated as bacteria which were engulfed by larger cells. How many times is it estimated that this occurred in the past? Are there any examples of this process being observed directly?&lt;/p&gt;&#xA;" OwnerUserId="37" LastEditorDisplayName="user59" LastEditDate="2011-12-14T21:50:36.617" LastActivityDate="2014-01-09T06:12:42.767" Title="How many times did endosymbiosis occur?" Tags="&lt;evolution&gt;&lt;mitochondria&gt;&lt;chloroplasts&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="12" PostTypeId="2" ParentId="2" CreationDate="2011-12-14T21:32:23.100" Score="14" Body="&lt;p&gt;You need to be careful about everything that comes in contact with your samples. Every spatula, beaker and every magnetic stir bar need to be RNAse-free. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For metal- and glassware we usually put everything into a drying closet at 200-250 °C for a few hours. That should get rid of RNAses pretty efficiently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The RNA chemicals should be seperated from other chemicals if not everyone in the lab is working with RNA. They shouldn't be weighed using spatulas, but just poured into an RNAse-free container to avoid contaminating the storage container.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Use disposable plastic wherever possible, you should be able to perform most stuff in falcons and Eppendorf tubes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Be careful with performing e.g. a DNA-prep at the same bench as the RNA work. The first buffer for the DNA-prep contains RNAse.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Avoid keeping your Eppendorf tubes or falcons open for long, that should reduce the potential for contamination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We've had pretty good experience with just using water from a Millipore system and autoclave it once, that seems to get rid of the RNAses. I know that this is not a sure thing as the RNAses can survive autoclaving, but it seems to work well enough.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2011-12-14T21:39:44.297" LastActivityDate="2011-12-14T21:39:44.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13" PostTypeId="1" CreationDate="2011-12-14T21:32:47.473" Score="12" ViewCount="1679" Body="&lt;p&gt;In high-throughput experiments where cells are cultured, treated, stained, and imaged in 384-well microplates, I frequently see significant edge effects. For instance, the following plot shows cell count (as measured by &lt;a href=&quot;http://cellprofiler.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;CellProfiler&lt;/a&gt; from images) for each well on such a plate:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RI3IQ.png&quot; alt=&quot;Example of edge effects&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can I reduce these effects? I can try to correct for them statistically, but it would be so much nicer to reduce them at the wet-work stage.&lt;/p&gt;&#xA;" OwnerUserId="23" LastActivityDate="2012-05-11T17:28:27.567" Title="How to reduce edge effects in cell-based high-throughput experiments?" Tags="&lt;high-throughput&gt;&lt;cell-based&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14" PostTypeId="2" ParentId="2" CreationDate="2011-12-14T21:33:06.500" Score="13" Body="&lt;p&gt;Here are some tips from what I routinely do:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;wipe all the surfaces (including pipettes and gloves) with RNAse Away or similar&lt;/li&gt;&#xA;&lt;li&gt;do everything on ice&lt;/li&gt;&#xA;&lt;li&gt;use a RNAse/DNAse free tubes. Use also commercial RNAse free water (it's worth the investment).&lt;/li&gt;&#xA;&lt;li&gt;keep all your RNA reagents separate from your cell culture/animal work reagents. Autoclave all your buffers and don't let them sit forever. Just make fresh buffers every now and then.&lt;/li&gt;&#xA;&lt;li&gt;don't talk over the tubes&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you keep having degradation following all the above, consider how you prepare your sample. Do you have enough RNAse inhibitors in there? Do you use a RNA-conserving solution? Is your tissue sitting for a long time before the lysis? If your extracting RNA from cells, try using trizol or a similar reagent to preserve the RNA right from the lysis. If your getting the RNA from tissue samples, try snap freezing them in liquid nitrogen.&lt;/p&gt;&#xA;" OwnerUserId="48" LastActivityDate="2011-12-14T21:33:06.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16" PostTypeId="1" AcceptedAnswerId="42" CreationDate="2011-12-14T21:36:18.410" Score="7" ViewCount="853" Body="&lt;p&gt;Has anyone tried the chew back-anneal in vitro DNA assembly method (known as Gibson Assembly) for difficult sequences, like GC-rich sequences? How big constructs could you efficiently assemble? Did you use the original protocol or some optimizations?&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="338" LastEditDate="2012-02-20T17:42:16.507" LastActivityDate="2014-10-15T09:35:11.977" Title="Has anyone tried Gibson Assembly Optimizations?" Tags="&lt;molecular-biology&gt;&lt;synthetic-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17" PostTypeId="2" ParentId="9" CreationDate="2011-12-14T21:37:15.867" Score="12" Body="&lt;p&gt;Did they try to centrifuge the tube when it got there to push all the liquid to the bottom? I know that especially when working with such little amounts that even shaking it up a little can disperse the contents all over the tube.&#xA;We have received plasmids from other labs before. Generally speaking the plasmids are sent in Screw-cap microcentrifuge tubes inside of some sort of canister. This is then packaged in a little foam cooler with dry ice to keep everything cold.&lt;/p&gt;&#xA;" OwnerUserId="41" LastActivityDate="2011-12-14T21:37:15.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="18" PostTypeId="2" ParentId="9" CreationDate="2011-12-14T21:38:37.183" Score="17" Body="&lt;p&gt;A quite safe way of shipping plasmids is to put them on filter paper (see &lt;a href=&quot;http://www0.hku.hk/biochem/research/tcf/protocols/Plasmid_shipment.html&quot;&gt;protocol&lt;/a&gt; and send a letter. Much cheaper.&lt;/p&gt;&#xA;" OwnerUserId="34" LastActivityDate="2011-12-14T21:38:37.183" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20" PostTypeId="2" ParentId="13" CreationDate="2011-12-14T21:42:56.987" Score="12" Body="&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1177/108705710325646&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lundholt et al.&lt;/a&gt; describe a very simple trick: let the plates settle in air at room temperature for a couple of hours before placing it in the incubator. We tried it out, and although the color scales are different in the following plots, it is easy to see that it really does help:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IBZJA.png&quot; alt=&quot;Transferred directly to incubator&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/6Eagk.png&quot; alt=&quot;Left out for 1 h&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/urgx8.png&quot; alt=&quot;Left out for 2 h&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Thanks to Sigrun Gustafsdottir and Kate Madden for testing this.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have seen some people &quot;pad&quot; the plate by using only the 308 interior wells and filling the  76 edge wells with only liquid, but I have no data for how well that works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Allison Tanner from Corning has &lt;a href=&quot;http://catalog2.corning.com/Lifesciences/media/pdf/an_hintsedgeeffecthts.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;collected&lt;/a&gt; a compendium of techniques to reduce the occurrence of irregular patterns of cell adhesion or “edge effect” in microplates. Brifly summarized:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Avoid bubble formation in the media when seeding cells.&lt;/li&gt;&#xA;&lt;li&gt;Use cell harvesting methods that foster adequate mixing of the cells in the media and complete dissociation of the monolayer into single cells.&lt;/li&gt;&#xA;&lt;li&gt;Seed cells at a density that will support attachment and growth.&lt;/li&gt;&#xA;&lt;li&gt;Allow cell attachment to occur in media of the proper formulation for the particular cell type.&lt;/li&gt;&#xA;&lt;li&gt;Dispense cells in an appropriate volume of media.&lt;/li&gt;&#xA;&lt;li&gt;Follow strict aseptic techniques according to respected microbiological practices.&lt;/li&gt;&#xA;&lt;li&gt;Cultures should be routinely monitored for mycoplasmal contamination.&lt;/li&gt;&#xA;&lt;li&gt;Minimize entrance to incubators to help reduce fluctuations in the internal environment.&lt;/li&gt;&#xA;&lt;li&gt;Allow cells to settle in the microplates while the microplates are on the benchtop.&lt;/li&gt;&#xA;&lt;li&gt;Culture cells in an environment that reduces the formation of static electrical charges.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="23" LastEditorUserId="23" LastEditDate="2012-05-11T17:28:27.567" LastActivityDate="2012-05-11T17:28:27.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22" PostTypeId="2" ParentId="10" CreationDate="2011-12-14T21:45:01.253" Score="13" Body="&lt;p&gt;Different genes will serve different purposes. For example, if you want to perform colocalization studies, then fluorescent genes like eGFP and DS-Red (or any variation of those, namely Emerald, mCherry, etc) will be quite useful, since you can use different filters on your microscope for the various fluorophores. For morphological assessments, perhaps a LacZ gene or alkaline phosphatase may be better suited, since the detection of these enzymes is compatible with standard histological techniques and you get usually much better contrast than with fluorescence. For quantification purposes, you would use probably firefly luciferase or CAT, since there are very good quantitative assays for these enzymes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The decision will also depend on the degree of experience of the lab with each detection technique and even in the availability of the constructs. If a reporter is already made by the lab next door and if it fits your needs, you'll just use it, instead of creating your own, even if the reporter gene would not have been your first choice.&lt;/p&gt;&#xA;" OwnerUserId="48" LastActivityDate="2011-12-14T21:45:01.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23" PostTypeId="1" AcceptedAnswerId="26" CreationDate="2011-12-14T21:47:06.820" Score="17" ViewCount="334" Body="&lt;p&gt;The whole question is&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What is the optimal frame size for the second and third generation protein secondary structure prediction methods? Justify your answer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I remember it has something to do with the average length of alpha-helix. More specifically, 3 on both side of a site. So in total the frame length should be 7. But I can't remember the reason behind the argument.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do you think?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;According to what my professor said in class, 2nd and 3rd generation of protein secondary structure reconstruction relies on statistics data of several consecutive residues.  I guess what he meant by &quot;frame size&quot;, is how many adjacent residues we should take into account in the algorithm.&lt;/p&gt;&#xA;" OwnerUserId="44" LastEditorUserId="112" LastEditDate="2011-12-15T08:33:31.000" LastActivityDate="2012-12-04T17:56:25.030" Title="What is the optimal frame size for protein secondary structure prediction methods?" Tags="&lt;bioinformatics&gt;&lt;homework&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24" PostTypeId="2" ParentId="5" CreationDate="2011-12-14T21:52:58.423" Score="13" Body="&lt;p&gt;I don't have any literature to back this up but I doubt that it occurs (at least frequently). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, imagine a simple three exon gene.  Upon splicing &lt;code&gt;exon 1&lt;/code&gt; to &lt;code&gt;exon 3&lt;/code&gt;, &lt;code&gt;exon 2&lt;/code&gt; would be excised as part of the intron lariat and subsequently degraded.  So in order for exon 2 to be spliced to exon three you would need to either have splicing between &lt;code&gt;exon 3&lt;/code&gt; and &lt;code&gt;exon 2&lt;/code&gt; in the lariat or another copy of the pre-mRNA.  This is typically called &lt;a href=&quot;http://en.wikipedia.org/wiki/Trans-splicing&quot;&gt;trans-splicing&lt;/a&gt; but it only occurs in specialized systems such as spliced-leader sequences in &lt;em&gt;C. elegans&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="12" LastActivityDate="2011-12-14T21:52:58.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25" PostTypeId="2" ParentId="8" CreationDate="2011-12-14T21:53:45.927" Score="12" Body="&lt;p&gt;Dendritic spines are thought to grow and recede under LTP and LTD, respectively. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21963169&quot; rel=&quot;nofollow&quot;&gt;(Bosch and Hayoshi 2011)&lt;/a&gt; for a review.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From there, much of the synaptogenesis occurs due to surface molecules present both on the dendrite and the presynaptic axon in the growth cone.  Localization and guidance are achieved through gradients of growth factors in the developing nervous system  See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21123392&quot; rel=&quot;nofollow&quot;&gt;(Kolodkin and Tessier-Lavigne 2011)&lt;/a&gt; for a review of all of these mechanics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How this maps back onto the human CNS and thinking/learning/memorizing is still up for debate, but some of these mechanisms must have been preserved in higher species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;References:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bosch M, Hayashi Y. (2012) Structural plasticity of dendritic spines. &lt;em&gt;Curr Opin Neurobiol.,22&lt;/em&gt;(3):383-8. (Epub 2011 Sep 28).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kolodkin AL, Tessier-Lavigne M. (2011). Mechanisms and molecules of neuronal wiring: a primer. &lt;em&gt;Cold Spring Harb Perspect Biol., 3&lt;/em&gt;(6). &lt;a href=&quot;http://dx.doi.org/10.1101/cshperspect.a001727&quot; rel=&quot;nofollow&quot;&gt;[DOI]&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-07-30T04:14:13.990" LastActivityDate="2012-07-30T04:14:13.990" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26" PostTypeId="2" ParentId="23" CreationDate="2011-12-14T21:57:19.003" Score="11" Body="&lt;p&gt;By frame size, do you mean sliding window?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that if you want to predict a secondary structure of a transmembrane protein, then your window size should be 20 amino acids (this is the average length of 1 transmembrane alpha helix spanning through the membrane). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found &lt;a href=&quot;http://dx.doi.org/10.1109/CIBCB.2006.330959&quot; rel=&quot;nofollow&quot;&gt;this paper by Chen, Kurgan, and Ruan&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It basically says that the window size depends on what kind of pattern you are looking for, but in general, 19 residues should be optimal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, secondary structure predictors rely on many features like hydrophobicity, missing coordinates in X-ray structures, B-factors, motifs, etc.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1109/CIBCB.2006.330959&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Chen K, Kurgan L, Ruan J&lt;/strong&gt;. 2006. Optimization of the Sliding Window Size for Protein Structure Prediction. CIBCB '06: 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, pp.1-7, 28-29, doi:10.1109/CIBCB.2006.330959.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="28" LastEditorUserId="43" LastEditDate="2012-12-04T17:56:25.030" LastActivityDate="2012-12-04T17:56:25.030" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27" PostTypeId="1" AcceptedAnswerId="39" CreationDate="2011-12-14T22:05:50.790" Score="17" ViewCount="237" Body="&lt;p&gt;We know from pop science that our psychological states have an effect on our immune systems (&quot;worrying ourselves sick&quot;, etc.), but what are the actual mechanisms through which our nervous systems pass information to the immune system?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cell mediators come to mind, but where in the body would a nerve cell release an interleukin or other factor? (Put another way, are neurons releasing these factors as a part of their normal cell metabolism and the side effect is a communicative effect with the immune system?)&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorDisplayName="user132" LastEditDate="2011-12-15T19:24:12.747" LastActivityDate="2016-06-24T03:10:37.183" Title="What are the main mechanisms of interaction between the nervous and immune systems?" Tags="&lt;neuroscience&gt;&lt;immunology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28" PostTypeId="1" AcceptedAnswerId="80" CreationDate="2011-12-14T22:11:46.060" Score="11" ViewCount="109" Body="&lt;p&gt;There are some bioinformatical considerations showing that there is a significant correlation of some between histone code and alternative splicing; but what are the hypothesis about the underlying mechanisms? Is there any experimental insight in the problem?&lt;/p&gt;&#xA;" OwnerDisplayName="user59" LastEditorUserId="948" LastEditDate="2014-01-13T21:36:30.677" LastActivityDate="2014-01-13T21:36:30.677" Title="What are the mechanism binding histone code with alternative splicing?" Tags="&lt;splicing&gt;&lt;histone&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29" PostTypeId="1" AcceptedAnswerId="41" CreationDate="2011-12-14T22:11:58.087" Score="9" ViewCount="217" Body="&lt;p&gt;I recently downloaded gene annotations for &lt;em&gt;Homo sapiens&lt;/em&gt; from Ensembl for some bioinformatic analysis. The vast majority of the gene annotations have 20 exons or less, although there are some that have as many as 250. I know enough about gene annotation to take these predictions with a grain of salt, but it got me thinking...what are the biologically relevant factors that might limit the length, exon number, etc of a gene? Is there any real possibility for a gene to have 50 exons? 100 exons? 250 exons? From a biological standpoint, where is the line drawn and why?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="4101" LastEditDate="2013-08-28T01:41:15.717" LastActivityDate="2013-08-28T01:41:15.717" Title="What are the limiting factors for gene length and number of exons?" Tags="&lt;genomics&gt;&lt;gene-annotation&gt;&lt;exons&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30" PostTypeId="2" ParentId="5" CreationDate="2011-12-14T22:13:21.310" Score="16" Body="&lt;p&gt;After performing a quick literature search, I am, as with GWW, unable to provide any literature against this occurring, although this paper by Black (2005) states that exons in multi-exon pre-mRNAs are always maintained in order.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0501414102&quot;&gt; &lt;strong&gt;Black DL&lt;/strong&gt;. 2005. A simple answer for a splicing conundrum. Proceedings of the National Academy of Sciences of the United States of America 102: 4927–8.&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Separate components of the spliceosome recognise sequences at the the start and end of each intron, along with a branch point adenine and some other conserved (highly in the case of yeast) regions upstream of the 3' end. The components seem to assemble in a particular order, which is 5' to 3' directional.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The general consensus seems to be that the spliceosome moves along the pre-mRNA from 5' to 3' removing the introns and splicing the exons together to form the mature transcript, ready for translation. The introns are subsequently degraded. In the case of eukaryotes some processing is required to transport the mRNA out of the nucleus to the ribosomes in the cytoplasm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mRNA would have a start codon near the 5' terminus and stop codon near the 3' end, at the boundaries of the CDS, and it isn't clear to me how this structure could be maintained if exon order didn't follow the 5' to 3' assemblage. I should imagine that the protein could be affected in much a similar way to exon skipping, possibly resulting in a truncated, inactive or ineffective protein. As protein folding is determined by the interactions between the amino acids, any change in exon order (secondary structure) is likely to result in a different tertiary structure.&lt;/p&gt;&#xA;" OwnerDisplayName="user49" LastEditorUserId="836" LastEditDate="2012-09-13T06:22:56.440" LastActivityDate="2012-09-13T06:22:56.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31" PostTypeId="2" ParentId="3" CreationDate="2011-12-14T22:20:18.817" Score="20" Body="&lt;p&gt;Unlike erythrocytes that have a very rigid shape and almost cannot change their size (hence the size distribution is indicative and can be used &lt;a href=&quot;http://en.wikipedia.org/wiki/Red_blood_cell_distribution_width&quot;&gt;for diagnostic purposes in medicine&lt;/a&gt;), lymphocytes can change their size in a wider range, this is why you see the numbers 6-9 and 10-15 μm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And they indeed cluster into several different groups: so-called &quot;large granular lymphocytes&quot;, also known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Natural_killer_cell&quot;&gt;NK-cells&lt;/a&gt; or &quot;natural killers&quot; (usually &gt;10μm) and &quot;small granular lymphocytes&quot;, constituted by a large family of &lt;a href=&quot;http://en.wikipedia.org/wiki/T_cell&quot;&gt;T-&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/B_cell&quot;&gt;B-lymphocites&lt;/a&gt;(usually &amp;lt;10μm). But this clustering is not really distinct, for as I said above, both NK and T/B-cells can shrink (if the osmolarity of the external medium grows due to acidosis, inflammation etc.) and swell (on binding many IgE/IgG complexes, on certain cell factor released etc.). Besides, there are also some intermediate size cells, called &lt;a href=&quot;http://en.wikipedia.org/wiki/Natural_Killer_T_cell&quot;&gt;NKT-cells&lt;/a&gt;, that also flatten the distribution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what you can definitely say is that the typical size distribution of lymphocytes has two peaks: around 8 and 12 μm respectively.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="69" LastEditDate="2012-01-04T05:09:26.713" LastActivityDate="2012-01-04T05:09:26.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32" PostTypeId="1" AcceptedAnswerId="34" CreationDate="2011-12-14T22:20:30.643" Score="20" ViewCount="3822" Body="&lt;p&gt;What do the strain designations for flu mean?&lt;br&gt;&#xA;For example avian flu is classified as &lt;code&gt;H5N1&lt;/code&gt;, what do the letters &lt;code&gt;H&lt;/code&gt;, &lt;code&gt;N&lt;/code&gt; and numbers &lt;code&gt;5&lt;/code&gt;, &lt;code&gt;1&lt;/code&gt; mean? Is it more than a simple string-identifier?&lt;/p&gt;&#xA;" OwnerUserId="61" LastEditorUserId="4101" LastEditorDisplayName="user132" LastEditDate="2015-06-02T14:35:23.777" LastActivityDate="2015-06-02T14:35:23.777" Title="How to understand influenza strain designations?" Tags="&lt;microbiology&gt;&lt;virology&gt;&lt;influenza&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="33" PostTypeId="1" AcceptedAnswerId="44" CreationDate="2011-12-14T22:26:55.820" Score="15" ViewCount="4093" Body="&lt;p&gt;I know the basics of epigenetics, but I do not know how epigenetic mechanisms are transmitted from parents to children (or if there is even enough literature to derive a consensus). My question is relates to surrogate motherhood, in which an egg is fertilized &lt;em&gt;in vitro&lt;/em&gt; and then implanted in the womb of a woman other than the egg donor. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are all the factors that affect epigenetic mechanisms encoded in the genome? Is it possible for the surrogate mother's epigenetics to influence the epigenetics of the child/children?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2012-02-20T18:12:53.977" LastActivityDate="2019-07-29T09:35:01.023" Title="Transmission of epigenetic regulation through surrogate mother" Tags="&lt;epigenetics&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34" PostTypeId="2" ParentId="32" CreationDate="2011-12-14T22:30:26.767" Score="22" Body="&lt;p&gt;The sub-type is named for the broad classes of the hemagglutinin (HA) or neuraminidase (NA) surface proteins sticking through the viral envelope. There are 16 HA sub-types (designated H1 - H16) and 9 NA sub-types (designated N1 - N9). All of the possible combinations of these influenza A subtypes infect birds, but only those containing the H1, H2, H3, H5, H7 and H9 and the N1, N2 and N7 surface proteins infect humans, and of these, so far, only H1, H2, H3 and N1 and N2 do so to any extent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Read more: &lt;a href=&quot;http://www.fluwiki.info/pmwiki.php?n=Science.NamingInfluenzaViruses&quot;&gt;http://www.fluwiki.info/pmwiki.php?n=Science.NamingInfluenzaViruses&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="79" LastActivityDate="2011-12-14T22:30:26.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35" PostTypeId="2" ParentId="32" CreationDate="2011-12-14T22:31:16.847" Score="9" Body="&lt;p&gt;The two letters represent the type of hemagglutinin (H) and neuraminidase (N) present on the viral surface. Those are the major surface proteins of the influenza virus and therefore crucial for the immune response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2380/#A214&quot;&gt;Immunology and Evolution of Infectious Disease&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;HA and NA reactivities with antibodies define the subtypes of&#xA;  influenza A (Cox and Subbarao 2000). Fifteen different HA antigenic&#xA;  subtypes occur, each subtype cross-reacting relatively little with the&#xA;  other subtypes. Nine distinct NA subtypes are known. The designation&#xA;  HxNy describes an influenza subtype with HA antigenic subtype x =&#xA;  1,...,15 and NA antigenic subtype y = 1,...,9.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The numbers represent different subtypes of the hemagglutinin and neuraminidase proteins.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2011-12-14T22:31:16.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36" PostTypeId="2" ParentId="9" CreationDate="2011-12-14T22:36:41.263" Score="12" Body="&lt;p&gt;&lt;strong&gt;Summary&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the 10 uL of plasmid miniprep may have been splattered in the cap of the tube (AnnaF)&lt;/li&gt;&#xA;&lt;li&gt;the eppendorf tube may have depressurized during air shipment and allowed the 10 uL to escape and evaporate&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;solution:&lt;/strong&gt; try air-drying or blotting (Jonas) your minipreps prior to air shipment &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Details&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As AnnaF wrote, the 10 uL of your plasmid could have been hidden in the cap or dispersed around the tube, making appear empty.  You should check with your collaborators to be sure they centrifuged it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to a &lt;a href=&quot;http://www.fedex.com/us/services/pdf/PKG_Pointers_Perishable.pdf&quot;&gt;fedex document on shipping perishables (pdf)&lt;/a&gt; and a &lt;a href=&quot;http://digitalcommons.calpoly.edu/cgi/viewcontent.cgi?article=1038&amp;amp;context=it_fac&quot;&gt;paper measuring the temp and pressure of air shipments (pdf)&lt;/a&gt;, fedex and ups air shipments may experience low pressure environments around 0.56 - 0.74 atmospheres (atm).  At these relatively low pressures, perhaps an eppendorf tube sealed at 1 atm might breach.  The papers also note that ground shipments that pass over the rockies (i.e. in Colorado) may experience ~ 0.64 atm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So perhaps your 1.5 ml eppendorf tube depressurized during the shipment?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be interesting to do some tests on the pressure-worthiness of eppendorf tubes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the original question, in 2007 I prepared and shipped (fedex) a library of thousands of minipreps to hundreds of users.  1uL of miniprep was dispensed into wells of 384-well plates and airdried, then sealed with aluminum, then mailed.  Users rehydrate a well with 10 uL of water.  Generally it works.&lt;/p&gt;&#xA;" OwnerUserId="51" LastActivityDate="2011-12-14T22:36:41.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="37" PostTypeId="2" ParentId="32" CreationDate="2011-12-14T22:36:50.217" Score="9" Body="&lt;p&gt;Adding to the other answers posted: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hemagglutinin  (HA or H) -  Helps the virus enter the cell by binding to sialic acid receptors on cell membrane. It then unfolds in a lysosome and fuses the viral and lysosome membranes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neuraminidase (NA or N) - Helps the virus exit the cell by cleaving the terminal sialic acid residues at the progeny virus release.&lt;/p&gt;&#xA;" OwnerUserId="78" LastActivityDate="2011-12-14T22:36:50.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="38" PostTypeId="1" AcceptedAnswerId="55" CreationDate="2011-12-14T22:39:06.687" Score="5" ViewCount="1122" Body="&lt;p&gt;I'm trying to find a good protocol for plasmid minipreps and I'm looking at 3 preps I've found:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://openwetware.org/wiki/One_step_%27miniprep%27_method_for_the_isolation_of_plasmid_DNA&quot; rel=&quot;nofollow&quot;&gt;Using phenol/chloroform&lt;/a&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;extract with phenol:chloroform:isoamylalcohol,&lt;/li&gt;&#xA;&lt;li&gt;isopropanol precipitation, 12,000g spin down,&lt;/li&gt;&#xA;&lt;li&gt;rinse with cold 70% ethanol. &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://openwetware.org/wiki/Miniprep/Kit-free_high-throughput_protocol&quot; rel=&quot;nofollow&quot;&gt;Using lysozyme&lt;/a&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;lyse with lysozyme,&lt;/li&gt;&#xA;&lt;li&gt;remove pellet, &lt;/li&gt;&#xA;&lt;li&gt;isopropanol precipitation,&lt;/li&gt;&#xA;&lt;li&gt;wash with cold 80% ethanol.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://biotech.biology.arizona.edu/labs/DNA_isolation_plasmid.html&quot; rel=&quot;nofollow&quot;&gt;Using alkaline lysis&lt;/a&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;open cells with 80% glucose in EDTA buffer,&lt;/li&gt;&#xA;&lt;li&gt;add SDS and NaOH,&lt;/li&gt;&#xA;&lt;li&gt;pellet protein/membrane with acetic acid/acetate,&lt;/li&gt;&#xA;&lt;li&gt;ispropanol precipitation,&lt;/li&gt;&#xA;&lt;li&gt;wash with cold 70% ethanol.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;They all differ in how to break open the cells and separate plasmids from the rest of the cell -- quite a bit.  Can anyone help me figure out which protocol is best here? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="6" LastEditDate="2011-12-22T10:27:15.480" LastActivityDate="2014-02-01T02:25:23.700" Title="What is a good miniprep protocol for the class room?" Tags="&lt;molecular-biology&gt;&lt;dna-isolation&gt;" AnswerCount="5" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="39" PostTypeId="2" ParentId="27" CreationDate="2011-12-14T22:40:13.317" Score="14" Body="&lt;p&gt;It is not only the immune system that prevents us from getting ill. Worrying much in my opinion won't make you catch a cold; rather, you can get problems with your cardiovascular system (arrhythmias, hypertension, angina pectoris) or limbic system (panic attacks, sweating attacks etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The connections are many; here are some possible ones:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;There are many glands in our body that are either densely innervated (like the thyroid gland) or are a part of nervous system (like pituitary gland, epiphysis). They can release hormones directly to our blood and make our hormone profile unstable, hence also impacting the immune system.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Sympathetic/parasympathetic nervous system is under direct control of the CNS (N.vagus, carotide sinus sinus etc.) and can dramatically change the peripheral resistance of our vascular system by constricting (=&gt; angina pectoris, hypertension) or dilating (swellings, bowel movements problems -&gt; constipations etc.) the small vessel. This alone can start so many different mechanisms resulting not only in being ill, but also being dead.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Speaking about connection between the nervous and immune system we must consider that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Many neuromediators, like adrenaline, for example, have clear effects on immune cells.&lt;/li&gt;&#xA;&lt;li&gt;The mediators and humoral factors released by nerve endings can easily diffuse outside of the synaptic cleft and act locally, attenuating immune response.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="66" LastEditorDisplayName="user132" LastEditDate="2011-12-15T19:22:50.893" LastActivityDate="2011-12-15T19:22:50.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="40" PostTypeId="2" ParentId="23" CreationDate="2011-12-14T22:40:35.267" Score="3" Body="&lt;p&gt;I found that 13 worked best for Neural Nets and SVM performance of secondary structure information when I ran this in R.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2011-12-14T22:40:35.267" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="41" PostTypeId="2" ParentId="29" CreationDate="2011-12-14T22:43:36.957" Score="10" Body="&lt;p&gt;This question drops firmly into the lap of molecular evolution and the constraints that are placed upon genes by the forces of mutation, selection, drift and recombination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are numerous situations, particularly gene duplication, that can result in a gene that is free from the selective constraints of it's parent, many of which will accumulate so many deleterious mutations as a result of stochastic processes that they will become non-functional e.g. psuedogenes. Some can be altered and rearranged, accumulating exons and introns, and if they infer a fitness benefit on the organism, may be moved to fixation within a population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution is a population genetics process, and there are many variables which can effect the outcome, not least the difference in populations size. The genomes of larger populations (such as those of bacteria) appear to have much smaller genomes, and of course no (at least not spliceosomal) introns, perhaps as a result of increased fitness due to the decreased generation time of an organism with a more slender genome. It would be a good idea to read &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0878934847&quot;&gt;The Origins of Genome Architecture&lt;/a&gt; by &lt;a href=&quot;http://www.indiana.edu/~lynchlab/&quot;&gt;Michael Lynch&lt;/a&gt;, as I think he answers your questions, better than I can.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many of the genes you retrieve from EnsEMBL will of course have experimental evidence to support them. The genes that are predicted in the pipeline can be looked upon with less confidence, but you can of course look at the alignments with closely related species to see if you think the introns/exons are indeed viable. An example of a gene with 79 exons is the Dystrophin (DMD) gene, the longest annotated gene at 2,217,347bp (see &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0888754383712255&quot;&gt;Roberts et al, 1993&lt;/a&gt; and &lt;a href=&quot;http://www.jci.org/articles/view/117417&quot;&gt;Nishio et al, 1994&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerDisplayName="user49" LastEditorDisplayName="user49" LastEditDate="2011-12-14T23:47:03.850" LastActivityDate="2011-12-14T23:47:03.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="42" PostTypeId="2" ParentId="16" CreationDate="2011-12-14T22:47:18.187" Score="5" Body="&lt;p&gt;I haven't tried Gibson Assembly myself, but I do know the &lt;a href=&quot;http://2011.igem.org/Team%3aCambridge/Project/Gibthon#/Project/Gibthon&quot;&gt;Cambridge iGEM Team in 2010 and 2011&lt;/a&gt; developed a web-based tool - &lt;a href=&quot;http://www.gibthon.org/&quot;&gt;Gibthon&lt;/a&gt; - for automatically generating primers for Gibson Assembly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could try running your difficult sequences through their tool to see what it suggests for primers.  It apparently gives you a &quot;value for the Gibbs free energy of the worst case secondary structure of the primer.&quot;&lt;/p&gt;&#xA;" OwnerUserId="51" LastActivityDate="2011-12-14T22:47:18.187" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="43" PostTypeId="2" ParentId="29" CreationDate="2011-12-14T22:49:47.150" Score="3" Body="&lt;p&gt;I doubt there is really any direct limitation; the best test would be to check if the size matches, i.e. that 1kbp gene with 100 exons would rather have to have way too short introns. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quick search over NCBI Genes show even a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene?term=%22000000000317%22%5BExon%20Count%5D&quot; rel=&quot;nofollow&quot;&gt;317-exon gene&lt;/a&gt;, although all those edge cases seem to be some unclear siblings of titin which is just huge on its own.&lt;/p&gt;&#xA;" OwnerDisplayName="user59" LastActivityDate="2011-12-14T22:49:47.150" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="44" PostTypeId="2" ParentId="33" CreationDate="2011-12-14T22:50:22.953" Score="11" Body="&lt;p&gt;Epigenetic information is information that can be inherited through cell division that is not encoded in the DNA sequence. This includes, but is not limited to, DNA methylation and histone modifications (there is also non-chromatin based epigenetic information). A nice example is the centromere, the chromosomal region that binds the kinetochore and is important to attach chromosomes to the mitotic spindle during cell division. The location of the centromere on the chromosome is encoded by a specific nucleosome composition and does not seem to rely on the DNA that wraps around those nucleosomes: The DNA sequence at centromeres is not even conserved from chromosome to chromosome (with the exception of budding yeast), and there are several known examples of people and families where the centromere is in a different place. However, all the mechanisms for maintaining this epigenetic mark are encoded genetically. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As epigenetic information is transmitted through cell division, it is directly inherited from the biological mother (with the exception of e.g. the centromere, most epigenetic marks from the father's chromosomes are removed when sperm is created). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, (some) epigenetic information can be &lt;em&gt;modified&lt;/em&gt;. This is obviously important during development where gene expression patterns of a liver cell need to be stable but different from gene expression patterns of a neuron, even though both descend from the same cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is evidence that the metabolism of the mother will influence the epigenetic program of the child; diet being one of the determinants. It has also been suggested that epigenetic changes may influence behavior. Thus, it is indeed possible for the surrogate mother's epigenetic state to influence the epigenetic information of the children.&lt;/p&gt;&#xA;" OwnerUserId="34" LastEditorUserId="69" LastEditDate="2012-01-11T14:50:14.360" LastActivityDate="2012-01-11T14:50:14.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="45" PostTypeId="2" ParentId="33" CreationDate="2011-12-14T22:56:50.610" Score="9" Body="&lt;p&gt;The idea of epigentics is that there is more info in chromatin than just in the DNA sequence it contains and that this info can be altered &lt;em&gt;in vivo&lt;/em&gt;.&lt;br&gt;&#xA;Thus, one cannot inherit epigenetic changes from a surrogate (which brings no new physical genetic material), but the fetus may develop some due to its interactions with her.&lt;/p&gt;&#xA;" OwnerDisplayName="user59" LastActivityDate="2011-12-14T22:56:50.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="46" PostTypeId="1" AcceptedAnswerId="53" CreationDate="2011-12-14T22:57:10.453" Score="9" ViewCount="175" Body="&lt;p&gt;Are the cells of marine animals and flora equipped with special ion exchange pumps to mitigate the effects of a saline-rich environment?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or have the cell's membranes adapted through structural changes to counter the osmotic forces?&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorDisplayName="user132" LastEditDate="2011-12-15T16:36:02.977" LastActivityDate="2015-04-30T11:06:08.680" Title="What specific membrane adaptations do cells have for saline-rich environs?" Tags="&lt;cell-membrane&gt;&lt;adaptation&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="47" PostTypeId="2" ParentId="38" CreationDate="2011-12-14T23:09:01.833" Score="7" Body="&lt;p&gt;The protocol I used in my genetics lab course was alkaline lysis followed by ethanol precipitation &lt;a href=&quot;http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=1667&quot;&gt;similar to this one&lt;/a&gt;.  Nothing terribly toxic or requiring a fume hood (at least at the small volumes used).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The more practical, reliable method is to use a miniprep kit (usually spin columns) from one of several suppliers (&lt;a href=&quot;http://www.qiagen.com/Products/Plasmid/QIAprepMiniprepSystem/QIAprepSpinMiniprepKit.aspx?r=912&quot;&gt;Qiagen&lt;/a&gt;, &lt;a href=&quot;http://www.promega.com/products/dna-and-rna-purification/plasmid-purification/pureyield-plasmid-miniprep-system/&quot;&gt;Promega&lt;/a&gt;, &lt;a href=&quot;http://www.bio-rad.com/prd/en/US/adirect/biorad?cmd=catProductDetail&amp;amp;vertical=LSR&amp;amp;country=US&amp;amp;lang=en&amp;amp;productID=732-6100&quot;&gt;Bio-Rad&lt;/a&gt;, etc.) which are fairly affordable at $1-2 per prep.&lt;/p&gt;&#xA;" OwnerUserId="25" LastActivityDate="2011-12-14T23:09:01.833" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="48" PostTypeId="2" ParentId="8" CreationDate="2011-12-14T23:09:35.773" Score="12" Body="&lt;p&gt;Spine formation (spinogenesis) is almost certainly due to chemical, rather than electrical, signalling between neurons. Although there are exceptions (gap junctions, for one), most forms of inter-cellular communication are mediated by chemicals released by one cell and detected by another. You are right that the cues for synaptogenesis are probably localized (the &quot;spatial condition&quot;), but I'm willing to bet the farm that those local cues are chemical in nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A recent paper from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21552280&quot;&gt;Kwon and Sabatini (2011)&lt;/a&gt; shows that local release of the neurotransmitter glutamate is sufficient to cause a functional spine to form. Glutamate receptors on the dendrite detect the glutamate and a spine forms (within seconds). At least under these conditions, the presynaptic machinery isn't required at all! Of course, in a less reduced preparation, electrical activity in the axon will signal the glutamate release from the presynaptic side. Thus, in this case, spine formation is activity-dependent but is mediated by chemical cues.&lt;/p&gt;&#xA;" OwnerUserId="72" LastActivityDate="2011-12-14T23:09:35.773" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="49" PostTypeId="2" ParentId="29" CreationDate="2011-12-14T23:11:01.533" Score="3" Body="&lt;p&gt;Agree with mbq - titan is the longest gene I know of and it has well over 100 exons. &lt;a href=&quot;http://en.wikipedia.org/wiki/Titin&quot; rel=&quot;nofollow&quot;&gt;Titin&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Dystrophin&quot; rel=&quot;nofollow&quot;&gt;dystrophin&lt;/a&gt; are well characterized genetically and not predictions.  titin is the champion exoner with 363 exons.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its only examples like this that can allow the gene predictors to run on as long as they do I think as the predictions are trimmed heuristically to resemble the known gene structures/lengths/junctions etc. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="112" LastEditDate="2011-12-15T19:22:27.180" LastActivityDate="2011-12-15T19:22:27.180" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="50" PostTypeId="1" AcceptedAnswerId="143" CreationDate="2011-12-14T23:14:43.633" Score="5" ViewCount="281" Body="&lt;p&gt;I'm looking for data - maybe CHP^2 data that shows chromatin binding to a prokaryotic genome under some specific conditions.  Can anyone point me to a source? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="948" LastEditDate="2014-01-13T21:43:09.413" LastActivityDate="2014-01-13T21:43:09.413" Title="Bacterial chromatin binding data?" Tags="&lt;transcription&gt;&lt;chromatin&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="51" PostTypeId="2" ParentId="6" CreationDate="2011-12-14T23:17:06.250" Score="4" Body="&lt;p&gt;Well, it depends if you just want to sequence your protein bound fragments.&#xA;If that is the case, I suppose you could go for a FAIRE-seq.&#xA;Basically, you perform several iterative phenol/chlo extractions, thus separating the bound and unbound fragments.&#xA;Then you sequence the unbound fragments that are present in the aqueous phase, and after the mapping, you can deduce the regions that were actually bound to proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know if it is possible to treat your bound fragments (that you isolate after a phenol/chlo extraction in the organic phase) with proteinase K, then perform another phenol/chlo extraction to purify your formerly bound fragments and sequence them. &#xA;Could be worth trying.&lt;/p&gt;&#xA;" OwnerUserId="36" LastActivityDate="2011-12-14T23:17:06.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="52" PostTypeId="1" AcceptedAnswerId="63" CreationDate="2011-12-14T23:34:01.983" Score="16" ViewCount="2838" Body="&lt;p&gt;Assuming that a longer distance between gaps in the myelin sheath is beneficial for an organism due to the increased propagation speed, what is the limiting factor in determining the maximum spacing between nodes?  I have previously encountered the analogy of the Nodes of Ranvier as forming a circuit between themselves and the previous node in order to pass on the action potential, which leads me into thinking that it is simply electrical resistance that is the cause however I assume the analogy is an over simplification and would be very interested in any alternatives.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, is there a significant variation in node separation between organisms?  Which organisms have the greatest gaps?&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2020-04-06T18:36:39.543" Title="What limits the maximum spacing of Nodes of Ranvier and which organisms tend to have the widest gaps?" Tags="&lt;biochemistry&gt;&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="53" PostTypeId="2" ParentId="46" CreationDate="2011-12-14T23:34:36.673" Score="9" Body="&lt;p&gt;&lt;a href=&quot;http://mic.sgmjournals.org/content/55/3/325.full.pdf+html&quot;&gt;This 1969 Steensland paper&lt;/a&gt; seems to suggest that the membranes of halophiles are stabilized by sodium ions and they rapidly denature at lower-salt conditions (2.2 vs. 4.3 M).  The protein composition of the membrane was generally acidic, stabilized by all the Na&lt;sup&gt;+&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as what the role of the halophile membrane is in sheltering the cell from the high ionic strength solution seems left unsaid.&lt;/p&gt;&#xA;" OwnerUserId="25" LastActivityDate="2011-12-14T23:34:36.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="55" PostTypeId="2" ParentId="38" CreationDate="2011-12-14T23:52:23.397" Score="4" Body="&lt;p&gt;In my experience, the P:C:I method will get you higher yields, and is a bit more simple (in steps and chems involved), but as @Mad Scientist has said, phenol use might be an issue. It depends on the age of your students.&lt;/p&gt;&#xA;" OwnerUserId="14" LastActivityDate="2011-12-14T23:52:23.397" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="57" PostTypeId="2" ParentId="32" CreationDate="2011-12-15T00:16:44.283" Score="17" Body="&lt;p&gt;&lt;strong&gt;Subtype&lt;/strong&gt; is denoted using the HxNy notation for the variant of hemagglutinin and neuraminidase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Strain names&lt;/strong&gt; are specified as: &lt;code&gt;[virus type]&lt;/code&gt;/&lt;code&gt;[location of origin]&lt;/code&gt;/&lt;code&gt;[sequential number of isolation]&lt;/code&gt;/&lt;code&gt;[year of isolation]&lt;/code&gt; (&lt;code&gt;[subtype]&lt;/code&gt;), such as &lt;a href=&quot;http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=CY069733&amp;amp;decorator=influenza&amp;amp;context=1323907641126&quot;&gt;&quot;A/Alabama/AF2070/2010(H1N1)&quot;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Virus type would be A, B, or C for the various forms of influenza (&lt;a href=&quot;http://en.wikipedia.org/wiki/Influenzavirus_A&quot;&gt;influenza A&lt;/a&gt; being the most common among humans)&lt;/li&gt;&#xA;&lt;li&gt;Location can be a country, state or city (e.g. Laos, Alabama, or Moscow)&lt;/li&gt;&#xA;&lt;li&gt;The number of isolation can be a simple number, but sometimes it goes beyond; e.g. &quot;AF2060&quot; or &quot;UR06-0455&quot;, possibly due to the tremendous number sequenced nowadays.&lt;/li&gt;&#xA;&lt;li&gt;Year, obvious.&lt;/li&gt;&#xA;&lt;li&gt;The subtype refers to the aforementioned HA/NA subtype.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Many more strains can be found on the &lt;a href=&quot;http://www.fludb.org/brc/home.do?decorator=influenza&quot;&gt;Influenza Research Database&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="25" LastActivityDate="2011-12-15T00:16:44.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="58" PostTypeId="1" CreationDate="2011-12-15T00:23:40.980" Score="9" ViewCount="247" Body="&lt;p&gt;We suspect a bi-directional transcription event is happening at a locus in our organism where two genes are directly adjacent to each other. The annotation data is not well established. The intergenic distance is probably less than 200 base pairs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two genes are expressed in opposite directions towards each other. Base on the preliminary transcriptomics data, it seems like one gene is over transcribing (3' UTR perhaps?) into the adjacent gene, possibly resulting in some kind of transcriptional regulation of the adjacent gene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a rough diagram of what we think might be happening:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;------------------------==========gene A================&amp;gt;----------------------&#xA;&#xA;----------------------------------------&amp;lt;====gene B=====-----------------------&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Of course we need to first confirm this by designing primers to see if this over transcription is actually happening. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is happening, we intend to do some knock down experiments. We have no transgenesis available in our organism, only RNAi by dsRNA. It is possible to specifically knock down geneA by introducing dsRNA to the 5' region of geneA that does not overlap with geneB. Perhaps this will lead to ectopic/over expression of geneB. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there anyway to knock down geneB specifically without knocking down geneA? It looks like designing dsRNA for geneB would knock down both A and B.&lt;/p&gt;&#xA;" OwnerUserId="90" LastEditorUserId="6" LastEditDate="2011-12-16T09:02:19.657" LastActivityDate="2011-12-26T03:29:45.240" Title="bi-directional transcription experiment" Tags="&lt;molecular-biology&gt;&lt;transcription&gt;&lt;rna-interference&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="59" PostTypeId="2" ParentId="1" CreationDate="2011-12-15T00:37:36.697" Score="22" Body="&lt;p&gt;I found an oldish paper on this topic (from 1994).  Here's a summary:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC523762/&quot;&gt;Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs.&lt;/a&gt; by Chen, Bjerknes, Kumar, &amp;amp; Jay. Nucleic Acids Research. (1994)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Experiment&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors constructed a series of synthetic RBS regions that varied the length separating a synthetic 5-nt Shine-Dalgarno sequence from the start codon.  The regions varied in size between 2 to 17 nt.  They assayed the activity of a downstream enzyme, chloramphenicol acetyltransferase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Conclusion&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors concluded that the optimal spacing between a consensus 5-nt Shine-Dalgarno sequence (5'-GAGGT-3') and the start site &lt;strong&gt;was 5 nt&lt;/strong&gt;. Note: this synthetic SD was made of the &lt;em&gt;last&lt;/em&gt; 5 nt of a 9 nt SD consensus sequence.  They also tested a synthetic SD made from the &lt;em&gt;first&lt;/em&gt; 5 nt (5'-TAAGG-3')of the consensus SD.  In this case they found the optimal distance was &lt;strong&gt;9 nt&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the optimal distance depends on where your desired SD aligns with the consensus SD sequence, which optimally is &lt;strong&gt;5 nt&lt;/strong&gt; from the start.  Read on for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Details&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;the RBS is considered to be large, extending 20bp on either side of a core Shine-Dalgarno (SD) sequence.  These days, I often hear of the RBS spoken of in sizes that are equivalent to the SD.  So in the parlance of the paper, you question is rephrased as &quot;how does distance of the SD from the start codon effect translation?&quot;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the canonical SD sequence referenced in the paper is 5'-UAAGGAGGU-3'.  It is 9 nucleotides long.  Distances between the SD and the start codon are defined as the number of nucleotides separate the 3' Uracil of the SD from the Adenine of the start AUG.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Example: the distance is 5 nt in the following mRNA&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;       5'.....UAAGGAGGUnnnnnAUG......3'&#xA;&lt;/code&gt;&lt;/pre&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;if the SD is not a complete 9 nt long, the distance is between the position of where the canonical Uracil &lt;em&gt;would&lt;/em&gt; occur.  In the following example, the distance is still calculated as 5 nt:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;       5'.....UAAGGAnnnnnnnnAUG......3'&#xA;&lt;/code&gt;&lt;/pre&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the average distance between the SD sequence and the start codon varies considerably and on average is 7 nt. Other investigators have found &quot;optimal&quot; spacing (circa 1994) ranged from 5 to 13 nt.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the SD site complements with region on the 16s rRNA. The start codon complements to the anticodon of fMet-tRNA loaded into the ribosomal P-site.  So there are two distinct sites on the ribosome that contact the mRNA during translation initiation.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Also good to read&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.elsevierdirect.com/product.jsp?lid=0&amp;amp;iid=5&amp;amp;sid=0&amp;amp;isbn=0123851203&quot;&gt;Designing Genes for Successful Protein Expression&lt;/a&gt; by Welch et al. Methods in Enzymology, Vol 498. (2011) (&lt;a href=&quot;http://mpec.ucsf.edu/pdfs_new/Pubs_77.pdf&quot;&gt;pdf&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nbt/journal/v27/n10/abs/nbt.1568.html&quot;&gt;Automated design of synthetic ribosome binding sites to control protein expression&lt;/a&gt; by Salis, Mirsky &amp;amp; Voigt. Nature Biotechnology. (2009). (&lt;a href=&quot;http://www.esf.edu/chemistry/nomura/fch530/files/nbt.1568.pdf&quot;&gt;pdf&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I enjoyed researching this question because I found my own knowledge to be lacking solid empirical details. I do not have any direct experience besides this little lit review with this topic.&lt;/p&gt;&#xA;" OwnerUserId="51" LastEditorUserId="51" LastEditDate="2011-12-15T00:53:52.397" LastActivityDate="2011-12-15T00:53:52.397" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="60" PostTypeId="2" ParentId="11" CreationDate="2011-12-15T00:39:45.057" Score="16" Body="&lt;p&gt;Well, it seems quite obvious that it was not a single I-eat-you-but-you-survived act but rather a convergence of endosymbiotic and host species into a greater and greater cooperation. &#xA;Of course this leaves a question if there was one or more species of endosymbionts involved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mitochondria are a very primeval story forced by the oxygen catastrophe, so it is hard to say, although great majority of mitochondria seems to have a single origin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plastids are much more divergent, however it seems that they did originated from a single source, diverged into chloroplasts, cyanelles and rhodoplasts and were later mixed up by numerous acts of secondary and even tertiary endosymbiosis (plus a further evolution); this variety can be especially seen within Euglenas, and they are the main group investigated in this manner. &lt;/p&gt;&#xA;" OwnerDisplayName="user59" LastActivityDate="2011-12-15T00:39:45.057" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="61" PostTypeId="2" ParentId="38" CreationDate="2011-12-15T00:47:21.393" Score="4" Body="&lt;p&gt;Using spin columns, my professor and I extracted ~30 plasmids from ~30 samples in a few hours.  It's easy, cheap, and it yields good quality plasmid.  My sample was quantified by UV spec and it was at about 200ng/ul.&lt;/p&gt;&#xA;" OwnerUserId="91" LastActivityDate="2011-12-15T00:47:21.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="62" PostTypeId="2" ParentId="4" CreationDate="2011-12-15T00:51:22.773" Score="3" Body="&lt;p&gt;As far as I know, that is fine.  Thats the temperature that Amp is regularly stored at.  I always do a negative control anyways to ensure that my antibiotics are still lethal.  Just don't stick it in the microwave to make plates&lt;/p&gt;&#xA;" OwnerUserId="91" LastActivityDate="2011-12-15T00:51:22.773" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="63" PostTypeId="2" ParentId="52" CreationDate="2011-12-15T04:40:30.013" Score="13" Body="&lt;p&gt;This is best answered via something called &lt;a href=&quot;http://en.wikipedia.org/wiki/Cable_theory&quot;&gt;cable theory&lt;/a&gt;.  Basically, as the action potential (AP) propagates along the membrane of the axon, it's tripping voltage gated channels that &quot;renew&quot; the flux of ions into the stream at the nodes. There are no ion channels under the sheathing (or they are there anatomically and inactive, but I don't remember), so the current is able to zip through that area.  There's no renewal of AP, but there's no loss due to leak of ions either.  Since there's no influx of ions from outside of the membrane until the next node, the capacitance and resistance of the membrane is exponentially decaying the voltage.  So, if the distance between the nodes was too long, the voltage would just die off and the AP wouldn't propagate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't have any anatomical data about individual species, but know that only the smaller diameter axons require sheathing to compensate for the slower ion flow due to higher resistance (e.g., the &lt;a href=&quot;http://en.wikipedia.org/wiki/Squid_giant_axon&quot;&gt;squid giant axon&lt;/a&gt;(not to be confused with the &quot;giant squid&quot; axon) has no myelination due to its large diameter).&lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2011-12-15T04:40:30.013" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="64" PostTypeId="1" AcceptedAnswerId="68" CreationDate="2011-12-15T05:53:56.750" Score="16" ViewCount="3169" Body="&lt;p&gt;What is the current consensus on whether or not humans have receptors that detect pheromones?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there are purported receptors, in what anatomical areas are they located?  With what organ systems do they interact? &lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="73" LastEditDate="2011-12-15T06:30:42.113" LastActivityDate="2020-03-19T03:12:00.117" Title="Do human beings have pheromone receptors?" Tags="&lt;neuroscience&gt;&lt;endocrinology&gt;&lt;human-biology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="66" PostTypeId="5" CreationDate="2011-12-15T06:37:09.927" Score="0" Body="&lt;p&gt;This tag is used for questions about the general biological features of human beings as opposed to the biology of non-humans. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human biology may be relevant to many fields of biology and appropriate complementary tags should be used.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also: &lt;a href=&quot;/questions/tagged/human-anatomy&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;human-anatomy&amp;#39;&quot; rel=&quot;tag&quot;&gt;human-anatomy&lt;/a&gt; &lt;a href=&quot;/questions/tagged/human-physiology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;human-physiology&amp;#39;&quot; rel=&quot;tag&quot;&gt;human-physiology&lt;/a&gt; &lt;a href=&quot;/questions/tagged/human-genetics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;human-genetics&amp;#39;&quot; rel=&quot;tag&quot;&gt;human-genetics&lt;/a&gt; &lt;a href=&quot;/questions/tagged/human-evolution&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;human-evolution&amp;#39;&quot; rel=&quot;tag&quot;&gt;human-evolution&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6703" LastEditorUserId="16866" LastEditDate="2019-12-13T04:34:03.283" LastActivityDate="2019-12-13T04:34:03.283" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="67" PostTypeId="4" CreationDate="2011-12-15T06:37:09.927" Score="0" Body="This tag is for questions about the general biological features of human beings (as opposed to the biology of non-humans)." OwnerUserId="73" LastEditorUserId="6289" LastEditDate="2014-05-23T02:50:50.787" LastActivityDate="2014-05-23T02:50:50.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="68" PostTypeId="2" ParentId="64" CreationDate="2011-12-15T06:56:10.043" Score="9" Body="&lt;p&gt;From what I have gathered, I would think that humans do have receptors that are able to detect pheromones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, some studies that have indicated human responses to pheromones.  Of these pheromone responses, some have been traced to the olfactory mucosa and olfactory epithelium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The trace amine-associated receptors (TAAR) for which humans have 7 genes (TAAR1, TAAR2, TAAR3, TAAR5, TAAR6, TAAR8, TAAR9) and 2 pseudogenes (TAAR4P, TAAR7P) are found in the olfactory epithelium whereas androstadienone receptors are found in the olfactory mucosa.  As suggested by the anatomical location, these receptors interact with the human sense of smell and the olfactory system&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More information: &lt;a href=&quot;http://en.wikipedia.org/wiki/Pheromone#Humans&quot;&gt;http://en.wikipedia.org/wiki/Pheromone#Humans&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="79" LastActivityDate="2011-12-15T06:56:10.043" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="69" PostTypeId="1" AcceptedAnswerId="74" CreationDate="2011-12-15T07:19:11.870" Score="8" ViewCount="2485" Body="&lt;p&gt;I understand that rooted and unrooted phylogenetic trees are similar in structure&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But how can they be easily identified as one or the other?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it simply based on the presence or lack of a named root (the root is identified as a particular ancestor) or outgroup?&lt;/p&gt;&#xA;" OwnerUserId="79" LastEditorUserId="20955" LastEditDate="2019-07-11T20:10:46.563" LastActivityDate="2019-07-11T20:10:46.563" Title="How can rooted and unrooted (phylogenetic) trees be distinguished from one another" Tags="&lt;bioinformatics&gt;&lt;phylogenetics&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="70" PostTypeId="2" ParentId="33" CreationDate="2011-12-15T07:47:11.347" Score="3" Body="&lt;p&gt;The definition of an epigenetic mark I work with is the following:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;impacts gene regulation without touching the DNA sequence,&lt;/li&gt;&#xA;&lt;li&gt;is reversible,&lt;/li&gt;&#xA;&lt;li&gt;is inheritable.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;With this definition in mind, you could say that only DNA methylation is a true epigenetic mark, leaving histone modifications and the like to canonical transcription regulation machinery. Yet it really depends on what scale you place yourself. Epigenetics at the scale of the cell is not the same thing as at the scale of the organism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if a surrogate mother can alter the epigenetic state of the pup or child or foetus, it will not be due to transmission of information in the traditional sense, but rather be due to her physiological state in the case of the foetus (many hormones act through nuclear receptors that can recruit chromatin remodelers), or as mbq mentioned it, due to her behaviour in the case of the child or pup.&lt;/p&gt;&#xA;" OwnerUserId="36" LastEditorUserId="14776" LastEditDate="2016-08-27T19:49:15.993" LastActivityDate="2016-08-27T19:49:15.993" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="71" PostTypeId="2" ParentId="69" CreationDate="2011-12-15T08:29:00.433" Score="2" Body="&lt;p&gt;Trees can not be distinguished from each other because every unrooted tree can be made rooted by adding a root and vice versa by deletion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you mean dendrograms... the root is always the one node where the distance to each leaf is the same. But I don't know of an unrooted dendrogram.&lt;/p&gt;&#xA;" OwnerUserId="120" LastActivityDate="2011-12-15T08:29:00.433" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="72" PostTypeId="1" AcceptedAnswerId="294" CreationDate="2011-12-15T08:36:32.913" Score="13" ViewCount="1325" Body="&lt;p&gt;For predicting genes from a sequenced genome, you need to set a maximum intron length. How long can introns get in animals? Is there some limit?&lt;/p&gt;&#xA;" OwnerUserId="112" LastEditorUserId="79" LastEditDate="2011-12-15T08:44:41.493" LastActivityDate="2011-12-22T17:33:31.267" Title="What are limiting factors for intron length?" Tags="&lt;splicing&gt;&lt;introns&gt;&lt;genetics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="73" PostTypeId="1" AcceptedAnswerId="1500" CreationDate="2011-12-15T08:36:53.350" Score="12" ViewCount="537" Body="&lt;p&gt;The T7 polymerase doesn't transcribe all sequences equally well, the transciption efficiency can vary widely for different sequences. One well known requirement of the T7 polymerase is that the sequence should begin with 2-3 guanines for efficient transcription.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any literature that quantified the effects of the sequence on the transcription efficiency? I'm mostly interested in the effect of the first few nucleotides, as changing other parts of the sequence is usually not possible.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2017-03-25T06:57:57.597" Title="Which sequence characteristics influence the transcription efficiency of T7 polymerase?" Tags="&lt;biochemistry&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="74" PostTypeId="2" ParentId="69" CreationDate="2011-12-15T08:40:15.060" Score="5" Body="&lt;p&gt;In case of a drawn figure, either look for the a short stem to the left, or for an explicitly labelled outgroup. Trees derived from phylogenetic analyses are normally unrooted by default, you need to root them by either making an arbitrary (but hopefully informed) decision or by adding an outgroup.&lt;/p&gt;&#xA;" OwnerUserId="112" LastEditorUserId="4579" LastEditDate="2014-06-19T14:50:19.097" LastActivityDate="2014-06-19T14:50:19.097" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="75" PostTypeId="1" AcceptedAnswerId="76" CreationDate="2011-12-15T08:46:07.467" Score="21" ViewCount="375" Body="&lt;p&gt;The existence of nanometer scale microorganisms has been proposed and used explain several phenomena  including morphological structures in a martian meteorite (ALH 84001) and implication in the formation of kidney stones (1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there now any consensus in the biology community whether these are biotic or abiotic in nature?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) &lt;a href=&quot;http://www.pnas.org/content/95/14/8274.full&quot;&gt;Kajander EO, Ciftcioglu N (1998) Nanobacteria: An alternative mechanism for pathogenic intra- and extracellular calcification and stone formation. Proc Natl Acad Sci U S A 95: 8274–8279&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-01-09T19:33:09.273" LastActivityDate="2012-01-09T19:33:09.273" Title="Is there any convincing evidence for the existence of nanobacteria?" Tags="&lt;microbiology&gt;&lt;astrobiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="76" PostTypeId="2" ParentId="75" CreationDate="2011-12-15T09:24:58.893" Score="20" Body="&lt;p&gt;There are two convincing papers (1,2) arguing that the observed &quot;nanobacteria&quot; are in fact mineral/protein complexes and not any living organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In (1) Martel and Young created very similar looking particles from calcium carbonate &lt;em&gt;in vitro&lt;/em&gt;. The calcium carbonate precipitations can even look similar to dividing cells:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After 5 days of serum incubation, a white precipitate formed and&#xA;  adhered on the bottom of each flask. When examined by scanning&#xA;  electron microscopy (SEM) and transmission electron microscopy (TEM),&#xA;  the precipitate was seen to consist of particles with a size ≈500 nm&#xA;  (Fig. 1 A, B, and E), an observation consistent with normal bacterial&#xA;  morphology, which peaks at one particular size specific to the strain&#xA;  on hand. Some forms resembled cells undergoing division (Fig. 1 D,&#xA;  arrow).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;One strong argument against those nanobacteria being living organisms is that they don't seem to contain any nucleic acids. Of course non-DNA based organisms are theoretically feasible, but that would be an absolutely extraordinary discovery.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The autors of (1) also observed these particles after filtration through a 0.1um filter. They argue that this size could not be sufficient to contain all the cellular machinery bacteria need:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because an earlier workshop commissioned by the NAS had suggested that&#xA;  the minimal cellular size of life on Earth must exceed 200 nm in&#xA;  diameter to harbor the cellular machinery based on DNA replication&#xA;  (19), it is unlikely that nanobacteria represent living entities&#xA;  unless they contain some other type of replicating mechanism.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(1) &lt;a href=&quot;http://www.pnas.org/content/105/14/5549.long&quot;&gt;Martel J and Young JD, Purported nanobacteria in human blood as calcium carbonate nanoparticles. PNAS 2008, 105(14):5549-54&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) &lt;a href=&quot;http://www.plospathogens.org/article/info%3adoi/10.1371/journal.ppat.0040041&quot;&gt;Raoult D. et al., Nanobacteria Are Mineralo Fetuin Complexes, PLoS Pathog. 2008, 4(2): e41.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2011-12-15T11:34:12.580" LastActivityDate="2011-12-15T11:34:12.580" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="77" PostTypeId="1" AcceptedAnswerId="78" CreationDate="2011-12-15T11:30:40.823" Score="12" ViewCount="1359" Body="&lt;p&gt;I've been thinking about starting a small private research project. In this project I need to find out whether a person is homozygous for a certain allele. The reason for this is that I'm really trying to find out whether has a mutation that makes him/her &lt;em&gt;not&lt;/em&gt; produce this chemokine. Thus I need to identify in an easy way which people are &quot;normal&quot;, which people have the mutation in one chromosome, and which people have the mutation in both. About 1% of the population have the mutation in both chromosomes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A primer would AFAIK not be able to differ between the heterozygous and the &quot;normal&quot; people.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do anyone know how to approach this?&lt;/p&gt;&#xA;" OwnerUserId="128" LastActivityDate="2011-12-15T12:17:15.060" Title="How can you identify if a person is homozygous for a certain allele?" Tags="&lt;dna&gt;&lt;primer&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="78" PostTypeId="2" ParentId="77" CreationDate="2011-12-15T12:17:15.060" Score="7" Body="&lt;p&gt;You could use a 3-primers strategy, where you have a common primer, one that only amplifies the mutant allele and one that only amplifies the wt. This may or may not be feasable depending on the type of mutation.&#xA;DNA from het people will amplify both product, while homozygous will only amplify one (wt or mutant).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course then, linking the mutation of a gene to the lack of a chemokine is not necessarily straightforward.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be honest, however, I would use a different approach: take people who don't produce the chemokine, and people who do (simply by dosing the chemokine in the blood). Now sequence the gene in the two groups and look for mutations.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2011-12-15T12:17:15.060" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="80" PostTypeId="2" ParentId="28" CreationDate="2011-12-15T13:09:06.027" Score="6" Body="&lt;p&gt;According to literature, histone marks seem to be affecting splicing both directly and indirectly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The indirect regulation appears to be due to biophysical hindrance, where a certain chromatin structure would cause Pol-II slowdown, allowing the splicing machinery to do its job. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The direct regulation seems to be essentially dependent on H3K36me3 and H3K4me1, marks that are recognized by MRG15, which in turn recruits the splicing regulator polypyrimidine tract-binding protein to splice sites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ref: &lt;a href=&quot;http://dx.doi.org/10.1126/science.1184208&quot;&gt;Luco, R. F. et al. Regulation of alternative splicing by histone modifications. Science 4 Feb 2010&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="36" LastEditorUserId="6" LastEditDate="2011-12-15T19:22:16.590" LastActivityDate="2011-12-15T19:22:16.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="81" PostTypeId="2" ParentId="4" CreationDate="2011-12-15T13:18:39.000" Score="3" Body="&lt;p&gt;I don't know about solutions, but we keep LB-Amp/Carb/Gm plates in 4°C for two-three weeks at a time, and the antibiotics seem to work.&lt;/p&gt;&#xA;" OwnerUserId="133" LastActivityDate="2011-12-15T13:18:39.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="82" PostTypeId="1" AcceptedAnswerId="88" CreationDate="2011-12-15T13:28:53.390" Score="18" ViewCount="386" Body="&lt;p&gt;Once upon a time, I chanced upon an old microbiology book that detailed the rather colorful world of enterobacteria. &lt;em&gt;Salmonella&lt;/em&gt; in particular stood out, as it seemed there were a lot of species: &lt;em&gt;typhi&lt;/em&gt; / &lt;em&gt;typhosa&lt;/em&gt;, &lt;em&gt;paratyphi&lt;/em&gt;, &lt;em&gt;gallinarum&lt;/em&gt;, &lt;em&gt;typhimurium&lt;/em&gt;, &lt;em&gt;choleraesuis&lt;/em&gt;, and quite a bunch of others that I have now forgotten.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Flipping through a newer book, it now seems that all of these &quot;species&quot; were collated under &lt;em&gt;choleraesuis&lt;/em&gt; (and now more recently &lt;em&gt;enterica&lt;/em&gt;), with all those species being demoted to &quot;strains&quot; (or maybe I should use the current term of art, &quot;serovar&quot;). Unfortunately, the book didn't give much in the way of explaining about this merger.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, why is there now only &lt;em&gt;S. enterica&lt;/em&gt;? If &quot;&lt;em&gt;S. typhi&lt;/em&gt;&quot; is a mere serovar, how come the species name is still used in the literature?&lt;/p&gt;&#xA;" OwnerDisplayName="user132" LastEditorDisplayName="user132" LastEditDate="2011-12-15T14:47:26.070" LastActivityDate="2011-12-15T14:47:26.070" Title="Why is there now only one Salmonella species?" Tags="&lt;microbiology&gt;&lt;history&gt;&lt;bacteriology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="83" PostTypeId="5" CreationDate="2011-12-15T13:33:24.163" Score="0" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/DNA&quot; rel=&quot;nofollow noreferrer&quot;&gt;Deoxyribonucleic acid (DNA)&lt;/a&gt; usually exists in a supermolecular form consisting of two hydrogen-bonded anti-parallel strands wound in the shape of a double helix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each strand is a directional polymer of mononucleotides. A DNA-mononucleotide consists of a phosphorylated 5-carbon sugar (deoxyribose) linked to heterocyclic nitrogenous bases by an N-glycosidic linkage. There are usually four types of bases in DNA: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Adenine (&lt;strong&gt;A&lt;/strong&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Guanine (&lt;strong&gt;G&lt;/strong&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Thymine (&lt;strong&gt;T&lt;/strong&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Cytosine (&lt;strong&gt;C&lt;/strong&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;They make up four different kinds of mononucleotides. Each mononucleotide is linked to each other through a phosphodiester bond [a mononucleotide is already a phosphoric ester (ester of sugar alcohol group and phosphoric acid). A second ester bond is formed between the 3-OH of a mononuclotide and the 5-phosphate of another nucleotide].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the DNA supermolecular structure, &lt;strong&gt;A&lt;/strong&gt; in a given strand is hydrogen bonded to &lt;strong&gt;T&lt;/strong&gt; in the other strand. Similarly, &lt;strong&gt;G&lt;/strong&gt;  is bound to &lt;strong&gt;C&lt;/strong&gt;.  This pattern of hydrogen bonding is called Watson-Crick base pairing, named for the discoverers of the double helix structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Questions should be on the synthesis, structure, function, and properties of DNA.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="16866" LastEditDate="2019-12-13T04:32:38.367" LastActivityDate="2019-12-13T04:32:38.367" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="84" PostTypeId="4" CreationDate="2011-12-15T13:33:24.163" Score="0" Body="Deoxyribonucleic acid (DNA) is the carrier of genetic information, including for all known living organisms. The only known exceptions are RNA viruses." OwnerDisplayName="user132" LastEditorUserId="16866" LastEditDate="2019-07-12T03:38:55.650" LastActivityDate="2019-07-12T03:38:55.650" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="85" PostTypeId="2" ParentId="82" CreationDate="2011-12-15T13:51:31.220" Score="4" Body="&lt;p&gt;Just open Wikipedia, your question is &lt;a href=&quot;http://en.wikipedia.org/wiki/Salmonella#Salmonella_nomenclature&quot; rel=&quot;nofollow&quot;&gt;answered there&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Initially, each Salmonella species was named according to clinical&#xA;  considerations,[15] e.g., Salmonella typhi-murium (mouse typhoid&#xA;  fever), S. cholerae-suis (hog cholera). After it was recognized that&#xA;  host specificity did not exist for many species, new strains (or&#xA;  serovar, short for serological variants) received species names&#xA;  according to the location at which the new strain was isolated. Later,&#xA;  molecular findings led to the hypothesis that Salmonella consisted of&#xA;  only one species,[16] S. enterica, and the serovar were classified&#xA;  into six groups,[17] two of which are medically relevant. But as this&#xA;  now formalized nomenclature[18][19] is not in harmony with the&#xA;  traditional usage familiar to specialists in microbiology and&#xA;  infectologists, the traditional nomenclature is common. Currently,&#xA;  there are two recognized species: S. enterica and S. bongori, with six&#xA;  main subspecies: enterica (I), salamae (II), arizonae (IIIa),&#xA;  diarizonae (IIIb), houtenae (IV), and indica (VI).[20] Historically,&#xA;  serotype (V) was bongori, which is now considered its own species. The&#xA;  serovar classification of Salmonella is based on the Kauffman-White&#xA;  classification scheme that permits serological varieties to be&#xA;  differentiated from each other. Newer methods for Salmonella typing&#xA;  and subtyping include genome-based methods such as pulsed field gel&#xA;  electrophoresis (PFGE), Multiple Loci VNTR Analysis (MLVA), Multilocus&#xA;  sequence typing (MLST) and (multiplex-) PCR-based methods.[21]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="66" LastActivityDate="2011-12-15T13:51:31.220" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="86" PostTypeId="5" CreationDate="2011-12-15T13:52:14.537" Score="0" Body="&lt;h2&gt;Useful Textbooks&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://books.google.co.uk/books?id=RawZTwEACAAJ&amp;amp;dq=brock+biology+of+microorganisms&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=lDmaUpeQMIPPhAeCw4HgCQ&amp;amp;ved=0CEEQ6AEwAA&quot; rel=&quot;nofollow noreferrer&quot;&gt;Brock's Biology of Microorganisms&lt;/a&gt;: A comprehensive undergraduate level textbook.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://books.google.co.uk/books?id=ToF6pwAACAAJ&amp;amp;dq=physiology+and+biochemistry+of+prokaryotes&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=lDiaUqr9Es7b7AbE_ID4CQ&amp;amp;ved=0CDIQ6AEwAA&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Physiology and Biochemistry of Prokaryotes&lt;/a&gt;: A thorough graduate-level textbook on the physiology and metabolism of bacteria and archaea. Does not include eukaryotes like fungi or protozoa.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://textbookofbacteriology.net/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Todar's Online Textbook of Bacteriology&lt;/a&gt;: a free online textbook on introductory microbiology, emphasizing bacteria.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Relevant tags: &lt;a href=&quot;/questions/tagged/bacteriology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;bacteriology&amp;#39;&quot; rel=&quot;tag&quot;&gt;bacteriology&lt;/a&gt; &lt;a href=&quot;/questions/tagged/virology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;virology&amp;#39;&quot; rel=&quot;tag&quot;&gt;virology&lt;/a&gt; &lt;a href=&quot;/questions/tagged/mycology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;mycology&amp;#39;&quot; rel=&quot;tag&quot;&gt;mycology&lt;/a&gt; &lt;a href=&quot;/questions/tagged/microbiome&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;microbiome&amp;#39;&quot; rel=&quot;tag&quot;&gt;microbiome&lt;/a&gt; &lt;a href=&quot;/questions/tagged/microscopy&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;microscopy&amp;#39;&quot; rel=&quot;tag&quot;&gt;microscopy&lt;/a&gt; &lt;a href=&quot;/questions/tagged/pathology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;pathology&amp;#39;&quot; rel=&quot;tag&quot;&gt;pathology&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4840" LastEditorUserId="16866" LastEditDate="2019-07-12T03:54:58.867" LastActivityDate="2019-07-12T03:54:58.867" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="87" PostTypeId="4" CreationDate="2011-12-15T13:52:14.537" Score="0" Body="Microbiology is the study of extremely small organisms. This includes organisms like bacteria, fungi, protozoa, and viruses." OwnerDisplayName="user132" LastEditorUserId="27029" LastEditorDisplayName="user132" LastEditDate="2016-11-23T21:10:58.460" LastActivityDate="2016-11-23T21:10:58.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="88" PostTypeId="2" ParentId="82" CreationDate="2011-12-15T13:53:33.427" Score="17" Body="&lt;p&gt;Simply put, old habits die hard; physicians and other medical personnel have grown up with the old species designations so will continue to use them.  This is somewhat the reverse of the case with &lt;em&gt;E. coli&lt;/em&gt;, where &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2974192/?tool=pmcentrez&quot;&gt;80-90% of the genome is variable&lt;/a&gt; across strains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17760271&quot;&gt;Lin-Hui gives a brief history&lt;/a&gt;, where strains identified early were given specific names within &lt;em&gt;Salmonella&lt;/em&gt; like &lt;em&gt;typhi&lt;/em&gt;, &lt;em&gt;typhimurium&lt;/em&gt;, &lt;em&gt;panama&lt;/em&gt;, etc.  In 1966 it was proposed to lump serovars together among three species &lt;em&gt;S.&#xA;choleraesuis&lt;/em&gt;, &lt;em&gt;S. typhosa&lt;/em&gt;, and &lt;em&gt;S. kauffmannii&lt;/em&gt;.  Shortly thereafter in 1972 with the advent of DNA techniques, it was shown they really should be all piled together.  There is one exception, &lt;em&gt;Salmonella choleraesuis subsp. bongori&lt;/em&gt;, separated in 1989.&lt;/p&gt;&#xA;" OwnerUserId="25" LastEditorUserId="25" LastEditDate="2011-12-15T14:00:03.230" LastActivityDate="2011-12-15T14:00:03.230" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="90" PostTypeId="1" AcceptedAnswerId="106" CreationDate="2011-12-15T14:20:56.700" Score="56" ViewCount="11437" Body="&lt;p&gt;I'm by no means an expert in the field, merely a curious visitor, but I've been thinking about this and Google isn't of much help. Do we know of any lifeforms that don't have the conventional double-helix DNA as we know it? Have any serious alternatives been theorized?&lt;/p&gt;&#xA;" OwnerUserId="26" LastEditorUserId="81" LastEditDate="2011-12-15T16:30:00.090" LastActivityDate="2015-07-16T03:57:37.623" Title="Life without DNA?" Tags="&lt;dna&gt;" AnswerCount="5" CommentCount="4" FavoriteCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="91" PostTypeId="1" AcceptedAnswerId="110" CreationDate="2011-12-15T14:27:37.170" Score="25" ViewCount="37943" Body="&lt;p&gt;The information between the brain and peripheral nerves is sent via electrical pulses or signals, How then does a non-metallic human cell manage to conduct an electrical &#xA;signal?&lt;/p&gt;&#xA;" OwnerUserId="135" LastEditorUserId="-1" LastEditDate="2018-10-04T14:28:19.050" LastActivityDate="2018-10-04T14:28:19.050" Title="How do the brain and nerves create electrical pulses?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="8" ContentLicense="CC BY-SA 4.0" />
  <row Id="92" PostTypeId="1" AcceptedAnswerId="97" CreationDate="2011-12-15T14:40:53.833" Score="21" ViewCount="576" Body="&lt;p&gt;It was somewhat new to me that mushrooms usually aren't individual organisms, but are merely the visible bodies of a bunch of fungi living in the soil. I know that mushrooms emit spores to reproduce, but what has been bizarre to me is how fairy rings form. Why do the fruiting bodies arrange themselves in a more or less circular shape, as opposed to the random scattering one would expect from wind-borne spores?&lt;/p&gt;&#xA;" OwnerDisplayName="user132" LastActivityDate="2011-12-19T14:18:36.823" Title="How do fairy rings propagate?" Tags="&lt;mycology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="93" PostTypeId="1" CreationDate="2011-12-15T14:45:59.303" Score="12" ViewCount="2228" Body="&lt;p&gt;I've seen &lt;em&gt;Taq&lt;/em&gt; polymerase being marketed as either &quot;native&quot; or &quot;recombinant&quot;. I understand that the recombinant version is produced by specially modified &lt;em&gt;Escherichia coli&lt;/em&gt; strains that have the gene for polymerase production spliced in them, but I am wondering about the &quot;native&quot; variant. I imagine that &lt;em&gt;Thermus aquaticus&lt;/em&gt; is rather difficult to culture in a medium; is it thus true that the archaeans have to be extracted from the springs they came from for producing &quot;native&quot; polymerase?&lt;/p&gt;&#xA;" OwnerDisplayName="user132" LastEditorDisplayName="user59" LastEditDate="2011-12-15T15:54:38.233" LastActivityDate="2015-03-18T20:15:08.163" Title="How is Taq polymerase produced?" Tags="&lt;molecular-biology&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="94" PostTypeId="1" AcceptedAnswerId="98" CreationDate="2011-12-15T14:58:09.603" Score="32" ViewCount="53513" Body="&lt;p&gt;Cerebrospinal fluid (CSF) is produced in the choroid plexus of the lateral ventricles and in the 4th ventricle of the brain.  CSF then circulates through the ventricles of the brain and the subarachnoid space of the meninges.  CSF is returned to the venous system via the arachnoid granulations connecting the subrachnoid space with the superior sagittal sinus at the superior portion of the neurocranium.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;What circulates the CSF such that it can return to the venous system against gravity?  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In other words, why does CSF not all just pool in the caudal cistern?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="137" LastActivityDate="2016-08-04T02:47:53.303" Title="How does cerebrospinal fluid circulate in the central nervous system?" Tags="&lt;neuroscience&gt;&lt;human-anatomy&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="95" PostTypeId="2" ParentId="90" CreationDate="2011-12-15T15:01:23.843" Score="24" Body="&lt;p&gt;There has been a recent report on Science, which had much return in the general press, in which a bacteria was identified that could live in an environment where arsenic was subsituted to phosphorus (one of the components of DNA, forming the backbone of the double helyx).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the original paper:&lt;br&gt;&#xA;&lt;a href=&quot;http://www.sciencemag.org/content/332/6034/1163.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus&lt;/a&gt;&lt;br&gt;&#xA;and the commentary appeared on Nature&lt;br&gt;&#xA;&lt;a href=&quot;http://www.nature.com/news/2010/101202/full/news.2010.645.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Arsenic-eating microbe may redefine chemistry of life&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is, however, much critique on the methodology used in the paper, and on whether arsenic would really be incorporated in DNA instead of phosphorus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Science published several of these critiques in an &lt;a href=&quot;http://www.sciencemag.org/content/early/2011/05/26/science.1208877&quot; rel=&quot;nofollow noreferrer&quot;&gt;Editor's Note&lt;/a&gt;&#xA;And here you will find the &lt;a href=&quot;http://www.sciencemag.org/content/early/2011/05/26/science.1202098.abstract?sid=056401d0-39ae-48b4-a069-76547475c618&quot; rel=&quot;nofollow noreferrer&quot;&gt;Response of the Authors&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other than that... well if you consider virus as life-forms, there's plenty that do not have double stranded DNA, but have instead single strand DNA or single strand RNA or double strand RNA.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://xkcd.com/829/&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;According to a new paper published in the journal Science, reporters are unable to thrive in an arsenic-rich environment.&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/b1WBH.png&quot; alt=&quot;XKCD on arsenic-based life&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="303" LastEditDate="2012-01-09T17:48:19.233" LastActivityDate="2012-01-09T17:48:19.233" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="96" PostTypeId="2" ParentId="90" CreationDate="2011-12-15T15:07:48.910" Score="13" Body="&lt;p&gt;It depends whether you call prions a life form, but prions do not make (direct) use of DNA to propagate themselves. They force other proteins into a misfolded protein state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, the question remains whether prions should be considered &quot;alive&quot;.&lt;/p&gt;&#xA;" OwnerUserId="138" LastActivityDate="2011-12-15T15:07:48.910" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="97" PostTypeId="2" ParentId="92" CreationDate="2011-12-15T15:17:46.470" Score="15" Body="&lt;p&gt;When a fungal spore germinates in a suitable location, the growing mycelium will spread underground in all directions. In the ideal situation, the result is that the mycelium will become circular. Over time, the center of the mycelium will die out whereas the newly formed mycelium (underground) will develop the familiar mushrooms above ground and this will result in a fairy ring.&lt;/p&gt;&#xA;" OwnerUserId="138" LastActivityDate="2011-12-15T15:17:46.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="98" PostTypeId="2" ParentId="94" CreationDate="2011-12-15T15:33:06.307" Score="19" Body="&lt;p&gt;There are several points here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Arachnoid granulations are not the only &quot;sinks&quot; for CSF.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even though it is true that most of the CSF is eliminated from ventricular system and subarachnoid space through these granulations, there are also suggestions that there are also other potential mechanism of shunting CSF into the venous system:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Cranial nerves leaving CNS go through &lt;em&gt;dura mater&lt;/em&gt; and these holes are not sealed, so it is suggested that some CSF can just go along the nerves and then accumulate in the lymphatic nodes in submucus. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Dura mater&lt;/em&gt; is mostly perforated at the area of &lt;em&gt;lamina cribrosa&lt;/em&gt;, that basically separates the nasal holes and our brain. Leaking through multiple small holes here CSF is accumulated into the lymphatic submucusal nodes, found in abundance here. &lt;em&gt;This way is considered to be primary CSF drainage way in newborns who don't have a well developed granularities in (sub)arachnoid space.&lt;/em&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Spinal nerves, especially in the upper part of the spinal cord, also leave unsealed holes and the presence of lymphatic nodes adjacent to the places where these nerves leave the verterbral column also make them a potential place for CSF drainage.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Arachnoid granularitis do not only drain, they are capable of active CSF uptake.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CFS is not just &quot;circulating&quot; here going from the place of its origin in lateral ventricles to venous system. The granularities are here to actively resorb this fluid, meaning that they effectively take it up forming vacuoles and then excrete it to the venous system. Constant uptake leads to the pressure gradient (see also below!) that acts as a driving force for CSF.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Venous system has generally low pressure, thus sucking the CSF up to drainage points.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Speaking about drainage we also should consider the fact that the venous system has a pressure lower than the atmospheric pressure and much lower than pressure in any middle-sized arterial vessels. This is reached by having elastic walls and by transmitting the negative pressure from the mediastinum during the inhale, when the diaphragm and the thorax expand. This negative pressure propagates mostly to the connected vessels, including sinus system. Due to the elastic wall other parts of venous system can accommodate this negative pressure constrict their lumen, but not the sinus system which has a hard external framework formed by &lt;em&gt;dura mater&lt;/em&gt; and bones. That is here we can measure the lowest pressure and this is the pressure that sucks CSF in into the venous system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope that answers your question.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2011-12-15T15:33:06.307" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="99" PostTypeId="1" AcceptedAnswerId="405" CreationDate="2011-12-15T15:47:46.337" Score="12" ViewCount="293" Body="&lt;p&gt;I'm trying to find a histochemical stain for beta-keratin, the type found in Reptilia which is organized in beta-sheets. It's different than alpha-keratin which is found in mammalian skin, hair, nails, etc., and is formed of alpha-helices. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Simple searches have produced results specific to mammals and alpha-keratin. Are there any good stains for beta-keratin?&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorDisplayName="user132" LastEditDate="2011-12-15T21:48:38.817" LastActivityDate="2012-01-01T18:03:44.507" Title="What histological stain can I use for beta-keratin?" Tags="&lt;histology&gt;&lt;staining&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="100" PostTypeId="1" CreationDate="2011-12-15T15:48:00.697" Score="14" ViewCount="706" Body="&lt;p&gt;It is known that there are animals that acquire toxins through their diet or through their surroundings. The examples I know of include butterflies stocking up on alkaloids/glycosides while in the caterpillar stage (monarchs snacking on milkweed come to mind), fish acquiring ciguatoxin or tetrodotoxin from marine bacteria, and arrow poison frogs and pitohuis acquiring batrachotoxin and other nasties from the insects they eat. Are there any other nice examples of animals like these?&lt;/p&gt;&#xA;" OwnerDisplayName="user132" LastActivityDate="2011-12-16T11:42:19.070" Title="Examples of animals that co-opt toxins?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="101" PostTypeId="1" CreationDate="2011-12-15T15:48:15.503" Score="5" ViewCount="3031" Body="&lt;p&gt;What are the optimal staining conditions when using Gel Red? So far, since we have started using it, the gels ran in our lab have been of very poor quality. The bands are very blurred and often indistinguishable. We have tried both pre- and post-staining, together with varying concentrations of Gel Red. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any advice about how to fix this problem?&lt;/p&gt;&#xA;" OwnerUserId="139" LastEditorUserId="6" LastEditDate="2011-12-15T19:25:11.513" LastActivityDate="2015-04-09T23:28:29.260" Title="What conditions should I use for Gel Red staining?" Tags="&lt;dna&gt;&lt;staining&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="102" PostTypeId="2" ParentId="90" CreationDate="2011-12-15T15:52:52.850" Score="12" Body="&lt;p&gt;There are serious speculations that the origins of life were using RNAs both as enzymes and genetic information carrier.&lt;br&gt;&#xA;Later this informative RNAs evolved into a more stable and less reactive DNAs, enzymatic role was delegated to proteins and RNA only remained into most crucial parts of expression chain (mRNA and rybosome) and some regulation mechanisms. &lt;/p&gt;&#xA;" OwnerDisplayName="user59" LastActivityDate="2011-12-15T15:52:52.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="103" PostTypeId="2" ParentId="92" CreationDate="2011-12-15T15:55:06.667" Score="13" Body="&lt;p&gt;In addition, the mycelia (the underground mass of hyphae which constitutes the bulk of the fungus) expand &lt;strong&gt;outwards&lt;/strong&gt; because they decompose organic matter in soil as they go, leaving very little organic matter in the soil in the interior of the ring. My Campbell &amp;amp; Reece textbook tells me that they can expand outwards at about 30 cm/yr. (1)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) Campbell, N.A., Reece, J.B. et al., &lt;em&gt;Biology&lt;/em&gt;, 8th edition, Pearson, 2008&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorDisplayName="user132" LastEditDate="2011-12-19T14:18:36.823" LastActivityDate="2011-12-19T14:18:36.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="104" PostTypeId="2" ParentId="91" CreationDate="2011-12-15T15:55:43.910" Score="18" Body="&lt;p&gt;So, let us introduce some keywords.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;electrical pulse&quot; that &quot;is sent from between brain and nerves&quot; is called an &lt;strong&gt;Action Potential&lt;/strong&gt; (AP). This is then &lt;strong&gt;propagated&lt;/strong&gt; along a nerve fiber until the target organ.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, a neuronal cell has a body and several long extended structures that &quot;sprout&quot; from the cell body. &lt;strong&gt;Dendrites&lt;/strong&gt; receive signals from other cells and they convey signals towards the cell body by creating small electrical currents. The &lt;strong&gt;axon&lt;/strong&gt; is a single &quot;sprout&quot; that is usually much thinner and longer than the dendrites and it conveys action potentials from the near the cell body to target cells and organs. Some axons can be as long as 80-90 cm (imagine!)! At the place where axon leaves the nerve cell body there is a small protrusion called the &lt;em&gt;axon hillock&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The AP originates at a special part of the axon called the &lt;em&gt;axon initial segment (AIS)&lt;/em&gt;. The initial segment is the first part of the axon as it leaves the cell body and sits immediately after the axon hillock.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The electrical pulse is the short electrical discharge, that can be seen as a sudden movement of many charged particles from one place to another. In our cells we have ions of Na&lt;sup&gt;+&lt;/sup&gt; (sodium), K&lt;sup&gt;+&lt;/sup&gt; (potassium) and Cl&lt;sup&gt;-&lt;/sup&gt; (chloride) (and in some cases also Ca&lt;sup&gt;2+&lt;/sup&gt;) that constitute these charged particles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two types of driving forces for these particles: besides the &lt;strong&gt;potential gradient&lt;/strong&gt;, e.g. the difference in the total charge in two different places there is also another force called &lt;strong&gt;concentration gradient&lt;/strong&gt;, e.g. the difference in concentration at two different places. These force can point into opposite directions, and thus by exploiting one force (let's say concentration gradient) we can influence another one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What we need here again is a so-called &lt;strong&gt;semi-permeable membrane&lt;/strong&gt;, this is just a barrier for ions, but only for specific ones. We need this because our main ions -- Na&lt;sup&gt;+&lt;/sup&gt; and K&lt;sup&gt;+&lt;/sup&gt; -- are both positively charged. Therefore the cell membrane acts as a semi-permeable membrane, letting K&lt;sup&gt;+&lt;/sup&gt; into the cells and Ca&lt;sup&gt;2+&lt;/sup&gt; ions outwards but not the opposite. Therefore we have two &lt;em&gt;concentration gradients&lt;/em&gt;: Na&lt;sup&gt;+&lt;/sup&gt; (outside is the peak) and K&lt;sup&gt;+&lt;/sup&gt; (inside is the peak).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to start the pulse we need to initiate a massive ionic drift from one place to another. This is done by the cell, and the first event here is the drastic change (increase) of the permeability for Na&lt;sup&gt;+&lt;/sup&gt; ions. Na&lt;sup&gt;+&lt;/sup&gt; ions massively enter the cell and their charges, moved into the cell, form the upstroke of the &lt;em&gt;action potential&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The protective mechanism of the cell immediately start working against the Na&lt;sup&gt;+&lt;/sup&gt; invasion and open the reserve shunts -- the K&lt;sup&gt;+&lt;/sup&gt; channels. K&lt;sup&gt;+&lt;/sup&gt; leaves the cell, taking away some charge and this is revealed as the decay of the action potential. But potassium channels are generally slower, that is why the decay of the pulse is more steady, not as sharp as the upstroke.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might be wondering now: what triggers the rapid change of membrane permeability then? There are several factors here that may contribute into this process.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Potential change of the membrane. Sodium and potassium channels are &lt;strong&gt;voltage-sensitive&lt;/strong&gt;, meaning if you manage to change the resting potential of the membrane, formed due to concentration gradients and normally being about -90..-80 mV (millivolts) up to about -40 mV it will trigger the sodium channels. This is how the impulse propagates -- having originated at one place it just decreases the resting potential of the adjacent membrane area, sodium enters the cell there and the AP travels along the nerve. The AIS is the site of AP initiation because this part of the cell has a very high density of voltage-gated sodium channels.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Chemical agents, called neurotransmitters, can be detected by receptors on the cell membrane. Some of these receptors are ion channels themselves and open directly when neurotransmitter is bound. Other receptors act through intracellular signals to open ion channels. This is how the signal appears at the sites of nerve cell contacts -- neurotransmitters, like acetylcholine or adrenaline, just act here as triggers for membrane permeability.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="66" LastEditorUserId="72" LastEditDate="2011-12-19T14:18:19.443" LastActivityDate="2011-12-19T14:18:19.443" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="105" PostTypeId="2" ParentId="4" CreationDate="2011-12-15T16:00:41.147" Score="16" Body="&lt;p&gt;&lt;a href=&quot;http://bitesizebio.com/articles/ye-olde-antibiotic-plates/&quot;&gt;This Bitesize Bio article&lt;/a&gt; is very informative on this issue.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC376956/&quot;&gt;The 1970 study&lt;/a&gt; they cite found negligible reduction in the the efficacy of non-beta-lactam antibiotics (kanamycin, chloramphenicol) over spans of 4 weeks or 60 days.  Ampicillin loses about 10% activity at 4 weeks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my lab, we only take care not to use LB/Amp plates that are older then 4 weeks, for LB/Km, we store them at 4 °C for more then a month, sealed in a plastic bag.&lt;/p&gt;&#xA;" OwnerUserId="139" LastEditorUserId="25" LastEditDate="2011-12-15T19:24:57.740" LastActivityDate="2011-12-15T19:24:57.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="106" PostTypeId="2" ParentId="90" CreationDate="2011-12-15T16:06:20.357" Score="39" Body="&lt;p&gt;To follow up what mbq said, there have been a number of &quot;origin of life&quot; studies which suggest that RNA was a precursor to DNA,  the so-called &quot;RNA world&quot; (1). Since RNA can carry out both roles which DNA and proteins perform today. Further speculations suggest things like a Peptide-Nucleic Acids &quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/Peptide_nucleic_acid&quot; rel=&quot;noreferrer&quot;&gt;PNA&lt;/a&gt;&quot;  may have preceded RNA and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Catalytic molecules and genetic molecules are generally required to have different features. For example, catalytic molecules should be able to fold and have many building blocks (for catalytic action), whereas genetic molecules should not fold (for template synthesis) and have few building blocks (for high copy fidelity). This puts a lot of demands on one molecule. Also, catalytic biopolymers can (potentially) catalyse their own destruction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RNA seems to be able to balance these demands, but then the difficulty is in making RNA prebiotically - so far his has not been achieved. This has lead to interest in &quot;metabolism first&quot; models where early life has no genetic biopolymer and somehow gives rise to genetic inheritance. However, so far this seems to have been little explored and largely unsuccessful (2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;edit&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just saw &lt;a href=&quot;http://www.newscientist.com/article/dn21335-before-dna-before-rna-life-in-the-hodgepodge-world.html&quot; rel=&quot;noreferrer&quot;&gt;this popular article&lt;/a&gt; in New Scientist which also discusses TNA (Threose nucleic acid) and gives some background reading for PNA, GNA (Glycol nucleic acid) and ANA (amyloid nucleic acid).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v319/n6055/abs/319618a0.html&quot; rel=&quot;noreferrer&quot;&gt;(1) Gilbert, W., 1986, Nature, 319, 618 &quot;Origin of life: The RNA world&quot;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17897696&quot; rel=&quot;noreferrer&quot;&gt;(2) Copley et al., 2007, Bioorg Chem, 35, 430 &quot;The origin of the RNA world: co-evolution of genes and metabolism.&quot;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="1402" LastEditDate="2015-07-16T03:57:37.623" LastActivityDate="2015-07-16T03:57:37.623" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="107" PostTypeId="1" AcceptedAnswerId="161" CreationDate="2011-12-15T16:12:35.400" Score="25" ViewCount="616" Body="&lt;p&gt;While investigating the rise of adult lactose tolerance, I came across the news that China has been encouraging its citizens to drink more milk, even though most of the Asian population lacks the SNP (single-nucleotide polymorphism) which conveys lactase persistence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it still possible for an adult without lactase persistence to build-up a tolerance for lactose over time? If so, what's the mechanism?&lt;/p&gt;&#xA;" OwnerUserId="42" LastEditorUserId="3632" LastEditDate="2012-07-05T18:24:43.210" LastActivityDate="2012-09-29T15:47:40.553" Title="Can an adult without genetic lactase persistence still develop a tolerance for dairy foods?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;enzymes&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="108" PostTypeId="1" CreationDate="2011-12-15T16:32:42.327" Score="46" ViewCount="4339" Body="&lt;p&gt;Cockroaches are very hardy insects. It is known that, among other things, they are able to withstand bursts of ionizing radiation that would kill a human being.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The explanations of this observed resistance I've seen include cell division not being that fast in cockroaches, and the relative simplicity of these insects compared to other organisms. I know that microbes are able to resist radiation by having &quot;tough&quot; DNA (more G-C base pairs) and ready repair systems. Do cockroaches also have mechanisms like these, or is it really as simple as them being, well, &quot;simple&quot;?&lt;/p&gt;&#xA;" OwnerDisplayName="user132" LastEditorUserId="69" LastEditDate="2012-01-22T21:29:43.107" LastActivityDate="2012-01-31T13:51:25.343" Title="How do cockroaches resist the effects of ionizing radiation?" Tags="&lt;dna&gt;&lt;zoology&gt;&lt;radiation&gt;&lt;entomology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="109" PostTypeId="1" CreationDate="2011-12-15T16:35:45.690" Score="8" ViewCount="242" Body="&lt;p&gt;Do clotting factors tpa and pai-1 lead to degenerative osteoarthritis in the same way that lupus anticoagulant and prothrombin might? Is one of these pathways particularly detrimental during formation of osteoarthritis or avascular necrosis (if these factors are inhibited or modified in some way)?&lt;/p&gt;&#xA;" OwnerUserId="140" LastEditorUserId="338" LastEditDate="2012-02-20T17:42:09.440" LastActivityDate="2012-09-30T22:41:42.237" Title="What are the clotting factors' effect on avascular necrosis development?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;enzymes&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="110" PostTypeId="2" ParentId="91" CreationDate="2011-12-15T17:26:25.013" Score="44" Body="&lt;p&gt;This is quite a big question! I'll try to outline the basic view.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, let's review how neurons signal between each other. The canonical way for a neuron to send a signal to a downstream neuron is by generating an &lt;strong&gt;action potential&lt;/strong&gt;, the &quot;electrical impulse&quot; you have heard of. This action potential causes the release of neurotransmitter at a point where the two cells are very close to each other called a &lt;strong&gt;synapse&lt;/strong&gt;. The downstream postsynaptic cell receives the neurotransmitter signal and converts it into a small electrical signal. If enough of these small electrical signals happen in a short time, they sum together and are likely to initiate an action potential in the second cell and the cycle repeats all along the circuit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is the electrical signal generated? The basics of how this works was worked out most famously by Hodgkin and Huxley in 1952. The short story is that the &lt;em&gt;plasma membrane is selectively permeable to ions&lt;/em&gt;. Let's build the concept from the ground up.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;The toolbox&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Imagine a sphere of plasma membrane that represents a simple neuron. For starters, we assume that this membrane is bare lipid with no membrane-associated proteins. Because of the hydrophobicity of the bilayer, charged particles cannot diffuse through the membrane. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The cell is bathed, inside and outside, in a solution containing many &lt;strong&gt;ions&lt;/strong&gt; (charged atoms), including sodium (Na+), potassium (K+), chloride (Cl-), and calcium (Ca2+). As we noted above, these ions cannot go through the membrane without &quot;help&quot;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Now we add an &lt;em&gt;ion pump&lt;/em&gt; protein into the membrane which will pump sodium ions out and potassium ions in. This particular pump, the &lt;strong&gt;Na-K ATPase&lt;/strong&gt;, creates an excess of sodium ions outside the cell and an excess of potassium ions inside.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Now we add a potassium &lt;strong&gt;ion channel&lt;/strong&gt; to the membrane. This protein creates a pore in the membrane that only allows potassium ions through. This particular protein's pore is always open. Now things start getting exciting...&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What do the potassium ions do now that they can go through the membrane? Ions will move based on the forces created by their &lt;strong&gt;electrochemical gradients&lt;/strong&gt;. The pump created a chemical gradient by putting excess K+ inside, so the K+ ions start to flow out through the ion channels. But K+ ions are positively charged, so when they flow out, positive charge starts building up outside and negative charge builds up inside. This electrical gradient opposes the chemical gradient, tending to pull the K+ ions into the cell while the chemical gradients pulls K+ ions out. The influx and efflux reach an equilibrium at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nernst_equation&quot;&gt;Nernst potential&lt;/a&gt;, where the electrical and chemical forces equal out. For physiological concentrations of K+ ions, the K+ equilibrium potential is about -80mV or -90mV. This means that K+ ions will flow until the outside of the cell is 80-90mV more positive than the inside of the cell. We started at 0mV, so K+ ions mostly flow out.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;We now have a &lt;strong&gt;membrane potential&lt;/strong&gt;, a difference in electrical potential between the inside and the outside of the cell at about -80mV (usually closer to -70mV or -60mV in &quot;real life&quot;). In particular, this membrane potential is the &lt;em&gt;resting potential&lt;/em&gt; that exists when the cell is not active. We can simplify for now and think of the resting potential as being set by a resting permeability of the membrane to potassium ions, but not to sodium ions. We call this membrane polarized, and thus &lt;strong&gt;depolarization&lt;/strong&gt; is when the membrane potential becomes more positive, and &lt;strong&gt;hyperpolarization&lt;/strong&gt; is when the membrane potential becomes more negative.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Now, we add to the membrane a &lt;strong&gt;voltage-gated sodium channel&lt;/strong&gt;, an ion channel that passes only sodium ions but is usually closed. The voltage-gating means that this ion channel is sensitive to the membrane potential. At the resting potential, the pore is closed and the membrane is still impermeable to sodium ions. When the membrane potential becomes slightly more positive, the channels opens and sodium ions can flow. This channel is also &lt;em&gt;inactivating&lt;/em&gt;, so that when it opens it only opens for a short period of time, letting in a limited amount of sodium.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What way will sodium flow when we open this channel? Because of the negative resting potential (-70mV) and the excess of sodium ions outside due to the pump, both the electrical and chemical gradient will drive sodium ions into the cell. The sodium equilibrium potential is usually around +60mV.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;To complete the machinery for generating an action potential, we also add a &lt;strong&gt;voltage-gated potassium channel&lt;/strong&gt; to the membrane. It works just like the voltage-gated sodium channel that is also closed at rest and opens when the membrane potential becomes more positive. This channel opens a bit more slowly than the sodium channel does, but it does not inactivate.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;h2&gt;Generating an action potential&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Ok, so how do these parts come together to create an electrical impulse?&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The cell sits at its resting membrane potential, with all of its voltage-gated channels closed. It receives a signal from an upstream cell that causes a slight depolarization. The action potential will initiate when the membrane potential hits the &lt;strong&gt;threshold potential&lt;/strong&gt;. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;At the threshold potential, the voltage-gated sodium channels open letting sodium ions flow into the cell. The sodium flux pulls the membrane from the resting potential (-70mV) towards the sodium equilibrium potential (+60mV). These values are far apart, so the driving force is large and the membrane depolarizes rapidly. This is the action potential &lt;strong&gt;upstroke&lt;/strong&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The depolarization also activates the (slightly slower) voltage-gated potassium channels. The potassium ions flow out and drive the depolarized membrane (about +20mV at the action potential peak) back towards the potassium equilibrium potential (-80mV). At the same time, the sodium channels are inactivating so that sodium is no longer depolarizing the membrane. The repolarization rate is usually slower than the depolarization rate. This is the action potential &lt;strong&gt;downstroke&lt;/strong&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The whole process of the action potential depolarization/repolarization cycle takes about 2-3 milliseconds in an &quot;average&quot; neuron. Once the cell reaches resting potentials again, the membrane is basically reset. The voltage-gated channels are turned off. The ion pump moves the potassium ions that flowed out and the sodium ions that flowed in. That patch of membrane is ready to fire another action potential!&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;As a final note, I'll mention that the voltage-gated sodium channel provides a mechanism for the action potential to &lt;strong&gt;propagate&lt;/strong&gt; down the axon. The action potential is initiated in one location of the cell, and creates a depolarization. This depolarization causes the voltage-gated sodium channels in neighbouring regions of the membrane to open and generate an action potential cycle of their own. This is how an action potential travel down axons (and sometimes dendrites too).&lt;/p&gt;&#xA;" OwnerUserId="72" LastEditorUserId="72" LastEditDate="2011-12-15T20:18:05.107" LastActivityDate="2011-12-15T20:18:05.107" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="111" PostTypeId="1" AcceptedAnswerId="114" CreationDate="2011-12-15T17:27:59.147" Score="21" ViewCount="1692" Body="&lt;p&gt;There are several examples where the largest animals were killed off preferentially due to a major ecological shift:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The KT extinction event&lt;/li&gt;&#xA;&lt;li&gt;The Holocene extinction, as well as the major megafauna humans killed off&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Mammaliaformes&quot;&gt;common ancestor of modern mammals&lt;/a&gt; is thought to be &quot;shrew-like&quot; in size, and it differentiated into most of the large animal species in the world today.  I imagine that a similar statement can be made for dinosaurs.  In general it seems that a major extinction event is likely to be best weathered by smaller creatures which can later, over time, increase in size to fill the niche that larger animals, and evolution dictates it will be profitable to do so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this limit large animals to only the branches of the tree of life?  Any given set of (Multicellular) species obviously share a common ancestor that is much smaller than them.  Is it possible for many species to share a common ancestor that is considerably larger than any of them?&lt;/p&gt;&#xA;" OwnerUserId="18" LastEditorDisplayName="user132" LastEditDate="2011-12-15T17:54:24.157" LastActivityDate="2011-12-15T18:16:29.323" Title="Do large animals often evolve into smaller animals?" Tags="&lt;evolution&gt;&lt;zoology&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="112" PostTypeId="5" CreationDate="2011-12-15T18:06:42.703" Score="0" Body="&lt;p&gt;Virology deals with the study of viruses, infectious entities that require the machinery of a host cell to replicate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;related: &lt;a href=&quot;/questions/tagged/microbiology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;microbiology&amp;#39;&quot; rel=&quot;tag&quot;&gt;microbiology&lt;/a&gt; &lt;a href=&quot;/questions/tagged/bacteriology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;bacteriology&amp;#39;&quot; rel=&quot;tag&quot;&gt;bacteriology&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="16866" LastEditDate="2019-08-25T03:53:53.973" LastActivityDate="2019-08-25T03:53:53.973" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="113" PostTypeId="4" CreationDate="2011-12-15T18:06:42.703" Score="0" Body="Virology deals with the study of viruses, infectious entities that require the machinery of a host cell to replicate." OwnerDisplayName="user132" LastEditorUserId="4101" LastEditorDisplayName="user132" LastEditDate="2013-08-28T04:57:25.337" LastActivityDate="2013-08-28T04:57:25.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="114" PostTypeId="2" ParentId="111" CreationDate="2011-12-15T18:16:29.323" Score="24" Body="&lt;p&gt;Your question brings up several important issues with regards to the evolution of body size. The rationale for concluding that the ancestral mammal had a small body size is that all of the taxa in that area of the tree tend to be small. In contrast, if all of those taxa had been cow-sized, then the most parsimonious conclusion would be that the ancestral mammal was cow-sized.&lt;/p&gt;&#xA;&lt;h2&gt;Identification of ancestors is difficult&lt;/h2&gt;&#xA;&lt;p&gt;Identification of a fossil species as &lt;em&gt;the most recent common ancestor&lt;/em&gt; of a pair of sister taxa is exceedingly difficult. The way that different species are diagnosed in fossils in by their unique derived characteristics (&lt;a href=&quot;http://en.wikipedia.org/wiki/Autapomorphy&quot; rel=&quot;noreferrer&quot;&gt;autapomorphies&lt;/a&gt;). So if a fossil is found with no autapomorphies, then it is plausibly an ancestor (i.e., at the split between two sister taxa). Some would argue that if you don't find any autapomorphies, then you just haven't looked closely enough.&lt;/p&gt;&#xA;&lt;h2&gt;Cope's Rule&lt;/h2&gt;&#xA;&lt;p&gt;The idea that lineages tend to evolve toward larger body size is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Cope%27s_rule&quot; rel=&quot;noreferrer&quot;&gt;Cope's Rule&lt;/a&gt;, named for the paleontologist Edward Drinker Cope. The success of Cope's Rule has been highly variable, with some lineages following and others not (&lt;a href=&quot;http://www.jstor.org/stable/2897758&quot; rel=&quot;noreferrer&quot;&gt;Polly, 1998&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;p&gt;Some clades following Cope's Rule&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Early reptiliomorphs (&lt;a href=&quot;http://dx.doi.org/10.1080/10635150490445706&quot; rel=&quot;noreferrer&quot;&gt;Laurin, 2004&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Pterodactyloidea (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2006.01284.x/abstract&quot; rel=&quot;noreferrer&quot;&gt;Hone and Benton, 2007&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Most Cambrian-Devonian marine invertebrates (&lt;a href=&quot;http://dx.doi.org/10.1666/0094-8373%282008%29034%5B0210:EBTICM%5D2.0.CO;2&quot; rel=&quot;noreferrer&quot;&gt;Novack-Gottshall, 2008&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;North American canids (&lt;a href=&quot;http://www.sciencemag.org/content/306/5693/101.short&quot; rel=&quot;noreferrer&quot;&gt;Van Valkenburgh et al., 2004&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Mesozoic birds (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2007.01483.x/full&quot; rel=&quot;noreferrer&quot;&gt;Hone et al., 2008&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Some clades not following Cope's Rule&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Early stegocephalians (&lt;a href=&quot;http://dx.doi.org/10.1080/10635150490445706&quot; rel=&quot;noreferrer&quot;&gt;Laurin, 2004&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;&amp;quot;Rhamphorhynchoid&amp;quot; pterosaurs (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2006.01284.x/abstract&quot; rel=&quot;noreferrer&quot;&gt;Hone and Benton, 2007&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Mesozoic birds (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2008.01594.x/full&quot; rel=&quot;noreferrer&quot;&gt;Butler and Goswami, 2008&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Note that many results depend on the methods used.&lt;/p&gt;&#xA;&lt;h2&gt;Evidence from experimental evolution&lt;/h2&gt;&#xA;&lt;p&gt;Several studies have addressed body size evolution in vertebrates both directly and indirectly. MacArthur (&lt;a href=&quot;http://www.jstor.org/stable/10.2307/2457976&quot; rel=&quot;noreferrer&quot;&gt;1944a&lt;/a&gt;, &lt;a href=&quot;http://www.jstor.org/stable/10.2307/2458253&quot; rel=&quot;noreferrer&quot;&gt;1944b&lt;/a&gt;) directly selected for large and small body mass in laboratory mice. Within 8 generations, mean body masses had increased or decreased by over 50%. Even when body mass is not directly selected upon, mass can change in a correlated way. &lt;a href=&quot;http://www.biology.ucr.edu/people/faculty/Garland.html&quot; rel=&quot;noreferrer&quot;&gt;Selection for high levels of voluntary activity&lt;/a&gt; has led to an approximately 25% reduction in body mass.&lt;/p&gt;&#xA;&lt;p&gt;Based on these studies, evolution of body size (larger or smaller) is certainly possible within relatively few generations.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2011-12-15T18:16:29.323" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="115" PostTypeId="1" AcceptedAnswerId="137" CreationDate="2011-12-15T18:38:36.700" Score="22" ViewCount="725" Body="&lt;p&gt;Are there any books or sites that detail, step-by-step, the evolution of the first single-celled organisms (bacteria, archaea) from a Miller-Urey-like beginning? That is, assumes only amino acids, then from there to self-replicating proteins, until culminating in the formation of a basic cell?&lt;/p&gt;&#xA;" OwnerUserId="42" LastEditorUserId="6" LastEditDate="2012-02-19T20:40:11.433" LastActivityDate="2012-02-19T20:40:11.433" Title="Good source that explains the evolution of single-celled organisms &quot;from scratch&quot;" Tags="&lt;evolution&gt;&lt;abiogenesis&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="116" PostTypeId="2" ParentId="11" CreationDate="2011-12-15T19:42:47.340" Score="6" Body="&lt;p&gt;It depends of what you call endosymbiosis. In the sense of mutualistic interaction between host cell and intracellular organism, it also include Rhizobium bacteria and Fabaceae plants, some Cnidaria and algea in their cells, and even some micorrhizal fungi that invade into plants cells. But parasitic interactions are also sometimes call symbiosis, as symbiosis means just “living together” and the balance between profits and costs for each partner are sometimes difficult to measure and even changes in time. So in this wider meaning even Trichinella worm that live in mammal cell is an endosymbiont and endosymbiosis is very common.&lt;/p&gt;&#xA;" OwnerUserId="68" LastActivityDate="2011-12-15T19:42:47.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="117" PostTypeId="1" CreationDate="2011-12-15T20:11:09.590" Score="8" ViewCount="227" Body="&lt;p&gt;I'd like to produce a specific DNA sequence on a milligram-scale and &lt;sup&gt;13&lt;/sup&gt;C&lt;sup&gt;15&lt;/sup&gt;N-label it. The sequence is around 35 nucleotides long, so chemical synthesis is out due to the exorbitant costs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm also only interested in the single-stranded DNA, so a method that produces double-stranded DNA without any way to easily separate the strands would also not be useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What methods are there to produce labelled DNA that fulfill these requirements?&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="25" LastEditDate="2011-12-16T07:10:18.770" LastActivityDate="2013-11-24T03:42:17.380" Title="How can I produce milligram quantities of an isotope-labeled DNA oligomer?" Tags="&lt;dna&gt;&lt;biochemistry&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="118" PostTypeId="2" ParentId="117" CreationDate="2011-12-15T20:44:39.030" Score="2" Body="&lt;p&gt;You can also design a plasmid that has your 35mers and raise the bacteria with isotopic carbon and nitrogen C13 acetate and N15 ammonium sulfate will work with E coli in a minimal medium.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;this is not cheap, but the cheapest available sources of the isotopes can be used.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2011-12-15T20:44:39.030" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="119" PostTypeId="2" ParentId="108" CreationDate="2011-12-15T20:48:23.657" Score="14" Body="&lt;p&gt;Studies of &lt;em&gt;Deinococcus radiodurans&lt;/em&gt;, the most radioactively tolerant microorganism we know, show that it has many genes for DNA repair.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of the cockroach, I would assume that in addition to repairing genes, and maybe some antioxidants produced in the cells to quench free radicals produced by radiation, the fact that the roaches lay many, many eggs is also useful. If the radiation kills 99.99% of the roaches, you will still have some insects coming from the egg clutches. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Selection is the insect's friend when you are a k-limited animal!&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="81" LastEditDate="2012-01-09T02:13:22.370" LastActivityDate="2012-01-09T02:13:22.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="120" PostTypeId="1" CreationDate="2011-12-15T21:04:24.057" Score="12" ViewCount="1695" Body="&lt;p&gt;I would like to perform a modified co-immunoprecipitation assay using a GFP-tagged protein.  We are going to bind the tagged protein to anti-GFP antibody then bind that to protein A/G beads, however we want to be able to selectively elute the tagged protein off the beads.  I know that you can elute a FLAG tagged protein off of M2 anti-FLAG antibody by adding excess FLAG, so can I use the same approach with my GFP tag?  If so, does anyone know a commercially available GFP monoclonal antibody who's epitope has been mapped so I can use excess epitope to elute my protein?  Or possibly a source of recombinant GFP?&lt;/p&gt;&#xA;" OwnerUserId="143" LastEditorUserId="6" LastEditDate="2011-12-16T23:08:20.467" LastActivityDate="2011-12-16T23:08:20.467" Title="Can I elute my GFP-tagged protein off anti-GFP antibody using a peptide?" Tags="&lt;molecular-biology&gt;&lt;green-fluorescent-protein&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="121" PostTypeId="1" AcceptedAnswerId="1150" CreationDate="2011-12-15T21:42:01.323" Score="6" ViewCount="1904" Body="&lt;p&gt;I'm looking for a protocol to get genomic DNA from an &lt;em&gt;E. coli&lt;/em&gt; sample so that I can clone a small portion of it using PCR into a plasmid.  (&amp;lt; 500 bp in this case). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems &lt;a href=&quot;http://openwetware.org/&quot; rel=&quot;nofollow&quot;&gt;OWW&lt;/a&gt; (Open Wet Ware) only discusses preparation of fragmented DNA. Does this mean I have to cut it up before I can clone from it?  Any pointers would be really appreciated.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1098" LastEditDate="2013-01-30T02:10:57.713" LastActivityDate="2013-01-30T07:14:28.710" Title="How do I prepare and clone from E. coli DNA?" Tags="&lt;molecular-biology&gt;&lt;cloning&gt;&lt;dna-isolation&gt;" AnswerCount="2" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="122" PostTypeId="1" CreationDate="2011-12-15T22:37:28.343" Score="6" ViewCount="6509" Body="&lt;p&gt;My learning of molecular biology ended in the early 90's (and with early 90's era information). While I don't aspire to &lt;em&gt;be&lt;/em&gt; a molecular biologist, I do aspire to better understand modern approaches better.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Short of going back to school and taking classes, what are good resources for learning on my own? I'd like to get to the point of being able to understand Nature, Science, Cell, etc. Is this even a feasible goal?&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="6" LastEditDate="2012-01-12T10:46:13.010" LastActivityDate="2012-01-12T10:46:13.010" Title="What are good resources for self-learning modern molecular biology concepts?" Tags="&lt;molecular-biology&gt;" AnswerCount="4" CommentCount="6" FavoriteCount="5" ClosedDate="2011-12-16T16:11:44.547" ContentLicense="CC BY-SA 3.0" />
  <row Id="123" PostTypeId="2" ParentId="107" CreationDate="2011-12-15T22:58:17.450" Score="6" Body="&lt;p&gt;Here are my thoughts on the topic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dairy good is not only milk, but also the following milk products: sour milk products (like yougurt, kefir, katik, buttermilk, etc.), cheese, etc. These products can contain less lactose than in the milk solids (due to fermentation during processing). It is also common for some of these products to contain living lactase-active bacteria, that can digest lactose.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regular intake of these products can lead to certain changes in our small intestine microflora, so that the lacking lactase activity is substituted by the bacteria and thereby the tolerance grows. Maybe this is the intend of the Chinese government? Maybe they encourage the intake of sour milk products and not solid milk?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is known, for example, that children with congenital/primary enzymatic deficiency develop the tolerance at the age of 6-10 years so that no special diet is needed anymore. This is true at least for such common enzymatic deficiencies like phenylketonuria and coeliacia. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Russia, where I got my medical degree, it is common to use bacteria in the treatment of many types of primary intolerance combining this treatment with dietary support.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="1433" LastEditDate="2012-09-29T15:47:40.553" LastActivityDate="2012-09-29T15:47:40.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="124" PostTypeId="2" ParentId="122" CreationDate="2011-12-15T23:16:02.713" Score="10" Body="&lt;p&gt;Sure it's feasible! Of course, there are lots of papers that I can't read even with a recent education, but you should be able to make a good dent by:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Getting a good modern textbook like &lt;a href=&quot;http://amzn.to/tzSvLC&quot;&gt;Molecular Biology of the Cell by Alberts et al&lt;/a&gt;. This is becoming a standard text and gives pretty good coverage of the field. I find that it doesn't always get as detailed as I would like, but such is the nature of textbooks I think. Another textbook that some people like is &lt;a href=&quot;http://amzn.to/vC0snC&quot;&gt;Molecular Cell Biology by Lodish et al&lt;/a&gt;, although I don't have experience with it myself.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Watch online lectures. MIT OpenCourseWare has a pretty &lt;a href=&quot;http://ocw.mit.edu/courses/biology/7-012-introduction-to-biology-fall-2004/&quot;&gt;good molecular biology course&lt;/a&gt;. It may get basic for you at times, but the lecturers are well-respected molecular biologists and geneticists.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Read reviews in things like Nature Reviews to get a 30,000-foot view. Review authors often touch on concepts that primary literature assume you know. Armed with a good text, you should be able to get a good idea of what people are talking about. On a similar note, the &quot;News and Views&quot; commentary articles that accompany &quot;high-impact&quot; papers are great for giving people unfamiliar with the field a taste of why a certain paper deserves attention.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Come back here and ask!&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="72" LastEditorUserId="72" LastEditDate="2011-12-15T23:27:22.740" LastActivityDate="2011-12-15T23:27:22.740" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="126" PostTypeId="1" AcceptedAnswerId="648" CreationDate="2011-12-15T23:20:10.467" Score="14" ViewCount="836" Body="&lt;p&gt;The pig is only an example, just an animal. Leydig cells have protein inclusions (Reinke crystals) that are mostly made of crystallised lipofuscin. They are secretory inclusions i.e. cells formed in secreting cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of Leydig cell in pig's testicle:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IJ3Hq.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My teacher told me that there is a difference in the existence of some cells between humans and animals. &#xA;However, I cannot find such a difference. I have not been provided a slide of human Leydig cell so I have not been able to compare.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the morphological difference between Leydig cell in human and pig?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="81" LastEditDate="2012-01-15T11:07:24.247" LastActivityDate="2012-02-02T16:05:02.680" Title="What is the morphological difference between Leydig cell in human and pig?" Tags="&lt;anatomy&gt;&lt;histology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="127" PostTypeId="2" ParentId="108" CreationDate="2011-12-15T23:25:42.773" Score="38" Body="&lt;p&gt;Off the top of head as a medical professional I can imagine the following mechanisms (everything is just speculative reasoning):&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Insects don't have blood&lt;/strong&gt;. Instead, they have hemolymph whose primary role is not oxygen transport (they have an additional tracheal system for this purpose), but rather that of nutrients. &lt;strong&gt;Thus they don't need&lt;/strong&gt; (and don't have) &lt;strong&gt;an intense proliferation of blood cell precusors&lt;/strong&gt; -- these (bone marrow, spleen) are the most susceptible to radiation in a human and animal body.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Insects have a rather primitive immune system that is mostly humoral&lt;sup&gt;[a]&lt;/sup&gt;&lt;/strong&gt;  and much less cellular&lt;sup&gt;[b]&lt;/sup&gt; compared to the immune system of animals and humans. This eliminates the next common weak place in the body: lymphatic nodes, thymus, again spleen and bone marrow etc.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Insects have generally a much primitive&lt;/strong&gt; and in many cases also rather &lt;strong&gt;decentralized nervous system&lt;/strong&gt;: the ganglia are organized in a sort of a cord and even though the capital ganglia are usually larger, these dominance is not as prominent as in case of CNS and PNS in animals and humans. Therefore this system is much more tolerant to losses.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;1.-3. Therefore, the only sensitive part of insects is the intestinal epithelium which gets renewed on a regular basis (similar to that of humans, also a known target of radiation), but...&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Insects&lt;/strong&gt; (and generally the arthropodes) are known to &lt;strong&gt;have exoskeleton&lt;/strong&gt;. This potentially serves as a good &quot;armor&quot; for vulnerable intestine cells, filtering out the most heavy particles (like alpha- and in some respect also the beta-particles). &#xA;&lt;strong&gt;EDIT&lt;/strong&gt;: This seems not to be real protection, see the discussion in comments.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Therefore it is not a surprise that insects generally show much higher resistance against radiation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;:&#xA;As it was correctly added in the comments, there are also gamets, that are most sensitive to radiation (because they bear only the half of the normal genetic information and cannot repair mutations). Even though the lesions in gamets do not lead to immediate death, the potential sterility can easily cause the extinction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, cockroaches (and insects generally) are known to be r-animals, meaning that &lt;a href=&quot;http://en.wikipedia.org/wiki/R/K_selection_theory&quot;&gt;they favor the quantity (r) over quality (K) of their off-spring&lt;/a&gt;. This strategy is optimal when dealing with radiation-induced changes in gametes: the high number of offsprings compensates for the genetic imperfections in gametes.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;[a]&lt;/sup&gt; -- meaning that is has secreted peptides in their hemolymph that protect them&lt;br&gt;&#xA;&lt;sup&gt;[b]&lt;/sup&gt; -- there are phagocytes, somewhat similar to tissue magrophages in humans, but the rest of the cell chains in immune response in vertrebrates, like T- and B-cells, are completely missing. Those are responsible for the mediation and amplification of the immune response in vertebrates and are the cells that are most susceptible to radiation damage.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-31T13:51:25.343" LastActivityDate="2012-01-31T13:51:25.343" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="128" PostTypeId="5" CreationDate="2011-12-15T23:29:22.503" Score="0" Body="&lt;p&gt;&lt;strong&gt;Some Basic Definitions:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biochemistry is the branch of science that explores the chemical processes within and related to living organisms. It is a laboratory-based science that brings together biology and chemistry. By using chemical knowledge and techniques, biochemists can understand and solve biological problems.&lt;sup&gt;(&lt;a href=&quot;http://www.biochemistry.org/?TabId=456&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;)&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biochemistry is the study of the chemical substances and vital processes occurring in living organisms. Biochemists focus heavily on the role, function, and structure of biomolecules. The study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry.&lt;sup&gt;(&lt;a href=&quot;https://en.wikipedia.org/wiki/Biochemistry&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;)&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Brief introduction:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;History:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The history of biochemistry can be said to have started with the ancient Greeks who were interested in the composition and processes of life, although biochemistry as a specific scientific discipline has its beginning around the early 19th century. Some argued that the beginning of biochemistry may have been the discovery of the first enzyme, diastase (today called amylase), in 1833 by Anselme Payen, while others considered Eduard Buchner's first demonstration of a complex biochemical process alcoholic fermentation in cell-free extracts to be the birth of biochemistry. Some might also point to the influential work of Justus von Liebig from 1842, Animal chemistry, or, Organic chemistry in its applications to physiology and pathology, which presented a chemical theory of metabolism, or even earlier to the 18th century studies on fermentation and respiration by Antoine Lavoisier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Main branches:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Animal_Biochemistry&quot; rel=&quot;nofollow noreferrer&quot;&gt;Animal Biochemistry&lt;/a&gt; (biochemistry of animals)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Plant_physiology#Biochemistry_of_plants&quot; rel=&quot;nofollow noreferrer&quot;&gt;Plant Biochemistry&lt;/a&gt; (biochemistry of plants)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Molecular_biology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Molecular Biology&lt;/a&gt; (concerns the molecular basis of biological activity between biomolecules in the various systems of a cell)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Cell_biology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cell Biology&lt;/a&gt; (study of the different structures and functions of the cell)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Metabolism&quot; rel=&quot;nofollow noreferrer&quot;&gt;Metabolism&lt;/a&gt; (conversion of food/fuel to energy to run cellular processes, conversion of food/fuel to building blocks for macromolecules, and the elimination of nitrogenous wastes)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Immunology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Immunology&lt;/a&gt; (study of immune systems in all organisms)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Genetics&quot; rel=&quot;nofollow noreferrer&quot;&gt;Genetics&lt;/a&gt; (study of genes, genetic variation, and heredity in living organisms)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Enzyme&quot; rel=&quot;nofollow noreferrer&quot;&gt;Enzymology&lt;/a&gt; (study of enzymes i.e. macromolecular biological catalysts)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Applications:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Testing&lt;/strong&gt;: in daignostic tests like &lt;a href=&quot;https://en.wikipedia.org/wiki/Ames_test&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ames test&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Pregnancy_test&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pregnancy test&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Breast_cancer_screening&quot; rel=&quot;nofollow noreferrer&quot;&gt;Breast cancer screening&lt;/a&gt;, &lt;a href=&quot;http://www.livescience.com/45949-prenatal-genetic-testing.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Prenatal genetic testing&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Phenylketonuria#Screening_and_presentation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Phenylketonuria test&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Genetic engineering&lt;/strong&gt;: &lt;a href=&quot;https://en.wikipedia.org/wiki/Genetic_engineering&quot; rel=&quot;nofollow noreferrer&quot;&gt;taking&lt;/a&gt; a gene from one organism and placing it into another.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Cloning&lt;/strong&gt;: &lt;a href=&quot;https://en.wikipedia.org/wiki/Cloning&quot; rel=&quot;nofollow noreferrer&quot;&gt;cloning&lt;/a&gt; is the process of producing similar populations of genetically identical individuals that occurs in nature when organisms such as bacteria, insects or plants reproduce asexually.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Gene therapy&lt;/strong&gt;: &lt;a href=&quot;https://en.wikipedia.org/wiki/Gene_therapy&quot; rel=&quot;nofollow noreferrer&quot;&gt;a&lt;/a&gt; modified or healthy gene is inserted into the organism to replace a disease-causing gene&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;When to use the &lt;code&gt;biochemistry&lt;/code&gt; tag?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As defined, this tag should be used for questions regarding chemistry within the scope of biology: the compounds involving/related to cellular metabolism, cellular biology, genetics, biomolecules, enzymes, immune system and the reactions involving them in living organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Links for further information:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Biochemistry&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Biochemistry&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Outline_of_biochemistry&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Outline_of_biochemistry&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Index_of_biochemistry_articles&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Index_of_biochemistry_articles&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/History_of_biochemistry&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://en.wikipedia.org/wiki/History_of_biochemistry&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="19099" LastEditorUserId="16866" LastEditDate="2019-07-12T03:09:37.683" LastActivityDate="2019-07-12T03:09:37.683" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="129" PostTypeId="4" CreationDate="2011-12-15T23:29:22.503" Score="0" Body="The study of chemistry within the scope of biology: the compounds that occur and the reactions involving them in living organisms." OwnerUserId="73" LastEditorUserId="4101" LastEditorDisplayName="user132" LastEditDate="2013-10-25T21:53:13.380" LastActivityDate="2013-10-25T21:53:13.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="130" PostTypeId="5" CreationDate="2011-12-15T23:33:33.890" Score="0" Body="&lt;p&gt;Questions should generally be on the biological action of enzymes, rather than on the chemistry of their action. Relevant tags may include &lt;a href=&quot;/questions/tagged/biochemistry&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;biochemistry&amp;#39;&quot; rel=&quot;tag&quot;&gt;biochemistry&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="16866" LastEditDate="2019-12-13T04:29:13.627" LastActivityDate="2019-12-13T04:29:13.627" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="131" PostTypeId="4" CreationDate="2011-12-15T23:33:33.890" Score="0" Body="Enzymes are globular proteins that catalyse a biochemical reaction, increasing the overall rate by reducing activation energy. Most chemical reactions in a cell need enzymes in order to occur at rates sufficient to sustain life." OwnerUserId="73" LastEditorUserId="1590" LastEditDate="2016-03-23T08:59:09.760" LastActivityDate="2016-03-23T08:59:09.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="132" PostTypeId="5" CreationDate="2011-12-15T23:40:09.910" Score="0" Body="&lt;p&gt;Genetics is the study of genes, genetic variation, and heredity in living organisms. Subfields and derived fields include &lt;a href=&quot;/questions/tagged/population-genetics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;population-genetics&amp;#39;&quot; rel=&quot;tag&quot;&gt;population-genetics&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/quantitative-genetics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;quantitative-genetics&amp;#39;&quot; rel=&quot;tag&quot;&gt;quantitative-genetics&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/molecular-evolution&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;molecular-evolution&amp;#39;&quot; rel=&quot;tag&quot;&gt;molecular-evolution&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/genomics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;genomics&amp;#39;&quot; rel=&quot;tag&quot;&gt;genomics&lt;/a&gt;, and &lt;a href=&quot;/questions/tagged/epigenetics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;epigenetics&amp;#39;&quot; rel=&quot;tag&quot;&gt;epigenetics&lt;/a&gt; (and questions should be tagged accordingly).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also: &lt;a href=&quot;/questions/tagged/human-genetics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;human-genetics&amp;#39;&quot; rel=&quot;tag&quot;&gt;human-genetics&lt;/a&gt; &lt;a href=&quot;/questions/tagged/dna&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;dna&amp;#39;&quot; rel=&quot;tag&quot;&gt;dna&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="16866" LastEditDate="2019-12-13T04:33:10.800" LastActivityDate="2019-12-13T04:33:10.800" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="133" PostTypeId="4" CreationDate="2011-12-15T23:40:09.910" Score="0" Body="Genetics is the branch of biology that deals with the transmission and variation of inherited characteristics." OwnerUserId="73" LastEditorUserId="4101" LastEditDate="2013-10-25T21:51:34.310" LastActivityDate="2013-10-25T21:51:34.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="134" PostTypeId="2" ParentId="122" CreationDate="2011-12-15T23:51:34.413" Score="0" Body="&lt;p&gt;Sorry, I just couldn't help but point out &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0470430664&quot; rel=&quot;nofollow noreferrer&quot;&gt;the following book&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/anAXw.jpg&quot; alt=&quot;Molecular biology for dummmies&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Joking aside, every book from this series I read was fantastic. I didn't read this particular one, but I would nonetheless recommend to give it a try. &lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="66" LastEditDate="2011-12-16T00:07:48.213" LastActivityDate="2011-12-16T00:07:48.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="135" PostTypeId="5" CreationDate="2011-12-16T00:14:20.173" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-16T00:14:20.173" LastActivityDate="2011-12-16T00:14:20.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="136" PostTypeId="4" CreationDate="2011-12-16T00:14:20.173" Score="0" Body="Splicing is a modification of an RNA after transcription, in which intervening nucleotide sequence sequences (introns) are removed and the remaining sequences (exons) are joined." OwnerUserId="73" LastEditorUserId="73" LastEditDate="2011-12-19T14:19:19.007" LastActivityDate="2011-12-19T14:19:19.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="137" PostTypeId="2" ParentId="115" CreationDate="2011-12-16T01:56:00.193" Score="20" Body="&lt;p&gt;&lt;a href=&quot;http://www.wiley.com/WileyCDA/WileyTitle/productCd-3906390500,subjectCd-CH83.html&quot;&gt;Origin of Life: Chemical Approach&lt;/a&gt; is an edited volume by Piet Herdewijn and M. Volkan Kisakürek.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;here is the book's description from the webpage:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dedicated to the fond memory of two great pioneers of this science, Leslie E. Orgel and Stanley L. Miller, this compilation of reviews and original manuscripts provides an overview of the current state of the art, written by some of the eminent &quot;players&quot; in this creative domain of &quot;explorative chemistry&quot;. &#xA;  Since we are still far from finding a definitive answer to the most fundamental of questions in science, &quot;chemistry&quot; here is defined in its broadest sense. It is against this background that the contributions cover such a wide range of theories, including chemistry and selection, evolution of the pioneer organism, chemical aspects of synthetic biology, ribozyme catalysis of metabolism in the RNA world, intractable mixtures and the&#xA;  origin of life, the chemical etiology of nucleic acids, interstellar amino acids, and even the chemistry that preceded life's origin. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="137" LastActivityDate="2011-12-16T01:56:00.193" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="138" PostTypeId="5" CreationDate="2011-12-16T01:56:43.917" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-16T01:56:43.917" LastActivityDate="2011-12-16T01:56:43.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="139" PostTypeId="4" CreationDate="2011-12-16T01:56:43.917" Score="0" Body="The scientific study of fungi." OwnerUserId="73" LastEditorUserId="3624" LastEditDate="2014-03-18T12:25:41.233" LastActivityDate="2014-03-18T12:25:41.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="140" PostTypeId="5" CreationDate="2011-12-16T02:50:54.667" Score="0" Body="&lt;p&gt;RNA, like &lt;a href=&quot;/questions/tagged/dna&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;dna&amp;#39;&quot; rel=&quot;tag&quot;&gt;dna&lt;/a&gt;, is a heteropolymer of mononucleotides connected by phosphodiester bonds. However, RNA mononucleotides have ribose instead of deoxyribose and Uracil instead of Thymine.  RNAs, unlike DNA form a variety of secondary and &lt;a href=&quot;http://dx.doi.org/10.1021/ar200098t&quot; rel=&quot;nofollow noreferrer&quot;&gt;tertiary&lt;/a&gt; structures.  Cellular RNAs are predominantly single stranded but can form intramolecular hydrogen bonds in DNA-like and other patterns such as Hoogstein base pairing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Three main classes of RNA incude:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;messenger RNA (&lt;a href=&quot;/questions/tagged/mrna&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;mrna&amp;#39;&quot; rel=&quot;tag&quot;&gt;mrna&lt;/a&gt;): serve as a template for protein synthesis&lt;/li&gt;&#xA;&lt;li&gt;non-coding RNA (ncRNA): serve diverse functions ranging from being a part of core-protein synthesis machinery to gene regulation&lt;/li&gt;&#xA;&lt;li&gt;genomic RNA: serve as genetic material of certain viruses&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;ncRNA is a diverse class including:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Ribosomal RNAs (&lt;a href=&quot;/questions/tagged/rrna&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;rrna&amp;#39;&quot; rel=&quot;tag&quot;&gt;rrna&lt;/a&gt;): structural and catalytic components of protein synthesis&lt;/li&gt;&#xA;&lt;li&gt;Transfer RNA (&lt;a href=&quot;/questions/tagged/trna&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;trna&amp;#39;&quot; rel=&quot;tag&quot;&gt;trna&lt;/a&gt;): carry charged amino-acids for protein synthesis]&lt;/li&gt;&#xA;&lt;li&gt;Long-noncoding RNA: diverse functions (yet to be characterized)&lt;/li&gt;&#xA;&lt;li&gt;MicroRNA (miRNA): small regulatory RNA which post transcriptionally regulate gene expression&lt;/li&gt;&#xA;&lt;li&gt;Small interfering RNA (siRNA) :small RNAs which silence target mRNA/lncRNA&lt;/li&gt;&#xA;&lt;li&gt;Piwi-associated RNA (piRNA): small RNAs that silence transposons&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="73" LastEditorUserId="16866" LastEditDate="2019-08-25T03:47:49.130" LastActivityDate="2019-08-25T03:47:49.130" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="141" PostTypeId="4" CreationDate="2011-12-16T02:50:54.667" Score="0" Body="RNA, or ribonucleic acid, is a biological macromolecule made of nucleotides used in cells to convey genetic information to protein. RNA also plays a role in catalyzing certain biological reactions as well as carrying genetic material in some viruses. " OwnerUserId="73" LastEditorUserId="4101" LastEditDate="2013-10-29T21:08:02.223" LastActivityDate="2013-10-29T21:08:02.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="142" PostTypeId="2" ParentId="100" CreationDate="2011-12-16T03:02:19.070" Score="9" Body="&lt;p&gt;&lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Glaucus_atlanticus&quot;&gt;Glaucus atlanticus&lt;/a&gt;&lt;/em&gt; consumes and reuses the nematocysts of &lt;strike&gt;jellyfish&lt;/strike&gt; siphonophores. Perhaps not quite what you were looking for, as the animal doesn't simply concentrate the toxin, but actually co-opts entire stinging cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further to your mention of dinoflagellate toxins being concentrated by fish, I seem to recall reading something about some toxins being modified in vivo into more toxic derivatives, but cannot find any mention of it.&lt;/p&gt;&#xA;" OwnerUserId="99" LastEditorUserId="99" LastEditDate="2011-12-16T11:42:19.070" LastActivityDate="2011-12-16T11:42:19.070" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="143" PostTypeId="2" ParentId="50" CreationDate="2011-12-16T03:13:55.643" Score="5" Body="&lt;p&gt;A large number of prokaryotes do indeed have nucleosome-like structures.  The most well studied is H-NS in &lt;em&gt;E. coli&lt;/em&gt;, &lt;em&gt;Salmonella&lt;/em&gt; and some other deltaproteobacteria.  H-NS like molecules have also been found in mycoplasma (Lsr2).  One of its roles is to bind AT-rich DNA and silence transcription.  The binding is usually to suppress the expression of foreign DNA which tends to have a lower GC content than the host organism.  There is a great paper that did ChIP on ChIP with H-NS in &lt;em&gt;Salmonella&lt;/em&gt; by &lt;a href=&quot;http://www.sciencemag.org/content/313/5784/236.short&quot;&gt;Navarre et al in Science&lt;/a&gt; (Pubmed ID: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16763111&quot;&gt;1676311&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note H-NS does compact DNA and there is a paper by &lt;a href=&quot;http://nar.oxfordjournals.org/content/28/18/3504.full&quot;&gt;Dame et al.&lt;/a&gt; that demonstrates it with atomic force microscopy.&lt;/p&gt;&#xA;" OwnerUserId="12" LastEditorUserId="12" LastEditDate="2011-12-16T03:22:15.803" LastActivityDate="2011-12-16T03:22:15.803" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="144" PostTypeId="2" ParentId="122" CreationDate="2011-12-16T03:20:35.073" Score="4" Body="&lt;p&gt;Drop by the &lt;a href=&quot;http://diybio.org&quot; rel=&quot;nofollow&quot;&gt;diybio.org&lt;/a&gt; &lt;a href=&quot;http://groups.google.com/forum/#!forum/diybio&quot; rel=&quot;nofollow&quot;&gt;mailing list&lt;/a&gt;, which is home to a bunch of autodidactic free thinkers like yourself.  They always can suggest fun projects and learning resources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also check out Nature's &lt;a href=&quot;http://www.nature.com/scitable&quot; rel=&quot;nofollow&quot;&gt;Scitable&lt;/a&gt; education resource (&quot;A collaborative learning space for science&quot;) &lt;/p&gt;&#xA;" OwnerUserId="51" LastActivityDate="2011-12-16T03:20:35.073" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="145" PostTypeId="2" ParentId="101" CreationDate="2011-12-16T03:37:55.903" Score="4" Body="&lt;p&gt;I have had success with 1.5% agarose gels in TBE pre-stained with gelred.  I use a 10,000x stock solution of gelred sold by &lt;a href=&quot;http://biotium.com&quot; rel=&quot;nofollow&quot;&gt;http://biotium.com&lt;/a&gt;.  I visualize the gel on an old fotodyne UV transilluminator.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After melting agarose in the appropriate volume of TBE in a microwave, I let it cool to about 50 C (I can touch the flask with the back of my hand without snatching it away) and then add the appropriate volume of stock gelred.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;For a 30 mL 1.5% agarose gel:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;mix 0.45g agarose + 30 mL 1x TBE&lt;/li&gt;&#xA;&lt;li&gt;microwave until agarose solution boils and clarifies&lt;/li&gt;&#xA;&lt;li&gt;let cool to around 50 C&lt;/li&gt;&#xA;&lt;li&gt;add 3 uL gelred&lt;/li&gt;&#xA;&lt;li&gt;swirl the mixture&lt;/li&gt;&#xA;&lt;li&gt;cast the gel (don't forget comb)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This typically works for me.  I run the gel in a 1x TBE buffer at around 120 volts.&lt;/p&gt;&#xA;" OwnerUserId="51" LastActivityDate="2011-12-16T03:37:55.903" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="146" PostTypeId="2" ParentId="122" CreationDate="2011-12-16T04:33:01.283" Score="5" Body="&lt;p&gt;You can watch the &lt;a href=&quot;http://ibioseminars.org/&quot;&gt;iBioSeminars&lt;/a&gt;, which are given by some of the best cell and molecular biologists out there. &lt;/p&gt;&#xA;" OwnerUserId="34" LastActivityDate="2011-12-16T04:33:01.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="147" PostTypeId="1" AcceptedAnswerId="444" CreationDate="2011-12-16T05:08:40.777" Score="5" ViewCount="147" Body="&lt;p&gt;On average, in a human being with no neurological deficits, how long does it take for a sound which is sensed in the ear to reach the cortex?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which brainstem structures are most responsible for the delay?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I'm interested in things like the effect of the Olivary n.)&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="86" LastEditDate="2012-06-07T13:36:05.163" LastActivityDate="2012-06-07T13:36:05.163" Title="Latency to audition in human beings?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;hearing&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="148" PostTypeId="5" CreationDate="2011-12-16T07:11:59.807" Score="0" Body="&lt;p&gt;Neuroscience deals with the structure and function of the nervous system and its components in biological organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For discussions about what neuroscience topics are on-topic, see:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://meta.biology.stackexchange.com/questions/129/line-between-cognitivesciences-se-and-biology-se&quot;&gt;Line between cognitivesciences.se and biology.se?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://meta.biology.stackexchange.com/questions/300/where-do-questions-about-optical-illusions-belong&quot;&gt;Where do questions about optical illusions belong?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://meta.biology.stackexchange.com/questions/188/should-cognitive-science-questions-be-asked-here&quot;&gt;Should cognitive science questions be asked here?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For an introduction to the subject, see: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0838577016&quot; rel=&quot;nofollow&quot;&gt;Principles of Neural Science&lt;/a&gt; (new edition forthcoming) &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0123740193&quot; rel=&quot;nofollow&quot;&gt;Fundamental Neuroscience&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0878936955&quot; rel=&quot;nofollow&quot;&gt;Neuroscience&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Journals include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jneurosci.org/&quot; rel=&quot;nofollow&quot;&gt;Journal of Neuroscience&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://jn.physiology.org&quot; rel=&quot;nofollow&quot;&gt;Journal of Neurophysiology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/neuro/index.html&quot; rel=&quot;nofollow&quot;&gt;Nature Neuroscience&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cell.com/neuron/home&quot; rel=&quot;nofollow&quot;&gt;Neuron&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="57" LastEditorUserId="4101" LastEditDate="2013-10-25T22:26:14.283" LastActivityDate="2013-10-25T22:26:14.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="149" PostTypeId="4" CreationDate="2011-12-16T07:11:59.807" Score="0" Body="The study of the structure and function of the nervous system and its components." OwnerDisplayName="user132" LastEditorUserId="4101" LastEditorDisplayName="user132" LastEditDate="2013-10-25T22:26:14.283" LastActivityDate="2013-10-25T22:26:14.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="150" PostTypeId="1" CreationDate="2011-12-16T07:14:41.810" Score="12" ViewCount="899" Body="&lt;p&gt;What are the olfactory chemicals in whiteboard/permanent markers and what do they bind to in the nose, lungs, and brain?&lt;/p&gt;&#xA;" OwnerUserId="61" LastEditorUserId="61" LastEditDate="2011-12-20T02:42:42.427" LastActivityDate="2011-12-24T06:02:00.600" Title="What are the olfactory chemicals in whiteboard/permanent markers and what do they bind to in the nose, lungs, and brain?" Tags="&lt;biochemistry&gt;&lt;organic-chemistry&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="151" PostTypeId="5" CreationDate="2011-12-16T07:16:53.217" Score="0" Body="&lt;p&gt;Evolution is a change in gene frequencies, resulting from four mechanisms (mutation, migration, drift, and selection) which can all affect the transmission of heritable genetic information within populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Charles Darwin described evolution with the term &lt;em&gt;&quot;Descent with modification&quot;&lt;/em&gt; to illustrate that (genetic) information, which can affect phenotypic traits, is inherited from parent to offspring, with the potential to be modified or altered with the passage of time.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;https://www.blackwellpublishing.com/ridley/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot; Evolution is [...] change between generations within a population lineage.&quot;&lt;/a&gt; &lt;sup&gt;1&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Questions on macro- and microevolutionary processes, speciation and divergence, the process of adaptation, effects of population genetics, etc. are generally on-topic. Questions about whether evolution is true, and other questions which would tend to illicit highly opinionated and poorly researched answers, are generally off-topic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before asking why a seemingly advantageous trait has not evolved see &lt;a href=&quot;http://biology.stackexchange.com/questions/35532/if-a-trait-would-be-advantageous-to-an-organism-why-hasnt-it-evolved&quot;&gt;this post&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/home.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;Understanding Evolution&lt;/a&gt; is a particularly useful introductory source and includes a large myth-busting section.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1405103450.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ridley, ISBN: 978-1-4051-0345-9&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="69" LastEditorUserId="16866" LastEditDate="2019-07-12T03:06:44.257" LastActivityDate="2019-07-12T03:06:44.257" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="152" PostTypeId="4" CreationDate="2011-12-16T07:16:53.217" Score="0" Body="Changes in the heritable attributes of populations of organisms over time. The mechanisms of evolution are mutation, migration, drift, and selection." OwnerDisplayName="user132" LastEditorUserId="1590" LastEditDate="2016-03-15T15:04:50.187" LastActivityDate="2016-03-15T15:04:50.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="153" PostTypeId="2" ParentId="72" CreationDate="2011-12-16T07:38:06.530" Score="6" Body="&lt;p&gt;If you examine the human genome ~99% of the introns are under 500 kb. I would assume that a limit between 250 kb - 500 kb is reasonable for gene prediction.  You may incorrectly predict the proper structure of a small number of genes that have these very large introns but this should be a small number.  Furthermore, most popular sequence aligners tend to set an intron length limit between 500 kb and 750 kb.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just keep in mind that you may increase the number of false positive introns you detect if you set this limit to high.  Therefore, it may be worthwhile to try a few settings and evaluate the results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My guess is that larger introns are constrained in mammals for two reasons&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;They are more difficult for the spliceosome to excise properly.  The spliceosome may have reduced assembly at the proper 5' / 3' splice sites and the branch point site.  There is also a higher chance that there will be cryptic / decoy splice sites witihin the intron.  &lt;/li&gt;&#xA;&lt;li&gt;They increase the time it takes to transcribe the gene&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="12" LastEditorUserId="12" LastEditDate="2011-12-16T17:04:49.593" LastActivityDate="2011-12-16T17:04:49.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="154" PostTypeId="2" ParentId="115" CreationDate="2011-12-16T07:55:20.100" Score="9" Body="&lt;p&gt;I quite like the account given in &lt;a href=&quot;http://www.biology-direct.com/content/6/1/36/&quot;&gt;Early evolution without a tree of life&lt;/a&gt;, where alkaline hydrothermal vents (like &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Lost_City_%28hydrothermal_field%29&quot;&gt;Lost City&lt;/a&gt;&quot;) are theorized to have formed pre-biotic compartments with a proton gradient (i.e. an energy source) from which cells could have evolved. &lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2011-12-16T07:55:20.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="155" PostTypeId="2" ParentId="64" CreationDate="2011-12-16T08:29:15.143" Score="8" Body="&lt;p&gt;Well... I'm excited that my first contribution to this site will include a study of strippers!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://whywereason.wordpress.com/2011/06/29/menstruation-attraction-why-females-shouldnt-flirt-while-menstruating-and-why-bears-can-smell-the-menstruation/&quot;&gt;http://whywereason.wordpress.com/2011/06/29/menstruation-attraction-why-females-shouldnt-flirt-while-menstruating-and-why-bears-can-smell-the-menstruation/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read other, more detailed analysis of this (and similar) research that suggests strongly that our noses are heavily involved in all sorts of entirely sub-conscious decision making, as it pertains specifically to sexual selection. &lt;/p&gt;&#xA;" OwnerUserId="148" LastActivityDate="2011-12-16T08:29:15.143" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="156" PostTypeId="1" AcceptedAnswerId="868" CreationDate="2011-12-16T09:00:36.947" Score="21" ViewCount="1013" Body="&lt;p&gt;Some years ago Hiroaki Kawasaki and  Kazunari Taira published an article called &lt;a href=&quot;http://www.nature.com/nature/journal/v431/n7005/full/nature02889.html&quot;&gt;&quot;Induction of DNA methylation and gene silencing by short interfering RNAs in human cells&quot;&lt;/a&gt; in Nature:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In plants, dsRNAs targeted to CpG islands within a promoter can also&#xA;  induce RNA-directed DNA methylation&lt;sup&gt;3, 4, 5, 6, 7, 8&lt;/sup&gt;; however, it&#xA;  remains unclear whether gene silencing mediated by DNA methylation can&#xA;  be induced by dsRNAs in mammalian cells. Here, we demonstrate that&#xA;  short interfering RNAs (siRNAs; 21–25-nucleotide RNA molecules) induce&#xA;  DNA methylation and histone H3 methylation in human cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This paper seemed to show that siRNA can also induce long-term silencing of genes by DNA methylation in mammalian cells, which hasn't previously been observed. Unfortunately, the &lt;a href=&quot;http://www.nature.com/nature/journal/v441/n7097/full/nature04952.html&quot;&gt;paper was retracted later&lt;/a&gt;, calling the results into question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found the paper very exciting at the time, as it suggested the possibility to perform gene therapy, to silence specficic genes, just by using RNA interference. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the current scientific consensus here, is there any convincing evidence that siRNA-induced DNA methylation is possible in mammalian cells? Was anyone able to replicate the results from Kawasaki and Taira?&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="948" LastEditDate="2014-01-13T21:40:20.367" LastActivityDate="2015-02-20T14:56:42.190" Title="Can siRNA induce DNA methylation in mammalian cells?" Tags="&lt;biochemistry&gt;&lt;histone&gt;&lt;rna-interference&gt;&lt;histone-modifications&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="157" PostTypeId="1" AcceptedAnswerId="185" CreationDate="2011-12-16T12:41:01.543" Score="7" ViewCount="660" Body="&lt;p&gt;I am trying to express functional NMDA receptors in HEK293 line cells for single channel recording experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The HEK cells are maintained in the standard way (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15862464&quot;&gt;Thomas &amp;amp; Smart 2005&lt;/a&gt;) and transfected with NR1 and NR2x subunit cDNAs and also GFP, using either lipofectamine or calcium phosphate precipitation. GFP expression suggests successful transfection, but cells exhibiting green fluorescence are uniformly swollen and dead and it's more or less impossible to obtain a successful patch. Untransfected cells seem to remain perfectly viable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the basis that the toxicity might be a consequence of Ca&lt;sup&gt;2+&lt;/sup&gt; influx through open NMDARs, I've tried including a cocktail of blockers in the growth medium, including AP5, kynurenic acid and Mg&lt;sup&gt;2+&lt;/sup&gt;, but the transfected cells continue to die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone suggest anything else I should be doing to keep the cells alive? Or am I just on a hiding to nothing? Other researchers seem to have managed this (eg &lt;a href=&quot;http://jp.physoc.org/content/482/Pt_3/567.long&quot;&gt;Medina et al 1995&lt;/a&gt;, &lt;a href=&quot;http://jn.physiology.org/content/79/2/555.long&quot;&gt;Vicini et al 1998&lt;/a&gt;) and do not seem to be doing anything substantially different, so I'm a bit at a loss.&lt;/p&gt;&#xA;" OwnerUserId="149" LastActivityDate="2016-02-25T21:41:04.583" Title="How can I keep HEK cells alive while expressing NMDA receptors?" Tags="&lt;cell-culture&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="158" PostTypeId="1" AcceptedAnswerId="403" CreationDate="2011-12-16T13:22:01.680" Score="10" ViewCount="194" Body="&lt;p&gt;In &lt;a href=&quot;http://www.bbc.co.uk/news/health-16107411&quot; title=&quot;Haemophilia gene therapy shows early success&quot;&gt;this BBC article&lt;/a&gt; a trial is described where patients with B-Haemophillia are infected with modified Adeno-associated Virus 8 which contained the genes for Factor IX clotting protein.  Trials seemed to be successful, however the article later mentions &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There was an immune response against the infected liver cells around seven to nine weeks after the virus was injected.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am interested to know why there was a delay period of such length?  Would this be true of all cells and is it due to a long duration of clonal selection in the humoral immune response or is something else at play?  Also, I'm presuming that the Adeno Virus would be attacked long before the cells it has infected?  &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="28778" LastEditDate="2017-05-06T07:26:45.370" LastActivityDate="2017-05-06T07:26:45.370" Title="Why is there an extended delay before G.M. liver cells are attacked by the immune system?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;liver&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="159" PostTypeId="2" ParentId="120" CreationDate="2011-12-16T13:27:00.367" Score="7" Body="&lt;p&gt;I found a paper that describes a method to purify GFP fusion proteins using affinity chromatography: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18342538&quot;&gt;&quot;Purification of GFP fusion proteins with high purity and yield by monoclonal antibody-coupled affinity column chromatography&quot; (1)&lt;/a&gt;. Unfortunately I don't have access to the full text, so I can't check how exactly they elute the GFP fusion protein from the column. They describe a specific monoclonal antibody they use, there should be information on how to obtain it in the paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Abstract:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;GFP has often been used as a marker of gene expression, protein&#xA;  localization in living and fixed tissues as well as for protein&#xA;  targeting in intact cells and organisms. Monitoring foreign protein&#xA;  expression via GFP fusion is also very appealing for bioprocess&#xA;  applications. Many cells, including bacterial, fungal, plant, insect&#xA;  and mammalian cells, can express recombinant GFP (rGFP) efficiently.&#xA;  Several methods and procedures have been developed to purify the rGFP&#xA;  or recombinant proteins fused with GFP tag. However, most current GFP&#xA;  purification methods are limited by poor yields and low purity. In the&#xA;  current study, we developed an improved purification method, utilizing&#xA;  a FMU-GFP.5 monoclonal antibody (mAb) to GFP together with a&#xA;  mAb-coupled affinity chromatography column. The method resulted in a&#xA;  sample that was highly pure (more than 97% homogeneity) and had a&#xA;  sample yield of about 90%. Moreover, the GFP epitope permitted the&#xA;  isolation of almost all the active recombinant target proteins fused&#xA;  with GFP, directly and easily, from the crude cellular sources. Our&#xA;  data suggests this method is more efficient than any currently&#xA;  available method for purification of GFP protein.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(1) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18342538&quot;&gt;Zhuang R. et al., Purification of GFP fusion proteins with high purity and yield by monoclonal antibody-coupled affinity column chromatography. &lt;em&gt;Protein Expr Purif&lt;/em&gt; 2008, &lt;strong&gt;59&lt;/strong&gt;(1), 138-43&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2011-12-16T13:27:00.367" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="160" PostTypeId="1" AcceptedAnswerId="162" CreationDate="2011-12-16T16:11:15.777" Score="23" ViewCount="690" Body="&lt;p&gt;For example, almost every dog I've met in my life (more than 20 subjects) uses their right paw touching one while asking for attention. Can it be used as a criterion for calling them dextral? If not, what?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I realize that even those dogs who live in the street might get influenced by dextral people:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There is no domestic animal which has so radically altered its whole&#xA;  way of living, indeed its whole sphere of interests, that has become&#xA;  domestic in so true a sense as the dog (Konrad Lorenz)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is there any research about it?&lt;/p&gt;&#xA;" OwnerUserId="121" LastEditorDisplayName="user132" LastEditDate="2011-12-19T14:18:39.477" LastActivityDate="2011-12-19T14:18:39.477" Title="Are there dextral/sinistral higher animals?" Tags="&lt;zoology&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ClosedDate="2017-03-23T20:50:48.657" ContentLicense="CC BY-SA 3.0" />
  <row Id="161" PostTypeId="2" ParentId="107" CreationDate="2011-12-16T16:17:44.640" Score="19" Body="&lt;p&gt;It seems that yes, it is possible to increase the tolerance for lactose over time, and it has to do with the adaptation of microbiota.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A simplistic explanation comes in the following article: &#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8694025&quot;&gt; &lt;strong&gt;Hertzler SR, Savaiano DA&lt;/strong&gt;. 1996. Colonic adaptation to daily lactose feeding in lactose maldigesters reduces lactose intolerance. The American journal of clinical nutrition 64: 232–6.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In which the authors claim the following: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;Colonic adaptation appears to reduce the symptomatic response to lactose via several mechanisms. (...)&lt;/li&gt;&#xA;&lt;li&gt;(...) increased β-galactosidase activity after regular lactose ingestion indicates that colonic bacteria are able to ferment lactose more rapidly. (...)&lt;/li&gt;&#xA;&lt;li&gt;(...) This metabolic shift is thought to result from the proliferation of lactose-fermenting, non-hydrogen producing organisms such as &lt;em&gt;Bifidobacteria&lt;/em&gt;.&quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This article makes reference to another one which supposedly explains the microbiota adaptation:&#xA;Hill Mi. Bacterial adaptation to lactase deficiency. In: &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/3805535465&quot;&gt;&lt;strong&gt;Delmont J, ed.&lt;/strong&gt; 1983. Milk intolerances and rejection. New York: Karger: 22–6.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But unfortunately I could not find the full text. I hope you are luckier than me.&lt;/p&gt;&#xA;" OwnerUserId="31" LastEditorUserId="836" LastEditDate="2012-08-19T01:56:56.383" LastActivityDate="2012-08-19T01:56:56.383" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="162" PostTypeId="2" ParentId="160" CreationDate="2011-12-16T16:41:53.440" Score="19" Body="&lt;p&gt;Handedness has been studied in several different species of toads. As basal tetrapods, the authors argue that these taxa are unlikely to be influenced by human hand dominance and are thus a better model for studying the evolution of handedness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15513053&quot;&gt;Bisazza et al. (1997)&lt;/a&gt; studied &quot;pawedness&quot; in &lt;em&gt;Bufo bufo&lt;/em&gt;, &lt;em&gt;B. viridis&lt;/em&gt;, and &lt;em&gt;B. marinus&lt;/em&gt; in wild-caught animals by determining which forelimb was used to remove a piece of paper from the animals' snout or a balloon placed over its head.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The results were mixed. &lt;em&gt;B. bufo&lt;/em&gt; preferred the right forelimb in both tests, but &lt;em&gt;B. viridis&lt;/em&gt; and &lt;em&gt;B. marinus&lt;/em&gt; did not. &lt;em&gt;B. marinus&lt;/em&gt; did preferentially turn its head left in another experiment, using the right forelimb for support.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A subsequent study by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15513184&quot;&gt;Malashichev and Nikitina (2002)&lt;/a&gt; showed that &lt;em&gt;Bombina viridis&lt;/em&gt; is &quot;lefthanded,&quot; while &lt;em&gt;Bombina bombina&lt;/em&gt; is &quot;ambidextrous.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So based on these studies, lateralization appears to have a long evolutionary history.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2011-12-16T16:53:18.140" LastActivityDate="2011-12-16T16:53:18.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="163" PostTypeId="1" AcceptedAnswerId="292" CreationDate="2011-12-16T16:59:56.130" Score="28" ViewCount="806" Body="&lt;p&gt;Much interest in the astrobiology community has been generated by the discovery of biological communities populating deep-ocean hydrothermal vents (i.e. &quot;black smokers&quot;). (1) These ecosystems rely on chemoautotrophic bacteria/archaea extremophiles as primary producers living at 40-80 C temperatures. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the lifetimes of these black smokers have been estimated to be of order 25 years. How  are these biological communities able to migrate to newer, active vent systems in conditions of extreme cold and high pressure?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0146629177904787&quot;&gt;(1) Lonsdale, P., 1977, Deep Sea Research, 24, 9&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2011-12-16T18:04:46.693" LastActivityDate="2012-09-17T12:23:32.533" Title="How do biological communities at deep-ocean hydrothermal vents migrate between vents?" Tags="&lt;ecology&gt;&lt;extremophiles&gt;&lt;astrobiology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="164" PostTypeId="2" ParentId="58" CreationDate="2011-12-16T18:58:10.430" Score="3" Body="&lt;p&gt;How well is gene A annotated? Do you have the gene A sequence (after post-transcriptional modifications)? If you do, you can order it from a company like DNA2.0 and they will synthesize it for you for like $0.35/base. Then you can transform the cells with this plasmid and do a knockout of gene B by inserting some sequence at the ~200bases overlap.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I guess you can transform the immediate transcript (without modifications). It will also be modified once it is in the cell. But it will be longer and more expensive to synthesize, but there are a few methods you can use to do that. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me know if this idea appeals to you. I can give you more info if you are interested.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2011-12-16T18:58:10.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="165" PostTypeId="1" AcceptedAnswerId="167" CreationDate="2011-12-16T19:07:08.793" Score="14" ViewCount="851" Body="&lt;p&gt;This is an assignment that had confused me for a long time.  So I think you guys who study computational biology might be interested. The original question is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Find the two most similar DNA sequences of length 20 that Blast using a word length of 5 will fail to align.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="44" LastEditorUserId="16866" LastEditDate="2017-03-23T16:27:35.083" LastActivityDate="2017-03-23T16:27:35.083" Title="When does BLAST fail to align 2 DNA sequences?" Tags="&lt;bioinformatics&gt;&lt;homework&gt;&lt;dna-sequencing&gt;&lt;blast&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="166" PostTypeId="1" AcceptedAnswerId="521" CreationDate="2011-12-16T19:54:42.633" Score="10" ViewCount="3072" Body="&lt;p&gt;Some proteins express well in a heterologous host; others- don't. A few requirements are known to determine the protein expression, like a strong promoter (like T7) for transcription and a strong ribosome binding site for translation. I am working with a protein, which consists of 2 subunits - alpha and beta. Both of them are on a plasmid with T7 promoter in front of the beta subunit (i.e. the construct is T7 promoter, CDS for beta subunit, CDS for the alpha subunit). The beta subunit expresses well, but the alpha doesn't. Do you thing this has something to do with the local environment (promoters, RBSs, etc) and how much does it depend on that? How can I increase the protein expression?&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-01-06T19:15:00.857" Title="What determines a successful protein expression in E. coli?" Tags="&lt;t7-promoter&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="167" PostTypeId="2" ParentId="165" CreationDate="2011-12-16T19:56:41.663" Score="14" Body="&lt;p&gt;BLAST works by finding a perfect match between sequences of a length equal to this &quot;word length&quot; and then enlarging it in a standard way -- yet there will be no alignment without this perfectly matched word.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in your case, you must look for two 20bp sequences with no common 5bp sub-sequence; for instance:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;AAAAAAAAAAAAAAAAAAAA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;AAAACAAAACAAAACAAAAC&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerDisplayName="user59" LastEditorDisplayName="user59" LastEditDate="2011-12-16T20:29:03.863" LastActivityDate="2011-12-16T20:29:03.863" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="169" PostTypeId="1" CreationDate="2011-12-16T20:14:50.447" Score="8" ViewCount="2051" Body="&lt;p&gt;I have to isolate a large plasmid from yeast and transform it in E. coli. After transformation, I often get no colonies. One reason for that is the yeast mini prep hasn't worked or the DNA concentration is too low. I tried two different isolation protocols:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.zymoresearch.com/zrc/pdf/D2001i.pdf&quot; rel=&quot;nofollow&quot;&gt;Zymoprep I yeast plasmid prep kit&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the doc: &quot;based on the old E.  coli alkaline lysis method with our Zymolyase added in the first  solution.&quot;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nprot/journal/v6/n1/pdf/nprot.2010.174.pdf&quot; rel=&quot;nofollow&quot;&gt;Phenol chloroform YAC isolation protocol&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;used by Dan Gibson et. al] for their huge constructs (&gt;100kb)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They use an expensive Qiagen large-construct column at the end, in order to purify and visualize the yeast extract on a gel, but I skip that step because the Qiagen column cost $40 per yeast clone which doesn't scale if we do many of these.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;How can I troubleshoot and optimize the above-mentioned protocols? Are there any other protocols that might be more suitable for a large plasmid and don't use too expensive materials?&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="338" LastEditDate="2012-02-21T09:48:13.683" LastActivityDate="2012-02-21T18:35:23.723" Title="What is causing my problem with very low yields when isolating a 42kb yeast plasmid?" Tags="&lt;molecular-biology&gt;&lt;yeast&gt;&lt;dna-isolation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="170" PostTypeId="2" ParentId="166" CreationDate="2011-12-16T20:31:15.873" Score="9" Body="&lt;p&gt;One important aspect when expressing a protein from a different organism in E. coli is that the codon usage of the original organism is likely different from the codon usage of the E. coli used for expression (&lt;a href=&quot;http://en.wikipedia.org/wiki/Codon_usage_bias&quot;&gt;Codon usage bias&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though the genetic code is degenerate, not all codons are equal. They might encode for the same amino acid, but organisms tend to favor specific codons over others and the tRNAs for those codons tend to be present in different concentrations. When you now have a lot of codons in your sequence that are very rare in E. coli, the expression will suffer because the tRNA for those codons is not present in high enough concentrations to sustain the translation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two ways of compensating for that, either you get your E. coli to produce more of the rare tRNAs, or you optimize your sequence to use different codons. For the first solution you can buy certain E. coli strains that contain plasmids encoding the tRNAs that are rare in E. coli, one of those strains is e.g. the Rosetta BL21 strain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For optimizing the codon usage there are several companies offering to synthesize optimized sequences. There are also tools available online, but I have no direct experience with those.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The optimization is also not as easy as just using the most prevalent codon every time, it has been shown that optimizing the codons to match the translation speed in the original organism can enhance the expression yields. For some proteins, pause sites during the translation might be necessary to ensure proper folding. If the protein doesn't fold correctly it will be quickly degraded and your yield will suffer. This is described in the article &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0002189&quot;&gt;&quot;Heterologous Protein Expression Is Enhanced by Harmonizing the Codon Usage Frequencies of the Target Gene with those of the Expression Host&quot; from Angov et al.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You'll find a nice overview about the whole topic in the article &lt;a href=&quot;http://rsif.royalsocietypublishing.org/content/6/Suppl_4/S467.long&quot;&gt;&quot;You're one in a googol: optimizing genes for protein expression&quot; from Welsh et al.&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2011-12-16T20:31:15.873" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="171" PostTypeId="1" AcceptedAnswerId="172" CreationDate="2011-12-16T20:57:09.470" Score="116" ViewCount="115046" Body="&lt;p&gt;What is the advantage gained by the substitution of thymine for uracil in DNA?  I have read previously that it is due to thymine being &quot;better protected&quot; and therefore more suited to the storage role of DNA, which seems fine in theory, but why does the addition of a simple methyl group make the base more well protected?&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="22057" LastEditorDisplayName="user132" LastEditDate="2017-01-26T13:31:12.117" LastActivityDate="2017-01-26T13:31:12.117" Title="Why is thymine rather than uracil used in DNA?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;rna&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="40" ContentLicense="CC BY-SA 3.0" />
  <row Id="172" PostTypeId="2" ParentId="171" CreationDate="2011-12-16T21:18:36.557" Score="116" Body="&lt;p&gt;One major problem with using uracil as a base is that &lt;a href=&quot;http://en.wikipedia.org/wiki/Deamination#Cytosine&quot;&gt;cytosine can be deaminated&lt;/a&gt;, which converts it into uracil. This is not a rare reaction; it happens around 100 times per cell, per day. This is no major problem when using thymine, as the cell can easily recognize that the uracil doesn't belong there and can repair it by substituting it by a cytosine again. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7vV8J.png&quot; alt=&quot;cytosine deamination&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an enzyme, &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_glycosylase#Uracil_DNA_glycosylases&quot;&gt;uracil DNA glycosylase&lt;/a&gt;, that does exactly that; it excises uracil bases from double-stranded DNA. It can safely do that as uracil is not supposed to be present in the DNA and has to be the result of a base modification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, if we would use uracil in DNA it would not be so easy to decide how to repair that error. It would prevent the usage of this important repair pathway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The inability to repair such damage doesn't matter for RNA as the mRNA is comparatively short-lived and any potential errors don't lead to any lasting damage. It matters a lot for DNA as the errors are continued through every replication. Now, this explains why there is an advantage to using thymine in DNA, it doesn't explain why RNA uses uracil. I'd guess it just evolved that way and there was no significant drawback that could be selected against, but there might be a better reason (more difficult biosynthesis of thymine, maybe?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You'll find a bit more information on that in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26879/#A835&quot;&gt;&quot;Molecular Biology of the Cell&quot; from Bruce Alberts et al.&lt;/a&gt; in the chapter about DNA repair (from page 267 on in the 4th edition).&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorDisplayName="user132" LastEditDate="2011-12-17T11:51:43.957" LastActivityDate="2011-12-17T11:51:43.957" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="173" PostTypeId="1" AcceptedAnswerId="179" CreationDate="2011-12-16T21:40:25.300" Score="7" ViewCount="269" Body="&lt;p&gt;Several &lt;a href=&quot;http://xenophilius.wordpress.com/2011/10/11/ocean-trawl-reveals-huge-virus-that-infects-amoebas/&quot; rel=&quot;nofollow&quot;&gt;large&lt;/a&gt; &lt;a href=&quot;http://www.pnas.org/content/early/2011/10/04/1110889108.abstract&quot; rel=&quot;nofollow&quot;&gt;viruses (Arslan 2011)&lt;/a&gt; form their own organelles within the amoebae they invade.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do these organelles form?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;Reference:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Arslan, D., Legendre, M., Seltzer, V., Abergel, C., Claverie, J-M. (2011) Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. &lt;em&gt;PNAS 108&lt;/em&gt;(42): 17486-17491 &lt;a href=&quot;http://dx.doi.org/10.1073/pnas.1110889108&quot; rel=&quot;nofollow&quot;&gt;[DOI]&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="57" LastEditDate="2012-07-30T04:30:42.987" LastActivityDate="2016-03-23T00:13:45.077" Title="How Do Large Ocean Viruses Form Their Own Organelles?" Tags="&lt;cell-biology&gt;&lt;virology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="174" PostTypeId="2" ParentId="171" CreationDate="2011-12-16T22:07:58.670" Score="54" Body="&lt;p&gt;The existence of thymine in DNA instead of uracil is apparently due to evolution process which made DNA more stable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thymine has greater resistance to photochemical mutation, making the genetic message more stable. A rough explanation of why thymine is more protected then uracil, can be found in the article&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Arthur M, L., &lt;a href=&quot;http://dx.doi.org/10.1016/0022-5193%2869%2990021-6&quot;&gt;&lt;strong&gt;&lt;em&gt;Why does DNA contain thymine and RNA uracil?&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt; Journal of Theoretical Biology, 1969. 22(3): p. 537-540.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;which gives three major reasons for it to happen:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&quot;Excitation  energy  in  DNA  is  mobile,  and  is  eventually  transferred  to &#xA;thymine  residues,  which  are  the  sites  of  radiation  damage.&quot;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&quot;Uracil but not thymine forms a stable photohydration product. The dimerization of thymine can be partially photoreversed by irradiation at relatively longer wavelengths, while this process is less effective for uracil dimers because of the competing photohydration reaction&quot;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&quot;Photochemical  mutation  is,  or  at  least  was  at  one  time,  a  serious &#xA;problem,  since  there  exists  a  series  of  enzymes  to  repair  radiation  damage.  Therefore  resistance  to  radiation  damage  was  an  important selective  advantage.&quot;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="31" LastEditorDisplayName="user132" LastEditDate="2011-12-19T14:18:51.410" LastActivityDate="2011-12-19T14:18:51.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="175" PostTypeId="1" CreationDate="2011-12-16T23:09:55.693" Score="8" ViewCount="2573" Body="&lt;p&gt;I am currently doing an experiment on cells to test the internalization of a protein.&#xA;Normally, I seeded my cells the day before the incubation. This worked well for Hela, CHL or PANC1 cells. However, when I did the same with INS1-E and MIN6 (both beta-cells) after the incubation and the washing step the majority of the cells were gone. This was better in the control where I did not put in the compound, but still a lot of cells were detached.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, I wonder if I should seed the INS1-E and MIN6 cells earlier, more like 2-3 days before. Do these cell lines need more time after splitting to attach again?&lt;/p&gt;&#xA;" OwnerUserId="126" LastEditorUserId="6" LastEditDate="2011-12-19T14:18:47.790" LastActivityDate="2017-12-14T07:55:20.990" Title="How much time do INS1-E and MIN6 cells need after splitting?" Tags="&lt;cell-culture&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="176" PostTypeId="1" CreationDate="2011-12-16T23:21:23.050" Score="9" ViewCount="85" Body="&lt;p&gt;Do you know if exendin, an analog of GLP-1 (glucagon like peptide-1), can be toxic for beta-cells? For example, what is the effect on INS1 or Min6 cells at a certain concentration or after 90 mins of incubation. And what is the impact on insulin secretion?&lt;/p&gt;&#xA;" OwnerUserId="126" LastEditorUserId="16299" LastEditDate="2015-12-27T01:16:10.347" LastActivityDate="2015-12-27T01:16:10.347" Title="What is the effect of exendin on beta-cells?" Tags="&lt;physiology&gt;&lt;metabolism&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="177" PostTypeId="1" AcceptedAnswerId="969" CreationDate="2011-12-17T00:22:10.603" Score="14" ViewCount="192" Body="&lt;p&gt;So I'm looking for some information on the infectious dose necessary to colonize a human with &lt;em&gt;Clostridium difficile&lt;/em&gt;. There's no human challenge studies, and since it's not a foodborne pathogen, little we can get from outbreak data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which leaves me looking at animal models, to at least get the &lt;em&gt;shape&lt;/em&gt; of the probability of infection based on a given dose. But the papers on hamsters makes it appear that they're infected rather easily, and that this infection is particularly severe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there another animal model that more closely mimics the infection dynamics of &lt;em&gt;C. difficile&lt;/em&gt; in humans?&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2012-02-10T07:04:34.887" Title="Are there animal models for Clostridium difficile that better replicate human infection than hamsters?" Tags="&lt;microbiology&gt;&lt;epidemiology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="178" PostTypeId="1" AcceptedAnswerId="181" CreationDate="2011-12-17T00:30:32.113" Score="12" ViewCount="260" Body="&lt;p&gt;I've gotten a staggering amount of use out of my copy of &lt;em&gt;Fields Virology&lt;/em&gt; as a general reference for &quot;getting me up to speed&quot; on whatever pathogen I'm currently looking at. I don't know of a similar type of reference for bacteria, but I only became aware of &lt;em&gt;Fields&lt;/em&gt; as I was moving &lt;em&gt;out&lt;/em&gt; of the field, rather than into it, so it's possible I've simply never heard of a suitable reference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any suggestions?&lt;/p&gt;&#xA;" OwnerUserId="67" LastEditorUserId="6" LastEditDate="2012-02-19T20:40:00.700" LastActivityDate="2012-02-19T20:40:00.700" Title="Is there an equivalent to &quot;Fields Virology&quot; for Bacteria?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="179" PostTypeId="2" ParentId="173" CreationDate="2011-12-17T03:10:06.107" Score="7" Body="&lt;p&gt;The organelle form in the same way they would if they were coded for by the host's genome, except in this case the virus uses its own genome to specify the type of organelle.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://xenophilius.wordpress.com/2011/10/11/ocean-trawl-reveals-huge-virus-that-infects-amoebas/&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; you link to indicates this.  The &quot;systems&quot; in the quote are in part the organelle that it needs&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A study of the giant virus’s DNA shows it to have over a thousand genes, the biochemical instructions it uses to build the systems it requires to replicate once inside its host.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="137" LastEditorUserId="22057" LastEditDate="2016-03-23T00:13:45.077" LastActivityDate="2016-03-23T00:13:45.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="180" PostTypeId="2" ParentId="166" CreationDate="2011-12-17T05:19:40.680" Score="2" Body="&lt;p&gt;Mad Scientist covered potential codon-bias issues (which can be ameliorated with Rosettas), but more generally, I've seen tremendous variability in expression rates between different vectors (pET-28 vs pET-24) without any apparent reason.  Our lab has had tremendous success with IPTG-inducible vectors (going from pBC-SK to pET-24 increased expression 50-fold).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beyond expression, the protein can be lost when preparing the cell-free extract.  It may not be in the cell pellet if exported courtesy of a signal peptide, or may be discarded in the &quot;debris&quot; pellet when spinning down lysed cells if it's poorly soluble.  I've heard a theory that solubility issues may be exaggerated by vectors that saturate the export machinery, which can both impede synthesis and/or be so effective they just cause precipitation.  The &lt;em&gt;&lt;a href=&quot;http://lifeserv.bgu.ac.il/wb/zarivach/media/protocols/Novagen%20pET%20system%20manual.pdf&quot; rel=&quot;nofollow&quot;&gt;pET System Manual&lt;/a&gt;&lt;/em&gt; suggests longer (overnight) expression times at lower (15-20 °C) can help solubility issues.  Whatever the reason, engineering away the signal peptide drastically increased expression for many of our proteins.&lt;/p&gt;&#xA;" OwnerUserId="25" LastActivityDate="2011-12-17T05:19:40.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="181" PostTypeId="2" ParentId="178" CreationDate="2011-12-17T09:05:06.367" Score="9" Body="&lt;p&gt;I might as well give this as an answer: the closest analog to Fields for bacteriology that I'm aware of are the two Bergey's manuals: &lt;a href=&quot;http://www.springer.com/series/4157&quot;&gt;&lt;em&gt;Bergey's Manual of Systematic Bacteriology&lt;/em&gt;&lt;/a&gt;, and &lt;a href=&quot;http://books.google.com/books?hl=en&amp;amp;id=jtMLzaa5ONcC&quot;&gt;&lt;em&gt;Bergey's Manual of Determinative Bacteriology&lt;/em&gt;&lt;/a&gt;. They deal with taxonomy and identification of bacteria (and even cyanobacteria and archaeans), with some emphasis on the medically important classes.&lt;/p&gt;&#xA;" OwnerDisplayName="user132" LastActivityDate="2011-12-17T09:05:06.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="182" PostTypeId="1" AcceptedAnswerId="422" CreationDate="2011-12-17T12:15:19.410" Score="10" ViewCount="478" Body="&lt;p&gt;In the sinusoids of the liver, venous blood from the hepatic portal system mixes with arterial blood from the hepatic arteries.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do oxygen molecules move between oxygenated RBCs and non-oxygenated RBCs, so that the partial oxygen saturation of the blood in the sinusoids reflect partial saturation of the RBCs? Or do RBCs retain their initial oxygen saturation, so that the partial saturation of the blood in the sinusoids reflects a mixture of saturated and unsaturated RBCs?&lt;/p&gt;&#xA;" OwnerUserId="137" LastEditorUserId="43480" LastEditDate="2018-07-31T20:17:08.027" LastActivityDate="2018-07-31T20:17:08.027" Title="Does the oxygen concentration equilibrate between red blood cells in the liver sinusoids?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;human-anatomy&gt;&lt;hematology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="183" PostTypeId="1" AcceptedAnswerId="191" CreationDate="2011-12-17T12:29:28.680" Score="10" ViewCount="122" Body="&lt;p&gt;Commercial suppliers of primary antibodies for given protein targets typically list recommended applications, for which the antibody has presumably been shown to work. I am usually looking to use them for immunofluorescence, and my impression (which admittedly may be based on an unrepresentative sample) is that most antibodies are recommended only for use with Western Blotting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is this? Is WB the most common application? The most general? Is it easier to test for than IF?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And, perhaps more to the point, how seriously should one take these recommendations? If an antibody is not recommended for IF, does that mean that it probably won't work? Or that it may well but no-one's bothered to check? Or that it almost certainly will?&lt;/p&gt;&#xA;" OwnerUserId="149" LastEditorUserId="149" LastEditDate="2011-12-17T18:49:02.503" LastActivityDate="2011-12-22T01:22:31.970" Title="Recommended applications for commercial antibodies" Tags="&lt;staining&gt;&lt;antibody&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="184" PostTypeId="2" ParentId="121" CreationDate="2011-12-17T13:57:43.250" Score="7" Body="&lt;p&gt;Yes, you must fragment the genome in order to insert it into a vector for cloning; you can't &quot;insert&quot; the whole 5 Mbp genome of &lt;em&gt;E. coli&lt;/em&gt; into a vector.  It's difficult to transform cells with huge plasmids, 2-20 kbp is an optimal range.  In any case, if you want a clone of the whole genome, wait 30 minutes and the cell will happily oblige you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most procedures that isolate genomic DNA will fragment it in the first place, as it is much too large and fragile to stay together, and if it did it, the majority would be caught up in other cell debris and discarded.  Vortexing with glass beads is a typical first step to randomly fragment it.  After this, you can digest the DNA and your vector to place matching ends on it, ligate it, and transform host cells.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want a targeted approach (to extract a specific gene, a technique with which I am unfamiliar), you may be able to use PCR on your extracted, fragmented DNA, as there would hopefully be one intact segment spanning what you want.&lt;/p&gt;&#xA;" OwnerUserId="25" LastActivityDate="2011-12-17T13:57:43.250" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="185" PostTypeId="2" ParentId="157" CreationDate="2011-12-17T18:48:48.070" Score="6" Body="&lt;p&gt;Try perhaps lowering the level of expression of your construct. HEK cells are notorious for expressing large quantities of your transfected insert. Do you have it under a CMV promoter? Try a milder one, such as an ubiquitin promoter or similar or, even better, a doxycyclin-inducible system (e.g., &lt;a href=&quot;http://www.clontech.com/US/Products/Inducible_Systems/Tetracycline-Inducible_Expression/Systems_1_and_2?sitex=10020:22372%3aUS&quot;&gt;clontech's tet off&lt;/a&gt;) so you can manage the expression levels through the dox concentration/time of induction.&lt;/p&gt;&#xA;" OwnerUserId="48" LastActivityDate="2011-12-17T18:48:48.070" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="186" PostTypeId="1" AcceptedAnswerId="331" CreationDate="2011-12-17T20:08:57.237" Score="31" ViewCount="1083" Body="&lt;p&gt;Several companies are commercializing tests for telomere length such as this one &lt;a href=&quot;http://www.telomehealth.com/index.html&quot;&gt;here&lt;/a&gt;. I understand the basic mechanism for why telomeres shorten during DNA replication, but how good is the evidence that telomere length is a reliable indicator of healthspan/lifespan?&lt;/p&gt;&#xA;" OwnerUserId="81" LastActivityDate="2017-09-18T14:04:04.107" Title="Is telomere length a reliable measure of health/lifespan?" Tags="&lt;human-biology&gt;&lt;dna&gt;&lt;telomere&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="187" PostTypeId="2" ParentId="186" CreationDate="2011-12-17T20:56:28.993" Score="9" Body="&lt;p&gt;It would be reliable if we don't take into account the environment, and if we are comparing two genetically identical persons. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, because there are many other factors that can cause genetic mutation and consequently shorten lifespan.&#xA;Second, giving an extreme example and not taking into account the environment and modern medicine, we cannot expect a hemophilic to have the same lifespan as a non-hemophilic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More, not all the individuals have the exactly same rate of cell division thus, two persons with the same telomere length can have slightly distinct ages, and consequently die at different ages. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would say, it is not 100% reliable since there are many other factors to take into account, but it could give a rough idea of lifespan&lt;/p&gt;&#xA;" OwnerUserId="31" LastActivityDate="2011-12-17T20:56:28.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="188" PostTypeId="1" AcceptedAnswerId="265" CreationDate="2011-12-17T22:07:45.247" Score="7" ViewCount="671" Body="&lt;p&gt;The title more or less says it all, but to contextualise a bit:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cerebellar molecular layer interneurons have been classified, probably since Cajal, into the &lt;em&gt;basket&lt;/em&gt; cells, which synapse onto the soma and axon initial segment of Purkinje cells, and &lt;em&gt;stellate&lt;/em&gt; cells, which synapse onto the dendrites. The types are distinguishable in tissue slices by positional and morphological differences, but it is at least arguable that the variation is continuous and the boundary somewhat arbitrary. Both types take basically the same inputs and deliver the same outputs, albeit in marginally different cellular locations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I'm aware -- and I would be &lt;em&gt;incredibly&lt;/em&gt; happy to be told otherwise -- there is no known difference in protein expression that can be used to distinguish between these interneuron types, for instance in dissociated culture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, is there in fact some identifying marker? And if not, is it still useful to classify them as separate types?&lt;/p&gt;&#xA;" OwnerUserId="149" LastActivityDate="2011-12-21T18:09:38.727" Title="Are cerebellar basket and stellate neurons actually different cell types?" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="189" PostTypeId="1" AcceptedAnswerId="199" CreationDate="2011-12-18T03:05:32.333" Score="50" ViewCount="57594" Body="&lt;p&gt;I am having some trouble understanding how salt water, a simple solution, could so effectively remove the pains of a sore throat. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do believe that the answer is closely related to hypo/hyper-tonic solutions, but why is this so, and how does this work?&lt;/p&gt;&#xA;" OwnerUserId="157" LastEditorUserId="69" LastEditDate="2012-08-03T22:49:38.840" LastActivityDate="2015-02-06T13:28:01.600" Title="Why Does Salt Water Help Sore Throats?" Tags="&lt;human-biology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="190" PostTypeId="1" AcceptedAnswerId="194" CreationDate="2011-12-18T08:31:28.737" Score="19" ViewCount="602" Body="&lt;p&gt;What are the major evolutionary pressures for Bioluminescence?&lt;/p&gt;&#xA;" OwnerUserId="161" LastEditorUserId="338" LastEditDate="2012-02-21T09:48:18.893" LastActivityDate="2012-05-30T06:38:17.600" Title="What are the major evolutionary pressures for Bioluminescence?" Tags="&lt;evolution&gt;&lt;bioluminescence&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="191" PostTypeId="2" ParentId="183" CreationDate="2011-12-18T10:18:27.490" Score="7" Body="&lt;p&gt;Maybe WB is easier for them to test?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, however, my recommendation is to check if they provide refs to paper using those antibodies and look at the images on the paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Be careful putting your trust in the supplier's pictures, I have seen obviously photoshopped images on commercial websites.&#xA;Also always double-check the referenced papers, as sometimes they don't really use the same product that is sold...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other than that, in my experience, the recommended application is just that: recommended. The antibody may as well work for other application.&#xA;That said, note that there is a rationale for an antibody working for WB and not IHC, for instance: perfusion with fixators such as PFA will change the 3D structure of the target protein and may mask (or reveal) certain epitops, so the antibody may be more or less efficient depending what form of the protein you're dealing with (native, fixed in PFA, fixed in glutaraldehyde, SDS-denaturated etc.)&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2011-12-18T10:18:27.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="192" PostTypeId="1" AcceptedAnswerId="197" CreationDate="2011-12-18T10:28:20.397" Score="13" ViewCount="465" Body="&lt;p&gt;The novel (and subsequently movie) &lt;em&gt;Jurassic Park&lt;/em&gt; featured a dinosaur called &lt;em&gt;Dilophosaurus&lt;/em&gt;, that was purported to be venomous and had an ability similar to that of the extant spitting cobra. Unfortunately, &lt;a href=&quot;http://people.hofstra.edu/J_B_Bennington/publications/JPerrors.html&quot;&gt;the whole setup isn't real&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This got me wondering though. Modern venomous snakes, to give a particular example, ought to have had ancestors that already had appropriately modified salivary glands, and similarly for most other extant venomous species. (I suppose I'll restrict myself to vertebrates so as not to be too broad.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I now ask: have fossils of animals that are likely to have been venomous ever been discovered?&lt;/p&gt;&#xA;" OwnerDisplayName="user132" LastEditorUserId="107" LastEditDate="2011-12-18T16:51:32.597" LastActivityDate="2012-01-06T21:27:26.133" Title="Are there any pre-Holocene venomous animals?" Tags="&lt;zoology&gt;&lt;evolution&gt;&lt;palaeontology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="193" PostTypeId="1" AcceptedAnswerId="256" CreationDate="2011-12-18T11:39:17.287" Score="23" ViewCount="2096" Body="&lt;p&gt;I've read that the amoeba is capable of learning.  Since these protists have no nervous system, it's safe to assume that even highly simplified learning mechanisms of the Aplysia are miles off in the evolutionary distance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this species learn?  I would presume that there is a complicated chain of receptor mediated transcription regulation, but what are the specifics?  What types of receptors does an amoeba have to sense its environs?&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="338" LastEditDate="2012-02-21T09:48:21.640" LastActivityDate="2021-03-08T02:20:14.927" Title="Are single-celled organisms capable of learning?" Tags="&lt;microbiology&gt;&lt;transcription&gt;&lt;learning&gt;&lt;receptor&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="194" PostTypeId="2" ParentId="190" CreationDate="2011-12-18T13:27:40.473" Score="18" Body="&lt;p&gt;In many cases, and in particular in marine invertebrates, the bioluminescence is in fact produced by symbiotic bacteria of the Vibrionaceae family. In most cases the bacteria can sense when they are being hosted by the animal through quorum sensing mechanisms, and start producing light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The evolutionary pressure for the bacteria to produce light is to be in the protected environment of the animal which often feeds them. On the animal side, there can be several reasons to host the luminescent bacteria. In many cases, the evolutionary pressure is linked to reproduction. In order to successfully reproduce in the immensity of oceans, marine animals need to know that they are among their kind before they release their gametes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example is the one of some deep see fish like the anglerfish which have developed a special &quot;flash light&quot; organ to host bio-luminescent bacteria. Fish can use the bacteria to emit a light to aid in camouflage, hunting, and attracting mates. See &lt;a href=&quot;http://microbewiki.kenyon.edu/index.php/Deep_sea_fish&quot;&gt;http://microbewiki.kenyon.edu/index.php/Deep_sea_fish&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="167" LastEditorUserId="167" LastEditDate="2011-12-18T13:32:52.767" LastActivityDate="2011-12-18T13:32:52.767" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="195" PostTypeId="1" AcceptedAnswerId="213" CreationDate="2011-12-18T14:32:34.567" Score="9" ViewCount="1190" Body="&lt;p&gt;When cold or in shock a person's blood vessels constrict in order to preserve heat or to move blood flow to protect vital organs.  I am interested in the mechanism by which this is achieved.  Does this occur along the entire length of the limb or are there 'pinch points' (for example is it possible to simply have a point of vasoconstriction just below the shoulder which would reduce blood flow to the entire arm)?  Am I correct in thinking that the response is neurological rather than endocrinological ?&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2011-12-19T13:39:12.047" Title="Where does vasoconstriction occur in limbs?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="196" PostTypeId="2" ParentId="190" CreationDate="2011-12-18T16:29:08.863" Score="6" Body="&lt;p&gt;Bioluminescence, in particular in marine organisms, has also been linked to way to get rid of reactive oxygen species (ROS). In fact, luciferases catalyse the photogenic oxydation of luciferins. In [&lt;a href=&quot;http://jeb.biologists.org/content/201/8/1211.full.pdf&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;], the authors propose that this system's function was primarily for antioxydation, while in deep seas, where the water is oxygen-poor, the lower selective pressure toward antioxydation would have given rise to light emitting functions in specialized organs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jeb.biologists.org/content/201/8/1211.full.pdf&quot; rel=&quot;nofollow&quot;&gt;THE ORIGINS OF MARINE BIOLUMINESCENCE: TURNING OXYGEN DEFENCE&#xA;MECHANISMS INTO DEEP-SEA COMMUNICATION TOOLS&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencemag.org/content/328/5979/704.abstract&quot; rel=&quot;nofollow&quot;&gt;Bioluminescence in the Ocean: Origins of Biological, Chemical, and Ecological Diversity&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="36" LastEditorUserId="36" LastEditDate="2012-05-30T06:38:17.600" LastActivityDate="2012-05-30T06:38:17.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="197" PostTypeId="2" ParentId="192" CreationDate="2011-12-18T16:34:06.730" Score="20" Body="&lt;h2&gt;Squamates&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Extant venomous snakes do have venomous ancestors. &lt;a href=&quot;http://dx.doi.org/10.1038/nature04328&quot;&gt;Fry et al. (2006)&lt;/a&gt; reported on finding venom toxins more broadly within Reptilia, beyond the well-known venomous snakes and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Helodermatidae&quot;&gt;helodermatid lizards&lt;/a&gt;. They show that varanid and iguanid lizards also have venom toxins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same group of authors (&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0810883106&quot;&gt;Fry et al., 2009&lt;/a&gt;) then reported on the use of venom in the extant varanid lizard, &lt;em&gt;Varanus komodoensis&lt;/em&gt; (Komodo monitor). This is a different hypothesis than the usual &quot;toxic bacteria&quot; hypothesis for predation in these animals. They then reinterpret the skull of the giant (~5.5 m) varanid &lt;em&gt;Varanus (Megalania) priscus&lt;/em&gt;. They conclude, based on anatomical similarity and the close phylogenetic relationship between it and &lt;em&gt;V. komodoensis&lt;/em&gt;, that &lt;em&gt;V. priscus&lt;/em&gt;' predatory mode was more similar to other varanid lizards, likely involving venom delivery.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Archosaurs&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Discovery of a venomous clade within squamates, including snakes and several clades of lizards, does not imply venom more broadly within Reptilia. Specifically, it would not parsimoniously reconstruct the presence of venom in Archosauria, the clade that includes dinosaurs. However, &lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0912360107&quot;&gt;Gong et al. (2009)&lt;/a&gt; interpret the teeth of the dromaeosaurid theropod dinosaur, &lt;em&gt;Sinornithosaurus&lt;/em&gt; as having venom grooves. These grooves are similar to grooves in the teeth of &lt;a href=&quot;http://en.wikipedia.org/wiki/Uatchitodon&quot;&gt;&lt;em&gt;Uatchitodon&lt;/em&gt;&lt;/a&gt;, a Triassic squamate from Arizona.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is currently no solid evidence that archosaurs could spit, nor is there ever likely to be.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Mammals&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Venomous extant mammals include the &lt;a href=&quot;http://dx.doi.org/10.1038/nature06936&quot;&gt;platypus&lt;/a&gt; (&lt;em&gt;Ornithorhynchus&lt;/em&gt;), &lt;em&gt;Solenodon&lt;/em&gt;, and some species of shrews. The venom gland in the platypus is a modified sweat gland on the hind limb, which includes an ossified spur. A similar structure has also been found in the basal mammalian taxa &lt;em&gt;Gobiconodon&lt;/em&gt; and &lt;em&gt;Zhangheotherium&lt;/em&gt; (Hurum et al., 2006). &lt;a href=&quot;http://www.app.pan.pl/article/item/app51-001.html&quot;&gt;Hurum et al. (2006)&lt;/a&gt; described a similar structure in the multituberculates. As the most basal clade of Mammalia, the authors conclude that an ossified spur is apomorphic for Mammalia and that the ancestral mammal may have used it for venom delivery. This structure would have been retained more-or-less unmodified in platypus and lost in other mammalian lineages. The authors' conclusions are supported by the presences of a non-venomous spur in the other clade of monotremes, the echidnas.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nature03646&quot;&gt;Fox and Scott (2005)&lt;/a&gt; report that the Palaeocene (~60 Ma) pantolestid &lt;em&gt;Bisonalveus browni&lt;/em&gt; also possessed teeth with venom delivery grooves.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Non-gnathostomes&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.4202/app.2009.0045&quot;&gt;Szaniawski, 2009&lt;/a&gt; used similar logic based on grooved &quot;tooth&quot; elements to conclude that some extinct jawless chordate &lt;a href=&quot;http://en.wikipedia.org/wiki/Conodont&quot;&gt;conodonts&lt;/a&gt; may also have been venomous.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorDisplayName="user132" LastEditDate="2012-01-06T21:27:26.133" LastActivityDate="2012-01-06T21:27:26.133" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="198" PostTypeId="2" ParentId="195" CreationDate="2011-12-18T16:53:33.197" Score="6" Body="&lt;p&gt;Vasoconstriction is a phenomenon that can be caused by many factors, from mechanical events (such as stretching) to hormones (epinephrin, neurepinephrin, angiotensin ...). But no matter what is the cause, the end-result is an increase in intracellular calcium concentration in smooth muscle cells (which compose the arteries and veins). So it seems that constriction does not happen in specific points but rather all along the limb. Furthermore angiotensin receptors are found in high concentration in smooth muscle cells [&lt;a href=&quot;http://www.clinsci.org/cs/100/0481/1000481.pdf&quot;&gt;1&lt;/a&gt;], suggesting that every such cell has the ability to change it's morphology in order to induce vasoconstriction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your second point, I think the response is as much endocrinological as neurological, since it involves both peripheral and central regulations. (Well, as a side note, endocrine systems rarely have no interaction with central ones).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.clinsci.org/cs/100/0481/1000481.pdf&quot;&gt;Angiotensin receptors : distribution,&#xA;signalling and function&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="36" LastEditorUserId="36" LastEditDate="2011-12-18T20:13:25.727" LastActivityDate="2011-12-18T20:13:25.727" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="199" PostTypeId="2" ParentId="189" CreationDate="2011-12-18T19:53:40.617" Score="47" Body="&lt;p&gt;Salt water may have &lt;strong&gt;anti-septic&lt;/strong&gt; properties due to the effect it has on water potential.  Pure water has a water potential (Ψ) of zero.  A concentrated salt solution has a lower (more-negative) water potential.  The water potential of the salt solution is likely to be more negative than that of the pathogen's cytoplasm; the salt solution is therefore referred to as hypertonic.  Therefore water osmoses out of the cell (osmosis being the net movement of water from a higher water potential to a lower water potential across a semi-permeable membrane).  The loss of water from the pathogenic cells causes osmotic crenation - the cell becomes shrivelled and dies.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A hypotonic solution (for example cells placed into pure water) would cause the opposite effect - osmotic lysis.  This is the bursting of the cell due to the movement of water into the cell.  The bacterial cell wall would first have to be damaged (e.g. by penicillin).  This would &lt;em&gt;not&lt;/em&gt; be the process by which a salt solution has effect, however.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fact that the salt water is warm in order to improve solubility may also have the side-effect of causing vasodilation around the infection, increasing the rate at which white blood cells can arrive at the infection site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has been more difficult to find a theory as to why a salt solution would have analgesic properties, see the comments below &amp;amp; previous versions of this answer.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2011-12-19T11:47:26.463" LastActivityDate="2011-12-19T11:47:26.463" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="200" PostTypeId="1" AcceptedAnswerId="203" CreationDate="2011-12-18T21:36:14.970" Score="3" ViewCount="93" Body="&lt;p&gt;Expression of extracellular protein Laminin 9 alpha-4 chain in human skeletal muscle.&#xA;Indirect immunostaining with HRP immunostain marker. Ob.x40.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have unsuccessfully searched NCBI -database, JSTOR and other major Biology databases for an answer. This suggests to me that I do not understand what is going on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1. What are the substrates of above cytochemical reactions for the given immunostaining above?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I need to give a simpler question where I apparently know the reaction exactly, since it is possible that people cannot answer the above question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mitochondria in Hep-2 cell line cells. Cytochemical test for mitochondria specific enzyme NAHD dehydrogenase. Ob.x40.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. What is the substrate of the cytochemical reaction?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My answer:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reaction of NADH dehydrogenase is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;NADH + H&lt;sup&gt;+&lt;/sup&gt; + CoQ → NAD&lt;sup&gt;+&lt;/sup&gt; + CoQH&lt;sub&gt;2&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Substrate: CoQ&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2011-12-20T10:31:47.170" LastActivityDate="2011-12-20T10:31:47.170" Title="Substrates of cytochemical reactions in this immunostaining" Tags="&lt;homework&gt;&lt;mitochondria&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="201" PostTypeId="1" AcceptedAnswerId="1770" CreationDate="2011-12-18T21:43:40.390" Score="7" ViewCount="308" Body="&lt;p&gt;Ankylosing Spondylitis (AS) causes inflammation around joints and the growth of syndesmophytes that may eventually fuse vertebrae. I'm familiar with the genetics (HLA-B27, IL1A) related to the condition, but I can't find any information about the mechanism that causes the actual growths to occur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My current assumption is that AS causes the over-production or under-production of a particular compound or enzyme at the growth site, but I can't find any studies or papers that explain this. Is the mechanism known? Is it directly related to abnormal levels of a particular substance?&lt;/p&gt;&#xA;" OwnerUserId="172" LastEditorUserId="172" LastEditDate="2011-12-19T10:00:47.230" LastActivityDate="2012-04-12T10:59:13.957" Title="Mechanism of syndesmophyte growth in AS" Tags="&lt;human-biology&gt;&lt;pathology&gt;&lt;joints&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="202" PostTypeId="1" AcceptedAnswerId="335" CreationDate="2011-12-18T21:45:16.950" Score="10" ViewCount="228" Body="&lt;p&gt;Isolating a gene or sets of genes in diseases sometimes isn't enough to determine penetrance - epigenetic factors can have a significant effect. What are the criteria in determining whether epigenetic factors are significant?&lt;/p&gt;&#xA;" OwnerUserId="173" LastEditorUserId="173" LastEditDate="2011-12-18T21:54:38.107" LastActivityDate="2011-12-26T12:40:12.687" Title="What are the criteria for determining the influence of epigenetic factors?" Tags="&lt;epigenetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="203" PostTypeId="2" ParentId="200" CreationDate="2011-12-19T02:50:10.963" Score="4" Body="&lt;p&gt;It's hard to understand the question, but in any immunocytochemical staining such as the above, you have two different types of reactions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the antibody binding to the target (in this case, some laminin) &lt;/li&gt;&#xA;&lt;li&gt;the peroxidase-based colorimetric reaction with DAB. DAB (3,3'-diaminobenzidine tetrahydrochloride) is oxidized in the presence of hydrogen peroxide to form a brown precipitate, which becomes the stain.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The fact that is an indirect immunostaining implies that you have a non-conjugated primary antibody against laminin and a secondary antibody against the Fc part of immunoglobulins of the species in which the first antibody was raised. This secondary antibody will be conjugated with HRP (horseradish peroxidase, the enzyme responsible of generating the peroxides that will oxidize the DAB).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a more complete reference of immunocytochemical stainings, you can read: &lt;a href=&quot;http://www.ihcworld.com/_books/Dako_Handbook.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.ihcworld.com/_books/Dako_Handbook.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="48" LastActivityDate="2011-12-19T02:50:10.963" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="205" PostTypeId="5" CreationDate="2011-12-19T11:16:56.360" Score="0" Body="&lt;p&gt;The process that produces a complementary strand of RNA from a section of DNA or (rarely) other RNA.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-29T09:09:42.523" LastActivityDate="2017-03-29T09:09:42.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="206" PostTypeId="4" CreationDate="2011-12-19T11:16:56.360" Score="0" Body="The process that produces a complementary strand of RNA from a section of DNA or (rarely) other RNA." OwnerUserId="69" LastEditorUserId="66" LastEditDate="2012-01-05T19:50:23.297" LastActivityDate="2012-01-05T19:50:23.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="207" PostTypeId="5" CreationDate="2011-12-19T11:18:07.387" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-19T11:18:07.387" LastActivityDate="2011-12-19T11:18:07.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="208" PostTypeId="4" CreationDate="2011-12-19T11:18:07.387" Score="0" Body="RNA Sequences corresponding to genomic regions which are retained in processed RNA (i.e., not spliced out)." OwnerUserId="69" LastEditorUserId="107" LastEditDate="2013-04-09T04:58:49.567" LastActivityDate="2013-04-09T04:58:49.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="209" PostTypeId="5" CreationDate="2011-12-19T11:19:03.483" Score="0" Body="&lt;p&gt;For questions purely relating to chemistry, see the &lt;a href=&quot;http://chemistry.stackexchange.com&quot;&gt;Chemistry Stack Exchange&lt;/a&gt; site.&lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="4101" LastEditDate="2013-10-31T19:18:37.633" LastActivityDate="2013-10-31T19:18:37.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="210" PostTypeId="4" CreationDate="2011-12-19T11:19:03.483" Score="0" Body="Chemistry relating to carbon-containing compounds.  Should relate to biology as opposed to being purely about chemistry." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T19:17:02.157" LastActivityDate="2013-10-31T19:17:02.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="211" PostTypeId="5" CreationDate="2011-12-19T11:55:31.227" Score="0" Body="&lt;p&gt;Mitochondira are maternally inherited and carry some genetic material. They are responsible for respiration in the cell. Relevant tags include &lt;a href=&quot;/questions/tagged/respiration&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;respiration&amp;#39;&quot; rel=&quot;tag&quot;&gt;respiration&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/cell-biology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;cell-biology&amp;#39;&quot; rel=&quot;tag&quot;&gt;cell-biology&lt;/a&gt; and &lt;a href=&quot;/questions/tagged/molecular-biology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;molecular-biology&amp;#39;&quot; rel=&quot;tag&quot;&gt;molecular-biology&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-03-23T11:17:14.240" LastActivityDate="2016-03-23T11:17:14.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="212" PostTypeId="4" CreationDate="2011-12-19T11:55:31.227" Score="0" Body="The organelle in eukaryotes where the main stages of respiration occur." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T14:05:14.543" LastActivityDate="2013-10-31T14:05:14.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="213" PostTypeId="2" ParentId="195" CreationDate="2011-12-19T13:39:12.047" Score="4" Body="&lt;p&gt;Reduced blood flow to a region of the body occurs through 2 principal mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) The smooth muscle fibers in the tunica media layer of the arteries contract and reduce the diameter of the artery, limiting blood flow due to increased resistance (this is the mechanism in @agrimaldi's answer).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Circularly oriented smooth muscle fibers at the junction of a metarteriole (the distal end of an arteriole) and a capillary bed form a precapillary sphincter, which serves as a valve and prevents blood flow into a the capillary bed.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to answer your question, it is both.  The narrowing of the arteries would occur rather continuously across the limb but there are &quot;pinch points&quot; where metarterioles joint the capillary beds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The endocrine and nervous systems are pretty integrated so in most cases it would be the result of the actions of both systems. &lt;/p&gt;&#xA;" OwnerUserId="137" LastActivityDate="2011-12-19T13:39:12.047" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="214" PostTypeId="5" CreationDate="2011-12-19T14:24:57.933" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-19T14:24:57.933" LastActivityDate="2011-12-19T14:24:57.933" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="215" PostTypeId="4" CreationDate="2011-12-19T14:24:57.933" Score="0" Body="Regions of a gene which do not form a part of the mature RNA product." OwnerUserId="69" LastEditorUserId="6307" LastEditDate="2017-05-25T05:36:06.587" LastActivityDate="2017-05-25T05:36:06.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="216" PostTypeId="5" CreationDate="2011-12-19T14:49:16.957" Score="0" Body="&lt;p&gt;Often circular segments of DNA that can replicate outside of the chromosomes.  Generally found in bacteria.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-29T16:00:08.920" LastActivityDate="2017-03-29T16:00:08.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="217" PostTypeId="4" CreationDate="2011-12-19T14:49:16.957" Score="0" Body="Often circular segments of DNA that can replicate outside of the chromosomes.  Generally found in bacteria." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T18:04:13.210" LastActivityDate="2013-10-31T18:04:13.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="218" PostTypeId="5" CreationDate="2011-12-19T14:50:29.933" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-19T14:50:29.933" LastActivityDate="2011-12-19T14:50:29.933" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="219" PostTypeId="4" CreationDate="2011-12-19T14:50:29.933" Score="0" Body="The organelle in which photosynthesis occurs" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2011-12-22T16:53:39.987" LastActivityDate="2011-12-22T16:53:39.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="220" PostTypeId="5" CreationDate="2011-12-19T15:05:49.097" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-19T15:05:49.097" LastActivityDate="2011-12-19T15:05:49.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="221" PostTypeId="4" CreationDate="2011-12-19T15:05:49.097" Score="0" Body="Messenger RNA is produced during transcription before it leaves the nucleus to be be translated by a ribosome.  This produces a sequence of nucleic acids for which mRNA is considered the template." OwnerUserId="69" LastEditorUserId="5144" LastEditDate="2014-03-16T22:10:07.947" LastActivityDate="2014-03-16T22:10:07.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="222" PostTypeId="1" AcceptedAnswerId="273" CreationDate="2011-12-19T15:11:53.750" Score="43" ViewCount="22020" Body="&lt;p&gt;Many plants (e.g. roses, palms) can be protected from frost during the winter if shielded with an appropriate coat that can be bought in garden shops. Do plants produce any heat that can be kept inside with these &quot;clothes&quot;?&lt;/p&gt;&#xA;" OwnerUserId="164" LastEditorDisplayName="user132" LastEditDate="2011-12-19T15:59:48.257" LastActivityDate="2015-04-15T04:25:25.647" Title="Do plants produce any heat?" Tags="&lt;plant-physiology&gt;&lt;botany&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="223" PostTypeId="2" ParentId="222" CreationDate="2011-12-19T15:38:39.183" Score="15" Body="&lt;p&gt;Plants will be respiring continuously, which is an exothermic process. Therefore the plants will be producing a small amount of heat. The protection from frost may be more a result of the vastly smaller convection current of the coat compared to the atmosphere rather than by reducing any conduction away of heat produced by the plant, however.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Keeping the plant out of the wind by 'dressing it' will reduce the rate of transpiration when the stomata are open.  I would &lt;em&gt;very tentatively&lt;/em&gt; suggest that, as water has a very high specific heat capacity, having a greater volume of water within the plant would help to retain any heat that was produced by respiration.  However this is entirely speculation on my part. &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2011-12-19T15:38:39.183" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="224" PostTypeId="5" CreationDate="2011-12-19T15:41:00.787" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-19T15:41:00.787" LastActivityDate="2011-12-19T15:41:00.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="225" PostTypeId="4" CreationDate="2011-12-19T15:41:00.787" Score="0" Body="Study of the normal functioning of plants and plant cells" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2011-12-22T16:53:56.027" LastActivityDate="2011-12-22T16:53:56.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="226" PostTypeId="5" CreationDate="2011-12-19T16:00:06.263" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-19T16:00:06.263" LastActivityDate="2011-12-19T16:00:06.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="227" PostTypeId="4" CreationDate="2011-12-19T16:00:06.263" Score="0" Body="A region of repeating DNA at the end of a chromosome that protects the chromosome from decaying." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T18:26:58.780" LastActivityDate="2013-10-31T18:26:58.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="228" PostTypeId="1" AcceptedAnswerId="231" CreationDate="2011-12-19T16:16:42.583" Score="23" ViewCount="1516" Body="&lt;p&gt;What statistical processes and methods are used by geneticists/molecular biologists to know where one gene starts and one ends?&lt;/p&gt;&#xA;" OwnerUserId="173" LastEditorUserId="81" LastEditDate="2012-01-09T19:30:11.167" LastActivityDate="2012-09-13T20:22:11.367" Title="How are the boundaries of a gene determined?" Tags="&lt;molecular-biology&gt;&lt;genetics&gt;" AnswerCount="4" CommentCount="6" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="229" PostTypeId="2" ParentId="228" CreationDate="2011-12-19T17:04:57.027" Score="3" Body="&lt;p&gt;Generally speaking you sequence the genome and then search for clues. There are usually specific sequences preceding a gene that help the translational equipment know &quot;hello this is where we begin&quot; as well as regions where proteins can bind that are used to enhance or inhibit translation of the gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Computers can be programmed to search through the sequence and bring up possible candidates for people to look at more closely.&lt;/p&gt;&#xA;" OwnerUserId="41" LastActivityDate="2011-12-19T17:04:57.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="230" PostTypeId="1" AcceptedAnswerId="244" CreationDate="2011-12-19T17:40:03.783" Score="26" ViewCount="262" Body="&lt;p&gt;Vaccines, especially those given in adulthood, usually have term limits attached, eg: 10 years for yellow fever or 3 years for typhoid. Since presumably the time course of an immune response is no great respecter of our calendrical conventions, and since there is also presumably a spectrum of responses across the population, how are these durations estimated? What are the criteria for deciding a cutoff time?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, do the estimates get revisited and updated as time goes on and new data become available? &lt;em&gt;Do&lt;/em&gt; new data become available? Is there continuing follow-up research into this, or does the estimate just get made before the vaccine comes to market and then get taken as gospel?&lt;/p&gt;&#xA;" OwnerUserId="149" LastEditorUserId="69" LastEditDate="2011-12-21T20:45:58.250" LastActivityDate="2012-09-16T22:52:18.593" Title="How is duration of efficacy estimated for vaccines?" Tags="&lt;immunology&gt;&lt;epidemiology&gt;&lt;vaccination&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="231" PostTypeId="2" ParentId="228" CreationDate="2011-12-19T18:02:45.533" Score="12" Body="&lt;p&gt;I know of only one naive approach to determining the boundaries of a gene : RACE-PCR. There are two kinds, 3' and 5' RACE, which allow to find the respective extremities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rationale is the following :&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;You perform a reverse transcription of the transcript of interest using a specific primer. At this step you have a specific single stranded cDNA.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Then you add a stretch of identical nucleotides called the homopolymeric tail in 5' of the cDNA.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Finally you perform a PCR using one specific primer and one universal primer that recognizes the homopolymeric tail. You can sequence your amplified cDNA and find where it is located in the genome with a 1 bp resolution. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For the 3'RACE, the concept is the same but the poly-A tail is used instead of generating it yourself with the terminal transferase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this paper for a detailed protocol :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1101/pdb.prot3989&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Sambrook J, Russell DW&lt;/strong&gt;. 2006. Rapid Amplification of 5’ cDNA Ends (5'-RACE). CSH protocols 2006.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Rapid_Amplification_of_cDNA_Ends&quot; rel=&quot;nofollow&quot;&gt;corresponding wikipedia article&lt;/a&gt; gives you more details about what is happening at each step, but beware, there is an error : it is said that for the 5'RACE, the terminal transferase appends the homopolymeric tail in 3' while it appends it in &lt;strong&gt;5'&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="36" LastEditorUserId="836" LastEditDate="2012-09-13T20:22:11.367" LastActivityDate="2012-09-13T20:22:11.367" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="232" PostTypeId="2" ParentId="228" CreationDate="2011-12-19T18:20:29.137" Score="8" Body="&lt;p&gt;There are various software in which you can enter your sequence (let's say the whole genome sequence) and it can identify for you the putative open reading frames (ORFs), i.e. the start codons and the stop codons. Then, by using these putative genes, you can do a sequence alignment by using BLAST and then, based on the scores you can confirm that those are really ORFs. As this being the statistical approach, you can then verify your results in the wet lab, like agrimaldi suggested.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2011-12-19T18:20:29.137" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="233" PostTypeId="5" CreationDate="2011-12-19T18:29:37.493" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/NMDA_receptor&quot; rel=&quot;nofollow&quot;&gt;NMDA receptors&lt;/a&gt; (NMDARs) are a family of ionotropic glutamate receptors that can bind the artificial agonist N-methyl-D-aspartate at their glutamate site. NMDARs also require binding of the co-agonist glycine (or D-serine).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At typical resting membrane potentials, NMDAR channels are blocked by Mg&lt;sup&gt;2+&lt;/sup&gt;. This block is relieved by depolarisation, which allows NMDARs to act as coincidence detectors, opening when presynaptic glutamate release coincides with post-synaptic depolarisation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NMDARs are cation channels with a high permeability for Ca&lt;sup&gt;2+&lt;/sup&gt;. In physiological conditions the greatest current through NMDA channels is usually carried by K&lt;sup&gt;+&lt;/sup&gt;, but the flow of Ca&lt;sup&gt;2+&lt;/sup&gt; through the channels is believed to be important for synaptic plasticity.&lt;/p&gt;&#xA;" OwnerUserId="149" LastEditorUserId="149" LastEditDate="2011-12-22T16:53:49.893" LastActivityDate="2011-12-22T16:53:49.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="234" PostTypeId="4" CreationDate="2011-12-19T18:29:37.493" Score="0" Body="Ionotropic glutamate receptors that respond to the artificial agonist N-methyl-D-aspartate. They act as coincidence detectors and are important for synaptic plasticity." OwnerUserId="149" LastEditorUserId="149" LastEditDate="2011-12-22T16:53:52.297" LastActivityDate="2011-12-22T16:53:52.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="235" PostTypeId="5" CreationDate="2011-12-19T18:44:51.960" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_culture&quot; rel=&quot;nofollow&quot;&gt;Cell culture&lt;/a&gt; is the process of taking living cells and growing them &lt;em&gt;in vitro&lt;/em&gt;: under controlled laboratory conditions, isolated from their original organism and natural environment. Cells may be cultured directly from tissues extracted from the parent organism (known as &quot;primary&quot; culture), or from immortalised cell lines such as HeLa, of which a great variety are now commercially available.&lt;/p&gt;&#xA;" OwnerUserId="149" LastEditorUserId="4101" LastEditDate="2013-10-31T00:53:52.327" LastActivityDate="2013-10-31T00:53:52.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="236" PostTypeId="4" CreationDate="2011-12-19T18:44:51.960" Score="0" Body="Cell culture is the process of growing and maintaining living cells in vitro." OwnerUserId="149" LastEditorUserId="69" LastEditDate="2012-02-12T23:41:06.423" LastActivityDate="2012-02-12T23:41:06.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="237" PostTypeId="5" CreationDate="2011-12-19T19:05:37.163" Score="0" Body="&lt;p&gt;A receptor is a molecular target for a chemical signal such as a neurotransmitter, hormone, or drug. Binding of the signal to the receptor initiates or modulates behaviour in the receiving cell.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-29T13:59:32.143" LastActivityDate="2017-03-29T13:59:32.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="238" PostTypeId="4" CreationDate="2011-12-19T19:05:37.163" Score="0" Body="A receptor is a molecular target for a chemical signal such as a neurotransmitter, hormone, or drug. Binding of the signal to the receptor initiates or modulates behaviour in the receiving cell." OwnerUserId="149" LastEditorUserId="4101" LastEditDate="2013-10-31T16:50:25.540" LastActivityDate="2013-10-31T16:50:25.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="239" PostTypeId="1" AcceptedAnswerId="254" CreationDate="2011-12-19T19:46:37.027" Score="64" ViewCount="3675" Body="&lt;p&gt;Darwin suggested that sexual selection, especially by female choice, may counter natural selection. Theoretical models, such as a Fisherian runaway process, suggest that evolution of preference and preferred phenotypes may drive each other in ever increasing speed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because one male may fertilize many females, one could imagine that natural selection against preferred but energetically costly phenotypes may be weak, and the whole process may not slow down fast enough (i.e., be sufficiently self-limiting). If male mortality is high and their number is low, the random fluctuations may easily cause the extinction of population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any fossil or experimental evidence that this may really happen?&lt;/p&gt;&#xA;" OwnerUserId="68" LastEditorUserId="3624" LastEditDate="2013-06-13T12:27:11.583" LastActivityDate="2013-06-13T12:27:11.583" Title="Is there any evidence that sexual selection may lead to extinction of species?" Tags="&lt;evolution&gt;&lt;theoretical-biology&gt;&lt;sexual-selection&gt;&lt;palaeontology&gt;&lt;extinction&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="240" PostTypeId="1" AcceptedAnswerId="241" CreationDate="2011-12-19T21:56:59.593" Score="18" ViewCount="1710" Body="&lt;p&gt;I know that the reference human genome is complied from DNA portions from different people, most of whom were European. Do you know how many of them were involved? Do you know which ones were involved? Perhaps scientists like James Watson and George Church's DNA were in the reference genome. Also, I would assume that the NIH funded Human Genome Project's reference genome must be slightly different from the privately funded one. &lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="69" LastEditDate="2012-01-13T10:08:12.637" LastActivityDate="2012-01-13T10:08:12.637" Title="How many people's DNA were involved in the compilation of the reference human genome?" Tags="&lt;genetics&gt;&lt;human-genome&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="241" PostTypeId="2" ParentId="240" CreationDate="2011-12-19T22:15:14.790" Score="14" Body="&lt;p&gt;&lt;strong&gt;tl;dr&lt;/strong&gt;: In the Human Genome Project, they used the DNA of four people (though one male provided &gt;70% of DNA. The Celera genome was compiled from five people.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the [...] Human Genome Project (HGP), [...] scientists used white&#xA;  blood cells from the blood of two male and two female donors (randomly&#xA;  selected from 20 of each) -- each donor yielding a separate DNA&#xA;  library. One of these libraries (RP11 [anonymous donor from Buffalo,&#xA;  NY]) was used considerably more than others, due to quality&#xA;  considerations. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;[...]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In the Celera Genomics private-sector project, DNA from five different&#xA;  individuals were used for sequencing. The lead scientist of Celera&#xA;  Genomics at that time, Craig Venter, later acknowledged (in a public&#xA;  letter to the journal Science) that his DNA was one of 21 samples in&#xA;  the pool, five of which were selected for use.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;On September 4, 2007, a team led by Craig Venter published his&#xA;  complete DNA sequence,[21] unveiling the six-billion-nucleotide genome&#xA;  of a single individual for the first time.)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_Genome_Project#Genome_donors&quot;&gt;Wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="34" LastActivityDate="2011-12-19T22:15:14.790" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="242" PostTypeId="1" AcceptedAnswerId="243" CreationDate="2011-12-20T01:41:31.647" Score="11" ViewCount="123" Body="&lt;p&gt;I was in the gym's steam-room today and a thought occurred to me: have I truly thwarted all possible mechanisms for maintaining thermal homeostasis?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's sweating, which is thwarted because the steam-room's atmosphere is as close to 100% humidity as possible, so there's almost no evaporative cooling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's convection, which is thwarted because the ambient temperature is above normal body temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And I can't get rid of heat by exhaling, because every lungful of air I inhale is already above normal body temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that, eventually, I should go into hyperthermia, but beside the above, are there any other last-ditch attempts to lower core temperature that my body could take?&lt;/p&gt;&#xA;" OwnerUserId="42" LastActivityDate="2011-12-20T04:57:16.660" Title="Last-ditch efforts to maintain thermal homeostasis" Tags="&lt;homeostasis&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="243" PostTypeId="2" ParentId="242" CreationDate="2011-12-20T04:57:16.660" Score="7" Body="&lt;p&gt;Another factor at play here is the cardiovascular system.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14610268&quot;&gt;Biro, Masudo, et al (2003)&lt;/a&gt; wrote an article about the benefits of the induction of systemic vasodilation for those with congestive heart failure.  This may be a short-term adaptation of the body stemming from the reduced ability to sweat in those conditions, or it may be a harbinger of the more serious circulation changes below.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21635561&quot;&gt;Epstein and Roberts (2011)&lt;/a&gt; explain how the eventual results of heatstroke (which isn't the phenomenon that you are describing, but a sauna might induce some of the features of these same pathways) can cause a circulatory collapse due to an initial overtaxing of the circulatory system to compensate as well as the activation of certain heat shock proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a lot of other references out there on sauna physiology, but many are not in evidence-based journals, so you can make your own decisions on those.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One factor that I didn't find mentioned explicitly was the basal metabolic rate.  It's probably safe to assume that the body will limit its own processes and reactions which produce heat.  I'm not clear on the extent to which factors such as the level of interleukins, etc. would play a role as they do in fever regulation.   &lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2011-12-20T04:57:16.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="244" PostTypeId="2" ParentId="230" CreationDate="2011-12-20T05:09:33.873" Score="16" Body="&lt;p&gt;Duration of efficacy is typically determined by tracking the antibody titers of a cohort of subjects who have gotten the vaccine, and estimating based on the trajectory of those titers where they will eventually cross the threshold to the point where the vaccine no longer confers immune resistance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These estimates do get revised and estimated as time goes on - you will occasionally see new recommendations for a second or third &quot;booster&quot; dose of a vaccine, which is meant to extend the duration of immunity beyond the duration of the original vaccine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two major types of studies track this over time. Phase IV clinical trials, which are clinical trials required post-licensure, and observational epidemiology trials, which tend to be performed when disease transmission starts to occur in supposedly vaccinated populations.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Mechanical snail has raised the issue of viral evolution, so I'll touch on it briefly. The duration of efficacy discussed above is based on how long a patient's body can mount an immune response to a particular challenge. That's a concern for &lt;em&gt;all&lt;/em&gt; vaccines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For some vaccines, there's a secondary process that's of concern - that of the virus evolving in such a way that the antigens targeted by the vaccine are no longer those on the virus itself. This is only a concern for some viruses, notably those that are particularly fast-evolving, like influenza or HIV, and less of an issue for say, measles and HPV.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But that's typically not what people are talking about when they say &quot;duration of efficacy&quot; because it's inherently unpredictable, and less a function of the vaccine and more a function of the virus.&lt;/p&gt;&#xA;" OwnerUserId="67" LastEditorUserId="67" LastEditDate="2012-09-16T22:52:18.593" LastActivityDate="2012-09-16T22:52:18.593" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="245" PostTypeId="5" CreationDate="2011-12-20T06:26:14.793" Score="0" Body="&lt;p&gt;The scientific study of plants, including their structure, physiology, genetics, molecular/cellular biology, ecology, distribution, classification, evolution, and economic importance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This tag is intended for questions about plants; i.e. pertaining to any of the angiosperms, gymnosperms, bryophytes, pteridophytes (ferns + allies), and algae.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Questions pertaining to bacteria, fungi, or viruses should be tagged as &lt;a href=&quot;/questions/tagged/bacteriology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;bacteriology&amp;#39;&quot; rel=&quot;tag&quot;&gt;bacteriology&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/mycology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;mycology&amp;#39;&quot; rel=&quot;tag&quot;&gt;mycology&lt;/a&gt;, or &lt;a href=&quot;/questions/tagged/virology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;virology&amp;#39;&quot; rel=&quot;tag&quot;&gt;virology&lt;/a&gt;, respectively, or &lt;a href=&quot;/questions/tagged/microbiology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;microbiology&amp;#39;&quot; rel=&quot;tag&quot;&gt;microbiology&lt;/a&gt; in general.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Botany is a fairly broad tag, so more precise tags should be used in conjunction with this tag. Commonly paired tags include: &lt;a href=&quot;/questions/tagged/plant-anatomy&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;plant-anatomy&amp;#39;&quot; rel=&quot;tag&quot;&gt;plant-anatomy&lt;/a&gt; &lt;a href=&quot;/questions/tagged/plant-physiology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;plant-physiology&amp;#39;&quot; rel=&quot;tag&quot;&gt;plant-physiology&lt;/a&gt; &lt;a href=&quot;/questions/tagged/plant-perception&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;plant-perception&amp;#39;&quot; rel=&quot;tag&quot;&gt;plant-perception&lt;/a&gt; &lt;a href=&quot;/questions/tagged/trees&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;trees&amp;#39;&quot; rel=&quot;tag&quot;&gt;trees&lt;/a&gt; &lt;a href=&quot;/questions/tagged/flowers&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;flowers&amp;#39;&quot; rel=&quot;tag&quot;&gt;flowers&lt;/a&gt; &lt;a href=&quot;/questions/tagged/fruit&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;fruit&amp;#39;&quot; rel=&quot;tag&quot;&gt;fruit&lt;/a&gt; &lt;a href=&quot;/questions/tagged/seeds&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;seeds&amp;#39;&quot; rel=&quot;tag&quot;&gt;seeds&lt;/a&gt; &lt;a href=&quot;/questions/tagged/photosynthesis&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;photosynthesis&amp;#39;&quot; rel=&quot;tag&quot;&gt;photosynthesis&lt;/a&gt; &lt;a href=&quot;/questions/tagged/transplantation&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;transplantation&amp;#39;&quot; rel=&quot;tag&quot;&gt;transplantation&lt;/a&gt; &lt;a href=&quot;/questions/tagged/pollination&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;pollination&amp;#39;&quot; rel=&quot;tag&quot;&gt;pollination&lt;/a&gt; &lt;a href=&quot;/questions/tagged/agriculture&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;agriculture&amp;#39;&quot; rel=&quot;tag&quot;&gt;agriculture&lt;/a&gt; &lt;a href=&quot;/questions/tagged/taxonomy&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;taxonomy&amp;#39;&quot; rel=&quot;tag&quot;&gt;taxonomy&lt;/a&gt; &lt;a href=&quot;/questions/tagged/terminology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;terminology&amp;#39;&quot; rel=&quot;tag&quot;&gt;terminology&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Botany can also be paired with other broad fields of study including: &lt;a href=&quot;/questions/tagged/molecular-biology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;molecular-biology&amp;#39;&quot; rel=&quot;tag&quot;&gt;molecular-biology&lt;/a&gt; &lt;a href=&quot;/questions/tagged/cell-biology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;cell-biology&amp;#39;&quot; rel=&quot;tag&quot;&gt;cell-biology&lt;/a&gt; &lt;a href=&quot;/questions/tagged/genetics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;genetics&amp;#39;&quot; rel=&quot;tag&quot;&gt;genetics&lt;/a&gt; &lt;a href=&quot;/questions/tagged/evolution&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;evolution&amp;#39;&quot; rel=&quot;tag&quot;&gt;evolution&lt;/a&gt; &lt;a href=&quot;/questions/tagged/ecology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;ecology&amp;#39;&quot; rel=&quot;tag&quot;&gt;ecology&lt;/a&gt; &lt;a href=&quot;/questions/tagged/species-identification&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;species-identification&amp;#39;&quot; rel=&quot;tag&quot;&gt;species-identification&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user132" LastEditorUserId="16866" LastEditorDisplayName="user132" LastEditDate="2019-07-12T03:37:37.243" LastActivityDate="2019-07-12T03:37:37.243" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="246" PostTypeId="4" CreationDate="2011-12-20T06:26:14.793" Score="0" Body="The study of plants and plant life." OwnerDisplayName="user132" LastEditorUserId="16866" LastEditorDisplayName="user132" LastEditDate="2019-07-12T03:37:37.243" LastActivityDate="2019-07-12T03:37:37.243" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="247" PostTypeId="5" CreationDate="2011-12-20T06:31:54.317" Score="0" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Paleontology&quot; rel=&quot;nofollow&quot;&gt;Palaeontology&lt;/a&gt;, also known as paleontology, palaeobiology or paleobiology,  is the study of organisms that lived in prehistoric times. Palaeontology deals with &lt;a href=&quot;https://en.wikipedia.org/wiki/Fossil&quot; rel=&quot;nofollow&quot;&gt;fossil&lt;/a&gt;-records.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Palaeontology broadly classified as &lt;a href=&quot;https://en.wikipedia.org/wiki/Paleozoology&quot; rel=&quot;nofollow&quot;&gt;palaeozoology&lt;/a&gt; (discussion on prehistoric animals) (sometimes the term palaeontology is used synonymously with palaeozoology)and &lt;a href=&quot;https://en.wikipedia.org/wiki/Paleobotany&quot; rel=&quot;nofollow&quot;&gt;palaeobotany&lt;/a&gt; (discussion on pre-historic plants). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But in case of ancient remains, their border is very fade because many specimens' taxonomic-nature could  &lt;em&gt;not&lt;/em&gt; be properly known (They grouped as &lt;a href=&quot;https://en.wikipedia.org/wiki/Incertae_sedis&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;incertae sedis&lt;/em&gt;&lt;/a&gt;). Another big branch of palaeontology, is &lt;a href=&quot;https://en.wikipedia.org/wiki/Micropaleontology&quot; rel=&quot;nofollow&quot;&gt;micropalaeontology&lt;/a&gt;, study of microfossils (including small-sized organisms (like bacteria, cyanobacteria, fungal hyphae, foraminifera, coccoliths, diatoms ) as well as microscopic remains of large organisms , say piece of barks, wood, pollens (&lt;a href=&quot;https://en.wikipedia.org/w/index.php?title=Paleopalynology&amp;amp;redirect=no&quot; rel=&quot;nofollow&quot;&gt;palaeoplynology&lt;/a&gt;), animal skeletal-parts of invertebrates and vertebrates), etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term &lt;a href=&quot;https://en.wikipedia.org/wiki/Paleoecology&quot; rel=&quot;nofollow&quot;&gt;Palaeoecology&lt;/a&gt; is applied for discussion about encien environment, climate, different inter-relationships of organisms, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Palaeontology is a very-much inter-disciplinary subject that is related with most-branches of biology, as well as Geology (Earth-science), Geography,  Astronomy, Cosmology, as well as the discussion on &lt;a href=&quot;https://en.wikipedia.org/wiki/Abiogenesis&quot; rel=&quot;nofollow&quot;&gt;origin of life&lt;/a&gt; is related to &lt;a href=&quot;https://en.wikipedia.org/wiki/Synthetic_biology&quot; rel=&quot;nofollow&quot;&gt;Synthetic-biology&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Astrobiology&quot; rel=&quot;nofollow&quot;&gt;Exobiology&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Palaeontology is the half of &lt;a href=&quot;http://http:/https://en.wikipedia.org/wiki/Evolution&quot; rel=&quot;nofollow&quot;&gt;Evolution&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Evolutionary_biology&quot; rel=&quot;nofollow&quot;&gt;Evolutionary biology&lt;/a&gt;, since fossil-records are only direct-evidence of ancient life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Palaeontology also have applied importance, like finding Coal and Petroleum, rock-layer correlation, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Portion of palaeontology discussing about origin of human, merges with &lt;a href=&quot;https://en.wikipedia.org/wiki/Archaeology&quot; rel=&quot;nofollow&quot;&gt;Archaeology&lt;/a&gt;.   &lt;a href=&quot;https://en.wikipedia.org/wiki/Bioarchaeology&quot; rel=&quot;nofollow&quot;&gt;Bioarchaeology&lt;/a&gt; discusses with later-condition of life-forms (other than human), especially those associated with archaeological-sites.&lt;/p&gt;&#xA;" OwnerUserId="25568" LastEditorUserId="25568" LastEditDate="2016-09-08T18:52:48.700" LastActivityDate="2016-09-08T18:52:48.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="248" PostTypeId="4" CreationDate="2011-12-20T06:31:54.317" Score="0" Body="Palaeontology is the study of organisms that lived in prehistoric times." OwnerDisplayName="user132" LastEditorDisplayName="user132" LastEditDate="2011-12-22T16:53:54.293" LastActivityDate="2011-12-22T16:53:54.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="249" PostTypeId="1" CreationDate="2011-12-20T06:53:18.900" Score="45" ViewCount="2360" Body="&lt;p&gt;The sensitive plant (&lt;em&gt;Mimosa pudica&lt;/em&gt;) is a remarkable little plant whose characteristic feature is its ability to droop its leaves when disturbed:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ti6oX.gif&quot; alt=&quot;sensitive plant animation&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently, this ability to droop rests on the cells in the leaves of the sensitive plant being able to draw water out of themselves through changes in intracellular ion concentrations, which makes the leaves less turgid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm hazy about is how the plant &quot;senses&quot; vibrations. Plants don't really have a nervous system to speak of; how then does the sensitive plant &quot;know&quot; to droop when disturbed?&lt;/p&gt;&#xA;" OwnerDisplayName="user132" LastEditorUserId="69" LastEditDate="2012-01-27T09:42:10.070" LastActivityDate="2012-09-13T06:20:49.097" Title="How does the sensitive plant detect vibrations?" Tags="&lt;botany&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="250" PostTypeId="2" ParentId="249" CreationDate="2011-12-20T08:18:02.647" Score="13" Body="&lt;p&gt;&lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822%2808%2900525-3&quot;&gt;Haswell, Peyronnet, et al (2008)&lt;/a&gt; have shown that plants have some of the same mechanosensitive ion channels that &lt;em&gt;E. coli&lt;/em&gt; does.  The work was on the roots of &lt;em&gt;Arabidopsis&lt;/em&gt; and not the plant you are investigating, but the mechanism could be similar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would not seem that vibration plays a role, as it the plant seems responsive to the touch of the human rather than his/her approach to the leaf. This could rule out air currents as a mechanism (but J.M. has noted in the comments that they do fold up when you blow on them).&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2011-12-20T08:27:35.147" LastActivityDate="2011-12-20T08:27:35.147" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="251" PostTypeId="1" AcceptedAnswerId="253" CreationDate="2011-12-20T10:45:20.340" Score="8" ViewCount="103" Body="&lt;p&gt;Scientists have been able to create artificial organs with varying degrees of success.  The mechanical heart (in its various forms, e.g. ventricular assist) is able to sustain life for some period of time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Efforts to grow whole organs in the lab will probably ultimately lead to a more pragmatic solution.  What aspects of the renal physiology are standing in the way of an implantable mechanical kidney (fashioned more so from tubules and membranes than simply being a shrunken down dialysis machine)?&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-10-01T22:30:55.127" LastActivityDate="2012-10-01T22:30:55.127" Title="Which aspects of renal physiology are standing in the way of an artificial (mechanical) kidney?" Tags="&lt;human-biology&gt;&lt;renal-physiology&gt;&lt;organs&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="252" PostTypeId="2" ParentId="249" CreationDate="2011-12-20T13:09:04.090" Score="29" Body="&lt;p&gt;In fact, the idea of a plant nervous system is quite serious and constantly developing; of course those are rather local, simple signal pathways rather than an &quot;animalian&quot; centralized global network, but they use similar mechanisms -- depolarisation waves, neurotransmitter-like compounds, specialized cells... Here is a &lt;a href=&quot;http://dx.doi.org/10.1016/j.tplants.2006.06.009&quot;&gt;review paper by Brenner &lt;em&gt;et al&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of &lt;em&gt;Mimosa&lt;/em&gt;, there is a &lt;a href=&quot;http://dx.doi.org/10.1007/BF02493405&quot;&gt;good paper&lt;/a&gt; summing up Takao Sibaoka's long research of the topic.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, it seems that its petioles' phloem has cells which have polarized membranes and can trigger depolarization due to a mechanical stimulation. The signal then propagates to the corresponding pulvinus by a mixture of electrical and Cl&lt;sup&gt;-&lt;/sup&gt; depolarization waves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the pulvinus, this signal triggers a second depolarization which coordinates the pulvinus' cells to trigger water pumping responsible for the leaf drop. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The transmission to the adjacent leaves is most likely mechanical, i.e. the movement of one dropping leaf excites another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.tplants.2006.06.009&quot;&gt; &lt;strong&gt;Brenner ED, Stahlberg R, Mancuso S, Vivanco J, Baluska F, Van Volkenburgh E&lt;/strong&gt;. 2006. Plant neurobiology: an integrated view of plant signaling. Trends in plant science 11: 413–9.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/BF02493405&quot;&gt; &lt;strong&gt;Sibaoka T&lt;/strong&gt;. 1991. Rapid plant movements triggered by action potentials. The Botanical Magazine Tokyo 104: 73–95.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerDisplayName="user59" LastEditorUserId="836" LastEditDate="2012-09-13T06:20:49.097" LastActivityDate="2012-09-13T06:20:49.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="253" PostTypeId="2" ParentId="251" CreationDate="2011-12-20T13:40:10.200" Score="5" Body="&lt;p&gt;The problem is that real organs are just damn complex - yes the kidney's prime role is just to be a filter, but in order to do so it must be plugged in to a dozen regulation mechanisms - osmotic balance, ion management, protein management and a plethora of more subtle ones. Moreover it is a part of body, so it must also follow all the standard protocols to live with immune system, obtain necessary resources to its function and maintenance, cooperate with nearby tissues... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Currently we only have rough knowledge about major processes, deciphering them all is a work for many, many years (if it is not futile at all).  Finally, our technology will be long not capable of implementing all those protocols; in peaks of perfection we can serially do simple parts in 100nm scale (microprocessors), while this is a scale of a complete molecular device.&lt;/p&gt;&#xA;" OwnerDisplayName="user59" LastEditorUserId="69" LastEditDate="2011-12-22T16:52:56.400" LastActivityDate="2011-12-22T16:52:56.400" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="254" PostTypeId="2" ParentId="239" CreationDate="2011-12-20T15:02:26.937" Score="53" Body="&lt;p&gt;&lt;strong&gt;TL;DR&lt;/strong&gt;: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;There is a dearth of actual experimental evidence. However:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;there is at least one study that confirmed the process&lt;/strong&gt; ([&lt;strong&gt;STUDY #7&lt;/strong&gt;] - Myxococcus xanthus; by Fiegna and Velicer, 2003). &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Another study experimentally confirmed higher extinction risk as well ([&lt;strong&gt;STUDY #8&lt;/strong&gt;] - Paul F. Doherty's study of dimorphic bird species an [&lt;strong&gt;STUDY #9&lt;/strong&gt;] - Denson K. McLain).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Theoretical studies produce somewhat unsettled results - some models support the evolutionary suicide and some models do not - the major difference seems to be variability of environmental pressures.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Also, if you include human predation based solely on sexually selected trait, examples definitely exist, e.g. Arabian Oryx&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;First of all, this may be cheating but one example is the extinction because a predator species specifically selects the species &lt;strong&gt;because&lt;/strong&gt; of selected-for feature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most obvious case is when the predator species is human. As a random example, Arabian Oryx was nearly hunted to extinction specifically because of their horns.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Please note that this is NOT a simple question - for example, the often-cited in unscientific literature example of Irish Elk that supposedly went extinct due to its antler size may not be a good crystal-clear example. For a very thorough analysis, see: &lt;em&gt;&quot;&lt;strong&gt;Sexy to die for? Sexual selection and risk of extinction&lt;/strong&gt;&quot; by Hanna Kokko and Robert Brooks, Ann. Zool. Fennici 40: 207-219&lt;/em&gt;. [&lt;strong&gt;STUDY #1&lt;/strong&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They specifically find that evolutionary &quot;suicide&quot; is unlikely in deterministic environments, at least if the costs of the feature are borne by the individual organism itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another study resulting in a negative result was &lt;em&gt;&quot;&lt;strong&gt;Sexual selection and the risk of extinction in mammals&lt;/strong&gt;&quot;, Edward H. Morrow and Claudia Fricke; The Royal Society Proceedings: Biological Sciences, Published online 4 November 2004, pp 2395-2401&lt;/em&gt; [&lt;strong&gt;STUDY #2&lt;/strong&gt;]&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The aim of this study was therefore to examine whether the level of&#xA;  sexual selection (measured as residual testes mass and sexual size dimorphism) was related to the risk of extinction that mammals are currently experiencing. We found no evidence for a relationship between these factors, although our analyses may have been confounded by the possible dominating effect of contemporary anthropogenic factors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;However, if one takes into consideration changes in the environment, the extinction becomes theoretically possible. From &lt;em&gt;&quot;&lt;a href=&quot;http://www.jstor.org/stable/2410506&quot;&gt;&lt;strong&gt;Runaway Evolution to Self-Extinction Under Asymmetrical Competition&lt;/strong&gt;&lt;/a&gt;&quot; - Hiroyuki Matsuda and Peter A. Abrams; Evolution Vol. 48, No. 6 (Dec., 1994), pp. 1764-1772&lt;/em&gt;: [&lt;strong&gt;STUDY #3&lt;/strong&gt;]&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We show that purely intraspecific competition can cause evolution of extreme competitive abilities that ultimately result in extinction, without any influence from other species. The only change in the model required for this outcome is the assumption of a nonnormal distribution of resources of different sizes measured on a logarithmic scale. This suggests that taxon cycles, if they exist, may be driven by within- rather than between-species competition. Self-extinction does not occur when the advantage conferred by a large value of the competitive trait (e.g., size) is relatively small, or when the carrying capacity decreases at a comparatively rapid rate with increases in trait value. The evidence regarding these assumptions is discussed. The results suggest a need for more data on resource distributions and size-advantage in order to understand the evolution of competitive traits such as body size. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;As far as supporting evidence, some studies are listed in &lt;em&gt;&quot;&lt;strong&gt;Can adaptation lead to extinction?&lt;/strong&gt;&quot; by Daniel J. Rankin and Andre´s Lo´pez-Sepulcre, OICOS 111:3 (2005)&lt;/em&gt;. [&lt;strong&gt;STUDY #4&lt;/strong&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They cite 3:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first example is a &lt;strong&gt;study on the Japanese medaka&#xA;  fish Oryzias latipes (Muir and Howard 1999 - [STUDY #5])&lt;/strong&gt;. Transgenic males which had been modified to include a salmon growth-hormone gene are larger than their wild-type counterparts, although their offspring have a lower fecundity (Muir and Howard 1999). Females&#xA;  prefer to mate with larger males, giving the larger&#xA;  transgenic males a fitness advantage over wild-type&#xA;  males. However, offspring produced with transgenic&#xA;  males have a lower fecundity, and hence average female&#xA;  fecundity will decrease. As long as females preferentially&#xA;  mate with larger males, the population density will&#xA;  decline. Models of this system have predicted that, if&#xA;  the transgenic fish were released into a wild-type&#xA;  population, the transgene would spread due to its mating&#xA;  advantage over wild-type males, and the population&#xA;  would become go extinct (Muir and Howard 1999).&#xA;  A recent extension of the model has shown that&#xA;  alternative mating tactics by wild-type males could&#xA;  reduce the rate of transgene spread, but that this is still&#xA;  not sufficient to prevent population extinction (Howard&#xA;  et al. 2004). &lt;strong&gt;Although evolutionary suicide was predicted&#xA;  from extrapolation, rather than observed in nature, this&#xA;  constitutes the first study making such a prediction from&#xA;  empirical data&lt;/strong&gt;.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In cod, Gadus morhua, the commercial fishing of large&#xA;  individuals has resulted in selection towards earlier&#xA;  maturation and smaller body sizes (&lt;strong&gt;Conover and Munch&#xA;  2002 [STUDY #6]&lt;/strong&gt;). Under exploitation, high mortality decreases the&#xA;  benefits of delayed maturation. As a result of this,&#xA;  smaller adults, which mature faster, have a higher fitness&#xA;  relative to their larger, slow maturing counterparts&#xA;  (Olsen et al. 2004). Despite being more successful&#xA;  relative to slow maturing individuals, the fast-maturing&#xA;  adults produce fewer offspring, on average. This adaptation,&#xA;  driven by the selective pressure imposed by&#xA;  harvesting, seems to have pre-empted a fishery collapse&#xA;  off the Atlantic coast of Canada (Olsen et al. 2004). &lt;strong&gt;As&#xA;  the cod evolved to be fast-maturing, population size was&#xA;  gradually reduced until it became inviable and vulnerable&#xA;  to stochastic processes.&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;The only strictly experimental evidence for evolutionary&#xA;  suicide comes from microbiology. In the social&#xA;  bacterium Myxococcus xanthus&lt;/strong&gt; individuals can develop&#xA;  cooperatively into complex fruiting structures (Fiegna&#xA;  and Velicer 2003 - [&lt;strong&gt;STUDY #7&lt;/strong&gt;]). Individuals in the fruiting body are&#xA;  then released as spores to form new colonies. Artificially&#xA;  selected cheater strains produce a higher number of&#xA;  spores than wild types. These cheaters were found to&#xA;  invade wild-type strains, eventually causing extinction of&#xA;  the entire population (Fiegna and Velicer 2003). The&#xA;  cheaters invade the wild-type population because they&#xA;  have a higher relative fitness, but as they spread through&#xA;  the population, they decrease the overall density, thus&#xA;  driving themselves and the population in which they&#xA;  reside, to extinction.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Another experimental study was &lt;em&gt;&quot;&lt;a href=&quot;http://www.pnas.org/content/100/10/5858.full.pdf&quot;&gt;&lt;strong&gt;Sexual selection affects local extinction and turnover&#xA;in bird communities&lt;/strong&gt;&lt;/a&gt;&quot; - Paul F. Doherty, Jr., Gabriele Sorci, et al; 5858–5862 PNAS  May 13, 2003 vol. 100 no. 10&lt;/em&gt; [&lt;strong&gt;STUDY #8&lt;/strong&gt;]&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Populations under strong sexual selection experience&#xA;  a number of costs ranging from increased predation and&#xA;  parasitism to enhanced sensitivity to environmental and demographic&#xA;  stochasticity. These findings have led to the prediction that&#xA;  local extinction rates should be higher for speciespopulations&#xA;  with intense sexual selection. We tested this prediction by analyzing&#xA;  the dynamics of natural bird communities at a continental&#xA;  scale over a period of 21 years (1975–1996), using relevant statistical&#xA;  tools. In agreement with the theoretical prediction, &lt;strong&gt;we found&#xA;  that sexual selection increased risks of local extinction (dichromatic&#xA;  birds had on average a 23% higher local extinction rate than&#xA;  monochromatic species)&lt;/strong&gt;. However, despite higher local extinction&#xA;  probabilities, &lt;strong&gt;the number of dichromatic species did not decrease&#xA;  over the period considered in this study. This pattern was caused&#xA;  by higher local turnover rates of dichromatic species&lt;/strong&gt;, resulting in&#xA;  relatively stable communities for both groups of species. Our&#xA;  results suggest that these communities function as metacommunities,&#xA;  with frequent local extinctions followed by colonization.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This result is similar to another bird-centered study: &lt;em&gt;&lt;a href=&quot;http://www.jstor.org/stable/3545671&quot;&gt;&lt;strong&gt;Sexual Selection and the Risk of Extinction of Introduced Birds on Oceanic Islands&lt;/strong&gt;&lt;/a&gt;&quot;: Denson K. McLain, Michael P. Moulton and Todd P. Redfearn. OICOS Vol. 74, No. 1 (Oct., 1995), pp. 27-34&lt;/em&gt; [&lt;strong&gt;STUDY #9&lt;/strong&gt;]&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We test the hypothesis that response to sexual selection increases the risk of extinction by examining the fate of plumage-monomorphic versus plumage-dimorphic bird species introduced to the tropical islands of Oahu and Tahiti. We assume that plumage dimorphism is a response to sexual selection and we assume that the males of plumage-dimorphic species experience stronger sexual selection pressures than males of monomorphic species. &lt;strong&gt;On Oahu, the extinction rate for dimorphic species, 59%, is significantly greater than for monomorphic species, 23%. On Tahiti, only 7% of the introduced dimorphic species have persisted compared to 22% for the introduced monomorphic species&lt;/strong&gt;. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Plumage is significantly associated with increased risk of extinction for passerids but insignificantly associated for fringillids. Thus, the hypothesis that response to sexual selection increases the risk of extinction is supported for passerids and for the data set as a whole. The probability of extinction was correlated with the number of species already introduced. &lt;strong&gt;Thus, species that have responded to sexual selection may be poorer interspecific competitors when their communities contain many other species.&lt;/strong&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="185" LastEditorUserId="185" LastEditDate="2011-12-20T16:14:40.903" LastActivityDate="2011-12-20T16:14:40.903" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="256" PostTypeId="2" ParentId="193" CreationDate="2011-12-20T23:34:42.340" Score="19" Body="&lt;p&gt;I'd like to know what is the reference for amoebic learning. I cannot comment directly on this, but there is some evidence for  &quot;adaptive anticipation&quot; in both prokaryotes and single-celled Eukaryotes which do not have a nervous system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of E. coli, it has been &lt;a href=&quot;http://www.nature.com/nature/journal/v460/n7252/abs/nature08112.html&quot;&gt;shown&lt;/a&gt; that the bacteria can anticipate the environment it is about to enter.  E. coli in the digestive tracts of mammals will typically be exposed to initially a lactose, and then later to a maltose environment as the bacteria pass down through the animal tract. This suggests that upon encountering a lactose environment, maltose operons are induced. I.e., upon encountering lactose, maltose is anticipated. This suggests a &quot;genetic memory&quot; of the sequence of sugar types where lactose is always encountered before maltose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further cultures (500 generations) of E. coli in the absence of maltose but in the presence of lactose reduced the maltose operon activity to negligible levels, suggesting that this is an adaptive prediction of environmental changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Mitchell, A et al.&lt;/em&gt;, &lt;strong&gt;Adaptive Prediction of environmental changes by microorganisms&lt;/strong&gt;, 2009, 460, 1038&lt;/p&gt;&#xA;" OwnerUserId="81" LastActivityDate="2011-12-20T23:34:42.340" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="257" PostTypeId="1" AcceptedAnswerId="266" CreationDate="2011-12-21T02:49:52.337" Score="15" ViewCount="5408" Body="&lt;p&gt;I am looking for video lectures to go through to guide my reading in intro molecular and cellular biology. I've had intro bio and I study evolutionary theory, but my molecule- and cell-level knowledge is weak. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm finding it impossible to know where to look in a big book like Alberts, or to read Lodish without a guide, so I really need lectures to help me out. I've tried the MIT OCW assignments and a few other similar sites, but I can't seem to find a course that includes lectures. Does anyone know of any? Ideally they'd follow Watson et al. for molecular and Lodish for cellular, but I can find other textbooks too.&lt;/p&gt;&#xA;" OwnerUserId="16" LastEditorUserId="6" LastEditDate="2012-01-12T10:48:24.050" LastActivityDate="2019-09-16T09:16:20.623" Title="Online Molecular and Cellular Biology Video Lectures?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;" AnswerCount="7" CommentCount="0" FavoriteCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="258" PostTypeId="2" ParentId="257" CreationDate="2011-12-21T08:53:32.680" Score="5" Body="&lt;p&gt;This one is not precisely molecular and cell biology, but rather systems biology. It might help you as some kind of introduction, though:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=Z__BHVFP0Lk&quot;&gt;Systems biology lecture 1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, if you are really really new to the subject, you can probably use &quot;Molecular and Cell Biology for Dummies&quot;. &lt;/p&gt;&#xA;" OwnerUserId="117" LastEditorUserId="115" LastEditDate="2011-12-21T13:28:18.340" LastActivityDate="2011-12-21T13:28:18.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="259" PostTypeId="2" ParentId="257" CreationDate="2011-12-21T09:43:20.657" Score="7" Body="&lt;p&gt;&lt;a href=&quot;http://ocw.mit.edu/index.htm&quot;&gt;MIT OpenCourseWare&lt;/a&gt; provides very interesting material, and not only on biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may be interested in seeing the video lectures from some of the Introductory biology courses, such as &lt;a href=&quot;http://ocw.mit.edu/courses/biology/7-014-introductory-biology-spring-2005/video-lectures/&quot;&gt;this one&lt;/a&gt;, &lt;a href=&quot;http://ocw.mit.edu/courses/biology/7-014-introductory-biology-spring-2005/video-lectures/&quot;&gt;this one&lt;/a&gt; or &lt;a href=&quot;http://ocw.mit.edu/courses/biology/7-013-introductory-biology-spring-2006/video-lectures/&quot;&gt;this other one&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is, however, much more, check out the index of the &lt;a href=&quot;http://ocw.mit.edu/courses/biology/&quot;&gt;available material for biology&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2011-12-21T09:43:20.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="260" PostTypeId="5" CreationDate="2011-12-21T13:16:50.710" Score="0" Body="&lt;p&gt;Related: &lt;a href=&quot;/questions/tagged/blood-circulation&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;blood-circulation&amp;#39;&quot; rel=&quot;tag&quot;&gt;blood-circulation&lt;/a&gt; &lt;a href=&quot;/questions/tagged/red-blood-cell&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;red-blood-cell&amp;#39;&quot; rel=&quot;tag&quot;&gt;red-blood-cell&lt;/a&gt; &lt;a href=&quot;/questions/tagged/blood-group&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;blood-group&amp;#39;&quot; rel=&quot;tag&quot;&gt;blood-group&lt;/a&gt; &lt;a href=&quot;/questions/tagged/blood-pressure&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;blood-pressure&amp;#39;&quot; rel=&quot;tag&quot;&gt;blood-pressure&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="16866" LastEditDate="2019-08-25T03:51:14.037" LastActivityDate="2019-08-25T03:51:14.037" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="261" PostTypeId="4" CreationDate="2011-12-21T13:16:50.710" Score="0" Body="The study of blood, the blood-forming organs, along with blood diseases and their treatment." OwnerUserId="57" LastEditorUserId="4101" LastEditDate="2013-10-31T00:46:09.533" LastActivityDate="2013-10-31T00:46:09.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="262" PostTypeId="5" CreationDate="2011-12-21T13:17:49.897" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-21T13:17:49.897" LastActivityDate="2011-12-21T13:17:49.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="263" PostTypeId="4" CreationDate="2011-12-21T13:17:49.897" Score="0" Body="Microanatomy of cells and tissues" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2011-12-22T16:53:45.933" LastActivityDate="2011-12-22T16:53:45.933" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="264" PostTypeId="1" AcceptedAnswerId="275" CreationDate="2011-12-21T13:45:26.553" Score="14" ViewCount="326" Body="&lt;p&gt;For someone who is interested in learning about the discovery of epigenetics, which are the foundational defining papers in the area?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="6" LastEditDate="2012-02-19T20:39:52.840" LastActivityDate="2012-09-12T17:37:59.183" Title="Defining paper(s) in epigenetics" Tags="&lt;epigenetics&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="265" PostTypeId="2" ParentId="188" CreationDate="2011-12-21T18:09:38.727" Score="4" Body="&lt;p&gt;You are completely right with your guess that is was Ramón y Cajal who first described these cells in his famous monograph &lt;em&gt;&quot;Histologie de systeme nerveux de l'homme et des vertebres&lt;/em&gt;.&quot; published in Paris Maloine in 1911. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the only method he had at his disposal was &lt;a href=&quot;http://en.wikipedia.org/wiki/Golgi%27s_method&quot; rel=&quot;nofollow&quot;&gt;Golgi's staining&lt;/a&gt; which is a pure anatomical staining (there is no living cell left in the tissue after the treatment with  potassium dichromate and silver nitrate) with silver chromate filling completely single cells at random.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using only this staining and his eyes Cajal did classify the neurons according to their size, location in the brain and their shape. This is why we have such names like basket, stellate, moss, pyramide etc. in neuron description. This classification is purely anatomical and does not reflect any intrinsic properties of these cell, as for example being motor neurons or interneurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I was studying histology at my medical school I was always told that there is new &quot;mollecular biology&quot;-based classification of neurons is about to come and to replace the existing classification by Cajal, many cell types were supposed to be merged there, among others also different anatatomical groups of interneurons. (This was one of the major research topic of the research facility where I studied neurohistology).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I can see, this classification is still not here...&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2011-12-21T18:09:38.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="266" PostTypeId="2" ParentId="257" CreationDate="2011-12-21T18:15:52.617" Score="7" Body="&lt;p&gt;MIT's OCW is weak when it comes to biology videos.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;UC Berkeley has some good video content for molecular and cell biology.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;See, for example, this playlist:&#xA;&lt;a href=&quot;http://www.youtube.com/playlist?list=59C08AE05E752758&quot;&gt;http://www.youtube.com/playlist?list=59C08AE05E752758&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;And explore the main UC Berkeley video lectures website here: &lt;a href=&quot;http://webcast.berkeley.edu/&quot;&gt;http://webcast.berkeley.edu/&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;UCSD, if I recall correctly, has had some pretty good life science lectures available online to the public, as well.  Possibly also UCLA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.apple.com/education/itunes-u/what-is.html&quot;&gt;iTunes U&lt;/a&gt; is your friend here. Unfortunately, to really take advantage of it, you &lt;em&gt;need&lt;/em&gt; to download iTunes -- but it's worth it.  The last time I looked, there was more there than I could possibly watch, and that was 4 years ago. &lt;/p&gt;&#xA;" OwnerUserId="184" LastEditorUserId="69" LastEditDate="2011-12-22T16:53:16.837" LastActivityDate="2011-12-22T16:53:16.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="267" PostTypeId="2" ParentId="11" CreationDate="2011-12-21T18:56:41.413" Score="16" Body="&lt;p&gt;I think @mbq has covered the frequency question better than I can.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is at least one modern example of this kind of new organelle formation.  Aphids have a deep, intracellular endosymbiont &lt;em&gt;Buchnera&lt;/em&gt; involving some genome transfer that has developed in the last 200 million years.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many articles about this topic (eg: &lt;a href=&quot;http://dx.doi.org/10.1038/35024074&quot;&gt;Nature from 2000&lt;/a&gt;), and it was a little controversial 15 years ago.  Now, it's largely accepted that this is a modern development of endosymbiosis, and a confirmation of the theory.  &lt;/p&gt;&#xA;" OwnerUserId="184" LastActivityDate="2011-12-21T18:56:41.413" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="268" PostTypeId="1" AcceptedAnswerId="308" CreationDate="2011-12-21T19:46:18.507" Score="6" ViewCount="546" Body="&lt;p&gt;Here are excerpts from an unknown ECG lead. I find it weird that the &quot;baseline&quot; changes after the T wave and doesn't return until after the following QRS complex. Is that normal/expected for any lead?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/OgLzO.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/OgLzO.png&quot; alt=&quot;sec 82-92&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/m6WSk.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/m6WSk.png&quot; alt=&quot;zoom sec 88-90&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Click for better resolution. I've got another 10 minutes of the ECG, if that would be helpful.&lt;/p&gt;&#xA;" OwnerUserId="194" LastEditorDisplayName="user12874" LastEditDate="2015-01-14T10:51:19.797" LastActivityDate="2015-01-14T10:51:19.797" Title="Is a raised baseline between T and QRS normal in any ECG lead?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;&lt;electrocardiography&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="269" PostTypeId="2" ParentId="178" CreationDate="2011-12-21T21:34:57.673" Score="5" Body="&lt;p&gt;The Manual of Clinical Microbiology from ASM is the bible we use in our Micro lab. It's often our first reference. There are a lot of other useful books in the ASM eStore. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://estore.asm.org/viewItemDetails.asp?ItemID=1021&quot;&gt;ASM eStore&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="200" LastActivityDate="2011-12-21T21:34:57.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="270" PostTypeId="2" ParentId="264" CreationDate="2011-12-21T21:59:15.627" Score="3" Body="&lt;p&gt;I found two nice review papers focused of epigenetics and human disease, one from &lt;a href=&quot;http://dx.doi.org/10.1146/annurev.genom.5.061903.180014&quot; rel=&quot;nofollow&quot;&gt;2004&lt;/a&gt;, and one from &lt;a href=&quot;http://dx.doi.org/10.1503/cmaj.050774&quot; rel=&quot;nofollow&quot;&gt;2006&lt;/a&gt;. But perhaps you are looking more for something like &lt;a href=&quot;http://www.oeb.harvard.edu/faculty/haig/publications_files/04epigeneticorigins.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also found this article in the BBC news: &lt;a href=&quot;http://www.bbc.co.uk/sn/tvradio/programmes/horizon/ghostgenes.shtml&quot; rel=&quot;nofollow&quot;&gt;The Ghost in Your Genes&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;They have shown that a famine at critical times in the lives of the grandparents can affect the life expectancy of the grandchildren. This is the first evidence that an environmental effect can be inherited in humans.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1146/annurev.genom.5.061903.180014&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Jiang Y-H, Bressler J, Beaudet AL&lt;/strong&gt;. 2004. Epigenetics and human disease. Annual review of genomics and human genetics 5: 479–510.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1503/cmaj.050774&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Rodenhiser D, Mann M&lt;/strong&gt;. 2006. Epigenetics and human disease: translating basic biology into clinical applications. CMAJ : Canadian Medical Association journal = journal de l’Association medicale canadienne 174: 341–8.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1101/sqb.2004.69.67&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Haig D&lt;/strong&gt;. 2004. The (dual) origin of epigenetics. Cold Spring Harbor symposia on quantitative biology 69: 67–70.&lt;/a&gt; [&lt;a href=&quot;http://www.oeb.harvard.edu/faculty/haig/publications_files/04epigeneticorigins.pdf&quot; rel=&quot;nofollow&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="28" LastEditorUserId="836" LastEditDate="2012-09-12T17:37:59.183" LastActivityDate="2012-09-12T17:37:59.183" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="271" PostTypeId="2" ParentId="9" CreationDate="2011-12-21T22:14:22.720" Score="5" Body="&lt;p&gt;Since tubes can be crushed in the mail, the safest way to ship plasmids is to drip a few uL into a filter paper, and then wrap it up to seal it with parafilm, and fill out a detailed form about its content.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good luck.&lt;/p&gt;&#xA;" OwnerUserId="201" LastActivityDate="2011-12-21T22:14:22.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="272" PostTypeId="2" ParentId="222" CreationDate="2011-12-21T23:10:00.150" Score="9" Body="&lt;p&gt;Some plants have mitochondrial pathways that produce heat. That's why skunk cabbage can be seen poking outing of the snow in late winter/early spring. Here's a review:  &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1744-7909.2010.01004.x/pdf&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1111/j.1744-7909.2010.01004.x/pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="123" LastActivityDate="2011-12-21T23:10:00.150" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="273" PostTypeId="2" ParentId="222" CreationDate="2011-12-21T23:10:31.427" Score="44" Body="&lt;p&gt;Cellular respiration in plants is slightly different than in other eukaryotes because the electron transport chain contains an additional enzyme called &lt;a href=&quot;http://en.wikipedia.org/wiki/Alternative_oxidase&quot; rel=&quot;noreferrer&quot;&gt;Alternative Oxidase&lt;/a&gt; (AOX). AOX takes some electrons out of the pathway prematurely - basically the energy is used to generate heat instead of ATP. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact purpose of AOX in plants is still unclear. Plants will make more AOX in response to cold, wounding, and oxidative stress. We know of at least one plant (skunk cabbage) that exploits this pathway to generate enough heat to melt snow. &lt;a href=&quot;http://scienceray.com/philosophy-of-science/hot-stinking-plants-and-thermogenesis/&quot; rel=&quot;noreferrer&quot;&gt;This link&lt;/a&gt; gives a pretty good overview. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6WL8Z.jpg&quot; alt=&quot;Eastern skunk cabbage melting a hole through the snow.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(AOX is dear to my heart, since my first 3 years working in a laboratory were spent studying this gene &amp;lt;3)&lt;/p&gt;&#xA;" OwnerUserId="204" LastEditorUserId="15339" LastEditDate="2015-04-15T04:25:25.647" LastActivityDate="2015-04-15T04:25:25.647" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="274" PostTypeId="2" ParentId="93" CreationDate="2011-12-21T23:15:13.307" Score="6" Body="&lt;p&gt;For recombinant &lt;em&gt;Taq&lt;/em&gt; polymerase, industrial-scale production produces &lt;em&gt;liters&lt;/em&gt; of highly concentrated enzyme in a single run.  It comes in such small, dilute quantities when sold that only a few preps a year would be necessary to satisfy research lab demand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know the &lt;em&gt;Thermus aquaticus&lt;/em&gt; protocol, but considering the achievements in yield for &lt;em&gt;E. coli&lt;/em&gt;, and the &lt;a href=&quot;http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/PCR/pcr-enzymes-master-mixes/taq-dna-polymerase-enzymes/taq_dna_polymerase.html&quot;&gt;minimal price difference&lt;/a&gt; between the two enzymes, I'd imagine that yields are similar there.  That would say to me that nobody's farming hot springs for &lt;em&gt;T. aquaticus&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&#xA;" OwnerUserId="184" LastEditorDisplayName="user132" LastEditDate="2011-12-22T16:53:20.970" LastActivityDate="2011-12-22T16:53:20.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="275" PostTypeId="2" ParentId="264" CreationDate="2011-12-21T23:38:10.807" Score="8" Body="&lt;p&gt;I understand that Robin Holliday was the first to discuss the possible role of DNA methylation &#xA;in the control of Gene expression. In his paper &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3310230&quot;&gt;The inheritance of epigenetic defects&lt;/a&gt;&quot;&#xA;he presents what is one of the first modern formulations of what we now regard as epigenetics. The term &quot;epigenetics&quot; itself was coined by Conrad Waddington although this predated our modern understanding of heredity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Holliday, R., &lt;strong&gt;The inheritance of epigenetic defects&lt;/strong&gt;, 1987, Science, 238, 4824&lt;/p&gt;&#xA;" OwnerUserId="81" LastActivityDate="2011-12-21T23:38:10.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="276" PostTypeId="2" ParentId="166" CreationDate="2011-12-21T23:41:31.707" Score="6" Body="&lt;p&gt;Have you tried putting your two genes on two separate plasmids (with different origins of replication and antibiotic selection, of course) and co-expressing that way? If the first of the two subunits is expressing well and the second isn't, that's probably because the ribosomes are falling off the mRNA before fully transcribing the second gene. Are the genes eukaryotic in origin? I think it is difficult to &quot;trick&quot; E. coli ribosomes into treating heterologous sequences as an operon, but maybe someone with more knowledge of prokaryotic translation could help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually, just adding a second T7 promoter in front of gene 2 would probably help quite a bit: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Genes are transcribed either from individual promoters or from a single promoter, leading to a long polycistronic mRNA. Polycistronic expression has been reported to lead to lower expression of the more downstream encoded protein, which can be exploited to influence the stoichiometry of a protein complex (9). Several-fold higher expression with individual promoters compared to polycistronic transcription has been reported (10). (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1874614/&quot;&gt;Source&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I do know from personal experience that co-expression using two plasmids can work very well with the right genes!&lt;/p&gt;&#xA;" OwnerUserId="204" LastActivityDate="2011-12-21T23:41:31.707" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="278" PostTypeId="2" ParentId="183" CreationDate="2011-12-22T01:22:31.970" Score="3" Body="&lt;p&gt;Antibodies for WB and for IF have fundamentally different requirements for the epitope structure. Antibodies for WB recognize denatured structures extended by SDS treatment. Antibodies for IF often will need to recognize a native-like structure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending on the supplier, some will have lots of antibodies for IF. I suggest looking around some more. &lt;/p&gt;&#xA;" OwnerUserId="209" LastActivityDate="2011-12-22T01:22:31.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="279" PostTypeId="1" CreationDate="2011-12-22T01:55:36.807" Score="5" ViewCount="5025" Body="&lt;p&gt;I am working with HepG2 cells, and they really like to form clumps.  Pipetting up and down in TrypLE does not seem to be very effective in breaking them up.&lt;/p&gt;&#xA;" OwnerUserId="210" LastActivityDate="2012-02-17T15:37:24.610" Title="How do you break up cell clumps when passaging?" Tags="&lt;cell-culture&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="280" PostTypeId="1" AcceptedAnswerId="508" CreationDate="2011-12-22T05:35:08.413" Score="9" ViewCount="194" Body="&lt;p&gt;Variations of the standard genetic code are pretty rare, but as the cost of high-throughput genome sequencing continues to drop, there is a greater possibility of discovering additional exceptions. That being said, there is a clear emphasis in genome projects on nucleotide (genome and transcriptome) sequencing, with much less (if any) effort put into proteomics work (correct me if I'm wrong there).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's assume we're sequencing the genome of a new organism and we're focusing completely on genome and transcriptome sequencing--no proteomics. Let's also assume this organism has slight variations to the standard genetic code. Would it be possible to annotate this genome (for protein-coding genes) completely incorrectly since the gene prediction software does not take into account these variations, or would it be pretty obvious? What would you expect to see in this case?&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-01-05T18:34:08.013" Title="Alternate genetic codes in newly sequenced organisms" Tags="&lt;dna-sequencing&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="281" PostTypeId="2" ParentId="222" CreationDate="2011-12-22T05:56:38.110" Score="7" Body="&lt;p&gt;Yes, respiration is exothermic and plants (like all living things) respire.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the effect of covering the plant has to more to do with reducing sensible heat loss , e.g. direct transfer of heat from plant to air) rather than latent heat loss (through evaporation). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cover is effectively reducing the mixing of the air near the plant (and closer to the temperature of the surface of the earth) with the free atmosphere (closer to the temperature reported by the weatherman)&lt;/p&gt;&#xA;" OwnerUserId="154" LastActivityDate="2011-12-22T05:56:38.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="282" PostTypeId="2" ParentId="280" CreationDate="2011-12-22T07:09:46.783" Score="2" Body="&lt;p&gt;The short answer is yes, you could end up with many errors.  See here for more detail:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi&quot; rel=&quot;nofollow&quot;&gt;NCBI: &quot;The Genetic Codes&quot;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="184" LastActivityDate="2011-12-22T07:09:46.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="283" PostTypeId="2" ParentId="38" CreationDate="2011-12-22T09:13:23.577" Score="6" Body="&lt;p&gt;I think the spin column kits are the way to go. As mentioned already, the benefits of the kits are that they are easy, safe, and (most importantly) how almost every actual lab does plasmid purification these days. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biggest criticism of the commercial kits is that you can get by easily without knowing anything about what is actually happening in the tube. However, as noted in the comments to Nick T's answer, there is no secret proprietary technology in the kits--they use the &lt;em&gt;alkaline lysis&lt;/em&gt; method. This means that you can still teach the mechanism in the class while getting the benefit of the spin columns.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One option, for teaching purposes, is to make all of your own solutions and just use the spin columns on the supernatant after pelleting the precipitated membrane/protein. That way, you get the benefit of insisting on real names for the solutions (NaOH is a more educational name than P2) and you get to use the spin columns in place of the ethanol precipitation. I believe there are cheap sources that just sell the spin columns, although I have never used them. You want to avoid the ethanol precipitation because it adds a bare minimum of 30 minutes to the protocol (for my protocols, it was more like an 1.5 hours or more). And waiting for ethanol to evaporate so you can resuspend is like watching paint dry unless you have a speed vac.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yield shouldn't be a big issue in a class situation, but you can boost yield with the column by prolonging the final elution step. I think the given instruction is to let the TE buffer (Tris) &quot;elute&quot; for 1 minute before the final spin, but I have routinely let the TE sit for about 15-30 minutes before spinning down. The difference in yield blew out the exposure on the gel camera.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are certain cases where phenol:chloroform extractions are still desirable, but this is definitely not one of them. I used to do P:Cs routinely when working with RNA and yeast genomic DNA. I have never seen anyone do anything other than a miniprep when preparing plasmids. What's more, the hassle of working in a fume hood and the risk of phenol burns encouraged &lt;em&gt;a lot&lt;/em&gt; of people in the lab to prefer the spin kits even when working with genomic DNA.&lt;/p&gt;&#xA;" OwnerUserId="72" LastActivityDate="2011-12-22T09:13:23.577" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="284" PostTypeId="2" ParentId="169" CreationDate="2011-12-22T09:40:16.747" Score="5" Body="&lt;p&gt;A dependable protocol for yeast DNA extraction I used to use was broadly similar to the protocols you cite but included an ethanol precipitation before and after the P:C extractions. The only expensive material was time. The general outline was:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Alkaline lysis&lt;/li&gt;&#xA;&lt;li&gt;Ethanol precipitation&lt;/li&gt;&#xA;&lt;li&gt;RNase A treatment of resuspended DNA for 15 minutes&lt;/li&gt;&#xA;&lt;li&gt;Phenol:chloroform extraction (x2)&lt;/li&gt;&#xA;&lt;li&gt;Ethanol precipitation&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;You probably know that the ethanol precipitation lore is that the yield is better the longer and colder you do your ethanol precipitations. I only ever did reverse transcriptase reactions a few times, but the template DNA I prepared spent the night in ethanol at -80C to maximize yield. Another place to double-check is that your yeast cultures are sufficiently dense before starting.&lt;/p&gt;&#xA;" OwnerUserId="72" LastActivityDate="2011-12-22T09:40:16.747" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="285" PostTypeId="1" AcceptedAnswerId="290" CreationDate="2011-12-22T09:45:59.497" Score="5" ViewCount="161" Body="&lt;p&gt;One quantification of the heart rate variability of an ECG is pNNx, i.e. the proportion of consecutive NN distances that differ by at least 50 ms. When a premature beat occurs, the preceding and following RR intervals are much shorter and longer than the mean. Are these intervals considered NN for the purpose of calculating the pNN50?&lt;/p&gt;&#xA;" OwnerDisplayName="user24" LastEditorUserId="69" LastEditDate="2011-12-22T11:23:15.327" LastActivityDate="2011-12-22T15:48:11.610" Title="Are ectopic beats considered sinus rhythm for pNN50 purposes?" Tags="&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="286" PostTypeId="1" CreationDate="2011-12-22T09:51:01.753" Score="7" ViewCount="1166" Body="&lt;p&gt;I want to measure alkaline phosphatase activity using PNPP in my mutant bacteria strains, but all the protocols I found involve purification of the phosphatase (which I have no need of).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know a good protocol which involves using only the supernatant, without purification of the enzyme? What is the preferred buffer for the reaction?&lt;/p&gt;&#xA;" OwnerUserId="133" LastEditorUserId="6" LastEditDate="2011-12-22T16:53:27.010" LastActivityDate="2012-09-13T20:29:40.127" Title="How can I measure bacterial alkaline phosphatase activity?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="287" PostTypeId="1" AcceptedAnswerId="411" CreationDate="2011-12-22T13:21:11.087" Score="14" ViewCount="6155" Body="&lt;p&gt;The chemical difference between RNA and DNA is the missing 2'-hydroxyl group in the nucleotides that build DNA. The major effect of that change that I know of is the higher stability of DNA compared to RNA. But I'm wondering whether this difference has significant implications for the ability of DNA to form compex, three-dimensional structures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RNA is known to be able to from complex tertiary structures and function as ribozymes. It clearly has the ability to form a wide range of structures and can catalyze a variety of chemical reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I know, there are no naturally occuring catalytic DNAs known. But a number of synthetic DNA enzymes have been created in the lab, so it is generally possible for DNA to form catalytic structures (see &lt;a href=&quot;http://dx.doi.org/10.1016/1074-5521%2894%2990014-0&quot;&gt;Breaker and Joyce 1994&lt;/a&gt; for the first created DNA enzyme).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm wondering whether the missing 2'-OH means that DNA has less potential to form complex structures compared to RNA? I imagine it changes the ability to create hydrogen bonds, but I don't know if it would significantly decrease the potential structures that DNA could adopt.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/1074-5521%2894%2990014-0&quot;&gt;Breaker RR, Joyce GF; (December 1994). &quot;A DNA enzyme that cleaves RNA&quot;. Chem Biol. 1 (4): 223–9&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="69" LastEditDate="2012-01-21T23:12:04.747" LastActivityDate="2016-05-23T17:38:36.757" Title="What implications has the missing 2'-OH on the capability of DNA to form 3D structures?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;rna&gt;&lt;structural-biology&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="288" PostTypeId="2" ParentId="280" CreationDate="2011-12-22T13:45:43.690" Score="3" Body="&lt;p&gt;You are correct to be a little concerned, especially with mitochondrial genomes (where non-standard genetic codes are more prevalent).  In addition to the use of non-standard codes you should also consider RNA editing (changed codons or deleted/inserted nucleotides to shift reading frames) and special amino acids (e.g., selenocysteine).  All together, the emphasis on DNA sequence to infer protein structure is safe in the bulk of cases, but don't be surprised by differences (for particular genes or for whole organisms).&lt;/p&gt;&#xA;" OwnerUserId="219" LastActivityDate="2011-12-22T13:45:43.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="289" PostTypeId="2" ParentId="264" CreationDate="2011-12-22T14:22:03.333" Score="3" Body="&lt;p&gt;There are few single papers that really drive the field by themselves, epigenetics has been a long slow progression (although more recently the definition has been muddied and started to include non-epigenetic modes of gene regulation).  A pretty good review of a lot of research, including a more circumspect discussion about what epigenetics is can be found in Youngson and Whitelaw's Annual Review (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18767965&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/18767965&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="219" LastEditorUserId="231" LastEditDate="2011-12-29T21:41:04.090" LastActivityDate="2011-12-29T21:41:04.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="290" PostTypeId="2" ParentId="285" CreationDate="2011-12-22T15:48:11.610" Score="3" Body="&lt;p&gt;No, the beats originating outside of the sinoatrial node are not considered for pNN50. Moreover, this metric cannot be applied to the rhythm featuring any type of ectopic or non-sinoatrial activity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;NN50 has its name from an acronym &quot;normal-to-normal&quot;, this acronym is used instead of RR (&quot;from R to R&quot;) to emphasize that &lt;strong&gt;only&lt;/strong&gt; the normal, e.g. sinoatrial beats &lt;a href=&quot;http://en.wikipedia.org/wiki/Heart_rate_variability&quot; rel=&quot;nofollow&quot;&gt;are considered for evaluation&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2011-12-22T15:48:11.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="291" PostTypeId="1" AcceptedAnswerId="293" CreationDate="2011-12-22T15:54:45.687" Score="17" ViewCount="193" Body="&lt;p&gt;My understanding is that gene expression, in response to some stimulus, generally occurs on the order of minutes. I'm curious about the extremes...the quickest and the slowest cases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is(are) the fastest time(s) recorded for genes being expressed in response to a stimulus? What are the slowest times?&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2011-12-23T06:39:50.667" Title="Time from stimulus to gene expression" Tags="&lt;gene-expression&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="292" PostTypeId="2" ParentId="163" CreationDate="2011-12-22T16:22:03.957" Score="14" Body="&lt;p&gt;I did some research on the topic and came accross &lt;a href=&quot;http://www.cryoung.org/www/pdfs/Johnson_et_al_biobull.pdf&quot;&gt;this paper&lt;/a&gt; by Johnson &lt;em&gt;et al&lt;/em&gt;. I am not a zoologist, so everything I write here is taken from the references paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors used genetics to estimate gene flow between different populations of limpets &lt;em&gt;Lepetodrilus fucensis&lt;/em&gt; which is considered to be an endemic hydrothermal vent animal. They used a mathematical demographic model &quot;isolation with migration&quot; to estimate the migration of the animals across different biotopes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The vents are distributed along the ridge segments and can be seen as small islands isolated by tens of kms from each other along the same ridge segment and thousands of kilometers between distinct ridges.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The results suggest that there is certain migration between the adjacent vent locations, that means that the flora of one vent can indeed survive the distance towards the next most proximal vent. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;So, from now on is my pure speculation. Since the distance between single vents along the same ridge segment seems not be to so high we can suggest that these organisms are capable to resist the pressure and temperature on the ocean bottom while travelling from one vent to another...&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2011-12-22T16:22:03.957" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="293" PostTypeId="2" ParentId="291" CreationDate="2011-12-22T17:23:28.567" Score="11" Body="&lt;p&gt;The fastest I know of is the heat shock locus in &lt;em&gt;Drosophila&lt;/em&gt;.  The transcription factor (HSF) accumulates within about 30 seconds, and RNA Polymerase can be seen to start accumulating within 3 minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Katie L. Zobeck, Martin S. Buckley, Warren R. Zipfel, John T. Lis.  2010. &lt;a href=&quot;http://www.sciencedirect.com/science?_ob=MiamiImageURL&amp;amp;_cid=272198&amp;amp;_user=10&amp;amp;_pii=S1097276510008889&amp;amp;_check=y&amp;amp;_coverDate=2010-12-22&amp;amp;view=c&amp;amp;_gw=y&amp;amp;wchp=dGLzVlt-zSkWA&amp;amp;md5=8be52df8fda06cadd3072a46310e2659/1-s2.0-S1097276510008889-main.pdf&quot;&gt;Recruitment Timing and Dynamics of Transcription Factors at the Hsp70 Loci in Living Cells&lt;/a&gt;.  &lt;em&gt;Molecular Cell&lt;/em&gt; 40(6): 965-975&lt;/p&gt;&#xA;" OwnerUserId="219" LastEditorUserId="107" LastEditDate="2011-12-23T06:39:50.667" LastActivityDate="2011-12-23T06:39:50.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="294" PostTypeId="2" ParentId="72" CreationDate="2011-12-22T17:33:31.267" Score="8" Body="&lt;p&gt;I think the above values (500-750 kb) are wrong.  &lt;a href=&quot;http://www.bioinfo.de/isb/2004040032/&quot;&gt;http://www.bioinfo.de/isb/2004040032/&lt;/a&gt; shows that most introns are less than about 10 kb (and personal experience in Drosophila confirms that - I've &lt;em&gt;rarely&lt;/em&gt; seen an intron bigger than about 5 kb).  There are some very large ones, but since it's nearly impossible to detect the splicing reaction, particularly if they're very large, it's not clear whether they are spliced as one BIG intron or are instead recursively spliced (in little steps, as in &lt;a href=&quot;http://www.genetics.org/content/170/2/661.full.pdf+html&quot;&gt;http://www.genetics.org/content/170/2/661.full.pdf+html&lt;/a&gt;).  I think its safe to say that we don't know how long the biggest introns can be.&lt;/p&gt;&#xA;" OwnerUserId="219" LastActivityDate="2011-12-22T17:33:31.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="295" PostTypeId="1" AcceptedAnswerId="301" CreationDate="2011-12-22T17:53:07.650" Score="2" ViewCount="6341" Body="&lt;p&gt;I got the question in my exam and wrote the following and I do not understand what is wrong in it:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Giemsa staining is a staining method to stain particularly malaria and other parasital diseases. G-bands occur because Giemsa stain&#xA;  consists of A,T rich material i.e. poor gene such that dark and white&#xA;  bands occur. Each chromosome has an unique reaction to Giemsa staining&#xA;  so G-bands occur.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;0 points. I do not understand what's wrong with it, since in their comments about the same question in my first exam they wrote also the extra questions: &lt;strong&gt;What are G-bands? How are they formed and why?&lt;/strong&gt; This time I answered the given things and got zero mark.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably, the mistake was that I did not answer to the question in the scope of medical Biology in some way. However, I am not exactly sure what it is exactly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How would you answer to the question when you know that the course was about medical biology?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please, add the tag Giemsa.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2011-12-22T18:06:03.773" LastActivityDate="2011-12-22T21:00:55.007" Title="What is the Giemsa staining of chromosomes?" Tags="&lt;homework&gt;&lt;staining&gt;&lt;histology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="296" PostTypeId="2" ParentId="287" CreationDate="2011-12-22T17:54:50.677" Score="6" Body="&lt;p&gt;This is not my field so I'm risking a wrong/incomplete answer here, but I'd say that the critical difference is the almost complete occurrence of double-stranded DNA that precludes the formation of the tertiary structures in single-stranded RNA, rather than the 2'OH difference. In fact, and following the link you posted, the authors even comment in the introduction that: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;It is well known that single-stranded DNA can assume interesting tertiary structures. A tRNA and its DNA analog form very similar structures [9]&quot;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I did not follow the citation 9&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1990.tb15485.x/pdf&quot; rel=&quot;nofollow&quot;&gt; [Paquette et al (1990), Eur. J. Biochem. 189,259-265]&lt;/a&gt;, but they seem to answer your question with that phrase. In essence, it probably does not have a major implication.&lt;/p&gt;&#xA;" OwnerUserId="48" LastEditorUserId="28" LastEditDate="2012-01-21T20:50:28.500" LastActivityDate="2012-01-21T20:50:28.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="297" PostTypeId="2" ParentId="295" CreationDate="2011-12-22T18:04:14.260" Score="1" Body="&lt;p&gt;Probably they want something like from &lt;a href=&quot;http://www.google.fi/url?sa=t&amp;amp;rct=j&amp;amp;q=giemsa%20staining%20filetype%3appt&amp;amp;source=web&amp;amp;cd=1&amp;amp;ved=0CBwQFjAA&amp;amp;url=http://wwwu.tsgh.ndmctsgh.edu.tw/cp/%25E8%258B%25B1%25E6%2596%2587%25E7%25B6%25B2%25E9%25A0%2581/%25E7%25B6%25B2%25E8%25B7%25AF%25E7%259B%25A7%25E4%25B8%25BB%25E4%25BB%25BB%2520infection%2520cases950316/sectin%2520II/Case%252016.ppt&amp;amp;ei=sm7zTtCzMcfe4QSpp8yNCA&amp;amp;usg=AFQjCNFyLGllzcCT_YnQ8uYz1WRJgDiiIA&amp;amp;sig2=z36FhqbIQC9URv8j-61-8A&amp;amp;cad=rja&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For differentiate nuclear and/or cytoplasmic morphology of platelets,&#xA;  RBCs, WBCs and parasites. In wright- and Giemsa-stain: the cytoplasm&#xA;  appears blue and the nucleus is relatively large, eccentrically&#xA;  located and red. The distinct, rod-shaped, red-staining kinetoplast (a&#xA;  specialized mitochondrial structure) contains extranuclear DNA&#xA;  arranged as catenated minicircles and maxicircles.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In my opinion, the question is not exact if they want the above thing. It should have been: What is the Giemsa staining of chromosomes &lt;strong&gt;morphologically&lt;/strong&gt;? if the above thing correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was the first medical biology course so answer should be from it.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2011-12-22T18:04:14.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="298" PostTypeId="2" ParentId="286" CreationDate="2011-12-22T19:07:45.283" Score="3" Body="&lt;p&gt;I found this &lt;a href=&quot;http://www.anaspec.com/products/product.asp?id=50319&quot; rel=&quot;nofollow&quot;&gt;kit&lt;/a&gt; that appears to be compatible with biological samples.  Rather than buying the kit you may also be able to imitate / modify their &lt;a href=&quot;http://www.anaspec.com/servePdf.asp?f=72146.pdf&amp;amp;t=datasheet&quot; rel=&quot;nofollow&quot;&gt;protocol&lt;/a&gt; to do the assay with your super natant.  &lt;/p&gt;&#xA;" OwnerUserId="12" LastActivityDate="2011-12-22T19:07:45.283" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="299" PostTypeId="1" AcceptedAnswerId="300" CreationDate="2011-12-22T19:54:58.220" Score="9" ViewCount="2601" Body="&lt;p&gt;My son has been diagnosed with Cystic Fibrosis.  I am not looking for medical advice regarding his condition, but I am very interested in understanding the genetic causes of his condition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to the common CF mutation Delta F508, my son's genetic testing revealed both 6T and 9T variants of the PolyT sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I understand it correctly, it seems that the variants (I have found repeated reference to 5T, 7T, and 9T variants, but almost nothing on 6T) are tied to errors in the RNA transcription of the CFTR protein, but I don't understand how, or what the difference between these variants are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does &quot;variant of the PolyT sequence&quot; mean in this context, what are the difference between 5T, 6T, 7T, and 9T, and how do they impact the production of the CFTR protein?&lt;/p&gt;&#xA;" OwnerUserId="225" LastActivityDate="2011-12-22T20:25:12.990" Title="What do the variants on the PolyT sequence mean?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="300" PostTypeId="2" ParentId="299" CreationDate="2011-12-22T20:25:12.990" Score="5" Body="&lt;p&gt;I haven't read too far into this, but from what I understand the variant PolyT sequence is the number of thymine bases in a short sequence within one of the introns of the CFTR gene. Introns and exons are both parts of a gene structure, but introns are spliced out of the final transcript before its converted to protein (for more information see this article on &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_splicing&quot;&gt;RNA splicing&lt;/a&gt;).   Studies have shown that the presence of a &lt;code&gt;5T&lt;/code&gt; sequence in this region may increasethe skipping of exon 9 in the CFTR gene (there is a nice picture showing what I mean &lt;a href=&quot;http://www.blackwellpublishing.com/korfgenetics/figure.asp?chap=13&amp;amp;fig=Fig13-7&quot;&gt;here&lt;/a&gt;).  This exon skipping will alter the final protein product translated from the spliced RNA species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could not find a lot of information about the 6T allele that your son has, however, I found one short article about a patient with 6T and F508 in the &lt;a href=&quot;http://www.nature.com/ejhg/journal/v13/n2/full/5201261a.html&quot;&gt;European Journal of Genetics&lt;/a&gt;. It references another &lt;a href=&quot;http://www.cell.com/AJHG/retrieve/pii/S0002929707619569&quot;&gt;paper&lt;/a&gt; that talks about the length of an additional repeat sequence of GT bases and its affect on individuals the the 5T variant.&lt;/p&gt;&#xA;" OwnerUserId="12" LastActivityDate="2011-12-22T20:25:12.990" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="301" PostTypeId="2" ParentId="295" CreationDate="2011-12-22T21:00:55.007" Score="3" Body="&lt;p&gt;Giemsa is not a particular methid to stain malaria or any other parasite. It stains DNA. As such, it can be used to stain any DNA-containing organism, or, in other words, any known cell.&lt;/p&gt;&#xA;&lt;p&gt;Regarding its particular use in chromosomal banding, you can refer to many online resources, such as &lt;a href=&quot;http://www.pathology.washington.edu/galleries/cytogallery/main.php?file=banding%20patterns&quot; rel=&quot;nofollow noreferrer&quot;&gt;this one of the University of Washington&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Chromosomes in metaphase can be identified using certain staining techniques, so called banding&lt;/p&gt;&#xA;&lt;p&gt;(...)&lt;/p&gt;&#xA;&lt;p&gt;G-bands are most commonly used. They take their name from the Giemsa dye, but can be produced with other dyes. In G-bands, the dark regions tend to be heterochromatic, late-replicating and AT rich. The bright regions tend to be euchromatic, early-replicating and GC rich.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="48" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2011-12-22T21:00:55.007" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="302" PostTypeId="2" ParentId="286" CreationDate="2011-12-22T21:31:51.503" Score="3" Body="&lt;p&gt;There's a paper from 1973 describing a very simple protocol: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4758599&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Wolf PL, Von der Muehll E, Praisler K&lt;/strong&gt;. 1973. A test for bacterial alkaline phosphatase: use in rapid identification of Serratia organisms. Clinical chemistry 19: 1248–9.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="48" LastEditorUserId="836" LastEditDate="2012-09-13T20:29:40.127" LastActivityDate="2012-09-13T20:29:40.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="303" PostTypeId="1" AcceptedAnswerId="479" CreationDate="2011-12-23T00:10:35.327" Score="7" ViewCount="775" Body="&lt;p&gt;DAPI is used as a stain for DNA heterochromatic and euchromatic regions. The Barr body is heterochromatic.&lt;/p&gt;&#xA;&lt;p&gt;In the slide of a normal human female cheek's somatic cells, there is apparently no other clear dark spot inside the nucleus than the Barr body against the nuclear inner membrane. - - I used an old microscope so my observation may be wrong as pointed in the comment.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;How can you deduce from the given slide that the spot really contains inactive satellite cells that are not used genetically?&lt;/p&gt;&#xA;&lt;p&gt;Why is the active X chromosome not visible by the same staining method? (It probably can be made visible by some other staining method.)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-01-05T14:04:43.313" Title="To understand why satellite cells are genetically inactive in Barr body" Tags="&lt;homework&gt;&lt;staining&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="304" PostTypeId="1" AcceptedAnswerId="397" CreationDate="2011-12-23T02:05:01.167" Score="18" ViewCount="1040" Body="&lt;p&gt;I wonder what are examples of organs/structures/behaviours/cooperation that evolutionary biologists themselves find most difficult to explain -- to explain how they could appear evolutionarily -- within known mutation rates, generation frequency, and known time frames.&#xA;Excluding issue of appearance of life itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Knowing rates of mutation and generation cycle (and population size), it would be possible to estimate time needed for appearance of new feature.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus it would be possible to spot counter-examples, such examples that are probabilistically beyond possibility to appear in given evolutionary time. Are such examples known ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I might be naive, but I think some rare behavioral trait can be a candidate, behavior that does not trigger even once in a lifetime of organism, on average, that triggers really rarely.&lt;/p&gt;&#xA;" OwnerUserId="226" LastEditorUserId="69" LastEditDate="2012-01-04T04:34:12.600" LastActivityDate="2012-05-06T20:41:05.423" Title="What is the most difficult feature to explain evolutionarily?" Tags="&lt;evolution&gt;" AnswerCount="3" CommentCount="8" FavoriteCount="6" ClosedDate="2012-05-08T09:53:14.373" ContentLicense="CC BY-SA 3.0" />
  <row Id="305" PostTypeId="1" AcceptedAnswerId="311" CreationDate="2011-12-23T02:14:31.003" Score="29" ViewCount="916" Body="&lt;p&gt;What is the smallest viable reproducing population, such as in a human population. By viable I mean a population which keeps genetic defects low (enough).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A very strongly related question: what is the expected number of generations a given population can survive?&lt;/p&gt;&#xA;" OwnerUserId="84" LastEditorUserId="3624" LastEditDate="2013-06-28T09:46:49.310" LastActivityDate="2013-06-28T09:46:49.310" Title="Smallest viable reproducing population" Tags="&lt;genetics&gt;&lt;ecology&gt;&lt;population-dynamics&gt;&lt;conservation-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="306" PostTypeId="1" AcceptedAnswerId="309" CreationDate="2011-12-23T04:27:46.433" Score="14" ViewCount="2513" Body="&lt;p&gt;I was wondering how many human proteins have a solved 3D structure. Is there a database with only human proteins? I looked at pdb but couldn't find a filter.  &lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="277" LastEditDate="2012-01-15T20:53:58.813" LastActivityDate="2015-04-19T05:53:54.600" Title="How many human proteins have a solved 3D structure?" Tags="&lt;proteins&gt;&lt;structural-biology&gt;&lt;3d-structure&gt;" AnswerCount="4" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="307" PostTypeId="2" ParentId="306" CreationDate="2011-12-23T04:45:17.950" Score="3" Body="&lt;p&gt;From your comments it doesn't seem like you are adverse to writing some custom scripts so one option would be to take advantage of the NCBI Structure database.  You can filter it by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/structure/?term=human%5BOrganism%5D&quot; rel=&quot;nofollow&quot;&gt;organism&lt;/a&gt; and then download the results as a text file / XML.  If you need access to the raw PDB data you could then download the PDB archive and examine the ones in your filtered list.&lt;/p&gt;&#xA;" OwnerUserId="12" LastActivityDate="2011-12-23T04:45:17.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="308" PostTypeId="2" ParentId="268" CreationDate="2011-12-23T07:25:13.013" Score="5" Body="&lt;p&gt;I am not sure if I understand your question correct. What I can see here is a clear ST depression, that might be indicative of myocardial ischemia/infarction. The underlying mechanism is the shortage of oxygen in myocytes leading to elevation of resting potential and slowing of the depolarization -- this accounts for the elevated baseline after T. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not at all an ECG expert, but I have seen the misplaces T-P segment many times while at medical school. It wasn't indicative for diagnosis, whereas all other segments were. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, why are you worrying about this segment?&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="1433" LastEditDate="2012-10-01T11:21:11.080" LastActivityDate="2012-10-01T11:21:11.080" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="309" PostTypeId="2" ParentId="306" CreationDate="2011-12-23T11:17:45.230" Score="19" Body="&lt;p&gt;6405 proteins mapping to 5220 genes, according to Ensembl. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Ensembl's &lt;a href=&quot;http://www.ensembl.org/biomart/martview&quot;&gt;BioMart&lt;/a&gt;, you can select the PDB ID as external reference. Export the results and count the unique proteins/genes that have a PDB ID.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2011-12-23T11:17:45.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="310" PostTypeId="2" ParentId="257" CreationDate="2011-12-23T16:22:45.887" Score="6" Body="&lt;p&gt;These are some of my favorite biology learning resources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ibioseminars.org/&quot;&gt;iBioSeminars&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://academicearth.org/subjects/biology&quot;&gt;Academic Earth - Biology&lt;/a&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Others include: &lt;a href=&quot;http://www.khanacademy.org/#biology&quot;&gt;Khan Academy - Biology&lt;/a&gt;, &lt;a href=&quot;http://www.hhmi.org/biointeractive/video/index.html&quot;&gt;HHMI BioInteractive video collections&lt;/a&gt;, W&lt;a href=&quot;http://www.wellcome.ac.uk/Education-resources/index.htm&quot;&gt;ellcome Trust education resources&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="230" LastEditorUserId="230" LastEditDate="2011-12-27T14:51:10.240" LastActivityDate="2011-12-27T14:51:10.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="311" PostTypeId="2" ParentId="305" CreationDate="2011-12-23T17:48:20.050" Score="23" Body="&lt;p&gt;The conservation biology literature has a great deal of information, particularly with reference to developing species survival plans (e.g., &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006320707002534&quot;&gt;Traill et al. [2007]&lt;/a&gt; report a minimum effective population size of ~4,000 will give a 99% persistence probability of 40 generations). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the question specifically mentions human populations, I'll focus my answer on the genetics of small human populations, though considerably less information is available.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v206/n4990/abs/2061232a0.html&quot;&gt;Hamerton et al. (1965; &lt;em&gt;Nature&lt;/em&gt; 206:1232-1234)&lt;/a&gt; studied chromosome abnormalities in 201 individuals from a total population size of 268 from the small island of &lt;a href=&quot;http://en.wikipedia.org/wiki/Tristan_da_Cunha&quot;&gt;Tristan da Cunha&lt;/a&gt;. These authors report increasing chromosome abnormalities (&lt;a href=&quot;http://en.wikipedia.org/wiki/Aneuploidy&quot;&gt;aneuploidy&lt;/a&gt;; hypo- or hyperdiploidy) with age and suggest that it may result in decreased mitotic efficiency. This population is thought to have developed from a founder population of only 15. According to &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2222.1974.tb01373.x/abstract&quot;&gt;Mantle and Pepys (2006; &lt;em&gt;Clin Exp Allergy&lt;/em&gt; 4:161-170)&lt;/a&gt; approximately two or three of the original settlers were asthmatic, which has led to a very high prevalence (32%) in the current population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC384945/&quot;&gt;Kaessmann et al. (2002; &lt;em&gt;Am J Hum Genet&lt;/em&gt; 70:673-685)&lt;/a&gt; present a more modern study of linkage disequilibrium in two small human populations (Evenki and Saami; ~58,000 and ~60,000 population sizes, respectively) compared to two large populations (Finns and Swedes; ~5 and ~9 million). The authors find significant LD in 60% of the Evenki population and 48% of Saami, but only 29% in Finns and Swedes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.life.umd.edu/faculty/wilkinson/BIOL608W/LiebermanNature07.pdf&quot;&gt;Lieberman et al. (2007; Nature 445:727-731)&lt;/a&gt; discuss the potential for human kin detection to avoid inbreeding. Such mechanisms have been found in other species, &quot;from social amoebas, social insects and shrimp, to birds, aphids, plants, rodents and primates.&quot; Lieberman et al. propose mechanisms contributing to sibling detection in humans, including &quot;maternal perinatal association&quot; and &quot;coresidence duration.&quot; Beyond these behavioral cues, the authors also suggest physiological cues such as major histocompatability complex as playing a role.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2011-12-23T17:48:20.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="312" PostTypeId="2" ParentId="304" CreationDate="2011-12-23T18:01:12.683" Score="7" Body="&lt;p&gt;The Nautilus eye used to be (still is?)  a &quot;problem&quot; and became a poster boy for creationist arguments. It has a pin-hole camera eye, which is the highest resolution non-lens eye. However, I understand that several genera arose during the Cambrian and the existing species haven't changed much since. So, the Nautilus saw fit to develop a sophisticated but non-optimal eye several hundred million years ago (other cephalopods have much better vision), but not develop it further.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This may hard to explain in evolutionary terms, although I note that they probably hunt via &lt;a href=&quot;http://content.karger.com/ProdukteDB/produkte.asp?doi=10.1159/000258669&quot;&gt;olfaction not vision&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2011-12-23T18:24:52.427" LastActivityDate="2011-12-23T18:24:52.427" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="313" PostTypeId="5" CreationDate="2011-12-23T18:38:12.277" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-23T18:38:12.277" LastActivityDate="2011-12-23T18:38:12.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="314" PostTypeId="4" CreationDate="2011-12-23T18:38:12.277" Score="0" Body="This tag is intended for requests for books, articles, online resources, etc. on some subject. Please don't use this as the only tag for a question; use this along with a tag related to the subject you're considering." OwnerDisplayName="user132" LastEditorDisplayName="user132" LastEditDate="2012-01-04T05:08:16.193" LastActivityDate="2012-01-04T05:08:16.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="315" PostTypeId="1" AcceptedAnswerId="316" CreationDate="2011-12-23T22:17:58.273" Score="12" ViewCount="3228" Body="&lt;p&gt;We all know restriction enzymes are proteins, but we never freeze them. They are instead provided in high glycerol containing solutions by companies and stored at -20C. Is there a reason why this is so?&lt;/p&gt;&#xA;" OwnerUserId="223" LastActivityDate="2011-12-24T22:01:30.440" Title="Why are restriction enzymes not frozen?" Tags="&lt;molecular-biology&gt;&lt;enzymes&gt;&lt;proteins&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="316" PostTypeId="2" ParentId="315" CreationDate="2011-12-23T22:56:50.360" Score="13" Body="&lt;p&gt;It's just so much more convenient to have the enzymes ready without having to thaw them. The main reason you freeze enzymes is to keep them active, if you figure out a buffer that keeps them unfrozen without compromising activity, that is a huge increase in convenience.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not having to thaw the enzymes before use saves a lot of time, if you can manage to keep the enzymes active in those non-freezing conditions that is a clear advantage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glycerol also &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19817484&quot;&gt;stabilizes proteins in solution&lt;/a&gt;, and multiple freeze and thaw cycles can negatively affect enzyme activity for some enzymes.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2011-12-24T08:43:21.983" LastActivityDate="2011-12-24T08:43:21.983" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="317" PostTypeId="2" ParentId="305" CreationDate="2011-12-24T04:28:44.380" Score="2" Body="&lt;p&gt;I suspect the answer would definitely include a parameter that would state how 'diverse' the reproducing population is to begin with - including how heterozygous each individual is (versus inbred);  as well as across individuals -  i.e. how different these individuals are from one another. &lt;/p&gt;&#xA;" OwnerUserId="237" LastActivityDate="2011-12-24T04:28:44.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="318" PostTypeId="2" ParentId="9" CreationDate="2011-12-24T04:45:15.650" Score="4" Body="&lt;p&gt;We have gotten into similar situations when other labs have sent us plasmids (or when we have taken out ancient tubes out from storage boxes at -20), and have since adopted the filter paper method. Another point to note is that you can just add, say, 10 &amp;mu;L of water to the &quot;empty&quot; tube (Mac) and use 1 &amp;mu;L for a transformation. It has always worked for us. DNA is seemingly invisible!&lt;/p&gt;&#xA;" OwnerUserId="223" LastActivityDate="2011-12-24T04:45:15.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="319" PostTypeId="1" AcceptedAnswerId="366" CreationDate="2011-12-24T05:41:13.107" Score="9" ViewCount="5635" Body="&lt;p&gt;Why do humans practice monophasic sleep cycles? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When altering one's circadian rhythm to a Polyphasic sleep schedule, how much would that affect development?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is Monophasic sleep (once per day) chosen because of biological evolution or is it due to cultural influence?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="69" LastEditDate="2012-01-04T04:43:46.483" LastActivityDate="2015-11-01T08:11:22.737" Title="Effects of Polyphasic vs Monophasic sleep in humans" Tags="&lt;human-biology&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="320" PostTypeId="1" AcceptedAnswerId="322" CreationDate="2011-12-24T05:52:25.497" Score="16" ViewCount="533" Body="&lt;p&gt;My teachers growing up told me it was impossible to decode the maize genome. But yet its been done. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why was decoding the genome so significant, and what made it so difficult?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="3340" LastEditDate="2014-11-11T14:04:09.483" LastActivityDate="2014-11-11T14:04:09.483" Title="Why was it so hard to decode the corn genome?" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;dna-sequencing&gt;&lt;genomics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="321" PostTypeId="2" ParentId="150" CreationDate="2011-12-24T06:02:00.600" Score="6" Body="&lt;p&gt;The smell of dry erase markers come from the chemicals ethanol, butanol and isopropyl alcohol. Like all chemicals inhaled through the nose, they bind to the Receptor neurons in the located in the back of the nose. The neurons interpret the chemicals using a 'lock-and-key' model but the specific way its coded and perceived in humans is still being researched and the process is not completely understood.&lt;/p&gt;&#xA;" OwnerUserId="238" LastActivityDate="2011-12-24T06:02:00.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="322" PostTypeId="2" ParentId="320" CreationDate="2011-12-24T06:48:35.510" Score="23" Body="&lt;p&gt;The short answer is that corn genome is large and has a huge amount of duplication events. Around 80% of the genome are repeated. It's hard to assemble genomes with large amount of duplications because our sequencing technology, practically, at best can give ~500 base pairs. Figuring out the ordering of duplicated regions relies on scaffold sequences or comparative assembly to rice genome.&lt;/p&gt;&#xA;" OwnerUserId="90" LastActivityDate="2011-12-24T06:48:35.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="323" PostTypeId="2" ParentId="228" CreationDate="2011-12-24T12:28:08.993" Score="6" Body="&lt;p&gt;If your goal is to define the boundaries of the transcription unit (the part of the DNA that is transcribed) the above answer is accurate, although many people merely use homology to cloned cDNAs rather than RACE reactions.  This approach has the benefit of defining alternative splice forms at the same time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your goal is to define the &quot;ends&quot; of the gene, it can only be done empirically and functionally because control elements (boundaries, enhancers, etc) are impossible to recognize using informatics, and even if one finds enhancers, it's not certain that those enhancers are used with specific genes.  Some genes can be &lt;em&gt;millions&lt;/em&gt; of base pairs long, so have hundreds of others genes interspersed.  The &quot;gold standard&quot; for defining the boundaries of genes is to rescue the loss-of-function phenotype of a mutation with a transgene that contains the gene of interest.  If the DNA that is transformed back into an organism can recover the wild-type condition of a mutation of a gene, it is assumed that all of the important parts of that gene are within the transgene.&lt;/p&gt;&#xA;" OwnerUserId="219" LastActivityDate="2011-12-24T12:28:08.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="324" PostTypeId="1" CreationDate="2011-12-24T15:10:50.830" Score="91" ViewCount="6554" Body="&lt;p&gt;The process of sleep seems to be very disadvantageous to an organism as it is extremely vulnerable to predation for several hours at a time. Why is sleep necessary in so many animals? What advantage did it give the individuals that evolved to have it as an adaptation? When and how did it likely occur in the evolutionary path of animals?&lt;/p&gt;&#xA;" OwnerUserId="62" LastEditorUserId="69" LastEditDate="2011-12-27T19:06:50.997" LastActivityDate="2019-09-27T16:52:51.230" Title="Why did the process of sleep evolve in many animals? What is its evolutionary advantage?" Tags="&lt;evolution&gt;&lt;sleep&gt;" AnswerCount="4" CommentCount="5" FavoriteCount="28" ContentLicense="CC BY-SA 3.0" />
  <row Id="325" PostTypeId="2" ParentId="324" CreationDate="2011-12-24T16:01:39.363" Score="54" Body="&lt;p&gt;&lt;a href=&quot;http://www.psychologytoday.com/blog/sleepless-in-america/200903/the-evolution-sleep&quot;&gt;This good non-scholarly article&lt;/a&gt; covers some of the usual advantages (rest/regeneration).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the research papers they mentioned (they linked to press release) was &lt;strong&gt;&lt;em&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2930986/&quot;&gt;Conservation of Sleep: Insights from Non-Mammalian Model Systems&lt;/a&gt;&lt;/strong&gt; by John E. Zimmerman, Ph.D.; Trends Neurosci. 2008 July; 31(7): 371–376. Published online 2008 June 5. doi:  10.1016/j.tins.2008.05.001; NIHMSID: NIHMS230885&lt;/em&gt;. To quote from the press release:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because the time of lethargus coincides with a time in the round worms’ life cycle when synaptic changes occur in the nervous system, they propose that &lt;strong&gt;sleep is a state required for nervous system plasticity.&lt;/strong&gt; In other words, in order for the nervous system to grow and change, there must be down time of active behavior. Other researchers at Penn have shown that, in mammals, synaptic changes occur during sleep and that deprivation of sleep results in a disruption of these synaptic changes. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="185" LastEditorUserId="267" LastEditDate="2011-12-29T21:41:41.703" LastActivityDate="2011-12-29T21:41:41.703" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="326" PostTypeId="2" ParentId="324" CreationDate="2011-12-24T17:49:36.830" Score="9" Body="&lt;p&gt;From what I've learned, there are two theories to answer that question:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Restoration - the body needs to rest in order to renew its metabolism (if an animal is active 24/7, it will constantly use up a lot energy and metabolism). It has been shown that mice that have gone a while without sleeping have a compromised immune system.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Preservation - sleep is assumed to confer a survival advantage. Night time is a dangerous time, so sleep sort of 'forces' an animal to lay low for a few hours.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="133" LastActivityDate="2011-12-24T17:49:36.830" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="327" PostTypeId="2" ParentId="315" CreationDate="2011-12-24T22:01:30.440" Score="5" Body="&lt;p&gt;Freeze-thaw cycles denature proteins through local pH change effects&lt;/p&gt;&#xA;" OwnerUserId="210" LastActivityDate="2011-12-24T22:01:30.440" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="328" PostTypeId="1" AcceptedAnswerId="427" CreationDate="2011-12-25T00:54:02.670" Score="18" ViewCount="1550" Body="&lt;p&gt;In what ways has DNA been studied to see if there a &quot;programmable&quot; aspect to it? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has nature produced anything resembling a Turing machine within the cell, perhaps using the &quot;junk DNA&quot; as its code? I expect nature's way would probably be very round-about and not compact.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NOTE: I am not asking about building DNA computers, as this question had recently been contorted to become.&lt;/p&gt;&#xA;" OwnerUserId="84" LastEditorUserId="84" LastEditDate="2012-01-05T17:01:56.580" LastActivityDate="2012-01-05T18:43:23.910" Title="Could Junk DNA be used as a Turing Machine by nature?" Tags="&lt;dna&gt;&lt;genetics&gt;&lt;introns&gt;" AnswerCount="6" CommentCount="7" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="329" PostTypeId="1" AcceptedAnswerId="330" CreationDate="2011-12-25T12:07:42.077" Score="11" ViewCount="1427" Body="&lt;p&gt;When a cat is growing, his nails are growing with him to some extent. A grown cat has a fixed nail length that is not extending.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By contrast, human finger nails just keep on growing, so we have to cut them to keep an aesthetically pleasing look.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nature clearly has a mechanism to control nail growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the most probable reason as to why this is not implemented in humans?&lt;/p&gt;&#xA;" OwnerUserId="245" LastEditorUserId="338" LastEditDate="2012-02-17T10:27:54.000" LastActivityDate="2012-02-17T10:27:54.000" Title="Why are there nail growth differences  between humans and other mammals?" Tags="&lt;evolution&gt;&lt;anatomy&gt;&lt;human-anatomy&gt;&lt;theoretical-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="330" PostTypeId="2" ParentId="329" CreationDate="2011-12-25T12:38:50.017" Score="12" Body="&lt;p&gt;Cat claws are growing all the time, like horse hooves, or human nails. However, cats and horses usually use their claws/hooves, so they get shortened through mechanical action.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.purina.co.uk/Home/All+About+Cats/Living+Together+Cat/Looking+Good+Feeling+Good+Cat/Nail+Care.htm&quot;&gt;An indoor cat may need their claws trimmed if it doesn't use them enough&lt;/a&gt; (that's why cats will want to scratch everywhere), or if has supernumerary toes that don't normally touch the ground. Similarly, cattle that doesn't get to move will suffer from hoof overgrowth, which appears to be very uncomfortable to the animal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consequently, if you were to use your fingernails more often for digging and scratching, you wouldn't have to trim them all the time. &lt;/p&gt;&#xA;" OwnerUserId="34" LastActivityDate="2011-12-25T12:38:50.017" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="331" PostTypeId="2" ParentId="186" CreationDate="2011-12-25T20:15:02.597" Score="20" Body="&lt;p&gt;I disagree with Ctina.  So many factors go into determining loss rate, activity of telomerase, gene conversion or unequal exchange at chromosome ends, etc to ever say that length is a function of age.  There is far more variation between individuals and between cells within an individual than aging ever shows.  Here is one study:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Das B, Saini D, Seshadri M. Telomere length in human adults and high level natural background radiation. PLoS One. 2009 Dec 23;4(12):e8440.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;however I've seen similar studies published elsewhere.  Telomere length as diagnostic for age is very poor at best.  Here's an article that gives a formula, but acknowledges the R&lt;sup&gt;2&lt;/sup&gt; is 0.04, which is useless: &lt;a href=&quot;http://preview.ncbi.nlm.nih.gov/pubmed/18378481&quot;&gt;http://preview.ncbi.nlm.nih.gov/pubmed/18378481&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="219" LastEditorUserId="219" LastEditDate="2011-12-30T13:40:29.917" LastActivityDate="2011-12-30T13:40:29.917" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="332" PostTypeId="2" ParentId="2" CreationDate="2011-12-25T23:07:26.010" Score="4" Body="&lt;p&gt;Apart from tips already mentioned, change your gloves every now and then.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, in my experience (with the Qiagen kit), keeping samples on ice shouldn't make much of a difference.&lt;/p&gt;&#xA;" OwnerUserId="251" LastEditorUserId="251" LastEditDate="2011-12-26T12:43:37.037" LastActivityDate="2011-12-26T12:43:37.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="333" PostTypeId="2" ParentId="58" CreationDate="2011-12-26T03:29:45.240" Score="3" Body="&lt;p&gt;If gene B makes a protein product, you can try designing a morpholino against the 5'-UTR of gene B. This can prevent translation initiation at the ribosome as the morpholino occludes mRNA entry into the ribosome. You can detect this by western blotting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If gene B makes some sort of regulator RNA, you will need to target expression of gene B at the DNA level. If gene B has well established splice sites, a morpholino can interfere with splicing enhancers and silencers, and therefore, should produce a non-functional or impaired RNA product. You can detect splice variants by amplifying gene B from cDNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Theoretically, the advantage of using a morpholino is due to it's single stranded nature. Morpholinos designed against gene B should have no effect on gene A due to non–complemenetarity.&lt;/p&gt;&#xA;" OwnerUserId="177" LastActivityDate="2011-12-26T03:29:45.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="335" PostTypeId="2" ParentId="202" CreationDate="2011-12-26T12:40:12.687" Score="6" Body="&lt;p&gt;First of all, the nature of penetrance is almost entirely unknown.  Likely it's a combination of epistasis and gene interactions, induced gene regulatory pathways, developmental noise, and other factors.  Epigenetics (imprinting, etc) may have little to do with penetrance, while chromatin structure may be a consequence of other things (most now regard histone modifications, etc, as consequence of transcription rather than heritable regulatory mechanism).  Currently, the field of epigenetics is undergoing a (long-overdue) reassessment.  Until that happens, anyone who wants to make claims of &quot;epigenetics&quot; is free to, so spurious claims are rampant.&lt;/p&gt;&#xA;" OwnerUserId="219" LastActivityDate="2011-12-26T12:40:12.687" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="337" PostTypeId="1" CreationDate="2011-12-26T17:41:53.323" Score="11" ViewCount="588" Body="&lt;p&gt;The attachment point of the umbilical cord in a baby girl is very close to where her own baby would develop. Is there something in the evolutionary history of mammals that explains this, or some anatomical constraint? Or is it just a coincidence?&lt;/p&gt;&#xA;" OwnerUserId="252" LastActivityDate="2015-08-19T21:08:17.023" Title="Coincidence that navel is near the womb?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="338" PostTypeId="2" ParentId="337" CreationDate="2011-12-26T17:53:07.590" Score="6" Body="&lt;p&gt;I would say it is a coincidence because:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;the navel is in the same place in males, so if it was there for some evolutionary advantage the charachter would be sexually dymorphic, which clearly is not the case.&lt;/li&gt;&#xA;&lt;li&gt;I cannot think of any specific function of the navel that is related to pregnancy or delivery (or of a specific function of the navel at all for that matters)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="115" LastActivityDate="2011-12-26T17:53:07.590" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="339" PostTypeId="1" AcceptedAnswerId="342" CreationDate="2011-12-26T20:54:58.497" Score="40" ViewCount="1078" Body="&lt;p&gt;I'm a biology amateur, but it seems like sexual selection is almost always performed based on physical characteristics, the outcome of physical contests, or some sort elaborate courtship. But do any non Homo-Sapiens perform sexual selection based on intelligence factors, like problem solving abilities? If so, how does the species accomplish this? I know natural selection as a whole would definitely favor intelligent individuals, but I'm curious if any species actually takes this into account when choosing mates. &lt;/p&gt;&#xA;" OwnerUserId="62" LastEditorUserId="277" LastEditDate="2012-01-04T14:52:33.457" LastActivityDate="2014-06-17T12:34:17.970" Title="Is there evidence that some non-human species perform sexual selection based primarily on intelligence? How do they do this?" Tags="&lt;evolution&gt;&lt;sexual-selection&gt;&lt;natural-selection&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="340" PostTypeId="1" AcceptedAnswerId="343" CreationDate="2011-12-26T23:31:20.647" Score="11" ViewCount="155" Body="&lt;p&gt;Are all carcinogens equally potent? Is the relationship between dose and probability of cancer roughly equal, or are there some carcinogens that provoke cancer significantly more than their cousins?&lt;/p&gt;&#xA;" OwnerUserId="42" LastEditorUserId="69" LastEditDate="2012-02-17T09:38:15.763" LastActivityDate="2012-02-17T09:38:15.763" Title="What is the base cancer rate for an arbitrary carcinogen?" Tags="&lt;cancer&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="342" PostTypeId="2" ParentId="339" CreationDate="2011-12-27T00:31:34.177" Score="41" Body="&lt;p&gt;Very intresting question. The problem is that animal intelligence is hard to measure not only for scientists, but probably also for the potential mate. Paradoxically, that is why selection for intelligence, if it occurred, may be very strong. One has to be smart in order to recognise smart behaviour, so preference and preferred feature are strongly connected. But that's only my opinion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Boogert et al., 2011 &lt;a href=&quot;http://beheco.oxfordjournals.org/content/22/3/447.abstract&quot;&gt;1&lt;/a&gt; reviews the current knowledge about animal preferences for cognition skills. They conclude that there is very little data on this subject. The given examples are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Preference for elaborating birds songs (as songs are not inborn and have to be learned)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Spatial abilities: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In meadow voles (Microtus pennsylvanicus), males with better spatial learning and memory abilities were not only found to have larger home ranges and to locate more females in the field (Spritzer, Solomon, et al. 2005 &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0003347204003781&quot;&gt;2&lt;/a&gt;) but were also preferred by females in mate-choice tests, even though the females did not observe males’ performance on spatial tests (Spritzer, Meikle, et al. 2005 &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S000334720500014X&quot;&gt;3&lt;/a&gt;).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In guppies (Poecilia reticulata), males that learned faster to swim through mazes to gain a food reward were found to be more attractive to females (Shohet and Watt 2009 &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8649.2009.02366.x/full&quot;&gt;4&lt;/a&gt;). However, females were not able to see the males’ performance in the mazes. Although male learning ability was weakly correlated with saturation of the orange patches on his body (a sexually selected trait (...)), orange saturation surprisingly did not correlate with female preferences. Thus, the cues leading female guppies to prefer faster learners are unknown.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is possible, that females base their choose on some factors that correlates with cognitive skills or on total wellness, what may depend on intelligence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) bowerbird's abilities to build bowers (courtship constructions):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Comparative studies across bowerbird species have shown that relative brain size is larger in species that build bowers than in closely related nonbuilding species (Madden 2001 &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/268/1469/833.short&quot;&gt;5&lt;/a&gt;). In addition, relative brain size increases with the species-typical complexity of the bower (Madden 2001 &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/268/1469/833.short&quot;&gt;5&lt;/a&gt;), and a comparative study on the relative size of specific brain regions showed that species with more complex bowers have a relatively larger cerebellum (Day et al. 2005 &lt;a href=&quot;http://content.karger.com/ProdukteDB/produkte.asp?Aktion=ShowAbstractBuch&amp;amp;ArtikelNr=85048&amp;amp;ProduktNr=230875&quot;&gt;6&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;4) foraging performance&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A recent experiment by Snowberg and Benkman (2009) &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2009.01699.x/full&quot;&gt;7&lt;/a&gt; using red crossbills (Loxia curvirostra) showed that, after observing 2 males extracting seeds from conifer cones, females associated preferentially with the more efficient forager of the 2. The authors were able to exclude female choice for correlated traits by experimentally manipulating foraging efficiency, such that fewer seeds were available in the cones of one of the males. The males were also swapped between treatments (i.e., slow vs. fast forager) so that male identity could not explain the females’ preferences for the most efficient forager.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Another way that intelligence may be favored by sexual selection is &quot;cheating&quot; during courtship. For example most frog species call to attract females. But this signal may also attract aggresive rivals or predators. Some males, especially the weaker ones, do not call  but stay near calling individual.  This allows them to avoid confrontation and wait for approaching females [8]. The successfulness of this strategy may depend on how &quot;smart&quot; the individual is (only my opinion).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://beheco.oxfordjournals.org/content/22/3/447.abstract&quot;&gt;&lt;strong&gt;[1] Boogert, N. J., Fawcett, T. W., &amp;amp; Lefebvre, L. (2011). Mate choice for cognitive traits: a review of the evidence in nonhuman vertebrates. Behavioral Ecology, 22(3), 447-459.&lt;/strong&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0003347204003781&quot;&gt;[2] Spritzer MD, Solomon NG, Meikle DB. 2005. Influence of scramble competition for mates upon the spatial ability of male meadow voles. Anim Behav. 69:375–386.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S000334720500014X&quot;&gt;[3] Spritzer MD, Meikle DB, Solomon NG. 2005. Female choice based on male spatial ability and aggressiveness among meadow voles. Anim Behav. 69:1121–1130.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8649.2009.02366.x/full&quot;&gt;[4] Shohet AJ, Watt PJ. 2009. Female guppies Poecilia reticulata prefer males that can learn fast. J Fish Biol. 75:1323–1330.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/268/1469/833.short&quot;&gt;[5] Madden J. 2001. Sex, bowers and brains. Proc R Soc Lond B Biol Sci. 268:833–838.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://content.karger.com/ProdukteDB/produkte.asp?Aktion=ShowAbstractBuch&amp;amp;ArtikelNr=85048&amp;amp;ProduktNr=230875&quot;&gt;[6] Day LB, Westcott DA, Olster DH. 2005. Evolution of bower complexity and cerebellum size in bowerbirds. Brain Behav Evol. 66:62–72&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2009.01699.x/full&quot;&gt;[7] Snowberg LK, Benkman CW. 2009. Mate choice based on a key ecological performance trait. J Evol Biol. 22:762–769.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[8] Bateson P. 1985. Mate choice. Cambridge University Press. 181-210&lt;/p&gt;&#xA;" OwnerUserId="68" LastEditorUserId="69" LastEditDate="2011-12-29T21:41:27.833" LastActivityDate="2011-12-29T21:41:27.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="343" PostTypeId="2" ParentId="340" CreationDate="2011-12-27T10:22:33.350" Score="8" Body="&lt;p&gt;To answer this question in its entirety we have to split it into two questions:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What are the underlying mechanisms of carcinogenity?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;One of the main mechanism behind carcinogenity is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Mutagen&quot;&gt;mutagenity&lt;/a&gt; of the cancerogens, i.e. the ability to cause mutations, that are abberations of the cell DNA leading to uncontrolled proliferation. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1569391/&quot;&gt;This classical paper&lt;/a&gt; investigates the relation between cancerogenity and mutagenity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One should mention here that there are many types of mutations possible, mutations are not equally dangerous for cells and some mutations can be successfully repaired using the intact strain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore the following parameters of the source substances need to be measured to estimate the cancerogenity:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Substance concentrations or absolute amounts (both being indirect measures of their chemical activities, the lower concentration is needed for causing cancer the higher is the chemical activity and vise versa).&lt;/li&gt;&#xA;&lt;li&gt;Substance radioactivity (for the mutagenesis due to radiation).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How can we measure the carcinogenity of different substances?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The most general approach here is to introduce certain amount of cancerogen into the animal body or to the cultured cell and to see the effect. The effect is calculated as the percentage of cells that undergo the transformation from normal into cancer cells. Two metrics are available here:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;DT&lt;/strong&gt; = Tumorigenic Dose (the amount of substance causing certain&#xA;  percentage of cancer in treated animals, all treated animals are taken&#xA;  for 100%)&lt;br&gt;&#xA;  &lt;strong&gt;CT&lt;/strong&gt; = Tumorigenic Concentration (same, but adjusted for&#xA;  concentration and used in cell cultures).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(They are written CT and DT because in science people tend to used Latin abbreviations where the adjective actually follows the noune).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The common metrics are DT5/CT5 (5% cells/animals get cancer) and DT50/CT50 (50% of the animals). Those are similar to other common metrics, the most common is LC50/LD50 -- lethal dose for 50% of the animals/cells.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Unfortunately I couldn't not find any pre-compiled list with most known cancerogens and their TD/TC values. These seem to be interesting primarily for scientists. But going back to your question: you are absolutely right: &lt;strong&gt;some cancerogens are much more potent in causing cancer than the others!&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2011-12-27T10:22:33.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="344" PostTypeId="1" AcceptedAnswerId="362" CreationDate="2011-12-27T10:54:11.907" Score="40" ViewCount="1957" Body="&lt;p&gt;There seem to be a number of ideas about why we age. Hypotheses include the gradual accumulation of cell metabolic products affecting organism function and the reduction of &lt;a href=&quot;https://biology.stackexchange.com/questions/186/is-telomere-length-a-reliable-measure-of-health-lifespan&quot;&gt;telomere length&lt;/a&gt; during cell division.&#xA;My hand-wavey idea would be &quot;wear and tear&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are we anywhere near a consensus theory of senescence?&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-10-30T21:29:50.690" Title="Why do we age? or Do we have a theory of senescence?" Tags="&lt;human-biology&gt;&lt;senescence&gt;" AnswerCount="6" CommentCount="2" FavoriteCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="345" PostTypeId="1" AcceptedAnswerId="376" CreationDate="2011-12-27T14:40:16.953" Score="18" ViewCount="741" Body="&lt;p&gt;The standard protocol for a person experiencing chest pains is to &lt;strong&gt;chew&lt;/strong&gt; a 300mg aspirin tablet, the argument being that chewing rather than swallowing the tablet results in the aspirin entering the blood stream faster.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a biological standpoint, why is this the case?  Given that the stomach and GI tract are specialised tissues to allow for maximum diffusion, why would it be faster to pass aspirin across the gums (&lt;em&gt;bucaal administration?)&lt;/em&gt; tongue and cheeks which are not specialised for this purpose? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not just a special case for aspirin either, as Hypostop&lt;sup&gt;TM&lt;/sup&gt;/Glucogel&lt;sup&gt;TM&lt;/sup&gt; (acute treatment for hypoglycaemic shock, essentially concentrated sugar) is applied directly to the gums or cheek with a similar argument that in critical situations it is faster.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only suggestion I could find was  very vague from the &quot;&lt;a href=&quot;http://www.merckmanuals.com/professional/clinical_pharmacology/pharmacokinetics/drug_absorption.html&quot; rel=&quot;nofollow&quot;&gt;Merck Manual&lt;/a&gt;&quot;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The stomach has a relatively large epithelial surface, but its thick mucous layer and short transit time limit absorption&#xA;  Which I assume could mean that it is the reduced absorption rate in the stomach that makes the oral membranes faster, yet it also says that the delay in the stomach is brief.  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'd be really interested to know the biology behind this!&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-08-11T18:37:32.653" LastActivityDate="2016-02-08T10:29:13.470" Title="Why would diffusion be faster across a non-specialised tissue?" Tags="&lt;human-biology&gt;&lt;pharmacology&gt;&lt;human-anatomy&gt;&lt;aspirin&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="346" PostTypeId="5" CreationDate="2011-12-27T14:54:29.397" Score="0" Body="&lt;p&gt;A field of biology focused on the study of the animal kingdom. Includes study of, but not limited to, natural history, ecology, anatomy, physiology, ethology (behavior), embryology, distributions, classification and evolutionary biology. Questions should explicitly seek answers on the biology of animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Zoology is a very broad field, so more focused tags should be included when using the zoology tag. Commonly paired tags with zoology include &lt;a href=&quot;/questions/tagged/species-identification&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;species-identification&amp;#39;&quot; rel=&quot;tag&quot;&gt;species-identification&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/anatomy&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;anatomy&amp;#39;&quot; rel=&quot;tag&quot;&gt;anatomy&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/physiology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;physiology&amp;#39;&quot; rel=&quot;tag&quot;&gt;physiology&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/ecology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;ecology&amp;#39;&quot; rel=&quot;tag&quot;&gt;ecology&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/ethology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;ethology&amp;#39;&quot; rel=&quot;tag&quot;&gt;ethology&lt;/a&gt;, and &lt;a href=&quot;/questions/tagged/genetics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;genetics&amp;#39;&quot; rel=&quot;tag&quot;&gt;genetics&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The study of specific animal groups also typically have dedicated tags: &lt;a href=&quot;/questions/tagged/mammals&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;mammals&amp;#39;&quot; rel=&quot;tag&quot;&gt;mammals&lt;/a&gt; &lt;a href=&quot;/questions/tagged/ornithology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;ornithology&amp;#39;&quot; rel=&quot;tag&quot;&gt;ornithology&lt;/a&gt; &lt;a href=&quot;/questions/tagged/arthropods&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;arthropods&amp;#39;&quot; rel=&quot;tag&quot;&gt;arthropods&lt;/a&gt; (&lt;a href=&quot;/questions/tagged/entomology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;entomology&amp;#39;&quot; rel=&quot;tag&quot;&gt;entomology&lt;/a&gt;&lt;strong&gt;/&lt;/strong&gt;&lt;a href=&quot;/questions/tagged/arachnology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;arachnology&amp;#39;&quot; rel=&quot;tag&quot;&gt;arachnology&lt;/a&gt;) &lt;a href=&quot;/questions/tagged/herpetology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;herpetology&amp;#39;&quot; rel=&quot;tag&quot;&gt;herpetology&lt;/a&gt; &lt;a href=&quot;/questions/tagged/ichthyology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;ichthyology&amp;#39;&quot; rel=&quot;tag&quot;&gt;ichthyology&lt;/a&gt; &lt;a href=&quot;/questions/tagged/invertebrates&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;invertebrates&amp;#39;&quot; rel=&quot;tag&quot;&gt;invertebrates&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also: &lt;a href=&quot;/questions/tagged/animal-husbandry&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;animal-husbandry&amp;#39;&quot; rel=&quot;tag&quot;&gt;animal-husbandry&lt;/a&gt; &lt;a href=&quot;/questions/tagged/animal-psychology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;animal-psychology&amp;#39;&quot; rel=&quot;tag&quot;&gt;animal-psychology&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="16866" LastEditDate="2019-07-12T03:26:22.620" LastActivityDate="2019-07-12T03:26:22.620" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="347" PostTypeId="4" CreationDate="2011-12-27T14:54:29.397" Score="0" Body="The biological study of animals. Very broad use so be sure to add additional clarifying tags" OwnerUserId="69" LastEditorUserId="16866" LastEditDate="2019-07-12T03:26:22.620" LastActivityDate="2019-07-12T03:26:22.620" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="348" PostTypeId="5" CreationDate="2011-12-27T14:56:28.393" Score="0" Body="&lt;p&gt;Proteins consist of one or more large amino acid residues and perform a vast array of functions in living organisms. Questions may need to draw on alternative related tags, such as &lt;a href=&quot;/questions/tagged/molecular-biology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;molecular-biology&amp;#39;&quot; rel=&quot;tag&quot;&gt;molecular-biology&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/cell-biology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;cell-biology&amp;#39;&quot; rel=&quot;tag&quot;&gt;cell-biology&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/amino-acids&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;amino-acids&amp;#39;&quot; rel=&quot;tag&quot;&gt;amino-acids&lt;/a&gt; and &lt;a href=&quot;/questions/tagged/proteomics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;proteomics&amp;#39;&quot; rel=&quot;tag&quot;&gt;proteomics&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additional, more-precise tags exist for proteins and should be additionally used as appropriate: &lt;a href=&quot;/questions/tagged/protein-structure&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;protein-structure&amp;#39;&quot; rel=&quot;tag&quot;&gt;protein-structure&lt;/a&gt; &lt;a href=&quot;/questions/tagged/protein-binding&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;protein-binding&amp;#39;&quot; rel=&quot;tag&quot;&gt;protein-binding&lt;/a&gt; &lt;a href=&quot;/questions/tagged/protein-folding&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;protein-folding&amp;#39;&quot; rel=&quot;tag&quot;&gt;protein-folding&lt;/a&gt; &lt;a href=&quot;/questions/tagged/protein-interaction&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;protein-interaction&amp;#39;&quot; rel=&quot;tag&quot;&gt;protein-interaction&lt;/a&gt; &lt;a href=&quot;/questions/tagged/protein-expression&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;protein-expression&amp;#39;&quot; rel=&quot;tag&quot;&gt;protein-expression&lt;/a&gt; &lt;a href=&quot;/questions/tagged/protein-evolution&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;protein-evolution&amp;#39;&quot; rel=&quot;tag&quot;&gt;protein-evolution&lt;/a&gt; &lt;a href=&quot;/questions/tagged/protein-engineering&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;protein-engineering&amp;#39;&quot; rel=&quot;tag&quot;&gt;protein-engineering&lt;/a&gt; &lt;a href=&quot;/questions/tagged/protein-identification&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;protein-identification&amp;#39;&quot; rel=&quot;tag&quot;&gt;protein-identification&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="16866" LastEditDate="2019-07-12T03:58:04.390" LastActivityDate="2019-07-12T03:58:04.390" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="349" PostTypeId="4" CreationDate="2011-12-27T14:56:28.393" Score="0" Body="Biopolymers consisting of amino acids that fold into 3D shapes and perform a large number of functions in living organisms." OwnerUserId="69" LastEditorUserId="6" LastEditDate="2013-06-09T20:51:40.037" LastActivityDate="2013-06-09T20:51:40.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="350" PostTypeId="5" CreationDate="2011-12-27T14:57:25.583" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-27T14:57:25.583" LastActivityDate="2011-12-27T14:57:25.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="351" PostTypeId="4" CreationDate="2011-12-27T14:57:25.583" Score="0" Body="The passive net movement of a substance from a high concentration to a lower concentration through a semi-permeable membrane." OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-04T04:45:04.280" LastActivityDate="2012-01-04T04:45:04.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="352" PostTypeId="5" CreationDate="2011-12-27T14:58:45.567" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-27T14:58:45.567" LastActivityDate="2011-12-27T14:58:45.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="353" PostTypeId="4" CreationDate="2011-12-27T14:58:45.567" Score="0" Body="The maintenance of a constant internal environment - for example temperature, carbon dioxide concentration or water concentration, etc. within an organism." OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-04T05:07:40.107" LastActivityDate="2012-01-04T05:07:40.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="354" PostTypeId="5" CreationDate="2011-12-27T15:00:44.737" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-27T15:00:44.737" LastActivityDate="2011-12-27T15:00:44.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="355" PostTypeId="4" CreationDate="2011-12-27T15:00:44.737" Score="0" Body="A collection of tissues which work together to accomplish a function.  The organisational unit above tissues and below systems.  " OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-04T05:08:02.743" LastActivityDate="2012-01-04T05:08:02.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="356" PostTypeId="5" CreationDate="2011-12-27T15:02:41.427" Score="0" Body="&lt;p&gt;Physiology is the study of how organisms, organs, cells, and biomolecules carry out the chemical or physical functions that exist in living systems. It can be subdivided into human, animal, plant, bacterial, etc. physiology. Questions should be about function, while the &lt;a href=&quot;/questions/tagged/anatomy&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;anatomy&amp;#39;&quot; rel=&quot;tag&quot;&gt;anatomy&lt;/a&gt; tag should be used for structure questions.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="16866" LastEditDate="2019-07-12T03:52:32.493" LastActivityDate="2019-07-12T03:52:32.493" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="357" PostTypeId="4" CreationDate="2011-12-27T15:02:41.427" Score="0" Body="The study of the normal function of living organisms and their anatomical parts and the means by which their normal functioning is achieved. " OwnerUserId="69" LastEditorUserId="16866" LastEditDate="2019-07-12T03:52:32.493" LastActivityDate="2019-07-12T03:52:32.493" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="358" PostTypeId="5" CreationDate="2011-12-27T15:03:42.500" Score="0" Body="&lt;p&gt;The study of the immune system, the system primarily responsible for fighting infection in living organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a list of books covering this topic, see &lt;a href=&quot;http://biology.stackexchange.com/q/13729/561&quot;&gt;Modern immunology textbooks&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;related: &lt;a href=&quot;/questions/tagged/immune-system&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;immune-system&amp;#39;&quot; rel=&quot;tag&quot;&gt;immune-system&lt;/a&gt; &lt;a href=&quot;/questions/tagged/immunity&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;immunity&amp;#39;&quot; rel=&quot;tag&quot;&gt;immunity&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="561" LastEditorUserId="16866" LastEditDate="2019-07-12T03:59:59.783" LastActivityDate="2019-07-12T03:59:59.783" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="359" PostTypeId="4" CreationDate="2011-12-27T15:03:42.500" Score="0" Body="The study of the immune system in organisms, primarily responsible for fighting infection." OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-04T05:07:54.370" LastActivityDate="2012-01-04T05:07:54.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="360" PostTypeId="5" CreationDate="2011-12-27T15:05:07.740" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2011-12-27T15:05:07.740" LastActivityDate="2011-12-27T15:05:07.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="361" PostTypeId="4" CreationDate="2011-12-27T15:05:07.740" Score="0" Body="The region at the rear of the brain that, among other things, controls the coordination, precision, and timing of movements.  Motor learning and postural control are largely governed by this area as well. " OwnerUserId="69" LastEditorUserId="57" LastEditDate="2012-01-15T09:09:47.700" LastActivityDate="2012-01-15T09:09:47.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="362" PostTypeId="2" ParentId="344" CreationDate="2011-12-27T15:38:16.167" Score="25" Body="&lt;p&gt;The 'wear and tear' argument is most likely true but it is also interesting to reason about ageing as inevitable from the evolutionary point of view.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To set up the argument, we need two things:&#xA;First, each individual has got a 'reproductive potential' which is realised throughout life. This means a deleterious mutation which has an effect in early life, will affect reproductive value more than a mutation which manifests itself in later life, after the individual has already had offspring. Thus selection will act strongly on genes which are expressed in early life than on those which are expressed later. For that reason, there's no strong selection against diseases such as diabetes or cancer. This argument can be applied not only to occurrence of disease but also to decay of ordinary functions of the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, cells in the body are constantly renewed and defects such as telomeric breaks are repaired. Mutations in the soma are taken care of by the immune system and can be in principle avoided. The fact that they tend to accumulate in later life can be explained by the first point: &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.2000.tb06651.x/full&quot;&gt;selection is weaker to oppose telomeric breaks and mutations in later life&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was trying to be brief here, but there are more sides to the argument (e.g. Williams' antagonistic pleiotropy). &lt;a href=&quot;http://www.amazon.co.uk/Modular-Evolution-Selection-Biological-Complexity/dp/0521728770&quot;&gt;Modular Evolution&lt;/a&gt; (Vinicius, CUP 2010) provides a good overview of the evolutionary aspect of theory of senescence (and many other interesting evolutionary arguments).&lt;/p&gt;&#xA;" OwnerUserId="9" LastEditorUserId="1590" LastEditDate="2013-07-08T08:50:40.680" LastActivityDate="2013-07-08T08:50:40.680" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="363" PostTypeId="1" AcceptedAnswerId="368" CreationDate="2011-12-27T15:47:03.053" Score="11" ViewCount="1749" Body="&lt;p&gt;I originally had planned to ask about whether there was any biological truth in the popular phrase &quot;shivering with fright&quot;.  However, after doing a fair bit of googling it seems that there is a lot more &lt;em&gt;medical&lt;/em&gt; reference to &lt;em&gt;trembling&lt;/em&gt; as a result of anxiety &lt;a href=&quot;http://www.rightdiagnosis.com/symptoms/shivering/common.htm&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt; (though I would imagine the distinction to be fairly minor).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was, after about an hour of fruitless searching, beginning to wonder if it was a phenomenon created only in literature (such as being 'frozen by fright') rather than genuine human physiology, however then a website described how many people often have minor trembling before exams, interviews or other high pressure situations - something I can attest to myself!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This hasn't really changed the biological purpose behind the question however - is there any advantage to shivering in a fight or flight situation or is it more a side effect of the release of adrenaline or another chemical response? I am struggling because I can only imagine it being a real disadvantage (consider for example an organism hiding from a predator - uncontrolled movement in a stressed situation can not be beneficial) so the only way that I can see is that the shivering must be linked to something that &lt;strong&gt;is&lt;/strong&gt; a definite advantage in a high stress situation.  What would that be? &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-10-02T22:40:15.543" LastActivityDate="2012-10-02T22:40:15.543" Title="Is trembling an advantageous response during periods of anxiety?" Tags="&lt;physiology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="364" PostTypeId="1" CreationDate="2011-12-27T16:00:29.167" Score="3" ViewCount="121" Body="&lt;p&gt;I am looking for a live-cell–impermeable dye for viability. (The cells cannot be permeabilized and fixed in this experiment.)  I would prefer with excitation and emission spectra similar to Cy5, but I can be flexible here as long as the spectra are far away from Hoechst.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried TOPRO3, but it seems to lose its brightness after a few exposures, so I would like something more resistant to photobleaching.&lt;/p&gt;&#xA;" OwnerUserId="23" LastEditorUserId="69" LastEditDate="2011-12-27T18:06:10.177" LastActivityDate="2011-12-27T18:06:10.177" Title="Is there a photobleaching-resistant, cell-permeant viability stain in the far red part of the spectrum?" Tags="&lt;staining&gt;&lt;high-throughput&gt;&lt;fluorescent-microscopy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="365" PostTypeId="2" ParentId="364" CreationDate="2011-12-27T16:32:57.947" Score="4" Body="&lt;p&gt;You could try SYTO Orange. Unlike SYTOX, which is a fixed-cell marker, SYTO works with both live and fixed cells.&lt;/p&gt;&#xA;" OwnerUserId="23" LastActivityDate="2011-12-27T16:32:57.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="366" PostTypeId="2" ParentId="319" CreationDate="2011-12-27T19:02:56.463" Score="6" Body="&lt;p&gt;Reading &amp;quot;&lt;a href=&quot;http://www.supermemo.com/articles/polyphasic.htm#Polyphasic%20sleep&quot; rel=&quot;noreferrer&quot;&gt;Polyphasic Sleep: Facts and Myths&lt;/a&gt; (Dr Piotr Wozniak)&amp;quot;, it is pointed out that infant humans do undergo polyphasic sleep. As this is where most of our development is obviously done, I do not know where I can further proceed with the question about how it would affect development?  Perhaps the issue is more how it would effect the day to day performance of a developed individual?  If this is the case then it is suggested by Dr Wozniak that this is likely to be highly disruptive to the individual&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Those well-defined effects of natural sleep affecting stimuli on sleep patterns lead to an instant conclusion: the claim that humans can adapt to any sleeping pattern is false. A sudden shift in the schedule, as in shift work, may lead to a catastrophic disruption of sleep control mechanisms. 25% of North American population may work in variants of shift schedule. Many shift workers never adapt to shifts in sleep patterns. At times, they work partly in conditions of harmful disconnect from their body clock, and return to restful sleep once their shift returns to their preferred timing. At worst, the constant shift of the working hours results in a loss of synchrony between various physiological variables and the worker never gets any quality sleep. This propels an individual on a straight path to a volley of health problems...&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;It appears that polyphasic sleep encounters the precisely same problems as seen in jet lag or shift-work. Human body clock is not adapted to sleeping in patterns other than monophasic or biphasic sleep.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It would therefore seem that polyphasic sleep is certainly detrimental to health, if not development.&lt;/p&gt;&#xA;&lt;p&gt;However studies into cognitive performance resulting from differing sleep patterns run by Dr Claudio Stampi (Published &lt;a href=&quot;http://sleepwarrior.com/Claudio_Stampi_-_Why_We_Nap.pdf&quot; rel=&quot;noreferrer&quot;&gt;ISBN 0-8176-3462-2&lt;/a&gt;), he concluded that polyphasic sleep was more efficient than monophasic sleep.  Therefore it may be possible that polyphasic sleep patterns have no detrimental effect on development.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Individuals sleeping for 30 minutes every four hours, for a daily total of only 3 hours of sleep, performed better and were more alert, compared to when they had 3 hours of uninterrupted sleep&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;There are a couple of theories mentioned in the above book (beginning pg 5) which support the development of monophasic sleep as evolution rather than a social convention:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Polyphasic sleep is regularly seen in smaller mammals that have very high metabolic rates, requiring them to spend most of their time foraging or hunting.  Therefore a long sleep would be highly impractical for them as they would wake without the energy required to hunt their next meal. Humans do not have this need as they are larger and do not require such regular meals.&lt;/li&gt;&#xA;&lt;li&gt;Monophasic sleep would be beneficial for the early human hunter gatherer as our eyes are not well adapted to see at night.  Therefore any time spent not using the daylight is wasted and any time without the light is not nearly as useful.  This makes it more beneficial to sleep for an extended period when the sun is down.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;I am sure that social factors would have an effect, however I would imagine the evolutionary pressures to be more significant.&lt;/p&gt;&#xA;&lt;p&gt;I really would recommend the book (&lt;a href=&quot;http://sleepwarrior.com/Claudio_Stampi_-_Why_We_Nap.pdf&quot; rel=&quot;noreferrer&quot;&gt;http://sleepwarrior.com/Claudio_Stampi_-_Why_We_Nap.pdf&lt;/a&gt;) if you have not yet encountered it as I found it very informative and packed with references to studies that you may find helpful.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2011-12-27T19:02:56.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="368" PostTypeId="2" ParentId="363" CreationDate="2011-12-28T10:21:48.213" Score="10" Body="&lt;p&gt;&lt;strong&gt;Some assumptions made in the question&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an implicit assumption in your question which I don't think to be correct: you assume that &lt;strong&gt;any reaction&lt;/strong&gt; of the human organism to stress (let's substitute &quot;fright&quot; by &quot;stress&quot; in your question) is a physiological reaction, meaning that this reaction somehow helps the organism to overcome the stressful situation. From medical viewpoint the reaction to any external action can be:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;physiological one (i.e. the one that is expected and is considered &quot;good&quot;, helping the organism to adapt to this action).&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;pathophysiological:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;as a side-effect of physiological reaction&lt;/li&gt;&#xA;&lt;li&gt;as a result of nervous/humoral system overlast and depletion&lt;/li&gt;&#xA;&lt;li&gt;as a reaction to unknown action&lt;/li&gt;&#xA;&lt;li&gt;as a reaction to something mistaken for known action that is indeed something else&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Mechanisms of tremor.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From mechanical viewpoint our body consists of dozens joints that are absolutely not fixed and have from two (moving in one plane) to three (for free movement in 3D, for example coxofemoral joint), thus giving our extremities an incredibly high number of degrees of freedom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to sustain a certain posture our joints are equipped with antagonistic muscles: muscles that move the joint into opposite direction. The muscles, again, by design are very badly adapted for isotonic action. That basically means they cannot keep the same pressure for long time and the only way to get a fix posture for the whole body is to keep sending repetitive pulses to antagonistic muscles so that none of them actually wins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Normally the impulses are very short and frequent. They also have to come synchronously and out-of-phase, meaning that whenever one muscles contracts its antagonist should dilate and vise versa, so that no muscle rupture takes place because of the simultaneous contraction of two opposite muscles. This synchrony accounts for very subtle trembling of the body, almost not seen by a naked eye in healthy humans. This trembling is also called &lt;strong&gt;physiological tremor&lt;/strong&gt; to designate its being normal, e.g. physiological.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two ways how this trembling can increase so that it becomes visible and sensible:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Due to impaired synchronisation between the pulses sent to the antagonistic muscles.&lt;/strong&gt; Since these pulses are generated in brainstem nervous centers, the impairment of those (in case of Parkinson's desease) or some inhibiting input into them (as in case of cerebellar deseases) leads to desync of these pulses, the frequency goes down whereas the amplitude might increase, making the trembling visible.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Due to attenuated cell sensitivity to the incoming impulses&lt;/strong&gt;. This happens if the muscle cells start to overreact to the normal impulses and respond with prolonged contraction (followed by longer refractory period when they are unable to respond any impulse, thereby missing frequent pulses and reducing the effective frequency). These is mainly caused due to special metabolic changes within and in the vicinity of the muscle cells. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The most common metabolic change within the cell is either the increased Calcium concentration within muscle cells, leading to much stronger contraction, or increased sensitivity for Calcium (via Ca and ryanodin receptors), that leads to much abrupter Calcium concentration rise in cells and results in the same.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for Ca to increase within the cells might be the intake of some known Calcium liberators, like caffein, increased concentration of the humoral factors that use Ca as second messenger, like adrenaline, insuline, thyroid factors etc. Those, again, can be released during some stress conditions, during artificial or temporal low sugar level and other factors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Shivering as a reaction to stress.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The shivering, or in medical terms &lt;a href=&quot;http://en.wikipedia.org/wiki/Tremor&quot;&gt;tremor&lt;/a&gt; might appear due to &lt;a href=&quot;http://en.wikipedia.org/wiki/Stress_%28biological%29&quot;&gt;the following mechanisms&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Massive release of adrenaline during the stress: both directly via the adrenaline receptors and indirectly by causing temporal hyperglycemia via the metabolic adrenaline receptors. The action of adrenaline is also increased due to concomitant release of corticosteroids.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;(muss less probable in case of fright, however might be common in many other cases) Overlast of the hypothalamic/amygdalic/brainstem structures responsible for stress reaction with probable weakening of deep nuclei controls over the posture and muscle contraction.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Conclusion.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, as you see, the tremor is rather a pathophysiological reaction when it appears as response to stress, a side-effect manifestation due to acute temporal increase in adrenaline concentration in blood. Funny enough, but exactly this tremor is referenced to as &quot;physiological tremor&quot; in medical literature, because this type of tremor is not indicative for any CNS or endocrine disorder, that is very common for other types of tremor (postural, intentional etc.).&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="66" LastEditDate="2011-12-28T21:15:35.167" LastActivityDate="2011-12-28T21:15:35.167" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="369" PostTypeId="5" CreationDate="2011-12-28T13:13:37.877" Score="0" Body="&lt;p&gt;Often refers to &lt;a href=&quot;/questions/tagged/dna-methylation&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;dna-methylation&amp;#39;&quot; rel=&quot;tag&quot;&gt;dna-methylation&lt;/a&gt; at &lt;a href=&quot;/questions/tagged/cpg&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;cpg&amp;#39;&quot; rel=&quot;tag&quot;&gt;cpg&lt;/a&gt; sites.&lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="4101" LastEditDate="2013-10-31T01:01:27.707" LastActivityDate="2013-10-31T01:01:27.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="370" PostTypeId="4" CreationDate="2011-12-28T13:13:37.877" Score="0" Body="Mechanisms for inheriting phenotype outside of the genomic DNA sequence." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T01:01:27.707" LastActivityDate="2013-10-31T01:01:27.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="371" PostTypeId="1" AcceptedAnswerId="372" CreationDate="2011-12-28T15:36:29.557" Score="25" ViewCount="1666" Body="&lt;p&gt;Can anyone summarize the mechanism by which when an object of a given temperature is placed in contact with, say, the skin on a human fingertip, the average speed of the particles of the object is converted into nerve signals to the brain?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you can answer that, how about the format of how the temperature is encoded in the nerve signals?&lt;/p&gt;&#xA;" OwnerUserId="263" LastEditorUserId="4101" LastEditDate="2013-10-26T14:39:40.400" LastActivityDate="2013-10-26T14:39:40.400" Title="How is temperature sensed?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;temperature&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="372" PostTypeId="2" ParentId="371" CreationDate="2011-12-28T16:07:03.757" Score="31" Body="&lt;p&gt;In the periphery (e.g. on our fingertips), our body senses external temperature through nerve terminals, expressing certain &lt;a href=&quot;http://en.wikipedia.org/wiki/Transient_receptor_potential_channel&quot;&gt;TRP channels&lt;/a&gt;. These are ion channels that are sensitive to temperature (note that TRP channels can be sensitive to several things, such as pH, light, and stretch) and allow entrance of cations in the cell when the temperature is higher or lower than a certain threshold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Six TRP channels have been described as been involved in sensing different temperature ranges&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15362149&quot;&gt;1&lt;/a&gt;,&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21591901&quot;&gt;2&lt;/a&gt;&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;TRPV1 is activated at &gt;43 °C&lt;/li&gt;&#xA;&lt;li&gt;TRPV2 at &gt;52 °C &lt;/li&gt;&#xA;&lt;li&gt;TRPV3 at ~&gt; 34-38 °C &lt;/li&gt;&#xA;&lt;li&gt;TRPV4 at ~&gt; 27-35 °C&lt;/li&gt;&#xA;&lt;li&gt;TRPM8 at ~&amp;lt; 25-28 °C&lt;/li&gt;&#xA;&lt;li&gt;TRPA1 at ~&amp;lt; 17 °C&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Not surprisingly, TRPV1 and TRPV2 are also involved in nociception (=pain perception).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact molecular mechanisms by which different temperatures open different TRP channels are unclear, although some biophysical models have been proposed.&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16537823&quot;&gt;3&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure of the exact &quot;format&quot; in which sensory fibers encode different temperature, but I would assume that the neuron would fire faster the more the temperature is distant from the specific threshold (hot or cold).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15362149&quot;&gt;&lt;sup&gt;1&lt;/sup&gt; Thermosensation and pain.&lt;/a&gt; - J Neurobiol. 2004 Oct;61(1):3-12.&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21591901&quot;&gt;&lt;sup&gt;2&lt;/sup&gt; Sensing hot and cold with TRP channels.&lt;/a&gt; - Int J Hyperthermia. 2011;27(4):388-98.&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16537823&quot;&gt;&lt;sup&gt;3&lt;/sup&gt; - Thermal gating of TRP ion channels: food for thought?&lt;/a&gt; - Sci STKE. 2006 Mar 14;2006(326):pe12.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="1320" LastEditDate="2012-12-16T12:22:38.267" LastActivityDate="2012-12-16T12:22:38.267" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="373" PostTypeId="1" AcceptedAnswerId="509" CreationDate="2011-12-28T16:16:50.993" Score="11" ViewCount="719" Body="&lt;p&gt;It seems like Müllerian mimicry would be an example of mutualism because both species would end up being eaten less by predators that only have to learn one pattern of warning symbols. But to what extent is Batesian mimicry a form a parasitism? It seems like predators who ended up consuming the harmless species would lose some of their conditioning to not eat prey that resembled it, thus harming the species that is actually protected. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How often might this happen in ecosystems where Batesian mimicry is present? Does the presence of a similar unprotected species cause the protected species to be a more common target for predators?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mimicry#Batesian&quot;&gt;Difference between Batesian and Mullerian mimicry on wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="62" LastActivityDate="2012-01-05T23:15:24.580" Title="Is Batesian Mimicry a form a parasitism? To what extent is the species with real defenses harmed by the defenceless species?" Tags="&lt;parasitism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="374" PostTypeId="2" ParentId="163" CreationDate="2011-12-28T18:23:57.550" Score="12" Body="&lt;p&gt;Following up on Alexander's response, I read a little more on the subject by looking at some of the references in the Johnson et al. paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/107/17/7829.full&quot; rel=&quot;noreferrer&quot;&gt;This paper&lt;/a&gt;  discusses an interesting case where researchers could study a hydrothermal vent ecology before and after a catastrophic eruption giving a &quot;natural clearance&quot; experiment. Since endemic organisms were eradicated, any pioneer species must come from other vent systems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A number of species, in the form of larvae caught in larval traps, were observed to arrive at the vent. These species, including &lt;em&gt;Cyathermia naticoides&lt;/em&gt;, &lt;em&gt;Lepetodrilus spp&lt;/em&gt; and &lt;em&gt;Gorgoleptis spiralis&lt;/em&gt;, arrived at a significantly different (P &amp;lt; 0.05, MANOVA and ANOVA) rate to the pre-eruption larval source population rate. Larvae of one gastropod species, &lt;em&gt;Ctenopelta porifera&lt;/em&gt;, which had been seen only once pre-eruption, arrived in significant numbers post eruption. The source of these larvae may have been from a vent 300 km away.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These authors associate this change in the populations pre- and post-eruption with the specifics of the &lt;a href=&quot;http://mit.whoi.edu/page.do?pid=34429&amp;amp;tid=1423&amp;amp;cid=62180&quot; rel=&quot;noreferrer&quot;&gt;hydrodynamic transport processes&lt;/a&gt; operating in the region.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A more general sequence of vent re-population is &lt;a href=&quot;http://www.nature.com/news/2010/100519/full/465284a.html&quot; rel=&quot;noreferrer&quot;&gt;given&lt;/a&gt; in this article.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the interesting thing for me was the significant, but changing fluxes of larval species at these deep-sea vents.&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-09-17T12:23:32.533" LastActivityDate="2012-09-17T12:23:32.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="375" PostTypeId="1" CreationDate="2011-12-28T21:12:15.403" Score="11" ViewCount="572" Body="&lt;p&gt;In the context of a Gram stain on a blood smear:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are the following acceptable substitutions and/or what differences could arise by substituting them? &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Using methylene blue instead of crystal violet &lt;/li&gt;&#xA;&lt;li&gt;Using carbol fuchsin instead of safranine&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I've seen text implying they are OK substitutes, but didn't find anything saying the if, why, or problems associated with replacement.&lt;/p&gt;&#xA;" OwnerUserId="96" LastEditorDisplayName="user132" LastEditDate="2012-01-09T02:13:14.553" LastActivityDate="2012-04-03T01:37:03.543" Title="Are these Gram stain substitutions acceptable?" Tags="&lt;microbiology&gt;&lt;staining&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="376" PostTypeId="2" ParentId="345" CreationDate="2011-12-28T21:47:39.467" Score="22" Body="&lt;p&gt;There are several issues here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) &lt;strong&gt;Any mucous membrane is a specialized tissue for absorption.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mucous membranes are indeed not so good for passive diffusion, that makes them absolutely perfect tools for active absorption of certain substances, almost independently from the membrane type. To provide some examples: many drugs like cocaine are inhaled and absorbed in nasal cavities, whereas the rectum is also known and favorite delivery way for medicines. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally the absorption force of the mucous membrane is dependent upon how well it is vasculated, for after going through the basal membrane the substance directly enters the blood flow and quickly travels away, thus the concentration gradient on both sides of the basal membrane -- the main barrier in mucosa -- remains relatively high.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://dx.doi.org/10.1016/0378-5173%2895%2904120-6&quot; rel=&quot;noreferrer&quot;&gt; &lt;strong&gt;Bhat P&lt;/strong&gt;. 1995. The limiting role of mucus in drug absorption: Drug permeation through mucus solution&lt;/a&gt; for an experimental model for this statement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) &lt;strong&gt;Mouth mucosa can absorb many substances.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a special term called &quot;oral absorption&quot; to describe the rapid drug absorption into blood flow from the mouth cavity. The mucous membrane is not specialized here, but small molecules are able to permeate here through all barriers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) &lt;strong&gt;Advantages of oral absorption.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;The mucous membrane in the mouth cavity is very highly vascularized.&lt;/em&gt; The whole mouth can be seen as a bundle of skeletal muscles and every muscle requires a lot of energy and oxygen, therefore they have one of the highest vascularity rates, having much less distance between single capillaries.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Blood flow is higher in the mouth cavity walls than in other inner organs&lt;/em&gt;. This is mostly because muscle contractions (during chewing) lead to increased propulsion of blood through capillaries and small vessels here.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Any substance that enters blood flow here bypasses the hepatic-portal system&lt;/em&gt;. This means that the substance does not have to wait until it is filtered by our liver, it is immediately distributed through the whole body.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;There are special reflexes from oral mucosa to inner organs.&lt;/em&gt; Even not so important in case of aspirin, this is very important for some placebo drugs like methyl valerate (known as &quot;Validol&quot; in many countries) used a lot for treating &lt;em&gt;angina pectoris&lt;/em&gt; whose only action is to activate the cold receptors in mouth and thereby leading to reflectory dilating of cardiac vessels.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;This is why many drugs, like for example loperamid, are administered only as sub-lingual tablets. And this also explains why in emergency medicine many remedies are injected directly into the tongue.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="836" LastEditDate="2012-09-13T20:30:02.263" LastActivityDate="2012-09-13T20:30:02.263" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="377" PostTypeId="2" ParentId="371" CreationDate="2011-12-29T00:04:14.737" Score="14" Body="&lt;p&gt;To complement on nico's answer (I don't have enough rep to comment), TRP channels seems to be also sensitive to increment or decrement of temperature as reported recently in a paper by Gallio &lt;em&gt;et al&lt;/em&gt;&lt;sup&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867411000675&quot;&gt;1&lt;/a&gt;&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably that channels have incomplete adaptative behavior that make them sensitive both to increment and absolute temperature values.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867411000675&quot;&gt;Gallio M, Ofstad TA, Macpherson LJ, Wang JW, Zuker CS (2011).  &lt;strong&gt;The coding of temperature in the Drosophila brain&lt;/strong&gt;. Cell 144: 614-624.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="151" LastEditorUserId="151" LastEditDate="2011-12-29T00:11:17.283" LastActivityDate="2011-12-29T00:11:17.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="378" PostTypeId="1" AcceptedAnswerId="382" CreationDate="2011-12-29T00:36:43.933" Score="31" ViewCount="735" Body="&lt;p&gt;I am very interested in the evolution of the evolution process itself. There are of course a lot of things that influence how evolution will work, but for this question, I am interested in things that are only related to the evolution process. Examples could be increase chance of mutations in newborns, change in reproduction age, and similar. I am specifically interested in observation where the evolution process itself has adapted to a change in the environment.&lt;/p&gt;&#xA;" OwnerUserId="205" LastEditorUserId="3952" LastEditDate="2013-08-09T00:44:54.830" LastActivityDate="2015-12-07T05:52:43.133" Title="Has there been any observation of species adapting the evolution process?" Tags="&lt;evolution&gt;&lt;life-history&gt;" AnswerCount="8" CommentCount="3" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="379" PostTypeId="2" ParentId="378" CreationDate="2011-12-29T00:51:51.650" Score="14" Body="&lt;p&gt;I think this falls into your criteria but correct me if i'm wrong :).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/HIV&quot;&gt;HIV&lt;/a&gt; reverse transcriptase protein has evolved to have relatively low fidelity (leading to a high mutation rate in replicated virus particles).  Reverse transcriptase is also recombinogenic, ie. it can switch templates during replication leading to even more variability.  Combined, these two properties lead to each individual having a large number of variant viral genomes, which leads to increased resistance to antiretroviral drugs etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought of &lt;a href=&quot;http://en.wikipedia.org/wiki/Influenza&quot;&gt;influenza&lt;/a&gt; as a second example.  The viral genome has evolved to be fragmented into 7-8 pieces of RNA, which can be swapped with other strains during co-infection of a single cell.  This can lead to more virulent or transmissible strains of influenza; these can also be helpful to create new strains that influenza vaccines are no longer useful against.&lt;/p&gt;&#xA;" OwnerUserId="12" LastEditorUserId="12" LastEditDate="2011-12-29T16:15:02.590" LastActivityDate="2011-12-29T16:15:02.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="380" PostTypeId="2" ParentId="378" CreationDate="2011-12-29T05:19:00.370" Score="3" Body="&lt;p&gt;How about species actively changing the factors that play a role in the selection process?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans are a species that have heavily modified this process. In the western world, we have gone away from selection by survival skills and genetic fitness to move to a social selection, where genome is secondary to social skills and adaptation to fashion, which are acquired skills.&lt;/p&gt;&#xA;" OwnerUserId="264" LastActivityDate="2011-12-29T05:19:00.370" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="381" PostTypeId="1" AcceptedAnswerId="383" CreationDate="2011-12-29T08:41:00.390" Score="10" ViewCount="231" Body="&lt;p&gt;Let's say you accidentally walk into a room pressurized with pure nitrogen (or you're &lt;a href=&quot;http://www.geoffreylandis.com/vacuum.html&quot;&gt;jettisoned into space&lt;/a&gt;). Within a couple of seconds, the partial pressure of oxygen within your lungs drops to 0. But there's still a (small?) reserve within your bloodstream.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, will the oxygenated blood travel to your lungs? If so, will the usual gas exchange reverse, with oxygen going &lt;em&gt;from&lt;/em&gt; your blood &lt;em&gt;to&lt;/em&gt; the oxygen-poor environment?&lt;/p&gt;&#xA;" OwnerUserId="265" LastActivityDate="2011-12-29T13:11:45.217" Title="Can oxygen diffuse out through the lungs?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;organs&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="382" PostTypeId="2" ParentId="378" CreationDate="2011-12-29T08:56:54.077" Score="33" Body="&lt;p&gt;Bacteria such as E. coli are known to increase their mutation rate (by switching to a more error prone polymerase among other things) when under stress. This can mean being placed in a medium where it's not adapted to grow (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088971/?tool=pmcentrez&quot;&gt;http://www.micab.umn.edu/courses/8002/Rosenberg.pdf&lt;/a&gt;) or when treated with antibiotics (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088971/?tool=pmcentrez&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088971/?tool=pmcentrez&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="9" LastActivityDate="2011-12-29T08:56:54.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="383" PostTypeId="2" ParentId="381" CreationDate="2011-12-29T13:11:45.217" Score="5" Body="&lt;p&gt;Yes.  Blood will continue to circulate (as long as you're alive and your heart is beating), so will eventually come in contact with your lungs.  Once there, the gasses (O2, CO2) will cross out into the lung and be exhaled.  All diffusion is driven down a concentration gradient.&lt;/p&gt;&#xA;" OwnerUserId="219" LastActivityDate="2011-12-29T13:11:45.217" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="384" PostTypeId="2" ParentId="378" CreationDate="2011-12-29T17:03:23.903" Score="15" Body="&lt;p&gt;The &quot;change in reproduction age&quot; you mention is one major aspect of life history evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A massive literature exists on this topic, including several books: e.g., &lt;em&gt;The evolution of life histories: Theory and analysis&lt;/em&gt; (Roff, 1992) and &lt;em&gt;The evolution of life histories&lt;/em&gt; (Stearns, 1992).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reznick and various colleagues have carried out extensive studies of experimental life history evolution in Trinidadian guppies going back ~30 years. For example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jstor.org/stable/10.2307/2407978&quot;&gt;Reznick, D.N. and Endler, J.A. 1982. The impact of predation on life history evolution in Trindadian guppies (&lt;em&gt;Poecilia reticulata&lt;/em&gt;). &lt;em&gt;Evolution&lt;/em&gt; 36:160-177&lt;/a&gt;. &lt;/li&gt;&#xA;&lt;li&gt;Reznick, D.N. and Bryga, H. 1987. Life-history evolution in guppies. 1. Phenotypic and genotypic changes in an introduction experiment.  &lt;em&gt;Evolution&lt;/em&gt; 41:1370-1385.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jstor.org/stable/10.2307/2409363&quot;&gt;Reznick, D.N. 1989. Life history evolution in guppies. 2. Repeatability of field observations and the effects of season on life histories. &lt;em&gt;Evolution&lt;/em&gt; 43:1285-1297&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencemag.org/content/275/5308/1934.short&quot;&gt;Reznick, D.N., Shaw, F.H., Rodd, F.H. and Shaw, R.G. 1997. Evaluation of the rate of evolution in natural populations of guppies (&lt;em&gt;Poecilia reticulata&lt;/em&gt;).  &lt;em&gt;Science&lt;/em&gt; 275: 1934-1937&lt;/a&gt;. &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9193894&quot;&gt;Reznick, D.N. 1997. Life history evolution in guppies (&lt;em&gt;Poecilia reticulata&lt;/em&gt;): guppies as a model for studying the evolutionary biology of aging. &lt;em&gt;Experimental Gerontology&lt;/em&gt; 32:245-258.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Life history evolution has also been documented in response to human pressures. Fisheries stocks are evolving in response to overfishing. For example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;ved=0CCgQFjAB&amp;amp;url=http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2005.00858.x/abstract&amp;amp;ei=tpv8TtzDEI6-gAfb69CbAg&amp;amp;usg=AFQjCNFioK4lBCfYb81DnmlPW2g_QDShKg&amp;amp;sig2=HCg_ywYhaZ04tFYMhg156Q&quot;&gt;Walsh, M.R., Munch, S.B., Chiba, S. and Conover, D.O. 2006. Maladaptive changes in multiple traits caused by fishing: impediments to population recovery. &lt;em&gt;Ecology Letters&lt;/em&gt; 9:142-148&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;ved=0CB8QFjAA&amp;amp;url=http://www.somas.stonybrook.edu/people/munchpdf/conover_etal_05_cjfas.pdf&amp;amp;ei=9Jv8To20F8jBgAe26uGdAg&amp;amp;usg=AFQjCNGCeA8otCOCiD89gsmDB3fV_ah3_Q&amp;amp;sig2=ypfDhTxkVQ2Oq6lPfkb70g&quot;&gt;Conover, D.O., Arnott, S.A., Walsh, M.R. and Munch, S.B.. 2005. Darwinian Fishery Science: lessons from the Atlantic silverside. &lt;em&gt;Canadian Journal of Fisheries and Aquatic Science&lt;/em&gt; 62:730-737&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="107" LastActivityDate="2011-12-29T17:03:23.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="385" PostTypeId="1" CreationDate="2011-12-29T17:40:18.430" Score="15" ViewCount="846" Body="&lt;p&gt;I have looked at every single Wikimedia commons photo in the category 'scanning electron microscope'. Unfortunately, I could not find any other repositories of such photos, but I would readily look at every single photograph there as well. It strikes me that such repositories are also bound to be useful to biologists and biology students. A simple Google search did not yield much. Can anyone help out?&lt;/p&gt;&#xA;" OwnerUserId="250" LastEditorUserId="69" LastEditDate="2012-08-03T22:39:45.043" LastActivityDate="2012-08-03T22:39:45.043" Title="Online repositories of scanning electron microscope photographs?" Tags="&lt;microscopy&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="386" PostTypeId="2" ParentId="385" CreationDate="2011-12-29T18:58:19.983" Score="10" Body="&lt;p&gt;David Orloff's &lt;a href=&quot;http://www.cellimagelibrary.org/&quot;&gt;The Cell – an Image Library&lt;/a&gt; has &lt;a href=&quot;http://www.cellimagelibrary.org/images?advanced_search=Advanced+Search&amp;amp;image_search_parms%5Bbiological_process%5D=&amp;amp;image_search_parms%5Bcell_line%5D=&amp;amp;image_search_parms%5Bcell_type%5D=&amp;amp;image_search_parms%5Bcellular_component%5D=&amp;amp;image_search_parms%5Bfoundational_model_anatomy%5D=&amp;amp;image_search_parms%5Bhuman_dev_anatomy%5D=&amp;amp;image_search_parms%5Bhuman_disease%5D=&amp;amp;image_search_parms%5Bidentity_bim%5D=&amp;amp;image_search_parms%5Bimage_mode_bim%5D=scanning+electron+microscopy+%28SEM%29&amp;amp;image_search_parms%5Bitem_type_bim%5D=&amp;amp;image_search_parms%5Bmolecular_function%5D=&amp;amp;image_search_parms%5Bmouse_gross_anatomy%5D=&amp;amp;image_search_parms%5Bmouse_pathology%5D=&amp;amp;image_search_parms%5Bncbi%5D=&amp;amp;image_search_parms%5Bparameter_imaged_bim%5D=&amp;amp;image_search_parms%5Bplant_growth%5D=&amp;amp;image_search_parms%5Bpreparation_bim%5D=&amp;amp;image_search_parms%5Bprocessing_history_bim%5D=&amp;amp;image_search_parms%5Brelation_to_intact_cell_bim%5D=&amp;amp;image_search_parms%5Bsource_of_contrast_bim%5D=&amp;amp;image_search_parms%5Bteleost_anatomy%5D=&amp;amp;image_search_parms%5Bvisualization_methods_bim%5D=&amp;amp;image_search_parms%5Bxenopus_anatomy%5D=&amp;amp;image_search_parms%5Bzebrafish_anatomy%5D=&amp;amp;k=&amp;amp;page=1&quot;&gt;thousands of SEM images&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="23" LastActivityDate="2011-12-29T18:58:19.983" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="387" PostTypeId="2" ParentId="385" CreationDate="2011-12-29T19:14:51.367" Score="12" Body="&lt;p&gt;First off I'd like to reccomend the University of Dartmouth's publicly available collection located &lt;a href=&quot;http://remf.dartmouth.edu/images/&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;.  They have both SEM and TEM images of a wide range of organisms and cells from algae to see urchins through everything from cholera to mammalian cells.  Images are high quality, fully captioned and properly attributed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm a little confused as to the problem you're having with google - see my original comment on your question.  However I have looked at the photos of Wikimedia Commons in the SEM category and see that they are either images taken with, images of SEM Microscopes or technical drawings regarding their function.  I assume that you're looking for the images taken with SEM.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was able to find a great number of similar images to those in the commons with a Google Image search - I read above that you were having problems with this approach so perhaps try the search term &quot;&lt;a href=&quot;http://www.google.co.uk/search?rls=en&amp;amp;q=SEM%20images&amp;amp;oe=UTF-8&amp;amp;redir_esc=&amp;amp;um=1&amp;amp;ie=UTF-8&amp;amp;hl=en&amp;amp;tbm=isch&amp;amp;source=og&amp;amp;sa=N&amp;amp;tab=wi&amp;amp;ei=M7j8TsS6I4OO8gPNkOjgAg&amp;amp;biw=1440&amp;amp;bih=728&amp;amp;sei=Nbj8ToPlFsnh8AOn-KnBAQ&quot; rel=&quot;noreferrer&quot;&gt;SEM images&lt;/a&gt;&quot; in image search (or &lt;a href=&quot;http://www.google.co.uk/search?q=SEM%20images%20-wikimedia&amp;amp;hl=en&amp;amp;safe=off&amp;amp;client=safari&amp;amp;rls=en&amp;amp;prmd=imvns&amp;amp;tbm=isch&amp;amp;tbo=u&amp;amp;source=univ&amp;amp;sa=X&amp;amp;ei=k7r8TumaLMLJ8gPKssXUAQ&amp;amp;ved=0CCEQsAQ&amp;amp;biw=1440&amp;amp;bih=728&quot; rel=&quot;noreferrer&quot;&gt;this search&lt;/a&gt; to avoid duplications from images you have already seen on Wiki Commons)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples found on just the first page:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/xLYZT.jpg&quot; alt=&quot;Mushroom Spores (Uni. Dartmouth &quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/NkVJ5.jpg&quot; alt=&quot;Ash Grain (USGS) - not biological but interesting nonetheless&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2011-12-29T19:14:51.367" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="388" PostTypeId="1" AcceptedAnswerId="398" CreationDate="2011-12-29T20:30:53.743" Score="16" ViewCount="28581" Body="&lt;p&gt;I'm struggling to find peer reviewed literature that explains the effect of changing the pH and the salt concentration on protein/protein complexes in solution. What effect does the pH and the salt concentration have and what is the physical basis behind this? &lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="62" LastEditDate="2012-01-03T19:51:16.887" LastActivityDate="2012-10-17T18:38:38.040" Title="What effect has changing pH and salt concentration on protein complexes?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="389" PostTypeId="2" ParentId="101" CreationDate="2011-12-29T21:25:07.847" Score="3" Body="&lt;p&gt;I don't think you should need to vary the concentration of the GelRed.  Mine came with instructions for the exact concentration and how to dilute.  Optionally salt can be added, which I did, and it has worked for me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have only done this with Post-staining.  1-2.5% agarose with TAE.  Used a 10,000x solution from Phenix research. The gelred stock and working solution needs to kept in the dark.  I am assuming you have a transilluminator and (optional) filters to visual though. GelRed has similar excitation and emission [wavelength] properties as EtBr, so a standard transilluminator and filter should work without any changes.  It will not be visible with the naked eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said there are a ton of things that can go wrong in casting the gel, eletrophoresis, staining, and visualization.  If bands are visible but just blurry I was suspect there is more of a problem with either the gel creation or eletrophoresis though. Make sure agarose is completely clear and cooled down a little before pouring. Otherwise voltage is one of the main things I have noticed that can have significant affects on how sharp or blurry bands appear.  You might try different % gels and different voltages.  There are formulas that can help you estimate the best value for each of those.&lt;/p&gt;&#xA;" OwnerUserId="96" LastActivityDate="2011-12-29T21:25:07.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="390" PostTypeId="2" ParentId="378" CreationDate="2011-12-29T22:46:22.150" Score="8" Body="&lt;p&gt;Species have been observed in controlled experiments to use different sources of energy, for instance axenic &lt;em&gt;E. coli&lt;/em&gt; cultures picking up citrate metabolism in &lt;a href=&quot;http://myxo.css.msu.edu/ecoli/&quot;&gt;Lenski's Lab at MSU&lt;/a&gt;.  They have also shown that mutations to the mutator gene mutT can accelerate the process of evolution, though it's evolution directed by fitness in a very specific setting.&lt;/p&gt;&#xA;" OwnerUserId="25" LastActivityDate="2011-12-29T22:46:22.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="391" PostTypeId="1" AcceptedAnswerId="392" CreationDate="2011-12-30T10:26:00.303" Score="13" ViewCount="1432" Body="&lt;p&gt;In most of the genome CpG sites are pretty much always methylated, but CpG islands are instead often unmethylated. This has been linked to the fact that they often are associated to transcripted genes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the current theories on the mechanisms involved in this preferential demethylation? &lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-09-13T21:25:10.187" Title="How do CpG islands remain unmethylated?" Tags="&lt;dna&gt;&lt;epigenetics&gt;&lt;transcription&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="392" PostTypeId="2" ParentId="391" CreationDate="2011-12-30T11:47:04.720" Score="11" Body="&lt;p&gt;Methylation is increasingly seen as a consequence of gene activity rather than a regulatory mechanism. There are cases where methylation is controlled &lt;em&gt;because&lt;/em&gt; of gene regulatory control, especially at the famous H19/Igf2 locus&lt;sup&gt;[&lt;a href=&quot;http://dx.doi.org/10.1042/BJ20111417&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]&lt;/sup&gt;. Here is a generally good recent review&lt;sup&gt;[&lt;a href=&quot;http://dx.doi.org/10.1101/gad.2037511&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]&lt;/sup&gt;, note they mention that DNA methylation does not cause transcriptional silencing, and likely methylated promoters are probably &lt;em&gt;more&lt;/em&gt; active than unmethylated, they just create silencing RNAs when methylated (resulting in an apparent silencing).  This may help explain some of the story&lt;sup&gt;[&lt;a href=&quot;http://dx.doi.org/10.1101/gad.11.18.2383&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;]&lt;/sup&gt;, but note how old that paper is, yet generally I'd say few people know of its existance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exception seems to be transposable elements&lt;sup&gt;[&lt;a href=&quot;http://dx.doi.org/10.1038/nature02886&quot; rel=&quot;nofollow&quot;&gt;4&lt;/a&gt;]&lt;/sup&gt;, but their control is probably also controlled by silencing RNAs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1042/BJ20111417&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Zampieri M, Guastafierro T, Calabrese R, Ciccarone F, Bacalini MG, Reale A, Perilli M, Passananti C, Caiafa P&lt;/strong&gt;. 2012. ADP-ribose polymers localized on Ctcf-Parp1-Dnmt1 complex prevent methylation of Ctcf target sites. The Biochemical journal 441: 645–52.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1101/gad.2037511&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Deaton AM, Bird A&lt;/strong&gt;. 2011. CpG islands and the regulation of transcription. Genes &amp;amp; development 25: 1010–22.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1101/gad.11.18.2383&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Rountree MR, Selker EU&lt;/strong&gt;. 1997. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes &amp;amp; Development 11: 2383–2395.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nature02886&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Bourc’his D, Bestor TH&lt;/strong&gt;. 2004. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431: 96–9.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="219" LastEditorUserId="836" LastEditDate="2012-09-13T21:25:10.187" LastActivityDate="2012-09-13T21:25:10.187" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="393" PostTypeId="1" AcceptedAnswerId="395" CreationDate="2011-12-30T13:57:32.017" Score="5" ViewCount="1113" Body="&lt;p&gt;Forgive me if my question does not belong here or if I'm using incorrect terms, but I'm not educated in biology at all. I'm investigating the workings of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_classification&quot; rel=&quot;nofollow&quot;&gt;biological classification system&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering if there is a list somewhere of all kingdoms, orders, classes, etc., both in Latin and common names?&lt;/p&gt;&#xA;" OwnerUserId="50" LastEditorDisplayName="user132" LastEditDate="2012-01-04T04:43:22.613" LastActivityDate="2012-03-07T09:11:18.407" Title="Where can I find the common names for the zoology taxonomy?" Tags="&lt;zoology&gt;&lt;taxonomy&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="394" PostTypeId="2" ParentId="393" CreationDate="2011-12-30T14:41:37.243" Score="3" Body="&lt;h1&gt;Kingdoms&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;The UK accepted system has five kingdoms, for some it's hard to describe a single word common name so I hope you don't mind that I have written brief summaries too:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Animalia&lt;/strong&gt; are multi-cellular organisms that have adaptations to allow them to move within their environment.  They have membrane bound organelle but not cell walls or chloroplasts. They must absorb nutrients by ingestion.  &lt;strong&gt;Common name is animals&lt;/strong&gt; ;-)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Plantae&lt;/strong&gt; are multi-cellular organisms that use photosynthesis to harness energy from sunlight.  Their cells contain cell walls &amp;amp; chloroplasts (where cells are exposed to the sun).  &lt;strong&gt;Common name is plants&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Fungi&lt;/strong&gt; are multi-cellular organisms with no adaptations to move independently.  They range in size from microscopic to the size of mushrooms (literally, of course).  They absorb their nutrients from their surroundings.  &lt;strong&gt;Common name could be mushrooms &amp;amp; molds&lt;/strong&gt;  &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Protista&lt;/strong&gt; are marine organisms that are eukaryotoic (have membrane bound organelles) and some can photosynthesise.  &lt;strong&gt;Common name &lt;em&gt;could be&lt;/em&gt; algae&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Prokaryota&lt;/strong&gt; (&lt;em&gt;a.k.a. Moneara&lt;/em&gt;) are single celled, with a cell wall but with no membrane bound organelles (i.e. they have no smaller 'bits' within the cell separated by a membrane).  They absorb nutrients directly across their membranes or can photosynthesise to make their own nutrients.  &lt;strong&gt;Common name &lt;em&gt;could be&lt;/em&gt; said to be Bacteria&lt;/strong&gt;.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Sources: &lt;a href=&quot;http://www.ruf.rice.edu/~bioslabs/studies/invertebrates/kingdoms.html&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;http://www.williamsclass.com/SixthScienceWork/Classification/ClassificationNotes/ClassificationNotes.htm&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;, &lt;a href=&quot;http://biology.clc.uc.edu/courses/bio106/protista.htm&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt; (for Protista)&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Phyla and Below&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;You may wish to try the following website:&#xA;&lt;a href=&quot;http://www.itis.gov/index.html&quot; rel=&quot;nofollow&quot;&gt;ITIS Database&lt;/a&gt; - enter a scientific or common name of an organism to get it's full taxonomic tree.  For example the tree for the &lt;em&gt;&lt;a href=&quot;http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&amp;amp;search_value=183803&quot; rel=&quot;nofollow&quot;&gt;Panthera leo&lt;/a&gt;&lt;/em&gt; (Lion).  This site also gives common names of Phylum, Class, Order &amp;amp; Genus - for example the lion is a member of genus Panthera (&quot;roaring cats&quot;). It may be slightly cumbersome but it is a way to get the info you want and is actually quite interesting once you get going, particularly if its just for your curiosity!&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Additions after comments by OP&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Have been hard at work, however it seems that a centralised repository is certainly elusive!  I've found some sites which go &lt;em&gt;a little&lt;/em&gt; of the way to amalgamating scientific and common names on a single page but I'm doubtful that you will be able to get much further than Phylum without having to write a script to harvest data from sites such as ITIS&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.earthlife.net/inverts/an-phyla.html&quot; rel=&quot;nofollow&quot;&gt;List of all Phyla for the Animalia Kingdom with common names&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.solpugid.com/cabiota/plants.htm&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;As above&lt;/em&gt; for Kingdom Plantae&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.backyardnature.net/f/funclass.htm&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;As above&lt;/em&gt; for Kingdom Fungi&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://biology.clc.uc.edu/courses/bio106/protista.htm&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;As above&lt;/em&gt; for Kingdom Protista&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2011-12-31T16:22:33.770" LastActivityDate="2011-12-31T16:22:33.770" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="395" PostTypeId="2" ParentId="393" CreationDate="2011-12-30T14:47:12.367" Score="9" Body="&lt;p&gt;The &lt;a href=&quot;http://tolweb.org/tree/&quot;&gt;Tree of Life&lt;/a&gt; project has a browse-able tree of all major taxa, but not necessarily all species. You can start at the &lt;a href=&quot;http://tolweb.org/Life_on_Earth/1&quot;&gt;root of the tree here&lt;/a&gt;. Tree of life uses modern &lt;a href=&quot;http://en.wikipedia.org/wiki/Phylogenetic_nomenclature&quot;&gt;phylogenetic nomenclature&lt;/a&gt; rather than more traditional Kingdom-Phylum-Class-etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Part of the problem that you will run into is that common names differ across regions/countries/languages. This is the point of species binomials. They are language-invariant.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2011-12-30T15:04:21.980" LastActivityDate="2011-12-30T15:04:21.980" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="396" PostTypeId="2" ParentId="304" CreationDate="2011-12-30T17:37:07.607" Score="13" Body="&lt;p&gt;To answer your question directly, there are a number of examples which creationists like to bring up, such as woodpecker's tongue which is wrapped around its brain or the archer fish which shoots down insects with water and has to adjust it's aim for refractive difference between water and air. These features supposedly 'couldn't have evolved' but of course one's disbelief doesn't make anything true or untrue. This is what Dawkins calls 'argument from personal incredulity'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me also point out a few evolutionary counter arguments to such reasoning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The presence of selection radically changes what is 'likely' or 'possible' to happen. For example, you wouldn't argue that it's highly improbable that the stones on the beach are ordered by size, if you know that the action of waves orders them in a certain way. Dawkins' weasel (&lt;a href=&quot;http://en.wikipedia.org/wiki/Weasel_program&quot;&gt;http://en.wikipedia.org/wiki/Weasel_program&lt;/a&gt;) also demonstrates this principle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another Dawkins' argument is that, contrary to what creationists claim, complex features such as eye don't have to be completely functional to be useful. In the early history of life, when no organism had eyes, any simple system which could distinguish light from darkness could provide a huge advantage to its owner. The simple system can then evolve to a more complex one to provide a competitive edge etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, evolution happens over time scales we cannot grasp. We don't have a good feeling of what billions of years of small changes which are selected for can add up to.&lt;/p&gt;&#xA;" OwnerUserId="9" LastActivityDate="2011-12-30T17:37:07.607" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="397" PostTypeId="2" ParentId="304" CreationDate="2011-12-30T21:45:28.687" Score="9" Body="&lt;p&gt;I won't claim that these are &lt;em&gt;the most difficult&lt;/em&gt; things to explain evolutionarily, but these two are hard:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Host-Pathogen dynamics. They start out easy enough, but the interaction between a pathogen and its host is intensely complex. You have the immune system, pathogen-pathogen interaction, the balance between weakening a host and killing a host, dozens of different transmission mechanisms, &lt;em&gt;at least&lt;/em&gt; two levels of evolutionary pressure (inter-host and population), etc.&lt;/li&gt;&#xA;&lt;li&gt;Social/Societal level traits. Evolutionary psychology has, for example, been criticized for not being able to get much past the level of &quot;Just So Stories&quot; in terms of its ability to explain human societal traits using evolutionary theory.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="67" LastEditorUserId="750" LastEditDate="2012-05-06T20:41:05.423" LastActivityDate="2012-05-06T20:41:05.423" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="398" PostTypeId="2" ParentId="388" CreationDate="2011-12-31T01:40:19.800" Score="14" Body="&lt;p&gt;The formation of protein complexes or aggregates in aqueous buffers is determined by a number of factors: physical properties of the protein itself, pH, temperature, type and concentration of the used cosolvent (salt). Solutes are often roughly divided by type into &lt;strong&gt;chaotropes&lt;/strong&gt; ('disorder-making'), which destabilise protein structures and &lt;strong&gt;kosmotropes&lt;/strong&gt; ('order-making'), which stabilize them. [&lt;a href=&quot;http://www.lsbu.ac.uk/water/kosmos.html&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19994836&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chaotropic salts interfere with intramolecular interactions mediated by non-covalent forces such as hydrogen bonds, van der Waals forces, and hydrophobic interactions, which, at high cosolvent concentrations, results in protein denaturation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kosmotropic salts, on the other hand, cause water molecules to favorably interact, which also stabilizes intermolecular interactions in proteins. The salt molecules readily interact with water from the protein's hydratation shell and remove it from the protein surface, which produces thermodynamically unfavourable interactions that are reduced when proteins associate to form complexes. With increase in salt concentration the protein precipitation (salting out) increases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both cations and anions have been ranked separately by their capacity to precipitate proteins, to form a &lt;strong&gt;Hofmeister series&lt;/strong&gt; [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15306378&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16821951&quot; rel=&quot;nofollow&quot;&gt;4&lt;/a&gt;] (first set in 1888 but still hotly debated), e.g.:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;SO&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;2−&lt;/sup&gt; &gt; H&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;−&lt;/sup&gt; &gt; CH&lt;sub&gt;3&lt;/sub&gt;COO&lt;sup&gt;−&lt;/sup&gt; &gt; Cl&lt;sup&gt;−&lt;/sup&gt; &gt; Br&lt;sup&gt;−&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At large salt concentrations protein solubility is given by the empirical &lt;strong&gt;Cohn equation&lt;/strong&gt; [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16814736&quot; rel=&quot;nofollow&quot;&gt;6&lt;/a&gt;]:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;lnS = α − βc&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where &lt;code&gt;S&lt;/code&gt; is the protein solubility, &lt;code&gt;c&lt;/code&gt; is the salt's ionic strength, &lt;code&gt;α&lt;/code&gt; and &lt;code&gt;β&lt;/code&gt; are empirical constants characteristic of particular salt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Salting-out agents are very widely used in protein purification (to concentrate proteins eg. with ammonium sulfate), chromatography or crystalization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The influence of pH&lt;/strong&gt; on protein-protein interactions in solution works through altering of the electrostatic properties of protein surfaces. At pH equal to the protein's isoelectric point (pI), where its net charge is neutral, charge repulsions of similar molecules are relatively low and many proteins will aggregate. Very low and very high pH will case proteins to denature; during digestion, for instance, proteins are in extremely low and then extremly high pH that exposes their backbones for enzymatic degradation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information, please refer to:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.lsbu.ac.uk/water/kosmos.html&quot; rel=&quot;nofollow&quot;&gt;Martin Chaplin, &lt;em&gt;Kosmotropes and Chaotropes&lt;/em&gt;, http://www.lsbu.ac.uk/water/kosmos.html&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19994836&quot; rel=&quot;nofollow&quot;&gt;Zangi R. &lt;em&gt;Can salting-in/salting-out ions be classified as chaotropes/kosmotropes?&lt;/em&gt; J Phys Chem B. 2010 Jan 14;114(1):643-50.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15306378&quot; rel=&quot;nofollow&quot;&gt;Pace CN, Treviño S, Prabhakaran E, Scholtz JM. &lt;em&gt;Protein structure, stability and solubility in water and other solvents&lt;/em&gt;. Philos Trans R Soc Lond B Biol Sci. 2004 Aug 29;359(1448):1225-34; discussion 1234-5.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16821951&quot; rel=&quot;nofollow&quot;&gt;Shimizu S, McLaren WM, Matubayasi N. &lt;em&gt;The Hofmeister series and protein-salt interactions&lt;/em&gt;. J Chem Phys. 2006 Jun 21;124(23):234905.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17035073&quot; rel=&quot;nofollow&quot;&gt;Zhang Y, Cremer PS. &lt;em&gt;Interactions between macromolecules and ions: The Hofmeister series&lt;/em&gt;. Curr Opin Chem Biol. 2006 Dec;10(6):658-63. Epub 2006 Oct 10.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16814736&quot; rel=&quot;nofollow&quot;&gt;Ruckenstein E, Shulgin IL. &lt;em&gt;Effect of salts and organic additives on the solubility of proteins in aqueous solutions&lt;/em&gt;. Adv Colloid Interface Sci. 2006 Nov 16;123-126:97-103. Epub 2006 Jun 30.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="277" LastEditorUserId="3632" LastEditDate="2012-10-17T18:38:38.040" LastActivityDate="2012-10-17T18:38:38.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="399" PostTypeId="1" AcceptedAnswerId="400" CreationDate="2011-12-31T05:57:12.643" Score="12" ViewCount="323" Body="&lt;p&gt;&lt;a href=&quot;http://rnajournal.cshlp.org/content/early/2006/12/12/rna.257607.full.pdf+html&quot;&gt;I just came across this abstract&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Aminoacyl-tRNA synthetases (aaRSs) are responsible for creating the pool of correctly charged aminoacyl-tRNAs that are&#xA;  necessary for the translation of genetic information (mRNA) by the ribosome. Each aaRS belongs to either one of only two&#xA;  classes with two different mechanisms of aminoacylation, making use of either the 29OH (Class I) or the 39OH (Class II) of the&#xA;  terminal A76 of the tRNA and approaching the tRNA either from the minor groove (29OH) or the major groove (39OH). Here,&#xA;  an asymmetric pattern typical of differentiation is uncovered in the partition of the codon repertoire, as defined by the&#xA;  mechanism of aminoacylation of each corresponding tRNA. This pattern can be reproduced in a unique cascade of successive&#xA;  binary decisions that progressively reduces codon ambiguity. The deduced order of differentiation is manifestly driven by the&#xA;  reduction of translation errors. A simple rule can be defined, decoding each codon sequence in its binary class, thereby&#xA;  providing both the code and the key to decode it. Assuming that the partition into two mechanisms of tRNA aminoacylation is&#xA;  a relic that dates back to the invention of the genetic code in the RNA World, a model for the assignment of amino acids in the&#xA;  codon table can be derived. The model implies that the stop codon was always there, as the codon whose tRNA cannot be&#xA;  charged with any amino acid, and makes the prediction of an ultimate differentiation step, which is found to correspond to the&#xA;  codon assignment of the 22nd amino acid pyrrolysine in archaebacteria.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Granted, this is a few years old, but I often find myself having to admit that &quot;I don't know&quot; when at the root of discussions on evolution.  That is, once abiogenesis has occurred, we can go on and explain the rich diversity of life, but sadly we really don't know much before that critical step.  Generally, those satisfied with &quot;magic&quot; as an answer posit their myths and fables, whereas I'd rather try to actually find out what happened.  Sadly, as the abstract shows, you actually need a level of education to understand papers such as this that is generally well beyond those who would deny the reality of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have a collection of papers on abiogenesis that are more accessible and understandable to laypeople?&lt;/p&gt;&#xA;" OwnerUserId="279" LastEditorUserId="279" LastEditDate="2012-01-16T01:01:30.053" LastActivityDate="2012-01-16T01:01:30.053" Title="Abiogenesis: Beyond the research journals as a lead in to discussions on evolution" Tags="&lt;evolution&gt;&lt;dna&gt;&lt;abiogenesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="400" PostTypeId="2" ParentId="399" CreationDate="2011-12-31T11:53:37.203" Score="13" Body="&lt;p&gt;The fascinating field of abiogenesis is, as Nick Lane put it, &quot;a wild west of ideas, theories, speculations, and even data&quot;. The stories we have involve a plethora of assumptions, there is no hypothesis where &lt;em&gt;all or most of the pieces&lt;/em&gt; would fit together. Usually scientists agree it was &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_world&quot;&gt;RNA&lt;/a&gt; that played central role in the process, as the molecule could both carry the genetic code, necessary for hereditary natural selection, and catalyze basic biochemical reactions. Where the energy came from and how it was harnessed to maintain RNA (a rather unstable molecule) and perform work is still debated. A fermentation in a 'primordial soup' or a primitive form of respiration, perhaps through a thin iron-sulphur membrane, have been proposed as possibilities. The second gave a start to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Iron%E2%80%93sulfur_world_theory&quot;&gt;iron-sulphur world&lt;/a&gt; hypothesis. Iron-sulphur minerals could catalyse the first organic reactions to synthetize sugars, amino-acids and nucleotides, and eventually RNA world, where natural selection could take over. Theories abound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually reviews will give you a sound and approachable picture of the current thought on the matter. Take a look into Nick Lane's book and these articles, too.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0192804812&quot;&gt;Lane N., &lt;em&gt;Origin of Life&lt;/em&gt; in: &lt;em&gt;Power, Sex, Suicide: Mitochondria and the Meaning of Life&lt;/em&gt;. Oxford University Press, 2005. p. 94-104.&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.americanscientist.org/issues/feature/first-life&quot;&gt;Russell, Michael (2006). &lt;em&gt;First Life&lt;/em&gt;. American Scientist 94 (1):32.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/news/2009/090513/full/news.2009.471.html&quot;&gt;Van Noorden R., &lt;em&gt;RNA world easier to make - Ingenious chemistry shows how nucleotides may have formed in the primordial soup&lt;/em&gt;. Nature 2009&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/news/2009/090108/full/news.2009.5.html&quot;&gt;Check Hayden E. &lt;em&gt;A never-ending dance of RNA - The recreation of life's origins comes a self-catalysing step closer.&lt;/em&gt; Nature 2009.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1989/cech-article.html&quot;&gt;Cech TR. Exploring the New RNA World. Nobel Prize articles&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16649141&quot;&gt;Müller UF. &lt;em&gt;Re-creating an RNA world&lt;/em&gt;. Cell Mol Life Sci. 2006 Jun;63(11):1278-93.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8681375&quot;&gt;Lazcano A, Miller SL. The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time. Cell. 1996 Jun 14;85(6):793-8.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="277" LastActivityDate="2011-12-31T11:53:37.203" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="401" PostTypeId="1" AcceptedAnswerId="402" CreationDate="2011-12-31T16:21:58.943" Score="74" ViewCount="53017" Body="&lt;p&gt;Why do most mammals produce their own Vitamin C?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do Humans not?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="69" LastEditDate="2012-06-16T11:15:39.477" LastActivityDate="2014-06-06T20:02:28.717" Title="Why do Humans not produce Vitamin C like other mammals?" Tags="&lt;human-biology&gt;&lt;vitamins&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="402" PostTypeId="2" ParentId="401" CreationDate="2011-12-31T16:44:19.150" Score="74" Body="&lt;p&gt;Humans do not produce Vitamin C due to a mutation in the GULO (gulonolactone oxidase) gene, which results in the inability to synthesize the protein.  Normal GULO is an enzyme that catalyses the reaction of D-glucuronolactone with oxygen to L-xylo-hex-3-gulonolactone.  This then spontaneously forms Ascorbic Acid (Vitamin C).  However without the GULO enzyme, no vitamin C is produced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has not been selected against in natural selection as we are able to consume more than enough vitamin C from our diet.  It is also suggested that organisms without a functional GULO gene have a method of &quot;recycling&quot; the vitamin C that they obtain from their diets using red blood cells (see &lt;a href=&quot;http://dx.doi.org/10.1016%2Fj.cell.2008.01.042&quot;&gt;Montel-Hagen et al. 2008&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A 2008 published study (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18764764&quot;&gt;Li et al. 2008&lt;/a&gt;) claimed to have successfully re-instated the ability to produce vitamin C in mice. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Simply as trivia: other than humans; guinea pigs, bats and dry-nosed primates have lost their ability to produce vitamin C in the same way.  &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Li, Y., Shi, C.-X., Mossman, K.L., Rosenfeld, J., Boo, Y.C. &amp;amp;&#xA;Schellhorn, H.E. (2008) Restoration of vitamin C synthesis in&#xA;transgenic Gulo-/- mice by helper-dependent adenovirus-based&#xA;expression of gulonolactone oxidase. Human gene therapy. [Online] 19&#xA;(12), 1349–1358. Available from: doi:10.1089/hgt.2008.106 [Accessed:&#xA;31 December 2011].&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Montel-Hagen, A., Kinet, S., Manel, N., Mongellaz, C., Prohaska, R.,&#xA;Battini, J.-L., Delaunay, J., Sitbon, M. &amp;amp; Taylor, N. (2008)&#xA;Erythrocyte Glut1 Triggers Dehydroascorbic Acid Uptake in Mammals&#xA;Unable to Synthesize Vitamin C. Cell. [Online] 132 (6), 1039–1048.&#xA;Available from: doi:10.1016/j.cell.2008.01.042 [Accessed: 31 December&#xA;2011].&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-06-16T11:15:03.660" LastActivityDate="2012-06-16T11:15:03.660" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="403" PostTypeId="2" ParentId="158" CreationDate="2011-12-31T17:57:57.800" Score="7" Body="&lt;p&gt;The delay in immune attack is common for many viral infectious deceases where auto-immune response plays substantial to significant role in pathogenesis of the decease. The classical example here are the viral hepatitis B, C and D where it is auto-immune attack that causes the massive death of liver cells (hepatocytes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The delay in immune attack is explained by the following mechanisms:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The immune attack is developed against the surface antigen&lt;/strong&gt;, in case of hepatitis it is the &lt;em&gt;HbS&lt;/em&gt; Antigen. &quot;Surface&quot; means that this antigen has to appear on the cell surface in order to elicit immune response: the virus itself as well as the parts of destroyed cells are not immunogenic enough for this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second point explaining why the attack takes so long to develop is that &lt;strong&gt;it is primarily cell-mediated attack&lt;/strong&gt;, the humoral factors play the secondary role here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the usual &quot;workflow&quot; in this case is the following:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Contamination with hepatitis virus.&lt;/li&gt;&#xA;&lt;li&gt;Virus propagation to hepatic cells and their infection.&lt;/li&gt;&#xA;&lt;li&gt;Processing of the viral DNA (either as DNA or first reversed-transcripted from RNA) so that it is integrated into cell normal processing pathways.&lt;/li&gt;&#xA;&lt;li&gt;Expression of viral proteins (=antigenes) and their anchoring in the cell membrane.&lt;/li&gt;&#xA;&lt;li&gt;Surface antigenes are detected by macrophagues, processed and expressed on their membrane for T-helpers&#xA;... (continuation of the usual cell-mediated immune response via T4 and T8 lymphocytes).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Every stage takes some time, the total duration can sum up to 4 to 12 weeks depending upon the viral activity and the immune system status.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-02T21:13:10.027" LastActivityDate="2012-01-02T21:13:10.027" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="404" PostTypeId="2" ParentId="344" CreationDate="2012-01-01T10:52:02.140" Score="6" Body="&lt;p&gt;Once could argue that we die because it is advantageous to get rid of mature individuals once they have reproduced.  Because mature individuals have no more offspring to convey beneficial genes, those offspring which will benefit from knocking off their ancestors will have an evolutionary advantage.&lt;/p&gt;&#xA;" OwnerUserId="285" LastActivityDate="2012-01-01T10:52:02.140" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="405" PostTypeId="2" ParentId="99" CreationDate="2012-01-01T18:03:44.507" Score="5" Body="&lt;p&gt;Not sure if this is what you are looking for, but I did some searching around for histochemicals and reptilia.  &lt;a href=&quot;http://lib.bioinfo.pl/pmid:11268059&quot;&gt;I did come across a paper by L Alibardi, Dipartimento di Biologia evoluzionistica e sperimentale, University of Bologna, Bologna, Italy&lt;/a&gt;.  Now, that exact application doesn't seem to answer your question, it did open up a web page that contained numerous papers on reptilia and their beta-keratin structure and investigations into that (citations of the original paper, as well as papers by the same author).  I didn't see any that specifically spoke to the exact stain used, but then this is a little outside my area of expertise.  Perhaps this link will give you an avenue to pursue?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wish I could help more.&lt;/p&gt;&#xA;" OwnerUserId="279" LastActivityDate="2012-01-01T18:03:44.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="406" PostTypeId="1" AcceptedAnswerId="407" CreationDate="2012-01-01T18:23:44.123" Score="51" ViewCount="2268" Body="&lt;p&gt;This particular question has been of a great deal of interest to me, especially since it dives at the heart of abiogenesis.&lt;/p&gt;&#xA;" OwnerUserId="279" LastActivityDate="2018-07-03T16:32:08.950" Title="Can scientists create totally synthetic life?" Tags="&lt;biochemistry&gt;&lt;synthetic-biology&gt;&lt;abiogenesis&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="15" ContentLicense="CC BY-SA 3.0" />
  <row Id="407" PostTypeId="2" ParentId="406" CreationDate="2012-01-01T18:24:30.830" Score="40" Body="&lt;p&gt;In 2010, Dr. Craig Venter actually used a bacterial shell and &lt;a href=&quot;http://www.guardian.co.uk/science/2010/may/20/craig-venter-synthetic-life-form&quot; rel=&quot;noreferrer&quot;&gt;wrote DNA for it&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Scientists have created the world's first synthetic life form in a landmark experiment that paves the way for designer organisms that are built rather than evolved.&lt;/p&gt;&#xA;&lt;p&gt;(Snip)&lt;/p&gt;&#xA;&lt;p&gt;The new organism is based on an existing bacterium that causes mastitis in goats, but at its core is an entirely synthetic genome that was constructed from chemicals in the laboratory.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Keep in mind, this is only a &lt;a href=&quot;http://articles.cnn.com/2010-05-21/health/venter.qa_1_synthetic-chromosome-genetic-code-synthetic-life?_s=PM:HEALTH&quot; rel=&quot;noreferrer&quot;&gt;synthetic genome&lt;/a&gt;, not a truly unique organism created from scratch.  Although I am confident that the technology will become available in the future.  As has been pointed out, the entire genome wasn't built &lt;em&gt;de novo&lt;/em&gt;, but rather most of it was copied from a baseline which was built up from the base chemicals with no biological processes, and then the watermarks were added &lt;strong&gt;(still damn impressive since they took inorganic matter and made a living cell function with it)&lt;/strong&gt;. But they are working at building a totally unique genome from &lt;a href=&quot;http://www.bu.edu/abl/files/nature_synthetic_genome.pdf&quot; rel=&quot;noreferrer&quot;&gt;scratch&lt;/a&gt; (PDF).&lt;/p&gt;&#xA;&lt;p&gt;This is actually quite an emerging field, so much so that the MIT press has set up an entire &lt;a href=&quot;http://www.mitpressjournals.org/loi/artl&quot; rel=&quot;noreferrer&quot;&gt;series of journals&lt;/a&gt;for this.  As far as to the purpose of these artificial organisms, most &lt;a href=&quot;http://money.cnn.com/2010/05/27/news/newsmakers/venter_artificial_life.fortune/index.htm&quot; rel=&quot;noreferrer&quot;&gt;research&lt;/a&gt; funded by companies are meant to be for specific purposes that biology hasn't solved yet (such as a bacteria that eats a toxic waste or something).  Although, a lot of people are concerned about scientists venturing into the domain of theology.&lt;/p&gt;&#xA;&lt;p&gt;In terms of abiogenesis, there are many resources to learn more about this.  &lt;a href=&quot;http://www.factsnotfantasy.com/abiogenesis.php&quot; rel=&quot;noreferrer&quot;&gt;Here&lt;/a&gt; is a list of 88 papers that discuss the natural mechanisms of abiogenesis (this list is a little old, so I am sure that there are many, many more papers at this time).&lt;/p&gt;&#xA;&lt;p&gt;I also found this list of &lt;a href=&quot;http://www.alcyone.com/max/links/alife.html&quot; rel=&quot;noreferrer&quot;&gt;links&lt;/a&gt; and resources for artificial life.  I cannot verify the usefulness of this since the field is a bit outside my area of expertise.  However, it does seem quite extensive.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;EDIT TO ADD&lt;/strong&gt;:  Now we have &lt;a href=&quot;http://arstechnica.com/science/news/2012/04/synthetic-dna-substitute-gets-its-own-enzymes-undergoes-evolution.ars?clicked=related_right&quot; rel=&quot;noreferrer&quot;&gt;&amp;quot;XNA&amp;quot;&lt;/a&gt; (a totally synthetic genome) on the way.&lt;/p&gt;&#xA;" OwnerUserId="279" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2018-07-03T16:32:08.950" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="408" PostTypeId="5" CreationDate="2012-01-01T18:30:07.300" Score="0" Body="" OwnerUserId="279" LastEditorUserId="4101" LastEditDate="2013-10-31T18:03:31.927" LastActivityDate="2013-10-31T18:03:31.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="409" PostTypeId="4" CreationDate="2012-01-01T18:30:07.300" Score="0" Body="The study of how biological life arises from inorganic matter through natural processes, and the method by which life on Earth arose." OwnerUserId="279" LastEditorUserId="279" LastEditDate="2012-01-04T04:44:33.877" LastActivityDate="2012-01-04T04:44:33.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="410" PostTypeId="1" AcceptedAnswerId="464" CreationDate="2012-01-01T19:22:42.757" Score="8" ViewCount="361" Body="&lt;p&gt;I was playing around with a simulation of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Hodgkin-Huxley_model&quot; rel=&quot;noreferrer&quot;&gt;Hodgkin-Huxley model&lt;/a&gt; using their original parameters for the squid giant axon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By applying a constant stimulation current to the model in resting state, an infinite train of action potentials is triggered, which seems reasonable. However, if the current exceeds a threshold, these APs die off very quickly as both the membrane potential and the ion conductances reach a steady state. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is this phenomenon called? Is it a real phenomenon, or just an artefact of the Hodgkin-Huxley model?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/kR5Hh.png&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/kR5Hh.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user24" LastEditorUserId="149" LastEditDate="2012-01-03T00:13:51.503" LastActivityDate="2012-01-04T15:06:56.323" Title="Is &quot;exhaustion&quot; of the Hodgkin-Huxley membrane at constant stimulation a real phenomenon?" Tags="&lt;cell-biology&gt;&lt;electrophysiology&gt;&lt;biophysics&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="411" PostTypeId="2" ParentId="287" CreationDate="2012-01-02T00:24:45.957" Score="13" Body="&lt;p&gt;To make sure I'm not comparing apples and pears, my (attempt to) answer the question will be broken into two parts: comparison of single-stranded nucleic acids and double stranded ones.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Single stranded DNA and RNA&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Both DNA and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10458781&quot;&gt;RNA&lt;/a&gt; can form single-stranded complex tertiary structures in which the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleic_acid_secondary_structure&quot;&gt;secondary structure elements&lt;/a&gt; are associated through van der Waals contacts and hydrogen bonds. The presence of a 2'-hydroxyl group makes ribose ring prefer different &lt;a href=&quot;http://online-media.uni-marburg.de/chemie/bioorganic/vorlesung1/kapitel1e.html?/chemie/bioorganic/vorlesung1/k1e-20.html&quot;&gt;conformations&lt;/a&gt; than deoxyribose in DNA. Also, since 2′-OH moiety is both a hydrogen donor and acceptor, it provides RNA with greater &lt;em&gt;flexibility&lt;/em&gt; to form 3D complex structures and &lt;em&gt;stability&lt;/em&gt; to remain in one of these conformations. As Aleadam notices, this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2338076&quot;&gt;paper&lt;/a&gt; shows that tRNA and its DNA analog form similar tertiary structures though tDNA is not as stable as tRNA:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Therefore, we submit that the global conformation of nucleic acids is primarily dictated by the interaction of purine and pyrimidine bases with atoms and functional groups common to both RNA and DNA. In this view the 2-hydroxyl group, in tRNA at least, is an auxiliary structural feature whose role is limited to fostering local interactions, which increase the stability of a given conformation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These authors also show that at least one loop in the tDNA analog is more susceptible to cleavage by a restriction endonuclease. In this region the tRNA has a water molecule hydrogen bonded to 2'hydroxyl group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was not able to find more of such interesting comparisons in the literature.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Double stranded DNA and RNA&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Both DNA and RNA can form double-stranded structures. Again, sugar conformation determines the shape of the helix: for DNA helix it's usually &lt;a href=&quot;http://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/DNA/DNA_structure#Secondary_Structures_of_DNA&quot;&gt;B-form&lt;/a&gt;, whereas helical RNA forms A-geometry under nearly all conditions. In RNA helix we find the ribose predominantly in the &lt;a href=&quot;http://online-media.uni-marburg.de/chemie/bioorganic/vorlesung1/kapitel1e.html?/chemie/bioorganic/vorlesung1/k1e-20.html&quot;&gt;C3’- endo&lt;/a&gt; conformation, as 2'-OH stericly disfavors the C2'-endo conformaion, necessary for B-form geometry.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Physiological significance&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;dsRNA and ssDNA often provide a signal to the cell that something is wrong. dsRNA is of course seen in normal processes like RNA interference but it can also stop protein synthesis and signal viral infections (cf. &lt;a href=&quot;http://en.wikipedia.org/wiki/Double-stranded_RNA_viruses&quot;&gt;double stranded RNA viruses&lt;/a&gt;). Similarly, ssDNA is much more prone to degradation than dsDNA, it often signals damage of DNA, or infections from &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_virus#Group_II%3a_ssDNA_viruses&quot;&gt;single stranded DNA viruses&lt;/a&gt; and induces cell death. Therefore, due to their functions, under normal conditions DNA 3D structure is mostly a double-stranded helix, whereas RNA has a single stranded, &quot;protein-like&quot;, complex 3D structure. &lt;/p&gt;&#xA;" OwnerUserId="277" LastEditorUserId="277" LastEditDate="2012-01-02T09:53:58.497" LastActivityDate="2012-01-02T09:53:58.497" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="412" PostTypeId="1" CreationDate="2012-01-02T00:35:41.310" Score="8" ViewCount="122" Body="&lt;p&gt;I hear that Oranges cultivated in tropical areas of the world tend to be greener when ripe, is that correct?&#xA;Even the same type of Orange differs in color if cultivated in California or Florida. I hear that's because of the climate (colder nights == &lt;em&gt;oranger&lt;/em&gt; oranges)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, at the same time, oranges tucked in between the tree leaves tend to be greener, for they need more chlorophyll to make the most use of less access to sun rays.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could someone correct my assumptions? Also, if possible, list the pigments and processes involved?&lt;/p&gt;&#xA;" OwnerUserId="286" LastEditorUserId="3971" LastEditDate="2013-08-29T14:40:49.963" LastActivityDate="2013-08-29T14:40:49.963" Title="What are the variables that control/influence the color of oranges(Citrus sinensis)?" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;pigmentation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="413" PostTypeId="2" ParentId="385" CreationDate="2012-01-02T00:57:27.153" Score="8" Body="&lt;p&gt;Have a look at:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.xtalent.com.au/gallery/thumbnails.php?album=2&quot;&gt;XTALENT Image Gallery&lt;/a&gt;, more than 600 images, last updated in 2006, though.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.denniskunkel.com/&quot;&gt;Dennis Kunkel Microscopy, Inc.&lt;/a&gt;, &quot;scientific stock photography library of light microscope pictures and electron microscopy images featuring science and biomedical microscopy photos&quot;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www-archive.mse.iastate.edu/microscopy/tutorials.html&quot;&gt;Iowa State University SEM library&lt;/a&gt;, includes pictures submitted by students from around the state of Iowa.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="277" LastActivityDate="2012-01-02T00:57:27.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="414" PostTypeId="2" ParentId="410" CreationDate="2012-01-02T01:51:09.290" Score="4" Body="&lt;p&gt;&lt;em&gt;(I probably ought to have a pat answer to this on the tip of my mind, but since I don't I'm going to wing it. This is probably just an opportunity to make an utter fool of myself. Please treat everything that follows with extreme suspicion.)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this is &lt;em&gt;effectively&lt;/em&gt; an artefact of the model. That may not be true in the strictest sense -- it is possible such behaviour could be produced in real experimental preparations -- but it would require driving them in drastically non-physiological ways. I am not aware of this having been done, but I'm sure that's just my ignorance -- I would be surprised if nobody has tried.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In physiological terms, though: where would such a large constant current come from in a real cell? Where would the charges go? How would that be sustained with realistic boundary conditions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While it is possible that such an effect can come into play very transiently in living systems, it seems unlikely that a true steady state of this kind could ever be reached.&lt;/p&gt;&#xA;" OwnerUserId="149" LastActivityDate="2012-01-02T01:51:09.290" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="417" PostTypeId="1" AcceptedAnswerId="1050" CreationDate="2012-01-02T12:50:30.270" Score="15" ViewCount="2387" Body="&lt;p&gt;I understand that in normal REM sleep the voluntary muscles are in effect paralysed in order to prevent an individual acting out their dreams.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579974/&quot;&gt;This paper&lt;/a&gt; indicates that there are likley to be multiple causes of this atonia. I am interested to know &lt;em&gt;what are some of these methods by which natural atonia is achieved by the body in periods of sleep&lt;/em&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, &lt;em&gt;what causes these mechanisms to fail in individuals who suffer from sleep-walking&lt;/em&gt;?&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-02T16:31:45.803" LastActivityDate="2014-04-30T18:26:11.580" Title="What causes REM atonia to be lost in sleepwalking?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;sleep&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="418" PostTypeId="2" ParentId="328" CreationDate="2012-01-02T13:05:14.800" Score="6" Body="&lt;p&gt;By programmable, I suppose you mean that it contains information or can be altered in response to some input or stimulus.  The answer is &quot;no&quot; for both.  Well, sort of.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does noncoding DNA contain information?  By definition, no.  There are probably many regions of the genome that appear to have no information, only later to be found to contain introns, regulatory elements such as enhancers, boundary element, MAR/SARs, targeting sites, etc.  Even functional tests (such as removing the region) may not reveal anything because the effects could be minor, or only evident under special conditions.  But arguably, if you remove a region and it has an effect on the organism, then it's not really a noncoding DNA, it's just you didn't see the coding before hand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the latter, can it altered, the answer is again &quot;no,&quot; or at least &quot;apparently not.&quot;  Intergenic regions (those stretches of DNA that do not contain obvious or characterized transcribed regions or their control elements) are very stable between organisms and even between species.  They seem to have a mutation rate expected for having no information, and thus free to mutate slowly without being swept away.  There is no evidence (as far as I know) of any region of the genome being purposefully altered, with the exception of a handful of specific genes whose regulation is controlled by DNA nicking or some such.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps I am missing your question, being a biologist and not really knowing what a &quot;Turing Machine&quot; is.  If I misunderstood, please clarify.&lt;/p&gt;&#xA;" OwnerUserId="219" LastActivityDate="2012-01-02T13:05:14.800" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="419" PostTypeId="2" ParentId="412" CreationDate="2012-01-02T13:51:51.290" Score="8" Body="&lt;p&gt;Naturally, ripe orange skins are usually green-yellow. In colder climates, they will turn orange over winter, since in the cold the chlorophyll will start degrading and stop masking out yellow/orange carotenoids in the skin. If the fruit is picked in fall (and not let ripen or &lt;em&gt;degreened&lt;/em&gt;) they will have green color.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ipt.us.com/produce-storage-and-transport/oranges-ethylene-gas&quot;&gt;Ehtylene gas&lt;/a&gt;, which is a natural plant hormone, is sometimes used to give them more uniform, orange color (&lt;em&gt;degreening&lt;/em&gt;). Also, some oranges cultivated in the US are dyed with &lt;a href=&quot;http://en.wikipedia.org/wiki/Citrus_Red_2&quot;&gt;Citrus Red 2&lt;/a&gt; to make their peels orange. &lt;/p&gt;&#xA;" OwnerUserId="277" LastActivityDate="2012-01-02T13:51:51.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="420" PostTypeId="2" ParentId="328" CreationDate="2012-01-02T13:56:02.157" Score="8" Body="&lt;p&gt;Depends on what you mean by &quot;non-coding&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are structural elements in telomeres &amp;amp; centromeres -- although the DNA there does not code for proteins, it contributes to the three dimensional structure of the chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Non-Coding&quot; DNA can also act as a binding substrate for many proteins: transcription factors,  enhancers, histone proteins; and thus control regulation indirectly through these intermediaries.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Promoter regions upstream of transcribed/translated regions are the combinatorial control switches/dials of our genome, and have tremendous regulatory importance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Non-Coding DNA also acts as repertoires of mobile DNA elements, which enable fast evolution / &quot;plasticity&quot; by copying&amp;amp;pasting exons around (L1 transductions) or by copying into coding regions &amp;amp; interrupting them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly,  they can act as the sandbox of evolution: Non-coding regions not genetically linked to functional regions are very likely to not suffer from  purifying selection, so they can act as templates of random evolution - where the vast majority of mutations won't have any impact positive or negative.  This enables exploring brand new combinations, which may then become new exons / miRNA / regulatory regions or get shuffled into other regions to enable new functionality. &lt;/p&gt;&#xA;" OwnerUserId="237" LastEditorUserId="237" LastEditDate="2012-01-04T11:15:29.520" LastActivityDate="2012-01-04T11:15:29.520" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="421" PostTypeId="1" AcceptedAnswerId="423" CreationDate="2012-01-02T16:35:19.230" Score="9" ViewCount="178" Body="&lt;p&gt;Are Schwann cells the only source of myelin for axons in the peripheral nervous system, or are there other neuroglia or other processes that result in myelination of PNS axons?&lt;/p&gt;&#xA;" OwnerDisplayName="user24" LastEditorDisplayName="user24" LastEditDate="2012-01-02T17:02:53.410" LastActivityDate="2012-01-02T21:44:10.257" Title="Are Schwann cells the sole source of myelination in PNS?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="422" PostTypeId="2" ParentId="182" CreationDate="2012-01-02T21:34:50.430" Score="6" Body="&lt;p&gt;The &lt;strong&gt;oxygen saturation&lt;/strong&gt; (in lungs) and desaturation (in target organs) &lt;strong&gt;takes place via diffusion&lt;/strong&gt; along the concentration gradient (i.e. partial pressure for gases). Therefore as long as &lt;strong&gt;RBCs&lt;/strong&gt; from two different sources and &lt;strong&gt;having different partial pressure&lt;/strong&gt; of oxygen mix up, the oxygen level &lt;strong&gt;starts to equilibrate&lt;/strong&gt; between these cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But &lt;strong&gt;diffusion&lt;/strong&gt; as a passive mechanism &lt;strong&gt;is not very fast&lt;/strong&gt; and can take some time. So the only possibility for the second variant (there is a mixture of two types of RBCs) is if the mixture exists for very short time in liver sinusoids, so that the blood leaves them without really mixing completely up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not true, &lt;strong&gt;at least &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8276352&quot; rel=&quot;nofollow&quot;&gt;in some animal models&lt;/a&gt; the blood within the liver seems to reach equilibrium very quickly&lt;/strong&gt; and its resulting partial pressure can be influenced by adjusting the blood flow from different sources (using vasoactive substances injected directly, as in the referenced paper). &lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="1433" LastEditDate="2012-10-01T12:38:18.730" LastActivityDate="2012-10-01T12:38:18.730" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="423" PostTypeId="2" ParentId="421" CreationDate="2012-01-02T21:44:10.257" Score="9" Body="&lt;p&gt;Schwann cells seem to be the most common type of glial cells outside of CNS, and &lt;strong&gt;the myelinating Schwann cells are the only known source of myelin in PNS&lt;/strong&gt;. Other types of neuroglia in PNS, for example &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC424114/&quot;&gt;non-myelinating Schwann cells&lt;/a&gt; and &lt;a href=&quot;http://www.jneurosci.org/content/3/11/2206.short&quot;&gt;astrocytes-like cells&lt;/a&gt; do not seem to take part in myelination, neither in CNS nor in PNS. &lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-01-02T21:44:10.257" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="424" PostTypeId="1" CreationDate="2012-01-02T23:50:18.883" Score="11" ViewCount="272" Body="&lt;p&gt;It's known (&lt;a href=&quot;http://ad-teaching.informatik.uni-freiburg.de/zbmed/APS/ajplegacy/ajplegacy_127_1.pdf/131.pdf&quot; rel=&quot;nofollow&quot;&gt;Hursh 1939&lt;/a&gt;) that myelinated axons exhibit the behavior $v = 6d$, where $v$ is the propagation speed [m/s] and $d$ is the axon diameter [μm].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A related relation for unmyelinated axons is (&lt;a href=&quot;http://www.bem.fi/book/02/02.htm&quot; rel=&quot;nofollow&quot;&gt;Malmivuo &amp;amp; Plonsey&lt;/a&gt;, eq. 2.1):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$v = \sqrt{\frac{i_\text{Na max}}{r_i c_m^2 V_\mathrm{th}}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to approximate the propagation speed that A-alpha nerve fibers would exhibit, if they were unmyelinated. How could I find values for the constants in the above equation? Is there an easier way to conduct these calculations, or has there already been a study done on this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the (myelinated) A-alpha fibers, d = 13-20 μm and v = 80-120 m/s according to &lt;a href=&quot;http://en.wikipedia.org/wiki/Axon&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="194" LastEditorUserId="3128" LastEditDate="2014-05-29T22:55:39.853" LastActivityDate="2014-05-29T22:55:39.853" Title="What would be the conduction speed of A-alpha fibers, were they unmyelinated?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="425" PostTypeId="5" CreationDate="2012-01-02T23:59:38.110" Score="0" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Hodgkin%2DHuxley_model&quot; rel=&quot;nofollow&quot;&gt;Hodgkin-Huxley model&lt;/a&gt; is a system of differential equations describing the behaviour of ion currents across a membrane that exhibits separate voltage-dependent conductances for different ion species. In particular, the model explains the propagating voltage pulse known as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Action_potential&quot; rel=&quot;nofollow&quot;&gt;action potential&lt;/a&gt;, a fundamental component of neuronal activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The model was published in 1952 in a series of papers for The Journal of Physiology, based on data from seminal voltage clamp experiments with the &lt;a href=&quot;http://en.wikipedia.org/wiki/Squid_giant_axon&quot; rel=&quot;nofollow&quot;&gt;squid giant axon&lt;/a&gt;. Alan Hodgkin and Andrew Huxley were awarded the 1963 Nobel Prize for Physiology &amp;amp; Medicine for this work.&lt;/p&gt;&#xA;" OwnerUserId="149" LastEditorUserId="149" LastEditDate="2012-01-04T05:07:32.330" LastActivityDate="2012-01-04T05:07:32.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="426" PostTypeId="4" CreationDate="2012-01-02T23:59:38.110" Score="0" Body="Mathematical model explaining neuronal action potentials in terms of separate voltage-dependant membrane conductances for different ion species." OwnerUserId="149" LastEditorUserId="149" LastEditDate="2012-01-04T05:07:36.140" LastActivityDate="2012-01-04T05:07:36.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="427" PostTypeId="2" ParentId="328" CreationDate="2012-01-03T05:48:46.913" Score="12" Body="&lt;p&gt;Perhaps this question is whether the regions between genes sometimes known as 'junk DNA' has any function. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the human genome, out of ~5 billion bases &lt;a href=&quot;http://www.ornl.gov/sci/techresources/Human_Genome/faq/genenumber.shtml&quot;&gt;there are something like 20-30,000 genes&lt;/a&gt; which take up perhaps 10s of millions of base pairs, depending on how you count it. 1% of all human DNA is the common figure.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is sometimes asked as if biologists commonly think of it as having no use, but in fact this is a researched topic, and few feel that it has no evolutionary or biological function at all. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the most common uses for intergenic DNA in eukaryotes (bacteria are an entirely different topic with very different responses.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Transcriptional Regulation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Outside the coding sequences of the gene, there can be an extensive set of binding sities for proteins which regulate the gene.  In this paper in Figure 1 the celebrated regulatory sequence of ENDO16 is &lt;a href=&quot;http://www.pnas.org/content/102/24/8591.full&quot;&gt;can be seen in Figure 1&lt;/a&gt;. As you can see for almoat 2000 bp there are numerous binding sites for many sorts of promotors and inhibitory factors, as well as factors which may splice the gene in various ways.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I recall, ENDO16 only  turns on for a brief period in the development of the sea urchin and so its very tightly controlled, which means that its got a lot of regulatory elements upstream of it, controlling transcription. Its one of the most exhaustively studied genes ever and the believe they have most of it.  Other human genes ive seen perusing medical literature have seen 20kb are necessary to reproduce the regulation of a gene. Still all this might at best only triple the amount of DNA actively involved.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Centromeres and Telomeres&#xA;The physiology of the chromosomes have large regions as Deniz mentions are necessary for cell reproduction and for development.  In animals (like humans) the regions are devoid of transcribed genes and might be 10-15% of the genome length (I'm eyeballing this from the UCSC genome browser on chr21 - in some organisms like yeast the centromere can be just a few hundred base pairs.  So anyway we are getting somewhere now!&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Non translated genes.&#xA;There are lots of pieces of DNA that might be copied into RNA and then do not function as templates for proteins.  some folks say there is a lot of this stuff.  The typical view is that there are a few thousand of these sorts of beasts known, and &lt;a href=&quot;http://mirbase.org/cgi-bin/browse.pl?org=hsa&quot;&gt;humans are currently thought to have about 1500 of them&lt;/a&gt;.  A small tweak in the number of genes, but they are there nonetheless.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Chromatin binding and organization sites&#xA;Although Centromeres are places where chromatin binds, the several families of proteins which bind DNA and wrap them &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleosome#Higher_order_structure&quot;&gt;into organized coiled coils thought to be like spools of telephone wire to form the Nucleosome&lt;/a&gt; which makes the chromosomes look like the little stick men you see in text books.  Chromatin can spool up just about any sort of DNA but seems to have a preference for regions which are at the ends of genes.  They can be modified by enzymes (acylated, methylated) to modulate their affinity for some classes of DNA sequence.  This is a hot topic of research.  The ability for RNA polymerase to find transcribe a gene is not good if its wound onto chromatin and though its not a precise binding like a transcription factor, chromatin binding and regulation must be affected greatly by changes in the distance between genes and the DNA sequences which surround a gene for thousands of base pairs, which is one of the main differences between species.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Of all biological systems (at least that I know of) this one accounts for the most bulk DNA sequence and is probably as related to the difference between different species as transcription factors and almost certainly is an older system of gene regulation, if you think about it. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Copy Number Variations and repetitive regions&#xA;just a side note, but small and very long repeat sequences can show up in the intergenic regions as well as inside a gene boundary to account for some of the differences between individuals.  they can be quite short or quite long.  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Well hope this helps?&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-01-03T05:48:46.913" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="428" PostTypeId="2" ParentId="424" CreationDate="2012-01-03T09:46:11.807" Score="4" Body="&lt;p&gt;The provided relation for unmyelinated axons only holds up to certain diameter value of the axon and is valid only as long as the sodium conductance i&lt;sub&gt;Na&lt;/sub&gt; is uniformly distributed along the cross-section of the axon. This explains why non-myelinated fibers are so thin, being only 0.2-1.5 μm in diameter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In axons having a larger diameter the axon potential can only move between Ranvier nodes. If this fiber gets unmyelinated the axon potential just stops propagating, due to several reasons:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Sodium concentration through the complete axon surface is too high so that it diffuses internally along the axon and reduces the concentration gradient in the direction of AP propagation.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;AP is propagated not only along the length of axon but also laterally, that leads to its flatenning over the axon surface, decreasing its amplitude etc.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Unfortunately I couldn't find the reprint of the original publication in Biofizika referenced by the webpage you provide the link to, so I cannot investigate the constraints of their model for AP propagation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to estimate the propagation velocity in unmyelinated axons of large diameter I would take some theoretical papers investigating the properties of nerve fibers undergoing demyelination. Z. J. Koles and M. Rasminsky &lt;em&gt;&quot;A computer simulation of conduction in demyelinated nerve fibres&quot;&lt;/em&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1331199/&quot; rel=&quot;nofollow&quot;&gt;J Physiol. 1972 December; 227(2): 351–364&lt;/a&gt;. seems to be one of the earliest publications on this topic and it is freely available online.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this paper the authors tried to simulate the conductance of demyelinated motor axon with diameter of 10μm and 5μm myelin sheath. They gradually decreases the amount of &lt;strong&gt;myelin&lt;/strong&gt; width until &lt;strong&gt;2.7% of the initial value where they saw the abolishment of AP propagation&lt;/strong&gt;. &lt;strong&gt;The propagation time was 12.5 times higher&lt;/strong&gt; than in normally myelinated fibers (for the distance where AP could travel). If we consider the initial propagation velocity being 80-120 m/s then &lt;strong&gt;after demyelination it is reduced down to 6-10 m/s and fade after a short travel&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-03T11:07:51.417" LastActivityDate="2012-01-03T11:07:51.417" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="429" PostTypeId="1" CreationDate="2012-01-03T09:57:36.150" Score="7" ViewCount="1425" Body="&lt;p&gt;How does a transgene (in vector) integrate to the host genome? (e.g. in glass bead method, neither biolistic nor agrobacterium).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I already cut some parts (NdeI-PciI) of the vector (pUC18) and wondering if it affects the integration procedure. Is there any recombination-like procedure same as gateway?&lt;/p&gt;&#xA;" OwnerUserId="295" LastEditorUserId="69" LastEditDate="2012-02-16T14:53:37.950" LastActivityDate="2012-02-16T14:53:37.950" Title="What is the mechanism of transgene integration (from expression vector to the host genome)?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="430" PostTypeId="2" ParentId="406" CreationDate="2012-01-03T11:07:55.783" Score="27" Body="&lt;p&gt;In principle it is possible. Life doesn’t contain some divine or intrinsically spiritual element that we would have to add to our &lt;em&gt;artificial organism potion&lt;/em&gt; to breathe life into it. At this moment we are limited by gaps in our knowledge and by the current state of technology. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We first have to better understand fundamental principles of life on a multi-level scale: from quantum mechanics, through biochemistry, structural biology, molecular evolution, to macroscopic function and behavior on the organism level. This, together with development of enabling technologies, will require decades of research but some steps have already been taken.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the promising approaches is &lt;em&gt;re-writing&lt;/em&gt;, as exemplified in this &lt;a href=&quot;http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html&quot;&gt;work&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We redesign the genome of a natural biological system, bacteriophage T7, in order to specify an engineered surrogate that, if viable, would be easier to study and extend. (...) The resulting chimeric genome encodes a viable bacteriophage that appears to maintain key features of the original while being simpler to model and easier to manipulate. The viability of our initial design suggests that the genomes encoding natural biological systems can be systematically redesigned and built anew in service of scientific understanding or human intention.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;or a &lt;a href=&quot;http://www.nature.com/msb/journal/v2/n1/full/msb4100090.html&quot;&gt;minimal cell synthesis&lt;/a&gt; project:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Construction of a chemical system capable of replication and evolution, fed only by small molecule nutrients, is now conceivable. This could be achieved by stepwise integration of decades of work on the reconstitution of DNA, RNA and protein syntheses from pure components. (...) Completion would yield a functionally and structurally understood self-replicating biosystem. (...) Our proposed minimal genome is 113 kbp long and contains 151 genes. We detail building blocks already in place and major hurdles to overcome for completion.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, technically it’s very difficult but definitely can be done, which is really exciting. &lt;/p&gt;&#xA;" OwnerUserId="277" LastEditorUserId="277" LastEditDate="2012-01-03T12:46:26.583" LastActivityDate="2012-01-03T12:46:26.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="432" PostTypeId="1" CreationDate="2012-01-03T15:35:27.610" Score="8" ViewCount="2014" Body="&lt;p&gt;While ethidium bromide works well for staining larger single-stranded RNA or double-stranded DNA molecules, it doesn't stain smaller nucleic acids very well. I observed that at around 20 bases and below single-stranded nucleic acids are difficult to see with EtBr-staining unless the nucleic acids are highly concentrated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are good alternatives for observing small nucleic acids in polyacrylamide gels? The main consideration would be ease-of-use, and it should be possible without any unusual equipment.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2012-01-03T16:10:26.757" LastActivityDate="2012-01-04T01:44:33.623" Title="Alternatives to ethidium bromide for staining small nucleic acids?" Tags="&lt;staining&gt;&lt;gel-electrophoresis&gt;&lt;nucleic-acids&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="433" PostTypeId="5" CreationDate="2012-01-03T15:36:34.690" Score="0" Body="&lt;p&gt;Often related to &lt;a href=&quot;/questions/tagged/biochemistry&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;biochemistry&amp;#39;&quot; rel=&quot;tag&quot;&gt;biochemistry&lt;/a&gt; and &lt;a href=&quot;/questions/tagged/genetics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;genetics&amp;#39;&quot; rel=&quot;tag&quot;&gt;genetics&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Molecular-biology involves study of biology at the molecular level including, but not limited to:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;transcription&lt;/li&gt;&#xA;&lt;li&gt;translation&lt;/li&gt;&#xA;&lt;li&gt;replication&lt;/li&gt;&#xA;&lt;li&gt;cell function&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Try to combine this with other relevant tags as molecular biology is a broad field.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="6307" LastEditDate="2017-05-19T01:23:02.700" LastActivityDate="2017-05-19T01:23:02.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="434" PostTypeId="4" CreationDate="2012-01-03T15:36:34.690" Score="0" Body="The study of the molecular processes underlying life." OwnerUserId="81" LastEditorUserId="6307" LastEditDate="2017-05-18T23:41:01.350" LastActivityDate="2017-05-18T23:41:01.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="435" PostTypeId="5" CreationDate="2012-01-03T15:46:43.320" Score="0" Body="&lt;h3&gt;Definition&lt;/h3&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;senescence /se·nes·cence/ (sĕ-nes´ens): the process of growing old, especially the condition resulting from the transitions and accumulations of the deleterious aging processes.&lt;/p&gt;&#xA;  &#xA;  &lt;blockquote&gt;&#xA;    &lt;p&gt;&lt;em&gt;Dorland's Medical Dictionary for Health Consumers. © 2007 by Saunders, an imprint of Elsevier, Inc. All rights reserved.&lt;/em&gt;&lt;/p&gt;&#xA;  &lt;/blockquote&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;h3&gt;Background&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Aging is an inevitable consequence of living.  As organisms live they are constantly damaged, both at the cellular level and at the level of the whole organism. Maintenance is required to keep cells replicating, or to keep a heart functioning for example, but aging, or senescence, cannot be avoided as damage builds up and the organism passes its prime.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cellular senescence can be caused by a range of sometimes inescapable damaging agents, including: ultra-violet radiation from exposure to sunlight, pathogens such as bacteria, chemicals such as alcohol or bisphenol A, or even by reactive-oxygen species - a by-product of respiration. Senescence is even proposed to have a causative role in promoting aging in a self-perpetuating manner [&lt;a href=&quot;http://dx.doi.org/10.1111/j.1474-9726.2012.00795.x&quot; rel=&quot;nofollow&quot; title=&quot;Senescent-cell bystander effect&quot;&gt;1&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Somatic cells of the body (i.e. not stem cells) also have a predefined &lt;em&gt;replicative lifespan&lt;/em&gt;, or Hayflick limit - the maximum number of times a cell can divide. This is determined by telomeres - lengths of DNA attached to the ends of chromosomes to keep them intact during cell division.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all cells have a replicative lifespan - they can express the enzyme &lt;em&gt;telomerase&lt;/em&gt; and replace their telomeres as they get run out. Embryonic stem cells have potentially unlimited lifespans, were it not for the inevitable build-up of damage that would occur through many rounds of cell division.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria also undergo aging, and can become uncultrable as the population enters a senescent state [&lt;a href=&quot;http://dx.doi.org/10.1371/journal.pgen.0030224&quot; rel=&quot;nofollow&quot; title=&quot;Nyström T (2007)&quot;&gt;2&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Questions?&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Questions can relate to any aspect of biological aging. Be it human aging and age-related diseases such as cardiovascular disease or dementia, or senescence at the cellular level, including the Hayflick limit, damaging agents that can trigger senescence, and the role of senescence in promoting aging.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Organismal and cellular aging are intrinsically linked, incredibly complex, and not yet fully understood. Theories around the evolution of cellular senescence are mixed, due to the simultaneous benefits and costs that come with a replicative lifespan [&lt;a href=&quot;http://dx.doi.org/10.1083/jcb.201009094&quot; rel=&quot;nofollow&quot; title=&quot;The four faces of cellular senescence&quot;&gt;3&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;References&lt;/h3&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Nelson G., &lt;em&gt;et al&lt;/em&gt; (2012) A senescent cell bystander effect: senescence-induced senescence. &lt;em&gt;Aging Cell&lt;/em&gt;. 2012 Apr;&lt;strong&gt;11&lt;/strong&gt;(2):345-9. doi: &lt;a href=&quot;http://dx.doi.org/10.1111/j.1474-9726.2012.00795.x&quot; rel=&quot;nofollow&quot;&gt;10.1111/j.1474-9726.2012.00795.x&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Nyström T (2007) A Bacterial Kind of Aging. &lt;em&gt;PLoS Genet&lt;/em&gt;. &lt;strong&gt;3&lt;/strong&gt;(12): e224. doi:&lt;a href=&quot;http://dx.doi.org/10.1371/journal.pgen.0030224&quot; rel=&quot;nofollow&quot;&gt;10.1371/journal.pgen.0030224&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Rodier F, Campisi J (2011) Four faces of cellular senescence. &lt;em&gt;J Cell Biol&lt;/em&gt;. &lt;strong&gt;192&lt;/strong&gt;(4): 547–556. doi:&lt;a href=&quot;http://dx.doi.org/10.1083/jcb.201009094&quot; rel=&quot;nofollow&quot;&gt;10.1083/jcb.201009094&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastEditorUserId="4101" LastEditDate="2013-10-31T00:45:53.547" LastActivityDate="2013-10-31T00:45:53.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="436" PostTypeId="4" CreationDate="2012-01-03T15:46:43.320" Score="0" Body="The process of biological aging or the state of an organism being biologically old. " OwnerUserId="81" LastEditorUserId="69" LastEditDate="2012-01-29T13:09:48.860" LastActivityDate="2012-01-29T13:09:48.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="437" PostTypeId="5" CreationDate="2012-01-03T15:48:30.997" Score="0" Body="&lt;p&gt;Questions about the biology and identification of members of &lt;a href=&quot;https://en.wikipedia.org/wiki/Insect&quot; rel=&quot;nofollow noreferrer&quot;&gt;Insecta&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Insecta is a group of arthropods with the following basic characteristics:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;body divided into head, thorax and abdomen&lt;/li&gt;&#xA;&lt;li&gt;three pairs of thoracic legs.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This group includes arthropods such as Butterflies/Moths (&lt;a href=&quot;/questions/tagged/lepidoptera&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;lepidoptera&amp;#39;&quot; rel=&quot;tag&quot;&gt;lepidoptera&lt;/a&gt;), Flies (&lt;a href=&quot;/questions/tagged/diptera&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;diptera&amp;#39;&quot; rel=&quot;tag&quot;&gt;diptera&lt;/a&gt;), Beetles (Coleopterans), Bees/&lt;a href=&quot;/questions/tagged/wasps&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;wasps&amp;#39;&quot; rel=&quot;tag&quot;&gt;wasps&lt;/a&gt; (Hymenopterans), and true bugs (Hemipterans).&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Insects do not include Chelicerates, myriapods, or crustaceans. If any of these (or arthropods in general) are the focus of your question, please use the &lt;a href=&quot;/questions/tagged/arthropod&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;arthropod&amp;#39;&quot; rel=&quot;tag&quot;&gt;arthropod&lt;/a&gt; tag.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;If the question is about arachnids (speiders, ticks, or mites) use tag &lt;a href=&quot;/questions/tagged/arachnology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;arachnology&amp;#39;&quot; rel=&quot;tag&quot;&gt;arachnology&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Questions about pest insects can include the &lt;a href=&quot;/questions/tagged/pest-control&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;pest-control&amp;#39;&quot; rel=&quot;tag&quot;&gt;pest-control&lt;/a&gt; tag or the &lt;a href=&quot;/questions/tagged/mosquito&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;mosquito&amp;#39;&quot; rel=&quot;tag&quot;&gt;mosquito&lt;/a&gt; tag if appropriate.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;If you are curious about or think you may have found &lt;strong&gt;bed bugs&lt;/strong&gt;, please see &lt;a href=&quot;https://biology.stackexchange.com/a/56204/16866&quot;&gt;this post&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;See also &lt;a href=&quot;/questions/tagged/species-identification&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;species-identification&amp;#39;&quot; rel=&quot;tag&quot;&gt;species-identification&lt;/a&gt; and use other tags to narrow the field of your question.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="16866" LastEditDate="2019-07-12T03:50:03.017" LastActivityDate="2019-07-12T03:50:03.017" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="438" PostTypeId="4" CreationDate="2012-01-03T15:48:30.997" Score="0" Body="The scientific study of Insects. If the question is about some other group of arthropod use 'arthropod' tag." OwnerUserId="81" LastEditorUserId="16866" LastEditDate="2019-07-12T03:50:03.017" LastActivityDate="2019-07-12T03:50:03.017" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="439" PostTypeId="5" CreationDate="2012-01-03T15:50:18.563" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-03T15:50:18.563" LastActivityDate="2012-01-03T15:50:18.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="440" PostTypeId="4" CreationDate="2012-01-03T15:50:18.563" Score="0" Body="The study of the function, chemistry and structure of cells." OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-01-04T04:44:52.207" LastActivityDate="2012-01-04T04:44:52.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="442" PostTypeId="5" CreationDate="2012-01-03T15:57:25.850" Score="0" Body="&lt;p&gt;Organelles responsible for protein synthesis in cells. They are distinguished into &quot;free&quot; and &quot;membrane-bound&quot; classes.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-27T12:19:24.770" LastActivityDate="2017-03-27T12:19:24.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="443" PostTypeId="4" CreationDate="2012-01-03T15:57:25.850" Score="0" Body="Organelles responsible for protein synthesis in cells. They are distinguished into &quot;free&quot; and &quot;membrane-bound&quot; classes." OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-01-04T05:08:24.083" LastActivityDate="2012-01-04T05:08:24.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="444" PostTypeId="2" ParentId="147" CreationDate="2012-01-03T16:27:46.073" Score="6" Body="&lt;p&gt;There are several ways to infer into the propagation delays of auditory system &lt;em&gt;in vivo&lt;/em&gt; that is applicable to humans (i.e. leaves the subjects intact).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of them is so-called &lt;a href=&quot;http://en.wikipedia.org/wiki/Auditory_brainstem_response&quot; rel=&quot;nofollow noreferrer&quot;&gt;ABR&lt;/a&gt; that stands for Auditory Brainstem Response. As it is clear from its name this method allows you to derive the brainstem response to an auditory stimulus (so, you can track the auditory pathway up to its input into thalamus), but its resolution is so fine that you can separate single components (&quot;waves&quot;) for the following path segments (from Wikipedia):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;&lt;pre&gt;&lt;code&gt;Wave I – generated by the peripheral portion of cranial nerve VIII&#xA;Wave II – generated by the central portion of cranial nerve VIII&#xA;Wave III – generated by the cochlear nucleus&#xA;Wave IV – generated by the superior olivary complex/lateral lemniscus&#xA;Wave V – generated by the lateral lemniscus/inferior colliculus&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, it takes only 10 ms for the signal to reach the input into thalamus. This correlates well with some auditory signal based activities, like &lt;a href=&quot;http://en.wikipedia.org/wiki/Startle_response&quot; rel=&quot;nofollow noreferrer&quot;&gt;startle reflex&lt;/a&gt;, which was also shown to have about 10 ms latency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried to search for some electrophysiological recordings from auditory cortex (temporal lobe) paired with auditory stimuli, but the first paper I came accross that is available for free (and which I can also link from my answer) is &lt;a href=&quot;http://www.cns.nyu.edu/events/earclub/artfiles/brosch.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this work&lt;/a&gt; done on monkeys.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at Figure 1:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/D8hN1.jpg&quot; alt=&quot;Figure 1 from Brosch et al.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the results from multiunit recordings and you see that the initial activity in the cortex starts approximately 20 ms after the stimulus onset with a short activity pattern, followed by some short break and then longer period of activity with broader frequences spectrum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my opinion the delays in signal propagation are not due to complex signal processing in the olivary nucleus or any other brainstem structures, rather they are due to electro-chemical transformations in CNS synapses. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The initial arrival of the signal into the cortex does not mean the perception of the sound, it definitely takes hundreds of millisecond until the conditioned cortex-mediated response to this stimulus.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-01-03T16:27:46.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="445" PostTypeId="1" AcceptedAnswerId="449" CreationDate="2012-01-03T17:51:03.200" Score="19" ViewCount="1959" Body="&lt;p&gt;The most annoying thing for me about being cold is a runny nose. Is there an advantage to having a runny nose when cold? What does having a runny nose achieve?&lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="86" LastEditDate="2014-04-29T18:17:12.737" LastActivityDate="2017-08-15T17:32:43.317" Title="Why do we get runny noses in the cold?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="446" PostTypeId="2" ParentId="328" CreationDate="2012-01-03T17:51:22.250" Score="4" Body="&lt;p&gt;Nature has done pretty well in the subject of formal computation. So much that we are still trying to keep its pace. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As about your question, it depends on your definition of &quot;non-coding DNA&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, DNA together with the machinery in charge of its maintenance &lt;em&gt;is&lt;/em&gt; Turing-complete in several senses. Take a look, for example, to the existence of mobile genetic  elements: some of them are &quot;subprograms&quot; coding for reverse transcriptases which in turn are able to reproduce the original program. I must note that for doing this with a Turing-complete formalism like the lambda-calculus, well, you need to do a fairly long and complicated program: &lt;a href=&quot;http://crpit.com/confpapers/CRPITV26Larkin.pdf&quot; rel=&quot;nofollow&quot;&gt;http://crpit.com/confpapers/CRPITV26Larkin.pdf&lt;/a&gt; .  And the lambda calculus is &quot;easier&quot; than bare Turing-machines, meaning that you can write shorter programs than with Turing machines for doing the same thing. So, my (somehow specious) argument is that any real-world information machine capable of self-replication is with high likelihood Turing-machine equivalent. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It just happens that the essential feature of mobile genetic elements is to ensure its survival, so, that's probably the reason we haven't found a fragment of DNA able to do something as interesting as calculating square root. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you refer to the part of DNA that can not do anything at all, well, for talking about Turing-machines and computation you need a way in which some &quot;data&quot; can be &quot;interpreted&quot;  as a program. A totally inert piece of DNA does not fill that role, by definition. &lt;/p&gt;&#xA;" OwnerUserId="117" LastEditorUserId="117" LastEditDate="2012-01-05T18:43:23.910" LastActivityDate="2012-01-05T18:43:23.910" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="447" PostTypeId="1" AcceptedAnswerId="633" CreationDate="2012-01-03T17:57:56.613" Score="23" ViewCount="8487" Body="&lt;p&gt;I can understand natural variation in alcohol dehydrogenase (ADH) in a population leading to variation in rate of inebriation (after controlling for other variables -- e.g., mass, food consumption, etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what physiological (adaptive?) process leads to increased alcohol tolerance over the long term in a single individual?&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorDisplayName="user132" LastEditDate="2012-01-16T00:28:57.960" LastActivityDate="2019-06-21T06:09:17.037" Title="What is the mechanism behind &quot;acquired&quot; alcohol tolerance?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;physiology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="448" PostTypeId="2" ParentId="432" CreationDate="2012-01-03T18:16:22.507" Score="8" Body="&lt;p&gt;A list of dyes is available &lt;a href=&quot;http://www.invitrogen.com/site/us/en/home/References/Molecular-Probes-The-Handbook/tables/Properties-of-classic-nucleic-acid-stains.html&quot;&gt;here&lt;/a&gt; and a list of dyes specific to nucleic acids is available &lt;a href=&quot;http://www.invitrogen.com/site/us/en/home/References/Molecular-Probes-The-Handbook/tables/Specialty-nucleic-acid-reagents-for-molecular-biology.html&quot;&gt;here&lt;/a&gt;. I think you have two choices the SYBR Gold nucleic acid gel stain (S11494) which can be detected under UV light (not sure if it can be used with polyacrylamide gels). Your other option which can be used with polyacrylamide gels is the SYBR Green II RNA gel stain (S7564, S7568, S7586), this stain can be detected with UV light post-electrophoresis. It states RNA in the name but it can also be used for ssDNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps&lt;/p&gt;&#xA;" OwnerUserId="158" LastActivityDate="2012-01-03T18:16:22.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="449" PostTypeId="2" ParentId="445" CreationDate="2012-01-03T18:24:44.300" Score="22" Body="&lt;p&gt;There are two reasons for this:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Nasal mucus helps warm inhaled air before it reaches the lungs. In cold weather, the mucus tends to dry out, so the membranes increase their production.&lt;/li&gt;&#xA;&lt;li&gt;At the same time, exhaled air is warmer than the surrounding air, so it contains more moisture than the outside air can hold. This moisture condenses around the tip of the nose.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Explanation found &lt;a href=&quot;http://www.npr.org/templates/story/story.php?storyId=99844567&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there's no particular advantage to getting a runny nose; it's just a normal reaction occurring in extreme conditions.&lt;/p&gt;&#xA;" OwnerUserId="104" LastActivityDate="2012-01-03T18:24:44.300" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="450" PostTypeId="1" AcceptedAnswerId="462" CreationDate="2012-01-03T19:11:43.617" Score="107" ViewCount="19905" Body="&lt;p&gt;I know plants are green due to chlorophyll.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Surely it would be more beneficial for plants to be red than green as by being green they reflect green light and do not absorb it even though green light has more energy than red light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there no alternative to chlorophyll? Or is it something else?&lt;/p&gt;&#xA;" OwnerUserId="299" LastEditorUserId="3952" LastEditDate="2013-08-06T23:46:17.440" LastActivityDate="2019-03-19T16:48:46.887" Title="Why do plants have green leaves and not red?" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;photosynthesis&gt;&lt;speculative&gt;&lt;chloroplasts&gt;" AnswerCount="8" CommentCount="11" FavoriteCount="39" ContentLicense="CC BY-SA 3.0" />
  <row Id="451" PostTypeId="2" ParentId="450" CreationDate="2012-01-03T19:55:01.747" Score="33" Body="&lt;p&gt;I believe it is because of a trade off between absorbing a wide range of photons and not absorbing too much heat.  Certainly this is a reason why leaves are not black - the enzymes in photosynthesis as it stands would be denatured by the excess heat that would be gained.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This may go some of the way towards explaining why green is reflected rather than red as you suggested - reflecting away a higher energy colour reduces the amount of thermal energy gained by the leaves.&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-01-03T19:55:01.747" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="452" PostTypeId="1" AcceptedAnswerId="456" CreationDate="2012-01-03T19:56:35.563" Score="40" ViewCount="13906" Body="&lt;p&gt;My biology teachers never explained why animals need to breathe oxygen, just that we organisms die if we don't get oxygen for too long. Maybe one of them happened to mention that its used to make ATP. Now in my AP Biology class we finally learned the specifics of how oxygen is used in the &lt;a href=&quot;http://www.science.smith.edu/departments/Biology/Bio231/etc.html&quot;&gt;electron transport chain&lt;/a&gt; due to its high electronegativity. But I assume this probably isn't the only reason we need oxygen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What other purposes does the oxygen we take in through respiration serve? Does oxygen deprivation result in death just due to the halting of ATP production, or is there some other reason as well? What percentage of the oxygen we take in through respiration is expelled later through the breath as carbon dioxide?&lt;/p&gt;&#xA;" OwnerUserId="62" LastEditorUserId="107" LastEditDate="2012-01-05T19:49:46.557" LastActivityDate="2020-02-16T11:58:43.107" Title="What does the human body use oxygen for besides the final electron acceptor in the electron transport chain?" Tags="&lt;biochemistry&gt;&lt;cellular-respiration&gt;" AnswerCount="5" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="455" PostTypeId="2" ParentId="452" CreationDate="2012-01-03T22:30:04.863" Score="28" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Superoxide&quot; rel=&quot;noreferrer&quot;&gt;Superoxide&lt;/a&gt;, O&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;−&lt;/sup&gt; is created by the immune system in &lt;a href=&quot;http://en.wikipedia.org/wiki/Phagocyte&quot; rel=&quot;noreferrer&quot;&gt;phagocytes&lt;/a&gt; (including neutrophils, monocytes, macrophages, dendritic cells, and mast cells) which use NADPH oxidase to produce it from O&lt;sub&gt;2&lt;/sub&gt; for use against invading microorganisms. However, under normal conditions, the mitochondrial electron transport chain is a major source of O&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;−&lt;/sup&gt;, converting up to perhaps 5% of O&lt;sub&gt;2&lt;/sub&gt; to superoxide. [1]&lt;/p&gt;&#xA;&lt;p&gt;As a side note, there are two sides to this coin.  While this is a useful tool against microorganisms, the formation of the reactive oxygen species has been incriminated in autoimmune reactions and diabetes (type 1). [2]&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;[1] Packer L, Ed. &lt;em&gt;Methods in Enzymology&lt;/em&gt;, Volume 349. San Diego, Calif: Academic Press; 2002&lt;/p&gt;&#xA;&lt;p&gt;[2] Thayer TC, Delano M, et al. (2011) &lt;em&gt;Superoxide production by macrophages and T cells is critical for the induction of autoreactivity and type 1 diabetes,60&lt;/em&gt;(8), 2144-51.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="57" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-02-02T16:12:46.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="456" PostTypeId="2" ParentId="452" CreationDate="2012-01-03T22:32:43.140" Score="28" Body="&lt;p&gt;Oxygen is actually highly toxic to cells and organisms – &lt;a href=&quot;http://en.wikipedia.org/wiki/Reactive_oxygen_species&quot; rel=&quot;noreferrer&quot;&gt;reactive oxygen species&lt;/a&gt; cause &lt;a href=&quot;http://en.wikipedia.org/wiki/Oxidative_stress&quot; rel=&quot;noreferrer&quot;&gt;oxidative stress&lt;/a&gt;, essentially cell damage and contributing to cell ageing. A lot of anaerobic organisms have never learned to cope with this and die almost immediately when exposed to oxygen. One classical example of this is &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/C._botulinum&quot; rel=&quot;noreferrer&quot;&gt;C. botulinum&lt;/a&gt;&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Oxygen &lt;em&gt;is&lt;/em&gt; incorporated in several molecules in the cell (for instance riboses and certain amino acids) but as far as I know, all of this comes into the cell as metabolic products, not in the form of pure oxygen.&lt;/p&gt;&#xA;&lt;p&gt;The oxygen (&lt;span class=&quot;math-container&quot;&gt;$\ce{O2}$&lt;/span&gt;) we breathe is completely used up during aerobic respiration. The stoichiometry of this is given by the following &lt;a href=&quot;https://en.wikipedia.org/wiki/Cellular_respiration#Aerobic_respiration&quot; rel=&quot;noreferrer&quot;&gt;simplified equation&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$\ce{C_6H12O6 + 6 O2 -&amp;gt; 6 CO2 + 6 H2O + heat}$$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;/a/35166/166&quot;&gt;WYSIWYG’s answer&lt;/a&gt; goes into more detail.&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-12T13:38:57.583" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="457" PostTypeId="1" AcceptedAnswerId="472" CreationDate="2012-01-03T22:45:31.850" Score="22" ViewCount="7495" Body="&lt;p&gt;I watched the documentary &quot;Evolve&quot; recently and in the segment on &quot;size&quot; Scott V. Edwards, Harvard evolutionary biologist mentioned the idea that humans might evolve to be 7' tall in 'hundreds of years'. (I think this may have been taken out of context... I have emailed him to find out, but do not expect a response from someone so busy)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reasoning goes that the trend in the past 100 years has been greater height, and women show a strong preference for men who are taller than they are. (Though a large share perhaps all of this difference has been due to diets higher in protein at an early age) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder, though, if this is only part of the story. The preference women have is not just for tall men, but for a man who is taller than she is. Likewise, men seem to prefer woman who are shorter than they are. There is even cultural pressure: the classic western image of a couple on wedding cake always shows a man who is about 4&quot; (to scale) taller than the bride.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, women who are short have an advantage as they have a greater pool of men to choose from. (Colloquially, simply ask any 6' tall woman if she feels her height helps her find dates.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say that men seek women who are shorter than they are, but no more than 8&quot; shorter. Women seek men who are taller than they are but no more than 8&quot; taller. Given that the current average height for men is 5'8&quot; and for women it is 5'4&quot; (and distributed normally SD 2.8&quot;) will we have selective pressure that leads to greater or lesser height? (This is, obviously, oversimplified, but it is a starting point.)&lt;/p&gt;&#xA;" OwnerUserId="301" LastEditorUserId="8186" LastEditDate="2014-07-21T13:23:36.223" LastActivityDate="2014-07-21T13:23:36.223" Title="Height and natural selection in humans?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;auxology&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="458" PostTypeId="2" ParentId="432" CreationDate="2012-01-04T01:44:33.623" Score="7" Body="&lt;p&gt;I would think GelRed or GelGreen would be an option too.  They claim to be more sensitive than EtBr and certainly less toxic (even moreso than SYBR Green).  I haven't personally used them against such a small bp product though.  GelRed has basically the same excitation/emission wavelengths as EtBr so no equipment change is needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biotium.com/product/product_info/Protocol/PI-41003.pdf&quot;&gt;Product sheet&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.phenixresearch.com/58CD49D6607546F99FCEC8576FFD74DB.asp?ccb_key=720827141BBE4E8E8AF862DAB80A6ABD&quot;&gt;Store link&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="96" LastActivityDate="2012-01-04T01:44:33.623" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="459" PostTypeId="2" ParentId="452" CreationDate="2012-01-04T08:44:53.543" Score="11" Body="&lt;p&gt;The overwhelming use of oxygen is to provide us (in combination with food) with energy.  We have a great need for energy in our cells, which is why we have these lungs, diaphragms, red blood cells, etc.; they assure we get the oxygen to obtain the energy (via the electron transport chain).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The overall metabolism of glucose (C&lt;sub&gt;6&lt;/sub&gt;H&lt;sub&gt;12&lt;/sub&gt;O&lt;sub&gt;6&lt;/sub&gt;) is a representative reaction:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt; C&lt;sub&gt;6&lt;/sub&gt;H&lt;sub&gt;12&lt;/sub&gt;O&lt;sub&gt;6&lt;/sub&gt; + 6 O&lt;sub&gt;2&lt;/sub&gt; --&gt; 6 CO&lt;sub&gt;2&lt;/sub&gt; + 6 H&lt;sub&gt;2&lt;/sub&gt;O + energy&lt;/pre&gt; &#xA;&#xA;&lt;p&gt;You can see that just as much oxygen goes out as gaseous CO&lt;sub&gt;2&lt;/sub&gt; as came in as gaseous oxygen (O&lt;sub&gt;2&lt;/sub&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The energy is temporarily kept in the form of the phosphate bond in ATP molecules so that it can be shuttled around the cell to the multitude of cellular processes that need energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Energy is so essential to the cellular processes that maintain animal cells that lack of that energy, which results quickly when there is oxygen deprivation, soon causes irreversible damage and death.&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2012-01-04T08:44:53.543" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="461" PostTypeId="2" ParentId="328" CreationDate="2012-01-04T09:55:23.630" Score="6" Body="&lt;p&gt;I am very suprised nobody mentioned the field of DNA-computing. It is proofen by Leonard Adleman and Richard Lipton that you can compute with DNA molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the article of Adleman they present an experiment to solve an instance of the Traveling-Salesman-Problem. Because this problem is in NP one can say that the DNA is turing-complete. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1126/science.7973651&quot;&gt;Article of Adleman&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/3540641963&quot;&gt;For a deeper understanding see&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="120" LastEditorUserId="120" LastEditDate="2012-01-04T11:41:09.183" LastActivityDate="2012-01-04T11:41:09.183" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="462" PostTypeId="2" ParentId="450" CreationDate="2012-01-04T11:25:55.573" Score="90" Body="&lt;p&gt;Surely it would be even more beneficial for plants to be black instead of red or green, from an energy absorption point of view. And &lt;a href=&quot;http://en.wikipedia.org/wiki/Solar_cell&quot; rel=&quot;noreferrer&quot;&gt;Solar cells&lt;/a&gt; are indeed pretty dark.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, as Rory &lt;a href=&quot;https://biology.stackexchange.com/a/451/303&quot;&gt;indicated&lt;/a&gt;, higher energy photons will only produce heat. This is because the chemical reactions powered by photosynthesis require only a certain amount of energy, and any excessive amount delivered by higher-energy photons cannot be simply used for another reaction&lt;sup&gt;1&lt;/sup&gt; but will yield heat. I don't know how much trouble that actually causes, but there is another point:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As explained, what determines the efficiency of solar energy conversion is not the energy per photon, but the amount of photons available. So you should take a look at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sunlight#Composition&quot; rel=&quot;noreferrer&quot;&gt;sunlight spectrum&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/File:Solar_Spectrum.png&quot; rel=&quot;noreferrer&quot; title=&quot;Solar Radiation Spectrum&quot;&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/4/4c/Solar_Spectrum.png&quot; alt=&quot;Solar Radiation Spectrum&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Irradiance is an energy density, however we are interested in photon density, so you have to divide this curve by the energy per photon, which means multiply it by λ/(hc) (that is higher wavelengths need more photons to achieve the same Irradiance). If you compare that curve integrated over the high energy photons (say, λ &amp;lt;&amp;nbsp;580 nm) to the integration over the the low energy ones, you'll notice that despite the atmospheric losses (the red curve is what is left of the sunlight at sea level) there are a lot more &quot;red&quot; photons than &quot;green&quot; ones, so making leaves red would waste a lot of potentially converted energy&lt;sup&gt;2&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, this is still no explanation why leaves are not simply black&amp;nbsp;— absorbing all light is surely even more effective, no? I don't know enough about organic chemistry, but my guess would be that there are no organic substances with such a broad absorption spectrum and adding another kind of pigment might not pay off.&lt;sup&gt;3&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1)&lt;/sup&gt; Theoretically that &lt;em&gt;is&lt;/em&gt; possible, but it's a highly non-linear process and thus too unlikely to be of real use (in plant medium at least)&lt;br&gt;&#xA;&lt;sup&gt;2)&lt;/sup&gt; Since &lt;a href=&quot;http://en.wikipedia.org/wiki/Electromagnetic_absorption_by_water&quot; rel=&quot;noreferrer&quot;&gt;water absorbs red light stronger than green and blue light&lt;/a&gt; deep sea plants are indeed better off being red, as Marta Cz-C &lt;a href=&quot;https://biology.stackexchange.com/questions/450/why-do-plants-have-green-leaves-and-not-red#comment-469&quot;&gt;mentioned&lt;/a&gt;.&lt;br&gt;&#xA;&lt;sup&gt;3&lt;/sup&gt;  And other alternatives, like the semiconductors used in Solar cells, are rather unlikely to be encountered in plants...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additional reading, &lt;a href=&quot;https://biology.stackexchange.com/review/suggested-edits/20188&quot;&gt;proposed&lt;/a&gt; by &lt;a href=&quot;https://biology.stackexchange.com/users/11677/dave-jarvis&quot;&gt;Dave Jarvis&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://pcp.oxfordjournals.org/content/50/4/684.full&quot; rel=&quot;noreferrer&quot;&gt;http://pcp.oxfordjournals.org/content/50/4/684.full&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691134/&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691134/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.life.illinois.edu/govindjee/photosynBook/Chapter11.pdf&quot; rel=&quot;noreferrer&quot;&gt;http://www.life.illinois.edu/govindjee/photosynBook/Chapter11.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.heliospectra.com/sites/default/files/general/What%20light%20do%20plants%20need_5.pdf&quot; rel=&quot;noreferrer&quot;&gt;https://www.heliospectra.com/sites/default/files/general/What%20light%20do%20plants%20need_5.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="303" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-09-28T06:40:54.027" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="463" PostTypeId="1" AcceptedAnswerId="465" CreationDate="2012-01-04T14:02:38.530" Score="7" ViewCount="267" Body="&lt;p&gt;I need a human cell line that does not express the GLP-1 (glucagon like peptide-1) receptor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm working with HeLa cells, do those express the GLP-1 receptor? Which other cell lines exist that don't express this specific receptor?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any general resources where I could find this kind of information?&lt;/p&gt;&#xA;" OwnerUserId="126" LastEditorUserId="6" LastEditDate="2012-01-05T19:49:43.437" LastActivityDate="2017-12-14T07:49:26.713" Title="Which human cell lines do not express the GLP-1 receptor?" Tags="&lt;cell-culture&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="464" PostTypeId="2" ParentId="410" CreationDate="2012-01-04T15:06:56.323" Score="6" Body="&lt;p&gt;This phenomenon is called &lt;em&gt;depolarization block&lt;/em&gt; and it occurs in real membranes in current-clamp experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key mechanism is that the membrane has not been allowed to repolarize sufficiently to relieve the inactivation of sodium channels. The Hodgkin-Huxley model reflects this in the &quot;inverted&quot; voltage-dependence of the h gate (sodium inactivation gate)--inactivation is greater at higher voltages. This means that sodium channels cannot open again, or trigger another action potential, until the membrane is repolarized. Canonically, the need to relieve inactivation of sodium channels is the reason for the afterhyperpolarization phase of an action potential where the AP downstroke becomes transiently more negative than the resting potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The relevance of depolarization block in &lt;em&gt;in vivo&lt;/em&gt; physiological conditions is not well studied. It is not likely that depolarization block occurs in well-behaved neurons under physiological conditions. However, it's possible that it does occur during pathological states.&lt;/p&gt;&#xA;" OwnerUserId="72" LastActivityDate="2012-01-04T15:06:56.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="465" PostTypeId="2" ParentId="463" CreationDate="2012-01-04T15:20:12.507" Score="5" Body="&lt;p&gt;AbCam suggests HeLa cells as positive controls for their &lt;a href=&quot;http://www.abcam.com/GLP1R-antibody-ab119287.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;antibody to GLP1R&lt;/a&gt;. They provide the following pictures of HeLa cells labeled with their antibody:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7mfyJ.jpg&quot; alt=&quot;HeLa cells labeled with anti-GLP1R&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(The image of the right is treated with synthesized peptide.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Glucagon-like_peptide_1_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;, GLP1R is also expressed in pancreatic beta cells and the brain.&lt;/p&gt;&#xA;" OwnerUserId="23" LastActivityDate="2012-01-04T15:20:12.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="466" PostTypeId="2" ParentId="457" CreationDate="2012-01-04T17:01:16.763" Score="13" Body="&lt;p&gt;&lt;em&gt;(This should have been a comment, but I don't have enough reputation yet. Sorry!)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You asked an interesting question, but I'm not sure about your reasoning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, the &quot;trend&quot; you describe, that in the past century humans grew taller that ever before, is a phenomenon known to most European countries, one of the so called &quot;secular trends&quot;: a uni-directional change in height (or growth rate) over a period of time. It was established that adult hight increased by 1 to 3 centimeters for each decade until 1980 (except for the times of World War 2, which had an opposite effect in some places). Such changes, however, happened much too quickly to be of genetic origin; and are much better explained by an increase in quality of life. In line with this explanation is the increase in height and growth tempo we see now in Third World countries, clearly the effect of improving life conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, in my opinion, womens' preference for higher men can be another manifestation of their wanting simply the best male. I don't see any particular advantage for a woman to want a man higher that she is, but, as you pointed out, anecdotal evidence suggests otherwise.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Based on:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Cole, T.J. &lt;a href=&quot;http://journals.cambridge.org/action/displayAbstract?fromPage=online&amp;amp;aid=796528&quot;&gt;Secular trends in growth&lt;/a&gt;. Proc Nutr Soc 59, 317–324 (2000), PMID: 10946801.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;See more on secular trends in:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Cole, T.J. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1570677X02000333&quot;&gt;The secular trend in human physical growth: a biological view&lt;/a&gt;. Economics &amp;amp; Human Biology 1, 161–168 (2003), PMID: 15463971.&lt;/li&gt;&#xA;&lt;li&gt;Sargent, M. &lt;a href=&quot;http://ebooks.cambridge.org/ebook.jsf?bid=CBO9780511546419&quot;&gt;Biomedicine and the human condition: challenges, risks, and rewards&lt;/a&gt;. (2005).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="251" LastEditorUserId="251" LastEditDate="2012-01-05T02:21:37.447" LastActivityDate="2012-01-05T02:21:37.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="469" PostTypeId="2" ParentId="345" CreationDate="2012-01-04T19:05:01.530" Score="15" Body="&lt;p&gt;It would also be logical to note that a chewed tablet increases its surface-area-to-volume ratio for absorption relative to an intact tablet, for any absorptive tissue.&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-01-04T19:05:01.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="470" PostTypeId="1" AcceptedAnswerId="474" CreationDate="2012-01-04T19:22:22.690" Score="11" ViewCount="2422" Body="&lt;p&gt;Many explanations of histone biochemistry isn't quite elucidating for the undergraduate student. How does histone structure (dimers, octomers) relate to their specific functions as core or linker histones? Also, how do both linker and core histones interact within nucleosomes to ultimately regulate gene expression?&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="948" LastEditDate="2014-01-13T21:37:51.573" LastActivityDate="2014-01-13T21:37:51.573" Title="What is the functional and structural distinction between core (H2A, H2B, H3,H4) and linker(H1/H5) histones?" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;histone&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="471" PostTypeId="2" ParentId="406" CreationDate="2012-01-04T20:02:28.150" Score="20" Body="&lt;p&gt;I would like to add a &lt;a href=&quot;http://www.youtube.com/watch?v=niQ0kkgPxJk&amp;amp;list=FLxdUC1zJmqWm08ib_SJn1tg&amp;amp;index=1&amp;amp;feature=plpp_video&quot;&gt;lecture&lt;/a&gt; on Synthetic Biology by &lt;a href=&quot;http://openwetware.org/wiki/Andrew_Hessel&quot;&gt;Andrew Hessel&lt;/a&gt;, who introduces the open source synthetic biology field, compares it to computing, and gives an overview of what are its applications, like the creation of the first synthetic organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also stumbled upon a &lt;a href=&quot;http://www.youtube.com/watch?v=219YybX66MY&amp;amp;feature=related&quot;&gt;talk&lt;/a&gt; from the famous physicist &lt;a href=&quot;http://en.wikipedia.org/wiki/Michio_Kaku&quot;&gt;Michio Kaku&lt;/a&gt;, who shares his vision about the world in 2030, when synthetic biology will change every-day-life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Enjoy!&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-01-04T20:02:28.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="472" PostTypeId="2" ParentId="457" CreationDate="2012-01-04T20:04:30.750" Score="15" Body="&lt;p&gt;@kate has what is probably the more correct answer for the observed pattern. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But as an experiment, I set up a basic simulation to approximate the conditions that you lay out:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Starting mean heights of 5'8&quot; (172.72 cm) and 5'4&quot; (162.56 cm) with standard deviations of 2.8&quot; (7.112 cm). I used cm, because it's easier than dealing with inches.&lt;/li&gt;&#xA;&lt;li&gt;Males will not mate with females that are taller than themselves.&lt;/li&gt;&#xA;&lt;li&gt;Females will not mate with males more than 8&quot; taller.&lt;/li&gt;&#xA;&lt;li&gt;Males will not mate with females more then 8&quot; shorter (follows from #3 above).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The problem that I quickly ran into was that, by truncating part of the normal distribution, the variance in height at each generation gradually decreased. After about 20 generations, the means weren't evolving because there was so little variation in height.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human height is one of the most studied quantitative traits, going back over 100 years to some of the very first statisticians (Fisher, Galton). Height is a polygenic trait with very high heritability (&lt;em&gt;h&lt;/em&gt;&lt;sup&gt;2&lt;/sup&gt; = 0.8)&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21340692&quot;&gt;1&lt;/a&gt;&lt;/sup&gt;. Genome-wide association studies have reported 54 genes involved in determination of human height&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18443579&quot;&gt;2&lt;/a&gt;&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine that each of these 54 genes has just two alleles: a and b. a gives a +1 to height. b gives a -1 to height. So aa would be +2, ab or ba 0, and bb -2. The sum of all those alleles is correlated to height. So if all 54 were aa, then the height would be +108.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem comes in when people only mate with taller people. Over time, the proportion of b's will decrease, and the proportion of a's will increase, but only to a point. Once all the alleles are fixed at a, there won't be any room left. The genetic variation will be exhausted. Without the input of new alleles, height will cease to evolve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1&lt;/strong&gt; Lettre, G. 2011. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21340692&quot;&gt;Recent progress in the study of the genetics of height&lt;/a&gt;. &lt;em&gt;Hum Genet&lt;/em&gt; 129:465–472.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2&lt;/strong&gt; Visscher, PM. 2008. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18443579&quot;&gt;Sizing up human height variation&lt;/a&gt;. &lt;em&gt;Nat Genet&lt;/em&gt; 40(5):489-90.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-01-04T20:04:30.750" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="473" PostTypeId="2" ParentId="452" CreationDate="2012-01-04T20:07:11.593" Score="19" Body="&lt;p&gt;You probably know by now that cytochrome &lt;em&gt;c&lt;/em&gt; oxidase, the last complex of the electron transport chain, belongs to a class of enzymes called oxidoreductases, that use oxygen atoms as electron acceptors. One type of oxidoreductases are oxidases, enzymes that (at least in theory [1]) use molecular oxygen--O&lt;sub&gt;2&lt;/sub&gt;, like in air--as their electron acceptor. From what I know, however, sometimes that isn't the case: xanthine oxidase, that converts xanthine to uric acid, gets its oxygen atoms from water [2]. Examples of the &quot;true&quot; oxidases include L-amino-acid oxidase and cytochrome P450 (aka. CYP family).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite cytochrome P450 being a numerous and important enzyme family, responsible for most of known drugs metabolism and some essential lipids transformations, it probably consumes only a fraction of oxygen that animals breathe in. I wasn't able to find any estimations, but would be surprised if it was more than perhaps 0,1%.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/intro.html&quot;&gt;Introduction to EC1 class&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] Metz, S. &amp;amp; Thiel, W. &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jp909999s&quot;&gt;A Combined QM/MM Study on the Reductive Half-Reaction of&#xA;Xanthine Oxidase: Substrate Orientation and Mechanism&lt;/a&gt;. J. Am. Chem. Soc. 2009, 131, 14885–14902, PMID: 20050623.&lt;/p&gt;&#xA;" OwnerUserId="251" LastEditorUserId="251" LastEditDate="2012-01-05T02:18:50.833" LastActivityDate="2012-01-05T02:18:50.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="474" PostTypeId="2" ParentId="470" CreationDate="2012-01-04T20:33:02.123" Score="7" Body="&lt;p&gt;The core histones are H2A, H2B, H3, and H4, and the linker histones are H1 and H5. The structure of the nucleosome is well explained in &lt;a href=&quot;http://en.wikipedia.org/wiki/Histone&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Two of each of the core histones assemble to form one octameric nucleosome core particle, and 147 base pairs of DNA wrap around this core particle 1.65 times in a left-handed super-helical turn. The linker histone H1 binds the nucleosome and the entry and exit sites of the DNA, thus locking the DNA into place and allowing the formation of higher order structure. The most basic such formation is the 10 nm fiber or beads on a string conformation. This involves the wrapping of DNA around nucleosomes with approximately 50 base pairs of DNA separating each pair of nucleosomes (also referred to as linker DNA). The assembled histones and DNA is called chromatin. Higher-order structures include the 30 nm fiber (forming an irregular zigzag) and 100 nm fiber, these being the structures found in normal cells. During mitosis and meiosis, the condensed chromosomes are assembled through interactions between nucleosomes and other regulatory proteins.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The core histones have a positive net charge, which facilitates the interaction with the negatively charged phosphate groups of DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from defining the nucleosome structure, the function of the core histones is regulatory: it can switch on/off gene expression by histone modifications like acetylation or methylation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The gene expression is ON when there is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;• DNA demethylation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;• histones acetylation&lt;br&gt;&#xA;• H3K4 methylation&lt;br&gt;&#xA;• H3K36 methylation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;• H3K9 demethylation&lt;br&gt;&#xA;• H3K27 demethylation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The gene expression is OFF when there is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;• DNA methylation&lt;br&gt;&#xA;• histones deacetylation&lt;br&gt;&#xA;• H3K4 demethylation&lt;br&gt;&#xA;• H3K36 demethylation&lt;br&gt;&#xA;• H3K9 methylation&lt;br&gt;&#xA;• H3K27 methylation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;// H3K4 demethylation is abbreviation for: Lysine 4 of H3 is demethylated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/S0959-437X%2802%2900279-4&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Berger SL&lt;/strong&gt;. 2002. Histone modifications in transcriptional regulation. Current Opinion in Genetics &amp;amp; Development 12: 142–148&lt;/a&gt; is also a nice review.&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="836" LastEditDate="2012-09-07T23:03:16.877" LastActivityDate="2012-09-07T23:03:16.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="475" PostTypeId="1" AcceptedAnswerId="480" CreationDate="2012-01-04T21:57:39.770" Score="22" ViewCount="734" Body="&lt;p&gt;It has been shown in several studies that regular aerobic exercise increases brain volume in aging humans. The changes were observed in hippocampus and were correlated with dramatic reduction of age-related dementia. Interestingly, the intensity of training had little influence on the results: walking, climbing stairs, gardening were just as effective at reducing dementia as more strenuous exercise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the biological mechanism behind this phenomena?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IS0pr.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fig. The aerobic exercise group showed an increase in the anterior hippocampus and no change in the posterior hippocampus.[&lt;a href=&quot;https://i.stack.imgur.com/IS0pr.jpg&quot;&gt;1&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Erickson et al. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21282661&quot;&gt;Exercise training increases size of hippocampus and improves memory&lt;/a&gt;. PNAS. 2011. &lt;/li&gt;&#xA;&lt;li&gt;Colcombe et al. &lt;a href=&quot;http://biomedgerontology.oxfordjournals.org/content/61/11/1166.abstract&quot;&gt;Aerobic exercise training increases brain volume in aging humans&lt;/a&gt;. J Gerontology. 2006&lt;/li&gt;&#xA;&lt;li&gt;Ravaglia, et al. &lt;a href=&quot;http://www.neurology.org/content/70/19_Part_2/1786.abstract&quot;&gt;Physical activity and dementia risk in the elderly&lt;/a&gt;. Neurology. 2008&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="277" LastActivityDate="2012-01-05T04:18:16.847" Title="Why does regular exercise increase brain volume?" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;&lt;senescence&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="476" PostTypeId="1" CreationDate="2012-01-04T22:43:51.473" Score="6" ViewCount="2156" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Golgi_apparatus&quot;&gt;Golgi Apparatus&lt;/a&gt; is an organelle with a great number of functions, I am particularly intrigued in the role it plays in packaging macromolecules and sending them to their target organelle or to leave the cell in exocytosis.  I would love to know more about how this process works.  How does the Golgi Apparatus recognise which molecules are which and how does the vesicle it places the molecule into navigate to where it is needed?  &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-01-05T12:45:46.763" Title="How does the Golgi Apparatus perform its function?" Tags="&lt;cell-biology&gt;&lt;eukaryotic-cells&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="477" PostTypeId="1" AcceptedAnswerId="478" CreationDate="2012-01-04T23:57:34.683" Score="31" ViewCount="270416" Body="&lt;p&gt;DNA replication goes in the 5' to 3' direction because DNA polymerase acts on the 3'-OH of the existing strand for adding free nucleotides. Is there any biochemical reason why all organisms evolved to go from 5' to 3'? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any energetic/resource advantages to using 5' to 3'? Is using the 3'-OH of the existing strand to attach the phosphate of the free nucleotide more energetically favorable than using the 3'-OH of the free nucleotide to attach the phosphate of the existing strand? Does it take more resources to create a 3' to 5' polymerase?&lt;/p&gt;&#xA;" OwnerUserId="90" LastEditorUserId="6" LastEditDate="2012-01-05T19:49:50.020" LastActivityDate="2018-05-05T22:33:14.900" Title="Why is DNA replication  performed in the 5' to 3' direction?" Tags="&lt;dna&gt;&lt;replication&gt;&lt;polymerase&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="478" PostTypeId="2" ParentId="477" CreationDate="2012-01-05T00:42:58.467" Score="31" Body="&lt;p&gt;Prof. &lt;a href=&quot;http://en.wikipedia.org/wiki/User%3aAgathman&quot;&gt;Allen Gathman&lt;/a&gt; has a great 10-minutes &lt;a href=&quot;http://www.youtube.com/watch?v=y4hKibS2fAo&quot;&gt;video&lt;/a&gt; on Youtube, explaining the reaction of adding nucleotide in the 5' to 3' direction, and why it doesn't work the other way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Briefly, the energy for the formation of the phosphodiester bond comes from the dNTP, which has to be added. dNTP is a nucleotide which has two additional phosphates attached to its 5' end. In order to join the 3'OH group with the phosphate of the next nucleotide, one oxygen has to be removed from this phosphate group. This oxygen is also attached to two extra phosphates, which are also attached to a Mg++. Mg++ pulls up the electrons of the oxygen, which weakens this bond and the so called nucleophilic attack of the oxygen from the 3'OH succeeds, thus forming the phospodiester bond.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you try to join the dNTP's 3'OH group to the 5' phosphate of the next nucleotide, there won't be enough energy to weaken the bond between the oxygen connected to the 5' phosphorous (the other two phosphates of the dNTP are on the 5' end, not on the 3' end), which makes the nucleophilic attack harder.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Watch the video, it is better explained there.&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-01-05T07:18:31.110" LastActivityDate="2012-01-05T07:18:31.110" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="479" PostTypeId="2" ParentId="303" CreationDate="2012-01-05T02:59:13.187" Score="6" Body="&lt;p&gt;DAPI (4',6-diamidino-2-phenylindole) preferentially binds AT-rich DNA (although it binds CG-rich DNA, too), which can give chromosomes distinctive banding patterns if they are polytene or in metaphase.  In interphase condensed chromosomes, such as the inactive X chromosomes of female mammals (Barr Body), the relatively high concentration of tightly-packed DNA makes the chromosome appear as a brighter spot in the nucleus.  When the DNA of a chromosome is decondensed (such as the rest of the chromosomes in interphase), it appears as more-or-less homogeneously stained DNA in the nucleus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A great picture is &lt;a href=&quot;http://www.pnas.org/content/98/15/8703/F2.expansion.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; (see below), A is the DAPI staining, B is a protein localized to the Barr Body, C is the RNA (Xist) which binds the Barr Body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xiLsp.jpg&quot; alt=&quot;Barr body&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the active X is not condensed, it appears as do the rest of the chromosomes, so cannot be identified among the mixture of autosomes.  The difference in DAPI appearance has nothing to do with activity per se, but rather differences in how tightly packaged the chromosomes are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not understand the first part of your question, though.  You cannot tell from a still image that the Barr Body is relatively inactive.  If your were doing experiments on live cells, you could measure RNA production (using a labeled nucleotide), immunofluorescence to show localization of e.g. RNA Polymerase, or reporter genes located on the inactive versus active X chromosomes.  If you clarify your question, I can answer better.&lt;/p&gt;&#xA;" OwnerUserId="219" LastEditorUserId="66" LastEditDate="2012-01-05T14:04:43.313" LastActivityDate="2012-01-05T14:04:43.313" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="480" PostTypeId="2" ParentId="475" CreationDate="2012-01-05T04:18:16.847" Score="10" Body="&lt;p&gt;Well, Erickson et al (2011) attribute the increase in brain volume in the aerobic exercise group to &lt;a href=&quot;http://en.wikipedia.org/wiki/BDNF&quot;&gt;brain-derived neurotrophic factor&lt;/a&gt; (BDNF).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically (p. 3020):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In fact, we found here that changes in serum BDNF levels were&#xA;  associated with changes in anterior hippocampal volume; an important&#xA;  link because the hippocampus is rich in BDNF, and BDNF levels increase&#xA;  with exercise treatments in both rodents and humans. BDNF is a&#xA;  putative mediator of neurogenesis and contributes to dendritic&#xA;  expansion and is also critical in memory formation. Our results suggest that &#xA;  cell proliferation or increased dendritic branching might explain increased &#xA;  hippocampal volume and improvements in memory after exercise&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;with the caveat:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;however, increased vascularization (15, 16, 33) and dendritic&#xA;  complexity (34) may also be contributing to increased volume&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-01-05T04:18:16.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="481" PostTypeId="1" AcceptedAnswerId="484" CreationDate="2012-01-05T04:36:03.560" Score="12" ViewCount="311" Body="&lt;p&gt;From all accounts, it seems as if the &lt;em&gt;Escherichia&lt;/em&gt;, &lt;em&gt;Enterobacter&lt;/em&gt;, etc. that live and thrive in the human gut are pretty well entrenched.  I know that these microbial populations are often analyzed as an ecosystem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What surprises me is that it seems like minor food poisoning can throw the whole ecosystem off.  I know superficially that &lt;em&gt;Clostridium&lt;/em&gt; are contenders in the fight because they remain viable after traveling through the acid of the stomach, but why are these populations so sensitive to other invading bacteria? &lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="69" LastEditDate="2012-01-07T12:18:12.643" LastActivityDate="2012-01-10T23:34:02.503" Title="Why is the  microbial ecosystem of the gut so susceptible to disruption by pathogens?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;digestive-system&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="482" PostTypeId="2" ParentId="477" CreationDate="2012-01-05T09:33:38.363" Score="21" Body="&lt;p&gt;DNA replications needs a source of energy to proceed, this energy is gained by cleaving the 5'-triphosphate of the nucleotide that is added to the existing DNA chain. Any alternative polymerase mechanism needs to account for the source of the energy required for adding a nucleotide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The simplest way one can imagine to perform reverse 3'-5' polymerization would be to use nucleotide-3'-triphosphate instead of the nucleotide-5'-triphosphate every existing polymerase uses. This would allow for a practically identical mechanism as existing polymerases, just with different nucleotides as substrates. The problem with this model is that ribonucleotide-3'-triphosphates are less stable under acidic conditions due to the neighbouring 2'-OH (though this obviously only applies for RNA, not for DNA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So any 3'-5' polymerase would likely need to use the same nucleotide-5'-triphosphates as the 5'-3' polymerase. This would mean that the triphosphate providing the energy for addition of a new nucleotide would be on the DNA strand that is extended, and not on the newly added nucleotide. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One disadvantage of this approach is that nucleotide triphosphates spontaneously hydrolyze under aqeuous conditions. This is no significant problem for the 5'-3' polymerase, as the triphosphate is on the new nucleotide and the polymerase just has to find a new nucleotide. For the 3'-5' polymerase spontaneous hydrolysis is a problem because the triphosphate is on the growing chain. If that one gets hydrolyzed, the whole polymerization needs to be either aborted or the triphosphate need to be readded by some mechanism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can take a look at the article &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0018881&quot;&gt;&quot;A Model for the Evolution of Nucleotide Polymerase Directionality&quot; by Joshua Ballanco and, Marc L. Mansfield&lt;/a&gt; for more information about this. They created a model on early polymerase evolution, though they don't reach any final conclusion.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2012-01-05T11:18:42.153" LastActivityDate="2012-01-05T11:18:42.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="483" PostTypeId="2" ParentId="476" CreationDate="2012-01-05T12:45:46.763" Score="6" Body="&lt;p&gt;This is actually is an awesome story: both how it happens and how it was discovered. This is one of those stories people get &lt;a href=&quot;http://www.nobelprize.org/nobel_prizes/medicine/laureates/1999/index.html#&quot;&gt;Nobel Prize&lt;/a&gt;, and this was &lt;a href=&quot;http://en.wikipedia.org/wiki/G%C3%BCnter_Blobel&quot;&gt;Günter Blobel&lt;/a&gt; who was awarded this highest possible prize for his discovery, which is according to his Nobel prize certificate:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;for the discovery that proteins have intrinsic signals that govern&#xA;  their transport and localization in the cell&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you &lt;a href=&quot;http://www.nobelprize.org/nobel_prizes/medicine/laureates/1999/award-video.html&quot;&gt;watch&lt;/a&gt; or &lt;a href=&quot;http://www.nobelprize.org/nobel_prizes/medicine/laureates/1999/presentation-speech.html&quot;&gt;read&lt;/a&gt; his Nobel prize lecture you will find answers to your question formulated much better than I can do it here. His Nobel lecture was opened with the following words which might already answer you question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Imagine a large factory that manufactures thousands of different items&#xA;  in millions of copies every hour, that promptly packages and ships&#xA;  each of them to waiting customers. Naturally, to avoid chaos, each&#xA;  product requires a clearly labeled address tag. Günter Blobel is being&#xA;  awarded this year's Nobel Prize in Physiology or Medicine for having&#xA;  shown that newly synthesized proteins, analogous to the products&#xA;  manufactured in the factory, contain built-in signals, or address&#xA;  tags, that direct them to their proper cellular destination.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Still, I recommend you to read (or watch) to the end, there are some interesting points on how it was discovered and what experiments were done to do it.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-01-05T12:45:46.763" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="484" PostTypeId="2" ParentId="481" CreationDate="2012-01-05T12:58:46.213" Score="11" Body="&lt;p&gt;There are two types of food poisoning:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Alimentary intoxication&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the case when you consume food which is contaminated with some toxins, and those are responsible for development of the poisoning symptoms. The source organisms of these toxins might not be present anymore (killed by heating during cooking, for example). In this case there is no massive invasion of any foreign organisms into the gut. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Alimentary toxico-infection&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This happens if you eat the food contaminated with microorganisms, and these start to massively proliferate in your alimentary system causing the symptoms of poisoning. The massive intake of the bacteria (even 2-3 spoons of contaminated food might contain millions of bacteria, like &lt;em&gt;Staphilococcus&lt;/em&gt; in contaminated diary products). In this case the balance of gut microflora is dramatically changed due to introduction of a considerable amount of foreign microorganisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, even the poisoning seems to be &quot;minor&quot; (e.g., its symptoms are not so dramatic), there could be different amounts of bacteria invading the guts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second important point here is the increased emptying of the gut due to diarrhea that leads to the washing out some of the &quot;good&quot; bacteria from the guts, especially in case of profuse diarrhea. The newly coming bacteria are not necessarily those that are present in normal microflora, and it takes days or even weeks until the microflora reaches homeostasis again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One last point: even without poisoning, microflora varies, and the amount of different bacterial fractions can fluctuate over time. This is normal and depends upon your eating habits, your environment, immune status, and many other factors.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="107" LastEditDate="2012-01-05T19:49:58.633" LastActivityDate="2012-01-05T19:49:58.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="485" PostTypeId="1" AcceptedAnswerId="506" CreationDate="2012-01-05T13:04:04.913" Score="12" ViewCount="4730" Body="&lt;p&gt;In this &lt;a href=&quot;http://highered.mcgraw-hill.com/sites/dl/free/0072835125/126997/12-06.swf&quot; rel=&quot;nofollow&quot;&gt;animation&lt;/a&gt;, towards the end (about three quarters) the process of transcription termination is shown. It states that the transcribed RNA forms a hairpin loop (or stem-loop), which halts the transcription process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, why does it halt the transcription process, considering that the RNA polymerase moves in the opposite direction of where the stem loop is created? Does it somehow change the RNA conformation such that no further bases can be added? Interpreting it as a physical obstacle doesn't seem to make any sense here.&lt;/p&gt;&#xA;" OwnerUserId="312" LastEditorUserId="43" LastEditDate="2012-09-14T15:56:02.863" LastActivityDate="2012-09-14T15:56:02.863" Title="How does the stem-loop cause intrinsic transcription termination?" Tags="&lt;molecular-genetics&gt;&lt;transcription&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="486" PostTypeId="2" ParentId="328" CreationDate="2012-01-05T13:16:19.053" Score="1" Body="&lt;p&gt;Let me answer your question by splitting it into two parts:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can DNA be used as an programmable medium (=band) for Turing machine?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer is &lt;strong&gt;YES.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Starting from the breaking &lt;a href=&quot;http://www.cs.duke.edu/bioComp/references/shapiroJohn/ShapiroNature2001explained.pdf&quot; rel=&quot;nofollow&quot;&gt;paper by Shapiro et al. in Nature&lt;/a&gt;, followed by another great article by &lt;a href=&quot;http://www.nature.com/embor/journal/v4/n1/full/embor719.html&quot; rel=&quot;nofollow&quot;&gt;Parker&lt;/a&gt;, there are many scientific publications about how to use DNA for computing. Unfortunately, these findings are still not applicable for classic computations and DNA computers will hardly substitute the normal ones in the nearest future.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can a junk DNA work as Turing machine?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a known principle in Computer Science called &quot;Junk In, Junk Out&quot;. Same in the case of DNA -- there is a way to use junk DNA for computing, but the result of the computation will mostly be junk too: as long as we don't know what this DNA is for, and this doesn't seem to operate as Turing machine on its own, there is hardly possible to get something reasonable by running this DNA on a turin machine...&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-01-05T13:16:19.053" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="487" PostTypeId="1" AcceptedAnswerId="538" CreationDate="2012-01-05T13:42:37.000" Score="10" ViewCount="751" Body="&lt;p&gt;When I studied biology at my medical school, we used to learn topics around a century old: the famous Darwin's voyage on &amp;quot;Beagle&amp;quot; to the Galapagos Islands, the classical triad of his Theory of Evolution, etc.&lt;/p&gt;&#xA;&lt;p&gt;At the same time we were told that there is no evidence found in nature for many of these statements of his evolutional theory. For example, people studied &lt;a href=&quot;http://www.wildsingapore.com/news/20060304/060420-5.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;wildlife&lt;/a&gt; around Chernobyl and found that no new species emerged due to much higher mutation rate as a consequence of radiation. On the contrary, there were &lt;a href=&quot;http://www.monstersandcritics.com/science/nature/features/article_1158689.php/Chernobyl_radiation_no_problem_-_almost_-_for_Mother_Nature&quot; rel=&quot;nofollow noreferrer&quot;&gt;no significant differences&lt;/a&gt; between the species living under elevated radiation level and those living in &amp;quot;normal&amp;quot; conditions.&lt;/p&gt;&#xA;&lt;p&gt;Do these facts somehow influence our understanding of the theory of evolution? Are there any breakthrough findings which happened in the last 20 years that prove or disprove it?&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="61039" LastEditDate="2020-09-14T10:17:46.147" LastActivityDate="2020-09-14T10:17:46.147" Title="What is the modern state of the theory of evolution?" Tags="&lt;evolution&gt;&lt;radiation&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="488" PostTypeId="5" CreationDate="2012-01-05T13:43:55.967" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-05T13:43:55.967" LastActivityDate="2012-01-05T13:43:55.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="489" PostTypeId="4" CreationDate="2012-01-05T13:43:55.967" Score="0" Body="The questions tagged with &quot;state-of-the-art&quot; ask for the modern state or current opinion on certain topic in science, especially compared to some known believes or fallacies." OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-05T19:50:21.143" LastActivityDate="2012-01-05T19:50:21.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="490" PostTypeId="5" CreationDate="2012-01-05T13:49:56.190" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-05T13:49:56.190" LastActivityDate="2012-01-05T13:49:56.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="491" PostTypeId="4" CreationDate="2012-01-05T13:49:56.190" Score="0" Body="Organs that play a role in digestion and/or absorption of nutrients: breaking down of food into smaller components that can be absorbed and used as for sources of energy, cellular/tissue building blocks, or cofactors for vital biochemical reactions." OwnerUserId="66" LastEditorUserId="16299" LastEditDate="2016-07-09T19:50:03.020" LastActivityDate="2016-07-09T19:50:03.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="492" PostTypeId="5" CreationDate="2012-01-05T13:50:57.313" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-05T13:50:57.313" LastActivityDate="2012-01-05T13:50:57.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="493" PostTypeId="4" CreationDate="2012-01-05T13:50:57.313" Score="0" Body="Copying the genome for the purpose of reproduction." OwnerUserId="66" LastEditorUserId="4101" LastEditDate="2013-10-31T19:16:03.370" LastActivityDate="2013-10-31T19:16:03.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="494" PostTypeId="5" CreationDate="2012-01-05T13:51:47.267" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-05T13:51:47.267" LastActivityDate="2012-01-05T13:51:47.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="495" PostTypeId="4" CreationDate="2012-01-05T13:51:47.267" Score="0" Body="Enzyme that catalyzes the serial addition of monomers to synthesize a polymeric biomolecule. This term usually applies to DNA/RNA polymerases which synthesize these nucleic acid polymers from mononucleotides. " OwnerUserId="66" LastEditorUserId="4101" LastEditDate="2013-10-31T19:31:36.877" LastActivityDate="2013-10-31T19:31:36.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="496" PostTypeId="5" CreationDate="2012-01-05T13:52:39.807" Score="0" Body="&lt;p&gt;The cell is the basic functional unit of all known life forms, and it is the smallest unit which can replicate independently. Cells are bound in membranes and filled with cytoplasm. They contain a variety of molecules, structures, and organelles, and they perform a variety of functions. Cell biology is a broad field so relevant complementary tags should also be considered.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="16866" LastEditDate="2019-07-12T03:12:45.073" LastActivityDate="2019-07-12T03:12:45.073" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="497" PostTypeId="4" CreationDate="2012-01-05T13:52:39.807" Score="0" Body="The study of cells and their physiological properties, structure, environmental interaction, division, life cycle, and death, as well as the organelles they contain. Also known as cytology." OwnerUserId="66" LastEditorUserId="16866" LastEditDate="2019-07-12T03:12:45.073" LastActivityDate="2019-07-12T03:12:45.073" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="498" PostTypeId="5" CreationDate="2012-01-05T13:53:16.157" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-05T13:53:16.157" LastActivityDate="2012-01-05T13:53:16.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="499" PostTypeId="4" CreationDate="2012-01-05T13:53:16.157" Score="0" Body="Specialized subunits within a cell that has a specific function, and is usually separately enclosed within its own lipid bilayer." OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-05T19:50:14.903" LastActivityDate="2012-01-05T19:50:14.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="500" PostTypeId="5" CreationDate="2012-01-05T13:54:36.247" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-05T13:54:36.247" LastActivityDate="2012-01-05T13:54:36.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="501" PostTypeId="4" CreationDate="2012-01-05T13:54:36.247" Score="0" Body="Organelle found in most eukaryotic cells that processes and packages proteins inside of the cell and before they make their way to their destination; it is particularly important in the processing of proteins for secretion. Named after Italian biologist Camillo Golgi." OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-05T19:50:11.160" LastActivityDate="2012-01-05T19:50:11.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="502" PostTypeId="5" CreationDate="2012-01-05T13:56:04.527" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-05T13:56:04.527" LastActivityDate="2012-01-05T13:56:04.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="503" PostTypeId="4" CreationDate="2012-01-05T13:56:04.527" Score="0" Body="Organisms whose cells contain organelles, complex structures enclosed within membranes, in particular a nucleus." OwnerUserId="66" LastEditorUserId="4101" LastEditDate="2013-10-31T19:07:23.587" LastActivityDate="2013-10-31T19:07:23.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="504" PostTypeId="5" CreationDate="2012-01-05T13:58:31.793" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-05T13:58:31.793" LastActivityDate="2012-01-05T13:58:31.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="505" PostTypeId="4" CreationDate="2012-01-05T13:58:31.793" Score="0" Body="Study of the anatomy and organization of the nervous system." OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-05T19:50:13.220" LastActivityDate="2012-01-05T19:50:13.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="506" PostTypeId="2" ParentId="485" CreationDate="2012-01-05T14:51:42.673" Score="8" Body="&lt;p&gt;There are two mechanisms of transcriptional termination in prokaryotes.  The one shown here is &quot;rho-dependent&quot; because it involves rho, a DNA-RNA helicase that loads on and unwinds the RNA from the DNA, terminating the elongation by the polymerase.  Check out [&lt;a href=&quot;http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=47221&amp;amp;tool=pmcentrez&amp;amp;rendertype=abstract&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;] which shows a model for how rho multimers move through the RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other mechanism involves just a hairpin. The paper [&lt;a href=&quot;http://dx.doi.org/10.1074/jbc.M707998200&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;], especially Page 23, part C, shows how &quot;rho-independent&quot; or &quot;intrinsic&quot; termination works.  Basically, the hairpin slows down the polymerase and destabilizes the transcription bubble, allowing the intrinsically-weaker A:U bonds to fall apart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no requirement for a hairpin in rho-dependent termination, and I think the movie is mixing them up.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=47221&amp;amp;tool=pmcentrez&amp;amp;rendertype=abstract&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Geiselmann J, Wang Y, Seifried SE, von Hippel PH&lt;/strong&gt;. 1993. A physical model for the translocation and helicase activities of Escherichia coli transcription termination protein Rho. Proceedings of the National Academy of Sciences of the United States of America 90: 7754–8.&lt;/a&gt; [&lt;a href=&quot;http://www.pnas.org/content/90/16/7754.full.pdf&quot; rel=&quot;nofollow&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1074/jbc.M707998200&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Datta K, von Hippel PH&lt;/strong&gt;. 2008. Direct spectroscopic study of reconstituted transcription complexes reveals that intrinsic termination is driven primarily by thermodynamic destabilization of the nucleic acid framework. The Journal of biological chemistry 283: 3537–49.&lt;/a&gt; [&lt;a href=&quot;http://www.jbc.org/content/early/2007/12/10/jbc.M707998200.full.pdf&quot; rel=&quot;nofollow&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="219" LastEditorUserId="836" LastEditDate="2012-09-13T21:24:29.067" LastActivityDate="2012-09-13T21:24:29.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="507" PostTypeId="2" ParentId="320" CreationDate="2012-01-05T18:13:33.583" Score="9" Body="&lt;p&gt;&lt;strong&gt;Why was decoding the genome so significant?&lt;/strong&gt;&#xA;Because decoding the genome gives us a complete picture of the genetic makeup of an organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What made it so difficult?&lt;/strong&gt;&#xA;The repetitive sequences as mentioned by other people is a main problem. Imaging you are trying to complete a big puzzle with millions of pieces. Each piece represents a sequencing reads that we get from the experiment. If there are repetitive sequences in the genome, basically the pieces that representing these regions would look very similar (or even entirely identical). Undoubtedly, this would make the puzzle very difficult to finish. To give a scale, the maize genome is ~2.3 billion base pairs and each sequencing reads is &amp;lt;1,000 base pairs.&lt;/p&gt;&#xA;" OwnerUserId="313" LastActivityDate="2012-01-05T18:13:33.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="508" PostTypeId="2" ParentId="280" CreationDate="2012-01-05T18:34:08.013" Score="6" Body="&lt;p&gt;If the organism uses an alternative code, the predicted protein sequences would always include the same type of amino acid substitution errors. This pattern should become apparent when you compare the proteins to other organisms.&#xA;In reality, the most common alternative code uses UGA for tryptophan instead of the usual stop. If you make the mistake of using the standard code for these genomes, the predicted genes would become highly fragmented so it is almost impossible not to notice.&lt;/p&gt;&#xA;" OwnerUserId="313" LastActivityDate="2012-01-05T18:34:08.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="509" PostTypeId="2" ParentId="373" CreationDate="2012-01-05T20:12:48.593" Score="5" Body="&lt;p&gt;In my own opinion, I would not classify this as parasitism, as more unpalatable species are eaten with Batesian mimicry (and eating causes death). Parasitic organisms often do not kill the host, whereas in this case, it does. However, you are correct in stating that a unpalatable species with aposematic coloring is detrimented by the presence of a palatable Batesian mimic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Predators often recognize the aposematic coloring of an unpalatable or dangerous species. They &quot;train&quot; themselves not to eat that particular prey, as it is detrimental. The presence of a Batesian mimic which is palatable or not harmful, in simple terms, &quot;untrains&quot; predators of the harmful nature of that particular aposematic coloring. Predators are &quot;confused&quot;, and are thus more likely to eat preys with that aposematic coloring, and results in more death of the species being mimicked, while providing protection to the species that is mimicking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I'm concerned, within an ecosystem, this phenomenon happens with any Batesian mimicry to some degree. Factors that may influence this degree is the recognizability of the aposematic coloring, as well as the ability of a predator to recognize this coloring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this clears things up.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-01-05T23:15:24.580" LastActivityDate="2012-01-05T23:15:24.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="510" PostTypeId="1" AcceptedAnswerId="516" CreationDate="2012-01-05T20:18:06.467" Score="121" ViewCount="5720" Body="&lt;p&gt;The accepted range for the wavelengths of light that the human eye can detect is roughly between 400nm and 700nm.  Is it a co-incidence that these wavelengths are identical to those in the  &lt;a href=&quot;http://en.wikipedia.org/wiki/Photosynthetically_active_radiation&quot;&gt;Photosynthetically Active Radiation&lt;/a&gt; (PAR) range (the wavelength of light used for normal photosynthesis)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively is there something &lt;em&gt;special&lt;/em&gt; about photons with those energy levels that is leading to stabilising selection in multiple species as diverse as humans and plants?  &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-02-10T22:40:00.617" LastActivityDate="2014-08-09T00:50:16.597" Title="Is there a reason why human eyesight and plants make use of the same wavelength of light?" Tags="&lt;human-biology&gt;&lt;botany&gt;&lt;photosynthesis&gt;&lt;vision&gt;&lt;eyes&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="24" ContentLicense="CC BY-SA 3.0" />
  <row Id="511" PostTypeId="5" CreationDate="2012-01-05T20:26:23.067" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-05T20:26:23.067" LastActivityDate="2012-01-05T20:26:23.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="512" PostTypeId="4" CreationDate="2012-01-05T20:26:23.067" Score="0" Body="The network of receptors, nerve cells, synapses and effectors that transmit electrical impulses around the body for sensation and movement." OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-06T21:29:10.093" LastActivityDate="2012-01-06T21:29:10.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="513" PostTypeId="2" ParentId="429" CreationDate="2012-01-06T02:14:54.267" Score="5" Body="&lt;p&gt;What is your host in this case? For integration into the genome of a bacterium, you would need to use an &quot;integration&quot; vector. Most commercial vectors (such as pUC18) will be maintained without integrating into the host genome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a description of an integration vector from the Bacillus Genetic Stock Center to give you an idea of how foreign DNA would be integrated into a Bacillus genome: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Integration vectors are plasmids that feature conditional replication&#xA;  coupled with a selectable marker. If the plasmid is transformed into&#xA;  an appropriate host under conditions that select for the plasmid’s&#xA;  presence but restrict its replication, all transformants will have&#xA;  integrated the plasmid into their chromosome (or some other resident&#xA;  DNA capable of replicating under the selective conditions). In&#xA;  practice, the selectable marker usually specifies antibiotic&#xA;  resistance. Conditional replication usually means that the plasmid has&#xA;  replication functions that work in E. coli but not in gram-positive&#xA;  bacteria, such as B. subtilis. Sometimes a temperature-sensitive&#xA;  replication phenotype is employed instead. Integration is targeted to&#xA;  a particular locus on the chromosome by including identical sequences&#xA;  on the plasmid. If there is a single homologous sequence, a single&#xA;  crossover will integrate the entire chromosome into the target locus&#xA;  by a Campbell-type mechanism. If there are two homologous sequences,&#xA;  and they are relatively close together on the chromosome, then a&#xA;  double crossover will result in a cassette integrating between the&#xA;  chromosomal targets. (&lt;a href=&quot;http://www.bgsc.org/Catpart4.pdf&quot;&gt;source&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For most routine molecular biology labwork, there is no need to integrate genes into the E. coli genome. Integration is usually used to generate &quot;knockout&quot; cell lines to study gene function in the bacteria of interest.  &lt;/p&gt;&#xA;" OwnerUserId="204" LastActivityDate="2012-01-06T02:14:54.267" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="514" PostTypeId="1" AcceptedAnswerId="515" CreationDate="2012-01-06T04:09:44.773" Score="12" ViewCount="273" Body="&lt;p&gt;I'm not a professional in biology nor a student, but I'm curious about this. To be more specific: why doesn't a plant virus affect animal cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect that different kinds of cells have different ways to replicate DNA and that this is the reason for the specialization of viruses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder if someone in the field can explain this to me. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="314" LastEditorUserId="314" LastEditDate="2014-12-24T19:57:16.817" LastActivityDate="2014-12-24T19:57:16.817" Title="Are there viruses that affect cells across different species?" Tags="&lt;dna&gt;&lt;virology&gt;&lt;replication&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="515" PostTypeId="2" ParentId="514" CreationDate="2012-01-06T05:21:22.307" Score="11" Body="&lt;p&gt;Firstly, it's important to recognize that &quot;plant viruses&quot; do not exist. There are only &quot;viruses that affect particular plant cells&quot;, or &quot;viruses that affect a particular cell type&quot;. You'll see why in a moment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the structural components of many virus is its protein coat. Different types of biological molecules protrude from the surface of this protein coat, deemed signalling molecules. The structure of these molecules are specific to a certain type of virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Analogously, specific cell types have specific biological molecules that protrude from their plasma membrane, deemed receptor molecules. For a virus to affect a particular type of cell, their signalling and receptor molecules must &quot;fit within each other&quot;, like lock and key. Once they do so, a virus may interact with this molecule, in whichever way it does.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although your hypothesis wasn't entirely correct, as viral contact with a cell must first be established, viruses do interact with DNA replication in different ways, as in the lytic or lysogenic cycle.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-04-07T01:04:55.713" LastActivityDate="2012-04-07T01:04:55.713" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="516" PostTypeId="2" ParentId="510" CreationDate="2012-01-06T11:42:01.337" Score="103" Body="&lt;p&gt;Good question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at the spectral energy distribution in the accepted answer &lt;a href=&quot;https://biology.stackexchange.com/questions/450&quot;&gt;here&lt;/a&gt;, we see that photons with wavelengths less than ~300 nm are absorbed by species such as ozone. Much beyond 750 infrared radiation is largely absorbed by species such as water and carbon dioxide. Therefore the vast majority of solar photons reaching the surface have wavelengths that lie between these two extremes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, I would suggest that surface organisms will have adapted to use these wavelengths of light whether it be used in photoreceptors or in photosynthesis since these are the wavelengths available; i.e., organisms have adapted to use these wavelengths of light, rather than these wavelengths being special &lt;em&gt;per se&lt;/em&gt; (although in the specific case of photosynthesis there is a photon energy sweet spot).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example &lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0000457&quot; rel=&quot;noreferrer&quot;&gt;this study&lt;/a&gt; suggests that some fungi might actually be able to utilize ionizing radiation in metabolism. This suggests that hypothetical organisms on a world bathed in ionizing radiation may evolve mechanisms to utilize this energy.&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-09-03T14:02:09.800" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="517" PostTypeId="1" AcceptedAnswerId="518" CreationDate="2012-01-06T14:25:17.427" Score="10" ViewCount="212" Body="&lt;p&gt;This is at least partly an historical question, and I am not even remotely a biologist of any sort, so apologies beforehand if it's a little obscure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I often wonder how many distinctions were made in pre-Renaissance times, between species of animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, though I'm sure there have always been those with enough of an interest in nature to tell subtle differences, how were lemmings or voles, for example, told apart from rats or mice? Or did this recognition of speciation only come later, once more detailed (intrusive) forms of analysis became common?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've looked up the etymologies for vole, lemming and hamster and all are dated post-Renaissance, so at least in these instances it &lt;em&gt;may&lt;/em&gt; be safe to assume that people might simply not have noticed the differences before closer study took place. But I guess there are other animals where the same question applies (particularly smaller, harder-to-scrutinise animals where there are a large number of species similar at a glance).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: &lt;em&gt;Vole&lt;/em&gt; means field (same root as &lt;em&gt;wold&lt;/em&gt;), giving rise to the 19th c. term &lt;em&gt;volemouse&lt;/em&gt;, meaning that originally, mouse and vole were indeed seen as one and the same -- proof of point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. Of course, this question need not apply solely to animal species.&lt;/p&gt;&#xA;" OwnerUserId="316" LastEditorUserId="16866" LastEditDate="2017-04-26T19:33:33.400" LastActivityDate="2017-04-26T19:33:33.400" Title="Acknowledging differentiation of species, in historical times" Tags="&lt;taxonomy&gt;&lt;nomenclature&gt;&lt;species&gt;&lt;history&gt;&lt;etymology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="518" PostTypeId="2" ParentId="517" CreationDate="2012-01-06T15:40:18.387" Score="10" Body="&lt;p&gt;The branch of science you are looking for is &lt;em&gt;taxonomy&lt;/em&gt;, that is the science of identifying and naming species, and arranging them into a classification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Modern taxonomy was born from the studies of the Swedish zoologist Carl Linnæus (1707-1778), who first introduced, in his books &lt;a href=&quot;http://en.wikipedia.org/wiki/Systema_Naturae&quot;&gt;&lt;em&gt;Systema Naturae&lt;/em&gt;&lt;/a&gt; (Systems of Nature) and &lt;a href=&quot;http://en.wikipedia.org/wiki/Species_Plantarum&quot;&gt;&lt;em&gt;Species Plantarum&lt;/em&gt;&lt;/a&gt; (Plants Species) the now common &lt;a href=&quot;http://en.wikipedia.org/wiki/Binomial_nomenclature&quot;&gt;binomial nomenclature&lt;/a&gt; where each different species is given a Latin name composed by two parts: one identifying the &lt;a href=&quot;http://en.wikipedia.org/wiki/Genus&quot;&gt;genus&lt;/a&gt; and one identifying the species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, various species of mice are in the genus &lt;em&gt;Mus&lt;/em&gt;: the common house mouse is &lt;em&gt;Mus musculus&lt;/em&gt;, but in the West Mediterranean you have another type of mouse, called &lt;em&gt;Mus spretus&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although this rigorous type of classification is quite recent, taxonomy existed much earlier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Shennong&quot;&gt;Shennong&lt;/a&gt;, Emperor of China somewhere around 4000BC apparently tasted hundred of plants to test their curative properties. He wrote his observations in a book called the &lt;em&gt;Shennong Ben Cao Jing&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a similar note the &lt;a href=&quot;http://en.wikipedia.org/wiki/Ebers_Papyrus&quot;&gt;Ebers Papyrus&lt;/a&gt;, dating ~1550 BC contains description of the properties of many plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To more &quot;&lt;em&gt;recent&lt;/em&gt;&quot; times, around 300BC Aristotle was the first who actually classified animals (e.g. vertebrates and invertebrates) and his student Theophrastus wrote a classification of plants in his &lt;a href=&quot;http://en.wikipedia.org/wiki/Historia_Plantarum&quot;&gt;Historia Plantarum&lt;/a&gt; (Hystory of the Plants).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some 400 years later Plinius in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Natural_History_%28Pliny%29&quot;&gt;Naturalis Historia&lt;/a&gt; (Natural History) enumerated many plants and animals and gave some of the first binomial names to certain species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the point of how did they distinguish species: well, with their eyes and ears, of course!&#xA;You can distinguish a mouse from a vole because it is skinnier and has a longer tail.&#xA;Even more similar species can be easily distinguished without needing special equipment.&#xA;A good birdwatcher can distinguish a chiffchaff from a willow warbler by listening to their songs, looking at how they behave how they fly, the subtly different tones of their feathers etc.&#xA;We can do that now, without any special equipment, so they could before the Renaissance!&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-01-06T15:40:18.387" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="519" PostTypeId="5" CreationDate="2012-01-06T15:43:42.770" Score="0" Body="&lt;p&gt;See also &lt;a href=&quot;/questions/tagged/phylogenetics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;phylogenetics&amp;#39;&quot; rel=&quot;tag&quot;&gt;phylogenetics&lt;/a&gt; for the study of relatedness between different organisms.&lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="4101" LastEditDate="2013-10-31T16:53:03.917" LastActivityDate="2013-10-31T16:53:03.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="520" PostTypeId="4" CreationDate="2012-01-06T15:43:42.770" Score="0" Body="Questions on the classification of biological organisms, and the methods used for classifying them." OwnerDisplayName="user132" LastEditorDisplayName="user132" LastEditDate="2012-01-06T21:29:12.027" LastActivityDate="2012-01-06T21:29:12.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="521" PostTypeId="2" ParentId="166" CreationDate="2012-01-06T19:15:00.857" Score="2" Body="&lt;p&gt;I found a very nice paper: &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=6&amp;amp;ved=0CFoQFjAF&amp;amp;url=http://mpec.ucsf.edu/pdfs_new/Pubs_77.pdf&amp;amp;ei=xkMHT-XmKqbdiAKv4JSHCQ&amp;amp;usg=AFQjCNFcrXypViPECyKyeUvRM2JmZtidGA&amp;amp;sig2=0BtAug3bPEHhzZDqzuFUjA&quot; rel=&quot;nofollow noreferrer&quot;&gt;Designing Genes for Successful Protein Expression&lt;/a&gt;, which covers most factors that determine protein expression. I post parts of it, because I am sure it will be useful to some of you.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Translation can be controlled at the level of initiation and elongation. Initiation of translation is primarily dependent on the sequence of the ribosome binding site (RBS) and early mRNA secondary structure. Other determinants of protein expression are less well understood but equally potent.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;1. Initiation of translation&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;A key component affecting initiation of translation in prokaryotes is the &lt;em&gt;RBS&lt;/em&gt; that occurs between 5 and 15 bases upstream of the open reading frame (ORF) AUG start codon. Binding of the ribosome to the Shine–Dalgarno (SD) sequence within the RBS localizes the ribosome to the initiation codon... &lt;em&gt;Affinity of the RBS&lt;/em&gt; for the ribosome is a critical factor controlling the efficiency with which new polypeptide chains are initiated. This interaction is in competition with possible base-pairing interactions involving the RBS region that may form within the mRNA itself. Thus, SD sequences with weaker base pairing to the ribosome are more susceptible to interference from mRNA structure. However, some experiments suggest that SD sequences with too strong affinity can be deleterious, particularly at lowering temperatures, by stalling initial elongation. Also critical is the distance between the RBS and the start codon with 5-7 bases from the consensus SD AGGAGG being optimal.&lt;/p&gt;&#xA;&lt;p&gt;Numerous lines of evidence suggest that the &lt;em&gt;initial 15–25 codons&lt;/em&gt; of the ORF deserve special consideration in gene optimization. Studies have shown that the impact of rare codons on translation rate is particularly strong in these first codons, for expression in both Escherichia coli and Saccharomyces cerevisiae. In E. coli, peptidyl-tRNA drop-off during translation of the initial codons appears to be accentuated by the presence of rare NGG codons. These effects appear to be independent of local mRNA secondary structure. It is also true that expression may be recovered by 5' sequence replacement even for sequences that do not show especially strong mRNA structure or contain rare codons or other obvious deleterious elements in this region.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;2. Codon bias&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;The second way in which host codon frequencies can be used is to match the &lt;em&gt;host codon frequencies&lt;/em&gt; in the designed gene. This can be done simply by choosing each codon with a probability that matches the host codon frequency...Using sets of genes broadly varied in gene design features, Welch et al. found that variation in synonymous codon usage frequencies had a profound effect on the amount of protein produced in E. coli, independent of local 5’ sequence effects. Variation of at least two orders of magnitude in expression was seen due to substitution beyond the initial 15 codons of the ORF. This variation was strongly correlated with the global codon usage frequencies of the genes, although the codon frequencies found in the highest expressed variants did not correspond to those found in the genome or in highly expressed endogenous genes of E. coli. Multivariate analysis showed that the frequencies of specific codons for about six amino acids could predict the observed differences in expression. It is not clear what the biochemical basis is for this correlation.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;3. mRNA structure and translational elongation&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;While much evidence suggests that mRNA structure can interfere with translational initiation in both prokaryotes and eukaryotes, the effects of structure on elongation are less well understood. This in part may be due to intrinsic helicase activity of ribosomes, which allows translation through even very strong hairpins and may preclude many structures from limiting the translation rate in either prokaryotes or eukaryotes. Perhaps more importantly, mRNA structure is difficult to predict, particularly for actively translated messages which are in continuous flux between various folded and unfolded states.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;4. Protein-specific factors providing additional complexity&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;The protein may be particularly unstable in the host, especially if it is poorly folded due to inherent instability, lack of sufficient prosthetic factors, or improper post-translational modification... Expression of secreted and membrane proteins may be limited by mechanisms for directing these proteins to the membrane. It is even possible that the protein amino acid sequence may limit translational efficiency. For example, proline is thought to be slowly translated in E. coli, regardless of which codon is used.&lt;/p&gt;&#xA;&lt;p&gt;Expression of the protein may be &lt;em&gt;toxic&lt;/em&gt; to the cell leading to instability of the expression vector or host suppression of protein synthesis...A common strategy to reduce toxicity is to lower expression to tolerable levels. Promoters varied in strength can be valuable tools for finding an optimal expression rate for maximal yield...One potential way to avoid toxicity of some proteins is to direct expression to the periplasm or media. This may be accomplished by N-terminal fusion of a secretion signal sequence.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;For more information, please read the whole paper. I also recommend reading &lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007002&quot; rel=&quot;nofollow noreferrer&quot;&gt;Design parameters to control synthetic gene expression in Escherichia coli&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-01-06T19:15:00.857" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="522" PostTypeId="1" AcceptedAnswerId="525" CreationDate="2012-01-06T20:04:55.320" Score="23" ViewCount="484" Body="&lt;p&gt;Clearly, a zygote does not harbor any microbes. As it develops, and the alimentary canal tissue is differentiated, I logically assume that there is still no microbial activity in the fetus's gut. I'm thus also assuming that the commencement of microbial activity in the intestines occurs after birth, but when, and how? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do newborn babies just happen to ingest only certain e.g., &lt;em&gt;E.coli&lt;/em&gt; strains? Is the gut a selective environment in which only certain &lt;em&gt;E.coli&lt;/em&gt; strains develop? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any mechanisms to ensure that harmful bacteria do not initially reside in the gut? Is a newborn's digestive tract particularly unstable and ineffective until the proper microbes are established?&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="24354" LastEditDate="2020-04-15T16:49:29.067" LastActivityDate="2020-04-15T16:49:29.067" Title="How does the microbial environment in your gut initiate?" Tags="&lt;physiology&gt;&lt;microbiology&gt;&lt;microbiome&gt;&lt;gut-bacteria&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="523" PostTypeId="2" ParentId="522" CreationDate="2012-01-06T20:41:56.167" Score="20" Body="&lt;p&gt;The initiation of gut flora come from maternal cervical and vaginal flora (Bezirtzoglou, 1997)&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16887585&quot;&gt;1&lt;/a&gt;&lt;/sup&gt;. These predominantly include facultative anaerobes (e.g., &lt;em&gt;Staphylococcus&lt;/em&gt;, Enterobacteriaceae and &lt;em&gt;Streptococcus&lt;/em&gt;). Birth by caesarean section can cause problems because these bacteria are not passed on in the  usual manner.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vael et al. (2011)&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118227/&quot;&gt;2&lt;/a&gt;&lt;/sup&gt; found an association between early gut flora and obesity later in life&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;High intestinal &lt;em&gt;Bacteroides fragilis&lt;/em&gt; and low &lt;em&gt;Staphylococcus&lt;/em&gt;&#xA;  concentrations in infants between the age of 3 weeks and 1 year were&#xA;  associated with a higher risk of obesity later in life.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;suggesting that monitoring or alterations of gut flora might be effective in reducing rates of obesity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16887585&quot;&gt;Bezirtzoglou E. 1997. The intestinal microflora during the first weeks of life. &lt;em&gt;Anaerobe&lt;/em&gt; 3:173-177.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118227/&quot;&gt;Vael, C., Verhulst, S.L., Nelen, V., Goossens, H., Desager, K.N. 2011. Intestinal microflora and body mass index during the first three years of life: an observational study. &lt;em&gt;Gut Pathog&lt;/em&gt; 3: 8.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-01-06T20:41:56.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="524" PostTypeId="1" AcceptedAnswerId="535" CreationDate="2012-01-06T22:33:49.853" Score="7" ViewCount="835" Body="&lt;p&gt;In prokaryotic organisms that have a slime layer or capsule, do intrinsic/extrinsic proteins and other molecules that could be used as antigens protrude through the capsule?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uhqVS.png&quot; alt=&quot;Diagram of typical Gram +ve prokaryote&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume that they must in order to maintain their function for the cell, yet am struggling to suggest another way in which the presence of a capsule/slime layer could serve as a defence against phagocytosis?  Unless the slime layer directly resists lysosomal activity &lt;em&gt;after&lt;/em&gt; the pathogen has been recognised and engulfed? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a related note, could the flagella of an organism (which must protrude through the capsule as above) trigger an immune response on its own?  &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-06T23:21:46.577" LastActivityDate="2012-11-25T16:56:26.253" Title="Do antigens protrude through the capsule/slime layer in prokaryotic organisms where these features are present?" Tags="&lt;immunology&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="525" PostTypeId="2" ParentId="522" CreationDate="2012-01-06T22:36:07.383" Score="16" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;The gastrointestinal tract of a normal fetus is sterile. During birth and rapidly thereafter, bacteria from the mother and the surrounding environment colonize the infant's gut. Immediately after vaginal delivery, babies may have bacterial strains derived from the mothers' feces in the upper gastrointestinal tract.[15] Infants born by caesarean section may also be exposed to their mothers' microflora, but the initial exposure is most likely to be from the surrounding environment such as the air, other infants, and the nursing staff, which serve as vectors for transfer.[16] The primary gut flora in infants born by caesarean delivery may be disturbed for up to six months after birth, whereas vaginally born infants take up to one month for their intestinal microflora to be well established.[citation needed] After birth, environmental, oral and cutaneous bacteria are readily transferred from the mother to the infant through suckling, kissing, and caressing. All infants are initially colonized by large numbers of E. coli and streptococci. Within a few days, bacterial numbers reach 108 to 1010 per gram of feces.[16][17] During the first week of life, these bacteria create a reducing environment favorable for the subsequent bacterial succession of strict anaerobic species mainly belonging to the genera Bifidobacterium, Bacteroides, Clostridium, and Ruminococcus.[18] Breast-fed babies become dominated by bifidobacteria, possibly due to the contents of bifidobacterial growth factors in breast milk.[19][20] In contrast, the microbiota of formula-fed infants is more diverse, with high numbers of Enterobacteriaceae, enterococci, bifidobacteria, Bacteroides, and clostridia.[21][22] By the second year of life, the fecal microflora resemble that of adults &lt;a href=&quot;http://en.wikipedia.org/wiki/Gut_flora&quot;&gt;(wiki source)&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-01-06T22:36:07.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="526" PostTypeId="5" CreationDate="2012-01-06T23:18:30.497" Score="0" Body="&lt;p&gt;&lt;strong&gt;Selection is an important mechanism of &lt;a href=&quot;http://biology.stackexchange.com/questions/11400/how-to-define-evolution/44309#44309&quot;&gt;evolution&lt;/a&gt;&lt;/strong&gt; which brings about changes in gene frequencies by inducing variance in reproductive success as a direct result of the genes possessed. Selection is the mechanism of evolution which underlies the process of adaptation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Darwin theorised that evolution could occur by natural selection in the 1800's, based on the idea that variance in heritable phenotypic characteristics could have a &lt;strong&gt;direct effect on reproductive success&lt;/strong&gt;. As such, individuals that posses genes which give them an advantage in reproduction should (assuming selection is constant between generations) also produce offspring of a higher fitness, and the offspring generation would more closely resemble that individual than the parental generation did.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A classic example is the peppered moth.&lt;/strong&gt; Before the industrial revolution most peppered moths were light in colour. Pollution from the industrial revolution caused the darkening of the environment. This gave an advantage to peppered moths that possessed genes causing a darker colouration, because predators were less able to spot them relative to lighter moths. The genes for dark phenotypes then spread through the population because these individuals were able to produce more offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Questions about how selection works, the effect of selection, population genetic interactions, and interactions with other mechanisms of evolution are generally on-topic. Subjective questions about the validity of evolution by selection are generally off-topic. Before asking why a seemingly advantageous trait has not evolved see &lt;a href=&quot;http://biology.stackexchange.com/questions/35532/if-a-trait-would-be-advantageous-to-an-organism-why-hasnt-it-evolved&quot;&gt;this post&lt;/a&gt;. &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/home.php&quot; rel=&quot;nofollow&quot;&gt;Understanding Evolution&lt;/a&gt; is a particularly useful introductory source and includes a large myth-busting section.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-03-15T15:04:59.640" LastActivityDate="2016-03-15T15:04:59.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="527" PostTypeId="4" CreationDate="2012-01-06T23:18:30.497" Score="0" Body="A mechanism of evolution that leads to non-random spread of genes due to the effect that genes have on reproductive success." OwnerUserId="69" LastEditorUserId="1590" LastEditDate="2016-03-15T17:18:15.103" LastActivityDate="2016-03-15T17:18:15.103" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="528" PostTypeId="5" CreationDate="2012-01-06T23:20:40.697" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-06T23:20:40.697" LastActivityDate="2012-01-06T23:20:40.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="529" PostTypeId="4" CreationDate="2012-01-06T23:20:40.697" Score="0" Body="The study of the distribution, incidence, and potential control of a disease." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T17:59:36.050" LastActivityDate="2013-10-31T17:59:36.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="530" PostTypeId="5" CreationDate="2012-01-06T23:22:37.713" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-06T23:22:37.713" LastActivityDate="2012-01-06T23:22:37.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="531" PostTypeId="4" CreationDate="2012-01-06T23:22:37.713" Score="0" Body="Cells which do not contain membrane bound organelle (a main example being bacteria)" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-09T02:13:29.610" LastActivityDate="2012-01-09T02:13:29.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="532" PostTypeId="1" AcceptedAnswerId="533" CreationDate="2012-01-07T02:41:03.803" Score="18" ViewCount="7907" Body="&lt;p&gt;I understand bacteria have become resistant to antibiotics due to selection pressures, but how do resistant bacteria process antibiotics when exposed to it, compared to non-resistant bacteria. Also, what research is being conducted to combat bacteria resistant to antibiotics?&lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="69" LastEditDate="2012-01-07T11:38:29.557" LastActivityDate="2016-07-09T19:54:17.483" Title="What causes the development of antibiotic-resistant strains of bacteria?" Tags="&lt;human-biology&gt;&lt;bacteriology&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="533" PostTypeId="2" ParentId="532" CreationDate="2012-01-07T04:03:13.163" Score="21" Body="&lt;p&gt;Bacteria usually gain resistance mechanisms through horizontal gene transfer (such as conjugation and phage infection). The four main mechanisms in which bacteria elude antibiotics are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Drug Inactivation&lt;/strong&gt;: For example, E. coli can produce beta-lactamase that inactivate many lactam based antibiotics such as penicillin.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Alteration of Target Site&lt;/strong&gt;: Mutations in genes encoding for target sites can reduce drug binding affinity. Example: Random mutations in DNA gyrase and topoisomerase IV reduces binding affinity to fluoroquinolone. &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Alteration of Metabolic Pathways&lt;/strong&gt;: Many drugs target certain parts of metabolic pathways by inactivating enzymes or sequestering substrates. Bacteria can use alternative metabolic pathways or find ways to uptake the necessary nutrients from the environment.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Reduced drug accumulation&lt;/strong&gt;: Caused by reduced drug permeability or the ability of the bacteria to transport drugs out of the cell (for example, tetA encodes for a tetracycline efflux transporter). They can gain these abilities through conjugation, phage infection (transduction), or uptake of environmental DNA (transformation).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Wikipedia has a pretty extensive and comprehensive article on antibiotic resistance. There's also a good list of references. &lt;a href=&quot;http://en.wikipedia.org/wiki/Antibiotic_resistance&quot;&gt;http://en.wikipedia.org/wiki/Antibiotic_resistance&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="177" LastEditorUserId="177" LastEditDate="2012-01-08T00:13:11.510" LastActivityDate="2012-01-08T00:13:11.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="534" PostTypeId="2" ParentId="532" CreationDate="2012-01-07T04:23:12.180" Score="12" Body="&lt;p&gt;The lead question you have answered yourself: bacteria become resistant because of the selection pressure caused by the antibiotic's effective suppression of the original non-resistant bacteria.  Those variants which resist the suppression are selected for as a natural consequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do resistant bacteria process antibiotics?  It depends on the details of the particular antibiotic, and perhaps the kind of resistance.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take the case of &lt;a href=&quot;http://en.wikipedia.org/wiki/Penicillin&quot;&gt;penicillin&lt;/a&gt; and related antibiotics, like &lt;a href=&quot;http://en.wikipedia.org/wiki/Amoxicillin&quot;&gt;amoxicillin&lt;/a&gt;.  These antibiotics act by inhibiting the formation of a layer of the cell wall which is essential for many kinds of bacteria.  This prevents multiplication of the bacteria and contributes to their distruction. Wikipedia gives &lt;a href=&quot;http://en.wikipedia.org/wiki/Beta-lactam_antibiotic&quot;&gt;some details on the action of these β-lactam antibiotics&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacterial resistance to drugs like penicillin usually takes the form of the bacteria producing an enzyme (called β-lactamase) which breaks apart a ring in the drug molecule, disabling it and thus removing its effect on cell wall synthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This resistance has become common because of the widespread use of  penicillin-like drugs and because of transfer of the gene for it between bacteria species as by &lt;a href=&quot;http://en.wikipedia.org/wiki/Plasmid&quot;&gt;plasmids&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Researchers managed in the 70s to discover and develop an auxilliary weapon in this war.  This was &lt;a href=&quot;http://en.wikipedia.org/wiki/Clavulanic_acid&quot;&gt;clavulanic acid&lt;/a&gt;, which has a structure partly similar to the penicillins and like them is attacked by the bacterial β-lactamase enzyme.  Unlike the penicilins though, it forms a permanent bond with the enzyme molecule, disabling its activity.  This has led to currently effective drugs like &lt;a href=&quot;http://en.wikipedia.org/wiki/Amoxicillin/clavulanic_acid&quot;&gt;Augmentin&lt;/a&gt; which include in the same pill both amoxicillin and its protector, clavulanic acid.&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2012-01-07T04:23:12.180" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="535" PostTypeId="2" ParentId="524" CreationDate="2012-01-07T11:44:08.267" Score="4" Body="&lt;p&gt;They don't have to -- there are times in life of a bacteria (cell division, hunger, mutations, attacks of lysozyme and other enzymes, cell lysis) when any possible antigen gets less or more exposed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;About escaping phagocitosis, there are numerous strategies to achieve it -- from forming a large slime-covered colony, through killing or disabling phagocytes up to stopping digestion, escaping the phagocyte back to the environment or even living inside it (&lt;em&gt;Listeria monocytogenes&lt;/em&gt; is a prime example -- it can even directly move from one cell to another).&lt;br&gt;&#xA;EDIT: &lt;a href=&quot;http://textbookofbacteriology.net/antiphago.html&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a nice overview.&lt;/p&gt;&#xA;" OwnerDisplayName="user59" LastActivityDate="2012-01-07T11:44:08.267" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="536" PostTypeId="2" ParentId="514" CreationDate="2012-01-07T12:12:20.997" Score="7" Body="&lt;p&gt;Further to LanceLafontaine's answer I'd just like to mention that, although as he mentioned viruses interact with DNA replication in different ways, DNA replication in itself is the same process in both plant and animal cells.  For example, a human cheek cell and a potato root cell replicate their DNA  in the same way (as both are eukaryotic cells - cells with internal membrane bound organelle): see &lt;a href=&quot;http://en.wikipedia.org/wiki/Eukaryotic_DNA_replication&quot;&gt;Eukaryotic DNA replication&lt;/a&gt; for more information.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-01-07T12:12:20.997" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="537" PostTypeId="1" AcceptedAnswerId="542" CreationDate="2012-01-07T17:47:59.053" Score="7" ViewCount="7741" Body="&lt;p&gt;My 2008 biology book (1) states that some 10% of the human genome consists of relatively short (~300 nucleotides long) &lt;em&gt;Alu&lt;/em&gt; elements which do not code for proteins but many of which are transcribed into RNA. Do these &lt;em&gt;Alu&lt;/em&gt; elements have any function in the cell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(1) Biology, 8th ed., Campbell &amp;amp; Reece, 2008&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="177" LastEditDate="2012-01-08T16:20:40.953" LastActivityDate="2012-01-08T16:20:40.953" Title="What are the function(s) of Alu elements in the cell?" Tags="&lt;genetics&gt;&lt;human-genome&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="538" PostTypeId="2" ParentId="487" CreationDate="2012-01-07T18:54:35.633" Score="18" Body="&lt;p&gt;My friend Brightblades is right in one thing.  It seems your teacher was working off a caricature of what the theory of evolution actually says.  &lt;a href=&quot;https://skeptics.stackexchange.com/questions/2057/demonstrable-and-repeatable-examples-of-evolution&quot;&gt;First of all, you should read Sklivvz's excellent answer at this question&lt;/a&gt;.  Now to address the elephant in the room, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Chernobyl_disaster&quot; rel=&quot;nofollow noreferrer&quot;&gt;accident at Chernobyl only happened in 1986&lt;/a&gt;.  &lt;em&gt;That was only 26 years ago&lt;/em&gt;.  In that timeframe, noticeable effects in an animal population really would not be at all noticeable.  Furthermore, the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677413/&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper cited by Marta Cz-C&lt;/a&gt; actually shows that there &lt;em&gt;have&lt;/em&gt; been some changes (in fungi though, not animals).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;fungi seem to interact with the ionizing radiation differently from other Earth’s inhabitants. Recent data show that melanized fungal species like those from Chernobyl’s reactor respond to ionizing radiation with enhanced growth. Fungi colonize space stations and adapt morphologically to extreme conditions. Radiation exposure causes upregulation of many key genes, and an inducible microhomology-mediated recombination pathway could be a potential mechanism of adaptive evolution in eukaryotes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Read the rest of the paper for more information on how there have been some other slight changes to fungi at Chernobyl as well as other locations throughout the world.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now I am going to repeat a bunch of stuff &lt;a href=&quot;http://factsnotfantasy.com/creationists.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;from one of my web pages that talks about evolution&lt;/a&gt;.  This web page is set up mostly to deal with creationist arguments, however, the caricature is so severe as to warrant this.  As I said earlier, evolution is a &lt;strong&gt;population phenomenon&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution acts upon heritable variation of characteristics, and you can only have variation of this sort within a population. A single individual organism, at least if its a multicellular eukaryote, has a fixed genome. It can't change what it has inherited. But a large number of organisms can all have different genomes, and can disseminate variation via inheritance to the next generation. It is upon the population as a whole that evolution acts, with various mechanisms coming into play to remove some variations from the population, and propel other variations to numerical dominance within the population. The organisms in question remain part of that population, and within a generation, those organisms don't change. But the moment a new generation is produced, dissemination of variation can result in the appearance of a new feature in one or more members of that population. If that new feature leads to greater reproductive success for the organism possessing it, that feature spreads through the population, as more and more future offspring inherit it. Over time, the population changes, and more and more organisms with new features appear within that population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Understanding inheritance basics and mechanisms for changes (genes), we have all that is needed for the appearance of cladogenesis events. Split a decent sized population of living organisms into two, and let's call these new, separate populations A and B. Now let a barrier be erected between population A and population B, so that individuals from one cannot reproduce with individuals from the other. This barrier can be an insurmountable physical obstacle, for example, but this need not be the only form such a barrier can take. Now, first of all, there is no reason whatsoever to think that population A and population B will start off in identical states to begin with. After all, those two populations were derived from an original population comprising lots of organisms with different genomes, and the likelihood of population A and population B being identical at the start of this process is vanishingly small. Then, once our barrier is erected, and our populations are allowed to reproduce separately from that point on, there is no reason to think that those populations will move in the same direction in the long term. Indeed, it is far more likely that they will be subject to different environmental and ecosystem influences, and those different environmental and ecosystem influences will shape the long term heredity of those populations. Indeed, that's all that natural selection IS - it's a single, concise term used to encapsulate all of those environmental and ecosystem influences succinctly, and additionally to encapsulate the fact that those influences affect the inheritance of characteristics within a population over the long term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a consequence, any two separated populations of living organisms, that originated from a single population, will diverge from each other. If the extant influences on those two populations are sufficiently different, that divergence will take place more rapidly. Eventually, we will arrive at a point where those two populations become sufficiently diverged from each other that individuals from population A can no longer produce viable offspring with individuals from population B, and vice versa. When this happens, we have a speciation event. Indeed, this has been observed taking place in the wild AND in the laboratory, and has been documented in the relevant scientific papers. So, if anyone wishes to assert that there are 'magic barriers' to speciation or other cladogenesis events, then reality doesn't agree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will not have any animals giving birth to any radically different animals as a result of radiation.  Most changed sue to radiation will not provide any particular advantage to an animal anyway.  Also, a change may also be dependent on a previous change and require many generations to fully manifest.  &lt;a href=&quot;http://myxo.css.msu.edu/ecoli/&quot; rel=&quot;nofollow noreferrer&quot;&gt;All this was &lt;em&gt;demonstrated&lt;/em&gt; by the long term evolution experiment led by Richard Lenski at Michigan State University&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in essence, your teacher was just plain wrong.  As for the findings of the past 20 years, we are always learning more and more.  For instance, there has been an explosive capability in DNA analysis and sequencing, which has only provided more support for the theory of evolution.  A mechanism that Charles Darwin could not have had any idea about in his day and age, yet it perfectly supports his conclusions.  Again, &lt;a href=&quot;https://skeptics.stackexchange.com/questions/2057/demonstrable-and-repeatable-examples-of-evolution&quot;&gt;read the answer provided at Skeptics&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="279" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2012-11-28T14:56:29.277" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="539" PostTypeId="2" ParentId="537" CreationDate="2012-01-07T20:21:46.550" Score="0" Body="&lt;p&gt;I've really not studied this, however &lt;a href=&quot;http://en.wikipedia.org/wiki/Alu_element&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt; does a good job talking about some of the functions, particularly the associated diseases that result from changed in those sequences.  Of particular interest is this sentence:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The discovery of Alu subfamilies led to the hypothesis of master/source genes, and provided the definitive link between transposable elements (active elements) and interspersed repetitive DNA (mutated copies of active elements).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The article goes on to discuss the effects of Alu changes:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Alu elements are a common source of mutation in humans, but such mutations are often confined to non-coding regions where they have little discernible impact on the bearer[citation needed]. However, the variation generated can be used in studies of the movement and ancestry of human populations[citation needed], and the mutagenic effect of Alu[9] and retrotransposons in general[10] has played a major role in the recent evolution of the human genome. There are also a number of cases where Alu insertions or deletions are associated with specific effects in humans:&lt;/p&gt;&#xA;&lt;p&gt;Associations with human disease&lt;/p&gt;&#xA;&lt;p&gt;Alu insertions are sometimes disruptive and can result in inherited disorders. However, most Alu variation acts as markers that segregate with the disease so the presence of a particular Alu allele does not mean that the carrier will definitely get the disease. The first report of Alu-mediated recombination causing a prevalent inherited predisposition to cancer was a 1995 report about hereditary nonpolyposis colorectal cancer.&lt;/p&gt;&#xA;&lt;p&gt;The following human diseases have been linked with Alu insertions:&lt;/p&gt;&#xA;&lt;p&gt;Breast cancer&lt;/p&gt;&#xA;&lt;p&gt;Ewing's sarcoma&lt;/p&gt;&#xA;&lt;p&gt;Familial hypercholesterolemia&lt;/p&gt;&#xA;&lt;p&gt;Hemophilia&lt;/p&gt;&#xA;&lt;p&gt;Neurofibromatosis&lt;/p&gt;&#xA;&lt;p&gt;Diabetes mellitus type II&lt;/p&gt;&#xA;&lt;p&gt;And the following diseases have been associated with single-nucleotide DNA variations in Alu elements impacting transcription levels:&lt;/p&gt;&#xA;&lt;p&gt;Alzheimer's disease&lt;/p&gt;&#xA;&lt;p&gt;Lung cancer&lt;/p&gt;&#xA;&lt;p&gt;Gastric cancer&lt;/p&gt;&#xA;&lt;p&gt;Other alu-associated human mutations&lt;/p&gt;&#xA;&lt;p&gt;The ACE gene, encoding Angiotensin-converting_enzyme, has 2 common variants, one with an Alu insertion (ACE-I) and one with the Alu deleted (ACE-D). This variation has been linked to changes in sporting ability: the presence of the Alu element is associated with better performance in endurance-oriented events (e.g. triathlons), whereas its absence is associated with strength- and power-oriented performance&lt;/p&gt;&#xA;&lt;p&gt;The opsin gene duplication which resulted in the re-gaining of trichromacy in Old World primates (including humans) is flanked by an Alu element, implicating the role of Alu in the evolution of three colour vision.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Of course, there is still a great deal to study on this.  For instance, the &lt;a href=&quot;http://news-releases.uiowa.edu/2011/february/022811genome_evolution.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;University of Iowa has a team studying this &amp;quot;junk&amp;quot; DNA&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Part of the answer to how and why primates differ from other mammals, and humans differ from other primates, may lie in the repetitive stretches of the genome that were once considered &amp;quot;junk.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;A new study by researchers at the University of Iowa Carver College of Medicine finds that when a particular type of repetitive DNA segment, known as a Alu element, is inserted into existing genes, it can alter the rate at which proteins are produced -- a mechanism that could contribute to the evolution of different biological characteristics in different species. The study was published in the Feb. 15 issue of the journal Proceedings of the National Academy of Sciences (PNAS).&lt;/p&gt;&#xA;&lt;p&gt;&amp;quot;Repetitive elements of the genome can provide a playground for the creation of new evolutionary characteristics,&amp;quot; said senior study author Yi Xing, Ph.D., assistant professor of internal medicine and biomedical engineering, who holds a joint appointment in the UI Carver College of Medicine and the UI College of Engineering. &amp;quot;By understanding how these elements function, we can learn more about genetic mechanisms that might contribute to uniquely human traits.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;Alu elements are a specific class of repetitive DNA that first appeared about 60 to 70 million years ago during primate evolution. They do not exist in genomes of other mammals. Alu elements are the most common form of mobile DNA in the human genome, and are able to transpose, or jump, to different positions in the genome sequence. When they jump into regions of the genome containing existing genes, these elements can become new exons -- pieces of messenger RNAs that carry the genetic information.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;There is a paper by Srikanta et al entitled &lt;a href=&quot;http://batzerlab.lsu.edu/publications/Srikanta_et_al_2009_Genomics.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair&lt;/a&gt; (PDF).&lt;/p&gt;&#xA;&lt;p&gt;Hope that helps.&lt;/p&gt;&#xA;" OwnerUserId="279" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-01-07T20:21:46.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="540" PostTypeId="2" ParentId="532" CreationDate="2012-01-07T22:05:30.697" Score="13" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Also, what research is being conducted to combat bacteria resistant to antibiotics?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You've gotten some decent answers for how antibiotic resistance arises, so I thought I'd touch on this a bit. There's three major thrusts to anti-resistance research:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Finding new targets and mechanisms. Essentially, creating new antibiotics that are subtly different enough that they slip past existing resistance mechanisms (usually by tacking a more elaborate side-group onto an existing antibiotic) or an entirely new class that targets a different mechanism to disrupt bacteria. This is essentially a drug development task, and is &lt;em&gt;hard&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Antimicrobial stewardship. This is largely clinical research examining how we use are existing antibiotics. Can we alter the duration/deployment/etc. of a course of antibiotics to minimize the chance of resistance. Can we minimize the number of times we use antibiotics inappropriately, giving rise to resistance with no gain to the patient?&lt;/li&gt;&#xA;&lt;li&gt;Alternate antimicrobial techniques. Can we use non-antibiotic techniques to prevent bacterial infections in the first place, or treat them when they occur? Antimicrobial surfaces, like copper or silver impregnated surfaces, improved surface cleaning, etc.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="67" LastActivityDate="2012-01-07T22:05:30.697" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="541" PostTypeId="2" ParentId="537" CreationDate="2012-01-07T22:06:19.233" Score="8" Body="&lt;p&gt;Because of the retrotransposon ability of Alu and other interspersed elements, insertion into parts of the genome can contribute to genetic diversity among the population. This can be analogous to random point mutations accumulated throughout a lifetime.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of these mutations can be beneficial and increase the overall fitness of the organism. However, many of these mutations and random insertions are harmful especially when elements insert themselves into essential genes or tumor suppressor genes (which leads to cancer). &lt;/p&gt;&#xA;" OwnerUserId="177" LastActivityDate="2012-01-07T22:06:19.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="542" PostTypeId="2" ParentId="537" CreationDate="2012-01-07T23:23:36.873" Score="9" Body="&lt;p&gt;Alu elements are a type of transposable element. They possess the means for their own duplication and movement.  Alu is a SINE-like element that is transcribed by RNA Pol III, and so a single DNA copy can make multiple RNA copies, each capable of inserting into DNA, so it's no wonder they have a very high copy number.  Here is a picture of one means of insertion &lt;a href=&quot;http://www.nature.com/nrg/journal/v3/n5/box/nrg798_BX1.html&quot;&gt;http://www.nature.com/nrg/journal/v3/n5/box/nrg798_BX1.html&lt;/a&gt;, although there are likely others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They do not have &quot;a function&quot; per se, in that they are not selected for, they are just rarely selected against and there are so many of them.  They do not add functionality, but rather are one half of the &quot;war&quot; between transposable elements and viruses versus the genome's evolution to mitigate the damage they cause.  They are, of course, commonly used as sources of new DNA for sequence evolution, or can be used to create transpositions or other chromosome rearrangements, but mostly they just fail to cause too much damage and so tend to accumulate in the genome.&lt;/p&gt;&#xA;" OwnerUserId="219" LastEditorUserId="219" LastEditDate="2012-01-08T11:39:30.943" LastActivityDate="2012-01-08T11:39:30.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="543" PostTypeId="1" AcceptedAnswerId="545" CreationDate="2012-01-08T02:14:59.570" Score="9" ViewCount="1851" Body="&lt;p&gt;What specific biochemical processes are involved in inducing meiosis rather than mitosis? Why are gonadal cells the only cells in the human body which do undergo meiosis? &lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-09-13T21:25:51.530" Title="What triggers meiosis in gonadal cells?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;cell-biology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="544" PostTypeId="2" ParentId="543" CreationDate="2012-01-08T02:40:21.117" Score="4" Body="&lt;p&gt;Let's start by answering the second part of your question first. I can ask you a similar question like &quot;Why do parietal cells secrete HCl?&quot; or &quot;Why are skeletal muscle cells multinucleated?&quot;. The reason why the cells in our body carry out different functions and undergo difference processes, despite having the same DNA, can be due to a multitude of factors. Here are some off the top of my head:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Differential gene expression&lt;/li&gt;&#xA;&lt;li&gt;Alternative splicing&lt;/li&gt;&#xA;&lt;li&gt;Regulation of gene expression at the mRNA level (silencing)&lt;/li&gt;&#xA;&lt;li&gt;Chromosomal inactivation (as seen in XX females)&lt;/li&gt;&#xA;&lt;li&gt;Cell-cell interactions&lt;/li&gt;&#xA;&lt;li&gt;Environmental factors that influence all of the above&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Now to answer what the specific mechanism in which gonadal cells undergo meiosis:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For one, histone modification (and therefore differential gene expression) has been implicated in the regulation of spermatogenesis. You can read about it in this paper: &lt;a href=&quot;http://dx.doi.org/10.1267/ahc.11027&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Song N, Liu J, An S, Nishino T, Hishikawa Y, Koji T&lt;/strong&gt;. 2011. Immunohistochemical Analysis of Histone H3 Modifications in Germ Cells during Mouse Spermatogenesis. Acta histochemica et cytochemica 44: 183–90.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At first glance, I didn't find anything on oogenesis; will update if I see anything.&lt;/p&gt;&#xA;" OwnerUserId="177" LastEditorUserId="836" LastEditDate="2012-09-13T21:25:51.530" LastActivityDate="2012-09-13T21:25:51.530" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="545" PostTypeId="2" ParentId="543" CreationDate="2012-01-08T15:22:32.310" Score="8" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;What specific biochemical processes are involved in inducing meiosis rather than mitosis?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's a difficult question because every step in the development of a germ cell is ultimately necessary for the final differentiation, which includes a meiotic division.  Meiosis requires a lot of specialized components to pair and segregate homologues, to induce and resolve recombination, etc.  What starts it all is still largely unknown.  There are plenty of mutants that halt the process, but these are required along the way, so damaging the pathway ultimately stops it from progressing.  At least one study has been able to initiate the program of meiosis in yeast:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC231241/pdf/162518.pdf&quot;&gt;Induction of meiosis in Saccharomyces cerevisiae depends on conversion of the transcriptional represssor Ume6 to a positive regulator by its regulated association with the transcriptional activator Ime1. I Rubin-Bejerano, S Mandel, K Robzyk, and Y Kassir&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, they turned on a transcription factor, which activated an entire suite of downstream genes necessary for meiosis.  In essence, they turned on the &quot;meiosis pathway.&quot;  Bear in mind this is yeast, so does't have separate germ cells, but the concept is probably the same.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why are gonadal cells the only cells in the human body which do undergo meiosis?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;All other cells are diploid.  Only in germ cells does the organism induce reductional divisions (to make haploid gametes for ultimate fusion in the zygote of the next generation). Creation of haploid somatic cells would uncover recessive lethal mutations and cells would die.  In sperm and eggs, which do not express any genes until after fertilization and karyogamy, this is not a problem.&lt;/p&gt;&#xA;" OwnerUserId="219" LastActivityDate="2012-01-08T15:22:32.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="546" PostTypeId="1" AcceptedAnswerId="548" CreationDate="2012-01-08T19:28:36.773" Score="47" ViewCount="242319" Body="&lt;p&gt;This is a question that has been in my mind since I was a kid. I'm not a doctor, nor even a biology student, just a curious person. What is the minimum and maximum temperature a human body can stand without dying or suffering severe consequences (eg. a burn or a freeze)? While at this subject, how much more global warming will the human body be able to take? Seeing as temperatures keep on rising, I'm just wondering how much longer until the temperature starts having drastic effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my country the temperature is about 35-40-45 degrees Celsius in mid-summer (I live in Romania, eastern Europe, and the climate is supposedly ideal here) which is very unhealthy. Does the human body suffer more and more as the temperatures change?&lt;/p&gt;&#xA;" OwnerUserId="324" LastEditorDisplayName="user12874" LastEditDate="2015-01-11T12:45:00.283" LastActivityDate="2015-01-11T12:45:00.283" Title="What's the maximum and minimum temperature a human can survive?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;temperature&gt;" AnswerCount="4" CommentCount="7" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="547" PostTypeId="2" ParentId="543" CreationDate="2012-01-08T19:39:07.793" Score="9" Body="&lt;p&gt;Ultimately, it seems that follicle-stimulating hormone (FSH), released from the pituitary gland, may be &lt;strong&gt;the direct signal&lt;/strong&gt; for spermatocytes to enter meiosis [1]. It's worth noting, though, that these results come from &lt;em&gt;in vitro&lt;/em&gt; studies, where spermatocytes were co-cultured with all cell types of seminiferous tubules in an artificial medium, which makes it a rather crude approximation of &lt;em&gt;in vivo&lt;/em&gt; conditions: mimicking the complete spermatogenic cycle &lt;em&gt;in vitro&lt;/em&gt; remains to be done [2].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a little bit more complicated with oocytes. They start meiosis during prenatal development, are arrested in diplotene stage of the first meiotic division, and then a surge of luteinizing hormone (LH), just before ovulation, makes them resume. But they are arrested again in the last phase, and only after conception do they finish meiosis. The pause occuring in prenatal development is thought to be induced by some kind of an &quot;arrester&quot; secreted by cells in the oocyte environment (specifically, mural granulosa cells) and sustained by high cAMP levels, that are produced in response to both intrinsic and extrinsic stimuli. [3]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another matter, and quite interesting, is the issue of timing: meiosis starts in a distinct moment of a male mammal develompent, and then goes on continuously, but mammal oogenesis is a series of starts and stops. More on this can be found in [3] and [4].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;[1] Tesarik, J., Guido, M., Mendoza, C. &amp;amp; Greco, E. &lt;a href=&quot;http://jcem.endojournals.org/content/83/12/4467.long&quot;&gt;Human spermatogenesis in vitro: respective effects of follicle-stimulating hormone and testosterone on meiosis, spermiogenesis, and Sertoli cell apoptosis&lt;/a&gt;. J. Clin. Endocrinol. Metab. 83, 4467–4473 (1998). PMID: 9851795. Free access.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] Sousa, M., Cremades, N., Alves, C., Silva, J. &amp;amp; Barros, A. &lt;a href=&quot;http://humrep.oxfordjournals.org/content/17/1/161.long&quot;&gt;Developmental potential of human spermatogenic cells co-cultured with Sertoli cells&lt;/a&gt;. Hum. Reprod. 17, 161–172 (2002). PMID: 11756382. Free access.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[3] Zhang, M. &amp;amp; Xia, G. &lt;a href=&quot;http://www.springerlink.com/content/4w0rtww88n813747/&quot;&gt;Hormonal control of mammalian oocyte meiosis at diplotene stage&lt;/a&gt;. Cell. Mol. Life Sci. Epub ahead of print. (2011). PMID: 22045555.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[4] Albertini, D.F. &amp;amp; Carabatsos, M.J. &lt;a href=&quot;http://www.springerlink.com/content/ca373exyt8h7hnnw/&quot;&gt;Comparative aspects of meiotic cell cycle control in mammals&lt;/a&gt;. J. Mol. Med. 76, 795–799 (1998). PMID: 9846949.&lt;/p&gt;&#xA;" OwnerUserId="251" LastActivityDate="2012-01-08T19:39:07.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="548" PostTypeId="2" ParentId="546" CreationDate="2012-01-08T21:58:43.707" Score="27" Body="&lt;p&gt;&lt;strong&gt;Hypothermia&lt;/strong&gt; (when the body is too cold) is said to occur when the core body temperature of an individual has dropped below 35° celsius.  Normal core body temperature is 37°C. (&lt;a href=&quot;http://www.nhs.uk/Conditions/Hypothermia/Pages/Causes.aspx&quot;&gt;1&lt;/a&gt;) Hypothermia is then further subdivided into levels of seriousness (&lt;a href=&quot;http://en.wikipedia.org/wiki/Hypothermia&quot;&gt;2&lt;/a&gt;) (although all can be damaging to health if left for an extended period of time)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Mild 35–32 °C&lt;/strong&gt;: &lt;em&gt;shivering, vasoconstriction, liver failure (which would eventually be fatal) or hypo/hyper-glycemia (problems maintaining healthy blood sugar levels, both of which could eventually be fatal)&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Moderate 32–28 °C:&lt;/strong&gt; &lt;em&gt;pronounced shivering, sufficient vasoconstriction to induce shock, cyanosis in extremities &amp;amp; lips (i.e. they turn blue), muscle mis-coordination becomes more apparent&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Severe 28–20 °C:&lt;/strong&gt; &lt;em&gt;this is where your body would start to rapidly give up.  Heart rate, respiratory rate and blood pressure fall to dangerous levels (HR of 30bpm would not be uncommon - normally around 70-100).  Multiple organs fail and clinical death (where the heart stops beating and breathing ceases) soon occurs&lt;/em&gt;. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;However, as with most things in human biology, there is a wide scope for variation between individuals. The Swedish media reports the case of a seven year old girl recovering from hypothermia of 13°C (&lt;a href=&quot;http://sverigesradio.se/sida/artikel.aspx?programid=2054&amp;amp;artikel=4296666&quot;&gt;3&lt;/a&gt;) (though children are often more resilient than adults).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Hyperthermia&lt;/strong&gt; (when the body is too hot - known in its acute form as heatstroke) and is medically defined as a core body temperature from 37.5–38.3 °C &lt;a href=&quot;http://en.wikipedia.org/wiki/Hyperthermia&quot;&gt;(4)&lt;/a&gt;.  A body temperature of above 40°C is likely to be fatal due to the damage done to enzymes in critical biochemical pathways (e.g. respiratory enzymes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you mentioned &lt;strong&gt;burns&lt;/strong&gt;, I will go into these too. Burns are a result of contact with a hot object or through infra-red (heat) radiation. Contact with hot liquid is referred to as a scald rather than a burn. Tests on animals showed that burns from hot objects start to take effect when the object is at least 50°C and the heat applied for over a minute. (&lt;a href=&quot;http://ep.physoc.org/content/32/1/67&quot;&gt;5&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Freeze-burn/frostbite&lt;/strong&gt;, which is harder to heal than heat burns(&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1345616/&quot;&gt;6&lt;/a&gt;) occurs when vaso-constriction progresses to the degree where blood flow to affected areas is virtually nil.  The tissue affected will eventually literally freeze, causing cell destruction. (&lt;a href=&quot;http://en.wikipedia.org/wiki/Frostbite&quot;&gt;7&lt;/a&gt;)  Similarly to hypothermia, frostbite is divided into four degrees (that can be viewed on Wikipedia).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the matter of global warming cooking us to death, I would imagine that it would be more indirect changes that got us first.  If the average temperature had risen  to the necessary 40°C to cause heat-stroke, sea levels would have risen hugely due to the melting of the polar ice caps.  Crops and other food sources would likely be affected too, therefore I don't think that global warming is overly likely to &lt;em&gt;directly&lt;/em&gt; kill humans.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="-1" LastEditDate="2012-12-01T16:04:48.923" LastActivityDate="2012-12-01T16:04:48.923" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="549" PostTypeId="1" AcceptedAnswerId="562" CreationDate="2012-01-09T01:03:10.047" Score="10" ViewCount="1217" Body="&lt;p&gt;When someone undergoes laser surgery to improve eyesight, how does it correct accommodation problems?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does it not help presbyopia?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="69" LastEditDate="2012-05-21T11:24:01.927" LastActivityDate="2012-05-21T11:24:01.927" Title="How does laser surgery correct accommodation problems?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="550" PostTypeId="1" AcceptedAnswerId="558" CreationDate="2012-01-09T01:09:17.980" Score="14" ViewCount="11709" Body="&lt;p&gt;If all the brain ever &quot;sees&quot; is action potentials, how do we know that one set of action potentials denotes a flash of light, another one signifies a loud sound, etc ?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="238" LastEditDate="2012-01-09T16:08:49.830" LastActivityDate="2012-01-10T09:40:43.000" Title="How does a brain distinguish stimuli?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="551" PostTypeId="1" AcceptedAnswerId="556" CreationDate="2012-01-09T03:14:58.000" Score="15" ViewCount="1986" Body="&lt;p&gt;I have many friends who are interested in Biology and want to know more about the subject in general (like a history of biology, from Darwin's theory, to DNA structure discovery, to the human genome project). Of course, I cannot suggest to them to read Alberts or Lenninger. Do you know whether such a book exist? I guess that a book that covers most fields of biology cannot be compiled, but even more focused book would do. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me try to narrow it down: something like the greatest discoveries in the field of biology (like &lt;a href=&quot;http://science.discovery.com/convergence/100discoveries/big100/biology.html&quot;&gt;this article&lt;/a&gt;) would be an interesting book to read.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure how appropriate this question is for SE, but I am sure that I will get the best answer here. Besides, it would be great if lay people can be more excited about biology and contribute to the site growth.&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="3059" LastEditDate="2013-05-02T01:12:09.583" LastActivityDate="2013-12-25T19:03:58.367" Title="A good book for history of biology/biotechnology for lay people" Tags="&lt;history&gt;&lt;biotechnology&gt;&lt;book-recommendation&gt;&lt;general-biology&gt;" AnswerCount="10" CommentCount="3" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="552" PostTypeId="2" ParentId="551" CreationDate="2012-01-09T03:36:20.133" Score="3" Body="&lt;p&gt;I don't know very many books that might be referred to as the Grand History of Biology or anything like that. That's...a big topic. Really big. How about some suggestions for good Biology/Medical History books accessible to lay people:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;And the Band Played On, by Randy Shilts, an account of the beginning of the AIDS epidemic in the U.S.&lt;/li&gt;&#xA;&lt;li&gt;The Great Influenza, by John Berry, which is about the 1918 influenza pandemic.&lt;/li&gt;&#xA;&lt;li&gt;The Demon Under the Microscope, by Thomas Hager, which is about sulfa and the development of early antibiotics.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Finally, I believe James Watson wrote a somewhat popular science-oriented account of the discovery of DNA, which would no doubt be interesting, though likely somewhat skewed in favor of his own awesomeness.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2012-01-09T03:36:20.133" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="554" PostTypeId="1" AcceptedAnswerId="566" CreationDate="2012-01-09T06:42:04.293" Score="8" ViewCount="460" Body="&lt;p&gt;I have some question, which I'm sure would fit better in the fitness section but proper answers should probably come from someone that knows biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is rather simple. How can a person that doesn't eat any vegetables at all be affected by such a diet? By no vegetables at all, I mean not eating any ever.&lt;/p&gt;&#xA;" OwnerUserId="324" LastEditorUserId="69" LastEditDate="2012-01-09T22:04:49.507" LastActivityDate="2014-03-11T17:29:55.290" Title="How does a veggie-less diet affect the human body?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="556" PostTypeId="2" ParentId="551" CreationDate="2012-01-09T08:48:41.333" Score="5" Body="&lt;p&gt;It doesn't have very many reviews, but &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/073820577X&quot;&gt;The Epic History of Biology&lt;/a&gt; sounds like it's perfect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Flipping through the first chapter in the preview, it doesn't seem overly technical in any way, so secondary school-level knowledge is probably enough.  If your associates have absolutely no biology experience, perhaps a run through a popular press book would provide all of the background necessary. &lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2012-01-09T08:48:41.333" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="557" PostTypeId="2" ParentId="551" CreationDate="2012-01-09T10:40:23.353" Score="12" Body="&lt;p&gt;Some that just come to mind, in random order:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One cannot skip reading:  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Richard Dawkins - &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0199291152&quot; rel=&quot;nofollow&quot;&gt;The selfish gene&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And, obviously:  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Charles Darwin - &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0451529065&quot; rel=&quot;nofollow&quot;&gt;The Origin of Species&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And, for those interested in the evolution of the brain (and its quirks):  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;David J Linden - &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0674030583&quot; rel=&quot;nofollow&quot;&gt;The Accidental Mind&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Oliver Sacks - &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0684853949&quot; rel=&quot;nofollow&quot;&gt;The Man Who Mistook His Wife for a Hat&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Not very DNA/evolution-oriented, but wonderful science books nonetheless:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Primo Levi - &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0679444637&quot; rel=&quot;nofollow&quot;&gt;The Periodic table&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;And the neveraging must-read:&lt;br&gt;&#xA;Isaac Asimov - &lt;a href=&quot;http://books.google.co.uk/books/about/A_short_history_of_chemistry.html?id=QszZAAAAMAAJ&amp;amp;redir_esc=y&quot; rel=&quot;nofollow&quot;&gt;A Short History of Chemistry&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2013-12-25T19:03:58.367" LastActivityDate="2013-12-25T19:03:58.367" CommentCount="2" CommunityOwnedDate="2012-01-09T10:40:23.353" ContentLicense="CC BY-SA 3.0" />
  <row Id="558" PostTypeId="2" ParentId="550" CreationDate="2012-01-09T13:43:43.907" Score="12" Body="&lt;p&gt;The fundamental way in which this works is by geography: signals triggered by different stimuli travel by different pathways to different regions of the brain that are specialised for dealing with the sorts of information they contain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, visual signals from the retina pass down the optic nerve and (after a few interesting twists and turns that, &lt;em&gt;inter alia&lt;/em&gt;, send the left and right halves of each visual field to different brain hemispheres) wind up in the visual cortex, which contains neuronal networks adapted for recognising different structures and regularities in the image. Whereas sound information from the ears, after an even more tortuous sequence of processing steps, winds up in the auditory cortex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Along the way, the signals will typically be split up across many neurons and reintegrated into new signals that pick out different kinds of information. So a particular stimulus will result in a complex spatio-temporal pattern of action potentials firing across many regions of the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conceptually, the further along this process you go, the more abstracted the signal probably becomes, so that it stands for a collection of events and ideas and thoughts rather than for excited photoreceptors or vibrating hair cells. But exactly how this parsing of the sensory content eventually turns into perception and conscious recognition is essentially unknown.&lt;/p&gt;&#xA;" OwnerUserId="149" LastActivityDate="2012-01-09T13:43:43.907" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="559" PostTypeId="1" AcceptedAnswerId="563" CreationDate="2012-01-09T17:13:47.853" Score="19" ViewCount="8511" Body="&lt;p&gt;Coming from an evolutionary approach, Is the only purpose of a scrotum to regulate the temperature of the testes? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Knowing all mammals are warm blooded, shouldn't all mammals have testes in a scrotum?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="238" LastEditDate="2012-01-09T18:48:26.857" LastActivityDate="2017-07-08T13:56:15.903" Title="Why do some mammals not have testes in a scrotum?" Tags="&lt;physiology&gt;&lt;reproduction&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="560" PostTypeId="2" ParentId="450" CreationDate="2012-01-09T19:59:52.897" Score="22" Body="&lt;p&gt;There is quite a fun article &lt;a href=&quot;http://www.ebscohost.com/uploads/imported/thisTopic-dbTopic-1033.pdf&quot;&gt;here&lt;/a&gt; which discusses the colours of hypothetical plants on planets around other stars. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stars are classified by their spectral type which is dictated by their surface temperatures. The Sun's is relatively hot, and it's spectral energy distribution peaks in the green region of the spectrum. However the majority of stars in the Galaxy are K and M type stars which emit mainly in the red and infrared. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is relevant to this discussion since any photosynthesis on these worlds would have to adapt to these wavelengths of light in order to proceed. On planets around cool stars plant life (or its equivalent) might well be black!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;OK, this is not entirely pie in the sky astrobiologist rubbish. It is actually quite relevant to the search for biosignatures and life on other planets. In order to model the reflectance spectrum of planets we observe (i.e. the light reflected from the primary star) we need to try and take into account any potential vegetation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, if we take a reflectance spectrum of the Earth, we see a characteristic peak in the red &quot;the red edge&quot; which is due to surface plant life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NASA also has a short page on this &lt;a href=&quot;http://www.nasa.gov/centers/goddard/news/topstory/2007/spectrum_plants.html&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="9644" LastEditDate="2014-10-14T20:05:13.063" LastActivityDate="2014-10-14T20:05:13.063" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="561" PostTypeId="1" CreationDate="2012-01-09T21:15:02.553" Score="9" ViewCount="342" Body="&lt;p&gt;The conduction velocity of the squid giant axon can reach 30 m/s. Is there any known example of an even faster conducting unmyelinated axons?&lt;/p&gt;&#xA;" OwnerDisplayName="user24" LastActivityDate="2012-01-10T05:52:42.410" Title="Is the squid giant axon the fastest conducting unmyelinated axon known?" Tags="&lt;neuroscience&gt;&lt;zoology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="562" PostTypeId="2" ParentId="549" CreationDate="2012-01-09T22:34:14.497" Score="14" Body="&lt;h1&gt;Overview&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Qx5zR.gif&quot; alt=&quot;Diagram of human eye&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Laser eye surgery works by altering the shape of the cornea.  The cornea works together with the lens to focus rays of light onto the retina.  The cornea accounts for two-thirds of the optical power of the eye (1) (i.e. the eyes capability to focus light), however unlike the lens is of fixed power. It is the lens that changes is shape by the action of suspensory ligaments and ciliary muscles in order to focus light by the correct amount depending on how far away the light originated from (and consequently the angle of incidence with the cornea).  I'm sure that you are aware of all this, however for the benefit of future readers this is fully explained diagrammatically &lt;a href=&quot;http://www.goodhope.org.uk/departments/eyedept/chroniceye.html&quot; rel=&quot;noreferrer&quot;&gt;on this webpage&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Specific Conditions&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;Three forms of accommodation problems can be treated by laser surgery:&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Hypermetropia&lt;/strong&gt; (long-sight) is where light focusses behind the retina:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jn3CO.gif&quot; alt=&quot;Hypermetropia&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Laser treatment is used to make the cornea thicker, resulting in a greater degree of refraction of light and correction of the focus.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Myopia&lt;/strong&gt; (short-sight) is where light focusses before the retina:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/f22LU.gif&quot; alt=&quot;Myopia&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Laser treatment is used to make the cornea thinner, resulting in a reduced degree of refraction of light and correction of the focus.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Astigmatism&lt;/strong&gt; is where the cornea is not the correct shape - it is closer to a rugby ball rather than the sweeping curve demonstrated in the first diagram.  This results in multiple focal points therefore a blurred image. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lPUsU.gif&quot; alt=&quot;Astigmatism&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Laser eye surgery is used to alter the shape of the cornea until it is more normal.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Presbyopia&lt;/strong&gt; is an age related condition where the lens becomes more rigid and is less able to change its shape to accommodate the light.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kvKU9.png&quot; alt=&quot;Presbyopia&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As this is a problem with the lens rather than the cornea, it can not be treated with laser eye surgery.  It must be corrected with glasses, as shown in the above diagram.  &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;(1) Cassin, B. and Solomon, S. Dictionary of Eye Terminology. Gainsville, Florida: Triad Publishing Company, 1990.&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-01-09T22:34:14.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="563" PostTypeId="2" ParentId="559" CreationDate="2012-01-09T23:02:52.453" Score="20" Body="&lt;p&gt;Having descended testes is a derived characteristic within mammals; monotremes and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Afrotheria&quot;&gt;Afrotheria&lt;/a&gt; (including elephants) all retain the ancestral character state (Kleisner, et al., 2010)&lt;sup&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Laurasiatheria&quot;&gt;2&lt;/a&gt;&lt;/sup&gt;. Among those mammals with descended testes, these can be ascrotal or scrotal. Testicular descent is hypothesized to have only occurred once within Mammalia, with the ascrotal &lt;a href=&quot;http://en.wikipedia.org/wiki/Laurasiatheria&quot;&gt;Laurasiatheria&lt;/a&gt;. Descended ascrotal testes are found in cetaceans, phocid seals, hippos, tapirs, rhinos, and some bats. Descended scrotal testes are found in horses, pigs, camels, and Carnivora.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since basal mammals would presumably have to regulate testicular temperature just as much as derived mammals, the temperature regulation hypothesis seems to not hold up. So the real question is: why have a scrotum? One hypothesis has to do with evolution of fast locomotion (e.g., galloping).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Frey (1991, 40)&lt;sup&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1439-0469.1991.tb00443.x/abstract&quot;&gt;4&lt;/a&gt;&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The strong flexions and extensions of the vertebral column during&#xA;  gallop should cause intense fluctuations of intra-abdominal pressure.&#xA;  Fluctuations of intra-abdominal pressure severely impede continuous&#xA;  flow of blood in the abdominal veins. Periodically reduced venous&#xA;  drainage resulting in fluctuations of intra-testicular pressure would&#xA;  impair the process of spermiohistogenesis, which is dependent on an&#xA;  absolutely constant pressure within the testis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Chance (1996)&lt;sup&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-7998.1996.tb05471.x/abstract&quot;&gt;5&lt;/a&gt;&lt;/sup&gt; suggests that the temperature hypothesis might represent a secondary adaptation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because in the human male, scrotal testes function optimally at&#xA;  temperatures below that of the body, much speculation, and a&#xA;  considerable amount of research, has gone into attempting to see what&#xA;  (metabolic) advantage might accrue from this lower temperature,&#xA;  without considering the possibility that this is a secondary&#xA;  adaptation to an enforced external position.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.springerlink.com/content/h378812x478u0417/&quot;&gt;Kleisner, K., Ivell, R., and Flegr, J. 2010. The evolutionary history of testicular externalization and the origin of the scrotum. &lt;em&gt;J Biosci&lt;/em&gt; 35:27-37&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1439-0469.1991.tb00443.x/abstract&quot;&gt;Frey, R. 1991. Zur Ursache des Hodenabstiegs (Descensus testiculorum) bei Säugetieren. &lt;em&gt;Z Zool Sys Evolut-Forsch&lt;/em&gt; 29:40–65&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-7998.1996.tb05471.x/abstract&quot;&gt;Chance, M.R.A. 1996. Reason for externalization of the testis of mammals. &lt;em&gt;J Zool&lt;/em&gt; 239:691–695&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2012-01-16T00:00:48.307" LastActivityDate="2012-01-16T00:00:48.307" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="564" PostTypeId="2" ParentId="551" CreationDate="2012-01-09T23:24:04.700" Score="3" Body="&lt;p&gt;I just came across &lt;a href=&quot;http://my.safaribooksonline.com/book/biotechnology/0131010115&quot; rel=&quot;nofollow&quot;&gt;Understanding Biotechnology&lt;/a&gt;. There is one very positive and one very negative review. I haven't read the book myself, but it looks that it is exactly what I was looking for: the table of content includes topics like small history overview, genetic engineering, gene therapy, pharmacogenomics, etc. It might be even useful for people with biology background. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has anyone heard about this book?&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-01-09T23:24:04.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="565" PostTypeId="2" ParentId="551" CreationDate="2012-01-10T00:03:36.987" Score="4" Body="&lt;p&gt;A fantastic book that covers the evolution of modern science since the Renaissance (including a great deal of biology) is &lt;a href=&quot;http://www.worldcat.org/title/scientists/oclc/690763545&quot; rel=&quot;nofollow&quot;&gt;The Scientists&lt;/a&gt; by John Gribbin. I found that by focusing on the people doing the science in the context of the society in which they lived, I got a much better understanding for why early scientists thought the way they did and researched the questions that they did.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the blurb from the publisher:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In this ambitious new book, John Gribbin tells the stories of the&#xA;  people who have made science, and of the times in which they lived and&#xA;  worked. He begins with Copernicus, during the Renaissance, when&#xA;  science replaced mysticism as a means of explaining the workings of&#xA;  the world, and he continues through the centuries, creating an&#xA;  unbroken genealogy of not only the greatest but also the more obscure&#xA;  names of Western science, a dot-to-dot line linking amateur to genius,&#xA;  and accidental discovery to brilliant deduction.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-01-10T00:03:36.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="566" PostTypeId="2" ParentId="554" CreationDate="2012-01-10T02:29:57.963" Score="11" Body="&lt;p&gt;There is a list of several implications of not eating vegetables (references &lt;a href=&quot;http://www.livestrong.com/article/468537-what-will-happen-if-you-dont-eat-vegetables/&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;http://commonsensehealth.com/Diet-and-Nutrition/Vegetables_List_with_Vegetable_Nutrition_Facts.shtml&quot;&gt;2&lt;/a&gt;, &lt;a href=&quot;http://www.ehow.com/facts_5809774_happens-eat-enough-fruits-vegetables_.html&quot;&gt;3&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Weight gain (by eating fat-rich products);&lt;/li&gt;&#xA;&lt;li&gt;Malnutrition (not reveiving enough vitamin A, C, D, K, etc);&lt;/li&gt;&#xA;&lt;li&gt;Digestive problems (low fiber intake leads to digestion disorders, which could lead to health problems);&lt;/li&gt;&#xA;&lt;li&gt;High risk of heart disease;&lt;/li&gt;&#xA;&lt;li&gt;High risk of certain cancers.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I also pulled up the nutrition fact sheets for vegetables, fruits, and seafood created by the &lt;a href=&quot;http://www.fda.gov/Food/LabelingNutrition/FoodLabelingGuidanceRegulatoryInformation/InformationforRestaurantsRetailEstablishments/ucm063367.htm&quot;&gt;US Food and Drug Administration&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to obtain all the necessary vitamins, one can substitute vegetables for fruits. For example, to obtain 100% of the daily value of vitamin A, one should eat as little as one carrot a day. In order to get the same amount of vitamin A from fruits, one should eat 134g of &lt;a href=&quot;http://en.wikipedia.org/wiki/Cantaloupe&quot;&gt;cantaloupe&lt;/a&gt;, or 462g of grapefruit, or 50 large apples a day. Although this could be difficult but possible, the sugar content of the above-mentioned fruits should be taken into account.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something else which needs to be considered is that vegetables are &lt;a href=&quot;http://www.livestrong.com/article/429695-what-are-the-nutritional-differences-between-fruits-vegetables/&quot;&gt;richer in minerals&lt;/a&gt; (iron, potassium, calcium), compared to fruits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All this in mind, perhaps all minerals and vitamins could be acquired from a source other than vegetables. &lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-01-10T02:39:48.673" LastActivityDate="2012-01-10T02:39:48.673" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="567" PostTypeId="1" AcceptedAnswerId="639" CreationDate="2012-01-10T03:24:39.017" Score="6" ViewCount="318" Body="&lt;p&gt;Full question: In C. elegans, why does knock-down of cco-1 via RNA interference in specific tissues like body wall muscle decreases life span, whereas knock-down in the nervous system and intestine increases life-span?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.wormbase.org/db/gene/gene?name=WBGene00000371;class=Gene&quot;&gt;http://www.wormbase.org/db/gene/gene?name=WBGene00000371;class=Gene&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also from paper 'The Cell-Non-Autonomous Nature of Electron Transport Chain-Mediated Longevity'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Supposedly, it's through hormesis. But why is there a differential effect from tissue to tissue?&lt;/p&gt;&#xA;" OwnerUserId="103" LastActivityDate="2012-02-01T12:02:20.840" Title="In C. elegans, why does knock-down of cco-1 in some tissues increase lifespan, and knock-down of cco-1 in other tissues decrease lifespan?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="568" PostTypeId="5" CreationDate="2012-01-10T04:17:23.917" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-10T04:17:23.917" LastActivityDate="2012-01-10T04:17:23.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="569" PostTypeId="4" CreationDate="2012-01-10T04:17:23.917" Score="0" Body="Biotechnology is a field of biology which utilizes biological systems like microorganisms to produce valuable products, such as biofuels, drugs, and vaccines." OwnerUserId="28" LastEditorUserId="4101" LastEditDate="2013-10-31T19:08:37.140" LastActivityDate="2013-10-31T19:08:37.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="570" PostTypeId="1" AcceptedAnswerId="595" CreationDate="2012-01-10T04:46:40.937" Score="14" ViewCount="221" Body="&lt;p&gt;I was watching an old Arnold Schwarzenegger movie (&quot;Commando&quot;) where he plays an elite soldier (surprise).  An enemy tries to sneak up on him, and Arnold says that he smelled the other guy approaching.  While this is possible, I find it to be more hyperbole than truth, but what modalities and areas of the brain would he would harness for this detection task?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of us not being super soldiers, we do occasionally get a feeling when someone has entered a room silently behind us.  Is it audible clues that fall below a certain threshold, is it the sensation of air moving in a the room, some sort of vibrational or proprioceptive sensation, or a combination of all three of these? &lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2012-01-11T19:54:03.917" Title="What portions of the brain have drastic changes in activation when we &quot;sense&quot; someone is there?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;sensation&gt;&lt;perception&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="571" PostTypeId="2" ParentId="561" CreationDate="2012-01-10T05:52:42.410" Score="6" Body="&lt;p&gt;The conductance velocity in the unmyelinated axon has been calculated and measured to be proportional to the square root of the axon diameter (see for example: &lt;a href=&quot;http://jp.physoc.org/content/115/1/101.full.pdf+html&quot;&gt;Rushton, 1951&lt;/a&gt;). Since the giant axon is, well, &lt;em&gt;giant&lt;/em&gt;, it conducts much faster than others. AFAIK, all other large neurons studied are myelinated. Maybe try to find bigger squids! ;)&lt;/p&gt;&#xA;" OwnerUserId="48" LastActivityDate="2012-01-10T05:52:42.410" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="572" PostTypeId="2" ParentId="550" CreationDate="2012-01-10T09:40:43.000" Score="6" Body="&lt;p&gt;Just adding some metaphors in support to the excellent answer by &lt;a href=&quot;https://biology.stackexchange.com/users/149/walkytalky&quot;&gt;walkytalky&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our brain is like a huge processing center that can be seen from techni's prospective as a sort of a data center with parallel processing of hundreds of thousands of inputs with processing cores scattered throughout the complete brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human brain (&lt;em&gt;medulla&lt;/em&gt;) is connected with the rest of the body through special types of nerves that convey the information to brain (sensory, centropetal nerves) or deliver information from brain to the target organs (motor or centrofugal nerves) or both (mixed nerves).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I intentionally use the term &quot;medulla&quot;, because this word comes from origin where it is applied to somwwhat more than brain: the spinal cord is also &quot;medulla&quot; (&lt;em&gt;medulla spinalis&lt;/em&gt;), as well as the part that connects the spinal cord with the brain itself (&lt;em&gt;medula oblongata&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nerves that come directly from the brain are called &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cranial_nerves&quot; rel=&quot;nofollow noreferrer&quot;&gt;cranial nerves&lt;/a&gt;&lt;/em&gt;. There are only 12 pairs of them in humans, numbered using Roman numbers (from I to XII) and every pair has a specific function: I bringing olfactory information (about smells), II -- the optic one, III -- moving the eyes etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The counterparts of these nerves in spinal cord are spinal nerves, which go through the holes between single vertebrae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brain and CNS in general can locate the information input and determine the information type judging by the input source using these nerves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides the classical sensory information, like those from eyes coming via optical nerves into CNS, there is also some sensory information that is conveyed through &lt;a href=&quot;http://en.wikipedia.org/wiki/Vegetative_nervous_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;autonomous nerve system&lt;/a&gt;, that is less specific and can not be localized as well as in case of sensory information coming via sensory input. Pain, for example, or the feeling of pressure belongs to the type of information coming via vegetative nerves. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The complete brain surface (so-called &lt;em&gt;cortex&lt;/em&gt;) is mapped into special zones, called &lt;a href=&quot;http://en.wikipedia.org/wiki/Brodmann_area&quot; rel=&quot;nofollow noreferrer&quot;&gt;Brodmann zones&lt;/a&gt;, depending upon prevailing neuron types and (secondary) role in information processing.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2012-01-10T09:40:43.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="573" PostTypeId="2" ParentId="551" CreationDate="2012-01-10T19:58:33.663" Score="7" Body="&lt;p&gt;A good recollection of the early days of micro and molecular biology is &lt;a href=&quot;http://www.cshlpress.com/default.tpl?cart=132622550197204983&amp;amp;fromlink=T&amp;amp;linkaction=full&amp;amp;linksortby=oop_title&amp;amp;--eqSKUdatarq=294&quot;&gt;&quot;The Eighth day of Creation&quot;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It covers the early use of &lt;em&gt;e. coli&lt;/em&gt;, the discovery of phage, transcriptional elements and the impact that DNA structure had.  It's very comprehensive and really useful if you are doing molecular biology today.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="69" LastEditDate="2012-01-31T22:57:34.747" LastActivityDate="2012-01-31T22:57:34.747" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="574" PostTypeId="1" AcceptedAnswerId="575" CreationDate="2012-01-10T20:44:51.373" Score="7" ViewCount="2032" Body="&lt;p&gt;If the &lt;em&gt;aim&lt;/em&gt; of evolution is to allow an organism to better compete against rivals, why would stabilizing selection ever happen? If you're not selecting the most highly adapted competitors at either end of the spectrum then how would a species progress?  &lt;/p&gt;&#xA;" OwnerUserId="318" LastActivityDate="2012-01-25T20:16:16.687" Title="Why would stablising selection ever happen?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="575" PostTypeId="2" ParentId="574" CreationDate="2012-01-10T21:36:54.393" Score="22" Body="&lt;p&gt;It occurs when a beneficial characteristic has been developed over time and it would be harmful to stray from it.  In these cases it is not the individuals at the fringe (as you put it the &lt;em&gt;most adapted&lt;/em&gt;) who are the best adapted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it may help if I answer with an example that is widely promoted by &lt;a href=&quot;http://web.aqa.org.uk/&quot; rel=&quot;nofollow noreferrer&quot;&gt;AQA&lt;/a&gt; in their A2 Biology syllabus. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Stabilising Selection in human birth weight&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;It is harmful for an infant to be born with a very low birth weight. They are much more vulnerable to heat loss due to their high surface area to volume ratio and consequently their respiratory demands are very high.  Pre-term babies (which account for 67% of low-birthweight infants(1)) are particularly susceptible to respiratory problems (lack of surfactant in the lungs), cardiac problems (Patent ductus arteriosus - the lungs are still bypassed when the umbilical cord has been cut) and dangerous intestinal problems (Necrotizing enterocolitis) amongst many other conditions can all be fatal (&lt;a href=&quot;http://www.marchofdimes.com/professionals/medicalresources_lowbirthweight.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;further information on mentioned conditions&lt;/a&gt;) and are reflected in high mortality rates at these low birth rates.  It is therefore &lt;strong&gt;not&lt;/strong&gt; beneficial to be on the extremes of birth weight.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, delivering a child of too high birth weight can cause complications with delivery if the head and shoulders are too wide to pass through the mother's hips.  Therefore the other extreme of high birth rate is also &lt;strong&gt;not&lt;/strong&gt; beneficial and will not be selected towards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leads to selective pressures in both directions, stabilising towards a mean birth weight as shown below:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ajwTt.gif&quot; alt=&quot;Human Birth Weight &amp;amp; Survival Rates&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is an example of evolution not pushing a species forward but ensuring that individuals have the best chance of getting to reproductive age themselves.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) Martin, J.A., et al. (2007). Births: Final Data for 2005. National Vital Statistics Reports, 56(6).&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-01-10T21:36:54.393" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="576" PostTypeId="1" AcceptedAnswerId="591" CreationDate="2012-01-10T21:54:52.207" Score="27" ViewCount="1223" Body="&lt;p&gt;When ATP is used as the energy currency to make, say, reaction X + Y → Z happen, is what happens on a physical level down at the molecular scale that during the reaction&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;ATP + H&lt;sub&gt;2&lt;/sub&gt;O → ADP + P&lt;sub&gt;i&lt;/sub&gt;&lt;/strong&gt; &amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; ΔG˚ = −30.5 kJ/mol (−7.3 kcal/mol)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;that 30.5 kJ/ mol is conferred by ATP molecules physically bumping around the reactants X and Y, the kinetic energy of the above reaction being what does it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I mean, is the energy coin of ATP conferred to reactions by molecular collisions, or is it an electric field effect in the spatial geometry the way the ATP molecule tends to break apart?&lt;/p&gt;&#xA;" OwnerUserId="263" LastEditorUserId="69" LastEditDate="2012-01-10T22:12:40.313" LastActivityDate="2019-02-17T12:20:12.417" Title="How, on a physical level, does ATP confer energy?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;biophysics&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="577" PostTypeId="5" CreationDate="2012-01-10T21:56:34.793" Score="0" Body="&lt;p&gt;Questions on identification, classification, and biology of bacteria are on topic. The &lt;a href=&quot;/questions/tagged/microbiology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;microbiology&amp;#39;&quot; rel=&quot;tag&quot;&gt;microbiology&lt;/a&gt; tag may also be useful for such questions, and the &lt;a href=&quot;/questions/tagged/pathology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;pathology&amp;#39;&quot; rel=&quot;tag&quot;&gt;pathology&lt;/a&gt; tag should be used for questions about bacterial disease. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Questions about viruses should use the &lt;a href=&quot;/questions/tagged/virology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;virology&amp;#39;&quot; rel=&quot;tag&quot;&gt;virology&lt;/a&gt; tag.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="16866" LastEditDate="2019-07-12T04:02:22.530" LastActivityDate="2019-07-12T04:02:22.530" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="578" PostTypeId="4" CreationDate="2012-01-10T21:56:34.793" Score="0" Body="A subdivision of microbiology dedicated to the study of bacteria. " OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-11T17:28:47.783" LastActivityDate="2012-01-11T17:28:47.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="579" PostTypeId="5" CreationDate="2012-01-10T21:57:52.623" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-10T21:57:52.623" LastActivityDate="2012-01-10T21:57:52.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="580" PostTypeId="4" CreationDate="2012-01-10T21:57:52.623" Score="0" Body="Questions relating to how the field of biology has developed over time." OwnerUserId="69" LastEditorUserId="3952" LastEditDate="2014-01-11T01:47:01.167" LastActivityDate="2014-01-11T01:47:01.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="581" PostTypeId="5" CreationDate="2012-01-10T21:59:55.307" Score="0" Body="&lt;p&gt;This tag is for questions about the general biological structure of human beings as opposed to the anatomy of non-human animals, &lt;em&gt;zootomy&lt;/em&gt;. Questions of &lt;a href=&quot;/questions/tagged/human-physiology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;human-physiology&amp;#39;&quot; rel=&quot;tag&quot;&gt;human-physiology&lt;/a&gt; should be tagged accordingly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also &lt;a href=&quot;/questions/tagged/human-biology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;human-biology&amp;#39;&quot; rel=&quot;tag&quot;&gt;human-biology&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/anatomy&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;anatomy&amp;#39;&quot; rel=&quot;tag&quot;&gt;anatomy&lt;/a&gt;, and &lt;a href=&quot;/questions/tagged/physiology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;physiology&amp;#39;&quot; rel=&quot;tag&quot;&gt;physiology&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6703" LastEditorUserId="16866" LastEditDate="2019-12-13T04:31:01.943" LastActivityDate="2019-12-13T04:31:01.943" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="582" PostTypeId="4" CreationDate="2012-01-10T21:59:55.307" Score="0" Body="This tag is for questions about the general anatomical features of human beings as opposed to the anatomy of non-human animals." OwnerUserId="69" LastEditorUserId="6703" LastEditDate="2014-05-22T22:16:02.233" LastActivityDate="2014-05-22T22:16:02.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="583" PostTypeId="5" CreationDate="2012-01-10T22:00:35.723" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-10T22:00:35.723" LastActivityDate="2012-01-10T22:00:35.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="584" PostTypeId="4" CreationDate="2012-01-10T22:00:35.723" Score="0" Body="The study of the structure of organisms and their parts." OwnerUserId="69" LastEditorUserId="9333" LastEditDate="2017-09-01T21:59:51.167" LastActivityDate="2017-09-01T21:59:51.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="585" PostTypeId="5" CreationDate="2012-01-10T22:02:03.087" Score="0" Body="&lt;p&gt;Should be paired with &lt;a href=&quot;/questions/tagged/botany&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;botany&amp;#39;&quot; rel=&quot;tag&quot;&gt;botany&lt;/a&gt; or &lt;a href=&quot;/questions/tagged/bacteriology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;bacteriology&amp;#39;&quot; rel=&quot;tag&quot;&gt;bacteriology&lt;/a&gt; as appropriate. &lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="16866" LastEditDate="2019-08-25T03:52:32.950" LastActivityDate="2019-08-25T03:52:32.950" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="586" PostTypeId="4" CreationDate="2012-01-10T22:02:03.087" Score="0" Body="The process by which light energy is harnessed to assemble organic compounds (esp. glucose) from inorganic carbon dioxide." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T00:49:29.223" LastActivityDate="2013-10-31T00:49:29.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="587" PostTypeId="5" CreationDate="2012-01-10T22:04:57.797" Score="0" Body="&lt;p&gt;Questions should be about the biology of cancer (such as the role of genetics or mutagens) or the biology of its treatment. Questions regarding medical advice are strictly off topic. &lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="9943" LastEditDate="2016-03-22T16:58:14.893" LastActivityDate="2016-03-22T16:58:14.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="588" PostTypeId="4" CreationDate="2012-01-10T22:04:57.797" Score="0" Body="A malignant group of uncontrollably dividing cells that form a tumour.  Questions regarding (proto)oncogenes and tumour-suppressor genes should also use this tag. " OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-03-18T11:47:31.657" LastActivityDate="2012-03-18T11:47:31.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="589" PostTypeId="2" ParentId="481" CreationDate="2012-01-10T23:34:02.503" Score="5" Body="&lt;p&gt;As requested, elaborating this into a full answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Three things to consider:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&quot;Alterations to gut microflora&quot; need not only be the invasion of a different, aggressive species of bacteria. One of the most common, and most dramatic forms of alteration to our gut flora is something we do to ourselves: antibiotics. Most ecosystems, micro or macro, are pretty vulnerable to the equivalent of a sustained firebombing.&lt;/li&gt;&#xA;&lt;li&gt;Some of the &quot;harmful bacteria&quot; that benefit from a disruption of the gut microflora are constituent components of said flora. &lt;em&gt;Clostridium difficile&lt;/em&gt; is part of the normal flora of many people - and acquired by many more transiently without incident - yet when the environment is sufficiently disrupted by antibiotics, peptic acid suppressors or some other factors, it proliferates and causes illness.&lt;/li&gt;&#xA;&lt;li&gt;While it may feel awful to you, many GI illnesses are really just a transient invasion before the body clears the infection, and are only marginally disruptive, or not disruptive at all. This can include the intake of toxins without the actual organism, or things like norovirus, which has a low enough infectious dose that even small amounts will make you ill.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="67" LastActivityDate="2012-01-10T23:34:02.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="590" PostTypeId="2" ParentId="574" CreationDate="2012-01-11T00:40:22.270" Score="6" Body="&lt;p&gt;&lt;strong&gt;Evolution has no aim&lt;/strong&gt;, you seem to be repeating a caricature of what the theory of evolution really says.  Evolution works by a mechanism where pressures on a population select for the traits that are best suited for that environment.  If there are no pressures on a population, then the selection of specific traits will be slowed down, as all members of the population have an equal chance at reproducing.&lt;/p&gt;&#xA;&lt;p&gt;Now to wax a bit philosophical on the issue.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.factsnotfantasy.com/15.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;As John Rennie said in Scientific American&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&amp;quot;Survival of the fittest&amp;quot; is a conversational way to describe natural selection, but a more technical description speaks of differential rates of survival and reproduction. That is, rather than labeling species as more or less fit, one can describe how many offspring they are likely to leave under given circumstances. Drop a fast-breeding pair of small-beaked finches and a slower-breeding pair of large-beaked finches onto an island full of food seeds. Within a few generations the fast breeders may control more of the food resources. Yet if large beaks more easily crush seeds, the advantage may tip to the slow breeders. In a pioneering study of finches on the Gal pagos Islands, Peter R. Grant of Princeton University observed these kinds of population shifts in the wild [see his article &amp;quot;Natural Selection and Darwin's Finches&amp;quot;; Scientific American, October 1991].&lt;/p&gt;&#xA;&lt;p&gt;The key is that adaptive fitness can be defined without reference to survival: large beaks are better adapted for crushing seeds, irrespective of whether that trait has survival value under the circumstances.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.factsnotfantasy.com/25.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;Michael Shermer states&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Living fossils (organisms that have not changed for millions of years) simply means that they evolved an adequate structure for a relatively static and unchanging environment, good enough to maintain a niche.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Or as a particularly brilliant writer that goes by the name of &lt;a href=&quot;http://factsnotfantasy.com/creationists.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;Calilasseia&lt;/a&gt; said:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;The static species fallacy.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;This is a particularly stupid canard, which the above discourse on inheritance, and variation brought about by meiosis, should flush down the toilet at a stroke. But, in order to reinforce how stupid this canard is, it is necessary to cover rigorously what a species is.&lt;/p&gt;&#xA;&lt;p&gt;A species is a population entity, and as a corollary thereof, a dynamic entity. A species is defined in rigorous biological work, as a population of living organisms, whose members can produce viable offspring with each other, but whose members can not produce viable offspring with a separate, distinct population. Actually, this is only one extant definition, but it is the one that matters with respect to evolution, because once again, it points to the central role of inheritance.&lt;/p&gt;&#xA;&lt;p&gt;Of course, part of the problem arises because of taxonomy. Because scientists need a reference point from which to launch further investigation, they have alighted, courtesy of our old friend Linnaeus, upon the process of cataloguing organisms and providing them with a unique, unambiguous identity. This, of course, has been most helpful in furthering our understanding of the biosphere, and indeed, Linnaeus himself, on the basis of comparative anatomy alone, alighted upon the idea that organisms were related to each other a hundred years before Darwin, which is why he constructed his taxonomic scheme in the manner he did. Yes, that's right, a creationist (though he was only a creationist because no other option existed in 1758) alighted upon the idea of biological interrelatedness, as a result of paying attention to reality. But the very same taxonomic practices that have been useful to science, have also led to a popular misconception. This is because taxonomists base their classification upon individually sampled organisms, one of which is chosen as a 'type specimen' that is henceforth declared to be the reference standard against which all others are compared. Other specimens are maintained in order to provide a record of likely variation in characteristics from that reference standard. The trouble is, of course, basing the entire classification system upon such reference standards promotes the illusion that those standards remain in place for all time. Scientists, of course, recognise that this is not the case, but it takes diligent intellectual effort to recognise that the taxonomic standards are merely particular snapshots of the state of the species at a given point in its history, which scientists then choose as their reference benchmark for current work. The species itself, however, courtesy of all that dissemination of variation across generations, does not stay still. It is NOT static.&lt;/p&gt;&#xA;&lt;p&gt;I cannot reinforce this strongly enough. A taxonomic classification is merely a historical snapshot of the state of a species, used as a reference point for further work, and does NOT constitute &amp;quot;the species&amp;quot; itself. The species itself, is the sum total of all the living organisms comprising that interfertile population, and with each new generation, that population undergoes change, because in the new generation, each of the organisms comprising that population are genetically different from those in the previous generation.&lt;/p&gt;&#xA;&lt;p&gt;So, if anyone wishes to erect the ridiculous idea that a species is a static entity, the simple retort is this. Look at your family album. Are you identical to either of your parents? No? There's your evidence for the dynamic nature of a species. Now replicate that evidence across millions of humans, and picture what happens with each new generation, remembering that across generations, inheritance is a dynamic process. There goes the static species fallacy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I hope that clears it up for you.&lt;/p&gt;&#xA;" OwnerUserId="279" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-01-25T20:16:16.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="591" PostTypeId="2" ParentId="576" CreationDate="2012-01-11T01:13:16.447" Score="21" Body="&lt;p&gt;Usually in biology (and being ATP, it most probably is biology), it's one of two things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The gamma-phosphate (the third one, the one farthest from the adenosine) is very unstable, meaning the phosphoanhydride bond is easy to break.  The cell &quot;allows&quot; it to break, but only at the cost of moving the phosphate to some other molecule, such as a serine or glycerol or fructose or whatever.  This phosphorylation creates a bond with lower energy than the phosphoanhydride, and so is overall favored.  Imagine the personification: the gamma phosphate hates being attached to anything, but hates being attached to an ADP the most.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, if ATP hydrolysis is coupled via an enzyme, it is usually done through transient storage of the energy is protein conformation.  An enzyme binds ATP, which makes the protein structure &quot;bend&quot; or conform around the ATP.  This puts loads of strain (energy = A) on the protein which is offset by the stabilization of binding the ATP (energy = B).  This strain can make an enzymatic surface open up on the protein which itself takes a lot of energy to make (energy = C).  The surface can catalyze some reaction (X+Y-&gt;Z in your example) that costs some energy (energy = D).  The completion of that reaction alters the enzyme's catalytic site to something new and higher energy (energy = E), which can be alleviated by cleavage of the ATP (-7.3 kcal/mol).  Alas, ADP and P do not fit well into that site of the enzyme, so they float out, restoring that original ATP-binding surface to it's original state.  Provided A&gt;B&gt;C&gt;D&gt;E&gt;-7.3, the cycle will continue until the ATP is exhausted or you have no more Z to make.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Typing &quot;enzyme catalysis cycle ATP&quot; gives a few examples. Here's a few:&lt;br&gt;&#xA;&lt;a href=&quot;http://www.pnas.org/content/108/34/14085/F5.large.jpg&quot;&gt;DNA gyrase&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.allometric.com/tom/courses/protected/ECB/CH16/16_37.jpg&quot;&gt;Actin-myosin cycle&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="219" LastEditorUserId="115" LastEditDate="2012-01-11T14:30:10.387" LastActivityDate="2012-01-11T14:30:10.387" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="592" PostTypeId="5" CreationDate="2012-01-11T02:30:42.407" Score="0" Body="&lt;p&gt;Synthetic biology is an approach to engineer biology. Core to the discipline is genetic engineering, which is made more akin to engineering by adding the levels of standardization, automation, and abstraction.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-29T16:00:26.890" LastActivityDate="2017-03-29T16:00:26.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="593" PostTypeId="4" CreationDate="2012-01-11T02:30:42.407" Score="0" Body="Synthetic biology is an approach to engineer biology. Core to the discipline is genetic engineering, which is made more akin to engineering by adding the levels of standardization, automation, and abstraction." OwnerUserId="28" LastEditorUserId="69" LastEditDate="2012-01-29T14:00:23.417" LastActivityDate="2012-01-29T14:00:23.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="594" PostTypeId="1" AcceptedAnswerId="615" CreationDate="2012-01-11T09:45:54.140" Score="44" ViewCount="1295" Body="&lt;p&gt;Why are nearly all amino acids in organisms left-handed (exception is glycine which has no isomer) when abiotic samples typical have an even mix of left- and right-handed molecules?&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-01-12T17:15:59.923" LastActivityDate="2017-08-08T22:02:10.710" Title="Why are amino acids in biology homochiral?" Tags="&lt;molecular-biology&gt;&lt;abiogenesis&gt;&lt;amino-acids&gt;&lt;chirality&gt;" AnswerCount="5" CommentCount="3" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="595" PostTypeId="2" ParentId="570" CreationDate="2012-01-11T10:13:14.293" Score="10" Body="&lt;p&gt;First of all one should tell that one can attribute the &lt;strong&gt;activation of certain brain zones&lt;/strong&gt; with some indepent events only when the activation takes place &lt;strong&gt;along the signal input&lt;/strong&gt; (receptors, sensory pathways towards the cortex and the sensory areas in cortex) &lt;strong&gt;or motor action&lt;/strong&gt; (=output) (along the motox cortex =&gt; motor neuron =&gt; target organ). Those zones in brain are also termed as primary ones, for there is a clear mapping between the event/action and the activity here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case of your &quot;sneak feeling&quot; as you describe in your post, there seems to be more not the sensory input from some unknown type of receptor, but rather &lt;strong&gt;a subconscious processing of the complete sensory input that reveals some potential danger and is percepted as a kind of &quot;smell of danger&quot;&lt;/strong&gt;. Since this processing happens in secondary zones and can be well distributed throughout the whole brain, there is no possibility to find a single focus with high activity change here (in my opinion, of course) -- those changes in activity are beyond the measuring/imaging capabilities of modern examination methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Possible sensory inputs here might include (but not limited to):&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Optical (some shades, moving asyncronously etc).&lt;/li&gt;&#xA;&lt;li&gt;Acustic (some sneaking sounds, normally disguised by the background sound).&lt;/li&gt;&#xA;&lt;li&gt;Air move, air stream blocking sense etc (tactile feeling).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So, everything you suggest might apply here.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-11T19:54:03.917" LastActivityDate="2012-01-11T19:54:03.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="596" PostTypeId="2" ParentId="109" CreationDate="2012-01-11T10:52:19.523" Score="7" Body="&lt;p&gt;First of all we should distinguish between the physiological clotting factors that are parts of the normal clotting pathways, and those that might affect clotting pathways but are not observed under healthy conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TPA (tissue plasminogen activation), PAI-1 (plasminogen activator inhibitor) and prothrombin are normal clotting factors that are essential for blood clotting. Any deficiency (congenital or acquired) might cause certain pathologic conditions, including the osteoarthritis and avascular bone necrosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lupus anticoagulant, however, is an antibody against cell membrane that is common for Lupus. This antibody can intervene into the process of clotting and increase the prothrombine time (the common lab method to test blood clotting properties), hence the name &quot;anticoagulant&quot;. But this effect is just a sort of &quot;side-effect&quot; of this antibody, that leads to certain symptoms in case of auto-immune attack against different target organs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, after this introduction I can rephrase your first question as: &lt;em&gt;&quot;Does the deficiency of clotting factors TPA and PAI-1 lead to degenerative arthritis in the same way that lupus anticoagulant and prothrombin deficiency might?&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The part of the answer is already in this question: &lt;strong&gt;yes&lt;/strong&gt;, the deficiency of these factors might and under certain conditions, leads to the development of osteoarhritis and avascular necrosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I must confess, I found no evidence whether the underlying mechanism is different or not. Papers just prove that these factors &lt;a href=&quot;http://ard.bmj.com/content/56/9/550.full&quot; rel=&quot;nofollow&quot;&gt;are discovered&lt;/a&gt; in the affected joins, and see the correlation in mice models between the factors and the articifially induced arthritis. But I found no study which would try to address the mechanisms of these actions or to show, whether these are different.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="107" LastEditDate="2012-09-30T22:41:42.237" LastActivityDate="2012-09-30T22:41:42.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="597" PostTypeId="2" ParentId="594" CreationDate="2012-01-11T10:58:56.223" Score="11" Body="&lt;p&gt;As far as I know, it is unknown why we only see left-handed and not right–handed amino acids. A &lt;a href=&quot;http://www.nature.com/news/frontier-experiments-tough-science-1.9723&quot;&gt;recent article&lt;/a&gt; speculates that the &lt;a href=&quot;http://en.wikipedia.org/wiki/Weak_force&quot;&gt;weak force&lt;/a&gt; could be responsible for a tiny asymmetry in energy levels between the stereo-isomers. However, if the effect is tiny, its hard to see why it should have biological implications. In 2004, &lt;a href=&quot;http://www.sciencemag.org/content/305/5688/1253.full&quot;&gt;Tamura and Schimmel&lt;/a&gt; showed that RNA has a preference for L-amino acids, whereas mirrored RNA has a preference for D-amino acids. They conclude:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These results suggest the possibility that the selection of L-amino acids for proteins was determined by the stereochemistry of RNA. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So the next question is: Why do we observe only one kind of RNA? It could just be by chance, that a polymer of one RNA configuration became self-replicating. &lt;/p&gt;&#xA;" OwnerUserId="112" LastEditorUserId="112" LastEditDate="2012-01-11T15:43:14.633" LastActivityDate="2012-01-11T15:43:14.633" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="598" PostTypeId="1" CreationDate="2012-01-11T13:22:40.710" Score="5" ViewCount="127" Body="&lt;p&gt;Exons are produced by more than one mechanism, e.g. splicing out introns after transcription, if I remember correctly. Please list all mechanisms.&lt;/p&gt;&#xA;" OwnerUserId="95" LastEditorUserId="66" LastEditDate="2012-01-11T19:28:21.540" LastActivityDate="2012-01-12T01:06:07.090" Title="What are the different ways an exon gets spliced?" Tags="&lt;molecular-biology&gt;&lt;genetics&gt;&lt;spliceosome&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="599" PostTypeId="2" ParentId="594" CreationDate="2012-01-11T14:26:19.177" Score="16" Body="&lt;p&gt;The ribosome holds the peptide-bound tRNA and aminoacyl-tRNA in the right orientation to catalyze the peptidyltransferase reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/103/36/13327/F1.expansion.html&quot;&gt;http://www.pnas.org/content/103/36/13327/F1.expansion.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the incoming aminoacyl-tRNA was the other enantiomer, the amino acid moiety would not fit properly into the ribosome active site.  In other words, the shape of the ribosome selects for specific amino acid enantiomers.  In abiotic mixes, the creation of amino acids and their polymerization is non-catalytic, and so there is no specificity or selection for certain enantiomers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're asking the &quot;biogenesis&quot; question, then I think the answer is that we don't know the original selection, and it may just be chance.  But once biochemistry began making and using them, of course they were all the same.  But frankly &quot;why not D-amino acids&quot; makes about as much sense as &quot;why not 22 amino acids, or 23, or 24, or 25?&quot;  Because that's what happened.&lt;/p&gt;&#xA;" OwnerUserId="219" LastActivityDate="2012-01-11T14:26:19.177" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="600" PostTypeId="5" CreationDate="2012-01-11T19:30:48.587" Score="0" Body="" OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-11T19:30:48.587" LastActivityDate="2012-01-11T19:30:48.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="601" PostTypeId="4" CreationDate="2012-01-11T19:30:48.587" Score="0" Body="Amino-acids are organic acids with an amino group in the alpha position (alpha-acids). They are the structural units of proteins and involved in many biochemical pathways." OwnerUserId="66" LastEditorUserId="4101" LastEditDate="2013-10-31T14:04:35.743" LastActivityDate="2013-10-31T14:04:35.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="602" PostTypeId="5" CreationDate="2012-01-11T19:36:47.813" Score="0" Body="" OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-11T19:36:47.813" LastActivityDate="2012-01-11T19:36:47.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="603" PostTypeId="4" CreationDate="2012-01-11T19:36:47.813" Score="0" Body="Set of methods to visualize certain properties (structure, gene expression, potential changes, etc.) of organisms or single cells. " OwnerUserId="66" LastEditorUserId="4101" LastEditDate="2013-10-31T19:08:07.577" LastActivityDate="2013-10-31T19:08:07.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="604" PostTypeId="1" AcceptedAnswerId="632" CreationDate="2012-01-11T23:21:15.577" Score="8" ViewCount="8218" Body="&lt;p&gt;Translation in &lt;em&gt;E. coli&lt;/em&gt; is usually initiated at an AUG codon, which encodes the amino acid methionine. In some cases, however, the start codon is GUG, which normally encodes valine. If GUG is used as the start codon, is a tRNA charged with methionine used or one charged with valine, and does the use of GUG as a start codon affect the efficiency of translation? &lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="22057" LastEditDate="2019-01-21T20:40:19.427" LastActivityDate="2019-01-21T20:40:19.427" Title="The GUG start codon in E. coli: identity of initiating tRNA and efficiency of translation" Tags="&lt;molecular-biology&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="605" PostTypeId="5" CreationDate="2012-01-11T23:25:00.343" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-11T23:25:00.343" LastActivityDate="2012-01-11T23:25:00.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="606" PostTypeId="4" CreationDate="2012-01-11T23:25:00.343" Score="0" Body="Translation is the process of protein synthesis. The information encoded in the mRNA is translated into an amino acid sequence through the joint activity of tRNAs and ribosomes." OwnerUserId="28" LastEditorUserId="4101" LastEditDate="2013-10-31T16:34:45.503" LastActivityDate="2013-10-31T16:34:45.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="607" PostTypeId="1" CreationDate="2012-01-11T23:44:48.940" Score="15" ViewCount="741" Body="&lt;p&gt;Intrinsically disordered proteins (IDPs) are a class of proteins that do not adopt a stable secondary or tertiary structure under physiological conditions &lt;em&gt;in vitro,&lt;/em&gt; but still have biological functions. Many IDPs are implicated in cancer, neurodegenerative diseases, and diabetes, which makes them attractive drug targets. Are there any successful examples of that? Are there any drugs which disrupt protein-protein interactions (as one of the protein being IDP)? &lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-01-15T01:05:41.397" LastActivityDate="2012-02-13T07:24:50.673" Title="Intrinsically disordered proteins as potential drug targets" Tags="&lt;molecular-biology&gt;&lt;proteins&gt;&lt;pharmacology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="608" PostTypeId="5" CreationDate="2012-01-11T23:45:19.187" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-11T23:45:19.187" LastActivityDate="2012-01-11T23:45:19.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="609" PostTypeId="4" CreationDate="2012-01-11T23:45:19.187" Score="0" Body="Intrinsically disordered proteins (IDPs) are a class of proteins that do not adopt a stable secondary or tertiary structure under physiological conditions in vitro, but still have biological functions." OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-01-12T13:51:19.107" LastActivityDate="2012-01-12T13:51:19.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="610" PostTypeId="5" CreationDate="2012-01-11T23:46:03.383" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-11T23:46:03.383" LastActivityDate="2012-01-11T23:46:03.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="611" PostTypeId="4" CreationDate="2012-01-11T23:46:03.383" Score="0" Body="PPIs stands for protein-protein interactions" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-01-12T13:51:22.943" LastActivityDate="2012-01-12T13:51:22.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="612" PostTypeId="5" CreationDate="2012-01-11T23:50:09.490" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-11T23:50:09.490" LastActivityDate="2012-01-11T23:50:09.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="613" PostTypeId="4" CreationDate="2012-01-11T23:50:09.490" Score="0" Body="Chemical substances that are used for treatment, cure, diagnostics, alleviation of symptoms of diseases, or stimulation of biological functions." OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-01-12T07:27:15.203" LastActivityDate="2012-01-12T07:27:15.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="614" PostTypeId="2" ParentId="598" CreationDate="2012-01-12T01:06:07.090" Score="9" Body="&lt;p&gt;There are several ways splicing can occur, which depends on the RNA molecule to be spliced and the catalyst that performs the splicing:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;mRNA splicing is carried out by spliceosome, which consists of small nuclear RNAs. There are sequences at the end of the introns and branch sties which indicate the splice sites. The so called lariat structure is formed when the 2'OH group of an adenosine residue in the branch site attacks the 5' splice site.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;self-splicing of ribosomal RNA precursor - it is performed with the absence of spliceosome.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;tRNA splicing - it requires three enzymes and ATP hydrolysis. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bcs.whfreeman.com/biochem5/default.asp?s=&amp;amp;n=&amp;amp;i=&amp;amp;v=&amp;amp;o=&amp;amp;ns=0&amp;amp;t=&amp;amp;uid=0&amp;amp;rau=0&quot;&gt;Biochemistry, L. Stryer, 5th eddition&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jbc.org/content/273/21/12685.full&quot;&gt;J. Abelson. tRNA Splicing&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-01-12T01:06:07.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="615" PostTypeId="2" ParentId="594" CreationDate="2012-01-12T02:03:13.033" Score="26" Body="&lt;p&gt;I know that you are referring to the commonly ribosome-translated L-proteins, but I can't help but add that there are some peptides, called nonribosomal peptides, which are not dependent on the mRNA and can incorporate D-amino acids. They have very important pharmaceutical properties. I recommend &lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.micro.58.030603.123615&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; (1) review article if you are interested in the subject. It is also worth mentioning that D-alanine and D-glutamine are incorporated into the peptidoglycane of bacteria.&lt;/p&gt;&#xA;&lt;p&gt;I read several papers (2, 3, 4) that discuss the problem of chirality but all of them conclude that there is no apparent reason why we live in the L-world. The L-amino acids should not have chemical advantages over the D-amino acids, as biocs already pointed out.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.springerlink.com/content/t746466251668633/&quot; rel=&quot;noreferrer&quot;&gt;Reasons for the occurrence of the twenty coded protein amino acids&lt;/a&gt; (2) has an informative and interesting outline. This is the paragraph on the topic of chirality:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;This is related to the question of the origin of optical&#xA;activity in living organisms on which there is a very&#xA;large literature (&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/4669121&quot; rel=&quot;noreferrer&quot;&gt;Bonner 1972&lt;/a&gt;; &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/722806&quot; rel=&quot;noreferrer&quot;&gt;Norden 1978&lt;/a&gt;; &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/7401179&quot; rel=&quot;noreferrer&quot;&gt;Brack and&#xA;Spack 1980&lt;/a&gt;). We do not propose to deal with this&#xA;question here, except to note that arguments presented&#xA;in this paper would apply to organisms constructed from&#xA;either D or L amino acids.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It might be possible that both L and D lives were present (L/D-amino acids, L/D-enzymes recognizing L/D-substrates), but, by random chance the L-world outcompeted the D-world.&lt;/p&gt;&#xA;&lt;p&gt;I also found the same question in a &lt;a href=&quot;http://forums.studentdoctor.net/archive/index.php/t-854644.html&quot; rel=&quot;noreferrer&quot;&gt;forum&lt;/a&gt; where one of the answers seems intriguing. I cannot comment on the reliability of the answer, but hopefully someone will have the expertise to do so:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;One, our galaxy has a chiral spin and a magnetic orientation, which causes cosmic dust particles to polarize starlight as circularly polarized in one direction only. This circularly polarized light degrades D enantiomers of amino acids more than L enantiomers, and this effect is clear when analyzing the amino acids found on comets and meteors. This explains why, at least in the milky way, L enantiomers are preferred.&lt;/p&gt;&#xA;&lt;p&gt;Two, although gravity, electromagnetism, and the strong nuclear force are achiral, the weak nuclear force (radioactive decay) is chiral. During beta decay, the emitted electrons preferentially favor one kind of spin. That's right, the parity of the universe is not conserved in nuclear decay. These chiral electrons once again preferrentially degrade D amino acids vs. L amino acids.&lt;/p&gt;&#xA;&lt;p&gt;Thus due to the chirality of sunlight and the chirality of nuclear radiation, L amino acids are the more stable enantiomers and therefore are favored for abiogenesis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.micro.58.030603.123615&quot; rel=&quot;noreferrer&quot;&gt;BIOSYNTHESIS OF NONRIBOSOMAL PEPTIDES&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.springerlink.com/content/t746466251668633/&quot; rel=&quot;noreferrer&quot;&gt;Reasons for the occurrence of the twenty coded protein amino acids&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.mdpi.com/1422-0067/12/7/4745/&quot; rel=&quot;noreferrer&quot;&gt;Molecular Basis for Chiral Selection in RNA Aminoacylation&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8749373&quot; rel=&quot;noreferrer&quot;&gt;How nature deals with stereoisomers&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/4669121&quot; rel=&quot;noreferrer&quot;&gt;The adaptation of diastereomeric S-prolyl dipeptide derivatives to the quantitative estimation of R- and S-leucine enantiomers. Bonner WA, 1972&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/722806&quot; rel=&quot;noreferrer&quot;&gt;The asymmetry of life. Nordén B, 1978&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/7401179&quot; rel=&quot;noreferrer&quot;&gt;Beta-Structures of polypeptides with L- and D-residues. Part III. Experimental evidences for enrichment in enantiomer. Brack A, Spach G, 1980&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="28" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2016-04-09T06:36:27.080" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="616" PostTypeId="2" ParentId="249" CreationDate="2012-01-12T02:18:33.337" Score="12" Body="&lt;p&gt;Some additional notes- I have grown TickleMe Plants (sensitive plants) for years and  I have seen the plants close their leaves as a reaction to the vibrations caused by my foot steps as well as blowing on the plant and placing the plant in cold, very hot and dark environments.  In addition I have found the plant's ablity to detect vibrations I have observed to be dependent on temperature and the time of day. Some of this information can be found in The TickleMe Plant Book found at &lt;a href=&quot;http://www.ticklemeplant.com&quot;&gt;http://www.ticklemeplant.com&lt;/a&gt;  I am unable to specifically say what the mechanism is that detects the vibrations and causes the TickleMe Plants turgor pressure to change. I look forward to more answers.&lt;/p&gt;&#xA;" OwnerUserId="337" LastEditorUserId="337" LastEditDate="2012-01-12T11:35:47.360" LastActivityDate="2012-01-12T11:35:47.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="617" PostTypeId="1" AcceptedAnswerId="621" CreationDate="2012-01-12T02:40:52.927" Score="4" ViewCount="2935" Body="&lt;p&gt;Many plants have pith, from walnut trees to corn to ragweed, but I can't think of anything it does them. What is pith and how is it useful to them?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="69" LastEditDate="2012-01-12T07:34:49.063" LastActivityDate="2017-06-23T03:35:13.727" Title="Why do plants have pith and how is it useful to them?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="618" PostTypeId="1" AcceptedAnswerId="620" CreationDate="2012-01-12T07:59:22.620" Score="11" ViewCount="61440" Body="&lt;p&gt;I extracted RNA from different cell lines, an I want to perform reverse transcription and then PCR. To get good results, in which range should the absorption ratios 260/280 nm and 260/230 nm be? And what is the idea behind measuring those ratios?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I got values for the 260/280 ratio from 2.1 to 2.13 and values for the 260/230 ratio from 0.98 to 2.01. Are these values acceptable, and what information can I gain from them?&lt;/p&gt;&#xA;" OwnerUserId="126" LastEditorUserId="223" LastEditDate="2012-08-02T12:53:01.143" LastActivityDate="2012-08-02T12:53:01.143" Title="Absorption ratios 260/280 and 260/230 for RNA" Tags="&lt;molecular-biology&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="619" PostTypeId="1" AcceptedAnswerId="636" CreationDate="2012-01-12T08:31:26.110" Score="6" ViewCount="1151" Body="&lt;p&gt;What is the ideal amount of RNA to use for the RT? and how much cDNA to use then for the PCR?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did RT with a solution of RNA of 0.36 ug/ul. Then for my PCR I used 1 ul of the cDNA obtained and used 25 cycles because I was hoping to see a difference between an endogenous level and an overexpression. However, I detected no band at the expected height of 500 bp but a diffuse band at 100 bp. What can this 100 bp represent? primer dimer? I switched to 35 cycles and I used either the same amount of cDNA or add 3 times more cDNA. In both cases I got bands at the expected height (but stronger when I put more cDNA) and still big bands at 100 bp. &lt;/p&gt;&#xA;" OwnerUserId="126" LastEditorUserId="28" LastEditDate="2012-01-12T20:02:47.367" LastActivityDate="2012-01-12T22:32:20.393" Title="Reverse transcription PCR optimization" Tags="&lt;molecular-biology&gt;&lt;rna&gt;&lt;reverse-transcription&gt;&lt;pcr&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="620" PostTypeId="2" ParentId="618" CreationDate="2012-01-12T08:42:34.023" Score="9" Body="&lt;p&gt;DNA and RNA absorb at 260nm. Proteins absorb at 280nm. The 260/280 ratio is a good estimate of how pure your sample is. For RNA, the 260/280 should be around 2. If it is lower, this might be an indication from contamination or proteins, phenol, or other contaminants in your sample. The 260/230 ratio is a second measure for purity of the sample, as the contaminants absorb at 230nm (like EDTA). The 260/230 ratio should be higher than the 260/280 ratio, as it is usually between 2 and 2.2. Lower ratio might be an indication of contamination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your case, I would be worried about the purity of the sample which gave you 260/230 ratio of 0.98. If you are using nanodrop, looking at the plot can also be a good indication of the quality of your sample. For a pure sample, a well defined peak (no shoulders or wiggles) at 260nm is expected. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take a look at the &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;ved=0CDIQFjAB&amp;amp;url=http://www.bio.davidson.edu/projects/gcat/protocols/NanoDrop_tip.pdf&amp;amp;ei=HZkOT8jWJ4rjiAKuxvC9DQ&amp;amp;usg=AFQjCNGBwjGNDiSKkXhOVf5JSl6543tnDA&amp;amp;sig2=CvtxjNrEC8lXmPQNcWVm6w&quot;&gt;NanoDrop manual&lt;/a&gt; for more information.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-01-12T08:42:34.023" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="621" PostTypeId="2" ParentId="617" CreationDate="2012-01-12T11:51:56.067" Score="8" Body="&lt;p&gt;The pith (medulla) forms part of the &lt;a href=&quot;http://www.uri.edu/cels/bio/plant_anatomy/glossary.html&quot;&gt;ground tissue system&lt;/a&gt; of a plant, and specifically it is the ground tissue which lies interior to a plants vascular tissues (xylem, phloem etc.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ground tissue system is responsible for much of a plants metabolic functioning, and contains various specialized cell types which aid in photosynthesis and storage of photosynthesis products. The pith is made from parenchyma cells.&lt;/p&gt;&#xA;" OwnerUserId="81" LastActivityDate="2012-01-12T11:51:56.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="623" PostTypeId="1" AcceptedAnswerId="1240" CreationDate="2012-01-12T14:15:14.970" Score="54" ViewCount="2544" Body="&lt;p&gt;From what I can tell and what thus far all people with whom I discussed this subject confirmed is that time appears to &quot;accelerate&quot; as we age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Digging a little, most explanations I found basically reduced this to two reasons:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;As we age physically, a time frame of constant length becomes ever smaller in contrast to the time we spent living&lt;/li&gt;&#xA;&lt;li&gt;As we age socially, we are burdened with an increasing amount of responsibility and thus an increasing influx of information which impairs our perception of the present&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;To be honest, neither sounds entirely convincing to me because:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;In my perception &quot;local time&quot; (short time frames that I don't even bother to measure on the scale of my lifetime) is also accelerating. Just as an example: When I wait for the bus, time goes by reasonably fast as opposed to my childhood tortures of having to wait an eternity for those five minutes to pass.&lt;/li&gt;&#xA;&lt;li&gt;Even after making a great effort to cut myself off from society and consciously trying to focus on the moment, the perceived speed of time didn't really change. (Although I did have a great time :))&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Which leads me to a simple question (and a few corollaries):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Am I just in denial of two perfectly plausible and sufficient explanations, or are there actual biological effects (e.g. changes in brain chemistry) in place, that cause (or at least significantly influence) this?&lt;/li&gt;&#xA;&lt;li&gt;Is there a mechanism, that &quot;stretches out&quot; time for the young brain so that weight of an immense boredom forces it to benefit from its learning ability, while it &quot;shrinks&quot; time as the brain &quot;matures&quot; and must now act based on what it has learned, which often involves a lot of patience?&lt;/li&gt;&#xA;&lt;li&gt;If there is such a mechanism, are there any available means to counter it? (not sure I'd really want to, but I'd like to know whether I could)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="340" LastEditorUserId="340" LastEditDate="2012-01-13T12:25:30.993" LastActivityDate="2015-09-21T15:10:31.750" Title="Human perception of time depending on age" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;neuroscience&gt;&lt;perception&gt;" AnswerCount="5" CommentCount="7" FavoriteCount="18" ContentLicense="CC BY-SA 3.0" />
  <row Id="624" PostTypeId="1" CreationDate="2012-01-12T14:28:13.750" Score="12" ViewCount="939" Body="&lt;p&gt;I &lt;a href=&quot;http://www.plosone.org/article/info%3adoi%2F10.1371%2Fjournal.pone.0006256&quot; rel=&quot;nofollow&quot;&gt;read&lt;/a&gt; that Japanese researchers have developed very sensitive camera that recorded bioluminescence in humans; is it possible and if so what is the mechanism behind it?&lt;/p&gt;&#xA;" OwnerUserId="333" LastEditorUserId="389" LastEditDate="2012-05-08T02:22:34.850" LastActivityDate="2012-05-08T02:22:34.850" Title="Does bioluminescence occur in humans too?" Tags="&lt;human-biology&gt;&lt;bioluminescence&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="625" PostTypeId="1" CreationDate="2012-01-12T15:26:36.133" Score="5" ViewCount="158" Body="&lt;p&gt;I'm curious to know if this is physically feasible because during my reading up on synthetic biology and just general research i realise that life is capable of producing some exquisitely complex materials and biological structures and wondered if they could potentially recreate artficial materials that aren't found in nature well not yet anyway. Could such a structure evolve naturally or would it have to be designed or directed via synthetic biology techniques?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your time.  &lt;/p&gt;&#xA;" OwnerUserId="342" LastActivityDate="2012-01-12T15:26:36.133" Title="Could an organism theoretically produce a metamaterial-like structure?" Tags="&lt;evolution&gt;&lt;synthetic-biology&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2012-02-05T15:39:37.957" ContentLicense="CC BY-SA 3.0" />
  <row Id="626" PostTypeId="2" ParentId="624" CreationDate="2012-01-12T16:07:56.793" Score="14" Body="&lt;p&gt;From the article you linked:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;virtually all living organisms emit extremely weak light, spontaneously without external photoexcitation. This biophoton emission is categorized in different phenomena of light emission from bioluminescence, and &lt;strong&gt;is believed to be a by-product of biochemical reactions in which excited molecules are produced from bioenergetic processes that involves active oxygen species&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They reference these two works. The first is a 1988 review from Popp et al. (1988):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3396653&quot;&gt;Biophoton emission&lt;/a&gt; - Experientia 44:543–600. (sorry, I cannot find the link to a full text...)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fritz-Albert_Popp&quot;&gt;Fritz-Albert Popp&lt;/a&gt; is the biophysicist who first developed the &lt;a href=&quot;http://en.wikipedia.org/wiki/Biophoton&quot;&gt;&lt;em&gt;biophoton theory&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second work they reference is by the same first author:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10498336&quot;&gt;In vivo imaging of spontaneous ultraweak photon emission from a rat's brain correlated with cerebral energy metabolism and oxidative stress.&lt;/a&gt; - Kobayashi M, et al.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=biophoton%20emission&quot;&gt;search in Pubmed&lt;/a&gt; reveals various other articles by different authors studying different species. &lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-01-12T16:07:56.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="627" PostTypeId="5" CreationDate="2012-01-12T16:10:18.063" Score="0" Body="&lt;p&gt;&lt;strong&gt;Homework questions are off-topic on Biology and are likely to be closed unless you have shown your attempt at an answer.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please see the &lt;a href=&quot;http://meta.biology.stackexchange.com/questions/266/draft-homework-policy-for-faq&quot;&gt;homework policy on meta&lt;/a&gt; or &lt;a href=&quot;https://biology.stackexchange.com/help/homework&quot;&gt;help center&lt;/a&gt; before posting a new homework question. This tag should be used in addition to other appropriate tags.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="16866" LastEditDate="2019-12-13T04:26:03.230" LastActivityDate="2019-12-13T04:26:03.230" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="628" PostTypeId="4" CreationDate="2012-01-12T16:10:18.063" Score="0" Body="This tag indicates that the question is likely based on a home assignment in biology-related university or high school courses or is about an elementary concept that may seem trivial to biology professionals. Please see the homework policy on meta before asking homework questions." OwnerUserId="66" LastEditorUserId="16460" LastEditDate="2017-06-04T12:41:59.860" LastActivityDate="2017-06-04T12:41:59.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="629" PostTypeId="2" ParentId="619" CreationDate="2012-01-12T16:12:47.507" Score="4" Body="&lt;p&gt;There is no single &quot;ideal amount&quot; of RNA. I would suggest you to do a titration curve to determine the best amount for your specific assay. The band at 100 bp could be a non-specific amplification. You could try to increase slightly the annealing temp to see if that removes (or reduces) the lower band. Alternatively, you can consider a different primer set or even a nested PCR. &#xA;Also, it is still possible that you may look at a splicing alternative in that band. Do your primers span more than one exon?&lt;/p&gt;&#xA;" OwnerUserId="48" LastActivityDate="2012-01-12T16:12:47.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="630" PostTypeId="5" CreationDate="2012-01-12T16:20:24.840" Score="0" Body="" OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-12T16:20:24.840" LastActivityDate="2012-01-12T16:20:24.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="631" PostTypeId="4" CreationDate="2012-01-12T16:20:24.840" Score="0" Body="This tag is not for asking questions about &quot;learning biology&quot;. Learning is acquiring new or modifying existing knowledge, behaviors, skills, values, or preferences and may involve synthesizing different types of information. It can be broken down to acquiring or modifying the reaction to the external input on its repetitive presentation.   " OwnerUserId="66" LastEditorUserId="69" LastEditDate="2013-02-09T11:28:37.743" LastActivityDate="2013-02-09T11:28:37.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="632" PostTypeId="2" ParentId="604" CreationDate="2012-01-12T17:12:24.560" Score="9" Body="&lt;p&gt;The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c#SG11&quot;&gt;NCBI translation table&lt;/a&gt; translates all alternative start sites as methionines. To my understanding, all translation is initiated by the fMet-tRNA. I don't know if there are any exceptions to this rule. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding translation efficiency, I only found a 1985 paper in PNAS (&lt;a href=&quot;http://www.pnas.org/content/82/17/5656.full.pdf&quot;&gt;Reddy et al, PNAS 82:5656-60&lt;/a&gt;), in which they compared the translation efficiency of adenilate cyclase's own UUG start vs GUG or AUG, obtaining a translation ratio 1:2:6 UUG:GUG:AUG, suggesting that AUG is the most efficient one, followed by GUG. Also, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/037810979190377M&quot;&gt;Romero and Garcia, FEMS microbiology letters 84:325-330 (1991)&lt;/a&gt; compared the efficiency of AUG vs AUC, AUA and AUU, showing a much lower efficiency for those codons, but they did not compare it to GUG.&lt;/p&gt;&#xA;" OwnerUserId="48" LastActivityDate="2012-01-12T17:12:24.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="633" PostTypeId="2" ParentId="447" CreationDate="2012-01-12T18:58:37.843" Score="15" Body="&lt;p&gt;The subject of alcohol tolerance is broader than it might appear. However, in most cases people refer to what is called metabolic alcohol tolerance. Based on your response to the comment made by Alexander Galkin, I assume that you also refer to metabolic alcohol tolerance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Metabolic alcohol tolerance is the result of drinking significant amounts of alcohol over a period of time as you describe. Both the amount of alcohol and the duration that it takes to develop an increased metabolic tolerance towards alcohol differ from person to person.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When most people drink alcohol, the liver will responds by activating alcohol degrading enzymes that break down the alcohol molecules, which results in the elimination of the intoxicating effect. The activation of those enzymes occurs much faster with people who have developed metabolic alcohol tolerance and the concentration of those enzymes is generally higher. This means that those people can break down alcohol faster than you and me, that is, they can &quot;tolerate&quot; more alcohol in the sense that they simply get rid of it much quicker.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a final note, being more alcohol tolerant is not exactly correct as metabolic tolerance doesn't necessarily mean that the organs affected/intoxicated (such as the brain) by alcohol aren't necessarily more tolerant. The alcohol is simply broken down much faster and can therefore have a limited impact.&lt;/p&gt;&#xA;" OwnerUserId="138" LastActivityDate="2012-01-12T18:58:37.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="634" PostTypeId="2" ParentId="594" CreationDate="2012-01-12T19:43:45.693" Score="9" Body="&lt;p&gt;The normal results of an attempt to assemble proteins with mixed chiral amino acids is a protein that fails to fold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The general assumption due to this result is a choice has to be made very early on to use all right-handed or all left-handed amino acids. There doesn't seem to be any particular reason to choose one way over the other except for prevalence.&lt;/p&gt;&#xA;" OwnerUserId="344" LastActivityDate="2012-01-12T19:43:45.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="636" PostTypeId="2" ParentId="619" CreationDate="2012-01-12T22:32:20.393" Score="6" Body="&lt;p&gt;I see big fuzzy bands around 100bp as well. They're most likely &lt;strong&gt;RNA contamination&lt;/strong&gt;. To get rid of them, digest your RT-PCR products with RNAse-H. But if you just need to visualize your band of interest, and the fuzzy bands aren't getting in the way, it shouldn't be a problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I usually input anywhere from 1-2 ug of RNA into my RT-PCR reaction using the Invitrogen Superscript III kit for a total volume of 20 ul. After the reaction, I use 1/10 the volume of that (2 ul) for downstream (PCR) applications. This usually gives me nice results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To optimize RT-PCR for detection of a specific target, consider using gene specific primers (make sure to use only anti-sense primers) in your RT-PCR instead of oligo-dT or random hexamers. This enriches your target when you use them for downstream applications. When you use GSPs though, make sure to run a parallel reaction with control (i.e. beta actin) primers to prove that your RT-PCR reaction is working.&lt;/p&gt;&#xA;" OwnerUserId="177" LastActivityDate="2012-01-12T22:32:20.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="637" PostTypeId="2" ParentId="447" CreationDate="2012-01-12T23:28:18.897" Score="10" Body="&lt;p&gt;So, judging by your answer to my comment you are most likely talking about so-called &lt;strong&gt;consumption-induced alcohol tolerance&lt;/strong&gt;, that one might develop by regular drinking of alcoholic beverages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can group the reasons for increased tolerance to the following groups: better adaptation for the elevated concentrations (functional) or increased break-down (metabolic).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Functional tolerance.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that your body and its organs, especially your CNS, &lt;strong&gt;adapt to compensate for the increased alcohol concentration&lt;/strong&gt; and manage to sustain its functioning despite the elevated blood alcohol concentrations (BAC). So, the dose of alcohol which previously led to trembling and disorientation now evokes only some coordinatory disturbances. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The physiological mechanisms involved here are:&#xA;1. Desensitization of the alcohol-sensitive (primarily GABA-ergic) receptors in CNS.&#xA;2. Changes in the neuron firing rates (to compensate for the deterioration of the GABA-ergic inhibition).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Metabolic tolerance.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This condition is characterized by the &lt;strong&gt;increased alcohol break-down&lt;/strong&gt; by the liver, that slows down the increase of blood alcohol concentration (BAC) upon its consumption leading to the attenuation or complete disguise of alcohol intoxication (inebriation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main enzyme that is responsible for alcohol transformation is the so-called  &lt;a href=&quot;http://en.wikipedia.org/wiki/Alcohol_dehydrogenase&quot;&gt;alcohol dehydrogenase&lt;/a&gt; (ADH), that represents a group of substances catalyzing the alcohol oxidation to aldehydes. This enzymes are located in the liver cells (hepatocytes) and the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1501558/&quot;&gt;increase in their activity&lt;/a&gt; (and most likely also the absolute amount) is not well understood. It happens, by the way, not only on alcohol consumption: the intake of barbiturates also leads to the increase of ADH and tolerance.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://alcoholism.about.com/cs/alerts/l/blnaa28.htm&quot;&gt;Here&lt;/a&gt; you can find much more information about acquired alcohol tolerance, but mostly from the behavioural viewpoint.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-01-12T23:28:18.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="638" PostTypeId="2" ParentId="126" CreationDate="2012-01-12T23:52:35.037" Score="6" Body="&lt;p&gt;I have studied all available (via University library) literature on the Leydig cells and I think your teacher might have &lt;a href=&quot;http://joe.endocrinology-journals.org/content/168/2/213.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt; summarizing the morphological studies on Leydig cells in different animal models in mind.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To put it straight, the most common animal models for studying Leydig cells are rats, mice and pigs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The development of Leydig cells in rats was shown to be bi-phasic: development of the Leydig cell population in fetus and its degradation while transforming into the mature cells. It has been believed for quite long that this is also true for human Leydig cells. However, some studies performed on pigs and monkeys delivered an evidence for an additional phase of cell degradation sometimes between the fetal and neonatal development shifts. These data are summarized on the following Figure (taken from the referenced paper):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eQPBB.jpg&quot; alt=&quot;Leydig cell development flowchart&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, by comparing the Leydig cells of rats and humans from the same fetus age or shortly after the birth (neonatal time) you might see the degradation of Leydig cells -- they decrease in size and many of them eventually die -- compared to normal state of these cells in rats.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-01-12T23:52:35.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="639" PostTypeId="2" ParentId="567" CreationDate="2012-01-13T00:14:29.493" Score="4" Body="&lt;p&gt;Let us first answer the question: what is the effect of cco-1 knock-down in &lt;em&gt;C. elegans&lt;/em&gt;. Durieux J., Wolff S. and Dillin A. in their &lt;a href=&quot;http://www.wormbase.org/db/misc/paper?name=WBPaper00037991;class=Paper&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; &quot;The cell-non-autonomous nature of electron transport chain-mediated longevity&quot;. Cell 144:79-91 (2011) provide the following explanation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The life span of &lt;em&gt;C. elegans&lt;/em&gt; can be increased via &lt;strong&gt;reduced function of&#xA;  the mitochondria&lt;/strong&gt;; however, the extent to which mitochondrial&#xA;  alteration in a single, distinct tissue may influence aging in the&#xA;  whole organism remains unknown.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, by &lt;strong&gt;slowing-down the mitochondria function you manage to slow-down the normal wear-and-tear of the mitochondrial enzymes&lt;/strong&gt;, which are normally responsible for the so-called respiratory chain -- one of the fundamental biological process for storing energy in cells (despite the common belief, ATP is rarely to store energy, but mostly to transfer it to the target!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we group the tissues where the knock-down leads to similar effects we will get muscle cells opposed by neurons and intenstine cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is just my suggestion, but if we approach those groups with the idea of energy storage and re-use in mind, we'll see that &lt;strong&gt;muscle cells have much higher turnover of energy&lt;/strong&gt; (for contraction and even more for dilation), whereas &lt;strong&gt;nerve and intestine cells&lt;/strong&gt; are not that dependent upon energy and &lt;strong&gt;have much lower baseline of energy consumption and turnover&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now we can &lt;strong&gt;suggest&lt;/strong&gt; that cco-1 knock-down &lt;strong&gt;decreases the functions of mitochondria in muscle cells below the acceptable level&lt;/strong&gt; and the decreased life span is due to depletion of mitochondrial energy storage under light stress conditions which would have been easily coped with under normal conditions. And vice versa, nervous/intenstine cells requiring a constant energy source at a much lower level just help the animal to cope with stress more effectively even during old age, leading to increased life span.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="430" LastEditDate="2012-02-01T12:02:20.840" LastActivityDate="2012-02-01T12:02:20.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="640" PostTypeId="1" AcceptedAnswerId="641" CreationDate="2012-01-13T04:07:56.757" Score="12" ViewCount="1150" Body="&lt;p&gt;Loperamide is frequently used to slow gastrointestinal motility.  It is available over the counter (in the US, I don't know about elsewhere) without any regulations whatsoever, yet it's derived from an opiate.  Knowing that the opiates slow the intestinal motility, it makes sense that it shares the same side effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What doesn't make sense to me is why it doesn't share the same primary effect of analgesia?  Clearly it binds to opiate receptors in the gut, but are they the same subtype as those in the CNS?  Or is it that the structure of the drug is such that hardly any crosses the blood brain barrier?&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-01-13T08:40:23.560" LastActivityDate="2012-01-13T09:25:37.510" Title="Why doesn't a substance like loperamide promote analgesia?" Tags="&lt;receptor&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="641" PostTypeId="2" ParentId="640" CreationDate="2012-01-13T09:25:37.510" Score="14" Body="&lt;p&gt;This is more of a chemical question I think, but the gist of it is that, unlike its predecessors difenoxin (Motofen) and diphenoxylate (Lomotil), it was specifically designed by Dr. Paul Janssen and other researchers at Janssen Pharmaceutica to have limited bioavailability from the gut (it is easily first-pass metabolized through cytochromes), as well as being too lipophilic to be dissolved in water and thus administered intravenously (and thus, junkies hoping to get a &quot;hit&quot; from loperamide through injections will be sorely disappointed), while still retaining its ability as a &lt;a href=&quot;http://jpet.aspetjournals.org/content/199/1/131.short&quot;&gt;μ-opioid receptor agonist to the receptors in the myenteric plexus&lt;/a&gt; (resulting in the slowing of peristalsis). (Difenoxin/diphenoxylate in fact is administered with small doses of atropine to discourage abuse.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, efflux mediated by P-glycoprotein in the blood-brain barrier helps retard the entry of loperamide into the CNS. The &lt;a href=&quot;http://dx.doi.org/10.1067/mcp.2000.109156&quot;&gt;concomitant administration of a P-gp inhibitor&lt;/a&gt; like quinidine (a stereoisomer of quinine used as an antiarrythmic) with loperamide, however, will cause respiratory depression and other CNS effects that are characteristic of μ-opioid receptor agonists.&lt;/p&gt;&#xA;" OwnerDisplayName="user132" LastActivityDate="2012-01-13T09:25:37.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="642" PostTypeId="1" AcceptedAnswerId="652" CreationDate="2012-01-13T09:33:05.563" Score="15" ViewCount="323" Body="&lt;p&gt;Hope this is within the scope of this site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Color-deficient persons lack the cells in their retina needed for differentiating some (or all) colors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the part of the brain that actually processes images is not deficient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to somehow make a color-deficient person &quot;see&quot; the missing colors by directly activating that part of the brain responsible for processing colors?&lt;/p&gt;&#xA;" OwnerUserId="58" LastEditorUserId="69" LastEditDate="2012-01-14T16:58:06.650" LastActivityDate="2012-09-07T18:25:48.537" Title="Can a color-deficient person be made to visualize the missing colors?" Tags="&lt;human-biology&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="643" PostTypeId="5" CreationDate="2012-01-13T13:06:56.907" Score="0" Body="&lt;p&gt;The study of drug action. Includes toxicology and drug composition. May be broken into pharmacokinetic and pharamcodynamic.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="16866" LastEditDate="2019-12-13T04:28:23.787" LastActivityDate="2019-12-13T04:28:23.787" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="644" PostTypeId="4" CreationDate="2012-01-13T13:06:56.907" Score="0" Body="Pharmacology is the study of the interactions that occur between a living organism and chemicals that affect normal or abnormal biochemical function." OwnerUserId="66" LastEditorUserId="16866" LastEditDate="2019-12-13T04:28:23.787" LastActivityDate="2019-12-13T04:28:23.787" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="645" PostTypeId="5" CreationDate="2012-01-13T13:08:41.413" Score="0" Body="&lt;p&gt;Perception involves the entire sensory system from the periphery (sensory receptors) to the higher processing centers in the brain (for example the somatosensory cortex for touch, or the visual cortices for vision). Perception is &lt;em&gt;subjective&lt;/em&gt; and may therefore be different from person to person. This tag is therefore suited for questions pertaining the subjective experience of physical stimuli, such as the perception of color, the perception of depth, or the perceptual differences between various odors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;perception&lt;/em&gt; tag refers to processes higher up in sensory systems than &lt;em&gt;sensation&lt;/em&gt;. The &lt;em&gt;sensation&lt;/em&gt; tag pertains to lower-level processes, such as the peripheral collection of inputs and their processing through earlier stages of processing, e.g. in the thalamus. The &lt;em&gt;perception&lt;/em&gt; tag is better suited for the subjective awareness of physical stimuli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;perception&lt;/em&gt; tag is less suitable for questions on sensory receptors &lt;em&gt;per se&lt;/em&gt;. For example, physiological questions on the molecular differences between various photoreceptor classes, or the mechanism of action of mechanoreceptors in the ear could better be tagged with the &lt;em&gt;neurophysiology&lt;/em&gt; tag, or others. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;perception&lt;/em&gt; tag relates to that field of Biology where it meets and overlaps with Psychology. If questions are aimed at the emotional consequences of &lt;em&gt;perception&lt;/em&gt;, or target otherwise higher-level cognitive areas such as intelligence or psychological states such as depression or psychosis, consider posting the question on CognitiveSciences.SE. Both Biology.SE and CognitiveSciences.SE consider Neurobiology on-topic, but when questions lean too much toward one side of the Biology - Cognitive Sciences spectrum, questions may face closure when posted on the other side.     &lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="9943" LastEditDate="2016-01-11T15:18:40.603" LastActivityDate="2016-01-11T15:18:40.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="646" PostTypeId="4" CreationDate="2012-01-13T13:08:41.413" Score="0" Body="Perception is the process of attaining awareness or understanding of the environment by organizing and interpreting sensory information coming from body receptors and sensory organs into CNS." OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-13T13:08:41.413" LastActivityDate="2012-01-13T13:08:41.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="647" PostTypeId="2" ParentId="115" CreationDate="2012-01-14T12:29:27.907" Score="7" Body="&lt;p&gt;From a more geology-oriented perspective:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Robert M Hazen (2007) - Genesis: The Scientific Quest for Life's Origins &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Noam Lahav (1999)- Biogenesis: Theories of Life's Origin&lt;/p&gt;&#xA;&#xA;&lt;p&gt;J William Schopf (2001) - Cradle of Life&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have watched Hazen's nice &quot;Origins of Life&quot; DVD/Video Course. There he says that the Miller-Urey stuff has gotten less popular. Their atmosphere contains too much Nitrogen, Hydrogen  and focuses on the water surface and the open water body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More recent research points to a more CO&lt;sub&gt;2&lt;/sub&gt;-rich atmosphere, and that life evolved deeper in hot water at the bottom of the ocean.&lt;/p&gt;&#xA;" OwnerUserId="349" LastActivityDate="2012-01-14T12:29:27.907" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="648" PostTypeId="2" ParentId="126" CreationDate="2012-01-14T19:06:02.843" Score="8" Body="&lt;p&gt;Perhaps what your teacher meant was not so much a difference in Leydig cell morphology, but in &lt;strong&gt;interstitial tissue morphology&lt;/strong&gt;, ie. tissue which occupies the space in between seminiferous tubules. Leydig cells are its most interesting component, others being small blood vessels (a lot of them), nerves and connective tissue (mostly fibroblasts, mastocytes, lymphocytes and macrophages). In different species interstitial tissue looks differently, for example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Leydig cells form clumps around blood vessels, and are surrounded by fibroblasts (which makes them more difficult to isolate) in guinea pig, but not in mice or rat; &lt;/li&gt;&#xA;&lt;li&gt;in human a lot of interstitial tissue is extracellular matter, Leydig cells are not so frequent, but more active;&lt;/li&gt;&#xA;&lt;li&gt;and, last but not least, in pig, there is little extracelluar matter and a lot of Leydig cells that are very easily isolated (and produce large amounts of estrogen). &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I found all this in some old lecture notes; I couldn't dig up any sensible reference, though.&lt;/p&gt;&#xA;" OwnerUserId="251" LastEditorUserId="251" LastEditDate="2012-02-02T16:05:02.680" LastActivityDate="2012-02-02T16:05:02.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="651" PostTypeId="1" AcceptedAnswerId="666" CreationDate="2012-01-14T19:46:56.583" Score="17" ViewCount="2976" Body="&lt;p&gt;Is there any hypothesis on the minimum number of amino acids required for life?&lt;/p&gt;&#xA;" OwnerUserId="84" LastEditorUserId="69" LastEditDate="2012-01-15T20:29:54.813" LastActivityDate="2019-03-30T05:47:41.963" Title="What is the smallest number of amino acids required for life?" Tags="&lt;genetics&gt;&lt;amino-acids&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="652" PostTypeId="2" ParentId="642" CreationDate="2012-01-14T20:00:14.910" Score="9" Body="&lt;p&gt;It is a very interesting question and I did some efforts to investigate the literature on this topic, but yet &lt;strong&gt;I don't have a definitive answer for you&lt;/strong&gt;. But let's start from the beginning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, the reason for color deficiency can be not only lack (rare) or impairment (more often) of certain types of color-perceiving cells (cones) in retina, but also &lt;a href=&quot;http://www.webexhibits.org/causesofcolor/2C.html&quot;&gt;brain injures&lt;/a&gt;: the central color blindness can develop after head trauma or as a result of some neurodegenerative deceases, like Parkinson's decease. In case of brain origin of the color blindness it is usually the complete color blindness (no color is percieved), whereas congenical primary color blindness (receptor-based) is usually just the unability to distinguish one or two colors, whereas the rest can be more or less separated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I searched Pubmed for the literature on the topic and found &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19276119&quot;&gt;a recent PNAS paper&lt;/a&gt; about the simulation of primary and secondary visual cortex on humans using intracranial electrodes. As they describe their results (bold font by me):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When percepts were elicited from late areas, subjects reported that&#xA;  they were simple shapes and &lt;strong&gt;colors&lt;/strong&gt;....&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But the paper investigated only healthy humans, no color impaired subjects were used for the tests, so cannot conclude from here whether we can elicit the perception of the color the person is incapable to see with the eyes using these stimulations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I took this paper as the starting point and did some reference research, looking for the paper referenced there and for newer publications referencing this one: PNAS is one of the top journals in this area with very high impact factor and if there were a publication about brain stimulation and color blindness I would have definitely identified it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During my investigations I came accross a series of interesting articles devoted to &quot;cortical visual neuroprosthesis for the blind&quot; (read &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16317227&quot;&gt;this paper&lt;/a&gt;&lt;sup&gt;&amp;lt;1&gt;&lt;/sup&gt; from 2005 for review on this topic), but this is the treatment of conventional blindness, not the color blindness. There was no intersection in keywords or titles for color blindness and brain stimulation, both in the referenced articles and in the complete article database.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I would suggest that you address some talented experimentalist with your question and maybe one day, who knows, we will read your name under the Nature article dedicated to the novel way to cure color blindness.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&amp;lt;1&gt;&lt;/sup&gt; -- unfortunately not available publicly for free, I am sorry.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-01-14T20:00:14.910" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="653" PostTypeId="1" AcceptedAnswerId="662" CreationDate="2012-01-14T20:40:33.610" Score="82" ViewCount="19858" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/651/minimal-number-of-amino-acids-required&quot;&gt;This question&lt;/a&gt; got me thinking about amino acids and the ambiguity in the genetic code. With 4 nucleotides in RNA and 3 per codon, there are 64 codons. However, these 64 codons only code for 20 amino acids (or 22 if you include &lt;a href=&quot;http://en.wikipedia.org/wiki/Selenocysteine&quot; rel=&quot;noreferrer&quot;&gt;selenocysteine&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Pyrrolysine&quot; rel=&quot;noreferrer&quot;&gt;pyrrolysine&lt;/a&gt;), so many of the amino acids are coded by multiple codons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any hypothesis as to why there are only 22 amino acids and not 64? Is it possible that there were 64 (or at least more than 22) at an earlier time?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2016-08-24T17:19:12.340" Title="Why 20 amino acids instead of 64?" Tags="&lt;biochemistry&gt;&lt;evolution&gt;&lt;genetics&gt;&lt;amino-acids&gt;" AnswerCount="3" CommentCount="9" FavoriteCount="25" ContentLicense="CC BY-SA 3.0" />
  <row Id="655" PostTypeId="1" AcceptedAnswerId="674" CreationDate="2012-01-14T22:30:20.270" Score="-2" ViewCount="1464" Body="&lt;p&gt;What kinds of plants live for more than one year and less than two years? Are there any categorical or taxonomical names for such plants?&lt;/p&gt;&#xA;" OwnerUserId="352" LastEditorDisplayName="user24" LastEditDate="2012-01-15T23:14:24.967" LastActivityDate="2012-01-15T23:14:24.967" Title="Which plants live for more than one year and less than two years?" Tags="&lt;botany&gt;&lt;taxonomy&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ClosedDate="2012-01-16T16:45:33.013" ContentLicense="CC BY-SA 3.0" />
  <row Id="656" PostTypeId="1" AcceptedAnswerId="54713" CreationDate="2012-01-14T23:16:18.687" Score="6" ViewCount="1633" Body="&lt;p&gt;What is the largest perennial herbaceous plant? My guess would be some kind of banana or bamboo.&lt;/p&gt;&#xA;" OwnerUserId="352" LastEditorUserId="352" LastEditDate="2016-12-31T19:34:47.857" LastActivityDate="2016-12-31T19:34:47.857" Title="What is the largest perennial herbaceous plant?" Tags="&lt;botany&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="657" PostTypeId="2" ParentId="607" CreationDate="2012-01-14T23:45:04.567" Score="14" Body="&lt;p&gt;IDPs are indeed attractive drug targets and there are ongoing efforts to develop drug molecules that block interactions between a disordered and a structured protein. According to this relatively recent &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559873/&quot;&gt;paper&lt;/a&gt;, however, these efforts have not brought a drug on the market, yet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few promising studies have shown drug-like molecules that inhibit protein-protein interactions based on intrinsic disorder of one of the partners and target:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;oncogenic fusion protein EWS-FLI1 and RNA helicase A. A small molecule has been &lt;a href=&quot;http://www.nature.com/nm/journal/v15/n7/full/nm.1983.html&quot;&gt;found&lt;/a&gt; that targets the disordered region of EWS-FLI1, blocks the interaction with the helicase and inhibits growth of &lt;a href=&quot;http://en.wikipedia.org/wiki/Ewing_sarcoma&quot;&gt;Ewing's sarcoma&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;p53 tumor supressor and its interactor Mdm2. Mdm2, by binding to an intrinsically disordered region of p53, targets p53 for ubiquitination and also causes it to be transported out of the nucleus. Promising &lt;a href=&quot;http://www.landesbioscience.com/journals/cc/article/801/&quot;&gt;small molecules &lt;/a&gt; have been found that associate with Mdm2 and thereby block its interaction with p53. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;c-Myc oncoprotein and the interaction with its partner Max protein. This &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1074552108003700&quot;&gt;study&lt;/a&gt; demonstrates two small molecules that bind to c-Myc and stabilize its disordered conformation, which inhibits its interaction with the Max protein.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The challenge in targeting protein-protein interactions for therapies stems largely from the fact, that the protein-protein contact surfaces are much larger than those involved in protein–small-molecule interactions (1,500–3,000 Å&lt;sup&gt;2&lt;/sup&gt; and (300–1,000 Å&lt;sup&gt;2&lt;/sup&gt;, respectively) &lt;a href=&quot;http://www.nature.com/nature/journal/v450/n7172/full/nature06526.html&quot;&gt;[2]&lt;/a&gt;. They are often flat and have no defined binding pocket. Also, IDPs often don't bind natural small ligands, that could act as starting points in developing drugs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may find this paper helpful:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Metallo SJ, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918680/&quot;&gt;Intrinsically disordered proteins are potential drug targets&lt;/a&gt;, Curr Opin Chem Biol. 2010 14(4): 481–488.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW: for a comprehensive, manually curated list of disordered proteins and regions, please check the &lt;a href=&quot;http://www.disprot.org/&quot;&gt;Database of Protein Disorder&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="277" LastActivityDate="2012-01-14T23:45:04.567" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="658" PostTypeId="2" ParentId="306" CreationDate="2012-01-15T00:06:53.097" Score="12" Body="&lt;p&gt;&lt;a href=&quot;http://www.pdb.org&quot;&gt;PDB&lt;/a&gt; is a good resource for answering such questions, since it will let you filter results by many additional parameters. To count and extract 3D structures of human proteins: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Open &lt;code&gt;Advanced&lt;/code&gt; search tab of the PDB website.&lt;/li&gt;&#xA;&lt;li&gt;Select &lt;code&gt;Biology&lt;/code&gt; -&gt; &lt;code&gt;Source organism&lt;/code&gt; from the menu.&lt;/li&gt;&#xA;&lt;li&gt;Type &lt;code&gt;Homo sapiens (human)&lt;/code&gt;.&lt;/li&gt;&#xA;&lt;li&gt;You can reduce redundancy by checking &lt;code&gt;Remove Similar Sequences at n% identity&lt;/code&gt; below.&lt;/li&gt;&#xA;&lt;li&gt;Submit query.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;To add further filters, click &lt;code&gt;Refine Query with Advanced Search&lt;/code&gt;. There you can extract structures by deposition date, quality (eg. resolution or R-factors for structures solved by X-ray diffraction), ligands, enzyme classification, etc. (by checking &lt;code&gt;Add Search Criteria&lt;/code&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Search for human proteins with removal of homologues with 90% identity cutoff fetches 7117 structures. The number of good quality X-ray protein structures (resolution &amp;lt; 2.5A) is currently 3964  (with the same identity cutoff).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can then download the fetched list or create custom reports (menus below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good tool (also used by PDB) for generating non-redundant protein datasets is &lt;a href=&quot;http://weizhong-lab.ucsd.edu/cd-hit/&quot;&gt;cd-hit&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="277" LastEditorUserId="277" LastEditDate="2012-01-15T09:50:50.997" LastActivityDate="2012-01-15T09:50:50.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="659" PostTypeId="5" CreationDate="2012-01-15T01:08:12.597" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-15T01:08:12.597" LastActivityDate="2012-01-15T01:08:12.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="660" PostTypeId="4" CreationDate="2012-01-15T01:08:12.597" Score="0" Body="PPIs stands for protein-protein interactions" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-01-15T09:09:57.683" LastActivityDate="2012-01-15T09:09:57.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="661" PostTypeId="2" ParentId="653" CreationDate="2012-01-15T02:27:40.450" Score="26" Body="&lt;p&gt;The &lt;em&gt;first&lt;/em&gt; position of the anti-codon, the &quot;Wobble&quot; position, forms hydrogen bonds less well than do the second two.  This means that the &lt;em&gt;last&lt;/em&gt; position of the codon has less coding potential than the first two.  The reason is that the anticodon is at the bottom of the anticodon loop of the tRNA, and so there backbone of the tRNA is bending back to pair with itself.  The nucleotides do not hold their bases flat and regular in relation to each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a picture of the &lt;a href=&quot;https://web.archive.org/web/20070223113929/http://library.thinkquest.org/C0123260/basic%20knowledge/images/basic%20knowledge/RNA/tRNA.jpg&quot; rel=&quot;nofollow&quot;&gt;anticodon loop&lt;/a&gt;.  In this case 5'-CAU-3' is the anticodon for 5'-AUG-3', so it would be the C, right at the sharpest part of the bend in the anticodon loop, that would pair poorest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is an &lt;a href=&quot;http://www.rcsb.org/pdb/101/motm.do?momID=121&quot; rel=&quot;nofollow&quot;&gt;interactive model&lt;/a&gt; where you can spin the tRNA/mRNA around and see that not all the hydrogen bonds are equal length, nor are all the bases coplanar.&lt;/p&gt;&#xA;" OwnerUserId="219" LastEditorUserId="15937" LastEditDate="2015-05-27T05:27:40.470" LastActivityDate="2015-05-27T05:27:40.470" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="662" PostTypeId="2" ParentId="653" CreationDate="2012-01-15T03:06:17.410" Score="58" Body="&lt;p&gt;Brian Hayes wrote a very interesting article from a mathematical point of view:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.americanscientist.org/issues/pub/the-invention-of-the-genetic-code&quot;&gt;http://www.americanscientist.org/issues/pub/the-invention-of-the-genetic-code&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;especially the &quot;Reality intrudes&quot; section. Basically people had created fancy mathematical reasons why it has to be exactly 20. Nature, being nature, does not follow the reasoning, but has its own ideas. In other words there was nothing especially special about 20. In fact there seems to be a slow grafting of a 21st amino acid, selenocysteine using the codon UGA. Also pyrrolysine is considered the 22nd. The last section suggests that the code was originally doublet, so coded for &amp;lt;16 amino acids. This can partly explain why the third base in each codon is not as discriminating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So perhaps in the year 2002012 someone will be asking on biology.stackexchange why there are only 40 amino acids.&lt;/p&gt;&#xA;" OwnerUserId="84" LastEditorUserId="84" LastEditDate="2012-01-17T14:11:41.300" LastActivityDate="2012-01-17T14:11:41.300" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="665" PostTypeId="2" ParentId="279" CreationDate="2012-01-15T13:52:12.050" Score="3" Body="&lt;p&gt;In some protocols for setting up primary cultures (for example from mouse bone marrow or rat endometrium), there is a step that requires pushing cell suspension through a large needle to get rid of clumps. Of course, this carries a high risk of damaging the cells, so sometimes collagenase is used instead.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It might also be helpful to wash your cells with PBS without ions before passaging and use tripsin with EDTA. That should get rid of at least some calcium from the plate, so that action of adhesion proteins would be inhibited.&lt;/p&gt;&#xA;" OwnerUserId="251" LastActivityDate="2012-01-15T13:52:12.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="666" PostTypeId="2" ParentId="651" CreationDate="2012-01-15T18:00:35.680" Score="11" Body="&lt;p&gt;You can divide the 22 (including &lt;a href=&quot;https://en.wikipedia.org/wiki/Selenocysteine&quot;&gt;selenocysteine&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Pyrrolysine&quot;&gt;pyrrolysine&lt;/a&gt;)  proteinogenic amino acids into broad groups of similar amino acids. There are the hydrophobic amino acids like trypthophane, valine and leucine, the charged amino acids like glutamate and arginine and the polar amino acids like serine and threonine. There are some amino acids with unique features like cysteine which can form disulfide bonds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some amino acids are very similar, for example isoleucine and leucine, it is plausible that one of those would suffice to create most protein folds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several examples of proteins designed with a smaller alphabet of amino acids, one example is the &lt;em&gt;E. coli&lt;/em&gt; orotate phosphoribosyltransferase (&lt;a href=&quot;http://www.pnas.org/content/99/21/13549.full&quot;&gt;Akanuma et al., 2002&lt;/a&gt;). The simplified enzyme consists of only 13 different amino acids and 88% of it are composed of only nine different amino acids. Even after those drastic changes the enzyme still folds correctly and has enzymatic activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is one study (&lt;a href=&quot;http://www.pnas.org/content/99/21/13549.full&quot;&gt;Fan and Wang, 2003&lt;/a&gt;) that tried to answer exactly the question you asked. They came to the conclusion that around 10 amino acids are necessary to create properly folding proteins:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;First, we study the minimum sequence complexity that can reserve the&#xA;  necessary structural information for detection of distantly related&#xA;  homologues. Second, we compare the ability of designing foldable model&#xA;  sequences over a wide range of reduced amino acid alphabets, which ﬁnd&#xA;  the minimum number of letters that have the similar design ability as&#xA;  20. Finally, we survey the lower bound of alphabet size of globular proteins in a non-redundant protein database. These different&#xA;  approaches give a remarkably consistent view, that the minimum number&#xA;  of letters required to fold a protein is around ten.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/99/21/13549.full&quot;&gt;Akanuma, S., Kigawa, T. &amp;amp; Yokoyama, S. Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set. Proceedings of the National Academy of Sciences 99, 13549 -13553 (2002).&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://biophy.nju.edu.cn/papers/jmb-328-921.pdf&quot;&gt;Fan, K. &amp;amp; Wang, W. What is the minimum number of letters required to fold a protein? J. Mol. Biol. 328, 921-926 (2003).&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="1306" LastEditDate="2012-10-24T16:01:29.777" LastActivityDate="2012-10-24T16:01:29.777" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="667" PostTypeId="1" AcceptedAnswerId="668" CreationDate="2012-01-15T19:05:49.393" Score="8" ViewCount="740" Body="&lt;p&gt;LTP was first described by Tim Bliss and Terje Lømo in their paper &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4727084&quot;&gt;Long-lasting potentiation of synaptic transmission in the dentate area of the anaesthetized rabbit following stimulation of the perforant path.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When was LTD first described? By whom?&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-01-15T20:05:37.817" Title="First discovery of long-term depression?" Tags="&lt;neuroscience&gt;&lt;history&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="668" PostTypeId="2" ParentId="667" CreationDate="2012-01-15T20:05:37.817" Score="7" Body="&lt;p&gt;The process of long-term depression (LTD) was first discovered in the cerebellum by Ito &lt;em&gt;et al.&lt;/em&gt; in 1982:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ito M, Kano M. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6298664&quot;&gt;Long-lasting depression of parallel fiber-Purkinje cell transmission induced by conjunctive stimulation of parallel fibers and climbing fibers in the cerebellar cortex.&lt;/a&gt; Neurosci Lett. 1982;33(3):253-8&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ito M, Sakurai M and Tongroach P. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1250696/&quot;&gt;Climbing fibre induced depression of both mossy fibre responsiveness and glutamate sensitivity of cerebellar Purkinje cells&lt;/a&gt;. Journal of Physiology 1982; 324: 113–134.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check this &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1038/npg.els.0000033/full&quot;&gt;source&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="277" LastActivityDate="2012-01-15T20:05:37.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="669" PostTypeId="1" AcceptedAnswerId="672" CreationDate="2012-01-15T20:09:56.157" Score="10" ViewCount="315" Body="&lt;p&gt;Can pollution and things in an organism's environment serve as hormones?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorDisplayName="user132" LastEditDate="2012-01-16T00:44:42.803" LastActivityDate="2012-01-17T07:57:40.050" Title="Can elements of one's environment act directly as hormones?" Tags="&lt;biochemistry&gt;&lt;endocrinology&gt;&lt;ecology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="671" PostTypeId="1" AcceptedAnswerId="687" CreationDate="2012-01-15T20:16:50.153" Score="9" ViewCount="7968" Body="&lt;p&gt;Some monocots (such as palms) are impressively thick and massive, yet botanists maintain that they don't have secondary growth. Why do botanists say this?  How can it get so big without secondary growth?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="277" LastEditDate="2012-01-15T20:58:24.190" LastActivityDate="2012-01-16T22:03:49.767" Title="How can a monocot get so massive?" Tags="&lt;botany&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="672" PostTypeId="2" ParentId="669" CreationDate="2012-01-15T20:36:44.800" Score="17" Body="&lt;p&gt;A hormone &lt;a href=&quot;http://en.wikipedia.org/wiki/Hormone&quot;&gt;is defined&lt;/a&gt; as &quot;a chemical released by a cell or a gland in one part of the body that sends out messages that affect cells in other parts of the organism&quot; (I'm just taking Wikipedia definition).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hormones work by binding to specific receptors present on their target cells so, if there is something in the environment that mimics the hormone, by binding to the same receptor they can act as hormones: these substances are called xenohormones and can often act as &lt;a href=&quot;http://en.wikipedia.org/wiki/Endocrine_disruptor&quot;&gt;endocrine disruptors compounds&lt;/a&gt; (EDC), by acting on various organs in the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably the most known xenohormones are &lt;a href=&quot;http://en.wikipedia.org/wiki/Xenoestrogens&quot;&gt;xenoestrogens&lt;/a&gt; that are been studied as possibly harmful for human health (e.g. linked to breast cancer), and as an environmental hazards, as they can, for instance, cause reproductive problems in fish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Xenohormones are not necessarily bad, though. Some analogs of human hormones are used in therapy, having being synthesised specifically, for instance, to have higher potency then their natural counterparts. &lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="66" LastEditDate="2012-01-16T16:49:10.577" LastActivityDate="2012-01-16T16:49:10.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="673" PostTypeId="2" ParentId="669" CreationDate="2012-01-15T22:09:29.020" Score="1" Body="&lt;p&gt;Yes, they can.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of a man-made chemical byproduct affecting hormone signaling is &lt;a href=&quot;http://en.wikipedia.org/wiki/Bisphenol_A&quot; rel=&quot;nofollow&quot;&gt;Bisphenol A (BPA)&lt;/a&gt;. &#xA;There is a vast body of evidence linking BPA to all manners of hormonal misregulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be impossible to try and enumerate all of the studies, and specific mechanisms or the extent of the signaling pathways impacted by BPA have yet to be clarified, however you can have a look to the huge amount of papers on the matter that you can &lt;a href=&quot;http://preview.ncbi.nlm.nih.gov/pubmed?term=bisphenol%20a&quot; rel=&quot;nofollow&quot;&gt;find on Pubmed&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="219" LastEditorUserId="115" LastEditDate="2012-01-17T07:57:40.050" LastActivityDate="2012-01-17T07:57:40.050" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="674" PostTypeId="2" ParentId="655" CreationDate="2012-01-15T22:13:16.860" Score="3" Body="&lt;p&gt;The plants are called &lt;strong&gt;Biennial plants&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples would be &lt;strong&gt;carrots&lt;/strong&gt; or &lt;strong&gt;dandelions&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="352" LastEditorUserId="69" LastEditDate="2012-01-15T23:13:53.437" LastActivityDate="2012-01-15T23:13:53.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="675" PostTypeId="1" AcceptedAnswerId="9246" CreationDate="2012-01-15T22:34:51.163" Score="7" ViewCount="178" Body="&lt;p&gt;I'm trying to get/renew basic knowledge of species. Could someone recommend a book for surveying &quot;important&quot;/&quot;representational&quot; species? I am looking for a book with good illustrations and that covers most &quot;important&quot;/&quot;representational&quot; species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am currently reading &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0674021835&quot; rel=&quot;nofollow&quot;&gt;The Tree of Life: A Phylogenetic Classification&lt;/a&gt;, and it is thicker than I want to read as a first book in this kind.&lt;/p&gt;&#xA;" OwnerUserId="352" LastEditorUserId="3952" LastEditDate="2013-07-12T17:34:15.413" LastActivityDate="2013-07-12T17:34:15.413" Title="Could someone recommend a book for surveying species?" Tags="&lt;taxonomy&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="676" PostTypeId="2" ParentId="669" CreationDate="2012-01-15T22:57:12.967" Score="10" Body="&lt;p&gt;Sure. Here are two anecdotes on xenohormones from unlikely sources.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;In the 1940s, Merino ewes imported to Australia were found to be infertile, as well as sometimes having stillbirths. A bit of detective work showed that the reproductive disorders observed were due to isoflavones like formononetin found in the clovers (&lt;em&gt;Trifolium&lt;/em&gt; spp.) that the Merino were grazing on. Due to the insufficient amounts of needed minerals in the soil, the clover plants were producing the phytoestrogens to defend themselves (sterilize your predators, and there will be less of them eating your kind). &lt;a href=&quot;http://dx.doi.org/10.1111/j.1751-0813.1946.tb15473.x&quot;&gt;(1)&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In the late 1950s, it was observed that Indiana sows feeding on moldy corn were exhibiting symptoms including engorgement of the vulva and stimulation of the mammaries. Researchers at Purdue University found that &lt;em&gt;Fusarium&lt;/em&gt; (&lt;em&gt;Gibberella&lt;/em&gt;) molds in the corn were producing a mycoestrogen, zearalenone, that were triggering those symptoms in swine.&#xA;&lt;a href=&quot;http://dx.doi.org/10.1038/1961318a0&quot;&gt;(2)&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user132" LastEditorDisplayName="user132" LastEditDate="2012-01-16T00:23:50.170" LastActivityDate="2012-01-16T00:23:50.170" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="677" PostTypeId="1" AcceptedAnswerId="727" CreationDate="2012-01-16T01:33:19.467" Score="18" ViewCount="332" Body="&lt;p&gt;As a followup to &lt;a href=&quot;https://biology.stackexchange.com/questions/653/why-20-amino-acids-instead-of-64&quot;&gt;Why 20 amino acids instead of 64?&lt;/a&gt; and &lt;a href=&quot;https://biology.stackexchange.com/questions/651/what-is-the-smallest-number-of-amino-acids-required-for-life&quot;&gt;What is the smallest number of amino acids required for life?&lt;/a&gt;, I am trying to understand the prehistory of amino acids in cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All living cells now use 20 (or 22 if you include selenocysteine and pyrrolysine) amino acids. Perhaps in the past there were fewer amino acids used in cells, especially if the theory of a 2-nucleotide codon is to be believed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any theory as to the order in which these amino acids were incorporated into cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This paper (by Akanuma, Kigawi, Yokoyama, &quot;Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set&quot;, &lt;a href=&quot;http://www.pnas.org/content/99/21/13549.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.pnas.org/content/99/21/13549.full&lt;/a&gt;) suggest that the full complement of 20 amino acids are not strictly necessary by reducing the number of amino acids in a certain enzyme to 13, yet still retain functionality.&lt;/p&gt;&#xA;" OwnerUserId="84" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2012-02-16T14:49:40.577" Title="What is the prehistory of amino acids in cells?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;amino-acids&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="680" PostTypeId="1" CreationDate="2012-01-16T10:14:33.367" Score="9" ViewCount="124" Body="&lt;p&gt;I want to change a pre-miRNA sequence (in my case the pre-miRNA is encoding in a 3'UTR of a gene) and then put it in a lentivirus to see if it is still processed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After modification (permutation of ten regions of ~20 nt) which kind of newly appeared pattern I've to be careful about? I do not want to disturb the gene in which the miRNA is encoded&lt;/p&gt;&#xA;" OwnerUserId="359" LastEditorUserId="6" LastEditDate="2012-01-16T12:56:29.023" LastActivityDate="2012-01-17T18:29:06.913" Title="Which patterns do I have to avoid when modifying the 3'-UTR?" Tags="&lt;genetics&gt;&lt;mrna&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="681" PostTypeId="1" AcceptedAnswerId="863" CreationDate="2012-01-16T13:47:26.117" Score="19" ViewCount="8361" Body="&lt;p&gt;Much discussion has been had about the affects of climate change on plantlife, but how will rising carbon dioxide concentrations affect the photosynthetic process itself? Since CO₂ is a reagent in photosynthesis, would we expect higher CO₂ to mean an increased rate of photosynthesis in a real-world context? Has there been any research on this? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking more of large-scale field tests rather than lab plants.&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="3340" LastEditDate="2014-10-09T13:59:21.473" LastActivityDate="2014-10-09T15:00:19.730" Title="How will rising carbon dioxide levels in the troposphere affect photosynthetic producers?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;ecology&gt;&lt;photosynthesis&gt;&lt;climate-change&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="682" PostTypeId="2" ParentId="653" CreationDate="2012-01-16T17:32:04.600" Score="17" Body="&lt;p&gt;There are two other ideas to throw in here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) just to add to KAM's thoughtful answer.  There was also a thought that the last base also gives a lot of flexibility for GC content which responds to some &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) lets not forget that redundancy in the genetic code helps give some resistance to mutations which might be disruptive.  the amino acids less disruptive to a typical protein fold are more common in the code. (we have some idea of this from studying mutations of protein structures.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) some biochemists have proposed that there is a sense that the 20 amino acids we have are a fairly stable set - that adding other amino acids don't help create better proteins.  Peter Schultz learned some of this as his group really wanted to add extra, human synthesized amino acids into native proteins. &#xA; I was at a talk where he noted that attempts to make cysteine with a longer side chain caused the amino acid to cyclize to form a thioolactone.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thinking along these lines adding another CH&lt;sub&gt;2&lt;/sub&gt; group to proline might not make packing better.  There is probably some value, but just not enough to disrupt all the sensitive machinery for making and realizing the genetic code.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3340" LastEditDate="2014-10-31T12:35:40.473" LastActivityDate="2014-10-31T12:35:40.473" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="684" PostTypeId="1" AcceptedAnswerId="685" CreationDate="2012-01-16T19:23:39.490" Score="10" ViewCount="443" Body="&lt;p&gt;In my research, I look at a lot of gene predictions / annotations. Frequently, I see loci where multiple gene models overlap. I haven't taken a systematic approach to analyzing these cases, but I do remember seeing quite a bit of variation in the direction of the overlapping genes (same vs different directions), the amount of overlap, and even the number of overlapping genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know enough about gene prediction to take any computational predictions with a grain of salt--even those supported by transcript and peptide alignments. However, these cases have me thinking--does overlap of genetic information &lt;em&gt;really&lt;/em&gt; occur in eukaryotes? I seem to remember learning (or hearing anecdotally) that it can happen in prokaryotes, and that seems to be understandable given the compactness of prokaryotic genomes. But can this happen in eukaryotes? Has this been studied, and are there cases that have been confirmed experimentally?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="69" LastEditDate="2012-01-17T15:28:58.087" LastActivityDate="2012-01-19T20:36:12.143" Title="Overlapping genetic information in eukaryotes" Tags="&lt;genetics&gt;&lt;gene-annotation&gt;&lt;eukaryotic-cells&gt;&lt;genomics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="685" PostTypeId="2" ParentId="684" CreationDate="2012-01-16T21:15:32.817" Score="9" Body="&lt;p&gt;You might be interested in the INK4A locus (chromosome 9p), encoding both p19 and p16 genes, very close to p15. You can read a description &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK13507/&quot;&gt;&lt;strong&gt;here&lt;/strong&gt;&lt;/a&gt;. All three proteins are known experimentally to exist. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, whether these are two different genes or the same gene with alternative splicing and start sites leading to different reading frames it's up to discussion. The point is that p19 and p16 share DNA coding sequence but not protein sequence nor function.&lt;/p&gt;&#xA;" OwnerUserId="48" LastActivityDate="2012-01-16T21:15:32.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="686" PostTypeId="1" AcceptedAnswerId="896" CreationDate="2012-01-16T21:59:28.027" Score="14" ViewCount="604" Body="&lt;p&gt;I know that most nitrogen is fixed through industrial processes and bacterial symbiotic relationships. However, are there any plants that can fix their own atmospheric nitrogen?&lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorDisplayName="user132" LastEditDate="2012-01-16T23:34:41.630" LastActivityDate="2012-06-06T20:46:03.673" Title="Are there any plants that fix their own nitrogen?" Tags="&lt;biochemistry&gt;&lt;botany&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="687" PostTypeId="2" ParentId="671" CreationDate="2012-01-16T22:03:49.767" Score="9" Body="&lt;p&gt;The vascular system is different in monocots and dicots. In dicots the vascular tissues are arranged in concentric circles; one of these rings is meristematic cells (undifferentiated cells that can differentiate into any cell type). This ring of meristem tissue is called the vascular cambium and is where secondary growth occurs - xylem grows inwards and phloem grows outwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whereas:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Monocots have a distinctive arrangement of vascular tissue known as an&#xA;  atactostele in which the vascular tissue is scattered rather than&#xA;  arranged in concentric rings. Many monocots are herbaceous and do not&#xA;  have the ability to increase the width of a stem (secondary growth)&#xA;  via the same kind of vascular cambium found in non-monocot woody&#xA;  plants. However, some monocots do have secondary growth, and because&#xA;  it does not arise from a single vascular cambium producing xylem&#xA;  inwards and phloem outwards, it is termed &quot;anomalous secondary&#xA;  growth&quot;. (&lt;a href=&quot;http://en.wikipedia.org/wiki/Monocot&quot;&gt;Wikipedia&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For palms specifically:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Palm trees increase their trunk diameter due to division and&#xA;  enlargement of parenchyma cells, which is termed diffuse secondary&#xA;  growth. (&lt;a href=&quot;http://en.wikipedia.org/wiki/Secondary_growth&quot;&gt;Wikipedia&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Parenchyma cells are type of cells found in plant ground tissue, which makes up the bulk of plant mass. &lt;/p&gt;&#xA;" OwnerUserId="204" LastActivityDate="2012-01-16T22:03:49.767" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="693" PostTypeId="2" ParentId="279" CreationDate="2012-01-17T03:40:10.103" Score="5" Body="&lt;p&gt;I find that I only get clumps (with HeLa and similar cell types) if I leave them in Tryple too long. Generally I leave them in room-temp (not hot) Tryple for ~8 minutes, then I angle the dish, lid off, so that I can see the &quot;sheen&quot; of cells on the dish (this happens in the hood, of course). Then I blast the sheen with Tryple using a 1000ul pipetter, which de-adheres the cells. These are generally much less clumped than if I let the Tryple de-adhere the cells.&lt;/p&gt;&#xA;" OwnerUserId="364" LastActivityDate="2012-01-17T03:40:10.103" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="695" PostTypeId="1" CreationDate="2012-01-17T10:36:00.333" Score="30" ViewCount="31837" Body="&lt;p&gt;From my basic understanding, antibiotics kill living things, bacteria for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do the antibiotics consumed by a human-being distinguish between what they kill? Or do they just kill every bacteria they find? And if that's the case, which bacteria do antibiotics find or do they find all bacteria in a human's body? Again, if that is the case, does that mean that after taking antibiotics for a certain time that the human body is free of all bacteria?&lt;/p&gt;&#xA;" OwnerUserId="367" LastEditorUserId="24354" LastEditDate="2020-07-06T18:41:53.160" LastActivityDate="2020-07-06T18:41:53.160" Title="If a human takes antibiotics are all bacteria in the body killed?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;bacteriology&gt;&lt;pharmacology&gt;&lt;antibiotics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="696" PostTypeId="2" ParentId="686" CreationDate="2012-01-17T10:55:58.657" Score="7" Body="&lt;p&gt;As far as I know, all biotic nitrogen fixation is performed by prokaryotic organisms such as &lt;em&gt;Rhizobium.&lt;/em&gt; I don't know of any plants which can carry out this function on their own.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants can't use atmospheric N&lt;sub&gt;2&lt;/sub&gt; because it is held essentially inert by the nitrogen triple bond. The process of reducing N&lt;sub&gt;2&lt;/sub&gt; to NH&lt;sub&gt;3&lt;/sub&gt; which is usable by plants can be summarized:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;N&lt;sub&gt;2&lt;/sub&gt; + 8e&lt;sup&gt;-&lt;/sup&gt; + 8 H&lt;sup&gt;+&lt;/sup&gt; + 16 ATP -&gt; 2 NH&lt;sub&gt;3&lt;/sub&gt; + H&lt;sub&gt;2&lt;/sub&gt; + 16 ADP + 16 P&lt;sub&gt;i&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(where P&lt;sub&gt;i&lt;/sub&gt; is a phosphate group)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nitrogenase catalyses the reaction reducing N&lt;sub&gt;2&lt;/sub&gt; to NH&lt;sub&gt;3&lt;/sub&gt; by adding H&lt;sup&gt;+&lt;/sup&gt; and electrons. The whole process requires 8 ATP and is therefore energy intense. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to perform this coversion, bacteria require sufficent carbohydrates from decaying matter or plant vascular tissues (this is how &lt;em&gt;Rhizobium&lt;/em&gt; derives energy from the host plant).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I should add that  bacteria often have a mutualistic relation with the plant to perform this function, so in this sense you could say that plants &lt;em&gt;can&lt;/em&gt; fix their own nitrogen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also &quot;free living&quot; ammonifying bacteria in soils.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ref&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Science and the Garden&lt;/em&gt;, eds. Ingram, D.S., Gregory, P.J., Blackwell,  2008&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-01-18T19:02:20.717" LastActivityDate="2012-01-18T19:02:20.717" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="697" PostTypeId="2" ParentId="695" CreationDate="2012-01-17T11:42:52.970" Score="19" Body="&lt;p&gt;Just a quick answer: &lt;strong&gt;No, there is no way to kill all bacteria in your body&lt;/strong&gt; once they are there. The only way to keep a person sterile is to prevent any bacteria entering the guts during and all time after the birth. Look for gnotobiology and gnotobionts to learn more about these organisms (including humans).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are some reasons why:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Most antibiotics have selective action&lt;/strong&gt; on certain type of bacteria. This is due to the mechanisms involved in their action, permeability through the bacterial wall, their effective concentrations etc. Even broad-spectrum antibiotics have selective action. None is universal (and it is hardly possible to create those).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Antibiotics can't reach all the places in your body.&lt;/strong&gt; Many bacteria either create some barrier against the immune response or the body eventually builds one. In the worst cases the whole bacterial infection is isolated and petrified (calcifications), as it is the case for tuberculosis and so-called Gohn's complex in lungs.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;As long as you are not isolated from the society and secluded into a sterile box you will have &lt;strong&gt;a steady contact with millions of bacteria&lt;/strong&gt; which re-invade your skin and guts. There is no way you can stop it and your gut flora will beging to restore spontaneously.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-18T10:57:49.787" LastActivityDate="2012-01-18T10:57:49.787" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="698" PostTypeId="2" ParentId="695" CreationDate="2012-01-17T12:08:13.903" Score="24" Body="&lt;p&gt;&lt;em&gt;No&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several reasons why this might not be true, as Alexander has discussed. An antibiotic often has a molecular target that isn't present in all bacteria, it's &lt;em&gt;extremely&lt;/em&gt; hard to get antibiotics to certain parts of your body, and some bacteria will be defended against a antibiotic attack by biofilms, resistance mechanisms, and sheer statistical probability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is not to say that many don't die. Indeed, one of the major causes of &lt;a href=&quot;http://en.wikipedia.org/wiki/Clostridium_difficile&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Clostridium difficile&lt;/em&gt;&lt;/a&gt; infection is that antibiotics kill most of your gut bacteria, allowing the somewhat better protected &lt;em&gt;C. diff&lt;/em&gt; to proliferate, start producing toxins, and send you to the hospital with symptoms ranging from diarrhea to perforated colon and worse. That disease is a direct consequence of &quot;Antibiotics kill some but not all bacteria in you&quot;.&lt;/p&gt;&#xA;" OwnerUserId="67" LastEditorUserId="5762" LastEditDate="2018-10-29T16:09:36.647" LastActivityDate="2018-10-29T16:09:36.647" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="699" PostTypeId="1" AcceptedAnswerId="703" CreationDate="2012-01-17T15:45:18.450" Score="7" ViewCount="1369" Body="&lt;p&gt;I'm reading some papers about prokaryotic transcription mechanisms, and I've come across a term I haven't heard before: &lt;em&gt;DNA melting&lt;/em&gt; or &lt;em&gt;promoter melting&lt;/em&gt;. After reading a bit, it's pretty clear that they're referring to the separation of DNA from the double stranded form to single strands.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe it's just because chemistry isn't my thing, but when I think of &lt;em&gt;melting&lt;/em&gt; I think of a solid gaining enough energy to become a liquid. How did the term &lt;em&gt;melting&lt;/em&gt; come to apply to DNA in this way? Does the term &lt;em&gt;melting&lt;/em&gt; have a more general definition in terms of thermal chemistry?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="338" LastEditDate="2012-02-16T14:42:16.967" LastActivityDate="2012-02-16T14:42:16.967" Title="What is the origin of &quot;melting&quot; in molecular genetics?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="700" PostTypeId="1" AcceptedAnswerId="705" CreationDate="2012-01-17T16:25:10.287" Score="15" ViewCount="2060" Body="&lt;p&gt;I know someone who bought earphones that shine light in you ears. According to what he was told, there are neurons that sense light and then make you feel wide awake when activated, which seemed like snake oil to me. Apparently the pineal gland may be able to sense light and it does secrete melatonin - a sleep regulating hormone. I'm still sceptical though as its stuck in the middle of your brain. Would shining lights in your ears be able to have any effect on how awake you feel?&lt;/p&gt;&#xA;" OwnerUserId="368" LastEditorUserId="6" LastEditDate="2012-01-17T19:50:20.187" LastActivityDate="2012-01-18T17:44:14.800" Title="Are there neurons that can sense light shining in your ears?" Tags="&lt;neuroscience&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="701" PostTypeId="2" ParentId="546" CreationDate="2012-01-17T16:40:02.807" Score="11" Body="&lt;p&gt;As Rory explained, internal body temperature needs to be highly regulated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sweating is the main built in mechanism for removing excess heat from the human body. According to my biology book, in (100%) humid conditions humans cannot survive in heats of above around 45C, but in a dry environment can survive in heats of over 100C just through sweating. &lt;/p&gt;&#xA;" OwnerUserId="368" LastEditorUserId="5132" LastEditDate="2013-12-10T16:30:05.937" LastActivityDate="2013-12-10T16:30:05.937" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="702" PostTypeId="2" ParentId="680" CreationDate="2012-01-17T18:29:06.913" Score="5" Body="&lt;p&gt;If your goal is to avoid regulatory elements, I would not believe any prediction program, since new regulatory elements are found every day.  The best way would be empirical and just clone and infect with a mutated 3'UTR and see if your gene's regulation is perturbed.  You could at least swap the entire 3'UTR with that from another gene to see if there are even any gene regulatory elements in the 3'UTR.&lt;/p&gt;&#xA;" OwnerUserId="219" LastActivityDate="2012-01-17T18:29:06.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="703" PostTypeId="2" ParentId="699" CreationDate="2012-01-17T19:05:09.150" Score="6" Body="&lt;p&gt;The &lt;em&gt;melting temperature&lt;/em&gt; (Tm) of a double stranded DNA tract is defined as the temperature at which 50% of the DNA molecules are dissociated into single strands (and 50% form duplexes). Sure, it has a different meaning than in physics... but it is a really common term in molecular biology and I doubt people will stop to use it anytime soon!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a vast amount of literature about the calculation of Tm, which is very important also for practical applications, such as &lt;a href=&quot;http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html&quot;&gt;designing PCR primers&lt;/a&gt;. &lt;a href=&quot;http://www.promega.com/techserv/tools/biomath/calc11.htm&quot;&gt;This page&lt;/a&gt; has some explanations and references about the maths behind it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure when the term first appeared, but it has clearly be used since the dawn of molecular biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA denaturation/renaturation dynamics were first studied in the '60s.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See for instance:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC222858/?tool=pubmed&quot;&gt;STRAND SEPARATION AND SPECIFIC RECOMBINATION IN DEOXYRIBONUCLEIC ACIDS: BIOLOGICAL STUDIES&lt;/a&gt; - J. Marmur and D. Lane - PNAS, 1960&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although Marmur and Lane do not talk about melting temperature, we can find the term already two years later in this 1962 paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1366401/?tool=pubmed&quot;&gt;Effect of Concentration on the Formation of Molecular Hybrids from T4 DNA&lt;/a&gt; - Andrzej W. Kozinski and Michael Beer - Biophys J., 1962&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evidently the term was already common there, as they don't care to define it (it's even in the abstract).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Who first used it? I'm not sure, if anyone knows feel free to add a comment or edit the answer.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-01-17T19:05:09.150" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="704" PostTypeId="2" ParentId="700" CreationDate="2012-01-17T20:30:09.060" Score="4" Body="&lt;p&gt;I believe there are light sensors (&lt;a href=&quot;http://en.wikipedia.org/wiki/TRPV3&quot; rel=&quot;nofollow&quot;&gt;TRPV3&lt;/a&gt;) in the skin for infrared light (heat), that convey that information back to the brain from the skin.  This is kind of light detection, but it is not direct detection like the rhodopsins in the eye. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, without passing information onto neurons, cells probably have a lot of sensors they may use to respond to their local environment.  This recent article talks about how &lt;a href=&quot;http://the-scientist.com/2011/12/01/taste-in-the-mouth-gut-and-airways/&quot; rel=&quot;nofollow&quot;&gt;olfactory receptors can be found in lung and gut cells&lt;/a&gt;.  so its quite possible that the conventional light detecting genes (rhodopsins) would be found in skin cells, but they may not convey information to neurons.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-01-17T20:30:09.060" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="705" PostTypeId="2" ParentId="700" CreationDate="2012-01-18T00:13:12.910" Score="13" Body="&lt;p&gt;There is no known mechanism for light detection through the ears in humans, as far as I know. It is certainly true that the pineal gland is part of the system that regulates the circadian rhythm (briefly, the daily sleep-wake cycle). However, while the pineal gland in birds and other non-mammalian vertebrates is directly sensitive to light, the mammalian pineal gland is not (see, for review, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18419310&quot;&gt;Doyle and Menaker, 2007&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16687306&quot;&gt;Csernus, 2006&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In all animals, the circadian rhythm is regulated by a photoperiod cue and therefore requires light detection. In mammals, the light sensors are found exclusively in the retina, the sensory portion of the eye. There are two classes of light detecting cells in the retina. First, rod and cone photoreceptors mediate vision in the usual sense of the word. These cells contain proteins called opsins that absorb photons of light and thereby excite the photoreceptors that contain them, informing the brain that light was detected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A second class of photosenstive cells in the retina are called intrinsically photosensitive retinal ganglion cells (ipRGCs) (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20959623&quot;&gt;Do and Yau, 2010&lt;/a&gt; for review). These cells mediate &quot;non-image-forming&quot; vision and are an important part of the circadian rhythm pathway. They also contain an opsin called &lt;em&gt;melanopsin&lt;/em&gt; which is a photosensitive pigment. This is not to be confused with &lt;em&gt;melatonin&lt;/em&gt;, which is the sleep hormone released by the pineal gland. The ipRGCs in the retina send the photoperiod cue to a brain area called the suprachiasmatic nucleus (SCN). The SCN then signals to the pineal gland.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we are generous and assume that these light-emitting headphones are the result of misunderstandings, we can guess that the confusion arises from (1) the fact that some animals have a directly photosensitive pineal gland, but not mammals and (2) that the pineal gland secretes melatonin but not the photosensitive pigment melanopsin.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt;: From a bit of research, it turns out that the company selling the headphones is not &quot;confused&quot; as I politely offered. I don't think this site is the appropriate forum to refute their research or claims. Suffice to say that the retina is the only part of the human brain shown to be photosensitive.&lt;/p&gt;&#xA;" OwnerUserId="72" LastEditorUserId="72" LastEditDate="2012-01-18T17:44:14.800" LastActivityDate="2012-01-18T17:44:14.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="709" PostTypeId="1" AcceptedAnswerId="710" CreationDate="2012-01-18T12:20:17.217" Score="13" ViewCount="738" Body="&lt;p&gt;In this new paper &lt;a href=&quot;http://dx.doi.org/10.1073/pnas.1115323109&quot;&gt;&quot;Experimental evolution of multicellularity&quot;&lt;/a&gt; found via &lt;a href=&quot;http://arstechnica.com/science/news/2012/01/researchers-evolve-a-multicellular-yeast-in-the-lab-in-2-months.ars&quot;&gt;Ars Technica&lt;/a&gt; the researchers describe having developed multicellularity and apoptosis within 60 days from a unicellular yeast species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible that what they have done is merely turn on an ability of that species that evolved previously and just lay dormant?  Do we know that that yeast species and all its ancestors were never multicellular?  The paper doesn't even mention the possiblity of this.&lt;/p&gt;&#xA;" OwnerUserId="377" LastEditorUserId="6" LastEditDate="2012-01-18T13:02:43.763" LastActivityDate="2012-01-19T05:39:13.173" Title="Did researchers evolve multicellular yeast or did they just turn on multicellularity?" Tags="&lt;evolution&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="710" PostTypeId="2" ParentId="709" CreationDate="2012-01-18T17:02:21.200" Score="14" Body="&lt;p&gt;You're right:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Within the Fungi, simple linear multicellularity of hyphae occurs in all major clades (see below), but only Ascomycota and Basidomycota display more complex two- and three- dimensional multicellularity in the form of sexual spore- producing fruiting bodies. &lt;strong&gt;In both of these groups, reversals to unicellular lifeforms have occurred&lt;/strong&gt;, for example, &lt;strong&gt;Saccharomyces&lt;/strong&gt; and many other related yeasts in the Saccharomycotina (Ascomycota) or Cryptococcus albidus and related species in the hymenomycete clade of Basidiomycota (de Hoog et al. 2000, p. 130).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Medina, M., A. G. Collins, J. W. Taylor, J. W. Valentine, J. H. Lipps, L. A. Amaral Zettler and M. L. Sogin (2003). &quot;Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa.&quot; International Journal of Astrobiology 2(3): 203-211. &lt;a href=&quot;http://dx.doi.org/10.1017/S1473550403001551&quot;&gt;doi:10.1017/S1473550403001551&lt;/a&gt;&#xA;(&lt;a href=&quot;http://nature.berkeley.edu/taylorlab/papers/medina2003.pdf&quot;&gt;PDF&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update: &lt;a href=&quot;http://blogs.discovermagazine.com/loom/2012/01/18/evolving-bodies-a-storify-follow-up/&quot;&gt;The authors responded to criticism like this on The Loom&lt;/a&gt;, here's an excerpt:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our yeast are not utilizing ‘latent’ multicellular genes and reverting back to their wild state. The initial evolution of snowflake yeast is the result of mutations that break the normal mitotic reproductive process, preventing daughter cells from being released as they normally would when division is complete. Again, we know from knockout libraries that this phenotype can be a consequence of many different mutations. This is a loss of function, not a gain of function. You could probably evolve a similar phenotype in nearly any microbe (other than bacteria, binary fission is a fundamentally different process). We find that it is actually much harder to go back to unicellularity once snowflake yeast have evolved, because there are many more ways to break something via mutation than fix it. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="112" LastEditorUserId="112" LastEditDate="2012-01-19T05:39:13.173" LastActivityDate="2012-01-19T05:39:13.173" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="711" PostTypeId="2" ParentId="385" CreationDate="2012-01-18T18:49:20.537" Score="4" Body="&lt;p&gt;Take a look at my website which has a section called Images.  &lt;a href=&quot;http://www.hssemgroup.com/&quot; rel=&quot;nofollow&quot;&gt;http://www.hssemgroup.com/&lt;/a&gt;&#xA;There are more than 13 sites listed which have hundreds of SEM images posted&lt;/p&gt;&#xA;" OwnerUserId="380" LastActivityDate="2012-01-18T18:49:20.537" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="712" PostTypeId="1" AcceptedAnswerId="716" CreationDate="2012-01-18T19:38:33.550" Score="6" ViewCount="6333" Body="&lt;p&gt;I'm taking a molecular genetics course, and we're currently discussing prokaryotic operons. The lacZ operon came up frequently for me as an undergraduate as an example for teaching regulatory control of transcription, and the focus was always on determining whether the operon was transcribed under certain conditions (mutations, nutrients, etc). I don't remember much discussion about what happens after transcription. Today, however, I noticed something I had never seen before: three of the genes in the lacZ operon are transcribed simultaneously on the same transcript--I don't know how I missed this before!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is what happens post-transcription. Obviously there are 3 protein products. How are these products derived from the transcript? Is the transcript broken into 3 pieces, or does a single ribosome translate all 3 proteins from a single transcript substrate, or do ribosomes translate a single protein from a single transcript substrate at a time? Where could I find the relevant literature that elucidated the translation process?&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-01-19T08:17:09.880" Title="Transcription and translation of prokaryotic operons" Tags="&lt;transcription&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="713" PostTypeId="2" ParentId="623" CreationDate="2012-01-18T19:42:38.623" Score="10" Body="&lt;p&gt;There may be some clues in neurobiology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A possibility may be that a person's general emotional state may affect their perception of the passage of time, as argued in this &lt;a href=&quot;http://www.robinson.cam.ac.uk/academic/robinson_rationality_luchini.pdf://&quot;&gt;article&lt;/a&gt; and references within.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Studies of people with damage to their orbitofrontal cortex (prefrontal cortex region) &lt;a href=&quot;http://brain.oxfordjournals.org/content/126/7/1691.short&quot;&gt;can experience sustained altered emotional states when compared to control samples.&lt;/a&gt; &#xA;These altered emotional states seemed to affect how they perceived future scenarios (specifically in a simulated gambling context) and the general passage of time compared to controls. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, emotions such as fear and anxiety tended to &quot;speed up&quot; the passage of time whereas positivity and excitement (particularly with regards to future events) lead to a subjective slowing down of time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Si it may be just that, as kids, we are just more &quot;excited&quot; in general which made for all those seemingly infinite long summers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another possibility is that perhaps it is related to the aging process? As we live longer, I can imagine a scenario where our perception of time would alter (slow down?). It would be interesting to study the perception of the passage of time between long-lived and shorter lived populations in this context.&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-03-12T11:05:28.573" LastActivityDate="2012-03-12T11:05:28.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="714" PostTypeId="1" AcceptedAnswerId="747" CreationDate="2012-01-18T22:10:34.793" Score="45" ViewCount="32633" Body="&lt;p&gt;All humans can be grouped into ABO and Rh+/- blood groups (at a minimum).  Is there any advantage at all to one group or the other?  &lt;a href=&quot;http://rajugurusamy.wordpress.com/2007/10/06/why-blood-types-and-any-advantage/&quot;&gt;This article&lt;/a&gt; hints that there are some pathogens that display a preference to a blood type (for example &lt;a href=&quot;http://Schistosomiasis&quot;&gt;Schistosomiasis&lt;/a&gt; &lt;em&gt;apparently&lt;/em&gt; being more common in people with blood group A, although it could be that more people have type A in the areas that the parasite inhabits).  Is there any literature out there to support or refute this claim or provide similar examples?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beyond ABO-Rh, is there any advantage or disadvantage (excluding the obvious difficulties in finding a donor after accident/trauma) in the 30 other blood type suffixes recognised by the International Society of Blood Transfusions (&lt;a href=&quot;http://www.isbtweb.org/home/&quot;&gt;ISBT&lt;/a&gt;)?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd imagine not (or at least very minimal) but it would be interesting to find out if anyone knows more. &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2019-03-22T02:15:45.553" Title="Is there any advantage to one blood type over another?" Tags="&lt;human-biology&gt;&lt;hematology&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="715" PostTypeId="2" ParentId="117" CreationDate="2012-01-18T23:04:29.733" Score="2" Body="&lt;p&gt;I found a couple of methods using M13 phage growing on E coli: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8723931&quot; rel=&quot;nofollow&quot;&gt;Reddy P, McKenney K. Improved method for the production of M13 phage and single-stranded DNA for DNA sequencing. Biotechniques. 1996 May;20(5):854-6, 858, 860. &lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC306708/&quot; rel=&quot;nofollow&quot;&gt;I Jupin and B Gronenborn. Abundant, easy and reproducible production of single-stranded DNA from phagemids using helper phage-infected competent cells.Nucleic Acids Res. 1995 February 11; 23(3): 535–536. &lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You could easily adapt these protocols to grow on 13C, 15N-containing medium. Then you could use a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC321909/&quot; rel=&quot;nofollow&quot;&gt;restriction enzyme able to cut ss DNA&lt;/a&gt; and purify your fragment through a PA gel. &lt;a href=&quot;http://www.clontech.com/US/Products/Nucleic_Acid_Purification/Plasmid_DNA_Purification_Endotoxin_Free/Gigaprep&quot; rel=&quot;nofollow&quot;&gt;Clontech's gigaprep kit&lt;/a&gt; (up to 50 mg of DNA) will cost you $546 (in the US, before any quote).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disclaimer: I've never done any of this!&lt;/p&gt;&#xA;" OwnerUserId="48" LastActivityDate="2012-01-18T23:04:29.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="716" PostTypeId="2" ParentId="712" CreationDate="2012-01-19T07:54:42.383" Score="6" Body="&lt;p&gt;As you pointed out, the repressor gene lacI is transcribed as a one mRNA, and three structural genes: lacZ, lacY and lacA are transcribed into a single polycistronic mRNA. The two mRNAs are translated independently of one another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The polycisronic mRNA is not broken into pieces. Rather, it is translated by ribosomes (at least three, explanation below), giving rise to three individual proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SyweF.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How from one mRNA three protein products are translated? The polycistronic DNA consists of a promotor (Plac), which ensures that transcription will be initiated, and three open reading frames (ORFs) for for lacZ, lacY, and lacA. Upstream of each of the ORFs, ribosome binding sites (RBSs) are located. Translation is initiated by the binding of the ribosome with both the RBS and the start codon. Thus, multiple ribosomes can bind upstream of the three ORFs and thus resulting into three proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is not very thorough literature on the translation of polycistronic RNA in prokaryotes, mainly because the condition which is necessary for translation is the RBS and there is nothing specific for polycistronic translation. A brief overview on the subject can be found in several places, as I recommend the following:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/scitable/topicpage/operons-and-prokaryotic-gene-regulation-992&quot; rel=&quot;noreferrer&quot;&gt;Ralston, A. (2008) Operons and prokaryotic gene regulation. Nature Education&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0471497835&quot; rel=&quot;noreferrer&quot;&gt;From Genes to Genomes: Concepts and Applications of DNA Technology&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0471497835&quot; rel=&quot;noreferrer&quot;&gt;Molecular cell biology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0470843802&quot; rel=&quot;noreferrer&quot;&gt;Analysis of Genes and Genomes&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-01-19T08:17:09.880" LastActivityDate="2012-01-19T08:17:09.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="717" PostTypeId="2" ParentId="714" CreationDate="2012-01-19T08:37:02.333" Score="21" Body="&lt;p&gt;The less antigens a woman (or in fact a female of any species close enough to humans for this phenomenon) has, the higher are the risks of triggering an immune reaction during her pregnancy, if the child has those antigens.&lt;br&gt;&#xA;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Rh_disease&quot;&gt;Rhesus incompatibility&lt;/a&gt; is probably the most common case of this problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One could thus assume that in populations that are genetically diverse in respect to blood groups, absence of antigens has negative effects on reproduction (unless countered by medicine).&lt;/p&gt;&#xA;" OwnerUserId="340" LastActivityDate="2012-01-19T08:37:02.333" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="718" PostTypeId="2" ParentId="714" CreationDate="2012-01-19T09:42:52.943" Score="14" Body="&lt;p&gt;These &lt;a href=&quot;http://dx.doi.org/10.1038/239165a0&quot;&gt;two&lt;/a&gt; &lt;a href=&quot;http://dx.doi.org/10.1603/0022-2585-41.4.796&quot;&gt;papers&lt;/a&gt; study whether there is a relationship between the ABO blood type of a person and his/her attractiveness to mosquitoes. It was found that people with type O blood are more likely to be bitten than people with other blood types. Additionally, the relationship between blood type and the secretion of oligosaccharides from the skin had any effect on attractiveness to mosquitoes. It was found that type O secretors are very attractive to mosquitoes compared to type O nonsecretors and type A nonsecretors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the flip side, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2396015/&quot;&gt;type A individuals are more susceptible to infection by plasmodia (i.e., malaria)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerDisplayName="user132" LastActivityDate="2012-01-19T09:42:52.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="719" PostTypeId="1" AcceptedAnswerId="744" CreationDate="2012-01-19T12:23:59.933" Score="14" ViewCount="635" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Cryptic_species_complex&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In biology, a cryptic species complex is a group of species which&#xA;  satisfy the biological definition of species—that is, they are&#xA;  reproductively isolated from each other—but whose morphology is very&#xA;  similar (in some cases virtually identical).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;How do members of these species know who to mate with?  Or would they unknowingly mate with incompatible partners?&lt;/p&gt;&#xA;" OwnerUserId="203" LastEditorUserId="1202" LastEditDate="2012-09-16T22:55:44.860" LastActivityDate="2012-09-16T22:55:44.860" Title="How do members of cryptic species know who to mate with?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;zoology&gt;&lt;ethology&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="720" PostTypeId="1" CreationDate="2012-01-19T13:12:01.450" Score="5" ViewCount="1085" Body="&lt;p&gt;It seems like a no-brainer than oxidation, playing the, er, role it does in the universe, would destroy prions just like it destroys everything else.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But when does it do that? I assume this has been studied, since people handle them in laboratories and may need to sterilize their instruments.&lt;/p&gt;&#xA;" OwnerUserId="250" LastActivityDate="2012-01-19T23:22:39.100" Title="When does oxidation destroy prions?" Tags="&lt;proteins&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="721" PostTypeId="5" CreationDate="2012-01-19T19:47:02.613" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-01-19T19:47:02.613" LastActivityDate="2012-01-19T19:47:02.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="722" PostTypeId="4" CreationDate="2012-01-19T19:47:02.613" Score="0" Body="Operon is a region of genomic DNA, which contains clustered genes under the regulatory control of a single promotor and terminator. They are generally transcribed into polycistronic mRNA and translated together." OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-01-19T20:02:05.723" LastActivityDate="2012-01-19T20:02:05.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="723" PostTypeId="2" ParentId="684" CreationDate="2012-01-19T20:36:12.143" Score="3" Body="&lt;p&gt;In general, the compactnes of genomes is a characteristic of prokaryotes, but there are several eykaryotes that have overlapping genes: many parasites and endosymbionts. The best studied of these are the fungal parasites of the phylum &lt;a href=&quot;http://en.wikipedia.org/wiki/Microsporidia&quot; rel=&quot;nofollow&quot;&gt;microsporidia&lt;/a&gt; and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleomorph&quot; rel=&quot;nofollow&quot;&gt;nucleomorphs&lt;/a&gt; (remnant nuclei of algal endosymbionts in cryptophytes and chlorarachniophytes). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;cDNA library was constructed from the microsporidian &lt;em&gt;Antonospora locustae&lt;/em&gt; and 1,146 cDNA clones were sequenced. Here is part of the expression profile (1):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Of the 871 clones found to encode recognizable genes, 97 transcripts (11%) from 70 distinct loci encoded sequence from more than one gene (Fig. 1 A ; see also Table 1, which is published as supporting information on the PNAS web site). The polyA sites of these clones do not correspond to polyA tracts in the genome, so they are unlikely to derive from DNA contamination (see also below), but instead come from polyA RNA. In prokaryotes, polycistronic mRNAs commonly code for multiple proteins (11), but with few exceptions (12) eukaryotic mRNAs encode a single gene. A. locustae multigene transcripts encode two or three genes or gene fragments in various orientations (Fig. 1 B–I ), but they cannot all be polycistronic messages because there is no bias for genes being on the same strand.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here is part of a review paper on the nucleomorphs genome (2):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As in other reduced genomes, the G. theta nucleomorph genome possesses a very high A+T content (75%) and gene density is extremely high: 1 gene per 977 bp and 44 genes overlap by as many as 76 nucleotides. Williams et al. (84) showed that transcription of the G. theta nucleomorph genome is affected by this compaction, with nucleomorph-derived messenger RNAs often possessing coding sequence for more than one gene, albeit with no strand bias. It appears that during the process of genome compaction, transcription regulatory elements (e.g., promoters, terminators) have moved from the intergenic spacers into the coding regions themselves (84).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I also have to point out that there are a few examples of overlapping genes in yeast: CCT6 overlaps with YDR187C and CCT8 overlaps with YJL009W (3).&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pnas.org/content/102/31/10936.full&quot; rel=&quot;nofollow&quot;&gt;A high frequency of overlapping gene expression in compacted eukaryotic genomes&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev-genet-102108-134809&quot; rel=&quot;nofollow&quot;&gt;Nucleomorph Genomes, Annual Review of Genetics&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencemag.org/content/320/5874/362.full&quot; rel=&quot;nofollow&quot;&gt;The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-01-19T20:36:12.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="724" PostTypeId="2" ParentId="656" CreationDate="2012-01-19T21:16:13.533" Score="5" Body="&lt;p&gt;As mentioned above, the largest perennial herbaceous plant is indeed the banana.  Whilst the main reference to this (&quot;Yes, we have more bananas&quot; - an article in the Royal Horticultural Society Journal from May 2002) has been removed from their website it would be I'm sure possible to order should you need to.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.scribd.com/arun_raja/d/48202430-Banana-files&quot; rel=&quot;nofollow&quot;&gt;summary of the banana&lt;/a&gt; mentions that the pseudo-stem of the banana plant grows to 6-7.6m in height - I haven't found anything taller when looking around so it doesn't generate any reason to doubt the removed article.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the comments on Bamboo, there are 7 genera containing bamboo species.  All of these (&lt;a href=&quot;http://delta-intkey.com/grass/www/arthrost.htm&quot; rel=&quot;nofollow&quot;&gt;Arthrostylidium Rupr&lt;/a&gt;, &lt;a href=&quot;http://herbarium.usu.edu/webmanual/info2.asp?name=Bambusa&amp;amp;type=treatment&quot; rel=&quot;nofollow&quot;&gt;Bambusa Schreb&lt;/a&gt;, &lt;a href=&quot;http://delta-intkey.com/grass/www/chusquea.htm&quot; rel=&quot;nofollow&quot;&gt;Chusquea Kunth&lt;/a&gt;, &lt;a href=&quot;http://www.inbar.int/publication/txt/tr17/Dendrocalamus/DE-r.htm&quot; rel=&quot;nofollow&quot;&gt;Dendrocalamus Nees&lt;/a&gt;, &lt;a href=&quot;http://delta-intkey.com/grass/www/phyllost.htm&quot; rel=&quot;nofollow&quot;&gt;Phyllostachys Siebold &amp;amp; Zucc.&lt;/a&gt;, &lt;a href=&quot;http://delta-intkey.com/grass/www/p_sasa.htm&quot; rel=&quot;nofollow&quot;&gt;Pseudosasa Makino&lt;/a&gt; and &lt;a href=&quot;http://delta-intkey.com/grass/www/sasa.htm&quot; rel=&quot;nofollow&quot;&gt;Sasa Makino &amp;amp; Shibata&lt;/a&gt;) are described as having persistent woody stems so don't meet your herbaceous requirement. &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-20T23:11:37.810" LastActivityDate="2012-01-20T23:11:37.810" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="725" PostTypeId="2" ParentId="720" CreationDate="2012-01-19T23:16:20.230" Score="5" Body="&lt;p&gt;Prions are fairly resistant to traditional method of sterilization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Citing from: &lt;a href=&quot;http://www.unc.edu/depts/spice/dis/ICHE-2010-Feb-p107.pdf&quot;&gt;Guideline for Disinfection and Sterilization of Prion-Contaminated Medical Instruments&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The prions that cause CJD and other TSEs exhibit an unusual resistance to conventional chemical and physical decontamination methods. Because the CJD agent is not readily inactivated by means of conventional disinfection and sterilization procedures and because of the invariably fatal outcome of CJD, the procedures for disinfection and sterilization of the CJD prion have been both cautious and controversial for many years.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The same paper also lists several effective and ineffective methods for sterilization (efficient method have &gt; 3log10 reduction in prion content within 1 hour)&#xA;I am not going to list them all here but you can see Table 2 in the paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just to answer your specific question about oxydation, certain oxydising agents are effective, others are not. Similarly certain autoclaving (=sterilising with heat) procedures are fine and others are not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another interesting paper &lt;a href=&quot;http://cid.oxfordjournals.org/content/43/6/757.full&quot;&gt;Methods to Minimize the Risks of Creutzfeldt-Jakob Disease Transmission by Surgical Procedures: Where to Set the Standard?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-01-19T23:16:20.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="726" PostTypeId="2" ParentId="720" CreationDate="2012-01-19T23:22:39.100" Score="3" Body="&lt;p&gt;If you google &quot;prion oxidation&quot; you'll see that there has been some research into this over the last 10 years, though it seems to be a minor focus of the overall field. There seems to be some interest currently in using ozone to inactivate prions. One company that offers a ozone-based sterilizer claims to be testing for effectiveness against prions, but that is an extremely long-term process (you have to isolate prions, subject them to your sterilization process, then inject them into the brains of mice or hamsters and wait to see if disease develops). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're curious as to how researchers sterilize material in the lab, I may be able to shed some light on that (I worked in a prion lab in 2006-07). Generally, disposable instruments and materials are used whenever possible and incinerated after use. Glassware is submerged in acidic detergent and autoclaved for 4 hours at (I believe) 132C. As far as I know, there is still no known way to completely sterilize stainless steel instruments - this was being studied at the time in the lab where I worked. Any piece of equipment that came in contact with human or bovine prions was kept in Biosafety Level 3 facilities permanently. I'm not sure what the decontamination process was for retired equipment. Separate equipment was maintained for &quot;non-human pathogen&quot; prions - hamster, mouse, etc. &lt;/p&gt;&#xA;" OwnerUserId="204" LastActivityDate="2012-01-19T23:22:39.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="727" PostTypeId="2" ParentId="677" CreationDate="2012-01-20T02:19:25.033" Score="10" Body="&lt;p&gt;Edward N. Trifonov is a professor at the Institute of evolution at University of Haifa, Israel. One of the main research topics in his group is the reconstruction of the origins of life. In one of his papers, &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;ved=0CCoQFjAB&amp;amp;url=http://www.colorado.edu/physics/phys7450/phys7450_sp05/downloads/tripletcode.pdf&amp;amp;ei=7akYT6uhG6bdiALtvd2YCA&amp;amp;usg=AFQjCNEVOQQXywtNVoaGZew50z7SLKgc0A&amp;amp;sig2=41seObNvcWSfbGAtfTt06g&quot;&gt;The triplet Code From First Principles&lt;/a&gt;, he proposes the the chronological appearance of the 20 amino acids. There are a lot of hypothesis and testable predictions, among which is the theory of S. Miller that some biological compounds have been abiotically produced in the atmosphere. This prediction has been confirmed by imitation experiments, yielding ten different amino acids, as glycine and alanine being the prevalent ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The author tries to predict the chronological order in which the 20 amino acids appeared by taking into account various criteria (studies, hypothesis and viewpoints) that propose some order, as each one of them contributes to the consensus order to a certain extent. This contribution is described in the form of rank. He compiles a list of 60 rankings of 60 different criteria to derive the consensus order. Some of the criteria are:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;N1’. Criteria based on various evaluations of complexity of amino-acids. N1, N34, N35,&#xA;  N37 – as in (5), and N44 (6). G, A, S, P, V, C, D, T, N, L, K, I, E, (MQ), H, R, F, Y, W&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;N2’. Criteria based on evolution of amino-acyl-tRNA synthetases. N2, N7 (5).&#xA;  (AG), (DFHKNPST), (CEILMQRV), (WY)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;N4’. Criteria based on amino-acid compositions of various sets of presumably ancient&#xA;  proteins. N4, N26 (5), N41 (7), N45 (8), N47 (9), N48 (10), and N58 (11).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The first ten (earliest) consensus amino acids are the same as in Millers’s experiments. The amino acids appeared last have their respective codons borrowed from already existing ones. The derived consensus order is G, A, D, V, P, S, E, (L, T), R, (I, Q, N), H, K, C, F, Y, M, W.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The author also proposes a reconstruction of the chronological order in which the 64 codons had appeared.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-01-20T02:19:25.033" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="728" PostTypeId="1" CreationDate="2012-01-20T02:26:14.117" Score="16" ViewCount="5999" Body="&lt;p&gt;In high school we studied the inheritance of eye color, as it was explained to us in the most simple way: blue eye color is a recessive, monogenic, autosomal trait. Now I know that it is a bit more complicated than that; there are several genes which determine the inheritance of eye color. That's as far as I my knowledge goes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which are these genes and what do they encode for? How is the eye color trait inherited? Provided that a man with blue eyes and a woman with brown eyes have a child, can the probability of their child to have blue eyes be calculated? &lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="107" LastEditDate="2012-01-27T00:09:06.977" LastActivityDate="2012-01-27T00:09:06.977" Title="How is eye color in humans inherited?" Tags="&lt;genetics&gt;&lt;human-anatomy&gt;&lt;human-genetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="729" PostTypeId="1" AcceptedAnswerId="736" CreationDate="2012-01-20T02:44:51.500" Score="8" ViewCount="592" Body="&lt;p&gt;Following up on &lt;a href=&quot;https://biology.stackexchange.com/questions/306/how-many-human-proteins-have-a-solved-3d-structure&quot;&gt;How many human proteins have a solved 3D structure?&lt;/a&gt;,is there a list of very well characterized human proteins / protein complexes?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My criteria for &quot;very well characterized&quot; includes, at least:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;a high quality 3D structure&lt;/li&gt;&#xA;&lt;li&gt;known activity &lt;em&gt;in vivo&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;known associates in its activities in the cell&lt;/li&gt;&#xA;&lt;li&gt;kinetics of its activity&lt;/li&gt;&#xA;&lt;li&gt;regulatory elements for expression&lt;/li&gt;&#xA;&lt;li&gt;etc..., and&lt;/li&gt;&#xA;&lt;li&gt;(probably most importantly) a general consensus among experts that it is well described&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This list would most likely include such proteins or protein complexes as: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;P53, &lt;/li&gt;&#xA;&lt;li&gt;polymerase alpha, and &lt;/li&gt;&#xA;&lt;li&gt;the nuclear pore complex,&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;to name a very small number.&lt;/p&gt;&#xA;" OwnerUserId="184" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2012-09-17T16:06:36.267" Title="How many human proteins are very well characterized?" Tags="&lt;proteins&gt;&lt;structural-biology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="730" PostTypeId="1" CreationDate="2012-01-20T03:12:27.423" Score="4" ViewCount="154" Body="&lt;p&gt;D1 and D2 both refer to specific types of dopamine receptors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure it has something to do with the fact that the D1 receptors are in regions different from D2 receptors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that adenylate cyclase usually triggers a signal transduction cascade that leads to increased cAMP+calmodulin, resulting in increased gene expression of proteins that help promote long-term potentiation of postsynaptic neurons (presumably lowering the absolute value of the voltage threshold that's needed to trigger another action potential, which increases neuron excitability).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But an increase in dopamine is going to cause more neuron excitability in postsynaptic neurons in some regions (those that have D1 receptors), and less in others (those that have D2 receptors). What then explains the fact that increased expression at all dopamine receptors can help modulate attention span? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that D3 and D4 are also involved, but they have to be either excitatory, inhibitory, or neutral.&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="103" LastEditDate="2012-01-22T00:31:58.097" LastActivityDate="2012-01-22T00:31:58.097" Title="If D1 receptors stimulate adenylate cyclase (through GPCRs) and D2 receptors inhibit it, then why do mutations in both have similar effects?" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;" AnswerCount="0" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="731" PostTypeId="1" AcceptedAnswerId="735" CreationDate="2012-01-20T03:19:25.540" Score="1" ViewCount="6578" Body="&lt;p&gt;Do they increase it, or is the effect mostly neutral?&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="66" LastEditDate="2012-01-20T06:47:52.050" LastActivityDate="2012-01-20T06:47:52.050" Title="How do dopamine agonists like amphetamine/methylphenidate affect acetylcholine signalling?" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="732" PostTypeId="1" AcceptedAnswerId="737" CreationDate="2012-01-20T04:29:52.003" Score="15" ViewCount="1426" Body="&lt;p&gt;I have a few protein models I want to take pictures of with various ligands bound.  It would be nice if I could do it from the same &quot;position&quot;, but the only way I can figure out to repeat the same view is with &lt;code&gt;zoom resi. 64, 152, 150&lt;/code&gt; or the like, which isn't framed that well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can I manually position the viewport, capture it's parameters, and repeat it in the script?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I have found &lt;strong&gt;get_view&lt;/strong&gt;, e.g. &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;PyMOL&amp;gt;get_view&#xA;### cut below here and paste into script ###&#xA;set_view (\&#xA;     0.590180993,    0.670941532,    0.448923886,\&#xA;    -0.507570565,    0.740831316,   -0.439937204,\&#xA;    -0.627747774,    0.031782545,    0.777776182,\&#xA;     0.000000000,    0.000000000, -417.497009277,\&#xA;     0.741809845,    7.078243256,   16.473480225,\&#xA;   329.157806396,  505.836212158,  -20.000000000 )&#xA;### cut above here and paste into script ###&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;but this doesn't work in a &lt;code&gt;.py&lt;/code&gt; script, where I need to modify it to &lt;code&gt;cmd.set_view(...)&lt;/code&gt;, as it complains it wants just (or up to 5) arguments, not 18.  &lt;a href=&quot;http://www.pymolwiki.org/index.php/Set_View&quot;&gt;The wiki is vague about it&lt;/a&gt;, it just says &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;h3&gt;PYMOL API&lt;/h3&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;cmd.set_view(string-or-sequence view)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="25" LastEditorUserId="112" LastEditDate="2012-01-20T08:03:23.997" LastActivityDate="2012-01-20T13:15:54.877" Title="How do I get the current &quot;camera position&quot; in PyMol so I can reuse it in scripts?" Tags="&lt;biochemistry&gt;&lt;bioinformatics&gt;&lt;structural-biology&gt;&lt;pymol&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="733" PostTypeId="1" AcceptedAnswerId="734" CreationDate="2012-01-20T05:10:48.260" Score="2" ViewCount="108" Body="&lt;p&gt;A &lt;a href=&quot;http://www.sciencedaily.com/releases/2012/01/120119143332.htm?utm_source=feedburner&amp;amp;utm_medium=feed&amp;amp;utm_campaign=Feed%3a%20sciencedaily%20%28ScienceDaily%3a%20Latest%20Science%20News%29&amp;amp;utm_content=Google%20Reader&quot; rel=&quot;nofollow&quot;&gt;ScienceDaily article&lt;/a&gt; says that the protein in teardrops can kill bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But how does it reach the bacteria?&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="66" LastEditDate="2012-01-20T06:29:22.297" LastActivityDate="2012-01-20T08:09:54.157" Title="Is the protein in teardrops still attached to cells, or is it released and free-flowing?" Tags="&lt;human-biology&gt;&lt;molecular-biology&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="734" PostTypeId="2" ParentId="733" CreationDate="2012-01-20T06:28:33.267" Score="6" Body="&lt;p&gt;I am not sure I understand your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the article you mention the proteins in teardrops kill the bacteria which are invading the eye (e.g. also present in the teardrops):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Those jaws chew apart the walls of the bacteria that are trying to&#xA;  get into your eyes and infect them,&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;: These proteins are enzymes called &lt;a href=&quot;http://en.wikipedia.org/wiki/Lysozyme&quot;&gt;lysozymes&lt;/a&gt;. Those are free-flowing proteins of the human tears. These proteins are actively produces in the lacrimal glands and actively &lt;a href=&quot;http://en.wikipedia.org/wiki/Secreted&quot;&gt;secreted&lt;/a&gt; into the &lt;a href=&quot;http://en.wikipedia.org/wiki/Tears&quot;&gt;lacrimal liquid&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-01-20T08:09:54.157" LastActivityDate="2012-01-20T08:09:54.157" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="735" PostTypeId="2" ParentId="731" CreationDate="2012-01-20T06:47:21.317" Score="2" Body="&lt;p&gt;&lt;strong&gt;Amphetamine and methylphenidate are not (direct) dopamine agonists.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dopamine agonists are the substances that would specifically bind to dopamine receptors and activate them, thereby mimicking the effects of dopamine release.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Amphetamine/methylphenidate are so-called &lt;strong&gt;indirect sympatomimetics.&lt;/strong&gt; This means that they stimulate the simpatyc nervous systems (with neurotransmitters noradrenaline and dopamine in CNS), but in indirect way: they don't bind to the receptors. Rather, they promote the massive neurotransmitter release from the presynaptic part. The released transmitter (DA, NA) then just diffuses to the postsynaptic membrane and binds to its own receptors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some works done on investigating the effect of these substances on parasympatic system with acetylcholine as neurotransmitter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sympatomimetics like amphetamine generally lead to increase of acetylcholine release throurout the nervous system: in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8405105&quot; rel=&quot;nofollow&quot;&gt;hippocampus and caudate nucleus&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9881866&quot; rel=&quot;nofollow&quot;&gt;nucleus accumbens&lt;/a&gt; and generally in &lt;a href=&quot;http://www.amphetamines.com/acetylcholine/index.html&quot; rel=&quot;nofollow&quot;&gt;forebrain and cortex&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This effect of amphetamine is indeed in many cases mediated through dopamine receptors. Same time some &lt;strong&gt;direct dopamine receptor agonists&lt;/strong&gt; were found to &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1986.tb21524.x/abstract&quot; rel=&quot;nofollow&quot;&gt;supress ACh release in some brain regions&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-01-20T06:47:21.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="736" PostTypeId="2" ParentId="729" CreationDate="2012-01-20T08:27:39.760" Score="9" Body="&lt;p&gt;To address your list:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;a high quality 3D structure: this you can easily get from PDB, using the answers to the question you linked as starting point. However, it is become increasingly clear that &lt;a href=&quot;http://en.wikipedia.org/wiki/Intrinsically_unstructured_proteins&quot;&gt;intrinsically unstructured proteins&lt;/a&gt; also play important roles in the cell, and for these you won't get a good 3D structure.&lt;/li&gt;&#xA;&lt;li&gt;known activity in vivo / known associates in its activities in the cell: interaction partners can be found in databases like &lt;a href=&quot;http://string-db.org&quot;&gt;STRING&lt;/a&gt;, although just knowing the partners doesn't mean we understand what's going on :)&lt;/li&gt;&#xA;&lt;li&gt;kinetics of its activity: I know of no good resource on this one except &lt;a href=&quot;http://www.brenda-enzymes.org/&quot;&gt;BRENDA&lt;/a&gt; for enzyme kinetics. But of course there are also kinetics to protein–protein interactions that would be interesting to know. (Update: There is &lt;a href=&quot;http://nar.oxfordjournals.org/content/34/suppl_1/D522.abstract&quot;&gt;AffinDB&lt;/a&gt;.)&lt;/li&gt;&#xA;&lt;li&gt;regulatory elements for expression: there are databases like &lt;a href=&quot;http://www.gene-regulation.com/pub/databases.html&quot;&gt;TransFac&lt;/a&gt;, but ChIP-Seq experiments show that we only know a tiny part of the regulation.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;But, I think the key to a good answer lies here:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(probably most importantly) a general consensus among experts that it is well described&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would check how often the genes are described in the literature. The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html&quot;&gt;GeneRIFs&lt;/a&gt; from NCBI may be a good starting point, because these are snippets from the literature that are curated and shown on the NCBI Gene pages. E.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/7157&quot;&gt;p53&lt;/a&gt; has &gt;3800 of these. The length of the summary could also be a good proxy. (Or, the length of the Wikipedia page?)&lt;/p&gt;&#xA;" OwnerUserId="112" LastEditorUserId="112" LastEditDate="2012-01-25T09:18:03.907" LastActivityDate="2012-01-25T09:18:03.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="737" PostTypeId="2" ParentId="732" CreationDate="2012-01-20T13:10:58.473" Score="10" Body="&lt;p&gt;Try to pass the matrix as a String containing 18 floats separated by commas, e.g. like&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;cmd.set_view ('''&#xA;     0.590180993,    0.670941532,    0.448923886,\&#xA;    -0.507570565,    0.740831316,   -0.439937204,\&#xA;    -0.627747774,    0.031782545,    0.777776182,\&#xA;     0.000000000,    0.000000000, -417.497009277,\&#xA;     0.741809845,    7.078243256,   16.473480225,\&#xA;   329.157806396,  505.836212158,  -20.000000000 ''')&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;cmd.get_view()&lt;/code&gt; seems to return a tuple, so you'll have to convert that to a String if you want to pass the same position to &lt;code&gt;cmd.set_view()&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried it in Pymol 1.3 on the command line (not in a script though) and it seemed to work.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2012-01-20T13:15:54.877" LastActivityDate="2012-01-20T13:15:54.877" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="738" PostTypeId="1" AcceptedAnswerId="739" CreationDate="2012-01-20T16:36:32.010" Score="6" ViewCount="119" Body="&lt;p&gt;In my book this is described as happening by kinetochores depolymerising from their attached microtubule spindle, then being dragged towards the spindle's centrosome by a dynein protein. I can understand this, but what it does not seem to answer is how different copies of chomatids beome attached to the correct spindles in the first place (i.e. spindles connected to opposing centrosomes). How does this work?&lt;/p&gt;&#xA;" OwnerUserId="368" LastEditorUserId="6" LastEditDate="2012-01-20T16:48:30.747" LastActivityDate="2012-01-20T18:24:18.477" Title="How are chromatids correctly segregated during mitosis?" Tags="&lt;cell-biology&gt;&lt;mitosis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="739" PostTypeId="2" ParentId="738" CreationDate="2012-01-20T18:24:18.477" Score="2" Body="&lt;p&gt;It's a spatial constraint.  As the DNA is replicated, the two resulting chromatids are kept stuck together by cohesin proteins.  The DNA sequence that corresponds to the centromere then coalesces the kinetochore.  It seems that the DNA-protein interactions at the centromeres creates a &lt;a href=&quot;http://www.genome.duke.edu/labs/sullivanlab/publications/Blower,Sullivan,Karpen.pdf&quot; rel=&quot;nofollow&quot;&gt;particular structure&lt;/a&gt; along the chromosome.  Since the two chromatids have their kinetochores pointing in opposite directions, when a spindle microtubule attaches to the kinetochore, it is nearly impossible for another microtubule from the same spindle to attach to the opposing kinetochore.&lt;/p&gt;&#xA;" OwnerUserId="219" LastActivityDate="2012-01-20T18:24:18.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="740" PostTypeId="1" AcceptedAnswerId="742" CreationDate="2012-01-20T18:38:59.143" Score="11" ViewCount="272" Body="&lt;p&gt;A while back there was a lot of noise about resveratrol, a naturally occurring phenol which was touted as a potential anti-aging drug due to its role in regulating the SIRT 1 gene. A number of studies suggested that it could extend the lifespans of model organisms such as &lt;em&gt;D. melanogaster&lt;/em&gt; and &lt;em&gt;C. elegans.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has there been any follow up on this? Have there been any human trials?&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-02-25T19:58:47.650" LastActivityDate="2012-06-27T07:54:31.443" Title="Does current evidence support the use of resveratrol as an anti-ageing drug?" Tags="&lt;human-biology&gt;&lt;pharmacology&gt;&lt;senescence&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="741" PostTypeId="2" ParentId="740" CreationDate="2012-01-20T19:46:18.430" Score="9" Body="&lt;p&gt;If you search clinicaltrials.gov (maintained by the NIH) for &quot;resveratrol&quot;, you'll find &lt;a href=&quot;http://clinicaltrials.gov/ct2/show/results/NCT01010009?term=resveratrol&amp;amp;rank=4&amp;amp;sect=X3015#evnt&quot;&gt;44 clinical trials&lt;/a&gt;, many of them ongoing or not yet started.&#xA;A &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21688389&quot;&gt;recent review by Smoliga JM et al&lt;/a&gt; states in the abstract: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Although the supporting research in laboratory models is quite substantial, only recently data has emerged to describe the effects of resveratrol supplementation on physiological responses in humans. The limited number of human clinical trials that are available has largely described various aspects of resveratrol's safety and bioavailability, reaching a consensus that it is generally well-tolerated, but have poor bioavailability. Very few published human studies have explored the ability of resveratrol to achieve the physiological benefits that have been observed in laboratory models, although many clinical trials have recently been initiated.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="48" LastActivityDate="2012-01-20T19:46:18.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="742" PostTypeId="2" ParentId="740" CreationDate="2012-01-20T20:10:59.583" Score="12" Body="&lt;p&gt;It's worth noting that earlier this month a large body of resveratrol research was retracted:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The University of Connecticut, in what clearly seems like an attempt to get ahead of damaging news, has announced an “extensive”&#xA;  investigation into research misconduct involving one of its&#xA;  scientists, Dipak K. Das.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;According to a press release, the university has notified 11 journals&#xA;  that published Das’ work about the alleged fraud. One area of interest&#xA;  for Das, a government-funded professor of surgery and director of the&#xA;  Cardiovascular Research Center, has been resveratrol, a substance in&#xA;  red wine that has allegedly been linked to improved cardiac health.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://retractionwatch.wordpress.com/&quot;&gt;Retraction Watch&lt;/a&gt;'s coverage has been pretty thorough and includes comments and citations:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://retractionwatch.wordpress.com/2012/01/11/uconn-resveratrol-researcher-dipak-das-fingered-in-sweeping-misconduct-case/&quot;&gt;UConn resveratrol researcher Dipak Das fingered in sweeping&#xA;misconduct case&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://retractionwatch.wordpress.com/2012/01/12/so-how-peripheral-was-dipak-das-resveratrol-work-really/&quot;&gt;So how peripheral was Dipak Das’ resveratrol&#xA;work, really?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://retractionwatch.wordpress.com/2012/01/12/resveratrol-fraud-case-update-dipak-das-loses-editors-chair-laywer-issues-statement-refuting-all-charges/&quot;&gt;Resveratrol fraud case update: Dipak Das loses&#xA;editor’s chair, lawyer issues statement refuting all charges&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="204" LastActivityDate="2012-01-20T20:10:59.583" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="743" PostTypeId="2" ParentId="728" CreationDate="2012-01-20T20:18:50.293" Score="8" Body="&lt;p&gt;It is mainly determined by the OCA2 gene, but it also likely involves several other genes, including TYR, TYRP1, HERC2, and several others. To complicate things further, it is not a &quot;mutant/wild type&quot; trait, but multiple normal alleles can be found in the population, and it is believed that the sum of these single nucleotide polymorphisms (SNPs) determine the final phenotype. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I took the info from a &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0168952504001593&quot;&gt;2004 review by Sturm and Frudakis&lt;/a&gt; and a more recent paper from &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0960982209005971&quot;&gt;Liu et al, 2009&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="48" LastEditorUserId="48" LastEditDate="2012-01-20T20:59:35.377" LastActivityDate="2012-01-20T20:59:35.377" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="744" PostTypeId="2" ParentId="719" CreationDate="2012-01-21T01:27:40.223" Score="11" Body="&lt;p&gt;As both @Rory M and @Alexander Galkin suggest, there are various non-visual mating behaviors to allow these species to select mates and also allow taxonomists and researchers to identify these species. And they hit on the two major ones, courtship rituals (mating calls, throat bulging, dancing) and pheromones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's have a look at some two examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The widespread amazonian frog &lt;em&gt;Allobates femoralis&lt;/em&gt; is now being approached as a species complex, with mating differences between the biologically distinct species varying from mating call note differences to cephalic amplexus (head grabbing during mate selection) and other various behavioral differences.&lt;a href=&quot;http://dx.doi.org/10.1080/03949370.2011.554884&quot;&gt;[1]&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Some crickets &lt;a href=&quot;http://dx.doi.org/10.1023/A:1021244812270&quot;&gt;mate preferentially based on their species-specific song&lt;/a&gt;. Though, there is probably some genetic mixing with those crickets.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I think it's important to note that the species are cryptic because we as humans have decided they're hard to tell apart. Now, that similar morphology is also potentially difficult for predators to tell apart, or may be used by one or both species to parasitize on the other, it may be kept similar by sexual selection, or it may just not have great selective pressures to change. But the important part is that &quot;cryptic species&quot; is a box that we've created to describe traits we see.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.tree.2006.11.004&quot;&gt;Cryptic species as a window on diversity and conservation&lt;/a&gt; is a decent overview paper. (it's avaliable &lt;a href=&quot;http://www.kevinwinker.org/Bickford%20et%20al%202007%20TREE%20cryptic%20species.pdf&quot;&gt;here&lt;/a&gt; if you don't have journal access)&lt;/p&gt;&#xA;" OwnerUserId="38" LastActivityDate="2012-01-21T01:27:40.223" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="745" PostTypeId="1" CreationDate="2012-01-21T03:58:03.113" Score="5" ViewCount="223" Body="&lt;p&gt;The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC535911/&quot; rel=&quot;nofollow&quot;&gt;reference below&lt;/a&gt; says that a higher AMP/ATP ratio is associated with lower lifespan in &lt;em&gt;C. elegans&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this finding also generalizable to vertebrates as well?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;br&gt;&#xA;Apfeld, J., O’Connor, G., McDonagh, T., DiStefano, P. S. &amp;amp; Curtis, R. The AMP-activated &#xA;protein kinase AAK-2 links energy levels and insulin-like signals to lifespan in C. elegans. &#xA;Genes Dev. 18, 3004–3009 (2004). &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC535911/&quot; rel=&quot;nofollow&quot;&gt;PMCID: PMC535911&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="66" LastEditDate="2012-01-21T20:56:43.270" LastActivityDate="2012-01-21T20:56:43.270" Title="Does AMP/ATP ratio affect lifespan in vertebrates?" Tags="&lt;senescence&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="747" PostTypeId="2" ParentId="714" CreationDate="2012-01-21T17:50:34.260" Score="32" Body="&lt;p&gt;I've been doing a little more digging myself and have found a couple of other advantages:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Risk of Venous-thromboembolism&lt;/strong&gt; (&lt;em&gt;deep vein thrombosis/pulmonary embolism &lt;sup&gt;&lt;a href=&quot;http://www.nhs.uk/conditions/thrombosis/Pages/Introduction.aspx&quot;&gt;(1)&lt;/a&gt;&lt;/sup&gt;&lt;/em&gt;).  Blood group O individuals are at lower risk of the above conditions due to reduced levels of von Willebrand factor&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17002642?dopt=Abstract&quot;&gt;(2)&lt;/a&gt;&lt;/sup&gt; and factor VIII clotting factors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cholera Infection Susceptibility &amp;amp; Severity&lt;/strong&gt;.  Individuals with blood group O are less susceptible to some strains of cholera (&lt;em&gt;O1&lt;/em&gt;) but are more likely to suffer severe effects from the disease if infected &lt;sup&gt;&lt;a href=&quot;http://iai.asm.org/content/73/11/7422.abstract?ijkey=874e927bc0c235214407900270e663e8deee3bbc&amp;amp;keytype2=tf_ipsecsha&quot;&gt;(3)&lt;/a&gt;&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;E. coli&lt;/em&gt; Infection Susceptibility &amp;amp; Severity.&lt;/strong&gt; A study in Scotland indicated that those with the O blood group showed higher than expected infection rates with &lt;em&gt;E. coli O157&lt;/em&gt; and significantly higher fatality rates (78.5% of fatalities had blood group O).&lt;sup&gt;&lt;a href=&quot;http://jid.oxfordjournals.org/content/185/3/393.abstract?ijkey=b285b74e38278f7c2423ce7a06e3555cf08f1d85&amp;amp;keytype2=tf_ipsecsha&quot;&gt;(4)&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Peptic Ulcers&lt;/strong&gt; caused by &lt;em&gt;Heliobacter pylori&lt;/em&gt; which can also lead to gastric cancer.  Group O are again more susceptible to strains of &lt;em&gt;H. pylori&lt;/em&gt; &lt;sup&gt;&lt;a href=&quot;http://www.sciencemag.org/content/262/5141/1892.abstract?ijkey=841510b71d793734a2791f975cdc77196289d266&amp;amp;keytype2=tf_ipsecsha&quot;&gt;(5)&lt;/a&gt;&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whether blood group antigens are displayed on other body cells or not has been linked to increased or decreased susceptibility to many diseases, notably norrovirus and HIV.  This is fully explained in the article that I was above summarising - &quot;&lt;a href=&quot;http://bloodjournal.hematologylibrary.org/content/115/23/4635.full&quot;&gt;The relationship between blood group and disease&lt;/a&gt;&quot; in addition to extended descriptions of the other two answers.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-02-19T21:57:59.027" LastActivityDate="2012-02-19T21:57:59.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="748" PostTypeId="2" ParentId="745" CreationDate="2012-01-21T20:32:50.543" Score="6" Body="&lt;p&gt;There are many papers suggesting a link between AMPK (the major cellular sensor of the AMP/ATP ratio) and lifespan.  As with most of these sorts of experiments, I think it is currently unclear precisely what the mechanism for this is, but AMPK regulates TORC1 and autophagy, both of which are also important for lifespan regulation.  Here is a PubMed link to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=ampk%20aging&quot;&gt;search results&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="235" LastEditorUserId="66" LastEditDate="2012-01-21T20:54:52.773" LastActivityDate="2012-01-21T20:54:52.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="749" PostTypeId="2" ParentId="728" CreationDate="2012-01-21T22:11:43.600" Score="5" Body="&lt;p&gt;There is &lt;a href=&quot;http://www.athro.com/evo/gen/genefr2.html&quot; rel=&quot;noreferrer&quot;&gt;a nice page&lt;/a&gt; that tries to explain this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The known Human Eye color genes are: EYCL1 (also called gey), the Green/blue eye color gene, &#xA;  located on chromosome 19 (though there is&#xA;  also evidence that another gene with similar activity exists but is&#xA;  not on chromosome 19). EYCL2 (also called bey1), the central brown eye&#xA;  color gene, possibly located on chromosome 15. EYCL3 (also called&#xA;  bey2), the Brown/blue eye color gene located on chromosome 15. EYCL3&#xA;  probably involves mutations in the regulatory region just before the&#xA;  OCA2 gene (which produces a protein that is expressed in melanocytes).&#xA;  A second gene for green has also been postulated. Other eye colors&#xA;  including grey and hazel are not yet explained. We do not yet know&#xA;  what these genes make, or how they produce eye colors. The two gene&#xA;  model (EYCL1 and EYCL3) used above explains only a portion of human&#xA;  eye color inheritance. Both additional eye color genes and modifier&#xA;  genes are almost certainly involved.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is even &lt;a href=&quot;http://www.athro.com/evo/gen/genefr2.html&quot; rel=&quot;noreferrer&quot;&gt;an interactive calculator&lt;/a&gt; available.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-01-21T22:11:43.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="750" PostTypeId="2" ParentId="117" CreationDate="2012-01-22T01:34:54.943" Score="1" Body="&lt;p&gt;The cheapest way to make that large quantity of DNA without the need of the whole oligomer being label would be to produce 34 nucleotides by chemical synthesis. The 35 nucleotide can be labeled and ligated to the remaining strands. This should reduce the costs of producing the oligomer since the most expensive stage, the labeling is limited to just the final nucleotide.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-01-22T01:34:54.943" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="752" PostTypeId="1" CreationDate="2012-01-22T15:53:36.657" Score="11" ViewCount="144" Body="&lt;p&gt;This is a follow-up question to &lt;a href=&quot;https://biology.stackexchange.com/questions/730/if-d1-receptors-stimulate-adenylate-cyclase-through-gpcrs-and-d2-receptors-inh&quot;&gt;If D1 receptors stimulate adenylate cyclase (through GPCRs) and D2 receptors inhibit it, then why do mutations in both have similar effects?&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a further question - I'd like to ask: do D1 dopamine receptors have the same (excitatory) effect everywhere in the brain? And do D2 dopamine receptors have the same (inhibitory) effect everywhere in the brain?&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-05-03T12:27:15.590" Title="Which brain regions are D1 dopamine receptors expressed, and which brain regions are D2 dopamine receptors expressed?" Tags="&lt;neuroscience&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="753" PostTypeId="1" AcceptedAnswerId="807" CreationDate="2012-01-22T18:34:43.187" Score="30" ViewCount="1208" Body="&lt;p&gt;Many flying insects tend to have very jagged trajectories. For moves of a fruit fly looks like a &lt;a href=&quot;http://en.wikipedia.org/wiki/Random_walk&quot;&gt;random walk&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any research on the properties of trajectories (e.g. their fractal dimension or mathematical models producing similar behaviour)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides the path of a single insect, I am also interested in the interaction of a small number of insects (e.g. 2 or 3).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am aware of the research in flocking and swarming (e.g. Tamas Vicsek, Anna Zafiris, &lt;a href=&quot;http://arxiv.org/abs/1010.5017&quot;&gt;Collective motion&lt;/a&gt; 2010) and of techniques of obtaining such trajectories (e.g. Danping Zou, Yan Qiu Chen, &lt;a href=&quot;http://dx.doi.org/10.1109/ICCVW.2009.5457649&quot;&gt;Acquiring 3D motion trajectories of large numbers of swarming animals&lt;/a&gt; or an &lt;a href=&quot;http://users.soe.ucsc.edu/~manazhao/files/iccv09_voec.pdf&quot;&gt;open access pdf&lt;/a&gt;, 2009). However, I haven't found within them an answer to my particular question.&lt;/p&gt;&#xA;" OwnerUserId="129" LastEditorUserId="69" LastEditDate="2012-02-16T14:49:26.287" LastActivityDate="2012-02-16T14:49:26.287" Title="What are the trajectories of flying insects?" Tags="&lt;zoology&gt;&lt;biophysics&gt;&lt;mathematical-models&gt;&lt;collective-behaviour&gt;&lt;entomology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="754" PostTypeId="1" CreationDate="2012-01-22T20:18:55.377" Score="19" ViewCount="10607" Body="&lt;p&gt;&lt;em&gt;I'm rather ashamed to say that this question is partly based on an episode of House.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have previously heard that, if there are multiple simultaneous painful stimuli, the mind will only feel the sensation of pain from the most severe injury.  A large amount of googling has turned up nothing and PubMed searches are proving tricky as I cant find the name of this effect (if it exists).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it does exist, is the mechanism solely effective for pain signals or would we for example only feel cold at our coldest points (i.e. from the face &lt;em&gt;or&lt;/em&gt; the hands rather than both) on a frosty morning? &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-25T20:11:35.743" LastActivityDate="2018-07-21T02:50:34.133" Title="Is it correct that the body only responds to the most painful stimulus?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="755" PostTypeId="1" AcceptedAnswerId="760" CreationDate="2012-01-22T20:39:06.623" Score="16" ViewCount="25396" Body="&lt;p&gt;In animals temporary anaerobic respiration leads to the breakdown of the pyruvate formed by glycolysis into lactate.  The buildup of lactate in the bloodstream is accompanied by a large number of protons causing lactic acidosis, which is detrimental to the health of the organism.  This is one of the main suggestions I have come across for why a lack of oxygen is fatal to cells, however the LD&lt;sub&gt;50&lt;/sub&gt; for lactic acid as referenced by the &lt;a href=&quot;http://www.sciencelab.com/msds.php?msdsId=9924446&quot;&gt;COSHH MSDS&lt;/a&gt; seem awfully high (even if the route is by ingestion rather than directly into the bloodstream) for this to be a cause of cell death:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Toxicological Data on Ingredients: &#xA;  ORAL (LD50): Acute:&lt;/strong&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;3543 mg/kg [Rat (Lactic Acid (CAS no. 50-21-5))]. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;4875 mg/kg [Mouse (Lactic Acid (CAS no. 50-21-5))].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I also wonder if this is a larger problem for an organism as a whole rather than on a cellular level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The alternative, I suppose, is that glycolysis alone does not provide sufficient ATP for vital cellular processes to occur.  If this is the case, which ATP requiring processes are most vital for the short term survival for a cell? &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2017-03-23T13:38:38.697" Title="Why is a lack of oxygen fatal to cells?" Tags="&lt;cellular-respiration&gt;&lt;anaerobic-respiration&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="756" PostTypeId="1" AcceptedAnswerId="771" CreationDate="2012-01-22T21:01:45.370" Score="8" ViewCount="704" Body="&lt;p&gt;For calculating the &lt;a href=&quot;https://en.wikipedia.org/wiki/Sievert#Effective_dose&quot;&gt;effective radiation dose in Sv&lt;/a&gt;, the equivalent dose absorbed by each body part is averaged according to tissue-specific weighting factors, which sum up to 1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not the whole body is irradiated, how are these factors used?&lt;/p&gt;&#xA;" OwnerUserId="392" LastActivityDate="2012-01-23T12:33:39.683" Title="How is the effective dose calculated when only part of the body is irradiated?" Tags="&lt;radiation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="757" PostTypeId="1" AcceptedAnswerId="7921" CreationDate="2012-01-22T23:02:38.443" Score="24" ViewCount="2869" Body="&lt;p&gt;As far as I understand, various abilities like flying, sight, hearing etc. were caused by slow evolution, where those with a greater ability to to these things had better chance of survival. (If this assumption is wrong, then I am happy to delete this question). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there, however, any documented examples of by evolutionary leaps being made, over the course of just a few generations? I understand, that some abilities have a tipping point where one gets the ability suddenly, but there is not a lot of physiological change made. An example of this would be the ability to climb a tree, which could suddenly be possible if the body weight is reduced with just a few percent. What my question is about, are sudden changes to the characteristics of a creature.&lt;/p&gt;&#xA;" OwnerUserId="205" LastActivityDate="2020-11-16T05:11:39.217" Title="Are there any examples of sudden leaps in evolution?" Tags="&lt;evolution&gt;" AnswerCount="5" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="758" PostTypeId="2" ParentId="753" CreationDate="2012-01-22T23:40:05.517" Score="23" Body="&lt;p&gt;&lt;a href=&quot;http://icb.oxfordjournals.org/content/45/2/274.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dickinson (2005)&lt;/a&gt; has a good review of insect flight, including behavior, biomechanics, electrophysiology, and neural control with links to more of the primary literature. What follows is a general summary thereof.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The jagged trajectories you mention are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Saccade&quot; rel=&quot;nofollow noreferrer&quot;&gt;saccades&lt;/a&gt; in the insect flight literature. In &lt;em&gt;Drosophila&lt;/em&gt;, saccades are ~90° turns accomplished in approximately 50 ms. Because flies can't move their eyes independently of their heads, saccades are though to allow a relatively constant visual field most of the time, interspersed with rapid reorientations during which the fly is &quot;blind.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The actual turn begins with the generation of a torque, which starts the fly turning. Shortly thereafter, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Haltere&quot; rel=&quot;nofollow noreferrer&quot;&gt;halteres&lt;/a&gt; sense this change and a counter-torque is produces, which stops the turn.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rather than random turns, &lt;em&gt;Drosophila&lt;/em&gt; are turning away from visual expansion as they near objects. So as they move closer to an object, it expands in their visual field, and they turn away from it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CxHuC.jpg&quot; alt=&quot;Schematic of fruit fly turning&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-01-22T23:40:05.517" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="759" PostTypeId="2" ParentId="757" CreationDate="2012-01-22T23:52:13.623" Score="21" Body="&lt;p&gt;&lt;a href=&quot;http://rsbl.royalsocietypublishing.org/content/2/4/521.full?sid=36ce9d7f-9cc9-4c07-92f4-4808ec90f451&quot;&gt;Zuk et al. (2006)&lt;/a&gt; document the rapid evolution of song-less crickets in a population of crickets that previously used song for courtship.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In less that 20 generations, over 90% of male crickets of the species &lt;em&gt;Teleogryllus oceanicus&lt;/em&gt; evolved to a novel morphology (&quot;flatwing&quot;) that rendered them unable to call to females. They hypothesize that this shift resulted from the presence of an North American invasive &quot;acoustically orienting parasitoid fly.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically the flies detect calling males and parasitize them, rendering them unable to reproduce. Were it not for the presence of the parasitoid fly, the flatwing flies would likely not have survived. Non-calling individuals rely on the presence of calling males to bring females near for mating.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2012-01-23T01:06:05.703" LastActivityDate="2012-01-23T01:06:05.703" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="760" PostTypeId="2" ParentId="755" CreationDate="2012-01-23T00:59:22.200" Score="11" Body="&lt;p&gt;Here's an illustrated example in neurons:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ATP, of course, is generated by aerobic respiration. The critical biochemical reaction in the brain that is halted due to lack of ATP (and therefore O2) is the glutmaine synthetase reaction, which is very important for the metabolism and excretion of nitrogenous wastes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lCUXV.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The body uses this reaction to dump excess ammonia (which is a metabolic waste product) on glutamate to make glutamine. The glutamine is then transported via the circulatory system to the kidney, where the terminal amino group is hydrolyzed by glutaminase, and the free ammonium ion is excreted in the urine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OX4lq.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, as you'd expect, under hypoxic conditions in the brain, excess ammonia builds up which is very toxic to the cells. Neurons are also highly metabolically active, which means they generate more waste products. A buildup of nitrogenous waste products in the cell (and bloodstream) can be potentially fatal due to it's effects on pH (screws up enzymes and a whole slew of biochemical reactions).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, the buildup of ammonia will cause glutamate dehydrogenase to convert ammonia + aKG to glutamate, which depletes the brain of alpha-ketoglutarate (key intermediate in TCA cycle). This basically creates a logjam in the central metabolic cycle which further depletes the cell of energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;This is just one example of many.&lt;/strong&gt; Of course, there are many, many other critical metabolic processes that require ATP (i.e. the Na+/K+ ATPase pump that regulates neuronal firing and osmotic pressure), but nitrogen metabolism was the first that came to mind :)&lt;/p&gt;&#xA;" OwnerUserId="177" LastActivityDate="2012-01-23T00:59:22.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="761" PostTypeId="1" AcceptedAnswerId="860" CreationDate="2012-01-23T01:44:59.433" Score="18" ViewCount="1897" Body="&lt;p&gt;I am curious how Gall Wasps, bacteria and other organisms induce &lt;a href=&quot;http://en.wikipedia.org/wiki/Gall&quot;&gt;galls&lt;/a&gt; to form. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, what chemicals induce gall formation?&lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="1590" LastEditorDisplayName="user132" LastEditDate="2015-07-10T07:06:17.570" LastActivityDate="2015-07-10T07:06:17.570" Title="How do plant galls form?" Tags="&lt;botany&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="762" PostTypeId="1" AcceptedAnswerId="766" CreationDate="2012-01-23T02:31:46.283" Score="22" ViewCount="19759" Body="&lt;p&gt;Humans have, in a relatively short amount of time, evolved from apes on the African plains to upright brainiacs with nukes, computers, and space travel.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Meanwhile, a lion is still a lion and a beetle is still a beetle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a specific reason for this?  Do we have a particular part of brain that no other animal has?&lt;/p&gt;&#xA;" OwnerUserId="393" LastEditorUserId="393" LastEditDate="2012-01-25T21:55:29.980" LastActivityDate="2016-12-26T07:15:46.877" Title="Why have humans evolved much more quickly than other animals?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;evolution&gt;" AnswerCount="9" CommentCount="7" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="763" PostTypeId="1" AcceptedAnswerId="773" CreationDate="2012-01-19T04:12:12.027" Score="0" ViewCount="31045" Body="&lt;p&gt;This is a follow-up question to &lt;a href=&quot;http://www.quora.com/Lincoln-Assassination/How-likely-would-Abraham-Lincoln-be-to-survive-his-wounds-today/answer/Laszlo-B.-Tamas&quot; rel=&quot;nofollow noreferrer&quot;&gt;How likely would Abraham Lincoln be to survive his wounds today?&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;You don't have to see a CT scan or autopsy to know if the brainstem is&#xA;injured (directly or indirectly), if it doesn't work right.&lt;/p&gt;&#xA;&lt;p&gt;The description of the first doc at the scene mentioned that Lincoln&#xA;was not breathing, and one pupil was dilated (the latter a clear and&#xA;unequivocal sign of dysfunction of the third cranial nerve or the&#xA;upper brainstem, from where it comes). Unfortunately, the second doc&#xA;described the enlarged pupil being the right one (it's extremely&#xA;unlikely to have been one and then the other - one of the doc's was&#xA;probably mistaken as to the side).&lt;/p&gt;&#xA;&lt;p&gt;By 3 hours after injury, both pupils were fixed and dilated, and&#xA;&lt;strong&gt;Lincoln showed extensor (decerebrate) posturing&lt;/strong&gt; - again, all signs of&#xA;profound brainstem dysfunction (but not yet brain death, though pretty&#xA;close to it).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Now, what is decerebrate posturing? See &lt;a href=&quot;http://en.wikipedia.org/wiki/Abnormal_posturing#Decerebrate&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Abnormal_posturing#Decerebrate&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Decerebrate posturing is also called decerebrate response, decerebrate&#xA;rigidity, or extensor posturing. It describes the involuntary&#xA;extension of the upper extremities in response to external stimuli. In&#xA;decerebrate posturing, the head is arched back, the arms are extended&#xA;by the sides, and the legs are extended.[6] A hallmark of decerebrate&#xA;posturing is extended elbows.[12] The arms and legs are extended and&#xA;rotated internally.[13] The patient is rigid, with the teeth&#xA;clenched.[13] The signs can be on just one or the other side of the&#xA;body or on both sides, and it may be just in the arms and may be&#xA;intermittent.[13]&lt;/p&gt;&#xA;&lt;p&gt;A person displaying decerebrate posturing in&#xA;response to pain gets a score of two in the motor section of the&#xA;Glasgow Coma Scale (for adults) and the Pediatric Glasgow Coma Scale&#xA;(for infants). Decerebrate posturing indicates brain stem damage,&#xA;specifically damage below the level of the red nucleus (e.g.&#xA;mid-collicular lesion). It is exhibited by people with lesions or&#xA;compression in the midbrain and lesions in the cerebellum&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="103" OwnerDisplayName="InquilineKea" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-09-09T22:58:06.543" Title="How reversible is decerebrate posturing caused by brain stem damage?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="764" PostTypeId="1" CreationDate="2012-01-19T04:37:11.143" Score="11" ViewCount="328" Body="&lt;p&gt;When we assume that peripheral touch receptor densities are equal in tall and short people, then tall people should have &lt;em&gt;more&lt;/em&gt; touch receptors than short people, given the larger amount of skin surface in the former. Hence my question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do taller people have larger somatosensory cortices than short people? And analogues to that, what about larger motor cortices in tall people? If tall people need larger somatosensory and motor areas, could this imply that they have less space devoted to other functions, like functions devoted to the prefrontal cortex?&lt;/p&gt;&#xA;" OwnerUserId="103" OwnerDisplayName="InquilineKea" LastEditorUserId="9943" LastEditDate="2016-03-10T20:56:36.833" LastActivityDate="2016-03-10T20:56:36.833" Title="Do taller people have larger somatosensory cortices than short people?" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;&lt;touch&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="765" PostTypeId="2" ParentId="757" CreationDate="2012-01-23T06:51:04.283" Score="12" Body="&lt;p&gt;The ability to drink milk by the inheritance of lactase persistence via a single allele change. Sociology and genetic studies have shown that the immigration of a few lactose tolerant people into large non-lactose tolerant populations, the lactase persistence gene quickly spreads through the population, a sign of a dominant mutation and survival of the fittest at work. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not in the mood to dissect the papers but here are a few commentaries:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://sciencelife.uchospitals.edu/2011/09/14/lactose-tolerance-in-the-indian-dairyland/&quot;&gt;http://sciencelife.uchospitals.edu/2011/09/14/lactose-tolerance-in-the-indian-dairyland/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://news.discovery.com/human/got-milk-drinking-common-ancestor-india-and-europe-do-110914.html&quot;&gt;http://news.discovery.com/human/got-milk-drinking-common-ancestor-india-and-europe-do-110914.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="389" LastEditorUserId="260" LastEditDate="2012-01-23T11:43:20.203" LastActivityDate="2012-01-23T11:43:20.203" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="766" PostTypeId="2" ParentId="762" CreationDate="2012-01-23T06:54:40.610" Score="32" Body="&lt;p&gt;We have the &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_accelerated_regions&quot;&gt;Human Accelerated Regions&lt;/a&gt; (HARs) which are some of the most rapidly evolving RNA genes elements. While heavily conserved in vertebrates, they go haywire in humans and are linked with neurodevelopment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks to @Nico, the following paper compares the human genome with that of the chimp and identifies genetic regions that show accelerated evolution. The most extreme, &lt;a href=&quot;http://en.wikipedia.org/wiki/HAR1F&quot;&gt;HAR1&lt;/a&gt; is expressed mainly in &lt;a href=&quot;http://en.wikipedia.org/wiki/Cajal-Retzius_cell&quot;&gt;Cajal-Retzius&lt;/a&gt; neuron cells which hints at its important role in human development.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nature05113&quot;&gt; &lt;strong&gt;Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, et al.&lt;/strong&gt;. 2006. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443: 167–72.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="836" LastEditDate="2012-09-13T06:21:09.673" LastActivityDate="2012-09-13T06:21:09.673" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="767" PostTypeId="2" ParentId="762" CreationDate="2012-01-23T08:55:35.633" Score="6" Body="&lt;p&gt;The ability to walk on two legs was hugely significant in human evolutionary development. This led to the hands being freed up to develop into precision tools rather than having to be durable for walking on rough terrain.  Increased dexterity in the hands led &lt;em&gt;in part&lt;/em&gt; to the leap forward in human development.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;~ &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Human_Body_%28TV_series%29&quot; rel=&quot;nofollow&quot;&gt;The Human Body&lt;/a&gt; (Prof. Robert Winston - &lt;a href=&quot;http://www.imdb.com/title/tt0200346/&quot; rel=&quot;nofollow&quot;&gt;BBC Documentary&lt;/a&gt; 1998 (&lt;a href=&quot;http://news.bbc.co.uk/1/hi/special_report/1998/05/98/the_human_body/114977.stm&quot; rel=&quot;nofollow&quot;&gt;BBC Text Summary&lt;/a&gt;)&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-25T22:24:06.267" LastActivityDate="2012-01-25T22:24:06.267" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="768" PostTypeId="1" AcceptedAnswerId="770" CreationDate="2012-01-23T10:37:03.930" Score="19" ViewCount="624" Body="&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;: From a physiological point of view, when sex is &lt;a href=&quot;http://en.wikipedia.org/wiki/XY_sex-determination_system&quot;&gt;determined&lt;/a&gt; in a human fetus, is it equally likely to be male or female?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Studies in this area typically measure age at birth, where the data would have already been biased.  There's a slight imbalance in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_sex_ratio&quot;&gt;human sex ratio&lt;/a&gt;, in that there's an overall tendency towards males.  However, this could be accounted for in numerous ways, such as abortion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fisher%27s_principle&quot;&gt;Fisher's principle&lt;/a&gt; suggests there would be an evolutionary tendency towards 50:50 chance.&lt;/p&gt;&#xA;" OwnerUserId="203" LastEditorUserId="231" LastEditDate="2013-08-17T05:27:13.650" LastActivityDate="2013-08-17T05:27:13.650" Title="Are human fetuses more likely to be male?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;reproduction&gt;&lt;sex-ratio&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="2" ClosedDate="2015-02-28T09:25:42.573" ContentLicense="CC BY-SA 3.0" />
  <row Id="769" PostTypeId="2" ParentId="287" CreationDate="2012-01-23T10:40:19.537" Score="3" Body="&lt;p&gt;The answer lies entirely in the thermodynamic stability that is provided with having a 2'-OH. As mentioned by Aleksandra, RNA will adopt only the C3'-endo conformation whereas DNA adopts both the C2'-endo and C3'-endo. Effectively, this makes the DNA strand more flexible not RNA. In doing so, a single stranded DNA oligomer will be able to adopt more states.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA/RNA helix formation is dominantly &lt;strong&gt;enthalpically&lt;/strong&gt; driven. When a helix forms, RNA will only adopt an A-form Helix where as DNA will adopt both a A-form and B-form. While there are more possible conformations for DNA, the reduction in the &lt;strong&gt;entropic&lt;/strong&gt; contributions make it significantly more unfavorable. Interestingly, this is why RNA analogs like PNA and morpholinos have good binding properties as they will form more entropically stable base-pairing with their target sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For these reasons, it is much more common so see structured Ribozymes and non-coding RNAs in nature even though it is physically possible to produce DNAzymes. Again, one of the many reasons why the RNA world hypothesis makes sense.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-01-23T10:40:19.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="770" PostTypeId="2" ParentId="768" CreationDate="2012-01-23T12:19:03.390" Score="15" Body="&lt;p&gt;&lt;strong&gt;The Fisher's principle is not applicable to the fetuses&lt;/strong&gt; because it has been formulated for parental expenditure and basically states that the ratio of male to female parents (implying that both parties have reached the age of fertility) will tend to 1:1. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several mechanisms that we can use and that are mentioned in the canonical paper by &lt;a href=&quot;http://dx.doi.org/10.1677/JOE-07-0446&quot; rel=&quot;nofollow&quot;&gt;James (2007)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(a) there are equal numbers of X and Y chromosomes in mammalian sperms&lt;br&gt;&#xA;  (b) X and Y stand equal chance of achieving conception&lt;br&gt;&#xA;  (c)&#xA;  therefore equal number of male and female zygotes are formed, and that&lt;br&gt;&#xA;  (d) therefore any variation of sex ratio at birth is due to sex&#xA;  selection between conception and birth.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;James brings much evidence that none of these conventional beliefs is true. Rather, they are dependent upon many factors: exposure to stress during pregnancy, glucose level etc. He reports that there is an excess of males at birth in almost all human populations, and the natural sex ratio at birth is usually between 1.02 and 1.08. However, the ratio may deviate significantly from this range for natural reasons. (I really recommend reading the paper I linked, it is available for free).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1093/humrep/dep255&quot; rel=&quot;nofollow&quot;&gt;Branum &lt;em&gt;et al&lt;/em&gt; (2009)&lt;/a&gt; analyze birth statistics in the US taking into account many factors like ethnicity, gestational age and plurality and show that the ratio can increase even more with growing gestational age and has different values among different races.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, taking everything together, I can say thay &lt;strong&gt;YES, the chances for human fetuses to be male are indeed higher&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="1306" LastEditDate="2012-09-29T12:07:59.650" LastActivityDate="2012-09-29T12:07:59.650" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="771" PostTypeId="2" ParentId="756" CreationDate="2012-01-23T12:33:39.683" Score="2" Body="&lt;p&gt;Not sure that I understood your question correctly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concept of &quot;effective dose&quot; was specially introduced to provide a mechanism for assessing the radiation detriment from partial body irradiations in terms of data derived from whole body irradiations. &lt;strong&gt;The effective dose is the mean absorbed dose from a uniform whole-body irradiation that results in the same total radiation detriment as from the nonuniform, partial-body irradiation in question&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is probably misleading you is the sum of the weighting factors to be 1. This is because we try to liken the partial body irradiation and the whole-body irradiation and the weighting factors represent the relative tissue sensitivity and susceptibility to the radiation. Your radiation should not go over all possible tissues and organs, you just assume the irradiation to be zero at them that cancels their summands so that they can be ignored in the final calculation. In other words, it is absolutely fine (and it is even so &quot;by design&quot;) to have only some of the W&lt;sub&gt;T&lt;/sub&gt;*H&lt;sub&gt;T&lt;/sub&gt; factors in your formula. &lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-01-23T12:33:39.683" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="772" PostTypeId="2" ParentId="754" CreationDate="2012-01-23T12:56:18.720" Score="5" Body="&lt;p&gt;Your question statement is a little bit incorrect or, better say, imprecise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all it is not clear what you mean by the &quot;body response&quot; here? Pain is sensed by peripherial receptors (several types of receptors, mostly purinergic, are assumed to play role in pain preception) and then this sensation is propagated into CNS. So, the local &quot;response to pain&quot; (like swelling, increase of the blood perfusion) is not the response to the pain stimulus, but rather a methabolic response to the cell injures and release of many humoral factors like interleukins, &quot;wound hormones&quot; etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And this is true that out of many different pain inputs the one with highest intensity seems to &quot;outshine&quot; all other inputs and ultimately the pain perception is constrained to a single body part. However, if you consciously focus your perception on other parts of your body you may be able to percieve the pain originating from these parts even if this pain is lower.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This principle is known as a smaller particular case of a more general principle known as &quot;the dominance principle of Ukhtomsky&quot;. Wikipedia has only the &lt;a href=&quot;http://ru.wikipedia.org/wiki/%D0%A3%D1%87%D0%B5%D0%BD%D0%B8%D0%B5_%D0%BE_%D0%B4%D0%BE%D0%BC%D0%B8%D0%BD%D0%B0%D0%BD%D1%82%D0%B5&quot; rel=&quot;noreferrer&quot;&gt;Russian language version&lt;/a&gt; about this principle (as well as about &lt;a href=&quot;http://ru.wikipedia.org/wiki/%D0%A3%D1%85%D1%82%D0%BE%D0%BC%D1%81%D0%BA%D0%B8%D0%B9,_%D0%90%D0%BB%D0%B5%D0%BA%D1%81%D0%B5%D0%B9_%D0%90%D0%BB%D0%B5%D0%BA%D1%81%D0%B5%D0%B5%D0%B2%D0%B8%D1%87&quot; rel=&quot;noreferrer&quot;&gt;Ukhtomsky&lt;/a&gt;, a prominent Russian physiologist) and it seems to be not really known outside of the Russian scientific community (this is &lt;a href=&quot;http://www.encyclopedia.com/doc/1G2-2830904408.html&quot; rel=&quot;noreferrer&quot;&gt;the only page&lt;/a&gt; I found about him in English).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The more general principle of Ukhtomsky postulates the following: one certain input may lead to the formation of the dominance center in the cortex. The domaninace center is characterized by the higher level of nerve cell excitation, whereas the rest of the cortex undergoes an inhibition so that different, even unrelated inputs converge here, helping this center to exist for longer time. The only way how this center can be ceased is to form another dominance center by a extremely high stimulus (for example a startle sound). Here the most insensive pain leads to the formation of such a center and all substantial pain stimuli just contribute to the persistence of this center: the pain is however percieved to originate from the place where the first stimulus, responsible for dominance center formation, originated from.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-01-23T12:56:18.720" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="773" PostTypeId="2" ParentId="763" CreationDate="2012-01-23T13:14:04.457" Score="2" Body="&lt;p&gt;The decerebrate posturing is a sign of major brainstem dysfunction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The reversibility&lt;/strong&gt; of this state (which is considered to be very critical and hardly reversible) &lt;strong&gt;depends upon the origin of the brainstem dysfunction&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The primary brainstem&lt;/strong&gt; dysfunction means that the brainstem was directly damaged (by a bullet) and there &lt;strong&gt;is no way&lt;/strong&gt; that this can be quickly &lt;strong&gt;reversed&lt;/strong&gt;. This is exactly the case here and there are no chances that the brainstem might recooperate with time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The secondary brainstem&lt;/strong&gt; dysfunction may be caused by cerebral edema and thereby dislocation of the brainstem towards &lt;em&gt;foramen magnum&lt;/em&gt;, where the brainstem is coned. The coning of the brainstem &lt;strong&gt;can be reversible&lt;/strong&gt; if the brain edema is treated quickly and effectively (by administration of diuretics in the intravenal catheter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With brainstem regaining its normal functions the decerebral posture will eventuall resolve and depending upon the residual brain injury the recooperation of the brain function (and compensation) may be almost entire.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-01-23T13:14:04.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="774" PostTypeId="2" ParentId="755" CreationDate="2012-01-23T14:52:32.840" Score="3" Body="&lt;p&gt;Energy production starts with glycolysis, which generates NADH and pyruvate.  Pyruvate goes to the mitochondria to make more NADH (or FADH2, which is similar to NADH) in the Krebs Cycle.  NADH is used to power the electron transport chain, which gives most of the energy the cell uses.  The &lt;em&gt;last&lt;/em&gt; step of the electron transport chain consumes oxygen (Complex IV reduces oxygen to water).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you do not have oxygen, the electron transport chain will not work.  If that doesn't work, the Krebs Cycle slows.  If that's not consuming pyruvate, glycolysis slows.  The cell dies from lack of energy.  It has less to do with the acid buildup as a consequence of lactate as it does with buildup of NADH and the consequent slowing of the central metabolism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The issue is most pronounced in multicellular organisms  because it's much more difficult to get oxygen to all your tissues, so &quot;think&quot; tissues have cells that are already close to hypoxia already.&lt;/p&gt;&#xA;" OwnerUserId="219" LastActivityDate="2012-01-23T14:52:32.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="775" PostTypeId="1" AcceptedAnswerId="778" CreationDate="2012-01-23T15:11:19.813" Score="33" ViewCount="3994" Body="&lt;h1&gt;Background&lt;/h1&gt;&#xA;&lt;p&gt;I am a computer programmer who is fascinated by artificial intelligence and artificial neural networks, and I am becoming more curious about how biological neural networks work.&lt;/p&gt;&#xA;&lt;h1&gt;Context &amp;amp; what I think I understand&lt;/h1&gt;&#xA;&lt;p&gt;In digesting all I have been reading, I am beginning to understand that there are layers to neural networks.  A front-line layer of neurons may receive, for example, a visual stimulus such as a bright light.  That stimulus is taken in by the front-line neurons, each of which produce a weighted electro-chemical response that results in a binary decision to pass an electrical charge through its axon to the dendrites of the tens of thousands of neurons to which it is connected.&lt;/p&gt;&#xA;&lt;p&gt;This process repeats through layers channeling the electrical signals and focusing them based on their permutations until ultimately a charge is passed to a focused response mechanism such as the nerves that control shrinking of the pupils.&lt;/p&gt;&#xA;&lt;p&gt;Hopefully I got that correct.&lt;/p&gt;&#xA;&lt;h1&gt;Preamble to the question ;)&lt;/h1&gt;&#xA;&lt;p&gt;Assuming that I am not completely off-base with my basic understanding of how a biological neural network operates, I am beginning to grasp how an input (stimulus) results in an output (response) such as motor movement or reflexes.  That would just seem to be basic electricity of open and closed circuits.&lt;/p&gt;&#xA;&lt;p&gt;HOWEVER, what confuzzles me still is how a memory is stored.  The analogy to an electrical circuit breaks down here, for in a circuit I can't really stop the flow of electrons unless I dam up said electrons in a capacitor.  If I do that, once the electrons are released (accessed), they are gone forever whereas a memory endures.&lt;/p&gt;&#xA;&lt;h1&gt;So. . .&lt;/h1&gt;&#xA;&lt;p&gt;How the heck are memories constructed and stored in the human brain?  Are they stored in a specific region?  If so, where?&lt;/p&gt;&#xA;" OwnerUserId="393" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-01T12:03:08.863" Title="How and where, in the human brain, are memories stored?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;molecular-biology&gt;&lt;neuroanatomy&gt;&lt;memory&gt;" AnswerCount="4" CommentCount="4" FavoriteCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="777" PostTypeId="7" CreationDate="2012-01-23T18:32:55.043" Score="0" Body="&lt;p&gt;Biology - Stack Exchange is for people studying biology at any level.  Questions are from students, academics and active researchers in biology and closely&#xA;  related fields, including:&lt;/p&gt;&#xA;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;general questions about biological concepts&lt;/li&gt;&#xA;  &lt;li&gt;questions about the biological mechanisms behind medical conditions&lt;/li&gt;&#xA;  &lt;li&gt;questions about techniques in a biological or biochemical laboratory&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&#xA;  &lt;p&gt;Questions on interdisciplinary subjects like bioinformatics are also&#xA;  welcome, as long as they focus on the biological part of the subject.&lt;/p&gt;&#xA;&#xA;  &lt;p&gt;&lt;strong&gt;Which questions are off-topic?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;personal medical questions&lt;/li&gt;&#xA;  &lt;li&gt;philosophical or ethical questions related to biology&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&#xA;  &lt;p&gt;&lt;strong&gt;Please see these &lt;a href=&quot;http://biology.stackexchange.com/questions/how-to-ask&quot;&gt;tips on writing a good question&lt;/a&gt; before posting&lt;/strong&gt;. &lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="69" LastEditDate="2012-02-17T10:22:58.670" LastActivityDate="2012-02-17T10:22:58.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="778" PostTypeId="2" ParentId="775" CreationDate="2012-01-23T18:41:31.333" Score="37" Body="&lt;p&gt;Unfortunately, we are all still &quot;confuzzled&quot; by how memory works. We are far from a complete understanding of how memory is stored and recalled. Nonetheless, we do know a &lt;em&gt;little&lt;/em&gt;, so read on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your understanding of basic neural function is &lt;em&gt;almost&lt;/em&gt; correct. First, an individual neuron will signal through its single axon onto the dendrites of many downstream neurons, not the other way around. Second, I am not sure what you mean by &quot;focusing them based on their permutations,&quot; but it is true that neural information can undergo many transformations as it propagates through a circuit. Third, if there is a behavioral outcome of the network activity like a muscle response or hormone release, those effects are mediated by nerves communicating with muscles and hormone-releasing cells. I'm not sure if that is what you meant by &quot;focused response mechanism.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, as you have discovered, the analogy of neural circuits to electrical circuits is relatively poor at any reasonably sophisticated level of analysis. My opinion is that biological systems are often poorly served by being framed as engineering problems. Others will disagree with that, but I think understanding a biological system on its own terms makes many things much clearer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key thing missing from the electrical circuit analogy turns out to be one of the keys to understanding information storage in neural circuits--&lt;em&gt;the synapse&lt;/em&gt;, the site where one neuron communicates with another. The synapse transforms the electrical signal from the upstream neuron into a chemical signal. That chemical signal is then converted back into an electrical signal by the downstream neuron. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The strength of the synapse can be adjusted in a long-term way by changing the level of protein expression--this is called &lt;strong&gt;long-term potentiation (LTP)&lt;/strong&gt; or &lt;strong&gt;long-term depression (LTD)&lt;/strong&gt;. LTP and LTD therefore can regulate the ease with which information can flow along a particular path. As a basic example (that should not be taken too seriously), imagine a set of neurons that represents &quot;New York City&quot; and another set of neurons that represents &quot;My Friend John.&quot; If you then happen to be in New York City with your friend John, both of those groups of neurons will be active and synapses &lt;em&gt;between&lt;/em&gt; these two networks will be strengthened because they are co-active (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Hebbian_theory&quot;&gt;Hebbian plasticity&lt;/a&gt;). In this way, the idea of NYC and the idea of John are now bound together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where are these neurons that represent NYC and John? We are still not totally clear on this, and the question is complicated because there are many different types of memory. For instance, your memory of how to ride a bike (procedural memory) is not treated the same as your memory of what you ate for breakfast (episodic memory). However, a best current answer is that the &lt;strong&gt;hippocampus&lt;/strong&gt; and its associated regions are important for the initial encoding of memories and the &lt;strong&gt;neocortex&lt;/strong&gt; is where longer term memories are stored. There is substantial communication between these two areas so that memories can be effectively adjusted over time.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Update&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;In response to Jule's comment asking for some resources, I realize it is important to make the point that the Hebbian model I outlined hasn't been definitively shown. Like with all aspects of neuroscience, there is a lot of good work at the molecular and cellular level and good work at the behavioral level, but the causal link between the two is not so clear. Nonetheless, Hebb's idea is still the mainstream working model for how memory works. Some reading might include: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) &lt;a href=&quot;http://dx.doi.org/10.1038/nrn2303&quot;&gt;Neves, G., Cooke, S.F., Bliss, T.V.P., 2008. Synaptic plasticity, memory and the hippocampus: a neural network approach to causality. Nature Reviews Neuroscience 9, 65–75.&#xA;&lt;/a&gt; A review on hippocampal memory and its relation to LTP/LTD and Hebbian theory. Notes the general difficulty of proving the theory and some ways for experiments to move forward.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) &lt;a href=&quot;http://dx.doi.org/10.1016/j.tins.2011.07.006&quot;&gt;Lisman, J., Grace, A.A., Duzel, E., 2011. A neoHebbian framework for episodic memory; role of dopamine-dependent late LTP. Trends in Neurosciences 34, 536–547.&#xA;&lt;/a&gt; A review proposing an elaboration of the Hebbian model that includes neuromodulatory influence on plasticity and memory process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) &lt;a href=&quot;http://dx.doi.org/10.1016/j.cell.2011.10.009&quot;&gt;Johansen, J.P., Cain, C.K., Ostroff, L.E., LeDoux, J.E., 2011. Molecular Mechanisms of Fear Learning and Memory. Cell 147, 509–524.&lt;/a&gt;. An excellent review on fear learning and memory with an extensive section on Hebbian theory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) &lt;a href=&quot;http://dx.doi.org/10.1038/nature11028&quot;&gt;Liu, X., Ramirez, S., Pang, P.T., Puryear, C.B., Govindarajan, A., Deisseroth, K., Tonegawa, S., 2012. Optogenetic stimulation of a hippocampal engram activates fear memory recall. Nature.&lt;/a&gt; A research article which is perhaps a realization of some of suggestions in the Neves et al review. They use light to reactivate a fear memory. This suggests that activation of the hippocampal network that was active during memory formation is sufficient to elicit the memory.&lt;/p&gt;&#xA;" OwnerUserId="72" LastEditorUserId="72" LastEditDate="2012-06-06T20:48:10.580" LastActivityDate="2012-06-06T20:48:10.580" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="779" PostTypeId="2" ParentId="762" CreationDate="2012-01-23T19:53:05.533" Score="1" Body="&lt;p&gt;I believe that it is significant that we spend so much of our brain-power on deciding who we want to mate with. For lions it seems like choosing a partner is much less based on rational thinking. The weakness of this theory is that I do not know how humans behaved earlier, and whether mating was strictly regulated by cultural rules to ensure that mating was not based upon convenience, but rational thinking about what who is the best partner in the long-term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for me believing that this is so important, is that a well-functioning couple in a well-functioning community, will have the time and energy to educate their children, who again will make wiser decisions on who they will choose as their partner.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would love to get this theory tested (and hopefully rejected, as that is the way I learn the most) by this community.&lt;/p&gt;&#xA;" OwnerUserId="205" LastActivityDate="2012-01-23T19:53:05.533" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="780" PostTypeId="2" ParentId="768" CreationDate="2012-01-23T20:16:14.060" Score="8" Body="&lt;p&gt;The following paper(1) studies the trends in male to female ratios among newborns over the period 1950-1994 in 29 countries (20 major European countries, USA, Canada, Japan, and others). In all countries at any time point, the male to female ratio was always higher than one. In some countries (Mexico and a few northern eastern European countries) the male proportion has been decreasing over the 1950-1994 period, whereas in southern Europe and Australia it has been increasing. Overall, the ratio has remained constant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors mention several factors that could contribute to the decrease of males. Among those factors are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;hormonally induced ovulation&lt;/li&gt;&#xA;&lt;li&gt;maternal nutrition&lt;/li&gt;&#xA;&lt;li&gt;environmental factors (like alcohol exposure of the fathers)  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;On another note, the increased male to female ratio in newborns could be explained with the size of the sex chromosomes. The X chromosome contains &lt;a href=&quot;http://vega.sanger.ac.uk/Homo_sapiens/Info/Index&quot; rel=&quot;nofollow&quot;&gt;~155 million base pairs&lt;/a&gt;, whereas the Y chromosome contains &lt;a href=&quot;http://vega.sanger.ac.uk/Homo_sapiens/Info/Index&quot; rel=&quot;nofollow&quot;&gt;~58 million base pairs&lt;/a&gt;. Thus, the X chromosome is heavier than the Y chromosome, and a sperm cell carrying the 22 autosomal chromosomes +Y chromosome will swim faster and have a slightly higher chance of fertilizing the egg. This explanation is purely my speculation.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1093/humrep/13.5.1394&quot; rel=&quot;nofollow&quot;&gt;Trends in male:female ratio among newborn infants in 29 countries from five continents&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-09-17T02:31:09.877" LastActivityDate="2012-09-17T02:31:09.877" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="781" PostTypeId="1" AcceptedAnswerId="784" CreationDate="2012-01-23T20:32:45.950" Score="7" ViewCount="165" Body="&lt;p&gt;Is it possible to trace the descent of a person only using his/her genome sequence?&lt;/p&gt;&#xA;" OwnerUserId="382" LastEditorUserId="338" LastEditDate="2012-02-16T14:41:51.773" LastActivityDate="2021-05-20T11:20:41.157" Title="Is it possible to trace of the ancestry of a person by only using his/her genetic information?" Tags="&lt;genetics&gt;&lt;genomics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="782" PostTypeId="1" AcceptedAnswerId="818" CreationDate="2012-01-23T20:43:09.227" Score="22" ViewCount="1275" Body="&lt;p&gt;Today I wondered what the first organism to evolve vision would have been. I assume that it would have been kind of primitive and basic, but of course extremely innovative and eventually useful to a wide variety of beings. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also makes sense that the evolution of vision would have accompanied the evolution of advanced brain functions in almost every case. So, do biologists have any idea as to what the first species to use vision would have been? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(By vision, I mean having some organ on your body that receives photons and has some signaling pathway that converts photons into a biochemical set of signals)&lt;/p&gt;&#xA;" OwnerUserId="250" LastEditorUserId="57" LastEditDate="2012-08-01T00:44:08.497" LastActivityDate="2017-02-02T04:57:29.337" Title="When did vision evolve for the first time?" Tags="&lt;evolution&gt;&lt;neuroscience&gt;&lt;eyes&gt;&lt;vision&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="783" PostTypeId="2" ParentId="762" CreationDate="2012-01-23T21:00:17.527" Score="37" Body="&lt;p&gt;This question appears to address at least two distinct concepts:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;the &amp;quot;speed&amp;quot; of evolution&lt;/li&gt;&#xA;&lt;li&gt;whether there is some &amp;quot;end goal&amp;quot; that evolution seeks&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;I will provide an explanation of each separately below:&lt;/p&gt;&#xA;&lt;h2&gt;The Speed of Evolution&lt;/h2&gt;&#xA;&lt;p&gt;The speed at which a species evolves—that is, the speed at which it acquires new heritable characteristics—can be affected by numerous factors. Among the most obvious which come to mind are:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;existing population size&lt;/li&gt;&#xA;&lt;li&gt;reproductive cycle rate&lt;/li&gt;&#xA;&lt;li&gt;number of offspring&lt;/li&gt;&#xA;&lt;li&gt;offspring survival rate&lt;/li&gt;&#xA;&lt;li&gt;environmental demands&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;h3&gt;That said, have humans evolved &lt;em&gt;faster&lt;/em&gt; than other species?&lt;/h3&gt;&#xA;&lt;p&gt;On the whole, I do not feel that I could say without a doubt that humans have evolved significantly faster than other organisms. Considering the above factors (we have a slow reproductive cycle, few offspring, etc.), it seems unlikely but this is where a zoologist would know better. The answer provided by &lt;a href=&quot;https://biology.stackexchange.com/a/766&quot;&gt;bobthejoe&lt;/a&gt; may provide insight as well.&lt;/p&gt;&#xA;&lt;p&gt;I would just raise a word of caution before leaping to the conclusion that we have evolved rapidly without looking into it, because while we often study human evolution quite extensively in biology classes and thus are more &lt;em&gt;&lt;strong&gt;aware&lt;/strong&gt;&lt;/em&gt; of changes like upright walking and opposable thumbs and increased brain size, that doesn't mean other animals didn't evolve that much as well (we just don't learn about them in as much detail). Being a psychologist and not a zoologist, I do not have the knowledge to say with any surety that other species did not evolve in their own ways to the same magnitude as we have in the last 3-4 million years, so perhaps someone else can help you there.&lt;/p&gt;&#xA;&lt;p&gt;But you ask &lt;strong&gt;whether we have a particular part of our brain that no other animal has&lt;/strong&gt;; the answer to this is no, but the parts of our brains which we do share with animals are often much larger than as seen in those other species.&lt;/p&gt;&#xA;&lt;h2&gt;The &amp;quot;Goal&amp;quot; of evolution&lt;/h2&gt;&#xA;&lt;p&gt;I would like to point out here that human technology has nothing to do with evolution. Not only have all of our notable technological achievements occurred in the last couple hundreds years when human evolution was at its slowest (early human evolution as we know it today dates back &lt;em&gt;at least&lt;/em&gt; 5-7 million years, and it was during this several million year period when all the genetic evolution you speak of happened), I would argue that human spaceships and computers are no more sophisticated to us than a &lt;a href=&quot;http://www.sciencedaily.com/releases/2009/11/091120000437.htm&quot; rel=&quot;noreferrer&quot;&gt;mushroom garden&lt;/a&gt; and &lt;a href=&quot;http://myportfolio.usc.edu/kentarom/2010/09/termites_friend_or_foe.html&quot; rel=&quot;noreferrer&quot;&gt;ventilation system&lt;/a&gt; are to a termite. I could be wrong here but &lt;strong&gt;it seems as if you are under the impression that evolution is striving &lt;em&gt;towards&lt;/em&gt; something&lt;/strong&gt;... That humans are somehow intrinsically &lt;em&gt;better&lt;/em&gt; than lions or sharks or beetles. On the contrary, each of these creatures is not significantly more or less adapted to their environments as we are to our own, and in many ways these creatures possess features which are beyond our own.&lt;/p&gt;&#xA;&lt;p&gt;I shall leave you with one of my favorite quotes:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&amp;quot;We need a wiser and perhaps a more mystical concept of animals. We&#xA;patronize them for their incompleteness, for their tragic fate having&#xA;taken form so far below ourselves. And therein we err, and greatly&#xA;err. For the animal shall not be measured by man. In a world older and&#xA;more complete than ours, they move finished and complete, gifted with&#xA;extensions of the senses we have lost or never attained, living by&#xA;voices we shall never hear. They are not brethren, they are not&#xA;underlings. They are other nations caught with ourselves in the net of&#xA;life and time, fellow prisoners of the splendor and travail of the&#xA;earth.&amp;quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;–Henry Beston, in &lt;em&gt;The Outermost House&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;sub&gt;I don't have a dog in this fight, and I could very well be falsely assuming that you think this particular way when you in fact don't (you only wrote 4 lines after all, it's hard to glean much from that), but I wanted to make sure that these concepts were clear either way, particularly for any future visitors who might get the wrong impression. :)&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="397" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-01-23T21:00:17.527" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="784" PostTypeId="2" ParentId="781" CreationDate="2012-01-23T21:06:29.420" Score="8" Body="&lt;p&gt;In short, yes, it is possible. There are companies that sequence part of your genome and then can trace it back to your ancestors. All human family trees can be traced back to their African origin 200 000 years ago, but the companies that sequence your genes do not do that. For example, &lt;a href=&quot;https://www.23andme.com/&quot;&gt;23andMe&lt;/a&gt; sequences only 1 million of your base pairs (single nucleotide polymorphisms (SNPs)). They trace your most recent heritage, which could lead to Europe, Africa, or Asia. They can basically trace which part of your chromosomes (and thus your ancestry) came from your mom or your dad:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Unlike the sex chromosomes and the mitochondrial DNA, which are inherited as blocks, the 22 biparental chromosomes, known as autosomes, are scrambled during reproduction. Through a process known as recombination, each parent pulls his or her paired set of 22 autosomes into chunks, then reassembles a new single set using half the material from each pair. The two single sets of chromomes from each parent are combined into a new paired set when a sperm fertilizes an egg. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can read more about 23andMe &lt;a href=&quot;https://www.23andme.com/ancestry/&quot;&gt;here&lt;/a&gt;. There are other companies that are specialized in tracing your ancestry: &lt;a href=&quot;http://www.dnaancestryproject.com/index.php&quot;&gt;Genetic Genealogy&lt;/a&gt;, &lt;a href=&quot;http://www.dnatribes.com/?g-dt&amp;amp;gclid=CL7UkOaF560CFQWDhwodAhyzTQ&quot;&gt;DNA Tribes&lt;/a&gt;, and &lt;a href=&quot;http://www.heirlines.com/?gclid=CJTN34OG560CFQJjhwodRXqVjQ&quot;&gt;Heirlines&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-01-23T21:06:29.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="785" PostTypeId="1" AcceptedAnswerId="5678" CreationDate="2012-01-23T21:50:44.403" Score="14" ViewCount="5352" Body="&lt;p&gt;I am well aware of traditional anaerobic respiration (lactic acid or alcohol produced - no Krebs cycle) and traditional aerobic respiration (O&lt;sub&gt;2&lt;/sub&gt; is used at the end of the Citric acid cycle).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering how to classify respiration that uses the Citric acid cycle, but consumes a nitrite/ate or sulfite/ate instead of O&lt;sub&gt;2&lt;/sub&gt;. Is that anaerobic or aerobic?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OqFkj.jpg&quot; alt=&quot;NADH and Nitrite&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could only find this image on Google image search catch but it said it was from &lt;a href=&quot;http://lecturer.ukdw.ac.id/dhira/Metabolism/RespAnaer.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://lecturer.ukdw.ac.id/dhira/Metabolism/RespAnaer.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="28" LastEditDate="2012-01-23T23:10:35.603" LastActivityDate="2016-02-04T09:27:16.533" Title="Where is the line between Anaerobic and Aerobic?" Tags="&lt;cellular-respiration&gt;&lt;anaerobic-respiration&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="786" PostTypeId="2" ParentId="785" CreationDate="2012-01-23T22:31:11.357" Score="11" Body="&lt;p&gt;Anaerobic respiration is a respiration where the final electron acceptor is different than oxygen. The final acceptor can be a less oxidizing than oxygen, like sulfate (SO&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;2-&lt;/sup&gt;), nitrate (NO&lt;sup&gt;3-&lt;/sup&gt;), or sulfur (S). For example bacteria that use sulfate are obligate anaerobs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Krebs cycle cannot take place in the absence of oxygen, although oxygen is not directly involved in the cycle. The oxygen is required for the electron transport chain, which oxidized NADH and FADH&lt;sub&gt;2&lt;/sub&gt; back to NAD&lt;sup&gt;+&lt;/sup&gt; and FAD&lt;sup&gt;+&lt;/sup&gt;, which are involved in the four reduction reactions of the cycle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, aerobic respiration includes both Krebs cycle and final electron acceptor of oxygen, whereas anaerobic respiration does not.&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-01-23T22:58:23.437" LastActivityDate="2012-01-23T22:58:23.437" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="787" PostTypeId="2" ParentId="762" CreationDate="2012-01-23T22:45:34.167" Score="13" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;It seems to me that humans have, in a relatively short amount of time evolved from apes on the African plains to upright brainiacs with nukes, computers, and space travel.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The question covers changes of two sorts: biological evolution and cultural evolution.  The other answers speak to biological evolution, but I want to point out that much of the most striking changes (&quot;nukes, computers...&quot;) are due to the evolution of our culture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By 40,000 years ago most of our biological evolution to the present had happened (perhaps the most notable exception being changes related to our coevolution with disease organisms).  Yet although we had achieved upright brainiac-hood by the apparent evidence, we were not strikingly different from other large animals.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We had sharpened rocks and sticks, and made better use of the surroundings, particularly in non-food categories, than other animals.  We had been successful enough to spread throughout much of the old world.  Nevertheless, the overall contrast with other animals seems rather muted when viewed by the differences with the modern world.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the visible changes since then are due to evolution happening outside our genes and bodies in what can be called culture.  Other animals have culture but our nature gives us many times the cultural capability.  We build upon the culture we find ourselves in and make it more effective.  The cultural presevation and advances come not just from aping ('monkey see, monkey do'), but from language, and from mechanisms of cultural distribution and preservation, most notably from the invention of written language.  These things have driven the cultural evolution of the largest visible changes, those of the last few millenia. &lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2012-01-23T22:45:34.167" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="788" PostTypeId="1" AcceptedAnswerId="1562" CreationDate="2012-01-23T23:22:56.607" Score="12" ViewCount="878" Body="&lt;p&gt;From &lt;a href=&quot;http://dx.doi.org/10.1016/j.tics.2010.01.008&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Raichle ME&lt;/strong&gt;. 2010. Two views of brain function. Trends in cognitive sciences 14: 180–90&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Alzheimer’s disease (AD) is the most common cause of progressive&#xA;  cognitive decline and dementia in adults. While the amyloid cascade&#xA;  hypothesis of AD posits an initiating role for the β-amyloid (Aβ)&#xA;  protein, there is limited understanding of why Aβ is deposited. &lt;strong&gt;A&#xA;  growing body of evidence based on in vitro, animal studies and human&#xA;  imaging work suggests that synaptic activity increases Aβ, which is&#xA;  deposited preferentially in multimodal brain regions that show&#xA;  continuous levels of heightened activation and plasticity across the&#xA;  lifespan&lt;/strong&gt;. Imaging studies of people with genetic predispositions to AD&#xA;  are consistent with these findings, suggesting a mechanism whereby&#xA;  neural efficiency or cognitive reserve may diminish Aβ deposition. The&#xA;  aggregated findings unify observations from cellular and molecular&#xA;  studies with human cognitive neuroscience to reveal potential&#xA;  mechanisms of AD development.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="103" LastEditorUserId="836" LastEditDate="2012-09-13T21:23:07.443" LastActivityDate="2012-09-13T21:23:07.443" Title="Could an &quot;overactive&quot; brain increase the chances of Alzheimer's Disease?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="789" PostTypeId="1" AcceptedAnswerId="791" CreationDate="2012-01-23T23:44:46.600" Score="13" ViewCount="946" Body="&lt;p&gt;I wonder whether there is any intelligent decision-making in mitochondria in the timing of their operation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do they simply begin ATP production as soon as the correct reactants are present?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or, because they have their own DNA, do they have more complex strategies that vary to benefit the mutual cooperation with the host cell? This assumes that the simple circular DNA is performing higher level decisions in switching.&lt;/p&gt;&#xA;" OwnerUserId="400" LastEditorUserId="69" LastEditDate="2012-01-24T19:54:18.890" LastActivityDate="2012-01-24T19:54:18.890" Title="Do mitochondria simply automatically convert glucose to ATP?" Tags="&lt;dna&gt;&lt;cellular-respiration&gt;&lt;mitochondria&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="790" PostTypeId="2" ParentId="789" CreationDate="2012-01-24T01:25:25.330" Score="6" Body="&lt;p&gt;The &lt;a href=&quot;http://www.wiley.com/legacy/college/boyer/0470003790/structure/pfk/pfk_intro.htm&quot;&gt;textbook&lt;/a&gt; version for the regulation of ATP involves a feedback loop with phosphofructokinase (PFK). The relative concentrations of ADP and ATP are characteristic of the energy state of the cell. If the cell is using energy, then there will be an excess of ADP. If not, then ATP. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ATP is an inhibitor of PFK, which in turn slows glycolysis (thus reducing the production of new ATP). In contrast, ADP is an allosteric activator of PFK, which in turn speeds up glycolysis (thus increasing the production of ATP).&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-01-24T01:25:25.330" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="791" PostTypeId="2" ParentId="789" CreationDate="2012-01-24T02:51:36.270" Score="12" Body="&lt;p&gt;Mitochondria are comprised of ~3000 proteins. However, the mitochondrial genome has only 13-14 protein-encoding genes. The remaining 99.6% of mitochondrial proteins are encoded by genes in the nuclear genome. (&lt;a href=&quot;http://en.wikipedia.org/wiki/Human_mitochondrial_genetics&quot;&gt;Wikipedia&lt;/a&gt;) Chloroplast genomes are only slightly larger (~100 genes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gene regulation and signaling between the nucleus and mitochondria (and between nucleus &amp;amp; chloroplast in plants/algae) occurs in both directions. &lt;strong&gt;Anterograde regulation&lt;/strong&gt; is the signalling from nucleus to mitochondria and was once thought to be the only method of regulating organelle function. We now also know that &lt;strong&gt;Retrograde regulation&lt;/strong&gt; occurs, in which the mitochondria sends signals to the nucleus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question directly (but not thoroughly), both the mitochondria and the nucleus are sensing the environment and needs of the cell and signaling to each other to regulate ATP production.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to learn more about retrograde signaling, &lt;a href=&quot;http://www.google.com/webhp?hl=en#sclient=psy-ab&amp;amp;hl=en&amp;amp;site=webhp&amp;amp;source=hp&amp;amp;q=retrograde%20regulation&amp;amp;pbx=1&amp;amp;oq=retrograde%20regulation&amp;amp;aq=f&amp;amp;aqi=g1g-sv1g-v1g-sv1&amp;amp;aql=&amp;amp;gs_sm=e&amp;amp;gs_upl=1663l5874l0l6628l21l16l0l3l3l2l928l5392l0.1.6.4.2.1.1l17l0&amp;amp;bav=on.2,or.r_gc.r_pw.,cf.osb&amp;amp;fp=90c1eb6c7005c121&amp;amp;biw=1272&amp;amp;bih=638&amp;amp;safe=active&quot;&gt;googling &quot;retrograde regulation&quot;&lt;/a&gt; will bring up lots of papers on this topic in different organisms. &lt;a href=&quot;http://www.biology.buffalo.edu/courses/bio402/Cullen_Visuals/Paper3.pdf&quot;&gt;This paper&lt;/a&gt; also has some diagrams of signalling pathways. &lt;/p&gt;&#xA;" OwnerUserId="204" LastEditorUserId="204" LastEditDate="2012-01-24T18:56:16.200" LastActivityDate="2012-01-24T18:56:16.200" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="792" PostTypeId="2" ParentId="761" CreationDate="2012-01-24T03:02:24.227" Score="13" Body="&lt;p&gt;It seems not much is known about how insects induce gall formation (perhaps someone with more of an entomology can jump in). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But we do know quite a bit about &lt;em&gt;Agrobacterium tumefaciens&lt;/em&gt;, which causes crown gall in roses, grapes, and other plants. &lt;em&gt;Agrobacterium&lt;/em&gt; invades cell tissue and inserts a piece of it's own DNA into the plant cell. The plant cells incorporates the DNA into its genome and begins expressing a number of new genes, including genes that lead to an over production of the plant hormones &lt;strong&gt;auxin&lt;/strong&gt; and &lt;strong&gt;cytokinin&lt;/strong&gt;.  These hormones cause the undifferentiation of the plant cell and uncontrolled cell division, leading to the formation of a tumor-like gall. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More on &lt;a href=&quot;http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens&quot;&gt;&lt;em&gt;Agrobacterium&lt;/em&gt; at Wikipedia&lt;/a&gt;. I can recommend some journal articles if you're interested. &lt;/p&gt;&#xA;" OwnerUserId="204" LastEditorUserId="107" LastEditDate="2012-01-24T03:34:45.920" LastActivityDate="2012-01-24T03:34:45.920" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="793" PostTypeId="1" CreationDate="2012-01-24T13:35:10.087" Score="15" ViewCount="654" Body="&lt;p&gt;I have a question I would like to pose to the community. I have recently received access to a bench-top ion torrent DNA sequencer. Our idea is to use this machine to sequence the DNA from patient’s tumors in order to guide treatment options. My job is to identify a list of all currently used anti-neoplastic drugs along with their known targets (i.e., specific genes and mutations) and accession numbers. I would like to put these data in a table in which each row corresponds to a different drug.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, a row in the table might read (column names are indicated in brackets): [disease] breast cancer, [drug] trastuzumab, [drug target] HER2/neu receptor, [gene] ERBB2, [location] chr17:37844393-37884915, [mutation type] amplification, [accession number] ENSG00000141736. The pathologists would then be able to use this database in order to select appropriate genes for sequencing whenever they receive a tumor specimen. If the patient’s tumor had an amplified ERBB2 gene, they could be given trastuzumab.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Currently our study is in pre-planning stages (i.e., we won’t actually be testing this on patients any time soon). I would appreciate it if anyone could give me on advice on how to go about creating such a database. I am aware of online databases including COSMIC, Sanger's Cancer Gene Census, and the Potential Drug Target Database (PDTD), but they don’t have everything that I’m looking for. I am familiar with R and could use it to combine data from multiple sources if necessary. If anyone else has comments or suggestions for further reading that would also be appreciated. Thanks!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: This question has also been posed on a Research Gate forum: &lt;a href=&quot;http://www.researchgate.net/topic/Cancer_Biology/post/Looking_for_a_cancer_drug_target_database_to_guide_sequencing_of_patient_tumor_DNA&quot;&gt;http://www.researchgate.net/topic/Cancer_Biology/post/Looking_for_a_cancer_drug_target_database_to_guide_sequencing_of_patient_tumor_DNA&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="403" LastActivityDate="2015-05-28T14:41:59.510" Title="Looking for a cancer drug target database to guide sequencing of patient tumor DNA" Tags="&lt;pharmacology&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;cancer&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="794" PostTypeId="1" AcceptedAnswerId="795" CreationDate="2012-01-24T14:31:41.007" Score="5" ViewCount="461" Body="&lt;p&gt;Mitochondria have their own DNA and appear to be loosely connected to the nucleus and it role. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why are the functions of mitochondria not in the nucleus? Why doesn't the nucleus control the mitochondria's functions as it controls regulation for other chemical reactions? &#xA;Are there evolutionary/competitive benefits for this separation?&lt;/p&gt;&#xA;" OwnerUserId="400" LastActivityDate="2012-01-24T15:55:48.700" Title="What is the benefit for cells having the ATP production regulated in mitochondria compared to being from the nucleus?" Tags="&lt;evolution&gt;&lt;dna&gt;&lt;cellular-respiration&gt;&lt;mitochondria&gt;&lt;eukaryotic-cells&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="795" PostTypeId="2" ParentId="794" CreationDate="2012-01-24T15:55:48.700" Score="5" Body="&lt;p&gt;For starters, see &lt;a href=&quot;https://biology.stackexchange.com/questions/11/how-many-times-did-endosymbiosis-occur&quot;&gt;this thread&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding is that the ancient predecessors of mitochondria were free-living unicellular organisms. Supposedly at one point, these mitochondria-like cells developed an endosymbiotic relationship with a larger cell. This relationship was advantageous for both cells: the smaller cell could focus on energy production, leaving tasks like homeostasis, nutrient collection, etc, to the larger cell. Over evolutionary time, this endosymbiosis caused the smaller cell to lose all functions unrelated to energy production, while the larger cell (as we now know it) came to rely heavily on the mitochondria for energy production.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it's possible that at one time the nucleus encoded machinery for ATP production, but apparently the modularity and separation of function provided by this ancient symbiosis turned out to be successful.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2012-01-24T15:55:48.700" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="796" PostTypeId="2" ParentId="788" CreationDate="2012-01-24T19:22:54.213" Score="3" Body="&lt;p&gt;Just out today: looks like it's exactly the other way around.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://healthland.time.com/2012/01/24/use-it-or-lose-it-keeping-brain-active-may-help-ward-off-alzheimers/&quot; rel=&quot;nofollow&quot;&gt;http://healthland.time.com/2012/01/24/use-it-or-lose-it-keeping-brain-active-may-help-ward-off-alzheimers/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.reuters.com/article/2012/01/24/us-alzheimers-protein-idUSTRE80N1EU20120124&quot; rel=&quot;nofollow&quot;&gt;http://www.reuters.com/article/2012/01/24/us-alzheimers-protein-idUSTRE80N1EU20120124&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://archneur.ama-assn.org/cgi/content/abstract/archneurol.2011.2748&quot; rel=&quot;nofollow&quot;&gt;http://archneur.ama-assn.org/cgi/content/abstract/archneurol.2011.2748&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="177" LastActivityDate="2012-01-24T19:22:54.213" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="797" PostTypeId="1" AcceptedAnswerId="799" CreationDate="2012-01-24T19:55:10.020" Score="13" ViewCount="565" Body="&lt;p&gt;I have just started reading up on structure-based methods for drug design (this is completely not my field so apologies for stupid questions that will be coming along!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clearly, some drugs are designed to target the central nervous system. However, I understand that the extracellular fluid of the central nervous system is separated from the blood by the &quot;blood-brain barrier&quot; which restricts the passage of large molecules between the two systems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is : how do you design a drug to be delivered to the CNS?&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="231" LastEditDate="2015-08-03T19:35:45.130" LastActivityDate="2015-08-03T19:35:45.130" Title="How do you design a drug to be delivered to the CNS?" Tags="&lt;pharmacology&gt;&lt;blood-brain-barrier&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="798" PostTypeId="1" AcceptedAnswerId="3583" CreationDate="2012-01-24T20:19:28.307" Score="9" ViewCount="9358" Body="&lt;p&gt;Here's the proximate physical implication of the ratio (from the Wikipedia article on NADH).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The balance between the oxidized and reduced forms of nicotinamide&#xA;  adenine dinucleotide is called the NAD+/NADH ratio. This ratio is an&#xA;  important component of what is called the redox state of a cell, a&#xA;  measurement that reflects both the metabolic activities and the health&#xA;  of cells. The effects of the NAD+/NADH ratio are complex,&#xA;  controlling the activity of several key enzymes, including&#xA;  glyceraldehyde 3-phosphate dehydrogenase and pyruvate dehydrogenase.&#xA;  In healthy mammalian tissues, estimates of the ratio between free NAD+&#xA;  and NADH in the cytoplasm typically lie around 700; the ratio is thus&#xA;  favourable for oxidative reactions. The ratio of total&#xA;  NAD+/NADH is much lower, with estimates ranging from 0.05 to 4. In&#xA;  contrast, the NADP+/NADPH ratio is normally about 0.005, so NADPH is&#xA;  the dominant form of this coenzyme. These different ratios are key&#xA;  to the different metabolic roles of NADH and NADPH.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So here's my question: how does this manifest in vertebrate aging? Is it something that's simply the resultant of other aging processes, or can the ratio also contribute to aging in a certain way?&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="107" LastEditDate="2012-01-26T16:02:42.347" LastActivityDate="2012-10-11T12:39:48.580" Title="How does the NAD+/NADH ratio affect lifespan in vertebrates?" Tags="&lt;senescence&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="799" PostTypeId="2" ParentId="797" CreationDate="2012-01-24T20:41:35.933" Score="10" Body="&lt;p&gt;In a nutshell: in order to pass through the blood-brain barrier (BBB) the substance has to mimick soee properties of the substances that are allowed to pass through. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are different types of &quot;transporters&quot; -- integral proteins going through the cell membranes and accounting for the active transport of the substances they can actively bind to. Smaller molecules of drugs can use solute carrier transporter (SLC), whereas bigger molecules (oligo- and polymeres) would use the receptor-mediated transporter (RMT).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is &lt;a href=&quot;http://www.sciencedaily.com/releases/2009/02/090205174546.htm&quot;&gt;a nice article&lt;/a&gt; on this topic published by ScienceDaily.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One technology for enabling active transport of small molecule drugs&#xA;  across the BBB involves targeting endogenous nutrient transporters.&#xA;  These transporters are members of the solute carrier (SLC) transporter&#xA;  superfamily. Transport of small molecules across the BBB by these&#xA;  membrane proteins is known as carrier-mediated transport (CMT).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In order to design drugs that utilize CMT to cross the BBB,&#xA;  researchers modify their chemical structures so that they resemble&#xA;  nutrients that are transported across the BBB by specific SLCs. The&#xA;  prototypical drug that uses this strategy (which was developed long&#xA;  before mechanisms of CMT were known) is L-DOPA, the major current drug&#xA;  for Parkinson's disease. L-DOPA is used to replace dopamine that is&#xA;  lost due to degeneration of dopaminergic neurons in the substantia&#xA;  nigra of the brain.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Another major system that is used in normal mammalian physiology to&#xA;  enable needed molecules to cross the BBB is receptor-mediated&#xA;  transport (RMT). The brain uses RMT to transport proteins, peptides,&#xA;  and lipoproteins that are needed for brain function across the BBB.&#xA;  Examples of biomolecules that are transported into the brain via RMT&#xA;  include insulin, insulin-like growth factor (IGF), leptin,&#xA;  transferrin, and low-density lipoprotein (LDL).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In RMT, molecules in the circulation may bind to specific receptors on&#xA;  the luminal surface of brain capillaries (i.e., the surface that&#xA;  interfaces with the bloodstream). Upon binding, the receptor-ligand&#xA;  complex is internalized into the endothelial cell by a process called&#xA;  receptor-mediated endocytosis. The ligand may then be transported&#xA;  across the abluminal membrane of the endothelial cell (i.e., the&#xA;  membrane that interfaces with brain tissue) into the brain. This whole&#xA;  process is called receptor-mediated transcytosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-01-24T20:41:35.933" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="800" PostTypeId="1" AcceptedAnswerId="804" CreationDate="2012-01-24T20:57:00.247" Score="9" ViewCount="2403" Body="&lt;p&gt;I understand what the enzyme ATP synthase does, but I'm not exactly sure &lt;em&gt;how&lt;/em&gt; it does it. I've heard that it uses rotary catalysis, but how exactly does this work? How is the energy from the H+ ion harnessed, turned into mechanical energy, and then finally into the chemical energy stored in ATP? Why does the spinning of parts of the enzyme need to occur for this to happen?&lt;/p&gt;&#xA;" OwnerUserId="62" LastActivityDate="2012-01-27T00:00:11.357" Title="How does the enzyme ATP Synthase use a proton concentration gradient to make ATP?" Tags="&lt;proteins&gt;&lt;enzymes&gt;&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="801" PostTypeId="1" CreationDate="2012-01-24T21:20:43.050" Score="28" ViewCount="175975" Body="&lt;p&gt;I know NADH is used in cellular respiration and NADPH is used in photosynthesis. What difference does the phosphate group make that the same one isn't or can't be used for both? Is there a greater reason for this separation or is it just coincidental? Why can't the two be interchanged?&lt;/p&gt;&#xA;" OwnerUserId="62" LastActivityDate="2014-10-15T18:31:40.900" Title="NADH vs. NADPH: Where is each one used and why that instead of the other?" Tags="&lt;biochemistry&gt;&lt;cellular-respiration&gt;&lt;photosynthesis&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="802" PostTypeId="1" AcceptedAnswerId="805" CreationDate="2012-01-25T00:00:42.320" Score="3" ViewCount="472" Body="&lt;p&gt;I can modify the colors of carbons in Coot under &lt;strong&gt;Edit&lt;/strong&gt;, &lt;strong&gt;Bond Colours...&lt;/strong&gt;, but that only gives me different hues.  Is there a way to change the color to something less-saturated (or perhaps slightly transparent) so I can identify the &quot;active&quot; molecule I'm working on versus a template?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The menus seem no help, I'm wondering if there's some scripting magic that can do this.&lt;/p&gt;&#xA;" OwnerUserId="25" LastEditorUserId="25" LastEditDate="2012-02-02T21:20:02.123" LastActivityDate="2012-02-02T21:20:02.123" Title="How do I change bond colors to something besides a different hue in Coot?" Tags="&lt;structural-biology&gt;&lt;coot&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="803" PostTypeId="2" ParentId="782" CreationDate="2012-01-25T01:01:34.707" Score="16" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;To me, it also makes sense that the evolution of sight would have accompanied the evolution of advanced brain functions in almost every case.&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not necessarily! For instance, think of &lt;a href=&quot;http://en.wikipedia.org/wiki/Phototropism&quot; rel=&quot;nofollow noreferrer&quot;&gt;phototropism&lt;/a&gt;: the plant detects the presence of light and uses it to grow towards the light, but that's a very simple process regulated by auxins. Or the &lt;a href=&quot;http://en.wikipedia.org/wiki/Phototaxis&quot; rel=&quot;nofollow noreferrer&quot;&gt;light-sensitivity (phototaxis)&lt;/a&gt; shown by &lt;a href=&quot;http://en.wikipedia.org/wiki/Euglena&quot; rel=&quot;nofollow noreferrer&quot;&gt;Euglena&lt;/a&gt;, a single-celled protist, which reorients its entire body towards a light source. Really simple vision (is there a light, and if so, where is it?) can help organisms absorb more energy than rivals, giving them an evolutionary advantage.&lt;/p&gt;&#xA;" OwnerUserId="87" LastEditorUserId="4880" LastEditDate="2017-02-01T21:02:53.037" LastActivityDate="2017-02-01T21:02:53.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="804" PostTypeId="2" ParentId="800" CreationDate="2012-01-25T07:47:03.777" Score="10" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uOcQo.png&quot; alt=&quot;ATP Synthase&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Image from wikipedia page on ATP synthase&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In brief, the addition and release of protons to the structure cause a conformational change that leads to another conformational change.  This series of conformational changes occurs in such a way that it induces a rotational motion.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rotation of the central axel that extends through both hemispheres of this large complex is driven by the proton gradient.  Specific residues in the c12 ring are protonated in order to drive this rotation.  A high concentration of protons (in this picture the high concentration is found &lt;em&gt;above&lt;/em&gt; the complex) allows each of the subunits in the membrane to be constantly loaded with H&lt;sup&gt;+&lt;/sup&gt; ammunition, ready to fire when it comes to be their turn.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The function of this axel is to slightly but significantly change the shape of one subunit at at a time in the red part.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Changing the conformation of subunits in the red part is what allows for the three steps in ATP synthesis to occur: binding of ADP and P&lt;sub&gt;i&lt;/sub&gt;, catalysis of the formation of ATP, and release of ATP. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of these changes occur at the molecular level.  The proton forms a bond with a single amino acid of the entire protein complex, but this is sufficient to cause a difference in the most stable 3-dimensional structure of the whole.  This could cause either a cascade of changes that result in a net rotation or it could cause a re-stabilization of the structure due to electrostatic forces.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Vinit K. Rastogi &amp;amp; Mark E. Girvin in their 1999 Nature paper on the subject, it's more like the former: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Earlier models proposed simple rotational diffusion of a rigid c12 ring, possibly driven by electrostatic forces. The structural data on protonation-linked conformational changes in subunit c indicate that the process may be more mechanical, with local rotations within subunit c driving larger-scale rotations of the c12 oligomer as a whole, in a `wheels within wheels' type of mechanism. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://dx.doi.org/10.1038/46224&quot; rel=&quot;noreferrer&quot;&gt;whole paper's&lt;/a&gt; a good read.  But this is as current as I am on the topic, and it's likely that a more detailed mechanism has been determined for the action of ATP synthase since 1999.&lt;/p&gt;&#xA;" OwnerUserId="184" LastEditorUserId="184" LastEditDate="2012-01-27T00:00:11.357" LastActivityDate="2012-01-27T00:00:11.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="805" PostTypeId="2" ParentId="802" CreationDate="2012-01-25T08:29:47.077" Score="5" Body="&lt;p&gt;You could try other visual differences, like make what you're interested in ball-and-stick, and everything else wireframe, like in this example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Qlfqt.png&quot; alt=&quot;like on this example&quot;&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;.... Because, from: &lt;a href=&quot;http://www.ysbl.york.ac.uk/~lohkamp/coot/doc/coot-python.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ysbl.york.ac.uk/~lohkamp/coot/doc/coot-python.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;procedure: hilight_binding_site (imol, centre_residue_spec,&#xA;  hilight_colour, radius): hilight-colour is specified in degrees (round&#xA;  the colour wheel - starting at yellow (e.g. 230 is purple))&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It looks from this like you only get to choose Hue (color_map_rotation) and not Saturation or Lightness, even with the script interface.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, &lt;a href=&quot;http://biop.ox.ac.uk/coot/doc/coot-reference-manual.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;text can be full RGB&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;3.28.3 (set-font-colour red green blue)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;where:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;red is an inexact number green is an inexact number blue is an inexact&#xA;  number&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="184" LastActivityDate="2012-01-25T08:29:47.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="806" PostTypeId="2" ParentId="801" CreationDate="2012-01-25T09:05:40.793" Score="36" Body="&lt;p&gt;The phosphate group in NADPH doesn't affect the redox abilities of the molecule, it is too far away from the part of the molecule involved in the electron transfer. What the phosphate group does is to allow enzymes to discriminate between NADH and NADPH, which allows the cell to regulate both independently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ratio of NAD&lt;sup&gt;+&lt;/sup&gt; to NADH inside the cell is high, while the ratio of NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH is kept low. The role of NADPH is mostly anabolic reactions, where NADPH is needed as a reducing agent, the role of NADH is mostly in catabolic reactions, where NAD&lt;sup&gt;+&lt;/sup&gt; is needed as a oxidizing agent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You'll find some more information about this in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26838/#A273&quot;&gt;chapter 2 of &quot;Molecular Biology of the Cell by Alberts et al.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2012-01-25T09:05:40.793" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="807" PostTypeId="2" ParentId="753" CreationDate="2012-01-25T12:34:52.357" Score="9" Body="&lt;p&gt;Quick search - Some articles that may interest you:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Random walk model of insect movements&#xA;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.springerlink.com/content/m525270k7647u074/&quot;&gt;Kareiva P. M., Shigesada N. (1983). Analyzing insect movement as a correlated random walk. Oecologia 56(2-3) 234-238&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Artificial life model of flying insects and its comparison to real insects navigation strategies.&#xA;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0960982201004183&quot;&gt;Dale K., Collett T. C. (2001). Using artificial evolution and selection to model insect navigation. Current Biology 11(17) 1305–1316&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) The last one is not about insects, but it's a trial to practical usage of the mathematical analisys of invertebrate movements.&#xA;&lt;br&gt;&#xA;&lt;a href=&quot;http://dx.doi.org/10.1002/tox.10077&quot;&gt;Shimizu N. et al. (2002). Fractal analysis of Daphnia motion for acute toxicity bioassay. Environmental Toxicology 17(5) 441–448&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="68" LastEditorUserId="81" LastEditDate="2012-01-25T19:49:41.437" LastActivityDate="2012-01-25T19:49:41.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="808" PostTypeId="2" ParentId="768" CreationDate="2012-01-25T17:00:37.730" Score="6" Body="&lt;p&gt;there is some evidence that the female reproductive system may also do some gender based selection and skew the chances of one or another outcome depending upon environment, if I recall the snake work correctly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found a recent (2002?) review: &lt;a href=&quot;http://dx.doi.org/10.1038/sj.hdy.6800018&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;West SA, Reece SE, Sheldon BC&lt;/strong&gt;. 2002. Sex ratios. Heredity 88: 117–24.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Furthermore, in some of these cases individuals appear to show&#xA;  extremely precise control of their offspring sex ratio. For example:&#xA;  (a) in the Seychelles warbler (described above), females vary the sex&#xA;  ratio of their offspring from 90% female to 80% male depending upon&#xA;  environmental conditions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It isn't so easily predictable what the outcome is for a given environmental set of conditions.  To me it is not surprising since sperm competition and selection in the oviducts is common to nearly all animals.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="836" LastEditDate="2012-09-13T21:23:33.793" LastActivityDate="2012-09-13T21:23:33.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="809" PostTypeId="1" AcceptedAnswerId="819" CreationDate="2012-01-25T18:16:28.277" Score="13" ViewCount="4361" Body="&lt;p&gt;I have heard and read about Peter's rule informally in the past, but never saw a formal definition or description. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Informally I have learned to understand Peter's rule as the assumed correlation between the amount of overlap between axons and dendrites and the post synaptic density in the synapse. Here is &lt;a href=&quot;https://www.google.com/#sclient=psy-ab&amp;amp;q=%22peter%27s+rule%22+neuroscience&quot;&gt;a sample&lt;/a&gt; of the search results in Google.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is my interpretation correct? Is there a more rigorous, perhaps quantitative,  definition of Peter's rule? &lt;/p&gt;&#xA;" OwnerUserId="17" LastEditorUserId="107" LastEditDate="2012-01-25T22:08:49.083" LastActivityDate="2013-04-22T16:14:40.330" Title="What is Peter's rule in neuroscience?" Tags="&lt;neuroscience&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="810" PostTypeId="5" CreationDate="2012-01-25T19:00:37.473" Score="0" Body="" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-25T19:00:37.473" LastActivityDate="2012-01-25T19:00:37.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="811" PostTypeId="4" CreationDate="2012-01-25T19:00:37.473" Score="0" Body="The process in which energy is liberated from organic molecules producing ATP." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T00:55:17.570" LastActivityDate="2013-10-31T00:55:17.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="812" PostTypeId="5" CreationDate="2012-01-25T19:12:18.483" Score="0" Body="" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-01-25T19:12:18.483" LastActivityDate="2012-01-25T19:12:18.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="813" PostTypeId="4" CreationDate="2012-01-25T19:12:18.483" Score="0" Body="A series of DNA bases in a chromosome that codes for a polypeptide protein, considered a unit of heredity. " OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T01:07:38.670" LastActivityDate="2013-10-31T01:07:38.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="814" PostTypeId="5" CreationDate="2012-01-25T19:13:16.610" Score="0" Body="&lt;p&gt;Endocrinology is the study of the various hormones and their actions and disorders. Many organ systems may secrete and/or responds to hormones (e.g., the brain, lungs, heart, intestine, skin and the kidney), the clinical specialty of endocrinology focuses primarily on the endocrine organs, namely those organs whose primary function is hormone secretion. These organs include the pituitary, thyroid, adrenals, ovaries, testes, and pancreas.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;See also:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&amp;amp;rid=endocrin.TOC&amp;amp;depth=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;British online textbook&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.endotext.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;American online textbook&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&amp;amp;term=Endocrinology&quot; rel=&quot;nofollow noreferrer&quot;&gt;US national library of Medicine Medical Subject Headings (MeSH)&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.hormone.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Hormone Foundation&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="69" LastEditorUserId="9943" LastEditDate="2017-04-13T18:38:57.130" LastActivityDate="2017-04-13T18:38:57.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="815" PostTypeId="4" CreationDate="2012-01-25T19:13:16.610" Score="0" Body="The area of physiology dealing with the production and effects of hormones." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-29T20:51:17.680" LastActivityDate="2013-10-29T20:51:17.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="816" PostTypeId="5" CreationDate="2012-01-25T19:15:05.327" Score="0" Body="&lt;p&gt;Questions about the biology of the heart, blood, and blood vessels. Medical advice questions are off topic, but biology of medicine related to the cardiovascular system may be on topic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also: &lt;a href=&quot;/questions/tagged/hematology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;hematology&amp;#39;&quot; rel=&quot;tag&quot;&gt;hematology&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="16866" LastEditDate="2019-08-25T03:53:23.340" LastActivityDate="2019-08-25T03:53:23.340" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="817" PostTypeId="4" CreationDate="2012-01-25T19:15:05.327" Score="0" Body="The study of the physiology and pathology of the heart and the cardiovascular system." OwnerUserId="69" LastEditorUserId="1590" LastEditDate="2016-03-23T08:58:04.323" LastActivityDate="2016-03-23T08:58:04.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="818" PostTypeId="2" ParentId="782" CreationDate="2012-01-25T19:15:48.430" Score="14" Body="&lt;p&gt;I'll address the question in the title &quot;At which time did sight evolve for the first time?&quot; by assuming that by the evolution of vision, we mean the evolution of the eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Molluscs are an excellent phylum to investigate this question because they exhibit a wide range of eye designs and levels of complexity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the most basic level, limpets such as &lt;em&gt;Patella&lt;/em&gt; exhibit small patches of &lt;strong&gt;photoreceptor&lt;/strong&gt; cells lying in a relatively flat configuration. Slightly more advanced is &lt;em&gt;Pleurotomaria&lt;/em&gt; which has photoreceptors and pigmentation cells held in an &lt;strong&gt;eyecup&lt;/strong&gt;. We then have the &lt;strong&gt;pinhole camera&lt;/strong&gt; style eye as seen in &lt;em&gt;Nautilus&lt;/em&gt; (&lt;a href=&quot;https://biology.stackexchange.com/questions/304/what-is-the-most-difficult-feature-to-explain-evolutionarily/312#312&quot;&gt;see this post&lt;/a&gt;), and more complex eyes with a cornea, retina, and lense such as those seen in squid (e.g. &lt;em&gt;Loligo&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that &quot;a patch of photoreceptors&quot; in an animal counts as an eye, then we should probably looking for marine invertebrates. The problem here is that if they had only soft body parts we might struggle to identify the oldest examples in sediments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One candidate for the &quot;earliest eye&quot; might be &lt;strong&gt;urbilatarians&lt;/strong&gt; - the hypothesized last common ancestor of the clade bilatarians - which probably evolved at the end of the Ediacaran period (~555 Myr). An example would be &lt;em&gt;Kimberella&lt;/em&gt; (described &lt;a href=&quot;http://palaeontology.palass-pubs.org/pdf/Vol%209/Pages%20599-628.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;) which might or might not have been a mollusc and might or might not have had photoreceptors!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/k8LEq.jpg&quot; alt=&quot;*Kimberella quadrata* fossil&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(credit : wikipedia)&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2012-01-27T00:07:19.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="819" PostTypeId="2" ParentId="809" CreationDate="2012-01-25T22:32:28.860" Score="7" Body="&lt;p&gt;I think that your interpretation is correct, although &lt;em&gt;Principles of Neural Science&lt;/em&gt; (Kandel et al.) doesn't mention Peter's rule (which is where I would have hoped to find a simple explanation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.neuro.cjb.net/content/24/39/8441.full&quot;&gt;Binzegger et al. (2004)&lt;/a&gt;, the idea behind Peter's rule dates back to Peters and Feldman (1976) and Peters and Payne (1993), though the Rule per se may have been coined by Braitenberg and Schultz (1991; at which point it was still called Peters' rule). Binzegger et al. describe it as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;They assumed that axons simply connect in direct proportion to the&#xA;  occurrence of all synaptic targets in the neuropil. The rule can be&#xA;  extended to provide more precise estimates by taking into account the&#xA;  detailed morphometrics of the dendritic and axonal trees of the&#xA;  different neuronal types.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To paraphrase Binzegger et al., in the simplest form of Peter's rule, the number of synapses in a cortical layer are evenly distributed across the potential target neurons. So there would be a direct proportionality between synapses and targets.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second sentence of the quote above is the meat of the Binzegger paper. They also present a mathematical model of a more complex and realistic variation of Peter's rule which takes into account different types of postsynaptic neurons and the fact that not all cells receive synapses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Braitenberg V, Schüz A (1991) Peters' Rule and White's Exceptions. In: &lt;em&gt;Anatomy of the Cortex&lt;/em&gt;, pp 109–112. Berlin: Springer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Peters A, Feldman ML (1976) The projection of the lateral geniculate nucleus to area 17 of the rat cerebral cortex. I. General description. &lt;em&gt;J Neurocytol&lt;/em&gt; 5:63–84.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Peters A, Payne BR (1993) Numerical relationships between geniculocortical afferents and pyramidal cell modules in cat primary visual cortex. &lt;em&gt;Cereb Cortex&lt;/em&gt; 3:69–78.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-01-25T22:32:28.860" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="820" PostTypeId="1" CreationDate="2012-01-26T03:00:17.430" Score="10" ViewCount="1465" Body="&lt;p&gt;All the sources I've read said that &lt;em&gt;Naegleria fowleri&lt;/em&gt; enters the brain through the nose. But lets say that someone had cuts on their arm or leg and they are swimming in water that is conducive to &lt;em&gt;Naegleria fowleri&lt;/em&gt; growth. Could it enter the cut into the bloodstream and then into the brain or cause some other type of damage if it enters the bloodstream? &lt;/p&gt;&#xA;" OwnerUserId="407" LastEditorUserId="107" LastEditDate="2012-01-26T16:03:50.427" LastActivityDate="2012-03-23T20:50:39.967" Title="Can Naegleria fowleri enter through wounds into the bloodstream?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;parasitism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="821" PostTypeId="1" CreationDate="2012-01-26T09:18:35.307" Score="9" ViewCount="1758" Body="&lt;p&gt;What is the evolution of hairs? Did they evolve from scales?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="16866" LastEditDate="2017-01-03T15:58:05.717" LastActivityDate="2017-01-03T15:58:05.717" Title="Did human hairs actually evolve from scales?" Tags="&lt;evolution&gt;&lt;human-anatomy&gt;&lt;hair&gt;&lt;scales&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="822" PostTypeId="2" ParentId="820" CreationDate="2012-01-26T11:16:43.500" Score="9" Body="&lt;p&gt;No, &lt;em&gt;Naegleria fowleri&lt;/em&gt; is a free-living excavate form of protist that lives in warm fresh water. &lt;em&gt;Fowleri&lt;/em&gt; finds its way into the brain by eating through the olfactory neurons in the nose where it multiplies itself greatly by feeding on nerve tissue. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once it penetrates the nervous tissue, &lt;em&gt;fowleri&lt;/em&gt;'s feeding  results in significant necrosis of and hemorrhaging in the olfactory bulbs. The protist then climbs along nerve fibers through the floor of the cranium via the cribriform plate and into the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the protist travels by feeding on nervous tissue, &lt;em&gt;fowleri&lt;/em&gt; could not enter the brain via bloodstream.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just some more facts about &lt;em&gt;Naegleria&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Death usually occurs within 14 days of exposure due to destruction the autonomic nerve cells of the medulla oblongata.&lt;/li&gt;&#xA;&lt;li&gt;Luckily for everyone this disease is rare. &lt;a href=&quot;http://td.rsmjournals.com/cgi/pmidlookup?view=long&amp;amp;pmid=18820207&quot; rel=&quot;nofollow&quot;&gt;There were only 300 cases as of 2008&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="238" LastEditorUserId="238" LastEditDate="2012-03-23T20:50:39.967" LastActivityDate="2012-03-23T20:50:39.967" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="823" PostTypeId="2" ParentId="821" CreationDate="2012-01-26T12:56:52.637" Score="6" Body="&lt;p&gt;From a little research I have been able to find some of the hypotheses and speculations but no papers &lt;em&gt;expressly&lt;/em&gt; confirming or denying the matter.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One theory displayed in &quot;The evolution of mammalian keratinized structures&quot; (&lt;a href=&quot;http://www.bcin.ca/Interface/openbcin.cgi?submit=submit&amp;amp;Chinkey=32482#&quot;&gt;abstract only&lt;/a&gt;) is that mammalian hair developed along the following pathway:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Hair follicles develop &lt;em&gt;between&lt;/em&gt; reptilian like scales.&lt;/li&gt;&#xA;&lt;li&gt;A granular layer formed in the pilosebaceous canal (see &lt;a href=&quot;http://en.wikipedia.org/wiki/File%3aSkin.jpg&quot;&gt;diagram of modern human skin&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;The granular layer extended into the epidermis.  &lt;em&gt;I read this as the point where scales started to more resemble mammalian skin&lt;/em&gt;.  It is suggested that this was as a result of a need for increased flexibility and agility.  &lt;/li&gt;&#xA;&lt;li&gt;Hairs began to protrude through the follicles (as seen in rat tails today).  Adaptations to organisms living in cold conditions led to the production of wool to help conserve heat.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So this paper would suggest that hair production evolved separately from but parallel to the movement away from reptilian scales.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;&lt;a href=&quot;http://www.jstor.org/stable/3881739&quot;&gt;Some Speculations on the Evolution of the Vertebrate Integument&lt;/a&gt;&quot; (Paul F. A. Maderson) suggests an entirely different origin of hairs.  He proposes that hairs ultimately evolved from sensory appendages that were involved in the detection of temperature in early synapsids.  The extension of these micro-limbs into hairs was selected towards as a result of their thermally insulating effect by-product rather than for their sensory role, however.&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-01-26T12:56:52.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="824" PostTypeId="1" AcceptedAnswerId="827" CreationDate="2012-01-26T18:12:10.613" Score="6" ViewCount="1277" Body="&lt;p&gt;What I mean by &quot;randomized&quot; is, in the place where an egg cell or sperm cell is made, what is the mechanism by which each one is not made identically? Though I am a layman, I'm pretty sure that if the sperm cell that was right next to &quot;me&quot; had made it to the egg instead of the one that did, the resultant human would have a different genomic sequence and different features.&lt;/p&gt;&#xA;" OwnerUserId="263" LastActivityDate="2012-01-27T17:19:55.767" Title="How are the gene sequences of individual sperm and egg cells &quot;randomized&quot;?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;reproduction&gt;&lt;human-genetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="825" PostTypeId="5" CreationDate="2012-01-26T19:22:17.427" Score="0" Body="" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2012-01-26T19:22:17.427" LastActivityDate="2012-01-26T19:22:17.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="826" PostTypeId="4" CreationDate="2012-01-26T19:22:17.427" Score="0" Body="The study of the molecular structure of biological macromolecules and how that structure relates to their function." OwnerUserId="6" LastEditorUserId="4101" LastEditDate="2013-10-31T00:42:03.160" LastActivityDate="2013-10-31T00:42:03.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="827" PostTypeId="2" ParentId="824" CreationDate="2012-01-26T21:09:07.160" Score="6" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Meiosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Meiosis&lt;/a&gt; is the type of cell division responsible for the diversification of genetic material among egg and sperm cells. The diversity comes primarily from &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosomal_crossover&quot; rel=&quot;nofollow noreferrer&quot;&gt;crossing over&lt;/a&gt; (&lt;em&gt;Prophase I&lt;/em&gt;) and the cell divisions (&lt;em&gt;Telophase I &amp;amp; II&lt;/em&gt;) later on in the process.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Meiosis begins with &lt;strong&gt;one diploid cell&lt;/strong&gt; containing two copies of each&#xA;  chromosome—one from the organism's mother and one from its father—and&#xA;  &lt;strong&gt;produces four haploid cells&lt;/strong&gt; containing one copy of each chromosome.&#xA;  Each of &lt;strong&gt;the resulting chromosomes in the gamete cells is a unique&#xA;  mixture of maternal and paternal DNA&lt;/strong&gt;, ensuring that offspring are&#xA;  genetically distinct from either parent. This gives rise to genetic&#xA;  diversity in sexually reproducing populations, which provides the&#xA;  variation of physical and behavioural attributes (phenotypes) upon&#xA;  which natural selection acts.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Further detail of the precise phases can be found in &lt;a href=&quot;http://en.wikipedia.org/wiki/Meiosis#Phases&quot; rel=&quot;nofollow noreferrer&quot;&gt;the Wikipeida article&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/12lFp.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/12lFp.jpg&quot; alt=&quot;meiosis&quot;&gt;&lt;/a&gt;&#xA;&lt;sub&gt;[picture from &lt;a href=&quot;http://en.wikipedia.org/wiki/Meiosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia]&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="397" LastEditorUserId="397" LastEditDate="2012-01-27T17:19:55.767" LastActivityDate="2012-01-27T17:19:55.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="828" PostTypeId="2" ParentId="824" CreationDate="2012-01-26T21:11:34.253" Score="1" Body="&lt;p&gt;I think we can attribute this to sheer probability. The human genome contains around 3 billion base pairs. When you consider recombination from chromosomal crossover that occurs in germ line cells, there is an astronomically huge number of possible unique combinations that can be made.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, males generate many many sperm, so some of these are bound to be similar. But the number of sperm produced by any individual doesn't come anywhere close to the number of possible unique sperm that he could produce.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-01-26T21:11:34.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="829" PostTypeId="2" ParentId="821" CreationDate="2012-01-26T23:49:09.973" Score="5" Body="&lt;p&gt;As to the early evolution of mammalian hair, &lt;a href=&quot;http://www.sciencemag.org/content/332/6032/955.abstract&quot;&gt;Rowe et al. (2011)&lt;/a&gt; hypothesized that the primitive function for hair was not thermoregulatory, but rather for tactile sensation (&lt;em&gt;contra&lt;/em&gt; the hypotheses of Spearman and Maderson). Rowe et al. say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Body hair develops as migrating neural crest cells induce patterns of&#xA;  tiny placodes that mature into hair follicles equipped with&#xA;  mechanoreceptors. These include lanceolate endings (velocity detectors&#xA;  excited by hair deflection), Ruffini receptors (tension receptors&#xA;  activated as hair is bent), and Merkel cells (slowly adapting&#xA;  sensors). In ontogeny, hair is first sensory, and only later does it&#xA;  insulate, as underfur thickens and thermoregulation matures.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So the developmental argument is in favor of tactile sensation.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-01-26T23:49:09.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="831" PostTypeId="1" CreationDate="2012-01-27T09:45:54.693" Score="7" ViewCount="171" Body="&lt;p&gt;Are there any experiments on growing artificial brains from brain tissue?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the constraints? Will such tissue grown to the mass greater than that of human brain surpass it in intellect or it would need additional conditions?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="81" LastEditDate="2012-01-27T13:50:09.183" LastActivityDate="2012-02-26T16:47:04.490" Title="What are the constraints when growing an artificial brain?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="832" PostTypeId="1" AcceptedAnswerId="833" CreationDate="2012-01-27T13:59:13.147" Score="12" ViewCount="2028" Body="&lt;p&gt;A student asked me this the other day and I thought that I would ask it again here. If one organism is said to be &quot;more evolved&quot; than another, what exactly does this mean?&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-01-30T18:02:08.033" LastActivityDate="2015-06-26T21:30:36.683" Title="What is meant in biology by the term &quot;evolved&quot;?" Tags="&lt;evolution&gt;" AnswerCount="5" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="833" PostTypeId="2" ParentId="832" CreationDate="2012-01-27T15:52:24.683" Score="26" Body="&lt;p&gt;&quot;More evolved&quot; is actually meaningless in all contexts. See terdon's answer for a good explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the strictest sense, an organism can be said to be more divergent than another when comparing both to an outgroup, such that there is an inferred most common ancestor in reference to which to make the comparison. In this case, one organism is more divergent if there are more changes to this organism than the other, relative to the reference point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, when speaking, many people get lazy, and use &quot;more evolved&quot; as shorthand, wishing it to mean something like &quot;more divergent&quot;. Even &quot;more divergent&quot; is meaningless in the following contexts:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;when there is no outgroup understood&lt;/li&gt;&#xA;&lt;li&gt;when describing increasing complexity (obligate parasites have lost complexity and have had more evolutionary changes than their non-parasitic relatives) &lt;/li&gt;&#xA;&lt;li&gt;when the outgroup is poorly chosen. Mammal vs reptile comparisons should not, in general, use prokaryotes as the outgroup.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edited 2013/12/06&lt;/strong&gt; to reflect the precision in the answer by terdon. &lt;/p&gt;&#xA;" OwnerUserId="184" LastEditorUserId="184" LastEditDate="2013-12-06T18:19:01.257" LastActivityDate="2013-12-06T18:19:01.257" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="834" PostTypeId="2" ParentId="832" CreationDate="2012-01-27T16:49:30.507" Score="18" Body="&lt;p&gt;I cannot improve on Thomas Ingalls' description of when &quot;more evolved&quot; is appropriately used, but the inappropriate/lazy use of the phrase is so prevalent that it deserves further comment. In my experience, the most common use of the phrase &quot;more evolved&quot; is when describing the increased complexity of one organism versus another. This usage is not just meaningless, but wrong and harmful, and springs from a misunderstanding of what evolution implies. Evolution is emphatically not the same as increased complexity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I try to avoid saying &quot;more evolved&quot; and tend to favor &quot;more complex&quot;, &quot;less simple&quot; or &quot;less primitive.&quot; &quot;Primitive&quot; has its own problems, since it sometimes brings with it the connotation of evolution (a &quot;primitive eye&quot; or &quot;primitive nervous system&quot; are common phrases), but it at least avoids an explicit misuse of &quot;evolved.&quot;&lt;/p&gt;&#xA;" OwnerUserId="72" LastEditorUserId="72" LastEditDate="2012-04-23T03:29:42.310" LastActivityDate="2012-04-23T03:29:42.310" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="835" PostTypeId="1" CreationDate="2012-01-27T18:31:25.567" Score="11" ViewCount="2794" Body="&lt;p&gt;I have been told the number of muscle fibers a particular muscle has varies from person to person. Unfortunately, the person who told me this did not know much more than this. Initial searching on the web did not reveal much detail on this; &lt;a href=&quot;http://www.ntcceagles.com/index.php?module=Pagesetter&amp;amp;func=viewpub&amp;amp;tid=18&amp;amp;pid=52&quot;&gt;some random sources&lt;/a&gt; suggested there was a correlation but they weren't referenced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a general correlation between the &lt;em&gt;number&lt;/em&gt; of muscle fibers and body type (mesomorph, endomorph, ectomorph)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about a correlation between muscle fiber &lt;em&gt;type&lt;/em&gt; (Type I/Type IIa/Type IIx/Type IIb) and body type?&lt;/p&gt;&#xA;" OwnerUserId="397" LastEditorUserId="6" LastEditDate="2012-01-30T07:28:53.290" LastActivityDate="2018-04-22T23:20:30.083" Title="Is there a correlation between muscle fibers and body types?" Tags="&lt;human-biology&gt;&lt;anatomy&gt;&lt;muscles&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="836" PostTypeId="1" CreationDate="2012-01-27T23:46:12.500" Score="11" ViewCount="2642" Body="&lt;p&gt;I would like to synthesize a 3.4kb gene (originally isolated from soil bacteria) and transform it into E. coli. There are several companies (&lt;a href=&quot;https://www.dna20.com/&quot;&gt;DNA2.0&lt;/a&gt;, &lt;a href=&quot;http://www.genscript.com/&quot;&gt;GeneScript&lt;/a&gt;, &lt;a href=&quot;http://www.blueheronbio.com/&quot;&gt;BlueHeron&lt;/a&gt;) which will synthesize the gene for you. I would like to know how these companies (or others) compare with each other in terms of:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Codon optimization - most of the companies are going to codon optimize the sequence and thus increase the protein expression in the desired host. Recently I learned that there are different algorithms that can be applied. I am mostly interested in how the codon-optimization is performed in the different companies and whether there are some direct comparisons of protein expression between them.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;cost per base - I would like to find the cheapest one. In general, the cost of gene synthesis usually depends on the size of the fragment, as well as the complexity of the sequence. But on the other hand, DNA2.0 can synthesize 1kb fragment and 5kb fragment for the same price.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Turn-around time - which company will synthesize the fragment the fastest? I think that this mainly depends on size. Of course I have an option of ordering 3 x 1.1kb fragments and joining them myself, but then I have to sequence-verify the final product. So, I need to find the trade-off.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Please, keep in mind that I am not asking about your favorite company, but about specific characteristics of the companies.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2016-12-30T01:45:56.890" Title="DNA synthesis companies: cost per base, turn-around time, codon-optimization algorithms" Tags="&lt;synthetic-biology&gt;&lt;gene-synthesis&gt;&lt;codon-usage&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="837" PostTypeId="1" AcceptedAnswerId="930" CreationDate="2012-01-28T00:58:18.677" Score="11" ViewCount="14987" Body="&lt;p&gt;I often hear that people who are taking antibiotics experience wild fluctuations between feeling full of energy and completely alert but soon after feeling impossibly fatigued and sick.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this have anything to do with the antibiotics being used by the body as anything? For example as a hormone or as a source of nutrition?  Is this this a reported side effect when used for other infections?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="238" LastEditDate="2012-02-05T16:21:11.677" LastActivityDate="2019-03-13T02:15:31.447" Title="Why would taking antibiotics increase stamina and energy?" Tags="&lt;human-biology&gt;&lt;bacteriology&gt;&lt;antibiotics&gt;&lt;pathology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="838" PostTypeId="2" ParentId="757" CreationDate="2012-01-28T06:26:24.527" Score="4" Body="&lt;p&gt;I think that this might refer to evolution in &lt;a href=&quot;http://www.scholarpedia.org/article/Punctuated_equilibria&quot; rel=&quot;nofollow&quot;&gt;punctuated equilibrium&lt;/a&gt; as described by Stephen Gould et al way back in the 70s.  If this is the case, it refers more to the idea that changes and speciations can be quite rapid in time and for long periods you don't see morphological changes or speciation events in the record.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, then this is influenced by the study of evolution in cases where there are large changes in the environment very rapidly. The classic case is when there is a bare island and new animals arrive only rarely. This is all very much inspired by Darwin's observations in the Galapagos, but has since been studied quite a bit.  In such cases you see just handful of sets of birds suddenly appear and you find a finch that can scrape bugs out of bark, another that can dig into narrow niches in the rock for food, where in a broader ecosystem two completely different species would be utilizing those 2 food sources. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It should be said that no evolutionary leap should be understood as an acceleration or deceleration of evolution.  Only a change in the rate of adoption of variations because of a wider set of possible advantages those variations can represent. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="500" LastEditDate="2013-04-14T21:46:43.540" LastActivityDate="2013-04-14T21:46:43.540" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="839" PostTypeId="1" CreationDate="2012-01-28T13:23:11.130" Score="75" ViewCount="15931" Body="&lt;p&gt;What is the impact of mental activity on the energy consumption of the human brain?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am most interested in intellectually demanding tasks (e.g., chess matches, solving a puzzle, taking a difficult exam) versus tasks with a similar posture but less demanding (e.g., reading a newspaper, watching TV). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I heard that energy consumption stays remarkably constant regardless of the mental activity (and energy consumption can be explained by elevated heart rate due to stress). However, it seems to contradict techniques such as fMRI, where the change in metabolism is measured (unless the relative change is really small).&lt;/p&gt;&#xA;" OwnerUserId="129" LastEditorUserId="57" LastEditDate="2012-08-01T00:39:48.890" LastActivityDate="2013-11-27T01:44:01.200" Title="How does the brain's energy consumption depend on mental activity?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="23" ContentLicense="CC BY-SA 3.0" />
  <row Id="840" PostTypeId="5" CreationDate="2012-01-28T22:21:10.827" Score="0" Body="&lt;p&gt;This tag is for questions about the biology of disease. Medical questions, other than those about the biology of medicine, may be off topic. See the &lt;a href=&quot;https://biology.stackexchange.com/help&quot;&gt;help center&lt;/a&gt; and &lt;a href=&quot;https://biology.meta.stackexchange.com/&quot;&gt;meta&lt;/a&gt; before posting your question on such topics.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="16866" LastEditDate="2019-08-25T03:36:47.230" LastActivityDate="2019-08-25T03:36:47.230" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="841" PostTypeId="4" CreationDate="2012-01-28T22:21:10.827" Score="0" Body="The study of diseases, including their causes and effects." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-29T20:55:44.363" LastActivityDate="2013-10-29T20:55:44.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="842" PostTypeId="1" AcceptedAnswerId="848" CreationDate="2012-01-29T03:26:12.433" Score="12" ViewCount="396" Body="&lt;p&gt;Over at skeptics, there were a couple questions asked as to the correlation of specific physical traits in relation to personality/behaviour.  For instance, the &lt;a href=&quot;https://skeptics.stackexchange.com/questions/7679/are-simian-lines-and-personality-correlated&quot;&gt;simian line&lt;/a&gt; as well as &lt;a href=&quot;https://skeptics.stackexchange.com/questions/7715/are-red-heads-more-likely-to-be-hot-headed&quot;&gt;red hair&lt;/a&gt;.  Now, I did my best to answer these questions, with what I understand as there being a long history of people attempting to correlate external physical characteristics with behaviour (see the disgraced &quot;art&quot; of phrenology for instance).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in answering the simian line question, I did come across some weak correlations.  It got me to wondering if this is an area of exploration in terms of perhaps one gene sequence for a physical trait somehow being tied with another gene sequence for behaviour.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, do any physical characteristics being expressed through genes correlate to behaviour?&lt;/p&gt;&#xA;" OwnerUserId="279" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2012-01-30T02:37:43.247" Title="Does the genetic expression of specific physical traits ever correlate to behaviour?" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;behaviour&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="843" PostTypeId="2" ParentId="324" CreationDate="2012-01-29T12:56:02.043" Score="27" Body="&lt;p&gt;I found &lt;a href=&quot;http://web.sbu.edu/biology/Benington/Prog%20Neurobiol%2045347.pdf&quot; rel=&quot;noreferrer&quot;&gt;this paper by Benington and Heller&lt;/a&gt; that expands on the previously mentioned theory of sleep as a mechanism to renew metabolism.  They hypothesise that sleep is necessary to replenish glycogen stores (mainly within astrocytes) in the brain.  These stores are normally used to supplement blood glucose due to the high energy demands of the brain.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is suggested that this may also result in the manifestation of feeling sleepy as a consequence of the exhaustion of glycogen supplies in specific small areas of the brain.  Brief and localised depletion of glycogen stores mean that cells are operating with less energy than they normally have to work with.  This causes an increase in synthesis of adenosine from the breakdown of AMP.  The paper maintains that the increased levels of adenosine are detected by adenosine receptors which then triggers or increases (as seen on EEG scans) the feeling of the need for sleep:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jF4cA.jpg&quot; alt=&quot;Flowchart of the relation of glycogen to sleep need and replenishment&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In NREM sleep (which may lend some support to the theory as NREM sleep accounts for 80% of sleep and is most physiologically different to waking), this glycogen is most efficiently replaced.  During NREM sleep the release of glycogenolysis inducing neurotransmitters is reduced, allowing glycogen-synthase to predominate and glycogen levels to be restored.  However, these same neurotransmitters are key in the processing sensory stimuli (by tonically depolarising neurons in the sensory cortex).  &lt;strong&gt;Therefore glycogen replenishment will always be associated with a (strongly) reduced response to stimuli&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leads to finally answering the question as to why sleep has an evolutionary advantage, which I will quote verbatim to maintain the authors momentum:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Glycogen replenishment during waking would be maladaptive because it would impair the organism's ability to to process and respond to sensory stimuli.  &lt;strong&gt;Sleep has therefore evolved as a state where animals retreat to a safe environment, behaviour is suppressed and glycogen stores are replenished&lt;/strong&gt;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-01-29T12:56:02.043" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="844" PostTypeId="5" CreationDate="2012-01-29T13:57:38.083" Score="0" Body="&lt;p&gt;Questions should be about the interactions among and between organisms and their environment. Examples of topics include: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Life processes, interactions, and adaptations&lt;/li&gt;&#xA;&lt;li&gt;Materials and energy in living communities&lt;/li&gt;&#xA;&lt;li&gt;The development of ecosystems&lt;/li&gt;&#xA;&lt;li&gt;Abundance and distribution of organisms&lt;/li&gt;&#xA;&lt;li&gt;Biodiversity&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;questions pertaining to specific hierarchical levels of ecology should use specific tags: &lt;a href=&quot;/questions/tagged/population-dynamics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;population-dynamics&amp;#39;&quot; rel=&quot;tag&quot;&gt;population-dynamics&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/community-ecology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;community-ecology&amp;#39;&quot; rel=&quot;tag&quot;&gt;community-ecology&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/landscape-ecology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;landscape-ecology&amp;#39;&quot; rel=&quot;tag&quot;&gt;landscape-ecology&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Questions pertaining to evolution should use &lt;a href=&quot;/questions/tagged/evolution&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;evolution&amp;#39;&quot; rel=&quot;tag&quot;&gt;evolution&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="16866" LastEditDate="2020-01-02T19:48:45.167" LastActivityDate="2020-01-02T19:48:45.167" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="845" PostTypeId="4" CreationDate="2012-01-29T13:57:38.083" Score="0" Body="The study of the spatial and temporal patterns of the distribution and abundance of organisms, including causes and consequences (Scheiner, S.M. and Willig, M.R., 2008. A general theory of ecology. Theoretical Ecology, 1(1), pp.21-28. doi:10.1007/s12080-007-0002-0)" OwnerUserId="69" LastEditorUserId="51090" LastEditDate="2020-10-20T16:21:38.343" LastActivityDate="2020-10-20T16:21:38.343" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="846" PostTypeId="2" ParentId="839" CreationDate="2012-01-29T17:05:35.223" Score="11" Body="&lt;p&gt;I answered on the facts of this question already on skeptics.SE, &lt;a href=&quot;https://skeptics.stackexchange.com/a/5128/3194&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;https://skeptics.stackexchange.com/a/4330/3194&quot;&gt;here&lt;/a&gt;. You should read both papers very carefully, I highlighted the most important facts but this is a very tricky question, esp. when it comes to defining what mental activitiy is. The papers also give an explanation of how fMRI signal is linked to NEURONAL activity, as far as I remember there is no strong direct link.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You assume in your question that a mathematician solving a differential equation needs higher mental activity than a child reading a book. Is this legitimate? It seems intuitive but also very subjective. &lt;strong&gt;In the paper they mention that for the highest and lowest energy consumption we lose consciousness.&lt;/strong&gt; I will not draw conclusions from this. However, you are talking about conscious mental activities so this may answer your question. To me it means more that the understanding of the human brain in neurobiololgy is on the level of the Rutherford Atomic Model in Physics at the beginning of the 20th century. We have not really got a clue how information is processed and how it's constrained by physical laws and principles of entropy and energy. By reading the 2 papers it looks more like the human brain is not raising energy consumption as a computer would (the computer analogy pretty much fails when compared to the human brain). Most of the energy is used for unconscious processes in &quot;standby mode&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As in physics, extreme cases such as savants and the mentally disabled are probably the best starting point to exclude possible models of human brain and physical boundary conditions as we cannot approach the questions of human brain in a reductionistic way. How can savants like &lt;a href=&quot;http://en.wikipedia.org/wiki/Kim_Peek&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kim Peek&lt;/a&gt; process such huge amounts of information AND save it. He is able to scan books pages just once and know them by heart thereafter. His brain does not, however, consume more energy than an average human brain. So mental activity is probably not a very good term, quantity, or even really suited to be scientifically used. Does neuronal activity mean mental activity (in the sense of your definition?) Reading the papers, the problem is the separation of mental and neuronal activities. At first you have to know what are the basic brain functions and processes that are consuming most of the energy. However the brain is not built in modular way like a computer (most energy is used here for constantly refreshing RAM). So there is not really a objective way to analyse and separate this modular energy consumption, &lt;em&gt;if it even is modular&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my opinion, most models about information processing in human brain are intuitive guessing (again Rutherford). We need much more detailed experiments and data (Blue Brain Project). fMRi is like analysing a atom with a magnifying glass. Also, the more prosperous approach from a biophysical perspective is probably not the level of &quot;mental activity&quot; but the hard-based amount of information processed by human brains and linked energy consumption (Kim Peek). But therefore we need a model of how this information is saved in human brain. Do normal humans save the same information as Kim Peek scanning a page or are we just unable to recall it consciouscly? When solving a differential equation, how much energy do you consume when recalling facts and is that experience not similar to reading a book? How much is mental logical tasks and is there really a difference at all? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will stop here, hope you gained some insight that the question is of course important but too early to be definitively answered. I think we will learn a lot more from projects like Blue Brain as we have from fMRI experiments.&lt;/p&gt;&#xA;" OwnerUserId="308" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2012-01-30T17:01:25.940" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="847" PostTypeId="1" AcceptedAnswerId="853" CreationDate="2012-01-30T01:34:32.157" Score="8" ViewCount="639" Body="&lt;p&gt;I'm familiar with the method to build Keio collection using single-gene deletion with an antibiotic cassette. However, what happens when there are gene clusters or overlapping ORFs and you still only wish to knockout a single gene?&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-01-30T03:44:23.133" LastActivityDate="2012-01-30T18:22:24.873" Title="How do you knockout an E. coli gene without disrupting the rest of the gene cluster?" Tags="&lt;molecular-biology&gt;&lt;ecoli&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="848" PostTypeId="2" ParentId="842" CreationDate="2012-01-30T01:43:23.143" Score="6" Body="&lt;p&gt;&lt;a href=&quot;http://www.molecularautism.com/content/2/1/15&quot;&gt;Aldridge et al. (2011)&lt;/a&gt; show a correlation between facial phenotypes and autism spectrum disorders (ASD) in a sample of 8-12 year old boys.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They studied two groups of boys, 65 that had been diagnosed with ASD and 41 who had not. They collected 3D images of the faces and looked for similar patterns among the two groups. They found a significant association between some phenotypes and ASD. But, as with most studies, the results are complex; there a distinct sub-groups within the ASD group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Keep in mind that this is an association study -- no causation is shown.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2012-01-30T02:37:43.247" LastActivityDate="2012-01-30T02:37:43.247" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="849" PostTypeId="1" AcceptedAnswerId="852" CreationDate="2012-01-30T06:17:42.057" Score="9" ViewCount="2949" Body="&lt;p&gt;I picture a neuron as having multiple trees of dendrites attached to the cell body with a single axon leaving the cell body.  I believe the cell body near the axon root makes the decision to fire or not fire an action potential.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;If the neuron has both excitatory and inhibitory synapses in the dendrite trees, how do these communicate to the cell body?  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Does something like an action potential get transmitted down the dendritic trees to the cell body?  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What is the difference between the excitatory and inhibitory signals that are transmitted?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="420" LastEditorUserId="57" LastEditDate="2012-08-01T00:36:44.417" LastActivityDate="2017-09-19T11:58:59.980" Title="How does an inhibitory synapse communicate to the cell body of a neuron?" Tags="&lt;neuroscience&gt;&lt;synapses&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="850" PostTypeId="2" ParentId="849" CreationDate="2012-01-30T08:32:50.963" Score="12" Body="&lt;p&gt;An inhibitory synapse works just like an excitatory one!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a presynaptic neuron fires it will release a neurotransmitter at its terminal(s). This neurotransmitter can be excitatory or inhibitory, the main excitatory one in the central nervous system being &lt;a href=&quot;http://en.wikipedia.org/wiki/Glutamate&quot; rel=&quot;nofollow noreferrer&quot;&gt;glutamate&lt;/a&gt; and the main inhibitory one &lt;a href=&quot;http://en.wikipedia.org/wiki/GABA&quot; rel=&quot;nofollow noreferrer&quot;&gt;GABA&lt;/a&gt;.&lt;sup&gt;*&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GABA and Glu are far from being the only neurotransmitters in the brain, they're just a classic example, so we'll stick with them. When the neurotransmitter is released it binds to receptors on the postsynaptic neuron (provided, of course, that the postsynaptic neuron expresses these receptors).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Various GABA and Glu receptors exist, both ionotropic (i.e. channel-receptors that let ions flow through the membrane upon binding of the ligand) and metabotropic (i.e. receptors which activate an intracellular pathway that does not &lt;em&gt;per se&lt;/em&gt; start the flow of ions, but that can induce it or prevent it indirectly).&#xA;For simplicity we'll stick to ionotropic receptors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glu binds to three types of ionotropic receptors: &lt;a href=&quot;http://en.wikipedia.org/wiki/AMPA_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;AMPA&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/NMDA_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;NMDA&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Kainate_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;kainate&lt;/a&gt; receptors. These have different kinetics/properties, but the bottom line is that they let cations (positively charged ions, such as Na+ and Ca++) into the cell. When this happens a postsynaptic depolarization happens, which is named EPSP (excitatory post-synaptic potential).&lt;br&gt;&#xA;So, if the resting membrane potential was, say, -57mV, it will become, for instance -52mV. &#xA;This means that, if the threshold potential for firing an action potential were -43mV the cell, which first needed a 14mV depolarization to fire now will need a 9mV depolarization.&#xA;If subsequent &lt;a href=&quot;http://en.wikipedia.org/wiki/Excitatory_postsynaptic_potential&quot; rel=&quot;nofollow noreferrer&quot;&gt;EPSP&lt;/a&gt; sum they can depolarize the cell sufficiently to reach threshold and let the cell fire.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This image from Wikipedia is quite self-explicatory: in this case 3 synaptic events generated 3 EPSPs that summed, making the cell depolarize enough to reach threshold potential, and generate an action potential, that will then propagate to the cell body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cdiDk.png&quot; alt=&quot;Sum of EPSP&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GABA, on the other hand, binds to the &lt;a href=&quot;http://en.wikipedia.org/wiki/GABA-A&quot; rel=&quot;nofollow noreferrer&quot;&gt;GABA-A&lt;/a&gt; receptor, which is a chloride channel. In most cases, upon binding of GABA, GABA-A lets Cl- in the cell, effectively hypopolarizing it and generating an &lt;a href=&quot;http://en.wikipedia.org/wiki/Inhibitory_postsynaptic_potential&quot; rel=&quot;nofollow noreferrer&quot;&gt;IPSP&lt;/a&gt; (inhibitory post-synaptic potential). The situation is the same (but opposite) to Glu, this time, though, the potential becomes more negative.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EPSP and IPSP can and do happen at the same time: as they can vary in frequency and intensity depending on the firing frequency and firing pattern of the presynaptic neuron, a pretty much continuous range of voltages can be achieved in the postsynaptic neuron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other controls over this process come from metabotropic receptors that can, for instance [de]phosphorylate (add or remove a phosphate group) ion channels modulating their permeability to ions or from the different kinetics of the different channels (for instance certain channels stay open for longer or open in a delayed manner etc), allowing for fine-tuning of the system. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;*&lt;/sup&gt;I am making a gross generalization here. A neurotransmitter is not excitatory or inhibitory &lt;em&gt;per se&lt;/em&gt;, it depends on the context. For instance excitatory GABA synapses do exist.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="36209" LastEditDate="2017-09-19T11:58:59.980" LastActivityDate="2017-09-19T11:58:59.980" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="851" PostTypeId="2" ParentId="839" CreationDate="2012-01-30T11:24:28.467" Score="33" Body="&lt;p&gt;The energy consumption doesn't vary that much between resting and performing tasks, as discussed in a &lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.neuro.29.051605.112819&quot; rel=&quot;noreferrer&quot;&gt;review by Marcus Raichle and Mark A. Mintun&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In the average adult human, the brain represents approximately 2% of&#xA;the total body weight but approximately 20% of the energy consumed&#xA;(Clark &amp;amp; Sokoloff 1999), 10 times that predicted by its weight alone.&#xA;Relative to this high rate of ongoing or “basal” metabolism (usually&#xA;measured while resting quietly awake with eyes closed), the amount&#xA;dedicated to task-evoked regional imaging signals is remarkably small.&lt;/p&gt;&#xA;&lt;p&gt;The regional increases in absolute blood flow associated with imaging&#xA;signals as measured with PET are rarely more than 5%–10% of the&#xA;resting blood flow of the brain. These are modest modulations in&#xA;ongoing circulatory activity that rarely affect the overall rate of&#xA;brain blood flow during even the most arousing perceptual and vigorous&#xA;motor activity (Fox et al. 1987, Friston et al. 1990, Lennox 1931,&#xA;Madsen et al. 1995, Roland et al. 1987, Sokoloff et al. 1955).&lt;/p&gt;&#xA;&lt;p&gt;[...]&lt;/p&gt;&#xA;&lt;p&gt;From knowledge of these relationships, one can estimate that if blood flow and glucose utilization increase by 10%, but oxygen consumption does not, the local energy consumption increase owing to a typical task-related response could be as little as 1%. It becomes clear, then, that the brain continuously expends a considerable amount of energy even in the absence of a particular task (i.e., when a subject is awake and at rest).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Techniques like fMRI measure relatively small differences, their existence does not contradict the claim that the energy consumption of the brain doesn't change a lot between the resting state and performing an activity.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.neuro.29.051605.112819&quot; rel=&quot;noreferrer&quot;&gt;1. Raichle ME, Mintun MA. BRAIN WORK AND BRAIN IMAGING. Annual Review of Neuroscience 2006 Jul;29(1):449-476.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-01-30T11:24:28.467" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="852" PostTypeId="2" ParentId="849" CreationDate="2012-01-30T16:22:07.353" Score="6" Body="&lt;p&gt;From your comment to nico's good answer, it seems that your question is really about how synaptic potentials propagate through dendrites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Canonically, synaptic potentials travel passively along membranes and is described by &lt;a href=&quot;http://en.wikipedia.org/wiki/Cable_theory&quot; rel=&quot;nofollow&quot;&gt;cable theory&lt;/a&gt;. The cable equation describes how the voltage will change over time and space along a cable. The theory was originally developed for signal decay in trans-Atlantic telegraph cables, but the principle holds for a voltage-independent length of membrane like a dendrite. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A key point is that the potential change &quot;seen&quot; by the cell body &lt;em&gt;is&lt;/em&gt; different from the potential change seen locally at the site of the synapse itself. In fact, the voltage decays exponentially with increasing distance from the synapse. The extent of the signal decay is governed by the axial resistance (influenced by dendritic diameter), the membrane resistance, and membrane capacitance, and the branching pattern. A common neuron modeling environment called &lt;a href=&quot;http://www.neuron.yale.edu/neuron/&quot; rel=&quot;nofollow&quot;&gt;NEURON&lt;/a&gt; is basically a fancy solver for the cable equation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You'll note that a consequence of this signal decay is that synaptic location matters a lot. Given an identical synaptic potential, a very distal synapse will have much less of an effect on the soma than a more proximal dendrite. Sometimes, the synaptic strengths are scaled to compensate for this location issue (a distal synapse will have a much larger local potential change). Many inhibitory synapses capitalize on this location dependence and are located close to the soma to act as shunts for all signals coming from the dendritic tree. When activated, an inhibitory synapse will decrease the local membrane resistance thereby decreasing cell excitability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, I'll note that although we often talk about dendrites as being passive conductors, dendrites are actually quite active and have many voltage-dependent channels. The voltage-dependent phenomena in the dendrite complicates the use of pure cable theory to understand the dynamics of synaptic potentials. However, cable theory is still the essential foundation upon which our growing understanding of the active dendrite is built.&lt;/p&gt;&#xA;" OwnerUserId="72" LastEditorUserId="72" LastEditDate="2015-11-01T19:33:11.637" LastActivityDate="2015-11-01T19:33:11.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="853" PostTypeId="2" ParentId="847" CreationDate="2012-01-30T18:22:24.873" Score="8" Body="&lt;p&gt;Let's say that we have gene A, followed by gene B so that they overlap with 100 bases. If you want to knock out only gene A, you can do the following:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;PCR gene A and clone it into a vector&lt;/li&gt;&#xA;&lt;li&gt;PCR gene B and clone it into another vector&lt;/li&gt;&#xA;&lt;li&gt;Insert a antibiotic resistance marker at the overlapping region of gene A and B&#xA;&lt;ul&gt;&#xA;&lt;li&gt;now you don't have functional gene A and gene B&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Transform your cells only with the vector that contains gene B&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now you have disrupted only gene A but you have a functional gene B.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-01-30T18:22:24.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="854" PostTypeId="1" CreationDate="2012-01-31T03:18:42.003" Score="12" ViewCount="146" Body="&lt;p&gt;How would one calculate the availability of nucleotides to an enzyme like a polymerase ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I imagine an answer in units like nucleotides per second per enzyme, but I'm also imagining an answer that is not a simple rate of reaction. k_on calculations and k_off do not offer mechanistic explanation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like to know, specifically, if there is a theoretical approach to this question:  how does a polymerase reject an incorrect nucleotide?&lt;/p&gt;&#xA;" OwnerUserId="184" LastEditorUserId="184" LastEditDate="2012-01-31T17:09:45.933" LastActivityDate="2012-11-07T18:28:27.330" Title="How would one calculate the availability of nucleotides to an enzyme?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="855" PostTypeId="1" AcceptedAnswerId="865" CreationDate="2012-01-31T04:49:18.513" Score="24" ViewCount="7663" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Vaccine&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A vaccine typically contains an agent that resembles a disease-causing&#xA;  microorganism, and is often made from weakened or killed forms of the&#xA;  microbe, its toxins or one of its surface proteins. The agent&#xA;  stimulates the body's immune system to recognize the agent as foreign,&#xA;  destroy it, and &quot;remember&quot; it, so that the immune system can more&#xA;  easily recognize and destroy any of these microorganisms that it later&#xA;  encounters.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;:  How does the immune system &quot;&quot;remember&quot;&quot; a foreign agent introduced via a vaccine?  And how does it learn how to deal with subsequent encounters?&lt;/p&gt;&#xA;" OwnerUserId="203" LastActivityDate="2017-08-21T07:29:54.303" Title="How does the immune system &quot;learn&quot; from a vaccine?" Tags="&lt;immunology&gt;&lt;epidemiology&gt;&lt;vaccination&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="856" PostTypeId="2" ParentId="855" CreationDate="2012-01-31T08:32:14.337" Score="6" Body="&lt;p&gt;In short, some of the B-cells (antibody producing lymphocytes) specified to deal with this agent go dormant after the vaccine stimulation -- when the real danger comes, they can proliferate quickly and flood it with new antibodies, also alerting the rest of the immune system.&lt;/p&gt;&#xA;" OwnerDisplayName="user59" LastEditorUserId="3522" LastEditDate="2013-05-07T15:44:58.680" LastActivityDate="2013-05-07T15:44:58.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="859" PostTypeId="1" CreationDate="2012-01-31T14:57:01.123" Score="10" ViewCount="226" Body="&lt;p&gt;There is increasing evidence (e.g. &lt;a href=&quot;http://www.sciencemag.org/content/334/6052/89.short&quot;&gt;&lt;em&gt;here&lt;/em&gt;&lt;/a&gt;) that &lt;em&gt;Homo sapiens&lt;/em&gt; interbred with contemporary homonins such as &lt;em&gt;Homo neanderthalensis&lt;/em&gt; and the &quot;Denisovans&quot;. Although these homonins do show differences in their mtDNA, since a species is generally defined as a group of organisms capable of interbreeding and producing viable offspring, should we not regard humans, neanderthals and denisovans as the same species and name them as such?&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="107" LastEditDate="2012-02-24T21:55:18.080" LastActivityDate="2012-02-24T21:55:18.080" Title="Is it correct to regard archeaic humans (i.e.n Neanderthals and Denisovans) as distinct species to Homo sapiens?" Tags="&lt;taxonomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="860" PostTypeId="2" ParentId="761" CreationDate="2012-01-31T18:22:36.370" Score="16" Body="&lt;p&gt;I'd like to add to Amy's excellent answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally, galls are induced by the forced accumulation of plant hormones at different levels to those naturally maintained by the plant, in a localised area. Usually the hormones targeted are auxins and cytokinins which are both involved in the regulation of normal growth patterns; disrupting these patterns leads to disorganised growth, or in some cases a differently organised growth. There are several methods that I know of:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The gall inducer directly synthesising the hormone.&lt;/li&gt;&#xA;&lt;li&gt;The inducer chemically inducing the host to synthesise more hormone.&lt;/li&gt;&#xA;&lt;li&gt;The inducer chemically inducing the host to transport more hormone to the site.&lt;/li&gt;&#xA;&lt;li&gt;The inducer genetically modifying the host to cause synthesis of the hormone in the host cell.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Some examples of the different methods:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Direct production:&lt;/strong&gt; The bacterium &lt;em&gt;Pseudomonas savastanoi&lt;/em&gt; directly produces indole-3-acetic acid (IAA, a type of auxin). This direct accumulation has been shown to be responsible for gall formation in oleander knot disease. Some key papers: Palm et al. 1989, link 1; Glickman et al. 1998, link 2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Chemical induction of transport:&lt;/strong&gt; Root-knot nematode worms induce root gall formation in clover. They probably do so by producing flavonoids which up-regulate transportation of auxin into cells (see link 3).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Genetic induction:&lt;/strong&gt; As already mentioned by Amy, &lt;em&gt;Agrobacterium tumefaciens&lt;/em&gt; is a very well characterised example of induction by genetic modification, however, &lt;em&gt;A. tumefaciens&lt;/em&gt; is also known to directly produce auxins in large quantities. Another interesting example of genetic modification is in viral gall-inducers. They are not so well studied as their bacterial counterparts, but in some cases (e.g. white clover mosaic potexvirus) it has been shown that virus infection initially leads to a complex change in the types of cytokinins produced by the plant (e.g. Clarke, 1999; see link 4). It has also been shown that if cytokinins are applied exogenously (i.e. injected into the plant) after viral infection, that the virus cannot replicate well. This suggests that the virus is manipulating the host's hormone production in a complex way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also the interesting case of &lt;em&gt;Rhodococcus fascians&lt;/em&gt;, which seems to produce a chemical which is not structurally similar to any known cytokinin, and yet has similar effects (Goethals et al., 2001; link 5).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You specifically asked about gall wasps, but unfortunately this mechanism is, as far as I can tell, not completely known. It is speculated (e.g. in Shorthouse &amp;amp; Rohrfritsch, 1992; link 6) that this involves direct injection of phytohormones. The evidence to support this is simply that other insects, particularly aphids, excrete phytohormones in their salivary sheaths when they inject them into a plant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, I'll just say that the fact that gall induction is carried out by bacteria, viruses, nematodes, fungi and wasps, and that some mechanisms are shared across all those associations,  demonstrates the ability of evolution to converge on the most elegant solution to a problem. It also shows that plants are so great, everyone wants a piece (but I would say that, because I'm a plant biologist).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC209694/&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC209694/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI.1998.11.2.156&quot;&gt;http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI.1998.11.2.156&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.publish.csiro.au/?paper=PP98157&quot;&gt;http://www.publish.csiro.au/?paper=PP98157&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plantphysiol.org/content/120/2/547.full&quot;&gt;http://www.plantphysiol.org/content/120/2/547.full&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.phyto.39.1.27&quot;&gt;http://www.annualreviews.org/doi/full/10.1146/annurev.phyto.39.1.27&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nhbs.com/biology_of_insect_induced_galls_tefno_3838.html&quot;&gt;http://www.nhbs.com/biology_of_insect_induced_galls_tefno_3838.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-02-01T21:16:39.960" LastActivityDate="2012-02-01T21:16:39.960" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="861" PostTypeId="1" CreationDate="2012-01-31T18:23:15.110" Score="7" ViewCount="76" Body="&lt;p&gt;Is it possible to reliably isolate and amplify DNA from individual sperm and/or eggs (from a fish)? I'd imagine that the small amount of DNA would make the PCR a bit wacky. We've considered irradiating sperm and attempting to create haploid females via gynogenesis, but I was wondering if there was a faster and easier method that could utilize gametes directly. &lt;/p&gt;&#xA;" OwnerUserId="55" LastEditorUserId="338" LastEditDate="2012-02-16T14:47:25.760" LastActivityDate="2014-01-02T10:31:26.973" Title="How are whole Haplotypes for Sequencing isolated?" Tags="&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="862" PostTypeId="1" CreationDate="2012-01-31T18:33:11.093" Score="11" ViewCount="2066" Body="&lt;p&gt;Using the Illumina platform, it is cheap and (relatively) easy to sequence huge amounts of DNA or RNA. There are various other platforms out there (Roche/454, SOLiD, PacBio, Ion Torrent) each with their own distinct advantages, but Illumina seems to be pretty popular for many applications, despite its limitations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ideally, we would like a sequencing technology that produces long, error-free reads with high throughput. However, at this point it seems we have to make a choice: throughput or length (and quality). PacBio seems promising, but the last I heard they have still been unable to deliver on their claims.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the molecular and biochemical limitations to our current sequencing technologies? Why &lt;em&gt;don't&lt;/em&gt; we already have long, error-free reads with high throughput?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2012-09-05T12:15:59.623" LastActivityDate="2014-01-02T13:09:27.930" Title="What are the limitations to current nucleotide sequencing technologies?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;dna-sequencing&gt;&lt;genomics&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="863" PostTypeId="2" ParentId="681" CreationDate="2012-01-31T19:06:05.340" Score="16" Body="&lt;p&gt;There are several key ways in which rising atmospheric CO₂ concentrations will affect photosynthesis, and these are related to the different types of photosynthesis. In order to properly answer your question, I'll provide some background about photosynthesis itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photosynthesis evolved in a high-CO₂ atmosphere, before the oxygen-enrichment of the atmosphere (which actually happened as a result of photosynthesis). Most plant species operate &lt;strong&gt;C3 photosynthesis&lt;/strong&gt;. In these plants, carbon dioxide diffuses into the cell where it is fixed by &lt;strong&gt;Ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO)&lt;/strong&gt; into a 3-carbon molecule (hence C3), which is then polymerised to make sugars. A crucial fact about RuBisCO is that it has both carboxylase (carbon-fixing) activity and oxygenase (oxygen-fixing) activity. This means that oxygen and carbon dioxide compete for the active site on the enzyme complex, leading to RuBisCO being quite inefficient and slow at fixing carbon in higher oxygen concentrations. That didn't matter in the high-CO₂ atmosphere of the early Earth, but in todays atmosphere O₂ concentrations are high enough that they severely limit the productivity of C3 plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, plants haven't just been growing slowly all that time - several mechanisms for increasing photosynthetic efficiency have evolved. The most influential systems involve concentrating carbon dioxide in a particular area, excluding oxygen, and concentrating RuBisCO in that same area. This avoids the oxygen competition for the active site and allows RuBisCO to operate more efficiently. The key adaptation here is &lt;strong&gt;C4 photosynthesis&lt;/strong&gt; - the system which is present in most grasses and many of the most productive plants on Earth (e.g. maize, sugarcane, Miscanthus). It has evolved at least 62 times independently. It works by having RuBisCO concentrated within 'bundle sheath' cells which are surrounded by a layer of suberin wax. This layer prevents CO₂ escaping and O₂ from getting in. CO₂ from the atmosphere is then fixed in different cells - 'mesophyll cells' - by another enzyme - &lt;strong&gt;Phosphoenolpyruvate carboxylase (PEPC)&lt;/strong&gt;, resulting in a four-carbon molecule (hence C4). This 4-carbon acid, (malate or oxaloacetate depending on the system) is then shuttled into the bundle sheath cells. There, the CO₂ is released again by a variety of enzymes depending on the system, creating a high CO₂ concentration in the cell where RuBisCO can then work efficiently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, C4 plants are much (about 50%) more efficient than their C3 counterparts, and they are particularly well adapted to high temperatures and moist environments. So, to answer your first question: as atmospheric CO2 levels continue to rise, C3 plants will gradually be able to photosynthesise more efficiently. Interestingly though, C4 plants are predicted to also benefit from increased atmospheric CO₂. If global temperatures rise as predicted, both C3 and C4 plants will be able to operate more efficiently than they currently do, up to a maximum temperature beyond which enzymes will begin to denature faster and efficiency will drop. One consideration is that the difference in efficiency between C3 and C4 systems will decrease, which may significantly alter the makeup of plant communities around the world.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a vast oversimplification, but it is accurate for the predicted overall effects. Localised effects (i.e. productivity changes in a particular region or for a particular crop) will depend on habitat, physiology, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some key papers to launch you into the literature: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Leakey, A.D.B., Bernacchi, C.J., Dohleman, F.G., Ort, D.R. &amp;amp; Long, S.P. (2004) &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1529-8817.2003.00767.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Will photosynthesis of maize (Zea mays) in the US Corn Belt increase in future [CO2] rich atmospheres? An analysis of diurnal courses of CO2 uptake under free‐air concentration enrichment (FACE)&lt;/a&gt;. Global Change Biology. [Online] 10 (6), 951–962. Available from: doi:10.1111/j.1529-8817.2003.00767.x [Accessed: 31 January 2012].&lt;/li&gt;&#xA;&lt;li&gt;Morgan, J.A., LeCain, D.R., Pendall, E., Blumenthal, D.M., Kimball, B.A., Carrillo, Y., Williams, D.G., Heisler-White, J., Dijkstra, F.A. &amp;amp; West, M. (2011) &lt;a href=&quot;http://www.nature.com/nature/journal/v476/n7359/full/nature10274.html&quot; rel=&quot;nofollow&quot;&gt;C4 grasses prosper as carbon dioxide eliminates desiccation in warmed semi-arid grassland&lt;/a&gt;. Nature. [Online] 476 (7359), 202–205. Available from: doi:10.1038/nature10274 [Accessed: 31 January 2012].&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="3340" LastEditDate="2014-10-09T15:00:19.730" LastActivityDate="2014-10-09T15:00:19.730" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="864" PostTypeId="2" ParentId="551" CreationDate="2012-01-31T20:00:57.283" Score="3" Body="&lt;p&gt;By far the best book I've read on the history of biology is &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0674032276&quot; rel=&quot;nofollow&quot;&gt;A Guinea Pig's History of Biology&lt;/a&gt;, by Jim Endersby. It tells the history of the field by focusing on experimental organisms and the contributions which were made by studying them. It has an engaging narrative style and the idea of focussing on organisms' stories is an excellent and original one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the best resource there is on the history of science is the TTC History of Science lecture series. It comes in two parts:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.thegreatcourses.com/tgc/courses/course_detail.aspx?cid=1200&quot; rel=&quot;nofollow&quot;&gt;Antiquity to 1700 by Lawrence M Principe of Johns Hopkins University&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.thegreatcourses.com/tgc/courses/course_detail.aspx?cid=1210&quot; rel=&quot;nofollow&quot;&gt;1700-1900 by Professor Frederick Gregory of Harvard&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The lecture series are VERY expensive - around $200 each. However, most good libraries will have them, and I strongly recommend getting hold of them if you can.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-01-31T20:00:57.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="865" PostTypeId="2" ParentId="855" CreationDate="2012-01-31T22:43:25.627" Score="18" Body="&lt;p&gt;Vaccines work by introducing an attenuated strain of the pathogen (or alternatively the antigens that are normally present on the pathogens surface) into the body, whereupon the body mounts an immune response.  As this will (hopefully) be the first time that the body has encountered the antigens on the pseudo-pathogen's surface, the response is called the primary response.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This consists of two main divisions: the cell mediated pathway and the humoral pathway.  In vaccination it is the humoral pathway that is important.  This is where a division of white blood cells (B-Cells) produce antibodies that are complementary to the antigens on the pathogen surface, causing a negative effect to the pathogen (death, inability to reproduce, de-activation of toxins, etc.).  However as each B-Cell produces a different antibody, there needs to be a mechanism to select the correct one:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Antigen Presentation&lt;/strong&gt; (technically part of the cell-mediated-response) - a phagocyte engulfs the pathogen and displays the pathogenic antigens on its own surface.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Clonal Selection&lt;/strong&gt; - B-Cells that are attracted to the invasion site attempt to bind their antibodies onto the pathogen's antigens.  &lt;strong&gt;It takes time for this to occur successfully&lt;/strong&gt; as you are essentially waiting for the correct mutation to happen. &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Clonal Expansion&lt;/strong&gt; - Once a complementary antibody producing B-Cell has been found it is then activated with the help of a T-Helper cell.  This causes it to divide rapidly whereupon these cloned specific B cells can secrete their antibodies which will cause detriment to the pathogen. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;It's at this point that I can start to answer your specific question.  The large clone of B cells will then sub-divide into two types.  Plasma Cells remain in the blood and produce antibodies to fight the infection.  The other type, much smaller in proportion, are called Memory Cells.  These cells have a very long lifetime and move to lymph nodes across the body (including the spleen), where they remain dormant until the same pathogen is found again.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When this is the case, the memory cells are activated by T-helpers so that they can divide into massive numbers of plasma cells to fight the infection the second time.  This secondary response is a much faster as the clonal selection stage does not have to wait for the right mutation - they are already waiting in the lymph nodes.  The response is also much stronger as each memory cell can produce large numbers of plasma cells - i.e. you can start with multiple activated B-cells (as many as you have memory cells) rather than just the one that has mutated into a complementary shape in the primary immune response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The aim of the vaccine is for the secondary response to be so quick that potentially life threatening symptoms do not occur; the body has time to find and store the correct antigen in a safe environment as the pathogen has been deactivated.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-01-31T22:43:25.627" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="866" PostTypeId="1" CreationDate="2012-01-31T22:44:03.520" Score="13" ViewCount="18109" Body="&lt;p&gt;I am attempting to reproduce results from a number of journal articles all referring to the same SNP. In doing this I'm using the same primer set outlined in the articles. When I attempted a run the other day I experienced what I can only assume was primer dimer (~40bp product, bands not visible at expected bps.) While the primers and restriction enzyme were the same among numerous articles, the annealing temperatures in the reaction varied a fair amount (52-59C). All were above the individual Tms of the primers which struck me as odd.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Calculating the Tm via primer blast here are the numbers:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Forward Tm: 50.14  [5'-GCTCTACTTCCTGAAGACCT-3']&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reverse Tm: 51.67  [5'-AGTCTCACTCACCTTTGCAG-3']&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other sites gave slightly higher numbers (54-55) but they are still below the 57C that I used in my reaction. I do not have access to a gradient thermocycler otherwise I would have tried a range myself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If an annealing temperature is chosen above the individual Tms how do the oligos have a chance to anneal with the template and eventually extend? I remember hearing the Tm calculation is more involved and includes finding where the melting curve changes direction. But on the surfance I would think the primers would never have a chance to anneal at such high temperature? What is wrong about my interpretation?&lt;/p&gt;&#xA;" OwnerUserId="96" LastActivityDate="2012-02-01T01:27:26.343" Title="Does an annealing temp higher than primer's Tm contribute to primer dimer?" Tags="&lt;dna&gt;&lt;pcr&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="867" PostTypeId="2" ParentId="866" CreationDate="2012-01-31T23:43:35.967" Score="6" Body="&lt;p&gt;I don't think primer dimers are your primary concern here. Usually in my experiences, I get primer dimers all the time, even if the reaction works and I get my bands of interest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe you ought to troubleshoot other aspects of your PCR that might account for why your reaction isn't working. Have you tried using a positive control with your primers? You may try varying the parameters of your PCR as well. Remember, standard Tms are calculated according to a 50mM salt concentration: is that what you're using? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally, if the annealing temperature is above the predicted Tms of your primers, this represents a more restrictive and selective amplification of your target. You usually use a high annealing temperature if you're seeing lots of non-specific products. Since you're seeing no products at all, consider lowering the Tm to that of your primers (50º).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you start seeing non-specific products at that Tm, I'd do what we call a &quot;Touchdown&quot; PCR -- that is, you start the reaction at a higher annealing temperature, and as each cycle progresses, it &quot;touches down&quot; to a lower annealing temperature. The principle behind this is that it starts it off at a restrictive temperature -- so your yield is very low initially, but then by gradually decreasing the &quot;restrictiveness&quot; of the reaction, your yield will improve. This will still prevent non-specific amplification b/c the less restrictive amplification will be on the fragments already amplified from the restrictive condition. Remember, biology is not exact science. Just because something says the Tm is such and such does not mean it's absolute and doesn't give you some margin of error. For example, we exploit that margin of error to optimize our experiments in the example I outlined above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyways, (might have went on a tangent a little bit) you also have to consider how you designed your primers. Primers wil high self-complementarity will self-anneal at higher Tms.&lt;/p&gt;&#xA;" OwnerUserId="177" LastActivityDate="2012-01-31T23:43:35.967" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="868" PostTypeId="2" ParentId="156" CreationDate="2012-02-01T00:05:32.563" Score="15" Body="&lt;p&gt;From a brief survey of the literature, it seems Kawasaki and Taira have been largely vindicated by the community before and since their paper. The retraction was by Taira alone, Kawasaki refused to co-sign because he maintained the data were valid. From the retraction it seems the reason for the retraction was a lost lab book.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prior to the Kawasaki and Taiga paper, there were already several other papers describing RNAi-induced epigenetic modification in mammals:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.ymthe.2005.03.003&quot;&gt;Castanotto, D., Tommasi, S., Li, M., Li, H., Yanow, S., Pfeifer, G.P. &amp;amp; Rossi, J.J. (2005) Short hairpin RNA-directed cytosine (CpG) methylation of the RASSF1A gene promoter in HeLa cells. Mol Ther. 12 (1), 179–183.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1126/science.1101372&quot;&gt;Morris, K.V., Chan, S.W.-L., Jacobsen, S.E. &amp;amp; Looney, D.J. (2004) Small Interfering RNA-Induced Transcriptional Gene Silencing in Human Cells. Science. [Online] 305 (5688), 1289 –1292.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Then there was another paper the next year by Kawasaki &amp;amp; Taira, which was not retracted:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/doi:10.4161/cc.4.3.1520&quot;&gt;Kawasaki, H. &amp;amp; Taira, K. (2005) siRNA Induced Transcriptional Gene Silencing in Mammalian Cells. Cell Cycle. [Online] 4 (3), 442–448.&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And it seems the idea is now generally accepted and supported by quite a few other studies, mainly looking at germline cells. For example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.devcel.2007.03.001&quot;&gt;Carmell, M.A., Girard, A., Kant, H.J.G. van de, Bourc’his, D., Bestor, T.H., Rooij, D.G. de &amp;amp; Hannon, G.J. (2007) MIWI2 Is Essential for Spermatogenesis and Repression of Transposons in the Mouse Male Germline. Developmental Cell. [Online] 12 (4), 503–514.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There is no review that I could find which really ties it all together convincingly, but there are several reviews on RNAi directed histone and chromatin modification in general which mention that the fact is now established in mammals:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1101/cshperspect.a003772&quot;&gt;Joshua-Tor, L. &amp;amp; Hannon, G.J. (2010) Ancestral Roles of Small RNAs: An Ago-Centric Perspective. Cold Spring Harbor Perspectives in Biology.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1101/cshperspect.a003731&quot;&gt;Volpe, T. &amp;amp; Martienssen, R.A. (2011) RNA Interference and Heterochromatin Assembly. Cold Spring Harbor Perspectives in Biology. 3 (9).&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="6" LastEditDate="2012-02-01T14:19:50.523" LastActivityDate="2012-02-01T14:19:50.523" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="869" PostTypeId="2" ParentId="866" CreationDate="2012-02-01T01:27:26.343" Score="6" Body="&lt;p&gt;Primer Tm calculations can vary significantly based on the method used. What I can tell you, is that the Tm really depend on the polymerase you are using for the PCR reaction and for each polymerase there is a set of PCR conditions you have to follow.  As I use &lt;a href=&quot;http://www.finnzymes.fi/pcr/phusion_hot_start_high_fidelity_dna_polymerase.html&quot;&gt;Phusion® Hot Start High-Fidelity DNA Polymerase&lt;/a&gt; from Finnzymes, I will give you an example with it:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, it is suggested to use the Finzymes &lt;a href=&quot;https://www.finnzymes.fi/tm_determination.html&quot;&gt;Tm calculator&lt;/a&gt; to determine the Tms of your primers. Usually the Tms are higher than the ones calculated by IDT. Then, according to the length of your primers, different annealing temperature should be set:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;for primers &gt; 20nt, anneal for 10 – 30 seconds at a Tm +3°C of the lower Tm primer&lt;/li&gt;&#xA;&lt;li&gt;for primers ≤ 20nt, use an annealing temperature equal to the Tm of the lower Tm primer&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;When calculating the Tm of your primers with the calculator:&#xA;Fwd primer Tm is 57.27&#xA;Rev primer Tm is 60.21&#xA;As they are 20bases long, your annealing temperature should be 57 degrees.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are right that the annealing temperature shouldn't be higher than the Tm of the primers. I think the problem is that different polymerases and different Tm calculators are used in the papers you are referring to. I can discuss other PCR optimizations but let me know first whether the problem is not just the anneaning temperature.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-02-01T01:27:26.343" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="870" PostTypeId="1" AcceptedAnswerId="1547" CreationDate="2012-02-01T05:12:44.247" Score="5" ViewCount="183" Body="&lt;p&gt;Conversion disorder has a set of DSM diagnosis criteria, which, among other things, includes ruling out all neurological disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, as the media has shown us (and one could argue a biased portrayal), many of these young people in &lt;a href=&quot;http://www.cnn.com/2012/01/28/health/new-york-students-illness/index.html?iref=allsearch&quot;&gt;Le Roy, NY&lt;/a&gt; who were diagnosed with conversion disorder have exhibited tics and starts that are highly reminiscent of Tourette's Syndrome, which is thought to have some basis in pathology of the basal ganglia (&lt;a href=&quot;http://en.wikipedia.org/wiki/Causes_and_origins_of_Tourette_syndrome#Pathophysiology&quot;&gt;and perhaps the thalamus and frontal cortex&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Granted, the issue is being looked into as having an environmental cause, so I can understand how the diagnosis may be reshaped, but I'm more curious about the initial diagnosis of &quot;mass hysteria&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this syndrome causes real physical symptoms and yet is &quot;psychogenic&quot;, through what physiological means is the disease acting?  Why would ruling out a neurological basis be a valid criterion? &lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-02-01T05:19:48.027" LastActivityDate="2012-03-24T11:48:56.627" Title="What evidence gives clues to the physiological basis for conversion disorder?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="871" PostTypeId="1" CreationDate="2012-02-01T10:31:50.917" Score="10" ViewCount="3962" Body="&lt;p&gt;Why do dendritic cells have CD4 or CD8 antigens on their surface? What is their function without the presence of a T-cell receptor?&lt;/p&gt;&#xA;" OwnerUserId="434" LastEditorUserId="3177" LastEditorDisplayName="user24" LastEditDate="2013-03-02T04:12:55.207" LastActivityDate="2016-06-20T03:06:22.180" Title="Why do dendritic cells have CD4/CD8 on their surface?" Tags="&lt;immunology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="872" PostTypeId="2" ParentId="551" CreationDate="2012-02-01T12:52:36.343" Score="1" Body="&lt;p&gt;There is a free video course &lt;a href=&quot;https://oli.web.cmu.edu/openlearning/forstudents/freecourses/biology&quot; rel=&quot;nofollow&quot;&gt;&quot;Modern Biology&quot;&lt;/a&gt; at Carnegie-Mellon University's Open learning initiative. This is very technical and does not cover history of biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I quite liked D.A. Sadava's non-free video course &lt;a href=&quot;http://www.thegreatcourses.com/tgc/courses/course_detail.aspx?cid=1533#&quot; rel=&quot;nofollow&quot;&gt;Understanding Genetics: DNA, Genes, and Their Real-World Applications&lt;/a&gt;. This is Genetics and Molecular Biology oriented, but also not a book. It is suitable for a reader with high-school knowledge of chemistry. Maybe it contains too few basics, so it is also not for the absolute layperson. He starts with Mendel and mentions many other 20th-century researchers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The author has co-authored one of those &lt;a href=&quot;http://www.whfreeman.com/Catalog/static/whf/thelifewirebridge2/&quot; rel=&quot;nofollow&quot;&gt;thick, expensive college-level biology textbooks&lt;/a&gt; as well. &lt;/p&gt;&#xA;" OwnerUserId="349" LastActivityDate="2012-02-01T12:52:36.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="875" PostTypeId="1" AcceptedAnswerId="15601" CreationDate="2012-02-01T20:20:01.200" Score="0" ViewCount="65207" Body="&lt;p&gt;An exam question asked what stage of meiosis corresponds with &quot;first meiotic arrest of oogenesis&quot;. I can't work out the answer from &lt;a href=&quot;http://en.wikipedia.org/wiki/Meiosis&quot; rel=&quot;nofollow&quot;&gt;the wiki page&lt;/a&gt; - can anyone explain which step this refers to?&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="430" LastEditDate="2012-02-06T16:57:04.030" LastActivityDate="2017-05-24T09:21:15.200" Title="At what stage of meiosis does &quot;first meiotic arrest of oogenesis&quot; occur?" Tags="&lt;meiosis&gt;&lt;oogenesis&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="876" PostTypeId="2" ParentId="836" CreationDate="2012-02-01T21:29:28.313" Score="5" Body="&lt;p&gt;Are you working in academia? It might be worthwhile to call the companies directly and see if there is a discounted rate for your institution (another lab or department may have already set something up). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You won't be able to get information on the different algorithms if they are proprietary.  However considering that codon usage data is public and shared knowledge, I can't imagine that the different algorithms are that much different. I think there are some tricks for choosing certain codons near the transcription start site in some organisms? From what I hear, the algorithms are constantly changing. I could tell you how my &lt;em&gt;E. coli&lt;/em&gt; optimized gene from GenScript worked two years ago, but they'd probably design it differently now. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Okay - GenScript calls their algorithm &quot;proprietary&quot;, so they are not sharing the details. DNA2.0 says their algorithm is patented, so it's out there for inspection. They published a PLOS paper on their &lt;em&gt;E. coli&lt;/em&gt; algorithm: &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0007002&quot;&gt;Welch et al.&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although, maybe all they do these days is spit out codon sequence randomly:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The results obtained in this study indicate that the codon&#xA;  randomization method is a superior strategy for codon optimization. A&#xA;  significant improvement in protein expression was obtained for the&#xA;  largely established process of chymosin production, showing the power&#xA;  of this strategy to reduce production costs of industrial enzymes in&#xA;  microbial hosts. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056764/?tool=pmcentrez&quot;&gt;(Menzella 2011)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Stitching smaller synthesized fragments works well if you're pressed for time, but it's usually more expensive. However, sometimes these companies do special pricing on synthesis for &amp;lt;1kb, which makes stitching a great choice. Turnaround is generally faster for three 1kb fragments than one 3kb fragment. &lt;/p&gt;&#xA;" OwnerUserId="204" LastEditorUserId="69" LastEditDate="2012-02-01T22:07:29.670" LastActivityDate="2012-02-01T22:07:29.670" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="877" PostTypeId="1" CreationDate="2012-02-01T23:10:13.140" Score="8" ViewCount="177" Body="&lt;p&gt;And is there any basis for believing that massage relieves that tension?&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="630" LastEditDate="2019-06-12T19:27:01.993" LastActivityDate="2019-06-12T19:27:01.993" Title="How exactly does long-term tension (over months) build up in the ligaments, tendons, muscles?" Tags="&lt;human-biology&gt;&lt;muscles&gt;&lt;tendons&gt;&lt;ligaments&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="878" PostTypeId="2" ParentId="855" CreationDate="2012-02-01T23:22:42.697" Score="14" Body="&lt;p&gt;MBQ and Rory M have already given decent answers on the &quot;hows&quot; of how the vaccine memory is formed. Now, for some twists:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are three (general) types of vaccine, all of which are meant to make your body &quot;think&quot; its being infected and provoke an immune response, while at the same time not causing active infection. They are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Live attenuated. These vaccines are made up of living pathogens that have, through a variety of methods, been rendered essentially harmless. Never the less, they are infecting you. It's a bit like getting into a shootout with people carrying Nerf guns. Good news is, the bullets are foam, but they're still shooting you. The advantages to these vaccines are that, generally speaking, they were easier to make, and because you are infected, you can shed the pathogen back into the environment, spreading the vaccine around a bit. The disadvantage? Sometimes the pathogens de-attenuate, and cause disease.&lt;/li&gt;&#xA;&lt;li&gt;Killed. Dead pathogen - your body responds to the presence of foreign antigens, develops an immune memory, and that's that. You gain safety, but lose the secondary spread of vaccinating attenuated pathogens.&lt;/li&gt;&#xA;&lt;li&gt;Virus-Like Particles. This is the sexy new class of vaccines, that is both dead and...not real. Synthetically produced, these vaccines (like the HPV vaccine) are both harmless and provoke an immune response, and can be customized - they can have antigens to different strains, etc. that you can't do just with attenuating or killing pathogens in the wild. They're awesome, and brilliant, and expensive as hell to develop and produce.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Once your body &quot;learns&quot; from the vaccine, how well it retains that memory also may vary. Some vaccines provoke a strong immune response, and the pathogen they target is genetically stable enough that you're pretty much set for life. Others, like the chicken pox vaccine, wane over time as your body isn't challenged by new exposures to the pathogen, and needs to be &quot;reupped&quot; now and again by giving you another dose of the vaccine, known as a booster. For some vaccines where your vaccine-triggered immunity may wane over time, we might not bother with a booster because you're now old enough that you're out of danger. The HPV vaccine comes to mind again - we're not &lt;em&gt;sure&lt;/em&gt; you're immune for life, but if we can make sure you're immune until say, 65 or 70, it doesn't really matter, because it will take years for cervical cancer from an HPV infection to develop anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still others target diseases that mutate rapidly enough that your body's memory doesn't last long. The yearly flu vaccine is an example of this. A year after you get your vaccine, you body may &quot;remember&quot; the previous year's strain well enough to fight it off, but that's not the strain of influenza going around that year. This is also a problem for the hypothetical development of an HIV vaccine.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2012-02-01T23:22:42.697" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="879" PostTypeId="1" AcceptedAnswerId="885" CreationDate="2012-02-02T04:52:54.663" Score="4" ViewCount="4139" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Apoptosis#Caspases&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt; just says...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The active effector caspases then proteolytically degrade a host of&#xA;  intracellular proteins to carry out the cell death program.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Okay, but what parts of the cell do they cleave up? And what happens to the rest of the cells' internal components, especially the parts that don't get cleaved up?&lt;/p&gt;&#xA;" OwnerUserId="103" LastActivityDate="2012-02-02T08:16:11.280" Title="How do caspase proteins kill a cell?" Tags="&lt;senescence&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="880" PostTypeId="1" AcceptedAnswerId="2060" CreationDate="2012-02-02T05:03:16.130" Score="5" ViewCount="346" Body="&lt;p&gt;&lt;a href=&quot;http://www.nytimes.com/2011/11/22/science/in-bodys-shield-against-cancer-a-culprit-in-aging-may-lurk.html?pagewanted=all&quot;&gt;New York Times&lt;/a&gt; article explains how killing p16-INK4a positive senescent cells can help keep the surrounding cells vigorous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So here's my question: why is p16-INK4a expressed in most cells other than heart and liver cells? What would happen if we knocked it out everywhere?&lt;/p&gt;&#xA;" OwnerUserId="103" LastActivityDate="2012-05-02T16:03:57.503" Title="Why isn't the p16-INK4a gene involved in apoptosis expressed in heart or liver tissues?" Tags="&lt;senescence&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="881" PostTypeId="1" CreationDate="2012-02-02T05:09:31.333" Score="6" ViewCount="1125" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/SA-beta-gal&quot;&gt;Wikipedia&lt;/a&gt; explains that it's a hypothetical hydrolase enzyme that catalyzes the hydrolysis of β-galactosides into monosaccharides only in senescent cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm just wondering - what causes it to be overexpressed in senescent cells - to the point that it often becomes a biomarker of senescence? And what exactly happens to the particular cell when you catalyze the hydrolysis of more β-galactosides (like lactose) into monosaccharides? &lt;/p&gt;&#xA;" OwnerUserId="103" LastActivityDate="2012-02-06T09:43:57.870" Title="Why are beta-galactosidase proteins overexpressed in senescent cells?" Tags="&lt;senescence&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="882" PostTypeId="2" ParentId="836" CreationDate="2012-02-02T05:28:53.727" Score="2" Body="&lt;p&gt;Here is a blog post from Ginkgo BioWorks that graphs the turn-times from 3 major suppliers:&#xA;&lt;a href=&quot;http://blog.ginkgobioworks.com/2012/01/14/commercial-gene-synthesis/&quot; rel=&quot;nofollow&quot;&gt;http://blog.ginkgobioworks.com/2012/01/14/commercial-gene-synthesis/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="437" LastActivityDate="2012-02-02T05:28:53.727" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="883" PostTypeId="1" AcceptedAnswerId="888" CreationDate="2012-02-02T05:51:57.693" Score="33" ViewCount="10067" Body="&lt;p&gt;I understand this might depend on the types of vegetables, but is there an average or studied specifics? Does it die immediately? Is there a way to precisely diagnose death in plants? If so, what are the conditions for it?&lt;/p&gt;&#xA;" OwnerUserId="438" LastActivityDate="2019-09-30T18:49:16.317" Title="How long will a vegetable live for after being harvested?" Tags="&lt;botany&gt;&lt;cell-biology&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="884" PostTypeId="1" AcceptedAnswerId="886" CreationDate="2012-02-02T05:59:14.690" Score="15" ViewCount="1004" Body="&lt;p&gt;This came up in a talk with a friend. I wanted to clear this doubt. I've read about it before and did again after her remark (my thoughts didn't change: her concept is Lamarck's, not Darwin's), but wanted to clarify.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding Evolution, nothing, absolutely nothing, that a person does to herself in life can be genetically inherited. It does not matter how much this person drinks, the changes they do to their body,  how dark their skin gets over life etc. Such changes can not be transmitted to their offspring in any way, correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Summary:*Is the assertion &quot;You can not change in life what will be genetically inherited in any possible way&quot; true?&lt;/p&gt;&#xA;" OwnerUserId="438" LastEditorUserId="69" LastEditDate="2012-02-02T19:35:39.290" LastActivityDate="2016-03-23T01:47:06.913" Title="Is it the case that all changes in phenotype during life are not inheritable?" Tags="&lt;evolution&gt;&lt;epigenetics&gt;" AnswerCount="5" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="885" PostTypeId="2" ParentId="879" CreationDate="2012-02-02T08:16:11.280" Score="10" Body="&lt;p&gt;Caspase do not directly kill the cell, but rather activate a process known as &lt;strong&gt;apoptosis&lt;/strong&gt;, or programmed cell death. The &lt;em&gt;programmed&lt;/em&gt; part is there to distinguish it from other types of cell death, such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Necrosis&quot;&gt;&lt;strong&gt;necrosis&lt;/strong&gt;&lt;/a&gt;, which are more aspecific death processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coming back to caspases, they are a series of proteasis, that can activate in cascade in response to a pro-apoptotic signal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To simplify matters a lot, the pro-apoptotic signal first activates &lt;em&gt;initiator caspases&lt;/em&gt;, such as caspase 8, 9, 10 (plus a series of other proteins).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These, in turn, cleave other &lt;em&gt;effector caspases&lt;/em&gt;, which are the ones who effectively do the &lt;em&gt;dirty job&lt;/em&gt;: caspase 3, 6, and 7.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now there are many things happening at the same time (see &lt;a href=&quot;http://www.abcam.com/ps/pdf/cancer/caspase.pdf&quot;&gt;this PDF from AbCam&lt;/a&gt; to get an idea of the complexity of the system).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the nuclear level you have, for instance:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;activation of DNA cleaving enzymes, such as CAD (caspase-activable DNAse), which is normally inactive, due to binding to its inhibitor I-CAD. The latter is a target of effector caspases and its degradation causes CAD to go in the nucleus and starting fragmenting DNA.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;cleavage of PARP (Poly(ADP-ribose) polymerase), a nuclear enzyme involved in finding and repairing single-strand breaks on DNA.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;cleavage of lamins (by effector caspases + other proteases), proteins that are important for the formation of nuclear lamina, and stability of the cell nucleus&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;cleavage of U1, a nuclear protein necessary for processing of mRNA.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Very complex events also happen at the mitochondria level: here you have a series of protein, which belong to the Bcl-2 family that control apoptosis mostly by regulating the levels of Ca2+ in the cell. There are 25 members of this family, that can be divided into two &quot;sides&quot;: pro-apoptotic proteins such as Bax, Bak, and BAD and anti-apoptotic proteins such as Bcl-2, Bcl-xL, and Bcl-w.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The functioning of the Blc-2 proteins is very complex and I am not up-to-date with the last literature but to simplify, essentially what happens is that when the balance between anti-apoptotic and pro-apoptotic proteins is shifted towards the pro-, there is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;liberation of cytochrome c from the mytochondria into the cytoplasm, which can activate effector caspases.&lt;/li&gt;&#xA;&lt;li&gt;induction of MPTPs (Mitochondrial Permeability Transition Pores), proteins which increases mitochondrial permeability which causes all sorts of trouble, eventually leading to swelling of mitochondria and loss of their function&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Different events also bring to an increase in cytoplasmic calcium concentration, which can, for instance, induce the activity of calcium-activated endonuclease or other pro-apoptotic calcium-dependent proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is far from being an exaustive list of what happens, but it gives you the idea of the complexity of the system.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-02-02T08:16:11.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="886" PostTypeId="2" ParentId="884" CreationDate="2012-02-02T09:37:13.153" Score="17" Body="&lt;p&gt;The assertion &quot;You cannot change in life what will be genetically inherited in any possible way&quot; is true, as you cannot (healthily) change the DNA in your germ cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the assertion &quot;You cannot change in life what will be inherited in any possible way&quot; is wrong, because of &lt;a href=&quot;http://en.wikipedia.org/wiki/Epigenetics&quot; rel=&quot;nofollow noreferrer&quot;&gt;epigenetics&lt;/a&gt;. Parts of your DNA are marked (in different ways), and this can be inherited and have an effect. E.g. the only causal difference between these two mice is the diet of their mothers:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1tmOP.jpg&quot; alt=&quot;Two mice of same genotype but different phenotype&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image source and a further explanation: &lt;a href=&quot;http://learn.genetics.utah.edu/content/epigenetics/nutrition/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nutrition and the epigenome&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-02-02T09:37:13.153" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="887" PostTypeId="2" ParentId="884" CreationDate="2012-02-02T10:14:48.597" Score="16" Body="&lt;p&gt;In general, Darwin's theory has been supported over and over again by experiments - our modern understanding of evolution is fundamentally what Darwin suggested. However, apart from appreciating many more details than Darwin ever could have, we also now know that Lamarck may not have been so crazy as he was later portrayed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Inheritance in the Darwinian sense involves the digital information of DNA, i.e the sequence of bases. But we also know that DNA can be altered structurally - i.e. in the way it folds, or whether bases are methylated - and that these structural alterations can affect the expression of genes. In some cases, these &lt;a href=&quot;http://en.wikipedia.org/wiki/Epigenetics&quot;&gt;epigenetic modifications&lt;/a&gt; can be trans-generational; they can be passed on to offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are the mechanisms that I know of (perhaps others can expand on this):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/scitable/topicpage/x-chromosome-x-inactivation-323&quot;&gt;X-chromosome inactivation&lt;/a&gt; (XCI): this is when one of two copies of the X-chromosome in females is completely inactivated by being packed into heterochromatin, preventing the DNA from being transcribed. Which chromosome (the maternal or paternal) is deactivated initially is random, but the decision can be inherited by all daughter cells. &lt;em&gt;Skewed&lt;/em&gt; x-inactivation is when a cell very early in the cell line passes on its XCI decision, and can result in a particular phenotype being activated in a whole organ or tissue (such as patches in tortoiseshell cats). It has been shown that in mice and in humans, the somatic cells can sometimes have their XCI decision influenced by the mother, and that this can lead to early skewing of the XCI in the offspring, thereby passing on a decision about which alleles are present without affecting the DNA sequence.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_imprinting&quot;&gt;Parental imprinting&lt;/a&gt;: in this case, individual alleles derived from one parent are preferentially activated or deactivated by &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_methylation&quot;&gt;methylation&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/Histone_modification#Chromatin_regulation&quot;&gt;histone modification&lt;/a&gt;. This change is passed on to the zygote, and alters expression in the offspring. Several human heritable diseases are associated with this kind of modification, such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Prader-Willi_syndrome&quot;&gt;Prader-Willi Syndrome&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Paramutation&quot;&gt;Paramutation&lt;/a&gt;: first discovered in maize, this is when the presence of one allele in a genome can affect another allele in a heritable way. I.e. if allele A is present in the same genome as allele B for a single generation, allele A is permanently inactivated so that if you breed out allele B, allele A will not be active in the offspring.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Finally, there is also a phenomenon called &lt;a href=&quot;http://en.wikipedia.org/wiki/Structural_inheritance&quot;&gt;structural inheritance&lt;/a&gt;, whereby a structural feature of an organism is inherited in a non-genetic way. There is less written about this, so the mechanism is not entirely clear as far as I know, but an example is that the 'handedness' of the spiral pattern on the shell of a protozoan &lt;em&gt;Tetrahymena&lt;/em&gt; is inherited without any genetic change (&lt;a href=&quot;http://dev.biologists.org/content/105/3/447.long&quot;&gt;Nelsen et al., 1989&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nelsen, E.M., Frankel, J. &amp;amp; Jenkins, L.M. (1989) Non-genic inheritance of cellular handedness. Development (Cambridge, England). 105 (3), 447–456.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-02-02T10:14:48.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="888" PostTypeId="2" ParentId="883" CreationDate="2012-02-02T10:36:23.477" Score="30" Body="&lt;p&gt;The short answer is that as long as the vegetable/fruit is fresh looking - i.e. the cells have not disintegrated - they will be respiring, many cells will be functioning quite normally, and the plant is still technically alive. In cases where the part of the plant we treat as a vegetable is a part intended for reproduction (e.g. a seed, or a tuber like a potato) the plant will keep growing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The point at which the plant dies is not clearly defined like it is in animals, but generally if you can still eat it, it's still alive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Death in plants is quite different from that in animals - we refer to it as senescence. The key difference is that it happens to tissues and organs which can die and separate from the organism. Individual leaves can die without the plant's health being affected. Once this has happened to all the parts, the organism is considered dead, but if there is any respiring tissue left, it's still alive.&lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-02-03T00:20:03.663" LastActivityDate="2012-02-03T00:20:03.663" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="889" PostTypeId="1" AcceptedAnswerId="890" CreationDate="2012-02-02T12:58:21.087" Score="7" ViewCount="627" Body="&lt;p&gt;Can anyone suggest a dye which specifically targets DNA, but is not fluorescent? We plan to mark DNA before observing it with RAMAN-Spectroscopy. Because of the weak signal, even a low emission would disturb the reading.&lt;/p&gt;&#xA;" OwnerUserId="405" LastEditorUserId="6307" LastEditDate="2017-04-02T20:12:48.977" LastActivityDate="2017-04-02T20:12:48.977" Title="What is a good non-fluorescent DNA dye?" Tags="&lt;dna&gt;&lt;materials&gt;&lt;spectroscopy&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="890" PostTypeId="2" ParentId="889" CreationDate="2012-02-02T13:12:54.960" Score="3" Body="&lt;p&gt;One option is to use &lt;a href=&quot;http://en.wikipedia.org/wiki/Biotinylation&quot; rel=&quot;nofollow&quot;&gt;biotin labelling&lt;/a&gt;. Most molecular biology supply companies do kits for this, and supply biotinylated nucleotides.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-02-02T13:12:54.960" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="891" PostTypeId="2" ParentId="884" CreationDate="2012-02-02T14:41:23.617" Score="4" Body="&lt;p&gt;Infections by a retro-virus (such as HIV) can, at least in principle, be inherited.&lt;br&gt;&#xA;These viruses integrate their genome into the host's DNA, and these changes pass to next generations as the cells split. So if a germ cell is infected, all the cells in the child would be.&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is whether there's a retro-virus that infects germ cells. I don't think HIV does (it can certainly pass from mother to child, but as a &quot;normal&quot; infection, not through the DNA).&lt;/p&gt;&#xA;" OwnerUserId="440" LastEditorUserId="22057" LastEditDate="2016-03-23T01:47:06.913" LastActivityDate="2016-03-23T01:47:06.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="892" PostTypeId="1" CreationDate="2012-02-02T20:53:37.710" Score="7" ViewCount="16907" Body="&lt;p&gt;Do you know of any peripheral blood mononuclear cells that would express any amount (beit low or high) of CD3 on their surface (other than T-cells)?&lt;/p&gt;&#xA;" OwnerUserId="434" LastActivityDate="2015-04-18T20:34:58.070" Title="What cells would have the CD3 marker on them (other than T-cells)" Tags="&lt;immunology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="893" PostTypeId="1" AcceptedAnswerId="920" CreationDate="2012-02-02T21:18:09.053" Score="5" ViewCount="717" Body="&lt;p&gt;I have a CIF file that I downloaded from the PDB, but if I try to use it in Coot, it complains that it is not a complete CIF definition.  &lt;a href=&quot;http://www.ccp4.ac.uk/html/libcheck.html#examples_complete&quot; rel=&quot;noreferrer&quot;&gt;This page&lt;/a&gt; provides a batch script that I may be able to tease apart to suit my needs, but I thought there was a way to do this from within the CCP4 Program Suite GUI/job manager.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maddeningly, I see in my project job history a couple &quot;dictionary&quot; jobs where I did this, but I utterly forgot how I set them up (forgive the asinine names):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/u6dhQ.png&quot; alt=&quot;CCP4 dictionary jobs&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I try to use the Monomer Library Sketcher (under Refinement/Restraint Preparation) and open a CIF (&quot;mmCIF&quot;) file, nothing happens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also under the sketcher, I can severely abuse the &quot;Load Monomer from Library&quot; and it looks like I get the right thing:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YlvtF.jpg&quot; alt=&quot;load monomer from library dialog&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, when setting up the above, it throws &quot;Error: can't read &quot;monomer_lib(code,n...&quot; warnings, then when running it generates the Geometry file (seemingly successfully) then says that Libcheck failed when trying to create the coordinate file.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;If there are other solutions, I'd be interested as well.  I've used &lt;a href=&quot;http://davapc1.bioch.dundee.ac.uk/prodrg/&quot; rel=&quot;noreferrer&quot;&gt;PRODRG&lt;/a&gt; to create CIF files before with its draw tool, but it can be a bit clumsy, it ignores how I drew my double bonds, and it creates new names for all the atoms.&lt;/p&gt;&#xA;" OwnerUserId="25" LastEditorUserId="25" LastEditDate="2012-02-03T01:12:54.177" LastActivityDate="2012-02-05T08:40:56.580" Title="How do you turn a minimal CIF description into a complete one?" Tags="&lt;structural-biology&gt;&lt;coot&gt;&lt;ccp4&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="894" PostTypeId="1" AcceptedAnswerId="895" CreationDate="2012-02-02T22:33:21.847" Score="16" ViewCount="1201" Body="&lt;p&gt;[Warning: this question is motivated by a prominent proponent of &quot;intelligent design&quot;: Prof. Michael Behe.  I'm not interested in debating creationism.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Wikipedia&lt;sup&gt;[&lt;a href=&quot;http://en.wikipedia.org/wiki/Michael_Behe&quot;&gt;1&lt;/a&gt;]&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In Darwin’s Black Box (Behe 1996) I claimed that the bacterial&#xA;  flagellum was irreducibly complex and so required deliberate&#xA;  intelligent design. The flip side of this claim is that the flagellum&#xA;  can’t be produced by natural selection acting on random mutation, or&#xA;  any other unintelligent process. To falsify such a claim, &lt;strong&gt;a scientist&#xA;  could go into the laboratory, place a bacterial species lacking a&#xA;  flagellum under some selective pressure (for mobility, say), grow it&#xA;  for ten thousand generations, and see if a flagellum--or any equally&#xA;  complex system--was produced.&lt;/strong&gt; If that happened, my claims would be&#xA;  neatly disproven.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;[emphasis mine.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I can tell, nobody has actually performed this experiment (although, my literature search was not comprehensive, so it is possible I simply haven't found the appropriate publications).  [However, there are arguments that the flagellum could have (or likely has) evolved from the type III secretory system, which shows similarity&lt;sup&gt;[&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0535335100&quot;&gt;2&lt;/a&gt;]&lt;/sup&gt;.]  This state of affairs strikes me as peculiar -- Behe's proposal sounds like an interesting experiment to perform (even disregarding any external debate).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;: Is the experiment proposed by Behe (or another experiment in the same spirit) plausible to implement in a laboratory experiment?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Experiments reproducing steps in evolution seem to turn out much easier than I would have expected &lt;em&gt;a priori&lt;/em&gt;, e.g. reproductive isolation of fruit flies&lt;sup&gt;[&lt;a href=&quot;http://dx.doi.org/10.2307/2409365&quot;&gt;3&lt;/a&gt;]&lt;/sup&gt;, experimental evolution of multicellularity&lt;sup&gt;[&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.1115323109&quot;&gt;4&lt;/a&gt;]&lt;/sup&gt;, so perhaps Behe's experiment would also be surprisingly easy to implement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Michael_Behe&quot;&gt;Wikipedia: Michael Behe&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0535335100&quot;&gt; &lt;strong&gt;Blocker A, Komoriya K, Aizawa S-I&lt;/strong&gt;. 2003. Type III secretion systems and bacterial flagella: insights into their function from structural similarities. Proceedings of the National Academy of Sciences of the United States of America 100: 3027–30.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.2307/2409365&quot;&gt; &lt;strong&gt;Dodd DMB&lt;/strong&gt;. 1989. Reproductive Isolation as a Consequence of Adaptive Divergence in Drosophila pseudoobscura. Evolution 43: 1308.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.1115323109&quot;&gt; &lt;strong&gt;Ratcliff WC, Denison RF, Borrello M, Travisano M&lt;/strong&gt;. 2012. Experimental evolution of multicellularity. Proceedings of the National Academy of Sciences of the United States of America 109: 1595–600.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="203" LastEditorUserId="740" LastEditDate="2012-09-13T21:27:21.963" LastActivityDate="2012-09-13T21:27:21.963" Title="Is Behe's experiment (evolving the bacterial flagellum) plausible in the lab?" Tags="&lt;evolution&gt;&lt;experimental-design&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="895" PostTypeId="2" ParentId="894" CreationDate="2012-02-02T23:13:10.487" Score="18" Body="&lt;p&gt;The experiment itself is technically feasible - but whether there is any point (as opposed to using the resources to perform a different experiment) is highly questionable. The problem is this: Behe's claim is that the mechanism is irreducibly complex, and that it could not have arisen by natural selection. This is theoretically falsifiable, but the experiment he proposed does not provide a good dichotomy - there is a very large chance that he is wrong but over the experimental term of 10,000 or 10,000,000 generations, the flagellum might not arise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The absence of the flagellum in the experiment is the most likely scenario, and doesn't either support or falsify his claim. It took evolutionary time, something on the order of 10&lt;sup&gt;10+&lt;/sup&gt; generations, to arise the first time (according to the consensus claim); we could not expect similar complexity to arise for the same purpose under conditions of directed evolution. That's a terrible experimental design: huge resource input, huge likelihood of no result.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be clear: it is technically feasible, but not a good experiment. He proposed it because he knew that nobody would do it (because it's a bad idea).&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-02-02T23:13:10.487" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="896" PostTypeId="2" ParentId="686" CreationDate="2012-02-02T23:31:19.140" Score="9" Body="&lt;p&gt;There are no known plants that fix their own nitrogen. &lt;strong&gt;However, there soon may be!&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because N is the major limiting factor in agricultural productivity, there is huge interest in plant systems which can fix their own. It's important enough that the Bill &amp;amp; Melinda Gates foundation have started a project aimed at reducing dependence on fertilisers by giving plants the ability to fix their own nitrogen. There are several potential strategies, the most obvious being encouraging more species to form symbioses with nitrogen fixing bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there's another proposal which builds on recent discoveries about the mechanism of nitrogen fixing in bacteria: we now know how the crucial enzyme complex is made (&lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.micro.62.081307.162737&quot;&gt;Rubio &amp;amp; Ludden, 2008&lt;/a&gt;). As a result, there are many people calling for efforts to engineer the system directly into a plant organelle (e.g. &lt;a href=&quot;http://www.sciencemag.org/content/333/6041/416.full&quot;&gt;Beatty &amp;amp; Good, 2011&lt;/a&gt;; &lt;a href=&quot;http://www.sciencemag.org/content/327/5967/812.full&quot;&gt;Godfray et al., 2010&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in 10-15 years time you can check back and the answer to this question might have changed! The most likely answer then will be &quot;just the usual suspects: rice, maize, wheat&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Beatty, P.H. &amp;amp; Good, A.G. (2011) Future Prospects for Cereals That Fix Nitrogen. Science. [Online] 333 (6041), 416 –417. Available from: doi:10.1126/science.1209467 [Accessed: 2 February 2012].&lt;/li&gt;&#xA;&lt;li&gt;Godfray, H.C.J., Beddington, J.R., Crute, I.R., Haddad, L., Lawrence, D., Muir, J.F., Pretty, J., Robinson, S., Thomas, S.M. &amp;amp; Toulmin, C. (2010) Food Security: The Challenge of Feeding 9 Billion People. Science. [Online] 327 (5967), 812 –818. Available from: doi:10.1126/science.1185383 [Accessed: 2 February 2012].&lt;/li&gt;&#xA;&lt;li&gt;Rubio, L.M. &amp;amp; Ludden, P.W. (2008) Biosynthesis of the Iron-Molybdenum Cofactor of Nitrogenase. Annual Review of Microbiology. [Online] 62 (1), 93–111. Available from: doi:10.1146/annurev.micro.62.081307.162737 [Accessed: 2 February 2012].&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-02-03T00:18:31.827" LastActivityDate="2012-02-03T00:18:31.827" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="897" PostTypeId="1" AcceptedAnswerId="903" CreationDate="2012-02-03T02:57:05.673" Score="24" ViewCount="5440" Body="&lt;p&gt;I am curious to know if insect muscles become stronger with exercise, because I have seen many insects get tired out, but I have never seen one get stronger. They always seem to become permanently weakened from excessive exercise. Do they get stronger like people do?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2014-07-08T23:59:16.773" LastActivityDate="2014-07-08T23:59:16.773" Title="Do insects' muscles become stronger with exercise?" Tags="&lt;entomology&gt;&lt;muscles&gt;&lt;growth&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="898" PostTypeId="1" CreationDate="2012-02-03T08:32:43.023" Score="7" ViewCount="1033" Body="&lt;p&gt;I am sorry if this is not appropriate for this site, but I think it fits so I am asking it here: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I went for a run yesterday, and it was about -8⁰C.  I was wearing a couple pairs of shorts, a t-shirt and a long sleeved shirt, which is not that much, so I went with the idea that I would warm up a lot while running.  After running for a while, I found that I was tired and out of breath much earlier on then I would normally be.  It raised the question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How does decreasing the ambient temperature affect the cardiovascular system?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There were two things I could think of that might directly affect it.  (1) The fact that my body's metabolism has to work to heat itself, and this takes energy.  However I am not sure how much of a role this plays since running warms you up anyway.  (2) The air being so cold, and entering the lungs, I imagine my body has to work much harder in some way to deal with it.  What exactly happens here, and how is the process different from breathing at 25⁰C?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, how much faster would we expect a runner to be able to finish a 10km run when it is 25⁰C outside versus -5⁰C outside?&lt;/p&gt;&#xA;" OwnerDisplayName="user443" LastEditorUserId="3340" LastEditDate="2014-10-09T15:08:47.443" LastActivityDate="2014-10-09T15:08:47.443" Title="What effect does ambient temperature have on the cardiovascular system?" Tags="&lt;cellular-respiration&gt;&lt;anaerobic-respiration&gt;&lt;cardiology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="899" PostTypeId="2" ParentId="884" CreationDate="2012-02-03T09:27:23.033" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is the assertion &quot;You can not change in life what will be genetically inherited in any possible way&quot; true?&#xA;  No. Does not seems the case, as other people already replied.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here, I just want to point to two recent research articles showing evidence against your assertion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first, published in Cell in 2010, is from Dr Oliver Rando, and suggests that &lt;a href=&quot;http://www.sciencedaily.com/releases/2010/12/101223130149.htm&quot; rel=&quot;nofollow&quot;&gt;you are what your father ate, too.&#xA;&lt;/a&gt;&#xA;The second, published in Nature in 2011, is from Dr Anne Brunet, and argues that &lt;a href=&quot;http://www.guardian.co.uk/science/2011/oct/19/worms-inherit-memory-longevity-parents&quot; rel=&quot;nofollow&quot;&gt;worms can inherit a 'memory of longevity'&lt;/a&gt; from long-lived parents.&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="444" LastEditDate="2013-08-23T07:26:49.413" LastActivityDate="2013-08-23T07:26:49.413" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="900" PostTypeId="2" ParentId="836" CreationDate="2012-02-03T09:40:13.173" Score="0" Body="&lt;p&gt;And here is a blog post from Reportergene that compares actual prices, even do I agree with Mad Scientist that the question about prize is probably too localized.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.reportergene.com/2011/08/gene-synthesis-review.html&quot; rel=&quot;nofollow&quot;&gt;http://www.reportergene.com/2011/08/gene-synthesis-review.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-02-03T09:40:13.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="901" PostTypeId="2" ParentId="875" CreationDate="2012-02-03T12:49:05.700" Score="9" Body="&lt;p&gt;Meiosis consists of two divisions. Both are somehow similar to &quot;ordinary&quot; type of cell division - mitosis, but there is no DNA replication between them. As mitosis, each of two meiosis divisions might be divided into 5 stages: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Profaze (condensation of chromosomes, formation of microtubular spindle apparatus between two centrosomes)&lt;/li&gt;&#xA;&lt;li&gt;Prometaphase (the nuclear membrane desintegrate and chromosomes and microtubules attach to kinetochores of chromosomes)&lt;/li&gt;&#xA;&lt;li&gt;Metaphase (The chromosomes align at the metaphase plate)&lt;/li&gt;&#xA;&lt;li&gt;Anaphase (segregation of chromosomes)&lt;/li&gt;&#xA;&lt;li&gt;Telophase (restoration of nuclear membrane, cytokinesis)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The first division is crucial for reducing number of chromosomes. The prophase is subdivided to following stages:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Leptotene (condensation of chromosomes)&lt;/li&gt;&#xA;&lt;li&gt;Zygotene (homologous chromosomes form tetrads )&lt;/li&gt;&#xA;&lt;li&gt;Pachytene (crossing over)&lt;/li&gt;&#xA;&lt;li&gt;Diplotene (chromosomes separate a little, sister chromosomes remain bounded in chiasmata)&lt;/li&gt;&#xA;&lt;li&gt;Diakinesis (futher condensation of chromosomes, the nuclear membrane desintegrates)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In animals the function of meiosis is producing gametes. In case of oogenesis (in human) this process starts during prenatal development. Between 12-th and 25-th week of female fetus development cells called oogonia become primary oocytes and enter meiosis, but become arrested in stage of dictyotene, which is prolonged diplotene of prophase of first division. Then they wait 12 up to 50 years (too long waiting increase risk of chromosomal disjunction disorders such as Down syndrome in children of old mothers), covered by a layer of cells - primordial follicle. At the beginning of each menstruation cycle one or a few of the follicles become growing (the follicle cells divide, but oocyte is still waiting). At the stage of Graafian follicle the follicle is about 75 times bigger and there is a cavity full of liquid between oocyte and surrounding cells. The hormone signal - LH from pituitary gland - brakes the meiosis block, the primary oocyte divide into secondary oocyte and small first polar body (which quickly degenerates). At this time the follicle breaks - its ovulation. The oocyte starts second division, but stops at the metaphase. This second arrest ends when sperm cell penetrates into oocyte. The second, small polar cell is released and haploid nuclei of ovum and spermatozoon fuse together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;more: &#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10008/&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK10008/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="68" LastEditorUserId="15824" LastEditDate="2015-05-20T10:18:05.013" LastActivityDate="2015-05-20T10:18:05.013" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="902" PostTypeId="1" AcceptedAnswerId="922" CreationDate="2012-02-03T12:58:46.340" Score="7" ViewCount="5662" Body="&lt;p&gt;A property of water is that it is slow to heat and cool. According to my biology book, some energy from an increase in temperature would spent breaking hydrogen bonds, so that temperature does not rise too fast - helping a cell to maintain homeostasis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I can tell, this answer does not explain how a drop in temperature would be slowed down by water in a cell. How does water slow down heat loss? Is it just because it is difficult for the heat that is already inside the cell to leave? &lt;/p&gt;&#xA;" OwnerUserId="368" LastEditorUserId="48636" LastEditDate="2019-01-07T08:56:35.497" LastActivityDate="2019-01-07T08:56:35.497" Title="How does water buffer a sudden drop in temperature?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;temperature&gt;&lt;thermodynamics&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="903" PostTypeId="2" ParentId="897" CreationDate="2012-02-03T13:10:37.467" Score="23" Body="&lt;p&gt;There are instances of insect muscle growth in response to increased use. The flight muscles of the tsetse fly (&lt;em&gt;Glossina morsitans&lt;/em&gt;) have been observed to grow at a faster rate when subjected to enforced exercise &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jmor.1051500205/abstract&quot;&gt;(Anderson and Finlayson, 1976)&lt;/a&gt;. Also larger mandibular adductor muscles (which power the feeding apparatus), and associated head capsule have been noted for caterpillars and grasshoppers feeding on particularly hard grasses &lt;a href=&quot;http://www.jstor.org/pss/1696716&quot;&gt;(Bernays, 1986)&lt;/a&gt;. However these examples occur immediately post-eclosion (i.e. after emergence as adults), and during immature stages respectively. Insect muscle typically grows during larval/nymphal (immature) stages, and often for a brief period at the start of adulthood - known as the teneral period. During immature stages, insects typically have a flexible membrane to allow for tissue growth and expansion, this can also be the case during the teneral period, before the inflexible exoskeleton has fully hardened. However at full maturity, insect growth is limited by the rigidity of their exoskeleton.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as excessive exercise is concerned, that some insects may be weakened permanently may be more to do with the fact that their life strategy is different to ours. Due to the vast number of offspring per adult, and subsequent low survival chance of any given individual, there could be an evolutionary advantage for individuals pushing themselves to possibly deadly extremes. This could lead to many deaths, whilst retaining a viable population and thus accelerate the emergence of a population of fitter individuals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Anderson, M. &amp;amp; Finlayson, L.H., 1976. The effect of exercise on the growth of mitochondria and myofibrils in the flight muscles of the tsetse fly, Glossina morsitans. &lt;em&gt;Journal of Morphology&lt;/em&gt;, 150(2), pp.321-326.&lt;/li&gt;&#xA;&lt;li&gt;Bernays, E.A., 1986. Diet-Induced Head Allometry among Foliage-Chewing Insects and its Importance for Graminivores. &lt;em&gt;Science&lt;/em&gt;, 231(4737), pp.495-497.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="445" LastEditorUserId="445" LastEditDate="2012-02-07T20:12:30.343" LastActivityDate="2012-02-07T20:12:30.343" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="904" PostTypeId="1" AcceptedAnswerId="907" CreationDate="2012-02-03T17:08:20.193" Score="11" ViewCount="10047" Body="&lt;p&gt;I recently extracted RNA from developing plant leaves for the first time, as part of a very long and intensive experiment. The samples were extremely precious because of the amount of effort that went into obtaining them (harvesting thousands of miniscule leaves, one from each plant, to get the required mass).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I extracted the RNA with TRIzol and chloroform. Nanodrop showed excellent yield as you would expect for actively growing young tissue, but some of the samples had really low 260/230 ratios. I know this suggests phenol or salt contamination, but what can I do to clean the samples without losing any of the precious RNA? And how can I avoid the contamination in the future?&lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-02-03T17:25:08.190" LastActivityDate="2014-03-19T12:18:21.617" Title="How do I clean phenol contaminated RNA without losing any of the sample?" Tags="&lt;molecular-biology&gt;&lt;rna&gt;&lt;lab-techniques&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="905" PostTypeId="1" CreationDate="2012-02-03T17:18:20.463" Score="6" ViewCount="666" Body="&lt;p&gt;It's often difficult to find the appropriate or best stain to use when I want to examine a new type of tissue. I think that's partly because many histological techniques were developed a long time ago, so the papers don't turn up in Google Scholar. Is there a standard reference which links tissues, cell types or states and their corresponding best stain?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm mostly interested in a reference text or website covering plant histology, but general references are welcome too.&lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="6" LastEditDate="2012-02-19T20:39:10.687" LastActivityDate="2012-06-23T04:52:44.073" Title="What's a good reference for choosing histological staining chemicals?" Tags="&lt;botany&gt;&lt;cell-biology&gt;&lt;staining&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="906" PostTypeId="1" AcceptedAnswerId="909" CreationDate="2012-02-03T17:45:40.223" Score="12" ViewCount="5079" Body="&lt;p&gt;Some plants have lobed leaves, like the English oak (&lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Quercus_robur&quot; rel=&quot;noreferrer&quot;&gt;Quercus robur&lt;/a&gt;&lt;/em&gt;), while other plants growing the same deciduous woodland habitats, and very often growing alongside oaks, such as the European beech (&lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fagus_sylvatica&quot; rel=&quot;noreferrer&quot;&gt;Fagus sylvaticus&lt;/a&gt;&lt;/em&gt;) don't have lobes. Here are two two leaves side by side for comparison:&lt;br /&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/eRUGC.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;br /&gt;&#xA;These two species should be subject to most of the same evolutionary pressures. Why would one evolve lobed leaves, whilst the other has only tiny serrations?&lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2017-01-03T15:46:38.370" Title="Why do some plant species have lobed leaves, while similar species in the same habitat don't?" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;ecology&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="907" PostTypeId="2" ParentId="904" CreationDate="2012-02-03T18:07:10.447" Score="9" Body="&lt;p&gt;You can clean up phenol by washing with choloroform, and then doing an isopropanol precipitation followed by a 75% EtOH wash (let me know if you'd like an exact protocol).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To avoid contamination (and sample loss), you have to be meticulous in your pipetting (which you'll get better with practice). You can always use those phase-lock tubes which basically jams a solid gel between the aqueous and organic phases so it's a lot easier to pipette.&lt;/p&gt;&#xA;" OwnerUserId="177" LastActivityDate="2012-02-03T18:07:10.447" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="908" PostTypeId="1" AcceptedAnswerId="919" CreationDate="2012-02-04T04:53:35.077" Score="7" ViewCount="434" Body="&lt;p&gt;There seems to be strong evidence to support the hypothesis that eating ginger helps reduce nausea e.g. during pregnancy (e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11275030&quot;&gt;Vutyavanich et al.&lt;/a&gt;).  It seems that &lt;a href=&quot;http://en.wikipedia.org/wiki/Gingerol&quot;&gt;gingerol&lt;/a&gt; is the active ingredient in preventing nausea (cf. &lt;a href=&quot;http://www.springerlink.com/content/j35x73316613760r/&quot;&gt;Qian et al.&lt;/a&gt;).  Wikipedia writes: &quot;Cooking ginger transforms gingerol into zingerone...&quot;.  Presumably, zingerone does not affect nausea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;: Does cooking ginger reduce its anti-nausea effect?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A Google search will reveal numerous suggestions for giving ginger tea to pregnant women to help with morning sickness.  But boiling the ginger could conceivably defeat the purpose of taking the ginger in the first place (and any effects are primarily due to the placebo).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's an article (&lt;a href=&quot;http://journals.tums.ac.ir/abs.aspx?org_id=59&amp;amp;culture_var=en&amp;amp;journal_id=2&amp;amp;issue_id=1476&amp;amp;manuscript_id=12755&amp;amp;segment=en&quot;&gt;Basirat et al.&lt;/a&gt;) which describes an experiment in which biscuits with ginger were given to patients (instead of ginger tablets), although their results alone have not convinced me one way or the other.  The authors conclude that their results indicate an anti-nausea effect, but some of their tests do not match that conclusion (i.e. a placebo was comparably effective).  Also, the group given the ginger biscuits started off with worse conditions on average.&lt;/p&gt;&#xA;" OwnerUserId="203" LastActivityDate="2012-02-05T06:43:51.620" Title="Does cooking ginger reduce its anti-nausea effect?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="909" PostTypeId="2" ParentId="906" CreationDate="2012-02-04T12:07:05.597" Score="11" Body="&lt;p&gt;This is a question for which, I think at the moment, we don't have a clear answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important to bear in mind that the leaf plays a number of important roles in the plant (photosynthesis, thermoregulation etc.) so leaf shapes probably evolved through a process of successive trade-offs. This may make it difficult to identify the exact selection processes operating on any one species. In contrast, something like the eye has a well-defined single function, which in principle at least, makes it easier to understand the link between form and function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From Niklas (1988):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Life history and optimisation theory suggest that the number of&#xA;  phenotypic solutions that allow for different equally successful trait&#xA;  combinations increases as the number of trade-offs increases – a&#xA;  conclusion that applies to traits within the leaf (e.g. for shape) as&#xA;  well as to leaf–branch relationships.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, there are a  number of ideas to explain leaf shape diversity which include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Thermoregulation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It has been shown that by adding lobes to leaves, the rate of heat transfer across a leaf is greater than that of an unlobed leaf of the same area (e.g. Gurevitch and Schuepp 1990). So, lobed leaves may be selected for under certain environmental conditions.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;hydromechanical constraints&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Lobed leaves may have greater hydraulic efficiency. For smaller veins, hydraulic pressure increases as they present an increased resistance to water flow. This places stress on the deliate outer leaf tissues. If  lobed leaves have relatively less mesophyll tissue than large, highly conductive veins, they may have reduced hydraulic resistance compared  unlobed leaves (Sack and Tyree 2005).&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;optimization for photosynthesis&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;adaptations against herbivorous animals&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;random (non-selected) variation. This is a possibility, although probably unlikely due to the importance of the leaf in plants.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, some or all of the above possibilities (which are not necessarily mutually exclusive) may shape the leaves of species which may appear to have undergone very similar selective pressures. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://geosci.uchicago.edu/pdfs/boyce/2011FunctionalPlantBiology.pdf&quot;&gt;This is a good read&lt;/a&gt; by Nicotra et al. (2011) which summarizes the state of play.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gurevitch J, Schuepp PH (1990) Boundary layer properties of highly dissected leaves – an investigation using an electrochemical fluid tunnel. Plant, Cell &amp;amp; Environment 13, 783–792. doi:10.1111/j.1365- 3040.1990.tb01094.x&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nicotra et al., The evolution and functional significance of leaf shape&#xA;in the angiosperms, Functional Plant Biology, 2011, 38, 535–552&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Niklas KJ (1988) The role of phyllotactic pattern as a developmental constraint on the interception of light by leaf surfaces. Evolution 42, 1–16. doi:10.2307/2409111&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sack L, Tyree MT (2005) Leaf hydraulics and its implications in plant structure and function. In ‘Vascular transport in plants.’ (Eds NM Holbrook, MA Zwieniecki) pp. 93–114. (Elsevier Academic Press: Burlington, MA, USA)&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-02-04T12:21:40.707" LastActivityDate="2012-02-04T12:21:40.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="910" PostTypeId="1" AcceptedAnswerId="918" CreationDate="2012-02-04T19:51:29.587" Score="12" ViewCount="51245" Body="&lt;p&gt;Will it travel more slowly since it hasn't had food for a day?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What if I left the cup there for longer?&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="107" LastEditDate="2012-03-11T03:03:48.523" LastActivityDate="2018-07-13T06:10:32.770" Title="If I put a cup over a spider, and leave it there for a day, will the spider survive?" Tags="&lt;zoology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="911" PostTypeId="1" AcceptedAnswerId="997" CreationDate="2012-02-04T21:14:39.090" Score="3" ViewCount="599" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/875/what-is-the-stage-of-meiosis-of-first-meiotic-arrest-of-oogenesis/901?iemail=1#901&quot;&gt;My old question&lt;/a&gt; raised this new question. After reading this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10008/&quot; rel=&quot;nofollow noreferrer&quot;&gt;page&lt;/a&gt; I can say now that metaphase is the stage in which the second meiotic arrest occurs within oogenesis:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The oocyte is arrested again in the metaphase of the second meiotic&#xA;  division.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is difficult to visualize the thing in my head. I could not find a video of specifically for oogenesis but probably the general model for meiosis holds true. The problem I am having is that I cannot see the arresting steps in this general &lt;a href=&quot;http://www.youtube.com/watch?v=D1_-mQS_FZ0&quot; rel=&quot;nofollow noreferrer&quot;&gt;meiosis video&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How do you see the second meiotic arrest of oogenesis in the above video?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I cannot even see clearly the first meiotic arrest. I only know that it is in prophase for the first and metaphase for the second.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2012-02-11T17:56:28.837" Title="How do you see the stage of the second meiotic arrest in oogenesis in the given video?" Tags="&lt;meiosis&gt;&lt;oogenesis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="915" PostTypeId="2" ParentId="881" CreationDate="2012-02-05T05:31:49.900" Score="3" Body="&lt;p&gt;Looking at the articles referenced in the Wikipedia article, there's probably no direct physiological link between senescence and beta-galactosides. &lt;a href=&quot;http://dx.doi.org/10.1111/j.1474-9726.2006.00199.x&quot; rel=&quot;nofollow&quot;&gt;Lee et al (2006)&lt;/a&gt; and others before them have shown that the &quot;hypothetical&quot; protein is just regular lysosomal beta-galactosidase, which is present in higher concentrations in aging and stressed cells because the number of lysosomes increase under those conditions. There's a collection of references in the Discussion section of the Lee paper that delves deeper into the aging-lysosome connection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm well out of my depth by this point, but if I were going to take a wild guess I'd suggest that lysosomal upregulation could be part of a stress response involving autophagy (i.e. the cell breaking down and recycling intracellular materials to meet critical demands), though I don't know the specific connection to aging. As far as beta-galactosides go: if you have any hanging around, you get to eat them, is all, I bet. I bet the references in Lee would tell you if I'm on track or not.&lt;/p&gt;&#xA;" OwnerUserId="452" LastEditorUserId="6" LastEditDate="2012-02-06T09:43:57.870" LastActivityDate="2012-02-06T09:43:57.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="917" PostTypeId="2" ParentId="892" CreationDate="2012-02-05T06:37:32.627" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;CD3 is initially expressed in the cytoplasm of pro-thymocytes, the&#xA;  stem cells from which T-cells arise in the thymus. The pro-thymocytes&#xA;  differentiate into common thymocytes, and then into medullary&#xA;  thymocytes, and it is at this latter stage that CD3 antigen begins to&#xA;  migrate to the cell membrane. &lt;strong&gt;The antigen is found bound to the&#xA;  membranes of all mature T cells, and in virtually no other cell type,&#xA;  although it does appear to be present in small amounts in &lt;em&gt;Purkinje&#xA;  cells&lt;/em&gt;.&lt;/strong&gt; This high specificity, combined with the presence of CD3 at&#xA;  all stages of T cell development, makes it a useful&#xA;  immunohistochemical marker for T cells in tissue sections. The antigen&#xA;  remains present in almost all T-cell lymphomas and leukaemias, and can&#xA;  therefore be used to distinguish them from superficially similar&#xA;  B-cell and myeloid neoplasms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://en.wikipedia.org/wiki/CD3_(immunology&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/CD3_(immunology&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="455" LastEditorUserId="6" LastEditDate="2012-02-05T07:26:07.637" LastActivityDate="2012-02-05T07:26:07.637" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="918" PostTypeId="2" ParentId="910" CreationDate="2012-02-05T06:39:47.490" Score="9" Body="&lt;p&gt;Just solely in terms of not having food (ignoring the importance of O&lt;sub&gt;2&lt;/sub&gt; that Ramkryp has pointed out), spiders don't necessarily have to feed on a daily basis anyway.  It's not the same species of spider as you ask about in your question, but consider:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The metabolic and water evaporation strategies in spiders may be part of a set of physiological adaptations to tolerate low or unpredictable food availability, buffering spiders against environmental fluctuations such as those of the high mountains of the central Andes. The aim of this study is to analyze experimentally the variations in metabolic rate and the rate of evaporative water with food and/or water restriction in a high mountain mygalomorph spider population (Paraphysa sp.). We found that the low metabolism of this spider was not affected by water restriction, but its metabolism was depressed after 3 weeks of food deprivation. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;from Canals M, Figueroa D, et al (2011). Effects of diet and water supply on energy intake and water loss in a mygalomorph spider in a fluctuating environment of the central Andes. J. Insect Physiol, 57(11), 1489-94.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biochemical makeup of the spider may be radically different than most other animals, and breaking down energy stores must take place over a longer timecourse.  &lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2012-02-05T06:39:47.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="919" PostTypeId="2" ParentId="908" CreationDate="2012-02-05T06:43:51.620" Score="5" Body="&lt;p&gt;Good news! Some Australians have published on the stability of aqueous gingerol at elevated temperatures: &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jps.1116/full&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1002/jps.1116/full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gingerol turns out to be stable enough to make a cup of tea with at neutral pH. They also note that gingerol and its primary decomposition product form a 50-50 mixture that doesn't degrade further over shortish time periods, and that the decomposition product is probably restored to gingerol in the stomach's acidic pH -- so you're good to make your tea, and probably to hold on to it for at least a few days.&lt;/p&gt;&#xA;" OwnerUserId="452" LastActivityDate="2012-02-05T06:43:51.620" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="920" PostTypeId="2" ParentId="893" CreationDate="2012-02-05T08:40:56.580" Score="2" Body="&lt;p&gt;Not quite as ideal as I had hoped, but it works:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Get and install &lt;a href=&quot;http://www.ccp4.ac.uk/download/os.php&quot; rel=&quot;nofollow&quot;&gt;CCP4&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Obtain minimal CIF file from PDB or elsewhere.  Save to some folder easy to get at with the console.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Launch console and &lt;code&gt;cd&lt;/code&gt; to folder with the minimal definition.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Run &lt;code&gt;libcheck&lt;/code&gt; by typing it and hitting return &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;If it complains it's not found, the CCP4 &lt;code&gt;bin&lt;/code&gt; directory may not be in your PATH environment variable.  You can get around this by specifing the full path to the program, e.g.: &lt;code&gt;c:\CCP4-Packages\ccp4-6.1.13\bin\libcheck.exe&lt;/code&gt; (may vary with version)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Say &quot;Y&quot; or &quot;A&quot; at the &lt;code&gt;_DOC:&lt;/code&gt; prompt for some more files, &quot;N&quot; if you don't care (I generally don't)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;At the &lt;code&gt;--&amp;gt;&lt;/code&gt; prompts, specify:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the input file, e.g.: &lt;code&gt;file_l: ABC.cif&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;the monomer: &lt;code&gt;mon: ABC&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;output file name: &lt;code&gt;file_o: ABC_out&lt;/code&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Leave a prompt blank and hit return to start processing.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;If it runs successfully it might look something like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;C:\Users\Nick&amp;gt;libcheck&#xA;&#xA;  --- LIBCHECK --- /Vers 4.2.8   ; 02.06.2009/&#xA;&#xA;&#xA;  Do you want to have FILE-DOCUMENT /libcheck.doc/ ? /&amp;lt;N&amp;gt;/Y/A :&#xA;    N - means without DOC-file&#xA;    Y - with new contents&#xA;    A - means to keep old contents and add new information&#xA;        with DOC-file program creates batch file: libcheck.bat&#xA; _DOC:n&#xA;&#xA;&#xA; #&#xA; #      Keywords:&#xA; #&#xA; #FILE_L:   &amp;lt; &amp;gt;  - additional library, &quot; &quot; means without this file&#xA; #MON:      &amp;lt; &amp;gt;  - give info about this monomer&#xA; ... (shortened) ...&#xA; #SRCH: &amp;lt;N&amp;gt;/Y/0  - Y - global search, 0 - for MON from PDB_file&#xA; #                 (only with NODIST = N)&#xA;&#xA; #---  type &quot;keyword   parameters&quot; and/or ---&#xA; #---  press key &quot;CR&quot; to run program      ---&#xA; --&amp;gt;file_l: ABC.cif&#xA; --&amp;gt;mon: ABC&#xA; --&amp;gt;file_o: ABC_out&#xA; --&amp;gt;&#xA; MON   : ABC&#xA; -------------&#xA; Output file   :ABC_comp&#xA; Input user lib:ABC.cif&#xA; _chem_comp.name &quot;DRUG INTERMEDIATE&quot;&#xA;&#xA;          17          55&#xA; &quot;DRUG INTERMEDIATE&quot;&#xA;&#xA; -------------&#xA; Keywords:&#xA; HFLAG : Y&#xA; COOR  : N&#xA; LCOOR : Y&#xA; SRCH  : 0&#xA; REF   : Y&#xA; NODIST: Y&#xA; ERROR ==&amp;gt; In the loop containing the item_chem_comp.three_letter_code&#xA; ERROR ==&amp;gt; The number of expected items and the number existing items do not match&#xA; ERROR ==&amp;gt; The number of expected items is    7&#xA;  NUMBER OF MONOMERS IN THE LIBRARY          :     1&#xA;                with complete description    :     0&#xA;  NUMBER OF MODIFICATIONS                    :     0&#xA;  NUMBER OF LINKS                            :     0&#xA;  I am reading libraries. Please wait.&#xA;      - energy parameters&#xA;      - monomer&quot;s description (links &amp;amp; mod )&#xA;  I am reading library. Please wait.&#xA;      - monomer&quot;s description&#xA;  WARNING : monomer:ABC      - has the minimal description.&#xA;  now monomer:ABC      - has complete description.&#xA;  I will check it.&#xA; * CIFile  : ABC_out_ABC.cif&#xA; * PDBfile : ABC_out_ABC.pdb&#xA; * Plotfile: ABC_out_ABC.ps&#xA;  I am writing new description to&#xA;  file: ABC_out.lib&#xA;&#xA;C:\Users\Nick&amp;gt;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;It yields the following output files:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;code&gt;(file_o)&lt;/code&gt;: looks like a CIF file with lots of whitespace and records stripped out&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;&lt;code&gt;(file_o)&lt;/code&gt;.lib: the desired, complete definition file&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;(file_o)&lt;/code&gt;_&lt;code&gt;(mon)&lt;/code&gt;.cif: an even more minimal CIF file with only XYZ coords&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;(file_o)&lt;/code&gt;_&lt;code&gt;(mon)&lt;/code&gt;.pdb: a PDB file&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;(file_o)&lt;/code&gt;_&lt;code&gt;(mon)&lt;/code&gt;.ps: a document with a stereo labeled diagram, and lists of bonds, angles, chirality (centers?) and planes.  Can convert it to the easier-to-use PDF format using this &lt;a href=&quot;http://www.ps2pdf.com/convert.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.ps2pdf.com/convert.htm&lt;/a&gt;, or other tools.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="25" LastActivityDate="2012-02-05T08:40:56.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="921" PostTypeId="1" AcceptedAnswerId="923" CreationDate="2012-02-05T13:07:37.810" Score="14" ViewCount="19029" Body="&lt;p&gt;I was wondering why, when you are cold, scar tissue turns bluish or purple while original skin stays the same color.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only thing I can think of, is that maybe scar tissue gets less circulation than regular skin, so when it gets cold it restricts circulation.&lt;/p&gt;&#xA;" OwnerUserId="135" LastActivityDate="2016-06-02T14:48:02.827" Title="Why does scar tissue change color?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="922" PostTypeId="2" ParentId="902" CreationDate="2012-02-05T14:11:30.113" Score="4" Body="&lt;p&gt;From pure biophysical viewpoint the question &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&quot;Why does water buffer sudden temperature changes?&quot;&lt;/strong&gt; can be answered in the following way: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Water has relatively high &lt;a href=&quot;http://en.wikipedia.org/wiki/Heat_capacity&quot; rel=&quot;nofollow&quot;&gt;specific heat capacity&lt;/a&gt;&lt;/strong&gt;. This is the measure of the energy required to raise the temperature of one kilogram of a substance by one kelvin without a change of state occurring. &quot;Relatively high&quot; means that &lt;strong&gt;water can absorb more energy without noticeable (for the cell) increase in temperature&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are some heat capacity values from the above-linked Wikipedia article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Animal (incl. human) tissue   3500 Jkg&lt;sup&gt;-1&lt;/sup&gt;&lt;br&gt;&#xA;  Water at 25 °C    liquid  &lt;strong&gt;4181.3&lt;/strong&gt; Jkg&lt;sup&gt;-1&lt;/sup&gt;&lt;br&gt;&#xA;  Methanol  liquid  2597 Jkg&lt;sup&gt;-1&lt;/sup&gt;&lt;br&gt;&#xA;  Ethanol       liquid  2440 Jkg&lt;sup&gt;-1&lt;/sup&gt;&lt;br&gt;&#xA;  Paraffin  wax solid   2500 Jkg&lt;sup&gt;-1&lt;/sup&gt;&lt;br&gt;&#xA;  Graphite  solid   710 Jkg&lt;sup&gt;-1&lt;/sup&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Water has relatively high &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_thermal_conductivities&quot; rel=&quot;nofollow&quot;&gt;thermal conductivity&lt;/a&gt;&lt;/strong&gt;. This means that the &lt;strong&gt;absorbed heat is quickly distributed over the complete cell volume&lt;/strong&gt;, leveling down the focal temperature increases in cell. Here are again some values for comparison:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Water &lt;strong&gt;0.6&lt;/strong&gt; Wm&lt;sup&gt;-1&lt;/sup&gt;K&lt;sup&gt;-1&lt;/sup&gt;&lt;br&gt;&#xA;  Wood 0.2  Wm&lt;sup&gt;-1&lt;/sup&gt;K&lt;sup&gt;-1&lt;/sup&gt;&lt;br /&gt;&#xA;  Paper 0.05  Wm&lt;sup&gt;-1&lt;/sup&gt;K&lt;sup&gt;-1&lt;/sup&gt;&lt;br&gt;&#xA;  Glycerol 0.3 Wm&lt;sup&gt;-1&lt;/sup&gt;K&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The follow-up questions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Why does water have relatively high heat capacity?&quot; and &quot;Why does water have relatively high thermal conductances?&quot; are not within the scope of this site. However, here exactly comes your explanation with hydrogen bonds in play (from Wikipedia):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hydrogen-containing polar molecules like ethanol, ammonia, and water&#xA;  have powerful, intermolecular hydrogen bonds when in their liquid&#xA;  phase. These bonds provide another place where heat may be stored as&#xA;  potential energy of vibration, even at comparatively low temperatures.&#xA;  Hydrogen bonds account for the fact that liquid water stores nearly&#xA;  the theoretical limit of 3 R per mole of atoms, even at relatively low&#xA;  temperatures (i.e. near the freezing point of water).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="66" LastEditorUserId="69" LastEditDate="2012-02-05T21:51:27.533" LastActivityDate="2012-02-05T21:51:27.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="923" PostTypeId="2" ParentId="921" CreationDate="2012-02-05T14:56:53.283" Score="14" Body="&lt;p&gt;The main mechanism behind the scar changing its color is the dilation of blood vessels within the scar tissue. The dilated vessels lead to the congestion of blood flow. The red blood cells moving more slowly leave more oxygen due to its diffusion to the tissue and the hemoglobin -- the oxygen holding protein -- changes its color from scarlet (bound to oxygen) to cyan (released/bound to CO&lt;sub&gt;2&lt;/sub&gt;). Since scars are not covered by skin, the blood vessels are clearly visible here and you see this characteristic color.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The triggering mechanism here is cold that increases the energy barrier for many biochemical reactions, first of all those required for smooth muscle contraction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cold-induced vessel dilation (that can be seen, for example, on cheeks and extremities) with mild circulatory disturbances ultimately undergoes into so-called cold vessel paralysis when smooth muscles of blood vessel walls completely loose their ability to contract and are maximally dilated. The cyan color of the scar is usually seen at the very last stage, that can occur unexpectedly quickly because scars do not have any warmth insulation layer compared to the regions covered by skin.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="66" LastEditDate="2012-02-05T22:09:49.893" LastActivityDate="2012-02-05T22:09:49.893" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="924" PostTypeId="2" ParentId="871" CreationDate="2012-02-05T15:15:47.090" Score="6" Body="&lt;p&gt;There is no direct connection between CD (cluster of differentiation) receptors and T-cell receptor (TCR).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CD-receptors are used to label and distinguish different cells belonging to immune system: &lt;a href=&quot;http://en.wikipedia.org/wiki/Macrophages&quot; rel=&quot;nofollow noreferrer&quot;&gt;macrophages&lt;/a&gt;, T- and B-cells etc. Dendtritic cells play a significant role as antigen presenting cells and belong to vertebrate (and human) immune system and thus bear certain CD receptor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These cells participate in the process of learning a new antigen by the immune system. During the very first phase the antigen is taken up by these cells, cleaved and processed. Depending upon the antigenic properties of the molecule it can be recognized as a valid antigen. In this case dentritic cells participate in the process of &lt;a href=&quot;http://en.wikipedia.org/wiki/Antigen_presentation&quot; rel=&quot;nofollow noreferrer&quot;&gt;antigen presentation&lt;/a&gt;, where this new antigen bound to the MHC receptor is expressed on the cell membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/THXjb.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TCR is the protein that binds to this complex (MHC + antigen) and as long as this binding takes place the signal about antigen is propagated further to the immune system (leading to formation or augmentation of immune response depending upon the cell type which connects to this complex).&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-02-05T15:15:47.090" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="925" PostTypeId="2" ParentId="764" CreationDate="2012-02-05T15:35:07.230" Score="4" Body="&lt;p&gt;I would say &lt;strong&gt;no&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question somehow implies that somatosensory cortex is equally distributed among the different sensory areas of the body, whereas in the reality this is the known &quot;&lt;em&gt;cortical homunculus&lt;/em&gt;&quot; &lt;a href=&quot;http://en.wikipedia.org/wiki/Cortical_homunculus&quot; rel=&quot;nofollow noreferrer&quot;&gt;concept&lt;/a&gt; of how this distribution looks:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qiaKD.png&quot; alt=&quot;cortical homunculus&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at this representation you'll see that chest and legs take only about one third to one fourth of the cortex, thus the changes between short and tall people don't seem to have noticeable contribution to the overall cortex size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we just walk away from cortex size and discuss the amount of nerve cells in these areas I would say that these numbers should correlate with the number of peripherial receptor cells that provide input for them, and since there is no known changes in receptor density among different body sizes, even the amount of nerve cells seems to be more or less same.&lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="9943" LastEditDate="2016-02-26T23:40:39.620" LastActivityDate="2016-02-26T23:40:39.620" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="926" PostTypeId="1" AcceptedAnswerId="981" CreationDate="2012-02-05T16:20:27.570" Score="23" ViewCount="4434" Body="&lt;p&gt;Is it possible for a virus to live symbiotically with its host?&#xA;Is the human body plagued with viral infections that do negligible harm, or even serve a beneficial role?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="238" LastEditDate="2012-02-14T03:01:17.283" LastActivityDate="2012-02-27T23:40:30.970" Title="Harmless virus?" Tags="&lt;immunology&gt;&lt;pathology&gt;&lt;virology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="927" PostTypeId="5" CreationDate="2012-02-05T16:25:07.137" Score="0" Body="&lt;p&gt;The use of data-analytical, mathematical modeling and computational techniques to study Biology.&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="238" LastEditDate="2012-02-05T16:27:28.543" LastActivityDate="2012-02-05T16:27:28.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="928" PostTypeId="4" CreationDate="2012-02-05T16:25:07.137" Score="0" Body="Use of data , mathematical modeling and computational techniques to study biology" OwnerUserId="238" LastEditorUserId="238" LastEditDate="2012-02-05T16:27:32.757" LastActivityDate="2012-02-05T16:27:32.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="930" PostTypeId="2" ParentId="837" CreationDate="2012-02-05T21:25:50.653" Score="9" Body="&lt;p&gt;I have never heard about this phenomenon from my patients or professors at the Medical School, but this is a possible mechanism that comes to my mind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the classification for antibiotics takes consideration the effect on bacteria. Two possible effects are either &lt;a href=&quot;http://en.wikipedia.org/wiki/Bacteriostatic&quot;&gt;stopping the proliferation&lt;/a&gt; (and letting the immune system to kill those that are currently present in the body) or &lt;a href=&quot;http://en.wikipedia.org/wiki/Bactericide#Bactericidal_antibiotics&quot;&gt;killing bacteria directly&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second approach is obviously more effective but has one big disadvantage: massive death of bacteria leads to the massive release of their toxins that are normally trapped within they bodies (so-called endotoxins). The symptoms you describe as &quot;impossible fatigue&quot; match exactly the symptoms of bacterial intoxication -- and this can increase upon the antibiotics intake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending upon the bioavailability and pharmacokinetics some antibiotics might not kill all bacteria &quot;on the first run&quot; and the symptoms of intoxication recur several times with decreasing severity of manifestations.  &lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-02-05T21:25:50.653" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="931" PostTypeId="1" AcceptedAnswerId="1172" CreationDate="2012-02-05T23:59:43.303" Score="13" ViewCount="10509" Body="&lt;p&gt;What is known about the targets of Golgi staining of neurons? Are larger neurons more likely to be stained? Are specific cell types more susceptible than others?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The current &lt;a href=&quot;http://en.wikipedia.org/wiki/Golgi%27s_method&quot;&gt;wikipedia article&lt;/a&gt; says the mechanism is still not fully understood. What is preventing us from using the advanced molecular biology techniques to understand the process?&lt;/p&gt;&#xA;" OwnerUserId="460" LastEditorUserId="452" LastEditDate="2012-02-06T06:33:50.530" LastActivityDate="2013-02-22T15:10:57.733" Title="How does Golgi's neural histological stain work?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="932" PostTypeId="1" CreationDate="2012-02-06T10:05:50.350" Score="8" ViewCount="8777" Body="&lt;p&gt;My last phrasing of this question did not go down well, so I will try again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genotype of species is not always the same. If you ask yourself why not all of these possible expressions except one have died out, a natural answer is each genotype occupies a specific niche: For example, different eye colors might be found attractive by different kinds of people. If the the genotype for one eye color became more rare for some reason, other individuals with this genotype had a higher mating chance; the frequency of that genotype would get pushed back up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But there seem to be genotypes (for example, having zits) that don't occupy any niche at all. Why didn't they die out?&lt;/p&gt;&#xA;" OwnerDisplayName="user458" LastActivityDate="2012-10-31T12:14:25.707" Title="Why does so much variation exist within species?" Tags="&lt;evolution&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="933" PostTypeId="2" ParentId="932" CreationDate="2012-02-06T11:30:32.557" Score="12" Body="&lt;p&gt;First of all, your assumption is incorrect: those are not genotypes and they do not occupy specific niches. You are talking about phenotypes (eye colour) or in the case of acne, not a trait at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll answer the question I think you're asking: &lt;strong&gt;why does biological variation exist?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Variation is constantly being generated by mutation, errors in the replication of the genome of an individual. If a mutation occurs in the gametic cells, it affects the genotype of the offspring. By affecting the genotype, it may or may not have a discernable effect on the phenotype. Where a gametic mutation isn't fatal, it has a chance of becoming established in the population when that mutant individual breeds. That chance is increased the further along the gradient from harmful to beneficial that effect of that mutation is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Variation also exists because development responds to environmental factors, not just genetics. Different individuals grow in different environments, and have unique combinations of factors influencing many traits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason variation persists is because, except under conditions of extreme selective pressure or genetic bottlenecks, many traits have no impact on survival or fecundity (reproductive success) or are determined only partly by genetics. Height, for example, only has a very slight impact on fecundity within quite a broad range of heights. It is partly genetically determined, and partly determined by environmental factors such as diet (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16140897&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eckhardt et al. 2005&lt;/a&gt;), exposure to toxins during development, muscular development etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If height were the key factor in human mate selection, we might see a gradual reduction in the range of heights, and a gradual increase in average height. However, what we see in reality is that height has changed through human history in concordance with economic factors like social status, inflation and war (e.g. &lt;a href=&quot;http://www.nber.org/papers/w8542&quot; rel=&quot;nofollow noreferrer&quot;&gt;Steckel, 2001&lt;/a&gt;), suggesting that nutrition is a major determinant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know it wasn't your choice of example, but for more detail on the effects of natural selection on human height, &lt;a href=&quot;https://biology.stackexchange.com/questions/457/height-and-natural-selection-in-humans&quot;&gt;see this question&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2012-02-06T16:14:49.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="934" PostTypeId="2" ParentId="339" CreationDate="2012-02-06T17:04:27.147" Score="6" Body="&lt;p&gt;I know nothing about biology however I did watch an amazing PBS documentary on cuttlefish that I think is fairly relevent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.pbs.org/wgbh/nova/nature/kings-of-camouflage.html&quot;&gt;http://www.pbs.org/wgbh/nova/nature/kings-of-camouflage.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;NARRATOR: During mating, males outnumber the females, sometimes 10 to&#xA;  one. And they're all looking for the chance to pass on their genes.&#xA;  While a female lays eggs beneath a rock, a big male tries to&#xA;  monopolize her, staving off the other hopeful suitors.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Sometimes intimidation alone won't work, and the competitors hurl&#xA;  themselves into a violent and bizarre looking wrestling match.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Like an octopus, they'll squirt out an inky smokescreen when it's time&#xA;  for a hasty retreat.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;But size and strength aren't the only ways to impress the ladies.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Thanks to the cuttlefish's skin morphing talents, the smaller males&#xA;  have a clever trick up their sleeve.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;MARK NORMAN: The really interesting thing in this system is actually&#xA;  far less obvious, and when you first dive with them, you don't see it.&#xA;  It takes a while before you realize what's going on.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The small males, who have no chance in a contest with a big male, are&#xA;  actually doing something completely different. They're effectively&#xA;  cross-dressing. They're dressing up as a female, by pulling in their&#xA;  webs and putting on this mottled color pattern and gliding past these&#xA;  big, aggressive male, pretending to be a female, and will come in to&#xA;  the female underneath.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;And what happens is, as another big male comes in and a potential&#xA;  conflict between these big guys starts up, the sneaker males start&#xA;  mating with her, successfully mate with the female, while the big guy&#xA;  isn't even aware of it.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;NARRATOR: The cross-dressers' success is all the more impressive&#xA;  because the females often play hard to get, as Roger Hanlon has seen&#xA;  firsthand.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;ROGER HANLON: These females are very picky. They reject 70 percent of&#xA;  approaches for mating. Yet they only reject 30 percent of the&#xA;  cross-dressing males. So this trick gets them in the door, so to&#xA;  speak, past the fighting male, and they're accepted by the female.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="462" LastActivityDate="2012-02-06T17:04:27.147" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="935" PostTypeId="1" AcceptedAnswerId="2552" CreationDate="2012-02-06T17:32:55.753" Score="46" ViewCount="12654" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Polyploid&quot;&gt;Polyploidy&lt;/a&gt; is the multiplication of number of chromosomal sets from 2n to 3n (triploidy), 4n (tetraploidy) and so on. It is quite common in plants, for example many crops like wheat or Brassica forms. It seems to be rarer in animals but still it is present among some amphibian species like Xenopus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I know in mammals polyploidy is lethal (I don't mean tissue - limited polyploidy). I understand that triploidy is harmful due to stronger influence of maternal or paternal epigenetic traits that cause abnormal development of placenta, but why there is no tetraploid mammals?&lt;/p&gt;&#xA;" OwnerUserId="68" LastEditorUserId="69" LastEditDate="2012-02-17T15:04:59.673" LastActivityDate="2015-08-31T01:11:51.847" Title="Why is polyploidy lethal for some organisms while for others is not?" Tags="&lt;evolution&gt;&lt;embryology&gt;&lt;chromosome&gt;&lt;polyploidy&gt;" AnswerCount="4" CommentCount="5" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="936" PostTypeId="2" ParentId="898" CreationDate="2012-02-06T19:19:26.777" Score="3" Body="&lt;p&gt;In relation to the cardio vascular system a combination of adrenaline from exercise and the bodies natural response to the cold causes constriction of blood vessels in the skin and extremities. This helps to reduce heat loss.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The movement from running increases the amount of cold air that runs across your body and into your lungs, which would offset the effect of heat generated from running. According to the article about &lt;a href=&quot;http://en.wikipedia.org/wiki/Thermoregulation#In_cold_conditions&quot; rel=&quot;nofollow&quot;&gt;Thermoregulation in cold conditions&lt;/a&gt; on Wikipedia, the offset is great enough to make shivering while standing still a better way to keep warm.&lt;/p&gt;&#xA;" OwnerUserId="368" LastEditorUserId="69" LastEditDate="2012-02-06T22:27:34.907" LastActivityDate="2012-02-06T22:27:34.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="937" PostTypeId="1" AcceptedAnswerId="939" CreationDate="2012-02-06T22:17:15.310" Score="153" ViewCount="6704" Body="&lt;p&gt;Evolution is often mistakenly depicted as linear in popular culture. One main feature of this depiction in &lt;a href=&quot;http://www.youtube.com/watch?v=faRlFsYmkeY&quot;&gt;popular&lt;/a&gt; &lt;a href=&quot;http://www.youtube.com/watch?v=R795KiMD4zs&quot;&gt;culture&lt;/a&gt;, but even &lt;a href=&quot;http://www.youtube.com/watch?v=jHoxZF3ZgTo#t=2m51&quot;&gt;in science popularisation&lt;/a&gt;, is that some ocean-dwelling animal sheds its scales and fins and crawls onto land.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, this showcases only &lt;em&gt;one&lt;/em&gt; ancestral lineage for &lt;em&gt;one&lt;/em&gt; specific species (&lt;em&gt;Homo sapiens&lt;/em&gt;). My question is: &lt;strong&gt;Where else did life evolve out of water onto land?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intuitively, this seems like a huge leap to take (adapting to a fundamentally alien environment) but it still must have happend several times (separately at least for plants, insects and chordates, since their respective most recent common ancestor is sea-dwelling). In fact, the more I think of it the more examples I find.&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="3340" LastEditDate="2017-04-01T09:56:11.917" LastActivityDate="2018-09-24T11:50:43.180" Title="How many times did terrestrial life emerge from the ocean?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="30" ContentLicense="CC BY-SA 3.0" />
  <row Id="938" PostTypeId="1" CreationDate="2012-02-07T01:05:23.177" Score="6" ViewCount="4825" Body="&lt;p&gt;I'm making a program that estimates a probable size (widest width and longest length) for a human's foot given the length and width of the leg to which it is attached. However, try as I might, &lt;strong&gt;I can't seem to find the average foot-to-leg size ratio. Does anyone know this?&lt;/strong&gt; It would be even better if you have different ratios for males and females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a note, I &lt;em&gt;don't&lt;/em&gt; want to know that this varies depending on certain circumstances, just a good average number that will let me generate people who aren't grossly out-of-proportion&lt;/p&gt;&#xA;" OwnerUserId="464" LastEditorUserId="69" LastEditDate="2012-02-16T14:45:48.320" LastActivityDate="2012-02-16T14:45:48.320" Title="What is the average Leg-to-Foot Length/Width Ratio?" Tags="&lt;anatomy&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="939" PostTypeId="2" ParentId="937" CreationDate="2012-02-07T01:22:03.080" Score="138" Body="&lt;p&gt;I doubt we know the precise number, or even anywhere near it. But there are several well-supported theorised colonisations which might interest you and help to build up a picture of just how common it was for life to transition to land. We can also use known facts about when different evolutionary lineages diverged, along with knowledge about the earlier colonisations of land, to work some events out for ourselves. I've done it here for broad taxonomic clades at different scales - if interested you could do the same thing again for lower sub-clades.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you rightly point out, there must have been at least one colonisation event for each lineage present on land which diverged from other land-present lineages before the colonisation of land. Using the evidence and reasoning I give below, at the very least, the following 9 independent colonisations occurred: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;bacteria&lt;/li&gt;&#xA;&lt;li&gt;cyanobacteria&lt;/li&gt;&#xA;&lt;li&gt;archaea&lt;/li&gt;&#xA;&lt;li&gt;protists&lt;/li&gt;&#xA;&lt;li&gt;fungi&lt;/li&gt;&#xA;&lt;li&gt;algae&lt;/li&gt;&#xA;&lt;li&gt;plants&lt;/li&gt;&#xA;&lt;li&gt;nematodes &lt;/li&gt;&#xA;&lt;li&gt;arthropods&lt;/li&gt;&#xA;&lt;li&gt;vertebrates&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Bacterial and archaean colonisation&lt;/strong&gt;&lt;br&gt;&#xA;The first evidence of life on land seems to originate from 2.6 (&lt;a href=&quot;http://www.nature.com/nature/journal/v408/n6812/full/408574a0.html&quot; rel=&quot;noreferrer&quot;&gt;Watanabe et al., 2000&lt;/a&gt;) to 3.1 (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC533871/&quot; rel=&quot;noreferrer&quot;&gt;Battistuzzi et al., 2004&lt;/a&gt;) billion years ago. Since molecular evidence points to bacteria and archaea diverging between 3.2-3.8 billion years ago (&lt;a href=&quot;http://www.pnas.org/content/94/24/13028.full&quot; rel=&quot;noreferrer&quot;&gt;Feng et al.,1997&lt;/a&gt; - a classic paper), and since both bacteria and archaea are found on land (e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20204349&quot; rel=&quot;noreferrer&quot;&gt;Taketani &amp;amp; Tsai, 2010&lt;/a&gt;), they must have colonised land independently. I would suggest there would have been many different bacterial colonisations, too. One at least is certain - cyanobacteria must have colonised independently from some other forms, since they evolved after the first bacterial colonisation (Tomitani et al., 2006), and are now found on land, e.g. in lichens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Protistan, fungal, algal, plant and animal colonisation&lt;/strong&gt;&lt;br&gt;&#xA;Protists are a polyphyletic group of simple eukaryotes, and since fungal divergence from them (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1689654/&quot; rel=&quot;noreferrer&quot;&gt;Wang et al., 1999&lt;/a&gt; - another classic) predates fungal emergence from the ocean (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0034666795000860&quot; rel=&quot;noreferrer&quot;&gt;Taylor &amp;amp; Osborn, 1996&lt;/a&gt;), they must have emerged separately. Then, since plants and fungi diverged whilst fungi were still in the ocean (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1689654/&quot; rel=&quot;noreferrer&quot;&gt;Wang et al., 1999&lt;/a&gt;), plants must have colonised separately. Actually, it has been explicitly discovered in various ways (e.g. molecular clock methods, &lt;a href=&quot;http://www.sciencemag.org/content/293/5532/1129.short&quot; rel=&quot;noreferrer&quot;&gt;Heckman et al., 2001&lt;/a&gt;) that plants must have left the ocean separately to fungi, but probably relied upon them to be able to do it (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1469-8137.2002.00397.x/full&quot; rel=&quot;noreferrer&quot;&gt;Brundrett, 2002&lt;/a&gt; - see note at bottom about this paper). Next, simple animals... Arthropods colonised the land independently (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC333434/&quot; rel=&quot;noreferrer&quot;&gt;Pisani et al, 2004&lt;/a&gt;), and since nematodes diverged before arthropods (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1689654/&quot; rel=&quot;noreferrer&quot;&gt;Wang et al., 1999&lt;/a&gt;), they too must have independently found land. Then, lumbering along at the end, came the tetrapods (&lt;a href=&quot;http://www.jstor.org/pss/10.1086/425183&quot; rel=&quot;noreferrer&quot;&gt;Long &amp;amp; Gordon, 2004&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note about the Brundrett paper: it has OVER 300 REFERENCES! That guy must have been hoping for some sort of prize.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1186/1471-2148-4-44&quot; rel=&quot;noreferrer&quot;&gt; &lt;strong&gt;Battistuzzi FU, Feijao A, Hedges SB&lt;/strong&gt;. 2004. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol 4: 44.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1046/j.1469-8137.2002.00397.x&quot; rel=&quot;noreferrer&quot;&gt; &lt;strong&gt;Brundrett MC&lt;/strong&gt;. 2002. Coevolution of roots and mycorrhizas of land plants. New Phytologist 154: 275–304.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Feng D-F, Cho G, Doolittle RF&lt;/strong&gt;. 1997. Determining divergence times with a protein clock: Update and reevaluation. Proceedings of the National Academy of Sciences 94: 13028 –13033.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1126/science.1061457&quot; rel=&quot;noreferrer&quot;&gt; &lt;strong&gt;Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL, Hedges SB&lt;/strong&gt;. 2001. Molecular Evidence for the Early Colonization of Land by Fungi and Plants. Science 293: 1129 –1133.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Long JA, Gordon MS&lt;/strong&gt;. 2004. The Greatest Step in Vertebrate History: A Paleobiological Review of the Fish‐Tetrapod Transition. Physiological and Biochemical Zoology 77: 700–719.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1186/1741-7007-2-1&quot; rel=&quot;noreferrer&quot;&gt; &lt;strong&gt;Pisani D, Poling LL, Lyons-Weiler M, Hedges SB&lt;/strong&gt;. 2004. The colonization of land by animals: molecular phylogeny and divergence times among arthropods. BMC Biol 2: 1.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s00248-010-9638-1&quot; rel=&quot;noreferrer&quot;&gt; &lt;strong&gt;Taketani RG, Tsai SM&lt;/strong&gt;. 2010. The influence of different land uses on the structure of archaeal communities in Amazonian anthrosols based on 16S rRNA and amoA genes. Microb Ecol 59: 734–743.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/0034-6667(95)00086-0&quot; rel=&quot;noreferrer&quot;&gt; &lt;strong&gt;Taylor TN, Osborn JM&lt;/strong&gt;. 1996. The importance of fungi in shaping the paleoecosystem. Review of Palaeobotany and Palynology 90: 249–262.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Wang DY, Kumar S, Hedges SB&lt;/strong&gt;. 1999. Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi. Proc Biol Sci 266: 163–171.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/35046052&quot; rel=&quot;noreferrer&quot;&gt; &lt;strong&gt;Watanabe Y, Martini JEJ, Ohmoto H&lt;/strong&gt;. 2000. Geochemical evidence for terrestrial ecosystems 2.6 billion years ago. Nature 408: 574–578.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="37383" LastEditDate="2018-09-24T11:50:43.180" LastActivityDate="2018-09-24T11:50:43.180" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="940" PostTypeId="1" AcceptedAnswerId="944" CreationDate="2012-02-07T07:38:57.893" Score="10" ViewCount="569" Body="&lt;p&gt;Each time I'm too lazy too cook I think it'd be cool to be able to just plug myselt into an outlet. Yet I know it is not possible - I need amino acids and a lot of other stuff that electricity can't replace.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can some simple organism live on electricity alone or is it just fundamentally impossible?&lt;/p&gt;&#xA;" OwnerUserId="466" LastEditorUserId="57" LastEditDate="2012-02-07T08:25:49.190" LastActivityDate="2015-11-28T11:20:43.783" Title="Can a living organism run on electricity?" Tags="&lt;biochemistry&gt;&lt;biophysics&gt;&lt;metabolism&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="941" PostTypeId="1" AcceptedAnswerId="966" CreationDate="2012-02-07T10:09:43.147" Score="7" ViewCount="9494" Body="&lt;p&gt;There seems to be strong evidence to support the claim that sodium benzoate (E211) causes hyperactivity &lt;em&gt;in young children&lt;/em&gt;, e.g. &lt;a href=&quot;http://adc.highwire.org/content/89/6/506.abstract&quot; rel=&quot;noreferrer&quot;&gt;Bateman et al. (2004)&lt;/a&gt; and &lt;a href=&quot;http://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2807%2961306-3/fulltext&quot; rel=&quot;noreferrer&quot;&gt;McCann et al. (2007)&lt;/a&gt;.  This leads me to consider whether or not E211 is harmful &lt;em&gt;during pregnancy&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A study by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17216947&quot; rel=&quot;noreferrer&quot;&gt;Mowafy et al. (2001)&lt;/a&gt; found a slight decrease in survival rates for pups of pregnant rats given sodium benzoate; they also found a more significant drop in mean weight of their pups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt; Could the consumption of sodium benzoate &lt;em&gt;by the mother&lt;/em&gt; be harmful during human pregnancy? How would this be the case?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Bateman, B., Warner, J.O., Hutchinson, E., Dean, T., Rowlandson, P., Gant, C., Grundy, J., Fitzgerald, C. &amp;amp; Stevenson, J. (2004) The effects of a double blind, placebo controlled, artificial food colourings and benzoate preservative challenge on hyperactivity in a general population sample of preschool children. Archives of Disease in Childhood. [Online] 89 (6), 506 –511.&lt;/li&gt;&#xA;&lt;li&gt;McCann, D., Barrett, A., Cooper, A., Crumpler, D., Dalen, L., Grimshaw, K., Kitchin, E., Lok, K., Porteous, L., Prince, E., Sonuga-Barke, E., Warner, J.O. &amp;amp; Stevenson, J. (2007) Food additives and hyperactive behaviour in 3-year-old and 8/9-year-old children in the community: a randomised, double-blinded, placebo-controlled trial. The Lancet. [Online] 370 (9598), 1560–1567.&lt;/li&gt;&#xA;&lt;li&gt;Mowafy, A.R., Darwish, A.M., El-Kholy, S.A. &amp;amp; Abdel-Mohsen, S.H. (2001) Effect of food preservatives on mother rats and survival of their offspring. The Journal of the Egyptian Public Health Association. 76 (3-4), 281–295.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="203" LastEditorUserId="430" LastEditDate="2012-02-09T01:26:32.827" LastActivityDate="2012-02-10T22:07:56.903" Title="Does consuming sodium benzoate (preservative E211) cause problems during pregnancy?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;teratology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="942" PostTypeId="1" CreationDate="2012-02-07T12:15:13.193" Score="6" ViewCount="145" Body="&lt;p&gt;&lt;a href=&quot;http://www.sbs.utexas.edu/shankland/BIO349/lc05clvg.htm&quot; rel=&quot;nofollow&quot;&gt;That for frog is 12&lt;/a&gt;, but what about mammalian embryos?&#xA;I cannot find the exact number anywhere.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="307" LastEditDate="2012-04-05T20:40:14.977" LastActivityDate="2012-11-21T05:09:16.720" Title="What is the total number of rounds of cleavage during mammalian embryonic development?" Tags="&lt;homework&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="943" PostTypeId="2" ParentId="607" CreationDate="2012-02-07T16:47:22.790" Score="10" Body="&lt;p&gt;I have been working on this problem for quite some time now and believe me getting specific binding is a real issue with IDRs. Also, since these regions dont form core structure of the protein, the residues are less conserved (more prone to mutations). So in case of evolving drug-resistance contributing proteins this become a bottleneck.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have done some work on IDPs as potential drug target: &lt;a href=&quot;http://pubs.rsc.org/en/content/articlelanding/2009/mb/b905518p&quot; rel=&quot;noreferrer&quot;&gt;Unraveling the potential of intrinsically disordered proteins as drug targets: application to &lt;em&gt;Mycobacterium tuberculosis&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the concept has been taken well by even the conventional structural biologists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the paper suggests, my work is focused on Mycobacterium tuberculosis. Multiple Drug resistance (MDR) and extremely drug resistance (XDR) form of TB have added to the tuberculosis loads not only in the developing but also developed nations. The drug resistance has been associated with proteins (mostly those involved in transport and metabolism) which have helped the pathogen grow resistant to first line of drugs or more. I refer such proteins as &quot;Drug resistance associated proteins&quot;.&lt;/p&gt;&#xA;" OwnerUserId="468" LastEditorUserId="6" LastEditDate="2012-02-13T07:24:50.673" LastActivityDate="2012-02-13T07:24:50.673" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="944" PostTypeId="2" ParentId="940" CreationDate="2012-02-07T17:16:16.483" Score="9" Body="&lt;p&gt;No; the problem is, as you pointed out, that no organism will manage to multiply, grow or even sustain itself without absorbing matter to create new cells and fill metabolic losses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even photoautotrophic organisms which get energy from light (which is in fact an E-M wave, so pretty close to electricity) collect matter from the environment -- plants for instance seem to grow out of nothing, but in fact gather significant part of their mass from atmospheric CO_2.&lt;/p&gt;&#xA;" OwnerDisplayName="user59" LastActivityDate="2012-02-07T17:16:16.483" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="945" PostTypeId="2" ParentId="938" CreationDate="2012-02-07T18:10:14.777" Score="3" Body="&lt;p&gt;A brief study I conducted of my peers (10 people of varying genders, ages, and races, all about average body type) revealed a rather consistent foot-to-leg length ratio of 1:3 for males and females (variance is insignificant), and width of 2:3 for males and 1:2 for females.&lt;/p&gt;&#xA;" OwnerUserId="464" LastEditorUserId="464" LastEditDate="2012-02-11T22:03:52.243" LastActivityDate="2012-02-11T22:03:52.243" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="946" PostTypeId="2" ParentId="935" CreationDate="2012-02-07T19:42:21.570" Score="5" Body="&lt;p&gt;Plants have a simpler anatomical structure than mammals (is &lt;em&gt;anatomical&lt;/em&gt; the right word, or would &lt;em&gt;physiological&lt;/em&gt; be more appropriate?). Mammals on average don't have more genes than plants, so my understanding is that this additional complexity is the result of finer and more complex regulatory mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you remove or duplicate an individual gene in an organism, that organism must compensate somehow. The more complex the regulatory system, more likely that even small perturbations will cause severe defects or even lethality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Extend this to the scale of a whole genome, and it shouldn't be surprising that polyploidy is lethal for a lot of organisms. It find it extremely fascinating that it's &lt;em&gt;not&lt;/em&gt; lethal for some organisms, but it makes sense that organisms with simpler regulatory mechanisms would be more successful handling a genome duplication event through gene subfunctionalization, neofunctionalization, etc.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-02-07T19:42:21.570" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="947" PostTypeId="2" ParentId="910" CreationDate="2012-02-07T19:48:43.647" Score="20" Body="&lt;p&gt;To answer the first part of your question: it is extremely unlikely that the spider will die or be weakened after just one day.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wolf spiders (Lycosids) are all predators. Due to variations in prey populations, and low efficiency of consumption at higher trophic levels, they are subject to inconsistent and unpredictable food supply (&lt;a href=&quot;http://www.jstor.org/stable/10.2307/1936843&quot; rel=&quot;noreferrer&quot;&gt;Greenstone and Bennett, 1980&lt;/a&gt;). They are very well adapted to this lifestyle and consequently, long periods of starvation often yield no behavioural changes (&lt;a href=&quot;http://www.susqu.edu/facstaff/p/persons/animalbehavior1999.pdf&quot; rel=&quot;noreferrer&quot;&gt;Persons, 1999&lt;/a&gt;). It is highly unlikely that the spider will die after just one day: &lt;a href=&quot;http://www.jstor.org/stable/10.2307/1935148&quot; rel=&quot;noreferrer&quot;&gt;Anderson, (1974)&lt;/a&gt; observed no changes in activity after starving &lt;em&gt;Lycosa lenta&lt;/em&gt; (a species of wolf spider) for 30 days; and &lt;a href=&quot;http://www.springerlink.com/content/v2k50682641n0l85/&quot; rel=&quot;noreferrer&quot;&gt;Tanaka and Ito, (1982)&lt;/a&gt; observed &lt;em&gt;Pardosa astrigera&lt;/em&gt; (another species of wolf spider) living for up to 54 days of starvation. Age and sex of the spider are more likely to affect its behaviour and performance than food or oxygen availability (&lt;a href=&quot;http://www.susqu.edu/facstaff/p/persons/animalbehavior1999.pdf&quot; rel=&quot;noreferrer&quot;&gt;Persons, 1999&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for oxygen consumption, &lt;a href=&quot;http://www.jstor.org/stable/10.2307/1936843&quot; rel=&quot;noreferrer&quot;&gt;Greenstone and Bennett, (1980)&lt;/a&gt; measure an oxygen consumption of 100µL/hr for wolf spiders. Assuming that your cup is of the size of the unit of volume of the same name, &lt;a href=&quot;http://en.wikipedia.org/wiki/Cup_%28unit%29&quot; rel=&quot;noreferrer&quot;&gt;the cup&lt;/a&gt; (~0.237L), a small calculation (see figure) shows that there will be enough oxygen for the spider to survive for over 98 days. The oxygen concentration within the cup may decrease as it is used by the spider, however this is likely to have a minimal effect as a cup placed on a surface is unlikely to be &lt;a href=&quot;http://en.wikipedia.org/wiki/Hermetic_seal&quot; rel=&quot;noreferrer&quot;&gt;hermetically&lt;/a&gt; sealed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AwOtn.png&quot; alt=&quot;equation for oxygen consumption&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, oxygen availability is unlikely to have an effect on the spider before other limitations (such as food) are reached. However neither of these effects are likely to cause behavioural changes during the first month.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Anderson, J.F., 1974. Responses to Starvation in the Spiders Lycosa Lenta Hentz and Filistata Hibernalis (Hentz). &lt;em&gt;Ecology&lt;/em&gt;, 55(3), pp.576-585.&lt;/li&gt;&#xA;&lt;li&gt;Greenstone, M.H. &amp;amp; Bennett, A.F., 1980. Foraging Strategy and Metabolic Rate in Spiders. &lt;em&gt;Ecology&lt;/em&gt;, 61(5), pp.1255-1259.&lt;/li&gt;&#xA;&lt;li&gt;Persons, M.H., 1999. Hunger effects on foraging responses to perceptual cues in immature and adult wolf spiders (Lycosidae). &lt;em&gt;Animal Behaviour&lt;/em&gt;, 57(1), pp.81-88.&lt;/li&gt;&#xA;&lt;li&gt;Tanaka, K. &amp;amp; Itô, Y., 1982. Decrease in respiratory rate in a wolf spider,Pardosa astrigera (L. Koch), under starvation. &lt;em&gt;Researches on Population Ecology&lt;/em&gt;, 24(2), pp.360-374.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="445" LastEditorUserId="445" LastEditDate="2012-02-07T20:05:08.587" LastActivityDate="2012-02-07T20:05:08.587" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="948" PostTypeId="1" AcceptedAnswerId="999" CreationDate="2012-02-07T21:15:52.803" Score="4" ViewCount="858" Body="&lt;p&gt;The mammalian blastocoel becomes yolk sac without yolk according to my professor. I have not found any evidence that such a thing happens in amphibians like frog.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I need to be able to compare and contrast cleavage and formation of blastula in amphibians and in humans.&#xA;My thoughts raised another question.&#xA;My friend says that blastula exists only when blastocoel exists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. Is the thing without blastocoel but with yolk sac the blastula?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="43" LastEditDate="2012-02-08T03:00:24.703" LastActivityDate="2012-02-12T08:24:28.943" Title="Does Amphibian embryo's blastocoel become a primitive yolk sac without yolk?" Tags="&lt;physiology&gt;&lt;homework&gt;&lt;development&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="949" PostTypeId="1" CreationDate="2012-02-07T22:58:47.483" Score="10" ViewCount="293" Body="&lt;p&gt;A mechanism for ADHD stimulant medication tolerance has now been found. See &lt;a href=&quot;http://neurosciencenews.com/adhd-medication-patient-brains-adapt-dat/&quot;&gt;http://neurosciencenews.com/adhd-medication-patient-brains-adapt-dat/&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the thing though: what exactly is the &quot;signal&quot; that the body uses to interpret whether or not it needs to upregulate the amount of DAT (dopamine transporter) that exist? Is it a dopamine-based signal  that somehow then gets carried to a transcription factor that gets carried to the nucleus for additional transcription?&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="806" LastEditDate="2013-01-28T12:56:48.973" LastActivityDate="2014-11-02T08:02:43.223" Title="How reversible is DAT upregulation from long-term ADHD medication use?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="950" PostTypeId="2" ParentId="904" CreationDate="2012-02-07T23:30:01.220" Score="6" Body="&lt;p&gt;An ethanol precipitation should work. But I have had great success using the Qiagen RNA cleanup columns, which are in my opinion easier.  Here is a URL to see the RNA cleanup columns Qiagen offers:  &lt;a href=&quot;http://www.qiagen.com/products/rnacleanupconcentration/default.aspx&quot;&gt;http://www.qiagen.com/products/rnacleanupconcentration/default.aspx&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also in the future you should consider using PhaseLock tubes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.5prime.com/products/nucleic-acid-purification/organic-nucleic-acid-extraction/phase-lock-gel-.aspx&quot;&gt;http://www.5prime.com/products/nucleic-acid-purification/organic-nucleic-acid-extraction/phase-lock-gel-.aspx&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That saved me from having your exact problem many times over.&lt;/p&gt;&#xA;" OwnerUserId="469" LastActivityDate="2012-02-07T23:30:01.220" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="951" PostTypeId="1" CreationDate="2012-02-08T09:39:45.877" Score="14" ViewCount="365" Body="&lt;p&gt;I just started working on predicting steady-state protein levels from different codon usage bias measures. I have whole-genome sequences (it's NGS data) from different strains of &lt;i&gt;S. cerevisiae&lt;/i&gt; and &lt;i&gt;S. paradoxus&lt;/i&gt; and I began to wonder if it's possible that different strains of the same species could have different copy numbers of tRNA genes? If so, would this be detectable in the sequencing data (presumably the reads were mapped onto a reference genome so maybe this copy number variation would be lost)?&lt;/p&gt;&#xA;" OwnerUserId="9" LastEditorUserId="9" LastEditDate="2012-02-24T09:19:13.597" LastActivityDate="2013-11-12T01:56:33.717" Title="What is the tRNA gene copy variation between different yeast strains?" Tags="&lt;yeast&gt;&lt;copy-number-variation&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="952" PostTypeId="1" AcceptedAnswerId="998" CreationDate="2012-02-08T15:37:19.020" Score="2" ViewCount="253" Body="&lt;p&gt;The picture shows the formation of early blastocyst and late blastocyst.&#xA;The middle embryo has embryoblast.&#xA;My professor says that blastocyst in general has embryoblast and trophoblast.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8vO0V.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Embryoblast is the inner cell mass but the thing has none of it.&#xA;The last embryo does not seem to have inner cell mass anymore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is the last embryo in the picture anymore blastocyst?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The given thing seems to be &quot;the single layered blastocyst that will give rise to gastrula&quot;, Wikipedia Gastrulation. The given stage seems to last very short time. It probably should be called phase between blastocyst and gastrula so that the thing is not blastocyst and not gastrula.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the right name for the given thing in mammalians?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-02-11T18:00:01.297" Title="Is this mammalian embryo blastocyst, gastrula or only phase between them?" Tags="&lt;homework&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="953" PostTypeId="1" AcceptedAnswerId="995" CreationDate="2012-02-08T19:40:15.380" Score="2" ViewCount="995" Body="&lt;p&gt;I am reading &lt;a href=&quot;http://wiki.answers.com/Q/What_is_the_difference_between_male_meiosis_and_female_meiosis_for_humans&quot; rel=&quot;nofollow&quot;&gt;one answer about meiosis&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;During meiosis I, the sex chromosomes separate and enter different&#xA;  sperm or egg cells (gametes).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I assume that sex chromosomes refer here to homologous chromosomes that experience crossing-over after meiosis that is exchange of genetical information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Meiosis I refers here to female meiosis I and to male meiosis I. &#xA;In both cases, homologous chromosomes separate resulting in haploid cells after meiosis I.&#xA;&lt;em&gt;These homologous chromosomes enter sperm or egg cells&lt;/em&gt; according to the writer, which I cannot understand, since the given chromosomes, now sister chromatids after meiosis I, do not enter physically anything, they just divide into haploid cells, gametes, after meiosis II.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the meaning of the word &quot;enter&quot; in the given sentence?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am confused by the word &quot;enter&quot;.&#xA;I am assuming that the word refers to enter something physically which is not the case in my opinion here.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="6" LastEditDate="2012-02-09T09:54:37.933" LastActivityDate="2012-02-11T17:37:22.527" Title="What does entering of sex chromosomes to gametes mean during meiosis I?" Tags="&lt;homework&gt;&lt;meiosis&gt;" AnswerCount="1" CommentCount="13" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="954" PostTypeId="1" AcceptedAnswerId="955" CreationDate="2012-02-08T21:51:56.683" Score="9" ViewCount="61627" Body="&lt;p&gt;I am reading &lt;a href=&quot;http://wiki.answers.com/Q/What_is_the_difference_between_male_meiosis_and_female_meiosis_for_humans#ixzz1lpTjjXvT&quot;&gt;the answer&lt;/a&gt; and I am getting confused by the sentence: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At the end of meiosis I females have two daughter cells and meiosis II&#xA;  only occurs if and when fertilization occurs by a sperm cell.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The clause suggests me that meiosis II starts after the sperm has ignited the fertilization process in female: I do not know how that exactly works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Human_fertilization&quot;&gt;Wikipedia&lt;/a&gt; says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The process of fertilization involves a sperm fusing with an ovum.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So female meiosis II must happen before the sperm fuses with the ovum. &#xA;Sperm must ignite some process in female that puts female meiosis II going on before sperm can fuse with egg. &lt;strong&gt;Is that right?&lt;/strong&gt; How is that going to happen?&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="6" LastEditDate="2012-02-09T09:53:56.530" LastActivityDate="2015-01-25T18:37:42.023" Title="Does Human Female Meiosis II occur after fertilization with sperm?" Tags="&lt;homework&gt;&lt;meiosis&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="955" PostTypeId="2" ParentId="954" CreationDate="2012-02-08T22:43:25.990" Score="10" Body="&lt;p&gt;Primary oocytes are formed prenatally and reain suspended in prophase of meiosis I for years until the onset of puberty. An oocyte completes meiosis I as its follicle matures (during ovulation) resulting in a secondary oocyte and the FIRST polar body. After ovulation, each oocyte continues to metaphase of meiosis II. Meiosis II is completed only if fertilization occurs, resulting in a fertilized mature ovum and the second polar body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in short, &lt;strong&gt;the egg is stuck in metaphase II until fertilization.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="177" LastActivityDate="2012-02-08T22:43:25.990" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="957" PostTypeId="1" AcceptedAnswerId="959" CreationDate="2012-02-08T23:01:14.967" Score="11" ViewCount="880" Body="&lt;p&gt;The chicken genome identifies two &quot;LGE&quot; sequences in the chicken genome.  Are these distinct chromosomes or some highly variable sequence from the genome that is put in a separate sequence? I'm thinking they are not really separate chromosomes.... It would be great to know a little bit about their biology.  the papers didn't seem to help me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/03o6I.gif&quot; alt=&quot; chromosome images for chicken genome&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="69" LastEditDate="2012-03-11T14:56:02.623" LastActivityDate="2012-03-11T14:56:02.623" Title="Chicken Genome what are the LGE 'chromosomes'?" Tags="&lt;chickens&gt;&lt;ornithology&gt;&lt;genomes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="959" PostTypeId="2" ParentId="957" CreationDate="2012-02-08T23:43:21.927" Score="8" Body="&lt;p&gt;LG stands for &quot;linkage group&quot;. It seems the Chicken Genome Sequence group (&lt;a href=&quot;http://www.nature.com/nature/journal/v432/n7018/full/nature03154.html&quot;&gt;Hillier et al., 2004&lt;/a&gt;) allocated several &lt;a href=&quot;http://en.wikipedia.org/wiki/Linkage_group&quot;&gt;linkage groups&lt;/a&gt; (alleles or genes which tend to be inherited together) to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Microchromosome&quot;&gt;microchromosomes&lt;/a&gt; (tiny chromosomes typical of birds and reptiles), in this case called &quot;linkage group E64&quot; and &quot;linkage group E22....&quot;. There are a load more microchromosomes which are the ones numbered 28-31 and 33-38 which haven't yet had their sequences resolved (&lt;a href=&quot;http://ps.fass.org/content/86/7/1460.full&quot;&gt;Burt, 2007&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Burt, D.W. (2007) Emergence of the Chicken as a Model Organism: Implications for Agriculture and Biology. Poultry Science. 86 (7), 1460 –1471. Available from:  [Accessed: 8 February 2012].&lt;/li&gt;&#xA;&lt;li&gt;Hillier, L.D.W., Miller, W., Birney, E., Warren, W., Hardison, R.C., Ponting, C.P., Bork, P., Burt, D.W., Groenen, M.A.M. &amp;amp; Delany, M.E. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 432 (7018), 695–716.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-02-08T23:43:21.927" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="960" PostTypeId="1" AcceptedAnswerId="964" CreationDate="2012-02-09T09:35:39.697" Score="16" ViewCount="2811" Body="&lt;p&gt;As I understand it the mechanism of death when a mammal is electrocuted is that the current disrupts the SAN/AVN in the heart causing it to fibrilate or arrest.  That's on a macro scale, however.  What damage, if any, does electricity cause on a cellular level?  I've noticed some sort of moss or lichen growing on the third rail of the train lines so I'm aware that they must be able to cope with the current, do they have adaptations ot allow this or is it just that they are not connected to the earth? &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2020-04-21T23:08:39.157" Title="Does electricity cause damage on a cellular level?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="961" PostTypeId="1" AcceptedAnswerId="962" CreationDate="2012-02-09T09:42:53.503" Score="12" ViewCount="13883" Body="&lt;p&gt;In protocols for polyacrylamide gel electrophoresis (PAGE) I often see instructions to degas the gel solution by putting it under vacuum for 10-15 minutes before polymerizing the gel. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I usually don't do this, and when I tried it once I couldn't see any difference. So I'm wondering what exactly the degassing is meant to achieve and how big the effect should be.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What effect is degassing the gel solution supposed to have?&lt;/li&gt;&#xA;&lt;li&gt;How important is degassing to achieve good gels?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Any literature that examines the effect of degassing would be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="69" LastEditDate="2012-02-10T20:33:05.497" LastActivityDate="2012-03-21T15:59:05.900" Title="Why should I degas my gel solution for polyacrylamide gels?" Tags="&lt;biochemistry&gt;&lt;lab-techniques&gt;&lt;gel-electrophoresis&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="962" PostTypeId="2" ParentId="961" CreationDate="2012-02-09T11:34:13.280" Score="20" Body="&lt;p&gt;The reason for degassing your gels is to remove oxygen. Oxygen in the gel interferes with polymerisation, slowing it down and making it less consistent, so degassing makes it faster and more uniform.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the &lt;a href=&quot;http://www.encorbio.com/protocols/SDS-PAGE.htm&quot;&gt;EncorBio SDS-PAGE protocol&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Polymerization is quicker and more uniform if you degas the first three solutions for a few minutes in an Ehrlenmeyer flask on a house vacuum prior to addition of the last three reagents. Molecular oxygen inhibits polymerisation by reacting with the free radical SO&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; ions, which is actually the reason why PAGE gels are poured in tubes or between plates and not in open top horizontal apparatuses, as can be done with agarose. Also it's a good idea to layer some isopropanol on top of the gel as this prevents oxygen getting in and inhibiting polymerisation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Oxygen can also lead to oxidation of protein products, which might be crucial if you then want to extract the products and use them for something else (e.g. &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/elps.200305800/abstract&quot;&gt;Sun &amp;amp; Anderson, 2004&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, having bubbles in your gel can distort the results and make them less reproducible, as the bubbles will not form consistently with each repetition and they disrupt the physical medium of the polyacrylamide. So another purpose of degassing is to ensure repeatability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.bio-rad.com/LifeScience/pdf/Bulletin_1156.pdf&quot;&gt;Bio-Rad acrylamide polymerisation info sheet&lt;/a&gt; has the best info I could find:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The formation of polyacrylamide gels proceeds via free radical&#xA;  polymerization. The reaction is therefore inhibited by any &#xA;  element or compound that serves as a free radical trap&#xA;  (Chrambach 1985). Oxygen is such an inhibitor. Oxygen,&#xA;  present in the air, dissolved in gel solutions, or adsorbed to&#xA;  the surfaces of plastic, rubber, etc., will inhibit, and in extreme&#xA;  cases prevent, acrylamide polymerization. Proper degassing&#xA;  is critical for reproducibility. Therefore, one of the most &#xA;  important steps in the preparation of polyacrylamide gels is&#xA;  the evacuation, or “degassing” of gel solutions immediately&#xA;  prior to pouring the gel. This is done by placing the flask of&#xA;  gel solution in a vacuum chamber or under a strong aspirator.&#xA;  In some cases, a vacuum pump may be required.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Buffer stock solutions and monomer stock solutions are usually&#xA;  stored at 4°C. Cold solutions have a greater capacity for &#xA;  dissolved oxygen. The process of degassing is faster and&#xA;  more complete if the gel solution is brought to room &#xA;  temperature (23–25°C)‚ before degassing begins.&#xA;  Furthermore, if a cold gel solution is placed under vacuum,&#xA;  the process of evacuation tends to keep the solution cold.&#xA;  Pouring a gel with a cold solution will have a substantial &#xA;  negative effect on the rate of polymerization and on the &#xA;  quality of the resulting gel.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Polymerization in which riboflavin is used as one of the &#xA;  initiators calls for degassing. The conversion of riboflavin from&#xA;  the flavo to the leuco form (the species active in initiation)&#xA;  actually requires a small amount of oxygen (Gordon 1973).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This explains why polymerization initiated primarily by riboflavin&#xA;  can be completely blocked by exhaustive degassing. However,&#xA;  oxygen in excess of that needed to convert riboflavin to the&#xA;  active form will inhibit polymer chain elongation, as it does in&#xA;  reactions initiated only by ammonium persulfate and TEMED.&#xA;  Thus, while degassing is still important for limiting inhibition, &#xA;  it must not be so extensive that it prevents conversion of&#xA;  riboflavin to the active form. For polymerization initiated by&#xA;  riboflavin/TEMED, or riboflavin/TEMED/ammonium persulfate&#xA;  systems, degassing should not exceed 5 min.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;A consequence of the interaction of riboflavin with oxygen is&#xA;  that riboflavin seems to act as an oxygen scavenger. This is&#xA;  supported by the observation that the addition of riboflavin &#xA;  (5 µg/ml) to stacking gel solutions containing ammonium &#xA;  persulfate/TEMED initiators results in cleaner, more uniform&#xA;  polymerization at gel surfaces exposed to oxygen (such as&#xA;  combs). The same effect could likely be achieved by more&#xA;  thorough degassing of solutions without riboflavin.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Whether using chemical polymerization (ammonium &#xA;  persulfate/TEMED) or photochemical polymerization&#xA;  (riboflavin/TEMED or riboflavin/TEMED/ammonium persulfate&#xA;  initiators), reproducible gel quality and separation &#xA;  characteristics require careful attention to gel solution &#xA;  temperature before degassing, and to degassing time, &#xA;  temperature, and vacuum. These parameters should be &#xA;  kept constant every time gels are prepared.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Sorry for the long quotes, but they are pasted here in case the original sources disappear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1002/elps.200305800&quot;&gt;Sun, G. &amp;amp; Anderson, V.E. (2004) Prevention of artifactual protein oxidation generated during sodium dodecyl sulfate‐gel electrophoresis. ELECTROPHORESIS. [Online] 25 (7‐8), 959–965.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="6" LastEditDate="2012-02-10T14:27:44.663" LastActivityDate="2012-02-10T14:27:44.663" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="963" PostTypeId="1" AcceptedAnswerId="1015" CreationDate="2012-02-09T12:01:15.257" Score="28" ViewCount="3984" Body="&lt;p&gt;I know that &lt;a href=&quot;http://en.wikipedia.org/wiki/Statistical_power&quot;&gt;power analysis&lt;/a&gt; is the statistically valid way to ensure you use the correct numer of samples or repeats in an experiment. But I have never seen any biologist actually conduct a power analysis. Mostly, researchers seems to use a rule of thumb (three technical, three biological replicates is a common one).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Should I be doing a power analysis each time I design an experiment, or can I just use one of the common biology rules of thumb? If not, what are the consequences for the validity of my results? And is there a situation where I will be &lt;em&gt;required&lt;/em&gt; to use power analysis, which makes it advantageous to get used to doing it now?&lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-02-09T13:22:30.070" LastActivityDate="2012-06-15T15:17:44.327" Title="Is it necessary to conduct a power analysis before beginning an experiment?" Tags="&lt;statistics&gt;&lt;experimental-design&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="964" PostTypeId="2" ParentId="960" CreationDate="2012-02-09T12:56:01.680" Score="18" Body="&lt;p&gt;Regarding the moss or lichen on the third rail on British train lines: there is no current passing through the moss/lichen as they are not completing a circuit. They are just sitting on one connector. If another connector passed over them, completing the circuit across them, then a current might pass across them for a very short time. But I doubt they grow on the top of the rail (which is the contact part in the UK system) as that is constantly being polished smooth by the contacts from trains sliding across it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding cell damage: Apart from fibrillation in animals, and burns caused by &lt;a href=&quot;http://en.wikipedia.org/wiki/Joule_heating&quot;&gt;Joule heating&lt;/a&gt;, electricity does cause cellular damage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At low frequencies (&amp;lt;10kHz), electricity disrupts cell membranes and makes them much more permeable (we actually harness this when we use &lt;a href=&quot;http://en.wikipedia.org/wiki/Electroporation&quot;&gt;electroporation&lt;/a&gt; to transform bacteria). All organisms rely on electrochemical potential differences across membranes for their metabolism (&lt;a href=&quot;http://www.springerlink.com/content/w99lc1m1a1kwtmld/&quot;&gt;Berry, 2002&lt;/a&gt;). The exact effect is dependent on the previous electrical state of the cells, for example the electrical potential difference across the membrane, and on the surface area to volume ratio of the cell (greater volume relative to surface area leads to more disruption). In any case, extreme electroporation can cause solutes to flow in or out of a cell, and generally disrupt the balance of solute concentrations and cause organelles and other bodies to move out of a cell. When the electrical stimulation stops, the contents are then fixed in a disrupted state. The cell then has to expend enormous amounts of ATP using ion channels and transport proteins in an attempt to reinstate the necessary chemiosmotic potentials, and in doing so exhausts the entire ATP supply and goes into biochemical arrest (no metabolism occurs), which is when a cell is dead. Dead cells break apart because there are is no maintenance occuring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At higher frequencies (10-100kHz) proteins become permanently denatured. Many proteins carry charges which give them an overall polarity. When placed in an electric field, the proteins reorient themselves and will undergo conformational change to achieve the optimum dipole moment in the direction of the field. Ion channels and pumps are particularly sensitive to these disruptions (since their charges are crucial to their function).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rather than provide lots of references, there is one excellent review from which I drew all this information, and which you should read for more of the physical detail (&lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.bioeng.2.1.477&quot;&gt;Lee et al., 2000&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Berry, S. (2002) The Chemical Basis of Membrane Bioenergetics. Journal of Molecular Evolution. [Online] 54 (5), 595–613. Available from: doi:10.1007/s00239-001-0056-3 [Accessed: 9 February 2012].&lt;/li&gt;&#xA;&lt;li&gt;Lee, R.C., Zhang, D. &amp;amp; Hannig, J. (2000) Biophysical injury mechanisms in electrical shock trauma. Annual Review of Biomedical Engineering. [Online] 2 (1), 477–509. Available from: doi:10.1146/annurev.bioeng.2.1.477 [Accessed: 9 February 2012].&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-02-09T18:10:37.957" LastActivityDate="2012-02-09T18:10:37.957" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="965" PostTypeId="2" ParentId="963" CreationDate="2012-02-09T14:45:09.013" Score="11" Body="&lt;p&gt;In order to calculate power, you need to know the &lt;em&gt;variance&lt;/em&gt; of the data being collected. You can only estimate this prior to actually gathering the data itself, so any &lt;em&gt;a priori&lt;/em&gt; power calculation is itself just an estimate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is why sometimes you will see small studies being conducted as &lt;em&gt;pilot studies&lt;/em&gt; (for example, see (1)), which enable variance to be more accurately determined, and a true power calculation to be performed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Knowing the power will enable you to state the probability that the effects you are observing are real (at a given sensitivity). The better idea you can get of this &lt;strong&gt;False Discovery Rate&lt;/strong&gt;, the more solid the conclusions you can draw will be (so it is almost always a good idea to calculate it, but it is not always a feasible thing to do).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1): &lt;a href=&quot;http://www.biomedcentral.com/1471-2105/11/48&quot;&gt;Power and sample size estimation in microarray studies&lt;/a&gt;, Lin &lt;em&gt;et al.&lt;/em&gt;, BMC Bioinformatics 2010, &lt;strong&gt;11&lt;/strong&gt;:48.&lt;/p&gt;&#xA;" OwnerUserId="82" LastEditorUserId="82" LastEditDate="2012-02-09T15:21:55.647" LastActivityDate="2012-02-09T15:21:55.647" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="966" PostTypeId="2" ParentId="941" CreationDate="2012-02-09T22:08:28.767" Score="5" Body="&lt;p&gt;There is some evidence to support the idea that sodium benzoate &lt;em&gt;may&lt;/em&gt; be detrimental to the development of the foetus:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;TERATOGENIC EFFECTS: Classified POSSIBLE for human&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;p&gt;DEVELOPMENTAL TOXICITY: Classified Reproductive system/toxin/female, Reproductive system/ toxin/male [SUSPECTED].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;sup&gt;&lt;a href=&quot;http://www.sciencelab.com/msds.php?msdsId=9927413&quot; rel=&quot;nofollow noreferrer&quot;&gt;MSDS for Sodium Benzoate&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;p&gt;This has been shown experimentally in rats by Minor &amp;amp; Becker in 1971.  They introduced high doses of up to 1000 mgkg&lt;sup&gt;-1&lt;/sup&gt; intraperitoneally and recorded reduction in foetal weight and &amp;quot;gross anomalies&amp;quot;.  Whilst I struggled to find a copy of their original paper, it is referenced in the &lt;a href=&quot;http://books.google.co.uk/books?hl=en&amp;amp;lr=&amp;amp;id=vBIl2OA6BK8C&amp;amp;oi=fnd&amp;amp;pg=PR9&amp;amp;dq=define:TERATOGENIC&amp;amp;ots=FJwao46YQv&amp;amp;sig=LpRE8XOSfKGNpKIYZFmopWlkpGo#v=onepage&amp;amp;q=sodium%20benzoate&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Catalog of Teratogenic Agents&lt;/a&gt;&lt;sup&gt;1&lt;/sup&gt; (Thomas H. Shepard).&lt;/p&gt;&#xA;&lt;p&gt;There is some evidence to refute this, however.  The Acceptable Daily Intake limits on sodium benzoate is a maximum of 5mgkg&lt;sup&gt;-1&lt;/sup&gt;, at this dose there is no noticeable effect of exposure. &lt;sup&gt;(2,3)&lt;/sup&gt;  The latter paper by EC food safety standards goes further:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;There appear to be sufficient studies to conclude &lt;strong&gt;absence of teratogenic potential&lt;/strong&gt;, with an overall NOAEL* for developmental toxicity of 500 mg/kg bw/day, based on effects on fetal weight.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;*(No observed adverse effect level)&lt;/p&gt;&#xA;&lt;p&gt;So the consensus from the food safety bodies suggests that E211 should not pose harm to an unborn child in the quantities allowed to be present as an additive.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;strong&gt;1&lt;/strong&gt; Emire, Ronald J. &amp;quot;&lt;a href=&quot;http://books.google.co.uk/books?hl=en&amp;amp;lr=&amp;amp;id=vBIl2OA6BK8C&amp;amp;oi=fnd&amp;amp;pg=PR9&amp;amp;dq=define:TERATOGENIC&amp;amp;ots=FJwao46YQv&amp;amp;sig=LpRE8XOSfKGNpKIYZFmopWlkpGo#v=onepage&amp;amp;q=sodium%20benzoate&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;306: Benzoate, Sodium.&lt;/a&gt;&amp;quot; Catalog of Teratogenic Agents. By Thomas H. Shepherd. JHU, 2004. 44-45. Google Books. Google. Web. 10 Feb. 2012.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;2&lt;/strong&gt; Nair, B. &amp;quot;&lt;a href=&quot;http://ijt.sagepub.com/content/20/3_suppl/23.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Final Report on the Safety Assessment of Benzyl Alcohol, Benzoic Acid, and Sodium Benzoate.&lt;/a&gt;&amp;quot; International Journal of Toxicology 20.3 (2001). International Journal of Toxicology. Web. 10 Feb. 2012.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;3&lt;/strong&gt; Scientific Committee on Food. &lt;a href=&quot;http://ec.europa.eu/food/fs/sc/scf/out137_en.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Opinion of the Scientific Committee on Food on Benzoic acid and its salts&lt;/a&gt;. Rep. 24 Sept. 2002. EUROPEAN COMMISSION HEALTH &amp;amp; CONSUMER PROTECTION DIRECTORATE-GENERAL. 10 Feb. 2012&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-02-10T22:07:56.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="967" PostTypeId="1" AcceptedAnswerId="11318" CreationDate="2012-02-09T22:08:48.313" Score="11" ViewCount="261" Body="&lt;p&gt;When carrying out some germination tests on species in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cucurbitaceae&quot;&gt;Cucurbitaceae&lt;/a&gt;, I notice that young plants of this family produce a lot of clear fluid when they are dissected. Most plants I dissect do not produce any fluid, even ones which appear to be turgid and have large cells. Why do cucurbits do this, and what's the fluid?&lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-02-10T12:42:20.427" LastActivityDate="2013-11-05T11:26:46.553" Title="Why do cucurbits produce so much fluid when their stems are cut?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="968" PostTypeId="1" AcceptedAnswerId="970" CreationDate="2012-02-10T01:54:57.160" Score="7" ViewCount="1190" Body="&lt;p&gt;The book said when you look at object close to you, the eye muscles contract and vice versa. I wonder what will be the status of the eye muscles when I stare at distance view (such as a mountain) inside an office through a glass wall. The mountain is far away but the glass wall is close to us. In this case, does the eye muscles relax?&lt;/p&gt;&#xA;" OwnerUserId="421" LastEditorUserId="43" LastEditDate="2012-02-17T11:55:37.083" LastActivityDate="2014-03-17T15:16:00.017" Title="What is the eye muscle status when you stare at distant view through a glass wall?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="969" PostTypeId="2" ParentId="177" CreationDate="2012-02-10T07:04:34.887" Score="4" Body="&lt;p&gt;Hamsters are considered the best animal model, most studied.&lt;br&gt;&#xA;C. difficile has been found in calves, ostriches, chickens, elephants, dogs, horses, and pigs, but its role in infection and &lt;a href=&quot;http://cmr.asm.org/content/23/3/529.full&quot; rel=&quot;nofollow&quot;&gt;its pathogenesis in animals are largely poorly understood and possibly underestimated&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="478" LastActivityDate="2012-02-10T07:04:34.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="970" PostTypeId="2" ParentId="968" CreationDate="2012-02-10T09:29:52.590" Score="5" Body="&lt;p&gt;In the situation you describe, the eye would be focused on the distant mountain.  This would mean that the lens would be stretched and thin in order to minimize the focussing power of the eye.  &lt;em&gt;Therefore the ciliary muscles would be relaxed&lt;/em&gt;.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you are looking out of the window, it is possible to make a conscious decision to focus on the window pane itself (thus adjusting the focus to be more powerful as the ciliary muscles contract), however then the distant object will be out of focus and uncomfortable to look at.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is because the light rays reflecting from the mountain are barely affected by the pane of glass, hence its transparency.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2014-03-17T15:16:00.017" LastActivityDate="2014-03-17T15:16:00.017" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="971" PostTypeId="1" AcceptedAnswerId="974" CreationDate="2012-02-10T12:30:04.450" Score="15" ViewCount="104852" Body="&lt;p&gt;All the DNA extraction protocols I have seen involve adding salts to the extraction buffer. What is the purpose of the salts? What happens if they aren't included?&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2019-08-23T12:31:44.387" Title="Why do we add salt when precipitating DNA?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;dna-isolation&gt;&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="972" PostTypeId="1" AcceptedAnswerId="976" CreationDate="2012-02-10T12:34:28.190" Score="10" ViewCount="5285" Body="&lt;p&gt;I work in a lab where all the pipettes are shared. We often have visiting students who come and use the pipettes for a short project. So when I work with them, they might have been handled by other people several times since I last used them. This leads me to worry that they might have been mishandled, or become less accurate somehow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do I clean and calibrate pipettes? And how often do I need to do it?&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-02-10T20:30:56.420" Title="How do I clean and calibrate pipettes, and how often should I do it?" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="973" PostTypeId="1" AcceptedAnswerId="1237" CreationDate="2012-02-10T12:36:21.760" Score="21" ViewCount="5591" Body="&lt;p&gt;If I extract RNA from a (leaf tissue) sample using a one-step phenol:chloroform extraction, how long can those samples be stored at -80°C? And how many times can I defrost and refreeze them before they will become degraded?&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2013-10-28T16:38:23.430" Title="How long can I store extracted RNA?" Tags="&lt;molecular-biology&gt;&lt;rna&gt;&lt;lab-techniques&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="974" PostTypeId="2" ParentId="971" CreationDate="2012-02-10T18:22:09.117" Score="22" Body="&lt;p&gt;The role of the salt is to neutralize the charge of the DNA's sugar phosphate backbone.  This makes the DNA less hydrophilic (less soluble in water).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ethanol has a lower dielectric constant than water so it's used to promote ionic bonds between the Na&lt;sup&gt;+&lt;/sup&gt; (from the salt) and the PO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; (from the DNA backbone) causing the DNA to precipitate.&lt;/p&gt;&#xA;" OwnerUserId="12" LastEditorUserId="12" LastEditDate="2012-02-10T19:37:55.670" LastActivityDate="2012-02-10T19:37:55.670" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="975" PostTypeId="1" AcceptedAnswerId="1020" CreationDate="2012-02-10T19:02:34.080" Score="11" ViewCount="145" Body="&lt;p&gt;Or is there documented evidence of even one homozygous carrier contracting HIV and staying infected?&lt;/p&gt;&#xA;" OwnerUserId="263" LastEditorUserId="69" LastEditDate="2013-01-12T11:20:57.273" LastActivityDate="2013-01-12T11:20:57.273" Title="Are homozygous carriers of the CCR5-Δ32 allele fully immune to all known strains of HIV?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;virology&gt;&lt;hiv&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="976" PostTypeId="2" ParentId="972" CreationDate="2012-02-10T20:14:11.623" Score="9" Body="&lt;p&gt;How often you should calibrate your pipettes depends on the tolerances of your application. For some applications, like quantitative PCR setup, one may care a great deal; for general lab work, one can probably be less particular. You can get a sense of how accurate your pipettes are by pipetting DI water onto the platform of a sensitive (and calibrated!) balance. Comparing the random and systemic error you get while doing that over several trials to the specifications published by the manufacturer will give you a good idea of whether pipette calibration will help and help give you a sense of how much you care. Note also that the error may vary with the volume; you should test error over the entire volume range you intend to use the pipette for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How to clean and calibrate pipettes is specific to each design. Some pipettes, like Gilson's, are not intended to be calibrated by the user. Others are. The pipette user guide published by the manufacturer should tell you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For some demanding applications, even well-calibrated and well-handled micropipettes may not be sufficiently accurate. In particular, I've made standard curves by serial 10-fold dilution for quantitative PCR both a) relying on my micropipettors to be correct and b) trusting pipettes only to get me into the right ballpark, and intentionally undershooting and correcting volumes with sequentially smaller pipettes until the reading on the balance is correct, if that's at all clear. In both cases I was using 900 ul of diluent and 100 ul of the previous dilution, which I feel are comfortably large volumes to handle. I found that the latter curve gave me noticeably better regressions.&lt;/p&gt;&#xA;" OwnerUserId="452" LastActivityDate="2012-02-10T20:14:11.623" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="977" PostTypeId="2" ParentId="972" CreationDate="2012-02-10T20:30:56.420" Score="2" Body="&lt;p&gt;When doing a recent investigation into methods of quantitatively determining the concentration of aspirin in solution I found &lt;a href=&quot;http://www.pipette.com/support/onlinelecture/sop%20sample%20of%20pipette%20calibration%20procedure.pdf&quot; rel=&quot;nofollow&quot;&gt;these procedures&lt;/a&gt; helpful.  They are a rough guide; design and procedure will vary by model.  It may be wise to check the manual that came with it, however in summary:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Calibration&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Performed at least once per week&lt;/li&gt;&#xA;&lt;li&gt;Performed in a room of the temperature indicated on the glassware (or at the very least in a room where the temperature will not fluctuate during the calibration).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;For example a pipette I was using was a 10ml graduated, the procedure for which was:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Rinse the 10 mL pipette with 10 mL of water. Pipette 2 mL into a tared vial containing water on a 2-place balance. Document the weight. Set the pipette to 5 mL, pipette 5 mL into the vial and document the weight. Set the pipette to 10 mL, pipette 10 mL into the vial and document the weight.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However procedures are given in the linked document for pipettes down to 100μL.   Then compare the values from the mass with the acceptable values in the appendix.  A calibrated pipette will give ±1% of the mass indicated in the appendix, for example the pipette I described above:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;1.98-2.02 g&lt;/li&gt;&#xA;  &lt;li&gt;4.95-5.05 g&lt;/li&gt;&#xA;  &lt;li&gt;9.90-10.1 g&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Cleaning can be achieved by pipetting up and rinsing with distilled water (in my case) or more likely for your case 'nanopure' water. &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-02-10T20:30:56.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="978" PostTypeId="5" CreationDate="2012-02-10T20:32:26.107" Score="0" Body="&lt;p&gt;When asking questions on lab techniques, the following should be considered:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A clear outline of the experimental problem should be presented.&lt;/li&gt;&#xA;&lt;li&gt;Standard names and units should be used for reagents and physical quantities.&lt;/li&gt;&#xA;&lt;li&gt;If question is asking for troubleshooting, the current protocol employed should be explained stepwise.&lt;/li&gt;&#xA;&lt;li&gt;The technique should be clearly important and specific to biology.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="69" LastEditorUserId="1590" LastEditDate="2016-03-22T13:25:08.947" LastActivityDate="2016-03-22T13:25:08.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="979" PostTypeId="4" CreationDate="2012-02-10T20:32:26.107" Score="0" Body="Questions relating to protocols, procedures, and good practice when using laboratory equipment." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-29T20:58:39.783" LastActivityDate="2013-10-29T20:58:39.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="980" PostTypeId="2" ParentId="926" CreationDate="2012-02-10T20:50:21.060" Score="6" Body="&lt;p&gt;As mentioned &lt;a href=&quot;https://biology.stackexchange.com/questions/158/why-is-there-an-extended-delay-before-g-m-liver-cells-are-attacked-by-the-immun&quot;&gt;in this question&lt;/a&gt; , Adeno-associated virus is often used for gene therapy.  This is due largely to its predictability when injecting genes (1), however it is also used as it &lt;strong&gt;is not implicated in any human pathology&lt;/strong&gt;. As it is a replication deficient/helper dependent virus, natural infection is much less likely.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The human immune system does mount an immune response against wild-type AAV, as Alexander Galkin discusses regarding an engineered AAV &lt;a href=&quot;https://biology.stackexchange.com/a/403/69&quot;&gt;here&lt;/a&gt;. Despite this, I think that AAV does meet your criteria for a 'harmless virus' , even if it is unlikely to infect without human encouragement.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;(1)  Kotin RM, Siniscalco M, Samulski RJ, et al. (1 March 1990). &quot;&lt;a href=&quot;http://www.pnas.org/content/87/6/2211.full.pdf+html?sid=b3e80d13-02c4-437f-95f7-a9032aaacb2a&quot; rel=&quot;nofollow noreferrer&quot;&gt;Site-specific integration by adeno-associated virus&lt;/a&gt;&quot; . doi:10.1073/pnas.87.6.2211 .&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2012-02-10T20:50:21.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="981" PostTypeId="2" ParentId="926" CreationDate="2012-02-10T21:19:33.457" Score="28" Body="&lt;p&gt;It is possible for viruses to live in mutualistic relationships with their hosts, these associations are often overlooked due to the devastating effect that many viruses can have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To give an example in humans, when HIV-1-infected patients are also infected with hepatitis G virus, progression to AIDS is slowed significantly (&lt;a href=&quot;http://jid.oxfordjournals.org/content/177/6/1723.short&quot; rel=&quot;noreferrer&quot;&gt;Heringlake &lt;em&gt;et al&lt;/em&gt;., 1998&lt;/a&gt;; &lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMoa010398&quot; rel=&quot;noreferrer&quot;&gt;Tillmann &lt;em&gt;et al&lt;/em&gt;., 2001&lt;/a&gt;). Also hepatitis A infection can surpress hepatitis C infection &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S016882780600451X&quot; rel=&quot;noreferrer&quot;&gt;(Deterding &lt;em&gt;et al&lt;/em&gt;., 2006)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many other notable examples within plants, fungi, insects, and other animals, reviewed by &lt;a href=&quot;http://jmm.sgmjournals.org/content/58/4/531&quot; rel=&quot;noreferrer&quot;&gt;Shen (2009)&lt;/a&gt;, and &lt;a href=&quot;http://www.nature.com/nrmicro/journal/v9/n2/abs/nrmicro2491.html&quot; rel=&quot;noreferrer&quot;&gt;Roossinck (2011)&lt;/a&gt;, in two excellent papers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The table below, summarises some beneficial viruses across all organisms, and is taken from &lt;a href=&quot;http://www.nature.com/nrmicro/journal/v9/n2/abs/nrmicro2491.html&quot; rel=&quot;noreferrer&quot;&gt;Roossinck (2011)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/a0TIt.png&quot; alt=&quot;Beneficial viruses&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Deterding, K. &lt;em&gt;et al&lt;/em&gt;., 2006. Hepatitis A virus infection suppresses hepatitis C virus replication and may lead to clearance of HCV. &lt;em&gt;Journal of Hepatology&lt;/em&gt;, 45(6), pp.770-778.&lt;/li&gt;&#xA;&lt;li&gt;Heringlake, S. &lt;em&gt;et al&lt;/em&gt;., 1998. GB Virus C/Hepatitis G Virus Infection: A Favorable Prognostic Factor in Human Immunodeficiency Virus-Infected Patients? &lt;em&gt;Journal of Infectious Diseases&lt;/em&gt;, 177(6), pp.1723 -1726.&lt;/li&gt;&#xA;&lt;li&gt;Roossinck, M.J., 2011. The good viruses: viral mutualistic symbioses. &lt;em&gt;Nature Reviews Microbiology&lt;/em&gt;, 9(2), pp.99–108.&lt;/li&gt;&#xA;&lt;li&gt;Shen, H.-H., 2009. The challenge of discovering beneficial viruses. &lt;em&gt;Journal of Medical Microbiology&lt;/em&gt;, 58(4), pp.531 -532.&lt;/li&gt;&#xA;&lt;li&gt;Tillmann, H.L. &lt;em&gt;et al&lt;/em&gt;., 2001. Infection with GB Virus C and Reduced Mortality among HIV-Infected Patients. &lt;em&gt;New England Journal of Medicine&lt;/em&gt;, 345(10), pp.715-724.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="445" LastActivityDate="2012-02-10T21:19:33.457" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="982" PostTypeId="1" CreationDate="2012-02-10T22:27:20.650" Score="9" ViewCount="8126" Body="&lt;p&gt;I have had some further thoughts after my previous question &lt;a href=&quot;https://biology.stackexchange.com/questions/345/why-would-diffusion-be-faster-across-a-non-specialised-tissue&quot;&gt;regarding the &lt;strong&gt;buccal delivery&lt;/strong&gt; of medication&lt;/a&gt;.  The active compound in aspirin (&lt;em&gt;acetylsalicylic acid&lt;/em&gt; or systematically 2-Acetoxybenzoic acid)  is salicylic acid (2-hydroxybenzoic acid).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that the hydrolysis reaction occurs as follows &lt;em&gt;within the stomach&lt;/em&gt; - therefore in the body it is an &lt;em&gt;acid&lt;/em&gt; hydrolysis:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BL0yN.gif&quot; alt=&quot;Hydrolysis of aspirin&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;N.B. The H&lt;sub&gt;2&lt;/sub&gt;O is not shown in the diagram.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However having done this experimentally I know that in the lab to ensure a decent yield of salicylic acid I had to &lt;strong&gt;&lt;em&gt;reflux&lt;/em&gt; the solution for several hours&lt;/strong&gt;.  Yet the onset of action of aspirin tablets is much faster than this.  To me this suggests some enzymatic activity, but I have no idea which enzyme this is likely to be.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To follow on directly from my previous question, if the aspirin is absorbed directly into the bloodstream bypassing the stomach then what causes the hydrolysis in the blood stream and is it the same factor that increases the rate of hydrolysis &lt;em&gt;in&lt;/em&gt; the stomach if the medication were to be taken orally?  &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2012-02-11T11:08:44.070" Title="What hydrolyses aspirin within the digestive tract and blood stream?" Tags="&lt;pharmacology&gt;&lt;aspirin&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="983" PostTypeId="5" CreationDate="2012-02-10T22:29:35.387" Score="0" Body="" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-02-10T22:29:35.387" LastActivityDate="2012-02-10T22:29:35.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="984" PostTypeId="4" CreationDate="2012-02-10T22:29:35.387" Score="0" Body="Questions relating to the pharmacology of Aspirin (Acetylsalicylic acid) and its decay product and active ingredient Salicylic acid.  " OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-02-10T22:29:35.387" LastActivityDate="2012-02-10T22:29:35.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="985" PostTypeId="5" CreationDate="2012-02-10T22:38:34.333" Score="0" Body="" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-02-10T22:38:34.333" LastActivityDate="2012-02-10T22:38:34.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="986" PostTypeId="4" CreationDate="2012-02-10T22:38:34.333" Score="0" Body="The generation of ATP from the breakdown of organic molecules in the absence of oxygen. " OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-02-10T22:38:34.333" LastActivityDate="2012-02-10T22:38:34.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="987" PostTypeId="5" CreationDate="2012-02-10T22:41:36.090" Score="0" Body="&lt;p&gt;The &lt;a href=&quot;/questions/tagged/eyes&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;eyes&amp;#39;&quot; rel=&quot;tag&quot;&gt;eyes&lt;/a&gt; tag is used for questions directly relating to the &lt;a href=&quot;/questions/tagged/anatomy&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;anatomy&amp;#39;&quot; rel=&quot;tag&quot;&gt;anatomy&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/physiology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;physiology&amp;#39;&quot; rel=&quot;tag&quot;&gt;physiology&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/pathology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;pathology&amp;#39;&quot; rel=&quot;tag&quot;&gt;pathology&lt;/a&gt; and &lt;a href=&quot;/questions/tagged/evolution&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;evolution&amp;#39;&quot; rel=&quot;tag&quot;&gt;evolution&lt;/a&gt; of the eyes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For related questions on how the brain interprets electrical messages from the eyes, see the &lt;a href=&quot;/questions/tagged/vision&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;vision&amp;#39;&quot; rel=&quot;tag&quot;&gt;vision&lt;/a&gt; tag.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-29T21:01:26.470" LastActivityDate="2013-10-29T21:01:26.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="988" PostTypeId="4" CreationDate="2012-02-10T22:41:36.090" Score="0" Body="The discussion of the anatomy and evolution of eyes.  Consider using the &quot;vision&quot; tag for questions regarding how the brain interprets information from the eyes. " OwnerUserId="69" LastEditorUserId="16866" LastEditDate="2019-08-25T03:54:14.757" LastActivityDate="2019-08-25T03:54:14.757" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="989" PostTypeId="5" CreationDate="2012-02-10T22:43:34.747" Score="0" Body="&lt;p&gt;The &lt;a href=&quot;/questions/tagged/vision&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;vision&amp;#39;&quot; rel=&quot;tag&quot;&gt;vision&lt;/a&gt; tag is for questions about how the brain and eyes combine to give and interpret signals to give vision, how an organism processes the electrical signals it receives from its visual organs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For questions on eye and brain anatomy, physiology and evolution see the &lt;a href=&quot;/questions/tagged/eyes&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;eyes&amp;#39;&quot; rel=&quot;tag&quot;&gt;eyes&lt;/a&gt; and &lt;a href=&quot;/questions/tagged/brain&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;brain&amp;#39;&quot; rel=&quot;tag&quot;&gt;brain&lt;/a&gt; tags respectively.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="1590" LastEditDate="2016-03-23T16:21:54.323" LastActivityDate="2016-03-23T16:21:54.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="990" PostTypeId="4" CreationDate="2012-02-10T22:43:34.747" Score="0" Body="Questions regarding how the brain interprets information from the eyes.  Consider using the &quot;eyes&quot; tag for discussion of eye anatomy, physiology and evolution." OwnerUserId="69" LastEditorUserId="16866" LastEditDate="2019-08-25T03:48:28.283" LastActivityDate="2019-08-25T03:48:28.283" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="991" PostTypeId="1" AcceptedAnswerId="1029" CreationDate="2012-02-10T23:51:05.203" Score="5" ViewCount="12385" Body="&lt;p&gt;Exam question which got lowest average points in my university: 1/5 average.&#xA;No markscheme available so my attempt below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume that embryonic disk prefers to germ disk such that Formation prefers to only to the &lt;a href=&quot;http://www.embryology.ch/anglais/hdisqueembry/planmoddisque.html&quot; rel=&quot;nofollow&quot;&gt;3rd developmental week&lt;/a&gt; because of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Embryonic_disc&quot; rel=&quot;nofollow&quot;&gt;Wikipedia fact&lt;/a&gt;. &#xA;I also went through the points during 2nd week of development and did not notice major differences. So let's consider only the 3rd week:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Formation of the primitive streak&lt;/li&gt;&#xA;&lt;li&gt;Genesis of the germ layers&lt;/li&gt;&#xA;&lt;li&gt;Genesis of the notochord&lt;/li&gt;&#xA;&lt;li&gt;Location of the epiblast cell target and the development of the primitive streak&lt;/li&gt;&#xA;&lt;li&gt;The bilaminar membranes&lt;/li&gt;&#xA;&lt;li&gt;Evolution of the mesoblast&lt;/li&gt;&#xA;&lt;li&gt;The intraembryonic coelom&lt;/li&gt;&#xA;&lt;li&gt;Induction of the neural plate – neurulation&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The following differences are based mostly on Gilbert's Developmental Biology 9e -book.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other Differences which seems to at least start at the 3rd week of development&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Chick meroblastic cleavage, human holoblastic. TODO do not know how that causes differences yet during the 3rd week.&lt;/li&gt;&#xA;&lt;li&gt;Chick has yolk, human not so human placenta development and implantation. Chick dependent on yolk nutrients, human not.&#xA;Human embryo gets mother nutrients through placenta.&#xA;Chorion formation and finally from it the fetal portion of the placenta.&#xA;Chorion also includes the uterine cells to form the maternal of the placenta, the decidua.&#xA;The decidua will come rich in the blood vessels that will provide oxygen &amp;amp; nutrients to the embryo.&#xA;Human oviduct expansion to the uterus.&lt;/li&gt;&#xA;&lt;li&gt;Chick embryo externally developing from the mother, human not. Chick egg is telocithal with a small disc of cytoplasm: blastodisc - sitting atop a large yolk. The yolk, eggs of birds undergo &lt;strong&gt;discoidal meroblastic cleavage.&lt;/strong&gt; Cleavage occurs only in the blastodisc which is about 2-3 mm in diameters &amp;amp; is located at the animal pole of the egg. The first cleavage furrow appears centrally in the blastodisc; other cleavages follow to create a single-layered &lt;strong&gt;blastoderm.&lt;/strong&gt;&#xA;The cleavages do not extend into the yolk, cytoplasm, so the early-cleavage cells are continuous with one another &amp;amp; with the yolk at their bases. &lt;/li&gt;&#xA;&lt;li&gt;One chick hypoblast streak, human multiple. Chick must have some control mechanism.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the differences between formation of embryonic disc in chick and mammal embryo?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2012-02-11T15:05:52.920" LastActivityDate="2014-11-04T17:16:00.703" Title="What are differences between formation of embryonic disc in chick and mammal embryo?" Tags="&lt;human-biology&gt;&lt;homework&gt;&lt;embryology&gt;&lt;chickens&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="992" PostTypeId="1" AcceptedAnswerId="1012" CreationDate="2012-02-11T00:28:16.467" Score="9" ViewCount="142" Body="&lt;p&gt;Occasionally, in hospitals and in eating establishments in the US, they have industrial grade UV lights in sconces attached to the wall (though they seem to be less prominent as the years go by).  I understand the anti-microbial properties of UV light, but are these devices anything more than show pieces?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have there been any lasting, significant public health gains that have been correlated with the use of UV light in public places?&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="67" LastEditDate="2012-02-12T23:32:42.023" LastActivityDate="2012-09-26T04:30:14.267" Title="Have there been any positive public health effects due to UV lights?" Tags="&lt;microbiology&gt;&lt;pathology&gt;&lt;epidemiology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="993" PostTypeId="2" ParentId="982" CreationDate="2012-02-11T11:00:42.603" Score="6" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Acetylsalicylate_deacetylase&quot;&gt;Acetylsalicylate deacetylase&lt;/a&gt; is the enzyme responsible for this reaction.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Precisely, the present investigation reveals that the hydrolysis of aspirin in liver, kidney and probably other tissues of&#xA;  rats is catalyzed by two highly substrate specific microsomal&#xA;  esterases, ASA esterase I and II active at acidic and slightly&#xA;  alkaline pH, respectively. The findings that ASA esterases have&#xA;  distinct organ distribution pattern and display responses to&#xA;  various inhibitors/activators that are different in many respects&#xA;  from those exhibited by cholinesterase and nonspecific carboxylesterase suggest that the latter esterases probably do not play&#xA;  a significant role in the hydrolysis of aspirin.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;From:&#xA;  &lt;em&gt;Ali B, Kaur S (1983) Mammalian tissue acetylsalicylic acid esterase(s): identification, distribution and discrimination from other esterases. J Pharmacol Exp Ther,226,589-594&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-02-11T11:08:44.070" LastActivityDate="2012-02-11T11:08:44.070" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="994" PostTypeId="1" AcceptedAnswerId="996" CreationDate="2012-02-11T15:59:39.873" Score="25" ViewCount="7870" Body="&lt;p&gt;Do the 46 human chromosomes form a single unbroken DNA helix?  Or is it rather that a human's genome consists of 46 disconnected helices?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it is the former, does the common numbering scheme for the chromosomes have any correlation to their actual ordering in the one large strand?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If is the latter, is there a convention on how the chromosomes are ordered in genomic datasets?  Also, is there a clear understanding of how sister chromosomes &quot;find&quot; each other in Meiosis I?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally, during periods when Mitosis/Meiosis are not occurring,  what's a good physical picture for how the chromosomes are physically arranged (e.g. a bowl of 46 spaghetti noodles, or maybe the sister chromosomes always stay close together, etc)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks! &lt;/p&gt;&#xA;" OwnerUserId="483" LastActivityDate="2015-06-22T20:20:46.627" Title="Are human chromosomes connected or separate molecules?" Tags="&lt;dna&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="995" PostTypeId="2" ParentId="953" CreationDate="2012-02-11T17:37:22.527" Score="0" Body="&lt;p&gt;I seem to now understand the sentence. I read the clause in other words:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;During meiosis I, the sex chromosomes of the gametogonia separate in&#xA;  anaphase I and II and become eventually different sperm or egg cells&#xA;  after cell differentiation and maturation: male spermiogenesis and&#xA;  female maturation into ovum.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Female thing does not seem to have a special name for the maturation thing.&#xA;Female does not seem to have differentiation part at the last part similarly as male, since only one ovum is formed after the sequence of events. &#xA;Sex chromosomes refer to your parents genotypes. [jg89]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Problem seems to be solved now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would not personally use the word &quot;enter&quot; in a such sequence. It is a shortcut. Better would be &quot;enter eventually&quot; or &quot;enter after a sequence of events&quot;. I prefer explicity instead of implicity.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-02-11T17:37:22.527" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="996" PostTypeId="2" ParentId="994" CreationDate="2012-02-11T17:39:38.603" Score="17" Body="&lt;p&gt;Each chromosome is a pair of distinct, separate DNA molecules.  A chromosome of an eukaryotic cell nucleus is a (long) helix of two linear molecules and so has two ends, which are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Telomere&quot; rel=&quot;noreferrer&quot;&gt;telomeres&lt;/a&gt;.  DNA naturally forms a &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleic_acid_double_helix&quot; rel=&quot;noreferrer&quot;&gt;double helix&lt;/a&gt; with its complementary DNA molecule, and the double helix can further curl in what are called &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA%20supercoil&quot; rel=&quot;noreferrer&quot;&gt;supercoils&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In humans, the chromosomes occur in 23 pairs (totaling 46). Except for the sex chromosome pair, each member of the pair is identical in appearance in a &lt;a href=&quot;http://en.wikipedia.org/wiki/Karyotype&quot; rel=&quot;noreferrer&quot;&gt;karyotype&lt;/a&gt; (picture) and each such pair has a number assigned from 1 to 22; the numbering generally follows the size of the chromosome, with chromosome 1 being the longest.  In mammals, the sex chromosomes in a male are quite different in size and are labelled X and Y; a female has two identical X chromosomes.&lt;/p&gt;&#xA;" OwnerUserId="231" LastEditorUserId="231" LastEditDate="2015-06-22T20:20:46.627" LastActivityDate="2015-06-22T20:20:46.627" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="997" PostTypeId="2" ParentId="911" CreationDate="2012-02-11T17:56:28.837" Score="1" Body="&lt;p&gt;I seem to understand the thing now. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The video is &lt;strong&gt;utterly simplified for animal cell&lt;/strong&gt; meiosis I and II. &#xA;In oogenesis, you get after every anaphase one cell with very little cytoplasm, polar body, and another cell with much cytoplasm. In the video, the amount of cytoplasm is equal so the thing is idealized.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The video is better to explain male gametogenesis: spermatogenesis, since the amount of cytoplasm does not differ after each anaphase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The video is too going too fast to teach you oogenesis, since in reality the things are arrested rather long time. The second meiotic arrest in oogenesis can lasts 12 - 50 years starting after puberty. The rupturing secondary oocytes lasts then again less in the second meiotic arrest of oogenesis, since they start to develop into ovum after the monthly release. &lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-02-11T17:56:28.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="998" PostTypeId="2" ParentId="952" CreationDate="2012-02-11T18:00:01.297" Score="0" Body="&lt;p&gt;Again, the thing (2) is idealized and probably does exists at all. It is an idealized picture. It is really a mistake to call such a thing blastocyst like Wikipedia does. The thing should be fixed not to confuse other people.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There should be real pictures instead of such idealized ones.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-02-11T18:00:01.297" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="999" PostTypeId="2" ParentId="948" CreationDate="2012-02-11T18:10:21.067" Score="0" Body="&lt;p&gt;Amphibians are produced externally so they do not get proteins and ATP from the mother during their maturation and differentiation. This means that they must have some way to get those things to protect themselves and survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The way that they get these things is yolk. Amphibians start to have yolk-filled endoderm during blastulation, [page 9, Gilbert, Developmental Biology]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am considering the frog here as an example of amphibian. To know that things need energy to survive and that they must get it somewhere, you can deduce this solution. So nutrition and external &quot;hatching&quot; or development outside of female is the key here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The overall answer to the question:&#xA;&lt;strong&gt;The organism must have a yolk sac, since it has yolk&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second question seems to be an idealized one.&#xA;Without blastocoele but with yolk-sac suggests me that the blastocoel has developed already to yolk-sac. If that is the case, then I would call the thing gastrula, since for instance some species' ectoderm develops into yolk-sac. I assume that the question refers with &quot;yolk-sac&quot; to complete yolk-sac, not to the developing one during gastrulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it is about developing yolk-sac, I would say that the cell is still blastula but is developing to gastrula. The yolk sac is not ready until gastrulation is complete.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2012-02-12T08:24:28.943" LastActivityDate="2012-02-12T08:24:28.943" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1000" PostTypeId="2" ParentId="898" CreationDate="2012-02-11T22:19:09.717" Score="2" Body="&lt;p&gt;I think you are correct to discount your first point as the cellular respiration proceeding to supply your muscles with ATP when running will produce heat anyway, as you say.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the lungs having to work harder in cold conditions, its an interesting proposition.  I would &lt;strong&gt;hypothesise&lt;/strong&gt; that this may indeed be the case:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gas exchange across the lungs occurs by diffusion.  Fick's law (simplified) states that the rate of diffusion is proportional to the difference in concentrations multiplied by the surface area along which diffusion is occurring, all divided by the length of the diffusion pathway:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$V_d=k\frac{\large a.([C_2]-[C_1])}{\large l}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the situation of the diffusion of O&lt;sub&gt;2&lt;/sub&gt; and CO&lt;sub&gt;2&lt;/sub&gt; across the alveolar membrane, k is dependent solely on the temperature of the diffusing particles. Therefore the rate of diffusion will almost certainly be reduced in lower temperatures.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The slower rate of diffusion will mean that the body will indeed have to 'work harder' to expel CO&lt;sub&gt;2&lt;/sub&gt; and take up O&lt;sub&gt;2&lt;/sub&gt;.  This would be achieved by increasing both the hearts stroke rate and the ventilation rate.  This holds true in theory, however I can not say for certain if it would occur in reality as I do not know how greatly V&lt;sub&gt;d&lt;/sub&gt; (diffusion rate) would be affected by the change in temperature and also crucially how much of a decrease in V&lt;sub&gt;d&lt;/sub&gt; would be sufficient to initiate the homeostatic responses mentioned above.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="3340" LastEditDate="2014-10-09T15:07:43.903" LastActivityDate="2014-10-09T15:07:43.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1001" PostTypeId="1" CreationDate="2012-02-12T01:37:42.420" Score="10" ViewCount="1241" Body="&lt;p&gt;Tickling is a rather interesting phenomenon: When humans or apes are touched in certain areas like the armpits or sides, we respond with laughter AND frantic attempts to stop the assault. Obviously our ticklish areas tend to be very vulnerable, so it makes sense that we would want to protect ourselves, but why do we respond with laughter? How might both of these reactions to tickling have evolved? Do they have the same evolutionary purpose or different ones?&lt;/p&gt;&#xA;" OwnerUserId="62" LastActivityDate="2013-04-19T14:31:19.737" Title="Is there are evolutionary explanation for why humans and primates are ticklish? How might it have evolved?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1002" PostTypeId="2" ParentId="1001" CreationDate="2012-02-12T08:25:08.420" Score="8" Body="&lt;p&gt;Tickling probably evolved from a defense mechanism but then gradually changed into a more social action, as explained in &lt;a href=&quot;http://www.chsbs.cmich.edu/hajime_otani/Classes/100/Extra1.pdf&quot;&gt;Provine, 2005&lt;/a&gt; (PDF):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The neurological mechanism of tickling probably evolved from a reﬂex defense mechanism that protects our body’s surface from external, moving stimuli, probably predators or parasites. Our response to tickle is more varied and complex than the typical reﬂex, but it has some stereotypic, reﬂex-like properties (i.e., we laugh when tickled, struggle to escape the tickler, huddle, fend off the tickling hand). Although you can be tickled to laughter by a machine (&lt;a href=&quot;http://scienceblogs.com/worldsfair/upload/2007/08/tickle.pdf&quot;&gt;Harris, 1999&lt;/a&gt;) (PDF), most everyday tickle is yet another social context for laughter and a form of communication.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="114" LastEditorUserId="445" LastEditDate="2012-02-12T14:33:25.553" LastActivityDate="2012-02-12T14:33:25.553" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1003" PostTypeId="2" ParentId="510" CreationDate="2012-02-12T13:47:28.340" Score="20" Body="&lt;p&gt;The selection you refer in multiple species could be due to a mutual advantage.&#xA;If fruits absorb visible wavelengths, they can be spotted by other animals and eaten together with the seeds. Seeds can then mature inside the host and, once eliminated with the feces, grow up a new plant in a different place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not only valid for light absorption, but for light emission also: for some fruits, the &lt;a href=&quot;http://www.reportergene.com/2009/01/banana-molecular-imaging-is-blue.html&quot;&gt;ripening causes a blue-UV luminescence&lt;/a&gt; that can be spotted by some insects.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-02-12T13:47:28.340" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1004" PostTypeId="1" AcceptedAnswerId="1006" CreationDate="2012-02-12T14:12:40.943" Score="5" ViewCount="10778" Body="&lt;p&gt;Kimball Biology 5e says&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Coelom is the main body cavity of many animals. It is lined with an epithelium derived from mesoderm. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Gilbert Embryonal Biology 9e says&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Coelom is the space between the somatic mesoderm and splanchnic mesoderm that becomes the body cavity. In mammals, the coelom becomes subdivided into the pleural, pericardial, and peritoneal cavities, enveloping the thorax, heart, and abdomen, respectively.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Then my lecture materials and the &lt;a href=&quot;http://www.newworldencyclopedia.org/entry/Body_cavity&quot; rel=&quot;noreferrer&quot;&gt;research site&lt;/a&gt; say&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Coelom is the secondary body cavity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Finnish Wikipedia says that Coelom is only with invertebrates.&#xA;Again &lt;a href=&quot;http://en.wikipedia.org/wiki/Peritoneum&quot; rel=&quot;noreferrer&quot;&gt;the Wikipedia page about peritoneum&lt;/a&gt; suggests that human has abdominal cavity and no coelom, and other mammalians coelom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Does human have Coelom?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The confusing thing is the use of the word &quot;OR&quot;, since I am not sure whether people are using it in different pages like &quot;XOR&quot; or like &quot;AND&quot; in normal speaking.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="81" LastEditDate="2012-02-12T19:20:55.627" LastActivityDate="2012-02-12T19:20:55.627" Title="Do humans have Coelom?" Tags="&lt;homework&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1005" PostTypeId="1" AcceptedAnswerId="1007" CreationDate="2012-02-12T14:52:40.397" Score="5" ViewCount="422" Body="&lt;p&gt;Related to my &lt;a href=&quot;https://biology.stackexchange.com/questions/1004/does-human-have-coelom&quot;&gt;other question&lt;/a&gt;.&#xA;I know that the coelom is derived from mesoderm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coelom seems to form during organogenesis within 3rd and 8th week of embryogenesis.&#xA;However, that answer is not either enough exact or it is wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am reading the thing in Kimball 5e and Gilbert 9e, but cannot find an exact mention about the thing. I know for sure that the coelom develops within gastrulation and organogenesis, since it is forming from mesoderm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;When does coelom form exactly?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2012-02-12T18:52:52.600" Title="When does Coelom form exactly?" Tags="&lt;homework&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1006" PostTypeId="2" ParentId="1004" CreationDate="2012-02-12T18:23:38.880" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Coelomates&quot;&gt;Wikipedia&lt;/a&gt; actually covers this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Most bilateral animals, including all the vertebrates, are coelomates.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now, some coelomates have subsequently lost their coelom but primates (actually, I believe, all vertebrates) are not among them. In humans, the coelom forms, amongst others, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Pleural_cavity#Development&quot;&gt;pleural cavity&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, &lt;strong&gt;yes&lt;/strong&gt;: humans do have a coelom that partitions into different, unconnected body cavities during development.&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="166" LastEditDate="2012-02-12T18:33:59.447" LastActivityDate="2012-02-12T18:33:59.447" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1007" PostTypeId="2" ParentId="1005" CreationDate="2012-02-12T18:52:52.600" Score="2" Body="&lt;p&gt;In humans, the coelom forms by the splitting of the lateral plate mesoderm, which occurs during weeks 4-5 (Sweeney, 1998).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sweeney, LJ. 1998. &lt;em&gt;Basic Concepts in Embryology&lt;/em&gt;. McGraw-Hill.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-02-12T18:52:52.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1008" PostTypeId="1" AcceptedAnswerId="1021" CreationDate="2012-02-12T20:17:48.317" Score="15" ViewCount="12225" Body="&lt;p&gt;There are numerous examples of sessile animals (sponges, barnacles etc.) but are there any examples of motile plants? If not, why not? Surely mobility would have conferred an evolutionary advantage to some plant species. I am specifically thinking of locomotion here.&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-02-13T10:38:35.867" LastActivityDate="2016-06-27T15:33:25.013" Title="Are there any motile plants?" Tags="&lt;botany&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1012" PostTypeId="2" ParentId="992" CreationDate="2012-02-12T23:32:30.853" Score="7" Body="&lt;p&gt;There have been some studies regarding the use of intensive UV light installations in surgical wards or other settings as a anti-microbial tool. Generally speaking, these are part of a general interest in non-cleaning based anti-microbials in hospitals, such as UV light, O3-based machines, and copper/silver coated surfaces.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer to your question will depend on what you consider &quot;lasting&quot; and &quot;significant&quot;. They're a relatively new technology, and haven't had a huge penetration into the market yet, so the only evidence you're likely to find is hospital-sized non-randomized trials.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So basically, the answer to your question, as I read it, is &quot;No, but...&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There hasn't been an opportunity for these technologies &lt;em&gt;to show&lt;/em&gt; any sort of lasting, significant reduction in hospital acquired infections. But there is some promise that these types of technologies, and those like them, may help reduce the burden of infections when they're used appropriately. The current state of research is figuring out just how workable they are, how to best use them, and what they can and cannot be expected to do. That kind of evaluation is actually what I'm doing as part of my dissertation work, though my focus is on the general concept, rather than a specific device.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2012-02-12T23:32:30.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1013" PostTypeId="5" CreationDate="2012-02-12T23:42:36.653" Score="0" Body="&lt;p&gt;Division of a diploid cell to produce four haploid cells for the purposes of reproduction.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="28834" LastEditDate="2017-03-29T16:00:47.077" LastActivityDate="2017-03-29T16:00:47.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1014" PostTypeId="4" CreationDate="2012-02-12T23:42:36.653" Score="0" Body="Division of a diploid cell to produce four haploid cells for the purposes of reproduction." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T14:18:36.263" LastActivityDate="2013-10-31T14:18:36.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1015" PostTypeId="2" ParentId="963" CreationDate="2012-02-12T23:55:12.277" Score="19" Body="&lt;p&gt;You've already gotten a decent answer to this, but I'll provide my own thoughts on the subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Yes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's necessary. It is absolutely something you should do before beginning an experiment, and preferably something you should do in collaboration with the person who is going to be helping you analyze your data. To address a couple points:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;You'll see all kinds of researchers doing all manner of sloppy things when it comes to statistics and data analysis. Reading some journals makes me groan. You won't necessarily find it a problem for your field, but one should ask oneself if the goal is merely not to get called out by your peers, or to actually run a well designed experiment.&lt;/li&gt;&#xA;&lt;li&gt;The consequences to the validity of your results lie in an increased risk of Type II error - the incorrect failure to reject the null hypothesis, or in slightly clearer English, finding no effect when an effect exists in reality. Which means, if you run an under powered study, you run the risk of doing the entire experiment, finding nothing, and being &lt;em&gt;wrong&lt;/em&gt;. The consequences of that are myriad - first, it likely harms your chances to get published, as null results are often quite difficult to get into press. Second, if it &lt;em&gt;does&lt;/em&gt; get into press, you've managed to get an &lt;em&gt;incorrect finding&lt;/em&gt; into the literature, which will then be propagated in meta-analysis, reviews, and the minds of impressionable future readers. And then there's the chance you'll abandon a potentially productive line of inquiry because you couldn't be bothered to do power analysis.&lt;/li&gt;&#xA;&lt;li&gt;One thing to also consider is that not having conducted power analysis somewhat limits your ability to chase after interesting sub-findings. If you've built your experiment on a shaky foundation, and then want to do a second analysis on a sub-set of your results, you almost certainly don't have the power for it.&lt;/li&gt;&#xA;&lt;li&gt;There are times when you'll be required to do power analysis. If you do research that's clinically relevant, and you ever want it to appear in one of those journals, you may very well be required to show you had a properly powered experiment. And many grant applications require you do so. Even if they don't require it, some people will do a napkin math estimation of your power if they don't see it appearing in your application anywhere.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;sjcockell is partially correct. To do power analysis, you at least need to have some notion of the effect measure you're likely to see. And these are indeed just estimations of what you'll see. But in nearly all circumstances, you'll likely have some ideas already. Are there similar experiments you can draw from? Your own pilot studies? A &quot;feel&quot; born of experience in your particular system?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also trivially easy to calculate power under a number of difference scenarios, to ensure your experiment is sufficiently powered if things go considerably worse than expected. For example, in a study I once did the power calculations for, we weren't sure what the ratio of exposed to unexposed subjects would be. So I ran it over a large range:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/aPPPG.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which left me with the confidence that even if I was in my &quot;worst case&quot; scenario, I'd have reasonably good power at realistic effect sizes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's the true strength of power calculations. They'll tell you things about your study. What you need. What doesn't matter. Whether or not before you spend time and money pursuing an idea if you have a reasonable chance at success. Sit down with someone, take an hour or two (at most for a simple experiment) and do it right. Or ask CrossValidated for advice.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2012-02-12T23:55:12.277" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1016" PostTypeId="1" AcceptedAnswerId="1019" CreationDate="2012-02-13T01:33:00.713" Score="7" ViewCount="941" Body="&lt;p&gt;What happens during a long sleep that makes people look odd when they have just woken up?  Why doesn't the same phenomenon occur in the case of a person who lies down for an extended period of time, but stays awake?  I've noticed that some nights seem to make a bigger difference than others in the appearance of the sleeper, but haven't noticed a pattern.&lt;/p&gt;&#xA;" OwnerUserId="489" LastActivityDate="2012-02-13T11:19:10.667" Title="Why do people look different after a long sleep?" Tags="&lt;human-biology&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1018" PostTypeId="1" AcceptedAnswerId="1043" CreationDate="2012-02-13T10:45:07.597" Score="16" ViewCount="4743" Body="&lt;p&gt;It's very costly to be a huge animal. Your mass grows in cube when you scale up, but you still only have two/four legs to support the same weight. This increases the pressure that your body needs to cope with.(this is easy to see if you compare an ant with an elephant. The elephants legs are much thicker and strudier in comparison to it's body)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at a T-rex for example, speciemns have been found that are believed to weight more than 9 tonnes, compared to an elephants 10 tonnes. T-rex has ofcorse has only two legs. The heaviest dionsaur is believed to have weight 80 tonnes. That is the weight of about 20 cars on each of their feet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How could they support such massive weights?&lt;/p&gt;&#xA;" OwnerUserId="491" LastEditorUserId="107" LastEditDate="2012-02-15T01:09:41.187" LastActivityDate="2016-09-12T16:17:50.940" Title="How did the huge dinosaurs cope with gravity and loads on bones, etc.?" Tags="&lt;evolution&gt;&lt;physiology&gt;&lt;palaeontology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1019" PostTypeId="2" ParentId="1016" CreationDate="2012-02-13T11:19:10.667" Score="5" Body="&lt;p&gt;Puffy eyes are caused by fluid build up in tear ducts from extended periods of lying down. Gravity from sitting or standing slowly drains them during the day. The crusty 'sleep' that accumulates in the corner of your eyes is the residue from basal tear liquid that has seeped out of the eye and evaporated during the night.&lt;/p&gt;&#xA;" OwnerUserId="368" LastActivityDate="2012-02-13T11:19:10.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1020" PostTypeId="2" ParentId="975" CreationDate="2012-02-13T15:03:33.563" Score="5" Body="&lt;p&gt;I would say no.&#xA;Some HIV strains are X4-tropic and not R5 tropic. That means that the virus uses the CXCR4 coreceptor and not the CCR5 coreceptor for entry into the CD4-positive cell.&lt;/p&gt;&#xA;" OwnerUserId="492" LastActivityDate="2012-02-13T15:03:33.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1021" PostTypeId="2" ParentId="1008" CreationDate="2012-02-13T15:13:10.967" Score="18" Body="&lt;p&gt;It depends how you define &lt;strong&gt;locomotion&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you take it to mean &lt;strong&gt;moving from one place to another&lt;/strong&gt;, then yes, almost all plants do this at some stage during their life cycle. Primarily seeds and pollen move around, and generally they do so by harnessing either natural forces like wind and rain, or by manipulating animals to do the leg-work, e.g.:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;by recruiting pollinating insects&lt;/li&gt;&#xA;&lt;li&gt;by having barbs which snag the fur of passing mammals&lt;/li&gt;&#xA;&lt;li&gt;by producing tasty fruit so monkeys eat them, seeds included, and deposit them with a dollop of fertiliser somewhere else&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you take it to mean &lt;strong&gt;moving around under ones own propulsion&lt;/strong&gt;, then yes, some plants do this. The example that springs to mind is the gametophyte generation of ferns:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/F4sq5.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The prothallus (i.e. the gametophyte) has rhizoids on the underside and uses them to slide around and find some space in which to start the next generation. I have seen this happen when fern spores are germinated on agar - when they reach the tiny prothallus stage, they start sliding around to avoid overlapping with one another. I can't find any references for this, but I'll keep looking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example of self-directed locomotion in plants is the motile sperm of bryophytes. The male sex cells have flagella, which they use to propel themselves through water to the female sex cells (reviewed by &lt;a href=&quot;http://www.tandfonline.com/doi/abs/10.1080/20013591099209&quot; rel=&quot;nofollow noreferrer&quot;&gt;Renzaglia &amp;amp; Garbary 2001&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Renzaglia, K.S. &amp;amp; Garbary, D.J. (2001) Motile Gametes of Land Plants: Diversity, Development, and Evolution. &lt;em&gt;Critical Reviews in Plant Sciences.&lt;/em&gt; [Online] 20 (2), 107–213.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-02-13T15:27:02.537" LastActivityDate="2012-02-13T15:27:02.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1023" PostTypeId="2" ParentId="1008" CreationDate="2012-02-13T18:15:23.227" Score="9" Body="&lt;p&gt;Many plants crawl by sending out ground vines and replant themselves in neighboring positions. But that's not what you are asking I think.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know if there are any land dwelling leaf bearing plant forms that move.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the water most chlorophyll bearing algae have flagellae and can migrate through the water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&#xA;&lt;a href=&quot;http://science.jrank.org/pages/205/Algae.html&quot;&gt;http://science.jrank.org/pages/205/Algae.html&lt;/a&gt;  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-02-13T18:15:23.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1024" PostTypeId="1" AcceptedAnswerId="1161" CreationDate="2012-02-13T18:26:00.133" Score="5" ViewCount="7564" Body="&lt;p&gt;Is there a difference between an F' plasmid that has taken up a chromosomal gene that conveys antibiotic resistance, and an R plasmid? Is a bacterium containing an R plasmid and yet lacking an F+ plasmid capable of horizontal gene transfer by conjugation?&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="338" LastEditDate="2012-02-22T08:36:01.143" LastActivityDate="2012-02-23T05:41:03.140" Title="What is the distinction between F' plasmid and R plasmid?" Tags="&lt;genetics&gt;&lt;microbiology&gt;&lt;bacteriology&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1025" PostTypeId="1" AcceptedAnswerId="2283" CreationDate="2012-02-13T19:54:22.513" Score="10" ViewCount="802" Body="&lt;p&gt;I'm reading about the use of x-ray crystallography to determine protein structure. According to my book, data is collected at 30-360 angles (dependent on the symmetry of the protein). An illustration is given with concentric rings labelled with distances - the further out the points are, the higher the resolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the image a composite (where the angle of the point point from the centre is equivalent to the angle of the reading) or is a separate image taken at each angle? Are there any other reasons why more images would be required?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="368" LastEditorUserId="6" LastEditDate="2012-02-13T22:38:21.157" LastActivityDate="2019-07-02T21:15:59.900" Title="Can protein structure be determined by X-Ray Diffraction in a single image?" Tags="&lt;proteins&gt;&lt;structural-biology&gt;&lt;xray-crystallography&gt;" AnswerCount="4" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1026" PostTypeId="1" AcceptedAnswerId="1040" CreationDate="2012-02-13T20:20:46.743" Score="9" ViewCount="43825" Body="&lt;p&gt;I'm trying to get my head around factors which affect transpiration in leaves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, how would applying petroleum jelly to the surface of plant leaves affect their rate of transpiration?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I get that it's basically going to decrease the trasnpiration rate because the stomata will be covered, but I'm not sure about these parts:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;How would it affect the rate of transpiration if only the top surface was covered?&lt;/li&gt;&#xA;&lt;li&gt;How would it affect the rate of transpiration if only the bottom surface was covered?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Also, I think I'm right in saying that increasing wind / applying a fan to plant leaves will increase the transpiration rate, but why?&lt;/p&gt;&#xA;" OwnerUserId="494" LastEditorUserId="338" LastEditDate="2012-02-16T14:36:45.023" LastActivityDate="2016-05-06T19:14:54.823" Title="What factors affect the rate of transpiration in plant leaves?" Tags="&lt;botany&gt;&lt;homework&gt;&lt;plant-physiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1027" PostTypeId="1" CreationDate="2012-02-13T20:59:58.190" Score="12" ViewCount="822" Body="&lt;p&gt;Different types of superoxide dismutase (SOD) contain different metal ions (Zn, Cu, Mn, Ni, or Fe), all of which allow them to catalyze one reaction, dismutation of superoxide anion, O&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;−&lt;/sup&gt;. Cyanide can block this reaction, but only in CuZnSOD.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the (bio)chemical mechanism behind cyanide inhibition of CuZnSOD and why doesn't it occur in FeSOD or MnSOD?&lt;/p&gt;&#xA;" OwnerUserId="251" LastEditorUserId="389" LastEditDate="2012-02-28T01:39:13.243" LastActivityDate="2012-03-05T14:20:28.837" Title="Why does cyanide inhibit CuZnSOD, but not MnSOD or FeSOD?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;&lt;bioinorganic-chemistry&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1029" PostTypeId="2" ParentId="991" CreationDate="2012-02-13T21:12:37.610" Score="1" Body="&lt;p&gt;Embryonic disc forms on top of yolk during cleavage on chicken embryo, while between amniotic sac and yolk sac inside blastocyst after implantation on human embryo.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Some further processes take place on and in the embryonic disc: specifically these &lt;a href=&quot;http://www.embryology.ch/anglais/hdisqueembry/planmoddisque.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; during the week 3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Embryonic disc formation includes still during the 3rd week of development:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Formation of the primitive streak&lt;/li&gt;&#xA;&lt;li&gt;Genesis of the germ layers&lt;/li&gt;&#xA;&lt;li&gt;Genesis of the notochord&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Formation of the primitive streak:&lt;/strong&gt; The process of primary neurulation appears to be similar in chick and mammalian. The embryonic disc becomes oval and then pear-shaped, the wider end being directed forward. Near the narrow, posterior end, the primitive streak makes its appearance and extends along the middle of the disc for about one-half of its length from migrated ectoderm cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MYQKv.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Genesis of the notochord:&lt;/strong&gt; “The notochord extends beneath the neural tube from the base of the head into the tail.” - As the mesoderm develops between the ectoderm and endoderm it is separated into lateral halves by the neural tube and notochord.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 2: Neurulation. NB the use of neural groove is correct. Notochord is below neural groove. - Genesis of germ layers here: from a flat thing to a developed one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lkX4a.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 3: Genesis of notochord and primitive streak. Yolk-sac surrounds notochord and primitive streak.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/725Ic.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2012-04-11T23:08:44.697" LastActivityDate="2012-04-11T23:08:44.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1030" PostTypeId="2" ParentId="1025" CreationDate="2012-02-13T21:24:08.700" Score="4" Body="&lt;p&gt;Not by analysing a single protein.  There is work with x-ray lasers.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You have to take a simultaneous image of millions of proteins and use that to get a structure.  It's not quite prime time.  People are also doing this with electron beams in electron microscopes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These methods will reconstruct 3D models of the molecules, sometimes in states which cannot be obtained from crystallography.  Examples being the structure of the many &lt;a href=&quot;http://www.sciencemag.org/content/306/5700/1387.short&quot; rel=&quot;nofollow&quot;&gt;megadalton nuclear pore complex&lt;/a&gt;, and the f-actin fiber.   The classic study is  3d model of bacteriorhodopsin, the first membrane protein structure which was at molecular resolution (this was a crystalline sample though). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While in principle, it sounds much simpler - get a pure sample of your protein, or complex and freeze it down and zap it with an Xray or Electron beam, its a lot more work to reconstruct the image and can take as long or longer than getting an x-ray structure.  The resolution is also usually poor as the crystal will reinforce coherence, that is all the proteins are aligned in the same way and have close to the same 3d shape in a crystal. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-05-17T14:34:18.133" LastActivityDate="2012-05-17T14:34:18.133" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1031" PostTypeId="1" AcceptedAnswerId="1766" CreationDate="2012-02-13T21:34:36.567" Score="2" ViewCount="258" Body="&lt;p&gt;I was given an explanation that birds and reptiles are polyspermic because they have an abundant yolk sac. But how does it explain the thing?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chicken as an adult is not using in my opinion yolk as an energy source.&#xA;Yolk is used during embryogenesis as the primary energy source with blastula and gastrula -stages and during organogenesis, since the embryo needs proteins and energy somewhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How does abundant yolk sac make birds and reptiles polyspermic?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-04-12T09:23:21.650" Title="Why are Birds and Reptiles with abundant yolk sac polyspermic?" Tags="&lt;homework&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1032" PostTypeId="1" CreationDate="2012-02-13T21:51:36.003" Score="6" ViewCount="378" Body="&lt;p&gt;In &lt;em&gt;The Road to Reality&lt;/em&gt;, Roger Penrose suggests that certain brain structures might play a role in consciousness&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Most particularly, lattice neuronal microtubules, as originally&#xA;  suggested by Stuart Hameroff but perhaps also other structures, like&#xA;  synaptic clathrins, whose structure closely resembles the c60&#xA;  molecules.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;He supposes this would have to do with some sort of quantum coherence:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...the scheme would require some kind of large scale quantum coherence,&#xA;  acting broadly across considerable regions of the brain having&#xA;  features in common with high temperature superconductivity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In general, which organisms have these structures? Are they common?&lt;/p&gt;&#xA;" OwnerUserId="250" LastActivityDate="2012-06-17T16:26:33.340" Title="Which organisms have the neuroanatomy Roger Penrose supposes play a role in consciousness?" Tags="&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1033" PostTypeId="1" AcceptedAnswerId="1204" CreationDate="2012-02-13T22:30:27.700" Score="3" ViewCount="356" Body="&lt;p&gt;I know that metaphase II ends at ampulla tuba uterina, but I am not completely sure where the telophase II ends. Is it in the triangular section of cervix uterii?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just have an intuition that the thing is not ending at the ampulla, since there is some time to get to the uterus. The thing must happen before implantation to the uterus, since the egg is blastocyst at the stage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. When does meiosis II of oogenesis end exactly?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-02-26T19:03:31.550" Title="Where does meiosis II of oogenesis end exactly in tuba uterina - uterus?" Tags="&lt;homework&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1034" PostTypeId="1" AcceptedAnswerId="1036" CreationDate="2012-02-14T00:58:00.267" Score="8" ViewCount="44520" Body="&lt;p&gt;I've heard that stomach lining has the fastest reproducing cells and the brain has the slowest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where in the human body does mitosis occur and at what rates do these cell reproduce? Is there a chart for the whole body available?&lt;/p&gt;&#xA;" OwnerUserId="84" LastActivityDate="2017-09-22T20:11:58.037" Title="Mitosis in human body" Tags="&lt;human-biology&gt;&lt;mitosis&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1035" PostTypeId="1" CreationDate="2012-02-14T01:37:18.450" Score="9" ViewCount="484" Body="&lt;p&gt;Which organism has the sharpest vision in terms of distance and spectrum. Please propose any other useful measure.&lt;/p&gt;&#xA;" OwnerUserId="95" LastEditorUserId="69" LastEditDate="2012-03-24T22:21:50.547" LastActivityDate="2012-03-24T22:21:50.547" Title="Which organism has the sharpest vision?" Tags="&lt;zoology&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1036" PostTypeId="2" ParentId="1034" CreationDate="2012-02-14T02:00:08.707" Score="7" Body="&lt;p&gt;In many cases cell division depends on the stage of development an organism is in. The rate of cell division is obviously much faster in a developing organism and from what I understand fully differentiated cells such as neuron and those in skeletal muscles don't divide (correct me if I'm wrong here).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In early development totipotent cells (stem cells that can become anything) begin to differentiate dependent on environmental factors, turning into multipotent (partially differentiated) cells that can only lead to certain cell types. For example: mesodermal precursors can differentiate to myoblasts, which can go on to differentiate into myotubes, later forming muscles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Epithelial and and blood cells are the two of the main types of cells that need to be constantly replaced in developed organisms. As far as I know cells lining the gut epithelium are fastest to divide. They are created from stem cells in 'crypts' (pockets) in the lining and are pushed outwards, where they are later broken down (by what I would assume would be abrasion and intestinal juices). My book gives them a lifespan of 3-5 days. External skin cells are much slower to divide (though I'n not sure by exactly how much). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Red blood cells have have a lifespan of approximately 120 days. They are replenished by stem cells in the marrow of certain bones (e.g. a femur). Neutrophils are the next most common blood cell, with a circulating life of 8 hours (but lifespan may be a few days). Per day, roughly equal numbers of RBCs and neutrophils are created and are most numerous new cells created per day. Lymphocytes, another white blood cell, are responsible for immune 'memory' can persist for years. The fastest recorded mitotic cycle for a mammalian cell (in culture) is ~8-10hrs.&lt;/p&gt;&#xA;" OwnerUserId="368" LastEditorUserId="368" LastEditDate="2014-04-01T19:02:59.323" LastActivityDate="2014-04-01T19:02:59.323" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1037" PostTypeId="1" AcceptedAnswerId="1039" CreationDate="2012-02-14T02:09:16.680" Score="33" ViewCount="157363" Body="&lt;p&gt;How did the red blood cell in humans get to lose its nucleus (and other organelles)? Does the bone marrow just not put the nucleus in, or is it stripped out at some stage in the construction of the cell?&lt;/p&gt;&#xA;" OwnerUserId="84" LastEditorUserId="1320" LastEditDate="2013-05-08T10:41:22.070" LastActivityDate="2016-10-23T00:16:22.383" Title="Why do mammalian red blood cells lack a nucleus?" Tags="&lt;human-biology&gt;&lt;hematology&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1038" PostTypeId="1" AcceptedAnswerId="1047" CreationDate="2012-02-14T03:51:34.363" Score="5" ViewCount="2099" Body="&lt;p&gt;In the antibody-mediated immune response, when the helper T cell gets activated by the costimulus (IL-2 and TNF-α secreted by the APC) which in turn produces IL-2, IL-2 acts in an autocrine manner. I'm just wondering why does IL-2 have to be secreted? Why doesn't it just exert an affect while it's already inside the helper T cell? What's the point of autocrine signalling? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope the answer isn't going to be, &quot;Well, that's just the way it is...&quot; because paracrine and endocrine make sense and have advantages, but autocrine just seems a bit extra. &lt;/p&gt;&#xA;" OwnerUserId="496" LastActivityDate="2012-02-15T09:25:29.637" Title="What's the advantage of autocrine signalling?" Tags="&lt;immunology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1039" PostTypeId="2" ParentId="1037" CreationDate="2012-02-14T06:09:08.147" Score="32" Body="&lt;p&gt;Red blood cells are initially produced in the bone marrow with a nucleus. They then undergo a process known as enucleation in which their nucleus is removed. Enucleation occurs roughly when the cell has reached maturity. According to one research (&lt;a href=&quot;http://www.nature.com/ncb/journal/v10/n3/abs/ncb1693.html&quot;&gt;Ji, &lt;em&gt;et al.&lt;/em&gt;, 2008&lt;/a&gt;), the way this occurs in mice is that a ring of actin filaments surrounds the cell, and then contracts. This cuts off a segment of the cell containing the nucleus, which is then swallowed by a macrophage. Enucleation in humans most likely follows a very similar mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The absence of a nucleus is an adaptation of the red blood cell for its role. It allows the red blood cell to contain more hemoglobin and, therefore, carry more oxygen molecules. It also allows the cell to have its distinctive bi-concave shape which aids diffusion. This shape would not be possible if the cell had a nucleus in the way. Because of the advantages it gives, it is easy to see why evolution would cause this to occur. However, since little is known about the genes the control enucleation, it is still not a fully understood process.             &lt;/p&gt;&#xA;" OwnerUserId="114" LastEditorUserId="107" LastEditDate="2013-06-25T18:54:05.607" LastActivityDate="2013-06-25T18:54:05.607" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1040" PostTypeId="2" ParentId="1026" CreationDate="2012-02-14T12:18:08.500" Score="7" Body="&lt;p&gt;The rate of transpiration is &lt;em&gt;very&lt;/em&gt; closely linked with the rate of evaporation from the leaf surface.  Increased air movement across the surface of the leaf (e.g. from a fan) increases the rate of evaporation of water from the leaf surface. This happens because water saturated air is moved away; making the osmotic gradient more pronounced.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the relative changes from adding an impermeable substance like petroleum jelly to the top and bottom surfaces of leaves, it's a question of plant-anatomy.  In the majority of plants, stomata are only located on the bottom surface of the leaf.  This is to prevent them getting 'clogged' during rainfall and to keep them out of the sun to minimise water loss (again more sunlight on the stomata would increase the rate of evaporation).  Therefore a plant with the underside covered would have a much slower rate of transpiration than one with the top surface of the leaf covered. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other factors that would affect the rate of transpiration:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Temperature (Positive Correlation) &lt;/li&gt;&#xA;&lt;li&gt;Humidity (Negative Correlation)&lt;/li&gt;&#xA;&lt;li&gt;Light Availability &lt;em&gt;Excluding CAM photosynthesis pathway plants&lt;/em&gt; (Positive Correlation - the stomata are in the main only open when photosynthesis is occurring, so transpiration is less at night or on a cloudy day in addition to light  heating the leaf surface)&lt;/li&gt;&#xA;&lt;li&gt;Water content of soil (Positive Correlation)&#xA;&lt;ul&gt;&#xA;&lt;li&gt;amount of salt in soil (negative correlation)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="69" LastEditorUserId="-1" LastEditDate="2013-01-02T20:51:09.747" LastActivityDate="2013-01-02T20:51:09.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1041" PostTypeId="1" AcceptedAnswerId="1042" CreationDate="2012-02-14T12:23:03.430" Score="20" ViewCount="15443" Body="&lt;p&gt;During photosynthesis, a plant translates CO&lt;sub&gt;2&lt;/sub&gt;, water and light into O&lt;sub&gt;2&lt;/sub&gt;. I assume the carbon C is further used for the growing process. I wonder how the plant grows &lt;em&gt;before&lt;/em&gt; the time where photosynthesis is possible, i.e. before there are even leaves, in which photosynthesis occurs.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;To what extent does the plant grow from the seed/the minerals in the ground?&lt;/p&gt;&#xA;&lt;p&gt;How much carbon are relevant for which parts of the plant and at what times of the evolution of the plant?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I don't know if there are only these life periods of the plant, i.e. if there are other major biochemist-of-growing changes, than in the comparison before and after the plant got leaves. So are there other relevant aspects to this? If there &lt;em&gt;are&lt;/em&gt; leaves present, is the rigid structure of the plant only coming from the CO&lt;sub&gt;2&lt;/sub&gt; in the air and not from the ground anymore?&lt;/p&gt;&#xA;&lt;p&gt;The answer will probably depend on the plant. So here is another formulation of the question:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;What are typical characteristics of different plants in this regard? I.e., how do common species of plants manage their C consumption before (and after) the development of leaves?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="498" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2017-04-13T04:17:02.407" Title="How does a plant grow before photosynthesis is possible?" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1042" PostTypeId="2" ParentId="1041" CreationDate="2012-02-14T13:59:57.380" Score="22" Body="&lt;p&gt;There are quite a few questions and thoughts in there, I'll try to cover them all:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, to correct your initial word equation: &lt;strong&gt;During photosynthesis, a plant translates CO&lt;sub&gt;2&lt;/sub&gt; and water into O&lt;sub&gt;2&lt;/sub&gt; and carbon compounds using energy from light (photons)&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are correct to assume the C is further used for the growing process; it is used to make sugars which store energy in their bonds. That energy is then released when required to power other reactions, which is how a plant lives and grows. C is also incorporated into all the organic molecules in the plant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants require several things to live: CO2, light, water and minerals. If any of those things is missing for a sustained period, growth will suffer. Most molecules in a plant require some carbon, which comes originally from CO&lt;sub&gt;2&lt;/sub&gt;, and also an assortment of other elements which come from the mineral nutrients in the soil. So the plant is completely reliant on minerals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most plants, before a leaf is established or roots develop, grow using energy and nutrients stored in the endosperm and cotyledons of the seed. I whipped up a rough diagram below. Cotyledons are primitive leaves inside the seed. The endosperm is a starchy tissue used only for storage of nutrients and energy. The radicle is the juvenile root. The embryo is the baby plant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/F80Hu.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the seed germinates the embryo elongates, the endosperm depletes, the testa ruptures, and the cotyledons emerge from the seed. The cotyledons are green, and like leaves can photosynthesise, so as soon as they are in the light the plant is able to make carbon compounds. The radicle elongates at the same time, and becomes the root, so the plant is very quickly able to obtain fresh nutrients from the soil (or whatever it's growing in).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At all stages of a plant's life it is using both energy stored in carbon compounds (from CO&lt;sub&gt;2&lt;/sub&gt;) and nutrients which it took up via its roots. At no point does the plant start to depend solely on the CO&lt;sub&gt;2&lt;/sub&gt; in the air for its growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are right that the way in which plants acquire energy and nutrients prior to leaves and roots being established varies between plants. Above I outlined the way &lt;em&gt;most&lt;/em&gt; plants use. But there are lots of variations. For example, orchids have very tiny seeds, some barely visible to the naked eye, like specks of dust. They have no endosperm or storage tissue, so they have to rely on a symbiotic &lt;a href=&quot;http://en.wikipedia.org/wiki/Mycorrhiza&quot; rel=&quot;noreferrer&quot;&gt;mycorrhizal fungus&lt;/a&gt; to get carbon and nutrients. The fungus grows through the coat of the orchid seed, then provides everything the growing plant needs until it has its own leaves. Then the orchid repays the fungus by providing sugars.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are lots of other examples, but we could go on all day! &lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-02-14T15:11:34.637" LastActivityDate="2012-02-14T15:11:34.637" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1043" PostTypeId="2" ParentId="1018" CreationDate="2012-02-14T16:36:27.603" Score="16" Body="&lt;p&gt;Assuming that gravity was essentially the same (other answers to this question notwithstanding), very large dinosaurs were dealing with the same forces that they would today. There are two clades of dinosaurs in which gigantism evolved, Sauropoda (quadrupdeal sauropods) and Theropoda (including &lt;em&gt;T. rex&lt;/em&gt;). Each &quot;solved&quot; the problem of large size in different (but also somewhat similar) ways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main reason why large size was not a problem was that, if posture changed to align the forces between the animal and the ground, the bones are compressed. Bone is very strong in compression.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Theropoda&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Theropod essential operate as a see-saw, with a large muscular tail balancing a large head. As such, they did not likely use much active muscular force to balance. The analogy is a human standing. Just standing, you don't need much muscle force to balance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hutchinson and Garcia (&lt;a href=&quot;http://www.rvc.ac.uk/aboutus/staff/jhutchinson/files/JRH5.pdf&quot;&gt;2002&lt;/a&gt;) showed that, because of a lack of plausibly large leg musculature, &lt;em&gt;T. rex&lt;/em&gt; could not run. For a range of postures, they estimated how much muscle would be required to balance the animal and found that running behavior was unlikely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hutchinson, J.R. and M. Garcia. 2002. &lt;em&gt;Tyrannosaurus&lt;/em&gt; was not a fast runner. &lt;em&gt;Nature&lt;/em&gt; 415:1018-1021.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sauropoda&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Sauropods show many similar adaptations as elephants, the largest extant land mammals. Their limbs were held upright (erect), which requires less energy for balance. Some sauropods had air-filled bones, which would also lighten the skeleton. Wilson and Carrano (&lt;a href=&quot;http://paleobiol.geoscienceworld.org/cgi/content/abstract/25/2/252&quot;&gt;1999&lt;/a&gt;) document the evolution of posture through sauropod evolution from a biomechanical perspective.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wilson, J.A. and M.T. Carrano. 1999. Titanosaurs and the origin of “wide-gauge” trackways: a biomechanical and systematic perspective on sauropod locomotion. &lt;em&gt;Paleobiology&lt;/em&gt; 25:252–267. &lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-02-14T16:36:27.603" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1045" PostTypeId="1" AcceptedAnswerId="1414" CreationDate="2012-02-14T20:12:20.687" Score="14" ViewCount="708" Body="&lt;p&gt;As my textbook &lt;em&gt;An Introduction to Genetic Analysis&lt;/em&gt; points out, yeast mitochondrial DNA has approximately 78 kb of genetic data, while the human mitochondrial DNA contains 17 kb. Is there any evolution reason for this drastic change in size? Also, are there any particularities about mitochondrial function that have been compromised with this reduction in size?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Griffiths, Anthony J. F.&lt;/strong&gt; &lt;em&gt;An Introduction to Genetic Analysis.&lt;/em&gt; New York: W.H. Freeman, 2000.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-07-26T23:13:16.003" LastActivityDate="2016-09-28T22:08:16.430" Title="Is there any reason for the variation in mitochondrial DNA size?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;physiology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1046" PostTypeId="2" ParentId="1045" CreationDate="2012-02-14T20:51:54.057" Score="3" Body="&lt;p&gt;Shorter DNA would allows easier synthesis, but more introns could  allow for more different transcription factors to influence gene expression. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human mitochondria probably does not need to be as adaptable as mitochondria in yeast, since the a human cell's environment tends to be more stable. This could provide a viable reason as to why human mitochondria does not need as many introns, but this is only how I imagine things. I have no proof or experience to validate any of this - its just a possiblility.&lt;/p&gt;&#xA;" OwnerUserId="368" LastActivityDate="2012-02-14T20:51:54.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1047" PostTypeId="2" ParentId="1038" CreationDate="2012-02-14T22:48:59.490" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Why doesn't it just exert an affect while it's already inside the helper T cell? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Because it interacts with membrane-bound receptors. Those are outside so there is no way IL-2 (or any autocrine factor) could signal while inside the cell. It &lt;em&gt;has&lt;/em&gt; to exit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the next question is why the receptor is membrane-bound and outside. As far as I understand there are two parts to this answer:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Receptors are evolutionarily related so they follow similar synthesis pathways.&lt;/li&gt;&#xA;&lt;li&gt;Membrane-bound receptors are (all?) transcribed while being secreted into the &lt;a href=&quot;http://en.wikipedia.org/wiki/Endoplasmic_reticulum&quot; rel=&quot;nofollow&quot;&gt;endoplasmic reticulum&lt;/a&gt;. This causes their agent-binding portion to reside &lt;em&gt;inside&lt;/em&gt; the ER. From there, vesicles bud off, are &lt;a href=&quot;http://en.wikipedia.org/wiki/Secretory_pathway&quot; rel=&quot;nofollow&quot;&gt;transported towards the cell membrane&lt;/a&gt;, merge with it, and hence the formerly inside portion of the protein ends up on the outside.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="166" LastActivityDate="2012-02-14T22:48:59.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1048" PostTypeId="2" ParentId="1025" CreationDate="2012-02-15T06:45:39.617" Score="4" Body="&lt;p&gt;Likely not. While one can get excellent diffraction data from a high quality crystal, it would be extremely difficult to solve the phase problem. The extra angles will help constraint the solutions.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-02-15T06:45:39.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1049" PostTypeId="2" ParentId="1038" CreationDate="2012-02-15T09:25:29.637" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;paracrine and endocrine make sense and have advantages, but autocrine&#xA;  just seems a bit extra.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Autocrine also have advantages compared to internal signaling. Even if when you study mechanisms you think at single cells, cells are never alone in the body. If the message (IL-2) would be internal, each cell will individually respond according to its internal signaling levels. With the 'extra' to secrete the message, and having it sensed at the exterior (the receptor is membrane-bound), all the cells in the nearby are going to contribute to the average signal and will respond with average magnitude. It's a form of communication between a single cell population that does not affect other cells populations (the ones that does not express the IL-2 receptor).&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-02-15T09:25:29.637" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1050" PostTypeId="2" ParentId="417" CreationDate="2012-02-15T11:05:17.627" Score="8" Body="&lt;p&gt;There's an excellent, comprehensive review article on the entire process of REM sleep:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Vetrivelan,R, Chang, C, Lu,J (2011). Muscle tone regulation during REM sleep:&#xA;  neural circuitry and clinical significance. Archives Italiennes de Biologie, 149 &lt;a href=&quot;http://dx.doi.org/10.4449/aib.v149i4.1272&quot; rel=&quot;nofollow&quot;&gt;[DOI]&lt;/a&gt; &lt;a href=&quot;http://www.architalbiol.org/aib/article/download/22205588/22205588&quot; rel=&quot;nofollow&quot;&gt;[Free PDF]&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Projections from the sublaterodorsal nucleus (SLD) of the Pons in the brainstem are responsible for the suppression of the spinal motor output/movement (for an anatomical schematic, see the article).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Descending SLD glutamatergic projections activating the premotor neurons&#xA;  in the ventromedial medulla and spinal cord interneurons bring about muscle atonia and suppress phasic muscle twitches in spinal musculature.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Lesions in this area in rats have resulted in REM sleep without atonia.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many studies have&#xA;  suggested that the ventromedial medulla (VMM),&#xA;  which receives glutamatergic inputs from the SLD,&#xA;  may be the relay site for the pontine inhibitory area&#xA;  on spinal motor neurons&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The SLD axons relay through the VMM, but also directly projects onto interneurons within the spinal cord, directly inhibiting their activation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the knowledge we have about this subject comes from animal studies, so it will take some time to verify whether these same mechanism and relays are the same in humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The area that is lending the most credence to these issues of REM atonia is not sleepwalking as much as REM sleep behavioral disorder (RBD).  In this condition, sufferers act out their dreams and generally lose atonia during REM sleep.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evidence points to the fact that such behavior is often seen decades before such conditions as Parkinson's and Lewy Body dementia.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ferini-Strambi,L (2011) Does idiopathic REM sleep behavior disorder (iRBD) really exist?&#xA;  What are the potential markers of neurodegeneration in iRBD? Sleep Medicine 12, S43–S49 &lt;a href=&quot;http://dx.doi.org/10.1016/j.sleep.2011.10.010&quot; rel=&quot;nofollow&quot;&gt;[DOI]&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They summarized two studies which explored these anatomical changes:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[Diffusion tensor imaging, a type of MRI scan] changes have been reported in the&#xA;  brainstem (pons, substantia nigra) as well as the fornix, the right&#xA;  visual stream, and the left superior temporal lobe suggestive of&#xA;  brain tissue disintegrity[1]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;significant decreases of [fractional aniosotropy] in the tegmentum&#xA;  of the midbrain and rostral pons and increases of [mean diffusivity]&#xA;  within the pontine reticular formation overlapping with a cluster&#xA;  of decreased [fractional anisotropy] in the midbrain [2]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, the answer is, we don't know for sure, but we have some clues from the animal models as to what stages of the signals to suppress movement are interrupted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;[1]Unger MM, Belke M, Menzler K, et al.(2010). Diffusion tensor imaging in idiopathic&#xA;REM sleep behavior disorder reveals microstructural changes in the brainstem,&#xA;substantia nigra, olfactory region, and other brain regions. Sleep,&#xA;33(6),767–73.&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881532/pdf/aasm.33.6.767.pdf&quot; rel=&quot;nofollow&quot;&gt;[FREE PDF]&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;[2]Scherfler C, Frauscher B, Schocke M, et al. (2011) White and gray matter abnormalities&#xA;in idiopathic rapid eye movement sleep behavior disorder: a diffusion-tensor&#xA;imaging and voxel-based morphometry study. Ann Neurol,69(2),400–7. &lt;a href=&quot;http://dx.doi.org/10.1002/ana.22245&quot; rel=&quot;nofollow&quot;&gt;[DOI]&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-07-13T08:28:23.523" LastActivityDate="2012-07-13T08:28:23.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1051" PostTypeId="1" CreationDate="2012-02-15T11:50:00.813" Score="17" ViewCount="5482" Body="&lt;p&gt;It is known that there are very few individuals having 44 chromosomes, not the usual 46 chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One example is a male in China: &lt;a href=&quot;http://www.asiahealthcareblog.com/2011/07/03/chinas-44-chromosome-man-may-be-missing-link-between-us-and-the-chimp/&quot;&gt;the first article&lt;/a&gt;, &lt;a href=&quot;http://www.thetech.org/genetics/news.php?id=124&quot;&gt;the second article&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://vimeo.com/6604325&quot;&gt;The other is a female in Turkey&lt;/a&gt;, unfortunately the article is in Turkish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is claimed in the links that they might reproduce and make healthy children if they mate. So I wonder &lt;strong&gt;if this already happened and such a couple is living&lt;/strong&gt;, or if it would be theoretically possible?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;: As requested, here is the Karyotype of Turkish female, which the professor in the video call her HomoNeoSapiens, with Robertsonian translocation between &lt;strong&gt;13 and 14&lt;/strong&gt; chromosomes. So, this translocation is different from Chinese Man's translocation, which is between &lt;strong&gt;14 and 15&lt;/strong&gt; chromosomes. So in this case they can't breed a healthy children? Gosh, I was about to create a new species :((&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/x0eCP.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="504" OwnerDisplayName="Comptrol" LastEditorUserId="504" LastEditDate="2012-12-23T21:43:31.977" LastActivityDate="2013-04-22T23:23:20.973" Title="Can two humans with 44 chromosomes produce viable offspring?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;genetics&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1052" PostTypeId="2" ParentId="1051" CreationDate="2012-02-15T14:55:00.023" Score="11" Body="&lt;p&gt;Interesting question. You refer to aneuploidy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't have idea, but I loved to make some calculations. Feel free to edit because there are some very approximative assumptions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Aneuploidy&lt;/strong&gt;, the loss or gain of a chromosome, is estimated to occur in 13-25% of oocytes, 1-4% of sperm, 20% conceptuses and 0.3% of newborns. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8768496&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The 46 chromosomes are made of 23 pairs, if the chromosome loss is evenly distributed, we have 0.3% / 23 newborns with the same chromosome loss (0.013 %).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, consider that the lost chromosome is likely not really lost, but just translocated on another of the 22 chromosomes. For instance, the individual you refer was having two chromosomes (the 14 and the 15) fused together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So individuals with the same chromosome loss (0.013%) should have also the same translocation on one of the remaining 22 chromosomes (0.013% / 22 = 0.00059%).**&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chances are now that two of the 0.00059% newborns with &lt;em&gt;exactly&lt;/em&gt; the same chromosome loss, will mate together. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming random mating between humans, we have 0.00059% x 0.00059% = 0.0000003 % of possibilities, which is 1 possibility every 333,333,333 human beings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We are now 7 billions on the Earth, so assume 3.5 billion couples all fertile despite of the age. If we assume also no spatial constraints, so that everyone could mate with every else one on the Earth, there could be no more than 10 couples with the same aneuploid mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Provided the mutation does not affect genes important for reproduction, for instance genes between the two chromosome junctions that get interrupted, this couple could reproduce I guess.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To find that child, chances are now that he/she will have a kariotype done. Quite difficult to find isn'it?&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-02-15T14:55:00.023" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1053" PostTypeId="2" ParentId="1051" CreationDate="2012-02-15T16:19:30.403" Score="14" Body="&lt;p&gt;The article says &quot;both his chromosome 14s are stuck to his chromosome 15s&quot; - meaning both his mom and his dad (46,XX,rob(14,15) and 46,XY,rob(14,15) had a Robertsonian Translocation which doesn't really result in the loss of any genetic material. The very small chance occurred which one sperm carrying the translocation chromosome fused with an oocyte carrying the other translocation chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the genotype of the dude is 44,XY,rob(14,15)(14,15), meaning he's normal because he technically has all the genomic information of a normal human.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If he mates with a normal woman (46,XX), then the resulting progeny will have an extra copy of chromosome 15, resulting in trisomy 15, which is non-viable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If one such 44 chromosome individual mates with another person of the same chromosomal arrangement, then probably a viable fetus would be produced if a translocation chromosome ends up with the same translocation chromosome from the mother. I wouldn't call it a new species per se because it still contains the genetic material from a human. For example, there are many humans with chromosomal abnormalities (I.e trisomy 21, XXY, etc...). Also the background rate of translocations and chromosomal aberrations in somatic cells is notable, so I wouldn't use this as a new species definition.&lt;/p&gt;&#xA;" OwnerUserId="177" LastEditorUserId="177" LastEditDate="2012-02-15T17:47:19.600" LastActivityDate="2012-02-15T17:47:19.600" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1054" PostTypeId="1" AcceptedAnswerId="1055" CreationDate="2012-02-15T18:17:01.527" Score="29" ViewCount="21917" Body="&lt;p&gt;I've found research that suggests that the reason we develop fingerprints is because they aid us with feeling surfaces (&lt;a href=&quot;http://www.sciencemag.org/content/323/5920/1503.abstract&quot;&gt;Scheibert, &lt;em&gt;et al.&lt;/em&gt; 2008&lt;/a&gt;) and not to increase friction  and help with the gripping of smooth objects (&lt;a href=&quot;http://jeb.biologists.org/content/212/13/i.1.short&quot;&gt;Warman and Ennos 2009&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One thing I am still curious about is at what stage of growth the pattern is formed and why a unique pattern is created in the fingerprint of each person (including identical twins). I assume it has something to do with the mechanism by which the patterns form, but I couldn't find any detailed research into this. Any insight would be very welcome.&lt;/p&gt;&#xA;" OwnerUserId="114" LastEditorUserId="307" LastEditDate="2012-07-19T21:17:09.977" LastActivityDate="2014-12-02T19:10:16.243" Title="What causes fingerprints to form and why is the pattern formed unique?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1055" PostTypeId="2" ParentId="1054" CreationDate="2012-02-15T20:47:19.537" Score="5" Body="&lt;p&gt;I would say genetic diversity is the primary reason which results in other reasons that you are looking for. At the lowest level, random crossing over at prophase I, random separation of homologous chromosomes at anaphase I, random separation of sister chromatids at anaphase II, and random fertilization: one sperm fertilizes one egg randomly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The skin is developed from ectoderm so need to look at the formation of embryonic disc and specifically to the &lt;a href=&quot;http://www.embryology.ch/anglais/hdisqueembry/triderm02.html&quot;&gt;genesis of germ layers&lt;/a&gt;: ectoderm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I would stick to the primary reasons, since it is extremely difficult to visualize the given formation - actually we do not have resources for it at the moment.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Very good question the last part. I have an intuition that skin develops randomly because of the above reasons. You would also need a lot of memory to make identical skins for twins! It has not been useful to have identical fingerprints between two people so evolution has not resulted into it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Feeling surfaces and gripping are movements - not much space taken things, in contrast to the memory needed in storing the exact surfaces of skin from one generation to another. - Learning is a way to save resources here and it is a lot more efficient and than storing static information to species from one generation to another.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-02-15T20:47:19.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1056" PostTypeId="1" AcceptedAnswerId="2097" CreationDate="2012-02-15T21:11:15.543" Score="6" ViewCount="1598" Body="&lt;p&gt;I found such a clause:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The general principle is that mitosis creates somatic cells and&#xA;  meiosis creates germ cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, I cannot agree. Each gametogonium needs to go through mitosis before it can enter meiosis I. So in that case mitosis is happening with germ cells so the clause is false.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would rephrase the sentence to be&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The general principle is that meiosis creates only germ cells with the possibility of a decrease in chromosome number, while mitosis can create both somatic and germ cells while the ploidy stays constant.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Ok, not perfect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How would you say the main general difference between mitosis and meiosis?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="43" LastEditDate="2012-05-04T01:13:40.433" LastActivityDate="2019-05-27T10:12:41.183" Title="What is the main general difference between Mitosis and Meiosis?" Tags="&lt;homework&gt;&lt;cell-biology&gt;&lt;meiosis&gt;&lt;mitosis&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1057" PostTypeId="1" AcceptedAnswerId="1059" CreationDate="2012-02-15T21:52:15.227" Score="2" ViewCount="903" Body="&lt;p&gt;Ok, it seems to be easy but I have probably ignored something by accident.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interphase is the phase where things are growing and the preparation for cell division happens. Its stages G1, S and G2. DNA replication in S stage. So the DNA in some chromosomes must have the pieces of information about how to do the DNA replication. - I am not sure  about thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would say to the part: structure that chromosomes are diploid at the given stage. - It does not feel right anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What would you answer to the main question?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-02-15T23:04:46.617" Title="What is the structure and function of chromosomes during interphase?" Tags="&lt;homework&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1058" PostTypeId="1" AcceptedAnswerId="5233" CreationDate="2012-02-15T22:12:52.270" Score="7" ViewCount="1226" Body="&lt;p&gt;Is one part of the day more prevalent then other when it comes to mammal animals mating? Is there an aggregating study that has been done to see if these living beings in nature mate mostly during day or night?&lt;/p&gt;&#xA;" OwnerUserId="245" LastEditorUserId="711" LastEditDate="2012-08-23T21:45:50.820" LastActivityDate="2012-11-13T22:43:34.803" Title="When do most mammals mate?" Tags="&lt;zoology&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="10" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1059" PostTypeId="2" ParentId="1057" CreationDate="2012-02-15T23:04:46.617" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;So the DNA in some chromosomes must have the pieces of information about how to do the DNA replication. - I am not sure about thing.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Genomes contain what is called the &quot;origin of replication&quot; - specific sequences in the DNA that tell DNA polymerase where to bind and to initiate replication. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your main question, I'm a little confused as to what you're asking. In a general sense, chromosomes function as carriers of genetic information. In eukaryotes, nuclear DNA is organized in the nucleus on linear chromosomes which carry most of the genetic information an organism needs to survive. In bacteria, the chromosome is a circular piece of DNA. In eukaryotes, the chromosome is also bound by histone proteins, which serves to regulate expression of certain genes and to help anchor the chromosomes to the inner nuclear membrane.&lt;/p&gt;&#xA;" OwnerUserId="177" LastActivityDate="2012-02-15T23:04:46.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1061" PostTypeId="2" ParentId="781" CreationDate="2012-02-16T17:08:59.393" Score="2" Body="&lt;p&gt;Back when I was doing my PhD, there was a group in the same department as me working on an interesting project exploring the extent to which surnames (generally paternally inherited, at least in the modern west) and Y chromosomes (always paternally inherited) shared their descent. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answers are always complicated, especially for more common surnames which have multiple origins. There are also confounding factors, such as the rate of non-paternity (which can be surprisingly high, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/014067369192013R&quot; rel=&quot;nofollow&quot;&gt;often around 1-2%&lt;/a&gt;). It is, however, striking just how much you can tell about a person's heritage, just from a relatively small amount of genetic information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more info about the surnames work, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19204044&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16488872&quot; rel=&quot;nofollow&quot;&gt;(2)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="82" LastActivityDate="2012-02-16T17:08:59.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1062" PostTypeId="1" AcceptedAnswerId="1063" CreationDate="2012-02-16T17:30:07.380" Score="8" ViewCount="2732" Body="&lt;p&gt;According to Wikipedia, the &lt;a href=&quot;http://en.wikipedia.org/wiki/X_chromosome#Function&quot; rel=&quot;noreferrer&quot;&gt;X chromosome&lt;/a&gt; has approximately 153 million base pairs, while the &lt;a href=&quot;http://en.wikipedia.org/wiki/Y_chromosome&quot; rel=&quot;noreferrer&quot;&gt;Y chromosome&lt;/a&gt; has only 60 million base pairs. Thus, the difference is roughly 93 million base pairs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: Could this &quot;extra&quot; 93 million base pairs in virtually every single female cell of the human body slightly contribute to the &quot;extra&quot; relative weight of the female as a whole, in comparison to a male (of course) with a similar amount of cells? Or would this weight be so small that we can consider it negligible?&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-02-16T21:20:56.413" LastActivityDate="2018-09-10T08:30:25.227" Title="X chromosome &quot;weight&quot;?" Tags="&lt;cell-biology&gt;&lt;cytogenetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1063" PostTypeId="2" ParentId="1062" CreationDate="2012-02-16T17:59:01.667" Score="15" Body="&lt;p&gt;Theoretically... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;93 million bp/cell x 650 daltons/bp x 10^13 cells/body x 1.66 * 10^-27 kg/dalton = 0.001 kg&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I would say it's not too much of a difference :P&lt;/p&gt;&#xA;&#xA;&lt;p&gt;however this ignores the rest of the chromosomal material: histones&lt;/p&gt;&#xA;" OwnerUserId="177" LastEditorUserId="-1" LastEditDate="2014-12-16T16:04:24.907" LastActivityDate="2014-12-16T16:04:24.907" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="1064" PostTypeId="1" AcceptedAnswerId="1065" CreationDate="2012-02-16T19:34:07.133" Score="4" ViewCount="106" Body="&lt;p&gt;My lab has an older large Fotodyne tabletop UV transilluminator for visualizing gels.  It has a UV blocking cover that hopefully reduces UV that passes through, but I've always been suspcious as to how effective it is.  Obviously this part can be replaced with a new one, but short of guessing on the recommended 50 hr lifetime, how would one know the level of UV passsing through?  I considered simply placing a gel on top, but that is far from quantitative.  I am really just curious if there is an easy to make and/or obtain sensor that could be used to know when UV expose could be considered dangerous.&lt;/p&gt;&#xA;" OwnerUserId="96" LastEditorUserId="69" LastEditDate="2012-02-17T10:04:52.593" LastActivityDate="2012-02-17T10:04:52.593" Title="Is there a cheap and easy way to check for potentially unsafe UV exposure?" Tags="&lt;gel-electrophoresis&gt;&lt;experimental-design&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1065" PostTypeId="2" ParentId="1064" CreationDate="2012-02-16T20:46:05.537" Score="3" Body="&lt;p&gt;The instrument you are looking for is probably an &lt;a href=&quot;http://www.google.com/cse?cx=004738989115247203233:09r2ltc-nlc&amp;amp;ie=UTF-8&amp;amp;q=UV-meter&quot; rel=&quot;nofollow&quot;&gt;UV-meter&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-02-16T20:46:05.537" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1066" PostTypeId="1" AcceptedAnswerId="1346" CreationDate="2012-02-16T21:07:17.917" Score="14" ViewCount="33006" Body="&lt;p&gt;We are 7 billion human beings on the Earth. But how many mice are there? How would you estimate such a number?&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2016-03-31T18:03:43.560" Title="How many mice are on the Earth?" Tags="&lt;zoology&gt;&lt;population-dynamics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1067" PostTypeId="2" ParentId="889" CreationDate="2012-02-16T22:09:21.440" Score="0" Body="&lt;p&gt;Methylene blue? Certainly not as sensitive or specific as other options but it's cheap and does not fluoresce.&lt;/p&gt;&#xA;" OwnerUserId="96" LastEditorUserId="96" LastEditDate="2012-02-16T22:18:38.463" LastActivityDate="2012-02-16T22:18:38.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1068" PostTypeId="2" ParentId="968" CreationDate="2012-02-16T23:53:40.343" Score="4" Body="&lt;p&gt;To increase long range focus, the ciliary muscle is relaxed so that the zonular fibres flatten the lens. This flattening increases the focal distance and far away objects appear sharp.&#xA;The process is reversed when increasing short range focus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your example you are watching out of the window into distance. To see the mountains sharp you need to increase range focus and this means relaxing the ciliary muscle. This is also the reason why it is recreative for your eyes to watch into the distance after hours of computer work for example.&#xA;The window itself does not play any role because your focus is not on the window pane but somewhere in the distance.&lt;/p&gt;&#xA;" OwnerUserId="508" LastActivityDate="2012-02-16T23:53:40.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1069" PostTypeId="1" CreationDate="2012-02-17T00:15:41.283" Score="3" ViewCount="55" Body="&lt;p&gt;If you solve collidally dispersed substances then the particles can form large colloids. This may block narrow passages and diffusion into dense structures may become completely impossible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What can you do to improve the solubility of such substances?&lt;/p&gt;&#xA;" OwnerUserId="508" LastActivityDate="2012-02-20T12:59:22.367" Title="How can you improve solubility of colloidally dispersed substances?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1070" PostTypeId="1" CreationDate="2012-02-17T01:06:53.537" Score="5" ViewCount="6495" Body="&lt;p&gt;I want to incubate my sample at 50ºC and then slowly cool it down to 4ºC at a rate of 0.1ºC/s. I am using  &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=3&amp;amp;sqi=2&amp;amp;ved=0CDMQFjAC&amp;amp;url=http://tools.invitrogen.com/content/sfs/manuals/cms_042832.pdf&amp;amp;ei=jKY9T66XCuji2AWFx7GTCA&amp;amp;usg=AFQjCNEnj5WKKDHWCxSR9da1giecngZzCw&amp;amp;sig2=bAQ17HeblDMc5Rbb3WnXAw&quot;&gt;AB Veriti thermal cycler&lt;/a&gt;. Does anyone know how to set up the rate of cooling? It has to do something with the ramp rate, which is given in % but I don't know how to convert this into a real rate.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-02-17T05:49:15.983" Title="How to set up a slow cooling on an AB Veriti thermal cycler?" Tags="&lt;protocol&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1071" PostTypeId="1" AcceptedAnswerId="1080" CreationDate="2012-02-17T02:22:36.777" Score="15" ViewCount="2998" Body="&lt;p&gt;Do insects with compound eyes have depth perception? They fly as if they do, but their eyes are so close together it seems like the image would be 2 dimensional.&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="16866" LastEditDate="2018-03-22T03:19:01.970" LastActivityDate="2018-03-22T03:19:01.970" Title="Do insects with compound eyes have depth perception?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;vision&gt;&lt;eyes&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1072" PostTypeId="1" AcceptedAnswerId="1073" CreationDate="2012-02-17T02:29:26.093" Score="19" ViewCount="2114" Body="&lt;p&gt;How do porcupines keep from pricking each other while mating? It seems like they would constantly be scratching each other.&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="1202" LastEditDate="2012-09-16T22:55:33.160" LastActivityDate="2012-09-16T22:55:33.160" Title="How do porcupines keep from pricking each other while mating?" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;sex&gt;&lt;antipredator-adaptation&gt;&lt;rodents&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1073" PostTypeId="2" ParentId="1072" CreationDate="2012-02-17T03:48:27.603" Score="14" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;The female stood with the tail held sharply to one side, and the quills on &#xA;  the back lying very flat.  The male stood on his hind legs, while the &#xA;  front legs grasped the sides of the female. There was no repetition  of the act.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The male's urethra is 115-120 mm long, and his penis is 75 mm, so the he doesn't need to be as close to the female as one might think.  The retractor muscles are attached to the lower portion of the pelvis, which is likely well below the level at which the male's quills end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently, a dozen or so porcupines will den up in close quarters for the winter, so one can probably guess they have a good sense of whether their spines are hurting another, but that's only conjecture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suppose the take-home message is, nature will find a way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Struthers, P.H. (1928) Breeding Habits of the Canadian Porcupine (&lt;em&gt;Erethizon dorsatum&lt;/em&gt;).  Journal of Mammalogy, 9(4), 300-308. &lt;a href=&quot;http://www.jstor.org/pss/1374084&quot;&gt;http://www.jstor.org/pss/1374084&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mirand,E.A., Shadle,A.R.(1953).  Gross anatomy of the male reproductive system of the porcupine&#xA;Journal of Mammalogy, 34(2), 210-220. &lt;a href=&quot;http://www.jstor.org/pss/1375622&quot;&gt;http://www.jstor.org/pss/1375622&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2012-02-17T03:48:27.603" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1074" PostTypeId="1" AcceptedAnswerId="1190" CreationDate="2012-02-17T04:19:30.093" Score="12" ViewCount="566" Body="&lt;p&gt;There are many arguments for what the unit of the neocortex is. &quot;Columns&quot; seem to be the standard, but what exactly those are is extremely contradictory between individuals, cortical regions, and species. Often times, when a column is referred to, it's actually a &lt;em&gt;functional&lt;/em&gt; column without any anatomical borders (such as Hubel and Wiesels ocular dominance columns). Sometimes, the &quot;column&quot; is semi anatomical, such as the rat barrel cortex. Other times, these functional columns are confabulated into anatomical units, without any evidence for a border.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is, could Mountcastle's &quot;minicolumns&quot; be the actual anatomical unit of the cortex? I've heard arguments that they are mere developmental relics. But they seem like the only reliable and consistent unit in the cortex.&lt;/p&gt;&#xA;" OwnerUserId="510" LastActivityDate="2012-02-25T21:38:06.950" Title="Is the minicolumn the unit of the neocortex?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1075" PostTypeId="2" ParentId="1070" CreationDate="2012-02-17T04:29:32.307" Score="4" Body="&lt;p&gt;If I recall correctly (from when I interned at ABI), you can't directly set this in the Veriti interface.  However, (again, I'm not 100% certain -- I couldn't find anything to confirm this after 30 minutes of googling,) the ramp rate percent refers to the percent of maximum ramp rate for the heating block.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the &lt;a href=&quot;http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/PCR/thermal-cyclers-realtime-instruments/thermal-cyclers/veriti-thermal-cycler.html&quot; rel=&quot;nofollow&quot;&gt;product website&lt;/a&gt;, the max heating block ramp rate is 5 °C/s while the max &lt;em&gt;sample&lt;/em&gt; ramp rate is 4.25 °C/s, so you need a ramp rate between 2% and 2.4%.&lt;/p&gt;&#xA;" OwnerUserId="184" LastActivityDate="2012-02-17T04:29:32.307" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1076" PostTypeId="2" ParentId="1070" CreationDate="2012-02-17T05:49:15.983" Score="3" Body="&lt;p&gt;As Thomas pointed out, there is a maximum ramp rate which you can set up on the thermocycler. Its value can go from 0% to 100%. I can then assume that a 100% ramp rate will corespond to the maximum ramp rate of 4.25°C/s for the heating block or 5°C/s for the sample. which means that a ramp rate of ~2.4%. Subsequently, I set up my reaction at a 2% ramp rate, as I started a timer at the time the ramp cycle started. To my surprise, the temperature was cooling down too slowly. Thus, I empirically found out that a ramp rate of 5% corresponds to ~0.1°C/s cooling speed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wished there was more precise way to calculate it. Perhaps the slope of the line changed at different temperature intervals. It would be great if I can talk to the AB people so that they could justify my finding.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-02-17T05:49:15.983" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1077" PostTypeId="2" ParentId="951" CreationDate="2012-02-17T07:23:58.537" Score="2" Body="&lt;p&gt;I would use an RNA microarray to look at those difference instead of sequencing. To delicately amplify your tRNAs in an unbiased manner would be a tricky molecular biology endeavor. I wouldn't be surprised if there were detectable and significant differences. Those experiments will be able to confirm your hypotheses regarding codon usage bias.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-02-17T07:23:58.537" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1080" PostTypeId="2" ParentId="1071" CreationDate="2012-02-17T09:55:59.470" Score="10" Body="&lt;p&gt;&quot;1001 questions answered about insects&quot; by Alexander Barrett and Elsie Broughton Klots includes the following passage:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Do insects have depth perception?&lt;/strong&gt; Depth perception of some sort is important to an animal who has to catch its prey; &lt;strong&gt;fortunately most&#xA;  insects have it to a degree&lt;/strong&gt;.  Although they do not have binocular&#xA;  vision that can be compared with man's, it is true that when one eye&#xA;  is covered their depth perception is markedly affected.  The criterion&#xA;  of depth seems to depend on the angle of simultaneous stimulation of&#xA;  two corresponding points of the retina of the two eyes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However it does not mention compound eyes specifically. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There may be other methods of obtaining a perception of distance rather than the binocular vision seen in humans.  &lt;a href=&quot;http://dx.doi.org/10.1016/S0376-6357%2803%2900054-8&quot;&gt;This paper&lt;/a&gt; suggests that there is 'clear evidence' that  some insects perceive depth by moving their head to artificially create parallax, which they can then recognise and interpret as depth and distance.  They cite the Praying Mantis as an example, which does have compound eyes.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-02-17T09:55:59.470" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1081" PostTypeId="5" CreationDate="2012-02-17T10:07:13.013" Score="0" Body="" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-02-17T10:07:13.013" LastActivityDate="2012-02-17T10:07:13.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1082" PostTypeId="4" CreationDate="2012-02-17T10:07:13.013" Score="0" Body="Questions on how to plan an experiment to gain the best results.  Also suitable for questions on why other researchers followed a certain procedure." OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-02-17T10:07:13.013" LastActivityDate="2012-02-17T10:07:13.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1083" PostTypeId="2" ParentId="1071" CreationDate="2012-02-17T11:10:58.917" Score="8" Body="&lt;p&gt;The sense of depth is required to us to orient ourselves in a 3D world. Insects do orient themselves in the exterior 3D world, thanks to the ability to detect the plane of sunlight polarization, that is used as a navigation compass in foraging expeditions and when coming back home.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find a good review on Current Biology (&lt;a href=&quot;http://dx.doi.org/10.1016/j.cub.2007.05.022&quot;&gt;Krapp 2007&lt;/a&gt;) and a &lt;a href=&quot;http://courses.cit.cornell.edu/ent201/vision.html&quot;&gt;lecture about insect vision&lt;/a&gt; from Cornell University. &lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-02-17T11:10:58.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1084" PostTypeId="1" CreationDate="2012-02-17T14:53:57.463" Score="13" ViewCount="991" Body="&lt;p&gt;I've done some transcriptomics work in the past with a polyploid organism, and this presented some unique challenges in the data processing and analysis. Since then, I have been brainstorming about the technical challenges one may face when sequencing and assembling the genomes of a polyploid organism. As far as I am aware, there are no polyploids whose genomes have been sequenced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If one wanted to sequence, for example, a tetraploid organism, one approach would be to prepare and sequence all of the DNA together and then rely on post-sequencing analysis to tease apart the two co-resident genomes. However, it would be difficult, if not impossible, with this approach to distinguish inter-genome variation from intra-genome variation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An alternative approach would be to isolate DNA from both co-resident genomes separately, and then sequence and assemble the genomes separately, so that inter-genome variation and homology need not be considered. However, I'm thinking at a very high level and have little intuition as to the technical feasibility of this approach. When there are two or more co-resident genomes, is it be possible to isolate DNA from only one of those genomes? What would this rely on (for example, would thorough cytogenetic/cytogenomic characterization help)? If this task is not possible, what types of limitations must be overcome to enable it?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2012-02-22T14:15:49.757" LastActivityDate="2012-02-22T22:02:26.427" Title="Sequencing the genomes of polyploid organisms" Tags="&lt;genomics&gt;&lt;polyploidy&gt;&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1085" PostTypeId="2" ParentId="279" CreationDate="2012-02-17T15:28:22.610" Score="3" Body="&lt;p&gt;Cell clumps that not dissociate with rigorous pipetting might very well be caused from free DNA in your cell suspension (i.e. if you trypsinized for too long). Free DNA attracts cells which bind altogether forming clumps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two possible ways to get rid of these clumps:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Centrifuge your cell suspension at 5000 rpm for 2 minutes with acceleration on (at 4) and brake (at 3) allowing the way heavier molecules to precipitate. Then aspirate ~0.5ml from the top of the suspension and transfer to a new flask. Repeat if needed.&lt;/li&gt;&#xA;&lt;li&gt;Use DNAse at concentrations from 20-100µg/ml (concentration resulted from personal use) as long as you will not intend to carry out DNA related experiments.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;You can always go back and buy a fresh ampule of the cell line you want clumps free :)&lt;/p&gt;&#xA;" OwnerUserId="512" LastEditorUserId="69" LastEditDate="2012-02-17T15:37:24.610" LastActivityDate="2012-02-17T15:37:24.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1086" PostTypeId="1" AcceptedAnswerId="1088" CreationDate="2012-02-18T02:16:01.320" Score="3" ViewCount="1778" Body="&lt;p&gt;I usually heat to boil in the microwave, and stain for 12 minutes. How often can I reuse this buffer?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-02-18T04:31:42.573" Title="How often can you reuse coomassie stain?" Tags="&lt;gel-electrophoresis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1088" PostTypeId="2" ParentId="1086" CreationDate="2012-02-18T04:31:42.573" Score="4" Body="&lt;p&gt;Since there's a lot of methanol in Coomassie stain, a significant amount would probably evaporate off each time you microwave it. Therefore, it'd be probably a good idea not to reuse it because (1) you're losing methanol, and (2) the concentration of everything else is thrown off.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do you boil the stain? I just pour mine at RT right on the gel and it works fine.&lt;/p&gt;&#xA;" OwnerUserId="177" LastActivityDate="2012-02-18T04:31:42.573" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1089" PostTypeId="1" AcceptedAnswerId="1094" CreationDate="2012-02-19T04:21:25.763" Score="11" ViewCount="1106" Body="&lt;p&gt;How does the cell regulate the number of mitochondria in a cell? What happens when there are too many or too few?&lt;/p&gt;&#xA;" OwnerUserId="84" LastEditorUserId="6" LastEditDate="2012-02-19T20:38:32.857" LastActivityDate="2012-02-19T20:38:32.857" Title="How is the number of mitochondria in a cell regulated?" Tags="&lt;cell-biology&gt;&lt;mitochondria&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1090" PostTypeId="1" AcceptedAnswerId="1091" CreationDate="2012-02-19T04:26:12.840" Score="36" ViewCount="14704" Body="&lt;p&gt;From what I understand, bacteria have circular DNA. What advantages does it have over linear strands like for eukaryotes? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do there exist bacteria with more than one ring of DNA?&lt;/p&gt;&#xA;" OwnerUserId="84" LastEditorUserId="84" LastEditDate="2012-02-19T16:25:45.340" LastActivityDate="2019-10-10T14:38:10.273" Title="What is the advantage of circular DNA in bacteria? " Tags="&lt;dna&gt;&lt;genetics&gt;&lt;bacteriology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1091" PostTypeId="2" ParentId="1090" CreationDate="2012-02-19T07:07:29.673" Score="31" Body="&lt;p&gt;Vibrio cholerae is known to have two circular chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria cell division is a lot simpler and efficient as compared to eukaryotic cell division, partly due in part to the nature of their chromosomes. They don't have to undergo mitosis -- condensation of chromosomes, segregation, spindle fibre formation, attachment et al aren't involved in bacterial cell division.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Circular DNA also circumvents the Hayflick limit (thus allowing it to be &quot;immortal&quot;), which is the number of times a cell population can divide before it stops, presumably due to the shortening of &lt;a href=&quot;http://en.wikipedia.org/wiki/Telomere&quot;&gt;telomeres&lt;/a&gt;, the sequences at the end of the chromosomes. Since circular DNA lacks telomeres, it does not get shorter with each replication cycle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Circular DNA can also facilitate horizontal gene transfer such as Hfr mediated conjugation. Remember, conjugation is analogous to a &quot;rolling-circle&quot; type replication which is of course, only possible on circular pieces of DNA. &lt;/p&gt;&#xA;" OwnerUserId="177" LastEditorUserId="115" LastEditDate="2012-02-19T07:30:26.130" LastActivityDate="2012-02-19T07:30:26.130" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1092" PostTypeId="2" ParentId="1090" CreationDate="2012-02-19T07:42:49.890" Score="22" Body="&lt;p&gt;To expand a little bit the other answer, I would also add that bacteria can have other (usually circular) DNA segments aside from their main chromosome. These are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Plasmid&quot; rel=&quot;nofollow noreferrer&quot;&gt;plasmids&lt;/a&gt; and are double stranded molecules of DNA that can replicate autonomously.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plasmids often carry genes that allow an organism to survive in certain conditions, for instance they could carry the resistance to an antibiotic, or the gene that encodes for a specific nutrient that may be absent in the environment and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the other answer says, plasmids can be transferred horizontally between bacteria in a process called &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Bacterial_conjugation&quot; rel=&quot;nofollow noreferrer&quot;&gt;bacterial conjugation&lt;/a&gt;&lt;/em&gt;, and that is made possible by the presence of a specific plasmid, called the F-plasmid in the donor. The F-plasmid encodes, amongst other things, for the F-pilus protein &lt;em&gt;pilin&lt;/em&gt;, that allows the formation of the pilus necessary for DNA transfer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of their properties, plasmids are widely used in laboratory as &lt;em&gt;vectors&lt;/em&gt;, to transfer genetic material to cells in order to give them specific &quot;abilities&quot; (e.g. you could insert a gene that encodes for a certain receptor normally not expressed by the cells to allow its expression and test its function). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, it is worth remembering that plasmids can also be found in eukaryotes (e.g. in yeast).&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="50613" LastEditDate="2019-10-10T14:38:10.273" LastActivityDate="2019-10-10T14:38:10.273" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="1093" PostTypeId="1" AcceptedAnswerId="1402" CreationDate="2012-02-19T15:03:56.307" Score="22" ViewCount="59191" Body="&lt;p&gt;Do cows produce more milk than it is required for their calves? It seems like cows are able to provide milk all the time (all year around). Is it so? Or do they, like other mammals, produce milk only in ammounts requeired by their offspring? &lt;/p&gt;&#xA;" OwnerUserId="245" LastEditorUserId="6440" LastEditDate="2019-03-13T21:16:52.847" LastActivityDate="2019-03-18T00:37:40.457" Title="Do cows produce milk excessively?" Tags="&lt;zoology&gt;&lt;mammals&gt;&lt;milk&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1094" PostTypeId="2" ParentId="1089" CreationDate="2012-02-19T19:52:57.573" Score="3" Body="&lt;p&gt;The concept you refer is recognized as mitochondrial biogenesis and it is regulated by AMPK which senses the cellular energy demand. If you have few mitochondria in the cell, the electron transport chain works suboptminally generating less ATP. When the AMP/ATP ratio is high (low ATP) AMPK is activated, and turns on the catabolic pathways required to produce more ATP, included mitochondrial biogenesis. &lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-02-19T19:52:57.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1096" PostTypeId="1" AcceptedAnswerId="1097" CreationDate="2012-02-20T02:28:57.260" Score="8" ViewCount="855" Body="&lt;p&gt;I haven't yet found a decent explanation for how water moves throughout plants. It does seem to travel more efficiently upward than out or down. Why is that?  How does it travel through the plant? &lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2012-02-20T03:24:51.130" Title="How does water move throughout plants?" Tags="&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1097" PostTypeId="2" ParentId="1096" CreationDate="2012-02-20T03:24:51.130" Score="9" Body="&lt;p&gt;Most water moves up through the xylem by &lt;em&gt;capillary action&lt;/em&gt;. Imagine dipping a pipette into a small pool of water; the water would rush up into the pipette. Or, imagine dipping the edge of a paper towel in water. The water &quot;runs&quot; up the paper towel. This is capillary action.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As water evaporates out of the leaves and such in higher regions of the plant, a capillary force pulls up more water. If for instance, you were to dry the top of your saturated paper towel, more water would be pulled up from the pool below to wet that top section.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for a molecular explanation, Wikipedia has a good explanation of &lt;a href=&quot;http://en.wikipedia.org/wiki/Xylem#Cohesion-tension_theory&quot;&gt;Cohesion-tension theory&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="510" LastActivityDate="2012-02-20T03:24:51.130" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1098" PostTypeId="2" ParentId="1069" CreationDate="2012-02-20T12:59:22.367" Score="2" Body="&lt;p&gt;In my case, three-four rounds of sonication greatly helps in having smaller and more homogeneous hydrophobic particles dispersed in water.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-02-20T12:59:22.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1099" PostTypeId="1" AcceptedAnswerId="1143" CreationDate="2012-02-20T14:39:51.713" Score="10" ViewCount="1388" Body="&lt;p&gt;Any cactus can be grafted onto any other cactus, and even the most unlike of them grow together. My latest graft was a &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=schlumbergera%20truncata&amp;amp;source=web&amp;amp;cd=1&amp;amp;ved=0CC8QFjAA&amp;amp;url=http://www.missouribotanicalgarden.org/gardens-gardening/your-garden/plant-finder/plant-details/kc/b669/schlumbergera-truncata.aspx&amp;amp;ei=7lhCT5q9B8Xx0gGiit2CCA&amp;amp;usg=AFQjCNEvu3Ll24MhP48MIywbRmD9gDFRBg&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Schlumbergera truncata&lt;/em&gt;&lt;/a&gt; scion on an &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=opuntia%20microdasys&amp;amp;source=web&amp;amp;cd=8&amp;amp;ved=0CE8QFjAH&amp;amp;url=http://ag.arizona.edu/pima/gardening/aridplants/Opuntia_microdasys.html&amp;amp;ei=p1lCT7PBGqbh0QGZvYXOBw&amp;amp;usg=AFQjCNFaBo8stGA7ImmCd4_TxXk9uufKoQ&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Opuntia microdasys&lt;/em&gt;&lt;/a&gt; rootstock. This kind of graft is always successful. Why can't garden trees be grafted in a similar way, between genera? &lt;img src=&quot;https://i.stack.imgur.com/tRSqi.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="81" LastEditDate="2012-02-20T16:48:58.963" LastActivityDate="2012-02-22T12:46:32.177" Title="Why can you graft two unrelated cacti successfully, but you cannot do this on garden trees?" Tags="&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1100" PostTypeId="1" CreationDate="2012-02-20T14:45:25.547" Score="5" ViewCount="182" Body="&lt;p&gt;If you took the chemicals a plant gains through photosynthesis and put it through the plants' roots or by injection, or used as a foliar application for intake through the stomata, would the plant need light? If not, how would it respond to the treatment?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2015-01-31T02:04:52.727" LastActivityDate="2015-01-31T02:04:52.727" Title="Would a plant need light if the chemicals gained by photosynthesis were given through the roots or as a foliar spray?" Tags="&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1101" PostTypeId="1" AcceptedAnswerId="1102" CreationDate="2012-02-20T14:49:02.403" Score="11" ViewCount="2587" Body="&lt;p&gt;Have any experiments been carried out involving sprouting and growing plants in a zero gravity environment? If so, what was the outcome? How did the plants sprout out of the soil without gravity? Did they grow outward or toward light sources?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="16866" LastEditDate="2017-04-13T04:27:15.487" LastActivityDate="2017-04-13T04:27:15.487" Title="How would a plant sprout and grow in a zero gravity environment?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1102" PostTypeId="2" ParentId="1101" CreationDate="2012-02-20T16:29:48.940" Score="10" Body="&lt;p&gt;There have been several experiments in growing plants in &lt;em&gt;microgravity&lt;/em&gt; (strictly speaking, we do not achieve &quot;zero-g&quot; since astronauts remain in orbit about the Earth).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Changes in plant growth due to the influence of a gravity field is sometimes called &lt;em&gt;gravimorphogenesis&lt;/em&gt;. More specifically, &lt;em&gt;gravitropism&lt;/em&gt; is a differential growth response of plant organs to gravity. For example, roots grow downwards (&lt;em&gt;positive gravitropism&lt;/em&gt;) and shoots grow upwards (&lt;em&gt;negative gravitropism&lt;/em&gt;) on Earth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://lib.bioinfo.pl/paper:11542611&quot;&gt;Studies&lt;/a&gt; (e.g. 1) suggest that in micro-g, there is no preferred direction; roots may grow &quot;up&quot; and shoots &quot;down&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is thought that this growth response is due to the relative distribution of auxin in the plant. On Earth, auxin will preferentially move down into the root-tips due to the location of amyloplasts in the root-cap cells. In micro-g, amyloplasts do not settle at the &quot;bottom&quot; of the plant, therefore there is a more generalized distribution of auxin, and therefore there will be no preferred growth direction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, changes in plant &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC166601/&quot;&gt;gene expression&lt;/a&gt; as a response to micro-g environments are also being investigated (2) and suggest that auxin transport inhibitors may block the activation of the auxin responsive promoters in &lt;em&gt;Nicotiana&lt;/em&gt; spp. (tabacco).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) Mechanisms in the Early Phases of plant Gravitropism CRC Crit Rev Plant Sci. 2000 ;19 (6):551-73  11806421  Cit:65 &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) Transcription Profiling of the Early Gravitropic Response in Arabidopsis Using High-Density Oligonucleotide Probe Microarrays, Plant Physiol. 2002 October; 130(2): 720–728.&#xA;doi:  10.1104/pp.009688&lt;/p&gt;&#xA;" OwnerUserId="81" LastActivityDate="2012-02-20T16:29:48.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1103" PostTypeId="1" AcceptedAnswerId="1108" CreationDate="2012-02-20T16:41:14.387" Score="11" ViewCount="1886" Body="&lt;p&gt;What is the most heat-tolerant (or heat loving - hyperthermophile) organism so far identified? What adaptations does this organism have in order to endure such high temperatures?&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-02-21T18:46:18.090" LastActivityDate="2012-06-18T18:26:43.657" Title="What is the most heat-tolerant organism?" Tags="&lt;extremophiles&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1104" PostTypeId="5" CreationDate="2012-02-20T18:56:50.883" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-02-20T18:56:50.883" LastActivityDate="2012-02-20T18:56:50.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1105" PostTypeId="4" CreationDate="2012-02-20T18:56:50.883" Score="0" Body="An organism which thrives in extreme chemical or physical conditions which would be harmful to most life forms. " OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-02-20T20:24:37.450" LastActivityDate="2012-02-20T20:24:37.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1106" PostTypeId="1" AcceptedAnswerId="1110" CreationDate="2012-02-20T20:09:37.800" Score="8" ViewCount="2427" Body="&lt;p&gt;For direct use as template in PCR runs. Chelex 100 5-10% w/v extraction. Without listing the whole protocol, in the end the supernate is decanted off and then stored at 4°C. I was under the impression that this could be stored and later used almost indefinately but two of four samples extracted several months back failed to produce a product (when it was known they should have). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming no mistakes were made and the reactions were the same, is there a technical reason the template would degrade to an unusable point?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a rule of thumb about how long it can reasonably be expected to last?&lt;/p&gt;&#xA;" OwnerUserId="96" LastActivityDate="2018-08-07T10:24:33.133" Title="Does extracted DNA degrade after a certain time period?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1107" PostTypeId="2" ParentId="16" CreationDate="2012-02-20T20:45:25.790" Score="2" Body="&lt;p&gt;I also haven't tried it, but theoretically GC-rich sequences will interfere with Gibson assembly. Since unique homology between the ends is key to the assembly process, repetitive sequences which cause non-unique overhangs will increase the possibility of incorrectly ordered assembly. One solution would be to use alternative codons where possible to decrease repetitiveness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure all the overlap design tools will try to avoid repetitive overlaps. &lt;a href=&quot;http://www.plantsci.cam.ac.uk/Haseloff/contact/contact.html&quot; rel=&quot;nofollow&quot;&gt;Prof Jim Hasselhoff&lt;/a&gt; at Cambridge Plant Science is a big proponent of Gibson assembly, it was one of his students who wrote Gibthon. If you email him I'm sure he'll give you specific advice.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-02-20T20:45:25.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1108" PostTypeId="2" ParentId="1103" CreationDate="2012-02-20T22:45:24.380" Score="12" Body="&lt;p&gt;&lt;em&gt;Methanopyrus kandleri&lt;/em&gt; has been able to grow and proliferate at temperatures of up to 122°C when under around 20atm (&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0712334105&quot; rel=&quot;nofollow&quot;&gt;Takai et. al. 2008&lt;/a&gt;).  This was achieved in the lab but the theory should hold true for deep sea thermal vents.  Another strain of &lt;em&gt;M. kandleri&lt;/em&gt; survived incubation to 130°C however was unable to reproduce at this temperature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the key adaptions for thermophiles is the selection towards an extremely thermo-stable copy of the enzyme DNA polymerase.  This allows DNA replication at high temperatures and is similar to the 'Taq' polymerase used in the polymer chain reaction in labs, derived from another thermophile, &lt;em&gt;Thermus aquaticus&lt;/em&gt;.    &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0712334105&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Takai K, Nakamura K, Toki T, Tsunogai U, Miyazaki M, Miyazaki J, Hirayama H, Nakagawa S, Nunoura T, Horikoshi K&lt;/strong&gt;. 2008. Cell Proliferation at 122°C and Isotopically Heavy CH4 Production by a Hyperthermophilic Methanogen Under High-Pressure Cultivation. PNAS 105: 10949–10954.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="69" LastEditorUserId="430" LastEditDate="2012-06-18T18:26:43.657" LastActivityDate="2012-06-18T18:26:43.657" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1109" PostTypeId="1" CreationDate="2012-02-20T22:45:53.990" Score="12" ViewCount="598" Body="&lt;p&gt;I've read that many plants have some sort of circadian rhythm where they perform a certain action on a cycle of about 24 hours, like the mimosa plant opening and closing its leaves. Obviously, this is done in order to synchronize with the sun, but many such plants continue to perform these actions even when left in constant darkness or light. It follows that this is the result of some sort of biochemical pathway, but whatever internal 'clock' is used is also independent of temperature.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;How can these plants perform certain actions every 24 hours at different temperatures when the chemical reactions most biochemical pathways use are temperature dependent?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;It would seem like the length of the cycle should vary widely according to the temperature as it affected the reactions involved, but instead it stays at a very constant length very close to 24 hours. How can this be?&lt;/p&gt;&#xA;&lt;p&gt;(This is in my textbook, but unfortunately the book doesn't cite any studies. I would greatly appreciate it if anyone could help me find one to link to so I can improve the  question. :)&lt;/p&gt;&#xA;" OwnerUserId="62" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2017-04-13T04:26:21.657" Title="How do plants 'tell time' for circadian rhythms based on a ~24 cycle?" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;plant-physiology&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1110" PostTypeId="2" ParentId="1106" CreationDate="2012-02-20T23:16:44.323" Score="7" Body="&lt;p&gt;My rule of thumb for DNA samples (in TE or water) - if I have plans to use it that week, I store at 4C. If I plan on using it within a month, I store at -20C. If I'm not sure when I will use it, I keep multiple aliquots at -80C. DNA can degrade by acid hydrolysis in water, because of contaminating nucleases in the sample, and by multiple freeze/thaw cycles.&lt;/p&gt;&#xA;" OwnerUserId="204" LastActivityDate="2012-02-20T23:16:44.323" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1111" PostTypeId="2" ParentId="1109" CreationDate="2012-02-21T00:27:39.327" Score="4" Body="&lt;p&gt;The short answer is that it is because the reaction chains dispensing time and enzymes doing those reactions have evolved to negate the impact of environmental factors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The true answer is that the plant clocks do gradually lose sync with 24h cycle when put in stable lighting conditions and move to some more-less random characteristic frequency of their  molecular clock which is quite likely dependent on environment (still it is obviously close to 24h) -- the sad truth is that every clock needs syncing to work properly.&lt;/p&gt;&#xA;" OwnerDisplayName="user59" LastActivityDate="2012-02-21T00:27:39.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1112" PostTypeId="1" AcceptedAnswerId="1123" CreationDate="2012-02-21T01:11:53.387" Score="14" ViewCount="356" Body="&lt;p&gt;RNA is known to act as an enzyme via its ability to fold itself in specific ways. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is DNA capable of such structures? Or is it some biochemical reason stopping the folding?&#xA;Have they been observed in nature?&lt;/p&gt;&#xA;" OwnerUserId="84" LastEditorUserId="338" LastEditDate="2012-02-21T06:36:56.067" LastActivityDate="2013-02-21T19:52:58.220" Title="Can DNA produce ribozyme-like structures?" Tags="&lt;dna&gt;&lt;rna&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1113" PostTypeId="1" CreationDate="2012-02-21T01:51:45.340" Score="22" ViewCount="459" Body="&lt;p&gt;The most obvious example of an approximately monthly biological cycle is the human menstrual cycle. My questions are the following:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Is it known when and where this cycle or one like it arose?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What exogenous cue(s) (if any) is/are this cycle based on? The moon's&#xA;orbit around the earth is seemingly obvious however the only cue that&#xA;I can think of that would be easily sensed by organisms is variance&#xA;in night-time illumination, which seems like a very weak phenomenon&#xA;when compared to day/night and seasonal cycles. King and neap tides may be a suitable cue however they have a half-monthly modulation.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The moon has been steadily retreating from the earth over the course&#xA;of its history, which means that months have been slowly getting&#xA;longer. Is there any fossil (e.g. biogeochemical) evidence of&#xA;organisms with biological cycles in synchrony with a 'short month'?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="99" LastEditorUserId="68" LastEditDate="2012-02-23T21:59:25.967" LastActivityDate="2012-05-16T03:06:03.337" Title="Evolutionary origin and exogenous cues of ~28 day infradian rhythm?" Tags="&lt;biochemistry&gt;&lt;evolution&gt;&lt;chronobiology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1114" PostTypeId="1" AcceptedAnswerId="1125" CreationDate="2012-02-21T02:27:58.413" Score="4" ViewCount="7100" Body="&lt;p&gt;Why did the sensitive plant, &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=sensitive%20plant&amp;amp;source=web&amp;amp;cd=1&amp;amp;ved=0CDgQFjAA&amp;amp;url=http://en.wikipedia.org/wiki/Mimosa_pudica&amp;amp;ei=4v9CT4nSEK-v0AGevKDMBw&amp;amp;usg=AFQjCNGQnTKwec6qFZKQdh4iPQzHoxZfLA&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Mimosa pudica&lt;/em&gt;,&lt;/a&gt; evolve its leaf closing mechanism? Does it help in a heavy storm? Does it scare off whatever animals might think it a good meal?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="9943" LastEditDate="2015-03-19T02:11:41.450" LastActivityDate="2015-03-19T02:11:41.450" Title="Why did the sensitive plant (Mimosa pudica) evolve its leaf-closing mechanism?" Tags="&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1115" PostTypeId="1" AcceptedAnswerId="2500" CreationDate="2012-02-21T02:36:32.833" Score="14" ViewCount="14694" Body="&lt;p&gt;If I were to graft two apple saplings together --  by bending the tops toward each other and lashing them together --  will the plants grow as one and benefit from one another, or will they be fighting each other for root space and light? If they would grow with each other, then I could theoretically grow a line of closely spaced fruit trees to any length, and they would be strengthened by each other in bad conditions. &lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="16866" LastEditDate="2017-04-13T04:24:24.137" LastActivityDate="2018-03-24T18:34:24.853" Title="If I graft two trees together while young, will they grow as one plant?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="2" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1116" PostTypeId="1" AcceptedAnswerId="7320" CreationDate="2012-02-21T02:47:54.333" Score="9" ViewCount="24175" Body="&lt;p&gt;My cat is about 1' high at the shoulder, and I am a little over 6', but my cat can easily jump onto something as high as I am. That is 6x it's height. If a cat can do this, then Why can't I jump up onto my barn roof? That is a little less than 36' up. I have a hard time jumping onto even a 4' platform. Now if my cat had trouble jumping onto an 8&quot; platform, I would think that pathetic. Do cats have muscles 20x stronger than humans, for their mass?&#xA;Is it just their skeleton providing leverage?&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2017-06-04T22:40:28.973" Title="Why is it that cats can jump so high for their size, compared with humans?" Tags="&lt;zoology&gt;&lt;muscles&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1117" PostTypeId="2" ParentId="1112" CreationDate="2012-02-21T03:00:38.070" Score="4" Body="&lt;p&gt;DNA has recently been designed to act as a targeted drug-delivery agent at George Church's lab.  This doesn't involve catalyzing a reaction between two substrates, but it does involve significant internal conformational changes based on binding to highly specific substrates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencemag.org/content/335/6070/831.abstract&quot;&gt;http://www.sciencemag.org/content/335/6070/831.abstract&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="184" LastActivityDate="2012-02-21T03:00:38.070" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1118" PostTypeId="1" CreationDate="2012-02-21T03:38:22.040" Score="10" ViewCount="2184" Body="&lt;p&gt;I wonder whether the eyes muscle relax when you close them. Common knowledge told us the eyes muscle get tense when you stare at nearby object. If you close your eyes, you eye lids have 0 distance with you eyes. Would the eyes muscle relax in this case?&lt;/p&gt;&#xA;" OwnerUserId="421" LastEditorUserId="81" LastEditDate="2012-02-23T10:38:44.590" LastActivityDate="2012-02-25T00:35:58.457" Title="Do eye muscles relax when you close your eyes?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1121" PostTypeId="2" ParentId="1116" CreationDate="2012-02-21T08:16:55.973" Score="7" Body="&lt;p&gt;There is not a linear relationship between the size of a muscle and its power. The cat weighs significantly less, but the decline in muscle power is not identical. If he weighs 20x less than you, but his muscle generate 1/5 as much force, he will still be able to jump way higher than you.&lt;/p&gt;&#xA;" OwnerUserId="510" LastActivityDate="2012-02-21T08:16:55.973" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1123" PostTypeId="2" ParentId="1112" CreationDate="2012-02-21T08:49:31.393" Score="9" Body="&lt;p&gt;There are no known natural DNA enzymes (deoxyribozymes), but there are various synthetic DNA enzymes. The first deoxyribozyme that has been reported (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9383394&quot; rel=&quot;nofollow&quot;&gt;Breaker and Joyce, 1994&lt;/a&gt;) catalyzed the Pb&lt;sup&gt;2+&lt;/sup&gt;-dependant cleavage of RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Various deoxyribozymes have been synthesized, they can catalyze RNA cleavage, RNA ligation and many other reactions like DNA phosphorylation or Thymine dimer photoreversion, and even a Diels-Alder reaction (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18373062&quot; rel=&quot;nofollow&quot;&gt;Baum and Silverman, 2008&lt;/a&gt; for a review).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA lacks the 2'-hydroxyl group that RNA posesses, but there is some evidence that this doesn't significantly decrease the potential of deoxyribozymes compared to ribozymes. In one experiment DNA and RNA enzymes that catalyze a Carbon-Carbon bond formation were compared and both achieved comparable catalytic rates (&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ja7111965&quot; rel=&quot;nofollow&quot;&gt;Chandra and Silverman, 2008&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information about DNA enzymes you can look at the publications from the &lt;a href=&quot;http://www.scs.illinois.edu/silverman/index.html&quot; rel=&quot;nofollow&quot;&gt;Silverman lab&lt;/a&gt;, they're probably the most active research group in this field.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18373062&quot; rel=&quot;nofollow&quot;&gt;Baum, D. A. &amp;amp; Silverman, S. K. Deoxyribozymes: useful DNA catalysts in vitro and in vivo. Cell. Mol. Life Sci. 65, 2156-2174 (2008).&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9383394&quot; rel=&quot;nofollow&quot;&gt;Breaker, R. R. &amp;amp; Joyce, G. F. A DNA enzyme that cleaves RNA. Chem. Biol. 1, 223-229 (1994).&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ja7111965&quot; rel=&quot;nofollow&quot;&gt;Chandra, M. &amp;amp; Silverman, S. K. DNA and RNA Can Be Equally Efficient Catalysts for Carbon−Carbon Bond Formation. J. Am. Chem. Soc. 130, 2936-2937 (2008).&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6" LastEditorUserId="1320" LastEditDate="2013-02-21T19:52:58.220" LastActivityDate="2013-02-21T19:52:58.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1124" PostTypeId="2" ParentId="193" CreationDate="2012-02-21T13:24:51.533" Score="9" Body="&lt;p&gt;In addition to the excellent response up top (by Poshpaws), one can also imagine how these systems work by looking at recent synthetic examples of single-celled organism memory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible to design various &lt;a href=&quot;http://en.wikipedia.org/wiki/Bistability&quot; rel=&quot;nofollow&quot;&gt;bistable&lt;/a&gt; switches using protein pathways, RNAi, or other means that will latch a particular state. In that way, an organism could effectively &quot;remember&quot; one bit of data by querying the state of the toggle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a specific example, see the Gardner 2000 paper [1]. It's a transcription-level circuit, that in response to a certain stimulus can latch either high or low. While the synthetic version itself is not terribly robust, one could see how in nature a highly evolved / refined circuit could maintain state and effectively serve as &quot;memory&quot; for a single-celled organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10659857&quot; rel=&quot;nofollow&quot;&gt;Gardner, et. al 2000 &quot;Construction of a genetic toggle switch in Escherichia coli.&quot;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="526" LastEditorUserId="389" LastEditDate="2012-10-02T03:37:29.693" LastActivityDate="2012-10-02T03:37:29.693" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1125" PostTypeId="2" ParentId="1114" CreationDate="2012-02-21T17:06:00.947" Score="4" Body="&lt;p&gt;There are many reasons why Mimosa pudica (More commonly now referred to as the &lt;strong&gt;&lt;a href=&quot;http://www.ticklemeplant.com&quot; rel=&quot;nofollow&quot;&gt;TickleMe Plant&lt;/a&gt;&lt;/strong&gt;) may have evolved it's leave- closing mechanism. I have observed the movement when insects have landed on my plants. The insects apprear to be frightened by the movement as they do move on rather quickly when the plant collapses. The movement of the TickleMe Plant also occurs when the sun sets or if I place the plant in a dark room. This may be a way to reduce water loss by transpiration as the leaves fold down upon each other. Another reason for the leave movement may be to expose the few thorns found on adult plants. This could be another warning for herbivores to stay away. In cold weather TickleMe Plants will close their leaves as well, could this be a way to maintain its body temperature. All in all, this is the most amazing house plant and I am always learning new things about this plant and its beautiful cotton candy like TickleMe Plant pink flowers. &lt;/p&gt;&#xA;" OwnerUserId="527" LastActivityDate="2012-02-21T17:06:00.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1126" PostTypeId="1" AcceptedAnswerId="1128" CreationDate="2012-02-21T17:40:59.567" Score="14" ViewCount="714" Body="&lt;p&gt;Some genes have been shown to be &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17667961&quot; rel=&quot;noreferrer&quot;&gt;associated with left-handedness&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Working with some clinicians, I've recommend them to ask their patients (whose genome will be sequenced) if they are &quot;right or left-handed&quot;.&#xA;It's a simple phenotype (without any ethical issue) that will be later fun/interesting to analyze through the sequencing data outside of the main study.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you know any other such kind of simple phenotype that we could ask to our patients ? :-)&lt;/p&gt;&#xA;" OwnerUserId="234" LastEditorUserId="69" LastEditDate="2012-02-23T18:50:07.717" LastActivityDate="2016-11-08T17:37:15.723" Title="Questions to ask to a panel of people that will be sequenced" Tags="&lt;dna-sequencing&gt;&lt;human-genetics&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1127" PostTypeId="2" ParentId="169" CreationDate="2012-02-21T18:35:23.723" Score="2" Body="&lt;p&gt;I've successfully used the Zymoprep kit, but only for smaller plasmids in 2-hybrid experiments. So their cell lysis enzyme/buffer system works well, but I'd guess that your 42kb plasmid is precipitating out with the genomic DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The standard Qiagen midi columns are capable of capturing large constructs. This has worked wonders for me when I was &lt;a href=&quot;http://www.qiagen.com/faq/faqview.aspx?faqid=881&amp;amp;SearchText=&amp;amp;FaqCategoryId=0&amp;amp;MenuItemId=0&amp;amp;catalog=1&amp;amp;ProductLineId=1000229&quot; rel=&quot;nofollow&quot;&gt;purifying large BACmids from E. coli&lt;/a&gt; - and gets the cost down to $10/sample (it does require additional buffer, but that's a minor expense). It might be worth trying the &lt;a href=&quot;http://www.qiagen.com/faq/faqview.aspx?faqid=853&amp;amp;SearchText=yeast%20large%20plasmid&amp;amp;FaqCategoryId=0&amp;amp;MenuItemId=0&amp;amp;ProductLineId=0&quot; rel=&quot;nofollow&quot;&gt;Qiagen yeast DNA protocols&lt;/a&gt; for the midi kit and see if you can isolate your large plasmid?&lt;/p&gt;&#xA;" OwnerUserId="204" LastActivityDate="2012-02-21T18:35:23.723" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1128" PostTypeId="2" ParentId="1126" CreationDate="2012-02-21T18:53:43.743" Score="7" Body="&lt;p&gt;&lt;a href=&quot;https://www.23andme.com/&quot;&gt;23andMe&lt;/a&gt; is a company that provides sequencing. Before they sequence your genome, they ask you to fill in a couple of surveys, one of which is about your physical features. Here is a list of some of the questions they ask: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;How much hair do you have on your upper/lower back?&lt;/li&gt;&#xA;  &lt;li&gt;When you walk, in what direction do your feet naturally face?&lt;/li&gt;&#xA;  &lt;li&gt;Do you have a line or indentation (dimple) in the middle of your chin?&lt;/li&gt;&#xA;  &lt;li&gt;Excluding any hair loss, does your natural hairline have a widow's peak (a V-shaped peak of hair at the front of the hairline)?&lt;/li&gt;&#xA;  &lt;li&gt;Can you flip your tongue over so that the underside is on top?&lt;/li&gt;&#xA;  &lt;li&gt;Can you lift one eyebrow while keeping the other eyebrow in place?&lt;/li&gt;&#xA;  &lt;li&gt;Which is longer, your big toe or the toe next to your big toe?&lt;/li&gt;&#xA;  &lt;li&gt;On your left hand, which finger is longer, your index finger or your ring finger?&lt;/li&gt;&#xA;  &lt;li&gt;What is your shoe size in U.S. shoe sizes?&lt;/li&gt;&#xA;  &lt;li&gt;How would you describe the arches of your feet?&lt;/li&gt;&#xA;  &lt;li&gt;Can you bend down and place your entire palms on the floor while keeping your legs straight (see above image)?&lt;/li&gt;&#xA;  &lt;li&gt;Which image best matches the natural shape of your face (with your hair pulled back)?&#xA;  ...&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That's a small list of phenotype questions you can ask ;-)&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-02-21T18:53:43.743" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1129" PostTypeId="1" AcceptedAnswerId="71895" CreationDate="2012-02-21T19:09:01.513" Score="18" ViewCount="1384" Body="&lt;p&gt;Based on pictures, it seems to me that a vast majority of fish species that have scales do NOT have scales on their heads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is that fact true?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To make this properly answerable:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;lets' define a &quot;majority&quot; as &gt;70% of fish species. But frankly, I'm more interested in actual numerical answer than whether it passes some arbitrary threshold or not.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The universe which I'm interested in measuring the percentage are fish species that have &quot;normal&quot; (Cycloid and ctenoid is the technical term, I believe?) scales on their bodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If that's not specific enough, you can restrict the universe to species in Actinopterygii (ray-finned) that have scales.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="185" LastEditorUserId="3624" LastEditDate="2018-03-30T20:21:10.587" LastActivityDate="2018-03-30T20:21:10.587" Title="Do the majority of fish lack scales on their heads?" Tags="&lt;zoology&gt;&lt;anatomy&gt;&lt;ichthyology&gt;&lt;scales&gt;" AnswerCount="2" CommentCount="12" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1130" PostTypeId="1" AcceptedAnswerId="1159" CreationDate="2012-02-21T20:18:42.493" Score="9" ViewCount="220" Body="&lt;p&gt;I understand that prions have been implicated in the passing on of epigentic information&lt;sup&gt;[&lt;a href=&quot;http://dx.doi.org/10.1016/j.cell.2009.02.044&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]&lt;/sup&gt;. Are prions thought to play a significant role in the evolution of organisms?&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.cell.2009.02.044&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Alberti S, Halfmann R, King O, Kapila A, Lindquist S&lt;/strong&gt;. 2009. A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell 137: 146–58.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="81" LastEditorUserId="836" LastEditDate="2012-09-14T19:47:07.683" LastActivityDate="2012-09-14T19:47:07.683" Title="Are prions an important driver in evolution?" Tags="&lt;epigenetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1132" PostTypeId="1" CreationDate="2012-02-22T02:39:31.087" Score="3" ViewCount="75" Body="&lt;p&gt;There exists 96 well plate setups for use with vacuum manifolds. Is it possible to use 6/12/24 plate inserts with the same setup?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2020-08-11T03:09:01.157" Title="Can a cell culture insert plate be used with a vacuum manifold?" Tags="&lt;cell-culture&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1133" PostTypeId="1" AcceptedAnswerId="9392" CreationDate="2012-02-22T03:14:17.953" Score="15" ViewCount="28083" Body="&lt;p&gt;I read somewhere (I think it was Bill Bryson's book on the origins of the English language) that of all animals, we are the only ones that can choke on food (having something to do with how our larynx is positioned).  I'm unable to find reference to this fact online, however, and am curious if this is just my having misunderstood something (or Bill having led me astray!). &lt;/p&gt;&#xA;" OwnerUserId="148" LastEditorUserId="16866" LastEditDate="2017-04-03T17:26:27.947" LastActivityDate="2019-05-13T00:17:42.877" Title="Can any other animal choke on food?" Tags="&lt;zoology&gt;&lt;human-anatomy&gt;&lt;food&gt;&lt;breathing&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1134" PostTypeId="1" CreationDate="2012-02-22T03:24:45.357" Score="24" ViewCount="503" Body="&lt;p&gt;I was wondering what is the protein concentration in an E. coli cell. When studying enzyme kinetics and activity &lt;em&gt;in vitro&lt;/em&gt;, I would argue that the substrate and enzyme concentrations resemble those &lt;em&gt;in vivo&lt;/em&gt;. As a result, conclusions made by such assays do not apply 100% to the naturally occurring reactions. Are there any examples in literature that address this issue? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Along those lines, what is the concentration of fatty acids/nucleic acids in the cell?&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="69" LastEditDate="2012-02-22T17:08:12.190" LastActivityDate="2015-09-16T06:16:12.853" Title="How crowded is the bacterial cell?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;enzymes&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1135" PostTypeId="2" ParentId="1134" CreationDate="2012-02-22T04:02:25.210" Score="9" Body="&lt;p&gt;The macromolecule concentration within E Coli is estimated to be around 0.3-0.4 g/ml [1]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concentrations of your substrate in respect to your enzyme are generally fairly analogous to &lt;em&gt;in vitro&lt;/em&gt; studies compared to &lt;em&gt;in vivo&lt;/em&gt; studies. However, this is heavily based on the assumption that the diffusion constants for both molecules stay consistent. In many cases that is true and errors can be corrected for using PEG to imitate the crowding effect. And yes, people have begun to look at the question [2]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, for larger macromolecules like DNA and chromosomes that do see effects from subdiffusive transport, the molecules don't obey diffusive random-wal behavior [3]. The classic model system is the lac repressor which exhibits non-diffusive kinetics due to its interactions with DNA.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1748995&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/1748995&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21237136&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/21237136&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://prl.aps.org/abstract/PRL/v104/i23/e238102&quot;&gt;http://prl.aps.org/abstract/PRL/v104/i23/e238102&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7317363&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/7317363&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-02-22T04:02:25.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1136" PostTypeId="1" AcceptedAnswerId="1169" CreationDate="2012-02-22T05:42:07.680" Score="8" ViewCount="170" Body="&lt;p&gt;Is there a technical/scientific term that scientists use to refer to tool making abilities found in certain types of animals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference &lt;a href=&quot;http://en.wikipedia.org/wiki/Animal_cognition#Tool_and_weapon_use&quot;&gt;http://en.wikipedia.org/wiki/Animal_cognition#Tool_and_weapon_use&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="530" LastEditorUserId="69" LastEditDate="2012-02-24T21:47:16.630" LastActivityDate="2013-02-21T16:50:04.460" Title="Is there a term for tool use in animals?" Tags="&lt;zoology&gt;&lt;ethology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1137" PostTypeId="1" CreationDate="2012-02-22T06:58:42.260" Score="12" ViewCount="1494" Body="&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Antibiotic_resistance#Causes&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Household use of antibacterials in soaps and other products, although not clearly contributing to resistance, is also discouraged (as not being effective at infection control).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Following the links led me to this paper:  Larson EL, Lin SX, Gomez-Pichardo C, Della-Latta P.,  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14996673&quot;&gt;Effect of antibacterial home cleaning and handwashing products on infectious disease symptoms: a randomized, double-blind trial&lt;/a&gt;.  Ann Intern Med. 2004 Mar 2;140(5):321-9.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They conclude:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The tested antibacterial products did not reduce the risk for symptoms of viral infectious diseases in households that included essentially healthy persons. This does not preclude the potential contribution of these products to reducing symptoms of bacterial diseases in the home.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Upon reading this, my thoughts were:  Why would one test whether antibacterial products have an effect on viral infections diseases?  Since the authors used a control group (those whose soaps didn't have an antibacterial agent), they are only testing for the effect of the antibiotic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leads me to the main question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;:  Which common diseases would likely be more affected by antibacterial hand soaps (and other antibacterial products) than their non-antibacterial counterpart?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="203" LastActivityDate="2012-02-26T03:06:46.237" Title="Antibacterial hand soaps (and related products); what are they good for?" Tags="&lt;microbiology&gt;&lt;antibiotics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1138" PostTypeId="1" CreationDate="2012-02-22T07:18:57.227" Score="7" ViewCount="1406" Body="&lt;p&gt;Were they developed anew or a heritage from fish?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="69" LastEditDate="2012-03-21T19:13:20.770" LastActivityDate="2015-12-22T16:33:01.223" Title="What did pangolin scales evolve from?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;scales&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1139" PostTypeId="2" ParentId="1134" CreationDate="2012-02-22T09:18:41.577" Score="7" Body="&lt;p&gt;For a great visualization of the macromolecules inside the cell, check out David Goodsell's illustrations.  He tries to reproduce the protein and DNA density within the cell to show how things might be in vivo.  Really great stuff.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer is - its very concentrated.  Compare the density of the cell to that of a typical crystallized protein, which is I believe 0.8 g/ml of protein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://mgl.scripps.edu/people/goodsell/&quot;&gt;http://mgl.scripps.edu/people/goodsell/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-02-22T09:18:41.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1140" PostTypeId="2" ParentId="1103" CreationDate="2012-02-22T09:28:02.640" Score="9" Body="&lt;p&gt;I'd add that biochemically speaking, animals and microorganisms from thermal vents tend to have a higher GC content in their genomes, which makes it more thermostable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of the proteins are adapted to work at higher temperature.  There are a higher number of salt bridges and specific hydrogen bonds in the proteins to stabilize them - more arginines, more glutamic acids, etc. While this reference says that Cysteine is less common, I imagine anything which is not in a reducing environment will have more disulfide bonds - e.g. for proteins on the cell surface.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sulferous deep sea vents would tend to be reducing as is the inside of the cell, but maybe in the case of fresh hot water spring extemophiles this may be the case. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&#xA;&lt;a href=&quot;http://peds.oxfordjournals.org/content/13/3/179.full&quot;&gt;http://peds.oxfordjournals.org/content/13/3/179.full&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-02-22T17:40:13.650" LastActivityDate="2012-02-22T17:40:13.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1141" PostTypeId="2" ParentId="1126" CreationDate="2012-02-22T09:33:48.670" Score="6" Body="&lt;p&gt;Another &lt;a href=&quot;http://bioweb.wku.edu/courses/biol114/genetics/human_genetics/human_genetics1.asp&quot; rel=&quot;nofollow noreferrer&quot;&gt;list of simple human traits&lt;/a&gt; can be found on the Western Kentucky University site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will ask also AB0 and Rh Blood Groups, you can use this also to check associations with other genotypes/phenotypes, see this &lt;a href=&quot;https://biology.stackexchange.com/questions/714/is-there-any-advantage-to-one-blood-type-over-another&quot;&gt;stackexchange question&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are going to sequence also the mitochondrial DNA, you may want to reflect on questions to ask also about their mother phenotypes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally you may want to find also the windows, mac or linux preference gene.&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2012-02-22T09:33:48.670" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1143" PostTypeId="2" ParentId="1099" CreationDate="2012-02-22T09:51:19.540" Score="6" Body="&lt;p&gt;Firstly, different genera of trees &lt;em&gt;can occasionally&lt;/em&gt; be successfully grafted. For example, quince, genus &lt;em&gt;Cydonia&lt;/em&gt;, may be used as a dwarfing rootstock for pear, genus &lt;em&gt;Pyrus&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it is true to say that this is the exception rather than the rule. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of plants in the family &lt;em&gt;Cactaceae&lt;/em&gt;, I would suggest that grafting is usually successful for two main reasons:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Genetic similarity.&lt;/strong&gt; Plants in the family &lt;em&gt;Cactaceae&lt;/em&gt; while known to be morphologically often very different, have relatively little &lt;a href=&quot;http://www.amjbot.org/content/89/2/312.full&quot;&gt;genetic diversity&lt;/a&gt;. This will increase the likelyhood of a successful graft.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Ease of aligning vascular cambium.&lt;/strong&gt; This is required for a successful graft, and in Cacti this is quite easy to achieve since the cambium is clearly visible when you prepare the scion and stock.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It is also possible that Cacti readily form callus tissue, which would also aid in the grafting process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Nyffeler, R., 2002, doi: 10.3732/ajb.89.2.312 Am. J. Bot. 1 February 2002 vol. 89 no. 2 312-326&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-02-22T12:46:32.177" LastActivityDate="2012-02-22T12:46:32.177" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1144" PostTypeId="2" ParentId="1100" CreationDate="2012-02-22T09:52:38.243" Score="0" Body="&lt;p&gt;I doubt this would work for the vast majority of plants.  I think it would cause root rot as the microorganisms in the soil would out-compete the plant.  Also the transport systems of the plant might not be efficient in this direction.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I mean might there be a plant somewhere where this might work?  Sure.  Fungi that grow in the dark would be a lot like such plants, so its biologically possible.  There might be a primitive plant that doesn't need its chloroplast to be active to live.  I've never heard of one and wikipedia is not helping here...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-02-22T09:52:38.243" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1145" PostTypeId="1" CreationDate="2012-02-22T13:59:29.350" Score="7" ViewCount="6945" Body="&lt;p&gt;I am completely confused by the images circulating on the internet of human gastrulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, lets see how it happens in deuterostomes. This image depicts the process:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1CHJj.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(&lt;a href=&quot;http://en.wikipedia.org/wiki/Deuterostome&quot; rel=&quot;nofollow noreferrer&quot;&gt;image is from Wikipedia&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From here we can conclude that blastula becomes gastrula when some of the ectoderm beecomes endoderm, the place where it goes inside becomes anus and then mesoderm is formed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ectoderm here is the outermost level and gastrula already has anus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in this image of human gastrulatuion we see completely different things:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5kWFK.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;(&lt;a href=&quot;http://scienceblogs.com/pharyngula/2008/03/reproductive_history_writ_in_t.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;image source&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mesoderm here is the outermost layer, ectoderm is inside and the gut cavity is formed by the separation of a part of the yolk sac. There is no anus and the posterior end of the gut is blind. Also other similar images suggest that a twins may be separated already after the mesoderm was formed (thus uniplacental twins). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lack of agreement between the images disturbs me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just to point out some of the differences in the depicted processes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;In first image mesoderm forms after gastrulation, on the second it forms far before gastrulation&lt;/li&gt;&#xA;&lt;li&gt;In the first image anus forms in the process of gastrulation, in the second image anus remains blind&lt;/li&gt;&#xA;&lt;li&gt;In the first image ectoderm is the outermost layer, while in the second picture mesodem is the outermost level that encloses all, including ectoderm.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="408" LastEditorUserId="408" LastEditDate="2013-08-15T10:03:34.060" LastActivityDate="2013-08-15T10:03:34.060" Title="Fetal development, gastrulation and embryonic disc" Tags="&lt;human-biology&gt;&lt;zoology&gt;&lt;embryology&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1146" PostTypeId="2" ParentId="1126" CreationDate="2012-02-22T15:21:15.617" Score="4" Body="&lt;p&gt;One that I wish we asked the subjects in our studies is: When do you normally go to sleep each evening and when do you normally wake up? This can get more detailed, but these 2 basic questions can allow segregation into morning or evening types (or both). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Deep phenotyping is critical to a better understanding of the genetic influence on disease risk phenotypes, and so one should collect lifestyle data - like diet, sleep, exercise - which all influence the genotype-phenotype association (these are called gene-environment interactions). If you can come up with phenotypes that distinguish different paths to the &quot;same&quot; disease outcome, that would be relevant to ask. In other words, there are often many paths to a very similar disease outcome, but as those paths are different, the disease may be slightly different. This requires sub-classification of disease - think of the different types of breast cancer. So, collecting these phenotypes, if you know them, in conjunction with diet, exercise, etc, will give you some very interesting possibilities.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-02-22T17:18:54.583" LastActivityDate="2012-02-22T17:18:54.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1147" PostTypeId="2" ParentId="1134" CreationDate="2012-02-22T16:00:02.777" Score="8" Body="&lt;p&gt;Composition of &lt;em&gt;E. coli&lt;/em&gt; (dry weight): 55% protein, 20% RNA, 10% lipid, 15% other&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Protein concentration is about 100 mg/ml or 3 mM. From the size of an &lt;em&gt;E. coli&lt;/em&gt; cell, 1 nM is about 1 molecule/cell. This is ~1000 molecules/cell for HeLa cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diffusion coefficient for an &quot;average&quot; protein: D ~ 5-15 microns^2/s, or ~10 ms to traverse an &lt;em&gt;E. coli&lt;/em&gt;. For reference, a small metabolite in water diffuses about 30-100x faster.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference: &lt;a href=&quot;http://www.rpgroup.caltech.edu/publications/SnapShot2010.pdf&quot;&gt;Cell 141:1262, Key Numbers in Biology&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="389" LastEditDate="2012-03-16T02:51:31.317" LastActivityDate="2012-03-16T02:51:31.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1148" PostTypeId="2" ParentId="1101" CreationDate="2012-02-22T16:10:31.033" Score="2" Body="&lt;p&gt;I find over 100 articles returned by a PubMed query for &quot;Arabidopsis microgravity.&quot; Arabidopsis was taken aboard at least one if not more Space Shuttle missions to answer this and other similar questions. A couple recent papers from this search are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Spaceflight transcriptomes: unique responses to a novel environment.&#xA;Paul AL, Zupanska AK, Ostrow DT, Zhang Y, Sun Y, Li JL, Shanker S, Farmerie WG, Amalfitano CE, Ferl RJ.&#xA;Astrobiology. 2012 Jan;12(1):40-56.&#xA;PMID: 22221117&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An endogenous growth pattern of roots is revealed in seedlings grown in microgravity.&#xA;Millar KD, Johnson CM, Edelmann RE, Kiss JZ.&#xA;Astrobiology. 2011 Oct;11(8):787-97. doi: 10.1089/ast.2011.0699.&#xA;PMID: 21970704&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Parabolic flight induces changes in gene expression patterns in Arabidopsis thaliana.&#xA;Paul AL, Manak MS, Mayfield JD, Reyes MF, Gurley WB, Ferl RJ.&#xA;Astrobiology. 2011 Oct;11(8):743-58. doi: 10.1089/ast.2011.0659.&#xA;PMID: 21970703&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gene expression changes in Arabidopsis seedlings during short- to long-term exposure to 3-D clinorotation.&#xA;Soh H, Auh C, Soh WY, Han K, Kim D, Lee S, Rhee Y.&#xA;Planta. 2011 Aug;234(2):255-70.&#xA;PMID: 21416242&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A novel phototropic response to red light is revealed in microgravity.&#xA;Millar KD, Kumar P, Correll MJ, Mullen JL, Hangarter RP, Edelmann RE, Kiss JZ.&#xA;New Phytol. 2010 May;186(3):648-56.&#xA;PMID: 20298479&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-02-22T16:10:31.033" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1149" PostTypeId="2" ParentId="1133" CreationDate="2012-02-22T16:18:17.793" Score="14" Body="&lt;p&gt;The veterinarian in our group offers this: For humans, who choke much more frequently than other mammals, it is likely to be a cognitive problem. We talk and eat at the same time and so give ample opportunity to allow food passed the epiglottis and choking. Animals do choke - dogs can, cats can. Not all animals can vomit and this is particularly a problem for horses, whose stomachs will rupture instead of releasing contents through the mouth.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-02-22T17:26:35.540" LastActivityDate="2012-02-22T17:26:35.540" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1150" PostTypeId="2" ParentId="121" CreationDate="2012-02-22T17:38:01.407" Score="0" Body="&lt;p&gt;Hey all I think I didn't know how to word this question properly.  After asking a colleague I was told that I don't need to prepare the DNA at all for this tiny non-library scenario. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;She told me to just take a little smear of bacteria on a toothpick and put it into the PCR reaction with the master mix and the enzyme and the heating cycles would do the rest.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe this question was too simple - sorry if it was. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;( Sure enough it worked fine.  ) &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-01-30T07:14:28.710" LastActivityDate="2013-01-30T07:14:28.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1151" PostTypeId="2" ParentId="1103" CreationDate="2012-02-22T18:12:05.390" Score="6" Body="&lt;p&gt;What about fire? A grass fire across the prairie or a forest fire generates temperatures in excess of those mentioned here and yet many organisms, mostly plants, need fire to allow for seeds to open and germinate. I know fire is a short-lived situation, but is extreme nonetheless. The bark of the burr oak, for example, is rather resistant to fire.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-02-22T18:12:05.390" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1152" PostTypeId="1" AcceptedAnswerId="1153" CreationDate="2012-02-22T19:32:12.290" Score="13" ViewCount="992" Body="&lt;p&gt;The field seems extremely divided on the debate. On one hand, artificial experiments have suggested that synonymous mutations don't correlate with gene expression but rather, the mRNA 5' structure is the most important &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19359587&quot;&gt;1&lt;/a&gt;. On the other hand, genome wide analysis suggests that tRNA biases are better associated with high expression &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20403328&quot;&gt;2&lt;/a&gt;. What other works balance out this discussion?&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19359587&quot;&gt;Coding-sequence determinants of gene expression in Escherichia coli&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pnas.org/content/107/8/3645.short&quot;&gt;Translation efficiency is determined by both codon bias and folding energy&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20403328&quot;&gt;An evolutionarily conserved mechanism for controlling the efficiency of protein translation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-03-12T20:10:09.177" LastActivityDate="2012-03-14T17:51:57.503" Title="Which is more important for protein expression mRNA structure or codon optimization?" Tags="&lt;gene-expression&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1153" PostTypeId="2" ParentId="1152" CreationDate="2012-02-22T20:21:22.710" Score="11" Body="&lt;p&gt;This is an excellent question! To my knowledge, there hasn't been a definite answer yet. Recently, I did tons of research on which factors influence protein expression and you should definitely check out the following questions which I asked: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/1/28&quot;&gt;What is the criticality of the ribosome binding site relative to the start codon in prokaryotic translation?&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/166/28&quot;&gt;What determines a successful protein expression in E. coli?&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I answered my second question by posting a concise version of &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=6&amp;amp;ved=0CFoQFjAF&amp;amp;url=http://mpec.ucsf.edu/pdfs_new/Pubs_77.pdf&amp;amp;ei=xkMHT-XmKqbdiAKv4JSHCQ&amp;amp;usg=AFQjCNFcrXypViPECyKyeUvRM2JmZtidGA&amp;amp;sig2=0BtAug3bPEHhzZDqzuFUjA&quot; rel=&quot;nofollow noreferrer&quot;&gt;a paper&lt;/a&gt; from DNA2.0 (a gene synthesis company) that discusses the protein expression. It summarizes all the important factors (RBS site, codon frequency match, 5' mRNA secondary structure), but it doesn't discuss the extend to which they influence expression. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a nature paper from Voigt lab about &lt;a href=&quot;http://www.nature.com/nbt/journal/v27/n10/full/nbt.1568.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;RBS calculator&lt;/a&gt;, which takes into account only the 5' mRNA secondary structure and it doesn't discuss at all the codon-optimization. The calculator was good, but far away from perfect: there is a 50% chance of predicting an expression level within a 2-fold range of the target one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, an &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16756672&quot; rel=&quot;nofollow noreferrer&quot;&gt;older paper from DNA2.0&lt;/a&gt; argues that the mRNA is covered with ribosomes practically all the time, so the secondary structure of the mRNA should have little effect. Besides, an actively translating ribosome can break up stem-loop structures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my opinion, we are still far off from predicting RNA secondary structure formation, although it might be highly implicated in protein expression. From what I read, I think that it is equally crucial that there is no strong secondary structure at the 5' end of the mRNA, the RBS sequence is close to the consensus one and it it appropriately spaced upstream of the start codon, and the first 60-100 codon frequencies match the frequency of your heterologous host. &lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2012-03-14T17:51:57.503" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1154" PostTypeId="2" ParentId="1084" CreationDate="2012-02-22T22:02:26.427" Score="7" Body="&lt;p&gt;Take a look at the strategies used to sequence the wheat genome. Wheat is hexaploid. The project is described at &lt;a href=&quot;http://www.wheatgenome.org/&quot;&gt;http://www.wheatgenome.org/&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For early work on the maize genome, we employed methyl filtration in order to reduce genome complexity and size - transposons are filtered out and genes + promoters and such remain. The gene sequences are different from the two genomes, so says the theory, and those can be distinguished. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10545948&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/10545948&lt;/a&gt; for the reference.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-02-22T22:02:26.427" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1155" PostTypeId="2" ParentId="1138" CreationDate="2012-02-23T00:34:50.057" Score="7" Body="&lt;p&gt;Pangolin scales are certainly not retained from fish. Pangolins are within the clade &lt;a href=&quot;http://tolweb.org/Pholidota/15954&quot;&gt;Pholidota&lt;/a&gt; (&lt;a href=&quot;http://tolweb.org/Eutheria/15997&quot;&gt;Tree of Life page for Eutheria&lt;/a&gt;) and their nearest relatives are anteaters, sloths, and armadillos.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the &lt;a href=&quot;http://www.ucmp.berkeley.edu/mammal/eutheria/pholidota.html&quot;&gt;University of California Museum of Paleontology&lt;/a&gt;, similarities between pangolin and armadillos are the results of convergent evolution. So the pangolin scales are a new feature that arose somewhere on the lineage leading to pangolins.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-02-23T00:34:50.057" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1156" PostTypeId="2" ParentId="1137" CreationDate="2012-02-23T01:38:39.160" Score="8" Body="&lt;p&gt;This may be related to this question on Skeptics SE:  &lt;a href=&quot;https://skeptics.stackexchange.com/questions/3234/does-regular-handwashing-with-antibacterial-soap-prevent-disease/&quot;&gt;Does regular handwashing with antibacterial soap prevent disease?&lt;/a&gt;  Since it is closely related, I will copy my answer from there to here:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://skeptics.stackexchange.com/questions/3222/is-it-good-to-be-germaphobic&quot;&gt;See this related answer&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;To answer your specific questions:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Has something changed?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Well, we have access to these products now, whereas we didn't before.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Does this sanitizing really make people healthier?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;That is a subject of debate.  While it can prevent rapid spread of some things, keep in mind that anti-bacterial soaps should only have specific uses.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cdc.gov/ncidod/eid/vol7no3_supp/levy.htm&quot; rel=&quot;noreferrer&quot;&gt;The CDC has concerns about the prevalent use of these products&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Scientists are concerned that the antibacterial agents will select bacteria resistant to them and cross-resistant to antibiotics. Moreover, if they alter a person's microflora, they may negatively affect the normal maturation of the T helper cell response of the immune system to commensal flora antigens; this change could lead to a greater chance of allergies in children. As with antibiotics, prudent use of these products is urged. Their designated purpose is to protect vulnerable patients.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Also, there is some concern as outlined by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hygiene_hypothesis&quot; rel=&quot;noreferrer&quot;&gt;hygiene hypothesis&lt;/a&gt; (WP).  However, that is mostly &lt;a href=&quot;http://www.sciencedaily.com/releases/2007/09/070905174501.htm&quot; rel=&quot;noreferrer&quot;&gt;associated with childhood immunities and allergies&lt;/a&gt; as opposed to the effects on adults.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;“The natural immune system does not have as much to do as it did 50 years ago because we’ve increased our efforts to protect our children from dirt and germs,” says McMorris.&lt;/p&gt;&#xA;&lt;p&gt;“Allergies are on the rise because our society has changed the way we live. As a result, people with allergies are having children with others who have allergies, which in turn creates a natural increase in the prevalence of allergies in our society.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The bottom line on this hypothesis is that &lt;a href=&quot;http://www.usc.edu/hsc/info/pr/hmm/00-01winter/germs.html&quot; rel=&quot;noreferrer&quot;&gt;more research is required&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;He (Richard G. Barbers, M.D., USC professor of medicine at the Keck School) also gives credence to the hygiene hypothesis in that &amp;quot;we may be over-protecting kids, and their immune systems, consequently, do not become well-developed.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;Barbers notes that only time and a lot more research will tell whether the hygiene hypothesis is valid, and whether, once again, parents should let their kids play in the dirt.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It is &lt;a href=&quot;http://www.physorg.com/news183810398.html&quot; rel=&quot;noreferrer&quot;&gt;generally understood that interaction with beneficial germs is good for you&lt;/a&gt;.  However, normal cleaning will not destroy these germs since they reside within you (unless his germaphobia induces him to take antibiotics).  The human immune response doesn't particularly work that way.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The investigators show that &amp;quot;good&amp;quot; bacteria in the gut keep the immune system primed to more effectively fight infection from invading pathogenic bacteria. Altering the intricate dynamic between resident and foreign bacteria - via antibiotics, for example -- compromises an animal's immune response, specifically, the function of white blood cells called neutrophils.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Using too many anti-bacterial soaps has &lt;a href=&quot;http://www.ama-assn.org/amednews/2005/11/14/hlsc1114.htm&quot; rel=&quot;noreferrer&quot;&gt;raised quite a few concerns even still&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Soaps and lotions that include antibacterial agents have no benefit over ordinary soap and water, but more research is needed to allay or substantiate concern that these substances may be leading to increased rates of antibiotic resistance. This is the conclusion of the Food and Drug Administration's Nonprescription Drugs Advisory Committee, which met last month to consider the use of these products outside of the health care setting.&lt;/p&gt;&#xA;&lt;p&gt;&amp;quot;In the absence of proven benefit, there's no real reason to encourage the use of these products,&amp;quot; said Alastair J.J. Wood, MD, committee chair and associate dean at Tennessee's Vanderbilt Medical School.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.health.com/health/article/0,,20433634,00.html&quot; rel=&quot;noreferrer&quot;&gt;That is not to say that their use should be discontinued entirely&lt;/a&gt;.  &lt;strong&gt;Two MDs weigh in and &lt;em&gt;conclude&lt;/em&gt;&lt;/strong&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Opt for regular soap and water, unless you’re at a hospital or doctor’s office, where it’s best to use antibacterial soap. But if you’re out and about and antibacterial soap is the only kind around, it’s fine to wash with it—and it’s worth keeping in the kitchen to use after handling raw meat.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Hope that helps.&lt;/p&gt;&#xA;" OwnerUserId="279" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-02-23T01:38:39.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1157" PostTypeId="1" AcceptedAnswerId="1162" CreationDate="2012-02-23T03:41:48.137" Score="6" ViewCount="188" Body="&lt;p&gt;The Guardian ran an article a while back talking about GM gene's &lt;a href=&quot;http://www.guardian.co.uk/science/2000/may/28/gm.food&quot; rel=&quot;noreferrer&quot;&gt;jumping to bacteria&lt;/a&gt; in an eater's intestine. Has other research confirmed this phenomenon?&lt;/p&gt;&#xA;" OwnerUserId="258" LastEditorUserId="115" LastEditDate="2012-02-23T06:17:16.603" LastActivityDate="2012-11-05T12:38:48.483" Title="Can genetically modified genes jump to bacteria in the eater's intestine?" Tags="&lt;genetics&gt;&lt;microbiology&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1158" PostTypeId="2" ParentId="1100" CreationDate="2012-02-23T05:04:04.583" Score="2" Body="&lt;p&gt;Not exactly the same thing, but a species of algae has been genetically altered to allow it to  uptake glucose, bypassing the need for photosynthesis: &lt;a href=&quot;http://www.unisci.com/stories/20012/0615013.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.unisci.com/stories/20012/0615013.htm&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="46" LastActivityDate="2012-02-23T05:04:04.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1159" PostTypeId="2" ParentId="1130" CreationDate="2012-02-23T05:12:53.347" Score="8" Body="&lt;p&gt;It is proposed that prions are a good mechanism for &quot;testing&quot; phenotypic variation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many identified proteins with prion-determining domains (PrD) in the yeast genome that can spontaneously switch between conformations with some low probability (eg: check &lt;a href=&quot;http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=S000002579&quot;&gt;SUP35&lt;/a&gt; for one example, and [1] for a good overview of more). The theory is that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;the low probability of switching from non-prion to prion state allows for many more mutations and variations to accumulate -- generating greater genetic diversity than in standard expressed gene variability where most mutations are silent or detrimental&lt;/li&gt;&#xA;&lt;li&gt;the prions provide a ready form of non-permanent inheritability that can be &quot;trialed&quot; by offspring and others in a colony of organisms -- this can be especially beneficial during say temporary changes in environment&lt;/li&gt;&#xA;&lt;li&gt;if the prion phenotype is widely successful, selective pressure can easily mutate it into a more permanent fixture in the genome.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Check out the excellent paper published just last week in Nature exploring this this topic [2]. To give a sense of just how evolutionarily-advantageous prions can be, in the author's experiments and analysis they note that 40% of the prion traits they analyzed were beneficial to growth (eg:  in the paper strain UCD939 gains additional resistance to acidic conditions from the prion [PSI+]).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming these hypothesis, prions would thus play a significant role in the evolution and variability of organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1084952111000413&quot;&gt;Crow, et. al. 2011. doi:10.1016/j.semcdb.2011.03.003&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] &lt;a href=&quot;http://www.nature.com/nature/journal/v482/n7385/full/nature10875.html&quot;&gt;Halfmann, et. al. 2012. doi:10.1038/nature10875&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="526" LastActivityDate="2012-02-23T05:12:53.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1161" PostTypeId="2" ParentId="1024" CreationDate="2012-02-23T05:41:03.140" Score="6" Body="&lt;p&gt;If I understand the nomenclature correctly, an R plasmid is just any plasmid containing an antibiotic (&lt;strong&gt;R&lt;/strong&gt;)esistance gene (eg. Amp, Kan, Cm, etc.). It's a bit of an outdated name from when people didn't know how exactly the plasmids conferred such resistance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An F-plasmid is any plasmid that contains the genes necessary for (&lt;strong&gt;F&lt;/strong&gt;)ertility, eg:horizontal gene transfer via the &lt;em&gt;tra&lt;/em&gt; operon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two do not have to appear together -- eg: Many F plamids will contain resistance genes (along with other random chunks from the genome), but resistance doesn't always have to be part of the payload. Likewise, it is common in labs to build pure resistance vectors that lack any horizontal transfer capability in order to select for particular clones.&lt;/p&gt;&#xA;" OwnerUserId="526" LastActivityDate="2012-02-23T05:41:03.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1162" PostTypeId="2" ParentId="1157" CreationDate="2012-02-23T08:33:00.123" Score="12" Body="&lt;p&gt;No.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is nothing special about a piece of GM DNA when compared to any other random piece of DNA. If this phenomenon happened at any detectable level, we'd have found eukaryotic DNA in bacterial genomes/plasmids long before the introduction of genetically modified crops. And that would be front page news in the field of horizontal gene transfer! Which has many talented people in it!&lt;/p&gt;&#xA;" OwnerUserId="204" LastActivityDate="2012-02-23T08:33:00.123" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1163" PostTypeId="2" ParentId="1157" CreationDate="2012-02-23T14:06:22.610" Score="5" Body="&lt;p&gt;Of far greater concern is the transfer of genetic material between bacteria in which antibiotic resistance is conferred. The &lt;em&gt;firmicutes&lt;/em&gt; in your poop is not at all the same genetically speaking as the &lt;em&gt;firmicutes&lt;/em&gt; in my poop. Polymorphisms and genetic transfer have changed members of the gut microbiome and that leads to differential extraction of energy from the ingested food and differential behavior with respect to antibiotics.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-02-23T14:06:22.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1164" PostTypeId="1" AcceptedAnswerId="1201" CreationDate="2012-02-23T14:47:06.457" Score="25" ViewCount="1712" Body="&lt;p&gt;How would you estimate the number of ATPs required to transcribe, export and translate a single eukariotic protein?&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="444" LastEditDate="2012-02-23T15:27:19.700" LastActivityDate="2012-02-26T17:25:50.423" Title="ATP cost for gene expression" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1165" PostTypeId="2" ParentId="951" CreationDate="2012-02-23T15:04:15.417" Score="4" Body="&lt;p&gt;I'd take that computational angle and run the sequence data through tRNAscan-SE (Lowe &amp;amp; Eddy, Nucl Acids Res 25: 955-964). Ideally, you'd install this locally. This tool is what the UCSC folks use and it has been the best known, most widely used tRNA predictor for years. It's what we all used on Arabidopsis thaliana genome annotation back in the late 1990's.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also a &lt;a href=&quot;http://gtrnadb.ucsc.edu/&quot; rel=&quot;nofollow&quot;&gt;genomic tRNA database&lt;/a&gt; that may have many of the predictions you seek, at least for some of your species/strains.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-02-23T15:04:15.417" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1166" PostTypeId="2" ParentId="1126" CreationDate="2012-02-23T15:15:07.907" Score="2" Body="&lt;p&gt;Some other ones:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Are you a Singer?&lt;/strong&gt; :-)  AVPR1A and SLC6A4 Polymorphisms in Choral Singers and Non-Musicians: A Gene Association Study &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031763&quot; rel=&quot;nofollow&quot;&gt;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031763&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Do you have sunbed sessions?&lt;/strong&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Do you dance?&lt;/strong&gt;  (via C.Dina. ) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1239939&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1239939&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="234" LastEditorUserId="69" LastEditDate="2012-02-24T15:22:47.950" LastActivityDate="2012-02-24T15:22:47.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1167" PostTypeId="1" AcceptedAnswerId="1207" CreationDate="2012-02-23T19:35:06.333" Score="15" ViewCount="1937" Body="&lt;p&gt;When reading my textbook I noticed that in all examples but one from eight the recognition site was an even number of bases.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wondered if this was just a co-incidence, so I took the data from &lt;a href=&quot;http://www.thelabrat.com/restriction/enzymesA.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;this site&lt;/a&gt; for over a thousand known recognition sites and put it into a spreadsheet (&lt;a href=&quot;http://www.mediafire.com/?m5i78wp7pgnii22&quot; rel=&quot;nofollow noreferrer&quot;&gt;XLS uploaded here&lt;/a&gt;).  The results are probably best summarised graphically:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EILPS.png&quot; alt=&quot;restriction enzymes pie chart&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/reKKN.png&quot; alt=&quot;restriction enzymes bar chart&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Stats Test&lt;/strong&gt;: Chi Squared Goodness of Fit.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Null Hypothesis: &#xA;There is no significant difference between the number of restriction sequences &#xA;that are an odd or even length.&#xA;&#xA;|---------|----------|----------|-----|-------|----------|&#xA;|  Trait  | Observed | Expected | O-E |(O-E)^2|(O-E)^2 /E|&#xA;|---------|----------|----------|-----|-------|----------|&#xA;|  Odd    |    172   |  231.5   |-59.5|3540.25|  15.293  |&#xA;|  Even   |    291   |  231.5   | 59.5|3540.25|  15.293  |&#xA;|---------|----------|----------|-----|-------|----------|&#xA;&#xA;Chi Squared Value = 30.586&#xA;&#xA;P=0.05, 1 Degree of Freedom: Critical Value of 3.841&#xA;&#xA;H0 rejected with 95% confidence (indeed with 99.9%+ confidence)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Can anyone explain or suggest why it is more common that restriction enzymes recognition sites have an even number of bases? &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Updates&lt;/h2&gt; &#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Expanded dataset to include &lt;a href=&quot;http://rebase.neb.com/cgi-bin/seqsget?L%20ed&quot; rel=&quot;nofollow noreferrer&quot;&gt;new recognition sites&lt;/a&gt; from the resource that &lt;a href=&quot;https://biology.stackexchange.com/users/444/96well&quot;&gt;96well&lt;/a&gt; linked to.  &lt;/li&gt;&#xA;&lt;li&gt;Removed all duplicate recognition sites leaving 465 distinct recognition sequences (&lt;em&gt;my fault for not removing them in the first instance&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Ran stats test on the data&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;&lt;a href=&quot;https://biology.stackexchange.com/revisions/1167/1&quot;&gt;See Previous Version&lt;/a&gt;&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="69" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2018-01-26T05:21:59.583" Title="Why do restriction enzymes tend to have an even number of bases in their recognition site?" Tags="&lt;dna-sequencing&gt;&lt;bioinformatics&gt;&lt;restriction-enzymes&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1168" PostTypeId="2" ParentId="1167" CreationDate="2012-02-23T20:27:10.720" Score="1" Body="&lt;p&gt;Most restriction enzymes recognize palindromes, hence the recognition site of an even number of residues. Why palindromes? This allows for a vast increase in complexity (or rarity) from a DNA sequence standpoint, while requiring very little added complexity from the protein. In other words, if a protein domain recognizes 2 or 3 or 4 bp of DNA, simply adding a second copy of that domain to the peptide chain (via duplication of the DNA encoding that domain) does the trick. It is much easier to duplicate a module than to build a new or second (perhaps complimentary) module.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-02-23T20:27:10.720" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1169" PostTypeId="2" ParentId="1136" CreationDate="2012-02-23T23:02:36.497" Score="8" Body="&lt;p&gt;Having read &lt;a href=&quot;http://www.eva.mpg.de/primat/staff/boesch/pdf/fol_prim_tool_use_making.pdf&quot;&gt;this article&lt;/a&gt; on tool use in Chimpanzees in full, I am inclined to say that if such a term existed then either the article itself or the titles of any of the 30 articles referenced would have included it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Searching a couple of online biological dictionaries and ethology sites hasn't yielded anything either, therefore until someone else points out that I'm missing the obvious I'd say you're free to coin the term yourself!  &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-02-23T23:02:36.497" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1170" PostTypeId="1" AcceptedAnswerId="1173" CreationDate="2012-02-24T03:37:29.623" Score="8" ViewCount="418" Body="&lt;p&gt;Let's assume for a minute that microbes themselves and their &lt;em&gt;direct&lt;/em&gt; toxic products (i.e. endotoxins) aren't toxic to humans. Let's also discount any innate immune responses the body mounts against the invading microbe (i.e. inflammation and production of cytokines).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens to food molecules (mechanistically) as it spoils and what deleterious effects do these &quot;spoil products&quot; have on the body if ingested? I'm looking for compounds that can result from the spontaneous breakdown of food or the byproducts of microbial metabolism (that is NOT a &quot;direct&quot; toxin) that is harmful to the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, do the proteins in food break down into some toxic nitrogenous substance?&lt;/p&gt;&#xA;" OwnerUserId="177" LastEditorUserId="177" LastEditDate="2012-02-24T04:12:23.810" LastActivityDate="2012-10-10T18:40:05.820" Title="What are the biochemical processes occurring when food spoils?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;digestive-system&gt;&lt;food&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1171" PostTypeId="1" AcceptedAnswerId="1187" CreationDate="2012-02-24T08:13:20.840" Score="7" ViewCount="2702" Body="&lt;p&gt;Could someone point out some relevant papers or resources (an online DB maybe?) describing the density of neurons (or, more in general, of cells) in different areas of the mouse brain?&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-06-27T17:08:18.953" Title="Density of neurons/cells in the mouse brain" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1172" PostTypeId="2" ParentId="931" CreationDate="2012-02-24T09:59:28.420" Score="7" Body="&lt;p&gt;&lt;strong&gt;Some background information.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all one should notice, that Golgi staining belongs to so-called morphological types of stainings in neuroscience, where the actual anatomy of different neurons is revealed (compared to other techniques, like Ca-imaging or potential imaging).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, Golgi staining is a type of &lt;a href=&quot;http://en.wikipedia.org/wiki/Silver_staining&quot;&gt;silver staining&lt;/a&gt;, there the sedimentation of silver or its salts (here: silver chromate) reveals the morphological traits of the cels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And, third, Golgi staining is applied to fixed preparation. This means that the tissue (normally a brain slice) is pre-treated (here: with formol) to kill all cells and arrest every biological process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is known about the targets.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The common description of the target is &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0165017307000033&quot;&gt;quoted&lt;/a&gt; as &quot;a limited number of cells at random in their entirety&quot;. This is the essence of Golgi staining:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Only single cells are stained&lt;/strong&gt;, therefore there is no impediment from adjacent cell staining while deriving the morphological structure of the cells (very important for light microscopy where you have integrated input from different depths).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;The cells are stained randomly&lt;/strong&gt;, there is no known preference among neuronal cells for Golgi staining and I haven't seen any other types of cells in CNS stained with Golgi, therefore it is quite &lt;strong&gt;specific for neuronal cells&lt;/strong&gt; (and leaving macro- and microglia, astrocytes etc. intact).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;The cells are stained in their entirety&lt;/strong&gt;, meaning that the complete cell is stained very nicely, showing detailed arborisation of dendritic tree, that was very important in studying of Purkinje cells in cerebellum.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are larger neurons more likely to be stained? Are specific cell types more susceptible than others?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Golgi staining is used mostly for brain slices (I have never seen or heard its application for other tissues). Traditionally one of the biggest cells here are pyramid neurons (NA, ACh-ergic) and one of the smallest are interneurons (often GABA-ergic) -- both are amenable to Golgi staining (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0006899383910764&quot;&gt;reference&lt;/a&gt;) and there is no seemingly clusterization of stained cells by their size or transmitter type.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is preventing us from using the advanced molecular biology techniques to understand the process?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can name several reasons for this:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Since Golgi staining is applied to fixed preparation the tissue is already &quot;damaged&quot; (formol leads to dessication of cells and shrumping), therefore it is difficult to use some fine mollecular biology methods to investigate these tissues.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There is no way to tell which cells get stained beforehand. And as long as  the microcrystallisation of silver chromate is started it can't be (easily) stopped and reversed. Therefore it is difficult to look at what caused the staining afterwards, then the whole cell is impregnated with silver.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I think there were no real attempts to crack the mistery of this staining: how intersting it might be, this seems to be an interdisciplinary question on the brink between biology and chemistry. So, maybe one day somebody will look into it and explain everything.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-02-24T09:59:28.420" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1173" PostTypeId="2" ParentId="1170" CreationDate="2012-02-24T11:25:05.773" Score="10" Body="&lt;p&gt;During putrefaction of animal tissue, lysine is decarboxylated into cadaverine and arginine is decarboxylated into putrescine. These compounds are deemed to be toxic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A serving of meat contains 8 g of protein, corresponding to 640 mg lysine and a little bit less of arginine. Let's go straight and say that a spoiled meat serving contains 640 mg cadaverine and a little bit less of putrescine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In rats, the acute oral toxicity for both polyamines is around 2000 mg/kg, let'assume that this is valid for humans also. According to these rough calculations, to have an acute toxic effect, a 70kg man that is resistant to the direct toxic effects of microbes, should eat 140 grams of cadaverine, corresponding to 218 smelly rotten meat servings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[composition and toxicity data taken from wikipedia]&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="444" LastEditDate="2012-10-10T18:40:05.820" LastActivityDate="2012-10-10T18:40:05.820" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1175" PostTypeId="1" AcceptedAnswerId="1189" CreationDate="2012-02-24T19:46:02.710" Score="8" ViewCount="287" Body="&lt;p&gt;I liked the &lt;a href=&quot;https://biology.stackexchange.com/questions/1024/what-is-the-distinction-between-f-plasmid-and-r-plasmid&quot;&gt;question about F' and R plasmids&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is a good resource that describes what is known about the functions and diversity of plasmids in the wild? &lt;a href=&quot;http://en.wikipedia.org/wiki/Prokaryote&quot; rel=&quot;nofollow noreferrer&quot;&gt;Prokaryotes&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/Eukaryote&quot; rel=&quot;nofollow noreferrer&quot;&gt;eukaryotes&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Plasmid&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia points&lt;/a&gt; to five kinds of plasmids (fertility (F), resistance (R), col plasmids (offensive genes that let a bacteria kill other bacteria), degradative function plasmids, and virulence plasmids). There is a brief section on yeast/euk plasmids too. It seems like plasmids could actually convey nearly any gene. &lt;a href=&quot;http://en.wikipedia.org/wiki/Restriction_enzyme&quot; rel=&quot;nofollow noreferrer&quot;&gt;Restriction enzymes&lt;/a&gt; are found mostly on plasmids and they would seem to be defensive - maybe those are degradative. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there references that are more detailed and nuanced? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2012-03-02T00:58:56.250" Title="Taxonomy for plasmids" Tags="&lt;plasmids&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1176" PostTypeId="1" CreationDate="2012-02-24T20:45:14.970" Score="7" ViewCount="1138" Body="&lt;p&gt;My expressed proteins are frequently truncated and I'm trying to figure out which bands are which. The first thing to come to mind is using PeptideCutter from ExPASy but there is just a data deluge of potential sites. I was curious what other strategies exists for determining the potential breaks asides using LC-MS.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-03-12T20:09:53.577" LastActivityDate="2012-03-12T20:09:53.577" Title="Determining potential protease sites within a recombinant protein" Tags="&lt;gene-expression&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1178" PostTypeId="2" ParentId="859" CreationDate="2012-02-24T21:54:40.000" Score="5" Body="&lt;p&gt;This question highlights the different &lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/VA1BioSpeciesConcept.shtml&quot;&gt;species concepts&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you go by the reproductive species concept (a population of actually or potentially interbreeding organisms), then yes. Apparently, the populations were interbreeding.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you go by the typological species concept (morphologically distinct), then no. &lt;em&gt;Homo neandertalensis&lt;/em&gt; and the &quot;Denosovian&quot; are morphologically distinct enough to be recognized as such.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-02-24T21:54:40.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1179" PostTypeId="1" AcceptedAnswerId="1293" CreationDate="2012-02-24T21:56:41.977" Score="6" ViewCount="1048" Body="&lt;p&gt;I am trying to understand the formation of embryonic disc for human and chick so the following question is related to &lt;a href=&quot;https://biology.stackexchange.com/questions/991/what-are-differences-between-formation-of-embryonic-disc-in-chick-and-mammal-emb&quot;&gt;here&lt;/a&gt; about formation of embryonic disc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I had thought that the amniotic sac forms only from embryonic disc in humans, particularly of lateral mesoderm and ectoderm of embryonic disc. However, my thought seems to be wrong as my professor says that amnion form only for birds from embryonic disc, but from many different parts besides of embryonic disc for human.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What, besides the embryonic disc, forms the human amniotic sac?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2012-03-09T20:27:14.843" Title="What forms the human amniotic sac?" Tags="&lt;human-biology&gt;&lt;homework&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1180" PostTypeId="1" AcceptedAnswerId="1183" CreationDate="2012-02-24T22:01:28.220" Score="8" ViewCount="181" Body="&lt;p&gt;I am attempting to find potential Hydrogen bonds between Hydrogen donors and aromatic ring acceptors.  I do this by predicting the location of Hydrogens on residues and then calculating how far these Hydrogens are from aromatic rings.  If a certain Hydrogen is &amp;lt;7.0 Angstroms from a certain aromatic ring, then I take it under consideration: I form the N-H vector, which is the vector created by the Hydrogen under question and the Nitrogen in the backbone of the residue that the Hydrogen belongs to.  I test that this N-H vector is pointing toward the plane of the aromatic ring, and I also test that the point of intersection between the plane of the aromatic and the N-H vector is within 6 Angstroms of the center of the aromatic ring.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If all of these conditions are met, then I consider it a Hydrogen bond between the Hydrogen and the aromatic ring.  However, my data must be incorrect, because I am seeing situations where a Hydrogen is &amp;lt; 1.0 Angstrom from the plane of the aromatic.  Atoms should not be getting that close to each other.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thoroughly tested my method by hand using an example situation where my code identified one of the sidechain Hydrogens on an ASN is 0.3 Angstroms from the plane of the aromatic of a TRP.  Unfortunately, I could not find any bugs.  You can find a PDF of this verification &lt;a href=&quot;https://docs.google.com/open?id=0B5ymj1_8HzRybjJfVFVWZWtTRzY3YkZ3WXM2U1VZZw&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any suggestions on how my method might be flawed would be greatly appreciated.&lt;/p&gt;&#xA;" OwnerUserId="543" LastActivityDate="2012-02-25T05:51:35.867" Title="PDB Mining: Why Do I Find Atoms Less than 1 Angstrom Apart?" Tags="&lt;molecular-biology&gt;&lt;proteins&gt;&lt;bioinformatics&gt;&lt;biophysics&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1181" PostTypeId="1" AcceptedAnswerId="1195" CreationDate="2012-02-25T00:22:07.007" Score="2" ViewCount="3171" Body="&lt;p&gt;Question originally asked on Quora. These proteins have many functional similarities, so why do cells need both to handle unfolded proteins?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-08-25T01:39:38.410" Title="What are the most important differences between HSP70 and HSP90?" Tags="&lt;proteins&gt;&lt;protein-folding&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1182" PostTypeId="2" ParentId="1118" CreationDate="2012-02-25T00:35:58.457" Score="4" Body="&lt;p&gt;I would guess that the eye muscle relaxes when the eye is closed. After having the eyes closed, just in the moment after opening them, it seems that the focus is in the distance. It takes a fraction of a second before you can read some text on your computer screen for example . This focusing-duration seems to be shorter when looking into the distance after opening the eyes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another effect is when you look at an object in short range for quite a moment and then close your eyes. You can feel the relaxation.&lt;/p&gt;&#xA;" OwnerUserId="508" LastActivityDate="2012-02-25T00:35:58.457" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1183" PostTypeId="2" ParentId="1180" CreationDate="2012-02-25T05:51:35.867" Score="7" Body="&lt;p&gt;if you are using NMR structures you might be making the mistake of using several superimposed structures - it would be nice to develop with x-ray structures at less than 2.0 A resolution for starters. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the models at low resolution can be sloppy, but submitted after 1994 or so will not have any center to center distances as that's when the x-ray structures used molecular models rather than just electron density rigorously and wierd steric violations in the structure should be rare. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still, this might not be wrong - the hydrogen might be pointing right into the aromatic ring's center.  This has been observed quite a bit.  In such a case, the atom to ring plane distance might be very small.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You only need to worry if the center to center distance between atoms is &lt;a href=&quot;http://en.wikipedia.org/wiki/Van_der_Waals_radius&quot;&gt;less than the vanderWaals&lt;/a&gt; radius.   I would filter for atom center to center distance and see if you see violations.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-02-25T05:51:35.867" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1184" PostTypeId="2" ParentId="6" CreationDate="2012-02-25T05:59:33.813" Score="1" Body="&lt;p&gt;This is a difficult experiment.  It's usually done by digesting the DNA under conditions where the binding protein is solidly attached.  DNAse is added, and then after some time, the DNAse is degraded with heat or the addition of an inhibitor.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you get depends on the length of the DNA protected by the protein and the tenacity by which the protein binds itself to the DNA.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="307" LastEditDate="2012-04-06T17:19:23.543" LastActivityDate="2012-04-06T17:19:23.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1185" PostTypeId="2" ParentId="6" CreationDate="2012-02-25T07:50:59.340" Score="3" Body="&lt;p&gt;Are you interested in transcription factor binding (and similar), or in histone modifications?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are looking at investigating something with a short binding motif that occurs redundantly across the genome, ChIP-exo works: &lt;a href=&quot;http://www.cell.com/abstract/S0092-8674(11)01351-1&quot; rel=&quot;nofollow&quot;&gt;http://www.cell.com/abstract/S0092-8674(11)01351-1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This technique involves digesting one strand of the DNA up until the bound protein-DNA complex via exonuclease, while leaving enough of a tag on the other end to uniquely identify it's location within the genome. I have no first-hand experience with it, and it's yet to be independently replicated, but it looks fantastic. I don't recall whether they investigated the extent to which off-target DNA was digested by the exonuclease, but theoretically I expect a significant portion would have been eaten up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in ChIP of histone modifications, you can use micrococcal nuclease (MNase) for your sample prep instead of sonication. Again, I have no first-hand experience, but I understand that this enzyme can be used to digest DNA until it reaches the nucleosomal core particle, and there are published ChIP-seq experiments employing this strategy. The MNase would be expected to digest unbound DNA fragments.&lt;/p&gt;&#xA;" OwnerUserId="544" LastEditorDisplayName="user560" LastEditDate="2012-02-29T00:34:06.360" LastActivityDate="2012-02-29T00:34:06.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1186" PostTypeId="1" AcceptedAnswerId="1213" CreationDate="2012-02-25T11:17:08.723" Score="13" ViewCount="23602" Body="&lt;p&gt;RNA is known to form an A-form helix, while DNA generally forms a B-form helix under physiological conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZqYhG.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;From left to right: A-form DNA, B-form DNA, Z-form DNA. Image created by &lt;a href=&quot;http://en.wikipedia.org/wiki/user:Zephyris&quot; rel=&quot;noreferrer&quot;&gt;Richard Wheeler&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The preference of RNA for the different conformation is supposed to be caused by the 2'-OH, my question is now how exactly this favors the A-helix? Which interactions are important and cause RNA to adopt an A-form helix?&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="43" LastEditDate="2012-02-27T14:06:58.310" LastActivityDate="2012-02-27T14:06:58.310" Title="Why does RNA adopt an A-form helix?" Tags="&lt;biochemistry&gt;&lt;rna&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1187" PostTypeId="2" ParentId="1171" CreationDate="2012-02-25T12:01:36.857" Score="7" Body="&lt;p&gt;The newest and most accurate method (far more accurate than older extrapolating/manual counting methods (Stereology) and yielding some surprising results) to estimate number/density of neurons/cells in brains is &lt;strong&gt;Isotropic Fractionator&lt;/strong&gt; to my knowledge. Using this keyword you find some recent papers, comparing different brain areas (cerebral cortex, cerebellum,...) among rodents:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Combining our estimates of total cell number and percentage of NeuN-containing nuclei in each brain region, we find that adult rat cortex contains ∼80 million cells, 40% of which (∼30 million) are neurons. In comparison, rat cerebellum contains more than twice as many cells (∼170 million), &gt;80% of which are neurons (Table 1, top). Therefore, the adult rat brain contains almost five times as many neurons in the cerebellum (∼140 million) than in the cerebral cortex. When all of the brain regions are taken into consideration, the cerebellum thus accounts for more than one-half of the cells and ∼70% of all of the neurons of the entire rat brain (Table 1, bottom). Overall, we estimate that of all of the cells in the adult rat brain, 60%, or 200.13 ± 21.17 million, are neurons. Glial cells, therefore, contrary to common belief, are not the most numerous cell type in the rat brain. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.jneurosci.org/content/25/10/2518.full&quot;&gt;Isotropic Fractionator: A Simple, Rapid Method for the Quantification of Total Cell and Neuron Numbers in the Brain&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/103/32/12138.full#sec-1&quot;&gt;Cellular scaling rules for rodent brains&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776484/&quot;&gt;The Human Brain in Numbers: A Linearly Scaled-up Primate Brain&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="45" LastActivityDate="2012-02-25T12:01:36.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1188" PostTypeId="1" CreationDate="2012-02-25T16:12:31.523" Score="11" ViewCount="567" Body="&lt;p&gt;Well, the question is in the title, no explanation need. &lt;/p&gt;&#xA;" OwnerUserId="546" LastEditorUserId="112" LastEditDate="2012-02-27T08:40:09.743" LastActivityDate="2013-01-23T18:04:16.680" Title="What can you tell about a person, having only their whole genome as information?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;genomics&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1189" PostTypeId="2" ParentId="1175" CreationDate="2012-02-25T17:36:22.993" Score="8" Body="&lt;p&gt;Not sure if generalized plasmid taxonomy is going to be relevant any longer. A lot of these old names were created before the exact sequence and function of the various DNA sequences were known. This is becoming especially true as synthetic biology allows us to mix and match parts of plasmids at will. If you want to dig through a lot of the old plasmid classification papers, a lot of them are published before 1980.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Back then I'd imagine conversations went more: &quot;oh look, I found an R plasmid conferring ampicillin resistance&quot;, instead our more modern understanding: &quot;oh, I have a plasmid conferring ampR via &lt;a href=&quot;http://en.wikipedia.org/wiki/Beta-lactamase&quot;&gt;&lt;em&gt;bla&lt;/em&gt;&lt;/a&gt; &quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, I think the more specific / specialized plasmid classifications will stick around for a while as they confer a lot of domain specific meaning.  Check out &lt;a href=&quot;http://en.wikipedia.org/wiki/Ti_plasmid&quot;&gt;Ti&lt;/a&gt; and &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0168945287900185&quot;&gt;Ri&lt;/a&gt; plamids which have very specific meanings in plant pathogens and are used in the genetic engineering of them.  You'll notice that the classification for these plasmids comes from a lot more than a single gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been some modern attempts to classify plasmids, but rely a lot more on the structure / lineage of the plasmid rather than the payload genes (replication origin, size, etc.). Check out [1] for an example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0147619X08000826&quot;&gt;Wang, et. al. 2009. Plasmid. &lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="526" LastEditorUserId="526" LastEditDate="2012-02-25T17:43:07.837" LastActivityDate="2012-02-25T17:43:07.837" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1190" PostTypeId="2" ParentId="1074" CreationDate="2012-02-25T21:38:06.950" Score="6" Body="&lt;p&gt;&lt;em&gt;I am skipping the background information (I will amend my question later) for now.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So, what is known about minicolumn?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The term was coined by Ramon y Cajal who saw narrow stripes, running from white matter to the surface (&lt;a href=&quot;http://williamcalvin.com/1990s/1995Handbook.htm&quot;&gt;reference&lt;/a&gt;) in his preparation with Nissl staining.&lt;/li&gt;&#xA;&lt;li&gt;The hypothesis about minicolumns to be anatomical units was proposed by Mountcastle in 1957, known as &quot;columnar hypothesis&quot; in neuroscience (&lt;a href=&quot;http://jn.physiology.org/content/20/4/408.full.pdf+html?ijkey=a4c3af74ac9060da578e8772cd4eca569fa7b1ec&amp;amp;keytype2=tf_ipsecsha&quot;&gt;reference&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;li&gt;It has been shown that minicolumns grow from progenitor cells within the embryo (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4624784?dopt=Abstract&quot;&gt;reference&lt;/a&gt;), and don't require brain functions to emerge.&lt;/li&gt;&#xA;&lt;li&gt;Minicolumns  contain neurons within multiple layers of the cortex (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15937015&quot;&gt;reference&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;li&gt;One of the latest review on the topic (&lt;a href=&quot;http://brain.oxfordjournals.org/content/125/5/935.full&quot;&gt;Buxhoeveden &amp;amp; Casanova, 2001&lt;/a&gt;) contains 121 references to experimental papers on this topic.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I wouldn't say that these columns are developmental relic, for there is a known heterogenity among these structures (like hypercolumns, macrocolumns and segregates) and it is rather improbable that all these types are relics. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So, as long as we stick to the term &quot;anatomical unit&quot;, I see no problems why columns (with all possible types and sizes of them) should not be it.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-02-25T21:38:06.950" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1191" PostTypeId="1" CreationDate="2012-02-25T23:20:28.093" Score="8" ViewCount="936" Body="&lt;p&gt;I have a new sequence and I want to add it to a pre-constructed BLAST database containing other sequences. The makeblastdb help does not give any hint on this regard. &lt;/p&gt;&#xA;" OwnerUserId="548" LastEditorUserId="6" LastEditDate="2012-02-26T14:06:18.663" LastActivityDate="2015-05-20T19:40:50.307" Title="Is it possible to add a new sequence to a blast database without recreating it from scratch?" Tags="&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1193" PostTypeId="2" ParentId="1137" CreationDate="2012-02-26T03:06:46.237" Score="4" Body="&lt;p&gt;I thought I would attempt to answer my own question.  The only other answer currently (by Larian LeQuella), while a helpful comment, I feel it doesn't answer my original question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To begin, we need to put the results into context.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fact&lt;/strong&gt;: Hand-washing using tap water alone will reduce the amount of bacteria and viruses on hands (they might not be actually killed, but no longer on your hands).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://aem.asm.org/content/55/12/3113.short&quot; rel=&quot;nofollow&quot;&gt;Ansari et al. (1989)&lt;/a&gt; performed an experiment where a fecal solution was placed on participants' hands and subsequently washed off using one of a range of soaps.  They found a reduction in around 83% of the human rotavirus and 90% of the E. coli.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0963996905002255&quot; rel=&quot;nofollow&quot;&gt;Shojaeia et al. (2006)&lt;/a&gt; randomly selected 150 food handlers in Iran, and instructed them to wash and scrub their hands with sterile water.  Before the intervention, around 73% were contaminated with bacteria (primarily with Staphylococcus aureus or E. coli), and afterwards 32%.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fact&lt;/strong&gt;: More bacteria and viruses are removed from hands by hand washing by using some type of soap (not necessarily antibacterial).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Ansari et al. (1989) (op. cit.) found that certain agents (e.g. 70% isopropanol) can increase the reduction in E. coli and human rotavirus to around 98%.  However, this was not true of all possible hand-washing agents.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://aem.asm.org/content/59/10/3463.abstract&quot; rel=&quot;nofollow&quot;&gt;Mbithi et al. (1993)&lt;/a&gt; also conducted a experiment consisting of placing a fecal solution on participants' hands that was subsequently washed off using one of a range of soaps.  In this case, the hepatitis A virus (HAV) and poliovirus type 1 (PV) was considered.  They found that tap water gave a reduction of HAV of around 80% and PV of around 85%.  The reduction increased to around 88-92% for HAV and 90-98% for PV for most soaps tested.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;[There will be zillions of additional examples to the above.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A large survey was conducted by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17683018&quot; rel=&quot;nofollow&quot;&gt;Aiello et al. (2007)&lt;/a&gt; which considered the efficacy of &lt;a href=&quot;http://en.wikipedia.org/wiki/Triclosan&quot; rel=&quot;nofollow&quot;&gt;triclosan&lt;/a&gt; (one of the common active ingredients used in antibacterial hand soap) found that, overall, previous research has indicated no significant additional benefit vs. ordinary hand soap.  They write:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Soaps containing triclosan within the range of concentrations commonly&#xA;  used in the community setting (0.1%–0.45% wt/vol) were no more&#xA;  effective than plain soap at preventing infectious illness symptoms&#xA;  and reducing bacterial levels on the hands.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is probably not the last word on the matter, e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18095447&quot; rel=&quot;nofollow&quot;&gt;Fischler et al. (2007)&lt;/a&gt; claimed a significant difference in the transmission and acquisition of E. coli and Shigella flexneri after using an antibacterial soap.  It is also plausible that antibacterial agents other than triclosan (where the focus has been) provide a health benefit (for example, &lt;a href=&quot;http://en.wikipedia.org/wiki/Methylchloroisothiazolinone&quot; rel=&quot;nofollow&quot;&gt;methylchloroisothiazolinone&lt;/a&gt;/&lt;a href=&quot;http://en.wikipedia.org/wiki/Methylisothiazolinone&quot; rel=&quot;nofollow&quot;&gt;methylisothiazolinone&lt;/a&gt;).  In fact, the Aiello et al. (op. cit.) paper itself indicates a non-negligible effect from &gt;1% triclosan.  Kimberly-Clark give a 99.9% or more bacterial killing efficacy for a range of bacteria in a 2003 in vitro experiment of their product; obtainable via Googling &quot;kimberly-clark killing efficacy&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Side note:  There is also a suspicion that the use of triclosan will give rise to triclosan resistance or cross-resistance to antibiotics (e.g. by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631814/&quot; rel=&quot;nofollow&quot;&gt;Levy (2001)&lt;/a&gt;, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1473309903007230&quot; rel=&quot;nofollow&quot;&gt;Aielloa and Larson (2003)&lt;/a&gt;, &lt;a href=&quot;http://online.liebertpub.com/doi/abs/10.1089/mdr.2006.12.83&quot; rel=&quot;nofollow&quot;&gt;Yazdankhah et al. (2006)&lt;/a&gt;).  Although, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12969278&quot; rel=&quot;nofollow&quot;&gt;Cole et al. (2003)&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17006819&quot; rel=&quot;nofollow&quot;&gt;Weber and Rutala (2006)&lt;/a&gt; claim otherwise in the case of antibiotic resistance.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leads to the original question:  &lt;em&gt;Which common diseases would likely be more affected by antibacterial hand soaps (and other antibacterial products) than their non-antibacterial counterpart?&lt;/em&gt;  I.e. if we wanted to test the claim that a certain antibacterial hand soap has some positive effect (vs. a non-antibacterial version), what would be some common diseases that we could test for, and expect to find a non-negligible result?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I offer the following candidate for a bacterial disease whose effect should be noticeably reduced by the use of antibacterial hand soaps:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Staphylococcus_aureus&quot; rel=&quot;nofollow&quot;&gt;Staphylococcus aureus&lt;/a&gt; is a bacterial species that causes a range of noticeable illnesses and can be transferred by skin-to-skin contact and contact with contaminated objects.  We can thus reasonably expect it to be affected by an effective antibacterial hand soap.  In fact, washing hands is recommended for reducing the prevalence of S. aureus, along with zillions of other diseases (by e.g. &lt;a href=&quot;http://www.betterhealth.vic.gov.au/bhcv2/bhcarticles.nsf/pages/Staphylococcus_aureus_golden_staph&quot; rel=&quot;nofollow&quot;&gt;Better health channel&lt;/a&gt;).  This is one of the bacteria that Kimberly-Clark give a 99.99% kill efficacy of their product in vitro.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Although, not directly related to hand-washing, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2255283&quot; rel=&quot;nofollow&quot;&gt;Brady et al. (1990)&lt;/a&gt; used a 1% triclosan preparation and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7677266&quot; rel=&quot;nofollow&quot;&gt;Zafar et al. (1995)&lt;/a&gt; used 0.3% triclosan to control methicillin-resistant Staphylococcus aureus.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The single additional measure of changing handwashing and bathing soap to a preparation containing 0.3% triclosan (Bacti-Stat) was associated with the immediate termination of the acute phase of the MRSA outbreak.  -- Zafar et al.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Similarly, a 1.5% &lt;a href=&quot;http://en.wikipedia.org/wiki/Triclocarban&quot; rel=&quot;nofollow&quot;&gt;triclocarban&lt;/a&gt; bath has been used to treat atopic detmatitis &lt;a href=&quot;http://ukpmc.ac.uk/abstract/MED/11109156&quot; rel=&quot;nofollow&quot;&gt;Breneman et al. (2000)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The antimicrobial soap regimen caused significantly greater&#xA;  improvement in the severity and extent of skin lesions than the&#xA;  placebo soap regimen, which correlated with reductions both in S&#xA;  aureus in patients with positive cultures at baseline and in total&#xA;  aerobic organisms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The above results suggest that antibacterial soaps could have a beneficial effect against S. aureus (more than a non-antibacterial counterpart).  However, it is unclear as to how much of this effect implies a comparable effect for hand washing alone (and in an ordinary household setting).  Moreover, there are many different antibacterial hand soaps and other products, whose active ingredients might be at different dosage, all of which would further affect the outcomes.&lt;/p&gt;&#xA;" OwnerUserId="203" LastActivityDate="2012-02-26T03:06:46.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1194" PostTypeId="2" ParentId="1188" CreationDate="2012-02-26T03:25:00.363" Score="5" Body="&lt;p&gt;Well - a lot if you knew what questions to ask...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most obvious thing is sex: if you can find the x and/or y chromosomes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other things like skin color, eye color, etc, or hereditary diseases and all that would involve running the genome through some sort of database which had values for both pheno and genotypes so you could correlate some of those things and find those physical characteristics. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scientists are discovering these correlations all the time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can go to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/omim&quot;&gt;http://www.ncbi.nlm.nih.gov/omim&lt;/a&gt; and search for something like eye color and find out more than you need probably.&lt;/p&gt;&#xA;" OwnerUserId="524" LastEditorUserId="69" LastEditDate="2012-02-26T11:46:20.407" LastActivityDate="2012-02-26T11:46:20.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1195" PostTypeId="2" ParentId="1181" CreationDate="2012-02-26T03:30:09.610" Score="4" Body="&lt;p&gt;Often cells have multiple types of the same protein — this redundancy can have different effects for different requirements such as having proteins function under different physiological conditions, or providing specificity to a certain class of ligand proteins or so on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But here, it seems like the two have some synergistic interaction, a tag team if you will. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s10254-003-0021-1&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Wegele H, Müller L, Buchner J&lt;/strong&gt;. 2004. Hsp70 and Hsp90 — a relay team for protein folding. Reviews of physiology, biochemistry and pharmacology 151: 1–44.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately this article's full version can only be accessed if you're at a university or somewhere that has a subscription to some of the large research databases, but the abstract is free and it may provide more clarification. &lt;/p&gt;&#xA;" OwnerUserId="524" LastEditorUserId="836" LastEditDate="2012-08-25T01:39:38.410" LastActivityDate="2012-08-25T01:39:38.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1196" PostTypeId="2" ParentId="775" CreationDate="2012-02-26T06:11:06.287" Score="9" Body="&lt;p&gt;I would like to point out some ways your understanding is wrong. &quot;Neural networks&quot; are usually a computer science term, only very, very loosely based on actual neural networks. The idea of layers in a neural network is pretty much an invention of computer science, it doesn't really reflect the reality. Also, neurons are not binary switches. It isn't so much about on/off, so much as a temporal rate code of action potentials. The actual brain sort of stochastic, and does not really work on the level of the single action potential. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The adaptation of the term &quot;neural networks&quot; by those devious computer scientists is unfortunate. Their work is virtually unrelated to actual neural networks.&lt;/p&gt;&#xA;" OwnerUserId="510" LastActivityDate="2012-02-26T06:11:06.287" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1197" PostTypeId="2" ParentId="1188" CreationDate="2012-02-26T06:13:27.720" Score="6" Body="&lt;p&gt;I've had a little encounter with this question in the past few months so I'm updating here...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The overall answer is 'really a lot about some things, but not as much as you'd like to think about others.'    There is a scientific genome interpretation 'contest' that has been going on for the past few years called CAGI (&lt;a href=&quot;https://genomeinterpretation.org/&quot; rel=&quot;nofollow&quot;&gt;Critical Assessment of Genome Interpretation&lt;/a&gt;).  This is meant to be a cutting edge set of challenges and its worth looking them over.  Last year there was in particular one challenge - &lt;a href=&quot;https://genomeinterpretation.org/content/pgp&quot; rel=&quot;nofollow&quot;&gt;answering questions about ten individuals given only a list of traits and their genome sequences&lt;/a&gt;.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was not so easy it turns out - simply looking up variants and cross referencing them to the literature led to poor predictions.  Glaucoma, asthma, migrane, irritable bowel syndrome, color blindness, lupus, lactose intolerance are examples from a list of 40-odd contest questions.  If you register onto the site you can get some of the results or there is a paper reporting the results, only four labs tried the challenge and the accuracies were sometimes not great, topping off with Rachel Karchin's lab with an AUC of 90%.  Even some of the phenotypes you think are easy are not a simple lookup.  Genetics is not as pre-determined as we think. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While we are good at inferring our history and geneology on the other hand.  A reasonable example of this is the &lt;a href=&quot;https://www.23andme.com/ancestry/&quot; rel=&quot;nofollow&quot;&gt;23andme analysis&lt;/a&gt;.  They have a lot less information about you than a complete genome sequence, but they do seem to make the most of the 0.0001% of the genome that they do have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They have a nice lookup of some of the hereditary disease data that is available.  &quot;Increased risk of skin cancer&quot; or for Alzheimers are only chances and its never clear how much your actual lifestyle has impact on 44 outcomes, but its there.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What they also have is your ancestral analysis which is crazy interesting. it shows where your maternal and paternal lineages come from and how strong.  they have a very pretty heatmap of the continents for this.  National Geographic's DB is probably more sophisticated and ancestry.com also does this.  This is pretty cool.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also included things like curly hair, color of skin eyes and hair.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like SimaPro says they are described in OMIM.  OMIM stands for 'online mendelian inheritance in man' and all the straightforward directly inheritable traits we know of are listed there.  its worth taking a look. There are not a lot of known single mutation genetically inheritable conditions.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the genome sequence includes methylation, then some other traits which are epigenetic, not genetic but would also be determined from a genome sequence.  Most famous example of this is &lt;a href=&quot;http://en.wikipedia.org/wiki/MEST_%28gene%29&quot; rel=&quot;nofollow&quot;&gt;MEST&lt;/a&gt; which will give an indicator of whether you are a doting parent or not.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-01-23T18:04:16.680" LastActivityDate="2013-01-23T18:04:16.680" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1198" PostTypeId="1" AcceptedAnswerId="1313" CreationDate="2012-02-26T07:54:20.963" Score="13" ViewCount="1257" Body="&lt;p&gt;I was reading the answers to the question: &lt;a href=&quot;https://biology.stackexchange.com/questions/775/how-and-where-in-the-human-brain-are-memories-stored&quot;&gt;How and where, in the human brain, are memories stored?&lt;/a&gt; and, as expected, LTP and LTD came out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Every time I read about LTP/LTD there is always something that bugs me a lot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I read papers about LTP/LTD (OK, I should really say &quot;when I browse&quot;, as I'm not exactly in that area of neurosciences, and that is probably the reason why I am confused by this) I always see these very neat experiments where stimulating a neuron in a certain way increases/decreases its further responses. Then, I look at the time axes on the graphs, or read the Methods, and I see that the LTP was induced and analysed few minutes after the stimulus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my questions are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Is there &lt;strong&gt;clear&lt;/strong&gt; evidence that LTP is involved in &lt;strong&gt;long-term&lt;/strong&gt; memory (not counting 1 hour as long-term...)?&lt;/li&gt;&#xA;&lt;li&gt;Has LTP/LTD been shown &lt;em&gt;in vivo&lt;/em&gt; after &lt;strong&gt;long&lt;/strong&gt; period of time (e.g. months).&lt;/li&gt;&#xA;&lt;li&gt;For those who work in the field, is there a strong belief that LTP/LTD are the &lt;strong&gt;only&lt;/strong&gt; phenomena underlying memory?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="115" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2012-09-14T20:20:02.577" Title="Long-term-potentiation and memory. Where do we stand?" Tags="&lt;neuroscience&gt;&lt;memory&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1200" PostTypeId="2" ParentId="1181" CreationDate="2012-02-26T08:55:47.980" Score="6" Body="&lt;p&gt;Hsp70 and Hsp90 are not single proteins, but entire protein families. And those two protein families are not the only ones of their kind. There are different groups of heat shock proteins, Hsp70 and Hsp90 are molecular chaperones that assist in protein folding. There are five major families of molecular chaperones: Hsp100, Hsp90, Hsp70, Hsp60 and Hsps. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hsp70 binds to nonnative, unstructured segments of proteins and helps folding them. Hsp90 doesn't bind to unfolded proteins, but to native-like proteins. Some substrates are also handed over to Hsp90 by Hsp70. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The whole area of chaperones and heat shock response is a very, very large and interesting field. I recommend to you to read the reviews below.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1101/cshperspect.a004390&quot;&gt;Vabulas, R. M., Raychaudhuri, S., Hayer-Hartl, M. &amp;amp; Hartl, F. U. Protein folding in the cytoplasm and the heat shock response. &lt;em&gt;Cold Spring Harb Perspect Biol&lt;/em&gt; &lt;strong&gt;2&lt;/strong&gt;, (2010).&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.molcel.2010.10.006&quot;&gt;Richter, K., Haslbeck, M. &amp;amp; Buchner, J. The heat shock response: life on the verge of death. &lt;em&gt;Mol. Cell&lt;/em&gt; &lt;strong&gt;40&lt;/strong&gt;, 253-266 (2010).&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6" LastActivityDate="2012-02-26T08:55:47.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1201" PostTypeId="2" ParentId="1164" CreationDate="2012-02-26T09:17:40.433" Score="18" Body="&lt;p&gt;The cost of transcribing and translating a hypothetical average gene in yeast has been calculated as 551 activated phosphate bonds ~P per second (&lt;a href=&quot;http://dx.doi.org/10.1093/molbev/msi126&quot;&gt;Wagner, 2005&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The median length of a yeast RNA molecule is 1,474 nucleotides, and&#xA;  the median cost of precursor synthesis per nucleotide (derived from&#xA;  the base composition of yeast-coding regions) is 49.3 ∼P. With a&#xA;  median mRNA abundance of R = 1.2 mRNA molecules per cell and a median&#xA;  mRNA decay constant of dR = 5.6 × 10−4 s−1, the mRNA synthesis costs&#xA;  calculates as 49.3 × 1,474 × 1.2 × (5.6 × 10−4) = 48.8 ∼P per second&#xA;  and cell. This is a fraction 48.8/1.34 × 107 = 3.6 × 10−6 of the total&#xA;  RNA synthesis cost per second. The median length of a yeast protein is&#xA;  385 amino acids, with a combined biosynthesis and polymerization cost&#xA;  of 30.3 ∼P per amino acid. The median abundance is 2,460 protein&#xA;  molecules per cell. No currently available data allows a meaningful&#xA;  estimate of the median protein half-life, but a protein of an&#xA;  intermediate half-life (see below) of 10 h (decay constant dP = 1.92 ×&#xA;  10−5 s−1) yields an overall synthesis cost of 30.3 × 385 × 2,460 ×&#xA;  (1.92 × 10−5) = 551 ∼P s−1.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For your question about a single gene, the cost would be 49.3 * 1474 ~P for the mRNA and 30.3 * 385 ~P for the translation, which would result in around 84 thousand ~P. This is probably a very misleading statistic as you can transcribe multiple proteins from a single mRNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How the cost of mRNA synthesis and translation are calculated is described in detail in the paper. A large part of the cost comes from the synthesis of the basic building blocks, the nucleotides and the amino acids.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1093/molbev/msi126&quot;&gt;Wagner, A. Energy Constraints on the Evolution of Gene Expression. &lt;em&gt;Mol Biol Evol&lt;/em&gt; &lt;strong&gt;22&lt;/strong&gt;, 1365-1374 (2005).&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2012-02-26T17:25:50.423" LastActivityDate="2012-02-26T17:25:50.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1202" PostTypeId="2" ParentId="1191" CreationDate="2012-02-26T14:01:59.740" Score="5" Body="&lt;p&gt;You can use &lt;code&gt;blastdbcmd&lt;/code&gt; to extract FASTA sequences from the BLAST database. Then you can append your extra sequence to the newly created FASTA file, and remake the BLAST DB using &lt;code&gt;makeblastdb&lt;/code&gt;. Assuming you have a protein BLAST database in the current working directory, and a sequence you want to add to it in &lt;code&gt;new.fa&lt;/code&gt;:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;$ blastdbcmd -db proteindb -dbtype prot -out db.fa -entry all&#xA;    $ cat new.fa &amp;gt;&amp;gt; db.fa&#xA;$ makeblastdb -in db.fa -out newproteindb -dbtype prot&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;(Replace &lt;code&gt;prot&lt;/code&gt; with &lt;code&gt;nucl&lt;/code&gt; if you have a nucleotide database)&lt;/p&gt;&#xA;" OwnerUserId="82" LastEditorUserId="89" LastEditDate="2013-12-26T14:24:33.350" LastActivityDate="2013-12-26T14:24:33.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1203" PostTypeId="2" ParentId="831" CreationDate="2012-02-26T16:47:04.490" Score="6" Body="&lt;p&gt;The comments above are quite relevant -- we are years / decades away from growing functional brains in the lab, so there are probably innumerable constraints that we have likely not even thought of yet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, you might find this paper interesting: &quot;&lt;a href=&quot;http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1556108&quot;&gt;Adaptive flight control with living neuronal networks on microelectrode arrays&lt;/a&gt;&quot; [1]. The authors are able to succesfully culture rat neurons and electrically interface with them in order to control pitch and yaw in the &lt;a href=&quot;http://www.x-plane.com&quot;&gt;XPlane&lt;/a&gt; flight simulation software.  It's a very crude system compared to an actual brain, but it's able to successfully use cells as rudimentary living neural networks. If you consider this to be a successful &quot;artificial brain,&quot; then your constraints are all the ones associated with &lt;a href=&quot;http://www.jove.com/video/152/culture-of-mouse-neural-stem-cell-precursors&quot;&gt;culturing neurons&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1556108&quot;&gt;DeMarse, et. al 2005&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="526" LastActivityDate="2012-02-26T16:47:04.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1204" PostTypeId="2" ParentId="1033" CreationDate="2012-02-26T19:03:31.550" Score="1" Body="&lt;p&gt;The location is exactly tuba uterina infundibulum, &lt;a href=&quot;http://www.embryology.ch/anglais/dbefruchtung/eisprung02.html&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;, since the processes results in the following things before LH peak:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;The correct placement of the uterine tube infundibulum upon the&#xA;  ovarian surface &lt;/li&gt;&#xA;  &lt;li&gt;The rupture of the follicle wall and the flow of the&#xA;  follicle fluid with the oocyte into the infundibulum &lt;/li&gt;&#xA;  &lt;li&gt;The inhibition of&#xA;  the maturation of further follicles&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-02-26T19:03:31.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1205" PostTypeId="1" AcceptedAnswerId="1741" CreationDate="2012-02-26T19:32:40.890" Score="4" ViewCount="4969" Body="&lt;p&gt;My note about which I am not sure:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Secondary oocyte is arrested in the metaphase II monthly after puberty until fertilization with sperm. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The following picture also satisfies my sentence: &lt;img src=&quot;https://i.stack.imgur.com/2GFHd.png&quot; alt=&quot;enter image description here&quot;&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you can see that the secondary oocyte that is arrested seems to be Graafian.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that Graafian develops during the second week.&#xA;I know that the secondary follicle is developing two days before &lt;a href=&quot;http://www.embryology.ch/anglais/dbefruchtung/eisprung02.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;ovulation&lt;/a&gt;.&#xA;It seems that the development of the secondary follicle ends and the formation of Graafian follicle occurs just before ovulation. &#xA;My lecture material suggests that Graafian follicle is arrested in metaphase II, since Graafian follicle is ovulated once in a month and waits sperm in tuba uterina infundibulum:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3Twn3.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer to my question is not also clear from &lt;a href=&quot;https://biology.stackexchange.com/questions/954/does-human-female-meiosis-ii-occur-after-fertilization-with-sperm&quot;&gt;my previous thread&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An oocyte completes meiosis I as its follicle matures (during ovulation) resulting in a secondary oocyte and the FIRST polar body. After ovulation, each oocyte continues to metaphase of meiosis II.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which follicle is arrested in the metaphase II of oogenesis?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-06-12T05:14:37.760" Title="Is secondary follicle or Graafian follicle arrested in the second metaphase of oogenesis?" Tags="&lt;homework&gt;&lt;oogenesis&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1206" PostTypeId="1" AcceptedAnswerId="1284" CreationDate="2012-02-26T19:51:20.680" Score="3" ViewCount="939" Body="&lt;p&gt;This thread is related to &lt;a href=&quot;https://biology.stackexchange.com/questions/991/what-are-differences-between-formation-of-embryonic-disc-in-chick-and-mammal-emb&quot;&gt;my previous thread&lt;/a&gt; which is still unsolved mainly. I need to be able to compare chick and human cleavage and blastulation of zygote. &#xA;My friend says that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Chicken have discoblast, human not. That is the main thing to get the idea of the difference.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I know that chicken have yolk sac with yolk, while human have yolk sac without yolk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My notes say that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cleavage in birds is partial discoidal (embryo forms disc and cells called blastodisc are on top of the yolk). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So embryo forms some disc, lets call it #1. Some cells called blastodisc are on top of the yolk. &lt;strong&gt;So are the cells called blastodisc on top of the yolk and the disc #1?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the name of the given disc that chick embryo forms?&lt;/strong&gt;&#xA;It seems that human is not forming the given disc. Apparently, the name of the given disc is discoblast, the thing he says is very important.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2018-03-02T04:17:05.390" Title="Does chicken embryo form the disc called &quot;discoblast&quot; in the cleavage and blastulation of chicken?" Tags="&lt;homework&gt;&lt;embryology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1207" PostTypeId="2" ParentId="1167" CreationDate="2012-02-26T21:51:04.377" Score="11" Body="&lt;p&gt;I think this is due to the over-representation of recognition sites with length 6:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;data&amp;lt;-c(16, 16, 12, 12, 6, 6, 6, 6, 4, 16, 6, 6, 6, 6, 15, 15, 6, 6, 6, 6, 11, 11, 6, 6, 4, 4, 6, 6, 11, 12, 6, 6, 23, 23, 6, 6, 6, 6, 9, 12, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 10, 10, 6, 4, 6, 6, 11, 11, 9, 9, 6, 6, 6, 6, 5, 5, 8, 8, 6, 6, 8, 8, 6, 9, 10, 10, 6, 6, 6, 5, 5, 6, 4, 6, 6, 5, 5, 14, 14, 6, 6, 6, 16, 6, 6, 6, 6, 15, 15, 6, 6, 6, 6, 6, 18, 18, 7, 7, 11, 11, 20, 20, 6, 13, 4, 4, 6, 6, 6, 6, 6, 6, 6, 11, 6, 6, 7, 7, 6, 6, 6, 6, 6, 12, 6, 6, 10, 10, 23, 23, 7, 7, 23, 23, 12, 12, 6, 6, 6, 6, 10, 10, 6, 6, 8, 8, 6, 6, 35, 35, 11, 11, 7, 7, 6, 6, 9, 9, 8, 8, 16, 16, 6, 6, 17, 17, 6, 6, 6, 6, 23, 23, 6, 6, 4, 4, 21, 21, 12, 12, 20, 20, 6, 6, 6, 6, 6, 7, 7, 6, 6, 6, 6, 5, 5, 11, 11, 6, 11, 11, 6, 6, 5, 5, 7, 7, 11, 11, 11, 11, 6, 6, 12, 12, 6, 6, 6, 21, 21, 9, 9, 8, 8, 7, 7, 16, 16, 4, 4, 6, 6, 6, 6, 7, 7, 18, 18, 6, 6, 6, 6, 6, 23, 23, 7, 34, 34, 39, 39, 6, 6, 12, 12, 5, 5, 19, 19, 8, 8, 8, 8, 4, 6, 6, 6, 6, 6, 5, 5, 6, 6, 6, 6, 7, 7, 4, 4, 15, 15, 7, 7, 7, 7, 14, 14, 11, 11, 27, 27, 12, 12, 4, 4, 10, 10, 6, 6, 8, 8, 7, 7, 8, 8, 7, 7, 5, 5, 7, 7, 6, 7, 7, 6, 6, 8, 8, 39, 39, 6, 6, 12, 12, 8, 8, 7, 13, 13, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 7, 17, 17, 17, 17, 11, 11, 15, 15, 6, 6, 6, 5, 5, 5, 6, 6, 5, 7, 7, 12, 6, 12, 6, 6, 6, 5, 6, 6, 7, 2, 5, 11, 5, 6, 4, 5, 7, 5, 4, 4, 6, 4, 5, 6, 7, 12, 6, 7, 7, 7, 6, 4, 4, 7, 5, 6, 6, 6, 7, 5, 12, 13, 5, 6, 6, 6, 5, 11, 11, 5, 6, 10, 5, 5, 11, 6, 5, 5, 6, 5, 6, 5, 6, 6, 7, 7, 6, 5, 5, 7, 6, 5, 6, 5, 6, 5, 5, 7, 6, 6, 6, 3, 5)&#xA;h&amp;lt;-hist(data, breaks=0.5:40.5)&#xA;df&amp;lt;-data.frame(counts=h$counts, mids=h$mids)&#xA;df$even &amp;lt;- (df$mids%%2 == 0)&#xA;ggplot(df, aes(x=mids, y=counts, fill=even))+geom_bar(stat=&quot;identity&quot;)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Q1Kfg.png&quot; alt=&quot;Histogram of recognition site length&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at the histogram of lengths, there is no bias towards even recognition site lengths except for length 6.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-02-26T21:51:04.377" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1208" PostTypeId="1" AcceptedAnswerId="1431" CreationDate="2012-02-27T02:38:09.333" Score="4" ViewCount="136" Body="&lt;p&gt;I am looking for a large collection (&gt;1000) of sequence files (eg. FASTA) from any real organism or a tool to create such a collection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sequence files would be used for teaching and for testing automation methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Students would be assigned one unique sequence file and asked to look at it (eg. using gORF) and to identify it (using BLASTn).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sequence file would thus need to contain only the sequence data (no meta data about species or gene).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would need an associated answer sheet.&lt;/p&gt;&#xA;" OwnerUserId="553" LastEditorUserId="553" LastEditDate="2012-03-30T10:53:34.500" LastActivityDate="2012-03-30T10:53:34.500" Title="How to create a collection of anonymous sequences for teaching and testing?" Tags="&lt;genetics&gt;&lt;dna-sequencing&gt;&lt;bioinformatics&gt;" AnswerCount="3" CommentCount="2" ClosedDate="2013-01-02T20:52:27.203" ContentLicense="CC BY-SA 3.0" />
  <row Id="1209" PostTypeId="2" ParentId="1176" CreationDate="2012-02-27T05:04:40.950" Score="2" Body="&lt;p&gt;You could also try induction at lower temperatures to minimize chances of protein degradation. Cells such as Arctic cells (&lt;a href=&quot;http://tinyurl.com/arcticecoli&quot; rel=&quot;nofollow&quot;&gt;http://tinyurl.com/arcticecoli&lt;/a&gt;) are optimized for low temperature expression although BL21 works just as good for the proteins we express (upto 140kDa in size)&lt;/p&gt;&#xA;" OwnerUserId="223" LastActivityDate="2012-02-27T05:04:40.950" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1210" PostTypeId="2" ParentId="1208" CreationDate="2012-02-27T05:24:01.580" Score="4" Body="&lt;p&gt;This is probably not the most elegant way but you could go to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore&quot; rel=&quot;nofollow&quot;&gt;NCBI&lt;/a&gt; and search for nucleotide sequences from a given organism (eg., txid9606[Organism:exp] gives all sequences from Homo sapiens). Then you could use the Send to dropdown to download all the results as a compiled FASTA file.&lt;/p&gt;&#xA;" OwnerUserId="223" LastEditorUserId="115" LastEditDate="2012-02-27T07:00:13.533" LastActivityDate="2012-02-27T07:00:13.533" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1213" PostTypeId="2" ParentId="1186" CreationDate="2012-02-27T06:20:58.310" Score="13" Body="&lt;p&gt;The beta-form of DNA and the alpha-form of DNA are based on the pucker on the sugar ribose. As DNA doesn't have a 2'-OH, it can obtain both conformations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iwQSC.jpg&quot; alt=&quot;schematic of Beta vs Alpha from riboses&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RNA does not have this luxury. The steric clash of the 2-OH with the 3'-OH makes the B-form to be very unfavorable thus constraining the RNA to adopt the A-form. Incidentally this steric limitation is also why RNA structures are more stable (see &lt;a href=&quot;https://biology.stackexchange.com/a/769/389&quot;&gt;https://biology.stackexchange.com/a/769/389&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2012-02-27T06:20:58.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1214" PostTypeId="1" AcceptedAnswerId="1239" CreationDate="2012-02-27T07:00:04.237" Score="6" ViewCount="385" Body="&lt;p&gt;There are internally threaded, externally threaded, natural caps. For the vials, there are skirts, star-footed, and various bottoms. Why do any of these things matter?&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorDisplayName="user560" LastEditDate="2012-03-02T12:23:56.050" LastActivityDate="2012-03-02T12:23:56.050" Title="Which cryogenic vials and caps are ideal for storing glycerol stocks?" Tags="&lt;ecoli&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1215" PostTypeId="2" ParentId="1188" CreationDate="2012-02-27T13:53:43.333" Score="4" Body="&lt;p&gt;The first place to look for answer to this is the 1000 Genomes Project. I feel that their efforts in data analysis offer lessons on what one can and cannot learn from such a dataset as posed in the question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One obvious thing that is easy to overlook is a whole genome sequence will tell you the mid- to large-sized insertions and deletions in that genome. Any of those that are novel, private or extremely rare (take a word of your choosing) &lt;em&gt;can be used&lt;/em&gt; to place that individual in a family tree (if other data are available) and to predict certain phenotypes (from the affected genes). This is also true for some SSRs - simple sequence repeats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good haplotype analysis from the genome sequence can predict ethnic ancestry - with a fair degree of accuracy. This is especially so as more genomes are sequenced and available for comparison. Haplotypes of the Y chromosome and mitochondrial genome, give paternal and maternal ancestry, respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the whole genome sequence gives accurate telomere lengths, then a prediction of age of the individual can be gained +/- 10 yrs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disease phenotypes or risk of disease is tricky. For monogenic diseases, this is more accurate and that accuracy falls off as the complexity of contribution to variance of the trait increases. At least a hundred loci contribute to risk of type 2 diabetes, but that risk is also age-dependent and so a young person may not have the disease but only be at increased risk. Furthermore, not everyone with elevated risk will acquire the disease and not all at reduced risk will remain disease-free - for that disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, if this analysis included epigenetic measures, such as methylation of the genomic DNA, then one can predict genome changes from environmental exposure such as tobacco smoking or air pollution. In addition, loci with differential methylation and showing a phenotypic consequence, such as elevated obesity status (BMI) or colorectal cancer risk, are beginning to be defined. This is in its infancy, but the data are growing.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-02-27T13:53:43.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1216" PostTypeId="1" CreationDate="2012-02-27T14:09:14.767" Score="9" ViewCount="9646" Body="&lt;p&gt;I presumed chimpanzees were the closest relatives of us. However, after watching &lt;a href=&quot;http://www.youtube.com/watch?v=a8nDJaH-fVE&quot;&gt;this TED Talk&lt;/a&gt;, it seems bonobos are closer to us both in &lt;a href=&quot;http://www.youtube.com/watch?v=a8nDJaH-fVE&amp;amp;t=3m10s&quot;&gt;skeleton&lt;/a&gt; and &lt;a href=&quot;http://www.youtube.com/watch?v=a8nDJaH-fVE&amp;amp;t=5m40s&quot;&gt;behavioral&lt;/a&gt; similarity than chimpanzees. I once read in &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1439192812&quot;&gt;The Magic of Reality&lt;/a&gt; that we share quite a lot of common &lt;a href=&quot;http://en.wikipedia.org/wiki/FOXP2&quot;&gt;FOXP2 gene&lt;/a&gt; letters with chimpanzees, but there isn't any mention on similarity between us and bonobos in that book. Here is the excerpt:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;You can tell that FoxP2 is the same gene in all mammals because the&#xA;  great majority of the code letters are the same, and that is true of&#xA;  the whole length of the gene, not just this stretch of 80 letters. Of&#xA;  the total of 2,076 letters in FoxP2, the chimpanzee has 9 letters&#xA;  different from ours, while the mouse has 139 letters different.   And&#xA;  that pattern holds for other genes too. That explains why chimpanzees&#xA;  are very like us, while mice are less so. Chimpanzees are our close&#xA;  cousins, mice are our more distant cousins. 'Distant cousins' means&#xA;  that the most recent ancestor we share with them lived a long time&#xA;  ago.   &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Monkeys are closer to us than mice but further from us than&#xA;  chimpanzees.   Baboons and rhesus macaques are both monkeys, close&#xA;  cousins of each other, and with almost identical FoxP2 genes. They are&#xA;  exactly as distant from chimps as they are from us; and the number of&#xA;  DNA letters in FoxP2 that separate baboons from chimps is almost&#xA;  exactly the same (24) as the number of letters that separate baboons&#xA;  from us (23).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So which species is closest to us, chimpanzees or bonobos?&lt;/p&gt;&#xA;" OwnerUserId="504" LastEditorUserId="59577" LastEditDate="2020-08-20T13:07:54.880" LastActivityDate="2020-08-20T13:07:54.880" Title="What is the closest species to humans in animal kingdom?" Tags="&lt;evolution&gt;&lt;human-genetics&gt;&lt;human-evolution&gt;&lt;anthropology&gt;" AnswerCount="5" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1217" PostTypeId="1" AcceptedAnswerId="1218" CreationDate="2012-02-27T15:14:21.097" Score="3" ViewCount="1156" Body="&lt;p&gt;How do I display a single nucleotide position from reads in a BAM file? I have been looking at variation using samtools mpileup, but I want to actually just display the nucleotide at the position I am interested in. This seems like you should be able to do it but I can't figure out how.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be clear I have a BAM file of a bunch of reads. I'm looking to do something like &lt;code&gt;samtools magic reads.bam chr3:10000&lt;/code&gt; where I get back something like:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;T T T T T T T T T T T T T T T T T T T A A A A A A A A A A A A A.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I just want to sanity check the output of bcftools by actually looking at the base calls.&lt;/p&gt;&#xA;" OwnerUserId="557" LastEditorUserId="6" LastEditDate="2012-02-27T15:20:51.947" LastActivityDate="2012-02-27T16:12:23.360" Title="Displaying nucleotide at a single position from RNA-seq reads in a BAM file" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1218" PostTypeId="2" ParentId="1217" CreationDate="2012-02-27T16:12:23.360" Score="3" Body="&lt;p&gt;Your best option is to create a tab delimited position list file:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;chr3    1000&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;You can then use the &lt;code&gt;samtools mpileup -l pos.txt&lt;/code&gt; option&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;-l FILE      list of positions (chr pos) or regions (BED)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This file can also be in &lt;a href=&quot;http://genome.ucsc.edu/FAQ/FAQformat#format1&quot; rel=&quot;nofollow&quot;&gt;bed&lt;/a&gt; format if you are interested in specific regions&lt;/p&gt;&#xA;" OwnerUserId="12" LastActivityDate="2012-02-27T16:12:23.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1219" PostTypeId="2" ParentId="1216" CreationDate="2012-02-27T16:34:15.840" Score="5" Body="&lt;p&gt;I'm don't have enough experience with this particular area to know whether experts have come to a consensus about this (although both your question and a brief literature search suggests they have not). What I do know is that when you begin looking at these types of questions at this level of detail, the answer that you get will depend on the characters used and the modeling strategy. The fact that you may arrive at a different conclusion when looking at a small number of morphological (skeletal) and behavioral characters versus genetic characters (sequence homology of a particular family of genes) is not surprising. Even when using the same characters, different methods (maximum parsimony vs maximum likelihood vs Bayesian) may give you different results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the answer is probably &quot;we don't know for sure&quot; (I'd be happy to be proven wrong here). But either way, the different conclusions you cite are not necessarily contradictory. Any conclusion will simply have to be justified in terms of the assumptions made, the data (characters) involved, and the method used.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-02-27T16:34:15.840" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1220" PostTypeId="1" AcceptedAnswerId="1233" CreationDate="2012-02-27T18:23:27.903" Score="14" ViewCount="6768" Body="&lt;p&gt;I'm volunteering for a biohacker lab - &lt;a href=&quot;http://www.biocurious.org&quot;&gt;biocurious&lt;/a&gt; in Sunnyvale.  The have a pretty good set of equipment - gel boxes, incubators, but they don't have a -80°C freezer yet.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like to set up some glycerol stab stocks of some E. coli strains, but i'm told even untransformed (i.e. no plasmid) bacteria will get funny after a while at -20°C.  It would also be good to hear how long you can keep a plasmid transformed strain at -20°C. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone be specific about what happens and how long it takes when you store them at -20°C for long periods of time? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have done a little reading for competent cells and I guess they stay active for about 4 days without a -80°C freezer.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="6" LastEditDate="2012-02-27T19:02:13.083" LastActivityDate="2014-01-29T20:10:17.657" Title="How long can E. coli stocks be stored at -20°C?" Tags="&lt;molecular-biology&gt;&lt;ecoli&gt;&lt;bacteriology&gt;" AnswerCount="3" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1221" PostTypeId="1" CreationDate="2012-02-27T19:22:26.067" Score="4" ViewCount="399" Body="&lt;p&gt;My bioinorganic and redox chemistry isn't up to par and I'm having a very difficult time understanding the chemical mechanism behind cystine bond formation. Most reactive environments are actually reductive whereas an oxidative environment is important for cystine bond formation. How does the oxidative environment oxidize the thiols, rearrange the orbitals and form a disulfide bond?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tirb0.png&quot; alt=&quot;Cystine bond&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-02-28T19:18:43.777" LastActivityDate="2012-03-02T16:41:23.123" Title="What is the molecular mechanism of cystine bond formation?" Tags="&lt;bioinorganic-chemistry&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1222" PostTypeId="2" ParentId="1216" CreationDate="2012-02-27T19:41:26.527" Score="9" Body="&lt;p&gt;Looking at one gene is not enough. Since each gene is free to evolve (or not), there can be different sister taxon relationships depending on the gene studied. A better estimate is made using several genes or combining the results of several analyses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.jstor.org/stable/56095&quot;&gt;Purvis (1995)&lt;/a&gt;, the extant sister taxon of &lt;em&gt;Homo sapiens&lt;/em&gt; is a clade with the bonobo (&lt;em&gt;Pan paniscus&lt;/em&gt;) and chimpanzee (&lt;em&gt;Pan troglodytes&lt;/em&gt;), with gorillas as an outgroup. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the answer is that neither is closer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Purvis, A. 1995. A Composite Estimate of Primate Phylogeny. &lt;em&gt;Philosophical Transactions: Biological Sciences&lt;/em&gt; 348: 405-421.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-02-27T19:41:26.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1223" PostTypeId="2" ParentId="1216" CreationDate="2012-02-27T19:45:32.763" Score="11" Body="&lt;p&gt;Chimpanzees and bonobos are equally close to us in time (which is the opportunity for evolutionary divergence).  Our &lt;a href=&quot;http://en.wikipedia.org/wiki/Most_recent_common_ancestor&quot;&gt;most recent common ancestor&lt;/a&gt; with either species is the same, as our line split from their common line &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Ancestor%27s_Tale#Primates&quot;&gt;about 6 million years ago&lt;/a&gt; (estimates are generally in the 4-8 mya range).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The split between the common chimp and the bonobo is much more recent, &lt;a href=&quot;http://en.wikipedia.org/wiki/Bonobo#Taxonomy_and_phylogeny&quot;&gt;probably less than one million years ago.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in terms of general closeness to us, these two species qualify equally.  For any particular gene, either one might be closer, as our version may be unchanged from our common ancestor, while one of the two &lt;em&gt;Pan&lt;/em&gt; (chimp) species may be the same and one different.  For most genes that have differences, we can expect that we are the odd man out, while the two &lt;em&gt;Pan&lt;/em&gt; species share a common gene.&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2012-02-27T19:45:32.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1224" PostTypeId="1" AcceptedAnswerId="1227" CreationDate="2012-02-27T20:16:13.697" Score="6" ViewCount="341" Body="&lt;p&gt;Say I have one dsDNA that undergoes normal PCR (where amplification is exponential).  If there is a mistake, say a G is swapped for an A during the 2nd round of replication, what percentage of the final DNA will have the mistake if there are 12 more rounds?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was talking to my teacher about this today.  I say 33%, my teacher said 12.5%.&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="558" LastEditDate="2012-03-03T23:39:01.647" LastActivityDate="2012-03-03T23:39:01.647" Title="PCR amplification and error propagation" Tags="&lt;pcr&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1225" PostTypeId="2" ParentId="1220" CreationDate="2012-02-27T20:18:14.937" Score="12" Body="&lt;p&gt;I think that cells get damaged at -20°C not because they are stored for a long period of time, but because they undergo cycles of thawing and freezing (the ice crystals that form damage them).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I never keep cells at -20°C. I store them at -80°C in 50% glycerol. The idea behind the glycerol is that it serves as cryoprotecor. It forms hydrogen bonds with the water molecules and thus it disrupts the water-water hydrogen bonds. As a result, it disrupts the crystal formation of ice, and the cells don't freeze. The freezing temperature of glycerol is −37.8 °C (60-70% glycerol in water), which means that at -20°C glycerol does not freeze and thus it cannot protect the cells from damaging from ice crystals formation.&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="223" LastEditDate="2012-02-27T21:50:59.890" LastActivityDate="2012-02-27T21:50:59.890" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1226" PostTypeId="2" ParentId="1224" CreationDate="2012-02-27T20:42:01.170" Score="8" Body="&lt;p&gt;Your teacher is indeed correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the first round you would get two identical molecules of the dsDNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the second round you would get 3 identical molecules and one molecular with an &lt;code&gt;A&lt;/code&gt; substituted for a &lt;code&gt;G&lt;/code&gt; in one of the strands.  ie.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No error (3 of the 4 molecules):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;------G-------&#xA;------C-------&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;One mismatch (1 of the 4 molecules):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;------A-------&#xA;------C-------&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So there are a total of 8 strands of DNA after the second round and one of those strands has the mismatch.  &lt;code&gt;1 / 8&lt;/code&gt; = 0.125 = 12.5%&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In round 3 you would have 8 dsDNA molecules and only one of those 8 dsDNA molecules would have the mismatch.&lt;/p&gt;&#xA;" OwnerUserId="12" LastActivityDate="2012-02-27T20:42:01.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1227" PostTypeId="2" ParentId="1224" CreationDate="2012-02-27T21:28:24.473" Score="7" Body="&lt;p&gt;I will format it to .ppt as soon as I have more time! If something is not readable, please let me know!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have to point out several things:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The fraction of incorrect DNA molecules does not depend on the number of cycles (as long as the number of cycles is higher than 2). &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There is one exception: if the mutation occurs outside of the region to be amplified (for example at the 4th molecule, downstream of the region of interest), the total number of wrong DNA molecules will be 0.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/B1EfJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-02-28T18:47:22.753" LastActivityDate="2012-02-28T18:47:22.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1228" PostTypeId="1" AcceptedAnswerId="1231" CreationDate="2012-02-27T22:27:41.127" Score="15" ViewCount="9715" Body="&lt;p&gt;I am working with an Arabidopsis mutant with an F-box protein knocked out. It has been shown that F-box proteins targets must first be phosphorylated (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867400804031&quot;&gt;Skowrya et al., 1997&lt;/a&gt;). I have heard of phosphorylation sites, but I can't find out whether every protein has them. Can any protein be phosphorylated?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867400804031&quot;&gt;Skowyra, D., Craig, K.L., Tyers, M., Elledge, S.J. &amp;amp; Harper, J.W. (1997) F-Box Proteins Are Receptors that Recruit Phosphorylated Substrates to the SCF Ubiquitin-Ligase Complex. &lt;em&gt;Cell&lt;/em&gt;. &lt;strong&gt;91&lt;/strong&gt; (2), 209–219.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-11-26T01:02:54.017" Title="Can any protein be phosphorylated?" Tags="&lt;proteins&gt;" AnswerCount="5" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1230" PostTypeId="2" ParentId="1228" CreationDate="2012-02-28T00:04:10.347" Score="7" Body="&lt;p&gt;Phosphorylation requires exposed serine, threonine, tyrosine, or histidine residues (in eukaryotes).  This is because the transfer of phosphate groups to proteins is mediated by a class of proteins called kinases.  Kinases can have broad or specific activity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This review ought to have most of the answers to your questions :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cell.com/abstract/S0092-8674(06)01274-8&quot;&gt;http://www.cell.com/abstract/S0092-8674(06)01274-8&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="184" LastActivityDate="2012-02-28T00:04:10.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1231" PostTypeId="2" ParentId="1228" CreationDate="2012-02-28T00:07:54.570" Score="15" Body="&lt;p&gt;Phosphorylation can occur on specific amino acids only, what you have called phosporylation sites. These amino acids are Ser, Tyr, Asp, Thr and His. In theory any of these amino acids may be phosphorylated, but in reality it may not actually occur for a number of reasons. Some of these are because of the change in overall charge of the protein which can influence the 3D conformation, or the amino acids are not accessible to specific kinases, etc. If you ask for the purposes of doing a Western blot, then the antibody specification sheet should indicate whether a phosphorylated form exists and there should be a reference to the literature describing this modification.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-02-28T00:07:54.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1232" PostTypeId="2" ParentId="1220" CreationDate="2012-02-28T00:39:19.117" Score="5" Body="&lt;p&gt;The answers already posted about glycerol being a cryoprotectant and ice crystals are correct. The other thing to consider is that enzymes still retain some activity at -20°C and though the reaction rate is slower, the cells will degrade until they are no longer viable. I always store glycerol stocks of bacteria at -80°C.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many common E. Coli strains commercially used for cloning are not protease-free and these are the enzymes that are responsible for cellular degradation.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="69" LastEditDate="2012-02-28T14:47:12.207" LastActivityDate="2012-02-28T14:47:12.207" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1233" PostTypeId="2" ParentId="1220" CreationDate="2012-02-28T01:18:32.967" Score="10" Body="&lt;p&gt;Gergana covered the &quot;why&quot; part of your question. +1&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If all you have at the moment is a -20°C and mostly what you want to store is &lt;em&gt;E. coli&lt;/em&gt; harboring plasmids, I'd recommend preparing plasmid DNA and storing that at -20°C. The DNA will stay stable in the medium term, and you can re-transform into &lt;em&gt;E. coli&lt;/em&gt; once you've got your -80°C freezer up and running. And ideally you want both DNA stocks and bacterial stocks on hand - you never know when a freezer will go down. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For your untransformed strains, you could make agar stabs or plates to store at 4°C. I would re-streak them every 1-2 weeks, grow overnight at 37°C, and then put them back in the fridge. &lt;/p&gt;&#xA;" OwnerUserId="204" LastActivityDate="2012-02-28T01:18:32.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1234" PostTypeId="2" ParentId="1167" CreationDate="2012-02-28T01:19:31.943" Score="6" Body="&lt;p&gt;Not sure why Larry Parnell was down-voted, he was not technically wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Crystal structures of the most popular restriction enzymes are already known and can easily be found the Protein Data Bank or Wikipedia for graphical reference. Any stretch of double-stranded DNA makes a complete 360 rotation (about it's helical axis) in 10-10.5 base pairs. A 180 degree rotation would then be half of that ~5 bases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A palindrome is not strictly necessary for a restriction enzyme site, but exploiting them has its advantages. Firstly, synthesizing one subunit of the enzyme requires half the occupied space of the genome, therefore translation is more efficient (2 products from half the instruction set).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some restriction enzymes take advantage of rotational symmetry, such as EcoRI and EcoRII (both odd and even palindromic enzymes). They recognize the same GAA (in the case of EcoRI) or NNGG (in the case of EcoRII), coming from each of the two DNA strands. For notation purposes we write the recognition site of the positive strand only (since the DNA code is symmetrical). Asymmetrical recognition sites are explained by enzymes binding to DNA as heterodimers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;New England Biolabs has a very good review of the kinds of restriction enzymes and the variations in their behaviour. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/overview.asp#.T0wqHYcgerY&quot;&gt;http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/overview.asp#.T0wqHYcgerY&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To sum up, palindromes are often, but not necessarily, comprised of even numbers of bases (domains bind to 2n bases). Many enzyme recognition sites are palindromic in the literal sense (CATTAC) or biological sense (GAATTC) because there is an axis of symmetry that is used. Palindromic sequences are more commonly used because enzymes are composed of homodimers.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-02-28T01:19:31.943" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1235" PostTypeId="2" ParentId="1176" CreationDate="2012-02-28T01:30:23.310" Score="2" Body="&lt;p&gt;One way to learn more about how your protein is being processed/degraded is to add two different tags on either end of your protein. Express your protein, then blot with the two antibodies for your tags. The most likely scenario here is that one end or another is being cleaved and then degraded - you'll be able to tell which end by what tag epitope remains. And since you'll know the approximate size, you can narrow down the region where the processing occurs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Small tags such as HA, cMyc, Flag or 6xHis work well because they are less likely to be cleaved off themselves. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only way to know for certain how and where your protein is being truncated is empirically: either by N-terminal sequencing of the fragment(s) by mass spec or by mutating the putative processing sites and testing the expression again. &lt;/p&gt;&#xA;" OwnerUserId="204" LastEditorUserId="204" LastEditDate="2012-02-28T01:39:09.977" LastActivityDate="2012-02-28T01:39:09.977" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1236" PostTypeId="2" ParentId="1198" CreationDate="2012-02-28T01:58:10.610" Score="2" Body="&lt;p&gt;Good questions. I don't think that LTP has been (or will be) shown to be THE mechanism for long term memory. It is one of many mechanisms, all with different time courses, that contribute to the modification of synaptic efficiencies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One mechanism not mentioned much anymore, but which I feel is absolutely crucial, is dendritic spine growth. Spines are malleable and formation/destruction of spines is probably very related to long term memory. But as always, the full picture is going to be a combination of mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a paper to have a look at: &lt;a href=&quot;http://dx.doi.org/10.1038/19978&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Engert F, Bonhoeffer T&lt;/strong&gt;. 1999. Dendritic spine changes associated with hippocampal long-term synaptic plasticity. Nature 399: 66–70.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="510" LastEditorUserId="836" LastEditDate="2012-09-14T20:19:47.290" LastActivityDate="2012-09-14T20:19:47.290" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1237" PostTypeId="2" ParentId="973" CreationDate="2012-02-28T02:01:14.457" Score="8" Body="&lt;p&gt;I've found that extracted RNA using commercial kits has stayed stable for many years at -80 C. I would certainly aliquot it before freezing however as RNA is particularly sensitive to freeze-thaw cleavage.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-02-28T02:01:14.457" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1238" PostTypeId="2" ParentId="1176" CreationDate="2012-02-28T02:18:36.993" Score="4" Body="&lt;p&gt;LC-MS is certainly quantitative and will give you a definitive answer, but it is costly and requires access to such a machine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I presume you're analyzing your protein based on western blotting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first thing you should always do is verify your DNA sequence is coding for the protein product you want. Once you're sure of this, the western blot will give you an indication as to where your protein is (approximately) being cleaved. Say you protein has a predicted size of 40 kDa and you see a band at 20 kDa, then your cleavage is somewhere in the middle of your sequence. There are a TON of proteases that could be potentially cleaving your peptide and you need to have a hypothesis as to what that could be. Your peptide could be cleaved by an endopeptidase (cutting within), or a carboxypeptidase (C-terminal cleavage) or an aminopeptidase (N-termainal cleavage). To go back to the 20/40 kDa example, it could be your peptide was cleaved N-terminally o C-terminally down to a size of 20 kDa, or that it was literally cleaved in the middle by an endopeptidase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something you may consider is the use of a general protease inhibitor cocktail (Roche makes a really good tablet product called Complete and Complete mini tab). These mixes have a bunch of general protease inhibitors which will stop most cleavage events. If you still see cleavage after using an inhibitor cocktail, you can reasonably expect that you are not inhibiting the protease with the tablet (thus narrowing down your search) and then you can better comb through Expasy's PepCutter data. You should also do a literature search to see what has been reported about your peptide or motif.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-02-28T02:18:36.993" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1239" PostTypeId="2" ParentId="1214" CreationDate="2012-02-28T03:12:18.710" Score="5" Body="&lt;p&gt;For any kind of frozen cell stock (for cell culture or bacteria) we routinely use freezing vials similar to these: &lt;a href=&quot;http://www.sigmaaldrich.com/catalog/ProductDetail.do?D7=0&amp;amp;N5=SEARCH_CONCAT_PNO%7CBRAND_KEY&amp;amp;N4=V9255%7CSIGMA&amp;amp;N25=0&amp;amp;QS=ON&amp;amp;F=SPEC&quot;&gt;http://www.sigmaaldrich.com/catalog/ProductDetail.do?D7=0&amp;amp;N5=SEARCH_CONCAT_PNO%7CBRAND_KEY&amp;amp;N4=V9255%7CSIGMA&amp;amp;N25=0&amp;amp;QS=ON&amp;amp;F=SPEC&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These tubes are internally threaded with a rubber grommet to seal the lid and make the tube air and water tight. I suspect the air tight seal prevents condensation from entering the tube and freezing within the tube, but I've never had a problem with either choice of tube.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The tubes don't really matter at -80 C for a glycerol stab. Freezing cells in liquid nitrogen on the other hand has a huge impact when storing in liquid nitrogen. Some tubes are meant to be stored in the liquid versus the vapour phase of nitrogen and not matching the tube to it's intended storage condition can result in explosion of the tube.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-02-28T03:12:18.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1240" PostTypeId="2" ParentId="623" CreationDate="2012-02-28T04:50:50.243" Score="28" Body="&lt;p&gt;This is not really a biological answer, but a psychological one:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One important fact to consider is that the perception of time is essentially a recollection of past experience, rather than perception of the present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Researchers who study autobiographical memory have suggested that part of this effect may be explained by the number of recallable memories during a particular time period. During one's adolescence, one typically has a large number of salient memories, due to the distinctness of events. People often make new friends, move frequently, attend different schools, and have several jobs. As each of these memories is unique, recollection of these (many) memories gives the impression that the time span was large.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In contrast, older adults have fewer unique experiences. They tend to work a single job, and live in a single place, and have set routines which they may follow for years. For this reason, memories are less distinct, and are often blurred together or consolidated. Upon recollection, it seems like time went by quickly because we can't remember what actually happened.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, it can be considered a special case of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Availability_heuristic&quot; rel=&quot;nofollow noreferrer&quot;&gt;availability heuristic&lt;/a&gt;: people judge a time span to be longer in which there are more salient/unique events.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incidentally, (and to at least &lt;em&gt;mention&lt;/em&gt; biology), episodic memory has been shown to be neurally distinct from semantic memory in the brain. In particular, a &lt;a href=&quot;http://en.wikipedia.org/wiki/Double_dissociation&quot; rel=&quot;nofollow noreferrer&quot;&gt;double dissociation&lt;/a&gt; has been shown for amnesics who suffer from semantic or episodic memory, but not both.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My apologies for the lack of citations, but a good bit about autobiographical memories can be found in:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1841695408&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eysenck, M.W., &amp;amp; Keane, M.T. (2010). Cognitive Psychology: A&#xA;  Student's Handbook.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You may also be interested in some responses or references to a related question on the Cognitive Science StackExchange:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://cogsci.stackexchange.com/q/129/55&quot;&gt;Perception of time as a function of age&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="562" LastEditorUserId="-1" LastEditDate="2017-04-13T12:56:15.910" LastActivityDate="2015-09-21T15:10:31.750" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1241" PostTypeId="2" ParentId="1228" CreationDate="2012-02-28T12:50:44.780" Score="9" Body="&lt;p&gt;One important thing is missing in the other answers: not only phosphorylation will happen only at selected aminoacids, but it will not happen at all of those.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, not all of the Ser/Thr/Tyr of a protein can be phosphorylated because they could be structurally unaccessible to protein kinase and because they need to be in a specific motif in order to be phosphorylated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.hprd.org/index_html&quot;&gt;Human Protein Reference Database&lt;/a&gt;, for instance, lists the phosphorylation motifs for many &lt;a href=&quot;http://www.hprd.org/tyrosine_motifs&quot;&gt;Tyr&lt;/a&gt; and &lt;a href=&quot;http://www.hprd.org/serine_motifs&quot;&gt;Ser/Thr&lt;/a&gt; kinases.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2012-02-28T16:07:28.750" LastActivityDate="2012-02-28T16:07:28.750" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1242" PostTypeId="1" CreationDate="2012-02-28T16:10:58.377" Score="30" ViewCount="4528" Body="&lt;p&gt;What is the lowest pressure at which plants can survive? How the plants behave in a Martian-type atmosphere? Is there any plant that can survive such atmosphere?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can a lichen grow at Martian pressure?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="81" LastEditDate="2012-02-29T11:37:44.337" LastActivityDate="2019-12-09T14:34:43.180" Title="What is the lowest pressure at which plants can survive?" Tags="&lt;botany&gt;&lt;astrobiology&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1243" PostTypeId="1" AcceptedAnswerId="1550" CreationDate="2012-02-28T19:29:34.047" Score="7" ViewCount="1696" Body="&lt;p&gt;Just a random question, would a sharp object pierce your muscle more(stabbed with the same amount of force) when the muscle is flexed or when relaxed?&lt;/p&gt;&#xA;" OwnerUserId="565" LastActivityDate="2012-03-24T12:06:45.393" Title="Stabbing muscles when flexed and when relaxed" Tags="&lt;muscles&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1244" PostTypeId="1" AcceptedAnswerId="1251" CreationDate="2012-02-28T19:34:34.927" Score="8" ViewCount="1317" Body="&lt;p&gt;Spider silk is pretty darn strong and all sorts of comparisons are made to steel. I'm more curious about the various moduli of spider silk and how it compares to other materials. What is the Young's modulus of spider silk? What is the bulk modulus of spider silk? What is the shear modulus of spider silk? In general how do those moduli describe the material properties of spider.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A simpler way to ask the question, what does it mean when it is said that spider silk is strong?&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="3545" LastEditDate="2013-05-12T14:28:41.827" LastActivityDate="2013-05-12T14:28:41.827" Title="How strong is spider silk?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1245" PostTypeId="1" AcceptedAnswerId="2279" CreationDate="2012-02-28T19:39:38.540" Score="8" ViewCount="4110" Body="&lt;p&gt;Considering that I have a diffraction pattern of a crystal, how would I calculate the resolution of a structure in Angstroms? How does that value differ from the information that I would get from the beta-factor?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm aware that the resolution can be calculated by Bragg's law but how does that provide details for the entire structure?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-05-16T03:36:17.973" Title="How does one calculate the resolution of a crystal structure?" Tags="&lt;structural-biology&gt;&lt;xray-crystallography&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1246" PostTypeId="2" ParentId="1221" CreationDate="2012-02-28T20:32:56.590" Score="3" Body="&lt;p&gt;If your question is with respect to a eukaryotic cell, the di-sulfide bridge/bond is formed in the rough endoplasmic reticulum which is an oxidative environment (unlike most other organelles which are reductive). This paper may be of relevance to you:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cell.com/trends/cell-biology/abstract/S0962-8924%2800%2901745-1&quot; rel=&quot;nofollow&quot;&gt;Pathways for protein disulphide bond formation&lt;/a&gt; - Frand et al, Trends Cell Biol. 2000 May;10(5):203-10.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="115" LastEditDate="2012-03-02T16:41:23.123" LastActivityDate="2012-03-02T16:41:23.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1247" PostTypeId="1" AcceptedAnswerId="1307" CreationDate="2012-02-28T20:39:42.457" Score="9" ViewCount="139" Body="&lt;p&gt;I'm measuring binding constants my system and I appreciate the usual methods of using replicates to measure standard errors and using those errors to calculate propagation of error. I'm curious if bootstrapping is a reasonable alternative to calculate uncertainty?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-03-04T03:51:37.467" Title="Is bootstrapping an acceptable way to determine standard error for binding constants?" Tags="&lt;biostatistics&gt;&lt;dissociation-constant&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ClosedDate="2015-01-23T19:10:07.317" ContentLicense="CC BY-SA 3.0" />
  <row Id="1248" PostTypeId="2" ParentId="1228" CreationDate="2012-02-28T21:33:13.847" Score="5" Body="&lt;p&gt;I like Nico's response best +1. I did find an interesting &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19751195&quot;&gt;review&lt;/a&gt; on phosphoarginine and phospholysine - the list of possible phosphorylation sites grows. Not only is it the spatial context of the amino acid to be (or not) phosphorylated, as Nico writes and Leonardo implies, but also the temporal. Are the target protein and protein kinase co-expressed? If you're looking at specific tissues (root, flower, leaf) and the kinase in question is only produced in seedlings, maybe that potential phosphorylation won't really occur.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-02-28T21:33:13.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1249" PostTypeId="1" CreationDate="2012-02-28T22:27:33.107" Score="6" ViewCount="147" Body="&lt;p&gt;I'm looking through the literature on the topic. It seems like hydrophilic PVDF membranes are ideal for low-protein binding but it also sounds like Regenerated Cellulose is an appropriate substitution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at one resource (http://www.zellnet.com/elispotplatescolumn/) &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When PVDF filter plates were introduced, some investigators chose to use PVDF plates and some continued to use NC.  The reasons for choosing one plate (membrane) over the other are highly varied and won’t be addressed in detail here.  The fact that some laboratories and individual researchers feel strongly that one membrane is superior to the other runs contrary to the large body of Western blotting experience:  Despite some clear-cut differences in how each of the membranes can be used, there is essentially no reported difference in terms of detection sensitivity or signal to noise on NC versus PVDF in the Western Blotting application.  This having been said, it is clear is that the two membranes and their properties are quite different.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The assay that I am looking at in particular is protein/nanoparticle binding to mammalian cells. I am looking for a balance that will enable me to remove free protein without fouling the membrane and/or killing my cells.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-02-28T22:59:24.547" LastActivityDate="2012-08-22T07:00:47.623" Title="Ideal low-protein binding membranes" Tags="&lt;protein-binding&gt;&lt;assay-development&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1251" PostTypeId="2" ParentId="1244" CreationDate="2012-02-28T22:55:51.733" Score="5" Body="&lt;p&gt;Wikipedia has a remarkably well-cited article on the subject of silks and their various biological isoforms and &lt;a href=&quot;http://en.wikipedia.org/wiki/Spider_silk#Properties&quot; rel=&quot;nofollow&quot;&gt;mechanical properties&lt;/a&gt;. With respect to tensile strength, spider's silk is as tough as high-grade steel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Explcitly, dragline silk was measured &lt;a href=&quot;http://dx.doi.org/10.1002/app.2072&quot; rel=&quot;nofollow&quot;&gt;by Pérez-Rigueiro &lt;em&gt;at al.&lt;/em&gt;&lt;/a&gt; to be 600 ± 50 MPa with a comparison to silkworm silk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1002/app.2072&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Pérez-Rigueiro J, Elices M, Llorca J, Viney C&lt;/strong&gt;. 2001. Tensile properties ofArgiope trifasciata drag line silk obtained from the spider’s web. Journal of Applied Polymer Science 82: 2245–2251&lt;/a&gt; [&lt;a href=&quot;http://www.mater.upm.es/Directorio/PDI/CU/Llorca_archivos/Argiope.pdf&quot; rel=&quot;nofollow&quot;&gt;pdf&lt;/a&gt;]&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="836" LastEditDate="2012-09-12T18:08:21.653" LastActivityDate="2012-09-12T18:08:21.653" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="1252" PostTypeId="2" ParentId="6" CreationDate="2012-02-28T23:30:40.737" Score="1" Body="&lt;p&gt;If your aim is to figure out which nucleosides are specifically recognized by the protein then once you narrow down the sequence with one of the above methods, you would have to perform sequential rounds of mutagenesis.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-02-28T23:30:40.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1253" PostTypeId="2" ParentId="175" CreationDate="2012-02-29T00:30:38.717" Score="2" Body="&lt;p&gt;Searching literature to see what the published protocols were is the best bet. I found a simple document for INS-1 cells &lt;a href=&quot;http://bcell.org/Tissue_culture_protocol_for_INS.htm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. There is also &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10868964&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; describing the isolation of an Ins-1-derived cell line 832/13 which my lab (though not me personally) have experience with. Cells should only be sub-cultured when nearly or fully confluent. With Ins-1 cells that would be a sub-culture ratio of 1:4 to 1:8 and will take 2-3 days. Something to note is that Ins-1 cells are poorly adherent to tissue culture plastic. That's a normal part of their characterization. I remember lab members having to take special precautions with respect to media ingredients to prevent them from detaching, as well as really delicately adding media to the dishes otherwise the force from pipetting too quickly will dislodge many cells and explain why your cells are washing away.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-02-29T00:30:38.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1254" PostTypeId="1" AcceptedAnswerId="1255" CreationDate="2012-02-29T00:43:26.307" Score="10" ViewCount="261" Body="&lt;p&gt;I'm looking to generation sequential deletions from a gene of interest. The total size of this region is 8 amino acids. I'm trying to determine which portion of this region is necessary within the gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, if this is my sequence:&#xA;&lt;br /&gt;&#xA;ABCDEFGH&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to generate:&#xA;&lt;br /&gt;&#xA;BCDEFGH, CDEFGH, DEFGH, and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the least expensive way to do this (by minimizing primer use, enzyme use, etc). I already have this gene sub-cloned into an expression vector.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-02-29T21:09:17.580" Title="What is the least costly method to generate sequential amino acid deletions?" Tags="&lt;molecular-biology&gt;&lt;pcr&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1255" PostTypeId="2" ParentId="1254" CreationDate="2012-02-29T07:28:04.940" Score="7" Body="&lt;p&gt;While it isn't the cheapest, it is certainly the fastest and simplest. I would quikchange out the amino acid. This would require no subcloning and only require &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;two ~25 nt primers ($10)&lt;/li&gt;&#xA;&lt;li&gt;1 shot of pfu (~$0.25)&lt;/li&gt;&#xA;&lt;li&gt;1 shot of DPNI ($0.05)&lt;/li&gt;&#xA;&lt;li&gt;competent cells (~$5)&lt;/li&gt;&#xA;&lt;li&gt;sequencing to confirm (~$4-6)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Overall, probably &gt;$20 a mutant all in 2-3 days of waiting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(edit) I'm going with quikchange rather than OE-PCR simply because it removes the cloning steps. You will potentially need to screen more colonies with conventional cloning vs. quikchange.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-02-29T20:42:07.237" LastActivityDate="2012-02-29T20:42:07.237" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="1256" PostTypeId="2" ParentId="1242" CreationDate="2012-02-29T11:31:50.820" Score="22" Body="&lt;p&gt;I like your question!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Low surface pressure on Mars (averaging 600 Pa or about 1/170 of Earth's at sea level) is only one difficulty that an organism would have to contend with. In addition, mean surface temperatures are ~210 K (- 63 °C), the surface ultraviolet flux is extremely high (no ozone layer) and an aridity comparable to the Atacama desert. On the plus side, a 95% CO&lt;sub&gt;2&lt;/sub&gt; atmosphere might promote photosynthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, higher plants are extremely unlikely to prosper on Mars. Purely in terms of pressure, &lt;a href=&quot;http://science.nasa.gov/science-news/science-at-nasa/2004/25feb_greenhouses/&quot; rel=&quot;noreferrer&quot;&gt;experiments suggest&lt;/a&gt; that at 1/10 Earth atmospheric pressure vascular plant transpiration increases significantly. So much so that they enter into a drought response which often leads to plant death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, lichens may be another matter. These are often adapted to low precipitation/pressure environments such as high mountains. Indeed, this &lt;a href=&quot;http://online.liebertpub.com/doi/abs/10.1089/ast.2009.0362&quot; rel=&quot;noreferrer&quot;&gt;article&lt;/a&gt; addresses exactly your question (sadly it is not open access). The authors suggest that the lichen &lt;a href=&quot;https://en.wikipedia.org/wiki/Xanthoria_elegans&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Xanthoria elegans&lt;/em&gt;&lt;/a&gt; experiences &lt;strong&gt;no loss&lt;/strong&gt; in vitality after 22 days exposure to laboratory Mars-like conditions (low pressure, low temperature etc.)!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having skimmed this article I am frankly amazed (and slightly dubious) at the result. However, it should be noted that they only ran the experiment for 22 days, applied no ionising radiation (to simulate the high UV flux) and make little mention of the precise metabolic state of the lichen. If it has entered into cryptobiosis (cessation of metabolic processes) then it can't exactly be regarded as prospering.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;de Vera et al., 2010, &lt;em&gt;Astrobiology&lt;/em&gt;, 10, 2, &lt;em&gt;Survival Potential and Photosynthetic Activity of Lichens Under Mars-Like Conditions : A Laboratory Study&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="81" LastEditorUserId="6194" LastEditDate="2017-12-23T17:38:57.360" LastActivityDate="2017-12-23T17:38:57.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1257" PostTypeId="1" CreationDate="2012-02-29T12:21:35.203" Score="6" ViewCount="677" Body="&lt;p&gt;I am doing a project on expression of GFAP in the zebrafish retina. GFAP is a marker for glial cells. &#xA;I have found that the glial cells are more abundant the closer they are to the optic nerve at the middle of the eye. This may just be because the cells are more tightly compacted here than at the edges of the eye... &#xA;But I am wondering if it may have something to do with the glial cells being involved with neuornal processes, and the optic nerve being the transmitter of signals from the eye to the brain? &lt;/p&gt;&#xA;" OwnerUserId="568" LastActivityDate="2012-09-12T18:07:06.463" Title="Why do glial cells of the retina become more abundant the closer they are to the optic nerve?" Tags="&lt;eyes&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1258" PostTypeId="2" ParentId="1254" CreationDate="2012-02-29T19:47:09.413" Score="8" Body="&lt;p&gt;Deletions may make sense if you are analyzing the N-terminus or C-terminus of a protein. If you are looking at an internal region however, keep in mind that the more AAs you delete, the more likely you are to disrupt the overall protein structure. If you delete any random selection of 8 AAs within a protein, there's a chance you'll knock out activity by changing the protein fold or stability. That's not useful information. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question is usually first addressed by alanine scanning - sequentially or additively changing amino acids to alanine. This is much more informative than deletions. Even better, you can choose to replace wild-type AAs with other AAs of similar size but differing charge or hydrophobicity. Then you are most likely to change the function of a region without changing the structure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The quickchange kit works great, but if &lt;em&gt;cost is an issue&lt;/em&gt; you can do whole plasmid mutagenesis PCR with your own reagents. And make your own competent cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my experience though, whole plasmid PCR can be tricky - if it doesn't work the first time it can be difficult to troubleshoot. If &lt;em&gt;time is an issue&lt;/em&gt;, I'd recommend doing overlap extension PCR with the same mutagenic primers, plus one set of amplification primers at the 5' and 3' end of your gene. Make a large batch of digested vector, test as a negative control, and use it for ligation of all of your different inserts.&lt;/p&gt;&#xA;" OwnerUserId="204" LastEditorUserId="204" LastEditDate="2012-02-29T21:09:17.580" LastActivityDate="2012-02-29T21:09:17.580" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1259" PostTypeId="1" AcceptedAnswerId="1260" CreationDate="2012-02-29T20:42:55.413" Score="5" ViewCount="230" Body="&lt;p&gt;I have a relatively simply gene regulatory network I would like to visualize, complete with the common arrow and bar symbols used to show, respectively, which genes enhance or repress with other genes. Is there a way to typeset a gene regulatory network using something like LaTeX or Graphviz? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For very simple networks, I guess something like Photoshop or Illustrator would probably be the quickest solution, but these programs become very tedious as the size of the network grows even a little bit. What do people typically use for this type of task?&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-03-01T09:56:15.920" Title="How to typeset gene regulatory networks" Tags="&lt;network&gt;&lt;visualization&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1260" PostTypeId="2" ParentId="1259" CreationDate="2012-02-29T22:15:36.503" Score="7" Body="&lt;p&gt;If you have simple 1:1 connections or can list your data in that manner, you can try Cytoscape (freely available). There are numerous plug-ins to customize what you have in mind in terms of visualization.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-02-29T22:15:36.503" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1261" PostTypeId="2" ParentId="1208" CreationDate="2012-03-01T02:24:46.677" Score="5" Body="&lt;p&gt;There are a couple key words in this question - anonymous and teaching. Yes, NCBI is a source for sequence data, but it is not anonymous (it is annotated, which means a student could also find it and copy/paste that annotation without doing the actual analysis). Notice, I am not assuming that the request is for human data. Now, if anonymous human data are needed, most available sequence data are anonymous but there remains that annotation issue: If it is annotated already, what will they learn?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good alternate source for some human genome data would be from Complete Genomics. They have released anonymized (de-identified) data for at least 69 subjects. The question asks about 1000 sequences, but how large? This is an important consideration. Other details are also lacking in the question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another source may be the 1000 Genomes data, also human. If you're interested in plants, there are sequence data out there from ~98 different Arabidopsis thaliana accessions/cultivars/strains.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-03-01T02:35:33.010" LastActivityDate="2012-03-01T02:35:33.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1262" PostTypeId="2" ParentId="23" CreationDate="2012-03-01T02:33:01.813" Score="4" Body="&lt;p&gt;OK, so 2 responses, each concerning different protein segments of different types/functions/structures, but not an answer really getting to the heart of the question. Because of the homework tag, I am tempted not to reply - this is something the student should accomplish on his/her own. So, I'll give a general answer to start you thinking. Basically, such a value - be it 7 or 20 for TMs or 13 - is determined empirically.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-03-01T13:33:17.900" LastActivityDate="2012-03-01T13:33:17.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1263" PostTypeId="2" ParentId="1259" CreationDate="2012-03-01T09:56:15.920" Score="2" Body="&lt;p&gt;I haven't tried it, but this &lt;a href=&quot;https://stackoverflow.com/questions/2278030/improving-graphviz-layout&quot;&gt;StackOverflow answer&lt;/a&gt; suggests that you can import a GraphViz network into &lt;a href=&quot;http://www.omnigroup.com/products/omnigraffle/&quot; rel=&quot;nofollow noreferrer&quot;&gt;OmniGraffle&lt;/a&gt; (for Mac), which makes it very easy to produce a pretty network (much easier than Photoshop/Illustrator). &lt;/p&gt;&#xA;" OwnerUserId="112" LastEditorUserId="-1" LastEditDate="2017-05-23T12:35:01.883" LastActivityDate="2012-03-01T09:56:15.920" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1264" PostTypeId="1" AcceptedAnswerId="1292" CreationDate="2012-03-01T11:15:32.703" Score="7" ViewCount="83" Body="&lt;p&gt;I am investigating the strength of binding of a small peptide to a protein by isolating the bound version and subjecting it to collisions with gas molecules (CID mass spectrometry) to dissociate the complex.&#xA;When I plot the collision energy against the proportion of bound and unbound proteins I get a curve that looks like a K&lt;sub&gt;d&lt;/sub&gt; curve.  However, as the interaction isn't in equilibria (i.e. it is in the gas phase) calculating the K&lt;sub&gt;d&lt;/sub&gt; value wouldn't be correct. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So is there another value I could calculate to describe the strength of the interaction?&lt;/p&gt;&#xA;" OwnerUserId="571" LastEditorUserId="69" LastEditDate="2012-03-03T12:07:00.783" LastActivityDate="2012-03-03T15:09:44.537" Title="Is there a binding affinity metric for interactions not in equilibria?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;dissociation-constant&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1266" PostTypeId="1" CreationDate="2012-03-01T12:18:15.167" Score="9" ViewCount="222" Body="&lt;p&gt;Currently it is possible and not so expensive for a person to have his genome. This is useful in general for understanding how life works. But, in practice, how is this useful for the specific person at this point in time?&lt;/p&gt;&#xA;" OwnerUserId="572" LastEditorUserId="572" LastEditDate="2012-03-01T13:12:04.583" LastActivityDate="2012-03-02T18:08:57.867" Title="How is the sequenced genome of a person useful to him in practice, now?" Tags="&lt;genomics&gt;&lt;human-genome&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1267" PostTypeId="1" AcceptedAnswerId="1273" CreationDate="2012-03-01T13:24:31.640" Score="23" ViewCount="6196" Body="&lt;p&gt;I cut my eyebrow and it grows until reach a certain length. Hair can grow without limit.&#xA;Why can hair grow without limit while eyebrow cannot?&lt;/p&gt;&#xA;" OwnerUserId="573" LastEditorUserId="16866" LastEditDate="2017-01-03T15:52:45.300" LastActivityDate="2017-01-03T15:52:45.300" Title="Why can hair grow without limit while eyebrow cannot?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;human-physiology&gt;&lt;hair&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1268" PostTypeId="2" ParentId="1266" CreationDate="2012-03-01T13:26:11.593" Score="9" Body="&lt;p&gt;A human genome sequence can uncover large deletions and insertions in the genome and would give the genotypes of both common and private (rare to very rare) small polymorphisms (e.g. SNPs) and SSRs (simple sequence repeats). From this information, one can learn about some curiosity traits (say, sensing asparagus metabolites in the urine, slow or fast twitch muscles, curly vs not curly hair) and, more importantly, about disease risk. Ancestry and family relationships can also be learned as in, for example, a half-sibling relationship.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As many diseases are polygenic with numerous loci each making small contributions to the variance, it becomes very difficult to fully describe the level of increased or decreased risk. In other words, we don't yet know all the players and so assessing their contribution to risk of disease can't be done with complete confidence. To further compound this problem are both epistasis and gene-environment interactions. Epistasis is a gene-gene (gene-gene-gene, etc) interaction, such that genes A and B separately make no contribution to the phenotype (disease risk), but do so in combination - say in ab/ab individuals. A gene-environment interaction can be described as when an allele associates with increased risk only when an environmental factor (e.g., exercise, fat in the diet, sun exposure, oxygen tension (altitude), etc), passes a certain threshold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still, the most powerful predictor of disease risk, onset and progression is family history. A genome sequence approaches that history (half your genome is from your mother and half from your father, of course), but remains fairly uninterpretable in terms of complex traits. You may carry a couple variants posing increased risk for heart disease, but what about the other hundred or so loci that also make small contributions to this affliction? Sure, if we knew exactly what those other hundred were and how much they each contribute and if they interact with each other or the environment. An incomplete picture emerges.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With rare diseases and altered genomes (say in cancer compared to normal) great strides are being made to either identify the small number of defective genes (rare diseases) or the commandeered pathways exploited for uncontrolled growth (cancer). In this regard, much can be learned and will have quicker, but still measurable in years, applications to the clinic.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-03-01T13:26:11.593" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1269" PostTypeId="1" CreationDate="2012-03-01T14:34:29.917" Score="8" ViewCount="119" Body="&lt;p&gt;I need to find a decent source of data for concentration of ATP and calcium in the pancreatic acinar cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far all I can find is ATP or calcium 'levels' based on fluorescence , which are not accompanied by a value of concentration in moles/molar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to find this information in a specific book or website, to avoid trawling though vast amounts of literature?&lt;/p&gt;&#xA;" OwnerUserId="574" LastEditorDisplayName="user560" LastEditDate="2012-03-01T19:18:51.387" LastActivityDate="2014-11-11T13:49:53.297" Title="Pancretic Acinar Cell - ATP, calcium concentration data" Tags="&lt;cell-biology&gt;&lt;mitochondria&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1272" PostTypeId="1" CreationDate="2012-03-01T18:57:09.170" Score="5" ViewCount="524" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Growing-degree_day&quot; rel=&quot;nofollow&quot;&gt;From Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Growing degree days (GDD), also called growing degree units (GDUs), are a heuristic tool in phenology. GDD are a measure of heat accumulation used by horticulturists, gardeners, and farmers to predict plant and pest development rates such as the date that a flower will bloom or a crop reach maturity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;GDD is calculated as $\frac{T_{min}-T_{max}}{2}- T_{base}$ - so a quick check of the units would indicate that they are in the same units as T, i.e., degrees C. However, they are usually presented without units.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is this?&lt;/p&gt;&#xA;" OwnerUserId="222" LastEditorUserId="57" LastEditDate="2012-10-24T08:19:50.867" LastActivityDate="2012-10-24T08:19:50.867" Title="Why dont &quot;growing degree days&quot; have units of degrees Celsius (or do they)?" Tags="&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1273" PostTypeId="2" ParentId="1267" CreationDate="2012-03-01T19:44:54.083" Score="37" Body="&lt;p&gt;Hair actually does have a limit to its growth. All hair cycles between periods where it grows, and when a new stand appears, which pushes the older, long hair out. Hairs that are generally shorter, like eyebrows or arm hairs, have a shorter growth period before a new hair pushes the old one out. The hair on your head actually grows much faster than many other hairs as well, so with the longer cycle and the faster growth, it can grow to be much longer before being replaced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I remember hearing that for many women (the cycle does vary from individual to individual, which explains why some men can't grow beards while others look like ZZ Top) the growth cycle ends between the waist and butt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My speculation would be that hair on the head could grow for longer because there are more capillaries in the scalp, which might lead to more nutrients, higher cell turnover (like you see in dandruff), and hence more hair. That's just a guess, mind you.&lt;/p&gt;&#xA;" OwnerUserId="575" LastActivityDate="2012-03-01T19:44:54.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1274" PostTypeId="2" ParentId="1264" CreationDate="2012-03-01T21:27:01.023" Score="5" Body="&lt;p&gt;You should be looking at the interactions in terms of kinetics and not thermodynamics. k_on and k_off should do the trick.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-03-01T21:27:01.023" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1275" PostTypeId="2" ParentId="1257" CreationDate="2012-03-02T00:11:53.817" Score="2" Body="&lt;p&gt;Any particular glial cell you're noticing this with?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that Astrocytes modify Calcium concentrations in the synaptic cleft. Perhaps at places where there are more synapses, more Astrocytes must exist to regulate such thing? Here's an interesting paper on a possible role of Astrocytes on associative networks:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.antanitus.com/&quot; rel=&quot;nofollow&quot;&gt;http://www.antanitus.com/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="510" LastActivityDate="2012-03-02T00:11:53.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1276" PostTypeId="2" ParentId="1266" CreationDate="2012-03-02T00:45:31.347" Score="0" Body="&lt;p&gt;I assume some people would have their genome sequenced not so much for &quot;My family has a history of heart disease - what risk factors have I inherited?&quot; but for &quot;I have my genome on this DVD - isn't that neat?&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason I suspect that is that I've heard that there are services that allow Europeans to find out which of the &quot;Seven daughters of Eve&quot; they're from, which seems to be more about curiosity than medical information.&lt;/p&gt;&#xA;" OwnerUserId="576" LastActivityDate="2012-03-02T00:45:31.347" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1277" PostTypeId="2" ParentId="1272" CreationDate="2012-03-02T08:05:49.117" Score="6" Body="&lt;p&gt;Actually, the units are &lt;em&gt;°C days&lt;/em&gt;  &amp;nbsp;or &lt;em&gt;°F days&lt;/em&gt;. The units are mostly given in the typical name, Growing &lt;em&gt;Degree Days&lt;/em&gt; where which temperature unit is meant is understood from the context.  Much more important is knowing the base temperature (&quot;T_base&quot;) since this value can be different in different usages, even for the same type of organism. &lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2012-03-02T08:05:49.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1278" PostTypeId="1" AcceptedAnswerId="1285" CreationDate="2012-03-02T13:47:44.133" Score="9" ViewCount="2263" Body="&lt;p&gt;I'm researching the possible connection between the dream content and the activity of various organ or hormonal systems within the human body. I'm looking for information on biological cycles within the human body that occur on a 24 hour cycle and may influence the sleep cycle, dream content or the overall state of awareness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far I was able to find:&#xA;&lt;strong&gt;Adrenaline, cortisol, testesterone - circadian endogenous cycle.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;leptin, glucose, insuline  -  peak with awakening, decline with bedtime&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What else within the human body is functioning on a predictable 24 hour cycle?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for any information!&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="69" LastEditDate="2012-03-03T11:54:51.547" LastActivityDate="2012-03-03T11:54:51.547" Title="Which human body hormonal systems exhibit 24 hour diurnal cyclical activity?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1279" PostTypeId="1" AcceptedAnswerId="1880" CreationDate="2012-03-02T14:26:04.213" Score="21" ViewCount="1246" Body="&lt;p&gt;Recently, I reviewed the different levels of chromatin structure. The primary level is nucleosomes, where DNA is bound to histones, and has structural similarity to &quot;beads on a string.&quot; The secondary level is a 30nm fiber, and the tertiary level is formed by radially looping the fibers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've also been learning about the histone code and how different modifications to the core histones relate to transcriptional regulation. Are these modifications the primary regulation mechanism for chromatin structure? In other words, does chromatin assume the most compact structure possible until histone modifications are made to enable transcription? Or have other regulatory mechanisms unrelated to transcription been discovered and characterized?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="948" LastEditDate="2014-01-13T21:38:45.343" LastActivityDate="2014-01-13T21:38:45.343" Title="Regulation of chromatin structure" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;epigenetics&gt;&lt;histone&gt;&lt;chromatin&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1280" PostTypeId="1" AcceptedAnswerId="1287" CreationDate="2012-03-02T14:34:25.620" Score="14" ViewCount="546" Body="&lt;p&gt;Recently I've been studying the p53 tumor suppressor gene as a model for regulation of gene expression. It's amazing how many different post-translational modifications are known to regulate p53 activity, and how many different factors are involved in this regulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is postulated that there are between 20,000 and 30,000 genes in the human genome. Is there an estimate for the percentage of these genes whose primary function is related to regulation of gene expression?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="810" LastEditDate="2012-05-09T15:06:16.013" LastActivityDate="2012-05-09T15:06:16.013" Title="Percentage of genome devoted to regulating gene expression" Tags="&lt;gene-expression&gt;&lt;genomics&gt;&lt;gene-regulation&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1281" PostTypeId="1" AcceptedAnswerId="1286" CreationDate="2012-03-02T16:54:01.313" Score="6" ViewCount="645" Body="&lt;p&gt;In other words, what products synthesized by ribosomes are actual parts of ribosomes (if any)?   How are they involved in their own synthesis otherwise? What is the cycle/chain of products starting with the proteins synthesized by ribosomes and actually ending with the synthesis of a ribosome?&lt;/p&gt;&#xA;" OwnerUserId="578" LastActivityDate="2012-03-02T20:35:43.850" Title="How do ribosomes contribute to their own synthesis?" Tags="&lt;ribosome&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1282" PostTypeId="2" ParentId="1266" CreationDate="2012-03-02T18:08:57.867" Score="4" Body="&lt;p&gt;&lt;strong&gt;How is the genome sequence useful right now?&lt;/strong&gt; There are several tests out there that rely on identifying single mutations that will lead to diseases, or that are associated with bad response to medication. Having the entire genome sequenced allows identifying all of them at once, and is cheaper than doing these diagnostic tests one by one. Thus, sequencing the genome gives you information about whether to expect certain diseases, and a list of medication that you shouldn't take, sort of as an insurance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sequencing also allows you to learn about your ancestry, which may be of interest especially to people from countries with a long history of immigration, such as the US. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How is the genome sequence useful in the mid-term?&lt;/strong&gt; Many diseases (including many cancers) are not caused by single mutations, but rather buy a combination of genetic and environmental risk factors that exceed some threshold. Thus, the genome sequence only allows to tell whether a person has increased risk for certain diseases, but not whether they'll get it. By itself, this information is not very useful. However, it has recently been suggested that blanket screening for cancer may not be the best idea due to bad side-effects and cost associated with treatment of false positives (which you'll get if you screen a sufficient number of people). Here, the genome sequence may help to identify who should get screened.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How is the genome sequence useful in the long term?&lt;/strong&gt; The more genomes are sequenced, and the more phenotypes and diseases get associated with them, the better the predictions become, and the easier it will be for basic science to understand how mutations cause/influence disease. Thus, getting the genome sequenced now may be extremely useful and informative for the people who get their genome sequenced five years from now. &lt;/p&gt;&#xA;" OwnerUserId="34" LastActivityDate="2012-03-02T18:08:57.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1283" PostTypeId="2" ParentId="1280" CreationDate="2012-03-02T19:30:35.757" Score="7" Body="&lt;p&gt;Yes, look at FANTOM and their work. There are about 2000 transcription factors and co-factors in the human genome. These are proteins, of course. If you add a couple (or few?) thousand microRNAs and a few dozen anti-sense transcripts, although small in size, you inch that percentage upwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With some 70% of the human genome transcribed, by some estimates, one could argue that many of these non-coding RNAs (short, long, trans-spliced) act in some way to regulate the DNA to mRNA to protein process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I can send you those 2000 or so FANTOM TFs if you wish. Contact me by email.)&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-03-02T19:30:35.757" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1284" PostTypeId="2" ParentId="1206" CreationDate="2012-03-02T19:53:57.457" Score="2" Body="&lt;p&gt;It is a mnemonic of two words: discoidal + blastula = discoblastula.&#xA;So it suggests that cleavage is partial discoidal in birds.&#xA;Embryo forms disc. &#xA;Cells called blastodisc are on top of the yolk.&#xA;It seems that the formed disc is blastodisc.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-03-02T19:53:57.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1285" PostTypeId="2" ParentId="1278" CreationDate="2012-03-02T20:28:55.993" Score="5" Body="&lt;p&gt;The real answer is probably more than you want, but its easy to do better than the list above.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I took a look through GEO for human circadian expression data and surprisingly I only found 2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE2703&quot;&gt;GSE2703&lt;/a&gt; - the rhesus circadian expression experiment, they have shown 355 genes that are rhythmically expressed.  This is not a great experiment because they only looked over a single 24 hour period.  Its only the adrenal gland.  Nonetheless they found 355 genes which seemed to be circadian.  the table is supplemental data to the article,  listed below. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see a fibroblast growth factor receptor, some hydrocarbon nuclear receptor components, sterol regulatory factors, bone morphogenic protein 2, glutamate receptor, thrombonspondin receptor, ryanodine receptor 3 (what is that?) , lysophosphatidic acid G-protein-coupled receptor 2, purinergic receptor P2Y, G-protein coupled.  You might find more if you know what you are looking for. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&amp;amp;form=html&amp;amp;view=brief&amp;amp;acc=GSE1832&quot;&gt;other circadian study was on human muscle&lt;/a&gt;, which will no doubt give different answers.  I imagine circadian behavior is highly tissue dependent. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://mend.endojournals.org/content/20/5/1164.long&quot;&gt;Reference&lt;/a&gt;: Lemos DR, Downs JL, Urbanski HF. Twenty-four-hour rhythmic gene expression in the rhesus macaque adrenal gland. Mol Endocrinol 2006 May;20(5):1164-76&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-03-02T20:37:01.680" LastActivityDate="2012-03-02T20:37:01.680" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1286" PostTypeId="2" ParentId="1281" CreationDate="2012-03-02T20:35:43.850" Score="5" Body="&lt;p&gt;The most important parts of the ribosome are not made by other ribosomes - 5 rRNA (ribosomal RNA) of the ribosome actually do most of the direct work of creating the protein and are made by RNA polymerase ( a protein, but not the ribosome).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there are 92 ribosomal proteins, which as a rule bind to ribosomal RNA to support their structure and keep everything going.  These are all made by ribosomes.  They are thought to have appeared later in the evolution of the ribosome though I imagine that it would not be possible to constitute a working ribosome without each one of them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;these numbers are for the eukaryotic ribosome, the prokaryotic ribosome has 3 rRNA and 52 ribosomal protein components. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ribosome&quot;&gt;http://en.wikipedia.org/wiki/Ribosome&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-03-02T20:35:43.850" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1287" PostTypeId="2" ParentId="1280" CreationDate="2012-03-03T00:18:22.323" Score="9" Body="&lt;p&gt;Okay, I'll take this out of the comments and put in an answer for all of us to work on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To directly answer your question: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Is there an estimate for the percentage of these genes whose primary&#xA;  function is related to regulation of gene expression?&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It depends on how you define &quot;gene expression.&quot; And what cellular processes you want to include in that definition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Larry's answer is the usual standard response, especially for people (such as me, ha) that have spent significant time studying transcription factors. About 1% of human genes have DNA binding domains and are thought to be directly involved in regulating the transcription of genes into mRNA - these are &lt;strong&gt;transcription factors&lt;/strong&gt; (TFs). Closely related are &lt;strong&gt;cofactors&lt;/strong&gt;, which regulate expression by binding to TFs or RNA polymerase machinery, but not directly to DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regulation of gene expression could also include modifications at the chromatin level - here you would include &lt;strong&gt;chromatin remodelers&lt;/strong&gt;, &lt;strong&gt;histone acetylases&lt;/strong&gt;, &lt;strong&gt;deacetylases&lt;/strong&gt;, &lt;strong&gt;methylases&lt;/strong&gt; and the &lt;strong&gt;histones&lt;/strong&gt; themselves. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;mRNA transcripts can also be regulated by &lt;strong&gt;miRNAs&lt;/strong&gt;: post-transcriptional regulators that bind to complementary sequences on target mRNAs, which leads to translational repression or target degradation and gene silencing. So you would also include the proteins involved in this process, most notably the &lt;strong&gt;RNA-induced silencing complex&lt;/strong&gt;, which includes Dicer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also proteins involved in mRNA stabilization and turnover, which effects gene expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure if anyone has added up all of the genes above to determine an overall percentage of the genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you include in your definition of &quot;gene regulation&quot; post-transcriptional modification, folding chaperones, intra-cellular transport, extra-cellular and intra-cellular signaling, and so on - then Shigeta is right, you begin approaching 100%. In the most basic sense, &lt;em&gt;life itself is gene regulation&lt;/em&gt;. &lt;/p&gt;&#xA;" OwnerUserId="204" LastEditorUserId="204" LastEditDate="2012-03-03T06:54:47.640" LastActivityDate="2012-03-03T06:54:47.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1288" PostTypeId="2" ParentId="623" CreationDate="2012-03-03T03:08:11.133" Score="7" Body="&lt;p&gt;Maybe the passage of time is perceived as a function of heart rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Waiting 5 minutes for a turn on the swings is 300 seconds for a 2 year old and 300 seconds for a 40 year old.  But that same wait is &lt;a href=&quot;http://www.ehow.com/about_5479822_normal-pulse-rate-children.html&quot;&gt;575 heart beats for the kid&lt;/a&gt;, but only 300 heart beats for the adult.&lt;/p&gt;&#xA;" OwnerUserId="579" LastActivityDate="2012-03-03T03:08:11.133" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1289" PostTypeId="1" CreationDate="2012-03-03T07:11:56.370" Score="12" ViewCount="1400" Body="&lt;p&gt;For example, how are infections of antibiotic resistant strains of MRSA, Streptococcus, or Gonorrhea treated?&lt;/p&gt;&#xA;" OwnerUserId="580" LastEditorUserId="19521" LastEditDate="2016-05-07T13:46:37.817" LastActivityDate="2017-09-15T13:13:40.247" Title="How are antibiotic resistant bacterial infections treated?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;antibiotics&gt;&lt;epidemiology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1290" PostTypeId="1" AcceptedAnswerId="9205" CreationDate="2012-02-28T16:36:29.093" Score="9" ViewCount="547" Body="&lt;p&gt;The past winter (2011-2012) was warmer than usual. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trees are normally tapped in late February when the daily maximum temperature goes above freezing. However, assuming that there have been relatively few days with a maximum temperature below freezing, &lt;strong&gt;how would this affect the timing and quantity of sap flow&lt;/strong&gt;?&lt;/p&gt;&#xA;" OwnerUserId="222" OwnerDisplayName="David" LastEditorUserId="3952" LastEditDate="2013-08-24T07:28:19.587" LastActivityDate="2013-08-24T07:28:19.587" Title="How would a warm winter affect maple sap production?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;climate-change&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1292" PostTypeId="2" ParentId="1264" CreationDate="2012-03-03T15:09:44.537" Score="3" Body="&lt;p&gt;Bobthejoe was pointing in the right direction  kcat and Km - Michaelis Menton parameters are measured to look at the relative rates of an enzyme in non equilibrium state.  Basically kcat is 'how fast does the enzyme work with little or no product in solution'. Km is 'how strongly does the enzyme bind the substrates that it uses. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pearsonhighered.com/mathews/ch11/c11kkkk.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.pearsonhighered.com/mathews/ch11/c11kkkk.htm&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-03-03T15:09:44.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1293" PostTypeId="2" ParentId="1179" CreationDate="2012-03-03T15:36:59.483" Score="5" Body="&lt;p&gt;In humans, the amnion (amniotic sac) persists from the primitive amniotic cavity&lt;sup&gt;&lt;strong&gt;1&lt;/strong&gt;&lt;/sup&gt;.  One side of this is formed from the cytoblast (a prismatic epithelium) and the plasmodioblast.  Together these two layers are the ectoplacenta or chorion.  They are also referred to as Rauber's layer.  These replace the lining epithelium of the uterus, whereupon internal cells undergo atrophy to create the amniotic sac.&lt;sup&gt;&lt;strong&gt;2&lt;/strong&gt;&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other side of the amniotic sac is formed of the epiblast/ectoderm (internally) and the hypoblast (externally).  Within the epiblast the other layer is comprised of prismatic cells whereas the inner layer are flattened (the hypoblast/entoderm).  This double layer forms the bilaminar blastodermic membrane.&lt;sup&gt;&lt;strong&gt;2&lt;/strong&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd really reccomend that you borrow the referenced books from your university library as I found the diagrams much easier to understand than the text.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;1&lt;/strong&gt;&lt;/sup&gt; Gray, Henry. &quot;Embryology: Formation of Membranes.&quot; Ed. Robert Howden. Anatomy Descriptive and Surgical. Ed. T. P. Pick. 15th ed. London: Chancellor, 1994. 90. Print. &lt;em&gt;Colloquially Gray's Anatomy&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;2&lt;/strong&gt;&lt;/sup&gt; Gray, Henry. &quot;Embryology: The Ovum.&quot; Anatomy Descriptive and Surgical. Ed. T. P. Pick and Robert Howden. 15th ed. London: Chancellor, 1994. 82-83. Print. &lt;em&gt;Colloquially Gray's Anatomy&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-03-03T15:36:59.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1294" PostTypeId="1" CreationDate="2012-03-03T16:07:09.903" Score="19" ViewCount="5292" Body="&lt;p&gt;If I have a brown eye gene which encodes the protein that is responsible for the brown color and have a blue eye gene as well, what is the reason that my eye color is brown? How does one gene maintain dominance over the other?&lt;/p&gt;&#xA;" OwnerUserId="566" LastEditorUserId="9943" LastEditDate="2015-01-12T10:52:23.720" LastActivityDate="2019-04-22T14:31:50.120" Title="Why are some genes dominant over others? What is the mechanism behind it?" Tags="&lt;molecular-biology&gt;&lt;genetics&gt;" AnswerCount="6" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1295" PostTypeId="1" AcceptedAnswerId="1298" CreationDate="2012-03-03T16:20:11.697" Score="9" ViewCount="921" Body="&lt;p&gt;I'm doing sleep and dreams research and have developed an iPhone application to help me track my bedtime, rise time, sleep onset and also mark dreams. The app also monitors overall activity overnight as an Actigraph, recording periods of elevated motion and inactivity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I have a lot of sleep cycle data that I have trouble analyzing.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that circadian rhythm is at play with 90-110 minute sleep cycles ehxibited over the course of the night, each one is a progression of various sleep stages, from NREM to REM. REM is more likely to result in a dream reported if awakened during REM. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What I'm seeing is a bunch of orderly patterns, and a lot of chaotic behavior that I cannot explain.&lt;/strong&gt; Particularly the times of going to sleep and awakening, while dreams exhibit more orderly behavior, with dreams reported at similar times on subsequent days.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm also interested in any insight as to what's causing me to wake up at certain times and report dreams. What could be involved in this kind of behavior? I saw research about deuretic hormones not being suppressed for the night, causing the urge to urinate to awaken the dreamer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Right now I have 90 days of sleep onset and dream data that looks like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7SJaf.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/krSWp.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://luciddreamingapp.com/my-90-day-sleep-history/&quot; rel=&quot;noreferrer&quot;&gt;Complete 90 day sleep history&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;In this case, each black marker indicates the sleep onset time for&#xA;the night&lt;/li&gt;&#xA;&lt;li&gt;The orange marker indicates the time of getting out of bed&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The green markers are dreams that I report upon awakening from a&lt;br&gt;&#xA;dream, so dreams occur prior to the marker's location. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Each green&lt;br&gt;&#xA;    marker's brightness indicates more clear dream content remembered&#xA;    and    recorded.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;Cyan markers are lucid dreams, where I was aware&#xA;    that I was    dreaming within a dream.&lt;/li&gt;&#xA;&lt;li&gt;Cyan color of a marker&#xA;    indicates that I    could control the dream's content from within a&#xA;    dream.&lt;/li&gt;&#xA;&lt;li&gt;Red markers    are periods of insomnia.&lt;/li&gt;&#xA;&lt;li&gt;The cyan line is&#xA;    number of hours after    bedtime&lt;/li&gt;&#xA;&lt;li&gt;The purple line is sleep cycle&#xA;    approximation (90 minutes).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The data is stacked with each row being a day of data. You will notice that your eyes start to automatically seek patterns within the vertical arrangement of markers. Because each marker is a dream reported upon awakening, they roughly trace the sleep cycles over the course of the night. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested in learning what influences the desire to go to bed at a particular time?&#xA;What influences the getting out of bed times?&#xA;is there some sort of analysis I can perform to understand the pattern within the sleep cycles as it evolves over multiple nights? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any input is appreciated!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-03-03T21:41:57.587" Title="Human sleep cycles and dream times, what influences the timing and intensity? Sleep history included" Tags="&lt;human-biology&gt;&lt;sleep&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1296" PostTypeId="1" AcceptedAnswerId="1297" CreationDate="2012-03-03T16:23:14.673" Score="9" ViewCount="1919" Body="&lt;p&gt;I'm trying to understand if the timing of human bowel movements in the morning is associated with the circadian rhythm, and can thus be used to make predictions about the circadian rhythm. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What influences the timing of bowel movements? Is it the timing of meals, caffeine intake or is it a biologically programmed time?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-01-13T21:29:50.033" Title="What influences the timing of human bowel movements in the morning?" Tags="&lt;human-biology&gt;&lt;circadian-rhythms&gt;&lt;digestive-system&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1297" PostTypeId="2" ParentId="1296" CreationDate="2012-03-03T16:42:29.267" Score="9" Body="&lt;p&gt;The bowel movements are influenced by a lot of factors. For example, when you eat a meal it induces a movement in your large intestines, to defecate and clear up space for new food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, there is MMC, migrating motor complex, which is responsible for the bowel movements when you are fasting. It causes a flushing effect, which prevents bacteria to overproduce in intestines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the daily bowel movements are mainly influenced by the timing and content of the food that you eat. But as I said there are many other factors. The gastrointestinal system has a very complex nervous system. Even psychological factors can effect the bowel movements greatly, for example extreme physical pain may induce the symphatetic system and cause constipation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also caffeine may affect it, like many drugs do.&lt;/p&gt;&#xA;" OwnerUserId="566" LastEditorUserId="566" LastEditDate="2012-03-05T20:56:09.843" LastActivityDate="2012-03-05T20:56:09.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1298" PostTypeId="2" ParentId="1295" CreationDate="2012-03-03T17:06:07.390" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I'm interested in learning what influences the desire to go to bed at&#xA;  a particular time? What influences the getting out of bed times?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is the circadian rhythm. Circadian rhythm is mediated by the suprachiasmatic nucleus of hypothalamus, which gets afferent nerves from optic nerve. So, the circadian rhythm is mediated by light. Initiation of the NREM Stage 1 sleep is controlled by the lateral preoptic nucleus, which is another area in the hypothalamus, so it is mainly the absence of light which starts sleep.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I'm also interested in any insight as to what's causing me to wake up&#xA;  at certain times and report dreams.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Sleep is not equal to absence of consciousness, it is just an diminished state of consciousness. Sleep consist of mainly 4 stages, NREM-1, NREM-2, NREM-3 and REM. Every stage, the &quot;depth&quot; of sleep, or the level of the decrease in your consciousness changes. REM is the stage in which dreaming most frequently occurs, and also it is the sleep stage where your consciousness is highest, so you are more likely to awake because of the stimulus coming from the environment. &lt;/p&gt;&#xA;" OwnerUserId="566" LastEditorUserId="69" LastEditDate="2012-03-03T21:41:57.587" LastActivityDate="2012-03-03T21:41:57.587" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1299" PostTypeId="5" CreationDate="2012-03-03T21:50:31.600" Score="0" Body="" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-03-03T21:50:31.600" LastActivityDate="2012-03-03T21:50:31.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1300" PostTypeId="4" CreationDate="2012-03-03T21:50:31.600" Score="0" Body="The study of the development of an embryo from fertilisation through to description as a foetus.  " OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T00:55:05.990" LastActivityDate="2013-10-31T00:55:05.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1301" PostTypeId="5" CreationDate="2012-03-03T21:51:42.177" Score="0" Body="&lt;p&gt;Polymerase Chain Reaction is a method of replicating DNA exponentially &lt;em&gt;in vitro&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="9943" LastEditDate="2017-03-27T10:27:39.993" LastActivityDate="2017-03-27T10:27:39.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1302" PostTypeId="4" CreationDate="2012-03-03T21:51:42.177" Score="0" Body="Polymerase Chain Reaction is a method of replicating DNA exponentially from even a single molecule." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T01:00:02.170" LastActivityDate="2013-10-31T01:00:02.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1303" PostTypeId="1" CreationDate="2012-03-03T23:33:51.183" Score="6" ViewCount="751" Body="&lt;p&gt;If auxotrophic strains grow on minimal media do they complement each other or not?  Also, is complementation the same thing as complementing each other?&lt;/p&gt;&#xA;" OwnerUserId="558" LastActivityDate="2012-06-10T17:08:27.710" Title="Auxotrophic complementation test with yeast" Tags="&lt;yeast&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1304" PostTypeId="1" AcceptedAnswerId="1309" CreationDate="2012-03-04T00:29:16.340" Score="7" ViewCount="130" Body="&lt;p&gt;And what are its effects on C. elegans?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper is &lt;a href=&quot;http://dx.doi.org/10.1038/nature10296&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Burnett C, Valentini S, Cabreiro F, Goss M, Somogyvári M, Piper MD, Hoddinott M, Sutphin GL, Leko V, McElwee JJ, et al.&lt;/strong&gt;. 2011. Absence of effects of Sir2 overexpression on lifespan in C. elegans and Drosophila. Nature 477: 482–5.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="836" LastEditDate="2012-09-12T17:41:22.017" LastActivityDate="2012-09-12T17:41:22.017" Title="Why is propanoic acid often added to the diet of C. elegans?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1305" PostTypeId="1" AcceptedAnswerId="3529" CreationDate="2012-03-04T00:37:58.543" Score="5" ViewCount="110" Body="&lt;p&gt;Can't we just overexpress regular Sir2 in the paper? Rather than overexpress a reduced-function gene?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper is &lt;a href=&quot;http://dx.doi.org/10.1038/nature10296&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Burnett C, Valentini S, Cabreiro F, Goss M, Somogyvári M, Piper MD, Hoddinott M, Sutphin GL, Leko V, McElwee JJ, et al.&lt;/strong&gt;. 2011. Absence of effects of Sir2 overexpression on lifespan in C. elegans and Drosophila. Nature 477: 482–5.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="836" LastEditDate="2012-09-12T17:41:09.223" LastActivityDate="2012-09-12T21:47:09.763" Title="Why would we overexpress Sir2 by overexpressing its hypomorph (dSir2-EP2300) in C. elegans?" Tags="&lt;molecular-biology&gt;&lt;senescence&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1306" PostTypeId="2" ParentId="9" CreationDate="2012-03-04T03:38:56.763" Score="1" Body="&lt;p&gt;I will also strongly recommend blotting a microgram of your plasmid DNA on a piece of filter paper (the filter paper is important for extraction on the receiving end). Also, it is very very helpful if you clearly indicate the amount of DNA (approximately) and circle the blotted DNA in pen so there is no ambiguity about cutting out the circle of filter paper containing the DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the receiving end, you should always freeze the paper right away or elute the DNA off of the paper in TE buffer or water and then freeze. Failure to do so will eventually lead to DNAase degradation of the plasmid DNA and then you'll have to wait for another shipment.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-03-04T03:38:56.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1307" PostTypeId="2" ParentId="1247" CreationDate="2012-03-04T03:51:37.467" Score="5" Body="&lt;p&gt;My understanding of bootstrapping is that you may estimate variance (and thus standard error of the population mean) iff your measurements are independent and have the same population distribution, in which case a number of sampling-with-replacement calculations can be done. I suspect that this method of estimation would be less desirable with small n values because of the effect that outliers or large standard deviations may have on the calculation. If you have a large dataset then it shouldn't be an issue.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-03-04T03:51:37.467" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1308" PostTypeId="2" ParentId="1027" CreationDate="2012-03-04T09:16:11.837" Score="1" Body="&lt;p&gt;One can argue that only the &quot;eukaryotic&quot; types of SOD are sensitive to cyanide treatment:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;FeSOD is designated as &quot;prokaryotic&quot; type of SOD which is uncommon (but possible) for eukaryotes (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/223343&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;li&gt;CuZnSOD is a cytosolic SOD, whereas MnSOD is located within mitochondria (&lt;a href=&quot;http://www.biolreprod.org/content/27/5/1109&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Taking into account the &lt;a href=&quot;http://en.wikipedia.org/wiki/Endosymbiotic_theory&quot; rel=&quot;nofollow&quot;&gt;endosymbiotic theory&lt;/a&gt; we might also suggest that MnSOD is also a sort of &quot;prokaryotic&quot; SOD.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-03-04T09:16:11.837" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1309" PostTypeId="2" ParentId="1304" CreationDate="2012-03-04T09:29:57.653" Score="10" Body="&lt;p&gt;Propanoic acid is toxic against many types of mold, fungi and bacteria (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0031942204002973&quot;&gt;wiki&lt;/a&gt;), but same time has almost no effect to C. elegans (&quot;fivefold less&quot;, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0031942204002973&quot;&gt;reference&lt;/a&gt;). This is why propanoic acids and (more commmon) its salts are used as conservants for C.elegans cultures (as well as for other animals, like Drosophila).&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-03-04T09:29:57.653" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1310" PostTypeId="1" AcceptedAnswerId="1312" CreationDate="2012-03-04T15:06:15.410" Score="14" ViewCount="1431" Body="&lt;p&gt;When are population dynamics models useful? There seems to have been a lot of research about it, but how does it help? If I need data about how a population will evolve under what conditions, I need it because I need data for a decision (such as &quot;can we kill 50% of population X without doing too much damage?&quot;), right? But for that, the model needs to be aware of what causes what. And for that, I have to do experiments, right? Like &quot;let's kill a significant amount of population X and see what happens in the next ten years&quot;. I really don't get it.&lt;/p&gt;&#xA;" OwnerUserId="585" LastEditorUserId="68" LastEditDate="2012-03-07T20:25:37.120" LastActivityDate="2016-05-16T09:09:33.257" Title="When are population dynamics models useful?" Tags="&lt;population-dynamics&gt;&lt;ecology&gt;&lt;theoretical-biology&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1311" PostTypeId="1" CreationDate="2012-03-04T15:38:18.793" Score="12" ViewCount="28990" Body="&lt;h1&gt;Background&lt;/h1&gt;&#xA;&lt;p&gt;I've heard from many people working in tourism or similar industries that, white Australians can be recognized as Australian solely by their facial features. Being Australian myself I've heard variants of the claim quite often and lean towards the claim being at least, a possibility.&lt;/p&gt;&#xA;&lt;p&gt;While it's true that people tend to see patterns when there are none or incorrectly attribute, why they correctly recognize something. I don't necessarily think that is the case here. Australians don't tend to dress in a distinguishing way when overseas, and people have recognized them before hearing them speak. Given the extent to which I hear this claim made, I can't completely dismiss it.&lt;/p&gt;&#xA;&lt;h1&gt;Examples of claims&lt;/h1&gt;&#xA;&lt;p&gt;This &lt;a href=&quot;http://news.google.com/newspapers?nid=1301&amp;amp;dat=19430222&amp;amp;id=mR8UAAAAIBAJ&amp;amp;sjid=1pYDAAAAIBAJ&amp;amp;pg=3044,3193641&quot; rel=&quot;noreferrer&quot;&gt;article&lt;/a&gt; from an Australian newspaper in 1943 interviews an artist who when asked if Australians have a racial type, says he thinks that it was generally possible to distinguish an Australian [from other Caucasians] due to differences in the nose and differences in the jaw.&lt;/p&gt;&#xA;&lt;p&gt;Googling for terms like &amp;quot;look Australian&amp;quot; returns examples of the claims strewn around the internet, such as this &lt;a href=&quot;http://www.disboards.com/showthread.php?t=2713859&quot; rel=&quot;noreferrer&quot;&gt;forum thread&lt;/a&gt; and &lt;a href=&quot;http://olivialooksaustralian.tumblr.com&quot; rel=&quot;noreferrer&quot;&gt;this blog&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Also of note is the art project to show the &lt;a href=&quot;http://www.smh.com.au/technology/technology-news/technology-plots-the-average-face-of-sydney--and-the-rest-of-the-world-20110211-1ap3w.html&quot; rel=&quot;noreferrer&quot;&gt;average face of Sydney&lt;/a&gt;, of which the following quote is relevant:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In many cases, however, the likeness is so strong that it's possible&#xA;to guess the nationality just by taking a cursory glance at the photo.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;h1&gt;Reasons for thinking it may be possible&lt;/h1&gt;&#xA;&lt;p&gt;I'm fairly ignorant when it comes to biology, although there are a few reasons I think this might be possible. The (relatively) small gene pool from when Australia was colonized could have led to features from a small group being inherited in a large population.&lt;/p&gt;&#xA;&lt;p&gt;There seems to be some evidence that environment can play a large role in influencing genetics more so than ethnicity. I can't find the paper investigating that, although will update this question if I am able to.&lt;/p&gt;&#xA;&lt;p&gt;It seems possible to me that facial features belonging to the original colonists could have spread through subsequent populations, becoming a defining characteristic for some Australians.&lt;/p&gt;&#xA;&lt;p&gt;I don't think most immigrants are relevant to this question as they will not have inherited distinguishing features (if they exist), nor will they or their parents/grandparents have been able to be influenced by the environment - if that is even a relevant factor.&lt;/p&gt;&#xA;&lt;h1&gt;So...&lt;/h1&gt;&#xA;&lt;p&gt;Do a significant number of white Australians, excluding 1st or 2nd generation immigrants, have distinct facial features unique or generally only found in Australia?&lt;/p&gt;&#xA;&lt;p&gt;Is it reasonable that some white Australians could be recognized as Australian, going only by facial features?&lt;/p&gt;&#xA;" OwnerUserId="586" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-28T04:28:54.393" Title="Do white Australians have a distinct look?" Tags="&lt;human-biology&gt;&lt;genetics&gt;" AnswerCount="2" CommentCount="14" FavoriteCount="2" ClosedDate="2016-07-01T17:42:55.493" ContentLicense="CC BY-SA 3.0" />
  <row Id="1312" PostTypeId="2" ParentId="1310" CreationDate="2012-03-04T18:08:55.860" Score="12" Body="&lt;p&gt;Population dynamics occupies a whole subset of mathematical biology. Perhaps the most pragmatic uses for modelling population dynamics come from the fields of epidemiology for modelling disease infection and transmission through a population (&lt;a href=&quot;http://www.springerlink.com/content/k7231j6848m0421u/&quot;&gt;one such article&lt;/a&gt;), or ecology modelling things like forestation, fishing dynamics, predator-prey relationships (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2656.1999.00258.x/full&quot;&gt;an example&lt;/a&gt;). Then there are more abstract uses, when you cannot measure a population to test a hypothesis because the labour is too intensive, or it's too costly, or no such surveillance mechanism exists. Theoretical models of population dynamics are built to gain an understanding of what the system as a whole may do under certain conditions. In this sense, population models are more of a theoretical exercise or a thought experiment.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-03-04T18:08:55.860" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1313" PostTypeId="2" ParentId="1198" CreationDate="2012-03-04T19:14:26.760" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there clear evidence that LTP is involved in long-term memory (not&#xA;  counting 1 hour as long-term...)?  Has LTP/LTD been shown in vivo&#xA;  after long period of time (e.g. months).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This &lt;em&gt;Journal of Neuroscience&lt;/em&gt; paper shows LTP &lt;em&gt;in vivo&lt;/em&gt; measured out to one year: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12417688&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Abraham WC, Logan B, Greenwood JM, Dragunow M&lt;/strong&gt;. 2002. Induction and experience-dependent consolidation of stable long-term potentiation lasting months in the hippocampus. The Journal of neuroscience : the official journal of the Society for Neuroscience 22: 9626–34.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="587" LastEditorUserId="836" LastEditDate="2012-09-14T20:20:02.577" LastActivityDate="2012-09-14T20:20:02.577" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1314" PostTypeId="1" CreationDate="2012-03-05T10:21:33.627" Score="8" ViewCount="737" Body="&lt;p&gt;How fast is the blood flow in different blood vessels, such as the aorta and capillaries? &lt;/p&gt;&#xA;" OwnerUserId="327" LastEditorUserId="16866" LastEditDate="2017-01-03T15:51:40.183" LastActivityDate="2017-01-03T15:51:40.183" Title="How fast is the blood flow in various vessels?" Tags="&lt;human-anatomy&gt;&lt;human-physiology&gt;&lt;blood-circulation&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1315" PostTypeId="2" ParentId="1027" CreationDate="2012-03-05T14:20:28.837" Score="3" Body="&lt;p&gt;I'm just taking a stab, because my inorganic chemistry is rusty.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;cyanate (CN-) is well known to bind to iron (it inhibits hemoglobin and causes anoxia), and it also forms a pretty strong complex with Zinc: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Zinc_cyanide&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Zinc_cyanide&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would guess that in the case of the SOD that the other liganding amino acids and the pocket of the enzyme are such that the affinity for cyanide is lowered to the point that oxygen can displace it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of hemoglobin, CN will coordinate to the heme iron in much the same fashion that O2 does, but it doesn't come off.   In the case of SOD, the enzyme will be looking to coordinate to superoxide O2(2-) which would be at a roughly tetrahedral angle to the metal.   This is not a favored geometry for CN coordination, which prefers to linearly coordinate to things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case CuZnSOD it seems likely that this enzyme has enough room and its Zn and Cu binding envirionments don't forbid CN binding. it would be an evolutionary accident really as to why one is sensitive and another is not. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;some structures at rcsb:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;SODs:&#xA;&lt;a href=&quot;http://www.rcsb.org/pdb/results/results.do?qrid=C0740111&amp;amp;tabtoshow=Current&quot; rel=&quot;nofollow&quot;&gt;http://www.rcsb.org/pdb/results/results.do?qrid=C0740111&amp;amp;tabtoshow=Current&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thiocyanate bound. the pocket is pretty open between the two ions.  no CN bound structure. &#xA;&lt;a href=&quot;http://www.rcsb.org/pdb/explore/jmol.do?structureId=1SXS&amp;amp;bionumber=1&quot; rel=&quot;nofollow&quot;&gt;http://www.rcsb.org/pdb/explore/jmol.do?structureId=1SXS&amp;amp;bionumber=1&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-03-05T14:20:28.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1316" PostTypeId="2" ParentId="1294" CreationDate="2012-03-05T16:04:39.300" Score="12" Body="&lt;p&gt;One version or allele of the gene for eye color may encode instructions to make the brown pigment, while the blue allele makes no pigment. Alternatively, it is possible, logically speaking, that the blue allele blocks the productions of brown pigment, but this is not the case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, brown vs blue is not a case of one gene and two alleles. After producing pigment, it must be transported, deposited and such. Many processes are involved. So, the pigment deposition process may be functional or not, but as above, it is often found that a non-functional version is simply non-functioning and not actively inhibiting the process. There are numerous cases where an aberrant form of a protein, encoded by a variant allele, acts as an active inhibitor of a given biological or biochemical process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key to your question as written is blue eye color is a lack of pigmentation.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-03-05T16:04:39.300" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1317" PostTypeId="1" CreationDate="2012-03-05T18:24:23.497" Score="9" ViewCount="881" Body="&lt;p&gt;Is there a negative net flow of blood in human arteries at any point of the cardiac cycle? I realise that blood flow can be turbulent, e.g. in the aorta or around stenotic arteries, but then the average is still flowing away from the heart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question was provoked by this graph, which admittedly I haven't seen in its context:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4qSMQ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A similar graph showed negative velocities in the aorta and innominate artery of humans.&lt;/p&gt;&#xA;" OwnerUserId="327" LastActivityDate="2013-05-31T10:55:54.337" Title="Does arterial blood always flow away from the heart?" Tags="&lt;human-biology&gt;&lt;cardiology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1318" PostTypeId="2" ParentId="1294" CreationDate="2012-03-05T19:12:42.983" Score="12" Body="&lt;p&gt;At the DNA level there are several mechanisms that  might be cited.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A mutation (change in the DNA sequence) of a gene may actually render one or both copies of the gene defective.  In the case of albino-ism, the skin is pink - no melanin pigment is made at all.  This is a case of both copies of a vital gene being defective and an ability lost completely. A &quot;loss of function&quot; recessive trait.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Blue eyes have no retinal pigment - they are a loss of function recessive. Some cases of genetically inherited diabetes (&amp;lt;1%) dwarfism and obesity are examples of this.  There are many others - many genetic diseases are like this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can be caused by a single mutation in each copy of the gene, and others an entire segment of the chromosome can be lost or disrupted by a new, often nonsensical sequence dropped into the gene region.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other changes can affect the way the genes turn on and off. - similar sequence changes in the regulatory sequences next to the gene sequence will make the gene behave differently. Even babies of african descent may be born with blonde hair and blue eyes and get the darker pigmentation later.  this is genetically caused by a change in they timing of the genes for hair and eye color turning on at other times (blonde hair and blue eyes have little or no pigment, so if the genes are off, then this is what you get).  So when genes are active can cause dominant (always on) versus recessive (sometimes off) patterns. which are because one copy of the gene behaves differently than the other copy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes a single mutation in one copy of the gene can cause rather interesting effects. A single good gene and a mutated, less effective gene might result in lost of activity because the mixture of the two genes is different between a wholly functional or wholly variant set of genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A classic example is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sickle-cell_disease&quot; rel=&quot;nofollow noreferrer&quot;&gt;sickle cell Anemia&lt;/a&gt;.  two copies of sickle cell hemoglobin causes the red blood cells to be stiff and misshapen which in turn causes a painful condition in the carrier.  a person with a single copy of the sickle cell gene does not have this problem - is nearly asymptomatic. So we say sickle cell anemia is recessive for the HbS mutation.  but in reality there is plenty of the HbS version of hemoglobin (Hb) in the blood cells, just that the mixture of the two does not cause the anemia.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Much rarer is an additive function from a genetic sequence change.  The immune system is where you will most often see this.  Since the sequences that drive immunity vary widely, some immune sequences are rare - such as &lt;a href=&quot;https://en.wikipedia.org/wiki/Innate_resistance_to_HIV&quot; rel=&quot;nofollow noreferrer&quot;&gt;inborn immunity to HIV&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2019-04-22T14:31:50.120" LastActivityDate="2019-04-22T14:31:50.120" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="1320" PostTypeId="2" ParentId="1314" CreationDate="2012-03-05T21:36:13.047" Score="5" Body="&lt;p&gt;In the middle cerebral artery blood flow at rest is 73.7 cm/s. After a period of 3 minutes of hyperventilation, blood flow in the same artery decreases to 37.6 cm/s. This is &lt;a href=&quot;http://www.ajnr.org/content/18/10/1929.full.pdf&quot;&gt;published&lt;/a&gt; work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://circres.ahajournals.org/content/23/3/349.short&quot;&gt;Vena cava measures&lt;/a&gt;: Peak velocities during ventricular systole ranged from 30 to 45 cm/sec in the inferior, and from 10 to 35 cm/sec in the superior, vena cava, also published.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-03-05T21:36:13.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1321" PostTypeId="2" ParentId="1317" CreationDate="2012-03-05T23:18:04.553" Score="8" Body="&lt;p&gt;Quick answer, no. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine a balloon; as you compress the balloon, there will be a lot of air that leaves it. But as you let it relax, the balloon pulls in surrounding air even as you fill  it from another side. When the aortic and tricuspid valves are closed, there is blood flow forward but due to conservation of mass, the blood goes back to fill in the empty region.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-03-05T23:18:04.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1322" PostTypeId="2" ParentId="1317" CreationDate="2012-03-06T01:06:39.260" Score="11" Body="&lt;p&gt;Simple answer, yes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It really is a matter of how technical you wish to be. By defintion, all arterial flow conveys blood away from the heart. The largest arteries exhibit the Windkessel effect which allows for the compression-based effects that bobthejoe inferred. Explicity, as blood is pumped out of the left ventricle, it stretches te aorta, and this tension in turn causes compression on the artery and pushes blood forward. On the flip side, venous vessels (except the pulmonary vein) return blood to the heart, but here you are likely to encounter local areas of reverse flow. This is counteracted to a degree by one-way valves present in the large veins to keep the net movement of blood in the body always toward the heart.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2013-05-31T10:55:54.337" LastActivityDate="2013-05-31T10:55:54.337" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1323" PostTypeId="2" ParentId="1310" CreationDate="2012-03-06T18:38:31.000" Score="9" Body="&lt;p&gt;Leonardo's already given you an excellent answer, but I thought I'd add my perspective. I'm a mathematical epidemiologist, so I'd at least like to believe these types of models are useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For me, there are a number of things population dynamics models are especially useful for:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Highlighting data requirements. Yes, models need data, as you've mentioned. But they don't need all their data to come from one source, one study, or even one &lt;em&gt;field&lt;/em&gt;. Models are also profoundly useful for showing where we &lt;em&gt;don't&lt;/em&gt; have the data we need to fully understand a system. &quot;To make a model where we understand A, we need the values for X, Y, and Z. X is well studied, but Y and Z aren't - though it turns out when we look over the entire parameter space for Z, nothing really changes in our answer. But guys? We could really use a study on Y.&quot;&lt;/li&gt;&#xA;&lt;li&gt;Eliminating guesswork. Models aren't perfect encapsulations of reality - there will always be some simplifying assumptions, etc. But it's better than &quot;going with your gut&quot; - especially for complex problems.&lt;/li&gt;&#xA;&lt;li&gt;Impossible studies. A ton of what mathematical epidemiology looks at it is areas where studies are either impossible, logistically difficult, or unethical. It would be very hard indeed to only be able to study pandemic response plans, or vaccination strategy only when we had an actual outbreak, or while a new vaccine is being rolled out.&lt;/li&gt;&#xA;&lt;li&gt;Highlighting potentially new directions. If you're considering an intervention, but no matter how effective you make it in your model it doesn't move the system much, it might not be worthwhile. Models can also highlight threshold effects - like the critical % of the population you'd need to vaccinate to achieve herd immunity.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="67" LastActivityDate="2012-03-06T18:38:31.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1324" PostTypeId="2" ParentId="1289" CreationDate="2012-03-06T19:25:46.113" Score="12" Body="&lt;p&gt;There are a number of ways to address antibiotic resistance in infectious bacteria. What one gets used depends on exactly what organism we're talking about. But below is a short list of some ways:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Changing the antibiotic being used. Not all antibiotics have the same molecular target within a bacterial cell. Some interfere with the formation of the cell wall, others interfere with protein synthesis, some mess with DNA replication, etc. Similarly, resistance mechanisms don't work equally well on all antibiotics. So often the solution is simply to switch antibiotics. Or, quite often, treating all infections with a combination of drugs that should get around most resistance. This is why you see people getting skittish about things like multi-drug resistant organisms - because it removes this solution.&lt;/li&gt;&#xA;&lt;li&gt;This isn't as much a treatment as a preventative measure, but increasing antimicrobial stewardship and the appropriate use of antibiotics to prevent widespread resistance from arising in the first place.&lt;/li&gt;&#xA;&lt;li&gt;The use of non-antibiotic antimicrobials. The most &quot;common&quot; of these is phage therapy - using preparations of bacteriophages that naturally prey on the infecting pathogen to help combat the infection. This was a major &quot;contender&quot; for how we treated antibiotic infections, but has fallen away due to a bad reputation early in its history (due to difficulties purifying phage treatments) and the discovery of antibiotics which were vastly easier to use. But there's still ongoing research, and it may pose a potential to help treat highly resistant infections in the future.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="67" LastActivityDate="2012-03-06T19:25:46.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1325" PostTypeId="2" ParentId="1294" CreationDate="2012-03-06T19:36:08.097" Score="8" Body="&lt;p&gt;Sorry to blockquote, but &lt;a href=&quot;http://en.wikipedia.org/wiki/Dominance_%28genetics%29&quot; rel=&quot;noreferrer&quot;&gt;this note from wikipedia&lt;/a&gt; gets to the heart of the question:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Which trait is dominant?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;The terms dominant and recessive refer to the interaction of alleles in producing the phenotype of the heterozygote. If there are two alternative phenotypes, by definition the phenotype exhibited by the heterozygote is called &amp;quot;dominant&amp;quot; and the &amp;quot;hidden&amp;quot; phenotype is called &amp;quot;recessive&amp;quot;. The key concept of dominance is that the heterozygote is phenotypically identical to one of the two homozygotes. That trait corresponding to the dominant allele may then be called the &amp;quot;dominant&amp;quot; trait.&lt;/p&gt;&#xA;&lt;p&gt;Dominance is a genotypic relationship between alleles, as manifested in the phenotype. It is unrelated to the nature of the phenotype itself, e.g., whether it is regarded as normal or abnormal, standard or nonstandard, healthy or diseased, stronger or weaker, or more or less extreme. It is also important to distinguish between the &amp;quot;round&amp;quot; gene locus, the &amp;quot;round&amp;quot; allele at that locus, and the &amp;quot;round&amp;quot; phenotype it produces. It is inaccurate to say that &amp;quot;the round gene dominates the wrinkled gene&amp;quot; or that &amp;quot;round peas dominate wrinkled peas.&amp;quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Recommended reading for an overview:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dominance_relationship&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Dominance_relationship&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dominant_negative&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Dominant_negative&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;You can also look to &amp;quot;dominant negative&amp;quot; phenotypes to get a good idea of what &amp;quot;dominance&amp;quot; entails (this was the concept that really locked it in for me in college). One example is Marfan syndrome, where the mutant allele of FBN1 (fibrillin-1) produces a version of the protein that is antagonistic to the protein produced by the &amp;quot;healthy&amp;quot; allele.&lt;/p&gt;&#xA;&lt;p&gt;Dominant negative and semi-dominant alleles can be seen when the protein forms dimers to function. Activin type receptors form dimers to transduce a signal from an extracellular ligand into the cell. A truncated receptor protein that has the dimerization domain but  lacks the intracellular domain necessary for signal transduction will act in a dominant negative fashion over the wildtype allele: Dimers are formed but the signal is not transduced. This has been implicated in hereditary colorectal cancers.&lt;/p&gt;&#xA;" OwnerUserId="204" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-03-06T19:36:08.097" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1326" PostTypeId="1" AcceptedAnswerId="1327" CreationDate="2012-03-06T21:01:51.797" Score="10" ViewCount="314" Body="&lt;p&gt;A friend of mine told me an anecdote about his mother, who drank too much caffeine, to the point she became hypotensive and would pass out. Because caffeine acts as a stimulant, I'm assuming the decreased blood pressure was some kind of tolerance effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How exactly would caffeine have disrupted her circulatory regulation and caused her normal pressure to decrease?&lt;/p&gt;&#xA;" OwnerUserId="575" LastEditorUserId="107" LastEditDate="2012-03-08T03:17:39.833" LastActivityDate="2021-05-07T15:01:24.020" Title="What are the effects of caffeine on the mammalian circulatory system?" Tags="&lt;physiology&gt;&lt;pharmacology&gt;&lt;metabolism&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1327" PostTypeId="2" ParentId="1326" CreationDate="2012-03-06T21:20:17.167" Score="7" Body="&lt;p&gt;I can't speak to the causes of hypotension, but you are indeed correct, caffeine is a stimulant. As a stimulant, there is a well documented acute period of &lt;em&gt;hypertension&lt;/em&gt; that lasts for up to 4 hours. Interestingly, there is no causal link established between caffiene consumption and chronic hypertension leading to cardiovascular disease (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21880846&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://eurheartj.oxfordjournals.org/content/32/24/3081.long&quot;&gt;here&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having said that, caffeine is also a diuretic, which could cause someone who is already fairly dehydrated to exacerbate that state. It's possible to faint from a result of severe dehydration but I think it would have to be pretty severe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's possible someone is prone to fainting for non-medical, purely physiological reasons, such as standing for long periods, standing up too quickly, hypoglycemia, or some other predisposition.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-03-06T21:20:17.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1328" PostTypeId="1" AcceptedAnswerId="1333" CreationDate="2012-03-07T08:34:34.233" Score="8" ViewCount="182" Body="&lt;p&gt;I'm working with luciferase and I want to be able to take a photo of it. The trouble is, I can see the luciferase glowing in all of its glory in front of me but no matter how hard I try, I can't take a photo of the luciferase with my DSLR (Nikon D80).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm curious if I'm missing a certain lens or if I should be shooting using a different lighting setup. I'm already exposing for 30&quot;. Perhaps longer?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-03-07T17:27:01.633" Title="What type of CCD system is required to take photos of luciferase" Tags="&lt;lab-techniques&gt;&lt;bioluminescence&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1330" PostTypeId="2" ParentId="393" CreationDate="2012-03-07T09:11:18.407" Score="3" Body="&lt;p&gt;EOL &lt;a href=&quot;http://eol.org/pages/328674/names/common_names&quot; rel=&quot;nofollow&quot;&gt;has large collections of common names&lt;/a&gt;, and &lt;a href=&quot;http://eol.org/api&quot; rel=&quot;nofollow&quot;&gt;a pretty comprehensive API&lt;/a&gt; which should be able to access them somehow (I haven't tried specifically downloading commons name before, though, so I can't promise that it'd work). If you need a list locally, ITIS has &lt;a href=&quot;http://www.itis.gov/downloads/index.html&quot; rel=&quot;nofollow&quot;&gt;downloadable pipe-delimited files&lt;/a&gt; containing scientific names and common names (although you'd need to do the mapping yourself). Hope that helps!&lt;/p&gt;&#xA;" OwnerUserId="87" LastActivityDate="2012-03-07T09:11:18.407" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1331" PostTypeId="2" ParentId="517" CreationDate="2012-03-07T09:26:27.373" Score="5" Body="&lt;p&gt;If I understand &lt;a href=&quot;http://www.goodreads.com/book/show/6518072-species&quot;&gt;John S. Wilkins' magnificent book on the history of the &quot;species&quot; concept&lt;/a&gt; correctly, the basis of biological taxonomy can be traced back to the Aristotelian idea of &lt;a href=&quot;http://en.wikipedia.org/wiki/Genus%E2%80%93differentia_definition&quot;&gt;&lt;em&gt;per genus et differentiam&lt;/em&gt;&lt;/a&gt;: you can define something as consisting of a general type (&quot;a plant&quot;) with a difference (&quot;made of wood&quot;) to define an entity (&quot;a tree&quot;), which could then itself become the general type for a more specific category (&quot;an oak tree&quot;). So the idea of an &lt;em&gt;infimae species&lt;/em&gt; (an entity that cannot be split any further) has been around since antiquity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whether or not a specific group of people would have split similar-looking species is a bigger unknown. I can't find a good online reference for Aristotle's classification of living things; you can &lt;a href=&quot;http://en.wikipedia.org/wiki/Aristotle#Classification_of_living_things&quot;&gt;read a summary on Wikipedia&lt;/a&gt;. Sorry I can't be more helpful!&lt;/p&gt;&#xA;" OwnerUserId="87" LastActivityDate="2012-03-07T09:26:27.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1332" PostTypeId="2" ParentId="1328" CreationDate="2012-03-07T13:32:01.663" Score="9" Body="&lt;p&gt;You are looking for a &lt;a href=&quot;http://www.google.com/cse?cx=004738989115247203233:09r2ltc-nlc&amp;amp;ie=UTF-8&amp;amp;q=luciferase#gsc.tab=0&amp;amp;gsc.q=bioluminescence%20imaging&quot;&gt;bioluminescence imaging device&lt;/a&gt;. These have very sensitive CCD camera and exposure times are around 5 minutes in complete darkness.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-03-07T13:32:01.663" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1333" PostTypeId="2" ParentId="1328" CreationDate="2012-03-07T17:27:01.633" Score="4" Body="&lt;p&gt;You'll also want to make sure that you are imaging in complete darkness because you may have very low photon emission from your luciferase system and any amount of background light can overwhelm your signal with noise.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-03-07T17:27:01.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1334" PostTypeId="2" ParentId="1311" CreationDate="2012-03-07T20:11:09.637" Score="4" Body="&lt;p&gt;It seems unlikely, but it's possible.  The mechanisms that might occur (that I can think of) are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) if the Australians had some rare genetic traits that became more common in the australian gene pool than in the UK gene pool, it is possible.  This is what happened with eastern Asia and the Y chromosome, which something like 40% from a single individual.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For this to be the case, it would be necessary that:  Australia's gene pool must be isolated - very little immigration to the company and mixing with other gene pools.  (i think not- what do you say?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) the diet of Australians caused their general body or face to be distinctive.  As there is a lot of fast food in Australia now (and obesity) I'm guessing that this is simply not the case, at least compared to the UK and US. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since there is no direct study (that I can find) all we can go on is anecdotal thought experiment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as cognitive bias goes, I'm Asian American and I've heard many many (maybe most Asians say that they can tell one nationality vs another just by appearance).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whenever I have tested myself or others I have not found anyone who can tell that i am 100% Japanese genetically.  This is probably because diet in the midwest where i grew up was so corn rich and I've been mistaken for nearly everything, including Latino backgrounds.  Most people think I'm Filipino, which is great except that I am not :)  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even when I ask Asians to look at other Asians and guess, it seems pretty rare that one can be consistently correct.  There has been a lot of gene migration between countries there, even though the national groups are much much older than Australia.  This is why I really doubt that Australians have been genetically isolated long enough or strongly enough for this to really be likely. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be pretty simple to get a bunch of pictures together, say 100, and test this if you really want to know.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="43" LastEditDate="2012-03-07T22:50:59.800" LastActivityDate="2012-03-07T22:50:59.800" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1335" PostTypeId="2" ParentId="1310" CreationDate="2012-03-07T20:19:41.030" Score="8" Body="&lt;p&gt;Two previous answers listed many applications of population dynamics models. I want to add that they are also important for conservation of endangered species. For example classical stage-class model (&lt;a href=&quot;http://www.esajournals.org/doi/abs/10.2307/1939225&quot;&gt;Crouse et al 1987&lt;/a&gt;, &lt;a href=&quot;http://www.google.com/url?q=http://depts.washington.edu/amath/courses/422-winter-2011/materials/crouse_et_al_sea_turtles.pdf&amp;amp;sa=U&amp;amp;ei=NMFXT9GpIYOXOt-SnJ0N&amp;amp;ved=0CAQQFjAA&amp;amp;client=internal-uds-cse&amp;amp;usg=AFQjCNHMllJA87MvU5XqxcxgjMQm3TNSAQ&quot;&gt;free copy&lt;/a&gt;) indicate that the most effective way to protect sea turtles is reducing mortality of large juveniles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, you don't have to perform such drastic experiments as killing 50% of  a population to estimate your model parameters. Information about number of offspring, breeding success, natural mortality, etc can usually be gain without serious perturbation of wild populations. The number of individuals in every natural population fluctuates because of random reasons, so it is possible (but sometimes needs more field work) to calculate, (possibly nonlinear) regression between density of population and some demographic indicators and then extrapolate it to non-examined densities. For some small, short-living species it is sometimes possible to measure that correlations in laboratory or semi-wild conditions. For some long-living species, especially if they are sedentary, like trees, it may be better to compare specimens living in different distance from its neighborhoods. For poorly-known species it is possible to take missing information from related or similar species.&lt;/p&gt;&#xA;" OwnerUserId="68" LastEditorUserId="43" LastEditDate="2012-03-07T22:49:56.027" LastActivityDate="2012-03-07T22:49:56.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1336" PostTypeId="1" AcceptedAnswerId="1337" CreationDate="2012-03-07T22:24:27.713" Score="21" ViewCount="33848" Body="&lt;p&gt;I've used HPLC (high performance liquid chromatography) before (once, so I'm barely even qualified to know what it stands for) so I was surprised when my labmate told me she would be using an alternate technique to isolate a protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What exactly are differences in HPLC and FPLC (fast protein liquid chromatography) instruments, and why would FPLC be a better technique than HPLC to use with proteins? What situations make HPLC preferable?&lt;/p&gt;&#xA;" OwnerUserId="575" LastEditorUserId="389" LastEditDate="2012-03-08T03:14:46.390" LastActivityDate="2014-08-07T08:35:22.817" Title="What is the difference between HPLC and FPLC and why is FPLC preferable for protein purification?" Tags="&lt;proteins&gt;&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1337" PostTypeId="2" ParentId="1336" CreationDate="2012-03-07T23:53:55.137" Score="18" Body="&lt;p&gt;The only difference between FPLC and HPLC is the amount of pressure the pumps apply to the column. FPLC columns have a maximum pressure of about of 3-4 MPa, whereas HPLC columns can withstand or require much higher pressures. As a general rule, HPLC columns won't work with old FPLC equipment; FPLC columns can go on HPLCs as long as the pressure can be regulated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Manufacturers have been marketing separate equipment to handle these different classes of columns, but the trend seems to be heading towards machines that can handle both types of columns without issue. A GE rep told me a few years ago that they've improved the pumps on the AKTAs to the point that &quot;they're technically HPLCs now.&quot; The term &quot;FPLC&quot; is probably on its way out. &lt;/p&gt;&#xA;" OwnerUserId="204" LastActivityDate="2012-03-07T23:53:55.137" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1338" PostTypeId="1" AcceptedAnswerId="2597" CreationDate="2012-03-08T01:00:48.633" Score="8" ViewCount="399" Body="&lt;p&gt;I am confused about the variable &quot;RuBisCO activity&quot;. How is it measured, and is it any different from the net assimilation rate?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on some background reading (e.g. &lt;a href=&quot;http://www.globalchange.umich.edu/globalchange1/current/lectures/kling/energyflow/energyflow.html&quot; rel=&quot;nofollow&quot;&gt;Kling, 2008&lt;/a&gt;; &lt;a href=&quot;http://books.google.com/books?id=PXBq6jsT5SYC&amp;amp;lpg=PA43&amp;amp;dq=%22rubisco%20activity%22&amp;amp;pg=PA43#v=onepage&amp;amp;q=%22rubisco%20activity%22&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Lambers et al 2011&lt;/a&gt;)  the only difference that I can find is the units. Both would have &quot;carbon fixed per unit time&quot;, but RuBisCO activity is expressed per unit mass of the enzyme, while assimilation rate is per unit leaf area (or less commonly, leaf mass).&lt;/p&gt;&#xA;" OwnerUserId="154" LastEditorUserId="69" LastEditDate="2012-03-08T11:32:42.230" LastActivityDate="2012-06-12T13:58:09.943" Title="Compare and contrast &quot;Rubisco activity&quot; and &quot;assimilation rate&quot; (is there a difference, and if so, what is it)?" Tags="&lt;plant-physiology&gt;&lt;enzymes&gt;&lt;photosynthesis&gt;&lt;ecology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1339" PostTypeId="1" AcceptedAnswerId="1340" CreationDate="2012-03-08T02:01:45.950" Score="15" ViewCount="4173" Body="&lt;p&gt;Do ants even breathe? If they don't, how do they stay alive? On what resources do they depend upon to stay alive? How are they different form mammals?&lt;/p&gt;&#xA;" OwnerDisplayName="user594" LastEditorUserId="69" LastEditDate="2012-03-08T11:30:10.877" LastActivityDate="2014-10-09T15:40:41.277" Title="How do insects breathe?" Tags="&lt;zoology&gt;&lt;physiology&gt;&lt;entomology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1340" PostTypeId="2" ParentId="1339" CreationDate="2012-03-08T02:37:18.430" Score="7" Body="&lt;p&gt;&lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=how%20do%20insects%20breathe&amp;amp;source=web&amp;amp;cd=4&amp;amp;ved=0CFEQFjAD&amp;amp;url=http://www.new-ecopsychology.org/en/insects/pages/p-8.htm&amp;amp;ei=6hpYT_rDEYPx0gGIpPmaDw&amp;amp;usg=AFQjCNHtfR2N6y7ig3tjv4RzjNJ-jiuebA&quot; rel=&quot;nofollow&quot;&gt;Insects breathe&lt;/a&gt; by simple diffusion through the cell walls. They do not breathe in the same sense that we humans do. They intake oxygen through &lt;a href=&quot;http://insects.about.com/od/s/g/def_spiracle.htm&quot; rel=&quot;nofollow&quot;&gt;spiracles&lt;/a&gt; in the insect's cuticle. It goes through the insect's trachea by dissolving into the tracheal liquid. From there it diffuses throughout the insect in tracheal tubes. At the ends of the tubes, the oxygen is taken by body cells. &lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="1320" LastEditDate="2013-11-22T14:06:17.123" LastActivityDate="2013-11-22T14:06:17.123" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1341" PostTypeId="1" CreationDate="2012-03-08T03:10:04.133" Score="8" ViewCount="448" Body="&lt;p&gt;I am interested in identifying the maximum potential dissolved sucrose (%w/w) that plant sap could have, and which (biological, physical, chemical) factors constrain the observed sucrose concentrations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, sugar maple has one of the highest sucrose contents at 6%, and the solution also contains fructose, glucose, organic acids, minerals (K, Ca, Mn, Zn, Na, Cl), amino acids, volatile organic compounds, phenols, enzymes  (according to &lt;a href=&quot;http://en.wikipedia.org/wiki/Maple_syrup#Food_and_nutrition&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;), and most sap flow occurs when temperatures cross the freezing point each day. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a way that I can calculate this theoretical maximum from &quot;first principles&quot; of organic- or bio-chemistry, or is this a question better suited for empirical study?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;this is a biological application of &lt;a href=&quot;https://physics.stackexchange.com/questions/22036/can-i-calculate-the-maximum-concentration-of-sucrose-that-will-dissolve-in-water&quot;&gt;my question&lt;/a&gt; at physics.SE&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="154" LastEditorUserId="-1" LastEditDate="2017-04-13T12:40:13.457" LastActivityDate="2012-03-12T15:15:01.320" Title="What is the maximum potential sucrose concentration of plant sap? What keeps plants below this potential?" Tags="&lt;biochemistry&gt;&lt;plant-physiology&gt;&lt;organic-chemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1342" PostTypeId="1" CreationDate="2012-03-08T12:49:52.437" Score="5" ViewCount="59" Body="&lt;p&gt;Is there anyone out there who has done much work with serological assays? We have antiserum for a manufactured viral protein but no luck so far getting it to detect native protein (unless today's attempt worked which we will find out tomorrow).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are any common problems or possible considerations that we should bear in mind when testing?&lt;/p&gt;&#xA;" OwnerUserId="596" LastActivityDate="2012-03-08T12:49:52.437" Title="Serological assays not detecting native proteins" Tags="&lt;botany&gt;&lt;assay-development&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2015-03-29T09:32:43.567" ContentLicense="CC BY-SA 3.0" />
  <row Id="1343" PostTypeId="1" CreationDate="2012-03-08T15:16:29.830" Score="9" ViewCount="347" Body="&lt;p&gt;I was wondering why the teeth of cats (And dogs, as far as I know, plus possibly some other animals or even humans) get darker if they are exposed to air / light?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rxp4q.jpg&quot; alt=&quot;Animal tooth&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(See the lower end of the tooth, which sticks out if the mouth is closed. No, the cat was not resisting, just slightly annoyed.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, my question is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why does this happen?&lt;/li&gt;&#xA;&lt;li&gt;Would it happen to human teeth, if they would stick out of the mouth like the ones of cats do?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My guess is that it has something to do with the teeth reacting to air and corroding, but all my knowledge about biology comes from two years of biology in school, so I'm asking here.&lt;/p&gt;&#xA;" OwnerUserId="597" LastEditorUserId="69" LastEditDate="2012-03-08T20:10:12.977" LastActivityDate="2013-08-19T16:54:32.223" Title="Why do animal teeth get darker if exposed?" Tags="&lt;zoology&gt;&lt;teeth&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1344" PostTypeId="2" ParentId="1311" CreationDate="2012-03-08T18:02:02.650" Score="7" Body="&lt;p&gt;Yes, it is possible (on some average basis, i.e. with chance better than random).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take a look at &lt;a href=&quot;http://www.geekologie.com/image.php?path=/2011/02/10/average-faces-full.jpg&quot;&gt;average women faces from 41 different countries&lt;/a&gt; (AFAIK created with &lt;a href=&quot;http://www.faceresearch.org/&quot;&gt;Face Research&lt;/a&gt; software; sadly no picture for Australia). Clearly, even from small and nearby European countries you can spot differences (which work on the average). I guess the case of Austriala vs other countries isn't an exception. Similar face averages are also on the project &lt;a href=&quot;http://www.faceoftomorrow.com/&quot;&gt;Face of Tomorrow&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, when dealing with a single subjects it it may be not a reliable method to tell of his/her nationality or country of origin, as:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;even within an relatively isolated group there is variance in genotype and phenotype,&lt;/li&gt;&#xA;&lt;li&gt;people do move (especially now) and do mix (so unless you are comparing isolated islands you should't expect to have homogenous genotype).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Moreover, when identifying a person we may (even subconsciously) look at different features (including clothes, accent, behaviour, context, ...).&lt;/p&gt;&#xA;" OwnerUserId="129" LastActivityDate="2012-03-08T18:02:02.650" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1345" PostTypeId="1" AcceptedAnswerId="1360" CreationDate="2012-03-08T18:03:22.223" Score="14" ViewCount="1146" Body="&lt;p&gt;Myosin, dynein and kinase all &quot;walk&quot; towards specific ends of the microtubule or actin filament they are on. I'm most familiar with the walking mechanism for myosin, where ATP fuels conformal changes in the binding region, but I don't understand how it chooses to go one direction over another. Actin fibers' positive and negative ends are fueled by the addition of G-actin via ATP and its subsequent reduction to ADP, so I suspect that this process is somehow involved in determining the direction of myosin's movement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As just a secondary thought, are there differences in the mechanisms of the movement between the three walking molecules listed above?&lt;/p&gt;&#xA;" OwnerUserId="575" LastEditorUserId="69" LastEditDate="2012-03-08T20:08:44.320" LastActivityDate="2012-03-15T17:00:40.957" Title="What is the mechanism that directs myosin walking?" Tags="&lt;biochemistry&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1346" PostTypeId="2" ParentId="1066" CreationDate="2012-03-08T18:53:20.390" Score="8" Body="&lt;p&gt;Mark-recapture is the most frequently used method for small mammals. It's best when combined with uncertainty estimates and population dynamics models (e.g. projection matrix). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fluctuations of small rodent populations have long fascinated scientists, and various models have been developed. Logistic regression models can be used to estimate likelihood of mice outbreak based on local rainfall data. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Estimates vary. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rat population in New York city, for example, was thought to be 1 rat to 15 humans in the mid 40s, 1:36 in the late 40s (Davis ratio), 12:1 in 2002. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The population of mice is often estimated per hectare - 0.25-60/ha in buildings and 1-200 in the field, over 1000/ha during outbreaks. 10^9-10^10 hectares of habitable land means &#xA;that populations of mice and men are, probably, of the same order of magnitude.&lt;/p&gt;&#xA;" OwnerUserId="478" LastActivityDate="2012-03-08T18:53:20.390" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1347" PostTypeId="1" AcceptedAnswerId="1426" CreationDate="2012-03-08T20:33:12.903" Score="9" ViewCount="123" Body="&lt;p&gt;FIA has a &lt;a href=&quot;http://www.fia.fs.fed.us/tools-data/docs/pdfs/FIADB_user%20guide_v3-0_P2_06_01_07.pdf&quot;&gt;nice database of forest Inventory data&lt;/a&gt;, this would be great except that it does not seem capable of handling data from non-tree species (e.g., grasslands, wetlands).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a standard database or flat-file format for collecting plant community data (e.g., biomass, cover, dbh as appropriate)?&lt;/p&gt;&#xA;" OwnerUserId="222" LastEditorUserId="16866" LastEditDate="2017-01-03T15:56:02.057" LastActivityDate="2017-01-03T15:56:02.057" Title="Is there a standard format for plant community composition data?" Tags="&lt;ecology&gt;&lt;database&gt;&lt;data&gt;&lt;community-ecology&gt;&lt;vegetation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1348" PostTypeId="1" CreationDate="2012-03-08T20:58:07.597" Score="15" ViewCount="392" Body="&lt;p&gt;Methylation on gene-body and 3'UTRs if copied to mRNA can potentially regulate post-transcription modifications or expression regulation. But I'm not sure if they are maintained after transcription or if they get all de-novo methylation.&lt;/p&gt;&#xA;" OwnerUserId="599" LastEditorUserId="389" LastEditDate="2012-03-09T19:46:10.650" LastActivityDate="2012-05-09T22:37:38.277" Title="Can methylation from DNA get copied to RNA during transcription?" Tags="&lt;dna&gt;&lt;rna&gt;&lt;epigenetics&gt;&lt;transcription&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1349" PostTypeId="2" ParentId="1348" CreationDate="2012-03-08T22:14:34.790" Score="10" Body="&lt;p&gt;I don't believe anything should change in the majority of DNA-&gt;RNA transcription. DNA methylation typically occurs on the non-watson crick side of Cytosine so it shouldn't affect the base-pairing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are a few hypothetical situations that would result in alterations of the transcribed RNA. The sponatneous deamination of the 4' amine would convert the base into uracil. If there is an additional 5' methyl, the 5-methyluracil would be recognized as Thymine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(edit) I've talked with several genomics folks about this topic and it turns out that M5Cytosine is very resistant to deamination due to the presence of the Methyl group. As a result, the instance that I have just described is actually very rare.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iTzNX.png&quot; alt=&quot;5mCytosine to Thymine deamination&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;5mCytosine to Thymine deamination&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other situation would be to errors in DNA proofreading. Does the 5mCytosine affect the fidelity of RNA polymerase? I honestly don't know but it would be worth examining.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-05-09T22:37:38.277" LastActivityDate="2012-05-09T22:37:38.277" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1350" PostTypeId="1" CreationDate="2012-03-09T06:42:41.210" Score="15" ViewCount="387" Body="&lt;p&gt;To start with, I am not a person having sound knowledge in biology. When I started my search for phyto-chemicals in a particular family in the plant kingdom, I got confused. The scientific papers use a particular name, and when I searched in &lt;a href=&quot;http://www.theplantlist.org&quot;&gt;these&lt;/a&gt; 2 &lt;a href=&quot;http://www.tropicos.org/Home.aspx&quot;&gt;websites&lt;/a&gt;, (just to name it) I got the message that some of the names are  &quot;not resolved&quot;  or &quot;synonyms&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions are &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Biologists do they accept  the names mentioned in  website 1? If not where can I find authentic names?&lt;/li&gt;&#xA;&lt;li&gt;Who controls / monitors the name of these plant species?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="602" LastEditorUserId="107" LastEditDate="2012-03-09T15:43:41.350" LastActivityDate="2012-06-08T08:20:08.500" Title="How to decide which is the correct scientific name for a particular species" Tags="&lt;botany&gt;&lt;taxonomy&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1351" PostTypeId="2" ParentId="1350" CreationDate="2012-03-09T10:14:10.243" Score="9" Body="&lt;p&gt;When it comes to plants and animals, common names clearly differ from region to region.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A first effort to univocally classify them was done in the 16th century by Carl Linnæus (see my answer to &lt;a href=&quot;https://biology.stackexchange.com/questions/517/acknowledging-differentiation-of-species-in-olden-times/518#518&quot;&gt;this question&lt;/a&gt; for some historical background).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nomenclature of plants is governed by the &lt;a href=&quot;http://en.wikipedia.org/wiki/International_Code_of_Nomenclature_for_algae,_fungi,_and_plants&quot; rel=&quot;nofollow noreferrer&quot;&gt;International Code of Nomenclature for algae, fungi, and plants (ICN)&lt;/a&gt;, and for animals from the &lt;a href=&quot;http://en.wikipedia.org/wiki/International_Code_of_Zoological_Nomenclature&quot; rel=&quot;nofollow noreferrer&quot;&gt;International Code of Zoological Nomenclature (ICZN)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fact that there are rules, however, does not imply that names are conserved over time, nor that there is a rule for everything!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As time goes by &lt;a href=&quot;http://en.wikipedia.org/wiki/International_Code_of_Nomenclature_for_algae,_fungi,_and_plants#History&quot; rel=&quot;nofollow noreferrer&quot;&gt;rules change&lt;/a&gt;, certain species may be assimilated by others, or a certain subspecies will separate and become its own, and at times name changing proposals even &lt;a href=&quot;http://www.nature.com/news/2010/100407/full/464825a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;raise havoc in the scientific community&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, it is important to remember that taxonomy poses rules that are there to facilitate talking about science. Those are not absolute rules, sometimes they are arbitrary, and therefore for certain species there is no univocal name (and surely there is no &lt;strong&gt;correct&lt;/strong&gt; name).&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2012-03-09T10:14:10.243" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1352" PostTypeId="1" AcceptedAnswerId="1361" CreationDate="2012-03-09T15:15:23.210" Score="11" ViewCount="672" Body="&lt;p&gt;According to the BBC documentary &quot;Wild About Pandas&quot;, about half of panda birth result in twins.  Why do they have such a high probability compared to other mammals?  What factor(s) control that fraction in general for mammals?&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Additional question about the allometry formula:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I am a little surprised that it is not the ratio between the neonatal mass and the adult body mass that enters the formula, but just the neonatal mass.  Any ideas on that?&lt;/p&gt;&#xA;" OwnerUserId="352" LastEditorUserId="69" LastEditDate="2012-03-13T22:27:52.727" LastActivityDate="2012-03-14T01:05:14.000" Title="Why do pandas have a high probability of giving birth to twins?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;embryology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1353" PostTypeId="2" ParentId="1350" CreationDate="2012-03-09T16:16:29.463" Score="7" Body="&lt;p&gt;Nico provides a nice answer, but implies that the names are more fluid than they actually are. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible to get an current standard nomenclature, and to update it each time the ICN releases a new edition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ICN requires that any changes be made by an international botanical congress, and changes are included when a new addition of the ICN is released. Also, note that the &lt;a href=&quot;http://en.wikipedia.org/wiki/International_Code_of_Nomenclature_for_Cultivated_Plants&quot;&gt;ICNCP&lt;/a&gt; is used for cultivated plants. &lt;/p&gt;&#xA;" OwnerUserId="154" LastActivityDate="2012-03-09T16:16:29.463" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1354" PostTypeId="1" CreationDate="2012-03-09T16:51:33.147" Score="8" ViewCount="2154" Body="&lt;p&gt;Why is methyl cellulose used as a pharmaceutical excipient? Is it due to certain chemical properties? What are the reasons for relying on the chemical properties of methyl cellulose?&lt;/p&gt;&#xA;" OwnerUserId="604" LastEditorUserId="107" LastEditDate="2012-03-09T18:15:37.587" LastActivityDate="2012-09-26T10:38:49.477" Title="Why is methylcellulose used in pharmaceuticals?" Tags="&lt;pharmacology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1355" PostTypeId="5" CreationDate="2012-03-09T23:25:08.573" Score="0" Body="" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-03-09T23:25:08.573" LastActivityDate="2012-03-09T23:25:08.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1356" PostTypeId="4" CreationDate="2012-03-09T23:25:08.573" Score="0" Body="Where one organism takes advantages from living alongside another organism to the detriment of the host.  " OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-03-09T23:25:08.573" LastActivityDate="2012-03-09T23:25:08.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1357" PostTypeId="5" CreationDate="2012-03-09T23:26:02.863" Score="0" Body="" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-03-09T23:26:02.863" LastActivityDate="2012-03-09T23:26:02.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1358" PostTypeId="4" CreationDate="2012-03-09T23:26:02.863" Score="0" Body="The study of animal behaviour." OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-03-09T23:26:02.863" LastActivityDate="2012-03-09T23:26:02.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1359" PostTypeId="2" ParentId="1198" CreationDate="2012-03-09T23:58:37.753" Score="2" Body="&lt;p&gt;Really good questions. As the guy who brought up LTP/LTD in the question you referenced, I thought I would weigh in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is the traditional definition of LTP/LTD as an increased/decreased synaptic efficacy at a single synapse or in a single cell. As you've noted, this is unlikely to be the only phenomena underlying memory and sometimes it's hard to see how some of these mechanisms can result in memory on behavioral timescales.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me propose, therefore, that the term &lt;strong&gt;long-term plasticity&lt;/strong&gt; is more relevant these days, as it can refer to a variety of mechanisms that relate to the ability of the nervous system to change in stable ways over time. Physiological mechanisms involving changes in protein expression include &lt;em&gt;traditional LTP/LTD at single synapses&lt;/em&gt;, but also &lt;em&gt;homeostatic plasticity&lt;/em&gt; and &lt;em&gt;long-term changes in intrinsic excitability&lt;/em&gt; where the tendency of the cell to fire changes independent of changes in synaptic weighting. Some structural mechanisms include the growth of new synapses, new spines, and new neurons--&lt;em&gt;synaptogenesis&lt;/em&gt;, &lt;em&gt;spinogenesis&lt;/em&gt;, and &lt;em&gt;neurogenesis&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the end, it is all of these mechanisms (and probably more) at play. Note, for instance, that the plasticity may move through structural changes in the system. This means that the lifetime of LTP in one cell or at one synapse does not necessarily have to be the same as the lifetime of the memory itself. All that said, I think all plasticity mechanisms ultimately reduce down to a change in the ability of an input to elicit an action potential somewhere in the brain (known as &lt;em&gt;EPSP-spike coupling&lt;/em&gt;). This is likely to be the basic underlying mechanism of memory.&lt;/p&gt;&#xA;" OwnerUserId="72" LastActivityDate="2012-03-09T23:58:37.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1360" PostTypeId="2" ParentId="1345" CreationDate="2012-03-10T01:11:11.377" Score="10" Body="&lt;p&gt;Good question that got me waist-deep in PubMed. It appears that the directionality of myosin motors is due to the angle at which the actin-binding catalytic domain is attached to the neck region. This review by &lt;a href=&quot;http://dx.doi.org/10.1126/science.288.5463.88&quot;&gt;Vale and Milligan, 2000&lt;/a&gt;, sums up the &quot;unzippering&quot; of the neck region that contributes the force for the movement (a &lt;a href=&quot;http://youtu.be/YAva4g3Pk6k&quot;&gt;video from the review&lt;/a&gt; adapted for Alberts' textbook is also informative).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most myosins move towards the plus end of actin, but myosin VI moves towards the minus end. The neck region of myosin VI attaches to the head region at a different angle than conventional myosins and this is the apparent reason for the change in direction preference (see Figure 1 in review by &lt;a href=&quot;http://dx.doi.org/10.1016/S0962-8924%2800%2901797-9&quot;&gt;Rodriguez and Cheney, 2000&lt;/a&gt;; also &lt;a href=&quot;http://dx.doi.org/10.1016/S0955-0674%2899%2900053-8&quot;&gt;Volkmann and Hanein, 2000&lt;/a&gt;; &lt;a href=&quot;http://dx.doi.org/10.1016/j.biosystems.2008.03.009&quot;&gt;Masuda, 2008&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And for your entertainment, an awesome movie of myosin V walking by &lt;a href=&quot;http://dx.doi.org/10.1038/nature09450&quot;&gt;Kodera et al, 2010&lt;/a&gt; on &lt;a href=&quot;http://youtu.be/edBRWl1vftc&quot;&gt;YouTube&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="72" LastEditorUserId="72" LastEditDate="2012-03-15T17:00:40.957" LastActivityDate="2012-03-15T17:00:40.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1361" PostTypeId="2" ParentId="1352" CreationDate="2012-03-10T06:17:08.760" Score="9" Body="&lt;p&gt;Charnov and Ernest (2006) present data on offspring number per year and neonatal mass for 532 species of mammals. The two are related by the linear regression equation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;ln(offspring/year) = 2.4 - ( 0.3 * ln(neonate mass) )&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Giant panda neonates &lt;a href=&quot;http://www.animalinfo.org/species/carnivor/ailumela.htm#Early&quot;&gt;weigh 100-200 g and are weaned at 46 weeks&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, according to the regression, pandas should have, on average, 2.8 to 2.2 offspring per year (for 100 and 200 g respectively). With a weaning time of 46 weeks, they could have 1.13 (52/46) litters per year. If every litter were exactly twins, that would be 1.13 * 2 = 2.26 offspring per year, which is within the predicted range.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans (neonatal mass of 3400 g) are predicted to have 0.96 offspring/year.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Charnov EL and SKM Ernest. 2006. The Offspring‐Size/Clutch‐Size Trade‐Off in Mammals. &lt;em&gt;American Naturalist&lt;/em&gt; 167:578-582.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-03-10T06:17:08.760" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1362" PostTypeId="1" AcceptedAnswerId="7167" CreationDate="2012-03-10T09:42:42.257" Score="9" ViewCount="1893" Body="&lt;p&gt;Why is blood pressure generally higher in more distal arteries?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4qSMQ.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="327" LastEditorUserId="69" LastEditDate="2012-03-10T15:56:30.137" LastActivityDate="2013-02-11T09:15:06.017" Title="Why is blood pressure higher the more distal an artery is?" Tags="&lt;zoology&gt;&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1365" PostTypeId="1" CreationDate="2012-03-10T21:39:50.403" Score="17" ViewCount="686" Body="&lt;p&gt;HIV compromises the human body to defend against infection. Yet people who are infected with herpes are at less risk of developing AIDS.&lt;/p&gt;&#xA;&lt;p&gt;How does this work?&lt;/p&gt;&#xA;&lt;p&gt;This question comes from this paper, which is hard for me to follow since I am uneducated on this field. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716975/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716975/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="238" LastEditDate="2020-12-13T20:01:31.493" LastActivityDate="2020-12-13T20:01:31.493" Title="How does herpes (HSV) infection suppress HIV?" Tags="&lt;immunology&gt;&lt;pathology&gt;&lt;virology&gt;&lt;hiv&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="1366" PostTypeId="1" CreationDate="2012-03-10T21:45:34.837" Score="5" ViewCount="125" Body="&lt;p&gt;Numerous sources like &lt;a href=&quot;http://www.nature.com/nature/journal/v460/n7253/full/nature08221.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; say that rapamycin increases lifespan. And mTOR antagonism appears to be a large part of this (mTOR antagonism also appears to be a large part of calorie restriction's mechanism too).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the effect of calorie restriction equal to that of rapamycin treatment or are there differences?&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="115" LastEditDate="2012-03-11T13:01:58.230" LastActivityDate="2012-05-11T14:01:21.337" Title="In what ways, if any, does administration of rapamycin *not* mimic calorie restriction?" Tags="&lt;pharmacology&gt;&lt;senescence&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1367" PostTypeId="1" AcceptedAnswerId="2041" CreationDate="2012-03-10T21:58:23.087" Score="2" ViewCount="193" Body="&lt;p&gt;Are the effects additive or subadditive? In many ways, rapamycin &lt;a href=&quot;http://www.nature.com/nature/journal/v460/n7253/full/nature08221.html&quot; rel=&quot;nofollow&quot;&gt;acts like a CR mimetic&lt;/a&gt;, but even CR can only go so far.&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="69" LastEditDate="2012-03-10T22:23:29.980" LastActivityDate="2012-05-02T14:11:17.120" Title="What are the effects of combining rapamycin with dietary restriction?" Tags="&lt;senescence&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1368" PostTypeId="1" CreationDate="2012-03-11T02:04:03.920" Score="4" ViewCount="62" Body="&lt;p&gt;RHEB (Ras homolog enriched in brain) senses amino acid levels in order to recruit mTOR. &#xA;See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21157483&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; review describing the process of how RHEB recruits mTOR. So does RHEB have differential selectivity towards different amino acids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We also discussed this in Matt Kaeberlein's class yesterday and I posed this question but no one could answer it (that said, Matt Kaeberlein called it a good question).&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="3340" LastEditDate="2014-12-06T11:42:58.420" LastActivityDate="2015-01-05T11:54:35.063" Title="Do we know if RHEB is more sensitive to some amino acids than other amino acids?" Tags="&lt;senescence&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1369" PostTypeId="1" CreationDate="2012-03-11T02:07:42.370" Score="1" ViewCount="90" Body="&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/P70S6_kinase&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/P70S6_kinase&lt;/a&gt;...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Phosphorylation of S6 induces protein synthesis at the ribosome.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;P70S6 kinase is in a signaling pathway that includes mTOR (the&#xA;  mammalian target of rapamycin). mTOR can be activated in distinct&#xA;  ways, thereby activating p70S6K. For example, branched chain amino&#xA;  acids such as leucine are sufficient to activate mTOR, resulting in an&#xA;  increase in p70S6K phosphorylation (and thereby activating it). mTOR&#xA;  is also in a pathway downstream of the kinase Akt. Akt is typically&#xA;  activated upon stimulation of a cell with a growth factor (such as&#xA;  IGF-1). Akt then activates mTOR (by inhibiting the Tsc complex),&#xA;  leading to p70S6K activation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;We also found a paper showing that downregulation of S6 kinase also results in a decrease in protein translation in yeast (but I'm waiting for Matt Kaeberlein to email me the slides from yesterday).&lt;/p&gt;&#xA;" OwnerUserId="103" LastActivityDate="2012-05-02T16:22:50.630" Title="If inhibiting S6 kinase decreases protein translation, then could inhibiting S6 kinase could possibly slow down long-term potentiation in neurons?" Tags="&lt;molecular-biology&gt;&lt;neuroscience&gt;&lt;senescence&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1370" PostTypeId="2" ParentId="1354" CreationDate="2012-03-11T03:26:13.350" Score="6" Body="&lt;p&gt;Methyl cellulose is a dry binder. It is used to make a pill with a small mass of active ingredient and as much binder as required to make the pill a manageable size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following properties make methyl cellulose a good dry binder:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;inexpensive&lt;/li&gt;&#xA;&lt;li&gt;non-allergic&lt;/li&gt;&#xA;&lt;li&gt;vegetarian&lt;/li&gt;&#xA;&lt;li&gt;soluble in cold water&lt;/li&gt;&#xA;&lt;li&gt;non-digestable&lt;/li&gt;&#xA;&lt;li&gt;nontoxic&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Most of this information is from the &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Methyl_cellulose&quot;&gt;Wikipedia&lt;/a&gt; article.&lt;/p&gt;&#xA;" OwnerUserId="154" LastEditorUserId="223" LastEditDate="2012-03-11T08:25:56.017" LastActivityDate="2012-03-11T08:25:56.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1371" PostTypeId="1" AcceptedAnswerId="1374" CreationDate="2012-03-11T07:30:13.590" Score="7" ViewCount="9276" Body="&lt;p&gt;Often, a smooth response to a hormone means that some processes must be sped up and others must be slowed down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can a single hormone have opposite effects like this?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="69" LastEditDate="2012-03-11T11:58:53.327" LastActivityDate="2012-03-12T13:14:27.540" Title="Single hormone opposite effects" Tags="&lt;biochemistry&gt;&lt;endocrinology&gt;&lt;chemical-communication&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1372" PostTypeId="1" AcceptedAnswerId="1373" CreationDate="2012-03-11T07:34:29.527" Score="9" ViewCount="274" Body="&lt;p&gt;From my understanding free radicals play a slight role in ageing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In what ways are they so damaging, and can a restricted diet reduce production of free radicals?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="69" LastEditDate="2012-03-11T11:52:47.093" LastActivityDate="2012-06-27T07:42:48.057" Title="Free Radicals for aging" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;senescence&gt;&lt;chemical-communication&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1373" PostTypeId="2" ParentId="1372" CreationDate="2012-03-11T11:30:46.817" Score="10" Body="&lt;p&gt;Free radicals are damaging because their unpaired electrons (or not fully filled valence shell) makes them highly reactive species. They are often considered together with highly oxidizing &quot;reactive oxygen species&quot; (ROS) such as peroxides. They are especially problematic for cell membranes and DNA. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12031895&quot;&gt;In the latter they can react with (oxidize) heterocyclic bases.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As suggested first by Gerschmann et al. (1954), since oxidative damage to cells and cell structures is seen to accumulate with age, the corollary of this could be that aging is a result of oxidative damage. The very fact that cells have antoxidant enzymes such as superoxide dismutase (SOD) suggests that suppression of these species is important in the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many (but not all) ROS originate from mitochondria during cell metabolism. Therefore, it has been suggested that by regulating metabolism (that is, reducing the metabolic rate) the &quot;rate of living theory&quot; (Harman 1981) the rate of oxidative damage can be reduced. One way to do this may be calorie restriction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This idea seems to fallen out of favour though. Another possibility is that the rate of mitochondrial ROS has nothing to do with metabolic rate per se; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12067594?dopt=Abstract&quot;&gt;rather it might simply be a longevity determinant.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, having said all this there is evidence that ROS are actually crucial in a number cellular pathways. &lt;a href=&quot;http://senescence.info/causes_of_aging.html#section3://&quot;&gt;It may be that it is the deregulation of pathways managing ROS that can contribute to aging rather than simply damage accumulation with age.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gerschman, R., Gilbert, D. L., Nye, S. W., Dwyer, P., and Fenn, W. O. (1954). &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/13156638&quot;&gt;Oxygen poisoning and x-irradiation: a mechanism in common.&lt;/a&gt;&quot; Science 119(3097):623-626. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Harman, D. (1981). &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6947277&quot;&gt;The aging process.&lt;/a&gt;&quot; Proc Natl Acad Sci U S A 78(11):7124-7128.&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-03-12T11:09:05.137" LastActivityDate="2012-03-12T11:09:05.137" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1374" PostTypeId="2" ParentId="1371" CreationDate="2012-03-11T12:30:37.380" Score="6" Body="&lt;p&gt;An hormone is not different from most other molecules. To have an effect on a cell it binds to a (more or less specific) receptor, located either on the plasma membrane or inside the cell, and it initiates an intracellular cascade of events&lt;sup&gt;1&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several ways an hormone can have different effects:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;there can be multiple receptors for the same hormone. For instance, &lt;a href=&quot;http://en.wikipedia.org/wiki/Prolactin&quot; rel=&quot;nofollow&quot;&gt;prolactin&lt;/a&gt; can bind to two receptors, called prolactin receptor (PRL-R) short and long form. The short form of the receptor has been shown to lack the ability to promote milk protein genes transcription (See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC50906/&quot; rel=&quot;nofollow&quot;&gt;Lesueur et al., PNAS - 1991&lt;/a&gt;).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the same receptor can be coupled to different intracellular pathways in different cell types / physiological conditions, thus resulting in different effects.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;each cell type/tissue expresses a set of protein that will interact in a different manner with the intracellular cascade promoted by the hormone.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;an hormone can interact with receptors for other molecules. For instance allopregnanolone, a metabolite of progesterone, is a potent agonist of the GABA-A receptor, giving it anxiolitic properties.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;An interesting example is that of estrogenic compound. Several receptors exist for estradiol (E2). The &quot;classical&quot; receptors are called ER-alpha and ER-beta, and they are located in the cytoplasm. The binding of E2 to the ER promotes their dimerization and entrance into the nucleus where they can promote the transcription of various genes. ERs can also bind to other transcription factors and modulate their activity. So, depending on which transcription factors are present different genes will be transcribed in response to E2. Moreover, ER-beta can have opposite effects then ER-alpha (see for instance &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC18537/&quot; rel=&quot;nofollow&quot;&gt;Weihua et al., PNAS - 2000&lt;/a&gt;). In addition, receptors like ERs can be activated also in absence of the endogenous hormone: for instance, dietary amino acids activate ER-alpha in liver by a mTOR-dependent phosphorylation (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21284987&quot; rel=&quot;nofollow&quot;&gt;Della Torre et al., Cell Metabolism 2011&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To make things more complicated, membrane receptor for estrogen have been described, such as GPR30 (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15705806&quot; rel=&quot;nofollow&quot;&gt;Revankar et al., Science - 2005&lt;/a&gt;), membrane &quot;versions&quot; of the classical ERs, plus various splicing variants of the ERs (mostly expressed in tumoral tissue).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GPR30 in breasts has been shown to activate certain molecular pathways (notably Erk1/2) that contribute to cellular growth (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11043579&quot; rel=&quot;nofollow&quot;&gt;Filardo et al., Mol Endocrinol. - 2000&lt;/a&gt;), possibly linking it to proliferation of ER-negative breast tumours. Other tissues that do not express GPR30 will lack this E2-induced proliferative stimulus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, tissue- or time- dependent modulation of the receptors and of the intracellular pathways associated with it can allow the body to respond to the same hormone (or, more in general, to the same molecule) in opposite ways.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt; This is a simplification, not every substance (and not every hormone) acts by binding to receptors, but let's keep things simple.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="444" LastEditDate="2012-03-12T13:14:27.540" LastActivityDate="2012-03-12T13:14:27.540" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1375" PostTypeId="1" AcceptedAnswerId="31179" CreationDate="2012-03-11T14:15:59.803" Score="10" ViewCount="1883" Body="&lt;p&gt;This morning I saw a bird that I have never seen before. Since it was quite big, I'm very interested in knowing its name.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bird was quite big, at least 2-3 times of a common blackbird. The wings were completely black but the whole back strip was quite yellow. Also the tail was yellow. The tail widens towards the end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bird flew very strange... it trundled towards the ground and then flew back up some meters before trundling down again. I observed the bird in Zurich, Switzerland at the outer border of the city. A big forest is quite near and there are some huge trees very close to the bird.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then one last thing to add: I'm not really sure about that, but it could be that the bird had a nest on top of a big tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any ideas which bird that could be?&lt;/p&gt;&#xA;" OwnerUserId="608" LastEditorUserId="69" LastEditDate="2012-03-11T14:53:09.477" LastActivityDate="2020-01-27T23:44:47.923" Title="What's the name of this bird?" Tags="&lt;zoology&gt;&lt;ornithology&gt;&lt;species-identification&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1376" PostTypeId="5" CreationDate="2012-03-11T14:56:53.417" Score="0" Body="" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-03-11T14:56:53.417" LastActivityDate="2012-03-11T14:56:53.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1377" PostTypeId="4" CreationDate="2012-03-11T14:56:53.417" Score="0" Body="Questions relating to the study of fish or icthyology." OwnerUserId="69" LastEditorUserId="6289" LastEditDate="2016-08-30T05:49:23.520" LastActivityDate="2016-08-30T05:49:23.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1378" PostTypeId="5" CreationDate="2012-03-11T14:57:12.123" Score="0" Body="&lt;p&gt;Ornithology is the study of birds including their anatomy, physiology, behaviour, ecology, and general biology. &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="16866" LastEditDate="2019-08-25T03:47:08.367" LastActivityDate="2019-08-25T03:47:08.367" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="1379" PostTypeId="4" CreationDate="2012-03-11T14:57:12.123" Score="0" Body="Questions relating to the study of birds." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T14:02:06.423" LastActivityDate="2013-10-31T14:02:06.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1380" PostTypeId="2" ParentId="1375" CreationDate="2012-03-11T15:39:22.340" Score="6" Body="&lt;p&gt;Hmmmm... the only one I can think of fitting at least in part your description would be the golden oriole (&lt;em&gt;Oriolus oriolus&lt;/em&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I say partly because it definitely is not 2-3 times a blackbird, could be slightly bigger, but on average it is the same size. Also it sounds extremely unlikely that you have spotted it in early March in Zurich, as they should be in Southern Africa right now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image, from Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/d/d2/Oriole_2.jpg&quot; alt=&quot;Golden Oriole&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could not find anything else fitting your description in my field guide (Mullarney &amp;amp; Svensson - Birds of Europe)&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.623" LastActivityDate="2012-03-11T15:39:22.340" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1381" PostTypeId="2" ParentId="1362" CreationDate="2012-03-11T18:40:34.823" Score="3" Body="&lt;p&gt;The cardiovascular system is affected by three types of pressure.  These are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Heamodynamic&lt;/strong&gt; - caused by the contraction of the heart, which would give the view of pressure being higher closer to the aorta as in Kevin's answer and my first thought too.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Kinetic&lt;/strong&gt;  - caused by the action of skeletal muscles in movement in squeezing primarily veins to return blood to the heart. &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Hydrostatic&lt;/strong&gt; - the combination of fluid density and gravity that leads to pressure on the vessel endothelium.  The pressure at a given point is proportional to the volume of fluid above it.  This means that pressure is highest at the bottom of the vessel.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Arteries can of course be treated as one long tube due to their lack of valves, therefore the hydrostatic pressure could be significant in contributing to total blood pressure.  If hydrostatic pressure is more significant than heamodynamic pressure then this would explain why pressure would be higher the more distal the artery is - when standing there is simply more blood pushing down on it.    &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://ccn.aacnjournals.org/content/22/2/60.full&quot; rel=&quot;nofollow&quot;&gt;Critical Care Nurse. 2002;22: 60-79&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-03-11T18:40:34.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1382" PostTypeId="1" AcceptedAnswerId="1392" CreationDate="2012-03-11T22:23:05.947" Score="25" ViewCount="6920" Body="&lt;p&gt;Which animal/plant/anything has smallest length genome? &lt;/p&gt;&#xA;" OwnerUserId="610" LastEditorUserId="69" LastEditDate="2012-03-11T23:12:26.173" LastActivityDate="2016-10-16T18:47:15.960" Title="Which organism has the smallest genome length?" Tags="&lt;dna&gt;&lt;genomes&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1383" PostTypeId="1" AcceptedAnswerId="1393" CreationDate="2012-03-11T22:56:59.807" Score="5" ViewCount="1002" Body="&lt;p&gt;A human male and female couple with normal colored ears discover that, in both of their families, their fathers (who have normal ears) each had siblings with red ears.  Red ears is a rare autosomal recessive disorder.  None of their grandparents had red ears.  Assume that the red ears in both families were caused by mutations in the same gene, that there were no new mutations within the pedigrees, and that the mothers of the couple were not carriers of the disease gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A) based on the information, what is the probability that the male in the couple is a carrier of the red ear disease gene?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B) if the couple had 1 child, what would be the probability that child would have red ears?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was discussing this problem over with a friend and we got different answers.  &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;A)I think the answer is 25%.  I multiplied 1/2 and 1/2.&#xA;B)6.25%.  I multiplied 1/4 and 1/4.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="558" LastEditorUserId="69" LastEditDate="2012-03-18T15:11:50.230" LastActivityDate="2012-03-18T15:11:50.230" Title="Genetic carrier Pedigree of Recessive Traits" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;genetic-diagrams&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1384" PostTypeId="1" AcceptedAnswerId="1394" CreationDate="2012-03-11T23:36:57.633" Score="8" ViewCount="4184" Body="&lt;p&gt;I have noticed when in a dark room light and color seem to be brighter and more intense in the corner of my eyes. For example the light that comes from my digital clock seems like a dark pink when I look straight at it. But when I see it in the corner of my eyes it looks red. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What causes this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this normal, does everyone perceive it that way?&lt;/p&gt;&#xA;" OwnerUserId="611" LastEditorUserId="6" LastEditDate="2012-03-12T09:54:02.940" LastActivityDate="2012-03-12T09:54:02.940" Title="What causes light to be brighter in the corner of the eyes?" Tags="&lt;human-biology&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1385" PostTypeId="2" ParentId="1382" CreationDate="2012-03-12T00:00:36.253" Score="10" Body="&lt;p&gt;I want to say &lt;em&gt;Mycoplasma genitalium&lt;/em&gt; with a genome size of 582,970 bp. Turns out the answer is &lt;em&gt;Nanoarchaeum eqitans&lt;/em&gt; with a genome of 490,885 bp.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Nanoarchaeum&quot;&gt;http://en.wikipedia.org/wiki/Nanoarchaeum&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14566062&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/14566062&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-03-12T00:00:36.253" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1386" PostTypeId="5" CreationDate="2012-03-12T00:06:49.023" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-03-12T00:06:49.023" LastActivityDate="2012-03-12T00:06:49.023" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1387" PostTypeId="4" CreationDate="2012-03-12T00:06:49.023" Score="0" Body="The use of methods from the physical sciences to aid in the study of biological systems." OwnerUserId="389" LastEditorUserId="4101" LastEditDate="2013-10-31T00:52:52.853" LastActivityDate="2013-10-31T00:52:52.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1388" PostTypeId="5" CreationDate="2012-03-12T00:10:15.430" Score="0" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/?title=Genomics&quot; rel=&quot;nofollow&quot;&gt;Genomics&lt;/a&gt; is essentially an extension of genetics such that many or all genes are studied simultaneously.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions that can have this tag:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Questions related to genome sequencing and assembly (See also &lt;a href=&quot;/questions/tagged/dna-sequencing&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;dna-sequencing&amp;#39;&quot; rel=&quot;tag&quot;&gt;dna-sequencing&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Questions related to variation in genomes (SNPs, CNVs)&lt;/li&gt;&#xA;&lt;li&gt;Questions related to genome-wide association studies (GWAS)&lt;/li&gt;&#xA;&lt;li&gt;Questions related to comparisons of genomes, e.g. its organization or function, between different organisms.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="4101" LastEditDate="2015-06-19T19:29:35.543" LastActivityDate="2015-06-19T19:29:35.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1389" PostTypeId="4" CreationDate="2012-03-12T00:10:15.430" Score="0" Body="The study of genomes, the entire set of genes in an organism." OwnerUserId="389" LastEditorUserId="3340" LastEditDate="2015-06-19T16:11:42.510" LastActivityDate="2015-06-19T16:11:42.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1390" PostTypeId="5" CreationDate="2012-03-12T00:16:13.350" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-03-12T00:16:13.350" LastActivityDate="2012-03-12T00:16:13.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1391" PostTypeId="4" CreationDate="2012-03-12T00:16:13.350" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-03-12T00:16:13.350" LastActivityDate="2012-03-12T00:16:13.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1392" PostTypeId="2" ParentId="1382" CreationDate="2012-03-12T00:17:57.237" Score="44" Body="&lt;p&gt;Since you said plant/animal/anything, I offer the smallest genomes in various categories...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Kb means Kilobases, Mb means Megabases. 1 Kb = 1000 base pairs, 1Mb = 1000Kb)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Smallest plant genome: &lt;em&gt;Genlisea margaretae&lt;/em&gt; at 63Mb (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1055/s-2006-924101/abstract;jsessionid=9DD396FA89FD33C27678C0FE3C7A0895.d01t04&quot;&gt;Greilhuber et al., 2006&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Smallest animal genome: &lt;em&gt;Pratylenchus coffeae&lt;/em&gt; (nematode worm) at 20Mb (&lt;a href=&quot;http://www.genomesize.com/statistics.php?stats=entire&quot;&gt;Animal Genome Size DB&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Smallest vertebrate genome: &lt;em&gt;Tetraodon nigroviridis&lt;/em&gt; (pufferfish) at 385Mb (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15496914&quot;&gt;Jailon et al., 2004&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Smallest eukaryote: &lt;em&gt;Encephalitozoon cuniculi&lt;/em&gt; (microsporidian) at 2.9Mb (&lt;a href=&quot;http://www.springerlink.com/content/j20626g827623n73/abstract/&quot;&gt;Vivarès &amp;amp; Méténier, 2004&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Smallest free-living bacterial genome: &lt;em&gt;Nanoarchaeum eqitans&lt;/em&gt; at 491Kb (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14566062&quot;&gt;Waters et al., 2003&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Smallest bacterial genome: &lt;em&gt;Carsonella ruddii&lt;/em&gt; (endosymbiont) at 160Kb (&lt;a href=&quot;http://www.sciencemag.org/content/314/5797/267&quot;&gt;Nakabachi et al., 2006&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Smallest genome of anything: &lt;em&gt;Circovirus&lt;/em&gt; at 1.8Kb (only 2 proteins!!) (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12745370&quot;&gt;Chen et al., 2003&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Refs...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12745370&quot;&gt;Chen, C.-L., Chang, P.-C., Lee, M.-S., Shien, J.-H., Ou, S.-J. &amp;amp; Shieh, H.K. (2003) Nucleotide sequences of goose circovirus isolated in Taiwan. Avian Pathology: Journal of the W.V.P.A. 32 (2), 165–171.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1055/s-2006-924101/abstract;jsessionid=9DD396FA89FD33C27678C0FE3C7A0895.d01t04&quot;&gt;Greilhuber, J., Borsch, T., Müller, K., Worberg, A., Porembski, S. &amp;amp; Barthlott, W. (2006) Smallest Angiosperm Genomes Found in Lentibulariaceae, with Chromosomes of Bacterial Size. Plant Biology. 8 (6), 770–777.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1055/s-2006-924101/abstract;jsessionid=9DD396FA89FD33C27678C0FE3C7A0895.d01t04&quot;&gt;Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., Nicaud, S., Jaffe, D., Fisher, S., Lutfalla, G., et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 431 (7011), 946–957.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencemag.org/content/314/5797/267&quot;&gt;Nakabachi, A., Yamashita, A., Toh, H., Ishikawa, H., Dunbar, H.E., Moran, N.A. &amp;amp; Hattori, M. (2006) The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella. Science. 314 (5797), 267–267.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.springerlink.com/content/j20626g827623n73/abstract/&quot;&gt;Vivarès, C.P. &amp;amp; Méténier, G. (2004) Opportunistic Infections: Toxoplasma, Sarcocystis, and Microsporidia. In: World Class Parasites. Springer US. pp. 215–242.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14566062&quot;&gt;Waters, E., Hohn, M.J., Ahel, I., Graham, D.E., Adams, M.D., Barnstead, M., Beeson, K.Y., Bibbs, L., Bolanos, R., Keller, M., Kretz, K., Lin, X., Mathur, E., Ni, J., et al. (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proceedings of the National Academy of Sciences of the United States of America. 100 (22), 12984–12988.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-03-12T00:34:47.637" LastActivityDate="2012-03-12T00:34:47.637" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1393" PostTypeId="2" ParentId="1383" CreationDate="2012-03-12T00:35:31.880" Score="6" Body="&lt;p&gt;&lt;strong&gt;Let's take Question A:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both fathers have siblings with red ears, and red ears are an autosomal recessive trait. The grandparents did not have red ears, we know then that they were carriers of the recessive allele. Each grandparent was Nr (for Normal and red alleles respectively).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fathers have normal ears, so they could be NN (probability 0.33) or Nr (probability 0.67).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer then is that each father independently has a 2/3 chance (0.67 probability) of carrying the red ears gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The male's mother, being RR, makes the male a carrier only if the male's father is himself a carrier. To put it mathematically, he has a 1/2 chance of being a carrier with 2/3 probability that he was a carrier to begin with. (2/3)*(1/2) = 1/3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore the male can be carrier with 1/3 chance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Now Question B:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Short answer:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the male and female have symmetrical pedigrees, and we just solved the chance of the male being a carrier with 1/3 chance, then the chance of them having a child with red ears is (1/3)*(1/3) = 1/9.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Long answer:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The male's and female's fathers may each be heterozygous or homozygous normal, given the information, with both mothers being homozygous normal (NN).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If Father A is NN (crossed with Mother A, also NN), there is a 0 probability of passing on the red ears allele.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If Father A is Nr, then Person A has a 0.5 probability of carrying the red ear allele.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Person A can now be NN (with 0.25 probability) or Nr (with 0.5 probability).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Likewise with Person B.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now lets consider all 4 combinations of genotypes that Person A and B can have when they have a child. I will write a table with one Person on each side of the table, with the probability of their genotype written in brackets beside. Each intersection will represent the frequency of carrying the red ears allele.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;                Person B&#xA;             (1/3)     (2/3)&#xA;Person A      NN        Nr&#xA;(1/3) NN      0/4       2/4&#xA;(2/3) Nr      2/4       2/4&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Carrying the red ear gene: (A more interesting example)&lt;/strong&gt;&#xA;There are a total of 6 outcomes in which the child carries the red ears allele, but these must be weighted by the probability that each parent has the associated genotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probability of carrying 'r' = [ (1/3)(1/3)(0/4) + (1/3)(2/3)(2/4) + (2/3)(1/3)(2/4) + (2/3)(2/3)(2/4) ] / [ (1/3)(1/3) + (1/3)(2/3) + (2/3)(1/3) + (2/3)(2/3) ]&#xA; &lt;strong&gt;= 0.25&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Having a child with red ears:&lt;/strong&gt;&#xA;Probability of having red ears = [ (1/3)(1/3)(0/4) + (1/3)(2/3)(0/4) + (2/3)(1/3)(0/4) + (2/3)(2/3)(1/4) ] / [ (1/3)(1/3) + (1/3)(2/3) + (2/3)(1/3) + (2/3)(2/3) ]&#xA; &lt;strong&gt;= 1/9 or about 0.11&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's left as an exercise to the student to derive the remaining probabilites.&#xA;Nr 4/9&#xA;NN 4/9&#xA;rr 1/9&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2012-03-12T01:05:45.853" LastActivityDate="2012-03-12T01:05:45.853" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1394" PostTypeId="2" ParentId="1384" CreationDate="2012-03-12T02:16:22.067" Score="9" Body="&lt;p&gt;Your retina has two kinds of light-sensing nerves: cones and rods. Cones are responsible for color vision, i.e. hue, while your rods handle differences in the value, as in how bright it is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans have adapted to have cones mostly in the center of the eye (which corresponds to what you're looking directly at), where the most distinguishing color information is needed. It's not often that you'd use your peripheral vision to identify the actual color of something, and this explains why you're seeing a difference between pink and red. The intensity of the color is correct, but you aren't able to identify the hue because of a lack of cone nerves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes, this is normal. A fun trick (and also totally helpful if you have a messy room) is to look a foot or so above the floor when you're walking in the dark. It allows you to see what you're walking on better, since you need intensity receptors more than color receptors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://regentsprep.org/Regents/physics/phys09/ceyes/sensing.htm&quot;&gt;http://regentsprep.org/Regents/physics/phys09/ceyes/sensing.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/vision/rodcone.html&quot;&gt;http://hyperphysics.phy-astr.gsu.edu/hbase/vision/rodcone.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="575" LastActivityDate="2012-03-12T02:16:22.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1395" PostTypeId="2" ParentId="1341" CreationDate="2012-03-12T12:30:41.323" Score="2" Body="&lt;p&gt;As the concentration of sugars in the sap increases, so does viscosity. At high viscosity, the sap will not flow at a sufficient rate to provide nourishment to the different plant tissues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, there are limitations to concentrating the solutes in the sap. As the sap becomes more concentrated, the plant would be working against a osmotic gradient to further increase that concentration. That energy cost may be too great.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-03-12T15:15:01.320" LastActivityDate="2012-03-12T15:15:01.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1396" PostTypeId="2" ParentId="1372" CreationDate="2012-03-12T12:42:01.900" Score="5" Body="&lt;p&gt;Nice answer by Poshpaws +1. Free radicals can damage membranes (especially important for mitochondrial and endoplasmic reticulum membrane function), DNA (genes, telomeres,  and mitochondrial DNA, eg), and microsomes. These are the things we consider with regard to ROS for our research on aging.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The role of diet is not clear. Smoking and alcohol may have greater effects on ROS levels than diet itself. However, people who smoke too much or drink too much generally have poorer diets (based on our (and others) epidemiological data). The role of homocysteine (Hcy) in ROS levels cannot be discounted and Hcy is influenced by genetics, diet, inflammation state in addition to other factors. In short, the evidence is not conclusive that a &quot;restricted diet&quot; (did you mean caloric restriction?) will certainly lower ROS levels.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-03-12T12:42:01.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1397" PostTypeId="1" CreationDate="2012-03-12T15:32:27.177" Score="3" ViewCount="1925" Body="&lt;p&gt;Has there been any serious scientific inquiries into answering this age old question?&lt;/p&gt;&#xA;" OwnerUserId="177" LastEditorUserId="307" LastEditDate="2012-04-06T04:06:00.647" LastActivityDate="2014-10-31T16:18:39.720" Title="Which came first: The Chicken or the Egg?" Tags="&lt;evolution&gt;" AnswerCount="4" CommentCount="5" FavoriteCount="2" ClosedDate="2012-04-05T18:55:01.693" ContentLicense="CC BY-SA 3.0" />
  <row Id="1398" PostTypeId="2" ParentId="1397" CreationDate="2012-03-12T15:39:39.420" Score="1" Body="&lt;p&gt;Dunno about any serious scientific inquiries into the answer but I always thought the answer is egg. At some point the modern chicken has come into being as the progeny of two pre-modern chickens, however it had to be an egg before it could be a chicken and its parents couldn't have been modern chickens.&lt;/p&gt;&#xA;&lt;p&gt;However, all that presupposes that you can draw a line in the evolutionary history of the modern (extant) chicken and say this is modern and what goes before is not. I dunno if that really can be done.&lt;/p&gt;&#xA;&lt;p&gt;Edit: came across this guardian article: &lt;a href=&quot;http://www.guardian.co.uk/science/2006/may/26/uknews&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.guardian.co.uk/science/2006/may/26/uknews&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&amp;quot;Whether chicken eggs preceded chickens hinges on the nature of chicken eggs,&amp;quot; said panel member and philosopher of science David Papineau at King's College London.&lt;/p&gt;&#xA;&lt;p&gt;&amp;quot;I would argue it's a chicken egg if it has a chicken in it. If a kangaroo laid an egg from which an ostrich hatched, that would surely be an ostrich egg, not a kangaroo egg. By this reasoning, the first chicken did indeed come from a chicken egg, even though that egg didn't come from chickens.&amp;quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;And from Prof. Brookfield of the University of Nottingham:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The first chicken must have differed from its parents by some genetic change, perhaps a very subtle one, but one which caused this bird to be the first ever to fulfil our criteria for truly being a chicken; Thus the living organism inside the eggshell would have had the same DNA as the chicken that it would develop into, and thus would itself be a member of the species of chicken&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="476" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-12-04T14:38:36.520" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1399" PostTypeId="2" ParentId="1397" CreationDate="2012-03-12T16:25:58.843" Score="14" Body="&lt;p&gt;Most theories about origin of life say that unicellular organisms were first and multicellularity (like chicken) evolved much later, so in that meaning egg (single cell)* was first. Also, almost all chicken ancestors lay eggs (primitive birds, non-avian reptiles, amphibians, fishes and so on...) so eggs existed much earlier than chickens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*in the meaning of zygote. The development of chicken embryo starts in hen's oviducts, so it's not a single cell at the moment when hen lays it (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10070/&quot; rel=&quot;nofollow&quot;&gt;Gilbert, 2000&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="68" LastEditorUserId="4579" LastEditDate="2014-10-31T16:18:39.720" LastActivityDate="2014-10-31T16:18:39.720" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1400" PostTypeId="2" ParentId="1365" CreationDate="2012-03-12T21:25:19.333" Score="15" Body="&lt;p&gt;Alright, having read the citation linked, and doing a little poking of my own, here's my approach at an answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Some&lt;/strong&gt; human herpes virus infections may compete with HIV infection. Essentially, some strains (not the ones you normally think of) infect CD4 cells - the same cells targeted by HIV. These strains down regulate transcription in CD4 cells, which in turn interferes with the HIV infection process. This pertains, it appears most notably, to HHV-7.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;However&lt;/em&gt; the actual impact on HIV disease isn't clear. Strain competition triggers some fascinating evolutionary pressures, but HIV is notoriously prone to mutation, and competition for CD4 cells might not impact HIV infection on a clinical - rather than microbiological - scale.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, the two most commonly thought of forms of herpesvirus infection, HSV-1 and HSV-2 are associated with &lt;em&gt;increased&lt;/em&gt; acquisition of HIV infection. The clearest reasons for this are genital lesions and inflammation at the site of HIV infection. There's also some interesting dynamics in play for active coinfection, such as the impact of acyclovir treatment for HSV impacting HIV, or HAART treatment for HIV impacting HSV.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2012-03-12T21:25:19.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1401" PostTypeId="2" ParentId="1397" CreationDate="2012-03-12T22:51:08.633" Score="3" Body="&lt;p&gt;This is a classic case of &quot;it depends on the context.&quot;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;The Egg&lt;/strong&gt;: As Marta Cz-C points out, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Amniotic_egg&quot; rel=&quot;nofollow&quot;&gt;amniotic eggs&lt;/a&gt; that chickens lay were inherited virtually unmodified from their &lt;a href=&quot;http://en.wikipedia.org/wiki/Theropoda&quot; rel=&quot;nofollow&quot;&gt;theropod dinosaur&lt;/a&gt; ancestors. So when considering the &lt;em&gt;type&lt;/em&gt; of eggs, the egg came first.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;The Chicken&lt;/strong&gt;: From a systematic perspective, you must first have an animal that you would call a chicken before it can lay a &quot;chicken&quot; egg. So considering the &lt;em&gt;animal&lt;/em&gt;, the chicken.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-03-12T22:51:08.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1402" PostTypeId="2" ParentId="1093" CreationDate="2012-03-12T22:52:44.933" Score="10" Body="&lt;p&gt;Dairy cows are bred, or selected to give milk.  So they do produce excessively.  The normal bovine wild type, like other mammals, not only produce less milk, but also will tend to stop lactating when the calf is not nursing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be interested to know if dairy cows stop giving milk if they are not milked every day.  I understand they can get very uncomfortable if they are not milked, but i don't know if they stop giving milk or if they are injured in some way. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-03-12T22:52:44.933" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1403" PostTypeId="1" AcceptedAnswerId="3380" CreationDate="2012-03-12T23:18:32.203" Score="7" ViewCount="700" Body="&lt;p&gt;How did accents first develop? Was it climate dependent? or was it a social behavioural issue?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any biological reason for the development of accents?&lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="3952" LastEditDate="2013-08-04T02:07:57.713" LastActivityDate="2013-08-04T02:07:57.713" Title="Is there a biological basis for different accents?" Tags="&lt;communication&gt;&lt;linguistics&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1404" PostTypeId="1" AcceptedAnswerId="1405" CreationDate="2012-03-12T23:20:54.727" Score="5" ViewCount="1019" Body="&lt;p&gt;I understand there are a number of protein-protein interactions, but what types of interactions exist? and what are the characteristics of them?&lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="158" LastEditDate="2012-03-13T11:26:55.273" LastActivityDate="2012-03-13T11:26:55.273" Title="What are the various types of protein-protein interactions" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1405" PostTypeId="2" ParentId="1404" CreationDate="2012-03-13T01:00:06.927" Score="6" Body="&lt;p&gt;There are so many types of protein-protein interactions via various domains, such as SH2 binding (in RTK signaling), Pleckstrin Homology domain (involved in signaling) among others. This site gives a nice list: &lt;a href=&quot;http://pawsonlab.mshri.on.ca/index.php?option=com_content&amp;amp;task=view&amp;amp;id=30&amp;amp;Itemid=63&quot;&gt;http://pawsonlab.mshri.on.ca/index.php?option=com_content&amp;amp;task=view&amp;amp;id=30&amp;amp;Itemid=63&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, protein-protein interactions rely on the premises of basic biochemistry:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;van-der waals interactions (at the most basic level)&lt;/li&gt;&#xA;&lt;li&gt;Electrostatic interactions&lt;/li&gt;&#xA;&lt;li&gt;&quot;Lock and Key&quot; model: Some proteins have specific binding pockets for domains of other proteins&lt;/li&gt;&#xA;&lt;li&gt;Induced fit&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are many ways to study protein-protein interactions, including, but not limited to&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Pull-down assays&lt;/li&gt;&#xA;&lt;li&gt;2D SDS-PAGE / MS&lt;/li&gt;&#xA;&lt;li&gt;Yeast two-hybrid&lt;/li&gt;&#xA;&lt;li&gt;Immunoprecipitation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="177" LastActivityDate="2012-03-13T01:00:06.927" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1406" PostTypeId="1" AcceptedAnswerId="1417" CreationDate="2012-03-13T11:21:59.497" Score="6" ViewCount="682" Body="&lt;p&gt;I would like to know, is there any enzyme which does the transformation of hydroxyl group to any other functional group using the enzyme. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The substrate is aromatic hydroxyl group. Product should not have hydroxyl group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How should these types of queries be searched for?&lt;/p&gt;&#xA;" OwnerUserId="602" LastEditorUserId="338" LastEditDate="2012-03-16T13:56:38.793" LastActivityDate="2018-02-12T22:38:10.473" Title="Is there an enzyme for the transformation of the hydroxyl group?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="1408" PostTypeId="2" ParentId="1152" CreationDate="2012-03-13T13:54:24.190" Score="3" Body="&lt;p&gt;Consider mRNA &lt;em&gt;primary&lt;/em&gt; structure in terms of uORFs, upstream open reading frames. These can cause ribosome pausing or slowing and even disassociation from the mRNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I agree that a definite answer is not known (+1). For different mRNAs, under different cellular conditions (eg, low levels of a given charged tRNA), the balance or interplay between structure- and codon usage-based control of translation could be different.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-03-13T13:54:24.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1409" PostTypeId="2" ParentId="854" CreationDate="2012-03-13T16:56:01.853" Score="1" Body="&lt;p&gt;I could read this question more than one way.  Are you talking about an enzyme in a cell or in a reaction in vitro?  Kinetics and mechanical explanations can overlap, but are not entirely the same and are usually dealt with separately - kinetics with watching the rate of reactions in a tube and mechanism in a crystal structure or possibly Nuclear Magnetic Resonance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Protein structures are usually static- you only get a time lapse snapshot of the reaction in most cases. kinetics allows you to see how fast these things go and can help you understand the order of binding when more than one component is needed for the reaction, etc.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The polymerase has a binding pocket where the template strand and the growing strand are used to build a double helix together.  if the base being introduced does not form Watson Crick base pair bonds, the geometry of the reaction will not allow the base to be added to the growing strand.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps? If I can make this clearer, can you drop me a comment and I'll revise...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-11-07T18:28:27.330" LastActivityDate="2012-11-07T18:28:27.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1410" PostTypeId="2" ParentId="862" CreationDate="2012-03-13T17:00:44.580" Score="4" Body="&lt;p&gt;It seems like you answered your own question,the signal from a few molecules running through an enzyme or a polymerase tend to fall out of synch after a few hundred bases.  If an enzyme for sequencing was more rigorously in time step that could help for instance.  The machines read traces in four channels with nice bumps for each base.  See &lt;a href=&quot;http://www.codoncode.com/GSAposter/GSA_Adap.html&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; for a nice example. You can see that if there are too many of the same base consecutively it gets hard to tell how many bases there are there.  Over time all four traces will start to smear out and you cant tell Adam from Thelma if you take my meaning. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But there are other bottlenecks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sequencers currently put out such a high volume of data that the analysis of the meaning of the output data can't be analyzed fast enough.  This follows the trend in biotech over the past 12 years or so - more sequence data, micro array data, more mutation data, more genomes than people who can actually use it to understand the biology.  There is a bit of an analysis bottleneck now. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So some of these sequencers have greater read lengths, which can make it easier to assemble a sequence.  These sequencers generally cost more.  For instance if you have a library to sequence a little fungal or algal genome - you will get the answer back in a day or less now.  In the form of 1 Tb of reads maybe 50 to 200 bp long.  It might take quite a bit of time to put that together into a novel genome sequence, still more to find the genes, build the gene networks from a template of pathways etc.  Just imagine a thousand sequencers pumping out day and night and you get the picture  I'm trying to paint here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;About cost.  Ion Torrent and the new oxford nanopore sequencers are really cheap - \$50k to perhaps \$900 for Oxford Nanopore's USB sequencer.  Most other systems cost hundreds of thousands of dollars.  Ion torrent and Nanopore have more disposables - you throw away a chip or even the entire sequencer - at a cost of hundreds of dollars a sample. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-01-02T13:09:27.930" LastActivityDate="2014-01-02T13:09:27.930" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1412" PostTypeId="2" ParentId="1352" CreationDate="2012-03-14T01:05:14.000" Score="2" Body="&lt;p&gt;Basically a summary and details-filled version of the above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ln(number of offspring/year) = 2.4 - ( 0.3 * ln(neonate mass) )&lt;br&gt;&#xA;(c.f. Charnov EL and SKM Ernest. 2006. The Offspring‐Size/Clutch‐Size &#xA;Trade‐Off in Mammals. American Naturalist 167:578-582.) &lt;/li&gt;&#xA;&lt;li&gt;litter/year = 1 / (pregnancy duration in years + weaning time in years) &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;it can be deduced that &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;number of offspring/litter = exp(2.4 - 0.3 ln(neonatal mass in grams)) / (pregnancy duration in years + weaning time in years) &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For pandas, the parameters have values &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;neonatal mass in grams = 150 - 200 &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;pregnancy duration in years = (95 - 160) (days/years) = &lt;a href=&quot;http://www.wolframalpha.com/input/?i=95+to+160+days+to+years&quot; rel=&quot;nofollow&quot;&gt;0.26 - 0.44&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;weaning time in years = 46 weeks/years = &lt;a href=&quot;http://www.wolframalpha.com/input/?i=46+weeks+to+years&quot; rel=&quot;nofollow&quot;&gt;0.88&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Therefore, for pandas, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;offspring/litter = exp(2.4 - 0.3 ln(200)) / (0.26+0.88) to exp(2.4 - 0.3 ln(200)) / (0.44+0.88) = &lt;a href=&quot;http://www.wolframalpha.com/input/?i=exp%282.4+-+0.3+ln%28200%29%29+%2F+%280.44%2B0.88%29&quot; rel=&quot;nofollow&quot;&gt;1.7&lt;/a&gt; to &lt;a href=&quot;http://www.wolframalpha.com/input/?i=+exp%282.4+-+0.3+ln%28200%29%29+%2F+%280.26%2B0.88%29&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means, pandas on average have slightly less than 2 offsprings per litter, which means a high probability of having twins, and sometimes single, but rarely higher multiples. Comparing to human which has about &lt;a href=&quot;http://www.wolframalpha.com/input/?i=exp%282.4+-+0.3+ln%283400%29%29+%2F+%28%2840%2a7%2B6%2a30%29%2F365%29&quot; rel=&quot;nofollow&quot;&gt;0.7 offsprings per litter&lt;/a&gt;, panda has higher probability of having twins mainly because of much lighter neonatal mass. &lt;/p&gt;&#xA;" OwnerUserId="352" LastActivityDate="2012-03-14T01:05:14.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1413" PostTypeId="2" ParentId="1093" CreationDate="2012-03-14T01:49:48.277" Score="27" Body="&lt;p&gt;The average domesticated dairy cow produces far more milk than would be required to feed their calf. All cows, wild and domesticated, will only lactate in the period between their calf's birth and weaning. Milk is calf-food, and when there's no calf, there's no evolutionary advantage in producing milk. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On dairy farms, cows are milked twice daily, from spring (when they give birth) until late autumn. This mechanical milking 'fools' the cow into continuing to lactate. When a cow has stopped lactating, they will only start again after giving birth. This means that you can't just start milking a cow and expect to get milk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally farmers milk their cows from spring (birth) until late autumn. The reason for stopping in autumn is simply because the grass grows much slower in winter, so there isn't enough food to support lactating cows. However, it is entirely possible to milk longer than a year; I know of farmers who milk their cows continuously for two years. These farmers will have to purchase a lot of supplimental food (like hay or silage) during winter. The advantage of milking for longer than one season is that the cows do not have to give birth every spring, but instead only every second spring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe (but can't guarantee) that in winter, most milk purchased in a shop comes from the opposite hemisphere. I do know that here in New Zealand, we export a &lt;em&gt;lot&lt;/em&gt; of milk to northern-hemisphere countries.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you were to suddenly stop milking a cow, they might get sick but generally they will survive. It's still something to avoid!&#xA;Although if the calf is left with their mother then the cow would be relieved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not have an 'official' source for these facts. However, I grew up on a dairy farm, so this was my life.&lt;/p&gt;&#xA;" OwnerUserId="620" LastEditorUserId="-1" LastEditDate="2019-03-18T00:37:40.457" LastActivityDate="2019-03-18T00:37:40.457" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="1414" PostTypeId="2" ParentId="1045" CreationDate="2012-03-14T01:57:56.037" Score="7" Body="&lt;p&gt;One of the contributing factors the size of the yeast mitochondrial genome are 'selfish' mobile genetic elements termed &lt;a href=&quot;http://en.wikipedia.org/wiki/Homing_endonuclease&quot;&gt;homing endonucleases genes&lt;/a&gt; (HEGs).  These genes are typically found in introns that encode site-specific DNA endonucleases.  These endnoclueases cleave the HEG&lt;sup&gt;-&lt;/sup&gt; alleles during yeast mating leading to DNA recombination using the HEG&lt;sup&gt;+&lt;/sup&gt; allele as template.  I suspect over time as organisms became more complex and HEGs become unable to mobilize they would become fixed in the organisms genome.  Upon being fixed there is no selection pressure to maintain the open reading frame of the HEG or the intron its encoded within (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0959437X04001571&quot;&gt;ref&lt;/a&gt;).  This causes the eventual loss of the HEG and intron since they provide no real benefit to the organisms genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know how much of the yeast mitochondrial genome is taken up by these introns.  I believe that there are 4 of them in yeast some of the introns also require reverse transcriptase for splicing and mobility.  Other fungal species can have many more introns and sometimes weird things like introns embedded within introns.&lt;/p&gt;&#xA;" OwnerUserId="12" LastEditorUserId="12" LastEditDate="2012-03-14T02:17:37.837" LastActivityDate="2012-03-14T02:17:37.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1415" PostTypeId="1" AcceptedAnswerId="9381" CreationDate="2012-03-14T02:10:37.037" Score="8" ViewCount="6680" Body="&lt;p&gt;In some white caladiums, there is less than a square inch of green space spread over the whole leaf. How do these plants perform the photosynthesis necessary to support the large leaves, the roots, the flowers, and build a corm?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/k6Bgs.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="3952" LastEditDate="2013-07-31T07:12:05.773" LastActivityDate="2014-05-20T14:41:13.940" Title="How do white Caladiums perform enough photosynthesis to support their mass?" Tags="&lt;plant-physiology&gt;&lt;photosynthesis&gt;&lt;botany&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1416" PostTypeId="1" AcceptedAnswerId="1807" CreationDate="2012-03-14T05:36:26.420" Score="4" ViewCount="2675" Body="&lt;p&gt;What's the distinction between a tetrad and a synaptonemal complex in meiosis?  Are they synonyms?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I ask because the concepts seem very closely related, but it seems like there may be a subtle distinction.  Unfortunately, none of the sources I've been consulting use both terms.&lt;/p&gt;&#xA;" OwnerUserId="623" LastActivityDate="2012-04-14T11:32:23.957" Title="What's the distinction between a tetrad and a synaptonemal complex in meiosis?" Tags="&lt;cell-biology&gt;&lt;meiosis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1417" PostTypeId="2" ParentId="1406" CreationDate="2012-03-14T09:15:23.730" Score="7" Body="&lt;p&gt;It is possible to search for enzymes or a series of enzymes that will take similar reactants to similar products. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.retro-biosynthesis.com/&quot;&gt;ReBIT&lt;/a&gt; allows you to query enzymes by your molecular structures of interest using their &lt;a href=&quot;http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_system&quot;&gt;SMILES&lt;/a&gt; code. Unfortunately, a quick search using coumarin didn't produce any results but searches for phenol and phenolate gave some hits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're seeking to do a more extensive search, I would suggest &lt;a href=&quot;http://www.brenda-enzymes.org/&quot;&gt;BRENDA&lt;/a&gt;. There you can search for reaction substrates and reaction products and even both. Both strategies may provide you with an enzyme that does the transformation chemistry that you're looking for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly there is always &lt;a href=&quot;http://enzyme.expasy.org/&quot;&gt;ENZYME&lt;/a&gt;, The Enzyme Data Bank. There you can search for chemical compounds. I did a search of coumarin and there are a few hits but they are for methyl-transferases and hydrolases. A more extensive search may give you a few leads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the concepts that I just suggested are explained in the following review: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18725289&quot;&gt;De novo biosynthetic pathways: rational design of microbial chemical factories.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-03-14T09:15:23.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1418" PostTypeId="1" AcceptedAnswerId="1420" CreationDate="2012-03-14T10:06:00.903" Score="6" ViewCount="9720" Body="&lt;p&gt;I have a protein gel and I'm comparing the reduced with the non-reduced gel. On the reduced gel, I have a few shorter bands but these bands appear with low intensity. In the non-reduced gel, I'm seeing more of the shorter product? What would case the protein to run &quot;smaller&quot; in the non-reduced conditions?&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-03-14T17:12:44.377" LastActivityDate="2012-03-14T17:12:44.377" Title="What would cause bands to appear lower on a nonreduced SDS-PAGE gel?" Tags="&lt;gel-electrophoresis&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1419" PostTypeId="1" AcceptedAnswerId="2115" CreationDate="2012-03-14T10:53:31.107" Score="9" ViewCount="472" Body="&lt;p&gt;There are many cases when people commit altruism. One is relationship. I am willing to die for 2 of my children or 8 nieces, say an evolutionary psychologist. Another is reciprocal altruism, which is just a selfish cooperation rather than true altruism.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the 1930s J.B.S. Haldane had full grasp of the basic quantities and&#xA;  considerations that play a role in kin selection. He famously said&#xA;  that, &quot;I would lay down my life for two brothers or eight cousins&quot;.[8]&#xA;  Kin altruism is the term for altruistic behaviour whose evolution is&#xA;  supposed to have been driven by kin selection.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is it possible that humans may be altruists not for their 2 children or 8 nieces but to say, 1000 people that are similar to them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, how does &quot;Be altruist to 1000 of people similar to you&quot; evolve?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: If the answer is negative, then we will have a hard time understanding voting. Why sacrifice your time. However, if the answer is positive that humans do love other humans &quot;a little bit&quot; then voting, or even suicide bombing make sense. Those humans sacrifice their little time to improve reproductive success of those who are similar to them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Answer DOES NOT have to be about humans. If you can show me why strong/weak chimps tend to help each other or whether alpha males like one another, that'll do. Of course, naturally we would expect that leaders need followers and followers need leaders. But sometimes there are behavior that defy even this complementary nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarity does not have to be genetic. For example, fellow programmers and fellow engineers tend to be gang up.... Or does it have to be genetic?&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="3952" LastEditDate="2013-08-02T14:09:33.223" LastActivityDate="2013-08-02T14:09:33.223" Title="How does &quot;be altruist to those who are similar to you&quot; evolve?" Tags="&lt;evolution&gt;&lt;sociality&gt;" AnswerCount="3" CommentCount="8" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1420" PostTypeId="2" ParentId="1418" CreationDate="2012-03-14T12:08:34.580" Score="7" Body="&lt;p&gt;The major effect of changing the redox environment of a protein is the formation or breakage of &lt;a href=&quot;http://en.wikipedia.org/wiki/Disulfide_bond&quot;&gt;disulfide bonds&lt;/a&gt;. Under sufficiently reducing conditions no disulfide bridges will be present, while under oxidizing conditions your protein will form disulfide bridges if it has the ability to do so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disulfide bridges can significantly change the tertiary structure of a protein and change the behaviour of the protein on a gel that way. Generally, disulfide bridges should make the protein more compact and make it run faster on a gel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is therefore plausible that your faster band is the protein with disulfide bridges, which will appear to run like a smaller protein as it is more compact. The slower band then is the protein without disulfide bridges which can adopt a more extended conformation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm assuming you're talking about native gels here, as denaturing gels usually contain DTT or beta-mercaptoethanol in the sample buffer to reduce any disulfide bonds and avoid this effect altogether.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2012-03-14T12:08:34.580" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1421" PostTypeId="2" ParentId="1419" CreationDate="2012-03-14T13:39:08.823" Score="9" Body="&lt;p&gt;The question's a little broad, but I'll answer the question in the title:  how does &quot;be altruist[ic] to those who are similar to you&quot; evolve.  It turns out one way is discussed by a simple theoretical model called the &quot;green-beard&quot; model.  In essence, it says that a gene for altruism can spread if it produces a characteristic that can be perceived by and recognized in others (the 'green beard') and promotes altruistic behaviour towards other greenbeards.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia has a &lt;a href=&quot;http://en.wikipedia.org/wiki/Green-beard_effect&quot;&gt;round-up&lt;/a&gt; of some examples of this in action;  my general feeling from reading on this is that though it's a good idea in theory, greenbeards won't be &lt;em&gt;too&lt;/em&gt; common in practice because of the difficulties involved in keeping out mimicry (as in many signaling systems) and because of the complexity involved in creating and maintaining all three parts of the greenbeard effect on the part of one gene.  For that reason, it's been &lt;a href=&quot;http://star.tau.ac.il/~eshel/Bio_complexity/11.%20Swarming%20Intelligence/Greenbeard.pdf&quot;&gt;suggested that it may be more common in smaller organisms like bacteria&lt;/a&gt;, where this machinery can all occur in the same cell.&lt;/p&gt;&#xA;" OwnerUserId="92" LastActivityDate="2012-03-14T13:39:08.823" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1422" PostTypeId="2" ParentId="1419" CreationDate="2012-03-14T13:53:57.290" Score="12" Body="&lt;p&gt;This is an important question in evolutionary biology, but you need to distinguish the biological terms 'altruism' vs 'cooperation'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Altruism in biology means giving up your chance to reproduce so that someone else can more readily.  This is not like a gorilla troop, where only one male breeds, and the rest contribute to mutual security.  A more typical example is a honeybee or an ant, where the vast majority of the hive have no ability to reproduce at all.  This happens in animals, but is relatively rare. Its causes are currently the subject of intense debate but as far as I know, the only cases are where you do this for others who are genetically similar to you.   That logic sort of plays out as you say: &quot;My brother has kids, why do I need to have any? I'll just help out a little bit there.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cooperation includes forming groups for mutual safety and increased competition for food resources are why you might vote or schlep down to the DMV to get a drivers license when simply getting in your car without might be just as good most of the time.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cooperation is incredibly common in biology.  It even happens between species.  A dolphin helps a ship navigate submerged rocks, symbiotic bacteria in our gut help us digest food, but also get enough to live and reproduce.  The benefit is always win-win in such situations.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To understand how cooperation occurs spontaneously, one of the best experiments to look at is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Prisoner%27s_dilemma&quot;&gt;Prisoners Dilemma&lt;/a&gt; experiment.  If individuals are in a situation where you are likely to see each other again later (like a society).  The most successful ones are the ones who treat each other reasonably well, even if you do look out for less reliable types.  Why do people from Northern climates have strong hospitality traditions?  &quot;Today you (are in trouble) tomorrow me.&quot;  As the saying goes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are individuals who are not cooperative, but the selection forces are positive enough that those folks will regularly disappear from the group, while more cooperative types will become more numerous. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a significant selective pressure that you can train robots with very simple reward mechanisms to cooperate.  &lt;a href=&quot;http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.144.2881&quot;&gt;http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.144.2881&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-03-14T13:53:57.290" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1423" PostTypeId="2" ParentId="1415" CreationDate="2012-03-14T14:00:29.110" Score="3" Body="&lt;p&gt;Any free growing (non parasitic) plant will rely on photosynthesis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants do not have to be green though. It says in &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=university%20of%20florida%20news%20white%20caladiums&amp;amp;source=web&amp;amp;cd=1&amp;amp;ved=0CDEQFjAA&amp;amp;url=http://news.ufl.edu/2002/02/26/caladiums/&amp;amp;ei=rqVgT6jMDqSN0QGaxNCZBw&amp;amp;usg=AFQjCNH_m0_PXdA0fXZ9o1rNfLNQQuqQ0g&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; that the white caladium has chlorophyll, but relatively little, or the white color may come from other pigments that reflect other kinds of light.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;“As with other white caladiums, there’s a little bit of mystery surrounding Florida Moonlight,” Miranda said. “Where’s the chlorophyll? Chlorophyll is a pigment that caladiums and other plants use to produce food by photosynthesis, and it gives the leaves their green color. White caladiums either get along with very little chlorophyll, or they somehow conceal its presence&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="338" LastEditDate="2012-03-14T14:26:14.690" LastActivityDate="2012-03-14T14:26:14.690" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1424" PostTypeId="1" AcceptedAnswerId="1427" CreationDate="2012-03-14T18:07:07.270" Score="8" ViewCount="1477" Body="&lt;p&gt;I have been reading a little about the size of cells and was curious as to how small they really were.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have noticed that on my finger, the outlines of the fingerprint are made up of thin lines. In fact, some of them are so thin that I have difficulty imagining anything thinner I can make out with the naked eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read that the naked eye has a resolution of 0.1 millimeters = 100 micrometers, whereas eukaryotic cells range in diameter of 10 - 100 micrometers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Putting this information together, would it be reasonable to conclude that the lines on my fingers have a width ranging from 1 - 10 skin cells? Is there any satisfactory method to verify this without fancy equipment? Is it even true?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there also more scientific names for these &quot;finger lines&quot; so that I can look it up somewhere? Googling &quot;finger lines&quot; brings up a lot of stuff about palm reading.&lt;/p&gt;&#xA;" OwnerUserId="600" LastEditorUserId="338" LastEditDate="2012-03-16T05:02:38.497" LastActivityDate="2012-03-16T05:02:38.497" Title="What is the number of cells in a line of a fingerprint?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1425" PostTypeId="1" CreationDate="2012-03-14T18:22:59.437" Score="4" ViewCount="6753" Body="&lt;p&gt;What is the role of acetylcholine in the cardiac cycle and in blood pressure regulation?&lt;/p&gt;&#xA;" OwnerUserId="622" LastActivityDate="2012-03-16T02:02:24.033" Title="What is the role of acetylcholine in blood pressure regulation?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1426" PostTypeId="2" ParentId="1347" CreationDate="2012-03-14T19:00:50.997" Score="6" Body="&lt;p&gt;There does not appear to be a current standard, but &lt;a href=&quot;http://wiki.tdwg.org/Vegetation/&quot; rel=&quot;nofollow&quot;&gt;Veg-X&lt;/a&gt; is a standard that has been developed to facilitate exchange of plot-based vegetation data, and may provide the closest to what you are looking for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Veg-X is described in &lt;a href=&quot;http://labs.bio.unc.edu/Peet/pubs/JVS-VegX.pdf&quot; rel=&quot;nofollow&quot;&gt;Wiser et al 2011&lt;/a&gt; and the project home page is &lt;a href=&quot;http://wiki.tdwg.org/Vegetation/&quot; rel=&quot;nofollow&quot;&gt;http://wiki.tdwg.org/Vegetation/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The exchange standard for plot-based vegetation data (Veg-X) allows&#xA;  for observations of vegetation at both individual plant and aggregated&#xA;  observation levels. It ensures that observations are ﬁxed to physical&#xA;  sample plots at speciﬁc points in space and time, and makes a&#xA;  distinction between the entity of interest (e.g. an individual tree)&#xA;  and the observational act (i.e. a measurement). The standard supports&#xA;  repeated measurements of both individual organisms and plots, allows&#xA;  observations of entities to be grouped following predeﬁned or&#xA;  user-deﬁned criteria, and ensures that the connection between the&#xA;  entity observed and taxonomic concept associated with that observation&#xA;  are maintained.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Wiser, S.K., N. Spencer, M. De Caceres, M. Kleikamp, B. Boyle, &amp;amp; R.K. Peet. 2011. Veg-X -- An international exchange standard for plot-based vegetation data. Journal of Vegetation Science 22:598-609.&lt;/p&gt;&#xA;" OwnerUserId="222" LastEditorUserId="222" LastEditDate="2012-03-22T02:22:07.637" LastActivityDate="2012-03-22T02:22:07.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1427" PostTypeId="2" ParentId="1424" CreationDate="2012-03-14T20:08:07.467" Score="3" Body="&lt;p&gt;I am not sure that this can be accurately estimated because the outer layer of skin is ill-defined in terms of cells and cell boundaries. The outer layer or epidermis is composed of dead cells and dead cell parts that is tough and interconnected by design. Individual cells are not readily discernible.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-03-14T20:08:07.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1428" PostTypeId="1" AcceptedAnswerId="1433" CreationDate="2012-03-15T01:38:35.367" Score="8" ViewCount="402" Body="&lt;p&gt;An animal such as a crayfish relies on gravity to keep its circulatory system running. If it is turned upside down, the gravity works against the system, suffocating the animal. Now if, instead of placing the animal on it's back, we were to take take it to a space station, gravity would not be working against it, and random blood flow plus capillary action should get some blood flowing. Would the animal survive this?&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2012-03-15T13:03:42.870" Title="Could an animal with an open circulatory system survive in a near-zero gravity environment?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1429" PostTypeId="1" AcceptedAnswerId="1572" CreationDate="2012-03-15T01:47:12.890" Score="10" ViewCount="3115" Body="&lt;p&gt;If the xylem of a tree is composed entirely of dead tissue, then that means the sapwood is dead. If so, how does it transform into heartwood, and what starts the process?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2FV8K.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2014-07-23T02:06:47.317" LastActivityDate="2017-03-14T14:55:24.813" Title="If the xylem of a woody plant is composed of dead tissue, how does sapwood become heartwood?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1430" PostTypeId="1" CreationDate="2012-03-15T05:26:49.793" Score="9" ViewCount="5414" Body="&lt;p&gt;Does anyone know? I'm curious to find out  as my human anatomy and physiology book doesn't go into much detail on &lt;em&gt;how&lt;/em&gt; the lungs function as such&lt;/p&gt;&#xA;" OwnerUserId="496" LastEditorUserId="69" LastEditDate="2012-03-15T18:01:18.643" LastActivityDate="2012-12-12T02:41:29.187" Title="How do the lungs act as a sieve to trap blood clots?" Tags="&lt;physiology&gt;&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1431" PostTypeId="2" ParentId="1208" CreationDate="2012-03-15T11:51:25.450" Score="5" Body="&lt;p&gt;Here is the approach I ended up using, in part thanks to all the contributions here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The associated R script is below or can be downloaded from:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://github.com/edielivon/Useful-R-functions/tree/master/Education&quot; rel=&quot;nofollow&quot;&gt;BOLDS SEQUENCE RECOVERY&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This creates 999 unique sequence files in plain text, with each sequence being identified to species level and few species being found across more than one sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also creates the matching answer key.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can start at a random location to so that files change every year/group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I used R to query the BOLDS database (Barcode of Life), to download a file and to split this huge file into separate sequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the R script&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;rm(list=ls())&#xA;&#xA;complete&amp;lt;-&quot;http://services.boldsystems.org/eFetch.php?record_type=full&amp;amp;id_type=sampleid&amp;amp;ids=(*)&amp;amp;return_type=text&quot;&#xA;write(complete, file=&quot;your location on disk&quot;)&#xA;&#xA;rm(list=ls())&#xA;&#xA;sequences.id&amp;lt;-data.frame(&quot;file.name&quot;, &quot;recordID&quot;, &quot;genus_name&quot;, &quot;species_name&quot;)&#xA;write.table(x=sequences.id, file=&quot;sequences_id.csv&quot;, append=F, sep = &quot;,&quot;, row.names=F, col.names=F)&#xA;&#xA;&#xA;&#xA;set.seed(10)&#xA;start&amp;lt;-sample(1:1000, size=1)&#xA;&#xA;i&amp;lt;-start&#xA;k&amp;lt;-1&#xA;&#xA;while(k &amp;lt; 1000){&#xA;&#xA;  sequences&amp;lt;-read.delim(file=complete, skip=i, nrows=1, header=F)&#xA;  sequence.compare&amp;lt;-read.csv(file=&quot;sequences_id.csv&quot;, skip=k-1, nrows=1, header=F)&#xA;&#xA;  if(! is.na(sequences$V24)){&#xA;    if(as.character(sequences$V24)!=as.character(sequence.compare$V4)){&#xA;      writeLines(text=as.character(sequences$V55), con=paste(k, &quot;.txt&quot;, sep=&quot;&quot;))&#xA;      sequences.id&amp;lt;-c(k, sequences[,c(&quot;V3&quot;,&quot;V22&quot;, &quot;V24&quot;)])&#xA;      write.table(x=sequences.id, file=&quot;sequences_id.csv&quot;, append=T, sep = &quot;,&quot;, row.names=F, col.names=F)&#xA;      print(&quot;kept&quot;)&#xA;      k&amp;lt;-k+1&#xA;    }&#xA;  }&#xA;  i&amp;lt;-i+1&#xA;  print(paste(k,&quot;/&quot;, i))&#xA;}&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="553" LastEditorUserId="553" LastEditDate="2012-03-30T10:51:20.277" LastActivityDate="2012-03-30T10:51:20.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1432" PostTypeId="2" ParentId="1430" CreationDate="2012-03-15T12:02:58.560" Score="3" Body="&lt;p&gt;I'll ask the lung experts I work with later today for a better answer. To my knowledge, the lungs, as an organ, have a very extensive capillary network that facilitates gas exchange. If blood clots become mobile in the blood stream, they can travel perfectly well in large vessels, but once they get down to a capillary, they are physically blocked from passing through. The blood clots don't have to be large in size, because the capillaries are only about 6 micrometres in diameter.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-03-15T12:02:58.560" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1433" PostTypeId="2" ParentId="1428" CreationDate="2012-03-15T13:03:42.870" Score="2" Body="&lt;p&gt;I believe that fruit flies have been taken aboard the Space Shuttle for &lt;a href=&quot;http://quest.nasa.gov/projects/flies/index.html&quot; rel=&quot;nofollow&quot;&gt;experiments&lt;/a&gt;. They survived and the adults have an open circulatory system.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-03-15T13:03:42.870" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1434" PostTypeId="1" AcceptedAnswerId="1468" CreationDate="2012-03-15T13:29:02.917" Score="3" ViewCount="578" Body="&lt;p&gt;I've heard that the only plants that have pith are dicots, because of the shape of their vascular bundle. If that is true, what is the foam inside of the corn plants, which are monocots?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="107" LastEditDate="2012-03-17T22:19:02.260" LastActivityDate="2012-03-17T22:20:48.200" Title="If only dicots have pith, what is the foam in the middle of cornstalks?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1435" PostTypeId="1" AcceptedAnswerId="1438" CreationDate="2012-03-15T14:42:39.767" Score="14" ViewCount="1075" Body="&lt;p&gt;So, as far as I understand (basic) evolutionary theories, diversity is generated by &quot;niching.&quot; That is, if there is an environmental factor that hasn't been fully used by any species to &quot;profit&quot; off, there will be a tendency to fill up that &quot;niche&quot; and thus speciation occurs (not in one day of course).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was standing in the kitchen earlier and was wondering: what is the niche that an apple fills in respect to a pear end vice versa? If I'm not mistaken they are form the same family and thus share a common ancestor (albeit I don't know if it is a &quot;recent&quot; ancestor). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it a geographical thing or do they genuinely vie for the same thing in a different way? (e.g. a pear aims to be eaten by animals that have small teeth and thus want a softer fruit, while an apple aims to be eaten by the bigger animals, that like a heartier bite).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;note: I know that this question might be too speculative and too localised to be any good, but hey, some of you might just know this!&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="626" LastEditorUserId="3952" LastEditDate="2013-12-20T21:06:11.910" LastActivityDate="2013-12-20T21:06:11.910" Title="What are the evolutionary niches differentiating an apple from a pear?" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;food&gt;&lt;ethnobiology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1437" PostTypeId="2" ParentId="1435" CreationDate="2012-03-15T15:07:07.817" Score="11" Body="&lt;p&gt;I wouldn't be suprised if no one has hard data on this. In any case there is more than one answer to this question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ecological_niche&quot; rel=&quot;nofollow noreferrer&quot;&gt;Niches&lt;/a&gt; are defined more than one way. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the narrowest definition, the niche might be defined as the ability of the different trees to grow in different terrains or be eaten by different animals in the same environment.  I can't comment on that, but in most environments, there is in practice little difference between the two.  The classic example of this is Darwin's finches - where a single species eventually becomes many, each specializing in a specific kind of lifestyle (what they eat/where they net) on the islands of the Galapagos where they were situated.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the broadest definition of niche, they do have a different niche because they are different species, and their differences allow them to be eaten by different people.  In their highly domesticated environs, apples and pears each have a niche defined by the fact that they are both stocked in the produce sections for people to eat as they choose. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5fwfd.jpg&quot; alt=&quot;Apple and Pear Niches&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its worth mentioning that Darwin determined that different organisms can inhabit the &lt;em&gt;same&lt;/em&gt; niche.  In his case he saw that on different islands of the Galapagos he saw that the finches had evolved into different species, each of which took up the role that a different bird might have back home.  so its possible that apples and pears may have substantially the same niche in their respective evolutionary histories. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-12-02T18:03:30.597" LastActivityDate="2013-12-02T18:03:30.597" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1438" PostTypeId="2" ParentId="1435" CreationDate="2012-03-15T17:02:33.697" Score="8" Body="&lt;p&gt;The ancestral apple is thought to originate in what is now Kazakhstan. See this &lt;a href=&quot;http://www.ars.usda.gov/is/AR/archive/jan06/apples0106.htm&quot;&gt;report&lt;/a&gt; from the USDA on this topic. Those early apples were small and likely eaten more often by non-human species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pears: From &lt;a href=&quot;http://en.wikipedia.org/wiki/Pear&quot;&gt;Wikipedia&lt;/a&gt;: &lt;em&gt;The genus is thought to have originated in present-day western China in the foothills of the Tian Shan, a mountain range of Central Asia, and to have spread to the north and south along mountain chains, evolving into a diverse group of over 20 widely recognized primary species.&lt;/em&gt; A citation for this is needed.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-03-15T17:02:33.697" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1439" PostTypeId="1" AcceptedAnswerId="1533" CreationDate="2012-03-15T18:42:58.703" Score="16" ViewCount="10396" Body="&lt;p&gt;A Chinese man has been &lt;a href=&quot;http://www.chinadaily.com.cn/photo/2011-07/12/content_12892492.htm&quot;&gt;drinking gasoline&lt;/a&gt; to relieve his pain for 25 years. How does the human body metabolize gasoline? Also, what are the side-affects to gasoline? &lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="107" LastEditDate="2012-03-23T00:36:13.163" LastActivityDate="2012-03-23T00:36:13.163" Title="How does the human body metabolize gasoline?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;toxicology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1440" PostTypeId="2" ParentId="1439" CreationDate="2012-03-15T20:02:46.967" Score="5" Body="&lt;p&gt;Prolonged exposure to high concentrations of n-hexane (&gt;1,000 ppm) has resulted in decreased sperm count and degenerative changes in the testes of rats but not those of mice.&#xA;Acute Data: Gasoline: Dermal LD50&gt;5 ml/kg (Rabbit) LC50&gt; 4500 ppm (Rat) Oral LD50= 18.75 ml/kg. (Rat)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carcinogenicity: Two year inhalation studies of wholly vaporized unleaded gasoline produced increased incidences of kidney tumors in male rats and liver tumors in female mice. Follow-up studies suggest that occurrence of the kidney tumors may be linked to alpha-2-u-globulin nephropathy, and most likely unique to the male rat. Epidemiology data collected from a study of more than 18,000 petroleum marketing and distribution workers showed no increased risk of leukemia, multiple myeloma, or kidney&#xA;cancer from gasoline exposure. Unleaded gasoline has been identified as a possible carcinogen by IARC.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because solvent extracts of gasoline exhaust particulates caused skin cancer in laboratory animals, IARC has categorized gasoline engine exhaust as a possible human cancer hazard.&#xA;Target Organ(s): A two year inhalation study of wholly vaporized unleaded gasoline producednephropathy in male rats, characterized by the accumulation of alpha-2-u- globulin in epithelial cells ofthe proximal tubules, and necrosis and hyperplasia of surrounding cells. Follow-up studies havedemonstrated that these changes are unique to the male rat. Although prolonged exposure to n-hexane, a component of gasoline, has resulted in adverse male reproductive effects in experimental animal studies, no adverse male reproductive effects were found in studies conducted with gasoline.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Developmental: No evidence of developmental toxicity was found in pregnant laboratory animals(rats and mice) exposed to up to 9,000 ppm vapor of unleaded gasoline via inhalation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All data taken from the &lt;a href=&quot;http://www.edrisoil.com/MSDS/MSDSUnbrandedConvGas.pdf&quot;&gt;Material Safety Data Sheet&lt;/a&gt; (MSDS) from Petroleum Products Corp. See this link for more information.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-03-15T20:02:46.967" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1442" PostTypeId="1" AcceptedAnswerId="1443" CreationDate="2012-03-15T22:32:17.417" Score="17" ViewCount="16562" Body="&lt;p&gt;Some protocols call for fluid samples to be mixed with a &quot;vortexer&quot; on the high setting.  What effect does the vortexing have on fluid samples that mechanical shaking does not?  Does it shear long molecules like DNA, for instance?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A friend is setting up a new lab and asked if vortexers were strictly necessary.  I am aware they are often called for in various protocols, but I actually don't know what specific effect the vortexing has that makes it better than manual shaking.  What do you think?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rI9yD.jpg&quot; alt=&quot;A typical lab vortexer&quot;&gt;  &lt;/p&gt;&#xA;" OwnerUserId="51" LastActivityDate="2017-03-25T22:03:52.477" Title="What effect does vortexing have on a fluid sample that simple mechanical shaking does not?" Tags="&lt;lab-techniques&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1443" PostTypeId="2" ParentId="1442" CreationDate="2012-03-16T00:02:39.157" Score="13" Body="&lt;p&gt;In my experience, shaking and mixing have different &quot;dead spaces&quot;. Supposed you had an eppendorf tube and you stirred it around with a pipet tip for thirty minutes. You would have great convective mixing in the radial direction but virtually no mixing in the Z-direction. Supposed you had a very viscous fluid like PEG. If you set the tube on a shaker for an hour it will virtually not mix. The vortexer provides a very different profile of mixing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instances where I wouldn't use the vortexer would be for sensitive objects like DNA and cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(update)&#xA;We had some interesting suggestions from the FDA (since the FDA pays attention to these type of discussions). To get proper mixing, it is often not considered enough to merely swirl a tube a bunch. Their actual recommendation is to train technicians to perform a 90 degree angle arc with their forearm to generate proper force in mixing.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2017-03-25T22:03:52.477" LastActivityDate="2017-03-25T22:03:52.477" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1444" PostTypeId="2" ParentId="1425" CreationDate="2012-03-16T02:02:24.033" Score="3" Body="&lt;p&gt;I hope this answers your question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the heart is an electrically excitable tissue: it pumps due to action potentials that start  from specialized heart cells called nodal cells and these nodal cells spread the action potential to surrounding heart cells. These nodal cells are found throughout the heart and they make up what's called the conducting system. These nodal cells don't need neural or hormonal input for them to spread action potentials, they have this mechanism to spontaneously start action potentials on their own called a pacemaker potential, BUT they can be influenced by neural (think sympathetic and parasympathetic) or hormonal input. These external inputs change the frequency (the pace) of the heart beat by influencing the pacemaker potential of the nodal cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sympathetic nerve fibers send out epinephrine which cause the pacemaker potential to occur at a faster rate, that's why during exercise (when epinephrine is released... hopefully) the heart beats faster. Parasympathetic nerve fibers send out acetylcholine which causes the pacemaker potential to occur at a slower rate, thus slowing down the heart. What does this mean in regards to the cardiac cycle? It influences how much blood (the volume) is ejected during the cycle. The volume of blood that is ejected from the ventricles, called cardiac output (CO), which is also how many liters/min, is determined by 2 other factors: stroke volume (volume of blood ejected during each ventricle during systole) and heart rate (CO = HR x SV). And therein lies a part of the answer to your question: when heart rate decreases because of parasympathetic stimulation, cardiac output should also decrease, granted stroke volume stays constant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I unfortunately do not know how acetylcholine affects blood pressure. I've read a paper of how acetylcholine induced relaxation in hypertensive rats, but I'm not sure of the mechanism, like how it affects systolic or diastolic BP.&lt;/p&gt;&#xA;" OwnerUserId="496" LastActivityDate="2012-03-16T02:02:24.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1445" PostTypeId="1" AcceptedAnswerId="1460" CreationDate="2012-03-16T07:17:10.640" Score="4" ViewCount="154" Body="&lt;p&gt;Is there any relation between age and the frequency of flatus? I often have this feeling that older people f*** more often than younger ones. Is this feeling scientifically correct? &lt;/p&gt;&#xA;" OwnerUserId="629" LastEditorUserId="69" LastEditDate="2012-03-16T09:11:21.500" LastActivityDate="2012-09-12T17:46:16.957" Title="Does age affect the frequency of flatus?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1446" PostTypeId="1" AcceptedAnswerId="1461" CreationDate="2012-03-16T11:27:39.430" Score="14" ViewCount="11434" Body="&lt;p&gt;I don't know if this question applies to only humans but why can cones see much greater detail than rods? Is it possible to have a rod that can detect light intensity and color?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="6" LastEditDate="2012-03-16T13:00:50.350" LastActivityDate="2016-09-01T20:12:21.613" Title="Why can cones detect color but rods can't?" Tags="&lt;vision&gt;" AnswerCount="5" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1447" PostTypeId="1" AcceptedAnswerId="1451" CreationDate="2012-03-16T11:42:36.073" Score="11" ViewCount="7891" Body="&lt;p&gt;After someone dies they become stiff, this is termed Rigor Mortis and happens because the cells run out of ATP (I think). But why do the cells need it to remain flexible?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="535" LastEditDate="2012-03-16T12:22:38.300" LastActivityDate="2012-03-16T15:33:44.043" Title="Why does Rigor Mortis occur after death?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1448" PostTypeId="1" CreationDate="2012-03-16T12:03:24.077" Score="13" ViewCount="806" Body="&lt;p&gt;&lt;a href=&quot;http://www.uniprot.org/uniprot/P36659&quot;&gt;CbpA&lt;/a&gt; is DNA binding protein found in E. coli and binds non-specifically to curved DNA (&lt;a href=&quot;http://dx.doi.org/10.1111/j.1365-2958.2010.07292.x&quot;&gt;Cosgriff et al., 2010&lt;/a&gt;), when the bacterium is in a static phase of growth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The use of &quot;curved DNA&quot; confuses me. Is the term &quot;curved DNA&quot; essentially the same as &quot;Circular DNA&quot;?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1111/j.1365-2958.2010.07292.x&quot;&gt;Cosgriff, S. et al. Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA. Mol. Microbiol. 77, 1289–1300 (2010).&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="6" LastEditDate="2012-03-16T12:49:57.493" LastActivityDate="2012-03-18T02:40:14.500" Title="What is Curved DNA?" Tags="&lt;dna&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1449" PostTypeId="1" AcceptedAnswerId="1528" CreationDate="2012-03-16T14:58:14.863" Score="10" ViewCount="297" Body="&lt;p&gt;I am interested in adding the ability to model &lt;a href=&quot;http://en.wikipedia.org/wiki/Coppice&quot;&gt;coppice&lt;/a&gt; tree production to a model of perennial crops (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1757-1707.2009.01019.x/abstract&quot;&gt;Miguez et al 2008&lt;/a&gt;)..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Implementing the biomass pools and allocation parameters required for tree growth is relatively straight-forward. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it is not clear to me if it will be necessary to account for any changes in growth form and physiology (e.g. allocation, allometry) associated with coppice management.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any models that explicitly model coppice regrowth? Are there any particular issues that I should consider?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Fernando E. Miguez , Xinguang Zhu, Stephen Humphries, German A. Bollero, and Stephen P. Long. GCB Bioenergy . 2009 . Volume 1 Issue 4, Pages 282 - 296 (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1757-1707.2009.01019.x/abstract&quot;&gt;link&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="222" LastEditorUserId="16866" LastEditDate="2017-01-03T15:57:24.627" LastActivityDate="2017-01-03T15:57:24.627" Title="(How) does coppicing fundamentally alter tree growth?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;theoretical-biology&gt;&lt;vegetation&gt;&lt;allometry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1450" PostTypeId="2" ParentId="1445" CreationDate="2012-03-16T15:07:18.830" Score="3" Body="&lt;p&gt;Could be that age has an effect. As humans age three important factors, with respect to this question, change:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Diet.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Immune system flexibility and its response to even minor disturbances and infections.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Gut microbiota composition.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-03-16T15:07:18.830" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1451" PostTypeId="2" ParentId="1447" CreationDate="2012-03-16T15:33:44.043" Score="15" Body="&lt;p&gt;You are right that ATP is needed in relation to Rigor Mortis: This for ion pumps to maintain concentration gradients in cells. Without a constant supply of ATP to the pumps, calcium starts to diffuse from the extracellular matrix (and other intracellular compartments with high concerntations of calcium) into the sarcomere where it binds to troponin, a regulatory protein in skeletal muscles. This holds myosin the actin filaments together creating the effect of rigor mortis. &lt;/p&gt;&#xA;" OwnerUserId="368" LastActivityDate="2012-03-16T15:33:44.043" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1452" PostTypeId="1" AcceptedAnswerId="1455" CreationDate="2012-03-16T17:04:21.300" Score="15" ViewCount="1005" Body="&lt;p&gt;According to my lecture notes testosterone generally increases sexual behavior.&#xA;Given that it's generally thought to be the male hormone I'm not quite sure whether they mean that it also increases sexual behavior in females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the effect of testosterone on female sexual behavior?&lt;/p&gt;&#xA;" OwnerUserId="152" LastEditorUserId="69" LastEditDate="2012-03-16T22:34:53.240" LastActivityDate="2012-06-16T17:37:40.357" Title="Does testosterone increase female sexual behavior?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1453" PostTypeId="2" ParentId="1442" CreationDate="2012-03-16T17:52:57.197" Score="11" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;what specific effect the vortexing has that makes it better than manual shaking&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In addition to @bobthejoe's answer about viscous fluids, (manual) mechanical shaking is also less consistent and more tiresome than vortexing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the vortexer is always at the same speed and each sample is vortexed for the same amount of time, then the shaking step will be less variable among samples. For example, the vigor of mixing an aqueous soil suspension could potentially affect the amount of aggregate decomposition and release of molecules into the suspension (I don't have a reference for this, but it is good practice to treat replicates the same to minimize any non-treatment effect).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Manual shaking is not only less consistent, it is also tiresome - especially with larger volumes (&gt;=10ml) and large sample sizes.&lt;/p&gt;&#xA;" OwnerUserId="222" LastActivityDate="2012-03-16T17:52:57.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1454" PostTypeId="2" ParentId="1446" CreationDate="2012-03-16T20:17:43.303" Score="14" Body="&lt;p&gt;Cone cells are each connected to their own neurone.  This allows them a great deal of resolution as the brain can interpret the exact position of the cone cell that was stimulated by a light photon.  However in order to improve low light vision, multiple rod cells are connected to a single neurone - this is called summation.  Whilst it does allow for an action potential to be generated in low light conditions, it greatly reduces resolution as the brain can not know precisely which rod cell was stimulated:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/15SFw.gif&quot; alt=&quot;Anatomy of the human retina&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rods can not detect colour as they only come in one variety - cone cells (in humans) come in a red, green and blue specific form to allow for the perception of colour by the brain due to the relative strength of these signals.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-03-16T20:17:43.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1455" PostTypeId="2" ParentId="1452" CreationDate="2012-03-16T20:31:40.710" Score="12" Body="&lt;p&gt;I'll point you to this article by &lt;a href=&quot;http://dx.doi.org/10.1001/archpsyc.57.2.149&quot; rel=&quot;nofollow&quot;&gt;A. Tuiten et al&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To quickly answer your question, yes,  &lt;strong&gt;testosterone does have an enhancing effect on the sexual behaviour of human healthy adult females&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The (admittedly small) study indicated that after an dose of testosterone was given to the women there was found:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;a statistically significantly &lt;em&gt;[sic]&lt;/em&gt; increase in genital responsiveness (P = .04)&lt;/li&gt;&#xA;&lt;li&gt;a statistically significant association between the increase in genital arousal and subjective reports of &quot;genital sensations&quot; (P = .02) and &quot;sexual lust&quot; (P = .01)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;A time lag was reported from the administering of the dose to effects being seen of approximately 4.5 hours. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1001/archpsyc.57.2.149&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Tuiten A&lt;/strong&gt;. 2000. Time Course of Effects of Testosterone Administration on Sexual Arousal in Women. Archives of General Psychiatry 57: 149–153.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-06-16T17:37:40.357" LastActivityDate="2012-06-16T17:37:40.357" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1456" PostTypeId="2" ParentId="1452" CreationDate="2012-03-16T20:33:04.297" Score="10" Body="&lt;p&gt;Although male testes are responsible for huge testosterone secretion, testosterone can be produced by other organs both in males and females. So, women do have testosterone. Similarly,  estrogen is also produced in men and not only in women. In addition, both sexes produce the androgen and the estrogen receptors, so endogeneous or external testosterone will be active in women. Among other things, testosterone supplementation have been shown to be useful in clinical studies conducted on women suffering from hypoactive sexual desire. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22392827&quot;&gt;Woodis et al.&lt;/a&gt;, Pharmacotherapy. 2012 Jan;32(1):38-53. doi: 10.1002/PHAR.1004.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-03-16T20:33:04.297" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1457" PostTypeId="2" ParentId="1448" CreationDate="2012-03-16T22:29:04.383" Score="3" Body="&lt;p&gt;I never heard of the term until today but a quick search implies that certain DNA sequences are more pliable than others. Most notable is the Widom sequence which binds to Histones. It is also noted that DNA isn't a free floating polymer but that there is also some directionality in its bend. It seems that the concept is bested explored in this review: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3905255&quot; rel=&quot;nofollow&quot;&gt;Curved DNA&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-03-16T22:29:04.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1458" PostTypeId="1" AcceptedAnswerId="1465" CreationDate="2012-03-17T04:40:11.547" Score="6" ViewCount="104" Body="&lt;p&gt;Is there any tool to search the biochemical action of a particular enzyme in a metabolic pathway of an organism? In other words, how can I find if enzyme &quot;E&quot;  is involved in the metabolic pathway for organism &quot;X&quot;.&lt;/p&gt;&#xA;" OwnerUserId="602" LastEditorUserId="69" LastEditDate="2012-03-17T18:11:53.920" LastActivityDate="2012-03-17T18:11:53.920" Title="Is there a tool to find the action of an enzyme in a metabolic pathway?" Tags="&lt;bioinformatics&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1459" PostTypeId="2" ParentId="1448" CreationDate="2012-03-17T06:29:17.220" Score="3" Body="&lt;p&gt;it is not necessarily circular - the transcription factors usually require a curvature that is much greater than what a plasmid will have, and the requirement can show up on eukaryotic proteins as well.  DNA binding proteins will cause a local loop or curvature that fit the transcription factor. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The classic picture is for the Gal and Lac repressor proteins which bind 2 strands simultaneously, causing a loop in the DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference: see fig 1 in: &#xA;&lt;a href=&quot;http://genesdev.cshlp.org/content/3/5/606.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;http://genesdev.cshlp.org/content/3/5/606.full.pdf+html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-03-17T06:29:17.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1460" PostTypeId="2" ParentId="1445" CreationDate="2012-03-17T07:04:55.610" Score="4" Body="&lt;p&gt;I do not have access to journals, but there is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8769291&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; claiming in its abstract that age DOES NOT play a role in flatus frequency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8769291&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Furne JK, Levitt MD&lt;/strong&gt;. 1996. Factors influencing frequency of flatus emission by healthy subjects. Digestive diseases and sciences 41: 1631–5.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="629" LastEditorUserId="836" LastEditDate="2012-09-12T17:46:16.957" LastActivityDate="2012-09-12T17:46:16.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1461" PostTypeId="2" ParentId="1446" CreationDate="2012-03-17T07:26:56.067" Score="21" Body="&lt;p&gt;The spectral sensitivity of photoreceptors expressed is the key to color vision. See figure below for the sensitivity of three-types of cone cells (S, M, L) and rod cell (R, dashed line).&#xA;&lt;img src=&quot;https://i.stack.imgur.com/fF2eT.png&quot; alt=&quot;Spectral sensitivity of photoreceptors&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this figure, one can say rod cells provide information about the &quot;blue-greenness&quot; of vision, however, despite their spectral sensitivity, it seems that in human vision rod cells do not contribute to color vision, because they are &lt;strong&gt;highly sensitive to intensity&lt;/strong&gt;, and thus they are mostly saturated in their response (does not induce firing of downstream bipolar cells) during normal daylight conditions. Rod cells specialize for night vision (&lt;a href=&quot;http://en.wikipedia.org/wiki/Scotopic_vision&quot; rel=&quot;noreferrer&quot;&gt;scotopic conditions&lt;/a&gt;) which is crucial for survival, and under this condition the cone cells are pretty much useless.&lt;/p&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2012-03-20T16:22:48.613" LastActivityDate="2012-03-20T16:22:48.613" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1462" PostTypeId="1" AcceptedAnswerId="1463" CreationDate="2012-03-17T07:38:40.113" Score="9" ViewCount="1585" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Swan&quot;&gt;the Wikipedia article on swans&lt;/a&gt;, swans are mostly monogamous but may sometimes separate, particularly after a &quot;nesting failure&quot;. What &quot;nesting failure&quot; may mean is not entirely clear to me. Does it mean that they they have literally failed to build a physical nest? Or is it that they have failed to produce offspring? Or is it something else entirely?&lt;/p&gt;&#xA;" OwnerUserId="600" LastEditorUserId="69" LastEditDate="2012-03-17T18:09:04.033" LastActivityDate="2012-03-17T18:09:04.033" Title="What does &quot;nesting failure&quot; mean?" Tags="&lt;ethology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1463" PostTypeId="2" ParentId="1462" CreationDate="2012-03-17T08:17:08.057" Score="6" Body="&lt;p&gt;Apparently it refers to the inability of nesting the eggs, because the nest was somehow destroyed, or environmental conditions were unfavourable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found a few examples pointing in this direction:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Trumpeter Swan page on the &lt;a href=&quot;http://www.nps.gov/yell/naturescience/trumpeterswan.htm&quot;&gt;Yellowstone National Park&lt;/a&gt; websites reports that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nest flooding is the primary cause of nest failure. Egg predation by coyotes, ravens, and otters does occur.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;From the abstract of: &lt;a href=&quot;http://www.jstor.org/discover/10.2307/1522356&quot;&gt;Nesting Ecology of Bewick's Swans on Vaygach Island, Russia&lt;/a&gt; - Syroechkovsky et al., Waterbirds, 2002&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nest failure was mostly due to abandonment of nests in cold weather rather then to predation. Climatic conditions in spring are the main determinants of nesting success for swans on Vaygach Island. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;From this article:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://elibrary.unm.edu/sora/Auk/v116n04/p1127-p1131.pdf&quot;&gt;Reproductive Success of Exotic Mute Swans in Connecticut&lt;/a&gt; - Conover et al., The Auk, 1999 (PDF)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Egg survival was defined as the proportion of eggs in successful nests that hatched (Johnson et al. 1992). Successful nests were those from which at least one egg hatched. Egg survival is referred to by some authors as hatching rate (Willey and Halla 1972). Eggs left in the nest after incubation ceased were considered abandoned.  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We determined the cause of failure for 33 nests: 46% were flooded, 27% were abandoned, 15% were disturbed by humans, 6% were lost to predators, and 6% failed after a parent died.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-03-17T08:17:08.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1464" PostTypeId="2" ParentId="1462" CreationDate="2012-03-17T09:23:31.213" Score="7" Body="&lt;p&gt;Actually, nesting failure means that nesting trial fail before offspring could even leave the nest. In case of precocial species (where chicks leave nest immediately after hatching, like swans) it means that eggs was destroyed or parents abandoned nest, as @nico point out. In case of altricial birds (offspring stay in nest) nesting failure may also mean that all nestlings died before leaving nest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;for example among House wrens (&lt;a href=&quot;http://elibrary.unm.edu/sora/Condor/files/issues/v088n04/p0483-p0486.pdf&quot;&gt;Belles-Isles &amp;amp; Picman 1986&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;About 81%&#xA;  of nesting failures (n = 30) were due to predation (contents disappeared before the expected fledgingdate). Females abandoned seven nests, and starvation (presumably because&#xA;  of desertion by parents) accounted for one nesting failure.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="68" LastActivityDate="2012-03-17T09:23:31.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1465" PostTypeId="2" ParentId="1458" CreationDate="2012-03-17T12:44:55.723" Score="8" Body="&lt;p&gt;I think the KEGG pathway database may be of some use to you. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Link is here: &lt;a href=&quot;http://www.genome.jp/kegg/pathway.html&quot;&gt;http://www.genome.jp/kegg/pathway.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This a database of manually drawn pathway maps, I have used the site myself and it is very useful in determining if your enzyme is in a pathway and where it lies in it. This is assuming though, your enzyme is in the database and has been mapped. &lt;/p&gt;&#xA;" OwnerUserId="158" LastActivityDate="2012-03-17T12:44:55.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1466" PostTypeId="1" CreationDate="2012-03-17T18:25:27.480" Score="11" ViewCount="11131" Body="&lt;p&gt;As I know all cells require oxygen. So my question is how efficiently can plants operate in no-oxygen atmosphere? Do all plants produce enough oxygen for themselves? Can they consume their own oxygen or the oxygen will be quickly lost to the air? Is there a plant that consumes more oxygen than they produce?&lt;/p&gt;&#xA;" OwnerUserId="408" LastActivityDate="2012-03-20T15:20:07.543" Title="What's the effect of oxygen deficit on plants?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1467" PostTypeId="2" ParentId="1466" CreationDate="2012-03-17T18:50:54.827" Score="9" Body="&lt;p&gt;During the daylight, the plant is photosynthesising faster than it is respiring so there is no net uptake of oxygen (the oxygen of course being produced in the as part of the photosynthesis).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, this only applies for tissues where photosynthesis is occurring.  In the roots of the plant, oxygen must always be present in the surrounding soil/growth medium for respiration.  Therefore if there is no oxygen in the roots then the root cells will be unable to produce ATP from respiration and consequently die.  This will eventually lead to the death of the entire plant as it is unable to take up nutrients due to the lack of a functioning root network.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the cause of plant death when soil is waterlogged - the water fills spaces in the soil that would otherwise contain air (i.e. oxygen).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Certain plants (often crop plants), rice being given as an example in the comments below, are able to survive being waterlogged and the resulting low oxygen supply. However they can only do so in the short term.  Rice plants in particular have adaptations that allow the transport of oxygen from the aerial parts of the plant down to the roots.  This does of course mean that the rice can not survive being totally submerged for an extended period of time.  Plants such as rice may have better adapted anaerobic fermentation pathways that become the main producer of ATP when aerobic respiration has arrested thus allowing them to better cope when transiently submerged than other plants.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jxb.oxfordjournals.org/content/51/342/89&quot;&gt;Molecular strategies for improving waterlogging tolerance in plants&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-03-20T15:20:07.543" LastActivityDate="2012-03-20T15:20:07.543" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1468" PostTypeId="2" ParentId="1434" CreationDate="2012-03-17T22:20:48.200" Score="3" Body="&lt;p&gt;Monocots &lt;a href=&quot;http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/Stems.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;do have pith&lt;/a&gt; in their stems. The link even has an image of a maize stem:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eyQQp.gif&quot; alt=&quot;Maize stem&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-03-17T22:20:48.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1469" PostTypeId="1" AcceptedAnswerId="1486" CreationDate="2012-03-17T23:12:11.240" Score="3" ViewCount="159" Body="&lt;p&gt;&lt;strong&gt;[EDIT]&lt;/strong&gt; - Have just found not &lt;a href=&quot;http://www.uniprot.org/citations/7791872&quot; rel=&quot;nofollow&quot;&gt;one&lt;/a&gt; but &lt;a href=&quot;http://www.nature.com/nsmb/journal/v3/n8/abs/nsb0896-723.html&quot; rel=&quot;nofollow&quot;&gt;two&lt;/a&gt; papers that address my structure problem. However they concern RAP-1A, so I guess my question is now what is the difference in  structure and function of RAP-1A and RAP-5? Does anyone know of X-ray structure analysis being used to examine RAP-5? &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;original question&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I'm a University Physics student writing a mock review article on what to me feels like a very 'un-physicsy' antibody - RAP-5. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although my knowledge of Biology is pretty poor, research is going quite well. I've found a lot of papers from the 80s talking about conducting immunohisto(/cyto)chemistry experiments, most of them finding that RAP-5 can be used to determine whether a cell has the ras in it, so they are able to measure the percentage of cells that are neoplastic (I believe this means cancerous) and contain ras and the percentage of cells which are normal and contain ras. (the ras-gene being a proto-oncogene which on mutation can result in permanently switched on ras proteins (p21?), which results in proliferation of cells and therefore can cause tumors). This is all very nice but on first glance immunohistochemistry doesn't seem to involve a huge amount of physics (for my bio-physics assignment), apart from using an optical microscope. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was hoping to be able focus a section of my article on the physical techniques involved in determining the structure of RAP-5. Although there seems to be plenty of literature on uses of RAP-5, I am struggling to find anything on the details on why it is able to be used in such experiments. In other words, I presume that its function is to bind on to an epitode specific to the ras protein (amino acids 10 -17 have popped up a few times) but I don't know if there is any imaging one can do to have a look at the structure and conclude 'yes this is why it binds to ras proteins and not to others'. Is there a technique that is likely to have been used to examine the structure of RAP-5? Is it's tertiary structure likely to be 'Y' shaped like other antibodies? Does it differ in structure from RAP1-4? (&lt;a href=&quot;http://books.google.co.uk/books?id=Ht1bypUY7c8C&amp;amp;pg=PA298&amp;amp;lpg=PA298&amp;amp;dq=ras%20Adenylate%20cyclase%20rap&amp;amp;source=bl&amp;amp;ots=WXvSq69THL&amp;amp;sig=ijXnD_UdHlkBumk2DmSOQUy3fu8&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=LABlT_eeGeOy0QWLg8iWCA&amp;amp;ved=0CDcQ6AEwAg#v=onepage&amp;amp;q=ras%20Adenylate%20cyclase%20rap&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;this book&lt;/a&gt; informs me that RAP1 and RAP2 have 60% sequence identity, but most sources seem to leave out RAP3-to-5, some evening telling me that the RAP family consists of RAP1A/B, RAP2A/B/C and no others!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, if RAP-5 is an antibody, does this mean that it is produced in the body and gets involved in the ras protein signal pathway in order to reduce too much ras expression? (am I right in saying the amount of expression is the amount of protein the ras-gene is producing?) or is it only synthetically produced and used in experiments to measure the amount and location of ras proteins? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also there seems to be little differentiation between the differences in the functions of each RAP. RAP-5 seems to be used quite a bit in experiments involving Ha-ras - but not exclusively. Do the different RAPs bind to different variants of ras? Ha-ras being the one unique to RAP-5. &lt;/p&gt;&#xA;" OwnerUserId="636" LastEditorUserId="389" LastEditDate="2012-03-19T02:22:13.650" LastActivityDate="2015-03-27T10:18:28.643" Title="Structure of RAP Antibodies (Specifically RAP-5)" Tags="&lt;biochemistry&gt;&lt;structural-biology&gt;&lt;biophysics&gt;&lt;antibody&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1470" PostTypeId="1" AcceptedAnswerId="9829" CreationDate="2012-03-18T01:47:30.100" Score="4" ViewCount="4431" Body="&lt;p&gt;Some insects, like the crickets pictured below, have such slender antennae it seems no blood could fit. How do they get blood through their antennae?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DMeVR.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/r37ZV.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="69" LastEditDate="2012-03-18T11:30:56.010" LastActivityDate="2013-08-20T10:00:50.243" Title="How do insects such as crickets circulate blood through their antennae?" Tags="&lt;entomology&gt;&lt;cardiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1472" PostTypeId="1" AcceptedAnswerId="1507" CreationDate="2012-03-18T01:56:50.883" Score="10" ViewCount="343" Body="&lt;p&gt;How do dragonflies manage to fly at such high speeds without their wings collapsing? Their wings are thinner than paper, but they do not even flutter. What gives them their strength?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="16866" LastEditDate="2017-01-03T15:59:06.497" LastActivityDate="2017-01-03T15:59:06.497" Title="Why don't dragonflies wings collapse?" Tags="&lt;physiology&gt;&lt;entomology&gt;&lt;biophysics&gt;&lt;anatomy&gt;&lt;flight&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1473" PostTypeId="2" ParentId="1448" CreationDate="2012-03-18T02:40:14.500" Score="3" Body="&lt;p&gt;I'm hardly an authority on this topic, but I distinctly recall an amazing report the mid-1990s of the co-crystal structure the yeast TATA binding protein in complex with DNA.  The structure shows that TBP bends the DNA axis by approximately 80 degrees, presumably in order to expose bases and improve recognition.  The structure is available at RCSB: &lt;a href=&quot;http://www.rcsb.org/pdb/explore.do?structureId=1ytb&quot; rel=&quot;nofollow&quot;&gt;http://www.rcsb.org/pdb/explore.do?structureId=1ytb&lt;/a&gt; . (Make sure you check out the Jmol view.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thermodynamically speaking, bending DNA would require energy. Therefore, DNA that was pre-bent (e.g., due to auxiliary binding proteins or composition bias) would improve binding. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I suspect that in the context DNA binding proteins, &quot;curved&quot; refers to the static curvature of unbound DNA or to the bending of DNA upon binding in order to facilitate recognition.&lt;/p&gt;&#xA;" OwnerUserId="639" LastActivityDate="2012-03-18T02:40:14.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1474" PostTypeId="2" ParentId="1470" CreationDate="2012-03-18T06:25:04.730" Score="5" Body="&lt;p&gt;Insects primarily get oxygen through diffusion of air through their skin.  I doubt the antennae need hemolymph circulation. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="4109" LastEditDate="2013-08-17T19:16:41.877" LastActivityDate="2013-08-17T19:16:41.877" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1475" PostTypeId="2" ParentId="932" CreationDate="2012-03-18T07:24:50.153" Score="3" Body="&lt;p&gt;It sounds like you're also trying to ask the question, &quot;how can non-adaptive or maladaptive traits evolve?&quot; and that you're not necessarily interested in acne specifically.  The following are just a few examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible that a gene that contributes to an undesirable trait, might also play a role in a strongly desirable trait. The classic textbook example of this is the gene involved in sickle-cell anemia, which causes the disease in homozygous individuals and is almost asymptomatic in heterozygous individuals. Since the gene helps with resistance to malaria, heterozygous individuals are actually better of than those with no mutation of this gene in areas where malaria is prevalent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this is not the only way a less than optimal genotype can persist. A gene may only produce an undesirable trait in combination with certain other genes, and there may not be enough selective pressure for it to be eliminated form a population.&lt;/p&gt;&#xA;" OwnerUserId="634" LastActivityDate="2012-03-18T07:24:50.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1476" PostTypeId="2" ParentId="1216" CreationDate="2012-03-18T07:43:26.683" Score="18" Body="&lt;p&gt;Others have given great answers, so I'll just support their answers with this diagram and a little further background on how to think about relatedness in evolutionary context. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CMOPT.png&quot; alt=&quot;Great Ape Phylogenetic Tree&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the author in this excerpt makes no mention of Bonobos, I would imagine that, by chimpanzee, he really meant the genus Pan, which includes both Bonobos and Common Chimps. But that does not necessarily matter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Relatedness, in modern taxonomy, depends purely on common ancestry, not necessarily on similarity of specific traits. As others have explained, we make theories about ancestry relationships based on many criteria and logic, not just variation in one gene. In this tree, you should think of A, B, and C as theoretical, extinct common ancestors of the species below them in the tree. The list of apes at the bottom represent the relevant extant species species only. Bonobos and Common Chimps have a more recent common ancestor (C) than either Bonobos and Humans (B) or Common Chimps and Humans (B). This is why @mgkrebs said that both qualify equally as most closely related, because the common ancestor of each pair is the same. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Few would disagree that Bonobos do seem to be more similar to humans than Chimps are to humans, but that actually does not mean they are more closely related evolutionarily! Theoretically there are two ways this could happen even if Bonobos and Chimps are equally related to humans, either our common ancestor with Chimps and Bonobos also shared the traits we have in common with Bonobos and Chimps changed, or Bonobos and Humans happened to develop these similarities independently. The former is a simpler explanation, but either are possible for each similarity. Again, the key in understanding this is in thinking about the theoretical ancestor species, B and C. The only way Humans could be more closely related to Bonobos than chimps is if the common ancestor, B, was a descendant of C, which seems extremely unlikely and as far as I know is not supported by the genetic research in this area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our common ancestor with Gorillas (A) on the other hand is much &quot;earlier&quot; than our common ancestor with Chimps and Bonobos, so Gorillas are less closely related to use than the group containing Bonobos and Chimps. &lt;/p&gt;&#xA;" OwnerUserId="634" LastActivityDate="2012-03-18T07:43:26.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1477" PostTypeId="5" CreationDate="2012-03-18T08:47:24.857" Score="0" Body="&lt;p&gt;The process by which information encoded in a gene is converted into a functional protein or RNA, resulting in or contributing to a phenotype.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-27T09:47:29.150" LastActivityDate="2017-03-27T09:47:29.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1478" PostTypeId="4" CreationDate="2012-03-18T08:47:24.857" Score="0" Body="The process by which information encoded in a gene is converted into a functional protein or RNA, resulting in or contributing to a phenotype." OwnerUserId="634" LastEditorUserId="4101" LastEditDate="2013-10-29T20:57:40.857" LastActivityDate="2013-10-29T20:57:40.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1479" PostTypeId="1" AcceptedAnswerId="1480" CreationDate="2012-03-18T13:26:48.227" Score="7" ViewCount="40455" Body="&lt;p&gt;Here is a pedigree: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/566Pu.png&quot; alt=&quot;Pedigree Chart&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The trait is autosomal recessive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is:  What is the probability that the bottom 2 people (4 and 5) have a child with the trait?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried doing &lt;code&gt;2/3 * 2/3 * 2/3 *1/4&lt;/code&gt; and got &lt;code&gt;2/27&lt;/code&gt; but this is wrong. I thought that the probability of III 1 being a carrier is 2/3.  The probability that IV 4 is a carrier is also 2/3.  The probability that III 6 is a carrier is 2/3 and IV 5 must be a carrier.  So IV 4 and IV 5 must be carriers.  The probability that they have a child with the trait is 1/4. But I am not getting the right answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The right answer is 1/6.&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="69" LastEditDate="2012-03-18T15:05:33.047" LastActivityDate="2017-02-22T20:58:03.950" Title="Pedigree Probability of Autosomal Recessive Trait" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;genetic-diagrams&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1480" PostTypeId="2" ParentId="1479" CreationDate="2012-03-18T15:03:35.577" Score="8" Body="&lt;p&gt;Starting with the left hand side of the diagram:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;III:2&lt;/em&gt; is definitely a carrier (Tt) as one parent (&lt;em&gt;II:2&lt;/em&gt;) is affected (tt).&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;III:1&lt;/em&gt; is also definitely a carrier (Tt) as when mating with &lt;em&gt;III:2&lt;/em&gt; they produce an affected (tt) offspring (&lt;em&gt;IV:1&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;li&gt;This means that we can work out the possibilities for &lt;em&gt;IV:4&lt;/em&gt; as we know the parent genotypes.  It follows the standard arrangement for two carrier parents giving the options of:&#xA;&lt;ul&gt;&#xA;&lt;li&gt;TT (1/4)&lt;/li&gt;&#xA;&lt;li&gt;Tt (2/4 = 1/2)&lt;/li&gt;&#xA;&lt;li&gt;tt (Normally 1/4 but in this case 0 as individual not marked as affected). &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Therefore for this scenario, the probabilities for &lt;em&gt;IV:4&lt;/em&gt; are :&#xA;&lt;ul&gt;&#xA;&lt;li&gt;TT (1/3)&lt;/li&gt;&#xA;&lt;li&gt;Tt (2/3)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now if we look at the right hand side of the diagram.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;IV:5&lt;/em&gt; is definitely a carrier (Tt) as one of their parents (&lt;em&gt;III:5&lt;/em&gt;) is affected.  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This gives two possible Punnett squares to be examined:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;|-------------------------------------------------------------------------------|&#xA;|                                        ♂ (IV:5)                               |&#xA;|                          T                                   t                |&#xA;|            -------------------------------------------------------------------|&#xA;|           |                                |                                  |&#xA;|         T |              TT                |                Tt                |&#xA;|           |                                |                                  |&#xA;| (IV:4)    |-------------------------------------------------------------------|&#xA;|    ♀      |                                |                                  |&#xA;|         T |              TT                |                Tt                |&#xA;|           |                                |                                  |&#xA;|-----------|-------------------------------------------------------------------|&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This gives nil affected offspring so we can disregard this option for your question (as we are ONLY looking for scenarios which produce affected individuals).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore the alternative is:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;|-------------------------------------------------------------------------------|&#xA;|                                        ♂ (IV:5)                               |&#xA;|                          T                                   t                |&#xA;|            -------------------------------------------------------------------|&#xA;|           |                                |                                  |&#xA;|         T |              TT                |                Tt                |&#xA;|           |                                |                                  |&#xA;| (IV:4)    |-------------------------------------------------------------------|&#xA;|    ♀      |                                |                                  |&#xA;|         t |              TT                |                tt                |&#xA;|           |                                |                                  |&#xA;|-----------|-------------------------------------------------------------------|&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Giving 1/4 affected offspring.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As mentioned above, in order to have affected offspring then &lt;em&gt;IV:4&lt;/em&gt; &lt;strong&gt;must&lt;/strong&gt; be Tt.  There is a &lt;code&gt;2/3&lt;/code&gt; chance of this being the case.  If this is the case, then there is a &lt;code&gt;1/4&lt;/code&gt; chance of the child being tt. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Both&lt;/strong&gt; conditions need to be true for this to happen so we multiply the fractions:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;2/3 * 1/4 = 1/6&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-03-18T15:03:35.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1481" PostTypeId="5" CreationDate="2012-03-18T15:14:17.777" Score="0" Body="" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-03-18T15:14:17.777" LastActivityDate="2012-03-18T15:14:17.777" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1482" PostTypeId="4" CreationDate="2012-03-18T15:14:17.777" Score="0" Body="Questions regarding the expression of genetic inheritance in the form of diagrams, including but not limited to questions about drawing and interpreting Punnett Squares, Pedigree Diagrams and genetic cross diagrams.  Please include images where possible. " OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-03-18T15:14:17.777" LastActivityDate="2012-03-18T15:14:17.777" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1483" PostTypeId="1" AcceptedAnswerId="1493" CreationDate="2012-03-18T18:02:46.090" Score="8" ViewCount="5602" Body="&lt;p&gt;I understand that many protein DNA binding domains bind to DNA via basic residues such as Arginine and Lysine. But what is the mechanism used to bind to DNA and where on the DNA would these residues bind?  &lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="158" LastEditDate="2012-03-19T13:26:20.817" LastActivityDate="2013-11-24T03:51:20.163" Title="Basic Amino Acid Residue Binding Mechanism to DNA" Tags="&lt;biochemistry&gt;&lt;dna&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1484" PostTypeId="1" CreationDate="2012-03-18T23:49:13.110" Score="4" ViewCount="582" Body="&lt;p&gt;I was asked this question on a test and got it wrong, but I'd like to know how to do it.  The answers are shown in the blanks below:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;You are studying two recessive mutations in the fruit fly D.&#xA;  melanogaster. The red_ mutation causes flies to have red bristles&#xA;  (wild-type flies have black bristles) and the shiny- mutation causes&#xA;  flies to have shiny eyes (wild-type flies have eyes that are pebbly).&#xA;  You mate females from a true-breeding strain with red bristles and&#xA;  pebbly (wild-type) eyes to males from a true-breeding strain with&#xA;  black (wild-type) bristles and shiny eyes. F1 females are then mated&#xA;  to males that have red bristles and shiny eyes to produce F2 progeny.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;If you analyzed 1000 male progeny in the F2 generation, how many flies&#xA;  of each possible phenotypic class would you expect, if:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The two traits are determined by two autosomal genes that are 15 cM&#xA;  apart: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Red bristles, pebbly eyes:_____ 425_______&#xA;Red bristles, shiny eyes: ______75____ &#xA;Black bristles, pebbly eyes:____ 75_____ &#xA;Black bristles, shiny eyes:____ 425______&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My attempt:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I know the 15cm=recombinants/parentals * 100 but I don't see how that formula can help.&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="6" LastEditDate="2012-03-19T13:30:05.687" LastActivityDate="2012-05-10T02:28:47.900" Title="Predicting progeny of recessive mutations using recombination" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1485" PostTypeId="1" AcceptedAnswerId="1514" CreationDate="2012-03-19T01:37:14.063" Score="9" ViewCount="346" Body="&lt;p&gt;With our fermentations we're noticing that it takes an appreciable amount of time for &lt;em&gt;E. coli&lt;/em&gt; (K12 variant) to change from being metabolically streamlined on amino acids to being metabolically streamlined to glucose. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How long does it take for such microorganisms to adjust to a new feedstock?&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="107" LastEditDate="2012-03-19T16:01:37.653" LastActivityDate="2012-03-23T01:24:41.427" Title="How long does it take for E. coli to shift feedstocks?" Tags="&lt;metabolism&gt;&lt;ecoli&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1486" PostTypeId="2" ParentId="1469" CreationDate="2012-03-19T02:21:27.270" Score="3" Body="&lt;p&gt;The confusion that you're facing is because RAP-5 is actually known as &lt;a href=&quot;http://en.wikipedia.org/wiki/RAB5C&quot; rel=&quot;nofollow&quot;&gt;RAB5C&lt;/a&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/5878&quot; rel=&quot;nofollow&quot;&gt;GENEID&lt;/a&gt;). The &lt;a href=&quot;http://en.wikipedia.org/wiki/Ras_superfamily&quot; rel=&quot;nofollow&quot;&gt;ras superfamily&lt;/a&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3145021&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt;) is divided into Ras, Rho, Rab, and Rap. But the Rap GTPases are divided only into two categories, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14570053&quot; rel=&quot;nofollow&quot;&gt;RAP1 and RAP2&lt;/a&gt;. On the other hand, there are multiple &lt;a href=&quot;http://en.wikipedia.org/wiki/Rab_%28G-protein%29&quot; rel=&quot;nofollow&quot;&gt;Rab GTPases&lt;/a&gt; which include &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/5868&quot; rel=&quot;nofollow&quot;&gt;RAB5A&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/5878&quot; rel=&quot;nofollow&quot;&gt;RAB5C&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a few crystal structures of both Rab5A and Rab5C in both human and murine forms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, for RAP-5. &lt;a href=&quot;http://www.nature.com/bjc/journal/v54/n6/abs/bjc1986256a.html&quot; rel=&quot;nofollow&quot;&gt;RAP-5&lt;/a&gt; &lt;strong&gt;is&lt;/strong&gt; a monoclonal murine antibody which has no relationship to the RAP family of proteins. It's probably called RAP because Spandidos and Wilkie weren't thinking clearly when they named their antibodies RAP1-5. In this case, you're probably better off looking at the antibody Y13-259 which is probably called that since its the 259th antibody they tried.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your questions, specifically, very few people have attempted to get a structure since it is an antibody and everyone knows what they look like. Secondly, the antibody is produced in a mouse and added to tissue. And yes, the RAP antibodies bind to different variants of Ras. Also, no one uses RAP-5 since anti-Ras &lt;a href=&quot;http://www.abcam.com/Ras-antibody-EP1125Y-ab52939.html&quot; rel=&quot;nofollow&quot;&gt;EP1125Y&lt;/a&gt; seems to be more popular.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you still want a crystal structure, I would hunt down the RAP5 patent and look up the peptide sequence. From there, you can look up similar structures in the &lt;a href=&quot;http://www.imgt.org/&quot; rel=&quot;nofollow&quot;&gt;IMGT database&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-03-19T02:21:27.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1488" PostTypeId="1" CreationDate="2012-03-19T12:03:55.433" Score="9" ViewCount="601" Body="&lt;p&gt;All life on Earth (bacteria, archaea, eukarya) is thought to have evolved from a common ancestor, or last universal common ancestor (LUCA). What do we know about the characteristics of LUCA based upon extant life?&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="231" LastEditDate="2015-12-03T21:13:10.283" LastActivityDate="2015-12-03T21:13:10.283" Title="What do we know about the Last Universal Common Ancestor (LUCA)?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1489" PostTypeId="1" AcceptedAnswerId="3163" CreationDate="2012-03-19T13:48:51.130" Score="11" ViewCount="8227" Body="&lt;p&gt;I have not yet found a plant that, when an insect eats a hole in one of its leaves, it can regenerate the lost tissue. Many plants will grow a new stem if the old one is cut, but it is not a perfect regeneration, and has no likeness in form to the previous stem. Are there any plants that can, even to a degree, regenerate missing tissue?&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2018-07-09T14:34:11.963" Title="Can any plant regenerate missing tissue?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1491" PostTypeId="1" AcceptedAnswerId="2472" CreationDate="2012-03-19T14:12:24.143" Score="14" ViewCount="2042" Body="&lt;p&gt;Can fruit tissue be grown in a tissue culture as is done to other plant tissues? From the answer to &lt;a href=&quot;https://biology.stackexchange.com/questions/883/how-long-will-a-vegetable-live-for-after-being-harvested&quot;&gt;this&lt;/a&gt; question, I learned that fruit is alive. Could it be possible to manufacture fruit products without plants, using this method?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2012-06-02T14:10:42.400" Title="Can fruit tissue be cultured and grown independent from the plant?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1492" PostTypeId="1" AcceptedAnswerId="1516" CreationDate="2012-03-19T17:15:12.703" Score="8" ViewCount="1264" Body="&lt;p&gt;What conditions are necessary for human pancreatic lipase to activate? Is there an optimal temperature or pH? How quickly does it take effect?&lt;/p&gt;&#xA;" OwnerUserId="502" LastEditorUserId="69" LastEditDate="2012-03-22T18:18:27.753" LastActivityDate="2012-10-16T12:25:43.357" Title="What conditions are necessary for HPL (human pancreatic lipase) to activate?" Tags="&lt;human-biology&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="1493" PostTypeId="2" ParentId="1483" CreationDate="2012-03-19T17:44:00.780" Score="5" Body="&lt;p&gt;This question has no particular answer.  There are several families of DNA binding proteins, some of them bind specifically (e.g. restriction enzymes like EcoRI which binds to and cuts GAATTC or transcription factors like &lt;a href=&quot;http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/L/LacOperon.html&quot; rel=&quot;nofollow&quot;&gt;lac repressor&lt;/a&gt; which binds a particular point of the e coli genome about 25 base pairs long) and some of them bind semi-specifically (e.g. zinc fingers which bind GC rich regions), others non specifically (e.g. &lt;a href=&quot;http://www.cs.stedwards.edu/chem/Chemistry/CHEM43/CHEM43/Projects04/Clamps/STRUCTURE.HTML&quot; rel=&quot;nofollow&quot;&gt;the sliding DNA clamp&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For all of these proteins, they will have a tendency to have positively charged amino acids facing the DNA because the DNA's phosphate backbone is negatively charged.  There are lots of protein motifs (like the helix turn helix motif) that fits into the major or minor groove of the DNA.  The lysine and argenine are important because they are the positively charged amino acids.  Histidine is also positively charged, but it is not as long and flexible, and doesn't seem to fit as often or as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/DNA-binding_protein&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/DNA-binding_protein&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-03-19T17:44:00.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1494" PostTypeId="2" ParentId="1446" CreationDate="2012-03-19T22:09:35.650" Score="12" Body="&lt;p&gt;While the answers to date are correct regarding the wiring of rods and cones in the primate (specifically human) eye, they are also fundamentally wrong. Neither rods nor cones perceive color. The brain does. The rods and cones are just the receptors providing signals. The first answer in fact says this in its very last sentence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As one answer says, during the day the rods are saturated (overstimulated) so the brain ignores them. It uses the components of the cone responses to invent the sensation &quot;color&quot;. At night the cones are usually only weakly stimulated, so the brain sees only with the more sensitive rods, and little or no color. This is why brightly colored stars such as Betelgeuse and Rigel still appear only faintly tinged (red and blue respectively).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, some primates have even better color perception than humans with four (or five) kinds of cones. It is speculated that color vision is so good in primates because of the need to judge fruit ripeness to eat. Many mammals have fewer cone types than primates.&lt;/p&gt;&#xA;" OwnerUserId="641" LastEditorUserId="69" LastEditDate="2012-03-20T08:42:19.227" LastActivityDate="2012-03-20T08:42:19.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1495" PostTypeId="1" AcceptedAnswerId="1496" CreationDate="2012-03-20T06:51:27.890" Score="25" ViewCount="2105" Body="&lt;p&gt;I know death and cancer doesn't hurt humans' reproductive success. It's not helping either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do we die? Why dying humans (all of us) are common? What's the point of dying?&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="5005" LastEditDate="2014-05-08T19:29:50.520" LastActivityDate="2020-08-08T00:19:57.740" Title="What evolutionary explanations are there for death?" Tags="&lt;evolution&gt;" AnswerCount="6" CommentCount="8" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1496" PostTypeId="2" ParentId="1495" CreationDate="2012-03-20T08:13:52.023" Score="23" Body="&lt;p&gt;Death is not only for humans. All 'complicated enough' organisms die (with a notable exception of &lt;a href=&quot;http://en.wikipedia.org/wiki/Hydra_(genus)&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hydra&lt;/a&gt;, though you may argue when it comes to the complexity). It is is easier to create a new organism from scratch than to repair both internal factors (free radicals, metabolic by-products, ...) and external (physical damage, exposure to toxins, ...).&lt;/p&gt;&#xA;&lt;p&gt;Underlying causes of death actually can be evolutionary beneficial. For example, shortening of &lt;a href=&quot;http://en.wikipedia.org/wiki/Telomere&quot; rel=&quot;nofollow noreferrer&quot;&gt;telomeres&lt;/a&gt; offers protection against cancer (on a cellular level), but also bounds lifespan.&lt;/p&gt;&#xA;&lt;p&gt;So actually they may be evolutionary competition (within the same species) of young and old. Mutations helping young but harming older may be preferred to the opposite ones.&lt;/p&gt;&#xA;" OwnerUserId="129" LastEditorUserId="46609" LastEditorDisplayName="user560" LastEditDate="2020-08-07T00:40:06.803" LastActivityDate="2020-08-07T00:40:06.803" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="1497" PostTypeId="2" ParentId="1495" CreationDate="2012-03-20T08:19:21.040" Score="9" Body="&lt;p&gt;Who is to say that having living Humans isn't hurting our reproductive success? Older non-reproducing humans cost the human network valuable resources and take up a sizeable portion of our living niche. Metabolically unstreamlined aged organisms are certainly not the most efficient and could potentially get in the way of better suited young'uns.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-03-20T08:19:21.040" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1498" PostTypeId="1" AcceptedAnswerId="1501" CreationDate="2012-03-20T13:12:22.210" Score="6" ViewCount="428" Body="&lt;p&gt;Do any animals become psychologically attached to any non-living object that is not useful to the animal for any of its physical needs, like some children do to stuffed animals? Some children are so attached to their toys that they take them with them whenever possible, and are upset when the toy goes missing or is taken by another.&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2014-07-23T02:11:02.573" LastActivityDate="2014-07-23T02:11:02.573" Title="Are there any other animals that become attached to a non-living object?" Tags="&lt;zoology&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1499" PostTypeId="1" AcceptedAnswerId="1527" CreationDate="2012-03-20T13:20:24.260" Score="7" ViewCount="1776" Body="&lt;p&gt;I know how plant cells and animal cells react to being cultured and grown this way, but what about mushrooms? Would they respond like plants, and result in embryos growing off the mass? Or does the mass just grow indefinitely as in animals? Has anyone done this? How do they react when grown this way?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="222" LastEditDate="2012-03-23T15:00:53.997" LastActivityDate="2012-03-23T15:00:53.997" Title="How do fungi react to being grown in a tissue culture?" Tags="&lt;mycology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1500" PostTypeId="2" ParentId="73" CreationDate="2012-03-20T13:28:07.333" Score="3" Body="&lt;p&gt;By far the most important part is the very beginning of the transcript, especially the positions +1 and +2. The conservered consensus sequence in class III T7 promoters is &lt;code&gt;GGGAGA&lt;/code&gt;, any changes in the first two nucleotides severely reduce the transcription efficiency. Changes at positions +3 to +6 have much smaller effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, changes that put many AU base pairs in that region (e.g. GGUUU) seem to affect the trancription efficiency negatively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other sequences that are problematic anywhere, not only in the beginning are long stretches of uridines or adenines. Sequences with eight or more uridines or adenines can cause the polymerase to slip, which results in transcripts with more uridines or adenines than in the template.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These characteristics are detailed in &lt;a href=&quot;http://rnaworld.bio.ku.edu/reprints/main/Milligan%281989%29Meth_Enzymol_180,51.pdf&quot; rel=&quot;nofollow&quot;&gt;the paper from Milligan and Uhlenbeck from 1989&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rnaworld.bio.ku.edu/reprints/main/Milligan%281989%29Meth_Enzymol_180,51.pdf&quot; rel=&quot;nofollow&quot;&gt;Milligan, J. F. &amp;amp; Uhlenbeck, O. C. Synthesis of small RNAs using T7 RNA polymerase. Meth. Enzymol. 180, 51–62 (1989).&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2012-03-20T13:28:07.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1501" PostTypeId="2" ParentId="1498" CreationDate="2012-03-20T14:09:27.040" Score="2" Body="&lt;p&gt;So, this is psychological attachment. From the question alone, I thought of physical attachment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you provide stuffed animals and human children, then I'd offer the television remote, a chair/sofa and the cellphone for human adults. In general, many adults are far too sedentary for their own health.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some non-human primates have exhibited behavior similar to that which you describe with the stuffed animals-children example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of an inanimate object, you can add the Internet. Certain behaviors like over-indulgence in alcohol, sex, gambling, hand-washing, and the like, could, broadly speaking, fit within the question as posed.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-03-20T14:15:45.813" LastActivityDate="2012-03-20T14:15:45.813" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1502" PostTypeId="1" AcceptedAnswerId="1504" CreationDate="2012-03-20T20:57:31.220" Score="15" ViewCount="1573" Body="&lt;p&gt;In humans the Appendix is a vestigial organ. Does it serve no apparent purpose in all the vertebrates that have one?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="107" LastEditDate="2012-03-20T21:50:49.223" LastActivityDate="2012-03-21T13:34:53.093" Title="Is the appendix a vestigial structure in all vertebrates?" Tags="&lt;zoology&gt;&lt;organs&gt;&lt;vestigial&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1503" PostTypeId="2" ParentId="1502" CreationDate="2012-03-20T21:40:32.517" Score="9" Body="&lt;p&gt;Aside from humans, it is largely rodents and most notably rabbits that have an appendix.  Therefore, using rabbits as my example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In rabbits, the appendix is thought to have a key role in the development of the immune system.  Specifically it has been shown experimentally that when neonatal rabbits are given an appendectomy levels of Immunoglobulin A and G (IgA/IgG) fall dramatically. Both these polypeptides are prominent antibodies - IgA plays a key role in mucosal immunity whilst IgGs in humoral immunity.  These effects were localised to the small intestine of the rabbits, however were statistically significant. &lt;sup&gt;1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;In infants&lt;/em&gt;, the rabbit appendix resembles the chicken bursa and sheep ileal Peyer's patch (both performing similar functions as described above).&lt;sup&gt;2&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has led to some ongoing research as to whether the human appendix has a similar properties in having function in infants &lt;sup&gt;3&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If the human appendix functions as a primary lymphoid organ, it may occur during the first few months of age when the GC T-cell density is low.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9427807&quot;&gt;Neonatal appendectomy impairs mucosal immunity in rabbits. Cell Immunol. 1997 Nov 25;182(1):29-37&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;2&lt;/sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7709830&quot;&gt;The appendix functions as a mammalian bursal equivalent in the developing rabbit. Adv Exp Med Biol. 1994;355:249-53.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10906392&quot;&gt;A morphological and immunohistological study of the human and rabbit appendix for comparison with the avian bursa. Dev Comp Immunol. 2000 Dec;24(8):797-814.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-03-20T21:40:32.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1504" PostTypeId="2" ParentId="1502" CreationDate="2012-03-20T21:49:12.610" Score="15" Body="&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2009.01809.x/full&quot; rel=&quot;noreferrer&quot;&gt;Smith et al. (2009)&lt;/a&gt; provide a survey of the morphology of the cecal appendix. One current hypothesis is that the appendix provides &quot;safe harbor&quot; for symbiotic gut bacteria. Among mammals, there is a vast array of cecal appendices:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RTFXa.gif&quot; alt=&quot;Morphology of the appendix&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A comparative anatomical approach reveals three apparent morphotypes&#xA;  of the cecal appendix, as well as appendix-like structures in some&#xA;  species that lack a true cecal appendix. Cladistic analyses indicate&#xA;  that the appendix has evolved independently at least twice (at least&#xA;  once in diprotodont marsupials and at least once in Euarchontoglires),&#xA;  shows a highly significant (P &amp;lt; 0.0001) phylogenetic signal in its&#xA;  distribution, and has been maintained in mammalian evolution for 80&#xA;  million years or longer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-03-20T21:49:12.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1505" PostTypeId="1" AcceptedAnswerId="1800" CreationDate="2012-03-20T23:02:01.027" Score="10" ViewCount="1693" Body="&lt;p&gt;So I was thinking that if each cell has P(X) of becoming cancerous, then the chance of cancer is 1-((1-P(X))^n) where n is the number of cells in the organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since larger organisms have more cells than smaller organisms (I'm guessing that larger organisms simply have more cells than smaller organisms as you can't have larger cells since there is an optimum surface area to volume ratio), does this mean then that larger creatures are more likely to have cancer cause they have more cells?&lt;/p&gt;&#xA;" OwnerUserId="648" LastActivityDate="2012-04-13T14:17:33.950" Title="Do larger multicellular organisms have an increased risk of mutation and thus cancer?" Tags="&lt;cell-biology&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1506" PostTypeId="1" CreationDate="2012-03-21T00:23:51.030" Score="7" ViewCount="108" Body="&lt;p&gt;Lets imagine that I have mammalian cells that I've immobilized on a filter. Now I want to keep providing small molecules to these immobilized cells without resolubilizing the cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The caveat is that I would like to do so without fixing the cells or waiting for them to adhere to the filter. The small molecules are small enough to diffuse through the filter.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2014-11-24T20:37:47.547" Title="Providing small molecules to cells on a filter plate" Tags="&lt;cell-culture&gt;&lt;assay-development&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1507" PostTypeId="2" ParentId="1472" CreationDate="2012-03-21T03:37:05.867" Score="10" Body="&lt;p&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.en.37.010192.000553&quot; rel=&quot;noreferrer&quot;&gt;Wootton (1992)&lt;/a&gt; reviewed the anatomy and biomechanics of insect wings. Basically the wing is a lightweight but strong scaffolding of &lt;em&gt;veins&lt;/em&gt;, supporting a thin membrane. The veins are composed by a sandwich of cuticle with a potential space in between. The membrane is also a double-layer but without the space.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the venous space are is circulating hemolymph and often nerves and tracheae. The wikipedia image is pretty good:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/O6ueq.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nerves carry sensory information and the tracheae oxygen.The hemolymph is continuous with the body and thus is able to circulate and hydrate the wing (important for maintaining flexibility). As Wootton says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;desiccation destroys both compliancy and toughness, and a dry cuticle would be mechanically disastrous&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So by maintaining a flexible tissue, insects have strong and tough wings that remain light enough.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-03-21T03:37:05.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1508" PostTypeId="2" ParentId="1488" CreationDate="2012-03-21T04:03:06.133" Score="9" Body="&lt;p&gt;Carl Woese has much to say on this subject, including:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;“The ancestor cannot have been a particular organism, a single&#xA;  organismal lineage. It was communal, a loosely knit, diverse&#xA;  conglomeration of primitive cells that evolved as a unit, and it&#xA;  eventually developed to a stage where it broke into several distinct&#xA;  communities, which in their turn become the three primary lines of&#xA;  descent [bacteria, archaea and eukaryotes].”&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is a 2000 Scientific American article by W.F. Doolittle that discusses much of Woese's (and others') work understanding this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, see a couple of Woese articles &lt;a href=&quot;http://dx.crossref.org/10.1073/pnas.132266999&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://dx.doi.org/10.1073/pnas.95.12.6854&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="649" LastEditorUserId="-1" LastEditDate="2012-04-15T00:45:20.947" LastActivityDate="2012-04-15T00:45:20.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1509" PostTypeId="1" AcceptedAnswerId="1524" CreationDate="2012-03-21T06:37:06.427" Score="38" ViewCount="919" Body="&lt;p&gt;Cells come in all sorts of sizes. How do they regulate their cell size to the point where similar cell types have a fairly mono-disperse size distribution?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reasked from &lt;a href=&quot;http://www.quora.com/How-Does-a-Cell-Know-Its-Size&quot;&gt;http://www.quora.com/How-Does-a-Cell-Know-Its-Size&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="22057" LastEditDate="2016-05-23T13:32:38.280" LastActivityDate="2016-05-23T13:32:38.280" Title="How does a cell sense its size?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="1510" PostTypeId="1" CreationDate="2012-03-21T10:09:35.177" Score="7" ViewCount="105" Body="&lt;p&gt;Intrinsic termination (rho-independent) relies on a stable hairpin with a subsequent uridine repeat. The common explanation on how these sequences cause the termination of the transcription are based on the thermodynamic stability of the sequence. The GC-rich stable hairpin together with the destabilizing U-repeat supposedly destabilize the binding of the polymerase enough to cause it to disassociate from the template.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm looking for are specific requirements on the termination sequences that are not based on thermodynamics. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Are there any specific requirements on the hairpin sequence beyond a certain thermodynamic stability. &lt;/li&gt;&#xA;&lt;li&gt;Are there any loop variants that are known to reduce the termination efficiency? &lt;/li&gt;&#xA;&lt;li&gt;Does the shape of the hairpin, e.g. any kinks or bulges in it, have an influence on termination efficiency?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The typical requirements I read are 5-14bp and GC-rich, and I'd like to know if there are any more specific requirements, especially ones related to the structure and not the stability of the hairpin.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="43" LastEditDate="2012-03-21T11:36:10.523" LastActivityDate="2012-05-28T22:11:12.240" Title="Which factors besides the thermodynamic stability are important for the hairpin in intrinsic transcription termination?" Tags="&lt;structural-biology&gt;&lt;transcription&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1512" PostTypeId="2" ParentId="1502" CreationDate="2012-03-21T13:34:53.093" Score="8" Body="&lt;p&gt;The appendix was thought to be vestigial in humans &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17936308&quot;&gt;until recently&lt;/a&gt;. Now it appears that, like rabbits, it is a safe harbour for symbiotic bacteria in the intestines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: Bollinger, Barbas, Bush, et al. J Theor Biol. 2007 Dec 21;249(4):826-31. Epub 2007 Sep 7.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-03-21T13:34:53.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1514" PostTypeId="2" ParentId="1485" CreationDate="2012-03-21T14:48:04.537" Score="6" Body="&lt;p&gt;This must depend upon the conditions in question, but I think it would not be very long.&#xA;The length of a generation for e coli can be 12 minutes or 24 hours, so that gives some idea of a typical time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did find this interesting &lt;a href=&quot;http://www.jbc.org/content/280/16/15921.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;case in the literature&lt;/a&gt;. They found that even as you subject e coli to minimal nutrients they are expressing genes that prepare them for a richer nutrient mix.  The bacteria are primed for a flood of carbohydrates succinate or amino acids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This study incubated the e coli overnight before taking their readings, so this puts an upper bound of about 12 hours.  The implication is that if you are moving the bacteria to rich media it might be just a short time before they are in log phase growth.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practice moving from LB plates to log phase growth is usually just like 4 hours.  This paper interestingly shows that cold adapted E coli moving to other media react in a few hours, &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1472-765X.2004.01593.x/pdf&quot; rel=&quot;nofollow&quot;&gt;but can show behavioral changes days out&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would say that 4 hours might be a typical expectation. 12 is typically used in the literature. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-03-23T01:24:41.427" LastActivityDate="2012-03-23T01:24:41.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1515" PostTypeId="1" AcceptedAnswerId="1539" CreationDate="2012-03-21T15:26:59.573" Score="19" ViewCount="19070" Body="&lt;p&gt;This is my first post here, so please be gentle. I recently learned that I have Rh- blood (I'm A-), and was idly looking into blood types on Wikipedia. I was surprised to find that relatively few (~15% of all) humans have it, and most of those seem to be European. Looking just a little further, I found a bunch of crackpot-looking sites that try to explain how people got Rh- blood, and what weird abilities they possess as a result.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I managed to find one site that seemed at least less laughable, which suggested that interbreeding with &lt;em&gt;Homo neanderthalensis&lt;/em&gt; (or possibly &lt;em&gt;Homo sapiens neanderthalensis&lt;/em&gt;, since the site seemed to indicate that there was some question about how different &lt;em&gt;H. s. sapiens&lt;/em&gt; were from &lt;em&gt;H. neanderthalensis&lt;/em&gt;) might have accounted for the introduction of the condition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that from more reputable (medical) sources, the only difference between Rh+ and Rh- is that complications can arise during pregnancy if the mother is Rh- and the fetus is Rh+. Indeed, most sites (e.g., WebMD) seem to explicitly state that there are no other differences of note.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not a biologist, or an anthropologist, or a life-science kind of guy at all. However, as a computer scientist, I like to think that I have both an open mind but one which demands scientific and/or logico-mathematical evidence for claims. Lots of the pseudo-scientific, paranormal, etc. theories on the web I basically dismiss out of hand, as explanations which are almost certainly fantasies, but most definitely baseless and untestable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What, if any, is the current scientific understanding of the origin, or source, of rhesus negative blood in human beings? Do individuals with Rh- blood have any common (in a statistically significant sense) characteristics or health issues, aside from the issue with pregnancy and tending to be more European than not? Is there anything to continuing to look into this?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For context, I got started down this rabbit hole while looking into different dieting strategies, and found the &quot;blood type diet&quot;. Just as an aside, I don't think there's a lot of merit to that diet... sounds like a fad thing. Any sources or information or help on this subject are appreciated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been looking a little more, and I stumbled across a paper entitled, &quot;The influence of RhD phenotype on toxoplasmosis and age-associated changes in personality profile of blood donors&quot; which looks at the effect of the Rh- trait on personality changes caused by toxoplasmosis (if you Google the title, you should be able to download). Using Cloninger's and Cattel's personality factors, they seem to show a variety of things, including (a) personality differences between Rh+ and Rh- individuals not affected by toxoplasmosis, and (b) different reactions to prolonged toxoplasmosis affection in Rh+ and Rh- individuals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I didn't even know that parasites could affect your behavior; that seems frightening on the one hand, but on the other, it's fascinating if it's for real, especially since the incidence of toxoplasmosis is not insignificant in most people. Anybody who knows anything about this or who reads the paper and can help me understand what it's saying would be doing me a great favor to answer/comment/chat. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="645" LastEditorUserId="107" LastEditDate="2012-03-22T22:37:28.943" LastActivityDate="2014-01-28T06:24:30.523" Title="Origin, or source, of rhesus negative in human blood" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;hematology&gt;" AnswerCount="5" CommentCount="4" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1516" PostTypeId="2" ParentId="1492" CreationDate="2012-03-21T15:43:56.807" Score="6" Body="&lt;p&gt;The protein referred to in the question is encoded by gene &lt;em&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/5406&quot; rel=&quot;nofollow&quot;&gt;PNLIP&lt;/a&gt;&lt;/em&gt;, pancreatic lipase. From this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/protein/NP_000927.1&quot; rel=&quot;nofollow&quot;&gt;annotation of the protein&lt;/a&gt;, I see that there is a signal peptide from amino acids 1 to 16. Thus, this signal peptide must be cleaved before the protein can be active in its digestion of emulsified triacylglyerides. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19113953/&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; describes the structural changes induced in human pancreatic lipase by lowering the pH. The secondary structure of the enzyme is stable within a pH range of 3.0 to 6.5. At this pH, a reversible opening of the lid controlling the access to the active site was observed. So, there is another aspect of activation - pH and the ability to open the enzyme lid so that the fat molecule enters the active site.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-10-16T12:25:43.357" LastActivityDate="2012-10-16T12:25:43.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1517" PostTypeId="2" ParentId="961" CreationDate="2012-03-21T15:59:05.900" Score="4" Body="&lt;p&gt;I have been running gels with different Acrylamide/Bisacrylamide ratios recently. People usually work with 1:37.5, 1:29 ratios which are commonly used for DNA and Protein gels. I have noticed that when you work with lower ratios 1:200 - 1:500, degassing becomes fundamental to guarantee reproducible resolution of my proteins. If I don't degass the mix in one of these gels some of the proteins I am resolving (which migrate really close to one another) won't separate well enough. Also, the time it takes to polymerize the gel can go from 20 to about 45 minutes if I don't degass the solution beforehand.&#xA;Degassing solutions with normal 1:29, 1:37.5 crosslinker ratios doesn't, in my experience, seem to have much of an effect other than having quicker polymerization times. Perhaps it makes a difference with lower concentration gels (8-5%), but I honestly wouldn't worry too much about this if I was routinely running 10-15% gels and reproducible resolution wasn't a concern.&lt;/p&gt;&#xA;" OwnerUserId="650" LastActivityDate="2012-03-21T15:59:05.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1518" PostTypeId="1" AcceptedAnswerId="1520" CreationDate="2012-03-21T16:08:43.320" Score="15" ViewCount="8096" Body="&lt;p&gt;I was quite fascinated by the feature &lt;a href=&quot;http://www.wired.com/wiredscience/2012/03/ff_antivirals/&quot;&gt;Should Science Pull the Trigger on Antiviral Drugs—That Can Blast the Common Cold?&lt;/a&gt; in this month's Wired magazine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They explain that Penicillin is effective at killing bacteria because it interferes with the growth of bacterial cell walls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does Penicillin do that exactly? And why does it not dissolve human cells as well?&lt;/p&gt;&#xA;" OwnerUserId="651" LastEditorUserId="69" LastEditDate="2012-03-27T21:26:56.183" LastActivityDate="2017-06-01T11:38:42.480" Title="Why does Penicillin only affect bacterial cell walls" Tags="&lt;pharmacology&gt;&lt;bacteriology&gt;&lt;antibiotics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1519" PostTypeId="1" AcceptedAnswerId="1531" CreationDate="2012-03-21T16:16:12.977" Score="13" ViewCount="170" Body="&lt;p&gt;Hymenoptera is an order of insects that includes bees, ants, and wasps. &lt;a href=&quot;http://www.etymonline.com/index.php?term=Hymenoptera&quot; rel=&quot;nofollow noreferrer&quot;&gt;A quick search&lt;/a&gt; gives the following etymological analysis of the term &lt;em&gt;hymenoptera&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;hymen&lt;/em&gt; (membrane) + &lt;em&gt;pteron&lt;/em&gt; (wing)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Does the term &lt;em&gt;hymenoptera&lt;/em&gt; have a firm basis in biology and physiology? In other words, what is different about membranes or wings (or membranous wings) in species of hymenoptera as opposed to species of other orders of insects?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="16866" LastEditDate="2017-04-26T19:29:20.500" LastActivityDate="2017-04-26T19:29:20.500" Title="To which distinctions does the term &quot;hymenoptera&quot; refer?" Tags="&lt;physiology&gt;&lt;entomology&gt;&lt;taxonomy&gt;&lt;nomenclature&gt;&lt;etymology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1520" PostTypeId="2" ParentId="1518" CreationDate="2012-03-21T16:21:19.867" Score="19" Body="&lt;p&gt;Bacteria have a mesh-like structure surrounding their plasma membrane called a cell wall.  The cell wall is made up of peptidoglycan polymers that form a rigid crystalline structure that helps protect the osmotic pressure of the bacterial cytoplasm.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Penicillin and other &amp;beta;-lactams work by inhibiting the final step of peptidoglycan synthesis, which prevents transpeptidation (crosslinking) of the peptidoglycan molecules. This leads to the death of the bacterium by osmotic pressure due to the loss of the cell wall.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This drug doesn't affect human cells because they lack a cell wall surrounding their plasma membrane.  &lt;/p&gt;&#xA;" OwnerUserId="12" LastEditorUserId="25" LastEditDate="2012-07-12T19:47:34.923" LastActivityDate="2012-07-12T19:47:34.923" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1521" PostTypeId="1" AcceptedAnswerId="1687" CreationDate="2012-03-21T17:35:58.210" Score="9" ViewCount="55377" Body="&lt;p&gt;Many fungi undergo a reproductive phase in which more than one genetically distinct nuclei (from 2 separate mating types) is present within the same cytoplasm. In the Ascomycota and Basidiomycota, this phase is termed &quot;dikaryotic&quot;, whereas in other fungal phyla the phase is &quot;heterokaryotic.&quot; What is the difference here? Is it purely number of nuclei per cell, or does the difference depend on how many genetically distinct nuclei are present (2 or &gt;2)? &lt;/p&gt;&#xA;" OwnerUserId="649" LastEditorUserId="649" LastEditDate="2012-03-21T19:56:02.150" LastActivityDate="2019-08-29T15:27:09.993" Title="What is the difference between &quot;dikaryotic&quot; and &quot;heterokaryotic&quot; states in the sexual lifecyles of fungi?" Tags="&lt;cell-biology&gt;&lt;mycology&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1522" PostTypeId="5" CreationDate="2012-03-21T19:00:05.077" Score="0" Body="" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-03-21T19:00:05.077" LastActivityDate="2012-03-21T19:00:05.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1523" PostTypeId="4" CreationDate="2012-03-21T19:00:05.077" Score="0" Body="Biologically-synthesized chemicals (or their derivatives) that cause growth suppression or death of bacteria. Other anti-microbials are often also considered under the class antibiotics these days." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T18:02:36.017" LastActivityDate="2013-10-31T18:02:36.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1524" PostTypeId="2" ParentId="1509" CreationDate="2012-03-21T20:17:11.827" Score="28" Body="&lt;p&gt;This is a question that has been the focus of study for the last century (e.g., &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/5875187&quot;&gt;Amodel of cell size regulation - Ycas et al, J. Theoret. Biol. (1965) 9, 444-470&lt;/a&gt;). Cell size regulation may be in part determined by ribosomal activity (through mTor regulation) and is a critical checkpoint in cell division.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How the cell senses its size, however, is not understood. In 2009, two reports suggested that protein gradients could be responsible for the sensing of cell size. You can read a commentary about those articles in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19619485&quot;&gt;Cell size control: governed by a spatial gradient. - Almeyda and Tyers, Dev. Cell. (2009) 17(1), 3-4&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The phenomenon of cell size homeostasis, whereby cells coordinate&#xA;  growth and division to maintain a uniform cell size, has been an&#xA;  outstanding issue in cell biology for many decades. Two recent studies&#xA;  in Nature in fission yeast demonstrate that a gradient of the polarity&#xA;  factor Pom1 is a sensor of cell length that determines the onset of&#xA;  Cdc2 activation and mitosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These articles demonstrate one way in which cells may sense their size, but most probably several other mechanisms are also in place.&lt;/p&gt;&#xA;" OwnerUserId="48" LastEditorUserId="115" LastEditDate="2012-03-21T21:14:32.223" LastActivityDate="2012-03-21T21:14:32.223" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1525" PostTypeId="1" CreationDate="2012-03-21T22:04:11.653" Score="5" ViewCount="234" Body="&lt;p&gt;Reposted from &lt;a href=&quot;http://www.quora.com/What-is-the-distance-between-the-3-18s-rRNA-the-Kozak-consensus-sequence-and-the-A-site-of-eukaryotic-ribosomes-during-protein-translation&quot; rel=&quot;nofollow&quot;&gt;Quora&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Kozak sequence is shown to be important in translation initiation, and the A-site is the anti-codon recognition site. If the distance is not known, how could I find out what it is? Is the crystal structure of the whole mRNA-rRNA-tRNA complex determined? If so, what modeling program would be best for establishing intermolecular distances?&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="3340" LastEditDate="2014-12-05T12:41:24.530" LastActivityDate="2014-12-05T13:05:03.630" Title="What is the distance between the 3' 18s rRNA (the Kozak consensus sequence) and the A-site of eukaryotic ribosomes during protein translation?" Tags="&lt;structural-biology&gt;&lt;ribosome&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1526" PostTypeId="1" CreationDate="2012-03-21T22:08:16.030" Score="7" ViewCount="243" Body="&lt;p&gt;Reposted from Quora: &lt;a href=&quot;http://www.quora.com/Does-the-MS2-RNA-binding-protein-have-any-translational-repression-effects&quot;&gt;http://www.quora.com/Does-the-MS2-RNA-binding-protein-have-any-translational-repression-effects&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm thinking of the MS2 protein binding to its RNA hairpin target. Would the interaction of the MS2 protein to the hairpin placed upstream of a ORF cause any translational repression?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2014-02-25T20:14:52.253" Title="Does the MS2 RNA binding protein have any translational repression effects?" Tags="&lt;molecular-biology&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1527" PostTypeId="2" ParentId="1499" CreationDate="2012-03-21T23:08:48.780" Score="7" Body="&lt;p&gt;Generally, fungi are cultured on agar with a food source such as malt extract. One way to do this is to clone a mushroom from the fruitbody of a mushroom or from colonized substrate (e.g. rotting wood). Another approach is to germinate spores. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fungus will grow as vegetative mycelia until it runs out of food. At that time, some species will grow tiny fruitbodies or sporulate before entering a more dormant phase, dying out. Unless refrigerated, standard agar plates dehydrate. Also, fungi may take on different textures: wispy, bumpy, root-like (rhizomorphic), leathery, powdery, and may darken or change color as they age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some cultures start to adapt their metabolism to the media after a large number of transfers (based on observation and discussed in Stamets' &quot;The Mushroom Cultivator&quot;.) at this point, cultures may also start to grow more slowly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mycelia can be transferred from one plate to another or to another media (substrate) such as a log, 'fortified sawdust' (sawdust with ~30% w/w wheat bran), or pasteurized compost. With the appropriate nutrition and environmental stimuli (CO2 levels, temperature, moisture, light, etc), the mycelia will fruit, creating mushrooms - generally after fully colonizing the substrate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a figure of 35 agar plates with 16 different fungal cultures that I isolated from the wild (soil, wood, mushrooms, as described in &lt;a href=&quot;https://webfiles.uci.edu/allisons/public/Pubs/allison2009.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Allison et. al, 2009&lt;/a&gt;; &lt;a href=&quot;https://netfiles.uiuc.edu/dlebauer/www/lebauer2010ldr.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;LeBauer, 2010&lt;/a&gt;), and have transferred from a mature culture (about a 2 months old) to a new plate, which are about two weeks old in this picture. Parent cultures are in the first and third row, with children below (they are genetic clones; instead of counting generations, I count number of transfers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/34gFY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also find cultures of fungi (Yeast) in unfiltered beer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have used many techniques to isolate and culture fungi (&lt;a href=&quot;https://netfiles.uiuc.edu/dlebauer/www/IsikhuemhenLeBauer2004GrowingPleurotustuberregium.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Isikhuemhen and LeBauer, 2004&lt;/a&gt;; &lt;a href=&quot;https://netfiles.uiuc.edu/dlebauer/www/lebauer2010ldr.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;LeBauer, 2010&lt;/a&gt;) but I would recommend the books &lt;a href=&quot;http://www.fungi.com/books/stamets.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;The Mushroom Cultivator&quot; and &quot;Growing Gourmet and Medicinal Mushrooms&quot; by Paul Stamets&lt;/a&gt; for more information on sterile culture techniques used in mushroom cultivation.&lt;/p&gt;&#xA;" OwnerUserId="222" LastEditorUserId="222" LastEditDate="2012-03-23T14:25:02.713" LastActivityDate="2012-03-23T14:25:02.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1528" PostTypeId="2" ParentId="1449" CreationDate="2012-03-22T00:08:54.153" Score="7" Body="&lt;p&gt;According to &lt;a href=&quot;http://dx.doi.org/10.1016/S0961-9534%2803%2900121-1&quot;&gt;Deckmyn et al (2004)&lt;/a&gt;, the primary effect of coppice management is that the fraction of total biomass in roots is relatively higher after coppicing, and that a substantial fraction of carbon in roots (~20% of root mass) is reallocated aboveground to support shoot growth in the spring following coppicing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of this large re-allocation, coppiced plants are able to grow more rapidly (and reach canopy closure sooner), than seedlings (&lt;a href=&quot;http://dx.doi.org/10.1016/0961-9534%2896%2900035-9&quot;&gt;Ceulemans et al 1996&lt;/a&gt;) it is important to consider that canopy closure (maximum leaf area index) occurrs more rapidly after coppicing &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Deckman et al, 2004 Poplar growth and yield in short rotation coppice: model simulations using the process model SECRETS. Biomass and Bioenergy &lt;a href=&quot;http://dx.doi.org/10.1016/S0961-9534%2803%2900121-1&quot;&gt;doi:10.1016/S0961-9534(03)00121-1&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Ceulemans et al, 1996. A comparison among eucalypt, poplar and willow characteristics with particular reference to a coppice, growth-modelling approach Original Research Article&#xA;Biomass and Bioenergy, Volume 11, Issues 2–3, Pages 215-231 &lt;a href=&quot;http://dx.doi.org/10.1016/0961-9534%2896%2900035-9&quot;&gt;doi:10.1016/0961-9534(96)00035-9&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="222" LastActivityDate="2012-03-22T00:08:54.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1529" PostTypeId="1" AcceptedAnswerId="1530" CreationDate="2012-03-22T02:13:51.863" Score="8" ViewCount="1805" Body="&lt;p&gt;How might I go about amplifying a gene transcript (mRNA) from animal tissue of which little is known about the genome? In some applications, I have used reverse transcriptase PCR to amplify all mRNA transcripts from cultured cells, but this required that I knew the sequence to PCR amplify.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do I go about this without knowledge of the gene or transcipt?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-09-14T20:19:53.437" Title="How to clone and sequence a gene transcript of unknown sequence?" Tags="&lt;dna-sequencing&gt;&lt;molecular-genetics&gt;&lt;pcr&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1530" PostTypeId="2" ParentId="1529" CreationDate="2012-03-22T03:39:37.433" Score="9" Body="&lt;p&gt;Perhaps you can draw inspiration from classic paper on lambda cloning: &lt;a href=&quot;http://dx.doi.org/10.1016/0092-8674%2878%2990036-3&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Maniatis T, Hardison RC, Lacy E, Lauer J, O’Connell C, Quon D, Sim GK, Efstratiadis A&lt;/strong&gt;. 1978. The isolation of structural genes from libraries of eucaryotic DNA. Cell 15: 687–701.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Try selecting tissues from the animal which you think is &quot;enriched&quot; (i.e. highly expressed) for the specific gene you're looking for. This might take a little bit of guessing. For example, if gene A is very highly expressed in tissue B, then you can &quot;assume&quot; most of the mRNA transcripts will be for that of gene A. Do a RNA purification, RT-PCR, and clone the cDNA into lambda vectors and pick plaques. With a little bit of luck, you'll be able to identify the gene by cloning, hybridisation, and subsequent chromosome &quot;walking&quot; to determine it's structural origin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This was done back in the day to identify novel genes way before genomics, sequencing, or even PCR!&lt;/p&gt;&#xA;" OwnerUserId="177" LastEditorUserId="836" LastEditDate="2012-09-14T20:19:53.437" LastActivityDate="2012-09-14T20:19:53.437" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1531" PostTypeId="2" ParentId="1519" CreationDate="2012-03-22T05:00:06.003" Score="8" Body="&lt;p&gt;I don't have a definitive answer, but I suspect Hymenoptera is &quot;just a name,&quot; albeit a name that has lasted through the &lt;a href=&quot;http://en.wikipedia.org/wiki/Phylogenetic_nomenclature&quot;&gt;phylogenetic nomenclature&lt;/a&gt; revolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hymenoptera was erected by &lt;a href=&quot;http://www.ucmp.berkeley.edu/history/linnaeus.html&quot;&gt;Linnaeus&lt;/a&gt; in the 10th edition of &lt;em&gt;&lt;a href=&quot;http://www.biodiversitylibrary.org/page/726888&quot;&gt;Systema Naturae&lt;/a&gt;&lt;/em&gt; (1758). The description of Hymenoptera (membrane wing; &lt;a href=&quot;http://www.biodiversitylibrary.org/page/727464&quot;&gt;p. 553&lt;/a&gt; [hope your Latin is better than mine]) follows that of Lepidoptera (scale wing) and Neuroptera (net wing) and precedes Diptera (two wing). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Classical taxonomy, which Linnaeus was more or less inventing at the time, was based on shared similarities. Those insects which Linnaeus thought more similar to each other than to other insects (e.g., ants, wasps, bees) all shared the characteristic of having a membrane based wing. The scaly wings of moths and butterflies made them more similar to each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He needed names for these groups, so he chose logical ones based on outward appearance of the wings: scaly, netted, membranous, or paired. That fact that these major groupings have more or less stood the test of time suggests that Linnaeus picked a good characteristic on which to name his classification of the major groups of insects.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-03-22T05:00:06.003" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1532" PostTypeId="2" ParentId="1439" CreationDate="2012-03-22T09:49:47.340" Score="16" Body="&lt;p&gt;Gasoline toxicity through ingestions seems to be a topic where there's not a great deal of in-depth information available. I don't know how this works for chronic use, as most literature refers to acute scenarios. Either way, orally ingested, 30-50g is said to be toxic to humans while 350g can be fatal.[3].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So...&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Gasoline's Constituents&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;A lot of components that make up gasoline are toxic to humans. This includes for example, benzene, toluene, xylene and butadiene. It's a mixture of more than 500 hydrocarbons and additives made up of:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;60–70% alkanes (paraffins)&lt;/li&gt;&#xA;&lt;li&gt;25–30% aromatics&lt;/li&gt;&#xA;&lt;li&gt;6–9% alkenes (olefins).[2].&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you really want to know specifics about metabolism of gasoline, you can probably check out how some of the constituents are metabolised (processed) and their effects. This is because different components have varying metabolic pathways. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to check this out, see Reese, et al at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1520023/pdf/envhper00383-0118.pdf.[3]. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Ingestion and Toxicity&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Apparently, most &lt;em&gt;reported&lt;/em&gt; cases of toxicity from gasoline occur from inhalation or absorption through the skin (intravenous use has also been reported). Even though ingestion is a frequent occurrence, there's not much data on outcomes after oral ingestion.[1],[2]. Gasoline can however be well absorbed through the gastrointestinal tract[2]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main target organ of gasoline toxicity is the nervous system and at high doses, this effect can cause death within minutes.[3]. However, generally, the primary cause of mortality seems to be related to gasoline's toxicity to the lungs. There are severe effects on the pulmonary system. Other effects of ingestion hasn't been as well documented.[1],[2]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's suggested that these compounds have a direct effect on lung tissue and  disrupts gas exchange and causes fluid buildup in the lungs (pulmonary edema). This in turn causes the oxygen levels in the body to drop (hypoxemia).[2]. There are many other toxic effects on the lungs as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, liver damage, kidney damage, damage to blood cells, gastric ulcers and toxicity in the heart can occur.[2],[3]. Again, this is discussed in Reese, et al.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps!&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Rahman I. &lt;em&gt;Gasoline ingestion: a rare cause of pancytopenia.&lt;/em&gt; Am J Med Sci. 2009. 338(5):433-4.&lt;/li&gt;&#xA;&lt;li&gt;Domej W. &lt;em&gt;Successful outcome after intravenous gasoline injection.&lt;/em&gt; J Med Toxicol. 2007. 3(4):173-7.&lt;/li&gt;&#xA;&lt;li&gt;Reese, et al. &lt;em&gt;Acute Toxicity of Gasoline and Some Additives&lt;/em&gt;. Environmental Health Perspectives. 1993. 115-131.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="653" LastEditorUserId="653" LastEditDate="2012-03-22T14:52:15.883" LastActivityDate="2012-03-22T14:52:15.883" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1533" PostTypeId="2" ParentId="1439" CreationDate="2012-03-22T11:10:18.147" Score="9" Body="&lt;p&gt;Just to add an answer to the 'how does the body process gasoline?' portion of the question, the liver and kidney would be doing most of the work of removing the stuff from the system once it was absorbed in the digestive tract.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The liver does most of the processing of toxins and their removal from the blood and would tend to do the most work in removing hydrocarbons from gasoline.  It has enzymes that oxygenate toxins (adds oxygens) which make them more soluable in the blood, usually less toxic, and also removable from the body by the liver or the kidney. In the case of gasoline the compounds are likely to be just as toxic.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The kidney works by actively filtering out excess water and mostly water soluable wastes like oxygenated hydrocarbons.  Kidney damage occurs when gasoline is ingested in excess.  This may be due to the toxicity of the gasoline, but also due to the compounds the liver is producing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gasoline will tend to be fat soluable too, so it will leave the system more slowly, even after being processed by the liver (benzene and toluene in gasoline will tend to become phenols which are quite toxic and fat soluable). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3379185&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/3379185&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-03-22T11:10:18.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1534" PostTypeId="2" ParentId="1430" CreationDate="2012-03-22T13:31:59.167" Score="9" Body="&lt;p&gt;Just as an intro...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heart pumps deoxygenated blood from the right ventricle, through the pulmonary arteries (&lt;a href=&quot;http://www.jawwad.org/uploads/attachments/1279476771.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;pic&lt;/a&gt;) which then eventually split into small capillary networks that surround the alveoli. The alveoli are formed by the trachea eventually branching off. So when you breathe in, the alveoli become filled with higher levels of oxygen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The blood then becomes oxygenated and returns to the heart via the pulmonary veins to be pumped to the rest of the body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The deoxygenated blood becomes oxygenated because there is a difference in oxygen and carbon dioxide concentration between the capillary network (O2 low / CO2 high) and the alveoli (O2 high / CO2 low) and so gas diffuses across because of the difference in concentrations (&lt;a href=&quot;http://anatomyhq.org/wp-content/uploads/2011/12/GCSE-Gas-Exchange-Revision.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;pic&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1piYT.jpg&quot; alt=&quot;Lung Anatomy&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Physiology textbooks explain these mechanisms but for blood clots in particular, you'll need to check out a pathophysiology book.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Blood clots&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;When a blood clot travels to the lungs, it's referred to as a &lt;em&gt;pulmonary embolus&lt;/em&gt; or PE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the time (90%), pulmonary emboli are formed in deep veins of the lower leg. These then travel to the pulmonary circulation system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Large emboli block larger vessels - the pulmonary arteries and their branches. The smaller ones travel further into the network.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Patients can sometimes be asymptomatic and the emboli can at times resolve on its own. The extent of the severity of a PE is determined by:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;how much blood flow is obstructed;&lt;/li&gt;&#xA;&lt;li&gt;how long the embolus has been there; and&lt;/li&gt;&#xA;&lt;li&gt;presence other underlying lung or heart disease.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are a number of things that a PE can cause physiologically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Reduced Gas Exchange&lt;/em&gt; - &lt;em&gt;alveolar dead space&lt;/em&gt; occurs when an alveolus is ventilated, but not perfused with blood. This, along with other factors, cause varying levels of hypoxemia (lack of oxygen).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Pulmonary Infarction&lt;/em&gt; - in a small amount of cases loss of blood flow to lung tissue can cause tissue death. This is fairly uncommon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Right Ventricular Failure&lt;/em&gt; - if there is a large enough blockage (&gt; 50 - 60%), the pressure in the pulmonary arteries increase. Subsequently, the load on the right ventricle is higher. &#xA;So in acute cases, the ventricle hasn't had time to adapt (hypertrophy) and so the right heart can fail. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At any rate, the haemodynamic balance can be disrupted when a PE is present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the elderly or people with underlying disease where their lung function is already decreased, PEs can have a significantly larger effect because they can't compensate. There are many more important points related to this but hopefully this is a useful (very) basic overview.&lt;/p&gt;&#xA;" OwnerUserId="653" LastEditorUserId="653" LastEditDate="2012-03-22T13:38:24.603" LastActivityDate="2012-03-22T13:38:24.603" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1535" PostTypeId="1" AcceptedAnswerId="1536" CreationDate="2012-03-22T17:28:00.640" Score="6" ViewCount="148" Body="&lt;p&gt;When did the change of official name from &lt;em&gt;Lactobacillus sanfrancisco&lt;/em&gt; to &lt;em&gt;Lactobacillus sanfranciscensis&lt;/em&gt; happen? An answer ((to the exact day OR within a few days) AND the name of the conference at which it happened) would be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="263" LastEditorUserId="87" LastEditDate="2012-03-23T06:44:49.397" LastActivityDate="2012-03-23T06:44:49.397" Title="On which date did the official name change of Lactobacillus sanfranciscensis change?" Tags="&lt;taxonomy&gt;&lt;history&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1536" PostTypeId="2" ParentId="1535" CreationDate="2012-03-22T18:22:19.730" Score="10" Body="&lt;p&gt;&lt;em&gt;Lactobacillus sanfranciscensis&lt;/em&gt; first shows up in pubmed in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106434/&quot;&gt;Gänzle et al. (1998)&lt;/a&gt;. They reference &lt;a href=&quot;http://ijs.sgmjournals.org/content/47/3/908.abstract&quot;&gt;Trüper and De'Clari (1997)&lt;/a&gt; for the name &lt;em&gt;Lactobacillus sanfranciscensis&lt;/em&gt;. The latter say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As none of them makes sense in the nominative apposition construction,&#xA;  we hereby correct these names to forms that are in agreement with Rule&#xA;  12c as follows. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;em&gt;Lactobacillus sanfrancisco&lt;/em&gt; (&quot;the city San Francisco&quot;) is corrected to &lt;em&gt;Lactobacillus sanfranciscensis&lt;/em&gt; (adjective: &quot;from San Francisco&quot;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That issue of &lt;em&gt;Int J Syst Bacteriol&lt;/em&gt; was published 1 July 1997, so I guess that's your date.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;References&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Gänzle M G, M Ehmann, and W P Hammes. 1998. Modeling of growth of &lt;em&gt;Lactobacillus sanfranciscensis&lt;/em&gt; and &lt;em&gt;Candida milleri&lt;/em&gt; in response to process parameters of sourdough fermentation. &lt;em&gt;Appl Environ Microbiol&lt;/em&gt; 64(7):2616–2623.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trüper H G, De'Clari L. 1997. Taxonomic note: necessary correction of specific epithets formed as substantives (nouns) &quot;in apposition.&quot; &lt;em&gt;Int J Syst Bacteriol&lt;/em&gt; 47:908–909.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2012-03-22T18:59:16.487" LastActivityDate="2012-03-22T18:59:16.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1537" PostTypeId="1" AcceptedAnswerId="1565" CreationDate="2012-03-22T19:36:40.023" Score="3" ViewCount="1442" Body="&lt;p&gt;I got the given question. They want the following pieces of information about protozoological human parasites:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;disease - parasite - vector.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are 10 proteogenic diseases at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Protozoa#Sub-groups&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;. I added the corresponding parasite and the vector next to them:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Malaria - Plasmodium - Apicomplexa&lt;/li&gt;&#xA;&lt;li&gt;Amoebiasis - Entamoeba histolytica - sarcomastigophora &lt;/li&gt;&#xA;&lt;li&gt;Giardiasis - Giardia lamblia - no vector&lt;/li&gt;&#xA;&lt;li&gt;Toxoplasmosis - Toxoplasma gondii - no vector&lt;/li&gt;&#xA;&lt;li&gt;Cryptosporidiosis - Cryptosporidium - Apicomplexa&lt;/li&gt;&#xA;&lt;li&gt;Trichomoniasis - Trichomonas vaginalis - no vector&lt;/li&gt;&#xA;&lt;li&gt;Chagas disease - Trypanosoma cruci - insect&lt;/li&gt;&#xA;&lt;li&gt;Leismaniasis - Leishmania donovani - sand fly vector&lt;/li&gt;&#xA;&lt;li&gt;Sleeping sickness - Trypanosoma brucei gambiense - tsetse fly vector&lt;/li&gt;&#xA;&lt;li&gt;Dysentery - Entamoeba histolytica - sarcomastigophora&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I am unsure what I should answer to the question since it is asking &quot;all&quot; possible vectors for unicellular human parasites. &#xA;There are many possible diseases, much more than the given ten in my opinion.&#xA;It seems also that there are many possible ways of getting the infection for each disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope that I am wrong in my statements.&#xA;It is my first course in Parasitology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What would you answer to the given question?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-03-25T18:44:28.607" Title="What are all possible vectors for unicellular human parasites?" Tags="&lt;homework&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1539" PostTypeId="2" ParentId="1515" CreationDate="2012-03-22T22:57:15.800" Score="10" Body="&lt;p&gt;Your question has many questions in it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the evolution of Rh factor, &lt;a href=&quot;http://jhered.oxfordjournals.org/content/91/3/205.abstract&quot;&gt;Blancher and Apoil (2000)&lt;/a&gt; attribute the high level of sequence similarity (92%) of the two &lt;em&gt;RH&lt;/em&gt; locus genes, &lt;em&gt;RHD&lt;/em&gt; and &lt;em&gt;RHCE&lt;/em&gt; to a gene duplication event in the common ancestor of human, chimps, and gorillas. Their analysis of the cDNA from these genes revealed &quot;complex recombination events&quot; after the lineages split.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically the most recent common ancestor of apes had the &quot;human&quot; &lt;em&gt;RH&lt;/em&gt; genes, which then differentiated after the lineages diverged. Duplicate and differentiate is a common theme in evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for why it's called rhesus antigen, that's just as experimental artifact:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The term &quot;Rhesus antigen&quot; was introduced by Landsteiner and Wiener,&#xA;  who found that rabbits (and later, guinea pigs) immunized with red&#xA;  blood cells (RBCs) from a rhesus monkey produced antibodies which&#xA;  agglutinated 85% of Caucasian blood samples (Landsteiner and Wiener&#xA;  1940, 1941).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They probably weren't even correct about the antibodies being rhesus:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In conclusion, if the term &quot;Rh&quot; was coined by Landsteiner and Wiener&#xA;  because of the source of antigens (the rhesus monkey) they used to&#xA;  obtain anti-Rh in rabbits, it is highly probable that, in fact, they&#xA;  produced anti-LW antibodies.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2012-03-23T00:23:00.687" LastActivityDate="2012-03-23T00:23:00.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1540" PostTypeId="2" ParentId="835" CreationDate="2012-03-23T15:18:42.527" Score="11" Body="&lt;p&gt;A recent paper called '&lt;em&gt;Genetic Influences in Sport and Physical Performance&lt;/em&gt;'[1] states:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;&lt;em&gt;Muscle fibre type determination is complex. Whilst initial composition is likely to be strongly influenced by genetic factors, training has significant effects on fibre shifts.&lt;/em&gt;&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They also go onto say that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;&lt;em&gt;However, the role of genetic variation in determining psychological state and responses remains poorly understood; only recently have specific genes been implicated in motivational behaviour and maintenance of exercise.&lt;/em&gt;&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Finally:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;&lt;em&gt;With the current state of knowledge, the field of genetic influences on sports performance remains in its infancy, despite over a decade of research.&lt;/em&gt;&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;An older paper which also examined fiber types stated that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;&lt;em&gt;These results reveal the existence of large interindividual variability and gender differences in the most common characteristics of the human skeletal muscle.&lt;/em&gt;&quot;[4].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Another study hypothesises that there may be racial differences in muscle fibre types.[2]. It's also said that a large variation in fiber composition of skeletal muscle within subgroups of athletic ability. This suggests that factors other than fiber-type composition contribute to performance.[3].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A small study carried out in the Croatian Navy found that ectomorphs had a better ability to sprint than endomorphs.[5]. They also found a positive correlation between calf girth and sprinting ability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The information is a bit disjointed and sparse. However, to finally come around to the question at hand, it seems that although there may be differences according to body type initially (which obviously also has a genetic basis), training and physical activity contributes significantly to what number and types of fibres individuals possess. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are lots of sport-specific research papers examining individuals' performance and suitability on body types.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;A note on somatotyping:&lt;/em&gt; I guess it might also be handy note that somatotyping (endomorph, ectomorph and mesomorph) is just one theory on measuring an individual and it does have critics. The theory was initially developed in an attempt to link body type to behaviour. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's been suggested that measurements like BMI are much more objective and useful.[6]. Another point made was that bodies change according to a number of environmental variables, nutrition etc.[7]. For example, one study suggested that intense labour during adolescence may affect somatotype (there are a few similar studies).[8]. So perhaps while using somatotypes to identify a person at one point in time is useful, it has limits in use as a long term classification. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This point probably has more relevance to the question at hand since with training and physical activity, a person can potentially change their somatotype at least to some extent; and also the number and types of muscle fibers (which evidence supports).&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Puthucheary Z, et al. &lt;em&gt;Genetic influences in sport and physical performance.&lt;/em&gt; Sports Med. 2011. 41:845-59.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Nielsen J. &lt;em&gt;Glucose intolerance in the West African Diaspora: a skeletal muscle fibre type distribution hypothesis.&lt;/em&gt; Acta Physiol. 2011. 202(4):605-16.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;DeLee: DeLee and Drez's Orthopaedic Sports Medicine. 3rd ed. Saunders.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Simoneau, et al. &lt;em&gt;Human variation in skeletal muscle fiber-type proportion and enzyme activities.&lt;/em&gt; AJP - Endo. 1989. 257(4):567-572.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Sporis G. &lt;em&gt;Impact of body composition on performance in fitness tests among personnel of the Croatian navy.&lt;/em&gt; Coll Antropol. 2011. 35(2):335-9.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Maddan, et al. &lt;em&gt;The BMI as a somatotypic measure of physique: A rejoinder to Jeremy E.C. Genovese.&lt;/em&gt; The Social Science Journal. 2009. 46:394–401.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Parnell. &lt;em&gt;Simplified somatotypes Original Research Article.&lt;/em&gt; Journal of Psychosomatic Research. 1964. 8(3):311-315.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Ozener, et al. &lt;em&gt;The effect of labour on somatotype of males during the adolescent growth period.&lt;/em&gt; Homo. 2008. 59(2):161-72.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="653" LastEditorUserId="653" LastEditDate="2012-03-23T17:26:00.217" LastActivityDate="2012-03-23T17:26:00.217" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1541" PostTypeId="1" CreationDate="2012-03-23T18:34:41.813" Score="12" ViewCount="1456" Body="&lt;p&gt;Most of the human genes are found to be highly methylated in their 3'UTR region (0.8-0.9%). I was wondering if there is any specific reason for this?&lt;/p&gt;&#xA;" OwnerUserId="601" LastEditorUserId="389" LastEditDate="2012-03-25T03:35:59.777" LastActivityDate="2012-03-27T16:10:13.223" Title="Why is the 3'UTR region highly methylated in most of the human genes?" Tags="&lt;dna&gt;&lt;epigenetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1542" PostTypeId="1" AcceptedAnswerId="1546" CreationDate="2012-03-23T23:12:44.393" Score="9" ViewCount="503" Body="&lt;p&gt;I understand that it's feasible the bacteria within the gastrointestinal tract originate from the food we eat and air we breath, but where does this population of microbes originate from?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="16651" LastEditDate="2015-12-13T13:30:18.017" LastActivityDate="2015-12-13T13:30:18.017" Title="Where do the bacteria within the vagina originate from?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;bacteriology&gt;&lt;microbiome&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1543" PostTypeId="2" ParentId="1542" CreationDate="2012-03-24T00:19:51.570" Score="3" Body="&lt;p&gt;There is some interesting information &lt;a href=&quot;http://www.hmpdacc.org/impacts_health/impact_health.php&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; from the Human Microbiome Project, but no details regarding the source of vaginal microflora. I would say that the sources would be gut and skin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ethical issues of manipulating a baby's microbiome are brought to light &lt;a href=&quot;http://the-scientist.com/2012/03/01/who-are-we-really/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-03-28T15:44:24.417" LastActivityDate="2012-03-28T15:44:24.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1544" PostTypeId="5" CreationDate="2012-03-24T01:50:06.723" Score="0" Body="&lt;p&gt;Bioinformatics is a broad field that interfaces a variety of life science disciplines (biology, genetics, biochemistry, etc.) with a variety of quantitative sciences (mathematics, statistics, computer science, etc.). Bioinformatic techniques typically involve developing and applying software and algorithms to computationally intensive biological questions, such as those common in structural biology, genomics, sequence analysis, and systems biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some scientists draw a distinction between the terms &lt;em&gt;bioinformatics&lt;/em&gt; and &lt;em&gt;computational biology&lt;/em&gt;. While these areas are indeed broad and diverse, the distinctions in terms is not consistent or well-defined, and some questions from computational biology should include the bioinformatics tag.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="1590" LastEditDate="2016-03-23T08:58:54.920" LastActivityDate="2016-03-23T08:58:54.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1545" PostTypeId="4" CreationDate="2012-03-24T01:50:06.723" Score="0" Body="The science of collecting and analyzing complex biological data such as genetic codes using informatics." OwnerUserId="43" LastEditorUserId="27029" LastEditDate="2016-11-23T21:10:29.637" LastActivityDate="2016-11-23T21:10:29.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1546" PostTypeId="2" ParentId="1542" CreationDate="2012-03-24T05:37:30.320" Score="11" Body="&lt;p&gt;Most of the initial colonisation is said to be coincidental ('happenstance' as the textbook puts it!) exposure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's then fairly predictable depending on:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;type of delivery (as Larry commented);&lt;/li&gt;&#xA;&lt;li&gt;feeding; and&lt;/li&gt;&#xA;&lt;li&gt;receipt of antibiotics.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In terms of feeding, there are differences in flora between babies fed human milk and those that are given cow's milk. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's a section called 'Establishment and Composition of Normal Flora' in chapter 187 of &lt;em&gt;Principles and Practice of Pediatric Infectious Diseases&lt;/em&gt; (3rd ed) by Long which discusses the above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also said that hormones may influence indigenous flora. For example, premenarcheal and postmenopausal vaginal flora are very different to those present during the childbearing period.[1].&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases. 7th ed. 2009. Churchill Livingstone.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="653" LastActivityDate="2012-03-24T05:37:30.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1547" PostTypeId="2" ParentId="870" CreationDate="2012-03-24T06:34:37.120" Score="2" Body="&lt;p&gt;It's usually important to rule out other medical conditions when considering many psychiatric diagnoses due to similarities in symptoms between them. There are many examples but I'm not sure if it's appropriate to note them here as a lot of symptoms have to be considered in a clinical context and might be mistaken as medical advice. It's also important to note that concurrent medical and psychiatric conditions frequently occur with individuals diagnosed with conversion disorder.(2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conversion disorder was previously combined with somatisation disorder and was known as hysteria.(2). Conversion disorder is a diagnosis of exclusion where the symptoms are not a result of:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;neurological or other medical condition;&lt;/li&gt;&#xA;&lt;li&gt;the effect of a substance; or &lt;/li&gt;&#xA;&lt;li&gt;cultural behavior or experience.(1).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The key is that these are not intentionally or medically driven symptoms but rather physical manifestations of psychological needs (&quot;&lt;em&gt;unconscious manifestations of emotional conflict&lt;/em&gt;&quot;(3)). Psychoanalytic theory suggests that &quot;&lt;em&gt;conversion disorder is caused by repression of unconscious intrapsychic conflict and conversion of anxiety into a physical symptom&lt;/em&gt;&quot;(2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of physiological basis of conversion disorder, it's been suggested that an imbalance in metabolism between the dominant and non-dominant brain hemispheres; and impaired communication between the two may be an issue.(2). There are some other points you can also read at &lt;a href=&quot;http://www.medscape.com/viewarticle/572542_5&quot; rel=&quot;nofollow&quot;&gt;MedScape&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Ferri. Ferri's Clinical Advisor. 2012. Mosby.&lt;/li&gt;&#xA;&lt;li&gt;Sadock. Kaplan &amp;amp; Sadock's Synopsis of Psychiatry. 10th ed. 2007. Wolters Kluwer.&lt;/li&gt;&#xA;&lt;li&gt;Jacobson. Psychiatric Secrets. 2nd ed. 2001. Hanley and Belfus.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="653" LastEditorUserId="653" LastEditDate="2012-03-24T11:48:56.627" LastActivityDate="2012-03-24T11:48:56.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1548" PostTypeId="2" ParentId="1035" CreationDate="2012-03-24T07:17:53.830" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://deepblue.lib.umich.edu/bitstream/2027.42/23426/1/0000374.pdf&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; suggests that bats have a comparatively high depth of focus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's believed that &lt;a href=&quot;http://landsat.gsfc.nasa.gov/education/compositor/em.html&quot; rel=&quot;nofollow&quot;&gt;butterflies&lt;/a&gt; (depending on species) have the widest visual spectrum.&lt;/p&gt;&#xA;" OwnerUserId="653" LastActivityDate="2012-03-24T07:17:53.830" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1549" PostTypeId="2" ParentId="344" CreationDate="2012-03-24T09:30:36.540" Score="4" Body="&lt;p&gt;There is a pretty good discussion on this topic in &lt;a href=&quot;http://books.google.com/books?id=OWD3V9bFWV8C&amp;amp;pg=PA17&amp;amp;lpg=PA17&amp;amp;dq=loose%20cannon%20and%20weak%20link%20theories&amp;amp;source=bl&amp;amp;ots=UPPbTZrB_t&amp;amp;sig=a_W4f5Ob1wuOQ5wT1r4DotJFy-E&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=uY5tT4W4I4nXrQejlMygDg&amp;amp;redir_esc=y#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;chapter 2&lt;/a&gt; of &lt;em&gt;Geriactric Medicine - An Evidence Based Approach (4th ed)&lt;/em&gt; by Cassel. This is the main reference for the info below which can hopefully add something to the answers already given.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of views on ageing, there's evidence to support both:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;general principles that may apply to it; and &lt;/li&gt;&#xA;&lt;li&gt;it being a consequence of a collection of degenerative processes (this is apparently the more supported view).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Since almost all biological systems in the body degenerates with age and this happens seemingly at random, it's been difficult to identify particular catalysts that cause this. Consequently, biologists apparently steer away from a general theory or mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are two classes of theories that have been floating around. That is 'loose cannon' and 'weak link'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Loose Cannon&lt;/em&gt; encompasses theories that support the 'wear and tear' proposition. Two popular theories under this banner are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1383768&quot; rel=&quot;nofollow&quot;&gt;free radicals&lt;/a&gt; and &lt;a href=&quot;http://www.springerlink.com/content/qq764j6548k56266/&quot; rel=&quot;nofollow&quot;&gt;glucose&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Weak Link&lt;/em&gt; suggests that particular physiological systems are vulnerable during senescence and if a system fails, the whole body begins to decline. It's suggested that the neuroendocrine and immune systems are particularly vulnerable. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also a limit on the ability of cells to replicate - this is called the Hayflick Phenomenon (or limit). The reduction of the enzyme &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933587/&quot; rel=&quot;nofollow&quot;&gt;Telomerase&lt;/a&gt;, which lengthens telomeres during mitosis, is implicated in limiting a cell's ability to replicate indefinitely.&lt;/p&gt;&#xA;" OwnerUserId="653" LastActivityDate="2012-03-24T09:30:36.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1550" PostTypeId="2" ParentId="1243" CreationDate="2012-03-24T12:06:45.393" Score="7" Body="&lt;p&gt;Well, if we look in &lt;em&gt;very basic&lt;/em&gt; detail at how muscle contraction works within a myofibril of the sarcomere:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dUcVs.gif&quot; alt=&quot;Animation of muscle contractions&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;N.b. this isn't on a loop and only plays through seven times&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The red lines represent actin filaments whilst the blue lines represent myosin filaments.  During muscle contraction the filaments move over each other:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0WDVE.jpg&quot; alt=&quot;Relaxed myofibril&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6y6TZ.jpg&quot; alt=&quot;Partially Contracted myofibril&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MBBOq.jpg&quot; alt=&quot;(Over)Contracted myofibril&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As shown in the above diagrams the &quot;more contracted&quot; a muscle is then the smaller the size of the H zone (the area where there are &lt;em&gt;just&lt;/em&gt; myosin filaments). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if we consider a penetrating impact that went through a plethora of identically aligned sarcomeres (obviously this is not the case in nature) then we could presume that (&lt;em&gt;et ceteris paribus&lt;/em&gt;) the object would not penetrate as deeply into a contracted muscle as it will hit more tissue on its route than in a relaxed muscle. &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-03-24T12:06:45.393" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1551" PostTypeId="5" CreationDate="2012-03-24T13:20:28.793" Score="0" Body="&lt;p&gt;DNA sequencing is a group of techniques that are used to obtain the sequence of nucleotides in &lt;a href=&quot;/questions/tagged/dna&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;dna&amp;#39;&quot; rel=&quot;tag&quot;&gt;dna&lt;/a&gt;. When DNA sequencing is done for the entire genome of an organism then it is called genome-sequencing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two main methodological principles for DNA sequencing:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Sequencing by termination: Sanger sequencing&lt;/li&gt;&#xA;&lt;li&gt;Sequencing by synthesis: Most next generation sequencing methods&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Sanger sequencing depends on termination of PCR reaction at different positions of a nucleotide. PCR termination happens because of the incorporation of a non-extensible di-deoxy-nucleotide (it lacks 3' OH; the triphosphate form is abbreviated as ddNTP), instead of a usual deoxy-nucleotide. This leads to formation of multiple products which indicate the location of a nucleotide in the DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sequencing by synthesis involves recording the nucleotide as it is inserted in the growing DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Refer to the &lt;a href=&quot;https://en.wikipedia.org/wiki/DNA_sequencing&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia page&lt;/a&gt; on DNA sequencing for basic details. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next generation sequencing (NGS) methods use a high level of automation that enables large scale sequencing. Refer to &lt;a href=&quot;http://www.cell.com/trends/genetics/abstract/S0168-9525%2814%2900112-7&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; review for more details on NGS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Applications and variants of DNA sequencing:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ChIP-seq: Chromatin Immunoprecipitation followed by DNA sequencing (ChIP-seq) is used to identify regions of DNA that is bound by a certain protein, which in most cases is a transcription factor.&lt;/li&gt;&#xA;&lt;li&gt;Nucleosome sequencing: Sequencing the regions bound the nucleosome; used to study chromatin architecture&lt;/li&gt;&#xA;&lt;li&gt;Bisulphite sequencing: Bisulphite to deaminate methylated cytosine to thymine. This when compared to untreated DNA sequence, reveals sites of cytosine methylation.&lt;/li&gt;&#xA;&lt;li&gt;MeDIP-seq: Methylated-DNA immunoprecipitation followed by sequencing: Also used to find methylated regions of DNA but uses an antibody to precipitate methylated DNA (cytosine). &lt;/li&gt;&#xA;&lt;li&gt;DNAse Hypersensitive region mapping: DNA is treated with DNAse to identify regions protected by protein binding. Used for studying chromatin architecture&lt;/li&gt;&#xA;&lt;li&gt;HiC: Genome level implementation of chromosome conformation capture (3C). Used for studying DNA-DNA interactions.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions that can have this tag:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Questions related to principle behind the sequencing techniques&lt;/li&gt;&#xA;&lt;li&gt;Questions related to principle behind any of the above mentioned implementations of DNA sequencing&lt;/li&gt;&#xA;&lt;li&gt;Questions related to experimental troubleshooting for any of these techniques&lt;/li&gt;&#xA;&lt;li&gt;Questions related to analysis of sequencing data&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Related tags are &lt;a href=&quot;/questions/tagged/genetics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;genetics&amp;#39;&quot; rel=&quot;tag&quot;&gt;genetics&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/dna&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;dna&amp;#39;&quot; rel=&quot;tag&quot;&gt;dna&lt;/a&gt; and &lt;a href=&quot;/questions/tagged/lab-techniques&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;lab-techniques&amp;#39;&quot; rel=&quot;tag&quot;&gt;lab-techniques&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="15950" LastEditDate="2019-12-31T14:44:17.190" LastActivityDate="2019-12-31T14:44:17.190" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="1552" PostTypeId="4" CreationDate="2012-03-24T13:20:28.793" Score="0" Body="Technique(s) by which the sequence of DNA is obtained. The principles are similar for RNA-sequencing." OwnerUserId="69" LastEditorUserId="15950" LastEditDate="2019-12-31T14:44:12.963" LastActivityDate="2019-12-31T14:44:12.963" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="1553" PostTypeId="1" CreationDate="2012-03-24T14:18:44.703" Score="9" ViewCount="7508" Body="&lt;p&gt;If the purpose of &quot;goosebumps&quot; is to keep us warm, why is it so ineffective? Or are the changes subtle, but important?&lt;/p&gt;&#xA;" OwnerUserId="660" LastActivityDate="2012-03-24T15:26:43.980" Title="Why are goosebumps so ineffective at keeping us warm?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1554" PostTypeId="2" ParentId="1553" CreationDate="2012-03-24T15:08:03.380" Score="10" Body="&lt;p&gt;When your brain, the hypothalamic temperature centers in particular, detects that the temperature is too warm or cold, it initiates a number of controls to try and correct this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Goosebumps appear due to &lt;em&gt;piloerection&lt;/em&gt;. This is one of the reactions that occur when the temperature is too low.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This causes hairs to stand on end as a result of contractions in muscles attached to hair follicles called &lt;em&gt;arrector pili&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This particular reflex is not actually important in human beings. However, in animals, this mechanism allows entrapment of a layer of air allowing insulation. This way, the heat loss is greatly reduced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other mechanisms are very adept at maintaining temperature in the human body. These include sweating, dilation (vasodilation) and constriction (vasoconstriction) of skin blood vessels and increasing and decreasing the body's heat production.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, when it's too hot, dilation of the skin blood vessels can increase heat transfer by up to eight times.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Source:&lt;/em&gt; Guyton and Hall. Medical Physiology. 11th ed. Elsevier Saunders.&lt;/p&gt;&#xA;" OwnerUserId="653" LastEditorUserId="653" LastEditDate="2012-03-24T15:21:55.693" LastActivityDate="2012-03-24T15:21:55.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1555" PostTypeId="2" ParentId="1553" CreationDate="2012-03-24T15:26:43.980" Score="5" Body="&lt;p&gt;&lt;em&gt;Cutis anserina&lt;/em&gt; (goosebumps) are caused when the sympathetic nervous system induces the &lt;em&gt;arrectores pilorum&lt;/em&gt; muscles at the base of each hair cell to contract and raise up the hair.  Zoidberg has posted an answer describing the mechanism as I was writing mine, so I'll move directly onto effectiveness. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason that, as you say, the mechanism is not particularly effective in humans is our relatively small amount of body hair.  As mentioned the purpose of the erector muscles causing the hairs to stand up is to allow for air to be trapped at the surface of the skin rather than absorbing heat from the body then taking it quickly away.  Mammals with denser fur/hair are likely to have a much better insulating effect from goosebumps.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some animals have adapted to use the mechanism for another purpose, however; the porcupine being a prime example.  When threatened, the porcupine uses its &lt;em&gt;arrectores pilorum&lt;/em&gt; muscles to elevate all its quills, making it appear larger and more threatening or to actively repel an attacker.  The extra rigidity that they gain from doing this&lt;sup&gt;1&lt;/sup&gt; also helps to contribute towards making their spines a very effective defence:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1xxM4.jpg&quot; alt=&quot;Dog after porcupine attack&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Goosebumps have also been reported in humans during periods of stress, anxiety and even sexual arousal.  This is related to the stimulatory effect that adrenaline has on the sympathetic nervous system which, as mentioned above, is responsible for the stimulation of the erector muscles. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-7998.1986.tb03620.x/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mechanical design of hedgehog spines and porcupine quills. Journal of Zoology&#xA;Volume 210, Issue 1, pages 55–75, September 1986&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-03-24T15:26:43.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1556" PostTypeId="1" AcceptedAnswerId="1561" CreationDate="2012-03-24T15:40:02.500" Score="15" ViewCount="1477" Body="&lt;p&gt;I'm sure that everyone is familiar with the sensation commonly known as &quot;butterflies in the stomach&quot;.  It is commonly experienced during periods of anxiety or stress (e.g. before high stakes job interviews or roller coaster rides) and apparently (after my web research) often felt in new romances without an obvious cause of tension.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, whilst my googling did turn up an inordinate amount of rubbish regarding love-sicknesnes, I have been unable to find even a suggestion as to a mechanism as to the physiology behind this feeling.  Is it a sensation of physical change in the stomach (some sites vaguely mentioned the restriction of blood flow to critical organs but it was entirely unsupported) or is it neurological in nature?  &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-03-25T19:55:29.497" Title="Is the 'fluttering feeling' when under stress neurological or physical?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1557" PostTypeId="2" ParentId="1556" CreationDate="2012-03-24T16:54:28.097" Score="7" Body="&lt;p&gt;Nervousness or excitement should cause an increase in activity in the sympathetic nervous system (the so-called &quot;fight or flight&quot; side of the autonomic system). Increased sympathetic activity will be associated with decreased parasympathetic activity (primarily digestion, but also crying and other &quot;emittive&quot; glandular activity).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't have a citation, but I suspect that the &quot;butterflies&quot; feeling is associated with the cessation of peristaltic activity in the gut, which puts the digestive and nervous systems in conflict. If you have just eaten, then there is a difference between what your gut wants to do (digest) and what your brain wants it to do (not digest) -- thus the frequently accompanying nausea.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-03-24T16:54:28.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1558" PostTypeId="2" ParentId="967" CreationDate="2012-03-24T19:34:34.697" Score="4" Body="&lt;p&gt;Looking through some papers it is not clear to me that botanists actually know why this should be the case, and I am sure that you are more qualified than me to comment on this Richard! However, there's some discussion of this in Zhang et al. (2012).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These authors argue that the &quot;exudate from curcubits is copious&quot; because of physiological adaptations due to their growth habit - i.e. they are vines and as such often require the structural support of other plants. Vines compensate for a lack of a supporting stem structure by having xylem vessels that are wider than comparable freestanding species  and &quot;high hydraulic conductivity&quot; (which is a measure of how readily water will flow through pores - in the case of curcubits - very readily). Similarly, sieve tubes and sieve pores are very wide compared to species in other families. Since these sieve tubes have such a large cross-section, they do not readily self-seal.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plantphysiol.org/content/early/2012/02/13/pp.112.194431&quot; rel=&quot;nofollow&quot;&gt;The Origin and Composition of Cucurbit Phloem Exudate&#xA;C Zhang, X Yu, BG Ayre, R. Turgeon - Plant Physiology, 2012 - Am Soc Plant Biol. 158, 3&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;See also:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.springerlink.com/content/p574mx10j2636041/&quot; rel=&quot;nofollow&quot;&gt;Why vines have narrow stems: Histological trends in Bauhinia (Fabaceae), Ewers, F., Fisher, J, Oecologia, 1991, 88, 2&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="81" LastActivityDate="2012-03-24T19:34:34.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1559" PostTypeId="1" AcceptedAnswerId="1598" CreationDate="2012-03-25T00:12:01.357" Score="9" ViewCount="805" Body="&lt;p&gt;I'm trying to make a script that will take a MTZ file (reflections), convert it into a CCP4 map, then pare that map down to only encompass a desired area to cut down on the size of my PyMol session files so they're email-able (a.k.a. not 200 MB) and ease the burden on my POS computer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I currently have a Python script that can &lt;code&gt;fft&lt;/code&gt; (CCP4) to create the map and &lt;code&gt;mapmask&lt;/code&gt; to fix unit cell tiling issues.  What I want to add now is something that can take a PDB file and strip out most of it except, for example, residues within 10 &amp;Aring; of #123.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been looking at &lt;a href=&quot;http://www.csb.pitt.edu/ProDy/index.html&quot;&gt;ProDy&lt;/a&gt;, but not quite sure where to start.  I would also be open to using something in the CCP4 toolkit.&lt;/p&gt;&#xA;" OwnerUserId="25" LastEditorUserId="43" LastEditDate="2012-03-25T03:28:07.653" LastActivityDate="2012-03-29T03:00:07.267" Title="How can I pare down a PDB file in Python to only include specific residues?" Tags="&lt;structural-biology&gt;&lt;bioinformatics&gt;&lt;ccp4&gt;&lt;pdb&gt;" AnswerCount="2" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="1560" PostTypeId="1" AcceptedAnswerId="1563" CreationDate="2012-03-25T10:56:34.623" Score="2" ViewCount="2608" Body="&lt;p&gt;I could not find the piece of information form Burton Human Parasitology -book and not by Google.&#xA;Yeast is divided to two phylums: one of them is Ascomycota. &#xA;Aspergillus clavatus belong to the given phylum.&#xA;Yeast is unicellular.&#xA;So it is possible that Aspergillus clavatus is unicellular.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can you tell whether the Aspergillus clavatus is an unicellular orgarism or not from the following picture?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VWJvQ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I need to find unicellular parasites that cause damage of brain. The fungus causes patulin so hemorrhaging of brain, but should still be unicellular to meet the criteria.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="43" LastEditDate="2012-03-25T15:50:32.680" LastActivityDate="2012-03-25T17:05:57.850" Title="Is Aspergillus clavatus an unicellular organism?" Tags="&lt;homework&gt;&lt;mycology&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1561" PostTypeId="2" ParentId="1556" CreationDate="2012-03-25T13:20:07.997" Score="12" Body="&lt;p&gt;If you want to find out about the the relationship of this response to romance in particular, there's a pretty comprehensive research paper called &lt;em&gt;Love is more than just a kiss: a neurobiological perspective on love and affection&lt;/em&gt;[1] which reviews a lot of the work done in this area. This is pretty good as it discusses all the different stages including breakup.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially, there seems to be a &lt;em&gt;lot&lt;/em&gt; factors at play which elicits various responses through different stages of love.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of anxiety and stress, initially, there's a large increase in levels of cortisol[2] and a marked drop in serotonin. Depletion of serotonin is found in many psychiatric conditions such as depression, anxiety and panic disorder. There's even been evidence that these levels at early stages of love are similar to those suffering with OCD. Obviously, the 'symptoms' of early love are quite similar to these conditions so it's hypothesised that this, at least in part contributes to those feelings.[1]. It was found that these levels are back to normal in 12-24 months.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The elevated levels of cortisol contribute to the feelings of stress but this hormone has also been shown to promote attachment.[2].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also changes in activity of the amygdala. Responsible for regulating a lot of emotions such as fear and sexual drive, the amygdala can activate autonomic nervous system responses through the mechanisms which Kevin described. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a bunch of other things at play here including dopamine, oxytocin, vasopressin, nerve growth factor (NGF), testosterone, increased activity in the hypothalamic-pituitary-axis (HPA) and variations in activity in other areas of the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, that first reference gives a pretty comprehensive overview of the mechanisms involved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer the actual question about the fluttering feeling, as Kevin mentioned, it's hypothesised that this is caused by reduced peristalsis in the intestines as a result of sympathetic stimulation. I don't have an academic reference for this but there are plenty of non-academic sources that talk about it (a quick Google of &lt;em&gt;butterflies in stomach and physiology&lt;/em&gt; will probably show them).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lot of the mechanisms noted above can contribute to, sensitise for or cause sympathetic activation. For example, panic attacks and anxiety, mentioned earlier with the serotonin relationship, can cause the same feeling.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Boer, et al. &lt;em&gt;Love is more than just a kiss: a neurobiological perspective on love and affection&lt;/em&gt;. Neuroscience. 2012. 201:114-124.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Marazziti, et al. &lt;em&gt;Hormonal changes when falling in love&lt;/em&gt;.&#xA;Psychoneuroendocrinology. 2004. 29(7):931-936.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Guyton and Hall. Medical Physiology. 11th ed. Elsevier Saunders.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="653" LastEditorUserId="653" LastEditDate="2012-03-25T19:55:29.497" LastActivityDate="2012-03-25T19:55:29.497" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1562" PostTypeId="2" ParentId="788" CreationDate="2012-03-25T16:01:54.910" Score="11" Body="&lt;p&gt;I think the article that quoted(1) is different to what the link shows now(2). However, both the article quoted and the one in the link are relevant to the question.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Alzheimer's Disease&lt;/em&gt; : In a nutshell, AD is the most common form of dementia. Although the exact cause is still under investigation, several genes have been implicated in the development of AD. One of the things you see in the brain with disease progression is &lt;em&gt;beta amyloid&lt;/em&gt; plaque deposition which &lt;a href=&quot;http://marjanlovsin.com/wp-content/uploads/2011/12/Red-light-and-green-tea-a-strange-brew-that-may-have-the-answer-to-Alzheimers-22.gif&quot; rel=&quot;noreferrer&quot;&gt;disrupts brain activity&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Brain Activity&lt;/em&gt; : While the brain consumes around 20% of our body's energy at a baseline, an increase in brain activity only increases this consumption by around 5%. Hans Berger, the first to record an EEG stated that &amp;quot;&lt;em&gt;mental work, as I explained elsewhere, adds only a small increment to the cortical work which is going on continuously and not only in the waking state&lt;/em&gt;&amp;quot;.(2)&lt;/p&gt;&#xA;&lt;p&gt;However, there are a few 'intrinsic' networks or regions that perform functions such as &amp;quot;information processing for interpreting, responding to and predicting environmental demands&amp;quot;. One of the areas active in this state of the brain is referred to as the 'default mode network' (DMN). It's thought that DMN is the main target of the amyloid plaques responsible for Alzheimer's Disease.(2)&lt;/p&gt;&#xA;&lt;p&gt;However, there are other &lt;em&gt;multimodal regions&lt;/em&gt; of the brain that perform processing of various types of information. It's now suggested that &lt;em&gt;&amp;quot;regions vulnerable to Ab deposition do not simply involve the DMN, but rather comprise multimodal brain regions that are highly interconnected, plastic, and capable of rapid ATP generation&amp;quot;&lt;/em&gt;(1).&lt;/p&gt;&#xA;&lt;p&gt;So it's a variation of activity in these particular areas - not all - that are implicated with Alzheimer's Disease. When you are performing a task, activity in these areas diminish.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Why keep the brain intentionally active&lt;/em&gt; : The reason for the hypothesis that actively engaging in challenging activity may reduce the risk of AD is that individuals with a high &lt;em&gt;cognitive reserve&lt;/em&gt; have been shown to cope with the pathological changes such as beta amyloid deposition better. Cognitive reserve has been linked to a bunch of factors including &amp;quot;&lt;em&gt;education, occupation, socioeconomic status, social networks and lifelong participation in cognitive and physical activity&lt;/em&gt;&amp;quot; and reflects &amp;quot;&lt;em&gt;lifelong patterns of behaviors, endogenous factors (including genetics) and exposure to environmental factors&lt;/em&gt;&amp;quot;(1).&lt;/p&gt;&#xA;&lt;p&gt;Moreover, it's suggested that perhaps higher cognitive reserve increases &lt;em&gt;neuronal efficiency&lt;/em&gt; which has been shown to reduce plaque deposition.(1).&lt;/p&gt;&#xA;&lt;p&gt;So InquilineKea's question and jp89's answer aren't really contradictory.&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;August, et al. &lt;em&gt;Lifespan brain activity, β-amyloid, and Alzheimer's disease&lt;/em&gt;.&#xA;Trends in Cognitive Sciences. 2011. 15(11):520-526.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Raiche. &lt;em&gt;Two views of the brain&lt;/em&gt;.&#xA;Trends in Cognitive Sciences. 2010. 14(4):180-190.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Hafkemeijer, et al. &lt;em&gt;Imaging the default mode network in aging and dementia&lt;/em&gt;.&#xA;Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 2012. 1822(3):431-441.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Harrison's Principles of Internal Medicine. 16th Ed. McGraw Hill.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="653" LastEditorUserId="-1" LastEditorDisplayName="user560" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-03-27T16:39:22.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1563" PostTypeId="2" ParentId="1560" CreationDate="2012-03-25T17:05:57.850" Score="5" Body="&lt;p&gt;You're right in saying that yeast is single celled. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, moulds are described to be filamentous fungi that are multicellular. The filaments of the mould give colonies &lt;em&gt;&quot;a woolly, fluffy, or velvety appearance, sometimes punctuated with a granular or powdery aspect that is produced by the formation of asexual reproductive structures&quot;&lt;/em&gt;(1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.uoguelph.ca/~gbarron/2008/parase1.jpg&quot;&gt;Aspergillus&lt;/a&gt; is such a species. The filaments are called &lt;em&gt;hyphae&lt;/em&gt;. In Aspergillus, hyphae have divisions or walls which separate it into multiple cells. This is called septate hyphae.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;McPherson, et al. &lt;em&gt;Henry's Clinical Diagnosis and Management by Laboratory Methods.&lt;/em&gt; 22nd ed. 2011. Saunders.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="653" LastActivityDate="2012-03-25T17:05:57.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1564" PostTypeId="1" AcceptedAnswerId="1567" CreationDate="2012-03-25T17:38:41.797" Score="10" ViewCount="3261" Body="&lt;p&gt;In this SE answer: &lt;a href=&quot;https://biology.stackexchange.com/questions/788/could-an-overactive-brain-increase-the-chances-of-alzheimers-disease#comment900_788&quot;&gt;Could an &amp;quot;overactive&amp;quot; brain increase the chances of Alzheimer&amp;#39;s Disease?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;user @nico used the word &lt;code&gt;inhibitory tone&lt;/code&gt; What does that mean?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More examples of it used:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18234887&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/18234887&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cell.com/neuron/abstract/S0896-6273(11)00479-X&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.cell.com/neuron/abstract/S0896-6273(11)00479-X&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2012-03-25T23:07:23.543" Title="What is a inhibitory tone when talking about neurons?" Tags="&lt;neuroscience&gt;&lt;cell-biology&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1565" PostTypeId="2" ParentId="1537" CreationDate="2012-03-25T18:44:28.607" Score="4" Body="&lt;p&gt;Based on my course material, I managed to get the following list:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Malaria - Plasmodium falciparum, p. malariae, p. vivax, p. ovale - female anopheline mosquito&lt;/li&gt;&#xA;&lt;li&gt;Babesiosis - Babesia devergens, babesia microti - tick ixodes ricinus&lt;/li&gt;&#xA;&lt;li&gt;Balantidiasis - Balantidium coli - waterborne&lt;/li&gt;&#xA;&lt;li&gt;Coccidiosis &amp;amp; toxoplasmosis - Eimeria species - waterborne&lt;/li&gt;&#xA;&lt;li&gt;Toxoplasmosis - Toxoplasma gondii - waterborne&lt;/li&gt;&#xA;&lt;li&gt;Amoebic dysentery - Entamoeba histolytica - waterborne&lt;/li&gt;&#xA;&lt;li&gt;Periodentitis - Entamoeba gingivalis - oral-oral contact&lt;/li&gt;&#xA;&lt;li&gt;PAM - Naegleria fowleri - waterborne&lt;/li&gt;&#xA;&lt;li&gt;GAM - Acanthamoeba species - waterborne&lt;/li&gt;&#xA;&lt;li&gt;BAE - Balamuthia mandrillaris - waterborne&lt;/li&gt;&#xA;&lt;li&gt;Trichomoniasis - Trichomonas vaginalis - sexual contact&lt;/li&gt;&#xA;&lt;li&gt;Trypanosomiasis - Trypanosoma brucei gambiense, trypanosoma brucei rhodesiense - bite of a tsetse fly&lt;/li&gt;&#xA;&lt;li&gt;Leukopenia - Leishmaniasis specieses - different genera of sandflies: Plebotonus &amp;amp; Lutzomyia&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Waterborne means that the parasite is transmitted to the host through contaminated food, water or hands, or by swimming in warm pools or mud pools, for instance.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-03-25T18:44:28.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1566" PostTypeId="2" ParentId="1559" CreationDate="2012-03-25T21:43:03.610" Score="7" Body="&lt;p&gt;With the program RasMol, you can select, as Mad Scientist explained it for PyMol, everything in a specific distance around an atom. RasMol can be run from command line, using a script (with the -script option under UNIX).&lt;/p&gt;&#xA;" OwnerUserId="663" LastActivityDate="2012-03-25T21:43:03.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1567" PostTypeId="2" ParentId="1564" CreationDate="2012-03-25T21:59:27.377" Score="10" Body="&lt;p&gt;Neurons communicate electrochemically. That is, when a signal arrives to a neuron it &lt;em&gt;fires&lt;/em&gt; a series of electrical signals, called &lt;strong&gt;action potentials&lt;/strong&gt;.&#xA;Action potentials are depolarization events that propagate along the neuronal membrane, down to the neuronal terminal. &#xA;The terminal of a neuron is (with some exceptions) in contact with another neuron, via a structure called &lt;strong&gt;synapse&lt;/strong&gt;.&#xA;When the depolarization arrives at the terminal, it allows the entry of calcium, which then mediates the release of a chemical substance, a &lt;strong&gt;neurotransmitter&lt;/strong&gt; into the synaptic space. Finally, neurotransmitters act on the postsynaptic neuron, by binding to specific receptors on its cell membrane and can either stimulate it, in which case the postsynaptic neuron will fire more and release more of its neurotransmitter or inhibit it, in which case the opposite happens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The textbook example of a stimulatory neurotransmitter is glutamate, and the inhibitory one is GABA&lt;sup&gt;1&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In various areas of the brain certain neurons are constantly receiving inputs from GABAergic afferents. This means that those neurons are constantly receiving a GABA stimulus that inhibits them, and are thus under a constant &lt;strong&gt;inhibitory tone&lt;/strong&gt;. This will prevent their firing until a sufficiently potent stimulatory stimulus arrives or until the inhibitory tone is somehow released (for instance if the inhibitory GABAergic afferents are themselves inhibited by some of their own afferents). &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt;note that this is not always true: GABA can also be stimulatory in various situations&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-03-25T21:59:27.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1568" PostTypeId="1" AcceptedAnswerId="1570" CreationDate="2012-03-26T08:55:47.323" Score="11" ViewCount="54768" Body="&lt;p&gt;In pretty much every transformation protocol I've seen SOC medium is used to grow the bacteria for a short while after the tranformation and before plating. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've usually substituted LB medium for this step for easy retransformations, but I gather that the SOC medium is supposed to make some difference in efficiency, or else the simpler LB medium would be recommended in the protocols.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is SOC medium used for transformations? What difference does substituting with LB medium cause for the transformation efficiency? &lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2019-02-05T16:39:20.940" Title="Why is SOC medium recommended for transformations?" Tags="&lt;molecular-biology&gt;&lt;transformation&gt;&lt;growth-media&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1569" PostTypeId="2" ParentId="1568" CreationDate="2012-03-26T09:07:19.880" Score="8" Body="&lt;p&gt;(&lt;a href=&quot;http://en.wikipedia.org/wiki/Super_Optimal_Broth&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Super Optimal&lt;/strong&gt; broth with &lt;strong&gt;Catabolite&lt;/strong&gt; Repression&lt;/a&gt;) SOC media contains glucose whereas &lt;a href=&quot;http://en.wikipedia.org/wiki/Lysogeny_broth&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Luria Broth&lt;/strong&gt;&lt;/a&gt; (LB) doesn't. SOB also has a more delicate salt balance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Naturally the glucose will help the cells recover and grow faster after the heat shock. Your transformation efficiency should improve since less cells will die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, the reason why SOC media isn't always used is because of the detrimental effects of having too much glucose. The glucose will be consumed in the Krebs cycle and produces a lot of acetate which can be pretty harsh on cells.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="22057" LastEditDate="2019-02-05T16:39:20.940" LastActivityDate="2019-02-05T16:39:20.940" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="1570" PostTypeId="2" ParentId="1568" CreationDate="2012-03-26T12:09:18.280" Score="12" Body="&lt;p&gt;To summarize from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6345791&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hanahan's paper&lt;/a&gt; (see below for reference), he carried out a systematic review of conditions necessary to improve transfection efficiency. Among the conditions tested were the presence of various cations (Ca&lt;sup&gt;2+&lt;/sup&gt;, Cs&lt;sup&gt;+&lt;/sup&gt;, Mn&lt;sup&gt;2+&lt;/sup&gt;, K&lt;sup&gt;+&lt;/sup&gt;, Mg&lt;sup&gt;2+&lt;/sup&gt;), DMSO, and growth temperatures (and a few other conditions not so commonly used these days). He worked with a strain that he subsequently isolated a derivative of, called DH1, which is now available commercially as DH1-alpha and other strain derivatives.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He defined transformation efficiency to be the number of transformed colonies on a plate, a measurement still used today. He found when the transforming media contained: certain cations, specifcally Mn&lt;sup&gt;2+&lt;/sup&gt;, Ca&lt;sup&gt;2+&lt;/sup&gt;, Rb&lt;sup&gt;+&lt;/sup&gt;; as well as DTT, hexamine cobalt (III) and DMSO; greatly improved the transfection efficiency compared to the standard Ca&lt;sup&gt;2+&lt;/sup&gt; treatment. He also found that sucrose and K&lt;sup&gt;+&lt;/sup&gt; were useful, though not strictly necessary for his experimental strain. It was stated in this paper, though not explained, that sucrose acted as a stabilizer, possibly to guard against his initial use of 0°C incubation and/or freeze/thaw cycling. For the rest of his work, he did not use sucrose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Among his conclusions, he states that DTT is necessary, as well as di-valent and mono-valent cations, but that they seem to be nonspecific. In other words, there is no strict requirement for having Ca&lt;sup&gt;2+&lt;/sup&gt;, since Mg&lt;sup&gt;2+&lt;/sup&gt; and Mn&lt;sup&gt;2+&lt;/sup&gt; perform equally well, nor is there a requirement for K&lt;sup&gt;+&lt;/sup&gt;, though it's admittedly easier to use than Rb+.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are today a number of &quot;rich&quot; media broths that are available: SOB, SOC (SOB + MgCl&lt;sub&gt;2&lt;/sub&gt; and sucrose), 2xYT, NZY+, TB, etc. All of these are superior to LB for transformation purposes because of the refined salt balance and in particular the inclusion of these di-valent and mono-valent cations. Sucrose seems to be included for the ease of metabolism and stability of the heat shock process (though I can't find a paper explicitly explaining why it is used, other than tradition).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two most common ways to transform bacteria are to have them chemically compentent (E. coli already in a rich media broth) or to electrically transform them (electroporation). The purpose of both of these is to induce holes into to cell membrane of the E. coli (chemical transformation relies on the heat shock process for this). Once these holes are made, DNA is free to enter into the bacteria. Naturally, this process is very traumatizing to the E. coli, especially since chemical transformation has the added insult of temperature shock (0°C to 42°C then back down to 0°C).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Substituting LB for any rich broth, such as SOC, will greatly improve transformation yield. If a protocol calls for SOC media, and you don't have any, you may substitute for another rich media. I have used 2xYT for SOC many times quite successfully, and as I stated earlier, only the valence number for the various ions seems to matter, so just make sure they are present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was my understanding that sucrose/glucose was added as an additional nutrient source for E. coli to expedite their recovery from the transformation protocol. I speculate that this is the case. Hanahan refers to sucrose as a stabilizer but does not define what it is stabilizing. I speculate that it acts as a cryopreservation aid and prevents ice crystal formation when undergoing cooling on ice in the heat shock method. Given the earlier bio.SE question &lt;a href=&quot;https://biology.stackexchange.com/q/1485/389&quot;&gt;about shifting E. coli feedstocks&lt;/a&gt;, it seems unlikely that sucrose will be used as a nutrient source in the one hour growth period immediately after transformation because that article quotes 4-12 hours as the common time range to shift metabolism from amino acids to carbohydrates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6345791&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol 1983 166(4):557-80.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2012-03-26T18:49:28.780" CommentCount="0" CommunityOwnedDate="2012-03-26T15:27:18.817" ContentLicense="CC BY-SA 3.0" />
  <row Id="1572" PostTypeId="2" ParentId="1429" CreationDate="2012-03-26T20:53:50.443" Score="7" Body="&lt;p&gt;I'm no expert, but I liked this question and did a quick literature search:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Xylem cells are certainly dead at maturity, and it is these cells that make up the majority of what we call wood. However, wood also contains other tissue types, some of which have live cells at maturity. From what I can glean &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1631069110000119&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://treephys.oxfordjournals.org/content/24/4/461&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;, it is ray parenchyma tissue that is responsible for many of the changes that take place during the transition from sapwood to heartwood. Ray parenchyma is formed at the vascular cambium, along with xylem, during stem secondary growth (wood formation). Ray parenchyma cells remain alive for years after the xylem cells in the sapwood die. Their functions are transporting nutrients radially in the stem, and storage of carbohydrates. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the stem grows in diameter, there is a zone of transition from sapwood to heartwood where the ray parenchyma tissue begins to die. Before it dies, the cells undergo some metabolic changes and begin to synthesize secondary phenolic compounds (many different kinds) from stored starch or sugars. Then, as ray parenchyma cells die, they dump these phenolics into the surrounding xylem tissue, and the accumulation of these durable, decay-resistant compounds in the xylem leads to the formation of heartwood. In many hardwood trees this parenchyma death and phenolic accumulation is preceded by vessel-plugging, in which the ray parenchyma cells form balloon-like growths that block the flow of water through the xylem. So, once sapwood changes to heartwood there should be no living cells left, and the water transport capacity of its xylem is gone or greatly diminished.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There appears to be quite a bit of variability between species in when heartwood formation occurs and what triggers it. From what I could see in my brief literature search, it is all under fairly complex genetic and hormonal control that remains an area of active research. I would suggest (and speculate a bit) that the trigger has something to do with maintaining an optimum amount of sapwood as the tree grows in leaf area (which increases demand for water transport) and height (which increases demand for support, or stem diameter).&lt;/p&gt;&#xA;" OwnerUserId="649" LastEditorUserId="649" LastEditDate="2012-03-27T14:37:11.860" LastActivityDate="2012-03-27T14:37:11.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1573" PostTypeId="1" AcceptedAnswerId="16984" CreationDate="2012-03-26T21:04:22.390" Score="19" ViewCount="11125" Body="&lt;p&gt;When humans get the common cold, a common symptom is a stuffy or runny nose. Is that the body's immune response or is that the virus's doing?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="1590" LastEditDate="2014-04-29T08:36:08.553" LastActivityDate="2016-06-28T11:52:57.890" Title="What causes a 'stuffy' or 'runny' nose when you have a cold?" Tags="&lt;human-biology&gt;&lt;virology&gt;&lt;epidemiology&gt;&lt;pathophysiology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1574" PostTypeId="1" AcceptedAnswerId="95184" CreationDate="2012-03-27T00:51:51.037" Score="3" ViewCount="426" Body="&lt;p&gt;In what ways are trichomes vital to the plant?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why have them on the plant shoots as well?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="238" LastEditDate="2012-03-27T11:41:26.100" LastActivityDate="2021-01-09T12:07:35.713" Title="Why are trichomes important for both the roots and shoots of plants?" Tags="&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1575" PostTypeId="1" CreationDate="2012-03-27T01:27:48.637" Score="31" ViewCount="5263" Body="&lt;p&gt;&lt;sub&gt;This question was considered unsuitable for Skeptics and I think it is more suited to BIology than Cognitive Sciences&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was reading &lt;a href=&quot;http://www.psy.fsu.edu/~baumeistertice/goodaboutmen.htm&quot;&gt;this&lt;/a&gt; article which I found interesting. It is not supported with references but was an invited address for the American Psychological Association.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It makes the claim that men go to more extremes than women.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;People can point to plenty of data that the average IQ of adult men is about the same as the average for women. So to suggest that men are smarter than women is wrong. No wonder some women were offended.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There are more males than females with really low IQs. Indeed, the&#xA;  pattern with mental retardation is the same as with genius, namely&#xA;  that as you go from mild to medium to extreme, the preponderance of&#xA;  males gets bigger.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;[...]&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Almost certainly, it is something biological and genetic. And my guess&#xA;  is that the greater proportion of men at both extremes of the IQ&#xA;  distribution is part of the same pattern.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;[...]&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nature rolls the dice with men more than women. Men go to extremes&#xA;  more than women. It’s true not just with IQ but also with other&#xA;  things, even height: The male distribution of height is flatter, with&#xA;  more really tall and really short men.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Another notable example of a similar claim was Lawrence Summer's speech &lt;a href=&quot;http://en.wikipedia.org/wiki/Lawrence_Summers#Differences_between_the_sexes&quot;&gt;regarding the possible reasons for dearth of women in tenured positions in science and engineering at top schools&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Summers outlined 3 possible reasons, with a major kerfuffle erupting - &lt;strong&gt;resulting in his firing from the job as a Harvard University President&lt;/strong&gt; - over his presented second reason [ quotes from Wiki ]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The second hypothesis, different availability of aptitude at the high end, caused the most controversy. In his discussion of this hypothesis, Summers said that &quot;even small differences in the standard deviation [between genders] will translate into very large differences in the available pool substantially out [from the mean]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Summers referenced research that implied differences between the standard deviations of males and females in the top 5% of twelfth graders under various tests. He then went on to argue that, if this research were to be accepted, then &quot;whatever the set of attributes... that are precisely defined to correlate with being an aeronautical engineer at MIT or being a chemist at Berkeley... are probably different in their standard deviations as well&quot;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;QUESTION:&lt;/strong&gt; Are there any studies or evidence to support the claim that men have more extreme variations than women (&lt;strong&gt;in other words, that the trait's distribution in males have fatter tails&lt;/strong&gt;) in a variety of traits? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Possible areas of research can be: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Intelligence (general IQ or specific linguistic or spacial abilities)&lt;/li&gt;&#xA;&lt;li&gt;Physical attributes (strength, height, weight)&lt;/li&gt;&#xA;&lt;li&gt;personality traits &#xA;&lt;ul&gt;&#xA;&lt;li&gt;for lack of anything better, let's take the &lt;a href=&quot;http://en.wikipedia.org/wiki/Big_Five_personality_traits&quot;&gt;FFM's Five&lt;/a&gt;: &lt;/li&gt;&#xA;&lt;li&gt;openness&lt;/li&gt;&#xA;&lt;li&gt;conscientiousness&lt;/li&gt;&#xA;&lt;li&gt;extroversion&lt;/li&gt;&#xA;&lt;li&gt;agreeableness&lt;/li&gt;&#xA;&lt;li&gt;neuroticism&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;In order for the answer to be &quot;yes&quot;, the research needs to show fat tails in at least 5-6 traits from all 3 of the buckets above (intelligence, physical, and personality), although precise trait mix may be arbitrary and not necessarily limited to my examples, as long as 5-6 somewhat independent traits fit. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order for the answer to be &quot;no&quot;, at least 8 of the 11 traits above should have no fatter tails in men. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anything else means &quot;inconclusive&quot;.&lt;/p&gt;&#xA;" OwnerUserId="586" LastActivityDate="2017-11-29T16:16:47.957" Title="Do men have more extreme variations than women?" Tags="&lt;evolution&gt;&lt;neuroscience&gt;&lt;physiology&gt;&lt;sexual-selection&gt;&lt;psychology&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="1576" PostTypeId="2" ParentId="1575" CreationDate="2012-03-27T04:24:53.037" Score="6" Body="&lt;p&gt;The biggest problem with this question, (not just here, but for everyone who asks it,) is drawing on our culturally constructed definition of maleness to look for mechanisms of &lt;em&gt;genetic&lt;/em&gt; inheritance of what are considered &quot;male&quot; traits.  We could measure frequency distributions of height, but we don't have a way to accurately probe &lt;em&gt;any&lt;/em&gt; of the other qualities you listed on a genetic level.  Since we can't make these mechanistic connections, any conclusions we draw would be confounded by the nature vs nurture debate.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, I don't know of any studies to this effect.  So this isn't much of an answer to your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I've been thinking about this question all day.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sources of heritable variation within genders that could be attributed to gender differences are (1) X and Y chromosome mutations and expression profiles, and (2) heritable epigenetic gender differences. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) might be more difficult to argue, since the currently known mechanism for epigenetic inheritance is the same in men and women.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One way to make this problem tractable is to look at transcriptome analysis -- it's an indirect approach to this question that gets from genome to phenotype quickly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A cursory pubmed search led me to a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16934145&quot; rel=&quot;nofollow&quot;&gt;study in &lt;em&gt;Drosophila&lt;/em&gt;&lt;/a&gt; that takes a different approach to this question.  They sought out previously undetected levels of gender difference.  Most current studies (and there are a &lt;em&gt;lot&lt;/em&gt; of them, including for humans) look to quantify differences in expression between genders for specific tissues. This is a prerequisite for estimating this within-genders variation, standardized against the number of genes expressed. &lt;/p&gt;&#xA;" OwnerUserId="184" LastEditorUserId="184" LastEditDate="2014-08-06T15:45:05.530" LastActivityDate="2014-08-06T15:45:05.530" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1577" PostTypeId="2" ParentId="1575" CreationDate="2012-03-27T04:37:30.770" Score="11" Body="&lt;p&gt;First of all for the first 22 chromosomes (and the mitochondrial chromsome) are the same between women and men. The X and the Y together are something like 1.5% of the total DNA in the human cell.  The X chromosome is also in common, so it has the same chromosomal (genetic) variations the same as women and men. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While I am not sure about the differences you point out, its for sure there are lots of differences between the biology of men and women!  The reason that women's traits might have different variances than men comes from the fact that in women there are 2 X chromosomes and in men there is only one, as well as the additional Y chromosome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there are any singular defects in the X chromosome a man carries, it will not be balanced out in the human male.  (other organisms have different sex chromosome schemes).  For instance because there is a cluster of genes that help the eye see in color, women's sense of color (i.e. from their cone cells) is sometimes better than men.  With 2 X chromosomes there is even the possibility of a woman who has &lt;a href=&quot;http://academic.evergreen.edu/curricular/anp07/Looking%20for%20Madam%20Tetrachromat.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;four different color receptors in their cones&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, why men see better in the dark (i.e. greater sensitivity in the rod cells), is possibly due to an extra Blue Rod pigment gene that remains on the Y chromosome (see above reference).  This is both an accident of genetics, but also an adaptive 'choice' that men would have different visual acuities than women. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its also known that woman and men may have different epigenetic patterns, with some epigenetic modifications coming from the mother and others from the father.  This is adaptive and also not the direct result of the XY chromosomes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, it turns out that for the most part women's 2 X chromosomes are mosaic.  That is, in each cell only one of the randomly selected X chromosomes are active.  Recessive/dominant X genes are often not the case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This could result in a greater observed genetic variance for women because when you have two chromosomes, often one of the genes is completely silenced.  Women display all of the alleles of their X chromsomes, whereas men have only one X chromosome entirely, the Y chromosome being much smaller.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in other words, I would say that while men and women actually have the same variation in their DNA sequences, there are different patterns in the X and Y Chromosomes that might create more variance in terms of what we see in women's displayed genetic traits.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2017-11-29T07:16:14.723" LastActivityDate="2017-11-29T07:16:14.723" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1578" PostTypeId="2" ParentId="1575" CreationDate="2012-03-27T12:34:44.067" Score="6" Body="&lt;p&gt;At least for physical data (heigth, weight etc) you can have a look of the DINED Anthropometric database &lt;a href=&quot;http://dined.io.tudelft.nl/dined/&quot;&gt;http://dined.io.tudelft.nl/dined/&lt;/a&gt;.  Here you can find mean and standard deviation data for Dutch population studies on numerous anthropometric measures, and you can stratify the results by sex.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-03-27T12:34:44.067" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1579" PostTypeId="1" AcceptedAnswerId="1583" CreationDate="2012-03-27T12:50:37.323" Score="6" ViewCount="132" Body="&lt;p&gt;I was watching the video at this link:&#xA;&lt;a href=&quot;http://www.bbc.co.uk/news/science-environment-17436365&quot; rel=&quot;noreferrer&quot;&gt;http://www.bbc.co.uk/news/science-environment-17436365&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The speaker says that a cell is taken and its original DNA content is stripped out and replaced with synthetic DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this mean scientists are not able to create a synthetic cell yet? Is this why they use existing cells, stripping them out and replacing the DNA?&lt;/p&gt;&#xA;" OwnerUserId="668" LastEditorUserId="43" LastEditDate="2012-03-27T16:07:41.930" LastActivityDate="2012-06-05T16:17:07.597" Title="Synthetic biology using existing cells" Tags="&lt;dna&gt;&lt;cell-biology&gt;&lt;synthetic-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1580" PostTypeId="1" AcceptedAnswerId="1600" CreationDate="2012-03-27T14:19:49.193" Score="5" ViewCount="924" Body="&lt;p&gt;I have a biology assignment and we have to explain various methods and strategies for conservation, two of which are:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Biological control&lt;br&gt;&#xA;  Introduced Species&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What is the difference between these? I was under the impression that they are essentially the same thing – &lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_control&quot; rel=&quot;nofollow&quot;&gt;biological control&lt;/a&gt; being the introduction of species to predate pests (eg. the abysmal failure of the cane toad).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any clarification would be great.&lt;/p&gt;&#xA;" OwnerUserId="669" LastEditorUserId="3624" LastEditDate="2015-09-11T08:25:57.097" LastActivityDate="2015-09-11T08:25:57.097" Title="Difference between biological control and introducing species for conservation?" Tags="&lt;homework&gt;&lt;ecology&gt;&lt;population-biology&gt;&lt;conservation-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1581" PostTypeId="1" AcceptedAnswerId="9980" CreationDate="2012-03-27T14:59:53.773" Score="17" ViewCount="6634" Body="&lt;p&gt;I've been thinking about this one, but I can't seem to find what causes this difference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All fishes that I've seen have their tail fin positioned vertical:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MCLkv.jpg&quot; alt=&quot;Fish&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But all the marine mammals I know have their tail positioned horizontal:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZwQZj.jpg&quot; alt=&quot;Dolphin&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is there this difference? Is it because it's mammals compared to fish? Or could fish as well have horizontal tail fins?&lt;/p&gt;&#xA;" OwnerUserId="611" LastEditorUserId="444" LastEditDate="2012-05-02T18:27:53.307" LastActivityDate="2018-08-04T01:43:36.517" Title="Why is there a difference in the rotation of the tail fin in fish compared to marine mammals?" Tags="&lt;zoology&gt;&lt;ichthyology&gt;&lt;marine-biology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1582" PostTypeId="2" ParentId="1541" CreationDate="2012-03-27T16:10:13.223" Score="8" Body="&lt;p&gt;According to &lt;a href=&quot;http://genomebiology.com/2009/10/9/R89&quot;&gt;Choi et al. Genome Biology 2009, 10:R89&lt;/a&gt;, DNA methylation at both coding boundaries may regulate transcription elongation and stabilize splicing by reducing the occurrences of exon skipping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Here we report a genome-wide observation of distinct peaks of&#xA;  nucleosomes and methylation at both ends of a protein coding unit.&#xA;  Elongating polymerases tend to pause near both coding ends immediately&#xA;  upstream of the epigenetic peaks, causing a significant reduction in&#xA;  elongation efficiency. Conserved features in underlying protein coding&#xA;  sequences seem to dictate their evolutionary conservation across&#xA;  multiple species. The nucleosomal and methylation marks are commonly&#xA;  associated with high sequence-encoded DNA-bending propensity but&#xA;  differentially with CpG density. As the gene grows longer, the&#xA;  epigenetic codes seem to be shifted from variable inner sequences&#xA;  toward boundary regions, rendering the peaks more prominent in higher&#xA;  organisms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Their data (figures 1 and S2), however, do not support a generalized increase in the 3' UTR regions in either human T cells, mouse liver, yeast or flies. &lt;/p&gt;&#xA;" OwnerUserId="48" LastActivityDate="2012-03-27T16:10:13.223" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1583" PostTypeId="2" ParentId="1579" CreationDate="2012-03-27T16:14:15.520" Score="5" Body="&lt;p&gt;The J. Craig Venter Institute recently has indeed created a synthetic, self-replicating cell (see the &lt;a href=&quot;http://www.jcvi.org/cms/press/press-releases/full-text/article/first-self-replicating-synthetic-bacterial-cell-constructed-by-j-craig-venter-institute-researcher/&quot; rel=&quot;nofollow&quot;&gt;press release&lt;/a&gt;). So it's definitely not impossible to create completely synthetic cells for use in synthetic biology, but that doesn't mean it makes much sense to do so. &lt;em&gt;E. coli&lt;/em&gt; in particular have been used as bench tools for decades: lots of protocols exist for using them in the lab, their genome has been extensively sequenced and is well studied, and they're cheap. I'm not a bench biologist anymore, but I'm guessing these are the reasons they stripped living bacteria and replaced their DNA rather than trying to build a completely synthetic microbe from scratch.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2012-03-27T16:38:35.817" LastActivityDate="2012-03-27T16:38:35.817" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1584" PostTypeId="2" ParentId="1581" CreationDate="2012-03-27T17:19:37.957" Score="11" Body="&lt;p&gt;Cetaceans (i.e., marine mammals) evolved from certain ancient land based mammals, thus the tail is essentially convergent evolution of the tail function.&lt;/p&gt;&#xA;" OwnerUserId="671" LastEditorUserId="107" LastEditDate="2012-03-27T20:43:45.477" LastActivityDate="2012-03-27T20:43:45.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1585" PostTypeId="1" AcceptedAnswerId="1586" CreationDate="2012-03-27T22:52:14.333" Score="8" ViewCount="3842" Body="&lt;p&gt;Every bloody protocol suggests adding in DTT when doing &lt;em&gt;in vitro&lt;/em&gt; RNA transcription. Why? The rationale seems to be that the cytoplasm traditionally has a reducing environment but as the only protein we care about is the T7 polymerase, why is this necessary.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2020-10-04T19:57:19.920" Title="Why does the T7 RNA Polymerase require a reducing environment ie. DTT" Tags="&lt;transcription&gt;&lt;t7-promoter&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1586" PostTypeId="2" ParentId="1585" CreationDate="2012-03-27T23:46:01.627" Score="6" Body="&lt;p&gt;A quick search on T7 cysteines gave some clues:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bacteriophage T7-induced DNA polymerase is composed of a 1: 1&#xA;  complex of phage-induced gene 5 protein  and Escherichia coli&#xA;  thioredoxin. Preparation of active  subunits in the absence of &#xA;  sulfhydryl  reagents  indicates  the reduced form of thioredoxin  is &#xA;  sufficient for formation of  the  active holoenzyme. The oxidized&#xA;  form of  thioredoxin, thioredoxin modified  at  one  active  site &#xA;  sulfhydryl by iodoacetate or methyl iodide, or thioredoxin modified&#xA;  at both  active  site  sulfhydryls  by N-ethylmaleimide,  are  all &#xA;  inactive,  being  defective  in  complex formation with  gene 5&#xA;  protein.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jbc.org/content/258/11/6956.full.pdf&quot;&gt;Adler and Modrich, J Biol Chem 258:6956 (1983)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's a more recent paper (&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ic900164j&quot;&gt;Aguirre et al, Inorganic Chemistry 48:4425 (2009)&lt;/a&gt;) that mentions the &quot;&lt;em&gt;the enzyme critical sulfhydryl cysteine groups&lt;/em&gt;&quot;, but unfortunately I only have access to the abstract.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt;: It seems to be an old finding, rather than a rationale concerning the cytoplasmic redox state. According to &lt;a href=&quot;http://www.jbc.org/content/248/6/2235.full.pdf+html&quot;&gt;Chamberlin and Ring, JBC 248:2235 (1973)&lt;/a&gt;, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;General Requirements-The general requirements for T7 RNA &#xA;  synthesis directed by T7 DNA polymerase are shown in Table &#xA;  I. As expected for a template directed polymerase, RNA &#xA;  synthesis shows an absolute requirement for DNA, the 4 &#xA;  ribonucleoside triphosphates and Mg++. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(no surprises there ;)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The activity of the &#xA;  enzyme is reduced significantly if a sulfhydryl reducing &#xA;  agent such as b-mercapto-ethanol is omitted from  the &#xA;  reaction. The addition of 10^-5 M p-hydroxymercuribenzoate to&#xA;  the assay system in the absence of b-mercaptoethanol &#xA;  abolished all activity, indicating that the enzyme contains a &#xA;  sulfhydryl group necessary for activity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, if you see the table I, the remaining activity after removing bme is still 74%&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There seems to be 7 exposed cysteines (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867402008152&quot;&gt;Mukherjee et al, Cell 110:81 (2002)&lt;/a&gt;), but I could not find any paper discussing their roles.&lt;/p&gt;&#xA;" OwnerUserId="48" LastEditorUserId="48" LastEditDate="2012-03-28T20:37:05.460" LastActivityDate="2012-03-28T20:37:05.460" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1587" PostTypeId="2" ParentId="1348" CreationDate="2012-03-28T00:56:11.940" Score="1" Body="&lt;p&gt;There is an article in PNAS &lt;a href=&quot;http://www.pnas.org/content/107/20/9027.full&quot; rel=&quot;nofollow&quot;&gt;Conservation and divergence in eukaryotic DNA methylation&lt;/a&gt; who used:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;next-generation sequencing to investigate the DNA methylation patterns&#xA;  in eight divergent species, including green algae, flowering plants,&#xA;  insects, and vertebrates. Their data allowed a comprehensive&#xA;  comparison of whole-genome methylation profiles across the plant and&#xA;  animal kingdoms, revealing both conserved and divergent features of&#xA;  DNA methylation in eukaryotes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So there is some conservation.&lt;/p&gt;&#xA;" OwnerUserId="395" LastActivityDate="2012-03-28T00:56:11.940" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1588" PostTypeId="1" AcceptedAnswerId="1592" CreationDate="2012-03-28T07:36:25.040" Score="10" ViewCount="1949" Body="&lt;p&gt;I've heard from several sources that trans FAs are bad for you and their consumption will lead to cardiac problems, and that they are indigestible.&#xA;But I also learned from biochemistry that they &lt;em&gt;are&lt;/em&gt; digestible. What is the reason for this, or is it true at all?&lt;/p&gt;&#xA;" OwnerUserId="673" LastEditorUserId="338" LastEditDate="2012-03-28T14:55:29.963" LastActivityDate="2013-09-27T15:35:22.643" Title="Why do people say that trans fatty acids are bad for your health?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;cardiology&gt;&lt;digestive-system&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1589" PostTypeId="1" AcceptedAnswerId="1590" CreationDate="2012-03-28T10:45:03.893" Score="11" ViewCount="10279" Body="&lt;p&gt;Many DNA isolation and protein expression protocols contain instructions to use a starter culture of E. coli that is then used to inoculate the main culture. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the advantages of using starter cultures compared to just let the bacteria grow in the same medium for a longer time? When should one use starter cultures and when can one safely skip that first culture?&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorDisplayName="user560" LastEditDate="2012-03-28T13:15:57.393" LastActivityDate="2012-03-29T03:43:54.380" Title="What is the advantage of using starter cultures for growing bacteria?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1590" PostTypeId="2" ParentId="1589" CreationDate="2012-03-28T13:02:22.980" Score="14" Body="&lt;p&gt;Growth can be quite slow for some species under certain conditions when the concentration of cells is too low. Log-phase growth is powerful, and so one would like to keep cells in this state for the experiment at hand. Different genes are expressed then compared to a stationary phase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, you'd like your culture to out-compete a contaminant if there is one. That is more easily accomplished with a starter culture, which is then used to inoculate a larger culture for scale-up. Inoculating directing into the large-sized flask may allow your bacteria to enter a stationary phase, thus giving an opportunity for other species to out-compete your bacteria.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-03-28T13:02:22.980" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1591" PostTypeId="1" AcceptedAnswerId="1593" CreationDate="2012-03-28T13:42:34.490" Score="8" ViewCount="3802" Body="&lt;p&gt;Most immature fruits are green: peppers, pine cones, plums, lots of them. I want to know if the green is from chlorophyll in the cells. Do the fruit cells perform photosynthesis? When you cover a green stem or leaf, it will turn pale and stretch. That is because the stems have little need for chlorophyll in the dark, which is why they are pale. They stretch because the auxins in the stems are not destroyed by the photons, and the stems stretch out and topple over. If a green fruit is covered, will it turn pale and stretch like that? &lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="69" LastEditDate="2012-03-28T21:13:47.967" LastActivityDate="2016-03-29T10:03:27.833" Title="Do immature fruits perform photosynthesis?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1592" PostTypeId="2" ParentId="1588" CreationDate="2012-03-28T18:14:29.197" Score="10" Body="&lt;p&gt;Trans fatty acids are digestible, but they cause an increase in LDL and a decrease in HDL, which is the leading mechanism for atherosclerosis. So, they increase the risk of a cardiac infarct. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;LDL means Low Density Lipoprotein, it's one of the 5 major lipoprotein groups. Lipoproteins carries the fatty acids and cholesterol which were absorbed from intestines (because lipids are hydrophobic and cannot be carried within the blood directly like glucose or proteins.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, LDL mainly carries cholesterol and fatty acids from intestines to tissues. (fatty acids and cholesterol are essential for cells.) But in excess levels, they tend to accumulate in vessel walls, which also starts and inflammatory response and makes the situation worse. (mainly includes macrophages and T cells) This is the main mechanism for atherosclerosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the other hand, HDLs serve as a reverse cholesterol transport system, which carries the cholesterol back, mostly to the liver (for bile secretion) or steroidogenic organs such as adrenals, ovary, and testes by direct and indirect pathways. So a high HDL reduces the atherosclerotic process.&lt;/p&gt;&#xA;" OwnerUserId="566" LastEditorUserId="566" LastEditDate="2012-03-28T20:44:36.590" LastActivityDate="2012-03-28T20:44:36.590" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1593" PostTypeId="2" ParentId="1591" CreationDate="2012-03-28T19:23:14.003" Score="4" Body="&lt;p&gt;The green pigment is indeed chlorophyll, and the fruits do perform photosynthesis.   It's not just &quot;fruiting&quot; plants that do this either.  Some shading experiments i saw estimated that  up to 30% of the sugars assimilated into the barley ears (basically the grain) can come from photosynthesis occurring in those organs.&lt;/p&gt;&#xA;" OwnerUserId="675" LastEditorUserId="338" LastEditDate="2014-05-20T03:44:45.977" LastActivityDate="2014-05-20T03:44:45.977" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1596" PostTypeId="2" ParentId="877" CreationDate="2012-03-28T21:10:53.103" Score="2" Body="&lt;p&gt;Tension is not a quantifiable thing, rather an abstract concept to describe feelings of stress in muscles.  I think I see what you are getting at but I would separate it into two questions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Is massage provably beneficial to muscles under physically induced stress?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Emphatically yes, however there are so many different types of massage, some are more medically viable than others.  Most massage stimulates muscles to encourage a release of tightening, much like exercise does, though I would assume that there's also a psychosomatic that plays a significant role as well due to human contact.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other question, more the point &quot;Are massage therapist's claims about relief true?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some are and some aren't.  Unless it's by a medical professional (prescribed physical therapy for instance) they can claim whatever they like.  &quot;Reiki contributes to your body balance and wellness by attuning your energy&quot;  This can not be proven, but not really disproven either, so they can claim it all they want though it's purely anecdotal (if not outright fabrication on the part of less ethical individuals.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary: Massage has tangible benefits, but if the claims of the therapist sound too good to be true, they probably are.  &lt;/p&gt;&#xA;" OwnerUserId="671" LastActivityDate="2012-03-28T21:10:53.103" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1597" PostTypeId="2" ParentId="1573" CreationDate="2012-03-28T21:21:39.017" Score="14" Body="&lt;p&gt;It's mainly caused by swelling of large veins and by an increase in vascular permeability that leads to an accumulation of fluids in the nasal mucosa. These effects are mediated, at least in part, by bradykinin and histamine, and can be counteracted by epinephrine. These mediators are part of the immune response to the viral particles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read more about it here:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cardiff.ac.uk/biosi/subsites/cold/commoncold.html&quot;&gt;http://www.cardiff.ac.uk/biosi/subsites/cold/commoncold.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://books.google.com/books?id=GFcQ2yVeniwC&amp;amp;lpg=PA520&amp;amp;ots=wbRN4d4w3M&amp;amp;vq=mechanism%20of%20nasal%20congestion%20after%20viral%20infections&amp;amp;dq=mechanism%20of%20nasal%20congestion%20after%20viral%20infections&amp;amp;pg=PA520#v=snippet&amp;amp;q=mechanism%20of%20nasal%20congestion%20after%20viral%20infections&amp;amp;f=false&quot;&gt;Chernick-Mellins basic mechanisms of pediatric respiratory disease&#xA;By Gabriel G. Haddad, Steven H. Abman, Victor Chernick (page 520)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="48" LastActivityDate="2012-03-28T21:21:39.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1598" PostTypeId="2" ParentId="1559" CreationDate="2012-03-29T02:44:27.770" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://www.csb.pitt.edu/ProDy/index.html&quot;&gt;ProDy&lt;/a&gt; works quite well, especially from within an existing Python script.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following code takes an existing PDB file, performs some &lt;a href=&quot;http://www.csb.pitt.edu/prody/reference/atomic/selection.html#selection-operations&quot;&gt;selection query&lt;/a&gt; on it, then saves it to another file.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;import prody&#xA;&#xA;def pdbsubset(inpdb, outpdb, selection):&#xA;    with open(inpdb) as protf:&#xA;        prot = prody.parsePDBStream(protf)&#xA;    atoms = prot.select(selection)&#xA;    prody.writePDB(outpdb, atoms)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;An example selection query builder&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;code&gt;residues&lt;/code&gt; is a list e.g. ['A12', 'A39'] with each element in the form &lt;code&gt;&amp;lt;chain&amp;gt;&amp;lt;residue number&amp;gt;&lt;/code&gt;.  They were captured from the command line using &lt;code&gt;argparse&lt;/code&gt; with &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;    parser.add_argument('-i', '--residues', nargs='+')&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;so you would specify &lt;code&gt;-i A12 A39&lt;/code&gt; or whatever.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;pdb&lt;/code&gt; and &lt;code&gt;outpdb&lt;/code&gt; are file paths&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;radius&lt;/code&gt; is the distance in angstroms to expand the selection by.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;reslist = [&quot;(chid {0} and resid {1})&quot;.format(res[0], res[1:]) for res in residues]&#xA;selector = 'within {0} of ({1})'.format(radius, ' or '.join(reslist))&#xA;&#xA;# and running it:&#xA;pdbsubset(pdb, outpdb, selector)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The documentation on ProDy selection queries is not the most straightforward, but fairly analogous to PyMol, so doable.&lt;/p&gt;&#xA;" OwnerUserId="25" LastEditorUserId="25" LastEditDate="2012-03-29T03:00:07.267" LastActivityDate="2012-03-29T03:00:07.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1599" PostTypeId="2" ParentId="1589" CreationDate="2012-03-29T03:43:54.380" Score="7" Body="&lt;p&gt;I agree that a starter culture would out-comete a contaminant (especially if there is no antibiotic in the media).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another advantage of inoculating with starter culture is that your results concerning plasmid preps or preparing competent cells will be easily reproducible. By inoculating with a colony, the starter number of cells is different each time you do that, so you might not know how long your cells have to grow to reach a certain OD (e.g. for preparing competent cells) or you have to measure the OD before you isolate DNA to be sure that your yields are comparable with your previous ones.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-03-29T03:43:54.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1600" PostTypeId="2" ParentId="1580" CreationDate="2012-03-29T08:33:44.167" Score="4" Body="&lt;p&gt;After talking to my teacher, he said that biological control is the introduction of species to control another species, however species may be introduced for other reasons (the &quot;Introduced Species&quot; method), such as to &quot;assist an ecosystem cope, flourish or re-establish itself.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The example he gave was the introduction of South African veldt grass to Western Australia in order to stabilise sand dunes, so that they can later be built upon further (eg. plants which may not perform well in sandy, unstable soil can then be planted).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully this helps anyone else with the same problem.&lt;/p&gt;&#xA;" OwnerUserId="669" LastActivityDate="2012-03-29T08:33:44.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1601" PostTypeId="1" AcceptedAnswerId="1607" CreationDate="2012-03-29T13:10:44.917" Score="6" ViewCount="1469" Body="&lt;p&gt;Precipitating nucleic acids using either isopropanol or ethanol is a very common operation, and I've read some very different protocols on the duration and temperature the precipitation should be performed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen anything from precipitating at room-temperature and centrifugating immediately without any delay to precipitating at -20 °C over night in various protocols.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any published data about the influence of duration and temperature on the yield of the nucleic acid precipitation?&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2012-03-29T22:09:12.380" Title="For how long and how cold should I perform ethanol/isopropanol precipitations of RNA or DNA?" Tags="&lt;biochemistry&gt;&lt;nucleic-acids&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1602" PostTypeId="1" CreationDate="2012-03-29T13:58:30.830" Score="11" ViewCount="1531" Body="&lt;p&gt;I just stumbled upon an article promoting 10 mM sodium borate as an alternative to the well-known TAE and TBE buffers for agarose gel electrophoresis of DNA (&lt;a href=&quot;http://www.biotechniques.com/multimedia/archive/00036/BTN_A_04362BM02_O_36180a.pdf&quot;&gt;Brody &amp;amp; Kern, 2004&lt;/a&gt;). They claim that sodium borate outperforms TBE and TAE at high-voltage conditions due to the significantly lower heat development.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm currently using TBE buffer and gels with 7M urea for my denaturing PAA gels, and I'm wondering if there are similar alternative conditions for those denaturing PAA gels of nucleic acids? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I couldn't find anything on using sodium borate for denaturing PAA gels, so I'm wondering if it should work the same as for the agarose gels or if it just isn't a good buffer for that kind of gel.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biotechniques.com/multimedia/archive/00036/BTN_A_04362BM02_O_36180a.pdf&quot;&gt;Brody, J. R. &amp;amp; Kern, S. E. Sodium boric acid: a Tris-free, cooler conductive medium for DNA electrophoresis. BioTechniques 36, 214–216 (2004).&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2013-06-27T11:43:08.100" Title="Alternatives to TBE buffer for denaturing polyacrylamide gel electrophoresis of DNA and RNA?" Tags="&lt;gel-electrophoresis&gt;" AnswerCount="1" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="1603" PostTypeId="2" ParentId="1601" CreationDate="2012-03-29T14:00:29.970" Score="2" Body="&lt;p&gt;As a first year molecular biology student, I did a class project on this very question:  trying to see if buffer temperature had an effect on yield during DNA precipitation. This is a far cry from peer reviewed research, but my finding was that there was no significant effect for a wide range of temperatures.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-03-29T14:00:29.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1604" PostTypeId="1" AcceptedAnswerId="1664" CreationDate="2012-03-29T14:04:54.310" Score="6" ViewCount="241" Body="&lt;p&gt;I need to demonstrate the effects of ethanol on a human brain (or other brain with developed telencephalon) &lt;em&gt;in vitro&lt;/em&gt;; ideally the effects on vigilance and/or memory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could you please suggest such an experiment?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What method would you suggest to demonstrate the effects of ethanol on NMDA receptors or membrane penetration by ethanol?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;Edit in respose to the first comment by @MadScientist:&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The point is to empirically demonstrate how ethanol affects the cognitive performance of brain (specifically vigilance and memory) and explain the biochemical nature of such an effect on an observable real example (not using computer simulations). It is aimed at mature layman audience.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The experiment has to be &lt;em&gt;in vitro&lt;/em&gt; due to ethical and environmental limitations (well, I am not permitted to intoxicate mature students nor animals).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Demonstrating the effect of ethanol in the role of an NMDAR antagonist would be satisfactory as the chain of implications would be illustrated on a theoretical basis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have access to standard laboratory equipment on a university level, but the simpler it is, the better. As to the material, the same is true while a fresh brain slice will hopefully be available as well.&lt;/p&gt;&#xA;" OwnerUserId="678" LastEditorUserId="678" LastEditDate="2012-03-29T14:52:18.303" LastActivityDate="2012-04-05T07:51:56.833" Title="Brain + ethanol experiment suggestions needed" Tags="&lt;neuroscience&gt;&lt;experimental-design&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1605" PostTypeId="1" AcceptedAnswerId="1623" CreationDate="2012-03-29T18:02:52.873" Score="11" ViewCount="2567" Body="&lt;p&gt;To start with, I do not have a sound knowledge in biology or any formal education in the area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was told that one of the definition of a species is a reproductive barrier, which means that if two animals can't reproduce, they are of different species. The barrier can be either the inability of the sperm to fertilize an egg, or a physical trait that inhibits reproduction, e.g. a cricket species that has a different mating song than another species or two species of flies, one that mates on yellow flowers, and the other on red flowers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what happens when, while two species can't reproduce, but there is a &quot;chain&quot; of &quot;intermediate&quot; sexual partners that can produce reproductive connection step by step. Like 6 degrees to Kavin Bacon, but with animal sex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll try to explain with an example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A Great Dane and a Miniature Pinscher dogs can't mate due to obvious size differences. But The Pincher can mate with a German Pincher (a slightly bigger breed of Pincher), which can mate with a Doberman Pincher. And the Doberman can mate with a German Shepard which can mate with a Great Dane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've also heard that such things happen with birds and crickets, where there is an original species, from which evolved several other, and while the original species (which still exists) can mate with all the new species. Some new species can't mate with some, or all of the other new species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How are such species are defined, and at what point dogs stop being dogs anymore?&lt;/p&gt;&#xA;" OwnerUserId="680" LastEditorUserId="1202" LastEditDate="2012-09-16T22:55:25.810" LastActivityDate="2013-03-19T20:12:27.487" Title="Species with reproduction barriers that can both reproduce with a third species" Tags="&lt;zoology&gt;&lt;reproduction&gt;&lt;taxonomy&gt;&lt;speciation&gt;" AnswerCount="3" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="1606" PostTypeId="2" ParentId="176" CreationDate="2012-03-29T18:39:57.320" Score="3" Body="&lt;p&gt;I recently tested exendin on INS1e cells in an Edu incorporation assay (similar to BrdU incorporation) to observe if this compound induces proliferation of the cells.  Compound incubation was for 24 hours.  I saw no incorporation of EdU with this compound over untreated levels.  In addition, during the assay I look at overall cell number with a DNA stain, but I did not see any effect on total cell number with exendin (ie, if it were toxic the total cell number should go down which I have observed with other compounds).&lt;/p&gt;&#xA;" OwnerUserId="681" LastActivityDate="2012-03-29T18:39:57.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1607" PostTypeId="2" ParentId="1601" CreationDate="2012-03-29T22:09:12.380" Score="6" Body="&lt;p&gt;I always did mine at -80 C, but I never compared the results to other protocols (&lt;em&gt;I don't fix what's not broken&lt;/em&gt;). But, I was curious about the same thing, so I looked around. I found one paper discussing this: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC333871/pdf/nar00242-0172.pdf&quot;&gt;Paithankar and Prasad, Nuc Acids Res 19(6):1346 (1991)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It shows that at low concentrations, EtOH at RT actually outperforms the precipitations at both 4 C and  dry ice/ethanol bath. That difference is quite big at 100ng/ml DNA and lost when there is more than 10 ug/ml DNA. For typical extractions, based on this data, I'd do it at RT.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, &lt;a href=&quot;http://books.google.com/books?id=3fDZqwC8ORwC&amp;amp;pg=PA11&amp;amp;dq=effect+of+temperature+on+ethanol+DNA+precipitation&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=rNV0T_yxD8600AHbyeyiDQ&amp;amp;ved=0CDUQ6AEwAQ#v=onepage&amp;amp;q=effect%20of%20temperature%20on%20ethanol%20DNA%20precipitation&amp;amp;f=false&quot;&gt;Hilario and Mackay&lt;/a&gt; say in their book that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;for genomic DNA isolation, different DNA precipitation temperatures&#xA;  and incubation times have little effect on recovery rates. One can&#xA;  directly centrifuge after adding ethanol without the -20 C incubation,&#xA;  and, it -20 C ethanol is not available, room temperature ethanol can&#xA;  be used.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They do not, however, provide any citation for that statement. &lt;/p&gt;&#xA;" OwnerUserId="48" LastActivityDate="2012-03-29T22:09:12.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1608" PostTypeId="1" CreationDate="2012-03-30T00:10:57.643" Score="5" ViewCount="81" Body="&lt;p&gt;I have a test in my upcoming Neuroscience class, one of the items on the study guide is: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Identify 2 means by which a maintained, constant stimulus produces only a transient excitation of the Pacinian corpuscle (phasic receptor). How does adaptation occur? &lt;/p&gt;&#xA;" OwnerUserId="622" LastActivityDate="2012-04-01T05:01:54.410" Title="Somatosensory System" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1609" PostTypeId="1" AcceptedAnswerId="1934" CreationDate="2012-03-30T07:13:46.417" Score="10" ViewCount="1893" Body="&lt;p&gt;I noticed it several times that when I drink beer (even one bottle) after some heavy workout, the next day my muscles are more stiff than other times, and not the same way... Is it because that lactate and NADH levels are raised both due to the anaerobic training and alcohol metabolism?&lt;/p&gt;&#xA;" OwnerUserId="673" LastEditorUserId="6" LastEditDate="2012-04-04T12:53:05.140" LastActivityDate="2012-04-25T05:36:43.070" Title="Effects of beer on muscle recovery after exercise" Tags="&lt;physiology&gt;&lt;metabolism&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1610" PostTypeId="1" AcceptedAnswerId="1616" CreationDate="2012-03-30T16:44:53.037" Score="4" ViewCount="70" Body="&lt;p&gt;My professor says&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nervus troclearis IV somatomotor fibers supply musculus obliquus superior.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and similarly for nervus oculomotorius III&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nervus oculomotorius postganglionic fibers supply musculus ciliaris, m. sphincter pupillae.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I understand the verb &quot;supply&quot; as &quot;stimulate&quot; or &quot;allow signal pass from the tract to the muscle that contracts or flexes&quot;. However, fibers must have some other functions too. So the verb &lt;em&gt;supply&lt;/em&gt; seems to be a general term for these functions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How do fibers control the muscle?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2012-03-30T17:58:48.563" LastActivityDate="2012-03-31T01:42:59.290" Title="How do fibers control muscles?" Tags="&lt;homework&gt;&lt;cranial-nerves&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1611" PostTypeId="1" AcceptedAnswerId="1615" CreationDate="2012-03-30T17:14:30.283" Score="7" ViewCount="2282" Body="&lt;p&gt;&quot;&lt;a href=&quot;http://www.boots.com/en/Boots-Pharmaceuticals-Cold-Defence-Nasal-Spray-20ml_1224268/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cold Defence&lt;/a&gt;&quot; nasal sprays are recommended to be taken either preventatively or in the early stages of a cold.  The active ingredient in these sprays is &lt;em&gt;Carrageenan&lt;/em&gt;.  After some research, the active compound is &lt;em&gt;Iota-Carrageenan&lt;/em&gt; (&lt;em&gt;ι-Carrageenan&lt;/em&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This study by &lt;a href=&quot;http://dx.doi.org/10.1186/1465-9921-11-108&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eccles et al&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt; shows that this drug is clinically effective.  The study was only designed to test efficacy rather than to explain the mechanism, however. A fleeting mention is provided in the discussion section:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The above results suggest that the treatment with Iota-Carrageenan reduces the viral replication. Consequently fewer cells are infected, the immune reaction against the viruses is less pronounced and fewer symptoms occur.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8hUS3.jpg&quot; alt=&quot;ι-Carrageenan&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How does &lt;em&gt;ι-Carrageenan&lt;/em&gt; produce an anti-viral effect?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1186/1465-9921-11-108&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Eccles R, Meier C, Jawad M, Weinmüllner R, Grassauer A, Prieschl-Grassauer E&lt;/strong&gt;. 2010. Efficacy and safety of an antiviral Iota-Carrageenan nasal spray: a randomized, double-blind, placebo-controlled exploratory study in volunteers with early symptoms of the common cold. Respiratory Research, 11:108, doi:10.1186/1465-9921-11-108.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="69" LastEditorUserId="43" LastEditDate="2012-09-16T18:08:28.183" LastActivityDate="2012-09-16T18:08:28.183" Title="How does Iota-Carrageenan achieve an antiviral effect?" Tags="&lt;pharmacology&gt;&lt;virology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1612" PostTypeId="1" CreationDate="2012-03-30T17:43:49.477" Score="5" ViewCount="218" Body="&lt;p&gt;We can localise cancer cells in the body. We can manufacture materials thin and hard enough to penetrate the body without harming it. So what stops us from creating an automated surgery where the patient lies down for some time whilst a machine locates cancerous cells and, using micro tubes, kills them one by one?&lt;/p&gt;&#xA;" OwnerUserId="518" LastEditorUserId="460" LastEditDate="2012-04-01T15:57:00.053" LastActivityDate="2012-09-08T07:38:32.810" Title="Robotic surgery for treating cancer?" Tags="&lt;cancer&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1613" PostTypeId="2" ParentId="1612" CreationDate="2012-03-30T18:27:25.970" Score="7" Body="&lt;p&gt;I'm assuming you are not talking about a single solid tumor, but rather one where the tumor is loose and is distributed throughout the tissue, or has metastasized &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess the answer is you could, but it would be one amazing machine.  This robot would have to examine each individual cell and destroy it based on what you could sense about the surface properties.  Identifying cancer cells on the basis of the proteins and glycosyl (carbohydrate) molecules on the cell surface is not embodied in a reliable way in a touch sensor.  Cancer can manifest lots of such patterns and it could quite easily be that if you looked at healthy cells, they look very similar.  Cancer cells don't have an obvious sign they are &lt;em&gt;always&lt;/em&gt; holding out saying 'im cancer'...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there is the structure of tumors. For instance glioma is one of the most difficult brain cancers you can have.  The glioma cells push out axons - they can be quite long.  Its hard to imagine a robot that could find that in a brain without tearing up all the neural connections.  In prostate cancers - one of the most common cancers in men, the cells are embedded in the tissue surrounded by necessary and healthy cells.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is why chemicals and nano  structures are the most commonly pursued means of combating cancer; they can enter into cells that are embedded in solid organs.  Differentiating the cancer cells from other sorts of cells in vivo is a pretty hard problem - some antibodies are given as a possible help there, but they are not reliable. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This blog post is a pretty up to date summary of where we are&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencebasedmedicine.org/index.php/personalized-medicine-vs-evolution/&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencebasedmedicine.org/index.php/personalized-medicine-vs-evolution/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-04-16T19:46:05.137" LastActivityDate="2012-04-16T19:46:05.137" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1614" PostTypeId="1" AcceptedAnswerId="2664" CreationDate="2012-03-30T19:01:25.503" Score="14" ViewCount="1603" Body="&lt;p&gt;Why do we turn images upside down again rather than dealing with them directly, still vertically rotated after passing through our lens? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't see how that would cause any problems, and how we'd ever be able to figure out if we are presented with flipped images after getting used to interacting based on visual input, whether flipped or not. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What am I missing?&lt;/p&gt;&#xA;" OwnerUserId="684" LastEditorUserId="43480" LastEditDate="2018-07-07T19:16:08.017" LastActivityDate="2018-07-07T19:16:08.017" Title="How do we know the brain flips images projected on the retina back around?" Tags="&lt;vision&gt;&lt;human-eye&gt;&lt;neurology&gt;&lt;perception&gt;" AnswerCount="3" CommentCount="11" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1615" PostTypeId="2" ParentId="1611" CreationDate="2012-03-30T21:52:48.460" Score="3" Body="&lt;p&gt;Through two different pathways, one relying on a non-specific (innate) response, and another through a reactive oxygen species, the level of NF-kB&lt;sup&gt;(**)&lt;/sup&gt; is amplified, as such a response would have happened as a result of the presence of the virus anyway. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In thousands of experiments, carrageenans have been used to&#xA;  induce inﬂammation, since inﬂammation is a predictable effect of&#xA;  exposure to carrageenan in animal and cell-based models. For the&#xA;  most part, these experiments were designed to test the effectiveness of anti-inﬂammatory agents or to study the mediators of inflammation&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The innate immune pathway is mediated by toll-like&#xA;  receptor (TLR)-4 and B-cell leukemia lymphoma (BCL)10, leading&#xA;  to increased Interleukin (IL)-8 secretion by both canonical and noncanonical pathways of NF-kB activation. The ROS-mediated&#xA;  pathway of inﬂammation does not involve TLR4-BCL10, but&#xA;  requires Hsp27 and IkB-kinase (IKK)b, leading to increased phosphorylation of IkBa, and thereby enabling the nuclear translocation&#xA;  of NF-kB.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From the intro to:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Yang B, Bhattacharyya S, Linhardt R, Tobacman J. (2012) Exposure to common food additive carrageenan leads to reduced sulfatase activity and increase in sulfated glycosaminoglycans in human epithelial cells.  Biochemie, Mar 5,epub ahead of print, &lt;a href=&quot;http://doi:10.1016/j.biochi.2012.02.031&quot; rel=&quot;nofollow&quot;&gt;doi&lt;/a&gt;  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(As an aside, the direct conclusions of this study are that these changes in GAGs may further influence transcription and play a role in determining cell fate, and perhaps may influence cell/cell interactions)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(**)NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) is a protein complex that controls the transcription of DNA. NF-κB is found in almost all animal cell types and is involved in cellular responses to stimuli such as stress, cytokines, free radicals, ultraviolet irradiation, oxidized LDL, and bacterial or viral antigens  &lt;a href=&quot;http://en.wikipedia.org/wiki/NF-%CE%BAB&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-03-30T21:58:48.640" LastActivityDate="2012-03-30T21:58:48.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1616" PostTypeId="2" ParentId="1610" CreationDate="2012-03-31T01:42:59.290" Score="5" Body="&lt;p&gt;Read &quot;supply&quot; as &quot;carry action potentials to.&quot; When the action potential reaches the junction with the muscle (i.e., the neuromuscular junction), neurotransmitters are released into synapse. A similar membrane depolarization occurs on the muscle cell, ultimately leading to contraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nerves visible to the naked eye are actually bundles of individual axons (hundreds, thousands, or tens of thousands of axons). Nerves have the appearance of branching because the individual axons that travel to muscle fibers don't all go to one muscle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example the oculomotor nerve branches:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wroNv.png&quot; alt=&quot;Oculomotor nerve&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what you see as the oculomotor nerve is really a collection of neurons. Some of these carry action potentials to the ciliary muscle and some to the sphincter pupillae. These are the parasympathetic components. There is a completely separate set of neurons (but still contained in the same nerve) that carry signals to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Extraocular_muscles&quot; rel=&quot;nofollow noreferrer&quot;&gt;extraocular muscles&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is really basic material that your professor should have explained to you.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-03-31T01:42:59.290" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1617" PostTypeId="2" ParentId="1612" CreationDate="2012-03-31T11:43:47.423" Score="13" Body="&lt;p&gt;Actually we aren't that good at localizing cancer cells.&#xA;There need to be around 100,000 cancer cells at a single location for the cancer to be visible on fMRI.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to treat a cancer via chemotherapy it's good to be able to see the cancer. It allows you to see whether the drug you are giving works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When dealing with a metastasized cancer where you don't think you know every location in which cancer is hiding it therefore often makes sense to avoid to take out everything you can see via surgery.&lt;/p&gt;&#xA;" OwnerUserId="152" LastActivityDate="2012-03-31T11:43:47.423" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1619" PostTypeId="1" CreationDate="2012-03-31T20:20:45.730" Score="6" ViewCount="360" Body="&lt;p&gt;Veterinarians often recommend spaying a female cat if the owner does not want her to have kittens. What does biology know about the effect of spaying on female cats' organism and health (apart from lack of fertility, of course)?&lt;/p&gt;&#xA;" OwnerUserId="688" LastEditorUserId="688" LastEditDate="2012-04-05T12:23:44.797" LastActivityDate="2012-04-05T12:23:44.797" Title="Effect of spaying on the female cat organism and health" Tags="&lt;zoology&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1620" PostTypeId="2" ParentId="1619" CreationDate="2012-04-01T00:19:25.350" Score="7" Body="&lt;p&gt;From the standpoint of the skeletal system, spaying is definitely not good for her health. Removal of the ovaries mimics what happens at menopause, when circulating estrogen levels fall. Estrogen is necessary for maintenance of bone mineralization. Without estrogen, bones start to demineralize (the same process that happens in human females after menopause, leading to &lt;a href=&quot;http://en.wikipedia.org/wiki/Osteoporosis&quot; rel=&quot;nofollow&quot;&gt;osteoporosis&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then again, some animals, if they do not get pregnant, will cycle indefinitely until they get anemic and die. Ferrets are an example. So it's better to have these spayed.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2012-04-02T15:36:43.220" LastActivityDate="2012-04-02T15:36:43.220" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1621" PostTypeId="2" ParentId="1608" CreationDate="2012-04-01T05:01:54.410" Score="2" Body="&lt;p&gt;I would consider physical filtering properties of the corpuscle sheath as well as adaptation of the neuron or downstream targets.&lt;/p&gt;&#xA;" OwnerUserId="689" LastActivityDate="2012-04-01T05:01:54.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1622" PostTypeId="1" AcceptedAnswerId="1624" CreationDate="2012-04-01T17:48:15.537" Score="8" ViewCount="1285" Body="&lt;p&gt;I have read that different optical imaging techniques such as  such as wide-field microscopy, confocal microscopy or STED microscopy can theoretically achieve a different spatial resolution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I was only able to find information about the STED microscopy's spatial resolution (5.8 nm) on Wikipedia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anybody know of any references or recommended reading (preferably free) where I can learn more about different optical microscopy methods and how the cope with the diffraction limit?&lt;/p&gt;&#xA;" OwnerUserId="17" LastActivityDate="2012-04-04T07:30:15.090" Title="Spatial resolutions in optical microscopy" Tags="&lt;fluorescent-microscopy&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1623" PostTypeId="2" ParentId="1605" CreationDate="2012-04-01T18:28:31.803" Score="7" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;How are such species are defined, and at what point dogs stop being&#xA;  dogs anymore?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is a bit like the is-Pluto-a-planet-discussion. A group of scientists have to come together and hold a big conference.&#xA;You have a few principles that you want to adhere to and then it's big groups of people making decisions. &lt;/p&gt;&#xA;" OwnerUserId="152" LastActivityDate="2012-04-01T18:28:31.803" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1624" PostTypeId="2" ParentId="1622" CreationDate="2012-04-01T23:38:54.633" Score="7" Body="&lt;p&gt;The theoretical resolution for an optical microscope depends on the wavelength used, but is close to 0.22 um (220 nm). Confocal microscopy does not greatly improve axial resolution; it dramatically improves the in-plane resolution (x and y directions, by excluding extraneous light). Theres not a lot to do to &quot;cope&quot; with that using those techniques. If you need more resolution, you can use the super-resolution techniques you mention, or the good old TEM.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is some more information on the Nikon website: &lt;a href=&quot;http://www.microscopyu.com/articles/formulas/formulasresolution.html&quot;&gt;http://www.microscopyu.com/articles/formulas/formulasresolution.html&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;and on Olympus website: &lt;a href=&quot;http://www.olympusconfocal.com/theory/resolutionintro.html&quot;&gt;http://www.olympusconfocal.com/theory/resolutionintro.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="48" LastEditorDisplayName="user560" LastEditDate="2012-04-02T00:55:08.620" LastActivityDate="2012-04-02T00:55:08.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1625" PostTypeId="2" ParentId="1622" CreationDate="2012-04-02T01:02:25.117" Score="3" Body="&lt;p&gt;A &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21929850&quot; rel=&quot;nofollow&quot;&gt;couple&lt;/a&gt; of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19489737&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt; articles you could read up on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Leung BO, Chou KC. Review of super-resolution fluorescence microscopy for biology. Appl Spectrosc. 2011 Sep;65(9):967-80.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Huang B, Bates M, Zhuang X. Super-resolution fluorescence microscopy. Annu Rev Biochem. 2009;78:993-1016.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-02T01:02:25.117" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1626" PostTypeId="1" AcceptedAnswerId="1628" CreationDate="2012-04-02T02:34:25.080" Score="17" ViewCount="646" Body="&lt;p&gt;There is a growing interest &lt;a href=&quot;http://www.nature.com/news/2011/110615/full/474272a.html&quot;&gt;in the applications of non-equilibrium quantum dynamics to describe biological processes&lt;/a&gt; (I'm not talking here about Penrose's old theories, but new stuff -- quantum coherence in light harvesting, magnetoreception etc.). What is the biologists' take on this? Is this just a whim of physicists looking for grants, or a serious part of biological research?&lt;/p&gt;&#xA;" OwnerUserId="688" LastEditorUserId="688" LastEditDate="2012-04-07T20:56:19.890" LastActivityDate="2012-04-07T20:56:19.890" Title="Quantum mechanics in biology" Tags="&lt;biophysics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1627" PostTypeId="1" AcceptedAnswerId="1630" CreationDate="2012-04-02T02:36:50.460" Score="7" ViewCount="848" Body="&lt;p&gt;I was asked the following question by my teacher:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A gene regulatory protein called HisP regulates the enzymes for&#xA;  histidine biosynthesis in the bacterium E. Coli.  HisP is a protein&#xA;  whoes activity is modulated by histidine.  Upon binding histidine,&#xA;  HisP alters its conformation, dramatically changing its affinity for&#xA;  the regulatory sequences in the promoters of the genes for the&#xA;  histidine biosynthetic enzymes.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;If HisP function sas a transcriptional repressor, would you expect&#xA;  that HisP would bind more tightly or less tightly to regulatory&#xA;  sequences when histidine is abundant? Why?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My own attempt at a solution: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Less tightly.  If histidine is abundant, HisP's job is to stop the histadine pathway as a &quot;repressor.&quot;  If HisP binds less tightly to promotors, the pathway should not produce as much histadine.  &lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="6" LastEditDate="2012-04-03T08:34:03.840" LastActivityDate="2012-04-03T08:34:03.840" Title="Effect of histidine on the binding affinity of HisP" Tags="&lt;molecular-biology&gt;&lt;homework&gt;&lt;transcription&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1628" PostTypeId="2" ParentId="1626" CreationDate="2012-04-02T04:29:51.793" Score="18" Body="&lt;p&gt;Absolutely a serious part of research - quantum mechanics &lt;em&gt;defines&lt;/em&gt; chemical structure and reactivity. Whenever you see a headline like '&lt;em&gt;Scientists find quantum effects important in protein activity, weird huh?&lt;/em&gt;', read it as '&lt;em&gt;Scientists find pragmatic classical approximations inadequate in describing protein activity&lt;/em&gt;'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In protein structure, for example, classical molecular dynamics/mechanics are important in generating computationally tractable problems, however they represent a tacit and streamlined parameterisation of underlying quantum mechanics. QM protein structures are usually too gnarly to compute (at least &lt;a href=&quot;http://www.petachem.com/&quot;&gt;historically speaking&lt;/a&gt;), except in regions of interest like an active site, where a model fine-tuned for sequences of amino acids will probably fail badly anyway. As a concrete example, the group that I'm in is in part interested in computationally modelling the active site of plant photosystem II, which contains a cluster of spin-coupled manganese atoms. To glean any useful understanding of how this cluster functions via a computational model, an explicit quantum mechanical level of theory that takes into account electron exchange and correlation must be used. This requirement can probably be extended to any metalloenzyme.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And this isn't touching upon the &lt;a href=&quot;http://en.wikipedia.org/wiki/F%C3%B6rster_resonance_energy_transfer&quot;&gt;resonance hole transfer&lt;/a&gt; that oxidises the active site, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Davydov_soliton&quot;&gt;Davydov solitons&lt;/a&gt; that manifest in protein alpha helices, or indeed the quantum electrodynamical origins of the Van der Waals interaction that causes everything to tend to stick to everything else.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this is interesting :D&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(note: I am not involved with PetaChem, I just think it's freaking awesome.)&lt;/p&gt;&#xA;" OwnerUserId="99" LastActivityDate="2012-04-02T04:29:51.793" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1629" PostTypeId="1" AcceptedAnswerId="1631" CreationDate="2012-04-02T06:23:19.187" Score="10" ViewCount="1313" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Start_codon&quot;&gt;wikipedia&lt;/a&gt; and the original complete sequence of the &lt;a href=&quot;http://www.sciencemag.org/content/277/5331/1453&quot;&gt;K-12 genome&lt;/a&gt;, there are multiple non-AUG start codons such as GUG and UUG. How is this possible? I'm particularly curious about the mechanism of translation initiation in the absence of the canonical tRNA&lt;sup&gt;fMet&lt;/sup&gt;.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-04-02T18:00:10.013" LastActivityDate="2012-04-02T18:23:10.767" Title="How are there alternative initiation codons?" Tags="&lt;molecular-biology&gt;&lt;gene-expression&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1630" PostTypeId="2" ParentId="1627" CreationDate="2012-04-02T15:20:33.770" Score="7" Body="&lt;p&gt;Still if you change your question as (If histidine is abundant, HisP's job is to stop the histidine pathway as a &amp;quot;repressor.&amp;quot; If HisP binds less tightly to promotors, the pathway should not produce as much histidine.)&lt;/p&gt;&#xA;&lt;p&gt;Then it should be under another assumption that what is the effect of HisP binding promoter of enzyme's gene. Is it suppressing the transcription or amplifying the transcription.&lt;/p&gt;&#xA;&lt;p&gt;If it suppresses transcription then answer is more tightly, if it amplifies the transcription then answer is less tightly. I suggest you put this clearly in your answer, as the question is not quest accurate.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;I guess your answer might be wrong.&lt;/p&gt;&#xA;&lt;p&gt;The question should be under another assumption that how does this protein HisP regulate histidine biosynthesis. positiver or negative feedback regulation.&lt;/p&gt;&#xA;&lt;p&gt;Generally, amino acids synthesis is regulated by negative feedback loops so that cells could control the amount of amino acids they want. In this case, the answer should be &lt;em&gt;&lt;strong&gt;more tightly&lt;/strong&gt;&lt;/em&gt;. As it functions as a repressor then it should bind promoter more tightly so that to repress the transcription more which then generate less histidine synthesis enzyme. (I believe this is what your teacher want you to answer)&lt;/p&gt;&#xA;&lt;p&gt;In the other case, biosystems sometimes have the positive feedback regulation so that they can amplify the sensitivity to the environment noise or generate bistability (phenotypic switching). In that case, the protein bind promoter &lt;em&gt;&lt;strong&gt;less tightly&lt;/strong&gt;&lt;/em&gt; in order to generate more histidine.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="322" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-04-03T08:32:28.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1631" PostTypeId="2" ParentId="1629" CreationDate="2012-04-02T18:23:10.767" Score="10" Body="&lt;p&gt;Actually, the start codon, no matter whether it is AUG or GUG/UGG, always encodes for Met. So the translation is initiated by tRNA&lt;sup&gt;fMet&lt;/sup&gt; (prokaryotic translation). The 30s ribosome subunit binds to the Shine-Dalgarno sequence and then it scans the dowstream mRNA sequence for AUG and the tRNA loaded with Met, which has the CAU anticodon form the most stable interaction. But apparently, only two-bases-interaction between the start codon (GUG, UUG) and the fMet-tRNA anticodon are sufficient for the initiation of translation (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0378111999002103&quot;&gt;1&lt;/a&gt;). I will look more into the literature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0378111999002103&quot;&gt;1. Initiation of translation in prokaryotes and eukaryotes&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-04-02T18:23:10.767" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1632" PostTypeId="1" AcceptedAnswerId="1634" CreationDate="2012-04-02T19:07:45.863" Score="1" ViewCount="148" Body="&lt;p&gt;I have the following tractus now:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;nucleus parasymphaticus sacrales -&gt; nervus splanchnic -&gt; ganglion&#xA;  terminalis -&gt; colon sigmoideum&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The tract is parasympathetic.&#xA;It suggests me that it should travel along CN 9 or CN 10, most likely with CN 10.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Does tractus colon sigmoideum travel with CN 10 and its nucleus dorsalis nervi vagi?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2012-04-03T23:45:59.710" LastActivityDate="2012-04-04T18:04:03.667" Title="Does the Parasympathetic Tract of Colon Sigmoideum Travel with Nervus Vagus and its Nucleus Dorsalis Nervi Vagi?" Tags="&lt;neuroscience&gt;&lt;cranial-nerves&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1633" PostTypeId="2" ParentId="1588" CreationDate="2012-04-02T19:33:11.003" Score="-2" Body="&lt;p&gt;You are right the biology text books claim that trans-“unsaturated” fatty acids can be metabolized. Note : - The text books make it clear that “Trans” means the fatty acid is unsaturated and can be monounsaturated or polyunsaturated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trans fatty acids are generally being blamed so as to keep to the unfortunate false “theory” that certain poly unsaturated fatty acids are essential for humans. This false “theory” is the basis for the epidemic of obesity and most of the strange and lifestyle diseases. The actual culprits of the epidemic of lifestyle diseases is the high levels of polyunsaturated fatty acids (both trans and cis) we consume through the processed unsaturated vegetable fats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check from your text books, atherosclerotic plaque is made up of oxidised polyunsaturated fatty acids and cholesterol (which has been labelled LDL cholesterol).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prostaglandins, which are produced in the body by polyunsaturated fatty acids, have been identified by many different research studies as the molecules underlying diseases and ailments such as diabetes, asthma, cancers, dysmenorrhea (menstrual pains), baldness, cramps and muscle pull, migraine, glaucoma, delivery and labour problems, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aspirin according to the research results, reduces the chances of cancer occurrence or dying early from cancer. Aspirin stops the production of prostaglandins in the body.&lt;/p&gt;&#xA;" OwnerUserId="690" LastActivityDate="2012-04-02T19:33:11.003" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1634" PostTypeId="2" ParentId="1632" CreationDate="2012-04-02T19:42:12.413" Score="0" Body="&lt;p&gt;I found the following from &lt;a href=&quot;http://webcache.googleusercontent.com/search?q=cache%3aBzi3WZBH4rMJ%3aen.wikipedia.org/wiki/Sigmoid_colon%20&amp;amp;cd=1&amp;amp;hl=fi&amp;amp;ct=clnk&amp;amp;gl=fi&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pelvic splanchnic nerves are the primary source for parasympathetic innervation [for Sigmoid colon].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The non-cranial nerve is extending the scope of the cranial nerve by a synapse between the two neurons. The neurons are transmitting the electrical impulse from one neuron to another.&#xA;So this way the splanchnic nerve does not need to be with CN 10 in the region of impact.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The parasympathetic tract of colon sigmoideum can travel with nervus vagus by having a synapse between pelvic splanchnic nerve and CN 10. I verified this from my professor.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2012-04-04T18:04:03.667" LastActivityDate="2012-04-04T18:04:03.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1635" PostTypeId="1" AcceptedAnswerId="1639" CreationDate="2012-04-02T21:38:37.650" Score="8" ViewCount="438" Body="&lt;p&gt;I recently came across &lt;a href=&quot;http://www.nature.com/news/cyborg-snails-power-up-1.10210&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; from Nature. In it, it states that the snails have &quot;tiny biofuel cells that extract electrical power from the glucose and oxygen in the snail’s blood&quot;, and that the power obtained is dependent on &quot;how quickly sugar and oxygen can be taken from the creatures' blood&quot;. They go on to say that the power obtained decreases over time, and that these implants could power future pacemakers in humans. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would this application in humans require that a patient eats more and &quot;breathes more&quot; than average? Why does the power output decrease over time, and couldn't that potentially lead to the malfunctioning of a pacemaker?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Van Noorden, Richard.&lt;/strong&gt; &lt;em&gt;“Cyborg Snails Power Up.”&lt;/em&gt; Nature (March 12, 2012). &lt;a href=&quot;http://www.nature.com/doifinder/10.1038/nature.2012.10210&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/doifinder/10.1038/nature.2012.10210&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-07-26T23:09:33.013" LastActivityDate="2012-07-26T23:09:33.013" Title="Electricity generated by the body and its applications?" Tags="&lt;biotechnology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1637" PostTypeId="1" AcceptedAnswerId="1644" CreationDate="2012-04-02T22:32:52.940" Score="5" ViewCount="202" Body="&lt;p&gt;It has been my thought for a long time that this is the case, but I am unsure currently, since the parasympathetic tract of colon sigmoideum does not seem to have connection with CN 10. It connects with pelvic splanchnic nerves. &#xA;Discussion about it &lt;a href=&quot;https://biology.stackexchange.com/questions/1632/does-the-parasympathetic-tract-of-colon-sigmoideum-travel-with-nervus-vagus-and&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is no connection from pelvic splanchnic nerves to CN 10, like CN 10 running within the nerves, then my though must be wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are CN3, CN7, CN9 and CN10 the only Parasympathetic Cranial Nerves?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-12-29T05:13:29.623" Title="Are CN3, CN7, CN9 and CN10 the only Parasympathetic Cranial Nerves?" Tags="&lt;neuroscience&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1638" PostTypeId="1" AcceptedAnswerId="42224" CreationDate="2012-04-03T01:01:20.687" Score="18" ViewCount="582" Body="&lt;p&gt;Please forgive the obviously silly appearance of this question, and/or of the tenor which may come across as flippant or dismissive of real world suffering. My intention is none of the above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a layperson, I have always understood that the expression of our various colds/flus etc, while frequently mis-understood as being caused by the virus, are actually just manifestations of our own immunity fighting same.  In other words, all the snot, and fever and inflammation are not caused *by the virus, they are a reaction *to the virus, as we fight it off. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question then is why do people with AIDS (or similar immunity destroying affliction) appear sick?  If they have weak or non-existent immune systems, following the above logic, would one expect to see them passing away while looking entirely healthy? &lt;/p&gt;&#xA;" OwnerUserId="148" LastActivityDate="2016-02-03T22:38:30.510" Title="Why do people dying of immune deficiency diseases appear sick?" Tags="&lt;immunology&gt;&lt;virology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1639" PostTypeId="2" ParentId="1635" CreationDate="2012-04-03T01:14:14.277" Score="6" Body="&lt;p&gt;You'd think if such devices were used in humans, they wouldn't require a change of lifestyle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They don't say the power &lt;em&gt;always&lt;/em&gt; decreases over time:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Katz’s snails, for example, produced up to 7.45 microwatts, but after&#xA;  45 minutes, that power had decreased by 80%. To draw continuous power,&#xA;  Katz’s team had to ramp down the power they extracted to 0.16&#xA;  microwatts.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is really a chemistry question. The glucose has to be brought to the fuel cell some way. In this case, the glucose is oxydized directly in the hemolymph. As oxygen PP in the hemolymph is always greater than glucose concentration(1), your limiting rate (which is related to the power you can get from the device) is that of glucose intake &lt;em&gt;at the fuel cell&lt;/em&gt;. Therefore, the more you oxidize glucose per unit time, the greater intake you need to keep the output from dropping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The glucose intake at the fuel cell is a function of biological parameters such as quantity eaten, metabolic efficiency, metabolic speed, blood flow, but also diffusion. The kinetics of glucose intake at the fuel cell are such that you can't ask for &lt;em&gt;too much&lt;/em&gt; power for &lt;em&gt;too long&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suggest you read the article to get a more detailed answer. Nature news is good, but there's nothing like reading the real paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1&lt;/strong&gt; &lt;a href=&quot;http://pubs.acs.org/doi/full/10.1021/ja211714w&quot;&gt;http://pubs.acs.org/doi/full/10.1021/ja211714w&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="691" LastActivityDate="2012-04-03T01:14:14.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1640" PostTypeId="1" AcceptedAnswerId="1647" CreationDate="2012-04-03T01:32:09.900" Score="15" ViewCount="792" Body="&lt;p&gt;Some fruits such as pumpkins can grow to be 100 lbs. Under different conditions, the same variety of pumpkin can produce a 15 lb. fruit. Both plants are healthy, and look the same except for their size difference. If I took two red apple trees and planted them in extreme opposite conditions, the fruit size would be nearly the same. The fruit quantity would be lowered in the tree grown under poor conditions. Why do fruits have such a variable range of acceptable sizes?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="307" LastEditDate="2012-04-06T17:19:06.210" LastActivityDate="2014-07-20T13:31:31.540" Title="Why do some fruits have a much wider range of acceptable sizes than others?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;fruit&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1641" PostTypeId="2" ParentId="375" CreationDate="2012-04-03T01:37:03.543" Score="3" Body="&lt;p&gt;I'm not a biologist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a chemist's point of view, these molecules should have similar polarity. Their structure is very similar, actually.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering your replacement rule is correct, I would say there wouldn't be much effect other than observing different colors. What is also plausible is that you'd have to reverse the interpretation of your results, e.g. methylene blue stains X, but crystal violet stains Y whereas carbol fuchsin stains Y and safranine stains X.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Was that clear?&lt;/p&gt;&#xA;" OwnerUserId="691" LastActivityDate="2012-04-03T01:37:03.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1642" PostTypeId="2" ParentId="1614" CreationDate="2012-04-03T02:31:04.007" Score="3" Body="&lt;p&gt;I think you're oversimplifying the problem. Think about gravitation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take this informal example: at any point on a massive sphere, you can define &quot;bottom&quot; such that any massive object with weight less than that of the sphere is subject to an attractive force towards that point. The direction of the force points in the direction of the &quot;bottom&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming this holds true for every massive object, the following is logical: for the purpose of orientation, it is a lot more energy efficient for an organism to simply invert the image using brain circuitry than invert &lt;em&gt;every single sensory input&lt;/em&gt; to effectively reverse the definition of &quot;bottom&quot;, which follows from physical laws to which the organism is &lt;em&gt;invariably&lt;/em&gt; bound.&lt;/p&gt;&#xA;" OwnerUserId="691" LastActivityDate="2012-04-03T02:31:04.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1643" PostTypeId="2" ParentId="1638" CreationDate="2012-04-03T04:35:51.873" Score="11" Body="&lt;p&gt;They appear sick because they &lt;em&gt;are&lt;/em&gt; sick, but with other, opportunistic infections. The &quot;immune deficiency&quot; part of AIDS means that the immune system is not functioning normally and, thus, is unable to protect them. Typical illnesses that are more found more frequently in AIDS patients are &lt;a href=&quot;http://en.wikipedia.org/wiki/Pneumocystis_pneumonia_%28PCP%29&quot;&gt;pneumocystis pneumonia&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Kaposi%27s_sarcoma&quot;&gt;Kaposi's sarcoma&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2012-04-03T05:47:13.797" LastActivityDate="2012-04-03T05:47:13.797" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1644" PostTypeId="2" ParentId="1637" CreationDate="2012-04-03T04:38:42.290" Score="4" Body="&lt;p&gt;Yes, only III, VII, IX, and X are cranial nerves that carry parasympathetic autonomic neurons. The key phrase is &quot;cranial.&quot; Pelvic splanchnic nerves also carry parasympathetics, but they arise from the pelvis, not the brain.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-04-03T04:38:42.290" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1645" PostTypeId="2" ParentId="1635" CreationDate="2012-04-03T09:41:30.837" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Would this application in humans require that a patient eats more and &quot;breathes more&quot; than average? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From the cellular standview, each glucose and O&lt;sub&gt;2&lt;/sub&gt; molecule that you substract to the cell for use in a second futile cycle, should be replaced. However, I doubt that the amount of glucose/O&lt;sub&gt;2&lt;/sub&gt; required per hour will be so important to require additional food intake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, each cell in the body &lt;strong&gt;normally&lt;/strong&gt; generates electricity from glucose and O&lt;sub&gt;2&lt;/sub&gt;: just think at the electron transport chain during the mitochondrial cellular respiration.&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="69" LastEditDate="2012-04-06T17:21:07.563" LastActivityDate="2012-04-06T17:21:07.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1646" PostTypeId="2" ParentId="1612" CreationDate="2012-04-03T10:51:41.920" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;We can manufacture materials thin and hard enough to penetrate the body without harming it.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It’s not a question of materials. After all, we have the materials to build flying cars – so why are there no flying cars? The problem is reliably &lt;em&gt;locating&lt;/em&gt;, &lt;em&gt;recognising&lt;/em&gt; and &lt;em&gt;selectively killing&lt;/em&gt; tumour cells.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;using micro tubes, kills them one by one?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;“one by one” … for &lt;strong&gt;billions&lt;/strong&gt; of cells? Even ignoring all the other technical problems already alluded to in other answers, this is simply a problem of insurmountable scale. In order to do this efficiently we’d need in the order of millions tiny robots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Either way, creating appropriate robots isn’t something we can do today, and even if we can someday do it, it will be easier (and much, much cheaper) to just &lt;a href=&quot;http://en.wikipedia.org/wiki/Synthetic_biology&quot; rel=&quot;nofollow&quot;&gt;bio-engineer&lt;/a&gt; a bacterium which &lt;a href=&quot;http://pubs.rsc.org/en/content/articlelanding/2011/mb/c1mb05016h&quot; rel=&quot;nofollow&quot;&gt;detects and kills tumour cells&lt;/a&gt;. While neither nanobots nor bio-engineered cancer killers are reality today, the bio-engineering approach is much easier, and much closer to realisation than the nanobot approach.&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="166" LastEditDate="2012-09-08T07:38:32.810" LastActivityDate="2012-09-08T07:38:32.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1647" PostTypeId="2" ParentId="1640" CreationDate="2012-04-03T12:48:26.250" Score="10" Body="&lt;p&gt;Pumpkins, squashes in general, grow on vines, while apples grow on trees. Vines are fast growing and trees are not. Zucchini can be quite large; cucumbers, too. Pears, plums, peaches and other tree fruits do have a reduced variation in fruit size. While I do not know the answer to your question, my background in plant biology tells me that this is an important part of the reason. For example, a watermelon or pumpkin rests on the earth, but a tree fruit hangs. If that fruit is too heavy it falls from the ground before it is ripe - before the seeds are fully differentiated that is. So, while &quot;evolution&quot; might be an answer, it is important to discuss what aspects are at play. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it has to do with vine vs tree, and how the fruit is attached and hangs/lays.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-04-03T12:48:26.250" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1648" PostTypeId="1" AcceptedAnswerId="2290" CreationDate="2012-04-03T15:29:50.887" Score="9" ViewCount="394" Body="&lt;p&gt;Regarding the bacteria found in Mono Lake, CA that scientists believe uses or can use arsenic in its DNA backbone where life as we know it uses phosphorus (according to their experiments depriving the microbes of phosphorus and providing much arsenic), have researchers conjectured and tested whether the energy currency molecule used is also arsenic-based instead of ATP?&lt;/p&gt;&#xA;" OwnerUserId="263" LastEditorUserId="43" LastEditDate="2012-04-03T16:02:53.980" LastActivityDate="2012-05-16T21:30:19.757" Title="Does GFAJ-1 use Adenosine triarsenate as its energy currency?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;extremophiles&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1649" PostTypeId="1" CreationDate="2012-04-03T16:52:13.180" Score="10" ViewCount="193" Body="&lt;p&gt;Many experiments showed that neurons tend to fire at some phase (usually trough) of local field potential (LFP) oscillations, such as theta or gamma rhythm. LFP is supposedly generated by a population of neurons with coherent currents induced by spikes. So there is a causal link from spiking activity to LFPs. &lt;strong&gt;Is there also a significant influence on the spikes directly from LFP (not via the hidden spikes that generated the LFP)?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it just an epiphenomenon, and or is there a possibility that it is partly a serious mechanism for neural computation?&lt;/p&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2012-04-03T19:48:40.793" LastActivityDate="2018-04-30T12:16:02.177" Title="Is there a biophysical causation from local field potential (LFP) to spikes?" Tags="&lt;neuroscience&gt;&lt;biophysics&gt;&lt;electrophysiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1651" PostTypeId="1" CreationDate="2012-04-03T19:48:21.013" Score="15" ViewCount="1062" Body="&lt;p&gt;Are there any significant differences in our genome compared to the genes of our ancestors from 1000-2000 years ago?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if there are significant differences, do they result in significant differences in phenotypic traits?&lt;/p&gt;&#xA;" OwnerUserId="693" LastEditorUserId="12909" LastEditDate="2015-04-20T11:53:58.500" LastActivityDate="2017-01-24T21:29:28.190" Title="Are there differences in DNA between humans of today and humans from 2000 years ago?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;dna&gt;&lt;genomics&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1652" PostTypeId="2" ParentId="1651" CreationDate="2012-04-03T21:33:12.460" Score="8" Body="&lt;p&gt;The larger differences are most likely in epigenetic marks on the DNA. The environment is a lot different today than it was 2000 years ago and those differences are stronger determinants of epigenetic change than sequence change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2000 years is only about 40 generations and that is not very much to see great differences in DNA sequence or allele frequencies - once founder populations are removed from the analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Height is highly influenced by genetics, but can be masked by environment - notably diet. Diets higher in protein content are more likely to elicit the expression of the &quot;height alleles&quot; but only to a point as too much protein is also unhealthy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Added in Edit 4 Apr 2012:&lt;/em&gt; I should add that my response is written from the perspective of frequency of alleles or epigenetic marks across a population.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-04-04T18:39:04.100" LastActivityDate="2012-04-04T18:39:04.100" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1655" PostTypeId="1" AcceptedAnswerId="1658" CreationDate="2012-04-04T07:08:20.577" Score="23" ViewCount="28419" Body="&lt;p&gt;How does caffeine (or any additional agents) act as a laxative when ingested? I'm interested in the metabolic/signaling pathway.&lt;/p&gt;&#xA;" OwnerUserId="673" LastEditorDisplayName="user560" LastEditDate="2012-11-22T22:52:20.753" LastActivityDate="2013-09-02T19:10:20.457" Title="Why is coffee a laxative?" Tags="&lt;physiology&gt;&lt;digestive-system&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1656" PostTypeId="2" ParentId="1622" CreationDate="2012-04-04T07:30:15.090" Score="5" Body="&lt;p&gt;You could also have a look at Leica Microsystems' Science Lab. You will find lots of articles and tutorials on the different microscopy methods, ranging from basic microscopy knowledge to specific know-how, including latest information on STED: www.leica-microsystems.com/science-lab&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example:&#xA;gCW-STED Microscopy: When the Arrival Time of a Photon Matters&#xA;&lt;a href=&quot;http://www.leica-microsystems.com/science-lab/gcw-sted-microscopy-when-the-arrival-time-of-a-photon-matters/&quot;&gt;http://www.leica-microsystems.com/science-lab/gcw-sted-microscopy-when-the-arrival-time-of-a-photon-matters/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From Molecules to Tissues – Optical Tools for Cancer Research&#xA;&lt;a href=&quot;http://www.leica-microsystems.com/science-lab/from-molecules-to-tissues-optical-tools-for-cancer-research/&quot;&gt;http://www.leica-microsystems.com/science-lab/from-molecules-to-tissues-optical-tools-for-cancer-research/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Disclosure: I have been involved in the launch of Leica Science Lab)&lt;/p&gt;&#xA;" OwnerUserId="697" LastActivityDate="2012-04-04T07:30:15.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1657" PostTypeId="2" ParentId="1651" CreationDate="2012-04-04T07:54:55.653" Score="6" Body="&lt;p&gt;In the literature, there are examples of DNA analysis from very old specimen. For instance, look at the analysis of both nuclear and mitochondrial DNA from 62 buried humans exhumed from a Mongolian cemetery &lt;strong&gt;dating from 2,000 years ago&lt;/strong&gt;, as described by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1180365/&quot;&gt;Keyser-Traqui et al. 2003&lt;/a&gt;, Am J Hum Genet 73(2): 247–260. Despite, the publication is open-access, the DNA sequences are not available, and no comparison with current mongolian DNA has been described in the study, but for sure your question should be answerable.&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="6" LastEditDate="2012-04-04T08:12:49.717" LastActivityDate="2012-04-04T08:12:49.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1658" PostTypeId="2" ParentId="1655" CreationDate="2012-04-04T12:00:17.457" Score="19" Body="&lt;p&gt;Coffee does have an effect on the peristaltic movement in the bowel.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Coffee increases rectosigmoid motor activity within 4 min after ingestion in some people. Its effects on the colon are found to be comparable to those of a 1000 kCal meal. Since coffee contains no calories, and its effects on the gastrointestinal tract cannot be ascribed to its volume load, acidity or osmolality, it must have pharmacological effects. Caffeine cannot solely account for these gastrointestinal effects.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Effectively, decaf and regular coffee stimulate peristaltic movement in the colon as effectively as a meal does. Caffeine is not the active agent then, but some other compound in coffee.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Source&lt;/strong&gt;: Boekema PJ, Samsom M, et al. Coffee and gastrointestinal function: facts and fiction. A review. Scand J Gastroenterol Suppl. 1999;230:35-9. PMID &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10499460&quot;&gt;10499460&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-04T12:00:17.457" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="1659" PostTypeId="1" AcceptedAnswerId="1669" CreationDate="2012-04-04T12:04:27.960" Score="9" ViewCount="387" Body="&lt;p&gt;What are the real consequences of never maintaining a circadian rhythm? &#xA;How is circadian rhythm important for health and function? Where did it arise in evolution?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="69" LastEditDate="2012-04-04T19:45:00.883" LastActivityDate="2012-04-05T08:31:38.097" Title="Why is maintaining a circadian rhythm important?" Tags="&lt;circadian-rhythms&gt;&lt;chronobiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1660" PostTypeId="1" AcceptedAnswerId="2207" CreationDate="2012-04-04T13:05:25.450" Score="11" ViewCount="7386" Body="&lt;p&gt;There is the famous saying about a frog that is put in water that are slowly boiling will not jump out until it's too late. I realize it happens because of the frog's cold blood that adjusts to the temperature change until it's too late.&#xA;Will this work as well on an animal with warm blood, or will the animal jump out ones it gets hot, but not hot enough to cause permanent damage?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit due to comments:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cold blooded animals, like the frog, can adjust easier to their surrounding when the surrounding changes temperature gradually as their body temperature adjusts with the surroundings. Will the same happen to a warm bodied creature, and will it find it easier to adjust to the surrounding if the change is gradual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, I don't like saunas, when I get in them I have problem breathing and I can't stand the heat, which means that I can be in a sauna for a very short time until I have had enough and get out. Will putting me in a sauna at room temperature and then turning it on to gradually begin to heat until its destination temperature will allow me to fill more comfortable and stay longer inside once it's at the normal sauna temperature?&lt;/p&gt;&#xA;" OwnerUserId="680" LastEditorUserId="680" LastEditDate="2012-04-04T21:08:36.973" LastActivityDate="2012-05-16T03:06:50.493" Title="Will the &quot;frog in boiling water not jumping out&quot; work on warm blooded animals" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1661" PostTypeId="1" AcceptedAnswerId="1860" CreationDate="2012-04-04T13:51:20.947" Score="18" ViewCount="55168" Body="&lt;p&gt;I've encountered a &lt;a href=&quot;http://www.youtube.com/watch?v=wwolYFGM9pU&amp;amp;feature=fvwrel&quot;&gt;clip on Youtube&lt;/a&gt; showing a goldfish thrown in liquid nitrogen and immediately after to normal water and swimming normally. In the explanation to the clip it says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For everyone that is worried about the goldfish, it survived and was perfectly fine until we fed him and a few of his friends to our turtles. (Which is what they were bought for in the first place!)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am wondering now as to several issues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the goldfish wasn't fed to the turtles and was allowed to live out its life, would it suffer any long term damages from the act?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is time an issue here, if the fish was kept frozen for a longer time, would it suffer more damage and would it be able to be revived?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the size and nature of the fish's body a factor? Would a larger animal or an animal with better resistance to frost that would take more time to completely freeze have damage due to gradual freezing of body and systems?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the fact that fish have cold blood affect the result of the experiment?&lt;/p&gt;&#xA;" OwnerUserId="680" LastEditorUserId="680" LastEditDate="2012-10-31T18:48:49.153" LastActivityDate="2015-02-25T23:51:14.707" Title="Fish &quot;coming back to life&quot; after being frozen" Tags="&lt;zoology&gt;&lt;experimental&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1662" PostTypeId="1" AcceptedAnswerId="5062" CreationDate="2012-04-04T13:52:28.170" Score="3" ViewCount="305" Body="&lt;p&gt;It's spring. The time of year that trees start to leaf out. I have been watching them, and noticed an interesting pattern. The unhealthy trees of a species leafs out first. I've noticed this especially with the wild black cherries. The hollow and damaged trees and the ones in poor conditions leaf out a week ahead of the good ones. The last ones to leaf out are the strongest in the area. This is not just a casual observation, and I have kept careful track of it. What causes this?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2012-04-05T01:21:10.303" LastActivityDate="2012-10-29T15:43:36.607" Title="Why do the sick and unhealthy trees leaf out first in spring?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="1663" PostTypeId="1" CreationDate="2012-04-04T18:34:17.303" Score="6" ViewCount="1844" Body="&lt;p&gt;Please see comments as to the appropriateness of this question on biology SE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All known life on Earth is made up of cells. It is thus safe to say that all known life is &lt;em&gt;characterized&lt;/em&gt; by the presence of cells. But is having cells as a basic unit a &lt;strong&gt;requirement&lt;/strong&gt; for life? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm thus asking if life is currently existent and/or possible without biomembranes, and to what degree cells actually matter in our present understanding of life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An all-encompassing, comprehensive and cited answer would be very much appreciated.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-04-05T17:13:55.357" LastActivityDate="2012-04-06T12:51:27.730" Title="Are cells really the basic unit of all life?" Tags="&lt;cell-based&gt;&lt;cell-membrane&gt;" AnswerCount="2" CommentCount="14" ClosedDate="2012-04-06T19:19:29.177" ContentLicense="CC BY-SA 3.0" />
  <row Id="1664" PostTypeId="2" ParentId="1604" CreationDate="2012-04-04T19:51:17.940" Score="6" Body="&lt;p&gt;The main problem with what you are asking is that you want to show effects on vigilance and memory &lt;em&gt;in vitro&lt;/em&gt;. That is just not possible: if you want vigilance and memory you need a live animal, there is no way around it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next point: you have an audience of non scientists, so you can lose them very quickly if you start speaking about NMDA, LTP or similar things without a clear explanation, so start with that: get a nice review (&lt;a href=&quot;http://goo.gl/eW8kl&quot; rel=&quot;nofollow&quot;&gt;Pubmed&lt;/a&gt; is a good start, as always), and give a simple theoretical explanation of one of the mechanisms involved. It is then important to clearly explain the experiment you will perform, and what you are expecting to see in case there is an effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately the best way to see effects on NMDA receptors would be electrophysiology. This is not trivial and, if you have never done it, I would not suggest going that way. However, if you have access to an electrophysiology setup you will most likely have access to someone who uses it, and that could make the experiment for you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not an expert on this topic, but a quick research on Pubmed seems to indicate that alcohol can, for instance, reduce LTP in hippocampal neuron.&#xA;Maybe what you could do is having someone patch hippocampal neurons and show how an LTP protocol is used. You don't necessary have to show them the whole thing (I doubt anyone in a right state of mind would bare to stay until the whole experiment is performed in control condition first, and alcohol later...).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, the results of these experiments are often non obvious to analyse, so you should have some data prepared and analysed earlier and quickly show how analysis is performed, before showing the final results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Calcium imaging experiments could also be used and would probably give results that are easier to understand for a laymen audience.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See for instance Fig. 1 or Fig. 5 of this paper (just the first one I found, there surely are other):&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21664257&quot; rel=&quot;nofollow&quot;&gt;Ethanol alters calcium signaling in axonal growth cones.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2012-04-05T07:51:56.833" LastActivityDate="2012-04-05T07:51:56.833" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1665" PostTypeId="1" AcceptedAnswerId="1783" CreationDate="2012-04-04T20:15:30.830" Score="10" ViewCount="339" Body="&lt;p&gt;Whilst on a recent refresher course it was highlighted that when considering risk of exposure to infection from bodily fluids we should be aware of two distinct risk levels:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;High Risk:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Blood&lt;/li&gt;&#xA;&lt;li&gt;Semen&lt;/li&gt;&#xA;&lt;li&gt;Vaginal Secretions&lt;/li&gt;&#xA;&lt;li&gt;Diarrhea&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Low Risk:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Saliva&lt;/li&gt;&#xA;&lt;li&gt;Vomit&lt;/li&gt;&#xA;&lt;li&gt;Urine&lt;/li&gt;&#xA;&lt;li&gt;CSF (Cerebrospinal fluid) &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Why is it that some bodily fluids are a greater infection risk than others?  Is it related to the fluids themselves or the species of pathogen that are located within them?&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-04-06T17:24:15.017" LastActivityDate="2012-04-12T18:09:25.310" Title="Why are some bodily fluids more of an infection risk than others?" Tags="&lt;pathology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1666" PostTypeId="2" ParentId="1663" CreationDate="2012-04-05T01:02:17.567" Score="3" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Gerald_Joyce&quot; rel=&quot;nofollow&quot;&gt;Gerry Joyce&lt;/a&gt;: &quot;Life is a self-sustained chemical system capable of undergoing Darwinian evolution.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a meta-analysis of 123 definitions of life: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21875147.1&quot; rel=&quot;nofollow&quot;&gt;&quot;Life is metabolizing material informational system with ability of self-reproduction with changes (evolution), which requires energy and suitable environment.&quot;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Alexander_Oparin&quot; rel=&quot;nofollow&quot;&gt;Alexander Oparin&lt;/a&gt;: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21875147.1&quot; rel=&quot;nofollow&quot;&gt;“Any system capable of replication and mutation is alive”.&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At hand are some key elements in order to match these criteria. Maintaining a Darwinian cycle requires replication, mutation, and selection. Thus, we can break down the above into 5 criteria (personal communication with Gerry Joyce).&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Life stores information&lt;/li&gt;&#xA;&lt;li&gt;Life reproduces its information&lt;/li&gt;&#xA;&lt;li&gt;Life alters that information&lt;/li&gt;&#xA;&lt;li&gt;Life does something with that information (uses energy)&lt;/li&gt;&#xA;&lt;li&gt;Life does all of this in a self-sustained manner&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I would point out that the above criteria is quite different from what is currently on &lt;a href=&quot;http://en.wikipedia.org/wiki/Life&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; described by metabolism and homeostasis. There are certainly additional criteria that certainly raise the threshold for what may be considered life. The common discussion revolves around viruses which do many of these things but not in a self-sustained way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question at hand then asks if cells are the minimum unit of life? What makes a cell a cell is that there is &lt;a href=&quot;http://www.mendeley.com/research/the-emergence-of-competition-between-model-protocells/&quot; rel=&quot;nofollow&quot;&gt;compartmentalization&lt;/a&gt;. The underlying reason behind this compartment is due to the necessity of tying the phenotype to the genotype. Paraphrasing using our definition of life, it links the information with the function that the information carries out. In the modern biological scheme, it keeps the proteins (phenotype) with the DNA (genotype).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The necessity of compartmentalization is negated when the phenotype is already linked with the genotype. The most frequent example is RNA where the material that carries the information is also the material that carries out its function. It tend, is reasonable to hypothesize that life can be made entirely with RNA without the need for compartmentalization (although compartmentalization certainly helps see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20659684&quot; rel=&quot;nofollow&quot;&gt;Paegal and Joyce&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16173749&quot; rel=&quot;nofollow&quot;&gt;Chen and Szostak&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recent &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19131595&quot; rel=&quot;nofollow&quot;&gt;experiments&lt;/a&gt; by Gerry Joyce and others have been able to satisfy several of the requirements of life. The have self-replicating RNAs, that store information, that reproduce their information, that introduce alterations to their information, and do it in a self-sustained manner. What Gerry and his colleagues agree on is that their current self-replication Ribozyme system doesn't do anything particularly novel. However, by introducing a larger variety of functional elements to their ribozymes perhaps they will.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-04-06T04:10:13.413" LastActivityDate="2012-04-06T04:10:13.413" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="1668" PostTypeId="1" CreationDate="2012-04-05T02:39:52.247" Score="5" ViewCount="235" Body="&lt;p&gt;And why can some felines roar while others meow?&lt;/p&gt;&#xA;" OwnerUserId="701" LastActivityDate="2012-04-05T18:10:20.540" Title="What evolutionary mechanism caused felines to develop purring?" Tags="&lt;evolution&gt;&lt;zoology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1669" PostTypeId="2" ParentId="1659" CreationDate="2012-04-05T08:31:38.097" Score="8" Body="&lt;p&gt;&lt;strong&gt;In theory&lt;/strong&gt;, having a circadian rhythm should help anticipating daily environmental changes (light, temperature etc.) so that the metabolic performance is maximized.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In practice&lt;/strong&gt;, mice chronically exposed to environmental light-dark cycles with a period length dramatically shorter or longer than that of their circadian clock are prone to become obese. Moreover, animals kept under short cycles die earlier than mice kept under normal or extended cycles. So, chronic circadian disturbance by a shortened light-dark cycle increases mortality (at least in mice). In humans, shift workers are likely the population that is more susceptible to circadian cycle derangements.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ref: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22154820&quot;&gt;Park et al., Neurobiol Aging. 2011&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-04-05T08:31:38.097" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1670" PostTypeId="2" ParentId="1663" CreationDate="2012-04-05T09:44:14.940" Score="1" Body="&lt;p&gt;Life is a physical entity that creates copies of itself,&lt;br&gt;sometimes in a slightly changed form.&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A cell is not the basic unit of a life but a large number of molecules that have bonded together to reap the benefits of specialization.&#xA;Like what is happening today, humans coming together to form a society which collectively starts to function like a single living organism again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So no, a cell is a far cry from being the basic unit of life, it is a very advanced form of life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All it takes for life to start is for a single self replicating molecule to form, that's it.&lt;br&gt;&#xA;Evolution takes over from there.&lt;/p&gt;&#xA;" OwnerUserId="542" LastEditorUserId="542" LastEditDate="2012-04-06T12:51:27.730" LastActivityDate="2012-04-06T12:51:27.730" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1671" PostTypeId="2" ParentId="1668" CreationDate="2012-04-05T10:03:19.040" Score="6" Body="&lt;p&gt;It makes sense that the ability to express your emotions improves the quality of the interaction you have with those around you. If a cat purrs those around it know it's feeling good, which can be useful information for future interaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure there have been cats who had a worse life because they didn't bond as well because they didn't purr, and consequently had a slightly lesser tendency to have their DNA end up in the next generation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This argument goes for every ability to express emotions.&lt;/p&gt;&#xA;" OwnerUserId="542" LastEditorUserId="542" LastEditDate="2012-04-05T18:10:20.540" LastActivityDate="2012-04-05T18:10:20.540" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1672" PostTypeId="2" ParentId="1397" CreationDate="2012-04-05T11:51:01.930" Score="2" Body="&lt;p&gt;The question makes the false assumption that chicken and eggs are different life forms.&lt;br&gt;&#xA;A life form at stage x is not a different life form than that very life form at stage y.&lt;br&gt;&#xA;You might as well ask of which came first, a 7 year old kid or an 8 year old kid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But they are the same thing and therefore this question is invalid.&lt;/p&gt;&#xA;" OwnerUserId="542" LastEditorUserId="542" LastEditDate="2012-04-05T17:57:34.767" LastActivityDate="2012-04-05T17:57:34.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1674" PostTypeId="2" ParentId="884" CreationDate="2012-04-05T12:17:24.773" Score="0" Body="&lt;p&gt;There's a related review paper: &quot;&lt;a href=&quot;http://www.nature.com/nrg/journal/v12/n7/full/nrg3028.html&quot; rel=&quot;nofollow&quot;&gt;Beyond DNA: integrating inclusive inheritance into an extended theory of evolution&lt;/a&gt;&quot; (&lt;a href=&quot;http://champagnelab.psych.columbia.edu/docs/ChampagneNR.pdf&quot; rel=&quot;nofollow&quot;&gt;PDF&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-04-05T12:17:24.773" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1675" PostTypeId="1" AcceptedAnswerId="26241" CreationDate="2012-04-05T13:13:36.990" Score="14" ViewCount="285" Body="&lt;p&gt;From a J. Neil Schulman article on &lt;a href=&quot;http://jneilschulman.rationalreview.com/2010/01/classic-j-neil-when-clones-are-outlawed-only-outlaws-will-have-clones/&quot;&gt;Organ Cloning&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cannibalizing organs from other people also entails the risk of&#xA;  rejection because of incompatibilities, not only for tissue-typing but&#xA;  also for gross anatomical mismatches. Cloning organs [...] has the&#xA;  potential of taking a human being's own genetic material and growing&#xA;  perfect replacement organs which are fully compatible with their&#xA;  genetic makeup.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The reason for using a person's own DNA, is obviously to avoid an allergic reaction to the antigen markers on a strange organ. But in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood_type&quot;&gt;blood typing system&lt;/a&gt;, there exist types which &lt;em&gt;don't&lt;/em&gt; have any trouble-making antigens (such as type O-negative, called a &quot;Universal Donor&quot;).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Would it be possible to grow an analogous &quot;universal&quot; internal organ, which didn't have any antigens indicating it was a foreign body? (By editing a DNA sample to remove certain expressed proteins, then growing it into an organ.)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I realize this is technically a science-fiction question :) But - A: it may not be in the near future, and B: I can rephrase it to remove the SF component:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the blood-typing system, the AB antigens don't appear necessary for proper functioning of red blood cells - are the antigens on a person's own cells, actually &lt;em&gt;needed&lt;/em&gt; for any essential functions, or could they be removed, without affecting that person's health?&lt;/p&gt;&#xA;" OwnerUserId="704" LastEditorUserId="69" LastEditDate="2012-04-05T14:46:46.193" LastActivityDate="2014-12-28T18:18:23.860" Title="Organ cloning - possible to make a non-antigenic organ?" Tags="&lt;immunology&gt;&lt;organs&gt;&lt;cloning&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1676" PostTypeId="1" AcceptedAnswerId="1678" CreationDate="2012-04-05T14:54:10.983" Score="8" ViewCount="203" Body="&lt;p&gt;I'm reading &lt;a href=&quot;http://prl.aps.org/pdf/PRL/v92/i3/e038102&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper about how neurons can connect. Wikipedia says, typically neurons connect via axon (transmitter) and dendrites (receiver) but there are also special cases where dendrites connect with dendrites, axons with with another axon, neurons with no axon etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now in the paper they refer to the soma-soma paired neurons and their strength of their cholinergic synapse.&#xA;Does that now mean that they neurons do directly interact via their soma? If so, how much different is that process to the generic axon-&gt;dendrite pathway?&lt;/p&gt;&#xA;" OwnerUserId="705" LastEditorUserId="5427" LastEditDate="2016-01-09T04:55:55.783" LastActivityDate="2016-01-09T04:55:55.783" Title="Soma-soma paired neurons" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1677" PostTypeId="1" CreationDate="2012-04-05T16:38:36.870" Score="5" ViewCount="248" Body="&lt;p&gt;I want to evaluate the level of gene expression by real-time PCR.  I have five controls that are &quot;clinically&quot; the same. I calculated the &quot;fold change&quot; of the target gene regarding each control.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What if the result of &quot;fold change&quot; for my target gene is different for each control? I mean it is up regulated according to three of them and down-regulated according to the rest two. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the intervention biased? Or should I consider the average?&lt;/p&gt;&#xA;" OwnerUserId="706" LastEditorUserId="6" LastEditDate="2012-04-05T16:51:48.380" LastActivityDate="2012-11-27T17:32:15.027" Title="Analysing the results of real-time PCR" Tags="&lt;pcr&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1678" PostTypeId="2" ParentId="1676" CreationDate="2012-04-05T17:44:18.617" Score="8" Body="&lt;p&gt;Yep, the soma-soma synapse in that paper appears to be a chemical synapse between two cell bodies. There are no axons or dendrites in that preparation so the synapse &lt;em&gt;must&lt;/em&gt; be between the somas. They are using two snail neurons that are far from each other (in different ganglia) &lt;em&gt;in vivo&lt;/em&gt;, but which are known to synapse. This &lt;em&gt;in vivo&lt;/em&gt; synapse is long-range and so must be mediated by an axon. In the dish, they can encourage the  synapse to form even without encouraging axons and dendrites to grow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that this is an artificial &lt;em&gt;in vitro&lt;/em&gt; preparation and they are, in some sense, forcing a synapse to occur in an unusual way in a cell culture dish. They do this because it makes it easy to study certain aspects of the signalling mechanisms for generating synapses. In your paper, they appear to be using it as an easy preparation for a proof of principle for the interface between a biological neuron and a non-biological semiconductor substrate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper you cited references this paper that outlines the soma-soma preparation with a pretty picture to make things clear: &lt;a href=&quot;http://www.jneurosci.org/content/19/21/9306&quot;&gt;http://www.jneurosci.org/content/19/21/9306&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="72" LastActivityDate="2012-04-05T17:44:18.617" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1680" PostTypeId="1" CreationDate="2012-04-05T20:44:23.357" Score="6" ViewCount="19388" Body="&lt;p&gt;Protein migrate differently in &lt;a href=&quot;http://en.wikipedia.org/wiki/Bis-tris_methane&quot; rel=&quot;nofollow&quot;&gt;Bis-Tris&lt;/a&gt; and Tris-Glycine gels. I was curious about the actual reasons why. Do certain gel systems result in a tighter resolution than others?&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-04-06T03:33:12.493" LastActivityDate="2012-09-13T17:12:14.447" Title="How do SDS-PAGE gels differ in a Bis-Tris system vs. a Tris-Glycine system?" Tags="&lt;gel-electrophoresis&gt;&lt;sds-page&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1681" PostTypeId="1" AcceptedAnswerId="2265" CreationDate="2012-04-05T20:47:22.570" Score="7" ViewCount="10747" Body="&lt;p&gt;My gels look significantly different in &lt;a href=&quot;http://en.wikipedia.org/wiki/MES_%28buffer%29&quot;&gt;MES&lt;/a&gt; (2-(N-morpholino)ethanesulfonic acid) and &lt;a href=&quot;http://en.wikipedia.org/wiki/MOPS&quot;&gt;MOPS&lt;/a&gt; (3-(N-morpholino)propanesulfonic acid). That is to be expected. What I don't understand is why the simple presence of the counter-ion significantly changes the velocity of certain proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this due to the different pH (MES is usually run at pH 8.0, MOPS is usually run at pH 7.0) or is the charge distribution on the counter-ion responsible for everything?&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-04-06T03:29:44.057" LastActivityDate="2012-05-15T00:13:44.480" Title="How do Proteins migrate in MES vs. MOPS" Tags="&lt;gel-electrophoresis&gt;&lt;sds-page&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1683" PostTypeId="1" AcceptedAnswerId="1689" CreationDate="2012-04-06T16:23:12.917" Score="7" ViewCount="282" Body="&lt;p&gt;I would like to conduct a simple dimerization experiment for some protein I'm collecting from a cultured cells. My thought is, that if I'm running a non-reducing, denaturing PAGE gel, then removing beta-mercaptoethanol/DTT from the sample buffer should be enough to allow di-sulfide bonds to form.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have seen several authors incubate the cells first with a drug called BSS that diffuses across membranes and creates protein cross-links. I may be wrong, but the use of this drug seems more appropriate when trying to follow up with an immunoprecipitation or a pull-down assay.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If anyone has any experience with this, could you please enlighten me?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-07T01:59:27.127" Title="When collecting cell lysates for a Western blot, how do I induce di-sulfide bonds?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1684" PostTypeId="5" CreationDate="2012-04-06T17:05:50.217" Score="0" Body="&lt;p&gt;The tag &lt;strong&gt;metabolism&lt;/strong&gt; can be used for questions concerning the biochemical reactions or the sequence of such reactions that are referred to as metabolic pathways. The emphasis of these questions will be on molecular processes. However the tag is also used for questions relating to the physiology of the whole organism, for example the effect of diet on the basal metabolic rate.&lt;/p&gt;&#xA;" OwnerUserId="16299" LastEditorUserId="16866" LastEditDate="2019-12-13T04:25:31.893" LastActivityDate="2019-12-13T04:25:31.893" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="1685" PostTypeId="4" CreationDate="2012-04-06T17:05:50.217" Score="0" Body="Metabolism is the set of defined biochemical transformations occurring within the cells of living organisms. " OwnerUserId="307" LastEditorUserId="16866" LastEditDate="2019-12-13T04:25:31.893" LastActivityDate="2019-12-13T04:25:31.893" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="1686" PostTypeId="1" AcceptedAnswerId="3042" CreationDate="2012-04-06T17:25:41.643" Score="11" ViewCount="54425" Body="&lt;p&gt;In practice, when you have vasoconstriction of the glomerular capillaries and subsequently an increase in blood pressure, glomerular filtration rate increases. However, this seems counterintuitive to Bernoulli's principle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;During vasoconstriction, because the radii of the capillaries are getting smaller, we should expect an increase in flow rate and blood velocity. According to Bernoulli's principle, the outward hydrostatic pressure should drop. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this lead to an increase in filtration rate?&lt;/p&gt;&#xA;" OwnerUserId="177" LastEditorUserId="57" LastEditDate="2012-07-28T05:00:02.093" LastActivityDate="2018-09-11T21:44:55.917" Title="Glomerular Filtration Rate" Tags="&lt;homeostasis&gt;&lt;renal-physiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1687" PostTypeId="2" ParentId="1521" CreationDate="2012-04-06T17:45:18.327" Score="5" Body="&lt;p&gt;A heterokaryon is a fungal cell which has &lt;em&gt;two or more genetically-distinct but allelically-compatible nuclei&lt;/em&gt;, as suggested by &lt;a href=&quot;http://crosswords911.com/heterokaryon.jsp?q=aHR0cDovL3d3dy5lYmkuYWMudWsvaW50ZXJwcm8vSUVudHJ5P2FjPUlQUjAxMDgxNg==&quot; rel=&quot;nofollow&quot;&gt;this resource&lt;/a&gt;, as well as &lt;a href=&quot;https://en.wikipedia.org/wiki/Heterokaryosis&quot; rel=&quot;nofollow&quot;&gt;this Wikipedia article&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A dikaryon is a fungal cell which has &lt;em&gt;precisely two genetically-distinct but allelically-compatible nuclei&lt;/em&gt;, as shown &lt;a href=&quot;http://www.fungionline.org.uk/7sexual/5dikaryon.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.ucmp.berkeley.edu/glossary/glossary_4.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this sense,  a heterokaryon is a general term, whereas a dikaryon is a specific term. A dikaryon and a trikaryon (although not often seen in literature) are both heterokaryons.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-04-06T22:03:25.843" LastActivityDate="2012-04-06T22:03:25.843" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1688" PostTypeId="1" CreationDate="2012-04-06T21:15:17.557" Score="7" ViewCount="497" Body="&lt;p&gt;I'm working with murine B-cells. The general protocol is to keep cells on ice to keep them from dying but I've noticed that it makes these cells aggregate and precipitate out. I've heard suggestions that these cells should just be kept at room temperature. How would I be able to determine which conditions at which I should be keeping my cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was trying to collect cells to prepare them for cell binding studies to antibodies and then assess the cells on a filterplate. Typically, you keep them on ice to pause the metabolic state as well as to prevent endocytosis of the bound molecules. However, that shift seems to cause settling. How do you troubleshoot the appropriate temperature to process cells and what are the usual scientific justification for making such decisions.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2015-02-06T22:53:58.233" LastActivityDate="2015-02-07T17:17:05.607" Title="What temperature should mammalian B-Cells be stored at outside of the incubator?" Tags="&lt;cell-culture&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1689" PostTypeId="2" ParentId="1683" CreationDate="2012-04-06T21:20:31.263" Score="4" Body="&lt;p&gt;For the introduction of new cystine bonds, you will probably need to maintain an appropriate redox potential when dialyzing your cell-lysate to allow your cystine bonds to reform. To break the current di-sulfide bonds, we have been adding in Disulfide Bond Isomerases (DsBC to be precise) which will allow your lysate to get to an appropriate equilibrium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for examining for disulfide bond formation that has already occured between proteins in your lysate, removing reducing equivalents like DTT and beta-mercaptoethanol should do the trick. You can even denature your proteins by incubating them in LDS or Laemmli buffer at 90C as those components will not reduce your cystine bonds. In our experience the bands typically run at the expected molecular weight on a SDS-PAGE.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-04-07T01:59:27.127" LastActivityDate="2012-04-07T01:59:27.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1690" PostTypeId="1" AcceptedAnswerId="1691" CreationDate="2012-04-06T21:51:37.683" Score="6" ViewCount="1251" Body="&lt;p&gt;I'm never going to run these type of experiments but I do need to have a good idea of their timescale. After I fix my cells, if I stained my cells with histology stains like DAPI, Fluorescein, and various labeled antibodies, how long do I have to wait before I can examine my cells with microscopy?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-04-07T00:26:49.347" Title="How long does it take to stain cells?" Tags="&lt;staining&gt;&lt;fluorescent-microscopy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1691" PostTypeId="2" ParentId="1690" CreationDate="2012-04-07T00:26:49.347" Score="6" Body="&lt;p&gt;For fluorescence immunocytochemistry, there are 3 main incubations that determine duration of the procedure. Generally it takes 2 days to stain your cells before you can visualize them. Once cells or tissue are fixed onto glass, you first incubate with a primary antibody to directly target a specific antigen(s), usually overnight. After primary labelling, a secondary antibody is applied to target the primary antibody, which usually takes a few hours. These secondary antibodies come conjugated to some fluorescent dye (Cy5, TRITC, FITC, AlexaFluors, etc). A nuclear counterstain is really quick, only 5 minutes. After all the labelling and nuclear stain, you can mount the coverslip with mounting media and once it cures you can visualize them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abcam has one of many quick &lt;a href=&quot;http://www.abcam.com/index.html?pageconfig=resource&amp;amp;rid=11459&quot;&gt;reference guides&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-07T00:26:49.347" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1692" PostTypeId="5" CreationDate="2012-04-07T01:42:50.080" Score="0" Body="&lt;p&gt;The scientific study of the structure and function of genes at the molecular level, particularly chromosomes and DNA.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-27T09:25:22.460" LastActivityDate="2017-03-27T09:25:22.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1693" PostTypeId="4" CreationDate="2012-04-07T01:42:50.080" Score="0" Body="The scientific study of the structure and function of genes at the molecular level, particularly chromosomes and DNA." OwnerUserId="307" LastEditorUserId="4101" LastEditDate="2013-10-25T21:50:57.587" LastActivityDate="2013-10-25T21:50:57.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1694" PostTypeId="5" CreationDate="2012-04-07T01:45:00.983" Score="0" Body="&lt;p&gt;Questions could include those that focus on the biology of reproduction, asexual and sexual reproduction, reproductive strategy, reproductive physiology and anatomy and physiology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Related: &lt;a href=&quot;/questions/tagged/sexual-reproduction&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;sexual-reproduction&amp;#39;&quot; rel=&quot;tag&quot;&gt;sexual-reproduction&lt;/a&gt; &lt;a href=&quot;/questions/tagged/asexual-reproduction&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;asexual-reproduction&amp;#39;&quot; rel=&quot;tag&quot;&gt;asexual-reproduction&lt;/a&gt; &lt;a href=&quot;/questions/tagged/pollination&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;pollination&amp;#39;&quot; rel=&quot;tag&quot;&gt;pollination&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="16866" LastEditDate="2019-08-25T03:40:31.463" LastActivityDate="2019-08-25T03:40:31.463" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="1695" PostTypeId="4" CreationDate="2012-04-07T01:45:00.983" Score="0" Body="The biological process by which new individuals are formed." OwnerUserId="307" LastEditorUserId="4101" LastEditDate="2013-10-29T20:50:27.130" LastActivityDate="2013-10-29T20:50:27.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1696" PostTypeId="5" CreationDate="2012-04-07T01:46:40.043" Score="0" Body="&lt;p&gt;Any biological process which displays an endogenous, entrainable oscillation of time.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-29T14:00:03.817" LastActivityDate="2017-03-29T14:00:03.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1697" PostTypeId="4" CreationDate="2012-04-07T01:46:40.043" Score="0" Body="Any biological process which displays an endogenous, entrainable oscillation of time." OwnerUserId="307" LastEditorUserId="4101" LastEditDate="2013-10-31T01:04:26.140" LastActivityDate="2013-10-31T01:04:26.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1698" PostTypeId="5" CreationDate="2012-04-07T01:48:40.290" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-04-07T01:48:40.290" LastActivityDate="2012-04-07T01:48:40.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1699" PostTypeId="4" CreationDate="2012-04-07T01:48:40.290" Score="0" Body="The biological process characterized by reversible unconsciousness, unresponsiveness to external stimuli and motor passivity." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-04-07T09:34:05.293" LastActivityDate="2012-04-07T09:34:05.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1700" PostTypeId="5" CreationDate="2012-04-07T01:49:53.753" Score="0" Body="&lt;p&gt;The contractile tissue of animals derived from the mesodermal layer of embryonic germ cells.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-27T12:19:18.070" LastActivityDate="2017-03-27T12:19:18.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1701" PostTypeId="4" CreationDate="2012-04-07T01:49:53.753" Score="0" Body="The contractile tissue of animals derived from the mesodermal layer of embryonic germ cells." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-04-07T09:33:41.563" LastActivityDate="2012-04-07T09:33:41.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1702" PostTypeId="5" CreationDate="2012-04-07T01:51:40.350" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-04-07T01:51:40.350" LastActivityDate="2012-04-07T01:51:40.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1703" PostTypeId="4" CreationDate="2012-04-07T01:51:40.350" Score="0" Body="The scientific study of short- and long-term changes in the size and age composition of populations and the processes driving these changes." OwnerUserId="307" LastEditorUserId="4101" LastEditDate="2013-10-31T18:05:13.603" LastActivityDate="2013-10-31T18:05:13.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1704" PostTypeId="5" CreationDate="2012-04-07T01:52:30.333" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-04-07T01:52:30.333" LastActivityDate="2012-04-07T01:52:30.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1705" PostTypeId="4" CreationDate="2012-04-07T01:52:30.333" Score="0" Body="Nerves that emerge directly from the brain." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-04-07T09:32:22.843" LastActivityDate="2012-04-07T09:32:22.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1706" PostTypeId="5" CreationDate="2012-04-07T01:54:03.187" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-04-07T01:54:03.187" LastActivityDate="2012-04-07T01:54:03.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1707" PostTypeId="4" CreationDate="2012-04-07T01:54:03.187" Score="0" Body="Escherichia coli, a gram-negative, rod-shaped bacterium commonly found in the lower intestines of warm-blooded animals.  Used extensively in laboratory research." OwnerUserId="307" LastEditorUserId="4101" LastEditDate="2013-10-31T14:04:14.273" LastActivityDate="2013-10-31T14:04:14.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1708" PostTypeId="5" CreationDate="2012-04-07T01:55:15.930" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-04-07T01:55:15.930" LastActivityDate="2012-04-07T01:55:15.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1709" PostTypeId="4" CreationDate="2012-04-07T01:55:15.930" Score="0" Body="The laboratory technique involving the extraction of DNA from a cell in a pure form." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-04-07T09:32:29.180" LastActivityDate="2012-04-07T09:32:29.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1710" PostTypeId="5" CreationDate="2012-04-07T01:57:18.987" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-04-07T01:57:18.987" LastActivityDate="2012-04-07T01:57:18.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1711" PostTypeId="4" CreationDate="2012-04-07T01:57:18.987" Score="0" Body="The scientific study of inheritance as it occurs specifically in human beings." OwnerUserId="307" LastEditorUserId="69" LastEditDate="2012-04-07T09:32:54.997" LastActivityDate="2012-04-07T09:32:54.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1712" PostTypeId="5" CreationDate="2012-04-07T01:58:34.257" Score="0" Body="&lt;p&gt;The scientific study of the origin, evolution, distribution, and future of life in the universe.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-27T12:18:41.210" LastActivityDate="2017-03-27T12:18:41.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1713" PostTypeId="4" CreationDate="2012-04-07T01:58:34.257" Score="0" Body="The scientific study of the origin, evolution, distribution, and future of life in the universe." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-04-07T09:30:10.850" LastActivityDate="2012-04-07T09:30:10.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1714" PostTypeId="5" CreationDate="2012-04-07T02:00:06.657" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-04-07T02:00:06.657" LastActivityDate="2012-04-07T02:00:06.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1715" PostTypeId="4" CreationDate="2012-04-07T02:00:06.657" Score="0" Body="The production and emission of light by a living organism." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-04-07T09:31:08.930" LastActivityDate="2012-04-07T09:31:08.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1717" PostTypeId="5" CreationDate="2012-04-07T02:00:43.583" Score="0" Body="&lt;p&gt;Eukaryotic chromosomes are often linear while prokaryotic chromosomes are usually circular, with individual chromosome sizes varying widely.&lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="4101" LastEditDate="2013-10-31T00:51:52.613" LastActivityDate="2013-10-31T00:51:52.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1718" PostTypeId="4" CreationDate="2012-04-07T02:00:43.583" Score="0" Body="A single piece of DNA coiled and organized along with RNA and proteins found in the cell." OwnerUserId="307" LastEditorUserId="4101" LastEditDate="2013-10-31T00:50:52.950" LastActivityDate="2013-10-31T00:50:52.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1719" PostTypeId="5" CreationDate="2012-04-07T02:01:55.983" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-04-07T02:01:55.983" LastActivityDate="2012-04-07T02:01:55.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1720" PostTypeId="4" CreationDate="2012-04-07T02:01:55.983" Score="0" Body="The field of biology that examines periodic phenomena in living organisms and their adaption to solar and lunar related rhythms." OwnerUserId="307" LastEditorUserId="69" LastEditDate="2012-04-07T09:32:01.097" LastActivityDate="2012-04-07T09:32:01.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1722" PostTypeId="2" ParentId="681" CreationDate="2012-04-07T08:24:35.830" Score="15" Body="&lt;p&gt;I wanted to add a little more to the excellent answer above, especially since the OP asks about research into this question in a &quot;real-world context&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a substantial body of evidence on exactly this question that comes from experiments at &quot;Free Air CO&lt;sub&gt;2&lt;/sub&gt; Enrichment&quot; (&lt;a href=&quot;http://www.bnl.gov/face/faceProgram.asp&quot;&gt;FACE&lt;/a&gt;) sites. FACE is an experimental method/technology in which standing ecosystems undergo CO&lt;sub&gt;2&lt;/sub&gt; enrichment without (much) disturbance to the ecosystem. It has been known that higher CO&lt;sub&gt;2&lt;/sub&gt; increases plant growth since the 1960s or so, but the motivation for FACE was to understand what the long-term and ecosystem scale effects of rising CO&lt;sub&gt;2&lt;/sub&gt; in the atmosphere would be. Many different ecosystem types (forests, crops, shrublands, etc) have been studied with this technique to date, some for fairly long periods of time. I think that  many of these sites are now being shut down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some key findings:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Net primary production (Plant C assimilation - Respiration) generally increased for plant species, but increases in productivity varied a lot between ecosystem types.&lt;/li&gt;&#xA;&lt;li&gt;This increase in productivity diminished over time, an effect that was largely mediated by changes in plant N availability.&lt;/li&gt;&#xA;&lt;li&gt;Different plant functional types show different responses. For example, herbaceous species saw less enhancement of assimilation (due to a decrease in leaf N) compared to woody plants at some sites.&lt;/li&gt;&#xA;&lt;li&gt;At the ecosystem level, primary production is often limited by factors other than available CO&lt;sub&gt;2&lt;/sub&gt; - nitrogen or water for example.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are a couple of excellent reviews available:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Nowak, R. S., Ellsworth, D. S. and Smith, S. D. (2004), Functional responses of plants to elevated atmospheric CO2– do photosynthetic and productivity data from FACE experiments support early predictions?. New Phytologist, 162: 253–280. doi: 10.1111/j.1469-8137.2004.01033.x &lt;a href=&quot;http://www.bnl.gov/face/pdfs/Nowak.pdf&quot;&gt;pdf&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Norby, R. J. and Zak, D. R. (2011), Ecological Lessons from Free-Air CO2 Enrichment (FACE) Experiments. Annual Review of Ecology, Evolution, and Systematics, 42: 181-203. doi: 10.1146/annurev-ecolsys-102209-144647 &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev-ecolsys-102209-144647&quot;&gt;link&lt;/a&gt;. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This article discusses the importance of nitrogen in limiting forest productivity under high CO&lt;sub&gt;2&lt;/sub&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Norby, R.J., Warren, J. M., Iversen, C. M., Medlyn, B. E., and McMurtrie, R. E. (2010), CO2 enhancement of forest productivity constrained by limited nitrogen availability. PNAS, 107 (45) 19368-19373. doi:10.1073/pnas.1006463107 &lt;a href=&quot;http://www.pnas.org/content/107/45/19368.short&quot;&gt;link&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="649" LastEditorUserId="649" LastEditDate="2012-04-20T20:05:32.997" LastActivityDate="2012-04-20T20:05:32.997" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1724" PostTypeId="1" CreationDate="2012-04-07T19:52:31.990" Score="44" ViewCount="54221" Body="&lt;p&gt;We touched on introns and exons in my bio class, but unfortunately we didn't really talk about why Eukaryotes have introns. It would seem they would have to have some purpose since prokaryotes do not have them and they evolved first chronologically, but I could easily be wrong. Did the junk sections of DNA just evolve there by some sort of randomness or necessity as opposed to an actual evolutionary advantage? Why hasn't evolution stopped us from having introns since they seem to be a 'waste' of time and DNA? Why do prokaryotes not have introns? &lt;/p&gt;&#xA;" OwnerUserId="62" LastEditorUserId="43" LastEditDate="2012-04-08T02:34:54.333" LastActivityDate="2017-11-05T20:36:06.447" Title="Why do eukaryotic organisms have introns in their DNA?" Tags="&lt;evolution&gt;&lt;dna&gt;&lt;rna&gt;&lt;molecular-genetics&gt;&lt;introns&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1725" PostTypeId="2" ParentId="1724" CreationDate="2012-04-08T02:33:00.063" Score="34" Body="&lt;p&gt;There is still a lot to be learned about the roles introns play in biological processes, but there are a couple of things that have been pretty well established.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Introns enable &lt;strong&gt;alternative splicing&lt;/strong&gt;, which enables a single gene to encode multiple proteins that perform different functions under different conditions. For example, a signal the cell receives could cause an exon that is normally included to be skipped, or an intron that is normally spliced out to be left in for translation (the &lt;a href=&quot;http://en.wikipedia.org/wiki/Alternative_splicing#Modes&quot;&gt;Wikipedia article&lt;/a&gt; on the subject has a basic overview of the possibilities). This would not be possible, or at least would be much more difficult, without the presence of introns.&lt;/li&gt;&#xA;&lt;li&gt;In recent years, we have discovered that RNA molecules (especially &lt;strong&gt;small RNAs&lt;/strong&gt; such as siRNAs and miRNAs) are much more involved in regulating gene expression than previously thought. Often the small regulatory RNAs are derived from spliced introns.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There is probably more, but essentially introns enable a finer level of regulatory control. Biological complexity is often not the result of having a larger complement of genes, but of having additional layers of regulation to turn genes on and off at the right times. Prokaryotic genes are often organized into operons, and a single polycistronic mRNA will often encode multiple proteins from multiple adjacent genes. Since the biological processes required to sustain microbial life are much less complicated than those required to sustain eukaryotic life, they can get away with much less regulatory control.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-04-08T02:33:00.063" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1726" PostTypeId="1" CreationDate="2012-04-09T03:22:54.267" Score="5" ViewCount="1076" Body="&lt;p&gt;I've searched everywhere.&lt;br&gt;&#xA;No Wikipedia page.&lt;br&gt;&#xA;No information on NCBI.&lt;br&gt;&#xA;I searched all occurrences of 34/70 in some primary research articles!&lt;br&gt;&#xA;The best I've found is &lt;a href=&quot;http://www.homebrewtalk.com/f163/weihenstephen-saflager-w34-70-a-318941/&quot;&gt;this brewery forum&lt;/a&gt; where someone asked the same question.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And the user rockfish42  answered:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;No idea why they use that number, but it's the catalog number at&#xA;  Weihenstephan's hefebank.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="719" LastEditorUserId="69" LastEditDate="2013-02-21T01:20:39.253" LastActivityDate="2013-02-21T01:20:39.253" Title="What does the 34/70 in Saccharomyces pastorianus Weihenstephan 34/70 stand for?" Tags="&lt;microbiology&gt;&lt;taxonomy&gt;&lt;nomenclature&gt;&lt;yeast&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1727" PostTypeId="2" ParentId="1726" CreationDate="2012-04-09T08:09:46.580" Score="3" Body="&lt;p&gt;I am not sure why you say there is no information... a quick Google search returned a few interesting pages...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18772282&quot; rel=&quot;nofollow&quot;&gt;Progress in Metabolic Engineering of Saccharomyces cerevisiae&lt;/a&gt; - Nevoigt, Microbiol Mol Biol Rev. 2008 &lt;/p&gt;&#xA;&#xA;&lt;p&gt;the author says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The identification of the entire genomic sequence of a commonly used lager brewer's yeast strain, i.e., Weihenstephan Nr. 34 (34/70), represents a breakthrough in the molecular analysis of lager brewer's yeast.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, it would look like 34/70 is just a catalogue number, with no specific meaning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Curiously, according to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Saccharomyces_pastorianus&quot; rel=&quot;nofollow&quot;&gt;Wikipedia page&lt;/a&gt; on &lt;em&gt;Saccharomyces pastorianus&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;S. pastorianus&lt;/em&gt; never grows above 34 °C (93 °F)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, I cannot exclude the hypothesis that 34 could come from there although, well, I personally propend for the catalogue number.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other interesting links:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper about the &lt;em&gt;S. pastorianus&lt;/em&gt; genome sequencing:&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19261625&quot; rel=&quot;nofollow&quot;&gt;Genome sequence of the lager brewing yeast, an interspecies hybrid.&lt;/a&gt; - Nakao et al., DNA Res. 2009&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An article comparing two different strains of &lt;em&gt;S. pastorianus&lt;/em&gt;, 34/70 and 34/78 (again, catalog number hypothesis seems to be the most obvious explanation)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16491465&quot; rel=&quot;nofollow&quot;&gt;Molecular species of phosphatidylethanolamine from continuous cultures of Saccharomyces pastorianus syn. carlsbergensis strains.&lt;/a&gt; - Tosch, Yeast. 2006&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/taxonomy/?term=520522&quot; rel=&quot;nofollow&quot;&gt;NCBI taxonomy page&lt;/a&gt; (entry #520522)&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-04-09T08:09:46.580" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1728" PostTypeId="2" ParentId="1726" CreationDate="2012-04-09T13:11:52.983" Score="6" Body="&lt;p&gt;I went to the &lt;a href=&quot;http://www.hefebank-weihenstephan.de/staemme.html&quot;&gt;Yeastbank website&lt;/a&gt; at Weihenstephan for some info. The keyword here is &quot;Stamm,&quot; which is German for stem, clade, clan, or strain. So, I would take this to mean that the 34/70 is an isolate (#70) of strain 34. Two of 34/70's strengths, according to the link above are it makes clean beer and gives a pleasant taste profile due to its low yeast-like aroma in the finished beer. I can attest to that firsthand, having had on numerous occasions the pleasure of partaking of &lt;a href=&quot;http://www.weihenstephaner.de/&quot;&gt;Weihenstephaner&lt;/a&gt; beer in its home city of Freising.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-04-09T13:11:52.983" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1729" PostTypeId="2" ParentId="894" CreationDate="2012-04-09T16:56:33.290" Score="8" Body="&lt;p&gt;You may be interested in &lt;a href=&quot;http://www.talkdesign.org/faqs/flagellum.html&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; paper and a &lt;a href=&quot;http://www.youtube.com/watch?v=SdwTwNPyR9w&quot; rel=&quot;noreferrer&quot;&gt;video&lt;/a&gt; that summarizes it. It seems to be made quite clear that 1) effectively all of the parts of the flagellum are not original to it, and 2) there is a reasonable evolutionary path (one involving only increment/refine steps) that could have been responsible for it.&lt;/p&gt;&#xA;&lt;p&gt;The video mentions but doesn't describe experiments that were in support of the proposed model. I assume they might involve refinement or statistical issues of the environment, &lt;em&gt;not&lt;/em&gt; the  whole-thing-at-once as Behe outlines. Obviously, if you can show that each step is independently adaptive, then the whole chain is shown to be possible evolutionarily, without trying to set up an experiment where you win the lottery &lt;em&gt;n&lt;/em&gt; times simultaneously.&lt;/p&gt;&#xA;&lt;p&gt;Personally I think the fact that the most awesome thing about the flagellum -- the rotation -- already exists in ATP synthase steals a lot of the flagellum's thunder. :)&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt; (Douglas S. Stones):  Following the above references led me to this paper:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;M.J. Pallen, N.J. Matzke &amp;quot;From &lt;em&gt;The Origin of Species&lt;/em&gt; to the origin of bacterial flagella&amp;quot; Nature Reviews Microbiology 4 (2006), 784-790. (&lt;a href=&quot;http://home.planet.nl/%7Egkorthof/pdf/Pallen_Matzke.pdf&quot; rel=&quot;noreferrer&quot;&gt;pdf&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;In this article the authors discuss the possibility of designing a lab experiment to reproduce (steps of) the evolution of the flagellum.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Scott_Minnich&quot; rel=&quot;noreferrer&quot;&gt;Scott Minnich&lt;/a&gt; speculated in his testimony that studies on flagellar&#xA;evolution need not be restricted to sequence analysis or theoretical&#xA;models, but that instead this topic could become the subject of&#xA;laboratory-based experimental studies. But obviously, one cannot&#xA;model millions of years of evolution in a few weeks or months.&lt;/p&gt;&#xA;&lt;p&gt;So how&#xA;might such studies be conducted? One option might be to look back in&#xA;time. It is feasible to use phylogenetic analyses to reconstruct&#xA;plausible ancestral sequences of modern-day proteins, and then&#xA;synthesize and investigate these ancestral proteins. Proof of&#xA;principle for this approach has already been demonstrated on several&#xA;NF proteins[69–75]. Similar studies could recreate plausible ancestors&#xA;for various flagellar components (for example, the common ancestor of&#xA;flagellins and HAP3 proteins). These proteins could then be reproduced&#xA;in the laboratory in order to examine their properties (for example,&#xA;how well they self-assemble into filaments and what those filaments&#xA;look like).&lt;/p&gt;&#xA;&lt;p&gt;An alternative, more radical, option would be to model&#xA;flagellar evolution prospectively, for example, by creating random or&#xA;minimally constrained libraries and then iteratively selecting&#xA;proteins that assemble into ever more sophisticated artificial&#xA;analogues of the flagellar filament.&lt;/p&gt;&#xA;&lt;p&gt;Another experimental option might&#xA;be to investigate the environmental conditions that favour or&#xA;disfavour bacterial motility. The fundamental physics involved&#xA;(diffusion due to Brownian motion) is mathematically tractable, and&#xA;has already been used to predict, for example, that powered motility&#xA;is useless in very small bacteria[76,77].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;[For readability, I've added some line breaks to the above.  There's too many cited references to list them all.]&lt;/p&gt;&#xA;" OwnerUserId="722" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-04-10T10:38:08.023" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1730" PostTypeId="1" AcceptedAnswerId="1743" CreationDate="2012-04-09T19:07:44.737" Score="4" ViewCount="3176" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Trichloroacetic_acid&quot; rel=&quot;nofollow&quot;&gt;Trichloroacetic Acid&lt;/a&gt; (TCA) is commonly used for protein precipitation but the wash waste needs to be neutralized prior to disposal. What exactly is required to effectively neutralize TCA waste? Do I just add caustic?&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-04-11T18:26:08.507" LastActivityDate="2015-07-16T08:19:32.557" Title="Neutralizing TCA washes" Tags="&lt;safety&gt;" AnswerCount="2" CommentCount="2" ClosedDate="2015-07-16T14:23:49.377" ContentLicense="CC BY-SA 3.0" />
  <row Id="1731" PostTypeId="1" AcceptedAnswerId="1864" CreationDate="2012-04-09T20:56:49.163" Score="11" ViewCount="244" Body="&lt;p&gt;Is there any method to do pulldown enrichment of DNA breakpoints from a cell? I have found this paper reporting a method to enrich for the DNA single-strand breakpoints from meiotic recombination events:&lt;br&gt;&#xA;&lt;a href=&quot;http://dx.doi.org/10.1101/gr.130583.111&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Khil PP, Smagulova F, Brick KM, Camerini-Otero RD, Petukhova GV&lt;/strong&gt;. 2012. Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA. Genome research 22: 957–65.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know if there is something like that which will work on any status of the cell cycle, not only meiosis.&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="836" LastEditDate="2012-09-13T06:21:01.123" LastActivityDate="2013-02-08T17:19:20.200" Title="protocol for pulldown of DNA breakpoints?" Tags="&lt;dna-sequencing&gt;&lt;meiosis&gt;&lt;protocol&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1732" PostTypeId="2" ParentId="1730" CreationDate="2012-04-10T00:23:29.713" Score="4" Body="&lt;p&gt;A neutralization reaction occurs between Brönsted acids and bases to form a salt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case, you have to add a Brönsted base to neutralize your acid. If the final pH is important, you should work out the exact quantity of base to add. Otherwise, just use litmus paper to check the pH of your solution, and add base until it's neutral.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In view of the other answer proposed, I want to stress the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do NOT dispose of your solution in the sink/sewer. Leave it in its plastic bin until a lab technician takes it to the furnace.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the base you use is sodium bicarbonate (NaHCO&lt;sub&gt;3&lt;/sub&gt;), there will be bubbling, caused by the decomposition of carbonic acid (H&lt;sub&gt;2&lt;/sub&gt;CO&lt;sub&gt;3&lt;/sub&gt;) into water (H&lt;sub&gt;2&lt;/sub&gt;O) and carbon dioxide (CO&lt;sub&gt;2&lt;/sub&gt;). You've successfully neutralized the TCA once there's no bubbling upon addition of NaHCO&lt;sub&gt;3&lt;/sub&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is indeed best to proceed slowly while adding your base.&lt;/p&gt;&#xA;" OwnerUserId="691" LastEditorUserId="691" LastEditDate="2012-04-11T00:04:23.797" LastActivityDate="2012-04-11T00:04:23.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1734" PostTypeId="1" CreationDate="2012-04-10T04:40:27.233" Score="13" ViewCount="276" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/In_vitro_compartmentalization&quot;&gt;&lt;em&gt;in vitro&lt;/em&gt; compartmentalization&lt;/a&gt; (IVC) is one of those technologies that everyone knows about, talks about, but never actual does due to the rather technical difficulties in setting the system up. I was wonder if anyone not named Tawfik, Griffiths or someone who did a post-doc with them have been successful in making IVC work? Details in how stable emulsions and a homogeneous mixture of cell-free components in the droplet are made would be wonderful.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2013-12-24T21:30:16.657" Title="How straightforward is in vitro compartmentalization?" Tags="&lt;protocol&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1735" PostTypeId="1" CreationDate="2012-04-10T07:12:21.407" Score="10" ViewCount="1545" Body="&lt;p&gt;The number of individuals constituting a population is called population size.  Over time population size does not remain constant, it fluctuates to different extent over generations because of several internal and external factors.  Populations with violent fluctuation in population size are called unstable and are more prone to extinction as they hit lower population sizes frequently.  And once a population in extinct, it is gone for ever.  Thus it would be interesting to investigate how population stability evolves.&lt;/p&gt;&#xA;" OwnerUserId="724" LastActivityDate="2012-06-06T20:06:56.727" Title="How does population stability evolve?" Tags="&lt;evolution&gt;&lt;ecology&gt;&lt;population-dynamics&gt;&lt;statistics&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1736" PostTypeId="1" CreationDate="2012-04-10T07:29:33.883" Score="7" ViewCount="16335" Body="&lt;p&gt;During translation ribosomes decode the genetic information present in the mRNA and protein synthesis takes place.  During this process which of those two does move, the ribosome or the mRNA?&lt;/p&gt;&#xA;" OwnerUserId="724" LastEditorUserId="6" LastEditDate="2012-04-10T09:58:12.713" LastActivityDate="2020-04-02T17:25:56.173" Title="RNA or ribosome, which one moves during translation?" Tags="&lt;cell-biology&gt;&lt;translation&gt;&lt;ribosome&gt;" AnswerCount="4" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1737" PostTypeId="2" ParentId="1735" CreationDate="2012-04-10T09:40:46.330" Score="5" Body="&lt;p&gt;I guess you meant the population size stability. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is considered that the biosystems will increase their capacity of adaptation when evolving in very fluctuating environments. I believe the population stability is embedded in the adaptability of individuals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a measurement about it, evolvability, when the environment changes, the faster the population adapted to the new environment, the higher evolvability it has. This means that if the population has higher evolvability then the population may be more stable to environmental variation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even so, there might be plenty of underlying mechanisms to enable a certain population stability. I recently read a paper about two mechanism: phenotypic switching and sensing machinery, which are common in bacteria and fungi. Please refer to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16123265&quot; rel=&quot;nofollow&quot;&gt;Edo Kussell and Stanislas Leibler's science paper (2005)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the organism increase its complexity, biosystems invented many more tools to make the individual survival from disasters. Such as human's intelligence. Well it would be an endless issue.&lt;/p&gt;&#xA;" OwnerUserId="698" LastEditorUserId="698" LastEditDate="2012-06-06T20:06:56.727" LastActivityDate="2012-06-06T20:06:56.727" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1738" PostTypeId="2" ParentId="1736" CreationDate="2012-04-10T09:47:07.557" Score="5" Body="&lt;p&gt;Movement is relative. The real events happening in translation are the conformational changes of ribosome makes itself continuous reading the base sequentially. Please refer the biochemistry textbook or cell biology textbook.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed, if the ribosome is anchored, you may say the mRNA is moving. &lt;/p&gt;&#xA;" OwnerUserId="698" LastEditorUserId="69" LastEditDate="2012-04-10T10:54:50.297" LastActivityDate="2012-04-10T10:54:50.297" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1739" PostTypeId="1" CreationDate="2012-04-10T10:10:01.257" Score="8" ViewCount="909" Body="&lt;p&gt;I require some clarification on copy number aberrations (structural gain and loss in chromosomes). From what I understand, gain/loss per se can be divided into two types.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider two alleles, A and B at the same locus on homologous chromosomes. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Allelic Balance: in one type of structural gain/loss, there is &lt;strong&gt;no&lt;/strong&gt; resulting allelic imbalance; examples: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;AB ==&gt; AABB (duplication),&lt;/li&gt;&#xA;&lt;li&gt;AB =&gt; -- (loss).&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Allelic Imbalance: in the other type of structural gain/loss, there is resulting allelic imbalance; examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;AB ==&gt; AAB (duplication of A),&lt;/li&gt;&#xA;&lt;li&gt;AB =&gt; -B (deletion LOH),&lt;/li&gt;&#xA;&lt;li&gt;AB ==&gt; BB (copy-neutral LOH).&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;First, is what I have described above correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, if it is correct, what is the biology underpinning these copy number aberration types? Are the mechanisms responsible for bringing about &lt;strong&gt;allelically-imbalanced&lt;/strong&gt; CN change distinct from the mechanisms for bringing about &lt;strong&gt;allelically-balanced&lt;/strong&gt; CN change? What are these mechanisms?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NB. I'm confining this to just copy number-related allelic imbalance.&lt;/p&gt;&#xA;" OwnerUserId="609" LastEditorUserId="609" LastEditDate="2012-04-11T16:22:44.213" LastActivityDate="2012-04-11T16:22:44.213" Title="What is the difference between copy number changes with and without allelic imbalance?" Tags="&lt;genetics&gt;&lt;copy-number-variation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1740" PostTypeId="2" ParentId="1736" CreationDate="2012-04-10T13:53:52.043" Score="2" Body="&lt;p&gt;The mRNA moves during translation. It is essentially threaded through the ribosome. This has been known ever since polyribosomes were discovered; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC300639/?tool=pmcentrez&quot; rel=&quot;nofollow&quot;&gt;see paper here&lt;/a&gt;. Polyribosomes are a cluster of ribosomes that read a series of mRNA molecules. Often, the ribosomes in a polyribosome will be translating the same mRNA.&lt;/p&gt;&#xA;" OwnerUserId="609" LastActivityDate="2012-04-10T13:53:52.043" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1741" PostTypeId="2" ParentId="1205" CreationDate="2012-04-10T17:54:33.637" Score="1" Body="&lt;p&gt;Graafian follicle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The secondary oocyte and thus Graafian follicle are arrested in the second metaphase of oogenesis.&#xA;After this the corpus luteum develops from the follicle during the luteal phase of the menstrual cycle.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2012-06-01T00:27:45.633" LastActivityDate="2012-06-01T00:27:45.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1742" PostTypeId="2" ParentId="1736" CreationDate="2012-04-10T22:50:23.953" Score="6" Body="&lt;p&gt;Here's an example &lt;strong&gt;in which the ribosome is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26841/&quot; rel=&quot;nofollow noreferrer&quot;&gt;fixed&lt;/a&gt;&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During co-translational translocation, the ribosome is essentially anchored onto the ER membrane through the Sec61 complex. It certainly cannot move along the mRNA. The mRNA is fed through the ribosome and the nascent peptide traverses into the ER lumen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rNKRJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="177" LastEditorDisplayName="user560" LastEditDate="2012-04-11T22:24:14.973" LastActivityDate="2012-04-11T22:24:14.973" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1743" PostTypeId="2" ParentId="1730" CreationDate="2012-04-10T23:33:52.900" Score="-3" Body="&lt;p&gt;I've been fortunate to find a protocol hidden away in my lab archives.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The acid waste can be accumulated for 10 days before it needs to be neutralized. The waste should be kept in a carboy in a &lt;strong&gt;fume hood&lt;/strong&gt;.&lt;/li&gt;&#xA;&lt;li&gt;50 mL 50% w/v Sodium Bicarbonate slurry should be added per liter of TCA waste. During neutralization fumes will be generated which may include &lt;strong&gt;chlorine gas&lt;/strong&gt;.&lt;/li&gt;&#xA;&lt;li&gt;When the pH reaches 6-8, dispose the waste into the sewer.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-04-10T23:33:52.900" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1745" PostTypeId="2" ParentId="1739" CreationDate="2012-04-11T03:53:12.303" Score="5" Body="&lt;p&gt;Allelic imbalance is a pretty broad phenomenon &lt;a href=&quot;http://www.nathansheffield.com/wordpress/2009/what-is-allelic-imbalance/&quot;&gt;difference in the expression of two alleles&lt;/a&gt;.  As such you have listed would probably cause allelic imbalance, but it could be the result of methylation or even differences in RNA sequences between the alleles which say interfere with post translational splicing say. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of copy number variations, if a copy number region (which is often a higly repetitive sequence in the genome and not a gene duplication) might interfere or not interfere with gene regulation. In cancer cells large segments of the genome may be copied or cut out though, so in that case the mechanism you put forth may be important. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-04-11T03:53:12.303" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1746" PostTypeId="5" CreationDate="2012-04-11T05:12:37.307" Score="0" Body="&lt;p&gt;See also &lt;a href=&quot;/questions/tagged/taxonomy&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;taxonomy&amp;#39;&quot; rel=&quot;tag&quot;&gt;taxonomy&lt;/a&gt; for the naming of species or higher taxa.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-03-31T09:04:55.283" LastActivityDate="2014-03-31T09:04:55.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1747" PostTypeId="4" CreationDate="2012-04-11T05:12:37.307" Score="0" Body="The principles, conventions, and terms used to systematically classify biological information, entities, processes, but also subfields of biology." OwnerUserId="43" LastEditorUserId="3624" LastEditDate="2014-03-31T09:05:06.313" LastActivityDate="2014-03-31T09:05:06.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1748" PostTypeId="5" CreationDate="2012-04-11T05:17:03.277" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-04-11T05:17:03.277" LastActivityDate="2012-04-11T05:17:03.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1749" PostTypeId="4" CreationDate="2012-04-11T05:17:03.277" Score="0" Body="Gene annotation refers to the characterization of a gene's exon-intron-UTR structure." OwnerUserId="43" LastEditorUserId="43" LastEditDate="2012-04-11T06:11:45.340" LastActivityDate="2012-04-11T06:11:45.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1750" PostTypeId="1" CreationDate="2012-04-11T08:53:04.413" Score="7" ViewCount="577" Body="&lt;p&gt;For interfacial studies, I would like to build an alanine scanning library for one of my proteins examining 20 sites. I will ultimately express the gene using &lt;em&gt;E.coli&lt;/em&gt; cell-free protein synthesis. I already have the template gene which was originally built using PCR assembly. Now, what's the best way to build a scanning library?&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-04-11T18:36:51.557" LastActivityDate="2014-11-11T14:41:48.303" Title="What is the fastest way to build an alanine scanning library?" Tags="&lt;molecular-biology&gt;&lt;protein-engineering&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1751" PostTypeId="1" CreationDate="2012-04-11T09:01:18.630" Score="24" ViewCount="711" Body="&lt;p&gt;If I'm using a bacteriophage for phage display and I'm trying to avoid avidity effects by using a helper phage what would be the best way to maintain a large library size while keeping everything monomeric? I'm asking in terms of maintaining an appropriate infection ratio and or phage tricks and tools to maintain the that stoichiometry.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-04-11T18:39:13.393" LastActivityDate="2014-07-15T22:26:46.523" Title="Phagemid display" Tags="&lt;protein-binding&gt;&lt;protein-engineering&gt;&lt;protein-evolution&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1752" PostTypeId="1" CreationDate="2012-04-11T12:03:37.320" Score="22" ViewCount="981" Body="&lt;p&gt;How is the blood-volume of an organism measured without killing it?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note:The blood-volume of an organism is defined as the total volume of blood present inside that organism.&lt;/p&gt;&#xA;" OwnerUserId="724" LastEditorUserId="14709" LastEditDate="2015-05-23T10:14:24.067" LastActivityDate="2015-05-23T10:14:24.067" Title="How is the blood volume of a living organism measured without killing it?" Tags="&lt;zoology&gt;&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1754" PostTypeId="1" CreationDate="2012-04-11T16:38:12.270" Score="13" ViewCount="531" Body="&lt;p&gt;One of the tenets of Darwin's theory is the survival of the fittest, ie adaptation of features that allow a species to adapt better to its surrounding environment. I am wondering that given the right conditions, is there a possibility of a more &quot;complex&quot; species, say humans, back-evolving into a less &quot;complex&quot; species, say a dog? Is there anything in Darwin's theory or some experimental proof that excludes such a possibility?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt; (4/19/12): Thanks for all the responses! I definitely agree with the fact that we are no more complex than dogs or Drosophila, hence the quotes surrounding complex in the question. I learnt a lot from the answers and don't think there is any one answer that is the best, but read together, they drive home the point. Thanks all!&lt;/p&gt;&#xA;" OwnerUserId="223" LastEditorUserId="223" LastEditDate="2012-04-20T03:58:13.583" LastActivityDate="2012-04-20T03:58:13.583" Title="Can species back-evolve?" Tags="&lt;evolution&gt;" AnswerCount="5" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1755" PostTypeId="2" ParentId="1754" CreationDate="2012-04-11T18:28:00.227" Score="19" Body="&lt;p&gt;Complexity is a lure. Evolution isn't defined by complexity, but by adaptation to one's environment, as you mentioned.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution is an ongoing, non-deterministic process. There's not &lt;em&gt;one&lt;/em&gt; definite evolutionary &quot;path&quot; that brings a unicellular to a modern human being. Nor is there a predictable evolutionary path that brings a dog into becoming a human. You also have to acknowledge that, because evolution is ongoing, the dog of yesterday is not the dog of tomorrow. That applies to all the living.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it &lt;em&gt;possible&lt;/em&gt; that given the &lt;em&gt;right amount of time&lt;/em&gt; and the &lt;em&gt;ideal environment&lt;/em&gt; the &lt;em&gt;modern human&lt;/em&gt; could evolve into the &lt;em&gt;modern dog&lt;/em&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, it is &lt;em&gt;possible&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it probable? &lt;strong&gt;No&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The chances are that if humanity were to find itself in such an exotic environment - to which dogs are &lt;strong&gt;100%&lt;/strong&gt; adapted, but humans &lt;strong&gt;0%&lt;/strong&gt;, which just shows how unprobable such an environment is - it would become extinct before it has a chance to adapt, much like a lot of other species &lt;a href=&quot;http://en.wikipedia.org/wiki/Extinction_event&quot;&gt;have done&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="691" LastEditorUserId="691" LastEditDate="2012-04-11T18:36:51.743" LastActivityDate="2012-04-11T18:36:51.743" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1756" PostTypeId="1" AcceptedAnswerId="1768" CreationDate="2012-04-11T19:34:08.507" Score="11" ViewCount="335" Body="&lt;p&gt;Were dinosaurs hot-blooded or cold-blooded? NOTE: The popular term 'hot-blooded' means having an internally maintained average body temperature, which is generally more than that of the surroundings, despite the variation of the temperature outside.  And obviously 'cold-blooded' is the opposite of 'hot-blooded'.&lt;/p&gt;&#xA;" OwnerUserId="724" LastEditorUserId="724" LastEditDate="2012-04-12T06:33:37.037" LastActivityDate="2012-04-12T10:31:31.450" Title="Were dinosaurs 'hot-blooded' or 'cold-blooded'?" Tags="&lt;physiology&gt;&lt;palaeontology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1758" PostTypeId="1" AcceptedAnswerId="1759" CreationDate="2012-04-11T21:26:27.227" Score="5" ViewCount="102" Body="&lt;p&gt;Looking at some more detailed &lt;a href=&quot;http://www.faculty.ucr.edu/~mmaduro/codonusage/codontable.htm&quot;&gt;codon usage tables&lt;/a&gt;, genes may be further clustered into three gene classes: Metabolic genes, highly expressed genes during exponential growth, and horizontal gene transfer. Looking at the original &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1762151&quot;&gt;paper&lt;/a&gt; by Medique et al., they clustered the genes based on the CAI and then by a variant of &lt;a href=&quot;http://en.wikipedia.org/wiki/K-means_clustering&quot;&gt;k-means&lt;/a&gt; determined 3 classes. Note that this is different from a class II gene which is determined by the types of RNA polymerase used.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How did they end up determining what the three classes are? It seems as if they made this generalization without any proteome data. Would the same genes be classified using a protein expression data during exponential growth and stationary growth?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-04-11T23:28:52.347" Title="How are the various classes of E coli genes determined?" Tags="&lt;gene-expression&gt;&lt;codon-usage&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1759" PostTypeId="2" ParentId="1758" CreationDate="2012-04-11T23:28:52.347" Score="3" Body="&lt;p&gt;I read through the paper. The author starts by stating that as of the time of writing, two different classes of codon usage profiles were known (or at least putatively so). All 782 unique CDS sequences used were subjected to a two-step classification method. In step one, each CDSs was broken down into a 61-dimensional vector representing each of the 61 possible codons. A factorial cluster analysis (the categorical, multi-variate equivalent of principle component analysis) was run on these vectors, condensing 61 dimensions down to 2 dimensions. Now that the data complexity has been reduced to 2D, it is more manageable for a k-means algorithm to partition the data. In the end, the genes were clustered into 3 orthogonal groups (classes I, II and III, with 502, 191 and 89 CDS, respectively).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Only after the authors clustered the gene set were they able to go back and look at the canonical definitions of each gene. It so happened, fortuitously, that each class of the genes had a strong bias for subsets of cellular function (eg, metabolism, protein biosynthesis, transport). They did not use proteome data, but they were able to define the role for a large number of these genes based on the body of literature at the time.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-11T23:28:52.347" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1760" PostTypeId="2" ParentId="1754" CreationDate="2012-04-11T23:49:30.913" Score="8" Body="&lt;p&gt;There are several &lt;a href=&quot;http://en.wikipedia.org/wiki/Immortalised_cell_line&quot;&gt;strains of mutant cells&lt;/a&gt; from humans, mice and various other species that have found themselves a niche as single-celled organisms living in lab dishes, and seem to be thriving there.  The well known &lt;a href=&quot;http://en.wikipedia.org/wiki/HeLa&quot;&gt;HeLa human cell line&lt;/a&gt;, in particular, appears to have adapted to this new existence well enough to have acquired a reputation as a &quot;weed&quot; that easily contaminates other cell cultures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nor is the phenomenon confined to artificial human-created habitats, either &amp;mdash; some species of animals, including dogs, hamsters and Tasmanian devils, are susceptible to infection by &lt;a href=&quot;http://en.wikipedia.org/wiki/Clonally_transmissible_cancer&quot;&gt;transmissible cancers&lt;/a&gt;, which are essentially unicellular pathogens deriving from mutant cells of the host (or a related) species.&lt;/p&gt;&#xA;" OwnerUserId="239" LastActivityDate="2012-04-11T23:49:30.913" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1761" PostTypeId="2" ParentId="1736" CreationDate="2012-04-12T00:42:57.210" Score="6" Body="&lt;p&gt;The ribosome moves relative to the mRNA by, in effect, pulling itself along it.  If both the ribosome and the mRNA are freely floating and not attached to anything else (as in &lt;a href=&quot;https://biology.stackexchange.com/a/1742/239&quot;&gt;jp89's answer&lt;/a&gt;), the relative amount of movement should depend on their relative masses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Actually, it also depends on how much drag each of them experiences with respect to the surrounding liquid medium, but since I have no idea how much that is, and since it's probably highly conformation-dependent anyway, I'm going to just ignore that and just assume that the drag is also more or less proportional to mass, at least to first order.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As it happens, a quick Google search and some back of the envelope calculation suggests that the mass of a ribosome and the average mass of an mRNA are both around a megadalton.  Of course, the length (and thus the mass) of an mRNA varies quite a lot, so it would seem likely that sometimes it's the ribosome that moves mostly, sometimes it's the mRNA, and sometimes it's both.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, as shigeta and others have pointed out, there can be more than one ribosome attached to the same mRNA strand.  That's going to make the mRNA move more (and, correspondingly, the ribosomes move less), since there are more ribosomes pulling it along.&#xA;Then there's also the protein being transcribed, which is attached to the ribosome but also being moved with respect to it.  And I really have no idea how negligible the interactions with the tRNAs and so on are.  It's a mess, but my &lt;em&gt;guess&lt;/em&gt; would be that, usually, it's mostly the mRNA that moves, but that the ribosomes aren't completely stationary either (unless they're attached to something, of course).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Ps. Here's an exercise for you, which you may try out if you happen to have a friend who works at a public swimming pool. Otherwise consider it a &lt;em&gt;gedankenexperiment&lt;/em&gt;. You know those floating ropes that separate the lanes in the pool? Try getting your friend to let you into the pool when it's not in use and to release one of the ropes from the walls.  Then get in, grab the rope with your arms and legs and try pulling yourself along it.  While doing so, try to decide whether it's you or the rope who moves more. (Also, to more closely approximate the Reynolds numbers involved inside a cell, imagine doing this in treacle instead of water.)&lt;/p&gt;&#xA;" OwnerUserId="239" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2012-04-12T01:00:41.027" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1762" PostTypeId="1" AcceptedAnswerId="1763" CreationDate="2012-04-12T01:15:33.940" Score="8" ViewCount="1802" Body="&lt;p&gt;Why do almost all plants in shade have a smaller stem structure and larger leaf than that same species grown in a well lit, sunny area? &lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2017-01-12T20:56:36.723" Title="Why do plants' leaves become enlarged in low light areas?" Tags="&lt;botany&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1763" PostTypeId="2" ParentId="1762" CreationDate="2012-04-12T01:35:07.083" Score="8" Body="&lt;p&gt;I have no idea of the biological mechanisms behind what I'm about to propose. Consider this a hypothesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the purpose of the leave is to collect sunlight for photosynthesis, then the behavior you mention is predictable. I order of &lt;em&gt;trying&lt;/em&gt; to maintain a healthy flux of light in dim conditions, the plant adapts by increasing the area of its leaves. Once back in a well-lit environment, the need for larger leaves fades and new leaves are thus smaller, but still catch as much light. Of course, there must be limits to the extent of leaf area variation that one plant can handle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the stem structure, I can only guess it's because plants spend more energy on leaf building than stem maintenance when under such stresses.&lt;/p&gt;&#xA;" OwnerUserId="691" LastActivityDate="2012-04-12T01:35:07.083" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1764" PostTypeId="2" ParentId="940" CreationDate="2012-04-12T06:46:59.203" Score="1" Body="&lt;p&gt;The cells would have to produce glucose directly from electricity. If we figured that out we could also solve our energy crisis.&lt;/p&gt;&#xA;" OwnerUserId="238" LastActivityDate="2012-04-12T06:46:59.203" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1766" PostTypeId="2" ParentId="1031" CreationDate="2012-04-12T09:23:21.650" Score="1" Body="&lt;p&gt;My professor says that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The yolk sac is not connected to the mechanism of polyspermy or&#xA;  monospermy. [Amount of yolk inside the oocyte is then again.]  The&#xA;  oocytes of reptiles and birds are yolk rich  - polylecithal  for instance.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;where&#xA;lecithal = yolk containing and some pieces of information about &lt;a href=&quot;http://answers.yahoo.com/question/index?qid=20070109144024AAsLkzy&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-04-12T09:23:21.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1767" PostTypeId="1" AcceptedAnswerId="1774" CreationDate="2012-04-12T09:23:24.327" Score="11" ViewCount="525" Body="&lt;p&gt;The dinosaurs, mammoths, giant plants etc are known to be bigger than modern animals. I wonder why they had been lived and why they are not living now? I really don't know much but is it something about oxygen balance or something similar? &lt;/p&gt;&#xA;" OwnerUserId="410" LastEditorUserId="66" LastEditDate="2012-04-12T11:06:26.770" LastActivityDate="2013-02-18T15:39:09.577" Title="What was the reason for some plant and animals to become giant in course of evolution?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;botany&gt;" AnswerCount="4" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1768" PostTypeId="2" ParentId="1756" CreationDate="2012-04-12T10:31:31.450" Score="6" Body="&lt;p&gt;This is a question I have often heard and there is no one certain answer to it. There are several scientific hypothesis about the methabolism of dinosaurs, but none of them has been ever proved or completely disproved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Arts of methabolism&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, the term &quot;cold-blooded&quot; and &quot;hot-blooded&quot; are not scientific. In biology the organisms are classified according to how constant their body temperature is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;homeothermic&lt;/strong&gt; (from greek &quot;hom(e)o&quot; = equal, same) -- organisms, who manage to maintain constant body temperature.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;poikilothermic&lt;/strong&gt; (from greek &quot;poikilos&quot; = changing, changeable) - ogranisms, whose body temperature fluctuates over time. It is implied here, that  the body temperature follows the fluctuation of the environment temperature, even though this is strictly not correct (see below)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There is another orthogonal classification, which takes into account the metabolic properties of the organisms:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;endothermic&lt;/strong&gt; organisms actively produce heat in their bodies, whereas&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;exotermic&lt;/strong&gt; organisms mostly rely upon external heat sources.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What do we know about dinosaurs' methabolism?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately there is no one living dinosaur, so we can only reason about their methabolism basing upon the fossils (and possible DNA from moskitos trapped into ambers).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the most cited works here is the &quot;Dinosaur Fossils Predict Body Temperatures&quot; (&lt;a href=&quot;http://www.plosbiology.org/article/info%3adoi/10.1371/journal.pbio.0040248&quot;&gt;link&lt;/a&gt; to the free full text), where the authors write:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Perhaps the greatest mystery surrounding dinosaurs concerns whether&#xA;  they were endotherms, ectotherms, or some unique intermediate form.&#xA;  Here we present a model that yields estimates of dinosaur body&#xA;  temperature based on ontogenetic growth trajectories obtained from&#xA;  fossil bones. The model predicts that dinosaur body temperatures&#xA;  increased with body mass from approximately 25 °C at 12 kg to&#xA;  approximately 41 °C at 13,000 kg. The model also successfully predicts&#xA;  observed increases in body temperature with body mass for extant&#xA;  crocodiles. These results provide direct evidence that dinosaurs were&#xA;  reptiles that exhibited inertial homeothermy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And exactly here we need the terminology I presented above to understand the findings:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Dinosarier were &lt;em&gt;endothermic&lt;/em&gt; -- they were able to actively produce heat in their bodies.&lt;/li&gt;&#xA;&lt;li&gt;The produced heat can only be taken away through their body surface. Due to the fact that the body surface increases quadratically (n&lt;sup&gt;2&lt;/sup&gt;) with the size, whereas the weight grows cubically (n&lt;sup&gt;3&lt;/sup&gt;), &lt;em&gt;the bigger dinosaurs were the higher temperature their bodies reached&lt;/em&gt;. That could be one of the growth limiting factors and explains why especially big species preferred to live in water.&lt;/li&gt;&#xA;&lt;li&gt;Even though the dinosaries were homeothermic, we don't know anything about their thermoregulation. Modern reptilia do not have the thermoregulation mechanisms that would keep the body temperature constant. &lt;em&gt;Dinosariers, however, due to increased heat production might have less fluctuations in their body temperature, than smaller reptilia.&lt;/em&gt; This is termed as &quot;inertial homeothermy&quot; here.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-04-12T10:31:31.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1769" PostTypeId="2" ParentId="1686" CreationDate="2012-04-12T10:45:33.803" Score="1" Body="&lt;p&gt;To my knowledge, capillaries in general and the renal capillaries in glomeruli in particular do not have muscle cells to constrict. The latters have only a basal layer with podocytes lying directly on it (&lt;a href=&quot;http://www.worldscibooks.com/etextbook/p186/p186_chap1.pdf&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt; to the open textbook).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, the vasoconstriction takes place only in arterioles before the glomeruli, and this vasoconstriction leads to the increased hydrostatic pressure which propagates to the glomerular cappilaries. The blood flow rate and velocity do not change, therefore &lt;em&gt;the increased hydrostatic pressure works against the constant pressure of Bowman's capsule and osmotic pressure of the colloid medium, leading to the increased net filtration pressure (NFP)&lt;/em&gt;. Filtration rate and filtration pressure are directly connected, so that the rate increases either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more details, please, refer to the textbook I provided the link to above.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-04-12T10:45:33.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1770" PostTypeId="2" ParentId="201" CreationDate="2012-04-12T10:59:13.957" Score="2" Body="&lt;p&gt;As far as I remember the pathology course from medical school, chronic long-lasting inflammation often leads to proliferation of connective tussie and ultimately to fibrosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The actual mechanism here is the lack of oxygen which is used-up by different immune system cells to produce peroxydes and superoxydes. &lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-04-12T10:59:13.957" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1771" PostTypeId="1" AcceptedAnswerId="1772" CreationDate="2012-04-12T11:04:36.587" Score="28" ViewCount="7198" Body="&lt;p&gt;I'm still not sure about the mechanics that lead to rabies being incurable. I know that it can be treated before any symptoms show up, but why is it that once symptoms show the person is a dead man walking?&lt;/p&gt;&#xA;" OwnerUserId="584" LastEditorUserId="69" LastEditDate="2012-04-13T13:01:14.137" LastActivityDate="2016-07-26T13:42:23.600" Title="Why is rabies incurable?" Tags="&lt;human-biology&gt;&lt;virology&gt;&lt;pathology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1772" PostTypeId="2" ParentId="1771" CreationDate="2012-04-12T12:32:11.037" Score="23" Body="&lt;p&gt;This is because &lt;a href=&quot;http://en.wikipedia.org/wiki/Rabies&quot;&gt;rabies&lt;/a&gt; is a viral infection of nervous tissue that propagates through peripheral nerves into the brain and causes brain tissue inflammation (encephalitis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As long as the virus is in the brain there is no way to get rid of it. The main trade-off here is that everything that would kill the virus will be as (or even more) aggressive against the brain tissue, and impairment of the latter will lead to really heavy deficits in vital functions like breathing and thermoregulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first manifestations of rabies are those due to brain damage. This means, the virus is already there and the brain is already fatally damaged. &lt;/p&gt;&#xA;" OwnerUserId="66" LastEditorUserId="1250" LastEditDate="2012-08-19T21:30:53.550" LastActivityDate="2012-08-19T21:30:53.550" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1773" PostTypeId="1" AcceptedAnswerId="1776" CreationDate="2012-04-12T14:07:39.527" Score="8" ViewCount="1932" Body="&lt;p&gt;I recently had a conversation with a rather &lt;em&gt;unusual&lt;/em&gt; gentleman who was, let's say, more than a little partial to conspiracy theories. He has this idea that governments are lowering &quot;nanowires&quot; from drones, to inject people with chemicals that modify their genetics in order to reduce their lifespan dramatically, or change their opinions and thoughts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clearly this man was a fruitcake, and the complexities of his psychology probably warrant a whole separate debate, but he did get me thinking about the theoretical side of how such a thing might be done.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, as such, I have a few questions on the matter:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Is it even &lt;em&gt;theoretically possible&lt;/em&gt; to alter human genetics using only an injected substance? I'd imagine trying to get a single DNA change to propogate through the entire body without being killed off by the immune system would be near impossible.&lt;/li&gt;&#xA;&lt;li&gt;Since we are aware of genetic markers that are related to predispositions to certain medical conditions (e.g. heart problems, cancers, high blood pressure, strokes, etc), is it possible to modify human DNA to create these issues in a living person?&lt;/li&gt;&#xA;&lt;li&gt;Has much research gone into how genetics affects thought and opinion, or the way we perceive and react to situations at an emotional level? If so, is it &lt;em&gt;theoretically&lt;/em&gt; possible to alter this at a biological level?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I'm certainly not advocating any of this, and I apologise for the unusual nature of the question, but it's something I certainly find interesting to think about!&lt;/p&gt;&#xA;" OwnerUserId="172" LastActivityDate="2017-02-25T23:42:44.937" Title="Altering the human genome" Tags="&lt;dna&gt;&lt;genetics&gt;&lt;human-genome&gt;&lt;splicing&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1774" PostTypeId="2" ParentId="1767" CreationDate="2012-04-12T15:16:56.153" Score="12" Body="&lt;p&gt;Thanks for asking an interesting question which made me think.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The short answer is that something evolves if there is an advantage to the genes involved, and, by 'advantage' I mean it produces more copies of the genes in the next generation so more individuals with that characteristic will be present in the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to what particular advantage increased body mass had to any particular species that would depend on the particular species and its environment at the time.  There is almost certainly not a 'one-fits-all' answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most very big land mammals are herbivores and there is an advantage in having a large digestive tract when you eat a lot of plant material with a fairly low nutrient level.  However, when there are also predators around, getting big and slow might be more of a disadvantage than staying small and fast. With evolution there is often a balance of competing forces which are traded of against one another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where large mammals have become isolated on islands with no predators, such as a species of now-extinct elephant on the Flores Island, they tend to become smaller so this suggests avoiding predators by simply being too big for them to kill might be an important factor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And of course with many species we have the effect of sex-selection. If females select for the biggest males, there will be a selection pressure towards greater size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With plants it could be something else entirely. Trees, for example, have long trunks basically for one of two reasons. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly to put their leaves and seeds out of the reach of herbivores, so we have a kind of arms race like that between giraffes and acacia trees in Africa.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, when they grow in close clumps like woods and forests, there will be competition for sunlight and soil resources like water. A species which can reach higher and put it's leaves above those of it's neighbours will win the competition and there will also then be pressure on it's neighbours to evolve longer trunks.  Long trunks mean that water must be pumped a long way to the leaves so the tree with the longest trunks will also need bigger root systems.  Again a trade off between making a long trunk and dominating the water supply underground.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many trees are also believed to have formed symbiotic associations with fungi in their root systems which help them take in the nutrients and water required to 'service' a long trunk and high-up leaf crown so they may be the only types of plants capable of doing this anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One thing you might like to think about is why some whales are very big and some are relatively small (dolphins, porpoises, killer whales). What is the difference in their life-style, food, habitat, and so on, which could drive these evolutionary differences.&lt;/p&gt;&#xA;" OwnerUserId="735" LastActivityDate="2012-04-12T15:16:56.153" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1775" PostTypeId="2" ParentId="1773" CreationDate="2012-04-12T15:49:52.053" Score="8" Body="&lt;p&gt;Concerning the first question, it is very well possible to alter human genetics by injecting a highly radio-active substance that will eventually cause mutations almost all cells. The lifespan will be dramatically reduced, however and the condition is known as &quot;radiation sickness&quot;(&lt;a href=&quot;http://en.wikipedia.org/wiki/Radiation_poisoning&quot;&gt;link&lt;/a&gt; to Wikipedia).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the person probably means so-called &quot;directed mutations&quot; (&lt;a href=&quot;http://en.wikipedia.org/wiki/Site-directed_mutagenesis&quot;&gt;link&lt;/a&gt; to Wikipedia), when the changes of genetic information is not random, but rather at a certain place and towards a certain function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second point, this is the area of extensive research: if we could specifically cure a gene than many diseases that are incurable now (like cystic fibrosis) could be effectively treated.  The complete nanotechnology (&lt;a href=&quot;http://en.wikipedia.org/wiki/Molecular_nanotechnology&quot;&gt;link&lt;/a&gt; to Wikipedia) is all about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the third point, this is also a very old discussion about the role of nature (=genetics) and nurture (environment). Answering this question in the scope of other questions I can suggest that (genetic) knocking-out some inhibiting receptor systems in brain can lead to certain malfunctions and deceases, including the lymbic system that is responsible for emotions and perception.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-04-12T15:49:52.053" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1776" PostTypeId="2" ParentId="1773" CreationDate="2012-04-12T16:19:43.503" Score="8" Body="&lt;p&gt;First of all it is important to note that, within certain limits, human DNA is not much different than, say, a mouse DNA: it has the same structure, it is constituted by the same bases etc etc. Therefore it is teorethically possible (leaving aside ethical issues, of course) to selectively modify it as you would do for a mouse. There are, however, some technical issues and obviously many ethical ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer specifically to your questions&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is it even theoretically possible to alter human genetics using only an injected substance? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes it is. Aside from the good example of radioactive substances given by Alexander, another good one (and probably one that is more common) is that of &lt;a href=&quot;http://en.wikipedia.org/wiki/Mutagen&quot;&gt;chemical mutagens&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important to understand that the mutation caused by these substances are random, or only partially selective.&#xA;For instance, certain substances, called &lt;a href=&quot;http://en.wikipedia.org/wiki/Intercalation_%28chemistry%29&quot;&gt;intercalating agents&lt;/a&gt; can interpose themselves in between the bases of the DNA, interfering and possibly giving rise to mutations during DNA replication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other substances such as alkilating agents are a bit more specific, although still not gene- or locus- specific.&#xA;For instance &lt;a href=&quot;http://en.wikipedia.org/wiki/Ethylnitrosourea&quot;&gt;ethylnitrosourea&lt;/a&gt; (ENU) favours A-&gt;T base transversions and AT-&gt;GC transitions.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I'd imagine trying to get a single DNA change to propogate through the entire body without being killed off by the immune system would be near impossible.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The immune system would not necessarily kill cells with mutations. Think of what happens during cancer developement.&#xA;Also, an extremely important point: mutating a somatic cell (i.e. not a sperm or an egg) can induce a mutant phenotype in the individual but it will not be transmitted to his/her progeny.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Since we are aware of genetic markers that are related to predispositions to certain medical conditions (e.g. heart problems, cancers, high blood pressure, strokes, etc), is it possible to modify human DNA to create these issues in a living person?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As Alexander says, there is much research in this field.&#xA;Some attempts of &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene_therapy&quot;&gt;gene therapy&lt;/a&gt; have indeed been made, and some have a big potential. We are, however, still far away for gene therapy to become a routine treatment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, remember that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;not all diseases are genetic diseases&lt;/li&gt;&#xA;&lt;li&gt;not all genetic diseases are &lt;a href=&quot;http://en.wikipedia.org/wiki/Monogenic_disorder#Single_gene_disorder&quot;&gt;monogenic&lt;/a&gt;: some derive from a complex interplay of different factors and hence curing them is not as simple as providing the correct version of the mutated gene.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Has much research gone into how genetics affects thought and opinion, or the way we perceive and react to situations at an emotional level? If so, is it theoretically possible to alter this at a biological level?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, but I would say that we are very very far away from a complete understanding of how thought and emotions are coded in our brain. The very difficult point is that one needs to study these events at multiple scales. We can study a big region of the brain and say that it is involved in fear coding, for instance. But then if you want to go deeper and study what happens at the single cell level you need to look at a lot of different cells to see how they interact between each other.&#xA;From the other side of the &quot;size scale&quot;, it is possible to study biochemical processes in the single neuron, but then again it is difficult to study how these processes are integrated in big networks of cells, especially &lt;em&gt;in vivo&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-04-12T16:19:43.503" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1777" PostTypeId="1" CreationDate="2012-04-12T17:33:16.510" Score="6" ViewCount="160" Body="&lt;p&gt;I have a couple structures that are nearly ready to be deposited in the PDB.  Out of curiosity, I ran them through the ADIT's precheck tool and they failed with one error after another, as I lacked all sorts of additional records (&lt;code&gt;TER&lt;/code&gt;, &lt;code&gt;SEQRES&lt;/code&gt;, &lt;code&gt;HETNAM&lt;/code&gt;, etc.) that my refinement and modelling tools don't seem to care about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I understand/guess, the online submission tool will help fill in all the metadata (&lt;code&gt;REMARK&lt;/code&gt;s, etc.), but how do I turn my coordinates into something acceptable?&lt;/p&gt;&#xA;" OwnerUserId="25" LastActivityDate="2012-10-11T11:58:44.107" Title="How do I prepare a PDB for submission to the Protein Data Bank?" Tags="&lt;bioinformatics&gt;&lt;structural-biology&gt;&lt;ccp4&gt;&lt;pdb&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1778" PostTypeId="2" ParentId="1767" CreationDate="2012-04-12T18:00:46.180" Score="5" Body="&lt;p&gt;to expand on Rose's answer, certain environmental factors are what people cite with unusual size changes in an animal over time as it diversifies into new species.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Island_gigantism&quot;&gt;Gigantism (and dwarfism) on islands&lt;/a&gt; are a particular example.  In this case an animal may arrive on an island and some of the predators or competitors that it is used to will not be there.  Then a single species will spin off many species, each one will fill one of the niches that are unfilled on the island - eating bugs from bark, breaking open nuts.  The lack of large carnivores will allow a nice juicy herbivore to get larger without fear of being eaten.  Similarly the Moa was a bird that became an aggressive carnivore in its island habitat, where it's very rare to see an aggressive land bird when a big cat or other carnivore is already present.  Such large changes in environment can also result in &lt;a href=&quot;http://www.wired.com/wiredscience/tag/island-dwarfism/&quot;&gt;dwarfism&lt;/a&gt; - smaller species as smaller animals like squirrels or mice might not be present to consume all the food that are available.  The &lt;a href=&quot;http://news.nationalgeographic.com/news/2009/01/090123-hobbit-skull.html&quot;&gt;Hobbits&lt;/a&gt; recently discovered in Indonesia are an example of island dwarfism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, selective pressure can probably make many animals larger or smaller - lots of the dog breeds are smaller than wolves that they descended from.  I think steers are as large as we can make them and are larger than native cattle stock. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as the environment that caused dinosaurs to be so large, the higher levels of oxygen on the planet at the time is a common theory for why they were so large.  I also think that at least early on, the selection conditions that favored larger animals were probably put in place as animals evolved without any competitors whatsoever (first animals on land or sea).  If this were to happen again, its not clear whether dinosaurs would have been so large - perhaps we could have had gigantic mammals or descendants of trilobites. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-04-12T18:00:46.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1779" PostTypeId="5" CreationDate="2012-04-12T18:04:06.550" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Statistics&quot; rel=&quot;nofollow&quot;&gt;Statistics&lt;/a&gt; is concerned with the analysis and interpretation of data. Statistical methods are applied frequently throughout biology, from planning experiments to validating results and drawing inferences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Use this tag if the use of statistics is a major part of your question, e.g. if you want to know whether a particular statistical test can be applied to your experimental results. Do not use the tag if the use of statistics is incidental. For example, if your question was &quot;Why did the average height of an adult American male increase over period XXXX-YYYY?&quot; you would probably be concerned with matters of nutrition, genetics, health and so on rather than how the data were collected and the averages calculated, so the &lt;a href=&quot;/questions/tagged/statistics&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;statistics&amp;#39;&quot; rel=&quot;tag&quot;&gt;statistics&lt;/a&gt; tag would not be appropriate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stack Exchange has an active site, &lt;a href=&quot;http://stats.stackexchange.com/&quot;&gt;Cross Validated&lt;/a&gt;, dedicated to statistics. If your question is primarily about statistics rather than biology, or requires dedicated statistical expertise, such as regarding the theoretical basis of a method, it is probably better asked there.&lt;/p&gt;&#xA;" OwnerUserId="149" LastEditorUserId="1590" LastEditDate="2016-03-23T11:17:19.083" LastActivityDate="2016-03-23T11:17:19.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1780" PostTypeId="4" CreationDate="2012-04-12T18:04:06.550" Score="0" Body="The study of the collection, analysis, and interpretation of data." OwnerUserId="307" LastEditorUserId="4101" LastEditDate="2013-10-31T14:03:49.630" LastActivityDate="2013-10-31T14:03:49.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1781" PostTypeId="5" CreationDate="2012-04-12T18:08:11.303" Score="0" Body="&lt;p&gt;Yeasts include organisms from the phyla Ascomycota and Basidiomycota and is therefore a polyphyletic group. In common practice, yeast or budding yeast refers to Saccharomyces cerevisiae. Fission yeast refers to Schizosaccharomyces pombe. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Saccharomyces is a commercially important organism, used in fermentative production of alcoholic beverages and breads.  It is also one of the simplest eukaryotes and is commonly used as a model organism to study basic eukaryotic cell-cycle and gene regulation pathways.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="4101" LastEditDate="2013-10-31T18:14:19.633" LastActivityDate="2013-10-31T18:14:19.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1782" PostTypeId="4" CreationDate="2012-04-12T18:08:11.303" Score="0" Body="Yeasts are a polyphyletic group of unicellular fungi. Usually the term yeast is used synonymously with baker's yeast - Saccharomyces cerevisiae." OwnerUserId="307" LastEditorUserId="4101" LastEditDate="2013-10-31T18:13:02.580" LastActivityDate="2013-10-31T18:13:02.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1783" PostTypeId="2" ParentId="1665" CreationDate="2012-04-12T18:09:25.310" Score="4" Body="&lt;p&gt;This is just about where the pathogens can be found that are dangerous to people.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vomit is highly acidic and less accommodating to microbe growth. Similarly saliva has many immune components in it as well as digestive enzymes that keep most microorganisms down. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Urine and CSF are actually quite sterile as they come from environments that are highly filtered - the kidney is an osmotic processor that essentially is a molecular filter and does not allow cells to pass, the spine is highly insulated from the blood and other direct exposure to microorganisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Compare that with the 'dangerous' list and you have organs that are open to human pathogens.  Venerial disease like HPV is so common that what - about 1 in 5 people under a certain age carry it.  That is a pretty high expectation of a biohazard.  most infections and viruses are blood bourne - influenza, cold, as well as any bacterial infections. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Feces is always a dangerous thing to handle as the digestive tract is rich in nutrients and essentially directly open to external bacteria and fungi.  (and its not acidified like the stomach).  Also parasites like tape worms and other multicelled animals! yum!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diarrhea is often caused by an infection of some sort, so its just more likely a hazard, but feces is always a place where you might find a pathogen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not to say that the 'safe' list is totally safe.  Its just less likely to bear disease causing agents. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-04-12T18:09:25.310" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1784" PostTypeId="1" CreationDate="2012-04-12T18:10:01.397" Score="40" ViewCount="7484" Body="&lt;p&gt;Most people have experienced the temporary loss of feeling and tingling in their leg resulting from sitting in an abnormal position for a short while. Usually you get a loss of feeling in your leg while it is being compressed/constricted at some point and then the tingling sensation as the pressure is removed. But what is actually happening? I understand the the blood vessels are probably constricted from the pressure, but how does this lead to loss of feeling and later the strange tingling sensation? Are there any other things that extended compression on the leg does to cause this? What exactly are the requirements to get the sensation of a one's leg or other limb falling tingling in that manner?&lt;/p&gt;&#xA;" OwnerUserId="62" LastEditorUserId="460" LastEditDate="2012-04-13T02:18:12.210" LastActivityDate="2014-09-14T17:07:23.390" Title="What actually happens when my leg 'falls asleep'?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;neuroscience&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1785" PostTypeId="5" CreationDate="2012-04-12T18:11:08.600" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-04-12T18:11:08.600" LastActivityDate="2012-04-12T18:11:08.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1786" PostTypeId="4" CreationDate="2012-04-12T18:11:08.600" Score="0" Body="The scientific study of behaviour and of the mind." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-04-12T19:14:36.773" LastActivityDate="2012-04-12T19:14:36.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1787" PostTypeId="5" CreationDate="2012-04-12T18:12:57.957" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-04-12T18:12:57.957" LastActivityDate="2012-04-12T18:12:57.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1788" PostTypeId="4" CreationDate="2012-04-12T18:12:57.957" Score="0" Body="A change in an organism's genomic sequence." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-04-12T19:14:32.327" LastActivityDate="2012-04-12T19:14:32.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1789" PostTypeId="5" CreationDate="2012-04-12T18:15:09.483" Score="0" Body="&lt;p&gt;Questions about cytokinesis should use the &lt;a href=&quot;/questions/tagged/cytokinesis&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;cytokinesis&amp;#39;&quot; rel=&quot;tag&quot;&gt;cytokinesis&lt;/a&gt; tag.&lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="4101" LastEditDate="2013-10-31T16:40:16.003" LastActivityDate="2013-10-31T16:40:16.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1790" PostTypeId="4" CreationDate="2012-04-12T18:15:09.483" Score="0" Body="The eukaryotic process characterized by replication of nuclear DNA and formation of a second identical nucleus. Separate from cytokinesis." OwnerUserId="307" LastEditorUserId="16866" LastEditDate="2020-01-02T19:22:16.943" LastActivityDate="2020-01-02T19:22:16.943" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="1791" PostTypeId="5" CreationDate="2012-04-12T18:17:46.890" Score="0" Body="&lt;p&gt;Literally anatomy means to cut something, so plant anatomy commonly mean the internal structures of plant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, practically, &lt;a href=&quot;https://en.wikipedia.org/wiki/Plant_anatomy&quot; rel=&quot;nofollow&quot;&gt;plant-anatomy&lt;/a&gt; is a &lt;em&gt;very broad-term&lt;/em&gt;, that includes &lt;em&gt;plant's &lt;a href=&quot;https://en.wikipedia.org/wiki/Histology&quot; rel=&quot;nofollow&quot;&gt;histology&lt;/a&gt; (studying plant-&lt;a href=&quot;https://en.wikipedia.org/wiki/Tissue_(biology)&quot; rel=&quot;nofollow&quot;&gt;tissue&lt;/a&gt;)&lt;/em&gt; and tissue-distribution patterns, &lt;em&gt;cellular-level anatomy&lt;/em&gt;, especially wall (&lt;a href=&quot;https://en.wikipedia.org/wiki/Extracellular_matrix&quot; rel=&quot;nofollow&quot;&gt;extracellular matrix&lt;/a&gt;)-structures like fibre-patterns, structure of cytoplasmic inclusions like &lt;a href=&quot;https://en.wikipedia.org/wiki/Starch&quot; rel=&quot;nofollow&quot;&gt;starch-grains&lt;/a&gt; , &lt;a href=&quot;https://en.wikipedia.org/wiki/Inulin&quot; rel=&quot;nofollow&quot;&gt;inulin&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Aleurone&quot; rel=&quot;nofollow&quot;&gt;aleurone&lt;/a&gt;, etc. or even organelles like plastid and mitochondria  structural variations.  as well as &lt;em&gt;large, macroscopic structures&lt;/em&gt;, such as topics of &lt;a href=&quot;https://en.wikipedia.org/wiki/Plant_morphology&quot; rel=&quot;nofollow&quot;&gt;plant morphology&lt;/a&gt;, like leaf venation, whole leaf, phyllotaxy, branching, etc. and &lt;a href=&quot;https://en.wikipedia.org/wiki/Plant_life-form&quot; rel=&quot;nofollow&quot;&gt;physiognomy&lt;/a&gt;, like overall-form, rhizosphere shape, rosette, boulting, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plant anatomy is not necessarily for internal structures. Various sorts of external structures like types hairs, scales, silica-impregnations, calcareous incrustations, and surface-topography. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Plant_morphology&quot; rel=&quot;nofollow&quot;&gt;Plant-morphology&lt;/a&gt;, though sometimes dealt as a separate subject from plant-anatomy, where plant morphology usually more focused to the big-picture as well placement-related concepts like 'apical', 'basal', 'radial', 'axial', etc, and &lt;a href=&quot;https://en.wikipedia.org/wiki/Metamorphosis_of_Plants&quot; rel=&quot;nofollow&quot;&gt;metamorphosis&lt;/a&gt; and actual-nature of the organs, practically there are no boundaries in between.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plant anatomy also discusses the organs/structures for ecological adaptation, and their detailed structure, including mycorrhizae, actinorrhizae, rhizobial-nodules, &lt;a href=&quot;https://www.britannica.com/topic/coralloid-root&quot; rel=&quot;nofollow&quot;&gt;coralloid roots&lt;/a&gt;, parasitic haustoria, succulent's water-storage tissue, floating-tissue etc. It also discusses about structures of plant-disease or &lt;a href=&quot;https://en.wikipedia.org/wiki/Plant_pathology&quot; rel=&quot;nofollow&quot;&gt;Plant-pathology&lt;/a&gt; and also about latex, wound-healing, knots, galls etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Palynology&quot; rel=&quot;nofollow&quot;&gt;Palynology&lt;/a&gt;, often considered a branch of plant-anatomy, discusses about structure of pollen-grains, spores, and other-sort of &lt;a href=&quot;https://en.wikipedia.org/w/index.php?title=Palynomorph&amp;amp;redirect=no&quot; rel=&quot;nofollow&quot;&gt;palynomorphs&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://biology.stackexchange.com/tags/dendrology/info&quot;&gt;Dendrology&lt;/a&gt;, a big branch of plant-anatomy, deals with different aspects of wood, the secondary xylem of plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plant anatomy is closely related to Plant developmental biology and plant physiology.&lt;/p&gt;&#xA;" OwnerUserId="25568" LastEditorUserId="25568" LastEditDate="2016-09-11T18:59:42.560" LastActivityDate="2016-09-11T18:59:42.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1792" PostTypeId="4" CreationDate="2012-04-12T18:17:46.890" Score="0" Body="The study of the form and internal structures of plants." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-04-12T19:14:34.650" LastActivityDate="2012-04-12T19:14:34.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1793" PostTypeId="2" ParentId="963" CreationDate="2012-04-12T20:06:04.440" Score="7" Body="&lt;p&gt;Due to my own woeful ignorance on the subject, I have been reading up on statistical methods recently. From what (little) I understand, the real answer to this question is:&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Yes, but only if you are doing &lt;a href=&quot;http://en.wikipedia.org/wiki/Neyman%E2%80%93Pearson_lemma&quot; rel=&quot;nofollow noreferrer&quot;&gt;Neyman-Pearson hypothesis testing&lt;/a&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Absolutely not, if you are using Fisher p-values&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;That is, the question isn't formulated correctly, because power analysis is only valid under one statistical framework (Neyman-Pearson). And you are probably not using that framework.&lt;/p&gt;&#xA;&lt;p&gt;In my experience, most experimental biologists use Fisher's p-value, which gives the probability of the data (or more extreme data) assuming that the null hypothesis is true. Under Fisher's framework, among other drawbacks, there is no quantitative measure of the test's power. However, it has the benefit that it allows scientists to do something close to what we would like to do--that is to draw conclusions from evidence obtained in individual experiments.&lt;/p&gt;&#xA;&lt;p&gt;The Neyman-Pearson framework does included the idea of a test's power, because you must formulate an alternative hypothesis as well as desired alpha and beta error rates before starting your experiment. However, it mostly denies us the ability to make inferences from individual experiments, and for that reason appears less suited to experimental science. To quote from Goodman (see below), under Neyman-Pearson, &amp;quot;we must abandon our ability to measure evidence, or judge truth, in an individual experiment.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;There is no clear &lt;em&gt;right&lt;/em&gt; frequentist framework, although what is clear is that you cannot mix Fisher and Neyman-Pearson. Finally, although it doesn't really address your question directly, it seems wrong not to mention Bayesian methods as an alternative to these two frequentist frameworks, which comes with its own baggage.&lt;/p&gt;&#xA;&lt;h3&gt;Further reading from people that understand this much better than me:&lt;/h3&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://stats.stackexchange.com/a/16071/10506&quot;&gt;Michael Lew's answer to &amp;quot;Setting the threshold p-value as part of hypothesis generation&amp;quot; at Cross Validated&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://stats.stackexchange.com/q/4551/10506&quot;&gt;Michael Lew's answer to &amp;quot;What are common statistical sins&amp;quot; at Cross Validated&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Hubbard, Raymond, and M. J Bayarri. “Confusion Over Measures of Evidence (          p’S) Versus Errors (α’S) in Classical Statistical Testing.” The American Statistician 57, no. 3 (August 2003): 171–178.  (&lt;a href=&quot;http://ftp.isds.duke.edu/WorkingPapers/03-26.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Working Paper PDF&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;h3&gt;Arguments for Bayesian statistics:&lt;/h3&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.annals.org/content/130/12/995&quot; rel=&quot;nofollow noreferrer&quot;&gt;Goodman, Steven N. “Toward Evidence-Based Medical Statistics. 1: The P Value Fallacy.” Annals of Internal Medicine 130, no. 12 (June 15, 1999): 995–1004.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Jaynes, E. T. &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0521592712&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Probability Theory: The Logic of Science&lt;/a&gt; (&lt;a href=&quot;http://omega.albany.edu:8008/JaynesBook.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Online version of some parts&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="72" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-06-15T15:17:44.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1794" PostTypeId="1" AcceptedAnswerId="1798" CreationDate="2012-04-12T21:07:09.203" Score="7" ViewCount="155" Body="&lt;p&gt;My apologies for possibly a naive question. I'm a statistics type and have been asked to assist with analysis of metabolic pathways (and networks). However, I would like to have at least a layman's understanding of how metabolic pathways/networks relate to DNA sequences. Been doing the Google for a few days and, given the results, it's clear I am not formulating the query correctly since nothing seems to be clicking. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something that helps me understand the mechanics behind going from a string of T,A,G, and C's to a network of substrates,enzymes, and products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance for your patience. &lt;/p&gt;&#xA;" OwnerUserId="738" LastActivityDate="2012-04-13T12:16:59.180" Title="Mechanics of going from DNA sequence to metabolic network" Tags="&lt;dna-sequencing&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1795" PostTypeId="1" AcceptedAnswerId="1797" CreationDate="2012-04-13T04:39:49.543" Score="6" ViewCount="850" Body="&lt;p&gt;There seems to be a lot of redundancy in PDB files.  These files can of course be compressed with general-purpose compression programs like gzip, but I can't help but imagine that these tools are overlooking a significant amount of redundancy in PDB files.  Are there compressors that specifically target PDB files?  If not, what are some aspects of PDB files that are ripe for compression?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at a typical PDB file, some redundancies are immediately apparent.  Other redundancies are less obvious.  Consider this excerpt of two residues from &lt;a href=&quot;http://www.rcsb.org/pdb/files/1MBO.pdb&quot; rel=&quot;nofollow&quot;&gt;1MOB&lt;/a&gt; (myoglobin):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ATOM    332  N   LYS A  42      16.481  27.122 -10.033  1.00 11.15           N  &#xA;ATOM    333  CA  LYS A  42      15.926  28.134  -9.159  1.00  8.64           C  &#xA;ATOM    334  C   LYS A  42      16.970  29.081  -8.512  1.00 16.74           C  &#xA;ATOM    335  O   LYS A  42      16.687  30.075  -7.799  1.00 11.84           O  &#xA;ATOM    336  CB  LYS A  42      15.093  27.489  -8.043  1.00 18.03           C  &#xA;ATOM    337  CG  LYS A  42      13.731  26.888  -8.502  1.00 19.65           C  &#xA;ATOM    338  CD  LYS A  42      12.679  27.912  -8.953  1.00 17.94           C  &#xA;ATOM    339  CE  LYS A  42      11.438  27.406  -9.703  1.00 24.82           C  &#xA;ATOM    340  NZ  LYS A  42      10.474  28.567  -9.803  1.00 19.81           N  &#xA;ATOM    341  N   PHE A  43      18.218  28.599  -8.544  1.00 12.28           N  &#xA;ATOM    342  CA  PHE A  43      19.311  29.318  -7.919  1.00 11.81           C  &#xA;ATOM    343  C   PHE A  43      20.223  30.024  -8.949  1.00 10.95           C  &#xA;ATOM    344  O   PHE A  43      21.201  29.462  -9.450  1.00 10.08           O  &#xA;ATOM    345  CB  PHE A  43      20.138  28.301  -7.137  1.00  9.30           C  &#xA;ATOM    346  CG  PHE A  43      19.494  27.689  -5.877  1.00  9.53           C  &#xA;ATOM    347  CD1 PHE A  43      19.572  28.376  -4.679  1.00 12.01           C  &#xA;ATOM    348  CD2 PHE A  43      18.837  26.465  -5.923  1.00 10.54           C  &#xA;ATOM    349  CE1 PHE A  43      18.993  27.861  -3.536  1.00  9.59           C  &#xA;ATOM    350  CE2 PHE A  43      18.261  25.959  -4.775  1.00  8.62           C  &#xA;ATOM    351  CZ  PHE A  43      18.341  26.666  -3.597  1.00  7.89           C  &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;These two residues occupy 1,638 bytes as plain text; when compressed with gzip, they occupy 467 bytes.  For reference, the format of ATOM records in PDB files is defined at wwpdb.org/documentation/format33/sect9.html#ATOM.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Almost all of the data in the above excerpt seems redundant.  The first field (ATOM), second field (atom index, e.g. 332 in the first row), sixth field (residue index, e.g. 42), tenth field (occupancy, e.g. 1.00) and last field (element name, e.g. N) seem clearly extraneous.  The fourth field (residue name) could be shortened from three characters to 1 character, or simply an integer.  I'm not a data compression expert, but I imagine gzip picks up most of this redundancy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Slightly less obviously, the atom names for each residue also seem unnecessary.  To my understanding, the atomic composition of all residues' backbones will always be the same, and represented in PDB files as &quot;N&quot;, &quot;CA&quot;, &quot;C&quot;, &quot;O&quot;.  The same for the atomic composition of the residues' respective sidechains: a lysine sidechain will always be &quot;CB&quot;, &quot;CG&quot;, &quot;CD&quot;, &quot;CE&quot;, &quot;NZ&quot; and a phenylalanine sidechain will always be &quot;CB&quot;, &quot;CG&quot;, &quot;CD1&quot;, &quot;CD2&quot;, &quot;CE1&quot;, &quot;CE2&quot;, &quot;CZ&quot;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A subtler redundancy, but one that might increase compressibility a lot, seems like it could be in the atomic coordinates themselves.  For example, in the backbone, would it be possible to deduce each residue atom's X, Y and Z coordinates (12 data points: 4 atoms * 3 coordinates) given only their phi, psi and omega &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Dihedral_angle&amp;amp;oldid=474965018#Dihedral_angles_of_biological_molecules&quot; rel=&quot;nofollow&quot;&gt;dihedral angles&lt;/a&gt; (3 data points)?  Could applying dihedral angles to atoms within sidechains similarly remove the need to explicitly list the 3D coordinates there?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could &quot;temperature  factor&quot; (the second to last field in the excerpt) be losslessly removed, or compressed in some non-obvious way?  What are some other possible optimizations that could be used to more efficiently compress PDB files?  Are there any obvious grave performance implications of these various compression techniques on the speed of a hypothetical decompressor to convert back to the official PDB format?  Have these questions been answered in the literature or an existing PDB-specific compression program?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance for any answers or feedback.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that no PDB-specific file compressors seem to be available, I suppose my specific goal is to develop one.  One potential application I see for this is in significantly decreasing fresh times-to-render in certain use cases of browser-based molecular visualization programs, e.g. &lt;a href=&quot;http://jmol.sourceforge.net/&quot; rel=&quot;nofollow&quot;&gt;Jmol&lt;/a&gt;, &lt;a href=&quot;http://web.chemdoodle.com/&quot; rel=&quot;nofollow&quot;&gt;ChemDoodle Web Components&lt;/a&gt; or &lt;a href=&quot;http://webglmol.sourceforge.jp/glmol/viewer.html&quot; rel=&quot;nofollow&quot;&gt;GLmol&lt;/a&gt;.  Another application could be decreasing the time and size of data needed to download archives of PDB files like those described &lt;a href=&quot;http://www.wwpdb.org/downloads.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This would of course require a way to efficiently decompress the packed PDB files, but this trade-off between decompression time and download time seems like it could be useful in at least some niche applications.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit 2&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a comment, nico asks &quot;How would compressing the file decrease render time?&quot;.  Decreasing gzipped PDB file size (e.g. by half or more) and thus decreasing time needed to download the file would decrease the time between when the PDB file was requested from a remote server and when the structure was rendered by a molecular visualization program running on a client machine. Apologies if that use of &quot;fresh time-to-render&quot; in that context was unclear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lossless compression could also involve encoding the PDB file to an object (e.g. JSON) that is faster to parse for the visualization program, and decrease render times that way.  Looking around further, if the application only required displaying the 3D structure and not also retaining data about specific atoms and residues, then using a binary mesh compression (e.g. &lt;a href=&quot;http://code.google.com/p/webgl-loader/&quot; rel=&quot;nofollow&quot;&gt;webgl-loader&lt;/a&gt;) seems like it would probably decrease time-to-render even more.&lt;/p&gt;&#xA;" OwnerUserId="739" LastEditorUserId="739" LastEditDate="2012-04-14T18:53:57.843" LastActivityDate="2016-06-14T23:31:07.193" Title="Compressing structural information in PDB files" Tags="&lt;bioinformatics&gt;&lt;pdb&gt;&lt;3d-structure&gt;&lt;visualization&gt;" AnswerCount="4" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1796" PostTypeId="2" ParentId="1795" CreationDate="2012-04-13T06:19:31.493" Score="3" Body="&lt;p&gt;The PDB file format was specified in the dawn of computing to fit on punch cards. So it has some shortcomings that have led to generations of scientists cursing the fixed-width column format. By now, it has been superseded by an XML-like format: PDBML. Of course XML is less space-efficient than a column layout, so you can see that disk space was not the main concern, but being able to parse the files. Nonetheless, the &lt;a href=&quot;http://pdbml.pdb.org/&quot; rel=&quot;nofollow&quot;&gt;PDBML page&lt;/a&gt; states that they offer three types of download files: &quot;fully marked-up files, files without atom records, files with a more space efficient encoding of atom records&quot; -- so you could check what they do in the latter case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your suggestions: in theory you could use only dihedral angles. However, the numerical errors would accumulate as you go along re-constructing the 3D coordinates, and different software architectures will give you different precision. So: explicit is better than implicit in scientific file formats.   &lt;/p&gt;&#xA;" OwnerUserId="112" LastEditorUserId="43" LastEditDate="2012-04-13T20:47:48.517" LastActivityDate="2012-04-13T20:47:48.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1797" PostTypeId="2" ParentId="1795" CreationDate="2012-04-13T08:41:39.110" Score="6" Body="&lt;p&gt;You are making a few assumptions that are likely not valid for all PDB files. For example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Residue indices are not necessarily sequential, nor do they have to start at 1&lt;/li&gt;&#xA;&lt;li&gt;Not all possible residues have 1-letter code equivalents, there are thousands of possible exotic residues, not only the standard amino acids&lt;/li&gt;&#xA;&lt;li&gt;PDB files are not only used for proteins, but also nucleic acids and small molecules (usually as ligands)&lt;/li&gt;&#xA;&lt;li&gt;Occupancy can be different from 1.0 if there are multiple conformations represented in the PDB file&lt;/li&gt;&#xA;&lt;li&gt;The element type is obvious for unmodified amino acids and nucleotides, but not necessarily for more exotic residues (though usually it's easy to identify)&lt;/li&gt;&#xA;&lt;li&gt;The distances between atoms are not necessarily the ideal distances, so you would need angles and distances to represent the coordinates.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The temperature factor is an experimentally determined value, there is no obvious compression for that. You can safely discard it if you don't need that data, and e.g. it has no meaning anyway in NMR structures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The advantage of the PDB format is that pretty much every program can (theoretically) handle it, though the implementations vary and subtle incompatibilities can cause a lot of headaches. The size of PDB files is almost never a problem, so there is no significant motivation to improve on the format in that regard.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2012-04-13T08:41:39.110" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1798" PostTypeId="2" ParentId="1794" CreationDate="2012-04-13T12:16:59.180" Score="6" Body="&lt;p&gt;The question is not too broad, just involves a fair bit of work to both do the research and compose a response. I'll do the latter, but in brief.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The strings of the four nucleotides encode genes. Sometimes these genes are broken into protein-coding portions (exons) and sometimes intervening, non-coding regions (introns). Bacteria, for example do not have introns within genes while most human genes do. The nucleotides in the protein-coding portion of the gene do just that - give instructions on how to synthesize the protein by directing which tRNAs the ribosome uses to translate the genetic code into a protein chain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A useful phrase is &lt;strong&gt;protein sequence dictates protein structure and that structure dictates function&lt;/strong&gt;. So, the proteins do things and many act as enzymes or modulators of enzyme activity. An enzyme catalyzes a biochemical reaction, lowering the activation energy to go from reactant(s) to product(s). One enzyme can be thought of as one unit within a metabolic network. A modulator might activate or deactivate an existing enzyme. A protein kinase is a good example of a modulator.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next, string some of those enzymes together to build a pathway. A common example is glycolysis. Think of this as a chain where the output or product of enzyme A serves as input to enzyme B, whose product is the input to enzyme C, and so on. These pathways are two-way, but it is exceedingly difficult to travel from the final product all the way up such a pathway to the initial input within the confines of a biological system. Thus, the pathways in practical terms are thought of as one-way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the pathways do not function in isolation. The final product may serve as input to one, two or more other pathways. Your pathway of choice may begin with the output of another process. Furthermore, pathways can branch: Glycolysis can proceed to glyceraldehyde 3-phosphate and pyruvate, or directly after glucose 6-phosphate formation can be shunted to the pentose phosphate pathway to yield reducing power and 5-carbon sugars (to be used in ATP, CoA, FAD, NAD+, DNA and RNA). Now, pathways leading to other pathways and branches and such make a network. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You and your colleagues might want to know if genes within a metabolic network are over- or under-represented in a test compared to control. Or, genes for a given network are not present in one species compared to several others. Or, one could estimate the flux through such a network given a set of measures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Peruse examples at both KEGG and Reactome, expecially at KEGG where you can view pathways pertinent to your organism(s) of choice.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-04-13T12:16:59.180" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1799" PostTypeId="1" CreationDate="2012-04-13T13:28:52.930" Score="6" ViewCount="240" Body="&lt;p&gt;It is commonly accepted that birds are descendants of dinosaurs. It is nice that not &lt;em&gt;all&lt;/em&gt; dinosaurs died out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there other animals, descendants of dinosaurs, &#xA; that survived ? (Maybe not till our time, but survived the time when most dinosaurs died).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, what made flying dinosaurs survive and not die like other dinosaurs?&lt;/p&gt;&#xA;" OwnerUserId="226" LastEditorUserId="69" LastEditDate="2012-04-13T13:32:21.230" LastActivityDate="2013-06-26T13:58:03.910" Title="Descendants of dinosaurs " Tags="&lt;palaeontology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1800" PostTypeId="2" ParentId="1505" CreationDate="2012-04-13T14:17:33.950" Score="6" Body="&lt;p&gt;As mentioned in the comments, this question is quite complicated. If the chance of a single cell from different organisms getting cancer was the same, then you would be correct, but this is not the case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Different organisms have evolved to live different lengths of time. This is rather obvious when you think about it: mice have a maximum lifespan of ~3 years, humans ~80years (these figures are of course &lt;em&gt;massive&lt;/em&gt; generalizations - but it doesn't really matter). Yet 'old' mice (&gt; 2 years) still get age-related diseases such as cardiovascular disease, and cancer. It should be fairly clear that the risk of a 2 year old mouse getting (age-related) cancer is much higher than a 2 year old human.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The explanation for this isn't exactly concrete, but it goes something like this; mice invest a lot more resources in growing very fast and reaching a reproductive age very early, whereas humans develop much more slowly, and invest a higher proportion of their resources in maintaining tissue function, thereby reaching reproductive maturity much later than the mouse. The &lt;em&gt;Hayflick limit&lt;/em&gt; for a mouse is about 10, whereas for humans this is closer to 60.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus the rate of aging in humans is much lower than that of the mouse, and it comes back to evolution: mortality in the wild is very high for the mouse, and thus mice that invest heavily in reaching early reproductive maturity are selected for - and those that invest in anti-cancer mechanisms take longer to reach reproductive maturity, and thus have less chance of actually doing it!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to answer your question - smaller organisms tend to have higher risks of getting cancer because their lifespans are comparatively shorter, and thus they 'age' at a faster rate and invest less resources in maintaining function (e.g. genome integrity).&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-04-13T14:17:33.950" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1801" PostTypeId="2" ParentId="1366" CreationDate="2012-04-13T14:38:54.080" Score="3" Body="&lt;p&gt;Rapamycin specifically inhibits the mTOR pathway (mTOR = mammalian target of rapamycin), which has numerous downstream functions including protein biogenesis, regulation of cell cycle, immune function and apoptosis. The upstream effectors of mTOR include growth factors and amino acid availability, so you can certainly see that the lifespan enhancing effects of caloric restriction will be (at least in part) mediated by the mTOR pathway. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But there are key differences. mTOR also receives signals relating to DNA damage and inflammatory changes (to name just 2) that are essential for healthy survival. So any direct inhibition of this pathway will affect all the functions - I can't find the reference now, but I have definitel read in one of the numerous rodent studies that rapamycin treated mice have reduced immune function (i.e. the lifespan increased effects can only be seen in a controlled lab environment - in the wild mTOR-inhibition to this degree would be a disadvantage).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think therefore it is fair to say that the effects of caloric restriction on longevity are mediated by mTOR, but administration of rapamycin is not an equivalent treatment.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Really great review came out last month (http://www.ncbi.nlm.nih.gov/pubmed/22500797) - I recommend you give that a skim if you want detail!&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-05-11T14:01:21.337" LastActivityDate="2012-05-11T14:01:21.337" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1803" PostTypeId="1" AcceptedAnswerId="1812" CreationDate="2012-04-13T21:00:38.503" Score="5" ViewCount="279" Body="&lt;p&gt;I'm working with a protein that doesn't have any homology to other proteins so it will likely require ab initio structure prediction. However, since I don't work for a structure prediction lab and I don't have a stringent requirement to have a high resolution structure, I'm fine with a 6-10 angstrom resolution prediction to help me visualize the protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm imagining I-TASSER to get an initial idea of the topology. SWISS-MODEL doesn't find any homologs to template against. I'm trying to avoid using Robetta since it will probably take a month. What other low-resolution webservers should I test?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, you could just tell me to suck it up and submit it to a month-long prediction.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-04-14T14:11:59.987" Title="First pass protein structure prediction" Tags="&lt;bioinformatics&gt;&lt;structure-prediction&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1804" PostTypeId="2" ParentId="1803" CreationDate="2012-04-13T22:46:17.573" Score="4" Body="&lt;p&gt;Robetta's the best service I've found for a protein I'm working on that doesn't have a solved structure. It's down right now for the CASP10 competition, but I would submit it and wait. The wait time lately has been ~2 months.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-13T22:46:17.573" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1805" PostTypeId="1" AcceptedAnswerId="1823" CreationDate="2012-04-13T23:02:25.103" Score="17" ViewCount="5292" Body="&lt;p&gt;Pretty much this. I've been wondering if any of the yogourt and other &quot;health&quot; foods containing living probiotic cultures survive digestion to populate our intestines? If so, is there peer-reviewed evidence you could point me to?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-07-17T16:36:09.950" Title="Do probiotics survive digestion?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1806" PostTypeId="2" ParentId="1805" CreationDate="2012-04-14T01:54:22.887" Score="9" Body="&lt;p&gt;When I took Microbio we had a entire lecture on this. My professor's view was that they do not survive due to the pH of the stomach.  He told us that there are microbiologist on both sides as to whether they do make it to the intestine (or enough of them to make much difference) or that they do survive and help. I have added a link below to a article by the American Society of Microbiology. Here it is saying that it may be helpful, but that more studies are being conducted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://cmr.asm.org/content/16/4/658.short&quot;&gt;http://cmr.asm.org/content/16/4/658.short&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="742" LastActivityDate="2012-04-14T01:54:22.887" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1807" PostTypeId="2" ParentId="1416" CreationDate="2012-04-14T11:32:23.957" Score="2" Body="&lt;p&gt;As far as I can tell there &lt;em&gt;is&lt;/em&gt; a distinction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;strong&gt;tetrad&lt;/strong&gt; refers to the &lt;em&gt;entire&lt;/em&gt; group of four chromatids after they have come together for crossing over in Prophase I (synapses).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;strong&gt;synaptonemal complex&lt;/strong&gt; as you would expect is formed in synapses.  This is a protein-RNA complex that connects the intervening regions of matched chromosomes in some circumstances - it is not required. Mutated yeast that can not form this complex has still been shown to be able to exchange genetic information. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, &lt;strong&gt;you can have a tetrad without a synaptonemal complex, but not vice versa&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-04-14T11:32:23.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1808" PostTypeId="1" AcceptedAnswerId="6833" CreationDate="2012-04-14T12:42:34.630" Score="11" ViewCount="221296" Body="&lt;p&gt;I am curious what animal is this. It is/lives inside some kind of cocoon, about 1 cm in length. They are attached to walls and to the ceiling, but sometimes they fall off. Inside the structure there is a small worm that can come out at both ends alternatingly. It can then hold on to the ground to move the cocoon around. They are said to feed on paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Yd5Lh.jpg&quot; alt=&quot;slightly better picture of animal&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="745" LastEditorUserId="745" LastEditDate="2012-04-23T14:43:55.413" LastActivityDate="2013-11-13T04:17:11.073" Title="Small worm living in some kind of cocoon, what are these animals?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1809" PostTypeId="2" ParentId="1752" CreationDate="2012-04-14T12:44:45.267" Score="12" Body="&lt;p&gt;It is easy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Method A, simple, is based on &quot;counting the fish in the pond&quot; method.  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Make rough estimate of amount of blood in the organism.&lt;/li&gt;&#xA;&lt;li&gt;Choose a component of blood that is replenished slowly [from liver or marrow etc]. That takes time to replenish. Red blood cells are probably OK. Some easily measurable and slowly replenished component of blood. Let's call this component of blood G.  &lt;/li&gt;&#xA;&lt;li&gt;Take small blood sample and measure level of G, denote result G1.  &lt;/li&gt;&#xA;&lt;li&gt;Drain N ml of blood, ands refill same amount back with infusion of normal saline.&lt;br&gt;&#xA;N can be taken as 10% of estimate of amount of blood.  &lt;/li&gt;&#xA;&lt;li&gt;Take small blood sample, measure level of G, denote result G2.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;G2 will be smaller than than G1. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now from G1, G2, and N it is easy to calculate organism's amount of blood.&#xA;You can derive exact formula yourself.&lt;/p&gt;&#xA;" OwnerUserId="226" LastEditorUserId="226" LastEditDate="2012-04-14T19:05:53.553" LastActivityDate="2012-04-14T19:05:53.553" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1810" PostTypeId="5" CreationDate="2012-04-14T13:31:44.553" Score="0" Body="&lt;h3&gt; Usage Guidelines:&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Species Identification questions get better answers if they include...&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;One or more &lt;em&gt;clear&lt;/em&gt; &lt;strong&gt;Photos&lt;/strong&gt;.&lt;/li&gt;&#xA;&lt;li&gt;A &lt;strong&gt;Location&lt;/strong&gt; where the specimen was found (city/region and/or habitat).&lt;/li&gt;&#xA;&lt;li&gt;An approximate &lt;strong&gt;Size&lt;/strong&gt; (or photo indicating size).&lt;/li&gt;&#xA;&lt;li&gt;Additional useful info (e.g., behavior, time of day/year, etc...)&lt;/li&gt;&#xA;&lt;li&gt;Indication of prior research performed by the asker. &lt;/li&gt;&#xA;&lt;li&gt;A tag for a specific taxanomic group (e.g., &lt;a href=&quot;/questions/tagged/botany&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;botany&amp;#39;&quot; rel=&quot;tag&quot;&gt;botany&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/entomology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;entomology&amp;#39;&quot; rel=&quot;tag&quot;&gt;entomology&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/arachnology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;arachnology&amp;#39;&quot; rel=&quot;tag&quot;&gt;arachnology&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/ornithology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;ornithology&amp;#39;&quot; rel=&quot;tag&quot;&gt;ornithology&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/ichthyology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;ichthyology&amp;#39;&quot; rel=&quot;tag&quot;&gt;ichthyology&lt;/a&gt;, etc...)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Some tag specific hints:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;/questions/tagged/botany&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;botany&amp;#39;&quot; rel=&quot;tag&quot;&gt;botany&lt;/a&gt;&lt;/strong&gt;: try to include photo of leaf, stem/trunk, &lt;em&gt;and&lt;/em&gt; flower/fruit. &lt;em&gt;All&lt;/em&gt; are often needed for accurate ID.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;/questions/tagged/entomology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;entomology&amp;#39;&quot; rel=&quot;tag&quot;&gt;entomology&lt;/a&gt;&lt;/strong&gt;/&lt;strong&gt;&lt;a href=&quot;/questions/tagged/arachnology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;arachnology&amp;#39;&quot; rel=&quot;tag&quot;&gt;arachnology&lt;/a&gt;&lt;/strong&gt;: there are many similar looking species. Add close-up photos (from multiple angles) if possible!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;/questions/tagged/ichthyology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;ichthyology&amp;#39;&quot; rel=&quot;tag&quot;&gt;ichthyology&lt;/a&gt;&lt;/strong&gt;: please indicate whether you found the fish in &lt;a href=&quot;https://biology.stackexchange.com/questions/tagged/marine-biology&quot;&gt;marine&lt;/a&gt; or &lt;a href=&quot;https://biology.stackexchange.com/tags/freshwater-biology&quot;&gt;fresh&lt;/a&gt; water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;/questions/tagged/mycology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;mycology&amp;#39;&quot; rel=&quot;tag&quot;&gt;mycology&lt;/a&gt;&lt;/strong&gt;: please include photo of top &lt;em&gt;and&lt;/em&gt; bottom of mushrooms!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please take a look &lt;a href=&quot;http://meta.biology.stackexchange.com/questions/3452/are-there-any-guideline-about-species-identification-questions&quot;&gt;&lt;strong&gt;here&lt;/strong&gt;&lt;/a&gt; for more hints.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h3&gt; General Info:&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;In-general; &lt;a href=&quot;https://en.wikipedia.org/wiki/Identification&quot; rel=&quot;nofollow noreferrer&quot;&gt;Identification&lt;/a&gt; is the process of determining the 'identity' or nature of a certain given object, out of a set of all known objects. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Identification is a part of Taxonomy. &lt;a href=&quot;https://en.wikipedia.org/wiki/Taxonomy_(general)&quot; rel=&quot;nofollow noreferrer&quot;&gt;Taxonomy&lt;/a&gt; is the science of arranging informations into groups and subroups on the basis of &lt;a href=&quot;https://en.wikipedia.org/wiki/Logic&quot; rel=&quot;nofollow noreferrer&quot;&gt;logic&lt;/a&gt;. &lt;em&gt;In biology&lt;/em&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Taxonomy_(biology)&quot; rel=&quot;nofollow noreferrer&quot;&gt;taxonomy&lt;/a&gt; means the science of classifying the organisms according to teir evolutionary distance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taxonomy in biology, have main 4 pillars (4-types of works), abbreviated as a mnemonic &lt;a href=&quot;https://books.google.co.in/books?id=Ia2eIPVksMMC&amp;amp;lpg=PA10&amp;amp;ots=CDFS5eFUcg&amp;amp;dq=D.I.N.C.%20of%20taxonomy&amp;amp;pg=PA10#v=onepage&amp;amp;q=D.I.N.C.%20of%20taxonomy&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;DINC&lt;/a&gt; , whose full form is description, identification, nomenclature and classification. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;https://en.wikipedia.org/wiki/Identification_(biology)&quot; rel=&quot;nofollow noreferrer&quot;&gt;biology&lt;/a&gt;, identification of a specimen means, determining the identity of that specimen out of a set of known organisms (which may be a museum or a &lt;a href=&quot;https://en.wikipedia.org/wiki/Herbarium&quot; rel=&quot;nofollow noreferrer&quot;&gt;herbarium&lt;/a&gt; an information-repertory or a database etc). Identification could be done upto a certain level or rank. Such as upto family-rank ('family-identification'), upto genus-rank ('Genus-identification'), upto species rank (species identification) etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term 'identification' is applicable only-when we have the object's record in the world's knowledge base. But if it a new discovery; then 'identification' or 'determining the identity'.  does not apply. Then we can do its &lt;em&gt;documentation&lt;/em&gt;. However still we can identify the upper-ranks of the specimen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To easily express or mention-about an organism of a certain identity, we use 'name' or '&lt;a href=&quot;https://en.wikipedia.org/wiki/Identifier&quot; rel=&quot;nofollow noreferrer&quot;&gt;identifiers&lt;/a&gt;'. On scientific-context it is the binomial scientific-name. After finish the identification we ends at the name or identifier for that organism. (However the name or identifier is not the 'identity' of the organism, but it is a short-cut or link to access the organism's identity within the knowledge base.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the group-of-organism, the identification could be &lt;a href=&quot;https://en.wikipedia.org/wiki/Animal_identification&quot; rel=&quot;nofollow noreferrer&quot;&gt;animal-identification&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Plant_identification&quot; rel=&quot;nofollow noreferrer&quot;&gt;plant identification&lt;/a&gt;, fungus identification, bacteria identification etc. &lt;a href=&quot;https://en.wikipedia.org/wiki/Fossil&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fossil&lt;/a&gt;-specimens too, are identified  out of the knowledge-base for records of other fossil and present-day specimens. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To identify an organism; we need look observable- '&lt;a href=&quot;http://www.ucmp.berkeley.edu/glossary/gloss1phylo.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;characters&lt;/a&gt;' (variables) and '&lt;a href=&quot;http://www.ucmp.berkeley.edu/glossary/gloss1phylo.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;character-states&lt;/a&gt;' (possible values of that variable). as simple example; 'colour' is a character. 'red' or 'green' or 'yellow' etc are different states of that character. or if branching-pattern is a character, then racemose or cymose branching patterns are 2 character states for it.   A character could be macroscopic or microscopic or biochemical or molecular or behavioral etc.&lt;br&gt;&#xA;The logical steps or &lt;a href=&quot;https://en.wikipedia.org/wiki/Algorithm&quot; rel=&quot;nofollow noreferrer&quot;&gt;algorithms&lt;/a&gt; required as tool for identification, are termed as &lt;a href=&quot;https://en.wikipedia.org/wiki/Identification_key&quot; rel=&quot;nofollow noreferrer&quot;&gt;identification keys&lt;/a&gt;. An identification key may be printed, or may be computerised. Even in case of identifying manually; we use some-or some key consciously or sub-consciously. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Before asking an identification question, Please include as much information as possible on habitat (esp. where in the world you found the organism), size, and behavior, and ideally provide images. Please take a look &lt;a href=&quot;http://meta.biology.stackexchange.com/questions/3452/are-there-any-guideline-about-species-identification-questions&quot;&gt;&lt;strong&gt;here&lt;/strong&gt;&lt;/a&gt; to get a basic idea.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="16866" LastEditDate="2019-07-12T03:08:10.813" LastActivityDate="2019-07-12T03:08:10.813" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="1811" PostTypeId="4" CreationDate="2012-04-14T13:31:44.553" Score="0" Body="Questions looking to find the name of a specific organism.  Please include as much information as possible on location/habitat, size/characteristics and behavior. Ideally, you should provide images.  " OwnerUserId="69" LastEditorUserId="16866" LastEditDate="2017-05-31T19:40:10.447" LastActivityDate="2017-05-31T19:40:10.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1812" PostTypeId="2" ParentId="1803" CreationDate="2012-04-14T14:11:59.987" Score="5" Body="&lt;p&gt;Have you used &lt;a href=&quot;http://toolkit.tuebingen.mpg.de/hhpred&quot;&gt;hhpred&lt;/a&gt; to search for homologues? What was your criteria for defining there was no homologues? You could potentially go down to around 30% sequence identity to model.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would submit the the query sequence to both I-Tasser and Rosetta and see if both of the servers agree on the topology. I-Tasser will always provide 5 models of your query sequence (even if they are rubbish) ranked by a confidence score.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While you wait for the above servers to finish, I would submit the sequence to a number of secondary structure prediction servers to come to a general consensus for the secondary structure of your protein. Some servers you could use are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.predictprotein.org/&quot;&gt;Predict Protein&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index&quot;&gt;Phyre2&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://raptorx.uchicago.edu/&quot;&gt;Raptor X&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.compbio.dundee.ac.uk/www-jpred/&quot;&gt;Jpred&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bioinf.cs.ucl.ac.uk/psipred/&quot;&gt;Psi-Pred&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If the servers come to a consensus, compare the secondary structure prediction with that of the secondary strucutre of the models, to see if the &lt;em&gt;ab initio&lt;/em&gt; modelling concurs with that of the secondary strucutre prediction. This will give you more reason to be confident in your model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would then validate your models using:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://prosa.services.came.sbg.ac.at/prosa.php&quot;&gt;Prosa&lt;/a&gt; - This calculates a Z-score, and plots where it fits with structures with a similar amino acid length, from the PDB.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Discrete_optimized_protein_energy&quot;&gt;DOPE Score&lt;/a&gt; - This is employed in Modeller and measures the &quot;nativeness&quot; of your model, the lower the score the better. But you will need to install Python and have some knowledge of how to use the command line. I can provide the code to Run Dope with modeller.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Finally, are there any constraints you could introduce such a oligomerisation site or a protein-protein interaction site, to help with the modelling?&lt;/p&gt;&#xA;" OwnerUserId="158" LastActivityDate="2012-04-14T14:11:59.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1813" PostTypeId="1" CreationDate="2012-04-14T15:10:58.227" Score="7" ViewCount="1309" Body="&lt;p&gt;I'm looking find a cheat sheet for protein biology to stick on my desk to remind of some of the key principles of protein biology. I seem to remember the specific and complex principles in protein biology but at the expense of the basics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone point me to a protein biology cheat sheet or formulate some suggestions to go on one?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;EDIT&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I am looking for:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Amount of amino acids in a helix turn&lt;/li&gt;&#xA;&lt;li&gt;Amino acids typically found in Beta sheets and Helices&lt;/li&gt;&#xA;&lt;li&gt;The types of protein interactions (i.e. ionic, hydrophobic) and the  amino acids usually involved.&lt;/li&gt;&#xA;&lt;li&gt;Definition of Globular and fibrous form&lt;/li&gt;&#xA;&lt;li&gt;Types of post-translational modifications&lt;/li&gt;&#xA;&lt;li&gt;Any other useful characteristics &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="158" LastEditorUserId="158" LastEditDate="2012-04-14T18:42:22.083" LastActivityDate="2012-04-18T13:41:08.387" Title="Protein Biology Cheat Sheet" Tags="&lt;proteins&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1814" PostTypeId="1" AcceptedAnswerId="1816" CreationDate="2012-04-14T16:41:42.443" Score="10" ViewCount="1167" Body="&lt;p&gt;I had this thought while bathing:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume a &lt;em&gt;perfectly&lt;/em&gt; developed physical human body and anatomy in terms of size, dimensions and proportions. In theory, if I cut the body vertically into two &lt;em&gt;exact halves&lt;/em&gt; from the center of the head downwards, &lt;strong&gt;would the two halves weigh the same?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tend to think that the 2 halves would weigh differently, and if so, I find this quite interesting because it is strange to me that our body would - &lt;em&gt;perhaps unecessarily&lt;/em&gt; - evolve in such a manner that requires it to balance itself on a symmetrical skeleton.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any topics that touches on this... phenomenon?&lt;/p&gt;&#xA;" OwnerUserId="746" LastEditorUserId="69" LastEditDate="2012-04-14T17:31:23.030" LastActivityDate="2012-05-23T14:34:10.733" Title="Weighing 2 vertical halves of the human body" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1815" PostTypeId="2" ParentId="1814" CreationDate="2012-04-14T17:36:23.070" Score="6" Body="&lt;p&gt;Humans, like all vertebrates, belong in subregnum &lt;a href=&quot;http://en.wikipedia.org/wiki/Bilateria&quot;&gt;bilateria&lt;/a&gt;, a broad class of animals whose characteristic trait is having a &lt;a href=&quot;http://en.wikipedia.org/wiki/Bilateral_symmetry&quot;&gt;bilaterally symmetric&lt;/a&gt; body plan at least in some of their life stages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Urbilaterian&quot;&gt;common ancestor of all bilaterians&lt;/a&gt; was presumably something like a small marine worm.  For a primitive animal living in water, an obvious advantage of bilateral symmetry is that it makes directed swimming easier.  If the animal were completely asymmetric, it would have to continually exert active control over its heading to be able to swim straight.   On the other hand, an even more symmetrical animal (such as one with 90&amp;deg; rotational symmetry) might have trouble controlling its vertical and lateral heading separately, which could be a problem in aquatic habitats where staying at a certain depth is often useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Indeed, in many ways these reasons are the same as why pretty much all &lt;a href=&quot;http://en.wikipedia.org/wiki/Aircraft&quot;&gt;aircraft&lt;/a&gt; are bilaterally symmetric: in the absence of active steering, we want them to fly straight and level.  That requires at least rough left&amp;ndash;right symmetry and generally also some degree of top&amp;ndash;down symmetry, although some breaking of the latter is usually needed both for landing and to account for the effects of gravity on flight dynamics.  We &lt;em&gt;could&lt;/em&gt; build completely asymmetric aircraft if we wanted, they just would be harder to fly.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for why this ancestral bilateral symmetry has survived so well throughout the course of evolution, that's presumably both because it's so deeply embedded in the genes that control our &lt;a href=&quot;http://en.wikipedia.org/wiki/Ontogeny&quot;&gt;ontogeny&lt;/a&gt;, but also because the basic reasons why such symmetry is useful still remain, even though our size, shape, habitat and locomotion are very different from those of the first &quot;urbilaterian&quot;.  Even though we mostly move by walking instead of swimming, it's still useful for us to be able to walk straight without having to pay constant attention to it.  Furthermore, once we've first learned to walk (or crawl) straight, it's useful that we can also learn to run, swim and jump (and ride a bike or drive a car) straight without having to always re-learn the exact amount of control needed to maintain a given heading with each of these modes of locomotion.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Ps. To answer your actual question, I'd guess, like Rory M, that the two halves of a human body probably won't weigh &lt;em&gt;exactly&lt;/em&gt; the same, both due to the asymmetrical distribution of the internal organs and also due to uneven muscle development.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the difference is quite small compared to the total mass of the human body, so that the center of mass is presumably still quite close to the body's centerline.  As I noted above, any significant deviation from that would cause issues with gait and balance.  Although such issues can certainly be adapted to and overcome with active control &amp;mdash; after all, even people who've lost a whole &lt;em&gt;leg&lt;/em&gt; manage to get around one way or another &amp;mdash; they're presumably still significant enough to be selected against over evolutionary timescales, which is why our body shape remains so nearly symmetrical.&lt;/p&gt;&#xA;" OwnerUserId="239" LastEditorUserId="239" LastEditDate="2012-04-14T17:51:43.270" LastActivityDate="2012-04-14T17:51:43.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1816" PostTypeId="2" ParentId="1814" CreationDate="2012-04-14T18:32:41.440" Score="10" Body="&lt;p&gt;The two halves likely do weigh approximately the same. Since the density of most tissues that are not filled with air is basically equal, it doesn't matter that, e.g., heart, spleen, and stomach are on the left and liver is (mostly) on the right. In the left/right axis, it evens out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the location of the center of mass of a human: it's located about 10 cm below the navel, at the level of the S2 vertebra approximately midway between dorsal and ventral surfaces of the body (assuming that the person in question is neither pregnant nor obese).&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-04-14T18:32:41.440" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1817" PostTypeId="2" ParentId="1754" CreationDate="2012-04-14T19:02:20.750" Score="8" Body="&lt;p&gt;Abundant example exist to this when it comes to organs. There are plenty of examples when organs that in the past served some function -- because they evolved to serve this function -- later degenerated or disappeared because environment changed. Examples: vision of species that came to live underground, wings/ability to fly of non-flying birds (penguins, ostriches etc), legs of snakes, some organs of sea mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We know what adaptations mammal species develop to life in the sea. However, these mammals do not turn to cold-blooded fish with scales and gills. They take different evoluionary path for adaptation to sea life. In particular, they remain warm blooded, milk-feeding, and  retain lungs. I do not think it is possible that lungs back-evolve into gils, but it is interesting question which mechanisms a mammal like dolphin would evolve if it needed to live all the time under the surface of the sea. It would be matter of inventiveness of mutations in the face of new (old :-) conditions not the issue of back-evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not think it was ever shown that genome has mechanism in which instead of mutations, &quot;old&quot; genetic trails (like gils) would be used. I think such mechanism does not exist, and in this sense, the answer to your question is &quot;no&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if chain of mutations exist that brings a species back to s atate resembling &quot;old&quot; state, this path might be taken. (degeneration of ograns). In this sense, the answer is &quot;yes&quot;.&lt;/p&gt;&#xA;" OwnerUserId="226" LastEditorUserId="226" LastEditDate="2012-04-14T19:41:22.400" LastActivityDate="2012-04-14T19:41:22.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1818" PostTypeId="1" CreationDate="2012-04-14T20:05:10.843" Score="5" ViewCount="450" Body="&lt;p&gt;Is there any way to design a PCR primer if region of interest is highly repetitive (tens of kilobases only SINE's &amp;amp; LINE's)?&lt;/p&gt;&#xA;" OwnerUserId="744" LastActivityDate="2012-04-14T22:02:25.657" Title="PCR primer in highly repetitive region" Tags="&lt;pcr&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1819" PostTypeId="2" ParentId="1818" CreationDate="2012-04-14T21:54:36.650" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://vertebrata.bio.msu.ru/Shedlock_Okada_2000_BE.pdf&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; describes some PCR strategies with LINE and SINE PCR identification (Shedlock and Okada. SINE Insertions: powerful tools for molecular systematics. BioEssays (2000) 22:148-160.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have no experience with PCR amplification of SINEs or LINEs, however I can think of two strategies right now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) You may be able to find a unique 18-20 nt region flanking those regions. If you can, great. If not, perhaps there is a unique site somewhere in the middle of these regions, then you can amplify from the middle outward to both upstream and downstream regions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) If there are no unique sites that you can exploit, that would imply a highly regular (ie, repetitive) pattern, but you can take advantage of this too. You can pick primers such that they are on the extremes of the repetitive subunit within these structures. For example, if your sequence looks like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;A------&amp;gt;BA------&amp;gt;BA------&amp;gt;BA------&amp;gt;BA------&amp;gt;B&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Then you can pick primers A and B for PCR use. You will have non-specific primers, and therefore when you amplify the DNA, you will get all possible permutations of DNA that these primers will produce. Specifically, you will get:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;A------&amp;gt;B&#xA;&#xA;A------&amp;gt;BA------&amp;gt;B&#xA;&#xA;A------&amp;gt;BA------&amp;gt;BA------&amp;gt;B&#xA;&#xA;A------&amp;gt;BA------&amp;gt;BA------&amp;gt;BA------&amp;gt;B&#xA;&#xA;A------&amp;gt;BA------&amp;gt;BA------&amp;gt;BA------&amp;gt;BA------&amp;gt;B&#xA;&#xA;         A------&amp;gt;BA------&amp;gt;BA------&amp;gt;BA------&amp;gt;B&#xA;&#xA;                  A------&amp;gt;BA------&amp;gt;BA------&amp;gt;B&#xA;&#xA;         A------&amp;gt;BA------&amp;gt;BA------&amp;gt;B&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and so forth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This last approach is obviously inefficient, because your possible products scale exponentially, and will be produced with equal likelihood, minimizing the DNA yield of any particular segment.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2012-04-14T22:02:25.657" LastActivityDate="2012-04-14T22:02:25.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1821" PostTypeId="2" ParentId="257" CreationDate="2012-04-15T01:04:19.673" Score="2" Body="&lt;p&gt;While not exclusively cell and molecular biology, I would also like to add the &lt;a href=&quot;http://www.jove.com/&quot; rel=&quot;nofollow&quot;&gt;Journal of Visualized Experiments&lt;/a&gt;. It's like Youtube for experiments. :)&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-15T01:04:19.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1822" PostTypeId="1" AcceptedAnswerId="1891" CreationDate="2012-04-15T02:05:36.197" Score="14" ViewCount="5216" Body="&lt;p&gt;After I cut trees into logs and remove the branches in winter, they start growing. They sprout out and grow completely normal looking stems and leaves and maintain them all summer. The sprouts mostly appear around the cut branches.  Sometimes they last all winter and grow for another year. How does it find the energy and water necessary to maintain and grow these stems without ground connection and a water source? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bUyEL.jpg&quot; alt=&quot;&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/O1IPT.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2014-05-21T00:09:39.777" LastActivityDate="2015-08-23T16:21:31.830" Title="How does a tree trunk sprout and grow after being cut?" Tags="&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1823" PostTypeId="2" ParentId="1805" CreationDate="2012-04-15T02:37:53.823" Score="7" Body="&lt;p&gt;Apparently, some do and some don't.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just tried searching for &lt;a href=&quot;http://www.google.com/search?q=yogurt+lactobacillus+survival&quot;&gt;&lt;em&gt;yogurt lactobacillus survival&lt;/em&gt;&lt;/a&gt; on Google, and the first hit I got was an article titled &lt;a href=&quot;http://www.ajcn.org/content/61/2/353.abstract&quot;&gt;&quot;Survival of yogurt-containing organisms and &lt;em&gt;Lactobacillus gasseri&lt;/em&gt; (ADH) and their effect on bacterial enzyme activity in the gastrointestinal tract of healthy and hypochlorhydric elderly subjects&quot;&lt;/a&gt; by Pedrosa &lt;em&gt;et al.&lt;/em&gt; (1995), published in the &lt;em&gt;American Journal of Clinical Nutrition&lt;/em&gt;, vol. 61, pp. 353&amp;ndash;359.  The abstract reads:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The effect of the live bacterial yogurt cultures, namely &lt;em&gt;Streptococcus thermophilus&lt;/em&gt; and &lt;em&gt;Lactobacillus bulgaricus&lt;/em&gt;, and a mucosal adhering strain of &lt;em&gt;Lactobacillus gasseri&lt;/em&gt; (ADH) on small intestinal and fecal bacterial characteristics was examined in 10 elderly subjects with atrophic gastritis and 23 elderly normal volunteers (11 received yogurt and 12 received ADH). Neither &lt;em&gt;S thermophilus&lt;/em&gt; nor &lt;em&gt;L bulgaricus&lt;/em&gt; was recovered from the stomach or small intestine of subjects fed yogurt or pasteurized yogurt. ADH was recovered from gastric or small intestinal aspirates in three of four subjects and in the stools of four of five subjects diagnosed with atrophic gastritis. In 11 of 12 normal subjects, ADH was isolated from stools. There was a significant reduction in fecal bacterial enzyme activity in both normal volunteers and subjects with atrophic gastritis after being fed with viable ADH. Adherent strains of bacteria such as ADH are likely to survive passage through the gastrointestinal tract and thus have greater metabolic effects.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Here's another result from the same search, &lt;a href=&quot;http://www.www-com.es/928892328/lactoacidophilus.pdf&quot;&gt;&quot;Survival and therapeutic potential of probiotic organisms with&#xA;reference to &lt;em&gt;Lactobacillus acidophilus&lt;/em&gt; and &lt;em&gt;Bifidobacterium&lt;/em&gt; spp.&quot;&lt;/a&gt; (PDF) by Kailasapathy &amp;amp; Chin, &lt;em&gt;Immunology and Cell Biology&lt;/em&gt; (2000) 78, 80–88, which says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;&lt;em&gt;Lactobacillus delbrueckii&lt;/em&gt; ssp. bulgaricus and &lt;em&gt;S. thermophilus&lt;/em&gt; (yoghurt starter cultures) are not bile resistant and do not survive the passage through the intestinal tract [Gilliland, 1978]. However, &lt;em&gt;L. acidophilus&lt;/em&gt; and &lt;em&gt;B. bifidum&lt;/em&gt; incorporated into the yoghurt starter culture have the ability to establish themselves among the gut flora [Tamime &amp;amp; Robinson, 1985].&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;but also points out that, for survival in the gastrointestinal tract to matter, the bacteria must first survive long enough to get there:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Strains of bifidobacteria used in some commercial products neither survive gastric transit nor product acidity during storage [Varnam &amp;amp; Sutherland, 1994]. [...] Eight commercial yoghurt samples claiming to contain viable bifidobacteria, sold in London, were enumerated for the presence of this organism. Only five of the eight yoghurts tested contained viable bifidobacteria at &gt; 10&lt;sup&gt;6&lt;/sup&gt; per mL, while the remaining three did not contain any bifidobacteria [Masuda &lt;em&gt;et al.&lt;/em&gt;, 1993]. Modler and Villa-Garcia [1993] reported that bifidobacteria do not survive in several yoghurt products in North America, due to highly acidic conditions. [...] It is considered misleading to describe probiotic yoghurt as having health promoting properties unless the minimum level of viable cells is present at the expiry date.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="239" LastEditorUserId="239" LastEditDate="2012-04-15T03:18:05.647" LastActivityDate="2012-04-15T03:18:05.647" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1824" PostTypeId="2" ParentId="1754" CreationDate="2012-04-15T03:21:11.477" Score="3" Body="&lt;p&gt;It should not have been &quot;survival of the fittest&quot; but rather &quot;survival by the most persistant.&quot;  Traits evolved by natural selection are not required to be optimal or even adaptive.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In response to your question, consider the case of the evolution of thermal reaction norms.  These mathematical representations quantify an organism's performance across a range of environmental temperatures.  Across the diversity of life, you'll find that some organisms have evolved narrow thermal tolerance windows while others have evolved broad thermal tolerance windows.  These specialist vs generalist strategies have benefits and constraints that depend on environmental and ecosystem stability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I think a way of answering your question would be to consider the evolution of thermal reaction norms.  Are there derived taxa that have switched between specialist vs generalist thermal preferences compared to their sister clades?  I'm sure the answer is yes -- but perhaps check out the papers by Kingsolver (Duke) for a more thorough answer!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, consider this:  As humans, we are just as much evolved as a fruit fly or a paramecium.  Since the generation time is much less for fruit flies and paramecia, you might even say they are more evolved than we are.  &lt;/p&gt;&#xA;" OwnerUserId="748" LastActivityDate="2012-04-15T03:21:11.477" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1825" PostTypeId="2" ParentId="1767" CreationDate="2012-04-15T03:37:17.073" Score="3" Body="&lt;p&gt;It needs to be recognized that this is an outstanding question in biology, i.e., there is no certain answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This review considers the various theoretical and empirical evidence for phenotypic selection on body size:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Blanckenhorn WU (2000) The Evolution of Body Size: What Keeps&#xA;Organisms Small? &lt;em&gt;Quarterly Review of Biology&lt;/em&gt; 75: 385-407.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Some have hypothesized a connection between body size and the evolution of endothermy:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Clarke A, Portner HO (2010) Temperature, metabolic power and the&#xA;evolution of endothermy. &lt;em&gt;Biological Reviews&lt;/em&gt; 85: 703-727.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And others have suggested a link to oxygen in the atmosphere:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Harrison JF, Kaiser A, VandenBrooks JM (2010) Atmospheric oxygen&#xA;level and the evolution of insect body size. &lt;em&gt;Proceedings of the Royal&#xA;Society B: Biological Sciences&lt;/em&gt; 277: 1937.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And I'll throw this hypothesis into the ring.  The large dinosaurs only went extinct 65 million years ago.  That's basically yesterday in terms of the geological time scales across which body size may evolve - they (dinosaurs) originally evolved 230 million years ago.  That means we've got at least 165 million years to go before you can see if our current diversity of life on earth can evolve similarly large organisms!&lt;/p&gt;&#xA;" OwnerUserId="748" LastEditorUserId="107" LastEditDate="2013-02-18T15:39:09.577" LastActivityDate="2013-02-18T15:39:09.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1827" PostTypeId="1" AcceptedAnswerId="1839" CreationDate="2012-04-15T18:40:34.717" Score="6" ViewCount="22187" Body="&lt;p&gt;When I checked it seemed trivial to answer: yes, all mammals can swim. But research on the internet provided different information. I found:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;people and primates cannot swim, but can be taught how to swim&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.arkive.org/giraffe/giraffa-camelopardalis/video-ti06.html&quot; rel=&quot;nofollow&quot;&gt;giraffes can't swim&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;someone claimed elephants can't swim, but &lt;a href=&quot;http://www.youtube.com/watch?v=-B7qlAeiXNE&quot; rel=&quot;nofollow&quot;&gt;this video ad shows the reverse&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://answers.yahoo.com/question/index?qid=20080517194505AAbU1wf&quot; rel=&quot;nofollow&quot;&gt;porcupines nor rhinos&lt;/a&gt; can't swim&lt;/li&gt;&#xA;&lt;li&gt;at least some bats &lt;a href=&quot;http://vimeo.com/2743336&quot; rel=&quot;nofollow&quot;&gt;can swim&lt;/a&gt;, but according to &lt;a href=&quot;http://www.si.edu/Encyclopedia_SI/nmnh/batfacts.htm&quot; rel=&quot;nofollow&quot;&gt;this source there's insufficient data&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Of each hit, I found other hits that claimed the reverse, sometimes with proof. Common sense tells me all mammals can swim, but is this true?&lt;/p&gt;&#xA;" OwnerUserId="750" LastEditorUserId="3952" LastEditDate="2015-06-22T15:52:42.773" LastActivityDate="2015-06-22T15:52:42.773" Title="Can all mammals swim?" Tags="&lt;zoology&gt;&lt;locomotion&gt;" AnswerCount="2" CommentCount="11" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1828" PostTypeId="2" ParentId="1605" CreationDate="2012-04-15T20:04:40.363" Score="6" Body="&lt;p&gt;There are many definitions of a species, which may or may not include the concept of reproductive barrier. The &lt;a href=&quot;http://www.encyclopedia.com/topic/biological_species_concept.aspx#1-1O6%3abiologicalspeciesconcept-full&quot; rel=&quot;noreferrer&quot;&gt;Biological Species Concept&lt;/a&gt; (BSC) is quite popular and involves a reproductive barrier, but other concepts such as the &lt;a href=&quot;http://www.encyclopedia.com/topic/phylogenetic_species_concept.aspx&quot; rel=&quot;noreferrer&quot;&gt;Phylogenetic Species Concept&lt;/a&gt; do not include a reproductive barrier. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Disagreements and confusion also happen over just what the best&#xA;  criteria are for identifying new species. In 1942 the famous biologist&#xA;  Ernst Mayr wrote that because biologists have different ways of&#xA;  identifying species, they actually have different species&#xA;  concepts. Mayr proceeded to list five different species concepts, and&#xA;  since then many more have been added. The question of which species&#xA;  concept is best has occupied many printed pages and many hours of&#xA;  discussion.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Some debates are philosophical in nature. One common disagreement is&#xA;  over whether a species is defined by the characteristics that&#xA;  biologists use to identify the species, or whether a species is an&#xA;  evolving entity in nature. Every named species has been formally&#xA;  described as a type of organism with particular defining&#xA;  characteristics. These defining traits are used to identify which&#xA;  species organisms belong to. But for many species, all of the&#xA;  individuals that fit the defining criteria also make up a single&#xA;  evolving unit. These two different ways of thinking about species, as&#xA;  a category and as an evolving population, are quite different from&#xA;  each other. &lt;a href=&quot;http://en.wikipedia.org/wiki/Species_Problem&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia Species Problem&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The Biological Species Concept does have it's problems:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is also true that there are many cases where members of different&#xA;  species will hybridize and produce fertile offspring when they are&#xA;  under confined conditions, such as in zoos. One fairly extreme example&#xA;  is that lions and tigers will hybridize in captivity, and at least&#xA;  some of the offspring have been reported to be fertile. (see also &#xA;  &lt;a href=&quot;http://en.wikipedia.org/wiki/Panthera&quot; rel=&quot;noreferrer&quot;&gt;Lions and Tigers&lt;/a&gt;)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Mayr's response to cases like these is that the reproductive barriers&#xA;  that are important for species are the ones that occur in the wild.&#xA;  But even so it is also the case that there are many cases of different&#xA;  species that are known to hybridize and produce fertile offspring in&#xA;  nature. &lt;a href=&quot;http://en.wikipedia.org/wiki/Species_Problem&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia Species Problem&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The Phylogenetic Species Concept also has its problems: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;it permits successive species to be defined even if they have evolved&#xA;  in an unbroken line of descent, with continuity of sexual fertility.&#xA;  However, because slight differences can be found among virtually any&#xA;  group of organisms, the concept tends to encourage extreme division of&#xA;  species into ever-smaller groups. &lt;a href=&quot;http://www.encyclopedia.com/topic/phylogenetic_species_concept.aspx&quot; rel=&quot;noreferrer&quot;&gt;Phylogenetic Species Concept&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;When does a dog stop being a dog? Technically all dogs are in the same species: See the definition of &lt;a href=&quot;http://en.wikipedia.org/wiki/Dog&quot; rel=&quot;noreferrer&quot;&gt;Dog&lt;/a&gt;, which is a subspecies of the species, Canis lupus, or Grey Wolf. The line between dog and wolf is poorly-defined as there may be hybrid wolf-dogs, since they are both from the same species. Up one level is the family &lt;a href=&quot;http://en.wikipedia.org/wiki/Canidae&quot; rel=&quot;noreferrer&quot;&gt;Canidae&lt;/a&gt;, which includes wolves, foxes, jackals, and coyote species. &lt;/p&gt;&#xA;" OwnerUserId="146" LastActivityDate="2012-04-15T20:04:40.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1829" PostTypeId="1" CreationDate="2012-04-15T21:09:02.070" Score="0" ViewCount="615" Body="&lt;p&gt;I regularly encounter students who believe humans came from amoebas and when asked why they often say Macro-Evolution has been scientifically proven. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Macroevolution&quot; rel=&quot;nofollow&quot;&gt;Macro-evolution&lt;/a&gt; is defined as evolution at or above the species level, which leads to the problem: Scientific evidence does exist for speciation at the &lt;a href=&quot;http://www.encyclopedia.com/topic/biological_species_concept.aspx#1-1O6%3abiologicalspeciesconcept-full&quot; rel=&quot;nofollow&quot;&gt;Biological Species Concept&lt;/a&gt; (BSC) level, but not for all species concepts and only if a helpful definition is employed. Lions and tigers are considered different species and have been know to reproduce--sometimes with fertile offspring. Therefore, what benefits are there to such a broad category as macro-evolution? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The distinction between lions and tigers is so much smaller than feathered vs. scaled creatures! Surely the current definition of macro-evolution is overly broad and confusing to newcomers. Only the fuzzy edge of the macro-evolution definition has been proven. Proving that 1 inch of a yardstick exists does not prove that the rest does. There is a distinct lack of rigor to the statement that &quot;macro-evolution has been scientifically proven.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Surely the definition of macro-evolution could be chopped in half with the goal of distinguishing between &lt;em&gt;relatively trivial changes&lt;/em&gt; (Lion vs. Tiger, but beyond micro-evolution) and &lt;em&gt;relatively non-trivial distinctions&lt;/em&gt; (either at and above the genus or the family level). The &quot;trivial&quot; changes could be termed &quot;Middle Evolution&quot; and work something like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1.) &lt;strong&gt;Middle evolution&lt;/strong&gt;: evolution at or above the species level, but below the family level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2.) &lt;strong&gt;Macro evolution&lt;/strong&gt;: evolution at or above the family level. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Substitute the word genus for family in the above definitions if that seems better. I admit that line would be somewhat arbitrary, but would not the term &quot;Middle Evolution&quot; be informative? &lt;/p&gt;&#xA;" OwnerUserId="146" LastActivityDate="2012-04-17T00:52:06.680" Title="How To Avoid Macro-Evolution Confusion?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2012-04-17T06:23:01.587" ContentLicense="CC BY-SA 3.0" />
  <row Id="1830" PostTypeId="1" CreationDate="2012-04-16T02:57:17.190" Score="18" ViewCount="13001" Body="&lt;p&gt;After sending a DNA sample for sequencing, the resulting sequence had N's in the beginning and end of the sequence.  I know the N's mean that the computer can't tell what the base pair is, but why is this?&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorDisplayName="user560" LastEditDate="2012-12-24T22:50:43.367" LastActivityDate="2020-05-26T18:55:24.110" Title="Why are there N's after Sanger sequencing?" Tags="&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1831" PostTypeId="2" ParentId="1830" CreationDate="2012-04-16T03:57:38.910" Score="8" Body="&lt;p&gt;Typically Sanger sequencing will run into a few errors. Sometimes the traces will overlap as below in red and the computer will call N. If you truly wanted to figure out the correct basepair, you can look at the trace.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6Bywy.jpg&quot; alt=&quot;Sample Trace&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="22057" LastEditDate="2020-05-26T18:55:24.110" LastActivityDate="2020-05-26T18:55:24.110" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="1832" PostTypeId="2" ParentId="1752" CreationDate="2012-04-16T04:20:22.163" Score="1" Body="&lt;p&gt;You can use &lt;a href=&quot;http://en.wikipedia.org/wiki/Medical_ultrasonography&quot; rel=&quot;nofollow noreferrer&quot;&gt;ultrasonography (echography)&lt;/a&gt; to measure blood &lt;a href=&quot;http://en.wikipedia.org/wiki/Ultrasonic_flow_meter&quot; rel=&quot;nofollow noreferrer&quot;&gt;flow&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the blood flow &lt;a href=&quot;http://www.umbjournal.org/article/0301-5629%2885%2990035-3/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;measurements&lt;/a&gt; and vessel dimensions you can then determine blood volume!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want a full explanation on how blood flow is measured by Doppler ultrasonography, make sure you ask the question to the &lt;a href=&quot;https://physics.stackexchange.com/&quot;&gt;right people&lt;/a&gt;. They'll help you with the technicalities.&lt;/p&gt;&#xA;" OwnerUserId="691" LastEditorUserId="-1" LastEditDate="2017-04-13T12:40:13.457" LastActivityDate="2012-04-16T04:20:22.163" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1833" PostTypeId="1" CreationDate="2012-04-16T05:22:59.223" Score="14" ViewCount="171" Body="&lt;p&gt;I'm interested in how the structure of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Thylakoid&quot;&gt;thylakoid&lt;/a&gt; forms into its characteristic highly rugose stacks of grana. What causes the thylakoid to invaginate and self-associate, albeit with what appear to be fairly large gaps in between folds?&lt;/p&gt;&#xA;" OwnerUserId="99" LastEditorUserId="500" LastEditDate="2012-07-20T04:19:26.417" LastActivityDate="2012-08-15T03:52:42.780" Title="Does a theory exist for the formation of thylakoid structure?" Tags="&lt;biochemistry&gt;&lt;plant-physiology&gt;&lt;cell-biology&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1834" PostTypeId="2" ParentId="1752" CreationDate="2012-04-16T05:54:55.117" Score="14" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/users/172/polynomial&quot;&gt;Polynomial&lt;/a&gt; gives a good hint. By adding in a known tracer of known amount that should only circulate in the blood stream, the concentration of the tracer when completely distributed will give the &lt;a href=&quot;http://en.wikipedia.org/wiki/Volume_of_distribution&quot; rel=&quot;nofollow noreferrer&quot;&gt;volume of distribution&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FbE0r.png&quot; alt=&quot;Volume of Distribution&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the tracer only stays in the bloodstream (and that's a fairly large IF), then the V&lt;sub&gt;D&lt;/sub&gt; will be equal to the V&lt;sub&gt;Blood&lt;/sub&gt;. However, as many pharmacologists know, interactions with proteins and cells can skew that number. The blood volume is also reduced by the volume of the blood cells. However, using &lt;a href=&quot;https://biology.stackexchange.com/users/226/andrei&quot;&gt;Andrei&lt;/a&gt;'s method of dilution, one can merely swap the cell counts with the tracer concentration.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2012-04-16T06:50:15.300" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1835" PostTypeId="1" CreationDate="2012-04-16T06:03:50.147" Score="8" ViewCount="226" Body="&lt;p&gt;Comments from the question &lt;a href=&quot;https://biology.stackexchange.com/q/1752/389&quot;&gt;How is the blood volume of a living organism measured without killing it?&lt;/a&gt; by @Nico discussed that the time of blood recirculation scales with the size of the organism. I was curious if there were a series of dimensionless numbers that characterize blood flow, blood volume, and time of blood recirculation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such dimensionless numbers exists for &lt;a href=&quot;http://www.nature.com/nature/journal/v261/n5556/abs/261129a0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;stride length&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18451160&quot; rel=&quot;nofollow noreferrer&quot;&gt;drug penetration&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;&#xA;I like @Nico's comment so much it's going to part of the question. Any description of the circulatory system doesn't necessarily have to be dimensionless. However, I would imagine that one could develop a characteristic time (lets call it &lt;em&gt;Tau&lt;/em&gt;) based on blood flow (L/t), cross-sectional area (L^2), and circulation time (t). From that characteristic time &lt;em&gt;Tau&lt;/em&gt;, interesting observations and appropriate comparisons about the various ratios and how they vary amongst species.  &lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-06-19T01:43:31.933" Title="Dimensionless number for blood volume" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1836" PostTypeId="1" AcceptedAnswerId="1888" CreationDate="2012-04-16T07:34:42.997" Score="14" ViewCount="588" Body="&lt;p&gt;Do we &lt;strong&gt;clearly&lt;/strong&gt; know what the &lt;em&gt;living closest relative of the dinosaurs&lt;/em&gt; are? And connected to the first question, in scientific manner how do we know these relationship between extinct species and living ones? &lt;/p&gt;&#xA;" OwnerUserId="410" LastEditorUserId="410" LastEditDate="2012-04-16T07:44:44.717" LastActivityDate="2017-05-27T11:02:11.507" Title="How do we know that dinosaurs were related to lizards and/or birds?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;palaeontology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1838" PostTypeId="1" AcceptedAnswerId="1844" CreationDate="2012-04-16T12:56:11.053" Score="8" ViewCount="8985" Body="&lt;p&gt;On news, articles etc. experts talking about &lt;strong&gt;Genetically Modified Foods and Organisms&lt;/strong&gt; often mentions about their disadvantages like, &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;their potential to harm human health&lt;/li&gt;&#xA;&lt;li&gt;allergies may become more intense, new allergy types may develop&lt;/li&gt;&#xA;&lt;li&gt;possible damages to the environment&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So I wonder, what's the aim of genetically modifying of foods/organisms? In other words, what are advantages of that? &lt;/p&gt;&#xA;" OwnerUserId="410" LastActivityDate="2015-09-18T14:48:14.320" Title="What's the aim of genetically modifying of foods/organisms?" Tags="&lt;genetics&gt;&lt;microbiology&gt;&lt;molecular-genetics&gt;" AnswerCount="5" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1839" PostTypeId="2" ParentId="1827" CreationDate="2012-04-16T13:27:41.073" Score="6" Body="&lt;p&gt;With respect to the giraffe claim, this article seems relevant:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D. M. Henderson, D. Naish, &lt;a href=&quot;http://dx.doi.org/10.1016/j.jtbi.2010.04.007&quot;&gt;Predicting the buoyancy, equilibrium and potential swimming ability of giraffes by computational analysis&lt;/a&gt;, J Theoretical Biology 265 (2010) 151-159.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It cites several non-&quot;random person on the internet&quot; claims that giraffes cannot swim:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is generally thought that giraffes cannot swim, but relevant&#xA;  observations are few. Shortridge (1934) and Goodwin (1954) state that&#xA;  giraffes were poor waders and unable to swim. Crandall (1964)&#xA;  discussed a case where a captive giraffe escaped from a carrying&#xA;  crate, ran to the end of a jetty, and fell into the water. The animal&#xA;  reportedly sank without making any attempt to swim. MacClintock (1973,&#xA;  p. 54) stated ‘Giraffes cannot swim. Rivers are barriers they do not&#xA;  cross’. Wood (1982, p. 20) noted that ‘Because of its extraordinarily&#xA;  anatomical shape the giraffe is one of the very few mammals that&#xA;  cannot swim – even in an emergency! Deep rivers are an impassable&#xA;  barrier to them, and they will avoid large expanses of water like the&#xA;  plague’.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They then go on to show that a model giraffe could plausibly swim, writing: &quot;For practical and ethical reasons we are unable to use live giraffes...&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They conclude:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In summary, the results and speculations of this study show that it is&#xA;  not impossible that a giraffe could propel itself in water, but in&#xA;  terms of energy efficiency relative to that of the horse, it would&#xA;  appear that the costs of aquatic locomotion might be too high. It is&#xA;  reasonable to expect that giraffes would be hesitant to enter water&#xA;  knowing that they would be at a decided disadvantage compared to being&#xA;  on solid ground.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="203" LastActivityDate="2012-04-16T13:27:41.073" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1840" PostTypeId="2" ParentId="1838" CreationDate="2012-04-16T16:00:45.653" Score="4" Body="&lt;p&gt;In terms of crops, plants that are grown for food, one advantage is the targeted modification of a single gene. Classical plant breeding is slow, imprecise and carries many traits of negative benefit. For example, if you cross plant variety A with variety B for the purpose of obtaining one of B's traits (say oil content of the seed), the resulting progeny will have half of the B genome (which half? each offspring a different half of all possible alleles, and many of the hybrids may carry less desirable traits of B like altered germination and maturation times, which would be quite problematic for a farmer). Back-crosses to variety A are then necessary in order to make, in successive generations, offspring that are 75% A, then 87% A, then 93% A and so on. This takes time - to do those back-crosses and to test that the trait of interest remains. Knowing the gene for oil content, or a set of genes, can speed this process by modifying that gene alone while maintaining all the other advantageous traits of variety A.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is but one example. If I think of others and find the time to describe those, I'll add such information here.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-04-16T17:04:32.953" LastActivityDate="2012-04-16T17:04:32.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1841" PostTypeId="1" AcceptedAnswerId="1845" CreationDate="2012-04-16T17:00:56.250" Score="8" ViewCount="240" Body="&lt;p&gt;Of course the sphincter muscle is at the exit point. To use a toothpaste tube analogy, if I want to squeeze out some toothpaste, it does me little to no good to jostle the nozzle; I need to squeeze the tube (which is analogous to the colon) to get the paste (payload) to come out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when a human is sitting on the toilet squeezing, is that squeezing flexing of the sphincter, or squeezing muscles along the sides of the colon pushing on it as one's fingers push on the tube to get toothpaste to come out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it's the sphincter that's getting flexed, how is that helping get a big log out?&lt;/p&gt;&#xA;" OwnerUserId="263" LastActivityDate="2012-04-16T21:32:16.567" Title="Is it the sphincter that flexes when a human pushes a bowel movement?" Tags="&lt;human-anatomy&gt;&lt;digestive-system&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1842" PostTypeId="1" AcceptedAnswerId="1881" CreationDate="2012-04-16T18:06:00.760" Score="32" ViewCount="1452" Body="&lt;p&gt;My question is out of curiosity and got me thinking. How did viruses with the head, tail and tail fibres actually evolve? These viruses look more like machines than biological entities. Are there any theories to how these viruses evolved?    &lt;/p&gt;&#xA;" OwnerUserId="158" LastActivityDate="2012-04-19T22:30:47.143" Title="How did viruses come to be?" Tags="&lt;evolution&gt;&lt;virology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1843" PostTypeId="1" AcceptedAnswerId="1932" CreationDate="2012-04-16T18:52:05.233" Score="12" ViewCount="386" Body="&lt;p&gt;The reason we cannot find a cure for the common cold is because viruses mutate rapidly. Where do the mutations occur in the DNA/mRNA of viruses and does this have any effect on the protein level? what has to change for the virus to be considered a new strain?&lt;/p&gt;&#xA;" OwnerUserId="158" LastActivityDate="2012-04-23T09:08:58.970" Title="What determines when a virus becomes a &quot;new strain&quot;?" Tags="&lt;virology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1844" PostTypeId="2" ParentId="1838" CreationDate="2012-04-16T19:56:37.217" Score="13" Body="&lt;p&gt;GMO foods have a huge potential to make food cheaper to produce and more nutritious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most common GMO foods have at least one gene added to them - an enzyme that makes the plant resistant to RoundUp - an herbicide made by the same company (Monsanto).  this makes the farmers able to grow their crops with much less intensive labor to keep the plants healthy. It does cost some money and people wonder whether using so much roundUp is good.  I won't come down on the benefits of this, but you can see how it might be more economical way to grow crops.  roundUp is biodegradable and does break down in about 3 weeks, just FYI. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other GMO foods can make the crops more resistant to drought, disease or insects. This might enable crops to be grown in areas and or with longer growing seasons - a big advantage for thirsy crops like tomatos or rice. Other GMO project may allow us to make the crops more nutritious.  A famous example of this is &lt;a href=&quot;http://www.goldenrice.org/&quot;&gt;golden rice&lt;/a&gt;, which has been enhanced to produce pro-vitaminA, which will help malnutrition in millions of children who can die annually because of a lack of vitamins in their diet.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also an effort in nutriceuticals, where vaccines and common drugs maybe produced by edible plants for easily processing or even direct distribution of pharmaceuticals.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For people who can afford organic food and free range beef, I think its great that its available, but at for a hungry world, GMO foods can help solve some vital problems. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-04-16T19:56:37.217" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1845" PostTypeId="2" ParentId="1841" CreationDate="2012-04-16T21:32:16.567" Score="8" Body="&lt;p&gt;The pressure that you apply when you push during a bowel movement derives from an increase in the pressure of the abdomino-pelvic cavity.  You generate this pressure by closing the glottis (the opening to the lungs) and contracting the anteriolateral abdominal muscles (i.e., the external oblique, internal oblique, and transversus abdominus).  This reduces the volume of the (now sealed) abdominopelvic cavity and increases pressure helping to drive feces from the rectum.  This is mechanism is also used to expel urine and during childbirth.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you do this with the glottis open, then you forcibly exhale because the increased pressure of the abdominopelvic cavity is transferred across the diaphragm and into the thoracic cavity compressing the lungs.&lt;/p&gt;&#xA;" OwnerUserId="137" LastActivityDate="2012-04-16T21:32:16.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1846" PostTypeId="2" ParentId="1838" CreationDate="2012-04-16T22:41:40.847" Score="7" Body="&lt;p&gt;On the example of &quot;golden rice&quot; already raised here I took the liberty of looking up some literature about this GMO varietal. &lt;a href=&quot;http://jn.nutrition.org/content/132/3/506S.short&quot;&gt;This article&lt;/a&gt; by Beyer et al. describes the introduction of the beta-carotene biosynthetic pathway into the strain of rice. About a decade later, &lt;a href=&quot;http://www.ajcn.org/content/89/6/1776.short&quot;&gt;Tang et al.&lt;/a&gt; followed this up with a clinical trial to measure how much beta-carotene a population defined to be clinically low in vitamin A are able to obtain. They found that there is efficient and significant conversion of beta-carotene into vitamin A within this population, providing evidence that the theoretical goal to reduce the vitamin deficiency is actually achievable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Larry pointed out, lab modified GMO plants allow a very specific gene or set of genes to be targeted, rather than crossing two plants together and screening the offspring for more desirable than undesirable characteristics. It is important to know that ever since &lt;em&gt;homo sapiens&lt;/em&gt; created the primitive form of agriculture called farming, we have been engaged in producing GMO plants. Every time a farmer select seeds form the plants that grew a little heartier in cold weather, or produced fruit just a little more juicy, it was a deliberate act to produce a higher quality crop (for some trait) the next season. The only difference between what we called and still call farming and GMO agricultural practices, is how finely controlled the individual genes are manipulated. The obvious by product from being able to sequence and manipulate a genome is that we can much more rapidly and broadly create and test new varietals at a pace that could have taken decades or generations earlier. This represents a very important opportunity to improve our quality of food and robustness of crops, and is just as &quot;natural&quot; as what has happened for 10,000 or so years.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-16T22:41:40.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1847" PostTypeId="2" ParentId="1829" CreationDate="2012-04-17T00:52:06.680" Score="7" Body="&lt;p&gt;The only place that the terms &quot;macro-evolution&quot; or &quot;micro-evolution&quot; are generally used, are in creationist rhetoric. They are not terms used by biologists. This is because there is no need to create distinct categories. In reality there is only &quot;microevolution&quot;. Macro-evolution is not a different thing, merely an accumulation of many micro-evolutions.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;what benefits are there to such a broad category as macro-evolution?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;None. Which is why such a term has been abandoned.&lt;/p&gt;&#xA;" OwnerUserId="510" LastActivityDate="2012-04-17T00:52:06.680" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1848" PostTypeId="2" ParentId="1754" CreationDate="2012-04-17T07:26:57.983" Score="3" Body="&lt;p&gt;Just to clarify, as one might read your question as if humans had evolved from dogs - humans and dogs have a common ancestor, one is not a direct descendant of the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of evolution running backwards, it has actually been experimentally tested in microorganisms, where you can check the phenotype (characteristics) of an organism over hundreds and thousands of generations. One example that comes to mind is Joe Thornton's research where he reconstructed a gene for an ancient protein and compared it to the more modern versions. They found out that the key mutations that modified the protein sequence could not be simply changed back to obtain the more ancient form, because in the meantime many neutral mutations had accumulated in that protein and while they did not change the protein sequence, they interacted with the protein-changing mutations and prevented the de-evolution of the protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper I have in mind (there are many more on this) is: Bridgham, Jamie T, Eric A Ortlund, and Joseph W Thornton. 2009. “&lt;a href=&quot;http://www.nature.com/nature/journal/v461/n7263/abs/nature08249.html&quot; rel=&quot;nofollow&quot;&gt;An Epistatic Ratchet Constrains the Direction of Glucocorticoid Receptor Evolution.&lt;/a&gt;” Nature 461 (7263) (September 24): 515–519. doi:10.1038/nature08249.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, in a sort of more esoteric example (as it is not directly de-evolution), blind cavefish have multiple mutations (and sometimes in multiple genes) that cumulatively result in loss of vision. Let's then say you have population of the fish that have sight-losing mutations in gene A and another population with mutations in gene B. Both populations are blind, but if you could cross the fish from the two populations, the eye-loss mutations in genes A and B would be substituted by 'correct' versions from the other population and thus both fish would be able to see again. While not de-evolution in itself, it shows that for relatively simple changes that were not influenced by other changes in the genome, you can rewind the clock and get the long-lost phenotypes, even like the sight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See here: Borowsky, Richard. 2008. “&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0960982207022622&quot; rel=&quot;nofollow&quot;&gt;Restoring Sight in Blind Cavefish.&lt;/a&gt;” Current Biology : CB 18 (1) (January 8): R23–4. doi:10.1016/j.cub.2007.11.023. (this is a description of the research, not the actual paper; but it links to it).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both these examples are super-cool (IMHO), and in my collection of all-time favorite evolutionary stories. But practically speaking, what you're asking for (from humans and dogs to their most common ancestor) is not possible. Too many variables (both genetic and environmental and stochastic) to control. The papers are behind the paywall, but if you want them, send me an email.&lt;/p&gt;&#xA;" OwnerUserId="752" LastActivityDate="2012-04-17T07:26:57.983" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1849" PostTypeId="2" ParentId="1838" CreationDate="2012-04-17T08:02:55.613" Score="2" Body="&lt;p&gt;I'd like to add that most of the GMOs that might most dramatically improve human condition (ie via drought/salt resistance, greatly increased yield or nutritional value) are all unfortunately still under development (or not even that), partially because of the general public resistance to GMO in some regions of the world (like Europe; anyone remembers the tomatoes?) and organized campaigns against GMO (not really fact-based; ie Greenpeace &amp;amp; Co).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes, GMO can lead to development of crops with increased nutritional value, better resistance to environmental conditions or changes and/or increased yield, but we're not there (yet).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above should not mean that what we have so far (insect resistant crops, disease-reducing GM insects or the golden rice) is not important, because it is, and it should not mean that the current legal/political context of GMO is fine, because it isn't.&lt;/p&gt;&#xA;" OwnerUserId="752" LastActivityDate="2012-04-17T08:02:55.613" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1851" PostTypeId="1" AcceptedAnswerId="3452" CreationDate="2012-04-17T12:43:42.137" Score="10" ViewCount="791" Body="&lt;p&gt;I’m currently reading on Tay-Sachs disease and have stumbled upon something regarding the typical “cherry red” macula symptom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the one hand it is mentioned that the macula is almost devoid of ganglion cells (GCs) and this actually the reason for the high acuity in this region since there is not obstruction of light [Suvarna JC, Hajela SA. Cherry-red spot. J Postgrad Med 2008;54:54-7].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand google books gives me numerous textbooks that highlight the fovea as the location of highest GC density and conclude that this leads to the high acuity because a GC only receives information from one or two cone cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess both are correct but how does one fit the other? It seems contradictory to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be precise some sources specifically mention the boundary regions of the central fovea to have the high GC density, this could leave the fovea devoid of them and therefore combine both facts, however if this is correct I still wonder:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1: Where are the GCs that the cones in the central fovea are connected to?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2: Why is the “cherry red” spot in the macula so large on all the pictures. If my explanation is correct only the tiny area of the central fovea should be red and the surroundings the complete opposite due to the high GC density, right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I’d really appreciate if someone could shed some light into this.&lt;/p&gt;&#xA;" OwnerUserId="754" LastEditorUserId="754" LastEditDate="2012-04-18T09:40:44.943" LastActivityDate="2012-09-06T21:58:41.030" Title="Foveal ganglion cell density (Tay-Sachs Disease)" Tags="&lt;human-anatomy&gt;&lt;neuroanatomy&gt;&lt;eyes&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1852" PostTypeId="1" CreationDate="2012-04-17T13:42:07.423" Score="5" ViewCount="337" Body="&lt;p&gt;&lt;strong&gt;Goal: To quantify the HIV-1 reverse transcriptase (RT) activity for a number of mutated RTs.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Idea: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Put RT into a vector in E.coli.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Deliver GFP mRNA to E.coli.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;RT will process the mRNA.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The resulting DNA will be integrated into E. coli.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;RT activity correlates with the GFP we observe.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;First question: Does this logic make sense?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second question: An alternative procedure? &lt;/p&gt;&#xA;" OwnerUserId="756" LastEditorUserId="43" LastEditDate="2012-04-18T03:28:51.630" LastActivityDate="2012-04-18T03:28:51.630" Title="Measuring reverse transcriptase activity in E. coli" Tags="&lt;molecular-genetics&gt;&lt;experimental-design&gt;&lt;ecoli&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1853" PostTypeId="1" AcceptedAnswerId="1919" CreationDate="2012-04-17T16:36:34.913" Score="18" ViewCount="18810" Body="&lt;p&gt;My PI showed a Ramachandran plot in class today with minimal explanation, but I'm interested in finding out more. I understand that the Ramachandran plot shows the relation between the omega phi and psi angleson either side of an amino acid alpha-carbon, but there are a few further points I'm confused about:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a.) What do these angles describe? Are they just dihedral angles that show translation around the bond-axis?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b.) Why are these angles important beyond the scope of identifying a secondary structure? Can they be used instead to identify the amino acid components, or only higher level structural units?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c.) What kind of instrument is used to collect the data and how are angles on either side of a single alpha-carbon correlated?&lt;/p&gt;&#xA;" OwnerUserId="575" LastEditorUserId="112" LastEditDate="2012-04-18T13:31:48.663" LastActivityDate="2016-12-06T00:45:41.330" Title="What is the significance and method behind Ramachandran plots?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1854" PostTypeId="2" ParentId="1852" CreationDate="2012-04-17T16:41:04.570" Score="5" Body="&lt;p&gt;the devil is in the details here - the logic is okay, but there is no experiment here. Too many unanswered questions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are you doing anything specific to see optimize RT activity?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How are you preventing your GFP mRNA from being turned into protein, producing much larger signal than you will ever see from RT activity? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once its integrated into the chromosome, how will this gene be expressed when it has been suppressed in all these other stages? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do you know that the plasmid isn't just being incorporated into the chromosome by some other means?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where is the RT coming from ?  E coli doesn't have the gene. this experiment is very likely to give no results.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When/how does this RT work?  If its some sort of phage RT ( i don't know if there are such things) any sort of viral RT will probably kill the cell the way normally it would. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;so many questions before this could work - need to do some homework here. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-04-17T16:41:04.570" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1855" PostTypeId="1" CreationDate="2012-04-17T18:02:21.077" Score="15" ViewCount="1626" Body="&lt;p&gt;Routinely, lysis of cells with hypotonic solutions is carried out along with some physical (douncing) or enzymatic (lysozyme) method to break open the cells. If one were not to do any of these and just resuspend cells in water, how long would it take to lyse the cells? I was discussing with a lab mate who claimed it would take hours while in my understanding, salt equilibrium should not take very long (maybe on the order of minutes?) and hence, lysis should be done within 20-30 minutes.&lt;/p&gt;&#xA;" OwnerUserId="223" LastActivityDate="2012-05-16T03:34:05.143" Title="How fast will cells lyse under hypotonic conditions?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1856" PostTypeId="2" ParentId="1852" CreationDate="2012-04-17T20:07:16.347" Score="4" Body="&lt;p&gt;I'm with @Mad Scientist. Save yourself the trouble and do this in an &lt;em&gt;in vitro&lt;/em&gt; system. At the moment, you don't even know if the HIV-RT will express or will be active in &lt;em&gt;E .coli&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rather, express mutated HIV-RT in T-Cells or Rabbit Lysate. Purify.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Add in a RNA template with the appropriate primer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hydrolyze your RNA&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Detect your cDNA.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-04-17T20:07:16.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1858" PostTypeId="2" ParentId="1852" CreationDate="2012-04-17T23:02:23.053" Score="3" Body="&lt;p&gt;I like that you are considering a simple and standardized approach. However, there are a number of potential pitfalls to consider with this proposal. First of all, what specific RT activity are you trying to quantify? Is the the transcription speed or accuracy, or are you trying to characterize something else entirely? If you are measuring speed, how and what will you measure, reliably and will be reproducible, for speed? If you are going for accuracy, you will need a whole lot of sequencing to check the bases are correct. Both of these can quickly become expensive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, is it necessary to use HIV-1 RT? Since you mention E. coli, would you want to consider using msr, a prokaryotic RT?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though I've never heard or tried it myself, is it possible to transform mRNA into bacteria? I would imagine that it would be degraded as a natural defense mechanism. You may need to consider some alternative form of gene delivery, such as a standard expression plasmid. Genomic integration may not be necessary to achieve your goal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As mentioned, you cannot just have naked cDNA to translate a protein. You need at least the promoter, RNA pol binding site and polyA signal. You could take advantage of viral infection systems (a replication defective HIV) to deliver your GFP and RT genes into a mammalian system (like HEK-293 cells), but this adds a lot of complexity and expense that may not be worthwhile.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The last thing off the top, you would benefit greatest from taking advantage of a directed evolution experiment to generate some potential leads. For example, you may PCR amplify the RT cDNA with an error-prone Taq to purpose create RT mutants for use in your assay.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Keep thinking about this, and maybe check the websites of the some of the RT commercial vendors. It is possible one of these companies have already done something similar.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-17T23:02:23.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1859" PostTypeId="1" CreationDate="2012-04-18T10:25:35.060" Score="48" ViewCount="7357" Body="&lt;p&gt;I've thoroughly read &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_sequencing&quot;&gt;the Wikipedia article on DNA sequencing&lt;/a&gt; and can't get one thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's some hardcore chemistry involved in the process that somehow splits the DNA and then isolates its parts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet DNA sequencing is &lt;a href=&quot;http://www.genome.gov/sequencingcosts/&quot;&gt;considered to be a very computationally-intensive process&lt;/a&gt;. I don't get what exactly is being computed there - what data comes into computers and what computers compute specifically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What exactly is being computed there? Where do I get more information on this?&lt;/p&gt;&#xA;" OwnerUserId="466" LastEditorUserId="15399" LastEditDate="2015-05-07T17:28:54.613" LastActivityDate="2020-07-08T13:18:04.393" Title="What exactly are computers used for in DNA sequencing?" Tags="&lt;bioinformatics&gt;&lt;dna&gt;&lt;dna-sequencing&gt;&lt;sequence-assembly&gt;" AnswerCount="4" CommentCount="7" FavoriteCount="15" ContentLicense="CC BY-SA 3.0" />
  <row Id="1860" PostTypeId="2" ParentId="1661" CreationDate="2012-04-18T10:44:58.023" Score="13" Body="&lt;p&gt;I have no idea what's the real reason for the survival of the poor fish, but I would guess this is all in the timing. I know for certain ;-) that one can submerge a hand in liquid nitrogen for a short time or in general one can pour liquid nitrogen on the skin with no harm done whatsoever.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason is that the difference in temperature that interface (-180 deg C or so for liquid nitrogen and 20-30 for the skin surface) is so large that nitrogen vaporizes instantly and does not penetrate/affect the tissue. The demonstrator could have pulled the fish with bare hands.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that for the goldfish the time was too short and while it was cooled/shocked a bit, it might have been too short to do any serious damage. But -&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a scientist, I can't help but notice that we don't really know the condition of the fish before or after the liquid nitrogen 'treatment'. We only see it flapping for a few seconds when back in water. I wonder what happened to the eyes and the mouth, both quite sensitive tissues for such a shock. Also, the water the fish was in was a factor probably, providing additional buffer between the fish and the liquid nitrogen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Last but not least, the ethical committee quite certainly did not approve that demonstration.&lt;/p&gt;&#xA;" OwnerUserId="752" LastActivityDate="2012-04-18T10:44:58.023" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1861" PostTypeId="2" ParentId="1859" CreationDate="2012-04-18T11:23:25.950" Score="7" Body="&lt;p&gt;In a genome, there are usually billions of base pairs. However, it's impossible to read all of them in one go. The DNA is fragmented, and the sequence of the fragments is determined. Next-generation sequencing techniques are faster and cheaper, but produce only short fragments (say, 100 base pairs, this depends on the technology). It's extremely computationally intensive to put these fragments back together. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More info: &lt;a href=&quot;http://www.cbcb.umd.edu/research/assembly_primer.shtml&quot;&gt;Genome sequence assembly primer&lt;/a&gt;; &lt;a href=&quot;http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1935.html&quot;&gt;intro in Nature Methods&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-04-18T11:23:25.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1862" PostTypeId="2" ParentId="1859" CreationDate="2012-04-18T11:25:46.043" Score="7" Body="&lt;p&gt;As you mentioned in the question, current sequencing platforms split the genomic DNA into many small pieces which the machine then analyzes. The product of a sequencing experiment is millions or even billions of short &quot;reads&quot;---strings of A, C, G, and T representing the nucleotides of a single fragment of DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The DNA reads in this form aren't particularly useful. The idea in the first place was to determine the sequence of the entire DNA molecule. This is where genome assembly software comes in---to determine the original sequence of the genomic DNA by finding the optimal arrangement of overlapping reads to reconstruct the original DNA sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Computers are crucial at 2 stages of this process---first, in the sequencing experiment itself, the platform must record and interpret fluorescent signals to generate the sequence reads in the first place; and second, very powerful computers are needed to assemble the reads back into a contiguous sequence to recover the original DNA sequence.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2015-02-25T14:21:50.770" LastActivityDate="2015-02-25T14:21:50.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1863" PostTypeId="2" ParentId="1677" CreationDate="2012-04-18T13:13:29.680" Score="4" Body="&lt;p&gt;Please provide more information: fold-change relative to what?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you did what I think you did (single control gene that you calculated fold change to of your gene of interest) I'd say this is the wrong approach. What you need is a set of genes which have similar expression levels across all your samples (controls and cases) to be able to compare your gene of interest to some common baseline. Selection of such genes should be the first step in the project, and it might be a good idea to use one of the established approaches - I recommend Jo Vandensompele's &lt;a href=&quot;http://genomebiology.com/2002/3/7/research/0034&quot; rel=&quot;nofollow&quot;&gt;GeNorm&lt;/a&gt; (link to the paper) method. It goes like this: from a panel of potential control genes you select two or three that are most stably expressed across your experimental conditions, and then use these two-three control genes along with your gene of interest in a qRT-PCR. You then normalize the signal from your gene to a mean of the control genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has been repeatedly shown that using a single control gene, even a so-called 'housekeeping gene' is misleading, because those genes do change their expression levels in some conditions. Also, using several control genes protects you against potential problems due to unequal amplification efficiency in different samples/groups. However, if you have multiple gene of interest, they all must have comparable amplification efficiency.&lt;/p&gt;&#xA;" OwnerUserId="752" LastActivityDate="2012-04-18T13:13:29.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1864" PostTypeId="2" ParentId="1731" CreationDate="2012-04-18T13:16:43.490" Score="3" Body="&lt;p&gt;The paper you cite says that the break points are single stranded DNA which have specific proteins bound to them.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not an expert here, but if thats the cause of meitotic break points there are some interesting possibilities for detecting them:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;you could detect them with a tiling array.  - that's an micro array which has an oligomer every 40 bp or so of the genome.  The array could be used in a CHP experiment that detects the same proteins as in this paper.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its possible that the array could possibly hybridize the single stranded DNA from the genome too if the conditions were right.  This sounds noisy though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the cheap side it might be possible to use PCR to copy the single stranded DNA from a chromosomal DNA prep.  if the oligos you use are labelled with streptavidin say, you could isolate it , re amplify it and sequence cheaply. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;any of these sound like a good bit of work :)&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-04-18T13:16:43.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1865" PostTypeId="2" ParentId="1813" CreationDate="2012-04-18T13:21:27.563" Score="0" Body="&lt;p&gt;You can find the answer in any university-level biochemistry textbook.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would recommend you &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/071677108X&quot; rel=&quot;nofollow&quot;&gt;Lehninger Principles of Biochemistry&lt;/a&gt;, if you could find it in your university library.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Skim the list of content, find corresponding chapters and write it down. It won't take you several hours.&lt;/p&gt;&#xA;" OwnerUserId="698" LastActivityDate="2012-04-18T13:21:27.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1866" PostTypeId="1" AcceptedAnswerId="1890" CreationDate="2012-04-18T13:30:20.977" Score="12" ViewCount="7779" Body="&lt;p&gt;I am in India where it is typically a custom to marry within one's caste. Basically the caste system originated with roots in people's professions - Each of priests, carpenters, troupers, etc had a caste of their own. My question is based on the genetic basis of marriages performed within one's caste.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I know the concept of alleles where there is a dominant allele and a recessive one, like the A and O resp. in blood groups and Rh+ and Rh- in Rhesus factors. Is there a similar genetic information based on our ancestral profession in our chromosomes? Is the son of a couple engaged in farming better suited to the same profession unless he receives a couple of recessive alleles from both parents?&lt;/li&gt;&#xA;&lt;li&gt;Generally there is a lot of unscientific information floating around about these matters. One of the grapevines is that it is genetically better for one to marry outside their caste to create diversity(?). Is such a thing true? &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If genetics or biology have any role to play in these fields, I will be happy to know and learn.&lt;/p&gt;&#xA;" OwnerUserId="629" LastEditorUserId="629" LastEditDate="2012-04-26T14:45:49.070" LastActivityDate="2015-01-24T08:33:10.873" Title="On the genetics behind caste marriages" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1867" PostTypeId="2" ParentId="1813" CreationDate="2012-04-18T13:34:53.340" Score="3" Body="&lt;p&gt;I think this is a question about what else should be on a protein cheat sheet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are clever you can format this to have a very high density of information. A good project.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's my list - I never made a sheet though.  Also I tend to be interested in protein structure, so there's a bias here.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The frequency of the amino acids in say e coli or the PDB &lt;/li&gt;&#xA;&lt;li&gt;The average molecular weight of an amino acid (~110 daltons)&lt;/li&gt;&#xA;&lt;li&gt;avg backbone width of a sheet (5 x 6 Ang) and helix (12 Ang.) DNAMajor groove is also 12 Ang btw.&lt;/li&gt;&#xA;&lt;li&gt;common non standard amino acids (ornithine, seleneomet, etc).&lt;/li&gt;&#xA;&lt;li&gt;common post translational modifications (e.g. T/Y phosphorylation)&lt;/li&gt;&#xA;&lt;li&gt;common non standard secondary structure (3-10 helix etc) or a small ramachandran diagram&lt;/li&gt;&#xA;&lt;li&gt;pKas of amino acids - remember that charge is defined at pH 7&lt;/li&gt;&#xA;&lt;li&gt;the genetic code&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For alpha/beta propensities, I would use chou-fasman's numbers.  Its annoying because there are some amino acids in &lt;em&gt;both&lt;/em&gt; lists.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will try to think of more and add later...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-04-18T13:34:53.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1868" PostTypeId="2" ParentId="1813" CreationDate="2012-04-18T13:41:08.387" Score="4" Body="&lt;p&gt;For 95% of the work I do with protein, I find this &lt;a href=&quot;http://en.wikipedia.org/wiki/File%3aGeneticCode22.svg&quot; rel=&quot;nofollow&quot;&gt;chart&lt;/a&gt; very helpful, showing common post-translational modifications, for each amino acid, with molecular weights, associated codons, pKa values, 1- and 3-letter amino acid codes, chemical structure and chemical properties (polar, non-polar, aromatic, acidic, basic).&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-18T13:41:08.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1869" PostTypeId="1" AcceptedAnswerId="1887" CreationDate="2012-04-18T13:57:22.357" Score="31" ViewCount="7264" Body="&lt;p&gt;I was walking down a road with these beautifully huge trees when this question occurred to me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Large trees with many thick branches have to grow equally in all directions, or they would tip over. Is there some sort of mechanism to ensure this uniform growth? Or is it just a happy coincidence arising from uniform availability of sunlight on all sides? If one branch of a tree becomes too heavy due to many sub-branches, does this somehow trigger growth on the opposite side of the tree? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have seen that potted plants in houses tend to grow towards sunlight. My mum often turns pots around by 180 degrees to ensure that plants don't bend in any one direction. I assume that this is because sunlight increases the rate of photosynthesis, leading to rapid growth of the meristem. &#xA;For trees growing in open spaces, this wouldn't be a problem. But there are many large trees that grow in the shadow of buildings without bending away from the buildings, even though this is the only direction from which they would receive any sunlight. Is there any explanation for this?&lt;/p&gt;&#xA;" OwnerUserId="753" LastEditorUserId="649" LastEditDate="2012-04-18T20:38:03.623" LastActivityDate="2019-04-18T17:53:31.880" Title="How do trees manage to grow equally in all directions?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="1870" PostTypeId="1" AcceptedAnswerId="1876" CreationDate="2012-04-18T14:00:50.780" Score="13" ViewCount="212" Body="&lt;p&gt;In the case of mammals like giraffes and koalas, is that bacteria common on the plants they eat so when a baby starts to try to stick something besides its mother's milk in its mouth, it can't digest the cellulose at all the first time, but along with the cellulose, into its mouth went some cellulose-digesting flora that then begins a lifelong colony in the animal's gut? Is that about how it happens?&lt;/p&gt;&#xA;" OwnerUserId="263" LastActivityDate="2012-07-11T08:58:42.337" Title="How do baby animals that primarily subsist on cellulose get their initial gut flora?" Tags="&lt;zoology&gt;&lt;microbiology&gt;&lt;digestive-system&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1871" PostTypeId="2" ParentId="1859" CreationDate="2012-04-18T15:00:38.787" Score="40" Body="&lt;p&gt;Think about it like this. Suppose you own a hundred copies of &quot;The Lord of the Rings&quot;, a 500000 word novel. Unfortunately, you have those hundred copies in the form of several million tiny scraps of paper, each of which contains about ten sequential words from the novel. Your task is to take those several million scraps of paper and put them in order so that you can read the novel from start to finish. Suppose for example you find the fragment&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;stab that vile creature, when he had a chance!&quot; &quot;Pity? &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;You could then search the other several million fragments for a fragment that overlaps this in some way. Perhaps you find&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;chance!&quot; &quot;Pity? It was Pity that stayed his hand. Pity, and Mercy: &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Odds are extremely good that those fragments go together into&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;stab that vile creature, when he had a chance!&quot; &#xA;&quot;Pity? It was Pity that stayed his hand. Pity, and Mercy: &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;But maybe not! Maybe either (1) there is another fragment of the novel that has &lt;code&gt;chance!&quot; &quot;Pity?&lt;/code&gt; that is the correct overlap, or oh, by the way did I mention (2) &lt;em&gt;some of those scraps of paper contain errors, and you have to also detect and eliminate them.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is an extremely computationally intensive job. DNA assemblers have the same problem: millions upon millions of of tiny scraps of DNA that overlap, that might contain errors, and that need to be sorted into order by analyzing their overlaps and gradually building up short fragments into longer and longer fragments. &lt;/p&gt;&#xA;" OwnerUserId="759" LastEditorUserId="759" LastEditDate="2012-04-18T15:06:30.013" LastActivityDate="2012-04-18T15:06:30.013" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1872" PostTypeId="2" ParentId="10" CreationDate="2012-04-18T15:48:00.150" Score="1" Body="&lt;p&gt;Reporter genes are also used when the experiment is trying to distinguish the effect of that gene that the scientist introduces (exogenous) and the same gene that the cell already has (endogenous). Ideally, one would like to choose a cell system that does not contain endogenous genes of interest because of this confounding effect, but it is not always feasible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reporter genes are also mainly used when it is impossible or very difficult to directly measure a gene of interest, especially if the gene of relatively obscure in the scientific literature. For example, cells that do not express a thymidine kinase gene are impossible to visualize by Positron Emission Tomography. It's not because there is anything wrong with the gene of interest, just that the cells need a way to retain a radioactive agent that can be detected by the PET machine. Likewise, fluorescent genes are very often used because there is often a need to see where the gene product is located within the cell, and the only way to do that is to combine it with something visible by microscopy which lets you see fluorescence and the cell structures. Lastly, a reporter gene is often used when the gene of interest is hard to detect because of limitations of commercial antibodies or detection kits, and the reporter, being very commonly used, is easy to detect with commercial products and antibodies.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-18T15:48:00.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1873" PostTypeId="2" ParentId="1859" CreationDate="2012-04-18T19:38:46.290" Score="53" Body="&lt;p&gt;Computers are used in several steps of sequencing, from the raw data to finished sequence:&lt;/p&gt;&#xA;&lt;h1&gt;Image processing&lt;/h1&gt;&#xA;&lt;p&gt;Modern sequencers usually use fluorescent labelling of DNA fragments in solution. The fluorescence encodes the different nucleobase (= “base”) types (generally called A, C, G and T). To achieve high throughput, millions of sequencing reactions are performed in parallel in microscopic quantities on a glass chip, and for each micro-reaction, the label needs to be recorded at each step in the reaction.&lt;/p&gt;&#xA;&lt;p&gt;This means: the sequencer takes progressive digital photographs of the chip containing the sequencing reagent. These photos have differently coloured pixels which need to be told apart and assigned a specific colour value.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QuyzW.png&quot; alt=&quot;Digital image of a sequencing chip&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;As can be seen, this (strongly magnified; the image is &amp;lt; 100 µm across!) image fragment is fuzzy and many of the dots overlap. This makes it hard to determine which colour to assign to which pixel (though more recent versions of the sequencing machine have improved focussing systems, and the image is consequently crisper).&lt;/p&gt;&#xA;&lt;h1&gt;Base calling&lt;/h1&gt;&#xA;&lt;p&gt;One such image is registered for each step of the sequencing process, yielding one image for each base of the fragments. For a fragment of length 75, that’d be 75 images.&lt;/p&gt;&#xA;&lt;p&gt;Once you have analysed the images, you get colour spectra for each pixel across the images. The spectra for each pixel correspond to one sequence fragment (often called a “read”) and are considered separately. So for each fragment you get such a spectrum:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EAHVb.png&quot; alt=&quot;Sequence trace spectrum&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;(This image is generated by an alternative sequencing process called &lt;a href=&quot;https://en.wikipedia.org/wiki/Sanger_sequencing&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sanger sequencing&lt;/a&gt; but the principle is the same.)&lt;/p&gt;&#xA;&lt;p&gt;Now you need to decide which base to assign for each position based on the signal (“base calling”). For most positions this is fairly easy but sometimes the signal overlaps or decays significantly. This has to be considered when deciding the base calling quality (i.e. which confidence you assign to your decision for a given base).&lt;/p&gt;&#xA;&lt;p&gt;Doing this for each read yields up to billions of reads, each representing a short fragment of the original DNA that you sequenced.&lt;/p&gt;&#xA;&lt;p&gt;Most bioinformatics analysis starts here; that is, the machines emit files containing the short sequence &lt;em&gt;fragments&lt;/em&gt;. Now we need to make a &lt;em&gt;sequence&lt;/em&gt; from them.&lt;/p&gt;&#xA;&lt;h1&gt;Read mapping and assembly&lt;/h1&gt;&#xA;&lt;p&gt;The key point that allows retrieving the original sequence from these small fragments is the fact that these fragments are (non-uniformly) &lt;em&gt;randomly distributed&lt;/em&gt; over the genome, and they are &lt;em&gt;overlapping&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;p&gt;The next step depends on whether you have a similar, already sequenced genome at hand. Often, this is the case. For instance, there is a high-quality “reference sequence” of the human genome and since all the genomic sequences of all humans are ~99.9% identical (depending on how you count), you can simply look where your reads align to the reference.&lt;/p&gt;&#xA;&lt;h2&gt;Read mapping&lt;/h2&gt;&#xA;&lt;p&gt;This is done to search for single changes between the reference and your currently studied genome, for example to detect mutations that lead to diseases.&lt;/p&gt;&#xA;&lt;p&gt;So all you have to do is to &lt;em&gt;map&lt;/em&gt; the reads back to their original location in the reference genome (in blue) and look for differences (such as base pair differences, insertions, deletions, inversions …).&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0jP4H.png&quot; alt=&quot;Mapped reads&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Two points make this hard:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;You have got &lt;strong&gt;billions&lt;/strong&gt; (!) of reads, and the reference genome is often several gigabytes large. Even with the fastest thinkable implementation of string search, this would take prohibitively long.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The strings don’t match precisely. First of all, there are of course differences between the genomes – otherwise, you wouldn’t sequence the data at all, you’d already have it! Most of these differences are single base pair differences – SNPs (= single nucleotide polymorphisms) – but there are also larger variations that are much harder to deal with (and they are often ignored in this step).&lt;/p&gt;&#xA;&lt;p&gt;Furthermore, the sequencing machines aren’t perfect. A lot of things influence the quality, first and foremost the quality of the sample preparation, and minute differences in the chemistry. All this leads to &lt;em&gt;errors&lt;/em&gt; in the reads.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;In summary, you need to find the position of billions of small strings in a larger string which is several gigabytes in size. All this data doesn’t even fit into a normal computer’s memory. And you need to account for mismatches between the reads and the genome.&lt;/p&gt;&#xA;&lt;p&gt;Unfortunately, this still doesn’t yield the complete genome. The main reason is that some regions of the genome are highly repetitive and badly conserved, so that it’s impossible to map reads uniquely to such regions.&lt;/p&gt;&#xA;&lt;p&gt;As a consequence, you instead end up with distinct, contiguous blocks (“contigs”) of mapped reads. Each contig is a sequence fragment, like reads, but much larger (and hopefully with less errors).&lt;/p&gt;&#xA;&lt;h3&gt;Assembly&lt;/h3&gt;&#xA;&lt;p&gt;Sometimes you want to sequence a new organism so you don’t have a reference sequence to map to. Instead, you need to do a &lt;em&gt;de novo assembly&lt;/em&gt;. An assembly can also be used to piece contigs from a mapped reads together (but different algorithms are used).&lt;/p&gt;&#xA;&lt;p&gt;Again we use the property of the reads that they overlap. If you find two fragments which look like this:&lt;/p&gt;&#xA;&lt;pre&gt;&lt;code&gt;ACGTCGATCGCTAGCCGCATCAGCAAACAACACGCTACAGCCT&#xA;ATCCCCAAACAACACGCTACAGCCTGGCGGGGCATAGCACTGG&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;p&gt;You can be quite certain that they overlap like this in the genome:&lt;/p&gt;&#xA;&lt;pre&gt;&lt;code&gt;ACGTCGATCGCTAGCCGCATCAGCAAACAACACGCTACAGCCT&#xA;                  ATCCCCATTCAACACGCTA-AGCTTGGCGGGGCATACGCACTG&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;p&gt;(Notice again that this isn’t a perfect match.)&lt;/p&gt;&#xA;&lt;p&gt;So now, instead of searching for all the reads in a reference sequencing, you search for head-to-tail correspondences between reads in your collection of billions of reads.&lt;/p&gt;&#xA;&lt;p&gt;If you compare the &lt;em&gt;mapping&lt;/em&gt; of a read to searching a needle in a haystack (an often used analogy), then &lt;em&gt;assembling&lt;/em&gt; reads is akin to comparing all the straws in the haystack to each other straw, and putting them in order of similarity.&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="166" LastEditDate="2020-07-08T13:18:04.393" LastActivityDate="2020-07-08T13:18:04.393" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="1874" PostTypeId="1" AcceptedAnswerId="1875" CreationDate="2012-04-18T20:18:14.643" Score="19" ViewCount="17212" Body="&lt;p&gt;I am quite sure that there is this blood-placental barrier between the mother and the baby so that nothing (except a type of antibody) can pass through it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I remember reading somewhere that when a pregnant woman suffers an organ damage, fetus would send stem cells to the damage organ to help repair it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anything to support that?&lt;/p&gt;&#xA;" OwnerDisplayName="user661" LastEditorUserId="444" LastEditDate="2012-04-19T13:00:52.683" LastActivityDate="2012-05-19T14:46:19.067" Title="Possible? When a pregnant woman suffers an organ damage, fetus would send stem cells to the damage organ to help repair it?" Tags="&lt;human-biology&gt;&lt;tissue-repair&gt;&lt;stem-cells&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1875" PostTypeId="2" ParentId="1874" CreationDate="2012-04-18T20:50:35.917" Score="15" Body="&lt;p&gt;Fetal RNA - mRNA and microRNA - has been detected in maternal blood as shown in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17885688&quot;&gt;this report&lt;/a&gt;. Here's a second &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22082491.1&quot;&gt;report&lt;/a&gt; showing how fetus gives back to repair the maternal myocardium - fetal cells traffic to an injured maternal myocardium and undergo cardiac differentiation.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-04-19T15:31:06.373" LastActivityDate="2012-04-19T15:31:06.373" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1876" PostTypeId="2" ParentId="1870" CreationDate="2012-04-18T20:54:38.327" Score="8" Body="&lt;p&gt;I would not expect this to be any different than other animals - they get the flora from the environment. Key components of the environment for newborns are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Birth canal&lt;/li&gt;&#xA;&lt;li&gt;Den / living quarters&lt;/li&gt;&#xA;&lt;li&gt;Skin / fur of mother, especially near the teats&lt;/li&gt;&#xA;&lt;li&gt;Diet&lt;/li&gt;&#xA;&lt;li&gt;Feces of family members (animals sniff this and aren't so clean)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-04-18T20:54:38.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1877" PostTypeId="2" ParentId="1869" CreationDate="2012-04-18T22:11:32.387" Score="11" Body="&lt;p&gt;They don't always.  For example, this apple tree grows just outside my window:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3kNWU.jpg&quot; alt=&quot;Tilted apple tree&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far, it hasn't fallen over yet.  The reason it grows that way is because all the light is coming from the right side of the picture: the tree leans roughly to southeast, while the building is to southwest of it and casts a shadow on the center of the yard for much of the day.  Also, to the left you can see the branches of other, taller trees that block pretty much all scattered skylight from that direction.&lt;/p&gt;&#xA;" OwnerUserId="239" LastActivityDate="2012-04-18T22:11:32.387" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1878" PostTypeId="2" ParentId="1870" CreationDate="2012-04-18T22:30:45.000" Score="8" Body="&lt;p&gt;I don't know about ruminants, but baby rabbits (and presumably other lagomorphs) apparently acquire the necessary intestinal flora by consuming their mother's &lt;a href=&quot;http://en.wikipedia.org/wiki/Cecotropes&quot;&gt;cecotropes&lt;/a&gt;.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;[1] Johnson-Delaney, C.A. (2006), &lt;a href=&quot;http://www.aemv.org/documents/2006_aemv_proceedings_2.pdf&quot;&gt;&quot;Anatomy and Physiology of the Rabbit and Rodent&#xA;Gastrointestinal System&quot;&lt;/a&gt; (PDF)&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="239" LastActivityDate="2012-04-18T22:30:45.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1880" PostTypeId="2" ParentId="1279" CreationDate="2012-04-19T00:50:04.560" Score="4" Body="&lt;p&gt;&quot;Are these modifications the primary regulation mechanism for chromatin structure?&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It depends on how you define primary, we might currently think of histone modifications as primary because other regulatory mechanisms have not yet been well studied. Something else you can think of are the various regulatory proteins that interact with histone marks to modify chromatin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think you should imagine chromatin as assuming &quot;the most compact structure possible until histone modifications are made to enable transcription&quot; but rather histone modifications being a dynamic process with various transcription factors (a class of proteins) coming in and adding/removing histone marks as well as 'remodeling chromatin' (adding/removing nucleosomes)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a sidenote, I don't believe much is known about the tertiary stage you initially mentioned so maybe that could play a huge role in the regulatory mechanisms of chromatin structure, it has just not been well explored.&lt;/p&gt;&#xA;" OwnerUserId="766" LastEditorUserId="766" LastEditDate="2012-04-19T01:01:37.307" LastActivityDate="2012-04-19T01:01:37.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1881" PostTypeId="2" ParentId="1842" CreationDate="2012-04-19T01:10:26.983" Score="17" Body="&lt;p&gt;I found a book chapter for you &lt;a href=&quot;http://books.google.com/books?id=ew1fR6ghsmgC&amp;amp;lpg=PA23&amp;amp;ots=K6oRDzsI3X&amp;amp;dq=origin%20of%20viruses&amp;amp;lr&amp;amp;pg=PA24#v=onepage&amp;amp;q=origin%20of%20viruses&amp;amp;f=false&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quick summary:&#xA;3 hypotheses to Origin of viruses&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;From pre-cellular world (virus first hypothesis)&lt;/li&gt;&#xA;&lt;li&gt;From reductive evolution of parasites (reduction hypothesis)&lt;/li&gt;&#xA;&lt;li&gt;From fragments of cellular genetic material (escape hypothesis)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Drawbacks:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;virus require cells (to infect) so how can they come first&lt;/li&gt;&#xA;&lt;li&gt;virus do not look like known reduced parasites from Bacteria/Eukarya/Archaea&lt;/li&gt;&#xA;&lt;li&gt;unlikely that genetic fragments form complex viral structures for viral function&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because of these drawbacks, the problem of virus origin was for a&#xA;  long time considered untractable and not worth serious consideration&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The rest of the chapter looks more in-depth into the 3 hypotheses&lt;/p&gt;&#xA;" OwnerUserId="766" LastEditorUserId="766" LastEditDate="2012-04-19T22:30:47.143" LastActivityDate="2012-04-19T22:30:47.143" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1883" PostTypeId="2" ParentId="1869" CreationDate="2012-04-19T01:27:49.803" Score="4" Body="&lt;p&gt;As shown in the &lt;a href=&quot;https://biology.stackexchange.com/questions/1869/how-do-trees-manage-to-grow-equally-in-all-directions/1877#1877&quot;&gt;answer by @IlmariKaronen&lt;/a&gt;, that is not always the case. most trees grown next to the shady sides of buildings tend to lean away from the building. Some trees can stand more shade than others, and these will send branches into the shade of buildings. They never grow as dense or robust in the shade. The reason for the plants growing toward the light is Phototropism. When light hits the plant stem, the auxins that determine the length of the stem are destroyed, decreasing the amount of growth on that side of the stem. When this happens, the stems bend toward the light source from the imbalance of auxins in the stem. The reason that the shady side is weaker is that all trees rely on photosynthesis for their energy. Of course, the side without direct sunlight will not perform as much photosynthesis, and so has that much less energy to grow with. Also, many large trees are imbalanced, sometimes all of the weight on one side. The roots hold them up.&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-10-15T13:30:27.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1884" PostTypeId="1" CreationDate="2012-04-19T07:16:32.303" Score="8" ViewCount="863" Body="&lt;p&gt;Suppose I sequence DNA of some organism (a human perhaphs) and now I have the entire DNA &quot;string&quot; - the sequence of nucleotides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the use of that? It's just a &quot;string&quot; where nucleotides encode something but I have no idea what they encode specifically. So to me it looks like some raw data, just represented as a sequence of elements.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is having the entire DNA sequenced useful?&lt;/p&gt;&#xA;" OwnerUserId="466" LastActivityDate="2017-01-26T21:12:29.730" Title="What's the use of DNA sequencing results?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1885" PostTypeId="2" ParentId="1884" CreationDate="2012-04-19T08:43:52.960" Score="9" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;It's just a &quot;string&quot; where nucleotides encode something but I have no idea what they encode specifically.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It sounds like you are describing a computer program, represented by a string of bytes on the hard drive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, the analogy breaks down very quickly because DNA is vastly more complex and a lot of aspects are still poorly understood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the basis is the same: a string of symbols encodes information. In the case of DNA, different parts encode different things in a different manner.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The elephant in the room are of course &lt;em&gt;coding sequences&lt;/em&gt;: stretches of DNA, contained in so-called “&lt;a href=&quot;http://en.wikipedia.org/wiki/Gene&quot;&gt;&lt;strong&gt;genes&lt;/strong&gt;&lt;/a&gt;” – which code for proteins and other stuff.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coding sequences use a fairly simple encoding schema that’s known as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_code&quot;&gt;&lt;strong&gt;genetic code&lt;/strong&gt;&lt;/a&gt;, decoded in 1961. The genetic code has the nice property of being (almost) universal across all species, and easy enough for a child to understand:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Three consecutive DNA base pairs form a &lt;em&gt;codon&lt;/em&gt;. Each codon stands for one &lt;em&gt;amino acid&lt;/em&gt; (except for a special “stop codon”). Amino acids form so-called &lt;em&gt;polypeptide chains&lt;/em&gt; – &lt;a href=&quot;http://en.wikipedia.org/wiki/Protein&quot;&gt;&lt;strong&gt;proteins&lt;/strong&gt;&lt;/a&gt;. There are codon tables, just as you have manuals for assembly mnemonics in computing:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EY6AL.jpg&quot; alt=&quot;Codon table of the genetic code&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, it’s not trivial to know &lt;em&gt;where&lt;/em&gt; genes are on the genome. Just by eyeballing the sequence there is nothing to distinguish one stretch of DNA from its surrounding. But there are certain recognisable stretches of DNA (“motifs”) which we can use to locate genes and other interesting regions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Grossly simplified, a gene is preceded by a &lt;a href=&quot;http://en.wikipedia.org/wiki/Promoter_%28biology%29&quot;&gt;&lt;em&gt;promoter region&lt;/em&gt;&lt;/a&gt; which is highly conserved between species (but gene-specific). Once you’ve identified one species’ promoter, you know it for other species. Furthermore, all promoters share highly similar elements, for instance the &lt;a href=&quot;http://en.wikipedia.org/wiki/TATA_box&quot;&gt;TATA box&lt;/a&gt; – literally the occurrence of “TATA” in the genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, just looking for occurrences of “TATA” would yield vastly more spurious hits than actual promoters but combined with other information you get a &lt;em&gt;gene model&lt;/em&gt; – a statistical machine which can tell you with high confidence where on a genome the genes are located.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Once you have found the genes in a sequence which you can trivially translate to amino acid sequences, you can try to form inferences about the function of the proteins (a protein’s function is an almost-direct consequence of its sequence). Unfortunately, discovering the function of a protein from its sequence alone isn’t possible but we &lt;em&gt;do&lt;/em&gt; know the functions of many proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When we now look at a genome and find a mutation in a protein-coding gene we can infer that the function of this protein is probably modified. Most mutations are so-called deleterious mutations (e.g. by deleting a single nucleotide you get a &lt;em&gt;frame shift&lt;/em&gt; in the codons, and all the subsequent codons no longer make sense), meaning that they &lt;em&gt;destroy&lt;/em&gt; the protein’s function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other, much rarer, mutations modify the protein’s function, making it more or less efficient, or giving it another function altogether.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the simplest case (but these are rare), a single such mutation can explain a complex phenotype. This is known as a &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_Mendelian_traits_in_humans&quot;&gt;Mendelian trait&lt;/a&gt; and can be used to explain a phenotypes such as eye colour, but also hereditary diseases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually, though, it is merely one of many adjusting screws which skew your susceptibility to a certain phenotype in one direction. For instance, you might be slightly more susceptible to &lt;a href=&quot;http://en.wikipedia.org/wiki/BRCA_mutation&quot;&gt;breast cancer&lt;/a&gt; or diabetes.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;This is &lt;em&gt;one&lt;/em&gt; use of the DNA sequence, there are many more; in the last decade, we have realised that &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene_regulation&quot;&gt;&lt;em&gt;regulation&lt;/em&gt;&lt;/a&gt; of gene activity plays a much larger role than anticipated, and most research today looks at regulatory patterns on the DNA level. This is also done with sequence data, but there doesn’t appear to be a simple schema analogous to the genetic code to understand regulation. Instead, it’s a complex interplay of many completely unrelated mechanisms.&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="166" LastEditDate="2012-04-19T08:59:03.517" LastActivityDate="2012-04-19T08:59:03.517" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1886" PostTypeId="2" ParentId="1884" CreationDate="2012-04-19T09:11:20.177" Score="1" Body="&lt;p&gt;There is a whole lot you can do with genome sequences, I'll focus on a specific example here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A gene encodes for a protein, but as long as you have only the DNA sequence of that gene you can't easily find out what exactly the protein that is encoded by the gene does. There are ways to predict certain characteristics of the protein, but you really want to have large amounts of the protein itself to be able to examine it in detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having the sequence of a gene allows you to put that gene into other cells, often bacteria but also yeast cells, insect or mammalian cell lines. Using those you can then mass-produce the protein, purify it and start to study its structure and function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Getting the protein without a sequence means you need to extract it from whatever organism produces it. This is only feasible for proteins that are produced in very large amounts, and even then it probably means you'll have to process a large amount of material to get enough protein. Having the sequence available enables us to study a lot more different proteins than we could by purifying them from their original source.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2012-04-19T09:11:20.177" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1887" PostTypeId="2" ParentId="1869" CreationDate="2012-04-19T09:22:45.827" Score="17" Body="&lt;p&gt;Growth in plants is tightly controlled by &lt;a href=&quot;http://en.wikipedia.org/wiki/Auxin&quot; rel=&quot;nofollow noreferrer&quot;&gt;auxins&lt;/a&gt; – plant hormones. Auxin itself usually has an &lt;del&gt;inhibitory&lt;/del&gt; effect on growth [EDIT: see comments and Richard’s answer for correction]. As far as I know there is no active control to restore plant symmetry once it has gone awry (but I could be wrong!) but the inhibitory effect of auxin synthesised at the meristem and diffusing in all directions causes a symmetrical pattern of inhibition and activation, forming shoots at symmetrical distances around the shoot apical meristem – this is very visible in the symmetry of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Romanesco_broccoli&quot; rel=&quot;nofollow noreferrer&quot;&gt;romanesco broccoli&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/4/4f/Fractal_Broccoli.jpg/320px-Fractal_Broccoli.jpg&quot; alt=&quot;Romanesco&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, there are several mechanisms involving auxin which shape the general growth of the plant. The most important ones are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Apical_dominance&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Apical dominance&lt;/strong&gt;&lt;/a&gt; which causes the apex (the stem) of the plant to grow more strongly than other parts of the plant, ensuring a general centring of the growth.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Phototropism&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Phototropism&lt;/strong&gt;&lt;/a&gt; causes the plant to grow towards sunlight. Unlike you hypothesised, this isn’t simply due to more photosynthesis and hence faster growth at the front of the plant facing the light, it’s actively controlled.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Geotropism&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Gravitropism&lt;/strong&gt;&lt;/a&gt; is a very interesting effect which causes the plant to grow generally &lt;em&gt;upwards&lt;/em&gt;. It’s interesting because the mechanism is actually using gravity: the auxin synthesised at the meristem diffuses downwards in the plant due to gravity, inhibiting the growth in lower regions (but note that in the root apical meristem the effect is somehow reversed).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hydrotropism&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Hydrotropism&lt;/strong&gt;&lt;/a&gt; causes the plant to grow towards water.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;All these effects combined cause the plant to grow in a generally upwards, laterally distributed fashion.&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.643" LastActivityDate="2014-12-26T21:41:41.763" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="1888" PostTypeId="2" ParentId="1836" CreationDate="2012-04-19T09:43:24.943" Score="16" Body="&lt;p&gt;In general the answer is always the same: you construct a &lt;a href=&quot;http://en.wikipedia.org/wiki/Phylogeny&quot;&gt;&lt;strong&gt;phylogenetic tree&lt;/strong&gt;&lt;/a&gt;. In order to locate different species on this tree in relation to each other, you use various features to compare which species are more similar to each other than others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best way of doing this is by comparing their DNA sequence, especially &lt;a href=&quot;http://en.wikipedia.org/wiki/Ortholog#Orthology&quot;&gt;orthologous genes&lt;/a&gt; (i.e. genes common to the species compared).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, genetic sequences usually aren’t available for extinct species. You can still compare &lt;a href=&quot;http://en.wikipedia.org/wiki/Ortholog#Orthology&quot;&gt;homologous features&lt;/a&gt; though. For instance, the class of &lt;a href=&quot;http://en.wikipedia.org/wiki/Mammals&quot;&gt;mammals&lt;/a&gt; are all characterised by the possession of mammary glands. Similarly, all vertebrates have a vertebral column and all aves are feathered, warm-blooded, egg-laying vertebrates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The collection of many such features from fossile records allows the creation of more or less detailed phylogenies. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Birds#Dinosaurs_and_the_origin_of_birds&quot;&gt;Wikipedia explanation&lt;/a&gt; mentions several transitional fossil forms which trace the evolution from dinosaurs to modern birds via several intermediates. All of the inferences are based on anatomical resemblance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This may sound weak evidence but in fact anatomical homology has proved to be sufficiently accurate in constructing other phylogenies, where we have been able to verify the correctness using genome comparison data. So while there is much uncertainty about the precise branching point of birds from dinosaurs (or maybe archosaurs), there is near-certainty that the common ancestor of birds and dinosaurs was, in fact, an archosaur.&lt;/p&gt;&#xA;" OwnerUserId="166" LastActivityDate="2012-04-19T09:43:24.943" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1889" PostTypeId="2" ParentId="1884" CreationDate="2012-04-19T12:55:36.437" Score="2" Body="&lt;p&gt;As the others mentioned, identifying and annotating protein coding genes is an important part of any genome sequencing project. However, there are a variety of other things you can do with a complete genome sequence. You can annotate other types of features, such as transposable elements and repetitive sequences, you can sequence mRNA and map it back to the genome to get a measure of gene expression for a particular tissue, and you can look for variations in the genome such as single nucleotide polymorphisms (SNPs), copy number variations (CNVs), and other large scale variations. If other related genomes are available, there are a lot comparative genomics questions you can ask about large-scale conservation (synteny), DNA substitution rates, relative DNA composition, etc. We are really just beginning to scratch the surface as to the wealth of information a genome contains and how that information is biologically processed.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2012-04-19T17:36:24.517" LastActivityDate="2012-04-19T17:36:24.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1890" PostTypeId="2" ParentId="1866" CreationDate="2012-04-19T19:36:16.783" Score="17" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is the son of a couple engaged in farming better suited to the same profession unless he receives a couple of recessive alleles from both parents?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not everything is coded in the genome, environmental cues play a very important role in shaping who you are. Profession is just one of those things that is not encoded in genes.&#xA;Many people do not continue doing the job of their parents, but they do very well in life.&#xA;Also note that, aside from the fact that there is no &quot;agriculture&quot; gene, having a recessive allele does not mean you will miss a certain phenotype.&#xA;What is true is that someone who has higher education will probably be more keen to have their kids studying. On the contrary, the kids of someone who is a poor farmer and is barely able to provide for his family will probably not have the opportunity of going to school (let alone university) and therefore will continue to work the land. It has nothing to do with genetics.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Generally there is a lot of unscientific information floating around about these matters. One of the grapevines is that it is genetically better for one to marry outside their caste to create diversity(?). Is such a thing true?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Continuing to reproduce in the same group of people will limit diversity in the genome, and create an accumulation of mutations, which is generally a bad thing. That is why it is very common to have particular illnesses in closed communities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance Amish people have an higher incidence of genetic disorders such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Ellis%E2%80%93van_Creveld_syndrome&quot;&gt;Ellis-van Creveld syndrome&lt;/a&gt; (a form of dwarfism)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8661097&quot;&gt;The Gene for the Ellis–van Creveld Syndrome Is Located on Chromosome 4p16&lt;/a&gt; - Ruiz-Perez et al., Nat. Genetics 2000&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Autosomal recessive transmission of the disorder is supported by&#xA;  multiple affected siblings with unaffected parents in families with&#xA;  known parental consanguinity. The largest known pedigree segregating&#xA;  with EVC is that reported by McKusick and his colleagues in the Old&#xA;  Order Amish (McKusick et al., 1964). The prevalence of living persons&#xA;  affected with EVC among the Lancaster County Amish was estimated to be&#xA;  2 in 1000, whereas the frequency of occurrence among live births was 5&#xA;  in 1000. McKusick et al. estimated that the frequency of heterozygous&#xA;  carriers in the Old Order Amish is as high as 13% (McKusick et al.,&#xA;  1964). All cases of EVC in the Amish at that time were traced to a&#xA;  common founding couple, Samuel King and his wife, who immigrated to&#xA;  Pennsylvania in 1744.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is a well known effect, called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Founder_effect&quot;&gt;founder effect&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for India, a study on the genetic behind casts has been done a couple of years ago. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842210/&quot;&gt;Reconstructing Indian Population History&lt;/a&gt; - Reich et al., Nature 2010&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Haldane wrote 45 years ago that “if inter-caste marriages in India become common, various… recessive characters will become rarer”. However, it has not been generally appreciated that this applies to groups throughout India, and not only to groups in the south where consanguinity is common. We hypothesize that founder effects are responsible for an even higher burden of recessive diseases in India than consanguinity. &#xA;  To test this hypothesis, we used our data to estimate the probability that two alleles from a group share a common ancestor more recently than that group’s divergence from other Indians, and compared this to the probability that an individual’s two alleles share an ancestor in the last few generations due to consanguinity. &lt;strong&gt;Nine of the 15 Indian groups for which we could make this assessment had a higher probability of recessive disease due to founder events than to consanguinity, including all the Indo-European speaking groups.&lt;/strong&gt;&#xA;  An additional reason why some diseases are expected to occur at elevated frequencies in India is shared descent from a common Indian ancestral population. An example is a 25 base pair deletion in MYBPC3 that increases heart failure risk by about 7-fold, and occurs at around 4% throughout India but is nearly absent elsewhere.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They conclude that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We have documented a high level of population substructure in India, and have shown that the model of mixture between two ancestral populations ASI and ANI provides an excellent description of genetic variation in many Indian groups. &#xA;  [...]&lt;br&gt;&#xA;  By showing that a large proportion of Indian groups descend from strong founder events, these results highlight the importance of identifying recessive diseases in these groups and mapping causal genes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is very important to understand that this results in no way show a genetic basis for the existence of casts, which remain purely social entities. They rather show that an &lt;strong&gt;environmental&lt;/strong&gt; constraint can influence the distribution of genetic traits, due to a restriction in the possibility of mixing genes in the population.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-04-19T19:36:16.783" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1891" PostTypeId="2" ParentId="1822" CreationDate="2012-04-19T20:10:39.567" Score="8" Body="&lt;p&gt;This is basically the same that happens after &lt;a href=&quot;http://en.wikipedia.org/wiki/Pruning&quot;&gt;pruning&lt;/a&gt; and involves a basic hormonal regulation mechanism in the plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens is that the cut piece of the wood forms a new &lt;a href=&quot;http://en.wikipedia.org/wiki/Meristem&quot;&gt;meristem&lt;/a&gt; which allows the growth of new organs. What’s important is that there is no other growth happening nearby, since that would hormonally inhibit any further growth. This is why such growths happen once you’ve cut the wood, not before (on the healthy stem). This inhibitory effect is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Apical_dominance&quot;&gt;apical dominance&lt;/a&gt;, which has now been disabled.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to where the energy and water comes from, to some extent it is stored within the branches themselves. That’s why you need to dry them before being able to use them in a fire. However, this growth is pretty limited. Further water is probably collected by condensation of water vapour in the air.&lt;/p&gt;&#xA;" OwnerUserId="166" LastActivityDate="2012-04-19T20:10:39.567" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1892" PostTypeId="1" CreationDate="2012-04-20T00:09:40.670" Score="10" ViewCount="1177" Body="&lt;p&gt;I am looking to find a highly competent E coli strain.  I am making a library of a ~6.6kb plasmid and I am not getting high enough efficiency.  Does anyone have a suggestion of a strain/protocol with ultrahigh efficiency (&gt;10&lt;sup&gt;10&lt;/sup&gt;).  &lt;/p&gt;&#xA;" OwnerUserId="770" LastEditorUserId="69" LastEditDate="2012-04-21T12:10:11.250" LastActivityDate="2012-04-21T12:10:11.250" Title="What is the highest competency possible for E coli?" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;synthetic-biology&gt;&lt;cloning&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1893" PostTypeId="2" ParentId="1892" CreationDate="2012-04-20T01:37:14.383" Score="9" Body="&lt;p&gt;This is a great question as I just made my own &quot;homebrew&quot; chemically competent cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a vast variety of &lt;em&gt;E. coli&lt;/em&gt; strains that are commonly used for cloning. They may be transformed chemically by heat shock method, or electrically by electroporation (a brief summary may be found &lt;a href=&quot;http://www.promega.com/resources/articles/pubhub/enotes/how-are-competent-bacterial-cells-transformed-with-a-plasmid/&quot;&gt;here&lt;/a&gt;). These can be made in the lab manually, or purchased commercially from reputable vendors (I recommend Invitrogen/Life Tech, NEB, Promega).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chemically competency is achieved using &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=6345791&quot;&gt;Hanahan&lt;/a&gt;'s method or some a variation thereof. The method involves washing the bacteria in a series of buffers containing various di-valent cation chloride salts (CaCl&lt;sub&gt;2&lt;/sub&gt;, RbCl&lt;sub&gt;2&lt;/sub&gt;, etc). &lt;strong&gt;Commercially available &lt;em&gt;E. coli&lt;/em&gt; are sold as &quot;regular&quot; and &quot;ultra&quot; competent, ranging from 10&lt;sup&gt;6&lt;/sup&gt; to 10&lt;sup&gt;6&lt;/sup&gt; for regular, and the highest I've seen is 10&lt;sup&gt;10&lt;/sup&gt; cfu/&amp;micro;g DNA.&lt;/strong&gt; For maximum efficiency, especially since a small plasmid such as yours will be easy to transform, &lt;strong&gt;electroporation is a more efficient technique, but requires specialized equpment&lt;/strong&gt;. &lt;strong&gt;Electroporation can yield &gt;10&lt;sup&gt;10&lt;/sup&gt; cfu/&amp;micro;g&lt;/strong&gt;. For standard cloning practices, regular or high efficiency chemically competent E. coli are perfectly adequate. Since you mentioned you are creating a library, you certainly want to go with ultra high efficiency chemical transformation or, if you have the necessary equipment, electroporation. &lt;em&gt;I have not seen electroporation efficiencies reported &gt; 5x10&lt;sup&gt;10&lt;/sup&gt;&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Transformation efficiencies are standardized by reporting a rate as the number of colony forming units (cfu) per &amp;micro;g of some control plasmid, typically pUC19. Transformation efficiency is very sensitive to many factors, including heat shock time, cooling times, thawing time, amount and size of plasmid DNA. All things being equal, the size and quantity of DNA are important for your purposes. Transformation efficiency generally increases with quantity of DNA, but there is a saturation point, and evenetually having too much DNA decreases the yield. Also, efficiency decreases linearly with plasmid size. For example, pUC19, the control vector, is ~2.7 kbp, and your library plasmid is ~6.6 kbp, so you should expect for the same mass of DNA you will have lost 60% transformation due to plasmid size. This loss is due to the physically larger size of DNA being more difficult to move into the bacteria.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2012-04-20T01:44:07.747" LastActivityDate="2012-04-20T01:44:07.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1894" PostTypeId="1" AcceptedAnswerId="1895" CreationDate="2012-04-20T07:20:04.627" Score="4" ViewCount="586" Body="&lt;p&gt;&lt;strong&gt;Hydroponics&lt;/strong&gt; is a subset of hydroculture and is a method of growing plants using mineral nutrient solutions, in water, without soil.&lt;a href=&quot;http://en.wikipedia.org/wiki/Hydroponics&quot; rel=&quot;noreferrer&quot;&gt; [wikipedia]&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;My question is if &lt;em&gt;is it possible to grow any kind of plant soilless (hydroponics)?&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="410" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-04-21T22:19:30.123" Title="Is it possible to grow any kind of plant soilless (hydroponics)?" Tags="&lt;botany&gt;&lt;plant-anatomy&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1895" PostTypeId="2" ParentId="1894" CreationDate="2012-04-20T08:15:04.000" Score="0" Body="&lt;p&gt;Yes, There are a few i know of, a quick &quot;air plant&quot; google search will get you quiet a lot. &#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Epiphyte&quot; rel=&quot;nofollow&quot;&gt;wiki 1&lt;/a&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Tillandsia&quot; rel=&quot;nofollow&quot;&gt;wiki 2&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: I just glanced through the hydroponics article, and now I wonder if my answer actual answers your question.&lt;/p&gt;&#xA;" OwnerUserId="565" LastActivityDate="2012-04-20T08:15:04.000" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1896" PostTypeId="1" AcceptedAnswerId="1898" CreationDate="2012-04-20T14:22:37.150" Score="11" ViewCount="448" Body="&lt;p&gt;I'm working on a project where I am taking DNA sequences and translating the codons into musical notes. I have some good ideas of how to do this, I'm just not sure what sequences to work with. My case study and a lot of my initial research showed that anything larger than a protein is too much to work with for now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question. Where can I find protein DNA sequences in some standard format. I've looked at NCBI but I have no idea what I'm looking at or if I'm downloading the right stuff. Is there a link that I can go to that will have a listing of a bunch of difference protein sequences that I can download? &lt;/p&gt;&#xA;" OwnerUserId="414" LastEditorUserId="389" LastEditDate="2012-04-21T06:32:15.300" LastActivityDate="2012-04-21T06:32:15.300" Title="Source of DNA sequences" Tags="&lt;dna&gt;&lt;bioinformatics&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1897" PostTypeId="2" ParentId="1896" CreationDate="2012-04-20T14:39:24.210" Score="7" Body="&lt;p&gt;A standard format would be the &lt;a href=&quot;http://en.wikipedia.org/wiki/FASTA_format&quot;&gt;FASTA format&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have a few proteins of interest that you would like to look at you can simply select 'Nucleotide' at the top of the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/guide/&quot;&gt;NCBI page&lt;/a&gt;, enter your protein's name and then press the FASTA button below each result you are interested in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you just need a large dataset of DNA sequences that code for proteins you could for example use the &lt;a href=&quot;ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz&quot;&gt;'nt'&lt;/a&gt; blast database.&#xA;(I believe this is only protein sequences not entirely sure though, I thought it would be easier to get)&lt;/p&gt;&#xA;" OwnerUserId="754" LastEditorUserId="754" LastEditDate="2012-04-20T14:57:36.513" LastActivityDate="2012-04-20T14:57:36.513" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1898" PostTypeId="2" ParentId="1896" CreationDate="2012-04-20T14:55:46.733" Score="8" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genbank/&quot;&gt;GenBank&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/RefSeq/&quot;&gt;RefSeq&lt;/a&gt; have a huge collection of DNA sequences that can be downloaded in Fasta format. GenBank makes it very easy to search for sequences (for example, using the organism name) but will often have redundant data and varied types (everything from whole chromosome sequences to mRNAs to gene sequences to ESTs). RefSeq has much cleaner, non-redundant data but might take a little more effort for you to find the sequences you want. Depending on whether this has any effect on your project, you might want to consider that. On the RefSeq page, under the &lt;strong&gt;FTP&lt;/strong&gt; menu you can click &lt;strong&gt;Genomes&lt;/strong&gt; to see which genomes have RefSeq data available. The Fasta sequences for a particular genome will be stored in a dedicated directory, possibly subdivided into further directories by chromosome. What you want are the Fasta files (ending in .fa, .fasta, .ffn, or something like that), keeping in mind they may be compressed (.fa.gz, fasta.gz, etc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, if you already have a specific organism in mind, then you could do a Google search to see if the genome for that organism has been sequenced. If so, there is almost always a dedicated website where you can download DNA sequences for that genome.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2012-04-20T15:24:31.050" LastActivityDate="2012-04-20T15:24:31.050" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1899" PostTypeId="1" AcceptedAnswerId="1903" CreationDate="2012-04-20T17:28:44.017" Score="9" ViewCount="402" Body="&lt;p&gt;Has there been any definitive research about handedness being genetic? Also, why is right-handedness clearly dominant in humans? I'm interested in evolutionary theories, as well as any molecular explanation (if known).&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-04-21T05:38:29.927" Title="Is there a dominant gene for right-handedness?" Tags="&lt;evolution&gt;&lt;molecular-genetics&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1900" PostTypeId="2" ParentId="1896" CreationDate="2012-04-20T18:31:54.020" Score="1" Body="&lt;p&gt;This is more of a comment, but too long to put in a comment box, so I'm putting it here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a fun idea you're doing. I have a half baked idea (assuming you're looking for input) if you want to explore it further -- or not ... by the time I finish writing this, I might realize it's too silly, but still ... let's see.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It might be fun to take the sequence of two organisms, let's say mouse and human and align certain regions to each other -- imagine this is like playing a piano where the &quot;left hand&quot; might be the mouse sequence, and the &quot;right hand&quot; is human.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, say you take a gene that are shared in both, like CCND1. You can align them against each other and you'll find large portions of the sequences are common (with some mismatches, obviously). In these regions, the left and right hands are playing together (different octaves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You'll also find gaps in the alignments where you'll have a stretch of &quot;mouse only&quot; or &quot;human only&quot; sequence, and in these regions the left or right hand play alone (solo).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, say the two alignments look like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;mouse: CGTGGGAGGCTCTTGAGCCTGGAAACACTATCGCAGTTTGTACGGAATGCACTTGTTCTTTACAAAAGG&#xA;human: CTTGGGCGACA---GAGC---GAGACTTTGTCTCAAAAAAGAAG--------------------AAAAG&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;In this case, you see stretches of the alignments where the mouse (left hand) will be playing a solo, and other times the two hands play in &quot;harmony.&quot;&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2012-04-20T18:31:54.020" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1901" PostTypeId="1" AcceptedAnswerId="1936" CreationDate="2012-04-20T19:25:30.503" Score="5" ViewCount="105" Body="&lt;p&gt;CD47 aka the &quot;don't eat me&quot; signal has recently been claimed &lt;a href=&quot;http://www.pnas.org/content/early/2012/03/20/1121623109.short&quot;&gt;to be expressed on all tumor cells&lt;/a&gt;. This doesn't seem to corroborate with other cell-biology experiments. On what other cells is CD47 expressed?&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="1214" LastEditDate="2014-01-26T18:35:16.547" LastActivityDate="2014-01-26T18:35:16.547" Title="How extensive is CD47?" Tags="&lt;cell-biology&gt;&lt;gene-expression&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1902" PostTypeId="1" AcceptedAnswerId="1906" CreationDate="2012-04-20T19:29:01.233" Score="2" ViewCount="74" Body="&lt;p&gt;I'm trying to get a sense of the variety of methods used for determining the number of cell surface antigens and receptors. This is notably different from determining the affinity of these surface markers. &lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-04-21T12:07:55.137" Title="Measuring the density of surface antigens" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1903" PostTypeId="2" ParentId="1899" CreationDate="2012-04-20T19:45:27.323" Score="6" Body="&lt;p&gt;There is a &lt;a href=&quot;http://omim.org/entry/139900&quot;&gt;lot of information&lt;/a&gt; at OMIM  - too much to summarize here - regarding the genetics of handedness and links to which hemisphere of the brain dominates (in an individual), to schizophrenia (slight association with non-right-handedness), and to hair whorl patterns on the scalp. References are provided at the above link. Basically, hand skill appears to be a complex multifactorial phenotype with a heterogeneous background.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-04-20T19:45:27.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1904" PostTypeId="2" ParentId="1892" CreationDate="2012-04-20T20:55:23.900" Score="6" Body="&lt;p&gt;I have heard that Epi300 electrocompetent cells (&lt;a href=&quot;http://www.epibio.com/item.asp?ID=384#Items&quot;&gt;1&lt;/a&gt;) from Epicentre are very efficient: &gt; 1 x 10&lt;sup&gt;10&lt;/sup&gt; cfu/µg of pUC19. Dan Gibson used them in his paper for the synthesis of the mitochondrial genome (&lt;a href=&quot;http://www.nature.com/nmeth/journal/v7/n11/full/nmeth.1515.html&quot;&gt;2&lt;/a&gt;). We were also thinking of using them for our assemblies, but they are pretty expensive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.epibio.com/item.asp?ID=384#Items&quot;&gt;1. TransforMax™ EPI300™ Electrocompetent E. coli&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nmeth/journal/v7/n11/full/nmeth.1515.html&quot;&gt;2. Chemical synthesis of the mouse mitochondrial genome, Gibson et. al.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-04-21T01:07:07.690" LastActivityDate="2012-04-21T01:07:07.690" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1906" PostTypeId="2" ParentId="1902" CreationDate="2012-04-21T02:53:26.247" Score="4" Body="&lt;p&gt;Do you mean to count numbers of both antigens and receptors in live cell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Possible ways:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;FRET (unlikely to work)&lt;/li&gt;&#xA;&lt;li&gt;imaging of receptors with single molecule resolution&lt;/li&gt;&#xA;&lt;li&gt;western blot to roughly estimate amount of receptors&lt;/li&gt;&#xA;&lt;li&gt;single cell proteomics techniques (not very suitable)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="698" LastEditorUserId="69" LastEditDate="2012-04-21T12:07:55.137" LastActivityDate="2012-04-21T12:07:55.137" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1907" PostTypeId="2" ParentId="1249" CreationDate="2012-04-21T03:48:08.560" Score="1" Body="&lt;p&gt;Apparently poly(ethylene oxide) is a biologically interesting polymer, with minimal protein interactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The apparently means that I haven't tried it myself, but my polymer teacher told us so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sigmaaldrich.com/materials-science/material-science-products.html?TablePage=20204110&quot; rel=&quot;nofollow&quot;&gt;http://www.sigmaaldrich.com/materials-science/material-science-products.html?TablePage=20204110&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Polyethylene_glycol&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Polyethylene_glycol&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nomenclature seems to favour poly(ethylene glycol). I prefer poly(ethylene oxide), because then I know from what monomer the polymer was synthesized.&lt;/p&gt;&#xA;" OwnerUserId="691" LastActivityDate="2012-04-21T03:48:08.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1908" PostTypeId="2" ParentId="1899" CreationDate="2012-04-21T05:38:29.927" Score="6" Body="&lt;p&gt;OMIM (online mendelian inheritance in man) is a good example to explain how complicated heritability usually is.  Simple Mendelian traits, where smooth or wrinkly peas will have wrinkly offspring, allow us to segregate individuals with pure dominant / heterologous and pure recessive traits.  When we have done so the chance of inheriting the trait can be predicted precisely (i.e. 25/50/25%).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The number of simple mendelian traits which are observed in an individual are pretty doggone rare. Even things that are dominant like dark hair are usually more complex.  I'm of 100% japanese descent, but my son was born with blonde hair and it looks like it won't go darker than mousy brown - black hair is not really dominant, he will have a color between my wife's and mine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also need to make a distinction between mendelian traits, which are observed in the individual organsim as opposed to specific DNA variants like a single site mutation (A-&gt;T, C-&gt;T etc)  which are &lt;em&gt;usually&lt;/em&gt; mendelian.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rarity of mendelian inheritance is because there are so many checks and balances in our gene networks that no single gene is solely responsible for any function.  Medical research has discovered many single mutation (Mendelian) diseases, but they are very rare in practice.  There are single mutations that cause diabetes like systems (called MODY diabetes) for instance, but more than 99% of diabetes are not caused by these mutations.  A single mutation advantage is quickly adapted so that single mutations cannot nullify the advantage.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Common mutations that cause diseases or other disadvantages are likewise relatively quick to disappear through adaptations.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I once saw the old text bound copy of &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Online_Mendelian_Inheritance_in_Man#Versions&quot;&gt;Mendelian Inheritance in Man&lt;/a&gt;&quot; It was not a small book, but it seemed to me that when I paged through it, when you look at traits like 'handedness'. there were only a few hundred simple mendelian traits identified.  Most of what we are is the result of the interplay of several or even many of our ~30,000 genes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an example of how this works, see this &lt;a href=&quot;http://www.sciencemag.org/content/330/6011/1682.full&quot;&gt;article&lt;/a&gt; about what happens to new fly genes. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-04-21T05:38:29.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1909" PostTypeId="1" AcceptedAnswerId="2211" CreationDate="2012-04-21T06:49:04.343" Score="8" ViewCount="449" Body="&lt;p&gt;The Solvent-Accessible Surface Area (SASA) is a valuable metric for looking at protein folding and protein-protein interactions. However, this measurement is typically done by calculating the SASA from a solved (and generally static) structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chemical probes like diazirine and hydroxyl radicals show some bias regarding where they tend to bind. I'm realizing while I'm writing this question that NMR is a perfectly valid method to determine a solution based structure and then calculate the SASA. Similar strategies has also been used to examine structured RNAs. I'm curious about the variety of these methods and how accurate they are.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="69" LastEditDate="2012-04-25T21:06:08.287" LastActivityDate="2018-06-28T05:50:51.537" Title="Solution based measurement of Solvent-Accessible Surface Area of macromolecules" Tags="&lt;biochemistry&gt;&lt;structural-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1910" PostTypeId="1" CreationDate="2012-04-21T11:42:30.920" Score="18" ViewCount="5776" Body="&lt;p&gt;For all domestic animals, and for all animals kept in laboratory, complete and precise composition of perfect food is figured out (cat food, dog food, cattle, rats, laboratory monkeys and apes) -- which contains precise composition of carbs, fats, proteins, aminoacids, minerals and vitamins. Everything is known. Convenient dry cat/dog food contains exactly that. Animals are healthy on this food. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The composition is also known for human babies. This is manufactured as &quot;baby formula&quot;. Everything baby's organism needs to be healthy (and to grow).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How let's take human adults. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Was ever attempt made to create &quot;dry human 'dog-food'&quot;? This sounds stupid, but there are emergency situation in which such food can come very useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is, is there anything special in human biology that prevents creation of complete &quot;dry human food&quot; that contains everything our organism needs to be healthy ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or it was created but tasted so disgusting that nobody would eat it ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or it actually exist somewhere ? Just curious.&lt;/p&gt;&#xA;" OwnerUserId="226" LastEditorUserId="69" LastEditDate="2012-04-22T11:57:53.350" LastActivityDate="2018-10-20T07:13:52.073" Title="Has there ever been an attempt to create nutritionally tailored food for adult human consumption?" Tags="&lt;food&gt;&lt;nutrition&gt;" AnswerCount="5" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1911" PostTypeId="1" AcceptedAnswerId="1912" CreationDate="2012-04-21T13:01:42.160" Score="10" ViewCount="535" Body="&lt;p&gt;I am struggling to think why horizontal gene transfer between bacteria would have persisted during the course of evolution as surely it puts the 'donor' at a disadvantage?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, consider a hypothetical situation where only one species of bacteria has a gene to resist a new (almost) omnipotent antibiotic.  When growing on this medium, this species of bacteria has nil inter-specific competition for the resources it needs.  Yet if it passes on the plasmid containing the resistance gene via conjugation to individuals of a different bacterial species, they then too are able to grow on the medium and potentially out-compete the first species - thus the conjugation could possibly be extremely detrimental to the survival of the original population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm obviously missing something as the feature &lt;em&gt;has&lt;/em&gt; persisted, &lt;strong&gt;so what is the advantage to the donor species of conjugation&lt;/strong&gt;? &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-04-21T13:24:48.497" Title="What advantage would the initial 'donor' in horizontal gene transfer by conjugation have received?" Tags="&lt;evolution&gt;&lt;bacteriology&gt;&lt;horizontal-gene-transfer&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1912" PostTypeId="2" ParentId="1911" CreationDate="2012-04-21T13:14:37.090" Score="8" Body="&lt;p&gt;The donor bacterium, viewed as a unit, may well gain no advantage from sharing its genes.  The genes that are shared, however, may gain a very substantial reproductive advantage from being able to spread to other strains.  If some of the genes that are capable of being shared also promote sharing, they may be selected for by evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a good example of the basic principle of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene-centered_view_of_evolution&quot;&gt;gene-centered view of evolution&lt;/a&gt;, famously popularized by Richard Dawkins is his book &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Selfish_Gene&quot;&gt;&lt;em&gt;The Selfish Gene&lt;/em&gt;&lt;/a&gt;: evolution selects for genes that are good at spreading themselves.  This may, but need not always, imply helping the organism containing the gene to survive and reproduce.&lt;/p&gt;&#xA;" OwnerUserId="239" LastEditorUserId="239" LastEditDate="2012-04-21T13:24:48.497" LastActivityDate="2012-04-21T13:24:48.497" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1914" PostTypeId="1" CreationDate="2012-04-21T19:27:41.710" Score="10" ViewCount="22208" Body="&lt;p&gt;As we all know, a few species of snakes swallow rodents as a whole. My question is what happens to the teeth and bones of these animals? Won't they cut into the flesh of the snake and hurt it? Are the digestive acids strong enough to dissolve bones and teeth? Even so, I'm sure the process takes time, and during this period won't the snake get injured? &lt;/p&gt;&#xA;" OwnerUserId="776" LastActivityDate="2017-10-02T18:36:21.053" Title="What happens to snakes that swallow rodents as a whole?" Tags="&lt;zoology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1915" PostTypeId="2" ParentId="1910" CreationDate="2012-04-21T19:34:38.907" Score="4" Body="&lt;p&gt;According to @Ilmari Karonen's comment and link, I have the answer. Such food does exist. However a person who tried to eat it and nothing else could bear it for only 7 days. He had cravings for &quot;normal&quot; food. The link was &lt;a href=&quot;http://www.angryman.ca/monkey.html&quot; rel=&quot;nofollow&quot;&gt;http://www.angryman.ca/monkey.html&lt;/a&gt;. Apparently the guy had weak will, but that's normal.&lt;/p&gt;&#xA;" OwnerUserId="226" LastEditorUserId="69" LastEditDate="2012-04-21T19:48:09.497" LastActivityDate="2012-04-21T19:48:09.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1916" PostTypeId="2" ParentId="1894" CreationDate="2012-04-21T22:19:30.123" Score="7" Body="&lt;p&gt;Yes it is possible, and as far as I can see, there should not be any plant which would be impossible to grow in a such an environment, just more or less difficult, although this is just my speculation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have myself grown tomatoes from only a liquid solution of minerals and nutrients, but you have to change the solution from time to time to prevent bacteria and fungi growing starting to grow in it. The reason why this is not a method used in industrious growing is because it is a lot more expensive than using soil and fertilisers, and more work.&lt;/p&gt;&#xA;" OwnerUserId="757" LastActivityDate="2012-04-21T22:19:30.123" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1917" PostTypeId="1" AcceptedAnswerId="1996" CreationDate="2012-04-22T00:19:55.810" Score="5" ViewCount="2762" Body="&lt;p&gt;I'm hoping to learn the basics of epidemiological methods, terminology, etc. I come from a background in statistical economics, and I'm moving into the economics of public health. I don't know if epidemiology uses separate statistical methods, but I presume it does. I know discussion questions aren't recommended, but please list any reasons you have (personal experience, ease of introduction, etc.) for texts you would recommend. &lt;/p&gt;&#xA;" OwnerUserId="777" LastActivityDate="2012-04-27T05:57:00.653" Title="Could someone recommend an introductory book on epidemiology?" Tags="&lt;epidemiology&gt;" AnswerCount="4" CommentCount="0" ClosedDate="2012-08-10T07:49:17.920" ContentLicense="CC BY-SA 3.0" />
  <row Id="1919" PostTypeId="2" ParentId="1853" CreationDate="2012-04-22T08:25:55.923" Score="14" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ramachandran_plot&quot;&gt;Ramachandran plots&lt;/a&gt; show the relationship between the phi and psi angles of a protein referring to dihedral angles between the N and the C-alpha and the C-alpha and the C-beta. As an aside, the omega angle between the C-beta and the N tends to be fixed due to pi-pi interactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Dihedral Angles&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JFHMD.jpg&quot; alt=&quot;Dihedral Angles&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are limits to possible distributions of phi and psi angles due to steric clashes between the side chains. Furthermore other limitations from higher order structure will result in the adoption of defined phi-psi angles. Using data from solved crystal structures, it can be seen that the dihedral angles will adopt specific conformations in a protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;RAMACHANDRAN PLOT from Lovell et al.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/47Op0.jpg&quot; alt=&quot;Ramachandran plot&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, it can be noted that some of these conformations relate to specific secondary structures. As seen above, peptides in alpha-helices and beta-sheets adopt a even more limited set of phi-psi angles. Certain amino acids like glycine and proline, which differ from from canonical amino acids have an unique Ramachandran plot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The angles from a Ramachandran plot are useful not only for determining a amino acids' role in secondary structure but can also be used to verify the solution to a crystal structure. Furthermore, it assists with constraining structure prediction simulations and helps with defining energy functions.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-04-22T08:25:55.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1920" PostTypeId="1" CreationDate="2012-04-22T10:25:37.270" Score="6" ViewCount="1357" Body="&lt;p&gt;I'd like monitor my resting heart rate and blood pressure to see how they are affected by regular cardiovascular training and other events in life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When should I take the measurements in order to reduce day-to-day variations? In the morning or evening? Before or after eating? Right after waking up?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course I'll make sure to follow good routines when measuring, but the ones I've found prescribed by hospitals don't state an appropriate time of the day.&lt;/p&gt;&#xA;" OwnerUserId="778" LastEditorUserId="69" LastEditDate="2012-04-22T11:39:36.977" LastActivityDate="2012-06-16T20:53:58.983" Title="When to measure resting heart rate and blood pressure for following day-to-day trend?" Tags="&lt;human-biology&gt;&lt;cardiology&gt;&lt;experimental-design&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1921" PostTypeId="2" ParentId="1920" CreationDate="2012-04-22T11:48:34.687" Score="5" Body="&lt;p&gt;I would be &lt;em&gt;very&lt;/em&gt; surprised if the time of day made a difference.  I've personally never heard mention of such a phenomenon in discussions with intensive care practitioners (where of course HR and BP are measured constantly).  However this is only the case during rest, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19142757&quot;&gt;this paper&lt;/a&gt; (on horses) suggests that there is some difference in HR and BP after exercise depending on time of day.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are right to attempt to control it however, I suppose.  &lt;strong&gt;It doesn't matter when you take your measurements, as long as you take them at the same time each day.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would say that one of your first suggestions of taking the measurements &lt;em&gt;almost&lt;/em&gt; immediately after waking.  Of course you would have to be relaxed as you assembled your equipment then rest for a few minutes in the posture you have chosen (this &lt;strong&gt;will&lt;/strong&gt; matter) before taking the measurements but otherwise I can't see you having too great a problem. &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-04-22T11:48:34.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1922" PostTypeId="1" AcceptedAnswerId="1924" CreationDate="2012-04-22T14:10:59.623" Score="4" ViewCount="529" Body="&lt;p&gt;We recently found a nest in the back garden and a little bird inside. Can you help us identify it? The nest is quite small like the bird so we are wondering whether this is the parent or a baby chick. Is there anything we can do to help it or are we better off leaving it alone?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update: I'm from the UK, currently in Oxfordshire to be more precise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/doFLY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="779" LastEditorUserId="16866" LastEditDate="2016-03-17T04:17:54.990" LastActivityDate="2016-10-02T08:33:16.640" Title="Can someone identify this bird?" Tags="&lt;zoology&gt;&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1923" PostTypeId="1" AcceptedAnswerId="1992" CreationDate="2012-04-22T14:54:32.113" Score="8" ViewCount="125" Body="&lt;p&gt;While tracing dendrites on &lt;a href=&quot;http://eyewire.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;EyeWire&lt;/a&gt; I encountered the following situation. They belong to an &lt;a href=&quot;http://wiki.eyewire.org/wiki/Orientation_Selective_Ganglion_Cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;Orientation Selective Ganglion Cell&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SzkFV.png&quot; alt=&quot;Dendrite hole&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's the first dendrite I've noticed with such a clear 'hole' in it, though which another dendrite passes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sQZPm.png&quot; alt=&quot;Passing dendrite&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible for one dendrite to pass through another? Perhaps I shouldn't have 'connected' the top part with the bottom part?&lt;/p&gt;&#xA;" OwnerUserId="780" LastEditorUserId="36209" LastEditDate="2017-11-07T15:03:17.307" LastActivityDate="2017-11-07T15:03:17.307" Title="Can one dendrite pass through another?" Tags="&lt;neuroscience&gt;&lt;dendrites&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1924" PostTypeId="2" ParentId="1922" CreationDate="2012-04-22T15:15:54.273" Score="6" Body="&lt;p&gt;It looks like a passerine bird, but I can't really tell the species without seeing the whole body. As for what to do with it, your best course of action is to leave it alone. Trust me. Once placed tissue paper over a pigeon's eggs to keep them warm, and the mother crushed them when she landed on the nest because she didn't see the eggs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there are eggs in the nest, try noting down what color they are. Passerines have colored eggs.&lt;/p&gt;&#xA;" OwnerUserId="584" LastActivityDate="2012-04-22T15:15:54.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1925" PostTypeId="2" ParentId="1914" CreationDate="2012-04-22T15:25:19.503" Score="5" Body="&lt;p&gt;Almost everything the snake eats is completely digested. They have a very efficient digestive system. Things that wouldn't be digested would be the rodent's claws and hair and feathers of birds. And during digestion, the snake's intestines go into overdrive mode and expand when necessary. When the snake isn't eating, the intestines are usually dormant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If something goes wrong though, or if the snake is threatened, the snake regurgitates everything in order to increase its mobility.&lt;/p&gt;&#xA;" OwnerUserId="584" LastEditorUserId="115" LastEditDate="2012-04-22T16:46:11.653" LastActivityDate="2012-04-22T16:46:11.653" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1926" PostTypeId="2" ParentId="1917" CreationDate="2012-04-22T15:32:09.023" Score="5" Body="&lt;p&gt;Here is an online book of epidemiology for the uninitiated. I used it to get a basic understanding of epidemiology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bmj.com/about-bmj/resources-readers/publications/epidemiology-uninitiated&quot;&gt;http://www.bmj.com/about-bmj/resources-readers/publications/epidemiology-uninitiated&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="584" LastActivityDate="2012-04-22T15:32:09.023" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1927" PostTypeId="1" AcceptedAnswerId="1930" CreationDate="2012-04-22T15:39:40.527" Score="4" ViewCount="79" Body="&lt;p&gt;Can someone provide me some information about the main method used to predict the &lt;em&gt;inferred electronic annotations&lt;/em&gt; in Gene Ontology?&lt;/p&gt;&#xA;" OwnerUserId="781" LastEditorUserId="166" LastEditDate="2012-04-22T18:26:04.307" LastActivityDate="2012-04-23T23:18:32.053" Title="Main methods used to predict functional annotations in GO" Tags="&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1928" PostTypeId="1" CreationDate="2012-04-22T18:09:36.837" Score="8" ViewCount="553" Body="&lt;p&gt;We are constantly shown nutritional information on food packaging stating this food contains &quot;x&quot; amount of your guided daily amount. A linked to the values is &lt;a href=&quot;http://www.gdalabel.org.uk/gda/gda_values.aspx&quot;&gt;here&lt;/a&gt;. How were these values calculated? How do we know that men as a recommendation must not consume more than 2500 calories, 55g of protein 300g of carbohydrate etc...   &lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="158" LastEditDate="2012-04-22T20:27:22.407" LastActivityDate="2012-08-28T12:45:29.443" Title="How was the guided daily amount (GDA) calculated?" Tags="&lt;human-biology&gt;&lt;nutrition&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1929" PostTypeId="2" ParentId="1922" CreationDate="2012-04-22T23:42:59.220" Score="4" Body="&lt;p&gt;The bird needs to be left alone; that's the best help you can give it.  Anything more than watching it is liable to lead to nesting failure (e.g. abandonment of the nest).  The bird looks attentive and quiet, and so is most likely an adult keeping the eggs or chicks warm.  The bill suggests a seed-eating bird, but there are large numbers of those (e.g. finches, sparrows, grosbeaks, ...) and I can say little more from the evidence.&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2012-04-22T23:42:59.220" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1930" PostTypeId="2" ParentId="1927" CreationDate="2012-04-23T05:08:47.147" Score="3" Body="&lt;p&gt;I believe the most common source of electronic annotations comes from analysis of peptide sequences.  A collection of InterPro to GO mappings were created manually and can generate GO annotations.  DNA binding domains of transcription factors would be given &quot;DNA binding&quot; GO annotations say. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This method has its flaws - if the domain detected has evolved away from the function used for the Interpro to GO listing, there is a potential for error in this method. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-04-23T05:08:47.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1931" PostTypeId="2" ParentId="1901" CreationDate="2012-04-23T05:17:00.257" Score="1" Body="&lt;p&gt;I can't give a comprehensive answer to this, but the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cluster_of_differentiation&quot; rel=&quot;nofollow&quot;&gt;CD&lt;/a&gt; proteins are found on white blood cells of various types.  If you think about it its impossible that a surface protein could be &lt;em&gt;only&lt;/em&gt; observed on cancer cells as cancer is a cell line which is a reproductive dead end.   You can see on the geneatlas box on the lower right side of the page - its gene is expressed, at least to a small amount, on nearly every major tissue type. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-04-23T05:17:00.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1932" PostTypeId="2" ParentId="1843" CreationDate="2012-04-23T09:08:58.970" Score="10" Body="&lt;p&gt;I don't know if this is a comprehensive enough answer, but viruses are taxonomically broken down into order (-virales), family (-viridae), subfamily (-virinae), genus (-virus) and species. This system was developed by the &lt;a href=&quot;http://ictvonline.org/&quot;&gt;ICTV&lt;/a&gt; and is concurrently used with the Baltimore System.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lot of species contain variations called virus strains. There are two types, serotype and genotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In serotypes, the differences are detected by variation in antigens. Genotypes are detected by differences in genome sequence.(1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason a vaccine is difficult to create for the common cold, or upper respiratory tract infections is not only because of the frequency of mutation but also due to the large number of serotypes present.(2),(3).&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Virology: Principles and Applications - Carter.&lt;/li&gt;&#xA;&lt;li&gt;Princuples and Practice of Infectious Diseases - Mendell, et al.&lt;/li&gt;&#xA;&lt;li&gt;E.g. Olszewska, et al. &lt;a href=&quot;http://bmb.oxfordjournals.org/content/62/1/99.full&quot;&gt;Development of vaccines against common colds&lt;/a&gt;. Br Med Bull. 2002. 62(1):99-111.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="653" LastActivityDate="2012-04-23T09:08:58.970" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1933" PostTypeId="2" ParentId="1784" CreationDate="2012-04-23T09:49:43.817" Score="-1" Body="&lt;p&gt;The explanation in the &lt;a href=&quot;http://health.howstuffworks.com/human-body/parts/question552.htm&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt; Polynomial posted is essentially correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whenever there is a reduced or blocked blood supply (ischaemia) to your extremities, the 'five P's' can occur: pulselessness, pain, pallor (colour), paresthesia (numbness) and paralysis (or weakness).(1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The numbness and weakness happen after the blood flow have been reduced for a particularly prolonged period.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cells in our body require a blood supply to stay alive (think about a stroke or heart attack for example). So a reduced supply can cause them to function abnormally or after a time (depending on the cell or tissue type) die. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So with a 'sleeping leg', staying in an awkward or particular position where arterial blood supply is blocked or reduced to the leg, the muscle, nerve tissue etc all lack supply hence causing sensory disturbance and weakness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The possible buildup of metabolites could also contribute to the symptoms (pain).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps!&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Miller's Anaesthesia - Miller.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="653" LastActivityDate="2012-04-23T09:49:43.817" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1934" PostTypeId="2" ParentId="1609" CreationDate="2012-04-23T10:03:40.297" Score="4" Body="&lt;p&gt;There are a few studies around related to this. One particular study(1) suggests that: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Neural drive is decreased following eccentric exercise leading to a reduction in muscle force. Alcohol may further reduce the already depressed neural drive.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Alcohol also has been shown to affect the innate immune system by altering the activity of a number of inflammatory proteins. A lot of these play &quot;important roles in the damage and repair processes occurring after eccentric exercise&quot;. Alterations in these proteins may affect muscle recovery post-exercise.(2).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The second point is maybe what's relevant to the question at hand? They say more research is required though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Edit&lt;/em&gt; (expanded discussion per comment below). The study itself was carried out using 8 (+/-1) standard drinks immediately following a workout. The article(1) itself doesn't hypothesise the point made earlier regarding inflammatory proteins, it rather points to earlier research(2), to suggest this may be the case. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whether a dose-dependant relationship exists, or the magnitude of it with regards to the alteration in inflammatory proteins is not discussed (except in the context of chronic versus acute alcohol use). Just that the possible effect on inflammatory proteins exists which may affect muscle recovery post-exercise.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Barnes, et al. Acute alcohol consumption aggravates the decline in muscle performance following strenuous eccentric exercise. Journal of Science and Medicine in Sport. 2010. 1:189-93.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Edit&lt;/em&gt;&#xA;2. Szabo. Consequences of alcohol consumption on host defence. Alcohol Alcohol. 1999. 1999:830–841.&lt;/p&gt;&#xA;" OwnerUserId="653" LastEditorUserId="653" LastEditDate="2012-04-25T05:36:43.070" LastActivityDate="2012-04-25T05:36:43.070" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1935" PostTypeId="2" ParentId="1917" CreationDate="2012-04-23T12:23:19.823" Score="1" Body="&lt;p&gt;Leon Gordis' &quot;&lt;a href=&quot;http://www.amazon.ca/Epidemiology-STUDENT-CONSULT-Online-Access/dp/1416040021/ref=sr_1_1?s=books&amp;amp;ie=UTF8&amp;amp;qid=1335183723&amp;amp;sr=1-1&quot; rel=&quot;nofollow&quot;&gt;Epidemiology&lt;/a&gt;&quot; was my textbook in undergrad and it was quite easy to follow. It's a small textbook as well so you can read through in no time.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-23T12:23:19.823" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1936" PostTypeId="2" ParentId="1901" CreationDate="2012-04-23T12:46:32.273" Score="2" Body="&lt;p&gt;I don't know how extensive. Let's run a simple data query and find out: Go to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/&quot; rel=&quot;nofollow&quot;&gt;GEO&lt;/a&gt; at NCBI. In the &quot;Gene profiles&quot; window, type CD47, and hit enter to launch the query. At the top of the resulting page, use the link labeled &quot;Limits&quot; to restrict the 7000+ results to human by entering the term &quot;human&quot; in the &quot;DataSet organism&quot; window. So, there are 3700+ results. Look through them to get an idea of which cell types and under which conditions &lt;em&gt;CD47&lt;/em&gt; is expressed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's try a second method. Go to the &lt;a href=&quot;http://biogps.org&quot; rel=&quot;nofollow&quot;&gt;BioGPS&lt;/a&gt; portal. Enter CD47 in the appropriate window and run the query. From the results, select the row with ID # 961 as this represents the human gene &lt;em&gt;CD47&lt;/em&gt;. The resulting gene expression/activity chart for Hs (human) will show you in more general terms where &lt;em&gt;CD47&lt;/em&gt; is expressed.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-04-23T12:46:32.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1937" PostTypeId="1" AcceptedAnswerId="7784" CreationDate="2012-04-23T14:50:47.343" Score="6" ViewCount="142" Body="&lt;p&gt;Does anybody have any estimate on the number of RNA pol II molecules in the nucleus of a given human cell? For example, how many RNA polymerase type II protein complexes would there be on average at a given time in, say, a human immortalized lymphoblastoid cell line (LCL)?&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2013-04-06T17:45:49.023" Title="number of RNA pol II molecules in a given human nucleus?" Tags="&lt;cell-biology&gt;&lt;polymerase&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1938" PostTypeId="1" CreationDate="2012-04-23T17:17:25.303" Score="2" ViewCount="127" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;This is an mRNA strand of mouse meta-globin:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;5'-ccccagauacggaauucgaau-3'&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;A) Which small RNA (below) is most likely to regulate expression of&#xA;  meta-globin?&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;5'-auucgaauuuucuaucugggg-3'&lt;/li&gt;&#xA;  &lt;li&gt;5'-ggggucuaucuuuuaagcuua-3'&lt;/li&gt;&#xA;  &lt;li&gt;5'-ccccagauacggaauucgaau-3'&lt;/li&gt;&#xA;  &lt;li&gt;5'-uaagcuuaaggcauagacccc-3'&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;  &#xA;  &lt;p&gt;B) This RNA most likely?&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;acts as an siRNA&lt;/li&gt;&#xA;  &lt;li&gt;inhibit meta-globin translation&lt;/li&gt;&#xA;  &lt;li&gt;increase meta-globin translation&lt;/li&gt;&#xA;  &lt;li&gt;help transport meta-globin mRNA back into the nucleus&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My attempt: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think A is 2 because the strand is complementary and will bind nicely to the mRNA strand.  For B, I'm between 2 and 3, but cant decide.&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="6" LastEditDate="2012-04-24T07:17:46.143" LastActivityDate="2014-12-02T12:13:46.630" Title="Mouse meta-globin mRNA problem" Tags="&lt;molecular-biology&gt;&lt;homework&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1939" PostTypeId="2" ParentId="1910" CreationDate="2012-04-23T17:59:13.960" Score="10" Body="&lt;p&gt;Shortest answer: there's nothing special in human biology, you could totally make it&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Short answer: Bachelor chow!&#xA;&lt;img src=&quot;https://i.stack.imgur.com/rBMIR.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would totally buy this stuff if they made it. The closest I have now to bland, flavorless, zero thought/effort food is Wheaties.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;longer answer:&#xA;Seriously though, dogfood for humans wouldn't be that hard to make. If you just took everything from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Reference_Daily_Intake&quot; rel=&quot;noreferrer&quot;&gt;RDI&lt;/a&gt; guidelines (the Recommended Daily Intake from which they calculate the percentages you find on food labels) and mashed it all together into a thick brown paste you would get all of the macro and micro nutrients that you theoretically require. Precise proportions are irrelevant because:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) everyone is a little different, and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) to some extent, our bodies are able to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21222652&quot; rel=&quot;noreferrer&quot;&gt;fine tune&lt;/a&gt; our digestive tracts to fit our specific diets (presumably this tuning would occur even faster if you ate the exact same thing for every meal). You're a mammalian omnivore. Enjoy it!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You probably shouldn't try to live on something like this for the rest of your life, since there's plenty of research suggesting that there are other micronutrients, such as phytocompounds (i.e. plant stuffs), that are poorly understood but may be beneficial to humans. One thing to note here is that any health claims about any antioxidant that is not on the list of essential vitamins (vitamin C is an antioxidant on the list) are almost certainly bunk and/or hokum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The upshot is that you would only need, at most, utterly minuscule quantities of these miscellaneous micronutrients. You would be fine(ish) for at least a few months. For related reasons, your statement:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The composition is also known for human babies. This is manufactured as &quot;baby formula&quot;. Everything baby's organism needs to be healthy (and to grow).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;is largely correct but somewhat flawed. While it is true that many babies are raised solely on formula and subsequently turn out just fine, there are some things that you can only get from mother's milk. For example, the mother passes on components of her own immune system to her baby through her milk, which then help to strengthen the baby's own immune system. These are the kind of subtle but useful compounds which are encountered in a &quot;natural&quot; diet but which could never realistically be included in people chow.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2012-04-23T20:08:55.743" LastActivityDate="2012-04-23T20:08:55.743" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1940" PostTypeId="1" AcceptedAnswerId="1941" CreationDate="2012-04-23T19:09:14.263" Score="6" ViewCount="2488" Body="&lt;p&gt;Thermophiles, heat-loving organisms, have been a popular topic of research for decades due in large part to the utility of their enzymes in various chemical reactions (Taq Pol single-enzymedly made PCR practical). One of the signatures of thermophiles is that their proteins resist heat denaturation up to much higher temperatures than their mesophilic (middle-loving) homologs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a corresponding group of extremophiles whose proteins resist cold denaturation down to much lower temperature than their mesophilic homologs? If so, could someone please point me towards a few good literature reviews on the topic? Or at least give me the proper name for this group of cold-loving extremophiles?&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2012-04-23T19:38:28.293" Title="What's the opposite of a thermophile?" Tags="&lt;proteins&gt;&lt;taxonomy&gt;&lt;extremophiles&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1941" PostTypeId="2" ParentId="1940" CreationDate="2012-04-23T19:37:52.193" Score="8" Body="&lt;p&gt;The term you are looking for is psychrophile or cryophile. There are examples of microbes adapted to very cold conditions in Bacteria, Archaea, and Eukarya. There are also fairly complex animals capable of surviving very low temperatures -  Tardigrades, for example. There are multiple issues that organisms face in withstanding extremely low temperatures - protein denaturation, membrane fluidity, intracellular ice-formation, just to name a few.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is this review that might be useful to you.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;D'Amico, S., Collins, T., Marx, J.-C., Feller, G., Gerday, C. Psychrophilic microorganisms: Challenges for life (2006) EMBO Reports, 7 (4), pp. 385-389. &lt;a href=&quot;http://www.nature.com/embor/journal/v7/n4/full/7400662.html&quot;&gt;link&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="649" LastActivityDate="2012-04-23T19:37:52.193" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1943" PostTypeId="1" AcceptedAnswerId="1946" CreationDate="2012-04-23T20:28:00.527" Score="20" ViewCount="2691" Body="&lt;p&gt;Do any animals other than humans undergo menopause?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, is there any difference between animals in captivity and animals in the wild as regards menopause? For example, even if menopause has been observed in a captive member of a particular ape species, do individuals of that species typically live long enough in the wild to also undergo menopause?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess here's what I'm really getting at: is menopause a common thing in the animal kingdom, or is it only a common thing in humans?&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2012-04-23T21:02:52.963" LastActivityDate="2018-11-20T03:07:28.803" Title="Do any animals other than humans undergo menopause?" Tags="&lt;zoology&gt;&lt;endocrinology&gt;&lt;ethology&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1944" PostTypeId="1" AcceptedAnswerId="1945" CreationDate="2012-04-23T20:30:37.743" Score="2" ViewCount="114" Body="&lt;p&gt;Does a public database exist that contains this information? I'm trying to make a simple gene annotation program that will let me input a DNA sequence and then optimize it based on one of these tables using the &lt;em&gt;E. coli&lt;/em&gt; preferences, for example.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-24T19:36:07.037" Title="Consensus codon optimization by organism" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;molecular-genetics&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1945" PostTypeId="2" ParentId="1944" CreationDate="2012-04-23T20:44:41.143" Score="5" Body="&lt;p&gt;Try the &lt;a href=&quot;http://www.kazusa.or.jp/codon/&quot;&gt;Codon Usage Database&lt;/a&gt; at Kazusa. You can search by organism. The database contains 35,799 organisms and compiled from 3,027,973 complete protein coding genes (CDS's), but last updated in 2007.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-04-23T20:44:41.143" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1946" PostTypeId="2" ParentId="1943" CreationDate="2012-04-23T20:58:18.757" Score="21" Body="&lt;p&gt;&lt;strong&gt;Yes. Menopause is common for long-lived mammals.&lt;/strong&gt; For instance, in the wild, killer whales go in a sort of menopause as reported in 2009 by Ward et al. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19192288&quot;&gt;Front Zool. 2009 Feb 3;6:4&lt;/a&gt;. So it is not due to captivity. According to a Nature review, reproductive cessation has also been documented in non-human primates, rodents, whales, dogs, rabbits, elephants and domestic livestock (Packer et al. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9572138&quot;&gt;Nature. 1998; 392(6678):807-11&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="444" LastEditDate="2012-04-23T21:07:32.503" LastActivityDate="2012-04-23T21:07:32.503" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1947" PostTypeId="2" ParentId="1917" CreationDate="2012-04-23T23:10:53.810" Score="2" Body="&lt;p&gt;I found &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0781752159&quot; rel=&quot;nofollow&quot;&gt;Clinical Epidemiology&lt;/a&gt; by Robert and Suzanne Fletcher extremely useful  to gain some quick insight in to the broad area of epidemiology during my first year of post-doc. It covers a wide-range of topic in clinical research and epidemiology in an accessible format with several examples and extensive illustrations. &lt;/p&gt;&#xA;" OwnerUserId="230" LastActivityDate="2012-04-23T23:10:53.810" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1948" PostTypeId="2" ParentId="1927" CreationDate="2012-04-23T23:18:32.053" Score="4" Body="&lt;p&gt;You can refer the &lt;a href=&quot;http://www.geneontology.org/GO.evidence.shtml#iea&quot; rel=&quot;nofollow&quot;&gt;IEA documentation&lt;/a&gt; maintained by GO consortium to get an idea about the automatically assigned evidence codes using IEA. Also please note that IEA is different from &lt;a href=&quot;http://www.geneontology.org/GO.evidence.shtml#computational&quot; rel=&quot;nofollow&quot;&gt;Computational Analysis Evidence Codes&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ISS: Inferred from Sequence or Structural Similarity &lt;/li&gt;&#xA;&lt;li&gt;ISO: Inferred from Sequence Orthology &lt;/li&gt;&#xA;&lt;li&gt;ISA: Inferred from Sequence Alignment &lt;/li&gt;&#xA;&lt;li&gt;ISM: Inferred from Sequence Model &lt;/li&gt;&#xA;&lt;li&gt;IGC: Inferred from Genomic Context &lt;/li&gt;&#xA;&lt;li&gt;IBA: Inferred from Biological aspect of Ancestor &lt;/li&gt;&#xA;&lt;li&gt;IBD: Inferred from Biological aspect of Descendant &lt;/li&gt;&#xA;&lt;li&gt;IKR: Inferred from Key Residues &lt;/li&gt;&#xA;&lt;li&gt;IRD: Inferred from Rapid Divergence &lt;/li&gt;&#xA;&lt;li&gt;RCA: inferred from Reviewed Computational Analysis&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="230" LastActivityDate="2012-04-23T23:18:32.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1949" PostTypeId="2" ParentId="1808" CreationDate="2012-04-24T02:52:28.220" Score="-2" Body="&lt;p&gt;This is a wild stab in the dark, so downvote me as you see fit: Caddis fly larvae (Insect Order Trichoptera). I thought caddis larvae were aquatic though.&lt;/p&gt;&#xA;" OwnerUserId="649" LastActivityDate="2012-04-24T02:52:28.220" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1951" PostTypeId="1" AcceptedAnswerId="1956" CreationDate="2012-04-24T05:23:56.957" Score="7" ViewCount="3222" Body="&lt;p&gt;Are the dark marks aka &quot;moles&quot; on our skin a patch of dead cells? If so, why is it not cleared over time? In a (probably) similar vein, why do scar marks from injuries remain long after new cells replace the dead cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[Feel free to edit out the second question if the answers are unrelated]&lt;/p&gt;&#xA;" OwnerUserId="223" LastActivityDate="2013-09-02T06:02:15.813" Title="What is the biology behind a skin &quot;mole&quot;?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1952" PostTypeId="5" CreationDate="2012-04-24T05:24:40.747" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-04-24T05:24:40.747" LastActivityDate="2012-04-24T05:24:40.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1953" PostTypeId="4" CreationDate="2012-04-24T05:24:40.747" Score="0" Body="The study of the skin and skin related diseases" OwnerUserId="223" LastEditorUserId="223" LastEditDate="2012-04-24T07:47:44.147" LastActivityDate="2012-04-24T07:47:44.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1955" PostTypeId="1" CreationDate="2012-04-24T10:42:17.683" Score="7" ViewCount="653" Body="&lt;p&gt;My understanding is that the concept &quot;genetic linkage&quot; can be expressed in quantitative form, like:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;A predisposing gene X was found in close genetic linkage to Y.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;And that linkage disequilibrium (LD) is a quality, like being pregnant, you are either in LD or your are not:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;A predisposing gene X was found in close genetic linkage to Y and in &#xA;linkage disequilibrium with Z.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Is this correct?&lt;/p&gt;&#xA;" OwnerUserId="787" LastEditorUserId="43" LastEditDate="2012-04-24T13:16:51.080" LastActivityDate="2012-05-01T13:35:53.760" Title="Linkage and LD: quantitative or qualitative?" Tags="&lt;genetics&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1956" PostTypeId="2" ParentId="1951" CreationDate="2012-04-24T12:59:35.127" Score="8" Body="&lt;p&gt;A &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanocytic_nevus&quot;&gt;mole&lt;/a&gt; is simply a benign tumour, i.e. a proliferated cell growth that hasn’t become cancerous. So moles are &lt;em&gt;not&lt;/em&gt; dead cells, they are very much alive. The colour is caused by a high concentration of the melanin, which is also responsible for normal darker skin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since moles are tumours, they can – but in most cases don’t – give rise to &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanoma&quot;&gt;melanomas&lt;/a&gt;, malignant skin tumours, when they lose susceptibility to cell growth regulation and start invading surrounding tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Scar&quot;&gt;Scar tissue&lt;/a&gt; is entirely unrelated and due to regular regrowth of epithelial cells after injury forming a linear collagen structure (as opposed to the skin’s normal collagen structure, which resembles a “weaved“ structure).&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="43" LastEditDate="2012-04-24T14:38:23.310" LastActivityDate="2012-04-24T14:38:23.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1957" PostTypeId="1" AcceptedAnswerId="1959" CreationDate="2012-04-24T13:23:21.447" Score="1" ViewCount="156" Body="&lt;p&gt;I'm wondering if it would be possible to create software (unless some already exists, but I couldn't find any) to generate human DNA (the base pairs on the double helix) containing genes representing specific permutations (eye colour, hair colour, etc.)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, something like the &quot;character builder&quot; from those &quot;Saints Row&quot;-style video games, except with actual human chromosomes, enabling you to essentially create a 'custom' human.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, that is assuming that all human DNA has a common structure, and that the entire sequence can either be assembled from individual chromosomes, or by using a reference genome and modifying specific genes/chromosomes according to user input. Is this the case?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One setback here, of course, could be the number of bases in each chromosome, which ranges between 100 million and 250 million, and the (approximately) 23000 human genes - a lot of data to manipulate.&lt;/p&gt;&#xA;" OwnerUserId="789" LastActivityDate="2012-04-24T16:18:02.607" Title="Generating custom human DNA sequences based on traits such as eye colour?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;human-genome&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1958" PostTypeId="1" AcceptedAnswerId="1971" CreationDate="2012-04-24T15:04:31.370" Score="9" ViewCount="10125" Body="&lt;p&gt;I would like to ask the difference between strand-specific and not strand-specific dataset.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I know, strand-specific data means that we know which strand the transcript is from.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not have biological background. Please confirm whether it is correct. If we have a transcript, which is from sense strand, when RNA-seq is producing reads, is that first the cDNA is synthesised. Then this cDNA is used for PCR to amplify the sample? Then the reads generated could be from both strands of the original DNA? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For strand-specific protocols, what is different?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;========================================================&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Follow up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please correct me if I am wrong. There are multiple protocols to produce strand-specific RNA-seq libraries. The basic process is like:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Get the RNA;&lt;/li&gt;&#xA;&lt;li&gt;Get its cDNA;&lt;/li&gt;&#xA;&lt;li&gt;Somehow mark the cDNA as sense or antisense when amplifying (PCR?) (here comes the differences between different protocols);&lt;/li&gt;&#xA;&lt;li&gt;Then REMOVE all antisense (or sense) cDNAs;&lt;/li&gt;&#xA;&lt;li&gt;Read the reads from clean cDNA library.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The result is that, the reads from this RNA can be used to assemble the sense cDNA. And for not strand-specific libraries, using the reads would be able to assemble both the anti-sense and sense cDNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am i right about this problem? Thanks.&lt;/p&gt;&#xA;" OwnerUserId="790" LastEditorUserId="790" LastEditDate="2012-04-26T05:12:42.630" LastActivityDate="2012-04-26T05:12:42.630" Title="Difference between strand-specific and not strand-specific RNA-seq data" Tags="&lt;bioinformatics&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="1959" PostTypeId="2" ParentId="1957" CreationDate="2012-04-24T16:18:02.607" Score="6" Body="&lt;p&gt;A major limiting factor in such an exercise is the complexity of the biological process under question (eye colour etc.,) and thus, our nascent understanding of these. What I mean is that there is not a single gene that determines a given characteristic, rather it is the complex interaction of a set of genes in different conditions responding to environmental cues and such. We are barely at the level of scratching the surface when it comes to understanding the mechanisms that underlie such outputs. And so, we are long ways off (maybe hundreds of years?) before we can even start thinking about coming up with feasible approaches to such objectives.&lt;/p&gt;&#xA;" OwnerUserId="223" LastActivityDate="2012-04-24T16:18:02.607" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1960" PostTypeId="1" CreationDate="2012-04-24T16:44:36.470" Score="5" ViewCount="337" Body="&lt;p&gt;Or as another example - what if you touch a surface that's contaminated with potentially pathogenic bacteria (like the ones at &lt;a href=&quot;http://arstechnica.com/hardware/news/2008/05/study-keyboards-make-excellent-homes-for-nasty-bacteria.ars&quot;&gt;http://arstechnica.com/hardware/news/2008/05/study-keyboards-make-excellent-homes-for-nasty-bacteria.ars&lt;/a&gt;) and introduce those bacteria into your body and don't get sick. Then could there be some other damage that the bacteria could do your body? Like, at the very least, maybe promote a not-particularly-noticeable increase in inflammation in the regions where the immune system decides to fight the bacteria? Inflammation only starts to get noticeable when some really high threshold gets crossed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By &quot;sick&quot;, I mean, that the symptoms of the infection become noticeable enough to cross the threshold of being unpleasant to the person carrying the infection. I'm sure that there may be some sub-threshold effects that come in first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And why is this important? We have to establish some sort of balance between using too much soap/other cleaning agents and not using enough of it. If we use too much, the bacteria could develop antibiotic resistance. And if we use too little, there could be an increase in the types of bacteria that cause chronic infections that don't get noticed, even though some of us might not even get physically sick more. &lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="103" LastEditDate="2012-04-24T16:49:41.487" LastActivityDate="2015-08-23T02:07:27.507" Title="Is it harmful for someone to consume things full of bacteria if they don't get physically sick from the bacteria at all?" Tags="&lt;pathology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1961" PostTypeId="2" ParentId="1944" CreationDate="2012-04-24T19:36:07.037" Score="3" Body="&lt;p&gt;Plenty of softwares doing that kind of functionality. A 2007 open access review lists &gt;30 such softwares &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17882154&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/17882154&lt;/a&gt;. However, No correlation between 'most common' codon and recombinant protein expression yield. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21102527&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/21102527&lt;/a&gt;. Thus, those &gt;30 softwares are pointless.&lt;/p&gt;&#xA;" OwnerDisplayName="user794" LastActivityDate="2012-04-24T19:36:07.037" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1962" PostTypeId="1" CreationDate="2012-04-24T19:52:46.257" Score="3" ViewCount="83" Body="&lt;p&gt;I'm talking about &lt;a href=&quot;http://en.wikipedia.org/wiki/Posttranslational_modification#PTMs_involving_addition_of_smaller_chemical_groups&quot; rel=&quot;nofollow&quot;&gt;this type of post-translational modifications&lt;/a&gt;. What I'm interested in is not whether some modifications can only occur on specific amino acids (that's clear), but if the nomenclature has examples of addition of slightly different chemical groups to different amino acids known under the same name.&#xA;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="793" LastActivityDate="2012-04-24T19:52:46.257" Title="Are there examples of PTMs that add different chemical groups (and mass) to different amino acids?" Tags="&lt;proteins&gt;&lt;amino-acids&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1963" PostTypeId="2" ParentId="1960" CreationDate="2012-04-25T01:43:37.493" Score="6" Body="&lt;p&gt;It really depends on what you consume, how much of it you consume, and the state of your immune system. Let me give you some examples. Yogourt is &lt;em&gt;full&lt;/em&gt; of bacteria, and yet we can eat it without issue. The bacteria likely don't survive digestion, but if they do, they will quite happily live in our intestines contributing to the already existing population of good bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Streptococcus&quot;&gt;Streptococcus&lt;/a&gt; is a genus of bacteria that contains some species that live all over us. They are on our skin, in our upper respiratory tract and intestine. If the species, S. pneumoniae makes it into our lungs, this can cause a bacterial pneumonia. There are likely few bacteria making it into our lungs on a regular basis, and normally our immune system can fight this off without concern. If we some how become immune depressed or compromised (for a number of medical reasons) then that's when we become symptomatic and ill.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a more extreme side, if we have a bacteremia it is called a bacteremia. There are benign cases of this every time your brush your teeth and bacteria are able to enter tiny cuts in your gums from the brushing action. A healthy person fights this off. If a bacteremia is left unchecked, because of a lack of immune response or trauma, this can develop into a sepetcemia, a toxic infection of the blood. This can be very life threatening and is quite serious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, we always have bacteria all over our hands which we likely transmit to our food or otherwise ingest. This is normally not a problem, but there is an appreciable risk of getting some kinds of viral or bacterial infection (eg, strep throat or a cold). Washing with soap (and to a lesser degree, using hand sanitizers) minimizes this risk.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-04-25T01:43:37.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1964" PostTypeId="1" AcceptedAnswerId="2285" CreationDate="2012-04-25T02:18:48.513" Score="7" ViewCount="147" Body="&lt;p&gt;Why do some plants have the ability to stand frost, while others can't? Does it have to do with the size of the water vacuoles in the plant cells?&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2012-05-16T18:20:01.650" Title="Why are some plants frost tender?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1965" PostTypeId="1" AcceptedAnswerId="1967" CreationDate="2012-04-25T03:34:59.493" Score="7" ViewCount="5716" Body="&lt;p&gt;I am learning RNA-seq analysis. I always encounter this phase &quot;poly(A)+ RNA&quot;. After searching, I got this: &quot;Most messenger RNAs contain a poly(A) tail, while structural RNAs do not. Poly(A) selection therefore enriches for messenger RNA. The technique has proved essential for construction of cDNA libraries.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it mean that when constructing the cDNA, we always use the ones with a A's tail? Then other RNAs like tRNA are filtered and not used to get their cDNA? I do find some RNAs records on UCSC where microRNAs are included.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When we say poly(A)+ RNA library, what is the difference between normal one? Or normal RNA library is a poly(A)+ RNA library? Thanks.&lt;/p&gt;&#xA;" OwnerUserId="790" LastEditorDisplayName="user560" LastEditDate="2012-04-26T23:23:49.827" LastActivityDate="2012-04-26T23:23:49.827" Title="Purpose of poly(A)+ RNA?" Tags="&lt;molecular-biology&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1966" PostTypeId="1" AcceptedAnswerId="1969" CreationDate="2012-04-25T03:41:21.873" Score="2" ViewCount="129" Body="&lt;p&gt;I am wondering whether majority of transcripts are transcribed from the 5'-&gt;3' strand? Because I encounter a lot of expressions like &quot;anti-sense transcripts&quot;. Could anybody help clarify this? Thanks.&lt;/p&gt;&#xA;" OwnerUserId="790" LastActivityDate="2020-07-06T12:40:24.327" Title="Majority of transcripts are from sense strand?" Tags="&lt;rna&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="1967" PostTypeId="2" ParentId="1965" CreationDate="2012-04-25T04:33:34.447" Score="11" Body="&lt;p&gt;One of the primary reasons to use poly(A) selection is to eliminate the massive amount of ribosomal RNA (rRNA) present in the samples.  The alternative is to use ribosomal RNA depletion kits / techniques to remove as much rRNA as possible before sequencing.  Without rRNA depletion a large proportion (~60-80%) of the reads would map to rRNAs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;poly(A) selection also reduces the amount of pre-mRNA in the samples, which reduces the number of intron aligned reads.&lt;/p&gt;&#xA;" OwnerUserId="12" LastActivityDate="2012-04-25T04:33:34.447" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1968" PostTypeId="1" AcceptedAnswerId="1979" CreationDate="2012-04-25T09:34:20.153" Score="5" ViewCount="3495" Body="&lt;p&gt;I am wondering what the correct method for primer design to introduce restriction sites. Specifically between two methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Primer first partially hybridises to the gene, has a mis-match where the restriction site and extra bases are on the primer, then has a hybridised site following the restriction site, to DNA upstream of the gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Primer first partially hybridises to the gene, then completely dangling and non-hybridising has the restriction site and extra bases.&lt;/p&gt;&#xA;" OwnerUserId="798" LastActivityDate="2012-04-26T08:55:39.230" Title="Primer design for introduction of restriction sites flanking a gene of interest" Tags="&lt;molecular-biology&gt;&lt;cloning&gt;&lt;restriction-enzymes&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1969" PostTypeId="2" ParentId="1966" CreationDate="2012-04-25T09:54:15.917" Score="10" Body="&lt;p&gt;From my understanding sense and anti sense is contextual. If you are looking at a gene from 5'-&gt;3'(which is convention) that strand is the sense strand and the complement to the gene is the anti sense strand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However further along the DNA there could be a gene on the 'original' anti sense strand, if you are discussing this new gene, there is a new context and it is now on the sense strand (oriented 5'-&gt;3'), and it's complement on the anti sense strand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope that's clear.&lt;/p&gt;&#xA;" OwnerUserId="798" LastActivityDate="2012-04-25T09:54:15.917" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1970" PostTypeId="1" AcceptedAnswerId="44250" CreationDate="2012-04-25T15:29:54.780" Score="14" ViewCount="1182" Body="&lt;p&gt;When food is scarce, the body slows its metabolic rate to conserve energy. Are there any other systems or processes that prioritize which organs receive nutrients?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="22057" LastEditDate="2016-03-13T22:02:43.613" LastActivityDate="2018-11-09T15:00:20.913" Title="During starvation, does the human body do anything to prioritize which organs receive nutrients?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;metabolism&gt;&lt;respiration&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1971" PostTypeId="2" ParentId="1958" CreationDate="2012-04-25T15:47:05.087" Score="7" Body="&lt;p&gt;It may be worth checking out the paper &quot;&lt;a href=&quot;http://www.nature.com/nmeth/journal/v7/n9/full/nmeth.1491.html&quot;&gt;Comprehensive comparative analysis of strand-specific RNA sequencing methods&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most common techniques sequentially ligate different RNA adapters to the 5' and 3' ends of each RNA molecule prior to cDNA synthesis.  You will end up with an RNA molecule that looks like this (where A and B are the two adapters):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;  5'-AAAAAA---------------BBBBBB-3'&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;These adapters are then used for cDNA synthesis and library preparation.  Finally, since each adapter is ligated to a specific end of the RNA the library can be generated in a stand-specific fashion; ie. the reads derived from the antisense strand &lt;strong&gt;should&lt;/strong&gt; align to the antisense strand of the genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;** Note that there are other variations of this technique but Illumina's protocol is one of the most popular.&lt;/p&gt;&#xA;" OwnerUserId="12" LastActivityDate="2012-04-25T15:47:05.087" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1972" PostTypeId="1" CreationDate="2012-04-25T17:36:59.080" Score="10" ViewCount="168" Body="&lt;p&gt;I'm trying to get the data for the Human and Mouse 12 and 23 Recomination &#xA;Signal Sequences (RSS), to run a classification algorithm on it. I'm not a &#xA;biologist, so I apologise in advance for my misunderstandings and &#xA;confusion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A version of the data is available &lt;a href=&quot;http://www.itb.cnr.it/rss/extratdata.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, but I thought I would try to &#xA;get it from www.imgt.org, if possible. There is also another slightly &#xA;different version available for the mouse &lt;a href=&quot;http://www.duke.edu/~lgcowell/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm trying to follow the instructions at &lt;a href=&quot;http://www.imgt.org/FAQ/#question43&quot; rel=&quot;nofollow&quot;&gt;IMGT-FAQ&lt;/a&gt; to obtain Recombination Signal &#xA;Sequences for the mouse.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is what I have selected at the &lt;a href=&quot;http://www.imgt.org/IMGT_GENE-DB/GENElect?livret=0&quot; rel=&quot;nofollow&quot;&gt;search page&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Identification:&#xA;Species : Mus Musculus&#xA;GeneType: any&#xA;Functionality: functional&#xA;MolecularComponent: any&#xA;Clone name: &amp;lt;blank&amp;gt;&#xA;&#xA;IMGT group: IGHV&#xA;IMGT subgroup: any&#xA;IMGT gene: &amp;lt;blank&amp;gt;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I'm not clear what &quot;Locus&quot;, &quot;Main locus&quot;, and &#xA;&quot;IGMT group&quot; mean here exactly. Specifically, what is the difference &#xA;between &quot;Locus&quot; and &quot;Main locus&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think, but am not sure, that IGHV corresponds to V genes in the &#xA;Immunoglobulin heavy locus (IGH@) on chromosome 14, where locus here &#xA;denotes collections of genes. Clarifications and corrections appreciated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would have expected that the IGH locus would correspond to &quot;IMGT group&quot;&#xA;entries like &quot;IGHJ, IGHV&quot; etc, and the IGK locus would correspond to IMGT &#xA;group entries like &quot;IGK, IGKJ, IGKV&quot;, but no matter what I select for &#xA;Locus, it does not change the possible entries for &quot;IMGT group&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Running the search gives&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Number of resulting genes : 218&#xA;Number of resulting alleles : 350&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As instructed, I went to the bottom, selected &quot;Select all genes&quot;, clicked &#xA;on &quot;Choose label(s) for extraction&quot;, and selected &quot;V-RS&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I got&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Number of results=98&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The first few results were&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt;X02459|IGHV1-4*02|Mus musculus_BALB/c|F|V-RS|395..432|38 nt|NR| | | | &#xA;|38+0=38| | |&#xA;cacagtggtgcaaccacatcccgactgtgtcagaaacc&#xA;&#xA;&amp;gt;X02064|IGHV1-54*02|Mus musculus|F|V-RS|295..332|38 nt|NR| | | | |38+0=38| &#xA;| |&#xA;cacagtgttgcaaccacatcctgagtgtgtcagaaatc&#xA;&#xA;&amp;gt;M34978|IGHV1-58*02|Mus musculus_A/J|P|V-RS|554..560|7 nt|NR| | | | &#xA;|7+0=7|partial in 3'| |&#xA;cacagtg&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Ok, now I'm confused. The lengths of the RSS should be 28 or 39. but I &#xA;counted lengths of 4,7, 31, 38, and 39. Are the results here not supposed &#xA;to contain the 12 and 23 RSS?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I must be misunderstanding things here. Possibly many things. Any &#xA;explanations and clarifications are appreciated.&lt;/p&gt;&#xA;" OwnerUserId="284" LastEditorUserId="3340" LastEditDate="2014-11-22T08:31:39.953" LastActivityDate="2015-01-08T15:42:05.530" Title="Using the IMGT/GENE-DB service to find RSS" Tags="&lt;bioinformatics&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1973" PostTypeId="2" ParentId="1968" CreationDate="2012-04-25T19:27:27.527" Score="5" Body="&lt;p&gt;I think the best way is option #2:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose that your gene of interest is AAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGG&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and you want to insert EcoRI restriction site GAATCC&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then your Fwd primer will be  GAATCC AAAAAAAAAAAAAAAA&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and your Rev primer will be GGATTC CCCCCCCCCCCCCCCC&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But in general, it shouldn't matter which option you choose, as long as you calculate the Tm of only the part of the primer that hybridizes to your template.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-04-25T19:27:27.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1974" PostTypeId="2" ParentId="1970" CreationDate="2012-04-25T20:53:58.147" Score="10" Body="&lt;p&gt;The glycogen in the liver begins providing blood glucose. Muscle glycogen is used as fuel by the muscles, fat cells (adipose tissue) release fatty acids to manufacture ketone bodies in the liver and to be used by the brain as fuel, and body proteins are converted to glucose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, the body's metabolism shifts to catabolic reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this continues for too long, you begin to see effects of starvation:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Inadequate tear production&lt;/li&gt;&#xA;&lt;li&gt;Enlarged/tender liver&lt;/li&gt;&#xA;&lt;li&gt;Muscle atrophy&lt;/li&gt;&#xA;&lt;li&gt;Rashes, sores, or peeling skin&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In short, deficiencies of energy, protein, iron, and zinc can really mess you up in the long term.&lt;/p&gt;&#xA;" OwnerUserId="584" LastEditorUserId="107" LastEditDate="2013-04-03T23:53:05.520" LastActivityDate="2013-04-03T23:53:05.520" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1975" PostTypeId="1" AcceptedAnswerId="1976" CreationDate="2012-04-25T23:38:17.413" Score="10" ViewCount="11655" Body="&lt;p&gt;What exactly does it mean when a plant has a scientific name that specifies a vairety, for example  &lt;em&gt;Nothofagus solandri var. cliffortioides&lt;/em&gt;, or when the name includes an &quot;x&quot;, as in &lt;em&gt;Populus maximowiczii Henry x trichocarpa&lt;/em&gt;, &lt;em&gt;Populus xcanadensis&lt;/em&gt;, or &quot;Crataegus x macrocarpa&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of these species are in the USDA Plants database (of plants that occur in the US). There are &gt; 6000 occurences of the string &quot; var. &quot; ~500 occurances of &quot; ssp. &quot; and only a handful occurences of &quot; x &quot; in the database, &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Does the x indicate that a plant is a hybrid, and are the varied uses indicate a different meaning?&lt;/li&gt;&#xA;&lt;li&gt;Does the use of &quot; var &quot; mean that the plant is a variety? &#xA;&lt;ul&gt;&#xA;&lt;li&gt;Does it mean that each of these species has been cultivated and/or bred by a human?&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Does &quot;ssp&quot;  mean that the plant is distinct yet compatible with others in the species? &lt;/li&gt;&#xA;&lt;li&gt;is there a way to identify a that a plant is cultivated based on its scientific name?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="222" LastEditorUserId="222" LastEditDate="2012-04-25T23:55:46.130" LastActivityDate="2017-02-08T16:54:17.780" Title="Does the use of &quot;var&quot;, &quot;x&quot;, and/or &quot;ssp&quot; in a scientific name provide specific information?" Tags="&lt;botany&gt;&lt;taxonomy&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1976" PostTypeId="2" ParentId="1975" CreationDate="2012-04-26T00:13:41.473" Score="7" Body="&lt;p&gt;Let me clarify my answer since it is lower quality than people may like.  To answer the question, my friend is a horticulist and has given a more detailed answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Subspecies is the most generic, &lt;a href=&quot;http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp&quot; rel=&quot;noreferrer&quot;&gt;taxonomically-defined&lt;/a&gt; term one rank order lower than species. The subspecies (either an individual subspecies, or collective group of subspecies) are defined to be genetically or morphologically distinct among other subspecies belonging to the same species, yet still produce viable offspring from interbreeding. For example, every type of dog is a sub-species of &lt;em&gt;Canis familiaris&lt;/em&gt;, and all dogs are capable of breeding with each other. &lt;a href=&quot;http://en.wikipedia.org/wiki/Subspecies&quot; rel=&quot;noreferrer&quot;&gt;Subspecies&lt;/a&gt;, abbreviated Ssp, may refer to an individual subspecies type, or a collective group of related subspecies when a distinct subset is difficult to define or unknown.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a variety of terms that are analogous to subspecies, when the strict definition does not apply, or a different term has been used historically. For example, a &lt;a href=&quot;http://en.wikipedia.org/wiki/Varietal&quot; rel=&quot;noreferrer&quot;&gt;varietal&lt;/a&gt; is the botanical term, and refers to a named subspecies. For example, grapes are a family of species, divided into the various subspecies, and a varietal is a specific subspecies that we refer to by a more common or familiar name, such as Riesling, Chardonnay, etc. (Grapes are a slightly different case in which most grapes are produced from hybrids or crosses for reasons of withstanding environmental conditions avoiding insect prey and fungal infections.) Microbiology has yet another distinction, called a strain. Strains are often genetically different, and yet all belong to a species. For example, several E. coli strains exist. In contrast, viruses are also given strain/subspecies names which don't technically fit the ICZN definition of interbreeding. Cultivar is a similar term, also from the field of botany. Cultivar is specifically applied to plants that are grown for some agricultural benefit, and have been bred or altered by humans for some reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, there is a zoological definition of subspecies set out in ICZN. This definition requires viable interbreeding among subspecies belonging to the same species. The term applies to individuals, or groups, as the context dictates. Analogous terms of subspecies are applied (adapted?) to other realms of biology, such as botany, microbiology and virology, but the definitions are slightly different, but consistent within the branch of biology (eg, viruses can't breed so they don't fit the ICZN definition, but the term applies). Ssp can also be qualitatively used to describe an unknown subset of a species (I've seen this used in microbiology mostly).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Crosses/hybrids are indicated with the &quot;x&quot; in the nomenclature. Since I found this confusing, I'm copying from &lt;a href=&quot;http://en.wikipedia.org/wiki/Hybrid_%28biology%29&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;From a taxonomic perspective, hybrid refers to offspring resulting&#xA;  from the interbreeding between two animals or plants of different&#xA;  species.&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;&lt;p&gt;Hybrids between different subspecies within a species&#xA;  (such as between the Bengal tiger and Siberian tiger) are known as&#xA;  intra-specific hybrids. Hybrids between different species within the&#xA;  same genus (such as between lions and tigers) are sometimes known as&#xA;  interspecific hybrids or crosses. Hybrids between different genera&#xA;  (such as between sheep and goats) are known as intergeneric hybrids.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;The second type of hybrid consists of crosses between populations,&#xA;  breeds or cultivars within a single species. This meaning is often&#xA;  used in plant and animal breeding, where hybrids are commonly produced&#xA;  and selected because they have desirable characteristics not found or&#xA;  inconsistently present in the parent individuals or populations. This&#xA;  flow of genetic material between populations or races is often called&#xA;  hybridization.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are some &lt;a href=&quot;http://en.wikipedia.org/wiki/Hybrid_%28biology%29#Examples_of_hybrids&quot; rel=&quot;noreferrer&quot;&gt;horticultural examples&lt;/a&gt; of crosses in which an example of interspecific and intergeneric hybrids, and others, are shown.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2012-05-03T01:58:39.330" LastActivityDate="2012-05-03T01:58:39.330" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="1977" PostTypeId="1" CreationDate="2012-04-26T00:39:21.600" Score="16" ViewCount="39841" Body="&lt;p&gt;I've read that hydrofluoric acid (HF) is extremely dangerous to touch, but what exactly makes it so toxic? It's weak acid ($K_a = 7.2 \times 10^{–4}$) and dissociates approximately 1/1000 as much as Hydrochloric acid does in water, so why is it so much more dangerous? Wouldn't a stronger acid cause more damage? What exactly happens when human skin comes into contact with Hydrofluoric acid that causes it to be so lethal?&lt;/p&gt;&#xA;" OwnerUserId="62" LastEditorUserId="9943" LastEditDate="2015-05-19T13:25:01.233" LastActivityDate="2015-05-19T13:25:01.233" Title="Why is hydrofluoric acid so dangerous if it is a weak acid?" Tags="&lt;toxicology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1978" PostTypeId="2" ParentId="1977" CreationDate="2012-04-26T06:43:02.673" Score="20" Body="&lt;p&gt;The confusion arises from the term &lt;em&gt;weak&lt;/em&gt;, which has only to be interpreted in chemical terms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Weak acid, as you say, just means that the acid does not readily dissociate, not that its effects are weak! Just to say one, HF corrodes glass, something that not even smoking HCl does.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hydrofluoric_acid#Health_.26_safety&quot;&gt;Wikipedia&lt;/a&gt; has a nice summary of HF toxicity (see also the references in the article itself):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hydrofluoric acid is a highly corrosive liquid and is a contact poison. It should be handled with extreme care, beyond that accorded to other mineral acids. Owing to its low dissociation constant, HF as a neutral lipid-soluble molecule penetrates tissue more rapidly than typical mineral acids. Because of the ability of hydrofluoric acid to penetrate tissue, poisoning can occur readily through exposure of skin or eyes, or when inhaled or swallowed. Symptoms of exposure to hydrofluoric acid may not be immediately evident. HF interferes with nerve function, meaning that burns may not initially be painful. Accidental exposures can go unnoticed, delaying treatment and increasing the extent and seriousness of the injury.&lt;br&gt;&#xA;  Once absorbed into blood through the skin, it reacts with blood calcium and may cause cardiac arrest. Burns with areas larger than 25 square inches (160 cm2) have the potential to cause serious systemic toxicity from interference with blood and tissue calcium levels. In the body, hydrofluoric acid reacts with the ubiquitous biologically important ions Ca2+ and Mg2+. Formation of insoluble calcium fluoride is proposed as the etiology for both precipitous fall in serum calcium and the severe pain associated with tissue toxicity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2015-03-16T17:49:48.400" LastActivityDate="2015-03-16T17:49:48.400" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1979" PostTypeId="2" ParentId="1968" CreationDate="2012-04-26T08:55:39.230" Score="2" Body="&lt;p&gt;The option #2 is most common. Do not forget to add 3 or more additional terminal base pairs for optimal restriction enzyme cutting (source: &lt;a href=&quot;http://www.biotechniques.com/multimedia/archive/00007/98244bm15_7837a.pdf&quot; rel=&quot;nofollow&quot;&gt;BioTechniques 1998, 24:582-584&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-04-26T08:55:39.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1980" PostTypeId="1" CreationDate="2012-04-26T10:47:53.803" Score="4" ViewCount="403" Body="&lt;p&gt;Recently, some research, for example &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919277/&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; has proposed that inflammation can cause innate immune cells to produce pro-inflammatory cytokines that act on the brain to cause sickness behaviour.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) What medication would potentially help to reduce the inflammation? I am not a biology expert so I do get a little confused reading the research articles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) What are cytokines in laymen's terms? Are they the same as histamines which cause allergies?&lt;/p&gt;&#xA;" OwnerUserId="801" LastEditorUserId="69" LastEditDate="2012-04-26T19:11:15.063" LastActivityDate="2012-04-26T19:11:15.063" Title="From inflammation to sickness and depression: when the immune system subjugates the brain" Tags="&lt;immunology&gt;&lt;pharmacology&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1981" PostTypeId="1" AcceptedAnswerId="1984" CreationDate="2012-04-26T13:53:54.853" Score="26" ViewCount="32671" Body="&lt;p&gt;Somewhere I have read we share more than 99% of our genes with every other other person and 98% of our genes with chimpanzees. What does this mean? Don't we share 50% of our genes with our mother and 50% with our father?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've found an another &lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=what-does-the-fact-that-w&quot;&gt;article&lt;/a&gt; stating that.&lt;/p&gt;&#xA;" OwnerUserId="695" LastEditorUserId="112" LastEditDate="2012-04-26T14:19:29.760" LastActivityDate="2019-08-06T21:40:40.520" Title="How many genes do we share with our mother?" Tags="&lt;human-biology&gt;&lt;genetics&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="1982" PostTypeId="1" AcceptedAnswerId="1985" CreationDate="2012-04-26T13:54:06.303" Score="12" ViewCount="614" Body="&lt;p&gt;I've noticed a peculiar phenomenon. A subject drinks 400 ml of water, then observes time until the urge to urinate is felt. The time is 15 minutes. The subject releases water. 14 minutes later another urge to urinate is felt. The subject releases water again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm particularly interested in what kinds of biological systems are involved in &lt;strong&gt;timing of such events&lt;/strong&gt;.&#xA;Does the time depend on how full the subject's stomach is? Does caffeine and other diuretics play a part? &#xA;Is it time of day (circadian rhythm) sensitive?&#xA;Does that predict anything about the suppression/release of diuretic hormones?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm trying to understand is if the timing between human urges to urinate after water consumption can be used to make predictions about the human biological clock and the state of various systems within the body (for example the digestive system). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will be conducting this experiment at different times of the day. &lt;strong&gt;My hypothesis is that at night, when diuretic hormones are suppressed, the timing would be longer for the same amount of water consumed.&lt;/strong&gt; This is based on my limited research in the area. &#xA;Update: I did perform the same experiment at night, the time was 75 minutes for the same amount of water. The experiment was performed at the end of one of sleep cycles, which makes me think that 75 minutes was the duration of the subsequent sleep cycle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I appreciate your input on the subject, along with any keywords that can help me advance my research in this area.&#xA;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="57" LastEditDate="2012-07-28T05:01:09.330" LastActivityDate="2012-07-28T05:01:09.330" Title="What can the timing of human urination tell about the human's physical condition and circadian rhythms?" Tags="&lt;human-biology&gt;&lt;circadian-rhythms&gt;&lt;renal-physiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1983" PostTypeId="2" ParentId="1981" CreationDate="2012-04-26T14:18:56.047" Score="17" Body="&lt;p&gt;In every cell of your body, you have &lt;strong&gt;two physical copies&lt;/strong&gt; of every gene (ignoring gametes, / copy number variations), one from your mother, one from your father. (Humans are &lt;a href=&quot;http://en.wikipedia.org/wiki/Diploid#Diploid&quot;&gt;diploid&lt;/a&gt;.) That's why it's correct to say that you got 50% from either parent (ignoring the 13 mitochondrial genes that are inherited from the mother only). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second approach is to look at &lt;strong&gt;genes as abstract entities&lt;/strong&gt;. In the abstract sense, you share 100% of your genes with fellow humans, and more distant species will have a number of different genes. (This difference can be quantified in many different ways.) &lt;/p&gt;&#xA;" OwnerUserId="112" LastEditorUserId="444" LastEditDate="2012-04-26T14:45:12.270" LastActivityDate="2012-04-26T14:45:12.270" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="1984" PostTypeId="2" ParentId="1981" CreationDate="2012-04-26T14:48:36.837" Score="33" Body="&lt;p&gt;There is a distinct difference between the 'genes' that we share, and the genome (the DNA) that the genes are made of.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All humans (excluding genetic disorders) have the same genes, but the same gene in different individuals may have a slightly different DNA sequence, and this may be manifested in the different traits you can observe between people (eye colour, height, etc) or be ’silent’ (have no observable effect).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you therefore have 100% of the genes that your mother has.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, as stated in another answer, you inherit the different 'alleles', or versions, of the genes from your parents, and end up with ~50% of the alleles from each parents (but all the genes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regard to species differences; many of the genes we inherit have evolved over millions (in fact billions) of years, and thus many of our genes are present in most other organisms (but in very different forms - the DNA). Chimpanzees are our closest relatives in evolutionary terms, and thus their genes are very similar to ours in the genome (~98% the same). But this only applies to the coding regions! Less than 2% of your genome actually codes for genes - the rest is mostly regulatory (not junk, as it used to be called), and this is where the true inter-species variation lies. So whilst we have ~98% homology in the protein-coding regions, this is MUCH less if you count the whole genome.&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="22057" LastEditDate="2019-08-06T21:40:40.520" LastActivityDate="2019-08-06T21:40:40.520" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="1985" PostTypeId="2" ParentId="1982" CreationDate="2012-04-26T14:55:10.260" Score="8" Body="&lt;p&gt;The fact that urine output (enuresis) and other kidney functions are circadian is well known, just search on pubmed 'circadian urine kidney'. This can be due both to the fact that liquid consumption is less during the night and to the fact that hormones regulating kidney function like aldosterone and plasma angiotensin II are circadian.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-04-26T14:55:10.260" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1986" PostTypeId="2" ParentId="1980" CreationDate="2012-04-26T15:06:04.397" Score="3" Body="&lt;p&gt;Cytokines are essentially signalling molecules of the immune system. Broadly speaking these can be classed as pro- or anti-inflammatory. Pro-inflammatory cytokines promote inflammation, and anti-inflammatory cytokines inhibit inflammation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Inflammation (again, broadly speaking) is associated with the 'innate' immune response - this is the immediate response by neutrophils and macrophages (among others), and these cells release a variety of molecules designed to damage cells around them. This is great if those cells are bacterial, or damaged host cells that need removing, but not so great if that is 'normally' functioning tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aging is associated with increased systemic inflammation - i.e. a greater proportion of pro- to anti-inflammatory cytokines. The causes of this aren't entirely certain, but it could be that the adaptive immune response (i.e. the memory T-/B- cells) is not as effective in older ages so the innate response is more important, or that it is just simply left 'unchecked'. Either way, the result this that the pro-inflammatory response can end up damaging host tissues, including the brain, without the corresponding repair instigated by anti-inflammatory cells/cytokines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any anti-inflammatory medication (e.g. aspirin, ibuprofen, or glucocorticoids) will, in theory, reduce inflammation, but by suppressing the immune system the risk of infection naturally rises, and there may be unforeseen consequences to prolonged use (the immune system does a lot more than just fend of bacteria - e.g. it is essential for tissue maintenance and regeneration), so I am by no means suggesting the use of anti-inflammatories to protect brain function!&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-04-26T15:06:04.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1987" PostTypeId="1" AcceptedAnswerId="2387" CreationDate="2012-04-26T15:29:51.957" Score="6" ViewCount="2488" Body="&lt;p&gt;I'm looking to understand the effects of sugary snacks and/or drinks on a human body. I'm particularly interested in the timing of the ingestion versus various hormonal levels that may be circadian in nature. Is the release of insulin circadian in nature? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scenario 1:&#xA;A person eats 50 grams of trail mix- raisins, sugared pineapple, sugared mango. &#xA;What happens in the next couple hours?&#xA;Which hormones get released and for how long? &#xA;Does the timing of ingestion produce different effects (ex: consumed at 11AM vs 3PM vs 8 PM?) on the body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scenario 2:&#xA;A person eats 100 grams of trail mix and drinks a can of sugary nectar (48 grams of sugar dissolved in water).&#xA;Will this cause the sugar &quot;crash&quot;?&#xA;Is there some grams per kilogram of weight guideline on how much refined sugar or corn syrup a human body can handle at once?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your response or any keywords that may help me search for this information!&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorDisplayName="user560" LastEditDate="2012-04-26T21:14:26.707" LastActivityDate="2012-05-25T18:55:07.440" Title="What happens to a human body once a sugary snack is consumed?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1988" PostTypeId="1" AcceptedAnswerId="1993" CreationDate="2012-04-26T15:33:57.550" Score="7" ViewCount="329" Body="&lt;p&gt;A while ago I picked up a book called &quot;Eat right for your metabolic type&quot;. The book discussed the effects of the endocrine system on the overall shape and the speed of metabolism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The book outlined few major metabolic types:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Adrenal&lt;/li&gt;&#xA;&lt;li&gt;Thyroid (hypo/hyper)&lt;/li&gt;&#xA;&lt;li&gt;Muscular&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The book proceeded to discuss the overall shape of the body, including shape of fingers to help identify the metabolic type and give suggestions on which foods to avoid for a particular type. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The book then gave examples of effects of foods on metabolic types - for example an Adrenal type who eats too much sugar would crash and compensate for this by sleeping. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since I can no longer find that book in print, &lt;strong&gt;I'm interested if there's really such a thing as a metabolic type that can be easily identified ? Are there indeed some foods that people should avoid eating?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="810" LastEditDate="2012-05-02T14:34:25.763" LastActivityDate="2012-05-02T14:34:25.763" Title="Is there such thing as a generic &quot;metabolic type&quot;?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;endocrinology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1989" PostTypeId="1" AcceptedAnswerId="1990" CreationDate="2012-04-26T18:37:59.270" Score="6" ViewCount="359" Body="&lt;p&gt;It is said that genes are &lt;em&gt;partly&lt;/em&gt; responsible for the choices we make in our life; our genes help to create our environment, and then that environment can influence our personality. So, beside genes, what else is responsible for the other choices? Is there something else at work?&lt;/p&gt;&#xA;" OwnerUserId="695" LastActivityDate="2012-05-03T20:18:03.887" Title="Genetic effects on personality" Tags="&lt;genetics&gt;&lt;human-genetics&gt;&lt;development&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1990" PostTypeId="2" ParentId="1989" CreationDate="2012-04-26T19:04:22.577" Score="5" Body="&lt;p&gt;Many genetic studies in this area have found that variation in serotonin receptors associates with differences in a number of personality traits. That one gene, or a very small number, turns up time and time again for something so complex as human personality makes me a bit suspicious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other factors at play:&#xA;Family dynamics&lt;br&gt;&#xA;Culture and cultural norms&lt;br&gt;&#xA;Society and societal norms (these could clash with the above two)&lt;br&gt;&#xA;Exposures - drugs, toxins, diet, and many others&lt;br&gt;&#xA;Traumatic events&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-05-03T20:18:03.887" LastActivityDate="2012-05-03T20:18:03.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1991" PostTypeId="2" ParentId="1988" CreationDate="2012-04-26T19:14:58.337" Score="8" Body="&lt;p&gt;That book was likely crap, but in short the answer is yes, probably there is a genetic basis in the metabolism, with human 'types' that could benefit from a personalized nutrition. The discipline studying these relationship is called nutrigenomics, and the main concept is similar to what is being told for personalized medicine. The bad news is that unfortunately this is not easy to identify, surely not from the form of your finger.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-04-26T19:14:58.337" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1992" PostTypeId="2" ParentId="1923" CreationDate="2012-04-26T19:33:47.717" Score="8" Body="&lt;p&gt;I can't think of any reason that would explicitly prohibit a dendrite from travelling through a space created by another dendrite's branching pattern. In non-EM images of dendritic branching patterns I don't think I have ever observed dendritic loops, but of course, that has nothing to do with whether or not they occur. Nonetheless, I think there are more likely explanations for what you are seeing in these particular images.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As shown, the upper and lower parts of the &quot;dendrite&quot; in the first image do not look like a continuous structure. I would guess that you are looking at a synapse or some other contact between two different processes in the first image. The 3-4'o'clock connection in the loop suggests this interpretation. Can you see vesicles in the images around those connections?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other dendrite that shows up in your second image might be a glial cell or some other cell's dendrite that participates in the synapse. Alternatively, the other dendrite may just be a chance passing of two dendrites that don't interact functionally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, it could be that you and the computer have just completely misunderstood the data. My understanding of the Eyewire interface is that the computer guides a lot of the identification and doesn't easily allow you to see the surrounding areas so you can't track structures all the way to their sources. In such a situation, it seems probable that you would end up with ambiguous instances like this that you would have a hard time resolving without more information/expertise. But maybe Seung or one his colleagues can come weigh in on that?&lt;/p&gt;&#xA;" OwnerUserId="72" LastActivityDate="2012-04-26T19:33:47.717" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="1993" PostTypeId="2" ParentId="1988" CreationDate="2012-04-26T20:31:19.023" Score="6" Body="&lt;p&gt;In general the answer is yes. However, the degree in which this is true and the degree in which the human body can adjust and adapt to new food types is larger misjudged. I am of the opinion that metabolism is largely controlled by the microbiome. It is largely &lt;a href=&quot;http://www.nature.com/nature/journal/v473/n7346/full/nature09944.html&quot;&gt;recognized&lt;/a&gt; that the gut biome does adjust depending on diet and will also vary depending on drug intake. From previous meta-analyses, it has been noted that there are &lt;a href=&quot;http://blogs.discovermagazine.com/notrocketscience/2011/04/20/divided-by-language-united-by-gut-bacteria-%E2%80%93-people-have-three-common-gut-types/&quot;&gt;three subtypes&lt;/a&gt; of microbiomes. In a particularly famous study, it has been noted that Japanese and only Japanese people have the microbiome to &lt;a href=&quot;http://blogs.discovermagazine.com/notrocketscience/2010/04/07/gut-bacteria-in-japanese-people-borrowed-sushi-digesting-genes-from-ocean-bacteria/&quot;&gt;digest seaweed&lt;/a&gt; due to the remarkable volumes of sushi that they eat.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-04-26T20:31:19.023" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1994" PostTypeId="1" AcceptedAnswerId="1997" CreationDate="2012-04-26T21:33:00.083" Score="8" ViewCount="246" Body="&lt;p&gt;Is there any evolutionary advantage to finding melodies or harmonies pleasurable? Does the ear pick up these particular oscillating waves differently from other sounds, and if so, how does that affect our perception of pleasure? I'm looking for some sort of signalling pathway (most likely involving neurotransmitters I realize).&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="86" LastEditDate="2012-06-07T13:36:34.630" LastActivityDate="2012-06-07T13:36:34.630" Title="Why are melodies/harmonies perceived as pleasurable by humans?" Tags="&lt;neuroscience&gt;&lt;perception&gt;&lt;hearing&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1995" PostTypeId="1" CreationDate="2012-04-27T00:30:58.413" Score="11" ViewCount="17937" Body="&lt;p&gt;One way to do an yeast transformation is by using lithium acetate, a single-stranded carrier DNA, and PEG &lt;a href=&quot;http://www.nature.com/nprot/journal/v2/n1/full/nprot.2007.13.html&quot;&gt;(1)&lt;/a&gt;. I was wondering why is the polyethylene glycol important for the efficient transformation. How does it affect the take-up of the foreign DNA? Yamakawa et al (2) showed that PEG is essential for the recovery of the cells but I couldn't access that paper to read more about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nprot/journal/v2/n1/full/nprot.2007.13.html&quot;&gt;1. R Daniel Gietz &amp;amp; Robert H Schiest (2007). High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=Intact%20cell%20transformation%20of%20Saccharomyces%20cerevisiae%20by%20polyethylene%20glycol&quot;&gt;2. Yamakawa, M., Hishinuma, F. and Gunge, N. (1985). Intact cell transformation of Saccharomyces cerevisiae by polyethylene glycol. Agric. Biol. Chem. 43, 869-&#xA;871.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2015-05-05T18:18:59.897" Title="Why is PEG important for efficient yeast transformation?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;yeast&gt;&lt;transformation&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="1996" PostTypeId="2" ParentId="1917" CreationDate="2012-04-27T05:57:00.653" Score="6" Body="&lt;p&gt;There are two books I'd highly recommend for someone starting to dabble in Epidemiology. The first is Kenneth Rothman's &lt;em&gt;Epidemiology: An Introduction&lt;/em&gt;, which I'm affectionately going to refer to as &quot;Baby Rothman&quot; from hereon out for reasons that will become obvious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Baby Rothman is an excellent &quot;getting your feet wet&quot; book. It's simplistic, and clearly designed for someone with no background in Epidemiology, so it starts from things that, if you have a statistical background, you might find a bit dull. But it accomplishes two key tasks:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;A basic treatment of the subject from a pre-eminent methodologist and advocate for the field that doesn't make some of the sloppy slight-of-hand mistakes many introductory books do.&lt;/li&gt;&#xA;&lt;li&gt;An introduction to the &quot;vocabulary&quot; of Epidemiology as a field - what we call things, how we thing about effect estimates, etc.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The second book I would buy would be &lt;em&gt;Modern Epidemiology: 3rd Edition&lt;/em&gt; by Rothman, Greenland and Lash. This is &lt;em&gt;the&lt;/em&gt; definitive reference book for most epidemiological methods  currently used in the field. As I said on a related &lt;a href=&quot;https://stats.stackexchange.com/questions/21405/good-reference-book-for-epidemiology&quot;&gt;CrossValidated&lt;/a&gt; question, ME3 is the only epidemiology book that has always come with me, regardless of what project I'm doing, and which I have routinely found invaluable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other benefit of the book is that it's &quot;platform agnostic&quot;. It's not going to try to teach you a statistics package - its going to teach you the science and philosophy of Epidemiology, the actual doing of the science, rather than the toolkit. Without that kind of methodological rigor, you can be a wizard at your language of choice and still do bad science.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I were only going to buy one book, it would be ME3.&lt;/p&gt;&#xA;" OwnerUserId="67" LastEditorUserId="-1" LastEditDate="2017-04-13T12:44:17.897" LastActivityDate="2012-04-27T05:57:00.653" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="1997" PostTypeId="2" ParentId="1994" CreationDate="2012-04-27T06:25:18.137" Score="7" Body="&lt;p&gt;There are strong connections between the auditory cortex and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Limbic_system&quot;&gt;limbic system&lt;/a&gt;, which includes such structures as the hippocampus and the amygdala.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A recent paper [1] builds on earlier notions of emotional &quot;significance&quot; of music without any lyrics.  It adds in lyrics, so giving a perspective of which portions of the brain are reacting to which component of the music.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Additionally, contrasts between sad music with versus without lyrics recruited the parahippocampal gyrus, the amygdala, the claustrum, the putamen, the precentral gyrus, the medial and inferior frontal gyri (including Broca’s area), and the auditory cortex, while the reverse contrast produced no activations. Happy music without lyrics activated structures of the limbic system and the right pars opercularis of the inferior frontal gyrus, whereas auditory regions alone responded to happy music with lyrics.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;One of the limitations of this particular study is that the subjects self-selected their own pieces, which may limit the reliability of the results.  Of course, defining &quot;happy&quot; or &quot;sad&quot; for every individual is slightly subjective and difficult.  They cited an earlier &quot;pioneering&quot; study which standardized the musical selection between subjects.  Without consideration of the lyrics:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first pioneer study using functional magnetic resonance imaging (fMRI) by Khalfa et al. (2005) chose a controlled manipulation of two musical features (tempo and mode) to vary the happy or sad emotional connotations of 34 instrumental pieces of classical music, lasting 10s each. Sad pieces in minor-mode contrasted with happy pieces in major mode produced activations in the left medial frontal gyrus (BA 10) and the adjacent superior frontal gyrus (BA 9). These regions have been associated with emotional experiences, introspection, and self-referential evaluation (Jacobsen et al., 2006; Kornysheva et al., 2010).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As an aside to answer your final thought, in cases like this I think trying to jam everything under an umbrella of one &quot;neurotransmitter system&quot; or another can make things overly simplistic to the point where you lose focus of the diversity of receptors expressed.  You can say a system is driven by Dopamine, but D1 and D2 &lt;a href=&quot;http://en.wikipedia.org/wiki/Dopamine_receptor&quot;&gt;receptors&lt;/a&gt; have exactly the opposite effects on the neuron.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[1] Brattico, E., Alluri, V., et al (2011) A functional MRI study of happy and sad emotions in music with and without lyrics.  Frontiers in Psychology, 2: 308.  doi: 10.3389/fpsyg.2011.00308 &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227856/pdf/fpsyg-02-00308.pdf&quot;&gt;(free pdf)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(see also, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0028393206003083&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0028393206003083&lt;/a&gt; and related)&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-04-27T06:39:06.077" LastActivityDate="2012-04-27T06:39:06.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1998" PostTypeId="2" ParentId="1989" CreationDate="2012-04-27T07:41:58.243" Score="2" Body="&lt;p&gt;Furthermore the genotype of the individual does not represent the phenotype, it is about the expression profile of the genes rather than just their presence.&lt;/p&gt;&#xA;" OwnerUserId="798" LastActivityDate="2012-04-27T07:41:58.243" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="1999" PostTypeId="1" CreationDate="2012-04-27T08:24:08.473" Score="15" ViewCount="319" Body="&lt;p&gt;Recently, &lt;a href=&quot;https://biology.stackexchange.com/questions/1988/human-biology-is-there-such-thing-as-a-generic-metabolic-type&quot;&gt;it has been asked&lt;/a&gt; whether there are 'metabolic types' between humans that can benefit from a sort of personalized nutrition. One answer suggested that one discerning factor could be the human microbiome. It is known that host–microbial symbiotic states might respond differently to diet and drug intake, but whether this can be useful for personalized nutrition is less clear to me. I wonder:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;does the microbiome affect food metabolism?&lt;/strong&gt; (useful for personalized nutrition)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;OR&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;is the food that we eat affecting the microbiome?&lt;/strong&gt; (less useful for personalized nutrition)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know the answer is probably both, but there are examples causally demonstrating one branch and excluding the other?&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-12-13T13:28:38.840" Title="Relationship between our microbiome and personalized nutrition" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;metabolism&gt;&lt;nutrition&gt;&lt;microbiome&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2000" PostTypeId="2" ParentId="1999" CreationDate="2012-04-27T11:04:26.623" Score="11" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;does the microbiome affect food metabolism?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Most definitely (and not surprisingly). The Arumugam paper [1] notes that&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The drivers of [&lt;strong&gt;enterotype 1&lt;/strong&gt;] seem to derive energy primarily from &lt;strong&gt;carbohydrates and proteins through fermentation&lt;/strong&gt;, … because genes encoding enzymes involved in the degradation of these substrates (galactosidases, hexosaminidases, proteases) along with glycolysis and pentose phosphate pathways are enriched in this enterotype […]&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Enterotype 2&lt;/strong&gt; … is enriched in Prevotella … and the co-occurring Desulfovibrio, which can act in synergy to &lt;strong&gt;degrade mucin glycoproteins present in the mucosal layer of the gut&lt;/strong&gt; […]&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Enterotype 3&lt;/strong&gt; is […] &lt;strong&gt;enriched in membrane transporters, mostly of sugars&lt;/strong&gt;, indicating the efficient binding of mucin and its subsequent hydrolysis as well as uptake of the resulting simple sugars by these genera. […]&lt;/p&gt;&#xA;&lt;p&gt;The enriched genera indicate that &lt;strong&gt;enterotypes use different routes to generate energy from fermentable substrates available in the colon&lt;/strong&gt;, reminiscent of a potential specialization in ecological niches or guilds. In addition to the conversion of complex carbohydrates into absorbable substrates, the gut microbiota is also beneficial to the human host by producing vitamins. Although all the vitamin metabolism pathways are represented in all samples, &lt;strong&gt;enterotypes 1 and 2 were enriched in biosynthesis of different vitamins&lt;/strong&gt; […]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;[All emphasis mine.]&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;is the food that we eat affecting the microbiome?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Yes, just as certainly. I don’t have a publication handy but it should be obvious that our food influences our gut microbiome – in the extreme case, it can kill it (consider &lt;a href=&quot;http://en.wikipedia.org/wiki/Antibiotic#Side-effects&quot; rel=&quot;noreferrer&quot;&gt;antibiotics side effects&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.nature.com/nature/journal/v474/n7353/full/nature10187.html&quot; rel=&quot;noreferrer&quot;&gt;Manimozhiyan Arumuga, Jeroen Raes &lt;em&gt;&amp;amp; al.&lt;/em&gt;, &lt;em&gt;Enterotypes of the human gut microbiome&lt;/em&gt;, Nature &lt;strong&gt;473&lt;/strong&gt;, 174–180, May 2011.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-04-27T11:04:26.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2001" PostTypeId="2" ParentId="1981" CreationDate="2012-04-27T11:09:47.677" Score="25" Body="&lt;p&gt;In addition to the other answers, let me show you a logical error in your reasoning:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Don't we share 50% of our genes with our mother and 50% with our father?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You &lt;em&gt;get&lt;/em&gt; 50% of our genes from each respective parent (disregarding mutations for now). But if you &lt;em&gt;shared&lt;/em&gt; only 50% with each parent, this would imply that your parents don’t share a single gene:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/f3QXo.png&quot; alt=&quot;Shared alleles between your parents and you&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But your parents &lt;em&gt;do&lt;/em&gt; share genes – or rather, &lt;a href=&quot;http://en.wikipedia.org/wiki/Allele&quot; rel=&quot;noreferrer&quot;&gt;alleles&lt;/a&gt;&lt;sup&gt;1&lt;/sup&gt; – which is why the you also share more than 50% of the alleles with each of your parent.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1)&lt;/sup&gt;  They share &lt;em&gt;all&lt;/em&gt; genes.&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="166" LastEditDate="2012-04-27T11:18:32.127" LastActivityDate="2012-04-27T11:18:32.127" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2002" PostTypeId="1" AcceptedAnswerId="2456" CreationDate="2012-04-27T12:15:07.580" Score="6" ViewCount="358" Body="&lt;p&gt;How do plants intake the fertilizer when it is sprayed all over the leaf surface as a foliar feed? &lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="16866" LastEditDate="2017-01-03T16:02:30.330" LastActivityDate="2017-01-03T16:02:30.330" Title="How do plants intake minerals through their leaves?" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2003" PostTypeId="2" ParentId="1994" CreationDate="2012-04-27T19:13:45.147" Score="1" Body="&lt;p&gt;&lt;strong&gt;In music&lt;/strong&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Harmony&quot; rel=&quot;nofollow&quot;&gt;harmonies&lt;/a&gt; are simultaneous combination of tones or chords that are concordant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In physics&lt;/strong&gt;, each note is actually a vibration with defined wavelenght, the concordance can be explained in mathemathical terms, for instance with regard to coincidence of phase oscillation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In physiology&lt;/strong&gt;, the ear perceives air vibrations and send them to the brain by means of trains of pulses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to some scientists, a music providing regular train of pulses (like harmonic music and rhytmic music) should be more pleasing, probably because of stimulation of the limbic system, as the other answer explains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://prl.aps.org/abstract/PRL/v107/i10/e108103&quot; rel=&quot;nofollow&quot;&gt;Ushakow et al. 2011&lt;/a&gt;, Physical Review Letters, DOI 10.1103/PhysRevLett.107.108103&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lay explanation: &lt;a href=&quot;http://www.newscientist.com/article/dn20930-why-harmony-pleases-the-brain.html&quot; rel=&quot;nofollow&quot;&gt;Why harmony pleases the brain&lt;/a&gt;, New Scientist, Sept 2011&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-04-27T19:13:45.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2004" PostTypeId="2" ParentId="1999" CreationDate="2012-04-27T20:07:30.230" Score="8" Body="&lt;p&gt;Yes, the microbiome affects food metabolism and the diet affects the composition of the microbiome. +1 to Konrad for his response. This is an area of research in which I and colleagues are engaged. Frankly, it is easier to assess the changes to the microbiome based on diet rather than looking at the fecal material to determine (unused) metabolic energy or potential given a certain input (i.e, from a controlled diet).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recently, we've fed humans a high number of servings of whole grains. The response is highly individualistic with some declines and others increases in Firmicutes, for example. Typically, Bacteroidetes numbers move opposite to Firmicutes, but not in all individuals. These observations are also seen by others in this growing field of research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;enterotypes&quot; paper Konrad cites is beginning to see some resistance in the field in that the three enterotypes defined by those authors are not really so cleanly defined when one takes a closer look at more individuals. Time will tell how well one view or the other holds.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-04-27T20:07:30.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2006" PostTypeId="1" AcceptedAnswerId="2008" CreationDate="2011-12-07T14:34:55.813" Score="14" ViewCount="89" Body="&lt;p&gt;I may be embarking on a project involving a fairly extensive healthcare records data set, looking for the use of a particular type of drug (for example, &quot;Proton Pump Inhibitors&quot;). But these drugs are usually listed by their trade or generic names - is there a well maintained resource for looking up what drugs are members of a certain class (if class is indeed the right word)?&lt;/p&gt;&#xA;" OwnerUserId="67" OwnerDisplayName="EpiGrad" LastEditorUserId="444" LastEditDate="2012-04-28T07:19:07.050" LastActivityDate="2012-04-28T07:19:07.050" Title="Resources for finding all drugs of a certain class" Tags="&lt;pharmacology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2007" PostTypeId="2" ParentId="2006" CreationDate="2011-12-07T17:59:11.350" Score="9" Body="&lt;p&gt;Comprehensive, up-to-date drug information including trade names and categories are available from &lt;a href=&quot;http://www.micromedex.com&quot;&gt;Micromedex&amp;reg;&lt;/a&gt; (a division of Thomson Reuters) in the &lt;a href=&quot;http://www.micromedex.com/products/redbook/&quot;&gt;RED BOOK&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's free to use anywhere (even on a mobile device) by anyone in your organization ... &lt;em&gt;after&lt;/em&gt; you pay the subscription fee.  The fee for research is much less than the fee for commercial use.&lt;/p&gt;&#xA;" OwnerDisplayName="David P. Hochman" LastActivityDate="2011-12-07T17:59:11.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2008" PostTypeId="2" ParentId="2006" CreationDate="2011-12-07T22:15:14.163" Score="11" Body="&lt;p&gt;The &lt;a href=&quot;http://www.who.int/en/&quot;&gt;WHO&lt;/a&gt; has their own methodology, the Anatomical Therapeutic Chemical (ATC, thank you commenter) &lt;a href=&quot;http://www.whocc.no/atc/structure_and_principles/&quot;&gt;classification system&lt;/a&gt;, for organizing such data (its impetus is comparing results between studies).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, if you have $900 sitting around, you can get a &lt;a href=&quot;http://store.usp.org/OA_HTML/usp2_ibeCCtpSctDspRte.jsp?section=10071&amp;amp;minisite=10020&quot;&gt;subscription&lt;/a&gt; for the United States Pharmacopeia.  I'm not sure if that can be spread across multiple subscriptions for an organization like the Red Book David mentions.&lt;/p&gt;&#xA;" OwnerUserId="57" OwnerDisplayName="jonsca" LastActivityDate="2011-12-19T01:29:38.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2009" PostTypeId="1" AcceptedAnswerId="2010" CreationDate="2012-01-31T09:42:20.767" Score="8" ViewCount="84" Body="&lt;p&gt;I am looking for a downloadable database of disease statistics. I have emailed the good folks over at &lt;a href=&quot;http://healthmap.org&quot; rel=&quot;nofollow&quot;&gt;HealthMap&lt;/a&gt;, but they haven't gotten back to me yet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I can tell, their data relevant to my project is gathered from the &lt;a href=&quot;http://www.who.int&quot; rel=&quot;nofollow&quot;&gt;World Health Organisation&lt;/a&gt;, &lt;a href=&quot;http://www.promedmail.org&quot; rel=&quot;nofollow&quot;&gt;ProMED Mail&lt;/a&gt;, &lt;a href=&quot;http://www.istm.org/geosentinel/main.html&quot; rel=&quot;nofollow&quot;&gt;GeoSentinel&lt;/a&gt;, &lt;a href=&quot;http://news.google.com&quot; rel=&quot;nofollow&quot;&gt;Google News&lt;/a&gt;, &lt;a href=&quot;http://www.moreover.com&quot; rel=&quot;nofollow&quot;&gt;Moreover&lt;/a&gt;, &lt;a href=&quot;http://www.baidu.com&quot; rel=&quot;nofollow&quot;&gt;Baidu&lt;/a&gt; and &lt;a href=&quot;http://www.soso.com&quot; rel=&quot;nofollow&quot;&gt;SOSO&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can scrape the data from each of these sites and aggregate it in the same way &lt;a href=&quot;http://healthmap.org&quot; rel=&quot;nofollow&quot;&gt;HealthMap&lt;/a&gt; has, but that is a large project in and of itself, and I only have a couple of months for this not-for-profit project.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do you know of a downloadable worldwide database of disease statistics?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4733" OwnerDisplayName="A T" LastEditorUserId="112" LastEditDate="2012-05-02T15:23:19.150" LastActivityDate="2012-05-02T15:23:19.150" Title="Downloadable worldwide database of disease statistics?" Tags="&lt;bioinformatics&gt;&lt;epidemiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2010" PostTypeId="2" ParentId="2009" CreationDate="2012-01-31T17:13:06.883" Score="4" Body="&lt;p&gt;I took a quick peek and HealthMap and their JavaScripts are publicly viewable.  As such, I believe cross site scripting would be quite feasible.  In other words, call their JavaScripts from a page you develop on your server to create a feed of the data you want.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this way, minimal effort on your part could leverage their data scraping efforts.  If you're adding your own data then you're basically doing a Mashup. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, my concern with doing this is potentially violating their copyright.  I would email them saying if their database is not available then you wish to use cross site scripting to access this data for your project, and unless they let you know otherwise by (specific date) you will assume this is acceptable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not a lawyer, so use this advice at your own risk.  =)  &lt;/p&gt;&#xA;" OwnerUserId="1016" OwnerDisplayName="Chris K" LastActivityDate="2012-01-31T17:13:06.883" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2011" PostTypeId="1" CreationDate="2012-02-21T21:11:36.807" Score="8" ViewCount="140" Body="&lt;p&gt;I was just looking at the &lt;a href=&quot;http://www.google.org/flutrends/&quot; rel=&quot;nofollow&quot;&gt;Google Flu Trends&lt;/a&gt; map.  &lt;a href=&quot;http://www.google.com/insights/search/&quot; rel=&quot;nofollow&quot;&gt;Google Insight&lt;/a&gt; could be used to gain similar information for other trends in disease keyword searches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I started wondering how valid are keyword searches to represent the spread of diseases.  In some ways I think it could be a good representative, but in others I think it would be susceptible to influence by mass media.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do maps of clinical data exist that could be compared to this Google data?  If so, where could I find some.  =)&lt;/p&gt;&#xA;" OwnerUserId="1016" OwnerDisplayName="Chris K" LastEditorUserId="57" LastEditDate="2012-04-27T23:11:22.773" LastActivityDate="2012-04-27T23:11:22.773" Title="What data / tools exist for mapping of disease trends?" Tags="&lt;epidemiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2012" PostTypeId="2" ParentId="2011" CreationDate="2012-03-07T05:13:59.347" Score="1" Body="&lt;p&gt;For myself, I've not been terribly impressed with the use of keyword searches and the like as methods of predicting influenza or other diseases. They are, when it comes down to it, somewhat glorified extensions of a syndromic surveillance system, just for &quot;I feel sick&quot; instead of &quot;Honey, pop down to CVS and pick up some NyQuil?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also apt to get you some odd results. I tried to use a &quot;Google-style&quot; analysis to match some rotavirus data to Google searches - I believe I was 7 entries down before I ever got to anything rotavirus related, and even that was &quot;rotavirus&quot;, which doesn't suggest it would be useful as a symptom detector, but rather people Googling a disease their doctor said they had. The top results, some of which fit &lt;em&gt;really&lt;/em&gt; well? A series of prom dress-related searches. In order for it to be useful, you'd have to extend Google's system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, as a thought experiment, if you'd like to match it to data, there's a number of potential data sources publicly available from the CDC. &lt;a href=&quot;http://www.cdc.gov/mmwr/&quot; rel=&quot;nofollow&quot;&gt;Morbidity and Mortality Weekly Report&lt;/a&gt; for example publishes weekly counts for a number of notifiable diseases.&lt;/p&gt;&#xA;" OwnerUserId="67" OwnerDisplayName="EpiGrad" LastActivityDate="2012-03-07T05:13:59.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2013" PostTypeId="2" ParentId="2011" CreationDate="2012-03-16T00:49:03.387" Score="2" Body="&lt;p&gt;You can use official sources such as hospital admissions, prescriptions for drugs fighting the disease you are tracking, sales of over-the-counter medicines.&#xA;CDC (cdc.gov/flu/weekly/, cdc.gov/outbreaknet/outbreaks.html, etc), WHO, EuroFlu Weekly Electronic Bulletin map official clinical data, Aurametrix uses these sources. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several scientific studies have compared GFT, twitter, even facebook with official sources.  Johns Hopkins study (pubmed/22230244) used data from local hospitals in addition to CDC.&#xA;My sampling studies too showed that social trends are surprisingly good, despite all the noise, but provide good estimates only for highly populated areas.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might also want to check Sickweather's algorithm, healthmap, usgs disease maps and industry databases providing coverage of pharmaceutical companies and product sales.&lt;/p&gt;&#xA;" OwnerUserId="478" OwnerDisplayName="Irene" LastActivityDate="2012-03-16T00:49:03.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2014" PostTypeId="1" CreationDate="2012-03-08T15:38:49.680" Score="4" ViewCount="665" Body="&lt;p&gt;Do you have any suggestions for a library which offers an algorithm to crop digital X-ray images automatically?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We receive full-size images (43x43cm) from a detector, independent of the collimator settings. If the collimator has been closed to 10x15cm, we need to crop this area. This should be done automatically, so that the user does not even see the full-size image because it contains a lot of information which is not needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now we are looking for a good library which offers such an algorithm. This sounds like a simple task, but depending on the dose and the collimation, it can be pretty hard to detect the collimated area of the image. Therefore, we are looking for a professional solution rather than implementing it ourselves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any suggestions?&lt;/p&gt;&#xA;" OwnerDisplayName="gehho" LastEditorUserId="115" LastEditDate="2012-04-28T14:25:01.050" LastActivityDate="2012-04-28T14:25:01.050" Title="Automatic cropping of collimated digital X-ray images" Tags="&lt;imaging&gt;&lt;software&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2015" PostTypeId="2" ParentId="2014" CreationDate="2012-03-08T18:29:09.640" Score="4" Body="&lt;p&gt;There is a software package ImageJ which can be used to what you are asking. Depending on your capability and the complexity of what you are doing you can either write a Macro in the program to crop images or you can extend the program in Java and write a custom plugin to do what you describe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I used this program for years it is a very strong program.&lt;/p&gt;&#xA;" OwnerDisplayName="Vill" LastActivityDate="2012-03-08T18:29:09.640" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2016" PostTypeId="1" CreationDate="2011-11-27T20:27:56.583" Score="13" ViewCount="947" Body="&lt;p&gt;Does anyone know of any good databases that contain symptoms for diseases and other ailments in humans? I've tried working with UMLS, but thats been impossible to work with. I've also tried working with the disease ontology website (&lt;a href=&quot;http://www.disease-ontology.org/&quot;&gt;http://www.disease-ontology.org/&lt;/a&gt;), but that doesn't seem to be very...comprehensive...in terms of symptoms for the diseases they have. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've tried looking at the the disease database (&lt;a href=&quot;http://www.diseasesdatabase.com/&quot;&gt;http://www.diseasesdatabase.com/&lt;/a&gt;), but they are reluctant to hand over the raw data, if I understand correctly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyone have better ideas? &lt;/p&gt;&#xA;" OwnerDisplayName="Vito" LastEditorUserId="57" LastEditDate="2012-04-27T23:13:55.313" LastActivityDate="2015-01-09T06:23:31.267" Title="Human disease and associated phenotype database?" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2018" PostTypeId="2" ParentId="2016" CreationDate="2012-01-11T00:18:44.367" Score="3" Body="&lt;p&gt;It seems to me like you're effectively wanting to make a decision matrix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So... As said above, ICD and SNOMED CT going to have codes for your diseases and symptoms. I'd lean toward SNOMED CT due to the way it organises concepts. Essentially from broad to specific. That way users can enter very specific symptoms, and your matrix only needs to have symptoms as specific as is required.&#xA;For example you can say &quot;vomitting&quot; is a symptom of &quot;alcohol poisoning&quot; in your db. And if a user enters &quot;projectile vomitting&quot; the SNOMED structure recognises this as a type of vomitting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;However&lt;/strong&gt; - Symptoms don't make the disease, and most diseases have a huge array of 'possible symptoms' (Which is why SNOMED CT doesn't have such relationships). So it's not an easy undertaking. Hence why those who've made such db's (as you've linked to) are reluctant to share their IP, at least without $$$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're going to make your own, here's some tips.&#xA;Consider:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;only diseases relevant to your use case - eg. Aged care doesn't require paediatric disorders;&lt;/li&gt;&#xA;&lt;li&gt;exclude non-specific symptoms;&lt;/li&gt;&#xA;&lt;li&gt;rank your symptoms by frequency - eg. 60% of pregnant women have morning sickness, where as 100% have an HCG &gt; 10*&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Hope this helps. And good luck.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;edit- there is a similar thread &lt;a href=&quot;http://www.linkedin.com/groupItem?view=&amp;amp;srchtype=discussedNews&amp;amp;gid=2099640&amp;amp;item=87855845&amp;amp;type=member&amp;amp;trk=eml-anet_dig-b_pd-ttl-cn&amp;amp;ut=2jUQx3DlSHql41&quot; rel=&quot;nofollow&quot; title=&quot;disease and symptom/measurement mappings&quot;&gt;on LinkedIn&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*&lt;em&gt;fabricated statistic :).&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="DougF" LastActivityDate="2012-01-17T00:53:59.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2020" PostTypeId="1" CreationDate="2012-04-28T01:15:05.303" Score="6" ViewCount="568" Body="&lt;p&gt;&lt;a href=&quot;http://news.sciencemag.org/sciencenow/2012/04/cocaine-may-age-the-brain.html?rss=1&quot; rel=&quot;nofollow&quot;&gt;http://news.sciencemag.org/sciencenow/2012/04/cocaine-may-age-the-brain.html?rss=1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cocaine-dependent individuals showed a significantly greater-than-normal age-related decline in gray matter in prefrontal and temporal regions compared with healthy controls. By contrast, parts of the striatum appeared resistant to age-related volume decline in the cocaine-using group. Enlarged striatal volume has frequently been reported in stimulant-dependent individuals,5, 6 possibly reflecting a marker of reduced dopamine neurotransmission in this dopamine-rich brain region where drugs like cocaine work. Decline in striatal dopamine receptor density has been associated with normal age-related cognitive decline.7 The relative absence of age-related changes in the striatum of cocaine-dependent people may thus reflect another feature of an abnormal brain ageing process.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Could it be related to possible neurotoxicity, or to the long-term effects of dopamine receptor downregulation? Could the effects also be generalizable to those who take dopamine-based ADD medications?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A link to the Letter to the Editor appeared in Molecular Psychiatry to which the ScienceNow article refers:&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22525488&quot; rel=&quot;nofollow&quot;&gt;Cocaine dependence: a fast-track for brain ageing?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="69" LastEditDate="2012-04-28T10:31:37.457" LastActivityDate="2013-09-04T10:33:55.790" Title="Why do the brains of cocaine-users shrink faster than the brains of non-cocaine users?" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;&lt;neuroanatomy&gt;&lt;addiction&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2021" PostTypeId="2" ParentId="1982" CreationDate="2012-04-28T18:02:56.330" Score="2" Body="&lt;p&gt;I would suggest a couple of papers&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21811695&quot; rel=&quot;nofollow&quot;&gt;Circadian rhythms in urinary functions: possible roles of circadian clocks?&lt;/a&gt; - Noh et al., Int Neurourol J., 2011&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20664559&quot; rel=&quot;nofollow&quot;&gt;Circadian regulation of renal function&lt;/a&gt; - Firsov and Bonny, 2010&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jneurosci.org/content/5/10/2771.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Neural regulation of the circadian vasopressin rhythm in cerebrospinal fluid: a pre-eminent role for the suprachiasmatic nuclei&lt;/a&gt; - Schwartz and Reppert, J Neurosci, 1985&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-04-28T18:02:56.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2022" PostTypeId="1" AcceptedAnswerId="2023" CreationDate="2012-04-28T21:55:32.580" Score="20" ViewCount="3700" Body="&lt;p&gt;I am currently reading 'The Selfish Gene' by Richard Dawkins, which I am sure many here have read. The topic are evolutionary stable strategies (ESS) regarding cooperation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I apologise for the long question. If you are already familiar with the topic and Dawkins' model of Cheat, Sucker and Grudger: my question is, how can Grudger be an ESS if it could be invaded both by Suckers (because they have no disadvantage against Grudger) and Cheats (because a Cheat minority is unlikely to meet the same Grudger twice, turning Grudger into Sucker effectively)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More detailed:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The model&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Near the end of chapter 10 (p 185 in my version), Dawkins uses a model of birds who clean each other of parasites, therefore helping in survival (as cleaning themselves they cannot reach every spot of their body). He defines three different behaviours for the model:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Sucker - birds who indiscriminately help and clean other birds&lt;/li&gt;&#xA;&lt;li&gt;Cheat - birds who let others help them but never do so themselves&lt;/li&gt;&#xA;&lt;li&gt;Grudger - birds who help others and remember who they helped. If the same bird does not help them later (reciprocate), they will not help that bird again.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Claim: Cheat and Grudger are ESS&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He claims that both Cheat and Grudger in themselves are ESS - that is, if all birds behave this way, none of the other behaviours can develop because they will be immediately penalised by lower chances of reproducing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The part that makes sense: Suckers is not an ESS, Cheat is&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sucker is of course not an ESS. If all birds were Suckers, any Cheat that developed would have a huge reproductive advantage and Cheat genes would overtake the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Being an ESS makes sense for Cheat. If all birds cheat, nobody will ever be helping each other. A minority of Suckers would be spending all their time helping and not getting anything in return, Cheats have the advantage and Suckers die out again. Grudger would be unlikely to meet a Cheat who they helped before again, so they too will spend all their time helping and die out again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The part that confuses: Grudger is an ESS?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But Dawkins also claims that Grudger is an ESS, and he seems very confident in that. Now I don't consider myself enough of a smartypants to claim that he's wrong, but I don't understand how Grudger can be an ESS. If all birds behave in this way, and for any reason some Sucker developed - the Sucker would have no disadvantage. All birds would still always be helping each other, so nothing would stop the Suckers from propagating equally well as the Grudgers, invading the gene pool. That's already the ESS broken, but even further, the presence of Suckers would mean that if Cheats came up, they would have a realistic chance of surviving - Grudgers would shun them after having helped once, but if the number of Suckers is large enough, Cheats will have an advantage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, back to the initial setting of Grudgers only - if a Cheat developed, he would be unlikely to meet the same Grudger twice, receiving the benefit all the time but never paying the cost. He would have an advantage and spread Cheat genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The problem&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not familiar enough with how these kinds of models are calculated in order to state chances that Cheats will take over completely, but however I think of it Grudger does not seem to be an ESS to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have an explanation why Dawkins is so sure that it is? Seeing as in nature we do see patterns like Sucker and Grudger all the time, I must be missing something important here. &lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="500" LastEditDate="2013-03-14T17:00:59.520" LastActivityDate="2014-10-03T18:53:46.480" Title="Why is 'Grudger' an evolutionary stable strategy?" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2023" PostTypeId="2" ParentId="2022" CreationDate="2012-04-29T07:22:50.363" Score="11" Body="&lt;p&gt;Unfortunately it is not necessary to invoke group selection to answer this question.  This is one of the reasons that Dawkins likes this discussion so much - he does not believe in group selection and so the discussion in SG does not invoke group selection.  ESSs are described in the book as the product of direct competition or interaction between genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ESSs in this case, can be described in terms of game theory.  In the famous Prisoner's Dilemma experiment, Grudger is similar to &lt;a href=&quot;http://en.wikipedia.org/wiki/Tit_for_tat&quot; rel=&quot;nofollow&quot;&gt;tit for tat&lt;/a&gt;, which 'won' the competition in the original Axelrod contest.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To see how this works you make a simple win/loss game matrix:  &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;     G        NG&#xA;G    win 1    win 3&#xA;NG   lose 3   lose 1&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;if you are groomed you win 1, if you are groomed, but you don't have to groom - even better win 3 (say)&#xA;If you groom but are not groomed, lose 3&#xA;If neither of you are groomed, you both lose 1&lt;/p&gt;&#xA;&#xA;&lt;p&gt;one might argue the exact proportions, but the point is that getting some thing for nothing is better than reciprocating, and getting nothing for your efforts and time are a loss, because you could have been getting groomed by someone else. As you can see cheaters end up in the top row all the time.  grudgers end up along the diagonal, and once in a while in the lower left, Suckers get stuck in the lower left a lot whenever there is a cheater around. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;now run this encounter over and over.  A behavior which scores negative the more times you run is not stable - they are going to disappear from the population, at least if this disadvantage is real&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has more than one stable outcomes in populations, a population that is full of Grudgers will all groom each other as before you know everyone, you assume they will reciprocate.  Everyone wins!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any invading Cheaters will quickly be at a disadvantage, in that they will not be groomed more than N times where N is the number of grudgers in the community.  Note that there is an equilibrium here - the Cheaters may exist in a small number - when N is large enough for a cheater to get enough grooming to make a 'living'.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suckers can also exist within a population of grudgers, but a population of Suckers where Cheaters show up are quickly sucked dry by the cheaters over several generations where you tally up 'points' and give more, healthier offspring to high scorers.  They are not ESS stable.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cheaters are also stable - nobody ever wins, but they don't lose big either and any invading grudgers can't get groomed.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-05-09T23:57:20.833" LastActivityDate="2012-05-09T23:57:20.833" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="2024" PostTypeId="1" AcceptedAnswerId="2029" CreationDate="2012-04-29T17:59:40.810" Score="7" ViewCount="60" Body="&lt;p&gt;Analyzing a genome, for a generic gene, which functional annotations (e.g from Gene Ontology) can help understanding its meaning/function or, at least, provide helpful informations?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Annotations of that gene&lt;/li&gt;&#xA;&lt;li&gt;Annotations of orthologous genes (?)&lt;/li&gt;&#xA;&lt;li&gt;Annotations of paralogous genes (?)&lt;/li&gt;&#xA;&lt;li&gt;Co-expressed genes (given a biological condition) (?)&lt;/li&gt;&#xA;&lt;li&gt;What else?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="781" LastActivityDate="2012-04-30T12:50:09.540" Title="Which functional annotations could be useful?" Tags="&lt;genomics&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2025" PostTypeId="1" AcceptedAnswerId="2722" CreationDate="2012-04-30T05:42:16.193" Score="8" ViewCount="997" Body="&lt;p&gt;Basically, I want to know if it would be humanely possible to sleep one day, skip the next, sleep, skip, sleep, skip, etc, with a 8 hour sleep time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you need any extra information, let me know.&lt;/p&gt;&#xA;" OwnerUserId="808" LastEditorUserId="535" LastEditDate="2012-04-30T12:51:05.563" LastActivityDate="2012-06-22T00:39:24.557" Title="Is it possible to live without health problems sleeping one day and not the other?" Tags="&lt;sleep&gt;&lt;circadian-rhythms&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2027" PostTypeId="1" AcceptedAnswerId="2036" CreationDate="2012-04-30T10:47:21.767" Score="7" ViewCount="142" Body="&lt;p&gt;Is there an easy, inexpensive, not too labor intensive way to normalise mRNA samples so that even though one loses information of gene expression levels, each of the transcripts in the transcriptome is equally represented in the sample for sequencing? This is to say, one has a uniform distribution of transcripts, so that the lowly-expressed transcripts still have a good chance of being sequenced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have seen a few papers mentioning protocols for mRNA normalization, but I can't tell if any of them are practical in real life wet lab situations.&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="6" LastEditDate="2012-05-01T08:20:05.887" LastActivityDate="2012-05-01T08:20:05.887" Title="How can I normalize mRNA samples for sequencing?" Tags="&lt;mrna&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2028" PostTypeId="1" AcceptedAnswerId="2032" CreationDate="2012-04-30T12:00:36.483" Score="6" ViewCount="1242" Body="&lt;p&gt;I'm just about to start working on a TOPO cloning after I couldn't get it to work with standard restriction/ligation. Does anyone have any tips for TOPO cloning?&lt;/p&gt;&#xA;" OwnerUserId="798" LastActivityDate="2012-04-30T23:14:28.073" Title="Does anyone have any TOPO directional cloning tips?" Tags="&lt;molecular-biology&gt;&lt;cloning&gt;" AnswerCount="1" CommentCount="9" ClosedDate="2012-05-01T08:21:49.613" ContentLicense="CC BY-SA 3.0" />
  <row Id="2029" PostTypeId="2" ParentId="2024" CreationDate="2012-04-30T12:50:09.540" Score="4" Body="&lt;ul&gt;&#xA;&lt;li&gt;I'd add genetic effects of the gene and its orthologs in that own&#xA;host. Knockouts and overexpression are powerful in uncovering&#xA;function.  &lt;/li&gt;&#xA;&lt;li&gt;In terms of baseline or normal expression, I would add    tissue,&#xA;developmental or differentiation time points, and conditions which stimulate or repress expression.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-04-30T12:50:09.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2030" PostTypeId="2" ParentId="2025" CreationDate="2012-04-30T12:53:48.100" Score="3" Body="&lt;p&gt;I'm not aware of any study testing this hypothesis. I would surmise that adverse health effects are likely because the circadian clock operates on a 24-hour time frame, and because lack of sleep for ~40 hours every second day will alter hormone, cytokine and other measures to levels not normally seen in 8-hour sleep/16-hour wake cycle.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="810" LastEditDate="2012-04-30T14:06:00.743" LastActivityDate="2012-04-30T14:06:00.743" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2031" PostTypeId="1" CreationDate="2012-04-30T17:47:02.477" Score="6" ViewCount="366" Body="&lt;p&gt;So heavier people generally have more blood than lighter people (this is why heavier people generally need to take higher doses of medication for the same effect of medication). They also have more blood to draw from. But this fails to differentiate between muscle mass and fat mass.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So here's my question: Is the net angiogenesis per gram of muscle more or less than the net angiogenesis per gram of fat?&lt;/p&gt;&#xA;" OwnerUserId="103" LastActivityDate="2013-06-09T11:10:02.610" Title="Does muscle growth trigger angiogenesis?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2032" PostTypeId="2" ParentId="2028" CreationDate="2012-04-30T21:10:55.473" Score="5" Body="&lt;p&gt;I have lots of experience with the TOPO TA kit which is very similar to the kit your using. Here's a link to the TOPO Directional cloning &lt;a href=&quot;http://www.invitrogen.com/site/us/en/home/brands/Product-Brand/topo/Directional-TOPO-cloning.reg.mx.html&quot; rel=&quot;nofollow&quot;&gt;product page&lt;/a&gt; which shows a schematic of the enzymatic ligation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From your comments, you said &lt;em&gt;you have doubly-digested the PCR product&lt;/em&gt;. &lt;strong&gt;This is likely your point of failure&lt;/strong&gt; unless you are absolutely confident that your enzymes work at blunt ended DNA (which I can almost guarantee does not work). Restriction digestion of PCR products will only work if there are at least a few bases on either side of the recognition site so that the restriction enzyme is able to &quot;grab on&quot; to the DNA. What you are mixing instead, is blunt-ended PCR product DNA + cohesive-ended vector. This will not work under any circumstances as is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;There is a simple solution.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Add 3'-A overhangs to your PCR product directly. The back of the TOPO manual tells you how to do this as well as many other sources. Ligate this using your TOPO kit to produce a shuttle vector that you can then doubly digest your insert out and gel purify it. Then you may ligate this purified, digested DNA with your previously digested destination vector.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note&lt;/strong&gt; that in my hands and in others in our lab, topoisomerase is unstable and has a short half-life. It is especially sensitive to temperature changes (warming from -20&amp;deg;C to 4&amp;deg;C) which you wouldn't expect since it is designed to work at room temperature. The vector is not affected, but without a working topoisomerase, the ligation step does not occur and the DNA does not transform.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;As an aside:&lt;/strong&gt; If you plan on doing more cloning in the future and need to replace the kit, I would recommend getting the basic TOPO TA cloning kit, clone your PCR product (with 3'-A overhangs) into the vector, transform, pick white/light blue colonies for screening then cut out from the TOPO vector (the shuttle vector) for downstream applications. The fact that it is directionally cloned or not into the TOPO vector is of no consequence unless it also happens to be your destination vector.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2012-04-30T23:14:28.073" LastActivityDate="2012-04-30T23:14:28.073" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2033" PostTypeId="1" CreationDate="2012-04-30T22:40:01.800" Score="8" ViewCount="3688" Body="&lt;p&gt;Terrific Broth will result in a greater density of cells compared to LB but I have certainly seen it isn't as effective for the protein production of certain proteins compared to LB or defined media. I was curious what other limits and constraints exist with TB.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Migrated and derived from Quora &lt;a href=&quot;http://www.quora.com/Under-what-circumstances-and-why-is-terrific-broth-preferred-to-LB-broth-for-E-coli-growth&quot;&gt;http://www.quora.com/Under-what-circumstances-and-why-is-terrific-broth-preferred-to-LB-broth-for-E-coli-growth&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2013-03-28T15:16:43.373" Title="Under what circumstances and why is terrific broth preferred to LB broth for E.coli growth?" Tags="&lt;growth-media&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2034" PostTypeId="2" ParentId="1836" CreationDate="2012-04-30T22:59:13.227" Score="10" Body="&lt;p&gt;Extending Konrad Rudolph's answer, research has been conducted into reconstructing the phylogenetic tree via protein sequence data of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Tyrannosaurus&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;T. rex&lt;/em&gt;&lt;/a&gt; (one of the latest living dinosaurs):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;C. L. Organ et al, &lt;a href=&quot;http://www.sciencemag.org/content/320/5875/499.short&quot; rel=&quot;noreferrer&quot;&gt;Molecular Phylogenetics of Mastodon and &lt;em&gt;Tyrannosaurus rex&lt;/em&gt;&lt;/a&gt;, Science 320 (2008), p. 499.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They use a variety of standard methods for the phylogenetic analysis.  The real challenge was collecting protein sequence data for the &lt;em&gt;T. rex&lt;/em&gt; (which has been extinct for ~65 million years).  They succeeded in collecting and sequencing collagen α1(I) from Mastodon and &lt;em&gt;T. rex&lt;/em&gt;, and compared it to the same protein in extant species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They write:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for &lt;em&gt;T. rex&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="203" LastEditorUserId="107" LastEditDate="2014-04-12T13:00:32.930" LastActivityDate="2014-04-12T13:00:32.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2035" PostTypeId="2" ParentId="2022" CreationDate="2012-04-30T23:07:19.800" Score="7" Body="&lt;p&gt;In an infinite, well mixed population with single pairwise encounters, Grudger is indeed not an ESS.  In fact, as you correctly note, in such a model the Grudger and Sucker strategies are indistiguishable, as the probability of anyone encountering the same individual twice is zero.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To make it possible for the Grudger strategy to survive against invasion by Cheaters, we must somehow extend the model to allow pairs of individuals to meet more than once.  Some ways to achieve this include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Finite population size:&lt;/strong&gt; if there are &lt;em&gt;n&lt;/em&gt; individuals and they each participate on average in &lt;em&gt;m&lt;/em&gt; encounters during their lifetime (or during the average time for which their memory persists), then each of them will encounter every other individual &lt;em&gt;m&lt;/em&gt; / (&lt;em&gt;n&lt;/em&gt;&amp;minus;1) times on average.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Viscous population:&lt;/strong&gt; this is a general term for populations that are not well mixed.  For example, if individuals live on a spatially extensive landscape, have limited movement rates and interact only with nearby individuals, then two individuals that meet once have a higher probability of meeting again due to spatial proximity.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Iterated encounters:&lt;/strong&gt; in these types of models, pairs of individuals are assumed to interact with each others some (fixed or random) number of times before parting and finding new partners to interact with.  In this way, repeat encounters can be included even in infinite, well mixed population models.  While this may be a reasonable approximation in some cases (e.g. for models of spousal cooperation in serially monogamous species), frankly the main reason for studying such models seems to be that they're mathematically simpler than finite or viscous populations.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Not entirely coincidentally, many of these mechanisms can also permit the survival of pure Sucker or altruist strategies against invasion by Cheaters through group and/or kin selection (or more general forms of assortment).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ps. Even with these mechanisms, Grudger will never be a &lt;em&gt;strict&lt;/em&gt; ESS anyway, since in any population consisting of only Grudgers and Suckers both have the same payoff.&lt;/p&gt;&#xA;" OwnerUserId="239" LastActivityDate="2012-04-30T23:07:19.800" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2036" PostTypeId="2" ParentId="2027" CreationDate="2012-05-01T08:11:31.013" Score="4" Body="&lt;p&gt;I found the link to a commercial product by Evrogen here:&#xA;&lt;a href=&quot;http://www.evrogen.com/technologies/normalization.shtml&quot; rel=&quot;nofollow&quot;&gt;http://www.evrogen.com/technologies/normalization.shtml&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They claim their method is compatible with nextgen sequencing platforms:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;cDNA normalization using duplex-specific nuclease (DSN) is a highly&#xA;  efficient approach that can be applied for normalization of&#xA;  full-length-enriched cDNA (Zhulidov et al., 2004; Zhulidov et al.,&#xA;  2005). The resulting cDNA contains equalized abundance of different&#xA;  transcripts and can be used for construction of cDNA libraries and for&#xA;  direct sequencing, including high-throughput sequencing on the next&#xA;  generation sequencing platforms (Roche/454, ABI/SOLiD or&#xA;  Illumina/Solexa).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And the most up-to-date reference seems to be this Curr Protoc Mol Biol. paper by Bogdanova et al.:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20373503&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/20373503&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2012-05-01T08:11:31.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2037" PostTypeId="1" CreationDate="2012-05-01T08:13:14.833" Score="2" ViewCount="148" Body="&lt;p&gt;I found the link to a commercial product by Evrogen to normalise cDNA samples for gene discovery projects here:&lt;br&gt;&#xA;&lt;a href=&quot;http://www.evrogen.com/technologies/normalization.shtml&quot; rel=&quot;nofollow&quot;&gt;http://www.evrogen.com/technologies/normalization.shtml&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most up-to-date reference seems to be this Curr Protoc Mol Biol. paper by Bogdanova et al.:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20373503&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/20373503&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They claim their method is compatible with nextgen sequencing platforms:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;cDNA normalization using duplex-specific nuclease (DSN) is a highly&#xA;  efficient approach that can be applied for normalization of&#xA;  full-length-enriched cDNA (Zhulidov et al., 2004; Zhulidov et al.,&#xA;  2005). The resulting cDNA contains equalized abundance of different&#xA;  transcripts and can be used for construction of cDNA libraries and for&#xA;  direct sequencing, including high-throughput sequencing on the next&#xA;  generation sequencing platforms (Roche/454, ABI/SOLiD or&#xA;  Illumina/Solexa).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Has anybody successfully used it for next-gen gene discovery projects?&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2012-05-01T08:13:14.833" Title="Has anybody used Evrogen's DSN-normalization protocol for cDNA normalization?" Tags="&lt;protocol&gt;&lt;mrna&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2012-08-27T21:37:20.630" ContentLicense="CC BY-SA 3.0" />
  <row Id="2038" PostTypeId="2" ParentId="1955" CreationDate="2012-05-01T09:03:33.980" Score="6" Body="&lt;p&gt;Linkage disequilibrium (LD) occurs when there is a non-random association or correlation between genotypes. Note I used the word correlation; this is a quantitative trait.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some genotypes may well correlate perfectly (R=1), i.e. they are always inherited together. Others may not be in 'perfect' linkage (e.g. R=0.9), but are still considered to be in LD because there is a strong correlation between the genotypes (I think 0.8 is generally seen in published papers as the 'cut-off').&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The correlation coefficient is derived from the D' value - this (simply) denotes the observed vs. expected frequencies of the genotypes (whether they are in linkage or not). Therefore either value can be used, but I think it is more common (and more interpretable) to express the correlation coefficient (or to be more precise, the coefficient of determination, R^2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you'd like an example: I might be interested to know if any SNPs are in LD with rs10757278 (located on 9p21, associated with heart disease). Using &lt;a href=&quot;http://www.broadinstitute.org/mpg/snap/ldsearch.php&quot;&gt;SNAP&lt;/a&gt; (by the BROAD) I can input my search, choose my options (e.g. use 1000 genomes data, and an R^2 cut-off of 0.8) and search. ~5 SNPs are found to be in 'perfect' LD (R^2=1), but a further ~40 are still considered to be in linkage with the input-SNP because their R^2 values are above 0.8.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in summary, both statements can be used correctly, but it is always more informative to state the degree of linkage (otherwise it might be assumed they are in perfect correlation).&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-05-01T13:35:53.760" LastActivityDate="2012-05-01T13:35:53.760" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2039" PostTypeId="1" AcceptedAnswerId="2040" CreationDate="2012-05-01T11:58:08.717" Score="13" ViewCount="21219" Body="&lt;p&gt;I am aware that circular DNA can be both relaxed and super coiled. However when running an agarose gel of the circular plasmid along with singly digested plasmid with BamHI and HindIII, I see 1 band for the linearized plasmid (lanes 2-5) (as expected) but 5 bands for the circular plasmid (lanes 6 and 7).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are these various conformations?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FTKGw.jpg&quot; alt=&quot;1% agarose gel, 1 and 2 indicate plasmid from prep&amp;#39;d from 2 colonies and are essentially replicates. Both plasmid from 1 and 2 was digested singly with BamHI and HindIII (apologies for incorrect label &amp;quot;BamH&amp;quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="798" LastActivityDate="2013-01-26T19:11:37.450" Title="How many agarose gel bands are typical for circularised DNA" Tags="&lt;dna&gt;&lt;gel-electrophoresis&gt;&lt;plasmids&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2040" PostTypeId="2" ParentId="2039" CreationDate="2012-05-01T13:46:04.207" Score="7" Body="&lt;p&gt;I don't have hands on it, but I will not be surprised if supercoiled DNA migrates at different distances according to some &lt;strong&gt;inner topological conformation&lt;/strong&gt; (i.e., more or less coiled AND/OR more or less nicked). Similarly, this picture highlights &gt;8 conformations. What is run in the gel is circularized phage DNA with some degree of knotting due to the circularization (phage DNA is otherwise linear).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pGZgg.gif&quot; alt=&quot;knotted DNA mobility on gel electrophoresis&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure from: Arsuaga et al. 2005, PNAS 102 (26) 9165-9169 (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1166588/&quot; rel=&quot;nofollow noreferrer&quot;&gt;free on PubMed Central&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Another theoretical possibility&lt;/strong&gt; is that two or more plasmids of different sizes were grown in the same maxiprep because of some contamination. But in this case, you will spot the problem also in the digestion, so it does not seem to be your case.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-05-01T13:46:04.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2041" PostTypeId="2" ParentId="1367" CreationDate="2012-05-01T14:42:50.170" Score="2" Body="&lt;p&gt;To clarify; administration of rapamycin (a drug) to lab organisms (including mice [1]) extends lifespan. Similarly, restricting the intake of nutrients to the &lt;em&gt;minimum without causing malnutrition&lt;/em&gt; also extends lifespan in lab animals (including primates [2]).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rapamycin inhibits the mTOR pathway (mammalian Target Of Rapamycin) - specifically mTORC1 (Complex 1) - which influences protein synthesis, autophagy and inflammation (among others). Upstream factors of mTOR include nutrient availability and insulin signaling (see &quot;Deconvoluting mTOR biology&quot; for good review [3]).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has been hypothesized that the lifespan-extending effects of caloric restriction (CR) are mediated by mTOR (one can see why - mTOR is affected by nutrient availability). In fact it may depend on the method of CR;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Greer &lt;em&gt;et al&lt;/em&gt; [4] report that different methods of CR in &lt;em&gt;C.elegans&lt;/em&gt;, for instance feeding them a diluted food source, or conversely feeding them on alternate days, do not necessarily require the same genetic pathways. Not only this but CR combined with a genetic mutant (&lt;em&gt;eat-2&lt;/em&gt;) have additive lifespan-enhancing effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So whilst the evidence is not concrete, and I look forward to other studies in mammals similar to the one by Greer &lt;em&gt;et al&lt;/em&gt;, it looks as though rapamycin and CR have similar but not exactly the same effects on lifespan; rapamycin specifically inhibits an individual pathway which is involved in many processes, and some of its effects are not necessarily desirable (e.g. rapamycin inhibits the immune system [5]). On the other hand, CR (most of the different types) seems to be &lt;em&gt;mediated&lt;/em&gt; by mTOR - this difference is critical: mTOR is not necessarily inhibited by CR, it is just required for its effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore combining rapamycin and CR is unlikely to have an additive effect as rapamycin may override any influence CR has on mTOR signaling, but I have not seen a study in which this has been tried. Combing different methods of CR (or developing drugs to do just that) may well have additive lifespan-enhancing effects.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Harrison DE, Strong R, Sharp ZD, et al. Rapamycin fed late in life extends lifespan in genetically heterogeneous mice. Nature. 2009;460(7253):392-5.&lt;/li&gt;&#xA;&lt;li&gt;Colman RJ, Anderson RM, Johnson SC, et al. Caloric restriction delays disease onset and mortality in rhesus monkeys. Science (New York, N.Y.). 2009;325(5937):201-4.&lt;/li&gt;&#xA;&lt;li&gt;Weber JD, Gutmann DH. Deconvoluting mTOR biology. Cell cycle (Georgetown, Tex.). 2012;11(2):236-48.&lt;/li&gt;&#xA;&lt;li&gt;Greer EL, Brunet A. Different dietary restriction regimens extend lifespan by both independent and overlapping genetic pathways in C. elegans. Aging cell. 2009;8(2):113-27.&lt;/li&gt;&#xA;&lt;li&gt;Thomson AW, Turnquist HR, Raimondi G. Immunoregulatory functions of mTOR inhibition. Nature reviews. Immunology. 2009;9(5):324-37.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-05-02T14:11:17.120" LastActivityDate="2012-05-02T14:11:17.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2042" PostTypeId="2" ParentId="2039" CreationDate="2012-05-01T15:08:09.640" Score="3" Body="&lt;p&gt;Gianpaolo is correct that you are seeing the different conformations of circular DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Growing plasmids up in bacteria produces 3 main forms: relaxed, coiled and super-coiled.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Relaxed tends to run a little higher than the expected size because it cannot travel as efficiently through the agarase;&lt;/li&gt;&#xA;&lt;li&gt;Coiled migrates a little farther than the expected size because it is a little more compact and therefore migrates more easil;&lt;/li&gt;&#xA;&lt;li&gt;Super-coiled, the most compact, migrates much farther than the expected size.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I would conclude from your picture the following:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;That the HindIII cuts are efficient, and have linearized nearly all of your plasmid.&lt;/li&gt;&#xA;&lt;li&gt;BamHI is cutting, but not as efficiently as HindIII for (presumably) the same amount of time. This should be digested longer if it's really important to digest with just BamHI, but for diagnostic purposes, it is fine. I say this because of the faint banding seen at ~4.5 and ~3.7 kb, which are likely your coiled and super-coiled plasmid DNA, respectively.&lt;/li&gt;&#xA;&lt;li&gt;From your linear digests, the plasmid is 6 kb.&lt;/li&gt;&#xA;&lt;li&gt;Looking at undigested control plasmid, your method of mini prep is not clean and looks to be contaminated, possibly by genomic DNA. Also, you see hints of streaking in the single digest lanes. Was this done using trizol?&lt;/li&gt;&#xA;&lt;li&gt;I would expect the band at 10 kb to possibly be the relaxed form of the plasmid, with much of the plasmid DNA existing in a super-coiled conformation.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;If these are important samples, I would consider purifying them using cleaner methods, for example using a column.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-05-01T15:08:09.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2044" PostTypeId="5" CreationDate="2012-05-01T20:00:41.357" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-01T20:00:41.357" LastActivityDate="2012-05-01T20:00:41.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2045" PostTypeId="4" CreationDate="2012-05-01T20:00:41.357" Score="0" Body="A method for analyzing or purifying samples. Molecules are separated by their relative weight, charge, or stereochemistry, which affect their speed of movement through a gel." OwnerUserId="806" LastEditorUserId="4101" LastEditDate="2013-10-31T14:05:50.920" LastActivityDate="2013-10-31T14:05:50.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2046" PostTypeId="5" CreationDate="2012-05-01T20:05:03.487" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-01T20:05:03.487" LastActivityDate="2012-05-01T20:05:03.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2047" PostTypeId="4" CreationDate="2012-05-01T20:05:03.487" Score="0" Body="Protein Data Bank, a publically available database of molecular structures of proteins" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-05-01T20:31:08.167" LastActivityDate="2012-05-01T20:31:08.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2049" PostTypeId="1" CreationDate="2012-05-01T21:42:33.553" Score="10" ViewCount="679" Body="&lt;p&gt;I am trying to determine a list of frequency ranges into which marine mammal vocalizations fall. &#xA;Ideally, I would like a list showing where the most popular marine mammal vocalizations fall, followed by the species name. That being said, I only &lt;em&gt;really&lt;/em&gt; care about frequencies above 20 kHz, should they exist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example: (Numbers fabricated)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Orcas       : 30-40 kHz&lt;/li&gt;&#xA;&lt;li&gt;Dolphins    : 100 kHz&lt;/li&gt;&#xA;&lt;li&gt;Blue Whales : 60-88 kHz&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if the list is 'quick and dirty', thats ok. The list will essentially point me to which species' songs/sounds I need to study.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some additional context, this &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_whale_vocalizations&quot; rel=&quot;noreferrer&quot;&gt;wikipedia&lt;/a&gt; link as well as &lt;a href=&quot;http://en.wikipedia.org/wiki/Whale_song#Toothed_Whale_Sound_Levels&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; one have some nice sound files of many marine mammals' songs/sounds. I am trying to avoid having to download each one and analyze their spectral content. (I could, but would rather not). &lt;/p&gt;&#xA;" OwnerUserId="816" LastEditorUserId="810" LastEditDate="2012-05-02T15:29:55.033" LastActivityDate="2018-12-11T14:03:17.890" Title="What are the frequency ranges of most marine mammal vocalizations?" Tags="&lt;zoology&gt;&lt;marine-biology&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2050" PostTypeId="1" AcceptedAnswerId="19623" CreationDate="2012-05-02T01:59:42.173" Score="17" ViewCount="4065" Body="&lt;p&gt;I have heard that there is no limit on the growth of trees, but then why do some trees, such as boxelders and poplars, tend to live shorter than redwoods, for example? Some advertisements for improved lombardy poplars state that their trees have an extended life span, up to 75 years? The trees with shorter life spans seem to weaken at a certain age, and then contract diseases more easily. &lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2014-07-09T00:08:10.847" LastActivityDate="2014-07-13T08:08:25.300" Title="Why do some trees have a life span, while some don't?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;senescence&gt;&lt;life-history&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2051" PostTypeId="1" AcceptedAnswerId="2052" CreationDate="2012-05-02T04:29:35.253" Score="25" ViewCount="156914" Body="&lt;p&gt;I was wondering what exactly a coupled reaction is and why cells couple them.  I read the wikipedia article as well as several others, such as &lt;a href=&quot;http://www.life.illinois.edu/crofts/bioph354/coupled.html&quot;&gt;life.illinois.edu&lt;/a&gt; but I still don't get it.  Could someone explain it to me?&lt;/p&gt;&#xA;" OwnerUserId="817" LastEditorUserId="43" LastEditDate="2012-05-02T15:20:15.990" LastActivityDate="2017-03-31T17:25:14.947" Title="What is a coupled reaction and why do cells couple reactions?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;thermodynamics&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="2052" PostTypeId="2" ParentId="2051" CreationDate="2012-05-02T06:15:43.267" Score="21" Body="&lt;p&gt;It's pretty simple. A reaction occurs that releases energy (like ATP losing a phosphate to become ADP + Pi). If this is uncoupled, the energy will merely turn into heat. If it is coupled, then it can be used to fuel some other process. For instance, if you couple the ATP -&gt; ADP reaction to a certain protein, the energy can be used to modify the shape of that protein.&lt;/p&gt;&#xA;" OwnerUserId="510" LastActivityDate="2012-05-02T06:15:43.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2053" PostTypeId="2" ParentId="2049" CreationDate="2012-05-02T09:07:21.507" Score="6" Body="&lt;p&gt;Dolphins can &lt;em&gt;hear&lt;/em&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/Hearing_range#Marine_mammals&quot;&gt;above 110 kHz&lt;/a&gt;, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Dolphin#Vocalizations&quot;&gt;produce vocalizations in this range&lt;/a&gt;.  Clicking has evolved in &lt;a href=&quot;http://en.wikipedia.org/wiki/Animal_echolocation#Toothed_whales&quot;&gt;proposes and sperm whales&lt;/a&gt; and is predominantly above 100 kHz (to avoid being heard by killer whales). It's a bit subjective, of course: if you do a frequency decomposition of a click, it will always have some component with very high frequency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That dolphins have evolved into such an niche highlights a problem with asking about &quot;most&quot; marine mammals, though: evolution often favors diversification between species, so you'd expect very different vocal ranges, to the point that many species have no overlap at all. (for the sake of illustration, ask yourself where &lt;em&gt;most&lt;/em&gt; people live)&lt;/p&gt;&#xA;" OwnerUserId="810" LastEditorUserId="810" LastEditDate="2012-05-02T09:17:01.933" LastActivityDate="2012-05-02T09:17:01.933" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2054" PostTypeId="1" CreationDate="2012-05-02T10:38:31.050" Score="5" ViewCount="363" Body="&lt;p&gt;It is known that zinc is an essential mineral that the body cannot store.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are other minerals, especially metals, that the body cannot store?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(other than water-soluble vitamins such as vitamin B and C)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sincere thanks.&lt;/p&gt;&#xA;" OwnerUserId="801" LastActivityDate="2012-07-10T17:06:18.087" Title="What are minerals (other than zinc) that the human body cannot store" Tags="&lt;nutrition&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2055" PostTypeId="1" AcceptedAnswerId="2923" CreationDate="2012-05-02T12:36:26.863" Score="29" ViewCount="1761" Body="&lt;p&gt;Most animals age via at least two mechinisms: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;at a &quot;macroscopic&quot; level, basically wear and tear to the point where (on evolutionary time scales) it's more genetically advantageous to optimize for reproduction rather than longer lifespans. &lt;/li&gt;&#xA;&lt;li&gt;at a microscopic level, e.g. shrinking of telomeres. This prevents cell division after a certain point (good to prevent cancer and other growths, bad for regeneration). &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Do plants also age microscopically? If so, how are we able to clone (in the horticultural sense) plants?  &lt;/p&gt;&#xA;" OwnerUserId="810" LastEditorUserId="810" LastEditDate="2014-06-16T09:12:07.687" LastActivityDate="2014-06-16T09:12:07.687" Title="Do trees age on a microscopic level?" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;senescence&gt;&lt;telomere&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2056" PostTypeId="1" AcceptedAnswerId="2069" CreationDate="2012-05-02T13:16:57.530" Score="22" ViewCount="31824" Body="&lt;p&gt;I am totally confused whether ask this question to physics or biology stackexchange.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I downloaded a mobile application which claims to repel mosquitoes. This application basically produces sound from 16kHz to 22kHz (I doubt that it even produces more than 20kHz because we can't hear more than 20kHz naturally).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I totally doubt this application. Do mosquitoes go away in higher frequency of sound?&lt;/p&gt;&#xA;" OwnerUserId="818" LastEditorUserId="338" LastEditDate="2012-05-03T01:21:02.043" LastActivityDate="2018-12-28T16:38:24.877" Title="Are mosquitoes repelled by high frequency sound?" Tags="&lt;entomology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2057" PostTypeId="2" ParentId="2049" CreationDate="2012-05-02T15:15:01.690" Score="9" Body="&lt;p&gt;&lt;a href=&quot;http://www.fathom.com/course/10701056/session3.html&quot;&gt;Here&lt;/a&gt; there are spectrograms from &lt;em&gt;Bottlenose dolphins&lt;/em&gt; (Tursiops truncatus), &lt;em&gt;Killer whales&lt;/em&gt; (Orcinus orca) and &lt;em&gt;False killer whales&lt;/em&gt; (Pseudorca crassidens).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.fathom.com/course/10701056/session4.html&quot;&gt;Here&lt;/a&gt; there are spectrograms for &lt;em&gt;Humpback whale&lt;/em&gt; (Megaptera novaeangliae) and from &lt;em&gt;Sperm whales&lt;/em&gt; (Physeter catodon or Physeter marcocephalus)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pmel.noaa.gov/vents/acoustics/specs_all.html&quot;&gt;Here&lt;/a&gt; there are spectrograms from &lt;em&gt;Blue whale&lt;/em&gt;, &lt;em&gt;Fin whale&lt;/em&gt; and &lt;em&gt;Minke whale&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some other google search for &quot;spectrogram + your preferred cetaceans&quot; should make your list. Enjoy.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-05-02T15:15:01.690" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2058" PostTypeId="5" CreationDate="2012-05-02T15:18:45.733" Score="0" Body="&lt;p&gt;Marine biology (&lt;a href=&quot;http://en.wikipedia.org/wiki/Marine_biology&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;) is the scientific study of organisms in the ocean or other marine or brackish bodies of water. Marine biology classifies species based on the environment rather than on taxonomy. See also the article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Large_marine_ecosystem&quot; rel=&quot;nofollow&quot;&gt;Large Marine Ecosystem&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="4101" LastEditDate="2013-10-31T14:16:56.080" LastActivityDate="2013-10-31T14:16:56.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2059" PostTypeId="4" CreationDate="2012-05-02T15:18:45.733" Score="0" Body="The study of organisms that dwell in the ocean or brackish waters." OwnerUserId="57" LastEditorUserId="4101" LastEditDate="2013-10-31T14:16:56.080" LastActivityDate="2013-10-31T14:16:56.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2060" PostTypeId="2" ParentId="880" CreationDate="2012-05-02T16:03:57.503" Score="6" Body="&lt;p&gt;p16-INK4a is a part of a very important checkpoint mechanism. It's the &quot;bad guy&quot; in the context of aging because it induces senescence, and too much senescence leads to aging-related  tissue degradation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But senescence is important. It's one of the responses cells take when something goes wrong-- DNA damage, viral infection, telomere depletion, that sort of thing. Senescent cells have stopped proliferating. We have a word for cells that don't stop proliferating, and that word is &quot;cancer&quot;. So, p16-INK4a is a major tumor suppressor. A universal p16-INK4a knockout would have a much harder time shutting down the proliferation of cells that had undergone DNA damage, and would therefore be much more prone to cancer. You'd have very young-looking tissues filled with tumors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the headline question is why INK4a is not expressed in the heart or liver if it's so important. This is speculation on my part, but I think it's because those tissues are especially prone to being damaged by fibrosis, and a build-up of senescent cells would lead to increased fibrosis. Senescence is just one possible response to DNA damage, though. Another is apoptosis. If the senescence-induction pathways aren't active in heart and lung tissue, I'd expect the apoptosis-induction pathways to be pretty active. &lt;/p&gt;&#xA;" OwnerUserId="819" LastActivityDate="2012-05-02T16:03:57.503" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2061" PostTypeId="1" AcceptedAnswerId="2062" CreationDate="2011-05-26T12:55:00.923" Score="25" ViewCount="1899" Body="&lt;p&gt;Why does looking at bright light trigger sneezing in some people?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any recent studies that have found a cause for this &lt;a href=&quot;http://en.wikipedia.org/wiki/Photic_sneeze_reflex&quot;&gt;Photic sneeze reflex&lt;/a&gt;? The Wikipedia article only references studies pertaining to the effect, stating that the cause is unknown. The article also states that &quot;the condition affects 18–35% of the population&quot;, which seems to be quite a large percentage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What could have lead to the development and persistence of such a genetic trait in humans? Are there any evolutionary advantages to this?&lt;/p&gt;&#xA;" OwnerUserId="33678" OwnerDisplayName="luvieere" LastEditorUserId="5239" LastEditDate="2013-12-29T15:31:19.327" LastActivityDate="2019-04-12T08:48:17.827" Title="Why does looking at bright light trigger sneezing in some people?" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;reflexes&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2062" PostTypeId="2" ParentId="2061" CreationDate="2011-05-26T13:06:48.260" Score="20" Body="&lt;p&gt;You are talking about the &lt;a href=&quot;http://en.wikipedia.org/wiki/Photic_sneeze_reflex&quot;&gt;photic sneeze reflex&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanisms are not entirely understood, but it affects &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8108024&quot;&gt;18-35% of the population&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Wikipedia (although this passage is not sourced):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The probable cause is a congenital&#xA;  malfunction in nerve signals in the&#xA;  trigeminal nerve nuclei. The fifth&#xA;  cranial nerve, called the trigeminal&#xA;  nerve, is apparently responsible for&#xA;  sneezes. Research suggests that some&#xA;  people have an association between&#xA;  this nerve and the nerve that&#xA;  transmits visual impulses to the&#xA;  brain. Overstimulation of the optic&#xA;  nerve triggers the trigeminal nerve,&#xA;  and this causes the photic sneeze&#xA;  reflex.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And, it could  be advantageous:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;On the other hand, some people with&#xA;  the trait feel that it is&#xA;  advantageous. In the event that nasal&#xA;  discomfort occurs, but to an extent&#xA;  that is insufficient to induce a&#xA;  sneeze, intentionally seeking and&#xA;  finding a light source facilitates the&#xA;  sneezing process and is in turn a mode&#xA;  of relief.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also, anecdotally, as I too photosneeze, I can see an advantage: should the atmosphere become weaker in the future, and allow more light to enter than we are accustomed to, it would discourage looking directly at the sun.&lt;/p&gt;&#xA;" OwnerDisplayName="Thomas O" LastActivityDate="2011-05-26T13:13:20.393" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2063" PostTypeId="2" ParentId="1369" CreationDate="2012-05-02T16:22:50.630" Score="2" Body="&lt;p&gt;I can't rule it out, but it sounds a lot like trying to tune a piano with sledgehammer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neuronal LTP depends on protein translation, but so does absolutely everything else in the cell. Inhibiting protein synthesis at the ribosome will block the formation of all proteins, not just the ones responsible for LTP. Unless there's a link I don't know about between LTP and &lt;em&gt;total&lt;/em&gt; levels of protein translation, you're really going to want to look into inhibiting the production of proteins specifically responsible for LTP and not protein synthesis in general.&lt;/p&gt;&#xA;" OwnerUserId="819" LastActivityDate="2012-05-02T16:22:50.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2064" PostTypeId="1" CreationDate="2012-05-02T18:34:29.287" Score="6" ViewCount="1238" Body="&lt;p&gt;I am particularly interested in MC3T3-E1 cells (mouse fibroblasts), which are adherent cells. Are &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemidesmosome&quot;&gt;hemidesmosomes&lt;/a&gt; involved in anchoring the cells to the plastic dish? What (if any) other molecules are involved? What happens at the molecular level?&lt;/p&gt;&#xA;" OwnerUserId="146" LastActivityDate="2012-05-02T21:25:19.720" Title="How Do Adherent Cells In Culture Attach To A Plastic Dish?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2065" PostTypeId="1" AcceptedAnswerId="2094" CreationDate="2012-05-02T21:03:22.997" Score="12" ViewCount="995" Body="&lt;p&gt;Thinking about how complex the interactions between different types of immune system cells (T-helpers, T-Killers, Phagocytes, B-Cells etc.) are, it's fascinating how they all combine to get the desired effect.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I assume that they didn't all evolve simultaneously!  Is there any way to tell which immune cell developed first or any theories to that effect?  Perhaps that question is too specific, in which case was it humoral or cell mediated immunity that developed first?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;You may find &lt;a href=&quot;http://www.nature.com/nri/journal/v10/n1/full/nri2686.html&quot;&gt;this paper&lt;/a&gt; helpful - unfortunately I'm still months off a campus so can't access it.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2013-06-17T19:30:55.027" Title="In which order did the cells of the immune system evolve?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2066" PostTypeId="2" ParentId="2064" CreationDate="2012-05-02T21:25:19.720" Score="2" Body="&lt;p&gt;I doubt that hemidesmosomes are much involved in 3T3 adhesion, just because they are characteristic of epithelial cells and fibroblasts are mesenchymal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You're on the right track, though. It's going to be the same basic processes as adhesion to the extracellular matrix. The major factors will probably be &lt;a href=&quot;http://en.wikipedia.org/wiki/Integrins&quot; rel=&quot;nofollow&quot;&gt;integrins&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Focal_adhesion&quot; rel=&quot;nofollow&quot;&gt;focal adhesion assemblies.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You're also raising an important point for in vitro work, which is that adhesion to plastic is a very imperfect substitute for ECM, and this probably has implications for the behavior of the cells. If you're interested in ECM-dependent processes like migration, adhesion, and invasion, consider coating your plates with collagen or Matrigel.&lt;/p&gt;&#xA;" OwnerUserId="819" LastActivityDate="2012-05-02T21:25:19.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2067" PostTypeId="1" CreationDate="2012-05-02T22:30:51.017" Score="8" ViewCount="402" Body="&lt;p&gt;I'm looking to comparing different protocols for minipreps for plasmid DNA purification. What factors should I be looking at? A few things come to mind:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Cost&lt;/li&gt;&#xA;&lt;li&gt;Yield &lt;/li&gt;&#xA;&lt;li&gt;Time per step&lt;/li&gt;&#xA;&lt;li&gt;Replacement with other reagents&lt;/li&gt;&#xA;&lt;li&gt;Spin vs. vacuum&lt;/li&gt;&#xA;&lt;li&gt;Color and caps or lack thereof&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-05-07T21:10:43.740" LastActivityDate="2012-07-27T06:27:23.853" Title="What are key factors when evaluating and comparing miniprep columns?" Tags="&lt;lab-reagents&gt;&lt;minipreps&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2068" PostTypeId="1" AcceptedAnswerId="2070" CreationDate="2012-05-03T02:18:25.507" Score="16" ViewCount="3317" Body="&lt;p&gt;As indicated by &lt;a href=&quot;https://biology.stackexchange.com/questions/594/why-are-amino-acids-in-biology-homochiral&quot;&gt;this&lt;/a&gt; question, most of the amino acids in the human body have the L-chirality. As enzymes also have handedness, what happens to the D-amino acids that end up within the human body? Are they simply excreted? Are there enzymes (perhaps not in humans) that convert a D-amino acid to a L- one?&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2012-08-28T12:06:56.753" Title="What happens to dextrorotatory amino acids in humans?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;metabolism&gt;&lt;amino-acids&gt;&lt;chirality&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2069" PostTypeId="2" ParentId="2056" CreationDate="2012-05-03T02:44:14.967" Score="18" Body="&lt;p&gt;After seeing your question, I decided to do a bit of research on the topic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;First Source: &lt;a href=&quot;http://www.eurekalert.org/pub_releases/2007-04/jws-mrt041607.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;EurekAlert!&lt;/a&gt;&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;&lt;a href=&quot;http://www.eurekalert.org/pub_releases/2007-04/jws-mrt041607.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.eurekalert.org/pub_releases/2007-04/jws-mrt041607.php&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Mosquito repellents that emit high-pitched sounds don't prevent&#xA;  bites&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Some key-points from the webpage:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;hr&gt;A Cochrane Systematic Review of the use of electronic mosquito repellents (EMRs) failed to find any evidence that they work. &#xA;  &lt;hr&gt;&#xA;  To test these claims a team of Cochrane Researchers conducted a systematic review looking for trials conducted with EMRs. They located ten field trials that had been carried out in various parts of the world. None of these trials showed any evidence that EMRs work.&#xA;  &lt;hr&gt;&#xA;  All ten studies found that there was no difference in the number of mosquitoes found on the bare body parts of the human participants with or without an EMR&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h1&gt;Second Source: &lt;a href=&quot;http://en.wikipedia.org/wiki/Insect_repellent&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Insect_repellent&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Insect_repellent&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These electronic devices have been shown to have no effect as a mosquito repellent by studies done by the EPA and many universities.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h1&gt;Third Source: &lt;a href=&quot;http://www.cbc.ca/news/story/2007/04/18/mosquito-repellent.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;CBCnews&lt;/a&gt;&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;&lt;a href=&quot;http://www.cbc.ca/news/story/2007/04/18/mosquito-repellent.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.cbc.ca/news/story/2007/04/18/mosquito-repellent.html&lt;/a&gt;&#xA;Key points from the article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;There was no evidence in the field studies to support any repelling effects of EMRs, hence &gt;no evidence to support their promotion or use&quot;&#xA;             &#xA;  -Ahmadali Enayati, researcher&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is a major point as well:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The study also said that in 12 of the 15 experiments, the landing rates of mosquitoes on subjects was in fact higher than in control groups.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The article also points out that female mosquitoes can't hear very well- Which supports the idea that high-frequency repellents are ineffective; Much more than you probably think. Why? Well, it's pretty simple:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Female Mosquitoes are the only Gender that Bite&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Overall, when you consider the countless studies and research put in to the effects of high-frequency sounds on mosquitoes, it's pretty obvious that:&#xA;&lt;h1&gt;No.&lt;/h1&gt;&lt;h3&gt;High Frequency Sounds do &lt;strong&gt;NOT&lt;/strong&gt; repel mosquitoes&lt;/h3&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7iauB.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="820" LastEditorUserId="15950" LastEditDate="2018-12-28T16:38:24.877" LastActivityDate="2018-12-28T16:38:24.877" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="2070" PostTypeId="2" ParentId="2068" CreationDate="2012-05-03T02:51:44.170" Score="13" Body="&lt;p&gt;For the most part they are not used.  there are amino acid racemases, which interconvert L- and D- forms of some specific amino acids, which may be used in some particular biosynthetic or metabolic pathways.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular I'm thinking of firefly luciferase which uses D-Cysteine as a re-dox reagent to regenerate the luciferin substrate that the light - generating enzyme consumes.  &lt;a href=&quot;http://openwetware.org/images/9/93/Firefly_Luciferase_How_to.pdf&quot;&gt;see slide 4 here&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.genome.jp/kegg/pathway/map/map01054.html&quot;&gt;Nonribosomal peptide synthases&lt;/a&gt; often use D amino acids too.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't believe that d- amino acids are really incorporated into proteins though.   &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-03T02:51:44.170" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2073" PostTypeId="1" AcceptedAnswerId="39769" CreationDate="2012-05-03T05:43:42.327" Score="54" ViewCount="7807" Body="&lt;p&gt;I'd be tempted to call nipples in men vestigial, but that suggests they have no modern function. They &lt;em&gt;do&lt;/em&gt; have a function, of course, but only in women. So why do &lt;em&gt;men&lt;/em&gt; (and all male mammals) have them? &lt;/p&gt;&#xA;" OwnerUserId="810" LastEditorUserId="810" LastEditDate="2012-05-03T20:00:25.973" LastActivityDate="2020-01-13T06:29:23.703" Title="Why do men have nipples?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;genetics&gt;" AnswerCount="4" CommentCount="6" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="2074" PostTypeId="1" AcceptedAnswerId="2080" CreationDate="2012-05-03T05:54:03.670" Score="25" ViewCount="9963" Body="&lt;p&gt;I've noticed that when I'm out at night stars seem to vanish when I focus on them. I assume the reason is physiological and not astronomic. Why does this happen? I would expect that things would be &lt;em&gt;more&lt;/em&gt; clear when I focus on them. &lt;/p&gt;&#xA;" OwnerUserId="810" LastEditorUserId="810" LastEditDate="2012-05-03T19:59:48.720" LastActivityDate="2017-05-24T09:34:24.987" Title="Why do stars disappear when I look at them?" Tags="&lt;human-anatomy&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2075" PostTypeId="1" AcceptedAnswerId="3471" CreationDate="2012-05-03T06:05:57.120" Score="36" ViewCount="53143" Body="&lt;p&gt;A number of companies have started marketing LED lamps that can be switched to a red mode. The claim is that red light is less harmful to one's night vision. Given that our eyes are less sensitive to red light, though, I'm not convinced that that red light is any better than dim white light. So if &quot;equivalent&quot; luminosity is defined where it's equally easy to, say, read a book in both light types, is there some physiological reason that red light is better than the equivalent white light? &lt;/p&gt;&#xA;" OwnerUserId="810" LastEditorUserId="810" LastEditDate="2012-09-08T14:55:02.880" LastActivityDate="2019-10-19T18:11:35.097" Title="Does red light preserve your night vision?" Tags="&lt;human-anatomy&gt;&lt;vision&gt;" AnswerCount="7" CommentCount="0" FavoriteCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="2076" PostTypeId="1" AcceptedAnswerId="2078" CreationDate="2012-05-03T06:13:28.873" Score="21" ViewCount="3486" Body="&lt;p&gt;We can encode sound and images in radio waves and send them, but presumably there's some physiological reason that we can't easily make a picture or video of a smell. Could we realistically break smells down into &quot;primary scents&quot;, in analogy with &quot;primary colors&quot; and encode the information for easy reproduction? &lt;/p&gt;&#xA;" OwnerUserId="810" LastEditorUserId="69" LastEditDate="2012-05-03T17:58:29.670" LastActivityDate="2015-07-24T03:57:45.843" Title="Could we transmit smells electronically?" Tags="&lt;human-anatomy&gt;&lt;chemical-communication&gt;&lt;sensation&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2077" PostTypeId="1" CreationDate="2012-05-03T06:38:37.697" Score="17" ViewCount="12233" Body="&lt;p&gt;The human ear (for example) is sensitive to frequencies from 20Hz to 20kHz. Any sound beyond that limit would not be heard by us naturally.&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Will it harm us (effect our ability to hear) when we hear sound more than 20kHz continuously?&lt;/p&gt;&#xA;&lt;p&gt;Or...&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Will it harm when we hear a 19,999Hz sound (which is upper limit) continuously?&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="818" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-05-19T18:16:54.900" Title="Will humans and animals be harmed by frequencies outside their hearing range? " Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;human-ear&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2078" PostTypeId="2" ParentId="2076" CreationDate="2012-05-03T06:39:42.607" Score="15" Body="&lt;p&gt;There are only &lt;a href=&quot;http://en.wikipedia.org/wiki/Cone_cell&quot;&gt;three kinds&lt;/a&gt; of optical receptors in the eye, but more than &lt;a href=&quot;http://en.wikipedia.org/wiki/Olfactory_receptor&quot;&gt;900 kinds&lt;/a&gt; of olfactory receptors. Thus you can encode pictures with the three primary colors, but there is no small set of primary scents. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To transmit a smell via &quot;primary scents&quot;, you'd have to create an artificial nose that monitors the response of each of the olfactory receptors, and then at the other end release a chemical mixture that has the exact same response pattern. (You won't find a one-to-one mapping of chemical compound to receptor.)&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-05-03T06:39:42.607" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2079" PostTypeId="1" AcceptedAnswerId="2082" CreationDate="2012-05-03T06:41:50.517" Score="6" ViewCount="25049" Body="&lt;p&gt;For those who use Qiagen miniprep columns, they may be aware that the P3 buffer is the acetic acid step to neutralize cell lysis. They may also be aware that the Qiagen P3 buffer cannot be interchanged with the proprietary N3 buffer. It is also known that the N3 buffer is particularly unique since it primes the miniprep columns for binding. I was wondering about that priming step and what chemically primes the columns. Would it be appropriate to use QBT buffer to prime the miniprep columns?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2013-05-13T16:23:42.887" Title="What is special about the N3 buffer for Qiagen minipreps?" Tags="&lt;minipreps&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2080" PostTypeId="2" ParentId="2074" CreationDate="2012-05-03T06:48:05.007" Score="25" Body="&lt;p&gt;When there is little light, the color-detecting &lt;a href=&quot;http://en.wikipedia.org/wiki/Cone_cell&quot; rel=&quot;noreferrer&quot;&gt;cone cells&lt;/a&gt; are not sensitive enough, and all vision is done by &lt;a href=&quot;http://en.wikipedia.org/wiki/Rod_cell&quot; rel=&quot;noreferrer&quot;&gt;rod cells&lt;/a&gt;. Cone cells are concentrated in the center of the eye, whereas &lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/vision/rodcone.html&quot; rel=&quot;noreferrer&quot;&gt;rod cells are very rare in the center (image source)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/D6o6S.gif&quot; alt=&quot;Density of rod and cone cells&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you focus on the star, the light is projected close to the center of the retina, where it will hit few rod cells. Thus the star appears to vanish.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-05-03T06:48:05.007" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2081" PostTypeId="2" ParentId="2077" CreationDate="2012-05-03T09:23:48.657" Score="12" Body="&lt;p&gt;The only sensible answer to these questions is &quot;sometimes&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason: even a simple monotone must be described by both frequency and amplitude. Any frequency can cause harm with enough amplitude, and any frequency can be harmless when the amplitude is low enough. If you want to actually quantify the damage, you'll need something like an &lt;a href=&quot;http://en.wikipedia.org/wiki/Equal-loudness_contour&quot;&gt;equal-loudness&lt;/a&gt; curve, but for damage rather than loudness. As a proxy, you could use the pain threshold of the equal-loudness curve. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the second question, there is nothing magical about 20kHz: physical damage will always fall on a spectrum, there is no single frequency and/or amplitude at which damage begins. If you set an oscillator to constant amplitude and slowly turn up the frequency, you'll notice that the sound &lt;em&gt;slowly&lt;/em&gt; dies out &lt;em&gt;around&lt;/em&gt; 20kHz. The damage threshold will behave the same way. &lt;/p&gt;&#xA;" OwnerUserId="810" LastActivityDate="2012-05-03T09:23:48.657" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2082" PostTypeId="2" ParentId="2079" CreationDate="2012-05-03T10:24:56.763" Score="8" Body="&lt;p&gt;The &lt;a href=&quot;http://www.qiagen.com/literature/render.aspx?id=370&quot;&gt;Qiagen manual for the Miniprep Kit&lt;/a&gt; states that buffer N3 contains guanidine hydrochloride and acetic acid. The &lt;a href=&quot;http://www.qiagen.com/support/msds/de/buffer_n3_de5.pdf&quot;&gt;MSDS for buffer N3&lt;/a&gt; gives a bit more information:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Guanidinium hydrochloride 25-50%&lt;/li&gt;&#xA;&lt;li&gt;Acetic acid 10-25%&lt;/li&gt;&#xA;&lt;li&gt;pH 4.3&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Buffer P3 uses 3M potassium acetate, the potassium is usually important in plasmid preparations as potassium SDS is used to precipitate the proteins in solution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This information might be enough to create a buffer that should work with the silica-gel columns.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also found a &lt;a href=&quot;http://www.google.de/patents?hl=de&amp;amp;lr=&amp;amp;vid=USPAT5234809&amp;amp;id=PdsgAAAAEBAJ&amp;amp;oi=fnd&amp;amp;dq=silica%20nucleic%20acids&amp;amp;printsec=abstract#v=onepage&amp;amp;q&amp;amp;f=false&quot;&gt;patent about a method for isolating nucleic acids&lt;/a&gt; that states that silica particles can bind nucleic acids in the presence of chaotropic salts, so the guianidinium hydrochloride is probably the important difference in the N3 buffer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.google.com/patents/pdf/Chromatographic_purification_and_separat.pdf?id=UZEKAAAAEBAJ&amp;amp;output=pdf&amp;amp;sig=ACfU3U37uL8a--9XoP1768CYwKk8EgF70w&quot;&gt;patent for this method from Qiagen&lt;/a&gt; goes into even more detail, according to this the buffer composition  is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;N3&lt;/strong&gt;: 4.2M guanidinium hydrochloride, 0.9M potassium acetate, pH 4.8&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2012-05-03T10:31:58.487" LastActivityDate="2012-05-03T10:31:58.487" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2083" PostTypeId="2" ParentId="2075" CreationDate="2012-05-03T12:21:28.663" Score="7" Body="&lt;p&gt;Another reason why red lights are now sponsorized for night illumination is because they are supposed to be safer in terms of interference on the circadian cycle. This is not related to better vision, but better health.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mammalian eye senses the light by the conventional rode and cone cells. However, a third light-sensing cell type &lt;a href=&quot;http://dx.doi.org/10.1038/nature01761&quot; rel=&quot;nofollow noreferrer&quot;&gt;has been recently identified&lt;/a&gt;. This third light-sensor is based on &lt;strong&gt;melanopsin&lt;/strong&gt;-positive cells. While rod and cone cells respond best to white, full spectrum light, melanopsin cells only respond to a specific bandwidth of blue light, in the range of 446-477 nanometers. These cells connect and regulate brain centers responsible for circadian rhythms. Therefore, during the night, blue-light exposure &lt;a href=&quot;http://dx.doi.org/10.1289/ehp.118-a22&quot; rel=&quot;nofollow noreferrer&quot;&gt;might interfere&lt;/a&gt; with circadian rhytms facilitating the onset of depression and other metabolic derangements associated with circadian cycle &lt;a href=&quot;https://biology.stackexchange.com/questions/1659/why-is-maintaining-a-circadian-rhythm-important&quot;&gt;see another SE question&lt;/a&gt;. White light contains also blue light, while red light does not. This is apparently the rationale to claim that red light is less harmful. However, no clinical evidence is available to my knowledge, and the threshold of blue light required to stimulate melanopsin receptors is probably over the common night illumination. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nature01761&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Hattar S, Lucas RJ, Mrosovsky N, Thompson S, Douglas RH, Hankins MW, Lem J, Biel M, Hofmann F, Foster RG, et al.&lt;/strong&gt;. 2003. Melanopsin and rod-cone photoreceptive systems account for all major accessory visual functions in mice. Nature 424: 76–81.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1289/ehp.118-a22&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Holzman DC&lt;/strong&gt;. 2010. What’s in a color? The unique human health effect of blue light. Environmental health perspectives 118: A22–7.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="444" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2012-09-08T14:08:59.187" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="2084" PostTypeId="1" AcceptedAnswerId="2364" CreationDate="2012-05-03T13:08:25.187" Score="12" ViewCount="435" Body="&lt;p&gt;Individuals that avoid age-related diseases into later life are known as 'exceptional survivors', and have increased longevity compared to their 'controls' (those that were born at a similar time, yet have 'aged' and died sooner). The Leiden Study determined that in these long-lived individuals there is a considerable genetic component contributing to the survival [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16251894&quot; rel=&quot;nofollow&quot;&gt;Schoenmaker &lt;em&gt;et al&lt;/em&gt;&lt;/a&gt;] (although this could equally be epigenetic - or even more likely, a combination of both).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read about studies that have identified genetic mutations that cause premature aging phenotypes (for instance mutations in the WRN gene cause Werner's Syndrome [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8602509&quot; rel=&quot;nofollow&quot;&gt;Yu &lt;em&gt;et al&lt;/em&gt;&lt;/a&gt;]).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I have yet to discover any studies that determine any genes/regions associated with resistance to age-related disease (i.e. those that age 'well'). My question is whether anyone knows of any such studies?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Arguably studies that have looked into predisposition to age-related diseases &lt;em&gt;have&lt;/em&gt; found some mutations - for instance mutations within the 9p21 genetic locus (i.e. p16INK4a/CDKN2A) have been associated with heart disease and stroke independently (2 age-related diseases) [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19293724&quot; rel=&quot;nofollow&quot;&gt;Wahlstrand &lt;em&gt;et al&lt;/em&gt;&lt;/a&gt;]. Therefore individuals without any of these risk-increasing alleles could be considered predisposed to exceptional survival - but I see this as separate to my question. Are there any protective alleles/genes/loci that increase 'global' survival? Are there a few protective alleles, or many with small effects? Or are the exceptional survivors just without any disease-causing/risk-increasing alleles?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested in published research (of course), but also in peoples general perceptions of the topic; there are plenty of theories of aging and longevity, but few facts - so please state what you 'believe', and explain why this is the case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;p.s. I am aware that you can genetically modify lab models (e.g. C. elegans &lt;em&gt;eat-2&lt;/em&gt; mutants [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9789046&quot; rel=&quot;nofollow&quot;&gt;Lakowski &lt;em&gt;et al&lt;/em&gt;&lt;/a&gt;]) to live longer. I am interested in naturally occurring variants, specifically in humans (or that at least relate to human aging).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt; (11 May 2012)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found a study, published earlier this year, that finds a single genetic polymorphism to be associated (after correction for multiple testing) with centenarians [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22279548&quot; rel=&quot;nofollow&quot;&gt;Sebastiani &lt;em&gt;et al&lt;/em&gt;&lt;/a&gt;]. The SNP is in TOMM40/APOE (in LD), which is certainly interesting given the previous links between APOE and Alzheimer's (an age-related disease). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I am not convinced by the experimental design; they use age-at-death in centenarians as their cases (having genotyped them), and they use &lt;em&gt;alive&lt;/em&gt; population controls as the controls. Whilst there is unlikely all these individual will become long-lived, a better design (to gain more power) would have been to use individuals who have died from 'premature' (e.g. between 60 and 70) age-related disease. So I am still waiting for a convincing study, but this does look promising!&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-05-23T09:15:45.550" LastActivityDate="2012-05-23T14:54:01.957" Title="Have any mutations or genetic loci been associated with exceptional longevity in humans?" Tags="&lt;genetics&gt;&lt;senescence&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2085" PostTypeId="2" ParentId="1989" CreationDate="2012-05-03T13:13:42.907" Score="5" Body="&lt;p&gt;The problem you are looking for is called the &quot;Nature vs nurture&quot; debate. Lots of scientists have written lots of books and papers and done lots of studies on the subject. As you can see, the title of the debate already includes the two main concerning factors: nature (genes) and nurture (environment).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These of course each include a variety of ways in which they influence personality. Genes provide the biological basis for your personality, they determine how everything in your body works&lt;sup&gt;1&lt;/sup&gt;. At the same time, these genes build a system that has a life of its own - your brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It consists of neurons, and nobody knows how personalitites comes about from them exactly but somehow they do. Neurons reshape all the time in ways that no other cells do. The connections between them, synapses, are formed, destroyed, reinforced or weakened all the time - in response to things that take effect on them, for example the things that you see and hear, smell, taste and feel. A very interesting subject in this field is the study of neuronal networks, giving some insight into how memory and learning may work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But while this may seem like external factors must then be more important for personality, it depends on the setup provided by your genes &lt;em&gt;how&lt;/em&gt; your neurons respond to certain influences - what concentrations of neurotransmitters they produce and secrete etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, the only thing that is really safe to say is that it is not &quot;either or&quot;, both definitely play a role.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt;But even the biological development of the body has non-genetic influences - at the moment I can think of epigenetic inheritance though this seems to be disputed (see comments). Apart from that as far as I know there are uterine influences on embryonic development. And then there are the more or less obvious external influences such as cutting things off before they develop.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-05-03T14:39:47.680" LastActivityDate="2012-05-03T14:39:47.680" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2086" PostTypeId="2" ParentId="2076" CreationDate="2012-05-03T13:31:09.123" Score="8" Body="&lt;p&gt;In expansion to biocs' excellent answer, I would like to highlight some practical limitations of this. Suppose we &lt;em&gt;did&lt;/em&gt; manage to create a huge database of exact chemical mixtures which produce all smells recognisable by humans. You would still meet some complications:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The output device (analogous to headphones or screen) would either need to be able to produce those substances on demand or have a large enough stack of them.&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The former would require a whole lab built into one device - even with our miniature technology this would probably end up rather large.&lt;/li&gt;&#xA;&lt;li&gt;The latter would require you to regularly stock up on all of the substances. You could sell these in an all-in-one package (again size becomes a problem) or in smaller &quot;smell sets&quot; (possibly practicable - but it would take a &lt;em&gt;long&lt;/em&gt; time until people would understand what this is about)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;The &quot;smell substances&quot; have to get to your nose somehow. At the same time, you probably don't want them in the rest of the room: While sound boxes are no problem because sound disappears rather quickly after being produced, smell can stick around for longer. The solution would be an apparatus that you insert into your nose. Not very practical, but people might do it.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I can't think of more at the moment but there probably are :)&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-05-03T13:31:09.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2087" PostTypeId="1" CreationDate="2012-05-03T14:23:27.240" Score="12" ViewCount="1238" Body="&lt;p&gt;It seems as though the act of crying when sad does nothing to relieve that sadness. Is there an advantage to crying from an evolutionary perspective, or is it the end result of a different process? Also, why is there the same physiological reaction of crying when in sadness &lt;strong&gt;or&lt;/strong&gt; in pain?&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-05-03T21:07:55.827" LastActivityDate="2012-07-20T21:23:16.707" Title="Is there an evolutionary advantage to crying when sad?" Tags="&lt;human-biology&gt;&lt;evolution&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="2088" PostTypeId="1" CreationDate="2012-05-03T17:54:40.127" Score="2" ViewCount="566" Body="&lt;p&gt;By default, &lt;code&gt;pymol&lt;/code&gt; seems to grab the number of cores on the system for rendering. How can I force it to only use one core?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Motivation:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a large collection time-series of of coordinate data from a computational protein folding experiment. I'd like batch render the generated pdb files into a movie in a programmatic way. Pymol however likes to eat up as many cores as it finds available. I'd like to retain some control of the computational burden (required for some computational cluster jobs). How can I force pymol to only use one (or n) core(s)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Solution:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the question was closed (as it was decided to not fit into biological criteria of the site) future visitors might find it useful to know the answer:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;set max_threads, 1&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The solution was found in a &lt;a href=&quot;http://biostars.org/post/show/44065/turn-off-multithreading-in-pymol&quot; rel=&quot;nofollow&quot;&gt;Biostars question&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="822" LastEditorUserId="822" LastEditDate="2012-06-27T18:14:02.923" LastActivityDate="2012-06-27T18:14:02.923" Title="Turn off multithreading in pymol" Tags="&lt;bioinformatics&gt;&lt;pymol&gt;" AnswerCount="0" CommentCount="11" ClosedDate="2012-05-04T20:02:40.023" ContentLicense="CC BY-SA 3.0" />
  <row Id="2089" PostTypeId="1" AcceptedAnswerId="2095" CreationDate="2012-05-03T18:21:18.987" Score="7" ViewCount="661" Body="&lt;p&gt;I have been previously told that the Patellar reflex (knee-jerk-reaction) exists to prevent the hyper-extension of the patellar tendon.  Yet if the impact to the tendon is delivered slowly - i.e. by pressing down on it rather than striking it - there is no reflex response.  Why is this, as surely the tendon is being extended by the same amount? &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-05-03T23:42:26.317" Title="Why is the Patellar reflex not triggered when the tendon is extended slowly?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;reflexes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2091" PostTypeId="1" CreationDate="2012-05-03T18:59:06.173" Score="11" ViewCount="1472" Body="&lt;p&gt;I was wondering what oxygen actually does in the body. I have seen a few answers to other questions that involve the electron chain and I am really not sure what that is. So I was wondering what oxygen does and could hydrogen do the same thing as a substitute?&lt;/p&gt;&#xA;" OwnerUserId="824" LastEditorUserId="806" LastEditDate="2012-05-03T22:35:27.073" LastActivityDate="2013-02-11T23:31:31.833" Title="Could hydrogen replace oxygen in cellular respiration?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;cellular-respiration&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2092" PostTypeId="2" ParentId="2091" CreationDate="2012-05-03T20:11:11.903" Score="16" Body="&lt;p&gt;No, hydrogen could not replace oxygen because it has entirely different characteristics. The most important one is probably its electronegativity - oxygen 'pulls' electrons much 'stronger' than hydrogen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Basics: Reduction potential&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oxygen is the so-called terminal electron acceptor of the electron transport chain in eukaryotes. You can see &quot;reduction potential&quot; as a kind of stored &quot;energy&quot; which molecules have, similar to the power stored in batteries (very similar actually). To make this text a bit shorter I'll call it &quot;RP&quot; from now on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One maybe confusing detail is that &lt;strong&gt;a substance with low RP has &quot;more energy&quot; than a substance with high RP&lt;/strong&gt;, so it is the opposite way of thinking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In very generalised terms, metabolism means that molecules with a low RP (glucose) are oxidised (burned) and turn into molecules with much higher RP (CO&lt;sub&gt;2&lt;/sub&gt;). Coupled with this, a different molecule with very high RP (oxygen) is reduced and becomes a molecule with slightly lower RP (H&lt;sub&gt;2&lt;/sub&gt;O). (You may have heard this before - it's called a redox reaction.) *&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The important part is that the RP &quot;released&quot; by the oxidisation (burning) is larger than the RP &quot;taken up&quot; by the reduction. The surplus leaves as energy - heat and light if you just burn the glucose. This is a spontaneous process, meaning it will occur just by itself - even if it takes a &lt;em&gt;long&lt;/em&gt; time if nobody drops a match on it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea of metabolism is to let that process happen - but use as much of the energy it releases as possible. This works by not just letting it burn, but intercepting that burning process at different stages so that at each step a bit of the RP can be taken off and stored in something else. This &quot;something else&quot; is NAD which I'm sure you've encountered before. Each step that glucose is burned down, another bit of NADH is made, which then has a respectable reduction potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NADH (leaving out NADPH here which is a bit different) is channeled into a process called oxidative phosphorylation which retrieves the reduction potential in an actual form of energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Basics: Terminal electron acceptor&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, the reduction potential I've been talking about all the time is really just electrons, involved in bonds which are &quot;happy&quot; to react. Passing down the reduction potential as I've explained is really a passing down of electrons into more and more stable, less reactive bonds. That's why it's called &quot;electron transport chain&quot;. At the end of oxidative phosphorylation, those electrons are dropped onto O&lt;sub&gt;2&lt;/sub&gt; and make it into H&lt;sub&gt;2&lt;/sub&gt;O. That's why O&lt;sub&gt;2&lt;/sub&gt; is called the &quot;terminal electron acceptor&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why Hydrogen can't replace Oxygen&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now to come back to why hydrogen cannot perform oxygen's function in our body. We use glucose as our source of reduction power and oxygen as our terminal electron acceptor. O has a high electronegativity (3.5) so it pulls electrons strongly towards it. H's electronegativity is only 2.1, so it's much weaker. O as a terminal electron acceptor works because it pulls them much stronger than H when they bond, so an O-H bond is almost like giving oxygen an electron. In order for hydrogen gas (H&lt;sub&gt;2&lt;/sub&gt;) to perform the same function, it would need to be possible to drop electrons onto hydrogen in a bond where it pulls them much stronger than the other partner. They do exist, and such compounds are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Hydride&quot; rel=&quot;nofollow&quot;&gt;hydrides&lt;/a&gt;. But the catch is: unlike H&lt;sub&gt;2&lt;/sub&gt;O, these are normally strong reducing agents, meaning that hydrogen would rather not be in that bond. This not a feasible option for cell respiration, at least in humans, because it requires a lot of RP input. Making oxygen into H&lt;sub&gt;2&lt;/sub&gt;O does &lt;em&gt;not&lt;/em&gt; require a lot, it's a very cheap electron acceptor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope I was able to put this in understandable terms. Let me know if I need to clarify anything.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;--&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*It works with other molecules than glucose-&gt;CO&lt;sub&gt;2&lt;/sub&gt; / O&lt;sub&gt;2&lt;/sub&gt;-&gt;H&lt;sub&gt;2&lt;/sub&gt;O too, many prokaryotes do that and in fact that's how batteries work&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-02-11T23:31:31.833" LastActivityDate="2013-02-11T23:31:31.833" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2093" PostTypeId="1" CreationDate="2012-05-03T21:43:00.620" Score="18" ViewCount="1061" Body="&lt;p&gt;A common question posed is, &quot;how did the eye evolve?&quot;, because the eye is so complex.  However, this has been answered rather clearly and there are several examples around the world of animals in which the eye has evolved independently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The human brain, however, only seems to have evolved once in the history of life on Earth - a brain which is capable of advanced speech, predicting the future given information on the past, producing art, imagining advanced abstract concepts such as algebra, creating advanced tools, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How, then, could the human brain have evolved?  What stimulus was there for progressive Homo individuals to have brains that were slightly more advanced than the previous one's?  I've heard Richard Dawkins summarize it as &quot;big brains are sexy&quot;, but that's a comment made in hindsight (and not even shared by all members of the human species today!)  At the time, why would a human female choose a male with a slightly larger brain, so slightly larger that the increased intelligence probably wouldn't be noticeable?  Or why would such an individual have an evolutionary advantage?&lt;/p&gt;&#xA;" OwnerUserId="826" LastEditorUserId="55096" LastEditDate="2019-11-11T09:29:55.197" LastActivityDate="2019-11-11T09:29:55.197" Title="How did the human brain evolve?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;brain&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2094" PostTypeId="2" ParentId="2065" CreationDate="2012-05-03T23:28:42.640" Score="8" Body="&lt;p&gt;As I'm lucky enough to have access to that article, I'm going to extract whatever I can find to answer your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To begin with, innate immunity must have evolved first - we can see it at almost all stages of evolution. According to Cooper &amp;amp; Herrin, ever since aerobic respiration gave rise to multicellular organisms which in turn needed protection from invasion by single-cell organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They state that around 500 million years ago, the first adaptive immune systems evolved in vertebrates, but do not explain &lt;em&gt;how&lt;/em&gt; although they attempt to. Instead, they explain why we are not able to discern at the moment how this evolution came about. The main reason given is that it is unknown when some key cells evolved (namely natural killer cells and dendritic cells) Additionally, mice and humans evolved two different kinds of natural killer cell receptors relatively recently while sharing a common ancestor only quite a long time ago.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently jawed and jawless vertebrates have also evolved two different kinds of adaptive immune systems. They both seem to rely on the same mechanisms but on a different molecular and genetic basis. Cooper &amp;amp; Herrin conclude that at the current level of research, we are not able to determine the evolution of our immune system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.nature.com/nri/journal/v10/n1/full/nri2686.html#B2&quot; rel=&quot;nofollow&quot;&gt;How did our complex immune system evolve?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally, if I'm allowed to give in to the temptation of speculation a bit, I would go by a similar strategy as the evolution of Krebs cycle - look which bits make sense even without the rest. There is of course the major obstacle that the cells of the immune system require an entirely new branch in haemopoiesis: all innate immune cells (aside from natural killer, NK cells) derive from the common myeloid progenitor, whereas all adaptive immune cells (and NK cells) derive from the common &lt;em&gt;lymphoid&lt;/em&gt; progenitor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this may even be a first hint: NK cells are innate immune cells but they derive from a different lineage at the highest level - they may have evolved as the first lymphoid cells after the myeloid innate immune cells. The next closest related cell is the cytotoxic T cell (CD8+, aka Tc), which utilises the exact same killing mechanisms (perforin+granzymes and Fas ligand) and attaches to other cells in almost the same way as the NK cell (immune synapse). It is also independent and can kill on its own, as long as it recognises its specific antigen. This is the main difference and also a very large step - the generation of the specific T cell receptor. Once the specific T cells receptor is developed, the step to helper T cells (CD4+, Th) is not far, although these perform a relatively bystander-like role in the immune response, steering the other immune cells from behind the scenes and not directly effecting any killing of the pathogen. Therefore I would guess that before helper T cells, B cells evolved, which are capable of producing antibodies. Antibodies themselves are very similar to the T cell receptor (not in gross structure but in the underlying genetic domains and their processing), so a 'detachable' antigen-specific T cell receptor may have evolved and ultimately caused the development of a new cell type. Once all these components are present, it is necessary (or beneficial) to control which cell types are the most active and in which way they act at the site of infection. This is exactly what helper T cells do, by steering the local immune response either into a Th1 (cytotoxic) or a Th2 ('humoral', anti-parasitic) response direction.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-06-17T19:30:55.027" LastActivityDate="2013-06-17T19:30:55.027" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2095" PostTypeId="2" ParentId="2089" CreationDate="2012-05-03T23:42:26.317" Score="6" Body="&lt;p&gt;This effect you are observing has to do with the nature of the afferent neurons (Ia fibers), which carry a signal into the spinal cord and synapse onto motor neurons directly.  See &lt;a href=&quot;http://neuroscience.uth.tmc.edu/s3/chapter01.html&quot;&gt;this text&lt;/a&gt; (scroll down to section 1.10) for a diagram.  At their other end, these Ia fibers penetrate into the muscle and wrap themselves around the body of the muscle spindles, &lt;code&gt;&quot;[which] are specialized receptors that signal (a) the length and (b) the rate of change of length (velocity) of the muscle.&quot;&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the main role of these spindles is to monitor the muscles for very rapid changes in length, the neurons have a static range which is optimized for these quick jerks (rather than firing over a wide range of velocities).  When you are stretching the muscle slowly, the Ia fiber is not building up a sufficient depolarization to fire off an action potential.    &lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2012-05-03T23:42:26.317" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2096" PostTypeId="2" ParentId="1056" CreationDate="2012-05-03T23:42:47.723" Score="2" Body="&lt;p&gt;According to all I've learned and heard, the only thing consistent about meiosis is that it  reduces ploidy because homologous chromosomes are separated. (Not necessarily diploid to haploid - it can be polyploid as well, although odd ploidies usually seem to mess it up.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mitosis on the other hand mainly serves to separate two copies of a genome into different cells.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-05-03T23:42:47.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2097" PostTypeId="2" ParentId="1056" CreationDate="2012-05-04T00:19:12.727" Score="7" Body="&lt;p&gt;If the question is about the one and only most important difference between mitosis and meiosis, then the answer &quot;meiosis reduces ploidy&quot; is probably correct. But if the list of important differences is open, it would be critical to add that mitosis generates identical cells (identical to each other and any ancestral cells, barring rare new mutations), while meiosis generates genetic diversity by creating cells, which are all different from each other and from any ancestral cells. It does so by independent segregation of homologs and by crossingover within chromosomes.&lt;/p&gt;&#xA;" OwnerUserId="828" LastActivityDate="2012-05-04T00:19:12.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2098" PostTypeId="2" ParentId="2068" CreationDate="2012-05-04T00:26:37.053" Score="0" Body="&lt;p&gt;many D-amino acids are not used at all, although some have rather elaborate metabolism, both synthesis and utilization: D-alanine for example.&lt;/p&gt;&#xA;" OwnerUserId="828" LastActivityDate="2012-05-04T00:26:37.053" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2099" PostTypeId="2" ParentId="2093" CreationDate="2012-05-04T04:38:05.757" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;why would such an individual have an evolutionary advantage?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;First thing to keep in mind, is that natural selection will seize upon even very slight advantages and evolve them until the point where evolving them is no longer viable. So, to you a slight increase in intelligence might be unnoticeable, but in a naturally selecting system it would be very noticeable. Don't mix up sexual selection (where the preference of one sex shapes the selection of genes) with natural selection (where fitness to the environment shapes the selection of genes). Sexual selection may or may not have helped shape brain evolution, I can't produce evidence that it did.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the increased fitness that slight gains in intelligence convey are easier to create evolutionary anecdotes about. It's simplistic to speak of just &quot;intelligence&quot; as evolving. Many different nervous structures evolved through out the animal kingdom, each with a function that directly increased fitness. I get the feeling that you're specifically talking about the evolution of the neocortex, because you reference human intelligence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what I guess you're really asking is what evolutionary advantage does the neocortex convey? The answer isn't that hard, once you understand a little about the neocortex. It is an organ that simply models the external and internal world as perceived by your sensory organs. By external world, I mean modeling things like vision, hearing, touch, etc... By internal world, I mean modeling the actions you can perform, the plans you make, and so on. Increasing the size of the neocortex is essentially increasing the possible complexity of these models. Not only can you find more subtle and complex patterns &lt;em&gt;out there&lt;/em&gt;, you can develop increasingly subtle plans and ruses too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Watching documentary footage of tribal hunters provides a really stark look at just how useful the neocortex is. It frames our intelligence in terms of a situation similar to one we evolved in. It's not hard to imagine why the growth has been explosive. Outsmarting other animals is a great niche that in our evolutionary history was virtually unexploited.&lt;/p&gt;&#xA;" OwnerUserId="510" LastActivityDate="2012-05-04T04:38:05.757" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2100" PostTypeId="2" ParentId="2087" CreationDate="2012-05-04T04:46:18.147" Score="5" Body="&lt;p&gt;First, here is a link to an article that discussion the answer to your question:&lt;br&gt;&#xA;&lt;a href=&quot;http://www.sciencedaily.com/releases/2009/08/090824141045.htm&quot;&gt;Why Cry? Evolutionary Biologists Show Crying Can Strengthen Relationships&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The original article to which it refers can be found here:&lt;br&gt;&#xA;&lt;a href=&quot;http://www.epjournal.net/wp-content/uploads/ep07363370.pdf&quot;&gt;Emotional Tears as Biological Signals&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To speculate a bit on Jez's question, crying in adults could be a result of our possible &lt;a href=&quot;http://en.wikipedia.org/wiki/Neoteny&quot;&gt;Neoteny&lt;/a&gt;. Crying in infant animals is extremely common as a way to elicit attention and sympathy from the mother. If we are neotenous apes, crying could be a left-over behavior that was seized by evolution, instead of being discarded.&lt;/p&gt;&#xA;" OwnerUserId="510" LastEditorUserId="115" LastEditDate="2012-05-04T06:47:00.927" LastActivityDate="2012-05-04T06:47:00.927" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2101" PostTypeId="2" ParentId="2093" CreationDate="2012-05-04T05:01:39.003" Score="6" Body="&lt;p&gt;You made a few statements in the beginning of your question, I'm just going to focus on the last paragraph (which seems like your question). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When people try to understand evolution, a common fallacy is to assume you're looking at a linear progression, in this case that each surviving child is &lt;em&gt;slightly&lt;/em&gt; more intelligent than his parents. This is confusing in part because it's at odds with day to day observation: dumb people have smart kids, tall people have short kids, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It may help to visualize a it as a cloud rather than a line, with the &lt;em&gt;really&lt;/em&gt; incompetent people being constantly clipped off the low end and the &lt;em&gt;really&lt;/em&gt; competent being, as Richard Dawkins puts it, &quot;sexy&quot;. Slowly, genes which tend to land people in the &quot;really dumb&quot; side are weeded out, genes that sometimes produced above-average intelligence are propagated. You can't think about evolution without considering the entire population. &lt;/p&gt;&#xA;" OwnerUserId="810" LastEditorUserId="810" LastEditDate="2012-05-04T06:35:10.413" LastActivityDate="2012-05-04T06:35:10.413" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2102" PostTypeId="2" ParentId="2073" CreationDate="2012-05-04T06:50:32.533" Score="28" Body="&lt;p&gt;I believe it is for this reason: the female body plan is the default one. Males are a variation upon that, in humans at least. Nipples are part of the basic body plan. For a man to &lt;em&gt;not&lt;/em&gt; have them, he would need to actively evolve something that would prevent nipples from developing. There is no selective pressure for the development of such a thing, so it hasn't happened. Keep in mind that the code for the general body plan is shared between males and females. The Y chromosome modifies the development of that body plan so the person becomes male.&lt;/p&gt;&#xA;" OwnerUserId="510" LastActivityDate="2012-05-04T06:50:32.533" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="2104" PostTypeId="1" CreationDate="2012-05-04T18:18:04.060" Score="5" ViewCount="4225" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nzW5O.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My attempt:  I looked for the TACs because I thought this would be AUG in mRNA and ultimately Methionine (the start codon). But apparently, that's not how you do this problem.  Im confused because the answer (shown in red) doesn't have any TACs and the boxes seem to start at random places.  I am also confused as to why my professor drew a box around both strands.  I thought only one strand at a time was turned into mRNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE:  It has occured to me that the entire strand is transcribed and then the introns are removed.  So I know why not to look for the TACs.  But now, how can I identify the exons?&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="558" LastEditDate="2012-05-04T18:28:45.357" LastActivityDate="2020-02-14T14:32:40.323" Title="Finding exons in DNA problem" Tags="&lt;dna&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2105" PostTypeId="1" AcceptedAnswerId="2108" CreationDate="2012-05-04T19:10:40.757" Score="24" ViewCount="2196" Body="&lt;p&gt;I'm sure the exact frequency varies, but does anyone know roughly how many revolutions per minute / second the rotating center part makes? &lt;/p&gt;&#xA;" OwnerUserId="810" LastEditorUserId="806" LastEditDate="2012-05-04T22:10:08.303" LastActivityDate="2020-01-12T19:21:13.283" Title="How fast does the rotor in ATP synthase spin?" Tags="&lt;enzymes&gt;&lt;cellular-respiration&gt;&lt;mitochondria&gt;&lt;chloroplasts&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2106" PostTypeId="2" ParentId="2104" CreationDate="2012-05-04T19:34:16.920" Score="6" Body="&lt;p&gt;After an RNA has been transcribed, in eukaryotes it is spliced before it leaves the nucleus. This means that parts of the RNA are removed (called introns) and the ends are capped. The parts left over in the mature mRNA after removing the introns are called exons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mRNA does not have to start with a start codon. There can be sequences before and after the bit which actually gets translated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, only one strand of DNA is transcribed into RNA. When you look at the mature mRNA below, read the first few bases and try to find their complements in the original DNA because this is where they were transcribed from. UCAUG is transcribed from the DNA AGTAC (with TCATG on the opposite side).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now you look for the end of the mRNA. Bear in mind that all the A's are the poly-A tail which is added during splicing and determines how long the mRNA will persist in the cytoplasm. So you look for CUAGG in the original DNA, which must be transcribed from GATCC (with CTAGG on the opposite strand).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, that's exactly where the two red boxes start and end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now since the mRNA you see here is mature (indicated by the poly-A tail and the 5'-cap), that means introns have already been taken out. So any bases that you can see in the DNA between the start and end that we just found but not in the mRNA must have been an intron. Or the other way round: all the bases that are in the mRNA which you can also find in the DNA must be exons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will notice that exactly the bit that isn't in the red boxes doesn't appear in the mRNA anymore. Or: All of the mRNA is in the red boxes. The sequence is interrupted by a short bit which you can't find in the mRNA anymore - so this must be an intron.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-05-04T19:34:16.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2107" PostTypeId="2" ParentId="2093" CreationDate="2012-05-04T19:34:55.720" Score="10" Body="&lt;p&gt;New work suggests a prominent role for genes in the SRGAP2 family, as explained &lt;a href=&quot;http://blogs.discovermagazine.com/notrocketscience/2012/05/04/a-duplicated-gene-shaped-human-brain-evolution%E2%80%A6-and-why-the-genome-project-missed-it/&quot;&gt;here&lt;/a&gt;. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867412004618&quot;&gt;Data&lt;/a&gt; suggest a mechanism where incomplete duplication - most likely at &lt;em&gt;SRGAP2C&lt;/em&gt; - created a novel gene function some 2–3 mya, which is a time corresponding to the transition from &lt;em&gt;Australopithecus&lt;/em&gt; to &lt;em&gt;Homo&lt;/em&gt; and the beginning of neocortex expansion. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S009286741200462X&quot;&gt;Further&lt;/a&gt;, in the mouse neocortex, &lt;em&gt;Srgap2&lt;/em&gt; promotes spine maturation and limits spine density, supporting sustained radial migration and leading to the emergence of human-specific features.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-05-04T19:34:55.720" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2108" PostTypeId="2" ParentId="2105" CreationDate="2012-05-04T19:52:13.640" Score="21" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.neuro.duke.edu/files/sites/yasuda/pub/0302207335.pdf&quot;&gt;&quot;Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase&quot;&lt;/a&gt; (Yasuda &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Nature&lt;/em&gt;, 2001), ATPase rotates at 130 revolutions per second when saturated with ATP.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-05-04T19:52:13.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2109" PostTypeId="1" AcceptedAnswerId="2113" CreationDate="2012-05-04T20:19:02.583" Score="9" ViewCount="293" Body="&lt;p&gt;Thinking of behaviours an organism can adapt, at the very base an action can always be either selfish or altruistic (cooperative).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually, selfish behaviour is assumed to be the preferred choice and the question is how altruistic behaviour comes about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if reciprocal altruism can give both participants a higher benefit than their respective costs (which it usually does), why would selfish behaviour (in the sense of behaviour which reaps benefit at another entity's expense) be what we assume to happen? If evolution tends to optimise things, why does it not optimise this?&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="500" LastEditDate="2013-03-14T17:07:04.193" LastActivityDate="2013-10-20T11:55:34.533" Title="Why is selfishness the 'obvious' strategy?" Tags="&lt;evolution&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2110" PostTypeId="5" CreationDate="2012-05-04T20:20:15.570" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-04T20:20:15.570" LastActivityDate="2012-05-04T20:20:15.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2111" PostTypeId="4" CreationDate="2012-05-04T20:20:15.570" Score="0" Body="Selfishness in evolutionary terms describes behaviour solely aimed (consciously or not) at an organism's own benefit." OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-05-04T20:21:34.973" LastActivityDate="2012-05-04T20:21:34.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2112" PostTypeId="1" AcceptedAnswerId="2114" CreationDate="2012-05-04T20:34:15.700" Score="9" ViewCount="857" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GyMQH.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My attempt: First I took the single letter AA codes and made them amino acids.  So, the first one is Trp which is 5'-UGG-3'.   From this I got the DNA sequence 3'-CCA-5'.  However, the correct answer (shown in red) doesn't have this sequence.  What did i do wrong?&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="43" LastEditDate="2012-05-04T20:51:10.460" LastActivityDate="2012-05-05T00:57:14.203" Title="Finding DNA from Amino Acid sequence problem" Tags="&lt;dna&gt;&lt;genetics&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2113" PostTypeId="2" ParentId="2109" CreationDate="2012-05-04T22:48:47.170" Score="9" Body="&lt;p&gt;It basically comes down to a question of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Unit_of_selection&quot;&gt;unit of selection&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the common viewpoint, in which natural selection is seen as acting on individual organisms, it's almost a tautology that the organisms favored by selection are those that maximize their own reproductive fitness.  Thus, the possibility that some organisms might engage in acts that help another organism at their own expense may seem like a paradox, or at least a puzzle in need of explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One solution to this puzzle is offered by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene-centered_view_of_evolution&quot;&gt;gene-centered view of evolution&lt;/a&gt;, where selection is viewed as acting on genes, with organisms being merely convenient (and usually, but not always, cooperative) collections of genes that (usually) reproduce together.  From this viewpoint, it is not at all surprising that evolution might favor genes that cause an organism to help other organisms, provided that there's a statistical tendency for those other organisms to also be carrying the same gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other mechanisms for the evolution of cooperation do also exist.  For example, organisms with sufficiently advanced cognitive capabilities may indeed engage in reciprocal altruism, where they help others only if those others have shown themselves willing to help them in exchange.  Such exchanges, being mutually beneficial, do indeed help both participating organisms, and are thus selected for even at the organism level.  However, to persist (in the absence of gene or group level selection effects), they generally need some form of enforcement and/or learning mechanism &amp;mdash; if cheaters can keep receiving help without ever helping anyone else, they'll do better than the cooperators and eventually displace them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, in some situations, an organism acting simply to help itself (e.g. by modifying its environment to be more suitable for itself) may also end up helping other organisms that just happen to be nearby.  In such a situation, selection indeed favors cooperative behavior in isolated organisms by default, with the evolution and persistence of &quot;freeloaders&quot; (who spend less effort on improving their surrounding, relying instead on others to do the work) being only possible as long as there are sufficiently many cooperators around.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, none of these mechanisms are mutually exclusive.  Indeed, the presence of &lt;em&gt;some&lt;/em&gt; gene-level selection effects tends to be unavoidable in any realistic situation involving cooperative interactions; it's hard to come up with a setting in which no two interacting organisms &lt;em&gt;ever&lt;/em&gt; share genes, and obviously the fact that two organisms share a common genetic predisposition to cooperate makes them more likely to do so when they meet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(However, one not-so-realistic theoretical limit case where that does happen is that of an infinitesimally rare cooperative mutant invading an infinitely large and well mixed population.  The popular use of this simplifying limit assumption in classical models of evolution may be one reasons why cooperative behavior is so often seen as something remarkable and hard to explain by evolutionary theorists.)&lt;/p&gt;&#xA;" OwnerUserId="239" LastEditorUserId="239" LastEditDate="2012-05-05T09:49:03.560" LastActivityDate="2012-05-05T09:49:03.560" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2114" PostTypeId="2" ParentId="2112" CreationDate="2012-05-04T22:59:12.900" Score="7" Body="&lt;p&gt;Your approach to translate the AA sequence, codon by codon, was correct. This was a bit of a trick question because to recognize it, you had to read the sequence backwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UGG-CAA-GGT-CAC etc is read directly off of the 3'-&gt;5' strand of the circled answer, reading from right to left.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bottom left is a red herring because it starts with a start codon, ATG, but reading beyond the start codon, the sequence wouldn't match.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2012-05-05T00:57:14.203" LastActivityDate="2012-05-05T00:57:14.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2115" PostTypeId="2" ParentId="1419" CreationDate="2012-05-05T09:56:25.003" Score="7" Body="&lt;p&gt;The above answers are good, but have unfortunately confused some of the concepts in the theory, I will do my best to explain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What we are assessing is how does one behaviour evolve, links with cooperation and altruism are applications of this. The process of selection in evolution removes the the worst individuals from the gene pool, thus those with comparatively good genes survive to reproduce. With physical traits these mechanisms are well understood, with behaviour there are still multiple theories which have not been concluded but our understanding of them is reasonably complete. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Inclusive fitness is the combination of direct and indirect fitness, direct being your personal fitness, indirect being fitness gained from others. In general this is measured in terms of reproductive success (RS) (the number of offspring you successfully raise to reproductive maturity). Out of this understanding came &lt;a href=&quot;https://en.wikipedia.org/wiki/Hamilton%27s_rule#Hamilton.27s_rule&quot;&gt;Hamilton's Rule&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;                               r.b &amp;gt; c&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Where &lt;em&gt;r&lt;/em&gt; is the relatedness, &lt;em&gt;b&lt;/em&gt; is the benefit &amp;amp; &lt;em&gt;c&lt;/em&gt; is the cost. In this scenario the cost is a reduction in RS, the benefit is a gain in RS. Benefits are multiplied by the relatedness to the offspring. In normal diploid organisms (Gets DNA from both parents) you are related by 0.5 (half from mother, half from father), but only related to your brother/sister's offspring by 0.25. Thus, if you have two children you have a &lt;em&gt;direct&lt;/em&gt; fitness of 1, if your brother has two children you gain an &lt;em&gt;indirect&lt;/em&gt; fitness of 0.5. Thus, you would prefer under normal circumstances to have your own children rather than raise your brothers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Altruism is suffering a cost for someone else's benefit, @Winawer mentions the greenbeard theory, which rests on the assumption that if you can tell someone has the same genes as you then you &lt;em&gt;know&lt;/em&gt; that you are related to them in someway and this will be on average be greater than to any other individual. Altruism is a behaviour, defined above, and not a specific action like giving up your own reproduction, thus it is a part of cooperation and not separate from it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is true that there are different forms of altruism however these are all just perspectives pertaining to the same theory. &lt;strong&gt;ALL&lt;/strong&gt; behaviour is selfish, reciprocal altruism is just an example of this. Reciprocal altruism, is &quot;If you scratch my back, I'll scratch yours&quot; (You need help now, I may need help in the future), it is altruistic because you suffer a cost for another's benefit but it is selfish because it is still in the individual's interest to help. This is where prisoners dilemma comes in, this is basically asking the question &quot;how do I pick the most optimal situation in this scenario?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For simplicity, it is generally ill advised to study behaviours in humans because of the implicit bias we have in our judgment on ourselves. From political and religious associations that cloud judgment to the fact that we always strive to see ourselves differently. Also, there are all sorts of ethical difficulties in actually testing and manipulating theories on us. Thus we normally study animals to get around this. However your question specifically talks about people so I will try and answer this based on biological theory alone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on the foundations above, why would someone behave altruistically to someone only 'similar' to you? The biggest difficulty is knowing that we understand all the costs and benefits involved, most of the time we only know some of them and its impossible that you can know all of them because you can't know what you don't know. Humans have effectively 'bootstrapped' behaviours which are 'for the good of society' building on from previously developed behaviours. However we are still fundamentally asking a question about Hamilton's Rule. Being seen as a part of society induces altruistic behaviour towards you (because you are seen as worth something), this is good for you and the costs associated with being altruistic are usually low. Thus you would never &lt;em&gt;rationally&lt;/em&gt; die for 1000 unrelated individuals unless you had at least had all the children you were going to have and raised them to be independent. But you would vote, by voting you suffer a tiny cost, your time, for a huge benefit. Benefits might include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Being seen as caring for others (altruism given to you)&lt;/li&gt;&#xA;&lt;li&gt;Possible benefits to yourself (less tax, more support, better roads, clean air.. etc)&lt;/li&gt;&#xA;&lt;li&gt;Possible benefits to others related to you&lt;/li&gt;&#xA;&lt;li&gt;General good moral of your community, leading to a better life.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There could be thousands of other benefits that I can't, off the top of my head, think of. The cost is negligible and the benefit is intangible but probably higher than the cost. Relatedness isn't important (so long as it is greater than 0), if the cost is sufficiently low or the benefit is sufficiently high. I hope this has helped clarify your thinking and answer the question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For further information:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia is great for getting an overview of terms and definitions, but remain critical of what you could be reading.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A decent book on animal behaviour in general is: &lt;a href=&quot;http://www.amazon.co.uk/Animal-Behavior-An-Evolutionary-Approach/dp/0878932259/ref=sr_1_1?ie=UTF8&amp;amp;qid=1336211529&amp;amp;sr=8-1&quot;&gt;Alcock J. (2009) Animal Behaviour: An evolutionary approach. 9Th edition. Sinaur Associates&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Academic papers; if you have access to them (i.e. are an academic)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Provides the foundations&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hamilton W.D. (1963) &lt;em&gt;Evolution of altruistic behaviour&lt;/em&gt;. The American Naturalist &lt;strong&gt;97&lt;/strong&gt; 354&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hamilton W.D. (1964) &lt;em&gt;The Genetical Evolution of Social Behaviour I&lt;/em&gt; . Journal of Theoretical Biology &lt;strong&gt;7&lt;/strong&gt; 1&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hamilton W.D. (1964)  &lt;em&gt;The Genetical Evolution of Social Behaviour II&lt;/em&gt;. Journal of Theoretical Biology &lt;strong&gt;7&lt;/strong&gt; 17&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The current controversy mentioned in another answer is from this paper, it is widely dislike but does have some support. It is slightly off topic from from the question here, but eusociality is fundamental to our understanding of evolutionary behaviour:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nowak M.A., Tarnita C.E. &amp;amp; Wilson E.O. (2010) &lt;em&gt;The Evolution of Eusociality&lt;/em&gt;. Nature &lt;strong&gt;466&lt;/strong&gt; 1057&lt;/p&gt;&#xA;" OwnerUserId="832" LastEditorUserId="69" LastEditDate="2012-05-05T10:09:19.187" LastActivityDate="2012-05-05T10:09:19.187" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2116" PostTypeId="1" AcceptedAnswerId="2117" CreationDate="2012-05-05T10:55:55.207" Score="7" ViewCount="2333" Body="&lt;p&gt;Well, I was just going through an article on eye, where in fun facts it was mentioned that newly born (for initial 1 to 3 months) babies do not produce tear while crying. Actually, I have found this true. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I am wondering why is it so? Does any one know the reason behind this?&lt;/p&gt;&#xA;" OwnerUserId="655" LastEditorUserId="69" LastEditDate="2012-05-05T11:49:08.407" LastActivityDate="2012-05-06T12:53:34.283" Title="Is it true that newborn babies don't produce tears while crying? Why?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2117" PostTypeId="2" ParentId="2116" CreationDate="2012-05-05T11:16:11.860" Score="9" Body="&lt;p&gt;It is not completely true.  Babies develop the lacrimal system at 42 days, &lt;em&gt;in utero&lt;/em&gt;.  The canals and ducts for tears are formed at 60 days [2].&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;At birth, tear production by the lacrimal gland is minimal. Normal tearing develops several days to 2 weeks after birth.[1]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Some 6% of newborns are born with a tear duct obstruction (in some online articles it stated up to 10%, but I think my source is more reliable).  The child still produces tears, but they can well up on the eyelid [2].&lt;/p&gt;&#xA;&lt;p&gt;Other more serious abnormalities can cause this problem.  Duct cysts or hemangiomas can also cause tear duct blockages in more severe cases.  Various factors, such as anatomical abnormalities and problems with pumping tears increase the propensity for the disorder in children with Trisomy-21 [2].  As nico has alluded to in the comments, there may be a lag in the development of the physiology of tear production even in non-Trisomy-21 children.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;[1] Thomas K. McInerny, MD, FAAP, ed. 2009. American Academy of Pediatrics Textbook of Pediatric Care. Elk Grove Village, IL. American Academy of Pediatrics, p1706.&lt;/p&gt;&#xA;&lt;p&gt;[2]M. E. Wilson et al. (eds.), Pediatric Ophthalmology, 2009, pp. 276-284.  DOI 10.1007/978-3-540-68632-3_1.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="57" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-05-06T12:53:34.283" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2119" PostTypeId="1" CreationDate="2012-05-05T15:27:15.747" Score="9" ViewCount="228" Body="&lt;p&gt;There are &lt;a href=&quot;https://biology.stackexchange.com/q/2073/810&quot;&gt;examples&lt;/a&gt; of structures which only serve a purpose in females, but it seems like the opposite could also be true. Are there any structures which exist in both mammalian sexes and only serve a purpose in males?&lt;/p&gt;&#xA;" OwnerUserId="810" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2012-05-07T14:27:00.327" Title="Are there any structures in mammals that are used only by males?" Tags="&lt;evolution&gt;&lt;zoology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2120" PostTypeId="2" ParentId="2075" CreationDate="2012-05-05T18:50:50.503" Score="10" Body="&lt;p&gt;Here is a comparison of the range of wavelength sensitivities for both rod cells (labelled R) to the 3 subtypes of cones cells (labelled S, M and L) from &lt;a href=&quot;http://en.wikipedia.org/wiki/Rod_cell&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qrlth.png&quot; alt=&quot;Cone and rod wavelength sensitivities.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If one is exposed to red light (above ~650 nm), it would activate the L-type cones mainly (possibly some M-type activation), but no rod activation. Rods are the low light receptor cells in our eyes, and as such, are very sensitive to the photon density, or brightness, entering the eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is just my speculation, but I think it's plausible that if you were in a completely dark environment with just a red light, filtering out the higher frequencies, night vision could be spared in the sense that we don't activate the rod cells.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-05-05T18:50:50.503" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2122" PostTypeId="1" CreationDate="2012-05-05T20:29:32.357" Score="9" ViewCount="1618" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Laughter&quot; rel=&quot;noreferrer&quot;&gt;This Wikipedia article&lt;/a&gt;  defines laughter in many terms, such as...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;a visual expression of happiness, or an inward feeling of joy&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;a part of &lt;strong&gt;human&lt;/strong&gt; behavior regulated by the brain, helping humans clarify their intentions in social interaction and providing an emotional context to conversations&quot;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Note: the emphasis was added by myself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article also states that laughter is &quot;probably genetic&quot;, and that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Scientists have noted the similarity in forms of laughter induced by tickling among various primates, which suggests that laughter derives from a common origin among primate species.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://ac.els-cdn.com/S0960982209011294/1-s2.0-S0960982209011294-main.pdf?_tid=92914468cf96a803efc412ea3fe1e4aa&amp;amp;acdnat=1336247635_d8d8d5459d87a3b2c552dff42f8370b4&quot; rel=&quot;noreferrer&quot;&gt;this report&lt;/a&gt; which the Wikipedia referenced, the expression of laughter in general is present among other great apes. Phylogenetic trees were reconstructed to represent the evolution of this trait among primates (which concludes that the ability to laugh must have a genetic basis, at least to some degree).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: I also found &lt;a href=&quot;http://wiki.answers.com/Q/Is_laughter_genetic&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; WikiAnswers post, but it &lt;em&gt;clearly&lt;/em&gt; can't be that reliable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A search on the OMIM database yielded &lt;a href=&quot;http://omim.org/entry/105830&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; result, where children with Angelman syndrome were characterized with &quot;excessive laughter&quot;, &lt;a href=&quot;http://omim.org/entry/614504&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; result, in which Charles Bonnet syndrome was characterized with &quot;inappropriate laughter&quot;, as well as many other genetic mutations which resulted in some sort of uncontrollable laughter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that laughter is a complex psychological expression of emotion likely associated with more abstract thought, and that there simply can't be &quot;a laughter gene&quot;, but my question is: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any known genetic or physiological origin of laughter? What is biologically different in great apes which allows for laughter, in comparison with a panoply of other animals? I'm looking for more of a molecular answer rather than an ecological or psychological one.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-05-06T21:39:32.410" LastActivityDate="2012-05-06T21:39:32.410" Title="The genetic and physiological origins of laughter?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;physiology&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2123" PostTypeId="2" ParentId="2122" CreationDate="2012-05-05T23:56:03.467" Score="12" Body="&lt;p&gt;I recommend this article: &lt;a href=&quot;http://www.jstor.org/stable/full/10.1086/498281&quot;&gt;The Evolution and Functions of Laughter and Humor: A Synthetic Approach&lt;/a&gt; by M Gervais and DS Wilson, 2005, University of Chicago Press.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For your question about the origin, firstly they explain that &lt;em&gt;all&lt;/em&gt; laughter is induced by stimuli which are unexpected or unpredictable, experienced in a non-serious (unthreatening, safe) context. Given examples include peek-a-boo, which can make a child laugh but also cry if the child is not perceiving the situation as safe. Also that we can't tickle ourselves and tickling is induced by stimulating vulnerable body areas. Similarily, apparently in apes laughter is mainly induced by &quot;tickling in conjunction with mock aggression and chasing&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They explain the function of (Duchenne, that is stimulus-driven &quot;honest&quot; as opposed to voluntary) laughter to be propagation of &quot;positive affect&quot; in a group, as it utilises the chameleon effect (it is contagious) which apparently has been shown to exist for its &quot;cooperative value&quot;. Other studies seem to have shown that a) we are thirty times more likely to laugh in a social context than by ourselves and b) the contagiousness of laughter response increases with group size, making it an efficient tool for coordinating a group and getting everyone into the same emotional state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for other animals, the article doesn't address that. It does seem like a different question to me so I would consider separating that into a second one.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-05-05T23:56:03.467" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="2124" PostTypeId="1" AcceptedAnswerId="2126" CreationDate="2012-05-06T04:19:09.497" Score="8" ViewCount="163" Body="&lt;p&gt;Watermelon is just starting to come in season in the northeastern U.S., and having a seedless watermelon is convenient.  The only downside is, the &quot;seedless&quot; almost always still have the immature, sterile white seeds in them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the mechanism for breeding these watermelons so that only these white seeds remain?  What is the genotype that results?  Could the genetics be modified so that there are virtually no seeds (short of any minor aberrations) left in the flesh of the fruit?&lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2016-09-12T03:05:16.490" Title="Why can't we breed watermelons without any remaining seeds in the flesh?" Tags="&lt;genetics&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2125" PostTypeId="2" ParentId="2091" CreationDate="2012-05-06T04:38:07.107" Score="2" Body="&lt;p&gt;I would say that while you could not just replace oxygen with hydrogen and expect life to just go on normally, it's possible for living things to be energetically provided for by H&lt;sub&gt;2&lt;/sub&gt; if it were found in the environment in enough plenty.  This is just speculation as Armatus points out metabolism does not work this way in animals, but I think that its quite possible a living organism could live off of H&lt;sub&gt;2&lt;/sub&gt; as an energy source. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Extremophiles can metabolize sulfur in underwater vents rather than oxygen.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the soil, anoxic metabolisms reduce nitrogn gas to ammonia.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photosynthesis uses light to reduce CO&lt;sub&gt;2&lt;/sub&gt; to glucose.  Atmospheric molecular oxygen is provided entirely by photosynthesis, and at one point there was little or none of it in the atmosphere and living things were found everywhere.  The glucose metabolism came after O&lt;sub&gt;2&lt;/sub&gt; appeared.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main point is that H&lt;sub&gt;2&lt;/sub&gt; stores a reasonable amount of energy even if free oxygen is not available to drive the formation of water from another oxide, or even more exotic chemistry. There's not thermodynamic reason that it couldn't work and biology on earth has proven to be versatile in getting chemical energy wherever it needs to. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its xenobiology and speculation, but I feel that if microorganisms evolved on a gas giant with a primarily hydrogen atmosphere, they could use the redox energy from H&lt;sub&gt;2&lt;/sub&gt;, which is quite reactive even without O&lt;sub&gt;2&lt;/sub&gt; present.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="69" LastEditDate="2012-05-06T10:41:26.650" LastActivityDate="2012-05-06T10:41:26.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2126" PostTypeId="2" ParentId="2124" CreationDate="2012-05-06T04:44:28.690" Score="7" Body="&lt;p&gt;The seedless watermelons, like bananas, are a crop that are specifically bred to be trisomic (three copies of a chromosome). The consequence is the seeds are non-viable.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-05-06T04:44:28.690" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2127" PostTypeId="2" ParentId="2119" CreationDate="2012-05-06T06:38:11.467" Score="4" Body="&lt;p&gt;Some researchers consider the neural circuitry responsible for orgasm vestigial in women. I disagree with this for a number of reasons, but here is a book exploring the hypothesis:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0674022467&quot; rel=&quot;nofollow&quot;&gt;http://www.amazon.com/The-Case-Female-Orgasm-Evolution/dp/0674022467/ref=sr_1_1?ie=UTF8&amp;amp;qid=1336286206&amp;amp;sr=8-1&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="510" LastActivityDate="2012-05-06T06:38:11.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2128" PostTypeId="1" AcceptedAnswerId="2129" CreationDate="2011-07-24T22:17:52.760" Score="34" ViewCount="11406" Body="&lt;p&gt;I heard you should wait some time until your eyes adapt to darkness and are able to see smallest luminosity differences, otherwise you might overlook faint objects in the ocular. Are there any rules of thumb here?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about looking for 5 minutes on your bright laptop, do you have to wait again the same time or wear some sunglasses? ;)&lt;/p&gt;&#xA;" OwnerUserId="45" OwnerDisplayName="Hauser" LastEditorUserId="69" LastEditDate="2012-05-06T10:42:02.747" LastActivityDate="2019-03-31T04:30:13.910" Title="How long do your eyes need to adapt to darkness and reach full contrast?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2129" PostTypeId="2" ParentId="2128" CreationDate="2011-07-25T00:43:29.550" Score="30" Body="&lt;p&gt;Actually, the US Army and &lt;a href=&quot;http://210.60.119.10/milmed/avitation/file-air/%B2%B4%AC%EC%B0%DD%C3D/NVG/NVG3-01.HTM&quot; rel=&quot;nofollow noreferrer&quot;&gt;Air Force&lt;/a&gt; (and I assume the Navy) teach their life support troops about this (as well as the aviators), since so many missions are conducted at night.  It is actually some very interesting physiology involved in this.  &lt;a href=&quot;http://usasam.amedd.army.mil/dl/Flight%20Provider%20Refresher/Lesson%203%20Aeromedical%20Physiology/Lesson%203%20part%20G,%20Night%20Vision.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;This Army Instructional manual should be of help&lt;/a&gt; (PDF File).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;On an average it takes 30 to 45 minutes for your rods to be fully dark adapted to night vision.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It also covers things such as Mesopic vision and Scotopic vision, eye health, and how to actually dark adapt.  I suggest it as a good read.  It's less than 14 pages.&lt;/p&gt;&#xA;" OwnerUserId="279" OwnerDisplayName="Larian LeQuella" LastEditorUserId="16866" LastEditDate="2019-03-31T04:30:13.910" LastActivityDate="2019-03-31T04:30:13.910" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="2132" PostTypeId="1" AcceptedAnswerId="7842" CreationDate="2012-05-06T12:08:57.060" Score="11" ViewCount="1707" Body="&lt;p&gt;When one exposes theirs body parts to cold environment (especially foot and hands), they may be numb, with temporarily blocked both muscles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is typical body temperature below which human muscles don't work properly?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, what is the mechanism behind it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interested in case when muscles almost cease to work (e.g one is not able to grasp a cup), not just in small perturbations to strength. &lt;/p&gt;&#xA;" OwnerUserId="129" LastEditorUserId="129" LastEditDate="2013-04-08T09:23:55.727" LastActivityDate="2013-04-13T01:17:59.203" Title="Below which temperature human muscles don't work?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;muscles&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2133" PostTypeId="1" CreationDate="2012-05-06T15:01:31.613" Score="14" ViewCount="1770" Body="&lt;p&gt;This question could be considered a follow-up question to &lt;a href=&quot;https://biology.stackexchange.com/questions/755/why-is-a-lack-of-oxygen-fatal-to-cells&quot;&gt;Why is a lack of oxygen fatal to cells?&lt;/a&gt;, although the top answer there does not address why damage starts to pop in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer says this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Neurons are also highly metabolically active, which means they&#xA;  generate more waste products. A buildup of nitrogenous waste products&#xA;  in the cell (and bloodstream) can be potentially fatal due to it's&#xA;  effects on pH (screws up enzymes and a whole slew of biochemical&#xA;  reactions)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But when the brain is deprived of oxygen, metabolism shuts down. So waste products aren't being generated anymore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;====&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically I'm wondering - what causes neurons, in particular, to die so quickly (relative to other cells, like kidney cells) after they're depleted of energy?&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2012-05-08T15:31:49.487" Title="Why do neurons die so quickly (relative to other cells) when deprived of oxygen?" Tags="&lt;neuroscience&gt;&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2134" PostTypeId="1" AcceptedAnswerId="2563" CreationDate="2012-05-06T15:09:11.683" Score="2" ViewCount="2484" Body="&lt;p&gt;The reaction is basically shown below. Dopamine hydroxylase is an enzyme, so I'm not sure if we can have a theory based on organic chemistry. On the other hand, maybe there is a theory that involves structural biology?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolutionarily speaking - the enzyme has evolved to add OH to the beta-carbon rather than somewhere else. I'm really wondering &lt;em&gt;what&lt;/em&gt; in the enzyme's shape makes the OH added to the beta carbon, rather than somewhere else. In other words, what is the structural mechanism behind substrate specificity?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EuR7O.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="806" LastEditDate="2012-05-07T20:10:04.660" LastActivityDate="2014-10-31T13:16:43.057" Title="What is the reaction mechanism of dopamine hydroxylase converting dopamine to norepinephrine?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2135" PostTypeId="1" CreationDate="2012-05-06T15:21:14.710" Score="8" ViewCount="354" Body="&lt;p&gt;This was a claim by Lynn Margulis explained over at &lt;a href=&quot;http://lymeunderground.com/bugs-within-us-sperm-tails-and-celia-come-from-spirochetes/&quot;&gt;this link&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The sense organs of vertebrates have modified cilia: The rods and cone&#xA;  cells of the eye have cilia, and the balance organ in the inner ear is&#xA;  lined with sensory cilia. You tilt your head to one side and little&#xA;  calcium carbonate stones in your inner ear hit the cilia.  This has&#xA;  been known since shortly after electron microscopy came in. Sensory&#xA;  cilia did not come from random mutations. They came by acquiring a&#xA;  whole genome of a symbiotic bacterium that could already sense light&#xA;  or motion. Specifically, I think it was a spirochete [a&#xA;  corkscrew-shaped bacterium] that became the cilium.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And why would our bodies incorporate spirochetes as part of our basic functionality?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There are many kinds of spirochetes, and if I’m right, some of them&#xA;  are ancestors to the cilia in our cells. Spirochete bacteria are&#xA;  already optimized for sensitivity to motion, light, and chemicals… If&#xA;  I’m right, the whole system—called the cytoskeletal system—came from&#xA;  the incorporation of ancestral spirochetes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="103" LastEditorUserId="307" LastEditDate="2012-05-06T21:27:49.220" LastActivityDate="2012-05-07T09:29:49.117" Title="Is it plausible that eukaryotic organelles like flagella and cilia are the result of endosymbiosis with spirochetes?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2136" PostTypeId="1" CreationDate="2012-05-06T17:45:03.567" Score="2" ViewCount="46" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Possible Duplicate:&lt;/strong&gt;&lt;br&gt;&#xA;  &lt;a href=&quot;https://biology.stackexchange.com/questions/839/how-does-brain-energy-consumption-depend-on-mental-activity&quot;&gt;How does brain energy consumption depend on mental activity?&lt;/a&gt;  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&#xA;&#xA;&lt;p&gt;Our brains consume about &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC124895/&quot; rel=&quot;nofollow noreferrer&quot;&gt;20%&lt;/a&gt; of our energy when we're at rest. How variable is a human brain's energy consumption? Will thinking harder consume more energy? Does this change significantly when we sleep? &lt;/p&gt;&#xA;" OwnerUserId="810" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2012-05-06T17:45:03.567" Title="How much does a human brain's metabolic rate vary?" Tags="&lt;human-anatomy&gt;&lt;metabolism&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ClosedDate="2012-05-06T22:12:56.830" ContentLicense="CC BY-SA 3.0" />
  <row Id="2137" PostTypeId="1" AcceptedAnswerId="2155" CreationDate="2012-05-06T19:01:51.477" Score="12" ViewCount="573" Body="&lt;p&gt;Looking at the swimming birds building nests just across my garden, I suddenly wondered how evolution came to swimming birds and whether flying birds started swimming or whether swimming bird like animals started flying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What came first and when and why?&lt;/p&gt;&#xA;" OwnerUserId="750" LastActivityDate="2012-05-07T09:58:42.903" Title="Did we first have swimming birds or flying birds?" Tags="&lt;evolution&gt;&lt;ornithology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2139" PostTypeId="5" CreationDate="2012-05-06T19:55:17.623" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-06T19:55:17.623" LastActivityDate="2012-05-06T19:55:17.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2140" PostTypeId="4" CreationDate="2012-05-06T19:55:17.623" Score="0" Body="Cells and organisms containing more than two paired (homologous) sets of chromosomes." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-05-06T21:28:55.490" LastActivityDate="2012-05-06T21:28:55.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2141" PostTypeId="5" CreationDate="2012-05-06T19:56:01.510" Score="0" Body="&lt;p&gt;Historically, these bacterially synthesized enzymes were called restriction endonucleases because they &lt;strong&gt;restricted&lt;/strong&gt; bacteriophages from infecting through digestion of viral DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are four types of restriction enzymess:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Type I: Can both methylate (SAM dependent) and digest DNA (ATP dependent). Cleave several nucleotides away from the restriction sites. &lt;/li&gt;&#xA;&lt;li&gt;Type II: Cleave at the restriction site. No methyl-transferase activity. &lt;/li&gt;&#xA;&lt;li&gt;Type III: Cleave 20-30 nt away from the restriction sites in ATP dependent way. Have methyl-transferase activity. &lt;/li&gt;&#xA;&lt;li&gt;Type IV: Cleave methylated DNA. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="4101" LastEditDate="2013-10-31T18:21:01.577" LastActivityDate="2013-10-31T18:21:01.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2142" PostTypeId="4" CreationDate="2012-05-06T19:56:01.510" Score="0" Body="Endonucleases are enyzmes (usually derived from bacterial sources) which cleave DNA at defined &quot;restriction&quot; sites." OwnerUserId="307" LastEditorUserId="5144" LastEditDate="2014-03-16T22:10:14.787" LastActivityDate="2014-03-16T22:10:14.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2143" PostTypeId="5" CreationDate="2012-05-06T19:56:37.997" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-06T19:56:37.997" LastActivityDate="2012-05-06T19:56:37.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2144" PostTypeId="4" CreationDate="2012-05-06T19:56:37.997" Score="0" Body="A complex of snRNA and protein subunits that removes introns from a transcribed pre-mRNA (hnRNA) segment." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-05-06T21:30:34.410" LastActivityDate="2012-05-06T21:30:34.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2145" PostTypeId="5" CreationDate="2012-05-06T19:59:00.070" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-06T19:59:00.070" LastActivityDate="2012-05-06T19:59:00.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2146" PostTypeId="4" CreationDate="2012-05-06T19:59:00.070" Score="0" Body="The medical specialty involving the diagnosis and treatment of all categories of disease involving the central, peripheral, and autonomic nervous systems, including their coverings, blood vessels, and all effector tissue, such as muscle." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-05-06T21:28:49.030" LastActivityDate="2012-05-06T21:28:49.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2147" PostTypeId="5" CreationDate="2012-05-06T20:00:08.117" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-06T20:00:08.117" LastActivityDate="2012-05-06T20:00:08.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2148" PostTypeId="4" CreationDate="2012-05-06T20:00:08.117" Score="0" Body="Thermodynamics in biology is the study of energy transfer within and between cells, organisms, and their environment, including the underlying chemical reactions." OwnerUserId="307" LastEditorUserId="4101" LastEditDate="2013-10-25T19:42:39.010" LastActivityDate="2013-10-25T19:42:39.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2149" PostTypeId="5" CreationDate="2012-05-06T20:00:50.737" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-06T20:00:50.737" LastActivityDate="2012-05-06T20:00:50.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2150" PostTypeId="4" CreationDate="2012-05-06T20:00:50.737" Score="0" Body="The branch of biology, chemistry, and medicine concerned with the study of the adverse effects of chemicals on living organisms." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-05-06T21:30:38.763" LastActivityDate="2012-05-06T21:30:38.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2151" PostTypeId="5" CreationDate="2012-05-06T20:02:42.937" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-06T20:02:42.937" LastActivityDate="2012-05-06T20:02:42.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2152" PostTypeId="4" CreationDate="2012-05-06T20:02:42.937" Score="0" Body="It concerns a type of molecule that has a non-superposable mirror image." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-05-06T21:28:19.187" LastActivityDate="2012-05-06T21:28:19.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2153" PostTypeId="5" CreationDate="2012-05-06T20:03:30.343" Score="0" Body="&lt;p&gt;A selectively-permeable biological membrane that separates the interior of all cells from the outside environment.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-29T09:10:15.020" LastActivityDate="2017-03-29T09:10:15.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2154" PostTypeId="4" CreationDate="2012-05-06T20:03:30.343" Score="0" Body="A selectively-permeable biological membrane that separates the interior of all cells from the outside environment." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-05-06T21:28:36.113" LastActivityDate="2012-05-06T21:28:36.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2155" PostTypeId="2" ParentId="2137" CreationDate="2012-05-06T22:18:32.860" Score="13" Body="&lt;p&gt;Flying came first, as far as we know. The earliest known bird (currently), &lt;a href=&quot;http://www.ucmp.berkeley.edu/diapsids/birds/archaeopteryx.html&quot;&gt;&lt;em&gt;Archaeopteryx lithographica&lt;/em&gt;&lt;/a&gt;, already had aerodynamic feathers (&lt;a href=&quot;http://www.sciencemag.org/content/203/4384/1021&quot;&gt;Feduccia and Tordoff, 1979&lt;/a&gt;). The &lt;a href=&quot;http://www.ucmp.berkeley.edu/mesozoic/jurassic/solnhofen.html&quot;&gt;Solnhofen Limestone&lt;/a&gt;, where it was discovered, is ~145 million years old, so we can place the &quot;when&quot; flight evolved to greater than or equal to that time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;a href=&quot;http://www.sciencemag.org/content/312/5780/1640&quot;&gt;Gansus yumenensis&lt;/a&gt;&lt;/em&gt; is regarded as the earliest aquatic bird and is dated from ~120 million years ago. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Hesperornithes&quot;&gt;Hesperornithiformes&lt;/a&gt; are the sister taxon of &lt;em&gt;Gansus&lt;/em&gt; (less derived) and also aquatic. However, they date from ~85 million years ago. It is not clear whether the ancestors of Hesperornithiformes were also aquatic. Because they branched off the main line of birds before &lt;em&gt;Gansus&lt;/em&gt;, these ancestors would likely predate &lt;em&gt;Gansus&lt;/em&gt;, but those relatives have not yet been discovered.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-05-06T22:18:32.860" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2157" PostTypeId="1" AcceptedAnswerId="2160" CreationDate="2012-05-07T07:15:00.863" Score="14" ViewCount="19564" Body="&lt;p&gt;Did animals evolve from plants? Did animals' ancestors have chloroplasts in their cells?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="4101" LastEditDate="2013-09-25T13:28:26.813" LastActivityDate="2013-09-25T13:28:26.813" Title="Did animals evolve from plants?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;botany&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2159" PostTypeId="2" ParentId="2157" CreationDate="2012-05-07T09:08:29.487" Score="10" Body="&lt;p&gt;No. Animals form the kingdom &lt;a href=&quot;http://en.wikipedia.org/wiki/Animalia&quot;&gt;Animalia&lt;/a&gt; (or Metazoa) which is distinct from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Plantae&quot;&gt;Plantae&lt;/a&gt; kingdom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both evolved independently from single-celled eukaryotes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, animals are more closely related to fungi than to plants.&lt;/p&gt;&#xA;" OwnerUserId="166" LastActivityDate="2012-05-07T09:08:29.487" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="2160" PostTypeId="2" ParentId="2157" CreationDate="2012-05-07T09:14:50.620" Score="23" Body="&lt;p&gt;See this paper &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1689654/pdf/10097391.pdf&quot;&gt;Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi&lt;/a&gt;&quot; for information on the divergence estimates (I'm not sure if there are more recent papers discussing this).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants, animals and fungi are eukaryotes, distinct from eubacteria and archaebacteria, which are prokaryotes. The difference being in the composition of the cell, particularly a nucleus contained within a membrane for eukaryotes, along with other membrane bound organelles, e.g. chloroplasts. They all share a common ancestor, according to this paper, that split 1.576 Bya (billion years ago) +/- 88 Mya (although it states the relationships are unresolved - it is often difficult to resolve relationships so deep in a tree). They form distinct groups known as Kingdoms under Linnaean based biological classification; the Fungi, Plantae and Animalia. Thus, in answer to your question, no, animals did not evolve from plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants have chloroplasts in their cells, which provide the ability to produce energy via photosynthesis. It is thought that the chloroplast resulted from a symbiotic relationship between early plants and a cyanobacteria in that they both relied on each other for survival and so coevolved. Animals don't contain chloroplasts and instead contain an organelle called the mitochondria (although most plants also have mitochondria), which is also thought to have been a bacterial endosymbiont, probably related to &lt;a href=&quot;http://genomebiology.com/2001/2/6/reviews/1018&quot;&gt;rikettsias&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Protists also contain chloroplasts. The protists are intermediate between all three groups and have been notoriously difficult to classify, being placed into a fourth Kingdom, the Protozoa, although this grouping has been contested. The current Cavalier-Smith system was proposed in 2004 and classifies life into &lt;a href=&quot;http://www.cladocera.de/protozoa/cavalier-smith_2004_prs.pdf&quot;&gt;6 Kingdoms&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chloroplasts are thought to have evolved from a single endosymbiotic event in Archaeplastida, although there are evidence to suggest some secondary endosymbiotic events. Check out &lt;a href=&quot;http://www.biomedcentral.com/1471-2148/9/197&quot;&gt;this paper&lt;/a&gt; for more information; figure 1 shows the relationships between the different groups and the endosymbiotic events. The Opisthokonts are the origin of the Fungi and Animalia kingdoms.&lt;/p&gt;&#xA;" OwnerDisplayName="user49" LastEditorUserId="430" LastEditDate="2012-06-10T14:02:52.717" LastActivityDate="2012-06-10T14:02:52.717" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="2161" PostTypeId="2" ParentId="2135" CreationDate="2012-05-07T09:29:49.117" Score="3" Body="&lt;p&gt;Well, since all cells in a multi-cellular organism originally come from the same precursor cells, it’s hard to argue that some of them have endosymbiotic compartments that are missing in others, and notably their precursor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notably, there are species which possess both ciliary and rhabdomeric photoreceptor cells, and their precursor is non-ciliary. This is incompatible with Margulis’ endosymbiosis hypothesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PZ Myers has a good &lt;a href=&quot;http://scienceblogs.com/pharyngula/2006/09/rhabdomeric_and_ciliary_eyes.php&quot; rel=&quot;nofollow&quot;&gt;summary&lt;/a&gt; of the relevant papers [1, 2].&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;[1] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15514158&quot; rel=&quot;nofollow&quot;&gt;D. Arendt, K Tessmar-Raible &lt;em&gt;&amp;amp; al.&lt;/em&gt;, &lt;em&gt;Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain&lt;/em&gt;, Science 306, 2004.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;[2] &lt;a href=&quot;http://www.ijdb.ehu.es/web/paper.php?doi=14756332&quot; rel=&quot;nofollow&quot;&gt;D. Arendt, &lt;em&gt;Evolution of eyes and photoreceptor cell types&lt;/em&gt;, Int J Dev Biol. 47, 2003.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="166" LastActivityDate="2012-05-07T09:29:49.117" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2163" PostTypeId="2" ParentId="2137" CreationDate="2012-05-07T09:58:42.903" Score="6" Body="&lt;p&gt;Another way to look at this is: &lt;em&gt;How do you evolve flight when you're aquatic?&lt;/em&gt; There are &lt;a href=&quot;http://en.wikipedia.org/wiki/Origin_of_avian_flight&quot;&gt;three proposed models&lt;/a&gt; (or even &lt;a href=&quot;http://www.ucmp.berkeley.edu/vertebrates/flight/origins.html&quot;&gt;five&lt;/a&gt;) for the evolution of flight:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;wings helped predators to better jump at prey from high positions&lt;/li&gt;&#xA;&lt;li&gt;wings helped a jumping animal to make longer jumps&lt;/li&gt;&#xA;&lt;li&gt;wings helped a tree-living animal to get around&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;All of these models assume that you have a high or solid surface to start flying from. Water, in contrast, is a difficult underground to start flying from (being flat and soft). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In contrast, to evolve swimming for &quot;terrestrial&quot; bird seems much more straightforward.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-05-07T09:58:42.903" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2165" PostTypeId="2" ParentId="2119" CreationDate="2012-05-07T14:27:00.327" Score="1" Body="&lt;p&gt;Females of Rangifer tarandus have horns which only used by males in competitions. Other species of deer only have males with horns.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from this, possibly, clitoris and vulvar lips have no purpose in women: the vulvar lips are underdeveloped halves of scrotum, and clitoris has no need to be so sensitive as it is because it plays no role in sexual reproduction in females.&lt;/p&gt;&#xA;" OwnerUserId="408" LastActivityDate="2012-05-07T14:27:00.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2166" PostTypeId="2" ParentId="2075" CreationDate="2012-05-07T14:56:28.823" Score="5" Body="&lt;p&gt;As mentioned in the other answer, red light does not affect the melanopsin receptors in eyes. These receptors not only regulate body rhythm but also &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12808468&quot; rel=&quot;nofollow&quot;&gt;regulate the diameters of the eye pupils&lt;/a&gt;. Once they are stimulated, the eye thinks that there is enough light around and the pupils get smaller to protect the eye against over-exposition, which reduces sensitivity.&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="810" LastEditDate="2012-05-07T15:27:41.903" LastActivityDate="2012-05-07T15:27:41.903" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2168" PostTypeId="2" ParentId="2067" CreationDate="2012-05-07T22:51:14.797" Score="3" Body="&lt;p&gt;Storage conditions and shelf life are some of the things that you should consider in comparing columns.&lt;/p&gt;&#xA;" OwnerUserId="798" LastEditorUserId="57" LastEditDate="2012-07-27T06:27:23.853" LastActivityDate="2012-07-27T06:27:23.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2169" PostTypeId="1" CreationDate="2012-05-08T01:03:25.713" Score="4" ViewCount="75" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Possible Duplicate:&lt;/strong&gt;&lt;br&gt;&#xA;  &lt;a href=&quot;https://biology.stackexchange.com/questions/2103/crossing-mutant-strains-on-minimal-media-problem&quot;&gt;Crossing mutant strains on minimal media problem&lt;/a&gt;  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&#xA;&#xA;&lt;p&gt;I'm studying this problem for my genetics final:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/D1y2P.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My Attempt:&lt;/strong&gt;   The answer for part B is met2 and the answer for part C is Df1.  Met2 and met 1 both have 1 no so i'm not sure how met2 is in the middle.  I didn't even know complementation tests could tell gene location. I think the answer to part C is because df1 has the most NOs, which means it's missing the most DNA.  (If it had that DNA, it would complement).&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2012-05-08T01:03:25.713" Title="Determine which gene is in the middle complementation" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2012-05-09T06:03:19.497" ContentLicense="CC BY-SA 3.0" />
  <row Id="2171" PostTypeId="1" CreationDate="2012-05-08T03:58:15.777" Score="8" ViewCount="126" Body="&lt;p&gt;In a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22031728&quot;&gt;large trial&lt;/a&gt;, screening yearly for lung cancer hasn't reduced mortality rates. Why is this? Isn't cancer best treatable when caught early? Is this because lung cancer is hard to treat anyway, because yearly is not frequent enough, or why?&lt;/p&gt;&#xA;" OwnerUserId="845" LastEditorDisplayName="user560" LastEditDate="2012-05-08T13:05:46.887" LastActivityDate="2012-05-09T09:10:42.003" Title="Why doesn't yearly screening for lung cancer decrease mortality rates?" Tags="&lt;epidemiology&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2172" PostTypeId="1" AcceptedAnswerId="2173" CreationDate="2012-05-08T08:44:54.210" Score="8" ViewCount="10533" Body="&lt;p&gt;I read &lt;a href=&quot;http://www.nature.com/?file=/ijo/journal/v21/n9/abs/0800473a.html&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://jas.fass.org/content/48/6/1530.full.pdf&quot;&gt;here&lt;/a&gt; that the function of lipoprotein lipase is to facilitate fat uptake and storage in adipose tissue. Could anyone provide a slightly more expanded explanation, without going into too much detail, and without the use of too much jargon (I am not a biologist). I have read the wikipedia page, but sadly I didn't understand it....Thanks !&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: One of the things that is confusing me is what &quot;fat uptake&quot; means in this context.&lt;/p&gt;&#xA;" OwnerUserId="835" LastEditorUserId="835" LastEditDate="2012-05-08T09:24:43.160" LastActivityDate="2016-11-28T03:26:34.670" Title="Primary function of the enzyme lipoprotein lipase" Tags="&lt;human-biology&gt;&lt;metabolism&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2173" PostTypeId="2" ParentId="2172" CreationDate="2012-05-08T10:18:23.130" Score="11" Body="&lt;p&gt;Fat uptake means cells eating fat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll try to keep it simple, so forget the many approximations. You need first to consider that most fat circulates in the blood under the form of &lt;a href=&quot;http://en.wikipedia.org/wiki/Triglyceride&quot; rel=&quot;noreferrer&quot;&gt;triglycerides (TG)&lt;/a&gt;. TG are not soluble in water, so how do they circulate? They are hidden inside cargo vehicles called &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipoprotein&quot; rel=&quot;noreferrer&quot;&gt;lipoproteins&lt;/a&gt;. When a circulating lipoprotein touches a cell, if the cell expresses lipoprotein lipase (LPL), first LPL would trap the lipoprotein cargo, and then will start to catabolize the TG.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Importantly, there are no efficient TG cargoes inside the cell, so &lt;strong&gt;the function of lipoprotein lipase&lt;/strong&gt; is to make fat easy to move inside the cell. TG are a chemical assembly of one glycerol and three fatty acids. Of note, there are good fatty acid cargoes inside the cell, so LPL will break TG into glycerol and fatty acids so that &lt;a href=&quot;http://www.wiley.com/legacy/college/boyer/0470003790/animations/fatty_acid_metabolism/fatty_acid_metabolism.htm&quot; rel=&quot;noreferrer&quot;&gt;they can be further metabolized&lt;/a&gt; depending on the cell type.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heart and muscle cells will bring fatty acids to mitochondria where they will be oxidized to produce energy. With reference to your question, adipocyte cells will bring fatty acids to other cellular compartments where they will be converted back to triglycerides and stored as fat. That's why you read that LPL facilitates fat uptake and storage in adipose tissue.&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="69" LastEditDate="2012-05-08T18:55:25.597" LastActivityDate="2012-05-08T18:55:25.597" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2174" PostTypeId="1" AcceptedAnswerId="2521" CreationDate="2012-05-08T12:16:44.443" Score="2" ViewCount="189" Body="&lt;p&gt;Is there a website or organization cataloging lists of biological species to have been recently found of great economic value? For example, a plant that wasn't of economic relevance a while ago but has been found recently to be important, due to advances in breeding varieties and more crops being planted. The same for species that were already important but have turned to be even more important in the last few years.&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="3952" LastEditDate="2013-08-08T00:09:42.657" LastActivityDate="2013-08-08T00:09:42.657" Title="List of species recently found of economic value" Tags="&lt;zoology&gt;&lt;botany&gt;&lt;ethnobiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2175" PostTypeId="2" ParentId="2133" CreationDate="2012-05-08T15:30:03.937" Score="10" Body="&lt;p&gt;There is a good review in the Journal of Experimental Biology (Bickler and Donohoe 2002, &lt;a href=&quot;http://jeb.biologists.org/content/205/23/3579.full.pdf&quot;&gt;JEB 205, 3579–3585&lt;/a&gt;) I will just summarize for those that do not have access to the review.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neurons use lot of energy to maintain their polarized state, this is not required to other cells. When O2 or blood flow is reduced, the neuronal ATP levels breaks down very fast, with 90% ATP depleted in less than 5 minutes. Without ATP, the neuron can not maintain the correct ion flux, so depolarization occurs causing &lt;a href=&quot;http://en.wikipedia.org/wiki/Excitotoxicity&quot;&gt;glutamate excitotoxicity&lt;/a&gt;, cell swelling and finally cell death.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-05-08T15:30:03.937" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2176" PostTypeId="1" AcceptedAnswerId="2178" CreationDate="2012-05-08T16:55:43.580" Score="4" ViewCount="293" Body="&lt;p&gt;As far as I've seen, this expression is almost always used in relation to gene expression profiling. Unfortunately, I have no background in this area. Can someone please explain this in layman terms?&lt;/p&gt;&#xA;" OwnerUserId="846" LastEditorUserId="307" LastEditDate="2012-05-08T17:34:38.553" LastActivityDate="2012-05-08T17:45:35.717" Title="What exactly is meant by the expression &quot;differentially expressed&quot;?" Tags="&lt;genetics&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2178" PostTypeId="2" ParentId="2176" CreationDate="2012-05-08T17:45:35.717" Score="7" Body="&lt;p&gt;Although each cell of your body essentially contains the same DNA and the same genes, cells in different tissues express (turn on) different genes under different conditions. Measuring differential gene expression involves looking at the amount of expression for a gene (or set of genes) in two contrasting scenarios. The contrast could be across different times, different tissues, different conditions, different related species, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When, you say a gene is &quot;differentially expressed&quot;, this is very context-specific. The phrase means nothing by itself, and it is only useful in terms of the applicable contrast. For example, the statement &quot;gene A is differentially expressed&quot; is uninformative, while the statement &quot;gene A is differentially expressed in liver and muscle tissue&quot; is descriptive--it tells you that liver tissues and muscle tissues have a significantly different level of gene A products. Often the terms &quot;up-regulated&quot; and &quot;down-regulated&quot; are also used to provide additional detail. In the context of the previous example, the statement &quot;gene A is up-regulated in muscle tissues&quot; tells you that the level of gene A products is higher in muscle tissues than in liver tissues.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-05-08T17:45:35.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2179" PostTypeId="1" AcceptedAnswerId="2233" CreationDate="2012-05-08T22:03:00.973" Score="7" ViewCount="130" Body="&lt;p&gt;A fairly recent meta-analysis of studies examining the association between adult obesity and polymorphisms of the FTO gene (&lt;a href=&quot;http://www.biomedcentral.com/1741-7015/9/71&quot; rel=&quot;nofollow&quot;&gt;Peng et al., 2011&lt;/a&gt;). The paper looked at 59 studies and concluded that, &quot;&lt;em&gt;FTO may represent a low-penetrance susceptible gene for obesity risk&lt;/em&gt;&quot;, although the association was weaker (or non-existent) for some ethnic groups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are other polymorphic genes which are currently known to be more strongly associated with obesity risk than the FTO gene?&lt;/p&gt;&#xA;" OwnerUserId="835" LastEditorUserId="16299" LastEditDate="2016-01-01T01:29:59.517" LastActivityDate="2016-01-01T01:29:59.517" Title="How many, and how severe, are known single gene polymorphisms for obesity?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;metabolism&gt;&lt;epidemiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2180" PostTypeId="1" AcceptedAnswerId="2243" CreationDate="2012-05-09T00:57:21.010" Score="8" ViewCount="26608" Body="&lt;p&gt;I'm aware that hair can be curly because of the disulfide bond interactions in between cysteine amino acids in alpha-keratin filaments. However, I'm curious as to the biochemistry involved in straightening hair with a straightening iron, as well as with &quot;perming&quot; hair. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens at the molecular level? I suspect that a straightening iron simply disrupts the present disulfide bonds, but I'm only speculating.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-05-09T01:31:18.677" LastActivityDate="2017-06-23T02:56:52.217" Title="Molecularly, why can you straighten or perm hair?" Tags="&lt;biochemistry&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2181" PostTypeId="1" AcceptedAnswerId="2210" CreationDate="2012-05-09T01:44:21.690" Score="7" ViewCount="117" Body="&lt;p&gt;Nuclear receptors can influence transcription far up- or downstream from their own binding sites by looping DNA (&lt;a href=&quot;http://dx.doi.org/10.1016/j.jmb.2004.08.070&quot; rel=&quot;nofollow&quot;&gt;Rubina et al.; J Mol Bio 2004&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure how exactly the receptors first attach to the DNA (dimers on each site first or the whole complex on one site), but in any case they will need to attach to one response element, then loop the DNA and bind the other response element. It seems like something that should be obvious, but I cannot stop wondering: How do the receptors &lt;em&gt;locate&lt;/em&gt; the other site?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Normally I would simply say: diffusion - it just randomly happens. But I imagine bending DNA in such a way would require a lot of energy; too much to just randomly waste it trying to find another site.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="810" LastEditDate="2012-05-09T15:05:30.913" LastActivityDate="2012-05-09T15:05:30.913" Title="How do nuclear receptors locate each other to form a DNA loop?" Tags="&lt;dna&gt;&lt;cell-biology&gt;&lt;molecular-genetics&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2182" PostTypeId="5" CreationDate="2012-05-09T02:25:21.947" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-09T02:25:21.947" LastActivityDate="2012-05-09T02:25:21.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2183" PostTypeId="4" CreationDate="2012-05-09T02:25:21.947" Score="0" Body="The entirety of an organism's hereditary information." OwnerUserId="851" LastEditorUserId="851" LastEditDate="2012-05-09T02:31:13.140" LastActivityDate="2012-05-09T02:31:13.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2184" PostTypeId="5" CreationDate="2012-05-09T02:26:00.013" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-09T02:26:00.013" LastActivityDate="2012-05-09T02:26:00.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2185" PostTypeId="4" CreationDate="2012-05-09T02:26:00.013" Score="0" Body="The motion of dispersed particles relative to a fluid under the influence of a spatially uniform electric field." OwnerUserId="851" LastEditorUserId="851" LastEditDate="2012-05-09T02:31:05.043" LastActivityDate="2012-05-09T02:31:05.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2186" PostTypeId="5" CreationDate="2012-05-09T02:26:43.520" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-09T02:26:43.520" LastActivityDate="2012-05-09T02:26:43.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2187" PostTypeId="4" CreationDate="2012-05-09T02:26:43.520" Score="0" Body="Homologous characters of organisms that have seemingly lost all or most of their original function in a species through evolution." OwnerUserId="851" LastEditorUserId="851" LastEditDate="2012-05-09T02:31:46.977" LastActivityDate="2012-05-09T02:31:46.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2188" PostTypeId="5" CreationDate="2012-05-09T02:27:16.953" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-09T02:27:16.953" LastActivityDate="2012-05-09T02:27:16.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2189" PostTypeId="4" CreationDate="2012-05-09T02:27:16.953" Score="0" Body="A method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions." OwnerUserId="851" LastEditorUserId="851" LastEditDate="2012-05-09T02:32:00.550" LastActivityDate="2012-05-09T02:32:00.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2190" PostTypeId="5" CreationDate="2012-05-09T02:27:49.043" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-09T02:27:49.043" LastActivityDate="2012-05-09T02:27:49.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2191" PostTypeId="4" CreationDate="2012-05-09T02:27:49.043" Score="0" Body="The administration of antigenic material to stimulate the immune system of an individual to develop adaptive immunity to a disease." OwnerUserId="851" LastEditorUserId="851" LastEditDate="2012-05-09T02:31:44.437" LastActivityDate="2012-05-09T02:31:44.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2192" PostTypeId="5" CreationDate="2012-05-09T02:28:24.610" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-09T02:28:24.610" LastActivityDate="2012-05-09T02:28:24.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2193" PostTypeId="4" CreationDate="2012-05-09T02:28:24.610" Score="0" Body="The genetic alteration of a cell resulting from the direct uptake, incorporation, and expression of exogenous genetic material from its surroundings." OwnerUserId="851" LastEditorUserId="4101" LastEditDate="2013-10-31T19:14:50.253" LastActivityDate="2013-10-31T19:14:50.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2194" PostTypeId="5" CreationDate="2012-05-09T02:29:15.267" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-09T02:29:15.267" LastActivityDate="2012-05-09T02:29:15.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2195" PostTypeId="4" CreationDate="2012-05-09T02:29:15.267" Score="0" Body="The study of parasites, their hosts, and the relationship between them." OwnerUserId="851" LastEditorUserId="851" LastEditDate="2012-05-09T02:31:22.983" LastActivityDate="2012-05-09T02:31:22.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2196" PostTypeId="5" CreationDate="2012-05-09T02:29:47.760" Score="0" Body="&lt;p&gt;Model organisms include &lt;a href=&quot;http://en.wikipedia.org/wiki/California_sea_hare&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Aplysia californica&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information, see &lt;a href=&quot;http://en.wikipedia.org/wiki/Memory&quot; rel=&quot;nofollow&quot;&gt;memory&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Short-term_memory&quot; rel=&quot;nofollow&quot;&gt;short-term memory&lt;/a&gt;, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Long-term_memory&quot; rel=&quot;nofollow&quot;&gt;long-term memory&lt;/a&gt; on Wikipedia. Scholarpedia has a &lt;a href=&quot;http://www.scholarpedia.org/article/Memory&quot; rel=&quot;nofollow&quot;&gt;comprehensive&lt;/a&gt; article on memory as well.  For a popular press introduction, see &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0393329372&quot; rel=&quot;nofollow&quot;&gt;Kandel's&lt;/a&gt; or &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0618219196&quot; rel=&quot;nofollow&quot;&gt;Schacter's&lt;/a&gt; books, written by two leading memory researchers.&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="4101" LastEditDate="2013-10-31T18:22:17.020" LastActivityDate="2013-10-31T18:22:17.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2197" PostTypeId="4" CreationDate="2012-05-09T02:29:47.760" Score="0" Body="The processes by which environmental information is encoded, stored, and retrieved." OwnerUserId="851" LastEditorUserId="4101" LastEditDate="2013-10-31T18:25:11.427" LastActivityDate="2013-10-31T18:25:11.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2198" PostTypeId="5" CreationDate="2012-05-09T02:30:13.500" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;What questions should have this tag?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Questions related to the biochemistry, synthesis, and properties of nucleic acids&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What questions should &lt;strong&gt;not&lt;/strong&gt; have this tag?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;General questions related to DNA replication and transcription, that don't exactly relate with the inherent properties of these nucleic acids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example: How is transcription elongation regulated by epigenetic factors? &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="4101" LastEditDate="2013-10-31T19:30:34.540" LastActivityDate="2013-10-31T19:30:34.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2199" PostTypeId="4" CreationDate="2012-05-09T02:30:13.500" Score="0" Body="Polymers/Oligomers of mononucleotides. Nucleotides are composed of heterocyclic bases such as Adenine, Guanine, Thymine, Cytosine, and Uracil linked to a backbone moeity such as ribose (RNA), deoxyribose (DNA), N-(2-aminoethyl)-glycine (PNA), etc. These monomers are usually linked by phosphodiester bonds as in the case of DNA and RNA but can be other bonds such as peptide bonds in the case of PNA." OwnerUserId="851" LastEditorUserId="4101" LastEditDate="2013-10-31T19:30:34.540" LastActivityDate="2013-10-31T19:30:34.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2200" PostTypeId="5" CreationDate="2012-05-09T02:30:56.543" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-09T02:30:56.543" LastActivityDate="2012-05-09T02:30:56.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2201" PostTypeId="4" CreationDate="2012-05-09T02:30:56.543" Score="0" Body="Sensation is dealing with the processing of the senses, including the traditional senses vision, hearing, taste, smell and touch, but also sense experiences such as vestibular and pain. It typically involves the higher-level cortical brain areas associated with the conscious experience of physical stimuli.  " OwnerUserId="851" LastEditorUserId="3624" LastEditDate="2015-11-06T01:28:23.627" LastActivityDate="2015-11-06T01:28:23.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2202" PostTypeId="5" CreationDate="2012-05-09T02:31:26.933" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-09T02:31:26.933" LastActivityDate="2012-05-09T02:31:26.933" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2203" PostTypeId="4" CreationDate="2012-05-09T02:31:26.933" Score="0" Body="The study of the electrical properties of biological cells and tissues." OwnerUserId="851" LastEditorUserId="851" LastEditDate="2012-05-09T06:03:46.667" LastActivityDate="2012-05-09T06:03:46.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2204" PostTypeId="5" CreationDate="2012-05-09T02:32:47.443" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-09T02:32:47.443" LastActivityDate="2012-05-09T02:32:47.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2205" PostTypeId="4" CreationDate="2012-05-09T02:32:47.443" Score="0" Body="The study of abnormalities of physiological development." OwnerUserId="851" LastEditorUserId="851" LastEditDate="2012-05-09T06:04:08.587" LastActivityDate="2012-05-09T06:04:08.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2206" PostTypeId="2" ParentId="2076" CreationDate="2012-05-09T03:23:28.387" Score="2" Body="&lt;p&gt;In my view, the reason we can't transmit smell is that we don't understand it. That is, we don't have a solid understanding of how odor information is coded, so it is hard to imagine how to build a system that could reproduce that information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is sometimes discussed in terms of a multi-dimensional &quot;odor space,&quot; where each odor could be described by its location along each dimension. The problem is that we don't really know what any of the dimensions are. By contrast, we know that visual space can be described by the intensity of a set of colors in a two-dimensional plane; auditory space is described by frequency and amplitude. It is clear that odors are comprised of chemicals, but we don't yet know where those chemicals fit in odor space. Understanding the odor space is a prerequisite to building a system that could transmit messages from it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, to a great extent, how to engineer a smell transmission system is only partly a biological question. For instance, a CMYK printing system does a fine job at generating images that our RGB photoreceptors understand just fine. A telephone wire can transmit sound without a care about how the cochlea actually works. Transmitted pictures and transmitted sounds work because they activate our photoreceptors and auditory hair cells in the same pattern that the original images and sounds would. We can build systems to do this because we understand the nature of the information sensory systems decode, and we don't need a really deep understanding of the physiology to do that. (Of course, I think figuring out that physiology is great fun, but that's another point.) That is, to build a smell system, it's probably not really necessary to know what every one of the many olfactory receptors does. That's a detail of the way the mammalian olfactory system evolved. The important thing is to understand the nature of odor information. Then it really may be theoretically feasible to create a system to transmit odors.&lt;/p&gt;&#xA;" OwnerUserId="72" LastActivityDate="2012-05-09T03:23:28.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2207" PostTypeId="2" ParentId="1660" CreationDate="2012-05-09T03:31:56.453" Score="13" Body="&lt;p&gt;This answer belongs on Skeptics. Sorry to disappoint, but the &quot;boiled frog&quot; phenomenon is an &quot;old folk warning&quot;. This essentially negates your original question altogether. Neither a cold-blooded animal (such as a frog) or warm-blooded animal will boil to death under the conditions implied by the warning (i.e. escape is permitted and water is heated very gradually).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.conservationmagazine.org/2011/03/frog-fable-brought-to-boil/&quot;&gt;1897 research by German scientist E. W. Scripture, upon which the fable may have first been based, has been deemed flawed by scientists:&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;From Scripture's research: “. . . a live frog can actually be boiled without a&#xA;  movement if the water is heated slowly enough; in one experiment, the&#xA;  temperature was raised at the rate of 0.002 degrees Celsius per&#xA;  second, and the frog was found dead at the end of 2.5 hours without&#xA;  having moved.&quot; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;According to Dr. Karl S. Kruszelnicki (Australian scientist): &quot;[T]he numbers just don’t seem right. If the water comes to a boil,&#xA;  that means a final temperature of 100 degrees Celsius. In that case,&#xA;  the frog would have to have been put into the water at 82 degrees&#xA;  Celsius. Surely, the frog would have died immediately.&quot;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;According to Dr. Victor H. Hutchinson (Herpetologist and Zoology Professor at University of Oklahoma): &#xA;  &quot;The legend is entirely incorrect! The 'critical thermal maxima' of many species of frogs have been&#xA;  determined by several investigators. In this procedure, the water in&#xA;  which a frog is submerged is heated gradually at about 2 degrees&#xA;  Fahrenheit per minute.  As the temperature of the water is gradually&#xA;  increased, the frog will eventually become more and more active in&#xA;  attempts to escape the heated water.  If the container size and&#xA;  opening allow the frog to jump out, it will do so.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://srel.uga.edu/ecoviews/ecoview071223.htm&quot;&gt;Whit Gibbons (University of Georgia) says that there is an important message behind the false legend:&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So where does that leave us with the boiling frog as a metaphor for&#xA;  the human response to economic change or environmental degradation?&#xA;  Well, it's not true that you can induce a frog to willingly remain in&#xA;  boiling water by starting it off in cold water. But that does not&#xA;  diminish the truth of the message that the accumulation of&#xA;  imperceptible changes can have a significant effect on the economy and&#xA;  the environment. We need to be aware of what changes are occurring and&#xA;  to respond to them in a timely fashion. The metaphor lies in the&#xA;  frog's ability to escape from the container: if there's no way out,&#xA;  then the frog's fate is a foregone conclusion.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="838" LastEditorUserId="838" LastEditDate="2012-05-16T03:06:50.493" LastActivityDate="2012-05-16T03:06:50.493" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2208" PostTypeId="1" CreationDate="2012-05-09T05:56:39.907" Score="8" ViewCount="106" Body="&lt;p&gt;This is a follow-up question to &lt;a href=&quot;https://biology.stackexchange.com/questions/2133/why-do-neurons-die-so-quickly-relative-to-other-cells-when-deprived-of-oxygen&quot;&gt;Why do neurons die so quickly (relative to other cells) when deprived of oxygen?&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm particularly interested in the case of reptiles, octopuses, and other invertebrates. Could it be that mammalian neurons are especially oxygen-demanding compared with the neurons of other animals?&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2012-09-04T04:52:12.577" Title="If a non-mammal is starved of oxygen for some time, how long would it take the animal's neurons to die?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2209" PostTypeId="2" ParentId="2171" CreationDate="2012-05-09T09:10:42.003" Score="3" Body="&lt;p&gt;There are a number of reasons, generally, why a screening test may fail to decrease cancer mortality rates:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The screening test may not be very good. I know this seems like an obvious one, but its something of a problem - a screening test will only reduce mortality if it catches cases that are both &lt;em&gt;treatable&lt;/em&gt; and wouldn't be detected in time to treat using other methods. For example, it may be that even if caught slightly later by other methods, lung cancer is equally treatable (or equally difficult to treat).&lt;/li&gt;&#xA;&lt;li&gt;Mortality from false positive tests and subsequent procedures in non-cases offsets any gain in survival among cases.&lt;/li&gt;&#xA;&lt;li&gt;Diagnosis is only one step toward treating a disease. Even if detected, if a disease is not treatable or isn't treated, knowing you have the disease doesn't change your mortality risk.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In this case it appears that a chest radiograph isn't good enough at detecting lung cancer to manifestly improve mortality outcomes. The author's of the paper don't really specify &lt;em&gt;why&lt;/em&gt; this is - though since they're just looking at lung cancer mortality, it's likely not #2.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2012-05-09T09:10:42.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2210" PostTypeId="2" ParentId="2181" CreationDate="2012-05-09T14:24:50.437" Score="3" Body="&lt;p&gt;This probably isn't the complete answer as I don't know so much about eukaryotic transcription, but maybe I can start the answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all DNA bending can be sequence dependent - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7836392&quot; rel=&quot;nofollow&quot;&gt;the double helix is not intrinsically straight&lt;/a&gt;.  DNA is also pretty easy to bend - it spends most of its time coiled pretty easily around histones, and eukaryotes, &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromatin&quot; rel=&quot;nofollow&quot;&gt;supercoiled into chromatin&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In transcription though, &lt;a href=&quot;http://www.nature.com/embor/journal/v8/n2/full/7400898.html&quot; rel=&quot;nofollow&quot;&gt;there are proteins that come along and effect bends in the DNA or even tight loops&lt;/a&gt;, so that the transcription initiation complex (TIC) can be activated by transcription factors (TFs) upstream as the DNA flops over. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;see this happening in this video at about :40:&#xA;&lt;a href=&quot;http://www.youtube.com/watch?v=5MfSYnItYvg&amp;amp;feature=related&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=5MfSYnItYvg&amp;amp;feature=related&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think in some cases there might be other proteins bound upstream of the TIC to make the influence of various TFs greater.   I know in highly regulated genes (such as developmental genes in animals) transcription regulation can be impossibly complicated with lots if internal logic.  The classic example is &lt;a href=&quot;http://www.bio.davidson.edu/people/macampbell/strategies/onegene.html&quot; rel=&quot;nofollow&quot;&gt;ENDO16 from sea urchin&lt;/a&gt; (see second image) which has scores of protein binding sites in front of it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was told that DNA binding proteins find their binding sites at a rate faster than diffusion.  The prof told me that she thought that there might be a tendency to diffuse along the length of the DNA because of its charge.  I have no reference for this, but it might help answer your question as to how the NRs pair up so quickly. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-09T14:24:50.437" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2211" PostTypeId="2" ParentId="1909" CreationDate="2012-05-09T14:38:26.427" Score="4" Body="&lt;p&gt;I only know of one method, but here it is.  You create a sphere the diameter of the &lt;a href=&quot;http://jmol.sourceforge.net/docs/surface/&quot; rel=&quot;nofollow noreferrer&quot;&gt;VdW radius of water, and then 'roll' it along the surface&lt;/a&gt;.  I know this as a Richards-Lee surface, wikipedia has another name for it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pBANE.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This looks complicated, but its not.  you move the probe sphere along the surface of the molecule in the XY plane until it just touches the vdW radius of the protein, keeping the center of the sphere as the surface, all the way around the molecule.  If you like, you can color the surface by the charge of the position too, which is useful for discussing solvent interactions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then you translate along the z axis and do another contour until you run out of protein.  Apparently jmol and other packages will do this for you. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Accessible_surface_area#Methods_of_calculating_ASA&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia references a more mathematical method LCPO&lt;/a&gt;, which I am not so familiar with.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this accurate?  As usual with such calculations its more of a guess than an answer.  You can do the calculation on any structure or any ensemble of structures (like NMR gives).  It doesn't understand how the molecule might be flexible or dynamic.  If you read up on your physical chemistry you see that proteins breathe and can allow diffusion into the core rather readily.  If I recall right, you can get rather large molecules quenching heme flouresence in hemoglobin at room temperature.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are looking to dock 2 proteins, SAS might be more useful.  Its an important piece of information, but not an ultimate answer.  I'm afraid with proteins that doesn't happen so easily. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;@bobthejoe asked about SAS for which no structure exists.&lt;br&gt;&#xA;This is an extremely difficult thing to even guess at.  The non helpful answer is that &lt;a href=&quot;http://www.nature.com/nature/journal/v277/n5696/pdf/277491a0.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;the surface of the protein goes as the cube root of the molecular weight of the protein&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By getting a solution of the protein and shooting it in a syhcrotron, you can get a mean radius of gyration pretty easily which will give you an ellipsoidal volume (and surface area) for a protein.  Again most of the particulars would be lost and this could easily be off by 25% for an irregularly shaped protein.  For a regular globular protein it might give an answer similar to the power law above.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have seen physical chemistry experiments that look for changes in osmotic pressure when the salt concentration in a solution of the protein changes substantially (Adrian Parsegian's work at NIH in the late 80s).   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I doubt you will find any of these answers useful as their mean error is going to be very large (20-200%) and also assumes the protein is soluable and amenable to the experimental conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Solvent probes can help too.  For instance exposing the protein to D20 then doing mass spectroscopy on the protein. This is still only going to give you a general idea of how much of the peptide is surface exposed.  Protein structure is still pretty necessary to getting any accurate measurement of SAS I think.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-05-14T20:20:15.520" LastActivityDate="2012-05-14T20:20:15.520" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2212" PostTypeId="1" AcceptedAnswerId="2221" CreationDate="2012-05-09T21:58:36.123" Score="37" ViewCount="3115" Body="&lt;p&gt;&lt;a href=&quot;http://rsbl.royalsocietypublishing.org/content/early/2012/04/26/rsbl.2012.0298&quot;&gt;A study&lt;/a&gt; was just released by researchers at Scripps Institute of Oceanography revealing a drastic increase in the amount of plastic adrift in the Pacific Ocean. According to the paper, the amount of plastic in the North Pacific Subtropical Convergence Zone has increased 100-fold over the last 40 years. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But most of the &lt;a href=&quot;http://www.huffingtonpost.com/2012/05/09/great-pacific-garbage-patch_n_1501544.html&quot;&gt;news&lt;/a&gt; stories coming out about this discovery are thin on facts about the dangers of plastic. And the research even suggests &lt;a href=&quot;http://blogs.discovermagazine.com/notrocketscience/2012/05/08/insects-that-skate-on-the-ocean-benefit-from-plastic-junk/&quot;&gt;marine wildlife may be benefiting&lt;/a&gt; from the artificial flotsam.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clearly this increase in trash can't be good. Can it?&lt;/p&gt;&#xA;" OwnerUserId="423" LastActivityDate="2012-05-10T11:24:00.957" Title="Is the &quot;Great Pacific Garbage Patch&quot; beneficial for marine wildlife?" Tags="&lt;marine-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2213" PostTypeId="1" AcceptedAnswerId="2226" CreationDate="2012-05-09T22:48:03.380" Score="6" ViewCount="1414" Body="&lt;p&gt;Circulating Tumor Cells (CTCs) are linked with metastasis and their presence can be used to indicate the onset of metastatic cancer. Likewise, the Cancer Stem Cell (CSC) hypothesis suggests that tumorigenic stem cells are the source of cancer. However, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21300848&quot;&gt;microscopy experiments and cytometry&lt;/a&gt; have suggested that the morphology of CTCs and CSCs are quite different. Essentially, we have not been able to find Circulating Cancer Stem Cells (asides Myeloma since they are circulating anyways).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is how similar are these cells? If they are different, is relapse caused by the CSCs from the primary tumor or CTCs in metasises that have become CSC-like?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2017-01-17T08:05:03.717" Title="How similar are Circulating Tumor Cells and Cancer Stem Cells?" Tags="&lt;cell-biology&gt;&lt;cancer&gt;&lt;stem-cells&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2214" PostTypeId="5" CreationDate="2012-05-09T22:53:55.763" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-09T22:53:55.763" LastActivityDate="2012-05-09T22:53:55.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2215" PostTypeId="4" CreationDate="2012-05-09T22:53:55.763" Score="0" Body="Cells which have not fully differentiated yet, i.e. with the potential to develop into other kinds of cells through asymmetric cell division." OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-05-10T03:01:59.607" LastActivityDate="2012-05-10T03:01:59.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2216" PostTypeId="2" ParentId="1484" CreationDate="2012-05-10T02:28:47.900" Score="2" Body="&lt;p&gt;First, the recombination equation is:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;cM = recombinants/(recombinants AND parentals) * 100&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Let's assign the following genotypes for clarity's sake:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;RR = black bristles&#xA;Rr = black bristles&#xA;rr = red bristles&#xA;SS = pebbly eyes&#xA;Ss = pebbly eyes&#xA;ss = shiny eyes&#xA;&#xA;F1 cross: rrSS x RRss = RrSs (all progeny)&#xA;F2 cross: RrSs (F1) x rrss = ?&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;You would have the following gametes: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Parent 1, RrSs = RS, Rs, rS, rs&#xA;Parent 2, rrss = rs, rs, rs, rs&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Draw your punnet square and you get the following genotypes of the offspring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So your GENOTYPES of your F2 cross will be &lt;strong&gt;RrSs, Rrss, rrSs, rrss&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's translate those to phenotypes.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;RrSs: black pebbly (parental)&#xA;Rrss: black shiny (recombinant)&#xA;rrSs: red pebbly (recombinant)&#xA;rrss: red shiny (parental)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Now let's look at recombination frequency. &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;15cM = (recombinants/(recombinants+parentals)*100&#xA;recombinants/(parentals+recombinants) = 15/100&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This tells you for every 15 recombinants, you have 85 parentals. If you scale this up to 1000, that's 150 recombinants for every 850 parentals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your 150 recombinants comes from 75 black/shiny and 75 red/pebbly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your 850 parentals ceoms from 425 black/pebbly and 425 red/shiny.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyways that was my attempt which appears to be directly opposite to what your answer key says. Did you copy it down correctly?&lt;/p&gt;&#xA;" OwnerUserId="177" LastActivityDate="2012-05-10T02:28:47.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2218" PostTypeId="1" CreationDate="2012-05-10T04:57:36.457" Score="7" ViewCount="988" Body="&lt;p&gt;I am trying to create some constructs of a certain protein deleting well defined domains (at either terminus) to determine interaction regions with other proteins etc., 3 constructs with varying start/end sites have ended up being aggregated in &lt;em&gt;E coli&lt;/em&gt; (while the full length protein expresses reasonably well). My question is what considerations one should use to determine start/end sites to maximize chances of getting soluble, purifiable protein. The criterion I used were:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Preferably loop region in known x-ray structure &lt;/li&gt;&#xA;&lt;li&gt;Use hydrophobicity plots to minimize hydrophobic residues at both termini &lt;/li&gt;&#xA;&lt;li&gt;3-4 residue linker between protein and affinity tag (GST/6xHis)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;From personal experience with an earlier construct, this can turn out to be an idiosyncratic exercise but I was wondering if I was missing any crucial parameters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;: I also played around with the PDB file of the non-truncated protein to check whether huge hydrophobic patches were exposed on deletion of the domain(s), and I didn't find any such patches that could potentially be exposed and lead to aggregation&lt;/p&gt;&#xA;" OwnerUserId="223" LastEditorUserId="43" LastEditDate="2012-05-10T13:22:20.823" LastActivityDate="2012-05-11T08:21:19.693" Title="Protein construct design" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;cloning&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2219" PostTypeId="2" ParentId="2218" CreationDate="2012-05-10T07:21:08.137" Score="5" Body="&lt;p&gt;Did you identify structural domains in the protein using Pfam or some other domain detecting peptide search?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's pretty useful to cut your constructs at the boundaries of structurally independent domins in the protein if you know where they are.  Hydrophobicity plots might lead you to cut right in the middle of a protein fold, only exascerbating inclusion body formation/protein precipitation. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="69" LastEditDate="2012-05-11T08:21:19.693" LastActivityDate="2012-05-11T08:21:19.693" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2220" PostTypeId="1" CreationDate="2012-05-10T09:47:18.493" Score="11" ViewCount="103" Body="&lt;p&gt;I've read &lt;a href=&quot;http://dx.doi.org/10.1038/nbt.2199&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; where they specifically modify a region in the rice genome to ablate the binding site of a pathogen, &lt;em&gt;Xanthomonas oryzae&lt;/em&gt;, and disrupt the hijacking of a gene network in the rice genome to the advantage of the pathogen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's an interesting concept but left me wondering how one would determine &lt;em&gt;de novo&lt;/em&gt; the binding of these pathogen effectors into the host if one didn't know them. What would be the steps to determine where are the pathogen's TFs binding the host genome?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: there is the possibility of not knowing which proteins bind to the host genome, so what would be the way of developing the antibodies in this case?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nbt.2199&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Li T, Liu B, Spalding MH, Weeks DP, Yang B&lt;/strong&gt;. 2012. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature biotechnology 30: 390–2.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="787" LastEditorUserId="836" LastEditDate="2012-09-13T06:22:42.120" LastActivityDate="2013-10-24T04:18:02.677" Title="determining genome-wide exogenous binding of pathogens to host genome?" Tags="&lt;transcription&gt;&lt;genomes&gt;&lt;protein-binding&gt;&lt;binding-sites&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2221" PostTypeId="2" ParentId="2212" CreationDate="2012-05-10T11:24:00.957" Score="38" Body="&lt;p&gt;There are very few things in the world that aren't beneficial to &lt;em&gt;some&lt;/em&gt; lifeform.  Even if you were to, say, spill a mixture of persistent broad-spectrum poisons on an area that killed off 99.9% of all species there, the remaining 0.1% that did survive would benefit from the lack of competition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;great garbage patch&quot; is hardly so extreme a phenomenon, but similar effects can be seen there: some species suffer, others benefit.  In that sense, it's no different from any other changing habitat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a conservation viewpoint, there are two issues here that one might find worrying:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;First, novel, extreme or rapidly changing habitats tend to have lower than average biodiversity, at least initially: the few species that thrive in the new environment tend to proliferate at the expense of others, forming a relatively simple (and often not very stable) food web.  Of course, over evolutionary timescales we'd expect the surviving species to adapt and diversify and the ecosystem to settle into a more stable state, but that tends to take a long time compared to the human timescale on which such novel habitats are created.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Also, the effects of the &quot;garbage patch&quot;, or ecological changes in general, are not limited to the directly changed area.  Creating a new habitat in one part of the ocean is one thing; disrupting the ecosystem of the &lt;em&gt;entire&lt;/em&gt; ocean is something else, as doing so leaves no unaffected refuge for the species that are harmed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, fish, birds and marine mammals passing even just occasionally through the patch might end up swallowing plastic and accumulating it in their gut; meanwhile, even for less motile organisms, the patch might act as a population sink, depleting their population density in nearby areas.  And if some organisms, such as the sea skaters mentioned in the article you cite, thrive in the patch, the increased population will likely spill into other areas, potentially harming their competitors or prey species.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;As for why the news are focusing on the beneficial effects of the garbage to the sea skaters, well, that's what the study that prompted this current batch of news stories was about.  It's also seen as newsworthy precisely because it seems so unexpected: we've all heard stories of plastic flotsam &lt;em&gt;harming&lt;/em&gt; wildlife, so finding out that some species are actually benefiting from it has some &quot;man bites dog&quot; style news value.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, it's a lot easier and more convincing to observe something that &lt;em&gt;is&lt;/em&gt; there than something that isn't: we can directly &lt;em&gt;see&lt;/em&gt; these insects laying their eggs on the bits of plastic, giving direct and incontrovertible proof of a causal connection.  Meanwhile, simply observing that some species used to be more common in the area of the patch than it is now is a lot less direct and informative: we might never be sure just &lt;em&gt;how&lt;/em&gt; the patch is harming that species, and it always leaves skeptics an opening to claim that the decline &lt;em&gt;might&lt;/em&gt; be caused by other factors.  With the sea skates, on the other hand, we're not just observing the effect, but the direct mechanism as well.&lt;/p&gt;&#xA;" OwnerUserId="239" LastActivityDate="2012-05-10T11:24:00.957" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2222" PostTypeId="2" ParentId="2220" CreationDate="2012-05-10T11:30:42.003" Score="9" Body="&lt;p&gt;The techniques used to do this are &lt;a href=&quot;http://en.wikipedia.org/wiki/ChIP-Seq&quot; rel=&quot;nofollow&quot;&gt;ChIP-seq&lt;/a&gt; and ChIP-chip.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, you&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;let the pathogen bind to the (highly replicated) DNA&lt;/li&gt;&#xA;&lt;li&gt;cut up the DNA into little random pieces by &lt;a href=&quot;http://en.wikipedia.org/wiki/Sonication&quot; rel=&quot;nofollow&quot;&gt;sonication&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;enrich (“pull down”) the pathogen-bound DNA fragments by using a known antibody which binds to the pathogen&lt;/li&gt;&#xA;&lt;li&gt;sequence the thus enriched DNA&lt;/li&gt;&#xA;&lt;li&gt;map the sequenced fragments back to their original location on the genome.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Wikipedia has a nice picture explaining this process in a little more detail:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/d/d8/Chromatin_immunoprecipitation_sequencing.svg/500px-Chromatin_immunoprecipitation_sequencing.svg.png&quot; alt=&quot;ChIP-seq workflow&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="4101" LastEditDate="2013-10-24T04:18:02.677" LastActivityDate="2013-10-24T04:18:02.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2223" PostTypeId="1" AcceptedAnswerId="2224" CreationDate="2012-05-10T12:50:24.773" Score="18" ViewCount="3903" Body="&lt;p&gt;I have seen a lot of research into molecular mechanisms of diseases/phenotypes use measures of RNA as a 'proxy' for the level of protein available in the cell. Is this actually valid? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My problem with the assumption that RNA levels correlate with that of the active product (i.e. the protein) is that a &lt;em&gt;lot&lt;/em&gt; of post translational regulation occurs, including co-factor binding and phosphorylation, to name but 2. Does anyone know of any studies that have looked into the correlation between RNA levels and protein levels, and separately into the correlations between RNA levels and &lt;em&gt;active&lt;/em&gt; protein?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It makes sense to me that RNA would correlate with protein certainly, but whether this relates to the proteins active function is what I wonder - i.e. there could be a pool that is replenished as and when the protein levels drop, but the proteins are only actually active for short periods in response to specific stimuli. So, does anyone know of any studies that have looked into the correlation between RNA levels and protein levels, and separately into the correlations between RNA levels and active protein?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h3&gt;Update (04.07.12)&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;I have not accepted any answers as yet because none address my question about levels of protein activation, but I concede to Daniel's excellent point that proteins are not all activated in the same way; some are constantly active, some require phosphorylation (multiple sites?), some binding partners... etc! So a study looking at 'global' activation is not yet possible. Yet I was hoping that someone may have read some specific examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I today found an &lt;a href=&quot;http://www.kendricklabs.com/WP1_mRNAvsProtein.pdf&quot; rel=&quot;nofollow&quot;&gt;unpublished review by Nancy Kendrick&lt;/a&gt; of 10 studies that have looked at the correlation between mRNA and protein &lt;em&gt;abundance&lt;/em&gt; - still not relating to &lt;em&gt;activation&lt;/em&gt;. However she finishes the paper as follows;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The conclusion from the ten examples listed above seems inescapable:  mRNA levels cannot be &#xA;  used as surrogates for corresponding protein levels without verification.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If this is her conclusion about protein levels, then any correlation between protein activation and mRNA abundance seems unlikely (as a rule. Some protein levels &lt;em&gt;do&lt;/em&gt; correlate with the RNA - see the paper).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am still interested in any answers that give any information about specific examples of protein activation and mRNA levels - it seems highly unlikely there are no such studies, but I have been as yet unable to find any!&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-07-04T17:30:00.883" LastActivityDate="2012-11-20T23:03:41.373" Title="Do gene expression levels necessarily correspond to levels of protein activation?" Tags="&lt;proteins&gt;&lt;mrna&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2224" PostTypeId="2" ParentId="2223" CreationDate="2012-05-10T13:45:37.783" Score="17" Body="&lt;p&gt;It has been well established that mRNA abundance serves as a poor proxy for protein abundance in most cases. &lt;a href=&quot;http://mcb.asm.org/content/19/3/1720.short&quot;&gt;This paper on yeast&lt;/a&gt; and &lt;a href=&quot;http://www.mcponline.org/content/1/4/304.short&quot;&gt;this paper on cancer&lt;/a&gt; both establish this, although using older techniques (SAGE and microarrays, respectively), while &lt;a href=&quot;http://dx.doi.org/10.1016/j.febslet.2009.10.036&quot;&gt;this more recent review&lt;/a&gt; discusses the topic in light of more recent technologies (e.g. RNA-seq).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps the difficulty with exploring the correlation between mRNA levels and levels of active, mature proteins is that we still know so little about so many proteins and and what makes them active and mature versus inactive, premature, etc. Not all proteins need post-translational modifications to be active, but some do. Currently, this is investigated on a very detailed protein-by-protein basis (as far as I know), so gathering enough data for a large-scale study could take a long time. On the other hand, there are a variety of (increasingly affordable) high-throughput methods for measuring the abundance of thousands of RNA species simultaneously. I think people are using mRNA levels to estimate expression not because it's the most biologically cogent course of action, but rather because it is much easier, more affordable, and more high-throughput (which is all the rage these days).&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-05-10T13:45:37.783" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2225" PostTypeId="2" ParentId="2220" CreationDate="2012-05-10T14:05:02.097" Score="2" Body="&lt;p&gt;A colleague of mine discovered the cipher that determines TAL effector DNA specificities, which is described in &lt;a href=&quot;http://dx.doi.org/10.1126/science.1178817&quot; rel=&quot;nofollow&quot;&gt;this short paper&lt;/a&gt;. These specificities were determined by observing TAL effectors bound to DNA and recording how often a given repeat-variable diresidue (RVD) would correspond to a given nucleotide (using a weight matrix).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now that the specificities have been determined, identifying TAL effector target sites is simply a matter of measuring the probability of that TAL effector's RVD sequence aligning to a novel sequence. Some applications are described &lt;a href=&quot;http://dx.doi.org/10.1534/genetics.110.120717&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://dx.doi.org/10.1093/nar/gkr218&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;https://boglab.plp.iastate.edu/&quot; rel=&quot;nofollow&quot;&gt;TALENT 2.0 server&lt;/a&gt; (invited paper under review) provides tools for designing custom TAL effectors to target specific DNA sequences, or for identifying potential off-target binding sites in a given sequence or genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1126/science.1178817&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Moscou MJ, Bogdanove AJ&lt;/strong&gt;. 2009. A simple cipher governs DNA recognition by TAL effectors. Science (New York, NY) 326: 1501.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1534/genetics.110.120717&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF&lt;/strong&gt;. 2010. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186: 757–61.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1093/nar/gkr218&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF&lt;/strong&gt;. 2011. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic acids research 39: e82.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="43" LastEditorUserId="836" LastEditDate="2012-09-13T06:21:59.373" LastActivityDate="2012-09-13T06:21:59.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2226" PostTypeId="2" ParentId="2213" CreationDate="2012-05-10T14:55:47.760" Score="5" Body="&lt;p&gt;There are several competing models of metastasis, and this question does go right to the differences between them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The primary thing to remember about CSCs is that all evidence suggests that they are a tiny, tiny subset of tumor cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CTCs, meanwhile, consist of whichever cells manage to acquire the right combination of motility, invasiveness, and resistance to anoikis (apoptosis caused by lack of attachment to neighboring cells or extracellular matrix).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, one possible explanation is that CTCs are drawn from the whole population of tumor cells, and that CSCs therefore make up a very small, nigh-undetectable subset of CTCs-- but that this is the subset that ends up founding the distant metastases while the rest of the CTCs get cleaned up by the immune system or lie dormant in the target tissue. You could call this the stochastic model: CSCs form some small, randomly determined fraction of the CTCs, but they preferentially survive and found secondary tumors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another model posits that the cells undergo substantial changes in phenotype driven by responses to their microenvironment. CSCs, like normal stem cells, presumably require a pretty specific niche to maintain their stemness. CTCs, meanwhile, acquire their invasiveness and anoikis-resistance in response to conditions in the tumor, such as hypoxia. So, another possiblity is that, in response to stimulus from the microenvironment, a cell with the potential to be a CSC undergoes some phenotypic changes and becomes a CTC. It circulates for a while, finds a target tissue, extravasates, invades the target microenvironment, &lt;em&gt;then&lt;/em&gt; starts re-setting up the microenvironmental niche to re-establish its stem-like properties. Call this the dynamic hypothesis: it's a single potential CSC the whole time, but it looks like a CTC while it's circulating and like a CSC only in its niche.&lt;/p&gt;&#xA;" OwnerUserId="819" LastActivityDate="2012-05-10T14:55:47.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2229" PostTypeId="1" AcceptedAnswerId="2230" CreationDate="2012-05-10T21:01:41.923" Score="9" ViewCount="190" Body="&lt;p&gt;There are several companies (most notably &lt;a href=&quot;http://23andme.com/&quot;&gt;23andMe&lt;/a&gt;) providing &lt;a href=&quot;http://en.wikipedia.org/wiki/SNP_genotyping&quot;&gt;SNP genotyping&lt;/a&gt; for individuals claiming that there is no sense for individual in obtaining full genome sequence since only small part of it could be interpreted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While this agrees with my understanding of the subject, I wonder whether there could be any use to perform full sequence of one's genome for means of personal health care?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only effect I recall which affects individual's health and could not be caught by SNP genotyping is &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_methylation&quot;&gt;DNA methylation&lt;/a&gt;, but complete sequencing procedure does not detect it either, as far as I know.&lt;/p&gt;&#xA;" OwnerUserId="836" LastEditorUserId="69" LastEditDate="2012-05-11T08:09:03.123" LastActivityDate="2013-01-04T23:15:04.027" Title="Is there any difference in terms of personal healthcare between complete DNA sequencing and SNPs genotyping?" Tags="&lt;dna-sequencing&gt;&lt;human-genetics&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2230" PostTypeId="2" ParentId="2229" CreationDate="2012-05-10T21:22:54.943" Score="8" Body="&lt;p&gt;This difference would have the greatest impact on treatment for cancer, in which a treatment protocol is based on genes deleted, amplified, altered in the tumor vs the reference genome for that patient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of health risks based on SNP genotypes, the data are far from complete. Sure, some level of risk can be assigned to a variant (SNP), say at certain markers within the &lt;em&gt;FTO&lt;/em&gt; gene and risk of obesity. However, the complete list of risk alleles for this and numerous other complex traits is not fully described. Furthermore, the impact of environmental factors (EF), or lifestyle choices, on those genetic variants is only beginning to gain wider attention. For example, a risk allele may not show itself as risk until the EF, such as amount of physical activity or percent energy from dietary polyunsaturated fat, passes a certain threshold. Such gene-environment interactions are thought to contribute to the variance in traits (phenotypes), but to what degree is not known.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Added in edit 15 May 2012: Epistasis, or gene-gene interactions, also are important but far from being cataloged for humans. A situation could arise where one allele elevates risk for a certain condition, but compensatory alleles elsewhere in the genome decrease that risk. We don't know the full extent of epistasis in humans.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, in terms of personal healthcare outside of something like cancer and monogenetic disorders, there may be little that is gained from genotyping or complete genome sequencing, little that is compared to other advice you already know. I carry risk alleles for certain conditions, but there is not really any advice one can give me that is specific for those alleles that I have, where that advice is different than or goes beyond general advice health care providers already have dispensed.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-05-15T12:40:41.120" LastActivityDate="2012-05-15T12:40:41.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2231" PostTypeId="1" AcceptedAnswerId="2257" CreationDate="2012-05-11T00:12:45.637" Score="14" ViewCount="8974" Body="&lt;p&gt;I know that there are companies that offer a kit+storage of your pet DNA for around $2k.&#xA;My question is if there is any other option for doing this yourself with a thought in mind that in 20+ years the technology will get so advanced that even this DIY sample can be utilized.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any ideas? Maybe drying a blood drop or mixing blood with alcohol/acetone?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I read somewhere that it is better if the pet is still very young, because if you take old pet DNA the clone will exhibit mature signs even as a youngster. Is this true? If yes then what is the top age that is safe?&lt;/p&gt;&#xA;" OwnerUserId="861" LastEditorUserId="861" LastEditDate="2012-05-11T00:28:04.917" LastActivityDate="2017-05-23T18:48:04.970" Title="How to DIY preserve pet DNA today so that it can be used in 20 years" Tags="&lt;dna&gt;&lt;cloning&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="2232" PostTypeId="1" AcceptedAnswerId="11082" CreationDate="2012-05-11T02:15:05.583" Score="9" ViewCount="182" Body="&lt;p&gt;If a human inbreeds with a relative, how distant does the relative have to be before the homozygosity in the child is no higher than if the mate were randomly chosen from the global population?&lt;/p&gt;&#xA;" OwnerUserId="864" LastActivityDate="2013-10-25T11:05:20.573" Title="What is the effective relatedness of inbreeding?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2233" PostTypeId="2" ParentId="2179" CreationDate="2012-05-11T06:14:28.950" Score="6" Body="&lt;p&gt;MC4R, TMEM18, GNPDA2, KCTD15, NEGR1, BDNF, ETV5, MTCH2, and SH2B1 have also been identified as being associated with adult onset obesity risk, however FTO currently appears to be the one with the strongest evidence. For example see &lt;a href=&quot;http://www.nature.com/ng/journal/v41/n1/abs/ng.274.html&quot;&gt;Thorleifsson et al. (2009)&lt;/a&gt;, &lt;a href=&quot;http://www.plosmedicine.org/article/info%3adoi/10.1371/journal.pmed.1000284&quot;&gt;Elks et al. (2010)&lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/ng/journal/v41/n1/abs/ng.287.html&quot;&gt;Willer (2009)&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="835" LastEditorUserId="69" LastEditDate="2012-05-11T08:03:40.027" LastActivityDate="2012-05-11T08:03:40.027" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2234" PostTypeId="2" ParentId="2232" CreationDate="2012-05-11T07:41:53.203" Score="6" Body="&lt;p&gt;In &quot;The Selfish Gene&quot; Dawkins claims a relatedness factor of 1/128 to be pretty much the same as the baseline chance for the rest of the population to have the same gene, so that would be a third cousin. (Or your great great great great great grandparents, though an incestuous relationship with them is quite unlikely I think.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure where he got that from though.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-05-11T09:47:02.987" LastActivityDate="2012-05-11T09:47:02.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2235" PostTypeId="1" AcceptedAnswerId="2238" CreationDate="2012-05-11T11:57:47.607" Score="7" ViewCount="2998" Body="&lt;p&gt;Inspired by the post about &lt;a href=&quot;https://biology.stackexchange.com/questions/2231/how-to-diy-preserve-pet-dna-today-so-that-it-can-be-used-in-20-years&quot;&gt;extracting pet DNA&lt;/a&gt;, how long would genomic DNA be stable for in a -20&amp;deg;C freezer? It is common practice to store DNA (double-stranded, plasmid) in a -20&amp;deg;C freezer in the lab, but would genomic DNA last longer in a -80&amp;deg;C freezer? With either method, how long would it be stable for?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-09-01T10:53:21.380" Title="How long is DNA stable in a freezer?" Tags="&lt;dna&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2236" PostTypeId="1" AcceptedAnswerId="2237" CreationDate="2012-05-11T18:15:43.913" Score="5" ViewCount="1880" Body="&lt;p&gt;What is the biological mechanism behind the variation within sexually reproducing species? Obviously, the children are combinations, to differing degrees, of their parents. But how does the variation originate in the parents to begin with?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not referring to evolution or mutations rather I have in mind things like facial structure and personality in humans, or fur coloring in dogs. I just thought I vaguely remembered there was some kind of driver of variation... For example, does the parent produce a variety of germ cells that purposely differ from the parent's geneome?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just think I'm missing something here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I'm familiar with DNA and genetics having taken a biology class in college and remembering much of it, I just can't seem to put my finger on this point...)&lt;/p&gt;&#xA;" OwnerUserId="866" LastActivityDate="2012-05-12T14:23:53.320" Title="What generates variation in a species?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2237" PostTypeId="2" ParentId="2236" CreationDate="2012-05-11T19:16:54.530" Score="5" Body="&lt;p&gt;After mutations, which probably is the source of most variation.  The classic biological model of variation comes from accidents of history and environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many mutations disappear over time because they aren't helpful (advantageous).  The reasons variations persist for more than a few generations is that our differences have helped us to live successful lives and (in biological terms of success) have offspring.  In europe the lactate dehydrogenase gene and others like it that help people digest milk is active through adult life as the result of domestication of milk producing animals,  in asia, this trait is rarer or non existent as agriculture does not produce milk there (in most cases). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a broad difference, but its true in smaller ways for all of our individual traits, or so the theory goes.  Individual family traits are helpful to create stronger family bonds, so even something like distinctive dimples or foreheads have claim to being an advantageous trait.  Its possible that blonde hair is the product of such an advantage - its a strong signal to paternity if the father is blonde for instance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another answer to your question I think, is that there are probably mechanisms in the cell or in mate selection that increase or decrease variation in the community at given times of stress.  For instance, snakes are among the animals who have a particular ability to select gender depending upon the conditions the female is experiencing.  more males may increase variation in the community - fewer males and more females will decrease it.  (not by a lot mind you, but a bit). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additional response added as requested:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see what you are getting at - why do children seem like such individual and unique things sometimes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In sexual reproduction, the offspring are the product of the shuffling of the parent's genomes through meiosis, where the pairs of chromosomes we have are combined to make a single chromosome that will be half of the children genome.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This process can result in completely novel combinations of genes while conveying many likenesses from the parent.  I would guesstimate that this is the major cause of the uniqueness of offspring/children.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also in mammals there are some cell lines which splice families of genes which will cause offspring to be potentially quite different from either parent.  Immune genes for instance are created from scratch from a bunch of genes that the parents give.  Making each offspring unique but also the product of the parent's genetic repertoire.  This can be significant as it affects health and also to some extent attraction - &lt;a href=&quot;http://en.wikipedia.org/wiki/Body_odor_and_subconscious_human_sexual_attraction&quot; rel=&quot;nofollow&quot;&gt;studies have shown that people who smell attractive to us are immunologically distinct from us&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;@David mentions epigenetic variation, which is a more recent significant development.  During our life, the germline (sperm/egg) DNA may be chemically labelled depending upon environmental conditions we experience.  A famous example is &lt;a href=&quot;http://epigenome.eu/en/2,48,872&quot; rel=&quot;nofollow&quot;&gt;experiencing famine conditions&lt;/a&gt;, which caused the children to be born on the small side amongst other effects.   More recent studies have shown that this is a &lt;a href=&quot;http://www.nature.com/nature/journal/v462/n7271/full/nature08514.html&quot; rel=&quot;nofollow&quot;&gt;widespread mechanism to control cells in our body during our lifetime as well as communicate to our offspring how life is&lt;/a&gt;.  It is expected that this labeling does not affect us forever - the epigenetic labels change over the course of a generation quite often (we believe). &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-05-12T14:23:53.320" LastActivityDate="2012-05-12T14:23:53.320" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2238" PostTypeId="2" ParentId="2235" CreationDate="2012-05-11T19:20:15.290" Score="5" Body="&lt;p&gt;If the DNA is pure, it should last quite a long time.  If there are enzymes and other biological molecules in there, -80C will work much better. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think you could keep pure DNA at -20C practically indefinitely. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Purity is the main issue there, also pH stabilized, sealed properly, etc.  That makes all the difference. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-11T19:20:15.290" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2239" PostTypeId="1" AcceptedAnswerId="2242" CreationDate="2012-05-11T19:48:42.797" Score="12" ViewCount="604" Body="&lt;p&gt;I can see from Wikipedia that there are possibly thousands of harmful mutations that have been cataloged and linked to disease. There are also unnumbered neutral mutations. But, does anyone know how many &quot;beneficial&quot; mutations have been cataloged in scientific literature?&lt;/p&gt;&#xA;" OwnerUserId="866" LastEditorUserId="69" LastEditDate="2012-05-14T10:39:19.860" LastActivityDate="2012-05-14T12:31:40.873" Title="Number of beneficial mutations cataloged?" Tags="&lt;genetics&gt;&lt;human-genetics&gt;&lt;mutations&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2240" PostTypeId="1" AcceptedAnswerId="2388" CreationDate="2012-05-11T20:09:40.703" Score="15" ViewCount="6989" Body="&lt;p&gt;Today I heard about a phenomenon called &quot;translational coupling&quot;, where the translation of one protein influences the translation of another protein. The messenger RNA levels don't seem influenced. How does this work? Do they need to be in the same operon?&lt;/p&gt;&#xA;" OwnerUserId="867" LastEditorUserId="6" LastEditDate="2012-05-13T09:05:09.873" LastActivityDate="2018-11-03T03:03:22.353" Title="How does translational coupling work in prokaryotes?" Tags="&lt;molecular-biology&gt;&lt;translation&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2241" PostTypeId="1" AcceptedAnswerId="2244" CreationDate="2012-05-11T20:39:51.953" Score="7" ViewCount="914" Body="&lt;p&gt;My girlfriend was watching some documentary on TLC about a paralyzed woman getting pregnant. I believe that woman still has some feeling, as she spoke about feeling the effects of a bladder inflamation. So supposedly, her brain could fire up her vagina to get ready for sex (in the sense that it gets lubricated and the labia get swollen).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But suppose a woman is paralyzed so they have no nervous connection from the brain to the vagina (or vice versa). Could she still be aroused in the sense of swollen labia, etc? (Presumably via some hormonal system?)&lt;/p&gt;&#xA;" OwnerUserId="868" LastEditorUserId="73" LastEditDate="2012-06-12T05:45:36.593" LastActivityDate="2012-06-12T05:45:36.593" Title="Is it purely the nervous system causing vaginal lubrication (arousal)?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;physiology&gt;&lt;endocrinology&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2242" PostTypeId="2" ParentId="2239" CreationDate="2012-05-12T03:02:11.923" Score="7" Body="&lt;p&gt;That would be hard to say because really beneficial mutations become well distributed through the genome.  Basically the differences between us and chimpanzees are a catalog of all the beneficial (or completely neutral) mutations since the ~4.7 M years since we diverged from each other.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Separating them from changes which have no special effect would be difficult too, but more to the spirit of your question, its difficult to explain what many mutations do, unless they cause significant changes in something we can observe in the individual (like height, weight, big nasty claws, etc).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For some more specific examples you can look at Online Mendelian Inheritance in Man.  Some mutations which are useful sometimes might be related to skin color for instance (really helps when there is a lot of sun about) or lactose tolerance (a variation which is popular amongst europeans who have been drinking dairy milk for thousands of years).  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-12T03:02:11.923" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2243" PostTypeId="2" ParentId="2180" CreationDate="2012-05-12T05:00:51.677" Score="8" Body="&lt;p&gt;&lt;strong&gt;For straightening hair with a flat iron&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ccmr.cornell.edu/education/ask/index.html?quid=708&quot;&gt;This source&lt;/a&gt; provided by bobthejoe states that temporarily straightening hair involves the breaking of hydrogen bonds between keratin molecules within hair.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One of the reasons hair is curly is because of hydrogen bonds between the proteins (keratin) that make up your hair [...]. Another way to alter hydrogen bonds is with heat; electric straighteners work because of this principle. The platters on electric straighteners are flat so that when your hair cools it takes the shape of &quot;flat&quot; as the hydrogen bonds reform. The same thing occurs with curling irons, but since the heating element is circular, the hair stays curled as it cools. The effect of heat, however, is temporary, over time the hydrogen bonds eventually return to their original form and the hairs goes back to the way they were. This rearrangement happens because moisture in the air hydrates the proteins. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ewg.org/hair-straighteners/our-report/how-to-get-straight-hair-whats-the-best-option/&quot;&gt;This source&lt;/a&gt; provides a similar explanation.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Running a flat iron through blown-dry hair breaks the hair’s hydrogen bonds. It flattens hair until water or water vapor (from humidity, drizzle or the shower) penetrates the hair fiber and allows the hydrogen bonds to revert to their natural positions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thus, the straightening of hair with an flat iron does not involve the breakage of disulfide bonds as I had originally hypothesized.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;For perming hair&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.yalescientific.org/2010/04/everyday-qa-how-does-a-perm-work/&quot;&gt;This article&lt;/a&gt; suggests that perming involves the chemical treatment of hair with reducing agents to break the present disulfide bonds between cysteine amino acids, followed by the reformation of the disulfide bonds in the desired curled shape.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In a standard “cold” perm, hair is put into curlers and the reducing agent ammonium thioglycolate is added. The disulfide bonds break and keratin molecules are now free to move around and adjust to the shape of the curl. Then a “neutralizer,” such as hydrogen peroxide, is added to reverse the effect of the reducing agent. New disulfide bonds form so the keratin molecules are locked into the shape of the curls.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Perm_%28hairstyle%29&quot;&gt;This Wikipedia article&lt;/a&gt; also suggests that the &lt;em&gt;chemical&lt;/em&gt; straightening of hair is obtained with the same process.&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-05-12T05:00:51.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2244" PostTypeId="2" ParentId="2241" CreationDate="2012-05-12T14:05:44.983" Score="9" Body="&lt;p&gt;There is a &lt;a href=&quot;http://joe.endocrinology-journals.org/content/186/3/411.full&quot;&gt;good open access review&lt;/a&gt; about the effects of different hormones on sexual arousal. In most instances, the hormone is acting on the brain, which signals the information to gonads and genitals via nerves (i.e., &lt;a href=&quot;http://en.wikipedia.org/wiki/Hypothalamic%E2%80%93pituitary%E2%80%93gonadal_axis&quot;&gt;the hypothalamic-pituitary-gonadal axis&lt;/a&gt;). However, in a study in which I have participated, we found a more direct and probably ancient signaling pathway where &lt;a href=&quot;http://www.reportergene.com/2011/02/eat-proteins-read-estrogens-said-liver.html&quot;&gt;the mouse liver, in response to protein intake&lt;/a&gt;, was sending a permissive signal to the uterus for reproduction. Whether this holds true for vagina lubrication was not investigated, but I would be optimistic that mechanisms other than nerve communication could play some roles.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-05-12T14:05:44.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2245" PostTypeId="2" ParentId="2239" CreationDate="2012-05-12T15:38:37.300" Score="6" Body="&lt;p&gt;Just continue scrolling down wikipedia: there are also listed two examples of &lt;a href=&quot;http://en.wikipedia.org/wiki/Mutation#Beneficial_mutations&quot;&gt;beneficial mutations&lt;/a&gt;: the one conferring HIV resistance, and the one conferring malaria resistance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that 'beneficial' is relative. The mutation associated to malaria resistance is actually causing sickle cell disease.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-05-12T15:38:37.300" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2246" PostTypeId="1" AcceptedAnswerId="2258" CreationDate="2012-05-12T19:00:21.327" Score="9" ViewCount="1592" Body="&lt;p&gt;I have a gene of of interest that I would like to compare between homologues. How does one go about finding a gene from known coding sequences across phyla? Afterwards I imagine I could do a Clustal sequence alignment to see how the sequences match.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-10-17T16:18:20.693" Title="Finding and Comparing Homologous Genes" Tags="&lt;bioinformatics&gt;&lt;phylogenetics&gt;" AnswerCount="5" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2247" PostTypeId="2" ParentId="2246" CreationDate="2012-05-13T01:41:22.507" Score="5" Body="&lt;p&gt;If I understand your question adequately, the &lt;a href=&quot;http://genome.ucsc.edu&quot;&gt;Genome Browser&lt;/a&gt; at UCSC is a great place to start. If you know the name of the gene, you can search for it. For example, &lt;a href=&quot;http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr2:227659726-227663454&amp;amp;hgsid=265444947&amp;amp;knownGene=pack&amp;amp;hgFind.matches=uc021vxn.1,&quot;&gt;here is the page for human insulin receptor 1&lt;/a&gt;. From there you can compare 46 genomes, with alignments. &lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-05-13T01:41:22.507" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2248" PostTypeId="2" ParentId="2246" CreationDate="2012-05-13T04:39:34.193" Score="4" Body="&lt;p&gt;maybe you'd like NCBI/Homologene instead.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/homologene&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/homologene&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or just using psiblast against NR if you have a nucleotide or protein sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi&quot; rel=&quot;nofollow&quot;&gt;http://blast.ncbi.nlm.nih.gov/Blast.cgi&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-13T04:39:34.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2249" PostTypeId="2" ParentId="2246" CreationDate="2012-05-13T05:18:02.537" Score="5" Body="&lt;p&gt;If you don't have any idea where your gene will have a match with other genes, try something like &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi&quot; rel=&quot;nofollow&quot;&gt;Blast at the NCBI website&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This will give you a list of hits that you can then use to align with a multiple sequence aligner (MSA). The same NCBI page can give you a tree reconstructed from the results of the searching process, although there is a variety of methods that can be used if you just download the sequences and attempt to build the gene family alignment yourself using &quot;[x] Select All -- Get selected sequences&quot; in the NCBI blast results page, then downloading them in FASTA or other format with &quot;Send to -- File -- Format FASTA -- Create File&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If what you want instead is to include your gene sequence into the best aligning place in an existing gene family alignment, you can try &lt;a href=&quot;http://code.google.com/p/pagan-msa/wiki/PAGAN&quot; rel=&quot;nofollow&quot;&gt;PAGAN&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="787" LastEditorUserId="166" LastEditDate="2012-05-13T08:39:49.030" LastActivityDate="2012-05-13T08:39:49.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2250" PostTypeId="1" AcceptedAnswerId="2253" CreationDate="2012-05-13T14:10:59.407" Score="83" ViewCount="123553" Body="&lt;p&gt;One of my friends said that I would die if I drank distilled water (we were using it in a chemistry experiment) I gave it a go and surprisingly did not die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did a bit of &lt;a href=&quot;https://www.google.com/search?ie=UTF-8&amp;amp;oe=utf-8&amp;amp;q=drinking+disti%3Blled+water+harmful%3F#hl=en&amp;amp;sa=X&amp;amp;ei=PLyvT9PvPMSIrAesu8mJBA&amp;amp;ved=0CB4QvwUoAQ&amp;amp;q=drinking+distilled+water+harmful%3F&amp;amp;spell=1&amp;amp;bav=on.2,or.r_gc.r_pw.r_cp.r_qf.,cf.osb&amp;amp;fp=311369616e4b455a&amp;amp;biw=1280&amp;amp;bih=652&quot;&gt;Googling&lt;/a&gt; and found &lt;a href=&quot;http://answers.yahoo.com/question/index?qid=20060919161158AAWqN9V&quot;&gt;this&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It said that drinking only this kind of water could definitely cause death, as distilled water was highly hypotonic and it would make the blood cells expand and finally explode and ultimately cause death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wanted to know exactly how much of this water on an average was needed to be consumed to cause death. &lt;/p&gt;&#xA;" OwnerUserId="872" LastEditorUserId="6194" LastEditDate="2014-09-26T13:09:12.237" LastActivityDate="2017-04-21T09:22:11.317" Title="Death because of distilled water consumption" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;experimental&gt;" AnswerCount="4" CommentCount="8" FavoriteCount="23" ContentLicense="CC BY-SA 3.0" />
  <row Id="2252" PostTypeId="1" CreationDate="2012-05-13T15:57:35.753" Score="18" ViewCount="68915" Body="&lt;p&gt;My wife and I are having a debate similar to &lt;a href=&quot;http://askville.amazon.com/store-vegetables-plastic-bag/AnswerViewer.do?requestId=3130523&quot;&gt;this one&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I claim that it's better to take the fresh veggies &lt;a href=&quot;http://in.answers.yahoo.com/question/index?qid=20110111002308AAGHxrs&quot;&gt;out of the bags&lt;/a&gt; and put them in the crisper with humidity control because:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;That's what the crisper with humidity control is for.&lt;/li&gt;&#xA;&lt;li&gt;If they are in the (plastic) bag, the humidity control is pointless.&lt;/li&gt;&#xA;&lt;li&gt;It's easier to notice vegetables in their early stage of rotting (it doesn't feel right to throw out an entire bag of rotten cucumbers or zucchinis before we got a chance to enjoy them). &lt;/li&gt;&#xA;&lt;li&gt;It's more pleasing to the eye. It's more convenient.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;She claims that it's better to leave the fresh veggies in their supermarket bags when putting them in the fridge because she could swear she noticed that they rot more slowly when left in their bags.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see from the few &lt;a href=&quot;http://vegtalk.blogspot.com/2008/04/best-way-to-store-veggies.html&quot;&gt;links&lt;/a&gt; in this question, I tried to conduct my own search on the subject, but all answers seem to be opinions or &quot;experiences&quot;, not an &lt;strong&gt;authoritative&lt;/strong&gt; answer based on &lt;strong&gt;scientific&lt;/strong&gt; research or knowledge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I am hoping that with the help of biology professionals (or students) I can finally find an &lt;strong&gt;authoritative&lt;/strong&gt; answer to the question: Do vegetables really last longer if they are kept in their (supermarket) plastic bags when put in the crisper?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt;: I found &lt;a href=&quot;http://kitchenaid.custhelp.com/app/answers/detail/a_id/2695/~/adjusting-crisper-humidity-control---side-by-side-refrigerator&quot;&gt;this formal excerpt&lt;/a&gt; from the refrigerator's manual:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Low&lt;/strong&gt; (open) lets moist air out of the crisper for best storage of fruits and vegetables with skins.&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;&lt;strong&gt;Fruit&lt;/strong&gt;: Wash, let dry and store in refrigerator in plastic bag or    crisper. Do not wash or hull berries until they are ready to&#xA;  use.    Sort and keep berries in original container in crisper, or&#xA;  store in a    loosely closed paper bag on a refrigerator shelf.&lt;/li&gt;&#xA;  &lt;li&gt;&lt;strong&gt;Vegetables with skins&lt;/strong&gt;: Place in plastic bag or plastic container and store in crisper.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;High&lt;/strong&gt; (closed) keeps moist air in the crisper for best storage of fresh, leafy vegetables.&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;&lt;strong&gt;Leafy vegetables&lt;/strong&gt;: Wash in cold water, drain and trim or tear off bruised and discolored areas. Place in plastic bag or plastic container and store in crisper.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;While this seems a bit more authoritative (because it comes from the manufacturer of the refrigerator), it still leaves quite a few questions open:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If leafy vegetables should be &quot;placed in plastic bag or plastic container and stored in crisper&quot;, why set the humidity on &quot;High&quot;? How does humidity get the lettuce inside the plastic bag or plastic container? (is it sealed?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that some humidity does get into the bag, why is the bag needed? Why not let humidity flow freely?&lt;/p&gt;&#xA;" OwnerUserId="873" LastEditorUserId="873" LastEditDate="2012-05-14T02:27:48.113" LastActivityDate="2015-02-25T17:12:40.287" Title="How to store vegetables in the refrigerator: In plastic bags or not?" Tags="&lt;botany&gt;&lt;cell-biology&gt;&lt;food&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2253" PostTypeId="2" ParentId="2250" CreationDate="2012-05-13T16:24:44.607" Score="47" Body="&lt;p&gt;Drinking a &lt;em&gt;&lt;strong&gt;little bit&lt;/strong&gt;&lt;/em&gt; of distilled water is not fatal. Drinking &lt;em&gt;&lt;strong&gt;only&lt;/strong&gt;&lt;/em&gt; this kind of water and ingesting nothing else will eventually be fatal because it is highly hypotonic as you've found out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Salt balance in the body is largely maintained by passive diffusion. Salts diffuse from areas of relatively high concentration (eg, stomach) down to areas of low concentration. For example, if you have just eaten a meal, the stomach contents are relatively higher in salt concentration compared to the surrounding tissue and the blood. Salt diffuses out of the stomach and into the stomach lining, intestines and blood. Tissues have to make sure they don't get too much salt or they will take in too much water and burst, so they have active transport mechanisms to remove excess salts and they go into the blood as well. Now that the excess salts are carried in the blood, they ultimately get filtered at the kidneys and excreted in urine. The kidneys are able to filter the salt by taking advantage of this gradient moving salt once again from high to low concentrations. The exact details are not important for this discussion, other than to know the kidneys need a highly concentrated store of salt to function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Distilled water on the other hand, has no salt. It is pure water. Distilled water will pull salt out of the tissues because now it is the absolute lowest concentration of salt. Tissues will also take in a lot of this water because it too passively diffuses and it is hypotonic. When this happens in the blood, red blood cells tend to burst because they can't tolerate a terribly large change in tonicity, and so some red blood cells die. The other problem is also that the salt control mechanisms in the kidneys malfunction because too much salt gets leeched out of them and passed in your urine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After drinking too much distilled water, electrolytes and important minerals get leeched out of your body and this creates electrical abnormalities in your body leading to irregular and weak heart beats (from hyponatremia and hypokalemia), poor muscle strength, high blood pressure and fatigue. Distilled water as mentioned, is fairly acidity (can be as low as pH 3 when freshly distilled) and leads to acidification of the blood (acidosis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no exact amount of water that one needs to drink to die. This mode of death is related to hyperhydration/water intoxication. This can happen from over-hydrating with regular tap water, but will take longer than distilled water because of the salt content in tap water.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2014-09-26T14:08:16.410" LastActivityDate="2014-09-26T14:08:16.410" CommentCount="15" ContentLicense="CC BY-SA 3.0" />
  <row Id="2254" PostTypeId="1" CreationDate="2012-05-13T18:22:57.893" Score="1" ViewCount="6008" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;pUWL22 is a circular, double stranded, 10.5 kb plasmid. It contains a&#xA;  gene encoding an enzyme that confers ampicillin resistance in the host&#xA;  bacterium. Cloning into the kpn I and Sst I sites abolishes ampicillin&#xA;  resistance, whereas cloning into other sites on the plasmid does not.&#xA;  Digestion with the following restriction enzymes singly and&#xA;  combination results in the following data:&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Enzyme Digest     ()()()()()()   Fragments Produced (kb)&#xA;&#xA;Hind III  ___________________________10.5&#xA;&#xA;Kpn I  _______________________________10.5&#xA;&#xA;Not I  _______________________________10.5&#xA;&#xA;Pvu II  ______________________________10.5&#xA;&#xA;Sst I  _______________________________10.5&#xA;&#xA;Stu I  _______________________________10.5&#xA;&#xA;Hind III + Kpn II  ___________________8.5  _______________2.0&#xA;&#xA;Hind III + Not I _________________8.0  __________________2.5&#xA;&#xA;Hind III + Pvu II ________________6.0  __________________4.5&#xA;&#xA;Hind III + Sst I _________________7.5  __________________3.0&#xA;&#xA;Hind III + Stu I _________________7.5  __________________3.0&#xA;&#xA;Stu I + Not I  ____________________10.0  __________________0.5&#xA;&#xA;Stu I + Pvu II  ____________________7.5  __________________3.0&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Now the actual questions:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A) Create a circular map of pUWL22, designating the Hind III site as&#xA;  the position 0 on the map. Once you have completed the map, indicate&#xA;  the relative position of the ampicillin gene.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My plasmid mapping: &lt;img src=&quot;https://i.stack.imgur.com/LHsY1.jpg&quot; alt=&quot;My Plasmid Mapping&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I need help with in indicating the relative position of the ampicillin gene. In the statement above it said &quot;Cloning into the Kpn I and Sst I sites abolishes ampicillin resistance.&quot; Does that mean its inbetween Sst 7.5 and Kpn 8.5? Please tell me where it is and why its there. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. I made a mistake on the on the Sst I enzyme, it's suppose to be @ 7.5 not 7.8.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question after that is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;B) Propose 2 other double digests that could be done to confirm your&#xA;  analysis. Predict the sizes of the fragments that would be generated&#xA;  from these digests.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Please answer this and explain why.&lt;/p&gt;&#xA;" OwnerUserId="877" LastEditorDisplayName="user560" LastEditDate="2012-05-13T22:39:00.363" LastActivityDate="2012-05-19T19:04:04.593" Title="Restriction Mapping of Plasmid Assignment" Tags="&lt;homework&gt;&lt;plasmids&gt;&lt;restriction-enzymes&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2255" PostTypeId="2" ParentId="2254" CreationDate="2012-05-13T19:35:31.243" Score="5" Body="&lt;p&gt;A) Here is the correct map:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/2ymc9.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You made a mistake on your map at the PvuII site (it is not on 6.5kB from the start of the plasmid, but on 6kB). &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Can the Kpn I not go on the 8.5 site, it still creates the 2 and 8.5, so isn't there more than 1 correct option for plasmid map?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes. What you need to do in order to make the correct map is try all possible positions of the restriction sites:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;You start with HindIII and place it at position 0 of your vector.&lt;/li&gt;&#xA;&lt;li&gt;The KpnII site can be either at 2kb (left of HindIII) or at 8.5kb (right of HindIII). Draw both versions of the plasmid.&lt;/li&gt;&#xA;&lt;li&gt;You place the NotI site that can either be at 2.5kb or at 8kb. Now you have four different possibilities for the plasmid:&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;HindIII[0], KpnII&lt;a href=&quot;https://i.stack.imgur.com/3rZpU.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;, NotI[2.5] &lt;/li&gt;&#xA;&lt;li&gt;HindIII[0], KpnII[8.5], NotI[2.5]&lt;/li&gt;&#xA;&lt;li&gt;HindIII[0], KpnII&lt;a href=&quot;https://i.stack.imgur.com/3rZpU.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;, NotI[8]&lt;/li&gt;&#xA;&lt;li&gt;HindII[0], KpnII[8.5], NotI[8]&lt;/li&gt;&#xA;&lt;/ol&gt;&lt;/li&gt;&#xA;&lt;li&gt;Then you do the same for the rest of the restriction sites. When you get to the last two digests, there is only one option for the correct plasmid left in the following order, depicted on the plasmid map below.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I have to point out though that StuI and SstI can both be at 3kb (they can be next to each other). Then the 2 fragments from the digest will be ~3kB and ~7.5kB. So technically, there are two possible versions:&#xA;correct           &lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) HindIII[0], KpnII&lt;a href=&quot;https://i.stack.imgur.com/3rZpU.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;, NotI[2.5], StuI[3], PvuII[6], SstI[7.5]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) HindIII[0], KpnII&lt;a href=&quot;https://i.stack.imgur.com/3rZpU.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;, NotI[2.5], StuI[3], SstI[3] PvuII[6]&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If u can, can u please elaborate on question b as to why there is one correct option for the plasmid map? Also, what do they mean by double digest to confirm ur analysis?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A double digest means that you cut your plasmid with two different restriction enzymes at the same time. As you already have a putative map of the plasmid, you can predict which would be the expected bands. If you observe the expected sizes, then your design is correct and your analysis are confirmed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To check which one is correct I would do a double digest with:&#xA;1) SstI and PvuII, generating a 1.5kb and a 9kb bands if design a) is correct or                              3kb and a 7.5kb bands if design b) is correct&#xA;2) StuI and SstI, generating a 4.5kb and a 6kb bands if design a) is correct or                             a 10.5kB band if design b) is correct           &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To confirm the &quot;ampicillin gene&quot; starts at kpn I 2.0 and end at the 3.0 stu I site right?? So the amp gene is 1 kB long?? So the relative position of the amp gene starts at 2.0 and ends at 3.0.&#xA;  Why is it that in the question it says cloning into the kpn I and sst I sites abolishes ampicillin resistance whereas cloning on other sites does not?&#xA;  What do they mean by this? Is the ampicillin resistance gene diff from the ampicillin gene??&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The ampicillin resistance gene and the ampicillin gene are the same. It refers to an enzyme (beta lactamase) which degrades ampicillin, and thus the cells that harbour the ampicillin-containing plasmid can survive when plated on ampicillin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are you sure that the resistance is disrupted if cloning into SstI site and not StuI? If this is really the case, then the StuI site and SstI sites are next to each other, as first you have the SstI site, followed by StuI. The amp gene &#xA;The gene is a little above 1kb, so it starts upstream of KpnII and ends right after SstI, but it doesn't disrupt StuI. If something is cloned into KpnII or SstI sites, then the open reading frame of amp is disrupted, and the protein cannot be functional.&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-05-15T06:39:56.590" LastActivityDate="2012-05-15T06:39:56.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2257" PostTypeId="2" ParentId="2231" CreationDate="2012-05-14T01:52:09.437" Score="10" Body="&lt;p&gt;For the impatient, I'm going to say that probably if you only have a regular home freezer, its unlikely that you will be able to do this. If you have access to a -80C or liquid nitrogen storage its possible, but also less likely. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v436/n7051/abs/436641a.html&quot;&gt;Cloning an animal typically starts with the transplantation of a nucleus into an egg cell whose nucleus has been removed&lt;/a&gt;.  So unless things change drastically in the next 20 years, just purifying DNA and keeping it in a tube of the fridge is not enough - you need to preserve epithelial (skin cells) or some other tissue in a state which can be revived to produce a live and intact cell when you want to do the cloning.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its possible that we will have machines that can take DNA from a DNA prep and produce a living cell - this is what we hope to do with the mammoth and other extinct animals from fossil tissue some day.  But whether that will be the case in 20 years is just a guess, whether it is affordable is also just a guess. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So from what we know now, you will need to preserve a piece of tissue from the animal when it is alive.  I'm not an expert on how to do this, but you might be able to get the skin cells to sort of turn into a cell line and then freeze them for not too much money.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you do this, regular freezers are not cold enough to prevent freezer burn.  This is what happens when you put a steak in to the freezer, wrapped in plastic even it will shrivel up and start to dry out as the water in the ice starts to sublime out of the package (the dry air in the freezer basically sucks the water out of the food).  If this happens to your animal tissue, its probably not going to revive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scientific labs use -80C freezers and liquid nitrogen storage because the water turns into a glass and all biochemical reactions are basically stopped. (besides drying out, the enzymes like DNAse are still nominally functioning in the cells at -20C and even simple bacterial cells don't live for more than a year at -20C, much less mammalian cells).  For preserving cell lines, liquid nitrogen is much more preferred.  I would say that properly produced cell lines can theoretically revive after indefinite liquid nitrogen storage.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So that's a quick answer.  Sorry to be a party pooper - things could change quite a bit in the next 20 years, but we just don't know how much.  popping a paw in a baggie or some DNA extract into the freezer might work, but its hard to say for sure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as the choice of where the DNA comes from in the animal, its true that skin cell lines are often producing imperfect animals - the DNA may be modified in the skin in various ways that cause the animal to be smaller, weaker, or even deformed compared to the donor.  At this time all the protocols I see (and i could be wrong) are skin cells.  I would expect that there is a better tissue to preserve, but that might be just a guess at this point.  Its likely that in the next 20 years the choice of cell line from the donor will change quite a bit as well.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-14T01:52:09.437" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2258" PostTypeId="2" ParentId="2246" CreationDate="2012-05-14T07:13:15.743" Score="6" Body="&lt;p&gt;There are various databases of homologs, for example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://eggnog.embl.de&quot;&gt;eggNOG&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Ensembl Compara (accessible via &lt;a href=&quot;http://www.ensembl.org/biomart/martview&quot;&gt;BioMart&lt;/a&gt;, I think)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/homologene&quot;&gt;Homologene&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://omabrowser.org/&quot;&gt;OMA&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.treefam.org/&quot;&gt;TreeFam&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The advantage of using an existing database is that more sophisticated methods for detecting orthologs than simple BLAST searches have been used (see &quot;&lt;a href=&quot;http://doi.org/cxwqpk&quot;&gt;Computational methods for Gene Orthology inference&lt;/a&gt;&quot; for a review), and everything is already precomputed, so it's much faster. The downside is that all precomputed methods need to use a snapshot of the genomes from the past, so not all currently available genomes will be there. &lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-05-14T07:13:15.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2259" PostTypeId="1" CreationDate="2012-05-14T09:28:51.723" Score="5" ViewCount="120" Body="&lt;p&gt;What is the difference between the terms &lt;em&gt;genetic network&lt;/em&gt; and &lt;em&gt;genetic architecture&lt;/em&gt;? I've heard both in a variety of contexts used by different people, so I am interested in what people think they mean, other than what is described in Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Genetic architecture&lt;/code&gt; refers to the underlying genetic basis of a phenotypic trait&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Genetic regulatory network&lt;/code&gt; (GRN) is a collection of DNA segments in a cell which interact with each other indirectly and with other substances in the cell, thereby governing the rates at which genes in the network are transcribed into mRNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: so what I take from the answers so far is that a &lt;code&gt;genetic network&lt;/code&gt; is the molecular wiring of all the interacting loci, whereas &lt;code&gt;genetic architecture&lt;/code&gt; describes the phenotypic consequence(s) one would be able to see from that network. Then, trying to bring the two definitions together, if we would assume we knew all the molecular details of a &lt;code&gt;genetic network&lt;/code&gt;, we would only need to add the other factors in the model, such as environmental perturbations, to end up with the description of the &lt;code&gt;genetic architecture&lt;/code&gt;, right? &lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="658" LastEditDate="2012-05-15T14:33:18.727" LastActivityDate="2012-05-15T14:33:18.727" Title="Genetic networks vs genetic architectures?" Tags="&lt;nomenclature&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2260" PostTypeId="2" ParentId="2239" CreationDate="2012-05-14T12:31:40.873" Score="5" Body="&lt;p&gt;Others have posted that the term beneficial in genetics is contextual - single mutations may be harmless, unless another mutation is co-inherited; this is called epistasis (where more than a single mutation/genotype/allele is required for the phenotype). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have not studied the list comprehensively, but there is a 'catalog' of all robust genome-wide association study results &lt;a href=&quot;http://www.genome.gov/gwastudies/&quot;&gt;here&lt;/a&gt;. Depending on your outlook, all mutations associated with a disease are therefore also 'beneficial' if you have the protective allele and not the risk allele. Using this logic there have been many SNPs identified that are &lt;em&gt;protective&lt;/em&gt;, rather than beneficial per se, and these are listed in the GWAS-catalog I linked to. As of 05/11/12, the catalog includes 1258 publications and 6400 SNPs.&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-05-14T12:31:40.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2262" PostTypeId="1" AcceptedAnswerId="2276" CreationDate="2012-05-14T16:08:05.560" Score="6" ViewCount="252" Body="&lt;p&gt;My russian friend says that the USSR agents used/use the trick that they offered the victim first vodka and then last wine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have noted that this puts you faster to hangover: decreasing the alcohol proof.&#xA;Some people lose their motor function immediately and some their memory only. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why does a decrease in the alcohol proof cause you a) faster intoxication and b) faster hangover?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably the change in the concentration of alcohol inside cells of brain tissue affects some parts of your brain like the cerebellum. I would like to have an explanation in Biochemistry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any truth in my friend's argument?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2012-05-15T00:08:38.210" LastActivityDate="2019-08-30T18:47:16.313" Title="Decreasing the alcohol proof and faster in hangover, why?" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2263" PostTypeId="1" CreationDate="2012-05-14T20:57:43.690" Score="13" ViewCount="1493" Body="&lt;p&gt;LB, TB media, and yeast extract are also yellow but at the heart of the question. What chemical(s) make E. coli yellow?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2015-06-22T19:57:50.650" Title="What makes E. coli yellowish?" Tags="&lt;ecoli&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2265" PostTypeId="2" ParentId="1681" CreationDate="2012-05-15T00:13:44.480" Score="2" Body="&lt;p&gt;Well, to rationalize everyone's comments, I think @leonardo is right.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a denaturing SDA PAGE gel.  The migration of the SDS Micelles which are negatively charged, depends upon the shielding of the solution around it.  The difference in mobility is because the SDS micelles will experience a slightly different field at pH ~6.2 (MES) vs 7.2 (MOPS).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thought that these have the same charge would be right at exactly the pH corresponding to the pKa.  For these two ions the proportions will not be the same when running 0.8 pH units from their respective pKas. the ion concentration goes as +/- log ([BH]/[B-]) and the charge environment of the buffer should not be the same.  I think that the higher pH for MOPS running will tend to create more negative charge in the solution from MOPS- but also OH- in solution, slowing the mobility of the micelles and favoring the resolution of the larger proteins with MOPS. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is all given even if &lt;a href=&quot;http://openwetware.org/wiki/Sauer%3abis-Tris_SDS-PAGE,_the_very_best&quot; rel=&quot;nofollow&quot;&gt;the buffering ion concentration is the same&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure the gory details are buried in the musty tomes of some physical biochemistry journals deep in the library, but this is how it sounds to me.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-15T00:13:44.480" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2266" PostTypeId="2" ParentId="2259" CreationDate="2012-05-15T08:50:29.717" Score="1" Body="&lt;p&gt;As I understand it &quot;gene network&quot; refers to functional 'pathways' that a gene is involved in. For instance there is an extensive gene network around the p53 tumour suppressor - many different gene-products regulate and are regulated by p53, which make up this particular network. These interactions are often visualized using flow-chart-like diagrams, with the stimuli at the top, and the 'outcome' of the network of interactions at the bottom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetic architecture refers to the actual structure of the gene itself. For instance, the coding sequence length, the intron:exon ratio, the 5' and 3' UTR lengths, are all traits relating to genetic architecture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You have presumably already read the Wiki pages so I've given you my take on the meanings, as I understand them in a general manner - this may well differ from others.&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-05-15T08:50:29.717" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2267" PostTypeId="1" CreationDate="2012-05-15T12:56:40.087" Score="6" ViewCount="111" Body="&lt;p&gt;In a scientific paper I have been studying (&lt;a href=&quot;http://dl.acm.org/citation.cfm?id=1719282&quot; rel=&quot;nofollow&quot;&gt;&quot;Predicting Novel Human Gene Ontology Annotations Using Semantic Analys&quot; S.Draghici et al., 2010&lt;/a&gt;), I have read that authors checked the accuracy of their annotation predictions by &lt;strong&gt;searching on available literature the scientific evidence&lt;/strong&gt; of their discoveries.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, for instance, if they predicted an annotation X, they would search for scientific papers that prove that the predicted annotation is correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think I could use the same method for my annotation prediction experiments, but how to do it? &lt;strong&gt;How to search&lt;/strong&gt; evidence of a certain annotation by browsing literature?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Should I just visit PubMed website and use annotation id as keyword for search? And which source (EntrezGene, etc) id should I use?&lt;/p&gt;&#xA;" OwnerUserId="885" LastEditorUserId="69" LastEditDate="2012-05-17T17:25:21.343" LastActivityDate="2012-05-17T17:25:21.343" Title="Question: Annotation search in scientific literature" Tags="&lt;gene-annotation&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2268" PostTypeId="2" ParentId="2259" CreationDate="2012-05-15T13:16:51.030" Score="3" Body="&lt;p&gt;You can think of a &lt;em&gt;genetic network&lt;/em&gt; as a network of interacting genes, turning each other on and off based on complex relationships and external stimuli. A genetic network is typically characterized in terms of graph theory--connectivity, density, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term &lt;em&gt;genetic architecture&lt;/em&gt;, on the other hand, typically refers to a trait or phenotype and the characteristics of the gene(s) that contribute to that phenotype (this is what the Wikipedia article means by &lt;em&gt;genotype-phenotype mapping&lt;/em&gt;). Characterization of a phenotype's genetic architecture involves describing how the phenotype(s) is/are related to the genotype(s). For example, for a particular trait or set of traits, is there a one-to-one relationship between gene and trait? Or do multiple genes contribute to a single trait? Or are multiple traits affected by changes in a single gene? The relevant terminology is discussed briefly in the Wikipedia article: polygeny, pleiotropy, etc.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-05-15T13:16:51.030" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2269" PostTypeId="1" AcceptedAnswerId="2271" CreationDate="2012-05-15T14:54:01.540" Score="1" ViewCount="653" Body="&lt;p&gt;Here's my theory:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;If you consume x calories each day with y amount of caloric expenditure each day you gain zero weight, regardless of x and y being out of balance.&lt;/p&gt;&#xA;&lt;p&gt;If you then mechanically remove a large percentage of body fat (surgically), the fat should not come back.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Is this a true theory or not? It seems to me that if the body is stable at the current consumption of x and expenditure of y then the removal of excess weight/fat should not affect anything.&lt;/p&gt;&#xA;&lt;p&gt;Anyone have thoughts on this? Is my thinking flawed? Why? Even if x and y were equal why might the fat come back if there is no net gain when the fat exists?&lt;/p&gt;&#xA;" OwnerUserId="886" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-05-15T17:57:55.903" Title="Human Body &quot;Fat&quot; Equilibrium" Tags="&lt;nutrition&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="2270" PostTypeId="1" AcceptedAnswerId="2339" CreationDate="2012-05-15T17:48:00.683" Score="6" ViewCount="336" Body="&lt;p&gt;I know that quaternary protein structures are formed exclusively via non-covalent bonds. My biochemistry professor discussed a viral capsid that is essentially one quaternary structure with 240 individual monomers of 4 kinds. I suspect that for this protein coat to be stable, the non-covalent bonds holding it together must be rather &lt;strong&gt;stable&lt;/strong&gt;. He also mentioned that different monomers can join to form the functional protein complex from relatively far distances, like across an entire cell, which once again leads me to believe that both monomers must be interacting with each other &lt;strong&gt;very strongly&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: Since a strong non-covalent interaction is required between (at least) two protein monomers to form the functional quaternary structure, can one particular protein be a monomer to an array of different quaternary complexes? Are there any examples of this? &lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-05-21T22:14:00.807" Title="Are quaternary protein monomers unique to a particular protein complex?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2271" PostTypeId="2" ParentId="2269" CreationDate="2012-05-15T17:52:48.127" Score="4" Body="&lt;p&gt;I'm not quite sure what you mean by&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;regardless of x and y being out of balance. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Surely it would make more sense to assume you gain 0 weight if x and y &lt;em&gt;are&lt;/em&gt; balanced? The prime reason why people get obese is probably because x and y are not balanced for them (there are other reasons though, as well as reasons why people can have it imbalanced and still not gain weight).&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Even if you consume exactly as many &lt;em&gt;calories&lt;/em&gt; as you expend in a day, you may gain weight depending on how (ratio of protein/fats/carbohydrates) and especially &lt;em&gt;when&lt;/em&gt; you consume the calories. The body may for example store consumed amounts as fat after eating and then use carbohydrate storage from liver and muscle when starving, so long term you would still gain weight.&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Adipose (fatty) tissue requires energy too. If you consume in the same manner after as before cutting a large amount of it away, you may just regain it until x=y again.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Also consider: if people ate just half an apple a day more than the exact amount of energy they need, they should gain more than a kilo on average every year. But they don't, and you can hardly assume that people manage on average to consume the exact amount their body needs.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The reason for that is probably &lt;a href=&quot;http://en.wikipedia.org/wiki/Leptin&quot; rel=&quot;nofollow&quot;&gt;leptin&lt;/a&gt;. It is a hormone produced by adipocytes (fat cells) and essentially indirectly reduces food uptake and increases expenditure, among others by decreasing your appetite. This has been regarded as a sort of &quot;adipostat&quot;; your leptin system creates a genetically determined level of body fat that you will tend to obtain. Dieting or cutting away fat will cause a drift to return to the previous weight because of a lower level of leptin (due to reduced fat cells). Of course it's not as simple as that though, so it's also possible that you will actually long-term reduce weight through those methods. E.g. exercise seems likely to be an &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19775494&quot; rel=&quot;nofollow&quot;&gt;exception&lt;/a&gt; somehow.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-05-15T17:57:55.903" LastActivityDate="2012-05-15T17:57:55.903" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2272" PostTypeId="1" AcceptedAnswerId="2273" CreationDate="2012-05-15T20:16:53.173" Score="4" ViewCount="85" Body="&lt;p&gt;I wanted to create a tool for some fields like SIFT, Phenotype, etc..so for example I know Phenotype will have &quot;Text&quot; values or SIFT will have some determined values from a drop down list...but what about Chrom Positions? what are some valid sample values for that? so I can know what type I can use for it.&lt;/p&gt;&#xA;" OwnerUserId="888" LastEditorUserId="806" LastEditDate="2012-05-15T22:57:44.330" LastActivityDate="2012-05-15T23:08:32.320" Title="What value type would a chromosome position be in a database or form?" Tags="&lt;bioinformatics&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2273" PostTypeId="2" ParentId="2272" CreationDate="2012-05-15T23:08:32.320" Score="2" Body="&lt;p&gt;Since it sounds like you are the one designing the database, you can make this a number of ways. The simplest is probably to reduce it to two variables, likely two decimals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this &lt;a href=&quot;http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/hbb.shtml&quot; rel=&quot;nofollow&quot;&gt;hemoglobin example&lt;/a&gt; for a chromosomal locus example.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;There are N chromosomes (23 for humans, if you like, sex chromosomes can be treated as a pair).&lt;/li&gt;&#xA;&lt;li&gt;There are 2 chromatids per chromosome.&lt;/li&gt;&#xA;&lt;li&gt;The part of the chromatid is either p or q (short or long arm).&lt;/li&gt;&#xA;&lt;li&gt;Then there is the location on the portion of the chromatid (eg, 15.5).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Chromatid can be easily represented as a decimal, where the integer portion is the chromosome number, and the decimal portion corresponds to the chromatid and arm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The chromosomal locus can be another decimal, such as 15.5 for the example above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is of course one way, and there are many other ways you could do this.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-05-15T23:08:32.320" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2274" PostTypeId="2" ParentId="935" CreationDate="2012-05-15T23:22:26.207" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;In animals, polyploidy is not tolerated and very few polyploid species&#xA;  are known to exist. Those that do exist are usually asexual,&#xA;  parthenogenetic, or hermaphroditic. Most of the problems resulting&#xA;  from polyploidy occur during synapsis of homologues during prophase I.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;As plants do not have a chromosomal mechanism for sex determination,&#xA;  synapsis and subsequent disjunction is not as great a problem. In&#xA;  fact, most plants are monoecious.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These paragraphs are taken from &lt;a href=&quot;http://academic.emporia.edu/mooredwi/genetics/note9.htm&quot; rel=&quot;nofollow&quot;&gt;these&lt;/a&gt; lecture notes from an Emporia State University genetics course.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Supporting information looks to be present in &lt;a href=&quot;http://www.jstor.org/stable/2456335&quot; rel=&quot;nofollow&quot;&gt;Why Polyploidy is Rarer in Animals Than in Plants&lt;/a&gt; (H. J. Muller, &lt;em&gt;The American Naturalist&lt;/em&gt;, 1925), but I didn't get a chance to access the article.&lt;/p&gt;&#xA;" OwnerUserId="864" LastActivityDate="2012-05-15T23:22:26.207" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2275" PostTypeId="1" AcceptedAnswerId="2303" CreationDate="2012-05-15T23:50:31.600" Score="2" ViewCount="1955" Body="&lt;p&gt;A &lt;a href=&quot;http://www.eurekalert.org/pub_releases/2012-05/uoc--smy051512.php&quot; rel=&quot;nofollow&quot;&gt;UCLA study&lt;/a&gt; seems to imply that insulin interferes with cognitive function.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The DHA-deprived rats also developed signs of resistance to insulin, a&#xA;  hormone that controls blood sugar and regulates synaptic function in&#xA;  the brain. A closer look at the rats' brain tissue suggested that&#xA;  insulin had lost much of its power to influence the brain cells.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&quot;Because insulin can penetrate the blood–brain barrier, the hormone&#xA;  may signal neurons to trigger reactions that disrupt learning and&#xA;  cause memory loss,&quot; Gomez-Pinilla said.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;He suspects that fructose is the culprit behind the DHA-deficient&#xA;  rats' brain dysfunction. Eating too much fructose could block&#xA;  insulin's ability to regulate how cells use and store sugar for the&#xA;  energy required for processing thoughts and emotions.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&quot;Insulin is important in the body for controlling blood sugar, but it&#xA;  may play a different role in the brain, where insulin appears to&#xA;  disturb memory and learning,&quot; he said. &quot;Our study shows that a&#xA;  high-fructose diet harms the brain as well as the body. This is&#xA;  something new.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;At the same time, &lt;a href=&quot;http://en.wikipedia.org/wiki/Insulin-like_growth_factor#IGF1.2FGH_Axis&quot; rel=&quot;nofollow&quot;&gt;increased levels of IGF-1 seems to be implicated in higher level of intelligence&lt;/a&gt;. IGF-1 is not the same thing as insulin, but it does seem to have many similar effects.&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="103" LastEditDate="2012-05-18T00:53:13.267" LastActivityDate="2012-05-18T11:31:50.060" Title="What are the positive and negative effects of insulin on cognitive function?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2276" PostTypeId="2" ParentId="2262" CreationDate="2012-05-16T01:13:17.360" Score="6" Body="&lt;p&gt;I would argue that your central point is intrinsically flawed. Your claim is that starting at a high alcohol percentage, then gradually decreasing alcohol content, gets you intoxicated faster. @nico is correct that you will get drunk faster this way (more alcohol sooner rather than later, so this is trivial). If we allow only one variable to change, the alcohol content (and therefore the water content), then the first drink is the most potent, and each drink afterwards is getting progressively more dilute, then this implies you are able to rehydrate better the more you drink. This argues exactly opposite to your claim. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since you offered up the example of vodka to wine, this introduces two new important aspects: fermentation impurities and sugar content. Vodka is distilled and relatively pure, so it offers little in addition to alcohol and therefore easy to process by the liver. Scotchs and whiskeys are low sugar, higher impurities, and so would be a bit more troubling to filter and process. As you move down to wine, impurities rise and sugar content is &lt;em&gt;much&lt;/em&gt; higher. This added sugar load dehydrates faster as well as causes a cascade of hormonal changes that are more immediately troubling than the alcohol. Beer would generally be the extreme end of the impurity and sugar continuum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since you bring up the USSR and the KGB, I imagine that if they did stick to this regimen of interrogation, it could be more effective by power of suggestion. The victim believes they are more intoxicated than they are, and perhaps more likely to offer up their secrets.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-05-16T01:13:17.360" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2277" PostTypeId="2" ParentId="1113" CreationDate="2012-05-16T03:06:03.337" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;A double-blind, prospective study during the fall of 1979 investigated&#xA;  the association between the menstrual cycles of 305 Brooklyn College&#xA;  undergraduates and their associates and the lunar cycles.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;.... Approximately 1/3 of the subjects had lunar period cycles, &lt;em&gt;i.e.&lt;/em&gt;&#xA;  a mean cycle length of 29.5 ± 1 day. Almost 2/3 of the subjects&#xA;  started their October cycle in the light 1/2 of the lunar cycle,&#xA;  significantly more than would be expected by random distribution. The&#xA;  author concludes that there is a lunar influence on ovulation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7246643&quot; rel=&quot;nofollow&quot;&gt;(Menstrual and Lunar Cycles, Friedmann E., &lt;em&gt;American Journal of Obstetrics and Gynecology&lt;/em&gt;, 1981)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://informahealthcare.com/doi/abs/10.3109/00016348609158228&quot; rel=&quot;nofollow&quot;&gt;Another source&lt;/a&gt; supports this conclusion, finding that &quot;a large proportion of menstruations occurred around the new moon.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Somewhat related, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851732/?tool=pmcentrez&quot; rel=&quot;nofollow&quot;&gt;this study&lt;/a&gt; found that light exposure shortened menstruation cycles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, there seems to be a good amount of data suggesting that lunar cycles do in fact calibrate the length of human menstrual cycles to some degree.&lt;/p&gt;&#xA;" OwnerUserId="864" LastActivityDate="2012-05-16T03:06:03.337" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2278" PostTypeId="2" ParentId="1855" CreationDate="2012-05-16T03:34:05.143" Score="5" Body="&lt;p&gt;In the case of red blood cells, hemolysis in pure water occurs at just over 1 minute, 30 seconds, according to &lt;a href=&quot;http://www.biolbull.org/content/63/2/224.abstract&quot;&gt;this&lt;/a&gt; paper. (Osmotic Properties of the Erythrocyte, M.H. Jacobs and Arthur K. Parpart, &lt;em&gt;The Biological Bulletin&lt;/em&gt;, 1932)&lt;/p&gt;&#xA;" OwnerUserId="864" LastActivityDate="2012-05-16T03:34:05.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2279" PostTypeId="2" ParentId="1245" CreationDate="2012-05-16T03:36:17.973" Score="6" Body="&lt;p&gt;Hi sorry i missed this one - not too hard for &quot;biology&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at a protein crystal (or any crystal really) in an x-ray beam, it scatters lots of spots (diffraction reflections).  If you look at &lt;a href=&quot;http://www.flickr.com/photos/sc63/2852072432/&quot;&gt;a picture of crystalline diffraction&lt;/a&gt;, at larger angles from the center of the x-ray beam, the reflections get weaker and weaker and basically just stop, if the wavelength is short enough (in all crystallography labs its plenty short - from 1.5 to 0.9 Angstroms).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The resolution is marked by the angle of scattering to the last measurable spot (aesthetics can vary here, but there is little variance from personal judgement here).  Once you have the angle of scattering, you can calculate the resolution from the Bragg scattering equation: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;lambda = 2d sin(theta)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;which is rearranged to solve for 'd'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;d = lambda / 2 * sin (theta)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where lambda is the wavelength of the incident radiation and theta is the scattering angle.&lt;br&gt;&#xA;d = the apparent width of the 'slit' which caused this highest resolution reflection is called the 'resolution' of the X-ray scattering experiment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is one part that's a bit tricky as in the &lt;a href=&quot;http://en.wikipedia.org/wiki/File%3aBraggPlaneDiffraction.svg&quot;&gt;typical diagram&lt;/a&gt;, depicting Bragg reflection/scattering, you would take the incident x-ray beam as first beam and the scattered angle as the beam of the high resolution scattering, which is more easily measured as 180 - 2* theta. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-16T03:36:17.973" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2280" PostTypeId="2" ParentId="1784" CreationDate="2012-05-16T13:33:29.117" Score="12" Body="&lt;p&gt;The feeling you describe is called &quot;paresthesia,&quot; and according to the &lt;a href=&quot;http://www.ninds.nih.gov/disorders/paresthesia/paresthesia.htm&quot;&gt;NINDS info page&lt;/a&gt;, it happens &quot;when sustained pressure is placed on a nerve.&quot;&lt;/p&gt;&#xA;" OwnerUserId="864" LastActivityDate="2012-05-16T13:33:29.117" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2281" PostTypeId="1" AcceptedAnswerId="2284" CreationDate="2012-05-16T16:38:46.683" Score="8" ViewCount="2363" Body="&lt;p&gt;Is it a myth that modern whales have been found with hind legs sticking out of their sides and full formed tibias, fibias, and toe bones? I keep finding assertions, but no citations. For example, the wikipedia page has no citation for it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Whales#Appendages&quot;&gt;http://en.wikipedia.org/wiki/Whales#Appendages&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="866" LastEditorUserId="69" LastEditDate="2012-05-16T17:31:20.327" LastActivityDate="2017-05-01T12:09:52.933" Title="Modern Whales with Vestigial legs Myth?" Tags="&lt;marine-biology&gt;&lt;vestigial&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2282" PostTypeId="2" ParentId="1648" CreationDate="2012-05-16T16:56:43.063" Score="8" Body="&lt;p&gt;This is a cool topic/question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question.  The hypothesis was based on the conjecture that there was so little phosphorus in the culture medium that phosphorous would have been replaced by arsenic in all its roles in the cell.  IF they had found arsenate DNA, it would have been derived from NTAs (nucleotide tri-arsenates) or a hybrid Phosphorous/Arsenic analog of the compound as DNA polymerase &lt;a href=&quot;http://wiki.cstl.semo.edu/agathman/DNA%20polymerase.ashx&quot;&gt;consumes NTPs to create DNA&lt;/a&gt;.  If there were only NTAs to drive DNA biosynthesis, then the cell's energy cycle would also have had to use ATA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;BUT&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The primary evidence was that the mono lake strain grew in a fermentor (culture) with lots of arsenic (which is impressive) and very little phosphorous. &lt;a href=&quot;http://rrresearch.fieldofscience.com/2012/01/growth-of-gfaj-1-under-phosphate.html&quot;&gt;how little&lt;/a&gt;? 3 micromolar. The investigators say that they did add a little phosphorus (3-5 micromolar), which, after some more careful accounting, appears to be enough to keep the bacteria growing at the observed rate &lt;a href=&quot;http://blogs.discovermagazine.com/badastronomy/2012/01/23/independent-researchers-find-no-evidence-for-arsenic-life-in-mono-lake/&quot;&gt;without using arsenate nucleotides&lt;/a&gt; (&lt;a href=&quot;http://rrresearch.fieldofscience.com/2012/04/latest-on-our-arseniclife-manuscript.html&quot;&gt;submitted to Science&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not completely surprising as the original publication in 2010 of a preliminary finding in &lt;em&gt;Science Express&lt;/em&gt; which only had x-ray abosorbtion fine edge spectroscopy work consistant with an arsenate like that found in a phosphorus backbone.  Given that they did not produce a more direct reading of the compounds such as mass spec or an NMR experiment, this looked pretty iffy in the first place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You an see why arsenic life was so improbable - a dozen (or more) vital pathways in the cell would have to adapt to use NTAs - pretty much all at once.  If they had I suspect Mono lake would be full of those suckers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its sort of a bummer, for those of us who want to discover new forms of life, but you can't find what isn't there.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-16T16:56:43.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2283" PostTypeId="2" ParentId="1025" CreationDate="2012-05-16T17:59:32.737" Score="9" Body="&lt;p&gt;You cannot solve a structure with a single frame, even with perfect diffraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason you need images over a large swath of angles is because the diffraction pattern is also in three dimensions, in the so-called &quot;reciprocal space&quot;.  At minimum, a 180° rotation of the crystal is needed to sweep the entire reciprocal space sphere with the plane of detection, though symmetry in the crystal structure can reduce this further (some of my proteins only required 90°, I think hexagonal unit cells with 6-fold symmetry can live with 30°).  Because crystals are real things (read: non-ideal, doubly so for protein crystals), the sweep is extended to gain some redundancy.&lt;/p&gt;&#xA;" OwnerUserId="25" LastActivityDate="2012-05-16T17:59:32.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2284" PostTypeId="2" ParentId="2281" CreationDate="2012-05-16T18:11:27.393" Score="11" Body="&lt;p&gt;The link you give doesn't mention limbs sticking out of the body wall, but only vestigial hind limb elements. Many whales do retain pelves and femora, as &lt;a href=&quot;http://bergenmuseum.uib.no/fagsider/osteologi/hvaler/e_bekken.htm&quot;&gt;this page at the Bergen Museum shows&lt;/a&gt;. Given the variation in limb development across vertebrates, it would not be surprising to find more distal elements (but I would be very surprised if they extended past the body wall).&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2012-05-16T18:24:17.660" LastActivityDate="2012-05-16T18:24:17.660" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2285" PostTypeId="2" ParentId="1964" CreationDate="2012-05-16T18:20:01.650" Score="3" Body="&lt;p&gt;All cells are susceptible to cold, but freezing is particularly difficult.  If the water in the cells freeze, it would usually burst the cells (water expands when it turns to ice) and tearing the cell membrane (totally killing it).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Antifreeze_protein&quot; rel=&quot;nofollow&quot;&gt;Some plants and animals have adapted to colder temperatures by putting antifreeze proteins in their cells&lt;/a&gt;.  A lot like adding antifreeze to the radiator of a car, this lowers the freezing temperature of the water in the cell.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the answer is that some plants have adapted to colder climates with the help of additional genes.  There are other things that have to change too - the chemical reactions in the cell will go haywire when temperature changes too, so lots of genes must make adjustment for a fully cold adapted plant.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-16T18:20:01.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2286" PostTypeId="1" AcceptedAnswerId="2287" CreationDate="2012-05-16T18:30:48.633" Score="4" ViewCount="162" Body="&lt;p&gt;A new study from MIT scientists &lt;a href=&quot;http://www.sciencedaily.com/releases/2012/05/120515181256.htm&quot; rel=&quot;nofollow&quot;&gt;suggests that long-term exposure to low-radiation poses no risk of DNA damage&lt;/a&gt; for mice (it is also important to note that mice are unusually susceptible to cancer). So apparently there may be a threshold for radiation damage to DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But is this study conclusive? What are some other studies that show the biological effects of long-term low-dose radiation on DNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some studies that &lt;a href=&quot;http://www.quora.com/Is-there-conclusive-medical-research-that-flying-in-airplanes-exposes-people-to-unsafe-amounts-of-radiation/answer/Alex-K-Chen&quot; rel=&quot;nofollow&quot;&gt;do show increased rates of cancer in frequent flyers&lt;/a&gt;. So are are we going to reconcile this finding with the finding above?&lt;/p&gt;&#xA;" OwnerUserId="103" LastEditorUserId="103" LastEditDate="2012-05-16T19:24:45.883" LastActivityDate="2016-03-23T01:47:28.803" Title="What risk to DNA does long-term exposure to low-dose radiation pose?" Tags="&lt;dna&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2287" PostTypeId="2" ParentId="2286" CreationDate="2012-05-16T19:56:42.933" Score="4" Body="&lt;p&gt;I agree with @Kevin - there are no ultimate statements in science. The answer is 'its all relative'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With radiation and risk, more radiation means more risk of cancer or any number of other types of damage that can result.  The question is is this significant?  And this is a somewhat subjective question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When someone says:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;'there is no health risk from XYZ' &lt;/p&gt;&#xA;&#xA;&lt;p&gt;what they mean is.. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;to the extent that we can determine, we can't see any more chance of adverse health if you are exposed to XYZ conditions than if you weren't&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA damage happens all the time.  The frequent flier study you cite is trying to see if the additional exposure to cosmic radiation while flying, which is largely blocked by the atmosphere, causes a change in the rate of some cancers.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Radiation and cancer is like a lottery.  If you buy just one ticket you might win.  If you step outside, the thousands of extra gamma rays you get outside might start a cancer that will eventually take your life.  If you buy 20 million tickets you will very likely win.  If you hang out next to high levels of radiation, even for a short while, you will get so much damage you will not live long.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its difficult to study the effect of low levels of radiation. The lower the levels of radiation we are asking about, the longer you will have to wait to see if there is an effect.  If 10% more people get cancer, you have a very real concern that some of these folks might have done something else, like sunbathe &lt;a href=&quot;http://en.wikipedia.org/wiki/Radon&quot; rel=&quot;nofollow&quot;&gt;or live in a poorly ventilated basement for too long&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The real question is, what is significant?  I once saw a 60 minutes segment where a dermatologist said that she simply never directly exposes her skin to direct sunlight.  I'm betting she never got a melanoma.  She carried a parasol and wore light gloves outdoors.  (sorry I can't find the link)  She was at least in her 50s and she had the skin of a teenager.  I still go out in the sun.  &lt;a href=&quot;http://www.cancer.gov/melanomarisktool/&quot; rel=&quot;nofollow&quot;&gt;I assume my risk of melanoma is 5-10 times more than hers was (this was a pretty old broadcast)&lt;/a&gt;.  (mine is 0.03% in the next 5 years btw).  Its just not worth it to me. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-16T19:56:42.933" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2288" PostTypeId="2" ParentId="1995" CreationDate="2012-05-16T20:04:42.690" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://www.protocol-online.org/biology-forums/posts/26634.html&quot;&gt;http://www.protocol-online.org/biology-forums/posts/26634.html&lt;/a&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this link - it says 'we don't really know'.  It says PEG binds DNA, I assume shielding the membrane from its negative charge and allowing internalization to happen.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would guess that the amphipathic nature of PEG, being partly hydrophobic, also helps soften up the membrane.  Interestingly, if you increase the PEG concentration beyond the limits, it decreases the efficiency of the procedure. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-16T20:04:42.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2289" PostTypeId="2" ParentId="2286" CreationDate="2012-05-16T20:18:42.093" Score="4" Body="&lt;p&gt;In the astrobiology community, radiation is a ubiquitous factor in the survival of life in space. It's the current understanding that, while high doses of radiation over a short period of time are lethal, an equivalent dose over a much longer time period (maybe 1000x longer) is much less harmful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The basis for radiation lethality lies in the ability of high-energy particles (that's what radiation &lt;em&gt;is&lt;/em&gt;) to damage DNA. When DNA gets damaged, there are some issues:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The normal, regular structure of the molecule gets disturbed. The genome is a very delicate structure. It is linearly sequence-dependent, and it is only singly redundant (there are two strands of DNA, so if one strand becomes damaged, it can be recopied from the other one).&lt;/li&gt;&#xA;&lt;li&gt;Our cells are under unrelenting barrage of oxidative stress, EM radiation, radioactive radiation and physiological stress--this is no exhaustive listing of the constant fight our bodies' cells put up all the time. There are repair mechanisms in place to automatically fix the damage done by high-energy radiation, and if it turns out that a particular cell has sustained too much damage--well, it commits suicide. This process is called apoptosis and its importance ranges from proper embryonic development to prevention of cancers.&lt;/li&gt;&#xA;&lt;li&gt;In short, there are two ways that excess radiation can cause an organism to die: a) DNA and cellular damage to an irreparable extent, and b) mutagenesis to cause cancers and other cell-cycle diseases.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;We don't quite know the full extent to which we can expose our bodies to long-term high-energy radiation, but the answer is sure very complex. Different tissues, cell lines, and regions of the body receive and cope with radiation in very different ways.&lt;/p&gt;&#xA;" OwnerDisplayName="user891" LastEditorUserId="22057" LastEditDate="2016-03-23T01:47:28.803" LastActivityDate="2016-03-23T01:47:28.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2290" PostTypeId="2" ParentId="1648" CreationDate="2012-05-16T20:39:27.480" Score="9" Body="&lt;p&gt;I'd have to agree that it's highly improbably that the GFAJ-1 strain used nucleoside triarsenates as an energy source. There are three main lines of evidence pointed out in the &lt;em&gt;Science&lt;/em&gt; reviews that were published after the initial publication of the paper.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The incorporation of arsenate ions into NTAs is not a plug-and-play process, &lt;em&gt;per se&lt;/em&gt;. Arsenate does not simply replace phosphate ions from molecules. In order for an NTA to form, it must arsenylate (like phosphorylate) a ribose molecule, then have the purine/pyrmidine ring form (and be attached to the ribose), and then two more arsenates have to be linked via ester bond to the other first arsenate. Mind you, this all happens in water. Arsenate esters are notoriously unstable in water, so it's difficult to imagine an NTA forming stably.&lt;/li&gt;&#xA;&lt;li&gt;The original team in Felisa Wolfe-Simon's lab didn't intentionally add phosphate ions to their growth media; instead, the approximate amount of phosphate impurity was measured and reported. The lab compared this level of phosphate with the minimal levels reported in &lt;em&gt;E. coli&lt;/em&gt; from another paper and basically said, &quot;There isn't enough phosphate in our growth media for our GFAJ-1 strain to grow solely on phosphorous.&quot; Well, that logic is a little &lt;em&gt;non sequitur&lt;/em&gt;  because GFAJ-1 is a halomonad (they said so themselves) and there is literature pointing to a species within &lt;em&gt;Halomonadaceae&lt;/em&gt; that can grow on phosphate levels &lt;strong&gt;lower than&lt;/strong&gt; that of the impurities reported.&lt;/li&gt;&#xA;&lt;li&gt;Although the Wolfe-Simon team added arsenate into their growth media, it's unlikely that any biologically-useful arsenic ended up in the cells at all. Under physiological electrochemical conditions, arsenate gets reduced to arsenite. Phosphate ions, on the other hand, are stable at physiological potentials.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;All in all, there's a reason why life chose phosphorous instead of arsenic. Although both elements have ions with a propensity to make ester bonds, maybe arsenic just doesn't fit into our anthropocentric view of what life is.&lt;/p&gt;&#xA;" OwnerDisplayName="user891" LastActivityDate="2012-05-16T20:39:27.480" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2291" PostTypeId="2" ParentId="1648" CreationDate="2012-05-16T21:30:19.757" Score="0" Body="&lt;p&gt;In my mind, this is definitively debunked in &lt;a href=&quot;http://www.microbeworld.org/index.php?option=com_content&amp;amp;view=article&amp;amp;id=1189%3atwim-32-not-the-shadow-biosphere&amp;amp;catid=107%3athis-week-in-microbiology&amp;amp;Itemid=275&quot; rel=&quot;nofollow&quot;&gt;episode 32&lt;/a&gt; of This Week in Microbiology. In short, no, GFAJ-1 does not use adenosine triarsenate as an energy currency, nor does not seem to incorporate any arsenic in its genetic material at all. One of the two well written answers above deserves the accepted status, but I thought I'd draw your attention to a scientific discussion behind this work.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-05-16T21:30:19.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2292" PostTypeId="1" AcceptedAnswerId="3269" CreationDate="2012-05-17T06:21:03.210" Score="5" ViewCount="66" Body="&lt;p&gt;We now have a collection of transcripts at hand. We would like to investigate some particular ones, which are ion/water channel related. How to perform this? Could anybody point out how to find the annotated genes those are ion/water channel related? If there are some places particularly for fish, that would be perfect. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="790" LastEditorUserId="223" LastEditDate="2012-08-21T20:07:17.573" LastActivityDate="2012-08-21T20:07:17.573" Title="How to find ion/water channel related genes" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2293" PostTypeId="1" AcceptedAnswerId="2735" CreationDate="2012-05-17T10:24:10.417" Score="29" ViewCount="9411" Body="&lt;p&gt;I've been wondering about head hair, facial hair in particular. Human males can grow very extensive beards should they choose to not shave - however you do not really see this in our chimpanzee cousins! Yes, they have little pseudo-beards, but the difference being that they do not shave, that is just the length they reach. Whereas in humans we can grow to our hearts content (*this may not be the case, see &lt;a href=&quot;https://biology.stackexchange.com/questions/1267/why-can-hair-grow-without-limit-while-eyebrow-cannot&quot;&gt;this question&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't really see why this would have been selected, unless it's simply that (evolutionarily speaking) women like men with long beards?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is: why can humans perpetually grow head hair, yet we have lost the majority of our body hair, in comparison to chimpanzees and other ape family members?&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2017-10-04T02:41:01.823" Title="Why do we grow so much hair on our heads compared to our bodies?" Tags="&lt;evolution&gt;&lt;zoology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2294" PostTypeId="2" ParentId="2267" CreationDate="2012-05-17T14:23:03.887" Score="4" Body="&lt;p&gt;Well here's my take. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Too bad there is no open access to this article.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see that they only had statistics for the top 50 annotations, which implies a fairly manual process - you are going to have to read a bunch of articles or abstracts to decide directly whether the software is right.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case, the authors are using a weighted latent semantic indexing method, which have started with a bunch of articles for each gene.  In this case they would need to only look over the data they put into their training. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That might not answer your question though.  If you wanted to search through the literature to confirm annotations generated by a different method...you could create a semi automated process perhaps like this: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do a rough search from NCBI in an automated fashion (I use biopython) and then read every article for validation of the Gene Ontology result. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its possible you could search for the gene and the GO term if to get a more focused result, load them into a database or just create a set of files with the data.  I would build a little website that would let me scan through the abstracts with links to the complete articles (pubmed supplies DOI numbers) and just check 'yea' or 'nay' on whether confirmation happened.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's other potential options on finding articles for search.  the Genbank record for the gene often has a few references in it. One might use pubmed's referencing feature, where you can start at these confirmed articles that describes the gene in question and use pubmed to show articles that have referenced that first article.  I'm not sure if this is accessible by API, but you can build an article graph by crawling the bibliographic references. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For anything that was neither directly contradicted nor confirmed you would have to go back to google and look until you found something.  Clearly there are genes for which you will find no reference at all, and you will have to avoid these for confirmation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure if they checked for any biases here. If something like interpro2go which generates GO mappings from protein domains was used to generate the annotations, you would want to take care that you weren't just rediscovering the references which helped generate the annotations in the first place. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-17T14:23:03.887" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2295" PostTypeId="1" CreationDate="2012-05-17T16:47:31.063" Score="7" ViewCount="1224" Body="&lt;p&gt;I am currently reading Richard Dawkins's book 'The Greatest Show On Earth: The proof for evolution' and in the second chapter he talks very much about the evolution of dogs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He says centuries ago there was only such dog-like creature as the wolf, but in a matter centuries the wolf has evolved into the many breeds of dog we have through artificial selection conducted by man. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This to me seemed very peculiar and quite frankly untrue, and I may be getting the wrong end of the stick and he is in fact being analogous, although I'm pretty sure he's not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, did wolves evolve into the many breeds of dog we have through artificial selection conducted by man?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, how many centuries did this take?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Dawkins's point was that if the wolf can evolve into the vast amount of breeds of dog we have at the moment from artificial selection over a matter of centuries, then surely over many millions of years, the evolution we claim to know of through natural selection could definitely have happened).&lt;/p&gt;&#xA;" OwnerUserId="839" LastEditorUserId="3952" LastEditDate="2013-08-08T00:14:43.680" LastActivityDate="2013-08-08T00:14:43.680" Title="The evolution of dogs through domestication and artificial selection" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;ethnobiology&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2296" PostTypeId="2" ParentId="2295" CreationDate="2012-05-17T19:09:29.540" Score="9" Body="&lt;p&gt;According to Serpell, 1995 (&lt;a href=&quot;http://books.google.co.uk/books?id=I8HU_3ycrrEC&quot;&gt;http://books.google.co.uk/books?id=I8HU_3ycrrEC&lt;/a&gt;, page 8), wolf bones in association with human bones have been found from as early as the middle pleistocene (126,000–781,000 years ago). I think we're talking about more than a few centuries here :) It's still relatively little in comparison to naturally selected evolution, but that's probably the point he is trying to emphasize.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-05-18T11:33:02.730" LastActivityDate="2012-05-18T11:33:02.730" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2298" PostTypeId="1" AcceptedAnswerId="2312" CreationDate="2012-05-17T19:56:00.717" Score="4" ViewCount="1785" Body="&lt;p&gt;Many DNA isolation protocols use a &lt;a href=&quot;http://en.wikipedia.org/wiki/Proteinase_K&quot; rel=&quot;nofollow&quot;&gt;Proteinase K&lt;/a&gt; digestion to remove proteins. This is often performed at 50&amp;nbsp;°C. Why is this?&lt;/p&gt;&#xA;" OwnerUserId="867" LastEditorUserId="355" LastEditDate="2012-05-17T23:07:12.570" LastActivityDate="2012-05-19T08:08:44.410" Title="Why is proteinase K digestion performed at 50 °C?" Tags="&lt;dna-isolation&gt;&lt;protocol&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2299" PostTypeId="1" AcceptedAnswerId="2856" CreationDate="2012-05-18T01:43:21.957" Score="10" ViewCount="666" Body="&lt;p&gt;Im an engineer by education and i program a lot, so the question sounds weird to people from other disciplines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Im trying to better understand the human biological clock. Yet i do not really know what it is. I read about clock genes, endogenous cycles, and other observed phenomena that is time sensitive or cyclical in nature. But is there a centralized model of what the circadian rhythm is or how itis exhibited within the human body? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example an electrical clock can be modelled with feedback loops or electrical flip flops that control the timing. Ive seen the heart modelled as Van Der Pol oscillator.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does modern science have some notion of how the &quot;master&quot; clock within the human body work? Is there a feedback or an oscillator model of the master clock?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for any articles or keywords that ican use to research this question!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-11-19T17:01:30.993" Title="How is human biological clock modelled in modern science?" Tags="&lt;human-biology&gt;&lt;circadian-rhythms&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2301" PostTypeId="2" ParentId="2295" CreationDate="2012-05-18T05:27:33.203" Score="9" Body="&lt;p&gt;I just wanted to add that although we are pretty confident that domestication of wolves created domestic dogs in pretty short order.  In addition to the fact that they can still interbreed and the taxonomical resemblence of dogs to wolves and finally the genome sequence, probably the most awesome evidence is &lt;a href=&quot;http://cbsu.tc.cornell.edu/ccgr/behaviour/History.htm&quot;&gt;the domestication of the silver fox&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Russian biologists at the Institute of Cytology and Genetics (ICG) in Novosibirsk, Russia in 1959 started with 130 foxes.  Even though they can be bred in captivity and they are close to dogs, they had never been domesticated.  By selecting the animals with the least aversion to human contact over 10 generations, they were able to breed foxes that were very much like domestic dogs.  They follow humans around, enjoy contact with humans, and generally act friendly.  In addition they also bred the most averse animals to human each generation as a control (sure enough these animals would rather nip your fingers off before letting you rub their belly!) there are &lt;a href=&quot;http://www.youtube.com/watch?v=-L58NPPQ5eI&quot;&gt;videos of these animals floating around&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ten generations of animals ended up being less than 20 years.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-18T05:27:33.203" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2302" PostTypeId="1" AcceptedAnswerId="2313" CreationDate="2012-05-18T07:23:44.127" Score="5" ViewCount="494" Body="&lt;p&gt;I trained myself to do intravenous injection on live mice. However, on anaesthetized mice you don't see the flux of your product showing that your injection was successful. In the same way, on live mouse a slight back pressure can be used to pull blood into the syringe to confirm proper placement in the vessel before injecting. On anaesthetized mice, I really have difficulty to obtain blood. All my following experiments rely on this injection, so I really need to be sure that the injection was successful and I have no choice that to do the injection on an anaesthetized mouse. Of course I warm the animals before injection to dilate the veins but I don't know how much I can warm an anaestethized mouse.&#xA;I thought to put a catheter before anesthetization the mouse but I don't know if it will stay in place until the mouse is anaestetized.&#xA;Do you have any tips?&lt;/p&gt;&#xA;" OwnerUserId="126" LastEditorUserId="69" LastEditDate="2012-05-19T15:58:15.857" LastActivityDate="2012-05-19T15:58:15.857" Title="intravenous (IV) in the tail vein of an anaesthetized mouse" Tags="&lt;zoology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2303" PostTypeId="2" ParentId="2275" CreationDate="2012-05-18T08:45:16.477" Score="1" Body="&lt;h3&gt;Diabetes&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;I've not read about any conclusive evidence for a link between insulin and differential cognitive function, but I have read studies that link &lt;em&gt;type-2 diabetes&lt;/em&gt; and impaired cognition (&lt;a href=&quot;http://care.diabetesjournals.org/content/29/3/560.full&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;). I will point out now that this is cross-sectional, so the study only reports associations (i.e. diabetes may not necessarily &lt;em&gt;cause&lt;/em&gt; the cognitive impairment).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The study I have mentioned does not conclude that this is caused by raised insulin, but rather the effects on the vascular system (specifically microvascular). They also find a significant interaction between diabetes and smoking status, in the context of cognitive impairment. Again, this seems likely to be the vascular system, rather than insulin levels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A recent review paper also refers to the links between diabetes and &lt;em&gt;executive&lt;/em&gt; function (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22268397&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;), but again makes no reference to insulin as the cause, but rather microvascular changes, hypertension, and other associated traits (again, the causes are not known, these are speculative based on the evidence).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diabetes may not be the best model for studying this though, as it can be characterized by either high insulin (tolerance), or low insulin (impairment) - therefore the association may not be found this way.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Insulin&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;In a separate review (this may be the best one for you if you only read one of the papers I've referenced) the author posits that whilst insulin &lt;em&gt;may&lt;/em&gt; have a neuroprotective role, it also increases amyloid-Beta metabolism and tau phosphorylation, possibly contributing to Alzheimer's-like pathologies (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22411248&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;). Studies have found that insulin directly improves cognitive performance (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11598383&quot; rel=&quot;nofollow&quot;&gt;4&lt;/a&gt;) after infusion of insulin, but the long term effects are less certain - it is unlikely to improve overall health having constantly raised insulin serum levels!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However the link between IGF-1 and improved cognition is less disputed, so you may well be right in thinking that the 'overall' effect of insulin on cognition may be protective, but this may just be a marker of good health overall, which is certainly protective!&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-05-18T11:31:50.060" LastActivityDate="2012-05-18T11:31:50.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2305" PostTypeId="1" CreationDate="2012-05-18T12:59:32.107" Score="4" ViewCount="14821" Body="&lt;p&gt;What are the differences between white and brown adipose tissue? Here are some that I have come across:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Brown Adipose Tissue                        White Adipose Tissue&#xA;&#xA;Thermogenic                                 Non-thermogenic&#xA;Multilocular                                Unilocular&#xA;Relatively many mitochondria                Relatively few mitochondria&#xA;Vascularised                                Relatively few capillaries&#xA;characterized by the presence of leptin     characterized by the presence of UCP-1&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="835" LastActivityDate="2016-12-06T05:01:32.193" Title="What are the differences between white and brown adipose tissue?" Tags="&lt;metabolism&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2307" PostTypeId="2" ParentId="2305" CreationDate="2012-05-18T18:32:36.287" Score="2" Body="&lt;p&gt;Not sure what you are asking, except to add to the list?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its worth mentioning that brown adipose tissue is the only organ in the human body whose primary purpose is to generate heat.  We are warm blooded, but the body temperature is regulated by other organs generating heat while they do work (like muscles or I suppose the stomach, kidney, etc).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brown Tissue is supposed to not a juvenile attribute - doesn't show up in adults to the same extent (usually being limited to neck and upper chest.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brown Tissue is thought to be present in only critical areas of the body - even in infants.  Its found in the inner body cavity around vital organs.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The color comes from the large number of mitochondria in the cells, which is where the heat is generated via uncoupling protein 1 (UCP1). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;White adipose tissue is what we more commonly call fat tissue - its primary function is to store energy in the chemical form of long chain fats.  Fat tissue as it grows can inhibit the function of insulin in the body, increasing insulin resistance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could almost call them 'good fat' and 'bad fat'&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-18T18:32:36.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2309" PostTypeId="1" CreationDate="2012-05-18T19:25:38.467" Score="12" ViewCount="940" Body="&lt;p&gt;According to the article &lt;a href=&quot;http://www.tandfonline.com/doi/abs/10.1080/07315724.2010.10719814&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;Green Tea Supplementation Affects Body Weight, Lipids, and Lipid Peroxidation in Obese Subjects with Metabolic Syndrome&quot;&lt;/a&gt;, Green tea increases metabolism and fat loss:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Green tea beverage consumption (4 cups/d) or extract supplementation&#xA;  (2 capsules/d) for 8 weeks significantly decreased body weight and&#xA;  BMI. Green tea beverage further lowered lipid peroxidation versus age-&#xA;  and gender-matched controls, suggesting the role of green tea&#xA;  flavonoids in improving features of metabolic syndrome in obese&#xA;  patients.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is there any information available concerning the mechanism of that metabolic increase?&lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="15695" LastEditDate="2017-03-04T12:44:28.630" LastActivityDate="2017-03-07T11:38:06.170" Title="How Does Green Tea Increase Metabolic Rate?" Tags="&lt;metabolism&gt;&lt;food&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2310" PostTypeId="2" ParentId="2298" CreationDate="2012-05-18T19:31:08.567" Score="2" Body="&lt;p&gt;In your linked wiki article: &quot;An elevation of the reaction temperature from 37 °C to 50 - 60 °C may increase the activity (of Proteinase K) several times.&quot; The enzyme works faster at 50°C.&lt;/p&gt;&#xA;" OwnerUserId="146" LastActivityDate="2012-05-18T19:31:08.567" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2311" PostTypeId="1" CreationDate="2012-05-19T05:40:21.793" Score="6" ViewCount="234" Body="&lt;p&gt;I'm learning about development via the example of &lt;em&gt;Drosophila&lt;/em&gt; embryogenesis. I understand that bicoid regulates hunchback, among other genes. My question whether the regulation is direct or indirect? In other words, does the level of bicoid directly govern the expression of hunchback, or are there steps in between?&lt;/p&gt;&#xA;" OwnerUserId="900" LastEditorUserId="43" LastEditDate="2012-11-29T15:32:37.513" LastActivityDate="2012-11-29T15:45:18.127" Title="Bicoid regulation of hunchback" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;development&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2312" PostTypeId="2" ParentId="2298" CreationDate="2012-05-19T08:08:44.410" Score="2" Body="&lt;p&gt;Proteinase K activity is greatly increased by addition of denaturing agents like SDS or urea (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1975.tb02211.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Hilz et al., 2008&lt;/a&gt;), indicating that the denaturation of the substrates helps Proteinase K to degrade them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Increasing the temperature to 50°C will also unfold some proteins already, making it easier for the Proteinase K to degrade them. The proteinase K seems to be a pretty stable enzyme, and  can still work at this temperature.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2012-05-19T08:08:44.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2313" PostTypeId="2" ParentId="2302" CreationDate="2012-05-19T10:15:52.753" Score="4" Body="&lt;p&gt;Cleaning the tail with ethanol is of some help and also, as you said, warming the tail. We sometimes put one of those flexible lamps (such as &lt;a href=&quot;http://www.ikea.com/us/en/images/products/forsa-work-lamp__66021_PE166226_S4.jpg&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;) to heat up only the tail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When anesthesized (ketamine/xylazine or isoflurane) we keep our mice on a &lt;a href=&quot;https://www.stoeltingco.com/stoelting/1671/1465/1473/Physio/Homeothermic-Blankets-for-Rodents&quot; rel=&quot;nofollow&quot;&gt;heated pad&lt;/a&gt; anyways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cannulation in the tail does not sound like a good idea to me, especially if you are going to have the animal wake up afterwards. If you're going to cannulate then go for the jugular, but be aware that doing it on a mouse requires quite a bit of experience and it's definitely way longer than a tail injection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It really depends on your experiment&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2012-05-19T10:48:07.457" LastActivityDate="2012-05-19T10:48:07.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2314" PostTypeId="2" ParentId="2309" CreationDate="2012-05-19T11:10:03.047" Score="5" Body="&lt;p&gt;May be because it contains xanthines that boosts Cyclic AMP and Subsequent Stimulation Of Oxidative Pathways .&lt;/p&gt;&#xA;" OwnerUserId="901" LastEditorUserId="901" LastEditDate="2012-05-19T16:56:49.280" LastActivityDate="2012-05-19T16:56:49.280" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2315" PostTypeId="2" ParentId="1874" CreationDate="2012-05-19T14:46:19.067" Score="4" Body="&lt;p&gt;I heard that as well and was skeptical at first, but apparently there IS science to support it- &lt;a href=&quot;http://mblogs.discovermagazine.com/80beats/2011/11/21/helpful-mouse-fetuses-naturally-send-stem-cells-to-mom-to-fix-her-damaged-heart/&quot; rel=&quot;nofollow&quot;&gt;http://mblogs.discovermagazine.com/80beats/2011/11/21/helpful-mouse-fetuses-naturally-send-stem-cells-to-mom-to-fix-her-damaged-heart/&lt;/a&gt; Officially found with mice, but it supports how some women that suffered damages while pregnant are sometimes found with their children's cells still in their body, in the formerly damaged organs, many years after birth.&lt;/p&gt;&#xA;" OwnerUserId="902" LastActivityDate="2012-05-19T14:46:19.067" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2316" PostTypeId="2" ParentId="2254" CreationDate="2012-05-19T19:04:04.593" Score="0" Body="&lt;p&gt;Heres the solution&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UM0Mc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;i got 1 mark off for the position of Not I&lt;/p&gt;&#xA;" OwnerUserId="877" LastActivityDate="2012-05-19T19:04:04.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2317" PostTypeId="1" CreationDate="2012-05-19T19:08:34.337" Score="11" ViewCount="8031" Body="&lt;p&gt;I am wondering if you were theoretically able to get vaccinations or antibodies for any and every diseases and/or illness, would there be a limit to how many you can get and keep in your body at one time? If so, what is the limiting factor?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would be the possible effects of this on the body and immune system? Thanks.&lt;/p&gt;&#xA;" OwnerUserId="904" LastActivityDate="2018-08-19T05:58:39.253" Title="Is there a maximum amount of antibodies your body can keep?" Tags="&lt;immunology&gt;&lt;antibody&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2318" PostTypeId="2" ParentId="2317" CreationDate="2012-05-19T20:49:07.467" Score="4" Body="&lt;p&gt;Antibodies are simply proteins and like any other protein have a relatively short &quot;life&quot;, so after clearing out an infection, they are not retained for long (most of them anyway). What the body keeps is memory cells which can produce a much more rapid response if they come in contact with the same pathogen again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could see it as a selective process: the body produces immune cells, one or more specific cells for nearly every potential antigen that might exist in the world (there are more steps involved of course but they are of little relevance here). Only those which are used at some point mature into memory cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, I just realised that I can't explain why the immune system goes through this selective process; producing cells equivalent to memory cells in the first place would make the immune response much stronger. One explanation I can think of for why the body produces naive cells first is that either a) their production or b) their maintenance is less costly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other explanation I could think of is that even immune cells in the periphery which have undergone the proofing mechanisms of immune cell development already, may not be perfect and target body cells every now and then - in that case it would be devastating if they would go all-out like a memory cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From my three explanations, only alternative b) would mean there could be a limitation to how many vaccinations our immune system can bear (if memory cells take more effort to maintain than naive cells, having too many of them may overstrain whatever systems maintain them). Otherwise I don't see any limiting factor for how many memory cells you can retain; except if their numbers become so large that your lymph nodes swell and that causes problems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit note: I'm not aware of any research about that question and couldn't find anything either.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-05-19T20:49:07.467" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2319" PostTypeId="1" AcceptedAnswerId="40982" CreationDate="2012-05-20T13:10:50.150" Score="3" ViewCount="397" Body="&lt;p&gt;From the Wikipedia page for the &lt;a href=&quot;http://en.wikipedia.org/wiki/Vermiform_appendix&quot; rel=&quot;nofollow&quot;&gt;vermiform appendix:&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This proposal is based on a new understanding of how the immune system supports the growth of beneficial intestinal bacteria, in combination with many well-known features of the appendix, including its architecture, its location just below the normal one-way flow of food and germs in the large intestine, and its association with copious amounts of immune tissue. Research...showed that individuals without an appendix were four times more likely to have a recurrence of Clostridium difficile.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This quote seems to be implying that the appendix can act as a breeding ground for certain gut flora that are slightly less common (like &lt;em&gt;C. difficile&lt;/em&gt;) and not as ubiquitous as &lt;em&gt;E. coli&lt;/em&gt; or &lt;em&gt;Enterobacter sp&lt;/em&gt;. The appendix could be seen as an ideal spot for this growth of microbial populations in the gut. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that, to a first approximation, anatomically, the appendix and a common diverticulum of the colon are both outcroppings of the large intestine: to what extent would a diverticulum also be able to support less common or more diverse flora, and how likely is this to be due to a difference in extracellular environment (pH, ion concentration) and how likely is it simply due to shape?&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="16651" LastEditDate="2015-12-26T20:20:51.937" LastActivityDate="2015-12-27T03:45:12.247" Title="Are the intestinal microbiota substantially different within a diverticulum of the colon?" Tags="&lt;bacteriology&gt;&lt;human-anatomy&gt;&lt;human-physiology&gt;&lt;gastroenterology&gt;&lt;microbiome&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2320" PostTypeId="1" AcceptedAnswerId="2321" CreationDate="2012-05-20T13:19:06.290" Score="39" ViewCount="66426" Body="&lt;p&gt;Laughing gas (N&lt;sub&gt;2&lt;/sub&gt;O), well, makes people laugh.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does just a gas make us do that, there has to be some hormones at work...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I wanted to know how this works?  What is the mechanism?&lt;/p&gt;&#xA;" OwnerUserId="771" LastEditorUserId="3340" LastEditDate="2015-01-14T15:59:38.443" LastActivityDate="2015-03-05T07:59:33.717" Title="How does laughing gas (N₂O) work?" Tags="&lt;human-biology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="2321" PostTypeId="2" ParentId="2320" CreationDate="2012-05-20T14:03:06.967" Score="40" Body="&lt;p&gt;This information is all strictly for Entonox - a brand of analgesic gas comprising 50% Oxygen (O&lt;sub&gt;2&lt;/sub&gt;) and 50% Nitrous Oxide (N&lt;sub&gt;2&lt;/sub&gt;O), Laughing Gas.  This mixture is known as 'Gas and Air' and is in very common use.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The active ingredient in Entonox is of course the nitrous oxide, so the discussion of the mechanism below refers solely to the N&lt;sub&gt;2&lt;/sub&gt;O as you asked for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nitrous oxide enters the blood by diffusion from the alveoli whilst it is being inhaled, but does not bind with haemoglobin.  It is fat soluble so quickly moves into cells, including synapse ends in the brain.  Because of the stability of the compound, N&lt;sub&gt;2&lt;/sub&gt;O is not metabolised by the body so has its effect as that molecule, then is eliminated by diffusion out of the lungs once inhalation has ceased (taking roughly 2 minutes for on and offset).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the material that BOC pharmaceuticals provide, the exact mechanism of the analgesia is not &lt;em&gt;fully&lt;/em&gt; understood.  It &lt;em&gt;is&lt;/em&gt; known, however, to induce &quot;inconsistent changes in the basal levels of thalamic nuclei&quot;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;N&lt;sub&gt;2&lt;/sub&gt;O inhibits NMDA receptors in the brain whilst simultaneously encouraging the stimulation of the parasympathetic GABA receptors.  This eventually produces an anaesthetic effect.  It is also understood that N&lt;sub&gt;2&lt;/sub&gt;O promotes the release of endogenous opioid neurotransmitters ('natural painkillers' e.g. endorphins) that specifically activate &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12034378&quot;&gt;descending pain pathways&lt;/a&gt;.  This inhibits the transmission of pain.  In this way the analgesia provided by nitrous oxide is antinociceptive (literally pain reducing) rather than a generalised limbic depressor.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, nitrous oxide also positively effects potassium ion channels too &lt;sup&gt;[&lt;a href=&quot;http://molpharm.aspetjournals.org/content/65/2/443.short&quot;&gt;ref&lt;/a&gt;]&lt;/sup&gt; - reducing the chance of an action potential being generated in affected neurons.  Research into this area of the effects of N&lt;sub&gt;2&lt;/sub&gt;O is ongoing.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Euphoria is a common side effect of N&lt;sub&gt;2&lt;/sub&gt;O usage, hence the name laughing gas.  This is as part of wider emotional changes that can occur when nitrous oxide is being administered.  For example, some people instead of laughing become scared or in other cases extremely aggressive towards those nearby. The emotional excitement may result in depressive or manic behaviour even to the point of psychosis and hallucinations especially in those who have a preexisting vulnerability to mental illness. The precise mechanism for these disinhibiting is again not fully understood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whilst it seems a lot of the answers are missing, the course I'm taking this information from is available online at &lt;a href=&quot;http://discover.entonox.co.uk/&quot;&gt;Discover Entonox&lt;/a&gt; - modules 8-10 have relevance to this question.  It's free to register and view the materials, they're all nicely narrated with diagrams etc.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="3340" LastEditDate="2015-03-05T07:59:33.717" LastActivityDate="2015-03-05T07:59:33.717" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2322" PostTypeId="1" CreationDate="2012-05-20T15:37:43.113" Score="3" ViewCount="116" Body="&lt;p&gt;In many spas and salons I have seen people place a cold cucumber on their eyes.&lt;br&gt;&#xA; I think this might be for coolness, but why a cucumber?&lt;br&gt;&#xA;And Is it actually for coolness or for something else (like lightening of dark circles, etc.)?&lt;/p&gt;&#xA;" OwnerUserId="771" LastEditorUserId="771" LastEditDate="2012-05-21T05:26:52.710" LastActivityDate="2012-05-22T06:03:02.617" Title="Cucumber on the eyes" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2323" PostTypeId="1" CreationDate="2012-05-20T18:18:45.347" Score="4" ViewCount="616" Body="&lt;p&gt;I recently had gone for an eye test. The doctor told that short sightedness/ far sightedness is caused due to shrinking or expanding of the eye.&lt;br&gt;&#xA;One thing i forgot o ask him was what causes that shrinking/expanding.&lt;br&gt;&#xA;Can anyone explain it to me?&lt;/p&gt;&#xA;" OwnerUserId="771" LastActivityDate="2012-05-30T20:25:02.440" Title="Cause of short sightedness/ far sightedness" Tags="&lt;eyes&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2324" PostTypeId="1" AcceptedAnswerId="2448" CreationDate="2012-05-20T21:47:09.313" Score="15" ViewCount="755" Body="&lt;p&gt;I'm interested in horizontal gene transfer in bacteria, viruses, and organisms such as Bdelloid Rotifers. I've just read in Carl Zimmer's 'A Planet of Viruses' the following passage:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As a host cell manufactures new viruses, it sometimes accidentally adds some of its own genes to them. The new viruses carry the genes of their hosts as they swim through the ocean, and they insert them, along with their own, into the genomes of their new hosts. By one estimate, viruses transfer a trillion trillion genes between host genomes in the ocean every year.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's interesting to consider the scale of DNA-swapping that has occurred given the frequency by which it happens and the evolutionary timescale.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any examples of genes in the human genome that we know were deposited by viruses that would have given an evolving human a physical/mental advantage? Where did they come from? What benefit did they provide?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested in genetic additions from non-human-ancestor species, rather than the transfer of genes that occurred as mutations from other humans.&lt;/p&gt;&#xA;" OwnerUserId="76" LastEditorUserId="69" LastEditDate="2012-05-21T11:20:37.250" LastActivityDate="2012-06-01T16:52:30.110" Title="What is the contribution of viruses to the evolution of mankind?" Tags="&lt;dna&gt;&lt;virology&gt;&lt;human-genetics&gt;&lt;human-genome&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2327" PostTypeId="1" AcceptedAnswerId="2408" CreationDate="2012-05-21T13:04:38.150" Score="1" ViewCount="785" Body="&lt;p&gt;(In particular primates)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know chimps do. Powerful alpha males chimp would beat up omega males that they caught mating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know gorillas do. Powerful alpha males gorillas would beat up omega males that they caught mating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know humans do. Politically powerful alpha males would jail or stone weaker omega &quot;peasant&quot; humans that they caught mating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know bonobo doesn't.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about other primates/animals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what's the difference and why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The alpha animals are given preference to be the first to eat and the&#xA;  first to mate; among some species &lt;strong&gt;they are the only animals in the&#xA;  pack allowed to mate. Other animals in the community are usually&#xA;  killed or ousted if they violate this rule&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Alpha_%28ethology%29&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Alpha_%28ethology%29&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do preventing and punishing others from mate improve ones' own gene pool survival? Are there similarity between primates (including humans) in this regard?&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="554" LastEditDate="2012-05-28T01:57:02.987" LastActivityDate="2012-05-29T16:46:22.940" Title="What animals stop other members of their species from mating and why?" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="2328" PostTypeId="1" AcceptedAnswerId="2329" CreationDate="2012-05-21T13:27:57.113" Score="10" ViewCount="6325" Body="&lt;p&gt;To clarify, I think the answer should be able to explain:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;What are animals?&lt;/li&gt;&#xA;&lt;li&gt;What are plants? &lt;/li&gt;&#xA;&lt;li&gt;What's the difference between animals and plants (How do biologists differentiate them, if they differentiate them by moving ability of course it's simple, but we know they don't)?&lt;/li&gt;&#xA;&lt;li&gt;How do those differences affect their evolutionary paths so that most animals can move around and most plants cannot? I know there are exceptions, but that's just the exceptions that show the rule.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="554" LastEditorUserId="43" LastEditDate="2012-05-21T14:56:10.787" LastActivityDate="2015-02-07T04:29:56.990" Title="Why animals can move and plants cannot in general?" Tags="&lt;zoology&gt;&lt;plant-physiology&gt;&lt;taxonomy&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2329" PostTypeId="2" ParentId="2328" CreationDate="2012-05-21T13:58:12.510" Score="12" Body="&lt;p&gt;Animals and plants are both classified as Eukaryotes, and as such can form large, complex, multi-cellular organisms. There are several major differences at the cellular level that distinguish the 2 &lt;a href=&quot;http://en.wikipedia.org/wiki/Kingdom_%28biology%29&quot; rel=&quot;noreferrer&quot;&gt;Kingdoms&lt;/a&gt; (Animalia and Plantae). Without getting technical, the most crucial difference in relation to your question is that plants contain &lt;a href=&quot;http://en.wikipedia.org/wiki/Chlorophyll&quot; rel=&quot;noreferrer&quot;&gt;chlorophyll&lt;/a&gt;, and as such can generate their own food using sunlight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is very important when you consider that plants (by definition, those Eukaryotes that contain chlorophyll) have therefore evolved to be very efficient at converting sunlight to 'energy', whereas animals have evolved without this option and have to eat what food they need. So they have instead evolved mechanisms that allow them to forage, or even to hunt, for their food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At some point, a unicellular organism incorporated chlorophyll, leading to multicellular plants in the course of evolution. The ancestor of animals evolved independently from the last common ancestor of plants and animals. Therefore, plants and animals are quite diverged, e.g. in mating 'rituals' (in plants this involves flowers and seeds - whereas in animals there are mating and gestation periods), and systemic changes, such as the immune system and the circulatory system (these are generally much more complex in animals than plants). All of which has stemmed from the difference in evolutionary pressures applied by the choice of food-source.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you have pointed out, there are exceptions to all rules, so not all plants have chlorophyll, but as a rule it is the case! (&lt;a href=&quot;http://en.wikipedia.org/wiki/Plant&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt;: &quot;Some plants are &lt;a href=&quot;http://en.wikipedia.org/wiki/Parasitic_plant&quot; rel=&quot;noreferrer&quot;&gt;parasitic&lt;/a&gt; and may not produce normal amounts of chlorophyll or photosynthesize.&quot;).&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-05-24T08:13:46.290" LastActivityDate="2012-05-24T08:13:46.290" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="2331" PostTypeId="1" CreationDate="2012-05-21T16:01:31.107" Score="5" ViewCount="359" Body="&lt;p&gt;I was reading &lt;a href=&quot;http://www.askamathematician.com/2012/05/q-is-quantum-randomness-ever-large-enough-to-be-noticed/&quot;&gt;http://www.askamathematician.com/2012/05/q-is-quantum-randomness-ever-large-enough-to-be-noticed/&lt;/a&gt; and saw:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] the evolution of entire species can be changed by a single &#xA;  mistake in the replication of a strand of DNA (this is one mechanism &#xA;  for mutation).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;... implying other mechanisms for mutation exist. Do they? &lt;/p&gt;&#xA;" OwnerUserId="910" LastActivityDate="2012-05-21T19:54:16.440" Title="Are there other mechanisms for mutation besides imperfect DNA replication?" Tags="&lt;evolution&gt;&lt;dna&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2332" PostTypeId="2" ParentId="2331" CreationDate="2012-05-21T16:06:42.223" Score="7" Body="&lt;p&gt;Absolutely. Ionizing (X-rays, neutrons, electrons, heavy ions) and non-ionizing radiation (UV), chemicals, etc. are able to induce DNA Damage, which is then imperfectly repaired. So it's not an issue of imperfect replication, but also of imperfect damage repair.&lt;/p&gt;&#xA;" OwnerUserId="852" LastActivityDate="2012-05-21T16:06:42.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2333" PostTypeId="2" ParentId="2295" CreationDate="2012-05-21T19:00:05.823" Score="3" Body="&lt;p&gt;Many dog breeds went through genetic bottlenecks about 200 years ago. Many of today's breeds either did not exist a couple to few hundred years ago or looked rather different than the breed looks today. It doesn't take long to change the characteristics when selective breeding occurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One may need to consider the co-evolution of &lt;em&gt;Homo sapiens&lt;/em&gt; and &lt;em&gt;Canis familiaris&lt;/em&gt;. &lt;a href=&quot;http://zeenews.india.com/news/eco-news/dogs-may-have-helped-modern-man-to-flourish_776168.html&quot; rel=&quot;nofollow&quot;&gt;Our close friendship with dogs tipped the balance in favour of modern man over the Neanderthals, who had previously occupied present-day Europe for a staggering 250,000 years&lt;/a&gt;. More on how dogs helped human hunt and be watchful is &lt;a href=&quot;http://www.theatlantic.com/technology/archive/2012/05/humanitys-best-friend-how-dogs-may-have-helped-humans-beat-the-neanderthals/257145/&quot; rel=&quot;nofollow&quot;&gt;explained here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This other report, just out, states that &lt;a href=&quot;http://www.eurekalert.org/pub_releases/2012-05/du-mdb051812.php&quot; rel=&quot;nofollow&quot;&gt;modern dog breeds are genetically disconnected from ancient ancestors&lt;/a&gt;. Cross-breeding of dogs over thousands of years has made it extremely difficult to trace the ancient genetic roots of today's pets, according to a new study.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-05-21T20:06:59.000" LastActivityDate="2012-05-21T20:06:59.000" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2334" PostTypeId="2" ParentId="2331" CreationDate="2012-05-21T19:54:16.440" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7678134&quot; rel=&quot;nofollow&quot;&gt;DNA methylation over CpG doublets can cause mutation&lt;/a&gt; since 5mC can undergo spontaneous deamination and covert to a thymine.&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2012-05-21T19:54:16.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2335" PostTypeId="1" CreationDate="2012-05-21T19:58:58.790" Score="4" ViewCount="137" Body="&lt;p&gt;Bt corn is genetically modified to kill borers, but &quot;regulations require farmers to plant conventional varieties as well, which is intended to stop the borers becoming resistant.&quot;&#xA;-&lt;a href=&quot;http://www.bbc.co.uk/news/science-environment-11496710&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do susceptible organisms prevent parasites from overcoming host resistance? &lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="16866" LastEditorDisplayName="user560" LastEditDate="2017-01-03T16:05:26.813" LastActivityDate="2017-01-03T16:05:26.813" Title="How do susceptible organisms prevent parasites from overcoming resistance?" Tags="&lt;ecology&gt;&lt;population-biology&gt;&lt;community-ecology&gt;&lt;parasitism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2336" PostTypeId="1" CreationDate="2012-05-21T20:08:18.560" Score="5" ViewCount="130" Body="&lt;p&gt;I seem to remember reading that embryonic cells will frequently replicate the section of their genome containing &lt;a href=&quot;http://en.wikipedia.org/wiki/Ribosomal_DNA&quot; rel=&quot;nofollow&quot;&gt;rDNA&lt;/a&gt; by splicing in duplicate genes. The cells use this to produce ribosomes at a rate which would be impossible with the DNA present in cells from full-grown organisms. Is this real? Are there other examples of cells altering their their own nucleotide sequence? &lt;/p&gt;&#xA;" OwnerUserId="810" LastEditorUserId="810" LastEditDate="2012-05-22T10:09:25.813" LastActivityDate="2012-05-22T10:09:25.813" Title="Do somatic cells alter their own nucleotide sequence?" Tags="&lt;dna&gt;&lt;replication&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2337" PostTypeId="2" ParentId="2335" CreationDate="2012-05-21T21:26:49.677" Score="4" Body="&lt;p&gt;In an environment where all plants are resistant to certain parasites, a rare breed which has a mechanism against this resistance has free play - lots of food and no competition. However, in plants which do not have the resistance, this rare parasite breed may be at a disadvantage compared to parasites who do not have the mechanism against that resistance (even if only because they do not waste energy on a defensive mechanism they don't need).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By mixing resistant and unresistant plants, it is probably possible to maintain high enough a competition of parasites without that defensive mechanism to prevent the ones with the mechanism from developing. It's natural selection at work :)&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-05-21T21:26:49.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2338" PostTypeId="2" ParentId="2336" CreationDate="2012-05-21T21:33:15.117" Score="3" Body="&lt;p&gt;I'm assuming you mean, physically changing the DNA polymer. &#xA;The answer is yes.  And how they do this depends upon which cells they are and what they are supposed to do.   A partial list: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In multicellular animals, cells DNA 'ages' where the telomeres, sequences at the ends of the chromosomes, will be degrade and shorten.  This relates to how many times the cells have divided and acts as a sort of clock for development and probably also ageing.  Telomere degradation does not happen in all cells - the germline cells are not modified of course.  This is one of the probable reasons that cloning animals sometimes doesn't make perfect copies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cells will also add Methyl groups to the DNA nucleotides.  Methylation is triggered when environmental or developmental conditions.  The textbook example for methylation is the markers on the DNA of children whose parents have experienced starvation conditions.  Methylation can disappear in subsequent generations.  It also happens to cells in the brain which mark different stages in their brain development.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Meiosis, When sexual mating happens, the cells that make the sperm and eggs shuffle the pairs of chromosomes, editing so that about half of the resulting single set of chromosomes contain half of each parent's chromosomes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, there is DNA repair. When radiation or chemicals breaks the chromosome, there are enzymes that repair them. Usually they read the opposite strand of the DNA to see how the repair happens. Sometimes the DNA is not reparable from the strand, and the result is not the same as the DNA the cell started with.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Short repeat DNA seem to show up in chromosomes - segments of short repeats can change length (AGGAGGAGGAGGAGT -&gt; AGGAGGAGGAGGAGGAGGAGTAGGAGG etc). I'm not sure how this happens, but its different between identical twins.  It also probably happens to cells in different parts of your body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What else have I forgotten everyone? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also enzymes that coil the DNA up onto nucleosomes, but don't really make any changes, but we won't count that. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-21T21:33:15.117" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2339" PostTypeId="2" ParentId="2270" CreationDate="2012-05-21T22:14:00.807" Score="4" Body="&lt;p&gt;If I understand the question correctly, you're thinking something along the lines of modular tertiary domains, but in a quaternary sense? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a reversible interaction, heterotrimeric G proteins spring to mind. Once activated by a G protein coupled receptor (GPCR), the alpha subunit and the beta-gamma complex dissociate from the receptor and from each other. They can both go on to affect signaling by binding to various effector proteins, depending on the particular pathway in which they are involved, and their activities can be mediated by other proteins (e.g. the alpha subunit GTPase regulated by GAP proteins). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I spoke to my Protein Engineering professor, and she also directed me to a few examples, although I'm not sure they're quite what you're looking for in the strictest sense.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Cyclin-dependent kinases, as @Armatus mentioned, bind to all sorts of different cyclins. (I get the sense that subunits found in multiple protein complexes will probably be more common in signal cascades. I don't have any real data on that, but it makes sense that a signal protein could interact with two or more protein complexes and even have slightly different functions in each.) &lt;/li&gt;&#xA;&lt;li&gt;Alcohol dehydrogenase (ADH) is an example of a protein with different quaternary structures between species. According to my professor, it occurs as a homodimer in mammals, but as a tetramer with some slightly different residues in budding yeast. I can't say whether the sequence changes are what affect the oligomerization, although my prof also mentioned &quot;oligomerization domains&quot; that could mediate protein-protein interactions.&lt;/li&gt;&#xA;&lt;li&gt;She also directed me toward a slightly more interesting example (in my opinion), though, again, it's also more along the lines of oligomerization. Small heat shock proteins (sHSPs) undergo something called &quot;dynamic subunit exchange&quot; and can take on a wide variety of oligomeric architectures. Binding is transient, but it's still kind of neat. There's a review here: &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0968000411001903&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0968000411001903&lt;/a&gt;. Figure 3 shows different oligomeric architectures from the one monomer.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It seems that pretty much any protein that interacts with two or more separate protein complexes could be considered an answer. Neither I nor my professor have managed to come up with an example of an irreversible assembly of common subunits, but she is of the opinion that, in all the different possible protein structures, there is probably at least one example of everything, no matter how outlandish it seems. &lt;/p&gt;&#xA;" OwnerUserId="889" LastActivityDate="2012-05-21T22:14:00.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2340" PostTypeId="2" ParentId="2336" CreationDate="2012-05-21T22:45:44.807" Score="7" Body="&lt;p&gt;One case where human cells alter their DNA occurs in the immune system.  In the early stages of the continuing production of &lt;a href=&quot;http://en.wikipedia.org/wiki/B_cell&quot;&gt;B-cells&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/T_cells&quot;&gt;T-cells&lt;/a&gt;, the developing cell recombines (shuffles) genes in a particular DNA region which codes for what are called &lt;em&gt;Variable, Diverse&lt;/em&gt;, and &lt;em&gt;Joining&lt;/em&gt; gene segments.  This shuffling is called &lt;em&gt;somatic recombination&lt;/em&gt; or &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/V%28D%29J_recombination&quot;&gt;V(D)J recombination&lt;/a&gt;&lt;/em&gt;.  This rearrangement gives the cell a genetic template for a random instance out of a enormous set of possible antigen-recognition proteins used by the immune system to recognize foreign molecules (in order to fight infection).&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2012-05-21T22:45:44.807" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2341" PostTypeId="1" AcceptedAnswerId="2342" CreationDate="2012-05-22T02:16:37.240" Score="2" ViewCount="437" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Definition&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;blockquote&gt;&#xA;    &lt;p&gt;Colloid is a dispresion of small particles of one material in another.&lt;/p&gt;&#xA;  &lt;/blockquote&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Definition 2 (&lt;a href=&quot;http://en.wikipedia.org/wiki/Colloid&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;)&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;blockquote&gt;&#xA;    &lt;p&gt;A colloidal system consists of two separate phases: a dispersed phase (or internal phase) and a continuous phase (or dispersion medium) in which the colloid is dispersed. A colloidal system may be solid, liquid, or gas.&lt;/p&gt;&#xA;  &lt;/blockquote&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am trying to answer &lt;a href=&quot;http://tenttiarkisto.fi/exams/8046.1.pdf&quot; rel=&quot;nofollow&quot;&gt;problem 2&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;em&gt;&quot;Colloidal particles: What are colloidal systems, give an example, what happens to colloidal particles in a liquid medium. How to stabilize colloidal systems in a liquid medium.&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My &lt;a href=&quot;https://noppa.aalto.fi/noppa/kurssi/tfy-125.2013/luennot/Tfy-125_2013_kolloidit.pdf&quot; rel=&quot;nofollow&quot;&gt;lecture slides&lt;/a&gt; mention this about gel: &lt;em&gt;&quot;a continuous network extending throughout the sample formed by association of colloidal particles or molecules in a liquid&quot;, &quot;formed in concentrated polymer solutions&quot; and &quot;formed by association of sol-gel particles&quot;&lt;/em&gt;. Next lecture slides is about &quot;liquid crystals&quot;, now I am confused -- not sure whether gel or &quot;liquid crystals&quot; is something to look here.&lt;/p&gt;&#xA;" OwnerDisplayName="user911" LastEditorUserId="166" LastEditDate="2012-05-22T11:16:29.567" LastActivityDate="2012-05-22T11:16:29.567" Title="What happens to colloidal particles in a liquid medium? And how to stabilize it?" Tags="&lt;biochemistry&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2342" PostTypeId="2" ParentId="2341" CreationDate="2012-05-22T03:04:36.697" Score="2" Body="&lt;p&gt;&lt;strong&gt;&quot;Colloidal particles: What are colloidal systems, give an example,--&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Milk, bear foam, paste, blood, ---&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&quot;what happens to colloidal particles in a liquid medium.&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I understand the q as solid in liquid so a gel. Examples about gel are &lt;code&gt;&quot;agar, gelatin, jelly and opal&quot;&lt;/code&gt; according to my lecture slides. The electrostatic forces are in some sort of middle phase: not enough to repulse into liquid form but not strong enough to form liquid either.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&quot;How to stabilize colloidal systems in a liquid medium.&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Wikipedia about stability&lt;/strong&gt; (&lt;a href=&quot;http://en.wikipedia.org/wiki/Colloid&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;)&lt;/p&gt;&#xA;  &#xA;  &lt;blockquote&gt;&#xA;    &lt;p&gt;&lt;em&gt;&quot;The stability of a colloidal system is the capability of the system&#xA;    to remain as it is. Stability is hindered by aggregation and by&#xA;    sedimentation phenomena, that determine phase separation.&quot;&lt;/em&gt;&lt;/p&gt;&#xA;  &lt;/blockquote&gt;&#xA;  &#xA;  &lt;p&gt;Now different things to consider are:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Electrostatic stabilization&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;  &#xA;  &lt;blockquote&gt;&#xA;    &lt;p&gt;&lt;em&gt;&quot;In a stable colloid, mass of a dispersed phase is so low that its buoyancy or kinetic energy is too weak to overcome the electrostatic&#xA;    repulsion between charged layers of the dispersing phase.&quot;&lt;/em&gt;&lt;/p&gt;&#xA;  &lt;/blockquote&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;steric stabilization &lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;  &#xA;  &lt;blockquote&gt;&#xA;    &lt;p&gt;&lt;em&gt;&quot;particles in polymers which prevents the particle to get close in the range of attractive forces.&quot;&lt;/em&gt;&lt;/p&gt;&#xA;  &lt;/blockquote&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerDisplayName="user911" LastEditorDisplayName="user911" LastEditDate="2012-05-22T03:09:47.923" LastActivityDate="2012-05-22T03:09:47.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2343" PostTypeId="1" CreationDate="2012-05-22T04:09:20.717" Score="2" ViewCount="178" Body="&lt;p&gt;I am trying to answer &lt;a href=&quot;http://tenttiarkisto.fi/exams/9605.1.pdf&quot; rel=&quot;nofollow&quot;&gt;q5&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;&quot;How can you manufacture micelles in A) nanometerer -scale B) and in ten nanometer -scale?&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;My Thinking&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;blockquote&gt;&#xA;    &lt;p&gt;&lt;strong&gt;Observations and some thinking&lt;/strong&gt;&lt;/p&gt;&#xA;    &#xA;    &lt;ol&gt;&#xA;    &lt;li&gt;Oil in water forms a micelle &lt;a href=&quot;http://en.wikipedia.org/wiki/Micelle&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, not making it soluble.&lt;/li&gt;&#xA;    &lt;li&gt;Whey protein in Water forms a micelle or is this due to other reason? Protein folding with hydrophopic-tailed-and-hydrophilic-headed-particels? Is this micelle or not?&lt;/li&gt;&#xA;    &lt;/ol&gt;&#xA;    &#xA;    &lt;p&gt;&lt;strong&gt;Required Vocabulary about one answer&lt;/strong&gt;&lt;/p&gt;&#xA;    &#xA;    &lt;ol&gt;&#xA;    &lt;li&gt;what is IVC? &lt;/li&gt;&#xA;    &lt;li&gt;PLoS? &lt;/li&gt;&#xA;    &lt;li&gt;&quot;[E]xtrusion step&quot; = some sort of burst? &lt;/li&gt;&#xA;    &lt;li&gt;PCR=Polymerase chain reaction &lt;a href=&quot;http://en.wikipedia.org/wiki/Polymerase_chain_reaction&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. &lt;/li&gt;&#xA;    &lt;li&gt;monodisperse = A collection of objects that &lt;code&gt;&quot;have the same size, shape, or mass.&quot;&lt;/code&gt; (source&#xA;    &lt;a href=&quot;http://en.wikipedia.org/wiki/Monodisperse&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;).&lt;/li&gt;&#xA;    &lt;/ol&gt;&#xA;  &lt;/blockquote&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerDisplayName="user911" LastEditorDisplayName="user911" LastEditDate="2012-05-23T13:32:22.263" LastActivityDate="2012-05-23T13:32:22.263" Title="How to manufacture different sized micelles in nano -scale?" Tags="&lt;biochemistry&gt;&lt;homework&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2344" PostTypeId="2" ParentId="2322" CreationDate="2012-05-22T06:03:02.617" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Cucumbers have an anti-inflammatory effect that reduces puffiness. The&#xA;  vegetable not only has a high water content, it but it's often stored&#xA;  in the refrigerator and comes out cold. This means that the water&#xA;  hydrates your skin, and the cool temperature decreases the flow of&#xA;  blood to the space around your eyes. Together, additional hydration&#xA;  and reduced blood flow can sooth the skin around your eyes and&#xA;  alleviate swelling&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://health.howstuffworks.com/skin-care/moisturizing/products/cucumbers-for-eyes.htm&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also it has silica.&lt;/p&gt;&#xA;" OwnerUserId="905" LastActivityDate="2012-05-22T06:03:02.617" CommentCount="3" CommunityOwnedDate="2012-05-22T20:32:11.043" ContentLicense="CC BY-SA 3.0" />
  <row Id="2345" PostTypeId="2" ParentId="2343" CreationDate="2012-05-22T06:50:20.397" Score="1" Body="&lt;p&gt;A key factor that determines the radii of a micelle is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Critical_micelle_concentration&quot; rel=&quot;nofollow noreferrer&quot;&gt;critical micelle concentration&lt;/a&gt;. The other is the the hydrophobicity of the micelles which can be measured using the &lt;a href=&quot;http://en.wikipedia.org/wiki/Contact_angle&quot; rel=&quot;nofollow noreferrer&quot;&gt;contact angle&lt;/a&gt;. A lipid nanoparticle has a minimum size on the order of 50 nm due to the surface tension of the lipid bilayer. However, micelles can be much smaller.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the creation of uniform nanoparticles, I am going to claim that what I say next can be in no way a reasonable answer to a HW problem. Why? Because the information is hidden in some obscure PLoS paper (&lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015275&quot; rel=&quot;nofollow noreferrer&quot;&gt;Stapleton and Swartz&lt;/a&gt;) with 7 citations using IVC. Typically, micelles created for emulsion-PCR are created by vigorous mixing and followed by an extrusion step. However, this creates a polydisperse droplets. Alternatively, if you were to use a microfluidic device, then more monodispersed droplets can be formed. The control of droplet size can be achieved by varying the flow rates of the aqueous phase and the oil phase as well as changing the surfactant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6zbEp.jpg&quot; alt=&quot;Micelles&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-05-22T06:50:20.397" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2348" PostTypeId="1" AcceptedAnswerId="2358" CreationDate="2012-05-22T13:51:14.730" Score="4" ViewCount="810" Body="&lt;p&gt;I always wondered why gametes from two different species dont fuse together to form an offspring. eg a donkey (sperm) and a female dog (egg)  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know this is not possible but I'm just curious.  &lt;/p&gt;&#xA;" OwnerUserId="771" LastEditorUserId="69" LastEditDate="2012-05-22T17:47:27.650" LastActivityDate="2016-05-20T20:54:26.530" Title="Gametes of two different species" Tags="&lt;genetics&gt;&lt;reproduction&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2351" PostTypeId="1" AcceptedAnswerId="2359" CreationDate="2012-05-22T16:28:47.090" Score="10" ViewCount="57489" Body="&lt;p&gt;My understanding is that the possible mechanisms of evolution are: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Environmental changes&lt;/li&gt;&#xA;&lt;li&gt;Cultural/mating preferences&lt;/li&gt;&#xA;&lt;li&gt;Population Immigration&lt;/li&gt;&#xA;&lt;li&gt;Genetic Mutation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Am I missing anything? I've heard that population shifts within a existing populaces will effect evolution, but imagining the most simplicity scenario, it's hard to see why the would make a difference. &lt;/p&gt;&#xA;" OwnerUserId="541" LastEditorUserId="-1" LastEditDate="2013-03-29T03:35:17.873" LastActivityDate="2018-04-14T14:25:14.063" Title="What factors are known to affect evolution?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="15" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2352" PostTypeId="1" CreationDate="2012-05-22T16:30:31.313" Score="10" ViewCount="6286" Body="&lt;p&gt;I know that it is usually considered a double membrane like those surrounding mitochondria and chloroplasts, but I read a review that stated &quot;according to topological details it is actually a single lipid bilayer; this distinction is important&quot;&lt;sup&gt;&lt;a href=&quot;http://www.molevol.de/publications/136.pdf&quot;&gt;1&lt;/a&gt;&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could anyone please explain how this is true and why the distinction is important? And why this topological analysis wouldn't apply to other membranous structures in the cell?&lt;/p&gt;&#xA;" OwnerUserId="913" LastActivityDate="2012-05-22T23:28:49.253" Title="Is the eukaryotic nucleus composed of a single or double membrane?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2353" PostTypeId="1" CreationDate="2012-05-22T19:16:56.820" Score="4" ViewCount="177" Body="&lt;p&gt;A few years ago, on my maths masters, I did a module in theoretical neuroscience. I was shown that the mathematical framework the course developed for neurons, with a small adjustment in the parameters, would produce spike trains similar to those observed during epileptic kindling. These parametric tweaks could be attributed to mutations in ion channel/receptor structures. This was one of the highlights of the course, and when I came to apply for a math/bio interdisciplinary doctoral program, I cited it as such in my personal statement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the interview is fast approaching, and I'm pretty sure it's going to come up, but for the life of me I can't track down a reference. After four years out of the game, my memory is hazy at best.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I recall, this had something to do with short term plasticity. Normal neurons' response to unrelentingly high frequency spike trains decayes over time, while pathological neurons' does not. &lt;em&gt;This may however be entirely wrong&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is a reference for the model I describe above?&lt;/strong&gt; An introductory/educational treatement is prefered, but the original paper is fine.&lt;/p&gt;&#xA;" OwnerUserId="914" LastEditorUserId="500" LastEditDate="2012-06-25T16:53:33.183" LastActivityDate="2012-06-25T16:53:33.183" Title="Epilepsy explained by computational neuroscience" Tags="&lt;neuroscience&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2355" PostTypeId="2" ParentId="2348" CreationDate="2012-05-22T20:30:03.853" Score="9" Body="&lt;p&gt;The biological environment in every cell and tissue of your body is an extremely complex, tightly controlled system. There are tens of thousands of genes in a typical eukaryotic genome, and depending on tissue types and environmental conditions, these genes are turned on and off in a very controlled manner. There is regulation at every point in the flow of genetic information: nucleosome disruption to expose DNA; RNA transcription from the DNA; protein translation from the RNA; and in some cases, additional modifications of proteins or intermediate mRNAs. At early stages in development, regulation of RNA and protein levels is even more crucial than, say, when an organism is fully developed and healthy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All living organisms share some basic building blocks--DNA, RNA, and proteins work pretty much the same in all of life (there are a few rare variations of the genetic code but the basic premise is identical). However, the way that &lt;em&gt;specific&lt;/em&gt; genes, transcripts, and proteins work together to sustain life varies widely between different organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a very rough analogy, imagine you want to bake a batch of cookies. Then consider the three following scenarios.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;You look at two different recipes for chocolate chip cookies. They will have some slight differences, but they will share a lot in common. If you put the ingredients for both recipes in one bowl, it's likely you can still come up with some pretty good chocolate chip cookies in the end.&lt;/li&gt;&#xA;&lt;li&gt;You look at two different recipes: one for chocolate chip cookies, and one for chocolate muffins. There will be some big differences in these recipes, but combining all the ingredients and baking, you still might be able to come up with something edible (and maybe even tasty).&lt;/li&gt;&#xA;&lt;li&gt;You look at two different recipes: one for chocolate chip cookies, and one for French onion soup. If you combine the ingredients from these recipes and try to cook or bake them, there is no way you will come up with something that anyone would want to eat.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The first example we can relate to two individuals of the same species mating. Of course there is natural variation in the population, but this doesn't typically lead to lethality during development. The second example we can relate to individuals of two related species (such as a horse and a donkey). Sometimes these matings can produce viable offspring, although these offspring are often sterile. The third example we can relate to individuals of two very divergent species (such as donkey and dog in your original question). The biological systems inside donkeys are just so different from those inside dogs that this mating cannot produce a viable offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Admittedly this is a rough analogy, but hopefully is sheds some light on the issue.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2012-05-23T13:25:26.140" LastActivityDate="2012-05-23T13:25:26.140" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2356" PostTypeId="2" ParentId="1808" CreationDate="2012-05-22T20:49:21.623" Score="0" Body="&lt;p&gt;This is probably caterpillar of one of the moth species from family &lt;a href=&quot;http://en.wikipedia.org/wiki/Bagworm_moth&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Psychidae&lt;/em&gt;&lt;/a&gt;. They larvae looks like &lt;a href=&quot;http://en.wikipedia.org/wiki/Caddisfly&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Trichoptera&lt;/em&gt;&lt;/a&gt; larvae and builds similar cases out of silk and material found in nearby surroundings. In contrast to &lt;em&gt;Trichoptera&lt;/em&gt;, &lt;em&gt;Psychidae&lt;/em&gt; caterpillars don't live in water, and some of them inhabit stones and walls, where they feed on lichens.&lt;/p&gt;&#xA;" OwnerUserId="68" LastActivityDate="2012-05-22T20:49:21.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2357" PostTypeId="2" ParentId="2352" CreationDate="2012-05-22T20:54:04.580" Score="9" Body="&lt;p&gt;The nucleus is topologically single membrane but functionally, and as visualized, double membrane.  Naturally, this is a bit confusing.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First consider the mitochondria and plastids.  One of these organelles has two entirely separate &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipid_bilayer&quot;&gt;lipid bilayers&lt;/a&gt;, one of which is nested inside the other.  If you start inside the organelle and draw a line to an external point, the line will pass through two lipid bilayers (assume there are no membrane folds to be encountered), first through the nested one and then through the entirely separate outer bilayer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nucleus at a gross level &lt;em&gt;appears&lt;/em&gt; to be structured similarly.  A line from the interior to the exterior will usually pass through two lipid bilayers, one that is the inner wall of the nucleus, then through the outer wall.  This may seem like the inner wall is separate from, and nested inside, the outer wall, but it is not.  As nicely illustrated in your reference (&lt;a href=&quot;http://www.molevol.de/publications/136.pdf&quot;&gt;Martin 2005&lt;/a&gt;), the two walls are continuous with each other and not nested.  Because of this, a line from nuclear interior to exterior may in fact not pass through any lipid bilayers; it may pass though a &lt;a href=&quot;http://en.wikipedia.org/wiki/Nuclear_pore&quot;&gt;nuclear pore&lt;/a&gt;.  Topologically (mathematically) speaking, the two walls are one surface, and the &quot;inside&quot; of the nucleus is on the same side of the surface as the outside.  (The topological interior is perinuclear space and the interior of the endoplasmic reticulum.)  Functionally though, the structure acts as a double membrane since it physically constrains its contents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The distinction is not very important for most biological contexts, but for a few purposes needs to be considered.  The main reason to pay attention to the distinction is that it probably is related to the evolutionary history of the nucleus: it is likely to have evolved from a single bilayer somehow.  In contrast, the mitochondria and plastids, with nested bilayers, evolved from two bilayers, one from a separate cell and one from an enveloping piece of a host cell.  This is why the distinction is important in the cited paper, which concerns the evolution of the nucleus. &lt;/p&gt;&#xA;" OwnerUserId="231" LastEditorUserId="231" LastEditDate="2012-05-22T23:28:49.253" LastActivityDate="2012-05-22T23:28:49.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2358" PostTypeId="2" ParentId="2348" CreationDate="2012-05-22T21:38:28.640" Score="8" Body="&lt;p&gt;Daniel's answer excellently explains the issue in an understandable fashion, though you may have been looking for a more cell biological approach.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=sperm%20cannot%20penetrate%20egg%20of%20other%20species&quot;&gt;&lt;em&gt;Immunological aspects of sperm receptors on the zona pellucida of mammalian eggs&lt;/em&gt;, 1976, Dunbar &amp;amp; Shivers&lt;/a&gt;, the egg cell has a receptor construction which is necessary for the sperm to attach. If the receptor is too different from what the sperm is built for (which will be the case in different species), it will not be able to attach and fertilise the egg.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-05-22T21:38:28.640" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2359" PostTypeId="2" ParentId="2351" CreationDate="2012-05-23T01:09:40.557" Score="16" Body="&lt;p&gt;Evolution is defined as a change in the allele frequency of population through time.  The Hardy-Weinberg model predicts that the allele frequency of a population will not change (i.e., evolution will not occur) if the following conditions are met:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;no natural or sexual selection&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;no gene flow (immigration or emigration from the population)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;no mutatation&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;no genetic drift (changes in allele frequency due to random events)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So we can conclude that if any of the above conditions are not met then there is a change in allele frequency and thus evolution, and thus that factor is the cause of evolution.&lt;/p&gt;&#xA;" OwnerUserId="137" LastEditorUserId="137" LastEditDate="2018-04-10T17:28:15.617" LastActivityDate="2018-04-10T17:28:15.617" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="2362" PostTypeId="1" CreationDate="2012-05-23T14:21:54.087" Score="20" ViewCount="133537" Body="&lt;p&gt;When we have an external wound, blood generally tends to clot there, forming a layer of solid scab.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yesterday, while brushing my teeth, I somehow hurt my gums and it got all bloody. However, it did not clot, neither did it hurt just after the incident. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After maybe like 12 or 15 hrs I had trouble opening my lips and when I looked at the spot in the mirror the gum tissue around and on the wound had colored white/yellowish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our mouths are supposed to be the among the most contaminated parts of the human body, so why do mouth wounds heal in just about a week and don't get infected?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the healing mechanism found in the mouth tissue, because I figure it is completely different from the processes in wounds occurring in the external skin.&lt;/p&gt;&#xA;" OwnerUserId="872" LastEditorUserId="9943" LastEditDate="2015-10-02T01:55:57.003" LastActivityDate="2015-10-02T01:55:57.003" Title="What is the healing process of mouth wounds?" Tags="&lt;human-biology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2363" PostTypeId="2" ParentId="1814" CreationDate="2012-05-23T14:34:10.733" Score="2" Body="&lt;p&gt;I also had this thought about the bilateral symmetry of the body and the weight distribution. I'm sure if we were to Q &amp;amp; A a kinesiologist about this particular query we would find that the arrangement of the organs left and right and the difference in weight muscular development left to right is off set by our arms which move in and out from our body to maintain balance. When we eat, we gain weight in the form of fat. A full belly makes us front heavy, but by leaning back we maintain the balance. I would wager that the two halves of our body are no more than ten pounds off from each other and the arms used as ballast keep us upright. Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="916" LastActivityDate="2012-05-23T14:34:10.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2364" PostTypeId="2" ParentId="2084" CreationDate="2012-05-23T14:54:01.957" Score="3" Body="&lt;p&gt;It looks like you have uncovered the majority of the corpus of molecular genetics related to aging.  There is a follow up analysis just published this year by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261167/?tool=pubmed&quot; rel=&quot;nofollow&quot;&gt;Sebastiani et al&lt;/a&gt;.  Pubmed has a feature that you can look at the publications that reference the paper you are looking at, and there are only reviews.  Nobody else seems to have done another yet.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are probably right to feel that the power of the study is not great.  The researchers did try though. The Centenarians have long lived relatives and the controls had both parents die before they were 73.  Although the controls were 68 y.o. and older.  Yes not great.  The controls are very difficult because you don't want people who would die from heart attacks, hypertension and all sorts of things that would color the background.  Its a hard study to do. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;No single gene will convey a phenotype like longevity.  Its basically impossible as the advantages would propogate through the population v quickly.  We could talk about how this trait is post-reproductive and about the &lt;a href=&quot;http://en.wikipedia.org/wiki/Grandmother_hypothesis&quot; rel=&quot;nofollow&quot;&gt;grandmother effect&lt;/a&gt;, but I'm setting that aside for now.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lack of statistical power of the study is also hampered because a mere 800 centenarians probably reflects dozens of different combinations of longevity groups.  (this is another reason all of these people are of specific european ancestry - to keep the number of variations in combinations down).  There are 281 significant mutations they found.   APOE is by far the most significant (fig1) but given the situation, just focusing on that one is not enough.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, even in flies it looks like &lt;a href=&quot;http://www.nature.com/news/2011/110921/full/news.2011.549.html&quot; rel=&quot;nofollow&quot;&gt;the sir2-1 gene is not a single mutant anti aging phenotype&lt;/a&gt;.  When they cross the mutant strain with wildtype, the sir2.1 mutants live 15% longer.  Its at least one other mutation they had not detected in that caused a 50% longevity bump in the mutants.  Its probable that if there were 5 other important mutations, that the average crossover has one or more of these mutations with it too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to try to understand how these loci might work together to expand life span, they created clusters of these SNPs (interestingly half of them are in genes which is relatively rare).  these clusters of genes look like they affect the lifespan together.  the paper is open and all the 281 genes are downloadable, each one of them has a known biological property you can look at.  how they fit together is still to be determined, but their clusters might point the way for now. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-23T14:54:01.957" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2365" PostTypeId="2" ParentId="2362" CreationDate="2012-05-23T15:02:12.647" Score="4" Body="&lt;p&gt;The mucosa (&quot;slimey&quot; skin) of course has different properties from your epidermis (outer skin) but the wound healing process is pretty much the same; the blood clotting process might be different though. About this I'm not entirely sure, but my best guess is that the &quot;scab&quot; is washed away by mucus and only the clots inside vessels remain, making them invisible from outside.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The white/yellowish colour is the underlying layer of fatty tissue. Chances are your wound &lt;em&gt;does&lt;/em&gt; get infected but your immune system is able to clear it away easily. If infection is a bit heavier, it can strain the immune cells a bit more and some of them may die - you can then see them as pus (which is mostly white blood cells).&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-05-23T15:02:12.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2366" PostTypeId="1" AcceptedAnswerId="2369" CreationDate="2012-05-23T15:18:54.693" Score="8" ViewCount="536" Body="&lt;p&gt;This is related to &#xA;&lt;a href=&quot;https://biology.stackexchange.com/questions/1419/how-does-be-altruist-to-those-who-are-similar-to-you-evolve&quot;&gt;How does &amp;quot;be altruist to those who are similar to you&amp;quot; evolve?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Altruism that is&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Not reciprocal&lt;/li&gt;&#xA;&lt;li&gt;Not familiar&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;has little explanation. One possible explanation is that the trait itself may correlate well with genetics. One great answer there is that often the cost of altruism is small anyway. It can explain why people vote. Here the expense is small anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still there seems to be some factors that are even bigger.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's take a look at people that die for their ideology. Christian martyrs, Muslim suicide bombers, or Communist guerilla fighters. They seem to get so little and well, die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And that's pretty common. It seems pretty easy for a leader or pedagogue to rouse men to be soldiers. Of course, becoming a soldier is a pretty shitty job, yet most men don't mind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These people make a huge sacrifice for the sake of their country, ideology, or people that are not even genetically related to them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why?&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2013-03-14T17:10:39.180" Title="Does becoming martyr have an evolutionary advantage?" Tags="&lt;evolution&gt;&lt;evolutionary-game-theory&gt;&lt;altruism&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2367" PostTypeId="1" CreationDate="2012-05-23T17:07:20.983" Score="4" ViewCount="94" Body="&lt;p&gt;I was reading about the Lenski experiments on the evolution of &lt;em&gt;E. coli&lt;/em&gt; bacterium and Dr. Elders's experiments on the evolution of the guppy. &#xA;These two experiments absolutely fascinated me, and seemed to happen relatively quickly by evolutionary standards. It was mentioned in the book that the fruit fly's productive turnover time is especially short.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am extremely interested and would very much like to conduct an experiment into the evolution of the fruit fly, in much the same way as the Lenski and Elder experiments when I'm older.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just so I can get a good idea, as I can find nothing on the internet, how long would it take for the fruit fly to get through, say, 10 generations?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, what would be the best way to go about beginning an experiment like this? Would there be certain people to contact? Would you need certain qualifications?&lt;/p&gt;&#xA;" OwnerUserId="839" LastEditorUserId="43" LastEditDate="2012-05-23T18:52:21.757" LastActivityDate="2012-05-23T19:53:09.360" Title="Productive turnover and generations in the fruit fly" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;experimental-design&gt;&lt;experimental&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2368" PostTypeId="2" ParentId="2366" CreationDate="2012-05-23T17:59:44.643" Score="6" Body="&lt;p&gt;There isn an effect called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Reciprocity_%28evolution%29#Indirect_reciprocity&quot;&gt;Indirect reciprocity&lt;/a&gt;&quot; where individuals just give to everyone they meet without direct requirement of reciprocity.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This sort of benefit to others is common - hospitality to strangers, general politeness, good customer service all fall along these lines.  You hope they will come back and benefit you again, but maybe they will tell someone else who will know you are a good community member. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is only sustainable in a system where the cost/benefit ratio is less than the reputation benefit of the act.  It sounds as if this is only good for public acts but if the benefit is transferred to a social entity that outlasts the individual (like your children, a relative's children, a religion or a corporation say), the result could still hold.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you think about typical morality/ethics really it still makes sense to think that what we call altruism must still have a net positive benefit.  If there is no benefit long term or to anyone, it really isn't useful or even good, its random.  What we usually call altruism is usually some sort of reciprocal cooperation.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A soldier who dies in combat or someone who dies for their beliefs but everyone knows about it as a public statement benefits from their act indirectly.  I don't think its altruism in the pure sense of the word. Defending the nation, ones' beliefs or whatever is, in its sense its own reward.  Veterans come back from a war are hopefully respected for their work.  Having a purple heart can be a good thing to show people.  I'm not saying these people are adequately compensated for what they have been through, but just trying to draw a distinction between pure biological altruism and 'indirect reciprocity'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples of Indirect reciprocity might be the use of tax money to build highways and build power and water infrastructure.  Its important - its the glue that holds a nation or a group together.  If you got &lt;em&gt;punished&lt;/em&gt; for doing these things we wouldn't be hanging as a nation very long!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A martyr with no family at all who would benefit would still count as an altruism I think, but most acts of public piety and sacrifice do benefit the individual by reputation. Something to think about. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-05-24T05:03:44.870" LastActivityDate="2012-05-24T05:03:44.870" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2369" PostTypeId="2" ParentId="2366" CreationDate="2012-05-23T18:07:50.507" Score="6" Body="&lt;p&gt;Your question is quite broad and asks for explanations for various behaviours which can lead to self-sacrifice. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Religious reasons:&lt;/em&gt; The genetic influence here may be a predisposition to let others influence you. This is what gives rise to culture in the first place, in other words: the predisposition to at some point &lt;em&gt;maybe&lt;/em&gt; sacrifice yourself because you are taught to do so can only die out if the basic behaviour which gives rise to culture dies out. Cultures which lead their members to die may decimate their own numbers, but they will not wipe out culture itself because in the bigger scale, those with culture do better than those without. (Plus, those who sacrifice themselves may have children as well, so any genetic influence on their behaviour can be carried on.) This also goes far into the field of memetic evolution, which is disputed but may be interesting to read about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Political reasons:&lt;/em&gt; As in, dying for one's nation or country rather than because of teachings. This probably has a defensive behaviour towards one's own group as the genetic influence. Also, reputation plays a big role: see shigeta's excellent answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You also mention willingness to subordinate oneself which is a very common pattern not only in humans. Richard Dawkins touches on this in &lt;em&gt;The Selfish Gene&lt;/em&gt;, but there are probably papers more focussed on this particular topic out there as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it is far-fetched to assume a genetic inheritance of in general &quot;willingness to die for something&quot; (which would be required for genetic evolution to work on it). Each thing that some people may be willing to die for can have completely different reasons. I think in these terms the willingness to die is usually an exaggeration of a behaviour which evolved for different reasons.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-05-23T18:07:50.507" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2370" PostTypeId="2" ParentId="2367" CreationDate="2012-05-23T18:23:51.207" Score="1" Body="&lt;p&gt;What do you mean by you couldn't find anything on the internet? &lt;a href=&quot;http://en.wikipedia.org/wiki/Drosophila_melanogaster#Life_cycle_and_reproduction&quot; rel=&quot;nofollow&quot;&gt;Drosophila generation time is explained here&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your other question is a bit off-topic here but I'll give all advice I have heard myself:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can leave out a banana skin and catch some fruit flies, then do the experiment in your kitchen :) Joke aside, unless you perform the experiment independently it will probably take a long time and it's well possible that you won't be able to do it at all (unless you become some famous scientist). I'm not familiar with the experiments you mention, but if you require equipment and/or funding, you will need a qualification and/or a good explanation why people should give you money or let you use their equipment for this experiment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know what stage of education you are at, but it sounds like you are still at school (&quot;when I'm older&quot;)? Most countries have some schemes where students (below uni) can apply for young researcher kind of things, so you could try and google that. Apart from that, the best bet is probably to try and get into a uni with good facilities and research programmes for their students. What you study shouldn't matter so much as long as it's science.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In response to Marta's commment: if you understand the experiment and you think you can gather everything they used at home, nothing speaks against just doing it on your own. Just make sure you don't let those flies swarm your house ;)&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-05-23T19:53:09.360" LastActivityDate="2012-05-23T19:53:09.360" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2373" PostTypeId="1" AcceptedAnswerId="2377" CreationDate="2012-05-23T22:44:20.917" Score="7" ViewCount="1679" Body="&lt;p&gt;Is there any skeletal muscle that does not have an antagonist? Excluding circular muscles such as around eye and mouth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason why I am wondering is because in biology normally nothing is ever just like that, there is always an exception. This would be the first biological rule without exception that I came across.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking of humans only for a start but feel free to include any other animal if any have skeletal muscles without antagonists :)&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-05-24T23:04:26.310" LastActivityDate="2012-05-24T23:04:26.310" Title="Skeletal muscle without antagonist" Tags="&lt;muscles&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2374" PostTypeId="1" CreationDate="2012-05-23T22:56:13.020" Score="4" ViewCount="3356" Body="&lt;p&gt;Can two plasmids with the same origin of replication (for example pBR322 ori) and thus from the same incompatibility group be successfully co-transformed in E. coli? What are the mechanisms that would prevent the two plasmids from co-existing together? Does it matter what is the dual resistance selection? How would the efficiency of co-transformation compare to the efficiency of a uni-transformation?&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-05-26T16:02:23.363" Title="Co-transformation of plasmids from the same incompatibility group" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;plasmids&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2375" PostTypeId="1" CreationDate="2012-05-24T09:48:53.383" Score="14" ViewCount="1984" Body="&lt;p&gt;What databases are available for gene regulatory network graphs starting from a given gene? For example, starting from p53 gene, where can I find a gene regulatory network image that can be exported or embedded to another website?&lt;/p&gt;&#xA;" OwnerUserId="787" LastEditorUserId="112" LastEditDate="2012-05-24T10:06:44.580" LastActivityDate="2015-07-10T19:53:48.243" Title="Databases for gene regulatory network graphs?" Tags="&lt;bioinformatics&gt;&lt;gene-expression&gt;&lt;gene-regulation&gt;&lt;network&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2376" PostTypeId="2" ParentId="2375" CreationDate="2012-05-24T13:31:20.323" Score="10" Body="&lt;p&gt;For a free resource, try &lt;a href=&quot;http://www.genmapp.org/default.html&quot;&gt;GenMAPP&lt;/a&gt;. Commercial products like &lt;a href=&quot;http://www.ingenuity.com/products/pathways_analysis.html&quot;&gt;Ingenuity Pathway Analysis&lt;/a&gt; do the same thing with prettier graphics and a curated approach to network-building, but access can be expensive if you're not affiliated with an institution that will foot the bill.&lt;/p&gt;&#xA;" OwnerUserId="819" LastActivityDate="2012-05-24T13:31:20.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2377" PostTypeId="2" ParentId="2373" CreationDate="2012-05-24T14:48:20.000" Score="6" Body="&lt;p&gt;I would argue that the orbiculares do have antagonists. To some extent, levator palpebrae superiorus antagonizes orbicularis oculi, and zygomaticus major/minor as well as risorius antagonize orbicularis oris.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can think of three muscle that don't have obvious antagonists:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Stapedius&lt;/li&gt;&#xA;&lt;li&gt;Tensor tympani&lt;/li&gt;&#xA;&lt;li&gt;Articularis genu&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;1 and 2 essentially perform the same action, to dampen sounds reaching the cochlea. 3 elevates the suprapatellar bursa.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2012-05-24T18:20:54.337" LastActivityDate="2012-05-24T18:20:54.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2378" PostTypeId="1" AcceptedAnswerId="2380" CreationDate="2012-05-24T17:02:57.507" Score="6" ViewCount="820" Body="&lt;p&gt;Tear gas (CCl&lt;sub&gt;3&lt;/sub&gt;NO&lt;sub&gt;2&lt;/sub&gt;) makes people cry, and crying doesn't seem to be a simple procedure. There has to be a triggering process somewhere. Can someone explain its mechanism / how it works?&lt;/p&gt;&#xA;" OwnerUserId="771" LastEditorUserId="107" LastEditDate="2012-05-24T18:22:35.567" LastActivityDate="2012-05-25T01:55:45.280" Title="Mechanism of Tear Gas (chloropicrin/Trichloro methane)" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2380" PostTypeId="2" ParentId="2378" CreationDate="2012-05-24T21:21:11.520" Score="5" Body="&lt;p&gt;The general belief is that these agents are irritants &lt;a href=&quot;http://science.howstuffworks.com/question340.htm%20its%20probab&quot; rel=&quot;nofollow&quot;&gt;which do not have a very specific effect&lt;/a&gt;.  That is to say that there is no specific cell or biological function that they set off, but that they irritate the cells, so the cells respond by putting up general defenses to insulate themselves from the noxious chemicals.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mucous and tears wash away the compounds.  I'm sure there are all sorts of things going on, but its hard to be more specific.  For instance, onions have many sulfhydryl (-SH) compounds,  many many of them.  In particular &lt;a href=&quot;http://www.chm.bris.ac.uk/motm/pso/psoc.htm&quot; rel=&quot;nofollow&quot;&gt;propanethial s-oxide causes the tears we get when we cut an onion&lt;/a&gt;. This compound is very reactive and reacts with all sorts of proteins and disrupts the membrane, etc.  Its perhaps an example of a specific irritant that is so reactive that it creates tears.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of a specific reaction would perhaps be capsaicin.  There is a specific protein that is a &lt;a href=&quot;http://www.chem.arizona.edu/miesfeld/teaching/Bioc471-2/pages/Lecture10/HotChili.pdf&quot; rel=&quot;nofollow&quot;&gt;heat receptor&lt;/a&gt; and the chemical capsaicin activates it, causing the feeling of heat/warmth.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tear gas and mustard gas appear to fall into the former category, which are chemicals so reactive that they just tear into the cell, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0027510779900599&quot; rel=&quot;nofollow&quot;&gt;damaging all sorts of things in there&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorDisplayName="user560" LastEditDate="2012-05-25T01:55:45.280" LastActivityDate="2012-05-25T01:55:45.280" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2381" PostTypeId="1" AcceptedAnswerId="2674" CreationDate="2012-05-24T23:22:10.180" Score="6" ViewCount="115" Body="&lt;p&gt;Overly simplified, macrophages recognise pathogenic patterns and endocytose anything that matches them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That also works on bacteria, which are quite often very mobile. What if a bacterium was just randomly twitching around when a macrophage recognised it - would it be possible for it to &quot;swim away&quot; (as a reaction to the macrophage or just randomly)? Or do macrophages employ some sort of fixation mechanism to keep anything they recognise close until it is engulfed? Or is engulfment in itself just so quick?&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-06-17T18:39:29.320" Title="Macrophage pathogen fixation" Tags="&lt;cell-biology&gt;&lt;immunology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2382" PostTypeId="1" AcceptedAnswerId="2412" CreationDate="2012-05-24T23:31:24.183" Score="11" ViewCount="2295" Body="&lt;p&gt;I'd like to know how antioxidants affect human metabolism and which ones are essential for metabolic processes.&lt;/p&gt;&#xA;" OwnerUserId="920" LastEditorUserId="9099" LastEditDate="2014-10-01T14:21:26.427" LastActivityDate="2014-10-01T14:21:26.427" Title="How do antioxidants affect human metabolism?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;metabolism&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2383" PostTypeId="2" ParentId="2353" CreationDate="2012-05-25T03:30:26.140" Score="3" Body="&lt;p&gt;Unfortunately, epileptic spiking can occur very easily in many neural modeling studies, and therefore one should be very careful in asserting the possibility of certain aspects of model as a cause for epileptic activity. One possibility, as you mentioned, is the lack of short-term depression which prevents long sustained firing. But again, a simple increase in the global excitatory coupling can also exhibit similar dynamics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good luck on your interview.&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2012-05-25T03:30:26.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2384" PostTypeId="2" ParentId="2375" CreationDate="2012-05-25T03:53:29.820" Score="8" Body="&lt;p&gt;If you can't afford ingenuity, KEGG has branched out into regulatory networks as well.  Here's the link to their version of the pathway. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.genome.jp/kegg/pathway/hsa/hsa04115.html&quot;&gt;http://www.genome.jp/kegg/pathway/hsa/hsa04115.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its free to use as a reference and for academic research. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-25T03:53:29.820" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2385" PostTypeId="1" CreationDate="2012-05-25T13:13:31.240" Score="5" ViewCount="234" Body="&lt;p&gt;I want to make a partially working model of the digestive system that could digest complex carbohydrates. My ultimate goal is to be able to cut up some bread, put it into the model, operate it, and eventually see some effect equivelent to glucose being used in a muscle. I obviously have a very limited buget. How could I simulate glucose being burned in some way that has a visible effect?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: I'm specifically looking for some way glucose can be &lt;em&gt;used&lt;/em&gt; to achieve some visible effect that makes sense as a metaphor for combustion, without dangerous/expensive chemicals.&lt;/p&gt;&#xA;" OwnerUserId="921" LastEditorUserId="921" LastEditDate="2012-05-25T20:24:52.097" LastActivityDate="2012-07-11T08:19:07.550" Title="What is an simple way to burn glucose for visible effect?" Tags="&lt;digestive-system&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2387" PostTypeId="2" ParentId="1987" CreationDate="2012-05-25T18:49:12.130" Score="4" Body="&lt;p&gt;The human/animal digestive tract breaks down food chemically (with low pH/acid), enzymatically (like proteases and glycolytic enaymes which break down protein and sugars respectively), as well as symbiotically (bacteria participates in the breakdown of some compounds in the gut).  The results are released into the blood stream for the most of the body to assimilate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With foods with complex carbohydrates (scenario 1), the results can be only a modest change in the glucose level in the serum.  This depends upon the specific food which you can understand better by researching the 'glycemic index'.  Highly glycemic foods result in rather short term release of simple carbohydrates glucose/sucrose into the blood.  Lower glycimic food contain complex carbohydrates (which are elaborate chains of sugars) which need to be broken up into simple carbohydrates before they are metabolized the the cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Foods which contain a lot of simple carbohydrates change the sugar levels in the blood nearly immediately and it can go quite high.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Carbohydrate&quot;&gt;simple carbohydrates are monomers or dimers of sugars&lt;/a&gt;.  BTW complex carbohydrates have few pictures on the web, but you can imagine them as chains and networks of many many simple carbohydrates linked together.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all simple carbohydrates are used by human beings for energy.  For instance the glycosamine in 'joint juice' is the sort that makes cartilidge, which just to show you how different some complex carbohydrates can be. BTW i don't recommend joint juice, just trying to give a familiar example.  Its unlikely that the glucosamine you drink will be directly used for your joints!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So glucose is the energy currency in the blood.  when the glucose level goes up &lt;a href=&quot;http://en.wikipedia.org/wiki/Insulin&quot;&gt;insulin&lt;/a&gt; is secreted by the pancreas which tells the cells to take up the glucose for glycogen (internal cell energy storage in a complex carbohydrate) or to be metabolized directly.  Diabetes results when insulin is not produced (type I) or when the cells stop responding to insulin (type II).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human tolerance to glucose in the blood is estimated to be up to about 100 mg/dl long term. higher than this on the average is not healthy and can go up to several hundreds and cause lots of degeneration in the kidney, liver, and eyes, and more.  Exercise and fasting increase insulin sensitivity and athletes have blood glucose that is quite low even if they have a sugary beverage.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;hope this helps - many keywords embedded within...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One last note.  Fructose, which is about 45-60% of high fructose corn syrup (the rest is sucrose) &lt;a href=&quot;http://en.wikipedia.org/wiki/Fructose#Liver_function&quot;&gt;is almost entirely metabolized in the liver&lt;/a&gt;.  This is why fructose can be harmful to people who drink too much sweetened beverages.  With the liver taking in the vast majority of fructose, it tends to make fat out of it, sort of overdosing it to make it fatter than the rest of you relatively quickly.  Fatty liver is a marginally disfunctional liver and can cause health problems down the way.  Abdominal body fat (not on your love handles, but amongst your chest cavity and internal organs) is particularly harmful as it interferes with all sorts of organ function.  Probably something everyone should be aware of.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-05-25T18:55:07.440" LastActivityDate="2012-05-25T18:55:07.440" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2388" PostTypeId="2" ParentId="2240" CreationDate="2012-05-25T21:40:17.533" Score="8" Body="&lt;p&gt;Translational coupling describes in how some cases an mRNA will code from more than one protein (i.e. will be polycistronic).  Translational coupling is thought to be mostly used as a way to make a set of genes are translated at roughly the same amount in the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Translational coupling is very common in prokaryotes and nearly half of e coli genes are found in a polycistronic operon.  What we know about them is revealing.  There are some fancy mechanisms to adjust &lt;a href=&quot;http://sheephapmap.org/news/Data_Access_OARv2p0.php&quot; rel=&quot;nofollow&quot;&gt;the ratios of these adjacent genes&lt;/a&gt;, which are still coupled, but with ratios that are not just 1:1.  Its shown that the later genes are often translated at somewhat lower frequency because the first genes are available more quickly before the mRNA degrades.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosgenetics.org/article/info%3adoi/10.1371/journal.pgen.0020096&quot; rel=&quot;nofollow&quot;&gt;Eric Alm @ MIT wrote this great paper on how operons evolve&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've only been able to find this reference to a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1190309/&quot; rel=&quot;nofollow&quot;&gt;eukaryotic case of &quot;translational coupling&quot;&lt;/a&gt; which is very rare, but does exist.  The most common cases of translationally coupled genes in eukaryotes are RNA viruses which usually contain only a single full length mRNA which codes for all the genes in the virus.  The selective pressures to keep the viral genome small and constrain the ratios of these genes, will cause these genes to even overlap, starting the next one before the current gene finishes. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="5662" LastEditDate="2014-04-10T20:13:37.793" LastActivityDate="2014-04-10T20:13:37.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2389" PostTypeId="2" ParentId="2328" CreationDate="2012-05-26T00:41:10.370" Score="6" Body="&lt;p&gt;Plants are multicellular organisms that utilize diffuse inorganic molecules (CO&lt;sub&gt;2&lt;/sub&gt;, NO&lt;sub&gt;3&lt;/sub&gt;, etc...) for energy and growth and thus they have evolved anatomical features that maximize the efficient concentration of these molecules (i. e., the root - shoot). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Animals are multicellular organisms that utilize concentrations of organic molecules for energy and growth (i.e., food) and thus they have evolved anatomical features that maximize the efficient harvest of these molecules.  Note that not all animals move.  There are many sessile filter feeders.&lt;/p&gt;&#xA;" OwnerUserId="137" LastEditorUserId="69" LastEditDate="2012-05-26T09:13:05.337" LastActivityDate="2012-05-26T09:13:05.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2390" PostTypeId="2" ParentId="2132" CreationDate="2012-05-26T06:20:01.180" Score="3" Body="&lt;p&gt;This seems complicated, but I found &lt;a href=&quot;http://jap.physiology.org/content/100/4/1361.full.pdf&quot; rel=&quot;nofollow&quot;&gt;a reference&lt;/a&gt; that might answer these questions (if its right). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sports physiology common wisdom is that human muscles regularly work in the range of 37C to 40C which is basically body temperature.  Since the muscles generate quite a bit of heath when they function, they are usually not functioning in colder temperatures and hyperthermia starts setting in.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thomas et al. put this to the test by cooling down some muscles in volunteers! &#xA;They say that the core body temperature is more important than the peripheral temperature in restoring muscle strength (torque produced).  Hypothermia makes the victim weaker and weaker apparently and it sets in below 37C pretty quickly apparently.  They speculate that the cooling might actually impair the nervous system from activating the muscles, which might be an answer to your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is probably not the final word, but its as far as I got...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="948" LastEditDate="2013-04-13T01:17:59.203" LastActivityDate="2013-04-13T01:17:59.203" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2391" PostTypeId="1" CreationDate="2012-05-26T09:23:19.927" Score="1" ViewCount="162" Body="&lt;p&gt;Well, insecticides are used to kill insects.&lt;br&gt;&#xA;I have always wondered why are herbal / natural insecticides more effective in killing insects than chemical ones. I have read this at many places but havent found a reason for it.&lt;br&gt;&#xA;Also why don't insects develop resistance to herbal insecticides while they do for chemical ones? &lt;/p&gt;&#xA;" OwnerUserId="771" LastActivityDate="2012-05-29T05:06:03.173" Title="Herbal vs Chemical Insecticides" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2012-08-20T10:53:47.347" ContentLicense="CC BY-SA 3.0" />
  <row Id="2392" PostTypeId="2" ParentId="2374" CreationDate="2012-05-26T15:02:39.863" Score="2" Body="&lt;p&gt;It turns out that &lt;a href=&quot;http://peds.oxfordjournals.org/content/20/7/309.full&quot; rel=&quot;nofollow&quot;&gt;there doesn't seem to be a specific mechanism to prevent multiple incompatible plasmids from coexisting&lt;/a&gt;.  Velappan et al put in more than one incompatible plasmid with different selection genes in them and put the bacteria on a single antibiotic and periodically checked for the second vector (by testing for  second antibiotic resistance).  It apparently took weeks for the second vector to disappear - many generations.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Higher copy number plasmids did better, with longer times to lose the second plasmid.  They seem to conclude that its just the natural rate of loss of plasmids that will cause the bacteria to lose the second plasmid without selection.  I imagine with two antibiotics in the culture it would take some months and you could potentially store the bacteria at -80C indefinitely.  Still in most experiments its going to be an additional headache where compatible origins of replication seem to have a more typical half life for retaining the plasmids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They also state that the frequency of double transformations is more frequent than is usually appreciated, which seems to imply that you will get some colonies from a typical high efficiency transformation from plasmid preps.  However, they introduced the multiple plasmids by phagemid infection rather than transformation in this study. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-05-26T16:02:23.363" LastActivityDate="2012-05-26T16:02:23.363" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2393" PostTypeId="1" AcceptedAnswerId="3382" CreationDate="2012-05-27T00:49:57.960" Score="4" ViewCount="303" Body="&lt;p&gt;I am trying to reproduce &lt;em&gt;E. coli&lt;/em&gt; interrupted mating using an HFR strain, and I read that the cultures should be vigorously shaken  at times to interrupt the DNA transfer from the F+(HFR) donors to the F- cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How vigorously(I'm OK with a qualitative answer) should I shake the culture for optimal results?&lt;/p&gt;&#xA;" OwnerUserId="922" LastEditorUserId="922" LastEditDate="2012-06-13T17:23:10.653" LastActivityDate="2012-08-28T23:46:44.773" Title="Vigorous shaking for HFR interrupted mating" Tags="&lt;microbiology&gt;&lt;molecular-genetics&gt;&lt;plasmids&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2396" PostTypeId="1" AcceptedAnswerId="2397" CreationDate="2012-05-28T02:12:15.787" Score="2" ViewCount="323" Body="&lt;p&gt;I need to make a model of the digestive system. It would be really nice to actually show it in action, such as by breaking down bread into glucose or something similar. Is this feasible with a small budget and non-dangerous chemicals? If so, how? This should be as similar too the real digestive system as possible.&lt;/p&gt;&#xA;" OwnerUserId="921" LastActivityDate="2012-05-28T13:32:28.677" Title="How might I break down bread into glucose in a model of the human digestive system?" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2397" PostTypeId="2" ParentId="2396" CreationDate="2012-05-28T08:14:40.603" Score="4" Body="&lt;p&gt;Amylase would be worth a try. The enzyme breaks down bread (starch), and you can buy it relatively cheaply online or probably at a chemist. Amylase is secreted in your saliva and in your stomach, so it would be most realistic if it was added in your model at those two points.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-05-28T08:14:40.603" CommentCount="20" ContentLicense="CC BY-SA 3.0" />
  <row Id="2398" PostTypeId="1" AcceptedAnswerId="2400" CreationDate="2012-04-25T20:28:07.653" Score="37" ViewCount="10803" Body="&lt;p&gt;I remember hearing that trees and other plants actually obtain a large amount of their mass from the carbon floating in the air, not the ground beneath them. Does the makeup of air actually contain enough carbon to support this theory, and is a tree's surface area actually large enough to obtain the amount of carbon it needs directly from the air?&lt;/p&gt;&#xA;" OwnerUserId="926" OwnerDisplayName="Elliot Bonneville" LastEditorUserId="806" LastEditDate="2012-05-28T20:19:55.597" LastActivityDate="2015-06-25T02:32:35.453" Title="Do trees really get a large share of their mass from the carbon in the air?" Tags="&lt;botany&gt;&lt;photosynthesis&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2400" PostTypeId="2" ParentId="2398" CreationDate="2012-04-25T20:43:51.003" Score="32" Body="&lt;p&gt;The vast majority of a tree's &lt;em&gt;carbon&lt;/em&gt; comes from the air, which &lt;a href=&quot;http://en.wikipedia.org/wiki/Carbon_dioxide_in_Earth%27s_atmosphere&quot;&gt;averages 0.03-0.04% by volume (300-400 ppmv) CO&lt;sub&gt;2&lt;/sub&gt;&lt;/a&gt;.  This is fixed through photosynthesis and eventually stored as glucose which the plant can then use for its metabolism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Doing some quick math, this means that in order to produce 1 kilogram of carbohydrates (e.g. cellulose) a plant needs to process on the order of 2000-3000 cubic meters of air (and &amp;approx;550 g or mL of H&lt;sub&gt;2&lt;/sub&gt;O), which would fill a cube measuring 13-14 meters on a side.  Note this is an ideal figure; a plant's fixing efficiency will likely fall as it depletes the air of CO&lt;sub&gt;2&lt;/sub&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants do take a great deal from the ground, namely water, fixed nitrogen (for proteins),  phosphorous (for nucleic acids), and several ions (sodium, potassium, calcium, among others)&lt;/p&gt;&#xA;" OwnerUserId="25" OwnerDisplayName="Nick T" LastActivityDate="2012-05-10T06:53:52.743" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2401" PostTypeId="2" ParentId="2398" CreationDate="2012-04-25T21:13:42.693" Score="14" Body="&lt;p&gt;Yes. In fact the organic compounds' mass comes &lt;em&gt;mostly&lt;/em&gt; from the air, since Photosynthesis essentially builds up glucose by only adding hydrogen to CO₂. The 2 H₂O → 2H₂ + O₂ reaction can be treated seperately, as was determined by Sam Ruben and Michael Kamen with ¹⁸O isotope tracing, i.e. in fact &lt;em&gt;only&lt;/em&gt; the hydrogen in the carbohydrates comes from the soil, and this has of course a much smaller mass.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As said by Nick T, the more complex compounds also incorporate other elements that the plants get from the soil, but most of them still consist mainly of C and O. The &lt;em&gt;total&lt;/em&gt; mass of a tree of course also has a lot of water and some minerals in it, but it's still safe to say that a tree &quot;consists mainly of air&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To your question about surface area and air CO₂ content, neither is usually the limiting factor: in nature, light exposure, water and mineral supply are (although in enclosed spaces like greenhouses CO2 fertilization is sometimes necessary).&lt;/p&gt;&#xA;" OwnerUserId="30093" OwnerDisplayName="leftaroundabout" LastEditorUserId="3952" LastEditDate="2015-06-25T02:32:35.453" LastActivityDate="2015-06-25T02:32:35.453" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2402" PostTypeId="2" ParentId="2398" CreationDate="2012-05-10T14:24:36.793" Score="20" Body="&lt;p&gt;I'm surprised nobody has mentioned Jan van Helmont. To summarise Blankenship's account, in the 17&lt;sup&gt;th&lt;/sup&gt; century, he (Helmont, not Blankenship) grew a tree in a known dry weight of soil and weighed the fallen leaves of the tree, and then eventually the whole tree including the root system. He found that the mass of the soil had barely diminished and concluded that the tree's mass was overwhelmingly due to watering (CO&lt;sub&gt;2&lt;/sub&gt; had not been discovered.)&lt;sup&gt;1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With the benefit of knowledge of CO&lt;sub&gt;2&lt;/sub&gt; we can conclude that the mass of trees comes from the fixation of CO&lt;sub&gt;2&lt;/sub&gt; and H&lt;sub&gt;2&lt;/sub&gt;O as well as the presence of H&lt;sub&gt;2&lt;/sub&gt;O as a biological solvent.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(1)&lt;/strong&gt; Blankenship, R. E., Molecular Mechanisms of Photosynthesis, Blackwell Science, 2002, p. 26&lt;/p&gt;&#xA;" OwnerUserId="99" OwnerDisplayName="Richard Terrett" LastEditorUserId="69" LastEditDate="2012-05-28T10:14:09.567" LastActivityDate="2012-05-28T10:14:09.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2403" PostTypeId="2" ParentId="2396" CreationDate="2012-05-28T13:32:28.677" Score="2" Body="&lt;p&gt;Generally speaking and as suggested by Rory, mechanical force probably plays a role in most instances (crustless bread may be different):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.modelgut.com/dmg.html&quot; rel=&quot;nofollow&quot;&gt;http://www.modelgut.com/dmg.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was hoping to post more about this but the websites of one of the institutes involved in developing the model gut doesn't provide much accessible information on first read.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe this still gives you something of a starting point:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ifr.ac.uk/info/about/index.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.ifr.ac.uk/info/about/index.htm&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="919" LastActivityDate="2012-05-28T13:32:28.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2405" PostTypeId="2" ParentId="1510" CreationDate="2012-05-28T22:11:12.240" Score="2" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Intrinsic_termination&quot; rel=&quot;nofollow&quot;&gt;RNA hairpin transcription terminator in prokaryotes&lt;/a&gt; is terminated by the GC rich hairpin followed by 4+ uracil bases as you describe it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/92/19/8793&quot; rel=&quot;nofollow&quot;&gt;The original reference describing the hairpin&lt;/a&gt;, described the sequence requirements as being for the thermodynamic stability of the hairpin, but the protein nusA has also been found to stimulate termination.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might think that there would be some protein that would precisely bind this motif and mediate the termination, but at least as far as I can find, it appears that the hairpin clogs up the polymerase itself, causing termination.  &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2443.2002.00563.x/full&quot; rel=&quot;nofollow&quot;&gt;This review linked here has some nice pictures of the RNAP bindig pocket model.&lt;/a&gt;  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-28T22:11:12.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2406" PostTypeId="1" CreationDate="2012-05-28T23:28:50.730" Score="7" ViewCount="160" Body="&lt;p&gt;In stem cell biology, it is recognized that embryonic stem cells are transcriptionally inactive for the first 3 days of development. However, during somatic cell nuclear transfer, the nucleus is likely to include various polymerases and RNA both coding and non-coding. Does this affect the success rates of cloning?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2021-05-04T10:08:20.823" Title="What metabolically happens when an egg fuses with the nucleus of a somatic cell" Tags="&lt;cell-biology&gt;&lt;eukaryotic-cells&gt;&lt;stem-cells&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2407" PostTypeId="2" ParentId="2391" CreationDate="2012-05-29T01:58:20.193" Score="1" Body="&lt;p&gt;I think you probably mean insect and pest control from plant extracts.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have seen posters where extracts from herbs were pretty effective in killing insects.  Really common herbs - rosemary, basi.   It makes sense that plants (and animals) would evolve chemical defenses against insects.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, a quick search under google scholar talks gives you an idea of the research going on (mostly not in the US) here.  Pestoban, &lt;a href=&quot;http://www.cabdirect.org/abstracts/19930515426.html;jsessionid=E48F7198553DCEC09DD03C03DFC8986C&quot; rel=&quot;nofollow&quot;&gt;an Indian herbal preparation&lt;/a&gt; is quite effective against some pests while less effective (~50% effective) in removing fleas from treated livestock. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also stands to reason that the compounds found in edible herbs and plants would tend to be selectively effective against insects found in the environment local to the plants.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another related topic is the search for antibiotics in herbs and spices.  &lt;a href=&quot;http://www.ingentaconnect.com/content/ben/cmc/2004/00000011/00000011/art00008&quot; rel=&quot;nofollow&quot;&gt;Tumeric is a common topic of research&lt;/a&gt;, which explains one of the possible reasons its used in cooking. &lt;a href=&quot;http://www.sciencedaily.com/releases/2012/05/120527115543.htm&quot; rel=&quot;nofollow&quot;&gt;Garlic components show interesting medical properties too&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While this may seem suspect to some, the research is done in the West too, but it is usually spun a different way. In general if you are looking for bioactive compounds that are not completely toxic (like heavy metals or cyanide for instance), you would want to look at compounds which are made by living things.  Nearly all pharmaceutical designs come from or are derived from plant or microbial / fungal extracts.   This is in fact the field of Natural Products Chemistry which is still a big thing in chemistry and biochemistry.  Few if any of the hot targets of organic synthesis are not some fancy compound found in a plant, fungus or sponge extract.  E.g. the surreally complex &lt;a href=&quot;http://en.wikipedia.org/wiki/Palytoxin&quot; rel=&quot;nofollow&quot;&gt;Palytoxin&lt;/a&gt;, the miracle breast cancer drug &lt;a href=&quot;http://en.wikipedia.org/wiki/Taxol&quot; rel=&quot;nofollow&quot;&gt;Taxol&lt;/a&gt;, and the venerable cholesterol control drugs, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Statin&quot; rel=&quot;nofollow&quot;&gt;Statins&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-05-29T05:06:03.173" LastActivityDate="2012-05-29T05:06:03.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2408" PostTypeId="2" ParentId="2327" CreationDate="2012-05-29T02:16:56.427" Score="2" Body="&lt;p&gt;As the comments suggest, I think a little basic reading so you understand the definitions involved here might be appropriate.  The questions are a bit anthocentric, and I think that's why folks with a bit more biological culture might be concerned about the answers.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alpha type structures can be found in all sorts of animals.  Sperm competition, where many males simply mate with the female and let the sperm work it out are also v common from snakes to mice to primates.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its hard to say without you asking a more specific question, but the essential question is whether the competition occurs between the animals themselves or between the intermixed sperm of the males inside the female.  If that sounds gross, that's a typical reaction if you are not a monkey, snake, duck or mouse to name a few.  Different species choose different social roles in mating and for reasons that may be difficult to divine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For animals in an alpha troop modality, the alpha male will eventually get older or weaker and the younger ones will have their chance to mate.  There is always tomorrow.  That's my very brief answer.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It might be worthwhile to take some time to read some about this - a page of response to your questions is not going to really answer your questions.  (I say this having answered several of them :).  I would recommend &lt;a href=&quot;http://en.wikipedia.org/wiki/Sarah_Blaffer_Hrdy#The_Woman_That_Never_Evolved&quot; rel=&quot;nofollow&quot;&gt;&quot;The woman that never evolved&quot;&lt;/a&gt; by Sarah Hrdy.  As a feminist in the 70s Hrdy decided to do a survey of primate male/female roles in mating, to try understand how human men and women became who they are (and who has not wondered this?).  This book will give you an idea of how so many different animals have come to different roles and possibly why.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since I have a little time today, I'm adding a couple of tangential references:  &lt;a href=&quot;http://www.nature.com/news/2010/100120/full/news.2010.22.html&quot; rel=&quot;nofollow&quot;&gt;Mice sperm have responded to sperm competition so much by evolving hooks on their heads and chain up together and swim together which enhances the chances of paternity&lt;/a&gt;.  Ducks are quite different.  they have a lot of forced copulation, but female choice of mate is still quite influential.  &lt;a href=&quot;http://io9.com/5433056/female-ducks-have-evolved-a-vagina-dentata&quot; rel=&quot;nofollow&quot;&gt;Duck vaginas are very complicated, with corkscrews and dead ends to make it difficult to copulate without 'consent'&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-05-29T16:46:22.940" LastActivityDate="2012-05-29T16:46:22.940" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2409" PostTypeId="1" AcceptedAnswerId="2424" CreationDate="2012-05-29T07:23:08.907" Score="4" ViewCount="686" Body="&lt;p&gt;Can sleeping patterns be trained, or are they genetic? I read that a human needs to sleep at least 4 hours. Can sleeping time be reduced without having a negative impact? &lt;/p&gt;&#xA;" OwnerUserId="410" LastEditorUserId="69" LastEditDate="2012-05-29T10:59:38.057" LastActivityDate="2012-05-30T03:57:54.553" Title="Can humans shorten their sleeping patterns?" Tags="&lt;human-biology&gt;&lt;human-genetics&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2410" PostTypeId="1" AcceptedAnswerId="2411" CreationDate="2012-05-29T10:05:30.197" Score="5" ViewCount="1751" Body="&lt;p&gt;It is quite the old wives tale that drinking a hot drink cools you down. If you don't really think about it it does seem somewhat logical: increasing temperature will cause your body to try and cool down faster. This is of course flawed by the fact that you have increased your temperature before cooling it back down again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have had a bit of a look, but have been unable to find any evidence that addresses the fact that drinking a hit drink may make you &lt;em&gt;feel&lt;/em&gt; cooler after sweating a little bit, rather than actually changing anything about your net temperature. Basically, is the 'cool down' just the placebo effect (you feel cooler because you think you feel cooler), or is there any evidence for a 'real' effect of hot drinks cooling you down? Or is there evidence that hot drinks do nothing at all except heat you up a bit before you come right back to the same temperature?&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-06-20T21:46:39.880" Title="Do hot drinks cool you down?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2411" PostTypeId="2" ParentId="2410" CreationDate="2012-05-29T10:49:48.867" Score="7" Body="&lt;p&gt;A Study by &lt;em&gt;&lt;a href=&quot;http://dx.doi.org/10.1080/02640410600959947&quot; rel=&quot;nofollow&quot;&gt;Lee &amp;amp; Shirreffs&lt;/a&gt;&lt;/em&gt; addresses this question.  Unfortunately I only have the abstract, but it's enough to summarise from:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Method&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Three groups exercised by  cycling before being given water at either &lt;strong&gt;10°C&lt;/strong&gt;, &lt;strong&gt;37°C&lt;/strong&gt; or &lt;strong&gt;50°C&lt;/strong&gt;.&lt;/li&gt;&#xA;&lt;li&gt;They then continued to exercise until exhausted. &lt;/li&gt;&#xA;&lt;li&gt;Mean skin temperature, core body temperature and heart rate were measured throughout.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Results&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mean skin temperature was highest in the hot drink category - half a degree warmer than in the cold group.  &lt;/li&gt;&#xA;&lt;li&gt;There was a heat difference between the two outlying groups of 33kJ.  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Irritatingly the pre-drink temperatures are not included in the abstract so it's hard to compare the effect that the drinks have had.  Certainly the hot drink has warmed skin temperature above the thermoneutral group but I suppose that could be due to increased vasodilation leading to better core heat dissipation (as you suggest).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In absolute terms, you are warmer than you would have been after having a neutral or cold drink, however it could be that you &lt;em&gt;feel&lt;/em&gt; cooler as your hotter skin loses heat energy at an increased rate due to the greater gradient.  &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1080/02640410600959947&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Lee JKW, Shirreffs SM&lt;/strong&gt;. 2007. The influence of drink temperature on thermoregulatory responses during prolonged exercise in a moderate environment. Journal of Sports Sciences 25: 975–985.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-06-20T21:46:39.880" LastActivityDate="2012-06-20T21:46:39.880" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2412" PostTypeId="2" ParentId="2382" CreationDate="2012-05-29T11:36:12.187" Score="5" Body="&lt;p&gt;This mainly depends on which kind of antioxidants you're talking about.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Vitamin A and E are antioxidants acquired from the food&lt;/li&gt;&#xA;&lt;li&gt;Superoxide dismutase, Catalase and the Glutathione system are enzymes produced by the cell.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Antioxidants keep the oxidative balance of the cell and quench free radicals which are generated by the mitochondrial respiratory chain. Very simplified: Antioxidants are thought to be anti-ageing compounds because free radicals destroy cellular compounds, which can be related to the ageing process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be very careful with products claiming to contain antioxidants and be therefore anti-aging. This whole anti-ageing marketing is far from being scientifically proven.&lt;/p&gt;&#xA;" OwnerUserId="852" LastActivityDate="2012-05-29T11:36:12.187" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2414" PostTypeId="1" AcceptedAnswerId="2416" CreationDate="2012-05-29T13:12:17.580" Score="7" ViewCount="1378" Body="&lt;p&gt;I once remember reading (15 years ago) that dinosaurs had two brains. One for their head and another one for their digestive functions. What is the current opinion on this theory? Has more evidence become available? &lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="3059" LastEditDate="2013-05-06T21:44:21.980" LastActivityDate="2020-11-11T20:14:04.413" Title="Did dinosaurs have more than one brain? If so, why?" Tags="&lt;zoology&gt;&lt;anatomy&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2415" PostTypeId="1" AcceptedAnswerId="2787" CreationDate="2012-05-29T13:13:41.540" Score="12" ViewCount="3673" Body="&lt;p&gt;Is it possible for any organisms in the animal kingdom to have more than one brain?&lt;/p&gt;&#xA;" OwnerUserId="238" LastActivityDate="2014-12-18T07:30:41.017" Title="Is it possible for any animals today to have more than one brain?" Tags="&lt;neuroscience&gt;&lt;general-biology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2416" PostTypeId="2" ParentId="2414" CreationDate="2012-05-29T13:22:49.377" Score="5" Body="&lt;p&gt;It would appear that at one time it was thought that a &amp;quot;gap&amp;quot; in the skeleton of a &lt;em&gt;Stegosaurus&lt;/em&gt; was a space for another brain. This is now thought to be a storage space for extra food.&lt;/p&gt;&#xA;&lt;p&gt;Googling your question brings up a number of answers along these lines:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Stegosaurus#%22Second_brain%22&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Stegosaurus#%22Second_brain%22&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://dinosaurs.about.com/od/dinosaurdiscovery/tp/dinoblunders.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://dinosaurs.about.com/od/dinosaurdiscovery/tp/dinoblunders.htm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://wiki.answers.com/Q/Did_a_dinosaur_have_two_brains&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://wiki.answers.com/Q/Did_a_dinosaur_have_two_brains&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="740" LastEditorUserId="62581" LastEditDate="2020-11-11T20:14:04.413" LastActivityDate="2020-11-11T20:14:04.413" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="2417" PostTypeId="1" AcceptedAnswerId="20229" CreationDate="2012-05-29T14:40:29.627" Score="6" ViewCount="63" Body="&lt;p&gt;I would like to know how easy/difficult it is to harvest fertilized eggs from Tetraodontidae species such as &lt;em&gt;Tetraodon nigroviridis&lt;/em&gt; or &lt;em&gt;Takifugu rubripes&lt;/em&gt; compared to zebrafish? Ultimately, I would like to know how much material would be obtainable from Tetraodontidae eggs to extract DNA from the nuclei.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know zebrafish lay lots of eggs, and other model fish species like medaka lay much fewer of them, but I couldn't find any information about &lt;em&gt;Tetraodon nigroviridis&lt;/em&gt; or &lt;em&gt;Takifugu rubripes&lt;/em&gt; after some googling.&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="8517" LastEditDate="2014-08-04T22:44:07.793" LastActivityDate="2014-08-04T22:44:07.793" Title="harvesting fertilized eggs from Tetraodontidae species?" Tags="&lt;genomes&gt;&lt;ichthyology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2418" PostTypeId="1" CreationDate="2012-05-29T15:42:22.807" Score="6" ViewCount="162" Body="&lt;p&gt;In mammals and birds the external reproductive organs and waste removal organs see to be the same. Is this always the case with other animals such as insects etc...? Are there any good reasons for it?&lt;/p&gt;&#xA;" OwnerUserId="84" LastEditorUserId="84" LastEditDate="2012-05-29T17:24:12.410" LastActivityDate="2012-05-29T17:24:12.410" Title="Reproduction and defecation" Tags="&lt;human-anatomy&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2419" PostTypeId="2" ParentId="2418" CreationDate="2012-05-29T16:42:37.113" Score="5" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Cloaca&quot;&gt;cloaca&lt;/a&gt;, which is the common opening of the urinary, excretory, and reproductive systems, is present in birds as well as in non-avian reptiles (and thus presumably dinosaurs), amphibians, and monotremes (e.g., duck-billed platypus). To answer your first question, yes, this condition does seem to be universal for those groups mentioned above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your second question, evolutionary history is as good a reason as I can think of. The cloacal system has worked &lt;em&gt;well enough&lt;/em&gt; for &gt;350 million years (in the case of amphibians).&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-05-29T16:42:37.113" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2420" PostTypeId="1" AcceptedAnswerId="3419" CreationDate="2012-05-29T18:19:17.833" Score="6" ViewCount="1303" Body="&lt;p&gt;Apparently, this has led to results with clinical significance, as we can see at &lt;a href=&quot;http://extremelongevity.net/2011/10/03/daily-fish-oil-consumption-may-reduce-lifespan/&quot; rel=&quot;noreferrer&quot;&gt;http://extremelongevity.net/2011/10/03/daily-fish-oil-consumption-may-reduce-lifespan/&lt;/a&gt;...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The researchers fed a special genetic variety of mice diets that&#xA;  either included 5% daily fish oil + 5% safflower oil or instead 10%&#xA;  daily safflower oil. The mice used were SAMP8 mutants that were bred&#xA;  to have accelerated aging and shortened lifespans. These mice are&#xA;  often used in longevity experiments because their average lifespans&#xA;  are only typically one year. They were fed these diets from 12 weeks&#xA;  of age on. The researchers hypothesized since fish oil is so easily&#xA;  oxidized it may lead to greater oxidative stress within cells and thus&#xA;  actually accelerate aging, a process believed in part due to&#xA;  accumulative damage from oxidative stress. Safflower oil is an omega-6&#xA;  fatty acid and is not readily oxidized – it could have beneficial&#xA;  effects without causing oxidative stress.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Let's not debate the clinical significance here - but I do wonder - why are omega-3 fatty acids so easily oxidized as compared to omega-6 fatty acids?&lt;/p&gt;&#xA;" OwnerUserId="103" LastActivityDate="2012-09-01T20:02:49.517" Title="Why are omega-3 fatty acids so easily oxidized when they're incorporated in cellular membranes?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2422" PostTypeId="1" AcceptedAnswerId="8145" CreationDate="2012-05-29T22:15:17.143" Score="7" ViewCount="291" Body="&lt;p&gt;A friend of mine asked me this today, and I didn't know. I remember studying the menstrual cycle a few years ago, but I can't remember the details (other than it was very hormone-related), and so I don't have a good base in the matter anyhow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What makes some women have irregular periods? Why?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-06-27T22:07:03.823" LastActivityDate="2013-05-26T02:31:20.080" Title="Why are some menstrual cycles irregular?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2423" PostTypeId="1" AcceptedAnswerId="2433" CreationDate="2012-05-30T03:45:57.707" Score="10" ViewCount="1038" Body="&lt;p&gt;The human genome is about 770 MB, the &lt;em&gt;C. elegans&lt;/em&gt; genome is about 100 MB, the yeast &lt;em&gt;S. cerevisiae&lt;/em&gt; is about 12 MB. Different other genomes have been sequenced: how many GB of genomic DNA we have now?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let say we would like to make a Noah hard-disk ark: how much space would it take to represent the genomes of all known species on earth? There is a way to provide an estimate?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm also interested in the total biodiversity: for instance, if two species each have 1 GB genomes and have half of their DNA in common this would count as 1.5 GB.&lt;/p&gt;&#xA;" OwnerUserId="570" LastEditorUserId="28778" LastEditDate="2018-09-14T02:14:36.690" LastActivityDate="2018-09-14T02:14:36.690" Title="How many gigabases of DNA are there on earth?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="11" ContentLicense="CC BY-SA 4.0" />
  <row Id="2424" PostTypeId="2" ParentId="2409" CreationDate="2012-05-30T03:57:54.553" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Polyphasic_sleep&quot;&gt;Polyphasic sleep&lt;/a&gt; can allow people to sleep at multiple regular intervals throughout the day and allows people to get by with less total sleep. I don't know of any training that can help people reduce the amount of monophasic sleep they need without a negative impact.&lt;/p&gt;&#xA;" OwnerUserId="570" LastActivityDate="2012-05-30T03:57:54.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2425" PostTypeId="1" CreationDate="2012-05-30T06:28:46.303" Score="9" ViewCount="405" Body="&lt;p&gt;I'm comparing 12 Metagenomes. I'm using HMM counts of a number of proteins known to exists as groups within certain operons. I have grouped the HMM counts for each type of operon and calculated the &lt;a href=&quot;http://en.wikipedia.org/wiki/Diversity_index#Shannon_index&quot; rel=&quot;noreferrer&quot;&gt;Shannon-Weaver index&lt;/a&gt; for each Metagenome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: Can I compare these Indices? Is there a better test to use than Mann Whitney U test? I would like to do this on the ungrouped data, but I have many zeroes for some fields?&lt;/p&gt;&#xA;" OwnerUserId="932" LastEditorUserId="115" LastEditDate="2012-08-07T16:29:46.713" LastActivityDate="2012-08-07T16:29:46.713" Title="Can I compare Shannon indices of metagenome gene data?" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;ecology&gt;&lt;statistics&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2426" PostTypeId="1" AcceptedAnswerId="2431" CreationDate="2012-05-30T07:32:03.117" Score="7" ViewCount="199" Body="&lt;p&gt;Similarly, what makes a wet down comforter so stinky? Why do they make no smell except when liquid is added?&lt;/p&gt;&#xA;" OwnerUserId="933" LastEditorUserId="57" LastEditDate="2012-05-30T08:03:12.063" LastActivityDate="2012-05-31T15:55:15.243" Title="What makes a wet dog so stinky?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2427" PostTypeId="1" CreationDate="2012-05-30T09:26:06.283" Score="5" ViewCount="68" Body="&lt;p&gt;What are commonly used tools to reconstruct the transcriptional regulatory circuits that govern diverse cellular responses and what input data sets do they accept?&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="43" LastEditDate="2012-05-30T14:49:17.280" LastActivityDate="2012-05-30T19:28:14.880" Title="tools to reconstruct the transcriptional regulatory circuits?" Tags="&lt;transcription&gt;&lt;gene-regulation&gt;&lt;software&gt;&lt;systems-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2429" PostTypeId="2" ParentId="2073" CreationDate="2012-05-30T13:39:59.130" Score="20" Body="&lt;p&gt;No one has mentioned the &lt;a href=&quot;http://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution&quot; rel=&quot;nofollow noreferrer&quot;&gt;Neutral Theory of Evolution&lt;/a&gt;, which explains mutations that are not necessarily motivated by increased &quot;fitness&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, (and more to the point for this question) there is no selective pressure with regards to men's nipples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Men have nipples because they find a purpose on women, but for men, there is no reason to not have them. From an evolutionary standpoint, it is simpler for men to have them. The more complex situation (women have nipples but men do not) would most likely only occur if there was some selective pressure for men to not have nipples.&lt;/p&gt;&#xA;" OwnerUserId="938" LastEditorUserId="49230" LastEditDate="2019-03-27T01:04:58.797" LastActivityDate="2019-03-27T01:04:58.797" CommentCount="6" ContentLicense="CC BY-SA 4.0" />
  <row Id="2431" PostTypeId="2" ParentId="2426" CreationDate="2012-05-30T14:55:07.107" Score="9" Body="&lt;p&gt;From &lt;a href=&quot;http://www.thenakedscientists.com/forum/index.php?topic=40705.0&quot;&gt;this source&lt;/a&gt;,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We answered this question on the show...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;We posed this question to Dr David williams from the Veterinary School&#xA;  at the University of Cambridge... David -  First of all, what actually&#xA;  makes something smell?   Molecules have to leave the smelly objects&#xA;  and get to your nose through the air and that means that these&#xA;  molecules must be very small and volatile.  That's to say they must be&#xA;  easily evaporated.  The chemicals that make dogs smell are mostly what&#xA;  we call volatile organic acids and they are produced by bacteria from&#xA;  the fats that are breaking down from sweat; and that's maybe why we&#xA;  find these body odours unpleasant.  They signal a presence of bacteria&#xA;  and decay and death to us.   &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Their [dogs] skins mostly have&#xA;  Staphylococcal bacteria, which don't produce much in the way of a&#xA;  smell at all, but they've also got some yeasts too which are really&#xA;  pongy.   But why does the smell seem worse when the dog is wet?  Here,&#xA;  I think we have to go into some physics.  The amount of evaporation of&#xA;  a substance is related to the concentration of the compound on a&#xA;  surface it’s evaporating from and the amount of compound that's in the&#xA;  air, just above the surface.  &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;So how might that change when it’s wet? &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Well, if the organic acids are dissolved in water on the fur of the&#xA;  wet dog, as the water evaporates, the concentration of those smelly&#xA;  acids increases, so they'll evaporate more, so there are more&#xA;  molecules in the air for us to smell.  Diana -   A bit of evaporation&#xA;  can effectively amplify the amount of volatile chemicals that emanate&#xA;  from a dog’s skin, and Dr. Williams thinks it’s the same effect that&#xA;  causes that damp earth smell when it rains.  It may also alter how&#xA;  dogs interact with each other when they're wet.  So, if you have a&#xA;  dog, watch to see if it sniffs differently at other dogs on a dry day&#xA;  versus a wet one...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There's a start, sounds legitimate to me...&lt;/p&gt;&#xA;" OwnerUserId="798" LastEditorUserId="307" LastEditDate="2012-05-31T15:55:15.243" LastActivityDate="2012-05-31T15:55:15.243" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2432" PostTypeId="2" ParentId="2427" CreationDate="2012-05-30T15:02:21.007" Score="3" Body="&lt;p&gt;Inferring transcriptional / regulatory networks from empirical data is an active area of research, and to my knowledge there aren't many mature tools for this type of analysis. I see mostly mathematicians, statisticians, and engineers working on this problem, probably because of the intense quantitative theory involved. Even if mature tools &lt;em&gt;do&lt;/em&gt; exist, I doubt they're tailored for the typical biologist--more likely, they are geared toward scientists with a more quantitative background.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, I am aware of 2 or 3 pieces of software that may provide a starting point for the curious or the adventurous: &lt;a href=&quot;http://dna.cs.byu.edu/airnet/&quot; rel=&quot;nofollow&quot;&gt;AIRnet&lt;/a&gt; (described &lt;a href=&quot;http://www.biomedcentral.com/1471-2164/11/S2/S6&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;), &lt;a href=&quot;http://www.async.ece.utah.edu/iBioSim/&quot; rel=&quot;nofollow&quot;&gt;iBioSim&lt;/a&gt; (described by Barker's PhD thesis, currently the second hit on &lt;a href=&quot;https://www.google.com/#hl=en&amp;amp;sclient=psy-ab&amp;amp;q=Learning+Genetic+Regulatory+Network+Connectivity+from+Time+Series+Data&amp;amp;oq=Learning+Genetic+Regulatory+Network+Connectivity+from+Time+Series+Data&amp;amp;aq=f&amp;amp;aqi=g-K1&amp;amp;aql=&amp;amp;gs_l=hp.3..0i30.166603.166603.4.167534.1.1.0.0.0.0.282.282.2-1.1.0...0.0.dr9esAhRzF8&amp;amp;pbx=1&amp;amp;bav=on.2,or.r_gc.r_pw.r_cp.r_qf.,cf.osb&amp;amp;fp=85a3745797f087a1&amp;amp;biw=1650&amp;amp;bih=914&quot; rel=&quot;nofollow&quot;&gt;this Google search&lt;/a&gt;), and maybe &lt;a href=&quot;http://www.ingenuity.com/products/pathways_analysis.html&quot; rel=&quot;nofollow&quot;&gt;Ingenuity Pathways Analysis&lt;/a&gt; (which requires a paid license). The only one of these tools I've even tried to use is iBioSim, and at the time (2 or so years ago) it was a very kludgy process.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-05-30T15:02:21.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2433" PostTypeId="2" ParentId="2423" CreationDate="2012-05-30T15:46:46.477" Score="14" Body="&lt;p&gt;If you simply take one order of insects, Coleoptera, there are just under 400,000 described species with estimates from 850,000 to 4,000,000 species total in just this order.  The number of primates is under 1,000.  If your assumption of say 10MB for all other primates would be accurate, just adding in the low end estimate of 850,000 at 10MB per 1000 we are quickly at 8,500GB which seems to be a factorial out of the GB range.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, we have a broad estimate of non-bacterial of plants, animals etc. at say 8,700,000.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Jason Gans found in a 1 gram of soil survey approximatly 1,000,000 bacterial species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;SO the total accounting for species number is totally impossible to estimate for anything at this time, let alone the genome&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even for something as &quot;common&quot; as a giraffe, there are up to 9 sub-species with genome differences within each subspecies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, once we get them all decribed, we can then work on the genome sequence for each and get you some answers!&lt;/p&gt;&#xA;" OwnerUserId="939" LastActivityDate="2012-05-30T15:46:46.477" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2434" PostTypeId="5" CreationDate="2012-05-30T15:54:07.510" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-05-30T15:54:07.510" LastActivityDate="2012-05-30T15:54:07.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2435" PostTypeId="4" CreationDate="2012-05-30T15:54:07.510" Score="0" Body="Computer programs that aid in the storage, processing, and analysis of biological data." OwnerUserId="43" LastEditorUserId="43" LastEditDate="2012-05-30T17:16:04.990" LastActivityDate="2012-05-30T17:16:04.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2436" PostTypeId="5" CreationDate="2012-05-30T15:56:33.453" Score="0" Body="&lt;p&gt;A system is defined as an assembly of mutually interacting components which, based on the dynamics of the interactions, performs specific functions. &#xA;Therefore one of the main features of systems biology is to understand the input-output characteristics of a biological system by integrating the fields of experimental biology and applied mathematics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a basic yet thorough introduction please read &lt;a href=&quot;http://www.weizmann.ac.il/mcb/UriAlon/bookUri.html&quot; rel=&quot;nofollow&quot;&gt;Introduction to Systems Biology -by Uri Alon&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-09T10:45:14.760" LastActivityDate="2013-04-09T10:45:14.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2437" PostTypeId="4" CreationDate="2012-05-30T15:56:33.453" Score="0" Body="An interdisciplinary area of study in the life sciences with a focus on complex interactions and large networks of biological molecules and processes." OwnerUserId="43" LastEditorUserId="43" LastEditDate="2012-05-30T17:16:15.990" LastActivityDate="2012-05-30T17:16:15.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2438" PostTypeId="2" ParentId="2427" CreationDate="2012-05-30T19:28:14.880" Score="1" Body="&lt;p&gt;I'd like to add &lt;a href=&quot;http://regulondb.ccg.unam.mx/&quot; rel=&quot;nofollow&quot;&gt;regulonDB&lt;/a&gt; which is not as integrated, but has a tremendous map of the e coli regulome which would be useful for any bacterial model. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I agree with @DanielStandage that this is not a well understood and there don't even appear to be standard representations for this sort of data. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-30T19:28:14.880" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2439" PostTypeId="2" ParentId="2323" CreationDate="2012-05-30T20:25:02.440" Score="1" Body="&lt;p&gt;The physical shape of the eye and lens are as @RoryM points out, the reason we become near/farsighted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most common cause of farsightedness is pretty well known.  &lt;a href=&quot;http://www.99main.com/~charlief/Blindness.htm&quot; rel=&quot;nofollow&quot;&gt;The lens of the eye allows us to focus as a ring of muscles pulls outward and flattens the lens, allowing it to focus on closer objects&lt;/a&gt;.  As we get older the lens of the eye becomes stiffer and inflexible, which means that the muscles that pull on the lens can't flatten it as easily and focusing on nearby objects becomes difficult or impossible.  This is why we need to get bifocals or reading glasses as we are older.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reasons for nearsightedness are '&lt;a href=&quot;http://www.webmd.com/eye-health/tc/nearsightedness-myopia-cause&quot; rel=&quot;nofollow&quot;&gt;natural changes in the shape of the eye&lt;/a&gt;'.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mentioned briefly in the WebMD link above is that close work (e.g. reading, web surfing, phone videos, reading and reading, etc) tends to cause nearsightedness.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://medical-dictionary.thefreedictionary.com/Near-sighted&quot; rel=&quot;nofollow&quot;&gt;25% of adults in the US and 40% of adults in Asia are myopic&lt;/a&gt; and it does look as if there is a strong genetic component to myopia.  If neither parents have myopia, the incidence is only about 7%. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm probably going to get ding-ed for this, but I am going to offer alternative explanation, which makes good scientific sense to me, so hear me out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This seems like a poor adaptive phenotype for humans who are otherwise so optimized for survival.  Why would we naturally lose our ability so young (often before the fifth grade)?  So many people who have myopia are so impaired that they can't find their way around their own house (or legally drive) without glasses/contacts/corrective surgery. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is supported by studies which show that &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8963918&quot; rel=&quot;nofollow&quot;&gt;non industrial societies have almost no natural myopia compared to industrialized ones&lt;/a&gt;.  This is just one example reference, not a survey of all evidence.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Physiologically the explanation for myopia is this: in the relaxed state, the eye is focused at the horizon (infinity).  If one habitually focuses on a book or screen within 1-2 feet from your face, the muscles might well adapt to a set point that is closer than infinity.  This would make myopia an adaptive response to modern life.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eye exercises are proposed as a way to correct myopia.  This is a bit controversial - some &lt;a href=&quot;http://www.livestrong.com/article/191866-free-eye-exercises-for-near-sightedness/&quot; rel=&quot;nofollow&quot;&gt;say they help&lt;/a&gt;, others say they &lt;a href=&quot;http://www.allaboutvision.com/buysmart/see_clearly.htm&quot; rel=&quot;nofollow&quot;&gt;do not&lt;/a&gt;. I would not be surprised that myopia developed in youth (8-15 y.o.) when the eye and body are developing can't be overcome by eye exercises when you are 25-30, but the jury is still out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are enough free descriptions of eye exercises out there that you don't really need to pay for them.  Getting young students outside to look around once in a while doesn't sound like a bad idea either, given this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are going to down vote or complain, I would appreciate it if you please cite counter reasoning other than 'this is not a popular explanation'. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-30T20:25:02.440" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2440" PostTypeId="1" AcceptedAnswerId="2794" CreationDate="2012-05-30T21:27:59.597" Score="9" ViewCount="10140" Body="&lt;p&gt;Recently, I heard on &lt;a href=&quot;http://www.bbc.co.uk/programmes/b01fhysj&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; health-related radio programme that it was better to take a half dose of paracetamol and a half dose of ibuprofen together, rather than the full dose of either one, for acute pain. Could anyone explain the reasons for this ? Could it be something along the lines of there being diminishing returns to higher doses, so you get more bang for the buck, as it were, for the first half of a dose than the second, but due to possible toxicity or drug interactions, two full doses are not recommended ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the same radio programme it was stated that caffeine also helps. Can anyone explain that ?&lt;/p&gt;&#xA;" OwnerUserId="940" LastEditorUserId="24354" LastEditDate="2020-07-06T04:08:54.573" LastActivityDate="2020-07-06T04:08:54.573" Title="Is it better to take a half dose of paracetamol and a half dose of ibuprofen together rather than a full dose of either?" Tags="&lt;pharmacology&gt;&lt;analgesia&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2442" PostTypeId="1" AcceptedAnswerId="2443" CreationDate="2012-05-31T04:17:34.307" Score="4" ViewCount="398" Body="&lt;p&gt;I was asking this first on philosophy forums, but it is suggested, that answer could be found from evolutionary view of point, so here we go:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again my question raised when thinking of myths, their origins, mysticism and religious institutions. It is said that prieshood came to existence, when ape first landed from trees to earth collecting and gathering fruits, hunting and then started to plant and farm. Whole agriculture was build organizating leadership of the society among whom were the priests and shamans who tried to understand natural forces with limited knowledge and superstition. Accelerating need for planning future, not only own family's, but whole society's future forced thinking process of humanized apes to become more involved with contemplating. &lt;em&gt;Did some of the deep thinkers find that there was a dimension on meditation which is next to impression of using herbs and drugs to bring mental experiences, were they hallucinations, visions, calmness or anything similar alive?&lt;/em&gt; Thus they became ascetics and adept on focusing mind toward itself while other part of high class of the society became adept on aiming mental activity outward, improving skills to master matter and physical nature. On ancient times both still shared same concept of need of supernatural forces to be placated or otherwise controlled to get or avoid certain every day results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This also brings up a huge evolutionary problem so to say. While apes, if they were just lead by rather unconscious instincts, they would have reproduced and build on the principle of the strongest is the leader. But when reasoning, ability to think &quot;cunning plans&quot; as stated by Baldric on Blackadder came to existence, then the most clever often won the game. But what is clever on the other extreme of the religious practice, self sacrificing and altruistic ethics? It feels almost unnatural, that religions evolved to direction, where ethic and moral rules fights against physical existence or surveillance of the individual. There is a strong hope of afterlife compensation, which explains some of it, but I'm still a bit struggled, &lt;strong&gt;why (and when) apes started to retire to the forests to meditate and rather practice altruistic ethics, loving enemies for example instead of getting justice and their own benefit fulfilled in first hand, instead of reproducing and fighting for their lives and space?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To bring whole question to modern life, I think zen buddhism is a good example of such practices brought to other level. While on the most plain form they don't expect belief on the existence of the self nor karmic relations of the acts, they still rather follow high ethics of the teachings of Buddha and live simple middle way life just being aware and mindfull of the things happening at the moment, which is the ultimate goal of the practice and life.&lt;/p&gt;&#xA;" OwnerUserId="941" LastActivityDate="2014-01-07T13:05:33.983" Title="Why apes started to contemplate and become altruistic?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;zoology&gt;&lt;physiology&gt;&lt;history&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ClosedDate="2012-05-31T14:15:21.157" ContentLicense="CC BY-SA 3.0" />
  <row Id="2443" PostTypeId="2" ParentId="2442" CreationDate="2012-05-31T05:25:49.730" Score="1" Body="&lt;p&gt;I think this is a difficult question all around, which is why its a little uncomfortable for some to be entertaining questions which are often seemingly metaphysical in nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think also that it is true that biology and neuroscience will have a big impact on the question, its also fair to say that the jury is still out on this question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genetic anthropologist Svante Paabo is one of the most engaging researchers in this question.  He started out studying the difference between the human gene sequences and &lt;a href=&quot;http://www.sciencemag.org/content/281/5382/1432.summary?sid=cd8b6f07-93ad-48da-9026-2b83593009fe&quot; rel=&quot;nofollow noreferrer&quot;&gt;the chimpanzee to try to suss out the specific genes which might be be responsible for out social selves&lt;/a&gt;.  So from this point of view, it might be that intelligence started at most about the time of human chimp divergence, &lt;a href=&quot;http://en.wikipedia.org/wiki/Chimpanzee-human_last_common_ancestor&quot; rel=&quot;nofollow noreferrer&quot;&gt;8-25 million years ago&lt;/a&gt;.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finding the specific genetic structures that convey our unique cognitive or social abilities would certainly pinpoint that time much more accurately.  There is just 1-4% difference between the chimp and human genome sequences (depending on how you calculate it), but even 1% of a 5 Gb genome is a lot of differences and no intelligent mutant chimp has been found (&lt;a href=&quot;http://www.imdb.com/title/tt1318514/&quot; rel=&quot;nofollow noreferrer&quot;&gt;that they've told us about!&lt;/a&gt;) .  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since then, a lot of interest has focused on assembling a &lt;a href=&quot;http://www.guardian.co.uk/science/2006/nov/16/fossils.research&quot; rel=&quot;nofollow noreferrer&quot;&gt;complete Neanderthal genome sequence&lt;/a&gt;.  Since Neanderthals diverged from humans about 500k years ago, and there's &lt;a href=&quot;http://en.wikipedia.org/wiki/Neanderthal_behavior&quot; rel=&quot;nofollow noreferrer&quot;&gt;plenty of evidence&lt;/a&gt; that they were intelligent, comparing the three genomes (human chimp and neanderthal) would help pinpoint the specific genetic elements which are distinctly human.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it is a mutation or set of mutations as the current thinking implies, there is a good chance that it is a combination of strong selection and accident.  Its true that cooperation is often enjoys a &lt;a href=&quot;https://biology.stackexchange.com/q/1419/77&quot;&gt;strong selective advantage&lt;/a&gt;, but it doesn't make you smart or hospitable.  When we talk in biology we don't say altruism, we say cooperation.  If such cooperation happened only because of selection, we would see such behavior in other primates.  So if we see this, I would lay odds to look for a rather complicated story...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another interesting person to read is anthropologist &lt;a href=&quot;http://anthropology.berkeley.edu/users/terrence-w-deacon&quot; rel=&quot;nofollow noreferrer&quot;&gt;Terrence Deacon&lt;/a&gt;, who is trying to understanding the terms with which we define intelligence.  About ten years ago there were actually experiments that showed that chimpanzee some strong candidate intelligence genes related to cognition could be put into people (who needed gene therapy because they had lost cognitive function) and restore that function.  Apologies, this is anecdotal - i saw him give a great talk, but he's moved on a bit and can't find the references.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is important I think because the fundamental definitions of human intelligence have failed over the years, from the old chestnut of &lt;a href=&quot;http://www.wired.com/wiredscience/2011/01/new-crow-tools/&quot; rel=&quot;nofollow noreferrer&quot;&gt;using tools&lt;/a&gt;, to a &lt;a href=&quot;http://www.kajama.com/index.php?file=articledetail&amp;amp;id=DC508A2E-0F28-42CA-882B-8B4818CFB53E&amp;amp;PageNum=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;recognition of mortality&lt;/a&gt;, &lt;a href=&quot;http://www.radiolab.org/2007/may/07/&quot; rel=&quot;nofollow noreferrer&quot;&gt;to awareness&lt;/a&gt;, &lt;a href=&quot;http://www.radiolab.org/2010/jan/11/spindle-cells/&quot; rel=&quot;nofollow noreferrer&quot;&gt;animals have surprised us, particularly primates&lt;/a&gt;.   I wonder whether we will be able to confirm these vital factors until we get a monkey asking for the keys to the car so that they can go get some pizza.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-01-07T13:05:33.983" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2445" PostTypeId="1" AcceptedAnswerId="2479" CreationDate="2012-05-31T08:49:48.797" Score="5" ViewCount="549" Body="&lt;p&gt;I've read the &lt;a href=&quot;http://dx.doi.org/10.1038/nature11119&quot; rel=&quot;nofollow&quot;&gt;tomato genome paper&lt;/a&gt; in Nature published recently, and they describe the tomato genetic resource as a rich &lt;code&gt;trait reservoir&lt;/code&gt; that &lt;em&gt;will provide biological knowledge and empower biodiversity-based breeding&lt;/em&gt;. What would be a formal definition of &lt;code&gt;trait reservoir&lt;/code&gt; in this context?&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="69" LastEditDate="2012-05-31T12:10:16.620" LastActivityDate="2012-06-02T23:07:41.060" Title="Formal definition of a 'genetic trait reservoir'?" Tags="&lt;nomenclature&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2446" PostTypeId="2" ParentId="2425" CreationDate="2012-05-31T09:22:37.177" Score="5" Body="&lt;p&gt;I'm not an expert on Shannon-Weaver Index, but according to &lt;a href=&quot;http://en.wikipedia.org/wiki/Diversity_index&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; it is the same as exponentially transformed &lt;a href=&quot;http://en.wikipedia.org/wiki/R%C3%A9nyi_entropy&quot; rel=&quot;nofollow&quot;&gt;Renyi entropy&lt;/a&gt;. If it is the case, you can compare them since they are scale invariant summary statistics. If you want error bars, you can always try resampling methods such as bootstrapping. Hypothesis testing can also be done with bootstrapping, although the power of the statistical test may not be very strong and fail to reject the null.&lt;/p&gt;&#xA;" OwnerUserId="460" LastEditorUserId="500" LastEditDate="2012-06-25T16:40:49.537" LastActivityDate="2012-06-25T16:40:49.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2447" PostTypeId="1" AcceptedAnswerId="2614" CreationDate="2012-05-31T13:15:53.060" Score="6" ViewCount="150" Body="&lt;p&gt;Are there any tools to do phylogenetic analysis of gene enrichment? This is, I have a list of genes from an experiment performed in several species, with a z-score that can be described as &quot;enrichment&quot; associated to each gene in each species. It's &lt;em&gt;not&lt;/em&gt; gene expression, it's enrichment of a certain marker n the gene. I would like to compare these lists, that are not fully overlapping, across the phylogeny of the species, to see significant changes in the trend of enrichment at the gene level, or at the branch level. What tools could I use for this?&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Species1 Z-score&#xA;Gene1    0.532&#xA;Gene2    0.531&#xA;...&#xA;&#xA;Species2 Z-score&#xA;Gene1    0.51&#xA;Gene3    0.505&#xA;...&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="658" LastEditorUserId="112" LastEditDate="2012-05-31T13:47:50.917" LastActivityDate="2012-06-13T22:05:39.823" Title="phylogenetic analysis of gene enrichment?" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;phylogenetics&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2448" PostTypeId="2" ParentId="2324" CreationDate="2012-05-31T13:55:39.497" Score="7" Body="&lt;p&gt;The processes that control the germline of metazoans (multicellular animals) are highly regulated compared to single cell bacteria and eukaryotes as well as plants.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At this point there are no clear stories of gene transfer into a complex animal, though there are some for plants:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.springerlink.com/content/k223q1668436n305/&quot;&gt;&quot;animals and fungi seem to be largely unaffected, with a few exceptions, while lateral gene transfer frequently occurs in protists with phagotrophic lifestyles, possibly with rates comparable to prokaryotic organisms.&quot;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria fungi and plants are more permissive and more susceptible to gene transfer and it probably is more important to their evolutionary path. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its been estimated that as much as eight percent of the human genome has been &lt;a href=&quot;http://www.popsci.com/science/article/2010-01/8-percent-human-dna-comes-virus-causes-schizophrenia&quot;&gt;affected by viral integration&lt;/a&gt;.  But viral genomes are highly selected against carrying non essential material - other genes rarely come along for the ride it seems.  What is probably more influential is that viral insertions could participate in rewiring the regulatory network of animal cells, &lt;a href=&quot;http://www.sciencedaily.com/releases/2010/06/100607101652.htm&quot;&gt;not adding genes, but modifying the conditions under which they are active&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-05-31T13:55:39.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2449" PostTypeId="1" CreationDate="2012-05-31T15:04:53.083" Score="0" ViewCount="134" Body="&lt;p&gt;CDC data show that American water consumption in restaurant meals is 600% of what it was in the 1950s while meal calorie density has decreased (kcal/oz). What impacts is this likely to have on the metabolism of Americans?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is based on this infographic:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/6FCph.jpg&quot; alt=&quot;http://i.imgur.com/e8XBN.jpg&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="942" LastEditorUserId="57" LastEditDate="2012-07-01T08:42:37.380" LastActivityDate="2012-07-01T08:42:37.380" Title="What impacts on metabolism are likely from the 6x increase in water consumption by Americans at restaurants since the 1950s?" Tags="&lt;metabolism&gt;&lt;food&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2450" PostTypeId="5" CreationDate="2012-05-31T15:43:01.623" Score="0" Body="" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-05-31T15:43:01.623" LastActivityDate="2012-05-31T15:43:01.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2451" PostTypeId="4" CreationDate="2012-05-31T15:43:01.623" Score="0" Body="The process in nature or in the lab by which a new organism is created that is genetically identical to its predecessor.  " OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T16:34:20.533" LastActivityDate="2013-10-31T16:34:20.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2452" PostTypeId="1" CreationDate="2012-05-31T16:53:39.593" Score="9" ViewCount="146" Body="&lt;p&gt;Has anyone optimized RT for long transcripts (9kb)? The downstream application will be PCR amplification and Illumina library prep.  It will be trivial to make internal primers sets for the PCR that are specific as long as there are no chimeric sequences.  If there are, they will probably get primed also.  If anyone knows of an optimization and/or other potential pitfalls, I would love to hear them.&lt;/p&gt;&#xA;" OwnerUserId="944" LastEditorUserId="69" LastEditDate="2012-05-31T22:12:29.713" LastActivityDate="2013-10-28T16:20:12.760" Title="Is there a Reverse Transcription optimization for long, 9kb, transcripts?" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;reverse-transcription&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2453" PostTypeId="2" ParentId="2449" CreationDate="2012-05-31T20:29:05.380" Score="5" Body="&lt;p&gt;As mentioned by nico in his comment, this infographic is very misleading in that it presents quite uninteresting data in a way as if it was a sensation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It claims the average meal drink has been soda which has increased by 6 times in size. Then it claims most of the volume is water. This is of course true. But while a substance solved in water barely increases its volume, it can still make a difference - soda and water are completely different things and the important statistic to look at here is not the amount of water drunk, but rather the fact that it is &lt;em&gt;soda&lt;/em&gt;. Where I live, soda usually contains around 27g of sugar per 240ml (8oz) which is 9% of the GDA. So according to this data, people consume half their energy needs of that day with the drink they get in their restaurant meal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other statistic is about calories per ounce of the food. What sense does a statistic about that make? The only relevance of the calorie density of food would be the effect on how well it is digested, and for that only a calorie number isn't really helpful. The relative ratios of fibre, carbohydrates and fats would be much more useful in that case. The only interesting statistic here is that meals have almost doubled in size. The fact that the volume of meals has increased much more hints that there is a higher portion of less calorific foods, such as salads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Impact on metabolism? Hard to say, this is a statistic about what people eat at restaurants, which is not really something that you expect to reflect their refular diet. It doesn't tell you anything about their general lifestyle, which would be the relevant statistic for effects on metabolism. If you only look at restaurant meals, those could look really unhealthy but on the larger scale, people balance it out in their every day diet and general lifestyle. If you had an additional statistic that shows that people actually eat a significiant amount of meals at restaurants, and they're the kind of meals described by the infographic you gave, that would have some implications.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-05-31T20:29:05.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2454" PostTypeId="1" CreationDate="2012-05-31T22:31:41.000" Score="4" ViewCount="413" Body="&lt;p&gt;I found a wasp in one of my coffee cups about 1 hour ago. There was barely any coffee left but it had managed to get itself pretty much drenched in coffee. I took it out. Put it on a piece of paper and put a pile of sugar next to it. It started eating but it was in a pretty bad state. I came back half an hour later to check up on it and it had fallen down on the floor. It's state seemed to have worsened. Went from walking around to lying still and moving it's limbs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What kind of damage did it suffer from the coffee and how would I go about maximizing it's chances for survival?&lt;/p&gt;&#xA;" OwnerUserId="945" LastActivityDate="2012-05-31T22:31:41.000" Title="How do I save a coffee damaged wasp?" Tags="&lt;zoology&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2012-06-01T14:42:48.183" ContentLicense="CC BY-SA 3.0" />
  <row Id="2455" PostTypeId="1" AcceptedAnswerId="2470" CreationDate="2012-06-01T00:17:16.853" Score="6" ViewCount="707" Body="&lt;p&gt;In the past I have used &lt;a href=&quot;http://www.springer.com/life+sciences/ecology/book/978-0-387-98928-0&quot; rel=&quot;noreferrer&quot;&gt;Limnological Analysis&lt;/a&gt; by Wetzel and Likens and &lt;a href=&quot;http://store.elsevier.com/Methods-in-Stream-Ecology/Richard-Hauer/isbn-9780123329073/&quot; rel=&quot;noreferrer&quot;&gt;Methods in Stream Ecology&lt;/a&gt; edited by Hauer and Lamberti to develop labs and research methods for courses and projects with an aquatic focus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These books detail the standard methods of lotic and lentic ecology with some emphasis on utilizing the methods in undergraduate or graduate level courses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am now developing a biogeochemistry course that is not limited to aquatic systems and I am looking for a summary of field methods for terrestrial systems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a book that summarizes terrestrial field ecology methods similar to Wetzel and Likens and Hauer and Lamberti?&lt;/p&gt;&#xA;" OwnerUserId="137" LastActivityDate="2012-10-20T15:13:27.800" Title="Is there a good field methods book that covers terrestrial ecology?" Tags="&lt;ecology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2456" PostTypeId="2" ParentId="2002" CreationDate="2012-06-01T01:21:24.527" Score="4" Body="&lt;p&gt;They absorb minerals through pores in the leaves known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Stoma&quot; rel=&quot;nofollow&quot;&gt;stomata&lt;/a&gt;, this is some what similar to the way a medicine patch is absorbed on human skin except for the fact that the human skin has sweat pores instead of stomata.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/3/3c/Tomato_stoma_observed_through_immersion_oil.gif&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a animation of them opening and closing on a tomato plant provided by Wikipedia:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;sources:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A nice review by &lt;a href=&quot;http://www.insad.pl/files/journal_pdf/journal_2004spec/full2004-24spec.pdf&quot; rel=&quot;nofollow&quot;&gt;Wocjik (2004)&lt;/a&gt; (from the comments)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;http://www.wisegeek.com/what-is-foliar-feeding.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.wisegeek.com/what-is-foliar-feeding.htm&lt;/a&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Foliar_feeding&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Foliar_feeding&lt;/a&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;http://cronodon.com/BioTech/Plant_Transport.html&quot; rel=&quot;nofollow&quot;&gt;http://cronodon.com/BioTech/Plant_Transport.html&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="946" LastEditorUserId="57" LastEditDate="2012-06-02T04:33:47.897" LastActivityDate="2012-06-02T04:33:47.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2457" PostTypeId="1" AcceptedAnswerId="2514" CreationDate="2012-06-01T02:49:56.977" Score="5" ViewCount="317" Body="&lt;p&gt;B vitamins and particularly the B6 vitamin appears to the one of the main ingredients in energy drinks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There has been anecdotal evidence from people interested in dreaming that ingestion of vitamin B6 at night time changes the pattern of dreaming and is likely to produce &quot;lucid&quot; dreams.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;From a biological standpoint, what is the effect of the B6 vitamin on the human body and brain?&lt;/strong&gt; Do other animals require the same vitamin?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are B vitamins in any way related to the circadian rhythm regulation within some organ systems? Does it speed up metabolism?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be grateful for any scholarly papers on the subject or keywords that I may look up myself. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-06-06T05:14:41.007" Title="What biological systems are affected by Vitamin B6 (or B vitamins in general)?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;circadian-rhythms&gt;&lt;vitamins&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2458" PostTypeId="1" CreationDate="2012-06-01T04:11:38.247" Score="9" ViewCount="1185" Body="&lt;p&gt;Many people like cracking their knuckles. I have always been curious about it.&#xA;What happens when we crack knuckles?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What creates the &lt;em&gt;POP&lt;/em&gt; sound?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do we get a relief-like feeling after doing it?&lt;/p&gt;&#xA;" OwnerUserId="771" LastEditorUserId="307" LastEditDate="2012-06-03T22:01:03.760" LastActivityDate="2015-04-21T23:28:51.337" Title="What causes knuckle &quot;popping&quot; and the feeling of relief that comes from it?" Tags="&lt;human-biology&gt;&lt;joints&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2459" PostTypeId="1" CreationDate="2012-06-01T05:16:53.080" Score="2" ViewCount="657" Body="&lt;p&gt;Bovine serum albumin, Avidin, Ficoll-70 and Dextran-70,are they&#xA;positively charged or negatively charged ? And which other solvents can be used as a substitute to water for preparing solutions in each case ?&lt;/p&gt;&#xA;" OwnerUserId="947" LastEditorUserId="947" LastEditDate="2012-06-01T05:22:49.220" LastActivityDate="2014-05-12T14:27:10.760" Title="Are Bovine serum albumin, Avidin, Ficoll-70 and Dextran-70 positively charged or negatively charged?" Tags="&lt;homework&gt;&lt;proteins&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2014-05-12T20:56:51.070" ContentLicense="CC BY-SA 3.0" />
  <row Id="2460" PostTypeId="2" ParentId="2458" CreationDate="2012-06-01T08:00:45.393" Score="6" Body="&lt;p&gt;Nobody really knows where it comes from. The currently most popular theory is that pulling the joint apart leads the gases in the joint's cartilage to accumulate and form a bubble which then pops when you let it spring back. The only thing that has been researched is whether it has an effect on the joint, but people who do it regularly don't seem to have any problems with their joints more than anyone else (I'll find the reference once I have time). Apart from that it's hard to get funding for this kind of research because it has little practical use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Relief like feeling? That must be subjective to you, I used to do it every now and then but I don't remember getting any relief from it. In that case, it's probably the same relief as other people get from picking their nose, their ears, biting their nails, etc. It's called compensation reaction.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-06-01T08:00:45.393" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2461" PostTypeId="1" AcceptedAnswerId="2465" CreationDate="2012-06-01T11:47:35.470" Score="6" ViewCount="741" Body="&lt;p&gt;Are there any computational tools to predict the binding affinity to specific DNA motifs from protein domain sequence information?&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="86" LastEditDate="2012-06-03T16:40:27.693" LastActivityDate="2012-06-03T16:40:27.693" Title="How can I predict DNA binding affinities from a protein sequence?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2462" PostTypeId="1" AcceptedAnswerId="2466" CreationDate="2012-06-01T12:07:42.060" Score="12" ViewCount="342" Body="&lt;p&gt;I attended a seminar about neurogenesis that presented results for PAX6 as an important TF that contains 3 domains with very distinct patterns of downstream expression. The speaker ended up saying that PAX6 can be considered as 3 TFs in one protein, acting independently in different situations:    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1186/1471-213X-10-39&quot;&gt;Relative roles of the different Pax6 domains for pancreatic alpha cell development&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anybody know of more examples like this?&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="69" LastEditDate="2012-06-01T14:37:31.120" LastActivityDate="2015-04-13T00:30:18.113" Title="Modularity of transcription factors" Tags="&lt;transcription&gt;&lt;gene-regulation&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2463" PostTypeId="1" AcceptedAnswerId="2464" CreationDate="2012-06-01T13:36:48.673" Score="7" ViewCount="957" Body="&lt;p&gt;Have there been any studies done on the animal use of their bodies to signal, communicate or express their emotions, particularly to members of other species (ex: humans)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been observing a very intelligent indoor-outdoor cat who has been doing the same sideways stretching posture every day he met me. There has been a number of other postures that the cat has been using - tearing at a carpet with claws, or dragging himself against the carpet by using claws that I've repeatedly observed.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/NUXRK.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another cat was thumping her head against a door to &quot;knock&quot; and indicate that the cat is outside. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To me, these gestures appeared as clear expressions of intent or emotional state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other experiment involved &quot;trained&quot; geese at a local pond who would indirectly approach humans to ask for food. Their body, neck and head position appear to indicate intent (is the animal grazing towards the human or away from the human). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet another experiment involves nesting birds who start to clearly express their displeasure at me located near their nesting area. They repeatedly produce high pitched screech until I move away.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example I repeatedly see geese assume this gesture to intimidate other geese.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/NXohS.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a human, I'm very conditioned to vocal and eye related coordination, and this &quot;non-verbal&quot; language is fascinating to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Have there been any studies in how indoor/outdoor - partially domesticated animals communicate with humans?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is it true that this communication uses their entire body and not just the vocal cords?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there some &quot;foundation&quot; language that would be similar among members of the same species, or is it entirely a learned skill that has nothing to do with evolutionary adaptation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, is there some sort of a brain complexity cut off at which level the animals can no longer understand if they are being communicated with? &lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="3952" LastEditDate="2013-08-02T14:12:20.783" LastActivityDate="2017-05-18T12:52:45.847" Title="Is there such thing as Animal non-verbal body language?" Tags="&lt;zoology&gt;&lt;adaptation&gt;&lt;language&gt;&lt;communication&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2464" PostTypeId="2" ParentId="2463" CreationDate="2012-06-01T15:07:36.453" Score="5" Body="&lt;p&gt;The closest reason that I know of for such behaviour is simple conditioning!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B. F. Skinner conducted some fairly famous experiments with pigeons, where he put hungry pigeons in cages, and randomly administered the food. The pigeons associated the foods arrival with whatever they happened to be doing at the time (be it looking to the right, or bobbing their heads). They would then keep trying this until more food came out (randomly), and the pigeons 'superstition' was confirmed. See the &lt;a href=&quot;http://en.wikipedia.org/wiki/B._F._Skinner#Superstition_in_the_pigeon&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize this is not concrete, but it seems to me that they are not 'communicating' as such, they are simply repeating what has worked before. It is your anthropomorphication that has meant this seems like deliberate communication in my opinion. Although I'm sure it could be argued that all communication is having been 'conditioned' to use words/gestures to get your meaning across.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt; (14.6.12)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just read the abstract for &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039145&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; (published yesterday) that finds that experts in dog behaviour can interpret the ('socially relevant') posture of a dog in a similar way to that of a human. We can therefore interpret the body language of an animal (in this case, dog), if we are familiar (you do not even have to have owned a dog necessarily) with the kinds of postures adopted. So the dog does not have to consciously 'communicate' for us to interpret their emotional state (happy/sad/angry/...).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of human-pet communication then, there seems to be more emphasis on the human interpretation of the natural postures adopted by animals, than the animals themselves. Pets may behave very differently to animals in the wild, but it comes back to what the specific human is used to. If you have had a lot of contact with pet dogs you are in a better position to associate the current behaviour of a pet dog with the correct emotional state. No doubt the animal with subconsciously adjust their behaviour to achieve the 'correct' human interpretation, and thus get fed, or whatever. &lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-06-14T12:40:40.073" LastActivityDate="2012-06-14T12:40:40.073" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2465" PostTypeId="2" ParentId="2461" CreationDate="2012-06-01T15:15:46.100" Score="3" Body="&lt;p&gt;Those that come up from a Google search (&quot;predict DNA binding from protein domain tool&quot;) seem pretty well suited to your question.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bioinfo.ggc.org/bindn/&quot; rel=&quot;nofollow&quot;&gt;BindN&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.imtech.res.in/raghava/dnabinder/help.html&quot; rel=&quot;nofollow&quot;&gt;DNAbinder&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Depending on your computational/statistical know-how you might also find these papers relevant&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21342579&quot; rel=&quot;nofollow&quot;&gt;Huang &lt;em&gt;et al&lt;/em&gt;, Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19911048/&quot; rel=&quot;nofollow&quot;&gt;Gao &lt;em&gt;et al&lt;/em&gt;, A threading-based method for the prediction of DNA-binding proteins with application to the human genome&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-06-01T15:15:46.100" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2466" PostTypeId="2" ParentId="2462" CreationDate="2012-06-01T16:14:25.950" Score="12" Body="&lt;p&gt;The &lt;a href=&quot;http://www.nf-kb.org&quot; rel=&quot;nofollow&quot;&gt;NF-κB&lt;/a&gt; family of transcription factors is very modular, with different combinations having different effects. The active (nuclear, DNA-bound) TF is a dimer, composed variously of &lt;a href=&quot;http://en.wikipedia.org/wiki/RELA&quot; rel=&quot;nofollow&quot;&gt;RelA/p65&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/RELB&quot; rel=&quot;nofollow&quot;&gt;RelB&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/REL&quot; rel=&quot;nofollow&quot;&gt;c-rel&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Nfkb1&quot; rel=&quot;nofollow&quot;&gt;NFKB1/p50&lt;/a&gt;, and/or &lt;a href=&quot;http://en.wikipedia.org/wiki/NFKB2&quot; rel=&quot;nofollow&quot;&gt;NFKB2/p52&lt;/a&gt; subunits. For example, the &quot;canonical&quot; p65/p50 dimer is activated in response to stimulants like &lt;a href=&quot;http://en.wikipedia.org/wiki/Tumor_necrosis_factor-alpha&quot; rel=&quot;nofollow&quot;&gt;TNF-α&lt;/a&gt; (tumor necrosis factor alpha, released in response to inflammatory signals like the presence of pathogens) and &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipopolysaccharide&quot; rel=&quot;nofollow&quot;&gt;LPS&lt;/a&gt; (lipopolysaccharide from the cell walls of &lt;a href=&quot;http://en.wikipedia.org/wiki/Gram-negative&quot; rel=&quot;nofollow&quot;&gt;Gram-negative&lt;/a&gt; bacteria), while the RelB/p52 dimer plays an important role in the development of &lt;a href=&quot;http://en.wikipedia.org/wiki/B_cell&quot; rel=&quot;nofollow&quot;&gt;B cells&lt;/a&gt; (the immune system component that produces antibodies). The &lt;a href=&quot;http://en.wikipedia.org/wiki/AP-1_%28transcription_factor%29&quot; rel=&quot;nofollow&quot;&gt;AP-1&lt;/a&gt; transcription factor is also heterodimeric, containing proteins from the Jun, Fos, JDP, and ATF families, and there are numerous other examples of multimeric transcription factor complexes. &lt;a href=&quot;http://www.nature.com/ni/journal/v13/n1/full/ni.2151.html&quot; rel=&quot;nofollow&quot;&gt;This recent article&lt;/a&gt; in Nature Immunology (disclaimer: I was not involved in that research, but my old lab did similar work) shows DNA sequence-specific binding by different NF-κB dimers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Polymerism in general, and dimerism in particular, are quite common modes of transcriptional activation and regulation. The large number of ways in which a relatively small number of transcription factors can be combined allows for the exquisite control of genes, responding to a huge variety of cellular situations. Unfortunately, it also means that mutations in key, common components can result in transformation, unrestricted growth, and the generation of tumors.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2015-04-13T00:30:18.113" LastActivityDate="2015-04-13T00:30:18.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2467" PostTypeId="2" ParentId="2324" CreationDate="2012-06-01T16:40:27.470" Score="3" Body="&lt;p&gt;Human endogenous retroviruses (HERVs) have been an interesting (and expanding) topic of research in evolutionary biology and medicine. A retrovirus has an RNA genome in the virus particle, and integrates with the host cell's DNA upon infection to hijack the transcription/translation machinery and produce copies of itself. For this reason, it is not possible to &quot;cure&quot; a cell of a retroviral infection; instead all of the infected cells must be destroyed or commit suicide through apoptosis, also known as programmed cell death. Common examples of retroviruses include HIV (causative agent of AIDS), HTLV (human T-cell leukemia virus), and the Hepatitis B virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Viral infections are most common in somatic cells, where any change in the DNA sequence is not passed along to the next generation. However, any retroviral infection in germ cells (eggs, sperm, and the progenitor cells that make them) could be passed on to the next generation, and over time spread throughout a population. Some HERV fragments are apparently completely inactive (at least as far as we are able to tell currently), and are a possible source for some of the so-called &quot;junk&quot; or non-coding non-regulatory DNA that makes up a significant part of our genome - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15044706&quot; rel=&quot;nofollow&quot;&gt;one estimate&lt;/a&gt; claims that 8% of our genetic material is of retroviral origin. Other HERVs have been implicated in various pathological conditions, including multiple sclerosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure that any human genes have been found that were picked up by a virus, stayed with it for a time (and potentially mutated), then was reinserted back into the human genome, if that's what you're asking. There are certainly many cases of genes and gene fragments (coding regions, promotors, enhancers, etc.) being moved around as a result of viral integration/splicing. &lt;a href=&quot;http://en.wikipedia.org/wiki/Endogenous_retrovirus#Genome_Evolution&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Endogenous_retrovirus#Genome_Evolution&lt;/a&gt; is a large, rather well-written section with numerous links to the primary literature showing how our genome has been altered over the years by HERVs.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2012-06-01T16:52:30.110" LastActivityDate="2012-06-01T16:52:30.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2469" PostTypeId="1" CreationDate="2012-06-02T06:07:36.790" Score="1" ViewCount="286" Body="&lt;p&gt;What is the recommended concentration of BSA to be mixed with water so as to prepare a very dilute solution in order to clearly study the intensity-intensity correlation with single scattering ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to plot the intensity vs time correlation curve/graph, and eventually calculate the hydrodynamic radius in each case. I've seen different journals and texts provide varied concentrations ranging from 0.001 g/L to 3 g/L.&lt;/p&gt;&#xA;" OwnerUserId="947" LastEditorUserId="6" LastEditDate="2012-06-07T07:18:20.633" LastActivityDate="2012-06-07T07:18:20.633" Title="Which concentration of BSA is recommended for dynamic light scattering experiments?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2470" PostTypeId="2" ParentId="2455" CreationDate="2012-06-02T06:17:32.993" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://books.google.com/books/about/Methods_in_Ecosystem_Science.html?id=N_pGrSntap0C&quot; rel=&quot;nofollow&quot;&gt;Methods in Ecosystem Science&lt;/a&gt; edited by Oswaldo Sala, Rob Jackson, Hal Mooney, and Robert Howarth is a classic standard reference used by many (most?) ecosystem ecologists.&lt;/p&gt;&#xA;" OwnerUserId="222" LastActivityDate="2012-06-02T06:17:32.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2471" PostTypeId="2" ParentId="2452" CreationDate="2012-06-02T13:14:56.590" Score="2" Body="&lt;p&gt;RT-PCR should be able to get you up to ~10kb. If you are finding that it is not working, then you can by long-range RT-PCR kits commercially (look at Stratagene and Qiagen, for example). The Qiagen can handle up to 12.5 kb in a two-step RT-PCR system.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2013-10-26T13:46:49.160" LastActivityDate="2013-10-26T13:46:49.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2472" PostTypeId="2" ParentId="1491" CreationDate="2012-06-02T14:10:42.400" Score="4" Body="&lt;p&gt;Plants are not a strong suit for me, but in general the answer is yes.  What I know mostly comes from animal tissue, so someone may have a better answer than I...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Botanists have been cloning plants from cuttings for thousands of years.  More recently, propagation from cell lines around for much longer than for animals.  Entire plants can often be grown from a &lt;a href=&quot;http://en.wikipedia.org/wiki/Plant_tissue_culture&quot; rel=&quot;nofollow&quot;&gt;plate of cells&lt;/a&gt;.  So you can grow roots or an entire plant from cells right now, but I can't find any mention of anyone trying to grow fruit without the rest of the plant, and there might not be any research for this.  Let me explain why this may be...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bioengineering animal tissue and organ growth has been an intensive area of research for the past 15 years or so.  In some cases, such as the growth of skin or liver, the technology has proven to be exceptionally valuable and useful. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using plastics with biological growth factors attached and 3D printing, even more complex organs such as &lt;a href=&quot;http://www.washingtonpost.com/wp-dyn/content/article/2006/04/03/AR2006040301387.html&quot; rel=&quot;nofollow&quot;&gt;bladders&lt;/a&gt; and &lt;a href=&quot;http://singularityhub.com/2010/11/02/wake-forest-creates-first-liver-in-lab-using-human-cells/&quot; rel=&quot;nofollow&quot;&gt;tracheas&lt;/a&gt; can be grown from the patients own cells, which avoids the problems of rejection and the complexities of donor matching.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More recently growing muscle tissue in an animal free culture has been tried, which would &lt;a href=&quot;http://en.wikipedia.org/wiki/In_vitro_meat&quot; rel=&quot;nofollow&quot;&gt;relieve some of the environmental and ethical problems&lt;/a&gt; of raising meat animals.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All this has been driven by a strong cost-benefit payoff.  A transplanted organ is highly valuable and improving that process and making organs more broadly available for patients has a high economic value.  The more often the structure is related to the tissue around, the more structurally complex, the more difficult it is to imagine growing that organ independently of the host organism (brain and eyes come to mind).  &lt;a href=&quot;http://singularityhub.com/2009/06/08/growing-organs-in-the-lab/&quot; rel=&quot;nofollow&quot;&gt;Other transplant worthy tissue cultures look quite promising&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Right now, it seems as if plant fruit like an apple or a kiwi might be difficult/expensive to grow in the lab as opposed to just picking them off the tree.  I think that growing a banana pulp or an apple sauce might be possible, though.  Who knows what we might be doing in 50 years or more though? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-06-02T14:10:42.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2473" PostTypeId="1" AcceptedAnswerId="2478" CreationDate="2012-06-02T14:14:53.110" Score="6" ViewCount="791" Body="&lt;p&gt;Lately, I've started exercising in the gym and outside. I've also started to look at the details of food I eat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Food usually has a label saying the amount of energy is inside it. For example, some chocolate says it has 400 kilocalorie for 100 grams.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have some questions about that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Does the label say the amount of total chemical energy exists inside the food, which will be released if burned, or the energy available to the human body after digested, and because digesting requires energy, the food contains actually MORE energy then written?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When I'm riding on a static bike, it has a screen which counts the kcal I burn. It has a thing connected to my arm, measuring my heart beat. After about an hour of riding, it said I used about 700 kcal. Is it the amount of work I did, i.e if there was a battery connected to the bicycle, I'd generate 700 kcal of electricity, OR, the amount of energy my body LOST, because muscle efficiency is far from 100% (so, I lost 700 kcal, but generated only 150 kcal of electricity, for example)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When doing a physical activity, the heart beat and breathing rate increases. Lets say I'm riding a bicycle or running. Whats the ratio between energy consumed by the muscle to energy consumed by the lungs or heart?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="951" LastEditorUserId="6" LastEditDate="2012-06-03T11:26:58.953" LastActivityDate="2012-06-03T11:26:58.953" Title="Energy use by muscles, actual work done by muscles and more" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;muscles&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2474" PostTypeId="2" ParentId="2473" CreationDate="2012-06-02T16:05:43.147" Score="1" Body="&lt;p&gt;1) It depends on each country and your minister. In Finland, the thing is done so that it says the energy stored in food, which will be released if burned.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) It is the energy pushed to the bike when the bike does not take into account your pulse. If the bike is smart one, it takes into account your pulse rate, then it tries to estimate the amount of energy released by your body. This is done differently among different manufacturers of those watches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) By the way heart is a bunch of muscles, a myogenic muscular organ! So consider instead heart and some part of lungs. Very broad problem otherwise.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-06-02T16:05:43.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2475" PostTypeId="2" ParentId="2462" CreationDate="2012-06-02T18:02:14.717" Score="4" Body="&lt;p&gt;There was a paper published in Cell last year that has shown that the binding motif of a Hox transcription factor will change depending on whether there's a co-factor bound to the Hox. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Slattery &lt;em&gt;et al.&lt;/em&gt; (2011) &lt;a href=&quot;http://dx.doi.org/10.1016/j.cell.2011.10.053&quot; rel=&quot;nofollow&quot;&gt;Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins&lt;/a&gt;. &lt;em&gt;Cell&lt;/em&gt;, &lt;strong&gt;147&lt;/strong&gt;(6) 1270-1282. doi: 10.1016/j.cell.2011.10.053 (&lt;a href=&quot;http://rohslab.cmb.usc.edu/Papers/2011_Cell_latent_specificity.pdf&quot; rel=&quot;nofollow&quot;&gt;pdf&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="953" LastEditorUserId="4202" LastEditDate="2015-04-12T21:06:53.030" LastActivityDate="2015-04-12T21:06:53.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2476" PostTypeId="1" CreationDate="2012-06-02T18:31:22.043" Score="3" ViewCount="64" Body="&lt;p&gt;Yesterday I thought about a question and asked it to my friend.  The question was&#xA;&lt;em&gt;which gene is completely the same for a male cell that made meiosis 1 recently&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My answer was the gene that starts meiosis 2, but he said he thought that there is no such gene - only a gene to start meiosis and meiosis 1 and 2 are just parts that scientists named.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is is there any gene that starts meiosis 2?&lt;/p&gt;&#xA;" OwnerUserId="954" LastEditorUserId="69" LastEditDate="2012-06-02T19:19:27.943" LastActivityDate="2012-06-02T19:19:27.943" Title="Is there a gene that starts meiosis 2?" Tags="&lt;genetics&gt;&lt;meiosis&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="0" ClosedDate="2014-08-01T21:01:55.830" ContentLicense="CC BY-SA 3.0" />
  <row Id="2477" PostTypeId="1" CreationDate="2012-06-02T20:53:39.417" Score="5" ViewCount="3415" Body="&lt;p&gt;After following a course in Permaculture, I realised that if I want to get serious about it, I need to be able to distinguish plants. So I am looking for an online Video course on Plant Taxonomy and Physiology. My understanding is that it is a fairly standard course in basic Botany degrees, and since there are more and more school that put their material online it is quite possible that one of them might have placed this online too. Any suggestion?&lt;/p&gt;&#xA;" OwnerUserId="955" LastEditorUserId="955" LastEditDate="2014-03-08T21:56:51.170" LastActivityDate="2018-03-31T08:25:02.550" Title="Online course on Plant Taxonomy and Physiology" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;taxonomy&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2478" PostTypeId="2" ParentId="2473" CreationDate="2012-06-02T22:41:12.153" Score="8" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;I speak only for the U.S. regulations: the calorie labels on wrappers refer to the energy released when burned. Sometimes these are inaccurate. Many dieticians recommend calculating the calories based on weights of protein, carbohydrates and fats in the serving: 4 kcal in each gram of protein and carbohydrate and 9 kcal in each gram of fat in your food. Multiply carbs, proteins and fats by the appropriate value and add them up.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The reading on the bike does not take into account your pulse. Just the raw work done turning the pedals. Some very smart bikes do take pulse into account, but the often inaccurate heart monitors lead to inaccurate calculations of total energy.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The heart and diaphragm (muscle primarily responsible for breathing) do use more energy when exercising than when you are sitting still. But that increase is small relative to the increase in the primary muscle sets involved in the exercise. Your resting heart rate is probably around 70 bpm, your exercising heart rate is probably around 160-180 bpm. So it has increased its rate and energy consumption by about 3 times. Your skeletal muscles maintain a basal metabolic rate during inactivity (one purpose of this is your body needs the heat from slightly tensed muscles to thermoregulate itself) - but during exertion, their metabolic rate increases enormously. Exercise increases their energetic demands by whole orders of magnitude.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The actual value of the (energy used by heart) / (energy used by skeletal muscles during exercise) depends on what exercise you do and how efficiently you do it. The change in the ratio between inactivity and activity depends on how much muscle mass you have (more muscle uses more energy during inactivity) and how strenuously you exercise. But the point is that the increased energetic demands by skeletal muscles far outpace the 3x increase in energetic demands by the heart and diaphragm - so the latter accounts for pretty much all total energy consumption at even moderate activity levels.&lt;/p&gt;&#xA;" OwnerUserId="956" LastActivityDate="2012-06-02T22:41:12.153" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2479" PostTypeId="2" ParentId="2445" CreationDate="2012-06-02T23:07:41.060" Score="5" Body="&lt;p&gt;In this context, &quot;trait reservoir&quot; refers to the set of all possible alleles for all the different genes in the organism. The more different alleles the organism has, the more possible genotypes it might have. The Nature paper might have referred specifically to the set of &lt;em&gt;known&lt;/em&gt; allelic variants. &lt;/p&gt;&#xA;" OwnerUserId="956" LastActivityDate="2012-06-02T23:07:41.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2480" PostTypeId="1" AcceptedAnswerId="2492" CreationDate="2012-06-03T17:21:33.010" Score="3" ViewCount="672" Body="&lt;p&gt;Does anyone know if the T7 phage promoter is efficient in mammalian systems?&lt;/p&gt;&#xA;" OwnerUserId="957" LastActivityDate="2012-06-04T19:33:21.210" Title="T7 phage promoter action in mammals" Tags="&lt;synthetic-biology&gt;&lt;t7-promoter&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2483" PostTypeId="1" AcceptedAnswerId="2487" CreationDate="2012-06-04T08:28:48.873" Score="9" ViewCount="4346" Body="&lt;p&gt;Obviously, a very large dog would have difficulties mating with a very small dog and vice versa. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7EVrA.jpg&quot; alt=&quot;big dog and small dog&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But putting that problem aside (using, say, insemination), considering the large variation of dog breeds, are there any two breeds that are so different genetically that they can't produce viable offspring together?&lt;/p&gt;&#xA;" OwnerUserId="960" LastEditorUserId="960" LastEditDate="2012-06-04T08:42:44.060" LastActivityDate="2012-06-04T13:57:09.450" Title="Are there dog breeds that are so far apart genetically that they can't produce viable offspring?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2484" PostTypeId="1" CreationDate="2012-06-04T08:36:34.507" Score="3" ViewCount="730" Body="&lt;p&gt;We do a lot of bioconjugation chemistry (click chemistry in particular but also NHS and Maleimide chemistries). Our method to valid the conjugation reactions have been to use SDS-PAGE gels followed with densitometry. However one particular challenge with such analyses is that proteins conjugated with non-proteins like DNA or PEG migrate with an inconsistent MW and also in a smear making it hard to isolate the relevant bands. I assume that this has to do with having a poly-disperse radius of gyration. Are there tricks that I can do to get tighter bands?&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="69" LastEditDate="2012-11-24T23:22:25.347" LastActivityDate="2012-11-24T23:22:25.347" Title="Troubleshooting bioconjugates migration in a SDS-PAGE gel?" Tags="&lt;biochemistry&gt;&lt;sds-page&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2485" PostTypeId="1" AcceptedAnswerId="2486" CreationDate="2012-06-04T11:12:46.203" Score="29" ViewCount="5919" Body="&lt;p&gt;The word natural here is meant in contrast to it being a sociological construct. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is &lt;em&gt;kissing&lt;/em&gt; in all its forms something natural for humans? Is it instinctively erotic? Or is it just a conventional form to show trust and intimicy, i.e. the association besically just comes via a social means?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Because the only other advantage of this mouth to mouth contact I could see is maybe for the immune system.&lt;/p&gt;&#xA;" OwnerUserId="498" LastEditorUserId="1320" LastEditDate="2013-01-07T08:39:16.330" LastActivityDate="2017-02-11T11:21:51.150" Title="Is kissing a natural human activity?" Tags="&lt;human-biology&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2486" PostTypeId="2" ParentId="2485" CreationDate="2012-06-04T13:40:51.297" Score="30" Body="&lt;p&gt;Wikipedia actually has a note on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Kiss#Biology_and_evolution&quot;&gt;evolution of kissing&lt;/a&gt;.  They point out that there are grooming behaviors such as licking and social behaviors like dogs touching noses in many species even insects.  They note that it is not decided at all whether kissing is learned or from some sort of instinct.  They also mention that its reminiscent of feeding behavior common in birds (and other animals) where food is pushed down the throats of young.  (try thinking about &lt;em&gt;that&lt;/em&gt; next time!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I seem to remember though that there are some culture which &lt;a href=&quot;http://people.howstuffworks.com/kissing.htm&quot;&gt;do not kiss&lt;/a&gt;. &lt;a href=&quot;http://www.kissingsite.com/differentcultureskissing.htm&quot;&gt;with their lips at least&lt;/a&gt;. This would favor kissing as a learned behavior, but these cases are very rare and isolated peoples and it might be simply a taboo to talk about kissing with researchers or at all, which is a hazard of that sort of work.  In addition, bonobos, one our our closest primate cousins, do kiss frequently with the lips, as a social and intimate gesture and the parallels with most human cultures &lt;a href=&quot;http://www.2think.org/bonobo.shtml&quot;&gt;are difficult to ignore&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-06-04T13:40:51.297" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2487" PostTypeId="2" ParentId="2483" CreationDate="2012-06-04T13:57:09.450" Score="8" Body="&lt;p&gt;I actually found some sort of reference for this.  Apparently in the case of a beagle and irish setter pairing, &lt;a href=&quot;http://sciencenetlinks.com/science-news/science-updates/dog-breeds/&quot;&gt;they had a lot of difficulty in producing pups&lt;/a&gt;, but as breeds have a lot of genetic quirks, this might be due to a genetic accident; this is probably a case of mutual infertility rather than speciation.  There are probably mutations in their genomes which are causing non viability in the pups the way that it does with some human parents who have difficulty having children - an immunological incompatibility or traits which cause most offspring non-viable.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact the discussion points out that the species designation does not always mean they cannot produce offspring, but simply do not.  Coyotes and wolves will produce offspring too if they are encouraged to do so, but are competing and antagonistic in the wild and so never do mate in practice.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the answer is probably no. (the beagle/setter pups did show up, but with a much smaller litter than usual with just 2 pups).  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-06-04T13:57:09.450" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2488" PostTypeId="2" ParentId="2484" CreationDate="2012-06-04T14:39:07.360" Score="4" Body="&lt;p&gt;The first step in troubleshooting is to run controls - run lanes with your protein input alone, and the conjugate alone (you may need to play with the type/percentage of the gel if the conjugate molecule is much smaller than your target protein - attaching biotin to a 50 kDa protein, for example) to see if the smear shows up. Depending on the type of conjugation you're using, the number of acceptor sites on the substrate, and the time and conditions of the conjugation reaction, you may be adding a highly variable number of conjugate molecules to your substrate. For example, when I first started working with adding fluorophores like Alexa and DyLight dyes to antibodies, the fluor/protein ratio was highly variable from reaction to reaction and between antibodies in the same reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is most likely what is happening in your case - the number of conjugate molecules being added to each substrate molecule is highly variable. If you haven't already, I'd suggest getting in touch with your conjugation kit vendor's tech support, as they likely encounter this problem all the time. You may need to change the type of conjugation chemistry, get a higher-quality conjugate, or purify the substrate before and/or after the reaction. One of the solutions to my antibody labeling problem I mentioned above was to purify the reaction products through a size-exclusion column. This had the dual effect of separating out the un-reacted antibody and fluorophore, and allowing us to pick different fractions of the conjugated product and decide which were best for our needs.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2012-06-04T14:39:07.360" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2489" PostTypeId="1" AcceptedAnswerId="2490" CreationDate="2012-06-04T14:51:05.087" Score="8" ViewCount="19564" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Active_Site#Models&quot; rel=&quot;noreferrer&quot;&gt;This Wikibook&lt;/a&gt; shows both proposed models of enzyme-substrate complementarity, the Lock and Key model and the Induced Fit model. I've always been taught that the Induced Fit model is  the proper one. However, my biochemistry professor mentioned that often times, enzymes behave as lock and key. I also noticed that the Wikibook doesn't mention which model is in fact true.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;The Lock and Key Model&lt;/em&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ekkPN.jpg&quot; alt=&quot;The Lock and Key Model&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;The Induced Fit Model&lt;/em&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/cBJ47.jpg&quot; alt=&quot;The Induced Fit Model&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there currently one accepted model? Which is it, and why?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-06-04T14:58:24.247" LastActivityDate="2012-06-04T19:53:14.103" Title="What is the correct model for enzyme-substrate complementarity?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;&lt;binding-sites&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2490" PostTypeId="2" ParentId="2489" CreationDate="2012-06-04T16:01:19.547" Score="9" Body="&lt;p&gt;This is true of all protein binding as well as the special case of enzyme-substrate interaction:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Various proteins are more dynamic than others: some have only one or two overall conformations and are relatively implastic otherwise. An example would be a receptor tyrosine kinase like Kit (or CD117, or Mast Stem Cell Growth Factor Receptor, whatever you want to call it), which has a very stable structure and binds its substrates in a lock and key manner.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Others, for example p53 (not an enzyme), have much more structural placiticity - even to the point of being mostly disordered when not bound. They tend to be induced fit binders (of other proteins, not catalytic substrates) and often exploit that to bind a broader range of possible targets than lock and key proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The point is, it is a continuum between lock and key &amp;lt;-----&gt; induced fit rather than discrete classes you can sort proteins into.&lt;/p&gt;&#xA;" OwnerUserId="956" LastEditorUserId="956" LastEditDate="2012-06-04T16:08:44.280" LastActivityDate="2012-06-04T16:08:44.280" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2491" PostTypeId="1" CreationDate="2012-06-04T18:54:13.950" Score="6" ViewCount="1557" Body="&lt;p&gt;I've found several sources that state that overall, the cytosol of a cell is electrically neutral. The extracellular fluid is also purportedly electrically neutral. How can that be when we have membrane potentials?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also in that regard, how do the ion transporters that set up the membrane potential know when to stop pumping ions to get a certain potential set up?&lt;/p&gt;&#xA;" OwnerUserId="965" LastEditorUserId="43" LastEditDate="2012-06-05T19:26:37.627" LastActivityDate="2012-06-05T19:26:37.627" Title="Are the cytosol and extracellular fluids electrically neutral?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2492" PostTypeId="2" ParentId="2480" CreationDate="2012-06-04T19:33:21.210" Score="3" Body="&lt;p&gt;Amazingly, yes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://dx.doi.org/10.1093/nar/17.21.8485&quot; rel=&quot;nofollow&quot;&gt;High level gene expression in mammalian cells by a nuclear T7-phage RNA polymerase&lt;/a&gt;. The authors recognize that the T7 RNA polymerase tends to work only in the cytoplasm thus is unable to transcribe genes in the nucleus. To remedy this limitation, the T7 polymerase was fused to a nuclear location signal peptide to localize the polymerase correctly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Promega sells a T7 expression system for RNAi production. &lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-06-04T19:33:21.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2493" PostTypeId="1" AcceptedAnswerId="2515" CreationDate="2012-06-04T19:45:22.703" Score="3" ViewCount="757" Body="&lt;p&gt;I'm not even sure if this claim is true, but...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://answers.yahoo.com/question/index?qid=20080201004454AAKGOq5&quot; rel=&quot;nofollow&quot;&gt;This source&lt;/a&gt; states that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Caffeine gives both types of sperm a boost, but the Y-sperm would get a little more of a boost. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.babyhopes.com/articles/how-to-conceive-a-boy.html&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; reinforces the quote. In fact, this &quot;tip&quot; can be seen all over the internet to preferentially conceive a male rather than a female.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is how. &lt;strong&gt;What is happening at the molecular to increase the overall mobility of sperm?&lt;/strong&gt; It clearly wouldn't work as a neurotransmitter (as it &quot;normally&quot; works).&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-06-06T06:11:01.707" Title="Does caffeine increase the speed at which sperm travels?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2494" PostTypeId="2" ParentId="2489" CreationDate="2012-06-04T19:53:14.103" Score="4" Body="&lt;p&gt;Both models are true depending on how you frame the mechanisms of catalysis. As mentioned by @Blues, proteins are highly dynamic. In that manner, a protein will adopt both the unbound active state shown in the induced fit model and the complementary shape shown in the lock and key model. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(apologies since this is the only figure that I could find to explain this concept). Using the above description the induced fit model (E) will change its structure to the E&lt;em&gt;S model. In the lock and key model, the E state will be equivalent to the E&lt;/em&gt;S state. According to the below figure, this would imply that the E&lt;em&gt;S state always exists but as it is a few kcals higher in free energy, the state is rarely seen. Thermodynamically, this means that the &quot;lock&quot; always exists but it is an unstable configuration. When the substrate is added to the system, it will stablize the lock and thermodynamically favor an E&lt;/em&gt;S state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cmqgv.gif&quot; alt=&quot;Thermodynamics&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Long story short, the induced fit model is a good explanation of how enzymes morph into an active state but depending on how you frame the mechanism, you are always seeing a lock-key model (at least according to my enzymology professor). Unfortunately, the majority of biochemistry textbook continue to teach using the induced fit model since it is a much easier concept to understand given the majority of undergrads; and 1st year graduates' understanding of statistical thermodynamics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The induced fit model is more appropriately used to understand the mechanisms of substrate specificity. As hinted by your professor, enzymes will perform their function in the lock-key mechanism. This is true for many serine proteases which all do the exact same reaction. However, substrate specificity can be incorporated by unstabilizing the E*S complex which largely has to do with the E state.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-06-04T19:53:14.103" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2496" PostTypeId="2" ParentId="2491" CreationDate="2012-06-04T20:55:14.367" Score="6" Body="&lt;p&gt;Membrane potentials are caused by different concentrations of ions on opposite sides of membranes in micro-environments along the membrane. The membrane can be, overall,  electrically and chemically neutral with small areas that have differences in electrochemical gradients. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For cells to produce these potentials they have proteins embedded in the lipid membrane. Ion pumps are the main players in creating potentials and gradients; through active transport (the use of ATP) the protein moves ions from one side to the other. When the concentration of that area of membrane is at one concentration the proteins are held in one conformation (active or inactive) and when the gradient is changed or meets a threshold the protein changes conformation and becomes activated or inactivated. So the actual electrochemical gradient dictates when the proteins are transporting. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also other proteins/messengers that are produced which can interact with the transmembrane proteins that keep them in one configuration or another to facilitate the production of an action potential. Once again, when this specific concentration is met the signaling molecule/transporter will become inactivate or activated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is just stuff I recall from some classes. Honestly, wikipedia is a fine general knowledge source. And more detailed than my explanation.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Membrane_potential#Ions_and_the_forces_driving_their_motion&quot;&gt;http://en.wikipedia.org/wiki/Membrane_potential#Ions_and_the_forces_driving_their_motion&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="929" LastActivityDate="2012-06-04T20:55:14.367" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2497" PostTypeId="1" AcceptedAnswerId="2519" CreationDate="2012-06-04T22:33:41.157" Score="6" ViewCount="400" Body="&lt;p&gt;I am studying a case of tendinopathies induced by an alteration of how the extracellular matrix is being remodeled. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From my understanding there has to be a careful balance of MMP (metallproteinases) and TIMP enzymes to maintain tendon homeostasis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which cells produce these enzymes?&lt;/p&gt;&#xA;" OwnerUserId="952" LastEditorUserId="630" LastEditDate="2019-06-14T13:26:40.107" LastActivityDate="2019-06-14T13:26:40.107" Title="Which cells are responsible for the extracellular matrix remodeling?" Tags="&lt;cell-biology&gt;&lt;tendons&gt;&lt;extra-cellular-matrix&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2498" PostTypeId="1" AcceptedAnswerId="2502" CreationDate="2012-06-05T00:29:12.690" Score="23" ViewCount="10556" Body="&lt;p&gt;A few friends of mine told me that salt provides zero nutritional value to us, and in fact can harm our bodies. Now, these guys are medical students, and being an engineering student myself, I decided not to argue with them. The rest of this question assumes that this fact is true, so if it's not, you can just go ahead and call me out now...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So here's my understanding of things: we 'like' doing things because of our instincts, which have slowly become refined over millions of years. For example, I 'like' eating foods with fat in it because my instinct compels me to do so. Fat is 'good' for my body, since it provides a lot of energy (obesity problems aside).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So are there certain things, such as eating salt, that are not in fact beneficial in any way, and we only do these things because we were trained to as children? This is the only thing I could come up with, but it's not a very satisfying explanation for a few reasons. First, I think humans have been eating salt for a long time. This would mean that most likely, it is actually our 'instinct' to eat salt. Also, salt is eaten in every culture today, which has the same implication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So is there some better explanation?&lt;/p&gt;&#xA;" OwnerUserId="970" LastActivityDate="2016-03-15T10:44:29.847" Title="Why do we like salt?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2499" PostTypeId="1" AcceptedAnswerId="2501" CreationDate="2012-06-05T04:02:45.143" Score="7" ViewCount="490" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;From wikipedia article &lt;a href=&quot;http://en.wikipedia.org/wiki/Resting_potential&quot; rel=&quot;nofollow&quot;&gt;RESTING potential&lt;/a&gt;: &quot;there is no actual measurable charge excess in either side. That occurs because the effect of charge on electrochemical potential is hugely greater than the effect of concentration so an undetectable change in concentration creates a great change on electric potential.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;the effect of charge on electrochemical potential significantly larger then the effect of charge on concentration - is this a general statement or true in all cases?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if charge is more significant then concentration in influencing electrochemical potential why does a small change in concentration greatly effect electropotential? Or does it mean electrochemical potential? Either way how does it make any sense, is it correct or nonsense and what is the exact meaning behind the message?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;other questions I have:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) What is the reason Na+ stays at its location right across the barrier on the extracellular side of the membrane? Diffusion? Electrochemical potential? Electric Charge.. if so because of Attraction or Repulsion?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) If the answer is the electrochemical gradient/potential, because it is trying to move to a &quot;less&quot; positive potential.. if its located extracellularlly isn't that the &quot;great unknown&quot; where any molecules/cells/protein etc. are able to float by and possibly influence it? What happens if one of these has a &quot;LESS&quot; positive potential then the membrane that Na+ is currently attracted?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Why can't Na+ be used for the entire process to establish the same voltage interactions leading from resting to action potential (as long as thier was less concentration intracellularly... if it is about LESS positivity ..Or vice versa for K+?)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am preparing for ACSM certification exam, so any help is appreciated.&lt;/p&gt;&#xA;" OwnerUserId="972" LastEditorUserId="72" LastEditDate="2012-06-06T16:23:59.993" LastActivityDate="2013-11-01T12:15:30.840" Title="Understanding Membrane / Resting Potential from the perspective of ions?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2500" PostTypeId="2" ParentId="1115" CreationDate="2012-06-05T04:20:15.313" Score="9" Body="&lt;p&gt;There are a couple of answers to this question.  Especially where trees are concerned, you can graft &lt;a href=&quot;http://inventorspot.com/articles/lemon_tree_japan_bears_eleven_ki_9572&quot; rel=&quot;noreferrer&quot;&gt;two or more trees onto the same rootstock, or even a single limb into a tree&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if the graft takes, it won't behave too much more differently than just more branches of the same tree.  Structurally intertwining them will not be different than if you had just taken a single tree's branches to support each other.  The graft will usually only have a single set of roots, from the host tree.  They will not compete.  The tendency will be for the branches to grow apart so that they can independently get their own light.  This is very much like any other single tree.  Not sure about fusing two halves of a tree together - exposing the roots would tend to kill the tree or unsettle it. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="338" LastEditDate="2014-05-19T01:43:00.500" LastActivityDate="2014-05-19T01:43:00.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2501" PostTypeId="2" ParentId="2499" CreationDate="2012-06-05T06:42:10.020" Score="8" Body="&lt;p&gt;Ah, what a classic biophysics problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One first needs to understand how a membrane gets a potential. The lipid bilayer is a large sea of hydrophobic interactions that essentially prevents any ion from crossing. As a result, Na&lt;sup&gt;+&lt;/sup&gt; and K&lt;sup&gt;+&lt;/sup&gt; concentrations remain constant and different on the cytoplasmic side and the extracellular side. However, ions can pass through ion channels like the &lt;a href=&quot;http://en.wikipedia.org/wiki/Potassium_channel&quot; rel=&quot;nofollow&quot;&gt;K&lt;sup&gt;+&lt;/sup&gt; channel&lt;/a&gt;. It is important to understand that in K&lt;sup&gt;+&lt;/sup&gt; channels, only K&lt;sup&gt;+&lt;/sup&gt; can pass and these channels are actually selective against Na&lt;sup&gt;+&lt;/sup&gt; (answer to question 1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two potentials at work here. First is a chemical potential created by the flux of K&lt;sup&gt;+&lt;/sup&gt; from high K&lt;sup&gt;+&lt;/sup&gt; to low K&lt;sup&gt;+&lt;/sup&gt;. The second is a counteracting membrane potential created by a charge imbalance. Note, that the swapping of a few ions will &lt;strong&gt;a)&lt;/strong&gt; result in a negligible change in the concentration ie. the chemical potential, &lt;strong&gt;b)&lt;/strong&gt; result in a large change in the membrane potential. At some point, the flux out due to the chemical potential and the flux in due to the membrane potential will be equilvant and the cell will reach a &lt;strong&gt;resting potential&lt;/strong&gt; otherwise known at the &lt;strong&gt;Nernst potential&lt;/strong&gt; or &lt;strong&gt;equilibrium potential&lt;/strong&gt; (technically a steady state).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a cell depolarizes by closing these channels, the local charge will quickly go back to an equilibrium or a non-charged state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why K&lt;sup&gt;+&lt;/sup&gt; rather than Na&lt;sup&gt;+&lt;/sup&gt;? For typical cells, the extracellular concentration of Na&lt;sup&gt;+&lt;/sup&gt; is 145 mM and cytoplasmic is 12 mM. For K&lt;sup&gt;+&lt;/sup&gt;, it is 4 mM and 155 mM respectively. Doing the appropriate calculations of the Nerst potential, for Na&lt;sup&gt;+&lt;/sup&gt; it is +67 mV and for K&lt;sup&gt;+&lt;/sup&gt; it is -98 mV. Qualitatively we can see that this would result in vastly different things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of this information can be found from Pollard and Earnshaw's &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0721639976&quot; rel=&quot;nofollow&quot;&gt;Cell Biology&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="1320" LastEditDate="2013-11-01T12:15:30.840" LastActivityDate="2013-11-01T12:15:30.840" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2502" PostTypeId="2" ParentId="2498" CreationDate="2012-06-05T09:16:03.370" Score="28" Body="&lt;p&gt;In developed countries we usually consume enough salt (sodium to be exact) without actually adding table salt to food. Everything can become toxic when consumed in excess - even water - and when we frequently add more salt to foods, we tend to consume sodium in potentially harmful excess. That's what your friends are referring to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, salt (sodium) is one of the most essential substances your body needs to stay alive, for several reasons. One of the main purposes of sodium is the upkeep of blood's osmolarity (i.e. concentrations of osmotically active compounds. Higher salt concentration on one side of a permeable membrane attracts water to that side - I'm sure you've heard that before). There are numerous systems in your body to make sure the osmolarity of blood is correct. If they fail and blood becomes hypo or hypertonic, your cells will be sucked dry or pumped full of water and in either case, burst and die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look up the renin-angiotensin-aldosterone system for example: when the kidney filters blood, it reabsorbs or lets through water depending on the current blood osmolarity; leading to higher or lower amount of higher or lower concentrated urine. You drink lots, your blood is diluted, it becomes less tonic, kidney registers that and lets water through more, you urinate more. There are many more elements involved there, including blood pressure, nerve signals stimulating thirst or hunger of different kinds, some hormones etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, there's a reason why the basic infusion given in hospitals to replace lost blood quickly isn't just water but normal saline.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Delayed update to pick up some side aspects of your description: 1) There are of course things that humans do which have absolutely no value to them whatsoever. Anything that plays into the feel-good-reward-circuit in our brain can become such an unhelpful habit. Take smoking and drug consumption as examples. 2) About evolutionary relevance: Being a key player in maintaining body function, evolution selected for instictively liking salt. Simultaneously, most people will not like food that is extremely salty - a protective mechanism against excess.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2016-03-15T10:44:29.847" LastActivityDate="2016-03-15T10:44:29.847" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2503" PostTypeId="1" CreationDate="2012-06-05T13:52:05.413" Score="8" ViewCount="1846" Body="&lt;p&gt;My BIO 101 book states that when human cells convert glucose to ATP, the process is only approx 35% efficient, and much of the potential energy is lost as heat.  However, that heat is useful to us in maintaining our overall body temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cold-blooded animals (reptiles, for example) are not as effective at maintaining their own body temperature.  Does that imply that their cellular metabolism (conversion of glucose to ATP) is more efficient than humans, and thus doesn't produce as much heat?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is cold-blooded- / warm-blooded-ness completely unrelated to heat released during cellular metabolism?&lt;/p&gt;&#xA;" OwnerUserId="912" LastActivityDate="2012-06-26T16:27:13.377" Title="Is there a relationship between efficiency of cellular metabolism and warm-blooded-ness?" Tags="&lt;human-biology&gt;&lt;zoology&gt;&lt;cell-biology&gt;&lt;metabolism&gt;&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2504" PostTypeId="2" ParentId="1579" CreationDate="2012-06-05T16:17:07.597" Score="4" Body="&lt;p&gt;There is this guy, Martin Hanczyc, working on protocells to better understand how the beginning of life occurred. He makes synthetic protocells. They don't have any DNA in them but they are pretty cool and maybe the beginnings to making synthetic cells. Perhaps once science has figured out how cells began and their very minimal needs they can create completely synthetic cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ted.com/talks/martin_hanczyc_the_line_between_life_and_not_life.html&quot; rel=&quot;nofollow&quot;&gt;http://www.ted.com/talks/martin_hanczyc_the_line_between_life_and_not_life.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, just thinking, what would we consider completely synthetic cells? If we took synthetic protocells and they eventually evolved into a cell with DNA would that still be synthetic? &lt;/p&gt;&#xA;" OwnerUserId="929" LastActivityDate="2012-06-05T16:17:07.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2505" PostTypeId="1" AcceptedAnswerId="7805" CreationDate="2012-06-05T18:39:42.767" Score="6" ViewCount="370" Body="&lt;p&gt;Which are the factors that modify the overall gene differential expression by introducing a vector for single-gene overexpression?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you overexpress a gene for a protein involved in signal transduction (e.g., a kinase, scaffold, or receptor) by vector cell transfection, then you overdrive the cell using this signaling pathway, it's useful to isolate the pathway and study them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any way to modify the overall gene expression or cell differential expression pattern by gene transfection? I think this would work if you delivered a gene for overexpression in proteins involved for RNA processing (e.g., splicing, ribosomal proteins, etc.), RNA transcription (e.g., TFs) or protein translation.&lt;/p&gt;&#xA;" OwnerUserId="973" LastEditorUserId="57" LastEditDate="2012-07-31T07:25:31.900" LastActivityDate="2013-05-08T09:13:47.790" Title="Effect of single-gene overexpression in the cell's response" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;genomics&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2506" PostTypeId="1" AcceptedAnswerId="2508" CreationDate="2012-06-05T18:47:54.617" Score="4" ViewCount="143" Body="&lt;p&gt;Of all the synthetic hormones we use, estrogens are probably the most common.  They are used for birth control as well as hormone replacement therapy.  This researcher also shows that there is plenty of it in milk because &lt;a href=&quot;http://news.harvard.edu/gazette/2006/12.07/11-dairy.html&quot; rel=&quot;nofollow&quot;&gt;dairy cows are often pregnant while they are being milked&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Estrogen is a sturdy compound, very much like cholesterol.  I was wondering if anyone had any idea how long it would survive in the environment, given that some people are concerned about it interrupting animals life cycles.  How fast does it break down in the wild? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="16866" LastEditDate="2017-01-03T16:01:39.933" LastActivityDate="2017-01-03T16:01:39.933" Title="How quickly do estrogens break down in the environment?" Tags="&lt;biochemistry&gt;&lt;endocrinology&gt;&lt;environment&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2507" PostTypeId="1" AcceptedAnswerId="2520" CreationDate="2012-06-05T20:52:20.790" Score="15" ViewCount="791" Body="&lt;p&gt;What are they, and do they share a common ancestor? How far back in evolutionary time must we go to find them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If none are known, what computational tools might be used to search for such examples?&lt;/p&gt;&#xA;" OwnerUserId="889" LastEditorUserId="889" LastEditDate="2012-06-06T20:02:57.823" LastActivityDate="2012-09-13T15:01:40.960" Title="Are there any examples of proteins with no or minimal sequence identity, but highly similar structure?" Tags="&lt;proteins&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2508" PostTypeId="2" ParentId="2506" CreationDate="2012-06-05T21:35:44.647" Score="7" Body="&lt;p&gt;Months to years - although the actual duration in a specific environment depends on the nature of that environment and is tied to oxygen level. Higher oxygen, faster degradation. Less oxygen, the estrogen molecules interconvert among various closely related molecules which hampers both their detection and their degradation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more info, please see: &lt;a href=&quot;http://dx.doi.org/10.1038/485441a&quot;&gt;Environmental science: The hidden costs of flexible fertility&lt;/a&gt; (&lt;em&gt;Nature 485, 441 (24 May 2012)&lt;/em&gt;)  and &lt;a href=&quot;http://www.sciencedaily.com/releases/2012/06/120605113723.htm&quot;&gt;this Science Daily article&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="956" LastEditorUserId="69" LastEditDate="2012-06-05T22:14:39.950" LastActivityDate="2012-06-05T22:14:39.950" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2509" PostTypeId="1" AcceptedAnswerId="2573" CreationDate="2012-06-05T23:54:53.663" Score="3" ViewCount="208" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Possible Duplicate:&lt;/strong&gt;&lt;br&gt;&#xA;  &lt;a href=&quot;https://biology.stackexchange.com/questions/1981/how-many-genes-do-we-share-with-our-mother&quot;&gt;How many genes do we share with our mother?&lt;/a&gt;  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&#xA;&#xA;&lt;p&gt;I went to a lecture that talked about the behavior of social insects in terms of their relatedness of genes. For instance, workers were 3/4ths related to each other, so it was in their gene's interest to care for each other instead of having their own, half-related offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However isn't it the case that members of the same species are much more related than 1/2 or 3/4s? I've read that we share anywhere from 95-99% of our genes with chimpanzees. Also I believe I've read (perhaps in Pinker) that we share some 60% of our genes with daffodils.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when they talk about the relatedness of social insects, and they say it's 1/2 or 2/3 or 1/4, aren't they really talking about the 1% to 5% of genes that are in play in sexual reproduction within the species? In other words, aren't I 97% + 1/2 * 3% related to my sister, assuming human beings share 97% of our genes?&lt;/p&gt;&#xA;" OwnerUserId="976" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-10-18T18:00:05.883" Title="How distantly related are eusocial insects? Aren't members of a species much more related than 1/4, 1/2, or 3/4?" Tags="&lt;dna&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ClosedDate="2012-08-15T15:40:12.240" ContentLicense="CC BY-SA 3.0" />
  <row Id="2510" PostTypeId="2" ParentId="2507" CreationDate="2012-06-06T01:26:45.487" Score="10" Body="&lt;p&gt;This &lt;a href=&quot;http://dx.doi.org/10.1109/TCBB.2009.28&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; published last year, address the answer for your question, about computational methods, they mention 3 principal algorithms for structural alignment&#xA;of proteins:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Structural alignment directly at the level of C atoms. &lt;/li&gt;&#xA;&lt;li&gt;The second class of algorithms first uses the SSEs (Secondary Structure Elements) to carry out an approximate alignment, and then uses the C atoms.&lt;/li&gt;&#xA;&lt;li&gt;The final class of algorithms uses geometric hashing.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And finally you could find useful this &lt;a href=&quot;http://dx.doi.org/10.1098/rstb.2005.1801&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; for an example of this kind of analysis with structural analyses of metabolic families.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1109/TCBB.2009.28&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Venkateswaran JG, Song B, Kahveci T, Jermaine C&lt;/strong&gt;. TRIAL: a tool for finding distant structural similarities. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 8: 819–31.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1098/rstb.2005.1801&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Marsden RL, Ranea JAG, Sillero A, Redfern O, Yeats C, Maibaum M, Lee D, Addou S, Reeves GA, Dallman TJ, et al.&lt;/strong&gt;. 2006. Exploiting protein structure data to explore the evolution of protein function and biological complexity. Philosophical transactions of the Royal Society of London Series B, Biological sciences 361: 425–40.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="973" LastEditorUserId="836" LastEditDate="2012-09-12T17:56:44.323" LastActivityDate="2012-09-12T17:56:44.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2511" PostTypeId="2" ParentId="2459" CreationDate="2012-06-06T01:51:23.513" Score="2" Body="&lt;p&gt;For charge, you could check this one by sequence level, for example for Bovine Albumin (Uniprot: P02769) you can get the theoretical pI of 5.82, as the mean of pKa aminoacid values, to do this can use &lt;a href=&quot;http://web.expasy.org/protparam/&quot; rel=&quot;nofollow&quot;&gt;protparm&lt;/a&gt;, so when the pH &gt; pI, the protein has a net negative charge and when the pH &amp;lt; pI, the protein has a net positive charge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And there are only two organic polar solvents I known to work proteins, DMSO (pKa = 35) and&#xA;Dimethylformamide (DMF, pKa=-0.01 (20ºC))&lt;/p&gt;&#xA;" OwnerUserId="973" LastEditorUserId="973" LastEditDate="2012-06-06T01:58:26.047" LastActivityDate="2012-06-06T01:58:26.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2512" PostTypeId="1" CreationDate="2012-06-06T03:07:55.980" Score="7" ViewCount="813" Body="&lt;p&gt;I'm currently investigating ChIP-seq vs. ChIP-exo for finding binding sites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I can tell, ChIP-exo seems to be better in every way than ChIP-seq... but then again, I'm not strong in this area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any weaknesses in the ChIP-exo approach?&lt;/p&gt;&#xA;" OwnerUserId="321" LastEditorUserId="948" LastEditDate="2014-04-20T04:16:04.253" LastActivityDate="2014-04-20T04:16:04.253" Title="ChIP-seq vs ChIP-exo" Tags="&lt;dna-sequencing&gt;&lt;transcription&gt;&lt;protein-binding&gt;&lt;binding-sites&gt;&lt;chip&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2514" PostTypeId="2" ParentId="2457" CreationDate="2012-06-06T05:14:41.007" Score="3" Body="&lt;p&gt;The main effect, of vitamin B6, is neurological, becouse  moderate variations in the intracellular concentration of pyridoxal 5'-phosphate (PLP), the biologically active form of vitamin B6, can have pronounced modulatory effects on steroid-induced gene expression. So you cannot get the effect of stress hormones. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also neurological damage has been reported on doses from excess of 500 mg/d. Check this papers &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2661220&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/2661220&lt;/a&gt; and &lt;a href=&quot;http://www.fasebj.org/content/8/3/343.short&quot; rel=&quot;nofollow&quot;&gt;http://www.fasebj.org/content/8/3/343.short&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="973" LastActivityDate="2012-06-06T05:14:41.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2515" PostTypeId="2" ParentId="2493" CreationDate="2012-06-06T06:11:01.707" Score="4" Body="&lt;p&gt;The cell response for caffeine, is at the molecular level of RyR (Ryanodine receptor), and the main effect could be a temporal rise in Ca+2 cytosolic concentration, so it can change the electrical behavior for the whole cell, and then affect their mobility. But the main area for RyR research is at spermatogenesis, there are a lot of papers like &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9770782&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt;, for that topic&lt;/p&gt;&#xA;" OwnerUserId="973" LastActivityDate="2012-06-06T06:11:01.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2516" PostTypeId="1" CreationDate="2012-06-06T07:30:10.587" Score="8" ViewCount="131" Body="&lt;p&gt;Title says it all. I've been searching for the best way of collecting macrofaunal priapulids and would like advice on sampling methods and particularly sampling tools. Since large priapulids are usually found in low densities any form of grab-sampler would probably be inefficient and a dredge/trawl would be preferred. Any ideas on what tool(s) would sample at the right depth and filter efficiently? &lt;/p&gt;&#xA;" OwnerUserId="978" LastActivityDate="2012-07-05T22:13:34.523" Title="What would be the best dredging/trawling tools to collect macrofaunal priapulids?" Tags="&lt;marine-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2517" PostTypeId="2" ParentId="2507" CreationDate="2012-06-06T08:25:03.570" Score="5" Body="&lt;p&gt;The &lt;a href=&quot;http://www.eb.tuebingen.mpg.de/research/departments/protein-evolution.html&quot; rel=&quot;nofollow&quot;&gt;group of Andrei Lupas&lt;/a&gt; studies this. He argues that the vast majority of folds arose only once, so that proteins that share a fold are homologous, even if their sequences have diverged. See for example this paper: &quot;&lt;a href=&quot;http://dx.plos.org/10.1371/journal.pone.0027336&quot; rel=&quot;nofollow&quot;&gt;Evolutionary Relationships of Microbial Aromatic Prenyltransferases&lt;/a&gt;&quot; where they show that there are subtle sequence similarities between two protein families of the same fold, arguing for a common ancestor. &lt;/p&gt;&#xA;" OwnerUserId="112" LastEditorUserId="112" LastEditDate="2012-06-06T11:57:25.207" LastActivityDate="2012-06-06T11:57:25.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2519" PostTypeId="2" ParentId="2497" CreationDate="2012-06-06T11:35:43.023" Score="3" Body="&lt;p&gt;Taken from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&amp;amp;cmd=Search&amp;amp;doptcmdl=Citation&amp;amp;defaultField=Title%20Word&amp;amp;term=Belvisi%5Bauthor%5D%20AND%20The%20role%20of%20matrix%20metalloproteinases%20%28MMPs%29%20in%20the%20pathophysiology%20of%20chronic%20obstructive%20pulmonary%20disease%20%28COPD%29%3a%20a%20therapeutic%20role%20for%20inhibitors%20of%20MMPs?&quot; rel=&quot;nofollow&quot;&gt;The role of matrix metalloproteinases (MMPs) in the pathophysiology of chronic obstructive pulmonary disease&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Metalloelastase (MMP-12) is (as the name suggests) capable of&#xA;  degrading elastin, as well as other extra-cellular matrix components.&#xA;  It is produced predominantly by infiltrating macrophages and appears&#xA;  essential for macrophage migration through extra-cellular matrix&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK6598/&quot; rel=&quot;nofollow&quot;&gt;Matrix Metalloproteinases in Cancer Cell Invasion&lt;/a&gt; gives a more thorough description of the various MMP and TIMP types &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;MMPs are mainly produced by nonmalignant stromal cells in malignant&#xA;  tumors. Tumor cells also secrete factors, such as extracellular MMP&#xA;  inducer (EMMPRIN), which enhance the expression of MMPs by stromal&#xA;  fibroblasts (see Toole, in this book). In addition, growth factors and&#xA;  cytokines secreted by tumor-infiltrating inflammatory cells as well as&#xA;  by tumor or stromal cells modulate MMP expression.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="953" LastActivityDate="2012-06-06T11:35:43.023" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2520" PostTypeId="2" ParentId="2507" CreationDate="2012-06-06T13:48:09.930" Score="10" Body="&lt;p&gt;The answer is that common folds are discovered in sequences which are completely divergent where essentially no alignment can be found by conventional means.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;David Eisenberg's group created profiles based on alignments from known structures which were more sensitive to discovering whether a given protein sequence was related to a given structure, solving what he called the '&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8577692&quot;&gt;inverse folding problem&lt;/a&gt;'.  More recently &lt;a href=&quot;http://pfam.sanger.ac.uk/&quot;&gt;HMMs&lt;/a&gt; have been used from raw aligned sequences which are even more sensitive to predicting whether a given protein structural family can be found in a query sequence.  &lt;a href=&quot;http://www.ebi.ac.uk/Tools/sss/psiblast/&quot;&gt;PsiBlast&lt;/a&gt; also deserves a mention as a method that builds such a profile on the fly.  It can come back with sequences that are so divergent that they are probably not really related (personal experience).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A classic example of this is hexokinase, an enzyme that phosphorylates sugars - which shows up in single cell eukaryotes and all animals.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Hexokinase#Variation&quot;&gt;When the structure of actin was solved, it proved to have the same core fold as hexokinase.&lt;/a&gt;  Actin is one of the most venerable proteins known in eurkaryotes, so this is now called the actin fold.  None of the software mentioned above would detect this relationship. (I just verified this with psiblast). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its probably not true all the time, but it probably happens a lot that sequences with the same protein fold are so different that they cannot be detected by any of these means.  Most genomes that are sequenced have dozens or hundreds of 'novel genes' - 40% of E coli is still uncharacterized.  Either there are novel folds popping up spontaneously over short evolutionary time frames or the possible sequences for many protein folds is quite large.  My expectation is that a novel protein sequence can emerge with the same fold in quite quickly, especially in bacteria. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-06-06T13:48:09.930" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2521" PostTypeId="2" ParentId="2174" CreationDate="2012-06-06T15:27:11.617" Score="6" Body="&lt;p&gt;I can only answer for plants. The short answer is no, there is no central source of information of that kind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are basically asking about the sub-classifications economic botany and ethnobotany, which cover the economy and human uses of plants respectively. Neither field is particularly fast-paced, so you could simply keep up to date with the latest issues of journals like &lt;a href=&quot;http://www.springerlink.com/content/120950/?MUD=MP&quot;&gt;Economic Botany&lt;/a&gt; or &lt;a href=&quot;http://www.ethnobotanyjournal.org/&quot;&gt;Ethnobotany&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One key area of development for new valuable crops is in crop wild relatives, but there is no particular publication you should watch for that. Keep an eye on the &lt;a href=&quot;http://www.croptrust.org/main/&quot;&gt;Crop Trust&lt;/a&gt; as they will shortly be releasing, in collaboration with us (the Millennium Seed Bank) some reports and data about this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I wanted to keep up to date with all those things over time, I would set up some saved search alerts on Google Scholar for key search terms like 'emerging crop', 'new crop', 'crop wild relative', etc. Just perform a search on &lt;a href=&quot;http://scholar.google.com/&quot;&gt;Scholar&lt;/a&gt; and then click the envelope button to the right of the search field to create a recurring search alert.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One other potential source of information would be to check &lt;a href=&quot;http://faostat3.fao.org/home/index.html&quot;&gt;FAOSTAT&lt;/a&gt; each year. You can examine global and local data about area under cultivation, yield, investment, commodity value, etc. of most crops. If something new were to emerge as a big player, it would appear on there.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-06-06T15:27:11.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2523" PostTypeId="1" CreationDate="2012-06-06T22:03:01.673" Score="8" ViewCount="143" Body="&lt;p&gt;There are a number of articles regarding nonsteroidal anti-inflammatory drugs&#xA; (NSAIDs) having a negative effect on healing conditions like tendonosis and tendinitis. From what I understand the channel through which they reduce inflammation disrupts healing. In general, many of them constrict vessels, thus reducing bloodflow even further to tendons. Are there other reasons, or interactions they can have with  cells that may also disrupt healing?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there advantages of using NSAIDs to promote healing?&lt;/p&gt;&#xA;" OwnerUserId="952" LastEditorUserId="630" LastEditDate="2019-06-01T07:00:24.290" LastActivityDate="2019-06-23T22:12:10.883" Title="Can NSAIDs impact negatively the healing of tendons?" Tags="&lt;cell-biology&gt;&lt;tendons&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="2524" PostTypeId="2" ParentId="2469" CreationDate="2012-06-07T02:21:07.187" Score="4" Body="&lt;p&gt;You can easly calculate the absorbance from Beer's Law &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A = εlc&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here you can get the values for Extinction coefficient by sequence at &lt;a href=&quot;http://web.expasy.org/cgi-bin/protparam/protparam1?P02769@25-607@&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://web.expasy.org/cgi-bin/protparam/protparam1?P02769@25-607@&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for your example 0.001 g/L  3 g/L with this R code, you can get the absorbance values for each concentration.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt; PM &amp;lt;- 66432.9 #g/mol&#xA;&amp;gt; c &amp;lt;- seq(0.001,3,0.05) #get values from 0.001 to 3, by 0.05 increment&#xA;&amp;gt; V &amp;lt;- 1 #liters&#xA;&amp;gt; M = c((c/PM)/V)&#xA;&amp;gt; #Lambert Beer Law&#xA;&amp;gt; e &amp;lt;- 42925&#xA;&amp;gt; l &amp;lt;- 1&#xA;&amp;gt; A &amp;lt;- c(e*l*M)&#xA;&amp;gt; plot(A ~ c, ylab=&quot;A (280nm)&quot;, xlab=&quot;g/l&quot;)&#xA;&amp;gt; data.frame(&quot;conc&quot;=c, M=M, A=A)&#xA;    conc            M            A&#xA;1  0.001 1.505278e-08 0.0006461407&#xA;2  0.051 7.676919e-07 0.0329531753&#xA;3  0.101 1.520331e-06 0.0652602099&#xA;4  0.151 2.272970e-06 0.0975672445&#xA;5  0.201 3.025609e-06 0.1298742792&#xA;6  0.251 3.778248e-06 0.1621813138&#xA;7  0.301 4.530888e-06 0.1944883484&#xA;8  0.351 5.283527e-06 0.2267953830&#xA;9  0.401 6.036166e-06 0.2591024176&#xA;10 0.451 6.788805e-06 0.2914094522&#xA;11 0.501 7.541444e-06 0.3237164869&#xA;12 0.551 8.294083e-06 0.3560235215&#xA;13 0.601 9.046722e-06 0.3883305561&#xA;14 0.651 9.799361e-06 0.4206375907&#xA;15 0.701 1.055200e-05 0.4529446253&#xA;16 0.751 1.130464e-05 0.4852516599&#xA;17 0.801 1.205728e-05 0.5175586946&#xA;18 0.851 1.280992e-05 0.5498657292&#xA;19 0.901 1.356256e-05 0.5821727638&#xA;20 0.951 1.431520e-05 0.6144797984&#xA;21 1.001 1.506784e-05 0.6467868330&#xA;22 1.051 1.582047e-05 0.6790938676&#xA;23 1.101 1.657311e-05 0.7114009023&#xA;24 1.151 1.732575e-05 0.7437079369&#xA;25 1.201 1.807839e-05 0.7760149715&#xA;26 1.251 1.883103e-05 0.8083220061&#xA;27 1.301 1.958367e-05 0.8406290407&#xA;28 1.351 2.033631e-05 0.8729360753&#xA;29 1.401 2.108895e-05 0.9052431100&#xA;30 1.451 2.184159e-05 0.9375501446&#xA;31 1.501 2.259423e-05 0.9698571792&#xA;32 1.551 2.334687e-05 1.0021642138&#xA;33 1.601 2.409950e-05 1.0344712484&#xA;34 1.651 2.485214e-05 1.0667782830&#xA;35 1.701 2.560478e-05 1.0990853177&#xA;36 1.751 2.635742e-05 1.1313923523&#xA;37 1.801 2.711006e-05 1.1636993869&#xA;38 1.851 2.786270e-05 1.1960064215&#xA;39 1.901 2.861534e-05 1.2283134561&#xA;40 1.951 2.936798e-05 1.2606204908&#xA;41 2.001 3.012062e-05 1.2929275254&#xA;42 2.051 3.087326e-05 1.3252345600&#xA;43 2.101 3.162590e-05 1.3575415946&#xA;44 2.151 3.237854e-05 1.3898486292&#xA;45 2.201 3.313117e-05 1.4221556638&#xA;46 2.251 3.388381e-05 1.4544626985&#xA;47 2.301 3.463645e-05 1.4867697331&#xA;48 2.351 3.538909e-05 1.5190767677&#xA;49 2.401 3.614173e-05 1.5513838023&#xA;50 2.451 3.689437e-05 1.5836908369&#xA;51 2.501 3.764701e-05 1.6159978715&#xA;52 2.551 3.839965e-05 1.6483049062&#xA;53 2.601 3.915229e-05 1.6806119408&#xA;54 2.651 3.990493e-05 1.7129189754&#xA;55 2.701 4.065757e-05 1.7452260100&#xA;56 2.751 4.141020e-05 1.7775330446&#xA;57 2.801 4.216284e-05 1.8098400792&#xA;58 2.851 4.291548e-05 1.8421471139&#xA;59 2.901 4.366812e-05 1.8744541485&#xA;60 2.951 4.442076e-05 1.9067611831&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;And you can get this plot from 0.001 to 3 g/l for albumine&#xA;&lt;img src=&quot;https://i.stack.imgur.com/AnnDS.png&quot; alt=&quot;plot from 0.001 to 3 g/l&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now you can choose the desired concentration for the absorbance you wanna work with&lt;/p&gt;&#xA;" OwnerUserId="973" LastEditorUserId="973" LastEditDate="2012-06-07T02:33:41.197" LastActivityDate="2012-06-07T02:33:41.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2527" PostTypeId="1" AcceptedAnswerId="2538" CreationDate="2012-06-07T06:22:29.790" Score="37" ViewCount="2234" Body="&lt;p&gt;Hydroxyapatite is the main component of tooth enamel. It contains phosphorus in the form of phosphates, pyrophosphates etc. that are found to exhibit the the property of phosphorescence. But why don't the teeth glow in the dark ?&lt;/p&gt;&#xA;" OwnerUserId="947" LastEditorUserId="947" LastEditDate="2012-06-07T15:43:35.987" LastActivityDate="2016-08-20T02:14:36.367" Title="Why don't teeth glow?" Tags="&lt;human-biology&gt;&lt;teeth&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2528" PostTypeId="1" AcceptedAnswerId="2531" CreationDate="2012-06-07T06:25:58.097" Score="3" ViewCount="222" Body="&lt;p&gt;Recently I was playing a quiz and a question was asked about the color of the fur coat of a polar bear. To my surprise the answer was black. I thought it was yellowish white or creamy. Why so ?&lt;/p&gt;&#xA;" OwnerUserId="947" LastActivityDate="2012-06-07T16:39:03.733" Title="Color of the Fur coat of Polar bears" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2529" PostTypeId="1" AcceptedAnswerId="13742" CreationDate="2012-06-07T06:39:18.987" Score="8" ViewCount="552" Body="&lt;p&gt;&lt;em&gt;Not sure if this is the best stackexchange to ask...&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have not been able to find a decent database of fossils on the web, does one exist?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are some of the links I have found through Wikipedia and Google:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.paleoportal.org/index.php?globalnav=doing_paleo&amp;amp;sectionnav=more_submissions&amp;amp;state_id=0&amp;amp;submission_type_id=27&amp;amp;type_id=5&quot;&gt;http://www.paleoportal.org/index.php?globalnav=doing_paleo&amp;amp;sectionnav=more_submissions&amp;amp;state_id=0&amp;amp;submission_type_id=27&amp;amp;type_id=5&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.morphobank.org/index.php/Projects/Index&quot;&gt;http://www.morphobank.org/index.php/Projects/Index&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://research.amnh.org/paleontology/&quot;&gt;http://research.amnh.org/paleontology/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_fossil_sites&quot;&gt;http://en.wikipedia.org/wiki/List_of_fossil_sites&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.fossilsites.com/STATES/AB.HTM&quot;&gt;http://www.fossilsites.com/STATES/AB.HTM&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://inyo.coffeecup.com/site/ammonoids/ammonoids.html&quot;&gt;http://inyo.coffeecup.com/site/ammonoids/ammonoids.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.historicalclimatology.com/&quot;&gt;http://www.historicalclimatology.com/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://geonames.usgs.gov/pls/gnispublic/f?p=gnispq:3:4473291015495555::NO::P3_FID:354414&quot;&gt;http://geonames.usgs.gov/pls/gnispublic/f?p=gnispq:3:4473291015495555::NO::P3_FID:354414&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.scotese.com/earth.htm&quot;&gt;http://www.scotese.com/earth.htm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.trilobites.info/biostratigraphy.htm&quot;&gt;http://www.trilobites.info/biostratigraphy.htm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://burgess-shale.rom.on.ca/en/&quot;&gt;http://burgess-shale.rom.on.ca/en/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.fossilmuseum.net/FossilGalleries.htm&quot;&gt;http://www.fossilmuseum.net/FossilGalleries.htm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.kumip.ku.edu/cambrianlife/Utah-Online-Fossil-Exhibits&amp;amp;Collections.html&quot;&gt;http://www.kumip.ku.edu/cambrianlife/Utah-Online-Fossil-Exhibits&amp;amp;Collections.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ucmp.berkeley.edu/collections/catalogs.html&quot;&gt;http://www.ucmp.berkeley.edu/collections/catalogs.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://peabody.yale.edu/collections/search-collections?vp&quot;&gt;http://peabody.yale.edu/collections/search-collections?vp&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://books.google.com/books?id=Ezm1OA_s6isC&amp;amp;printsec=frontcover&amp;amp;dq=hartwig+primate&amp;amp;cd=1&amp;amp;hl=en#v=onepage&amp;amp;q&amp;amp;f=false&quot;&gt;http://books.google.com/books?id=Ezm1OA_s6isC&amp;amp;printsec=frontcover&amp;amp;dq=hartwig+primate&amp;amp;cd=1&amp;amp;hl=en#v=onepage&amp;amp;q&amp;amp;f=false&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;What are the best places to get fossil data and images of the fossils? Or are museums and textbooks the only alternative?&lt;/p&gt;&#xA;" OwnerUserId="985" LastEditorUserId="806" LastEditDate="2012-10-31T13:06:38.247" LastActivityDate="2013-12-01T19:56:45.090" Title="Is there a comprehensive database of fossils (with images) online?" Tags="&lt;evolution&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2530" PostTypeId="2" ParentId="2527" CreationDate="2012-06-07T07:24:36.717" Score="19" Body="&lt;p&gt;Firstly, phosphorus does not exhibit phosphorescence on its own (don't let words mislead you, they often don't mean what they seem like): See &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphorescence#Materials&quot;&gt;http://en.wikipedia.org/wiki/Phosphorescence#Materials&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphor#Standard_phosphor_types&quot;&gt;http://en.wikipedia.org/wiki/Phosphor#Standard_phosphor_types&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if phosphorus did do so on its own, it would not do so in the body because it is always (almost always?) present as phosphate (PO4-), and this again is most often incorporated in other compounds such as nucleotides.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-06-07T07:24:36.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2531" PostTypeId="2" ParentId="2528" CreationDate="2012-06-07T11:15:17.227" Score="9" Body="&lt;p&gt;The fur coats of polar bears are in fact clear tubes - not white fur as is often believed. It is their &lt;em&gt;skin&lt;/em&gt; that is black, to absorb the most warmth from the sun (and the clear tubes allow the majority of the light to pass through to the skin).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I recently watched the BBC's Frozen Planet TV series (with David Attenborough), where I heard the above answer. If you haven't already, I recommend watching it.&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-06-07T11:15:17.227" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2532" PostTypeId="5" CreationDate="2012-06-07T13:32:27.180" Score="0" Body="&lt;p&gt;Related tags: &lt;a href=&quot;/questions/tagged/human-anatomy&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;human-anatomy&amp;#39;&quot; rel=&quot;tag&quot;&gt;human-anatomy&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Questions concerned about the physiology of ears (i.e., &lt;em&gt;hearing&lt;/em&gt;) should consider the following tags as appropriate: &lt;a href=&quot;/questions/tagged/hearing&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;hearing&amp;#39;&quot; rel=&quot;tag&quot;&gt;hearing&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/sensation&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;sensation&amp;#39;&quot; rel=&quot;tag&quot;&gt;sensation&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/senses&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;senses&amp;#39;&quot; rel=&quot;tag&quot;&gt;senses&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/sensory-systems&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;sensory-systems&amp;#39;&quot; rel=&quot;tag&quot;&gt;sensory-systems&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="16866" LastEditDate="2020-01-02T19:44:21.103" LastActivityDate="2020-01-02T19:44:21.103" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="2533" PostTypeId="4" CreationDate="2012-06-07T13:32:27.180" Score="0" Body="Questions regarding the structure, morphology, and function of the human ear." OwnerUserId="86" LastEditorUserId="4101" LastEditDate="2013-10-31T19:28:14.543" LastActivityDate="2013-10-31T19:28:14.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2534" PostTypeId="5" CreationDate="2012-06-07T13:42:24.497" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hearing_%28sense%29&quot; rel=&quot;nofollow&quot;&gt;Hearing&lt;/a&gt; is the ability to perceive sound by detecting vibrations through an organ such as the ear. The inability to hear is called deafness.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="4101" LastEditDate="2013-10-31T19:06:57.413" LastActivityDate="2013-10-31T19:06:57.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2535" PostTypeId="4" CreationDate="2012-06-07T13:42:24.497" Score="0" Body="Hearing is the ability to perceive sound by detecting vibrations through an organ such as the ear." OwnerUserId="86" LastEditorUserId="4101" LastEditDate="2013-10-31T19:06:57.413" LastActivityDate="2013-10-31T19:06:57.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2536" PostTypeId="1" CreationDate="2012-06-07T13:58:46.153" Score="7" ViewCount="63137" Body="&lt;p&gt;(Sorry if this question is only partly biological)&lt;/p&gt;&#xA;&lt;p&gt;I have noticed that several cats (including the one that keeps sleeping in my house), are fond of the odor of bleach (eau de Javel) and chlorine.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Among examples, chlorine is used in small quantities in tape water and the cat is fond of licking the faucet in acrobatic positions even if there is mineral freshwater nearby.&lt;/p&gt;&#xA;&lt;p&gt;I was one day not careful enough using a bleach based gel cleaning product and some of it got on my hand. Even after cleaning my hands, they still had a bleach &amp;quot;perfume&amp;quot; and my cat cling to me and even cleaned my hands with his tongue for minutes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Why is this so ? Are there other animals known to have this taste ?&lt;/p&gt;&#xA;&lt;p&gt;Might it be in fact acquired through living with humans ?&lt;/p&gt;&#xA;&lt;p&gt;Is this potentially detrimental to their physiology ?&lt;/p&gt;&#xA;" OwnerUserId="207" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-26T01:27:24.153" Title="Why are (some) cats attracted by bleach?" Tags="&lt;zoology&gt;&lt;physiology&gt;&lt;perception&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2538" PostTypeId="2" ParentId="2527" CreationDate="2012-06-07T16:00:57.433" Score="32" Body="&lt;p&gt;Just to add a little more on the interface between optics and dentistry:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whilst teeth do not phosphoresce, they do in fact autofluoresce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The differential auto fluorescence of healthy tooth and carious tooth has been used for the early diagnosis of caries. (&lt;a href=&quot;http://www.jcd.org.in/article.asp?issn=0972-0707;year=2011;volume=14;issue=4;spage=418;epage=422;aulast=Gugnani&quot;&gt;Gugnani N, Pandit IK, Srivastava N, Gupta M, Gugnani S. Light induced fluorescence evaluation: A novel concept for caries diagnosis and excavation. J Conserv Dent 2011;14:418-22&lt;/a&gt; and &lt;a href=&quot;http://www.opticsinfobase.org/boe/abstract.cfm?uri=boe-2-1-149&quot;&gt;http://www.opticsinfobase.org/boe/abstract.cfm?uri=boe-2-1-149&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To see teeth glow, or rather, fluoresce, they should be illuminated with short wavelength light, like blue light (wavelength 450 nm) and the teeth will glow green, which will be visible if the the blue light is filtered out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also see &lt;a href=&quot;http://www.inspektor.nl/dental/qlfmain.htm#QLF%99%20Basic%20Principle&quot;&gt;http://www.inspektor.nl/dental/qlfmain.htm#QLF%99%20Basic%20Principle&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="798" LastEditorUserId="4101" LastEditDate="2013-09-25T13:26:26.243" LastActivityDate="2013-09-25T13:26:26.243" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2540" PostTypeId="2" ParentId="2512" CreationDate="2012-06-07T19:38:10.087" Score="4" Body="&lt;p&gt;ChIP-exo does seem to be the &quot;ChIP-seq killer.&quot; I've seen Dr. Pugh present it a few times, and the audience is pretty much always impressed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One thing I'd do if I were of the &quot;experimental bent&quot; would be to add random degenerate barcodes in the library prep to control for potential PCR artifacts. I imagine that since the &quot;peaks&quot; in ChIP-exo seem to be quite a bit narrower than ChIP-seq, I reckon it'd harder to use some coverage-in-local-neighborhood to remove such biases (assuming you wanted to do so).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To give you an idea of what I'm thinking of -- it would be somehow similar to what &lt;a href=&quot;http://www.pnas.org/content/109/4/1347/F1.expansion.html&quot; rel=&quot;nofollow&quot;&gt;is depicted here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2012-06-07T19:38:10.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2541" PostTypeId="1" AcceptedAnswerId="2542" CreationDate="2012-06-07T21:23:30.877" Score="4" ViewCount="20198" Body="&lt;p&gt;I read that both hemoglobin and ferritin are for storing iron in the body. So, what is the difference between them in terms of storing/binding iron?&lt;/p&gt;&#xA;" OwnerUserId="989" LastEditorUserId="6" LastEditDate="2012-06-08T05:52:43.750" LastActivityDate="2017-06-15T14:43:52.803" Title="What is the functional difference between hemoglobin and ferritin?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2542" PostTypeId="2" ParentId="2541" CreationDate="2012-06-07T22:22:54.937" Score="8" Body="&lt;p&gt;Hemoglobin is the protein of erythrocytes (red blood cells) which has ferrous ions (Fe2+) bound in its subunits. These are able to keep oxygen bound which enables the cell to transport oxygen through the circulation. It's not really for storage of iron, it's for using it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ferritin#Iron_storage&quot; rel=&quot;nofollow&quot;&gt;Ferritin&lt;/a&gt; is the actual storage protein, cells express it to store iron in case of deficiency and also to regulate the amount they have in the cell. According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16448386&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;, it's mainly expressed in muscle, liver and kidney cells (but I'm not too sure about the details of that study so I might have got that wrong).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: just found this in one of my old lectures; unfortunately it doesn't quote sources: ferritin stores iron in liver and heart. The total iron in the body is ~3.9g, of which 2.5g are in use in hemoglobin, 500mg in stores (an additional 250mg in the liver), 150mg in bone marrow, 300mg in myoglobin and 150mg in other enzymes. The remaining 5mg are bound to transferrin in the plasma.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-06-09T23:39:42.360" LastActivityDate="2012-06-09T23:39:42.360" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2543" PostTypeId="2" ParentId="2536" CreationDate="2012-06-07T22:31:14.283" Score="9" Body="&lt;p&gt;I can't give a definite answer, and there's nothing in the literature about this specifically, but perhaps some relevant information and a suggested behavioural experiment will help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt; &lt;br&gt;&#xA;Firstly, I assume you are talking about sodium hypochlorite (which is usually what people mean by bleach)? If so, there are several compounds your cat could be reacting to. Chlorine is an obvious candidate, which is released as sodium hypochlorite decomposes in solution. Additionally, bleach can react with various organic materials to release a variety of volatile organic compounds (VOCs), which your cat might be able to smell. In addition to also releasing chlorine gas, the same suite of VOCs are released when the chlorine in chlorinated tap water reacts with organic contaminants (Odabasi, 2008). The VOCs include chloroform and carbon tetrachloride.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next, cats are known to exhibit modified behaviour in response to a variety of compounds. Some are suspected pheromone components of cat urine, such as felinine (Hendriks et al, 1995) and its breakdown products, such as MMB (Miyazaki et. al, 2006). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some cats also react to externally-produced compounds with a particular response called the 'catnip response', which involves rubbing the face on the ground or other objects, shaking the head, rolling, etc. (Tucker &amp;amp; Tucker, 1988). Not all cats exhibit the response, around 50-50% do, and susceptibility is genetic and heritable. Some sources eliciting the catnip response include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;nepetalactone released from catnip (&lt;em&gt;Nepeta cataria&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;li&gt;actinidine released from valerian (&lt;em&gt;Valeriana officinalis&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;li&gt;essential oil of &lt;em&gt;Actinidia macrosperma&lt;/em&gt; (Zhao et al., 2006)&lt;/li&gt;&#xA;&lt;li&gt;the compounds epinepetalactone, dihydronepetalactone, isodihydronepetalactone, neonepetalactone, iridomyrmecin, boschnialactone, onikulactone, boschniakine, actinidiolide and dihydroactinidiolide (Tucker &amp;amp; Tucker, 1988)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In general all the catnip response elicitors share a two-ring structure, which is not to my knowledge shared by any of the volatiles given off by bleach.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A possible experiment&lt;/strong&gt;&lt;br&gt;&#xA;So, two obvious possibilities (regarding what type of behavioural response is being elicited) are that either:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;your cat is interpreting the volatile as a pheremone and therefore as some sort of sexual or territorial signal, or&lt;/li&gt;&#xA;&lt;li&gt;it is showing the catnip response&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;As a first experiment, you could check whether your cat (and any others you can get hold of - in an ethical way) respond to bleach and/or to catnip. If the cats do not exhibit the catnip response to catnip, they aren't exhibiting it in response to bleach, and thus some other explanation is more likely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a second experiment, you could make a detailed observation of the precise behaviour shown in response to bleach. Compare it to that exhibited when the cats encounter catnip (depending on the outcome of the first experiment) and when they are oestrous (if female) or encounter an oestrous female (if male). You could also compare to the response to the urine of other (male and female, familiar and unfamiliar) cats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;An experiment you shouldn't do&lt;/strong&gt;&lt;br&gt;&#xA;If you wanted to find out which chemical your cat is responding to, you could allow your cat to sniff pure chlorine which hasn't encountered organic contaminants, as well as chloroform, and carbon tetrachloride. However, &lt;strong&gt;all three of those compounds are extremely dangerous&lt;/strong&gt; and could easily kill you or your cat, so please don't. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I general, I would caution against exposing your cat to bleach, because it can induce serious health effects depending on dose and mode of exposure, ranging from asthma to third-degree burns to carcinogenesis. If they are attracted to it, that is a good reason to keep it away from them to prevent them ingesting it, which is more harmful than inhaling the fumes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't comment on whether the behaviour is acquired as result of domestication, but that too could be tested by comparing the reaction of a large sample of wild cats (!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0305049195001301&quot;&gt;Hendriks, Wouter H., Paul J. Moughan, Michael F. Tarttelin, and Anthony D. Woolhouse. “Felinine: a Urinary Amino Acid of Felidae.” Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 112, no. 4 (December 1995): 581–588.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cell.com/chemistry-biology/abstract/S1074-5521%2806%2900309-7&quot;&gt;Miyazaki, Masao, Tetsuro Yamashita, Yusuke Suzuki, Yoshihiro Saito, Satoshi Soeta, Hideharu Taira, and Akemi Suzuki. “A Major Urinary Protein of the Domestic Cat Regulates the Production of Felinine, a Putative Pheromone Precursor.” Chemistry &amp;amp; Biology 13, no. 10 (October 1, 2006): 1071–1079.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1021/es702355u&quot;&gt;Odabasi, Mustafa. “Halogenated Volatile Organic Compounds from the Use of Chlorine-Bleach-Containing Household Products.” Environ. Sci. Technol. 42, no. 5 (2008): 1445–1451.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.springerlink.com/content/f613756573257t02/abstract/&quot;&gt;Tucker, Arthur, and Sharon Tucker. “Catnip and the Catnip Response.” Economic Botany 42, no. 2 (1988): 214–231.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1559795/&quot;&gt;Zhao, Yun-peng, Xiao-yun Wang, Zhi-can Wang, Yin Lu, Cheng-xin Fu, and Shao-yuan Chen. “Essential Oil of Actinidia Macrosperma, a Catnip Response Kiwi Endemic to China.” Journal of Zhejiang University. Science. B 7, no. 9 (September 2006): 708–712.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-06-07T22:41:29.570" LastActivityDate="2012-06-07T22:41:29.570" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2544" PostTypeId="1" CreationDate="2012-06-08T01:33:34.853" Score="2" ViewCount="210" Body="&lt;p&gt;I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is my running command:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;python scripts/oases_pipeline.py -m 25 -M 29 -o output -d &quot; -strand_specific -shortPaired data/reads.fa&quot; -p &quot; -min_trans_lgth 100 -ins_length 300&quot;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;My library is strand-specific and pair-ended with length 67bp. The reads are shuffled as:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt;0(left_mate_forwarded)&#xA;ACTC...&#xA;&amp;gt;1(right_mate_reverse_complemented)&#xA;TATA...&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I got some transcripts, but are far from the transcripts annotated, also far from the result of Trinity. The longest contig from Oases is ~2500bp (vs. ~10000bp from cufflinks and ~6000bp from Trinity). The N50 value is also low. It only reports 20 contigs those cover full-length of some transcripts from Cufflinks (totally ~4000), while Trinity reports ~650.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The dataset I am using is a subset of &lt;em&gt;S. pombe&lt;/em&gt;. Does it matter?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could somebody help me point out whether something wrong here?&lt;/p&gt;&#xA;" OwnerUserId="790" LastEditorUserId="6" LastEditDate="2012-06-09T12:38:11.600" LastActivityDate="2012-06-09T12:38:11.600" Title="Too few transcripts from transcriptome assembler Oases" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;&lt;rna-sequencing&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2545" PostTypeId="2" ParentId="2223" CreationDate="2012-06-08T05:55:41.497" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20671182&quot;&gt;This study&lt;/a&gt; in E.coli is useful in setting out some additional issues at play here, in a system where post-translational modifications are basically a non-issue.  The authors see clearly a correlation between mRNA and Protein levels (Fig. 3C) and theorize that differences translation rate and protein turnover are responsible for differences in protein level for two genes with similar mRNA level.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They investigate the issue on a single-cell level and find no correlation between a single cell's mRNA level and protein level for a given gene (Fig. 4).  This is attributed to the time-scale separation between mRNA turnover (usually a few minutes) and protein turnover (in many cases degradation is so slow, protein turnover is driven by dilution/cell division).  One way to understand this is there are several &quot;generations&quot; of mRNA contributing to a the population of protein at a given moment, which is not inconsistent with the central dogma.  However this result raises serious problems for using mRNA as a proxy for protein in comparing single-cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However generally, in populations of bacteria, using mRNA as a proxy for protein works pretty well, especially when comparing levels of a gene under perturbations.  Unless we believe translation or protein degradation is affected mRNA level should be a good proxy, though there can be issues with using this quantitatively because regulation is often not linear (i.e. double mRNA doesn't produce double protein).  See, for example, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17713988&quot;&gt;sRNA regulation&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="991" LastActivityDate="2012-06-08T05:55:41.497" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2546" PostTypeId="1" AcceptedAnswerId="2559" CreationDate="2012-06-08T06:20:40.527" Score="9" ViewCount="2640" Body="&lt;p&gt;My initial objection is that nose filters air, mouth is for eating but is used for breathing also, plus they both are used to create sounds. What is the cause and reason in this case, why do we need two &quot;holes&quot; and one is not good enough?&lt;/p&gt;&#xA;" OwnerUserId="941" LastActivityDate="2012-06-10T05:17:38.797" Title="How and why did mouth and nasal cavity evolve separate?" Tags="&lt;evolution&gt;&lt;human-anatomy&gt;&lt;language&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2547" PostTypeId="1" AcceptedAnswerId="3560" CreationDate="2012-06-08T06:27:18.680" Score="9" ViewCount="1745" Body="&lt;p&gt;I came to wonder this when studying language (as well as other same theme question posted just few ago). For example the word &quot;fantastic&quot; we use upper teeth and lower lip to produce F sound, instead of using lower teeth and upper lip, which would work as well with a small practice.&lt;/p&gt;&#xA;" OwnerUserId="941" LastActivityDate="2012-09-16T05:08:09.870" Title="Why are we using upper teeth and lower lip on labiodental sounds?" Tags="&lt;human-anatomy&gt;&lt;language&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2549" PostTypeId="1" AcceptedAnswerId="2550" CreationDate="2012-06-08T09:01:17.870" Score="0" ViewCount="6432" Body="&lt;p&gt;Roughly, what I know is, when we eat food it goes into our: Stomach &gt; Small Intestine &gt; Large Intestine &gt; Rectum. So, it just moves through a digestive pipe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I don't understand is, &lt;strong&gt;what part of the food is responsible for blood's color and how does the food that we eat mixes with blood?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="994" LastEditorUserId="16866" LastEditDate="2017-04-03T17:55:34.110" LastActivityDate="2019-05-25T16:32:46.413" Title="What part of food gives the blood red color?" Tags="&lt;human-biology&gt;&lt;food&gt;&lt;hematology&gt;&lt;digestive-system&gt;&lt;pigmentation&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2550" PostTypeId="2" ParentId="2549" CreationDate="2012-06-08T11:02:17.790" Score="19" Body="&lt;p&gt;The red colour of blood isn't actually to do with food at all.  The primary purpose of the blood is to carry oxygen to all the cells that require it to release energy.  Red Blood Cells are filled with an iron containing pigment called &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemoglobin&quot; rel=&quot;noreferrer&quot;&gt;haemoglobin&lt;/a&gt;.  When it has oxygen bonded to it, haemoglobin  has a bright red colour - it is this that gives blood its red colour.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of how food enters the bloodstream, it is first broken down into extremely small constituents.  This is done by mechanical action (i.e. chewing and the squeezing movement of your digestive system) and by chemical action through the use of enzymes.  Enzymes are proteins that are secreted by various glands in the mouth (and are therefore contained in saliva), stomach and both intestines.  These chemically break large food molecules down into small products such as glucose (sugar) and amino acids (protein-building blocks) amongst other things.  These then move across the wall of the intestines and into the bloodstream, which are separated by only one cell:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4n3bt.gif&quot; alt=&quot;Diagram of villus&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately that's the best image I could find.  The intestine is everything outside of the pink layer (which is the wall of the intestine).  The small molecules are able to pass through the pink layer and straight into the blood stream.  The picture shows a fold in the wall of the gut, which increases its surface area so allows more molecules to diffuse across.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2013-06-30T22:46:25.020" LastActivityDate="2013-06-30T22:46:25.020" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2551" PostTypeId="2" ParentId="2549" CreationDate="2012-06-08T13:01:26.300" Score="5" Body="&lt;p&gt;In essence, some of your food contains iron (especially red meat). This is taken up by your body and integrated into the haemoglobin protein which red blood cells contain in high amounts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The iron in haemoglobin can bind oxygen (it does this when it passes through the lungs) which enables the red blood cell to carry it through your blood circulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The colour of blood comes from this haemoglobin. When the iron is binding oxygen, it is red. Otherwise, blueish-red. (&lt;a href=&quot;http://www.ebi.ac.uk/interpro/potm/2005_10/Page1.htm&quot; rel=&quot;noreferrer&quot;&gt;http://www.ebi.ac.uk/interpro/potm/2005_10/Page1.htm&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-06-08T13:01:26.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2552" PostTypeId="2" ParentId="935" CreationDate="2012-06-08T13:50:07.643" Score="30" Body="&lt;p&gt;Great question, and one about which there has historically been a lot of speculation, and there is currently a lot of misinformation. I will first address the two answers given by other users, which are both incorrect but have been historically suggested by scientists. Then I will try to explain the current understanding (which is not simple or complete). My answer is derived directly from the literature, and in particular from Mable (2004), which in turn is part of the &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/bij.2004.82.issue-4/issuetoc&quot;&gt;2004 special issue of the Biological Journal of the Linnean Society&lt;/a&gt; tackling the subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The 'sex' answer...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In 1925 HJ Muller addressed this question in a famous paper, &quot;Why polyploidy is rarer in animals than in plants&quot; (Muller, 1925). Muller briefly described the phenomenon that polyploidy was frequently observed in plants, but rarely in animals. The explanation, he said, was simple (and is approximate to that described in Matthew Piziak's answer):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;animals usually have two sexes which are differentiated by means of a process involving the diploid mechanism of segregation and combination whereas plants-at least the higher plants-are usually hermaphroditic.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Muller then elaborated with three explanations of the mechanism:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;He assumed that triploidy was usually the intermediate step in chromosome duplication. This would cause problems, because if most animals' sex was determined by the ratios of chromosomes (as in Drosophila), triploidy would lead to sterility. &lt;/li&gt;&#xA;&lt;li&gt;In the rare cases when a tetraploid was accidentally created, it would have to breed with diploids, and this would result in a (presumably sterile) triploid.&lt;/li&gt;&#xA;&lt;li&gt;If, by chance, two tetraploids were to arise and mate, they would be at a disadvantage because, he said, they would be randomly allocated sex chromosomes and this would lead to a higher proportion of non-viable offspring, and thus the polyploid line would be outcompeted by the diploid.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, whilst the first two points are valid facts about polyploids, the third point is incorrect. A major flaw with Muller's explanation is that it only applies to animals with chromosomal ratio-based sex determination, which we have since discovered is actually relatively few animals. In 1925 there was comparatively little systematic study of life, so we really didn't know what proportion of plant or animal taxa showed polyploidy. Muller's answer doesn't explain why most animals, e.g. those with Y-dominant sex determination, exhibit relatively little polyploidy. Another line of evidence disproving Muller's answer is that, in fact, polyploidy is very common among dioecious plants (those with separate male and female plants; e.g. Westergaard, 1958), while Muller's theory predicts that prevalence in this group should be as low as in animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The 'complexity' answer...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another answer with some historical clout is the one given by Daniel Standage in his answer, and has been given by various scientists over the years (e.g. Stebbins, 1950). This answer states that animals are more complex than plants, so complex that their molecular machinery is much more finely balanced and is disturbed by having multiple genome copies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This answer has been soundly rejected (e.g. by Orr, 1990) on the basis of two key facts. Firstly, whilst polyploidy is unusual in animals, it does occur. Various animals with hermaphroditic or parthenogenetic modes of reproduction frequently show polyploidy. There are also examples of Mammalian polyploidy (e.g. Gallardo et al., 2004). In addition, polyploidy can be artificially induced in a wide range of animal species, with no deleterious effects (in fact it often causes something akin to hybrid vigour; Jackson, 1976).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also worth noting here that since the 1960s Susumo Ohno (e.g. Ohno et al. 1968; Ohno 1970; Ohno 1999) has been proposing that vertebrate evolution involved multiple whole-genome duplication events (in addition to smaller duplications). There is now significant evidence to support this idea, reviewed in Furlong &amp;amp; Holland (2004). If true, it further highlights that animals being more complex (itself a large, and in my view false, assumption) does not preclude polyploidy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The modern synthesis...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And so to the present day. As reviewed in Mable (2004), it is now thought that:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Polyploidy is an important evolutionary mechanism which was and is probably responsible for a great deal of biological diversity.&lt;/li&gt;&#xA;&lt;li&gt;Polyploidy arises easily in both animals and plants, but reproductive strategies might prevent it from propagating in certain circumstances, rather than any reduction in fitness resulting from the genome duplication.&lt;/li&gt;&#xA;&lt;li&gt;Polyploidy may be more prevalent in animals than previously expected, and the imbalance in data arises from the fact that cytogenetics (i.e. chromosome counting) of large populations of wild specimens is a very common practise in botany, and very uncommon in zoology.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In addition, there are now several new suspected factors involved in ploidy which are currently being investigated:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Polyploidy is more common in species from high latitudes (temperate climates) and high altitudes (Soltis &amp;amp; Soltis, 1999). Polyploidy frequently occurs by the production of unreduced gametes (through meiotic non-disjunction), and it has been shown that unreduced gametes are produced with higher frequency in response to environmental fluctuations. This predicts that polyploidy should be more likely to occur in the first place in fluctuating environments (which are more common at higher latitudes and altitudes).&lt;/li&gt;&#xA;&lt;li&gt;Triploid individuals, the most likely initial result of a genome duplication event, in animals and plants often die before reaching sexual maturity, or have low fertility. However, if triploid individuals do reproduce, there is a chance of even-ploid (fertile) individuals resulting. This probability is increased if the species produces large numbers of both male and female gametes, or has some mechanism of bypassing the triploid individual stage. This may largely explain why many species with 'alternative' sexual modes (apomictic, automictic, unisexual, or gynogenetic) show polyploidy, as they can keep replicating tetraploids, thus increasing the chance that eventually a sexual encounter with another tetraploid will create a new polyploid line. In this way, non-sexual species may be a crucial evolutionary intermediate in generating sexual polyploid species. Species with external fertilisation are more likely to establish polyploid lines - a greater proportion of gametes are involved in fertilisation events and therefore two tetraploid gametes are more likely to meet.&lt;/li&gt;&#xA;&lt;li&gt;Finally, polyploidy is more likely to occur in species with assortative mixing. That is, when a tetraploid gamete is formed, if the genome duplication somehow affects the individual so as to make it more likely that it will be fertilised by another tetraploid, then it is more likely that a polyploid line will be established. Thus it may be partly down to evolutionary chance as to how easily a species' reproductive traits are affected. For example in plants, tetraploids often have larger flowers or other organs, and thus are preferentially attractive to pollinators. In frogs, genome duplication leads to changes in the vocal apparatus which can lead to immediate reproductive isolation of polyploids.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Furlong, R.F. &amp;amp; Holland, P.W.H. (2004) Polyploidy in vertebrate ancestry: Ohno and beyond. Biological Journal of the Linnean Society. 82 (4), 425–430.&lt;/li&gt;&#xA;&lt;li&gt;Gallardo, M.H., Kausel, G., Jiménez, A., Bacquet, C., González, C., Figueroa, J., Köhler, N. &amp;amp; Ojeda, R. (2004) Whole-genome duplications in South American desert rodents (Octodontidae). Biological Journal of the Linnean Society. 82 (4), 443–451.&lt;/li&gt;&#xA;&lt;li&gt;Jackson, R.C. (1976) Evolution and Systematic Significance of Polyploidy. Annual Review of Ecology and Systematics. 7209–234.&lt;/li&gt;&#xA;&lt;li&gt;Mable, B.K. (2004) ‘Why polyploidy is rarer in animals than in plants’: myths and mechanisms. Biological Journal of the Linnean Society. 82 (4), 453–466.&lt;/li&gt;&#xA;&lt;li&gt;Muller, H.J. (1925) Why Polyploidy is Rarer in Animals Than in Plants. The American Naturalist. 59 (663), 346–353.&lt;/li&gt;&#xA;&lt;li&gt;Ohno, S. (1970) Evolution by gene duplication.&lt;/li&gt;&#xA;&lt;li&gt;Ohno, S. (1999) Gene duplication and the uniqueness of vertebrate genomes circa 1970–1999. Seminars in Cell &amp;amp; Developmental Biology. 10 (5), 517–522.&lt;/li&gt;&#xA;&lt;li&gt;Ohno, S., Wolf, U. &amp;amp; Atkin, N.B. (1968) EVOLUTION FROM FISH TO MAMMALS BY GENE DUPLICATION. Hereditas. 59 (1), 169–187.&lt;/li&gt;&#xA;&lt;li&gt;Orr, H.A. (1990) ‘Why Polyploidy is Rarer in Animals Than in Plants’ Revisited. The American Naturalist. 136 (6), 759–770.&lt;/li&gt;&#xA;&lt;li&gt;Soltis, D.E. &amp;amp; Soltis, P.S. (1999) Polyploidy: recurrent formation and genome evolution. Trends in Ecology &amp;amp; Evolution. 14 (9), 348–352.&lt;/li&gt;&#xA;&lt;li&gt;Stebbins, C.L. (1950) Variation and evolution in plants.&#xA;Westergaard, M. (1958) The Mechanism of Sex Determination in Dioecious Flowering Plants. In: Advances in Genetics. Academic Press. pp. 217–281.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;(I'll come back and add links to the references later)&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-06-08T13:50:07.643" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2553" PostTypeId="1" AcceptedAnswerId="2562" CreationDate="2012-06-08T18:06:27.060" Score="4" ViewCount="308" Body="&lt;p&gt;Are there substances that can promote TIMP enzyme production, or MMP enzyme production or supression in tendons?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there medical tests that measure quantities of MMP and TIMP enzymes in tendons?&lt;/p&gt;&#xA;" OwnerUserId="952" LastEditorUserId="69" LastEditDate="2012-06-18T15:28:59.550" LastActivityDate="2012-06-18T15:28:59.550" Title="Regarding TIMP and MMP enzymes" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2554" PostTypeId="1" AcceptedAnswerId="2556" CreationDate="2012-06-08T19:49:14.850" Score="8" ViewCount="200" Body="&lt;p&gt;In genetics, does the word &quot;polymorphism&quot; properly refer to genes, to phenotypes, or both? For example, if there are two alleles that lead to differences in the structure of the D2 neuroreceptor, would I talk about &quot;a polymorphism in the gene for the D2 neuroreceptor&quot; or &quot;a polymorphism in the D2 neuroreceptor&quot;? I've seen both uses in the literature, but it's not my primary field, so I don't have a feel for whether one is more widely accepted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bonus question: is there a preference regarding &quot;polymorphism of,&quot; &quot;polymorphism in,&quot; and &quot;polymorphism on&quot;? &lt;/p&gt;&#xA;" OwnerUserId="827" LastEditorUserId="69" LastEditDate="2012-06-08T20:37:36.213" LastActivityDate="2012-06-09T02:43:46.097" Title="Does the word &quot;polymorphism&quot; refer to the gene, the phenotype, or both?" Tags="&lt;genetics&gt;&lt;nomenclature&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2555" PostTypeId="1" AcceptedAnswerId="2557" CreationDate="2012-06-08T20:10:06.890" Score="3" ViewCount="757" Body="&lt;p&gt;I've always simply assumed quaternary structure to be characterized by non-covalent interactions such as hydrogen bonding, van der Waals interactions and whatnot. However, if two distinct polypeptides were &lt;em&gt;only&lt;/em&gt; connected by one covalent disulfide bridge, would this be considered as quaternary structure, assuming that non-covalent interactions between the subunits are either negligible or even repulsive?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, &lt;strong&gt;can a disulfide bridge, on its own, convey quaternary structure?&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a side note, are there any notable examples of this type of interaction?&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-06-08T21:06:24.743" LastActivityDate="2012-06-09T01:27:15.507" Title="Two subunits connected by only one disulfide bridge: quaternary structure?" Tags="&lt;proteins&gt;&lt;structural-biology&gt;&lt;protein-binding&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2556" PostTypeId="2" ParentId="2554" CreationDate="2012-06-08T20:55:04.150" Score="9" Body="&lt;p&gt;The term &quot;polymorphism&quot; itself is more generally defined as &quot;&lt;em&gt;the quality or state of existing in or assuming different forms&lt;/em&gt;&quot; (&lt;a href=&quot;http://www.merriam-webster.com/dictionary/polymorphism&quot;&gt;Merriam-Webster dictionary&lt;/a&gt;). So I guess semantically, it would be correct to say that there is polymorphism in a gene that can occur in different allelic variants, or polymorphism in phenotype because of variant traits (such as sexual dimorphism).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, when biologists today speak of polymorphisms, often they refer to variations at the level of individual nucleotides (single nucleotide polymorphisms or SNPs; some people use the terms polymorphism and SNP interchangeably). These SNPs have become popular for genotyping and for correlation with a variety of diseases or other observable phenotypes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And regarding the bonus question, I think &quot;polymorphism in&quot; is the most correct usage--it's definitely the most widely used. For example, you could say &quot;there is a polymorphism in nucleotide 257 of...&quot; or simply &quot;there is polymorphism in nucleotide 257 of...&quot; or even &quot;nucleotide 257 of ... exhibits polymorphism&quot;.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2012-06-08T21:13:27.573" LastActivityDate="2012-06-08T21:13:27.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2557" PostTypeId="2" ParentId="2555" CreationDate="2012-06-08T23:36:49.543" Score="4" Body="&lt;p&gt;I don't know of any examples of this but I would say no doubt, that's quarternary structure. Quarternary isn't so much defined by the kind of interaction but much more the fact that it's between different polypeptides; all lower-level structures are within one polypeptide. (&lt;a href=&quot;http://en.wikipedia.org/wiki/Protein_quaternary_structure&quot; rel=&quot;nofollow&quot;&gt;Wikipedia agrees&lt;/a&gt;.)&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-06-08T23:36:49.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2558" PostTypeId="2" ParentId="2555" CreationDate="2012-06-09T01:27:15.507" Score="2" Body="&lt;p&gt;I've always just gone with the name hetereodimer but there isn't any technical reason why it isn't a quaternary structure. As for an example, I work with antibody fragments or FAbs and cys-diabodies which are exactly that, two distinct polypeptides that are connected by a disulfide bond linkage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These do have a significant amount of non-covalent interactions. For something with less, maybe ricin?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-06-09T01:27:15.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2559" PostTypeId="2" ParentId="2546" CreationDate="2012-06-09T01:36:10.237" Score="11" Body="&lt;p&gt;Neither the nostrils nor the mouth originally evolved for breathing.  Fish have (two pairs of) nostrils which they use to smell and mouths which they use to eat, but they breathe through their gills.  Some lobe-finned fishes (the ancestors to tetrapods) evolved a connection between the posterior nostrils and the oral cavity called choanae.  A fossil called Kenichthys is a transitional form in this development.  The evolutionary reasons behind this development are not particularly well understood.  (This should not be surprising when discussing something that happened in the Devonian.  It's only recently that the discovery of Kenichthys ended the controversy of whether chonae in tetrapods are homologous to posterior nostrils in fish.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basal reptiles have nostrils and mouths and can breathe through both of them, but do not have a separation between the oral and nasal cavities.  The next important development is a secondary palate (which separates the nasal and oral cavities).  This allows animals to continue breathing while swallowing food.  Animals without such a separation must hold their breath while swallowing.  This ability is certainly useful in many situations, and unsurprisingly several solutions to this problem have evolved in different lineages.&lt;/p&gt;&#xA;" OwnerUserId="997" LastEditorUserId="997" LastEditDate="2012-06-10T05:17:38.797" LastActivityDate="2012-06-10T05:17:38.797" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2560" PostTypeId="2" ParentId="937" CreationDate="2012-06-09T02:14:15.697" Score="52" Body="&lt;p&gt;Richard's answer is fantastic, and I'm not going to be as thorough.  But here's some other examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Turtles (which did sea to land to sea back to land!)  &lt;/li&gt;&#xA;&lt;li&gt;Gastropoda (snails and slugs)&lt;/li&gt;&#xA;&lt;li&gt;Tardigrada (water bears)&lt;/li&gt;&#xA;&lt;li&gt;Onychophora (velvet worms)&lt;/li&gt;&#xA;&lt;li&gt;Planaria (flatworms)&lt;/li&gt;&#xA;&lt;li&gt;Annelida (annelid worms)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Together with Richard's examples that includes all the examples of &lt;a href=&quot;http://en.wikipedia.org/wiki/Terrestrial_animal&quot;&gt;terrestrial animals&lt;/a&gt; given at wikipedia.&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2012-06-09T02:14:15.697" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2561" PostTypeId="2" ParentId="2554" CreationDate="2012-06-09T02:43:46.097" Score="0" Body="&lt;p&gt;A difference in phenotypes might result from polymorphisms, but one doesn't refer to those differences as polymorphisms.&lt;/p&gt;&#xA;" OwnerUserId="1001" LastActivityDate="2012-06-09T02:43:46.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2562" PostTypeId="2" ParentId="2553" CreationDate="2012-06-09T03:22:50.230" Score="2" Body="&lt;p&gt;For your first question&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both enzymes, are components of Epidermal growth factor receptor (EGFR) signalling pathway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MMP is a matrix metalloproteinase, that triggers EGFR signalling, this can be done by a mechanism called transactivation &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WkH9W.jpg&quot; alt=&quot;transactivation&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, A signal from G-coupled receptor, or cytokine receptor could activate the cleavage of MMP,  then MMP converts to a ligand for EGFR activation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example Angiotensin II type 1 receptor (AT1R) and type 2 receptor (AT2R) which are GPCR, there are evidence for crosstalk with EGFR, look for this &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022282800912720&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper&lt;/a&gt;. This could be linked with hypertension or inflamation. Also cancer, could trigger EGFR receptors by NMP's.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And finally tissue inhibitors of metalloproteinases (TIMPs) are the negative regulator of MMP's&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This are only an overview of the whole biological process involving MMP, so I think there is no single answer to your question, but you can delimit the topic for a specific disease, and look for papers at google scholar. &lt;/p&gt;&#xA;" OwnerUserId="973" LastActivityDate="2012-06-09T03:22:50.230" CommentCount="2" CommunityOwnedDate="2012-06-09T03:22:50.230" ContentLicense="CC BY-SA 3.0" />
  <row Id="2563" PostTypeId="2" ParentId="2134" CreationDate="2012-06-09T08:29:38.070" Score="4" Body="&lt;p&gt;There are various studies on the mechanism of action of dopamine beta-hydroxylase (DBH).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This review (sorry, non-free article) by Kaufman and Friedman was written less than 10 years after the discovery of the reaction of conversion of tyrosine into [nor]adrenaline in the adrenal gland:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14294032&quot; rel=&quot;nofollow noreferrer&quot;&gt;DOPAMINE BETA-HYDROXYLASE&lt;/a&gt; - Kaufman S., Friedman S. - Pharmacol Rev. &lt;strong&gt;1965&lt;/strong&gt; Jun;17:71-100.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It makes for an interesting read, as they start detailing the history of our knowledge on adrenaline synthesis (well, at least at that point in time!), the various hypotheses and models that were thought of, experiments with radioactive labeled precursors and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They then procede to talk about the mechanism of the enzyme. Without going too much in detail, they report experiments showing that oxygen, ATP and Mg&lt;sup&gt;++&lt;/sup&gt; stimulate dopamine beta-hydroxylase enzymatic activity, with the following note on Mg&lt;sup&gt;++&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] Mg&lt;sup&gt;++&lt;/sup&gt; is required for the uptake of catecholamines by the adrenal vesicles. EDTA inhibits the uptake of the precursor, hydroxytyramine, but does not inhibit the enzymatic conversion to norepinephrine if the vesicles are intact. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They also list the requirement for two cofactors: ascorbate and copper&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first indication that Dopamine-beta-hydroxylase is a mixed-function oxidase was the demonstration of a requirement for ascorbate. It was found that this reducing agent&#xA;  could stimulate the hydroxylation reaction even in adrenal particles, and the requirement for ascorbate became more pronounced as the enzyme was purified.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Bringing to the reaction:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dopamine + ascorbate + O&lt;sub&gt;2&lt;/sub&gt; → L-norepinephrine + dehydroascorbate + H&lt;sub&gt;2&lt;/sub&gt;O &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For the Cu:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Only recently, however, was the enzyme obtained in a pure state and the metal characterized by direct analysis. The metal is copper and it is present in a concentration of 0.65 to 1.0 ug per mg enzyme (4 to 7 moles of copper per mole of protein). It can be removed by treatment with concentrated potassium cyanide. This copper-free enzyme is inactive but can be reactivated by addition of Cu.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They then proceed to detail some basic mechanism of action, which I will not report here for briefness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few years later, researchers from the same group authored a book chapter for the American Chemical Society entitled:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ba-1968-0077.ch073&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Mechanism of Action of Dopamine β-Hydroxylase&lt;/a&gt; - Kaufman S., Bridgers W.F., Baron J - in &lt;a href=&quot;http://pubs.acs.org/isbn/9780841200784&quot; rel=&quot;nofollow noreferrer&quot;&gt;Oxidation of Organic Compounds&lt;/a&gt;, Chapter 73, pp 172–176, &lt;strong&gt;1968&lt;/strong&gt; - Chapter DOI: 10.1021/ba-1968-0077.ch073&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the abstract (I do not have access to the full text of this):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dopamine β-hydroxylase catalyzes the side-chain hydroxylation of dopamine and other phenylethylamine derivatives. Ascorbic acid serves as a specific electron-donating cofactor. The enzyme from bovine adrenal glands contains Cu&lt;sup&gt;2+&lt;/sup&gt; and a smaller amount of Cu&lt;sup&gt;+&lt;/sup&gt;. When the enzyme oxidizes ascorbate to dehydroascorbate, most of the Cu&lt;sup&gt;2+&lt;/sup&gt; is reduced to Cu&lt;sup&gt;+&lt;/sup&gt;. Added substrate is hydroxylated, and Cu+ is reoxidized to Cu&lt;sup&gt;2+&lt;/sup&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To get to some more recent years... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this review&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11028916&quot; rel=&quot;nofollow noreferrer&quot;&gt;New insights into copper monooxygenases and peptide amidation: structure, mechanism and function.&lt;/a&gt; - Prigge ST, Mains RE, Eipper BA, Amzel LM. - Cell Mol Life Sci. &lt;strong&gt;2000&lt;/strong&gt; Aug;57(8-9):1236-59.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A mechanism for Peptidylglycine alpha-hydroxylating monooxygenase (PHM; EC 1.14.17.3) is proposed, and  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Since PHM is homologous in sequence and mechanism to dopamine beta-monooxygenase (DBM; EC 1.14.17.1), the enzyme that converts dopamine to norepinephrine during catecholamine biosynthesis, these structural and mechanistic insights are extended to DBM.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/A8IzG.jpg&quot; alt=&quot;DBM mechanism&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A structure of PHM along with a modeling of DBH is shown in Fig 14. You can see the two catalytic copper atoms and the possible binding of dopamine to the site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6syM5.jpg&quot; alt=&quot;PHM structure and DBH model&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They also show a mechanism of action for PHM. Essentially, through the oxydation of ascorbate the Cu&lt;sup&gt;++&lt;/sup&gt; becomes Cu&lt;sup&gt;+&lt;/sup&gt; and can then bind an oxygen molecule that will be used to hydroxylate the product:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TNndc.jpg&quot; alt=&quot;PHM mechanism&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, a detailed computational model of the enzyme, and its active site is shown in this paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026509&quot; rel=&quot;nofollow noreferrer&quot;&gt;Structural Insight of Dopamine β-Hydroxylase, a Drug Target for Complex Traits, and Functional Significance of Exonic Single Nucleotide Polymorphisms&lt;/a&gt; - Kapoor A, Shandilya M, Kundu S - PLoS One. &lt;strong&gt;2011&lt;/strong&gt;;6(10):e26509. Epub 2011 Oct 20.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The active site is shown in Fig. 7, where you can clearly see the two copper atoms in purple and green, the most important aminoacids at the active site and two water molecules in red:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0026509.g007&amp;amp;representation=PNG_M&quot; rel=&quot;nofollow noreferrer&quot;&gt;Active site of DBH http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0026509.g007&amp;amp;representation=PNG_M&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 10C shows the interaction of dopamine with the aa of the active site (Fig 10A and B show superposition between rat and human enzymes and Fig 10D shows the interaction of a drug with the enzyme):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0026509.g010&amp;amp;representation=PNG_M&quot; rel=&quot;nofollow noreferrer&quot;&gt;Residues important for catalysis http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0026509.g010&amp;amp;representation=PNG_M&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Finally, a remark on your question. You say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Evolutionarily speaking - the enzyme has evolved to add OH to the beta-carbon rather than somewhere else.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As I said somewhere else: not everything has an evolutionary explication, and evolution is not finalistic. This specific enzyme structure appeared at some point and it was evidently working fairly well, and at the time the rest of the pathway may or may not have been like it is at present, but the important thing is that the enzymatic network managed to work together. It could had well evolved to hydroxylate another position, but probably in that case we would have different enzymes downstream. The important thing to remember is that the enzyme did NOT evolve with the &lt;em&gt;finality&lt;/em&gt; of oxydating the beta carbon.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="3340" LastEditDate="2014-10-31T13:16:43.057" LastActivityDate="2014-10-31T13:16:43.057" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2564" PostTypeId="1" AcceptedAnswerId="3094" CreationDate="2012-06-09T20:35:30.197" Score="8" ViewCount="1244" Body="&lt;p&gt;It is said that the human body turns over all cells or molecules in 7 year cycles. This is not quite correct, because there are different organs changing at different speeds. My interest is what is the scale of change and especially, is it possible to measure and how fast do:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) cells change&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) molecules change&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) atoms change&lt;/p&gt;&#xA;&#xA;&lt;p&gt;High, medium and max rate organ examples would be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="941" LastEditorUserId="806" LastEditDate="2012-06-09T20:53:39.387" LastActivityDate="2012-08-01T16:15:59.930" Title="How fast do different organs turn over cells?" Tags="&lt;human-biology&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2565" PostTypeId="1" AcceptedAnswerId="2590" CreationDate="2012-06-09T21:38:11.613" Score="3" ViewCount="984" Body="&lt;p&gt;I read this in a paper&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Keller and Ross describe their greenbeard gene as an ‘&lt;strong&gt;outlaw&lt;/strong&gt;’.&#xA;  Admittedly, the comment is only made in passing, but are they correct?&#xA;  In this context &lt;strong&gt;an outlaw is usually defined as a gene whose action&#xA;  favours itself, but opposes the reproductive interests of the&#xA;  individual organism.&lt;/strong&gt; Where there are outlaws, natural selection at&#xA;  different loci is pulling the organism in different directions.&#xA;  Theoretically speaking, green-beard genes...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes: &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0140175083901562&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0140175083901562&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically loving your children is outlaw because it makes you sacrifice resources for your children. However, if your interest is defined as maximizing the number of children, then it's just your stuff working properly. Outlaw genes will be something that makes you die for a cause or stuff like that I suppose.&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="554" LastEditDate="2012-06-11T09:02:42.717" LastActivityDate="2012-06-12T05:16:52.853" Title="What are samples of &quot;Outlaw Genes&quot;" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2566" PostTypeId="2" ParentId="1981" CreationDate="2012-06-09T21:43:11.340" Score="3" Body="&lt;p&gt;Say x is the percentage of an allele in your mom (or cousin, or brother). Say c is the filial similarity (brother=.5, son=.5, cousins=.125, etc.) of the allele. Say y is the general probability of having that allele in that population (assuming mom is the same species with you). Say f(x,y) is the expected value of the number of allele that you have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then f(x,y)= c * x+ (1-c) *y&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other word. There is no contradiction in the idea that we are 98% similar with monkeys and yet only 50% similar with our own mom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here, the world similar is used in totally different sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;f(x,y) is 99% for most allele. Now let gy(x)=f(x,y) then&lt;/p&gt;&#xA;&#xA;&lt;p&gt;gy'(x) is c.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other word, for every allele your mom have, it'll improve the expected value of you having the same allele by half. For each allele your cousin has, it'll improve the expected value of you having the same allele by 1/8th. That is for the same y. For &lt;strong&gt;most y&lt;/strong&gt;, similarity is 100% nevertheless.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Say Ann, Beth, and Cindy has AA, Aa, and aa alleles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then Ann's sons have 25% higher expected value of having A alleles than Beth, and Beth have 25% higher expected value of having A alleles than Cindy. I say nothing of actual probability distribution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ann's cousins have .0625% higher expected value of A occurrence than Beth's cousins and .125% expected value of A occurrence than Cindy's cousins&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disclaimer: We do not take into account that people mate with those who are genetically similar but not too similar (i.e. no inbreeding).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way to see this is to look at y. For rare genes y is small. Hence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;50-50 is for genes that are &lt;strong&gt;rare&lt;/strong&gt; and family specific. If your mother is color blind (100% carrier), the expected value of the number of color blind carrier is improved by 50%. It doesn't mean you'll be color blind. We'll have to go to the technicality of dominant vs recessive. But that's the idea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For genes that are &lt;strong&gt;NOT rare&lt;/strong&gt;, say genes that make you have 2 feet and 2 hand, you still share all your mom's genes. That's because everybody have that. Your mom have that, and your dad have that, and so is everyone else, including chimps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this what most directly answer your question?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again the issue is rarity. For rare genes P(You have it|mom have it) is 50%.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For common genes, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;P(You have it|mom have it) = P(You have it and mom have it)/P(mom have it). //By bayesian rule&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is 1/1, which is true.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's just obvious, probability = 1, that everybody has it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: selfish gene by Richard Dawkins&#xA;I am a mathematician. Now prove me wrong.&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="5005" LastEditDate="2013-12-09T14:40:20.063" LastActivityDate="2013-12-09T14:40:20.063" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2567" PostTypeId="1" CreationDate="2012-06-10T06:48:08.013" Score="5" ViewCount="8673" Body="&lt;p&gt;As far as I know for evolution to work mutations  are necessary. Mutations are the raw material on which natural selection works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But mutations are always completely random and human beings have no control over it.Then my question is how artificial selection works? Would it have been possible to domesticate dogs from wolves, if there would have been no mutations in wolves to begin with?&lt;/p&gt;&#xA;" OwnerUserId="1003" LastEditorUserId="3952" LastEditDate="2013-08-08T00:16:47.363" LastActivityDate="2017-12-05T23:29:18.583" Title="How does Artificial Selection work?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;ethnobiology&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2568" PostTypeId="1" CreationDate="2012-06-10T06:56:51.170" Score="3" ViewCount="151" Body="&lt;p&gt;What exactly does the term Haplogroup or Haplotype means?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is it claimed that people belonging to the same haplogroups have common ancestors?&lt;/p&gt;&#xA;" OwnerUserId="1003" LastActivityDate="2012-06-10T07:52:28.440" Title="What are Haplogroups?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2569" PostTypeId="2" ParentId="2567" CreationDate="2012-06-10T07:38:18.653" Score="6" Body="&lt;p&gt;You seem to have a few different concepts in there...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But mutations are always completely random and human beings have no control over it.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Aside from the fact that mutations are not completely random (not always, at least), it is not true that humans have no control over them. Imagine you grow plants, and you start to cross those plants that have a larger stalk, allowing them to be more resistent to wind: you are effectively selecting a certain mutation. Surely, you cannot choose which specific sequence you want to mutate, but still you are enriching your population of plants with a specific mutation.&#xA;Nowadays of course you can specifically mutate the genome in the lab, but that is a different matter.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Would it have been possible to domesticate dogs from wolves, if there would have been no mutations in wolves to begin with?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Note that artificial selection has been used to generate the different breeds of dogs, by breeding animals with specific characters.&lt;br&gt;&#xA;However, domestication is a different matter. Wolves and dogs are the same species (&lt;em&gt;Canis lupus&lt;/em&gt;) and domestication is not strictly dependent on selective breeding. You can domesticate an &lt;strong&gt;adult&lt;/strong&gt; animal without inducing mutations in its DNA. Probably &lt;a href=&quot;http://en.wikipedia.org/wiki/Epigenetics&quot;&gt;epigenetics&lt;/a&gt; plays an important role there, and epigenetic patterns could possibly be &lt;a href=&quot;http://en.wikipedia.org/wiki/Transgenerational_epigenetics&quot;&gt;transmitted to the offspring&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, then you will use selective breeding to expand the domesticated population, and to select those traits you are interersted into. With artificial selection you are just selecting the mutations you want, the way you generate them is irrelevant to the matter: for instance you can irradiate plants to enhance mutation rate, and consequently the appearance of new favorable traits.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2012-06-10T07:50:52.117" LastActivityDate="2012-06-10T07:50:52.117" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="2570" PostTypeId="2" ParentId="2567" CreationDate="2012-06-10T07:40:23.717" Score="2" Body="&lt;p&gt;Accumulated mutations over generations will make up the genetic variation present in a population for a species. For example, wolves naturally had a certain amount of genetic variation, or diversity, before humans started domesticating wolves. They still do, but to a lesser extend now since their populations have decreased.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Artificial selection is different from natural selection in that is forced artificially by us, humans, upon a species, like wolves, to change the traits to our liking. The first few traits that were artificially selected from wolves were probably related to their behavior: being more submissive and less erratic in their behavior. Then different people started crossing different breeds with interesting traits to try and combine the desired traits into new breeds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the consequences of such dramatic breeding efforts is a decrease in haplotype diversity in dog breeds and higher incidence of undesired diseases. That is, during the crossing of breeds, part of the natural variability in the original populations was lost, and the resulting breeds only had one identical haplotype (in both copies) for many areas of the genome where there used to be two distinct ones, and if that haplotype was bearing an allele for a recessive disease, it showed up in homozygosis. This is the reason why for many important species of plants and animals, there are efforts to try and keep the original wild populations alive, in case we need to draw from the genetic diversity when the domesticated breeds need more. &lt;/p&gt;&#xA;" OwnerUserId="787" LastActivityDate="2012-06-10T07:40:23.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2571" PostTypeId="2" ParentId="2568" CreationDate="2012-06-10T07:52:28.440" Score="3" Body="&lt;p&gt;I understand haplogroup as the group of people that share the same given haplotype for a region of the genome.&#xA;A haplotype is the readout of the DNA sequence for a part of the genome in one of the two copies that diploid organisms have. If you start reading the DNA sequence for a given point in the genome from one of your copies and someone else's copies, it will coincide up until a point where there is a change. It is more probable to have longer identical haplotypes if the two people that are compared are related. The closest the relation, the longer their haplotypes will be identical. What breaks haplotype identity are recombination events that happen in the germinal line in the previous generation, and mutations that happen both in the germinal line and the soma (the rest of your body) along time. &lt;/p&gt;&#xA;" OwnerUserId="787" LastActivityDate="2012-06-10T07:52:28.440" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2572" PostTypeId="2" ParentId="2509" CreationDate="2012-06-10T08:02:39.623" Score="0" Body="&lt;p&gt;The part that is probably specific to this question is that some species of insects divide their population in the reproducing individuals, that are usually diploid and the working individuals, that are sometimes haploids, meaning they only have one copy of their set of chromosomes. This means that the workers have about half the amount of DNA material compared to reproducing individuals, although they share that copy in full with the diploid individuals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are variations of this mechanism in different species. Some species keep the copies but epigenetically &quot;shut down&quot; one of the copies. Others shed specific bits of the genome in the somatic cells. Sometimes this loss of DNA is not perfect, so different parts of the genome are lost just by chance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We humans don't lose any material at all, we just epigenetically &quot;shut down&quot; one of the X chromosomes in XX individuals -- females.&lt;/p&gt;&#xA;" OwnerUserId="787" LastActivityDate="2012-06-10T08:02:39.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2573" PostTypeId="2" ParentId="2509" CreationDate="2012-06-10T09:47:50.447" Score="3" Body="&lt;p&gt;In evolutionary genetic comparison, you are talking about members within species. They will share almost &lt;em&gt;all&lt;/em&gt; genes, because if they didn't they would belong to a different species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, within species there exist different &lt;em&gt;versions&lt;/em&gt; of the same genes, called 'alleles'. When we say that you are 0.5 related to each of your parents, we mean that statistically, 50% of your alleles should be those which your father has, and 50% of your alleles are those passed down from your mother.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eusocial insects have different mechanisms. Bee males are produced without fertilisation, meaning that they only have one copy of each bee gene. When the male produces sperm, it only has this one set, so all sperms end up carrying the same set of alleles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Females on the other hand have the normal double set, with two different versions of each gene. So if you look at one gene, half of the female's egg should have one version and the other half should have the other version. All females of one hive are produced by the same queen and the one male that she mated with. Remember, the male only has one set, so the versions coming from the male are the same in all female offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means a female's genes are made up of: 50% from the father (these are the same across all females) and 50% from the mother (where half the females have one version and half have the other version). Statistically, this means that looking at one gene, there is a 75% chance that two bees will have the same version of that gene.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-06-10T09:47:50.447" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2574" PostTypeId="1" AcceptedAnswerId="2612" CreationDate="2012-06-10T11:09:11.753" Score="15" ViewCount="2133" Body="&lt;p&gt;The main paper for the &lt;em&gt;Plasmodium palciparum&lt;/em&gt; genome project (Gardner et al., 2002) repeatedly mentioned that the unusually high A+T content (~80%) of the genome caused problems. For example they imply that it prevented them using a clone-by-clone approach:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Also, high-quality large insert libraries of (A + T)-rich P. falciparum DNA have never been constructed in Escherichia coli, which ruled out a clone-by-clone sequencing strategy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And that it made gene annotation difficult:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The origin of many candidate organelle-derived genes could not be conclusively determined, in part due to the problems inherent in analysing genes of very high (A + T) content. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt;&lt;BR&gt;&#xA;What is the biological significance of high A+T content, and why would it cause problems in genome sequencing?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Ref:&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://dx.doi.org/10.1038/nature01097&quot;&gt;Gardner, M.J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R.W., Carlton, J.M., Pain, A., Nelson, K.E., Bowman, S., Paulsen, I.T., James, K., Eisen, J.A., Rutherford, K., et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 419 (6906), 498–511.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="1320" LastEditDate="2013-06-30T18:49:07.703" LastActivityDate="2016-02-15T21:10:28.727" Title="Why did high A+T content create problems for the Plasmodium falciparum genome project?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;genomics&gt;" AnswerCount="5" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2575" PostTypeId="2" ParentId="2574" CreationDate="2012-06-10T14:23:10.553" Score="6" Body="&lt;p&gt;I can't comment on how A+T richness complicates the sequencing process itself, but I can comment on complications that arise when annotating the sequence. &lt;em&gt;Ab initio&lt;/em&gt; gene predictors are often based on hidden Markov models that are very sensitive to base composition in the genome (di-nucleotides, tri-nucleotides, etc). These gene finders typically perform very poorly if they are run on a genome that has a much different base composition than the one on which it was trained. This could explain some of the difficulty they has with analyzing genes in the genome.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-06-10T14:23:10.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2576" PostTypeId="2" ParentId="1303" CreationDate="2012-06-10T17:08:27.710" Score="2" Body="&lt;p&gt;If the yeast strain A is auxotrophic for AA 1 and the yeast strain B is auxotrophic for AA 2, neither would be able to grow in minimal medium by itself. But combined they complement the lack of AA1 in strain A by strain B and vice versa. That is metabolic complementation.&lt;/p&gt;&#xA;" OwnerUserId="1004" LastActivityDate="2012-06-10T17:08:27.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2577" PostTypeId="2" ParentId="2567" CreationDate="2012-06-10T17:41:31.147" Score="8" Body="&lt;p&gt;Both natural selection and artificial selection require genetic variation in the underlying population to work.  The exact source of this genetic variation is not particularly important theoretically.  In reality this genetic variation originally comes from mutations of various sorts (not just point mutations, but also duplications, recombinations, etc.).  If you had no genetic variation then artificial selection would not be effective.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might be interested in Stephen Jay Gould's essay &quot;A Dog's Life in Galton's Polyhedron&quot; (found in the collection &quot;Eight Little Piggies&quot;), where he explains that domestic dogs have very little variation in skull length (relative to body size), but large variation in skull width.  It seems that it is very difficult to artificially select for dogs whose skull and body don't have the correct ratio, even though you can wildly change the sizes of dogs, the width of their skulls, the length of their legs, etc.&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2012-06-10T17:41:31.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2580" PostTypeId="1" CreationDate="2012-06-11T10:28:31.427" Score="12" ViewCount="756" Body="&lt;p&gt;I am a computer engineer (MSc in Computer Engineering) who's looking to switch into the field of synthetic / systems biology. I have a comprehensive layman's understanding of evolution, genetics, transcription, etc, but my academic studies have been in the areas informatics, computer science, computer engineering and mathematics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have a good recommendation for standard literature in the field, to get me up to speed? &lt;/p&gt;&#xA;" OwnerUserId="1006" LastEditorUserId="24354" LastEditDate="2018-05-07T16:29:45.923" LastActivityDate="2018-05-08T10:02:57.263" Title="Introductory literature for synthetic / systems biology" Tags="&lt;bioinformatics&gt;&lt;literature&gt;&lt;synthetic-biology&gt;&lt;systems-biology&gt;" AnswerCount="5" CommentCount="1" FavoriteCount="11" ContentLicense="CC BY-SA 4.0" />
  <row Id="2581" PostTypeId="2" ParentId="2580" CreationDate="2012-06-11T11:29:54.473" Score="6" Body="&lt;p&gt;I have a similar background (CS switching to systems biology) and I learned a great deal by reading &quot;Systems Biology: A Textbook&quot; by Edda Klipp et al [1]. It's a very good overview of different sub-areas and it's written in a way that's friendlier to a technical mind than most other bio-related books (i. e. concise, to the point, not shy with formulas). The section about experimental techniques is a real treasure, at least for me getting used to the ways in which we can look into cells was the biggest challenge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another text you might look into is &quot;An Introduction to Systems Biology&quot; by Uri Alon, but it's very dynamic modelling-oriented and will give you less of an overview.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.amazon.co.uk/Systems-Biology-Textbook-Edda-Klipp/dp/3527318747/ref=sr_1_1?ie=UTF8&amp;amp;qid=1339413559&amp;amp;sr=8-1&quot;&gt;http://www.amazon.co.uk/Systems-Biology-Textbook-Edda-Klipp/dp/3527318747/ref=sr_1_1?ie=UTF8&amp;amp;qid=1339413559&amp;amp;sr=8-1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1584886420&quot;&gt;http://www.amazon.com/Introduction-Systems-Biology-Mathematical-Computational/dp/1584886420&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9" LastActivityDate="2012-06-11T11:29:54.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2582" PostTypeId="2" ParentId="2580" CreationDate="2012-06-11T12:44:09.073" Score="13" Body="&lt;p&gt;&lt;strong&gt;Systems Biology&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wingreen &amp;amp; Botstein who run the graduate systems biology course at Princeton wrote a paper about how to teach the subject (Wingreen &amp;amp; Botstein, 2006). In the paper they highlight the key concepts they think are crucial to understanding modern systems biology, and they teach the course through discussion of seminal papers in the field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the reference...&#xA;&lt;a href=&quot;http://dx.doi.org/10.1038/nrm2023&quot;&gt;Wingreen, N. &amp;amp; Botstein, D. (2006) Back to the future: education for systems-level biologists. Nature Reviews Molecular Cell Biology. 7 (11), 829–832.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;del&gt;The paper is unfortunately not open access, so for those who can't access the paper &lt;/del&gt; edit: @uvesten &lt;a href=&quot;http://www.princeton.edu/genomics/botstein/publications/2006_Wingreen_Back.pdf&quot;&gt;found a free PDF copy&lt;/a&gt;! I have listed their choices below, along with the key concept they think each provides...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Robustness (i.e. retaining function despite fluctuations)&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://dx.doi.org/10.1038/43199&quot;&gt;Barkai, N. &amp;amp; Leibler, S. (1997) Robustness in simple biochemical networks. Nature. 387913–917.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Evolutionary perspective&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://dx.doi.org/10.1093/nar/26.18.4291&quot;&gt;Eisen, J.A. (1998) A phylogenomic study of the MutS family of proteins. Nucleic Acids Res. 264291–4300.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Microarray analysis (and more generally, the importance of data visualisation)&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.95.25.14863&quot;&gt;Eisen, M.B., Spellman, P.T., Brown, P.O. &amp;amp; Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA. 9514863–14868.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Individuality of elements in a system:&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://dx.doi.org/10.1126/science.1070919&quot;&gt;Elowitz, M.B., Levine, A.J., Siggia, E.D. &amp;amp; Swain, P.S. (2002) Stochastic gene expression in a single cell. Science. 2971183–1186.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Maximum likelihood&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://dx.doi.org/10.1007/BF01734359&quot;&gt;Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17368–376.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Ultrasensitvity&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.78.11.6840&quot;&gt;Goldbeter, A. &amp;amp; Koshland, D.E. (1981) An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl Acad. Sci. USA. 786840–6844.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Biophysical modelling&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.jstor.org/stable/10.2307/83088&quot;&gt;Hodgkin, A.L. (1958) Croonian Lecture, ionic movements and electrical activity in giant nerve fibres. Proc. R. Soc. Lond. B. Biol. Sci. 1481–37.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Specificity&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.71.10.4135&quot;&gt;Hopfield, J.J. (1974) Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. Natl Acad. Sci. USA. 714135–4139.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Random processes and distributions:&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.genetics.org/content/28/6/491&quot;&gt;Luria, S.E. &amp;amp; Delbruck, M. (1943) Mutations of bacteria from virus sensitivity to virus resistance. Genetics. 28491–511.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Stable switching between states:&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.43.7.553&quot;&gt;Novick, A. &amp;amp; Wiener, M. (1957) Enzyme Induction as an all-or-none phenomenon. Proc. Natl Acad. Sci. USA. 43553–566.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sequence similarity&lt;/strong&gt;&#xA;&lt;a href=&quot;http://dx.doi.org/10.1016/0022-2836%2881%2990087-5&quot;&gt;Smith, T.F. &amp;amp; Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147195–197.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Synthetic Biology&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good place to start in this subject is the Synthetic Biology network:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://syntheticbiology.org/&quot;&gt;Syntheticbiology.org&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://igem.org&quot;&gt;iGEM.org&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://biobricks.org/&quot;&gt;BioBricks.org&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-06-11T14:59:32.370" LastActivityDate="2012-06-11T14:59:32.370" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2583" PostTypeId="1" AcceptedAnswerId="2587" CreationDate="2012-06-11T15:36:59.343" Score="7" ViewCount="426" Body="&lt;p&gt;All winged vertebrates have wings which are homologous to each other and to the forelimbs of the non-winged vertebrates. But what about insect wings? Are all insect wings homologous, and are there any homologies between insect wings and any vertebrate limbs?&lt;/p&gt;&#xA;" OwnerUserId="996" LastEditorUserId="430" LastEditDate="2012-06-11T19:53:24.983" LastActivityDate="2019-06-15T03:43:46.253" Title="Homologies to insect wings" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;entomology&gt;&lt;homology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2584" PostTypeId="1" AcceptedAnswerId="2585" CreationDate="2012-06-11T15:40:45.077" Score="-2" ViewCount="2408" Body="&lt;p&gt;I understand that the protein helps to repair body tissues. If I increase the intake of protein, would it help to cure the wound more quickly? I would like to know how does the protein reaches the wound and how does it help to heal?&lt;/p&gt;&#xA;" OwnerUserId="994" LastActivityDate="2012-06-11T16:15:43.133" Title="How does protein help to cure wound?" Tags="&lt;human-biology&gt;&lt;proteins&gt;&lt;tissue-repair&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2012-06-11T18:16:01.360" ContentLicense="CC BY-SA 3.0" />
  <row Id="2585" PostTypeId="2" ParentId="2584" CreationDate="2012-06-11T16:03:46.843" Score="2" Body="&lt;p&gt;Saying protein in general helps to heal wounds is a very far step. Different proteins are essential for nearly every process that happens anywhere in your body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a range of proteins which is required specifically for wound healing. The first step of wound healing is blood clotting in order to close wounds. This uses several so-called clotting factors, all of which are proteins. Some of these help the platelets (small cells in the blood) stick to the walls of the blood vessels which have been damaged, others are responsible for forming a tight clot around them to make sure no more blood leaks out. Most clotting factors also require vitamin K for their production.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The next step is wound healing. This involves several cell types gathering at the wound and laying down what is called connective tissue, a network made mostly of proteins. Cells of the skin will need to replicate themselves in order to close the wound, and they will require lots of proteins for this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Protein reaches all cells of the body from the intestines via the blood flow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eating a diet high in protein would surely not be a bad thing to do - your body needs it everywhere. But it is important that you consume it mixed with healthy amounts of carbohydrate (needed for energy) and fats (needed for many structures and hormones).&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-06-11T16:15:43.133" LastActivityDate="2012-06-11T16:15:43.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2586" PostTypeId="2" ParentId="2580" CreationDate="2012-06-11T17:39:17.757" Score="4" Body="&lt;p&gt;There is a recent published book, from Garland Science for systems biology&#xA;&lt;a href=&quot;http://www.garlandscience.com/product/isbn/9780815344674&quot; rel=&quot;nofollow&quot;&gt;http://www.garlandscience.com/product/isbn/9780815344674&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and a clasic textbook: Physical Biology of the Cell&#xA;&lt;a href=&quot;http://www.garlandscience.com/product/isbn/9780815341635&quot; rel=&quot;nofollow&quot;&gt;http://www.garlandscience.com/product/isbn/9780815341635&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="973" LastActivityDate="2012-06-11T17:39:17.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2587" PostTypeId="2" ParentId="2583" CreationDate="2012-06-11T19:43:48.257" Score="6" Body="&lt;p&gt;Insects and vertebrates are extremely distantly related: they're on opposite sides of the oldest split among bilaterally symmetric animals.  Their most recent common ancestor lived in the pre-cambrian and was almost certainly worm-shaped with no limbs at all.  There's no way that insect wings are homologous to any body parts of vertebrates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The evolution of insect wings is a somewhat difficult topic, because it happened 350 million years ago in animals that do not fossilize well.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Insect_wing#Evolution&quot;&gt;Wikipedia&lt;/a&gt; discusses several possible theories for what parts of non-winged insects are homologs of insect wings.  Currently the situation does not seem to be resolved.&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2012-06-11T19:43:48.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2588" PostTypeId="1" AcceptedAnswerId="7715" CreationDate="2012-06-11T20:33:43.747" Score="5" ViewCount="915" Body="&lt;p&gt;In stratified (not pseudostratified) epithelia such as the epidermis, what purpose does the basal lamina serve for the outer layer cells which do not even stand in contact with it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, how do these cells attach, all just through tight junctions to lower layers?&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-06-11T23:31:44.360" LastActivityDate="2013-03-30T23:03:25.433" Title="Significance of basal lamina for outer layers of epithelium" Tags="&lt;cell-biology&gt;&lt;histology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2589" PostTypeId="1" CreationDate="2012-06-12T01:17:53.383" Score="1" ViewCount="2184" Body="&lt;p&gt;In order to run my microbial community samples from my experiments through &lt;a href=&quot;https://en.wikipedia.org/wiki/Dgge#Denaturing_gradient_gel_electrophoresis&quot; rel=&quot;nofollow&quot;&gt;DGGE&lt;/a&gt;, I was required to use multiple gels.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus it is necessary to compare banding patterns across more than one gel.  This means that I need some way of assessing whether the 4th band on gel #1 is the same OTU as the 4th band on gel #2.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The industry standard for this procedure seems to be the &lt;a href=&quot;http://gelcompar.com/&quot; rel=&quot;nofollow&quot;&gt;Gelcompar&lt;/a&gt; software.  Unfortunately this software is greater than $10,000 and is proprietary (thus, not open science friendly).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Does there exist a free (ideally as in speech and beer) alternative to Gelcompar?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="137" LastActivityDate="2013-09-12T14:26:11.577" Title="Is there a free alternative to Gelcompar for comparing banding patterns across multiple gels?" Tags="&lt;microbiology&gt;&lt;gel-electrophoresis&gt;&lt;software&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2590" PostTypeId="2" ParentId="2565" CreationDate="2012-06-12T05:16:52.853" Score="4" Body="&lt;p&gt;The &lt;em&gt;t&lt;/em&gt; locus, which is described in detail in this book by &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0674017137&quot; rel=&quot;nofollow&quot;&gt;Robert Trivers&lt;/a&gt;, is the classic 'outlaw' or 'selfish' gene.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a heterozygous (single) &lt;em&gt;t&lt;/em&gt; allele is present in the paternal mouse, the t locus is evident in sperm 95% of the time.  Talk about &quot;Breakin' the Law&quot;!  As a locus whose main phenotype seems to be for mitotic cheating, t seems to convey little or no benefit to the other genes by way of helping the host survive.  &lt;em&gt;t/t&lt;/em&gt; homozygotes are sterile.  Nice summary &lt;a href=&quot;http://bio.research.ucsc.edu/~barrylab/classes/animal_behavior/LEVELS.HTM#anchor190660&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-06-12T05:16:52.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2591" PostTypeId="1" CreationDate="2012-06-12T05:37:56.413" Score="7" ViewCount="2580" Body="&lt;p&gt;For a school project I need to find the number of chromosomes of an organism (specifically the adelie penguin, &lt;em&gt;Pygoscelis adeliae&lt;/em&gt;). After several internet searches and a look through the encyclopedia at school, I am unable to find a definite answer to this question. Sources on the internet claim anything from 38 to 96 for diploid cells (with none of them citing a trustable study).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any database that records the chromosome number for organisms?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, if this information is unavailable, what is the best way to estimate this value? On the Wikipedia article for number of chromosomes for various organisms, it listed the value for some birds, most of them in the 70-80 range. Is it safe then to assume that the number for penguins in general would be somewhere in this range?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="1010" LastEditorUserId="223" LastEditDate="2012-08-13T22:14:33.217" LastActivityDate="2012-08-13T22:14:33.217" Title="Finding the number of chromosomes of an organism" Tags="&lt;chromosome&gt;&lt;cytogenetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2592" PostTypeId="1" AcceptedAnswerId="2594" CreationDate="2012-06-12T05:56:27.453" Score="10" ViewCount="904" Body="&lt;p&gt;Are there any examples of two species taxonomically classified in &lt;strong&gt;different &lt;a href=&quot;http://en.wikipedia.org/wiki/Family_%28biology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;biological families&lt;/a&gt;&lt;/strong&gt; that have successfully hybridized and produced viable offspring? If not, is there an example of where reproduction occured with non-viable offspring?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be clear, I mean regular sexual reproduction that could occur in the natural world outside a lab. Even so, I'd be curious to know if it could even occur in a lab without direct genetic manipulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, grolar bears which are &lt;a href=&quot;http://en.wikipedia.org/wiki/Ursid_hybrid&quot; rel=&quot;nofollow noreferrer&quot;&gt;ursid hybrids&lt;/a&gt; between different species in the &lt;em&gt;Ursus&lt;/em&gt; genus are known to exist. Also ursid hybrids between bear species in different genuses have been produced in captivity (sloth bear &lt;em&gt;Melursus ursinus&lt;/em&gt; x Malayan sun bear &lt;em&gt;Ursus malayanus&lt;/em&gt; and sloth bear x Asiatic black bear &lt;em&gt;Ursus thibetanus&lt;/em&gt;). Would an extra-familial hybridisation be possible? Would this be more likely in the plant kingdom?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question is inspired by a &lt;a href=&quot;https://gardening.stackexchange.com/questions/2491/can-i-cross-pollinate-basil-and-chili-peppers&quot;&gt;separate question on the Gardening SE&lt;/a&gt; which hints at a general lack of understanding of the genetic similarity required for cross-pollination in plants. It made me wonder whether there are any exceptions to the general assumption that extra-familial hybridisation is impossible.&lt;/p&gt;&#xA;" OwnerUserId="73" LastEditorUserId="-1" LastEditDate="2017-04-13T12:42:26.137" LastActivityDate="2013-10-28T15:16:54.960" Title="Is sexual reproduction outside the same biological family possible? Has it ever occured successfully?" Tags="&lt;genetics&gt;&lt;reproduction&gt;&lt;taxonomy&gt;&lt;hybridization&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2593" PostTypeId="2" ParentId="2589" CreationDate="2012-06-12T07:03:22.253" Score="1" Body="&lt;p&gt;Try this one&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pavel, A. B. &amp;amp; Vasile, C. I. &lt;a href=&quot;http://dx.doi.org/10.1186/1471-2105-13-9&quot; rel=&quot;nofollow&quot;&gt;PyElph - a software tool for gel images analysis and phylogenetics&lt;/a&gt;. BMC Bioinformatics 13, 9+ (2012).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can download here&#xA;&lt;a href=&quot;http://sourceforge.net/projects/pyelph/&quot; rel=&quot;nofollow&quot;&gt;http://sourceforge.net/projects/pyelph/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="973" LastActivityDate="2012-06-12T07:03:22.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2594" PostTypeId="2" ParentId="2592" CreationDate="2012-06-12T11:00:46.547" Score="14" Body="&lt;p&gt;Interfamilial hybrids have never, to my knowledge, been recorded occurring naturally (without human intervention).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In plants, somatic inter-familial hybrids have been produced for a wide variety of species pairs in the lab (e.g. between carrot and barley; Kisaka et al. 1997). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In animals, there are some historical reports of hybrids between chickens (Mathis &amp;amp; MacDougald 1987) or peafowl (Serebrovsky 1929), both in Phasianidae, and guineafowl (in Numididae). The animal example meets your condition of being outside the lab, although they were produced by breeders.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Refs&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s001220050403&quot;&gt;Kisaka, H., Kisaka, M., Kanno, A. &amp;amp; Kameya, T. (1997) Production and analysis of plants that are somatic hybrids of barley (Hordeum vulgare L.) and carrot (Daucus carota L.). TAG Theoretical and Applied Genetics. 94 (2), 221–226.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3442527&quot;&gt;Mathis, G.F. &amp;amp; McDougald, L.R. (1987) Evaluation of interspecific hybrids of the chicken, guinea fowl, and Japanese quail for innate resistance to coccidia. Avian Diseases. 31 (4), 740–745.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/BF02984211&quot;&gt;Serebrovsky, A. (1929) Observations on interspecific hybrids of the fowl. Journal of Genetics. 21 (3), 327–340.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-06-12T11:14:59.647" LastActivityDate="2012-06-12T11:14:59.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2595" PostTypeId="1" AcceptedAnswerId="2598" CreationDate="2012-06-12T12:56:56.950" Score="4" ViewCount="156" Body="&lt;p&gt;I am a computer scientist that studies biology and bioinformatics. &#xA;In the last weeks, I have been trying to study new research directions, and I would like to deepen my knowledge on the role and behavior of genes and proteins in learning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By &lt;em&gt;learning&lt;/em&gt;, I mean the human process: the information &lt;em&gt;I&lt;/em&gt; is absent at time &lt;em&gt;T&lt;/em&gt;, and present at time &lt;em&gt;T+1&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to study more this problem, and I am wondering: how do proteins and genes behave during learning?&#xA;I have read that proteins that participate in learning are called marker proteins. Is it true? Which role do they have?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Where could I find some resources to study this fascinating problem?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you very much!&lt;/p&gt;&#xA;" OwnerUserId="885" LastEditorUserId="43" LastEditDate="2012-06-12T14:55:12.993" LastActivityDate="2012-06-12T19:04:46.607" Title="How do proteins and genes participate in learning?" Tags="&lt;molecular-biology&gt;&lt;proteins&gt;&lt;genetics&gt;&lt;learning&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2597" PostTypeId="2" ParentId="1338" CreationDate="2012-06-12T13:58:09.943" Score="3" Body="&lt;p&gt;Both are measures of carbon fixation rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RuBisCO activity specifically refers to the rate at which the enzyme RuBisCO fixes carbon to RuBP, and is measured by isolating the enzyme from tissue samples and, usually, using radiolabelled CO2 to measure how much carbon is fixed in a set amount of time in controlled conditions and with controlled supply of substrate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carbon assimilation rate is generally a whole-plant or whole-leaf variable, measured on a larger scale. It is usually measured by measuring leaf sugar carbon before and after a set period, again using radiolabelling. Conditions may or may not be controlled, and it can be measured in the field (unlike RuBisCO activity).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RuBisCO activity might differ from net fixation in the short term in plants which have an intermediate carbon fixation step, such as in CAM or C4 plants, if the net fixation measurement includes the intermediates - the pool of intermediate carbon-containing molecules have technically been fixed but not by RuBisCO. However, over longer time periods this effect will disappear, as ultimately all CO2 is fixed or re-fixed through RuBisCO.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-06-12T13:58:09.943" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2598" PostTypeId="2" ParentId="2595" CreationDate="2012-06-12T14:41:03.590" Score="6" Body="&lt;p&gt;The storage of memories in cells is rarely thought of on the protein level of the cell.  Cells are usually given a developmental state, but no memory.  A cell may become a liver cell, cancerous, or diabetic, but this is not memory, but a physiological change in the cell which is usually not reversible to a previous state.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example cancer treatments are entirely focused on identifying the cancerous cells and &lt;a href=&quot;http://www.cancer.gov/cancertopics/treatment/types-of-treatment&quot;&gt;killing them&lt;/a&gt;.   &lt;a href=&quot;http://publications.icr.ac.uk/9196/&quot;&gt;Internally the genomes of cancer cells often have deletions and duplications.&lt;/a&gt;  They are cancerous, they have not learned to be cancerous. Though not as dramatic, it is now thought that cellular differentiation which creates different types of cells is heavily influenced by epigenetic modification of the genome; &lt;a href=&quot;http://en.wikipedia.org/wiki/Cellular_differentiation#Mechanisms&quot;&gt;the DNA is marked by methyl groups which dictates the state of the cell by modifying the gene&lt;/a&gt;.  This is mediated by proteins for sure, but is quite complex and not well understood at this time. Epigenetic markers can even change gene behavior between generations of offspring as well, though that is not usually called memory. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is information stored in the brain?  This is thought to be reflected in the organization of the neurons in the brain.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Neuron#Classes&quot;&gt;There are many kinds of neurons.&lt;/a&gt;  They can be distinguished by the sorts of axons and dendrites that emanate from the cell body.  They can also be distinguished by the chemical variety of neurotransmitter they use (there are a score of different molecules).  So to a great extent the type of cell and the specific proteins it chooses to use to mediate information is very important.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, information is currently thought to highly related to the placement of the axons and dendrites connecting the neuron to sometimes scores of other cells, sometimes touching the cell body, other times other dendrites or neurons.  As neural activity ensues, &lt;a href=&quot;http://en.wikipedia.org/wiki/Neuroplasticity#Neurobiology&quot;&gt;the cells will reconfigure their connections by physically moving them&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More recently, investigators have tried to understand the genes which internally modulate the neural signals within the cells.  &lt;a href=&quot;http://mcb.berkeley.edu/courses/mcb160/Fall2006/readings/Kandel%20review%202001.pdf&quot;&gt;This nobel prize lecture discusses how the CREB/MAPK pathway can modulate Long Term Potentiation - the shape of the neuron response to a signal over time (days or hours)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taken as a whole, you can see that memory is likely to be stored on several levels at once - the kinds of cells (dictated by differentiation) involved, structural arrangement of the neurons (axons and dendrites connecting to various cells and places on cells), as well as internal signaling circuitry that generates and modulate the electrical and chemical activity within the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Marker protein&quot; only refers to a protein that you can follow to see some sort of activity in the cell. A typical example is Green Fluorescent Protein, which is colored, fused with a protein of interest.  It has no specific meaning regarding learning I think. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-06-12T14:41:03.590" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2599" PostTypeId="1" AcceptedAnswerId="2600" CreationDate="2012-06-12T15:28:13.700" Score="3" ViewCount="5539" Body="&lt;p&gt;$Q_{10}$ is the increase in a rate (e.g. activity of an enzyme) observed with a 10&amp;deg; temperature increase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Q10_%28temperature_coefficient%29&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$Q_{10}=\left(\frac{R_2}{R_1}\right)^{{10}/\left({T_2-T_1}\right)}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is apparent that the units of $R$ (e.g. $mol/g/s$) cancel out, but what about the units of temperature? Does $Q_{10}$ have units? It seems the units would be &quot;&lt;em&gt;per 10 &amp;deg;C&lt;/em&gt;&quot;, but it is not clear how this comes from the referenced equation&lt;/p&gt;&#xA;" OwnerUserId="154" LastEditorUserId="6703" LastEditDate="2015-02-13T22:19:40.820" LastActivityDate="2015-02-13T22:19:53.327" Title="What are the units of Q10 (temperature sensitivity)?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2600" PostTypeId="2" ParentId="2599" CreationDate="2012-06-12T17:07:33.297" Score="6" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qqVuB.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure. A schematic diagram showing the effect of the temperature on the stability of an enzyme catalysed reaction. The curves show the percentage activity remaining as the incubation period increases. From the top they represent equal increases in the incubation temperature (50 &amp;deg;C, 55 &amp;deg;C, 60 &amp;deg;C, 65 &amp;deg;C and 70 &amp;deg;C).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The $Q_{10}$ is a unitless number, that summarizes the effect of raising temperature 10&amp;deg;C on the rate of a chemical reaction. A $Q_{10}$ of 2.0 suggests that raising the temperature of a system by 10 &amp;deg;C will effectively double the rate of the reaction. This value would be expected for most chemical reactions occurring within normal physiological temperatures.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematically, $Q_{10}$ can be represented by the following expression:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$Q_{10}=\left(\frac{k_2}{k_1}\right)^{\frac{10}{t_2-t_1}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$t_2$ = higher temperature&lt;br&gt;&#xA;$k_2$ = rate at $t_2$&lt;br&gt;&#xA;$t_1$ = lower temperature&lt;br&gt;&#xA;$k_1$ = rate at $t_1$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually the temperature difference is about 10 &amp;deg;C, then you can simplify the equation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$Q_{10}=\left(\frac{k_1}{k_2}\right)^{\frac{10}{10}}=\frac{k_1}{k_2}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: You can easily calculate $k$ form Arrhenius equation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$k=Ae^{\frac{-\Delta G^*}{RT}}$$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $k$ is the kinetic rate constant for the reaction, $A$ is the Arrhenius constant, also known as the frequency factor, $-\Delta G^*$ is the standard free energy of activation ($kJ/mol$) which depends on entropic and enthalpic factors, $R$ is the gas law constant and $T$ is the absolute temperature. &lt;/p&gt;&#xA;" OwnerUserId="973" LastEditorUserId="6703" LastEditDate="2015-02-13T22:19:53.327" LastActivityDate="2015-02-13T22:19:53.327" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2601" PostTypeId="2" ParentId="2595" CreationDate="2012-06-12T19:04:46.607" Score="2" Body="&lt;p&gt;If you're interested in understanding the maintenance of state, history, and information, I would look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Hysteresis&quot; rel=&quot;nofollow&quot;&gt;hysteresis&lt;/a&gt;. The classic biophysics model for studying hysteresis has been the &lt;a href=&quot;http://en.wikipedia.org/wiki/Lambda_phage&quot; rel=&quot;nofollow&quot;&gt;Lambda phage&lt;/a&gt; which has been extensively detailed in Mark Ptashne's &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0879697164&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;A Genetic Switch&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-06-12T19:04:46.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2602" PostTypeId="1" AcceptedAnswerId="20890" CreationDate="2012-06-12T20:02:53.290" Score="25" ViewCount="7208" Body="&lt;p&gt;I'm curious how much damage is potentially inflicted by shear stress by pipetting. I know that syringes used for stem cell injection can cause a lot of damage. However, to what extent does this happen with P20 and P200 pipette tips? Understandably the shear modulus of bacterial cells is significantly different from that of cancer cells, which will be different from that of stem cells.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="22057" LastEditDate="2017-01-10T19:45:56.023" LastActivityDate="2017-08-11T13:27:47.320" Title="Pipetting damage to cells" Tags="&lt;cell-culture&gt;" AnswerCount="7" CommentCount="1" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2603" PostTypeId="2" ParentId="2602" CreationDate="2012-06-12T20:11:37.440" Score="12" Body="&lt;p&gt;It's an easy experiment to do. Take your cells aliquot them into 10 microfuge tubes, and pipette each suspension increasing amount of times, stain with trypan blue and count.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most important factors will be which pipette-type you use; I would expect a p1000 to cause more damage then a p200 then a p20 due to velocity of the fluid. Also the most important factor will be the skill of the scientist, if you pipette slowly it should decrease stress as opposed to pipetting quickly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my experience it depends on the pipette-type and the skill of the operator. The only way to answer this for you is to try it empirically. &lt;/p&gt;&#xA;" OwnerUserId="990" LastActivityDate="2012-06-12T20:11:37.440" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2604" PostTypeId="2" ParentId="2602" CreationDate="2012-06-12T20:13:25.577" Score="9" Body="&lt;p&gt;Anecdotally I have not observed any cell death upon pipetting of &lt;em&gt;E. coli&lt;/em&gt; DH5alpha or TOP10, however as competent cells, mixing by pipetting up and down is discouraged due to the compromised cell wall.&lt;/p&gt;&#xA;" OwnerUserId="798" LastActivityDate="2012-06-12T20:13:25.577" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2605" PostTypeId="1" CreationDate="2012-06-12T23:38:53.140" Score="1" ViewCount="119" Body="&lt;p&gt;Usually adult organisms are more sophisticated than corresponding larva, i. e. frogs, mosquitoes, fish. Are there species where the opposite is true?&lt;/p&gt;&#xA;" OwnerUserId="1013" LastEditorUserId="1013" LastEditDate="2012-06-13T01:55:07.353" LastActivityDate="2012-06-15T18:06:23.833" Title="Are there any organisms with larva more advanced than adult form?" Tags="&lt;homework&gt;&lt;reproduction&gt;&lt;development&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2606" PostTypeId="1" CreationDate="2012-06-13T07:53:10.887" Score="8" ViewCount="15583" Body="&lt;p&gt;Psychologically this might be a tough question, but in means of biology, what are the effects of total celibacy on the gonads and the nervous system concerning both man and woman in short and long term? Has there any research made in medical terms and as a bonus question, is there anything similar on other animal kingdom like deliberate celibacy?&lt;/p&gt;&#xA;" OwnerUserId="941" LastEditorUserId="941" LastEditDate="2012-06-13T09:23:58.793" LastActivityDate="2012-06-15T11:24:39.670" Title="What are the consequences of voluntary total celibacy?" Tags="&lt;human-biology&gt;&lt;organs&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2607" PostTypeId="1" CreationDate="2012-06-13T08:28:30.503" Score="7" ViewCount="304" Body="&lt;p&gt;That is, they don't differ throughout the entire population. I understand of course that we can't DNA sequence every human, so by &quot;fully&quot; I mean there's an incredibly small probability of there being a mutation retained in a living individual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also by the genome I'm referring to the consensus of all the cells composing in the individual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess my question is really, where are the crucially important sections of DNA that are simply unmodifiable without being incompatible with life?&lt;/p&gt;&#xA;" OwnerUserId="1014" LastActivityDate="2012-06-13T10:19:54.407" Title="Are there any DNA base sequences that are fully conserved between the genomes of all humans?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;human-genome&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2608" PostTypeId="2" ParentId="2607" CreationDate="2012-06-13T10:19:54.407" Score="11" Body="&lt;p&gt;In 2004 &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15131266&quot;&gt;Bejerano &lt;em&gt;et al.&lt;/em&gt;&lt;/a&gt; identified &quot;481 segments longer than 200 base pairs (bp) that are absolutely conserved (100% identity with no insertions or deletions) between orthologous regions of the human, rat, and mouse genomes&quot;. These were found to be mostly in/around genes related to RNA processing, which is perhaps unsurprising given that it is such a primitive/inherent biological process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bejerano's paper has been cited &lt;a href=&quot;http://www.scopus.com/results/citedbyresults.url?sort=plf-f&amp;amp;cite=2-s2.0-2542542256&amp;amp;src=s&amp;amp;imp=t&amp;amp;sid=rnObiJAHVmr8LbB21Qi2qbD%3a200&amp;amp;sot=cite&amp;amp;sdt=a&amp;amp;sl=0&amp;amp;origin=recordpage&amp;amp;txGid=rnObiJAHVmr8LbB21Qi2qbD%3a20&quot;&gt;over 500 times on Scopus&lt;/a&gt;, with numerous papers reporting variants in such regions that cause diseases such as colorectal adenocarcinomas.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;So few conserved regions exist because there is plenty of redundancy in the genome; many genes functionally overlap with others, and many genetic variants are 'silent' - they have no effect on the phenotype. Having this variability is advantageous in Darwinian terms because this increases the &lt;em&gt;evolvability&lt;/em&gt; of the species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many regions of very high homology between individuals (protein-coding regions are highly conserved even between species), but there will still be natural variation; each mutations effect will be dependent on the &lt;em&gt;rest&lt;/em&gt; of the genome. Genes work together to produce a working organism - they do not each code for a little 'bit', and therefore a change in one portion of the DNA may be 'balanced' by a change elsewhere. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is only in 'ultra-conserved' sequences that mutations are presumably incompatible with life because the process is so finely-tuned and indispensable.&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-06-13T10:19:54.407" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2609" PostTypeId="1" AcceptedAnswerId="2636" CreationDate="2012-06-13T12:41:29.053" Score="8" ViewCount="2520" Body="&lt;p&gt;I don't understand why darker skin is advantageous in hotter climates. Wouldn't it absorb more of the heat? I have heard that it reduces the incidence of cancer, but I would think absorbing more radiation would increase the risk?&lt;/p&gt;&#xA;" OwnerUserId="258" LastEditorUserId="3971" LastEditDate="2013-08-29T16:04:52.603" LastActivityDate="2016-10-18T16:18:05.003" Title="Why do people have darker skin in sunnier climates?" Tags="&lt;human-biology&gt;&lt;pigmentation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2610" PostTypeId="2" ParentId="2609" CreationDate="2012-06-13T13:04:54.500" Score="4" Body="&lt;p&gt;I heard one proposition that has to do with cancer, and the other side of the coin is related to vitamin D and calcium. If I remember correctly, living in a sunnier climate can affect your skin and cause cancer. The trick is to produce pigments in the epidermis so that the radiation is absorbed by the pigments and doesn't go further inside into the dermis, where it could cause DNA damage to the living dermis cells. The epidermis is constantly shedding dead cells out, so apart from absorbing more heat, there is no problem in absorbing radiation in the pigments at the epidermis level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having lighter skin in cloudier climates favors the absorption of sunlight, which is necessary for the production of Vitamin D, which in turn is necessary for the regulation of the levels of usable calcium in the body. Not having enough calcium is associated to all sorts of diseases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The claims for VitD/calcium/sunlight are sometimes also associated to lactose tolerance in adults. The scene we see in pictures where someone wakes up in the middle of the night, opens the fridge and downs a gallon of fresh milk is actually not applicable to most of the human populations. We are lactose tolerant during our infancy, but for most of us, lactase production slowly shuts down when we grow up. The claim related to calcium metabolism is that human populations living in cloudier climates became adapted to lactose tolerance in adulthood so that they could make use of the calcium available in milk, and that extra calcium would contribute to a balanced calcium metabolism given that there is not much sunlight in their climates.&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2012-06-13T13:04:54.500" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2611" PostTypeId="2" ParentId="2606" CreationDate="2012-06-13T13:08:00.753" Score="4" Body="&lt;p&gt;I was told in my undergraduate degree that males produce sperm all the time, and that under conditions of no sexual stimulation, that sperm is excreted involuntarily every 15-16 days, at night, while dreaming. I was also told that the renewal rate of sperm is higher under regular sexual stimulation, which increases the fertility of the sperm that is excreted.&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2012-06-13T13:08:00.753" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="2612" PostTypeId="2" ParentId="2574" CreationDate="2012-06-13T13:14:43.070" Score="10" Body="&lt;p&gt;The sequencing technologies that were developed in the last 20 years have a range of optimal use at an average A+T/G+C rate. Both highly AT-rich and GC-rich regions are complicated to process by the different sequencing technologies. Each technology has different ranges of usage, but to name one, &lt;a href=&quot;http://www.illumina.com/technology/sequencing_technology.ilmn&quot;&gt;Illumina technology&lt;/a&gt; prefers sequences in the middle range. If you try to sequence an AT-rich genome with the Illumina standard protocol, you will sequence an incomplete genome, the fragments of which are not a perfect reflection of the original complete genome. Other technologies claim to be completely unbiased to nucleotide content. &lt;a href=&quot;http://www.pacificbiosciences.com/products/&quot;&gt;Pacific Biosciences&lt;/a&gt; is one of them, and people seem to agree on that claim, after having analyzed the data that is produced by their machines. &lt;a href=&quot;http://www.nanoporetech.com/&quot;&gt;Oxford Nanopore Technologies&lt;/a&gt; claims that they have almost no biases, but as of today (2012-06-13), there is no confirmation of that by external analyses. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beyond sequencing problems, the software used to assemble and annotate the sequences may also be prone to errors in AT-rich and GC-rich regions. But many of those problems stem from the incompleteness of the sequencing.&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2012-06-13T13:14:43.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2613" PostTypeId="2" ParentId="2050" CreationDate="2012-06-13T13:37:34.693" Score="-3" Body="&lt;p&gt;Although most plants can potentially reproduce sexually, there are some plants that effectively always reproduce by shedding off branches which, when they fall in the right conditions, grow into new 'clones' of the same tree, which the exact genetic material. In these cases, it is advantageous for the tree to be able to survive as long as possible. Plants that reproduce sexually by the cross of two different individuals have a recombined genetic material in every generation, and the survival of that plant with that new genome is usually shorter.&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="338" LastEditDate="2014-07-09T00:01:52.137" LastActivityDate="2014-07-09T00:01:52.137" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2614" PostTypeId="2" ParentId="2447" CreationDate="2012-06-13T16:53:48.490" Score="4" Body="&lt;p&gt;Phylogenetically analyzing genes that are not present in every species may present you with some problems, but it is completely feasible to simultaneously analyze the relatedness of the species (based on your enrichment score), and the relatedness of the scores themselves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Forgive me if this is too 'simple' an analysis, but you have not said what you have tried.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My choice of approach would be to use &lt;a href=&quot;http://www.r-project.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;R (open source stats package)&lt;/a&gt; to generate a heatmap of your matrix of data. There are plenty of options for the method of clustering, but the defaults tend to produce quite a nice heatplot, with hierarchical cluster analysis performed on both dimensions of the data (you can specify only 1, or even none, if you prefer). I have used the following code to simulate some data to generate the below heatmap;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;# generate 10x10 matrix using random data&#xA;x &amp;lt;- as.matrix(data.frame(rnorm(10),rnorm(10),rnorm(10),rnorm(10),rnorm(10),rnorm(10),rnorm(10),rnorm(10),rnorm(10),rnorm(10)))&#xA;# use heatmap function on the data. &quot;labRow&quot; and &quot;labCol&quot; simply remove the labels.&#xA;heatmap(x, xlab=&quot;Genes&quot;, ylab=&quot;Species&quot;, labRow=&quot;&quot;, labCol=&quot;&quot;)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rvZsW.png&quot; alt=&quot;Heatmap generated using R&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Because it is randomly generated data there are no patterns really, but if you were to stick you real data in there it would look better no doubt. (In an actual analysis you will want to leave the labels on, I was just simplifying the plot). The function can handle missing values, so you could put all the genes you want to analyze in there, even if not all species have them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using this method you could see the most closely related species by gene enrichment, and also which are the most closely related genes (in terms of enrichment for your TF).&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-06-13T16:53:48.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2615" PostTypeId="1" AcceptedAnswerId="2621" CreationDate="2012-06-13T17:38:40.840" Score="12" ViewCount="501" Body="&lt;p&gt;For most people (my earliest memories are of perhaps when I was 2 or so) their earliest memories would be when they were over a year old. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How old does the average baby have to be before it can retain memories? &#xA;Are there any preconditions that need to be fulfilled?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="45" LastEditDate="2012-06-14T00:58:43.720" LastActivityDate="2015-05-29T13:56:27.640" Title="How old does a baby have to be before it can retain memories?" Tags="&lt;neuroscience&gt;&lt;memory&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2616" PostTypeId="1" CreationDate="2012-06-13T17:51:47.530" Score="6" ViewCount="177" Body="&lt;p&gt;I'm designing a gene in DNAWorks, and I'm unable to find a set of conditions that gives an &quot;overall score&quot; of zero (which is what I normally insist on). People that have used DNAWorks: what's the highest nonzero score you've been able to successfully assemble?&lt;/p&gt;&#xA;" OwnerUserId="1015" LastActivityDate="2012-06-15T03:23:29.767" Title="Designing genes with DNAWorks: Maximum nonzero score?" Tags="&lt;synthetic-biology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2617" PostTypeId="2" ParentId="2447" CreationDate="2012-06-13T18:17:38.307" Score="2" Body="&lt;p&gt;From your example&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Species1 Z-score&#xA;Gene1    0.532&#xA;Gene2    0.531&#xA;...&#xA;&#xA;Species2 Z-score&#xA;Gene1    0.51&#xA;Gene3    0.505&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;You need to get a matrix for all the Z-scores from your species, like this&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Genes    Species1    Species2&#xA;Gene1    0.532         0.51&#xA;Gene2    0.531         NA&#xA;Gene3    NA            0.505         &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;And then, you can easly &lt;a href=&quot;http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dist.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;calculate the distance matrix&lt;/a&gt; for your enrichment set, to do phylogenetic analysis with R &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;genes &amp;lt;- c(paste(rep(&quot;gene&quot;,10), seq(1,10,1), sep=&quot;&quot;))&#xA;Species &amp;lt;- c(rep(rnorm(10, 0.5 ,0.3), 10))&#xA;Species.name &amp;lt;- c(paste(rep(&quot;Species&quot;, 10), seq(1,10,1), sep=&quot;&quot;))&#xA;&#xA;gene.matrix &amp;lt;- data.frame(Species1=Species[1:10], Species2=Species[11:20], &#xA;                          Species3=Species[21:30], Species4=Species[31:40],&#xA;                          Species5=Species[41:50], Species6=Species[51:60],&#xA;                          Species7=Species[61:70], Species8=Species[71:80],&#xA;                          Species9=Species[81:90], Species10=Species[91:100],&#xA;                          row.names=genes)&#xA;&#xA;d.gene.matrix &amp;lt;- dist(gene.matrix, method = &quot;euclidean&quot;)&#xA;&#xA;tree &amp;lt;- hclust(d.gene.matrix)&#xA;plot(tree)&#xA;&#xA;    &amp;gt; gene.matrix&#xA;         Species1   Species2   Species3   Species4   Species5   Species6   Species7&#xA;gene1  0.97128393 0.97128393 0.97128393 0.97128393 0.97128393 0.97128393 0.97128393&#xA;gene2  0.85378459 0.85378459 0.85378459 0.85378459 0.85378459 0.85378459 0.85378459&#xA;gene3  0.85152911 0.85152911 0.85152911 0.85152911 0.85152911 0.85152911 0.85152911&#xA;gene4  0.52703866 0.52703866 0.52703866 0.52703866 0.52703866 0.52703866 0.52703866&#xA;gene5  0.49145958 0.49145958 0.49145958 0.49145958 0.49145958 0.49145958 0.49145958&#xA;gene6  0.70815764 0.70815764 0.70815764 0.70815764 0.70815764 0.70815764 0.70815764&#xA;gene7  0.66739808 0.66739808 0.66739808 0.66739808 0.66739808 0.66739808 0.66739808&#xA;gene8  0.47487837 0.47487837 0.47487837 0.47487837 0.47487837 0.47487837 0.47487837&#xA;gene9  0.13635000 0.13635000 0.13635000 0.13635000 0.13635000 0.13635000 0.13635000&#xA;gene10 0.07511424 0.07511424 0.07511424 0.07511424 0.07511424 0.07511424 0.07511424&#xA;         Species8   Species9  Species10&#xA;gene1  0.97128393 0.97128393 0.97128393&#xA;gene2  0.85378459 0.85378459 0.85378459&#xA;gene3  0.85152911 0.85152911 0.85152911&#xA;gene4  0.52703866 0.52703866 0.52703866&#xA;gene5  0.49145958 0.49145958 0.49145958&#xA;gene6  0.70815764 0.70815764 0.70815764&#xA;gene7  0.66739808 0.66739808 0.66739808&#xA;gene8  0.47487837 0.47487837 0.47487837&#xA;gene9  0.13635000 0.13635000 0.13635000&#xA;gene10 0.07511424 0.07511424 0.07511424&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PdDV5.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="973" LastEditorUserId="973" LastEditDate="2012-06-13T22:05:39.823" LastActivityDate="2012-06-13T22:05:39.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2618" PostTypeId="1" AcceptedAnswerId="2620" CreationDate="2012-06-13T19:38:14.900" Score="1" ViewCount="439" Body="&lt;p&gt;Somewhere, I have read that we need to consume proteins to make amino acids to make new proteins. What does it suggest? How do we make proteins from proteins?&lt;/p&gt;&#xA;" OwnerUserId="994" LastEditorUserId="43" LastEditDate="2012-06-14T00:50:37.847" LastActivityDate="2014-06-05T22:11:37.137" Title="How are proteins formed?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;proteins&gt;&lt;amino-acids&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2619" PostTypeId="2" ParentId="2618" CreationDate="2012-06-13T20:29:53.490" Score="3" Body="&lt;p&gt;You ingest daily dietary protein which your body &lt;a href=&quot;http://en.wikipedia.org/wiki/Protein_hydrolysis&quot; rel=&quot;nofollow&quot;&gt;hydrolyzes&lt;/a&gt; to get all the building blocks for other proteins (amino acids).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, from diet you can get &lt;a href=&quot;http://en.wikipedia.org/wiki/Essential_amino_acid&quot; rel=&quot;nofollow&quot;&gt;essential amino acids&lt;/a&gt; that cannot be synthesized &lt;em&gt;de novo&lt;/em&gt; by the organism which is more economical than amino acid synthesis. Other amino acids can be constructed by metabolic processes.&lt;/p&gt;&#xA;" OwnerUserId="973" LastEditorUserId="5762" LastEditDate="2014-06-05T22:11:37.137" LastActivityDate="2014-06-05T22:11:37.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2620" PostTypeId="2" ParentId="2618" CreationDate="2012-06-13T21:21:55.753" Score="7" Body="&lt;p&gt;Essentially, yes, &quot;proteins that we consume form new proteins that are different&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The processes are each of them topics for themselves. In short, consumed proteins are digested by &lt;a href=&quot;http://en.wikipedia.org/wiki/Peptidase&quot;&gt;peptidases&lt;/a&gt; (enzymes) in the stomach, breaking them down into their consituent &lt;a href=&quot;http://en.wikipedia.org/wiki/Amino_acid&quot;&gt;amino acids&lt;/a&gt;. These are absorbed in the gut and transported in the blood to all cells. These take up amino acids and attach them to &lt;a href=&quot;http://en.wikipedia.org/wiki/tRNA&quot;&gt;tRNA molecules&lt;/a&gt; which are used in &lt;a href=&quot;http://en.wikipedia.org/wiki/Translation_%28biology%29&quot;&gt;translation&lt;/a&gt; to form new body proteins.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-06-13T21:21:55.753" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2621" PostTypeId="2" ParentId="2615" CreationDate="2012-06-14T00:57:57.823" Score="11" Body="&lt;p&gt;Surely an important question. But there are different kinds of memory (classified mainly as declarative and procedural) which you don't specify exactly in your question. Wikipedia and Scholarpedia list here many known facts. I will give you some short hints and links for introduction and overview instead of pasting that stuff here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are probably referring to &lt;em&gt;autobiographical&lt;/em&gt; or &lt;em&gt;episodic memory&lt;/em&gt;, that is memorizing consciously particular events within one's own life within a context. And for this type of memory researchers agree that &lt;em&gt;self-awareness&lt;/em&gt; seems to be a necessary precondition. The existence of this cognitive ability can be checked by the &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mirror_test&quot; rel=&quot;nofollow&quot;&gt;mirror test&lt;/a&gt;&lt;/em&gt;. Human infants pass this test normally around a age of 18 months (also some animals). The cognitive self develops between &lt;a href=&quot;http://en.wikipedia.org/wiki/Memory_development#Cognitive_Self&quot; rel=&quot;nofollow&quot;&gt;21 and 24 months&lt;/a&gt; and marks the end of &lt;em&gt;infantile amnesia&lt;/em&gt;. &lt;/p&gt;&#xA;" OwnerUserId="45" LastEditorUserId="9943" LastEditDate="2015-05-29T13:56:27.640" LastActivityDate="2015-05-29T13:56:27.640" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2622" PostTypeId="1" CreationDate="2012-06-14T09:01:22.297" Score="2" ViewCount="146" Body="&lt;p&gt;Are there any resources out there for TFBS (transcription factor binding site) predictions for the yeast (&lt;em&gt;S. cerevisiae&lt;/em&gt;) and &lt;em&gt;S. pombe&lt;/em&gt; genomes? Even if these are only &lt;em&gt;de novo&lt;/em&gt; predictions, I would like to have access to them.&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="43" LastEditDate="2012-06-14T13:19:41.687" LastActivityDate="2015-12-28T19:50:21.883" Title="TFBS predictions for yeast and pombe?" Tags="&lt;bioinformatics&gt;&lt;transcription&gt;&lt;genomes&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2624" PostTypeId="2" ParentId="954" CreationDate="2012-06-14T11:11:38.693" Score="4" Body="&lt;p&gt;Untill puberty the follicles grown from primordial to antral stage (secondary folliccle) and oocytes are arrested in diplotene of profase I of meiosis I, without polar body, with a nucleous called germinative vesicle. After puberty, with gonadotrophis, they can grow more and ovulate. With LH surge they are stimulated to continuing meiosis and they lose the nucleous and became metafase I oocytes (MI) and extrude the first polar body to became secondary oocytes (MII oocytes) just before ovulation. So, the Graaf folicle, last stage of follicular development, has a secondary oocyte arrested in metafase II. Only after ovulation and with fecundation it is possible to escape from MII arrest and extrude the second polar body.&lt;/p&gt;&#xA;" OwnerUserId="1021" LastActivityDate="2012-06-14T11:11:38.693" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2625" PostTypeId="1" CreationDate="2012-06-14T11:12:24.570" Score="1" ViewCount="41" Body="&lt;p&gt;I am looking for a database where I could find a transcriptome (say obtained with a microarray analysis) of one (or ideally many) normal uveal melanocytes ?&lt;/p&gt;&#xA;" OwnerUserId="1020" LastEditorUserId="57" LastEditDate="2012-06-14T19:55:29.730" LastActivityDate="2012-06-14T19:55:29.730" Title="Where can I find a transcriptome of a normal uveal melanocyte?" Tags="&lt;cell-biology&gt;&lt;bioinformatics&gt;&lt;transcription&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2626" PostTypeId="1" AcceptedAnswerId="2757" CreationDate="2012-06-14T14:14:24.737" Score="7" ViewCount="1204" Body="&lt;p&gt;Physiological measurements such as respiration rate and assimilation rate depend on temperature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most papers report tissue temperature (e.g. leaf temperature for leaf measurements), although some report air temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My goal is to compare measurements in the literature.  I use leaf temperature at time of measurement to adjust the rates to a common temperature. Currently, I assume that if leaf temperature is not available, it is the same as air temperature. (This is often assumed in papers where the leaf temperature was not measured).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a way to estimate the difference between air temperature and leaf temperature? I can get fairly good estimates of other physiological traits (e.g. leaf thickness, albedo, stomatal conductance) as well as climate data (e.g. humidity, soil moisture content).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My model is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;$T_{leaf} = T_a + X + \epsilon$&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And I currently assume X = 0 in my calculations&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a better way to estimate X?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under what conditions would X &amp;lt; 0? X &gt; 0?&lt;/p&gt;&#xA;" OwnerUserId="154" LastEditorUserId="57" LastEditDate="2012-10-24T07:33:55.150" LastActivityDate="2012-10-24T07:33:55.150" Title="Can I estimate leaf temperature from air temperature? What other information would be required?" Tags="&lt;physiology&gt;&lt;plant-physiology&gt;&lt;photosynthesis&gt;&lt;ecophysiology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2627" PostTypeId="2" ParentId="2622" CreationDate="2012-06-14T15:36:48.150" Score="2" Body="&lt;p&gt;Try YEASTRACT &lt;a href=&quot;http://www.yeastract.com/&quot; rel=&quot;nofollow&quot;&gt;http://www.yeastract.com/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus&#xA;  Tracking) is a curated repository of more than 48333 regulatory&#xA;  associations between transcription factors (TF) and target genes in&#xA;  Saccharomyces cerevisiae, based on more than 1200 bibliographic&#xA;  references. It also includes the description of 298 specific DNA&#xA;  binding sites for more than a hundred characterized TFs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="973" LastActivityDate="2012-06-14T15:36:48.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2628" PostTypeId="2" ParentId="2625" CreationDate="2012-06-14T15:47:10.290" Score="1" Body="&lt;p&gt;I can't find any transcriptome data, but I did find miRNAome data from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18381&quot; rel=&quot;nofollow&quot;&gt;GEO at NCBI&lt;/a&gt; and &lt;a href=&quot;http://www.ebi.ac.uk/arrayexpress/browse.html?keywords=uveal%20melanocytes&quot; rel=&quot;nofollow&quot;&gt;Array Express at EMBL&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="973" LastEditorUserId="43" LastEditDate="2012-06-14T16:07:21.553" LastActivityDate="2012-06-14T16:07:21.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2629" PostTypeId="1" AcceptedAnswerId="2630" CreationDate="2012-06-14T17:42:05.480" Score="6" ViewCount="12602" Body="&lt;p&gt;From what I've read,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bioavailability is the degree to which food nutrients are available&#xA;  for absorption and utilization in the body.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;How would you explain this with an example?&lt;/p&gt;&#xA;" OwnerUserId="695" LastEditorUserId="695" LastEditDate="2012-06-14T17:52:52.113" LastActivityDate="2017-06-07T04:12:14.807" Title="What does the term 'bioavailability' mean?" Tags="&lt;nutrition&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2630" PostTypeId="2" ParentId="2629" CreationDate="2012-06-14T19:00:14.743" Score="11" Body="&lt;p&gt;Bioavailability is a concept which applies to nutrients and drugs which pass through &lt;a href=&quot;http://en.wikipedia.org/wiki/First-pass_metabolism&quot; rel=&quot;noreferrer&quot;&gt;first-pass metabolism&lt;/a&gt;, i.e. orally (and to some extent nasally) consumed substances. Anything absorbed in the gut first passes through the liver before reaching the rest of the circulation, and both the gut and liver may metabolise it to some extent. The liver in specific has the powerful &lt;a href=&quot;http://en.wikipedia.org/wiki/P450&quot; rel=&quot;noreferrer&quot;&gt;Cytochrome P450&lt;/a&gt; system, a huge variety of enzymes to break down all sorts of substances, although in some cases it can actually produce more active or even toxic forms instead of breaking them down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can lead to drastic reductions in the amount available in the systemic circulation after oral administration. E.g. propanolol (a beta blocker) needs to be given in 100mg doses orally while intravenously (avoiding first-pass metabolism) only 5mg are needed.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-06-15T00:09:18.670" LastActivityDate="2012-06-15T00:09:18.670" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2632" PostTypeId="2" ParentId="2616" CreationDate="2012-06-15T03:23:29.767" Score="4" Body="&lt;p&gt;You might want to read Gibson's paper on the step-wise assembly of the mouse mitochondrial genome &lt;a href=&quot;http://www.nature.com/nmeth/journal/v7/n11/full/nmeth.1515.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;(1)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SfkXC.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He started with 60b long oligos with 20b overlap, as he assembled 5 of those 60-mers into a backbone, obtaining 384b fragments. On the next step, he joined 5 of those 384mers, obtaining 1.2kb constructs. You can do the same, but on the second step use 2x 384mers to get you ~600bp gene. Gibson didn't use DNAWorks to chop up the sequence. He just started from base 1, so that his fragments were F1 [1:60], F2[41:100], F3[81:140], etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that 15b homology is pretty low (Gibson used 20b for assembling the 60mers in the first step, and 40bp homology for the next assemblies). 60b oligo length is standard.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also try one step assembly with all of your oligos (via PCA) as you planned, but I think that the two step assembly might be more efficient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me know if you need more help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nmeth/journal/v7/n11/full/nmeth.1515.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;1. Gibson et al, 2009. Chemical synthesis of the mouse mitochondrial genome&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-06-15T03:23:29.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2633" PostTypeId="1" CreationDate="2012-06-15T07:35:42.900" Score="3" ViewCount="339" Body="&lt;p&gt;To study DNA-protein interaction, I want to do a DNA retardation test by mixing the protein with DNA and afterwarts loading it on an agarose gel to see if the DNA migrates slower. I've found some articles where they do this and they state that they mix the DNA with protein in an 1:8 charge ratio, but I can't really figure out how to interpret this&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could anyone tell me how to calculate a DNA:protein charge ratio? If 1:8 is stated, how should I interpret this?&lt;/p&gt;&#xA;" OwnerUserId="1026" LastEditorUserId="6" LastEditDate="2012-06-16T06:47:55.173" LastActivityDate="2012-06-16T16:51:15.330" Title="What is the DNA/protein charge ratio?" Tags="&lt;dna&gt;&lt;gel-electrophoresis&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2634" PostTypeId="1" AcceptedAnswerId="2637" CreationDate="2012-06-15T08:55:07.803" Score="6" ViewCount="376" Body="&lt;p&gt;I would like to know of any publication studying the relative power of GWAS studies in different species. For example, I've seen reports that say genotyping and GWAS in dog breeds is much more powerful than in humans due to the extent of linkage disequilibrium and other population genetics considerations. Some claims say that many GWAS studies in dogs are 10-20x more powerful than many GWAS studies in humans. I have also heard from pigeons (pigeon-omics) to be a similar case. I would like to know if there are other comparisons for other species and the relative power of discovery for GWAS studies compared to human. For example, are there any numbers for yeast, &lt;em&gt;Drosophila sp.&lt;/em&gt;, &lt;em&gt;C.elegans&lt;/em&gt;, zebrafish and then also for plants like maize, rice, etc.?&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="107" LastEditDate="2012-06-15T17:56:19.343" LastActivityDate="2016-03-31T16:08:05.153" Title="What is the relative power of GWAS studies in different species?" Tags="&lt;genetics&gt;&lt;genomics&gt;&lt;gwas&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2635" PostTypeId="2" ParentId="2606" CreationDate="2012-06-15T11:24:39.670" Score="3" Body="&lt;p&gt;Not entirely on your question but I think sufficiently relevant:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1046/j.1464-410X.2003.04319.x&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; (freely available) identified a &lt;em&gt;non-causal&lt;/em&gt; link between ejaculatory frequency and incidence of prostate cancer.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Men were asked their age at first ejaculation, the maximum number of ejaculations ever experienced in 24 h, and to estimate the average number of times that they had ejaculated per week in their most sexually active year in each of three decades of age (i.e. third, fourth and fifth). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Leading to results indicating that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Greater ejaculatory frequency in the most sexually active year in each of the three decades was associated with a significantly lower risk, with men in the upper quartile of ejaculatory frequency having about two-thirds the risk of those in the lower quartile for the third and fourth decade, and four-fifths the risk for the fifth. Ejaculatory frequencies in each of the decades were correlated with one another (r = 0.5–0.7). A similar finding related to the total number of ejaculations over the three decades. Those who reported an average of four to five or more ejaculations per week had two-thirds the risk compared with those who, on average, ejaculated less than three times per week.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Giles, G.G., Severi, G., English, D.R., McCredie, M.R.E., Borland, R., Boyle, P. and Hopper, J.L. (2003), &lt;em&gt;Sexual factors and prostate cancer. BJU International&lt;/em&gt;, 92: 211–216. doi: 10.1046/j.1464-410X.2003.04319.x&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-06-15T11:24:39.670" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2636" PostTypeId="2" ParentId="2609" CreationDate="2012-06-15T11:48:27.930" Score="11" Body="&lt;p&gt;One of the important pigments that the earlier answer hinted at is &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanin&quot; rel=&quot;noreferrer&quot;&gt;melanin&lt;/a&gt;.  Melanin is a brown pigment with photoprotectant properties.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you correctly identified in your question, exposure to EM radiation (particularly UV and shorter λ waves) is damaging (indirectly) to DNA, which can cause mutations and therefore possibly cancer.  Melanin production is one of the defence mechanisms the body has evolved to deal with this threat.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When DNA is damaged by the UV-B radiation, melanogenesis (the increased production of melanin pigment) is induced.&lt;sup&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.mrfmmm.2004.11.016&quot; rel=&quot;noreferrer&quot;&gt;(1)&lt;/a&gt;&lt;/sup&gt;  Therefore, people often exposed to more UVB (i.e. in sunnier climates) are likely to have more melanin in their skin, which makes it appear darker in colour.  It is likely to be the increased incidence of melanin proteins in your skin which leads to the formation of a tan.     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Melanin and its derivatives work as photo-protectors (protecting the body from the damaging effects of ultra-violet exposure) by absorbing UV-B photons and converting them into much less damaging infra-red wavelengths (heat energy).  It does this extremely rapidly by &lt;a href=&quot;http://en.wikipedia.org/wiki/Internal_conversion_%28chemistry%29&quot; rel=&quot;noreferrer&quot;&gt;internal conversion&lt;/a&gt; and extremely efficiently - efficiency in excess of 99.9% &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15068035&quot; rel=&quot;noreferrer&quot;&gt;has been reported&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the melanin removes the danger posed by the UV within a few femtoseconds (x10&lt;sup&gt;-15&lt;/sup&gt; s), the more melanin that is present in skin tissues (and consequently the darker the skin), the lesser the chance of the UV damaging molecules in the skin so the lesser the risk of developing skin cancer. &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-08-29T21:03:41.603" LastActivityDate="2013-08-29T21:03:41.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2637" PostTypeId="2" ParentId="2634" CreationDate="2012-06-15T13:01:08.667" Score="5" Body="&lt;p&gt;Part of the increase in power to detect a genetic association via GWAS-genotyping comes from long haplotypes. Many dog breeds went through selective breeding bottlenecks 100-200 years ago. Many lab model organisms, such as flies, worms and plants, have recombinant inbred lines that aid in GWAS discovery as well. The price one pays for this increased power, say for canine GWAS, is &lt;strong&gt;not&lt;/strong&gt; being able to pinpoint the casual variant. The association SNP(s) found may be far, far away from the gene responsible for the phenotype, because of that long LD.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another aspect not to neglect is the phenotype. In humans, there may be a 3-fold range in phenotype &lt;em&gt;p&lt;/em&gt;, while in dog that value is just 35% (1.35x). That may mean that the phenotype is difficult to measure (accurately) and to assign to a given allele with statistical certainty.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A third aspect to consider is the effect size of the association, say on a per (risk) allele basis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, while I am not aware of any papers specifically taking such elements as haplotype length, phenotype range and effect size into an analysis of GWAS power across species, I feel that one versed in genetics of the organism of choice can readily accomplish this for the specific trait(s) of interest.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-06-15T13:01:08.667" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2638" PostTypeId="1" CreationDate="2012-06-15T14:48:37.953" Score="7" ViewCount="222" Body="&lt;p&gt;When modeling &lt;a href=&quot;http://en.wikipedia.org/wiki/Selective_sweep&quot; rel=&quot;nofollow&quot;&gt;selective sweeps&lt;/a&gt; as a micro-building block in models of &lt;a href=&quot;http://en.wikipedia.org/wiki/Macroevolution&quot; rel=&quot;nofollow&quot;&gt;macroevolution&lt;/a&gt; (not to be confused with misuses of this in creationist arguments), I use the fittest-win model of selection as a first approximation, or &lt;a href=&quot;http://en.wikipedia.org/wiki/Moran_process&quot; rel=&quot;nofollow&quot;&gt;Moran process&lt;/a&gt; model when I want a more reasonable approximation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the fittest win model the probability for a mutant of fitness r to invade a host population of fitness 1 is 100% if r &gt; 1 and 0 otherwise. In the Moran process model, the mutant of fitness r invades with probability $\frac{1 - r^{-1}}{1 - r^{-n}}$ for a finite population. Alternative in the limit as n goes to infinite, a mutant with r &gt; 1 invades with probability $1 - \frac{1}{r}$ and 0 otherwise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general I am interested in simple models of selection of a single (or small concentration of) mutant invading an asexual host population of fitness 1 (with fitness constant and independent of frequency). &lt;strong&gt;Are there other common mathematical models for selection of this type?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="57" LastEditDate="2012-10-24T07:30:37.090" LastActivityDate="2013-04-01T00:11:10.363" Title="Alternatives to fittest-win and Moran processes as simple mathematical models of selection" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2639" PostTypeId="2" ParentId="1920" CreationDate="2012-06-15T15:23:29.187" Score="2" Body="&lt;p&gt;It kind of depends.  If you want to compare apples to apples, check it first thing in the morning.  However, that's going to be at the lowest point. It's also important to know what your blood pressure is during the day, when you're living your normal daily life.  I recommend checking fairly regularly in the morning so you'll know what your true baseline is and whether it's trending up or down, and to &quot;spot-check&quot; occasionally at different times of the day to see how your body is handling the normal daily stress&lt;/p&gt;&#xA;" OwnerUserId="1027" LastActivityDate="2012-06-15T15:23:29.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2640" PostTypeId="2" ParentId="551" CreationDate="2012-06-15T15:35:22.513" Score="2" Body="&lt;p&gt;This book, although a little dated, has given me an incredible appreciation of biology that I never gained in school:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/What_Is_Life%3F&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;What is Life?&lt;/em&gt;&lt;/a&gt; by Erwin Shrodinger&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am not a biologist, but I occasionally work on mathematical-biology and have training in physics and theoretical computer science. This book was much more accessible to me that other books on biology. Before reading the book I perceived biology as a collection of fun facts (what Rutherford would call &quot;stamp collecting&quot;). Shrodinger's presentation was well tailored to the typical reductionist and &quot;everything must have a reason&quot; thinking of a theoretical physicists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the book does a good job of explaining the basics and providing intuition and grounding. The excited reader can then move on to more orthodox treatments.&lt;/p&gt;&#xA;" OwnerUserId="500" LastActivityDate="2012-06-15T15:35:22.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2641" PostTypeId="2" ParentId="2605" CreationDate="2012-06-15T18:06:23.833" Score="1" Body="&lt;p&gt;First let me agree with the commenters that your question doesn't really make sense.  Nonetheless here's an example that you may find interesting. Arachnocampa are insects that spend almost their entire lives as larva. These larva spin silk trap lines which capture and poison prey. They can only live in windless places (wind will mix up the lines) so to lure insects into caves they glow. By contrast their imago forms are short-lived poor fliers which are unable to eat.&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2012-06-15T18:06:23.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2642" PostTypeId="2" ParentId="2591" CreationDate="2012-06-15T19:44:50.590" Score="4" Body="&lt;h2&gt;Answer&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;An comprehensive online database of the chromosome numbers of all living species most likely doesn't exist. &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_organisms_by_chromosome_count&quot; rel=&quot;nofollow&quot;&gt;This Wikipedia article&lt;/a&gt; is the best and most complete reference comprising animals that I can personally find on the internet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.scielo.org.ar/scielo.php?script=sci_arttext&amp;amp;pid=S0073-34072003000100009&amp;amp;lng=pt&amp;amp;nrm=iso&quot; rel=&quot;nofollow&quot;&gt;This source in Spanish&lt;/a&gt;, which I've translated with Google Translate reads:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Canedo Delgado (1999) performed the karyotype description of the three species of the genus Pygoscelis , noting that there is a high homology both numerically and morphologically: Pygoscelis antarctica presented 2n = 92, Pygoscelis papua 2n = 94 and Pygoscelis adeliae 2n = 95 in females and 2n = 96 in males.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also, note that chromosome number cannot be &quot;guessed&quot; or &quot;assumed&quot; for closely-related species. As shown above, the three &lt;em&gt;Pygoscelis&lt;/em&gt; species have a high homology, but have very different chromosome numbers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other chromosome number you found for the species (38) is actually that of the Emperor penguin, as a simple Google search shows.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Ledesma, Mario A., T. R. O. Freitas, J. Da Silva, Fernanda Da Silva, and R. J. Gunski.&lt;/strong&gt; &lt;em&gt;“Descripción Cariotípica De Spheniscus Magellanicus (Spheniscidae).”&lt;/em&gt; El Hornero 18, no. 1 (August 2003): 61–64.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-08-12T19:36:32.517" LastActivityDate="2012-08-12T19:36:32.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2643" PostTypeId="2" ParentId="2591" CreationDate="2012-06-15T20:57:35.363" Score="3" Body="&lt;p&gt;Since you didn't specify animals, I will add here for anyone coming from google that plant chromosome numbers are stored in the &lt;a href=&quot;http://www.tropicos.org/Project/IPCN&quot; rel=&quot;nofollow&quot;&gt;Index to Plant Chromosome Numbers&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be surprised if such a database exists for animals (except maybe insects) as historically C-numbers of plants and other cytogenetics were important for taxonomy (and still is important), whilst this was not the case so much in zoology.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-06-15T20:57:35.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2644" PostTypeId="1" CreationDate="2012-06-15T21:41:42.673" Score="4" ViewCount="140" Body="&lt;p&gt;Where can I find an online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried the following: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Batch tool for GSFS: PROBLEM: It says that my input yeast genes are not human genes (which probably means that the tool will work only with Human genes).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://bioinformatics.clemson.edu/G-SESAME/Program/geneCompareTwo1.php&quot; rel=&quot;nofollow&quot;&gt;http://bioinformatics.clemson.edu/G-SESAME/Program/geneCompareTwo1.php&lt;/a&gt; : PROBLEM: provides score for every gene pair input. I have ~3600 genes. Impossible to do it for eveyr pair. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;DAVID batch viewer gives a 1xN matrix (functional similarity score of one gene to a set of N genes, when I want all possible pairs of similarities which will give an NxN matrix) &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;GO funsimmat- I am unable to get this to work, so I'm not sure if it will give me the desied results. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;GO FastSemSim- same as 4.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1030" LastEditorUserId="57" LastEditDate="2012-06-16T08:12:22.430" LastActivityDate="2012-07-01T08:35:47.390" Title="Online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology" Tags="&lt;bioinformatics&gt;&lt;genetics&gt;&lt;yeast&gt;&lt;software&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2645" PostTypeId="1" AcceptedAnswerId="2648" CreationDate="2012-06-15T23:05:56.607" Score="8" ViewCount="27226" Body="&lt;p&gt;I've read that they all share some genes, internal structure, and behaviour with each other, but with different degrees of overlap depending of what the function is. E.g., archaea have some eukaryotic and some bacterial function, and eukaryotes have bacterial function in the form of mitochondria and plastids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However I'm finding the nitty-gritty of all this rather confusing. Could anyone please explain some of the detail for me as I can't seem to make any sense of this from reading Wikipedia, etc.&lt;/p&gt;&#xA;" OwnerUserId="1031" LastEditorUserId="57" LastEditDate="2012-06-16T08:14:04.813" LastActivityDate="2012-06-19T12:47:50.253" Title="How do archaea relate to eukaryotes and bacteria?" Tags="&lt;evolution&gt;&lt;cell-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2646" PostTypeId="2" ParentId="1869" CreationDate="2012-06-15T23:32:54.433" Score="20" Body="&lt;p&gt;There are some other good answers which provide part of the picture, but I think there is a fundamental organising principle which has been missed. Konrad has touched on it in his answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The reason trees, and most plants, tend to grow equally in all directions is that they have iteratively generated branching and radial symmetry which is controlled in a feedback loop of the growth promoting hormone auxin and auxin-sensitive auxin transporters. This is an elegant biological algorithm which explains all branching growth.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The things Konrad identifies (phototropism, gravitropism, etc.) serve as orientation cues which help the plant determine which axes to grow along, but fundamentally the process is about auxin gradients. There are exceptions, as others have pointed out in their answers, and they usually result from severe imbalances in the orientation cues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll try to explain the growth process clearly (and it gives me an opportunity to try my hand at diagramming again ^_^)...&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Auxin is a plant hormone (actually a class of hormones, but mostly when people say auxin, they mean &lt;a href=&quot;http://en.wikipedia.org/wiki/Indole-3-acetic_acid&quot; rel=&quot;noreferrer&quot;&gt;indole-3-acetic acid&lt;/a&gt;) which promotes cell elongation and division. The basic principle which allows auxin to act in the organising way it does is that auxin is produced inside cells, and proteins which export auxin from a cell develop on the side of the cell which has the highest auxin concentration (see figure below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VGbXI.png&quot; alt=&quot;cells export auxin more on the side which has the highest auxin concentration&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So auxin gets transported up the concentration gradient of auxin!&lt;/strong&gt; Thus if you get an area of high auxin concentration developing somehow, more auxin is then transported towards that area. An area of high auxin concentration relative to the surrounding tissue is called an &lt;strong&gt;auxin maximum&lt;/strong&gt; (plural 'maxima').&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For most of the life of the plant, auxin is produced pretty much equally in most cells. However, at the very early stages of embryo development, it gets produced preferentially along the embryonic axis (see figure below, &lt;strong&gt;part 1&lt;/strong&gt;). That creates a &lt;strong&gt;meristem&lt;/strong&gt; - a group of cells where cell division is taking place - at the auxin maximum at each end of the embryo. Since this particular meristem is at the apex of the plant, it is called the &lt;strong&gt;apical meristem&lt;/strong&gt;, and it is usually the strongest one in the plant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bSY6i.png&quot; alt=&quot;auxin patterning of plant growth&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So by having a meristem at each end, the embryo then elongates as cell division is only taking place at those points. This leads to &lt;strong&gt;part 2&lt;/strong&gt; of the image above, where the two meristems get so far apart that the auxin gradient is so weak as to no longer have its organising effect (area in the red square). When that happens, the auxin produced in cells in that area concentrates in a chaotic way for a short time until another center of transport is created. This happens, as the first one did, when a particular area of the tissue has a slightly higher concentration of auxin, and so auxin in the surrounding tissue is transported towards it. This leads to &lt;strong&gt;part 3&lt;/strong&gt; of the figure, in which two new meristems are created on the sides of the plant (called &lt;strong&gt;lateral meristems&lt;/strong&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lateral meristems are where branches occur on plants. If you then imagine this process continuing to iterate over and over, you will see that the branches, as they elongate, will develop meristems at the tips and along the sides. The main stem will also continue elongating, and develop more lateral stems. The root will begin to branch, and those branches will branch, etc. If you can understand how this elegant system works, you understand how plants grow, and why they grow in repeating units as opposed to in a body plan like animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also explains why, if you cut off the tip of a stem, it promotes branching. By removing the apical meristem, you get rid of the auxin gradient and enable the creating of multiple smaller meristems which each develop into branches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far I've explained regular branching, but the same system causes the radial symmetry which makes trees (usually) grow in all directions equally...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/81e6B.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine taking a cross section through a stem and looking down all the way through it (as depicted crudely above). Just as auxin gradients act to coordinate growth along the length of the plant, they also coordinate it radially, as the maxima will tend to space themselves out as far from one another as possible. That leads to branches growing in all directions equally (on average).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I welcome comments on this answer, as I think its so important to understanding plant growth that I'd like to hone my answer to make it as good as possible.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-06-15T23:32:54.433" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2647" PostTypeId="2" ParentId="2645" CreationDate="2012-06-15T23:53:25.627" Score="2" Body="&lt;p&gt;Indeed the situation is a bit complicated and not totally well understood.  Archaea and bacteria are superficially very similar, they're both small, have circular chromosomes, and not a lot of internal complexity.  However, there are some very important differences, most notably they have very different cell membranes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The origin of the eukaryotic cell is a very difficult subject, as it evolved over 2 billion years ago in organisms that don't fossilize well and there are no living descendants of intermediate forms.  (E.g. every known Eukaryote is descended from a eukaryote that already had mitochondria.)  My understanding is that the leading theory is that the eukaryotic cell was formed by endosymbiosis between an archaeon and two bacteria.  In that model the nucleus is descended from a methanogenic archaeon, the cell membrane is descended from a myxobacteria, and the mitochondria is descended from a proteobacteria.  But this is not fully understood, and there are several competing theories on the details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One place to start reading about this (beyond wikipedia) is a nice &lt;a href=&quot;http://carlzimmer.com/articles/2009.php?subaction=showfull&amp;amp;id=1249671744&amp;amp;archive=&amp;amp;start_from=&amp;amp;ucat=12&amp;amp;&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; by Carl Zimmer in Science.&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2012-06-15T23:53:25.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2648" PostTypeId="2" ParentId="2645" CreationDate="2012-06-16T00:10:09.443" Score="5" Body="&lt;p&gt;The relationship between the three is so overly complicated because of horizontal gene transfer, i.e. cells sharing parts of their genome with others instead of the normal passing-down to the next generation. This works between eukaryotes, archaea and bacteria and causes the mixing of the three.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An overview (originally proposed by &lt;a href=&quot;http://www.pnas.org/content/87/12/4576.long&quot; rel=&quot;nofollow&quot;&gt;Woese &lt;em&gt;et al&lt;/em&gt;&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Bacteria are simplest considering cellular organisation. They have no nucleus or other internal membranes and no cytoskeleton. Their DNA is generally &quot;junk-free&quot;* (i.e. no introns), not bound by histones (&quot;organising&quot; proteins) and the organisation of regulatory sequences is relatively straightforward, typically with one 'operator' sequence before a gene.&lt;/li&gt;&#xA;&lt;li&gt;Eukaryotes are complex cells in comparison. They have a nucleus and are full of internal membranes (ER, golgi, vesicles,...). Their complex cytoskeleton allows them to grow very large in comparison. Their DNA is usually full of more or less &quot;junk&quot;*, organised into tight bundles by histones and they tend to have a ridiculous amount of regulatory sequences way before, just at the start and even &lt;em&gt;inside&lt;/em&gt; genes. Very importantly, they possess endosymbionts as you mentioned - mitochondria or plasmids, derived probably from some protobacterium.&lt;/li&gt;&#xA;&lt;li&gt;Archaea at first appear to be a mixture between the two. A nice way to sum it up (though not very accurate) is &quot;eukaryote in a bacterium's clothing&quot;. Their cells look a lot like prokaryotes because they are similar size, have no nucleus, endomembranes or cytoskeleton. However, some archaeas' DNA &lt;em&gt;is&lt;/em&gt; bound by histones and they use similar machinery as eukaryotes for DNA replication, transcription and translation.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;One possible explanation for this (theory by &lt;a href=&quot;http://www.amazon.co.uk/Five-Kingdoms-Illustrated-Guide-Phyla/dp/0716730278&quot; rel=&quot;nofollow&quot;&gt;Margulis &amp;amp; Schwartz&lt;/a&gt; as explained by my tutor) is: From the last universal common ancestor, first prokaryotes and archaea diverged. After this branching, the differences in genetic machinery evolved. Archaea then branched, producing a protoeukaryote line which went on to endosymbiosis with some protobacteria. That would explain the similarities I outlined above: similar cell structure between archaea and prokaryotes but similar genetic machinery between archaea and eukaryotes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It gets a bit more complicated though, because archaea and bacteria can exchange genetic material, and eukaryotes incorporated a lot of their endosymbionts' DNA in their own genome, so you end up with all of them having a huge mix of genes from the others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: Genetic machinery refers to the enzymes used for DNA replication and transcription (DNA and RNA polymerase and the transcription initiation factors) and translation (ribosomes and several other translation factors involved). For example: Prokaryotes only have one type of RNA polymerase which uses sigma factor to bind the initiaion site. Eukaryotes and archaea both have three types of RNA polymerase which use TATA-binding protein for initiation. Or: In Prokaryotes, the translation start codon codes for formyl-methionine while in eukaryotes and archaea it codes for &quot;normal&quot; methionine. (&lt;a href=&quot;http://dx.doi.org/10.1016/S0092-8674%2800%2980284-6&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*) Unrelated to your question, but in my own defence: I am aware that the usage of the word &quot;junk&quot; is somewhat unaccepted nowadays, because it supposes that there is &quot;useful&quot; and &quot;unuseful&quot; genetic material. Also, some of what was thought to be junk has been identified to have regulatory function etc. However, it's also a fact that a lot has been identified to have no function to the cell whatsoever, most of it parasitic DNA which is dead or still happily replicating away (LINEs and SINEs). That is, &quot;junk&quot; to the cell.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-06-19T12:47:50.253" LastActivityDate="2012-06-19T12:47:50.253" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2649" PostTypeId="1" CreationDate="2012-06-16T00:58:54.373" Score="11" ViewCount="407" Body="&lt;p&gt;I was wondering if anyone has ever seen large deletions (~40-50 bp) occur when using phusion polymerase to clone a gene.  I have recently tried using Circular Polymerase Extension cloning to clone a 200 bp insert into a 6.5kb plasmid and obtained two separate clones with 40bp+ deletions in the center of the insert.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phusion has a 5'-&gt;3' exonuclease activity, but I didn't think it could cut in the center of a sequence.  While our inserts were created with oligo synthesis, it is my understanding that such large deletions are rare with oligo synthesis. If you have heard of this happening please let me know.  &lt;/p&gt;&#xA;" OwnerUserId="1032" LastActivityDate="2014-01-10T04:15:58.967" Title="Deletion errors with Phusion Polymerase?" Tags="&lt;cloning&gt;&lt;pcr&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2650" PostTypeId="1" AcceptedAnswerId="2652" CreationDate="2012-06-16T02:17:06.100" Score="12" ViewCount="1256" Body="&lt;p&gt;The most recent &lt;a href=&quot;http://en.wikipedia.org/wiki/Race_%28human_classification%29#CITEREFLiebermanHamptonLittlefieldHallead1992&quot;&gt;survey&lt;/a&gt; I could find was from 1985 which said that 16% of biologist disagreed that &quot;[t]here are biological races in the species Homo sapiens.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering if there's been a change in this position.&lt;/p&gt;&#xA;" OwnerUserId="1033" LastEditorUserId="1033" LastEditDate="2012-06-16T02:23:28.627" LastActivityDate="2015-01-05T08:52:50.733" Title="Is there a consensus on whether or not race exists on a biological level?" Tags="&lt;human-biology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2651" PostTypeId="1" AcceptedAnswerId="2702" CreationDate="2012-06-16T05:21:35.040" Score="3" ViewCount="852" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ligation-independent_cloning&quot; rel=&quot;nofollow&quot;&gt;Ligase Independent Cloning&lt;/a&gt; is a protocol that allow an insert to be integrated into a vector without ligation.  It uses T4 DNA polymerase with only ATP to first chew back from blunt ends to create long sticky ends and then a polymerase treatment with full dNTP compliments to fill in the vector.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While there are several &lt;a href=&quot;http://bitesizebio.com/articles/get-your-clone-90-of-the-time-with-ligation-independent-cloning/&quot; rel=&quot;nofollow&quot;&gt;nice&lt;/a&gt; &lt;a href=&quot;http://bitesizebio.com/articles/ligation-independent-cloning-primer-design/&quot; rel=&quot;nofollow&quot;&gt;articles&lt;/a&gt; and &lt;a href=&quot;http://bioinfo.clontech.com/infusion/convertPcrPrimersInit.do&quot; rel=&quot;nofollow&quot;&gt;resources&lt;/a&gt; that describe the procedure, I really would like a protocol with concentrations, temperatures and timing, which I'm having problems finding.  OpenWetWare for instance has only &lt;a href=&quot;http://openwetware.org/wiki/Duffy%3aLIC_Cloning&quot; rel=&quot;nofollow&quot;&gt;stub pages&lt;/a&gt; with &lt;a href=&quot;http://openwetware.org/wiki/T4_DNA_Polymerase&quot; rel=&quot;nofollow&quot;&gt;no details&lt;/a&gt;.  Can anyone point to a full step by step recipe to make this work, once you have designed the primers? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2015-02-09T22:43:47.870" Title="Open protocol for Ligase Independent Cloning" Tags="&lt;cloning&gt;&lt;protocol&gt;&lt;polymerase&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2652" PostTypeId="2" ParentId="2650" CreationDate="2012-06-16T11:00:06.247" Score="7" Body="&lt;p&gt;This has been &lt;a href=&quot;https://skeptics.stackexchange.com/q/399/82&quot;&gt;investigated extensively&lt;/a&gt; on &lt;a href=&quot;https://skeptics.stackexchange.com/&quot;&gt;skeptics.stackexchange.com&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, it’s not easy to determine a scientific consensus since nobody has cited a relevant survey. On the other hand, here are some salient quotes from scientific literature (stolen from the answers to the above-mentioned question) which I find worth repeating:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A subspecies (race) is a distinct evolutionary lineage within a species. This definition requires that a subspecies be genetically differentiated due to barriers to genetic exchange that have persisted for long periods of time; that is, the subspecies must have historical continuity in addition to current genetic differentiation. [Templeton, 1998], cited in [Long &amp;amp; Kittles, 2003]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Which speaks &lt;strong&gt;against&lt;/strong&gt; the existence of races as a meaningful biological concept.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, Jorde &amp;amp; Wooding (2004) contend that,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Genetic variation is geographically structured, as expected from the partial isolation of human populations during much of their history. Because traditional concepts of race are in turn correlated with geography, &lt;strong&gt;it is inaccurate to state that race is &quot;biologically meaningless&quot;&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But they concede that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;there is no scientific support for the concept that human populations are discrete, nonoverlapping entities.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Finally, it’s worth noting that &lt;strong&gt;in the universally agreed-on taxonomy&lt;/strong&gt;, formalised in the &lt;a href=&quot;http://en.wikipedia.org/wiki/International_Code_of_Zoological_Nomenclature&quot; rel=&quot;nofollow noreferrer&quot;&gt;International Code of Zoological Nomenclature&lt;/a&gt; &lt;strong&gt;there simply is no category for races&lt;/strong&gt;, whether they would make sense or not. Whether or not this view enjoys a majority vote in biology, it’s the de facto consensus.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://muse.jhu.edu/login?auth=0&amp;amp;type=summary&amp;amp;url=/journals/human_biology/v075/75.4long.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Jeffrey C. Long &amp;amp; Rick A. Kittles, &lt;em&gt;Human Genetic Diversity and the Nonexistence of Biological Races&lt;/em&gt;, Human Biology 75 (&lt;strong&gt;4&lt;/strong&gt;), pp. 449–471, Aug 2003&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/ng/journal/v36/n11s/full/ng1435.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lynn B. Jorde &amp;amp; Stephen P. Wooding, &lt;em&gt;Genetic variation, classification and ‘race’&lt;/em&gt;, Nature Genetics 36, pp. 28–33, 2004&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="166" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2012-06-16T11:00:06.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2653" PostTypeId="1" AcceptedAnswerId="2654" CreationDate="2012-06-16T12:23:42.510" Score="9" ViewCount="213" Body="&lt;p&gt;If there are three different alleles to a gene, is it possible that the first is dominant to the second, but recessive to the third?&lt;/p&gt;&#xA;" OwnerUserId="1034" LastActivityDate="2012-06-17T15:03:25.400" Title="Relative Property of Alleles" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2654" PostTypeId="2" ParentId="2653" CreationDate="2012-06-16T13:37:24.853" Score="10" Body="&lt;p&gt;Sure it is!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When we say that an allele is dominant on another what we really mean is that the phenotype obtained from that specific mutation of the gene somehow &quot;masks&quot; the phenotype of the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The easiest example would be that of pigment. A gene X could code for an enzyme which produces a red pigment. A mutation in X could result in a allelic variant x coding for a non-functional enzyme that does not produce pigment. In this case X will be dominant on x, as in the presence of both the pigment will still be produced (because you will have half functional and half non-functional enzyme molecules).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Things can, however be slightly complicated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, if the allele R codes gives a red pigment and r gives a white pigment Rr could give pink. This is called &lt;strong&gt;incomplete dominance&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand you could have &lt;strong&gt;co-dominance&lt;/strong&gt;, where WW is white, ww is black and Ww is black and white.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The example you are asking for is called &lt;strong&gt;serial dominance&lt;/strong&gt; and the &quot;classical&quot; example given is that of the rabbit coat color where you have for alleles with a dominance hierarchy like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c+ &gt; c&lt;sup&gt;ch&lt;/sup&gt; &gt; c&lt;sup&gt;h&lt;/sup&gt; &gt; c&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c+ gives a fully functional enzyme, called tyrosinase&lt;br&gt;&#xA;c gives a non-functional enzyme, resulting in an albino phenotype&lt;br&gt;&#xA;c&lt;sup&gt;ch&lt;/sup&gt; (chincilla phenotype) and c&lt;sup&gt;h&lt;/sup&gt; (hymalayan phenotype) give partly functional enzyme (interestingly, the latter gives a temperature sensitive fur color). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In reality the rabbit coat genetics is even more complex, see &lt;a href=&quot;http://www.amysrabbitranch.com/Color%26Genetics/Biochemistry-CoatColor.pdf&quot; rel=&quot;nofollow&quot;&gt;this documents (PDF)&lt;/a&gt; for a more complete list of all the various loci and possible alleles involved.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2012-06-17T15:03:25.400" LastActivityDate="2012-06-17T15:03:25.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2655" PostTypeId="2" ParentId="2650" CreationDate="2012-06-16T16:25:05.050" Score="13" Body="&lt;p&gt;Anatomically modern humans are less than 200K years old, left Africa (or possibly Africa and Arabia) only 60K years ago, and migrate quite a lot (think of the Mongol invasion).  So you would not expect to have clear divisions into subspecies.  And indeed a quick search of google scholar pulls up no claims in the literature for human subspecies of anatomically modern humans (i.e. no subspecies of homo sapiens since Neanderthals and Denisovans).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, it's certainly the case that you can work out a rough phylogenetic tree of humans.  Native americans are descended from certain northern and eastern asians, and so in the 1400s were more closely related to them then they were to other humans.  Similarly, Austronesians (of Indonesia and Polynesia, e.g.) are more closely related to Taiwanese aborigines than they are to Australian aborigines.  This tree is complicated by how much more migration there has been in the last 1000 years than there was previous to that, but it's still biologically meaningful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But here's the striking thing: traditional notions of &quot;race&quot; do not match up well with this tree.  The deepest and most fundamental phylogenetic splits in the human tree are &lt;em&gt;within Africans&lt;/em&gt;.  If you were going to try to &quot;scientifically&quot; come up with races, you'd end up with something vaguely like one for Khoisan, one for other Africans, and one for all non-Africans.  Even ignoring modern admixture, traditional races are not monophyletic.  Any clade including all &quot;black&quot; people includes all people, any clade including all &quot;east asians&quot; includes all native americans.  (Also note that traditional notions of &quot;race&quot; are not stable over time, remember that &quot;Irish&quot; used to be a &quot;race&quot; on the US census.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Modern admixture even more clearly shows the non-genetic nature of traditional &quot;races.&quot;  One genetic &lt;a href=&quot;http://www.eurekalert.org/pub_releases/2009-12/uop-gsc121809.php&quot;&gt;study&lt;/a&gt; of people who identify as African-American, found that African ancestry can be as low as 1% and as high as 99%, with the median African-American having 18.5% European ancestry (with 30% having European y-dna).  Furthermore, relatively ancient admixture (for example, in the Northern Africa, Northeastern Africa, Middle East region or in Madagascar) also complicates the situation significantly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To summarize, although human genetic diversity is a real biological phenomenon which can be used to figure out the geographical history of people's ancestors, traditional notions of race do not match up well with the biologically meaningful concepts.&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2012-06-16T16:25:05.050" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2656" PostTypeId="2" ParentId="2633" CreationDate="2012-06-16T16:51:15.330" Score="1" Body="&lt;p&gt;This is really sounds like a guideline, a starting place, not necessarily your best protocol. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practice its hard to be more specific as MS says.  The pH of the buffer will affect the charge of the protein, and to a lesser extent the DNA.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also the protein may have an ideal pH for binding which you could guess is in the range of &lt;a href=&quot;http://en.wikipedia.org/wiki/Cytosol#Water&quot; rel=&quot;nofollow&quot;&gt;7.0-7.4&lt;/a&gt;, but might find that the strongest binding depends on unexpected pH and salt concentrations, or the addition of a small molecule.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The affinity of araC for &lt;a href=&quot;http://en.wikipedia.org/wiki/L-arabinose_operon#Activation&quot; rel=&quot;nofollow&quot;&gt;instance is greatly increased by&lt;/a&gt; the presence of arabinose in sufficient concentration.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;lac Repressor, in contrast releases itself from DNA in the presence of IPTG or  lactose.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-06-16T16:51:15.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2658" PostTypeId="1" AcceptedAnswerId="2749" CreationDate="2012-06-16T18:49:56.980" Score="4" ViewCount="827" Body="&lt;p&gt;According to wikipedia, &lt;a href=&quot;http://en.wikipedia.org/wiki/Progerin&quot; rel=&quot;nofollow&quot;&gt;progerin&lt;/a&gt; is activated in senescent cells. The protein itself is known to be the cause of a rare affliction '&lt;a href=&quot;http://en.wikipedia.org/wiki/Progeria&quot; rel=&quot;nofollow&quot;&gt;progeria&lt;/a&gt;' - a disease marked by accelerated aging of the body. This disease is not accompanied by neurodegeneration.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Is progerin the key factor in the aging process?&lt;/li&gt;&#xA;&lt;li&gt;If yes, could inhibition of progerin formation control the rate at which a body ages?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2012-06-26T15:12:01.180" Title="Could inhibition of progerin formation slow the rate at which a body ages?" Tags="&lt;human-biology&gt;&lt;senescence&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2659" PostTypeId="2" ParentId="1920" CreationDate="2012-06-16T20:53:58.983" Score="1" Body="&lt;p&gt;Actually in my research into circadian events, the hourly differences in blood pressure was the first thing that I found. Based on this, &lt;strong&gt;I'd state that there are hourly differences in blood pressure and cardiovascular efficiency.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because these changes are circadian, measuring these values at the same time every day (ex: 1 hour after wake up time or 1 hour before bedtime) would reduce variation. Just be aware of your caffeine intake - it may skew the measurements.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not have access to the scholarly library that I used then, so the chances of finding the article are slim to none. &lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-06-16T20:53:58.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2660" PostTypeId="1" CreationDate="2012-06-16T21:03:57.040" Score="5" ViewCount="461" Body="&lt;p&gt;A little background: I'm an avid dreamer and have great dream recall, sometimes up to 5-7 per night. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my experience, I can sometimes trace some elements of the dream to an event that occured within a 1-3 day window prior to the dream. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've done similar experiments with the process of idea generation, where an idea that I have can be traced to experiences from the previous 1-3 days. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This makes me interested if there have been some kind of studies on how rapidly the brain absorbs and assimilates information from short term memory over to the long term memory. &lt;strong&gt;Has there been any studies on how long the brain keeps information before discarding or processing/assimilating it into dreams or new ideas?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-06-16T21:03:57.040" Title="What is the timing of information assimilation within a human brain?" Tags="&lt;human-biology&gt;&lt;sleep&gt;&lt;brain&gt;&lt;dreaming&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ClosedDate="2014-06-04T14:28:13.293" ContentLicense="CC BY-SA 3.0" />
  <row Id="2663" PostTypeId="2" ParentId="1032" CreationDate="2012-06-17T01:17:54.867" Score="4" Body="&lt;p&gt;Microtubules are a structure in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cytoskeleton&quot; rel=&quot;nofollow&quot;&gt;cytoskeleton&lt;/a&gt;, they are rope like polymers that grow to a length of about 25 micrometers (25000 nm), and have an outer-diameter of around 25 nm. For comparison, the mean spacing between atoms is on the order of 0.1  to 0.2 nm; so the micro tubule really is micro: about 200 atoms across. In terms of quantum effects though, this is pretty big but not unreasonable. Researchers commonly use &lt;a href=&quot;http://en.wikipedia.org/wiki/Quantum_dot&quot; rel=&quot;nofollow&quot;&gt;quantum dots&lt;/a&gt; to play with quantum effects, and these are typically spheres on the order of 10 to 50 atoms in diameter. Note, that we don't know how to couple 5000 quantum dots in one coherent chain (how many you would need to get the length of a microtubule).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So microtubules are small, but they are common! &lt;strong&gt;Microtubules are found in all dividing &lt;a href=&quot;http://en.wikipedia.org/wiki/Eukaryote&quot; rel=&quot;nofollow&quot;&gt;eukaryotic cells&lt;/a&gt; and in most differentiated cell types&lt;/strong&gt;. In other words, that mosquito you just smacked and that philosophers always give as an example of something non-conscious is &lt;em&gt;full of&lt;/em&gt; microtubules. This should raise some red flags, but we don't need to go into more detail of microtubules to discredit Penrose and Hammeroff. However, if you love cell biology, take a look at &lt;a href=&quot;http://mitchison.med.harvard.edu/publications/AnnRevCelDevBioV13p83.pdf&quot; rel=&quot;nofollow&quot;&gt;Desai &amp;amp; Mitchison (1997)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So microtubules are probably a bad basis, but why did Penrose want quantum effects in the brain? In &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Emperor%27s_New_Mind&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;The Emperor's New Mind&lt;/em&gt;&lt;/a&gt;, Penrose suggests consciousness is non-algorithmic and suggests that a magical quantum computer could do these non-algorithmic tasks. The reason I use 'magical' is because a real quantum computer is Turing-complete, &lt;strong&gt;if a classical computer cannon solve a problem then neither can a quantum one&lt;/strong&gt; (of course, if a classical computer can solve a problem, then quantum one can as well and might be able to do it qualitatively faster). For a nice computer science debunking of this part of Penrose's argument take a look a Scott Aaronson's &lt;a href=&quot;http://www.scottaaronson.com/democritus/lec10.5.html&quot; rel=&quot;nofollow&quot;&gt;lecture notes&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why did Hammeroff want quantum-ness? To avoid dualism in explaining consciousness. However, he has gone so far down the reductionist rabbit-hole that he popped out on the other side. He arrived at the same 'magic' we feared in dualism except now he called it 'quantum mechanics'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biggest irony of this approach is that Penrose was inspired in many ways by Schrodinger's beautiful take on life. Although Schrödinger does bring in quantum mechanics (both as a useful reduction and as an analogy) he uses completely different parts of it (he uses the discritization of energy levels, and specially avoids issues of the uncertainty principle and superposition of states that made him famous).  Schrödinger would completely disagree with Penrose and Hameroff::&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[I]f we were organisms so sensitive that a single atom, or even a few atoms, could make a perceptible impression on our senses -- Heaves, what would life be like! To stress one point: an organism of that kind would most certainly not be capable of developing the kind of orderly thought which, after passing through a long sequence of earlier stages, ultimately results in forming, among many other ideas, the idea of an atom.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This response can be made precise through quantum decoherence (&lt;a href=&quot;http://pre.aps.org/abstract/PRE/v61/i4/p4194_1&quot; rel=&quot;nofollow&quot;&gt;Tegmark, 2000&lt;/a&gt;) and &lt;strong&gt;there is little regard for the physical importance of quantum mechanics in the brain&lt;/strong&gt; (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1207/s15516709cog0000_59/abstract&quot; rel=&quot;nofollow&quot;&gt;Litt et al., 2006&lt;/a&gt;) although &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1080/03640210701704004/full&quot; rel=&quot;nofollow&quot;&gt;Hammeroff (2007)&lt;/a&gt; still defends it.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="166" LastEditDate="2012-06-17T16:26:33.340" LastActivityDate="2012-06-17T16:26:33.340" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2664" PostTypeId="2" ParentId="1614" CreationDate="2012-06-17T02:25:08.590" Score="15" Body="&lt;p&gt;The basis of this question is a &lt;a href=&quot;https://cogsci.stackexchange.com/q/337/29&quot;&gt;common misconception&lt;/a&gt;, and unfortunately the accepted answer by @CHM is also based on this common misconception. The misconception is based on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Homunculus_argument&quot; rel=&quot;nofollow noreferrer&quot;&gt;homunculus falacy&lt;/a&gt;: the tendency for people to think that the image that lands on the retina is &lt;a href=&quot;https://cogsci.stackexchange.com/q/1125/29&quot;&gt;somehow 'assembled'&lt;/a&gt; and presented for something (the 'consciousness') to view. This is not the case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/1614/how-do-we-know-the-brain-flips-images-projected-on-the-retina-back-around#comment2032_1614&quot;&gt;As the comment by @mgkrebbs&lt;/a&gt; explains, there is no orientation (up or down) in the brain, there is only neural firing. The information of the visual scene is distributed over the brain, and information does not have physical properties like orientation. Although as &lt;a href=&quot;https://biology.stackexchange.com/questions/1614/how-do-we-know-the-brain-flips-images-projected-on-the-retina-back-around#comment2039_1614&quot;&gt;@nico pointed out&lt;/a&gt; the neurons that process the information do have a spatial structure that mimics that of the retina, this is a topological property (i.e. stimuli that are close on the retina are processes by neurons that are close in V1) and such a topological property does not induce an orientation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The root of the problem is really that the question &quot;How do we know the brain flips images projected on the retina back around?&quot; is a pseudo-question. Although it is grammatically well-formed, it makes no semantic sense. When the image is 'in the' (i.e. being processed by the) brain it no longer has physical properties like orientation. Thus you cannot ask if it has been flipped or not.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2017-04-13T12:56:15.910" LastActivityDate="2016-12-27T01:20:40.160" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2665" PostTypeId="1" AcceptedAnswerId="2666" CreationDate="2012-06-17T04:47:14.480" Score="7" ViewCount="6253" Body="&lt;p&gt;From what I read on wikipedia they are made of collagen. Collagen is just a protein. Right? How is this collagen structured (I imagine like fibers). Aren't there cells in this fibers as well?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this picture:&lt;br&gt;&#xA;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/6/66/Tendon_-_very_high_mag.jpg&quot; alt=&quot;Tendon H&amp;amp;E&quot;&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the pink stuff the collagen? and the purple stuff the tenocytes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If someone can expand on this with a picture preferably, it would be great.&lt;/p&gt;&#xA;" OwnerUserId="952" LastEditorUserId="630" LastEditDate="2019-06-12T19:27:16.147" LastActivityDate="2019-06-30T06:28:23.240" Title="What are tendons made of specifically" Tags="&lt;human-biology&gt;&lt;tendons&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2666" PostTypeId="2" ParentId="2665" CreationDate="2012-06-17T05:33:08.370" Score="10" Body="&lt;p&gt;As you correctly say, tendons are made up of collagen fibers. Collagen is one of the most important proteins (or, to be more specific, family of proteins, as there are many types of collagen) forming connective tissue in the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Collagen molecules have a particular structure that allows them to form long fibers, composed by three different strands that form a triple helix. This is a schema of a collagen helix (each ball represents one aminoacid):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/d/d1/Collagentriplehelix.png/120px-Collagentriplehelix.png&quot; alt=&quot;Collagen helix&quot;&gt;&lt;br&gt;&#xA;(source: &lt;a href=&quot;http://en.wikipedia.org/wiki/Collagen&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These helices can then be bound together to form a collagen fiber, through the action of an enzyme called &lt;em&gt;lysyl oxidase&lt;/em&gt; which binds two lysine residues from two different helices together (lysine is one of the aminoacids that makes up collagen).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a scanning electron microscope of a collagen fiber:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://www.sciencephoto.com/image/80742/530wm/C0016340-Synovial_collagen_fibres,_SEM-SPL.jpg&quot; alt=&quot;Collagen fiber, SEM&quot;&gt;&lt;br&gt;&#xA;(source: &lt;a href=&quot;https://www.sciencephoto.com/media/80742/enlarge&quot; rel=&quot;nofollow noreferrer&quot;&gt;Science photo library&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Collagen is secreted out of the cells that produce it so, although there may be cells around the collagen molecules, it is important to understand that it is part of what is called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Extracellular_matrix&quot; rel=&quot;nofollow noreferrer&quot;&gt;extracellular matrix&lt;/a&gt;, the extracellular structure that supports the cells in our body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the photo you linked, it is an &lt;a href=&quot;http://en.wikipedia.org/wiki/H%26E_stain&quot; rel=&quot;nofollow noreferrer&quot;&gt;hematoxylin and eosin (H&amp;amp;E) stain&lt;/a&gt; of a tendon. Hematoxylin colours cell nuclei in dark blue, so the dark spots are definitely cells.&#xA;The pink &quot;waves&quot; are indeed collagen fibers, the cells are probably the tenocytes, the specialized fibroblasts of the tendon, which produce the collagen.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.693" LastActivityDate="2012-06-17T05:33:08.370" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2668" PostTypeId="1" AcceptedAnswerId="6849" CreationDate="2012-06-17T12:06:20.373" Score="11" ViewCount="1157" Body="&lt;p&gt;Single crossovers in circular pieces of DNA do not seem to be a big topic, because if they happened, they would lead to a kind of combined chromosome with two inner strands and one large outer strand. (A bit like an 8)&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; ________&#xA;|  ____  |&#xA;| |    | |&#xA;| |____| |&#xA;|  ____  |&#xA;| |    | |&#xA;| |____| |&#xA;|________|&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;But do these single crossovers actually not &lt;em&gt;occur&lt;/em&gt;, for example because the crossover machinery is physically not able to do it, or do we just not &lt;em&gt;observe&lt;/em&gt; them because they will inevitably lead to cell death and/or the chromosome somehow breaking?&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-01-24T09:17:59.517" LastActivityDate="2016-08-28T16:46:20.577" Title="Do single crossovers occur in circular polynucleotides?" Tags="&lt;molecular-genetics&gt;&lt;plasmids&gt;&lt;chromosome&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2670" PostTypeId="1" CreationDate="2012-06-17T17:15:42.950" Score="7" ViewCount="185" Body="&lt;p&gt;My question is simple:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that evolution is described by random genetic mutations allowing certain members of a species to gain a reproductive advantage over others that coexist in the particular environment- I am curious- single genetic mutations do not seem to really explain complex morphic changes such as the length of a giraffes neck. Instead it appears it must be a compilation of many such mutations. So what are the statistics for mutations? How long does it really take for so many to favorably compile? How does this compare with the reproductive time of the species?&lt;/p&gt;&#xA;" OwnerUserId="1038" LastEditorUserId="1038" LastEditDate="2012-06-19T16:53:47.263" LastActivityDate="2012-06-19T16:53:47.263" Title="Genetic Models for Natural Selection?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2672" PostTypeId="2" ParentId="2381" CreationDate="2012-06-17T18:00:22.817" Score="2" Body="&lt;p&gt;The explanation one of my tutors offered was this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In cell recognition, it is very common for interactions between proteins to be based on weak interactions, but a certain degree of binding can trigger a (conformational) change which will instead establish a very strong interaction between the proteins involved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, if the contact is specific enough to 'count as a recognised pathogen', the interactions will immediately change to strong forces and the pathogen will not be able to move away.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-06-17T18:00:22.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2673" PostTypeId="2" ParentId="2670" CreationDate="2012-06-17T18:29:13.687" Score="13" Body="&lt;p&gt;The rate of mutation has been studied since the early 1900s, which is when your question was put to rest in a prescient paper by JBS Haldane (1949). Essentially the answer is that it varies a lot between organisms and environmental conditions, but for any given gene a mutation occurs once in about 50,000 sexual replications. That is equivalent to, in a human, several hundred new mutations in each person born. Impressively, Haldane's calculations have since been confirmed by a variety of other methods (e.g. Nachman &amp;amp; Crowell, 2000; Xue et al., 2009).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Faster rates of evolution have been recorded in other organisms, and there have been many, many studies looking at the rate of increase in sizes of the whole body or of particular organs of a wide variety of animals and plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, Azevedo et al. (2002) look at the rate of mutations affecting size (trying to select for decrease in body size) in C. elegans, and found mutations affecting size occured at a rate of ~0.0025 per haploid genome per generation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In another example, with a result more definite regarding your question, Keightley (1998) investigated the rate of change in average body weight under conditions of selection for increased body size, over 50 generations in mice. They recorded an average increase of 0.23-0.57% body weight per generation from new mutations. That's pretty huge, and demonstrates how rapidly a complex trait can change by mutation under selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wrote a small piece of python code to calculate the increase after x generations at the same rate (the formula is very simple)...&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;initial = 1&#xA;rate = 0.35&#xA;generations = 1000&#xA;result = initial * (1.0 + rate) ** generations&#xA;print result&#xA;&amp;gt;&amp;gt;&amp;gt;20.10655586861808&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Thus if we assume that approximately the average rate found in the mouse study (0.35%) could be the rate at which giraffes' necks might increase under strong selection, after 1000 generations the mean neck length would be over 20 times the original length. A low estimate for wild giraffe longevity is around 20 years, thus for giraffe necks to increase around 20x might take 20,000 years. Of course this basic estimate is making a whole lot of assumptions, but the point is that rates of mutation are actually very high, easily enough to explain the diversity of traits we see in the world.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.genetics.org/content/162/2/755&quot;&gt; &lt;strong&gt;Azevedo RBR, Keightley PD, Laurén-Määttä C, Vassilieva LL, Lynch M, Leroi AM&lt;/strong&gt;. 2002. Spontaneous Mutational Variation for Body Size in Caenorhabditis Elegans. Genetics 162: 755–765.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1111/j.1601-5223.1949.tb03339.x&quot;&gt; &lt;strong&gt;Haldane JBS&lt;/strong&gt;. 1949. THE RATE OF MUTATION OF HUMAN GENES. Hereditas 35: 267–273.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.genetics.org/content/148/4/1931&quot;&gt; &lt;strong&gt;Keightley PD&lt;/strong&gt;. 1998. Genetic Basis of Response to 50 Generations of Selection on Body Weight in Inbred Mice. Genetics 148: 1931–1939.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.genetics.org/content/156/1/297&quot;&gt; &lt;strong&gt;Nachman MW, Crowell SL&lt;/strong&gt;. 2000. Estimate of the Mutation Rate Per Nucleotide in Humans. Genetics 156: 297–304.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.cub.2009.07.032&quot;&gt; &lt;strong&gt;Xue Y, Wang Q, Long Q, Ng BL, Swerdlow H, Burton J, Skuce C, Taylor R, Abdellah Z, Zhao Y, et al.&lt;/strong&gt;. 2009. Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree. Current Biology 19: 1453–1457.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-06-17T20:56:19.477" LastActivityDate="2012-06-17T20:56:19.477" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2674" PostTypeId="2" ParentId="2381" CreationDate="2012-06-17T18:39:29.320" Score="2" Body="&lt;p&gt;As an alternative explanation I refer to this video.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=I_xh-bkiv_c&quot; rel=&quot;nofollow&quot;&gt;Crawling Neutrophil Chasing a Bacterium&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to a high affinity between the target bacterium and the macrophage, sensing the bacterium will also trigger amoeboid movement to chase down a pathogen.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-06-17T18:39:29.320" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2675" PostTypeId="1" AcceptedAnswerId="2676" CreationDate="2012-06-17T19:39:03.667" Score="7" ViewCount="273" Body="&lt;p&gt;Just what the title states. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any plants/trees that exhibit a growth spurt at a definite interval after the shoot appears? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2013-08-27T03:05:45.370" Title="Do any plants exhibit hormonal changes similar to puberty?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2676" PostTypeId="2" ParentId="2675" CreationDate="2012-06-17T20:49:59.293" Score="11" Body="&lt;p&gt;In flowering plants (the angiosperms) there are several developmental transitions in the life of the plant. I won't list the plants, because the list includes pretty much all of them (although the magnitude in the change of developmental pace differs widely between taxa and environments).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First there is &lt;strong&gt;seed germination&lt;/strong&gt;, which is controlled hormonally. Absence of germination is usually imposed by abscisic acid, whilst germination is caused at the appropriate time by gibberellic acid and ethylene (among other things; &lt;a href=&quot;http://dx.doi.org/10.1111/j.1469-8137.2008.02437.x&quot; rel=&quot;nofollow&quot;&gt;Holdsworth, Bentsink &amp;amp; Soppe, 2008&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next, in many herbaceous species there is a &lt;strong&gt;transition between a spreading growth stage (e.g. rosette growth) and the flowering stage&lt;/strong&gt;. The 'growth spurt' here is the differentiation and elongation of the flowering stem, and then subsequently the sudden flowering of buds. The transition is also controlled hormonally, by a variety of hormones including auxin (&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev-arplant-042809-112308&quot; rel=&quot;nofollow&quot;&gt;Zhao, 2010&lt;/a&gt;), gibberellic acid, ethylene (&lt;a href=&quot;http://dx.doi.org/10.1186/1741-7007-10-9&quot; rel=&quot;nofollow&quot;&gt;Schaller, 2012&lt;/a&gt;), and the long anticipated, recently confirmed florigen (&lt;a href=&quot;http://dx.doi.org/10.1371/journal.pbio.1001311&quot; rel=&quot;nofollow&quot;&gt;Choi, 2012&lt;/a&gt;). Ethylene and abscisic acid then play important roles in the next developmental transition when seeds and fruits are produced and dehisced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Small RNAs are also now being revealed to play a large role in controlling the timing of developmental, but they are upstream of the hormonal changes. In particular some key miRNAs are involved in auxin-based regulation of branching, and in embryogenesis (&lt;a href=&quot;http://dx.doi.org/10.1101/gad.1986710&quot; rel=&quot;nofollow&quot;&gt;Nodine &amp;amp; Bartel, 2010&lt;/a&gt;), and RNA silencing is involved in the switch from rosette growth to flowering growth (reviewed in &lt;a href=&quot;http://dx.doi.org/10.1016/j.gde.2009.06.001&quot; rel=&quot;nofollow&quot;&gt;Poethig, 2009&lt;/a&gt; and &lt;a href=&quot;http://dx.doi.org/10.1016/j.cell.2006.05.005&quot; rel=&quot;nofollow&quot;&gt;Baurle &amp;amp; Dean 2006&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.cell.2006.05.005&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Bäurle I, Dean C&lt;/strong&gt;. 2006. The Timing of Developmental Transitions in Plants. Cell 125: 655–664.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1371/journal.pbio.1001311&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Choi CQ&lt;/strong&gt;. 2012. A Blossoming Field of Research: How Florigen Is Transported to Create Flowers. PLoS Biol 10: e1001311.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1111/j.1469-8137.2008.02437.x&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Holdsworth MJ, Bentsink L, Soppe WJJ&lt;/strong&gt;. 2008. Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination. New Phytologist 179: 33–54.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1101/gad.1986710&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Nodine MD, Bartel DP&lt;/strong&gt;. 2010. MicroRNAs Prevent Precocious Gene Expression and Enable Pattern Formation During Plant Embryogenesis. Genes Dev 24: 2678–2692.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.gde.2009.06.001&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Poethig RS&lt;/strong&gt;. 2009. Small RNAs and developmental timing in plants. Curr Opin Genet Dev 19: 374–378.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1186/1741-7007-10-9&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Schaller GE&lt;/strong&gt;. 2012. Ethylene and the regulation of plant development. BMC Biology 10: 9.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev-arplant-042809-112308&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Zhao Y&lt;/strong&gt;. 2010. Auxin Biosynthesis and Its Role in Plant Development.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="3952" LastEditDate="2013-08-27T03:05:45.370" LastActivityDate="2013-08-27T03:05:45.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2677" PostTypeId="2" ParentId="2670" CreationDate="2012-06-17T21:22:24.420" Score="5" Body="&lt;p&gt;You might have a look at the &lt;a href=&quot;http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment&quot;&gt;E. coli long-term evolution experiment&lt;/a&gt; lead by Lenski.  They've traced over 50 thousand generations of E. Coli and measured how they evolved when growing in a minimal growth medium.  Since these E. Coli reproduce asexually and do not trade genes via bacterial conjugations, the only genetic changes over time come from mutations.  Since they keep frozen samples of earlier generations, it's possible to test exactly what changed and when (and even to go back in time and rerun the experiment again).  The experimenters estimate that there were hundreds of millions of mutations during the first 20K generations.  Of those 20K, approximately 100 reached fixation (that is, where everything without those mutations died), and of those there were between 10 and 20 beneficial mutations.  During those 20K generations the fitness (measured by how quickly the population grew when introduced to a new media) grew by 70%.  Later studies have looked directly at the DNA and identified the precise mutations which lead to important increases in fitness.&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2012-06-17T21:22:24.420" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2678" PostTypeId="1" CreationDate="2012-06-17T22:03:18.973" Score="4" ViewCount="84" Body="&lt;p&gt;As I understand it, a population with high variation is something sought after, since it makes the population better equipped to face a dynamic environment.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, I guess features in an individual which causes it's population's variation to be high, should be selected for (high mutation rate, other features.. ?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, does this manifest itself partly as individuals preferring to mate with individuals from another population? (With genetic difference within reason, perhaps a norm for a proffered genetic difference between individuals)&lt;/p&gt;&#xA;" OwnerUserId="945" LastEditorUserId="945" LastEditDate="2012-06-19T07:58:01.987" LastActivityDate="2012-06-19T08:57:51.680" Title="Features in individuals causing high population variation" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2679" PostTypeId="1" CreationDate="2012-06-18T14:02:49.577" Score="7" ViewCount="1564" Body="&lt;p&gt;When collagen is digested is it broken up into usable components that the body can use to produce its own collagen? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What evidence is there that supplementing with collagen type I &amp;amp; II etc.. can help connective tissue disorders?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What evidence is there that supplementing with collagen from animal products is not useful?&lt;/p&gt;&#xA;" OwnerUserId="952" LastEditorUserId="630" LastEditDate="2019-06-19T09:37:59.080" LastActivityDate="2020-09-27T20:02:23.443" Title="Is collagen supplementation useless?" Tags="&lt;cell-biology&gt;&lt;tissue&gt;&lt;tissue-repair&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2680" PostTypeId="1" CreationDate="2012-06-18T14:14:41.640" Score="8" ViewCount="168" Body="&lt;p&gt;Is there any relationship between DNA methylation as a level of stability to epigenetic states and genome size? For example, it is claimed that DNA methylation is not required for epigenetic stability in &lt;em&gt;Drosophila melanogaster&lt;/em&gt; and yeast, both genomes much smaller than mammalian or plant genomes. Could it be that DNA methylation is needed to help activate/repress certain genomic regions on top of other epigenomic marks when the genome is so vast that there is a need for an extra level of marking? Is there any evidence along those lines?&lt;/p&gt;&#xA;" OwnerUserId="787" LastEditorUserId="787" LastEditDate="2012-06-18T14:32:38.670" LastActivityDate="2020-02-06T20:12:58.473" Title="DNA methylation and genome size" Tags="&lt;genomics&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2681" PostTypeId="1" CreationDate="2012-06-18T14:38:19.050" Score="5" ViewCount="174" Body="&lt;p&gt;In the philosophy of biology it has been claimed many times that a popular position regarding the question of what species are, among biologists, is &lt;em&gt;cladism&lt;/em&gt;. For my current purposes, the defining trait of cladism is captured in the following quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;According to cladism, a species becomes extinct whenever it sends forth a new side species. (LaPorte 2004, 54)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, for example, if &lt;em&gt;Homo floresiensis&lt;/em&gt; is truly a species, and it derives, via a speciation event, from &lt;em&gt;Homo sapiens&lt;/em&gt;, then, after the speciation, there is no &lt;em&gt;Homo sapiens&lt;/em&gt;: there is &lt;em&gt;Homo floresiensis&lt;/em&gt; and a new species, very similar to &lt;em&gt;sapiens&lt;/em&gt;. In general, whenever there is speciation the mother species disappears.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am under the impression that this description of the situation is not the one most mainstream biologists would endorse. I take it that a more common description would be one under which, if a number of &lt;em&gt;Homo sapiens&lt;/em&gt; get isolated in an island and go on to form a new species, &lt;em&gt;Homo sapiens&lt;/em&gt; exists both before and after this speciation event. I would like to know whether cladism, described as above, is really a popular position, or whether I am right about what most biologists would say about the relation between &lt;em&gt;floresiensis&lt;/em&gt; and &lt;em&gt;sapiens&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It might also be that biologists declare themselves cladists when explicitly theorizing about the nature of species, but fall back to a less extreme form of cladism in the actual practice. Evidence in favour of or against this possibility (coming from biology, not the philosophy of biology) would also be appreciated.&lt;/p&gt; &#xA;&#xA;&lt;p&gt;&lt;p&gt;As Noah has pointed below, what I have called &lt;em&gt;extreme cladism&lt;/em&gt; might be very far from cladism, as usually interpreted. This is precisely the kind of claim I would like to see substantiated.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;LaPorte, Joseph. 2004. &lt;em&gt;Natural Kinds and Conceptual Change&lt;/em&gt;. Cambridge University Press.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1040" LastEditorUserId="57" LastEditDate="2012-06-18T16:41:55.400" LastActivityDate="2012-08-08T17:17:28.007" Title="Is extreme cladism a mainstream position in the species debate?" Tags="&lt;evolution&gt;&lt;speciation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2682" PostTypeId="2" ParentId="2680" CreationDate="2012-06-18T15:03:51.910" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there any relationship between DNA methylation as a level of&#xA;  stability to epigenetic states and genome size?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would say yes, because methylation is used to disable genes in differentiated cells. Disabled genes in differentiated cells generally need to stay disabled to maintain normal behavior for the cell type. Larger genomes usually encode more different types of cells.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;it is claimed that DNA methylation is not required for epigenetic&#xA;  stability in Drosophila melanogaster and yeast, both genomes much&#xA;  smaller than mammalian or plant genomes. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;According to my book (S377 molecular and cell biology, book 2, p140) Drosphila don't need methylation because they perform transcriptional regulation by persistent chromatin remodelling instead. Yeast being single celled would have less need for this type of control.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Could it be that DNA methylation is needed to help activate/repress certain genomic regions on top of other epigenomic marks when the genome is so vast that there is a need for an extra level of marking?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is used as a repressor because it inhibits  hydrogen bonding of transcription factors and the like. I have not heard of it functioning as an activator.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also other uses for methylation, for example  newly synthesized DNA is hemimethylated - where the parent strand is methylated and the child one not. From this it can be determined which is the parent strand during DNA repair.&lt;/p&gt;&#xA;" OwnerUserId="368" LastEditorUserId="368" LastEditDate="2012-06-18T15:09:31.263" LastActivityDate="2012-06-18T15:09:31.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2683" PostTypeId="1" CreationDate="2012-06-18T15:18:08.660" Score="3" ViewCount="5217" Body="&lt;p&gt;In my biology book I read about an experiment where the genes encoding telomerase were 'knocked out', but they could still live a normal life and no adverse effects were noticed until the 6th generation of offspring (although it did not say what the effects were). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have often often heard how longer telomeres indicate longer life potential, but what happens when you run out of them? Would rapidly proliferating cells be affected before others? Do the cells then just stop dividing or would they continue to divide? If they continue to divide what would the effects be?&lt;/p&gt;&#xA;" OwnerUserId="368" LastActivityDate="2013-09-14T07:13:26.790" Title="What happens when cells in your body run out of telomeres?" Tags="&lt;dna&gt;&lt;replication&gt;&lt;telomere&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2684" PostTypeId="1" CreationDate="2012-06-18T16:42:43.950" Score="14" ViewCount="78572" Body="&lt;p&gt;I know that we get half of our genes from each parent, but does it necessarily mean we get 1/4 of our genes from each grandparent? Or is it possible that we might get say 30% from one grandparent, 20% from other, 15% from another, 35% from another?&lt;/p&gt;&#xA;" OwnerUserId="1041" LastActivityDate="2016-05-28T14:33:21.130" Title="Do we get 1/4 of our genes from each grandparent?" Tags="&lt;genetics&gt;" AnswerCount="5" CommentCount="2" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2685" PostTypeId="2" ParentId="2684" CreationDate="2012-06-18T18:06:00.390" Score="14" Body="&lt;p&gt;I have answered a similar question before: &quot;&lt;a href=&quot;https://biology.stackexchange.com/questions/1981/how-many-genes-do-we-share-with-our-mother&quot;&gt;How many genes do we share with our mother?&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not that you &quot;get half your genes&quot; from each parent, and thus a quarter from each grandparent, it is that you inherit the &lt;em&gt;versions&lt;/em&gt; of the genes (we all have the 'same' genes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The method that determines which traits are inherited from each parent by the offspring is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Homologous_recombination&quot; rel=&quot;nofollow noreferrer&quot;&gt;homologous recombination&lt;/a&gt;, and this process is (essentially) random, and thus you end with ~50% of your traits (the &lt;em&gt;alleles&lt;/em&gt; of the genes) from each parent, and ~25% from each grandparent, so you are right in this respect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is, however, a generalization; due to the chance nature of the recombination it is entirely plausible that you may inherit more traits from one grandparent in comparison to another, but this is unique to each individual (with the exception of course of genetically identical twins).&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2012-06-18T18:06:00.390" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2687" PostTypeId="1" CreationDate="2012-06-18T20:04:28.733" Score="2" ViewCount="277" Body="&lt;p&gt;I'm trying to add on the order of 10-50 mammalian cells to a mixture of other cells (order of 1e6 cells). What is the best way to do this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(edit) I guess this wasn't clear. I would really like to emphasize how to sort 10-50 cells to give me an precise (not necessarily accurate but that would be nice too) method of getting a desired number of cells.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-06-19T07:22:03.683" LastActivityDate="2012-06-19T16:32:54.710" Title="What is an efficient way to spike 10-50 cells to a culture" Tags="&lt;cell-culture&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2688" PostTypeId="1" AcceptedAnswerId="5686" CreationDate="2012-06-18T22:41:06.670" Score="5" ViewCount="268" Body="&lt;p&gt;The adrenal medulla is less of a 'real' endocrine organ like the others in the endocrine system and much more an extension of the sympathetic nervous system. In fact, its chromaffin cells are modified neurons by descent and secrete adrenalin and some noradrenalin upon stimulation by sympathetic preganglionic fibres, effectively turning the medulla into a sort of 'endocrine ganglion' with the whole cardiovascular system as its 'postganglionic fibres'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adrenalin in the circulation seems to have pretty much the same effect as all the adrenergic neurons of the sympathetic nervous system (which innervates all blood vessels, organs etc.): arteriole constriction, cardiac output increase, breath rate increase, pupil dilation, glucagon secretion and insulin inhibition, stimulation of glycolysis and glycogenolysis etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what is the purpose of the adrenal medulla, if all of the effects which the endocrine adrenalin produces are essentially the same as those produced by the sympathetic mass response?&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2012-06-18T22:51:37.530" LastActivityDate="2013-01-06T10:53:49.870" Title="What is the purpose of the adrenal medulla?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;endocrinology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2690" PostTypeId="1" AcceptedAnswerId="2691" CreationDate="2012-06-19T04:18:07.820" Score="3" ViewCount="8800" Body="&lt;p&gt;How do you calculate or predict the charge of a protein at pH 7 given a fasta sequence?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any papers or online servers to do this is well appreciated.&lt;/p&gt;&#xA;" OwnerUserId="95" LastEditorUserId="1320" LastEditDate="2013-01-13T15:14:45.210" LastActivityDate="2013-05-09T13:11:20.383" Title="How do you calculate or predict the charge of a protein at pH 7?" Tags="&lt;amino-acids&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2691" PostTypeId="2" ParentId="2690" CreationDate="2012-06-19T04:54:11.177" Score="4" Body="&lt;p&gt;ExPASy to the rescue! Although I didn't comb through all the tools, this nifty website provides quite the myriad of bioinformatics resources which most certainly contains the tool to calculate what you want.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bear in mind though, most tools will tell you the &lt;em&gt;isoelectric point&lt;/em&gt; of your protein. However, bearing in mind the relationship between pI and pH (i.e. if pI &amp;lt; pH, then protein is - charged, and vice versa), you can easily figure out the charge of a protein at pH 7.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://expasy.org/tools/&quot; rel=&quot;nofollow&quot;&gt;http://expasy.org/tools/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Update&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the exact tool to calculate isoelectric points: &lt;a href=&quot;http://web.expasy.org/compute_pi/&quot; rel=&quot;nofollow&quot;&gt;http://web.expasy.org/compute_pi/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="177" LastActivityDate="2012-06-19T04:54:11.177" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2692" PostTypeId="1" CreationDate="2012-06-19T05:44:38.487" Score="7" ViewCount="266" Body="&lt;p&gt;Is there any gland in which there are no stem cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;sebaceous gland is maintained by unipotent stem cells&lt;/li&gt;&#xA;&lt;li&gt;thyroid gland - some stem cells, apparently unipotent&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Glands about which potency I am not sure&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;pancreas gland - contains probably many types stem cells, at least unipotent&lt;/li&gt;&#xA;&lt;li&gt;pituitary gland - not sure if any exist&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I cannot find any such gland that does not have stem cells.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1292" LastEditDate="2012-08-22T14:50:05.003" LastActivityDate="2012-08-22T14:50:05.003" Title="Does every gland type have stem cells for regeneration?" Tags="&lt;stem-cells&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2693" PostTypeId="2" ParentId="2687" CreationDate="2012-06-19T06:11:46.850" Score="1" Body="&lt;p&gt;If you are you working with primary cell cultures or cell lines may be you could do this when cells are in suspension, after tripsinization, mix them well with a 5mL serologial pipete in a falcon 50mL tube and plate to a 100mm2 with a final volume of 7mL. And finaly draw an eight with the plate in the hood more than 3 times to mix them well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt; For the addition of 10-50 cells, count these cells with trypan blue, and do a 1:100 dilution, for example if you have 1e6 cells in 10mL you could take 0.01 mL (10 microliters) to get 1, 000 cells &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2QTk3.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/I8vGT.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And then you add the 0.01mL into 1mL of cell media to get 1 cell per 1 microliter, and then if you wanna get 10 cells, take 10 microliters, and so on&lt;/p&gt;&#xA;" OwnerUserId="973" LastEditorUserId="973" LastEditDate="2012-06-19T16:32:54.710" LastActivityDate="2012-06-19T16:32:54.710" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2694" PostTypeId="2" ParentId="2678" CreationDate="2012-06-19T08:52:39.783" Score="1" Body="&lt;p&gt;I believe there are evidences in both directions in terms of mechanisms to favor variation in a population: outbreeding and crossing within individuals that look alike. There is a fine line between the two. Outbreeding helps in keeping variation and mixing variants that appeared in different parts of the population, but too much outbreeding can generate inviable offspring. Too much inbreeding also reduces viability. Certain plants have features that are selected to favor outbreeding and make inbreeding incompatible by rejecting incompatible (&quot;self&quot;) pollen (&lt;a href=&quot;http://en.wikipedia.org/wiki/Self-incompatibility_in_plants&quot; rel=&quot;nofollow&quot;&gt;self-incompatibility mechanisms&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="658" LastEditDate="2012-06-19T08:57:51.680" LastActivityDate="2012-06-19T08:57:51.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2695" PostTypeId="1" AcceptedAnswerId="2696" CreationDate="2012-06-19T09:20:03.897" Score="7" ViewCount="13633" Body="&lt;p&gt;Many protocols suggest that beta-mercaptoethanol is necessary for growing cells. It is a reducing agent but what does it mechanistically do for your cells. When would one not add it.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-06-19T09:26:29.880" Title="Why is beta-mercaptoethanol often added to cell culture media" Tags="&lt;cell-culture&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2696" PostTypeId="2" ParentId="2695" CreationDate="2012-06-19T09:26:29.880" Score="2" Body="&lt;p&gt;2-me is a reducing agent necessary to be added to help keep free radical oxygen from affecting mouse cells.  It is generally not necessary for human cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1467329&quot; rel=&quot;nofollow&quot;&gt;S Bannai&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3680392&quot; rel=&quot;nofollow&quot;&gt;Ishii et al.&lt;/a&gt;, 2-mercaptoethanol improves tumor cell uptake of cystine by creating a reducing environment.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-06-19T09:26:29.880" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2697" PostTypeId="2" ParentId="2574" CreationDate="2012-06-19T13:59:40.777" Score="4" Body="&lt;p&gt;Often sequencing involves a step of amplification of genomic material. The standard way to perform this is with PCR, but PCR is biased and does not amplify very AT-rich regions well. With multiple rounds of PCR, even low-abundance regions that are not as AT-rich might come to dominate the sample and hide the AT-rich sequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not only a problem for de novo sequencing, but for many sequencing-based techniques (RNA-seq, ChIP-seq, your-favorite-seq...). Alternative methods have been employed in plasmodium, but they are not as standard (yet?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See, for example, &lt;em&gt;H2A.Z Demarcates Intergenic Regions of the Plasmodium falciparum Epigenome That Are Dynamically Marked by H3K9ac and H3K4me3&lt;/em&gt; at &lt;a href=&quot;http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001223&quot; rel=&quot;nofollow&quot;&gt;http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001223&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="29" LastEditorUserId="29" LastEditDate="2013-05-30T16:38:43.873" LastActivityDate="2013-05-30T16:38:43.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2698" PostTypeId="1" AcceptedAnswerId="5338" CreationDate="2012-06-19T14:09:12.510" Score="14" ViewCount="53206" Body="&lt;p&gt;When is it best to use Hoechst vs. DAPI for nuclear staining? They seem to be very similar on paper. Are there situations where one is clearly preferable?&lt;/p&gt;&#xA;" OwnerUserId="29" LastEditorUserId="852" LastEditDate="2012-11-26T09:55:22.490" LastActivityDate="2014-11-07T19:19:21.010" Title="Hoechst or DAPI for nuclear staining?" Tags="&lt;cell-culture&gt;&lt;fluorescent-microscopy&gt;&lt;flow-cytometry&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2699" PostTypeId="1" AcceptedAnswerId="4948" CreationDate="2012-06-19T17:19:02.977" Score="4" ViewCount="1055" Body="&lt;p&gt;If streamlining makes movement/locomotion quicker and easier, why didn't the apes evolve into life-forms that had streamlined bodies (much like fish)?&lt;/p&gt;&#xA;" OwnerUserId="1034" LastEditorUserId="3952" LastEditDate="2013-08-02T14:19:27.283" LastActivityDate="2013-08-02T16:48:13.347" Title="Why Didn't Evolution Cause the Human Body to become Streamlined?" Tags="&lt;evolution&gt;&lt;speculative&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2700" PostTypeId="1" AcceptedAnswerId="2703" CreationDate="2012-06-19T19:28:14.157" Score="2" ViewCount="243" Body="&lt;p&gt;I know from reading that a human in vacuum needs a space-suit to survive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the body of any organism on Earth capable of living equally in vacuum, and on/below Earth's surface within the atmosphere?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="3952" LastEditDate="2014-04-16T19:25:56.897" LastActivityDate="2014-04-16T19:25:56.897" Title="Can the body of any organism on Earth live without impairment both in vacuum, and within Earth's atmosphere?" Tags="&lt;physiology&gt;&lt;speculative&gt;&lt;extremophiles&gt;" AnswerCount="2" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="2701" PostTypeId="1" AcceptedAnswerId="2779" CreationDate="2012-06-19T19:46:52.977" Score="11" ViewCount="3400" Body="&lt;p&gt;Why does the butterfly have a cocoon stage in its life cycle? It could have simply grown up within the egg/cocoon, and emerged as a butterfly. Instead it is first an egg, then a worm, then a chrysalis, and finally after some time a butterfly. &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2012-06-29T19:54:56.463" LastActivityDate="2012-06-29T19:54:56.463" Title="Why does the butterfly have a cocoon stage in its life cycle?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;entomology&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2702" PostTypeId="2" ParentId="2651" CreationDate="2012-06-19T21:31:04.687" Score="1" Body="&lt;p&gt;You can look up Gibson Assembly or Circular Polymerase Extension cloning (CPEC).  For both of these the website for J5 has some good protocols.  Here is the one for CPEC:  &lt;a href=&quot;http://j5.jbei.org/j5manual/pages/80.html&quot; rel=&quot;nofollow&quot;&gt;http://j5.jbei.org/j5manual/pages/80.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For CPEC you can look at the 2011 Quan paper: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21293463&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/21293463&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully that helps.  &lt;/p&gt;&#xA;" OwnerUserId="1032" LastActivityDate="2012-06-19T21:31:04.687" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2703" PostTypeId="2" ParentId="2700" CreationDate="2012-06-19T23:27:42.570" Score="6" Body="&lt;p&gt;Remarkably, &lt;a href=&quot;http://en.wikipedia.org/wiki/Tardigrade&quot;&gt;Tardigrades&lt;/a&gt; are multi-cellular animals which can &lt;a href=&quot;http://www.newscientist.com/article/dn14690-water-bears-are-first-animal-to-survive-space-vacuum.html&quot;&gt;survive the vacuum of space&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2012-06-19T23:27:42.570" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2704" PostTypeId="1" CreationDate="2012-06-20T04:44:20.513" Score="0" ViewCount="1849" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Green-beard_effect&quot; rel=&quot;nofollow&quot;&gt;Green-beard effects&lt;/a&gt; are genes that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Produce an effect that can be detected&lt;/li&gt;&#xA;&lt;li&gt;Produce preference to others with the same effect&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Are there any examples of this in humans?&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="6" LastEditDate="2012-06-21T12:47:26.053" LastActivityDate="2012-06-21T12:47:26.053" Title="Are there examples of the green beard effect in humans?" Tags="&lt;human-biology&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2705" PostTypeId="1" AcceptedAnswerId="2708" CreationDate="2012-06-20T08:44:50.627" Score="16" ViewCount="13597" Body="&lt;p&gt;Imagine that we take a population of horses, split them in half and place them in completely different environments. The two species will evolve separate from each other and because the environment is different, the outcome of evolution will be different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But at what point can you say that these horses have evolved into two different species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I do know that they would probably go extinct if we conducted this exact experiment, but this experiment is just to give an example)&lt;/p&gt;&#xA;" OwnerUserId="611" LastActivityDate="2012-08-17T13:45:59.950" Title="When has an organism evolved enough to be called a new species?" Tags="&lt;evolution&gt;&lt;taxonomy&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2706" PostTypeId="2" ParentId="2705" CreationDate="2012-06-20T09:14:06.693" Score="1" Body="&lt;p&gt;The biological definition of a &lt;em&gt;species&lt;/em&gt; on &lt;a href=&quot;http://dictionary.reference.com/browse/species&quot; rel=&quot;nofollow&quot;&gt;Dictionary.com&lt;/a&gt; is as follows;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The major subdivision of a genus or subgenus, regarded as the basic category of biological classification, composed of related individuals that resemble one another, are able to breed among themselves, but are not able to breed with members of another species. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So what we take from this is that a species, by definition, are those individuals/organisms that can successfully breed together. It is worth pointing out that some members of closely related species can breed together (e.g. a male horse and a female donkey can produce a 'mule'), but these animals are not fertile, so this is not considered 'successful' breeding, and the two organisms (in this case the horse and the donkey) are of different (if closely related) species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your example, the populations of horses would be said to have sufficiently &lt;em&gt;diverged&lt;/em&gt; from one-another when they can no longer successfully breed.&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-06-20T09:14:06.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2707" PostTypeId="1" AcceptedAnswerId="3074" CreationDate="2012-06-20T10:54:09.337" Score="8" ViewCount="2312" Body="&lt;p&gt;What are examples of intracellular parasites of medical or economic importance? I have read that &lt;em&gt;Xanthomonas oryzae&lt;/em&gt; is an intracellular parasite in rice that produces proteins able to cause changes in the gene regulation of the rice cells in order to feed off the sugars produced by the rice cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know of other examples of intracellular parasites of medical or economic importance that would be potentially (even if not tested) able to interact with the host's genome in a similar manner.&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="57" LastEditDate="2012-06-20T13:04:30.420" LastActivityDate="2012-08-01T00:31:37.513" Title="Examples of intracellular parasites of medical or economic importance?" Tags="&lt;genomes&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2708" PostTypeId="2" ParentId="2705" CreationDate="2012-06-20T13:12:35.043" Score="23" Body="&lt;p&gt;I think LuketheDuke's answer is an oversimplification of the biological species concept (possibly resulting from the dictionary having a poor definition). The definition he gives is one of many which are in current use, and is made redundant by many types of organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important to recognise that because reproduction is not the same process in all organisms, genetic differentiation between individuals occurs in different ways for different groups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's take the definition given in LuketheDuke's answer...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The major subdivision of a genus or subgenus, regarded as the basic category of biological classification, composed of related individuals that resemble one another, are able to breed among themselves, but are not able to breed with members of another species.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Under this definition, lions and tigers (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Liger&quot;&gt;ligers&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Tiglon&quot;&gt;tiglons&lt;/a&gt;, which are sterile hybrids between the two) would be considered one species, as would donkeys and horses (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Mule&quot;&gt;mules&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Hinny&quot;&gt;hinnys&lt;/a&gt;, again sterile hybrids). There are hundreds of other examples of pairs of animal species which can hybridise to produce sterile offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, these animal hybrids usually only take place with human intervention, by delibrate breeding efforts. Thus we could extend the previous definition to include them...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The major subdivision of a genus or subgenus, regarded as the basic category of biological classification, composed of related individuals that resemble one another, are able to breed among themselves, but &lt;strong&gt;do not breed freely with members of another species in the wild&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That last part takes care of the ligers and tiglons. But what if we consider plants? Under the definition I just gave, most grasses (around 11,000 species) would have to be considered as one species. In the wild, most grasses will freely pollinate related species and produce hybrid seed, which germinates. You might then think we could just modify the definition to specify that the offspring must be fertile (i.e. able to reproduce with one another)...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The major subdivision of a genus or subgenus, regarded as the basic category of biological classification, composed of related individuals that resemble one another, are able to breed among themselves, but &lt;strong&gt;do not breed freely with members of another species in the wild to produce fertile progeny&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, the situation is still more complicated (we've barely started!). Often wild hybridisation events between plants lead to healthy, fertile offspring. In fact common wheat (&lt;em&gt;Triticum aestivum&lt;/em&gt;) is a natural hybrid between &lt;strong&gt;three&lt;/strong&gt; related species of grass. The offspring are able to breed freely with one another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps we could account for this by taking into account whether the populations &lt;em&gt;usually&lt;/em&gt; interbreed, and whether they form distinct populations...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The major subdivision of a genus or subgenus, regarded as the basic category of biological classification, composed of &lt;strong&gt;populations or meta-populations of&lt;/strong&gt; related individuals that resemble one another, are able to breed among themselves, but &lt;strong&gt;do tend not to breed freely with members of another species in the wild to produce fertile progeny&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This accounts for the grasses, but it still leaves a messy area when you have a hybridisation which establishes - until the hybrid population is segregated away from the parent populations it is unclear whether they still count as the same species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We could probably live with this situation, except for the fact that bacteria refuse to conform to it at all. Bacteria of the same species, or even very different species, can freely transfer genes from one to the other in &lt;a href=&quot;http://en.wikipedia.org/wiki/Bacterial_conjugation&quot;&gt;conjugation&lt;/a&gt;, which combined with fission can result in perfectly replicable hybrids. This is such a common occurence that it breaks even the 'tend to' part of the previous definition, and members of a population can be doing this almost constantly, which negates the segregation requirement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Richard Dawkins had a go at defining around this, by stating that...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;two organisms are conspecific if and only if they have the same number of chromosomes and, for each chromosome, both organisms have the same number of nucleotides &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This partly gets around the bacterial problem and means that bacteria which result from conjugation are a new species. Unfortunately under this definition we might as well not ever bother trying to classify bacteria as billions of new species would be created every day - something which the medical profession might have something to say about. This definition would also mean that those with genetic diseases like trisomy 21 are not human. The final nail in the coffin of this attempt is that there are many species, including frogs and plants, which are very certainly considered a single species by taxonomists but which have some variety in the presence of small accessory chromosomes, which occur in different combinations between individuals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's consider one last option. We now live in the era of genomics where data about genomes of thousands of organisms is accumulating rapidly. We could try to use that data to build a species definition based upon similarity at the nucleotide level. This is often used for bacteria, by considering organisms with less than 97% nucleotide similarity to be different species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The major point I've been trying to make, though, is that species is not a natural concept. Humans need to be able to classify organisms in order to be able to structure our knowledge about them and make it accessible to people trying to link ideas together. But the natural world doesn't care about our definitions. Ultimately the species concept is different for different groups of organisms and will continue to change over time as our analytical methods and the requirements of our knowledge change. Note that I've deliberately skipped over many historical species concept ideas.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The direct answer to your horse question is &quot;it depends how you want to define a horse&quot;.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-06-20T13:12:35.043" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="2709" PostTypeId="1" CreationDate="2012-06-20T18:18:38.370" Score="5" ViewCount="266" Body="&lt;p&gt;I'm not an expert in plant physiology. I was wondering if, per square centimeter, leaves are converting more or less energy than photovoltaic systems. Can this be estimated? How?&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="444" LastEditDate="2012-06-21T12:53:34.700" LastActivityDate="2012-06-21T13:31:29.643" Title="How high is the energy yield of photovoltaics compared to photosynthesis?" Tags="&lt;photosynthesis&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2710" PostTypeId="2" ParentId="2709" CreationDate="2012-06-20T18:28:00.320" Score="6" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Photosynthetic_efficiency&quot;&gt;wikipedia&lt;/a&gt;, plants typically convert around 5% of the energy of the sunlight that hit the leaves into energy usable by the plant.  Sugarcane seems to be the best, it converts up to 8% of the energy into actual biomass.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best solar panels on the market, &lt;a href=&quot;http://www.independent.co.uk/environment/worlds-most-efficient-solar-cells-ready-for-use-in-the-uk-2200508.html&quot;&gt;according to the Independent&lt;/a&gt;, convert 21% of energy from sunlight into usable electricity.  Experimental prototypes do much better, and there are some that get over 40%.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Solar_cell_efficiency&quot;&gt;Wikipedia&lt;/a&gt; has a nice graph of the most efficient solar cell prototypes.&lt;/p&gt;&#xA;" OwnerUserId="997" LastEditorUserId="997" LastEditDate="2012-06-20T21:26:08.970" LastActivityDate="2012-06-20T21:26:08.970" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2711" PostTypeId="1" CreationDate="2012-06-20T18:41:18.857" Score="5" ViewCount="80" Body="&lt;p&gt;If we discover an association between a disease and a particular HLA type (MHC class I or class II molecule) then it may provide us with some insight into the disease in a very basic way. However, will it provide us with a therapeutic target? Or second best, will it provide us with information that is useful for diagnosis or management? I am looking for examples. Do you know of any?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most obvious is in transplantation where one would use HLA typing to match donor to recipient but that is not the same as using knowledge of an HLA type to target, treat, diagnose, prognosticate.&lt;/p&gt;&#xA;" OwnerUserId="1045" LastEditorUserId="4101" LastEditDate="2013-10-13T15:51:24.360" LastActivityDate="2014-10-16T03:54:24.403" Title="Do you know of any disease where HLA / MHC association discovery has led to better treatment or management?" Tags="&lt;immunology&gt;&lt;hla&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2712" PostTypeId="2" ParentId="2704" CreationDate="2012-06-20T22:51:51.407" Score="7" Body="&lt;p&gt;Your examples are way too broad. A green-beard effect only applies to the effects of a single gene or group of linked genes, not to just any trait. Racism and your Mongol war example are too complex to be explained by this effect. In reality examples will mostly be found in single-celled organisms where expression of a single protein can have whole-organism effects such as causing aggregation, or in larger organisms where some highly visible effect is possible such as a colour change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are very few real known examples of the green-beard effect, but four are listed on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Green-beard_effect&quot;&gt;Wikipedia page&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The killing of red ant queens carrying a particular allele by workers with a different allele (Keller &amp;amp; Ross, 1998)&lt;/li&gt;&#xA;&lt;li&gt;Altruism in social amoeba resulting from homophilic adhesion of a protein (Queller et al., 2003)&lt;/li&gt;&#xA;&lt;li&gt;A multi-locus example in which similarly-coloured male lizards protect one another (Sinervo et al., 2006)&lt;/li&gt;&#xA;&lt;li&gt;A neat example in yeast whereby individuals sharing an allele for a particular locus selectively aggregate, preventing those without the allele from benefiting by proxy from their trait (Smukalla et al., 2008)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/29064&quot;&gt; &lt;strong&gt;Keller L, Ross KG&lt;/strong&gt;. 1998. Selfish genes: a green beard in the red fire ant. Nature 394: 573–575.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1126/science.1077742&quot;&gt; &lt;strong&gt;Queller DC, Ponte E, Bozzaro S, Strassmann JE&lt;/strong&gt;. 2003. Single-Gene Greenbeard Effects in the Social Amoeba Dictyostelium Discoideum. Science 299: 105–106.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0510260103&quot;&gt; &lt;strong&gt;Sinervo B, Chaine A, Clobert J, Calsbeek R, Hazard L, Lancaster L, McAdam AG, Alonzo S, Corrigan G, Hochberg ME&lt;/strong&gt;. 2006. Self-recognition, color signals, and cycles of greenbeard mutualism and altruism. Proc Natl Acad Sci U S A 103: 7372–7377.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.cell.2008.09.037&quot;&gt; &lt;strong&gt;Smukalla S, Caldara M, Pochet N, Beauvais A, Guadagnini S, Yan C, Vinces MD, Jansen A, Prevost MC, Latgé J-P, et al.&lt;/strong&gt;. 2008. FLO1 Is a Variable Green Beard Gene that Drives Biofilm-like Cooperation in Budding Yeast. Cell 135: 726–737.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-06-20T22:51:51.407" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2713" PostTypeId="1" CreationDate="2012-06-20T23:31:31.800" Score="8" ViewCount="108" Body="&lt;p&gt;My questions are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;What techniques are available for doing so?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are they destructive ?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What is their accuracy ?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="207" LastEditorUserId="57" LastEditDate="2012-07-27T06:30:21.227" LastActivityDate="2012-07-27T07:05:18.980" Title="How does one measure the length of telomeres?" Tags="&lt;dna&gt;&lt;telomere&gt;&lt;cytogenetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2714" PostTypeId="2" ParentId="2701" CreationDate="2012-06-21T13:23:01.650" Score="4" Body="&lt;p&gt;The butterfly is the reproductive stage while the larvae all it does is eat an accumulates energy to be succesfull during the reproductive phase. &#xA;In terms of adaptation this life cycle would be much more efficent.&lt;/p&gt;&#xA;" OwnerUserId="1004" LastActivityDate="2012-06-21T13:23:01.650" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2715" PostTypeId="2" ParentId="2709" CreationDate="2012-06-21T13:31:29.643" Score="0" Body="&lt;p&gt;Photovoltaics made from organic sources, like Graphene, (OPVs) have the potential for efficiencies exceeding 24% in a stacked structure. A theoretical max efficiency has not been  proposed, but it is expected to be less than silicon. The main benefit of OPVs is the rock-bottom price and the ability to make very tiny panels.&lt;/p&gt;&#xA;" OwnerUserId="238" LastActivityDate="2012-06-21T13:31:29.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2716" PostTypeId="1" AcceptedAnswerId="2720" CreationDate="2012-06-21T14:17:16.810" Score="3" ViewCount="893" Body="&lt;p&gt;I'm having a conceptual nightmare trying to understand when a group of cells may become cancerous and the more resources I consult the more confused I seem to get.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order for a cell to become cancerous, does it have to mutate to knock out tumour suppressor genes &lt;strong&gt;and&lt;/strong&gt; have a proto-oncogene become an oncogene?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm  currently working on the basis that that is the case, or at least that a mutated TSG on its own will not cause uncontrolled division.  However wikipedia seems to suggest that an oncogene alone can cause uncontrolled division with a functional TSG in place.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It could be a flaw in the idea I have that tumour suppressor genes only trigger apoptosis once a cell has started to divide rapidly, are they actually carrying it out to a regular schedule independent of oncogene presence?   &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-06-21T14:24:26.707" LastActivityDate="2013-06-18T17:21:50.843" Title="Do both TSG and Proto-oncogenes have to suffer mutations to cause cancer?" Tags="&lt;cancer&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2717" PostTypeId="2" ParentId="2716" CreationDate="2012-06-21T15:38:24.983" Score="2" Body="&lt;p&gt;The typical idea is that several &quot;hits&quot; are required. The difference between proto-oncogene and TSG is mainly in their heritability - TSG mutations are usually recessive (because a heterozygote will still express sufficient suppressor, e.g. p53) whereas proto-oncogenes are dominant (if a consitutively active agent e.g. Ras is present, it doesn't matter if the other allele is under normal control).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A single &quot;hit&quot; in this way (TSG or proto-oncogene) may just cause the cell to die, which isn't a bad thing (in fact, TSG such as p53 often work by inducing apoptosis because proliferative errors make them accumulute). A tumour only results when a single cell accumulates sufficient mutations and genomic damage to gain a reproductive advantage over the cells in its vicinity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, you are asking about &lt;em&gt;cancer&lt;/em&gt;, which is not simply a tumour. Tumours are any sort of abnormal growth, i.e. neoplasms, but they can be benign! This means they stay in their tumour capsule, do not grow at a fast rate and do not invade or metastasise other tissues. The distinct characteristics that define a cancer are very well-known and were published in a well recognised paper by Weinberg &amp;amp; Hanahan, 2002, &quot;The Hallmarks of Cancer&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The six primary hallmarks of cancer. The first two are the ones most people know, but the other ones are just as essential for &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Independence from external growth signals&lt;/strong&gt;: Cancer cells produce their on autocrine growth factors or have mutated signal pathways active without GF receptor stimulation (&lt;strong&gt;Oncogenes&lt;/strong&gt;).&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Resistance to anti-growth signals&lt;/strong&gt;: Cancer cells do not respond to growth-inhibitory factors from outside or inside (&lt;strong&gt;Tumour suppressor genes&lt;/strong&gt;).&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Evasion of apoptosis&lt;/strong&gt;: Cancer cells resist signals which cause normal cells to die (apoptose) (these are also tumour suppressor genes).&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Limitless replication / Evasion of cell senescence&lt;/strong&gt;: Apart from stem cells, all normal cells can only replicate their genome a certain number of times before the ends of the chromosomes known as telomeres are too short, disintegrate and cause the cell to enter senescence or die. Cancer cells express telomerase, which extends telomeres and maintains replicative potential.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Sustained angiogenesis&lt;/strong&gt;: Tumours and cancers form massive cell heaps. Tumours may stall growth because blood vessels do not grow into the heap and supply the cells with the nutrients needed to proliferate. Cancer cells have found a way to induce blood vessel growth (VEGF) and sustain it in order to maintain nutrient supply.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Invasion and metastasis&lt;/strong&gt;: This is the crucial, most distinguishing difference between benign neoplasm (tumour) and malign neoplasm (cancer). Cancer cells degrade the extracellular matrix around them (by secreting metallo-matrix-proteases, MMP), which allows them to move away from where they are and invade into neighbouring tissues. They can also spill into blood vessels this way (especially if the neoplasm is well-vascularised thanks to hallmark number 5), where they can travel to other sites in the body and grow new cancerous tumours in other locations.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;There are four more emerging hallmarks and enabling characteristics (immune evasion, inflammation induction, modification of energy metabolism, genomic instability), which allow better cancer growth and make a cancer more dangerous if it acquires them, but these are outside the scope of this answer.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-06-18T17:21:50.843" LastActivityDate="2013-06-18T17:21:50.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2719" PostTypeId="1" AcceptedAnswerId="2726" CreationDate="2012-06-21T22:23:03.273" Score="1" ViewCount="1921" Body="&lt;p&gt;It is my understanding that the hair on the head is there to protect us from sunburn.  I've never seen a bald animal, so isn't evolution in charge of addressing these type of things? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is it that evolution gave us a thumb, but hasn't found a way to keep the hair on our heads?&lt;/p&gt;&#xA;" OwnerUserId="1048" LastEditorUserId="3632" LastEditDate="2012-06-24T16:07:14.800" LastActivityDate="2021-05-21T05:02:09.100" Title="Shouldn't evolution have taken care of baldness already?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="2720" PostTypeId="2" ParentId="2716" CreationDate="2012-06-21T22:52:12.630" Score="1" Body="&lt;p&gt;There is a nice &lt;a href=&quot;http://www.nature.com/nature/journal/v458/n7239/full/nature07943.html&quot; rel=&quot;nofollow&quot;&gt;nature paper&lt;/a&gt; by Dr. Micheal Stratton et al. that I think might be a good place to start.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think answering you question is complex, because different cancers will actually have different mechanisms that trigger their onset and aggressiveness and as such some have more complex mutational landscapes than others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good question to ask yourself is : what is a driver mutation and what is a passenger mutation. A driver mutation is usually what is driving the cancer, and it can be a proto-oncogene or TSG. Passenger mutations don't really have as much of an impact and result from the destructive tendencies of the driver mutations.&lt;/p&gt;&#xA;" OwnerUserId="1049" LastActivityDate="2012-06-21T22:52:12.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2721" PostTypeId="1" AcceptedAnswerId="2731" CreationDate="2012-06-21T23:05:32.467" Score="15" ViewCount="635" Body="&lt;p&gt;Do genes that occupy a similar locus on the genome have correlated function, specifically in human beings? It is my understanding that adjacent genes are inherited together, and so location plays a role there. However it terms of function, I don't know to what extent location plays a role. Furthermore, if say two adjacent genes have the same expression, does this necessarily mean that their function is correlated, or is that interpretation stretch?&lt;/p&gt;&#xA;" OwnerUserId="1049" LastEditorUserId="10276" LastEditDate="2015-01-16T11:53:00.667" LastActivityDate="2017-02-17T15:37:28.567" Title="Is the function of adjacent genes correlated?" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;human-genetics&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2722" PostTypeId="2" ParentId="2025" CreationDate="2012-06-22T00:39:24.557" Score="3" Body="&lt;p&gt;(too long to be a comment)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may be interested in &lt;a href=&quot;http://en.wikipedia.org/wiki/Phase_response_curve&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Phase_response_curve&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This graph shows how the body's circadian rhythm normally works: &lt;a href=&quot;http://en.wikipedia.org/wiki/File:Body_Temp_Variation.png&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/File:Body_Temp_Variation.png&lt;/a&gt;.  Body temperature decreases during the night (apparently due to more melatonin production.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I conjecture that the proposed schedule would interfere with the Circadian rhythm.  Melatonin is the hormone that regulates sleep--it causes drowsiness.  It is suppressed by blue light (because we get exposed to blue light in the daytime).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aside from this, I am also very interested in the effects because I have personally wondered about the same question.  The thing I am worried about is significant immunosuppression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A larger question might be--&quot;Why is sleep necessary?&quot;  Does it serve only to conserve food (which is very useful if you are living on subsistence) or does it serve a greater purpose? (whenever I have asked anyone about it, they always cite &quot;regeneration&quot; and some have cited the recycling of neurotransmitters.  Personally, I'm a little skeptical.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One final study: there was a study by Dement on the effect of dream deprivation: he took several people and woke them up whenever they went into REM sleep.  Then, there was a period when the patients were not woken up.  He found that there was a &quot;REM rebound&quot;--that they would go into more REM sleep after they had been deprived of it.  This seems to indicate that dreaming, specifically, may serve a significant purpose.&lt;/p&gt;&#xA;" OwnerUserId="1050" LastActivityDate="2012-06-22T00:39:24.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2724" PostTypeId="1" AcceptedAnswerId="2727" CreationDate="2012-06-22T00:53:35.777" Score="8" ViewCount="372" Body="&lt;p&gt;What's the state of the art for solving the following problem. You imagine a set of features that you want a life-form to have. Just to take an arbitrary example, say you want your life-form to have a) a strong sense of smell, b) the ability to fly and c) a comfortable couch shaped saddle on its back. What's the sequence of steps you need to take so that you can create this life-form in the lab?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize that we are probably far away from solving this very general problem. But perhaps there are some smaller subproblems that we do know how to solve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, as far as I gather, you can probably make any living being fluorescent green in color by inserting into its genome the gene responsible for expressing the Green Fluorescent Protein. So may be if we limit the set of features one is allowed to choose from, the above problem can be solved. So my first question of the set of questions is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1)  What features can be easily inserted into almost any organism easily?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next, I imagine that to design and create an artificial life-form will consist of three steps: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Figure out which proteins will give rise to those feaures, &lt;/li&gt;&#xA;&lt;li&gt;Design a genome that will express those proteins in the right quantities and &lt;/li&gt;&#xA;&lt;li&gt;Implant that genome into a cell and actually let the being grow.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;2)  Is the above sequence of steps correct, or am I missing something?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3)  What is the state of the art for each of these steps?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, in light of the recent spur in the open source biology groups and DIYbio enthusiasts, I feel that there might be some very simple but really cool things related to my question that you can already do in your garage. For example, may be there is some very simple single-cell life-form that's so well understood that you can add or subtract tons of features from it with a budget of a few hundred dollars. So my final question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) What is the cheapest experiment you can perform at your own home without access to a biology lab which involves changing the genome of a living organism in a way that's functionally visible? (An arbitrary example: Can you create an apple that's blue in color with a budget of $500? By create, I mean you should be able to hold the blue apple in your hand.)&lt;/p&gt;&#xA;" OwnerUserId="485" LastEditorUserId="6" LastEditDate="2012-06-23T15:51:18.623" LastActivityDate="2018-06-28T14:11:49.680" Title="What's the state of the art in designing and creating your own life forms?" Tags="&lt;molecular-biology&gt;&lt;synthetic-biology&gt;" AnswerCount="2" CommentCount="10" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2725" PostTypeId="2" ParentId="2719" CreationDate="2012-06-22T03:57:19.937" Score="1" Body="&lt;p&gt;The closest research I can find with a little poking is &lt;a href=&quot;http://www.springerlink.com/content/e7r8547719j242m6/&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;.  The results are somewhat inconclusive, because AGA (the technical term for male pattern baldness) has many separate genetic components.  Nonetheless, there appears to be evidence that AGA is under &lt;em&gt;positive&lt;/em&gt; selective pressure in Europeans and possibly Asians.  That is, there appears to be a fitness advantage to baldness in some circumstances.  However, there are other possibilities, for example, it may be that an adjacent gene is being selected for and this gene is coming along for the ride.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that AGA is less frequent in Africans than Europeans, which suggests that indeed there may be selective pressure against baldness in sunnier climates for the reason you suggest.  Note that in cold climates, on the other hand, there can be selection for increased UV exposure to avoid Vitamin D deficiency (&lt;a href=&quot;http://en.wikipedia.org/wiki/Human_skin_color#Evolution_of_skin_color&quot; rel=&quot;nofollow&quot;&gt;the evolution of lighter skin&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2012-06-22T03:57:19.937" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2726" PostTypeId="2" ParentId="2719" CreationDate="2012-06-22T04:28:01.457" Score="7" Body="&lt;p&gt;As is typical for questions about fitness, this question has more than one valid answer.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The essential question @AndrewSalmon is answering is the right one:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;If evolution eliminates disadvantages, why can xyz trait still be seen the population?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a more complete list, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) The trait is not eliminated by evolution since it is manifested after reproduction.  The classic example of this sort of trait is senescence.  Why do we grow old and die?  Clearly it doesn't stop us from having offspring.  I generally don't find this sort of answer informative. Its not a bad argument for the traits of bipolar and schitzophrenic tendencies which can manifest as a chronic mental condition, often in the 30s after many people have children.&lt;br&gt;&#xA;These traits are fairly common (1 in 6) in the population.&lt;br&gt;&#xA;It is usually arguable that these traits are of some sort of advantage from some perspective (including my examples).  In this case @Andrew argues this.  I'm not sure I agree, but you can read his post for the argument. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) &lt;a href=&quot;http://www.nature.com/scitable/topicpage/pleiotropy-one-gene-can-affect-multiple-traits-569&quot;&gt;Pleiotropy&lt;/a&gt;. The idea that the negative trait evidences more than one trait.  In this case one might say that baldness is tied with another trait that is beneficial.  Some say that the cause of male pattern baldness, &lt;a href=&quot;http://en.wikipedia.org/wiki/Baldness#Evolutionary_hypotheses&quot;&gt;which is an excess of testosterone&lt;/a&gt;, would be tied in with other masculine signals, which can often outweigh disadvantages of being bald and trying to find a mate.  A trait like baldness could also for instance be tied to a desirable trait in women, causing it to persist in men as a result of the advantage of say, less hairy women.  I probably wouldn't take this stand either, though its conceivable. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) &quot;Neutral variant&quot; The third explanation that I will put out is that baldness simply isn't a trait with enough disadvantage (if any) that it should be removed from the gene pool.  While there is &lt;a href=&quot;http://www.nytimes.com/2011/01/23/fashion/weddings/23FIELD.html&quot;&gt;evidence that baldness&lt;/a&gt; is a &lt;a href=&quot;http://blog.timesunion.com/kristi/women-5-times-more-likely-to-go-for-men-with-hair/9687/&quot;&gt;disadvantage come friday night&lt;/a&gt;, to say that a trait is disadvantageous we have to see, &lt;em&gt;in the long run&lt;/em&gt; - over the lifetime - really is a disadvantage.  I think I would agree with those who say that while some women do not find bald men attractive, &lt;a href=&quot;http://www.helium.com/items/1530613-women-dating-bald-men&quot;&gt;its not enough to stop them from having kids&lt;/a&gt;, which is all evolution cares about. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if you happen to be balding probably what you should care about, guys!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If evolution should eliminate male baldness, then why not eliminate sterility, homeliness, impotence, poverty, obesity, being dull, living with your parents and adolescent awkwardness?  These are probably even more important obstacles to finding a mate? All of these traits are beneficial traits that are maladapted to modern life or genetic accidents.  Evolution can't get rid of them at all I think.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an even more complete discussion of the general subject, see Dawkin's &quot;The Extended Phenotype&quot;.  Baldness is not discussed however.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-06-22T04:28:01.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2727" PostTypeId="2" ParentId="2724" CreationDate="2012-06-22T06:38:16.833" Score="7" Body="&lt;p&gt;The problem is of course very complex so take my answers as simplifications.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most transgenesis so far has been done on unicellular beings (bacteria, yeast), which we can change as much as we want fairly &quot;easily&quot;, plants, insects and some mammals. Notably, for the latter case, mice are the species which has been used the most for transgenesis, as they are cheap (compared to, say, using pigs), do not take lots of space, have big litters and a quick reproductive cycle (~20 days). Aside from mice we've seen GFP rats, pigs, dogs, cats, sheep and probably there is more, but I will mostly restrict my answers to mice (as far as I know there are big technical difficulties in applying transgenics procedures to something bigger than a mouse, but to be honest I could not explain you the details on this as I have never done it).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What features can be easily inserted into almost any organism easily?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, essentially, it is easy to give rise to monogenic traits (i.e. traits that depend on a single gene). Generally speaking, when you want to have more traits, or need more than 1 gene to have the trait you create single transgenics and then breed them together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if your phenotype depends on the presence of gene A and B you will generate a (mouse) line expressing A, one expressing B, you breed them together and, if you are lucky, a part of the pups will be expressing both.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Next, I imagine that to design and create an artificial life-form will consist of three steps: 1. Figure out which proteins will give rise to those feaures, 2. Design a genome that will express those proteins in the right quantities and 3. Implant that genome into a cell and actually let the being grow.&lt;br&gt;&#xA;  Is the above sequence of steps correct, or am I missing something?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No, that is not how it is done!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There has been, to my knowledge, only one (very impressive) attempt to do that, a project led by Craig Venter at Celera Genomics. The project resulted in the creation of the first synthetic life form, named &lt;a href=&quot;http://en.wikipedia.org/wiki/Mycoplasma_laboratorium#Minimal_genome_project&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mycoplasma laboratorium&lt;/a&gt; (see also the &lt;a href=&quot;http://www.sciencemag.org/content/329/5987/52.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;original paper on Science&lt;/a&gt;). Doing this for a multicellular being is, presently, science-fiction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What normally you would do is to insert or remove just the piece of DNA you need in the genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are different approaches to do that: for instance, you can start from embryonic stem cells, from fertilized oocytes or from spermatozoa.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the general process for making a transgenic mouse:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://web.archive.org/web/20160423165056im_/http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transgenics.gif&quot; alt=&quot;Making a transgenic mouse&quot;&gt;&lt;br&gt;&#xA;Source: &lt;a href=&quot;https://web.archive.org/web/20161212170103/http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/TransgenicAnimals.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://web.archive.org/web/20161212170103/http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/TransgenicAnimals.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, depending on how you inject your gene you can distinguish between transgenics and knock-in mice. In a transgenic mouse you insert the gene somewhere in the genome and, although there are method to understand where it ended up you generally do not know.&#xA;Knock-in animals, instead, target a specific region of the genome. This is usually used in order to change an existing gene, to improve its function or to remove its function (knock-out animals). This process, called &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene_targeting&quot; rel=&quot;nofollow noreferrer&quot;&gt;gene targeting&lt;/a&gt; relies on the biological process called &lt;a href=&quot;http://en.wikipedia.org/wiki/Homologous_recombination&quot; rel=&quot;nofollow noreferrer&quot;&gt;homologous recombination&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, why don't we just synthesize a new genome each time?&#xA;Aside from Venter's dream, the process would:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;have incredibly high cost&lt;/li&gt;&#xA;&lt;li&gt;be extremely complicated technically&lt;/li&gt;&#xA;&lt;li&gt;be extremely long (mostly for reason 2)&lt;/li&gt;&#xA;&lt;li&gt;suffer from the problem that there is so much we do not know about genome regulation in a bacteria, let alone in a mouse! You have to think that the genome is not just a series of genes one after another: there is a big part of regulatory regions that define things like the 3D form of the genome, which determines when and how much genes are accessible for transcription, when and where they are activated and so on. Also, more and more attention is now drawn to something called &lt;a href=&quot;http://en.wikipedia.org/wiki/Epigenetics&quot; rel=&quot;nofollow noreferrer&quot;&gt;epigenetics&lt;/a&gt; marks, modifications of the DNA, or its associated proteins that can also modulate its transcription.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What is the cheapest experiment you can perform at your own home without access to a biology lab which involves changing the genome of a living organism in a way that's functionally visible? (An arbitrary example: Can you create an apple that's blue in color with a budget of $500? By create, I mean you should be able to hold the blue apple in your hand.)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Quick answer: no you cannot.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Health authorities will be not very happy if you start to produce transgenic organisms in your garage&lt;/li&gt;&#xA;&lt;li&gt;The sole cost of the reagents which you will need to create the transgene will be &gt;$500. You would then need various machines (e.g. a &lt;a href=&quot;http://en.wikipedia.org/wiki/Thermal_cycler&quot; rel=&quot;nofollow noreferrer&quot;&gt;thermocycler&lt;/a&gt;, probably a &lt;a href=&quot;http://en.wikipedia.org/wiki/Spectrophotometry&quot; rel=&quot;nofollow noreferrer&quot;&gt;spectrophotometer&lt;/a&gt;, a hood, etc etc.).&lt;/li&gt;&#xA;&lt;li&gt;I personally don't have a clue how one creates a transgenic plant, but I suspect it is not much easier than an animal. And definitely you don't want a mouse colony in your garage, do you?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;An easy experiment you can do is &lt;a href=&quot;http://www.york.ac.uk/res/sots/activities/diydna.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;extracting (fairly unpurified) DNA&lt;/a&gt; with stuff you have at home. More than that it gets really complicated.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="9686" LastEditDate="2018-06-28T11:58:43.120" LastActivityDate="2018-06-28T11:58:43.120" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="2728" PostTypeId="1" CreationDate="2012-06-22T07:07:22.850" Score="-3" ViewCount="517" Body="&lt;p&gt;In many personal improvement books I've read, people make a distinction between 2 parts of our brain:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the logical brain, dealing with logic, judgement, thinking; what makes Humans different than Animals&lt;/li&gt;&#xA;&lt;li&gt;the lizard brain inherited from our ancestors, dealing with emotions and instincts, which takes shortcuts to react to the immediate problems, such as a saber tiger croping up to eat us.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The facts are, the lizard brain sometimes take actions/decisions without making the logical brain aware of that, which is at the origin of many brain biases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering if there's a sound reason why Mother Nature didn't evolve us so that we would be made aware of our lizard brain decisions after the fact (i.e. a kind of summary for our logical brain). I mean, is there's something physical or an evolutionary reason that would prevent that?&lt;/p&gt;&#xA;" OwnerUserId="1052" LastEditorUserId="3632" LastEditDate="2012-06-24T16:09:07.607" LastActivityDate="2012-06-24T16:09:07.607" Title="Why hasn't mother nature made us aware of our lizard brain?" Tags="&lt;evolution&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2012-07-01T12:11:49.760" ContentLicense="CC BY-SA 3.0" />
  <row Id="2729" PostTypeId="2" ParentId="2700" CreationDate="2012-06-22T08:57:20.573" Score="2" Body="&lt;p&gt;Adding to Noah's answer, some lichens can survive the vacuum of space too. In an experiment led by Leopoldo Sancho from the Complutense University of Madrid, two species of lichen - &lt;em&gt;Rhizocarpon geographicum&lt;/em&gt; and &lt;em&gt;Xanthoria elegans&lt;/em&gt; - were sealed in a capsule and launched on a Russian Soyuz rocket on 31 May 2005. The &lt;a href=&quot;http://www.newscientist.com/article/dn8297-hardy-lichen-shown-to-survive-in-space.html&quot; rel=&quot;nofollow&quot;&gt;lichens&lt;/a&gt; were in perfect condition when observed after the return to earth. &lt;/p&gt;&#xA;" OwnerUserId="1053" LastActivityDate="2012-06-22T08:57:20.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2730" PostTypeId="2" ParentId="2728" CreationDate="2012-06-22T15:57:12.707" Score="6" Body="&lt;p&gt;Just to echo what others have said here, the term lizard brain is a remnant of &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Recapitulation_theory#Modern_status&quot;&gt;recapitulation theory&lt;/a&gt;&quot; which rigorously proposed that the embryo develops through more primitive animals.  This is an intriguing idea when looking at embryos - early stage embryos of flies, birds, fish and primates really do resemble each other.  So the idea was that our lower brain, near the spinal chord was the brain of a lizard, whereas the prefrontal cortex, which is highly developed in humans compared to lizards, birds etc was 'added later' and represents a 'human brain'.  This idea is flawed because it basically assumed that the lizard part of us never evolved and was based on a linear idea of phylogeny, as opposed to Darwin's idea of evolutionary trees where lizards and insect continue to evolve.  In evolution there are no 'lower animals'.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practice, the parts of the brain we have in common with lizards do handle more physiologically autonomous functions (heart rate, etc).  While cortex and prefrontal cortex do show greater activity in emotional and rational decision making.  &lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/IIIC6aOntogeny.shtml&quot;&gt;This is now more of a rule of thumb&lt;/a&gt;, not a rigorous statement or a theory of development, merely the result that structures that were developed later tend to have newer functions.  A good discussion of this can be found in &lt;a href=&quot;http://en.wikipedia.org/wiki/Ontogeny_and_Phylogeny_%28book%29&quot;&gt;Gould's &quot;Ontogeny and Philogeny&quot;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question also asks why we can't rationally understand our lower brain functions...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Awareness itself is not an intrinsic property of the brain.  Some aspects of the rational mind and articulate self consciousness are so far fairly unique amongst brains.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I should mention at this point that I do not mean that conscious thought is unique to humans - its clear that &lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=monkey-in-the-mirror&quot;&gt;primates&lt;/a&gt; are aware that they exist and have empathy for &lt;a href=&quot;http://en.wikipedia.org/wiki/Koko_%28gorilla%29#Koko.27s_pets&quot;&gt;feelings of others&lt;/a&gt;. Its likely that other animals have similar amazing &lt;a href=&quot;http://www.wired.com/wiredscience/2011/01/new-crow-tools/&quot;&gt;abilities we think of as human&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just the same, the level of development in humans is distinctly unique.  Insofar as it is a unique development, not a typical brain function, we should understand that it is far from all encompassing.  Given all this, its not surprising that the physiological functions of the brain such as regulation of breathing, many hormonal levels, stress are not conscious.  I usually only know I've run too far and too hard because I can feel my chest heave - its actually only something I'm aware of because my brain is receiving signals from my chest that its heaving and my heart is beating rapidly.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The limits of our consciousness are the subject of much study now.  From cognitive psychology and behavioral economics we've been surprised over and over in the past 20 years how there are limits to the amount of information we can process at a time and, how limited we are in being rational to the point that we can make foolish decisions, and lastly how much of those decisions are made subconciously, only to be rationalized later by our thoughts.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will give three examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Experiments in cognitive psych show that as subjects turn over cards in a deck, our pulse and respiration indicate they know that the deck is stacked before they consciously know.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Psychologist/Philosopher Joshua Greene is famous for observing that moral decisions are made in parallel in more than one region of the brain before the decision is rationally made.  This is a &lt;a href=&quot;http://www.radiolab.org/2007/aug/13/&quot;&gt;great radiolab podcast&lt;/a&gt; on this story. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Behavioral economists have shown that we don't even know a good deal when we see it.  We are often convinced by cues in the environment about the profitability of our decisions which comes from pre-set processes embodied in our minds.  Studies showing what happens when we &lt;a href=&quot;http://www.mercurynews.com/ci_15272782&quot;&gt;pay CEOs too much money&lt;/a&gt;, manipulate decision making &lt;a href=&quot;http://www.economist.com/node/17723028&quot;&gt;by offering too many choices&lt;/a&gt; and &lt;a href=&quot;http://www.psychologytoday.com/blog/hidden-motives/201008/why-are-the-poor-more-generous&quot;&gt;how poor people are more generous than wealthy ones&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This discussion goes back to Descartes, who felt we could be fooling ourselves to the point that we might even be deluding ourselves to believe in mathematics.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there are ever times when people do things that don't make sense, we have often found that the faults go back to the limitations of our brains.   If you have never had that experience ... &quot;Ill have what @Sylvain's having&quot;!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at references for cognitive dissonance, optical illusions will tell you a dozen more fascinating stories.  Highly recommend it :)&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-06-23T14:51:56.613" LastActivityDate="2012-06-23T14:51:56.613" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2731" PostTypeId="2" ParentId="2721" CreationDate="2012-06-22T16:02:44.353" Score="7" Body="&lt;p&gt;In bacteria, this is often true.  This is because more than one gene is often transcribed onto a single RNA.  This grouping of genes is called an operon.  It is usually true that these have a related function because they are being translated to protein in very much the same proportion - a convenient way to regulate the function as a whole. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you get into eukaryotes this is no longer true (except for v. rare cases most of which are viral genes), one mRNA transcript contains just one translation region.  This is true even for yeast and other single celled organisms.  Gene regulation can be correlated, but the relationship on the genome has little to do with it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is some importance to the genomic relationship of two genes because of the crossing over that occurs in meiosis, but this is more of a relationship that is important in speciation and evolution, it doesn't have any recognized importance to how the genes act within the eukaryotic cell. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-06-23T14:37:57.317" LastActivityDate="2012-06-23T14:37:57.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2732" PostTypeId="1" AcceptedAnswerId="3480" CreationDate="2012-06-21T21:08:02.233" Score="13" ViewCount="7678" Body="&lt;p&gt;I know there's a similar question &lt;a href=&quot;https://skeptics.stackexchange.com/questions/734/do-men-have-a-monthly-cycle&quot;&gt;here&lt;/a&gt;. But that discussion dissolved into lunar cycle and a correlation with it.  I want to find more towards the original question of is there a periodic hormone cycle in men. &#xA;The &lt;a href=&quot;http://answers.google.com/answers/threadview?id=431376&quot; rel=&quot;nofollow noreferrer&quot;&gt;links&lt;/a&gt; i have read suggest that there's probably a daily one for sure. But few hint at monthly ones &lt;a href=&quot;http://www.theirritablemale.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;too&lt;/a&gt;.&#xA; That link seems to have very shaky science, but my biology is too weak for me to find the actual studies. Anyone else with more informed opinions? Any studies tracking purely hormone levels in men over a period of couple of months/years?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[EDIT]&#xA;   I understand it's clear there are cycles within the day or around the 24-hr mark now. I still am looking for studies focusing on longer term cycles like week,months etc.&lt;/p&gt;&#xA;" OwnerUserId="1055" OwnerDisplayName="Anand Jeyahar" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2012-09-09T06:40:49.323" Title="Do men have significant hormonal cycles?" Tags="&lt;endocrinology&gt;&lt;circadian-rhythms&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2733" PostTypeId="1" CreationDate="2012-06-22T19:11:36.607" Score="1" ViewCount="123" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Possible Duplicate:&lt;/strong&gt;&lt;br&gt;&#xA;  &lt;a href=&quot;https://biology.stackexchange.com/questions/2250/death-because-of-distilled-water-consumption&quot;&gt;Death because of distilled water consumption&lt;/a&gt;  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&#xA;&#xA;&lt;p&gt;I know about the effects and myths about drinking distilled and/or deionized water. I'm not asking about such substances.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder if a semi-immediate effect of drinking, say 1L pure 100% H2O is deadly or harmful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My intuition says yes: either the reverse osmosis effect also present in distilled water is amplified so much that critical systems shut down due to extremely low concentrations in the organs/cells/... or the reverse happens, where the water is absorbed into cells making them burst, leading to among other things (massive) internal bleeding.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm particularly interested in scientific studies (if any) that were done (link to publication would be very welcome, my Web of Knowledge search-fu doesn't seem to work for this subject).&lt;/p&gt;&#xA;" OwnerUserId="1058" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2012-06-22T21:04:06.053" Title="Is pure (100% H20, (near to no) solutes) water toxic to living organisms?" Tags="&lt;toxicology&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2012-06-23T08:18:19.870" ContentLicense="CC BY-SA 3.0" />
  <row Id="2734" PostTypeId="2" ParentId="2701" CreationDate="2012-06-22T22:52:55.037" Score="9" Body="&lt;p&gt;The cocoon phase allows lepidopterans (and other holometabolous insects) to reorganize their body and undertake the dramatic metamorphosis from larvae to adult in a safe environment. Cocoons and pupae are typically attached to branches by silk (oftentimes after climbing high into the canopy), thereby removing them from many predatory interactions and providing a protected environment to breakdown the larval body and develop into the adult phase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my mind, the main adaptive significance of the cocoon/pupal phase is to provide an environment within which the animal can metamorphose while reducing exposure to both predators and any harsh elements. &lt;/p&gt;&#xA;" OwnerUserId="1060" LastActivityDate="2012-06-22T22:52:55.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2735" PostTypeId="2" ParentId="2293" CreationDate="2012-06-23T04:39:27.863" Score="11" Body="&lt;p&gt;Wheeler (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/004724849290086O&quot;&gt;1992&lt;/a&gt;; and &lt;a href=&quot;http://scholar.google.com/scholar?hl=en&amp;amp;q=hominid%20loss%20of%20hair&quot;&gt;previous&lt;/a&gt;) discusses the evolutionary loss of &quot;non-functional&quot; hair in hominids from the perspective of water balance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wheeler's hypothesis is that naked, bipedal hominids could have tolerated higher ambient temperatures as well as elevated metabolic heat production. Naked skin would confer higher levels of evaporative cooling, but would have entailed more water loss. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wheeler argues that bipedalism necessarily would have preceded loss of hair, which seems to agree with Carrier's (&lt;a href=&quot;http://www.jstor.org/discover/10.2307/2742907?uid=3739560&quot;&gt;1984&lt;/a&gt;) hypothesis that early hominids were distinguished not by large brains but by upright, bipedal postures with striding gaits. Humans are unique among similarly sized mammals in their capacity for endurance running.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-06-23T04:39:27.863" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2736" PostTypeId="2" ParentId="905" CreationDate="2012-06-23T04:52:44.073" Score="3" Body="&lt;p&gt;If you want to go way back, google books has &lt;em&gt;Methods in Plant Histology&lt;/em&gt; (&lt;a href=&quot;http://books.google.com/books?id=InIxAQAAMAAJ&quot; rel=&quot;nofollow&quot;&gt;Chamberlin, 1905&lt;/a&gt;) with a PDF. It details stains and the tissues they are used for and even has a section titled &quot;Selection of a Stain.&quot;&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-06-23T04:52:44.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2738" PostTypeId="1" AcceptedAnswerId="2796" CreationDate="2012-06-23T09:30:07.783" Score="24" ViewCount="7832" Body="&lt;p&gt;Why, from the natural selection point of view, do only two sexes exist for animals?&lt;/p&gt;&#xA;" OwnerUserId="1061" LastEditorUserId="239" LastEditDate="2015-08-28T10:00:39.817" LastActivityDate="2017-06-26T05:56:01.120" Title="Why do only two sexes exist for animals?" Tags="&lt;natural-selection&gt;" AnswerCount="4" CommentCount="12" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2739" PostTypeId="1" AcceptedAnswerId="3352" CreationDate="2012-06-23T09:43:48.680" Score="21" ViewCount="1398" Body="&lt;p&gt;Shortly before his untimely passing, the computing pioneer Alan Turing published his most cited paper &lt;a href=&quot;http://www.cecm.usp.br/~cewinter/aulas/artigos/2010/Turing_1952.pdf&quot;&gt;&lt;em&gt;The Chemical Basis of Morphogenesis&lt;/em&gt;&lt;/a&gt; (1952). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The central question for Turing was: how does a spherically symmetric embryo develop into a non-spherically symmetric organism under the action of symmetry-preserving chemical diffusion of &lt;em&gt;morphogens&lt;/em&gt; (as Turing calls them, an abstract term for arbitrary molecules relevant to development)? The insight that Turing made is that very small stochastic fluctuations in the chemical distribution can be amplified by diffusion to produce stable (i.e. not time varying except slow increases in intensity; although also potentially time-varying with 3 or more morphogens) patterns that break the spherical symmetry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The theory is beautifully simple and abstract, and produces very important qualitative results (and also quantitative results through computer simulation, which unfortunately Turing did not get to fully explore). However, even in the definition Turing discusses some potential limitations such as ignoring mechanical factors, and the inability to explain preferences in handedness. The particular models he considers -- a cycle of discrete cells and a circular tissue -- do not seem particularly relevant. As far as I understand, the key feature is his observation of symmetry breaking through small stochastic noise and instability. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What was the most important contribution of Turing's paper to developmental biology? Is his approach still used, or has the field moved on to other models? If his approach is used, how was the handedness problem resolved?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="500" LastActivityDate="2021-01-18T23:10:03.770" Title="Impact of Alan Turing's approach to morphogenesis" Tags="&lt;embryology&gt;&lt;history&gt;&lt;development&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2740" PostTypeId="2" ParentId="2732" CreationDate="2012-06-23T10:52:27.753" Score="10" Body="&lt;p&gt;Short answer: yes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although clearly the infradian changes in steroid hormones in females are quite &quot;obvious&quot;, other changes are less evident, but happen nonetheless in males as well as in females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the hormones produced by endocrine organs such as the hypothalamus (a region at the base of the brain) or the hypophisis are not secreted in a continuous manner but rather in pulses. The exact frequency/amplitude etc. of these pulses can be different depending on the species considered, but (as fare as we know) the undelying mechanism are fairly conserved.*&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, you can find circadian (~24 h), ultradian (&amp;lt;24h) and infradian (&gt;24h) rhythms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance these graphs show the concentration of cortisol, aldosteron and renin in a man, showing a strong circadian rhythm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2gno0.jpg&quot; alt=&quot;Cortisol, aldosteron and renin secretion in man&quot;&gt;&lt;br&gt;&#xA;From: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9886949&quot; rel=&quot;nofollow noreferrer&quot;&gt;Charloux et al. - Am J Physiol Endocrinol Metab 1999&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see that on top of the circadian rhythm, an ultradian pulsatility (every ~2-3h) is also quite clear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example is that of GH (growth hormone): here you see secretion of GH in an healthy women (top) and an healthy men (bottom)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SZg2u.jpg&quot; alt=&quot;GH secretion in women and men&quot;&gt;&lt;br&gt;&#xA;From: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8675561&quot; rel=&quot;nofollow noreferrer&quot;&gt;van den Bergh et al. - J Clin Endocrinol Metab. 1996&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many other hormones show this type of rhythmicity in males, such as testosterone, LH, GnRH, and probably many other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not aware of long term studies on this matter.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;*&lt;/sup&gt; Actually, the mechanisms underlying pulsatility are still poorly understood.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="3632" LastEditDate="2012-09-08T02:08:22.437" LastActivityDate="2012-09-08T02:08:22.437" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2742" PostTypeId="1" AcceptedAnswerId="2743" CreationDate="2012-06-23T12:54:48.920" Score="5" ViewCount="766" Body="&lt;p&gt;Just what the title states.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given identical, necessary and favourable conditions (Probably nutrients, humidity, and light but what I mean is all &lt;strong&gt;necessary&lt;/strong&gt; requirements are fulfilled) - Is photosynthesis equally efficient in terms of the amount of sugar/carbohydrates generated by all plants/trees, or are some plants/trees more adept at it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My background in biology/botany is high-school, so my list of necessary requirements may be lacking for which I crave your indulgence&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="649" LastEditDate="2012-06-26T21:58:42.860" LastActivityDate="2012-06-28T00:26:14.617" Title="Do all plants photosynthesize with equal efficiency?" Tags="&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2743" PostTypeId="2" ParentId="2742" CreationDate="2012-06-23T22:15:21.493" Score="7" Body="&lt;p&gt;If you mean the efficiency at which plants convert light energy to chemical energy (in sugar or other reduced C compounds) then there is definitely variability between plants, both at the species and individual level. The &lt;a href=&quot;https://en.wikipedia.org/wiki/Photosynthetic_efficiency&quot; rel=&quot;nofollow&quot;&gt;photosynthetic efficiency&lt;/a&gt; WP page gives ranges of between 0.1 and 8% of total solar radiation converted to &quot;biomass&quot;, but these values are not cited. In their review, &lt;a href=&quot;http://naldc.nal.usda.gov/download/36097/PDF&quot; rel=&quot;nofollow&quot;&gt;(Zhu et al, 2008)&lt;/a&gt; state that the maximum maximum efﬁciency with which photosynthesis can convert solar energy into biomass is 3.5% and 4.3% for C3 and C4 plants (both observed for crops), respectively. Biomass is not a measure of energy, but perhaps they mean potential chemical energy in that biomass.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its a pretty complicated question though. Photosynthesis is a complex process involving many interdependent chemical reactions and physical processes. All species (or even individuals) of plants have different morphology, physiology, and biochemistry that influences overall photosynthetic efficiency. In addition, they each inhabit different ecological niches and climate space. Therefore, all species or individuals would have a slightly unique maximum potential efficiency. Here are a couple other efficiency related concepts to consider:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are 2 systems in photosynthesis that work in tandem, the light reaction and the dark reaction.  The &lt;a href=&quot;https://en.wikipedia.org/wiki/Photosynthesis#Light_reactions&quot; rel=&quot;nofollow&quot;&gt;light reaction&lt;/a&gt; uses light energy, pigments like chlorophyll, and a bunch of electron transport chain proteins to generate ATP and NADPH. These 2 molecules then provide the reducing power for use in the &lt;a href=&quot;https://en.wikipedia.org/wiki/Photosynthesis#Light-independent_reactions&quot; rel=&quot;nofollow&quot;&gt;dark reaction&lt;/a&gt; (the Calvin Cycle). In the dark reaction, the enzyme &lt;a href=&quot;https://en.wikipedia.org/wiki/RuBisCO&quot; rel=&quot;nofollow&quot;&gt;RuBisCO&lt;/a&gt; joins CO&lt;sub&gt;2&lt;/sub&gt; and RuBP, creating simple reduced carbon chains which are then used to assemble sugars. This is an over-simplification, as both reactions are very complex systems with lots of biochemical machinery, but this is the basic process used to convert light energy to chemical energy. To operate at peak efficiency, the entire process must not be limited by incoming energy (light), substrate supply (CO&lt;sub&gt;2&lt;/sub&gt;, RuBP), or nutrients used to construct all the needed cellular and molecular machinery (N, P, K, and many others). In reality, there are limits that vary from plant to plant, species to species. For example, a species or individual with a very reflective leaf surface converts less of the light reaching the leaf surface to chemical energy, thus lowering the output of ATP and NADPH. This reduces the chemical energy supplied to the dark reaction and limits the amount of carbon fixed by RuBisCO. So the reflective surface of the leaf, which might be advantageous to the plant in other ways, has a large impact on overall photosynthetic efficiency (compared to a less reflective leaf or leaves).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to search for more information, there are a number of terms that plant physiologists and ecologists use when describing a plant's (or communities of plants) photosynthetic efficiency. Each of these is used in different ways and can have many variations in units.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Light use efficiency&lt;/strong&gt;: The amount of carbon fixed per unit of light incident.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Water use efficiency&lt;/strong&gt;: The amount of carbon fixed per unit of water transpired&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Nutrient use efficiency&lt;/strong&gt;: The amount of carbon fixed per unit of nutrient concentration (usually in leaves).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;reference: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://naldc.nal.usda.gov/download/36097/PDF&quot; rel=&quot;nofollow&quot;&gt;Zhu, Ort, and Long 2008 &quot;What is the maximum efﬁciency with which photosynthesis can&#xA;convert solar energy into biomass?&quot; Current Opinion in Biotechnology.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="649" LastEditorUserId="222" LastEditDate="2012-06-28T00:26:14.617" LastActivityDate="2012-06-28T00:26:14.617" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2745" PostTypeId="2" ParentId="2738" CreationDate="2012-06-24T16:05:38.423" Score="6" Body="&lt;p&gt;@emanuele you seem to be asking why there are only 2 sexes for animals, in contrast to f&lt;a href=&quot;http://blog.mycology.cornell.edu/?p=1060&quot; rel=&quot;nofollow&quot;&gt;ungi which can have many sexes&lt;/a&gt; or maybe bacteria which have mobile sex - the ability to donate genetic information can be acquired or lost. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some animals - worms and fish for instance are hemaphrodites - they can accept sperm or donate them to produce offspring. Fungi are even simpler - the mating is by haploid fusion on the cellular level, since they have single celled life cycles.  The mating type allows mating with any cell that is not of the same mating type.  Its just a matter of how much genome space you want to dedicate to mating and there can be 2 mating types of 10,000 mating types - the only rule is that you can't mate with your own mating type.  Its a simple mechanism to restrict mating with yourself - probably to encourage genetic diversity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Physiologically, for single celled animals and simple egg layers like fish and worms, you can see why sexual roles might not need to be specialized; its a matter of which gamete you will deposit.  If the egg is no more than an especially fat cell, becoming male is not necessarily a big change.  But when eggs are more complicated structures or live birth becomes an adaptation, the expense of being the gamete donor (male) or recipient (female) becomes a significant commitment and changing roles is not so easy to do in an evolutionary system.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultimately, Unlike worms or snakes, committed females are specialized such that turning into a male, with the requisite development of a womb, changes in bone structure, etc is such an elaborate phenomenon that we don't observe it.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-06-30T19:16:57.110" LastActivityDate="2012-06-30T19:16:57.110" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2748" PostTypeId="2" ParentId="1914" CreationDate="2012-06-25T11:44:53.443" Score="0" Body="&lt;p&gt;Owing to their narrow structure, no chewing mechanism nor limbs, a snake has to swallow its prey as a whole. In fact, their success and diversity is partly due to their ability to swallow  prey relatively larger than their own body size. So inevitably, they need to process the parts like teeth, bones, exoskeleton and things of such nature.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Snake saliva not only eases swallowing by lubrication, but also&#xA;  contains powerful enzymes to break down tissues and even egg shells.&#xA;  But snakes generally cannot digest keratin (claws, hair) or chitin&#xA;  (arthropod exoskeleton). Many prey are covered with tough hide and if&#xA;  a snake relied solely on its digestive juices, it would take a long to&#xA;  time to get through to the nutrients. So this is speeded up by snake&#xA;  venom. Venom not only immobilises prey but also starts digesting the&#xA;  prey from the inside. A study showed that when a fer-de-lance&#xA;  (&lt;em&gt;Bothrops asper&lt;/em&gt;) is deprived of its venom it took 12 days to digest&#xA;  a rat instead of the usual 2-3 days.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, there is no consensus among different theories arguing the utility of a snake's venom. The above mentioned opinion is based on digestion hypothesis of venom utility. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please refer to &lt;a href=&quot;http://www.mccuescience.com/uploads/Venom_review.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; excellent review and a &lt;a href=&quot;http://www.szgdocent.org/resource/rr/c-eat2.htm&quot; rel=&quot;nofollow&quot;&gt;summary&lt;/a&gt; of a snake's eating habits&lt;/p&gt;&#xA;" OwnerUserId="1053" LastEditorUserId="69" LastEditDate="2012-06-25T12:33:51.260" LastActivityDate="2012-06-25T12:33:51.260" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2749" PostTypeId="2" ParentId="2658" CreationDate="2012-06-25T14:37:51.493" Score="3" Body="&lt;p&gt;Progeria (and related) syndromes are essentially a collection of 'accelerated aging' phenotypes caused by single mutations; Progerin is a shortened version of the protein Lamin A, and is therefore &lt;em&gt;not&lt;/em&gt; found in individuals without a loss-of-function mutation in the &lt;em&gt;LMNA&lt;/em&gt; gene (&lt;a href=&quot;http://en.wikipedia.org/wiki/Progerin&quot; rel=&quot;nofollow&quot;&gt;the wiki page you reference&lt;/a&gt;). As far as we are aware these genes do not 'cause' aging in individuals without the mutations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;LMNA&lt;/em&gt; is a normal component of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nuclear_lamina&quot; rel=&quot;nofollow&quot;&gt;nuclear lamina&lt;/a&gt; (a structure inherent to the nucleus). &lt;a href=&quot;http://www.goldmanlab.northwestern.edu/articles/MattoutCOCB2006.pdf&quot; rel=&quot;nofollow&quot;&gt;This review&lt;/a&gt; discusses the various diseases associated with mutations in this gene, some of which present 'accelerated aging' phenotypes. However, as far as I know, there is limited evidence to suggest that &lt;em&gt;LMNA&lt;/em&gt;, or indeed any Lamina associated protein, is involved in 'normal aging'. A &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22340368&quot; rel=&quot;nofollow&quot;&gt;recent GWAS meta-analysis&lt;/a&gt; found a variant in &lt;em&gt;LMNA&lt;/em&gt; that is associated with longevity in humans, however the association is relatively weak (OR=1.18, P=7(x10)-4), so even if this is a true association, it seems that (as usual in aging research) there are &lt;em&gt;many&lt;/em&gt; other factors to consider, and it is not a single gene that is doing the aging.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to stress the point: &lt;strong&gt;progerin has no function in 'normal' human aging - it is a defective protein caused by a germline (or novel) mutation in the &lt;em&gt;LMNA&lt;/em&gt; gene.&lt;/strong&gt;  Accelerated aging is the &lt;em&gt;symptom&lt;/em&gt; of this genetic disorder, and is not completely analogous to normal aging (as you point out, there is no cognitive decline that is associated with normal human aging).&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-06-26T15:12:01.180" LastActivityDate="2012-06-26T15:12:01.180" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2750" PostTypeId="1" CreationDate="2012-06-25T17:08:09.673" Score="4" ViewCount="255" Body="&lt;p&gt;Just what the title states--given an absurdly large number of assignments to perform in a limited time-frame we usually attempt to do the most important ones first. Is this ability to define and execute by priority a universal feature in all sentients, or is it a socially learnt behaviour of us &lt;em&gt;Homo sapiens&lt;/em&gt;?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="107" LastEditDate="2012-06-25T20:35:52.943" LastActivityDate="2012-11-12T02:36:26.927" Title="Is Homo sapiens the only species capable of prioritization?" Tags="&lt;learning&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2751" PostTypeId="1" AcceptedAnswerId="2769" CreationDate="2012-06-25T21:33:46.340" Score="6" ViewCount="213" Body="&lt;p&gt;This might come off as a really silly question. But I'm wondering (especially in the case of food) if there is any reason a fly would continue to try and sit on top of a piece of food even after swatting it away. I assume (it could be misconception) that it is instinctive that animals and insects would leave an area if it is harmful / dangerous to their existence after having close encounters more than once. Is this not the same for the fly? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have this question mainly because I recall waving a fly away several times while eating lunch, and I couldn't understand why the fly wouldn't just find another place where there is food or somewhere safer.&lt;/p&gt;&#xA;" OwnerUserId="1064" LastEditorUserId="16866" LastEditDate="2017-01-03T16:07:38.827" LastActivityDate="2017-01-03T16:07:38.827" Title="Is there any reason the common housefly continues to return to an area?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;ethology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2753" PostTypeId="1" AcceptedAnswerId="2755" CreationDate="2012-06-26T13:23:04.593" Score="2" ViewCount="2593" Body="&lt;p&gt;I have a universal tube with 10 mg mL-1 ampicillin. When I got it, it was supposed to be sterile. It was opened for approximately 20 minutes for an experiment and has since been standing around sealed for a good month now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within the last couple weeks, it has gradually turned yellow. Right now the colour is faint, with a green-ish tint.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why would it turn yellow? I know NADH is yellow, so that was my first guess. But I couldn't exaplain why ampicillin would cause NADH to accumulate, so I discarded that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Side info: Ampicillin acts on bacterial cell walls, maybe that might help.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-06-26T16:48:31.940" Title="Why does ampicillin in solution turn yellow?" Tags="&lt;bacteriology&gt;&lt;antibiotics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2754" PostTypeId="2" ParentId="2503" CreationDate="2012-06-26T16:27:13.377" Score="4" Body="&lt;p&gt;While heat is lost during glycolysis, a lot more heat can be lost during chemiosmosis.  This is the movement of H+ (protons) across the inner mitochondrial membrane.  The energy potential of having a greater concentration of H+ on one side of the membrane usually powers ATP synthesis through ATP synthase.  In mammals, however, special proteins called uncoupling proteins (UCPs) can make the membrane 'leaky' to H+, so the energy is lost as heat, instead of being used to make ATP.  This is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Thermogenesis&quot; rel=&quot;nofollow&quot;&gt;non-shivering thermogenesis&lt;/a&gt;, and usually happens in brown adipose tissue (because fatty acids are used to enable UCP production).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not that glycolysis in ectotherms is less efficient (as far as I'm aware), but that ectotherms have different levels of different types of UCPs. Some UCP genes may have their expression altered in response to colder conditions (e.g. UCP2 and 3 may be upregulated) or the genes may not be present at all (e.g. UCP1 is not present in birds and crocodiles).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A better summary of UCPs in reptiles etc. can be found in this abstract:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/275/1637/979.long&quot; rel=&quot;nofollow&quot;&gt;http://rspb.royalsocietypublishing.org/content/275/1637/979.long&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1017" LastActivityDate="2012-06-26T16:27:13.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2755" PostTypeId="2" ParentId="2753" CreationDate="2012-06-26T16:48:31.940" Score="7" Body="&lt;p&gt;Why is NADH the first thing to come to mind? Time for some physical chemistry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beta-lactams has a shorter ring structure which give it a different absorbance (around 322 nm apparently (source needed)) which gives it a blueish hue. Typically Penicillin and Ampicillin start off as an off-white. As hinted by @Mad Scientist, the beta-lactam rings are unstable and will undergo acid-catalyzed hydrolysis which breaks the 4-membered ring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Penicillin core also near a ketone which can attack the ketone in the lactam (I'm pretty sure this qualifies as enol chemistry but it has been awhile). The cyclization will form a 5-membered oxazole ring. Based on my experience, unsaturated 5-membered rings will absorb at a higher wavelength tending to result in a yellowish color (570-590 nM) so I am going to suggest that is the source of your color.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZTLzo.png&quot; alt=&quot;Penicillin core&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jps.2600580412/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ampicillin degradation&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-06-26T16:48:31.940" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2756" PostTypeId="1" AcceptedAnswerId="2765" CreationDate="2012-06-26T18:02:23.967" Score="19" ViewCount="4308" Body="&lt;p&gt;The question is pretty simple: what is happening molecularly when hair turns grey or white? I would imagine that it is due to the lack of a particular compound. I'm also interested in why some people's onset of grey hair happens much later than others.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="3971" LastEditDate="2013-08-29T16:04:48.680" LastActivityDate="2020-11-02T04:03:55.653" Title="Why does hair turn grey or white, and why does it happen later for some?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;senescence&gt;&lt;pigmentation&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2757" PostTypeId="2" ParentId="2626" CreationDate="2012-06-26T19:37:57.433" Score="3" Body="&lt;p&gt;One way to do this is to use the &quot;humid operative temperature&quot; equation, or something similar. A variant of this equation, specifically for estimating leaf temperature, is derived using a leaf energy balance equation in chapter 14.1 of the Environmental Biophysics book (cited below). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll let you look up the actual equation since I'm not sure how to do math symbols here. But, in addition to air temperature, you will need to know a few pieces of information:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Vapor pressure deficit - calculated from humidity and temperature.&lt;/li&gt;&#xA;&lt;li&gt;Incoming radiation - Measured, or you could model this using time of day, latitude, etc.&lt;/li&gt;&#xA;&lt;li&gt;Emissivity of your leaves - you can probably look this up for your species or a similar one.&lt;/li&gt;&#xA;&lt;li&gt;Windspeed&lt;/li&gt;&#xA;&lt;li&gt;Characteristic dimension of leaves - measure, or look up a value for your species (Use this with windspeed to calculate boundary layer heat conductance).&lt;/li&gt;&#xA;&lt;li&gt;Leaf vapor conductance - a combination of stomatal and boundary layer conductance to water vapor. You must know something about where the stomata are on your leaf (both sides or one side), but you can often look this value up for a given species.&lt;/li&gt;&#xA;&lt;li&gt;A few other constants that are easy to look up.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;That's about it - its a somewhat hairy calculation, but if you have standard weather data and a little knowledge of the plants you are estimating the leaf temperature of, it should be manageable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This equation and other relevant info are in &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0387949372&quot; rel=&quot;nofollow&quot;&gt;this book&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Campbell, G.S. and Norman, J.M. &lt;em&gt;An Introduction to Environmental Biophysics&lt;/em&gt;. Springer Science, 1998&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="649" LastEditorUserId="649" LastEditDate="2012-06-26T21:55:35.843" LastActivityDate="2012-06-26T21:55:35.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2758" PostTypeId="1" CreationDate="2012-06-27T00:30:24.703" Score="5" ViewCount="1458" Body="&lt;p&gt;Can a gene be expressed under the T7 promoter in an E. coli strain (e.g. DH5 alpha), which does not have the T7 polymerase gene encoded in its genome? In other words, is T7 promoter leaky? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be more specific, how is it possible that a regular E. coli strain, which does not encode for the T7 polymerase, can grow on kan selective media if it was transformed with a plasmid that has the kanR gene under T7 promoter?&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-06-27T15:24:04.590" LastActivityDate="2018-07-24T18:47:19.630" Title="T7 promoter leakiness" Tags="&lt;genetics&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2759" PostTypeId="2" ParentId="2713" CreationDate="2012-06-27T03:36:23.313" Score="7" Body="&lt;p&gt;Again, not an expert, but I found &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC115301/&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; seems to say it pretty well: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Telomere's are most commonly measured by qPCR of the repetitive regions with degenerate oligomer sequences such as &quot;TTAGGG and CCCTAA repeats&quot;  Although articles like this one appear to advance measurements in vertebrates, this &lt;a href=&quot;http://umdnj.technologypublisher.com/technology/6197&quot; rel=&quot;nofollow&quot;&gt;reference from 2011&lt;/a&gt; implies two techniques continue to be most common: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) &lt;a href=&quot;http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction&quot; rel=&quot;nofollow&quot;&gt;qPCR&lt;/a&gt; with the appropriate oligos and then running them on an agarose gel&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) &lt;a href=&quot;http://en.wikipedia.org/wiki/Southern_blot&quot; rel=&quot;nofollow&quot;&gt;Southern blot&lt;/a&gt; of a restriction digest that leaves the telomeres intact  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clearly sequencing techniques don't do well with repetitive sequences such as this, so in general this still seems like the most common method.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This would indeed be quite destructive, at least for the cells used, though a biopsy would be enough, though apparently micrograms of DNA are required.  Kind of a large amount. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The accuracy would then be limited to that of the gel or blot.  That would generally be a percentage of total length, I think 2% might be obtainable, but I'm not sure about that part. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="115" LastEditDate="2012-07-27T07:05:18.980" LastActivityDate="2012-07-27T07:05:18.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2760" PostTypeId="2" ParentId="2758" CreationDate="2012-06-27T03:39:51.530" Score="2" Body="&lt;p&gt;Apparently not, &lt;a href=&quot;http://openwetware.org/wiki/E._coli_genotypes#High-Control.28tm.29_BL21.28DE3.29_.28Lucigen.29&quot; rel=&quot;nofollow&quot;&gt;leakiness can be controlled by tightly regulating the T7 polymerase with a tight promoter (in this case lacUV5)&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-06-27T03:39:51.530" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2761" PostTypeId="1" AcceptedAnswerId="2862" CreationDate="2012-06-27T03:41:02.463" Score="5" ViewCount="150" Body="&lt;p&gt;There have recently been several papers on using 16S rRNA as a way of identifying species (&lt;a href=&quot;http://jb.asm.org/content/173/2/697.abstract&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, and &lt;a href=&quot;http://aem.asm.org/content/73/1/278.long&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;). I'm wondering if it's possible to sequence either just that subunit of the ribosome or just the sequence of DNA that it comes from (probably not, I know). That way you can use only the sequence you need to compare against other 16S rRNA sequences to test for novel species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, what is the process involved?&lt;/p&gt;&#xA;" OwnerUserId="1051" LastEditorUserId="1051" LastEditDate="2012-06-27T07:04:38.913" LastActivityDate="2012-07-10T16:42:41.737" Title="Is it possible to sequence only the 16S rRNA component? If so, how?" Tags="&lt;dna-sequencing&gt;&lt;rna&gt;&lt;ribosome&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2762" PostTypeId="2" ParentId="1372" CreationDate="2012-06-27T07:42:48.057" Score="3" Body="&lt;p&gt;ROS can inflict DNA damage in cells and if this damage is persistant and cannot be repaired, the cell can undergo cellular senescence.  Cellular senescence appears to play a major role in ageing (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19234764&quot; rel=&quot;nofollow&quot;&gt;see here&lt;/a&gt; for example). When cells become senescent they can no longer divide and replace damaged tissue.  Also, they secrete pro-inflammatory factors which can damage the microenvironment leading to disease and ageing.  Senescent cells also have dysfunctional mitochondrial leading to increase ROS levels and possibly further damage.  &lt;/p&gt;&#xA;" OwnerUserId="1067" LastActivityDate="2012-06-27T07:42:48.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2763" PostTypeId="2" ParentId="740" CreationDate="2012-06-27T07:54:31.443" Score="4" Body="&lt;p&gt;Resveratrol has recently been shown to induce cellular senescence (at least at high concentrations, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21318333&quot; rel=&quot;nofollow&quot;&gt;see here&lt;/a&gt;) which has the potential to accelerate ageing.  Senescent cells display and highly inflammatory phenotype which could damage tissues if not removed.  However, Resveratrol itself is rapidly metabolised and it may be these metabolites that have health benefits, but this needs to be researched further.  &lt;/p&gt;&#xA;" OwnerUserId="1067" LastActivityDate="2012-06-27T07:54:31.443" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2764" PostTypeId="2" ParentId="344" CreationDate="2012-06-27T08:19:54.267" Score="3" Body="&lt;p&gt;&quot;WHY&quot; we age is a different question from &quot;HOW&quot; we age.  The &quot;WHY&quot; refers to ageing from an evolutionally standpoint, whereas the &quot;HOW&quot; refers to biology of ageing.  As for the &quot;WHY&quot; I would read a few papers on the antagonistic pleiotropy hypothesis (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22329645&quot; rel=&quot;nofollow&quot;&gt;click here&lt;/a&gt;).  As for the &quot;HOW&quot;, there is no definitive understanding of mechanisms of ageing.  However, the role of cellular senescence in ageing and age-related disease is a major player in the biology of ageing (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19234764&quot; rel=&quot;nofollow&quot;&gt;click here&lt;/a&gt; for example).  When cells become senescent (due to either telomere shortening/DNA-damage) they can no longer divide to regenerate damaged tissue.  Additionally, senescent cells are highly pro-inflammatory and so have the potential to damage the surrounding tissue if the are not removed.  In younger organisms, senescent cells are most likely removed my the immune system, but as organisms age, the immune system also ages and can no longer effectively remove senescent cells.&lt;/p&gt;&#xA;" OwnerUserId="1067" LastActivityDate="2012-06-27T08:19:54.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2765" PostTypeId="2" ParentId="2756" CreationDate="2012-06-27T08:40:15.997" Score="17" Body="&lt;p&gt;Each individuals &lt;a href=&quot;http://en.wikipedia.org/wiki/Hair_color&quot;&gt;hair colour&lt;/a&gt; is determined by the particular pigment they produce (called melanin - the same stuff in your skin that makes you tan).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the body ages this pigment (produced by the melanonocytes - cells that reside in the hair follicle) is produced less and less, until the hair is no longer coloured, and appears grey.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is unique to each individual because it is a genetic (and therefore highly heritable) trait. Because it is in no way linked to mortality there is no selection pressure against greying hair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;reason&lt;/em&gt; that the pigment is not longer produced is the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17917134&quot;&gt;gradual depletion of the stem-cell pool with age&lt;/a&gt;. This is common to many tissues, hair follicles being just one. As the 'pool' of stem cells is depleted, the melanocytes are no longer replaced as frequently, and thus less pigment is produced as we age.&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-06-27T10:58:30.640" LastActivityDate="2012-06-27T10:58:30.640" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2766" PostTypeId="2" ParentId="186" CreationDate="2012-06-27T08:49:25.943" Score="3" Body="&lt;p&gt;A number of studies have compared replicative capacity of cells with lifespan.  Since Replicative capacity of cells is linked to telomere-length, these studies may provide indirect evidence for the association between telomere length and lifespan.  One interesting study in particular compared animal life spans and in vitro replicative capacity of skin fibroblasts in groupings of small, middle, large, and very large breeds of dogs of specific ages (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8914489&quot; rel=&quot;nofollow&quot;&gt;Li et al, 1996&lt;/a&gt;). It was found that the life spans were inversely correlated to the frame sizes of the breeds. It was shown that all the small breeds studied have a longer life span than that of the large breeds. The replicative capacity of fibroblasts from the large dogs (Great Dane and Irish Wolfhound) was significantly decreased compared with that of the small dogs. The reasoning behind these observations may again be due to varying degrees of cell turnover between the species. Large dogs consist of more cells than small dogs and as a result more cell turnover was initially required in their development compared to small dogs. This increase in cell turnover would subsequently lead to a decrease in replicative potential (due to telomere shortening) and an increase in the rate of senescent cell formation.&lt;/p&gt;&#xA;" OwnerUserId="1067" LastEditorUserId="1067" LastEditDate="2012-06-27T10:08:52.367" LastActivityDate="2012-06-27T10:08:52.367" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2767" PostTypeId="1" CreationDate="2012-06-27T09:00:46.117" Score="2" ViewCount="80" Body="&lt;p&gt;I am reading a GWAS paper that found a SNP associated to predisposition to colon cancer and was assessed for gene expression of the nearby gene. They found that the genotype accounted for 55% of the variation in the nearby gene expression. 55% sounds like a lot to me, what is the usual percent accounted for a significant SNP in a study like this?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/ng.2293&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Dunlop MG, Dobbins SE, Farrington SM, Jones AM, Palles C, Whiffin N, Tenesa A, Spain S, Broderick P, Ooi L-Y, et al.&lt;/strong&gt;. 2012. Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. Nature genetics 44: 770–776.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="658" LastEditorUserId="836" LastEditDate="2012-09-13T06:23:04.040" LastActivityDate="2012-09-13T06:23:08.470" Title="variation in expression accounted for a SNP -- what's a usual percent?" Tags="&lt;gene-expression&gt;&lt;gwas&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2768" PostTypeId="2" ParentId="2767" CreationDate="2012-06-27T09:47:32.977" Score="3" Body="&lt;p&gt;eQTLs (expression quantitative trait loci) are variants that affect the expression of one or more genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been several 'genome-wide' studies of SNPs that directly affect expression. The actual effect sizes are hard to pin down in most of them, but in the supplementary data for &lt;a href=&quot;http://dx.doi.org/10.1093/hmg/ddr328&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; is a list of the SNPs with the largest effects and coefficients of determination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several common SNPs (cis-acting) that account for &gt;50% of the variation in that genes expression in this (European) population cohort. That being said, that vast majority of variants account for &lt;em&gt;much&lt;/em&gt; less variation in the expression, but this is to be expected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I therefore can fully suppose that a disease-linked SNP could affect the expression of a gene to that degree, particularly if it is an oncogene or tumour suppressor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1093/hmg/ddr328&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Wood AR, Hernandez DG, Nalls MA, Yaghootkar H, Gibbs JR, Harries LW, Chong S, Moore M, Weedon MN, Guralnik JM, et al.&lt;/strong&gt;. 2011. Allelic heterogeneity and more detailed analyses of known loci explain additional phenotypic variation and reveal complex patterns of association. Human molecular genetics 20: 4082–92.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="740" LastEditorUserId="836" LastEditDate="2012-09-13T06:23:08.470" LastActivityDate="2012-09-13T06:23:08.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2769" PostTypeId="2" ParentId="2751" CreationDate="2012-06-27T13:16:07.477" Score="6" Body="&lt;p&gt;I don't think it's a silly question, but it is a common error to &lt;a href=&quot;http://en.wikipedia.org/wiki/Anthropomorphise&quot;&gt;anthropomorphise&lt;/a&gt; animals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Insects respond to cues which they have evolved to respond to, and this is how they 'make decisions'. They do not have free will or any more complex decision-making process like common sense. This is evident is lots of insect behaviour: flying repeatedly at a closed window; landing on brightly coloured clothes instead of flowers; and returning to a food source when they are in real danger of being swatted!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a fly senses the food (often by olfactory receptors), they are 'programmed' to fly towards it in response to some chemical they sense depending on the species and food. They may not have adapted a response to swatting, or perhaps the food cue overrides others. In nature swatting is not so much of a threat to a fly. Some animals may brush them away, but since they are not really doing any harm in feeding from another animal's food, they are mostly ignored.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CO2 traps are used to entice and kill mosquitoes. The mosquitoes are attracted to CO2 (as it is dispelled from the animals from which they blood feed), they will only evolve to avoid the traps if there is another cue which they could eventually associate with a negative effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another thing to remember when thinking about insect behaviour is that their life strategy is very different to ours. Insects are more &lt;a href=&quot;http://en.wikipedia.org/wiki/R/K_selection_theory&quot;&gt;r-selected&lt;/a&gt; than humans, meaning that each individual life has not had so much energy put into it as a more &lt;a href=&quot;http://en.wikipedia.org/wiki/R/K_selection_theory&quot;&gt;K-selected&lt;/a&gt; animal (such as humans), and to compensate for this, many more young are produced. This often results in more risks being taken by individuals since there will still be a viable population even after many deaths.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chapter 4 of '&lt;a href=&quot;http://www.amazon.co.uk/The-Insects-An-Outline-Entomology/dp/1444330365/ref=sr_1_1?ie=UTF8&amp;amp;qid=1340802822&amp;amp;sr=8-1&quot;&gt;The Insects&lt;/a&gt;' by Gullan &amp;amp; Cranston gives a good introduction to the sensory responses of insect behaviour. There are other books on the subject, '&lt;a href=&quot;http://www.cabdirect.org/abstracts/19800575094.html&quot;&gt;Introduction to insect behaviour&lt;/a&gt;' by Atkins looks like a good starting point, but I have not read it yet.&lt;/p&gt;&#xA;" OwnerUserId="445" LastActivityDate="2012-06-27T13:16:07.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2770" PostTypeId="2" ParentId="1339" CreationDate="2012-06-27T15:05:39.213" Score="9" Body="&lt;p&gt;The main difference between tracheal gas exchange, and other forms of gas exchange (except simple diffusion) is that it is generally a passive process. Organisms with lungs, gills, or other modified respiratory organs can actively pump the oxygen-containing medium (usually air or water) across their respiratory surface, and some also pump their blood across in the opposite direction to cause a &lt;a href=&quot;http://en.wikipedia.org/wiki/Countercurrent_exchange&quot; rel=&quot;nofollow&quot;&gt;countercurrent exchange&lt;/a&gt; to enable maximum efficiency of oxygen/CO₂ transfer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The tracheal system is a more efficient mode of gas exchange than diffusion since it does not only involve the oxygen passing over the organism's body surface (a &lt;a href=&quot;http://en.wikipedia.org/wiki/Semi-permeable_membrane&quot; rel=&quot;nofollow&quot;&gt;semi-permeable membrane&lt;/a&gt;) which limits the rate of movement. Instead the epidermis is invaginated to form tracheae (tubes) through which air can travel passively. The tracheal system is highly branched and terminates at tracheoles (fluid-filled sacs) which closely line respiring tissues to provide oxygen and allow release of CO₂.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tracheal respiration limits the size of insects since their oxygen demands will not be able to be met if the air has to diffuse very far. Some insects require more oxygen than others: many larger insects and more active insects have evolved to supplement the tracheal system with pumps, gas gills (permanent or temporary bubbles of air which aquatic insects carry), or mechanically ventilated air sacs (honeybees have these, see &lt;a href=&quot;http://www.amazon.co.uk/The-Insects-An-Outline-Entomology/dp/1444330365/ref=sr_1_1?ie=UTF8&amp;amp;qid=1340808083&amp;amp;sr=8-1&quot; rel=&quot;nofollow&quot;&gt;Gullan &amp;amp; Cranston, 2005&lt;/a&gt;; and Snodgrass, 1956). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, tracheal systems can be 'open', 'closed', or the insect can engage in &lt;a href=&quot;http://en.wikipedia.org/wiki/Discontinuous_gas_exchange&quot; rel=&quot;nofollow&quot;&gt;discontinuous gas exchange&lt;/a&gt;. Insects with open tracheal systems have spiracles (holes in their cuticle). Closed tracheal systems are more common in aquatic insects, they come in two major designs: highly branched systems over the internal surface, allowing cutaneous gas exchange; and filamentous or lamellate  arrangements, which are analogous to a primitive gill (see &lt;a href=&quot;http://www.amazon.co.uk/THE-LIFE-OF-INSECTS-Wigglesworth/dp/B0006AYOQK/ref=sr_1_2?ie=UTF8&amp;amp;qid=1340808693&amp;amp;sr=8-2&quot; rel=&quot;nofollow&quot;&gt;Wigglesworth, 1964&lt;/a&gt; or &lt;a href=&quot;http://www.amazon.co.uk/The-Insects-An-Outline-Entomology/dp/1444330365/ref=sr_1_1?s=books&amp;amp;ie=UTF8&amp;amp;qid=1340808812&amp;amp;sr=1-1&quot; rel=&quot;nofollow&quot;&gt;Gullan &amp;amp; Cranston, 2005&lt;/a&gt; chapter 10 for more on aquatic insect adaptations). Discontinuous gas exchange involves co-ordinated opening and closing of different spiracles which results in a uni-directional current allowing more effective ventilation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Gullan, P.J. &amp;amp; Cranston, P.S. (2010) The Insects: An Outline of Entomology. John Wiley &amp;amp; Sons.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Snodgrass, R. (1956) Anatomy of the honey bee, Comstock Publ. Assoc. Ithaca, New York,.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wigglesworth, S.V.B. (1968) The Life of Insects. New American Library.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="445" LastEditorUserId="3340" LastEditDate="2014-10-09T15:40:41.277" LastActivityDate="2014-10-09T15:40:41.277" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2771" PostTypeId="1" AcceptedAnswerId="2775" CreationDate="2012-06-27T15:15:17.470" Score="9" ViewCount="3989" Body="&lt;p&gt;The Kakapo can be seen in &lt;a href=&quot;http://www.youtube.com/watch?v=9T1vfsHYiKY&quot;&gt;this video&lt;/a&gt; by BBC. It is said that the species is strongly sexually attracted to humans. Why could this be the case? &lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="16866" LastEditDate="2017-01-03T16:08:35.000" LastActivityDate="2017-01-03T16:08:35.000" Title="Why is the Kakapo more attracted to humans than its own kind?" Tags="&lt;evolution&gt;&lt;ornithology&gt;&lt;ethology&gt;&lt;sexual-selection&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2772" PostTypeId="2" ParentId="2067" CreationDate="2012-06-27T16:45:17.093" Score="2" Body="&lt;p&gt;Seems like you have covered the essentials here. I can't think of anything else.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the Qiagen patent on spin prep columns ran out, these kits are very cheap - $0.40 each?  In the 3 or 4 kits Ive used, they all seem to use the same protocol and about the same buffers, so there might be differences in quality or yield but if so, they are small.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can even make your own buffers &lt;a href=&quot;http://openwetware.org/wiki/Qiagen_Buffers&quot; rel=&quot;nofollow&quot;&gt;as the recipes are on open wet ware&lt;/a&gt;.  None of the kits i've used has suggested that these buffers can't be used.  They even usually call the buffers by the same names. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So your application would have be pretty discriminating to differentiate.  Even if this were the case, the quality could probably be improved a lot just by washing the column more.  Can you provide more details about how a few percent one way or another might be an issue? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-06-27T16:45:17.093" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2773" PostTypeId="2" ParentId="1171" CreationDate="2012-06-27T17:03:17.210" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/cne.902860404/abstract&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; seems to be at least part of what you're looking for (although I can only access the abstract at the moment). They report that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In this study the density of neurons and synapses was measured in three different areas (8, 6, and 17) of the neocortex of the mouse. [...] The total average was 9.2 × 104 neurons/mm3 and 7.2 × 108 synapses/mm3.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It would only make sense for the neuron and synapse density of the different areas of the mouse brain to be reported in the full-text article.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-06-27T17:08:18.953" LastActivityDate="2012-06-27T17:08:18.953" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2775" PostTypeId="2" ParentId="2771" CreationDate="2012-06-27T18:53:31.130" Score="17" Body="&lt;p&gt;The male kakapo (&lt;em&gt;Strigops habroptila&lt;/em&gt;) in that video is called Sirocco. Kakapo were (and still are) very close to extinction, so in the 1980s the &lt;a href=&quot;http://www.kakaporecovery.org.nz/&quot;&gt;Kakapo Recovery Programme&lt;/a&gt; was launched. As part of this programme, rangers monitor all known kakapo in the wild, visiting their nests and generally ensuring they are in good health. When Sirocco was a young chick, a ranger discovered him in his mothers nest with severe breathing problems. He was brought back to the Kakapo care hut and raised by humans. As a result of this, he imprinted on his carers (&lt;a href=&quot;http://www.kakaporecovery.org.nz/index.php?option=com_content&amp;amp;view=article&amp;amp;id=92&amp;amp;Itemid=191&quot;&gt;see his website!&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imprinting is common in birds, and takes several different forms. The most well-known form is filial imprinting, where young birds (and some other animals) develop a strong fixated image of who their mother is. They then learn their behaviour almost exclusively from the animal they fixated on. This is well studied in geese, for example by Konrad Lorenz.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, Sirocco was demonstrating sexual imprinting. This is where young animals (including humans, see e.g. Bereczkei et al., 2004) learn which characteristics are sexually desirable by fixing an image of their parent(s). In Sirocco's case, he imprinted on a human and subsequently saw humans as his species, and therefore potential mates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact purpose of sexual imprinting has been widely discussed (e.g. see Immelmann, 1972). Lorenz suggested that it allowed animals to recognise their own species. However, some imprintable birds will show a preference toward individuals resembling the one they imprinted on, but when introduced to their own species will still recognise them as potential sexual partners. It may therefore be the case that imprinting allows a juvenile firstly to supplement a genetic predisposition toward its own species, but secondly to recognise closely related and less related individuals. Bateson (1978) suggested that this would enable a sexual strategy of choosing mates which are sufficiently unrelated so as not to cause inbreeding depression, but sufficiently related so as not to cause outbreeding depression, and he found an example which bore out the predicted behaviour in Japanese quails.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sirocco seems not to have the genetic ability to recognise his own species, and according to his website does not associate with other birds.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/273659a0&quot;&gt; &lt;strong&gt;Bateson P&lt;/strong&gt;. 1978. Sexual imprinting and optimal outbreeding. Nature 273, 659 - 660.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1691703/&quot;&gt; &lt;strong&gt;Bereczkei T, Gyuris P, Weisfeld GE&lt;/strong&gt;. 2004. Sexual imprinting in human mate choice. Proceedings of the Royal Society of London, Series B: Biological Sciences 271: 1129–1134.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0065345408600091&quot;&gt; &lt;strong&gt;Immelmann K&lt;/strong&gt;. 1972. Sexual and Other Long-Term Aspects of Imprinting in Birds and Other Species. In Advances in the Study of Behavior, Vol. Volume 4 of, pp. 147–174, Academic Press&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-06-27T19:02:54.923" LastActivityDate="2012-06-27T19:02:54.923" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2776" PostTypeId="1" CreationDate="2012-06-27T21:24:29.740" Score="12" ViewCount="623" Body="&lt;p&gt;The aquatic ape theory suggests that many features that distinguish humans from their nearest evolutionary relatives emerged because the ancestors of humans underwent a period when they were adapting to an aquatic or semiaquatic way of life, but returned to terrestrial life before having become fully adapted to the aquatic environment.  Is there any new evidence of this?&lt;/p&gt;&#xA;" OwnerUserId="1067" LastEditorUserId="107" LastEditDate="2016-01-10T15:47:10.103" LastActivityDate="2016-01-10T15:47:10.103" Title="Is there any recent evidence for the aquatic ape theory of human evolution?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="2778" PostTypeId="1" AcceptedAnswerId="2782" CreationDate="2012-06-28T03:21:37.703" Score="5" ViewCount="11321" Body="&lt;p&gt;We are planning to send an ecoli strain to another lab. What is the appropriate way to do so. No MTA is required but the options seem to be using filter paper or sending a glycerol stock on dry ice.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-06-28T14:24:13.543" Title="What is the appropriate method to send a strain?" Tags="&lt;ecoli&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2779" PostTypeId="2" ParentId="2701" CreationDate="2012-06-28T10:22:14.603" Score="18" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Holometabolism&quot; rel=&quot;noreferrer&quot;&gt;Holometaboly&lt;/a&gt; is believed to have evolved only once (&lt;a href=&quot;http://www.bioone.org/doi/abs/10.1664/10-RA-011.1&quot; rel=&quot;noreferrer&quot;&gt;Labandeira, 2011&lt;/a&gt;), but is arguably the most successful mode of development we know of in terms of species richness (&lt;a href=&quot;http://katz.entu.cas.cz/pdfarticles/310/eje_096_3_237_Kristensen.pdf&quot; rel=&quot;noreferrer&quot;&gt;Kristensen, 1999&lt;/a&gt; - PDF link). Insects which have adopted this method are far more diverse than their &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemimetabolism&quot; rel=&quot;noreferrer&quot;&gt;hemimetabolous&lt;/a&gt; counterparts. A conservative estimate by Hammond (1992) is that holometabolous insects comprise more than 60% of all living organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The subclass &lt;a href=&quot;http://en.wikipedia.org/wiki/Pterygota&quot; rel=&quot;noreferrer&quot;&gt;Pterygota&lt;/a&gt; (winged insects) is divided into (super orders) &lt;a href=&quot;http://en.wikipedia.org/wiki/Endopterygota&quot; rel=&quot;noreferrer&quot;&gt;endopterygota&lt;/a&gt; (wings develop interiorly) which are holometabolous, and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Exopterygota&quot; rel=&quot;noreferrer&quot;&gt;exopterygota&lt;/a&gt; (external wing development) which are hemimetabolous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hemimetabolous insects (usually) develop from an egg to an adult through a series of immature forms (known as nymphs or instars) which are slightly modified (and usually slightly larger) forms of the preceding form. There are exceptions to this mode within the exopterygota including asexual parthenogenesis which is common in aphids. The general life cycle is well illustrated in the Dermaptera (earwigs). All stages inhabit the same ecological niche and so maintain the same general body plan.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/K8LHR.png&quot; alt=&quot;Dermaptera lifecycle, from Wikimedia commons&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image file from Wikimedia Commons &lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Earwig_life_cycle_2.svg&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although hemimetaboly is a more gradual process than holometaboly, it happens in a small number (often four or five nymphal instars) of discrete steps rather than the more continuous development of other animals such as mammals. Although all insects fall into either the exopterygote or endopterygote categories (i.e. wings either develop externally or internally), there are examples of intermediate processes which lie somewhere between hemi- and holometaboly. A notable example are the Cicadas. Cicadas are Hemiperans (true bugs) which lie in the exopterygota and so are, by default hemimetabolous. However there is a considerable difference between their immature and mature stages:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HK9tn.jpg&quot; alt=&quot;Cicada (Auchenorrhyncha: Hemiptera) development&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Illustration by Debbie Hadley, using drawings from Insects - Their Ways and Means of Living by Robert Evans Snodgrass, U.S. Bureau of Entomology. These drawings are in the public domain. From &lt;a href=&quot;http://insects.about.com/od/growthmetamorphosi1/ss/typesmetamorph_3.htm&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During the immature stages, the larva (or nymph) will burrow underground, sometimes for many years. This requires strong front appendages, which they also use when they surface to grip onto a surface whilst they shed their final skin to become an adult. This differential niche exploitation is likely to have given rise to the morphological differences between immature and mature life stages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exploiting different niches during different developmental stages not only reduces intra-specific competition between young and adult, it also enables the insect to be more specialised to fulfill their specific role, which changes as they develop. The role of the immature is to grow, they do not yet need to be able to reproduce or disperse; whereas the role of the adult is to find a mate and reproduce. Young often develop below ground where there are fewer predators, adults often fly to enhance dispersal (further reducing competition and also decreasing inbreeding). These two activities call for vastly different body designs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some other common holometabolous insect orders are Coleoptera (beetles), Hymenoptera (bees, wasps, and ants), and Diptera (true flies), whereas hemimetabolous groups include Orthoptera (grasshoppers, crickets etc.), Mantodea (praying mantids), and Blattaria (cockroaches).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the chrysalis which Lepidoptera (butterflies and moths) have evolved to surround their pupal stage, the main role is likely to be protection. Larvae (caterpillars) are a highly nutritious and energetic food source and thus have adapted defensive mechanisms such as mimicry, warning colours, and dropping to the ground when disturbed. This drop would damage the metamorphosing pupa (the most vulnerable stage as it is usually relatively immobile), as the cuticle softens to allow for cell-rearrangement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The process of insect development is regulated by juvenile hormone (JH), see &lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028728#pone.0028728-Kristensen1&quot; rel=&quot;noreferrer&quot;&gt;Konopova&lt;/a&gt; &lt;em&gt;et al&lt;/em&gt;, (2011) for more on this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Hammond, P. (1992) Species Inventory. Global Biodiversity (ed B. Groombridge), pp. 17–39. Chapman and Hall, London.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Konopova, B., Smykal, V. &amp;amp; Jindra, M. (2011) Common and Distinct Roles of Juvenile Hormone Signaling Genes in Metamorphosis of Holometabolous and Hemimetabolous Insects. PLoS ONE, 6, e28728.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Kristensen, N.P. (1999) Phylogeny of endopterygote insects, the most successful lineage of living organisms. European Journal of Entomology, 96, 237–253.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Labandeira, C.C. (2011) Evidence for an Earliest Late Carboniferous Divergence Time and the Early Larval Ecology and Diversification of Major Holometabola Lineages. Entomologica Americana, 117, 9–21.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="445" LastActivityDate="2012-06-28T10:22:14.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2780" PostTypeId="1" CreationDate="2012-06-28T10:49:54.823" Score="3" ViewCount="106" Body="&lt;p&gt;What are different foetal conditions during pregnancy that could be treated with appropriate prenatal genetic testing?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I only know that pregnant women are encouraged to take certain supplements to make sure certain conditions won't develop in the foetus, and which are apparently also the case for deficiencies in human growth hormone, but I imagine there must be other specific cases that are treatable for specific conditions diagnosed to only a small number of cases?&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="69" LastEditDate="2012-06-29T18:03:27.193" LastActivityDate="2012-07-01T13:17:46.367" Title="What are treatable foetal conditions during pregnancy?" Tags="&lt;genetics&gt;&lt;teratology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2781" PostTypeId="2" ParentId="2778" CreationDate="2012-06-28T12:37:53.450" Score="2" Body="&lt;p&gt;I think the best way is to use &lt;a href=&quot;http://en.wikipedia.org/wiki/Freeze-drying&quot; rel=&quot;nofollow&quot;&gt;lyophilization&lt;/a&gt;. The American Type Culture Collection send the strains that way.&lt;/p&gt;&#xA;" OwnerUserId="1004" LastActivityDate="2012-06-28T12:37:53.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2782" PostTypeId="2" ParentId="2778" CreationDate="2012-06-28T14:24:13.543" Score="5" Body="&lt;p&gt;I believe Addgene send strains as bacterial stabs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the protocol from Qiagen.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;E. coli strains can also be stored for up to 1 year as stabs in soft&#xA;  agar. Stab cultures are used to transport or send bacterial strains to&#xA;  other labs. Prepare stab cultures as follows:&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;&lt;p&gt;Prepare and autoclave LB agar (standard LB medium containing 0.7% agar) as described in the last issue of QIAGEN News (1).&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Cool the LB agar to below 50°C (when you can hold it comfortably) and add the appropriate antibiotic(s). While the agar is still liquid,&#xA;  add 1 ml agar to a 2-ml screw-cap vial under sterile conditions, then&#xA;  leave to solidify.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;  &#xA;  &lt;p&gt;Vials of agar can be prepared in batches and stored at room&#xA;  temperature until required.&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;Using a sterile straight wire, pick a single colony from a freshly streaked plate and stab it deep down into the soft agar several times&#xA;  (Figure 1).&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;  &#xA;  &lt;p&gt;￼￼￼￼￼￼￼￼￼4. Incubate the vial at 37°C for 8–12 h leaving the cap&#xA;  slightly loose.&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;Seal the vial tightly and store in the dark, preferably at 4°C.&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;  &#xA;  &lt;p&gt;When recovering a stored strain, it is advisable to check the&#xA;  antibiotic markers by streaking the strain onto a selective plate.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I believe if the shipping is &amp;lt;24hrs you could send a stab in ice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ben&lt;/p&gt;&#xA;" OwnerUserId="798" LastActivityDate="2012-06-28T14:24:13.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2783" PostTypeId="1" AcceptedAnswerId="2784" CreationDate="2012-06-28T15:05:33.320" Score="8" ViewCount="14501" Body="&lt;p&gt;To check a protein expression I pelleted a small amount of &lt;em&gt;E. coli&lt;/em&gt; before and after induction and lysed them by redissolving them in SDS-PAGE loading buffer and heating them to 95 °C for 1 minute.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This lead to a solution with some very sticky and viscous parts in it, that make pipetting the sample into the gel wells extremely annoying. As far as I heard, this is probably genomic DNA, and my usual way to deal with this is to centrifuge the samples and only pipet a small part out from the top. This does seem to help sometimes, but not always.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can I avoid the formation of that sticky and viscious stuff or how can I avoid pipetting that stuff into my wells?&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2017-08-29T12:55:51.193" Title="How do I deal with sticky and viscous samples from cell lysates?" Tags="&lt;gel-electrophoresis&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2784" PostTypeId="2" ParentId="2783" CreationDate="2012-06-28T18:09:29.420" Score="9" Body="&lt;p&gt;Yes, it is the genomic DNA that is causing you trouble. Although a brief 1000g spin should bring it all down, the pellet is never tight and you almost always are going to pull up some gunk with the clear supernatant. A better solution is to include a quick sonication step (5-10s) before the 1000g spin. That way, the DNA is sheared and it should pellet better. It has worked for me most times. Also, remember to use a reasonable volume of SDS buffer when you lyse the cells. Too little buffer and its always going to be hard. For comparison, I use about 200ul per 1ml culture pellet and this volume works well for both pre- and post-induced cells.&lt;/p&gt;&#xA;" OwnerUserId="223" LastActivityDate="2012-06-28T18:09:29.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2785" PostTypeId="1" AcceptedAnswerId="2795" CreationDate="2012-06-29T02:01:49.510" Score="41" ViewCount="16713" Body="&lt;p&gt;I was surprised to learn that worker ants in some species live many years. I would have expected a lifespan of a few weeks or months (which is apparently the case for many species).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What factors might account for the length (and/or variation) in ants' lifespans?   (ie, is there some evolutionary preference? Some fundamental limit on the reproductive capacity of the queen?) Is there any relationship between these lifespans and different structures of ant communities? &lt;/p&gt;&#xA;" OwnerUserId="589" LastEditorUserId="28778" LastEditDate="2017-05-08T14:43:37.777" LastActivityDate="2017-05-08T14:43:37.777" Title="Why do ants live so long?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;ant&gt;&lt;lifespan&gt;&lt;collective-behaviour&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="2786" PostTypeId="1" CreationDate="2012-06-29T09:12:45.557" Score="3" ViewCount="440" Body="&lt;p&gt;What are known extreme examples of protein translation/effect coupling/decoupling? For example, examples of proteins that are immediately used at the time the have been translated and vice versa, cases of proteins that are translated but then only used much later in time in/outside the cell?&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="69" LastEditDate="2012-06-29T18:01:39.847" LastActivityDate="2014-12-15T08:26:27.170" Title="Extreme examples of protein translation/use coupling/decoupling?" Tags="&lt;genetics&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2787" PostTypeId="2" ParentId="2415" CreationDate="2012-06-29T18:01:23.077" Score="14" Body="&lt;p&gt;To some degree the answer depends on your definition of what counts as a brain.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bilaterally symmetrical organisms tend to have some level of &lt;a href=&quot;https://en.wikipedia.org/wiki/Cephalization&quot;&gt;cephalization&lt;/a&gt;, which involves the concentration of sensory and inter-neurons at one end of the organism (the head).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This aggregation of neurons at the head is typically more complex than aggregations of neurons elsewhere in the body and so it gets designated as a &lt;em&gt;brain&lt;/em&gt; whereas the others are designated as &lt;em&gt;ganglia&lt;/em&gt; (if they are outside the central nervous system or &lt;em&gt;nuclei&lt;/em&gt; if they are within the central nervous system).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In vertebrates, cephalization is very well developed so the brain is typically much more complex than the ganglia (although the &lt;a href=&quot;https://en.wikipedia.org/wiki/Enteric_nervous_system&quot;&gt;enteric nervous system&lt;/a&gt; is pretty awesome, its not the brain). However in many invertebrates, the ganglia at the head of the organism (its &lt;em&gt;brain&lt;/em&gt;) is not much more complex than the other ganglia around the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For this reason, many invertebrates can survive decapitation (at least for a while) and some like the &lt;a href=&quot;https://en.wikipedia.org/wiki/Planarian&quot;&gt;flat worm&lt;/a&gt;, can famously survive and regenerate their head after decapitation.  &lt;/p&gt;&#xA;" OwnerUserId="137" LastActivityDate="2012-06-29T18:01:23.077" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2789" PostTypeId="2" ParentId="344" CreationDate="2012-06-30T03:20:11.470" Score="2" Body="&lt;p&gt;I know this question has closed out, but I wanted add this recent reference.  The reactivation of telomerase (which inhibits telomere shortening) &lt;a href=&quot;http://www.guardian.co.uk/science/2010/nov/28/scientists-reverse-ageing-mice-humans&quot; rel=&quot;nofollow&quot;&gt;seems to have rejuvinated mice, including neuronal growth in the brain&lt;/a&gt;.  This is crazy awesome for a couple of reasons.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One being that we may all get to see our 140th birthday.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But since there were a reversal of aging from telomere extension, that implies that aging is adaptive and not a 'wear and tear' phenomenon, at least in animals like mice (and hopefully humans).  hard to believe.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;i.e. If there was a mutant that turned on telomerase, why is it not a ubiquitous trait?  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-06-30T03:20:11.470" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2790" PostTypeId="1" AcceptedAnswerId="2806" CreationDate="2012-06-30T06:18:32.350" Score="16" ViewCount="10030" Body="&lt;p&gt;When people try to explain evolution, they tell me that evolution is a cumulative result of mutations &amp;amp; natural section of the more superior individuals of a particular species. I think I'm fairly convinced with this explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But when I think about it, all of them assume that there was an organism, however simple, that was capable of self replication &amp;amp; occasionally mutate. How did such an organism come into existence? Can anyone explain this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An answer I found &lt;a href=&quot;http://www.reddit.com/r/explainlikeimfive/comments/upb42/eli5_evolution_how_can_human_beings_pop_out_of/c4zdmf4&quot;&gt;on Reddit&lt;/a&gt; didn’t really convince me.&lt;/p&gt;&#xA;" OwnerUserId="1039" LastEditorUserId="997" LastEditDate="2012-07-02T02:43:41.450" LastActivityDate="2015-12-25T20:25:19.543" Title="How did the first self replicating organism come into existence?" Tags="&lt;evolution&gt;&lt;abiogenesis&gt;" AnswerCount="7" CommentCount="7" FavoriteCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="2791" PostTypeId="2" ParentId="2783" CreationDate="2012-06-30T06:54:14.840" Score="0" Body="&lt;p&gt;In addition to gkadam's suggestion, for my protein gels, I heat my samples at 95C for 10 minutes. I would also look into different lysing conditions. Rather than using SDS loading buffer, look into more vigorous lysing steps either with a kit like bug-buster or using a homogenizer. When pelleting your lysate, I've traditionally done a 10,000g spin for 10 minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe I just work with really soluble proteins...&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-06-30T06:54:14.840" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2792" PostTypeId="2" ParentId="1649" CreationDate="2012-06-30T09:19:57.820" Score="3" Body="&lt;p&gt;I am not sure that kind of action would be a &quot;significant influence&quot;, but the general understanding is that LFP and spike frequency are inter-correlated (&lt;a href=&quot;http://dx.doi.org/10.1523/JNEUROSCI.0009-08.2008&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;http://dx.doi.org/10.1152/jn.00919.2007&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;). An interesting recent publication on the topic (&lt;a href=&quot;http://dx.doi.org/10.1152/jn.00642.2010&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;), however, doubts this correlation as the nature of LFP recording and signal processing might introduce some artifacts to the recordings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be interesting to see a correlation between the spike shapes and LFP, but I failed to find a relevant paper here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1523/JNEUROSCI.0009-08.2008&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Belitski A, Gretton A, Magri C, Murayama Y, Montemurro MA, Logothetis NK, Panzeri S&lt;/strong&gt;. 2008. Low-frequency local field potentials and spikes in primary visual cortex convey independent visual information. The Journal of neuroscience : the official journal of the Society for Neuroscience 28: 5696–709.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1152/jn.00919.2007&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Rasch MJ, Gretton A, Murayama Y, Maass W, Logothetis NK&lt;/strong&gt;. 2008. Inferring spike trains from local field potentials. Journal of neurophysiology 99: 1461–76.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1152/jn.00642.2010&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Zanos TP, Mineault PJ, Pack CC&lt;/strong&gt;. 2011. Removal of spurious correlations between spikes and local field potentials. Journal of neurophysiology 105: 474–86.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="66" LastEditorUserId="836" LastEditDate="2012-09-13T06:21:22.090" LastActivityDate="2012-09-13T06:21:22.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2793" PostTypeId="2" ParentId="2790" CreationDate="2012-06-30T09:46:36.240" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;They teach us in Physics that the entropy of an isolated system is always increasing or at least constant. Then how can an organism be born under these conditions?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The sun sends energy to the Earth, allowing for a decrease in entropy on Earth at the expense of the sun's entropy.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But when I think about it, all of them assume that there was an organism, however simple, that was capable of self replication &amp;amp; occasionally mutate. How did such an organism come into existence? Can anyone explain this?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That organism you're talking about is just a molecule that copies itself. Exactly how it has come about is not clear to me but it's not hard to imagine the possibility. A vast planet with molecules flying all over being bathed in ultraviolet light and if any molecule anywhere acquires the characteristic of copying itself, it will start growing exponentially and quickly spread all over the world.&lt;/p&gt;&#xA;" OwnerUserId="542" LastEditorUserId="542" LastEditDate="2012-07-01T20:01:28.873" LastActivityDate="2012-07-01T20:01:28.873" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2794" PostTypeId="2" ParentId="2440" CreationDate="2012-06-30T09:51:30.073" Score="5" Body="&lt;p&gt;There are many different reasons for an acute pain and inflammation (both directly via pain receptors, and indirectly via swelling etc.) plays not the least role in this phenomenon. Therefore the combination of a classic analgesic without anti-inflammatory activity (as &lt;a href=&quot;http://en.wikipedia.org/wiki/Paracetamol&quot; rel=&quot;noreferrer&quot;&gt;paracetamol&lt;/a&gt;) with a strong &lt;a href=&quot;http://en.wikipedia.org/wiki/Non-steroidal_anti-inflammatory_drug&quot; rel=&quot;noreferrer&quot;&gt;anti-inflammatory agent&lt;/a&gt; (as ibuprofen) is a reasonable one and potentially alleviates the pain manifestations in more cases than a single administration of every agent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are right with you suggestion that the doubled dose could be dangerous: even though the complications of Paracetamol administrations are not often, they are &lt;a href=&quot;http://en.wikipedia.org/wiki/Paracetamol_toxicity&quot; rel=&quot;noreferrer&quot;&gt;very dram&lt;/a&gt;atic (acute liver failure) with rather pessimistic prognosis. This is why one generally tries to half the doses if combined with other similar-acting agents (historically paracetamol was for the long time a member of the non-steroid anti-inflammatory agents).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Caffeine is generally believed to be a pain reliever, especially as concerns the pains with migraine background (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21425885&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;). One review, however, points out that there are still not enough data to support this belief (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22656684&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-06-30T09:51:30.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2795" PostTypeId="2" ParentId="2785" CreationDate="2012-06-30T17:45:27.790" Score="40" Body="&lt;p&gt;There will always be a tradeoff in terms of resource allocation between reproduction and self maintenance. Since worker ants forego reproduction to perform other roles (gathering resources, caring for young etc.) within the colony, it makes sense that this would favour a longer lifespan. This idea works for most animals (i.e. higher reproduction = lower lifespan across species in general) and is well documented (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0022191087900606&quot; rel=&quot;noreferrer&quot;&gt;Partridge &lt;em&gt;et al&lt;/em&gt;. 1987&lt;/a&gt;, &lt;a href=&quot;http://www.ucl.ac.uk/~ucbtdag/Gems_1996.pdf&quot; rel=&quot;noreferrer&quot;&gt;Gems &amp;amp; Riddle 1996&lt;/a&gt; (PDF link), &lt;a href=&quot;http://www.nature.com/nature/journal/v396/n6713/abs/396743a0.html&quot; rel=&quot;noreferrer&quot;&gt;Westendorp &amp;amp; Kirkwood 1998&lt;/a&gt; - to name a few). However the relationship is reversed in &lt;a href=&quot;http://en.wikipedia.org/wiki/Eusocial&quot; rel=&quot;noreferrer&quot;&gt;eusocial&lt;/a&gt; animals: the queens of ants, some bees and naked mole rats (which are all eusocial) tend to be longer lived than their sterile workers (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2003.tb00254.x/abstract&quot; rel=&quot;noreferrer&quot;&gt;Hartmann &amp;amp; Heinze 2003&lt;/a&gt;). Aging patterns within ants and other eusocial organisms are a very popular research topic at the moment, but the mechanisms causing differences between social castes are not fully understood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eusociality is strongly associated with increased lifespan, indeed many studies on the evolution of aging have focussed on eusocial animals which have appeared to overcome aging effects to an extent (&lt;a href=&quot;http://content.karger.com/ProdukteDB/produkte.asp?Aktion=ShowAbstractBuch&amp;amp;ArtikelNr=22115&amp;amp;ProduktNr=225839&quot; rel=&quot;noreferrer&quot;&gt;Keller &amp;amp; Genoud, 1999&lt;/a&gt;, &lt;a href=&quot;http://biomedgerontology.oxfordjournals.org/content/60/11/1369.short&quot; rel=&quot;noreferrer&quot;&gt;Buffenstein 2005&lt;/a&gt;). The naked mole rat is one of very few species of eusocial mammals and the relationship between its lifespan and body mass is very dissimilar to that of other rodents (ignore the bat points):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zP1Ui.jpg&quot; alt=&quot;Naked mole rat lifespan vs body mass&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image from &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0303720708002888&quot; rel=&quot;noreferrer&quot;&gt;Buffenstein &amp;amp; Pinto (2009)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a queen has a longer reproductive lifespan then over the course of its life it will create a higher number of offspring. This will cause their increased longevity genes to be more prevalent in the gene pool over time - &lt;strong&gt;as long as they are able to reach the limit of their reproductive lifespan and are not killed by externalities (accident or attack) in the meantime.&lt;/strong&gt; Therefore this trait (longer reproductive lifespan) will be selected for as long as the queen is protected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within eusocial colonies, there is often a protective environment (&lt;a href=&quot;http://sageke.sciencemag.org/cgi/content/full/2002/21/pe7#R4&quot; rel=&quot;noreferrer&quot;&gt;Buffenstein &amp;amp; Jarvis 2002&lt;/a&gt;): there is usually a physical structure (nest or burrow); symbiotic bacteria and/or fungi creating a more hygienic microflora; and queens are also protected by other castes. This gives queens a lower incidence of death due to accident or attack which (from the reasoning in the previous paragraph) supports the selection of a longer reproductive life. This is likely to lead to longer lived workers since they share the same genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However queens do tend to live much longer than their workers (&lt;a href=&quot;http://beheco.oxfordjournals.org/content/6/3/269.short&quot; rel=&quot;noreferrer&quot;&gt;O'Donnell &amp;amp; Jeanne 1995&lt;/a&gt;). This is probably due to their reproductive role. All the ants in the colony are investing in reproduction (whether by physically giving birth to young or by providing it with food and protection) therefore the normal relationship (reproduction and lifespan tradeoff) mentioned at the start is not relevant, but since the queen is the only individual reproducing, it will be the only one for whom lengthened lifespan is beneficial evolutionarily.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A mean lifespan of 20 years has been observed in &lt;em&gt;Formica exsecta&lt;/em&gt;, and a maximum lifespan of 28.5 years observed in &lt;em&gt;Lasius niger&lt;/em&gt;. &lt;em&gt;Pogonomyrmex owyheei&lt;/em&gt; has an observed maximum of 30 years, and mean of 17 years. These (and many more) figures were obtained from a review by &lt;a href=&quot;http://www.springerlink.com/content/nd4tn4an7f5xaq9y/&quot; rel=&quot;noreferrer&quot;&gt;Keller (1998)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other references on this subject include &lt;a href=&quot;http://www.jstor.org/discover/10.2307/3546674?uid=3738032&amp;amp;uid=2&amp;amp;uid=4&amp;amp;sid=21100883579231&quot; rel=&quot;noreferrer&quot;&gt;(Svensson &amp;amp; Sheldon 1998)&lt;/a&gt;, &lt;a href=&quot;http://web.mac.com/redifiori/Russell_Di_Fiori/Anthropocene_files/extraordinary%20lifesapns.pdf&quot; rel=&quot;noreferrer&quot;&gt;(Keller &amp;amp; Genoud 1997)&lt;/a&gt; (PDF link), &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0022191089901273&quot; rel=&quot;noreferrer&quot;&gt;(Calabi &amp;amp; Porter 1989)&lt;/a&gt;, and &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022519302925452&quot; rel=&quot;noreferrer&quot;&gt;(Amdam &amp;amp; Omholt 2002)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Amdam, G.V. &amp;amp; Omholt, S.W. (2002) The Regulatory Anatomy of Honeybee Lifespan. Journal of Theoretical Biology, 216, 209–228.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Buffenstein, R. (2005) The naked mole-rat: a new long-living model for human aging research. The Journals of Gerontology Series A: Biological Sciences and Medical Sciences, 60, 1369–1377.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Buffenstein, R. &amp;amp; Jarvis, J.U.M. (2002) The Naked Mole Rat--A New Record for the Oldest Living Rodent. Sci. Aging Knowl. Environ., 2002, pe7.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Buffenstein, R. &amp;amp; Pinto, M. (2009) Endocrine function in naturally long-living small mammals. Molecular and cellular endocrinology, 299, 101–111.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Calabi, P. &amp;amp; Porter, S.D. (1989) Worker longevity in the fire ant Solenopsis invicta: Ergonomic considerations of correlations between temperature, size and metabolic rates. Journal of Insect Physiology, 35, 643–649.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Hartmann, A. &amp;amp; Heinze, J. (2003) Lay eggs, live longer: division of labor and life span in a clonal ant species. Evolution, 57, 2424–2429.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Keller, L. (1998) Queen lifespan and colony characteristics in ants and termites. Insectes Sociaux, 45, 235–246.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Keller, L. &amp;amp; Genoud, M. (1997) Extraordinary lifespans in ants: a test of evolutionary theories of ageing. Nature, 389, 958–960.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Keller, L. &amp;amp; Genoud, M. (1999) Evolutionary Theories of Aging. Gerontology, 45, 336–338.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;O’Donnell, S. &amp;amp; Jeanne, R.L. (1995) Implications of senescence patterns for the evolution of age polyethism in eusocial insects. Behavioral Ecology, 6, 269–273.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Svensson, E. &amp;amp; Sheldon, B.C. (1998) The social context of life evolution history. Oikos, 83, 466–477.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="445" LastActivityDate="2012-06-30T17:45:27.790" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2796" PostTypeId="2" ParentId="2738" CreationDate="2012-06-30T18:08:39.440" Score="21" Body="&lt;p&gt;To get a non-circular answer to why humans and other mammals have only two sexes, it's helpful to take a look at our evolutionary history.  While mammals possess several adaptations to a terrestrial life cycle, including internal fertilization and gestation, which require substantial anatomic specialization between males and females, these are all secondary features that evolved long after our aquatic ancestors had acquired two distinct sexes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed, if we look at animals like fish, which reproduce via external fertilization, it's not at all obvious why they might not have more than two sexes.  After all, for many aquatic animals, mating involves little more than the female and the male releasing their respective gametes into the water, where they meet and fuse to a form new zygote, which can then divide and grow into a new adult.  Seen that way, there seems to be no reason why there could not be more than two &quot;mating types&quot;, as in many fungi, such that gametes of any two distinct types could fuse into zygote.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer lies in the fact that the male and female gametes aren't actually that similar: the female gametes, or eggs, are typically large cells that contain all the nutrients necessary for the new zygote to develop into a viable individual, whereas the male gametes, or sperm, are tiny and produced in huge numbers.  This asymmetry is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Anisogamy&quot;&gt;anisogamy&lt;/a&gt;, and modeling its origin has been an important topic in the theoretical study of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Without going into details on the evolution of anisogamy, once it exists, it clearly forces the mating types to also split into two groups: there's no advantage in two microgametes (sperm) fusing, since the resulting zygote would lack the nutrients it needs to be viable, whereas the fusion of two macrogametes (eggs) would simply be inefficient &amp;mdash; eggs, being large, are comparatively rare and expensive, and wasting two of them to produce only one offspring would be suboptimal even if the resulting zygote was viable.  Nor is there really room in such a scheme for gametes of intermediate size: they'd be too small to fuse into a viable zygote with sperm, but too large to be produced in sufficient amounts to be effective in fertilizing eggs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, there's nothing that would stop a single adult from producing both micro- and macrogametes, but such an adult would not really be a third sex &amp;mdash; it would just be male and female at the same time, a mating strategy known as (simultaneous) hermaphroditism, which indeed occurs relatively often in nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if pretty much all animals are anisogamous, why do fungi remain isogamous (and often have multiple mating types), then?  Well, one explanation is that the main drivers for the evolution of anisogamy &amp;mdash; sperm competition and transportation risk &amp;mdash; don't really apply to fungi, which mate when two sessile haploid mycelia grow and come into contact with each other.  Since the gametes are not motile, there's no advantage for either/any sex to produce more of them (at the cost of smaller size) in order to increase the chance of successful mating.  Thus, isogamous mating works fine for the lifestyle of fungi, and having multiple mating types is then a useful adaptation to make successful mating between neighboring mycelia more likely.&lt;/p&gt;&#xA;" OwnerUserId="239" LastActivityDate="2012-06-30T18:08:39.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2797" PostTypeId="2" ParentId="2790" CreationDate="2012-06-30T19:42:03.827" Score="9" Body="&lt;p&gt;We don't know how self-replicating molecules first arose (and probably never will know exactly) but the Earth is large and had 500 million years (i.e. the prebiotic Earth timescale) or so to experiment in organic chemistry. The land-sea interface (such as tidal pools) are a good candidate site since these are areas where high concentrations of organic goodies can be found.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this context, one focus that researchers have been looking at is self-replicating molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, one lab in &lt;a href=&quot;http://www2.mrc-lmb.cam.ac.uk/groups/ph1/pub.html&quot;&gt;Cambridge,UK&lt;/a&gt; has come up with tC19Z.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;tC19Z is the name of a RNA enzyme that acts like a self-replicating molecule. It can copy chunks of RNA almost 50% as long as itself. It can also make copies of other RNA enzymes. This molecule is not &quot;alive&quot; itself, but clearly demonstrates how greater complexity can arise.&lt;/p&gt;&#xA;" OwnerUserId="81" LastActivityDate="2012-06-30T19:42:03.827" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="2798" PostTypeId="2" ParentId="2644" CreationDate="2012-06-30T23:51:09.267" Score="2" Body="&lt;p&gt;I think that you could try a similar approach to GSFS:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;use transduction in proteins (if you don't know star code, then you must use 3 strings for each gene)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;use a basic tool (a stand alone like UNIPROT tools) to identify the proteic domain type (chain alpha, ..)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;divide the genes by proteic domain type (pdt): which contains which pdt and the pdt order frequencies&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now, you could use DAVID or similar (try wconsensus: it's old, basic but very custom) to compare similar sequence and obtain your scores.&lt;/p&gt;&#xA;" OwnerUserId="1084" LastEditorUserId="57" LastEditDate="2012-07-01T08:35:47.390" LastActivityDate="2012-07-01T08:35:47.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2799" PostTypeId="2" ParentId="2679" CreationDate="2012-07-01T12:47:33.117" Score="1" Body="&lt;p&gt;This seems to be an interesting and ambiguous topic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On one hand, the collagen as any other protein is cleaved into small-sized chunks (oligopeptides) and single aminoacids before absorption. The chunks of proteins which were not completely digested before absorption are broken up further in the body and cannot be selectively used for collagen re-building in the body. Therefore, there should be no difference between the collagen of different types and, basically, no difference between the supplements containing collagen and just a mixture of aminoacids. This also explains the fact why collagen supplement is in most cases taken in the lysate (pre-cleaved) form.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, a quick search in PubMed and I found an interesting article on the topic (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22500661&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;), where the authors claim:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At 6 months, the proportion of clinical responders to the treatment,&#xA;  according to VAS scores, was significantly higher in the collagen&#xA;  hydrolysate (CH) group 51.6%, compared to the placebo group 36.5%&#xA;  (p&amp;lt;0.05).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This study suggests that collagen hydrolysate 1200 mg/day could&#xA;  increase the number of clinical responders (i.e. improvement of at&#xA;  least 20% on the VAS) compared to placebo. More studies are needed to&#xA;  confirm the clinical interest of this food supplement.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, if the article is not a bogus (I failed to get the full version of it and the journal does not seem to belong to the top journal in the field of medicine), there could be some mechanisms yet to be discovered.&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-07-01T12:47:33.117" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2800" PostTypeId="2" ParentId="2780" CreationDate="2012-07-01T13:17:46.367" Score="1" Body="&lt;p&gt;Your question probably expresses a subtle confusion about the prenatal diagnostics and genetic testing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, genetic testing is one of the diagnostic methods in prenatal diagnostics (among with the other methods, see the &lt;a href=&quot;http://en.wikipedia.org/wiki/Prenatal_testing#Methods_of_prenatal_screening_and_diagnosis&quot; rel=&quot;nofollow&quot;&gt;list&lt;/a&gt;) which is used to diagnose genetic disorders of the foetus, whereas the disorders that are diagnosed on this stage are mostly genetic anomalies with dramatic impact on the feotus development, for example chromosome aberrations (like Down or Turner Syndromes). Should these conditions be diagnosed, the woman is given a choice to interrupt the pregnancy prematurely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Less dramatic conditions (like &lt;a href=&quot;http://en.wikipedia.org/wiki/Sickle_cell_anemia&quot; rel=&quot;nofollow&quot;&gt;sickle-cell disease&lt;/a&gt;) can be diagnosed at this time too, but are not treated before the birth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genetic disorders that are amenable to the dietary or medical treatment (like phenylketonuria or congenital hypothyroidism) are usually diagnosed in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Newborn_screening&quot; rel=&quot;nofollow&quot;&gt;newborn screening tests&lt;/a&gt; (newborn heel prickle test), because these screening is more precise and less dangerous compared to the pre-born diagnostics. &lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-07-01T13:17:46.367" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2801" PostTypeId="1" CreationDate="2012-07-01T14:39:21.833" Score="4" ViewCount="66" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Possible Duplicate:&lt;/strong&gt;&lt;br&gt;&#xA;  &lt;a href=&quot;https://biology.stackexchange.com/questions/107/can-an-adult-without-genetic-lactase-persistence-still-develop-a-tolerance-for-d&quot;&gt;Can an adult without genetic lactase persistence still develop a tolerance for dairy foods?&lt;/a&gt;  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&#xA;&#xA;&lt;p&gt;In my younger years, I don't seem to have a problem drinking milk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nowadays, when I drink milk, I keep farting away.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After searching around the Internet, &lt;a href=&quot;http://www.dairycare.sg/resource_faq.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;this site&lt;/a&gt; claimed that it is due to lactose intolerance. They have a product that claims to be able to repopulate the enzymes in the body so that it can digest milk. Is this product based on sound principles? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone (other than the Dairy Care company itself) refute or support its claims?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="1079" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2012-07-01T14:39:21.833" Title="Is it possible to repopulate lactase in the stomach?" Tags="&lt;enzymes&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2012-07-03T09:08:35.253" ContentLicense="CC BY-SA 3.0" />
  <row Id="2802" PostTypeId="2" ParentId="2440" CreationDate="2012-07-01T17:58:12.367" Score="0" Body="&lt;p&gt;Whilst Alexander Galkin gives some great information, I think there's a fundamental reason why that particular pain relief strategy is best, and it hasn't been mentioned yet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason is simply that when you take Ibuprofen or Paracetamol (a full dose) you can only take it once every 4 hours. However, the pain relief doesn't last for 4 hours, so if you take either or both together every four hours you will experience pain after the medication wears off and before you are allowed your next dose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So instead you can follow either of two strategies:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Take a full dose of Paracetamol at 0 hours, 4 hours, 8 hours, as well as taking a full dose of Ibuprofen at 2 hours, 6 hours, 10 hours. This will give you less time when no pain medication is in effect. But if your pain is inflammation related you might want to keep the anti-inflammatory effects of Ibuprofen topped up, so you can...&lt;/li&gt;&#xA;&lt;li&gt;Take a half dose of Paracetamol + a half dose of Ibruprofen every 2hours. This gives you a mix of pure pain relief and anti-inflammation and ensures minimum time when each medication has no effect.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I don't think human biology has to come into it (apart from the fact that you can take the two substances together with no ill effects), it's just a good pain-avoidance strategy.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-07-01T17:58:12.367" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2804" PostTypeId="1" AcceptedAnswerId="2819" CreationDate="2012-07-02T00:57:53.847" Score="5" ViewCount="252" Body="&lt;p&gt;As far as I understand it, PCR can be used to make many copies of one gene. My question is, is it possible to sequence DNA after PCR and is it easier than sequencing it via other methods. If it is possible, how would you do it?&lt;/p&gt;&#xA;" OwnerUserId="1051" LastActivityDate="2012-07-04T10:04:39.467" Title="Sequencing from PCR" Tags="&lt;dna-sequencing&gt;&lt;pcr&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2805" PostTypeId="2" ParentId="2804" CreationDate="2012-07-02T02:44:35.357" Score="4" Body="&lt;p&gt;We do it all the time. You can use one of your end/flanking primers and use that as a primer for sequencing. Companies will typically have a setup where they can take a &quot;premixed&quot; sample.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since we tend to use sequetech, here are their details: &lt;a href=&quot;http://www.sequetech.com/requirements.php?premixed=1&quot; rel=&quot;nofollow&quot;&gt;http://www.sequetech.com/requirements.php?premixed=1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a second opinion look at Elimbio's: &lt;a href=&quot;http://www.elimbio.com/Sample_Preparation.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.elimbio.com/Sample_Preparation.htm&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-07-02T02:44:35.357" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2806" PostTypeId="2" ParentId="2790" CreationDate="2012-07-02T03:02:49.337" Score="14" Body="&lt;p&gt;Evolution or (as Darwin called it) &quot;descent with modification&quot; is a theory which explains the origin of the species NOT the origin of life.  How the first life arose is &lt;strong&gt;completely irrelevant&lt;/strong&gt; to the theory of evolution.  What evolution does explain is how and why we have such variety of life on earth all descending from the same organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you're asking about is not a theory of &quot;evolution&quot; but rather a theory of &quot;abiogenesis.&quot;  Although there are many interesting hypothesis for how abiogenesis happened (e.g. the RNA world, the &quot;metabolism first&quot; theory, etc.), the fact is we simply do not know yet how life first arose.  What we do know is that life first arose between 3.5 and 3.9 billion years ago.  That's a really long time ago compared to lots of other important events in natural history (even the Cambrian explosion where modern animal phyla evolved was only half a billion years ago), and so it shouldn't be surprising that it's a hard problem.&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2012-07-02T03:02:49.337" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2809" PostTypeId="1" AcceptedAnswerId="2810" CreationDate="2012-07-02T23:35:08.580" Score="5" ViewCount="379" Body="&lt;p&gt;Yes, there is the &lt;a href=&quot;http://en.wikipedia.org/wiki/R-factor_%28crystallography%29&quot; rel=&quot;noreferrer&quot;&gt;wikipedia definition&lt;/a&gt;, but how would one explain this concept to a non structural biologist?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-07-03T05:53:38.930" Title="How would one describe the R-factor in crystallography?" Tags="&lt;structural-biology&gt;&lt;definitions&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2810" PostTypeId="2" ParentId="2809" CreationDate="2012-07-03T05:53:38.930" Score="6" Body="&lt;p&gt;Crystallography requires the collection of many measurements (could be a few thousand to even millions depending on the size of the molecule and complexity of the crystal (technically speaking, the size of the crystal's unit cell is a major determining factor for the size of the data set).  I'm not going to assume this is a small molecule crystal like a salt or a large molecule like a protein.  its not necessary here.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll call this a set of intensity measurements, even though what is actually used is the square root of the intensities measured, called the structure factor.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only way we really know that the molecular structure model is correct is that it generates as accurately as possible the intensities that were experimentally measured. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;R, which I believe stands for residual, is a fractional difference between the measured intensities and what any proposed molecular model gives.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The residual is calculated as the absolute value of F(model)-F(measured).  This means that 0.0 is a perfect match while 1.0 is a perfectly awful fit that shows the model is perfectly awful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practice 0.60 is usually as bad as random model will give you (there's a statistical argument as to why it doesn't go higher).  Also the measurements are usually not perfect - they contain errors in measurements or artifacts from imperfect crystals or the detector, so an R value of &amp;lt; 0.20 (20%) is typically what you see in a reasonable paper.  I think its commonly less than 0.15 for most structures now in fact.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-07-03T05:53:38.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2811" PostTypeId="1" AcceptedAnswerId="2812" CreationDate="2012-07-03T11:00:43.593" Score="9" ViewCount="1804" Body="&lt;p&gt;I mean, what if a person is for a long time submitted to conditions in which his mental capacities are not explored, are the synapses undone? I've heard that drugs may cause such an effect, but what if the person is not submitted to drugs or any severe accident, may the forgetfulness be related to the simple lack of usage of a certain knowledge?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the lack of brain usage the main cause for Alzheimer's?&lt;/p&gt;&#xA;" OwnerUserId="1092" LastEditorUserId="430" LastEditDate="2012-07-03T11:36:11.907" LastActivityDate="2012-07-03T14:05:58.867" Title="Is it possible to lose synapses over time?" Tags="&lt;brain&gt;&lt;synapses&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2812" PostTypeId="2" ParentId="2811" CreationDate="2012-07-03T11:23:49.517" Score="14" Body="&lt;p&gt;Regarding your question about losing synapses; yes, synapses are regularly lost in a process called &lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Synaptic_pruning&quot;&gt;Synaptic Pruning&lt;/a&gt;&lt;/strong&gt;. From the Wikipedia article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A decrease in synapses is seen after adolescence reflecting synaptic pruning, and approximately 50% of neurons during development do not survive until adulthood. Pruning is influenced by environmental factors and is widely thought to represent learning.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Synaptic pruning is most significant during development due to &quot;excessive&quot; &lt;a href=&quot;http://en.wikipedia.org/wiki/Neurogenesis&quot;&gt;Neurogenesis&lt;/a&gt; that creates a large number of neurons, many of which will later be pruned. It's not excessive in a bad way, it's simply the case that more neurons are generated than necessary and thus pruning is needed to keep the connections efficient. There's no &quot;measure twice, cut once&quot;, instead pruning is used to refine connections.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Synaptic Pruning really doesn't have anything to do with forgetting; &lt;a href=&quot;http://en.wikipedia.org/wiki/Forgetting&quot;&gt;Forgetting&lt;/a&gt; is natural and simply happens because connections (via Recall/Rehersal) are not made strongly enough to fully encode memories into Long Term Memory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that Synaptic Pruning is not the cause for Alzheimer's or other age related degenerative disorders. From Wikipedia again:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Synaptic pruning is classified separately from the regressive events seen during older ages. While developmental pruning is experience dependent, the deteriorating connections that are synonymous with old age are not. The stereotyped pruning can be related to the chiseling and molding of stone into a statue. Once the statue is complete, the weather will begin to erode the statue and this represents the experience independent deletion of connections.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Synaptic Pruning is a normal process of development and occurs in all individuals. Alzheimer's is a very visible disorder due to media focus, but not part of normal developmental/aging effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead I suggest you read more specifically about &lt;a href=&quot;http://en.wikipedia.org/wiki/Alzheimer%27s_disease&quot;&gt;Alzheimer's disease&lt;/a&gt;, there's quite a bit of information on it.&lt;/p&gt;&#xA;" OwnerUserId="711" LastEditorUserId="711" LastEditDate="2012-07-03T14:05:58.867" LastActivityDate="2012-07-03T14:05:58.867" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2813" PostTypeId="1" AcceptedAnswerId="2815" CreationDate="2012-07-03T10:50:03.647" Score="2" ViewCount="14623" Body="&lt;p&gt;My girlfriend is in her very early pregnancy, and has provided several blood samples by now where the doctors measure her hCG levels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hCG hormone level is measure in a unit called &lt;code&gt;mIU/ml&lt;/code&gt; which I figure is milli-something per milliliter blood. But what is that something? What is the &lt;code&gt;IU&lt;/code&gt;?&lt;/p&gt;&#xA;" OwnerUserId="1127" OwnerDisplayName="bjarkef" LastEditorUserId="6" LastEditDate="2012-07-03T14:02:13.567" LastActivityDate="2017-06-23T17:56:08.017" Title="What is the mIU unit as used in hCG hormone levels?" Tags="&lt;endocrinology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2814" PostTypeId="1" CreationDate="2012-07-03T14:16:34.330" Score="14" ViewCount="278" Body="&lt;p&gt;Has anybody tested if paralogous genes are over-represented among the genes identified by genome-wide association studies (GWAS)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, if a GWAS study finds 200 genes associated to the disease/trait, and a number X of those can be classified as belonging to Y different gene families, is there a test to see if X and Y are bigger than expected, given the total number of genes and gene paralogies in a genome? Here I am talking long established copies within a species, not CNVs in different individuals of the same species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking there is an interesting question behind this: if a gene has duplicated during the evolution of a genome, and the different gene copies have taken specialized, yet related, roles, an unbiased analysis like GWAS should be able to find cases where different paralogous copies associate to different subdiseases/subtraits within the same global disease/trait.&lt;/p&gt;&#xA;" OwnerUserId="787" LastEditorUserId="3340" LastEditDate="2014-11-12T10:13:22.580" LastActivityDate="2014-11-12T10:13:22.580" Title="Paralogous genes in genome-wide association studies?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;genomics&gt;&lt;gwas&gt;&lt;homology&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2815" PostTypeId="2" ParentId="2813" CreationDate="2012-07-03T16:36:04.700" Score="4" Body="&lt;p&gt;IU stands for &quot;International Units&quot; and it is an arbitrarily chosen unit of measure used mostly to quantify hormones, vitamins or various substances found in the blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea is well explained by the &lt;a href=&quot;http://en.wikipedia.org/wiki/International_unit&quot; rel=&quot;nofollow&quot;&gt;Wikipedia article on international units&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many biological agents exist in different forms or preparations (e.g. vitamin A in the form of retinol or beta-carotene). The goal of the IU is to be able to compare these, so that different forms or preparations with the same biological effect will contain the same number of IUs. To do so, the WHO Expert Committee on Biological Standardization provides a reference preparation of the agent, arbitrarily sets the number of IUs contained in that preparation, and specifies a biological procedure to compare other preparations of the same agent to the reference preparation. Since the number of IUs contained in a new substance is arbitrarily set, there is no equivalence between IU measurements of different biological agents. For instance, one IU of vitamin E cannot be equated with one IU of vitamin A in any way, including mass or efficacy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For hCG, in the 55th report for of the WHO Expert Commitee on Biological Standardization, you could find:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Expert Committee on Biological Standardization, after consideration of this issue (11), concluded that the choice of unit should be made on a case-by-case basis and reflect, and be based on, the biological and medical as well as the physicochemical information available. &#xA;  Many biologicals exist in both active and inactive states, and the clinically relevant form of the analyte may depend on the diagnostic aim. For example, the active state of the placental hormone chorionic gonadotrophin (hCG) is the relevant molecule to measure in the diagnosis of pregnancy, whereas the biologically inactive free beta subunit (hCG-beta) is measured to diagnose choriocarcinoma. Generally, a measurement of biological activity is expressed in IU, whereas measurement of the amount of a protein or of a specific protein structure is expressed in SI. In this case there would be a compelling reason to relate the measurement of hCG to a unit of biological activity, and the measurement of hCG-beta to an SI unit of quantity. Accordingly WHO has established a reference preparation for hCG (currently the fourth International Standard, with an assigned content of 650 IU/ampoule) (7) and a reference preparation for hCG-beta (currently the first WHO Reference Reagent for immunoassay of hCG beta subunit, with an assigned content of 0.88nmol/ampoule) (18). The former preparation was assigned a value based on bioassay, whereas the latter preparation had been extensively characterized by physicochemical and&#xA;  immunological methods and calibrated in nanomol by amino acid analysis. Applying these considerations of the properties of biological analytes, and their measurement in the clinical situation allowed the WHO biological reference standard for hepatitis B surface antigen, assigned a value in arbitrary IU rather than in SI units, to be adopted by the medical devices sector of the European Commission as the standard required for the fulfilment of the so-called Common Technical Specifications (CTS) for in vitro diagnostic devices. The Common Technical Specification document supporting the European (IVD) Medical Devices Directive 98/79 EC is a legally binding document within the 25 countries of the European Union.&#xA;  Where it is appropriate for a WHO biological reference standard to be calibrated in SI units, the principles outlined in ISO 17511 (8) should be followed. This will necessitate the existence and use of an appropriate single reference method and an assignment of uncertainty, derived from calibration data. Such a reference method should not be a biological assay because the factors that affect the results of such assays are not fully understood. Where they are used, SI units assigned to biological reference standards should be derived from, and traceable to, physicochemical procedures.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Note that IU are &lt;strong&gt;not&lt;/strong&gt; the same as &lt;a href=&quot;http://en.wikipedia.org/wiki/Enzyme_unit&quot; rel=&quot;nofollow&quot;&gt;enzyme units&lt;/a&gt; (U) which is a measure of enzymatic activity&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-07-03T16:36:04.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2817" PostTypeId="1" AcceptedAnswerId="2830" CreationDate="2012-07-04T06:09:45.003" Score="16" ViewCount="1431" Body="&lt;p&gt;The selected answer to &lt;a href=&quot;https://biology.stackexchange.com/questions/1041/how-does-a-plant-grow-before-photosynthesis-is-possible&quot;&gt;How does a plant grow before photosynthesis is possible?&lt;/a&gt; indicates that a sprout grows beneath the soil using the food stored within the seed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this limited ready food place a restriction upon the depth to which a seed may be placed and still develop into a plant? What depth will be best applicable for a given plant/tree seed? Is there a mathematical relationship known?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2019-02-01T16:13:03.763" Title="How deep in the soil can a seed be placed and still develop into a plant/tree?" Tags="&lt;botany&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2818" PostTypeId="1" CreationDate="2012-07-04T08:19:53.720" Score="7" ViewCount="1444" Body="&lt;p&gt;What are the algorithms / methods in use for the calculation of primer dimers and hairpins?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an example, IDT's &lt;a href=&quot;http://www.idtdna.com/analyzer/applications/oligoanalyzer/&quot;&gt;OligoAnalyzer tool&lt;/a&gt; will generate these analysis given particular sequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The homo-dimer analysis seems to me to just be a sliding scan of two sequences across each other. I assume this doesn't take into account possible hairpin issues? or are such structures less likely compared to the myriad of other more common problems.  In addition, how are the ΔG values calculated given a particular dimerization pattern?&lt;/p&gt;&#xA;" OwnerUserId="526" LastActivityDate="2012-07-04T21:10:33.453" Title="Primer Dimer / Hairpin Algorithms" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;pcr&gt;&lt;primer&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2819" PostTypeId="2" ParentId="2804" CreationDate="2012-07-04T10:04:39.467" Score="9" Body="&lt;p&gt;All sequencing methods, be it classical Sanger sequencing or next-generation sequencing (or even third generation) need a certain amount of DNA to work with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You either need to extract DNA from a large-ish tissue sample or you need to amplify DNA content from a smaller sample. The first approach is often impractical, or downright impossible (when you want to work with single cells or very small organisms).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So PCR is used routinely to amplify DNA before sequencing. The sequencing itself isn’t influenced by this – you use whatever technique is appropriate. However, the PCR may introduce biases into the data because not all DNA fragments amplify equally efficiently. This needs to be taken care of in the downstream analysis of the sequence data if quantitative information is required (as in RNA-seq or ChIP-seq).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coming back to your question, PCR isn’t a sequencing method in itself. It just helps getting the necessary amount of raw material in order for sequencing to work. Furthermore, most sequencing methods actually &lt;em&gt;include&lt;/em&gt; PCR steps as well, since they rely on the generation of of overlapping DNA fragments to be stitched together.&lt;/p&gt;&#xA;" OwnerUserId="166" LastActivityDate="2012-07-04T10:04:39.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2820" PostTypeId="2" ParentId="2649" CreationDate="2012-07-04T20:10:29.893" Score="3" Body="&lt;p&gt;In my own personal lab experience, I got some unexpected results using Phusion polymerase. However, I have not seen deletions, only insertions (ranging from single bases to 3 tandem copies of a primer sequence). This is not an answer to your deletion question, but it does suggest unusual things might happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have seen deletions with T4 DNA polymerase during &quot;blunting&quot; reactions. According to the NEB website:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Q10: Is T4 DNA Polymerase active at room temperature?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A10: We suggest 12°C. The DNA ends &quot;breathe&quot; at higher temperatures allowing the exonuclease to remove nucleotides past blunt.&lt;/p&gt;&#xA;" OwnerUserId="867" LastActivityDate="2012-07-04T20:10:29.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2821" PostTypeId="2" ParentId="2818" CreationDate="2012-07-04T21:10:33.453" Score="2" Body="&lt;p&gt;It is important visualize more faces to design primer or oligo and PCR experiments:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;- calculate thermodynamic parameters of DNA Hybridization (Oligo/Template)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;compute hairpin-loop, dimer, bases penality and melting temperature about primer or pair primer&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;calculate statistics about melting temperature with the change in composition and mix PCR concentration&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;with google you could find more tools but you must choose a tool of a sequencing team.&#xA;almost all tools use mfold algorithm, it's simple and effective:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;M. Zuker, D. H. Mathews &amp;amp; D. H. Turner. Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide In A Biochemistry and Biotechnology, 11-43, J. Barciszewski and B. F. C. Clark, eds. , NATO ASI Series, Kluwer Academic Publishers, Dordrecht, NL, 1999.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I worked in a sequencing team and there was a programmer. he developed a fantastic tools. he is a little english, but he could support you: &lt;a href=&quot;http://promix.cribi.unipd.it/cgi-bin/promix/melting/melting_main.exe&quot; rel=&quot;nofollow&quot;&gt;http://promix.cribi.unipd.it/cgi-bin/promix/melting/melting_main.exe&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1084" LastActivityDate="2012-07-04T21:10:33.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2822" PostTypeId="1" CreationDate="2012-07-05T05:15:05.593" Score="0" ViewCount="10250" Body="&lt;p&gt;I learned recently that given a pedigree it is possible to tell whether a disease is autosomal recessive by observing if the trait skips a generation. If the disease does skip a generation, then the disease is autosomal recessive. But the converse is false. That is a disease that is autosomal recessive does not necessarily mean the disease skips a generation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does someone know of a proof of this fact?&lt;/p&gt;&#xA;" OwnerUserId="325" LastActivityDate="2012-07-10T16:41:34.407" Title="Autosomal Recessive Trait when skipping one generation" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2823" PostTypeId="2" ParentId="2790" CreationDate="2012-07-05T09:08:21.760" Score="4" Body="&lt;p&gt;This is an extremely interesting and extremely fundamental question, indeed, and thus far, biologists have failed at coming up with a satisfying answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We know that all the parts are there, we just don't know how they were arranged, or which ones go where.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is, in essence, composed of three sub-questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;How did the fundamental building blocks of life come about?&lt;/li&gt;&#xA;&lt;li&gt;How did the first self-replicating molecules come about?&lt;/li&gt;&#xA;&lt;li&gt;How did cell membranes come about?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The answer generally takes the form of &quot;On primordial Earth, a small selection of the billions of organic compounds generated when UV-light hits a mess of carbon dioxide, nitrogen and water where captured in a tide pool where concentration and foam led to random chance producing self-replicating molecules in proto-cells.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This answer, while almost certainly true, is also incredibly dissatisfying, because all it tells us is what deductive logic has already taught us, almost intuitively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incidentally, the fact that all of this happens with a million to one odds isn't a problem: The Earth is big, and the time frame for this happening is along the lines of hundreds of millions of years: Anything that might happen once per year by a million to one shot would likely happen hundreds of times in that timeframe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;In any case&lt;/em&gt;&lt;/strong&gt;, when it comes to evolution, or Darwin's Theory of Evolution, or any other theory of evolution, this is all irrelevant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution is something that happens in any sufficiently complex (open) system, assuming it has the capacity to change at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is most easily observed in living organisms, because they are at the right scale, and incredibly diverse, but it happens on all scales of the universe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, the easiest way to explain how life first originated, is just to keep counting backwards when you reach the Last Common Ancestor (of All Life on Earth), and propose models for how this proto-bacterium could be even simpler, until you're left with CO₂, N₂ and H₂O, and other simple molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At that end of the spectrum it is well-understood that e.g. H₂O &quot;evolves&quot; from H₂ and O₂, because H₂O has a quality that makes it more &quot;fit&quot; than either of its components, chemical stability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, H2 &quot;evolves&quot; from free hydrogen by a similar mechanism, and free hydrogen &quot;evolves&quot; from protons and electrons, because it has the property of being electrically neutral, which is also a desirable property.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, at the level of protons and electrons, things get a little muddy, and evolution kind of breaks down as a method for explaining how things come about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt; For reference: &lt;a href=&quot;http://en.wikipedia.org/wiki/Abiogenesis#Current_models&quot; rel=&quot;nofollow&quot;&gt;Current Models of Abiogenesis&lt;/a&gt; on Wikipedia.&lt;/p&gt;&#xA;" OwnerUserId="1095" LastEditorUserId="3340" LastEditDate="2014-10-09T16:50:44.553" LastActivityDate="2014-10-09T16:50:44.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2824" PostTypeId="1" AcceptedAnswerId="2825" CreationDate="2012-07-05T12:06:13.310" Score="15" ViewCount="5060" Body="&lt;p&gt;I found this image on Google+&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5HTA7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you shake your head you can see a portrait of a person. Can anyone explain how the image is constructed in the brain?&lt;/p&gt;&#xA;" OwnerUserId="1039" LastEditorUserId="238" LastEditDate="2012-07-05T13:03:43.560" LastActivityDate="2015-09-18T01:50:22.423" Title="How does this illusion work?" Tags="&lt;neuroscience&gt;&lt;eyes&gt;&lt;vision&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2825" PostTypeId="2" ParentId="2824" CreationDate="2012-07-05T13:15:47.073" Score="19" Body="&lt;p&gt;If you zoom in on the image, you can see that it is not just composed of black vertical lines, but also has pixels with different gray tones in the white areas. When you move your head sideways, you perceive the gray tones more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you were to remove the black lines, you could see the face clearly. Initially I thought that by blurring the gray shapes when your head moved, they became more visible as they seemed larger. On reflection though I think that actually what's happening is that the high contrast between the black lines and the mostly white background causes your perception to adjust so it doesn't easily see the mid tones. This is because we have a low &lt;strong&gt;dynamic range&lt;/strong&gt; in our vision (relative to absolute brightness, but compared to camera CCDs we have a high dynamic range) - we have to adjust the light sensitivity to compensate for the overall brightness of the image. This is called &lt;strong&gt;brightness adaptation&lt;/strong&gt;. &lt;a href=&quot;http://webvision.med.utah.edu/book/part-viii-gabac-receptors/light-and-dark-adaptation/&quot; rel=&quot;noreferrer&quot;&gt;There's a good free textbook for further reading about this at Utah U's Webvision&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you move your head, the black and white lines blur together which makes the overall brightness appear to be the average brightness of the black and white. So against that background your light sensitivity increases and the areas where the pixel tone is different from the average - the gray pixels of the face - start to stand out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By reducing the brightness you can see the faint image in the background much more clearly...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YmaQU.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-07-05T16:27:31.590" LastActivityDate="2012-07-05T16:27:31.590" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2826" PostTypeId="2" ParentId="2790" CreationDate="2012-07-05T16:34:32.957" Score="2" Body="&lt;p&gt;While many point to RNA, or a variant of it, as being the first molecule of &quot;life&quot; very few people know where it came from. Some suggest that it came from outer space because it's uncertain how the material for &lt;a href=&quot;http://www.nature.com/scitable/definition/phosphate-backbone-273&quot; rel=&quot;nofollow&quot;&gt;sugar-phosphate backbones&lt;/a&gt; could have developed on earth and that the perhaps these materials found their way here &lt;a href=&quot;http://www.pnas.org/content/108/34/13995&quot; rel=&quot;nofollow&quot;&gt;via meteorites&lt;/a&gt;. There are several hypotheses as to how an early earth environment may have promoted the properties of these molecules, but it's difficult to ascertain what exactly happened.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Somewhere within that abiogenesis wikipedia article is the mention of the role of deep-sea vents. The deep-sea vents and the currents that surround them basically facilitated a PCR reaction. Some of the early emerging DNA, maybe with some RNA and free nucleotides floating around, could have leveraged such an environment for replication and by sheer number (and some chance) entered into symbiotic relationship with other molecules to form the first cellular structures.&lt;/p&gt;&#xA;" OwnerUserId="1049" LastEditorUserId="1306" LastEditDate="2012-10-09T01:19:15.220" LastActivityDate="2012-10-09T01:19:15.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2827" PostTypeId="1" AcceptedAnswerId="2828" CreationDate="2012-07-05T17:12:49.820" Score="2" ViewCount="1147" Body="&lt;p&gt;With practice one can create a bonsai; no complicated modification of the DNA in a high-end lab required. The bonsai will even beget bonsai fruit. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I am curious about is - if such bonsai fruit is planted again, will it give rise to a normal, or a bonsai tree? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2012-07-05T17:37:00.353" Title="Will fruit/seed of a bonsai yield another bonsai plant/tree?" Tags="&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2828" PostTypeId="2" ParentId="2827" CreationDate="2012-07-05T17:37:00.353" Score="8" Body="&lt;p&gt;No, seed from a bonsai tree will not automatically produce another bonsai tree. Bonsai are dwarfed due to restriction of root growth in their small containers - unless the offspring are also grown in environmentally dwarfing conditions, they will tend to grow normally.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-07-05T17:37:00.353" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="2829" PostTypeId="2" ParentId="2817" CreationDate="2012-07-05T18:03:48.627" Score="8" Body="&lt;p&gt;To answer your specific questions...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Does nutrient availability limit emergence depth?&lt;/strong&gt;&lt;br&gt;&#xA;Yes, the size of the nutrient store in the seed does impose a theoretical limit on the maximum depth at which seed germination and emergence can take place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the best depth for a given species?&lt;/strong&gt;&lt;br&gt;&#xA;The specific depth which gives &lt;strong&gt;best germination&lt;/strong&gt; for any given species is very unlikely to be the &lt;strong&gt;maximum&lt;/strong&gt; depth at which seeds of that species can germinate. This is because other factors also impose limits on germination depth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably the most important other factor is &lt;strong&gt;light&lt;/strong&gt; - most seeds require the perception of red light in order to trigger germination. For most species then, you are unlikely to find seeds germinating and successfully emerging from depths greater than the penetrance of light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another important factor in some latitudes is temperature - many seeds (from 26 families) use dormancy as a way of preventing germination in the wrong seasonal conditions. In species where temperature serves as a cue to alleviate dormancy, there will be a maximum depth at which a given seed can detect the temperature fluctuations at the surface. Beyond a certain depth, surface temperature changes will not perceptibly affect local temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you ever need to find out the best depth of germination for a given species, many can be found on google, or failing that it is trivial to perform a simple experiment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there a mathematical relationship?&lt;/strong&gt;&lt;br&gt;&#xA;There is a general mathematical relationship, an &lt;strong&gt;allometric&lt;/strong&gt; relationship (i.e. relating size to another trait), between seed size and maximum depth of emergence, described by Bond et al. (1999):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;                                     &lt;img src=&quot;https://i.stack.imgur.com/YRgjA.gif&quot;/&gt;&#xA;where:&#xA;d&lt;sub&gt;max&lt;/sub&gt; = maximum depth of emergence&lt;br&gt;w = seed weight&lt;br&gt;c = a constant which varies with phylogeny and environmental conditions.&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Many species however will not submit to this equation. For example some large-seeded species (incl. coconut, coco-de-mer, avocado), have large seeds because they may need to enable long-distance growth along the ground in order to locate optimum growth conditions. Seeds of these species will therefore not conform to the depth-size relationship above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s004420050841&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Bond WJ, Honig M, Maze KE&lt;/strong&gt;. 1999. Seed size and seedling emergence: an allometric relationship and some ecological implications. Oecologia 120: 132–136.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-07-05T18:03:48.627" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2830" PostTypeId="2" ParentId="2817" CreationDate="2012-07-05T18:09:19.003" Score="10" Body="&lt;p&gt;The general mathematical relationship requires an allometric equation. There are not as many for seedlings as there are for mature trees (but see the answer by @Richard-smith for a specific example). But lets start with a basic assumption that the emerging seedling will be a very tall cone (tall = high &lt;em&gt;h&lt;/em&gt; to &lt;em&gt;r&lt;/em&gt; ratio).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The volume of a cone is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;$V = \frac{1}{3} \pi r^2h$&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Then we need to know the density of the seedling to figure out how much carbon a seedling of height &lt;em&gt;h&lt;/em&gt; would require. Lets say that the density is 1.5 g/cc (excluding water). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, assume that the biomass is 1/2 carbon (a fairly reasonable assumption).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To figure out how tall a seed could grow given carbon reserves, it would be necessary to determine the amount of carbon in storage in the seed. Say there were 5 grams. There will be a carbon cost of reallocating this to growth, say 50%. So, for a seed that has 5g of carbon, its total volume might be calculated as:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; (5g * 50% growth respiration)/(50% C content of biomass) * 1.5 g/cc = 7.5 cc&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;assuming that the seedling will have a radius of 0.2 cm, the height could be calculated as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;$h = \frac{V}{(3 \pi * 0.2^2)} &#xA;    = \frac{V}{0.38}$&#xA;          = 20 cm (for V = 7.5)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Note: this is just a very quick &quot;back of the envelope&quot; calculation with many assumptions. C is 50% of plant biomass is pretty close (the actually number is closer to 48%). The growth respiration cost is a very rough estimate, and will vary with nitrogen content of the tissue, soil temperature, and etc.. The plant will likely need carbon left to build a leaf, and another resource may be limiting.&lt;/p&gt;&#xA;" OwnerUserId="222" LastEditorUserId="57" LastEditDate="2012-10-24T07:43:36.107" LastActivityDate="2012-10-24T07:43:36.107" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2831" PostTypeId="2" ParentId="2574" CreationDate="2012-07-05T18:24:05.550" Score="1" Body="&lt;p&gt;In the past, before massively parallel sequencing, they made a library of cloned sequences and transformed these into &lt;em&gt;E. coli&lt;/em&gt;. High AT sequences are difficult to maintain in &lt;em&gt;E. coli&lt;/em&gt; (perhaps due to similarity to promoters?).&lt;/p&gt;&#xA;" OwnerUserId="867" LastEditorUserId="43" LastEditDate="2012-09-04T17:08:24.680" LastActivityDate="2012-09-04T17:08:24.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2832" PostTypeId="2" ParentId="623" CreationDate="2012-07-05T20:24:12.767" Score="7" Body="&lt;p&gt;Perception of time can change drastically during an &lt;a href=&quot;http://www.livescience.com/2117-time-slow-emergencies.html&quot;&gt;emergency&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When we are younger, much like during an emergency, the brain hasn't activated very many filters for sensory data.  The young have much to learn about the world and more detail is needed for the brain to make appropriate decisions.  Sensory information is recorded in great detail, making time seem to relatively crawl.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As we age, the brain learns to filter out more and more of what it considers inconsequential data.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good example of these filters at work is the morning commute.  If the same route is driven at roughly the same time every workday, the brain begins to leave out much of the repetitive events and scenery from it's historical record of time.  Given enough repetition, the record of the event will include so little detail in memory as to almost seem not to have occurred at all.  A 30 minute commute will be perceived to have taken very little time -- if it's remembered at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Ferris Bueller so aptly put it, &quot;Life moves pretty fast... You don't stop and look around once in a while, you could miss it.&quot;&lt;/p&gt;&#xA;" OwnerUserId="1096" LastActivityDate="2012-07-05T20:24:12.767" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2833" PostTypeId="2" ParentId="2516" CreationDate="2012-07-05T22:13:34.523" Score="2" Body="&lt;p&gt;My first question would be is there any external indication of them such as air holes or anything else that you can assess from the surface?  I would think that if there is, you could use transects and a quadrat.  If you need to dive for them you can obviously make a weighted quadrat by filling pvc pipe with sand and gluing it together.  Then take an area and lay out transects and and randomly choose different lengths along each transect to put the quadrat down and that will give you an estimate of density.  If you actually need to extract them from the mud, I imagine that varies by species and you could make due with a grab sampler of the right size, something on the small end I would imagine.  That way you aren't dredging up tons and tons of mud to sort through.  If they are even rarer than I imagine, you could just lay out transects and swim them until you see something and do away with the quadrat.  Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="1097" LastActivityDate="2012-07-05T22:13:34.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2834" PostTypeId="2" ParentId="551" CreationDate="2012-07-06T12:32:13.953" Score="2" Body="&lt;p&gt;My two favorite books are &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1889899097&quot; rel=&quot;nofollow&quot;&gt;Molecular Biology made simple and fun&lt;/a&gt; and &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0123735815&quot; rel=&quot;nofollow&quot;&gt;Biotechnology for Beginners&lt;/a&gt;. Both are well written and fun to read. As their names suggest, the former covers the basics of biology and the latter covers the basics of biotechnology.&lt;/p&gt;&#xA;" OwnerUserId="22" LastActivityDate="2012-07-06T12:32:13.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2835" PostTypeId="1" AcceptedAnswerId="2836" CreationDate="2012-07-06T16:11:03.540" Score="13" ViewCount="543" Body="&lt;p&gt;I am conducting an investigation into the effect of two different grass management techniques (grazing vs. machine-mowing) upon floral biodiversity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have collected my data and now need to process it in a way that will yield meaningful and valid results. My data is in the form of 25 samples per area with %-abundance measured for each species in a 0.25m&lt;sup&gt;2&lt;/sup&gt; quadrat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am currently using a non-standard diversity quantification technique, called Disney's index (which I have been led to believe is named eponymously after R.H.L Disney, however I am unable to find any references describing this), in which we assign each species a weight based on percentage abundance, as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/cMdor.png&quot; alt=&quot;Table showing weights for %-abundances&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We then use these weights to calculate the index as follows (i.e. by computing the sum of the weights of the species, over the number of species):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/HXHiB.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know if this is the best possible diversity index I could use for this type of analysis, or whether there are others which I should be considering.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance!&lt;/p&gt;&#xA;" OwnerUserId="1081" LastEditorUserId="3624" LastEditDate="2013-10-28T19:45:21.997" LastActivityDate="2013-10-28T19:45:21.997" Title="Most suitable biodiversity index" Tags="&lt;botany&gt;&lt;ecology&gt;&lt;biodiversity&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2836" PostTypeId="2" ParentId="2835" CreationDate="2012-07-06T17:48:52.630" Score="4" Body="&lt;p&gt;It sounds like you are interested in &lt;a href=&quot;https://en.wikipedia.org/wiki/Beta_diversity&quot; rel=&quot;nofollow noreferrer&quot;&gt;beta diversity&lt;/a&gt; which is the change in taxa composition (i.e., alpha diversity) between plots.  There are a number of approaches to calculating beta diversity and the correct choice generally depends on the question(s) you are trying to answer.  The most common approaches are very well described in this paper: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anderson, M. J. et al. 2011. Navigating the multiple meanings of Beta diversity: a roadmap for the practicing ecologist. Ecology Letters 14:19-28&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. I am not familiar with Disney's index so I cannot comment on its merits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.P.S. You may also be interested in &lt;a href=&quot;https://stats.stackexchange.com/questions/9281/what-test-to-compare-community-composition/9293#9293&quot;&gt;this question&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="137" LastEditorUserId="-1" LastEditDate="2017-04-13T12:44:17.897" LastActivityDate="2012-07-06T17:48:52.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2838" PostTypeId="1" CreationDate="2012-07-06T23:14:16.210" Score="13" ViewCount="499" Body="&lt;p&gt;Suppose that we have the ability to make mosquitoes extinct, what would be the likely effects (on disease and ecosystems for example) of such extinction? Essentially, what roles in nature do mosquitoes perform?&lt;/p&gt;&#xA;" OwnerUserId="1107" LastEditorUserId="1590" LastEditDate="2016-03-31T09:40:14.290" LastActivityDate="2016-03-31T09:40:14.290" Title="Are there any side-effects from a mosquitoes extinction?" Tags="&lt;ecology&gt;&lt;extinction&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2839" PostTypeId="1" AcceptedAnswerId="2842" CreationDate="2012-07-07T19:13:45.710" Score="5" ViewCount="16871" Body="&lt;p&gt;Why do we sweat after running? &#xA;Also we sweat sometime after drinking lots of water. Why it is so?&#xA;Can someone please enlighten me in this regard?    &lt;/p&gt;&#xA;" OwnerUserId="1110" LastEditorUserId="69" LastEditDate="2012-07-07T21:36:30.927" LastActivityDate="2014-09-11T09:43:42.960" Title="Why do we sweat after drinking water and running?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2841" PostTypeId="1" CreationDate="2012-07-07T20:02:11.900" Score="7" ViewCount="4153" Body="&lt;p&gt;How much carbon dioxide and oxygen from/for respiration are in the bloodstream at any one time? (mass per litre of blood or similar) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And would there be much more aside from the blood in tissue, e.g. muscle, brain, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far the figures I have are as follows (please double check for me, I dont have a clue)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;O₂ molecules per red blood cell: 1 billion. Red blood cells per micro litre of blood in males: 4.7 to 6.1 million. Molecules per mole: 6 x 10^23. Therefore moles of O2 per litre of blood: approx 0.01 (correct?) This seems quite low, since an inhalation is typically 0.5L and about a quarter of the oxygen is absorbed (oxygen by volume, 5% of the air) (1 thousandth of a mole of oxygen absorbed per inhalation?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="1113" LastEditorUserId="3340" LastEditDate="2014-10-09T13:30:17.933" LastActivityDate="2018-03-16T15:21:55.113" Title="Total amount of CO₂ / Oxygen in Bloodstream in Humans" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2842" PostTypeId="2" ParentId="2839" CreationDate="2012-07-07T21:43:31.937" Score="8" Body="&lt;p&gt;Exercise, such as running, increases muscle activity.  This increases the energy demand of these tissues, which increases the rate of cellular respiration.  Respiration releases heat as a by-product, therefore the body is hotter during and after exercise. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sweating is a homoeostatic mechanism to keep core body temperature constant. It is a response to lower the body temperature. When the body becomes too hot, sweat is released onto the surface of the skin.  The water from the sweat then takes some of the excess heat energy from the body and uses it to evaporate.  Because water has a relatively large specific heat capacity a lot of heat can be carried away by this method.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-07-07T21:43:31.937" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2843" PostTypeId="1" AcceptedAnswerId="7372" CreationDate="2012-07-08T02:16:45.657" Score="14" ViewCount="1282" Body="&lt;p&gt;I just witnessed a small jumping spider &lt;em&gt;jump&lt;/em&gt; on some kind of louse or bed bug on the ceiling. How does it do that without falling? I have yet to find a high-speed-camera video of a jumping spider jumping on a ceiling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My hypothesis is that the spider would spit silk and anchor it on the ceiling, then jump, and allow itself to be swung by the silk onto the prey. But I don't have a high speed camera to prove that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&#xA;I now have some evidence that supports my hypothesis: I just saw a jumping spider attempt to jump on a prey and failing to land properly. It didn't fall directly to the floor. Instead, it dangled from its own silk, at about 2 cm from the ceiling, then climbed right back up the thread of silk, onto the ceiling.&lt;/p&gt;&#xA;" OwnerUserId="1114" LastEditorUserId="1114" LastEditDate="2012-07-18T15:08:04.337" LastActivityDate="2013-02-26T23:38:28.433" Title="How does a jumping spider manage to &quot;jump&quot; on the ceiling?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2844" PostTypeId="2" ParentId="2838" CreationDate="2012-07-08T02:49:38.873" Score="5" Body="&lt;p&gt;There was actually just such an article in &lt;a href=&quot;http://www.nature.com/news/2010/100721/full/466432a.html&quot; rel=&quot;noreferrer&quot;&gt;Nature recently&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;They don't occupy an unassailable niche in the environment,&quot; says entomologist Joe Conlon, of the American Mosquito Control Association in Jacksonville, Florida. &quot;If we eradicated them tomorrow, the ecosystems where they are active will hiccup and then get on with life. Something better or worse would take over.&quot;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-07-08T02:49:38.873" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2845" PostTypeId="1" AcceptedAnswerId="2849" CreationDate="2012-07-08T06:47:06.053" Score="4" ViewCount="4161" Body="&lt;p&gt;Please correct me if my understanding is incorrect; I understand branch/stem, and root are composed of different types of cells. Yet in some plants (e.g. rose, bougainvillea) a cutting from the stem is capable of developing and taking root. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this transformation from stem to root come about? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an aside - I believe such root-generation happens only in plant cuttings, and not in a tree branch. Why? Is it a matter of the volume of nutrition required? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2012-07-08T09:33:11.597" LastActivityDate="2017-11-14T17:43:36.633" Title="How does a plant cutting develop roots?" Tags="&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2846" PostTypeId="1" AcceptedAnswerId="2847" CreationDate="2012-07-08T09:45:33.030" Score="6" ViewCount="572" Body="&lt;p&gt;A family member suffers from migraines so I have been reading a little around the subject. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There seem to be any number of &quot;triggers&quot;, but I have seen mention several times of the role of histamine in migraine activation as an active area of research. The suggestion is that high histamine levels in the body can cause migraines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there solid evidence that histamine can trigger migraines?  How does this mechanism operate?&lt;/p&gt;&#xA;" OwnerUserId="81" LastActivityDate="2013-02-04T16:49:17.077" Title="What is the relationship between migraines and histamine?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2847" PostTypeId="2" ParentId="2846" CreationDate="2012-07-08T11:59:10.680" Score="5" Body="&lt;p&gt;Yes, this is true.&lt;/p&gt;&#xA;&lt;p&gt;Histamine is thought to induce the enzyme Nitric Oxide (NO) Synthase.  NO is then available to act locally on the vasculature as a vasodilator.&lt;/p&gt;&#xA;&lt;p&gt;NO binds to guanylyl cyclase in vascular smooth muscle cells, which leads to the production of cyclic GMP, which in turn forms phosphorylated protein kinase G. PKG phosphorylates Ca&lt;sup&gt;2+&lt;/sup&gt; channels, slowing the influx of calcium into the cell, which leads to smooth muscle relaxation, and vasodilation, which leads to migraine.&lt;/p&gt;&#xA;&lt;p&gt;The only silver lining is that there is a check in place: with the binding of histamine to H3 receptors on c-fibers in the central nervous system, feedback inhibition prevents the further release of histamine from these sites.&lt;/p&gt;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Akerman S, Williamson DJ, Kaube H, Goadsby PJ. (2002).  The role of histamine in dural vessel dilation.  Brain Res. 956(1):96-102.&lt;/p&gt;&#xA;&lt;p&gt;Gupta, S., Nahas, S.J.,Peterlin, B.L. (2011) Chemical Mediators of Migraine:&#xA;Preclinical and Clinical Observations.  Headache: The Journal of Head and Face Pain, 51(6): 1029–1045.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="57" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-07-08T11:59:10.680" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2848" PostTypeId="1" AcceptedAnswerId="2850" CreationDate="2012-07-08T17:28:53.627" Score="6" ViewCount="828" Body="&lt;p&gt;What is the difference between Photosynthetic Pigments and Chloroplasts? I know plants have both but Prokaryotes (Bacteria and Archeae) only have the former.&lt;/p&gt;&#xA;" OwnerUserId="1083" LastEditorUserId="3971" LastEditDate="2013-08-29T16:04:35.460" LastActivityDate="2013-08-29T16:04:35.460" Title="Photosynthetic Pigments vs. Chloroplasts" Tags="&lt;botany&gt;&lt;photosynthesis&gt;&lt;pigmentation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2849" PostTypeId="2" ParentId="2845" CreationDate="2012-07-08T18:55:19.867" Score="2" Body="&lt;p&gt;Plants grow only from regions at the tips of the roots and shoots called meristems.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within the meristem areas there are stem cells (&quot;blank&quot; unspecialised cells).  Unlike animal stem cells, plant stem cells are totipotent - meaning that they can differentiate into &lt;em&gt;any&lt;/em&gt; type of cell.  Therefore when the cutting is taken from the end of the shoot, the stem cells can differentiate into root cells or shoot cells depending on their conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the meristems (therefore the &lt;em&gt;unspecialised&lt;/em&gt; stem cells) are only located at the tips of shoots, you cant grow a cutting from the middle of a branch.&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-07-08T18:55:19.867" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2850" PostTypeId="2" ParentId="2848" CreationDate="2012-07-08T20:09:42.210" Score="10" Body="&lt;p&gt;Photosynthetic pigments are the chemicals which take part in photosynthesis, in particular they are they ones which absorb photons and fluoresce (emit photons of a different wavelength) or emit electrons. Pigments are molecules, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Chlorophyll&quot;&gt;chlorophyll&lt;/a&gt; is a key example. These pigments are required for photosynthesis to take place, as they generate the electrons which create the electrochemical gradients which power photosynthesis, thus all photosynthetic organisms will have photosynthetic pigments of some kind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Chloroplast&quot;&gt;Chloroplasts&lt;/a&gt; are membrane-bound organelles in plant cells, made up of many hundreds of thousands of molecules including pigments. Plant photosynthesis takes place on their internal membrane, the thylakoid. Specifically, the thylakoid membrane of chloroplasts is the membrane across which the aforementioned electrochemical gradients are created in plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chloroplasts originated from a free-living bacterium, probably a cyanobacterium, entering a eukaryotic cell. So prokaryotes don't have them because the chloroplast endosymbiosis event was one way in which plants diverged from their non-plant ancestors. So you can think of a cyanobacterium as a free-living chloroplast - they have their own internal membranes similar to the thylakoid across which electrochemical gradients are created for photosynthesis. Conversely, you can think of a chloroplast as a small cyanobacterium living symbiotically inside a plant cell.&lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-07-08T20:15:19.083" LastActivityDate="2012-07-08T20:15:19.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2851" PostTypeId="1" AcceptedAnswerId="3029" CreationDate="2012-07-09T09:01:51.900" Score="16" ViewCount="9127" Body="&lt;p&gt;In general, you want to be consistent with running your gels either at constant volts or constant amps. However, it is very clear that during the progression of both PAGE and agarose gels, the free parameter changes due to the change in resistance of the gel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While there are safety reasons why you run one vs. the other, I'm curious how these difference affect the migration of your gel.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="16299" LastEditDate="2015-12-29T05:05:08.570" LastActivityDate="2019-01-17T03:12:42.820" Title="When running gels what is the difference between constant volts or constant amps?" Tags="&lt;lab-techniques&gt;&lt;gel-electrophoresis&gt;&lt;sds-page&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2852" PostTypeId="1" CreationDate="2012-07-09T15:28:40.263" Score="5" ViewCount="111" Body="&lt;p&gt;Has anyone looked at the effect of &lt;a href=&quot;http://en.wikipedia.org/wiki/Natural_selection&quot; rel=&quot;nofollow&quot;&gt;background selection&lt;/a&gt; on the levels of conservation of promoter regions compared to distant enhancers? Do promoter regions have a higher conservation due to background selection from nearby genes compared to more distant enhancer regions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My attempts to google for this only gave me a 2004 Drosophila paper on a few genes survey:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://mbe.oxfordjournals.org/content/21/2/374.full&quot; rel=&quot;nofollow&quot;&gt;http://mbe.oxfordjournals.org/content/21/2/374.full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering if this has been looked at before or if there are any other relevant bits of genetics one should consider first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: a bit more of explanation into the hypothesis below, and a reference that could be useful:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's start supposing a region near a coding gene that can gain regulatory potential via a new point mutation or small translocation. This new regulatory potential needs to be positively selected after it appears, or it will gradually accumulate more mutations and disappear. But if the region is close enough to the coding gene, recombination rate between the region and the nearby gene body will be low, proportional to their distance. If the gene body is assumed under selective constraint, there will be a hitchhiking effect of the nearby regulatory region by the gene nearby. The background levels of mutation on the regulatory region are then going to be lower (lower background mutation) than in a region that is not near a gene under strong selective constraint. So one way of explaining why close promoter/enhancer regions are more conserved than distant enhancer regions would simply be due to linkage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A second part of the hypothesis would be about the presence or absence of recombination hotspots in upstream regions of a coding region: if nearby promoter/enhancers are kept via linkage to the closest gene, unbiased measures of cross-over (e.g. &lt;a href=&quot;http://genome.cshlp.org/content/22/5/957.long&quot; rel=&quot;nofollow&quot;&gt;PRDM9 experiments in mouse testis&lt;/a&gt;) should indicate if there is an &lt;a href=&quot;http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11089.html&quot; rel=&quot;nofollow&quot;&gt;increased linkage of functional genomic blocks&lt;/a&gt;, like enhancer/promoter/gene blocks (Hi-C, 4C, 3C data), whereas if recombination doesn't play a role, regulatory blocks wouldn't necessarily be kept in the same haplotype block.&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="658" LastEditDate="2012-07-11T09:27:02.643" LastActivityDate="2012-07-11T09:27:02.643" Title="effect of background selection on promoter regions compared to distant enhancers?" Tags="&lt;genetics&gt;&lt;natural-selection&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2853" PostTypeId="1" CreationDate="2012-07-09T16:47:56.153" Score="7" ViewCount="7383" Body="&lt;p&gt;In humans is it possible to fertilize a ovum with another ovum from the same female subject? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I already found some works in which the ovum is fertilized by a somatic cell (see e.g. &lt;a href=&quot;http://news.sciencemag.org/sciencenow/2001/07/12-01.html&quot;&gt; this &lt;/a&gt;), but I am looking for fertilization specifically by another ovum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Around a year ago I found in the internet a Japanese (ongoing) study on this, but cannot locate it any more. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would greatly appreciate any help. &lt;/p&gt;&#xA;" OwnerUserId="1119" LastActivityDate="2018-05-17T18:53:40.983" Title="Is ovum + ovum fertilization possible for human?" Tags="&lt;molecular-genetics&gt;&lt;reproduction&gt;&lt;human-genetics&gt;&lt;cytogenetics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2854" PostTypeId="2" ParentId="2853" CreationDate="2012-07-09T17:37:37.233" Score="3" Body="&lt;p&gt;Using a somatic cell in an a ovum is what is typically done in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Somatic_cell_nuclear_transfer&quot; rel=&quot;nofollow&quot;&gt;process of cloning&lt;/a&gt;.  It was the same process used to &lt;a href=&quot;http://en.wikipedia.org/wiki/Dolly_%28sheep%29&quot; rel=&quot;nofollow&quot;&gt;create Dolly the Sheep&lt;/a&gt;. What you're asking about is something very different:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider that somatic cells are properly &lt;a href=&quot;http://en.wikipedia.org/wiki/Ploidy&quot; rel=&quot;nofollow&quot;&gt;diploid&lt;/a&gt;.  Whereas an ovum itself just contains a haploid number of chromosomes. In &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_fertilization&quot; rel=&quot;nofollow&quot;&gt;typical sexual reproductio&lt;/a&gt;n the sperm fertilizes the ovum which would than bring the chromosome number to to correct tally.  So combining the genetic material in two ovum should bring the chromosome count to the correct tally as well, but scientists would need to somehow motivate the  activities that happen when typical  sexual reproduction occurs. It's likely very challenging to do that if not highly improbable. Should it work, this process could only produce female children. &lt;/p&gt;&#xA;" OwnerUserId="1049" LastActivityDate="2012-07-09T17:37:37.233" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2856" PostTypeId="2" ParentId="2299" CreationDate="2012-07-10T07:15:42.197" Score="4" Body="&lt;p&gt;The situation is quite complex, and there are certain things that we do not fully understand, but I will try to give you an explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, at the cellular level, you have the genetic components of the circadian clock, the clock genes and their protein products.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can divide clock proteins into positive and negative regulators: the positive regulators modulate transcription of clock-controlled genes and are inhibited by the negative regulators in a loop that lasts approximately 24 hours (in Latin: &lt;em&gt;circa&lt;/em&gt; = around and &lt;em&gt;dies&lt;/em&gt; = day).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance the &lt;em&gt;Clock&lt;/em&gt; and &lt;em&gt;Bmal1&lt;/em&gt; nuclear proteins, when present in sufficiently large amount, will dimerize and act as transcription factors on a series of genes that contain a region in their promoter element called &lt;a href=&quot;http://en.wikipedia.org/wiki/E-box&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;E-box&lt;/em&gt;&lt;/a&gt;. Amongst these are the &lt;em&gt;Period&lt;/em&gt; (&lt;em&gt;Per&lt;/em&gt;) genes.&lt;br&gt;&#xA;&lt;em&gt;Per&lt;/em&gt; is then synthesised, and exported to the cytoplasm. Here, if in a sufficiently large amount, it can heterodimerize with the &lt;em&gt;Cryptocrome&lt;/em&gt; (&lt;em&gt;Cry&lt;/em&gt;) proteins: the dimer will then enter the nucleus and inhibit the transcription actions of the &lt;em&gt;Clock/Bmal&lt;/em&gt; couple. This will in turn, block the transcription of &lt;em&gt;Per&lt;/em&gt;, that will therefore not be able to dimerize with &lt;em&gt;Cry&lt;/em&gt; and stop the inhibition of &lt;em&gt;Clock/Bmal&lt;/em&gt; and so on. All of this takes approximately 24 hours.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This basic loop (and some more) is nicely schematised in this review by Reppert and Weaver&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12198538&quot; rel=&quot;nofollow noreferrer&quot;&gt;Coordination of circadian timing in mammals.&lt;/a&gt; - Reppert and Weaver, &lt;em&gt;Nature.&lt;/em&gt; &lt;strong&gt;2002&lt;/strong&gt; Aug 29;418(6901):935-41.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xsvOj.jpg&quot; alt=&quot;Schematics of circadian clock - from Reppert and Weaver, Nature 2002&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I report here the legend of the figure:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The clock mechanism comprises interactive positive (green) and negative (red) feedback loops. CLOCK (C, oval) and BMAL1 (B, oval) form heterodimers and activate transcription of the Per, Cry and Rev-Erbalpha genes through E-box enhancers. As the levels of PER proteins increase (P, blue circle), they complex with CRY proteins (C, diamond) and CKI&amp;epsilon;/CKI&amp;delta; (&amp;epsilon;/&amp;delta;, circle), and are phosphorylated (p). In the nucleus, the CRY–PER–CKI&amp;epsilon;/CKI&amp;delta; complexes associate with CLOCK–BMAL1 heterodimers to shut down transcription while the heterodimer remains bound to DNA, forming the negative feedback loop. For the positive feedback loop, increasing REV-ERB&amp;alpha; levels (R, circle) act through Rev-Erb/ROR response elements in the Bmal1 promoter to repress (-) Bmal1 transcription. CRY-mediated inhibition of CLOCK–BMAL1-mediated transcription de-represses (activates) Bmal1 transcription, because REV-ERB&amp;alpha;-mediated repression is inhibited. An activator (A, circle) may positively regulate Bmal1 transcription (?) alone or by interacting with mPER2. There are probably kinases (?) other than CKI&amp;epsilon; and CKI&amp;delta; that participate in phosphorylation of clock proteins.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The clock machinery, however, is even more complex than this and different tissues need to integrate different signals (e.g. light, hormonal concentrations and so on).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, as nice as this may be, our bodies are not constituted by one single cell... if we &quot;zoom out&quot; a little bit and we go to the tissue or the whole body level, we see that circadian rhytms are present in all sorts of tissues and involve all sorts of different physiological processes. A very interesting question is then: how do cells from different organs coordinate each other so that the interrelation of different circadian processes is always the same? For instance, the release of cortisol peaks in the morning, our body temperature has a peak in the late afternoon and a trough in the early hours of the morning, and our heart rate is higher during the daytime.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In 1972, an article by Moore and Eichler was published, showing that lesioning the suprachiasmatic nucleus (SCN) of the hypothalamus (a region at the base of the brain) resulted in the &quot;breakage&quot; of the circadian rhythm of corticosterone (the stress hormone). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/5047187&quot; rel=&quot;nofollow noreferrer&quot;&gt;Loss of a circadian adrenal corticosterone rhythm following suprachiasmatic lesions in the rat.&lt;/a&gt; - Moore and Eichler, &lt;em&gt;Brain Res.&lt;/em&gt; &lt;strong&gt;1972&lt;/strong&gt; Jul 13;42(1):201-6&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fact that lesioning a bit of the brain resulted in loss of circadian rhythm in the adrenal gland was obviously a very big deal: the central circadian clock of the organism had been discovered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will not going too much into that but, since 1972 many advances have been made and nowadays we know that, although the role of the SCN is very important, it is not the only clock in the body. Several peripheral clock exist, in organs such as the pituitary gland, the liver or the pancreas. How all these clocks communicate between each other and what is their contribution to the generation of non-circadian rhythms (ultradian and infradian) are questions that still have to be solved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few interesting papers on the matter:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19712475&quot; rel=&quot;nofollow noreferrer&quot;&gt;A riot of rhythms: neuronal and glial circadian oscillators in the mediobasal hypothalamus.&lt;/a&gt; - Guilding et al., &lt;em&gt;Mol Brain.&lt;/em&gt; &lt;strong&gt;2009&lt;/strong&gt; Aug 27;2:28.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12894240&quot; rel=&quot;nofollow noreferrer&quot;&gt;A clockwork web: circadian timing in brain and periphery, in health and disease.&lt;/a&gt; - Hastings et al., &lt;em&gt;Nat Rev Neurosci.&lt;/em&gt; &lt;strong&gt;2003&lt;/strong&gt; Aug;4(8):649-61.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12828282&quot; rel=&quot;nofollow noreferrer&quot;&gt;Peripheral circadian oscillators in mammals: time and food.&lt;/a&gt; - Schibler et al., &lt;em&gt;J Biol Rhythms.&lt;/em&gt; &lt;strong&gt;2003&lt;/strong&gt; Jun;18(3):250-60.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-07-10T07:15:42.197" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2859" PostTypeId="2" ParentId="2822" CreationDate="2012-07-10T16:12:16.830" Score="1" Body="&lt;p&gt;A proof that autosomal recessive not necessarily skips a generation would be parents who both have the genotype and where one forth of the offspring would show the full phenotype.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-07-10T16:12:16.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2860" PostTypeId="2" ParentId="2385" CreationDate="2012-07-10T16:27:39.040" Score="4" Body="&lt;p&gt;You could combine the demonstration that glucose can be burned with the principle of catalysis: a sugar cube won't burn by itself if you hold a match at it. Using a bit of MnO2 or even simple ash on the cube will make it inflammable through catalysis: the MnO2 acts as catalysator (is not used up).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MnO2 (manganese(IV) oxide), a dark powder, is a safe chemical that only reacts with acids, and is insoluble in water.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-07-11T08:19:07.550" LastActivityDate="2012-07-11T08:19:07.550" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2861" PostTypeId="2" ParentId="2822" CreationDate="2012-07-10T16:41:34.407" Score="3" Body="&lt;p&gt;What you are saying is very similar to the statement that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Absence of evidence is not evidence of absence&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Suppose you have an autosomic gene A, which has a mutant allele a, causing an illness (or any other phenotype, for that matters). The particular nature of a makes its associated phenotype recessive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You have three possibilities:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;AA -&amp;gt; no illness  &#xA;Aa (or aA) -&amp;gt; carrier, with no illness &#xA;aa -&amp;gt; ill&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Now, let's take an aa individual (ill) and cross it with a sane AA individual:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;aa x AA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;All of the individuals of the first generation (F1) will be carriers (Aa) because the father will always give a and the mother always A.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now if we breed them together&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;aA x aA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;both parents have 1/2 probability of giving a and 1/2 of giving A. We will then have &lt;strong&gt;a proportion of&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;1/4 aa&#xA;1/2 Aa (1/4 A from mother and a from father, 1/4 vice-versa) &#xA;1/4 AA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;But this is just down to statistics. You have only 1/4 chances of seeing the trait reappearing, so you are much less likely to see it if they have 1 offspring then if they have 20.&#xA;Moreover, you have Aa offsprings in the progeny... this means that these could pass the mutant allele to the third or fourth generation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another important thing is that all we said is true if the first cross is&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;aa * AA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;If it was&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;aa * aa&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;or&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;aa * Aa&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The trait will (surely in the first case, and with 1/2 chance in the second) appear directly in the first generation.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-07-10T16:41:34.407" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2862" PostTypeId="2" ParentId="2761" CreationDate="2012-07-10T16:42:41.737" Score="3" Body="&lt;p&gt;Basically, all 16S genes are highly conserved, i.e., they share much identical bases. This means one can bind the 16S gene piece (after DNA was cut) to a specific other piece of DNA, even if you don't know exactly the 16S gene bases. Everything else is discarded then. Now finally, using PCR the rest is amplified and sequenced. Sequencing 16S only is much less work, so that's how they did it years ago. Today, whole microbiomes are sequenced by professional labs.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-07-10T16:42:41.737" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2863" PostTypeId="2" ParentId="2054" CreationDate="2012-07-10T16:50:09.153" Score="5" Body="&lt;p&gt;Essential &quot;minerals&quot;, i.e., metal cations are magnesium, zinc, iron, potassium, sodium, manganese, molybdenum, selenium, cobalt, copper and even calcium, as we lose a tiny amount of it through urine and sweat. They are all &quot;stored&quot; in some way, but only temporally, so some amount has to be taken up daily. It would show only weeks later, however, if you have a deficiency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia adds phosphorus and iodine but they are not metals.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-07-10T17:06:18.087" LastActivityDate="2012-07-10T17:06:18.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2864" PostTypeId="1" AcceptedAnswerId="2872" CreationDate="2012-07-10T23:37:45.597" Score="3" ViewCount="3832" Body="&lt;p&gt;After wading through a sea of information, I understand the main differences between the white matter and grey matter of the spinal cord.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that white matter contains myelinated axons in the ascending and descending nerve tracts from the brain to the spinal cord. I know that grey matter contains somata which contribute to sensory and motor functions from and to the peripheral nerve fibers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With the differences in mind, I am confused about the relationship between the two.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main question being: What signaling, if any, takes place between the myelinated axons of white matter and the somata of grey matter? More pointedly, do the myelinated axons from the nerve tracts in white matter ever synapse with dendrites from somata in grey matter?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My guess is yes, that this is a key aspect in how the brain and the spinal cord communicate. But I haven’t yet found any definitive source that addresses this question directly.&lt;/p&gt;&#xA;" OwnerUserId="972" LastEditorUserId="69" LastEditDate="2012-07-12T10:25:07.313" LastActivityDate="2012-07-12T10:25:07.313" Title="SPINAL CORD: Do the axons from white matter synapse with the cell bodies in grey matter?" Tags="&lt;neuroscience&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2868" PostTypeId="1" AcceptedAnswerId="3093" CreationDate="2012-07-11T08:38:13.953" Score="7" ViewCount="343" Body="&lt;p&gt;With which bacterial infection in humans has it been shown that bacterial DNA can be found in the blood? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If any is found it is likely not to be very much, and even difficult to distinguish from human DNA, but presumably recent advances in sequencing should have made it possible.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="57" LastEditDate="2012-07-31T07:30:12.253" LastActivityDate="2012-08-01T14:19:47.333" Title="Is there a detectable amount of bacterial DNA in the blood of infected persons?" Tags="&lt;dna-sequencing&gt;&lt;bacteriology&gt;&lt;pcr&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2869" PostTypeId="2" ParentId="1870" CreationDate="2012-07-11T08:58:42.337" Score="2" Body="&lt;p&gt;We now know that humans acquire not only their initial gut flora but also that of the skin from swallowing and touching mother's vaginal mucus. This doesn't apply to Caesarean birth, however.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For reference, see my answer at skeptics: &lt;a href=&quot;https://skeptics.stackexchange.com/questions/9994/do-c-section-born-babies-have-worse-immune-systems/10078#10078&quot;&gt;https://skeptics.stackexchange.com/questions/9994/do-c-section-born-babies-have-worse-immune-systems/10078#10078&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2012-07-11T08:58:42.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2870" PostTypeId="1" CreationDate="2012-07-11T13:36:06.070" Score="4" ViewCount="28525" Body="&lt;p&gt;I am looking to purchase Pyruvate Kinase from the &lt;a href=&quot;http://www.sigmaaldrich.com/catalog/search?interface=All&amp;amp;term=P9136&amp;amp;lang=en&amp;amp;region=GB&amp;amp;focus=product&amp;amp;N=0%20220003048%20219853121%20219853286&amp;amp;mode=match%20partialmax&quot; rel=&quot;nofollow&quot;&gt;Sigma Website&lt;/a&gt;, they state the volume in Kilo Units (KU) i.e. 1, 5 or 25 KU. It also states there are 350-600 units / mg protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this mean one unit is one protein? so 1KU is 1000 units of protein?&#xA;What is the relationship between the KU and mg? and how can I use this relationship to calculate my concentration in um or mg.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;EDIT&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jp906242m&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; (look at the methods section) they calculated the concentration of 25,000 units of calmodulin in 0.5 ml to be approximately 75um which is 40,000 units/mg. How did they calculate this? &lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="3460" LastEditDate="2013-05-07T00:24:21.007" LastActivityDate="2014-01-15T22:19:42.583" Title="Calculating Protein Concentration from Kilo Units (KU)" Tags="&lt;proteins&gt;&lt;terminology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2871" PostTypeId="2" ParentId="2870" CreationDate="2012-07-11T13:41:01.670" Score="5" Body="&lt;p&gt;From the page linked from your link:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Unit Definition&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;One unit will convert 1.0 μmole of phospho(enol)pyruvate to pyruvate&#xA;  per min at pH 7.6 at 37 °C.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, the unit is defined by activity, and there is no way to know how many molecules or milligrams of protein are included&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-07-11T13:41:01.670" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="2872" PostTypeId="2" ParentId="2864" CreationDate="2012-07-11T16:58:11.013" Score="4" Body="&lt;p&gt;Here is a great diagram (from &lt;a href=&quot;http://en.wikipedia.org/wiki/Pyramidal_tracts&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;) that outlines all of the different white matter tracts running up (blue) and down (red) the cord.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/0dhRo.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The portion in the center, as you have found in your research, is the gray matter.  In there are the different interneurons (cells that exist in the network to integrate information from descending controls and do further processing on it) and all of the different motor neurons.  The corticospinal tract descends to the appropriate level (for example, a neuron in charge of moving your arm, to keep it simple, will have a cell body in the brain, and descend to the thoracic level), enters into the gray matter and either synapse on an interneuron or directly onto a motor neuron).&lt;/p&gt;&#xA;&lt;p&gt;The sensory neurons are a slightly different animal.  Some (pseudo-unipolar cells) have what are basically two &amp;quot;legs&amp;quot;, one that runs out into the periphery, which will take the signal from something like a Pacinian corpuscle in the skin, propagates a signal to the cell body, which is outside of the spinal cord in the dorsal root (see below), and the other &amp;quot;leg&amp;quot; runs all the way up the dorsal column into the medulla of the brainstem.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/urL4z.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;sup&gt;from &lt;a href=&quot;http://en.wikipedia.org/wiki/Posterior_root_of_spinal_nerve&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;p&gt;So that should give you some idea of the two major tracts.  To see some of the finer detail, you can look into the different layers (laminae) that the gray matter is composed of, so that you can trace the connections all the way in.&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-07-11T16:58:11.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2873" PostTypeId="2" ParentId="2841" CreationDate="2012-07-11T23:10:33.283" Score="4" Body="&lt;p&gt;Your calculation for O2 is along the right direction, but missing a factor I think. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each red blood cell holds millions of molecules of hemoglobin, each &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemoglobin&quot; rel=&quot;nofollow noreferrer&quot;&gt;hemoglobin&lt;/a&gt; molecule, when saturated (at the lung), holds four O2 molecules.  So this is off by a factor of millions at least.  Wikipedia estimates that hemoglobin makes up about 35% of the total weight of blood.  We can use this figure and an average of 4.5 l of blood for a human being ( numbers vary, but it will be within 30%).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;4.5l blood * &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood#Constituents_of_human_blood&quot; rel=&quot;nofollow noreferrer&quot;&gt;1.060 g/ml density of blood&lt;/a&gt; * 1000 ml/l water * 35% = 1667 g hemoglobin &lt;/p&gt;&#xA;&#xA;&lt;p&gt;4 molecules O2/molecule hemoglobin * 1667 g hemoglobin / (64000 g/mol molecular weight of hemoglobin)  = 0.104 moles O2&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so I get: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;0.104 moles O2 * 30 g/mol for O2 = &lt;strong&gt;3.12 g O2 in the blood at a time.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the muscle and tissues it gradually depletes so that all four molecules will usually end up somewhere in your tissue.  So this is all assuming that counting all the hemoglobin bound O2 will approximate the count of O2 in the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We know this is a crude estimate as myoglobin in mammal muscle will store O2 for use later, and the average hemoglobin is not in the lungs and will have given up some of its O2.  It also doesn't count the O2 which diffuses into the blood and is carried by the water.  This is about 0.035 g / l, which is why we need hemoglobin - total blood saturation would carry about 1.15 g of O2.  Hemoglobin multiplies the oxygen carrying capacity of blood by 100 fold. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;CO2 is much more soluble in water (blood/tissue) than O2 is- about 1g/l.  There is I think only 2 CO2 binding sites for hemoglobin, which means it carries out only half the CO2 oxygen that it carries  in.  Hemoglobin is &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemoglobin#Binding_for_ligands_other_than_oxygen&quot; rel=&quot;nofollow noreferrer&quot;&gt;is only considered to account for 10% of the total CO2 carrying capacity of humans&lt;/a&gt;.  So calculating CO2 respiration by hemoglobin is not a good way to estimate blood CO2.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2018-03-16T15:21:55.113" LastActivityDate="2018-03-16T15:21:55.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2874" PostTypeId="1" CreationDate="2012-07-12T01:59:05.087" Score="27" ViewCount="13712" Body="&lt;p&gt;Does someone know why DNA is composed of four nucleobases? In particular, is there an explanation for the number? Why four and not two, or eight?&lt;/p&gt;&#xA;" OwnerUserId="1125" LastEditorUserId="43" LastEditDate="2013-01-25T15:52:41.780" LastActivityDate="2020-08-18T18:23:57.307" Title="Why are there exactly four nucleobases in DNA?" Tags="&lt;evolution&gt;&lt;biochemistry&gt;&lt;dna&gt;" AnswerCount="7" CommentCount="1" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2875" PostTypeId="1" AcceptedAnswerId="2876" CreationDate="2012-07-12T05:47:28.373" Score="29" ViewCount="6455" Body="&lt;p&gt;A friend of mine told me once about a documentary movie he saw some years ago. On this movie he saw scientists talking about particular experiment. This experiment involved rats and probably electrical traps. The rat had to get to the cheese, there were traps on the shortest route to it, and obviously it got shocked few times. What is interesting is that my friend says that when they took its offspring (probably born later) they avoided those traps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm aware that its not how &quot;genetic memory&quot; works. Its not memory of individual, but of species (so it requires evolution). This is what I'm trying to explain to him, but he says &quot;he knows what he saw&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway &lt;strong&gt;maybe someone&lt;/strong&gt; here &lt;strong&gt;is aware of such an experiment&lt;/strong&gt;. I believe that he is wrong about something (or conclusions drawn where changed later), so I would like to find out more about it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To sum up:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Its not Tryon's Rat Experiment&lt;/li&gt;&#xA;&lt;li&gt;It involved: rats, traps (probably electrical), more then one path to cheese, rat's offspring and some sort of memory/learning amongst rats.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1126" LastEditorUserId="3952" LastEditDate="2013-08-04T02:10:00.147" LastActivityDate="2020-02-15T06:39:59.870" Title="Can rats pass on memories of a maze to their offspring?" Tags="&lt;epigenetics&gt;&lt;memory&gt;&lt;communication&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2876" PostTypeId="2" ParentId="2875" CreationDate="2012-07-12T08:17:23.780" Score="50" Body="&lt;p&gt;The phenomenon you're talking about was a fad in the 60's, called 'interanimal memory transfer'. It started out when &lt;a href=&quot;http://en.wikipedia.org/wiki/James_V._McConnell&quot;&gt;James McConnell&lt;/a&gt; performed a later-discredited experiment in which he found that if you chopped up flatworms which had been exposed to some stresses, and fed them to other unexposed flatworms, the unexposed worms became wary of the source of stress quicker after eating their dead companions. He jumped to the conclusion that a 'memory molecule' was being transferred, and that the cannibal worms gained the food worms' memories of the stress.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;People then started looking to see if they could:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;repeat the experiments&lt;/li&gt;&#xA;&lt;li&gt;find the same phenomenon in other animals&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In the first case, nobody could replicate the experiments in worms, but because McConnell was such a PR genius he managed to convince the public that his results were valid (see Rilling, 1996 for more on this).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the second case, Frank et al. (1970) and others tried working with rats - I think this is the experiment you're talking about in the question. They found various interesting results including that if you trained rats to run through a maze by using particularly stressful negative reinforcement (like electrocution), then those rats' children would be able to learn the new maze much faster. However, Frank et al. didn't make the same mistake as McConnell - first of all they wondered if the parent rats might be leaving a scent trail. So they used duplicate mazes with the exact same design, putting the children into clean mazes. The children of adults who had already learned the maze continued to outperform the control rats - the explanation was not scent trails.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next they wondered whether it might be that the second generation rats had been born with a higher wariness as a result of the stress their parents suffered; i.e. it could be a hormonal transfer from mother to child (e.g. cortisol, the stress hormone).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Frank et al. tested their hypothesis by torturing some rats for a while (rules about animal welfare were not strict in the 70's). They would lock some rats in a small jar and bash them about for a long time, then kill them, chop them up, and take out their livers. They fed the livers to other rats, and found that after eating the livers the other rats learned the maze much faster. They interpreted the results in what now seems a sensible light: &lt;strong&gt;the stressed rats were producing high concentrations of a stress-signalling molecule. When those rats either had children or were fed to other rats, they passed on high doses of the stress molecule. This raised the alterness and wariness of the receipient rats so that they were much quicker to learn which parts of the maze were dangerous.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no evidence that the child rats actually 'remembered' the maze - they still had to find their way around, but they were extremely wary of the electrocution plates and so avoided them, finding the safest way to the end. &lt;strong&gt;This is not a case of genetic memory&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1126/science.169.3943.399&quot;&gt; &lt;strong&gt;Frank B, Stein DG, Rosen J&lt;/strong&gt;. 1970. Interanimal “Memory” Transfer: Results from Brain and Liver Homogenates. Science 169: 399–402.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1037/0003-066X.51.6.589&quot;&gt; &lt;strong&gt;Rilling M&lt;/strong&gt;. 1996. The mystery of the vanished citations: James McConnell’s forgotten 1960s quest for planarian learning, a biochemical engram, and celebrity. American Psychologist 51: 589–598.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-07-19T07:04:15.213" LastActivityDate="2012-07-19T07:04:15.213" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2877" PostTypeId="1" AcceptedAnswerId="2882" CreationDate="2012-07-12T08:41:24.417" Score="8" ViewCount="717" Body="&lt;p&gt;Multidrug resistant probiotics are often recommended by doctors in various cases. But since bacteriae can easily exchange genes by conjugation or other means they could promote the drug resistance of other dangerous bacteriae residing in the bowels. (Which could be just &quot;visitors&quot; otherwise causing infections somewhere else) &lt;br/&gt;&#xA;Or there is something that withholds this transfer? I think not and so my former genetics professor.&lt;/p&gt;&#xA;" OwnerUserId="673" LastEditorUserId="673" LastEditDate="2012-07-12T08:51:30.443" LastActivityDate="2012-07-12T17:25:00.910" Title="Aren't antibiotic resistant probiotics dangerous?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;antibiotics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2879" PostTypeId="1" CreationDate="2012-07-12T09:18:19.970" Score="18" ViewCount="2819" Body="&lt;p&gt;Following from this question: &lt;a href=&quot;https://biology.stackexchange.com/questions/1495/what-is-the-evolutionary-advantage-of-death&quot;&gt;What is the evolutionary advantage of death?&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any evidence that human bodies have systemic self-destruction built into their developmental program? I'm not talking about the cell death response, which I know is an important part of growth, development and cancer prevention.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've read some things about telomere-shortening but don't know if this is a cause or an effect.&lt;/p&gt;&#xA;" OwnerUserId="1128" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2021-03-05T07:08:44.023" Title="Are human bodies programmed to die?" Tags="&lt;human-biology&gt;&lt;senescence&gt;&lt;human-genome&gt;&lt;development&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2880" PostTypeId="2" ParentId="2879" CreationDate="2012-07-12T10:00:07.723" Score="18" Body="&lt;p&gt;From a certain point of view you could argue that our bodies have an inherently limited lifespan;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Telomeres are extensions to the end of chromosomes that prevent damage or loss of genetic information during cell division. Telomeres are not replaced (in normal cells), which gives rise to a &lt;em&gt;replicative lifespan&lt;/em&gt;; the number of times a cell can divide before permenantly leaving the cell cycle (senescence).&#xA;&lt;ul&gt;&#xA;&lt;li&gt;This is generally viewed as an anti-cancer mechanism to protect against errors creeping in to the genome through many cell divisions. In order to become cancerous, a cell must first overcome its replicative lifespan [&lt;a href=&quot;http://dx.doi.org/10.1093/carcin/bgp268&quot;&gt;ref.&lt;/a&gt;]. This is achieved by activating the (normally inactive) &lt;em&gt;telomerase&lt;/em&gt; enzyme that extends the telomeres - embryonic stem cells are one of the few cell types that normally express this enzyme.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are other ways in which you could argue that our lifespans are fundamentally limited, but &lt;strong&gt;it is important to note that the objective is not 'to die', but to increase &lt;em&gt;fitness&lt;/em&gt;&lt;/strong&gt; (in a Darwinian sense) &lt;strong&gt;earlier in life&lt;/strong&gt;. This is known as &lt;em&gt;antagonistic pleiotropy&lt;/em&gt;; when an advantageous trait early in life is disadvantageous later in life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Telomere shortening is just one example of antagonistic pleiotropy (protects against cancer when younger, but limits the number of times your cells can divide).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other traits that inherently limit lifespan include;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Neurons (as a rule) do not replicate, and last for your whole life time. This certainly excludes them from replicate senescence, however it means they are highly susceptible to 'wear and tear'; oxidative stress is a natural by-product of respiration, and the vast majority of damage done by these species (e.g. reactive oxygen species) is repaired by the cell, however some will always remain unchecked, and eventually this leads to neurological dysfunction and cognitive decline. &lt;strong&gt;Without intervention this is inevitable in each individual (the &lt;em&gt;rate&lt;/em&gt; of aging differs between people, but aging and age-dependent diseases are disorders are a natural part of living)&lt;/strong&gt;.&lt;/li&gt;&#xA;&lt;li&gt;The same is true for cardiac and smooth muscle - whilst much repair can be carried out, it is inevitable that damage will creep in over a life time, and thus the vast majority of human age-related deaths are due to cardiac problems in one way or another.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So there is no 'programmed' limit to life span, in that we have not evolved to die, but our bodies are inherently limited by the systems that have evolved. Life expectancy a few thousand years ago was ~20 years (if you lived beyond infancy!), whereas now in the developed world this is ~80 years, so our bodies can already survive way beyond our 'natural' life span, and thus we now succumb to age-related disease. &lt;strong&gt;Evolution has spent millions of years giving us every possible advantage that leads to reproductive success. Natural selection of traits beyond reproduction are secondary to those beforehand&lt;/strong&gt;, and thus we have fundamentally limited life spans.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;There is an argument for an evolutionary advantage of limited lifespan. This seems at first counter-intuitive, until you consider that natural selection does not act on individuals, but genes. It is proposed to be advantageous (in some circumstances) for an organism to have a shorter life span, as this increases the turn-over of individuals in that population. This in turn increases their &lt;em&gt;evolvability&lt;/em&gt; - clearly advantageous for the gene(s) influencing this trait if it increases the likelihood of successful reproduction and thus passing on that gene/allele/trait...  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I like this hypothesis, and can see that natural selection may favour it. I think mice are great examples here; they have much shorter lifespans than us, yet they 'age' (biologically) the same (cardiac problems, diabetes, cancer) but at a faster rate to give a higher population turnover). In a high mortality environment, the most adaptable animals will be more successful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I think this is likely to be secondary to the pressures on other survival traits that  more directly increase the chances of successful reproduction.&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-07-13T15:06:16.733" LastActivityDate="2012-07-13T15:06:16.733" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="2881" PostTypeId="1" CreationDate="2012-07-12T17:10:07.277" Score="7" ViewCount="1052" Body="&lt;p&gt;I'm working with a GFP-tagged protein and am routinely using a fluorescence imager (GE Typhoon) and a standard optical scanner to capture fluorescent and absorption images, respectively, of my SDS-PAGE gels.  The Typhoon supports multiple channels, so is there some way that I can scan for the two on the same device (GFP + total protein)?  I assume I can't do absorption on a fluorescence scanner..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could manually register the two images, but it would be laborious as they are at different resolutions, slightly different rotations, and the gel can stretch ever-so-slightly when placing it on the platens.&lt;/p&gt;&#xA;" OwnerUserId="25" LastActivityDate="2012-10-21T13:58:39.753" Title="Can I image Coomassie and GFP in gels at the same time with a fluorescence scanner?" Tags="&lt;lab-techniques&gt;&lt;sds-page&gt;&lt;imaging&gt;&lt;green-fluorescent-protein&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2882" PostTypeId="2" ParentId="2877" CreationDate="2012-07-12T17:25:00.910" Score="5" Body="&lt;p&gt;Usually, resistance genes are located on plasmids---additional DNA rings in the bacterium that are part of the genome. These plasmids cause their own exchange with other bacteria, even from other species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;B. clausii&lt;/em&gt;, the probiotics organism in question here, appears to be special, though, in that it has no plasmids. His resistance genes come with the primary ring-shaped genome and should not be transferred via plasmid exchange to other bacteria. This doesn't rule out other means of gene transfer like phages or conjugation, however. In one study, it was unsuccessfully tried to transfer a macrolide resistance gene to other bacteria. They conclude&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A potential hazard is transfer of resistance to microorganisms&#xA;  pathogenic for humans. The risk that this event will occur and the&#xA;  consequences in terms of morbidity and mortality have not been&#xA;  evaluated. Parameters required for risk assessment include studies on&#xA;  the nature and mobility of the resistance genes of probiotics.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The only other paper on a &lt;em&gt;B.clausii&lt;/em&gt; resistance gene didn't look at its transferability. That clearly shows we don't know enough.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;B. Bozdogan, S. Galopin, R. Leclercq: &lt;em&gt;Characterization of a new erm-related macrolide resistance gene present in probiotic strains of Bacillus clausii.&lt;/em&gt; In: &lt;em&gt;Applied and environmental microbiology.&lt;/em&gt; Band 70, Nummer 1, Januar 2004, S.&amp;nbsp;280–284, {{ISSN|0099-2240}}. PMID 14711653. PMC 321311. &lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-07-12T17:25:00.910" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2883" PostTypeId="1" AcceptedAnswerId="3630" CreationDate="2012-07-12T17:46:34.540" Score="9" ViewCount="1428" Body="&lt;p&gt;From my reading on &lt;em&gt;M. tuberculosis&lt;/em&gt;, I know that this organism has a pretty high mutation rate due to uncorrected sloppy replication, which leads to a high rate of development of spontaneous resistance to treatment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there species that can beat &lt;em&gt;M. tuberculosis&lt;/em&gt; in this degree of mutation, due to polymerase sloppiness or other mechanism?&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="57" LastEditDate="2012-07-15T19:24:05.927" LastActivityDate="2012-11-11T02:00:37.173" Title="Which bacteria have the highest mutation rate?" Tags="&lt;genetics&gt;&lt;bacteriology&gt;&lt;replication&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2884" PostTypeId="1" AcceptedAnswerId="2890" CreationDate="2012-07-12T18:00:08.203" Score="6" ViewCount="262" Body="&lt;p&gt;What is the possible health issue the women would face in this record?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The record for most children born to a single couple belongs to the&#xA;  first wife of Feodor Vassilyev of Russia. In 27 pregnancies between&#xA;  1725 and 1765 she gave birth to 16 pairs of twins, 7 sets of triplets,&#xA;  and 4 sets of quadruplets for a grand total of 69 children.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="69" LastEditDate="2012-07-14T16:27:43.463" LastActivityDate="2015-12-23T11:40:40.223" Title="What are possible health risks to women having large numbers of children?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2885" PostTypeId="1" AcceptedAnswerId="8077" CreationDate="2012-07-12T18:06:30.100" Score="1" ViewCount="713" Body="&lt;p&gt;Cockroaches are known to live in very dirty places like sewers. Does this cause them to evolve to be stronger against parasites and bacteria? Recently I read online that cockroaches can sustain radioactive harm 6-15 more than humans, so does that mean that cockroaches are less likely to get cancer?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;refernece for the radioactive exposure:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.abc.net.au/science/articles/2006/02/23/1567313.htm?site=science/greatmomentsinscience&quot; rel=&quot;nofollow&quot;&gt;http://www.abc.net.au/science/articles/2006/02/23/1567313.htm?site=science/greatmomentsinscience&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="69" LastEditDate="2012-10-11T21:42:39.543" LastActivityDate="2013-04-24T23:19:04.660" Title="Do cockroaches have less health issues than humans?" Tags="&lt;zoology&gt;&lt;immunology&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2886" PostTypeId="1" AcceptedAnswerId="2894" CreationDate="2012-07-12T18:12:03.463" Score="10" ViewCount="358" Body="&lt;p&gt;I recently watched a clip on Discovery Channel, where I saw deer crossing a river full of crocodiles, ignoring the fact that some of them would have been killed doing so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a possible evolutionary reason for this behaviour?&lt;/p&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="16651" LastEditDate="2015-12-29T03:57:10.220" LastActivityDate="2015-12-29T03:57:10.220" Title="Why would deer continue to cross a river full of crocodiles even though some of them have been killed?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2887" PostTypeId="1" AcceptedAnswerId="2889" CreationDate="2012-07-12T18:41:23.613" Score="5" ViewCount="3593" Body="&lt;p&gt;Recently, I discovered a &quot;bite&quot; by a cockroach, and not only is the &quot;bitten&quot; area red and swallowing, and more specifically, it have a big hole in that area, but when I clean it with hydrogen peroxide solution, something is happening, that is, a yellowish/greenish thing comes out from the holes from each infecting area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do cockroaches lay eggs in human flesh when they &quot;bite&quot;, and much more importantly, would hydroxide solution kill the eggs and parasites inside those of those holes?&lt;/p&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="21009" LastEditDate="2016-08-06T08:20:26.917" LastActivityDate="2016-08-06T08:20:26.917" Title="Do cockroaches lay eggs in human flesh when they &quot;bite&quot;?" Tags="&lt;zoology&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2889" PostTypeId="2" ParentId="2887" CreationDate="2012-07-12T19:15:16.133" Score="10" Body="&lt;p&gt;No, cockroaches do not lay eggs into human flesh. You most likely received an infection of some sort from the bug, or it wasn't a cockroach.&lt;/p&gt;&#xA;" OwnerUserId="1130" LastActivityDate="2012-07-12T19:15:16.133" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2890" PostTypeId="2" ParentId="2884" CreationDate="2012-07-12T21:58:49.477" Score="9" Body="&lt;p&gt;A common problem for any woman who has experienced pregnancy and childbirth is damage to the &lt;em&gt;levator ani&lt;/em&gt; muscle, which comprises a portion of the &quot;pelvic floor.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5jZmr.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt; from &lt;a href=&quot;http://en.wikipedia.org/wiki/Pelvic_floor&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; &lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can cause a number of &lt;a href=&quot;http://en.wikipedia.org/wiki/Pelvic_floor&quot; rel=&quot;nofollow noreferrer&quot;&gt;symptoms&lt;/a&gt;, including urinary incontinence (due to an increase in pressure on the bladder from less effective muscular support), and possible prolapse of the bladder, uterus, or rectum into the vagina, again due to the weakening of the pelvic floor.&lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2012-07-12T21:58:49.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2891" PostTypeId="1" CreationDate="2012-07-13T02:31:11.830" Score="10" ViewCount="206" Body="&lt;p&gt;Popular science features on wildlife typically capture camera images using natural light, or high-speed exposures. This is not possible where the ambient light is extremely poor. &#xA;E.g. Caves, Undersea&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For beings accustomed to the stygian dark, the high illumination for a video camera and/or the flash of a still camera could both be the equivalent of a 1&quot; spanner wallop on the head or worse. Do we, inadvertently, injure the local ecosystem this way?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="3952" LastEditDate="2014-04-22T14:44:27.827" LastActivityDate="2014-04-22T14:44:27.827" Title="Does artificial high intensity light damage permanently dark ecosystems?" Tags="&lt;zoology&gt;&lt;ecology&gt;&lt;light&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2892" PostTypeId="1" AcceptedAnswerId="3011" CreationDate="2012-07-13T07:01:38.653" Score="2" ViewCount="6730" Body="&lt;p&gt;(after some deliberation in the comments, I've decided to make the question more general)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An &lt;a href=&quot;http://en.wikipedia.org/wiki/Eschar&quot; rel=&quot;nofollow&quot;&gt;eschar&lt;/a&gt; or &quot;dry scab&quot; often forms at a site of injury over a large cut or sore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems as though the healing scab portion binds more strongly to the other scab cells than to those of the surrounding healthy tissue initially, as evidenced by the ability to remove the scab &lt;em&gt;en masse&lt;/em&gt; without disturbing the edges of the actual wound (in surgical debridement or when the area is &quot;picked&quot; at).  Then, the eschar bonds then bonds more strongly with the edges of the wounds (so it's more difficult to remove), and then finally, the underlying newly formed skin seems to push it off completely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this accurately describe the &quot;lifecycle&quot; of a common dry scab, or are there other well defined stages in the process?  What types of cells (platelets in the beginning?  epithelials at the end?) are involved with each stage of the process?&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-07-22T03:40:23.010" LastActivityDate="2018-06-30T21:42:57.180" Title="What is the &quot;lifecycle&quot; of an average eschar and what types of cells are involved in each stage?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;pathology&gt;" AnswerCount="2" CommentCount="10" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2893" PostTypeId="1" CreationDate="2012-07-13T08:40:10.280" Score="16" ViewCount="409" Body="&lt;p&gt;I have a technical question regarding the syntax in Protein Data Bank files.  In the protein with PDB# &lt;a href=&quot;http://www.rcsb.org/pdb/explore.do?structureId=1ae9&quot; rel=&quot;noreferrer&quot;&gt;1AE9&lt;/a&gt; (&lt;a href=&quot;http://www.rcsb.org/pdb/files/1AE9.pdb&quot; rel=&quot;noreferrer&quot;&gt;pdb file&lt;/a&gt;), there are two lines in the .pdb file:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;HELIX    4   4 MET A 255  ILE A  265  1                                  11    &#xA;&#xA;SHEET    2   B 2 ILE A 253  MET A 255 -1  N  ILE A 253   O  ILE A 248           &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Now, as I understand the documentation, this means there is an alpha helix starting from residue &quot;MET A 255&quot; to the residue &quot;ILE A  265&quot;.  There is also a beta strand from &quot;ILE A 253&quot; to &quot;MET A 255&quot;.  We see that the alpha helix and beta strand share the residue &quot;MET A 255&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.wwpdb.org/documentation/format33/sect5.html&quot; rel=&quot;noreferrer&quot;&gt;documentation&lt;/a&gt; describes these as:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;Name of the initial residue.&quot;&lt;/li&gt;&#xA;&lt;li&gt;&quot;Name of the terminal residue of the helix.&quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The wording suggests that the &quot;initial&quot; residue is included, but I'm unsure of whether or not the &quot;terminal&quot; residue would be included.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;:  Should I consider this residue as belonging to both the alpha helix and beta strand?  Or should I consider the &quot;terminal&quot; residue as not belonging to the secondary structure element?  (Or something else?)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="203" LastEditorUserId="3553" LastEditDate="2016-06-01T06:58:02.847" LastActivityDate="2016-06-01T06:58:02.847" Title="Can two protein secondary structures &quot;overlap&quot; in the PDB?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;database&gt;&lt;structural-biology&gt;&lt;pdb&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2894" PostTypeId="2" ParentId="2886" CreationDate="2012-07-13T13:33:11.867" Score="11" Body="&lt;p&gt;The reason for their behavior is that exactly the fact that even though some of them do indeed get killed, most of them survive -- what you have said.  The deer cross the river because that allows for the better continuation of the species rather than if they had stayed on the original side of the river. You could think of it this way: If there was a crowd of 5000 people crossing a field of grass and aliens were abducting them one by one, the actual chances of them abducting you are rather little.&lt;/p&gt;&#xA;" OwnerUserId="1130" LastEditorUserId="69" LastEditDate="2012-08-17T15:36:23.060" LastActivityDate="2012-08-17T15:36:23.060" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2895" PostTypeId="1" AcceptedAnswerId="2896" CreationDate="2012-07-13T15:56:52.650" Score="4" ViewCount="226" Body="&lt;p&gt;What happens in liver when large amount of fructose is consumed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I vaguely remember my biochemistry lecturer telling us that the enzymes that process fructose in the liver does not have negative feedback to control the rate of reaction. But I cannot find a reliable source. How is it regulated if it is?&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2012-07-13T17:50:33.517" Title="Negative feedback in the fructose metabolism in liver" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;metabolism&gt;&lt;digestive-system&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2896" PostTypeId="2" ParentId="2895" CreationDate="2012-07-13T17:50:33.517" Score="5" Body="&lt;p&gt;The main reaction of fructose in liver is phosphorylation, catalyzed by ketohexokinase (&lt;a href=&quot;http://www.uniprot.org/uniprot/P50053&quot;&gt;UniProt P50053&lt;/a&gt;). In one paper with rats it was shown that fructose load can deplete the liver of nucleotide triphosphates (ATP, GTP) although ADP and GDP are inhibitors of the enzyme. This shows there is no effective regulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;M. I. Phillips, D. R. Davies: &lt;em&gt;The mechanism of guanosine triphosphate depletion in the liver after a fructose load. The role of fructokinase.&lt;/em&gt; In: &lt;em&gt;The Biochemical journal.&lt;/em&gt; Vol 228, Nr 3, Jun 1985, p.&amp;nbsp;667–671, {{ISSN|0264-6021}}. PMID 2992452. PMC 1145036. &lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-07-13T17:50:33.517" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2897" PostTypeId="1" CreationDate="2012-07-14T06:41:08.080" Score="10" ViewCount="262" Body="&lt;p&gt;Is there a website where I can input pairs of species and get an &quot;evolutionary similarity score&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.g. (numbers are completely made up)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Input: Chimp and Human, Output: 97%&lt;/li&gt;&#xA;&lt;li&gt;Input: Cat and Human, Output: 85%&lt;/li&gt;&#xA;&lt;li&gt;Input: Is Cat closer to Human or Chimp, or Snake, Output: Cat is closer to Chimp (87%), second is Human (85%) and Snake is last with 50%.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I have no idea what the actual scale should be, but I imagine there is at least one interesting scale, perhaps several.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.quora.com/Evolutionary-Biology/Is-there-an-%E2%80%9Cevolutionary-species-similarity-calculator%E2%80%9D&quot;&gt;Cross posted to Quora&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="288" LastActivityDate="2012-07-16T11:16:20.577" Title="Is there an &quot;evolutionary species similarity calculator&quot;?" Tags="&lt;evolution&gt;&lt;genetics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2898" PostTypeId="2" ParentId="2897" CreationDate="2012-07-14T07:24:22.427" Score="11" Body="&lt;p&gt;Since the simple value of percentage of nucleic acid identity over whole genomes isn't very useful in taxonomy, you won't find these values published in a database, even if they were computed by someone in the process of other work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One project that provides ready-for-consumption phylogenetic trees based on similarity metrics, by using orthologous genes between species, is OMA. They compute all orthologous genes between two species, and they are now at 1,235 species:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biorecipes.com/Orthologues/status.html&quot;&gt;http://www.biorecipes.com/Orthologues/status.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could then read off the &quot;distance&quot; between cat and mouse from the eukaryotes tree. This value would then be more meaningful than the nucleic acid identity percentage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from the trees, using their OMAbrowser you can get for any species pair the number of common orthology groups, i.e., the number of common genes between those two species.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-07-14T07:30:44.213" LastActivityDate="2012-07-14T07:30:44.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2901" PostTypeId="2" ParentId="2870" CreationDate="2012-07-15T08:15:51.633" Score="5" Body="&lt;p&gt;The figure of 350 - 600 Units per mg refers to the &lt;strong&gt;specific activity&lt;/strong&gt; of the enzyme. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;Unit&lt;/strong&gt; is &lt;strong&gt;International Unit&lt;/strong&gt; or &lt;strong&gt;IU&lt;/strong&gt; and is usually defined as that amount of enzyme that will catalyze the transformation of 1 micromole of substrate (or product) per min, under defined assay conditions (such as pH, &lt;strong&gt;temperature&lt;/strong&gt;, substrate concentration, presence of Mg&lt;sup&gt;++&lt;/sup&gt;, etc). It is thus a measure of &lt;em&gt;activity&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the enzyme is pure (no other extraeneous proteins present), the specific activity provides important information about the catalytic capacity of the enzyme.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is usually calculated by measuring&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA; &lt;li&gt;the &lt;i&gt;activity&lt;/i&gt; of the enzyme preparation under defined assay conditions&lt;/li&gt;&#xA;&lt;li&gt;the &lt;i&gt;protein concentration of the same enzyme preparation&lt;/i&gt; (using, say, the Lowry or Biuret method for protein estimation). &lt;br /&gt;&lt;br /&gt;&#xA;Alternatively, if the E(1%, 280) is known (see below) &lt;i&gt;and the enzyme is pure&lt;/i&gt;, measurement of the absorbance at 280 nm gives a very good estimate of protein content (and the enzyme may be recovered 'unharmed' at the end of the measurement).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Thus, taking a figure of 450 Units/mg for the specific activity of pyruvate kinase, &#xA;25 KU (25 Kilo-Units, I presume) contains 500/9 mg (~55 mg) protein.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I notice that the Sigma product sheet provides a figure for  &lt;strong&gt;E(0.1%, 280)&lt;/strong&gt; = 0.54.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;This means that a 1 mg/ml solution of the protein will have an absorbance at 280 nm of 0.54&lt;/strong&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;E(0.1%, 280) can be used as a very convenient measure of the protein content &lt;em&gt;provided that the enzyme preparation supplied by Sigma is pure&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;A 'rule of thumb', useful when the E(0.1%, 280) is unknown, is that a 1mg/ml protein solution has an A&lt;sub&gt;280&lt;/sub&gt; of 1.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thus if, say, the A&lt;sub&gt;280&lt;/sub&gt; (absorbance at 280 nm) of the resuspended lyophilized powder is 1.08 and you have 5 ml of this, the protein concentration is 2mg/ml and you have 10 mg of protein in total.  You may wish to assay the enzyme yourself to determine an accurate specific activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The EC (Enzyme Commission) Number may also be of interest.  For pyruvate kinase (EC 2.7.1.40) see &lt;a href=&quot;http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/7/1/40.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a great ref on PK (pdf may be downloaded) see &lt;a href=&quot;http://www.biochemj.org/bj/209/bj2090401.htm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; (Ainsworth et al.) &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;For your &lt;strong&gt;second question&lt;/strong&gt;, I do not have access to that paper from home.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if calmodulin has a specific activity of 40 000 Units/mg,&lt;/p&gt;&#xA;&#xA;&lt;ul&gt; &lt;li&gt;25 000 Units is equivalent to 0.625 mg; this is in a volume of&#xA;0.5 ml.  Therefore, the calmodulin concentration is 1.25mg/ml.&lt;/li&gt;  &#xA;&#xA;&lt;li&gt;Taking the molecular weight of calmodulin to be 16 000, &#xA;then 16 000 mg /ml (theoretical) would be a 1 Molar solution.&#xA;Thus a 1.25 mg/ml solution is about 78 micromolar.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="1136" LastEditDate="2012-07-21T18:11:33.160" LastActivityDate="2012-07-21T18:11:33.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2902" PostTypeId="1" AcceptedAnswerId="27574" CreationDate="2012-07-15T09:05:57.077" Score="7" ViewCount="906" Body="&lt;p&gt;If a person were administered a mydriatic, would the subsequent application of a miotic neutralize the action of the former? If the sequence were reversed would a mydriatic neutralize the effect of a miotic?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="9943" LastEditDate="2015-03-09T11:48:12.480" LastActivityDate="2015-03-09T11:48:12.480" Title="Does a mydriatic drug neutralize the action of a miotic?" Tags="&lt;pharmacology&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2903" PostTypeId="2" ParentId="2051" CreationDate="2012-07-15T14:13:59.810" Score="28" Body="&lt;p&gt;A reaction where the the free energy of a thermodynamically favorable transformation, such as the hydrolysis of ATP, and a thermodynamically unfavorable one, are mechanistically joined  &lt;em&gt;into a new reaction&lt;/em&gt; (or may be envisaged to be so joined) is known as a coupled reaction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To put it another way, two or more reactions may be combined mechanistically such that a spontaneous reaction may be made 'drive' a non-spontaneous one,   and we may speak of the combined reaction as being 'coupled' (see, for example, Silby &amp;amp; Alberty (2001), quoted below). The combined reaction may be catalyzed by an enzyme, in which case the 'thermodynamic push' is provided by the coupling agent (such as ATP) and the 'kinetic push' is provided by the enzyme. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We need to take into account a very important point. As pointed out by Atkinson (1977),  the coupled reaction is &lt;em&gt;a different reaction&lt;/em&gt; to the reaction we are trying to 'drive', with different overall stoichiometry &lt;em&gt;and hence a different overall equilibrium constant&lt;/em&gt; (Atkinson, 1977, p52). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A coupled reaction does &lt;em&gt;not&lt;/em&gt; &quot;push a reaction past its equilibrium&quot; (see Atkinson, 1977, p52). No enzyme, for example, can push any reaction past its position of equilibrium. This is forbidden by the second law. (If your favourite kinetic mechanism does not obey the second law there is, as &lt;a href=&quot;https://en.wikiquote.org/wiki/Arthur_Eddington&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eddington&lt;/a&gt; put it, &quot;no hope&quot;). An enzyme (or enzymes) &lt;em&gt;can&lt;/em&gt; however, cause a reaction to proceed further than it normally would by catalyzing a different reaction (or series of reactions). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps (in lysine biosynthesis from aspartate), nature requires the the (NADH-linked) reduction of a carboxylic acid to an aldehyde, a reaction normally considered  irreversible. And lets spell this one out: the equilibrium constant for a reaction such as the following:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;        NADH + carboxylic acid = NAD&lt;sup&gt;+&lt;/sup&gt; + aldehyde        (1)  &lt;/pre&gt;&#xA;&#xA;&lt;p&gt;greatly favors aldehyde dehydrogenation so much so that the left-to-right transformation has never (to the best of my knowledge) been demonstrated (more on this below).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lets first phosphorylate the carboxylic acid using ATP as coupling agent to give aspartyl-phosphate (&lt;a href=&quot;https://en.wikipedia.org/wiki/Aspartate_kinase&quot; rel=&quot;nofollow noreferrer&quot;&gt;aspartate kinase&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;         aspartate + ATP = aspartate-4-phosphate + ADP        (2) &lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Now let's reduce the 'activated' acid (aspartate-4-phosphate) using NADPH as electron donor, where the equilibrium constant of the following reaction is  very much to the right  (&lt;a href=&quot;https://en.wikipedia.org/wiki/Aspartate-semialdehyde_dehydrogenase&quot; rel=&quot;nofollow noreferrer&quot;&gt;aspartate semialdehyde dehydrogenase&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;  aspartate-4-phosphate + NADPH + H&lt;sup&gt;+&lt;/sup&gt; ⇌ L-aspartate 4-semialdehyde + P&lt;sub&gt;i&lt;/sub&gt; + NADP&lt;sup&gt;+&lt;/sup&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So we have got our product (the aldehyde) from our 'starting material' (the carboxylic acid), but at the 'expense' (as we would see it) of  ATP hydrolysis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We may think of the above reactions as being 'mechanistially coupled' by the formation of aspartyl-phosphate such that the overall equilibrium constant for the following reaction is much more favourable than that of Eqn (1)&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;  aspartate + ATP + NADPH + H&lt;sup&gt;+&lt;/sup&gt; ⇌ L-aspartate 4-semialdehyde + P&lt;sub&gt;i&lt;/sub&gt; + NADP&lt;sup&gt;+&lt;/sup&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Or, perhaps in more abstract terms, the coupled reaction may be represented as folows:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;  carboxylic acid + ATP + NADPH + H&lt;sup&gt;+&lt;/sup&gt; ⇌  aldeyde + P&lt;sub&gt;i&lt;/sub&gt; + NADP&lt;sup&gt;+&lt;/sup&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The reduction of a carboxylic acid to an aldehyde has been given a thermodynamic 'push' by the coupling agent  (and a kinetic 'push' by the enzymes). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before we move on to some specific examples let's consider three further points. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(i) What makes ATP a good coupling agent? To again quote Atkinson (1977, p48), a good coupling agent has two requirements: firstly, it must be thermodynamically unstable. That is, it must be &quot;far from equilibrium in terms of some useful conversion&quot; (Atkinson, 1977, p48). The hydrolysis of ATP nicely fills this criterion. Secondly, a good coupling agent must be kinetically stable. Again ATP 'fits the bill': solutions of ATP in water are stable (Atkinson, 1977, p48). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ATP (-39.7 kJ/mol), of course, is not the only useful coupling agent, or even the 'best' one. phosphoenol-pyruvate (-61.9 kJ/mol) , creatine-phosphate (-43.5 kJ/mol)  and acetyl-phosphate (-43.1 kJ/mol) are others. The figures in brackets refer to free energy of hydrolysis and are taken from Silby and Alberty (2001, p 282).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(ii) The coupled reaction need &lt;em&gt;not&lt;/em&gt; involve direct hydrolysis of coupling agent. Any reaction in which ATP is converted to ADP has received a 'thermodynamic push equivalent to the free energy of hydrolysis of ATP' (Atkinson, 1977, p49). In essence, the concept of a coupled reaction is an abstraction, created by us for our convenience.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(iii) To state the obvious, a coupled reaction is exactly that: &lt;em&gt;coupled&lt;/em&gt;.  The coupling may be 'chemical', as in many of the examples below, or may be conformational (as in ATP synthase), but there must be in some sense a mechanistic joining into a new (real) reaction. Two reactions occurring in isolation, even if one is ATP hydrolysis, are not coupled. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Specific Examples&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of a coupled reaction is the  glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12; GAPDH) reaction [see &lt;a href=&quot;http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/2/1/12.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here] &lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt; Glyceraldehyde-3-phosphate + NAD&lt;sup&gt;+&lt;/sup&gt; + P&lt;sub&gt;i&lt;/sub&gt; → 1,3-diPhosphoGlycerate + NADH + H&lt;sup&gt;+&lt;/sup&gt; &lt;/pre&gt;&#xA;&#xA;&lt;p&gt;We can think of this reaction in terms of two separate reactions which are coupled mechanistically by the enzyme. (i) The NAD&lt;sup&gt;+&lt;/sup&gt; linked oxidation of an aldehyde to a carboxylic acid (the aldehyde dehydrogenase reaction) and (ii) the phosphorylation of a carboxylic acid. (Like ATP, a phosphorylated carboxylic acid may be considered a 'high energy' compound, that is one where the equilibrium for hydrolysis lies very much to the left in reaction 2 below). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reaction 1&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt; RCHO + NAD&lt;sup&gt;+&lt;/sup&gt; + H&lt;sub&gt;2&lt;/sub&gt;O → RCOOH + NADH + H&lt;sup&gt;+&lt;/sup&gt; &lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reaction 2&lt;/strong&gt; (P&lt;sub&gt;i&lt;/sub&gt; is inorganic &lt;em&gt;phosphate&lt;/em&gt;). &lt;/p&gt;&#xA;&#xA;&lt;pre&gt; RCOOH + P&lt;sub&gt;i&lt;/sub&gt; → RC(=O)(O-P&lt;sub&gt;i&lt;/sub&gt;) + H&lt;sub&gt;2&lt;/sub&gt;O &lt;/pre&gt;&#xA;&#xA;&lt;p&gt;As stated above, the NAD&lt;sup&gt;+&lt;/sup&gt;-linked oxidation of an aldehyde (reaction 1) is practically irreversible. That is, at equilibrium it has proceeded almost totally to the right. As stated above, the position of equilibrium of reaction 2 lies very much to the left.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can one 'drive' the formation of a phosphorylated carboxylic acid by coupling it to the (spontaneous) NAD&lt;sup&gt;+&lt;/sup&gt;-linked oxidation of an aldehyde?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A simplified version of the GAPDH reaction is as follows (a more complete mechanism, supported by a lot of experimental evidence, may be found in Fersht (1999), which I quote below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Step 1.&lt;/strong&gt;  Formation on an enzyme-linked thiohemiacetal.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt; E-SH + RCHO → E-S-C(R)(H)(OH) &lt;/pre&gt;&#xA;&#xA;&lt;p&gt;A sulphydryl on the enzyme (part of a Cys residue) reacts with the aldehyde group on the substrate to give a thiohemiacetal.  (In the representation above, groups in brackets are all connected to a single (tetrahedral) carbon atom). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Step 2.&lt;/strong&gt; The thiohemiacetal is oxidized by enzyme-bound NAD&lt;sup&gt;+&lt;/sup&gt; to a thiol-ester (the key step).&lt;/p&gt;&#xA;&#xA;&lt;pre&gt; E-S-C(R)(H)(OH) + NAD&lt;sup&gt;+&lt;/sup&gt; → E-S-C(=O)(R) + NADH + H&lt;sup&gt;+&lt;/sup&gt; &lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This (enzyme-bound) thiol-ester is a 'high energy' intermediate wherein, it may be envisaged, the free energy of aldehyde oxidation has been 'trapped'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The final step of the GAPDH reaction is now spontaneous (proceeds to the right).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Step 3.&lt;/strong&gt; Attack on the thiol-ester by inorganic phosphate &lt;br/&gt;&lt;br/&gt;(P&lt;sub&gt;i&lt;/sub&gt; is inorganic &lt;em&gt;phosphate&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;E-S-C(=O)(R) + P&lt;sub&gt;i&lt;/sub&gt; → E-SH + R-C(=O)(O-P&lt;sub&gt;i&lt;/sub&gt;)&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Thus, the free energy of NAD&lt;sup&gt;+&lt;/sup&gt;-linked aldehyde oxidation has been 'sequestered' and used to 'drive' the thermodynamically unfavourable phosphorylation of a carboxylic acid, by coupling the two reactions via a ('high energy') thiol-ester: the coupled reaction &lt;em&gt;is a different reaction&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The 'thermodynamic price' is that the GAPDH reaction (unlike NAD&lt;sup&gt;+&lt;/sup&gt;-linked aldehyde oxidation) is freely reversible: the coupled reaction has a &lt;em&gt;different overall equilibrium constant&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As stated above, this is a simplified version of the GAPDH reaction.  The (tetrameric) enzyme contains a tightly bound NAD&lt;sup&gt;+&lt;/sup&gt; for a start, and this needs to be taken account of.  A fuller account may be found in the following reference:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Fersht, Alan. (1999) &lt;em&gt;Structure and Mechanism in Protein Science&lt;/em&gt;, pp 469 - 471, W.H. Freeman &amp;amp; Co. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For a fuller treatment of coupled biochemical reactions, see&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Silbey, R.J. &amp;amp; Alberty, R.A. (2001) Physical Chemistry (3rd Edn) pp 281 - 283.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://books.google.ie/books/about/Cellular_energy_metabolism_and_its_regul.html?id=NpZqAAAAMAAJ&amp;amp;redir_esc=y&quot; rel=&quot;nofollow noreferrer&quot;&gt;Atkinson&lt;/a&gt;, D. E. (1977) Cellular Energy Metabolism and Its Regulation. &#xA;Academic Press, New York&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr/&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Pyruvate kinase&lt;/strong&gt; (EC 2.7.1.40) [see &lt;a href=&quot;http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/7/1/40.&quot; rel=&quot;nofollow noreferrer&quot;&gt;here] &lt;/a&gt;is another great example of a coupled biochemical reaction.  In this case the reaction is almost irreversible in the direction of ATP synthesis! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The standard transformed free energy (&amp;Delta;G&lt;sup&gt;o'&lt;/sup&gt;) for the hydrolysis of phosphoenol-pyruvate (PEP) to pyruvate and phosphate is ~ - 62 kJ/mol.  This represents an equilibrium constant of about 10&lt;sup&gt;10&lt;/sup&gt; in favour of hydrolysis! (see Walsh, quoted below, pp 229-230).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For comparison,  &amp;Delta;G&lt;sup&gt;o'&lt;/sup&gt; for ATP + H&lt;sub&gt;2&lt;/sub&gt;O → ADP + P&lt;sub&gt;i&lt;/sub&gt; is about - 40 kJ/mol.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus the pyruvate kinase reaction may be viewed as a coupled biochemical reaction where the free energy of PEP hydrolysis is coupled to (&lt;em&gt;almost irreversible&lt;/em&gt;) ATP synthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does PEP have such a large negative &amp;Delta;G&lt;sup&gt;o'&lt;/sup&gt;? The enol form of pyruvate does not exist in appreciable quantites in aqueous solution at pH 7 (&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/j100843a015&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pocker &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 1969; &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ja00034a049?journalCode=jacsat&amp;amp;quickLinkVolume=114&amp;amp;quickLinkPage=3081&amp;amp;selectedTab=citation&amp;amp;volume=114&quot; rel=&quot;nofollow noreferrer&quot;&gt;Damitio &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 1992).  PEP may be considered a 'trapped' form of a thermodynamically unstable enol which is released upon hydrolysis, thus 'pulling' the equilibrium to the right. (see &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1016/0307-4412(81)90250-8/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Walsh&lt;/a&gt;, quoted below, p 230, for a more thorough explanation). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally, I have always considered the reaction catalyzed by PK to be pretty amazing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In response to &lt;a href=&quot;https://biology.stackexchange.com/q/57699/1136&quot;&gt;this&lt;/a&gt; question on the standard free energy of hydrolysis of phosphoenolpyruvate (PEP), I'll add the following. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thermodynamically stable form of PEP in solution at 'physiological' pH is the enol form.  That is, the enol from predominates. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;PEP hydrolysis may be formally divided  into two parts: &#xA;(i) the hydrolysis of the phosphate ester to give the enol form of pyruvate,&#xA;followed by (ii) tautomerization to the (thermodynamically stable)  keto form of pyruvate (&lt;a href=&quot;http://pubs.acs.org/doi/pdf/10.1021/ja00034a053&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chiang et al.&lt;/a&gt;, 1992). &#xA;Thus it is the enol form of PEP that predominates in aqueous solution at pH 7, but pyruvate exists predominately in the keto form under similar conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In their in-depth study, &lt;a href=&quot;http://pubs.acs.org/doi/pdf/10.1021/ja00034a053&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chiang&lt;/a&gt; and co-workers attribute 47% of &#xA;the free energy liberated by  the hydrolysis PEP to the ketonization of the enol form of pyruvate, and &#xA;conclude that &quot;nearly half of the high energy content of this molecule resides in its masked  enol function&quot; (And of course, they mean 'high energy' in the &lt;a href=&quot;http://centennial.rucares.org/index.php?page=CoenzymeA&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lipmann&lt;/a&gt; ('&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/9780470122464.ch4/summary&quot; rel=&quot;nofollow noreferrer&quot;&gt;squiggle&lt;/a&gt;') sense, that is PEP has a high standard free energy of hydrolysis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We need to be careful with the following and acknowledge that the language is somewhat loose: we may&#xA;think of PEP as a molecule where the thermodynamically unstable form of &lt;em&gt;pyruvate&lt;/em&gt; (the enol form) &#xA;is 'trapped' in a (thermodynamically stable) phosphate-ester linkage, which will be 'released' on hydrolysis. And to emphasize, the thermodynamically stable form of PEP is the enol form.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;IMO, &lt;a href=&quot;http://pubs.acs.org/doi/pdf/10.1021/ja00034a053&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chiang et al.&lt;/a&gt; (1992) is a very nice paper that rigorously backs up conclusions with strong experimental evidence, but it is surprising that they did not quote &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1016/0307-4412(81)90250-8/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Walsh&lt;/a&gt;&#xA; who (again, IMO) is the first to give the correct explanation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://pubs.acs.org/doi/pdf/10.1021/ja00034a053&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chiang&lt;/a&gt;,Y., Kresge, A. J. &amp;amp; Pruszynski, P. (1992) Keto-Enol Equilibria in the Pyruvic Acid System: Determination of the &#xA;Keto-Enol Equilibrium Constants of Pyruvic Acid and Pyruvate and the &#xA;Acidity Constant of Pyruvate Enol in Aqueous Solution  J. Am. Chem. Soc. 114, 3103-3107&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ja00034a049?journalCode=jacsat&amp;amp;quickLinkVolume=114&amp;amp;quickLinkPage=3081&amp;amp;selectedTab=citation&amp;amp;volume=114&quot; rel=&quot;nofollow noreferrer&quot;&gt;Damitio&lt;/a&gt;, J.,  Smith , G.,  Meany , J. E.,  Pocker, Y. (1992).  A comparative study of the enolization of pyruvate and the reversible dehydration of pyruvate hydrate&#xA;&lt;em&gt;J. Am. Chem. Soc&lt;/em&gt;.,  &lt;strong&gt;114&lt;/strong&gt;, 3081–3087&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/9780470122464.ch4/summary&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lipmann&lt;/a&gt;, F. (1941). Metabolic generation and utilization of phosphate bond energy.  Adv. Enzymol. 1, 99 - 162.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/j100843a015&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pocker&lt;/a&gt;, Y., Meany, J. E., Nist, B. J., &amp;amp;  Zadorojny, C.  (1969) The Reversible Hydration of Pyruvic Acid. I. Equilibrium Studies.  &lt;em&gt;J. Phys. Chem.&lt;/em&gt;&#xA;&lt;strong&gt;76&lt;/strong&gt;, 2879 – 2882. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1016/0307-4412(81)90250-8/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Walsh&lt;/a&gt;, C. (1979) &lt;em&gt;Enzymatic Reaction Mechanisms&lt;/em&gt;.  W.H. Freeman &amp;amp; Co. &#xA;&lt;hr/&gt;&#xA;&lt;strong&gt;Oxidative Phosphorylation&lt;/strong&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Perhaps the most important coupled reaction is that which occurs in &lt;strong&gt;oxidative phosphorylation&lt;/strong&gt; where the oxidation of  fuels via the respiratory redox chain is coupled to  the  'synthesis' of ATP.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have 'steered clear' up to this point, as it is a very complex area and difficult to do justice to in a few lines.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the chemiosmotic theory of oxidative phosphorylation (due primarily to &lt;a href=&quot;http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1978/mitchell.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Peter Mitchell&lt;/a&gt;)  electron transport via the respiratory chain to molecular oxygen creates a proton  gradient across the inner mitochondrial membrane by pumping protons outwards. This proton gradient, or protonmotive force, is used to 'drive' the following  reaction to the right:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;ADP + P&lt;sub&gt;i&lt;/sub&gt; ⇌  ATP + H&lt;sub&gt;2&lt;/sub&gt;O&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This is commonly referred to as 'ATP synthesis' but, more correctly perhaps, it  maintains our coupling agent  &quot;far from equilibrium in terms of some useful conversion&quot; (Atkinson, 1977, p48), that is far from equilibrium in the hydrolysis of ATP.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although all of oxidative phosphorylation may be considered a coupled reaction, all that will be (very briefly) looked at here is the reaction catalyzed by ATP synthase, which may be considered to catalyze the following coupled reaction. &lt;/p&gt;&#xA;&#xA;&lt;pre&gt; ADP + P&lt;sub&gt;i&lt;/sub&gt; + H&lt;sup&gt;+&lt;/sup&gt;(Out) ⇌ ATP + H&lt;sub&gt;2&lt;/sub&gt;O + H&lt;sup&gt;+&lt;/sup&gt;(In)&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This is an example of &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.bi.46.070177.005024?journalCode=biochem&quot; rel=&quot;nofollow noreferrer&quot;&gt;vectorial catalysis&lt;/a&gt;, but it is much more. The ATP synthetase has been described as a &quot;splendid molecular machine&quot; (Boyer, 1997b). &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;It is an example of sequential, cooperative catalysis between 3 active sites where the the release of products (ATP) at one site is dependent on binding of substrates (ADP and P&lt;sub&gt;i&lt;/sub&gt; ) at another. &lt;/li&gt;&#xA;&lt;li&gt;It is an example of indirect conformational coupling where the proton gradient effects the release of of tightly bound ATP by eliciting sequential conformational changes in all active sites . &lt;/li&gt;&#xA;&lt;li&gt;It is an example of a binding-change mechanism, where the proton gradient is responsible release of ATP from the enzyme, but plays no role in its synthesis. &lt;/li&gt;&#xA;&lt;li&gt;Perhaps most dramatically,  it is an example of rotational catalysis, where the indirect rotation of a protein subunit brings about the sequential conformational  changes in the active sites. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Much of the mechanism of ATP synthetase is due to Boyer: this includes the prediction of rotational catalysis and the formulation (and defense) of the binding-change mechanism (see Boyer, 1997a,b). For some nice dynamic diagrams on the mechanism of action, see &lt;a href=&quot;https://biology.stackexchange.com/a/57742/1136&quot;&gt;this SO answer&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps the most important considerations from the standpoint of the present discussion is the subtlety  of the coupling effect or 'mechanistic joining': it is brought about by a conformational change due to rotation of a protein subunit, and it is mediated though the dissociation of ATP from a subunit and not through its 'synthesis' from ADP and P&lt;sub&gt;i&lt;/sub&gt; at an active site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;[Aside] In a most famous experiment, rotary catalysis was 'physically' demonstrated by &lt;a href=&quot;http://www.k2.phys.waseda.ac.jp/Publications.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kinoshita&lt;/a&gt; and  co-workers by attaching an actin filament to the rotating subunit of the enzyme and viewing under a fluorescent microscope (see &lt;a href=&quot;http://www.k2.phys.waseda.ac.jp/PDF/1997Nat_Noji_F1rot.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;), which showed that rotation is anti-clockwise (viewing the enzyme from the 'membrane' side) when the enzyme is hydrolyzing ATP. A nice YouTube video, which seems to be base on the original &lt;a href=&quot;http://www.k2.phys.waseda.ac.jp/PDF/1997Nat_Noji_F1rot.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Noji&lt;/a&gt; experiment, may be found &lt;a href=&quot;https://www.youtube.com/watch?v=0y7n-vK1AJE&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; . &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Abeles, R.H., Frey, P.A. &amp;amp; Jencks, W.P. (1992) &lt;em&gt;Biochemistry&lt;/em&gt;.  Jones &amp;amp; Barlett, Publishers.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Boyer, P. D. (1997a) [Nobel Lecture] &lt;em&gt;Energy, Life, and ATP&lt;/em&gt; (pdf available &lt;a href=&quot;http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1997/boyer-lecture.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Boyer, P. D. (1997b) The ATP Synthase. A splendid molecular machine Annu. Rev. Biochem.  66, 717–749&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Mitchell, P. (1978) [Nobel Lecture] &lt;em&gt;David Keilin's Respiratory Chain Concept and Its Chemiosmotic Consequences&lt;/em&gt; (pdf available &lt;a href=&quot;http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1978/mitchell-lecture.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Walker, J. E. (1997) [Nobel Lecture] &lt;em&gt;ATP Synthesis by Rotary Catalysis&lt;/em&gt; (pdf available  &lt;a href=&quot;http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1997/walker-lecture.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2017-03-31T17:25:14.947" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2904" PostTypeId="1" CreationDate="2012-07-15T13:48:27.750" Score="3" ViewCount="92" Body="&lt;p&gt;The novice often performs population calculations using&#xA;what is referred to as Mendelian Genetics. Soon after the&#xA;publication of Mendel's results; Hardy and Weinberg presented&#xA;their results after the interjection of a collection of axioms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a difference between Medelian genetics and the&#xA;Hardy-Weinberg model?&lt;/p&gt;&#xA;" OwnerDisplayName="Schenectady" LastEditorUserId="57" LastEditDate="2012-07-15T22:30:51.117" LastActivityDate="2012-07-16T07:12:12.363" Title="What's in a Name: Statistical Genetics" Tags="&lt;genetics&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2905" PostTypeId="1" CreationDate="2012-07-16T06:22:46.840" Score="3" ViewCount="808" Body="&lt;p&gt;JMol can be used to identify Hydrogen bonds in proteins by the script &quot;calculate HBONDS&quot;.  By outputting the state of the network, we can obtain a lisdt of H-bonds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's one line from an example output (PDB ID number 1a1x):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;74    540    4096    0.001    -2.507   hbond;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I believe the correct interpretation of the first two numbers is that atom 74 is H-bonded to atom 540.  (I'm not really sure what the other numbers mean.)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;: How can we determine which atom is the donor and which is the acceptor?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the above example, atom 74 is a Nitrogen atom and atom 540 is a Carbon atom, so presumably the Nitrogen atom is the donor.  But, how can we tell in general?&lt;/p&gt;&#xA;" OwnerUserId="203" LastEditorUserId="112" LastEditDate="2012-07-16T11:12:14.827" LastActivityDate="2012-12-16T15:14:16.747" Title="JMol &quot;calculate HBONDS&quot;: which atom is the donor/acceptor?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;structural-biology&gt;&lt;software&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2906" PostTypeId="1" AcceptedAnswerId="2910" CreationDate="2012-07-16T06:37:46.710" Score="10" ViewCount="141" Body="&lt;p&gt;Pretty much what the title states.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some cells/structures in the human body undergo rejuvenation periodically by flushing away older cells and growth of new ones.&#xA;E.g Skin, Blood&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this (for want of a better word) 'rejuvenation' apply to Rods/Cones within the eye too? If so, how are the old cells flushed out - or do the old cells become part of the local humour?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="69" LastEditDate="2012-07-16T10:34:05.700" LastActivityDate="2012-07-16T14:11:26.623" Title="Are rods/cones rejuvenated periodically?" Tags="&lt;eyes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2907" PostTypeId="2" ParentId="2904" CreationDate="2012-07-16T07:12:12.363" Score="4" Body="&lt;p&gt;Mendel published his results 1866 but they were rediscovered only in 1900. The Hardy-Weinberg model is an application of Mendel's rules to a population that is not under selection forces. So the one builds on the other, and Hardy-Weinberg is a simplification model-wise, and Mendel's rules are not detailed enough either. It's the same relation as with a physical law like gravitation and a mathematical model of its consequences applied on many entities, like models of a solar system's gravitational behaviour.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-07-16T07:12:12.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2908" PostTypeId="2" ParentId="2897" CreationDate="2012-07-16T11:16:20.577" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://www.timetree.org/&quot;&gt;TimeTree&lt;/a&gt; gives you an estimate for time of divergence, which is also nice to know. But of course different species have different rates of evolution.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-07-16T11:16:20.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2909" PostTypeId="1" CreationDate="2012-07-16T12:39:45.293" Score="7" ViewCount="1194" Body="&lt;p&gt;With a lack of mitochondria, can red blood cells perform intrinsic apoptosis and do they have another way of generating cytochrome c to attach to a CARD domain and assemble the apoptosome?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or are they dependent on killer lymphocytes to bind via the fas ligand and activate procaspase 8 or 10 in extrinsic apoptosis? Do red blood cells even have fas ligand receptors for this process?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is there an entirely different method for red blood cells?&lt;/p&gt;&#xA;" OwnerUserId="1083" LastActivityDate="2017-09-15T08:54:21.900" Title="Intrinsic apoptosis in erythrocytes" Tags="&lt;cell-biology&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2910" PostTypeId="2" ParentId="2906" CreationDate="2012-07-16T14:00:58.553" Score="9" Body="&lt;p&gt;The answer can be found in the excellent lecture from 1983 &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1312450/&quot;&gt;&lt;em&gt;The Life History of Retinal Cells&lt;/em&gt;&lt;/a&gt; which also has gorgeous microscope fotos. The renewal time of rod outer membrane proteins is less than two weeks. Cells stay indefinitely, as I understand, but are periodically rebuilt in a logistical nightmare/wonder.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-07-16T14:11:26.623" LastActivityDate="2012-07-16T14:11:26.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2911" PostTypeId="1" CreationDate="2012-07-16T14:29:53.783" Score="5" ViewCount="1910" Body="&lt;p&gt;This post is regarding a follow up on my initial post on &quot;Properties and life cycle of chondrocytes and tenocytes&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am elaborating on my question on the lifespan of tenocytes and chondrocytes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I have read, tenocytes and chondrocytes form from mature stem cells, more specifically Mesenchymal stem cells. These cells can replicate through mitosis, and are present in the body in different tissues like bone marrow. These cells are the key in the regeneration of diverse tissues. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the cells that inhabit tendons or cartilage die, do new MS cells travel to the tendon or cartilage area and diffentiate into a new tenocyte or chondrocyte? Are tenocytes and chondrocytes continuously replaced?&lt;/p&gt;&#xA;" OwnerUserId="952" LastEditorUserId="630" LastEditDate="2019-06-17T21:02:31.557" LastActivityDate="2019-06-17T21:02:31.557" Title="Lifespan of connective tissue cells" Tags="&lt;cell-biology&gt;&lt;tendons&gt;&lt;cartilage&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2912" PostTypeId="1" CreationDate="2012-07-16T15:53:13.990" Score="3" ViewCount="906" Body="&lt;p&gt;I tried to make the probe several times but it failed again and again. It usually turns out that the probe after hydrolysis is very very short (maybe around 50nt). I did not check the RNA before hydrolysis except last time. However, I saw a band (though very weak) last time, but it still produce very very short probe after hydrolysis.I use Sp6 polymerase to synthesize RNA, and the original length of the DNA is 1.5kb. My expected length after hydrolysis is 500nt. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm guessing maybe it's the phenol contamination of the phenol:chloroform extraction step because my 260/280 value is low (around 1.6-1.7), and my 260/230 is also low, which is like 1.6-1.8. Also the peak is not at 260, it's almost at 270.&lt;/p&gt;&#xA;" OwnerUserId="1141" LastEditorUserId="3340" LastEditDate="2014-02-19T10:50:29.807" LastActivityDate="2014-02-19T10:50:29.807" Title="How do I create a probe for in situ hybridization?" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2913" PostTypeId="1" AcceptedAnswerId="2914" CreationDate="2012-07-17T10:40:38.597" Score="3" ViewCount="105" Body="&lt;p&gt;I read in New Scientist recently that microchimerism occurs between previously born siblings and grandparents, not just the mother.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do we know which parts of the genome are likely to be transferred? Is it possible, given a genetic sample of relatives, to predict which genetic traits might be transferred by microchimerism?&lt;/p&gt;&#xA;" OwnerUserId="172" LastActivityDate="2012-07-20T08:02:28.433" Title="Predictable microchimerism" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;reproduction&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2914" PostTypeId="2" ParentId="2913" CreationDate="2012-07-17T11:04:07.227" Score="2" Body="&lt;p&gt;Microchimerism, as defined by wiki, is the presence of a small number of cells in an organism that are genetically distinct, and originated from a separate organism. The example they give is an unborn child and the mother can 'swap' immune cells, and retain these for many years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question about which parts of the genome are transferred is therefore not really valid, because the cells are transferred, rather than bits of genetic information. Therefore 'traits' are not transferred either, but distinct immune cell lineages can be transferred and persist - this can confer an immune advantage, so this 'trait' could be said to have transferred, but no genetic information has been swapped by the cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although it does not say it on wiki, this presumably only applies to cells of the same species, but a different organism, otherwise infections would also count.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h3&gt;Update 20th July 2012&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;The New Scientist article you have linked to in the comments can be found online &lt;a href=&quot;http://www.newscientist.com/article/mg21428695.100-you-may-carry-cells-from-siblings-aunts-and-uncles.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It says that we may be more microchimeric than we imagined, because a recent study in Blood found that half of the mothers studied were positive for male T-cells (&lt;a href=&quot;http://dx.doi.org/10.1182/blood-2012-02-410571&quot; rel=&quot;nofollow&quot;&gt;Dierselhuis, 2012&lt;/a&gt;). The authors note that it is remarkable that the immune cells from neither the parent or the offspring attack the other, and that this may explain the observation that siblings make better donors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another finding that mothers are found positive for cells from their own mothers, and even their own grandmothers, and that the cell numbers increase during pregnancy (due to clonal expansion of the inherited immune cells) reinforces the opinion that microchimerism is commonplace (&lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0024101&quot; rel=&quot;nofollow&quot;&gt;Gammill, 2011&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to reiterate, immune cells can be inherited from your mother, and she may also end up with leukocytes from her offspring, which can in turn be passed on. This is a very fascinating way in which the immune system seems even more complex and helpful.&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-07-20T08:02:28.433" LastActivityDate="2012-07-20T08:02:28.433" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="2915" PostTypeId="1" AcceptedAnswerId="15772" CreationDate="2012-07-17T11:33:52.213" Score="4" ViewCount="2854" Body="&lt;p&gt;I would like to do a quick freeze on pancreas from mice. I want to then make sections (30 µm thick).  The idea is to preserve a fluorescent staining done &lt;em&gt;in vivo&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not know if I should place my fresh tissue directly into liquid nitrogen, then embed the tissue in OCT, and then freeze everything in cold isopentane? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or do I have to embed the fresh tissue in OCT first, prior to putting everything in nitrogen?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is there another protocol to do quick freezing in order to do sectioning?&lt;/p&gt;&#xA;" OwnerUserId="126" LastEditorUserId="5144" LastEditDate="2014-03-16T21:59:30.523" LastActivityDate="2014-03-17T03:19:35.960" Title="What is the proper quick freezing /snap freezing protocol for pancreatic tissue?" Tags="&lt;histology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2916" PostTypeId="1" AcceptedAnswerId="2917" CreationDate="2012-07-17T21:05:14.873" Score="9" ViewCount="259" Body="&lt;p&gt;I am trying to understand the Y2H screening method. I can understand how we can check if two specific proteins interact with each other. For example, if we want to check whether protein A and protein B interact, we fuse A with the Activation Domain (AD) of a transcription factor and B with the Binding Domain (BD) of another transcription factor. When the two fusion proteins are transfected into a yeast cell, the reporter gene is expressed only if the AD and the BD get together and form a complete transcription factor and that happens only if proteins A and B interact with each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I have seen claims that Y2H is a high throughput system, i.e., it can be used to detect several interactions at once. But most articles online that attempt to describe it, seem vague to me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, suppose I fuse the &quot;bait&quot; protein to the BD and several different cDNA's to the AD and let the yeast grow. Next, I observe that the reporter gene is expressed. Doesn't this observation only imply that there exists some protein from the cDNA library that interacts with our bait protein? How do we know exactly which of the target proteins have interacted with the bait and resulted in the expression of the reporter gene?&lt;/p&gt;&#xA;" OwnerUserId="485" LastActivityDate="2012-07-18T00:05:28.887" Title="How does Yeast-two-hybrid detect interactions between several proteins in one experiment?" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2917" PostTypeId="2" ParentId="2916" CreationDate="2012-07-18T00:05:28.887" Score="10" Body="&lt;p&gt;You use a library of many yeast in which each expresses only one target, or 'prey' protein. Then you grow each yeast colony separately, for example in different wells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's definitely not a high-throughput method if you do it the old-fashioned way, i.e. making your own yeast library, or if you do it with only a few targets.  But these days you can buy pre-made yeast libraries with thousands of target proteins, each separated into a well on a plate, then you run the experiment for all the targets simultaneously. With a visible marker you can then easily see which wells have produced successful interactions, and thus which targets interacted with your bait.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-07-18T00:05:28.887" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2919" PostTypeId="1" CreationDate="2012-07-18T11:12:33.993" Score="10" ViewCount="1502" Body="&lt;p&gt;The human body can repair skin/organ laceration, fractures, even repair nerves - albeit the duration and rate of recovery differ. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why can the heart muscles not repair themselves?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="16866" LastEditDate="2017-04-13T03:56:18.717" LastActivityDate="2017-04-13T03:56:18.717" Title="Why is the human body able to repair a broken bone and not a heart muscle?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;&lt;healing&gt;" AnswerCount="5" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2921" PostTypeId="2" ParentId="2919" CreationDate="2012-07-18T15:46:46.533" Score="5" Body="&lt;p&gt;Part of the answer may be(*) that in bone, you have still stem cells everywhere (blood capillaries that grow until checked and osteoblasts), i.e., also in the vicinity of the wound. The same applies to skin, by the way, where the epidermis continues to produce skin layers until eternity. This facilitates repair enormously, as new cells won't have to move far to take their place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Contrast this with heart or spinal cord, where the placement of the cells took place in early development when distances were small and most cells were undifferentiated. Also, no tissue like epidermis was left in the vicinity that could act as a near source of new cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(*) I said &quot;may be&quot; because 1. I have no ref for this, and 2. I have no idea to what extent other factors are involved. I would be thankful for counterexamples.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-07-18T15:46:46.533" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2922" PostTypeId="1" AcceptedAnswerId="23217" CreationDate="2012-07-18T20:29:22.023" Score="9" ViewCount="944" Body="&lt;p&gt;I know that the non-steroidal anti-inflammatory drugs (e.g., aspirin, ibuprofen, naproxen) affect the enzymes cyclooxygenase (types I and II).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any difference in the degree to which these drugs manipulate/inhibit the enzymes (I assume their affinities for COX-1 and COX-2 are at least somewhat different)?  Is there any evidence as to whether the the NSAIDs collect in certain areas of the body in a compartmental fashion?&#xA;Are there differences in fat solubility, etc., between the different drugs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, are there any known phenotypes of COX-1 and COX-2 enzymes that are present in the general population that affect the ability of these drugs to act? &lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="86" LastEditDate="2014-10-18T11:06:30.213" LastActivityDate="2014-10-18T11:10:21.293" Title="How do the pharmacodynamics of the NSAIDs differ and are there &quot;resistant&quot; COX phenotypes?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;pharmacology&gt;&lt;human-genetics&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2923" PostTypeId="2" ParentId="2055" CreationDate="2012-07-18T22:30:12.053" Score="22" Body="&lt;p&gt;I've been doing some reading, and have come up with the following interesting information.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Telomeres&quot; rel=&quot;nofollow noreferrer&quot;&gt;Telomeres&lt;/a&gt;&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;During cell division the DNA is replicated, but the mechanism is imperfect and in each round of cell division a small section is lost from the end of each chromosome. To compensate and protect the genetic information there are caps – regions of excess nucleotides – at the ends called telomeres (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22759812&quot; rel=&quot;nofollow noreferrer&quot;&gt;Silvestre, 2012&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mammalian cells do not replenish their telomeres after cell division, giving them a replicative lifespan;  a maximum number of cell divisions before the telomeres run out. The cells then either enter a state of senescence and no longer divide, or initiate programmed cell death. However each cell has the genetic information for telomerase – the enzyme that can replenish the telomeres – but cannot use it. Only embryos and stem cells are able to express telomerase in mammalian cells - this protects against the build up of damage to DNA causing uncontrolled cell cycle progression. Activated telomerase is a core feature of many cancers (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22341437&quot; rel=&quot;nofollow noreferrer&quot;&gt;Campbell, 2012&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Plant Telomeres&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;You mention telomeres in your question, and it is an interesting question I had never considered. Plants have no germline preserved, so their progeny must bear all the defects of their particular parent cell, and that plant cells must therefore all have the capacity to regenerate their telomeres. I found a paper by Fajkus and colleagues that finds telomerase activity in plant cuttings grown in culture (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9894917&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fajkus, 1998&lt;/a&gt;). Their hypothetical Plant Telomere-Length Regulating (PTLR) protein must arise in the early stages of the culture and last only a few cycles. Interestingly it seems that the efficiency of this process varies between different plant species. The authors note that their plant of choice – tobacco – is particularly proliferative and that other plants such as barley were harder to grow from cuttings, which may be down to a different way of regulating the telomerase (for instance it could only be activated occasionally at low amounts).&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Do Plants Get Cancer?&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;It seems to me the next obvious question. One of the first papers I came across (published in 1916 by the Journal of Cancer Research!) talks of Crown Gall in plants and its relation to human cancer (&lt;a href=&quot;http://cancerres.aacrjournals.org/content/jcanres/1/2/231.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Smith, 1916&lt;/a&gt;). Many websites cite galls as being the equivalent to cancer in plants, but it appears that the outgrowths (galls) that appear very tumour-like are in fact caused by bacteria encouraging their surrounding cells to proliferate. (See &lt;a href=&quot;https://biology.stackexchange.com/questions/761/how-do-galls-form&quot;&gt;this question&lt;/a&gt; for more detail on galls).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I later found an abstract (I cannot access the full paper) from a paper published in Nature in 2010 called “Walls around tumours — why plants do not develop cancer” (&lt;a href=&quot;http://dx.doi.org/10.1038/nrc2942&quot; rel=&quot;nofollow noreferrer&quot;&gt;Doonan, 2010&lt;/a&gt;). It appears that Plants can and do develop tumours, but they are less frequent and less lethal due to fundamental differences in development between plant and animal cells. Singh and colleagues found that in 2 plant species (&lt;em&gt;Arabidopsis&lt;/em&gt; and rice) there were DNA damage repair pathways well conserved but with variation; there were several gene duplications in different DNA repair pathways (&lt;a href=&quot;http://dx.doi.org/10.1186/1471-2164-11-443&quot; rel=&quot;nofollow noreferrer&quot;&gt;Singh, 2010&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Plants Do Not “Age” As We Do&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Although I could find no conclusive evidence, it seems to me likely that plants may also have enhanced maintenance against other cellular stresses than DNA damage, such as build-ups of aberrant proteins. It therefore appears that in a protected environment some plants could live indefinitely. I say some, because others deliberately end their lives after reproduction. Traits such as longevity are inherently hard to be selected for, as the advantages come long after reproductive maturity and are therefore under much less selective pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We see plants wither and die, but this is because they are constantly subject to environmental insult. Animals and insects may eat them, there may not be enough food or water, or sunlight, or the plant may become infected. All of which are at the macroscopic level. Due to completely different evolutionary constraints and pressures plants are highly resilient to cellar stresses, possibly due to differences in metabolic rate, and apparently have indefinite replicative potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt;&#xA;Although the more I think about it, the more it seems that most plant must have an ultimate lifespan, in that as they forever grow and expand their tissues would gradually harden and become less functional (I am mostly imagining bark plants here). Although as the layers of bark are pushed out the layers below take the place. In this way a tree could possibly live indefinitely by continuously remodelling it's layers.&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2012-07-19T08:51:01.493" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2924" PostTypeId="1" AcceptedAnswerId="2932" CreationDate="2012-07-18T23:54:18.530" Score="7" ViewCount="131" Body="&lt;p&gt;Is it possible to sequence rRNA directly, that is, using the ribosome rather than the DNA from the nucleus? For example, this paper, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC336208/&quot;&gt;Complete nucleotide sequence of a 16s rRNA gene from E. coli&lt;/a&gt;,  suggests that it uses DNA to find the sequence. Would it be possible to isolate the rRNA and derive the sequence from that?&lt;/p&gt;&#xA;" OwnerUserId="1051" LastActivityDate="2019-01-21T08:58:14.067" Title="Sequence of ribosomal RNA" Tags="&lt;dna-sequencing&gt;&lt;rna-sequencing&gt;&lt;ribosome&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2925" PostTypeId="2" ParentId="2705" CreationDate="2012-07-19T03:10:19.423" Score="3" Body="&lt;p&gt;The story of the ability to interbreed is even more complicated than the ambiguity posed by horses, donkeys, lions and tigers. In California and Mexico, there are a series of species of lizards which form a geographical 'horseshoe'. Neighboring lizards can interbreed, but species at either end of the horseshoe cannot breed. In other words, lizards at the ends of the horseshoe are clearly of different species, but any pair of geographically close groups of lizards can be argued to be the same species. There's no place to draw the line to say where one species ends, and the next begins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that this lies at the heart of the question... the concept of a species is an artificial construct. By and large, there are large enough separations of space and time that the lines are easy to draw, but during the split, the lines are in no way clear.&lt;/p&gt;&#xA;" OwnerUserId="1153" LastActivityDate="2012-07-19T03:10:19.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2926" PostTypeId="1" CreationDate="2012-07-19T06:27:09.200" Score="5" ViewCount="1862" Body="&lt;p&gt;This days I read some debates on evolution. That made me more interested to read something reliable on topic - I mean books. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm christian - although I think it doesn't matter on that topic - and I would like to read a book that presents all weaknesses and strengths (as much as possible) of evolution. I want that not to be presented as a debate on creationism, but to be a book on evolution theory explanation and presentation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also would appreciate if you know to give some details about the author that wrote the recommended book. I mean if he/she is atheist or a christian or a skeptic. &lt;/p&gt;&#xA;" OwnerUserId="1154" LastEditorUserId="6" LastEditDate="2012-07-19T14:07:37.087" LastActivityDate="2015-02-18T01:08:52.683" Title="Introductory books about evolution" Tags="&lt;evolution&gt;" AnswerCount="7" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2927" PostTypeId="2" ParentId="2926" CreationDate="2012-07-19T07:02:10.863" Score="18" Body="&lt;p&gt;You won't find a good book that presents the 'weaknesses' of the theory of evolution, and for good reason. There has to date been no convincing challenge to the theory, whilst it has been supported by experimental and circumstantial evidence as well as clear logic over and over and over again, as well as actually being observed taking place numerous times. The closest to what looking for is a book which presents our best understanding of how evolution works, or which discusses competing ideas about &lt;em&gt;how&lt;/em&gt; evolution works - there's no question about whether it works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Selfish Gene by Richard Dawkins, whilst it contains some errors, has some very clear thinking about evolution in it, and in particular explains why group selection is a misguided idea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Logic of Chance: The Nature and Origin of Biological Evolution by Eugene Koonin is a more up-to-date coverage of our current understanding of evolution, in particular with insights from modern genomics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are plenty of terrible books about the weaknesses of evolution, but they are deeply flawed. Pick one and I'll be happy to debunk it for you.&lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-07-19T07:13:04.937" LastActivityDate="2012-07-19T07:13:04.937" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2928" PostTypeId="2" ParentId="2926" CreationDate="2012-07-19T11:25:08.383" Score="11" Body="&lt;p&gt;Almost anything by &lt;a href=&quot;http://www.amazon.com/Richard-Dawkins/e/B000AQ3RBI&quot;&gt;Richard Dawkins&lt;/a&gt; would be excellent value. I especially like his &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0393316823&quot;&gt;Climbing Mount Improbable&lt;/a&gt; as a short but gripping account of why evolution can achieve such astoundingly complex results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Richard Dawkins&lt;/strong&gt; (from my link above)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Richard Dawkins taught zoology at the University of California at Berkeley and at Oxford University and is now the Charles Simonyi Professor of the Public Understanding of Science at Oxford.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;He is definitely an atheist.&lt;/p&gt;&#xA;" OwnerUserId="1156" LastActivityDate="2012-07-19T11:25:08.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2929" PostTypeId="2" ParentId="2926" CreationDate="2012-07-19T12:20:02.450" Score="7" Body="&lt;p&gt;Another book by Dawkins which I find quite excellent is &lt;a href=&quot;http://www.amazon.co.uk/The-Greatest-Show-Earth-Evolution/dp/055277524X&quot;&gt;&lt;em&gt;The Greatest Show on Earth&lt;/em&gt;&lt;/a&gt;. Unfortunately, you might find it a bit preachy in episodes since Dawkins gets – rightfully! – exasperated with some vocal, stupid critics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nevertheless, it’s a very compelling and interesting read, especially since it tackles some very complementary avenues of evidence for evolution. A similar outline is followed by Sean B. Carroll in &lt;a href=&quot;http://www.amazon.co.uk/The-Making-Fittest-Ultimate-Evolution/dp/1847247245&quot;&gt;&lt;em&gt;The Making of the Fittest&lt;/em&gt;&lt;/a&gt; although he clearly focuses on the most compelling evidence for evolution: DNA – hence the subtitle: “DNA and the Ultimate Forensic Record of Evolution”.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have no idea whether Carroll is religious or atheist – but shouldn’t that be strictly irrelevant?&lt;/p&gt;&#xA;" OwnerUserId="166" LastActivityDate="2012-07-19T12:20:02.450" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2930" PostTypeId="2" ParentId="2926" CreationDate="2012-07-19T16:47:34.240" Score="9" Body="&lt;p&gt;Two recommendations:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1 - The Origin of Species by Charles Darwin.  This is a very accessible book, filled with clear explanations and examples, and conveys the wealth of evidence that Darwin collected as he developed his theory.  It includes a chapter on issues that people might see as &quot;weaknesses&quot;, and convincing explanations as to why they are not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Darwin began life as a Unitarian, and considered a career as a minister.  By the end of his life he had no belief in God.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2 - The Blind Watchmaker by Richard Dawkins, mentioned several times above.&lt;/p&gt;&#xA;" OwnerUserId="1157" LastActivityDate="2012-07-19T16:47:34.240" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2931" PostTypeId="1" AcceptedAnswerId="2947" CreationDate="2012-07-19T18:20:55.137" Score="10" ViewCount="269" Body="&lt;p&gt;Going by the assumption that stress eventually triggers a flight/fight response, and the subsequent realization that flight/fight puts the body in a system of readiness to use it's available resources (mental, physical).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it make sense to think that stress physically ages a person? I am specifically referring to characteristics identified with aging such as  bleached hair, telomere shortening, wrinkles around the eyes, etc.&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorDisplayName="user560" LastEditDate="2012-11-02T21:43:16.467" LastActivityDate="2012-11-02T21:43:16.467" Title="Does stress physically age our body?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2932" PostTypeId="2" ParentId="2924" CreationDate="2012-07-19T19:12:33.010" Score="0" Body="&lt;p&gt;As far as I know it'spossible to reverse transcribe a rRNA gene, you may not get the best yields though.  The secondary / tertiary structures will be a problem, however, there are reverse transcriptase's commercially available that can handle secondary structure: Thermo-X™ Reverse Transcriptase from Invitrogen or Sensiscript™ from Qiagen.  &lt;/p&gt;&#xA;" OwnerUserId="12" LastActivityDate="2012-07-19T19:12:33.010" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2934" PostTypeId="1" AcceptedAnswerId="2964" CreationDate="2012-07-19T19:59:32.480" Score="25" ViewCount="18071" Body="&lt;p&gt;Is there any evolutionary reason for glucose being the &quot;main&quot; molecule used as a source of energy, beginning with glycolysis and subsequently cellular respiration (after being converted to two pyruvate molecules)? Or did this particular biochemical pathway arise &quot;by fluke&quot; early on in the history of life?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A colleague of mine told me that it was because as shown below, all of beta-D-glucose's hydroxyl substituents are all equatorially positioned (when in the correct chair conformation), which lends to its general stability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4I3b7.png&quot; alt=&quot;Beta-D-Glucose&quot;&gt;&#xA;Image taken from &lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/thumb/b/bb/Beta-D-Glucose.svg/620px-Beta-D-Glucose.svg.png&quot; rel=&quot;noreferrer&quot;&gt;the Wikimedia Commons&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could this have played a factor in the beginnings of energy metabolism, and if so, why? &lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="561" LastEditDate="2013-10-23T18:55:22.617" LastActivityDate="2018-01-23T18:00:49.807" Title="Why is glucose our primary source of energy?" Tags="&lt;evolution&gt;&lt;biochemistry&gt;&lt;metabolism&gt;&lt;glucose&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2935" PostTypeId="1" CreationDate="2012-07-19T20:08:33.983" Score="17" ViewCount="56282" Body="&lt;p&gt;The question is rather straight forward: I have always been curious as to why, but cannot find an explanation online.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can imagine that the mechanism is different for each, but &lt;strong&gt;why does brain tissue and red blood cells use specifically and only glucose for energy metabolism?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2015-06-10T02:11:03.623" Title="Why can't the brain and red blood cells use fuels other than glucose?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2936" PostTypeId="1" CreationDate="2012-07-19T20:20:53.853" Score="1" ViewCount="711" Body="&lt;p&gt;I find it interesting that all life on earth use DNA. I've seen video on how helicase and ribosomes work together to copy DNA sequences (to RNA) with helicase then recreate them using ribosomes. Does this process work the same way in the simplest life forms? Bacteria and other unicellular life that reproduce through mitosis, for example?&lt;/p&gt;&#xA;" OwnerUserId="1083" LastEditorUserId="166" LastEditDate="2012-07-20T12:50:52.020" LastActivityDate="2012-07-20T16:52:48.080" Title="Do the simplest bacteria have ribosomes and helicase?" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2937" PostTypeId="1" AcceptedAnswerId="2960" CreationDate="2012-07-19T20:25:29.063" Score="12" ViewCount="3260" Body="&lt;p&gt;Why are insects so energy-efficient while flying? Is it because of their light weight and aerodynamics or due to very efficient biochemical transformations (food-&gt;energy)?&lt;/p&gt;&#xA;" OwnerUserId="1158" LastActivityDate="2012-07-21T17:33:32.103" Title="Why insects are so energy-efficient while flying?" Tags="&lt;biochemistry&gt;&lt;entomology&gt;&lt;flight&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2939" PostTypeId="2" ParentId="2937" CreationDate="2012-07-19T20:37:02.373" Score="10" Body="&lt;p&gt;The smaller an animal is the easier it becomes for it to fly. That is because surface area increases to the second power of the diameter of the animal whereas mass increases to the third. So the larger a thing is the more mass per surface are it has.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And since insects tend to be small they tend to be good at flying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for any other reason, I don't think insects are any more energy efficient than say, birds.&lt;/p&gt;&#xA;" OwnerUserId="542" LastEditorUserId="542" LastEditDate="2012-07-20T20:10:18.060" LastActivityDate="2012-07-20T20:10:18.060" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="2941" PostTypeId="2" ParentId="1054" CreationDate="2012-07-19T21:14:04.177" Score="5" Body="&lt;h2&gt;Answer&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Fingerprint pattern formation has two components to it: developmental and genetic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, &lt;a href=&quot;http://iopscience.iop.org/0295-5075/68/1/141&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;'s abstract describes how fingerprints are physically formed in the womb.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] fingerprint patterns are created as the result of a buckling instability in the basal cell layer of the fetal epidermis. Analysis of the well-known von Karman equations informs us that the buckling direction is perpendicular to the direction of greatest stress in the basal layer. We propose that this stress is induced by resistance of furrows and creases to the differential growth of the basal layer and regression of the volar pads during the time of ridge formation. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also, &lt;a href=&quot;http://omim.org/entry/125590&quot; rel=&quot;nofollow&quot;&gt;this OMIM entry&lt;/a&gt; describes a study which suggests the function of genes directly related to fingerprint formation. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An assumption is that the basic pattern is all ulnar loops and that a variety of genes cause deviations from the basic pattern. These include (1) a semidominant gene for whorls on the thumbs (one homozygote has whorls on both thumbs, the other homozygote has ulnar loops on both thumbs, and the heterozygote has two ulnar loops or one ulnar loop and one whorl); (2) a semidominant gene for whorls on the ring fingers that acts like the gene for whorls on the thumbs; (3) a dominant gene for arches on the thumbs and often on other fingers; (4) one or more dominant genes for arches on the fingers; (5) a dominant gene for whorls on all fingers except for an ulnar loop on the middle finger; (6) a dominant gene for radial loops on the index fingers, frequently associated with an arch on the middle fingers; and (7) a recessive gene for radial loops on the ring and little fingers. They suggested that these genes may act independently or epistatically.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The first source explains why everyone has different fingerprints, but the second explains why family members and identical twins have increasingly similar patterns.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Kücken, M, and A. C Newell. “A Model for Fingerprint Formation.” Europhysics Letters (EPL) 68, no. 1 (October 2004): 141–146.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Slatis, H M, M B Katznelson, and B Bonné-Tamir. “The Inheritance of Fingerprint Patterns.” American Journal of Human Genetics 28, no. 3 (May 1976): 280–289.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-08-12T19:32:32.950" LastActivityDate="2012-08-12T19:32:32.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2942" PostTypeId="1" AcceptedAnswerId="2950" CreationDate="2012-07-19T21:35:58.033" Score="11" ViewCount="386" Body="&lt;p&gt;The Murchison meteorite is an important piece of evidence for abiogenesis, because it contained nucleobases from extraterrestrial origin, as &lt;a href=&quot;http://en.wikipedia.org/wiki/Murchison_meteorite&quot;&gt;this Wikipedia article&lt;/a&gt; explains.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These results demonstrate that many organic compounds which are components of life on Earth, were already present in the early solar system and may have played a key role in life's origin.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My question is: &lt;strong&gt;How did these nucleobases arise? Is it possible for these nucleobases to have been synthesized naturally from simpler molecules in a specific environment, like in the Miller-Urey experiment for amino acids?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-07-20T13:23:22.807" LastActivityDate="2014-10-09T15:43:43.937" Title="How did the nucleobases in the Murchison meteorite form?" Tags="&lt;abiogenesis&gt;&lt;astrobiology&gt;" AnswerCount="2" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="2943" PostTypeId="2" ParentId="2935" CreationDate="2012-07-19T22:49:18.327" Score="8" Body="&lt;p&gt;The brain and heart &lt;em&gt;can&lt;/em&gt; take advantage of &lt;a href=&quot;http://en.wikipedia.org/wiki/Ketone_bodies&quot;&gt;ketone bodies&lt;/a&gt; when the amount of glucose is low.  These are byproducts of fat metabolism and can be converted to acetyl-coA via the citric acid cycle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overproduction of these products can cause pathological conditions:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When the rate of synthesis of ketone bodies exceeds the rate of utilization ,their concentration in blood increases , this is known as ketonemia. This is followed by ketonuria- excretion of ketone bodies in urine. The overall picture of ketonemia and ketouria is commonly referred as ketosis. Smell of acetone in breath is a common feature in ketosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="57" LastActivityDate="2012-07-19T22:49:18.327" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2944" PostTypeId="1" AcceptedAnswerId="44228" CreationDate="2012-07-20T03:08:52.007" Score="10" ViewCount="1497" Body="&lt;p&gt;I am somewhat new to evolutionary biology, having studied it on my free time as a computer science student.  There is one particular thing that has always bothered me for which I have not seen a good treatment, relating to adaptations to the environment with respect to genetic diversity.  If it is possible for a population to adapt to rapid environmental changes, and they don't have an adaptation for dealing with change directly (such as a complex brain), it seems to me that every generation must have present within them almost every possible environmental adaptation that the population is capable of expressing (including many irrelevant ones and a few relevant to the particular environmental challenge).  Otherwise, it may take too many generations to deal with a change, which may be disastrous for the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question would be: how does an evolutionary biologist explain the mechanics behind the ability for a population to adapt quickly?  Are most environmental changes slow or gradual enough that the population has a few generations to happen upon the mutations that will allow it to survive, and have generally been successful in this regard for 3.5 billion years?  Or, are a large majority of possible adaptations present in almost every generation, and just serve no purpose or advantage for most of the population if the provided &quot;benefit&quot; is unneeded (i.e., are effectively neutral)?  Or something in between?&lt;/p&gt;&#xA;" OwnerUserId="1161" LastEditorUserId="1590" LastEditDate="2016-03-15T06:38:21.287" LastActivityDate="2016-03-23T18:50:51.087" Title="Genetic Diversity and Adaptation" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;population-dynamics&gt;&lt;adaptation&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2945" PostTypeId="2" ParentId="2926" CreationDate="2012-07-20T03:34:05.727" Score="7" Body="&lt;p&gt;Evolution is only fun when it is used to try to explain something. So to depart from the theme of Dawkins-books, consider:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0307277453&quot;&gt;Your Inner Fish&lt;/a&gt; by &lt;a href=&quot;http://pondside.uchicago.edu/oba/faculty/shubin_n.html&quot;&gt;Neil Shubin&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Shub is a Professor of Organismal Biology and Anatomy, Associate Dean of Organismal Biology and Anatomy and Professor on the Committee of Evolutionary Biology at the University of Chicago. He is famous for disocovering the &lt;a href=&quot;http://en.wikipedia.org/wiki/Tiktaalik_roseae&quot;&gt;&lt;em&gt;Tiktaalik roseae&lt;/em&gt;&lt;/a&gt; or 'fish-with-hands'. The reason the book is fun is that it not only explains the basics of evolution, it uses it to show you something: why the human body is the way it is.&lt;/p&gt;&#xA;" OwnerUserId="500" LastActivityDate="2012-07-20T03:34:05.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2946" PostTypeId="1" AcceptedAnswerId="21027" CreationDate="2012-07-20T12:14:13.853" Score="4" ViewCount="174" Body="&lt;p&gt;In the mid 2000s in the US, due to issues of drug enforcement, pseudoephedrine containing medications were brought behind the pharmacy counter and in most cases require ID, and phenylephrine was substituted in most over-the-counter products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pseudoephedrine increases the amount of endogenous norepinephrine, whereas phenylephrine works on α1-adrenergic receptors directly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are numerous cases where &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenylephrine#Questions_about_effectiveness&quot; rel=&quot;nofollow&quot;&gt;experts&lt;/a&gt; have spoken out about the effectiveness of phenylephrine, so it likely is a less effective substitute for pseudoephedrine in its main role as a decongestant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm curious about is whether there are clinical indications for which the phenylephrine is actually preferred (so situations where the α1-agonist nature without the increase of endogenous NE is sought after)?    &lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2014-09-04T17:40:44.233" Title="Are there any situations in which phenylephrine is preferred to pseudoephedrine?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2947" PostTypeId="2" ParentId="2931" CreationDate="2012-07-20T14:18:54.630" Score="4" Body="&lt;p&gt;The fight/flight situation, through activation of the sympathetic part of the autonomous nerve system, leads to secretion of catechol amines, i.e. adrenaline and noradrenaline. The effects of these hormones, if excreted continously or without real resting time, are thought to be bad for your health. If you recall the possible effects of those two substances (which are both similar to amphetamine, by the way), and look at what big studies have found about the impact of high blood pressure then you know the most important negative effect of stress, IMHO.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sympathetic_nervous_system&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Sympathetic_nervous_system&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-07-20T15:10:53.447" LastActivityDate="2012-07-20T15:10:53.447" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2948" PostTypeId="2" ParentId="2942" CreationDate="2012-07-20T14:25:17.357" Score="5" Body="&lt;p&gt;I think it's fair to say that we don't really know how these more complex organic molecules formed abiotically, but we can say that carbonaceous chondrites - a class of carbon and organic molecule bearing meteorites to which Murchison belongs (specifically CM2) - have experienced at least three distinct chemical histories:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;In the interstellar medium (ISM) in cool (10 - 30 K), dense clouds where cold gas phase chemistry can lead to the formation of species such as HCN, C₂O₂ and CO.Polycyclic aromatic hydrocarbons (PAHs) have also be identified here.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In the early solar nebula. These simple organics can stick to dust grains forming &quot;tarballs&quot;. The ultraviolet radiation field from the young star can then create some interesting chemistry through things like radical reactions and during the evaporation of ices. Things like diethyl ether have been detected in the pre/proto stellar nebulae of young stars.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;In the parent body of the meteorite, such as in a meteoroid. Here most chemistry would occur through hydrothermal alteration over long timescales as the body orbited the parent star. As these bodies will invariably describe elliptical  orbits, it will undergo many freeze-thaw cycles all in the presence of an intense radiation field.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Carbonaceous chondrites in particular undergo aqueous alteration due to the presence of water in liquid form.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 2 of &lt;a href=&quot;http://www.gb.nrao.edu/astrobiology/gbtModel/astroBioARAA.38.1.427.pdf&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; gives an basic overview of some of the chemistry involved. It actually refers to the chemistry in cold molecular clouds, but is almost equally applicable to that in things like meteroids/asteroids/comets.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ehrenfreund, P, and Charnley, S.B., 2000, Annual Reviews of Astronomy and Astrophysics, 38, 427&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="3340" LastEditDate="2014-10-09T15:43:43.937" LastActivityDate="2014-10-09T15:43:43.937" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2949" PostTypeId="2" ParentId="2936" CreationDate="2012-07-20T14:38:56.750" Score="1" Body="&lt;p&gt;First, mitosis is a eukaryotic process where not only genome replication and cell division is involved but quite a few more processes, not the least because there is a nucleus in eukaryotes. Bacteria simply divide after replication. And yes, even the simplest bacteria (and even some symbionts) use ribosomes for protein production. Example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The smallest bacteria are from species &lt;em&gt;Mycoplasma&lt;/em&gt;. The &lt;em&gt;Mycoplasma&lt;/em&gt; species with the smallest annotated proteome on UniProt is &lt;em&gt;Mycoplasma genitalium&lt;/em&gt; (strain ATCC 33530 / G-37 / NCTC 10195, with 484 genes. I have attached links to the set, as well as to its helicase. (For the 16S gene you would look that up in a gene not protein database)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.uniprot.org/uniprot/?query=taxonomy:243273&quot; rel=&quot;nofollow&quot;&gt;http://www.uniprot.org/uniprot/?query=taxonomy:243273&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.uniprot.org/uniprot/P47340&quot; rel=&quot;nofollow&quot;&gt;http://www.uniprot.org/uniprot/P47340&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-07-20T14:38:56.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2950" PostTypeId="2" ParentId="2942" CreationDate="2012-07-20T16:00:31.043" Score="6" Body="&lt;p&gt;It is interesting to note that, in the Wikipedia article, it states that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The amino acids were racemic (that is, the chirality of their enantiomers are equally left- and right-handed), indicating that they are not present due to terrestrial contamination&quot;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This implies that, if a 'life form' did create these proteins, they are fundamentally quite different to life on earth. (Particularly in light of the 70 unique amino acids they described!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We cannot ever 'know' how they were made, unless a pretty revolutionary discovery is made that undisputably confirms evidence for extra-terrestrial life (although this is the best evidence yet!), so we are left to speculation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nucleobases either formed 'randomly' in one of the countless celestial events (although the chances of this seem pretty remote given the complexity of the molecules and the homogeneity in the sample), or they were made by extra-terrestrial 'life' (much more exciting, and indeed probably more likely, as we will see). (Or the 3rd option: intelligent design, however this is &lt;a href=&quot;http://www.secularhumanism.org/library/fi/dawkins_18_3.html&quot; rel=&quot;nofollow&quot;&gt;dramatically less probable&lt;/a&gt; than either of the other two). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Miller-Urey experiment to which you refer has been subsequently enhanced, and evidence for the &quot;catalytic potential of cosmic dust&quot; is now reasonably robust (&lt;a href=&quot;http://dx.doi.org/10.1089%2F153110703769016389&quot; rel=&quot;nofollow&quot;&gt;Hill, 2004&lt;/a&gt;). They demonstrate that simple nebular iron silicate catalysts can yield methane and water from CO₂ and H₂, and ammonia from N₂ and H₂. Allowing these to react yields nitrogen-containing organics such as methyl amine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not a huge jump to suppose that with enough time, mass and energy, these reactants could combine and form a molecule (chain of amino-acid-like molecules - a protein) capable of faithfully replicating itself, and thus initiate life. There is no reason to suppose that Earth is unique in this respect; there are billions of suns in our galaxy alone, and billions of years of time for these reactions to take place.&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="3340" LastEditDate="2014-10-09T15:43:12.730" LastActivityDate="2014-10-09T15:43:12.730" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2951" PostTypeId="1" CreationDate="2012-07-20T16:07:46.213" Score="10" ViewCount="1420" Body="&lt;p&gt;I have recently been doing a lot of research into the interplay between the innate and adaptive immune systems in humans, and mammalian laboratory models. This has led to my reading some &lt;a href=&quot;http://www.cnrs.fr/Cnrspresse/en40a2.html&quot;&gt;interesting information on the immune response in insects&lt;/a&gt;;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Insects have a highly efficient immune system.  In response to a bacterial attack, their fat body (the equivalent of the liver in mammals) synthesizes a whole range of peptides with an antibacterial and antifungal effect.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This fascinated me, as the clear inference is that there are no ‘dedicated’ immune cells, but that adipose tissue has far more diverse functions that I had realized.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have done a little more reading, and also looked at plant immune systems, which seems far more analogous to those in insects than mammals;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Plants, unlike mammals, lack mobile defender cells and a somatic adaptive immune system. Instead, they rely on the innate immunity of each cell and on systemic signals emanating from infection sites.&#xA;  (&lt;a href=&quot;http://dx.doi.org/10.1038/nature05286&quot;&gt;Jones, 2006&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My questions relates to the &lt;em&gt;need&lt;/em&gt; of an adaptive immune response in mammals. The immune systems in insects and plants - a more 'systemic' immunity due to the lack of dedicated/mobile immune cells - seems much simpler. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that evolution works incrementally (there are no 'jumps' - for instance, going from a non-dedicated immune system, to a dedicated immune system), I would hypothesise that organisms less distantly related to insects and plants may have tissues with duel functions (similar to insects?), but that specialize further as immune cells until gradually (down the evolutionary tree) a complex and specific immune system emerges. (This is complicated by the fact that our immune systems do have multiple roles - e.g. tissue remodelling, but I wasn't going to go into that here. Feel free in your answers if it is necessary!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My overall curiosity can be summarized as 2 questions;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;What are the possible reasons why a dedicated and immensely complex immune system evolved in some lineages of organism?&lt;/li&gt;&#xA;&lt;li&gt;Is there any evidence of 'half-way' organisms, and about what ecological time-frame might the dedicated immune system have developed?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-07-20T16:13:26.503" LastActivityDate="2017-05-11T12:20:35.423" Title="How and when did a dedicated immune system evolve?" Tags="&lt;evolution&gt;&lt;immunology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2953" PostTypeId="2" ParentId="2951" CreationDate="2012-07-20T16:47:11.470" Score="3" Body="&lt;p&gt;Immunity has probably evolved more than once as it is completely necessary for survival.  You might even argue that defenses such as antibiotics and predatory behavior are immune defenses for single celled creatures.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you point out, plants have a different immune system than animals do.  Insects do too.  They don't have innate immune memory which many animals have, where pools of cells embody the immune response to a specific antigen.  (i.e. encode for a specific immunoglobin or a tCell Receptor variant).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this reference that this appears to be the collective property of &lt;a href=&quot;http://jeb.biologists.org/content/213/5/661.long&quot; rel=&quot;nofollow&quot;&gt;jawed vertebrates&lt;/a&gt;.  Even so, there are many late innovations in the immune system, where reptilian and mammalian immune responses vary substantially. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its not clear to me whether other animals have the insect system. Animals that branched off before insect lines such as radiates probably have their own way of dealing with immune response.  That's just a guess though. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-07-20T16:47:11.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2954" PostTypeId="2" ParentId="2936" CreationDate="2012-07-20T16:52:48.080" Score="3" Body="&lt;p&gt;I've had a direct look at Carsonella rudii, which is I believe is the bacterial genome with the smallest number of genes so far - &lt;a href=&quot;http://www.sciencemag.org/content/314/5797/267.abstract&quot; rel=&quot;nofollow&quot;&gt;184 as well as being only 160 kb in length&lt;/a&gt;.   It has a putative DNA helicase encoded in it.  37 of those genes encode for ribosomal components as well.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there was ever a bacterium or any living cell (non virus that is) discovered without a ribosome, you would have heard about it.  nobel prizes all around. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I would say that your answer is yes.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-07-20T16:52:48.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2955" PostTypeId="1" AcceptedAnswerId="2956" CreationDate="2012-07-20T20:11:37.967" Score="24" ViewCount="18451" Body="&lt;p&gt;It may be different for other people, but for me, anything above 32°C (90°F) is very uncomfortable, and my body is inclined to seek cooler temperatures.  But I would think that at 32°C, the body would have less work to do to get itself to 37°C.  So why is it not comfortable in those temperatures?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My theory is this, but I don't know if it's right:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The body's abilities for warming itself are much more sophisticated than its abilities for cooling itself (which are non-existent, possibly?). So it likes to be in an environment 20-30 degrees below optimal because it can easily handle that.  But up in the 32's and we're dangerously close to going over the optimal, and the body doesn't know how to get it back down after that, so we are inclined to seek safer temperatures.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it something like that?&lt;/p&gt;&#xA;" OwnerUserId="1163" LastEditorUserId="115" LastEditDate="2012-07-21T07:02:18.147" LastActivityDate="2018-08-01T17:59:12.583" Title="If body temperature is 37°C (98.6°F), why are most people more comfortable at around 21°C (70°F)?" Tags="&lt;human-biology&gt;&lt;homeostasis&gt;" AnswerCount="4" CommentCount="5" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="2956" PostTypeId="2" ParentId="2955" CreationDate="2012-07-20T20:38:25.800" Score="15" Body="&lt;p&gt;The body can never stop working. If the body stops working, you die.&#xA;And while the body is working it cannot avoid generating heat.&#xA;Being in an environment somewhat colder than the body makes getting rid of this excess heat easier, and is thus more comfortable.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;The body's abilities for warming itself are much more sophisticated than&#xA;its abilities for cooling itself (which are non-existent, possibly?).&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The body can cool itself down by sweating.&lt;/p&gt;&#xA;" OwnerUserId="542" LastActivityDate="2012-07-20T20:38:25.800" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2958" PostTypeId="1" AcceptedAnswerId="2962" CreationDate="2012-07-20T21:44:49.720" Score="17" ViewCount="6323" Body="&lt;p&gt;I've been wondering lately how evolution manages to produce complex organs. It is pretty obvious to me how evolution would select some minor traits like size, resistnce to illness or climate. There is a mutation where some organisms are slightly different and better traits are selected. However I cannot imagine how an organism will mutate to have lets say lungs at once and unless organism has a functional organ there is no reason for the trait to be selected. So how does evolution produce complx organs?&lt;/p&gt;&#xA;" OwnerUserId="1164" LastActivityDate="2016-10-22T14:16:17.107" Title="How does evolution produce complex organs" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2959" PostTypeId="2" ParentId="2955" CreationDate="2012-07-20T23:55:03.183" Score="9" Body="&lt;p&gt;Your body requires energy to function.  Just like in a powerplant, the energy comes from oxidizing fuel (food, instead of coal or gas).  The efficiency Of conversion is rather low, and results in excess heat, which must be rejected to the environment.  When it's cool, the heat is easily convected to the surrounding air.  When it's warmer, or you're producing more waste heat than can be rejected through simple convection, your body relies on evaporative cooling, i.e. sweating.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When it's very cold, the normal waste heat is not sufficient to keep you warm enough for normal bodily functions, so you shiver.  This is physical activity which your body performs solely to create waste heat, which warms you up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's an article about &lt;a href=&quot;http://en.wikipedia.org/wiki/Muscle#Efficiency&quot; rel=&quot;nofollow&quot;&gt;muscle efficiency&lt;/a&gt; on Wikipedia, indicating that the human body is about 25% efficient.  This means that about 75% of the energy consumed must be rejected as heat.&lt;/p&gt;&#xA;" OwnerUserId="1157" LastEditorUserId="7974" LastEditDate="2015-01-11T18:59:19.010" LastActivityDate="2015-01-11T18:59:19.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2960" PostTypeId="2" ParentId="2937" CreationDate="2012-07-21T10:40:56.240" Score="21" Body="&lt;p&gt;Insect flight muscle is capable of achieving the highest metabolic rate of all animal tissues, and this tissue may be considered an exquisite example of biochemical adaptation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Locusts, for example, may (almost instantaneously) increase their oxygen consumption up to 70-fold when starting to fly.  In humans, excercise can increase O&lt;sub&gt;2&lt;/sub&gt; consumption a maximum of 20-fold, and for birds in flight the figure is about 10-fold (Wegener, 1996; Sacktor, 1976).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Wegener (1996) has put it (in his definitive paper):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The aerobic scope (the ratio of maximal to basal rate of respiration) of insects is unrivalled in the animal kingdom&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Flight is powered by ATP hydrolysis, and these impressive metabolic rates are achieved by very effective control of ATP hydrolysis and regeneration.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt; Metabolism is &lt;i&gt;aerobic&lt;/i&gt;, thus allowing for much more efficient ATP production from hexoses (as compared with, say, anaerobic metabolism).&lt;/li&gt;&#xA;&#xA;&#xA;&lt;li&gt; Flight muscle may account for up to 20% of body mass.&lt;/li&gt;&#xA;&#xA;&lt;li&gt; In insects, haemoglobin and myoglobin are absent. Instead, gaseous O&lt;sub&gt;2&lt;/sub&gt; is transported to the tissues by a system of tubules and deposited so close to the site of consumption that (seemingly) it may reach mitochondria by diffusion. &lt;/li&gt; &#xA;&#xA;&lt;li&gt;Locusts fuel flight by burning sugars in the early stages, gradually changing to use lipids as fuel. (In bees, flight is totally fuelled by hexose consumption). &#xA;&#xA;This is achieved by effective control of glycogen breakdown and glycolysis, by modifying the activity glycogen phosphorylase (glycogen breakdown) and phosphofructokinase (PFK), a key control enzyme of glycolysis. &lt;/li&gt;&#xA;&#xA;&lt;li&gt;There is an enormous literature on these topics, but suffice it to say, in the case of glycolysis, control is very efficiently achieved by allosteric regulation of PKF, where fructose 1,6-bisphosphate and fructose 2,6-bisphosphate play key roles (see Sacktor, 1976).&lt;/li&gt;&#xA;&#xA;&lt;li&gt;This allosteric control very effectively allows glycolysis to be (almost instantaneously) turned on and operate at a maximum value, and to be (almost instantaneously) turned off.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wegener, G. (1996) &lt;em&gt;Flying insects: model systems exercise physiology&lt;/em&gt;&#xA;Experientia May 15;52(5):404-12. (See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8641375&quot;&gt;here&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sacktor B. (1976) &lt;em&gt;Biochemical adaptations for flight in the insect.&lt;/em&gt;&#xA;Biochem Soc Symp. 1976;(41):111-31. (See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/788715&quot;&gt;here&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="1136" LastEditDate="2012-07-21T17:33:32.103" LastActivityDate="2012-07-21T17:33:32.103" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2961" PostTypeId="1" AcceptedAnswerId="3120" CreationDate="2012-07-21T13:06:29.647" Score="9" ViewCount="2675" Body="&lt;p&gt;I'm looking for data to build a timeline of the odds for survival of a fertilized egg, i.e., &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What are the odds it'll last a week? &lt;/li&gt;&#xA;&lt;li&gt;What are the odds it'll last a month?  &lt;/li&gt;&#xA;&lt;li&gt;2 months? &lt;/li&gt;&#xA;&lt;li&gt;(and so on until)&lt;/li&gt;&#xA;&lt;li&gt;What are the odds of it being born?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am interested in the odds with the usual level of care in an industrialized nation (and a mother that is not trying to abort the fetus).&lt;/p&gt;&#xA;" OwnerUserId="1167" LastEditorUserId="57" LastEditDate="2012-07-23T02:00:39.313" LastActivityDate="2012-08-07T16:34:56.383" Title="A timeline of the odds for survival for fertilized eggs and fetuses" Tags="&lt;human-biology&gt;&lt;reproduction&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2962" PostTypeId="2" ParentId="2958" CreationDate="2012-07-21T13:42:47.123" Score="5" Body="&lt;p&gt;The best introduction to evolution of complex phenotypes via master control genes is &lt;em&gt;Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom&lt;/em&gt; by Sean B. Carroll. You might also want to have a look at a more recent Evolutional developmental biology (Evo Devo) book like those you get when searching for &quot;Evo Devo&quot; in Google Books.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, it is possible for a mutation to change a shape by changing the spatial distribution of a transcription factor during embryo development. What's more, by changing the distribution of two mutually dependent factors, formation of any shape is possible if the distributions overlap. Such transcription factors are highly conserved in evolution and the most important cause of the endless forms we see.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-07-21T14:32:17.577" LastActivityDate="2012-07-21T14:32:17.577" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="2963" PostTypeId="2" ParentId="2934" CreationDate="2012-07-21T14:06:03.583" Score="6" Body="&lt;p&gt;This is only a guess but I hope somewhat educated, so refute me. The establishment of glucose as nutritional molecule is mainly linked with the availability of carbohydrates in the environment, i.e. plants as nutrition. Before plants evolved however, there were only bacteria and they use glucose as one of many oligosaccharides. But more important than glucose is trehalose because it is less toxic and can be collected in large amounts in the cell. The only reserves for glucose are glycogen and the bacterial cell wall which can be catabolized. So, in my guess, the reason for the mere existence of glycolysis/gluconeogenesis pathways is the bacterial cell wall that has to be synthesized and catabolized. Only later were these pathways differentiated when land plants came up and animals that et them.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-07-21T14:06:03.583" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2964" PostTypeId="2" ParentId="2934" CreationDate="2012-07-21T15:34:46.247" Score="11" Body="&lt;p&gt;I thought this was a great question.  In particular because it hints at two questions.  The first is 'why carbohydrates are used to store energy' in general. The second being 'why glucose rather than other carbohydrates?' in particular. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glucose metabolism (and glycogen storage) is a core gene pathway - its found in &lt;a href=&quot;http://www.nature.com/nature/journal/v220/n5167/abs/220606a0.html&quot;&gt;bacteria&lt;/a&gt; archaea and eukaryotes.  So probably the most that we can readily say about question one is that as @rwst points out this pathway has proven to be useful at a critical juncture of the formulation of living things on earth.  If you look at &lt;a href=&quot;http://www.genome.jp/kegg-bin/show_pathway?ko00010&quot;&gt;glucose metabolism pathways&lt;/a&gt;, you can see that glycerate compounds and pyruvate are the actual intermediates that are used to create energy.  The first thing about these molecule worth noting is that they have a good mix of carbon and oxygen, which would make it easier to extract energy - creating CO2 from these compounds may even predates the existence of atmospheric oxygen.  So glucose and fructose (which is actually derived from glucose in the metabolic pathway) are actually storage molecules themselves, easily broken down to smaller molecules. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the second question: there are quite a few ways to arrange oxygen around the carbohydrate ring.  why glucose?  The advantages of glucose is probably a subtle one.  The structural properties of glycogen might be a reason that the use of glucose monomer is so important for glycogen. There is no evidence that I can find for this, so its always possible that glucose was just the first hexose carbohydrate to be biologically used.  Its sort of hard to imagine that the structure of glucose does not play some sort of role in cell structure though. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-07-21T15:34:46.247" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2965" PostTypeId="1" CreationDate="2012-07-22T11:08:19.963" Score="10" ViewCount="240" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction&quot;&gt;Protein-protein interactions&lt;/a&gt; are when two or more proteins bind together, possibly for some important biological function.  Recently, I'm starting to look more into proteins, and in particular, networks related to proteins, such as protein-protein interaction networks.  I found myself thinking about the following question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;:  Does the relative size of two proteins significantly affect how likely they are to interact?  Does it affect &lt;em&gt;how&lt;/em&gt; they interact?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It would be plausible for me to download a protein-protein interaction network, and calculate their relative size from the proteins' &lt;a href=&quot;http://www.pdb.org/&quot;&gt;PDB&lt;/a&gt; files.  However, I predict that the results from such a computation would not offer much insight into why (or why not) the protein sizes affect binding.&lt;/p&gt;&#xA;" OwnerUserId="203" LastEditorUserId="43" LastEditDate="2012-09-04T17:00:33.397" LastActivityDate="2013-07-26T00:16:10.177" Title="What role does a protein's size have on protein-protein interactions?" Tags="&lt;biochemistry&gt;&lt;bioinformatics&gt;&lt;proteins&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2966" PostTypeId="2" ParentId="894" CreationDate="2012-07-22T11:38:20.037" Score="3" Body="&lt;p&gt;[I'm answering my own question, but this seems too important not to include as an answer.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;http://myxo.css.msu.edu/ecoli/&quot; rel=&quot;nofollow&quot;&gt;long-term E. coli evolution experiment&lt;/a&gt; (&lt;a href=&quot;http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;) was begun in February 1988 by Richard Lenski.  He took 12 initially identical populations of Escherichia coli, and let them grow, having now completed over 50,000 generations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One striking observation made through this research, is that one sample of E. coli evolved the ability to metabolise citrate, which took over 30,000 generations (see Blount, Borland, Lenski, &quot;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0803151105&quot; rel=&quot;nofollow&quot;&gt;Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli&lt;/a&gt;&quot; PNAS (2008)).  This evolutionary step was achieved in a glucose-limited medium, thereby adding evolutionary pressure.  Moreover, their results suggest that a necessary &quot;potentiating change&quot; occurred at around 20,000 generations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These results demonstrate that significant evolutionary change is possible to observe in the laboratory, and gives a feel for how long it might take for something as complicated as the flagellum.&lt;/p&gt;&#xA;" OwnerUserId="203" LastActivityDate="2012-07-22T11:38:20.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2968" PostTypeId="2" ParentId="2965" CreationDate="2012-07-22T13:42:26.213" Score="4" Body="&lt;p&gt;Protein interactions occur mostly (if not all) through residues that are on the &quot;surface&quot; and exposed to the milieu in which they exist, be it cytoplasmic or extracellular. So, a naive thought would be to guess that a greater surface area means a greater swathe of exposed regions and probable interacting parts. One protein can bind many others, even simultaneously, through different such interaction surfaces. However, other factors also determine whether a given set of two proteins interact, most important being where they localize in a given cell. If one protein is nuclear but the other on the plasma membrane, it is highly unlikely that they ever interact even if thermodynamics highly favors complex formation. Interaction between two proteins also depends on their respective conformations, which can further be regulated by events such as post translational modifications (eg., phosphorylation by a kinase), bound nucleotide state (eg., GTP vs GDP in a G protein). Last, scaffolds can also sequester and organize protein clusters together spatially and increase the probability of them interacting. All put together, I think it is highly unlikely that just looking at 3D surface area of a protein will say much about its &quot;interactability&quot; with other proteins.&lt;/p&gt;&#xA;" OwnerUserId="223" LastActivityDate="2012-07-22T13:42:26.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2970" PostTypeId="1" AcceptedAnswerId="2972" CreationDate="2012-07-22T21:38:27.210" Score="11" ViewCount="604" Body="&lt;p&gt;Today in &lt;a href=&quot;http://maps.google.pl/maps?q=55.684575,12.580501&amp;amp;num=1&amp;amp;t=m&amp;amp;z=16&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kongens Have&lt;/a&gt;, I noticed a lot of white dots on bark of trees. There are plenty of them, and they were usually on 'bottom' side of branches. Does anyone know what this could be?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I took a photo:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gQcZQ.jpg&quot; alt=&quot;Kongens Have photo&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect some pupa of insects, but it is just a quess.  &lt;/p&gt;&#xA;" OwnerUserId="1171" LastEditorUserId="57" LastEditDate="2012-07-23T01:21:01.930" LastActivityDate="2012-07-23T08:09:26.217" Title="What are the white dots on the tree in this photo?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2972" PostTypeId="2" ParentId="2970" CreationDate="2012-07-23T08:09:26.217" Score="13" Body="&lt;p&gt;I'm not 100% sure, but I think they look like scale insects (&lt;a href=&quot;http://en.wikipedia.org/wiki/Scale_insect&quot; rel=&quot;nofollow noreferrer&quot;&gt;Coccoidea&lt;/a&gt;). In particular it looks at bit like a hermaphrodite &lt;a href=&quot;http://en.wikipedia.org/wiki/Icerya_purchasi&quot; rel=&quot;nofollow noreferrer&quot;&gt;cottony cushion scale insect (&lt;em&gt;Icerya purchasi&lt;/em&gt;)&lt;/a&gt;...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/o7XxD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The white fluffy thing underneath the insects is the ootheca (egg case). The mature insect migrates to the main trunk of its host tree and attaches to the bark. It then secretes the cottony sack between itself and the bark. Hundreds of eggs are laid into the case, which eventually hatches and the nymphs disperse to the tips of branches where they feed on leaves. As they get older they gradually move first to twigs, then to branches and finally back to the main trunk to breed again.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-07-23T08:09:26.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2973" PostTypeId="1" AcceptedAnswerId="2974" CreationDate="2012-07-23T09:51:33.530" Score="3" ViewCount="7814" Body="&lt;p&gt;I have a lingering question which stems from an answer that I gave to &lt;a href=&quot;https://biology.stackexchange.com/questions/982/what-hydrolyses-aspirin-within-the-digestive-tract-and-blood-stream/993#993&quot;&gt;What hydrolyses aspirin within the digestive tract and blood stream?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a drug or any other substance is absorbed into the bloodstream in the stomach or small intestine, it ultimately passes through the hepatic portal vein and into the liver sinusoids, where it is processed by hepatocytes and introduced into the general circulation via the vena cava.  In terms of metabolism, this is what causes a &quot;first-pass&quot; effect for drugs that are ingested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For drugs that are delivered either by intravenous, intramuscular, or sub-lingually (as in the other Biology.SE question), this first-pass effect is avoided, and the drug is introduced into the general circulation without being metabolized by the liver first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even though the first pass is avoided, the blood in the body still makes its way back through the liver eventually via the hepatic artery, which is a branch off of the celiac artery.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The issue I still have is, does the incoming blood from the hepatic artery merge with the blood from the hepatic portal vein?  If not, does the blood from the hepatic artery still interact with the hepatocytes in some way? (it makes sense that it does, and I have also read that one of the main functions of the hepatic artery was to deliver blood supply for the liver's metabolic needs)  If this is not the case, where in the body would these drugs that were introduced via IV, etc., be metabolized? &lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2012-07-23T13:11:11.460" Title="Circulation through the liver in light of drug metabolism" Tags="&lt;metabolism&gt;&lt;human-anatomy&gt;&lt;pharmacology&gt;&lt;liver&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2974" PostTypeId="2" ParentId="2973" CreationDate="2012-07-23T13:11:11.460" Score="5" Body="&lt;p&gt;Yes, the blood from the hepatic artery (proper) and the portal vein mix in the sinusoids of the liver. The hepatic vein supplies about 75% of the blood to the liver, and the hepatic artery the remaining 25%. Because the portal vein provides such a large part of the blood supply to the liver, then any disease that causes the blood to build up can cause portal hypertension.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hepatic artery carries oxygen-rich blood from the heart. The portal vein is part of the portal system and connects the capillary beds of the gastrointestinal tract to those of the liver. Because of the larger volume through the portal vein, I think that each vessel carries about half the oxygen supply to the liver.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For drugs introduced through an injection, for example, metabolism occurs throughout the circulatory system and in the liver. Remember that it's all the same blood supply, but the first-pass effect just refers to the blood that goes to the liver before entering the systemic circulation (by which it can travel to its target).&lt;/p&gt;&#xA;" OwnerUserId="1166" LastActivityDate="2012-07-23T13:11:11.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2975" PostTypeId="1" CreationDate="2012-07-23T16:02:54.147" Score="2" ViewCount="5235" Body="&lt;p&gt;While shopping in the local supermarket yesterday, I was surprised to find this display on one of the shelves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/477t6.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also realize that I should have taken a pamphlet with me, as well as a picture of the boxes for the glasses, as seen in the picture to read more about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://skeptics.stackexchange.com/questions/7648/do-raster-glasses-work-for-improving-eyesight&quot;&gt;This answer at Skeptics.SE&lt;/a&gt; shows that there are in fact probably no long-term benefits of wearing pinhole glasses, but my question is...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What potential harm/side effects can be caused in the short and long-term from wearing this type of eyewear?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2017-05-27T22:47:39.467" Title="What negative effects can pinhole glasses have on the body?" Tags="&lt;human-anatomy&gt;&lt;eyes&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2976" PostTypeId="1" AcceptedAnswerId="2994" CreationDate="2012-07-23T17:44:54.363" Score="4" ViewCount="2995" Body="&lt;p&gt;A reflex is an unconscious action in response to some specific stimulus, e.g., blinking an eye, or pulling the hand away from a hot pin&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know from school biology, and reading online that withdrawal reflexes are quick because&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;CNS is involved&lt;/li&gt;&#xA;&lt;li&gt;Danger receptors send impulses to prevent inhibition of flexion&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;When a person is extremely obese, do these flexion impulses take longer? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is a withdrawal reflex in an obese person noticeably slower than in case of a reasonably fit person? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="57" LastEditDate="2012-07-24T04:15:19.557" LastActivityDate="2012-07-29T12:47:00.567" Title="Does body mass have a bearing on reflex speed?" Tags="&lt;neuroscience&gt;&lt;reflexes&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2977" PostTypeId="1" AcceptedAnswerId="4991" CreationDate="2012-07-23T18:36:24.650" Score="4" ViewCount="342" Body="&lt;p&gt;I was reading through the &lt;a href=&quot;http://www.cell.com/abstract/S0092-8674(12)00776-3&quot; rel=&quot;nofollow noreferrer&quot;&gt;Karr et al. (2012)&lt;/a&gt; whole-cell computational model. One of the things they did was to induce single-gene disruptions in their model. They observed several to be fatal, but:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In some cases (Figure 6B, fifth column), the time required for the levels of specific proteins to fall to lethal levels was greater than one generation (Figures 6C and 6D).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;As far as I understand this is because when a single-cell divides, daughters get not only get a copy of the mother DNA, but also have their initial levels of proteins and RNA set to those of their mother (or similar, with some statistical fluctuation).&lt;/p&gt;&#xA;&lt;p&gt;To me this screams of &lt;a href=&quot;http://en.wikipedia.org/wiki/Lamarckism&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lamarkism&lt;/a&gt;: if an organism during its lifetime came in contact with an environment that caused a greater expression of some protein that in had at birth, its children will also have a higher initial expression of the same protein. In other words, the trait of &amp;quot;level of this protein&amp;quot; seems to be being passed down in a Lamarkian way. &lt;strong&gt;Is my understanding correct, or am I missing the point?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;If my understanding is correct, then &lt;strong&gt;what are some standard methods to account for this short-term Lamarkism in mathematical models of evolution?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h3&gt;Notes&lt;/h3&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;I am primarily &lt;strong&gt;interested in mathematical (or other formal) treatments&lt;/strong&gt; of this. I have a background in mathematics and some work in mathematical modeling for population biology and evolutionary game theory. I have &lt;strong&gt;no background in biochemistry or microbiology&lt;/strong&gt;. I would appreciate answers or references that cater to this awkward background but I am not adverse to plowing through some microbio if it is for something awesome.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Similar partial arguments can be made for non-single-cell and sexual organism by considering hormone expressions of the mother during pregnancy, as &lt;a href=&quot;https://biology.stackexchange.com/a/2876/500&quot;&gt;in this answer&lt;/a&gt;. I am satisfied with an explanation for asexual single-cell organisms, but bonus points if it can also say something about non-single-cell and/or sexual organisms.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Follow up question on modeling the mechanism behind this: &lt;a href=&quot;https://biology.stackexchange.com/q/3020/500&quot;&gt;Macromolecule levels in daughter cells after fission&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-02-09T11:27:59.493" Title="Short-term Lamarckism in asexual single cell organisms" Tags="&lt;evolution&gt;&lt;microbiology&gt;&lt;epigenetics&gt;&lt;mathematical-models&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="2978" PostTypeId="2" ParentId="2912" CreationDate="2012-07-23T19:46:19.520" Score="1" Body="&lt;p&gt;Later I found out that the length of RNA read from the gel is not trustworthy. I guess it's because the RNA is in hybridyzation solution that even when it's running on the gel, it cannot reflect the actually length of the probe. The only way to test the probe quality is to do the in situ. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the pheno contamination problem, I think it's a separate problem of myself. Once RNA can be synthesized in vitro, it means there should not be pheno contamination. &lt;/p&gt;&#xA;" OwnerUserId="1141" LastActivityDate="2012-07-23T19:46:19.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2979" PostTypeId="1" AcceptedAnswerId="2981" CreationDate="2012-07-23T19:48:45.243" Score="6" ViewCount="1019" Body="&lt;p&gt;Hard water is water with high mineral/salt content. I'm told that a potted plant watered with a salt solution dries out sooner or later. Is this true? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, would a plant survive if watered using hard-water? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="57" LastEditDate="2012-07-24T06:04:25.640" LastActivityDate="2016-12-13T00:10:11.340" Title="Would a plant survive if it was watered using hard-water?" Tags="&lt;plant-physiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2980" PostTypeId="1" CreationDate="2012-07-23T20:27:13.857" Score="3" ViewCount="100" Body="&lt;p&gt;Something analogous to an encyclopedia on baseball players with a list of all thier stats would be ideal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not looking for just generic muscle names, locations and illustrations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good answers would include links to resources, textbooks etc. which include stats for most or all of the following of every skeletal muscle in the human anatomy:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Language of origin/LOO definition&lt;/li&gt;&#xA;&lt;li&gt;Labeled by ? shape, location, size etc.&lt;/li&gt;&#xA;&lt;li&gt;Type of Shape (i.e., fusiform, pennate, bipennate, multipennate, convergent, parrellel etc)&lt;/li&gt;&#xA;&lt;li&gt;Angle(s) of pennation (if applicable)&lt;/li&gt;&#xA;&lt;li&gt;# of motor neuron innervations&lt;/li&gt;&#xA;&lt;li&gt;# of proprioceptors in muscle&lt;/li&gt;&#xA;&lt;li&gt;# of fibers&lt;/li&gt;&#xA;&lt;li&gt;Length of muscle&lt;/li&gt;&#xA;&lt;li&gt;Length of fibers&lt;/li&gt;&#xA;&lt;li&gt;Typical fuel system reliance (determined off of biomechanical placement and architecture..CPr, oxidative, etc.)&lt;/li&gt;&#xA;&lt;li&gt;Biomechanical function (structure of corresponding bone/tendon anchors and corresponding movement manipulation)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="972" LastEditorUserId="57" LastEditDate="2012-07-24T04:12:00.733" LastActivityDate="2014-07-05T20:34:30.087" Title="Text/resource with information on all skeletal muscles and their motor units" Tags="&lt;neuroscience&gt;&lt;anatomy&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2981" PostTypeId="2" ParentId="2979" CreationDate="2012-07-23T20:29:26.207" Score="2" Body="&lt;p&gt;It would depend on the content of the hard-water. If the water contained heavier metals like lead or radioactive elements like tritium (Hydrogen-3), the plant would most likely die. Most land plants cannot survive when watered with massive amounts of salt water as the salt would absorb the water from the leaves.&lt;/p&gt;&#xA;" OwnerUserId="1130" LastActivityDate="2012-07-23T20:29:26.207" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2982" PostTypeId="1" AcceptedAnswerId="2983" CreationDate="2012-07-23T23:00:47.820" Score="7" ViewCount="540" Body="&lt;p&gt;&lt;a href=&quot;http://www.cell.com/abstract/S0092-8674%2812%2900776-3&quot; rel=&quot;nofollow&quot;&gt;Karr, Sanghvi, et al. (2012)&lt;/a&gt; propose a whole-cell computational model for predicting phenotype from genotype in &lt;em&gt;Mycoplasma genitalium&lt;/em&gt;. Their model simulates myriad cell processes such as DNA replication, RNA transcription and regulation, protein synthesis, metabolism and cell division at the molecular level over the life-cycle of the organism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They achieve this by combining many existing mathematical and computational models into one piece of &lt;a href=&quot;https://simtk.org/project/xml/team.xml?group_id=714&quot; rel=&quot;nofollow&quot;&gt;software&lt;/a&gt;. The article suggests that this is the first comprehensive whole-cell model at the molecular level in detail. They cite previous molecular-level models for their sub-modules, but don't go on to discuss more coarse-grained genotype-to-phenotype models. Their model is exciting, but the 10 hours of simulation on a top-end computer cluster to follow the life-cycle of a single organism is unreasonable for someone who wants to study evolutionary processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are there prior reasonably accurate computational (or even better, analytic) genotype-to-phenotype models? If there are, what are some of the best coarse-grained genotype-to-phenotype models for commonly studied organisms such as &lt;em&gt;E.Coli&lt;/em&gt;?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="57" LastEditDate="2012-07-24T04:08:13.700" LastActivityDate="2012-07-24T04:08:13.700" Title="Computational/mathematical models for predicting phenotype from genotype" Tags="&lt;evolution&gt;&lt;cell-biology&gt;&lt;genomics&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2983" PostTypeId="2" ParentId="2982" CreationDate="2012-07-23T23:50:02.070" Score="6" Body="&lt;p&gt;The Karr et al. paper attempts to capture most of the details in their model by combining features from the genome, transcriptome, proteome, and metabolome. This work heavily builds off of the coarse-grained models that you ask of especially on the work from Bernhard Palsson from which Markus Covert did his training. The answer to your question rests entirely on the type of question that you seek and what you want the model to do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the most part, most of your questions can be answered using &lt;a href=&quot;http://opencobra.sourceforge.net/openCOBRA/Welcome.html&quot;&gt;COBRA&lt;/a&gt;, the COnstratins Based Reconstruction and Analysis Toolbox. You can get a good idea of what genotypes can be knocked out and see how it affects the phenotype as long as the phenotype is a known pathway that gets affected by that gene and you don't care about temporal and dynamic information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also the &lt;a href=&quot;http://www.e-cell.org/ecell/about/history&quot;&gt;E-Cell Project&lt;/a&gt; for &lt;em&gt;E. coli&lt;/em&gt;. I personally don't know much about it but it has created some basic models for &lt;em&gt;E. coli&lt;/em&gt; and that may be good enough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to build your own models, you should check out &lt;a href=&quot;http://www.biomedcentral.com/1471-2105/11/213&quot;&gt;BiGG&lt;/a&gt; where all of the large-scale reconstructions exists. A good chunk of the code is stored at the &lt;a href=&quot;http://systemsbiology.ucsd.edu/Downloads&quot;&gt;Palsson lab website&lt;/a&gt; where you can attempt to use COBRA and start generating your own hypotheses.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-07-23T23:50:02.070" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="2984" PostTypeId="1" AcceptedAnswerId="3024" CreationDate="2012-07-24T02:08:08.207" Score="5" ViewCount="1570" Body="&lt;p&gt;I am trying to understand the importance of proliferation limits and cell senescence. In particular, I would like to compare the proliferation limit of Embryonic Stem cells (ES) and fibroblasts (which would be trans-differentiated) and describe how this difference plays a role when thinking about engineering organs, for example a heart transplant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do ES cells and fibroblasts compare with regards to the Hayflick limit?&lt;/p&gt;&#xA;" OwnerUserId="1083" LastEditorUserId="57" LastEditDate="2012-07-24T04:05:34.623" LastActivityDate="2012-07-26T16:50:00.260" Title="Cell proliferation limit and senescence of embryonic stem cells and fibroblasts" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2985" PostTypeId="5" CreationDate="2012-07-24T06:49:58.330" Score="0" Body="&lt;p&gt;Questions should relate to the structure, physiology, and other biological aspects of the brain. Questions on psychology or health are generally off topic.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-03-22T21:07:47.313" LastActivityDate="2016-03-22T21:07:47.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2986" PostTypeId="4" CreationDate="2012-07-24T06:49:58.330" Score="0" Body="The primary component of the central nervous system, which, along with the spinal cord, controls the body of bilaterally symmetrical beings. " OwnerUserId="57" LastEditorUserId="4101" LastEditDate="2013-10-29T20:50:52.680" LastActivityDate="2013-10-29T20:50:52.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2987" PostTypeId="5" CreationDate="2012-07-24T06:55:01.800" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-07-24T06:55:01.800" LastActivityDate="2012-07-24T06:55:01.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2988" PostTypeId="4" CreationDate="2012-07-24T06:55:01.800" Score="0" Body="The branch of physiology that deals with the kidneys, and their role in reabsorption, filtration, acid-base and electrolyte balance." OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-07-24T07:16:57.420" LastActivityDate="2012-07-24T07:16:57.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2989" PostTypeId="5" CreationDate="2012-07-24T07:03:18.157" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-07-24T07:03:18.157" LastActivityDate="2012-07-24T07:03:18.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2990" PostTypeId="4" CreationDate="2012-07-24T07:03:18.157" Score="0" Body="Involuntary movements in response to stimuli which usually employ circuits local to the spinal cord or in the cranial nerves, though not exclusively." OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-07-24T07:16:59.217" LastActivityDate="2012-07-24T07:16:59.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2991" PostTypeId="1" AcceptedAnswerId="2993" CreationDate="2012-07-24T08:45:51.633" Score="7" ViewCount="1087" Body="&lt;p&gt;I have been tasked with writing a program for computing properties of a give set of peptides. These peptides are given as 1-letter amino acid sequences and I need to compute the following :&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Length of peptide&lt;/li&gt;&#xA;&lt;li&gt;Number of Each Amino Acid&lt;/li&gt;&#xA;&lt;li&gt;Percent composition of each amino acid&lt;/li&gt;&#xA;&lt;li&gt;Molecular weight&lt;/li&gt;&#xA;&lt;li&gt;Net charge of peptide &lt;/li&gt;&#xA;&lt;li&gt;Positive charge &lt;/li&gt;&#xA;&lt;li&gt;Negative charge&lt;/li&gt;&#xA;&lt;li&gt;Isoelectric point (pI) &lt;/li&gt;&#xA;&lt;li&gt;Hydropathicity&lt;/li&gt;&#xA;&lt;li&gt;Percent polar amino acids &lt;/li&gt;&#xA;&lt;li&gt;Percent positive amino acids &lt;/li&gt;&#xA;&lt;li&gt;Percent negative amino acids &lt;/li&gt;&#xA;&lt;li&gt;Percent hydrophobic amino acids &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hydrophobicity_scales&quot;&gt;Hydrophobicity&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Lipophilicity&quot;&gt;Lipophilicity&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Amphiphilicity&lt;/li&gt;&#xA;&lt;li&gt;Water-Octanol Partition Coefficient&lt;/li&gt;&#xA;&lt;li&gt;Steric Bulk&lt;/li&gt;&#xA;&lt;li&gt;Side chain bulk&lt;/li&gt;&#xA;&lt;li&gt;Net donated hydrogen bonds&lt;/li&gt;&#xA;&lt;li&gt;Percent \alpha helix&lt;/li&gt;&#xA;&lt;li&gt;Percent random coil&lt;/li&gt;&#xA;&lt;li&gt;Percent \beta sheet&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;While some of these properties are self explanatory ( eg. size, num. of amino acids, percentage of amino acids. ) and easy to compute. Other properties ( like Molecular weight, Net. charge, Positive charge, Hydorphobicity etc ) have been difficult for me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I donot have Chemistry or Biology background and hence have found these difficult to compute. I would be appreciative if someone could point me in the correct direction ( I have already been through Wikipedia ) containing methods to compute the above mentioned properties or to a standard text which would explain the above mentioned properties and also provide methods to compute them. Thank you all.&lt;/p&gt;&#xA;" OwnerUserId="1175" LastEditorUserId="476" LastEditDate="2012-07-24T13:56:05.333" LastActivityDate="2012-07-24T13:56:05.333" Title="How to compute properties of peptides ?" Tags="&lt;biochemistry&gt;&lt;bioinformatics&gt;&lt;proteins&gt;&lt;amino-acids&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2992" PostTypeId="2" ParentId="2991" CreationDate="2012-07-24T10:04:02.690" Score="6" Body="&lt;p&gt;That's quite a laundry list, and I doubt someone is going to sit down and give you hints for all of them. Note that some of the properties (like percent alpha helix) rely on prediction method (secondary structure prediction, in this case). &quot;Net donated hydrogen bonds&quot; sounds like it makes sense only for a given complex with a solved 3D structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nonetheless, you will probably find some of the stats implemented in &lt;a href=&quot;http://emboss.sourceforge.net/apps/&quot;&gt;EMBOSS&lt;/a&gt;, for example in the &lt;a href=&quot;http://emboss.open-bio.org/wiki/Appdoc%3aPepstats&quot;&gt;pepstats&lt;/a&gt; app.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-07-24T10:04:02.690" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="2993" PostTypeId="2" ParentId="2991" CreationDate="2012-07-24T10:19:04.713" Score="7" Body="&lt;p&gt;Biopython and the other bio-programming languages typically have examples of how to do this kind of thing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example here is some python code for calculating some of these:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://biopython.org/w/index.php?title=ProtParam&amp;amp;redirect=no&quot;&gt;http://biopython.org/w/index.php?title=ProtParam&amp;amp;redirect=no&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many of the propensity scales are in this database:&#xA;&lt;a href=&quot;http://www.genome.jp/aaindex/&quot;&gt;http://www.genome.jp/aaindex/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And there are also biojava classes for accessing these. Essentially you will need to know what these physicochemical properties are and get access to a scale for converting the letter to a numerical value. &lt;/p&gt;&#xA;" OwnerUserId="476" LastActivityDate="2012-07-24T10:19:04.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2994" PostTypeId="2" ParentId="2976" CreationDate="2012-07-24T12:50:30.517" Score="1" Body="&lt;p&gt;No, what would weight have to do it? An obese person has more fat than a person of a normal weight, but fat isn't innervated by nerves (or motor neurons, at least). What about very muscular people? In this case, they actually have more muscles that require innervation, and this comes from increased branching at the nerve terminal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since you mentioned muscles, let's focus on motor neurons (or motoneurons). Remember that the cell body of motor neurons is actually in the spinal cord. In the case of &lt;a href=&quot;http://en.wikipedia.org/wiki/Alpha_motoneurons&quot; rel=&quot;nofollow&quot;&gt;alpha motor neurons&lt;/a&gt;, which innervate skeletal muscle, the cell body is in the ventral horn. What you think of as a &quot;nerve [bundle]&quot; is really just a collection of cell axons. The axons can regrow if cut in the middle, but you don't grow more axons very easily.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, a spinal reflex is very quick because it involves the CNS, &lt;em&gt;but not the brain&lt;/em&gt;. Look at the example of the &lt;a href=&quot;http://apbrwww5.apsu.edu/thompsonj/Anatomy%20&amp;amp;%20Physiology/2010/2010%20Exam%20Reviews/Exam%204%20Review/CH%2013%20Proprioception%20and%20Types%20of%20Reflexes.htm&quot; rel=&quot;nofollow&quot;&gt;patellar (knee-jerk) reflex&lt;/a&gt;. The stretch is sensed and transmitted to the spinal cord, causing contraction of the quadriceps while simultaneously inhibiting the antagonist muscle, the hamstrings.&lt;/p&gt;&#xA;" OwnerUserId="1166" LastActivityDate="2012-07-24T12:50:30.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2995" PostTypeId="1" CreationDate="2012-07-24T12:52:09.953" Score="3" ViewCount="62" Body="&lt;p&gt;I'm looking for some information about the cycles of increased/decreased activity, mental performance or endurance that are related to a mammal's age and the time of a season. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, I'm not sure what such cycles would be called. I know of circadian rhythm, which is an ~24 hour cycle. The other cycle I've heard about was circa-septan (7 days?). &lt;strong&gt;What keywords should I use to search for cycles that may have period of a month to several months?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second question is - are there are episodes of increased activity/performance over a mammal's lifetime? I can think of two example - mating rituals may involve fighting and hibernation involves almost no movement at all.  &lt;strong&gt;Are there additional events that may last more than a month?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The final question is if the age comes into equation of increased/decreased activity. Lets say a younger rat an and older rat are put into the same maze, would their ability to &quot;solve&quot; the maze be related to age?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question is rather broad. Maybe there are some keywords or a science branch that deals with these questions and I can refine my search?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I appreciate your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-07-24T16:25:30.697" Title="Is there such thing as &quot;biological cycles&quot; of activity/performance/etc in mammals?" Tags="&lt;zoology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="2996" PostTypeId="2" ParentId="2975" CreationDate="2012-07-24T13:00:27.680" Score="1" Body="&lt;p&gt;Probably not many side effects except in specific instances, but no benefits either. My guess is that there are potential side effects because these glasses reduce the amount of light that the eye receives and restrict the visual field. Therefore, the restricted visual field would be bad for activities such as driving, in which you need your peripheral vision. And the reduced light makes objects appear dimmer, so it is harder to see with them at night. I also imagine (just a guess) that they would be bad for very young infants, who are almost always born without perfect vision and require some visual stimulation to correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are probably many reasons why optometrists use a &lt;a href=&quot;http://en.wikipedia.org/wiki/Pinhole_occluder&quot; rel=&quot;nofollow&quot;&gt;pinhole occluder&lt;/a&gt; for diagnostic purposes, but never prescribe it as treatment...&lt;/p&gt;&#xA;" OwnerUserId="1166" LastActivityDate="2012-07-24T13:00:27.680" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="2997" PostTypeId="2" ParentId="2995" CreationDate="2012-07-24T16:25:30.697" Score="1" Body="&lt;p&gt;With regard to episodes of increased activity/performance over a mammal's lifetime, I can add migration to breeding/mating and hibernation or torpor. Birds of course are better known for migration, but some mammals, notably in Africa migrate over an extended time.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-07-24T16:25:30.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="2998" PostTypeId="1" CreationDate="2012-07-24T17:59:04.967" Score="1" ViewCount="1261" Body="&lt;p&gt;A person may have a cold or any other disease that is an airborne-infection. &#xA;Is their sperm also contagious? Should the person take any precautions?&lt;/p&gt;&#xA;" OwnerUserId="608" LastEditorUserId="1005" LastEditDate="2012-07-25T10:13:19.153" LastActivityDate="2012-07-25T15:32:54.833" Title="Is sperm contagious?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="2999" PostTypeId="5" CreationDate="2012-07-25T06:57:41.903" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-07-25T06:57:41.903" LastActivityDate="2012-07-25T06:57:41.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3000" PostTypeId="4" CreationDate="2012-07-25T06:57:41.903" Score="0" Body="The 23 chromosome pairs, made up of 3 billion base-pairs, 22 chromosomes of which are autosomal and one which is an allosome, or sex chromosome." OwnerUserId="57" LastEditorUserId="4101" LastEditDate="2013-10-31T16:35:32.630" LastActivityDate="2013-10-31T16:35:32.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3001" PostTypeId="5" CreationDate="2012-07-25T06:59:15.850" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-07-25T06:59:15.850" LastActivityDate="2012-07-25T06:59:15.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3002" PostTypeId="4" CreationDate="2012-07-25T06:59:15.850" Score="0" Body="A predetermined methodology for carrying out an experiment." OwnerUserId="57" LastEditorUserId="4101" LastEditDate="2013-10-31T14:09:01.383" LastActivityDate="2013-10-31T14:09:01.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3003" PostTypeId="5" CreationDate="2012-07-25T07:01:31.493" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-07-25T07:01:31.493" LastActivityDate="2012-07-25T07:01:31.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3004" PostTypeId="4" CreationDate="2012-07-25T07:01:31.493" Score="0" Body="The processes by which gene products (largely RNA and proteins) are increased or decreased." OwnerUserId="57" LastEditorUserId="4101" LastEditDate="2013-10-31T18:15:00.137" LastActivityDate="2013-10-31T18:15:00.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3005" PostTypeId="5" CreationDate="2012-07-25T07:02:57.250" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-07-25T07:02:57.250" LastActivityDate="2012-07-25T07:02:57.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3006" PostTypeId="4" CreationDate="2012-07-25T07:02:57.250" Score="0" Body="The process through which a biological organism grows to maturity.  In certain contexts it can mean the changes the organism goes through over its entire lifetime." OwnerUserId="57" LastEditorUserId="4101" LastEditDate="2013-10-31T00:48:41.780" LastActivityDate="2013-10-31T00:48:41.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3007" PostTypeId="5" CreationDate="2012-07-25T07:08:54.200" Score="0" Body="&lt;p&gt;Theoretical biology can refer both to biological theory in general (as a scientific theory) or to theoretical developments that deals with biological processes, using either verbal models or as formal models that apply tools of applied mathematics.  See also &lt;a href=&quot;/questions/tagged/mathematical-models&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged 'mathematical-models'&quot; rel=&quot;tag&quot;&gt;mathematical-models&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="3624" LastEditDate="2015-01-21T09:25:08.187" LastActivityDate="2015-01-21T09:25:08.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3008" PostTypeId="4" CreationDate="2012-07-25T07:08:54.200" Score="0" Body="Questions relating to biological theory or theoretical developments that deals with biological processes.&#xD;&#xA; " OwnerUserId="57" LastEditorUserId="3624" LastEditDate="2015-01-21T09:25:08.187" LastActivityDate="2015-01-21T09:25:08.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3009" PostTypeId="5" CreationDate="2012-07-25T07:11:20.937" Score="0" Body="&lt;p&gt;Mathematical models in biology can refer to many different types of models, with the common feature that they use the tools of applied mathematics and statistics to model biological processes. For general biological theory, see &lt;a href=&quot;/questions/tagged/theoretical-biology&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged 'theoretical-biology'&quot; rel=&quot;tag&quot;&gt;theoretical-biology&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematical models can be classified based on several aspects, but the most common classification is based on the type of equations that are used to define the system:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Deterministic models&lt;/em&gt;: Algebraic and differential equations that describe a system which is assumed to have a predictable non-random behaviour (e.g., accelerated motion as defined by Newton's laws).&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Stochastic models&lt;/em&gt;: Probabilistic equations that describe a system which has an element of randomness (e.g., Brownian motion).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What questions should have this tag:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Questions involving formulation, implementation and analysis of mathematical models &lt;strong&gt;pertaining to biological systems&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="3624" LastEditDate="2015-01-21T09:35:47.197" LastActivityDate="2015-01-21T09:35:47.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3010" PostTypeId="4" CreationDate="2012-07-25T07:11:20.937" Score="0" Body="Models that analyse biological systems or processes using the tools of applied mathematics. " OwnerUserId="57" LastEditorUserId="3624" LastEditDate="2015-01-21T09:35:47.197" LastActivityDate="2015-01-21T09:35:47.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3011" PostTypeId="2" ParentId="2892" CreationDate="2012-07-25T10:11:09.140" Score="2" Body="&lt;p&gt;Response to cutaneous tissue damage occurs is several distinct but overlapping phases. First an scab is formed as the blood is 'allowed' to clot. A matrix is formed as the platelets adhere to one another, which contracts and 'dries' (forces out the serum) to form a scab. This process clearly happens prior to tissue regeneration/formation to reduce further blood loss.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Fibrinogen&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;In response to damage to blood vessels a signaling cascade is initated that results in the &lt;em&gt;massive&lt;/em&gt; production of &lt;strong&gt;fibrin&lt;/strong&gt;, which is deposited at the site of wounding and subsequently forms blood clots by activating platelets and stabilising the matrix by cross-linking (&lt;a href=&quot;http://www.ebi.ac.uk/interpro/potm/2006_11/Page1.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;see PDB's protein of the month 2006&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So this is why clots do not appear to be attached to the surrounding tissue; the fibrin causes the blood to form a matrix that is very tightly bound to itself. Only after clot formation does the tissue remodeling occur, and it is during this stage that the scab will 'bind' more stongly to the surrounding tissue.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;The Cell Types and Processes of Wound Healing&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;This figure (from (&lt;a href=&quot;http://dx.doi.org/10.1016/j.clindermatol.2006.09.007&quot; rel=&quot;nofollow noreferrer&quot;&gt;Li, 2007&lt;/a&gt;)) shows the various stages that occur and cells that are involved in acute wound healing  (wounds such as burns and cuts that heal &quot;in a timely fashion&quot;);&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/I3ITN.jpg&quot; alt=&quot;Major cells and their effects on wound healing&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-07-25T10:11:09.140" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3012" PostTypeId="1" AcceptedAnswerId="8828" CreationDate="2012-07-25T10:19:19.113" Score="6" ViewCount="114" Body="&lt;p&gt;Other than 5-Methylcytosine and the more recently discovered 5-Hydroxymethyl, 5-formil and 5-carboxylcytosine DNA modifications found in DNA sequences, what are other DNA modifications present in vertebrate genomes? There is apparently a whole bunch of modifications that can be found in prokaryotic and eukaryotic genomes, but I would like to know which ones have been found relevant in vertebrate/mammalian genomes of the eukaryotic ones.&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2013-06-17T14:59:04.570" Title="DNA modifications other than 5-mC/5-hmC/5-fC/5-caC in vertebrate genomes?" Tags="&lt;dna&gt;&lt;genomes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3013" PostTypeId="1" CreationDate="2012-07-25T11:34:47.163" Score="3" ViewCount="101" Body="&lt;p&gt;If a plant, say a ficus or a teak, as a sapling were exposed to radiation, and a tree of the same species were present at the same distance, which of the two would be more likely to mutate?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="57" LastEditDate="2012-07-26T22:04:00.867" LastActivityDate="2012-07-26T22:04:00.867" Title="Are mature trees as susceptible to mutation from exposure to radiation as seedlings?" Tags="&lt;botany&gt;&lt;mutations&gt;" AnswerCount="0" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="3014" PostTypeId="2" ParentId="2998" CreationDate="2012-07-25T15:25:11.580" Score="2" Body="&lt;p&gt;I'm unsure about the use of the word &quot;contagious&quot; here. If you would describe it as an organism &quot;catching something&quot; from another &lt;em&gt;only once&lt;/em&gt;, this answer applies (vaguely perhaps).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One example of &quot;contagious&quot; sperm: sea urchins &lt;em&gt;spray&lt;/em&gt; their sperm (called milt) into the surrounding water, so that it can hopefully fertilize roe, which are fish eggs. The eggs are also expulsed for some species, but for others they stay on the surface of the female sea urchin, as &lt;a href=&quot;http://en.wikipedia.org/wiki/Sea_urchin#cite_note-IZ-0&quot; rel=&quot;nofollow&quot;&gt;this Wikipedia article&lt;/a&gt; explains.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The gonads are lined with muscles underneath the peritoneum, and these allow the animal to squeeze its gametes through the duct and into the surrounding sea water where fertilization takes place.&#xA;  ...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In most cases, the eggs float freely in the sea, but some species hold onto them with their spines, affording them a greater degree of protection.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thus, it's entirely possible for a female sea urchin to be bombarded by free-floating sperm, to ultimately fertilize the eggs on its surface. I don't know if one would strictly consider this a contagion, but it's what I initially thought of after reading the question.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;When referring to sexually transmitted disease however, sperm &lt;em&gt;in itself&lt;/em&gt; is not contagious, as it would require the pathogen to &quot;tag along with it&quot; in whichever environment (whether it be airborne or aquatic). Also, if considering impregnation as &quot;contagious&quot;, physical contact would certainly be required.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short: &lt;strong&gt;For humans, no. For sea urchins (and likely other aquatic animals), sort of.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-07-25T15:32:54.833" LastActivityDate="2012-07-25T15:32:54.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3015" PostTypeId="1" AcceptedAnswerId="3019" CreationDate="2012-07-25T16:15:27.777" Score="12" ViewCount="963" Body="&lt;p&gt;This is another image I found on &lt;a href=&quot;https://plus.google.com/103488786418978849574/posts/TrBkrqTJvJ9&quot; rel=&quot;nofollow noreferrer&quot;&gt;Google+&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VnYNz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All lines are absolutely straight, parallel and perpendicular but why does it appear to have a curvature?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Related: &lt;a href=&quot;https://biology.stackexchange.com/questions/2824/how-does-this-illusion-work&quot;&gt;How does this illusion work?&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1039" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2012-07-25T23:02:18.113" Title="Why does this illusion work?" Tags="&lt;neuroscience&gt;&lt;eyes&gt;&lt;vision&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="3016" PostTypeId="1" AcceptedAnswerId="3023" CreationDate="2012-07-25T16:54:25.503" Score="4" ViewCount="139" Body="&lt;p&gt;Does the data indicate that if you have one, the probability of you having the other is higher than that of someone who doesn't have the one? &lt;/p&gt;&#xA;" OwnerUserId="263" LastActivityDate="2012-07-26T13:07:38.853" Title="Is there a correlation between incidence of type 1 diabetes and vitiligo?" Tags="&lt;human-biology&gt;&lt;pathology&gt;&lt;biostatistics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3019" PostTypeId="2" ParentId="3015" CreationDate="2012-07-25T23:02:18.113" Score="21" Body="&lt;p&gt;Like these questions :) Many of these illusions come from &lt;a href=&quot;http://en.wikipedia.org/wiki/Akiyoshi_Kitaoka&quot; rel=&quot;nofollow noreferrer&quot;&gt;Prof. Akiyoshi Kitaoka&lt;/a&gt;, a japanese Psychologist and expert for Gestalt Psychology. &lt;a href=&quot;http://www.ritsumei.ac.jp/~akitaoka/index-e.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;On his website&lt;/a&gt; you'll find some more fascinating illusions and questions to ask here ;) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The illusion above is named &lt;strong&gt;&lt;em&gt;Cafe Wall illusion&lt;/em&gt;&lt;/strong&gt; and the newest model to explain those illusions is the &lt;strong&gt;&lt;em&gt;contrast-polarity model&lt;/em&gt;&lt;/strong&gt;. &lt;a href=&quot;http://www.psy.ritsumei.ac.jp/~akitaoka/checkerede.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Short explanation&lt;/a&gt; from his webpage:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/i0CKX.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper explained it better to me:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Kitaoka, Pinna, and Brelstaff (2004) proposed a phenomenal model to&#xA;  explain the Café Wall illusion, which stressed the importance of&#xA;  contrast polarities of a solid square and its adjacent line segment.&#xA;  When a dark/light square is accompanied by a dark/light line segment,&#xA;  the apparent tilt is the direction of contraction of  the square angle&#xA;  (Figure 18a,b). In contrast, when a dark/ light square is accompanied&#xA;  by a light /dark line segment, the apparent tilt is the direction of&#xA;  expansion of the square angle (Figure 18c,d).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bUKj4.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This explains why you perceive a tilt. If you position the smaller squares now in distinct edges of the big squares, you can achieve 2- and 3-dimenional illusions. Here you see a increasing of the tilt due to more smaller squares:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JHZiF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here you can see that the positioning of the smaller squares is critical to achieve the 3D effect of the orignial bulge effect in your question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qqsyX.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notice that &lt;em&gt;Gestalt Psychology&lt;/em&gt; is a non-reductionistic theory approach and investigates mainly the phenomenology and underlying &lt;em&gt;Gestalt Laws&lt;/em&gt; of visual perception. How these &lt;em&gt;Gestalt Laws&lt;/em&gt; developed on a deeper level is a question of neurobiological evolution similar to, &quot;why have some species of apes color-vision and some not&quot;. The ellipses in the explaining picture above show you, that our cognitive visual machine somehow tries to group divided objects (square and line of same contrast/brightness) in one line and we see a tilt. I'm guessing here, but this is probably due to cognitive brain algorithm that saves things and objects we see and perceive mainly by countor and shapes, rather than pixel by pixel like a computer and digital camera do it, which of course don't perceive any tilt or 3D illusion in any of those trick images :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Read the papers for more explanations and examples, not behind a paywall:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.psy.ritsumei.ac.jp/~akitaoka/corner.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Apparent contraction of edge angles, A Kitaoks, Perception, 1998&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.psy.ritsumei.ac.jp/~akitaoka/tiltillusionreview2007.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tilt illusions after Oyama (1960): A review. Kitaoka, A,  Japanese Psychological Research, 49, 7-19.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="45" LastActivityDate="2012-07-25T23:02:18.113" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3020" PostTypeId="1" CreationDate="2012-07-26T02:39:35.130" Score="6" ViewCount="163" Body="&lt;p&gt;&lt;strong&gt;When a prokaryote undergoes binary fission, how are the non-DNA macromolecules distributed between the two daughter cells?&lt;/strong&gt; This is motivated by comments on a &lt;a href=&quot;https://biology.stackexchange.com/q/2977/500&quot;&gt;previous question&lt;/a&gt; and a &lt;a href=&quot;https://plus.google.com/u/0/101780559173703781847/posts/e7Q7eQKasC8&quot; rel=&quot;noreferrer&quot;&gt;G+ discussion&lt;/a&gt;. I am primarily interested in explicit mathematical models.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h3&gt;Naive model&lt;/h3&gt;&#xA;&lt;p&gt;For DNA, each copy is attached to a different part of the cell membrane, to ensure each of the daughters receives a copy. As far as I understand, there isn't such specific mechanism in place for other macromolecules. If we are allowed to assume that non-DNA macromolecules are distributed uniformly through the parent cell than this would mean the two daughter cells would receive half the proteins within statistical fluctuation. This has a specific meaning: if there are &lt;span class=&quot;math-container&quot;&gt;$N$&lt;/span&gt; molecules of type A in the parent, then the difference in number of type A molecules in the two daughters after fission will be on the order of &lt;span class=&quot;math-container&quot;&gt;$\sqrt{N}$&lt;/span&gt;.&lt;/p&gt;&#xA;&lt;p&gt;However, this model might be wrong. For instance, as the new cell-wall is being formed it could have in it specific pumps that either balance the protein levels below chance (producing an average difference lower than &lt;span class=&quot;math-container&quot;&gt;$\sqrt{N}$&lt;/span&gt;) or to create asymmetries higher than chance. Altenrnatively, the initial distribution of macromolecules in the parent could be far from symmetric for some other reasons. Which is the case?&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;If the naive model is correct, is there experimental evidence explicitly showing this?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-09-01T15:39:47.233" Title="Macromolecule levels in daughter cells after fission" Tags="&lt;cell-biology&gt;&lt;proteins&gt;&lt;reproduction&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3021" PostTypeId="1" AcceptedAnswerId="3022" CreationDate="2012-07-26T05:03:53.880" Score="9" ViewCount="713" Body="&lt;p&gt;I cut an underripe avocado in half and put half of it, without the pit but with the peel, in the refrigerator. A day later, I see very small black bumps along the cut surface. What are they? What causes them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/Ml3ZD.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ml3ZD.jpg&quot; alt=&quot;A view.&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/V9f7n.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/V9f7n.jpg&quot; alt=&quot;Another.&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="988" LastActivityDate="2012-07-26T11:11:13.947" Title="Black bumps on the cut surface of an avocado" Tags="&lt;plant-physiology&gt;&lt;fruit&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3022" PostTypeId="2" ParentId="3021" CreationDate="2012-07-26T08:17:29.983" Score="13" Body="&lt;p&gt;It looks to me (although I'd want to use a microscope to check) like the black dots are &lt;a href=&quot;http://en.wikipedia.org/wiki/Xylem&quot;&gt;xylem&lt;/a&gt;. When you cut the fruit, you've severed the xylem and also exposed the flat surface. Three main things have then happened:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The increased surface area has led to the 'fleshy' part of the fruit contracting as the cells dehydrate.&lt;/li&gt;&#xA;&lt;li&gt;The stiffer, lignified xylem tubes have retained their structure and have not contracted with the rest of the fruit, so they've become exposed. &lt;/li&gt;&#xA;&lt;li&gt;The exposed xylem have blackened due to oxidation - this eventually happens to all the flesh but, again speculating here, the oil in the fleshy tissue might protect it from oxidation longer than the exposed xylem which don't have the oil coating.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="430" LastEditorUserId="115" LastEditDate="2012-07-26T11:11:13.947" LastActivityDate="2012-07-26T11:11:13.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3023" PostTypeId="2" ParentId="3016" CreationDate="2012-07-26T13:07:38.853" Score="1" Body="&lt;p&gt;It has been associated with polymorphisms with the CD4 gene, which is usually implicated in type I diabetes. The wikipedia article for vitiligo also mentions studies for the NALP1 gene. NALP1 is expressed at high levels in T cells and Langerhan cells, white blood cells that are involved in skin autoimmunity.&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2012-07-26T13:07:38.853" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3024" PostTypeId="2" ParentId="2984" CreationDate="2012-07-26T16:50:00.260" Score="4" Body="&lt;p&gt;Telomeres (caps on the ends of chromosomes that are gradually shortened during each cell division) determine the maximum number of times a cell can divide, known as the 'Hayflick limit'. Cells that are able to express &lt;em&gt;telomerase&lt;/em&gt;, an enzyme capable of extending the telomeres, can divide indefinitely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are various types of stem cell in a body which replenish the 'pool' of cells in the tissue once they reach the end of their useful lifespan. Each stem cell expresses telomerase to lengthen the telomeres after a round of cell division. The inhibition of telomerase in somatic (normal) cells is a major 'challenge' for cancerous cells - in order to achieve uninhibited proliferation, they must express telomerase. Thus, there are many molecular similarities between stem cells and cancerous cells (well, with regards to telomerase, anyway!) [&lt;a href=&quot;http://dx.doi.org/10.1126/science.1218370&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fibroblasts are somatic cells - they are the 'normal' cells that make up the vast majority of organsisms. The only cells not known as somatic are gametes/germ cells and stem cells. They thus do not express telomerase, and have a &lt;em&gt;replicative lifespan&lt;/em&gt;, also known as a Hayflick limit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regard to your question about engineering organs, there are many resident stem cells in tissues (and thus organs) that 'top-up' the somatic cells when required. As organisms age, this pool of stem cells becomes depleted [&lt;a href=&quot;http://dx.doi.org/10.4161/cc.7.24.7214&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;]. Artificially engineering an organ such as the heart (I assume this is what you mean) would be inherently difficult, as many vascular cells are not replaced, but can last a whole lifetime - this is also true for many neuronal cells. So replicative lifespan is not necessarily related to lifespan! &lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-07-26T16:50:00.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3025" PostTypeId="1" AcceptedAnswerId="3033" CreationDate="2012-07-26T19:52:26.920" Score="5" ViewCount="103" Body="&lt;p&gt;Does anyone know the details about which line they are using to sequence as the &lt;em&gt;Drosophila melanogaster&lt;/em&gt; reference genome?&lt;/p&gt;&#xA;" OwnerUserId="1141" LastEditorUserId="57" LastEditDate="2012-07-26T21:50:24.020" LastActivityDate="2012-07-27T16:59:34.943" Title="Drosophila reference genome" Tags="&lt;genetics&gt;&lt;genomes&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3026" PostTypeId="2" ParentId="2926" CreationDate="2012-07-26T20:01:20.777" Score="6" Body="&lt;p&gt;I also recommend Jerry Coyne's book, &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0143116649&quot;&gt;&quot;Why Evolution is True.&quot;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an introductory text book, I recommend &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0878932232&quot;&gt;&quot;Evolution&quot;&lt;/a&gt; by Douglas J. Futuyma. This is a very good introductory book covers almost everything about evolution. It aims to give you an overview not the detail.&lt;/p&gt;&#xA;" OwnerUserId="1141" LastEditorUserId="57" LastEditDate="2012-07-26T22:02:14.787" LastActivityDate="2012-07-26T22:02:14.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3027" PostTypeId="1" CreationDate="2012-07-26T21:16:45.457" Score="7" ViewCount="70" Body="&lt;p&gt;I've heard time and again that living in São Paulo (a large city in Brasil) takes 1.5 years from your life expectancy. The allegation is that this happens because of air pollution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am just wondering &lt;em&gt;how&lt;/em&gt; air pollution harms humans. Is the effect cumulative? Or is it a more immediate effect that makes the elderly die sooner?&lt;/p&gt;&#xA;" OwnerUserId="1167" LastEditorUserId="1167" LastEditDate="2012-07-27T00:28:37.760" LastActivityDate="2012-07-28T07:46:22.583" Title="On the effect of polluted air on health. Is it more gradual, or more immediate?" Tags="&lt;human-biology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3028" PostTypeId="1" CreationDate="2012-07-27T12:33:03.850" Score="3" ViewCount="193" Body="&lt;p&gt;I'm interested in which biological systems or hormones are involved in the following phenomenon:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before sleep it may be difficult to find a comfortable position, and muscular aches and pains are more evident.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After 8 hours of sleep, many more positions are comfortable, and muscle aches/tension are non-existent. Some time after awakening, the feeling disappears.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What causes the difference in feeling between prior to falling asleep and after? Are there some hormones involved? Is it caused by some form of thought/feeling inhibition (e.g., part of a brain &quot;falls asleep&quot;)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I remember correctly, after long running muscles accumulate some compound that is a result of metabolizing energy without enough oxygen, which causes muscles to ache. Could a similar process be involved?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="57" LastEditDate="2012-07-28T02:22:04.863" LastActivityDate="2012-07-28T02:22:04.863" Title="What controls the feeling of discomfort/comfort before and after sleep?" Tags="&lt;human-biology&gt;&lt;muscles&gt;&lt;sleep&gt;&lt;pain&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3029" PostTypeId="2" ParentId="2851" CreationDate="2012-07-27T12:34:45.507" Score="10" Body="&lt;p&gt;I'll answer only for &lt;a href=&quot;http://en.wikipedia.org/wiki/SDS-PAGE&quot; rel=&quot;nofollow&quot;&gt;SDS-Page&lt;/a&gt;, which is the system I am most familiar with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With a discontinuous buffer system, such as the well-known &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/5432063&quot; rel=&quot;nofollow&quot;&gt;Laemmli&lt;/a&gt; system, resistance &lt;strong&gt;increases&lt;/strong&gt; during electrophoresis, as (very mobile) chloride ions are replaced by glycinate (glycine ions). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Ohm%27s_law&quot; rel=&quot;nofollow&quot;&gt;Ohms law&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Voltage (V) = Current (I)  x Resistance (R)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and the definition of power (Watts): &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Watts (W) = Current (I) x Voltage (V) = I&lt;sup&gt;2&lt;/sup&gt; x R&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;At &lt;b&gt;constant current&lt;/b&gt; electrophoresis will proceed at a uniform rate, however, as the resistance increases, so too will the voltage and the amount of heat generated.  &lt;br /&gt;&lt;br /&gt;&#xA;&#xA;In some discontinuous buffer systems, such as the Tricine/SDS system due to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2449095&quot; rel=&quot;nofollow&quot;&gt;Schägger &amp; von Jagow&lt;/a&gt;, this may be enough to crack the gel plates!&lt;/li&gt;&#xA;&#xA;&lt;li&gt;At &lt;b&gt;constant voltage&lt;/b&gt;, the current will decrease during electrophoresis; as a result less heat will be generated than &lt;b&gt;constant current&lt;/b&gt; electrophoresis, but &lt;b&gt;the rate of migration of the sample will decrease with the decrease in current&lt;/b&gt;. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. &lt;em&gt;Nature&lt;/em&gt; &lt;b&gt;227&lt;/b&gt;, 680-685. [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/5432063&quot; rel=&quot;nofollow&quot;&gt;PubMed&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Schägger, H. &amp;amp; von Jagow, G (1987).&#xA;Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. &lt;em&gt;Anal Biochem&lt;/em&gt; &lt;strong&gt;166&lt;/strong&gt;, 368-379.[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2449095&quot; rel=&quot;nofollow&quot;&gt;PubMed&lt;/a&gt;]&lt;/p&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="16651" LastEditDate="2015-12-29T14:11:01.420" LastActivityDate="2015-12-29T14:11:01.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3030" PostTypeId="1" AcceptedAnswerId="5098" CreationDate="2012-07-27T13:01:59.367" Score="3" ViewCount="199" Body="&lt;p&gt;I'm interested in learning more about the biological systems or hormones or parts of the brain that affect short term (&amp;lt;15 minutes) ability to concentrate attention on the task and be aware of the situation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I'm particularly interested in humans who are engaged in an activity that can be perceived as threatening:&lt;/strong&gt; martial arts, competitive video games, sports and other activities which may be considered &quot;fight or flight&quot;, but a scenario in which the person has chosen to stay and fight. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To clarify the question further: &lt;strong&gt;What is involved in the ability to make decisions based on the competitive situation itself, instead of responding with pre-learned techniques and tactics?&lt;/strong&gt; In one case, a person may be aware of what his/her opponents are doing, while in other cases the same person may &quot;rush in blindly&quot; and attempt to execute techniques that were learned and worked before, but will not work in the current situation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What influences this choice of responding versus acting on prior knowledge?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="57" LastEditDate="2012-07-28T02:26:11.553" LastActivityDate="2012-11-02T21:30:32.930" Title="What is the biological basis for a human's ability to think clearly and be aware while &quot;fighting/competing&quot;?" Tags="&lt;human-biology&gt;&lt;behaviour&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3031" PostTypeId="2" ParentId="3027" CreationDate="2012-07-27T14:25:28.240" Score="5" Body="&lt;p&gt;The main factors of urban air pollution are nitric oxides, carbon monoxide, and what is called in german &quot;Feinstaub&quot; (very small carbon-rich particles from diesel exhaust). However, do not forget heavy metals: street dust is especially metal-rich and is swept into the soil near the streets where children and farmed plants can take it up. Lead is a heavy metal that can be breathed in with the air. Last not least noise over a certain threshold is proven to be a cause of illness, even loss of life time (10 years near an airport, if I recall correctly, but airport noise is getting better while machines become more fuel-efficient).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question one would have to look at every single factor. Lead accumulates in bones and destroys your brain. I just see Brazil banned it too in the 80's so this one killer is no more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Tetraethyllead&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Tetraethyllead&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found a meta-study that reviews about 80 papers on the subject, especially the Sao Paulo studies, so this should fit exactly your questions:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093800/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093800/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-07-28T07:46:22.583" LastActivityDate="2012-07-28T07:46:22.583" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3033" PostTypeId="2" ParentId="3025" CreationDate="2012-07-27T16:59:34.943" Score="5" Body="&lt;p&gt;That &lt;em&gt;was&lt;/em&gt; surprisingly buried. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this in a &lt;a href=&quot;http://genomebiology.com/2002/3/12/research/0079&quot;&gt;paper describing genome build 3&lt;/a&gt; - See &quot;Materials and Methods&quot;.  I imagine that this is consistent through to the current build.  In any case it should get you started. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Sequencing templates were made from P1, BAC and WGS DNA libraries using the D. melanogaster strain yellow (y1); cinnabar (cn1) brown (bw1) speck (sp1).&quot;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-07-27T16:59:34.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3034" PostTypeId="5" CreationDate="2012-07-28T04:46:34.090" Score="0" Body="&lt;p&gt;Neurotransmitters are used to cross the synaptic cleft to bind with post-synaptic receptors, and in certain cases retrograde messengers are passed back to the presynaptic cell.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term is thought to have been coined by &lt;a href=&quot;http://en.wikipedia.org/wiki/Charles_Scott_Sherrington&quot; rel=&quot;nofollow&quot;&gt;Sir Charles Scott Sherrington&lt;/a&gt;, an early pioneer in neuroscience and pathology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also &lt;a href=&quot;/questions/tagged/neuroscience&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;neuroscience&amp;#39;&quot; rel=&quot;tag&quot;&gt;neuroscience&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="4101" LastEditDate="2013-10-31T19:31:14.107" LastActivityDate="2013-10-31T19:31:14.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3035" PostTypeId="4" CreationDate="2012-07-28T04:46:34.090" Score="0" Body="A connection between neurons, which is either continuous (in electrical synapses) or interrupted by a cleft (in chemical synapses), through which communication is established." OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-07-28T10:06:47.190" LastActivityDate="2012-07-28T10:06:47.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3036" PostTypeId="5" CreationDate="2012-07-28T04:50:08.860" Score="0" Body="&lt;p&gt;Involves library preparation and sequencing. Library preparation might slightly vary for different classes of RNAs.  The general procedure for mRNA and most ncRNA sequencing involves:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Enrichment of polyA RNAs using oligo-dT beads to remove ribosomal RNA. Alternatively, ribosomal RNAs can be selectively removed. Refer to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20688152&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;. &lt;/li&gt;&#xA;&lt;li&gt;cDNA preparation&lt;/li&gt;&#xA;&lt;li&gt;Adapter ligation&lt;/li&gt;&#xA;&lt;li&gt;PCR amplification&lt;/li&gt;&#xA;&lt;li&gt;Sequencing&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;See also &lt;a href=&quot;/questions/tagged/dna-sequencing&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;dna-sequencing&amp;#39;&quot; rel=&quot;tag&quot;&gt;dna-sequencing&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="4101" LastEditDate="2013-10-31T14:13:20.173" LastActivityDate="2013-10-31T14:13:20.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3037" PostTypeId="4" CreationDate="2012-07-28T04:50:08.860" Score="0" Body="Determining the sequence of RNA. This technique is used for discovery and quantification of mRNAs and ncRNAs. " OwnerUserId="57" LastEditorUserId="3340" LastEditDate="2013-04-09T13:26:32.043" LastActivityDate="2013-04-09T13:26:32.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3038" PostTypeId="5" CreationDate="2012-07-28T04:52:06.737" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-07-28T04:52:06.737" LastActivityDate="2012-07-28T04:52:06.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3039" PostTypeId="4" CreationDate="2012-07-28T04:52:06.737" Score="0" Body="The study of the appropriate provisions required to sustain life in an organism or the provisions themselves." OwnerUserId="57" LastEditorUserId="4101" LastEditDate="2013-10-31T00:55:44.477" LastActivityDate="2013-10-31T00:55:44.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3040" PostTypeId="5" CreationDate="2012-07-28T04:55:53.923" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-07-28T04:55:53.923" LastActivityDate="2012-07-28T04:55:53.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3041" PostTypeId="4" CreationDate="2012-07-28T04:55:53.923" Score="0" Body="The concepts of mate choice and competition over eligible members of the opposite sex in animals, including humans." OwnerUserId="57" LastEditorUserId="4101" LastEditDate="2013-10-31T18:23:23.370" LastActivityDate="2013-10-31T18:23:23.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3042" PostTypeId="2" ParentId="1686" CreationDate="2012-07-28T16:32:00.817" Score="6" Body="&lt;p&gt;The previous answer isn't quite correct, because, well, blood flow is complicated and the body has autoregulatory mechanisms. As Alex mentioned, &lt;a href=&quot;http://en.wikipedia.org/wiki/Vasoconstriction&quot; rel=&quot;nofollow noreferrer&quot;&gt;vasoconstriction&lt;/a&gt; doesn't occur in capillaries because they lack a muscle layer. It does occur in the small arterioles before and after the glomerulus (the afferent and efferent arterioles, respectively).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bernoulli's principle mainly applies to larger arteries and arterioles, and not capillaries. Capillaries are so tiny that the red blood cell is a significant portion of the diameter, so the assumption of no viscosity is no longer valid. See &lt;a href=&quot;http://www.physicsforums.com/archive/index.php/t-207950.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this discussion&lt;/a&gt; for an explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To address your question, here's a basic picture of the glomerulus, from Gray's Anatomy.&#xA;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/f/fd/Gray1129.png&quot; alt=&quot;image&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The afferent arteriole is in red, and the efferent arteriole in blue. The glomerular filtration rate (GFR) depends on the pressure difference between the two, which affects the hydrostatic pressure at the glomerulus. Also, note that vasodilation has the opposite effect of vasoconstriction on GFR.  (For a nice image and explanation, look at &lt;a href=&quot;http://alexandria.healthlibrary.ca/documents/notes/bom/unit_2/L-51%20Renal%20Clearances%20%20GFR%20and%20Renal%20iqbglo.xml&quot; rel=&quot;nofollow noreferrer&quot;&gt;Figure 6 here&lt;/a&gt;) So:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Constriction of the &lt;strong&gt;afferent&lt;/strong&gt; arteriole decreases the blood flow &lt;em&gt;into&lt;/em&gt; the glomerulus and thus the glomerular hydrostatic pressure, which leads to a &lt;strong&gt;decrease&lt;/strong&gt; in GFR.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In contrast, constriction of the &lt;strong&gt;efferent&lt;/strong&gt; arteriole decreases blood flow &lt;em&gt;out&lt;/em&gt; of the glomerulus, and this increases the glomerular hydrostatic pressure and leads to an &lt;strong&gt;increase&lt;/strong&gt; in GFR.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Both the afferent and efferent arterioles are regulated through hormones (and drugs that inhibit the hormones). Prostaglandins dilate the afferent arterioles, and NSAIDs inhibit this action. Angiotensin II preferentially constricts the efferent arteriole, and this action is restricted by an ACE inhibitor. (Source: First Aid for the USMLE Step 1)&lt;/p&gt;&#xA;" OwnerUserId="1166" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.710" LastActivityDate="2012-07-28T16:39:07.110" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3043" PostTypeId="1" AcceptedAnswerId="3047" CreationDate="2012-07-29T09:59:37.360" Score="9" ViewCount="6270" Body="&lt;p&gt;Just read &lt;a href=&quot;https://biology.stackexchange.com/questions/1466/whats-the-effect-of-oxygen-deficit-on-plants&quot;&gt;What&amp;#39;s the effect of oxygen deficit on plants?&lt;/a&gt; ; and wondered whether the opposite would have any effect on a plant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is to say, if a potted plant were placed under a bell-jar and the air within replaced by pure oxygen would the plant starve? If the environment/soil were loosely radioactive, would it make a difference?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2020-12-01T16:40:47.067" Title="What is the effect of a pure-oxygen environment on a plant?" Tags="&lt;plant-physiology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3044" PostTypeId="1" AcceptedAnswerId="3096" CreationDate="2012-07-29T10:18:42.530" Score="7" ViewCount="625" Body="&lt;p&gt;One argument often given in favour of saving current and planting additional plants/saplings is the roots hold soil together and prevent soil erosion. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unlike plants that may be uprooted, a large tree may only be chopped down; its roots continue to remain buried. Do these, now dead, roots continue to prevent soil erosion, or does the plant have to be alive and kicking?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My guess is the latter, perhaps because absorption of water possibly 'compresses' the soil over the root.&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="57" LastEditDate="2012-07-29T10:31:10.987" LastActivityDate="2012-08-01T17:18:00.453" Title="Does a plant have to be alive for its roots to prevent erosion?" Tags="&lt;plant-anatomy&gt;&lt;environment&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3045" PostTypeId="1" CreationDate="2012-07-29T12:30:26.773" Score="6" ViewCount="419" Body="&lt;p&gt;How do hibernation/aestivation happen? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read on wikipedia that a squirrel injected with the body fluids of a hibernating fellow is more prone to hibernation. If hibernation/aestivation are driven by biochemicals and not merely the weather, can the process be induced in higher beings such as humans to replace surgical (etc) anesthesia? How is the one different from the other?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strike&gt;p.s. Or perhaps to induce hibernation for the trip across the Solar System (+: &lt;/strike&gt;&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2012-07-29T14:48:07.390" LastActivityDate="2014-06-23T20:45:54.610" Title="How is hibernation/aestivation different from anesthesia?" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3046" PostTypeId="2" ParentId="2976" CreationDate="2012-07-29T12:47:00.567" Score="2" Body="&lt;p&gt;I went into this with the same assumptions that &lt;code&gt;jello&lt;/code&gt; did, but I found two studies that had some interesting results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20019633&quot; rel=&quot;nofollow&quot;&gt;Isojärvi (2010)&lt;/a&gt; found that in obese and under-exercised adults, physical fitness level predicted, among other things, a significant proportion of the variance of nerve conduction velocity and &lt;a href=&quot;http://en.wikipedia.org/wiki/F_wave&quot; rel=&quot;nofollow&quot;&gt;F-wave&lt;/a&gt; latency.  So, these individuals may theoretically have a slower response to noxious stimuli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While Type II diabetes is not always a result of obesity, there is often a high correlation between the two.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15727946&quot; rel=&quot;nofollow&quot;&gt;Oltman (2005)&lt;/a&gt; found that, in &quot;Zucker diabetic &lt;em&gt;fatty&lt;/em&gt;&quot; rats (an animal model of Type II diabetes), motor nerve conduction velocity in the sciatic was significantly slowed.  This effect, too, would affect the rate with which an individual could withdraw a limb from a noxious stimuli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I don't think that anatomical changes in the bodies of individuals who are obese would have any effect, but clearly there are physiological changes in the neurons of these individuals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;References:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isojärvi H, Keinänen-Kiukaanniemi S, Kallio M, Kaikkonen K, Jämsä T, Korpelainen J, Korpelainen R. (2010). Exercise and fitness are related to peripheral nervous system function in overweight adults. &lt;em&gt;Med Sci Sports Exerc. 42&lt;/em&gt;(7):1241-5.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oltman CL, Coppey LJ, Gellett JS, Davidson EP, Lund DD, Yorek MA. (2005).  Progression of vascular and neural dysfunction in sciatic nerves of Zucker diabetic fatty and Zucker rats. &lt;em&gt;Am J Physiol Endocrinol Metab. 289&lt;/em&gt;(1):E113-22.&lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2012-07-29T12:47:00.567" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3047" PostTypeId="2" ParentId="3043" CreationDate="2012-07-29T14:46:09.920" Score="6" Body="&lt;p&gt;Ask yourself, where would the plant take the carbon for construction of all kind of molecules, most important the cell membrane and cell wall of newly divided cells. Plants do not eat! So they have to get their carbon from somewhere else.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-07-29T14:46:09.920" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3048" PostTypeId="1" CreationDate="2012-07-29T21:45:28.433" Score="7" ViewCount="3620" Body="&lt;p&gt;Does a female animal that lays eggs experience a pregnancy-like period of time, where she will feel and behave differently as if she were fertilized and her body is prepared to lay a fertile egg, not a sterile egg (like the chicken eggs we eat)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;does the egg takes more time to be formed? &lt;/li&gt;&#xA;&lt;li&gt;is it different in size?&lt;/li&gt;&#xA;&lt;li&gt;maybe the animal will feel hormonal changes that cause it to increase body heat to help her sit on the egg, etc.?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="680" LastEditorUserId="43" LastEditDate="2012-08-03T13:09:52.200" LastActivityDate="2013-05-03T06:40:57.977" Title="Do egg laying animals experience a pregnancy?" Tags="&lt;zoology&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3049" PostTypeId="1" AcceptedAnswerId="3073" CreationDate="2012-07-30T08:22:21.963" Score="10" ViewCount="1887" Body="&lt;p&gt;I have been wondering for some time whether several drugs really have an expiration date. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's narrow the scope and think about only &quot;common&quot; drugs, e.g NSAIDs, antibiotics etc. &#xA;For example, would antibiotics in the pills get deactivated or decomposed? &lt;/p&gt;&#xA;" OwnerUserId="673" LastEditorUserId="57" LastEditDate="2012-07-30T18:35:21.623" LastActivityDate="2012-08-01T00:05:07.373" Title="Do drugs always degrade after they have passed their expiration date?" Tags="&lt;pharmacology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="3050" PostTypeId="1" AcceptedAnswerId="3054" CreationDate="2012-07-30T10:45:17.067" Score="7" ViewCount="3695" Body="&lt;p&gt;Since the new queens-to-be have wings, it means that ants either evolved from insects that can fly, or insects that can fly evolved from ants, or that we have a case of parallel evolution (which is unlikely).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, what evolutionary benefit is there to &lt;em&gt;not&lt;/em&gt; have wings?&lt;/p&gt;&#xA;" OwnerUserId="1185" LastEditorUserId="55929" LastEditDate="2020-01-06T00:33:24.173" LastActivityDate="2020-01-06T00:33:24.173" Title="Why don't all ants have wings?" Tags="&lt;evolution&gt;&lt;entomology&gt;&lt;ant&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3051" PostTypeId="1" AcceptedAnswerId="3141" CreationDate="2012-07-30T13:34:57.097" Score="11" ViewCount="1233" Body="&lt;p&gt;I recently finished an experiment where I analyzed the rate of ATP hydrolysis of Heat shock protein 104 in three species of fungi. They have shown to all have different rates of ATPase activity. How would I explain these findings based on structure/ATP affinity?  The experiment was done &lt;em&gt;in vitro&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The species under consideration:&#xA;&lt;em&gt;Candida albicans,&#xA;Saccharomyces cerevisiae,&#xA;Schizosaccharomyces pombe&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1186" LastEditorUserId="1186" LastEditDate="2012-07-30T14:43:41.937" LastActivityDate="2012-08-12T13:17:37.490" Title="How would I explain different properties of the same protein in different species?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3052" PostTypeId="1" CreationDate="2012-07-30T14:33:25.770" Score="12" ViewCount="6262" Body="&lt;p&gt;I suppose that the question should be turned around to &quot;Why is it extremely rare to see black people competing in professional swimming?&quot; because it is the absence of this phenotype while watching the Olympics that caused me to ask this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So,&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;why are there very few black people competing at world class level swimming?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;While I'm here I may as well ask the question:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Why are black people faster sprinters than white people when it comes to world class level?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;And of course I want biological reasons.&lt;/p&gt;&#xA;" OwnerUserId="839" LastEditorUserId="839" LastEditDate="2012-11-04T14:09:23.683" LastActivityDate="2019-07-31T14:39:56.180" Title="Is there any biological reason that professional swimming is dominated by white people?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="7" ClosedDate="2019-08-16T21:56:45.227" ContentLicense="CC BY-SA 3.0" />
  <row Id="3053" PostTypeId="1" CreationDate="2012-07-30T17:00:52.337" Score="4" ViewCount="2397" Body="&lt;p&gt;I am wondering whether a behavioral trait (e.g. fear or stress experienced in the lifetime of the parent) can be transmitted genetically to its offspring?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that a behavioral tendency for stress acquired through evolutionary time can be transmitted from parent to child, but I'm wondering whether a trait not present before can be transmitted between 2 generations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example many studies claim that offsprings of holocaust survivors inherit psychopathological disorders. I'm wondering how this inheritance could occur genetically given such a short time period?&lt;/p&gt;&#xA;" OwnerUserId="1187" LastEditorUserId="430" LastEditDate="2012-07-31T08:37:31.910" LastActivityDate="2016-04-21T20:36:32.337" Title="Can parents' learned traits be transmitted genetically?" Tags="&lt;evolution&gt;&lt;genetics&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3054" PostTypeId="2" ParentId="3050" CreationDate="2012-07-31T04:56:22.647" Score="13" Body="&lt;p&gt;Certainly ants evolved from insects that could fly.  All the earliest wasps (ants are specialized wasps) could fly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Building and maintaining wings is expensive in terms of energy.  That's an obvious evolutionary advantage to not having wings.  So if there's insufficient benefit from having wings then there's selective pressure against having wings.&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2012-07-31T04:56:22.647" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3056" PostTypeId="2" ParentId="3052" CreationDate="2012-07-31T07:22:43.733" Score="21" Body="&lt;p&gt;It's not biological, it's simply an education issue, and googling would give you:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Just under 70% of African-American children surveyed said they had no or low ability to swim. Low ability merely meant they were able to splash around in the shallow end. A further 12% said they could swim but had &quot;taught themselves&quot;.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bbc.co.uk/news/world-us-canada-11172054&quot;&gt;http://www.bbc.co.uk/news/world-us-canada-11172054&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Unlike the UK, where learning to swim is enshrined in the national curriculum except in Scotland, the ultimate responsibility in the US often lies with parents.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-07-31T07:22:43.733" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3059" PostTypeId="2" ParentId="2835" CreationDate="2012-07-31T07:39:31.340" Score="2" Body="&lt;p&gt;I don't know anything about the &quot;Disney index&quot; but the equation you use looks like it's a version of Simpson's D, a very common biodiversity index.  If you're just estimating two different kinds of sites (your two management strategies) I would suggest a rarefaction method.  This can be estimated in either the vegan package in R, or EstimateS &lt;a href=&quot;http://viceroy.eeb.uconn.edu/EstimateS/&quot; rel=&quot;nofollow&quot;&gt;http://viceroy.eeb.uconn.edu/EstimateS/&lt;/a&gt; by Robert Colwell.  Rarefaction takes into account the number of samples you have when calculating an estimate of the number of species you find.  You could also use straight forward species richness estimators like Chao1 and Chao2.  The best &quot;diversity index&quot; in my opinion is &lt;a href=&quot;http://www.edinburgh.ceh.ac.uk/Archive_scaling/6687.htm&quot; rel=&quot;nofollow&quot;&gt;Hurlbert's PIE&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="1097" LastActivityDate="2012-07-31T07:39:31.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3060" PostTypeId="1" AcceptedAnswerId="3061" CreationDate="2012-07-31T08:36:02.630" Score="6" ViewCount="156" Body="&lt;p&gt;It is common knowledge that when you're cold you could get a cold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the mechanism linking temperature and viral infection?&lt;/p&gt;&#xA;" OwnerUserId="1190" LastActivityDate="2012-07-31T09:42:53.980" Title="What is the biological mechanism linking temperature and probability to be infected with a virus?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;virology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3061" PostTypeId="2" ParentId="3060" CreationDate="2012-07-31T09:42:53.980" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;It is common knowledge that when you're cold you could get a cold.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This may be a nice illustration why we need to be wary of “common knowledge”.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What is the mechanism linking temperature and viral infection?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This isn’t clear. There are a few proposed mechanisms but a likely explanation is: &lt;a href=&quot;http://www.straightdope.com/columns/read/997/why-is-winter-the-season-for-colds-flu-etc&quot;&gt;“there is no mechanism”&lt;/a&gt; – and the assumed correlation between cold temperature and catching a cold might be nothing more than an illusion – a form of &lt;a href=&quot;http://en.wikipedia.org/wiki/Confirmation_bias&quot;&gt;confirmation bias&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, we don’t even know for sure that the cold season coincides with cold temperatures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, a 2007 review [1] found that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;… most of the available evidence from laboratory and clinical studies suggests that &lt;strong&gt;inhaled cold air, cooling of the body surface and cold stress induced by lowering the core body temperature cause pathophysiological responses such as vasoconstriction in the respiratory tract mucosa and suppression of immune responses&lt;/strong&gt;, which are responsible for increased susceptibility to infections.&#xA;   [emphasis mine]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So according to their results, potential mechanisms which link temperatures and viral infection are indirect:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The lowered core body temperature would imply, in my interpretation, that the body has to expend more energy to maintain its temperature, and hence less energy to power its immune system (which is expensive).&lt;/li&gt;&#xA;&lt;li&gt;Lack of respiratory tract mucosa removes an important physical barrier between the environment and the body, and allows pathogens to enter the body with much less resistance.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17705968&quot;&gt;Mourtzoukou &amp;amp; Falagas: &lt;em&gt;Exposure to Cold and respiratory tract infections&lt;/em&gt;, in Int J Tuberc Lung Dis. (2007), pp 938–943&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="166" LastActivityDate="2012-07-31T09:42:53.980" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3062" PostTypeId="2" ParentId="3043" CreationDate="2012-07-31T10:11:27.127" Score="9" Body="&lt;p&gt;As hinted in other answers, the key problem with a pure oxygen environment would be the inability to photosynthesise caused by the absence of carbon dioxide.&lt;/p&gt;&#xA;&lt;p&gt;The overall equation for photosynthesis (the process in which energy from the sun is harnessed to fix inorganic &lt;em&gt;carbon dioxide&lt;/em&gt; into organic molecules that  are of use to the plant) is:&lt;/p&gt;&#xA;&lt;h1&gt;6CO&lt;sub&gt;2&lt;/sub&gt; + 6H&lt;sub&gt;2&lt;/sub&gt;O → 6O&lt;sub&gt;2&lt;/sub&gt; + C&lt;sub&gt;6&lt;/sub&gt;H&lt;sub&gt;12&lt;/sub&gt;O&lt;sub&gt;6&lt;/sub&gt;&lt;/h1&gt;&#xA;&lt;p&gt;The carbon dioxide required for photosynthesis is obtained from the atmosphere by diffusion through stomata on the leaves.  Therefore if the atmosphere contains no carbon dioxide (i.e. in the scenario you suggest) photosynthesis would not progress, meaning glucose used by the plant in respiration would not be replaced.&lt;/p&gt;&#xA;&lt;p&gt;This would eventually lead to the cessation of cellular respiration due to a lack of reactant.  This would cause the plant to die.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-07-31T10:11:27.127" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3063" PostTypeId="1" AcceptedAnswerId="3065" CreationDate="2012-07-31T11:04:23.293" Score="11" ViewCount="1151" Body="&lt;p&gt;I've read a little about hybrid animals, and have been amazed by the fact that the sex of the parent species determine the species of the offspring, in some hybrids.&#xA;A male horse and a female donkey will give birth to a &lt;a href=&quot;http://en.wikipedia.org/wiki/Hinny&quot; rel=&quot;nofollow&quot;&gt;Hinny&lt;/a&gt;, while a female horse and a male donkey will give birth to a &lt;a href=&quot;http://en.wikipedia.org/wiki/Mule&quot; rel=&quot;nofollow&quot;&gt;Mule&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same goes for tigers and lions, male lion and a female tigress will give birth to a &lt;a href=&quot;http://en.wikipedia.org/wiki/Liger&quot; rel=&quot;nofollow&quot;&gt;Liger&lt;/a&gt;, while a male tiger and a female lioness mating will result in a &lt;a href=&quot;http://en.wikipedia.org/wiki/Tiglon&quot; rel=&quot;nofollow&quot;&gt;Tiglon&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought that the only difference between the male and female reproductive cell's DNA code is the X-Y chromosome that determines gender, not differences that can define the phenotypical result of the offspring. Why does this happen?&lt;/p&gt;&#xA;" OwnerUserId="680" LastEditorUserId="14629" LastEditDate="2015-06-19T20:28:58.267" LastActivityDate="2015-06-20T20:20:57.017" Title="Why does the sex of the parent species determines the species of a hybrid offspring" Tags="&lt;zoology&gt;&lt;reproduction&gt;&lt;hybridization&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3064" PostTypeId="1" AcceptedAnswerId="23355" CreationDate="2012-07-31T12:52:35.617" Score="11" ViewCount="713" Body="&lt;p&gt;What length are the shortest strings of DNA not present in any known person's genome, and what are they?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And is there a database online by which I could find this out?&lt;/p&gt;&#xA;" OwnerUserId="1191" LastEditorUserId="112" LastEditDate="2012-08-01T08:05:42.713" LastActivityDate="2014-10-22T02:56:33.257" Title="Shortest strings not present in the human genome" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;&lt;human-genome&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3065" PostTypeId="2" ParentId="3063" CreationDate="2012-07-31T13:34:22.680" Score="11" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I thought that the only difference between the male and female reproductive cell's DNA code is the X-Y chromosome that determines gender, not differences that can define the species of the offspring. Why does this happen?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well that is not the only difference, there are certain characters that are only transmitted by one of the parents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all you have to think that the &lt;a href=&quot;http://en.wikipedia.org/wiki/Zygote&quot;&gt;zygote&lt;/a&gt; (the cell deriving from the fusion of two gametes) contains the nucleus of the egg and of the sperm &lt;strong&gt;but the cytoplasm of the egg only&lt;/strong&gt; (or at least in great part).&#xA;One thing that is present in the cytoplasm are mithocondria, which contain DNA, called mtDNA. &lt;a href=&quot;http://en.wikipedia.org/wiki/MtDNA&quot;&gt;mtDNA&lt;/a&gt; is therefore transmitted only by the mother (at least, in most species). Therefore a hinny will have donkey mtDNA, while a mule will have horse mtDNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, cytoplasm contains transcription factors and various proteins that will influence the subsequent development of the zygote into an embryo and, again, these are maternally derived.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another thing that changes is that there are certain genes on nuclear DNA which are expressed in a single-parent manner. That is, you have 2 copies of these genes, called &lt;a href=&quot;http://en.wikipedia.org/wiki/Genomic_imprinting&quot;&gt;&lt;em&gt;imprinted genes&lt;/em&gt;&lt;/a&gt;, one from the mother and one from the father but only one of these copies -that of the mother or of the father, depending on the gene- will be expressed.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-07-31T13:34:22.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3066" PostTypeId="1" AcceptedAnswerId="3070" CreationDate="2012-07-31T14:34:11.793" Score="11" ViewCount="5877" Body="&lt;p&gt;What is the difference between a naive p-value and an adjusted p-value in the results of a GWAS study? See from &lt;a href=&quot;http://www.nature.com/ng/journal/v44/n8/full/ng.2344.html&quot;&gt;this paper&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After Bonferroni adjustment, a single gene, DCTN4 (encoding dynactin 4) on chromosome 5q33.1, was significantly associated with time to chronic P. aeruginosa infection (naïve P = 2.2 × 10−6; adjusted P = 0.025; Supplementary Fig. 1).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="658" LastEditorUserId="67" LastEditDate="2012-08-11T21:28:38.713" LastActivityDate="2014-01-15T16:56:56.447" Title="What is the difference between naive and adjusted p-values in a GWAS study?" Tags="&lt;epidemiology&gt;&lt;statistics&gt;&lt;gwas&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3067" PostTypeId="1" CreationDate="2012-07-31T14:37:29.067" Score="9" ViewCount="1408" Body="&lt;p&gt;Is there something encoded within us that makes us attracted to, e.g., someone&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;taller or shorter&lt;/li&gt;&#xA;&lt;li&gt;with blonde or brunette hair &lt;/li&gt;&#xA;&lt;li&gt;with green or blue eyes? &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Or, is this phenomenon completely based on our social/cultural environment? &lt;/p&gt;&#xA;" OwnerUserId="1193" LastEditorUserId="57" LastEditDate="2012-07-31T21:53:28.713" LastActivityDate="2012-07-31T21:53:28.713" Title="Is there a biological basis to physical attraction?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3069" PostTypeId="2" ParentId="3067" CreationDate="2012-07-31T17:00:40.263" Score="9" Body="&lt;p&gt;Yes, there is a biological basis. Your examples seem a little social/cultural to me, though. In any case, here are some examples I came across. One &lt;a href=&quot;http://www.berkeley.edu/news/media/releases/2007/02/06_sweat.shtml&quot;&gt;study&lt;/a&gt; that showed that women's hormones rose in response to smelling male sweat.  There's also a large &lt;a href=&quot;http://www.psychworld.com/psychology-of-beauty-2011-06&quot;&gt;psychological component&lt;/a&gt; that, for example, shows people find symmetry important in beauty.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1467-2494.2005.00286.x/abstract&quot;&gt;review&lt;/a&gt; discusses various aspects of facial beauty, and mentions that several studies have shown certain physical attractiveness standards are common across ethnic groups. It also mentions &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1090513801000666&quot;&gt;another study&lt;/a&gt; that shows how women are more attracted to a &quot;masculine&quot; face during the high-risk phase of their menstrual cycle.&lt;/p&gt;&#xA;" OwnerUserId="1166" LastActivityDate="2012-07-31T17:00:40.263" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3070" PostTypeId="2" ParentId="3066" CreationDate="2012-07-31T19:13:38.940" Score="18" Body="&lt;p&gt;There’s an XKCD comic which &lt;a href=&quot;http://xkcd.com/882/&quot; rel=&quot;nofollow&quot;&gt;explains the problem&lt;/a&gt;. Unfortunately, that comic is too big to post here. Briefly, a &lt;em&gt;p&lt;/em&gt;-value of 0.1 says (roughly) that there’s a 10% chance (0.1) of the observed result being as extreme&lt;sup&gt;1&lt;/sup&gt; as it is simply due to chance (sampling variation from a population), &lt;em&gt;assuming the null hypothesis is true&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Often, 5% is more or less arbitrarily chosen as “cut-off”: results with &lt;em&gt;p&lt;/em&gt;-values below that (which occur by chance 1 time out of 20) are called &lt;em&gt;significant&lt;/em&gt; – results above are insignificant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this directly implies that when doing multiple studies, say 20, there’s a very high chance of getting a “significant” result by pure chance, without there being a real effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GWAS studies essentially perform experiments on many (hundreds or thousands) of factors simultaneously. Therefore, reporting the pure &lt;em&gt;p&lt;/em&gt;-values would be very misleading since there would be a lot of spurious results with “significant” &lt;em&gt;p&lt;/em&gt;-values. The probability of getting one or more spurious hits is called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Familywise_error_rate&quot; rel=&quot;nofollow&quot;&gt;familywise error rate (FWER)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The FWER can be reduced by &lt;em&gt;adjusting&lt;/em&gt; the &lt;em&gt;p&lt;/em&gt; values, for instance by performing the &lt;a href=&quot;http://en.wikipedia.org/wiki/Bonferroni_correction&quot; rel=&quot;nofollow&quot;&gt;Bonferroni correction&lt;/a&gt;. The resulting &lt;em&gt;p&lt;/em&gt;-values are quite a bit higher, which reflects the reduced certainty that the result is due to chance, i.e. the reduced significance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It doesn’t generally make sense to report the unadjusted &lt;em&gt;p&lt;/em&gt;-value. It was probably reported here because correcting for FWER is quite conservative (i.e. it trades a low false-positive rate for an increased false-negative rate) and the authors feared that the adjusted &lt;em&gt;p&lt;/em&gt;-value looked less impressive than it should. This involves a fair bit of interpretation.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt; extreme = different from the expected result under the null hypothesis&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="166" LastEditDate="2014-01-15T16:56:56.447" LastActivityDate="2014-01-15T16:56:56.447" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3072" PostTypeId="2" ParentId="3053" CreationDate="2012-07-31T23:45:19.040" Score="4" Body="&lt;p&gt;Strictly speaking no. There are ideas about cultural inheritance though that seem relevant here: see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11425279&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/11425279&lt;/a&gt;.  Cultural inheritance theory uses the plasticity of the human brain as the evidence for the underlying genetics of culture.  I.e. we aren't born with the ability to speak English because our parents learned it but we have an the underlying brain structure that is controlled by genetics to learn cultural traits.  It seems far more likely that the phenomenon you describe with holocaust survivors is more related to some environmental effects (from their parents) than anything genetic.  In the comments stress hormones in pregnant mothers were mentioned.  Any impact these have on the offspring are not truly &quot;genetic&quot;, they're termed &quot;maternal effects&quot; in the evolution literature.  In fact most selection studies go to great lengths to control for them or eliminate them.  They aren't truly genetic because these traits would never get passed down to the grandoffspring of the original mother.  &lt;/p&gt;&#xA;" OwnerUserId="1097" LastActivityDate="2012-07-31T23:45:19.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3073" PostTypeId="2" ParentId="3049" CreationDate="2012-08-01T00:05:07.373" Score="3" Body="&lt;p&gt;Drugs do not have to degrade after their expiration date and passing the expiration date has more than one possible meaning. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all chemical compounds vary in their susceptibility to breakdown over time.  If they are kept away from oxygen, high temperatures (or kept in very low temperatures), and they are of a robust chemical nature, they might be stored for much longer than their expiration date and remain just as strong. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Over time, pharma compounds will chemically break down and lose their potency.  In many cases, you will find that they simply don't do anything when you take them.  This link cites a study that &lt;a href=&quot;http://www.health.harvard.edu/fhg/updates/update1103a.shtml&quot; rel=&quot;nofollow&quot;&gt;many drugs can retain their potency 15 years after they are made&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are important exceptions.  Two examples are &lt;a href=&quot;http://en.wikipedia.org/wiki/Tetracycline_antibiotics#Cautions&quot; rel=&quot;nofollow&quot;&gt;tetracycline&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Tylenol#Dangers&quot; rel=&quot;nofollow&quot;&gt;acetaminophen&lt;/a&gt; (tylenol) whose breakdown products can increase the tendency for these drugs to induce liver damage. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-08-01T00:05:07.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3074" PostTypeId="2" ParentId="2707" CreationDate="2012-08-01T00:31:37.513" Score="4" Body="&lt;p&gt;As Armatus pointed out above, all viruses are obligately intracellular, and their medical and economic importance cannot be overstated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many bacterial species live intracellularly. The arthropod specific &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Wolbachia&quot; rel=&quot;nofollow&quot;&gt;Wolbachia&lt;/a&gt;&lt;/em&gt; has a wide variety of consequences for its host, including alteration of reproduction and sex ratios, induction of reproductive isolation possibly driving speciation, and conferring protection from some viral infections.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eukaryotes can be intracellular parasites as well: Malaria is a well-known example. &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Toxoplasma_gondii&quot; rel=&quot;nofollow&quot;&gt;Toxoplasma gondii&lt;/a&gt;&lt;/em&gt; is another intracellular parasite that uses cats as a primary host, but can use other warm-blooded animals (such as humans, rats, and birds) as intermediate hosts. &lt;em&gt;T. gondii&lt;/em&gt; infection has been shown to induce behavioral changes in rats, causing an attraction to cats (thereby increasing the chance that the parasite will infect the cat and sexually reproduce). There is also some evidence that &lt;em&gt;T. gondii&lt;/em&gt; infection in humans causes behavioral and psychological changes such as decreased reaction times, and links to depression and suicide.&lt;/p&gt;&#xA;" OwnerUserId="1197" LastActivityDate="2012-08-01T00:31:37.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3075" PostTypeId="2" ParentId="3064" CreationDate="2012-08-01T00:53:05.130" Score="8" Body="&lt;p&gt;The human genome contains less than 4&lt;sup&gt;16&lt;/sup&gt; base pairs, so, even after including a factor of 2 for the two strands and another to allow for some genetic variation, there must certainly exist some 17-base string not found in either strand of the genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, 4&lt;sup&gt;17&lt;/sup&gt; bits is two gigabytes, which fits easily within the memory of a typical desktop computer these days, so a simple and efficient algorithm for finding such a string would be to set up an array of 4&lt;sup&gt;17&lt;/sup&gt; bits, initialize them all to zero, and then simply iterate over the entire genome (including all known variations), taking each 17-base subsequence (and its complement), mapping them to base-4 integers and setting the bits in the array at the positions given by those integers to one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you're done, any remaining zero bits will correspond to strings not found in the genome.  More to the point, the longest consecutive block of zero bits will give you the shortest base string not present in the genome.&lt;/p&gt;&#xA;" OwnerUserId="239" LastEditorUserId="239" LastEditDate="2012-08-01T00:59:44.933" LastActivityDate="2012-08-01T00:59:44.933" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="3076" PostTypeId="2" ParentId="3064" CreationDate="2012-08-01T01:00:53.327" Score="4" Body="&lt;p&gt;This actually wouldn't be &lt;em&gt;too&lt;/em&gt; difficult to find. A common algorithm in genome assembly first takes stretches of DNA and finds all the substrings of length k that are present. (These are known as k-mers and the algorithm then builds the assembly based on how k-mers overlap.) So, given a genome(s) it's not that difficult to find all the k-mers of a certain length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Ilmari's answer points out, there are definitely 17-base k-mers that don't exist in a string of DNA the size of the human genome. Given the amount of repetitive content present in actual genomes, the actual shortest string will almost certainly be less than 17 base pairs.&lt;/p&gt;&#xA;" OwnerUserId="1197" LastActivityDate="2012-08-01T01:00:53.327" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3077" PostTypeId="2" ParentId="2944" CreationDate="2012-08-01T02:04:31.390" Score="4" Body="&lt;p&gt;Great question! A lot of things affect how quickly a population or species can adapt to a new environment, including population size, mutation rate, generation time, standing genetic diversity, and selective pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The diversity of life encompasses practically all combinations of those variables. A bacterial population might very well contain enough diversity to allow a portion of the population to overcome a rapid change. In fact, applying antibiotics to a bacterial population and counting the survivors is a common measure of mutation rates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, organisms with small populations and long generation times will be much less likely to overcome a rapid environmental change. This is why there is so much concern over anthropogenic changes to the environment, including climate change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's hard to provide a definitive answer, since &quot;rapid change&quot; is a relative term, and the difficulty of adapting isn't known. Some striking adaptations can be caused by a single base pair mutation, such as in beetles and Monarch butterflies that are &lt;a href=&quot;http://mbe.oxfordjournals.org/content/21/2/218.abstract&quot; rel=&quot;nofollow&quot;&gt;insensitive&lt;/a&gt; to toxic plant compounds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's important to point out that natural selection is based on &lt;em&gt;relative&lt;/em&gt; fitness. Therefore, an adaptive mutation will spread because it's likely that carriers will be more fit than all of their neighbors. This does not necessarily mean that individuals without the mutation will die or fail to reproduce, only that those with the mutation will do it better.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Likewise, adaptation is not necessarily caused by the environment changing and wiping out all but a few lucky mutants like in the bacteria example. Instead, the environmental change might make things more difficult, but as long as the population can persist, then mutations will continue to enter the population which could confer a selective advantage against the change. So, no, a population does not (cannot) carry all possible adaptations. A population cannot adapt to an environment it hasn't encountered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, it's worth pointing out that a species can expand its range through migration. A new, unsuitable environment can act as a migration sink (that is, migrants make it there but fail to establish) for a nearby population. If this happens for long enough, some of the migrants may have a mutation allowing them to establish in the new environment.&lt;/p&gt;&#xA;" OwnerUserId="1197" LastActivityDate="2012-08-01T02:04:31.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3078" PostTypeId="5" CreationDate="2012-08-01T05:40:12.863" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-08-01T05:40:12.863" LastActivityDate="2012-08-01T05:40:12.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3079" PostTypeId="4" CreationDate="2012-08-01T05:40:12.863" Score="0" Body="Embryos of chickens (*Gallus gallus domesticus*) are often used in genetic experimentation and testing.  To a lesser extent, adult chickens can be used as a laboratory animal." OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-08-01T05:42:37.083" LastActivityDate="2012-08-01T05:42:37.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3080" PostTypeId="5" CreationDate="2012-08-01T05:53:48.043" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-08-01T05:53:48.043" LastActivityDate="2012-08-01T05:53:48.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3081" PostTypeId="4" CreationDate="2012-08-01T05:53:48.043" Score="0" Body="The locations at which two bones make contact.  They may be movable or unmovable." OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-08-01T06:06:41.697" LastActivityDate="2012-08-01T06:06:41.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3082" PostTypeId="5" CreationDate="2012-08-01T05:58:03.013" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-08-01T05:58:03.013" LastActivityDate="2012-08-01T05:58:03.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3083" PostTypeId="4" CreationDate="2012-08-01T05:58:03.013" Score="0" Body="The set of actions performed by an organism within a given environment" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-08-01T06:06:32.640" LastActivityDate="2012-08-01T06:06:32.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3084" PostTypeId="5" CreationDate="2012-08-01T06:04:11.993" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-08-01T06:04:11.993" LastActivityDate="2012-08-01T06:04:11.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3085" PostTypeId="4" CreationDate="2012-08-01T06:04:11.993" Score="0" Body="A protein produced by the B-cells of the immune system which binds to a particular antigen, a foreign substance to the body." OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-08-01T06:06:21.953" LastActivityDate="2012-08-01T06:06:21.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3086" PostTypeId="5" CreationDate="2012-08-01T06:11:03.200" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-08-01T06:11:03.200" LastActivityDate="2012-08-01T06:11:03.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3087" PostTypeId="4" CreationDate="2012-08-01T06:11:03.200" Score="0" Body="Movement through the atmosphere using wings or other structures to generate lift." OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-08-01T06:58:38.767" LastActivityDate="2012-08-01T06:58:38.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3088" PostTypeId="5" CreationDate="2012-08-01T06:29:21.757" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-08-01T06:29:21.757" LastActivityDate="2012-08-01T06:29:21.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3089" PostTypeId="4" CreationDate="2012-08-01T06:29:21.757" Score="0" Body="The process of gathering visual studies of tissue or the body for purposes of research or diagnostics." OwnerUserId="57" LastEditorUserId="57" LastEditDate="2012-08-01T06:58:43.167" LastActivityDate="2012-08-01T06:58:43.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3090" PostTypeId="1" CreationDate="2012-08-01T11:10:40.277" Score="5" ViewCount="84" Body="&lt;p&gt;At some point in the past I found a cancer portal site which had aggregated data for the relationships between various mutations and their prevalence in cancer types and tumor data. The data was presented in various pleasantly coloured interactive histograms and you could search per-gene or per-disease. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However after spending a few hours, I cannot find the site again. Though I have found many sites with a great deal of data and nice visualizations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nearest looking site, was this one:&#xA;&lt;a href=&quot;http://plugins.biogps.org/data_chart/data_chart.cgi?id=673&quot; rel=&quot;nofollow&quot;&gt;http://plugins.biogps.org/data_chart/data_chart.cgi?id=673&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But that doesn't have the level of detail that I remember.&lt;/p&gt;&#xA;" OwnerUserId="1198" LastEditorUserId="1214" LastEditDate="2014-01-26T18:35:48.750" LastActivityDate="2015-12-15T16:12:19.207" Title="Where can I find histograms and tables of prevalence of mutations in cancer?" Tags="&lt;bioinformatics&gt;&lt;gene-expression&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3091" PostTypeId="2" ParentId="3050" CreationDate="2012-08-01T11:54:34.220" Score="6" Body="&lt;p&gt;Building on Noah Snyder's answer…&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having wings could also be &lt;em&gt;expensive&lt;/em&gt; in other ways. For example, energy aside, maybe the growth of wings relies on some special nutrients, which were scarce in the environment of the first ancestors of modern ants. So the ant colonies that grew smaller wings (or no wing at all) thrived.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having wings could also cost them their lives. Maybe the workers in ancestor colonies used to be small and had a tendency to get stuck in spider webs (not having enough in-flight momentum or brute strength to break off the web), and somehow the queens and drones are less affected (because they don't tend to go to the same places as the workers to begin with, maybe; but that's unlikely: I see plenty of queens stuck in spider webs in Hong Kong in the mating season).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, I believe the nutrient-driven path is quite likely. When you think about it, there is a &lt;em&gt;huge&lt;/em&gt; behavioural component to this trait. If I remember correctly, all female ants are equal at birth. Whether a certain female becomes a worker, a soldier, or a queen depends on what it is fed as it develops. So the scenario could be that some ancestor colonies arrived in a place that didn't have an abundance in nutrients for wings. Some of those colonies tended to reserve the said nutrients to the reproductive casts (queens and drones), and this strategy proved successful, so the trait got amplified over time. So it becomes a matter of &lt;em&gt;less&lt;/em&gt; wings, not &lt;em&gt;smaller&lt;/em&gt; wings.&lt;/p&gt;&#xA;" OwnerUserId="1114" LastEditorUserId="1114" LastEditDate="2012-08-02T01:44:28.823" LastActivityDate="2012-08-02T01:44:28.823" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3092" PostTypeId="2" ParentId="3090" CreationDate="2012-08-01T13:43:22.373" Score="2" Body="&lt;p&gt;Perhaps you mean &lt;a href=&quot;http://www.sanger.ac.uk/perl/genetics/CGP/cosmic?action=bygene&amp;amp;ln=BRCA1&amp;amp;start=1&amp;amp;end=1864&amp;amp;coords=AA%3aAA&quot; rel=&quot;nofollow&quot;&gt;COSMIC&lt;/a&gt;? The &lt;a href=&quot;http://www.ebi.ac.uk/gxa/gene/ENSG00000012048&quot; rel=&quot;nofollow&quot;&gt;EBI Gene Expression Atlas&lt;/a&gt; also has pretty charts, but now mutations.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-08-01T13:43:22.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3093" PostTypeId="2" ParentId="2868" CreationDate="2012-08-01T14:19:47.333" Score="4" Body="&lt;p&gt;Everything depends upon the infection and on the general immune status of the patient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally, the prerequisite for DNA to freely circulate in the blood is the presence of bacteria themselves in the blood (&lt;a href=&quot;http://en.wikipedia.org/wiki/Bacteremia&quot; rel=&quot;nofollow&quot;&gt;bacteraemia&lt;/a&gt;). This means that the infection left its original site (where it is usually kept isolated from the blood flow by the immune system). Depending upon the body reaction to this breakthrough, &lt;a href=&quot;http://en.wikipedia.org/wiki/Sepsis&quot; rel=&quot;nofollow&quot;&gt;sepsis&lt;/a&gt; and/or &lt;a href=&quot;http://en.wikipedia.org/wiki/Systemic_inflammatory_response_syndrome&quot; rel=&quot;nofollow&quot;&gt;SIRS&lt;/a&gt; can be the consequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under these conditions (not necessarily as severe as sepsis, but in case of proven bacteriemia), the bacteria cells get attacked by the immuno cells, that leads to their eventual lyzing and releasing their content to the blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PCR can be used as a method to prove the existence of bacterial DNA. (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/hep.21286/full&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a publicly available paper on this topic).&lt;/p&gt;&#xA;" OwnerUserId="66" LastActivityDate="2012-08-01T14:19:47.333" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3094" PostTypeId="2" ParentId="2564" CreationDate="2012-08-01T16:15:59.930" Score="5" Body="&lt;p&gt;1) cell growth&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should look into chemotherapy and cancer medicine in general.  Because chemo is mostly effective because it kills fast dividing cells, this has been worked out reasonably well.  the 7-10 year number is not really correct, &lt;a href=&quot;http://askanaturalist.com/do-we-replace-our-cells-every-7-or-10-years/&quot;&gt;some cells are replaced a lot more slowly&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is why hair often falls out in cancer treatment, because the follicle cells are growing quickly.  Neurons divide very slowly - if at all - and often are never replaced.  Fat cells are in between - probably replaced in the 7-10 year range.  Heart cells are replaced albeit quite slowly - less than 1% per year, which implies that many cells are with you your entire lifetime.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) atoms/molecules change&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cell itself is in a continuous state of flux, but different parts of the cell, like cells in the body, change at different rates. Some proteins which make up the cell matrix or the DNA in the nucleus are replaced very rarely (through repair or rearrangement of the chromosome for instance) and most of the chromosome DNA is with the cell for the entire life of the cell.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://mcponline.org/content/1/8/579.full&quot;&gt;Most proteins are labelled for degradation and are recycled after a few hours of function&lt;/a&gt;.  Metabolic compounds such as sugars or salt might drift in and out of the cell continuously, maybe turning over in an hour or so. Fats can be incorporated into the cell and last for years I think.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-08-01T16:15:59.930" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3095" PostTypeId="1" CreationDate="2012-08-01T16:16:08.090" Score="8" ViewCount="1863" Body="&lt;p&gt;A 10 year old child does not have the intellectual power to accurately calculate the energy required to throw a ball an arbitrary distance. Yet they are able to accurately throw a ball at a distinctive target.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarily, we often &quot;instinctively&quot; know an approximation of the amount of energy and force required to accomplish certain tasks, even considering that many of us have minimal knowledge of the mathematical complexity behind the tasks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How does the human brain know the values of force, energy etc. required when accomplishing certain tasks, while being ignorant of the mathematics behind the Newtonian Physics of the task? Is it just a game of &quot;guess and check&quot;?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1199" LastEditorDisplayName="user1199" LastEditDate="2012-08-01T18:53:34.317" LastActivityDate="2018-01-28T14:51:22.203" Title="How does the brain instinctively know the math behind Newtonian Physics?" Tags="&lt;human-biology&gt;" AnswerCount="3" CommentCount="10" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3096" PostTypeId="2" ParentId="3044" CreationDate="2012-08-01T17:18:00.453" Score="5" Body="&lt;p&gt;The roots do actually continue to hold soil without being alie.  The stabilizing properties are structural in nature.  You begin to lose those though as the roots decompose, and the important roots against erosion, millions of fine root hairs, will go first. But leaving the roots in on a dead tree will help for a bit, but isn't a long term solution.&lt;/p&gt;&#xA;" OwnerUserId="1097" LastActivityDate="2012-08-01T17:18:00.453" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3097" PostTypeId="1" AcceptedAnswerId="3099" CreationDate="2012-08-01T19:04:28.517" Score="6" ViewCount="1959" Body="&lt;p&gt;For some species the Darwin's theory evolution makes perfect sense. I can easily imagine how, for example, the giraffe has evolved to its current appearance: the natural selection was favoring individuals that could consume more vegetable food from trees using longer necks, and some individuals were getting at birth necks longer than average by pure genetic randomness and the long neck trait was being propagated to descendant individuals by means of genetic inheritance. I have no problem with understanding this kind of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now let's have a look at the bat and its relatives. The bat is one of the few mammals that have something to do with flying and the only one that took flying to the bird level. Paleontologically, first mammals date to the dinosaur era and initially looked similar to the present-day shrew (which looks much like a mouse). The question is: how in the world prehistoric mouse-like creatures could grow wings over time? It impossible to believe that some mouse-like individuals were getting wing-like limbs by mutation and the &quot;wings&quot; were growing out accompanied with the knowledge of how the &quot;wings&quot; can actually be used. Ok, then maybe first wings were tiny moth-size wings and then grew larger? But where natural selection would come into play in this case? Such mouse-like individuals would have no advantage over their wingless relatives and thus would not be able to transfer those wing-growing genes to their descendants, quite the contrary, such individuals with useless mutations that interfere with their ability to walk would be suppressed by natural selection and therefore &quot;weeded out&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what is the story behind the bat's wings and is the Darwin's theory really able to support it?&lt;/p&gt;&#xA;" OwnerUserId="1200" LastEditorUserId="1200" LastEditDate="2012-08-03T14:24:56.817" LastActivityDate="2013-02-03T23:34:20.830" Title="Is the theory of evolution being disproved by bats?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;zoology&gt;" AnswerCount="3" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="3098" PostTypeId="2" ParentId="3097" CreationDate="2012-08-01T20:32:14.497" Score="18" Body="&lt;p&gt;Perhaps you didn't realise that bats' wings are equivalent to the front limbs of other mammals? They aren't extra limbs, just adapted ones, and the wings are formed from flaps of skin between the 'fingers'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taking that into account, I don't even see how anyone can think this is a challenge to the theory of evolution. It's obvious that increased skin webbing between fingers, eventually combined with increased finger length, provides an adaptive benefit to tree-dwelling small mammals. Initially it gives increased air resistance to allow controlled falling, then to allow gliding (like in flying squirrels), and in the most extreme cases to allow flying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These kinds of questions are always about a failure of imagination, or a misunderstanding of the basic facts, and never about the theory of evolution being wrong. (edit: that doesn't mean the theory of evolution can't be challenged - it is a &lt;em&gt;theory&lt;/em&gt; - but that this isn't a valid way to challenge it).&lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2012-08-02T23:39:54.920" LastActivityDate="2012-08-02T23:39:54.920" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3099" PostTypeId="2" ParentId="3097" CreationDate="2012-08-01T20:32:27.993" Score="43" Body="&lt;p&gt;Take a look at this little fellow:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Polatouche-estonien.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/2/2e/Polatouche-estonien.jpg&quot; alt=&quot;Flying squirrel&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a &lt;a href=&quot;http://en.wikipedia.org/wiki/Flying_squirrel&quot; rel=&quot;noreferrer&quot;&gt;flying squirrel&lt;/a&gt; &amp;mdash; a shy little nocturnal rodent which lives in trees and, despite its name, does not actually fly.  It does, however, have a skin membrane called a &lt;em&gt;patagium&lt;/em&gt; between its fore and hind limbs which allows it to glide from tree to tree and thus evade ground predators.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's not hard to see how the flying squirrel's patagium may have evolved: after all, ordinary squirrels, to which the flying squirrel is indeed related, also spend most of their time in trees and avoid the ground, often performing quite impressive leaps to cross from one tree to another.  With sufficient pressure to minimize time spent on the ground, any little morphological changes that allowed longer leaps would be favored by natural selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed, there are &lt;a href=&quot;http://en.wikipedia.org/wiki/Flying_and_gliding_animals#Mammals&quot; rel=&quot;noreferrer&quot;&gt;plenty of other groups of mammals which have independently evolved very similar adaptations to gliding&lt;/a&gt;.  Given how many small arboreal mammals there are, this is perhaps not surprising.  What's special about bats is not the fact that they possess flight membranes &amp;mdash; it's that they're the only group of mammals, so far, to have taken the next step to actual powered flight.&lt;/p&gt;&#xA;" OwnerUserId="239" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.727" LastActivityDate="2012-08-01T20:32:27.993" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3100" PostTypeId="1" CreationDate="2012-08-01T21:11:33.427" Score="38" ViewCount="1709" Body="&lt;p&gt;What exactly at the molecular level is itching? What physiological function does itching serve, if any? I cant remember the reference but a PLCb3 null mice lost the itch phenotype, so presumably it is mediated by the Gq-PLCbeta pathway through a cell surface GPCR. Since a physical action of scratching relieves it, could it be a case of a mechanosensitive channel at work?&lt;/p&gt;&#xA;" OwnerUserId="223" LastActivityDate="2012-09-21T17:51:03.743" Title="What is itching?" Tags="&lt;cell-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3101" PostTypeId="2" ParentId="3097" CreationDate="2012-08-01T22:36:52.063" Score="24" Body="&lt;p&gt;Check out this famous paper by &lt;a href=&quot;http://www.life.illinois.edu/ib/443/Gould%20&amp;amp;%20Lewontin.pdf&quot;&gt;Gould and Lewontin, the Spandrels of San Marco&lt;/a&gt;.  It's essentially a criticism of your question as it's not really the right question to ask.  You're engaging in what they call &quot;adaptive storytelling&quot;.  The truth is that barring fossil intermediaries it's almost impossible to infer how a species transitioned from primitive ancestors.  Secondly you're assuming constant selective pressure over time. It certainly can be the case that traits evolve in certain environments but are conserved over time despite no longer serving their original function (why do flightless birds have feathers still? etc.).&lt;/p&gt;&#xA;" OwnerUserId="1097" LastEditorUserId="-1" LastEditDate="2013-02-03T23:34:20.830" LastActivityDate="2013-02-03T23:34:20.830" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3105" PostTypeId="1" AcceptedAnswerId="3107" CreationDate="2012-08-02T21:53:12.607" Score="15" ViewCount="431" Body="&lt;p&gt;In &lt;a href=&quot;https://biology.stackexchange.com/questions/3097/is-the-theory-of-evolution-being-disproved-by-bats&quot;&gt;this question&lt;/a&gt;, the OP uses giraffe necks as a supportive example of evolution. Is the mechanism described in this post accurate? At some point, I thought I remember hearing that giraffes did not evolve long necks to reach higher food resources, but instead longer, stronger necks gave some sort of mating advantage (male competition perhaps?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a consensus in the scientific community as to evolutionary mechanism(s) that contributed most to the evolution of long necks in giraffes?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2012-08-29T16:49:46.300" Title="Evolution of long necks in giraffes" Tags="&lt;evolution&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3106" PostTypeId="2" ParentId="3050" CreationDate="2012-08-03T01:02:25.977" Score="2" Body="&lt;h2&gt;When is it good to have wings?&lt;/h2&gt;&#xA;&lt;p&gt;When you need to move a great distance in as short a time as possible with minimal risk.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Clearly wings would have enormous benefit at a time when you need to get far away from the nest really quickly, perhaps at a time when you believe the weather would be particularly favourable. This benefit increases exponentially when procreation is involved.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;h2&gt;When is it bad to have wings?&lt;/h2&gt;&#xA;&lt;p&gt;&lt;em&gt;Almost any other time.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;When it is raining.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Rain and wings just do &lt;strong&gt;not&lt;/strong&gt; go well together. If you get hit by a raindrop while wearing wings you are basically stuck where the drop lands until it evaporates completely.&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;When it is windy.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;I rest my case.&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;When you are under attack.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Agility, while wearing wings, just cannot be considered one of your evolutionary advantages.&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;When you are trying to gather/carry food back to the nest.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Surely an ant trying to carry a piece of a leaf, however small, would consider wings a severe burden.&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;When times are hard foodwise&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;The protein investment in wings would surely be better spent on survival when food is scarce.&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Encounters with birds suck&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Wings make you incredibly easy to grab hold of in mid-air, unless of course you can shed your wings when stressed, and many ants can (while obviously butterflies and moths cannot).&lt;/p&gt;&#xA;&lt;h1&gt;Wings or No Wings?&lt;/h1&gt;&#xA;&lt;p&gt;Surely my arguments suggest that having no wings would be a serious advantage in almost any situation except on the rare occasion when you need to move a long way really fast. Clearly the ant has an amazing skill to &lt;strong&gt;only have wings when they are needed&lt;/strong&gt; and not at any other time.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Added after a number of comments&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;You have to remember that much of an ant's work is maintaining the colony as a collective. Preserving its cohesion, feeding the young, caring for eggs. The whole point of having a colony is to have far fewer individuals spread out, in danger, gathering food. This is to reduce the risk of complete colony death, which is essentially the death of the queen and therefore the gene pool of the colony.&lt;/p&gt;&#xA;&lt;p&gt;You have to look at each ant colony as a single individual when you look at them on an evolutionary scale. In this way the life or death of one, or even 1,000 ants is not important, it is the survival of the &lt;strong&gt;colony&lt;/strong&gt;. From this perspective, wings are dangerous for all my reasons above. The only time they are of value is during diaspora and that is the only time ants have them, which I think is incredibly clever.&lt;/p&gt;&#xA;&lt;p&gt;Evolving a detachable appendage to an ant is like humans evolving detachable breasts at menopause. An astonishing achievement even humans have failed to achieve.&lt;/p&gt;&#xA;" OwnerUserId="1156" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-08-03T12:48:17.030" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="3107" PostTypeId="2" ParentId="3105" CreationDate="2012-08-03T04:32:26.957" Score="15" Body="&lt;p&gt;There seems to consensus that it is not competition for tall food.  Giraffes actually often feed on resources that are lower than their maximum possible height.    See: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1086/285955&quot;&gt;&lt;strong&gt;Simmons, R. E. &amp;amp; Scheepers, L.&lt;/strong&gt; 1996. Winning by a Neck: Sexual Selection in the Evolution of Giraffe. The American Naturalist 148: 771–786&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This paper put forth the idea that sexual selection is the reason behind long necks.  The idea is that longer necked males are dominant.  But this  theory has also been questioned.  See:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1111/j.1469-7998.2009.00573.x&quot;&gt;&lt;strong&gt;G. Mitchell, S. J. Van Sittert, J. D. Skinner.&lt;/strong&gt; 2009.Sexual selection is not the origin of long necks in giraffes. Journal of Zoology 278, Issue 4: 281–286&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in the end there's no clear consensus.  Some papers have returned to the theory of competition for research in the past few years.To put it simply, no there is no consensus.&lt;/p&gt;&#xA;" OwnerUserId="1097" LastEditorUserId="836" LastEditDate="2012-08-08T18:48:30.620" LastActivityDate="2012-08-08T18:48:30.620" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3108" PostTypeId="1" AcceptedAnswerId="3109" CreationDate="2012-08-03T13:25:43.217" Score="6" ViewCount="1991" Body="&lt;p&gt;Recently we have started suspecting that one of our children has hypolactasia (lactose intolerance), and so accordingly I have had my first exposure to lactose-free dairy- and dairy-like products. In addition to soy milk and almond milk, we have recently purchased actual dairy milk that was labeled lactose-free. This gave me the impression that they had used some process to remove the lactose, but looking at the ingredients more closely, it seems that they simply added lactase enzyme to the milk to assist breaking down the sugars.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is this: when is the lactase enzyme active? Does the lactase activity begin right as it is added to the milk, or will it not become active until ingested?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially, I'm wondering if this type of milk can/should be used in cooking or baking. High temperatures will certainly denature the lactase enzymes in the milk, but if the lactose has already been broken down, this shouldn't be a problem.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2019-11-27T00:59:14.070" Title="When is the lactase in lactose-free milk active?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3109" PostTypeId="2" ParentId="3108" CreationDate="2012-08-03T13:57:18.620" Score="6" Body="&lt;p&gt;Having done an inordinate number of rather mind-numbing A.S. practicals involving milk and enzymes the year before last, in my experience lactase always began breaking down the lactose immediately and converting a boiling tube worth of milk in less than 50 minutes at below room temperature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To further allay your concerns, &lt;a href=&quot;http://www.ochef.com/1407.htm&quot; rel=&quot;nofollow&quot;&gt;this website&lt;/a&gt; suggests that most Lactose Free milk has undergone UHT treatment - therefore cooking shouldn't be a problem as the enzymes have presumably been added before the pasteurisation, and are therefore denatured - I can't see why you'd then go to the extra trouble of adding the lactase aseptically after pasteurisation; and if the lactase shows in the ingredient list it presumably wasn't done with immobilised enzymes in the factory.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="430" LastEditDate="2012-08-03T16:11:48.283" LastActivityDate="2012-08-03T16:11:48.283" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3110" PostTypeId="1" CreationDate="2012-08-03T14:14:04.333" Score="8" ViewCount="103" Body="&lt;p&gt;I know it is usually stated as the threonine residue near the N-terminus of either light harvesting complex (lhc) b1 or lhcb2, but if this is somehow lost, say in a mutant, is the system flexible enough to compensate by phosphorylation at another site such as a serine residue or will state transitions just cease?&lt;/p&gt;&#xA;" OwnerUserId="1211" LastEditorUserId="1122" LastEditDate="2012-08-03T16:23:35.233" LastActivityDate="2012-08-06T18:03:39.923" Title="Exactly which amino acids are phosphorylated in higher plants during state transitions?" Tags="&lt;plant-physiology&gt;&lt;proteins&gt;&lt;photosynthesis&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3112" PostTypeId="2" ParentId="3110" CreationDate="2012-08-03T16:20:34.970" Score="3" Body="&lt;p&gt;The protein in question from &lt;em&gt;Arabidopsis&lt;/em&gt; has &lt;a href=&quot;http://www.uniprot.org/uniprot/P0CJ48&quot; rel=&quot;nofollow&quot;&gt;this UniProt entry&lt;/a&gt;. In the comments you read: &lt;em&gt;The N-terminus of the protein extends into the stroma where it is involved with adhesion of granal membranes and post-translational modifications; both are believed to mediate the distribution of excitation energy between photosystems I and II.&lt;/em&gt; As known PTMs we have (see Sequence Annotations) Threonine-38 and Arginine-36; below you can see known mutations. My guess, though, is that they are a few years behind and so it's better to look at recent work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let us then take the PMID 11113141 referred to in the above entry and see the citing papers, e.g., via &lt;a href=&quot;http://www.ebi.ac.uk/citexplore/performQuery.do?queryString=cites:11113141_MED&amp;amp;sortOrder=&quot; rel=&quot;nofollow&quot;&gt;CiteXplore&lt;/a&gt; where I see at least a few relevant references on the topic of LHC phosphorylation. If there were a review, it would be listed there. Apparently, there is also a plant phosphorylation site database PhosPhAt which might help, see PMID 22723801.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, not much is known, lacking even a single review on the subject.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-08-03T16:26:27.837" LastActivityDate="2012-08-03T16:26:27.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3113" PostTypeId="5" CreationDate="2012-08-03T20:01:19.157" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-08-03T20:01:19.157" LastActivityDate="2012-08-03T20:01:19.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3114" PostTypeId="4" CreationDate="2012-08-03T20:01:19.157" Score="0" Body="in vitro compartmentalization" OwnerUserId="184" LastEditorUserId="184" LastEditDate="2012-08-03T20:55:49.460" LastActivityDate="2012-08-03T20:55:49.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3116" PostTypeId="5" CreationDate="2012-08-03T22:37:51.143" Score="0" Body="" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-08-03T22:37:51.143" LastActivityDate="2012-08-03T22:37:51.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3117" PostTypeId="4" CreationDate="2012-08-03T22:37:51.143" Score="0" Body="This question has no tags, either as a result of migration from another site, tag expiry or mass tag removal.  Please add appropriate tags!" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-08-03T22:37:51.143" LastActivityDate="2012-08-03T22:37:51.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3118" PostTypeId="1" CreationDate="2012-08-04T08:48:52.530" Score="9" ViewCount="178" Body="&lt;p&gt;Anybody know which traits of bird plumage are accurate indicators of a birds health? For example feather coloration, feather brightness, amount of feather wear, number of feathers, moult timing, moult duration etc.&lt;/p&gt;&#xA;" OwnerUserId="1216" LastEditorUserId="3971" LastEditDate="2013-08-29T16:14:49.303" LastActivityDate="2013-08-29T16:14:49.303" Title="Plumage as indicator of health in birds" Tags="&lt;ornithology&gt;&lt;pigmentation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3119" PostTypeId="1" AcceptedAnswerId="3122" CreationDate="2012-08-04T12:07:35.900" Score="7" ViewCount="157" Body="&lt;p&gt;I'm reading about how synaptobrevin is used to identify synaptic vesicles for tethering near the synaptic cleft. Since neurons have a synapse and dendrites, I'd like to know how exactly  the vesicles get moved from the Golgi to the synapse. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I can tell, they are transported along microtubules by dynamins as opposed to floating freely in the cytosol (correct?). If so how do the dynenins identify synaptic vesicles - would they form a SNARE complex that gets released near the synapse or by some other means?&lt;/p&gt;&#xA;" OwnerUserId="368" LastEditorUserId="43" LastEditDate="2012-08-05T17:55:12.730" LastActivityDate="2012-08-07T05:55:06.147" Title="How are synaptic vesicles brought to the synapse?" Tags="&lt;neuroscience&gt;&lt;cell-biology&gt;&lt;synapses&gt;&lt;intracellular-transport&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3120" PostTypeId="2" ParentId="2961" CreationDate="2012-08-04T18:03:44.687" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://discovermagazine.com/2004/may/cover/article_view?b_start%3aint=1&amp;amp;-C&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; I found an answer. Not sure how accurate is is, though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Data seems to be from the US&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a rewrite of parts of that article:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;266 days before birth, all we have is a fertilized egg.  (~33% chance of living birth).&lt;br&gt;&#xA;The odds are calculated using data from &lt;em&gt;in-vitro&lt;/em&gt; fertilization, and the next stage is 66%.&lt;br&gt;&#xA;In in-vitro, some 50% of the eggs cannot fix to the uterine wall  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;262 days before birth, the egg has implanted (~66% chance of living birth)&lt;br&gt;&#xA;After implantation, there is still a decent chance that the embryo will be aborted (and maybe the woman will not even know that she was pregnant).&lt;br&gt;&#xA;Half of the embryos that die from here on will die because of chromosome abnormalities.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;241 days before birth (~88%) &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;178 days before birth, entering the second trimester (~97%)&#xA;At this stage, problems are more likely to stem from the mother, not the fetus' genome. Problems with the cervix, the uterus or the placenta are (some ?) likely causes of death.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;89 days before birth, entering the third trimester (~99%)&#xA;At this stage, doctors will consider the fetus a patient, and treat it if needed.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1167" LastEditorUserId="115" LastEditDate="2012-08-07T16:34:56.383" LastActivityDate="2012-08-07T16:34:56.383" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3122" PostTypeId="2" ParentId="3119" CreationDate="2012-08-05T07:31:56.487" Score="4" Body="&lt;p&gt;You are looking for a review on vesicle cargoing along the cytoskeleton. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19653898&quot; rel=&quot;nofollow&quot;&gt;This open access article&lt;/a&gt; is the most recent I found on the subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the abstract: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How synaptic cargos achieve specificity, directionality and timing of transport is a developing area of investigation. Recent studies demonstrate that the docking of motors to their cargos is a key control point. Moreover, precise spatial and temporal regulation of motor-cargo interactions is important for transport specificity and cargo recruitment. Local signaling pathways Ca2+ influx, CaMKII signaling and Rab GTPase activity regulate motor activity and cargo release at synaptic locations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;M. A. Schlager, C. C. Hoogenraad: &lt;em&gt;Basic mechanisms for recognition and transport of synaptic cargos.&lt;/em&gt; In: &lt;em&gt;Molecular brain.&lt;/em&gt; Vol. 2, 2009, p.&amp;nbsp;25. DOI:10.1186/1756-6606-2-25. PMID 19653898. PMC 2732917.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="6" LastEditDate="2012-08-07T05:55:06.147" LastActivityDate="2012-08-07T05:55:06.147" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3123" PostTypeId="2" ParentId="3110" CreationDate="2012-08-06T18:03:39.923" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;is the system flexible enough to compensate by phosphorylation at another site such as a serine residue&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If we are just talking about substituting a residue, I think that functionality would be dependent on the associated kinases. Perhaps the plant phosphorylation database rwst mentioned could be of help?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to my biology book (S377 Book 3), threonine-serine kinases can usually phosphorylate both residues due to their similarity. There are also tyrosoine kinases, and hystidine kinases; the latter occurring in plants only. The book states that these are the only residues that are known to be phosphorylated. It is uncommon for a threonine-serine kinase to be able to phosphorylate tyrosine, but some rare kinases can do both.&lt;/p&gt;&#xA;" OwnerUserId="368" LastActivityDate="2012-08-06T18:03:39.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3124" PostTypeId="2" ParentId="2835" CreationDate="2012-08-07T00:55:28.067" Score="2" Body="&lt;p&gt;You might want to look at Koleff's paper (open access @ JAE &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2656.2003.00710.x/abstract&quot; rel=&quot;nofollow&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2656.2003.00710.x/abstract&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that you have quantitative data, you should look at the difference between presence/absence and quantitative measures. A Bry-Curtis measure or something to that effect would be way better than a Sorensen or Whittaker here, lest you lose information.&lt;/p&gt;&#xA;" OwnerUserId="1225" LastActivityDate="2012-08-07T00:55:28.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3125" PostTypeId="2" ParentId="2425" CreationDate="2012-08-07T00:58:08.140" Score="1" Body="&lt;p&gt;It is fairly simple to normalize this measure by the number of observations, so you can have values in the 0-1 range at the end, which are way easier to compare.&lt;/p&gt;&#xA;" OwnerUserId="1225" LastActivityDate="2012-08-07T00:58:08.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3127" PostTypeId="1" AcceptedAnswerId="3128" CreationDate="2012-08-07T23:54:45.127" Score="7" ViewCount="268" Body="&lt;p&gt;I've been thinking about the development of an embryo from the zygote stage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is it that when cytokinesis takes place at that stage, the cells all stick together in a little ball, but later in life, some are not bound to others (red blood cells, sperm cells, etc.)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, how is it that some cells are stuck together and some are separated? How does this property develop?&lt;/p&gt;&#xA;" OwnerUserId="1083" LastEditorUserId="1122" LastEditDate="2012-08-08T17:13:17.520" LastActivityDate="2012-08-08T17:13:17.520" Title="Free-flowing cells and those that are stuck together?" Tags="&lt;cell-biology&gt;&lt;development&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3128" PostTypeId="2" ParentId="3127" CreationDate="2012-08-08T11:13:39.307" Score="8" Body="&lt;p&gt;Cell-cell adhesion is a well-regulated mechanism, cells don't just stick together randomly, this interaction is mediated by specific molecules on the cell surfaces. The responsible proteins for that are the Cell Adhesion Molecules (CAMs) like integrins, cadherins and selectins. Which of these CAMs are present on the surface of a cell determines if those cells will bind to each other or not. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cells can change their ability to adhere to each other or the extracellular matrix by expressing or not expressing different kinds of these molecules. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find a lot more information about this topic in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26937/&quot;&gt;the cell-cell adhesion chapter of &quot;Molecular Biology of the Cell&quot;, available on the NCBI homepage&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2012-08-08T11:13:39.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3129" PostTypeId="2" ParentId="3095" CreationDate="2012-08-08T16:33:05.367" Score="9" Body="&lt;p&gt;Trial and error.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The CNS is very much a living, changing organ system - much more so before you are an adult. While you are a child your neurons fire, muscles contract, and force is exerted on objects - then your CNS modifies itself (either through redistribution of neural contacts or growth of new neurons spurned by chemical changes) to account for the results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is why &quot;practice makes perfect.&quot; As you continuously perform a task, like throwing a ball, your body is keeping track of the results. Did X muscle fibers contracting in Y muscles overshoot your buddy? You register the failure and compensate by utilizing X-N muscle fibers that contract in Y muscles until you consistently satisfy your goal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your CNS is keeping track of everything, all the time. There isn't a single instant in your life - asleep or awake - that's not being monitored, so your body has copious amounts of data to work with when making its estimates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is also why simulations take time to adapt to, even if the person is fully aware of the basics behind the physics involved.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-08T16:33:05.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3130" PostTypeId="2" ParentId="2911" CreationDate="2012-08-08T17:07:29.593" Score="3" Body="&lt;p&gt;Not that I'm aware of. There isn't &lt;em&gt;any&lt;/em&gt; blood flow to either tendons or cartilage as an adult, so the pathway for migration doesn't exist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tendons and cartilage are tissues composed of dead cells after their formation (the cartilage growth plates cease to exist in your teen and completely ossify, tendons I'm not sure on). Damage to tendons and cartilage is permanent, and can cause arthritis (when the cartilage is completely worn away and bone-on-bone contact occurs at joints).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unlike living tissue, because tendon cells are dead, they are much, much easier to transplant - they do not produce any signaling molecules or have any surface proteins which would trigger an immune reaction for the vast majority of people. Shoulder surgeries often utilize this to the benefit of the patient, especially acromio-clavicular injuries.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If living cells are brought to the dead tissue, some repair is initiated, as I do recall a technique where surgeons tapped into the marrow of a patient's femur to stimulate cartilage reconstruction, but I also remember reading that the new cartilage formed wasn't the same hyaline cartilage produced by chondrocytes of the growth plate, so the repairs were temporary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Artificially produced tendons do exist, and many are braided in order to foster interaction with host tissues (when you suffer from tendonitis, the tendon itself isn't repaired - the tissue around the tendon is repaired and strengthened). I'm not aware of any successful attempts to regrow tendons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Attempts to grow cartilage &lt;em&gt;in vitro&lt;/em&gt; have been successful, but re-introducing it into the body to produce a surface to articulate against has presented significant difficulties. Because we cannot (currently) reproduce biological articular surfaces, joint replacement often uses composites or surgical grade metals (both of which present problems of their own, but arthritis is not one as there's no living tissue to feel pain).&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="57" LastEditDate="2012-08-09T00:32:40.760" LastActivityDate="2012-08-09T00:32:40.760" CommentCount="15" ContentLicense="CC BY-SA 3.0" />
  <row Id="3131" PostTypeId="2" ParentId="2681" CreationDate="2012-08-08T17:17:28.007" Score="1" Body="&lt;p&gt;I've never heard of it, actually - though I can't speak for my professors or researchers I know, none have ever presented the Cladism argument as an argument for the delineation of species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I'm aware, the attempts to define a species fall along three lines:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ability to produce fertile offspring in the wild.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Distinct physical characteristics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An arbitrary amount of genetic divergence.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-08T17:17:28.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3132" PostTypeId="1" AcceptedAnswerId="3133" CreationDate="2012-08-08T18:15:03.283" Score="6" ViewCount="2048" Body="&lt;p&gt;I've heard that the aplication of &lt;a href=&quot;http://www.agroline.com.br/produto/ver/377/monovin-a-20-ml-bravet-vitamina-a.html&quot; rel=&quot;nofollow&quot;&gt;Monovin A&lt;/a&gt; in the hair would allow it to grow faster. Monovin A seems to be only &lt;a href=&quot;http://en.wikipedia.org/wiki/Vitamin_A&quot; rel=&quot;nofollow&quot;&gt;A vitamin&lt;/a&gt;, according to the first website. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Could the application of A vitamin in the hair make it grow?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm thinking it's not very probable that applying it to the hair and the scalp would affect the hair growth. References will also be useful.&lt;/p&gt;&#xA;" OwnerUserId="783" LastEditorUserId="1122" LastEditDate="2012-08-09T14:42:56.397" LastActivityDate="2019-06-12T16:28:52.127" Title="Is it possible for a substance to be absorbed by the hair or the scalp?" Tags="&lt;pharmacology&gt;&lt;toxicology&gt;&lt;vitamins&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3133" PostTypeId="2" ParentId="3132" CreationDate="2012-08-09T14:39:14.763" Score="5" Body="&lt;p&gt;As to the subject line, yes, lipid substances or any non-polar small molecule will enter the skin cells and the body below. The reason is because cell membranes simply consist of fatty substance that behaves like a solvent for other lipids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the specific question about this product, Monovin A. This is a veterinary product and the producer, Laboratórios Bravet, intends it to be injected into animals in case of a vitamin A deficiency. The main ingredients is a retinol ester in the amount of 2,000,000 IU (which usually means retinol equivalents in this respect).[1]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed, retinol is a lipid and long-chain esters like retinol esters are non-polar, too, and can readily be de-esterified by esterases, making vitamin A (=retinol, retinal, retinyl palmitate, retinoic acid) immediately available to the surrounding cells and, via transport in the blood stream, to the liver, which is the body's store for it. Daily doses of 25,000 IU are known to be toxic when administered over a long time. Doses of 50,000 IU can be dangerous over weeks. In general, it appears that single high doses are better tolerated than long over-exposure.[2][3] So, do the math and dilute the stuff such that you get at most one hundredth of an ampoule, else...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the effects. Indeed, hair loss is one of the symptoms of heavy vitamin A-deficiency, and logically, that symptom can be cured with vitamin A. That does not mean that more results in more. While retinoids are important therapeutic agents for the management of many skin diseases, notably acne vulgaris, psoriasis, ichthyosis, and palmoplantar keratoderma, there exists something like &lt;strong&gt;retinoid-induced effluvium&lt;/strong&gt; which is a side effect of such medication with tretinoin (ATRA).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Retinoid-induced hair loss (telogen effluvium) is among the most&#xA;  frequent and psychologically most distressing adverse effects of&#xA;  retinoid therapy, which results in premature termination of a&#xA;  clinically desired and often highly effective systemic therapy with&#xA;  retinoids.[4]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Since ATRA is readily produced from retinal, its concentration would be expected to be up, even if the original stuff was retinyl ester. In summary, I would expect no effect, or even hair loss, for you don't simply put such potent stuff on your head and elsewhere, and have no reaction from the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.bravet.com.br/pr-ceg-monovina.asp&quot;&gt;http://www.bravet.com.br/pr-ceg-monovina.asp&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] Vitamin A: Toxicity from Supplements In: Medical Sciences Bulletin 1995; Pharmaceutical Information Associates, Ltd.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[3] Hartmann S, Brørs O, Bock J, et al.: Exposure to retinyl esters, retinol, and retinoic acids in non-pregnant women following increasing single and repeated oral doses of vitamin A. In: Ann. Nutr. Metab.. 49, Nr. 3, 2005, p. 155–64. doi:10.1159/000086879. PMID 16006784&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[4] K. Foitzik, T. Spexard u.&amp;nbsp;a.: &lt;em&gt;Towards dissecting the pathogenesis of retinoid-induced hair loss: all-trans retinoic acid induces premature hair follicle regression (catagen) by upregulation of transforming growth factor-beta2 in the dermal papilla.&lt;/em&gt; In: &lt;em&gt;The Journal of investigative dermatology.&lt;/em&gt; Vol. 124, Nr 6, June 2005, p.&amp;nbsp;1119–1126. DOI:10.1111/j.0022-202X.2005.23686.x. PMID 15955085. &lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-08-09T14:39:14.763" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3134" PostTypeId="1" AcceptedAnswerId="3326" CreationDate="2012-08-09T22:40:36.247" Score="4" ViewCount="192" Body="&lt;p&gt;Say a sophiscated scientist in the 19th century noted that applying soy sauce on a dead octopus leads to movement of the legs, as a result of the voltage differences resulting from the salt in the soy sauce. (For example, see &lt;a href=&quot;http://www.youtube.com/watch?v=xxgcnU9FpAo&quot; rel=&quot;nofollow&quot;&gt;this video&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a way for that scientist to prove, using only the methodologies available at that time, that the decapitated octopus doesn't regain the functions that a octopus brain normally has, for even a few seconds, when the soy sauce is applied?&lt;/p&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="223" LastEditDate="2012-08-10T19:34:45.393" LastActivityDate="2012-08-26T16:24:49.650" Title="Is there a way for a 19th century scientist to prove that the octopus doesn't revive?" Tags="&lt;neuroscience&gt;&lt;zoology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="3135" PostTypeId="1" AcceptedAnswerId="3137" CreationDate="2012-08-10T01:07:21.440" Score="12" ViewCount="328" Body="&lt;p&gt;Is there a computer program that simulates biology on a molecular level? Software that has rules that simulates the rules of molecular-biology?&lt;/p&gt;&#xA;" OwnerUserId="1236" LastEditorUserId="500" LastEditDate="2012-08-10T04:10:02.763" LastActivityDate="2015-12-24T16:48:30.023" Title="Is there a program that simulates biology on a molecular level?" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;software&gt;&lt;theoretical-biology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3136" PostTypeId="2" ParentId="3118" CreationDate="2012-08-10T02:28:16.680" Score="6" Body="&lt;p&gt;&lt;a href=&quot;http://www.drsfostersmith.com/pic/article.cfm?aid=327&quot; rel=&quot;noreferrer&quot;&gt;This resource&lt;/a&gt; provides a short list of which general components of plumage are good indicators of a healthy bird.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Your pet's plumage should be. . .&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Soft&lt;/em&gt; - feathers should be strong, yet flexible.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Smooth&lt;/em&gt; - no rough feather shafts; no uneven or split edges&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Glossy&lt;/em&gt; - sheen extends over the entire coat&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Full&lt;/em&gt; - thick, where it needs to be&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Vivid&lt;/em&gt; - color should be deep, bright and uniform&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Clean&lt;/em&gt; - free of dust, dander, waste, or soil&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Parasite-Free&lt;/em&gt; - no lice or mites&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Also, &lt;a href=&quot;http://www.birdcageoutlet.com/bird-safety/article-things-you-can-tell-from-feathers.htm&quot; rel=&quot;noreferrer&quot;&gt;this website page&lt;/a&gt; discusses the signs of malnutrition or disease in plumage in more detail.&lt;/p&gt;&#xA;&lt;p&gt;Stress bars, dark lines which transect a feather, are directly caused by an inefficient absorption or lack of required nutrients. Stress bars can be found on all feathers during the period of malnutrition, and remain even after this period.&lt;/p&gt;&#xA;&lt;p&gt;Assymetrical moulting is also a sign of bad health. There should not be any bald patches present during the moult.&lt;/p&gt;&#xA;&lt;p&gt;The resource states that if a moult is delayed due to malnutrition, an incorrect photoperiod or a metabolic problem, plumage will become depigmented. However, the appearance of &amp;quot;dirty&amp;quot; feathers can also be due to overpreening or damage done to feathers by physical contact.&lt;/p&gt;&#xA;&lt;p&gt;Finally, a change in the usual plumage color of the bird in question is indicative of a lack  or oversupply of a particular nutrient.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-08-10T02:28:16.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3137" PostTypeId="2" ParentId="3135" CreationDate="2012-08-10T03:34:35.197" Score="21" Body="&lt;p&gt;There is a recent paper that introduced the first molecular-level whole-cell simulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Karr, J.R., Sanghvi, J.C., Macklin, D.N., Gutschow, M.V., Jacobs, J.M., Bolival, B., Assad-Garcia, N., Glass, J.I., &amp;amp; Covert, M.W. (2012). &lt;a href=&quot;http://www.cell.com/retrieve/pii/S0092867412007763&quot; rel=&quot;nofollow noreferrer&quot;&gt;A whole-cell computational model predicts phenotype from genotype&lt;/a&gt;. &lt;em&gt;Cell&lt;/em&gt; 150:389-401 DOI: 10.1016/j.cell.2012.05.044&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors combined 28 different sub-modules of various biological processes from the literature. Each one operates at the level of macromolecules, although models them in different ways: some by ODEs, some by logic; some by agent-based approaches. If you want to fool around their code is &lt;a href=&quot;https://simtk.org/home/wholecell&quot; rel=&quot;nofollow noreferrer&quot;&gt;available online&lt;/a&gt; and I wrote a basic &lt;a href=&quot;http://egtheory.wordpress.com/2012/07/23/whole-cell-model/&quot; rel=&quot;nofollow noreferrer&quot;&gt;introduction/summary of the paper&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are some related bio.SE questions motivated by that model:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/2977/500&quot;&gt;Short-term Lamarckism in asexual single cell organisms&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/2982/500&quot;&gt;Computational/mathematical models for predicting phenotype from genotype&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/3020/500&quot;&gt;Macromolecule levels in daughter cells after fission&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2012-10-16T03:38:23.503" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3138" PostTypeId="1" AcceptedAnswerId="3139" CreationDate="2012-08-10T11:26:23.323" Score="11" ViewCount="241" Body="&lt;p&gt;To spawn, salmon return to the river in which they were born. Is it because the individuals &lt;em&gt;remember&lt;/em&gt; the specific river, or because populations are &lt;em&gt;genetically conditioned&lt;/em&gt; to follow specific environmental cues that guide them to the specific river?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, if a salmon is artificially taken to lay eggs in a &lt;em&gt;different&lt;/em&gt;, (&quot;wrong&quot;) river, will its progeny return, when grown, to the river where they were born, or that where their mother was born?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If salmon that was grown in a fish-farm is taken to the sea, does it return to a river? How does it choose which?&lt;/p&gt;&#xA;" OwnerUserId="226" LastEditorUserId="3952" LastEditDate="2013-08-10T02:53:31.970" LastActivityDate="2013-08-10T02:53:31.970" Title="Salmon returning to lay eggs" Tags="&lt;ichthyology&gt;&lt;memory&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3139" PostTypeId="2" ParentId="3138" CreationDate="2012-08-10T14:43:32.803" Score="10" Body="&lt;h2&gt;Answer&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The mechanism for salmon natal homing isn't exactly known, but there are really two good hypotheses out there.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Salmon have an extremely good sense of smell. One hypothesis is that they retain an imprint of their birthplace's odor, and manage to recognize it again at a later time (as explained by &lt;a href=&quot;http://jeb.biologists.org/content/199/1/83.abstract&quot;&gt;this article&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;li&gt;Another hypothesis: the Earth's magnetic field guides the salmon to their birthplace via geomagnetic navigation. They then use chemical cues to recognize the stream in which they were born (supported by &lt;a href=&quot;http://www.pnas.org/content/105/49/19096.abstract&quot;&gt;this scientific article&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;These hypotheses were mentioned in &lt;a href=&quot;http://en.wikipedia.org/wiki/Natal_homing#cite_ref-Lohmann_2-0&quot;&gt;this Wikipedia article&lt;/a&gt;. Note that there was a third pheromone-related hypothesis which was disproved (as shown &lt;a href=&quot;http://www.springerlink.com/content/w60223331428uw64/&quot;&gt;here&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would say that both memory and &quot;genetic conditioning&quot; &lt;em&gt;could potentially&lt;/em&gt; be factors in how these animals perform this natal homing, among other things. However, it is difficult to pinpoint which one if any, because neither hypothesis has yet to be confirmed, and both function on completely different mechanisms. Not to mention that &lt;em&gt;we can't tell what exactly a fish is thinking&lt;/em&gt;, and also &lt;em&gt;what chemical we're looking for, if there is one.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, for your personal information, salmon aren't the only animals to do this: sea turtles return to their birthplace as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;TLDR:&lt;/strong&gt; If a salmon was displaced right before birth, or birthed in a pool, I &lt;em&gt;would imagine&lt;/em&gt; it returning to that particular location at sexual maturity.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Lohmann, K. J., N. F. Putman, and C. M. F. Lohmann.&lt;/strong&gt; &lt;em&gt;“Movement Ecology Special Feature: Geomagnetic Imprinting: A Unifying Hypothesis of Long-distance Natal Homing in Salmon and Sea Turtles.”&lt;/em&gt; Proceedings of the National Academy of Sciences 105, no. 49 (December 5, 2008): 19096–19101.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Dittman, A., and T. Quinn.&lt;/strong&gt; &lt;em&gt;“Homing in Pacific Salmon: Mechanisms and Ecological Basis.”&lt;/em&gt; Journal of Experimental Biology 199, no. 1 (January 1, 1996): 83–91.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Black, Geoff, and J. Dempson.&lt;/strong&gt; &lt;em&gt;“A Test of the Hypothesis of Pheromone Attraction in Salmonid Migration.”&lt;/em&gt; Environmental Biology of Fishes 15, no. 3 (1986): 229–235.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-08-10T23:49:20.937" LastActivityDate="2012-08-10T23:49:20.937" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3140" PostTypeId="1" CreationDate="2012-08-10T18:31:28.247" Score="4" ViewCount="106" Body="&lt;p&gt;Say both parent and child are genotyped for all SNPs. In this setup we are only looking at variant positions between one parent and child - so neither parent nor child are homozygous reference (no AA/AA) in the millions of positions we are studying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume all variants are biallelic and there is no &lt;em&gt;de novo&lt;/em&gt; mutation (no AA/BB or BB/AA)&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;P    C&#xA;AA   AB&#xA;AB   AA&#xA;AB   AB&#xA;AB   BB&#xA;BB   AB&#xA;BB   BB&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;What is the fraction of AB/AB among these possibilites?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We are looking at all positions in the genome so the minor allele frequency (MAF) of B allele varies. You can choose whatever B frequency you like.&lt;/p&gt;&#xA;" OwnerUserId="1241" LastEditorUserId="1590" LastEditDate="2016-08-19T12:35:53.883" LastActivityDate="2016-08-19T12:35:53.883" Title="What is the frequency of double-hets between parent and child?" Tags="&lt;genetics&gt;" AnswerCount="0" CommentCount="6" ClosedDate="2016-08-23T09:21:51.457" ContentLicense="CC BY-SA 3.0" />
  <row Id="3141" PostTypeId="2" ParentId="3051" CreationDate="2012-08-11T12:33:47.147" Score="12" Body="&lt;p&gt;As nobody has answered this good question, I'll have a go.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, let me state that I have little-or-no knowledge of heat-shock &#xA;proteins. What follows are some general observations and thoughts.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;It would not be unusual for the same enzyme from different &#xA;species to have different kinetic properties. For example, yeast and &#xA;horse liver alcohol dehydrogenase (&lt;a href=&quot;http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/1/1/1.html&quot;&gt;EC 1.1.1.1&lt;/a&gt;) vary quite dramatically in this regard&#xA;(see below).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It &lt;i&gt;is &lt;/i&gt; to be expected that the same &#xA;protein from different species will have different amino acid sequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even the sequence of cytochrome C (~104 amino acids), one of the most &#xA;conserved proteins, differs between species. There are 44 amino-acid differences &#xA;between human and yeast cyctochrome C, for example (although there is no&#xA;difference in amino acid sequence between the human and chimpanzee &#xA;proteins) [see Creighton, 1993, p116, quoted below].&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;This fact alone could explain the kinetic variation, but it might be &#xA;very difficult (and require a lot of work) to pinpoint what differences &#xA;in amino acid sequence (if any) account for the observed differences in &#xA;kinetic constants. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In the case of hsp104, a quick alignment (out of curiosity) &#xA;of the amino acid sequence of the  &lt;i&gt;Saccharomyces &#xA;cerevisiae&lt;/i&gt; and &lt;i&gt;Candida albicans&lt;/i&gt; enzymes showed quite a number of amino acid differences between these obviously homologous proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I used the &#xA;&lt;a href=&quot;http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi?stage1=1&amp;amp;daction=TCOFFEE%3a%3aAdvanced&quot;&gt;TCoffee&lt;/a&gt;&#xA;sequence alignment algorithm (a new version of ClustalW) at the &#xA;&lt;a href=&quot;http://expasy.org/proteomics/similarity_search_alignment&quot;&gt;xPASy&lt;/a&gt; server. (I received an alignment score of 98).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the record, the accession numbers used are the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;hsp140 from &lt;i&gt; Saccharomyces cerevisiae&lt;/i&gt;, 908 amino &#xA;acids, Accession Number &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/protein/AAA50477.1&quot;&gt;AAA50477&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;hsp140 from &lt;i&gt;Candida albicans&lt;/i&gt;, 899 amino acids, Accession &#xA;Number &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/protein/AAK60625.1&quot;&gt;AAK60625&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Of course, the observed kinetic differences may not be due to &#xA;amino acid sequence differences at all, or may not be &#xA;&lt;i&gt;only&lt;/i&gt; due to such differences.  Post-translational &#xA;modification (such as phosphorylation) and differences in quaternary &#xA;structure are other possibilities.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I notice from &lt;a href=&quot;http://www.jbc.org/content/269/6/4480.full.pdf&quot;&gt;this &#xA;reference&lt;/a&gt; (Parsell &#xA;&lt;i&gt;et al&lt;/i&gt;., 1994)  that hsp104 from &#xA;&lt;i&gt;Saccharomyces cerevisiae&lt;/i&gt; forms oligomers in the &#xA;presence of ATP, and this might be very important in any explanation of &#xA;kinetic differences. (My whole knowledge of hsp140 does not extend &#xA;beyond this excellent paper). &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Yeast and horse liver alcohol dehydrogenase (ADH) are &#xA;homologues and &lt;a href=&quot;http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/1/1/1.html&quot;&gt;catalyze an identical reaction&lt;/a&gt;.  Both also contain zinc.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the yeast enzyme is a &#xA;tetramer, whereas horse liver ADH is dimeric. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another difference worth &#xA;pointing out is that &lt;i&gt;in vivo&lt;/i&gt; yeast ADH functions as &#xA;an aldehyde reductase (making ethanol), whereas liver ADH functions as &#xA;an ethanol dehydrogenase (in alcohol elimination). [I am aware there are&#xA;other isozymes of yeast ADH, which may have different functions]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;As an ethanol dehydrogenase&lt;/strong&gt;, the yeast enzyme has a &#xA;&lt;i&gt;k&lt;/i&gt;&lt;sub&gt;cat&lt;/sub&gt; value of 455 &#xA;s&lt;sup&gt;-1&lt;/sup&gt; (pH 7.05, 25&lt;sup&gt;o&lt;/sup&gt;C; &#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1177466/?tool=pubmed&quot;&gt;Dickinson &amp;amp; Monger&lt;/a&gt;, 1973) whereas the horse liver enzyme has a &#xA;&lt;i&gt;k&lt;/i&gt;&lt;sub&gt;cat&lt;/sub&gt; value (for ethanol &#xA;dehydrogenation) of only 1.67 s&lt;sup&gt;-1&lt;/sup&gt; (pH 6.0, &#xA;25&lt;sup&gt;o&lt;/sup&gt;C; Dalziel, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1243656/?tool=pubmed&quot;&gt;1962&lt;/a&gt;, &lt;a href=&quot;http://www.jbc.org/content/238/8/2850.long&quot;&gt;1963&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the reverse direction, the&lt;i&gt; &#xA;k&lt;/i&gt;&lt;sub&gt;cat&lt;/sub&gt; for &lt;strong&gt;acetaldehyde reduction&lt;/strong&gt; is &#xA;3850 &#xA;s&lt;sup&gt;-1&lt;/sup&gt; for the yeast enzyme (pH 7.05, &#xA;25&lt;sup&gt;o&lt;/sup&gt;C, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1177466/?tool=pubmed&quot;&gt;Dickinson &amp;amp; Monger&lt;/a&gt;, 1973), whereas it &#xA;is only 125 s&lt;sup&gt;-1&lt;/sup&gt; for the liver oxidoreductase (pH &#xA;6.0, 25&lt;sup&gt;o&lt;/sup&gt;C; Dalziel, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1243656/?tool=pubmed&quot;&gt;1962&lt;/a&gt;, &lt;a href=&quot;http://www.jbc.org/content/238/8/2850.long&quot;&gt;1963&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can we explain these kinetic differences from an analysis of &#xA;structure? In my view this is a very tough question.  It may be due to some or all or none of the differences I have highlighted.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Perhaps the question needs to be rephrased as follows: Is there any fundamental &#xA;difference, at any level, in the catalytic mechanism, or in the form of the enzyme in &#xA;solution, or in the amino acid sequence, or in the tertiary or quaternary structure, that can reasonably account for the observed kinetic variation? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are the differences worth explaining?  Perhaps one needs to go no further than to record the individual variation under rigorously-defined reproducible conditions? &lt;hr/&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Before such questions may be answered, it is important to establish the nature of the observed kinetic differences.  What follows are merely some guidelines, most of which you are probably aware of.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Is the velocity versus enzyme plot linear in all cases at both high and low substrate concentrations? That is, in kinetic jargon, is the   &lt;i&gt;&amp;#957;&lt;/i&gt; vs [E&lt;sub&gt;o&lt;/sub&gt;] linear?  As the enzyme is known to form oligomers in the presence of nucleotides (see above), this might be an important control.  Does doubling the enzyme concentration exactly double the rate, and does halving the enzyme concentration exactly half the rate (at both high and low substrate concentrations)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of an enzyme where the &lt;i&gt;&amp;#957;&lt;/i&gt; vs [E&lt;sub&gt;o&lt;/sub&gt;] is often not linear is phosphofructokinase.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I notice you are using a &lt;a href=&quot;http://www.bjsycy.com/WebEdit/UploadFile/20084392717141.pdf&quot;&gt;coupled assay&lt;/a&gt; with two coupling enzymes.  What effect does doubling the amount of one and/or both of these enzymes have on the observed rate?  &lt;strong&gt;It should have none&lt;/strong&gt;, otherwise the assay is not valid. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The substate is ATP.  &lt;strong&gt;Almost certainly, the 'true' substrate for the enzyme is MgATP&lt;sup&gt;2-&lt;/sup&gt;&lt;/strong&gt; (correct me if I am wrong about heat-shock proteins). How much Mg&lt;sup&gt;++&lt;/sup&gt; do you have there?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In determining kinetic parameters for ATP-utilizing enzymes one needs to be aware of ionic equilibria during experimental design. Failure to do so may give rise to spurious kinetic effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A solution containing ATP and Mg&lt;sup&gt;++&lt;/sup&gt; will contain many ions, probably only one of which is the substrate for the enzyme, and whose proportion will vary with concentration.  It is essential that this is taken into account. The problem and posssible solutions are explained very well by Cornish-Bowden (2003, pp 86 - 89) and by &lt;a href=&quot;http://www.biochemj.org/bj/159/0001/1590001.pdf&quot;&gt;Storer &amp;amp; Cornish-Bowden&lt;/a&gt; (1976). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One experimental design is to keep the concentration of MgCl&lt;sub&gt;2&lt;/sub&gt; &lt;strong&gt;in constant excess&lt;/strong&gt; over total ATP concentration (CB recommends 5mM).  This is an important one.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are Michaelis-Menten kinetics obeyed in &#xA;all cases? Is there any evidence for substrate inhibition, or substrate &#xA;activation? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are the double-reciprocal plots (Hanes plot, &#xA;Lineweaver-Burk plot, Eadie-Hofstee plot) linear in all cases?.  Non-linearity may be an indicator of kinetic complexity, or of poor experimental design. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you plot the kinetic data for all three enzymes on a single double-reciprocal plot what sort of a pattern do you get?  Competitive? (no &#xA;differences in &lt;i&gt;k&lt;/i&gt;&lt;sub&gt;cat&lt;/sub&gt;, but &#xA;differences in Michaelis constants). &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In comparing enzyme kinetic parameters the Michaelis constant has the big advantage that it is independent of enzyme concentration.  Thus any differences are likely to be 'real' and not due to errors in, say, protein concentration.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what about &lt;em&gt;V&lt;/em&gt;&lt;sub&gt;max&lt;/sub&gt;? If, say, you determine that the maximum velocites differ by a factor of 1.4, can you be certain that you are not inadvertently adding slighly more enzyme in the higher case, and that the catalytic constants are in fact identical? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;As I said above, these are just personal thoughts.  Most you probably already aware of.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;hr/&gt;&#xA;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Creighton, T.E. (1993) Proteins. Strutures and Molecular Properties. 2&lt;sup&gt;nd&lt;/sup&gt; Edn. W.H. Freeman &amp;amp; Company.&lt;/li&gt;&#xA;&lt;li&gt;Cornish-Bowden (2004) Fundamentals of Enzyme Kinetics 3&lt;sup&gt;rd&lt;/sup&gt; Edn. Portland Press, London. &lt;/li&gt;&#xA;&lt;li&gt;Dalziel, K. (1962) Kinetic Studies of Liver Alcohol Dehydrogenase. &lt;em&gt;Biochemical Journal&lt;/em&gt;, &lt;strong&gt;84&lt;/strong&gt;, 244-254.[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1243656/?tool=pubmed&quot;&gt;pdf&lt;/a&gt;]&lt;/li&gt;&#xA;&lt;li&gt;Dalziel, K (1963) Kinetic Studies of Liver Alcohol Dehydrogenase and pH&#xA;with Coenzyme Preparations of High Purity.  &lt;em&gt;J. Biol. Chem&lt;/em&gt;., &lt;strong&gt;238&lt;/strong&gt;,2850-2858. [&lt;a href=&quot;http://www.jbc.org/content/238/8/2850.long&quot;&gt;pdf&lt;/a&gt;]&lt;/li&gt;&#xA;&lt;li&gt;Dickinson, F.M. &amp;amp; Monger, G.P. (1973)  A study of the kinetics and mechanism of yeast alcohol dehydrogenase with a variety of substrates. &lt;em&gt;Biochemical Journal&lt;/em&gt;,  &lt;strong&gt;131&lt;/strong&gt;, 261-270.  [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1177466/?tool=pubmed&quot;&gt;pdf&lt;/a&gt;]&lt;/li&gt;&#xA;&lt;li&gt;Parsell, D.A., Kowal, A.S &amp;amp; Lindquist, S. (1994) &lt;em&gt;Saccharomyces cerevisiae&lt;/em&gt; Hsp104 Protein. Purification and Characterization of ATP-Induced Structural Changes. &lt;em&gt;J. Biol. Chem&lt;/em&gt;.,  &lt;strong&gt;269&lt;/strong&gt;, 4480-4467. [&lt;a href=&quot;http://www.jbc.org/content/269/6/4480.full.pdf&quot;&gt;pdf&lt;/a&gt;]&lt;/li&gt;&#xA;&lt;li&gt;Storer, A.C. &amp;amp; Cornish-Bowden, A. (1976) Concentration of MgATP&lt;sup&gt;2-&lt;/sup&gt; and Other Ions in Solution. Calculation Of the True Concentrations of Species Present in&#xA;Mixtures of Associating Ions. &lt;em&gt;Biochemical Journal&lt;/em&gt; &lt;strong&gt;159&lt;/strong&gt;, 1-5 [&lt;a href=&quot;http://www.biochemj.org/bj/159/0001/1590001.pdf&quot;&gt;pdf&lt;/a&gt;]&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="1136" LastEditDate="2012-08-12T13:17:37.490" LastActivityDate="2012-08-12T13:17:37.490" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3142" PostTypeId="1" AcceptedAnswerId="3155" CreationDate="2012-08-11T20:48:05.100" Score="6" ViewCount="121" Body="&lt;p&gt;I'm trying to assemble metagenomic data that comes from termite guts. The sequences comes from SOLiD and no paired, so the reads are extremely short (25bp). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried multiple assemblers (CLC, velvet, metavelvet, Meta-IDBA) but all produce few contigs (15 contigs, 1000bp average). The contig output is scarce considering the amount of raw data (5 Gpb).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has anybody has any success in a task such as this?.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="1004" LastEditorUserId="43" LastEditDate="2012-08-12T12:20:02.840" LastActivityDate="2012-08-13T04:37:10.207" Title="Assembly of metagenomic data" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3143" PostTypeId="2" ParentId="3066" CreationDate="2012-08-11T21:26:44.987" Score="2" Body="&lt;p&gt;I'd argue this actually belongs on CrossValidated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially, the problem is one of how a GWAS study is conducted. By looking over an entire genome for associations, you're actually conducting thousands or millions of experiments, not the single experiment most statistics were designed to handle. As such, you're going to find many results that meet the traditional threshold for &quot;significance&quot; purely by chance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Early genomics studies had this problem - they'd generate tons of false-positives, and because of the numbers involved, their very small p-values would give an incorrect perception of the precision of their results. One way to handle this is to adjust for multiple comparisons to essentially penalize the p-value to enable you to still use the p &amp;lt; 0.05 threshold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another very common choice is to recognize that 0.05 is something of an arbitrary boundary, and simply choose a much, much stricter criteria for significance. This is, as far as I'm aware, what most state of the art GWAS epidemiology studies do.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2012-08-11T21:26:44.987" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3147" PostTypeId="1" AcceptedAnswerId="3150" CreationDate="2012-08-12T15:46:00.000" Score="14" ViewCount="2858" Body="&lt;p&gt;We work with a membrane protein system where measuring the affinity between the enzyme and the upstream activating protein has been difficult, and when measured in detergent solution, it is almost 100 fold lesser (ie ~100nM) whereas the EC50 in an enzymatic assay using vesicles in ~1-2nM. Would it be reasonable to say that the &quot;real&quot; affinity is ~1nM than 100s of nM based on the biochemical assay?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternately, is there a documented system where a huge discrepancy exists between measurements from direct binding and biochemical assays?&lt;/p&gt;&#xA;" OwnerUserId="223" LastActivityDate="2012-08-25T15:25:36.587" Title="Is the EC50 of an activating protein for an enzyme a good indicator for the binding affinity Kd?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;&lt;biophysics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3150" PostTypeId="2" ParentId="3147" CreationDate="2012-08-12T18:27:39.763" Score="9" Body="&lt;p&gt;You can certainly get massive differences between EC&lt;sub&gt;50&lt;/sub&gt; and affinity. This is especially true for cell-based assays and membrane protein systems. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason why is because the appropriate time scales to achieve binding equilibrium (hrs for nM affinity, days for picomolar, feptomolar affinity according to back of the envelope calculations) may be and likely will be different from the appropriate time scales of activation, endocytosis, degradation, etc. Furthermore, you can have avidity effects that would not be apparent in a dilute membrane assay compared to a cell's surface. It could very much be that the dominant terms in mass transport change depending on the geometry and antigen density and while I'm not entirely sure bout vesicles vs. emulsions it is true for cancer models. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12649189&quot; rel=&quot;nofollow noreferrer&quot;&gt;Theoretical analysis of antibody targeting of tumor spheroids: importance of dosage for penetration, and affinity for retention.&#xA;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Case study number I:&lt;/strong&gt; hGH:hGHR interactions have been extensively studied and high affinity hGH have been produced. However, none of the variants showed improved EC&lt;sub&gt;50&lt;/sub&gt;. It turns out that the binding was primarily influenced by the off-rates which were so slow, that affecting those values did little to the kinetics of the system. &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/bi9817008&quot; rel=&quot;nofollow noreferrer&quot;&gt;Growth Hormone Binding Affinity for Its Receptor Surpasses the Requirements for Cellular Activity&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Case study number II:&lt;/strong&gt; CEA-antibodies have been affinity matured to have pM activity compared to the wild-type nM affinity. However, the antibody had minimal effect on tumor uptake. As CEA gets endocytosed on the order of 30 minutes, all of the antibody was simply getting endocytosed rather than acting as an inhibitor. &lt;a href=&quot;http://peds.oxfordjournals.org/content/17/4/293.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Directed evolution of an anti-carcinoembryonic antigen scFv with a 4-day monovalent dissociation half-time at 37°C&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(edit)&#xA;I realized that this answer is more applicable to IC&lt;sub&gt;50&lt;/sub&gt;s vs. the EC&lt;sub&gt;50&lt;/sub&gt; experiments described above. However, many of the points remains. The Km between a substrate and its enzyme is a thermodynamic property where as the EC&lt;sub&gt;50&lt;/sub&gt; also has dynamic factors that may influence its measurement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would also add that simply adjusting the pH 2 units may result in a 2 orders of magnitude change in activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(edit2)&#xA;A further point to make about enzymatic assays is that from an observation of Michaelis-Menten kinetics, the K&lt;sub&gt;M&lt;/sub&gt; of the reaction isn't the K&lt;sub&gt;D&lt;/sub&gt; of the enzyme but alternatively the effective binding constant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recall that:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Vb9Lm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is a non-trivial k&lt;sub&gt;cat&lt;/sub&gt; comparable to the dissociation rate k&lt;sub&gt;r&lt;/sub&gt;, the enzyme will have an effective half maximal concentration that is significantly higher than the K&lt;sub&gt;d&lt;/sub&gt;. There are multiple ways how your assay can result in the discrepancies that you're seeing. The first would your strategy in measuring your EC&lt;sub&gt;50&lt;/sub&gt;. If one is an enzymatic readout and the other is a binding readout, you would naturally have very different results.  Alternatively, the enzyme in the detergent system may be catalytically more active than the vesicle system resulting in a higher effective K&lt;sub&gt;M&lt;/sub&gt;. Again, the pH thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, there is always that awkward moment when you realized that you might accidentally have measured a titration curve rather than a binding curve.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-08-17T07:33:27.927" LastActivityDate="2012-08-17T07:33:27.927" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3153" PostTypeId="1" AcceptedAnswerId="3161" CreationDate="2012-08-12T19:52:34.010" Score="7" ViewCount="185" Body="&lt;p&gt;We had a lecture about the balancing systems of the body (mainly the otolith organ / semilunar canals) in which a case was described where a pilot crashed into a ship. He was supposed to keep his altitude and had not been looking at his instruments, but was guiding the plane by feeling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, he was under the illusion that the plane was gaining altitude when it wasn't and so steered it downwards, dropping and eventually crashing into a ship which happened to be at that particular spot that moment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the otolith organs detect de- and acceleration in all directions (that just comes from how the mechanism works), if the pilot was flying at steady altitude, why would they signal that he is rising?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Will add an article later if I find one.)&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-08-19T09:37:33.380" Title="Why are pilots under the illusion of gaining altitude without doing so?" Tags="&lt;human-biology&gt;&lt;perception&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3155" PostTypeId="2" ParentId="3142" CreationDate="2012-08-13T04:37:10.207" Score="2" Body="&lt;p&gt;This depends on your coverage and the number and relative proportion of species in the mixture.  this seems unlikely to produce results unless the protocol biases the library (rRNA universal primers for instance.)  I think at 25 bp sequences, even 30x coverage would not give full assembly sequences. Typically I believe 25 bp reads are only used to resequence close variants from similar or reference genomes.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-08-13T04:37:10.207" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3156" PostTypeId="1" AcceptedAnswerId="3157" CreationDate="2012-08-13T14:34:27.580" Score="2" ViewCount="145" Body="&lt;p&gt;Question is pretty straight forward. Are there generally any chemical cues?&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-08-13T19:26:46.000" Title="How do parasitic fungi sense optimal fruiting conditions from inside the host?" Tags="&lt;mycology&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3157" PostTypeId="2" ParentId="3156" CreationDate="2012-08-13T19:07:57.527" Score="3" Body="&lt;p&gt;In model fungi, the G protein coupled receptor Gpr1 is known to sense sugars and upregulate a cAMP linked PKA pathway, while in pathogenic strains, it senses Methionine. This probably is the environmental cue that sets off fruiting. There is a recently published extensive review too: &lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.micro.61.080706.093432&quot; rel=&quot;nofollow&quot;&gt;Heterotrimeric G protein signaling in filamentous fungi&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Reference&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Li, Liande, Sara J. Wright, Svetlana Krystofova, Gyungsoon Park, and Katherine A. Borkovich.&lt;/strong&gt; &lt;em&gt;“Heterotrimeric G Protein Signaling in Filamentous Fungi.”&lt;/em&gt; Annual Review of Microbiology 61, no. 1 (October 2007): 423–452.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="223" LastEditorUserId="307" LastEditDate="2012-08-13T19:26:46.000" LastActivityDate="2012-08-13T19:26:46.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3158" PostTypeId="1" AcceptedAnswerId="3159" CreationDate="2012-08-13T20:42:52.890" Score="6" ViewCount="1297" Body="&lt;p&gt;I was going over slides of energy expenditure in muscle cells. It mentions that in muscle tissue, the cell's energy charge ([ATP] / [AMP]) is the principle factor controlling glycolytic activity, and also that glycolysis’ primary role here is to provide ATP for contraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the slides also mentions that &quot;Keep in mind that [ATP] + [ADP] + [AMP] remains relatively constant in the cell over short time frames&quot; with no further explanation. I was under the impression that ATP was &lt;em&gt;actively consumed&lt;/em&gt; in muscle tissue during intense activity (which is why lactic acid builds up in muscles: oxidative phosphorylation can't keep up with your rate of energy expenditure).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, my question is &lt;strong&gt;Are my slides wrong? During muscle activity, is there a general lack or constancy of ATP?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-08-13T21:28:38.220" LastActivityDate="2012-08-13T21:28:38.220" Title="Why does muscle tissue have relatively constant AMP + ADP + AMP?" Tags="&lt;metabolism&gt;&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3159" PostTypeId="2" ParentId="3158" CreationDate="2012-08-13T21:18:16.140" Score="6" Body="&lt;p&gt;Adenosine triphosphate (ATP) is often thought of as the energy currency of cells. It is not &quot;used up&quot; per se, but energy is released from the conversion of ATP to ADP (adenosine diphosphate), and yet more can be obtained by removing another phosphate to make AMP (adenosine monophosphate). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a chemical schematic of ATP, you can see the three phosphates to the left.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/P49xp.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your slides state that the amount of (ATP + ADP + AMP) remains constant in the muscle, which makes sense because ATP is not used up, but converted to ADP. So as cells use energy, they do not actually reduce the total concentration of (ATP + ADP + AMP). Energy is required to add the phosphates back onto an ADP or AMP molecule - the process is called oxidative phosphorylation in cellular respiration (although this is not the only way).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope I didn't misunderstand your question.&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-08-13T21:18:16.140" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3160" PostTypeId="1" AcceptedAnswerId="3162" CreationDate="2012-08-13T21:39:56.900" Score="9" ViewCount="14559" Body="&lt;p&gt;There doesn't seem to be a lot of information available on research done on warts.  What is the life cycle of a wart?  How does it spread? -- specifically how does it recruit cells to spread it?  What is the life cycle of a PV-infected dermal cell? &lt;/p&gt;&#xA;" OwnerUserId="1249" LastEditorUserId="1249" LastEditDate="2012-08-15T17:56:02.637" LastActivityDate="2012-08-15T17:56:02.637" Title="What is the life cycle of a wart?" Tags="&lt;virology&gt;&lt;pathology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3161" PostTypeId="2" ParentId="3153" CreationDate="2012-08-13T23:54:05.883" Score="5" Body="&lt;p&gt;See &lt;a href=&quot;http://flightsafety.org/hf/hf_jul-aug95.pdf&quot;&gt;this&lt;/a&gt; link. It provides a great overview. The answer you want is in the otolith section. To paraphrase, it states that our otolith organs are designed to help us lean forward while running to maintain our center of gravity when in motion; however, in a plane this reflex can backfire by causing a pilot to believe he is going straight when in actuality he may be going downward.&lt;/p&gt;&#xA;" OwnerUserId="1250" LastEditorUserId="1250" LastEditDate="2012-08-14T00:14:27.427" LastActivityDate="2012-08-14T00:14:27.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3162" PostTypeId="2" ParentId="3160" CreationDate="2012-08-13T23:58:23.553" Score="8" Body="&lt;p&gt;&lt;a href=&quot;http://www.scielo.br/scielo.php?script=sci_arttext&amp;amp;pid=S0365-05962011000200014&amp;amp;lng=en&amp;amp;nrm=iso&amp;amp;tlng=en&quot;&gt;This&lt;/a&gt; article has some good information. It's certainly more than I want to know about warts.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Isolated warts may remain unaltered for&#xA;  months or years, or a large number of new lesions&#xA;  may develop rapidly in a short period of time. The&#xA;  development of warts is not predictable.&#xA;  Approximately 65% of warts disappear spontaneously&#xA;  within two years. The patient’s age and number of&#xA;  lesions do not seem to affect the prognosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are many different types of &lt;a href=&quot;http://en.wikipedia.org/wiki/Wart&quot;&gt;warts&lt;/a&gt; and of &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_papillomavirus&quot;&gt;HPV&lt;/a&gt;. Since warts cause a type of &lt;a href=&quot;http://en.wikipedia.org/wiki/Dysplasia&quot;&gt;dysplasia&lt;/a&gt; their life cycle can be very variable and unpredictable.&lt;/p&gt;&#xA;" OwnerUserId="1250" LastEditorUserId="1250" LastEditDate="2012-08-14T00:05:29.763" LastActivityDate="2012-08-14T00:05:29.763" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3163" PostTypeId="2" ParentId="1489" CreationDate="2012-08-14T02:11:45.440" Score="12" Body="&lt;p&gt;In general, plant cells only undergo differentiation at special regions in the plant known as meristems. Two of the primary types of meristem are the root apical meristem (at the tips of roots) and the shoot apical meristem (at shoot tips)^. Within the shoot apical meristem the plant cells divide and begin to differentiate into different cell types (such as different cells of the leaf, or vascular cells). Later growth (of, say, a leaf) is largely a result of cell expansion (although cell division does &lt;a href=&quot;http://jxb.oxfordjournals.org/content/11/1/68.abstract&quot;&gt;still occur&lt;/a&gt;, but drops off as the leaf expands). Therefore, if you punch a hole in a leaf, it probably won't be filled in because the cells in that leaf have finished growing and dividing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, as a shoot grows, more meristems are created. These are found in the axillary buds, just above where the leaf meets the stem. The meristems in the axillary buds can grow to form branches. Different plants obviously make different numbers of branches, but there is a common control mechanism known as apical dominance, where the meristem at the tip of the shoot suppresses the growth of the lower axillary buds. This is why a shoot with no branches can be made to grow branches by cutting off the tip (gardeners often do this to make &quot;leggy&quot; plants more bushy).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of that was a long explanation to say, no, a plant doesn't normally^^ regenerate in the sense of filling in cells that have gone missing. However, if you cut off a shoot, the next remaining bud might begin to grow and, in a sense, replace the part that was lost. In that case, an existing bud is recruited to form a new branch and replace lost functionality, but I wouldn't say that qualifies as regenerating missing tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;^There are other types of meristem as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;^^If you torture plant cells enough you can force them to become &quot;stem cells&quot; and thereby make an entirely new plant, but this is rare in nature.&lt;/p&gt;&#xA;" OwnerUserId="1197" LastActivityDate="2012-08-14T02:11:45.440" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3164" PostTypeId="1" CreationDate="2012-08-14T08:11:39.750" Score="5" ViewCount="122" Body="&lt;p&gt;It is now well established that human ageing is accompanied by an increase in systemic, low-grade (chronic) inflammation, sometimes termed &lt;em&gt;inflammaging&lt;/em&gt; (&lt;a href=&quot;http://dx.doi.org/10.1111/j.1753-4887.2007.tb00358.x&quot; rel=&quot;noreferrer&quot;&gt;Franceschi, 2007&lt;/a&gt;). This is in part due to more global changes to the body, including an increased number of senescent cells, but of interest to me currently is the change in the composition of the circulating immune cell sub-types that may either cause, or be affected by, the increase in 'global' inflammation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I imagine the answer to this question is a study that samples individuals of different ages and separates the various leukocyte fractions. Using this it could be determined which immune sub-types are over-/under-represented in the aged, and at what age the changes occur (e.g. monocyte numbers may decrease from age 40, whereas neutrophil numbers may increase...). I have done some fairly extensive research, but have been unable to find a study that has done this - however it seems likely that it has been performed. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-08-16T04:05:26.547" Title="During human ageing, which immune cell sub-types are most affected?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;senescence&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3165" PostTypeId="1" AcceptedAnswerId="5165" CreationDate="2012-08-14T10:52:11.917" Score="15" ViewCount="1218" Body="&lt;p&gt;Having watched a lot of olympians the last few weeks, I was struck by how many of them have actually spent their wholes lives/careers training for their one event (be in running a marathon, or throwing a javelin). This is of course unsurprising - a lot of people take their sport very seriously - but I wondered to what degree these athletes are predisposed to becoming atheletes, and to what degree they just 'happened' to end up doing it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've had a bit of a search around, but have been unable to find any studies (although there is an awful lot of media attention to the topic) that actually study the interaction between nature (genetics) and nurture (environment/training etc) in the context of top-end athletes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is quite clear to me that the answer is of course 'both', but to what degree? Have any common genetic variants/loci been identified, or is 'athleticism' a far too complex trait for this? Thanks.&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2013-02-06T10:57:22.180" Title="Athletes: nature vs. nurture?" Tags="&lt;human-biology&gt;&lt;genetics&gt;" AnswerCount="3" CommentCount="11" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3166" PostTypeId="1" CreationDate="2012-08-14T11:43:50.473" Score="9" ViewCount="305" Body="&lt;p&gt;In software engineering, an analogy is sometimes made using biological cells. I would like to know whether it has basis in fact.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;People say (&lt;a href=&quot;http://userpage.fu-berlin.de/~ram/pub/pub_jf47ht81Ht/doc_kay_oop_en&quot;&gt;Alan Kay was first&lt;/a&gt;) that &quot;objects&quot; in software should be like cells: separate from one another, communicating by passing messages. This separateness has been argued by saying that &lt;strong&gt;a cell spends much of its metabolic energy keeping its insides in and its outsides out&lt;/strong&gt;. The implication is that programmers should likewise spend significant effort maintaining boundaries between parts of a system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this actually true? What percentage of its energy does a cell generally spend maintaining its contents?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(My guess is that the answer varies wildly depending on the cell and its environment, but some ballpark example numbers would be nice.)&lt;/p&gt;&#xA;" OwnerUserId="1251" LastEditorUserId="1251" LastEditDate="2012-08-14T12:22:14.563" LastActivityDate="2015-05-13T06:23:01.790" Title="How much energy does a cell expend maintaining its contents?" Tags="&lt;cell-biology&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3167" PostTypeId="1" CreationDate="2012-08-14T12:52:12.410" Score="8" ViewCount="1371" Body="&lt;p&gt;Mitochondria and plastids have their own DNA, their own membranes, and their reproduction is not tied to the reproductive cycle of the host cell. However, they are considered to be organelles rather than a separate species in symbiosis with eukaryotes. Granted, mitochondria and plastids are incapable of living outside their parent cells, and likewise eukaryotes are incapable of surviving without the help of mitochondria and plastids. But this is also true of many other symbiotic pairs in Eukarya. So where does the distinction lie? What makes mitochondria and plastids organelles rather than separate organisms? &lt;/p&gt;&#xA;" OwnerUserId="864" LastEditorUserId="43" LastEditDate="2012-08-14T13:50:07.300" LastActivityDate="2012-08-18T18:54:20.160" Title="Why aren't mitochondria and plastids considered symbiotes of eukaryotic cells?" Tags="&lt;cell-biology&gt;&lt;mitochondria&gt;&lt;eukaryotic-cells&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3168" PostTypeId="2" ParentId="3167" CreationDate="2012-08-14T13:15:32.000" Score="7" Body="&lt;p&gt;I would say it has to do with the amount of mitochondrial or sequence that has been transferred to the host genome. As a consequence of all this information stored in the host genome, mitochondria cannot reproduce without the host. In this way, they are not their own organisms, but rather organelles.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Over evolutionary time, the line between organelle and intracellular endosymbiont gets blurry, but in their current state, mitochondria are organelles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same goes for for plastids, in general.&lt;/p&gt;&#xA;" OwnerUserId="184" LastActivityDate="2012-08-14T13:15:32.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3169" PostTypeId="1" AcceptedAnswerId="97284" CreationDate="2012-08-14T13:48:13.190" Score="8" ViewCount="314" Body="&lt;p&gt;Other than CO₂ and Methane what other gases do humans produce or emit?&lt;/p&gt;&#xA;&lt;p&gt;For example, does  skin decomposition, or aerobic respiration emit any special gases that people don't normally realize or know about.&lt;/p&gt;&#xA;&lt;p&gt;I ask because of a discovery I made during research is that while being poisonous to the central nervous system, methanol is a natural endogenous compound found in normal, healthy human individuals.&lt;/p&gt;&#xA;&lt;p&gt;One study found a mean of 4.5 ppm in the exhaled breath of the subjects. &lt;a href=&quot;https://iopscience.iop.org/article/10.1088/0967-3334/27/7/007&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://iopscience.iop.org/article/10.1088/0967-3334/27/7/007&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="238" LastEditDate="2020-12-13T19:58:16.163" LastActivityDate="2020-12-15T10:39:59.377" Title="What gaseous substances do humans emit?" Tags="&lt;cell-biology&gt;&lt;physiology&gt;&lt;endocrinology&gt;&lt;digestive-system&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="3170" PostTypeId="2" ParentId="3166" CreationDate="2012-08-14T14:54:53.093" Score="6" Body="&lt;p&gt;I'm going to take a stab at this.  Its a difficult question to get right, just to put is in the right mood here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lets leave energy out of this as the proper term is structure.  The cell is designed to compartmentalize itself to differentiate its own living tissue from other cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this regard Alan Kay's analogy is pretty good.  In multicellular organisms, individual cells (mostly) each maintain their own DNA and energy storage, though they get their nutrients and energy from outside.  They create the organism as a whole by differentiation; each cell changes to take on a specialized role and depends on other cells to support it. E.g. in animals some cells/organs digest the food and distribute nutrients to the rest, others form the lung and help distribute oxygen and others scrub the blood of waste.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is somewhat like good code design where functions are partitioned out into specialized parts of the software for the sake of maintainability and organization. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Somewhere after this point I think the analogy breaks down since after all the point of good coding practice is to organize the code for understanding within reasonable human conceptual limits.  The cells and how they organize themselves are still plenty mysterious to us as they have their own definition of roles and function much of which is still being discovered today.  For instance the many kinds of neurons in the brain and the sorts of structures they form are extremely diverse.  We have few organizing principles for predicting how many cell types would exist in a system and these only create partial answers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After all its just an analogy...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;getting close to an answer? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-08-14T14:54:53.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3171" PostTypeId="1" AcceptedAnswerId="3184" CreationDate="2012-08-14T15:15:18.833" Score="10" ViewCount="6722" Body="&lt;p&gt;Studies of human traits and diseases are inherently confined to observational studies, known as epidemiological studies. This can make it very hard to determine what actually causes a particular disease or trait, and what is just a by-product or biomarker of the disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Mendelian randomization&lt;/strong&gt; is a statistical technique used by genetic epidemiologists to determine &lt;em&gt;causal&lt;/em&gt; effects, for instance whether a biomarker actually influences disease risk, or whether it is just a statistical association.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From basics, how can genetics be used to determine causal associations between traits (such as blood markers) and increased risk of disease, and on what assumptions is this based?&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2016-03-15T09:58:07.057" Title="What is Mendelian Randomization, and how is it used to infer causality in epidemiology?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;bioinformatics&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3172" PostTypeId="2" ParentId="1833" CreationDate="2012-08-14T15:42:27.560" Score="4" Body="&lt;p&gt;I think I found a reference.  Most of these papers are behind paywalls - its a pretty obscure topic in biology, though not because it isn't interesting...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For those not familiar with the question, the thylakoid membranes are an organelle structure in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Chloroplast&quot; rel=&quot;nofollow&quot;&gt;chloroplast&lt;/a&gt;, which contains all the photosynthetic machinery in the plant cell.  The chloroplast is though to be a symbiotic cyanobacterium captured to make eukaryotic plants.  Like mitochondria, the chloroplast maintains its own chromosome and some ribosomal machinery. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The stack (grana) and extended (stromal lamallae) structures of the thylakoid no doubt help optimize light/energy capture by distributing the light gathering proteins in an advantageous way.  It was previously believed that the electrostatic charge of the thylakoid membrane helped make the stacks, but this &lt;a href=&quot;http://jfallen.org/~john/webstar/john/pdf/124.pdf&quot; rel=&quot;nofollow&quot;&gt;Trends in Plant Science review article (Allen and Forsberg, 2001)&lt;/a&gt; discusses how the distribution of photosystem (PS) I and II are more concentrated in the stroma and grana respectively.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They put forth that Light Harvesting complex II (LHC II), which gathers photons for PSII tends to cluster in a trans fashion - forming contacts with LHCII in membranes above it, specifically forming the grana stacks enriched in PSII. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-08-15T03:52:42.780" LastActivityDate="2012-08-15T03:52:42.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3173" PostTypeId="1" AcceptedAnswerId="3215" CreationDate="2012-08-14T16:15:56.337" Score="6" ViewCount="90" Body="&lt;p&gt;I need a model of in-gene DNA drift. I'm not interested in bacterial phylogenies alone. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is what I understand:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Sequences corresponding to genes have both exons and introns, but in bacteria the proportion of introns is low.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Because I'm talking about genes, sequence changes are not very neutral but subject to selection. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I have checked a few papers linked in Wikipedia about this subject, but I notice that they are tuned for entire sequences, and many of them almost predate the genomic era. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are some current, canonical sources in this area?&lt;/p&gt;&#xA;" OwnerUserId="117" LastEditorUserId="57" LastEditDate="2012-08-14T19:54:01.970" LastActivityDate="2012-08-17T14:32:13.140" Title="(Rough) Model for DNA evolution in E. coli genes" Tags="&lt;dna&gt;&lt;sequence-analysis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3175" PostTypeId="2" ParentId="3160" CreationDate="2012-08-14T21:46:03.180" Score="4" Body="&lt;p&gt;Conner's response contained just the type of source material I was looking for.  Thanks Conner -- let us all +1 him.  Allow me to summarize the specifics of the &lt;a href=&quot;http://www.scielo.br/scielo.php?script=sci_arttext&amp;amp;pid=S0365-05962011000200014&amp;amp;lng=en&amp;amp;nrm=iso&amp;amp;tlng=en&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; in relation to my question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Transmission&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;PVs are transmitted through direct or indirect contact with an&#xA;  individual who has the lesion. Dysfunctions in the epithelial barrier&#xA;  by trauma, minor injuries or maceration cause loss of solution of&#xA;  continuity in the skin, thus allowing viral infection. After&#xA;  inoculation, the incubation period varies from 3 weeks to 8 months.&#xA;  Spontaneous regression is observed in most cases.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Infection&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Infection begins when the PV reaches the cells of the basal layer;&#xA;  there is no viral replication at this location and the virus just&#xA;  keeps its genome by amplification of a low number of copies.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Replication&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The replicative phase and protein synthesis occur in the suprabasal&#xA;  differentiated &lt;a href=&quot;http://en.wikipedia.org/wiki/Keratinocyte&quot; rel=&quot;nofollow&quot;&gt;keratinocytes&lt;/a&gt;. Progression time and type of lesion&#xA;  correlates with the quantity of viral particles detected. Younger&#xA;  warts present a higher viral amount when compared to old warts.&#xA;  Plantar warts have a higher viral load than common warts. The center&#xA;  of the lesion appears to be the main site of viral concentration.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Latency&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;PVs appear to remain in their host for long periods of life. A variety&#xA;  of different types of PVs can be detected in random sites of normal&#xA;  skin in humans and animals. This reinforces that a latent life cycle&#xA;  is often a characteristic of these viruses.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Interesting Notes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;There are no known PVs that infect more than one species.&lt;/li&gt;&#xA;&lt;li&gt;To date, about 100 different types of HPVs have been fully characterized.&lt;/li&gt;&#xA;&lt;li&gt;Human PVs does not grow on conventional culture media. The diagnosis of HPV infection is made by histopathology of lesions&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1249" LastActivityDate="2012-08-14T21:46:03.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3176" PostTypeId="2" ParentId="3169" CreationDate="2012-08-15T06:58:32.260" Score="6" Body="&lt;p&gt;The gases NO, H₂S, CO even have a function in the human body!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nitric oxide is produced in endothel and neurons as messenger, and in macrophages as cause of nitrosative stress for imprisoned bacteria. Hydrogen sulfide is produced in cysteine catabolism and functions as messenger (only recently discovered). Carbon monoxide appears to act as messenger, too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_functions_of_nitric_oxide&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Biological_functions_of_nitric_oxide&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hydrogen_sulfide#Function_in_the_body&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Hydrogen_sulfide#Function_in_the_body&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wu, L; Wang, R (December 2005). &quot;Carbon Monoxide: Endogenous Production, Physiological Functions, and Pharmacological Applications&quot;. Pharmacol Rev 57 (4): 585–630. doi:10.1124/pr.57.4.3. PMID 16382109&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="3340" LastEditDate="2014-10-09T13:32:22.620" LastActivityDate="2014-10-09T13:32:22.620" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3177" PostTypeId="1" AcceptedAnswerId="3180" CreationDate="2012-08-15T07:26:03.653" Score="40" ViewCount="5026" Body="&lt;p&gt;We use electromagnetic communication everywhere these days. Cell phones, wifi, old-school radio transmissions, television, deep space communication, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm curious about some of the possible reasons we have never seen biological systems having evolved to use electromagnetic, i.e. radio, for communication. The one obvious exception to this are organisms that generate their own light, i.e. bioluminescence. Cuttlefish are masters of this, and many other species as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems like bio-radio could have offered all kinds of evolutionary advantages for animals capable of using it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are their basic physical limits in chemistry, or excess energy requirements or something that would basically have made this impossible? Or was this perhaps just something that life never evolved to use, but would otherwise be possible in evolution?&lt;/p&gt;&#xA;" OwnerUserId="1253" LastEditorUserId="3952" LastEditDate="2013-08-04T02:17:39.870" LastActivityDate="2015-07-10T20:44:05.650" Title="Why did life not evolve to use radio?" Tags="&lt;evolution&gt;&lt;vision&gt;&lt;electrophysiology&gt;&lt;speculative&gt;" AnswerCount="5" CommentCount="5" FavoriteCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="3178" PostTypeId="2" ParentId="3177" CreationDate="2012-08-15T08:15:01.900" Score="2" Body="&lt;p&gt;A quick comparison between light and sound vs. Radio&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Light&quot; rel=&quot;nofollow noreferrer&quot;&gt;Light&lt;/a&gt;: Wavelength 380 nm -740 nm&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sound&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sound&lt;/a&gt;: 17 mm - 17 m&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Radio_frequency&quot; rel=&quot;nofollow noreferrer&quot;&gt;Radio&lt;/a&gt;: 1mm - 10e5 km&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gSMxk.png&quot; alt=&quot;EM spectrum&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the Planck relation, the energy of a wave is inversely proportional to the wavelength. As a result light is stronger than sound which is stronger than FM radio which is stronger than AM radio. Very likely, the energy density provided by radio is far too weak to have meaningful signal processing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are some uses in the radio frequency. &lt;a href=&quot;http://en.wikipedia.org/wiki/Animal_echolocation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bat echolocation&lt;/a&gt; occurs at a frequency of 14,000 to 100,000 Hz which is well within the radio frequency. &lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-08-15T08:15:01.900" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3179" PostTypeId="1" CreationDate="2012-08-15T11:59:10.683" Score="2" ViewCount="1065" Body="&lt;p&gt;Say I am studying a particular disease and I know that its incidence is 0.8 per 100000 children below the age of 18, how would I find the incidence of a whole bunch of other pediatric diseases (or even not just limited to pediatrics)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially I want to find diseases that would be familiar to a medical audience and provide an example of a disease with an incidence of about 0.8 per 100000, another one that is one tenth the incidence and another one that is ten times the incidence.&lt;/p&gt;&#xA;" OwnerUserId="1045" LastActivityDate="2012-08-23T04:14:29.417" Title="Where can I find a list of diseases and their incidence?" Tags="&lt;epidemiology&gt;&lt;statistics&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3180" PostTypeId="2" ParentId="3177" CreationDate="2012-08-15T12:03:59.370" Score="31" Body="&lt;p&gt;There is a very different mechanism for generation (and detection) of ultraviolet, visible and infrared light vs radio waves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the first, it is possible to generate it using chemical reactions (that is, &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemiluminescence&quot;&gt;chemiluminescence&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Bioluminescence&quot;&gt;bioluminescence&lt;/a&gt;) with a typical energy of order of 2 eV (&lt;a href=&quot;http://en.wikipedia.org/wiki/Electronvolt&quot;&gt;electronovolts&lt;/a&gt;). Also, it is easy to detect with similar means - coupling to a bond (e.g. using &lt;a href=&quot;http://en.wikipedia.org/wiki/Opsin&quot;&gt;opsins&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For much longer electromagnetic waves, and much lower &lt;a href=&quot;http://halas.rice.edu/conversions&quot;&gt;energies per photon&lt;/a&gt;, such mechanism does not work. There are two reasons:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;typical energy levels for molecules (but it can be worked around),&lt;/li&gt;&#xA;&lt;li&gt;thermal noise has energies (0.025 eV) which are higher than radio wave photon energies (&amp;lt;0.001 eV) (it rules out both controlled creation and detection using molecules).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In other words - radiation which is less energetic than thermal radiation (far infrared) is not suitable for communication using molecular mechanisms, as thermal noise jams transmission (making the sender firing at random and making the receiver being blind by noise way stronger than the signal).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, one can both transmit, and detect it, using wires. In principle it is possible; however, without good conductors (like metals, not - salt solutions) it is not an easy task (not impossible though).&lt;/p&gt;&#xA;" OwnerUserId="129" LastEditorUserId="129" LastEditDate="2012-08-15T12:16:39.560" LastActivityDate="2012-08-15T12:16:39.560" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3181" PostTypeId="1" CreationDate="2012-08-15T12:54:13.287" Score="3" ViewCount="176" Body="&lt;p&gt;I am trying to optimize annealing temperature for some primer pairs. I have tried optimization using cDNA, genomic DNA, Taq polymerase, phusion polymerase etc., but every time I am either getting non-specific amplification, a band of larger size than expected or no amplification. Every time I am getting a primer-dimer. Can anybody help me optimize the annealing temperature?&lt;/p&gt;&#xA;" OwnerUserId="1255" LastEditorUserId="1250" LastEditDate="2012-08-15T16:44:00.500" LastActivityDate="2014-07-10T23:30:17.710" Title="Optimization of annealing temperature" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3182" PostTypeId="2" ParentId="3179" CreationDate="2012-08-15T14:06:20.823" Score="3" Body="&lt;p&gt;About diseases in general, that would concern the health dept. of the respective country government, and the govt. is the most probable source for such numbers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, orpha.net has two reports with numbers concerning hereditary diseases, have a look at &lt;a href=&quot;http://www.orpha.net/consor/cgi-bin/Education_Home.php?lng=EN#REPORT_RARE_DISEASES&quot; rel=&quot;nofollow&quot;&gt;http://www.orpha.net/consor/cgi-bin/Education_Home.php?lng=EN#REPORT_RARE_DISEASES&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-08-15T14:06:20.823" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3184" PostTypeId="2" ParentId="3171" CreationDate="2012-08-15T14:35:48.633" Score="17" Body="&lt;p&gt;Epidemiological studies analyze human observational cohort data to try to statistically link disease risk and biomarkers. For instance, it is know a well know fact that smoking increases the risk of lung cancer, yet before the 1950s it was widely considered otherwise until observational evidence proved irrefutable (&lt;a href=&quot;http://dx.doi.org/10.1001/jama.1950.02920090056026&quot; rel=&quot;noreferrer&quot;&gt;Levin, 1950&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Confounding&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;However, inferring causality using observational data can be tricky. For instance, there is a very strong statistical association between ice-cream sales and risk of drowning in the UK. In this example it is quite clear that the association is &lt;em&gt;confounded&lt;/em&gt; - that is, there is a 'hidden' variable we have not accounted for that links the 2. It is easy to infer that ice-cream sales don't increase your risk of drowning, but the 2 are correlated because both ice-cream sales and risk of drowning increase at the same time of year; both are positively correlated with 'nice weather' traits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the above example it is easy to say that the relationship is confounded. However, in a hypothetical study on type-2 diabetes that finds higher blood hematocrit (% volume of blood made up of red blood cells) is associated with increased odds of being diabetic, it is less clear whether higher hematocrit increases susceptibility/risk of becoming diabetic, or whether diabetes increases hematocrit. Longitudinal studies that follow the same individuals for many years help determine &lt;em&gt;which came first&lt;/em&gt; - this is based on the assumption that if raised hematocrit is associated with increased risk of diabetes 5 years later, it is more likely that hematocrit is &lt;em&gt;causal&lt;/em&gt;, and you have a biomarker for diabetes risk (although you still cannot say it is causal, it may just be a proxy for another 'hidden' trait, or the effect may be &lt;em&gt;mediated&lt;/em&gt; by another unmeasured marker).&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Causality&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Genome-wide association (GWA) studies have become increasingly popular since the completion of the human genome project, and there are currently (15th August 2012) 7039 genetic variants (SNPs, single-nucleotide polymorphisms) documented in the catalogue of published GWA studies (&lt;a href=&quot;http://www.genome.gov/gwastudies/&quot; rel=&quot;noreferrer&quot;&gt;www.genome.gov/gwastudies&lt;/a&gt;). These SNPs have been robustly associated with traits such as 'risk of type-2 diabetes', or 'blood adiponectin levels', by large genetic epidemiological studies, usually with many thousands of participants sampled. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key point about SNP associations is that the direction of effect is always known; a particular SNP may affect your adiponectin levels, but adiponectin does not affect the SNPs you inherit.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Mendelian Randomization&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;In an observational study that finds an association between (for example) circulating triglyceride levels and type-2 diabetes (using fasting glucose and insulin as 'proxies') it is not possible to determine the causal direction; do triglycerides increase risk of diabetes or vice versa? (This is an actual case study by &lt;a href=&quot;http://dx.doi.org/10.2337/db10-1317&quot; rel=&quot;noreferrer&quot;&gt;De Silva, &lt;em&gt;et al&lt;/em&gt;. 2011&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using the assumption that the inheritance of SNPs is essentially random (i.e. not affected by the trait you are measuring - in this example triglycerides) it is possible to determine the causal effect of triglycerides on the risk of diabetes. Note: this is only possible for traits (such as serum triglyceride levels) that have SNPs identified by GWA studies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, you have already calculated the association between triglyceride levels (in this study a 1 standard-deviation (SD) increase in triglycerides was associated, with an Odds Ratio (OR) of 2.68, with type-2 diabetes in almost 10,000 human participants). Because it is a cross-sectional study, only an association is reported, with no causal implications... yet!&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Enter the SNPs&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Having identified the SNPs that increase triglyceride levels (at the time of the study, 10 were reported in the literature), each participants genotype for these SNPs needs to be measured or inferred (generally this is performed in large cohort studies, which are then used for many different individual projects).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A combined 'score' is then derived for each individual. This is conceptually very simple; if an individual has 4 of the 10 triglyceride raising alleles, they are given a score or 4, and so on. This is complicated by the fact that the SNPs have different effects on the triglycerides, so a 'weighted allele score' is derived instead (simply put, the coefficient of the SNP~triglyceride association is taken into account when adding risk allele scores). By using this kind of score, a 'per allele' estimation of the effects can be estimated;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The association between the triglyceride levels and the allele score is then determined (by linear regression analysis - adjusted for age and sex, as these are known to affect triglycerides). There are actually 2 ways of performing the next analysis, the first of which is conceptually simpler, but the second of which is more robust.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Method 1: the 'triangulation' approach&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;The two observed associations calculated so far (per-SD trig. levels are associated with diabetes, and the per-allele SNP score are associated with per-SD trig. levels) can then be used to calculate an &lt;em&gt;expected&lt;/em&gt; association. This is simply derived by multiplying the 2 coefficients together. Below is the 'triangulation' representation of this;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0ItJ0.png&quot; alt=&quot;Triangulation approach for Mendelian Randomization&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;em&gt;expected&lt;/em&gt; association between the triglyceride-raising SNPs and risk of diabetes is only true if raised triglycerides increase the risk of diabetes. The &lt;em&gt;observed&lt;/em&gt; association between the SNP-score and diabetes can then be calculated. If the expected and observed estimates are similar, then triglycerides raise diabetes risk, and are a causal biomarker. If the observed association is null (or, at least, much smaller), then triglycerides are likely to be secondary.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Method 2: the instrumental variable analysis&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;This method is for the more hardy statisticians. Instrumental variables are derived variables, and represent an intermediate between a proposed 'cause' and the 'effect', or outcome (in this case the triglyceride raising alleles are proposed to 'cause' diabetes, and this is mediated by the triglyceride levels themselves).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using a linear regression, the &quot;fitted values&quot; from a model with triglyceride levels as the outcome, and the weighted SNP score as the only independent variable, are extracted. These fitted values represent the variance in the triglycerides that is predicted by the SNP score. We are using the SNPs as the &lt;em&gt;instrument&lt;/em&gt; here, as they directly influence the biomarker (exposure, i.e. triglycerides), and are not affected by either the exposure or the outcome (diabetes). &lt;strong&gt;The important assumption here is that the effect of the SNPs on the outcome is not confounded, and can only be mediated by the exposure - this is true for genotypes (&lt;a href=&quot;http://dx.doi.org/10.1002/sim.3034&quot; rel=&quot;noreferrer&quot;&gt;Lawlor, &lt;em&gt;et al&lt;/em&gt;. 2008&lt;/a&gt;)&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By then determining the association between the derived variable and diabetes, you will know whether the proportion of the triglyceride variance predicted by the SNPs is associated with diabetes - if so, then triglycerides increase the risk of diabetes.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Results&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;The study performed both types of Mendelian Randomization analysis and found no evidence to suggest a causal association between triglycerides and diabetes phenotypes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So Mendelian Randomization is a useful tool for inferring causality with biomarkers. It is not necessarily conclusive evidence, but it can help distinguish biomarkers of particular importance and interest (with regard to interventions) from those that are just markers of the disease.&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-08-15T14:35:48.633" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3186" PostTypeId="1" CreationDate="2012-08-15T20:34:20.433" Score="21" ViewCount="11445" Body="&lt;p&gt;I am familiar with the structure and function of ATP synthase, but one small detail doesn't seem to make sense. It also happens to be a detail that seems very hard to express.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Depending on the organism, there can be from 10 to 14 c-subunits in the c-ring of ATP synthase. For practicality/consistency's sake, let's assume 10. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Every c-subunit is protonated (from the cytoplasmic side of the mitochondrion) and rotated almost 360 degrees within the lipid membrane before it is ultimately deprotonated, which releases a proton into the matrix. Thus, since the c-ring is 10 subunits big (in this case), 10 protons are being introduced to the matrix every 360 degree turn, which mean that &lt;em&gt;1 proton = a 36 degree turn&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These protons allow for the gamma-subunit to be turned at the inside of the hexamer (of 3 alpha-subunits and 3 catalytic beta-subunits) found below the rotor. The b-subunits are thus located 120 degrees apart. &lt;em&gt;Every 120 degrees precisely&lt;/em&gt;, that beta-subunit changes shape, &lt;em&gt;dictated by the rotation of the gamma-subunit&lt;/em&gt;, and enters one of the three states that ultimately catalyze one ATP from ADP and inorganic phosphate (since &lt;strong&gt;only one of the three states actually forms ATP&lt;/strong&gt;). Since the gamma-subunit catalyses the formation of 1 ATP every 120 degrees, a &lt;em&gt;full 360 degree rotation would yield 3 ATPs&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is where things go awry in my mind. Within 360 degrees, 10 protons and 3 ATPs are made. Thus, that makes (10/3) protons per ATP, or 3.33 protons/ATP. When the gamma-subunit receives a proton, it rotates 36 degrees, but &lt;em&gt;ATP formation only happens at precisely 120 degrees&lt;/em&gt;, and the only common interval between 36 and 120 is 360 (when 3 as opposed to 1 ATPs are made)!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;: The gamma-subunit &lt;em&gt;must&lt;/em&gt; rotate in exactly 120 degree increments, because we observe it do so, as shown &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK22388/&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;More detailed analysis in the presence of lower concentrations of ATP revealed that the γ subunit rotates in 120-degree increments, with each step corresponding to the hydrolysis of a single ATP molecule.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Logically, this &lt;em&gt;shouldn't happen though&lt;/em&gt;, since the closest increments of 36 to 120 degrees are 108 and 144.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;To summarize: How can 3.33 protons ultimately synthesize one, and only one ATP, knowing that a literal third of a proton doesn't exist (excluding quarks) and that increments of 36 degrees can never add up to exactly 120 degrees?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;“A Proton Gradient Powers the Synthesis of ATP - Biochemistry - NCBI Bookshelf”, n.d. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK22388/&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK22388/&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-08-15T23:09:02.497" LastActivityDate="2019-01-21T17:43:28.003" Title="Given ATP synthase's structure, how can 3.33 protons ultimately synthesize one and only one ATP?" Tags="&lt;proteins&gt;&lt;cellular-respiration&gt;" AnswerCount="2" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3188" PostTypeId="1" AcceptedAnswerId="3190" CreationDate="2012-08-16T03:11:52.570" Score="6" ViewCount="2006" Body="&lt;p&gt;I'm confused as to why, when exposed to bright light, rod cells cease to function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that exposure to bright light bleaches all of the rhodopsin, but...so what?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why doesn't the bleached product (opsonin/retinal) simply get re-synthesised back into rhodopsin as it does in dim light, and therefore continue the cycle and enable impulses?&lt;/p&gt;&#xA;" OwnerUserId="1083" LastEditorUserId="69" LastEditDate="2012-08-16T16:02:47.397" LastActivityDate="2012-08-16T22:49:28.100" Title="Why do rod cells not recover after bleaching upon exposure to bright light?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3189" PostTypeId="2" ParentId="3164" CreationDate="2012-08-16T04:05:26.547" Score="2" Body="&lt;p&gt;From my Immunology notes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Decrease in hematopoietic stem cells resulting in a reduction of Affector cells. Erythroid and myeloid progeny cells don't seem to be affected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Fewer pro-B cells, resulting in fewer affector B-cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Lymphoid progenitors in the bone marrow and thymus mature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Lymphocytes in secondary lymphoid organs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the Innate system:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Neutrophils have a reduced capacity for Oxidative bursts, Batericidal activity, and Chemotaxis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Macrophages have a reduced capacity for phagocytic activity, oxidative bursts, and MHC II expression (which impairs their ability to present antigen and initiate CD4 Helper T-Cell responses).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*NK Cells have a reduced capacity for Cytotoxicity, proinflammatory cytokines and chemokines,and proliferation in response to IL-2. However, the total number of NK cells increases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sources: Both clinical (it was at a teaching hospital) and &lt;em&gt;Aging and Immune System&lt;/em&gt;, Chapter 33 of the class text: &lt;strong&gt;Cellular and Molecular Immunology&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-16T04:05:26.547" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3190" PostTypeId="2" ParentId="3188" CreationDate="2012-08-16T04:28:30.463" Score="3" Body="&lt;p&gt;In rods, the pigment Rhodopsin can be thought of as a receptor protein with a pre-bound chemical agonist. The receptor protein is called Opsin, and the pre-bound agonist is called retinal. The absorption of light causes a change in the conformation of retinal so that it activates the opsin, causing bleaching (changing the wavelengths absorbed by rhodopsin). The bleaching of rhodopsin stimulates a G-protein called transducin in the membrane, which activates phosphodiesterase, which in turn breaks down cGMP that is normally present in the cytoplasm of the rod and is necessary for the continued operation of the sodium channel sending the neural signal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the dark, the channel is open and the Rods are active. In bright light, due to the amplification from cascade effects, all of the channels will be closed, stopping the Rods from sending their normal signals until cGMP levels are able to compensate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My guess is that the bleaching ceases fairly quickly and the proteins return to their original conforms shortly, but it's the cGMP levels (remember, cGMP is destroyed, so any new cGMP replacing the old must be synthesized first) that take a long time to recover as the signal to destroy the cGMP initiates a cascade that results in strong amplifications.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-16T04:28:30.463" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3192" PostTypeId="1" AcceptedAnswerId="3194" CreationDate="2012-08-16T09:01:25.367" Score="29" ViewCount="6480" Body="&lt;p&gt;Are &quot;computational biology&quot; and &quot;bioinformatics&quot; simply different terms for the same thing or is there a real difference?&lt;/p&gt;&#xA;" OwnerUserId="1176" LastEditorUserId="43" LastEditDate="2013-05-03T16:23:52.130" LastActivityDate="2020-12-02T09:47:42.643" Title="Is &quot;computational biology&quot; different from &quot;bioinformatics&quot;?" Tags="&lt;bioinformatics&gt;&lt;terminology&gt;" AnswerCount="4" CommentCount="10" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3193" PostTypeId="2" ParentId="3192" CreationDate="2012-08-16T13:06:34.420" Score="10" Body="&lt;p&gt;I think this question is on topic here, although yes you would definitely get a lot of answers  at &lt;a href=&quot;http://biostars.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;BioStars&lt;/a&gt;. But consider this from the &lt;a href=&quot;https://biology.stackexchange.com/tags/bioinformatics/info&quot;&gt;bioinformatics tag wiki&lt;/a&gt; on this site.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bioinformatics is a broad field that interfaces a variety of life&#xA;  science disciplines (biology, genetics, biochemistry, biophysics, etc)&#xA;  with a variety of quantitative sciences (mathematics, statistics,&#xA;  computer science, engineering, etc). Bioinformatics techniques&#xA;  typically involve developing and applying software and algorithms to&#xA;  computationally intensive biological questions, such as those common&#xA;  in structural biology, genomics, sequence analysis, and systems&#xA;  biology.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Some scientists draw a distinction between the term &lt;em&gt;bioinformatics&lt;/em&gt; and&#xA;  &lt;em&gt;computational biology&lt;/em&gt;. While these areas indeed broad and diverse,&#xA;  these distinctions in terms are not consistent or well-defined.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Case in point: @GWW's answer cites two different definitions, while another has already been suggested in response to his answer (as a comment). More definitions are sure to come from additional answers, comments, and edits. None of these definitions are necessarily wrong, but in the same way none are &quot;right&quot; as there is no objective way to determine which of the definitions is &quot;better&quot; than the others. If you were to ask 5 experts in the field, you are likely to get 5 different definitions.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2012-08-22T19:39:45.310" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3194" PostTypeId="2" ParentId="3192" CreationDate="2012-08-16T14:24:23.270" Score="24" Body="&lt;p&gt;I found &lt;a href=&quot;http://rbaltman.wordpress.com/2009/02/18/bioinformatics-computational-biology-same-no/&quot;&gt;this&lt;/a&gt; post by Russ Altman quite good.  Below is his opinion about the two similar but distinct fields:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Computational biology&lt;/strong&gt;: the study of biology using computational&#xA;  techniques.  The goal is to learn new biology, knowledge about living&#xA;  sytems.  It is about science.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Bioinformatics&lt;/strong&gt;: the creation of tools (algorithms, databases) that&#xA;  solve problems.  The goal is to build useful tools that work on&#xA;  biological data.  It is about engineering.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Just as a note:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is just one persons opinion and I have heard many other definitions for both of these terms.  For example, one person I know mentioned that he believes computational biology is concerned with very theoretical research such as NP-hardness (ie. articles published in the Journal of Computational Biology). Other people think that bioinformatics is an applied field that is essentially using already published tools.  &lt;/p&gt;&#xA;" OwnerUserId="12" LastEditorUserId="12" LastEditDate="2012-08-16T17:22:21.137" LastActivityDate="2012-08-16T17:22:21.137" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3195" PostTypeId="1" AcceptedAnswerId="3198" CreationDate="2012-08-16T15:29:56.103" Score="5" ViewCount="190" Body="&lt;p&gt;Thermodynamic efficiency can be expressed as the ratio of Work done(W) to Energy invested (Q).&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Thermodynamic efficiency= W/Q&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;How can one measure work done by a biological system?&lt;/p&gt;&#xA;" OwnerUserId="1176" LastEditorUserId="1176" LastEditDate="2012-08-16T21:12:12.210" LastActivityDate="2012-08-16T21:28:10.713" Title="How to quantitatively measure work done by a biological system?" Tags="&lt;biophysics&gt;&lt;thermodynamics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3198" PostTypeId="2" ParentId="3195" CreationDate="2012-08-16T21:19:51.880" Score="3" Body="&lt;p&gt;Measuring the work done by a biological system seems pretty impossible. Imagine how many different ways one cell of your body uses energy (ATP). You can't really measure all the work done by every cell on a macro scale. Metabolic efficiency has been defined as... &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Health&quot; rel=&quot;nofollow&quot;&gt;health&lt;/a&gt;&quot;. That seems just a little ambiguous. That's why we use things like averages to determine if energy use is normal or not, such as in &lt;a href=&quot;http://en.wikipedia.org/wiki/Metabolic_age&quot; rel=&quot;nofollow&quot;&gt;metabolic age&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, work is a more tangible term in discrete physics examples, but there is so much complicated energy use in biological systems that total systemic work can't be easily defined.&lt;/p&gt;&#xA;" OwnerUserId="1250" LastEditorUserId="1250" LastEditDate="2012-08-16T21:28:10.713" LastActivityDate="2012-08-16T21:28:10.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3200" PostTypeId="1" CreationDate="2012-08-17T00:42:19.923" Score="8" ViewCount="1077" Body="&lt;p&gt;What is the lowest level attribute that all cancers share? Also, what is the highest level attributes that all cancers share?&lt;/p&gt;&#xA;" OwnerUserId="1236" LastActivityDate="2018-04-13T05:14:18.497" Title="What is the lowest common denominator of cancer?" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;cancer&gt;" AnswerCount="6" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3201" PostTypeId="1" CreationDate="2012-08-17T01:38:23.830" Score="9" ViewCount="17704" Body="&lt;p&gt;Can someone give me some references showing the average concentration of ATP in a cell?&lt;/p&gt;&#xA;" OwnerUserId="1186" LastEditorUserId="115" LastEditDate="2012-08-17T09:08:50.250" LastActivityDate="2012-09-17T20:56:09.603" Title="What is the concentration of ATP in an average cell?" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3202" PostTypeId="2" ParentId="3200" CreationDate="2012-08-17T02:06:30.557" Score="2" Body="&lt;p&gt;Could you define your terms a bit more? How do you define levels?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most common trait shared by cancerous cells is a regulatory malfunction somewhere. Whether it's a failure to regulate apoptosis, failure to recognize boundaries composed of regular cells, or failure to enter states of the cell cycle - a metabolic process somewhere goes awry, which leads to the unwanted proliferation of the cell and its daughter cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was recently discovered that some (but not all) tumors spring from a set of &quot;cancer stem cells&quot; which originally incurred the mutation and serve as the epicenter. They have the capacity to regrow tumors if they are not destroyed or harvested during treatment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the &quot;highest&quot; level trait they all share is that all cancers are unwanted. Other than that, cancers vary so widely that there's practically no universals between them that I'm aware of.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I'm not an Oncoligst or a researcher.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-17T02:06:30.557" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3203" PostTypeId="2" ParentId="3201" CreationDate="2012-08-17T02:08:27.647" Score="11" Body="&lt;h2&gt;Answer&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1172435/pdf/biochemj00546-0037.pdf&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; covers the energy charge and ATP concentrations of an array of muscle cells from many different organisms. Since many factors come into play (amount of glucose available, rate and regulation of glycolysis and cellular respiration, use of energy in metabolism, etc.) it is expected for the ATP concentration within the cell to vary significantly. The ATP concentrations reported span from approximately 1 to 10 mM.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1172435/pdf/biochemj00546-0037.pdf&quot; rel=&quot;nofollow&quot;&gt; - &lt;strong&gt;Beis, I, and E A Newsholme.&lt;/strong&gt; &lt;em&gt;“The Contents of Adenine Nucleotides, Phosphagens and Some Glycolytic Intermediates in Resting Muscles from Vertebrates and Invertebrates.”&lt;/em&gt; Biochemical Journal 152, no. 1 (October 1975): 23–32.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-09-17T20:56:09.603" LastActivityDate="2012-09-17T20:56:09.603" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3204" PostTypeId="2" ParentId="3200" CreationDate="2012-08-17T02:20:07.133" Score="7" Body="&lt;p&gt;Cancer is such a diverse group of diseases that they really only share one commonality, unregulated cell growth with the potential ability to invade or transfer to other tissue types.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many types of cancer share certain characteristics and can thus be grouped, but as a whole the only characteristic all cancers share is that they are classified as cancer. That classification is based on a number of markers and evaluations used to differentiate between benign and malignant neoplasms. Malignancy is determined by an expert pathologist who uses these markers and evaluations to determine his or her diagnosis based on experience. Some examples of indicators are circumscription, pleomorphism, presence of a capsule, nuclei number and morphology, amount of cytoplasm, number of mitoses, size, depth, particular gene mutations and so on. Even with all of these indicators, it can't be known with certainty beforehand whether or not neoplasms will metastasize.&lt;/p&gt;&#xA;" OwnerUserId="1250" LastActivityDate="2012-08-17T02:20:07.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3205" PostTypeId="1" CreationDate="2012-08-17T02:39:53.997" Score="4" ViewCount="926" Body="&lt;p&gt;In regards to cancer why do cells replicate themselves? If it's a mutation, what kind of mutation would this be classified as?&lt;/p&gt;&#xA;" OwnerUserId="1236" LastActivityDate="2015-02-19T23:19:53.033" Title="In cancer, why do cells duplicate themselves?" Tags="&lt;molecular-biology&gt;&lt;pathology&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3206" PostTypeId="2" ParentId="3205" CreationDate="2012-08-17T03:07:56.133" Score="7" Body="&lt;p&gt;&lt;a href=&quot;http://www.cancerquest.org/mutation-and-cancer.html&quot; rel=&quot;noreferrer&quot;&gt;This article&lt;/a&gt; covers some of the key issues of cancer in layman's terms.&lt;/p&gt;&#xA;&lt;p&gt;Essential, cancer is caused by &lt;em&gt;multiple&lt;/em&gt; mutations in key regulatory genes which function in maintaining the cell cycle. This provokes uncontrollably rapid cell division, with only furthers the problem with genetic mutation. Here are some quotes from the article to strengthen your understanding in cancer cell mutations.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lCXSk.png&quot; alt=&quot;The cell cycle: Wikimedia Commons&quot; /&gt;&#xA;&lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/thumb/e/e0/Major_events_in_mitosis.svg/800px-Major_events_in_mitosis.svg.png&quot; rel=&quot;noreferrer&quot;&gt;Image source&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The cells become progressively more abnormal as more genes become damaged. Often, the genes that are in control of DNA repair become damaged themselves, rendering the cells even more susceptible to ever-increasing levels of genetic mayhem.&lt;/p&gt;&#xA;&lt;p&gt;[...] Most cancers are thought to arise from a single mutant precursor cell. As that cell divides, the resulting 'daughter' cells may acquire different mutations and different behaviors over a period of time. Those cells that gain an advantage in division or resistance to cell death will tend to take over the population. In this way, the tumor cells are able to gain a wide range of capabilities that are not normally seen in the healthy version of the cell type represented.&lt;/p&gt;&#xA;&lt;p&gt;[...] Mutations in key regulatory genes (tumor suppressors and proto-oncogenes) alter the behavior of cells and can potentially lead to the unregulated growth seen in cancer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="307" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-08-17T03:07:56.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3207" PostTypeId="1" CreationDate="2012-08-17T03:24:16.713" Score="-1" ViewCount="154" Body="&lt;p&gt;In detail, what causes mutations in regulatory genes?&lt;/p&gt;&#xA;" OwnerUserId="1236" LastEditorUserId="307" LastEditDate="2012-08-17T03:47:31.623" LastActivityDate="2012-08-17T06:21:16.707" Title="What causes mutations in regulatory genes?" Tags="&lt;pathology&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2012-08-17T06:50:57.940" ContentLicense="CC BY-SA 3.0" />
  <row Id="3208" PostTypeId="2" ParentId="3207" CreationDate="2012-08-17T06:21:16.707" Score="1" Body="&lt;p&gt;nothing causes mutations in any specific genes.  mutations actually occur as the result of random processes and can mutate any given point in the genome.  mutations may be found more often in some genes or regions of the genome more often because they have a positive selective force that gives them more staying power in the gene pool over time.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its better to think of it this way: mutations happen everywhere, but they stay in the gene pool more often if they do something useful.  Genes are the active portions of the genome so mutations in genes are more likely to stay around. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-08-17T06:21:16.707" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3209" PostTypeId="2" ParentId="3201" CreationDate="2012-08-17T07:36:10.653" Score="3" Body="&lt;p&gt;Alternatively: &lt;a href=&quot;http://bionumbers.hms.harvard.edu/search.aspx?log=y&amp;amp;task=searchbytrmorg&amp;amp;trm=atp+concentration&amp;amp;org=&quot; rel=&quot;nofollow&quot;&gt;http://bionumbers.hms.harvard.edu/search.aspx?log=y&amp;amp;task=searchbytrmorg&amp;amp;trm=atp+concentration&amp;amp;org=&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As LanceLafontain answered, most of the numbers fall within the range of .5-10 mM&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-08-17T07:36:10.653" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3210" PostTypeId="1" CreationDate="2012-08-17T07:45:10.897" Score="9" ViewCount="181" Body="&lt;p&gt;This is mainly a followup question to the recent paper &lt;a href=&quot;http://www.sciencemag.org/content/early/2012/08/15/science.1226355.abstract&quot;&gt;Next-Generation Digital Information Storage in DNA&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally, while I agree about the data density of the format, I can't help point out the large issues with the inability to rewrite and recopy the data efficiently and potential issues regarding the &quot;immutability&quot; of the data. I'm curious about other takes on the publication and whether or not the stability of the DNA as well as the &quot;writing&quot; inefficiencies are better than I'm believing.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-10-16T18:35:09.140" Title="How realistic is to use DNA for long term storage?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;synthetic-biology&gt;&lt;gene-synthesis&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3211" PostTypeId="1" AcceptedAnswerId="3221" CreationDate="2012-08-17T11:20:18.100" Score="6" ViewCount="554" Body="&lt;p&gt;Flies have a short lifespan, therefore evolution should technically happen over a shorter period of time (years).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Flies die all the time from getting hit by cars on the motorway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Those flies that don't go near the motorways have a greater chance of reproducing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this was an advantage (motorway avoidance = not dying), shouldn't more and more flies be avoiding the motorway?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cars have been around since, roughly ~1950. That's 60 years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why don't flies avoid the motorway?&lt;/p&gt;&#xA;" OwnerUserId="1264" LastEditorUserId="115" LastEditDate="2012-08-20T15:55:56.683" LastActivityDate="2012-08-20T15:55:56.683" Title="Why don't flies avoid the motorway?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;entomology&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3212" PostTypeId="2" ParentId="2926" CreationDate="2012-08-17T13:07:26.877" Score="2" Body="&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/E6k1I.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Ancestor's Tale&lt;/a&gt; .&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is an utterly, utterly fascinating book.&lt;/p&gt;&#xA;" OwnerUserId="1265" LastEditorUserId="1265" LastEditDate="2012-08-17T13:15:38.863" LastActivityDate="2012-08-17T13:15:38.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3214" PostTypeId="1" CreationDate="2012-08-17T13:49:09.527" Score="2" ViewCount="74" Body="&lt;p&gt;I was wondering if somebody could recommend a book on the history of medicine, be it comprehensive or an introduction to the history of medicine. I know there are a lot of medical books that cover this subject, but given that I have a limited amount of time for reading I was wondering which book would make the best use of my time.&lt;/p&gt;&#xA;" OwnerUserId="584" LastEditorUserId="69" LastEditDate="2012-12-02T15:51:40.577" LastActivityDate="2012-12-02T15:51:40.577" Title="Recommendation of a comprehensive book on the history of medicine" Tags="&lt;history&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3215" PostTypeId="2" ParentId="3173" CreationDate="2012-08-17T14:32:13.140" Score="1" Body="&lt;p&gt;Bacterial DNA evolution is like other evolution in the sense that the mutation rates are probably random and biased somewhat by the physical and chemical structure of DNA as well as the presence and activity of DNA repair enzymes.  The mutation protocols for preparing mutant libraries from UV or chemical mutagens are a good place to start I would think - like this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC48854/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;. Most of this stuff is oriented towards protocols used in the lab, not in the wild.  Like how much UV does E coli get in your gut?  Not much.  Still it does happen and is a typical baseline factor in evolution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria also mediate their own adaptation via phage transfer as well as direct lateral gene transfer, chromosomal rearrangement.  The dynamics of this evolution is just as interesting I think as site mutation as the bacteria can use its repair mechanisms and even actively upregulate some adaptation itself, responding to environmental changes.  The fundamental differences between bacterial evolution and say evolution of animals and plants come from the fact that life is relatively cheap - a single well adapted survivor can repopulate very quickly and so that even radical genetic diversity has a benefit even if some of the population dies off every generation from being a bad adaptive experiment.  (BTW animals do this too, but in the short lived haploid gamete phase, not so much as diploid animals). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well anyway back to bacteria.  &lt;a href=&quot;http://almlab.mit.edu/ALM/Publications.html&quot; rel=&quot;nofollow&quot;&gt;Eric Alm's lab at MIT&lt;/a&gt; started with his work with operon evolution.  Genes grouped together on a single mRNA leap from one cluster to another across evolution, allowing for coordination of biochemical processes in the cell.  Lately they have been looking more intensely at the evolution of bacterial species, and how the selective environment influences bacterial adaptation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its hard to be more specific since I'm not completely clear on your focus and needs here, but this is what I know. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-08-17T14:32:13.140" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3216" PostTypeId="2" ParentId="3210" CreationDate="2012-08-17T14:56:08.123" Score="2" Body="&lt;p&gt;I can at least answer the question about the stability of the stored information. With my colleagues, I worked for several years to estimate the rate of DNA degradation at room temperatures. Our results showed that the information could  be retrieved after 100,000 years storage.&lt;/p&gt;&#xA;" OwnerUserId="1266" LastEditorUserId="43" LastEditDate="2012-09-16T18:09:59.523" LastActivityDate="2012-09-16T18:09:59.523" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3217" PostTypeId="2" ParentId="3211" CreationDate="2012-08-17T15:36:17.037" Score="6" Body="&lt;p&gt;Flies can and do evolve quickly thanks to a short generational time. However, your question seems to stem from a misunderstanding of what evolution entails.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution occurs when the genome mutates. Why it mutates isn't particularly relevant, but a gene (or genes) mutates and as a result of that mutation a characteristic of the organism changes. It doesn't have to be a big change. Maybe a single protein somewhere operates 2% less efficiently, giving practically no outward signs of evolution. Sometimes it can be big - changes in coloration, changes in sensory perception, lifespan, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order for mutations (beneficial or detrimental) to have a significant effect across an entire population, the population itself has to be fairly small or the mutation has to give a large advantage over the old version.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Flies are not avoiding motorways because a mutation that specifically codes &quot;AVOID CARS&quot; is going to be very unlikely given that it would you would first have to encode what a &quot;CAR&quot; is in order to avoid it. That probably won't happen because on the time scale that evolution usually acts over very large populations (which flies have) we won't be driving cars by the time necessary for deaths due to cars has a serious effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Flies have huge populations and breed extremely quickly, so even if a few million are killed by cars, it doesn't put a dent in their population numbers. There's no reason for the change to occur. Combined with the extreme difficulty of actually encoding a gene specific to cars, the odds are it just won't happen in any realistic time-frame.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-17T15:36:17.037" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3218" PostTypeId="2" ParentId="3200" CreationDate="2012-08-17T15:40:50.673" Score="13" Body="&lt;p&gt;Hanahan and Weinberg's &quot;Hallmarks of Cancer&quot; articles should answer your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their original, highly cited (14k+ citations), &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867400816839&quot; rel=&quot;noreferrer&quot;&gt;[Six] Hallmarks of Cancer article&lt;/a&gt; list these six common attributes of all cancers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Sustaining proliferative signaling&lt;/li&gt;&#xA;&lt;li&gt;Evading growth suppressors&lt;/li&gt;&#xA;&lt;li&gt;Activating invasion and metastasis&lt;/li&gt;&#xA;&lt;li&gt;Enabling replicative immortality&lt;/li&gt;&#xA;&lt;li&gt;Inducing angiogenesis&lt;/li&gt;&#xA;&lt;li&gt;Resisting cell death&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The new article, &lt;a href=&quot;http://www.cell.com/abstract/S0092-8674%2811%2900127-9&quot; rel=&quot;noreferrer&quot;&gt;Hallmarks of Cancer: The Next Generation&lt;/a&gt; includes additional &quot;emerging hallmarks&quot; and &quot;enabling characteristics&quot; (Figure 3) common among cancers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The capability to modify, or reprogram, cellular metabolism in order to most effectively support neoplastic proliferation; and&lt;/li&gt;&#xA;&lt;li&gt;The ability to evade immunological destruction, in particular by T and B lymphocytes, macrophages, and natural killer cells.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="192" LastEditorUserId="192" LastEditDate="2012-09-17T02:18:40.987" LastActivityDate="2012-09-17T02:18:40.987" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3220" PostTypeId="2" ParentId="3200" CreationDate="2012-08-17T17:17:43.003" Score="1" Body="&lt;p&gt;All cancers are very different, even when they are the same type of cancer. Breast Cancer, for example, falls into ER+, HER+ and Triple Negative subtypes, all which have different survival outcomes and response to therapeutics.  We didn't realise the extent of diversity until we started to analyse the tumours at a higher level of resolution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, there can be some common pathways that are affected. &lt;a href=&quot;http://en.wikipedia.org/wiki/P53&quot; rel=&quot;nofollow&quot;&gt;p53&lt;/a&gt; mutations tend be common in all cancer types, &lt;a href=&quot;http://en.wikipedia.org/wiki/Ras_subfamily&quot; rel=&quot;nofollow&quot;&gt;RAS&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Epidermal_growth_factor_receptor&quot; rel=&quot;nofollow&quot;&gt;EGFR&lt;/a&gt;  are some examples. When we analyze the details at the genomic level(SNP level,Copy Number variants, insertions-deletions), mutations can be very variable, but as you zoom out we see that they target similar genes and furthermore similar pathways. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But recall: people used to die just of fever back in the day, we know now that fever is a symptom not the disease. Technology will allow us to understand whether Cancer is just a catch-all, or whether they are actually different diseases.&lt;/p&gt;&#xA;" OwnerUserId="1049" LastActivityDate="2012-08-17T17:17:43.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3221" PostTypeId="2" ParentId="3211" CreationDate="2012-08-17T17:50:00.850" Score="5" Body="&lt;p&gt;&quot;in the long run we're all dead men&quot; - John Keynes&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First is the fact that flies have adapted their way around cars long long ago by giving up longevity for faster breeding; flies are cheap and they just don't care if they get hit by a car.  The average flying insect lays large clutches of eggs - hundreds at a go is common.  &lt;a href=&quot;http://www.uam.es/personal_pdi/ciencias/egb/download/bodysize.pdf&quot; rel=&quot;noreferrer&quot;&gt;See this reference on butterflies as an example.&lt;/a&gt;  In table 2 the potential fecundity (FEC) is I believe the number of eggs laid in a lifetime.  The smallest number is 53, the largest is 1500, the average is hundreds.  As long as one or two fly from each lifetime of breeding survives, the species holds on just fine, more and there is a population explosion.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another side of the question is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It would still be an advantage to be smart and stay off the road wouldn't it?  If they adapt so quickly why doesn't a mutant braniac fly come along that can see the cars and in short order all flies would have this trait... its just selection too, right? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The answer there is that not everything is available to adaption.   Flies could become that smart, heck maybe even smarter than us, but they have lots of pressure on them from many things they could do well, and their system is already doing many things very well enough for them to survive as they are without making such a large change that might require some short term disadvantages that prevent them from becoming entirely different animals.  The essay &quot;&lt;a href=&quot;http://www.lrb.co.uk/v29/n20/jerry-fodor/why-pigs-dont-have-wings&quot; rel=&quot;noreferrer&quot;&gt;why pigs don't have wings&lt;/a&gt;&quot; is a pretty good reading for a longer more detailed answer.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where I live its temperate and there is a good amount of water- lots of food and hospitable for all kinds of plants and animals can thrive here. On the hillsides where updraft currents blow flying insects.  The spiders 'figured this out' and the bushes and trees are often covered with cobwebs on this side of a house.  The flies don't avoid the wind just because so many of them are eaten - they would not themselves be able to mate or eat.&lt;br&gt;&#xA;Note that the spiders haven't become 'smart' - just lucky to have landed in that area.  But then there are many many spiders there that they probably don't get a lot more food than a spider living on the other side of the house who has the only web for a space of several cubic feet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Everything balances itself out in a competitive landscape because there are so many other living things ready to take advantage of a break like this.  Cars just aren't enough to budge the other things the flies have to watch out for. For more reading about how competition affects evolution read about the &lt;a href=&quot;http://en.wikipedia.org/wiki/Red_Queen%27s_Hypothesis&quot; rel=&quot;noreferrer&quot;&gt;Red Queen&lt;/a&gt; and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Tangled_bank_hypothesis&quot; rel=&quot;noreferrer&quot;&gt;Tangled bank&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-08-17T17:50:00.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3222" PostTypeId="2" ParentId="3214" CreationDate="2012-08-17T17:53:48.580" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://books.google.com/books?id=hVePdRGsX2sC&amp;amp;printsec=frontcover&amp;amp;dq=doctors%20the%20history%20of%20medicine&amp;amp;source=bl&amp;amp;ots=nDEwXGoe0i&amp;amp;sig=urP38zlQn2Ypq_IMQUc2N6zBzbg&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=4IQuUPCJJ9POyAG85oDAAQ&amp;amp;ved=0CDYQ6AEwAA#v=onepage&amp;amp;q=doctors%20the%20history%20of%20medicine&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;I enjoyed &quot;Doctors: the biography of Medicine&quot; by Sherwin Nuland&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not comprehensive, but covers the major eras of medicine.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Im sure there are many others. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-08-17T17:53:48.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3223" PostTypeId="1" CreationDate="2012-08-17T20:02:12.767" Score="7" ViewCount="676" Body="&lt;p&gt;Given the recent failure of the Bapi clinical trial, there is a lot of questions that have arised from he amyloid hypothesis. However, I can't really think of many other mechanisms that don't involved plaque formation via protein aggregation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the other dominant proposed mechanisms for the biochemistry of Alzheimers?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference: &lt;a href=&quot;http://www.nytimes.com/2012/07/24/business/alzheimers-drug-fails-its-first-clinical-trial.html&quot; rel=&quot;nofollow&quot;&gt;Alzheimer’s Drug Fails Its First Big Clinical Trial&lt;/a&gt;. Unfortunately, the results of the study have yet to be presented at a medical conference but will be in September.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-08-20T06:14:09.987" LastActivityDate="2012-08-26T17:10:08.860" Title="What alternatives are there to the amyloid hypothesis?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;neuroscience&gt;&lt;pathology&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3225" PostTypeId="1" AcceptedAnswerId="3433" CreationDate="2012-08-18T02:00:46.067" Score="2" ViewCount="113" Body="&lt;p&gt;Why would the expression of an ancestral gene and comparing the product to a modern protein give misleading conclusions about heredity?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update:&#xA;By ancestral gene I mean a gene which was used by an ancestor but than changed slightly through evolution, though it still serves the same purpose. And by the misleading conclusion I mean that using this similarity between the product of the ancestral gene and the modern protein as evidence that the organism is descended from the ancestor.&lt;/p&gt;&#xA;" OwnerUserId="584" LastEditorUserId="5144" LastEditDate="2015-01-16T12:53:08.503" LastActivityDate="2015-01-16T12:53:08.503" Title="Expression of an ancestral gene" Tags="&lt;genetics&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3226" PostTypeId="2" ParentId="2252" CreationDate="2012-08-18T02:11:18.967" Score="4" Body="&lt;p&gt;Based on what I've been able to locate on the USDA website:&#xA;&lt;a href=&quot;http://www.fsis.usda.gov/FactSheets/Refrigeration_&amp;amp;_Food_Safety/index.asp&quot; rel=&quot;nofollow&quot;&gt;Refrigeration &amp;amp; Food Safety&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be better to take the foods out of the bags and put them in the crisper if you're using the crisper solely for vegetables:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Some refrigerators have special features such as adjustable shelves, door bins, crispers, and meat/cheese drawers. These features are designed to make storage of foods more convenient and to provide an optimal storage environment for fruits, vegetables, meats, poultry, and cheese. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sealed crisper drawers provide an optimal storage environment for fruits and vegetables. Vegetables require higher humidity conditions while fruits require lower humidity conditions. Some crispers are equipped with controls to allow the consumer to customize each drawer’s humidity level. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Therefore, keeping your stuff in the bag would negate the purpose of these specialized compartments. Too bad the USDA doesn't specifically address the issue of bags...&lt;/p&gt;&#xA;" OwnerUserId="584" LastActivityDate="2012-08-18T02:11:18.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3227" PostTypeId="1" AcceptedAnswerId="3232" CreationDate="2012-08-18T02:28:21.053" Score="10" ViewCount="253" Body="&lt;p&gt;I have just read &lt;a href=&quot;http://www.guardian.co.uk/science/2012/aug/18/edward-wilson-harvard-biologist-interview&quot;&gt;this article on E. O. Wilson&lt;/a&gt; and I don't understand what the difference is between what he is arguing and &quot;standard&quot; natural selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read &quot;the extended phenotype&quot; some years ago and from what I vaguely remember that argued that everything about selection comes down to genes: they are the units of what is inherited and drive everything else (and their reach can be quite surprising).  At first glance that seems inconsistent with the article, since it mentions &quot;group selection&quot;.  But when you read the details it includes things like&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Group selection begins when a colony of creatures develops a behaviour&#xA;  that gives it a competitive advantage over other groups. Initially,&#xA;  this could be down to a &lt;strong&gt;random genetic mutation&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;which sounds like it's gene-based too (and examples seem to come from ants and the like which I thought were closely genetically-related across a colony too...).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what is the fuss about?  And how will it be resolved?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe the difference is easier to explain in terms of some difference between mathematical models?  If so, that's fine (I hope - it might make more sense than jargon in a field I am unfamiliar with ;o).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[Is this too &quot;general public&quot; for this site?  Apologies if so.]&lt;/p&gt;&#xA;" OwnerUserId="1267" LastEditorUserId="3952" LastEditDate="2013-08-02T14:09:09.753" LastActivityDate="2013-08-02T14:40:52.443" Title="What is the Edward O. Wilson fuss about?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;sociality&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3229" PostTypeId="2" ParentId="3214" CreationDate="2012-08-18T02:56:26.630" Score="2" Body="&lt;p&gt;While it's not meant to be a history of all of medicine, I thought the &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1439107955&quot; rel=&quot;nofollow&quot;&gt;The Emperor of All Maladies&lt;/a&gt; touched on a good deal of the history as the author took us through how cancers were diagnosed and treated since long ago.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Great book, that was.&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2012-08-18T02:56:26.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3230" PostTypeId="1" CreationDate="2012-08-18T03:16:54.213" Score="3" ViewCount="77" Body="&lt;p&gt;I know that the details of the process of sleep aren't entirely known, but have always wondered why I feel rested after sleep. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Biologically, what differences can be directly observed in the human body before and after a good night's sleep?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1240" LastActivityDate="2012-08-18T03:16:54.213" Title="Physiological or molecular difference before and after sleep?" Tags="&lt;physiology&gt;&lt;sleep&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3232" PostTypeId="2" ParentId="3227" CreationDate="2012-08-18T04:57:17.657" Score="5" Body="&lt;p&gt;After reading the article, the fuss is about this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In currently accepted theory Eusociality or &quot;kin selection&quot; explains altruistic behavior (the sacrifice of yourself or resources you control for the betterment of something else besides you) by relating the act to the amount of genetic information passed on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The relevant equation is &lt;a href=&quot;https://en.wikipedia.org/wiki/Hamilton%27s_rule#Hamilton.27s_rule&quot; rel=&quot;nofollow&quot;&gt;Hamilton's rule&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;   $rB &amp;gt; C$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;C is the cost to the actor (the person giving up resources). B is the number of others involved, and r is the relationship value to the actor in terms of genetic similarity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if you and two full-siblings (who each share on-average 50% of your genome) and a bus comes straight at the group, and you have the capability to push them out of the way while dying yourself, kin selection suggests you shouldn't because the genetic cost is equivalent. You eliminate yourself from the gene pool, and save the equivalent of yourself for future generations (2 x 1/2 = 1). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if you and &lt;strong&gt;three&lt;/strong&gt; siblings were in the situation, then it's evolutionarily advantageous to be altruistic. You would die (a cost of 1), but you would save the equivalent of 1.5x your genome (3 x 1/2 = 1.5) to pass on to future generations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, communal and social behaviors like those of ants basically boil down to: Everybody is so closely related that spending resources to help your kin is essentially spending resources to ensure the majority of your genome survives (which is the big point of evolution, after all).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wilson's argument, what I can glean from the small brief of the study and the article, is that you don't need the relatedness equation to explain altruistic behavior in social situations (basically the row is he's saying the currently accepted theory is wrong). All you need to start with is a genetic mutation somewhere along the line that &lt;strong&gt;causes the offspring to stick close to home.&lt;/strong&gt; Once you have a few generations that don't leave the nest, you start to develop social behavior that results in altruism because you've gone from selfish individuals to a group setting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article and Wilson don't give any more insight other than altruism apparently develops spontaneously from the formation of groups. Simply being social is the explanation for why some individuals will give resources to others to ensure the success of the others. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whether or not Wilson is correct isn't really discussed. He openly admits to needing a lot of research, some of which is being performed. &lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1306" LastEditDate="2013-08-02T14:40:52.443" LastActivityDate="2013-08-02T14:40:52.443" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3234" PostTypeId="2" ParentId="3223" CreationDate="2012-08-18T09:53:39.753" Score="4" Body="&lt;p&gt;Alzheimer is also considered a tauopathy due to abnormal aggregation of the tau protein. There has been succesful research in that direction, recently, which was a bit neglected, presumably because of vested interests in the amyloid hypothesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Tauopathy&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Tauopathy&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, &lt;strong&gt;another alternative to amyloid (and tau)&lt;/strong&gt; is the hypothesis that Alzheimer is caused or enhanced by Herpes Simplex virus (HSV-1). One landmark paper found HSV DNA in amyloid plaques and another hint is the association of a lysin-poor/arginine-rich diet with Alzheimer risk (the connection being that HSV thrives in Arg-rich tissue). Also, a cohort study found a direct association.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;N. Zilka, Z. Kazmerova, S. Jadhav, P. Neradil, A. Madari, D. Obetkova, O. Bugos, M. Novak: &lt;em&gt;Who fans the flames of Alzheimer's disease brains? Misfolded tau on the crossroad of neurodegenerative and inflammatory pathways.&lt;/em&gt; In: &lt;em&gt;Journal of neuroinflammation.&lt;/em&gt; Vol.9, 2012, p.&amp;nbsp;47 doi:10.1186/1742-2094-9-47. PMID 22397366. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22397366/&quot; rel=&quot;nofollow&quot;&gt;PMC 3334709.&lt;/a&gt; (Review).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A. M. Geppert: &lt;em&gt;[Alzheimer's disease and HSV-1 infection].&lt;/em&gt; In: &lt;em&gt;Neurologia i neurochirurgia polska.&lt;/em&gt; 40, 1, 2006 Jan-Feb, 57–61. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16463223&quot; rel=&quot;nofollow&quot;&gt;PMID 16463223.&lt;/a&gt; (Review).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;M. A. Wozniak, A. P. Mee, R. F. Itzhaki: &lt;em&gt;Herpes simplex virus type 1 DNA is located within Alzheimer's disease amyloid plaques.&lt;/em&gt; In: &lt;em&gt;The Journal of pathology.&lt;/em&gt; 217, 1, Jan 2009, 131–138. doi:10.1002/path.2449. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18973185&quot; rel=&quot;nofollow&quot;&gt;PMID 18973185.&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Letenneur, L; Pérès, K, Fleury, H, Garrigue, I, Barberger-Gateau, P, Helmer, C, Orgogozo, JM, Gauthier, S, Dartigues, JF (2008): &lt;em&gt;Seropositivity to herpes simplex virus antibodies and risk of Alzheimer's disease: a population-based cohort study.&quot;&lt;/em&gt; In: &lt;em&gt;PLoS ONE&lt;/em&gt; 3 (11): e3637. doi:10.1371/journal.pone.0003637. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18982063/&quot; rel=&quot;nofollow&quot;&gt;PMC 2572852.&lt;/a&gt; PMID 18982063.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-08-26T17:10:08.860" LastActivityDate="2012-08-26T17:10:08.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3235" PostTypeId="2" ParentId="3223" CreationDate="2012-08-18T12:03:59.293" Score="9" Body="&lt;p&gt;Alzheimer's disease is a very complex field, and I am going to restrict my answer to two particular areas: the neuritic plaques and the neurofibrillary tangles. This area is also of interest to me, hence the protracted answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two pathological hallmarks of Alzheimer's disease, first described by &lt;a href=&quot;http://en.wikipedia.org/wiki/Alois_Alzheimer&quot;&gt;Alois Alzheimer&lt;/a&gt; in about 1906, are the extracellular &lt;strong&gt;neuritic plaques&lt;/strong&gt; and the intracellular &lt;strong&gt;neurofibrillary tangles&lt;/strong&gt; which occur (exclusively) in the brain of humans with this disease.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;The Neuritic Plaques (Amyloid Precursor Protein and &amp;beta;-Amyoid)&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;[References to the information given below may be found in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9530504&quot;&gt;Price &amp;amp; Sisodia&lt;/a&gt; (1998) and in &lt;a href=&quot;http://www.jbc.org/content/266/29/19842.full.pdf&quot;&gt;Lowery &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt; (1991)]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The major component of the extracellular neuritic plaques is a small, appromimately 4 kDa protein known as the &lt;strong&gt;&amp;beta;-Amyloid (A&amp;beta;)&lt;/strong&gt;,  or A4-protein.  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The A&amp;beta;, whose tertiary structure is that of a &amp;beta;-pleated sheet, is itself derived by proteolysis (see below) from a much larger protein known as the &lt;strong&gt;Amyloid Precursor Protein (APP)&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A number of isoforms of A&amp;beta; are known which contain between 36 and 43 amino acids, the most common of which are  A&amp;beta;&lt;sub&gt;40&lt;/sub&gt; and A&amp;beta;&lt;sub&gt;42&lt;/sub&gt;. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The Amyloid Precursor protein (APP) is a very large protein (&amp;ge; 695 amino acids) of unknown function which is a normal component of brain. It is predicted to have a single transmembrane span. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A number of isoforms of this protein are also known, which contain  695, 714, 751 &amp;amp; 770 amino acids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The AA&lt;sub&gt;751&lt;/sub&gt; and AA&lt;sub&gt;770&lt;/sub&gt; isoforms contain a domain (Kunitz domain) homologous to a class of protease inhibitors, strongly suggesting the proteolysis plays a key role in normal function, and perhaps in (abberant?)  A&amp;beta; formation. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;One of the cleavages which produces the A&amp;beta;, that catalyzed by &amp;gamma;-secretase, occurs &lt;strong&gt;within the transmembrane-spanning domain&lt;/strong&gt; of APP.  How the protease has access to its substrate within the lipid bilayer is a major source of interest. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Researchers who believe that neuritic plaques and  A&amp;beta; hold the key to Alzheimer's disease are known as &lt;strong&gt;baptists&lt;/strong&gt;. Their counterparts, who believe that the neurofibrillary tangles are key, are known as &lt;strong&gt;tauists&lt;/strong&gt;, for reasons that will become obvious (see also &lt;a href=&quot;http://www.tangledneuron.info/the_tangled_neuron/2007/01/alzheimers_tang.html&quot;&gt;here&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the past number of years, baptists have been to the forefront. In my view, the tauist story is even more interesting, and must surely be important in any final understanding of Alzheimer's disease.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt; Neurofibrillary Tangles, Paired Helical Filaments and &lt;i&gt;Tau&lt;/i&gt; Protein&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Examination of the neurofibrillary tangles under the electron microscope revealed that they had a twisted ribbon-like structure which was called the &lt;strong&gt;paired helical filament (PHF)&lt;/strong&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14188276&quot;&gt;Kidd&lt;/a&gt;, 1964; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6542129&quot;&gt;Wisniewksi &lt;i&gt; et al.,&lt;/i&gt;&lt;/a&gt; 1984). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;PHFs are practically insoluble and for a long time this impared progress.  However, extraction using the detergent sarkosyl, followed by sequence analysis and immunological investigations, produced a  major surprise:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A component of the paired helical filament is the&#xA;  microtubule-associated protein &lt;em&gt;tau&lt;/em&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC280359/&quot;&gt;Goedert &lt;i&gt;et al&lt;/i&gt;&lt;/a&gt;., 1988;&#xA;  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC280541/&quot;&gt;Wischik &lt;i&gt;et al&lt;/i&gt;.&lt;/a&gt;, 1988), a most unusual and interesting &lt;em&gt;soluble&lt;/em&gt; protein&#xA;  which had already been purified to homogeneity and extensively characterized by Kirschner &amp;amp; co-workers&#xA;  (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC432646/&quot;&gt;Weingarten &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 1975; Cleveland &lt;i&gt; et al&lt;/i&gt;., &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/599557&quot;&gt;1977a&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/146092&quot;&gt;1977b&lt;/a&gt;). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A perusal of pubmed shows that at this stage interest in &lt;em&gt;tau&lt;/em&gt; increased dramatically!&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is now accepted that microtubule-acssociated protein &lt;em&gt;tau&lt;/em&gt; &lt;strong&gt;in a&#xA;  hyper-phosphorylated state&lt;/strong&gt; is the major structural component of the&#xA;  paired helical filament (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1899488&quot;&gt;Lee &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 1991; Kosik &amp;amp; Greenberg, 1994).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Some key properties of &lt;em&gt;tau&lt;/em&gt; are the following.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Tau&lt;/em&gt; was first isolated as  a series of closely related proteins (isoforms) which co-purify with porcine tubulin during successive cycles of polymerization/depolymerization (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC432646/&quot;&gt;Weingarten &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 1975).  On an SDS gel, one sees (with bovine brain &lt;em&gt;tau&lt;/em&gt;) 4 bands quite close together from (say) 58 - 64 kDa.&lt;/li&gt;&#xA;&lt;li&gt;Interaction with tubulin is the only known 'normal' function of &lt;em&gt;tau&lt;/em&gt;.  It promotes the polymerization of tubulin into microtubules under polymerization conditions, for example (Cleveland &lt;i&gt; et al&lt;/i&gt;., &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/599557&quot;&gt;1977a&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/146092&quot;&gt;1977b&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Tau&lt;/em&gt; is encoded by a single gene, located on chromosome 17, and differential mRNA splicing gives rise to the brain isoforms (six in humans and four in cow) [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1420178&quot;&gt;Andreadis &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 1989; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2484340&quot;&gt;Goedert &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 1989; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC362555/&quot;&gt;Himmler&lt;/a&gt;, 1989], and a single high molecular weight &lt;em&gt;tau&lt;/em&gt; ('big &lt;em&gt;tau&lt;/em&gt;') in peripheral tissues (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC48578/?tool=pmcentrez&quot;&gt;Goedert &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 1992).  &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Tau&lt;/em&gt; contains a series of imperfect amino-acid repeats, located in the C-terminus of the protein.  These repeats are thought to be responsible for microtubule binding (see, for example, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=Lee%201990%20tau%20protein%20an%20update&quot;&gt;Lee&lt;/a&gt;, 1990).&lt;/li&gt;&#xA;&lt;li&gt;Although &lt;em&gt;tau&lt;/em&gt; occurs in a hyper-phosphorylated state in the PHF, and may be phosphorylated in normal brain, phosphorylation &lt;em&gt;is not necessary&lt;/em&gt; for formation of paired-helical filaments (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8849730&quot;&gt;Goedert &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 1996).  &lt;/li&gt;&#xA;&lt;li&gt;The &lt;em&gt;tau&lt;/em&gt; gene may be knocked out without any visible alteration of phenotype! (experiments done in mice) (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8202139&quot;&gt;Harada &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 1994).  &lt;/li&gt;&#xA;&lt;li&gt;Mutations in the &lt;em&gt;tau&lt;/em&gt; gene are &lt;em&gt;not known to cause&lt;/em&gt; Alzheimer's disease, but &lt;em&gt;are&lt;/em&gt; associated with very rare 'taupathies', such as an inherited dementia called frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17; possibly identical with Pick's disease) [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9641683&quot;&gt;Hutton &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 1994].  &lt;/li&gt;&#xA;&lt;li&gt;The crystal structure of &lt;em&gt;tau&lt;/em&gt; has not been obtained to date.  Current thinking is that the soluble form of &lt;em&gt;tau&lt;/em&gt; is mainly a random coil (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17047358&quot;&gt;von Bergen &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 2006).  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The fact that &lt;em&gt;tau&lt;/em&gt; can be knocked  without serious consequence, together with the lack of mutations causing Alzheimer's,  has led to much criticism of the tauist story. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However it still &lt;em&gt;is&lt;/em&gt; the major structural component of the paired helical filament (neurofibrillary tangles), and must surely be a key player in the understanding of Alzheimer's disease. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr/&gt;&#xA;This is not to imply that A&amp;beta; and &lt;em&gt;tau&lt;/em&gt; are the only shows in town.  As stated above, the field of Alzheimer's disease is very complex&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An allele of Apolipoprotein E (&amp;epsilon;4 allele) is &lt;em&gt;genetically&lt;/em&gt; associated with an increased risk in late-onset Alzheimer's, for example (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8346443&quot;&gt;Corder &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 1993).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations in the presenilin genes are also associated with the disease (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7596406&quot;&gt;Sherrington &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 1995).  Presenilins form part of the &amp;gamma;-secretase protease complex involved in A&amp;beta; formation (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=Takeo%2C%20K%2C%20Watanabe%2C%20N%2C%20Tomita%2C%20T%2C%20Iwatsubo%2C%20T.&quot;&gt;Takeo &lt;em&gt;et al&lt;/em&gt;.&lt;/a&gt;, 2012). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not know enough about these fields to comment any further (although this does not usually stop me). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It should be emphasized, however, that most cases of Alzheimer's disease are sporadic, and only a small subset has a genetic component. It is a disease of the brain, and of aging. There is no known cure, no known cause and no reliable (biochemical) pre-mortem test (although a clinic diagnosis may of course be made). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr/&gt;&#xA;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Andreadis, A., Brown, W. M. &amp;amp; Kosik, K. S. 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(1988)  Structural characterization of the core of the paired helical filament of alzheimer disease. &lt;em&gt;Proc. Natl. Acad. Sci. USA&lt;/em&gt;,   &lt;strong&gt;85&lt;/strong&gt;, 4884-32768. [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC280541/&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wisniewski, H. M., Merz, P. A. &amp;amp; Iqbal, K. (1984) Ultrastructure of paired helical filaments of Alzheimer's neurofibrillary tangle. &lt;em&gt;J. Neuropathol. Exper. Neurol&lt;/em&gt;.,  &lt;strong&gt;43&lt;/strong&gt;,  643-656.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="1136" LastEditDate="2012-08-19T10:01:39.280" LastActivityDate="2012-08-19T10:01:39.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3237" PostTypeId="2" ParentId="1724" CreationDate="2012-08-18T19:27:48.503" Score="6" Body="&lt;p&gt;Evolution - Douglas J. Futuyma, Chapter 19, p. 461&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://chaos.physics.swarthmore.edu/courses/Physics120_2008/docs/lynchm.pdf&quot; rel=&quot;nofollow&quot;&gt;Michael Lynch and John Conery (2003)&lt;/a&gt; have pointed out that a variety&#xA;  of genomic features that appear to have little fitness advantage for&#xA;  organisms-introns, transposable elements, large tracts of noncoding&#xA;  DNA-may be more prevalent in species with small effective population&#xA;  sizes. They have suggested that viruses and bacteria have extremely&#xA;  large population sizes that facilitate the sweep of advantageous&#xA;  mutations that enable genomic streamlining. By contrast, eukaryotes&#xA;  have smaller population sizes that facilitate the fixation of&#xA;  nonadaptive traits. This is the best hypothesis advanced&#xA;  so far that would explain the diversity of genome sizes and&#xA;  structures.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1265" LastEditorUserId="1265" LastEditDate="2012-11-20T08:50:20.687" LastActivityDate="2012-11-20T08:50:20.687" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3238" PostTypeId="1" CreationDate="2012-08-18T21:09:22.083" Score="8" ViewCount="106" Body="&lt;p&gt;Wikipedia definition of &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hybrid_%28biology%29&quot; rel=&quot;noreferrer&quot;&gt;hybrid&lt;/a&gt;&quot; offers many competing definitions. But most seem to be centered on sexual-reproduction gene transfer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there an official (in a textbook or widely accepted peer reviewed work) definition of a &quot;hybrid&quot;/&quot;hybridization&quot; that would clearly include ANY genetic mixing, &lt;strong&gt;most specifically obtaining genes via horizontal gene transfer&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, is it specifically because &quot;hybrid&quot; requires sexual reproduction, or merely because it requires a certain minimal amount of inherited genetic material from both sides, and horisontal genetic transfer in practice involves significantly less genetic material being inherited?&lt;/p&gt;&#xA;" OwnerUserId="185" LastEditorUserId="1270" LastEditDate="2012-08-19T10:26:04.080" LastActivityDate="2012-08-19T10:26:04.080" Title="Can an organism obtaining a part of its genome via horizontal gene transfer be called a &quot;hybrid&quot;?" Tags="&lt;genetics&gt;&lt;horizontal-gene-transfer&gt;&lt;definitions&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3239" PostTypeId="2" ParentId="3177" CreationDate="2012-08-18T21:53:27.707" Score="5" Body="&lt;p&gt;Actually, electromagnetic communication is used by certain fish, the mormyrids and the gymnotids.  Pulse modulated in the former and amplitude modulated in the latter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the frequencies used are not much greater than 1Khz, which is not what we ordinarily consider to be in the radio frequency spectrum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is, too,  another biological species in which the use of the full RF spectrum has evolved. Its activities even extend to the use of the UV and X-ray frequencies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That species is our own. I am not being flippant here. We must not fall into the trap of considering ourselves as apart from nature.  Contrary to our usual intuitions, technologies have evolved autonomously within the collective imagination of our species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The broader evolutionary model which supports this contention is outlined, very informally, in &quot;The Goldilocks Effect: What Has Serendipity Ever Done For Us?&quot; , a free download in e-book formats from the &quot;Unusual Perspectives&quot; website.   &lt;/p&gt;&#xA;" OwnerUserId="1271" LastActivityDate="2012-08-18T21:53:27.707" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3240" PostTypeId="2" ParentId="3238" CreationDate="2012-08-18T23:55:14.267" Score="3" Body="&lt;p&gt;As you point out, there isn't a singularly accepted biological defnition of 'hybrid.' The most basic would be a single organism that exhibits traits of two individual organisms, but that will find perfectly acceptable disagreement depending on who you talk to. You, for instance, are human - but a hybrid of your parents' genomes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I would personally say that horizontal gene transfer is equivalent to gene inheritance, and that as long as the organism exhibited traits of both 'parent' individuals - then yes, it is a hybrid. Some might include that even if it didn't exhibit traits and merely contained the genes in any inherited genomic data that the hybrid label would be appropriate.&lt;/p&gt;&#xA;" OwnerUserId="1274" LastActivityDate="2012-08-18T23:55:14.267" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3241" PostTypeId="1" AcceptedAnswerId="3913" CreationDate="2012-08-19T00:58:05.560" Score="8" ViewCount="2217" Body="&lt;p&gt;Is is well known fact that marine mammals and some birds can &lt;a href=&quot;http://en.wikipedia.org/wiki/Unihemispheric_slow-wave_sleep&quot; rel=&quot;nofollow noreferrer&quot;&gt;sleep with one brain hemisphere at a time&lt;/a&gt;, since it's essential for their survival.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, at least in my opinion, such mechanism would give significant advantage to many other species (e.g. to antelops) because it helps avoiding predators.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While answers to &lt;a href=&quot;https://biology.stackexchange.com/q/324/836&quot;&gt;this question&lt;/a&gt; explain why sleep is necessary, animals with unihemispheric sleep mode does not seem to suffer from any of mentioned drawbacks of non-sleeping (except maybe increased energy consumption).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any particular disadvantages of unihemispheric sleep versus &quot;normal&quot; sleep?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I've stumbled upon the following paper: &lt;a href=&quot;http://dx.doi.org/10.1016/S0149-7634(00)00039-7&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Rattenborg N., Amlaner C., Lima S.&lt;/strong&gt;. 2000. Behavioral, neurophysiological and evolutionary perspectives on unihemispheric sleep. Neuroscience &amp;amp; Biobehavioral Reviews 24: 817–842&lt;/a&gt;, which discusses several possible reasons for absense of unihemispheric sleep in most mammals, but does not present any evidence to support their hypothesis. The main reason (from authors' point of view, at least) is the need for very loose coupling of both hemispheres to allow them sleep independently, which might negatively affect overall brain effectiveness.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Along these lines, sleep may play a role in integrating the&#xA;  functions of different brain regions. Thus, BSWS&lt;sup&gt;1&lt;/sup&gt; in terrestrial&#xA;  mammals may be superior to the BSWS in animals with USWS&lt;sup&gt;2&lt;/sup&gt; &#xA;  because it allows integration within and between hemispheres, rather than&#xA;  just within a particular hemisphere.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Specifically, the reorganization of the central nervous system&#xA;  required for USWS may interfere with other adaptive brain functions,&#xA;  such as integrating the functions of both hemispheres.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;sup&gt;1&lt;/sup&gt; Bihemispheric Slow Wave Sleep; &lt;sup&gt;2&lt;/sup&gt; Unihemispheric Slow Wave Sleep&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They also argue that the unihemispheric sleep might have been present in first mammals, but wasn't giving any advantages on first stages of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this paper was published more that 10 years ago, so there might have been some advances in the field since then.&lt;/p&gt;&#xA;" OwnerUserId="836" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2012-10-13T23:21:26.747" Title="Disadvantages of unihemispheric sleep" Tags="&lt;evolution&gt;&lt;sleep&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3245" PostTypeId="1" AcceptedAnswerId="3249" CreationDate="2012-08-19T15:29:40.167" Score="14" ViewCount="4167" Body="&lt;p&gt;I know that mitochondria of eukaryotes have their own DNA, more similar to that of bacteria than to the rest of the cell's DNA. I also know that a cell can have plenty of mitochondria, and I understand each of them has it's own DNA. Is it the same DNA? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that when a human is conceived, the mitochondria of the sperm are destroyed and don't contribute to the new cell. If there were no mutations and the process started with a cell with homogenous mDNA, that would mean that the mDNA not only within one cell but among all of the descendants was the same. But there are mutations because we have different mDNAs. Then shouldn't the mutations cause variety within single cells? It's hard for me to believe that there can even be a single human cell in the world that has homogenous mDNA because, if I understand correctly, an ovum retains many mitochondria during conception, not just one, so at least some of the variety within the ovum should be passed over to the conceived human. But perhaps it's extremely difficult for a cell with variously DNAed mitochondria to survive? Can it be estimated what the percentage of human cells with homogenous or nearly homogenous mDNA is across the world?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm asking this because I've heard that the mDNA can be considered another chromosome. I wonder if then every single piece of mitochondrial DNA should be considered another chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please note that all I know about biology is what I learned in high school several years ago and the bits I know from Wikipedia and other internet sources. I would like to ask for possibly accessible answers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Reading up on this, I came across the term &lt;a href=&quot;http://en.wikipedia.org/wiki/Heteroplasmy&quot;&gt;heteroplasmy&lt;/a&gt;. So it does happen that mitochondria of an organism can store different genetic information. But the article seems to suggest that it is an anomaly rather than the normal course of things. That seems strange to me. I understand of course that &lt;em&gt;some&lt;/em&gt; mutations have to be harmful, but shouldn't some mutations and some kinds of in-cell variety turn out to be neutral or even advantageous?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've also just read that a mitochondrion stores more than one copy of its DNA. That seems to allow for variation even within a single mitochondrion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT 2: I think it's possible that my question is unclear. There seem to be four levels on which mDNA variety can be considered: a species, an organism, a cell, a mitochondrion. I ask the answerers to focus on the third one. I will be happy to learn about the other levels too and I will consider such information on-topic, but my main question is about what happens in a cell. &lt;/p&gt;&#xA;" OwnerUserId="1278" LastEditorUserId="1278" LastEditDate="2012-08-19T19:27:44.977" LastActivityDate="2012-08-19T19:27:44.977" Title="Does every mitochondrion in a cell contain the same DNA?" Tags="&lt;dna&gt;&lt;cell-biology&gt;&lt;mitochondria&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3246" PostTypeId="1" AcceptedAnswerId="3248" CreationDate="2012-08-19T16:48:48.447" Score="7" ViewCount="3422" Body="&lt;p&gt;I know that there are two most important directions of genetic information transfer in living organisms: DNA-&gt;DNA and DNA-&gt;RNA. The first is replication, and the second is transcription. I wonder if there is a reason for this choice of directions. According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology#General_transfers_of_biological_sequential_information&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;, all other directions are possible. Why do we use DNA for example? RNA is capable of self-replication since it happens in viruses. And why do we use RNA, not DNA, as messenger molecules? Is it just an accident or is it possible to explain why this is the right way of doing it?&lt;/p&gt;&#xA;" OwnerUserId="1278" LastEditorUserId="43" LastEditDate="2012-08-24T14:48:05.517" LastActivityDate="2012-09-17T13:37:07.753" Title="Why do DNA and RNA have the functions they have?" Tags="&lt;dna&gt;&lt;molecular-genetics&gt;&lt;rna&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3247" PostTypeId="1" AcceptedAnswerId="3251" CreationDate="2012-08-19T17:03:43.240" Score="4" ViewCount="916" Body="&lt;p&gt;In the past, when there was no pasteurization, could making yogurt from milk lower the chance of getting infected by bovine tuberculosis (or other diseases from infected milk)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, would yogurt cultures reduce the amount of &quot;bad&quot; bacteria or create a less hospitable environment for them?&lt;/p&gt;&#xA;" OwnerUserId="1279" LastEditorUserId="69" LastEditDate="2012-08-19T17:21:53.270" LastActivityDate="2014-07-13T16:05:32.263" Title="Does making yogurt from non-pasteurized milk work against possible disease bacteria?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;bacteriology&gt;&lt;pathology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3248" PostTypeId="2" ParentId="3246" CreationDate="2012-08-19T18:56:15.933" Score="5" Body="&lt;p&gt;DNA is &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA#Comparison_with_DNA&quot;&gt;more chemically stable&lt;/a&gt; than RNA, which makes it ideal for long-term storage. RNA viruses like HIV have a short lifespan and must replicate to survive, which is why they can get by with a less chemically stable genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RNA is a useful format to transcribe since it has multiple forms and functions (e.g. rRNA, mRNA, tRNA, siRNA, snRNA, miRNA, &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_RNAs&quot;&gt;etc.&lt;/a&gt;). RNA can sometimes function like a protein in which it carries out cellular actions without needing to be translated. It has been &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_world_hypothesis&quot;&gt;hypothesized&lt;/a&gt; that RNA were the first molecules as precursors to life since they can function for both storage and action. The theory is that RNA was the first molecule but was then able to be translated into proteins (which were more variable/useful) and able to be stored as DNA (which was more stable as a storage medium).&lt;/p&gt;&#xA;" OwnerUserId="1250" LastEditorUserId="1250" LastEditDate="2012-08-19T19:26:53.497" LastActivityDate="2012-08-19T19:26:53.497" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="3249" PostTypeId="2" ParentId="3245" CreationDate="2012-08-19T19:23:39.977" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://www.genetics.edu.au/Information/Genetics-Fact-Sheets/Mitochondial-Inheritance-Complex-Patterns-of-Inheritance-2-FS12&quot; rel=&quot;noreferrer&quot;&gt;This link&lt;/a&gt; seems to have good information that answers most of your questions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my mind, there are two types of mitochondria: ones that work and ones that don't. Mitochondria do have DNA but that mDNA is there to encode proteins for their specific functions (e.g. to create ATP). So, although the mDNA may not be uniform for every mitochondrion in your body, it is most likely functional unless you have a mitochondrial disease. If you do have a mitochondrial disease then it suggests that some of your mitochondria are functional and some are not (otherwise you would be inviable).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As discussed in the comments, all DNA undergoes mutations so that even identical mDNA genomes may vary after undergoing some mutations. It's possible that only one genetic line of mitochondria was passed to you from your mom. In this case all the mitochondria in your body would be identical (except for minor mutations). It's also possible that your mom inherited and passed on to you more than one genetic line (as is the case in viable mitochondrial disease).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mitochondrial repair mechanisms do exist but &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16050976&quot; rel=&quot;noreferrer&quot;&gt;they differ&lt;/a&gt; in various ways from nuclear DNA repair and may be more prone to damage.&lt;/p&gt;&#xA;" OwnerUserId="1250" LastActivityDate="2012-08-19T19:23:39.977" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3250" PostTypeId="2" ParentId="3147" CreationDate="2012-08-19T20:11:23.277" Score="7" Body="&lt;p&gt;In what follows I am going to attempt to answer your question using a specific example of  (competitive) reversible activation, and I hope to show what a misleading parameter EC&lt;sub&gt;50&lt;/sub&gt; can be.  (Rate law derivation is an area of interest, hence the long-winded answer). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It &lt;em&gt;can&lt;/em&gt; of course give information, but IMO it needs to be used with extreme care.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am restricting my comments to the case where A is a &lt;em&gt;reversible&lt;/em&gt; activator and where  [A] &gt;&gt; e&lt;sub&gt;o&lt;/sub&gt; and [S] &gt;&gt; e&lt;sub&gt;o&lt;/sub&gt;.  (All constants are defined below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, I am not treating irreversible activation, and I am not treating the case where A is considered a tight-binding activator (so that [A] &amp;asymp; e&lt;sub&gt;o&lt;/sub&gt;). In other words, I am making the steady-state approximation (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1259181/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Briggs &amp;amp; Haldane&lt;/a&gt;, 1925)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider the following simple mechanism for activation in a single-substrate enzyme:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A Mechanism for Competitive, Reversible Activation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/99fZ1.gif&quot; alt=&quot;Competitive Activation DIAGRAM&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The substrate (S) cannot bind to the free enzyme (E) unless the activator (A) is present.  That is, only the activator can bind (reversibly) to E, and the substrate binds (reversibly) to the EA complex.  Reaction occurs within the EAS complex (giving EAP). Dissociation of product (P) from EAP gives EA.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The (steady-state) &lt;strong&gt;initial-rate law&lt;/strong&gt; for the above mechanism is the following: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/O5Tu3.gif&quot; alt=&quot;Basic Rate law in three parts eqn1&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As stated, all constants are defined below and follow the usual definitions in enzyme kinetics.  I'll mention just one here: &lt;em&gt;K&lt;sub&gt;A&lt;/sub&gt;&lt;/em&gt; is the &lt;em&gt;dissociation constant&lt;/em&gt; for the activator, and has units of concentration. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I derived these equations using a computerized version of the King &amp;amp; Altman method (&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/j150544a010&quot; rel=&quot;nofollow noreferrer&quot;&gt;King &amp;amp; Altman&lt;/a&gt;, 1956), but it is &lt;em&gt;not&lt;/em&gt; difficult to do. It was pure laziness that prevented a 'first principles' derivation. Rate law derivation is treated in depth in most books on enzyme kinetics and good accounts may be found in Segel (1975) and Cornish-Bowden (2004).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One can now make the following points&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;There is no activity without A (as one would expect).&lt;/li&gt;&#xA;&lt;li&gt;When [A]  &gt;&gt;  &lt;em&gt;K&lt;/em&gt;&lt;sub&gt;A&lt;/sub&gt;, the rate law becomes identical with the Michaelis-Menten equation (as one would expect).&lt;/li&gt;&#xA;&lt;li&gt;The equation is similar to the case of &lt;strong&gt;competitive inhibition&lt;/strong&gt;, but (note subtle change) with (1&amp;nbsp;+&amp;nbsp;&lt;em&gt;K&lt;sub&gt;A&lt;/sub&gt;&lt;/em&gt;&amp;nbsp;/&amp;nbsp;[A]) substituted for (1&amp;nbsp;+&amp;nbsp;[I]&amp;nbsp;/&amp;nbsp;&lt;em&gt;K&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;li&gt;One can consider this mechanism an example of &lt;strong&gt;competitive activation&lt;/strong&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Defining&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;&amp;nu;&lt;sub&gt;i&lt;/sub&gt;&lt;sup&gt;exc&lt;/sup&gt;&lt;/em&gt; &amp;nbsp;&amp;nbsp;&amp;nbsp; = &amp;nbsp; &amp;nbsp; the initial velocity when A is in vast &lt;i&gt;exc&lt;/i&gt;ess [&lt;em&gt;ie&lt;/em&gt; setting [A] equal to &amp;infin; in eqn (1) ].&lt;/li&gt;&#xA;&lt;li&gt;EC&lt;sub&gt;50&lt;/sub&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp; = &amp;nbsp; &amp;nbsp; the concentration of A that gives &lt;em&gt;&amp;nu;&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt; equal to &lt;em&gt;&amp;nu;&lt;sub&gt;i&lt;/sub&gt;&lt;sup&gt;exc&lt;/sup&gt;&lt;/em&gt; / 2 (half-maximal activation)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;allows the following two equations to be derived:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4zKwJ.gif&quot; alt=&quot;Ratio of velocities eqn3&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Setting the left-hand side of the above equal to 2, and solving for [A], gives &lt;strong&gt;the following all-important equation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AE22T.gif&quot; alt=&quot;EC50 definition eqn3&quot;&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;One can now draw the following conclusions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;When [S] = K&lt;sup&gt;S&lt;/sup&gt;&lt;sub&gt;m&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rTrFv.gif&quot; alt=&quot;Conclusion1 S equals to Km&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In words, when the substrate is present at a concentration equal to the Michaelis constant the value of EC&lt;sub&gt;50&lt;/sub&gt; is &lt;em&gt;half&lt;/em&gt; the value of &lt;em&gt;K&lt;sub&gt;A&lt;/sub&gt;&lt;/em&gt;!.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When [S] &gt;&gt; K&lt;sup&gt;S&lt;/sup&gt;&lt;sub&gt;m&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3j6DB.gif&quot; alt=&quot;Conclusion 2 S greater than Km&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When [S] = 10 x K&lt;sup&gt;S&lt;/sup&gt;&lt;sub&gt;m&lt;/sub&gt;, for example, EC&lt;sub&gt;50&lt;/sub&gt; is one-tenth the value of &lt;em&gt;K&lt;sub&gt;A&lt;/sub&gt;&lt;/em&gt;, and when  [S] = 100 x K&lt;sup&gt;S&lt;/sup&gt;&lt;sub&gt;m&lt;/sub&gt; the figure is one-hundreth. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When [S] &amp;lt;&amp;lt; K&lt;sup&gt;S&lt;/sup&gt;&lt;sub&gt;m&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LlKuo.gif&quot; alt=&quot;Conclusion 3 S less than Km&quot;&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Thus, &lt;em&gt;for a competitive activator&lt;/em&gt;, it is only when [S] &amp;lt;&amp;lt; K&lt;sup&gt;S&lt;/sup&gt;&lt;sub&gt;m&lt;/sub&gt;&#xA;that EC&lt;sub&gt;50&lt;/sub&gt; gives a reasonable estimate of &lt;em&gt;K&lt;sub&gt;A&lt;/sub&gt;&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The substrate concentration in a 'normal' enzyme assay will probably be equal to or greater than the Michaelis constant (in order to 'see' activity), and thus EC&lt;sub&gt;50&lt;/sub&gt; will be an underestimate of &lt;em&gt;K&lt;sub&gt;A&lt;/sub&gt;&lt;/em&gt;.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the substrate is present at a 'saturating' concentration (say 10 x K&lt;sup&gt;S&lt;/sup&gt;&lt;sub&gt;m&lt;/sub&gt;) then one is in real trouble.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this is &lt;em&gt;not&lt;/em&gt; the only consideration.  As well as being substrate-concentration dependent, the manner in which EC&lt;sub&gt;50&lt;/sub&gt; depends on [substrate] &lt;em&gt;depends on mechanism&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As briefly discussed below, the competitive activation case is analogous to that of competitive inhibition. However for &lt;em&gt;uncompetitive inhibition&lt;/em&gt; the &lt;em&gt;K&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt; (inhibition constant) is only equal to IC&lt;sub&gt;50&lt;/sub&gt; (the concentration of inhibitor giving half-maximal inhibition) &lt;em&gt;at high substrate concentration&lt;/em&gt;! (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1152414/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Naqui&lt;/a&gt;, 1982). By analogy, one can conclude that the same is true of uncompetitive activation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is very difficult to see how EC&lt;sub&gt;50&lt;/sub&gt; can be of any practical use, except perhaps when the mechanism of activation is known.  At the very least, conclusions drawn from EC&lt;sub&gt;50&lt;/sub&gt; data should otherwise not be considered definitive.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, I have discussed the only the case of a single-substrate reaction.  Two-substrate reactions have the potential for even greater complexity. &lt;/p&gt;&#xA;&#xA;&lt;hr/&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Illustrative Example (Competitive Activation)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's take an example, and check some conclusions: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;k&lt;/em&gt;&lt;sup&gt;f&lt;/sup&gt;&lt;sub&gt;cat&lt;/sub&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;=&amp;nbsp;&amp;nbsp;&amp;nbsp;1000 s&lt;sup&gt;-1&lt;sup&gt;&lt;/li&gt;&#xA;&lt;li&gt;e&lt;sub&gt;o&lt;/sub&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;=&amp;nbsp;&amp;nbsp;&amp;nbsp;1&lt;/li&gt;&#xA;&lt;li&gt;K&lt;sup&gt;S&lt;/sup&gt;&lt;sub&gt;m&lt;/sub&gt; &amp;nbsp;&amp;nbsp;&amp;nbsp;=&amp;nbsp;&amp;nbsp;&amp;nbsp;10 &lt;i&gt;&amp;micro;&lt;/i&gt;M&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;K&lt;/em&gt;&lt;sub&gt;A&lt;/sub&gt; &amp;nbsp; &amp;nbsp; &amp;nbsp;=&amp;nbsp;&amp;nbsp;&amp;nbsp;50 &lt;i&gt;&amp;micro;&lt;/i&gt;M&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It may be calculated that:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;When [S] equals  10 &lt;i&gt;&amp;micro;&lt;/i&gt;M (ie when [S] is equal to K&lt;sup&gt;S&lt;/sup&gt;&lt;sub&gt;m&lt;/sub&gt;) and when [A] is 'saturating' (for the sake of argument set equal to &amp;infin;) the velocity is 500 &lt;i&gt;&amp;micro;&lt;/i&gt;M s&lt;sup&gt;-1&lt;/sup&gt; [from eqn (1) ].  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From eqn (2), the concentration of A required to achieve half this value (half maximal activation) is 25 &lt;i&gt;&amp;micro;&lt;/i&gt;M (EC&lt;sub&gt;50&lt;/sub&gt; equals 25 &lt;i&gt;&amp;micro;&lt;/i&gt;M)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This value can be directly calculated from eqn (3)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When [S] equals  100 &lt;i&gt;&amp;micro;&lt;/i&gt;M (ie [S] equals 10 x K&lt;sup&gt;S&lt;/sup&gt;&lt;sub&gt;m&lt;/sub&gt;) and when [A] is 'saturating' the velocity is now 909&amp;nbsp;&lt;i&gt;&amp;micro;&lt;/i&gt;M s&lt;sup&gt;-1&lt;/sup&gt; [from eqn (1) ].  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From eqn (2), the concentration of A required to achieve half this value  is now only ~4.5 &lt;i&gt;&amp;micro;&lt;/i&gt;M &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This value can be directly calculated from eqn (3) [EC&lt;sub&gt;50&lt;/sub&gt; equals (50 / 11) &lt;i&gt;&amp;micro;&lt;/i&gt;M]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When [S] equals  1 &lt;i&gt;&amp;micro;&lt;/i&gt;M (ie [S] equal to one-tenth the Michaelis constant) and when [A] is 'saturating' the velocity is now only ~91 &lt;i&gt;&amp;micro;&lt;/i&gt;M s&lt;sup&gt;-1&lt;/sup&gt; [from eqn (1) ].  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From eqn (2), the concentration of A required to achieve half this value is ~45.5 &lt;i&gt;&amp;micro;&lt;/i&gt;M (now almost equal to &lt;em&gt;K&lt;sub&gt;A&lt;/sub&gt;&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This value can be directly calculated from eqn (3) [EC&lt;sub&gt;50&lt;/sub&gt; equals (500 / 11) &lt;i&gt;&amp;micro;&lt;/i&gt;M]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr/&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reversible Inhibition &amp;amp; IC&lt;sub&gt;50&lt;/sub&gt;.  A Brief Comment&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is nothing much new in any of the above. In the field of enzyme inhibition, the inadequecies of IC&lt;sub&gt;50&lt;/sub&gt; (the concentration of inhibitor giving 50% inhibition) and the relationship to the Inhibition constant are well-known  [see, for example,  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=Relationships%20between%20inhibition%20Constants%20and%20Fractional%20Inhibition%20in%20Enzyme-Catalyzed%20Reactions&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chou&lt;/a&gt; (1974), Segel (1975), &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1152414/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Naqui&lt;/a&gt; (1982) &amp;amp; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=Tsou%20the%20screening%20of%20enzyme%20targeted%20drugs&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tsou&lt;/a&gt; (1987)], but (it seems to me) often ignored. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1152414/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Naqui&lt;/a&gt; gives a very succinct analysis of the situation and the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1152414/&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf&lt;/a&gt; is freely available to all. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reversible inhibitors may be divided into four classes, depending on the pattern of inhibition: &lt;strong&gt;competitive, uncompetitive, non-competitive&lt;/strong&gt; and &lt;strong&gt;'mixed'&lt;/strong&gt; (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1152414/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Naqui&lt;/a&gt;, 1982, and references therein). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In all cases except non-competitive inhibition, &lt;em&gt;K&lt;/em&gt;&lt;sub&gt;i&lt;/sub&gt; &amp;ne; IC&lt;sub&gt;50&lt;/sub&gt;, and IC&lt;sub&gt;50&lt;/sub&gt; is substrate- dependent. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Non-competitive inhibition is the 'fluky' one where it just so happens that the catalytic constant and the specificity constant (&lt;em&gt;k&lt;/em&gt;&lt;sup&gt;f&lt;/sup&gt;&lt;sub&gt;cat&lt;/sub&gt; / K&lt;sup&gt;S&lt;/sup&gt;&lt;sub&gt;m&lt;/sub&gt;) are changed to the same extent or, to put it another way, the slope and intercept of a Lineweaver-Burk plot (it just so happens) are changed to the same extent)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an uncompetitive inhibitor (as stated) the IC&lt;sub&gt;50&lt;/sub&gt; only equals &lt;em&gt;K&lt;/em&gt;&lt;sub&gt;i&lt;/sub&gt; &lt;em&gt;at high substrate concentration&lt;/em&gt; (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1152414/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Naqui&lt;/a&gt;, 1982).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like the case of competitive activation, IC&lt;sub&gt;50&lt;/sub&gt;  equals &lt;em&gt;K&lt;/em&gt;&lt;sub&gt;i&lt;/sub&gt; for a competitive inhibitor only at low susbstrate concentrations (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1152414/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Naqui&lt;/a&gt;, 1982).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;'Mixed' inhibition is even more complex, and the inhibition constant may be greater than or less than IC&lt;sub&gt;50&lt;/sub&gt; depending on experimental conditons (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1152414/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Naqui&lt;/a&gt;, 1982).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Great question, BTW. &lt;/p&gt;&#xA;&#xA;&lt;hr/&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Addendum&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I have derived the full form of the rate law (as opposed to the initial-rate law), it is probably worth posting it. The initial-rate law is obtained from this equation by setting [P] equal to zero. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yVW5p.gif&quot; alt=&quot;Full Rate Law for Competitive Activation Kinetic Constant form&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Kinetic Constants defined in terms of Rate Contants&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rate constants are numbered (as subscripts) &lt;em&gt;from species, to species&lt;/em&gt;, with numbering as in diagram.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus the rate constant k&lt;sub&gt;1,2&lt;/sub&gt; is that from E (species 1) to EA (species 2).  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Catalytic Constants&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ntDTK.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uXgJV.gif&quot; alt=&quot;kcatreverse rate constant form&quot;&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Michaelis Constants&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WyHqP.gif&quot; alt=&quot;KmS Rate Constant Form&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mpdsh.gif&quot; alt=&quot;KmP Rate Constant Form&quot;&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Specificity Constants&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8Spnf.gif&quot; alt=&quot;Specificity Constant for S rate constant form&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UWDXD.gif&quot; alt=&quot;Specificity Constant for P rate constant form&quot;&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Activation (Dissociation Constant) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5r4KB.gif&quot; alt=&quot;Ka Rate Constant Form&quot;&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr/&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Kinetic Constant Definition&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&amp;nu;     velocity &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;&amp;nu;&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;the initial velocity&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;K&lt;sup&gt;S&lt;/sup&gt;&lt;sub&gt;m&lt;/sub&gt; &amp;nbsp;&amp;nbsp;&amp;nbsp;the Michaelis Constant for S&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;K&lt;sup&gt;P&lt;/sup&gt;&lt;sub&gt;m&lt;/sub&gt; &amp;nbsp;&amp;nbsp;&amp;nbsp;the Michaelis Constant for P&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;k&lt;/em&gt;&lt;sup&gt;f&lt;/sup&gt;&lt;sub&gt;cat&lt;/sub&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;the catalytic constant (in the &lt;i&gt;f&lt;/i&gt;orward direction)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;k&lt;/em&gt;&lt;sup&gt;r&lt;/sup&gt;&lt;sub&gt;cat&lt;/sub&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;the catalytic constant (in the &lt;i&gt;r&lt;/i&gt;everse direction)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;V&lt;/em&gt;&lt;sub&gt;max&lt;/sub&gt; &amp;nbsp;&amp;nbsp;&amp;nbsp;the maximum velocity, equal to &lt;em&gt;k&lt;/em&gt;&lt;sup&gt;f&lt;/sup&gt;&lt;sub&gt;cat&lt;/sub&gt; &lt;em&gt;e&lt;/em&gt;&lt;sub&gt;o&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;e&lt;/em&gt;&lt;sub&gt;o&lt;/sub&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;the total enzyme concentration&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NUAUp.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;K&lt;/em&gt;&lt;sub&gt;A&lt;/sub&gt; &amp;nbsp; &amp;nbsp; &amp;nbsp;the dissociation constant for (activator), equal to &lt;em&gt;k&lt;/em&gt;&lt;sub&gt;2,1&lt;/sub&gt; / k&lt;sub&gt;1,2&lt;/sub&gt;, with units of concentration (Molarity, say) [rate constants are numbered &lt;em&gt;from species&lt;/em&gt;, &lt;em&gt;to species&lt;/em&gt;, numbering as in diagram].&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;&amp;nu;&lt;sub&gt;i&lt;/sub&gt;&lt;sup&gt;exc&lt;/sup&gt;&lt;/em&gt; &amp;nbsp;&amp;nbsp;&amp;nbsp;the initial velocity when A is in &lt;i&gt;exc&lt;/i&gt;ess ([A] = &amp;infin;).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;EC&lt;sub&gt;50&lt;/sub&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;the concencentration of A that gives &lt;em&gt;&amp;nu;&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt; equal to &lt;em&gt;&amp;nu;&lt;sub&gt;i&lt;/sub&gt;exc&lt;/sup&gt;&lt;/em&gt; / 2 (half-maximal activation)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;[A]  &amp;nbsp;&amp;nbsp;&amp;nbsp;The &lt;em&gt;initial&lt;/em&gt; concentration of activator. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;[S]  &amp;nbsp;&amp;nbsp;&amp;nbsp;The &lt;em&gt;initial&lt;/em&gt; concentration of substrate.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The rate law and the diagrams were obtained using &lt;a href=&quot;http://www.wolfram.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mathematica&lt;/a&gt;.  For Matematica at SE see &lt;a href=&quot;https://mathematica.stackexchange.com/questions&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr/&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Briggs, G. E. &amp;amp; Haldane, J. B. S. (1925). A note on the kinetics of enzyme action.  &lt;em&gt;Biochem. J&lt;/em&gt;. &lt;strong&gt;19&lt;/strong&gt;, 338 - 339.[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1259181/&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Chou, T.C. (1974) Relationships between inhibition constants and fractional inhibition in enzyme-catalyzed reactions with different numbers of reactants, different reaction mechanisms, and different types and mechanisms of inhibition. &lt;em&gt;Mol. Pharmacol&lt;/em&gt;., &lt;strong&gt;10&lt;/strong&gt;, 235-247 [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=Relationships%20between%20inhibition%20Constants%20and%20Fractional%20Inhibition%20in%20Enzyme-Catalyzed%20Reactions&quot; rel=&quot;nofollow noreferrer&quot;&gt;pubmed&lt;/a&gt;]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Cornish-Bowden, A. (2004). Fundamentals of Enzyme Kinetics. 3rd&lt;/sup&gt; edn. Portland Press Ltd, London.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;King, E. L. &amp;amp; Altman, C. (1956). A schematic method of deriving the rate laws for enzyme-catalyzed reactions.  &lt;em&gt;J. Phys. Chem&lt;/em&gt;. &lt;strong&gt;60&lt;/strong&gt;, 1375 - 1378. [&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/j150544a010&quot; rel=&quot;nofollow noreferrer&quot;&gt;ACS site&lt;/a&gt;]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Naqui, A. (1982). What does I50&lt;/sub&gt; mean? (1983)  &lt;em&gt;Biochem. J&lt;/em&gt;.  &lt;strong&gt;215&lt;/strong&gt;,  429-430 [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1152414/&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Segel, I. H. (1975). Enzyme Kinetics.  Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems. John Wiley &amp;amp; Sons, Inc., New York.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Tsou, C. L. (1987) The screening of enzyme-targeted drugs.  &lt;em&gt;Bioessays&lt;/em&gt;, &lt;strong&gt;6&lt;/strong&gt;, 237-238. [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=Tsou%20the%20screening%20of%20enzyme%20targeted%20drugs&quot; rel=&quot;nofollow noreferrer&quot;&gt;pubmed&lt;/a&gt;]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="-1" LastEditDate="2017-04-13T12:56:10.857" LastActivityDate="2012-08-25T15:25:36.587" CommentCount="0" CommunityOwnedDate="2012-08-25T15:25:36.587" ContentLicense="CC BY-SA 3.0" />
  <row Id="3251" PostTypeId="2" ParentId="3247" CreationDate="2012-08-20T00:35:41.537" Score="3" Body="&lt;p&gt;In short, 'No.'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yogurt, in and of itself, is the product of milk with specific strains of bacteria that are not particularly unique. Yogurt is just as hospitable to harmful bacteria as beneficial bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two mechanisms which spring to my mind that would prevent infection by harmful bacteria in yogurt would be the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*The already dominant beneficial bacteria outcompete for the harmful bacteria, effectively limiting the capacity for harmful bacterial growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*The already present beneficial bacteria create extracellular products which damage harmful bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second, if it happens at all, doesn't happen on a scale that I'm aware of. The first &lt;em&gt;could&lt;/em&gt; happen, but I highly doubt it. It seems, to me, that it would be more likely to happen in cheese when most of the easy resources have been consumed, which in yogurt they haven't.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yogurt, and all products stemming from milk, are inherently safer not because of any bacteria that take up residence, but because the mammary glands inside the animal producing the milk &lt;em&gt;are&lt;/em&gt; effective filters for a variety of infections. Milk is a &lt;em&gt;product&lt;/em&gt; that is constructed in the mammary glands, and the cells are selective about the output. Keep in mind, however, that it is &lt;strong&gt;by no means&lt;/strong&gt; &lt;em&gt;sterile&lt;/em&gt;. There are dozens of virii and diseases which can be imparted by breastmilk, and nursing women must adhere to guidelines concerning exposure to medications and diet. It's also possible for DDT and other compounds to become concentrated in breastmilk, resulting in harm to the child.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.breastfeedingbasics.org/cgi-bin/deliver.cgi/content/Drugs/pre_pass.html&quot; rel=&quot;nofollow&quot;&gt;http://www.breastfeedingbasics.org/cgi-bin/deliver.cgi/content/Drugs/pre_pass.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, yes, while milk in and of itself is safer than other options, it is not risk free. A virus could easily infect the mammal or herd producing the milk for sale to humans, and only exhibit dangerous symptoms after the milk had been sold. This is why it's illegal to sell unpasteurized milk for human consumption in most U.S. states.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2014-07-13T16:05:32.263" LastActivityDate="2014-07-13T16:05:32.263" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3252" PostTypeId="1" CreationDate="2012-08-20T04:17:21.657" Score="4" ViewCount="302" Body="&lt;p&gt;There are many ads nowadays advertising cellulite removal, and it causes me to wonder if there is an advantage to having cellulite or if it is just a result of too much fat unevenly spread?  Is it structurally more efficient at storing energy or providing insulation?&lt;/p&gt;&#xA;" OwnerUserId="817" LastActivityDate="2012-08-20T05:11:23.090" Title="Is there an advantage to having cellulite" Tags="&lt;human-biology&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3253" PostTypeId="2" ParentId="1771" CreationDate="2012-08-20T04:21:49.310" Score="9" Body="&lt;p&gt;It may actually be curable, as shown by success stories involving the &lt;a href=&quot;http://en.wikipedia.org/wiki/Milwaukee_protocol&quot;&gt;Milwaukee protocol&lt;/a&gt; in which the brain is effectively shut down to allow for the immune system to eradicate the virus.  In most cases, however, it is fatal once symptomatic.  Note that the Milwaukee protocol boasts an imporessive (sarcastic) survival rate of under 15%&lt;/p&gt;&#xA;" OwnerUserId="817" LastActivityDate="2012-08-20T04:21:49.310" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3254" PostTypeId="2" ParentId="3252" CreationDate="2012-08-20T05:11:23.090" Score="1" Body="&lt;p&gt;There's no advantage or disadvantage (beyond personal perception of attractiveness).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a benign condition that can occur with hormone changes, weight changes, and &lt;em&gt;especially&lt;/em&gt; genetic predisposition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It occurs in most women (up to 90% will have it at some point) and some men, and physicians consider it 'normal.'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mayoclinic.com/health/cellulite/DS00891&quot; rel=&quot;nofollow&quot;&gt;http://www.mayoclinic.com/health/cellulite/DS00891&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-20T05:11:23.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3255" PostTypeId="2" ParentId="3211" CreationDate="2012-08-20T07:40:04.630" Score="2" Body="&lt;p&gt;I also got an answer via email that I think is worth sharing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mrs Price:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not answering officially as I’m probably wrong but…&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main point mentioned is that because flies have such a short&#xA;lifespan, so they should evolve faster than elephants or other slow&#xA;growing species.  While this is true, and there are many examples of r&#xA;(ruderal) species evolving rapidly* evolution is not a predictable or&#xA;sensible process, and there are many other factors that contribute to&#xA;evolution other than a short generation time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One main question to consider is… how many flies are there?  And how&#xA;much of that population is affected by the road fatalities?  Whilst&#xA;there are over 23,000 insect species in the UK, your question&#xA;specifically concerned flies so… An average fly lives for around 35&#xA;days and can lay roughly 750 eggs in her lifetime, so fly numbers are&#xA;bloody huge!  Although a small proportion of flies may be killed by a&#xA;car, the proportion will be so small as to make no impact to the&#xA;overall population; therefore the driver for evolution is not strong&#xA;enough to have an impact on the species as a whole.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another reason why motorway deaths may not have a significant impact&#xA;on the fly population is due to when the flies breed.  Even if&#xA;motorways killed 90% of all flies, the fact that many insects breed&#xA;hours after hatching from their egg means that the population is still&#xA;able to reproduce.  Killing something after it has bred is again not a&#xA;driver for evolution, it would have to be a very strong force that&#xA;kills a high number of individuals before they have chance to breed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, motorway deaths affect such a small amount of individuals&#xA;that it does not have a significant impact upon their populations, I&#xA;imagine that many many more of them get killed in spider webs each&#xA;day, however the idiots are still flying into those too!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps :)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;*The peppered moth changed colour from mottled to black due to the&#xA;population from the industrial revolution and then to white once the&#xA;air pollution had cleared as the ones that stood out had such a high&#xA;predation rate&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;*in the last 50 years some fish species have evolved a much smaller&#xA;body size due to the advantage of escaping through a net and being&#xA;able to carry on breeding&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1264" LastActivityDate="2012-08-20T07:40:04.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3256" PostTypeId="1" CreationDate="2012-08-20T08:46:07.823" Score="4" ViewCount="167" Body="&lt;p&gt;I'm beginning to do some cell-binding assays and I would like for my proteins to not be endocytosed by my mammalian cells. Typical suggestions are for the cells to be kept on ice and that the binding experiment also occurs when the cells are chilled.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, to be sure it has been suggested that I use endocytosis inhbitors. So my questions are, when are the endocytosis inhibitors necessary? How would I know that endocytosis inhibitors are necessary? Which ones would I actually use?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I recognize that there are both clathrin and non-clathrin mechanisms of internalization. Which mechanism would be more useful to study for an antibody-receptor interaction?&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="3340" LastEditDate="2015-01-08T12:53:55.513" LastActivityDate="2015-01-08T23:19:38.240" Title="When should endocytosis inhibitors be used in cell binding assays?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;experimental-design&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3257" PostTypeId="2" ParentId="3223" CreationDate="2012-08-20T12:34:51.287" Score="2" Body="&lt;p&gt;Whilst there are several competing ideas for the cause of Alzheimer's, it seems to me that the deposition of β-amyloid (Aβ) is key to the understanding of the disease progression. In many of the papers I will go on to cite, they suggest that prevention of Alzheimer's may be the only cure, as neurons (once damaged) cannot be replaced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During aging there is a progressive increase in the systemic pro-inflammatory state (sometimes called 'inflammaging'). This is also true for the brain (commonly known as neuroinflammation), and is known to contribute to neurodegenerative diseases by promoting the destruction of local tissues (i.e. neurons) [&lt;a href=&quot;http://dx.doi.org/10.1186/1742-2094-1-14&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under normal circumstances microglia (resident macrophages of the brain) clear any excess protein depositions (plaques), such as Aβ, in much the same way as macrophages respond to carotid plaques (as can occur during cardiovascular disease). With age, the immune system becomes less functional - a process known as immunosenescence - which contributes to the pro-inflammatory state of aging [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16859761&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the immune system becomes less functional, the clearance of Aβ deposits is reduced, possibly contributing to the increased plaque deposition [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20552234&quot; rel=&quot;nofollow&quot;&gt;ref.1&lt;/a&gt;][&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20002526&quot; rel=&quot;nofollow&quot;&gt;ref.2&lt;/a&gt;]. There is also discussion on whether it is the decreased effectiveness of the blood-brain barrier that allows peripheral (from the blood) immune cells to infiltrate the central nervous system, possibly kick-starting the degeneration [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/196698920&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many more factors than this, but this is certainly one that interests me as I can see that individuals will have different responses and predispositions to plaques formation in the first place (i.e. the ApoE risk allele, exposure to certain pathogens over the lifetime).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I therefore don't think the study rules out the amyloid hypothesis, in that removal Aβ does not restore the lost neurons (did they really expect it to?). What it does show is that the emphasis should be on prevention, not cure, as 'early-warning' signs, such as biomarkers of Aβ deposits, will be the best way to &lt;em&gt;prevent&lt;/em&gt; the loss of neurons.&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-08-20T12:34:51.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3258" PostTypeId="1" CreationDate="2012-08-20T17:15:29.970" Score="10" ViewCount="4010" Body="&lt;p&gt;GTP gamma S is routinely used in studies of G proteins to stably activate the G protein. Comparing the structures of GTP gamma S and GTP, the Sulphur atom replaces the Oxygen attached to the leaving Phosphate group. However, this is not the bond that is hydrolyzed (dashed line). What makes it non-hydrolyzable then?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GTP: &lt;img src=&quot;https://i.stack.imgur.com/Li5sz.png&quot; alt=&quot;GTP&quot;&gt;                   GTPgS: &lt;img src=&quot;https://i.stack.imgur.com/HOAqr.png&quot; alt=&quot;GTPgS&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="223" LastActivityDate="2012-08-20T19:47:40.270" Title="Why is GTP gamma S non hydrolyzable?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3259" PostTypeId="1" CreationDate="2012-08-20T19:35:03.617" Score="6" ViewCount="1439" Body="&lt;p&gt;I was looking at &lt;a href=&quot;http://www.uic.edu/classes/bios/bios100/labs/graph05.jpg&quot;&gt;this&lt;/a&gt; graph of turnip &lt;a href=&quot;http://en.wikipedia.org/wiki/Peroxidase&quot;&gt;peroxidase&lt;/a&gt; activity and I saw that they use units of 1/sec for enzyme activity. What does this unit intuitively represent and how is it calculated?&lt;/p&gt;&#xA;" OwnerUserId="1186" LastEditorUserId="1250" LastEditDate="2012-08-20T21:07:53.560" LastActivityDate="2012-08-20T22:18:32.737" Title="What are the units of enzyme activity?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3260" PostTypeId="2" ParentId="3258" CreationDate="2012-08-20T19:47:40.270" Score="5" Body="&lt;p&gt;Gamma thiophosphate-analogues of nucleotides were first synthesized in the 70s &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ja00752a042&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Goody and Eckstein, &lt;em&gt;J. Am. Chem. Soc.&lt;/em&gt;, 1971)&lt;/a&gt; and have been used to decipher many intracellular pathways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To understand why GTP-&amp;gamma;-S is not (or very slowly) hydrolysed by GTPases, we can look at the structure of a GTPase-GTP complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GTP binds to various sites on GTPases. This is the binding of GTP to Rap2A, as described in &lt;a href=&quot;http://www.nature.com/emboj/journal/v16/n18/full/7590533a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Cherfils et al., &lt;em&gt;EMBO J.&lt;/em&gt; 1997)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cAyfK.jpg&quot; alt=&quot;Binding site of GTP on Rap2A&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see four different sites bind to the &amp;gamma; phosphate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The interaction of Tyr32 with GTP suggests that its general conservation in small G proteins may have structural or functional advantages. Tyr32 is located three amino acids upstream of a threonine (Thr35 in Ras) which is extremely conserved in most G domains. The alpha subunits of heterotrimeric G proteins have a conserved arginine equivalent in sequence to Tyr32, which was shown from crystal structures to interact with the &amp;gamma;-phosphate of GTP&amp;gamma;S&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In particular, the position of Tyr&lt;sup&gt;32&lt;/sup&gt; is different, when Rap2A is crystallised with GTP-&amp;gamma;-S. This figure shows the position of the Tyr&lt;sup&gt;32&lt;/sup&gt; with GDP (A), GTP (B) and GTP-&amp;gamma;-S (C)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ssNwP.jpg&quot; alt=&quot;Tyr32 position&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Crystals of Rap2A–GTP&amp;gamma;S, whose structure we also report at 3Å resolution, are isomorphous to the Rap2A–GTP crystals. Both structures are essentially similar, except that &lt;strong&gt;Tyr32 no longer forms a hydrogen bond with the corresponding atom of the &amp;gamma;-thiophosphate, which is probably the sulfur atom&lt;/strong&gt;. The Tyr32–&amp;gamma;-thiophosphate distance is 7.2 Å. The conformation of switch I and II and their interaction with the nucleotide are otherwise identical. Thus, the Tyr32–&amp;gamma;-phosphate hydrogen bond forms only in the presence of the true ligand, but is probably not essential for the triphosphate conformation of Rap2A nor for proper binding of the nucleotide. In particular, the position of Thr61 compares well between the GTP and GTP&amp;gamma;S complexes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The author conclude that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our study shows that the complex with the natural ligand GTP is similar to the complex with GTP&amp;gamma;S, and thus justifies most conclusions obtained from previous structures of G proteins with GTP analogues. However, the structure of Rap2A with GTP reveals a novel interaction of Tyr32 with an oxygen of the &amp;gamma;-phosphate of GTP and with the amide group of Gly13. &lt;strong&gt;In the GTP&amp;gamma;S complex, Tyr32 is shifted away from the corresponding atom&lt;/strong&gt;. The Rap2A–GTP and Rap2A–GTP&amp;gamma;S complexes are otherwise identical, and form isomorphous crystals. Thus, the interaction of Tyr32 with GTP&amp;gamma;S is prevented solely by the presence of the gamma-sulfur, but the conformation of switch I and II is similar whether GTP or a GTP analogue is bound. &lt;strong&gt;GTP&amp;gamma;S probably introduces a different charge distribution on the gamma-(thio)-phosphate and/or modifies the polarizability of the &amp;beta;–&amp;gamma; P–O bonds as compared with GTP&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-08-20T19:47:40.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3261" PostTypeId="2" ParentId="3259" CreationDate="2012-08-20T21:34:29.060" Score="7" Body="&lt;p&gt;This refers to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Turnover_number&quot;&gt;turnover number&lt;/a&gt; (a.k.a k&lt;sub&gt;cat&lt;/sub&gt; or k&lt;sub&gt;2&lt;/sub&gt;) of an enzyme and is usually calculated using &lt;a href=&quot;http://en.wikipedia.org/wiki/Michaelis-Menten_kinetics&quot;&gt;Michaelis-Menten&lt;/a&gt; kinetics. Jump to the summary at the end if you want a simple answer. If you want a more thorough answer, consider the following chemical equation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[E] + [S] ⇌ [ES] → [E] + [P]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This says that a certain concentration of enzyme mixed with a certain concentration of substrate will first combine and form a complex depending on the enzyme's &lt;a href=&quot;http://en.wikipedia.org/wiki/Affinity&quot;&gt;affinity&lt;/a&gt; for the substrate. Then the enzyme complex will generate a product depending on the enzyme's ability to convert the transition state into product. The k&lt;sub&gt;1&lt;/sub&gt; constant is the arrow moving from [E] + [S] → [ES] and the k&lt;sub&gt;-1&lt;/sub&gt; is the arrow moving from [ES] → [E] + [S] (they oppose each other). The k&lt;sub&gt;2&lt;/sub&gt; constant is the arrow moving from [ES] → [E] + [P].&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;V&lt;sub&gt;o&lt;/sub&gt; = [ES]k&lt;sub&gt;2&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;V&lt;sub&gt;o&lt;/sub&gt; - this is the rate that product is being formed, which can be measured.&lt;/li&gt;&#xA;&lt;li&gt;[ES] - this is the concentration of enzyme-substrate complexes.&lt;/li&gt;&#xA;&lt;li&gt;k&lt;sub&gt;2&lt;/sub&gt; - this is a constant value comparing the two.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This can also be expressed in terms of maximum rate:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;V&lt;sub&gt;max&lt;/sub&gt; = [E]&lt;sub&gt;T&lt;/sub&gt;k&lt;sub&gt;2&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;V&lt;sub&gt;max&lt;/sub&gt; - V&lt;sub&gt;max&lt;/sub&gt; is catalytic rate when [E]&lt;sub&gt;T&lt;/sub&gt; = [ES] (when all of the enzyme present is bound to substrate/saturated).&lt;/li&gt;&#xA;&lt;li&gt;[E]&lt;sub&gt;T&lt;/sub&gt; - [E]&lt;sub&gt;T&lt;/sub&gt; is the total enzyme concentration. [E]&lt;sub&gt;T&lt;/sub&gt; = [E] + [ES].&lt;/li&gt;&#xA;&lt;li&gt;k&lt;sub&gt;2&lt;/sub&gt; - the k&lt;sub&gt;cat&lt;/sub&gt; is the catalytic constant. It is a constant indicating how quickly an enzyme can convert substrates into products. It is easily observed by this equation.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h3&gt;Summary&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;So k&lt;sub&gt;2&lt;/sub&gt; is basically an indicator of how efficiently or quickly an enzyme operates. Not all enzymes follow standard &lt;a href=&quot;http://en.wikipedia.org/wiki/Michaelis-Menten_kinetics&quot;&gt;Michaelis-Menten&lt;/a&gt; kinetics. For example, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Allosteric_regulation&quot;&gt;allosteric properties&lt;/a&gt; of some enzymes cause a non-linear saturation curve. Because of this, the turnover number is commonly referred to. The turnover number's units of s&lt;sup&gt;-1&lt;/sup&gt; indicate one product molecule per second, so a turnover rate of 3000 means you can create 3000 products in 1 second at V&lt;sub&gt;max&lt;/sub&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1250" LastEditorUserId="1250" LastEditDate="2012-08-20T22:18:32.737" LastActivityDate="2012-08-20T22:18:32.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3262" PostTypeId="1" AcceptedAnswerId="3264" CreationDate="2012-08-21T05:29:39.117" Score="4" ViewCount="115" Body="&lt;p&gt;Pretty self explanatory question. I have a basic grasp on the &quot;How&quot; and &quot;Why&quot; of Reversal/Action Potential in and between neurons, but this question lingers.&lt;/p&gt;&#xA;" OwnerUserId="972" LastEditorUserId="1122" LastEditDate="2012-08-21T16:30:56.137" LastActivityDate="2012-08-21T16:30:56.137" Title="Why isn't there any repulsive force between Na+ and K+ disrupting thier roles in transmembrane voltage/ action potentials" Tags="&lt;biochemistry&gt;&lt;electrophysiology&gt;&lt;intracellular-transport&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3263" PostTypeId="1" AcceptedAnswerId="3265" CreationDate="2012-08-21T05:48:31.647" Score="8" ViewCount="809" Body="&lt;p&gt;Many species of mosquitoes have bloodsucking females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When they bite a host, do they need to pump? Or does the sheer blood pressure combined with capillary action suffice to make the blood rush into the mosquito's stomach?&#xA;If the blood pressure is enough, can the mosquito &quot;explode&quot; or simply die from having too much blood rushing in?&lt;/p&gt;&#xA;" OwnerUserId="1114" LastActivityDate="2012-09-17T15:02:33.770" Title="Do mosquitoes need to pump blood out of the host?" Tags="&lt;physiology&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3264" PostTypeId="2" ParentId="3262" CreationDate="2012-08-21T06:46:07.810" Score="7" Body="&lt;p&gt;The carriers of the charge are ions and they get repelled from each other well enough. Other than their charge there is only the size in which they differ (for all practical purposes). This means, as long as we are talking about membrane potential, the actors are just a mix of 1+ ions which don't come near each other. When size matters, for example in an ion channel, we are talking about single particles, so there is no action of a repulsive force between K+ and Na+.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From another angle: The charge is a force that emerges from a sea of particles, regardless if they are all of one kind or mixed K+/Na+. If you talk about a force between K+ and Na+ then you would have to separate all 10^15 or so K+ ions from 10^15 or so Na+ ions which is simply impossible, as they are mixed up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Brownian_motion&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Brownian_motion&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ion&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Ion&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ion_channel&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Ion_channel&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-08-21T16:17:23.127" LastActivityDate="2012-08-21T16:17:23.127" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3265" PostTypeId="2" ParentId="3263" CreationDate="2012-08-21T10:36:18.407" Score="8" Body="&lt;p&gt;Take a look at &lt;a href=&quot;http://dx.doi.org/10.1088/1748-3182/3/4/046001&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ramasubramanian &lt;em&gt;et al&lt;/em&gt;.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt; The authors have some great SEM images of the proboscis and fascicle tip and derive a mathematical model for the &quot;bite&quot; itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They mention that there are two types of feeding: pool feeding, where the mosquito creates a hemmorrhage and feeds slowly via capillary action, and capillary feeding, wherein the mosquito taps into a capillary and the feeding process is much faster, as the blood is driven under pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another source to check, one that the authors above cite, is by &lt;a href=&quot;http://dx.doi.org/10.1016/0022-1910%2866%2990143-0&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kashin&lt;sup&gt;[2]&lt;/sup&gt;&lt;/a&gt;. This only links to the abstract, however.  You'd have to hit the stacks to get the article, I'd imagine.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bibliotecavirtual.ranf.com/i18n/catalogo_imagenes/grupo.cmd?path=1002130&quot; rel=&quot;nofollow noreferrer&quot;&gt;This source&lt;sup&gt;[3]&lt;/sup&gt;&lt;/a&gt; indicates that: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The blood is imbibed by action of the cibarial and pharyngeal pump muscles via the food canal formed by the labrum and hypopharynx. Blood then passes into the midgut.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For @Luke, and others:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zbyZo.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/uadZq.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/pddvm.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ehCi6.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All images are from &lt;a href=&quot;http://dx.doi.org/10.1088/1748-3182/3/4/046001&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ramasubramanian &lt;em&gt;et al&lt;/em&gt;.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1088/1748-3182/3/4/046001&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Ramasubramanian MK, Barham OM, Swaminathan V&lt;/strong&gt;. 2008. Mechanics of a mosquito bite with applications to microneedle design. Bioinspiration &amp;amp; Biomimetics, 3: 046001, doi:10.1088/1748-3182/3/4/046001.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/0022-1910%2866%2990143-0&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Kashin P&lt;/strong&gt;. 1966. Electronic recording of the mosquito bite. Journal of Insect Physiology, 12(3): 281-286, doi:10.1016/0022-1910(66)90143-0.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bibliotecavirtual.ranf.com/i18n/catalogo_imagenes/grupo.cmd?path=1002130&quot; rel=&quot;nofollow noreferrer&quot;&gt;Robert V, Brey PT. 1998. Biting physiology of &lt;em&gt;Anopholes&lt;/em&gt; affecting &lt;em&gt;Plasmodium&lt;/em&gt; transmission. Research and Reviews in Parasitology, 58 (3-4): 203-208.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1210" LastEditorUserId="112" LastEditDate="2012-09-17T15:02:33.770" LastActivityDate="2012-09-17T15:02:33.770" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3266" PostTypeId="1" AcceptedAnswerId="3268" CreationDate="2012-08-21T11:46:29.197" Score="9" ViewCount="276" Body="&lt;p&gt;Curiosity is on the Martian surface and is equipped with a slew of laboratory equipment. What would Curiosity need to discover to prove there is or has been life on Mars? Would it have to find DNA (or its Martian equivalent)?&lt;/p&gt;&#xA;" OwnerUserId="1284" LastEditorUserId="1284" LastEditDate="2012-08-22T23:37:27.630" LastActivityDate="2012-08-22T23:37:27.630" Title="What would need to be discovered to prove there is extraterrestrial life?" Tags="&lt;dna&gt;&lt;astrobiology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3267" PostTypeId="2" ParentId="3266" CreationDate="2012-08-21T13:33:32.547" Score="5" Body="&lt;h3&gt;Answer to your title:&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dictionary.reference.com/browse/extraterrestrial?s=t&quot;&gt;ex•tra•ter•res•tri•al&lt;/a&gt; [ek-struh-&lt;em&gt;tuh&lt;/em&gt;-&lt;strong&gt;res&lt;/strong&gt;-tree-&lt;em&gt;uhl&lt;/em&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;adjective&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;outside, or originating outside, the limits of the earth&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;h3&gt;Answer to your post:&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;There is a whole field of study revolving around these questions called &lt;a href=&quot;http://en.wikipedia.org/wiki/Astrobiology&quot;&gt;astrobiology&lt;/a&gt;. It is assumed that extraterrestrial life forms will have some sort of information storage similar to DNA but that it will probably not be identical. Accessible water is considered the most important indicator for the potentiality of life. Oxygen or some kind of reducing element is also considered to be very important.&lt;/p&gt;&#xA;" OwnerUserId="1250" LastActivityDate="2012-08-21T13:33:32.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3268" PostTypeId="2" ParentId="3266" CreationDate="2012-08-21T13:54:49.423" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Curiosity is on the Martian surface and is equipped with a slew of laboratory equipment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.news-press.com/videonetwork/1769239255001/Curiosity-not-looking-to-detect-life-on-Mars&quot;&gt;But not, incidentally, equipment to detect life.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What would Curiosity need to discover to prove there is or has been life on Mars? Would it have to find DNA …?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No. In fact, DNA would be lousy evidence of life on Mars, it would almost certainly be a &lt;a href=&quot;http://www.space.com/12827-mars-rover-curiosity-landing-contamination-risks.html&quot;&gt;contamination from Earth&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lacking equipment, I’m not even sure how Curiosity would go about finding traces of DNA but assuming that it did (through some sort of chemical assay), it has no way of telling the origin of said DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And even if the genetic material could be sequenced there are a number of scenarios. It could be very similar to what is found in extremophiles on Earth, in which case we wouldn’t necessarily know the origin (but due to the aforementioned contamination risk, the prior probability of it being Earth life would be very high). If it were completely different, that might be compelling enough to consider it extraterrestrial.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But maybe not: estimates for &lt;a href=&quot;http://en.wikipedia.org/wiki/Species#Numbers_of_species&quot;&gt;the number of existing species on Earth vary drastically&lt;/a&gt;. One thing is certain, though: we’ve only scratched the surface of prokaryotic life in particular. So if we find something new, that wouldn’t even be very surprising.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More interesting would be an &lt;em&gt;alternative&lt;/em&gt; genetic material, neither DNA nor RNA. So far, we haven’t discovered anything like this on Earth (&lt;a href=&quot;http://www.bbc.co.uk/news/science-environment-18770964&quot;&gt;despite earlier hopes&lt;/a&gt;) so it would be more likely of extraterrestrial origin. But again, as the refuted study shows, we cannot entirely exclude the possibility of such life being found on Earth either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All this is just to show that proving microbial life to be extraterrestrial is quite hard. It would be much easier if we were to find non-microbial life on Mars (i.e. something multicellular). However, I don’t know of any serious scientist who seriously entertains this possibility.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the reason to prefer such a discovery is simple: the bigger the life form, the less likely that we haven’t found it yet on Earth, and the smaller its viable niche. So if we find multicellular life adapted to the surface of Mars there aren’t many places on Earth where it could have originated from, never mind the low chance of having survived the ride aboard the probe.&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="166" LastEditDate="2012-08-21T14:00:20.443" LastActivityDate="2012-08-21T14:00:20.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3269" PostTypeId="2" ParentId="2292" CreationDate="2012-08-21T13:55:21.373" Score="1" Body="&lt;p&gt;I think your best bet is to blast your transcripts against the &lt;a href=&quot;http://www.tcdb.org&quot; rel=&quot;nofollow&quot;&gt;TCDB&lt;/a&gt; which has all ion channel templates you can get in the literature. Second best would be to blast against a general protein database like UniProt.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-08-21T13:55:21.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3270" PostTypeId="1" CreationDate="2012-08-21T14:55:37.243" Score="1" ViewCount="36" Body="&lt;p&gt;Could silicon oil block Na+ ion channels in the membrane of an axon and prevent Na+ influx?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been wondering if Na+ influx could have been a diluting factor in anterograde fills.  If so, could coating the axon with silicon oil prevent this?&lt;/p&gt;&#xA;" OwnerUserId="1285" LastEditorUserId="1122" LastEditDate="2012-08-21T16:29:19.720" LastActivityDate="2012-08-21T17:10:56.883" Title="Could silicon oil block Na+ ion channels in the membrane of an axon and prevent Na+ influx?" Tags="&lt;neuroscience&gt;&lt;cell-membrane&gt;&lt;intracellular-transport&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3271" PostTypeId="2" ParentId="3266" CreationDate="2012-08-21T15:06:50.623" Score="3" Body="&lt;p&gt;In the simplest sense, extraterrestrial life is life found beyond the Earth. Defining what life itself is notoriously difficult - perhaps the best is a system which is subject to Darwinian evolution?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the term &quot;extraterrestrial life&quot; does not necessarily imply that said life (if found) originated &lt;em&gt;in situ&lt;/em&gt;. For example, if we do find (presumably microbial) life on Mars, I would not be completely surprised if it had a DNA/RNA (or PNA or similar) information system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The amount of material exchange (due primarily to asteroid impacts) between the Earth and Mars is large - significant quantities of Martian rocks have been found on Earth, and the reverse is presumably also true. Earth's higher escape velocity would reduce the amount of material ejected from the surface, but Mars' thinner atmosphere would facilitate the successful &quot;landing&quot; of any ejected rock without being burned up on re-entry beforehand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, Mars may have been seeded by Earth life traveling on rocks ejected by impacts. Whether this life could adapt to extreme cold, saline regolith, ionising radiation, dessication etc. is another matter although extremophiles on Earth are seen to (individually) have some of these qualities (psychrophiles, halophiles, &quot;radiophiles&quot;, etc. Deinococcus radiodurans actually does quite well in all these areas. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, Earth life may  have been seeded by Mars rocks traveling the other way. If Mars was warm and wet in the past as some advocate, this idea may not be so crazy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look for &quot;panspermia&quot; and &quot;lithopanspermia&quot; for more information.&lt;/p&gt;&#xA;" OwnerUserId="81" LastActivityDate="2012-08-21T15:06:50.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3272" PostTypeId="2" ParentId="3270" CreationDate="2012-08-21T16:24:45.470" Score="2" Body="&lt;p&gt;No, silicon oil couldn't block an ion channel. Oil is a nonpolar substance, just like the membrane lipids, so if you can get your oil to that cell, it will mix with the lipids within the membrane. The ion channel, which sits in the membrane, too, is rather closed to the membrane interior and opens to the inside and outside of the cell which, contrarily, is a polar solution of soluble molecules in water. So, to block one of the openings you better have a polar molecule that is water-soluble.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ion_channel&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Ion_channel&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Polarity_%28chemistry%29&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Polarity_%28chemistry%29&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-08-21T17:10:56.883" LastActivityDate="2012-08-21T17:10:56.883" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3275" PostTypeId="1" AcceptedAnswerId="3288" CreationDate="2012-08-22T00:30:05.637" Score="5" ViewCount="562" Body="&lt;p&gt;I was wondering this as I considered how effective panting would be for humans as a means of cooling.&lt;/p&gt;&#xA;" OwnerUserId="1289" LastEditorUserId="43" LastEditDate="2012-08-22T01:31:06.263" LastActivityDate="2012-08-22T18:12:49.310" Title="Do dogs have something different about their physiology that allows them to pant without hyperventilating?" Tags="&lt;zoology&gt;&lt;physiology&gt;&lt;breathing&gt;&lt;respiration&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3276" PostTypeId="2" ParentId="2477" CreationDate="2012-08-22T00:56:11.203" Score="2" Body="&lt;p&gt;Well, I wasn't able to find an online video course. The closest I came was &lt;a href=&quot;http://www.ces.ncsu.edu/depts/hort/consumer/hortinternet/classes_online.html&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt;, which links to courses that put their material online. Most of these are compilations of the lecture notes. There's also &lt;a href=&quot;http://www.geog.ubc.ca/biodiversity/eflora/IntroductiontoPlantTaxonomy.html&quot; rel=&quot;nofollow&quot;&gt;this page&lt;/a&gt; from the University of British Columbia, that has a nice little overview of the field of plant taxonomy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my experience, botany and plant identification are subjects where one really needs to learn by doing. You really need to grab a plant and take a close look at it while noting why its in the group that its in. A great way to get started might be to join a local gardening club or native plant society. The people in those groups can provide their tips for ID-ing plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the primary skills you'll want to learn is identifying what family a plant is in. Plant families have (mostly) consistent characters, and learning how to spot the most common families in your area will be a big help.&lt;/p&gt;&#xA;" OwnerUserId="1197" LastActivityDate="2012-08-22T00:56:11.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3277" PostTypeId="2" ParentId="3275" CreationDate="2012-08-22T02:12:36.637" Score="1" Body="&lt;p&gt;Not knowing the physiology or the literature, I can say based on personal observations that dogs, even when extremely hot or exhausted, mix in a routine of deep inhales and exhales to their panting.  Perhaps this prevents unwanted side effects of their cooling mechanisms.  &lt;/p&gt;&#xA;" OwnerUserId="1210" LastActivityDate="2012-08-22T02:12:36.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3278" PostTypeId="1" AcceptedAnswerId="10573" CreationDate="2012-08-22T04:55:57.093" Score="44" ViewCount="39270" Body="&lt;p&gt;This question has always mystified me since young. For beetles, I can reason that they flip over because they have a higher centre of gravity causing them to be in unstable equilibrium when they tuck in their legs when they are about to die. For cockroaches with a lower profile, I would expect them to stay upright. But why do they flip over? Is it more comfortable for them to die this way or is there a scientific explanation for this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/l9cdg.jpg&quot; alt=&quot;image for reference&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As noted in some of the comments below, this is a general observation based on cockroaches being killed by insecticide. I haven't got the chance to observe (or notice) cockroaches that die in other ways and therefore do not want to limit the scope of my question to just insecticide poisoning.&lt;/p&gt;&#xA;" OwnerUserId="1283" LastEditorUserId="1283" LastEditDate="2012-08-28T02:24:07.297" LastActivityDate="2015-04-02T09:56:02.553" Title="Why do cockroaches flip over when they die?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3279" PostTypeId="1" AcceptedAnswerId="3284" CreationDate="2012-08-22T06:41:36.610" Score="7" ViewCount="2954" Body="&lt;p&gt;Typically when proteins aggregate, they will get stuck at the top of the well. However, we're seeing some protein aggregate in the stacking layer even when we're treating the loading volume with DTT.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One peculiar attribute of this experiment is that we're trying to carry out a Cu(I) catalyzed Azide-Alkyne Click rxn. Without the Cu(I), the proteins run normally. However, after Click rxn, we do see some of our expected clicked product, one of our proteins is disappearing into the top band. Hypothesis is that either the copper(I) is changing the migration or oxidative damage from the Cu(I)-&gt; Cu(II) transition is altering the protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Returning to the original question, what would cause a protein to stop at the stacking layer vs. at the combs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[edit]&#xA;According to my labmate who was having this problem, the protein was crosslinking with itself to create fairly sizeable polymers. We also saw ladders of the protein with ascending size. Spinning the clicked reaction removed the issue but also resulted at a lost of the protein. It sounds like he wasn't treating with a sufficient amount of DTT to break up the mixture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This unfortunately still doesn't differentiate between proteins stuck at the combs vs stuck at the stacking layer.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="389" LastEditDate="2012-09-05T07:19:08.790" LastActivityDate="2012-09-05T07:19:08.790" Title="What would cause proteins to get stuck in the stacking layer of a SDS-Page gel" Tags="&lt;sds-page&gt;&lt;experimental&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3280" PostTypeId="1" AcceptedAnswerId="5072" CreationDate="2012-08-22T08:26:59.227" Score="8" ViewCount="119" Body="&lt;p&gt;I believe that there are predator/prey combinations where the prey can easily spot that the predator is not hungry and will not try to flee from it. I’m thinking, for example, of gazelles who will happily graze in sight of sleeping lions. (Please correct me if this is already wrong.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to be sensible (in an evolutionary sense) for the predator to not put unnecessary stress on the prey. First question: Are there predator who &lt;em&gt;actively&lt;/em&gt; signal that they are not hungry, e.g. by a certain sound?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And my second question: Is there such a combination where the predator will, in times of severe hunger, &lt;em&gt;pretend&lt;/em&gt; not to be hungry in order to more easily catch a prey?&lt;/p&gt;&#xA;" OwnerUserId="1291" LastEditorUserId="43" LastEditDate="2012-08-22T09:58:09.727" LastActivityDate="2012-10-30T23:14:42.140" Title="Predators faking to be not hungry?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3281" PostTypeId="1" AcceptedAnswerId="3283" CreationDate="2012-08-22T11:46:01.567" Score="5" ViewCount="281" Body="&lt;p&gt;I have an ensemble of homology models of a protein, and I now wish to remove those models which have backbone clashes. I could obviously check by eye but this is subjective and probably will not be accepted for publication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the best (reproducible) method to determine if a particular protein model contains a backbone clash?&lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="43" LastEditDate="2012-08-22T12:17:52.780" LastActivityDate="2012-08-22T13:58:53.037" Title="Determining if a Protein Model Contains a Backbone Clash" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3282" PostTypeId="2" ParentId="2692" CreationDate="2012-08-22T12:44:45.043" Score="3" Body="&lt;p&gt;Stem cells are not all 'unipotent' - they cannot necessarily differentiate into any type of cell. For instance, resident stem cells in tissues such as muscle - myo-satellite cells - are &lt;em&gt;partially differentiated&lt;/em&gt; and during cell division one daughter differentiates further to become a myocyte (for example), and the other daughter the replacement myosatellite cell. As far as I'm aware, the majority of tissues have resident stem cells in varying degrees of differentiation (exceptions might include neurons and cardiac muscle, where cells are not replaced over the lifespan of the organism). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is some evidence for resident stem cells in glands;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The adult &lt;strong&gt;pituitary&lt;/strong&gt; gland shows stem/progenitor cell activation in response to injury and is capable of regeneration (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22518061&quot; rel=&quot;nofollow&quot;&gt;Fu &lt;em&gt;et al&lt;/em&gt;, 2012&lt;/a&gt;),&lt;/li&gt;&#xA;&lt;li&gt;The &lt;strong&gt;pancreas&lt;/strong&gt; has been heavily studied from the perspective of diabetes research, with many studies looking to implant stem cells from elsewhere (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22740171&quot; rel=&quot;nofollow&quot;&gt;Rezania &lt;em&gt;et al&lt;/em&gt;, 2012&lt;/a&gt;). However there is some evidence for resident stem cells of the pancreas that may turn out to be more promising as treatment strategies in the future (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18243096&quot; rel=&quot;nofollow&quot;&gt;Xu &lt;em&gt;et al&lt;/em&gt;, 2004&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21934353&quot; rel=&quot;nofollow&quot;&gt;Venkatesan &lt;em&gt;et al&lt;/em&gt;, 2011&lt;/a&gt;),&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Sebaceous&lt;/strong&gt; glands are found throughout the skin, and secrete 'sebum' which keeps the skin waxy and waterproof. There is plenty of evidence for epidermal stem cells (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22820019&quot; rel=&quot;nofollow&quot;&gt;Eckert &lt;em&gt;et al&lt;/em&gt;, 2012&lt;/a&gt;),&lt;/li&gt;&#xA;&lt;li&gt;There is also recent evidence for the existence of &lt;strong&gt;thyroid&lt;/strong&gt; stem cells too (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22028390&quot; rel=&quot;nofollow&quot;&gt;Fierabracci, 2012&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22691885&quot; rel=&quot;nofollow&quot;&gt;Malaguarnera &lt;em&gt;et al&lt;/em&gt;, 2012&lt;/a&gt;),&lt;/li&gt;&#xA;&lt;li&gt;Saliva is mainly produced by the &lt;strong&gt;submandibular&lt;/strong&gt; glands also contain resident stem cells, with this paper stating that stem cells have been isolted from salivary glands in humans (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22550510&quot; rel=&quot;nofollow&quot;&gt;Okumura &lt;em&gt;et al&lt;/em&gt;, 2012&lt;/a&gt;),&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Given the limited (and very recent) evidence for the above (relatively well characterizd) glands, it seems likely that other glands will also have resident stem cells that remain to be identified.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ageing: The so-called stem-cell pool gets depleted over a lifetime, so tissues lose the regenerative potential. However rejuvenation medicine is becoming a heavily invested in area of research (see &lt;a href=&quot;http://www.sens.org/&quot; rel=&quot;nofollow&quot;&gt;www.SENS.org&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-08-22T12:44:45.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3283" PostTypeId="2" ParentId="3281" CreationDate="2012-08-22T12:58:28.743" Score="4" Body="&lt;p&gt;The way to check for steric clashing between any two atoms, backbone or otherwise, is to compute their Euclidean distance. If &lt;code&gt;a&lt;/code&gt; and &lt;code&gt;b&lt;/code&gt; represent two atoms (with &lt;code&gt;a_x&lt;/code&gt; being the X coordinate of atom &lt;code&gt;a&lt;/code&gt; and so forth), you can calculate their Euclidean distance as follows.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;code&gt;d(a, b) = sqrt( (a_x - b_x)^2 + (a_y - b_y)^2 + (a_z - b_z)^2) )&lt;/code&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So essentially the idea would be to calculate the pairwise distance between each of the backbone atoms. For any pair of atoms, there is steric clashing if the distance between them falls below a certain threshold. If I remember correctly, this threshold is the sum of the van der Waals radii of the two atoms.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2012-08-22T13:58:53.037" LastActivityDate="2012-08-22T13:58:53.037" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3284" PostTypeId="2" ParentId="3279" CreationDate="2012-08-22T14:18:27.387" Score="2" Body="&lt;p&gt;Sounds like the copper cross linking the protein or creating aggregates that the SDS  buffer can't break up.  add EDTA to your loading buffer before you cook it? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-08-22T14:18:27.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3286" PostTypeId="2" ParentId="3275" CreationDate="2012-08-22T16:15:35.660" Score="0" Body="&lt;p&gt;Our physiology is quite different. I guess their larger surface-area tongue is one obvious difference, and the fact that they have limited sweat glands. I actually thought they had none, but &lt;a href=&quot;http://www.psychologytoday.com/blog/canine-corner/201011/do-dogs-sweat&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; states that they have them on their feet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another fun fact there is that they don't just use panting -- they can apparently  constrict/dilate vessels in their face and ears..&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2012-08-22T16:15:35.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3287" PostTypeId="2" ParentId="3192" CreationDate="2012-08-22T17:38:12.983" Score="3" Body="&lt;p&gt;Computational Biology - usually involves creating a model (software or other logic) where you attempt to shed light on some process of biology by building information flows using known physics/chemistry/biology --- (how to cells divide ? -&gt; build a biomechanic model of mitotic spindles ...) --- You are building up complexity in your model to simulate biology to ever increasing levels of accuracy&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bioinformatics --&gt; measure biology then analyze the data --- biology already has the complexity --- You are attempting to understand this complexity by identifying patterns in measurement data&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both of these fields drive research efforts to create better sensors used to measure biological processing&lt;/p&gt;&#xA;" OwnerUserId="1068" LastEditorUserId="1068" LastEditDate="2018-04-11T13:43:22.100" LastActivityDate="2018-04-11T13:43:22.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3288" PostTypeId="2" ParentId="3275" CreationDate="2012-08-22T18:12:49.310" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://host.madison.com/wsj/news/local/ask/article_2c020ce8-f82a-11e0-b065-001cc4c03286.html&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; quotes a professor of respiratory physiology that says &quot;dogs are built to pant just right. The mechanics of their lungs and chest set a precise rate for panting that minimizes the amount of work while maximizing cooling power.&quot; They also don't breathe fully when panting, so they can still cool themselves without increasing gas exchange. This is different than humans, who will hyperventilate to get rid of carbon dioxide (or you can intentionally hyperventilate and cause respiratory alkalosis).&lt;/p&gt;&#xA;" OwnerUserId="1166" LastActivityDate="2012-08-22T18:12:49.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3289" PostTypeId="2" ParentId="3179" CreationDate="2012-08-22T22:40:17.943" Score="1" Body="&lt;p&gt;The Center for Disease Control is a great source for disease statistics. I didn't find a chart with common disease incidence on their website, but if you search for a specific disease you should be able to find the incidence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cdc.gov/nchs/&quot; rel=&quot;nofollow&quot;&gt;http://www.cdc.gov/nchs/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1295" LastActivityDate="2012-08-22T22:40:17.943" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3290" PostTypeId="1" AcceptedAnswerId="3292" CreationDate="2012-08-23T00:01:18.173" Score="3" ViewCount="4696" Body="&lt;p&gt;From my experience on SE sites, I believe this is the right site to ask this question under &quot;terminology&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been trying to find out whether English has one-word verbs for &quot;undergo mitosis&quot; and &quot;undergo meiosis&quot;. I haven't been able to find confirmation on Google, but my linguistic imagination is limited, and I may have failed to google the right things. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could you tell me if there are such verbs in common use in biology? I mean, if such verbs exist, can I find them in modern biology books or papers? &lt;/p&gt;&#xA;" OwnerUserId="1278" LastEditorUserId="43" LastEditDate="2012-08-23T10:11:24.290" LastActivityDate="2019-09-06T19:23:50.553" Title="Are there verbs for &quot;undergo mitosis&quot; and &quot;undergo meiosis&quot;?" Tags="&lt;cell-biology&gt;&lt;meiosis&gt;&lt;mitosis&gt;&lt;terminology&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3291" PostTypeId="1" CreationDate="2012-08-23T00:32:16.013" Score="9" ViewCount="150" Body="&lt;p&gt;In my attempt to create a metabolic model of &lt;em&gt;E. coli&lt;/em&gt;, I have found a comprehensive list of metabolic reactions and their stoichiometry. The one I am currently using is &lt;em&gt;E. coli&lt;/em&gt; model iJO1366 (&lt;a href=&quot;http://ecoliwiki.net/colipedia/index.php/Metabolic_Network_Reconstructions#iJO1366&quot; rel=&quot;nofollow&quot;&gt;more here&lt;/a&gt;). What I have not yet found is a comprehensive list of kinetic rate constants associated with these reactions. I also require a data source of concentrations of these enzymes and metabolites at steady state in &lt;em&gt;E. coli&lt;/em&gt;. Where can I find information on concentrations and rate constants?&lt;/p&gt;&#xA;" OwnerUserId="1296" LastEditorUserId="43" LastEditDate="2012-08-31T01:31:07.043" LastActivityDate="2013-03-19T21:02:45.803" Title="E. coli values for [enzymes], [metabolites] and kinetic rates" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3292" PostTypeId="2" ParentId="3290" CreationDate="2012-08-23T03:06:02.033" Score="3" Body="&lt;p&gt;I'm actually not sure myself. If I were to use something, I would go with &quot;Mitos'd&quot; and &quot;Meios'd&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, you may not win over many fans, depending on the audience. If it's with students or maybe a professor, you could get away with shortening the processes. If it's in any formal setting, be as precise and descriptive as possible. It's not a lot of trouble to be more accurate and add &quot;underwent&quot; to the sentence. &lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-23T03:06:02.033" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3293" PostTypeId="2" ParentId="3179" CreationDate="2012-08-23T04:14:29.417" Score="0" Body="&lt;p&gt;A couple resources that might be of use:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you subscribe to it (annoyingly, I cannot get at my copy), the American Academy of Pediatric's &lt;em&gt;Red Book&lt;/em&gt; may contain incidence figures. I don't recall, but it contains a remarkable amount of information in it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For viral diseases, most if not all entries in &lt;em&gt;Fields Virology&lt;/em&gt; have an Epidemiology section, and many of these touch on the incidence rate, especially for more common diseases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to the CDC (listed in another answer), take a look at the Agency for Healthcare Quality Research (AHRQ)'s Healthcare Cost and Utilization Project (HCUP) data. While this will only give you incidence in terms of hospitalizations rather than all cases, it may be potentially useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beyond that, I'd suggest looking for particular papers, or search for &quot;DISEASE OF INTEREST&quot; meta-analysis in Google Scholar or PubMed for overall incidence figures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, a useful formula:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prevalence = Incidence * Duration. Which in turn means Prevalence/Duration = Incidence. If you can find those two pieces of information, you can calculate the incidence for what you want.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's also a way to extract incidence from a mathematical modeling paper about a disease which reports an R0 figure, but that may be a touch technical given your stated desires.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2012-08-23T04:14:29.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3294" PostTypeId="2" ParentId="3247" CreationDate="2012-08-23T04:20:07.257" Score="1" Body="&lt;p&gt;There have been studies regarding whether or not the bacterial load in yogurt (which would be the &quot;Live and active cultures&quot; part of yogurt - or the part where Jamie Lee Curtis talks about how you'll go back to pooping on schedule) helps protect the gut against the proliferation of certain pathogenic bacterias like &lt;em&gt;C. difficile&lt;/em&gt; when we've otherwise wiped out the gut's natural flora - say with antibiotics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far, the results from that have been middling and inconclusive. And honestly, that's the best shot the cultures in yogurt have of showing a good effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the scenario you ask about, you'd be trying to protect against diseases that &lt;em&gt;haven't&lt;/em&gt; been handed a competitive advantage in the form of an obliterated gut flora, and have added in the risk of introducing pathogenic bacteria from the milk itself. A staggering proportion of milk-related food-born illness in the U.S. is due to unpasteurized milk. I'd say the chances of that being net-positive as slim, and more importantly I don't think you could slip that study past an IRB - at least in the U.S.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From Nico's question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://wwwnc.cdc.gov/eid/article/18/3/pdfs/11-1370.pdf&quot; rel=&quot;nofollow&quot;&gt;http://wwwnc.cdc.gov/eid/article/18/3/pdfs/11-1370.pdf&lt;/a&gt; Would be a decent place to start. Dairy is, admittedly, responsible for a small number of food born outbreaks overall - various fruits and vegetables, chicken and beef are still the top causes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The issue is in how many outbreaks are caused by raw milk given how little of it is consumed in the U.S. The study I link above looks at known dairy outbreaks from 1993-2006. Of the 121 outbreaks, 60% of them were from unpasturized products, with a ~2 to 1 split between milk and cheese. All of them were caused by bacteria (addressing the idea that it might be a viral pathogen that wouldn't have been deactivated anyway).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem is though that many states prohibit the sale of raw milk products, and its relatively rare. If you weight the incidence of disease according to consumption patterns, one finds that the incidence per unit of dairy consumed is ~150x greater in non-pasturized products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So while the overall numbers are not huge (though far from zero, and I've seen people consider lesser things public health emergencies), for such a rare product it's a big deal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen no suggestion that the patterns in Europe are different. For example (in Finnish) from this year: &lt;a href=&quot;http://www.vsshp.fi/fi/7273/58327/&quot; rel=&quot;nofollow&quot;&gt;http://www.vsshp.fi/fi/7273/58327/&lt;/a&gt; from this summer. But only the really massive outbreaks catch major media attention.&lt;/p&gt;&#xA;" OwnerUserId="67" LastEditorUserId="67" LastEditDate="2012-08-23T16:44:10.667" LastActivityDate="2012-08-23T16:44:10.667" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="3296" PostTypeId="1" AcceptedAnswerId="89250" CreationDate="2012-08-23T08:16:01.610" Score="11" ViewCount="338" Body="&lt;p&gt;I know that parasitic wasp larvae can live for a long time inside their live host (eg. caterpillar), but I always thought that they kill the host when they eventually get out of it. But I've seen a &lt;a href=&quot;http://www.youtube.com/watch?v=vMG-LWyNcAs&quot; rel=&quot;nofollow noreferrer&quot;&gt;film&lt;/a&gt;, where it's shown that not only can a caterpillar survive the emergence of a wasp larva, but also the parasites infect the host with some kind of virus that changes the behaviour of the caterpillar to protect the wasp’s pupa. Is it possible and common among parasitic wasps? What species of wasps and viruses cause such effect?&lt;/p&gt;&#xA;" OwnerUserId="68" LastEditorUserId="22057" LastEditDate="2019-12-16T09:13:36.013" LastActivityDate="2019-12-16T09:13:36.013" Title="Is it possible for a parasitic wasp to alter the behaviour of its host after emerging from it?" Tags="&lt;entomology&gt;&lt;virology&gt;&lt;behaviour&gt;&lt;parasitology&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="3297" PostTypeId="1" AcceptedAnswerId="3298" CreationDate="2012-08-23T09:21:12.113" Score="4" ViewCount="2667" Body="&lt;p&gt;I read somewhere that a mature neuron loses its ability to divide, except for very specific situations. I was unable to find the description of those situations. What are they?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I'm sorry I'm not saying where I read that, but I simply can't find it.)&lt;/p&gt;&#xA;" OwnerUserId="1278" LastActivityDate="2012-09-15T21:20:55.650" Title="Under what circumstances will a human neuron divide?" Tags="&lt;neuroscience&gt;&lt;cell-biology&gt;&lt;mitosis&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3298" PostTypeId="2" ParentId="3297" CreationDate="2012-08-23T11:38:54.863" Score="6" Body="&lt;p&gt;Mature, differentiated neurons do not divide (undergo mitosis), but apparently there is a small population of self-renewing &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10920/&quot; rel=&quot;nofollow&quot;&gt;neural stem cells&lt;/a&gt; in adults that can produce new neurons. &lt;a href=&quot;http://en.wikipedia.org/wiki/Neurogenesis&quot; rel=&quot;nofollow&quot;&gt;Neurogenesis&lt;/a&gt; predominantly occurs in the subventricular and subgranular zones of the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Peripheral nerves can &lt;a href=&quot;http://en.wikipedia.org/wiki/Neuroregeneration&quot; rel=&quot;nofollow&quot;&gt;regenerate&lt;/a&gt; along its axon as long as the endoneurial tube and the Schwann cells are intact. Here's a &lt;a href=&quot;http://chen2820.pbworks.com/w/page/11951452/Biomaterials%20for%20nerve%20regeneration&quot; rel=&quot;nofollow&quot;&gt;picture&lt;/a&gt; of a neuron regenerating.&lt;/p&gt;&#xA;" OwnerUserId="1166" LastEditorUserId="740" LastEditDate="2012-08-24T12:35:26.703" LastActivityDate="2012-08-24T12:35:26.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3299" PostTypeId="1" AcceptedAnswerId="3357" CreationDate="2012-08-23T12:20:46.957" Score="6" ViewCount="3423" Body="&lt;p&gt;Some butterflies, such as the UK native Peacock butterfly (&lt;a href=&quot;https://www.google.co.uk/search?q=butterfly&amp;amp;sugexp=chrome,mod=5&amp;amp;um=1&amp;amp;ie=UTF-8&amp;amp;hl=en&amp;amp;tbm=isch&amp;amp;source=og&amp;amp;sa=N&amp;amp;tab=wi&amp;amp;ei=0B02UP7HLYWa0QXLpoCgCQ&amp;amp;biw=1600&amp;amp;bih=775&amp;amp;sei=0h02UJPQB6KI0AXNwYA4#um=1&amp;amp;hl=en&amp;amp;safe=off&amp;amp;tbm=isch&amp;amp;sa=1&amp;amp;q=peacock%20butterfly&amp;amp;oq=peacock%20butterfly&amp;amp;gs_l=img.3..0l9j0i5.7042.10989.0.11060.24.19.3.2.2.1.277.2983.1j10j6.17.0...0.0...1c.yTA7IQEyKSw&amp;amp;pbx=1&amp;amp;bav=on.2,or.r_gc.r_pw.r_qf.&amp;amp;fp=2434384cfc018328&amp;amp;biw=1600&amp;amp;bih=775&quot;&gt;Google Image Search&lt;/a&gt;) have markings on their wings that look just like eyes, complete with a white fleck to imitate a convex, transparency effect, as though the &quot;eye&quot; is reflecting sunlight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Presumably, this pattern is designed to deter prospective predators, because the predator will see a creature with massive eyes looking at them and think twice before attacking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But how did the pattern evolve?  Was the first one a fluke / a genetic mutation that happened to work, or is there another explanation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For possible bonus points, is there any way of telling when this occurred, and therefore making a guess as to which creature's eye is being imitated?&lt;/p&gt;&#xA;" OwnerUserId="1297" LastActivityDate="2012-08-28T00:10:41.007" Title="How did butterflies evolve to have eyes on their wings?" Tags="&lt;evolution&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3300" PostTypeId="2" ParentId="3299" CreationDate="2012-08-23T13:35:15.947" Score="7" Body="&lt;p&gt;You're correct with the genetic mutation bit. A basic explanation would be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some gene or genes became mutated that lead to the coloration you see, and the end result was that the butterfly or butterflies with the mutated gene were able to produce more offspring or offspring which survived better than the eyeless versions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are ways of dating genetic mutations by comparing one organism's genes to another, but accuracy can be an issue without some significant genomic study to confirm mutation rates and other aspects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the butterfly wouldn't be purposefully imitating another creature's eye. It may be by chance and/or predator behaviors that the eyespots &lt;em&gt;look&lt;/em&gt; like the eyes of another creature, but the adaptation wasn't a willful act. It was a random genetic mutation or mutations that lead to beneficial coloring, and the eyespots may have improved over time as more mutations occurred.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-23T13:35:15.947" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3301" PostTypeId="2" ParentId="3296" CreationDate="2012-08-23T21:48:01.750" Score="6" Body="&lt;p&gt;The species of wasp in the video you link to is &lt;em&gt;Cotesia glomerata&lt;/em&gt;. Furthermore, there is at least one other species, &lt;em&gt;Glyptapanteles&lt;/em&gt;, which parasitizes other caterpillar species in the same way and induces the same behaviour in its host.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure which virus it is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.newscientist.com/article/dn14053-zombie-caterpillars-controlled-by-voodoo-wasps.html?feedId=online-news_rss20&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.newscientist.com/article/dn14053-zombie-caterpillars-controlled-by-voodoo-wasps.html?feedId=online-news_rss20&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible? Of course, you have an example! Though, there is a small caveat. Some of the offspring sacrifice themselves to induce the behavioral change after the rest of the brood has emerged.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it common among parasitic wasps? No. While injecting offspring into host species &lt;em&gt;is&lt;/em&gt; a common theme for parasitic wasps, and while there are a handful which somehow induce behavioral changes in the host animals - continuing the manipulation after leaving the host animal is extremely rare among parasites in general.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="55929" LastEditDate="2019-12-16T08:53:12.033" LastActivityDate="2019-12-16T08:53:12.033" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="3302" PostTypeId="2" ParentId="2683" CreationDate="2012-08-24T11:46:03.300" Score="3" Body="&lt;p&gt;During mitosis the genetic material in the cell is replicated to produce a copy of the genome for each resulting daughter cell. Due to the nature of the process, the ends of the chromosomes are not completely replicated, resulting in a slightly shorter copy of each chromosome after each round of replication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Telomeres&lt;/strong&gt; are extensions to the end of chromosomes that prevent damage or loss of genetic information during cell division. Telomeres are not replaced (in 'normal'/somatic cells), which gives rise to a &lt;em&gt;replicative lifespan&lt;/em&gt;; the number of times a cell can divide before permenantly leaving the cell cycle (known as &lt;em&gt;cellular senescence&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;This is generally viewed as an anti-cancer mechanism to protect against errors creeping in to the genome through many cell divisions. In order to become cancerous, a cell must first overcome its replicative lifespan [&lt;a href=&quot;http://dx.doi.org/10.1093/carcin/bgp268&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref.&lt;/a&gt;]. This is achieved by activating the (normally inactive) &lt;em&gt;telomerase&lt;/em&gt; enzyme that extends the telomeres - embryonic stem cells are one of the few cell types that normally express this enzyme, so they have unlimited replicative potential - a very important trait for stem cells.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;So a rapidly proliferating cell would indeed 'use up' it's telomeres before a different cell type. The cell would then either enter a state of senscence (permenant cell-cycle arrest), or apoptose. There are a lot of factors governing which outcome is realized, but the senscent cell population increases with age, and is proposed to contribute to many aging phenotypes (there is a recent fascinating study published in Nature where the authors remove all the senscent cells from aging mice, and the mice actually get healthier! Can't wait for studies that relate to human aging and senescent cell clearance (&lt;a href=&quot;http://dx.doi.org/10.1038/nature10600&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref.&lt;/a&gt;)).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I have elaborated on the function of telomeres in the context of organismal aging in my answer to &lt;a href=&quot;https://biology.stackexchange.com/questions/2879/are-human-bodies-programmed-to-die/&quot;&gt;this question&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2012-08-24T11:51:27.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3303" PostTypeId="2" ParentId="3246" CreationDate="2012-08-24T13:35:51.660" Score="3" Body="&lt;p&gt;If you had a complex life form which used only DNA or RNA, it would have no way to tell transcribed mXNA from genomic gXNA. This would cause problems during cellar replication, as you could also replicate your mXNA along with your gXNA. It would also cause problems repairing breaks in your gXNA, as you would run the risk of including mXNA during the repair process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore it seems advantageous to have a storage system for information which is not currently being translated into protein (i.e., DNA), as compared to just having RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand a completely DNA organism would need RNA for functional ribosomes anyway. If RNA is being used for ribosomes, using it for mRNA as well to avoid confusion with genomic DNA seems advantageous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to test this hypothesis, you would need to create a completely RNA/DNA based lifeform and investigate its properties. Short of starting life from scratch as RNA based and monitoring its evolution over a few million years, a conclusive proof as to why things are the way they are as opposed to being down to an evolutionary historical accident is difficult to obtain!&lt;/p&gt;&#xA;" OwnerUserId="1300" LastEditorUserId="43" LastEditDate="2012-09-17T13:37:07.753" LastActivityDate="2012-09-17T13:37:07.753" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3304" PostTypeId="1" AcceptedAnswerId="3305" CreationDate="2012-08-24T13:55:58.930" Score="29" ViewCount="6106" Body="&lt;p&gt;Layman here. So I have never really quite understood this facet of human evolution, (or any other for that matter), in that, I understand the evolutionary process, but I get lost on the 'border' cases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, we, as humans, evolved from monkeys, (to use the colloquial term, I am not a biologist by any measure). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, doesn't this mean that at some, discrete point, there had to have been a human, whose parents were not? If that is true, how does that work, in the sense that we now have species1 giving birth to species2. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, then how exactly does this border case work? The only other alternative I see, is that the borders are 'fuzzy', but then that necessarily means that the definition of a species is itself fuzzy, which I understand is not the case. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="816" LastEditorUserId="3952" LastEditDate="2013-08-05T02:09:00.433" LastActivityDate="2016-09-29T09:36:49.907" Title="Human evolution: Where *exactly* did the first human come from, whose parents were not?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;taxonomy&gt;" AnswerCount="7" CommentCount="4" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3305" PostTypeId="2" ParentId="3304" CreationDate="2012-08-24T15:04:59.777" Score="23" Body="&lt;p&gt;Actually, your last paragraph is more the case than not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;There are currently three common definitions for delineating discrete species:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Phenotypically different from related species (looks or acts differently).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Produces viable offspring in the wild.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Some % of genetic difference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;There are strengths to all three:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Very easy to ascertain and measure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Most common conception of a species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Genes control the first two, so genetic divergence gets to the heart of the matter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;There are also weaknesses to all three:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Is notorious for mis-labeling and missing species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Some species which can mate and produce fertile offspring under enclosed conditions do not do so in the wild (Tigers and Lions, for instance).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) The &lt;em&gt;amount&lt;/em&gt; of divergence has, thus far, been completely arbitrary. If there is a certain % or patterns of mutation required in the genome, science hasn't yet discovered it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fuzzy definition of species, combined in the not-exactly-intuitive generational-type thinking required for understanding evolution, and the answer to your question is (at least to the best of my understanding) the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, at some point one of our ancestors gave birth to the first &lt;em&gt;Homo sapien&lt;/em&gt; that was somehow genetically different from its parents. However, the magnitude of the difference is probably not as great as you might think. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We've already observed our closest evolutionary cousins, the Bonobos, making basic tools through flint napping: &lt;a href=&quot;http://www.newscientist.com/article/dn22197-bonobo-genius-makes-stone-tools-like-early-humans-did.html&quot;&gt;http://www.newscientist.com/article/dn22197-bonobo-genius-makes-stone-tools-like-early-humans-did.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also possible that disputes between male chimpanzees are mediated by an older female: &lt;a href=&quot;http://www.cpradr.org/Resources/ALLCPRArticles/tabid/265/ID/121/Primates-and-Me-Web.aspx&quot;&gt;http://www.cpradr.org/Resources/ALLCPRArticles/tabid/265/ID/121/Primates-and-Me-Web.aspx&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And that both Chimpanzees and Capuchin monkeys can be taught the concept of currency (which, somewhat comedically, they then used for prostitution): &lt;a href=&quot;http://www.nytimes.com/2005/06/05/magazine/05FREAK.html?ei=5090&amp;amp;en=af2d9755a2c32ba8&amp;amp;ex=1275624000&amp;amp;partner=rssuserland&amp;amp;emc=rss&amp;amp;adxnnlx=1118160068-1EGJuan4FJH1LooxHYd5/g&amp;amp;pagewanted=all&quot;&gt;http://www.nytimes.com/2005/06/05/magazine/05FREAK.html?ei=5090&amp;amp;en=af2d9755a2c32ba8&amp;amp;ex=1275624000&amp;amp;partner=rssuserland&amp;amp;emc=rss&amp;amp;adxnnlx=1118160068-1EGJuan4FJH1LooxHYd5/g&amp;amp;pagewanted=all&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there's the everlasting impact of Koko, the Silverback Gorilla who was taught - and perfectly capable of replying in - sign language: &lt;a href=&quot;http://en.wikipedia.org/wiki/Koko_%28gorilla%29&quot;&gt;http://en.wikipedia.org/wiki/Koko_%28gorilla%29&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea that humans jumped onto the scene with unforeseen amounts of intelligence and capability probably isn't what happened. Obviously we are capable of constructing and using the most advanced tools on the planet, but this is after several thousand generations of innovation. The very first human might have been more intelligent (or at least had the capacity to be), but otherwise probably fit in pretty well with its parents and other relatives since the &lt;em&gt;vast majority&lt;/em&gt; of what we learn comes from our parents and personal experience.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then over time the number of individuals with the capacity for higher modes of thinking increased as a result of the genetic inheritance of whatever mutation created the first human. The first human, to put it simply, was successfully able to pass on their mutation which gave them our unique traits, and their offspring were also successful - until you have an entire population of humans living amongst each other. Eventually our innovative capacity lead, step by step, to our dominant position on the planet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even now humans are yet evolving. Lactose tolerance (the ability to consume dairy products after childhood) is a &lt;em&gt;very&lt;/em&gt; new trait among humans (and unprecedented among all mammals) only a few hundred generations old (roughly 10,000 years) that evolved &lt;strong&gt;twice&lt;/strong&gt; in separate populations of humans (North Africa and Northern Europe). Our jaws are getting progressively smaller (which is why some people have to remove their wisdom teeth to maintain a straight smile - and some people don't have wisdom teeth at all), some muscles are disappearing (the Palmaris Longus is one example - it's present in about 80% of humans), and other subtle changes are occurring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just don't make the mistake of equating &quot;evolved&quot; with &quot;superior.&quot; Evolution is dictated by the ever-changing demands of the environments we find ourselves in, and what's beneficial today isn't guaranteed to be beneficial forever. &lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2012-08-24T15:11:08.817" LastActivityDate="2012-08-24T15:11:08.817" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="3306" PostTypeId="2" ParentId="3304" CreationDate="2012-08-24T16:25:46.747" Score="36" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;but I get lost on the 'border' cases.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not surprisingly, since there are no borders, and this is probably the greatest misunderstanding: Evolution is gradual. It’s not generally possible to say where a complex feature (or a species) starts and another one ends. We &lt;em&gt;could&lt;/em&gt; in theory say, for individual mutations on the genetic level, in which generation they first occurred, or when they became fixed in the population. But we cannot infer from these atomic changes where our ancestors started becoming humans. So the whole concept of “first human” is not biologically meaningful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best analogy remains a gradient between two colours. Going from the left, where does blue end and red start?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3ltqb.png&quot; alt=&quot;Colour gradient&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, you spotted this very well by yourself:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[if there is no first human] then that necessarily means that the definition of a species is itself fuzzy&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Exactly, that’s the case. For more details on definitions of species, refer to MCM’s answer. But it’s indeed crucial to note that the definition of species (or any other biological classification) is an ever-changing approximation which tries to fit a definitive yes/no answer onto a gradually changing scale.&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="166" LastEditDate="2013-01-28T10:19:02.913" LastActivityDate="2013-01-28T10:19:02.913" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="3307" PostTypeId="2" ParentId="378" CreationDate="2012-08-24T16:29:11.047" Score="2" Body="&lt;p&gt;If you look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Adaptive_immune_system&quot; rel=&quot;nofollow&quot;&gt;the adaptive immune system&lt;/a&gt;, the process of &lt;a href=&quot;http://en.wikipedia.org/wiki/V%28D%29J_recombination&quot; rel=&quot;nofollow&quot;&gt;B-cell recombination&lt;/a&gt;, clonal expansion and &lt;a href=&quot;http://en.wikipedia.org/wiki/Somatic_hypermutation&quot; rel=&quot;nofollow&quot;&gt;somatic hypermuation&lt;/a&gt; is, in essence, induced evolution.&lt;/p&gt;&#xA;" OwnerUserId="1300" LastActivityDate="2012-08-24T16:29:11.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3308" PostTypeId="1" AcceptedAnswerId="3309" CreationDate="2012-08-24T19:58:41.930" Score="0" ViewCount="3033" Body="&lt;p&gt;At school we were told on scale of 0 through 1000 the animal kingdom ranges from amoeba the simplest/primitive being at 0, and Humans the most complex animals at 1000; what are the equivalent complexity species (?) in the plant kingdom? What is the least complex plant, and the most complex?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2012-08-26T22:29:53.580" Title="What is the most complex plant form?" Tags="&lt;taxonomy&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3309" PostTypeId="2" ParentId="3308" CreationDate="2012-08-24T23:52:47.247" Score="14" Body="&lt;p&gt;That whole thing of being more complex is non-sense, you can't say that for animals and you can't say that for plants either. It all depends on how you look at it. Average number of cells? Size of genome? Size of the proteome? Adaptability to different environments? Mental abilities? You can't place human on the top of any of them (maybe we could argue about if you define it as mental abilities but that doesn't sound right) and you can't place amoeba at the bottom either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, if you look at a phylogenetic tree, an organism is also not more complex by the number of nodes it has behind them (I've seen people thinking this means more evolved and associate that with more complex).&lt;/p&gt;&#xA;" OwnerUserId="1303" LastActivityDate="2012-08-24T23:52:47.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3310" PostTypeId="1" CreationDate="2012-08-25T04:47:48.320" Score="7" ViewCount="225" Body="&lt;p&gt;When I was investigating the differences between protein structures obtained by X-ray crystallography and NMR spectroscopy, I found the paper [1] compairing structures of several proteins resolved both with X-ray and NMR. The average root-mean-square deviation (RMSD) between NMR and Xray structures is 1.4Å (max. 3.6Å), and the average RMSD between different NMR structures for same protein is 0.4Å (max. 1.3Å). I've checked some proteins studied in this paper, and they are mostly within 100–200 residues long.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are plenty of papers (e.g. [2], [3], dealing with similarly sized proteins) that base their statements about conformational transitions on structures with RMSD difference 1–2Å.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder what is considered reliable RMSD between two structures to draw any solid conlusions about conformational transitions (e.g. upon ligand binding) as opposed to simple thermal fluctuations or perturbance caused by the method to obtain structure?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, the best way (at least in my opinion) to distinguish actual conformational transition from thermal fluctuations is to measure its lifetime, but it is often not an option.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1002/prot.21507&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Andrec M, Snyder DA, Zhou Z, Young J, Montelione GT, Levy RM&lt;/strong&gt;. 2007. A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Proteins 69: 449–65.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1371/journal.pcbi.1000325&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Grant BJ, Gorfe AA, McCammon JA&lt;/strong&gt;. 2009. Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Computational Biology 5(3): e1000325.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.jmb.2010.03.011&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Kumaraswami M, Newberry KJ, Brennan RG&lt;/strong&gt;. 2010. Conformational plasticity of the coiled-coil domain of BmrR is required for bmr operator binding: the structure of unliganded BmrR. Journal of Molecular Biology 398: 264–75.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="836" LastEditorUserId="6307" LastEditDate="2017-04-02T20:10:20.077" LastActivityDate="2018-02-06T12:40:16.937" Title="RMSD during conformational transition in proteins" Tags="&lt;structural-biology&gt;&lt;xray-crystallography&gt;&lt;spectroscopy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3311" PostTypeId="2" ParentId="3304" CreationDate="2012-08-25T06:41:17.050" Score="1" Body="&lt;p&gt;While the definition of species certainly is fuzzy, the process of species generation is easily defined: &lt;strong&gt;migration&lt;/strong&gt; of a population part leads to two &lt;strong&gt;geographically isolated gene pools&lt;/strong&gt; which do not communicate genetic information. Both pools will, through &lt;strong&gt;genetic drift&lt;/strong&gt; (mutations/inserts/deletions), develop away from each other to the point that, if they were to meet again, they could no longer produce offspring with each other. Voilà, a new species.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-08-25T06:41:17.050" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3312" PostTypeId="2" ParentId="3279" CreationDate="2012-08-25T10:02:40.867" Score="4" Body="&lt;p&gt;At the interface of the stack gel and resolving gel is a pH change and a change in gel density.  If you feel certain that your protein is not crosslinking so much that it can not enter the gel than I would think about the pH of the sample and the effect of Cu ions on the stacking effect of the stacingk gel.  Is your sample the normal blue color (indication of pH) when you load it (compared to other samples you load)?  Are you overloading the gel?  I have seen overloading cause the effect you describe because the proteins get concentrated to a very high degree before entering the resolving gel.  Could the Cu ions be affecting stacking itself?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Read &lt;a href=&quot;http://en.wikipedia.org/wiki/SDS-PAGE&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/SDS-PAGE&lt;/a&gt;.  Specifically the section on buffer systems.  You might want to try a different buffer system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, you could try an acetone precipitation to try to remove the Cu ions and other chemical and see if that helps.&lt;/p&gt;&#xA;" OwnerUserId="1305" LastActivityDate="2012-08-25T10:02:40.867" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3313" PostTypeId="2" ParentId="3304" CreationDate="2012-08-25T12:41:10.387" Score="6" Body="&lt;p&gt;I'd just like to expand on Konrad and MCM's answers. If I understand you correctly, your main question is &quot;what were the 1st human's parents&quot;. You cannot really get an answer to that because the question itself is wrong. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea that evolution moves in discrete bounds, that is that &lt;a href=&quot;https://en.wikipedia.org/wiki/Speciation&quot; rel=&quot;nofollow&quot;&gt;speciation&lt;/a&gt; occurs suddenly, from one generation to the next (also known as &lt;a href=&quot;https://en.wikipedia.org/wiki/Lamarckism&quot; rel=&quot;nofollow&quot;&gt;Lamarckian evolution&lt;/a&gt;) has been abandoned years ago. That is simply not how evolution works (our modern knowledge of &lt;a href=&quot;https://en.wikipedia.org/wiki/Epigenetics&quot; rel=&quot;nofollow&quot;&gt;epigenetics&lt;/a&gt; notwithstanding). The color analogy given by Konrad is indeed a good one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, there was never an individual 'proto human'. This is also the case for all other species. What you &lt;em&gt;do&lt;/em&gt; get, usually, is that a change in a species' environment (e.g. temperature, atmospheric pH, the introduction of a new predator etc) causes a particular mutation, or set of mutations, to become advantageous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One has to remember that a &lt;a href=&quot;https://en.wikipedia.org/wiki/Genome&quot; rel=&quot;nofollow&quot;&gt;genome&lt;/a&gt; (an organism's genetic material, their DNA) is &lt;em&gt;not&lt;/em&gt; stable. It is in fact extremely dynamic and constantly undergoing mutational changes. Most of these mutations are neutral, they do not affect the organism in any way. However, when an external change such as I mentioned before occurs, some of these mutations may become advantageous. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine a random mutation that causes an individual of a species to be more resistant to cold. If this occurs at the beginning of an ice age, that individual is more likely to reproduce, passing the mutation to its offspring. Over time, since the mutation-carriers are likelier to survive and reproduce, this mutation will spread across the population and become &quot;fixed&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At some point these changes accumulate past a certain &lt;em&gt;indefinable&lt;/em&gt; point and we call a speciation event. This does not occur at the &lt;em&gt;individual&lt;/em&gt; but at the &lt;em&gt;species&lt;/em&gt; level. A good analogy here is the &lt;a href=&quot;https://en.wikipedia.org/wiki/Sorites_paradox&quot; rel=&quot;nofollow&quot;&gt;sorites paradox&lt;/a&gt;. How many stones does it take to make a pile?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to sum up, &lt;strong&gt;humans did not evolve &lt;em&gt;from&lt;/em&gt; monkeys&lt;/strong&gt;. Humans &lt;em&gt;and&lt;/em&gt; monkeys at some point shared a common ancestor. Then, over a long time period, successive changes caused the two species to diverge. That is not the same thing. The linear concept of evolution that has one species morphing into the next is one of the greatest misrepresentations of a scientific concept ever perpetrated by the media and inflicted upon the unsuspecting public.  &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-08-05T01:31:58.760" LastActivityDate="2013-08-05T01:31:58.760" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="3314" PostTypeId="2" ParentId="3304" CreationDate="2012-08-25T14:32:22.883" Score="5" Body="&lt;p&gt;There are a lot of good answers here, but let me try to streamline things a bit: @Konrad's analogy to the color spectrum is spot on - where does red begin in that spectrum? This is essentially your question - where in the continuum of generations does the &lt;em&gt;Homo sapiens&lt;/em&gt; species begin?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just like our definition of color is imprecise (we usually can identify bright red and deep blue, but we cannot be sure about the shades in between), our definition of species is imprecise. We can identify a modern human and we could identify a far ancestor as such, but if we were presented with somebody from an intermediate generation, we could not confidently say if they are &lt;em&gt;Homo sapiens&lt;/em&gt; or not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We could, arbitrarily, point to a particular individual and say it was the first human, but it would not have any scientific meaning.&lt;/p&gt;&#xA;" OwnerUserId="1307" LastEditorUserId="43" LastEditDate="2012-09-17T15:04:59.270" LastActivityDate="2012-09-17T15:04:59.270" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3315" PostTypeId="1" AcceptedAnswerId="3317" CreationDate="2012-08-26T03:53:55.960" Score="4" ViewCount="21915" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hijra_%28South_Asia%29&quot; rel=&quot;nofollow&quot;&gt;Hijra&lt;/a&gt; are people who have a penis (not sure if sexually active) but look much like a female (perhaps for some feminine biological property). Wikipedia says they are &lt;em&gt;&quot;physiological males who have feminine gender identity&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I just came to know there are some more types of &lt;a href=&quot;http://en.wikipedia.org/wiki/Third_gender&quot; rel=&quot;nofollow&quot;&gt;third gender&lt;/a&gt; people.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, &lt;strong&gt;is there really any &lt;em&gt;BIOLOGICAL&lt;/em&gt; third gender&lt;/strong&gt; which cannot be categorized as male or female? Or its always possible to categorize them to male or female?&lt;/p&gt;&#xA;" OwnerUserId="1308" LastEditorUserId="43" LastEditDate="2012-08-27T13:48:24.627" LastActivityDate="2015-09-08T14:37:05.140" Title="Can the third sex be categorized as Male or Female?" Tags="&lt;genetics&gt;&lt;reproduction&gt;&lt;terminology&gt;" AnswerCount="5" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3317" PostTypeId="2" ParentId="3315" CreationDate="2012-08-26T05:30:37.970" Score="21" Body="&lt;p&gt;When dealing with &lt;em&gt;humans&lt;/em&gt;, there are only two &lt;strong&gt;Biological&lt;/strong&gt; genders as defined by the presence or absence of the Y-Chromosome. If the Y-Chromosome is not present, or through some process gets totally deactivated, the human will appear and function as a Female.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;XX = Female&lt;/p&gt;&#xA;&#xA;&lt;p&gt;XY = Male&lt;/p&gt;&#xA;&#xA;&lt;p&gt;XXY = Male (Klinefelter's Syndrome)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;XYY = Male (Aneuploidy - Normal Functioning Males)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;XXX = Female (Aneuploidy - Normal Functioning Females)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;X = Female (Turner's Syndrome - Generally infertile, other issues)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Y = Fatal (The Y-Chromosome is drastically smaller than the X-Chromosome, which contains many &lt;em&gt;necessary&lt;/em&gt; genes)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;XXYY = Male&lt;/p&gt;&#xA;&#xA;&lt;p&gt;...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The list goes on, since there have been records of up to XXXXX.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is a Y-Chromosome present, the human born will be male.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, that is not to say that a person cannot &lt;strong&gt;psychologically&lt;/strong&gt; identify as something else. It's also worth noting that the majority of known species are asexual and do not have genders, and that those which do have genders do not always follow the same rules (Fruit Flies, for instance, use the &lt;em&gt;ratio&lt;/em&gt; of genes to determine sex).&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-26T05:30:37.970" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3318" PostTypeId="2" ParentId="3315" CreationDate="2012-08-26T05:38:40.967" Score="0" Body="&lt;p&gt;As I read the Wikipedia article you reference, its useful to remember that conventional chromosomal definitions of gender, the genitals are soft tissue which has many recorded morphological abnormalities.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Hermaphrodite#Humans&quot; rel=&quot;nofollow&quot;&gt;hermaphrodites&lt;/a&gt; and a &lt;a href=&quot;http://en.wikipedia.org/wiki/Intersex&quot; rel=&quot;nofollow&quot;&gt;spectrum of tissue shapes do occur&lt;/a&gt; to the extent that the conventional gender identity is not acceptable.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Physiological definition of gender, despite the chromosomes do need to be medically and socially addressed.  I am not sure that all these 'intersex' people really should be grouped into a single 'third sex', but some way of recognizing their essential human rights should be out there in my opinion. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-08-26T05:38:40.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3319" PostTypeId="1" AcceptedAnswerId="3322" CreationDate="2012-08-26T12:00:10.763" Score="3" ViewCount="237" Body="&lt;p&gt;I asked a &lt;a href=&quot;https://biology.stackexchange.com/q/3315/1308&quot;&gt;question&lt;/a&gt; related to the third sex, and I came to know that its always possible to categorize a human to male or female with presence of Y chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I have another question. Is there a way to say if someone has Y chromosome &lt;strong&gt;only with external physical test&lt;/strong&gt;? More specifically:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Someone has a penis, can we say that s/he will have Y chromosome?&lt;/li&gt;&#xA;&lt;li&gt;Some one has Y chromosome, can we say that he will have a penis?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1308" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-05-06T11:13:35.947" Title="Is it possible to correctly identify presence of Y chromosome with external physical test only?" Tags="&lt;human-biology&gt;&lt;chromosome&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3320" PostTypeId="1" CreationDate="2012-08-26T12:55:02.467" Score="3" ViewCount="128" Body="&lt;p&gt;As a plant grows, at some point the first branch forms. As it continues, branches grow new branches, and so on, in a seemingly random way. Is it random, or is it driven by the environment (heat or cold, sunshine, wind)? Or is it somehow defined in the plant's DNA, that each branch will grow at in such and such a direction, at such and such a time?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this generalize down to successively smaller branches, and eventually leaves?&lt;/p&gt;&#xA;" OwnerUserId="1313" LastEditorUserId="43" LastEditDate="2012-09-16T02:23:59.110" LastActivityDate="2012-09-16T02:23:59.110" Title="How does a plant decide when to grow a branch?" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2013-09-26T12:24:24.863" ContentLicense="CC BY-SA 3.0" />
  <row Id="3322" PostTypeId="2" ParentId="3319" CreationDate="2012-08-26T13:41:06.483" Score="7" Body="&lt;p&gt;No, an external physical examination would be inconclusive. The reason is the TDF&#xA;gene. To be more specific, if a person has XY and the gene is not active then the subject&#xA;would have a female appearance. Also we cannot conclude that a person has a Y&#xA;chromosome even if it has penis because that gene could be transferred on the X chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a reference: &lt;a href=&quot;http://en.wikipedia.org/wiki/Testis_determining_factor&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Testis_determining_factor&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1304" LastEditorUserId="43" LastEditDate="2012-09-17T13:42:29.357" LastActivityDate="2012-09-17T13:42:29.357" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3323" PostTypeId="2" ParentId="3304" CreationDate="2012-08-26T14:06:34.907" Score="16" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://books.google.com.tr/books?id=rR9XPnaqvCMC&amp;amp;pg=PA308&amp;amp;lpg=PA308&amp;amp;dq=Ernst%20Mayr,%20distinguished%20elder%20statesman%20of%20twentieth-century%20evolution,%20has%20blamed%20the%20delusion%20of%20discontinuity%20%E2%80%94%20under%20its%20philosophical%20name%20of%20Essentialism%20%E2%80%94%20as%20the%20main%20reason%20why%20evolutionary%20understanding%20came%20so%20late%20in%20human%20history.&amp;amp;source=bl&amp;amp;ots=4QD7rcrxpk&amp;amp;sig=8AaXVIAvov9aDk4jKtIuSZTxQwk&amp;amp;hl=tr&amp;amp;redir_esc=y#v=onepage&amp;amp;q=Ernst%20Mayr,%20distinguished%20elder%20statesman%20of%20twentieth-century%20evolution,%20has%20blamed%20the%20delusion%20of%20discontinuity%20%E2%80%94%20under%20its%20philosophical%20name%20of%20Essentialism%20%E2%80%94%20as%20the%20main%20reason%20why%20evolutionary%20understanding%20came%20so%20late%20in%20human%20history.&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ernst Mayr, distinguished elder statesman of twentieth-century&#xA;  evolution, has blamed the delusion of discontinuity — under its&#xA;  philosophical name of Essentialism — as the main reason why&#xA;  evolutionary understanding came so late in human history.&lt;/a&gt; Plato, whose&#xA;  philosophy can be seen as the inspiration for Essentialism, believed&#xA;  that actual things are imperfect versions of an ideal archetype of&#xA;  their kind. Hanging somewhere in ideal space is an essential, perfect&#xA;  rabbit, which bears the same relation to a real rabbit as a&#xA;  mathematician’s perfect circle bears to a circle drawn in the dust. To&#xA;  this day many people are deeply imbued with the idea that sheep are&#xA;  sheep and goats are goats, and no species can ever give rise to&#xA;  another because to do so they’d have to change their ‘essence’.&#xA;  There is no such thing as essence.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;h2&gt;&lt;img src=&quot;https://i.stack.imgur.com/OGqvi.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/h2&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://books.google.com.tr/books?id=rR9XPnaqvCMC&amp;amp;pg=PA310&amp;amp;lpg=PA310&amp;amp;dq=Actually%20it%20isn%E2%80%99t%20paradoxical%20to%20anybody%20but%20a%20dyed-in-the-wool%20essentialist.%20It%20is%20no%20more%20paradoxical%20than%20the%20statement%20that%20there%20is%20never%20a%20moment%20when%20a%20growing%20child%20ceases%20to%20be%20short%20and%20becomes%20tall.%20Or%20a%20kettle%20ceases%20to%20be%20cold%20and%20becomes%20hot.&amp;amp;source=bl&amp;amp;ots=4QD7rcrwlj&amp;amp;sig=bPXlGriqB6ne6cDjHt0eK31X66A&amp;amp;hl=tr&amp;amp;redir_esc=y#v=onepage&amp;amp;q=Actually%20it%20isn%E2%80%99t%20paradoxical%20to%20anybody%20but%20a%20dyed-in-the-wool%20essentialist.%20It%20is%20no%20more%20paradoxical%20than%20the%20statement%20that%20there%20is%20never%20a%20moment%20when%20a%20growing%20child%20ceases%20to%20be%20short%20and%20becomes%20tall.%20Or%20a%20kettle%20ceases%20to%20be%20cold%20and%20becomes%20hot.&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;The barrier would not come suddenly.&lt;/a&gt; There would never be a generation&#xA;  in which it made sense to say of an individual that he is Homo sapiens&#xA;  but his parents are Homo erectus. You can think of it as a paradox if&#xA;  you like, but there is no reason to think that any child was ever a&#xA;  member of a different species from its parents, even though the daisy&#xA;  chain of parents and children stretches back from humans to fish and&#xA;  beyond. &lt;strong&gt;&lt;em&gt;Actually it isn’t paradoxical to anybody but a&#xA;  dyed-in-the-wool essentialist. It is no more paradoxical than the&#xA;  statement that there is never a moment when a growing child ceases to&#xA;  be short and becomes tall. Or a kettle ceases to be cold and becomes&#xA;  hot.&lt;/em&gt;&lt;/strong&gt; The legal mind may find it necessary to impose a barrier&#xA;  between childhood and majority — the stroke of midnight on the&#xA;  eighteenth birthday, or whenever it is. But anyone can see that it is&#xA;  a (necessary for some purposes) fiction. If only more people could see&#xA;  that the same applies to when, say, a developing embryo becomes&#xA;  ‘human’.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://t.co/RR0L23ld&quot;&gt;The Ancestor’s Tale&lt;/a&gt; &lt;a href=&quot;http://www.youtube.com/watch?v=j4ClZROoyNM&amp;amp;feature=player_embedded&quot; rel=&quot;nofollow noreferrer&quot;&gt;Richard Dawkins&lt;/a&gt;, &lt;/p&gt;&#xA;" OwnerUserId="1265" LastEditorUserId="1265" LastEditDate="2012-08-26T15:46:20.147" LastActivityDate="2012-08-26T15:46:20.147" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3325" PostTypeId="1" AcceptedAnswerId="3340" CreationDate="2012-08-26T15:52:00.827" Score="16" ViewCount="2529" Body="&lt;p&gt;Some time ago, I read James Gleick's &quot;Genius: The Life and Science of Richard Feynman&quot;, a wonderful biography of &lt;a href=&quot;https://en.wikipedia.org/wiki/Richard_Feynman&quot; rel=&quot;noreferrer&quot;&gt;Feynman&lt;/a&gt; and, by extension, most of modern physics.&#xA;In this book, the author mentions that Feynman spent a year working in a biology lab and that during that year he made an important discovery.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I remember that when reading the book as an undergraduate biology student, I knew the discovery in question well enough to be immensely impressed that it had been discovered by someone foreign to the field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, I no longer have the book and cannot remember what that discovery was. Does anyone know?&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-03-08T02:33:39.223" LastActivityDate="2014-03-08T03:17:39.380" Title="What did Richard Feynman contribute to molecular biology?" Tags="&lt;molecular-biology&gt;&lt;history&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3326" PostTypeId="2" ParentId="3134" CreationDate="2012-08-26T16:24:49.650" Score="3" Body="&lt;p&gt;Yes. The scientist could cut a small piece of the octopus's tentacle and perform the experiment again. If the same result is observed, no other organs are involved.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2012-08-26T16:24:49.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3327" PostTypeId="1" CreationDate="2012-08-26T19:35:19.567" Score="24" ViewCount="58798" Body="&lt;p&gt;How many human cells are there in our body, on average?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Human_microbiome&quot;&gt;Wikipedia&lt;/a&gt; says 10&lt;sup&gt;13&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bacterial cells are much smaller than human cells, and there are at least ten times as many bacteria as human cells in the body (approximately 10&lt;sup&gt;14&lt;/sup&gt; versus 10&lt;sup&gt;13&lt;/sup&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.nobelprize.org/nobel_prizes/medicine/laureates/2001/press.html&quot;&gt;Nobel site&lt;/a&gt; says 10&lt;sup&gt;14&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An adult human being has approximately 100 000 billion cells, all originating from a single cell, the fertilized egg cell.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://hypertextbook.com/facts/1998/StevenChen.shtml&quot;&gt;Physics fact book&lt;/a&gt; insists it's 10&lt;sup&gt;13&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(length of 1 bp)(number of bp per cell)(number of cells in the body)&lt;br&gt;&#xA;  (0.34 × 10&lt;sup&gt;-9&lt;/sup&gt; m)(6 × 10&lt;sup&gt;9&lt;/sup&gt;)(10&lt;sup&gt;13&lt;/sup&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Finally, &lt;a href=&quot;https://www.wolframalpha.com/input/?i=number+of+cells+in+body&quot;&gt;Wolfram Alpha&lt;/a&gt; gives 1.0 &amp;times; 10&lt;sup&gt;14&lt;/sup&gt; as fact:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Estimated number of eukaryotic (human) cells in the human body: 1.0×10&lt;sup&gt;14&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am quite confused: &lt;em&gt;who is right here?&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1315" LastActivityDate="2015-11-16T22:19:41.647" Title="How many human cells are there in our body, on average?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3328" PostTypeId="1" CreationDate="2012-08-26T20:28:40.763" Score="5" ViewCount="2402" Body="&lt;p&gt;Some actions, almost behaviour, exist that are common across a species. For instance, based on personal observation, human babies try to taste anything new they encounter until they are a few score months old. Similarly most dogs will go round-and-round before they finally settle down to sleep. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We probably use the term 'instinctive' to indicate there is no conscious thought behind that action, albeit the action is not a reflex either. Anyway, what causes instinctive behaviour? Is it genetic in nature? Are there some basic rules/behaviour hard-coded into our brains sort of like BIOS in a computer? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2013-05-29T13:29:52.943" Title="What causes instinctive behaviour?" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3329" PostTypeId="2" ParentId="3327" CreationDate="2012-08-26T20:42:27.613" Score="10" Body="&lt;p&gt;In Mike Lynch's &lt;a href=&quot;http://www.sinauer.com/detail.php?id=4843&quot;&gt;&quot;The Origins of Genome Architecture&quot;&lt;/a&gt;, he claims 10^13.  I forget the primary source he cited, and since the book is in my office I can't check it now. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;** Found the snippet that contained the reference.  I think it's really worth including in its entirety.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A crude estimate of the amount of DNA within currently living&#xA;  organisms can be made by noting that the length spanned by one base of&#xA;  DNA is ~0.3x10^-12 km (Cook 2001).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The number of viral particles in the open oceans is ~10^30 (Suttle&#xA;  2005).  Assuming that there are twice as many viruses on land and in&#xA;  fresh water does not change the global estimate very much at the&#xA;  order-of-magnitude level.  Thus, assuming an average viral genome size&#xA;  of 10^4 bp, the total length of viral DNA if all chromosomes were&#xA;  linearized and placed end to end is ~10^22 km.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The estimated global number of prokaryotic cells is ~10^30 (Whitman et&#xA;  al. 1998), and assuming an average prokaryotic genome size of 3x10^6&#xA;  bp yields an estimated total DNA length of 10^24 km.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;With a total population size of 6x10^9 individuals, 10^13 cells per&#xA;  individual (Baserga 1985), and a diploid genome size of 6x10^9 bp, the&#xA;  amount of DNA occupied by the human population is ~10^20 km.  Assuming&#xA;  there are ~10^7 species of eukaryotes on Earth (~6 times the number&#xA;  that have actually been identified), that the average eukaryotic&#xA;  genome size is ~1% of humans, and that all species occupy&#xA;  approximately the same amount of total biomass, total eukaryotic DNA&#xA;  is ~10^5 times that for humans, or ~10^25 km.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Given the very approximate nature of these calculations, any one of&#xA;  these estimates could be off by one or two orders of magnitude, but it&#xA;  is difficult to escape the conclusion that the total amount of DNA in&#xA;  living organisms is on the order of 10^25 km, which is equivalent to a&#xA;  distance of 10^12 light years, or 10 times the diameter of the known&#xA;  universe.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1210" LastEditorUserId="-1" LastEditDate="2012-08-26T21:33:05.090" LastActivityDate="2012-08-26T21:33:05.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3330" PostTypeId="2" ParentId="3308" CreationDate="2012-08-26T22:29:53.580" Score="0" Body="&lt;p&gt;The venus fly trap would certainly appear one of the most complex plants.&#xA;The plant almost 'bridges' a lifeform gap.&lt;/p&gt;&#xA;" OwnerUserId="1310" LastActivityDate="2012-08-26T22:29:53.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3332" PostTypeId="2" ParentId="3299" CreationDate="2012-08-26T22:54:24.550" Score="-2" Body="&lt;p&gt;I read above ;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;''Some gene or genes became mutated that lead to the coloration you see, and the end result was that the butterfly or butterflies with the mutated gene were able to produce more offspring or offspring which survived better than the eyeless versions.''&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, for the genes to mutate randomly, an eye would not form, but a mess.&#xA;Further,  how strange it is, that neither the butteryfly nor the genes are able to see this manifestation. Yet any preditors, from above sees it clearly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To apply that this random mutation and natural selection, makes up everything that we know, is in itself blind and calls for an eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will state, it is positive variation and nothing more nothing less.&#xA;No lifeform goes downhill in terms of evolution. Random anything would render any 'random' lifeform , lifeless.&lt;/p&gt;&#xA;" OwnerUserId="1310" LastActivityDate="2012-08-26T22:54:24.550" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="3333" PostTypeId="1" CreationDate="2012-08-26T22:59:27.130" Score="4" ViewCount="3950" Body="&lt;p&gt;The definition of an organism Wikipedia gives is&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An organism is any contiguous living system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I understand that these are not organisms according to this definition:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A bird and a tree it's perching on are living and contiguous, but they don't form a system.&lt;/li&gt;&#xA;&lt;li&gt;All humans are living and form a system, but they are not contiguous.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;But some things are unclear to me. My veins and my skin are contiguous and living. Do they form a system? I think so, at least according to what I read about systems in Wikipedia. They are definitely interconnected; they have behavior; and I believe they have structure, though I'm not really sure what structure is. Perhaps if we carefully define what we want &quot;structure&quot; to mean, we can save the definition from allowing (skin + veins) to be an organism?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is (mother + her unborn child) an organism? I think it definitely is according to the definition. Is the unborn child an organism? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is an apple that's just fallen off a tree an organism? Was it an organism before it fell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is (human + their microbiome) an organism? Is a human without the microbiome an organism? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the part of the definition that the least clear to me is the word &quot;system&quot;, and in the definition of the word &quot;system&quot;, it's the word &quot;structure&quot;.&lt;/p&gt;&#xA;" OwnerUserId="1278" LastEditorUserId="16651" LastEditDate="2015-12-13T13:35:30.353" LastActivityDate="2015-12-13T15:18:23.083" Title="What is an organism?" Tags="&lt;definitions&gt;&lt;microbiome&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3334" PostTypeId="2" ParentId="3333" CreationDate="2012-08-27T01:08:24.537" Score="0" Body="&lt;p&gt;I believe you are using the incorrect definition of &quot;Contigous.&quot; The most common usage is basically &quot;sharing a border,&quot; but it can also be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-touching or connected throughout in an unbroken sequence contiguous row of houses&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.merriam-webster.com/dictionary/contiguous&quot; rel=&quot;nofollow&quot;&gt;http://www.merriam-webster.com/dictionary/contiguous&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You also need to include the part about what defines &quot;living&quot;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;... can react to stimuli, reproduce, grow, and maintain homeostasis.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your organs form a system, which results in you. A mother and her unborn child could also be considered an organism under this definition. The apple would not, nor would the tree and bird combination. &lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-27T01:08:24.537" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3335" PostTypeId="1" AcceptedAnswerId="3338" CreationDate="2012-08-27T02:01:53.417" Score="2" ViewCount="154" Body="&lt;p&gt;I'm looking at this link : &lt;a href=&quot;http://en.wikipedia.org/wiki/Homocysteine#Neuropsychiatric_illness&quot; rel=&quot;nofollow&quot;&gt;Homocysteine and cognitive impairments&lt;/a&gt; and &lt;strong&gt;am looking for more information on specific cognitive impairments associated with elevated levels Homocysteine&lt;/strong&gt;. That article is not very clear on that point. I've seen some research papers about the study of this in elderly people and cardiovascular studies. I'm interested in average adults.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been fascinated with the effect/lack of thereof of vitamin B6 on dreaming and Homocysteine is the first thing that I've stumbled upon in quite some time that is directly related to the B family of vitamins. &lt;strong&gt;Has there been any research about what Homocysteine gets metabolized to if exposed to B-Complex vitamins versus Vitamin B6 alone?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input! &lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-08-27T04:37:32.710" Title="What is the role of Homocysteine in cognitive function?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;amino-acids&gt;&lt;vitamins&gt;&lt;homocysteine&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3336" PostTypeId="2" ParentId="3319" CreationDate="2012-08-27T03:22:34.597" Score="3" Body="&lt;p&gt;An interesting condition is &lt;a href=&quot;http://en.wikipedia.org/wiki/Androgen_insensitivity_syndrome&quot; rel=&quot;nofollow&quot;&gt;androgen insentivity syndrome&lt;/a&gt;. In AIS, the body is unable to respond to androgens, the male sex hormone, of which testosterone is the best known. The most common cause is a defective androgen receptor, and most of these diseases are X-linked. In extreme cases, &lt;a href=&quot;http://en.wikipedia.org/wiki/Complete_androgen_insensitivity_syndrome&quot; rel=&quot;nofollow&quot;&gt;complete androgen insensitivy syndrome (CAIS)&lt;/a&gt; can occur. Genetic males (XY) with CAIS appear outwardly as females due to the lack of androgens that would normally lead to masculinzation. However, the SRY gene (sex-determining region Y) that encodes TDF still causes testes to develop, although they are usually internal. Individuals with CAIS generally identify as females.&lt;/p&gt;&#xA;" OwnerUserId="1166" LastActivityDate="2012-08-27T03:22:34.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3337" PostTypeId="2" ParentId="3315" CreationDate="2012-08-27T03:59:34.457" Score="18" Body="&lt;p&gt;I think you might be confusing &lt;em&gt;sex&lt;/em&gt; and &lt;em&gt;gender&lt;/em&gt;. The terms are often used interchangeably, but strictly speaking, they have different biological meanings. &lt;a href=&quot;http://en.wikipedia.org/wiki/Sex&quot;&gt;Sex&lt;/a&gt; refers to the biological categorization based on genetics, reproductive organs, or similar things, whereas &lt;a href=&quot;http://en.wikipedia.org/wiki/Gender&quot;&gt;gender&lt;/a&gt; is based on social identity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For humans, there are only two sex chromosomes, X and Y, and they determine the male and female sexes. But there are many situations that don't fall under the XX/XY categorization, and people with these conditions are usually referred to as &lt;a href=&quot;http://en.wikipedia.org/wiki/Intersex&quot;&gt;intersex&lt;/a&gt;. These can include conditions such as congenital adrenal hyperplasia, androgen insensitivity syndrome, and 5-alpha-reductase deficiency. So in short, there is no biological third &lt;em&gt;sex&lt;/em&gt;, but that doesn't mean you can always categorize a person as biologically male or female.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you quoted, the hijira are usually physiologically male but have a different &lt;em&gt;gender&lt;/em&gt; identity.&lt;/p&gt;&#xA;" OwnerUserId="1166" LastActivityDate="2012-08-27T03:59:34.457" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3338" PostTypeId="2" ParentId="3335" CreationDate="2012-08-27T04:37:32.710" Score="2" Body="&lt;p&gt;I'm not sure if this answers your question, but I'll give it a try anyway. Here's a diagram of &lt;a href=&quot;http://lpi.oregonstate.edu/infocenter/vitamins/vitaminB6/b6diag.html&quot; rel=&quot;nofollow&quot;&gt;homocysteine metabolism&lt;/a&gt;. Vitamin B12 is a cofactor for homocysteine methyltransferase, and folic acid is required for tetrahydrofolate (THF). As both vitamins are involved in homocysteine metabolism, the symptoms of &lt;a href=&quot;http://en.wikipedia.org/wiki/Folate_deficiency&quot; rel=&quot;nofollow&quot;&gt;folate&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Vitamin_B12_deficiency&quot; rel=&quot;nofollow&quot;&gt;vitamin B12&lt;/a&gt; deficiency are similar. Vitamin B12 deficiency can result in neurological symptoms due to abnormal myelin, but folate deficiency does not. Vitamin B12 also metabolizes methylmalonyl-CoA to succinyl-CoA as &lt;a href=&quot;http://www.ganfyd.org/index.php?title=Vitamin_B12&quot; rel=&quot;nofollow&quot;&gt;seem here&lt;/a&gt;, so the methylmalonic acid level is often measured to test for vitamin B12 deficiency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hyperhomocysteinemia&quot; rel=&quot;nofollow&quot;&gt;Hyperhomocysteinemia&lt;/a&gt; is the condition of high levels of homocysteine, but it is usually due to low vitamin B12 or folate.&lt;/p&gt;&#xA;" OwnerUserId="1166" LastActivityDate="2012-08-27T04:37:32.710" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3339" PostTypeId="1" CreationDate="2012-08-27T05:21:46.367" Score="6" ViewCount="172" Body="&lt;p&gt;Do bugs love light bulbs because they resemble the stars or is it the sun? How do they sense the bulb? What is the purpose of this &quot;brightophilia&quot; that has evolved in insects?&lt;/p&gt;&#xA;" OwnerUserId="339" LastEditorUserId="43" LastEditDate="2012-09-17T13:43:19.917" LastActivityDate="2012-09-17T13:43:19.917" Title="Bugs' love for light" Tags="&lt;neuroscience&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3340" PostTypeId="2" ParentId="3325" CreationDate="2012-08-27T06:46:07.060" Score="17" Body="&lt;p&gt;According to Gleick, Feynman spent the summer of 1960 in Delbr&amp;uuml;ck's lab at Caltech and discovered &lt;strong&gt;intragenic supression&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is where the expression of a gene which has been knocked out by a mutation may be restored by a second mutation within the same gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fenynman worked with the &lt;a href=&quot;http://en.wikipedia.org/wiki/T4_rII_system&quot;&gt;rII mutant of phage T4&lt;/a&gt; and was looking for back mutations in &lt;em&gt;E.coli&lt;/em&gt; strain K. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;He noted some unusual plaques which he labelled &lt;strong&gt;idiot r's&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Feynman correctly deduced that these revertants were due to a second mutation which cancelled the effect of the first, but he did not publish the result, possibly because he had no molecular explanation for what was going on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Delbr&amp;uuml;ck lab referred to these revertants as &lt;strong&gt;Feyntrons&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cricks and co-workers in Cambridge, UK, correctly explained the phenomenon.  If, for example, a mutation caused a gene to be read out of sequence (a frameshift mutation) then a second mutation &lt;em&gt;within the same gene&lt;/em&gt; could put the message back 'in phase', thus cancelling out the effect of the first mutation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All the above is taken from James Gleick (1992) &lt;em&gt;Genius.  Richard Feynman and modern physics&lt;/em&gt;, a great book.    &lt;/p&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="3632" LastEditDate="2014-03-08T03:17:39.380" LastActivityDate="2014-03-08T03:17:39.380" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3342" PostTypeId="2" ParentId="2935" CreationDate="2012-08-27T11:58:10.350" Score="12" Body="&lt;p&gt;In the case of red blood cells: human erythrocytes (red blood cells) have no mitochondria. Since the mitochondria are the cellular site for oxidative metabolism of fatty acids, erythrocytes cannot oxidise fatty acids to release energy. The erythrocytes also cannot fully oxidise glucose (to carbon dioxide and water) because this is also a mitochondrial process, so they have to rely upon anaerobic glycolysis. The end product of anaerobic glycolysis is pyruvate, and erythrocytes reduce this to lactate (to recycle the NADH that is produced during glycolysis) and then export this lactate into the blood for further metabolism by the liver.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-08-27T11:58:10.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3344" PostTypeId="1" AcceptedAnswerId="3372" CreationDate="2012-08-27T14:02:50.847" Score="6" ViewCount="1997" Body="&lt;p&gt;I'm looking at this diagram of homocysteine metabolism and see two distinct pathways that the amino acid may get metabolized to: with vitamin B12 it gets converted back into methionine, while with B6 it gets converted to cysteine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've followed the links for the products that Cysteine gets metabolized to and could not find any references to cognitive effects. &lt;strong&gt;Are there any cognitive effects of Cysteine or other amino acids that it gets metabolized to?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YPQLV.jpg&quot; alt=&quot;Diagram of homocysteine metabolism&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested in learning what are the possible effects of pharmacological (50mg - 100mg) doses of vitamin B6 on this metabolic cycle, while folate and B12 levels stay at the baseline levels. It seems to me that if vitamin B6 is more readily available, there will be a higher chance of homocysteine metabolized into Cysteine. Is this assumption correct? &lt;strong&gt;What are the implications to this metabolic cycle that may be caused  by elevated levels of vitamin B6, while keeping folate and B12 at baseline levels?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm particularly interested in the implications of this process on dreaming. There has been numerous reports among dreamers that &lt;strong&gt;50-100mg of vitamin B6, taken in the 3rd-5th sleep cycle produces very intense and vivid dreams, sometimes featuring spontaneous awareness&lt;/strong&gt; (lucid dreams), while B-complex vitamins (B6, B12, Folate, Niacin, etc) appear to produce the opposite effect - very vague dream recall. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm trying to understand if there is indeed a connection between the metabolic pathway that homocysteine may take and the vividness of dreams, capacity to recall them clearly and the phenomenon of being able to spontaneously realize the fact that the person is dreaming while still asleep. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://lpi.oregonstate.edu/infocenter/vitamins/vitaminB6/b6diag.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Diagram obtained from here&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2014-10-31T13:20:49.927" Title="Are there any effects of elevated Cysteine levels on cognitive function?" Tags="&lt;human-biology&gt;&lt;amino-acids&gt;&lt;vitamins&gt;&lt;dreaming&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3345" PostTypeId="2" ParentId="3333" CreationDate="2012-08-27T14:45:39.080" Score="3" Body="&lt;p&gt;I think the definition in Wikipedia is simply bad because it depends on another debatable definition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I prefer something which follows from an observation made by Ricard Dawkins in &lt;em&gt;The Extended Phenotype&lt;/em&gt; (the following is &lt;em&gt;my&lt;/em&gt; definition, but I think Dawkins had something similar in mind):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;An organism is any system of components which depend on each other for survival and cooperate in proliferating potentially unboundedly.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A single-celled organism is by this definition an organism since it proliferates by coordination of its components.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A single-celled organism with organelles deriving from endosymbiosis (think mitochondria) is an organism: even though mitochondria &lt;em&gt;do&lt;/em&gt; proliferate on their own inside the cell, they don’t do so outside of the cell, hence have a bounded proliferation only; and they depend on the cell as a host. On the other hand, they cooperate with the cell division.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Endosymbionts, on the other hand, &lt;em&gt;are&lt;/em&gt; organisms because even though they depend on a host (and the host on them), they may theoretically &lt;em&gt;switch&lt;/em&gt; host or even survive a limited time without a host.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, the cells in a multi-cellular organism can sometimes divide independently (in organs) but they cannot survive without the rest of the organism, and the unbounded reproduction of any organ in fact requires going via the germ line of said organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A virus which depends on a host to proliferate does &lt;em&gt;not&lt;/em&gt; form an organism with the host since it doesn’t use the host’s germ line; if, on the other hand, it &lt;em&gt;does&lt;/em&gt; use the host’s germ line (consider virally derived pseudo-genes on our DNA) then, yes, it forms a common organism with its host.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is (mother + her unborn child) an organism?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I wouldn’t say so, since the child is only temporally part of the host.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is an apple that's just fallen off a tree an organism?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Interesting; I’d say yes, as long as it retains the potential ability to proliferate (it’s a &lt;em&gt;separate&lt;/em&gt; organism from the tree though).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is (human + their microbiome) an organism?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No. Humans can survive (albeit only shortly) without a microbiome; in the same vein, the bacteria of the microbiome can change their host.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, this definition also has a drawback: there are organisms which cannot reproduce because they are sterile, yet they are clearly still organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that other definitions (e.g. “an organism is a collection of components sharing common genetic material”) also don’t work universally since they also break down – the example of genetic commonality would preclude &lt;a href=&quot;http://en.wikipedia.org/wiki/Mosaicism&quot; rel=&quot;nofollow&quot;&gt;mosaicism&lt;/a&gt; and organelles derived from endosymbiosis.&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="166" LastEditDate="2012-08-27T14:51:12.847" LastActivityDate="2012-08-27T14:51:12.847" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="3346" PostTypeId="1" AcceptedAnswerId="3397" CreationDate="2012-08-27T16:51:39.963" Score="7" ViewCount="489" Body="&lt;p&gt;I've read a lot on both sides of the debate of low carb vs low fat diets trying to make some sense of what is being proposed. The lipid hypothesis runs roughly along the lines that we have lots of observational epidemiological evidence that eating a high fat diet correlates heart disease/obesity/enter disease of choice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An alternative hypothesis is that high carbohydrate diets cause these things. Since the studies haven't been done, there is not the correlation to point to. This hypothesis is believable (to some people) due to the well-understood biological pathway: Carbohydrates turn to glucose, which causes an insulin release, and insulin regulates fat storage, so high carbohydrate diets lead to weight gain (see a biochemsitry textbook for a more detailed explanation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: Does the lipid hypothesis have any biological pathway for which there could be proposed a causal relation rather than just a correlation? Of all the speakers/writers on this topic, the low carb advocates always clearly describe the causal relation, whereas the low fat advocates never say &lt;em&gt;why&lt;/em&gt; eating fat should cause weight gain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: I'm not interested in discussing the merits of the studies, but rather the proposed causal mechanism.&lt;/p&gt;&#xA;" OwnerDisplayName="user1323" LastActivityDate="2012-08-30T17:07:57.723" Title="Biological Pathway of Lipid Hypothesis" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;endocrinology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3347" PostTypeId="1" CreationDate="2012-08-27T17:07:20.643" Score="13" ViewCount="1632" Body="&lt;p&gt;My wife and I recently found out that we are going to have twins and so nearly everyone asks if we have a family history of twins.  Now I know that the answer for me is that it doesn't matter&amp;mdash;as a man, I have no influence on my wife's tendency to &lt;a href=&quot;http://en.wikipedia.org/wiki/Twin#Statistics&quot;&gt;hyper-ovulate&lt;/a&gt;.  And, of course, if we turn out to have monozygotic twins (we don't know yet), genetics plays no part.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore the question only matters on my wife's side and only if dizygotic twins are known in her heritage. As it happens, we don't know of any twins on her side.  Given that many factors besides genetics are relevant to twins being born and we only know her family history for a half-dozen generations with any confidence, what are the odds that we would observe twins in her family history if she is genetically predisposed to having them? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or, to put in another way, can I respond that nutrition and other factors were probably more important than genetics?&lt;/p&gt;&#xA;" OwnerUserId="1324" LastEditorUserId="43" LastEditDate="2012-08-27T18:52:45.077" LastActivityDate="2012-08-28T09:07:52.677" Title="Do twins &quot;run in the family&quot;?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;reproduction&gt;&lt;embryology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3348" PostTypeId="2" ParentId="2684" CreationDate="2012-08-27T19:01:18.300" Score="5" Body="&lt;p&gt;I agree with the person above. But it might be more correct to say we get 1/4 of our total DNA from each of our grandparents, because though the genes are really important to code for specific proteins, there are tons of non-coding DNA in between them. In fact, 98% of our genome is non-coding! Although we are discovering awesome novel functions for this DNA slowly but surely. But it is important to think of it as 1/4 of your DNA and not genes because it is in this non-coding DNA where a lot of mutations can occur, and these mutations are what we inherit and make things like DNA fingerprinting for forensic analysis possible, like in CSI. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just wanted to add three more thoughts:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though it is true that 1/4 of your DNA would come from each grandparent, that is only true for your autosomal genes, not your necessarily for your sex chromosomes. The X chromosome does recombine regularly in the mother, but in the father the X and the Y do not recombine. (Actually I think part of the Y can recombine, but for the most part, the sex-determining part of the Y and its associated genes stay completely intact). This means that if you are a male, your father, and his father, and his father all share the same Y chromosome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally for the women, because the woman makes the egg, and thus all the early embryonic organelles and RNA's, the woman donates the mitochondrial DNA, which has its own sets of genes that are really important and have been linked to many diseases. So every child of a woman, shares their mother's mitochondrial DNA, as she shares her mother's and her mother's mother, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If ~1/4 of our DNA comes each grandparent, then 1/8 of your DNA comes from each great-grandparent. So then 1/16 of our DNA comes from each great-great grandparent, which are your grandparent's grandparents. And thus it continues exponentially upward. The result is that there comes a point where your ancestors have contributed so little to your actual DNA, that it becomes almost negligible. So if you are an American, who most likely has ancestors from all over the world, even if you have 1 great-great-great-great grandparent who was a French immigrant while the rest of your ancestors were all British, the French DNA is only 1/64 of your total DNA. So even if you are a complete mix, there comes a point where so many different people have contributed to you being you, that you can establish a cut-off and just say, 3/4 of my ancestors were born in America, I'm American!&lt;/p&gt;&#xA;" OwnerUserId="1325" LastActivityDate="2012-08-27T19:01:18.300" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3349" PostTypeId="2" ParentId="3339" CreationDate="2012-08-27T19:26:21.500" Score="5" Body="&lt;p&gt;I think the answer to your question is relatively unknown. The answer I have heard the most often, which is largely the most accepted, is that many insects orient themselves in space using light. So if they are flying at night, the soft light of the moon tells them which relative direction they are going. Light bulbs end up confusing them, because they think they can orient themselves to it, but they are wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.npr.org/templates/story/story.php?storyId=12903572&quot;&gt;http://www.npr.org/templates/story/story.php?storyId=12903572&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, insects do have very similar photoreceptors as humans and vertebrates. Fruit fly eyes are a major research topic because of the similarity of the photoreceptor proteins as well as the amazing genetics that can be done.&lt;/p&gt;&#xA;" OwnerUserId="1325" LastActivityDate="2012-08-27T19:26:21.500" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3350" PostTypeId="2" ParentId="3347" CreationDate="2012-08-27T19:39:27.580" Score="2" Body="&lt;p&gt;Nutrition and environment don't have a huge affect, if any, that I could find. Age can, as women above 35 have a greater propensity for bearing twins. &lt;a href=&quot;http://en.wikipedia.org/wiki/Twin#Fraternal_.28sororal.2Fdizygotic.29_twins&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Twin#Fraternal_.28sororal.2Fdizygotic.29_twins&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, because fraternal twins can be the result of a gene on the X-Chromsome, the answer is yes &lt;em&gt;in this specfic case&lt;/em&gt;. &lt;a href=&quot;http://genetics.thetech.org/ask/ask86&quot; rel=&quot;nofollow&quot;&gt;http://genetics.thetech.org/ask/ask86&lt;/a&gt;  If a mother is, herself, a fraternal twin then her chances of bearing fraternal twins is 2.5x higher than normal and it can be inherited from the mother's side even if she's not a twin herself. It's definitely not guaranteed, as the normal chances are so low to begin with, but there is definitely an increase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, for all other types of twins I have not yet been able to find anything implying there's a genetic component.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-27T19:39:27.580" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3351" PostTypeId="2" ParentId="3347" CreationDate="2012-08-27T20:06:19.120" Score="6" Body="&lt;p&gt;The propensity for heterozygotic twins seems to be driven primarily by genetics, with additional factors playing a role (http://152.98.160.29/contents/p/staff/CV162Lewis_UQ_Copy.pdf', &lt;a href=&quot;http://www.sciencelearn.org.nz/Contexts/Uniquely-Me/Looking-Closer/Twins&quot; rel=&quot;nofollow&quot;&gt;info site&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;hormones (&lt;a href=&quot;http://genetics.thetech.org/ask/ask86&quot; rel=&quot;nofollow&quot;&gt;&quot;Mothers of fraternal twins tend to be taller, and have earlier and shorter menstrual cycles&quot;&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;ethnic background (which is really genetic) - African women are more likely than Caucasian women to have them, and Caucasian women are more likely than Asian women to have fraternal twins&lt;/li&gt;&#xA;&lt;li&gt;mother's age&lt;/li&gt;&#xA;&lt;li&gt;nutrition&lt;/li&gt;&#xA;&lt;li&gt;previous births&lt;/li&gt;&#xA;&lt;li&gt;fertility drugs&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I also found a link to a genetic study published in Nature that claims to have linked a DNA region to dyzotic twins, but the Nature website seems to be down - maybe it will work later: &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=9&amp;amp;ved=0CG4QFjAI&amp;amp;url=http%3A%2F%2Fwww.nature.com%2Fng%2Fjournal%2Fv26%2Fn4%2Ffull%2Fng1200_398.html&amp;amp;ei=_tA7UP3OAsjQ4QSpkYCoCQ&amp;amp;usg=AFQjCNGtEN6yFQ_DKxlSBSgiDtUqQV0qnQ&amp;amp;sig2=9lMDpGXbLiGOa-s-Obfy1A&amp;amp;cad=rja&quot; rel=&quot;nofollow&quot;&gt;A region on chromosome 3 is linked to dizygotic twinning - Nature&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the father does not contribute to the chance of having heterozygotic twins, but a male offspring could pass the gene to daughter.&lt;/p&gt;&#xA;" OwnerUserId="1307" LastEditorUserId="1307" LastEditDate="2012-08-28T09:07:52.677" LastActivityDate="2012-08-28T09:07:52.677" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3352" PostTypeId="2" ParentId="2739" CreationDate="2012-08-27T20:26:28.823" Score="8" Body="&lt;p&gt;This is a very interesting question. Many people have researched this topic, and many still are. But regardless, I had never heard of Alan Turing's contributions, so thank you!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, I cannot actually find who first coined the term morphogen. Though people had hypothesized that chemicals could play a critical role in development through much of the 20th century, I cannot actually find the first person to use &lt;em&gt;morphogen&lt;/em&gt;. But the most important paper really came from a guy named Lewis Wolpert, who came up with the model of a gradient of morphogens leading to differential cell fates. The idea being that if some area of an embryo produces a morphogen at a very high concentration, then as you move away from that area, the concentration goes down. So if this morphogen is required at or above a certain threshold for activity, then only those cells with that concentration will have a certain cell fate, while at lower concentrations, the cells can become something different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But this does not really answer your question. You are asking how a single cell, which is spherically symmetrical, can determine a particular axis. Though most organisms do this is in slightly different ways, the most common feature is that sperm entry point breaks the symmetry. The best way to explain this is to show you a diagram of Xenopus (frog) eggs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/h0qJw.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image from: &lt;a href=&quot;http://studentreader.com/nieuwkoop-center/&quot; rel=&quot;noreferrer&quot;&gt;http://studentreader.com/nieuwkoop-center/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Xenopus egg, first of all, is inherently not spherically symmetrical. There is a black animal pole, and a white vegetal pole. The sperm can only enter a marrow region of the egg about 30˚ north of the animal/vegetal line. Upon fertilization, an event occurs where the pigmented areas turn toward the sperm entry point, leaving a gray crescent. Nearby the gray crescent, in the vegetal pole, a structure called the organiser develops. This organiser creates many of the morphogens that then pattern the rest of the embryo. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Researchers have studied this a lot in many different organisms, but a few things really remain constant: eggs are not exactly spherically symmetrical, and the sperm entry point provides asymmetry.&lt;/p&gt;&#xA;" OwnerUserId="1325" LastActivityDate="2012-08-27T20:26:28.823" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3353" PostTypeId="2" ParentId="2068" CreationDate="2012-08-27T21:22:48.607" Score="7" Body="&lt;p&gt;You may also be interested in &lt;strong&gt;D-amino-acid oxidase&lt;/strong&gt; (&lt;a href=&quot;http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/4/3/3.html&quot;&gt;EC 1.4.3.3&lt;/a&gt;), a flavoprotein  (FAD) highly specific for the D-form of amino acids, which was discovered by Hans Krebs in 1935 (see &lt;a href=&quot;http://www.biochemj.org/bj/029/1620/0291620.pdf&quot;&gt;here&lt;/a&gt;), and which has a wide distribution (including in humans). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The enzyme has been very thoroughly investigated, in particular by Massey &amp;amp; co-workers (see &lt;a href=&quot;http://www.jbc.org/content/269/50/31666.full.pdf&quot;&gt;here&lt;/a&gt; for example)   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;D-amino-acid oxidase (&lt;a href=&quot;http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/4/3/3.html&quot;&gt;EC 1.4.3.3&lt;/a&gt;) catalyzes the reaction which results in the following &lt;a href=&quot;http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/4/3/3.html&quot;&gt;transformation&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;D-amino acid + H&lt;sub&gt;2&lt;/sub&gt;O + O&lt;sub&gt;2&lt;/sub&gt; = 2-oxo carboxylate + NH&lt;sub&gt;3&lt;/sub&gt; + H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;2-Oxo-carboxylates are what used to be called &amp;alpha;-keto acids.  For example, pyruvate is produced from D-Ala.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The product of the enzymatic reaction is the imino-acid&lt;/strong&gt; which is nonenzymatically&#xA;hydrolyzed to a-keto acid (see &lt;a href=&quot;http://www.jbc.org/content/269/50/31666.full.pdf&quot;&gt;Pollegioni&lt;/a&gt; &lt;em&gt;et al&lt;/em&gt;., 1994, and references therein) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An excellent review&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;D-Amino Acid Oxidase: Physiological Role and Applications&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;by S. V. Khoronenkova &amp;amp; V. I. Tishkov,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Biochemistry (Moscow)&lt;/em&gt; is freely available from &lt;a href=&quot;http://protein.bio.msu.ru/biokhimiya/contents/v73/full/73131511.html&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;These authors have some intersting things to say about D-Serine, D-Proline and D-Alanine, and much more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Additional Reference&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Pollegioni L, Fukui K, Massey V. (1994) Studies on the kinetic mechanism of pig kidney D-amino acid oxidase by site-directed mutagenesis of  tyrosine 224 and tyrosine 228.  &lt;em&gt;J. Biol. Chem.&lt;/em&gt; &lt;strong&gt;269&lt;/strong&gt;, 31666-31673. [&lt;a href=&quot;http://www.jbc.org/content/269/50/31666.full.pdf&quot;&gt;pdf&lt;/a&gt;]&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="1136" LastEditDate="2012-08-28T12:06:56.753" LastActivityDate="2012-08-28T12:06:56.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3354" PostTypeId="1" CreationDate="2012-08-27T21:55:07.753" Score="4" ViewCount="141" Body="&lt;p&gt;I have read that a chimera is an organism with two or more sets of DNA, with every cell having one of the sets. Is it possible and common for the two or more sets to be present in the cells of a single organ? I'm confining my question to vertebrates because I don't remember much about the biology of invertebrates from high school, but please don't hesitate to add anything interesting about them.&lt;/p&gt;&#xA;" OwnerUserId="1278" LastEditorUserId="1278" LastEditDate="2012-08-28T16:02:01.400" LastActivityDate="2012-08-29T17:46:57.670" Title="In a vertebrate chimera, are particular organs homogenous genetically?" Tags="&lt;genetics&gt;&lt;chimerism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3355" PostTypeId="1" AcceptedAnswerId="3362" CreationDate="2012-08-27T23:00:44.350" Score="5" ViewCount="5987" Body="&lt;p&gt;I'm looking at &lt;a href=&quot;https://biology.stackexchange.com/questions/3344/are-there-any-effects-of-elevated-cysteine-levels-on-cognitive-function&quot;&gt;my question about homocysteine metabolism&lt;/a&gt; and am doing a followup inquiry into vitamins B6(Pyroxidine) and B12(Cyanocobalamin). I've found this interesting bit about vitamin B12 and am looking at its implications:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Approximately 56% of a 1 mcg oral dose of vitamin B12 is absorbed, but &lt;strong&gt;absorption decreases drastically when the capacity of intrinsic factor is exceeded&lt;/strong&gt; (at 1–2 mcg of vitamin B12) &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://ods.od.nih.gov/factsheets/VitaminB12-HealthProfessional/#en8&quot; rel=&quot;nofollow noreferrer&quot;&gt;Quote from vitamin B12 fact sheet&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I'm trying to understand the implications of an intrinsic factor involved in B12 absorption.&lt;/strong&gt; Lets say that a person gets vitamin B12 from both food and a single supplement pill. Will taking that pill &quot;use up&quot; the absorption factor and prevent food's vitamin B12 from being absorbed over time? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the first time I'm hearing of additional &quot;factors&quot; that may limit vitamin absorption in the human body. Is this common across vitamins, or is it B12 specific?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2016-04-16T13:52:49.043" Title="What does vitamin B6 and B12 absorption depend upon?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;vitamins&gt;&lt;vegetarianism&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3356" PostTypeId="1" AcceptedAnswerId="3653" CreationDate="2012-08-27T23:43:37.437" Score="8" ViewCount="575" Body="&lt;p&gt;I'm not versed in either biology or linguistics so please forgive any naiveties I may commit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've learned that Noam Chomsky thinks that language is a result of a single genetic mutation in humans. It would be a mutation allowing the human brain to conceive of natural numbers as I understand. Have there been any (even speculative) attempts by biologists to locate that mutation in the human genome and/or in time? Is it even feasible?&lt;/p&gt;&#xA;" OwnerUserId="1278" LastEditorUserId="3952" LastEditDate="2013-08-04T02:05:35.530" LastActivityDate="2021-05-29T09:10:12.267" Title="Have there been attempts to identify Chomsky's &quot;language mutation&quot; in humans?" Tags="&lt;genetics&gt;&lt;mutations&gt;&lt;linguistics&gt;&lt;communication&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3357" PostTypeId="2" ParentId="3299" CreationDate="2012-08-28T00:02:52.527" Score="7" Body="&lt;p&gt;There has been quite a bit of study on the development of &lt;em&gt;eyespots&lt;/em&gt;. How did they evolve is still unclear, but several experiments have elucidated the molecular mechanisms underlying their formation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Eyespot_%28mimicry%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia page about eyespots&lt;/a&gt; gives a good basic introduction and some interesting references.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, first of all, how does an eyespot form?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During the development of wings, eyespots arise at specific locations called &lt;em&gt;foci&lt;/em&gt; (singular &lt;em&gt;focus&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you take cells from a focus in a developing wing, and transplant them into another region of the wing, an eyespot will develop at the transplanted site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3eI9D.jpg&quot; alt=&quot;Transplanted focus&quot;&gt;&#xA;Adapted from: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7004953&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pattern Formation on Lepidopteran Wings: Determination of an Eyespot&lt;/a&gt; - Nijhout, &lt;em&gt;Dev. Biol&lt;/em&gt;, &lt;strong&gt;1980&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The photo on the left is a normal wing from an adult Buckeye butterfly, &lt;em&gt;Precis coenia&lt;/em&gt;. In the middle and right photos, some cells of the big eyespots have been transplanted in a new position during development. As you can see, a third eyespot develops. Note that the middle photo is from an autograph, that is, the cells were transplanted on the same wing. This results in a shrinkage of the normal eyespot. In the right picture, instead, cells were transplanted in another individual, and this does not result in shrinkage of the eyespot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors conclude that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is evident from these experiments that the development of the large eyespot on the forewing of &lt;em&gt;Precis coenia&lt;/em&gt; depends on the presence of a small group of cells that lie at or near its center. This group of cells corresponds to a &quot;focus&quot;: a small region, occurring in each wing cell, that is postulated&#xA;  to be responsible for the induction of most color pattern elements in butterflies and moths (Nijhout, 1978). Cautery experiments establish an upper limit for the size of this focus in the neighborhood of 300 epidermal cells, though it is probable that the actual size of the focus is much smaller.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They further speculate that a specific &lt;a href=&quot;http://en.wikipedia.org/wiki/Morphogen&quot; rel=&quot;nofollow noreferrer&quot;&gt;morphogen&lt;/a&gt; may be involved:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The response of the eyespot pattern to cautery or transplantation of the focus is most readily interpreted if we assume that the focus is the source of a morphogen that is somehow able to induce synthesis of specific pigments.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The idea that a morphogen was involved has been confirmed in later years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12809139&quot; rel=&quot;nofollow noreferrer&quot;&gt;Development, plasticity and evolution of butterfly eyespot patterns&lt;/a&gt; - Brakefield et al., &lt;em&gt;Nature&lt;/em&gt;, &lt;strong&gt;1996&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The focus is proposed to be a signalling source for a morphogen, the levels of which determine the pigmentation of surrounding cells. Recent investigations have indicated that regulatory genes, such as the &lt;em&gt;Distalless&lt;/em&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/Homeobox&quot; rel=&quot;nofollow noreferrer&quot;&gt;homeobox gene&lt;/a&gt;, are specifically espressed in the eyespot focus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XxM86.jpg&quot; alt=&quot;Wing development&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During the development of the wing the expression of the &lt;em&gt;Distalless (Dll)&lt;/em&gt; protein (shown in green in the picture) corresponds to the location of the future eyespots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several mutations exist that will provoke changes in the eyespots patterns. Some of this with the evoking names of &lt;em&gt;Cyclops&lt;/em&gt;, &lt;em&gt;Spotty&lt;/em&gt; and &lt;em&gt;Bigeye&lt;/em&gt; were analysed in the paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, without going much into insects genetics (which is far from being my domain of interest), you can clearly see that, although the number, position and size of the foci are affected by the mutations, their position always correspond with an increased expression of &lt;em&gt;Dll&lt;/em&gt; during development.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/G9WPr.jpg&quot; alt=&quot;wing pattern mutants&quot;&gt;&lt;br&gt;&#xA;Left column: ventral hindwing patterns of a wild type (top), &lt;em&gt;Cyclops&lt;/em&gt; (middle) and &lt;em&gt;Bigeye&lt;/em&gt; mutants. Right column: forewing pattern in a wild type (top) and &lt;em&gt;Cyclops&lt;/em&gt; mutant (bottom).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the conclusion of the paper (bold mine):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;The selection experiments on &lt;em&gt;B. anynana&lt;/em&gt; rapidly produced dramatic differences in eyespot size which were due to genes of small phenotypic effect.&lt;/strong&gt; The mutants described here show that genes also exist with large phenotypic effect on eyespot development (including size) that have no perceptible effect on other wing or body patterns. It is likely that the evolution of eyespot patterns in nature involves both genes with large and small effects on eyespots development. [...]&lt;br&gt;&#xA;  These observations suggest that the regulation of the eyespot developmental pathway is such that &lt;strong&gt;eyespot patterns can evolve rapidly and independently of other wing-pattern elements and body structures&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Finally, another interesting read is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19243218&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wings, Horns, and Butterfly Eyespots: How Do Complex Traits Evolve?&lt;/a&gt; - Monteiro and Podlaha - &lt;em&gt;PLoS Biol.&lt;/em&gt;, &lt;strong&gt;2009&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where the authors propose that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Complex traits require co-ordinated expression of many transcription factors and signaling pathways to guide their development. Creating a developmental program de novo would involve linking many genes one-by-one, requiring each mutation to drift into fixation, or to confer some selective advantage at every intermediate step in order to spread in the population. While this lengthy process is not completely unlikely, it could be circumvented with fewer steps by recruiting a top regulator of an already existing gene network, i.e., by means of gene network co-option. Subsequent modifications of the co-opted network could further optimize its role in the new developmental context.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2012-08-28T00:10:41.007" LastActivityDate="2012-08-28T00:10:41.007" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3358" PostTypeId="1" CreationDate="2012-08-28T00:19:39.090" Score="3" ViewCount="2410" Body="&lt;p&gt;Say I have three unicellular organisms: a eukariote, a bacterium and an archaeon. If I cut off nutrition from them at the same time, how long will it take for them to die? What will their death look like, and do they actually need to die? If so, why?&lt;/p&gt;&#xA;" OwnerUserId="1278" LastActivityDate="2016-09-27T18:44:42.823" Title="How long can a unicellular organism live without nutrition? What happens after that? Does it depend on the domain?" Tags="&lt;cell-biology&gt;&lt;death&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3359" PostTypeId="2" ParentId="2875" CreationDate="2012-08-28T00:32:10.213" Score="7" Body="&lt;p&gt;This is somewhat unrelated, and for that, I apologize, but I find it truly fascinating, and I believe you will too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Zebra finches are a song bird that have become a popular model organism for behavioral research. They have a very stereotypical pattern for song learning: at about 70 days after hatching, the baby male song bird starts to listen to his father's song, copy it, practice it, and ultimately learn it. Female birds do not have a courtship song to learn.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, if the baby male bird does not learn their father's song, they end up just kind of screeching, and never singing a song. This, in nature, makes them unable to court a female.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But in the lab, this research group did an experiment, where they took these screeching males, let them grow to adulthood, then teach their child as best as they can. The child, wanting to learn a song, takes what it can from the father. After 4 generations of this, the group was able to get de novo song production from these birds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unbelievable!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v459/n7246/full/nature07994.html&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;De novo&lt;/em&gt; establishment of wild-type song culture in the zebra finch&lt;/a&gt; - Fehér et al. - &lt;em&gt;Nature&lt;/em&gt;, &lt;strong&gt;2009&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1325" LastEditorUserId="115" LastEditDate="2013-08-04T12:22:09.487" LastActivityDate="2013-08-04T12:22:09.487" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3360" PostTypeId="1" AcceptedAnswerId="3364" CreationDate="2012-08-28T00:37:11.967" Score="19" ViewCount="1541" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QK3T6.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/5kNYH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/eF4zk.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just spotted this fruit while walking to school. It's the size of a small coin.The taste is almost sour and tangy and somewhat sweet (I only tried one of them and very little of it).  I admit, I've never seen it before. Does anyone know what this is?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update: Location is two or three blocks north of UC Berkeley (Berkley, CA, USA).&lt;/p&gt;&#xA;" OwnerUserId="1326" LastEditorUserId="19468" LastEditDate="2017-10-14T18:24:54.793" LastActivityDate="2017-10-14T18:24:54.793" Title="What kind of fruit is this?" Tags="&lt;species-identification&gt;&lt;botany&gt;&lt;fruit&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3361" PostTypeId="2" ParentId="3358" CreationDate="2012-08-28T00:52:17.537" Score="4" Body="&lt;p&gt;This is very dependent on the organism within each of the groups you mention. While for the most part, archea are the extremophiles and have the ability to withstand many extreme conditions, nutrient limitation survival greatly varies. I think you could easily find organisms in each group that could withstand nutrient limitation well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good example would be yeast, which is a single celled organism you may have actually worked with. If you take laboratory yeast, in their diploid state, and starve them, they will undergo meiosis, and in their spore form, live for a very very long time without nutrients, protected by their ascus (which is actual their dead mother cell). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yeast can also completely desiccate and still live. When you pick up an active yeast packet for baking, those yeast have not only been starved, but have been completely sucked dry of their water. Yet when you add water back, they live (though a great number of them will die).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think in general, most single celled organisms have a certain tolerance for low nutrient conditions. This does happen to them a lot. All it means is they slow their cell cycle down, stop dividing, and just undergo a caution period. There is all sorts of signaling in the cells that sense the nutrients, and slow growth based on their conditions.&lt;/p&gt;&#xA;" OwnerUserId="1325" LastActivityDate="2012-08-28T00:52:17.537" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3362" PostTypeId="2" ParentId="3355" CreationDate="2012-08-28T01:15:22.730" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Vitamin_B12&quot; rel=&quot;nofollow&quot;&gt;Vitamin B12&lt;/a&gt; (cobalamin) is a water-soluble vitamin required for homocysteine methyltransferase. In order to be absorbed, it must bind to &lt;a href=&quot;http://en.wikipedia.org/wiki/Intrinsic_factor&quot; rel=&quot;nofollow&quot;&gt;intrinsic factor&lt;/a&gt; (IF), which is produced by the parietal cells of the stomach. The absorption of the vitamin B12-IF complex occurs in the terminal ileum (of the small intestine). The quote just means that if there isn't enough IF, then you can't absorb vitamin B12.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many things that limit absorption of vitamins, and even vitamin B12. Because vitamin B12 is found in animal products, vegetarians and vegans may need to supplement it. Pernicious anemia is an autoimmune disease that destroys IF or the parietal cells, Gastric bypass surgery can lead to vitamin B12 deficiency. Anything that affects vitamin B12 absorption in the terminal ileum, such as in Crohn's, celiac disease, or enteritis, can lead to &lt;a href=&quot;http://en.wikipedia.org/wiki/Vitamin_B12_deficiency&quot; rel=&quot;nofollow&quot;&gt;deficiency&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question, no. Yes, it will use some IF (provided you have IF), but that would allow your body to absorb vitamin B12. For people who have diseases mentioned above, they can take vitamin B12 via injections, subligually (under the tongue), or intranasal gels, according to the fact sheet you cited.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because all the B vitamins and vitamin C are water-soluble, they are &lt;a href=&quot;http://www.sharecare.com/question/how-water-soluble-vitamins-absorbed&quot; rel=&quot;nofollow&quot;&gt;easily absorbed&lt;/a&gt; through the intestinal wall. Excess amounts are usually excreted in urine. I believe vitamin B12 is the only vitamin that needs to be bound to a factor, due to its larger size. It can be stored in the liver for several years. Fat-soluble vitamins (A, D, E, K) are absorbed with lipids.&lt;/p&gt;&#xA;" OwnerUserId="1166" LastActivityDate="2012-08-28T01:15:22.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3364" PostTypeId="2" ParentId="3360" CreationDate="2012-08-28T09:21:23.693" Score="18" Body="&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/8/80/Arbutus_unedo%2C_Livorno.JPG&quot; alt=&quot;strawberry tree&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's probably &lt;a href=&quot;http://en.wikipedia.org/wiki/Arbutus_unedo&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Arbutus unedo&lt;/em&gt;, strawberry tree&lt;/a&gt;. Native to Mediterranean region and some part of western Ireland. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: I've just spot that you found it in California, so it's probably one of north american &lt;a href=&quot;http://en.wikipedia.org/wiki/Arbutus&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Arbutus&lt;/em&gt;&lt;/a&gt; species, eg. &lt;a href=&quot;http://en.wikipedia.org/wiki/Arbutus_menziesii&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Arbutus menziesii&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="68" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.747" LastActivityDate="2012-09-11T08:22:32.460" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3365" PostTypeId="1" AcceptedAnswerId="3378" CreationDate="2012-08-28T10:40:08.173" Score="5" ViewCount="30352" Body="&lt;p&gt;I have an AP Bio class where I have to name 3 properties of water and I chose adhesion and cohesion for one of them. I'm having trouble finding out how exactly trees use adhesion and cohesion to move water. There is a lot of different answers out there on the net. How do trees use adhesion and cohesion to move water against gravity?&lt;/p&gt;&#xA;" OwnerUserId="1330" LastEditorUserId="43" LastEditDate="2012-08-28T17:42:22.070" LastActivityDate="2019-01-23T02:15:05.077" Title="How do trees use Adhesion and Cohesion to move water against gravity?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;homework&gt;&lt;biophysics&gt;" AnswerCount="6" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3366" PostTypeId="2" ParentId="1928" CreationDate="2012-08-28T11:01:51.217" Score="1" Body="&lt;p&gt;In the USA, they refer to this as the recommended daily values (DVs) for a variety of nutrients. All I can find regarding &lt;a href=&quot;http://www.fda.gov/Food/GuidanceComplianceRegulatoryInformation/GuidanceDocuments/FoodLabelingNutrition/FoodLabelingGuide/ucm064928.htm&quot; rel=&quot;nofollow&quot;&gt;these recommendations&lt;/a&gt; is that they were calculated for adults and children over 4 years old with a daily energy intake of 2000 kilocalories (often referred to as calories in the US).&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-08-28T11:01:51.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3367" PostTypeId="2" ParentId="3365" CreationDate="2012-08-28T12:34:46.573" Score="8" Body="&lt;p&gt;The mechanism is called &quot;capillary action&quot;. It requires a tube of a small diameter and happens because of the adhesion of water to the walls and the cohesion within the water (=surface tension).&lt;/p&gt;&#xA;" OwnerUserId="1307" LastActivityDate="2012-08-28T12:34:46.573" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3368" PostTypeId="2" ParentId="1928" CreationDate="2012-08-28T12:45:29.443" Score="2" Body="&lt;p&gt;The total calories are not in fact a recommended value - they are an example amount that is derived from some calorie intake that seemed reasonable to someone (I don't know the details). It does not mean that the government is recommending that you eat exactly 2000 calories per day.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The relative content &lt;em&gt;is&lt;/em&gt;, however, a recommended value, based on presumably research. So, if you do take 2000 calories a day, then you know how much of it should be fat/carbs/proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that there is some controversy about whether the recommended values were influenced by industry lobbying. Moreover, science is definitely not clear on what the optimal food content for a human is, which is why we keep having the different diet fads, oscillating from no-fat to no-carbs.&lt;/p&gt;&#xA;" OwnerUserId="1307" LastActivityDate="2012-08-28T12:45:29.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3369" PostTypeId="1" CreationDate="2012-08-19T10:36:18.957" Score="5" ViewCount="1228" Body="&lt;p&gt;In a Flow Cytrometry, one can add an Isotype Control Antibody to allow another antibody to bind more specific to the cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, how can the Isotype Control Antibody add specificity to the other antibody?&#xA;My thought was, that the Isotype Control Antibody binds to all the antibody receptors, but with a &quot;weak&quot; binding. When the other antibody (e.g. CD73) tries to bind, it can make a stronger binding with the CD73 antibody receptor, kicking the Isotype Control Antibody off it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However i'm entirely not sure this is correct... Could anyone explain how the Isotype Control Antibody helps the other antibody (eg.g CD 73) to bind more specific?&lt;/p&gt;&#xA;" OwnerDisplayName="Jeffrey" LastEditorUserId="948" LastEditDate="2013-12-08T17:54:51.997" LastActivityDate="2013-12-08T17:54:51.997" Title="Isotype control antibodies in Flow Cytometry" Tags="&lt;biochemistry&gt;&lt;antibody&gt;&lt;flow-cytometry&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3370" PostTypeId="2" ParentId="3369" CreationDate="2012-08-22T07:13:07.743" Score="3" Body="&lt;p&gt;I don't believe that the Isotype Control Antibody makes the antibody bind more specifically but rather ensures that your signal is specific to your antibody.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Isotype Control Antibodies tend to bind to the non-binding domain of the antibody, typically the constant (Fc) domain. By measuring the concentration of the control antibody, you can determine what percentage of your light signal comes from your primary antibody and not from non-specific binders to your light source.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is very similar to having secondary antibodies in your assay.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ebioscience.com/isotype-controls.htm&quot; rel=&quot;nofollow&quot;&gt;Random link showing that I'm not making stuff up&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" OwnerDisplayName="bobthejoe" LastEditorUserId="389" LastEditDate="2012-11-16T18:56:29.737" LastActivityDate="2012-11-16T18:56:29.737" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3371" PostTypeId="2" ParentId="2739" CreationDate="2012-08-28T13:57:21.500" Score="2" Body="&lt;p&gt;I would think this is very much still &quot;used.&quot; 60 years later, we finally have the first experimental support for it: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this &lt;a href=&quot;http://www.sciencedaily.com/releases/2012/02/120219143321.htm&quot; rel=&quot;nofollow&quot;&gt;blog article about&lt;/a&gt; this &lt;a href=&quot;http://www.nature.com/ng/journal/v44/n3/full/ng.1090.html&quot; rel=&quot;nofollow&quot;&gt;journal piece&lt;/a&gt; the authors studied the ridges that form on the roof of mouse mouths. They manipulated the signaling molecules that induce their formation and observed changes in line with Turing's theory. Of course, this doesn't preclude other mechanisms from occurring, but supports that of Turing. &lt;/p&gt;&#xA;" OwnerUserId="1332" LastEditorUserId="69" LastEditDate="2012-08-28T18:31:36.150" LastActivityDate="2012-08-28T18:31:36.150" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3372" PostTypeId="2" ParentId="3344" CreationDate="2012-08-28T14:31:10.787" Score="3" Body="&lt;p&gt;Your shown homocysteine pathway is way too simple. Especially the production of the neuromodulator H&lt;sub&gt;2&lt;/sub&gt;S from excess sulfur amino acids is not shown. In the last years many more enzymes and reactions have been discovered. I have summarized human sulfur amino acid metabolism in reactome.org, so &lt;a href=&quot;http://reactome.oicr.on.ca/cgi-bin/link?SOURCE=Reactome&amp;amp;ID=REACT_115639.1&quot; rel=&quot;nofollow&quot;&gt;please use this link&lt;/a&gt; to discover all the details and new papers. I'll also append some of the relevant papers below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brosnan, JT, Brosnan, ME The sulfur-containing amino acids: an overview 2006 J Nutr &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16702333&quot; rel=&quot;nofollow&quot;&gt;PMID 16702333&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remethylation of homocysteine to methionine can also happen using betaine as a methyl donor. This reaction is also part of choline catabolism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Li, F, Feng, Q, Lee, C, Wang, S, Pelleymounter, LL, Moon, I, Eckloff, BW, Wieben, ED, Schaid, DJ, Yee, V, Weinshilboum, RM Human betaine-homocysteine methyltransferase (BHMT) and BHMT2: common gene sequence variation and functional characterization 2008 Mol Genet Metab &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18457970&quot; rel=&quot;nofollow&quot;&gt;PMID 18457970&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bearden, SE, Beard RS, Jr, Pfau, JC Extracellular transsulfuration generates hydrogen sulfide from homocysteine and protects endothelium from redox stress 2010 Am J Physiol Heart Circ Physiol &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20817827&quot; rel=&quot;nofollow&quot;&gt;PMID 20817827&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dominy, JE, Stipanuk, MH New roles for cysteine and transsulfuration enzymes: production of H2S, a neuromodulator and smooth muscle relaxant 2004 Nutr Rev &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15497768&quot; rel=&quot;nofollow&quot;&gt;PMID 15497768&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stipanuk, MH, Ueki, I Dealing with methionine/homocysteine sulfur: cysteine metabolism to taurine and inorganic sulfur 2011 J Inherit Metab Dis &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20162368&quot; rel=&quot;nofollow&quot;&gt;PMID 20162368&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chiku, T, Padovani, D, Zhu, W, Singh, S, Vitvitsky, V, Banerjee, R H2S biogenesis by human cystathionine gamma-lyase leads to the novel sulfur metabolites lanthionine and homolanthionine and is responsive to the grade of hyperhomocysteinemia 2009 J Biol Chem &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19261609&quot; rel=&quot;nofollow&quot;&gt;PMID 19261609&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="3340" LastEditDate="2014-10-31T13:20:49.927" LastActivityDate="2014-10-31T13:20:49.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3373" PostTypeId="2" ParentId="3346" CreationDate="2012-08-28T14:43:12.283" Score="2" Body="&lt;p&gt;You are mistaken in that the &quot;lipid hypothesis&quot; has no physiological basis like the carbohydrate biological pathways. Lipids and carbohydrates are produced and catabolized mutually from each other in the body. It's all the calories that matter (okay, proteins have a few too). Once the fat is in the body it gets turned into an energy source but it appears you are more interested what comes before. I'll quote from Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Digestion of some fats can begin in the mouth where lingual lipase&#xA;  breaks down some short chain lipids into diglycerides. The presence of&#xA;  fat in the small intestine produces hormones that stimulate the&#xA;  release of pancreatic lipase from the pancreas and bile from the liver&#xA;  for breakdown of fats into fatty acids. Complete digestion of one&#xA;  molecule of fat (a triglyceride) results in 3 fatty acid molecules and&#xA;  one glycerol molecule.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;After that, fatty acids are packed into chylomicrons and transported through the blood to where they are catabolized.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This process, however, is strongly dependend on the right mixture of bile acids and pancreas enzymes. Any deviation from the ideal leads to undigested fat in the intestine, which is usually then partly digested by bacteria (winds as byproduct) or simply excreted as fatty stool.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Digestion#Fat_digestion&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Digestion#Fat_digestion&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fatty_acid_metabolism&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Fatty_acid_metabolism&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-08-28T17:08:44.607" LastActivityDate="2012-08-28T17:08:44.607" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3374" PostTypeId="1" AcceptedAnswerId="3375" CreationDate="2012-08-28T15:31:02.433" Score="3" ViewCount="1711" Body="&lt;p&gt;With many foods today containing chemicals, agents and preservatives etc... What biological criteria must a new food and its constituent components satisfy biologically, to be defined as edible?   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example do they look at the chronic/acute affects of chemicals in the body? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question is just limited to chemicals, if a new fruit was discovered, how would it be decided if it was edible or not?&lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="43" LastEditDate="2012-08-28T15:55:51.737" LastActivityDate="2012-08-28T17:23:33.637" Title="What Defines a Food as Edible?" Tags="&lt;nutrition&gt;&lt;food&gt;&lt;toxicology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3375" PostTypeId="2" ParentId="3374" CreationDate="2012-08-28T16:19:27.720" Score="4" Body="&lt;p&gt;As far as I know, edibility (wow, I'm surprised that passes the spell checker!) is not a strictly defined term, biologically or otherwise. Humans have been around eating and drinking stuff long before the scientific method was around to study this question rigorously, and before there were regulatory agencies charged with approving new products as &quot;safe.&quot; As one might imagine, knowledge of what is and is not edible was likely passed down by oral tradition and personal experience.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Honestly, I'm not even sure designating a food (or a substance) as edible or inedible really makes much sense. Let's consider wild fruit, as mentioned in your question. If ingesting 5 or more berries of hypothetical fruit X causes your body to have a nasty reaction, then we could probably agree that fruit X is toxic and inedible (even if eating only 1 or 2 berries might not elicit the same reaction). On the other hand, ingesting berries of hypothetical fruit Y causes no reaction unless consumed in much larger quantities (maybe 100 or more berries). Although fruit Y does cause a reaction when ingested in excessive amounts, it would be a stretch to call it inedible. This principle applies to many foods that we typically consider edible but can be unhealthy or even dangerous when taken in excess.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So where do we draw the line? How much of a substance do you have to ingest without an adverse reaction to deem it edible? I don't think there is an objective answer to this question. It is complicated further by the vast amounts of variation in the human population: food allergies, differences in tolerance to certain substances, etc.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-08-28T16:19:27.720" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3376" PostTypeId="2" ParentId="3374" CreationDate="2012-08-28T17:22:55.983" Score="0" Body="&lt;p&gt;This is more a legal question, so I'll quote from what is lex in the EU:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regulation (EC) No 178/2002 of the European Parliament and of the Council of 28 January 2002 laying down the general principles and requirements of food law, establishing the European Food Safety Authority and laying down procedures in matters of food safety&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Article 2&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Definition of &quot;food&quot;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;For the purposes of this Regulation, &quot;food&quot; (or &quot;foodstuff&quot;) means any&#xA;  substance or product, whether processed, partially processed or&#xA;  unprocessed, intended to be, or reasonably expected to be ingested by&#xA;  humans.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&quot;Food&quot; includes drink, chewing gum and any substance, including water,&#xA;  intentionally incorporated into the food during its manufacture,&#xA;  preparation or treatment. It includes water after the point of&#xA;  compliance as defined in Article 6 of Directive 98/83/EC and without&#xA;  prejudice to the requirements of Directives 80/778/EEC and 98/83/EC.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&quot;Food&quot; shall not include:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(a) feed;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(b) live animals unless they are prepared for placing on the market&#xA;  for human consumption;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(c) plants prior to harvesting;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(d) medicinal products within the meaning of Council Directives&#xA;  65/65/EEC(21) and 92/73/EEC(22);&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(e) cosmetics within the meaning of Council Directive 76/768/EEC(23);&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(f) tobacco and tobacco products within the meaning of Council&#xA;  Directive 89/622/EEC(24);&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(g) narcotic or psychotropic substances within the meaning of the&#xA;  United Nations Single Convention on Narcotic Drugs, 1961, and the&#xA;  United Nations Convention on Psychotropic Substances, 1971;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(h) residues and contaminants.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=CELEX:32002R0178:EN:NOT&quot; rel=&quot;nofollow&quot;&gt;http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=CELEX:32002R0178:EN:NOT&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-08-28T17:22:55.983" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3377" PostTypeId="2" ParentId="3374" CreationDate="2012-08-28T17:23:33.637" Score="4" Body="&lt;p&gt;Much like Daniel Standage suggests, I think &quot;edible&quot; is more inferried than defined, sort of like looking at a black hole - its absence is defined by the activity around it. Human bodies are capable of metabolizing lots of compounds that become poisonous pass some threshold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In medical terms there are LDmin and MLD and LD50: miminum Lethal Dose, Median Lethal Dose, Lethal Dose for 50% of the Population respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also compounds that aren't lethal, but are definitely harmful. Trans-Fats are one, where the FDA hasn't determined any safe levels of Trans-Fats in foods; they're always dangerous and harm your system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there are materials or chemicals that will simply pass through your system without being absorbed or interferring with anything. Cellulose (refined wood pulp) is a popular additive in pre-made diet foods because it adds mass and texture while being completely indigestable since humans do not produce cellulase. The same can be said for silicone dioxide (sand), which is also very unreactive and passes through your digestive system benignly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I'd say as long as whatever is eaten is below the LDmin and/or can benignly pass through your system without damage, it is 'edible.' &lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-28T17:23:33.637" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3378" PostTypeId="2" ParentId="3365" CreationDate="2012-08-28T17:30:43.290" Score="8" Body="&lt;p&gt;In high school, we did an experiment that showed this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, if you take a glass of water, and let it sit out, perhaps in front of an open window, it will eventually lose water due to evaporation. It may take a few days/weeks to really see a large difference, but the level will go down. But, if you take a few flexible straws, put them in so the bendy part is submerged, the water level will drop much more quickly. (I'm not exactly sure if the bendy straw part is really that important here. Logically, I don't think it is, but I haven't done the experiment so I can't really say.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason the straws cause evaporation to happen more quickly is because as wind blows across the top of the straws, it pulls some of the water with it. And because, as the last person said, of cohesion and adhesion, the column of water is pulled up with it and thus it evaporates faster.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, these fluid mechanics are why toilets and siphoning work. When you siphon, you create a low pressure area inside the tube, like you are sucking out of a straw. Because of this low pressure, liquid is pulled into the tube. If you fill the tube with liquid, and turn the tube down toward the ground so the liquid starts coming out the end, the force of the liquid coming out of the tube creates low pressure in the tube again, thus causing more liquid to be sucked up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is very similar to how trees work. In the stomata, or the pores in the leaves that allow the leaves to &quot;breathe,&quot; wind helps to pull the water out of the pores. But because of the decrease in pressure cause by the liquid being sucked out of the pore, water gets pulled up the tubes in the tree (xylem).&lt;/p&gt;&#xA;" OwnerUserId="1325" LastActivityDate="2012-08-28T17:30:43.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3379" PostTypeId="1" AcceptedAnswerId="3383" CreationDate="2012-08-28T18:38:36.180" Score="11" ViewCount="1036" Body="&lt;p&gt;A healthy immune response to a bacterial infection includes &quot;memory&quot; to permit the body to thwart subsequent exposure to same bacteria.  What are the dynamics of using antibiotics on initial exposure to the bacteria regarding a possible degradation of the quality of this &quot;memory&quot; and thus the body's possibly compromised ability to fight a repeat exposure to same bacteria ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not speaking of vaccines ... focus here is on bacteria &lt;/p&gt;&#xA;" OwnerUserId="1068" LastEditorUserId="1068" LastEditDate="2019-02-14T21:45:18.730" LastActivityDate="2019-02-14T21:45:18.730" Title="Do antibiotics attenuate immune response on subsequent exposure to same bacteria?" Tags="&lt;molecular-biology&gt;&lt;immunology&gt;&lt;bacteriology&gt;&lt;antibiotics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="3380" PostTypeId="2" ParentId="1403" CreationDate="2012-08-28T18:51:47.123" Score="4" Body="&lt;p&gt;No. Accent is purely environmental. The ability to pick up the unique sounds of a language or variation of a language ceases around puberty: &lt;a href=&quot;http://en.wikipedia.org/wiki/Language_acquisition&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Language_acquisition&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is why adults learning a second language have trouble distinguishing the unique sounds of the second language. For learners of English, the &quot;th&quot; sounds and the difference between &quot;l&quot; and &quot;r&quot; can be difficult. For languages based on Sanskrit, there are a variety of aspirated/unaspirated consonants somewhere between &quot;b&quot; and &quot;v&quot; that English-speakers have a hard time distinguishing, much less imitating.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="3952" LastEditDate="2013-08-04T02:07:48.963" LastActivityDate="2013-08-04T02:07:48.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3381" PostTypeId="2" ParentId="3379" CreationDate="2012-08-28T19:19:00.777" Score="2" Body="&lt;p&gt;Edited for Clarity:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to invoke a memory response or create a memory response, there &lt;em&gt;must&lt;/em&gt; be interaction with the Adaptive Immune System (usually CD40+ &quot;Helper&quot; T-Cells), and the interaction &lt;em&gt;must&lt;/em&gt; come in the form of a protein since the MHC receptors only respond to proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antibiotics are usually smaller macromolecules that directly cause slower growth or kill the microbe. They will &lt;strong&gt;*&lt;em&gt;not&lt;/em&gt;*&lt;/strong&gt; create or illicit a memory response because they are not presented to the immune system to initiate the proper procedure, and may not be proteins and unable to be presented in the first place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're asking about vaccines (which was my inference before the edit), then they stimulate what is basically the same memory creation mechanisms that normal infections do. Antibody counterparts recognized by B-Cells are paired with proteins from the disease you want to immunize against, called the Hapten and Carrier respectively. Then the protein is processed via the B-Cells, presented to T-Cells, and a memory response is made.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My apologies if the previous answer was more ambiguous.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2012-08-28T21:43:03.783" LastActivityDate="2012-08-28T21:43:03.783" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3382" PostTypeId="2" ParentId="2393" CreationDate="2012-08-28T21:17:48.320" Score="1" Body="&lt;p&gt;I remember doing this experiment many years ago in an undergraduate practical where we used vigorous vortexing of culture samples in glass tubes to achieve interruption and separation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21351/&quot; rel=&quot;nofollow&quot;&gt;Griffiths AJF, Gelbart WM, Miller JH, &lt;em&gt;et al.&lt;/em&gt; &lt;strong&gt;Modern Genetic Analysis&lt;/strong&gt;. Bacterial Conjugation&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... sampling is accomplished by using a kitchen blender to separate&#xA;  the joined cells, resulting in interrupted conjugation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="836" LastEditDate="2012-08-28T23:46:44.773" LastActivityDate="2012-08-28T23:46:44.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3383" PostTypeId="2" ParentId="3379" CreationDate="2012-08-29T08:04:26.420" Score="8" Body="&lt;p&gt;A quick search on ISI Web of Knowledge yielded this paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;R J North, P A Berche and M F Newborg (1981) Immunologic consequences of antibiotic-induced abridgement of bacterial infection: effect on generation and loss of protective T cells and level of immunologic memory. Journal of Immunology &lt;strong&gt;127&lt;/strong&gt;: 342-346&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors investigated the effects of ampicillin treatement in mice infected with Listeria monocytogenes. They reported an abridgement of T cell-mediated antibacterial immunity and in particular an effect upon the development of memory:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Moreover, Ampicillin-induced abridgement of infection, either before or at the time of peak primary response, resulted in the expression of greatly reduced levels of immunologic memory at a later time. This indicates that memory cells are generated throughout the entire course of the primary anti-Listeria response, including the period of its decay.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Presumably any treatment that reduces the need for an immune response will have an effect upon the production of useful memory T cells.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-08-29T08:04:26.420" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3384" PostTypeId="1" AcceptedAnswerId="3385" CreationDate="2012-08-29T12:35:32.647" Score="5" ViewCount="907" Body="&lt;p&gt;Humans normally have 46 chromosomes (two copies - one from each parent - of each of the 24 chromosomes: [1:22] + [XX or XY]). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aneuploidy is an abnormal number of chromosomes - Down's syndromes is an example of this, where individuals have an additional copy of chromosome 21.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read a little about gender-related aneuploidy, where individuals can have additional sex-specific chromosomes (for example XXY). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering what (roughly) the prevalence of the different combinations are, what the specific phenotypes are, and what (if any) medical complications can arise from these combinations, or indeed, what advantages could be conferred by the additional chromosome!&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;47,XXX&lt;/li&gt;&#xA;&lt;li&gt;47,XXY&lt;/li&gt;&#xA;&lt;li&gt;47,XYY&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;My question also stretches to whether the different combinations display a hermaphroditic phenotype?&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2012-08-29T13:08:15.213" LastActivityDate="2012-08-29T18:39:56.737" Title="What phenotypes can arise from gender-related aneuploidy?" Tags="&lt;genetics&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3385" PostTypeId="2" ParentId="3384" CreationDate="2012-08-29T13:14:21.080" Score="11" Body="&lt;p&gt;Note that anyone with a Y chromosome is considered a genetic male. Also, aneuploidy is usually a result of nondisjunction (but can have other causes as well) and is usually not inherited.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;47,XXX is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Triple_X_syndrome&quot; rel=&quot;nofollow&quot;&gt;Triple X syndrome&lt;/a&gt; and occurs in approximately 1 in 1,000 female births. These individuals usually appear normal, but may have tall stature, a small head, and delayed development. According to &lt;a href=&quot;http://content.karger.com/produktedb/produkte.asp?DOI=10.1159/000076532&quot; rel=&quot;nofollow&quot;&gt;this case report&lt;/a&gt;, the tall stature is possibly due to SHOX gene triplication, in some cases. The &lt;a href=&quot;http://en.wikipedia.org/wiki/SHOX_gene&quot; rel=&quot;nofollow&quot;&gt;short stature homeobox gene (SHOX)&lt;/a&gt; gene is a gene on the X and Y chromosome and is associated with short stature if a copy of the gene is missing or mutated. The case report states, &quot;The enhancing effect of SHOX gene triplication on growth was ascribed to the concomitant absence of gonadal steroids in cases of gonadal dysgenesis, allowing a prolonged period of growth.&quot;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;47,XXY is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Klinefelter%27s_syndrome&quot; rel=&quot;nofollow&quot;&gt;Klinefelter's syndrome&lt;/a&gt;. Here is an &lt;a href=&quot;http://men.webmd.com/male-with-klinefelter-syndrome&quot; rel=&quot;nofollow&quot;&gt;image/diagram of symptoms&lt;/a&gt;. These people may have gynecomastia (enlarged breasts), less muscle, less body hair, and hypogonadism (decreased testicular function, also resulting in smaller testicles and penis) due to lower testosterone production. These &lt;a href=&quot;http://www.mayoclinic.com/health/klinefelter-syndrome/DS01057/DSECTION=symptoms&quot; rel=&quot;nofollow&quot;&gt;symptoms&lt;/a&gt; become more obvious after puberty, because individuals with Klinefelter's have less &quot;masculinization&quot; (for lack of a better word). Cognitive problems are usually present. It occurs in roughly 1 in 500 to 1 in 1,000 male births.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;47,XYY is &lt;a href=&quot;http://en.wikipedia.org/wiki/XYY_syndrome&quot; rel=&quot;nofollow&quot;&gt;XYY syndrome&lt;/a&gt; and has an incidence of 1 in 1,000 male births. They appear normal but may be slightly taller than average. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2876236/&quot; rel=&quot;nofollow&quot;&gt;This study&lt;/a&gt; looked at the cognitive and motor phenotypes of boys with Klinefelter's and XYY syndromes. It found that both groups have generalized cognitive impairment, but XYY has more profound language impairment and Klinefelter's has more significant motor impairment. Their hypothesis is that &quot;the more severe language-based cognitive phenotype in XYY versus KS is likely to be genetically determined on the basis of abnormal dosage of specific Y chromosome genes, but not abnormal levels of testosterone because XYY is not associated with testicular failure.&quot;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;There's also 45, X0 (&lt;a href=&quot;http://en.wikipedia.org/wiki/Turner_syndrome&quot; rel=&quot;nofollow&quot;&gt;Turner syndrome&lt;/a&gt;), in which girls have a webbed neck,  broad chest, low-set ears, short stature, gonadal dysfunction, and often other conditions such as a bicuspid aortic valve, coarctation of the aorta, and vision problems. &lt;a href=&quot;http://turnersyndromepictures.com/Noonan-Syndrome.php&quot; rel=&quot;nofollow&quot;&gt;Image of symptoms&lt;/a&gt;. It occurs in 1 in 2,000 live births. Individuals usually have 1 X chromosome, but may also have 2 X chromosomes, with 1 of them being incomplete (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001417/&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;). The single copy of the SHOX gene (mentioned above) has been linked to the short stature in Turner syndrome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, people with 47,XYY and 47,XXX people often have normal fertility, but not in the other two cases. My uneducated guess is that the extra &quot;normal&quot; chromosome (for the person's sex) doesn't disrupt gonadal function.&lt;/p&gt;&#xA;" OwnerUserId="1166" LastEditorUserId="1166" LastEditDate="2012-08-29T18:39:56.737" LastActivityDate="2012-08-29T18:39:56.737" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3386" PostTypeId="2" ParentId="3354" CreationDate="2012-08-29T17:46:57.670" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.vivo.colostate.edu/hbooks/genetics/medgen/chromo/mosaics.html&quot; rel=&quot;nofollow&quot;&gt;Chimerism&lt;/a&gt; (or genetic mosaicism if the cells come from the same zygote) is possible in the same organ or tissue. I don't think you will see a homogeneous distribution of the chimeric tissue because the tissue in any vertebrate organ is rarely homogeneous to begin with. &lt;a href=&quot;http://en.wikipedia.org/wiki/Microchimerism&quot; rel=&quot;nofollow&quot;&gt;Microchimerism&lt;/a&gt; may occur in a small number of cells. That's about all I know.&lt;/p&gt;&#xA;" OwnerUserId="1335" LastActivityDate="2012-08-29T17:46:57.670" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3388" PostTypeId="1" CreationDate="2012-08-29T18:28:07.997" Score="6" ViewCount="87" Body="&lt;p&gt;Presently I am working on metagenomics of coal biomethenation by bacterial consortium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have got the sequence result (Illumina). The sequence is huge and I can't predict anything from the sequence.&#xA;I have gone through different database like Metacyc, Biocyc etc.&#xA;Please help me that how can I draw an inference towards the metabolic enzyme that are involved in biomethenation of coal.&lt;/p&gt;&#xA;" OwnerUserId="1337" LastEditorUserId="69" LastEditDate="2012-08-29T20:29:26.317" LastActivityDate="2012-08-30T07:28:48.457" Title="Predicting and identifying microbes and enzymes DNA sequence with metabolic prediction" Tags="&lt;metabolism&gt;&lt;enzymes&gt;&lt;sequence-analysis&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3390" PostTypeId="2" ParentId="3388" CreationDate="2012-08-29T20:51:41.747" Score="0" Body="&lt;p&gt;Well first off, we don't know how you sequenced the data. What did you actually sequence? Did you look at transcriptional activity using RNA-seq or did you do a full genome sequencing. Were there any paired-end reads? How did you create your library? Did you enrich the bacterial consortium for biomethanation activity?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where do you reads map? The consortium complicates things but you will likely need to build a quality contig library before you do anything else. Without a doubt, much of your library will not map to anything interesting but you should still annotate the library by seeing where the reads map up. Identifying ORFs will be useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Likely, you will have a set of genes that will be involved with biomethanation. You should BLAST the bejesus out of your contig library for hits. Do they match any of your ORFs? Going the otherway, do your ORFs match any of the genes in EcoCyc or BioCyc. Do you need to use a larger database? &lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-08-29T20:51:41.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3391" PostTypeId="2" ParentId="3388" CreationDate="2012-08-30T06:44:54.410" Score="2" Body="&lt;p&gt;The first step after sequencing is finding probable genes. After that, genes and their proteins can be classified to belong to protein classes. This is the most what you can do with completely unknown genes. It's possible nowadays to predict the final structure using contact maps (if there is no homologous structure known) but this will still leave you unclear on ligands in many cases. So, the final step is to clarify the function with biochemical lab methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if you are stuck with a huge sequence, first try to find the genes in it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Gene_prediction&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Gene_prediction&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For subsequent annotation/classification, I recommend InterPro and PROSITE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ebi.ac.uk/Tools/pfa/iprscan/&quot; rel=&quot;nofollow&quot;&gt;http://www.ebi.ac.uk/Tools/pfa/iprscan/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://prosite.expasy.org/scanprosite/&quot; rel=&quot;nofollow&quot;&gt;http://prosite.expasy.org/scanprosite/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-08-30T07:28:48.457" LastActivityDate="2012-08-30T07:28:48.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3392" PostTypeId="1" CreationDate="2012-08-30T06:55:34.830" Score="5" ViewCount="245" Body="&lt;p&gt;I would like to measure the surface density of &lt;em&gt;Staphylococcus&lt;/em&gt; bacteria and Rhinoviruses (only those two, to be specific) within my home.  What's the cheapest way?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The textbook procedure is to:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;rub a clean wet cotton swab on the surface in a controlled way&lt;/li&gt;&#xA;&lt;li&gt;dip the swab into a clean agar (or some living media to detect viruses?) dish&lt;/li&gt;&#xA;&lt;li&gt;incubate the dish&lt;/li&gt;&#xA;&lt;li&gt;&quot;look for genetic patterns from special enzyme reactions&quot;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Is it possible to do the last step at home?  Or, is there some easier way if I only care about &lt;em&gt;Staphylococcus&lt;/em&gt; bacteria or Rhinoviruses?&lt;/p&gt;&#xA;" OwnerUserId="1339" LastEditorUserId="16866" LastEditDate="2017-01-11T22:58:13.123" LastActivityDate="2017-06-11T18:24:39.347" Title="Cheapest way to measure S. aureus and Rhinoviruses density at home" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;virology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3393" PostTypeId="1" AcceptedAnswerId="3396" CreationDate="2012-08-30T12:31:56.183" Score="15" ViewCount="57593" Body="&lt;p&gt;In humans, each cell normally contains 23 pairs of chromosomes, for a total of 46. Monkeys, chimpanzees, and Apes have 24 pairs (twenty-four pairs), for a total of 48. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What caused humans to have 46?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&#xA;@TomD is right, I was asking why we have one less chromosome pair than chimpanzees (for example) [23 pairs instead of 24].&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="43" LastEditDate="2014-05-19T20:07:22.180" LastActivityDate="2017-01-31T22:32:49.780" Title="Evolutionarily speaking, why do humans have 46 chromosomes" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;dna&gt;&lt;chromosome&gt;&lt;cytogenetics&gt;" AnswerCount="4" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3394" PostTypeId="2" ParentId="3393" CreationDate="2012-08-30T13:38:47.037" Score="8" Body="&lt;p&gt;@nico is right.  the number of chromosomes is the result of an evolutionary timeline, puncutated by sometimes spontaneous events which shape the DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These events occur in the course of evolution:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Chromosomal rearrangements.  Large sections of the genome can flip around or become integrated in other chromosomes.  By homologous recombination, regions of the genome can clip themselves out or duplicate themselves as well.  If you look at the alignment of human to say chimp, there are many segments that move relative to each other. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) chromosomal breaking or combination.  Two smaller chromosomes may combine to form a larger one, or a larger one may break into two smaller chromosomes.  An example of this is human chromosome 2, which is found as two smaller chromosomes in the great apes (&lt;a href=&quot;http://en.wikipedia.org/wiki/Chimpanzee_genome_project&quot; rel=&quot;noreferrer&quot;&gt;see figure in wikipedi&lt;/a&gt;a).  We infer that this is a combination event exclusive to humans by comparing the other apes on the evolutionary tree.  Birds and reptiles tend to have lots of chromosomal breakage, even to the point  where the number of &lt;a href=&quot;http://en.wikipedia.org/wiki/Microchromosome&quot; rel=&quot;noreferrer&quot;&gt;microchromosomes&lt;/a&gt; (less than 20 million bases).  Mammals tend to be more conservative and not allow viable chromosomal breaks - chickens have 78 chromosomes to our 23..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) idiomatic chromosomal behavior.  Sex determining chromosomes are examples of chromosomes where a pair becomes distinctly different in size and composition.&lt;br&gt;&#xA;Another example is in trypanosome which has many tiny DNA segments which code for variant surface coat proteins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) @rwst points, what I clean forgot, that occasionally (like maybe just a few times) there have been &lt;a href=&quot;http://genomevolution.org/wiki/index.php/Whole_genome_duplication#Detecting_paleopolyploidy&quot; rel=&quot;noreferrer&quot;&gt;whole genome duplications&lt;/a&gt;.  This can be identified by chromosomal alignments within a single genome and has not happened very often since we became eukaryotic metazoans.  Not sure how many times, but perhaps just once or twice in our lineage.  If anyone knows about animals/humans that would be great. As you can see the link shows whole genome duplications in plants, which don't seem care how many chromosomes there are.  Plants have polyploidy, you see, so such duplication events are much better tolerated.  On the other hand plants can't play video games. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;P. Dehal, J. L. Boore: &lt;em&gt;Two rounds of whole genome duplication in the ancestral vertebrate.&lt;/em&gt; In: &lt;em&gt;PLoS biology.&lt;/em&gt; 3, 10, Oct 2005, e314, &lt;a href=&quot;http://dx.plos.org/10.1371/journal.pbio.0030314&quot; rel=&quot;noreferrer&quot;&gt;doi:10.1371/journal.pbio.0030314&lt;/a&gt;. PMID 16128622. PMC 1197285.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see that these events happen at particular moments and help shape the species and the composition of the chromosomes.  It is not a priori possible to predict the number or type of chromosomes just by looking at an animal, but only by looking at the related animals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fungi and Plants have even more variations in chromosomal composition than animals.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1122" LastEditDate="2012-09-01T16:54:29.183" LastActivityDate="2012-09-01T16:54:29.183" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="3395" PostTypeId="2" ParentId="3393" CreationDate="2012-08-30T14:15:42.990" Score="7" Body="&lt;p&gt;Here is a paper you might want to take a look at:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://genome.cshlp.org/content/10/5/644.abstract&quot;&gt;Phylogenetic Origin of Human Chromosomes 7, 16, and 19 and their Homologs in Placental Mammals&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;From their origin, these chromosomes underwent the following rearrangements to give rise to current human chromosomes: centromeric fission of the two submetacentrics in ancestors of all primates (∼80 million years ago); fusion of the HSA19p and HSA19q sequences, originating the current HSA19, in ancestors of all simians (∼55 million years ago); fusions of the HSA16p and HSA16q sequences, originating the current HSA16 and the two components of HSA7 before the separation of Cercopithecoids and Hominoids (∼35 million years ago); and finally, pericentric and paracentric inversions of the homologs to HSA7 after the divergence of orangutan and gorilla, respectively. Thus, compared with HSA16 and HSA19, HSA7 is a fairly recent chromosome shared by man and chimpanzee only.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1210" LastActivityDate="2012-08-30T14:15:42.990" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3396" PostTypeId="2" ParentId="3393" CreationDate="2012-08-30T14:38:33.093" Score="17" Body="&lt;p&gt;I think the OP is asking why we have &lt;strong&gt;one less chromosome pair&lt;/strong&gt; than chimpanzees (for example) [23 pairs instead of 24].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The is an abundance of evidence, as alluded to &lt;a href=&quot;https://biology.stackexchange.com/a/3394/1136&quot;&gt;above&lt;/a&gt; by &lt;a href=&quot;https://biology.stackexchange.com/users/77/shigeta&quot;&gt;shigeta&lt;/a&gt;, that human chromosome 2 is the result of a &lt;strong&gt;telomere-to-telomere fusion of two ancestral chromosomes&lt;/strong&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC52649/pdf/pnas01070-0197.pdf&quot; rel=&quot;noreferrer&quot;&gt;IJdo&lt;/a&gt; &lt;em&gt;et al&lt;/em&gt;., 1991).  This event did not occur in our closest ancestors, hence we have one less chromosome pair.  In fact the sequence of human chromosome 2 contains the relic of an ancestral telomere-telomere fusion (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC52649/pdf/pnas01070-0197.pdf&quot; rel=&quot;noreferrer&quot;&gt;IJdo&lt;/a&gt; &lt;em&gt;et al&lt;/em&gt;., 1991).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pdf of this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC52649/pdf/pnas01070-0197.pdf&quot; rel=&quot;noreferrer&quot;&gt;key reference&lt;/a&gt; is freely available to all from PNAS &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;IJdo, J.W, Baldini, A, Ward, D.C, Reeders, S.T, Wells, R.A. (1991) Origin of human chromosome 2: an ancestral telomere-telomere fusion  &lt;em&gt;Proc Natl Acad Sci U S A.&lt;/em&gt;, &lt;strong&gt;88&lt;/strong&gt; 9051-9055.[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC52649/pdf/pnas01070-0197.pdf&quot; rel=&quot;noreferrer&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually it has now been shown that Neanderthals and Denisovans also exhibit the same chromosomal fusion as humans - &lt;a href=&quot;http://m.motherjones.com/politics/2014/02/evolution-creationism-bonobos-neanderthals-denisovans-chromosome-two&quot; rel=&quot;noreferrer&quot;&gt;http://m.motherjones.com/politics/2014/02/evolution-creationism-bonobos-neanderthals-denisovans-chromosome-two&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2016-07-31T19:41:16.227" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3397" PostTypeId="2" ParentId="3346" CreationDate="2012-08-30T15:02:32.303" Score="3" Body="&lt;p&gt;I think you're confounding two separate things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Lipid Hypothesis is about the creation of atherosclerosis (&lt;em&gt;only&lt;/em&gt; atherosclerosis) and was proposed as an explanation for why plaques of cholesterol, fatty acids, and somatic cells form in arteries. It does not try to explain adipocyte behavior, which would result in weight gain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the Lipid Hypothesis, after the glycerol has been removed from fatty acids, they are free to diffuse into the blood and can start plaques.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Weight Gain/Loss due to adipocyte behavior is significantly more complicated. One of the weight-related regulatory hormones present in adipose tissue is Leptin: &lt;a href=&quot;http://en.wikipedia.org/wiki/Leptin&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Leptin&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And a more scholarly article from 1995 discussing Leptin:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v395/n6704/abs/395763a0.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nature/journal/v395/n6704/abs/395763a0.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Leptin helps inhibit appetite, along with Ghrelin and a host of other molecules that control hunger and keep track of nutrient levels. However, as the wiki article states, Leptin and Insulin based activities are the primary functions of adipocytes, so a high-fat diet would conceivably deal with either or both of those molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the quirks of Leptin is that fad dieting or starvation techniques have a very undesirable affect on Leptin levels (for &lt;em&gt;years&lt;/em&gt; after a starvation diet, sometimes) that cause adipocytes to accumulate lipids that they normally would not have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obesity can also cause Leptin resistance (which &lt;em&gt;might&lt;/em&gt; be aggravated by Fructose intake: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11723062&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/11723062&lt;/a&gt; ), much the same way that a diet rich in simple sugars can cause Type II Diabetes: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8532024&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/8532024&lt;/a&gt;  The Leptin levels are at the expected concentrations in obese individuals, but the proper neuro-receptor activity isn't taking place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Come to think of it, this may be what you're after. High fat diets will result in more Leptin and thus quicker/more Leptin resistance. Once Leptin resistance occurs, the mechanisms for controlling hunger are no longer as effective as they once were, resulting in more food intake and more weight gain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the actual satiatory signal of Leptin is still debated. Some researchers have proposed that it's more of a &quot;starvation&quot; signal than a &quot;satiation&quot; signal, and thus Leptin resistance might be a normal condition when energy-dense foods are widely available: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19644451&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/19644451&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-08-30T15:02:32.303" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="3398" PostTypeId="2" ParentId="3346" CreationDate="2012-08-30T17:07:57.723" Score="0" Body="&lt;p&gt;First, dietary fat itself accumulates without big biochemical modifications: indeed dietary triglycerides are preferentially uptaken in white adipose tissue according to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17192479&quot; rel=&quot;nofollow&quot;&gt;Bickerton et al. Diabetes 2007 56(1):168-76&lt;/a&gt;. So no complicated pathway: you eat fat, you store fat. If you eat more fat than the amount you dispose, you accumulate fat and get obese.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, continuted ingestion of dietary fat, and particularly &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12643169&quot; rel=&quot;nofollow&quot;&gt;saturated fat, facilitates insulin resistance&lt;/a&gt;. Therefore, insulin is less effective to drive glucose entering in the cells. Sometimes, you may want to eat something sweet as well, but because insulin is less effective, more glucose remains in the blood driving the typical complicances of the metabolic syndrome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At this point, the increased glycemia causes the same interferences described in the carb hypothesis.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-08-30T17:07:57.723" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3399" PostTypeId="1" CreationDate="2012-08-30T18:17:10.823" Score="3" ViewCount="300" Body="&lt;p&gt;Sunlight doesn't penetrate beyond a couple of hundred feet from the surface of the ocean. Species that exist at greater depth probably live in a state of perpetual night; yet from a quick google image search (i agree it isn't a very authoritative source) for deep ocean species I see that plenty of these have eyes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So ...&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Are the sight organs in deep oceans species merely a remnant from an earlier era?&lt;/li&gt;&#xA;&lt;li&gt;If they are a remnant, has evolution/mutation modified these organs over time? &lt;/li&gt;&#xA;&lt;li&gt;Regardless of whether the organs of sight are vestigial organs for deep ocean species, how do the eyeballs withstand the extreme pressure of water in the deeps?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="43" LastEditDate="2012-08-30T20:08:57.650" LastActivityDate="2018-06-29T18:01:47.447" Title="Is vision a vestigial sense for deep ocean species?" Tags="&lt;evolution&gt;&lt;physiology&gt;&lt;mutations&gt;&lt;ichthyology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3400" PostTypeId="2" ParentId="3399" CreationDate="2012-08-30T19:47:56.303" Score="6" Body="&lt;p&gt;I can't answer your third, but I can answer your first two. With one word, in fact:&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;Bioluminescence&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://brightnepenthe.blogspot.com/2010/08/palate-cleanser-90.html&quot; rel=&quot;noreferrer&quot;&gt;http://brightnepenthe.blogspot.com/2010/08/palate-cleanser-90.html&lt;/a&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/c4a6A.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;That's the deep ocean at night for ya. Unlike underground environments and caves, it's not pitch black pretty much anywhere in the ocean. There are things to see everywhere, and they play an important role in predator/prey relationships and/or mating. The absence of natural light does make things harder to see, but that's why you see the enormous eyes on species which live far down. So, nope! The eyes on deep ocean critters are not vestigial. They're very functional (and, if anything, probably increased in sensitivity).&lt;/p&gt;&#xA;&lt;p&gt;The basics are summed up here: &lt;a href=&quot;http://www.lifesci.ucsb.edu/%7Ebiolum/functions.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.lifesci.ucsb.edu/~biolum/functions.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-08-30T19:47:56.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3401" PostTypeId="1" AcceptedAnswerId="3416" CreationDate="2012-08-30T20:04:11.270" Score="7" ViewCount="178" Body="&lt;p&gt;In the scifi novel &lt;a href=&quot;http://en.wikipedia.org/wiki/Lucifer%27s_Hammer&quot; rel=&quot;nofollow&quot;&gt;Lucifer's Hammer&lt;/a&gt;, one of the characters (a biologist, if I remember correctly) finds himself in a post-apocalyptic world and tries to make penicillin to save his own life. To do this, he repeatedly states that he needs &quot;a goat&quot; - for some reason which is never explained.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that penicillin (in its various forms) is a byproduct of some types of fungi (see Wikipedia), but I can't make sense of the statement &quot;I need a goat to make it&quot;. Assuming you don't have a chemical lab at your disposal (think &quot;post-apocalyptic world&quot;), does this requirement make any sense to any of you (apart from &quot;I need to eat the goat to stay alive long enough to find a deserted biochemical lab&quot; :-) )?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, how would you go about finding or making penicillin in such an environment?&lt;/p&gt;&#xA;" OwnerUserId="1344" LastEditorUserId="69" LastEditDate="2012-12-02T15:48:37.510" LastActivityDate="2012-12-02T15:48:37.510" Title="Making penicillin using animals - specifically, a goat" Tags="&lt;biochemistry&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3402" PostTypeId="1" AcceptedAnswerId="3411" CreationDate="2012-08-30T22:26:22.167" Score="4" ViewCount="196" Body="&lt;p&gt;Typically, when performing gene-knockout, the experimenters select one gene to remove/replace-with-junk and then see if the prokaryote can still undergo fission. If it continues to reproduce then the gene is labeled as non-essential; if the organism cannot reproduce then the gene is labeled as essential; and some-times (if the organism can reproduce but only for a &lt;a href=&quot;https://biology.stackexchange.com/q/2977/500&quot;&gt;certain number of generations&lt;/a&gt;) the gene is labeled as quasi-essential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Typically, if gene X is essential, and you knock-out both gene X and some other gene Y then the organism still dies; this is an example of monotonic behavior. However, this doesn't always have to be the case, it could be that gene X is essential only in the presence of gene Y (for instance if the two proteins produced are in a delicate feedback loop). &lt;strong&gt;Is there examples when knocking out gene X makes the organism nonviable, but knocking out gene X &lt;em&gt;and&lt;/em&gt; Y maintains viability?&lt;/strong&gt; In the most extreme case, &lt;strong&gt;is there an example where both gene X and Y are essential, but if both are knocked-out then the organism is still viable?&lt;/strong&gt; I am primarily interested in simple prokaryotes (an answer for &lt;em&gt;Mycoplasma genitalium&lt;/em&gt; or &lt;em&gt;Escherichia coli&lt;/em&gt; would be best) but more complicated organisms are preferred over no answer.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2016-05-27T13:42:29.913" Title="Non-monotonic knock-out effects in prokaryotes" Tags="&lt;genetics&gt;&lt;microbiology&gt;&lt;mycoplasma&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3403" PostTypeId="1" AcceptedAnswerId="3522" CreationDate="2012-08-31T01:44:21.117" Score="4" ViewCount="128" Body="&lt;p&gt;What are the different, &lt;strong&gt;high-level&lt;/strong&gt;, &lt;strong&gt;disjunct&lt;/strong&gt; (mutually exclusive at one particular point in time) programs or pathways along which a eukaryotic animal cell can follow? Examples of programs would include growth, cell division, senescence and quiescence. Are there programs that differ between cell types?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any I'm missing? If so, references much appreciated.&lt;/p&gt;&#xA;" OwnerUserId="609" LastEditorUserId="609" LastEditDate="2012-09-12T13:59:22.113" LastActivityDate="2012-09-16T18:25:42.343" Title="What are the different, high-level programs along which a eukaryotic animal cell can follow?" Tags="&lt;cell-biology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3404" PostTypeId="1" CreationDate="2012-08-31T01:51:40.683" Score="6" ViewCount="465" Body="&lt;p&gt;I find a number of contradictory sources regarding the tissues in which hTERT - the protein - is expressed. Does anybody know some resource that authoritatively (as authoritative or widely-accepted as is possible) lists the various tissues and hTERT's protein expression levels?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any similar resource for gene expression of hTERT?&lt;/p&gt;&#xA;" OwnerUserId="609" LastActivityDate="2012-08-31T14:06:42.873" Title="Where can I find the tissue-specific protein expression levels for hTERT (telomerase subunit)?" Tags="&lt;proteins&gt;&lt;gene-expression&gt;&lt;telomere&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3405" PostTypeId="2" ParentId="3404" CreationDate="2012-08-31T07:16:26.540" Score="3" Body="&lt;p&gt;I have found that biogps.org has all expression data I need:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biogps.org&quot; rel=&quot;nofollow&quot;&gt;https://biogps.org&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biogps.org/#goto=genereport&amp;amp;id=7015&quot; rel=&quot;nofollow&quot;&gt;https://biogps.org/#goto=genereport&amp;amp;id=7015&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-08-31T14:06:42.873" LastActivityDate="2012-08-31T14:06:42.873" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3406" PostTypeId="2" ParentId="2935" CreationDate="2012-08-31T14:57:24.043" Score="8" Body="&lt;p&gt;Lipid catabolism provides energy mainly through fatty acid beta-oxidation. This process goes through a spiral of four mitochondrial enzymatic steps: one is catalyzed by the mitochondrial trifunctional3-ketoacyl-CoA thiolase (gene HADH). The activity of this thiolase is very low in neurons, explaining the brain need of alternative energy sources. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3654601&quot;&gt;Yang et al., JBC 1987&lt;/a&gt;. As previosly mentioned, developing erythrocytes eliminates mitochondria trough autophagy (mitophagy), therefore they became unable to efficiently perform lipid catabolism. &lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-08-31T14:57:24.043" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3407" PostTypeId="1" AcceptedAnswerId="3414" CreationDate="2012-08-31T17:14:11.607" Score="9" ViewCount="9430" Body="&lt;p&gt;Often, genetics studies, especially genome wide ones, talk about &quot;focal copy number variations&quot; in genes or regions of the chromosome. I know what a copy number variation is. What does &quot;focal&quot; mean, exactly?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there non-focal CNVs? What are they? Where did the term &quot;focal&quot; originate? Is there a specific paper that coined (and hopefully unambiguously defined) the term?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A search for &quot;focal copy number variation&quot; on Google Scholar should turn up plenty of papers &lt;em&gt;about it&lt;/em&gt;. The GISTIC algorithm is a popular computational method for finding putative CNVs- so information about this algorithm may have some clues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;ftp://ftp.broadinstitute.org/pub/genepattern/modules_public_server_doc/GISTIC.pdf&quot;&gt;documentation text&lt;/a&gt; for one GISTIC implementation on the Broad Institute's website states the following:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(8) Broad or Focal: Identifies whether the region reaches significance due &#xA;  primarily to broad events (called “broad”), focal events (called “focal”), or &#xA;  independently significant broad and focal events (called “both”).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2012-08-31T17:22:50.110" LastActivityDate="2012-09-02T15:18:44.307" Title="What is a focal copy number variation?" Tags="&lt;genetics&gt;&lt;terminology&gt;&lt;copy-number-variation&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3408" PostTypeId="1" AcceptedAnswerId="3438" CreationDate="2012-08-31T18:31:58.847" Score="3" ViewCount="442" Body="&lt;p&gt;From &lt;a href=&quot;http://newswatch.nationalgeographic.com/2012/08/29/university-of-cape-town-researchers-believe-they-have-found-a-single-dose-cure-for-malaria/&quot; rel=&quot;nofollow&quot;&gt;National Geographic&lt;/a&gt;, there has been a lot of hype on Kelly Chibale's work from University of Cape Town on the aminopyridine MMV390048. Unfortunately, this was from an announcement from an internal meeting so there is very little literature on the compound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I ask, does anyone have good literature on the compound?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-09-18T12:25:48.753" Title="Looking for Kelly Chibale's paper on Malaria cure" Tags="&lt;pharmacology&gt;&lt;literature&gt;&lt;malaria&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3409" PostTypeId="1" AcceptedAnswerId="3418" CreationDate="2012-08-31T18:40:27.210" Score="3" ViewCount="151" Body="&lt;p&gt;Which part of a female mantises's DNA causes her to be a few times larger than a male mantis?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do other species have that part of DNA?&lt;/p&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="62" LastEditDate="2012-09-02T03:10:28.847" LastActivityDate="2013-08-12T06:12:17.793" Title="Which part of a female mantises's DNA causes her to be a few times larger than a male mantis?" Tags="&lt;genetics&gt;&lt;entomology&gt;&lt;genomics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3410" PostTypeId="2" ParentId="3296" CreationDate="2012-08-31T20:24:34.643" Score="3" Body="&lt;p&gt;In the study by Whitfield 1990 (&lt;a href=&quot;http://dx.doi.org/10.1016/0169-4758%2890%2990146-U&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;) I found the information that the parasitic wasp from family &lt;em&gt;Ichneumonidae&lt;/em&gt; have interesting symbiotic viruses called polydnaviruses. This virus stay as provirus in the wasps genome and is transmitted vertically between subsequent generations of parasitoid. It does not harm the wasp and it is transmitted to the wasps hosts (usually caterpillar). The virus does not replicate in the caterpillar, but alter it's physiology: supress immune response and metamorphosis and increases the amount of nutrients in caterpillars hemolymph. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still, I have not found any references about this kind of virus altering the behaviour of the caterpillar after the emergence of wasps larvae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/0169-4758%2890%2990146-U&quot; rel=&quot;nofollow&quot;&gt;[1] Whitfield, J. B. (1990). Parasitoids, Polydnaviruses and Endosymbiosis. Parasitology Today, 6(12), 381-384.&lt;/a&gt; (&lt;a href=&quot;http://insects.tamu.edu/students/grad/gcourses/ento621/password/discusstopics/pdv1.pdf&quot; rel=&quot;nofollow&quot;&gt;free PDF&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="68" LastActivityDate="2012-08-31T20:24:34.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3411" PostTypeId="2" ParentId="3402" CreationDate="2012-08-31T21:44:58.367" Score="2" Body="&lt;p&gt;Here is an example in which the knockout of a non-essential gene in yeast (Saccharomyces cerevisiae) suppresses the lethal effects of a different knockout.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Amy L. Kistler and Christine Guthrie (2001) Deletion of MUD2, the yeast homolog of U2AF65, can bypass the requirement for Sub2, an essential spliceosomal ATPase. Genes &amp;amp; Development 15:42-49&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The SUB2 gene encodes a protein which is a component of the TREX complex required for nuclear mRNA export. Deletion of the SUB2 gene is lethal. The MUD2 gene encodes a non-essential protein involved in pre-mRNA splicing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors show that - &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;...the essential requirement for the SUB2 ATPase can be bypassed by deletion of the nonessential splicing factor MUD2...&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Detailed information about these (and all other) Saccharomyces cerevisiae genes is freely available at the &lt;a href=&quot;http://www.yeastgenome.org/&quot; rel=&quot;nofollow&quot;&gt;Saccharomyces Genome Database&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-09-01T11:58:25.950" LastActivityDate="2012-09-01T11:58:25.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3412" PostTypeId="2" ParentId="3408" CreationDate="2012-09-01T06:57:51.647" Score="5" Body="&lt;p&gt;This may be the paper you are looking for:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.bmcl.2012.06.010&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Ongaroraa DSB, Gutb J, Rosenthalb PJ, Masimirembwac CM, Chibale K&lt;/strong&gt;. 2012. Benzoheterocyclic amodiaquine analogues with potent antiplasmodial activity: Synthesis and pharmacological evaluation. Bioorganic &amp;amp; Medicinal Chemistry Letters, 22(15): 5046–5050, doi:10.1016/j.bmcl.2012.06.010.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1345" LastEditorUserId="43" LastEditDate="2012-09-18T12:25:48.753" LastActivityDate="2012-09-18T12:25:48.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3413" PostTypeId="2" ParentId="3408" CreationDate="2012-09-01T07:54:56.767" Score="5" Body="&lt;p&gt;I don't know anything about this topic, but I did find this recent paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Kamaljit Singh,Hardeep Kaur, Kelly Chibale, Jan Balzarini, Susan Little, Prasad V. Bharatam (2012) 2-Aminopyrimidine based 4-aminoquinoline anti-plasmodial agents. Synthesis, biological activity, structure–activity relationship and mode of action studies. European Journal of Medicinal Chemistry 52:82–97&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors analyse a range of compounds for in vitro anti-plasmodial activity. The most active is named 5-isopropyloxycarbonyl-6-methyl-4-(2-nitrophenyl)-2-[(7-chloroquinolin-4-ylamino)butylamino] pyrimidine (referred to as 10r in the paper).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although the code name MMV390048 does not appear in the paper the strategy that this group is following is discussed in detail. My guess would be that MMV390048 is a development of 10r.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the structure of 10r as depicted in Table 1 of the paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IRFAi.png&quot; alt=&quot;structure of 10r&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-01T07:54:56.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3414" PostTypeId="2" ParentId="3407" CreationDate="2012-09-01T10:48:14.567" Score="6" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;A copy number variation (CNV) is when the number of copies of a particular gene varies from one individual to the next.&lt;/p&gt;&#xA;&lt;p&gt;From: &lt;a href=&quot;http://ghr.nlm.nih.gov/glossary=copynumbervariation&quot; rel=&quot;nofollow noreferrer&quot;&gt;the NIH Glossary&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Focal CNVs are regions of repeated genetic information that only span a small proportion  (&amp;lt;25%) of the chromosome arm (although this does not seem to be a consistent rule), and can contain few genes. CNVs greater than this are termed either 'large-scale' or 'broad'.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;Here are some relevant papers I came across (no doubt there are more);&lt;/p&gt;&#xA;&lt;p&gt;This paper is about a program (VarScan2) the authors have made to robustly detect somatic mutations and CNVs;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;To identify SCNAs [&lt;em&gt;somatic copy number alterations&lt;/em&gt;], VarScan 2 compares Q20 (base quality &amp;gt;=20) read depths between tumor and normal samples for contiguous regions of coverage ... Therefore, we apply a circular binary segmentation (CBS) algorithm (Seshan and Olshen 2010) to delineate segments by copy number and identify significant change-points. &lt;strong&gt;A subsequent joining procedure merged adjacent segments of similar copy number and classified them as either large-scale (&amp;gt;25% of chromosome arm) or focal events.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;From: &lt;a href=&quot;http://dx.doi.org/10.1101/gr.129684.111&quot; rel=&quot;nofollow noreferrer&quot;&gt;Koboldt D, &lt;em&gt;et al&lt;/em&gt;, 2012&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I continued searching, as I wondered whether this was a standard definition, or just one used by the authors.&lt;/p&gt;&#xA;&lt;p&gt;This paper is reporting bacterial genes that drive focal chromosomal aberrations, but do not give a great definition (as it seem quite arbitrary to me);&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Many of these [chromosomal] aberrations concern large chromosomal regions, which makes it difficult to identify actual driver genes. Increased resolution has led to the detection of &lt;strong&gt;focal chromosomal aberrations, defined as 3 Mb or smaller in size&lt;/strong&gt; [5–8]. Inherent to their size, focal aberrations contain a small number of genes, facilitating driver gene identification&lt;/p&gt;&#xA;&lt;p&gt;From: &lt;a href=&quot;http://dx.doi.org/10.1002/path.2724&quot; rel=&quot;nofollow noreferrer&quot;&gt;Brosens R, &lt;em&gt;et al&lt;/em&gt;, 2010&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This extract is from one of the studies referenced by the previous paper (when they mention their definition of focal CNVs). This paper is about CNVs in different tumour cells;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Primary tumors contain varying proportions of nonneoplastic cells thereby obscuring focal amplifications, defined by the increased copy number of a small region of the genome, from simple gains of whole chromosome arms.&lt;/p&gt;&#xA;&lt;p&gt;From: &lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0808041105&quot; rel=&quot;nofollow noreferrer&quot;&gt;Leary RJ, &lt;em&gt;et al&lt;/em&gt;, 2008&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-09-02T15:18:44.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3415" PostTypeId="2" ParentId="3403" CreationDate="2012-09-01T14:10:21.667" Score="5" Body="&lt;p&gt;To see the width of your question, have a look at what the Gene Ontology considers a cellular process:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0009987#term=children&quot; rel=&quot;noreferrer&quot;&gt;http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0009987#term=children&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think you can agree on what's high-level, so it's better to see them all, I think. Also, for completeness, there is a list with cell types which is admirably maintained:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_distinct_cell_types_in_the_adult_human_body&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/List_of_distinct_cell_types_in_the_adult_human_body&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-09-01T14:10:21.667" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3416" PostTypeId="2" ParentId="3401" CreationDate="2012-09-01T15:17:24.080" Score="4" Body="&lt;p&gt;Here is a link to a &lt;a href=&quot;http://www.doomandbloom.net/2011/05/making-penicillin-at-home.html&quot; rel=&quot;nofollow&quot;&gt;survivalist blog&lt;/a&gt; with a protocol for making penicillin. (I'm not recommending this by the way.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible that the reference to the goat in Lucifer's Hammer is for the extraction of insulin (from the pancreas)? Have a look at the Wikipedia entry for Eva Saxl - in Shanghai during WWII her husband kept her alive with insulin extracted from water buffalo pancreas.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-01T15:17:24.080" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="3417" PostTypeId="2" ParentId="3020" CreationDate="2012-09-01T15:39:47.233" Score="2" Body="&lt;p&gt;Many years ago I worked in the field of bacterial chemotaxis, and your question brought this paper to mind:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;JL Spudich &amp;amp; DE Koshland Jr. (1976) Non-genetic individuality: chance in the single cell. Nature &lt;strong&gt;262&lt;/strong&gt;:467-471.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors report an analysis of the chemotactic behaviour of individual bacterial cells from a single homogeneous culture. They find marked differences between individuals, and their favoured model is what they refer to as a Poissonian variation in the inheritance of key proteins that are present in small numbers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to ISI Web of Science this paper has been cited 241 times - presumably at least some of those papers might be about other more recent examples of this type of phenomenon.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-01T15:39:47.233" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3418" PostTypeId="2" ParentId="3409" CreationDate="2012-09-01T16:19:32.203" Score="7" Body="&lt;p&gt;Insects and spiders have tremendous sexual dimorphism, with males often being much smaller than females.  They are pretty much just sperm carriers and sometimes do not eat.  &lt;a href=&quot;http://www.nature.com/scitable/topicpage/genetic-mechanisms-of-sex-determination-314&quot; rel=&quot;nofollow&quot;&gt;Insects may have two or one sex chromosome, where males my have only one chromosome&lt;/a&gt;.   As is pointed out in the comments, &lt;a href=&quot;http://www.keepinginsects.com/praying-mantis/distinguishing-males-and-females/&quot; rel=&quot;nofollow&quot;&gt;not all mantis' species display this dimorphism&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since such dimorphism is probably due to small changes in the genome due to environmental selection pressures and the genetic mechanisms of control are probably not simple.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its difficult to say which genes are responsible for size per-se.  Recent studies of human height indicate that scores of genes may be involved in human size and insects have at least as many genes as humans do; &lt;a href=&quot;http://www.nature.com/ng/journal/v42/n7/abs/ng.608.html&quot; rel=&quot;nofollow&quot;&gt;it is pretty hard to look at a human genome sequence and say what height that person is without some other help&lt;/a&gt;.  I imagine for specific insect species this too would be difficult. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-08-12T06:12:17.793" LastActivityDate="2013-08-12T06:12:17.793" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3419" PostTypeId="2" ParentId="2420" CreationDate="2012-09-01T20:02:49.517" Score="2" Body="&lt;p&gt;I think the explanation for this description of fish oils as &quot;easily oxidised&quot; can be found in the Introduction to the actual paper (Nutrition 27 (2011) 334–337) that is cited in the article linked to in the question.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fish oil contains high levels of eicosapentaenoic acid (EPA; 20:5 omega-3) and docosahexaenoic acid (DHA; 22:6 omega-3), which are omega-3 polyunsaturated fatty acids. EPA, DHA, and fish oil have been shown to have protective effects against coronary heart disease, thrombosis, inflammatory processes, carcinomatosis, and metabolic syndrome. Therefore, fish oils and components of the oils are marketed as health supplements. However, the effects of omega-3 polyunsaturated fatty acids on aging and lifespan are unclear compared with those of omega-6 polyunsaturated fatty acids contained in safflower oil and soybean oil. EPA and DHA are oxidized easily compared with linoleic acid (18:2 omega-6) and oleic acid (18:1 omega-9) in vitro . &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In other words, the fish oil omega-3 fatty acids EPA and DHA have, respectively, 5 and 6 double bonds, whereas the omega-6 fatty acids in safflower oil, linoleic acid and oleic acid have, respectively, just 2 and 1 double bonds. So the fatty acids in fish oil are more prone to oxidation simply because they have so many more double bonds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incidentally, as you can see from the two structures below, both of the omega-3 fatty acids, EPA and DHA, also have an omega-6 double bond.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EPA:&lt;/strong&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/NpNVF.png&quot; alt=&quot;The structure of EPA&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;DHA:&lt;/strong&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/hQS0U.png&quot; alt=&quot;The structure of DHA&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-01T20:02:49.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3420" PostTypeId="1" AcceptedAnswerId="3577" CreationDate="2012-09-02T02:38:18.110" Score="7" ViewCount="481" Body="&lt;p&gt;Below are two quotes from the CDC about Hantavirus:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Researchers believe that people may be able to get the virus if they&#xA;  touch something that has been contaminated with rodent urine,&#xA;  droppings, or saliva, and then touch their nose or mouth.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;You cannot get the virus from touching or kissing a person who has HPS.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is hard to believe.  So, since human saliva is not a problem, can you be contaminated&#xA;by human urine or human droppings?  The only way for me to interpret this logically is to&#xA;say that this virus lives at the end of the digestive tract (for both rodents and humans)&#xA;and people can be kissed because they have much better hygiene than rodents.  Is there a&#xA;better interpretation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, is there a simple reason why Hantavirus leaves the mouth (moving to the end of the&#xA;digestive tract) of an infected animal, but influenza does not?&lt;/p&gt;&#xA;" OwnerUserId="1339" LastEditorUserId="43" LastEditDate="2012-09-16T23:52:28.033" LastActivityDate="2012-09-16T23:52:28.033" Title="Why are some viruses not communicable person-to-person?" Tags="&lt;virology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3421" PostTypeId="2" ParentId="3420" CreationDate="2012-09-02T07:24:04.783" Score="0" Body="&lt;p&gt;This paper is referred to in the Wikipedia entry for hantavirus as an example of human-human transmission. It may discuss the reasons why transmission is not normally via this route.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Martinez VP &lt;em&gt;et al&lt;/em&gt;. (2005) Person-to-person transmission of Andes virus. Emerg Infect Dis. &lt;strong&gt;11&lt;/strong&gt;:1848-53&lt;/p&gt;&#xA;&lt;p&gt;Despite the fact that rodents are considered to be the infectious source of hantavirus for humans, another route of transmission was demonstrated. Andes virus (ANDV) has been responsible for most of the cases recorded in Argentina. Person-to-person transmission of ANDV Sout lineage was described during an outbreak of hantavirus pulmonary syndrome in southwest Argentina. In this study, we analyzed 4 clusters that occurred in 2 disease-endemic areas for different ANDV lineages. We found new evidence of interhuman transmission for ANDV Sout lineage and described the first event in which another lineage, ANDV Cent BsAs, was implicated in this mechanism of transmission. On the basis of epidemiologic and genetic data, we concluded that person-to-person spread of the virus likely took place during the prodromal phase or shortly after it ended, since close and prolonged contact occurred in the events analyzed here, and the incubation period was 15-24 days.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-09-02T07:24:04.783" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3422" PostTypeId="1" AcceptedAnswerId="3424" CreationDate="2012-09-02T18:34:30.993" Score="8" ViewCount="2479" Body="&lt;p&gt;Mammals have lungs, so do marine mammals. Nevertheless some marine mammals seem to die rather quickly when they strand on a beach.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As they have lungs and can breath while on land, why do they die so quickly? Not being in water only restricts them from food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do they maybe try to get back into the water so rudely that they get hurt by rocks and/or break bones? Pressure difference doesn't seem to be a problem as they can jump out of the water as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering after reading &lt;a href=&quot;http://www.dailymail.co.uk/news/article-2197167/It-like-aircraft-crash-Horror-sixteen-pilot-whales-die-mass-stranding-rescuers-battle-save-rest-pod.html&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; on stranded pilot whales that got spot but died rather quickly after.&lt;/p&gt;&#xA;" OwnerUserId="1224" LastEditorUserId="43" LastEditDate="2012-09-17T13:34:02.860" LastActivityDate="2012-09-17T13:34:02.860" Title="Why do stranded marine mammals die so quickly?" Tags="&lt;zoology&gt;&lt;marine-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3423" PostTypeId="2" ParentId="3422" CreationDate="2012-09-02T18:48:52.037" Score="0" Body="&lt;p&gt;That's not exactly true, you are generalizing. For example seals are marine mammals (that's a rather large non-official group I think)  and they don't die so quickly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, breathing is not the only thing necessary for survival. If you leave a human inside a 50°C room he can still breath but won't live for long.&lt;/p&gt;&#xA;" OwnerUserId="1303" LastActivityDate="2012-09-02T18:48:52.037" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3424" PostTypeId="2" ParentId="3422" CreationDate="2012-09-02T18:56:12.917" Score="15" Body="&lt;p&gt;In the case of whales, I always thought that it was something to do with the fact that they rely upon buoyancy to support their weight and &lt;a href=&quot;http://whale.wheelock.edu/archives/ask99/0532.html&quot;&gt;this&lt;/a&gt; seems to support that view:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When whales, including small whales or dolphins become stranded on beaches&#xA;  they suffer from the pressure of their own weight on their organs,in the&#xA;  water they are weightless.  They also suffer from overheating as they have&#xA;  blubber that insulates them in the water and outside of the water causing&#xA;  them to overheat.  This is why we place wet towels and cold water on their&#xA;  fins and flukes when do they strand to help keep their body temperature&#xA;  down.  Unfortunately most stranded whales do not survive once they have&#xA;  beached themselves.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-02T18:56:12.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3425" PostTypeId="2" ParentId="2208" CreationDate="2012-09-02T22:34:09.853" Score="2" Body="&lt;p&gt;Medically, &lt;a href=&quot;http://en.wikipedia.org/wiki/Clinical_death#Limits_of_reversal&quot; rel=&quot;nofollow&quot;&gt;recovery of brain function after 3 minutes of oxygen deprivation at body temperature is rare&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further down here in &lt;a href=&quot;http://en.wikipedia.org/wiki/Clinical_death#Limits_of_reversal&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt; it indicates that at lower temperatures the time can be much longer.  At 13C, the record is 80 minutes for people.  Animals cooled to 0C have a record of recovery of three hours!  Not sure how much like themselves they feel after that though...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-09-04T04:52:12.577" LastActivityDate="2012-09-04T04:52:12.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3426" PostTypeId="2" ParentId="3227" CreationDate="2012-09-03T09:49:11.530" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;So what is the fuss about?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The fuss isn’t so much about biology as it is about the circumstances of the argument. in particular, I gather that there are two complaints people have with E. O. Wilson’s (and his collaborators’) arguments:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The Wilsonians pretend that kin selection (inclusive fitness) is just a quaint, outdated theory which is trivially dismantled because its mathematics don’t work, while in reality it represents the view of most people in the of field evolutionary biology, and has for years. Regardless of its actual scientific value, it certainly isn’t outdated – &lt;a href=&quot;http://whyevolutionistrue.wordpress.com/2012/06/26/did-human-social-behavior-evolve-via-group-selection-e-o-wilson-defends-that-view-in-the-nyt/&quot; rel=&quot;nofollow&quot;&gt;it’s the majority view among experts.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Proponents of kin selection feel that the &lt;a href=&quot;http://whyevolutionistrue.wordpress.com/2012/06/26/did-human-social-behavior-evolve-via-group-selection-e-o-wilson-defends-that-view-in-the-nyt/&quot; rel=&quot;nofollow&quot;&gt;Wilsonians misrepresent their views by citing and attacking outdated knowledge rather than the state of the art&lt;/a&gt;, thus creating a &lt;a href=&quot;http://en.wikipedia.org/wiki/Straw_man_argument&quot; rel=&quot;nofollow&quot;&gt;straw man argument&lt;/a&gt;. In the same vein, they argue that since Wilsonians obviously don’t know the state of the art, they cannot contribute meaningfully to the debate.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In addition, proponents of kin selection argue that &lt;a href=&quot;http://edge.org/conversation/the-false-allure-of-group-selection&quot; rel=&quot;nofollow&quot;&gt;group selection theory simply doesn’t hold up in theory&lt;/a&gt;&lt;sup&gt;1&lt;/sup&gt;. I find those arguments highly compelling. At the same time, I’m not an expert and the Wilsonians argue that kin selection is equally flawed so I won’t weigh in on the debate.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt; The article is &lt;em&gt;not&lt;/em&gt; written by an expert in the field but it has been endorsed by experts as a lucid explanation of the matter.&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="166" LastEditDate="2012-09-04T15:59:26.360" LastActivityDate="2012-09-04T15:59:26.360" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3427" PostTypeId="1" AcceptedAnswerId="3434" CreationDate="2012-09-03T10:24:53.157" Score="15" ViewCount="13199" Body="&lt;p&gt;I've recently seen the term &lt;em&gt;synthetic biology&lt;/em&gt; being used to describe research involving genetic modification of organisms. What is the difference between &lt;em&gt;synthetic biology&lt;/em&gt; and &lt;em&gt;genetic engineering&lt;/em&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it just a new term for the same thing, or is it something different? Does one of the two terms encompass the other?&lt;/p&gt;&#xA;" OwnerUserId="1350" LastEditorUserId="43" LastEditDate="2012-09-03T17:54:14.650" LastActivityDate="2019-02-21T14:27:35.097" Title="Difference between genetic engineering and synthetic biology" Tags="&lt;genetics&gt;&lt;synthetic-biology&gt;&lt;terminology&gt;" AnswerCount="6" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3428" PostTypeId="2" ParentId="3427" CreationDate="2012-09-03T10:56:17.067" Score="3" Body="&lt;p&gt;In genetics engineering we use and manipulate natural genetic elements but in synthetic biology we make new gene elements and network.&lt;/p&gt;&#xA;" OwnerUserId="1351" LastActivityDate="2012-09-03T10:56:17.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3429" PostTypeId="2" ParentId="3427" CreationDate="2012-09-03T11:32:25.413" Score="8" Body="&lt;p&gt;It seems to me that the difference is mainly semantic, although the aims of synthetic biology are undoubtedly more ambitious than those of genetic engineering in, say, the 80s and 90s.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Wikipedia page on &lt;a href=&quot;https://en.wikipedia.org/wiki/Genetic_engineering&quot;&gt;genetic engineering&lt;/a&gt; has this definition of the difference: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Synthetic biology is an emerging discipline that takes genetic engineering a step further by introducing artificially synthesized genetic material from raw materials into an organism.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I must say that for me this doesn't really stand up to close scrutiny. To give just just one example from my own experience - for a long time now yeast geneticists have used PCR to make DNA for targetted gene disruption. This seems to me to fit the definition in the quote: the primers were made chemically and the PCR product was made in vitro using dNTPs as raw materials. (Admittedly the template DNA would be normally produced in vivo.) But I don't think we ever thought that we were doing synthetic biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps the term &lt;em&gt;synthetic biology&lt;/em&gt; was intended to herald a new approach that would be more fundable?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I look forward to reading the responses to this rather cynical answer :)&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-03T11:32:25.413" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3430" PostTypeId="2" ParentId="1611" CreationDate="2012-09-03T14:09:20.990" Score="3" Body="&lt;p&gt;In the publication by &lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0014320&quot; rel=&quot;nofollow&quot;&gt;Leibbrandt et al.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt;, it could be shown that the iota-carrageenan directly binds to viruses and thereby prevents the attachment to cells. This is a critical step in the viral life-cycle and therefore replication is reduced. Iota carrageenan rather acts unspecifically and besides influenza also other viruses such as human Rhinoviruses are inhibited&lt;a href=&quot;http://dx.doi.org/10.1186/1743-422X-5-107&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[2]&lt;/sup&gt;&lt;/a&gt;. Similarly, a direct binding to viruses has been shown for iota-carrageenan and papillomaviruses&lt;a href=&quot;http://dx.doi.org/10.1371/journal.ppat.0020069&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[3]&lt;/sup&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In contrast to lambda carrageenan that is widely used as proinflammatory compound in animal experiments, iota carrageenan lacks this activity and therefore a pharmacological / immunological mode of action can be excluded. In addition carrageenans have a high molecular weight which makes it very unlikely that it acts systemically.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0014320&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Leibbrandt A, Meier C, König-Schuster M, Weinmüllner R, Kalthoff D, Pflugfelder B, Graf P, Frank-Gehrke B, Beer M, Fazekas T, Unger H, Prieschl-Grassauer E, Grassauer A&lt;/strong&gt;. 2010. Iota-Carrageenan Is a Potent Inhibitor of Influenza A Virus Infection. PLoS ONE, 5(12): e14320 doi:10.1371/journal.pone.0014320.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1186/1743-422X-5-107&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Grassauer A, Weinmuellner R, Meier C, Pretsch A, Prieschl-Grassauer E, Unger H&lt;/strong&gt;. 2008. Iota-Carrageenan is a potent inhibitor of rhinovirus infection. Virology Journal, 5:107, doi:10.1186/1743-422X-5-107.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1371/journal.ppat.0020069&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Buck CB, Thompson CD, Roberts JN, Müller M, Lowy DR, Schiller JT&lt;/strong&gt;. 2006. Carrageenan Is a Potent Inhibitor of Papillomavirus Infection. PLoS Pathogens, 2(7): e69, doi:10.1371/journal.ppat.0020069.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1352" LastEditorUserId="43" LastEditDate="2012-09-16T12:50:56.653" LastActivityDate="2012-09-16T12:50:56.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3431" PostTypeId="2" ParentId="3427" CreationDate="2012-09-03T14:51:17.773" Score="5" Body="&lt;p&gt;They seem to be practically the same, with the exception of the goals. &lt;em&gt;Genetic Engineering&lt;/em&gt; is the direct modification of the genes of an organism which results in capabilities being added or taken away. &lt;em&gt;Synthetic Biology&lt;/em&gt; aims to modify the behaviors of an organism or integrate the behaviors of multiple organisms into a singular whole.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As is explained in &lt;a href=&quot;http://dx.doi.org/10.1038/msb4100073&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Andrianantoandro E, Basu S, Karig DK, Weiss R&lt;/strong&gt;. 2006. Synthetic biology: new engineering rules for an emerging discipline. Molecular systems biology 2: 2006.0028&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One useful analogy to conceptualize both the goal and methods of synthetic biology is the computer engineering hierarchy (&lt;a href=&quot;http://www.nature.com/msb/journal/v2/n1/fig_tab/msb4100073_F1.html&quot; rel=&quot;nofollow&quot;&gt;Figure 1&lt;/a&gt;). Within the hierarchy, every constituent part is embedded in a more complex system that provides its context. Design of new behavior occurs with the top of the hierarchy in mind but is implemented bottom-up. At the bottom of the hierarchy are DNA, RNA, proteins, and metabolites (including lipids and carbohydrates, amino acids, and nucleotides), analogous to the physical layer of transistors, capacitors, and resistors in computer engineering. The next layer, the device layer, comprises biochemical reactions that regulate the flow of information and manipulate physical processes, equivalent to engineered logic gates that perform computations in a computer. At the module layer, the synthetic biologist uses a diverse library of biological devices to assemble complex pathways that function like integrated circuits. &lt;strong&gt;The connection of these modules to each other and their integration into host cells allows the synthetic biologist to extend or modify the behavior of cells in a programmatic fashion.&lt;/strong&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2012-09-04T12:24:09.767" LastActivityDate="2012-09-04T12:24:09.767" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3432" PostTypeId="1" CreationDate="2012-09-03T16:53:44.077" Score="3" ViewCount="64" Body="&lt;p&gt;I would like you to point me out some literature about putative epigenetic state changes in mouse/mammal sequences after cloning steps in &lt;em&gt;Escherichia coli&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This are the last search details I used in NCBI PubMed:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;epigenomics&quot;[MeSH Terms] AND &quot;cloning, molecular&quot;[MeSH Terms] OR&#xA;  &quot;molecular cloning&quot;[All Fields] AND &quot;sequence&quot;[All Fields] AND&#xA;  (&quot;escherichia coli&quot;[All Fields] OR &quot;e. coli&quot;[All Fields])&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1353" LastActivityDate="2015-01-20T20:30:11.243" Title="Literature about putative epigenetic state changes in mammal sequences after cloning steps in Escherichia coli" Tags="&lt;epigenetics&gt;&lt;cloning&gt;&lt;ecoli&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3433" PostTypeId="2" ParentId="3225" CreationDate="2012-09-04T04:52:18.147" Score="2" Body="&lt;p&gt;Your updated question is still very vague, but I'm going to assume it is basically: &quot;Why would the ancestral version of a gene be mistaken for a more recent version than the modern gene?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is incorrect, please let me know and modify your question to clarify.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The simple answer to that question is that the mutations that occurred after the &lt;em&gt;Ancestral&lt;/em&gt; gene resulted in less apparent divergence than the LCA (last common ancestor), which would cause the &lt;em&gt;Ancestral&lt;/em&gt; gene to seemingly have more polymorphisms - and the general assumption is that the more polymorphisms (mutations) that a gene has undergone, the more recent it is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So let's say you have the following DNA sequences:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5' - AAAT - 3' = LCA (Template)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5' - AAAG - 3' = Sample 1 : # Differences = 1 Nucleotide&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5' - AACG - 3' = Sample 2 : # Differences = 2 Nucleotides&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;general&lt;/em&gt; assumption is that the larger the difference from the LCA, the more mutations have occurred over time. So, under the general assumption, &lt;em&gt;Sample 2&lt;/em&gt; is probably the most recent version of the sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;However&lt;/strong&gt;, and this is what I think is the answer to your question, because mutations can occur in any order and at any place in the genome, it is &lt;strong&gt;entirely possible&lt;/strong&gt; for the third (from left) Nucleotide to have followed this mutation path: A -&gt; C -&gt; A&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That would make &lt;em&gt;Sample 2&lt;/em&gt; &lt;strong&gt;appear&lt;/strong&gt; to be more recent than it is because it essentially mutated &quot;back&quot; to the LCA version of the gene, despite being a linearly older version than &lt;em&gt;Sample 1&lt;/em&gt;. In this way, an Ancestral gene can be mistaken for a more recent evolution of a gene. This is also why genomic data is never as strong as when paired with fossil records or other corroborating data that also aligns with the genomic data's proposed timeline; though the odds of a mistake being made grow exponentially less as more of the genome is compared and analyzed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With very recent mutations; on the scale of hundreds to thousands of years, it's sometimes necessary to analyze thousands of base pairs to calculate an adequately confident answer.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-09-04T04:52:18.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3434" PostTypeId="2" ParentId="3427" CreationDate="2012-09-04T12:53:37.170" Score="9" Body="&lt;p&gt;My understanding is that synthetic biology is genetic engineering 2.0. The difference is in the approach. Whereas genetic engineering projects are usually ad hoc, synthetic biology aims to apply proper engineering principles such as standardisation, modularisation, and reusability. Synthetic biologists create and use libraries of standard parts that are characterised, so they can be easily reused in projects. A part could be a gene, a terminator, a promoter, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Synthetic biology also has greater ambitions. The focus is on creating whole systems/circuits of genetic regulation. This means there is a need for computational modelling and understanding of how biological systems work. In this aspect synthetic biology is a sister of systems biology a bit like synthetic chemistry (engineering) is a sister of chemistry (science).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could of course argue that it's just a marketing ploy to invent a new name for something that is just the next step in genetic engineering, but the differences in approach are quite large and a new name signifies it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regards to synthesised vs. PCRed DNA: It doesn't really matter which you use in synthetic biology. However, cheap synthesis is one of the technologies that enable easier synthetic biology. The idea for the future is that you will be able to synthesise whole plasmids and chromosomes instead of having to &quot;cut and paste&quot; DNA. When that happens physical parts repositories will be obsolete, but they will remain crucial &lt;em&gt;in silico&lt;/em&gt;. Cheap synthesis is nice, but doesn't make or brake synthetic biology.&lt;/p&gt;&#xA;" OwnerUserId="1355" LastEditorUserId="1355" LastEditDate="2012-09-05T15:32:13.180" LastActivityDate="2012-09-05T15:32:13.180" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3435" PostTypeId="1" CreationDate="2012-09-04T19:03:01.493" Score="8" ViewCount="713" Body="&lt;p&gt;I have designed several proteins which I predict have interactions with another protein using the sequence based Conjoint Triad Method. I would like to know which ones structurally are predicted to dock and have interactions. I have Rosetta installed and have looked at the examples a little. Rosetta doesn't have much &quot;how to&quot; documentation on protein design and fitness selection. Could someone please walk me through the process line by line of taking a fasta with a series of proteins through rosetta's ab initio pdb generation and then how to and where to look for a fitness of each proteins interaction/docking? Also I read in &lt;a href=&quot;http://web.mit.edu/biology/keating/extra_files/scottchen_thesis_020612.pdf&quot; rel=&quot;nofollow&quot;&gt;&quot;Design of Protein-Protein Interaction Specificity Using Computational Methods and Experimental Library Screening&quot;&lt;/a&gt; page 91 that it was possible to generate specific protein combinations that map to a structure using Rosetta. How do you do that?&#xA;thank you :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.rosettacommons.org/manuals/rosetta3_user_guide/file_fragments.html&quot; rel=&quot;nofollow&quot;&gt;Rosetta commons&lt;/a&gt; links to additional software add ins but omits the crucial Sparks-X. I found Sparks-X from at this &lt;a href=&quot;http://sparks.informatics.iupui.edu/yueyang/download/index.php&quot; rel=&quot;nofollow&quot;&gt;webpage&lt;/a&gt;. And I found that the code for make_fragments.pl needs to have many changes made for it to run properly. Several files are listed in make_fragments.pl. Two files without links pdb_seqres.txt and entries.idx are found at RSCB, below. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The NCBI nr database requires about 100 gigs of free space to properly load and process. Anything less than that results in errors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;make_fragments.pl requires a single gene in a fasta file. multiple genes in the fasta file cause it it crash.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Psipred nolonger has a dat4 so this line needs in make_fragments needs to have the dat4 removed. &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&quot;$PSIPRED sstmp.mtx $PSIPRED_DATA/weights.dat $PSIPRED_DATA/weights.dat2 $PSIPRED_DATA/weights.dat3 $PSIPRED_DATA/weights.dat4 &amp;gt; psipred_ss&quot;,&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;My make_fragments does not always finish it sometimes gives an error &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ERROR: Error reading in FragmentPicker::read_spine_x(): does not match size of query!&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This error was caused by a ^M in the fasta file removed with vi.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm attempting to bypass the fragment picker with csrosetta toolkit from .csrosetta.org/&lt;/p&gt;&#xA;&#xA;&lt;p&gt;libstdc++6 32bit version must be used for talos+&#xA;I used a Ubuntu 32 bit machine to copy the /usr/lib/libstdc++.so.6 and uploaded it here.&#xA;&lt;a href=&quot;http://www.mediafire.com/?j0133qqwiilsuz1&quot; rel=&quot;nofollow&quot;&gt;http://www.mediafire.com/?j0133qqwiilsuz1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;cs-rosetta does not create fragments for unknown reason. I have emailed the creator and I have emailed rosetta commons support as well. For now I recomend the on-line server roberta. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are examples of how to use prepacking and docking in rosetta_tests.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PPI can be designed by docking a protein to another protein then running sequence tolerance. Though the resfile doesn't seem to be able to limit the changes to certain nt at this point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sequence tolerance has an extra rotamer bug and fills up memory and the page file for certain proteins if the &quot;ex&quot; series flags are use. It also sometimes ignores the resfile so double check the initial scripts results before begining a multi-generational study. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ab initio relax has a bug which prevents it from running twice in the same directory. Remove default.out to rerun the structure prediction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Docking can be forced to one location by using a constraints file but the radomize and spin options must be turned off for it to work properly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;-constraints:cst_weight integer&#xA;-constraints:cst_file cstfile&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/de/d50/constraint_file.html&quot; rel=&quot;nofollow&quot;&gt;http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/de/d50/constraint_file.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/summaries.html&quot; rel=&quot;nofollow&quot;&gt;http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/summaries.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2012-09-18T20:57:02.870" LastActivityDate="2013-12-18T19:50:48.460" Title="Rosetta ab initio prediction and protein-protein interaction fitness help" Tags="&lt;proteins&gt;&lt;structural-biology&gt;&lt;protein-binding&gt;&lt;protein-engineering&gt;&lt;structure-prediction&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="1" ClosedDate="2014-03-23T13:33:38.883" CommunityOwnedDate="2012-09-07T02:21:22.767" ContentLicense="CC BY-SA 3.0" />
  <row Id="3436" PostTypeId="1" CreationDate="2012-09-04T21:37:03.960" Score="0" ViewCount="331" Body="&lt;p&gt;From what ancestors did humans inherit orgasm?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do fish experience orgasm?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are the male and female orgasm the homologues that can be traced to the time when there was no difference in sex between individuals (as in fish) or developed independently?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="408" LastEditDate="2012-09-05T08:16:53.563" LastActivityDate="2012-09-05T13:42:32.580" Title="From which ancestor species did humans inherit orgasm?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="3438" PostTypeId="2" ParentId="3408" CreationDate="2012-09-05T05:55:22.870" Score="0" Body="&lt;p&gt;It turns out that TomD is the winner. That particular paper is an amino-pyridine class and exhibits single-dose efficacy. Amazingly, the other two papers mentioned by Satz and Alan Boyd are leads for other classes of compounds with Satz's paper focused on an amodiaquine derivative and Alan's paper focused on an alternative 2 amino-pyridine backbone also based off amodiaquine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jm3001373&quot; rel=&quot;nofollow noreferrer&quot;&gt;3,5-Diaryl-2-aminopyridines as a Novel Class of Orally Active Antimalarials Demonstrating Single Dose Cure in Mice and Clinical Candidate Potential&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vUfA7.png&quot; alt=&quot;MMV390048&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-09-05T05:55:22.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3439" PostTypeId="1" CreationDate="2012-09-05T07:15:38.813" Score="6" ViewCount="2252" Body="&lt;p&gt;At least according to a few sources &lt;a href=&quot;http://www.prozyme.com/faqs/pjg0006.html&quot;&gt;Prozyme&lt;/a&gt; and &lt;a href=&quot;http://www.protocol-online.org/biology-forums/posts/20105.html&quot;&gt;Protocols-Online&lt;/a&gt;, it is possible to reuse desalting columns and since I'm cheap I would like to also.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Key things seem to be washing with several column volumes of your buffer of choice. Also certain columns like crosslinked desalting columns are not amenable to regeneration. I'm curious about other factors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm mainly using Bio-Rad micro-spins&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-09-05T11:40:14.943" Title="What are good practices with reusing desalting columns" Tags="&lt;lab-techniques&gt;&lt;lab-reagents&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3440" PostTypeId="2" ParentId="3439" CreationDate="2012-09-05T11:40:14.943" Score="2" Body="&lt;p&gt;Regardless of what protocol you use, and what the advertised efficacy of that protocol might be, in any situation like this I think the important thing to consider is: what would happen if the material taken from a re-used column was contaminated by a previous application? Can you live with the consequences of such contamination? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are preparing DNA for further use (PCR and/or cloning and/or transformation) then you run the risk of propagating a contaminant through subsequent steps and getting into a real mess. I worked in a lab once where one postgrad ended up spending several weeks working with a cloned fragment that was actually derived from someone else's work in the same lab (although not due to re-use of a column as far as I remember). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are preparing protein samples then the risks are possibly reduced, but if the protein sample is going to be subjected to sensitive methods (blotting, MS) then again, could get messy.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-05T11:40:14.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3441" PostTypeId="2" ParentId="3436" CreationDate="2012-09-05T13:42:32.580" Score="3" Body="&lt;p&gt;Let's assume that pleasure from sexual intercourse might be indicative of some sort of orgasm. Then this would suggest that any evidence of autoerotic behaviour would point to the existence of orgasm, or certanly physical pleasure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this quotation on the Wikipedia page for &lt;a href=&quot;http://en.wikipedia.org/wiki/Animal_sexual_behaviour&quot; rel=&quot;nofollow&quot;&gt;Animal sexual behavior&lt;/a&gt;, amongst a lot of information about mammals :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many birds masturbate by mounting and copulating with tufts of grass, leaves or mounds of earth...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;apparently from Bruce Bagemihl: Biological Exuberance: Animal Homosexuality and Natural Diversity. St. Martin's Press, 1999. ISBN 0-312-19239-8&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is taken to imply that the last common ancestor of birds and mammals experienced this pleasure then we have got fairly deep into evolutionary history, although not as far as fish.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-05T13:42:32.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3442" PostTypeId="1" CreationDate="2012-09-05T14:01:35.933" Score="2" ViewCount="53504" Body="&lt;p&gt;Semen is a thick, nutritious liquid, rich in vitamins (such as C, B12), amino acids, lipids, monosaccharides (fructose), &lt;em&gt;et cetera&lt;/em&gt;. Can semen's ability to fulfill the needs of human organism provide enough essential nutrients to keep the body alive and functional? And if so, would it be a healthy life? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can a glass of ejaculate a day keep The Reaper/doctor away? If not, how long could a person survive on a &quot;diet&quot; like this?&lt;/p&gt;&#xA;" OwnerUserId="1359" LastEditorUserId="1306" LastEditDate="2012-10-09T16:25:17.607" LastActivityDate="2015-09-03T09:57:50.167" Title="Ramifications and possibility of a diet consuming exclusively of human semen" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3443" PostTypeId="2" ParentId="3442" CreationDate="2012-09-05T15:01:49.500" Score="16" Body="&lt;p&gt;No, you cannot live off of semen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://goaskalice.columbia.edu/nutritional-value-serving-semen&quot;&gt;A source from Columbia.edu&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A typical ejaculation fills up about one teaspoon; the actual amount is determined by a man's age (younger men usually make more semen), when he last ejaculated, and how long he's aroused before ejaculating, among other factors. Contrary to what you've heard, semen is not loaded with calories. Each teaspoon of ejaculate has about 5 - 7 calories and some 200 - 500 million sperm. Since sperm make up only about 1 percent of semen, what accounts for the other 99 percent? Well, its other ingredients include:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Fructose sugar&lt;/li&gt;&#xA;  &lt;li&gt;Water&lt;/li&gt;&#xA;  &lt;li&gt;Ascorbic acid (a.k.a., vitamin C)&lt;/li&gt;&#xA;  &lt;li&gt;Citric acid&lt;/li&gt;&#xA;  &lt;li&gt;Enzymes&lt;/li&gt;&#xA;  &lt;li&gt;Protein&lt;/li&gt;&#xA;  &lt;li&gt;Phosphate and bicarbonate buffers (bases)&lt;/li&gt;&#xA;  &lt;li&gt;Zinc&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;  &#xA;  &lt;p&gt;Can swallowing semen enrich a protein poor diet? Unless you're gulping gallons of it each day, it's no substitute for real nutritious cuisine! &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From a &lt;a href=&quot;http://wiki.answers.com/Q/What_is_the_nutritional_content_of_human_semen&quot;&gt;non-academic, but apparently well-informed&lt;/a&gt; source, semen contains:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Semen contains only 15 calories and boy does it have a lot of stuff in it. So let's have a look. Ejaculate contains &lt;strong&gt;ascorbic acid&lt;/strong&gt;, blood-group antigens, &lt;strong&gt;calcium&lt;/strong&gt;, chlorine, &lt;strong&gt;cholesterol&lt;/strong&gt;, &lt;strong&gt;choline&lt;/strong&gt;, citric acid, creatine, deoxyribonucleic acid (DNA), &lt;strong&gt;fructose&lt;/strong&gt;, glutathione, hyaluronidase, inositol, lactic acid, &lt;strong&gt;magnesium&lt;/strong&gt;, nitrogen, &lt;strong&gt;phosphorous&lt;/strong&gt;, &lt;strong&gt;potassium&lt;/strong&gt;, purine, pyrimidine, pyruvic acid, &lt;strong&gt;sodium&lt;/strong&gt;, sorbitol, spermidine, spermine, urea, uric acid, &lt;strong&gt;vitamin B12&lt;/strong&gt;, and &lt;strong&gt;zinc&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I've highlighted the nutritionally-relevant ingredients. You'll notice that there is some overlap - with the Columbia source. What you won't notice, though, are the rest of the Essential Vitamins and Minerals:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Vitamin A (retinol)&#xA;Vitamin B1 (thiamin)&#xA;Vitamin B2 (riboflavin, vitamin G)&#xA;Vitamin B3 (niacin, vitamin P, vitamin PP)&#xA;Vitamin B5 (pantothenic acid)&#xA;Vitamin B6 (pyridoxine, pyridoxamine, or pyridoxal)&#xA;Vitamin B7 (biotin, vitamin H)&#xA;Vitamin B9 (folic acid, folate, vitamin M)&#xA;Vitamin D (ergocalciferol, or cholecalciferol)&#xA;Vitamin E (tocopherol)&#xA;Vitamin K (naphthoquinoids)&#xA;Chloride (Cl−)&#xA;Chromium (Cr)[4]&#xA;Cobalt (Co) (as part of Vitamin B12)&#xA;Copper (Cu)&#xA;Iodine (I)&#xA;Iron (Fe)&#xA;Manganese (Mn)&#xA;Molybdenum (Mo)&#xA;Nickel (Ni)&#xA;Selenium (Se)&#xA;Sulfur (S) numerous roles[5]&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I should also mention that the specific amounts of each ingredient will vary from person to person, as &lt;a href=&quot;http://www.bbc.co.uk/sn/humanbody/truthaboutfood/sexy/spermtaste.shtml&quot;&gt;diet can play a major role in flavor&lt;/a&gt; resulting from the changed nutritional content (i.e. - higher fructose levels).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As perhaps the most reliable source I could find, there is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Semen#Composition_of_human_semen&quot;&gt;Wikipedia article with references concerning the makeup of human seminal fluid&lt;/a&gt; and has this information:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;amino acids&lt;/strong&gt;, citrate, enzymes, flavins, &lt;strong&gt;fructose&lt;/strong&gt; (2–5 mg per mL semen,&lt;a href=&quot;http://www.bbc.co.uk/sn/humanbody/truthaboutfood/sexy/spermtaste.shtml&quot;&gt;3&lt;/a&gt; the main energy source of sperm cells, which rely entirely on sugars from the seminal plasma for energy), &lt;strong&gt;phosphorylcholine&lt;/strong&gt;, prostaglandins (involved in suppressing an immune response by the female against the foreign semen), &lt;strong&gt;proteins&lt;/strong&gt;, &lt;strong&gt;vitamin C&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;acid phosphatase, citric acid, fibrinolysin, prostate specific antigen, proteolytic enzymes, &lt;strong&gt;zinc&lt;/strong&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It echoes the other sources closely, and still yields insufficient evidence that a person could live off of semen exclusively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for how long you can live? From a &lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=how-long-can-a-person-sur&quot;&gt;Scientific American article concerning starvation&lt;/a&gt; there have been confirmed instances of hungers strikes lasting up to 40 days. Assuming you could consume enough semen to sustain your body's daily Caloric requirements, you would die of malnutrition eventually. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567249/&quot;&gt;Scurvy&lt;/a&gt; - the inadequate intake of Vitamin C (Ascorbic Acid) - would probably be the culprit, as deficiency becomes clinical in 1 to 3 months with the later stages of Scurvy being: &lt;em&gt;&quot;...more severe and life threatening; common manifestations include generalized edema, severe jaundice, hemolysis, acute spontaneous bleeding, neuropathy, fever, convulsions, and death.&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that there is enough Vitamin C in semen, you would die of other deficiencies. Since Vitamin B1 (Thiamine) is water-soluble (is not stored in your fatty tissues), not found in semen at all, and the body only reserves about a month's worth, after 30 days you would start to experience &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001379/&quot;&gt;Beriberi&lt;/a&gt; - which is only slightly less fun than Scurvy.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2012-09-05T16:57:07.503" LastActivityDate="2012-09-05T16:57:07.503" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3444" PostTypeId="1" AcceptedAnswerId="3466" CreationDate="2012-09-05T15:27:04.983" Score="7" ViewCount="104" Body="&lt;p&gt;What causes a group of disembodied neurons in a dish to fire after a silence? If there are no neurons providing a stimulus for more firing (as in a dish of disembodied rat neurons), then why don't they simply cease firing after the synchronized burst completes?  &lt;/p&gt;&#xA;" OwnerUserId="1360" LastActivityDate="2012-09-07T15:14:53.513" Title="on/off behavior of neural networks" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3445" PostTypeId="1" CreationDate="2012-09-05T15:44:05.873" Score="11" ViewCount="3024" Body="&lt;p&gt;It's a curiosity question. When I'm doing minipreps after pelleting the bacteria sometimes it's very easy to resuspend them in P1 (Qiagen kit), but sometimes they form a rubbery clump that is very hard to break up with a pipette and I have to vortex the tubes. It interests me because it adds more time to my lab work and I wish I could avoid it.&lt;/p&gt;&#xA;" OwnerUserId="1355" LastEditorUserId="389" LastEditDate="2012-10-31T21:35:06.680" LastActivityDate="2014-09-02T01:32:44.307" Title="Why is it sometimes difficult to resuspend E. coli in P1?" Tags="&lt;ecoli&gt;&lt;protocol&gt;&lt;minipreps&gt;" AnswerCount="4" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3446" PostTypeId="2" ParentId="3445" CreationDate="2012-09-05T16:42:22.660" Score="4" Body="&lt;p&gt;What I do to avoid this is to ressuspend the cells by pipetting up and down the P1 (ressuspension) buffer on the side of the tube. This way, every time takes only a bit of cells every time and big clumps are avoided. The  only times I used to get big clumps hard to ressuspend were when I went poking at the pellets first.&lt;/p&gt;&#xA;" OwnerUserId="1303" LastActivityDate="2012-09-05T16:42:22.660" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3447" PostTypeId="2" ParentId="3445" CreationDate="2012-09-05T18:35:36.403" Score="8" Body="&lt;p&gt;This is particularly an issue when you do maxipreps and the pellet is 200x the size of the pellet from a miniprep. The reasons why? Maybe you're pelleting at too high of a g-force (pure speculation). Alternatively, you could be growing the cells too long. I typically miniprep after a 12 hr culture. If you're seeing any darker colors in your pellet, you have a significant amount of dead cells. Those dead lysed cells will spill out their genomic DNA which is very viscous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For maxipreps, you can't break up the pellet merely by pipetting up and down a few times and calling it a day. What you can do is swirl the side where the pellet is and breakup the clumps. Alternatively you can use a different pipet tip (for an extensive discussion on this very topic see &lt;a href=&quot;https://biology.stackexchange.com/q/2602/389&quot;&gt;Pipetting damage to cells&lt;/a&gt;). I change to a P200 for my minipreps and pipetting only the area around the pellet seems to do the trick for me. For maxipreps I use a P1000 which is better than using a 5mL syringe. &lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2012-09-05T18:35:36.403" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="3448" PostTypeId="1" CreationDate="2012-09-06T02:57:25.093" Score="4" ViewCount="140" Body="&lt;p&gt;Let us consider a gene FOO with novel type foo.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I were discussing an organism that has inherited foo in every cell during classical zygote formation, then I would ordinarily just say that the organism &lt;em&gt;has&lt;/em&gt; foo.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I were discussing a SNP of FOO that gives rise to foo in a tumor cell of an organism, I wouldn't say that the organism &lt;em&gt;has&lt;/em&gt; foo, but I might say that the &lt;em&gt;tumor has&lt;/em&gt; it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I were discussing a chimeric or mosaic organism in which some fraction of the chimera had foo and the other fraction had FOO, I would have to say something like &quot;in foo-containing cells ...&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what if I wanted to particularly draw attention to the scope of applicability of the allele in question? That is, I want to talk about the scope explicitly, rather than implicitly. How could I directly refer to the scope of applicability of an allele? Is there a single adjective that captures the concept of &quot;This organism has foo in every cell except in rare ones where a point mutation may have occurred; it's probably been inherited during normal meiosis&quot; and is there a contrasting term for &quot;The organism only has foo in a particular subset of its cells and there is some other genetic process necessary to explain that.&quot;? &lt;/p&gt;&#xA;" OwnerUserId="1364" LastEditorUserId="1364" LastEditDate="2012-09-06T12:06:53.290" LastActivityDate="2014-12-31T11:44:06.303" Title="Terminology question: the scope of an allele in an organism" Tags="&lt;genetics&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3449" PostTypeId="2" ParentId="3200" CreationDate="2012-09-06T14:25:46.090" Score="1" Body="&lt;p&gt;There definitely has to be an upstream factor that drives ALL cancers.  The fundamental common denominator of all cancers is growth and survival, basic life processes.  If you can figure out what ultimately drives these processes, you can figure out what ultimately drives ALL cancer types and subtypes.  Cancer is just diversified growth.  With an open toolbox to employ.  All cancer cells originate because of one point factor, one switch point that alters their developmental trajectory.  There are lot of variables it could be.&lt;/p&gt;&#xA;" OwnerUserId="1365" LastActivityDate="2012-09-06T14:25:46.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3450" PostTypeId="1" AcceptedAnswerId="3463" CreationDate="2012-09-06T16:07:38.300" Score="6" ViewCount="289" Body="&lt;p&gt;What are the current models/ideas describing the mechanisms explaining inheritance of methylation on DNA resp. histone level?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there evidance of this &quot;setup&quot; information being really duplicated/inherited during a cell division process?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pointers? Articles? What is the current state of knowledge regarding this?&lt;/p&gt;&#xA;" OwnerUserId="578" LastEditorUserId="948" LastEditDate="2014-01-13T21:37:01.083" LastActivityDate="2014-01-13T21:37:01.083" Title="How does &quot;inheritance of methylation&quot; of DNA and/or histones work?" Tags="&lt;dna&gt;&lt;epigenetics&gt;&lt;histone&gt;&lt;histone-modifications&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3451" PostTypeId="1" AcceptedAnswerId="5393" CreationDate="2012-09-06T19:20:36.447" Score="5" ViewCount="335" Body="&lt;p&gt;A cell is 'senescent' when is has permanently left the cell-cycle. This can be caused by stresses, or by reaching the 'Hayflick limit' (the cell has reached its replicative lifespan, as defined by its telomeres).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cells cultured &lt;em&gt;in vitro&lt;/em&gt; can be used as models to study senescence (or sometimes 'ageing', although the distinction there is not necessarily within scope of this question) by growing the same population of cells for a long time (many passages). A common method to identify a senescent cell population is to use &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11017877&quot; rel=&quot;noreferrer&quot;&gt;beta-galactosidase staining&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering to what degree senescent cells in culture (identified by beta-gal staining) are actually comparable to those you might expect &lt;em&gt;in vivo&lt;/em&gt;. I ask because it seems to me that a terminally senescent cell may not actually survive long in an organism, so what we refer to as senescent cells &lt;em&gt;in vivo&lt;/em&gt; are actually pre-senescent cells? I haven't got any basis for this, just a feeling. (Very scientific I know).&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-12-01T13:17:29.070" Title="Is cell senescence in culture comparable to that in vivo?" Tags="&lt;senescence&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3452" PostTypeId="2" ParentId="1851" CreationDate="2012-09-06T21:58:41.030" Score="3" Body="&lt;p&gt;As you've already mentioned, cells near the primate macula tend to make one to one connections.  Due to this lack of convergence they can be somewhat smaller than normal cells (particularly in the size of their dendritic arbors) earning them the moniker &quot;midget&quot; ganglion and bipolar cells (also P cells).  By reducing the magnitude of photoreceptor convergence onto ganglion cells, the retina sacrifices luminal sensitivity for spatial acuity.  Or put another way, a downstream neuron in the LGN/V1 can be more &quot;certain&quot; about which photoreceptor is sending information when light is bright, but less certain that any information is being sent when light is dim.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other side of the question you bring up is how the retinal ganglion cells themselves alter the image formed onto the photoreceptor layer.  For those that don't already know, photoreceptors are located at the very back of the retina.  Since they're the major light sensitive part of the retina, that means light has to go through the ganglion cells, bipolar cells, amacrine cells, and all of their associated processes before reaching the actual photosensitive part of the eye.  So, why not put photoreceptors at the front of the eye?  One major reason is metabolic, photoreceptors are tightly coupled with the retinal pigment epithelium which helps to re-process used photopigment as part of &lt;a href=&quot;http://en.wikipedia.org/wiki/Retinal#Visual_cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;the retina's vitamin A cycle&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can those two factors, a one to one correspondence and a decrease in thickness be present at the same time?  For reference, let's locate a cross section of a primate macula&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FUeS8.jpg&quot; alt=&quot;monkey retina h&amp;amp;e&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dark areas are cell nuclei.  The innermost layer of cells (bottom of the image) are ganglion cells, the next layer of cells up is bipolar cells (the inner nuclear layer) and the next layer up is photoreceptor cell bodies.  you can make out the cilial stalks of the photoreceptors pointing upwards toward the RPE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this image we can see a few transformations happening in the macula:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The photoreceptor layer is thicker, up to 7 or 8 cell bodies deep.  This means higher photoreceptor density.&lt;/li&gt;&#xA;&lt;li&gt;The outer plexiform layer (photoreceptors to bipolar cell connections) is considerably thicker.  A single cone should connect to fewer bipolar cells in the retina, so how does this make sense?  We'll find the answer in #3.&lt;/li&gt;&#xA;&lt;li&gt;The outer nuclear layer is only one cell thick.  This is the first layer that is actually thinner in the foveal region.  The cell bodies for photoreceptors from tis region have been displaced laterally, and the outer plexiform layer from #2 had to be larger to accommodate this lateral shift&lt;/li&gt;&#xA;&lt;li&gt;The inner plexiform layer, connections between bipolar cells and ganglion cells, is nonexistent.  Also absent is the ganglion cell layer itself.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So how do these observations resolve your question?  Quite simply, the lateral movement of information from the foveal/macular photoreceptors happens predominantly in the &lt;strong&gt;outer&lt;/strong&gt; plexiform layer.  That buys the inner plexiform layer considerably more space to further spread those signals laterally to ganglion cells, and avoids the problematic situation you suggested of having an extra-thick ring of ganglion cells immediately around the fovea.  The end result is that ganglion cells that respond to photoreceptors in the foveal region of space are even further out from the retina than the bipolar cells they connect to, which are themselves displaced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as why a cherry red spot looks so large, that honestly depends on two factors: the disease or disorder in question and the zoom used.  Bear in mind that the red color comes from, as far as I know, the blood vessels in the choroid itself.  It would therefore not necessarily correspond exactly to the size of the macula, but instead to any area which is thinned in that vicinity.  I think you'll become more comfortable with that idea if you look back at the thickness of the total retina in the above figure and notice that even outside of the foveal region it is still growing thicker.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think your question shows good instincts, because I believe that if the eye evolved to have a larger &quot;true&quot; fovea then you would get exactly what you describe: a large area of super high density vision surrounded by a region with non-linearly worse vision designed to support the central region.  Instead it appears that the primate macula is just large enough that we have a moderate sized central acute region and a (relatively) linear drop in spatial acuity moving out from it.&lt;/p&gt;&#xA;" OwnerUserId="1367" LastActivityDate="2012-09-06T21:58:41.030" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3453" PostTypeId="2" ParentId="1257" CreationDate="2012-09-06T23:30:45.683" Score="1" Body="&lt;p&gt;Glia serve the classic support role in the retina, similar to that served by neuroglia elsewhere in the CNS.  That role mostly consists of taking used neurotransmitters and recycling them such as in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Glutamate-glutamine_cycle&quot; rel=&quot;nofollow&quot;&gt;glutamate-glutamine cycle&lt;/a&gt;.  As Preece suggested, glial cells are a heterogenous group, and with a general marker like GFAP you could very well be observing two different types of glial cell, one with a uniform presentation and one specifically in the central retina.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, the most familiar type of glial cell in the retina is the Muller glial cell.  It is particularly interesting in zebrafish, where it has been shown to &lt;a href=&quot;http://dx.doi.org/10.1523/JNEUROSCI.1624-07.2007&quot; rel=&quot;nofollow&quot;&gt;act as a neural progenitor cell upon tissue damage in adult animals&lt;/a&gt;  As you can see from that article, it fits your requirement of being GFAP expressing, although I couldn't find any good flat mount pictures showing whether it was preferentially expressed in the central retina.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So that gives us two potential roles for glial cells in the zebrafish: as potential multipotent retinal stem cells and as housekeeping neurons present to clean things up.  You could come up with reasons either of those might be important in the central retina, but for my money the arguments are all pretty hypothetical: &quot;the central retina is more active and therefore has a higher requirement for removing neurotransmitter&quot; or &quot;the central retina needs to be protected from potential damage more than the peripheral&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One thing I think we have a good basis to rule out is that it's the optic nerve.  From a retinal point of view, you refer to the point where the optic nerve passes through the rest of the retina as the optic nerve head or optic disc.  Axons from ganglion cells all across the retina stretch out from their soma toward this single point.  By the time they reach the optic nerve, the vast majority of axons are far from their axon hillock.  That means that they're being propagated from one node of Ranvier to the next.  Because that process requires voltage gated ion and not neurotransmitter gated channels, there is no neurotransmitter release associated with that process and consequently no additional reason for glial cells to be present to clean up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1523/JNEUROSCI.1624-07.2007&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Bernardos RL, Barthel LK, Meyers JR, Raymond PA&lt;/strong&gt;. 2007. Late-stage neuronal progenitors in the retina are radial Müller glia that function as retinal stem cells. The Journal of neuroscience : the official journal of the Society for Neuroscience 27: 7028–40.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1367" LastEditorUserId="836" LastEditDate="2012-09-12T18:07:06.463" LastActivityDate="2012-09-12T18:07:06.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3454" PostTypeId="2" ParentId="642" CreationDate="2012-09-06T23:55:08.483" Score="4" Body="&lt;p&gt;Yes!  And no.  But first, some background.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your central nervous system has (or is believed to have, as do other primates) a number of different organizational structures.  Cells within a column (the cortex is composed of about 7 layers, and a column would be a vertical group of neurons from these layers) respond to stimuli with similar features.  There are also higher order structures of collections of columns, such as &lt;a href=&quot;http://www.nature.com/nature/journal/v442/n7105/fig_tab/nature05019_F1.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;orientation pinwheels&lt;/a&gt;&lt;sup&gt;(1)&lt;/sup&gt; &lt;img src=&quot;https://i.stack.imgur.com/xsVku.jpg&quot; alt=&quot;orientation pinwheel&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that in the above picture, color is used to indicate orientation and not what color the column responds to.  Color sensitivity itself is (as far as I'm up to date on things) simply known to occur in color opponency columns, see this &lt;a href=&quot;http://neurosciences.us/courses/vision2/Color/tso88.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper by T'So&lt;/a&gt;&lt;sup&gt;(2)&lt;/sup&gt; where for instance red and green color opponent columns would be found together more often than not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key point to take away from that is that your cortex &lt;strong&gt;has&lt;/strong&gt; to develop these columns.  Without them you wouldn't have normal color vision, even if you circumvented the retina and LGN entirely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That brings us to the &quot;Yes!&quot; part of my answer.  If you've got a person that lost their color vision late in life, they should have relatively developed color columns in their visual cortex and assuming that we could wire to those areas in a meaningful way, in sufficient resolution, and could manipulate their voltages in a directed manner (we can't) then they certainly should be able to see in color with direct cortical stimulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However if someone was born without color vision, I do not believe this would be possible.  Not without more work than simply sending a signal in, since there is &lt;a href=&quot;http://dx.doi.org/10.1038/290332a0&quot; rel=&quot;nofollow noreferrer&quot;&gt;strong evidence&lt;/a&gt;&lt;sup&gt;(3)&lt;/sup&gt; that development of the columnar organization of V1 requires visual input during later stages of development.  I have read some cases where they took people with very simple retinal diseases (photoreceptor loss) and attempted to restore their vision.  There was an extremely strong positive correlation between how old the patient was when they lost vision and the degree to which any sight could be restored.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nature05019&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Ohki K, Chung S, Kara P, Hübener M, Bonhoeffer T, Reid RC&lt;/strong&gt;. 2006. Highly ordered arrangement of single neurons in orientation pinwheels. Nature 442: 925–8.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3367218&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Ts’o DY, Gilbert CD&lt;/strong&gt;. 1988. The organization of chromatic and spatial interactions in the primate striate cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience 8: 1712–27.&lt;/a&gt; [&lt;a href=&quot;http://neurosciences.us/courses/vision2/Color/tso88.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf&lt;/a&gt;]&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/290332a0&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Swindale NV&lt;/strong&gt;. 1981. Absence of ocular dominance patches in dark-reared cats. Nature 290: 332–333.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1367" LastEditorUserId="836" LastEditDate="2012-09-07T18:25:48.537" LastActivityDate="2012-09-07T18:25:48.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3455" PostTypeId="1" AcceptedAnswerId="3459" CreationDate="2012-09-07T01:23:04.950" Score="22" ViewCount="8637" Body="&lt;p&gt;The DNA copying enzymes have a hard time working to the end of a chromosome. For circular chromosomes this is not a problem, since there is not a sharp 'end'. However, for a linear chromosome, without extra mechanisms in place, a bit of DNA is lost off the end of the chromosome after each replication. Because of this, eukaryotes have a &lt;a href=&quot;http://en.wikipedia.org/wiki/Telomere&quot; rel=&quot;noreferrer&quot;&gt;telomere&lt;/a&gt; to cap off their chromosomes.&lt;/p&gt;&#xA;&lt;p&gt;In most cells of a mutli-cellular organism, this telomere is slowly worn away after each reproduction leading to &lt;a href=&quot;http://en.wikipedia.org/wiki/Apoptosis&quot; rel=&quot;noreferrer&quot;&gt;apoptosis&lt;/a&gt;. Cells that need to reproduce indefinitely such as germ and stem cells have to invest in extra mechanisms to replenish the telomere. For multi-cellular eukaryotes I can see how this might be usefull (for instance as a cancer counter mechanism). However, multi-cellular organisms evolved from single-cell eukaryotes.&lt;/p&gt;&#xA;&lt;p&gt;I cannot see a reason for wanting apoptosis in a single-cell organism. However, single cell eukaryotes (say yeast) still have linear chromosomes with telomere caps. &lt;strong&gt;What advantage did linear chromosomes provide single-cell eukaryotes to offset the extra investment in reparing the telomere?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h3&gt;Related questions&lt;/h3&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/1090/500&quot;&gt;What is the advantage of circular DNA in bacteria? &lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-03-16T03:16:15.633" Title="Is there an advantage to linear chromosomes?" Tags="&lt;evolution&gt;&lt;dna&gt;&lt;cell-biology&gt;&lt;senescence&gt;&lt;chromosome&gt;" AnswerCount="2" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="3456" PostTypeId="1" AcceptedAnswerId="3458" CreationDate="2012-09-07T01:24:13.990" Score="6" ViewCount="207" Body="&lt;p&gt;If experiments like those of Luria and Delbruck on &lt;em&gt;E. coli&lt;/em&gt; and T1 phage are the main source of our confidence in the mutation-immunity model, is it then highly unlikely that there are other types of bacteria for which an encounter with a phage is the mutagenic (or immunity-conferring) event? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are the two possibilities in principle mutually exclusive? &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="57" LastEditDate="2012-09-07T01:37:08.043" LastActivityDate="2012-09-07T07:30:48.890" Title="Mutation-immunity in Luria-Delbruck experiment" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3457" PostTypeId="1" CreationDate="2012-09-07T05:02:14.997" Score="0" ViewCount="1465" Body="&lt;p&gt;I noticed that I sometimes get dizzy when I accidentaly breathe in too much Axe. Also, I find the smell of alchohol rich deodorants quite unpleasant. But, I was wondering, is it actually dangerous? Can some chemical (alchohol) pass the blood-brain barrier and hurt my brain? Can it hurt other organs? It might be that I'm just dizzy because of the lack of oxygen...&lt;/p&gt;&#xA;" OwnerUserId="1369" LastActivityDate="2012-09-07T12:17:59.030" Title="Is breathing in deodorant fumes dangerous for my brain?" Tags="&lt;biochemistry&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3458" PostTypeId="2" ParentId="3456" CreationDate="2012-09-07T07:30:48.890" Score="2" Body="&lt;p&gt;No. Surprisingly, there is an adaptive immune system in prokaryotes. This is still widely unknown. The newest review is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;S. Al-Attar, E. R. Westra et al: &lt;em&gt;Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes.&lt;/em&gt; In: &lt;em&gt;Biological chemistry.&lt;/em&gt; 392, 4, April 2011, 277–289. doi:10.1515/BC.2011.042. PMID 21294681. (Review).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cited from abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many prokaryotes contain the recently discovered defense system&#xA;  against mobile genetic elements. This defense system contains a unique&#xA;  type of repetitive DNA stretches, termed Clustered Regularly&#xA;  Interspaced Short Palindromic Repeats (CRISPRs). CRISPRs consist of&#xA;  identical repeated DNA sequences (repeats), interspaced by highly&#xA;  variable sequences referred to as spacers. The spacers originate from&#xA;  either phages or plasmids and comprise the prokaryotes' 'immunological&#xA;  memory'. CRISPR-associated (cas) genes encode conserved proteins that&#xA;  together with CRISPRs make-up the CRISPR/Cas system, responsible for&#xA;  defending the prokaryotic cell against invaders.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An application of the CRISPR/Cas system is the immunization of&#xA;  industry-relevant prokaryotes (or eukaryotes) against mobile-genetic&#xA;  invasion. In addition, the high variability of the CRISPR spacer&#xA;  content can be exploited for phylogenetic and evolutionary studies.&#xA;  Despite impressive progress during the last couple of years, the&#xA;  elucidation of several fundamental details will be a major challenge&#xA;  in future research.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-09-07T07:30:48.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3459" PostTypeId="2" ParentId="3455" CreationDate="2012-09-07T07:48:27.297" Score="10" Body="&lt;p&gt;I think it is the wrong question. You assume that eukaryotes developed from a single-cell organism with circular DNA. Then, clearly, there must have been an advantage of (newly) developing a linear genome. But eukaryotes could have developed from an organism with linear DNA, too. There are still a few bacterial species with linear chromosomes, so this is not unlikely. We don't know, however.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, if linearisation developed independently, you can learn from bacteria why it might have occurred:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;J. N. Volff, J. Altenbuchner: &lt;em&gt;A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution.&lt;/em&gt; In: &lt;em&gt;FEMS microbiology letters.&lt;/em&gt; 186, 2, May 2000, 143–150, PMID 10802162. (Review).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bacterial circular chromosomes have sporadically become linearised&#xA;  during prokaryote evolution. Unrelated bacteria, including the&#xA;  spirochete Borrelia burgdorferi and the actinomycete Streptomyces,&#xA;  have linear chromosomes. Linear chromosomes may have been formed&#xA;  through integration of linear plasmids. Linear chromosomes use linear&#xA;  plasmid strategies to resolve the 'end-of-replication problem', but&#xA;  they have generally retained from their circular ancestors a central&#xA;  origin of replication. Streptomyces linear chromosomes are very&#xA;  unstable and at high frequency undergo amplifications and large&#xA;  deletions, often removing the telomeres. At least in Streptomyces,&#xA;  chromosome linearity is reversible: circular chromosomes arise&#xA;  spontaneously as products of genetic instability or can be generated&#xA;  artificially by targeted recombination. Streptomyces circularised&#xA;  chromosomes are very unstable as well, indicating that genetic&#xA;  instability is not confined to the linearised chromosomes. Bacterial&#xA;  linear chromosomes may contain telomere-linked regions of enhanced&#xA;  genomic plasticity, which undergo more frequent genetic exchanges and&#xA;  rearrangements and allow differential evolution of genes, depending on&#xA;  their chromosomal location.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-09-07T07:48:27.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3460" PostTypeId="1" AcceptedAnswerId="3461" CreationDate="2012-09-07T08:50:55.903" Score="12" ViewCount="1454" Body="&lt;p&gt;I've been reading a bit about &quot;junk DNA&quot; and how much of our genome consists of this &quot;non coding DNA&quot; in comparison to &quot;coding DNA&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm just an interested layperson but I thought all combinations of three base pairs encoded one amino acid, with some amino acids being encoded by more than one combination of base pairs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if that were true then all of our DNA would encode something.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or if only a tiny percentage of our DNA is &quot;coding&quot; that would mean that the vast majority of possible combinations of three base pairs don't represent any amino acid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or it could mean that there are a small number of &quot;meaningless&quot; combinations of three base pairs, but that those combinations are vastly overrepresented in our genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which is correct? What am I missing?&lt;/p&gt;&#xA;" OwnerUserId="224" LastEditorUserId="22057" LastEditDate="2017-11-05T20:39:42.147" LastActivityDate="2017-11-05T20:39:42.147" Title="What distinguishes &quot;coding&quot; from &quot;noncoding&quot; DNA?" Tags="&lt;dna&gt;&lt;genomics&gt;&lt;human-genome&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3461" PostTypeId="2" ParentId="3460" CreationDate="2012-09-07T10:24:26.140" Score="8" Body="&lt;p&gt;You are correct in thinking that any sequence of bases corresponds, via the genetic code, to a sequence of amino acids. However not all stretches of DNA are actually transcribed into mRNA for translation into proteins. For this to happen the stretch of DNA requires (DNA-encoded) elements to promote and regulate the transcription and translation processes, and this, very broadly, is what defines a gene: a segment of DNA which has the required components to direct the synthesis of a protein (or in some cases an RNA that will not be translated into a protein). The segments of DNA that correspond to mRNA for proteins and to other RNA molecules are referred to as coding sequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I've omitted lots of details here: some genes encode RNA molecules, such as ribosomal RNAs, which are not translated into proteins; eukaryotic genes include stretches of sequence (called introns) that are spliced out of the transcript before the mRNA&gt;protein step. The original definition (if there ever was a definition) of &quot;junk&quot; DNA included these introns, as well as regions of DNA lying outside the coding sequences. We now know that there is useful information stored in much of this DNA, even though it doesn't code for anything directly via the genetic code.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-07T10:24:26.140" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3462" PostTypeId="2" ParentId="3460" CreationDate="2012-09-07T10:27:53.347" Score="7" Body="&lt;p&gt;You bring up a good point. &quot;Coding&quot; is a term that obviously carries some historical baggage that is gradually becoming less and less relevant. &quot;Coding DNA&quot; has typically been used to refer to DNA that encodes one or more functional protein products, which are constructed from an mRNA intermediate. As we've been learning over the last several years (and as was confirmed by the recent release of 30+ coordinated, high-profile publications from the &lt;a href=&quot;http://www.nature.com/encode/&quot; rel=&quot;nofollow&quot;&gt;ENCODE project&lt;/a&gt;), DNA that is not &quot;coding DNA&quot; is not &quot;junk&quot; or &quot;meaningless&quot;--it simply does not, to our knowledge, encode a protein. There is still a lot to learn about what precisely the function and purpose of this DNA is, but we do know that a lot of it is transcribed into RNA and that a lot of it has been associated with human disease.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2012-09-07T15:34:00.390" LastActivityDate="2012-09-07T15:34:00.390" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3463" PostTypeId="2" ParentId="3450" CreationDate="2012-09-07T11:36:51.333" Score="6" Body="&lt;p&gt;Jon Wilkins has a &lt;a href=&quot;http://jonfwilkins.blogspot.com/p/primers-on-imprinting.html&quot; rel=&quot;noreferrer&quot;&gt;nice introduction to imprinting&lt;/a&gt;.  He does a nice job of introducing the idea methylation and how these patterns are maintained during development and cell division.  Further, he links to some interesting papers on the subject.&lt;/p&gt;&#xA;" OwnerUserId="1210" LastActivityDate="2012-09-07T11:36:51.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3464" PostTypeId="2" ParentId="3457" CreationDate="2012-09-07T11:57:55.213" Score="2" Body="&lt;p&gt;You can definitely absorb alcohols by breathing them in.  But doing do is far less efficient than drinking alcohol, so you don't have anything to worry about on that front.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To address your concern we have to answer two questions: how much alcohol is transfered per unit time and is there a local dosing effect due to proximity to the blood brain barrier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is probably pretty obvious that while alcohol evaporates rapidly compared to water, it still takes quite awhile. Imagine trying to inhale a glass of whiskey. You would get a serious headache but 30 minutes in you would still have an almost full glass of whiskey and no alcohol buzz. For an amusing anecdote relating how hard it is to get drunk off of inhaling even from a machine designed for it, &lt;a href=&quot;http://www.msnbc.msn.com/id/6011716/ns/health-addictions/t/booze-vapor-machine-dangerous-or-not/&quot; rel=&quot;nofollow&quot;&gt;see here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the second point - Fortunately, the blood brain barrier is a two way street for alcohol, which means that you can't get drunk in your brain if you don't have high levels of alcohol in your bloodstream. The two would dialyze into a reasonably balanced equilibrium.&lt;/p&gt;&#xA;" OwnerUserId="1367" LastEditorUserId="1367" LastEditDate="2012-09-07T12:17:59.030" LastActivityDate="2012-09-07T12:17:59.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3465" PostTypeId="1" AcceptedAnswerId="3468" CreationDate="2012-09-07T14:13:11.530" Score="3" ViewCount="1457" Body="&lt;p&gt;As we have heard in the summaries of the human ENCODE project, &lt;strong&gt;80 per cent of junk DNA appears to have an essential function&lt;/strong&gt;. Many fish have a genome with only one tenth the size of a usual vertebrate genome. Why can fish have 1/10th of junk DNA and be still fully functional? What has a frog more than a fish has? I'm especially interested if we can see the difference somewhere, complexity of physiology or anatomy, or such.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Jap. puffer fish genome: 390 Megabases, 47,800-49,000 genes (UniProt)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Medaka genome: 690 Megabases, 24,600 genes&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clawed frog: 1,500 Megabases, 23,500 genes&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1320" LastEditDate="2013-01-03T15:29:08.340" LastActivityDate="2013-01-03T15:29:08.340" Title="Why is the frog genome so much larger than a fish's?" Tags="&lt;zoology&gt;&lt;physiology&gt;&lt;genomes&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3466" PostTypeId="2" ParentId="3444" CreationDate="2012-09-07T14:54:02.187" Score="4" Body="&lt;p&gt;There are a number of different wiring scenarios that could lead to this type of behavior, even in a &lt;a href=&quot;http://en.wikipedia.org/wiki/Cultured_neuronal_network&quot; rel=&quot;nofollow&quot;&gt;dissociated neuronal cell culture&lt;/a&gt;.  The two major cases are neurons that are truly isolated from each other, and collections of neurons that connect together.  Since your question refers to firing and synchronized bursts, I'll restrict my discussion to the generation of spontaneous action potentials - but keep in mind that not all synaptic communication requires an action potential (the vast majority of internal connections within the retina, for example)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of ensembles neurons in vitro, &lt;a href=&quot;http://en.wikipedia.org/wiki/Cultured_neuronal_network#Spontaneous_Network_Activity&quot; rel=&quot;nofollow&quot;&gt;spontaneous activity is fairly typical&lt;/a&gt;.  One simple way to get this activity is for a subset of cells in the network to be inherently spontaneously active.  In the case of single, isolated neurons, this kind of individual cell spontaneous activity could also result in a single neuron firing spikes in a periodic fashion.  So for example purposes, let's explore how a single cell could produce this kind of activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since action potentials are triggered by a sufficiently strong depolarization, we need to identify potential membrane polarizing sources.  When dealing with single cells, the major controllers of cell membrane voltage potential are the &lt;a href=&quot;http://en.wikipedia.org/wiki/Voltage-gated_ion_channel&quot; rel=&quot;nofollow&quot;&gt;voltage gated ion channels&lt;/a&gt;.  When open these channels can cause, depending on their type and cellular/extracellular conditions, either a depolarization or hyperpolarization in the cell.  And, most interestingly, whether they are open or not &lt;strong&gt;depends on the cell membrane's polarization state&lt;/strong&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That makes voltage gated channels excellent at feedback: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;a depolarizing channel that is depolarization gated will further activate itself once activated, leading to yet more activation.  This is a positive feedback cycle.&lt;/li&gt;&#xA;&lt;li&gt;a hyperpolarizing channel that is depolarization gated will, upon depolarization of the cell open and serve to hyperpolarize the cell until the initial depolarization has been removed.  In this way it would serve as a negative feedback source.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Physiologists have thoroughly characterized many of these cells, and they have many more states beyond an &quot;open&quot; and &quot;closed&quot;, such as different levels of &quot;inactivated&quot;.  But we don't need to know about those to answer your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The last piece we do need is &lt;a href=&quot;http://en.wikipedia.org/wiki/Brownian_motion&quot; rel=&quot;nofollow&quot;&gt;brownian motion&lt;/a&gt; which is the movement of particles due to their bombardment by other particles.  This motion can with some frequency &lt;a href=&quot;http://nerve.bsd.uchicago.edu/FB/PhysiolRev.pdf&quot; rel=&quot;nofollow&quot;&gt;cause voltage gated channels to spontaneously open or close&lt;/a&gt;, which introduces noise into the system.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can imagine, if you have a positive feedback channel that is gated spontaneously, it will make it briefly more likely for other depolarization gated channels to be activated.  Positive feedback can quickly lead to a rapid depolarization of the cell, which could be observed as a burst of spikes.  If you include a set of slower reacting depolarization gated hyperpolarizing channels, then it's easy to construct a scenario where the cell would depolarize spontaneously with no apparent input, then have a quiescent period where a prolonged hyperpolarization makes it less likely to fire spontaneously.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Voila, bursting in an isolated neuron.  Place a set of those neurons in a network and you can get generate a lot of spontaneous activity.&lt;/p&gt;&#xA;" OwnerUserId="1367" LastEditorUserId="1367" LastEditDate="2012-09-07T15:14:53.513" LastActivityDate="2012-09-07T15:14:53.513" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3467" PostTypeId="2" ParentId="3465" CreationDate="2012-09-07T15:04:04.363" Score="5" Body="&lt;p&gt;See &lt;a href=&quot;http://genomeinformatician.blogspot.co.uk/2012/09/encode-my-own-thoughts.html&quot;&gt;here&lt;/a&gt; for an ENCODE author's reflections on their use of the word &quot;functional&quot;. (I don't think anyone is using the word &quot;essential&quot;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is clear from this that, for them, one class of functional DNA is intronic DNA: i.e. introns are defined by ENCODE as functional DNA. It is well known that puffer fish have reduced genomes and that this is largely due to the presence of much smaller introns, although the number and positioning of these introns is broadly similar to what is seen in other vertebrates. One classic example of this is the huntingtin gene which is 7.5 times shorter in pufferfish than in humans even though both genes have 67 introns. In fact the average fish genome size is 5-6 times bigger than that for pufferfish (zebrafish is around this average value).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although ENCODE are defining intronic DNA as functional I don't think that they are claiming a specific function for each and every intron, let alone each base in those introns. So there is still  a lot of scope for the observed differences in genome size.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-07T15:04:04.363" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3468" PostTypeId="2" ParentId="3465" CreationDate="2012-09-07T15:31:45.857" Score="7" Body="&lt;p&gt;Genome size is a poor indicator of an organism's &lt;em&gt;complexity&lt;/em&gt; (already an ill-defined term). We cannot assume by any means that a larger genome corresponds to a more &quot;complex&quot; organism. There are some plants whose genomes are larger than most mammals, and indeed &lt;a href=&quot;http://dx.doi.org/10.1111/j.1095-8339.2010.01072.x&quot;&gt;the largest eukaryotic genome&lt;/a&gt; (at least as of 2010) is the plant &lt;em&gt;Paris japonica&lt;/em&gt;, weighing in at 1C = 152.23 pg (compared to &lt;em&gt;Homo sapiens&lt;/em&gt; at 1C = 3 pg). Anecdotally, in my previous research lab I discussed with a colleague a fungal species whose genome size differed &lt;em&gt;by orders of magnitude&lt;/em&gt; between different individuals of that species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It should &lt;em&gt;never&lt;/em&gt; surprise you to see an organism with a larger genome size than what you may consider to be a more complex organism.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-09-07T15:31:45.857" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3469" PostTypeId="1" AcceptedAnswerId="8250" CreationDate="2012-09-07T15:44:07.520" Score="4" ViewCount="105" Body="&lt;p&gt;My understanding and experience is that during the night photoreceptors are less tightly coupled to the retinal pigment epithelium.  Does this make it more likely for a retinal detachment to happen at night?&lt;/p&gt;&#xA;" OwnerUserId="1367" LastEditorUserId="107" LastEditDate="2013-05-07T12:09:22.793" LastActivityDate="2013-08-06T04:01:21.880" Title="Does retinal detachment happen more frequently at night?" Tags="&lt;vision&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3470" PostTypeId="1" CreationDate="2012-09-07T16:23:01.070" Score="3" ViewCount="473" Body="&lt;p&gt;Can you tell me is there any good softwares and tutorials which can be used to learn DNA Origami. I am new to this and want to learn from basics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Advance thanks for your help&lt;/p&gt;&#xA;&#xA;&lt;p&gt;edited: INSILICO&lt;/p&gt;&#xA;" OwnerUserId="834" LastEditorUserId="834" LastEditDate="2012-09-08T05:35:36.503" LastActivityDate="2012-09-08T05:35:36.503" Title="How to learn DNA Origami" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3471" PostTypeId="2" ParentId="2075" CreationDate="2012-09-07T16:27:32.113" Score="20" Body="&lt;p&gt;This is a very good question.  Red light is routinely used by scientific laboratories to do low light dissections of retinas, and of course it is used in other low light contexts such as printing plate development.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In both of the above contexts, you have a clear subject: the retina being dissected or the printing plate being developed.  In the case of the printing plate the film has been designed to be specifically non-reactive to red light, so red light is used because &lt;strong&gt;your eyes can see it, but the film doesn't react to it&lt;/strong&gt;.  Similarly in some scientific settings it makes sense to use red light during dissections.  Mice lack a long wavelength opsin, and therefore using a dim red light allows the experimenter to have a &lt;strong&gt;relative sight advantage compared to the mouse&lt;/strong&gt; when keeping the mouse dark adapted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But in the case you're asking about, there is no film or animal to serve as a second party.  So is there any intrinsic advantage to using red light?  As it turns out, there is.  The fovea, which is in the center of our eye and used for high acuity vision, has no rods and primarily L- or red sensitive cones.  Note the high density center area which lacks blue sensitive cones and has &lt;a href=&quot;http://www.psych.ndsu.nodak.edu/mccourt/Psy460/Color%20Vision/Color%20Vision.html&quot; rel=&quot;noreferrer&quot;&gt;2:1 red to green cones&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wIbcE.jpg&quot; alt=&quot;retinal mosaic&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So by having red light present, you stimulate this area.  But red light is present in white light, too, why not just use that?  Leonardo's answer comes the closest, but it's a little off.  &lt;strong&gt;Red light is used because it preferentially stimulates L cones more than rods&lt;/strong&gt;, but you are definitely not able to preserve night vision by using red light.  Why not?  Well it may look like it is possible to exclusively stimulate cones from the chromatic sensitivity figure &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UvNmc.png&quot; alt=&quot;chromatic sensitivity&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But that figure is 1) normalized and 2) not indicative of synaptic signal processing.  1000's of rods can converge onto a single ganglion cell, where cone convergence in the fovea can be on the order of a single cone per ganglion cell.  When it comes to perception, in order to compare the black rod line above with the red L-cone line you'd have to magnify it dramatically in size.  Practically speaking, it is nearly impossible to stimulate cone pathways without stimulating rod pathways when using a relatively broad spectrum LED that you're powering with a battery.  Maybe with a high power infrared laser.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So &lt;strong&gt;the purpose of using red light is to attempt to balance the activation of high sensitivity (red insensitive) rods with that of the low sensitivity (but red sensitive) cones in the fovea.&lt;/strong&gt;  While using a similar level of rod activation with blue light, you would perceive a &quot;blind spot&quot; where your fovea is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, instrinsically photosensitive cells (the melanopsin cells brought up) do not factor into this processing.  These cells are activated only with extraordinarily bright levels of light, and the therefore do not enter into conversations dealing with night vision.&lt;/p&gt;&#xA;" OwnerUserId="1367" LastEditorUserId="1367" LastEditDate="2012-09-07T16:33:31.370" LastActivityDate="2012-09-07T16:33:31.370" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="3472" PostTypeId="2" ParentId="3470" CreationDate="2012-09-07T16:53:36.310" Score="1" Body="&lt;p&gt;Try &lt;a href=&quot;http://cadnano.org/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;cadnano simplifies and enhances the process of designing three-dimensional DNA origami nanostructures. Through its user-friendly 2D and 3D interfaces it accelerates the creation of arbitrary designs. The embedded rules within cadnano paired with the finite element analysis performed by cando, provide relative certainty of the stability of the structures.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-07T16:53:36.310" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3473" PostTypeId="2" ParentId="839" CreationDate="2012-09-07T19:29:46.420" Score="8" Body="&lt;p&gt;This answer relates closely to the classic myth&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We only us 10% of our brain power&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As with many truisms it holds a grain of truth.  Large areas of the brain are specialized for tasks like the visual and motor cortices.  Other areas are known to be responsible for spatial memory (hippocampus) and emotional learning (amygdala).  Higher order functions like you're describing are classically assigned to the prefrontal cortex, but that means little.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because there is some level of functional specificity throughout the brain, the fMRI studies you mention generally look at many places in the brain (nearly) simultaneously.  They then compare relative activation in different areas under different conditions, and are clever about how they frame their experiments to determine which areas are associated with which responses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most common method of measuring activity is through the BOLD response, which measures haemoglobin's oxygenation state as a proxy for the amount of blood flowing into the area under the presumption that there is high metabolic demand there.  For the purposes of this discussion, this is fairly useful since glucose delivery should be a reasonable proxy for metabolic demand even if it &lt;a href=&quot;http://www.nature.com/nature/journal/v453/n7197/full/nature06976.html&quot;&gt;has limitations when it comes to predicting neural activity.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So which areas are metabolically more active while doing a cognitive activity?  In &lt;a href=&quot;http://sheng-lab.psych.umn.edu/pdf_files/Atherton_fMRI_chess.pdf&quot;&gt;this study&lt;/a&gt; they test exactly that.  Their basic finding is that chess does increase mental activity in certain areas of the brain, particularly the parietal and occipital lobes in real game conditions, and that the activation was relatively bilteral between the left and right hemispheres.  I just glanced through it, but it looks like the authors were surprised that the activation was less pre-frontal and more visuospatial.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I believe this supports the logical conclusion: thinking takes energy&lt;/strong&gt;.  But your brain is used for many things, so the change in activation is best understood in a relative sense.  Watching TV also takes energy, preferentially in the visual cortex.  As does playing ultimate frisbee, in the motor cortex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Logothetis, Nikos K., 2008. What we can do and what we cannot do with fMRI, Nature 453, 869-878&lt;/li&gt;&#xA;&lt;li&gt;Atherton M, Zhuang J, Bart WM, Hu X, He S, 2003. A functional MRI study of high-level cognition. I. The game of chess, Cognitive Brain Research 16.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1367" LastActivityDate="2012-09-07T19:29:46.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3476" PostTypeId="1" AcceptedAnswerId="14037" CreationDate="2012-09-08T09:44:56.157" Score="4" ViewCount="219" Body="&lt;p&gt;The mushrooms are gilled with a light-brown cap. The stem is widened to the base.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What species is it? Is it considered edible?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are found in mixed forest in Moscow, Russia. They grow in the ground quite separated from each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0zzZ8.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="408" LastEditDate="2012-09-08T10:27:36.853" LastActivityDate="2013-12-17T09:08:37.037" Title="What is the species of these mushrooms?" Tags="&lt;taxonomy&gt;&lt;species-identification&gt;&lt;mycology&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3477" PostTypeId="2" ParentId="3476" CreationDate="2012-09-08T10:46:07.367" Score="1" Body="&lt;p&gt;I had a quick look in my books (for the British Isles and Europe) but although I found a couple of candidates I don't feel confident in either identification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suggest that you have a look at &lt;a href=&quot;http://www.rogersmushrooms.com/&quot; rel=&quot;nofollow&quot;&gt;Roger Phillips' online identification guide&lt;/a&gt;  - this will suggest a few identification criteria that you haven't considered in your question.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-08T10:46:07.367" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="3478" PostTypeId="1" CreationDate="2012-09-08T19:18:40.530" Score="17" ViewCount="548" Body="&lt;p&gt;Is there any documented evidence for suicide among vertebrates other than humans? Lemmings not accepted !&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-09-20T16:28:51.637" LastActivityDate="2015-11-19T23:13:25.103" Title="Is there any documented evidence for suicide among vertebrates other than humans?" Tags="&lt;zoology&gt;&lt;ethology&gt;" AnswerCount="4" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="3479" PostTypeId="1" AcceptedAnswerId="3492" CreationDate="2012-09-08T21:19:19.413" Score="2" ViewCount="128" Body="&lt;p&gt;I am no biologist, but as a physicist, a spontaneous mutation (seen as a chemical transformation) should lower the energy of the system, at least locally. So I wonder if any research has been done along these lines for the DNA. &lt;/p&gt;&#xA;" OwnerUserId="1371" LastEditorUserId="43" LastEditDate="2012-09-09T22:33:20.150" LastActivityDate="2012-09-12T17:35:55.480" Title="Is DNA mutation locally energetically stabilizing the DNA molecule" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;molecular-biology&gt;" AnswerCount="3" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="3480" PostTypeId="2" ParentId="2732" CreationDate="2012-09-08T21:31:29.737" Score="6" Body="&lt;p&gt;I found this -&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Celec et al. (2003) Circatrigintan cycle of salivary testosterone in human male. Biological Rhythm Research 34: 305-315&lt;/p&gt;&#xA;&lt;p&gt;Conclusion. We believe that this is the first study demonstrating the existence of circatrigintan and circavigintan rhythms of testosterone in human males. Our findings might have implications in human physiology and pathophysiology.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;(circatrigintan = ~30 day period; circavigintan = ~20 day period&lt;/p&gt;&#xA;&lt;p&gt;also:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Celec et al (2006) Infradian rhythmic variations of salivary estradiol and progesterone in healthy men Biological Rhythm Research 37: 37-44&lt;/p&gt;&#xA;&lt;p&gt;Discussion. We believe that this is the first study to describe a 12-day (duodecimal) rhythm of salivary estradiol in men. This finding might be of importance for physiological and pathophysiological research though the pattern needs to be investigated in larger studies.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However these papers have not been widely cited so their significance is unclear. The citing articles do not lead to a body of literature on this topic.&lt;/p&gt;&#xA;&lt;p&gt;Finally, the entire text of this book:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;INTRODUCING BIOLOGICAL RHYTHMS A Primer on the Temporal Organization of Life,&#xA;with Implications for Health,Society,Reproduction and the Natural Environment &#xA;Willard L. Koukkari and Robert B. Sothern. (2006) Springer, New York.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;is available &lt;a href=&quot;http://www.scribd.com/doc/73609918/161/Infradian-Cycles&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;. There is a long discussion of infradian rhythms in men starting at page 273.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-09-09T06:40:49.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3481" PostTypeId="1" AcceptedAnswerId="5046" CreationDate="2012-09-08T23:04:03.500" Score="10" ViewCount="1067" Body="&lt;p&gt;Here's the reason why I'm asking: I've heard that it takes some time for pets(cats/dogs) to adjust to a different dry feed, where the new feed has to be mixed with the old one, slowly replacing the old one. I'm wandering if this advice has any truth in it, and if so, does this apply to humans as well?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, a cat eats the same kind of food for months at a time, but humans vary their diet  much more dramatically. &lt;strong&gt;Are there any benefits to eating the same kind of food over extended period of time?&lt;/strong&gt; I'm interested in knowing if the digestive system/symbiotic bacteria in the gut adapts to the food, resulting in better digestion/absorption of nutrients.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2014-10-02T01:04:11.553" Title="Does human digestive system benefit from eating same kind of food consistently?" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;&lt;food&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3482" PostTypeId="1" AcceptedAnswerId="3484" CreationDate="2012-09-09T01:12:51.763" Score="3" ViewCount="638" Body="&lt;p&gt;I've been researching neuromodulators and have taken a look at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Norepinephrine#Norepinephrine_system&quot; rel=&quot;nofollow&quot;&gt;Norepinephrine/Noradrenaline  system&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The diagram of &lt;strong&gt;biosynthesis of Norepinephrine&lt;/strong&gt; is presented in the wikipedia article:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/File%3aCatecholamines_biosynthesis.svg&quot; rel=&quot;nofollow&quot;&gt;Catecholamines_biosynthesis&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The diagram appears to state that Dopamine gets converted to Norepinephrine , which gets converted to Epinephrine, and as a side effect, Homocysteine cycle gets advanced too (or is it involved?).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This article describes the &lt;a href=&quot;http://en.wikipedia.org/wiki/Homocysteine&quot; rel=&quot;nofollow&quot;&gt;homocysteine biosynthesis&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to understand what this means when two biosynthesis cycles are related like that. If I envision two cycles as connected gears, then turning one would turn the other, and if one is malfunctioning, so will the other. Is this a correct analogy?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the implications of the Homocysteine and Norepinephrine cycles touching each other?&lt;/strong&gt; As far as I understand, Epinephrine(Adrenaline) is a stress related hormone, &lt;strong&gt;does this mean that stress also results in elevating the levels of Homocysteine ?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your clarification!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-09-09T20:14:59.940" Title="What is the relationship between Homocysteine and Norepinephrine metabolic cycles?" Tags="&lt;human-biology&gt;&lt;homocysteine&gt;&lt;neuromodulation&gt;&lt;neurotransmitter&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3484" PostTypeId="2" ParentId="3482" CreationDate="2012-09-09T12:02:21.747" Score="3" Body="&lt;p&gt;Norepinephrine is converted to epinephrine by phenylethanolamine &lt;em&gt;N&lt;/em&gt;-methyltransferase (PNMT). In mammals PNMT is just one member of a large family of methyltransferases which use &lt;em&gt;S&lt;/em&gt;-adenosylmethionine (AdoMet) as a cofactor to provide a methyl group. These methyltransferases are involved in a very diverse set of pathways including the synthesis of nucleic acids and of certain phospholipids, as well as the methylation of DNA and histones. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you point out, these reactions generate homocysteine via &lt;em&gt;S&lt;/em&gt;-adenosylhomocysteine. However, because AdoMet is such a critically important cofactor it is thought that cellular levels are tightly regulated. As part of this regulation, homocysteine is re-methylated to methionine via two different routes requiring either methionine synthase or betaine-homocysteine methyltransferase. Methionine synthase obtains the required methyl group from 5-methyltetrahydrofolate in a vitamin B&lt;sub&gt;12&lt;/sub&gt; (actually methylcobalamin)-dependent reaction. This latter reaction links the AdoMet-based methyl transfer system to the other part of the cellular one-carbon economy, the folate pool. This is why vitamin B&lt;sub&gt;12&lt;/sub&gt; deficiency leads to hyperhomocysteinemia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hDglw.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This Figure is reproduced from Luka &lt;em&gt;et al&lt;/em&gt;. (2009) Glycine &lt;em&gt;N&lt;/em&gt;-methyltransferase and regulation of &lt;em&gt;S&lt;/em&gt;-adenosylmethionine levels. J. Biol. Chem. &lt;strong&gt;284&lt;/strong&gt;:22507–22511. I show it here just to illustrate the point that there are, in fact, many gears interacting in this system. The minireview is interesting and I recommend it to you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion, my answer to your question is that it is unlikely that stress leads to elevated levels of homocysteine as long as all of the relevant regulatory machinery is functioning correctly. If there is a problem with homocysteine recycling then yes, homocysteine levels would rise, but given that there so many AdoMet-dependent methylation reactions it is unclear how big a contribution PNMT would make to the overall homocysteine load. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-09T12:02:21.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3485" PostTypeId="1" AcceptedAnswerId="3499" CreationDate="2012-09-09T12:13:05.837" Score="5" ViewCount="257" Body="&lt;p&gt;Can someone please point me in the direction of a good academic article on the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are possible sources of phenotypic variation of different 400 day weights of cattle? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore how much variation is likely to be due to each contributing source?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried the following searches in google scholar:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Phenotypic, genetic, environmental cattle weight&lt;/li&gt;&#xA;&lt;li&gt;Phenotypic variation cattle weight&lt;/li&gt;&#xA;&lt;li&gt;Phenotypic variation&lt;/li&gt;&#xA;&lt;li&gt;Phenotypic variation, genetic&lt;/li&gt;&#xA;&lt;li&gt;genetic variation, dam, sire&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1374" LastEditorUserId="185" LastEditDate="2012-09-09T12:50:31.187" LastActivityDate="2012-09-10T06:13:01.893" Title="Phenotypic Variation of cattle - looking for academic sources" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3486" PostTypeId="1" AcceptedAnswerId="3495" CreationDate="2012-09-09T12:26:20.430" Score="4" ViewCount="3979" Body="&lt;p&gt;Can one become addicted to tea like coffee addicts or smokers? I heard there are some common substances in tea and coffee, do they cause addiction?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastEditorUserId="43" LastEditDate="2012-09-18T12:16:21.413" LastActivityDate="2013-02-19T14:48:38.650" Title="Can a person become addicted to tea?" Tags="&lt;pharmacology&gt;&lt;addiction&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3487" PostTypeId="1" AcceptedAnswerId="3500" CreationDate="2012-09-09T13:19:11.873" Score="9" ViewCount="1419" Body="&lt;p&gt;When a biologist or a layman tries to reason the evolutionary explanation for something, they would simply use English with some math thrown in (for a random example, pick any explanation out of &quot;The Selfish Gene&quot; -- for example, the reasoning why &quot;discriminate in favor of one's own eggs&quot; strategy is employed by Guillemots, in &quot;Genesmanship&quot; chapter, page 103. I won't quote it in full since it's a page worth of text).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example of such a wall of English is (Dawkins-inspired) Bio.SE question: &quot; &lt;a href=&quot;https://biology.stackexchange.com/questions/2022/why-is-grudger-an-evolutionary-stable-strategy&quot;&gt;Why is &amp;#39;Grudger&amp;#39; an evolutionary stable strategy?&lt;/a&gt; &quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a biologist tries to actually model evolutionary development to see which traits would win, they would need to somehow teach the computer to implement that model: what the environmental factors are, what the genotype involved is, how exactly it's expressed in different phenotypal and extended phenotypal traits, and how environment would affect an individual with that phenotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: &lt;strong&gt;is there some sort of standard way to build such a model? A domain specific language&lt;/strong&gt; (in computer science terminology) that is used by many different biologists or some standard modeling packages/software? E.g. some sort of special XML format, etc...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is it always just hand-built custom implementation by individual researchers for their current model?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Just to clarify:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;I'm NOT asking what the models look like theoretically. &lt;strong&gt;I'm asking what language/format (if any standard one exists) is used to encode them to run simulations&lt;/strong&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If there are discrepancies between the type/purposes of models, the ones I'm most interested in are game theoretical ones.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="185" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-03-14T16:58:10.040" Title="How exactly are game theoretical evolutionary models described during implementation for computer simulations?" Tags="&lt;evolution&gt;&lt;bioinformatics&gt;&lt;mathematical-models&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3488" PostTypeId="2" ParentId="3487" CreationDate="2012-09-09T14:08:43.103" Score="-1" Body="&lt;p&gt;There is no single way to build such a model.  They can vary from a simple mathematical statement like &lt;a href=&quot;http://en.wikipedia.org/wiki/Kin_selection#Hamilton.27s_rule&quot; rel=&quot;nofollow&quot;&gt;Hamilton's rule&lt;/a&gt; (rB&gt;C) to the chemical diffusion models used to describe the &lt;a href=&quot;http://www.sjsu.edu/faculty/watkins/murray.htm&quot; rel=&quot;nofollow&quot;&gt;patterns in animal skin coloring&lt;/a&gt; (like zebra stripes, leopard spots and the like). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are efforts to build molecular models of entire cells like this &lt;a href=&quot;http://www.nytimes.com/2012/07/21/science/in-a-first-an-entire-organism-is-simulated-by-software.html&quot; rel=&quot;nofollow&quot;&gt;model of mycobacterium genitalium dividing&lt;/a&gt;, which integrates nearly 30 different mathematical models to describe different aspects of the organism.  There are efforts to build such a model of an entire brain as well.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another common sort of model for evolutionary biology is the use of game theory, where different strategies can be posed one against another as in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Prisoner%27s_dilemma&quot; rel=&quot;nofollow&quot;&gt;prisoner's dilemma&lt;/a&gt; competition Dawkins describes in the Selfish Gene.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It goes on and on.  Basically biological modeling is driven by the sorts of mathematical models that we know.   New models will reveal new paradigms of how biology works.  They can be highly mathematical, but their relative importance and when they apply and what they mean are more analogy than proof.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance in the prisoner's dilemma, the first contests showed that Tit for Tat was the strongest model - generally assisting others, but betraying when there is a history of betrayal.  The ideas at the time moved towards general cooperation in populations.  More recent replays have shown that if there is a team of entrants that make extraordinary gifts to each other (allow betrayal without retribution), then they can compete against other models quite well.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One can never prove that a selfish model for the prisoner's dilemma will not show up, though biological systems to seem to be highly cooperative.  That is a model, not a proof. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-09-09T14:08:43.103" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3489" PostTypeId="2" ParentId="3479" CreationDate="2012-09-09T14:28:11.247" Score="1" Body="&lt;p&gt;I'm going to attempt an answer to this at the level of undergraduate biochemistry: apologies in advance if this is not sufficiently sophisticated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most frequent spontaneous mutation is deamination of cytosine to uracil (hydrolysis with loss of ammonia). Strictly in terms of the double helical structure of the DNA molecule this, it seems to me, would be &lt;strong&gt;destabilizing&lt;/strong&gt; because of the change from a GC base pair (3 hydrogen bonds) to a GU base pair (2 hydrogen bonds). &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-09T14:28:11.247" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3490" PostTypeId="2" ParentId="3427" CreationDate="2012-09-09T14:47:43.307" Score="3" Body="&lt;p&gt;In general:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;genetic engineering = cutting and pasting existing DNA extracted from organisms&lt;/p&gt;&#xA;&#xA;&lt;p&gt;synthetic biology = chemically synthesizing DNA from scratch, which is used to create new genes and constructs from scratch. The synthetic sequences may not exist or may exist in nature.&lt;/p&gt;&#xA;" OwnerDisplayName="user1377" LastEditorDisplayName="user1377" LastEditDate="2012-10-26T08:27:36.940" LastActivityDate="2012-10-26T08:27:36.940" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3491" PostTypeId="1" AcceptedAnswerId="3626" CreationDate="2012-09-09T15:20:45.390" Score="3" ViewCount="1407" Body="&lt;p&gt;I find that people generally distinguish between love and infatuation. Is there a physiological difference between the two? Or are they biologically identical, and the difference is circumstantial?&lt;/p&gt;&#xA;" OwnerUserId="1378" LastActivityDate="2012-09-23T23:15:44.823" Title="Is there a physiological difference between love and infatuation?" Tags="&lt;psychology&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3492" PostTypeId="2" ParentId="3479" CreationDate="2012-09-09T15:30:17.060" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;a spontaneous mutation (seen as a chemical transformation) should lower the energy of the system&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why do you think that? Because it’s an endothermic reaction?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider that mutations don’t happen “just like that” (at least to my knowledge) –they are triggered by external energy influx from things like reactive oxygen species or ionising radiation. So yes, they cost energy but that energy doesn’t come energetically unstable chemical bonds; it is supplemented from external sources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it’s not necessarily true that mutations produce lower-energy chemical bonds.&lt;/p&gt;&#xA;" OwnerUserId="166" LastActivityDate="2012-09-09T15:30:17.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3493" PostTypeId="1" CreationDate="2012-09-09T17:26:32.413" Score="3" ViewCount="108" Body="&lt;p&gt;How is it possible to access microbiome data like that found &lt;a href=&quot;http://www.exploredata.net/Downloads/Microbiome-Data-Set&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;? I'd like to perform analyses on similar type of data, but cannot find OTU data like that at the &lt;a href=&quot;http://commonfund.nih.gov/hmp/&quot; rel=&quot;nofollow&quot;&gt;Human Biome Project&lt;/a&gt;. Thanks for any leads. &lt;/p&gt;&#xA;" OwnerUserId="1379" LastEditorUserId="16651" LastEditDate="2015-12-13T13:31:06.133" LastActivityDate="2015-12-13T13:31:06.133" Title="Microbiome Data" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;genomics&gt;&lt;microbiome&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3494" PostTypeId="2" ParentId="3493" CreationDate="2012-09-09T18:23:49.433" Score="2" Body="&lt;p&gt;The data that you are pointing to are files in .csv (comma-separated value) format. They can be opened, after downloading, by any standard spreadsheet programme, including Excel, as well as programmatically (e.g. in Python using the csv module)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apologies if you understood this and were asking for something more.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-09T18:23:49.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3495" PostTypeId="2" ParentId="3486" CreationDate="2012-09-09T19:13:55.690" Score="6" Body="&lt;p&gt;Yes, both tea (black tea at least, English speakers usually mean black tea when they say tea anyway) and coffee have caffeine which is addictive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently, being able to correctly reply to this question involves defining the word &quot;addiction&quot;. My guess is that the negative connotation of the word &quot;addiction&quot; will cause some pressure to not use it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a recent review on &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17127537&quot; rel=&quot;nofollow&quot;&gt;caffeine addiction&lt;/a&gt; that says that caffeine is &lt;em&gt;not&lt;/em&gt; addictive. I do not agree with their arguments but I'll leave it to the reader to judge.&lt;/p&gt;&#xA;" OwnerUserId="1303" LastEditorUserId="1303" LastEditDate="2013-02-19T14:48:38.650" LastActivityDate="2013-02-19T14:48:38.650" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="3497" PostTypeId="1" CreationDate="2012-09-09T22:49:39.277" Score="7" ViewCount="697" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Spasmodic_torticollis#Secondary&quot;&gt;Torticollis&lt;/a&gt; (wryneck, cervical dystonia) is a neurologic movement disorder causing involuntary muscle spasms in the neck. Often, neuroleptics can cause such a side effect.  I'm wondering if this condition could also be part of the side-effect profile of  tricyclic antidepressants, like &lt;a href=&quot;http://en.wikipedia.org/wiki/Amitriptyline&quot;&gt;amitriptyline&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some potential indications:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Often the &lt;a href=&quot;http://en.wikipedia.org/wiki/Basal_ganglia&quot;&gt;basal ganglia&lt;/a&gt; are associated with neurological conditions such as movement disorders. -&gt; Do amitriptylines effect the basal ganglia?&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16208529&quot;&gt;Dressler and Benecke&lt;/a&gt; claim that &lt;em&gt;&quot;Of all patients treated with neuroleptics approximately 2 to 3% develop acute dystonic reactions within days of therapy initiation .When highly potent neuroleptics are used this rate may increase to over 50 %.Young men are at a particularly high risk. Cranial, pharyngeal, cervical and axial muscles are most commonly affected causing oculogyric crisis, grimacing, fixation of the jaw, retrocollis, torticollis or even opisthotonic posturing.&quot;&lt;/em&gt; -&gt; Do tricyclic antidepressants operate similar to neuroleptics?&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1474442206705476&quot;&gt;Geyer and Bressman&lt;/a&gt; claim that dystonia can be caused by certain drugs: &lt;em&gt;&quot;In addition to inherited forms of secondary dystonia (dystonia-plus syndromes and neurodegenerative diseases), a variety of acquired insults can cause secondary dystonia in previously unaffected individuals. Many cases are iatrogenic, resulting from drugs that block dopamine receptors; antipsychotic and antiemetic drugs are the most common culprits.&quot;&lt;/em&gt; -&gt; even though &lt;a href=&quot;http://whatmeds.stanford.edu/medications/amit_perp.html&quot;&gt;amitriptyline doesn't seem to block dopamine&lt;/a&gt;, maybe there is some kind of connection?&lt;/li&gt;&#xA;&lt;li&gt;Tricyclic antidepressants sometimes &lt;a href=&quot;http://web.squ.edu.om/med-lib/med_cd/e_cds/Griffith%27s%20Instructions%20Patients/pdf/Pg496.pdf&quot;&gt;seem to be used to treat torticollis&lt;/a&gt;, so is the reverse effect of causing the condition also thinkable?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1380" LastEditorUserId="57" LastEditDate="2012-09-10T03:44:00.903" LastActivityDate="2014-07-16T19:10:51.170" Title="Pharmacologically, can tricyclic antidepressants have a side-effect profile similar to neuroleptics?" Tags="&lt;biochemistry&gt;&lt;neuroscience&gt;&lt;pharmacology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3498" PostTypeId="2" ParentId="3487" CreationDate="2012-09-09T23:46:08.077" Score="6" Body="&lt;p&gt;The particular language a bioligist uses depends on the trade-offs between speed and ease of programming.  Many models are written in C or Fortran if speed is paramount.  On the other hand people will write models in higher level languages if speed is less important.  These would be Python, R, MatLab, etc...  In my models, which are written mostly in Python, I write all the classes from scratch and then all the simulation components by hand as well.  Since almost all models are mathematical in nature, the language is inconsequential.  Algorithms should behave similarly across platforms.  If you're looking for examples of easy ways to code up game theoretic models, consider NetLogo, &lt;a href=&quot;http://ccl.northwestern.edu/netlogo/models/community/GameTheory&quot;&gt;they have some nice examples using game theory.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1097" LastActivityDate="2012-09-09T23:46:08.077" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3499" PostTypeId="2" ParentId="3485" CreationDate="2012-09-10T06:13:01.893" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/omia&quot; rel=&quot;nofollow&quot;&gt;Online Mendelian Inheritance in Animals (OMIA)&lt;/a&gt; is a database of genes, inherited disorders and traits in more than 135 animal species (other than human and mouse). At the moment, it has &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/omia?term=bos&quot; rel=&quot;nofollow&quot;&gt;about 400 entries for &lt;em&gt;Bos taurus&lt;/em&gt;&lt;/a&gt;, mostly disease phenotypes. This is probably the only attempt to exhaustively list such phenotypes.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-09-10T06:13:01.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3500" PostTypeId="2" ParentId="3487" CreationDate="2012-09-10T12:35:22.800" Score="7" Body="&lt;p&gt;The field most closely associated with game theoretic models in biology is evolutionary game theory. If modeling is required, then the typical paradigm is agent-based modeling, and a good introductory book is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Yoav Shoham and Kevin Leyton-Brown&#xA;  [2009], &quot;Multiagent systems:&#xA;  algorithmic, game-theoretic, and&#xA;  logical foundations&quot;, Cambridge&#xA;  University press.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As for actually building the model, and what to describe/how, I will take you through my usual procedure since this is a field I specialize in:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Define what type of strategies you think are relevant to the interactions you are modeling. Select what you expect the payoff of those strategies to be. For instance, if you are studying the evolution of cooperation, you might select 'Cooperate' and 'Defect' as your strategies and the Prisoner's dilemma as your pay-off matrix, but maybe you will pick something &lt;a href=&quot;http://egtheory.wordpress.com/2012/03/14/uv-space/&quot;&gt;more general&lt;/a&gt;. Unfortunately, in most of EGT a clear distinction between genotype and phenotype is not drawn, and they are usually equated. At the end of this step you have a game matrix G. Sometimes when mutation or innovation are explicitly necessary even in the inviscid model, further analytic approaches are taken at this stage. I recommend &lt;a href=&quot;http://www.ams.org/journals/bull/2003-40-04/S0273-0979-03-00988-1/home.html?pagingLink=%3Ca+href%3D%22%2Fjoursearch%2Fservlet%2FDoSearch%3Ff1%3Dmsc%26jrnl%3Dall%26msctype%3D2000%26timingString%3DQuery%2Btook%2B100%2Bmilliseconds.%26v1%3D34D20%26startRec%3D1%22%3E&quot;&gt;Hofbauer &amp;amp; Sigmund (2003)&lt;/a&gt; for a broad treatment of step 1.&lt;/li&gt;&#xA;&lt;li&gt;Now you need a basic intuition of what the 'default' behavior in this interaction is, so solve the &lt;a href=&quot;http://en.wikipedia.org/wiki/Replicator_equation&quot;&gt;replicator dynamics&lt;/a&gt; of G.&lt;/li&gt;&#xA;&lt;li&gt;The main interest in EGT right now is &lt;a href=&quot;http://egtheory.wordpress.com/2012/03/21/spatial-structure/&quot;&gt;structured populations&lt;/a&gt;. This is where computational modeling is typically used. However, before I turn to simulation, I first try the best analytic approach I know. I use the Ohtsuki-Nowak transform on G to analytically solve the interaction for &lt;a href=&quot;http://egtheory.wordpress.com/2012/03/29/random-regular-graphs/&quot;&gt;random graphs&lt;/a&gt; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022519306002426&quot;&gt;(Ohtsuki &amp;amp; Nowak, 2006)&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;If I am still interested in the question, and steps 2 and 3 didn't capture all the subtlety of the system I want to study, then I start building a multi-agent computational model. I make sure that my model has some way to scale to the completely inviscid case of replicatory dynamics, and the simply-structured case of ON-transform. If my computational model disagrees with the analytic approach in these regimes, then I become worried. Otherwise, I continue with standard agent-based modeling techniques. Personally, I code in Matlab. I have never seen a modern EGT simulation that required the performance of C/Fortran. As suggested in another answer, if you don't have a programming background then you can use &lt;a href=&quot;http://ccl.northwestern.edu/netlogo/&quot;&gt;NetLogo&lt;/a&gt;. However, my experience is that the models are typically simple enough to implement from scratch, and NetLogo models typically hide from you some very important subtleties (like which reproduction rule to use: death-birth, birth-death, immitation?) and usually lead to weaker papers. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Note the broad theme. These models are typically described as differential equations, and this approach is preferred to agent-based models. However, if a clean differential equations approach does not capture all the subtleties of what you are studying, then an ABM paradigm is adopted.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="500" LastEditDate="2012-09-10T12:42:19.487" LastActivityDate="2012-09-10T12:42:19.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3501" PostTypeId="1" AcceptedAnswerId="3502" CreationDate="2012-09-10T12:59:51.920" Score="14" ViewCount="6985" Body="&lt;p&gt;In my understanding, the evolutional function of berries is to be eaten and pood out somewhere else, so that the seeds of the plant spread. Is this so? Then why are some berries poisonous?&lt;/p&gt;&#xA;" OwnerUserId="1384" LastActivityDate="2016-06-30T19:15:37.113" Title="Why are some berries poisonous?" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;ecology&gt;&lt;food&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3502" PostTypeId="2" ParentId="3501" CreationDate="2012-09-10T14:09:07.470" Score="20" Body="&lt;p&gt;While poison affects not every organism equally, plants did develop some poisons to avoid being eaten. However, if you look at the great multitude of so-called secondary metabolites, most of them are poisonous to either viruses, bacteria, fungi or other microorganisms, or insects, or even other plants. Plant evolution just hasn't had time to adapt to humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if some substance from plants is a poison to us, it's accidentally so, and the target was another organism. Examples: nicotine is first and foremost an insecticide, nematistat, and herbicide; aconitine, atropine, caffeine are insecticides; many essential oils (causing allergies in human) are antimicrobial and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has also to do with the fact that nerve cell physiology has not much changed since they developed in the first multi-celled animals, and poisons for insect nerves have at least some effect on human nerves.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-09-10T14:16:47.303" LastActivityDate="2012-09-10T14:16:47.303" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3503" PostTypeId="2" ParentId="3493" CreationDate="2012-09-10T14:18:25.273" Score="3" Body="&lt;p&gt;This .csv files (comma-separated value) can be imported into Galaxy (&lt;a href=&quot;http://usegalaxy.org&quot; rel=&quot;nofollow&quot;&gt;usegalaxy.org&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I recommend that you take a look at that web app, it has many build in applications for analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also this site has a lot of quick video tutorials.&lt;/p&gt;&#xA;" OwnerUserId="1004" LastActivityDate="2012-09-10T14:18:25.273" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3504" PostTypeId="1" AcceptedAnswerId="3506" CreationDate="2012-09-10T15:27:09.203" Score="2" ViewCount="259" Body="&lt;p&gt;A few years back I heard at biology class that sugar's molecule consists of half the number of elements of a glucose molecule. So not counting the energy needed to transform two sugar molecules in one glucose molecule, isn't it almost the same (eating N amount of sugar) as eating N/2 of glucose?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2012-09-10T17:42:21.507" Title="Is consuming sugar with food as beneficial as consuming glucose (~half of the amount of sugar)?" Tags="&lt;physiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3505" PostTypeId="2" ParentId="3504" CreationDate="2012-09-10T15:39:53.887" Score="4" Body="&lt;p&gt;&lt;em&gt;&lt;strong&gt;Is consuming sugar with food as beneficial as consuming glucose (~half of the amount of sugar)?&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is referred to in everyday language as &quot;sugar&quot; is sucrose. Each sucrose molecule consists of one glucose molecule and one fructose molecule linked by a chemical bond. These two, glucose and fructose are, in terms of energy value, identical. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whether they are equally beneficial, or indeed beneficial at all (from a nutritional point of view), is a very big question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;P.S. (in response to MCM):&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But... fructose metabolism is largely carried out by the liver. If you are consuming sucrose then the glucose component will raise insulin levels and the liver will be in anabolic mode. The fructose will be converted to liver glycogen via glucose-6-phosphate (as shown in your diagram) and also to triglyceride for export to adipose tissue where it is stored as fat. So the energy yield from fructose will be deferred, whereas the glucose will be used by all tissues immediately. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Later on, as insulin levels fall (and glucagon levels rise) the liver glycogen will be mobilised as glucose for export to other tissues. Some of the triglyceride will be mobilised from the adipose tissue for use as fuel too, but it is widely believed that with a typical Western diet there is a net movement from fructose&gt;fat which contributes to the rise in levels of obesity. Indeed some scientists believe that fructose is the main culprit.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-09-10T17:42:21.507" LastActivityDate="2012-09-10T17:42:21.507" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3506" PostTypeId="2" ParentId="3504" CreationDate="2012-09-10T16:59:23.170" Score="9" Body="&lt;p&gt;You have it backwards. One sugar molecule is equivalent to &lt;strong&gt;two&lt;/strong&gt; glucose molecules, though the actual structure of sugar (&lt;em&gt;Sucrose&lt;/em&gt;) is a &lt;em&gt;Glucose&lt;/em&gt; + &lt;em&gt;Fructose&lt;/em&gt; combination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While Glucose is metabolized via Glycolysis into two molecules of Pyruvate (which are then used in the Citric Acid Cycle), Fructose enters the Glycolysis metabolism at a later stage as shown here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rS4lh.jpg&quot; alt=&quot;Fructose metabolic pathway.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The GA-3-P is then turned into 2-Phosphoglycerate and then into 2x Pyruvate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The end result is that a single Sucrose molecule (Glucose + Fructose) [aka - Sugar] is equivalent to 4x Pyruvate, whereas Glucose alone is equivalent to 2x Pyruvate. Or, if you prefer, a single Glucose molecule results in about 32-36 ATP produced, whereas Sucrose will result in 64-72 ATP produced - with ATP being the primary energy carrier of the cell.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-09-10T16:59:23.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3507" PostTypeId="1" AcceptedAnswerId="3517" CreationDate="2012-09-10T17:33:55.580" Score="6" ViewCount="460" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Quorum_sensing&quot;&gt;Quorum sensing&lt;/a&gt; is a system of stimulus and responses correlated to population density that is used by bacteria to coordinate gene-expression. I am looking for a simple computational/mathematical model of quorum sensing that abstracts away from the details of the mechanism implementing it inside the agent, but keeps the key inter-agent properties like diffusion rate, range, and timing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there a standard abstract mathematical model of quorum sensing used by biologists?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not interested in the particulars of a specific organism, but would like a general model I could apply to capture the 'gist' for any organism that relies on quorum sensing for part of its behavior.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0304397506007493&quot;&gt;Bernardini et al. (2007)&lt;/a&gt; provided an extension to &lt;a href=&quot;http://en.wikipedia.org/wiki/P_system&quot;&gt;P-systems&lt;/a&gt; incorporating the basics of quorum sensing, and &lt;a href=&quot;http://www.mitpressjournals.org/doi/abs/10.1162/artl.2008.14.1.95&quot;&gt;Romero-Campero &amp;amp; Pérez-Jiménez (2008)&lt;/a&gt; have used their approach to model bioluminosity in &lt;em&gt;vibrio fischeri&lt;/em&gt;. This approach is conceptually appealing to me, but that is because I am predominantly a computer scientists. Although P-system can be used for modeling biological systems &lt;a href=&quot;http://www.springerlink.com/content/p7u550426528m676/&quot;&gt;(Ardelean &amp;amp; Cavaliere, 2003)&lt;/a&gt;, they still feel fundamentally computer-science-y and are typically not published in orthodox biological venues. This makes me suspect there is a more standard approach among biologists, probably via dynamic systems and diffusion equations.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="4101" LastEditDate="2013-10-31T01:43:08.410" LastActivityDate="2013-10-31T01:43:08.410" Title="Models of quorum sensing for multi-agent systems" Tags="&lt;bioinformatics&gt;&lt;microbiology&gt;&lt;mathematical-models&gt;&lt;cell-signaling&gt;&lt;quorum-sensing&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3509" PostTypeId="1" CreationDate="2012-09-10T18:20:52.297" Score="8" ViewCount="1679" Body="&lt;p&gt;I'm trying to label a protein with fluorescent dye (TMR succinimidyl ester), but having trouble getting the protocol to work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The protein seems to be stable in distilled water at a the recommended concentration of about 2mg/ml (determined by OD280 with an absorption coefficient calculated from its sequence).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the protocol calls for the addition of 1:10 1M sodium bicarbonate to raise the pH to ~8.5. When I perform this step the solution immediately turns cloudy. I have also encountered this precipitation problem when dialyzing against PBS. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What steps can I take to get around this? I assume a lower concentration of protein might prevent precipitation, but I have read that the labeling reaction becomes very inefficient below 1mg/ml.&lt;/p&gt;&#xA;" OwnerUserId="46" LastEditorUserId="223" LastEditDate="2012-09-11T22:38:18.837" LastActivityDate="2013-10-23T02:03:21.967" Title="How to prevent protein precipitation?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3510" PostTypeId="1" AcceptedAnswerId="3621" CreationDate="2012-09-11T05:25:59.453" Score="16" ViewCount="440" Body="&lt;p&gt;According to &lt;a href=&quot;http://dx.doi.org/10.1200/JCO.2009.25.5729&quot;&gt;Korde et al.&lt;/a&gt; (2010):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Male breast cancer accounts for less than 1% of all cancers in men and less than 1% of breast cancers.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This raises the question: &lt;em&gt;Why do most breast cancers occur in women?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two plausible explanations I can think of:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;A male is less likely to get breast cancer for anatomical reasons (such as a smaller quantity of breast tissue, or breast tissue that is less susceptible to cancer),&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Women have higher significantly levels of estrogen, which is linked to mutations that cause breast cancer (see &lt;a href=&quot;http://dx.doi.org/10.1016/j.bbcan.2006.03.001&quot;&gt;Cavalieria et al.&lt;/a&gt; (2006)).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Although, I have no evidence to suggest that either of these is predominant factor.&lt;/p&gt;&#xA;" OwnerUserId="203" LastActivityDate="2018-10-21T01:30:10.753" Title="Why do most breast cancers occur in women?" Tags="&lt;human-biology&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3511" PostTypeId="2" ParentId="3509" CreationDate="2012-09-11T08:06:31.700" Score="3" Body="&lt;p&gt;Alas, the great problems with protein formulation. I assume that the labeling chemistry forces you to use the 8.5 pH. (I don't think this is necessarily true since succinimidyl chemistry does work at pH=7.2 and the NHS ester is fairly unstable above pH=8.6)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We usually tackle this problem entirely by brute force ie. testing multiple buffer condition with different bases and different salt concentrations. First attempt would be to try out all of the Good's Buffers notablely HEPES, TRIS, MOPS, Tricine, Maybe you should look at both zwitterionic buffers and non-zwitterionic buffers. In your case, the succinimidyl is vunerable to primary amines so avoid things like Tris/Glycine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second thing to test would be various salt concentrations. Since you're already dumping in Sodium Bicarb, NaCl should be great. Unfortunately, this is where things get tricky since it is hard to know if your protein precipitates at low salt or high. A test from 20 mM, 50 mM, 100 mM, 150 mM, 200 mM, 500 mM should cover most of the interesting regimes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively the sudden change in the ionic environment around your protein may be causing it to precipitate. You probably should dialyze or purified your protein in PBS to allow it to refold appropriately.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-09-11T08:06:31.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3513" PostTypeId="1" AcceptedAnswerId="3518" CreationDate="2012-09-11T18:47:04.587" Score="10" ViewCount="1399" Body="&lt;p&gt;I'm reading over the ENCODE Nature papers, and one of the papers referred to is &quot;Global mapping of protein-DNA interactions in vivo by digital&quot; by Hesselberth et al&lt;sup&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nmeth.1313&quot;&gt;[1]&lt;/a&gt;&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genomic footprinting is a massively parallel variant of DNAse I hypersensitivity screening, which I feel I have a good handle on, but I don't understand this paragraph from the beginning of the results (the troublesome part is in &lt;strong&gt;bold&lt;/strong&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To visualize regulatory protein occupancy across the genome of Saccharomyces cerevisiae, we coupled DNase I digestion of yeast nuclei with massively parallel DNA sequencing to create a dense whole-genome map of DNA template accessibility at nucleotide-level. We analyzed a single well-studied environmental condition, yeast a cells treated with the pheromone α-factor, which synchronizes cells in the G1 phase of the cell cycle. &lt;strong&gt;We isolated yeast nuclei and treated them with a DNase I concentration sufficient to release short (&amp;lt;300 bp) DNA fragments while maintaining the bulk of the sample in high molecular weight species (Supplementary Fig.1). These small fragments derive from two DNase I “hits” in close proximity, and therefore their isolation minimizes contamination by single fragment ends derived from random shearing.&lt;/strong&gt; Because each end of the released DNase I ‘double-hit’ fragments represents an in vivo DNase I cleavage site, the sequence and hence genomic location of these sites can be readily determined by sequencing (Supplementary methods).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There's a reference to another paper by Sabo et al.&lt;sup&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nmeth890&quot;&gt;[2]&lt;/a&gt;&lt;/sup&gt; about genome-scale DNase assays using microarrays in that paragraph that I'm reading, but if someone understands the biology well, I'd really appreciate an answer.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nmeth.1313&quot;&gt;&lt;strong&gt;Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA&lt;/strong&gt;. 2009. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nature Methods 6(4): 283–289, doi:10.1038/nmeth.1313.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nmeth890&quot;&gt;&lt;strong&gt;Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A, Weaver M, Shafer A, Lee K, Neri F, Humbert R, Singer MA, Richmond TA, Dorschner MO, McArthur M, Hawrylycz M, Green RD, Navas PA, Noble WS, Stamatoyannopoulos JA&lt;/strong&gt;. 2006. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nature Methods 3: 511-518, doi:10.1038/nmeth890.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1387" LastEditorUserId="43" LastEditDate="2012-09-16T12:38:13.037" LastActivityDate="2012-09-16T12:38:13.037" Title="Digital Genomic Footprinting for ENCODE" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3514" PostTypeId="1" AcceptedAnswerId="3528" CreationDate="2012-09-11T23:39:00.777" Score="6" ViewCount="324" Body="&lt;p&gt;It is well known that the first DNA polymerase, &lt;em&gt;Taq&lt;/em&gt;, is quite error prone. Newer generation commercial enzymes that have either been isolated from different thermophile species or have been improved by recombination are less error prone. How are these error rates compared? For instance, if this is done by Sanger sequencing, the average signal will dominate in reading the output and so it will be very unlikely to pick up on errors by this method.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="43" LastEditDate="2012-09-12T22:21:23.597" LastActivityDate="2012-09-12T22:21:23.597" Title="How are DNA polymerase error rates measured?" Tags="&lt;dna&gt;&lt;proteins&gt;&lt;molecular-genetics&gt;&lt;pcr&gt;&lt;polymerase&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3515" PostTypeId="1" AcceptedAnswerId="3516" CreationDate="2012-09-12T01:10:36.623" Score="1" ViewCount="32507" Body="&lt;p&gt;My attempt:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Transcription - RNA polymerase &#xA;Translation - aminoacyl tRNA synthetase &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that the ribosome almost runs translation, but I don't think ribosomes are enzymes, which is why I went with aminoacyl tRNA synthetase.  Is this right? &lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="1320" LastEditDate="2012-09-15T17:31:16.020" LastActivityDate="2012-09-15T17:31:48.300" Title="Which enzyme catalyzes transcription and which translation?" Tags="&lt;homework&gt;&lt;transcription&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3516" PostTypeId="2" ParentId="3515" CreationDate="2012-09-12T02:30:32.497" Score="2" Body="&lt;p&gt;Sorry, but you started on the right track. What you're looking for is called the central dogma of protein synthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genomic DNA is transcribed in the nucleus into messenger RNA (mRNA) by RNA polymerase. RNA polymerase is DNA-dependent; it needs a DNA template to make an RNA version of the message.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The messenger RNA moves into the cytoplasm where it gets translated by ribosomes into an a polypeptide (protein). Ribosomes are the enzyme that do the translating, and perhaps your confusion is because ribosomes are made up of both RNA molecules and proteins (a ribonucleotide complex).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aminoacyl tRNA synthetases are the enzymes that make aminoacyl tRNAs (tRNA for short). These tRNA bring individual amino acids to the ribosome as the ribosome is extending the polypetide product of the mRNA message.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="1320" LastEditDate="2012-09-15T17:31:48.300" LastActivityDate="2012-09-15T17:31:48.300" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3517" PostTypeId="2" ParentId="3507" CreationDate="2012-09-12T07:33:32.353" Score="2" Body="&lt;p&gt;I found &lt;a href=&quot;http://dx.doi.org/10.1371/journal.pcbi.1002361&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt;, which might be relevant; it uses is a more chemically inspired approach. &lt;a href=&quot;http://dx.doi.org/10.1103/PhysRevE.84.041921&quot; rel=&quot;nofollow&quot;&gt;Another paper&lt;sup&gt;[2]&lt;/sup&gt;&lt;/a&gt; also might be interesting, it takes a more dynamical systems approach.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My personal instinct would be to use ordinary differential equations: generate a population of cells in random positions, assign each cell levels of any relevant molecular species, and come up with a list of ODEs that describe the rates of change of the species in a particular cell in terms of gene expression, degradation, and diffusion. You should then be able to simulate the time evolution of the system just by solving the (large) system of ODEs given your initial conditions. Something like the approach in &lt;a href=&quot;http://dx.doi.org/10.1073/pnas.1015302108&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;sup&gt;[3]&lt;/sup&gt;&lt;/a&gt; (read the supplemental info), only your cells would move around during the simulation, rather than remaining still as part of a tissue. The implementation would get thorny, because you would have to accommodate the motion of the cells as you solve the ODEs. I imagine that this could be accomplished by simply treating the initial positions of the cells as part of the system's initial conditions and then defining the ODEs that govern the rate of change in each dimension (either randomly, or perhaps they move in a coordinated manner) so that this aspect of the system can evolve during the integration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1371/journal.pcbi.1002361&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Rai N, Anand R, Ramkumar K, Sreenivasan V, Dabholkar S, Venkatesh KV, Thattai M&lt;/strong&gt;. 2012. Prediction by promoter logic in bacterial quorum sensing. PLoS computational biology 8: e1002361.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1103/PhysRevE.84.041921&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Chiang W-Y, Li Y-X, Lai P-Y&lt;/strong&gt;. 2011. Simple models for quorum sensing: Nonlinear dynamical analysis. Physical Review E 84.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.1015302108&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Lubensky DK, Pennington MW, Shraiman BI, Baker NE&lt;/strong&gt;. 2011. A dynamical model of ommatidial crystal formation. Proceedings of the National Academy of Sciences of the United States of America 108: 11145–50.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1389" LastEditorUserId="43" LastEditDate="2012-09-16T02:20:07.850" LastActivityDate="2012-09-16T02:20:07.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3518" PostTypeId="2" ParentId="3513" CreationDate="2012-09-12T08:59:48.737" Score="9" Body="&lt;p&gt;After reading the paper cited I think the logic goes like this: DNAse I will create free ends at accessible sites in the genome. However shearing during subsequent DNA isolation is also a source of free ends, and these represent noise in the analysis. You have to put in a lot of energy to shear DNA to very small fragments, so I infer that mild shearing during DNA isolation is very unlikely to create a new end that is near to an existing DNase I-generated end. Therefore, under the conditions used, any small fragments are much more likely to have been generated by two closely-spaced DNase I hits. By limiting the analysis to these fragments the noise from shearing is minimised.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now that I've written this answer it doesn't seem like much more than a rewrite of the emboldened sentence, but I hope it is helpful anyway.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-12T08:59:48.737" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3519" PostTypeId="1" AcceptedAnswerId="3520" CreationDate="2012-09-12T11:07:14.733" Score="11" ViewCount="3897" Body="&lt;p&gt;How do fish separate oxygen from H&lt;sub&gt;2&lt;/sub&gt;0 &amp;amp; consume it? Do they break the water molecule and absorb  the oxygen only?&lt;/p&gt;&#xA;" OwnerUserId="1390" LastEditorUserId="69" LastEditDate="2012-12-11T13:35:39.813" LastActivityDate="2016-08-03T15:42:36.487" Title="Do fish break a water molecule to absorb oxygen?" Tags="&lt;zoology&gt;&lt;cellular-respiration&gt;&lt;ichthyology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="3520" PostTypeId="2" ParentId="3519" CreationDate="2012-09-12T12:21:00.637" Score="30" Body="&lt;p&gt;The answer to this, I reckon, &lt;em&gt;is that they don't&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They use molecular oxygen (O&lt;sub&gt;2&lt;/sub&gt;) dissolved in the water for respiration, where it acts as a terminal electron acceptor, just as we use molecular oxygen in the air for respiration. We can speak of the water as being &lt;em&gt;oxygenated&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Water &lt;em&gt;is&lt;/em&gt; split in photosynthesis, where &lt;strong&gt;reducing equivalents from water&lt;/strong&gt; are used to reduce NADP&lt;sup&gt;+&lt;/sup&gt; (giving NADPH).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the great discoveries of biology, IMO, &lt;strong&gt;is that the oxygen formed in green-plant photosynthesis comes from water, not CO&lt;sub&gt;2&lt;/sub&gt;&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Tricarboxylic Acid Cycle (Krebs Cycle) Rant&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite claims to the contrary, most infamously by Racker (1976, pp 28 - 29) and Wieser (1980), but also by Madeira (1988) and Mego (1986) for example, water is &lt;em&gt;not&lt;/em&gt; split in the tricarboxylic acid cycle (Krebs Cycle). Banfalvi (1991) also sails pretty close to the wind on this one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is, reducing equivalents from water are &lt;em&gt;not&lt;/em&gt; passed down the respiratory chain, or in any way used to make ATP, or are in any way a 'source' of free energy.  Such claims, IMO, are nonsense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The definitive answers to the Wieser (1980) paper are given by Atkinson (1981) and Herreros &amp;amp; Garcia-Sancho (1981). Both of these articles are models of clarity, and categorically refute the claims of Wieser (1980).  Nevertheless, as shown by the references above, the controversy surfaces periodically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only sources of reducing equivalents in the TCA cycle are carbon compounds, and the only electrons passed down the respiratory chain are those 'held' in C-H and C-C bonds (Herreros &amp;amp; Garcia-Sancho, 1981).  An ionization is neither an oxidation nor a reduction (see Atkinson, 1981) and neither is a hydration. Adding water to (say) a double bond &lt;em&gt;does not&lt;/em&gt; make the compound any more oxidized or reduced.  As far as oxygen and electrons are concerned, and to generalize from a biological point of view, what is has it holds - except in photosynthesis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you may have guessed, the splitting of the water in the TCA cycle is a pet rant of mine.  Thanks for the opportunity of airing my views! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit 3&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Found &lt;a href=&quot;http://ajpcell.physiology.org/content/291/6/C1114.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;this one&lt;/a&gt; when searching Google (Bri&amp;egrave;re &lt;em&gt;et al&lt;/em&gt;, 2006).  In an invited review for the American Journal of Physiology (Cell Physiology) at that!&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Finally, TCA cycle should also be considered as a water-splitting process generating oxygen for acetyl-CoA oxidation [they quote Wieser]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So now the TCA cycle is producing oxygen from water.  Wonders will never cease!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(end edit)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(end rant)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit 2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As &lt;a href=&quot;https://biology.stackexchange.com/users/1122/rwst&quot;&gt;rwst&lt;/a&gt; and &lt;a href=&quot;https://biology.stackexchange.com/users/1320/alan-boyd&quot;&gt;Alan Boyd&lt;/a&gt; have drawn attention to, the concentration of dissolved oxygen in water is all important, and varies with (for example) temperature.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In air-saturated buffer at 25&lt;sup&gt;o&lt;/sup&gt;C the concentration of oxygen (O&lt;sub&gt;2&lt;/sub&gt; molecules) is about 0.24 mM (0.24 &amp;mu;moles/ml, or about 0.474 &amp;mu;g-atoms of oxygen per ml). [&lt;a href=&quot;http://www.biochemj.org/bj/090/0225/0900225.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chappell&lt;/a&gt; (1964)]. This figure decreases with increasing temperature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Great question, BTW.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Apologies for the &lt;strong&gt;incomplete Atkinson and Herreros &amp;amp; Garcia-Sancho references&lt;/strong&gt;. I have a photocopy of these papers but have been unable to trace the full source. They are both in the 'Letters to the Editor' section of the February 1981 edition of &lt;em&gt;Trends in Biochemical Sciences&lt;/em&gt;. They do not appear to be in Pubmed, or anywhere else on-line.  &lt;strong&gt;Has anyone ever seen these references quoted, or can provide me with a full source?&lt;/strong&gt;.  I'll update if I find anything)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Atkinson, D.E. (1981) TCA Cycle Confusion.  &lt;em&gt;Trends in Biochemical Sciences&lt;/em&gt; (February 1981 edition; full ref to follow)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Banfalvi,G. (1991)  Conversion of Oxidative Energy to Reductive Power in the Citrate Cycle. &lt;em&gt;Biochemical Education&lt;/em&gt;, &lt;strong&gt;19&lt;/strong&gt;, 24 - 26  [see &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1016/0307-4412%2891%2990138-X/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;] (pdf apparently free to all)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Brière, J.J., Favier, J, Gimenez-Roqueplo, A.P. &amp;amp; Rustin, P (2006) Tricarboxylic acid cycle dysfunction as a cause of human diseases and tumor formation.  &lt;em&gt;Am J Physiol Cell Physiol&lt;/em&gt;, &lt;strong&gt;291&lt;/strong&gt;, C1114-20. [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=briere%20rustin%20american%20journal%20of%20physiology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pubmed&lt;/a&gt;]  [&lt;a href=&quot;http://ajpcell.physiology.org/content/291/6/C1114.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Chappell (1964) The oxidation of citrate, isocitrate and cis-aconitate by isolated mitochondria. &lt;em&gt;Biochem J.&lt;/em&gt;, &lt;strong&gt;90&lt;/strong&gt;, 225-237.[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4378636&quot; rel=&quot;nofollow noreferrer&quot;&gt;pubmed&lt;/a&gt;]  [&lt;a href=&quot;http://www.biochemj.org/bj/090/0225/0900225.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Herreros, B. &amp;amp; Garcia-Sancho, J. (1981) TCA Cycle Confusion.  &lt;em&gt;Trends in Biochemical Sciences&lt;/em&gt; (February 1981 edition; full ref to follow)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Madeira, V.M.C. (1988) Stoichiometry of Reducing Equivalents and Splitting&#xA;of Water in the Citric Acid Cycle.  &lt;em&gt;Biochemical Education&lt;/em&gt; &lt;strong&gt;16&lt;/strong&gt;, 94 - 96 [&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1016/0307-4412%2888%2990069-6/pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf&lt;/a&gt;] (apparently free to all.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Mego, J.L. (1986)  The Role of Water in Glycolysis &lt;em&gt;Biochemical Education&lt;/em&gt;,  &lt;strong&gt;14&lt;/strong&gt;, 130 - 131. (see &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1016/0307-4412%2886%2990175-5/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Racker, E. (1976) A New Look at Mechanisms in Bioenergetics.  Academic Press, New York.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wieser (1980) Textbook Errrors: The splitting of water by the tricarboxylic acid cycle.  Textbook error or textbook omission? &lt;em&gt;Trends in Biochemical Sciences&lt;/em&gt;, &lt;strong&gt;5&lt;/strong&gt; (Issue 11), 284. [see &lt;a href=&quot;http://www.sciencedirect.com/science/journal/09680004/5/11&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;].  [&lt;a href=&quot;http://download.cell.com/trends/biochemical-sciences/pdf/PII0968000480901590.pdf?intermediate=true&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf&lt;/a&gt;], apparently free to all.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit 4&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have not been able to locate the exact reference for the incomplete &lt;strong&gt;Atkinson and Herreros &amp;amp; Garcia-Sancho&lt;/strong&gt; references cited above but, in response to &lt;a href=&quot;https://biology.stackexchange.com/q/49214/1136&quot;&gt;this&lt;/a&gt; great question, I have put a copy of a very bad scanned version &lt;a href=&quot;https://dl.dropboxusercontent.com/u/27195641/tca_cycle_confusion_tibs.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another great reference to this controversy which I should have quoted is the&#xA;following:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Losada, Manuel&#xA;. (1978) Energy-Transducing Redox Systems and the Mechanism of Oxidative Phosphorylation. &lt;em&gt;Bioelectrochemistry and Bioenergetics,&lt;/em&gt; &lt;strong&gt;5&lt;/strong&gt;, 296-310 [&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0302459887870393&quot; rel=&quot;nofollow noreferrer&quot;&gt;Science Direct&lt;/a&gt;]. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The following is the relevant section, for those who do not have access:&#xA;&lt;a href=&quot;https://i.stack.imgur.com/xS6VW.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/xS6VW.png&quot; alt=&quot;Losada Quote&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/baP4k.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/baP4k.png&quot; alt=&quot;Losada Refs&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A more complete version of the Racker reference quoted above by Losada (1978): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;However, pyruvate has only 4 hydrogens to donate to 2 oxygens and with a P:O ratio of 3 should therefore yield only 6 molecules of ATP (Table 1.2). Where are the other 6 hydrogens coming from so that 15 ATP can be formed? The answer to this question gives us what I think is the key to the puzzle why nature has designed the complex acrobatic scheme of the Krebs cycle. Its major purpose I believe is to increase the energy yield by catalyzing cleavage of water.&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;There are three steps at which water enter the Krebs cycle. - one at the transformation of fumarate to malate an the other two somewhat more indirectly during the utilization of acetyl-CoA and succinyl-CoA. In the course of the Krebs cycle the hydrogens of these water molecules are separated from oxygen and are donated to DPN or to a flavoprotein (e.g., succinate dehydrogenase) and then transported via the oxidation chain of mitochondria as electrons and protons as we shall discuss later.&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[Racker, E. (1976).  A New Look at Mechanisms of Bioenergetics, pp 5-6, Academic Press].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;IMO, the last sentence of this quote is complete rubbish. (For DPN, read NAD. DPN, or &lt;em&gt;diphospo-pyridine-nucleotide&lt;/em&gt; (or something close), is an old name for NAD) &lt;/p&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2016-08-03T15:42:36.487" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="3521" PostTypeId="1" AcceptedAnswerId="3523" CreationDate="2012-09-12T13:51:17.467" Score="10" ViewCount="6824" Body="&lt;p&gt;I read &lt;a href=&quot;http://www.independent.co.uk/news/science/success-isnt-written-in-the-stars-its-in-the-length-of-your-fingers-1334251.html&quot;&gt;this&lt;/a&gt; article which has the following quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The ratio between index and ring finger is believed to be linked to exposure to the male hormone testosterone in the womb.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And I wonder what determines the amount of exposure to testosterone in the womb. Is it testosterone produced by the fetus itself, in which case the baby's own genetics is the answer, or does this exposure the article speaks of more likely refer to testosterone produced by the mother and exposed to the baby?&lt;/p&gt;&#xA;" OwnerUserId="263" LastEditorUserId="69" LastEditDate="2012-10-26T16:33:52.283" LastActivityDate="2018-02-24T16:13:20.317" Title="What determines testosterone exposure in womb, baby's genetics or mom's body?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;endocrinology&gt;&lt;embryology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3522" PostTypeId="2" ParentId="3403" CreationDate="2012-09-12T13:57:55.870" Score="0" Body="&lt;p&gt;I'm going to answer my own question with suggestions collected from the comments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A multipotent stem cell:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Growth&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Growth and clonal division&lt;/li&gt;&#xA;&lt;li&gt;Growth, division and differentiation&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Division and no growth&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A differentiated cell:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Senescence (irreversible)&lt;/li&gt;&#xA;&lt;li&gt;Programmed cell death&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Apoptosis.&lt;/li&gt;&#xA;&lt;li&gt;Autophagic cell death.&lt;/li&gt;&#xA;&lt;li&gt;Necrotic cell death.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Quiescence (reversible)&lt;/li&gt;&#xA;&lt;li&gt;Growth ==&gt; Immortality (cancer cells)&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Growth and division&lt;/li&gt;&#xA;&lt;li&gt;Growth and no division (endocycles)&lt;a href=&quot;http://www.nature.com/nature/journal/v480/n7375/full/nature10579.html&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Division and no growth&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v480/n7375/full/nature10579.html&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;:  &lt;a href=&quot;http://www.nature.com/nature/journal/v480/n7375/full/nature10579.html&quot; rel=&quot;nofollow&quot;&gt;Norman Zielke, Kerry J. Kim, Vuong Tran, Shusaku T. Shibutani, Maria-Jose Bravo, Sabarish Nagarajan, Monique van Straaten, Brigitte Woods, George von Dassow, Carmen Rottig, Christian F. Lehner, Savraj Grewal, Robert J. Duronio, and Bruce A. Edgar: Control of Drosophila endocycles by E2F and CRL4Cdt2&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="609" LastEditorUserId="609" LastEditDate="2012-09-16T18:25:42.343" LastActivityDate="2012-09-16T18:25:42.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3523" PostTypeId="2" ParentId="3521" CreationDate="2012-09-12T15:34:50.333" Score="9" Body="&lt;p&gt;Fetal testis produces testosterone from cholesterol. There is a peak of production around 15 weeks of gestation (the &quot;masculinization programming window&quot;). So the genotype of the fetus can affect testosterone levels directly via effects on the biosynthesis of the hormone, or indirectly by defective regulation of the pathway's activity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, exposure to chemicals in the mother's environment is also thought to play a part in determining testosterone levels. The classic example of this is the phthalate esters used as plasticizers.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Scott et al. (2009) Steroidogenesis in the Fetal Testis and Its Susceptibility to Disruption by Exogenous Compounds. Endocrine Reviews 30: preprint freely available &lt;a href=&quot;http://www.cefic-lri.org/uploads/Project%20publications/Scott09%20Endo%20Rev.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-10-26T19:27:04.237" LastActivityDate="2012-10-26T19:27:04.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3525" PostTypeId="1" CreationDate="2012-09-12T17:27:38.740" Score="2" ViewCount="107" Body="&lt;p&gt;Age-associated neurodegenerative diseases encompass Alzheimer's Disease and Parkinson's Disease. What other neurodegenerative diseases could be described as age-associated? Multiple Sclerosis? Brain tumors? What might be the criteria for defining a disease as age-associated, specifically in the realm of neurobiology?&lt;/p&gt;&#xA;" OwnerUserId="609" LastEditorUserId="609" LastEditDate="2012-09-12T17:42:45.813" LastActivityDate="2012-09-12T17:55:47.130" Title="Age-associated neurodegenerative diseases" Tags="&lt;senescence&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3526" PostTypeId="2" ParentId="3479" CreationDate="2012-09-12T17:35:55.480" Score="1" Body="&lt;p&gt;The reaction kinetics of DNA mutations are complicated by the fact that the DNA doesn't exist in isolation, and in fact is actively processed and maintained by the cellular machinery.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, as Alan Boyd notes, the most common spontaneous mutation is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Deamination#Cytosine&quot; rel=&quot;nofollow&quot;&gt;deamination of cytosine to uracil&lt;/a&gt;: Cyt + H&lt;sub&gt;2&lt;/sub&gt;O &amp;rarr; NH&lt;sub&gt;3&lt;/sub&gt; + Ura.  On its own, the reverse of this reaction, i.e. spontaneous amination of uracil to cytosine, would be very unlikely, if only because the low concentration of ammonia compared to water in cellular fluid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in a living cell, there are DNA repair enzymes that actively &lt;a href=&quot;http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase&quot; rel=&quot;nofollow&quot;&gt;look for uracil in DNA and remove it&lt;/a&gt;, allowing &lt;a href=&quot;http://en.wikipedia.org/wiki/Base_excision_repair&quot; rel=&quot;nofollow&quot;&gt;other enzymes&lt;/a&gt; to come along and replace it with the original cytosine.  This keeps the &lt;em&gt;effective&lt;/em&gt; Cyt &amp;rarr; Ura mutation rate far below what it would be in the absence of active repair.&lt;/p&gt;&#xA;" OwnerUserId="239" LastActivityDate="2012-09-12T17:35:55.480" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3527" PostTypeId="2" ParentId="3525" CreationDate="2012-09-12T17:55:47.130" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Dementia with Lewy bodies (DLB):&lt;/strong&gt; It is characterized anatomically by the presence of Lewy bodies, clumps of alpha-synuclein and&#xA;  ubiquitin protein in neurons, detectable in post-mortem brain&#xA;  histology.[1] Lewy Body dementia affects 1.3 million individuals in&#xA;  the United States alone.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dementia_with_Lewy_bodies&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Dementia_with_Lewy_bodies&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Binswanger disease&lt;/strong&gt; is a form of small vessel vascular dementia caused by damage to the white brain matter.[1] White matter atrophy&#xA;  can be caused by many circumstances including chronic hypertension as&#xA;  well as old age.[2] This disease is characterized by loss of memory&#xA;  and intellectual function and by changes in mood. These changes&#xA;  encompass what are known as executive functions of the brain.[3] It&#xA;  usually presents between 54 and 66 years of age, and the first&#xA;  symptoms are usually mental deterioration or stroke.[4]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Binswanger%27s_disease&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Binswanger%27s_disease&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To name the two with the highest prevalence after Alzheimer's and Parkinson's.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-09-12T17:55:47.130" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3528" PostTypeId="2" ParentId="3514" CreationDate="2012-09-12T19:21:51.877" Score="5" Body="&lt;p&gt;According to their website &lt;strong&gt;&lt;em&gt;New England Biolabs&lt;/em&gt;&lt;/strong&gt; use a version of the approach pioneered by Wayne Barnes, as described in:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Kermekchiev, M.B., Tzekov, A and Barnes, W.M. (2003) Nucl. Acids Res. 31, 6139–6147&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is basically an assay for the mutation rate in a PCR-amplified &lt;em&gt;lacZ&lt;/em&gt; (&amp;beta;-galactosidase) gene, assayed by transforming &lt;em&gt;E. coli&lt;/em&gt;, plating on the chromogenic &amp;beta;-galactosidase substrate Xgal, and then scoring white colonies as mutated genes. Also according to NEB, Agilent Technologies use a similar mutational assay, but based upon the &lt;em&gt;lacI&lt;/em&gt; (lac repressor) gene.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-12T19:21:51.877" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3529" PostTypeId="2" ParentId="1305" CreationDate="2012-09-12T21:47:09.763" Score="0" Body="&lt;p&gt;I have had a little time to look over this paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They do overexpress a native sir2 clone in high doses, called sir2.1 OE.  Which seems to be native and also appears in high copy numbers. This strain was found in previous publication to have a high lifespan... that is old news. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This paper sees sir2.1 expression levels as an oversimplification of the causes of longevity.  When they create crosses of the sir2.1 OE strain with wildtype, you can see the Outcross, which is verified to have a high level of sir2 expressed no longer has an extraordinary lifespan.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can be seen in Figure 1.  &lt;a href=&quot;http://www.nature.com/nature/journal/v477/n7365/fig_tab/nature10296_F1.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nature/journal/v477/n7365/fig_tab/nature10296_F1.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So this paper is now asking, if sir2 levels do not convey the information that creates an extended lifespan, then what does?  It must be some modulation of some protein that sir2 affects.  They implies that the actual cause of the lifespan increase may have been a mutation somewhere else in the organism.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;However, longevity was not suppressed by sir-2.1 RNA interference (RNAi) ... indicating causation by factors other than sir-2.1, either on mDp4 or elsewhere in the genome.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;This implies that lifespan extension is due to transgene-linked genetic effects other than the overexpression of dSir2.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the second half of the paper (figure2) the investigators have moved on to drosophila work, where they look at how expressing constructs or inhibiting sir2 protein levels might affect lifespan.  Although the dSir(EP2300) / + construct (drosophila sir2) with a wild type gene promoter did not live quite as long as dSir2(EP2300) with a fancy promoter (dSir2(EP2300) / tub-GAL4), the promoter construct (tub-GAL4/+) alone also had just as long a lifespan.  How can this be?  Not sure, but the expression of sir2 is clearly not the panacea we had hoped.  Note however that &lt;em&gt;the reduced power gene still gave the same boost to lifetime&lt;/em&gt;.   &lt;strong&gt;This shows dramatically that sir2 activity alone does not drive the longer lifetime.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, deletion constructs (dSir4.5/1.7) , which should have lower than wild type protein levels for sir2 had completely normal lifetimes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the answer to your question; you need to test a hypothesis going in both directions - does increase of the protein really create a strong effect?  Does decreasing it have a negative effect then?  There are lots of other reasons to use knockouts and non functional genes in such an experiment, but those are the broad strokes. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-09-12T21:47:09.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3530" PostTypeId="1" AcceptedAnswerId="3531" CreationDate="2012-09-13T04:12:34.507" Score="2" ViewCount="370" Body="&lt;p&gt;Each of these types below contains a DNA mutation. Which type(s) will affect the children of the individual whose cell it is.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Red blood cell&lt;/li&gt;&#xA;&lt;li&gt;T cell&lt;/li&gt;&#xA;&lt;li&gt;Skin (epithelial) cell&lt;/li&gt;&#xA;&lt;li&gt;Neuron from the brain&lt;/li&gt;&#xA;&lt;li&gt;Sperm cell&lt;/li&gt;&#xA;&lt;li&gt;Cell from lining of the uterus&lt;/li&gt;&#xA;&lt;li&gt;Placenta cell&lt;/li&gt;&#xA;&lt;li&gt;Stem cell&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;My attempt&lt;/em&gt;: I think it's only a sperm cell, because that is the only cell to get passed on.  Is this right?&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="107" LastEditDate="2013-08-08T19:49:46.920" LastActivityDate="2013-08-08T19:52:14.880" Title="Which cells will pass cancer to offspring?" Tags="&lt;homework&gt;&lt;cancer&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3531" PostTypeId="2" ParentId="3530" CreationDate="2012-09-13T04:56:07.030" Score="4" Body="&lt;h2&gt;Red blood cell&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Will probably not. You inherit blood type, but not actual erythrocytes (though the mother's erythrocytes do interact with a fetus).&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;T cell&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Will probably not. However, while in the uterus and for the first few weeks outside the uterus the Mother's immune system is effectively the newborn's immune system. While the mother doesn't pass on any myeloid progenitor cells, a disease affecting a leukocyte might also be passed on to the child (HIV).&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Skin (epithelial) cell&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Will not. You inherit many traits to do with skin (melanocyte activity resulting in melanin concentrations, for instance), but no skin cells are involved in the creation of the fetus.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Neuron from the brain&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Will not.  Neurons are the last time of cell I'd expect to vertically pass on a mutation, not only because their environment is usually tightly controlled (Schwann Cells, Blood-Brain Barrier, etc.), but also because the fetus will develop the beginnings of its nervous system very early on and I'm not aware of the mother's CNS or PNS interacting with the fetus in any significant way.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sperm cell&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Can certainly pass on a mutation as long as the mutation is part of the sperm's DNA. Though the particular gene the mutation exists on may be inactivated, it would still be passed on to the offspring and potential future generations.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Cell from lining of the uterus&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I'm not positive on this one. The fertilized egg cell must implant itself in the lining of the uterus, and the landing location eventually becomes the umbilical cord. I suppose it's possible, particularly if the mutation occurs closer to the child's end - like the obliterated artery.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Placenta cell&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Probably not, though like &lt;em&gt;Cell from lining of the uterus&lt;/em&gt; I'm not super positive on this one. Given that the placenta is detached from both the mother and child soon after birth, a mutation in a placental cell that hasn't metasticized won't affect either. However, there may be interactions I'm not aware of.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Stem cell&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&quot;Stem cell&quot; is a little vague. The body has many specific types of stem cells, and the fertilized egg itself basically turns into all of the stem cells the developing fetus will ever have. If it's referring to the daughter cells of a fertilized egg, then only the child will have the cancer, as the genetic inheritance is unidirectional (the mother's genome is not modified to resemble the child's in any way).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If someone has better knowledge on the interaction between the fetus and the uterus/mother or can come up with some references, listen to them. It's been a while since I've studied development.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="107" LastEditDate="2013-08-08T19:52:14.880" LastActivityDate="2013-08-08T19:52:14.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3532" PostTypeId="2" ParentId="5" CreationDate="2012-09-13T08:36:24.423" Score="5" Body="&lt;p&gt;There are references in the literature to the phenomenon of &amp;quot;exon scrambling&amp;quot; which seems to be what you are asking about, but the prevailing view is that the evidence for this process, which comes from comparing EST sequences with genome sequences, can be explained by cloning artefacts occurring during EST characterisation. Certainly I agree that there is no evidence for a gene in which the rearrangement of exons is part of the normal pathway for mRNA generation.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Shao et al. (2006) Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans. Bioinformatics 22: 692-698&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;There is also more recent evidence from deep sequencing for rearrangement of exon order via circular RNAs:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Salzman et al. (2012), Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types PLOS ONE 7: e30733   DOI: 10.1371/journal.pone.0030733   &lt;/p&gt;&#xA;&lt;p&gt;Most human pre-mRNAs are spliced into linear molecules that retain the exon order defined by the genomic sequence. By deep sequencing of RNA from a variety of normal and malignant human cells, we found RNA transcripts from many human genes in which the exons were arranged in a non-canonical order. Statistical estimates and biochemical assays provided strong evidence that a substantial fraction of the spliced transcripts from hundreds of genes are circular RNAs. Our results suggest that a non-canonical mode of RNA splicing, resulting in a circular RNA isoform, is a general feature of the gene expression program in human cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Incidentally it is perhaps worth mentioning that in the case of the lectin concanavalin A the equivalent effect is produced post-translationally when the protein rearranges.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Carrington et al. (1985) Polypeptide ligation occurs during post-translational modification of concanavalin A. Nature 313:64-67&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-09-13T08:36:24.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3533" PostTypeId="1" AcceptedAnswerId="3535" CreationDate="2012-09-13T11:06:09.320" Score="5" ViewCount="209" Body="&lt;p&gt;In a hospital I can see a long queue of pregnant women waiting for their turn for ultrasound.  Is it safe to go through the ultrasound during pregnancy, especially during last few weeks? &#xA;Is ultrasound really required?  What if it is not done? How does ultrasound affect baby?&lt;/p&gt;&#xA;" OwnerUserId="1110" LastEditorUserId="69" LastEditDate="2012-12-02T15:50:57.927" LastActivityDate="2012-12-02T15:50:57.927" Title="Ultrasound during pregnancy" Tags="&lt;human-biology&gt;&lt;imaging&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3534" PostTypeId="2" ParentId="3533" CreationDate="2012-09-13T12:11:41.650" Score="6" Body="&lt;p&gt;The U.S. Food and Drug Administration (FDA) has the following information regarding the risks of ultrasound imaging;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Ultrasound imaging has been used for over 20 years and has an excellent safety record. It is non-ionizing radiation, so it does not have the same risks as x-rays or other types of ionizing radiation.&lt;/p&gt;&#xA;&lt;p&gt;Even though there are no known risks of ultrasound imaging, it can produce effects on the body. When ultrasound enters the body, it heats the tissues slightly. In some cases, it can also produce small pockets of gas in body fluids or tissues (cavitation). The long-term effects of tissue heating and cavitation are not known.&lt;/p&gt;&#xA;&lt;p&gt;Because of the particular concern for fetal exposures, national and international organizations have advocated prudent use of ultrasound imaging. Furthermore, the use of diagnostic ultrasound for non-medical purposes such as fetal keepsake videos has been discouraged.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.fda.gov/Radiation-EmittingProducts/RadiationEmittingProductsandProcedures/MedicalImaging/ucm115357.htm&quot; rel=&quot;noreferrer&quot;&gt;FDA &amp;gt; Radiation Emitting Products &amp;gt; Medical Imaging &amp;gt; Ultrasound Imaging&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.fda.gov/downloads/ForConsumers/ConsumerUpdates/UCM095487.pdf&quot; rel=&quot;noreferrer&quot;&gt;Further information&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;I had a bit of a look through PubMed and Scopus for any papers relating to ultrasound risk, but didn't find any.&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-09-13T12:16:48.677" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3535" PostTypeId="2" ParentId="3533" CreationDate="2012-09-13T12:36:22.747" Score="5" Body="&lt;p&gt;As Luke points out, the ultrasound is very safe. However, in many cases it is not required. Typically by 20 weeks into the pregnancy, and sometimes earlier, a baby's sex can be determined by examining the genitals via ultrasound. My experience is that this is the most common reason for an ultrasound during pregnancy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course if there are complications during the pregnancy, an ultrasound might be helpful to visualize the fetus and diagnose any problems. However there is no definite &lt;em&gt;need&lt;/em&gt; for an ultrasound during the course of a normal pregnancy.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-09-13T12:36:22.747" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3536" PostTypeId="1" CreationDate="2012-09-13T12:40:22.933" Score="2" ViewCount="147" Body="&lt;p&gt;A protein that catalyzes one reaction can theoretically be modified by mutations and natural selection and eventually catalyze another reaction completely unrelated to the original. Has this been observed, documented, or at least postulated to be where a certain protein(s) came from?&lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="146" LastEditDate="2015-12-17T06:37:36.993" LastActivityDate="2015-12-17T06:37:36.993" Title="Have proteins been observed to come into existence through mutations and natural selection?" Tags="&lt;evolution&gt;&lt;proteins&gt;&lt;natural-selection&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3537" PostTypeId="2" ParentId="2507" CreationDate="2012-09-13T13:34:14.290" Score="3" Body="&lt;p&gt;An example possibly worth taking a look at is the variable surface glycoprotein of the bloodstream form of &lt;em&gt;Trypanosoma brucei&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trypanosomes are the causative agent of sleeping sickness, and the entire cell surface is covered by a single glycoprotein called the variable surface glycoprotein, or VSG. (see &lt;a href=&quot;http://tryps.rockefeller.edu/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for more information)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These parasitic protozoans have the ability to 'fool' the immune response by antigenic variation.  At any one time just a single VSG is expressed on the surface, but (very rarely) a trypanosome may express a different VSG gene product.  Thus if the immune response succeeds in eliminating all trypanosomes expressing VSG-A, but there exists in the population just one parasite which has switched coat, this variant will poliferate as it effectively presents a different antigen to the host's defenses (and a second immune response will result).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is litte sequence identity between different VSGs but they are homologous (descended from a common ancestor). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The crystal structure of the N-terminal domain of two different VSGs (MITat1.2 and ILTat1.24) have been solved (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8464512?dopt=Abstract&quot; rel=&quot;nofollow&quot;&gt;Blum&lt;/a&gt; &lt;em&gt;et al.&lt;/em&gt; 1993; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2231728?dopt=Abstract&quot; rel=&quot;nofollow&quot;&gt;Freymann&lt;/a&gt; &lt;em&gt;et al&lt;/em&gt;., 1993).  Despite the low sequence identity (~16%), &lt;strong&gt;the structures are almost identical&lt;/strong&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One other very interesting property of all VSGs is that they are covalently anchored to the plasma membrane via a (C-terminus) glycosylphosphatidylinositol anchor (or GPI anchor).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Blum, M. L., Down, J. A., Gurnett, A. M., Carrington, M., Turner, M. J., and Wiley, D. C. (1993) &lt;em&gt;Nature&lt;/em&gt; &lt;strong&gt;362&lt;/strong&gt;, 603-609 [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8464512?dopt=Abstract&quot; rel=&quot;nofollow&quot;&gt;pubmed&lt;/a&gt;]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Freymann, D., Down, J., Carrington, M., Roditi, I., Turner, M., and Wiley, D. (1990) 2.9 A resolution structure of the N-terminal domain of a variant surface glycoprotein from &lt;em&gt;Trypanosoma brucei&lt;/em&gt;.  &lt;em&gt;J. Mol. Biol&lt;/em&gt;. &lt;strong&gt;216&lt;/strong&gt;, 141-160  [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2231728?dopt=Abstract&quot; rel=&quot;nofollow&quot;&gt;Pubmed&lt;/a&gt;]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The following reference contains much useful background information, and is free to all. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Chattopadhyay, A, Jones, N.G, Nietlispach,D, Nielsen, P.R., Voorheis, H.P., Mott H.R., Carrington, M. (2005)  Structure of the C-terminal domain from &lt;em&gt;Trypanosoma brucei&lt;/em&gt; variant surface glycoprotein MITat1.2. &lt;em&gt;J. Biol. Chem.&lt;/em&gt;, &lt;strong&gt;280&lt;/strong&gt;, 7228-7235 [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15557330&quot; rel=&quot;nofollow&quot;&gt;Pubmed&lt;/a&gt;] [&lt;a href=&quot;http://www.jbc.org/content/280/8/7228.long&quot; rel=&quot;nofollow&quot;&gt;pdf&lt;/a&gt;]&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="1136" LastEditDate="2012-09-13T15:01:40.960" LastActivityDate="2012-09-13T15:01:40.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3538" PostTypeId="2" ParentId="3536" CreationDate="2012-09-13T14:01:19.477" Score="2" Body="&lt;p&gt;From the following free review:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Here we review some of the successful strategies in creating protein&#xA;diversity and the more recent progress in directed protein evolution&#xA;in a wide range of scientific disciplines and its impacts in chemical,&#xA;pharmaceutical, and agricultural sciences.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Quoting three examples, but the article has much more:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Directed evolution has been successfully applied to DNA polymerase for&#xA;enhanced activity (233) and conversion to an efficient RNA polymerase&#xA;(232, 333).&lt;/p&gt;&#xA;&lt;p&gt;Naumann and Reznikoff (216) used directed evolution to generate a&#xA;mutated Tn5 bacterial transposase that could function on transposons&#xA;with mutated end binding sequences.&lt;/p&gt;&#xA;&lt;p&gt;Organophosphate-degrading enzymes have been evolved and selected for&#xA;broadened substrate specificity (53, 335). Broadened substrate&#xA;specificity of a biphenyl dioxygenase has also been achieved (33, 87,&#xA;164, 291). Efforts in cleaning underground water contamination&#xA;prompted the evolution of an enzyme for chlorinated ethene degradation&#xA;(41).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;L. Yuan, I. Kurek et al: &lt;em&gt;Laboratory-directed protein evolution.&lt;/em&gt; In: &lt;em&gt;Microbiology and molecular biology reviews : MMBR.&lt;/em&gt; 69, 3, September 2005, 373–392. doi:10.1128/MMBR.69.3.373-392.2005. PMID 16148303. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/16148303/&quot; rel=&quot;nofollow noreferrer&quot;&gt;PMC 1197809.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-09-13T14:01:19.477" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3539" PostTypeId="2" ParentId="1680" CreationDate="2012-09-13T17:12:14.447" Score="2" Body="&lt;p&gt;SDS PAGE system rely on the fact that protein is denatured and surrounded by the SDS negatively charged detergent micelle.  This eliminates most of the charge and idiosyncratic solubility differences from one protein to another and gives a reasonable separation based only on size of the protein which is related to the size of the SDS micelle around each molecule.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bis-Tris and Tris-glycine buffers have quite different charge shielding characteristics.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Bis-tris_methane&quot; rel=&quot;nofollow&quot;&gt;Bis&lt;/a&gt; (also known as 2-[Bis(2-hydroxyethyl)amino]-2-(hydroxymethyl)-1,3-propanediol) has a tertiary amine with a pKa of 6.46 and a pKb of 7.54.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Glycine&quot; rel=&quot;nofollow&quot;&gt;glycine&lt;/a&gt; is a zwitterion at any pH between 2.3 and 9.6.  This creates a difference in the way that the buffer shields the SDS PAGE micelles from the rest of the electrical field, slowing down (probably glycine slows things down a bit) the time to resolution, but also giving the micelles more time to migrate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for SDS PAGE systems, the resolution of the gel has at least as much to do with the size of the gel pores (based on the acrylamide and bis-acrylamide percentages), the amount of protein you are putting into a given volume of loading well, and the size differences of the bands you are tying to separate. (you need to get pretty lucky to separate a 100.54 kda band from a 100.85 kDa band, but 1.5 to 1.8 kDa is easier 10 to 14 kDa is even easier). Also consider adjusting the current or voltage of the power supply.  The buffer system is only one consideration in planning your experiment and often not the primary factor of quality. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-09-13T17:12:14.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3540" PostTypeId="2" ParentId="3536" CreationDate="2012-09-13T17:56:34.463" Score="6" Body="&lt;p&gt;How about &lt;a href=&quot;http://en.wikipedia.org/wiki/FLI1#Clinical_significance&quot;&gt;EWS-FLI1&lt;/a&gt; and other &lt;a href=&quot;http://www.google.com?q=oncofusion+proteins&quot;&gt;oncofusion proteins&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One could argue that cancer progression is as close to viewing &quot;evolution in real time&quot; (as you say) as possible.&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2012-09-13T17:56:34.463" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3541" PostTypeId="2" ParentId="2455" CreationDate="2012-09-13T17:58:27.553" Score="5" Body="&lt;p&gt;Take a look at &lt;a href=&quot;http://books.google.com/books/about/Field_and_laboratory_methods_for_general.html?id=WFfwAAAAMAAJ&quot; rel=&quot;nofollow&quot;&gt;Field and Laboratory Methods for General Ecology&lt;/a&gt; by James E. Brower, Jerrold H. Zar, and Carl N. von Ende.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are only interested in plant sampling techniques, an great resource published by U.S. Bureau of Land Management is &lt;a href=&quot;http://www.blm.gov/nstc/library/pdf/MeasAndMon.pdf&quot; rel=&quot;nofollow&quot;&gt;Measuring &amp;amp; Monitoring Plant Populations&lt;/a&gt; by Caryl L. Elzinga, Daniel W. Salzer, and John W. Willoughby.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another great resource that covers wildlife research and management techniques (2 volume set) is &lt;a href=&quot;http://joomla.wildlife.org/techniquesmanual/&quot; rel=&quot;nofollow&quot;&gt;The Wildlife Techniques Manual&lt;/a&gt; published by The Wildlife Society and edited by Nova J. Silvy.&lt;/p&gt;&#xA;" OwnerUserId="1396" LastEditorUserId="1396" LastEditDate="2012-10-20T15:13:27.800" LastActivityDate="2012-10-20T15:13:27.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3542" PostTypeId="2" ParentId="762" CreationDate="2012-09-13T19:40:20.230" Score="2" Body="&lt;p&gt;Many animals have actually reached an optimal solution to their evolutionary path.&#xA;That means that from where their genome is right now, pretty much all changes are harmful to expected reproduction. Over time such species start to have less variability within their genome and start to evolve less. Evolving is simply not sensible anymore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans on the other hand are in an extremely open evolutionary path, that means there is much variability within the human genome that leads to greatly varied expected reproduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is why humans are evolving so fast.&lt;/p&gt;&#xA;" OwnerUserId="542" LastEditorUserId="542" LastEditDate="2012-09-13T19:57:36.493" LastActivityDate="2012-09-13T19:57:36.493" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3544" PostTypeId="1" AcceptedAnswerId="3556" CreationDate="2012-09-14T08:39:17.067" Score="7" ViewCount="92" Body="&lt;p&gt;In the new citizen science project (see: &lt;a href=&quot;http://www.seafloorexplorer.org/&quot; rel=&quot;nofollow&quot;&gt;Sea Floor Explorer&lt;/a&gt;), numbers of seastars, scallops, crustaceans and other animals are counted. Already one can see a heavy bias in favor of seastars, both the fat and brittle kind. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be interested in why this creature is so succesful, especially if it is poisonous to e.g., crustaceans, and what poisons exactly are responsible.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1550" LastEditDate="2012-10-19T18:14:48.110" LastActivityDate="2012-10-19T18:14:48.110" Title="Which poison makes seastars inedible to possible predators?" Tags="&lt;marine-biology&gt;&lt;ecophysiology&gt;&lt;invertebrates&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3545" PostTypeId="1" AcceptedAnswerId="3546" CreationDate="2012-09-14T14:30:43.143" Score="9" ViewCount="1816" Body="&lt;p&gt;I am reading through the ENCODE papers, which is taking me well out of my comfort zone in terms of modern laboratory techniques. At the risk of asking a question which may well be thoroughly answered somewhere else on the internet, I was hoping for a brief explanation of nuclear transfection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://genomebiology.com/2012/13/9/R50&quot;&gt;Whiteld et all&lt;/a&gt;, they describe the direct assay of transcription factor binding site efficacy in human cells.  To do this, they transfect a luciferase plasmid, presumably into the nucleus of the cell (because they subsequently observe that the luciferase plasmid is transcribed).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reading through Materials and Methods and getting to the supplementary file, they disclosed their transfection protocol. The relevant reagants appear to be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;FuGene 6 &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a nonliposomal formulation designed to transfect plasmid DNA into a wide variety of cell lines with high efficiency and low toxicity. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(From Promega's website.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lipofectamine LTX&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;efficient reagent for plasmid delivery and protein expression&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(From Invitrogen's website.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PLUS reagent&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;PLUS™ Reagent is used in conjunction with transfection reagents, such as Lipofectamine™, to enhance transfection in adherent cell lines. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(From Invitrogen's website.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently, the protocol is to combine the DNA plasmid with transfection reagent, wait a few minutes, and then add in the cells, and incubate at 37ºC for 24 hours. That's all that is required to get the plasmid into the nucleus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have consulted Wikipedia and Strachan and Read's Human Molecular Genetics 4th edition, but been unable to answer my question about this technique.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think I have a pretty clear understanding of how these reagents are able to get through the cell's lipid membrane, but I don't have a similar understanding of &lt;strong&gt;how the DNA then passes to the nucleus&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Human Molecular Genetics 4th edition, I can find only one paragraph about plasmid transfer across a nuclear membrane, page 704: &quot;Transport of plasmid DNA to the nucleus of non-dividing cells is very inefficient because the plasmid DNA often cannot enter nuclear membrane pores. Various methods can be used to faciliate nuclear entry such as conjugating specific DNA sequences or protein sequences (nuclear localization seuqences) that are known to facilitate nuclear entry, or compacting the DNA to a small enough size to pass through the nuclear pores.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But nothing in the materials and methods section of Whiteld et. all mentions any of these techniques. I'm sure they would have mentioned if their plasmid included a DNA conjugation sequence, so that can't be it. Perhaps these reagents implicitly include some sort of DNA compaction polycation, such as PEG-CK30?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isn't the cytoplasm an extremely hostile place for DNA plasmids? Shouldn't they just flail around in the cytoplasm until they are digested?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or perhaps these vectors sneak into the nucleus during mitosis? (This is a theory that just occurred to me when contemplating the &quot;non-dividing&quot; qualification in the Strachan quote.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the question isn't addressed in the paper, I can only assume the answer is elementary and something that a professional cell biologist would be expected to know. I've run out of obvious next steps for finding the answer, so I beg pardon in advance for asking it.&lt;/p&gt;&#xA;" OwnerUserId="1364" LastEditorUserId="69" LastEditDate="2012-10-26T16:31:59.103" LastActivityDate="2015-07-16T14:23:24.550" Title="Methods of nuclear transfection - nuclear transport" Tags="&lt;cell-biology&gt;&lt;molecular-genetics&gt;&lt;eukaryotic-cells&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3546" PostTypeId="2" ParentId="3545" CreationDate="2012-09-14T15:41:32.047" Score="8" Body="&lt;p&gt;My attempt to find an answer has suggested that no-one knows how the DNA gets into the nucleus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This fairly recent paper reports attempts to track the pathway of DNA entry and transfer to the nucleus.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Le Bihan &lt;em&gt;et al&lt;/em&gt;. (2010) Probing the in vitro mechanism of action of cationic lipid/DNA lipoplexes at a nanometric scale. Nucl. Acids Res. &lt;strong&gt;39&lt;/strong&gt;:1595-1609&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The technique used was transmission electron microscopy. Complexes of plasmid DNA + cationic lipids (lipoplexes) were labelled with silica-based nanoparticles to allow visualization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors describe a transfection pathway with five steps:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(i) binding of the lipoplexes to the cell surface;&lt;br&gt; &#xA;  (ii) entry of the lipoplexes into the cells mainly via endocytosis (a direct fusion with cell membrane cannot be excluded);&lt;br&gt; &#xA;  (iii) DNA release into the cytosol;&lt;br&gt;&#xA;  (iv) transport through the cytosol; and&lt;br&gt; &#xA;  (v) entry of DNA into the nucleus and nuclear transcription.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors were able to follow each of the first four steps but:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;our data show nanoparticles close to, but not within, the nucleus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They speculate about what this might mean, but they do not refer to any previously published data. My conclusion is that the answer to your question is, as I said at the beginning of my answer: no-one knows how the transfected DNA enters the nucleus.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-09-14T16:06:16.193" LastActivityDate="2012-09-14T16:06:16.193" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3547" PostTypeId="1" CreationDate="2012-09-15T01:14:31.663" Score="5" ViewCount="417" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Paracerceis_sculpta&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Paracerceis sculpta&lt;/em&gt;&lt;/a&gt; is a marine isopod species known for its unusual reproductive strategy:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;female: medium-sized; lives in harems run by an α male&lt;/li&gt;&#xA;&lt;li&gt;α male: large; keeps a harem of females&lt;/li&gt;&#xA;&lt;li&gt;β male: medium; mimics a female in order to enter a harem and mate&lt;/li&gt;&#xA;&lt;li&gt;γ male: small; mimics a juvenile in order to slip into a harem and mate&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mchy8.png&quot; alt=&quot;P. sculpta illustration&quot;&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How does this 4-way sex differentiation occur?&lt;/strong&gt; That is, what determines which of the morphs an individual develops into?&lt;/p&gt;&#xA;" OwnerUserId="1202" LastEditorUserId="1202" LastEditDate="2012-09-16T22:38:39.480" LastActivityDate="2012-09-16T22:38:39.480" Title="How does sex differentiation work in Paracerceis sculpta, the sexually tetramorphic isopod?" Tags="&lt;genetics&gt;&lt;zoology&gt;&lt;development&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3548" PostTypeId="1" AcceptedAnswerId="3550" CreationDate="2012-09-15T01:35:35.747" Score="9" ViewCount="1582" Body="&lt;p&gt;Here's &lt;a href=&quot;http://theearlybirder.com/corvids/am-crow/pages/6002831%20American%20Crow.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;a picture&lt;/a&gt; (by Rob Curtis) of a crow carrying and eating the corpse of what looks a bit like a small hawk or falcon:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TZ4p9.jpg&quot; alt=&quot;Crow carrying dead bird&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://theearlybirder.com/corvids/am-crow/pages/6003000%20American%20Crow.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Other&lt;/a&gt; &lt;a href=&quot;http://theearlybirder.com/corvids/am-crow/pages/6002847%20American%20Crow.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;pictures&lt;/a&gt; clearly show the crow is eating the dead bird. &lt;a href=&quot;http://theearlybirder.com/corvids/am-crow/pages/6002847%20American%20Crow.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;This image&lt;/a&gt; shows the underside of the head and beak; &lt;a href=&quot;http://theearlybirder.com/corvids/am-crow/pages/6002825%20American%20Crow.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;this one&lt;/a&gt; shows its legs, which are grayish.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;What bird is being eaten?&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Is this bird a usual part of the corvid diet?&lt;/strong&gt; Or did the crow just opportunistically scavenge a dead bird?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1202" LastActivityDate="2013-08-01T10:09:04.950" Title="What is this crow eating, and is it a common part of the corvid diet?" Tags="&lt;zoology&gt;&lt;species-identification&gt;&lt;ornithology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3549" PostTypeId="1" AcceptedAnswerId="3551" CreationDate="2012-09-15T07:33:23.190" Score="7" ViewCount="1103" Body="&lt;p&gt;As I am not related to biology, I would appreciate if you can keep your answers as simple as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is about the influence of alcohol on the brain. As far as I know, drinking alcohol is killing cells in the brain. But is it linear? E.g. if I have 1.0 per mil and it kills 1000 cells will 2.0 per mil kill 2000 cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(An equation would be nice) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks &lt;/p&gt;&#xA;" OwnerUserId="1405" LastEditorUserId="43" LastEditDate="2012-09-17T13:30:15.653" LastActivityDate="2014-03-30T07:39:57.737" Title="Influence of alcohol on brain cells" Tags="&lt;human-biology&gt;&lt;brain&gt;&lt;toxicology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3550" PostTypeId="2" ParentId="3548" CreationDate="2012-09-15T10:17:05.673" Score="13" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Crow#Diet&quot; rel=&quot;nofollow noreferrer&quot;&gt;Crows&lt;/a&gt; are omnivorous, and will eat almost anything they find or can kill.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case the prey looks like a &lt;a href=&quot;http://en.wikipedia.org/wiki/Northern_flicker&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yellow-Shafted Flicker&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Yo6Xy.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="3952" LastEditDate="2013-08-01T10:09:04.950" LastActivityDate="2013-08-01T10:09:04.950" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3551" PostTypeId="2" ParentId="3549" CreationDate="2012-09-15T11:13:55.080" Score="16" Body="&lt;p&gt;The situation is definitely an extremely complex one, and you should probably forget about having an &lt;strong&gt;exact&lt;/strong&gt; equation to define it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When talking about the effects of a substance on the organism there are several factors to take into account. These are generally put together under the term &lt;a href=&quot;http://en.wikipedia.org/wiki/Pharmacodynamics&quot; rel=&quot;noreferrer&quot;&gt;pharmacodynamics&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the factor to take into account are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The dose of the substance&lt;/li&gt;&#xA;&lt;li&gt;The route of administration&lt;/li&gt;&#xA;&lt;li&gt;The metabolism of the substance&lt;/li&gt;&#xA;&lt;li&gt;The target organ&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The problem is, &lt;strong&gt;not all ethanol you drink will go to the brain&lt;/strong&gt;, and it will not necessarily go there immediately, or all at the same time. All of this will change the effects on the brain. Also, there are several confounding factors, some of which I have tried to list.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have summarized here a few information about ethanol metabolism, taken mostly from &lt;a href=&quot;http://books.google.com/books?id=k7BInEQ-iqgC&amp;amp;pg=PA157&amp;amp;lpg=PA157&quot; rel=&quot;noreferrer&quot;&gt;Principles of Forensic Toxicology&lt;/a&gt; - Chapter 10 by Barry Levine and Yale H. Caplan&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ethanol is normally taken through drinking, which means that it will have to pass through the gastrointestinal (GI) tract (i.e. stomach and intestine) before getting into the bloodstream. This route permits practically 100% of absorption of ethanol in the body, with the major site of absorption being the small intestine, absorbing ~75% of a dose of ethanol. The rest will be absorbed in the stomach and in the other parts of the intestine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The absorption in the GI tract is dependent on the type of beverage: for instance carbonated alcoholic beverages are absorbed faster than &quot;plain&quot; ones. &#xA;The alcohol content also is important: a very diluted drink is absorbed slower than one with 10-30% of ethanol, as the latter will generate a bigger concentration gradient between the GI tract and the circulation, so it will diffuse faster. However, &gt;30% ethanol will enhance mucus formation, which will slow down absorption. Furthermore, absorption depends on the status of the GI tract: preexisting conditions (e.g. inflammation) can modify the rate at which the alcohol enters the bloodstream.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, we are still far away from the brain! After being absorbed, ethanol goes into the vena cava, and passes through the liver, where it can be metabolized (destroyed) by an enzyme called &lt;a href=&quot;http://en.wikipedia.org/wiki/Alcohol_dehydrogenase&quot; rel=&quot;noreferrer&quot;&gt;alcohol dehydrogenase&lt;/a&gt; (ADH), which converts ethanol into acetaldheyde, effectively reducing the ethanol concentration in the blood. &#xA;This is a well-known phenomenon for many drugs, and it is called &lt;a href=&quot;http://en.wikipedia.org/wiki/First_pass_effect&quot; rel=&quot;noreferrer&quot;&gt;first pass effect&lt;/a&gt;&#xA;Importantly, the human stomach also expresses ADH, so this first pass effect can start even before reaching the liver! The effects of ADH in the stomach obviously depends on how long the ethanol stays in there. So, it will be lower for an empty stomach then after a big meal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Food, in fact, is also a well known factor that reduces the amount of ethanol in the blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, these graphs show blood ethanol content in four healthy subjects after a 10 hour fast (filled circles) or after breakfast (empty circles), after drinking the same dose of 0.80 g ethanol/kg body weight, in 30 minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FLK2L.jpg&quot; alt=&quot;Blood EtOH levels and food&quot;&gt;&lt;br&gt;&#xA;From: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8064267&quot; rel=&quot;noreferrer&quot;&gt;Food-Induced Lowering of Blood-Ethanol Profiles and Increased Rate of Elimination Immediately After a Meal&lt;/a&gt; - Jones AW and Jönsson KA - &lt;em&gt;J Forensic Sci.&lt;/em&gt;, &lt;strong&gt;1994&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, eating strongly decrease the ethanol blood content. Also see how there is quite a bit of variation between the different subjects (if you open the paper you will also see the graphs from other 6 subjects).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, you can look for instance at this paper (just got a random study, there seems to be a ton of them around):&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8974331&quot; rel=&quot;noreferrer&quot;&gt;First pass metabolism of ethanol.&lt;/a&gt; - Lieber CS et al. - &lt;em&gt;Alcohol Alcohol Suppl.&lt;/em&gt;, &lt;strong&gt;1994&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coming out of the liver, ethanol goes into the right side of the hearth, and from there to the lungs. This poses no particular issue for most drugs, but ethanol is volatile! So, part of the ethanol is released through respiration (in fact the &quot;classic&quot; way of saying if someone has drunk alcohol is to smell his breath). However, this only accounts for a minor decrease in blood ethanol levels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, ethanol can start going around the body. Being a water-soluble molecule it will tend to diffuse into water-containing parts of our body (i.e. you will not find much ethanol in fat), which include the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the meantime, however, the process of elimination has started: ethanol can be excreted in urine, sweat and breath, although the major route of elimination is epathic metabolism by ADH, accounting for &gt;90% of ethanol elimination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a neat formula to express all of this, called the Widmark equation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$A=\frac{Wr(C_t+\beta*t)}{0.8z}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$A$ = number of drinks consumed&lt;br&gt;&#xA;$W$ = body weight (important because of the content of water in the body)&lt;br&gt;&#xA;$r$ = Widmark constant (depends on sex, age, etc.)&lt;br&gt;&#xA;$C_t$ = blood ethanol concentration at time t&lt;br&gt;&#xA;$\beta$ = acohol elimination rate&lt;br&gt;&#xA;$t$ = time since the first drink&lt;br&gt;&#xA;$z$ = volume of alcohol per drink  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find examples of this formula in &lt;a href=&quot;http://www.wsp.wa.gov/breathtest/docs/webdms/Studies_Articles/Widmarks%20Equation%2009-16-1996.pdf&quot; rel=&quot;noreferrer&quot;&gt;this PDF about Widmark equations&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And now to the brain: ethanol does indeed have various effects on neurons. Short term effect essentially involve depression of neuronal activity, ethanol being able to modulate GABA signalling in the brain. Long term effect range from reduced neurogenesis (i.e. birth of new neurons) to reduced volume of certain brain areas, probably due to loss of neurons, to inflammation in the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, the situation is very complex and it depends on the frequency of drinking, the amount of each drink and many other factors. A single dose of ethanol will probably have irrelevant effects on your neurons... as the amount needed (in one shot) for serious neurotoxicity will probably send you into ethilic coma. The exact mechanisms for these effects are only partially known and very likely to be derived by the interaction of numerous diverse effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This article explains some of the mechanisms for loss of neurons in the cerebellum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18418667&quot; rel=&quot;noreferrer&quot;&gt;Mechanisms of ethanol-induced degeneration in the developing, mature, and aging cerebellum.&lt;/a&gt; - Jaatinen and Rintala - &lt;em&gt;Cerebellum&lt;/em&gt;, &lt;strong&gt;2008&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These mechanisms include: (i) excitotoxicity; (ii) dietary factors, especially thiamine depletion; (iii) glial abnormalities; (iv) changes in growth factors; (v) apoptotic mechanisms; (vi) oxidative stress; and (vii) compromised energy production.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I will not go into the details of all of this, but it should be clear by now that all the things I mentioned so far (and many other factors I did not talk about) make it &lt;strong&gt;extremely difficult to give an exact quantification of the number of cells killed by ethanol&lt;/strong&gt;. Surely the relationship is not linear, in fact, for instance, positive effects of small doses of alcohol have been reported numerous times.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few more references on effects of alcohol on the brain:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reduced neurogenesis&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20534463&quot; rel=&quot;noreferrer&quot;&gt;Long-lasting reduction in hippocampal neurogenesis by alcohol consumption in adolescent nonhuman primates.&lt;/a&gt; - Taffe et al. - &lt;em&gt;PNAS&lt;/em&gt;, &lt;strong&gt;2010&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21484803&quot; rel=&quot;noreferrer&quot;&gt;Adolescent binge alcohol exposure alters hippocampal progenitor cell proliferation in rats: effects on cell cycle kinetics.&lt;/a&gt; - McClain et al. - &lt;em&gt;J Comp Neurol.&lt;/em&gt;, &lt;strong&gt;2011&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Brain volume decrease&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18374900&quot; rel=&quot;noreferrer&quot;&gt;Decreased volume of the brain reward system in alcoholism.&lt;/a&gt; - Makris et al. - &lt;em&gt;Biol Psychiatry&lt;/em&gt;, &lt;strong&gt;2008&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18593776&quot; rel=&quot;noreferrer&quot;&gt;Amygdala volume associated with alcohol abuse relapse and craving.&lt;/a&gt; - Wrase et al. - &lt;em&gt;Am J Psychiatry.&lt;/em&gt;, &lt;strong&gt;2008&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12531462&quot; rel=&quot;noreferrer&quot;&gt;Hyperhomocysteinemia as a new risk factor for brain shrinkage in patients with alcoholism.&lt;/a&gt; - Bleich et al. - &lt;em&gt;Neurosci Lett.&lt;/em&gt;, &lt;strong&gt;2003&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2014-03-30T07:39:57.737" LastActivityDate="2014-03-30T07:39:57.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3552" PostTypeId="1" AcceptedAnswerId="39054" CreationDate="2012-09-15T15:48:08.833" Score="8" ViewCount="233" Body="&lt;p&gt;Two publications, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1527604&quot; rel=&quot;nofollow&quot;&gt;Roe et al, 1992&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt; and &lt;a href=&quot;http://www.pnas.org/content/86/1/357&quot; rel=&quot;nofollow&quot;&gt;Metin &amp;amp; Frost, 1989&lt;sup&gt;[2]&lt;/sup&gt;&lt;/a&gt;, describe results pertaining to the ability of a region of cortex to process information from a different sensory mode than the one that it normally does.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, they describe studies in which:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;input from the retinas of newborn rodents was rerouted, by&#xA;surgical methods, to parts of the cortex other than the visual; &lt;/li&gt;&#xA;&lt;li&gt;the rodents were allowed to mature;&lt;/li&gt;&#xA;&lt;li&gt;the responses of cortical cells in the new target region to visual stimuli were assess.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Now it's 20 years later, so I'm sure there have been many others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something of which these publications seem to make no mention is the behavior that developed in the test subjects. For example, did they appear to be completely blind from a behavioral standpoint?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is anyone aware of any publication, relating to these studies or other, similar experiments, which addresses this question?&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1527604&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Roe AW, Pallas SL, Kwon YH, Sur M&lt;/strong&gt;. 1992. Visual projections routed to the auditory pathway in ferrets: receptive fields of visual neurons in primary auditory cortex. Journal of Neuroscience, 12(9): 3651-64.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pnas.org/content/86/1/357&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Métin C, Frost DO&lt;/strong&gt;. 1989. Visual responses of neurons in somatosensory cortex of hamsters with experimentally induced retinal projections to somatosensory thalamus. Proceedings of the National Academy of Sciences USA, 86(1): 357-361.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1406" LastEditorUserId="9943" LastEditDate="2015-09-25T11:35:17.827" LastActivityDate="2015-09-26T13:28:05.797" Title="How well does it actually work to surgically reroute the optical nerve?" Tags="&lt;neuroscience&gt;&lt;vision&gt;&lt;behaviour&gt;&lt;neurophysiology&gt;&lt;neuroplasticity&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3553" PostTypeId="2" ParentId="3547" CreationDate="2012-09-15T19:21:54.893" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Shuster, SM &amp;amp; C Sassaman (1997)&#xA;  Genetic interaction between male mating strategy and sex ratio in a marine isopod. Nature &lt;strong&gt;388&lt;/strong&gt;: 373-377&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As described in this paper, the chromosomal system of sex determination in &lt;em&gt;Paracerceis sculpta&lt;/em&gt; is ZW=females, ZZ=males. Genetic evidence indicates that the morph of a ZZ male is determined by a second locus, &lt;em&gt;Ams&lt;/em&gt; (&lt;em&gt;alternative mating strategy&lt;/em&gt;) which exists in three allelic forms whose dominance relationship is &lt;em&gt;Ams&lt;sup&gt;&amp;beta;&lt;/sup&gt;&lt;/em&gt; &gt; &lt;em&gt;Ams&lt;sup&gt;&amp;gamma;&lt;/sup&gt;&lt;/em&gt; &gt; &lt;em&gt;Ams&lt;sup&gt;&amp;alpha;&lt;/sup&gt;&lt;/em&gt;. So for example, to be an &amp;alpha; type male, an individual must be ZZ &lt;em&gt;Ams&lt;sup&gt;&amp;alpha;&lt;/sup&gt;&lt;/em&gt; / &lt;em&gt;Ams&lt;sup&gt;&amp;alpha;&lt;/sup&gt;&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's the end of the answer, what follows is supplementary information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper also describes an additional layer of complexity in the sex-determining system of &lt;em&gt;P. sculpta&lt;/em&gt; involving sex changes in both directions. This is explained by a model in terms of two other factors: an autosomal locus &lt;em&gt;Tfr&lt;/em&gt; (&lt;em&gt;transformer&lt;/em&gt;) and a cytoplasmic factor ECF (extra-chromosomal factor) which interact as shown in the Table below (taken from the paper). However, this doesn't really add anything to the &lt;em&gt;Ams&lt;/em&gt; story as far as male morphs are concerned, except that some of them start as females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ugaPB.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-15T19:21:54.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3554" PostTypeId="1" AcceptedAnswerId="3558" CreationDate="2012-09-15T20:59:47.950" Score="7" ViewCount="1192" Body="&lt;p&gt;I went to give blood the other day, and they take an &quot;iron&quot; measurement prior to actually drawing the blood. My level was 16.4 -- but what specific type of iron were they measuring? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've heard of ferritin, transferrin, iron binding cap, total, etc., but when I asked what the upper limit was, she said 19, which didn't really fit within the healthy ranges I can find for the above types.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thoughts?&lt;/p&gt;&#xA;" OwnerUserId="1407" LastEditorUserId="69" LastEditDate="2013-02-22T11:03:15.220" LastActivityDate="2013-02-22T11:03:15.220" Title="When giving blood, what is the specific Iron measurement they take?" Tags="&lt;biochemistry&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3555" PostTypeId="2" ParentId="3297" CreationDate="2012-09-15T21:20:55.650" Score="2" Body="&lt;p&gt;As was pointed out by @jello differentiated neurons do not divide, instead new neurons are recruited into existing networks from undifferentiated cells. This process is called neurogenesis. A high level summary of &lt;a href=&quot;http://www.scholarpedia.org/article/Adult_neurogenesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;adult neurogenesis&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Neural &lt;a href=&quot;http://en.wikipedia.org/wiki/Progenitor_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;progenitor cells&lt;/a&gt; differentiate into new neurons that have zero (or very few) synaptic connections, but are sensitive to the local chemistry.&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;(Optional)&lt;/em&gt; Sometimes (such as in adult neurogenesis in the olfactory bulb) these immature neurons-to-be are produced far away from where they are needed and follow standard pathways to migrate to the correct brain region&lt;/li&gt;&#xA;&lt;li&gt;The immature neuron extends dendrites towards upstream neurons and starts to develop an axon&lt;/li&gt;&#xA;&lt;li&gt;The immature neuron extends axon towards downstream neurons, and&lt;/li&gt;&#xA;&lt;li&gt;The neuron matures and becomes indistinguishable from the network it joined.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;For more information, consider the question: &lt;a href=&quot;https://cogsci.stackexchange.com/q/318/29&quot;&gt;How are newly created neurons recruited into existing networks?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2017-04-13T12:56:15.910" LastActivityDate="2012-09-15T21:20:55.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3556" PostTypeId="2" ParentId="3544" CreationDate="2012-09-15T22:53:18.107" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Crown-of-thorns_starfish#Toxins&quot; rel=&quot;nofollow&quot;&gt;Asterosaponins&lt;/a&gt; are the class of compounds - &lt;a href=&quot;http://books.google.com/books?id=8Ugmrew2EqEC&amp;amp;pg=PA314&amp;amp;lpg=PA314&amp;amp;dq=asterosaponins&amp;amp;source=bl&amp;amp;ots=RF4cXY5Myb&amp;amp;sig=pSz43IVy6FaSorNFzQT01jsHj-8&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=XwZVUNaiB6jmiwKv_oGwDQ&amp;amp;ved=0CDgQ6AEwAg#v=onepage&amp;amp;q=asterosaponins&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;they have a cholesterol like organic core&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently, these saponins make &lt;strong&gt;pore-forming&lt;/strong&gt; complexes with Δ&lt;sup&gt;5&lt;/sup&gt;-sterols of cell membranes, and so are deadly to all usual kind of life, including bacteria and fungi. Quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Starfish and sea cucumber cell membranes are resistant to their own&#xA;  saponines due to the presence of Δ&lt;sup&gt;7&lt;/sup&gt;- and&#xA;  Δ&lt;sup&gt;9,11&lt;/sup&gt;-sterols, sulfated Δ&lt;sup&gt;5&lt;/sup&gt;-sterols, and&#xA;  β-xylosides of sterols instead of the free Δ&lt;sup&gt;5&lt;/sup&gt;-sterols.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-09-16T22:54:06.547" LastActivityDate="2012-09-16T22:54:06.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3558" PostTypeId="2" ParentId="3554" CreationDate="2012-09-16T04:28:40.090" Score="10" Body="&lt;p&gt;Most likely they were measuring the &lt;a href=&quot;https://en.wikipedia.org/wiki/Hemoglobin&quot;&gt;hemoglobin&lt;/a&gt; concentration, in units of g/dL (i.e. 10&lt;sup&gt;1&lt;/sup&gt; kg/m&lt;sup&gt;3&lt;/sup&gt;). Assuming by your username you are male, the reference range for [Hb] is approximately 13.8 to 18.0 g/dL (sources vary somewhat), which roughly matches the &quot;19&quot; you were told was the upper bound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia also notes that [Hb] &quot;is typically tested before or after blood donation&quot;, making it likely that that was what they measured.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Calling it &quot;iron&quot; isn't strictly correct. The human Hb tetramer's molecular weight is about 65 kDa, yet it contains only 4 iron atoms, so the actual concentration of iron in your blood is actually much less.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Useful resource: &lt;a href=&quot;https://en.wikipedia.org/wiki/Reference_ranges_for_blood_tests&quot;&gt;Wikipedia's list of reference ranges for blood tests&lt;/a&gt; has a very detailed chart of commonly cited reference ranges for many substances, with citations.&lt;/p&gt;&#xA;" OwnerUserId="1202" LastActivityDate="2012-09-16T04:28:40.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3559" PostTypeId="2" ParentId="230" CreationDate="2012-09-16T04:54:26.853" Score="0" Body="&lt;p&gt;I read somewhere (I don't have a citation) that duration of efficacy is limited by the evolution of viral antigens; eventually the population will evolve to the point where the immune system no longer recognizes them effectively. RNA viruses have more volatile genomes and so their antigens drift faster. This explanation makes some sense but it conflicts with @Epigrad's answer.&lt;/p&gt;&#xA;" OwnerUserId="1202" LastActivityDate="2012-09-16T04:54:26.853" CommentCount="2" CommunityOwnedDate="2012-09-16T04:54:26.853" ContentLicense="CC BY-SA 3.0" />
  <row Id="3560" PostTypeId="2" ParentId="2547" CreationDate="2012-09-16T05:08:09.870" Score="4" Body="&lt;p&gt;The alternative articulation, called &lt;em&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Dentolabial_consonant&quot; rel=&quot;nofollow noreferrer&quot;&gt;dentolabial&lt;/a&gt;&lt;/em&gt;, is more difficult to articulate, so it is very rarely used in human language. However, it apparently is common enough in disordered speech to be allocated an &lt;a href=&quot;https://en.wikipedia.org/wiki/ExtIPA&quot; rel=&quot;nofollow noreferrer&quot;&gt;ExtIPA&lt;/a&gt; diacritic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason labiodentals are easier: Humans normally have a slight overbite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4MKuC.jpg&quot; alt=&quot;lower lip near upper teeth&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the jaw and lips are in a &quot;neutral&quot; position, the lower lip is close to or touching the upper teeth, so with a small vertical movement of the jaw (together with tensing the lip) one can articulate a labiodental. Articulating a dentolabial requires moving the jaw a fair distance forward, to go around the upper teeth before reaching the upper lip. As Ben pointed out in the comments, front-back jaw movement is unusual, a less &quot;common movement in terms of other vocalisations and eating&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, since labial articulations are directly visible to observers, learners are especially likely to imitate others' exact articulation. Thus even though labiodentals and dentolabials sound similar, everyone in the population of speakers uses the same articulation (rather than having both articulations in free variation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps dentolabials would instead be more common if most people were &lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Maxillary_Hypoplasia_2.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;like this&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3qAdK.jpg&quot; alt=&quot;maxillary hypoplasia&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1202" LastActivityDate="2012-09-16T05:08:09.870" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3561" PostTypeId="1" CreationDate="2012-09-16T05:45:10.980" Score="4" ViewCount="599" Body="&lt;p&gt;Most tissue is comprised of cells.  Why? It would seem inefficient to have so many individual nucleus, membranes, etc.?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically: Not all tissue is cellular.  Much tissue is extracellular matrix.  Since the body &lt;em&gt;can&lt;/em&gt; use noncellular tissue, what is the role of cells in cellular tissue?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way to ask my question: Do the cellular organelles directly contribute to the tissue and organ's function? Or are they just there to maintain the cell itself?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My hypothesis is:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;In some cases, the cellular organelles directly provide the tissue's function.  Eg endocrine system - synthesized at the cellular level.&lt;/li&gt;&#xA;&lt;li&gt;In other cases, individual cells function discretely in the tissue.  Eg, nervous or muscular tissue.&lt;/li&gt;&#xA;&lt;li&gt;In other cases, the cell doesn't directly support the tissue's function.  But it's needed to grow and preserve the tissue.  Eg connective tissue.&lt;/li&gt;&#xA;&lt;li&gt;And finally, in cases where preserving and growing the tissue is a small enough task, a small number of cells simply extracellular tissue.  Eg bone tissue.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The above is my hypothesis.  Is it correct? Fix, revise, or replace it with something better!&lt;/p&gt;&#xA;" OwnerUserId="1409" LastEditorUserId="1122" LastEditDate="2012-09-16T07:15:34.597" LastActivityDate="2012-09-27T15:52:43.890" Title="Why is most tissue cellular?" Tags="&lt;cell-biology&gt;&lt;physiology&gt;&lt;organs&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3562" PostTypeId="1" CreationDate="2012-09-16T05:52:20.190" Score="9" ViewCount="729" Body="&lt;p&gt;It's well known that genetic information is stored in DNA.  As far as I know, DNA only has information at the &lt;em&gt;protein&lt;/em&gt; level.  What about higher levels, such as organelles, cells, tissue, organs? Is there any known carrier of information at that level? If not, what guides those levels of structure?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hypothesis: Above the protein level, there is no real genotype/phenotype.  Instead, it's all done through cell division.  So, there is no split between information and embodiment.  Instead, it's through a prototype-duplication model: cells grow and split, creating more cells.  As for differentation into different types of cells, and organization into tissue and organs: the information and control systems for that are currently unknown.&lt;/p&gt;&#xA;" OwnerUserId="1409" LastEditorUserId="43" LastEditDate="2012-09-16T11:42:45.070" LastActivityDate="2012-09-21T13:36:19.100" Title="Does DNA contain information beyond protein synthesis?" Tags="&lt;genetics&gt;&lt;cell-biology&gt;&lt;bioinformatics&gt;&lt;genomics&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3563" PostTypeId="2" ParentId="3561" CreationDate="2012-09-16T07:14:38.000" Score="1" Body="&lt;p&gt;Since cells are the origin of every life, any tissue must at least be based on cells. Some tissue matter is outside the cells (plant cell walls), some apparently non-cellular tissue is really a bloated organelle. Both happens. As to your theses,&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;yes, an example are oil reservoirs in plants&lt;/li&gt;&#xA;&lt;li&gt;no, these are just big cells. A striking example is spinal cord nerves that can be very long; irreparable if injured, because you can't repair single cells&lt;/li&gt;&#xA;&lt;li&gt;connective tissue is cartilage, bone, adipose tissue, blood, hematopoietic tissue and lymphatic tissue. These together fit in both the organelle and extracellular substance slots, so you would have to differentiate&lt;/li&gt;&#xA;&lt;li&gt;bone belongs to connective tissue&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So, yes, you can differentiate between functions belonging to whole cells, cell organelles, or extracellular material. And there is no reason to narrow this question to humans.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-09-16T07:14:38.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3564" PostTypeId="1" AcceptedAnswerId="5185" CreationDate="2012-09-16T09:55:13.973" Score="10" ViewCount="621" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Antibody&quot;&gt;Antibodies&lt;/a&gt; have the ability of recognising highly specific peptide sequences and bind it at their antigen-binding site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This ability is harnessed as a tool in research to purify target structures in the cell (e.g. in &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromatin_immunoprecipitation&quot;&gt;chromatin immunoprecipitation&lt;/a&gt;, ChIP).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now let’s say that I’ve identified an interesting target structure (such as a particular transcription factor) and I want to design an antibody to use in ChIP against said target. How would I go about producing such an antibody, taking into account that it should be both highly sensitive and specific?&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="166" LastEditDate="2012-09-16T16:51:07.903" LastActivityDate="2013-12-28T00:58:14.997" Title="How are antibodies designed?" Tags="&lt;molecular-biology&gt;&lt;immunology&gt;&lt;antibody&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3565" PostTypeId="2" ParentId="3562" CreationDate="2012-09-16T10:50:30.160" Score="11" Body="&lt;p&gt;What a timely question.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Does DNA contain information beyond protein synthesis?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Yes&lt;/strong&gt;. In fact, protein-coding genes only constitute a tiny part – less than 2% – of the whole DNA. There are of course many other genes which aren’t protein coding: there are genes for &lt;a href=&quot;http://en.wikipedia.org/wiki/Ribosomal_RNA&quot;&gt;ribosomal RNA&lt;/a&gt; and we find more and more genes which code for small RNAs, such as &lt;a href=&quot;http://en.wikipedia.org/wiki/TRNA&quot;&gt;tRNA&lt;/a&gt;. But even if we count all those genes we won’t come above maybe 10% of the total DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the DNA is instead devoted to the regulation of gene expression, most importantly via the binding of transcription factors (but the picture is much more complex than that). With the conclusion of the &lt;a href=&quot;http://genome.ucsc.edu/ENCODE/&quot;&gt;ENCODE project&lt;/a&gt;, a &lt;a href=&quot;http://www.nature.com/encode/&quot;&gt;whole slew of papers&lt;/a&gt; were published which show that in fact most of the DNA is actively implicated in the binding of various factors (although it’s not known how much of that actually contributed to the cell’s fitness).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I’ve hijacked your question a bit here. So let’s come back to what you’re actually interested in:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What about higher levels, such as organelles, cells, tissue, organs?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is no known mechanism (beyond the already mentioned regulation) which would encode such information in the DNA. Excluding its existence categorically may be hard but given that we haven’t found &lt;em&gt;any&lt;/em&gt; machinery which would be necessary to read such information, we can be pretty confident that it doesn’t exist.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If not, what guides those levels of structure?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The higher levels of organisation are to all appearances emergent. That is, they are a &lt;em&gt;consequence&lt;/em&gt; of the lower level organisation. For instance, take the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cytoskeleton&quot;&gt;cytoskeleton&lt;/a&gt; which carries much of the cell’s physical structure. It is composed of different protein complexes which form spontaneously through assembly of globular proteins (such as actin). The are several ways in which the process can be guided but strikingly &lt;a href=&quot;http://en.wikipedia.org/wiki/Actin#Formation_of_thin_filament&quot;&gt;it’s largely stochastic&lt;/a&gt; – i.e. mostly unguided, and it still succeeds in building a stable skeleton, simply by virtue of molecular properties encoded in the proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this is a common theme of cell organisation: the elementary building blocks are encoded by the DNA, and their abundance is tightly regulated. Everything else, i.e. higher-level organisation – follows from that: abundance and localisation of the right proteins.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As for differentation into different types of cells, and organization into tissue and organs: the information and control systems for that are currently unknown.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In fact, much &lt;em&gt;is&lt;/em&gt; known here, and it goes back to regulation on the level of DNA: we know that genes are differentially expressed depending on the cell type and stage of development (and the stage in the cell cycle). This regulation is highly complex and decoding it is a slow process. Nevertheless, the factors involved here are decoded one by one. This is the domain of &lt;a href=&quot;http://en.wikipedia.org/wiki/Developmental_biology&quot;&gt;developmental biology&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="166" LastActivityDate="2012-09-16T10:50:30.160" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="3566" PostTypeId="1" AcceptedAnswerId="3716" CreationDate="2012-09-16T17:46:33.917" Score="8" ViewCount="410" Body="&lt;p&gt;It is a &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_countries_by_life_expectancy#List_by_the_United_Nations_.282005.E2.80.932010.29&quot;&gt;well-known fact&lt;/a&gt; that women tend to outlive men. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I often hear people unscientifically stating that men generally generally die younger because of the higher stress encountered in their work lives. I would personally immediately rule this out, as who's to say that that women's (past) home lives just weren't as stressful? Also, shouldn't we see a narrowing of difference in age with the recent gender equality issues? Since the trend in question still occurs in virtually all countries of the world, I think it's safe to assume that the phenomenon is purely physiological. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am curious as to &lt;em&gt;the most sound scientific theories or known reasons&lt;/em&gt; for why women typically outlive men. Finally, I understand that aging in itself is not a process that's completely understood, and thus am not expecting a &quot;complete list&quot; of factors.&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2013-06-06T10:34:11.117" Title="What reasons allow for women to outlive men?" Tags="&lt;senescence&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3567" PostTypeId="1" CreationDate="2012-09-16T18:33:00.710" Score="2" ViewCount="410" Body="&lt;p&gt;I'm familiar with the use of alpha-complementation of beta-galactosidase with the pUC alpha-peptide and the M15 lacZ gene product, and would like to hypothetically apply alpha-complementation in other settings with different enzymes. I do have a few questions, but hopefully they are similar enough to all be answered here.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;What specifically allows for the non-covalent association between both truncated protein products to form a functional beta-galactosidase? How is beta-galactosidase unique in that separating it into two portions still yields a functional enzyme (in other words, why wouldn't other enzymes remain functional if I split them)?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What other proteins, if any, have been engineered to perform similar alpha-complementation? What steps were taken to accomplish this?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-09-16T18:33:00.710" Title="What specifically allows alpha-complementation in beta-galactosidase?" Tags="&lt;proteins&gt;&lt;biotechnology&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3568" PostTypeId="5" CreationDate="2012-09-16T18:48:00.197" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-09-16T18:48:00.197" LastActivityDate="2012-09-16T18:48:00.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3569" PostTypeId="4" CreationDate="2012-09-16T18:48:00.197" Score="0" Body="Any substance consumed to provide nutritional support for the body." OwnerUserId="307" LastEditorUserId="4101" LastEditDate="2013-10-29T20:57:11.340" LastActivityDate="2013-10-29T20:57:11.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3570" PostTypeId="5" CreationDate="2012-09-16T18:48:57.687" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-09-16T18:48:57.687" LastActivityDate="2012-09-16T18:48:57.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3571" PostTypeId="4" CreationDate="2012-09-16T18:48:57.687" Score="0" Body="Questions regarding organic compounds required by an organism as a vital nutrient in limited amounts." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-09-16T18:50:01.780" LastActivityDate="2012-09-16T18:50:01.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3572" PostTypeId="5" CreationDate="2012-09-16T18:49:45.190" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-09-16T18:49:45.190" LastActivityDate="2012-09-16T18:49:45.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3573" PostTypeId="4" CreationDate="2012-09-16T18:49:45.190" Score="0" Body="A branch of genetics that is concerned with the study of the structure and function of the cell, especially the chromosomes." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-09-16T18:50:32.700" LastActivityDate="2012-09-16T18:50:32.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3574" PostTypeId="5" CreationDate="2012-09-16T18:50:42.333" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2012-09-16T18:50:42.333" LastActivityDate="2012-09-16T18:50:42.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3575" PostTypeId="4" CreationDate="2012-09-16T18:50:42.333" Score="0" Body="Questions regarding substances which may have medicinal, intoxicating, performance enhancing or other effects when taken or put into a human body or the body of another animal and is not considered a food or exclusively a food." OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-09-16T18:51:04.633" LastActivityDate="2012-09-16T18:51:04.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3577" PostTypeId="2" ParentId="3420" CreationDate="2012-09-16T23:13:51.040" Score="2" Body="&lt;p&gt;Viruses can have many different conditions necessary for transmission.  Viruses which have membrane surface coats (like HIV ) need to be in water all the time to survive.  Cold and flu viruses are more resilient and can survive on a &lt;a href=&quot;http://www.nytimes.com/2009/12/15/health/15real.html&quot; rel=&quot;nofollow&quot;&gt;surface such as a doorknob with a halflife of 18 hours&lt;/a&gt;(!).  Fortunately we are also have a reasonable intrinsic resistance to cold and flu and I think most infections do not result in symptoms.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Viruses often only infect some parts of the body.  Venerial diseases are a classic example of this where only contact of genitalia might cause transmission. Its probable that Hantavirus is not excreted through the sweat glands or in saliva.  If it did it would certainly be a more devastating disease.   It may also only be serious when the virus is introduced into the lungs, which may make transmission difficult. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For Hantavirus human to human transmission looks possible as observed by &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0042682297989765&quot; rel=&quot;nofollow&quot;&gt;these folks&lt;/a&gt;. Even so, transmission is still so rare that there is no accounting for it in public health policy.  (they might also have been mistaken!).   Its possible that the virus requires transmission from a mouse to be virulent in humans. Its possible that the human transmission mechanism is so improbable (ingestion of faeces of infected human for instance) that you just dont' see it happening with the few cases of Hantavirus infection we have on the books. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-09-16T23:13:51.040" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3578" PostTypeId="2" ParentId="729" CreationDate="2012-09-17T16:06:36.267" Score="1" Body="&lt;p&gt;Many of these questions can be answered by UniProt:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;around 4,600 proteins with some 3D structure (&lt;a href=&quot;http://www.uniprot.org/uniprot/?query=%28organism:9606%29%20AND%20reviewed%3ayes%20AND%20keyword%3aKW-0002&amp;amp;sort=score&quot; rel=&quot;nofollow&quot;&gt;this query&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;of these 3,800 with annotated function in the Gene Ontology (&lt;a href=&quot;http://www.uniprot.org/browse/uniprot/by/go/?query=%28organism%3A9606%29+AND+reviewed%3Ayes+AND+keyword%3AKW-0002#3674&quot; rel=&quot;nofollow&quot;&gt;this query&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-09-17T16:06:36.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3581" PostTypeId="1" AcceptedAnswerId="3582" CreationDate="2012-09-17T22:56:34.707" Score="6" ViewCount="2466" Body="&lt;p&gt;I'm reading a booklet on melatonin published in 1996, titled &quot;Melatonin and the Biological Clock&quot;. This particular paragraph caught my attention and I would like to better understand what it means:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The requirement of intact beta-receptor function for melatonin&#xA;  synthesis, and the stimulatory effect of norepinephrine on melatonin&#xA;  synthesis and release, point up a theoretic relationship of melatonin&#xA;  to depression.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I've been looking at the &lt;a href=&quot;http://en.wikipedia.org/wiki/File%3aCatecholamines_biosynthesis.svg&quot; rel=&quot;nofollow&quot;&gt;biosynthesis of norepinephrine &lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/File%3aTryptophan_metabolism.png&quot; rel=&quot;nofollow&quot;&gt;tryptophan metabolism&lt;/a&gt; and do not see how the two cycles are connected. &lt;strong&gt;Is there a connection between the norepinephrine system and the melatonin synthesis in humans?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="500" LastEditDate="2012-09-18T15:17:18.843" LastActivityDate="2017-03-22T01:28:56.207" Title="Is there a relationship between Melatonin, Norepinephrine and depression in humans?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3582" PostTypeId="2" ParentId="3581" CreationDate="2012-09-18T14:38:41.900" Score="1" Body="&lt;p&gt;This answer addresses your question about a link between norepinephrine and melatonin, but I have nothing to say about depression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In vertebrates, the link between norepinephrine (NE) and melatonin lies in the regulation of the melatonin biosynthetic pathway. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Arylalkamine N-acetyltransferase (AANAT) is an enzyme in the biosynthetic pathway for melatonin, and controls the diurnal rhythm of melatonin production in the pineal gland. NE is released as a neurotransmitter by neurons innervating the pineal gland, and which themselves are regulated by the circadian pacemaker of the hypothalamus. One of the effects of NE on the pineal gland is to elevate the transcription of the AANAT gene via adrenoreceptors and cAMP levels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper cited below describes this, and other relevant diurnal rhythms in the viscacha, a rodent of the chinchilla family. This animal was chosen because it has an interesting diurnal behaviour pattern with two apparent peaks in melatonin biosynthesis. It's a good starting point for further research into the literature on this topic.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Calderon,C et al. (2008) Daily rhythms of norepinephrine, &amp;beta;1-adrenoceptor mRNA, serotonin, arylalkylamine N-acetyltransferase mRNA, arylalkylamine N-acetyltransferase and hydroxyindol-O-methyltransferase activities, and melatonin in the pineal gland of viscacha. Biological Rhythm Research 39: 93-107&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-18T14:38:41.900" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3583" PostTypeId="2" ParentId="798" CreationDate="2012-09-18T14:58:06.057" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/%20doi:10.1371/journal.pone.0019194&quot; rel=&quot;nofollow noreferrer&quot;&gt;This study&lt;/a&gt; found a statistically significant decline in NAD+:NADH ratios and in intracellular NAD+ with age in the organs of rats. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They discuss that the activation of  PARP - the  NAD-dependent enzyme Poly(ADP-ribose) polymerase-1 instrumental in DNA repair - increases in aging organs (heart, liver, kidneys). This depletes cellular NAD+ levels via poly(ADP-ribosylation) of proteins. This reduced cellular  NAD+ then reduces the effectiveness of Sirtuins (Sirt1) which can &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12220851&quot; rel=&quot;nofollow noreferrer&quot;&gt;deacetylate tumor-suppressor proteins such as p53.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's schematic showing the basic idea from their figure 10:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mp6zF.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the inference is that oxidative stress in vertebrates increases with age due to lowered cellular NAD+ - i.e.,  consistent with the free-radical theory of aging.  This could mean that lowered cellular NAD+, NAD+/NADH in any given individual may well decrease said individuals lifespan.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors of the first study (Braidy et al 2011) suggest that therapies involved in maintaining high NAD+ levels may alleviate age-associated disorders.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/%20doi:10.1371/journal.pone.0019194&quot; rel=&quot;nofollow noreferrer&quot;&gt;Braidy N, Guillemin GJ, Mansour H, Chan-Ling T, Poljak A, et al. (2011) Age Related Changes in NAD+ Metabolism Oxidative Stress and Sirt1 Activity in Wistar Rats. PLoS ONE 6(4)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12220851&quot; rel=&quot;nofollow noreferrer&quot;&gt;Smith, J., (2002) Human Sir2 and the 'silencing' of p53 activity, Traneds, Cell Biol. 12, 404&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-10-11T12:39:48.580" LastActivityDate="2012-10-11T12:39:48.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3585" PostTypeId="1" AcceptedAnswerId="3665" CreationDate="2012-09-18T15:25:16.493" Score="5" ViewCount="161" Body="&lt;p&gt;If some time in the future, we can know exactly what a cell (for example simple prokaryote bacteria) contains, (I mean, exactly which molecules, the shape of them, the density of each, everything), Then can we create a new cell (not from another cell)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I mean, if we have such technology, then create a soup just like what that cell contains, and a DNA exactly same as that bacteria cell, and then put some of it inside a Cell membrane, will it start living?&lt;/p&gt;&#xA;" OwnerUserId="1419" LastEditorUserId="112" LastEditDate="2012-09-18T15:44:36.407" LastActivityDate="2013-02-22T23:31:31.800" Title="Creating a cell, not from another cell. Will it be possible?" Tags="&lt;cell-biology&gt;&lt;synthetic-biology&gt;" AnswerCount="2" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="3587" PostTypeId="1" CreationDate="2012-09-18T16:19:01.363" Score="5" ViewCount="999" Body="&lt;p&gt;If I kept &lt;em&gt;E. coli&lt;/em&gt; transformed with plasmid at -20˚C without making glycerol stock, will it survive? Actually I have kept it this way for 18 hours. What will happen with it? Will it grow in fresh media?&lt;/p&gt;&#xA;" OwnerUserId="1420" LastEditorUserId="43" LastEditDate="2012-09-18T16:34:27.447" LastActivityDate="2012-09-19T12:35:51.790" Title="Survival of E. coli on agar plate at -20 degree C without glycerol stock" Tags="&lt;microbiology&gt;&lt;ecoli&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3588" PostTypeId="2" ParentId="3587" CreationDate="2012-09-18T17:33:44.810" Score="2" Body="&lt;p&gt;Over time I suspect that ice crystals will form in the colonies from defrost cycles in the freezer and the moisture in the agar.  This will cause rupture of the bacteria membranes and over time may destroy the bulk of the bacteria cells.  The plates will also desiccate over time as well from the defrosting cycles of the freezer.  You may be able to leave them in the freezer for a while but I can't foresee them surviving indefinitely.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the strains are really important I recommend just sucking it up and spending the small amount of time necessary to make the glycerol stock.  Glycerol is used in bacteria stocks as a cryoprotectant to prevent the crystallization of the stock.  &lt;/p&gt;&#xA;" OwnerUserId="12" LastActivityDate="2012-09-18T17:33:44.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3589" PostTypeId="2" ParentId="171" CreationDate="2012-09-18T19:19:55.127" Score="16" Body="&lt;p&gt;Thymine has a greater resistance to photochemical mutation, making the genetic message more stable. This offers a rough explanation of why thymine is more protected then uracil.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the real question is: Why does thymine replace uracil in DNA? The important thing to notice is that while uracil exists as both uridine (U) and deoxy-uridine (dU), thymine only exists as deoxy-thymidine (dT). So the question becomes: Why do cells go to the trouble of methylating uracil to thymine before it can be used in DNA? and the easy answer is: methylation protects the DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides using dT instead of dU, most organisms also use various enzymes to modify DNA after it has been synthesized. Two such enzymes, &lt;code&gt;dam&lt;/code&gt; and &lt;code&gt;dcm&lt;/code&gt; methylate adenines and cytosines, respectively, along the entire DNA strand. This methylation makes the DNA unrecognizable to many nucleases (enzymes which break down DNA and RNA), so that it cannot be easily attacked by invaders, like viruses or certain bacteria. Obviously, methylating the nucleotides before they are incorporated ensures that the entire strand of DNA is protected. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thymine also protects the DNA in another way. If you look at the components of nucleic acids, phosphates, sugars, and bases, you see that they are all very hydrophilic (water soluble). Obviously, adding a hydrophobic (water insoluble) methyl group to part of the DNA is going to change the characteristics of the molecule. The major effect is that the methyl group will be repelled by the rest of the DNA, moving it to a fixed position in the major groove of the helix. This solves an important problem with uracil - though it prefers adenine, uracil can base-pair with almost any other base, including itself, depending on how it situates itself in the helix. By tacking it down to a single conformation, the methyl group restricts uracil (thymine) to pairing only with adenine. This greatly improves the efficiency of DNA replication, by reducing the rate of mismatches, and thus mutations.&lt;/p&gt;&#xA;" OwnerUserId="1421" LastEditorUserId="57" LastEditDate="2012-09-18T21:03:58.280" LastActivityDate="2012-09-18T21:03:58.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3590" PostTypeId="1" AcceptedAnswerId="3609" CreationDate="2012-09-18T19:38:17.533" Score="16" ViewCount="457" Body="&lt;p&gt;Biological systems are pretty good at measuring fairly long times, for example, menstrual cycles (month), or puberty (years). Counting days or years seems to be implausible, and chemical concentration also seems implausible. What are the physiological processes that are involved in keeping track of such long periods? Is it just a long sequence of finite state changes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand there are environmental correlates such as seasonal changes and relative position of celestial objects to measure the relative time, but regardless of these external cues, I suspect that a pretty good internal clock for longer time scale could exist. For example, the time to menopause can actually be thought of as a counting mechanism of a shorter clock which is the menstrual cycle. But, how does the body know when to stop growing? I cannot think of biological processes with such long time constants that is stable.&lt;/p&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2012-09-19T09:14:46.867" LastActivityDate="2013-04-16T01:38:56.980" Title="How are long time periods measured in biological systems?" Tags="&lt;physiology&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3591" PostTypeId="1" AcceptedAnswerId="3632" CreationDate="2012-09-18T20:35:08.603" Score="25" ViewCount="132347" Body="&lt;p&gt;When you get a shot for a vaccine (for example, the annual flu vaccine), the nurse frequently indicates that your arm will ache for a day or two, maybe more. This ache is typically not just a pain from having your skin punctured, but is actually an ache of the entire arm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What mechanism causes the entire arm to ache from a vaccine? Why doesn't that ache extend to other parts of the body, like the hands or the shoulders? Why do non-vaccine arm punctures (such as drawing blood, injecting drugs) not cause the ache?&lt;/p&gt;&#xA;" OwnerUserId="1422" LastEditorUserId="16651" LastEditDate="2015-12-17T05:14:54.230" LastActivityDate="2015-12-17T05:14:54.230" Title="Why do vaccines cause your arm to hurt?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;pharmacology&gt;&lt;vaccination&gt;&lt;immune-system&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3592" PostTypeId="2" ParentId="3100" CreationDate="2012-09-18T21:43:03.907" Score="17" Body="&lt;p&gt;Like all tough questions, this one has no well understood answer.  Itching &quot;&lt;a href=&quot;http://pubs.acs.org/doi/pdf/10.1021/cen-v089n027.p027&quot;&gt;is one of the most poorly understood sensations.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The obvious facts: The urge to scratch part of your skin is the result of stimulus of the skin which causes some of the nerves to register an irritation (you can get an itch in internal organs too - which sounds excruciating).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biochemically, following the effects of poison Ivy oils, &lt;a href=&quot;http://pubs.acs.org/doi/pdf/10.1021/cen-v089n027.p027&quot;&gt;the cathechols break down to orthoquinones and may stimulate local mast cells to release histimine&lt;/a&gt;.  So in this case you can see that itching, like many irritations are linked to the immune system which is highly variable from one individual to another, as such it is still a bit of a black box.&lt;br&gt;&#xA;The histamine pathway is well studied and histamine stimulates an ion channel protein in nerve cells called TRPV1, which is also known as the capsaicin receptor, which means it is also related to sensing heat.  This explains why itching can be relieved (temporarily) by exposing the skin to water that is as hot as the patient can stand without burning them.  This is one of the ways pain and itching are highly intertwined. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still, not all itching is stimulated by histamine release; that isn't the whole story.  Antihistamine allergy pills don't help itching.  Other nerve channel proteins can be activated to stimulate itching.  One example found in an itchy mutant strain of mice is TRPA1, and maybe the G protein coupled receptor, Gastrin Releasing Protein Receptor (GRPR). Its hard to imagine that there will not be more mechanisms discovered later.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mediated both by immune systems and nerve cells, which literally have a mind of their own and whose signal processing is highly individualized and sensitive to local conditions in the body make itching a fairly mysterious phenomenon.  Its also likely that itching can be entirely initiated as a mental condition (&lt;a href=&quot;http://psychology.wikia.com/wiki/Pruritus&quot;&gt;Pruritus&lt;/a&gt;), so it is not entirely a biochemical phenomenon, which only serves to illustrate the point I guess. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-09-21T17:51:03.743" LastActivityDate="2012-09-21T17:51:03.743" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3593" PostTypeId="1" CreationDate="2012-09-18T22:29:19.550" Score="3" ViewCount="73" Body="&lt;p&gt;I have &lt;em&gt;E. coli&lt;/em&gt; with transformed plasmid on agar in a vial.  It has been stored at -20 degree C without glycerol stock for 18 hours.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a continuation of: &lt;a href=&quot;https://biology.stackexchange.com/questions/3587/survival-of-e-coli-on-agar-plate-at-20-degree-c-without-glycerol-stock&quot;&gt;Survival of E. coli on agar plate at -20 degree C without glycerol stock&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have transfered this vial from -20 degrees to 4 degrees after 18 hours when I determined that I had made a mistake. Since this is a very important vial and I don't have another one, what should I do in this stage? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the procedure for saving the plasmid if I am unable to save the whole cell? &lt;/p&gt;&#xA;" OwnerUserId="1420" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2012-09-19T04:59:51.823" Title="Salvaging a plasmid from a cell culture stored at the incorrect temperature" Tags="&lt;microbiology&gt;&lt;ecoli&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3594" PostTypeId="1" CreationDate="2012-09-19T04:06:10.280" Score="4" ViewCount="66" Body="&lt;p&gt;I was wondering if there are any spatial ecologists out there who can provide some insight on the trouble I'm having with my Masters research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking at the association a bat species to high density aggregations of a flowering plant. The bats were tracked throughout the night with a point taken at approximately 10 minute intervals. The bats were tracked over consecutive nights until an asymptote in their space use was reached. So now I have point patterns for each bat that pretty much covers the entirety of their space use at that period. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the data is displayed visually there is a clear pattern of the bats that were tracked during the flowering period moving into the aggregations of the plant however they also spend a lot of time foraging around their roost sites. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have simulated the point pattern of each bat 999 times by randomly shifting and rotating the points within the study window (the internal structure of the observed pattern was maintained in the simulations to account for autocorrelation). I then did randomisation tests to see if the average distance to the nearest plant aggregation for the observed data is within the lower 5% of the distribution of the averages for the simulated point patterns. However because the majority of the points collected are highly associated with the roosts the average distance is primarily effected by the position of the roost in relation to any of the plant aggregations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been thinking of ways to disentangle the association with roosts and the association with the plant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First I was thought about putting a buffer around the roosts and removing the points falling within these buffers from the analysis. The problem is deciding on a buffer. In the other areas I have been using a buffer equal to the circular error probable of the radio tracking error but placing this around the roost will only incorporate the points where the bat was actually inside the roost not foraging around it. All the bats have different foraging patterns around their roosts and I can't see how to assign a buffer distance that is not completely arbitrary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second method we have been looking into is taking out the points that are more closely associated (closer in distance) with the roost than the nearest plant aggregation and then running the randomisation to look at the association of the remaining points to the plant. I want to get an idea of whether or not removing the association with the roosts in this way will potentially bias the analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any thoughts or further suggestions?!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance!    &lt;/p&gt;&#xA;" OwnerUserId="1424" LastActivityDate="2012-09-19T04:06:10.280" Title="Help with designing the analysis of radio telemetry study" Tags="&lt;zoology&gt;&lt;ecology&gt;&lt;experimental-design&gt;" AnswerCount="0" CommentCount="5" ClosedDate="2012-09-20T16:09:36.197" ContentLicense="CC BY-SA 3.0" />
  <row Id="3595" PostTypeId="2" ParentId="3593" CreationDate="2012-09-19T04:59:51.823" Score="4" Body="&lt;p&gt;I would rinse the cells off the agar using a small volume of LB or similar rich medium. Then use a small aliquot (10 &amp;mu;l) to inoculate a 5 ml culture under selection to see if anything will grow. Meanwhile the remainder of the cell suspension from the vial can be used as input for your favourite miniprep procedure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If necessary, the DNA that you recover should then be used to transform a suitable &lt;em&gt;E. coli&lt;/em&gt; strain. Don't bother trying to analyse the rescued DNA first since polysaccharide contaminants from the agar will probably inhibit any restriction enzyme that you might use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good luck!&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-19T04:59:51.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3597" PostTypeId="2" ParentId="3587" CreationDate="2012-09-19T08:29:08.647" Score="1" Body="&lt;p&gt;&lt;strong&gt;Trehalose&lt;/strong&gt;&lt;sup&gt;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.142314099&quot; rel=&quot;nofollow&quot;&gt;[1]&lt;/a&gt;,&lt;a href=&quot;http://en.wikipedia.org/wiki/Trehalose&quot; rel=&quot;nofollow&quot;&gt;[2]&lt;/a&gt;&lt;/sup&gt; is the cryoprotectant used by bacteria to keep things going when all else freezes (or dries up), and they grow in it, too!&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Trehalose accumulates dramatically in microorganisms during heat shock&#xA;  and osmotic stress and helps protect cells against thermal injury and&#xA;  oxygen radicals. Here we demonstrate an important role of this sugar&#xA;  in cold-adaptation of bacteria.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.142314099&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Kandror O, DeLeon A, Goldberg AL&lt;/strong&gt;. 2002. Trehalose synthesis is induced upon exposure of Escherichia coli to cold and is essential for viability at low temperatures. Proceedings of the National Academy of Sciences USA, 99(15): 9727-9732, doi:10.1073/pnas.142314099&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Trehalose&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Trehalose&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="43" LastEditDate="2012-09-19T12:35:51.790" LastActivityDate="2012-09-19T12:35:51.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3598" PostTypeId="1" CreationDate="2012-09-19T10:31:31.160" Score="5" ViewCount="388" Body="&lt;p&gt;How is the &quot;time axis&quot; of memories encoded in the brain? I guess the time of the event could be &quot;stored&quot; with each event, but how is this translated into neurons etc.?&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-09-19T19:52:50.527" Title="What is the biological basis for the perception of time?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3599" PostTypeId="1" AcceptedAnswerId="10092" CreationDate="2012-09-19T12:07:03.340" Score="4" ViewCount="172" Body="&lt;p&gt;I'm reading this article, which discusses the influence of Long Photoperiod (LP) and Short Photoperiod (SP) on melatonin production:&#xA;&lt;a href=&quot;http://ajpregu.physiology.org/content/278/5/R1339.full&quot; rel=&quot;nofollow&quot;&gt;HIOMT drives the photoperiodic changes in the amplitude of the melatonin peak of the Siberian hamster&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I'm interested in knowing what light intensity is interpreted as the onset and end of a light-dark photoperiod&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The referenced article indicates that animals were kept in cages, with a pre-set photoperiod duration, this sounds to me like it was done indoors. If it has been done indoors, then artificial lighting was involved, and I would guess it was an on-off affair, rather than gradual change or jumps in intensity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason why I'm asking is that I'm trying to understand the implications of this article for humans, who may wake up before dawn, and spend some time under &lt;strong&gt;artificial lighting of various intensity&lt;/strong&gt; before sunrise, and continue to function after sunset. For example a person may be looking at a TV or a monitor, and I would like to get an idea if this &quot;presence of light&quot; is enough to trigger photoperiod-related changes in the brain. &lt;strong&gt;Is there some &quot;critical&quot; density (or density at a specific wavelength) of light that signals the start/end of a photoperiod?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://ajpregu.physiology.org/content/278/5/R1339.full&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Ribelayga C, Pévet O, Simonneaux V&lt;/strong&gt;. 2000. HIOMT drives the photoperiodic changes in the amplitude of the melatonin peak of the Siberian hamster. Regulatory, Integrative, and Comparative Physiology, 278(5), R1339-R1345.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="577" LastEditorUserId="43" LastEditDate="2012-09-19T12:28:04.917" LastActivityDate="2013-08-28T21:03:36.040" Title="What light intensity determines the start/end of a photoperiod in humans?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;endocrinology&gt;&lt;photoperiod&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3601" PostTypeId="1" CreationDate="2012-09-19T13:19:52.623" Score="6" ViewCount="446" Body="&lt;p&gt;Are some non-coding RNA spliced like mRNA? I tried to find some information but I don't find anything...&lt;/p&gt;&#xA;" OwnerUserId="359" LastEditorUserId="14852" LastEditDate="2016-05-09T15:57:03.433" LastActivityDate="2016-05-09T15:57:03.433" Title="Are some non-coding RNA spliced?" Tags="&lt;molecular-genetics&gt;&lt;rna&gt;&lt;splicing&gt;&lt;noncoding-rna&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3602" PostTypeId="1" AcceptedAnswerId="3608" CreationDate="2012-09-19T13:37:36.253" Score="4" ViewCount="72" Body="&lt;p&gt;I'm reading a booklet on melatonin published in 1996, titled &quot;Melatonin and the Biological Clock&quot;. And see the following statement:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;HIOMT (HydroxyIndole-O-MethylTransferase), one of enzymes of melatonin&#xA;  synthesis, rises and falls in an annual rhythm, with troughs in March&#xA;  and October and peaks in January and July.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Seeing how HIOMT is the last methyltransferase involved in Melatonin synthesis in humans, &lt;strong&gt;I'm interested in learning if there's indeed a yearly variation in this MT production in humans, and if it is regulated by genetics or photoperiod duration.&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-09-19T18:16:19.737" Title="Are there yearly variations in HIOMT (HydroxyIndole-O-MethylTransferase) availability?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3603" PostTypeId="2" ParentId="3590" CreationDate="2012-09-19T13:49:04.163" Score="3" Body="&lt;p&gt;Though chemical concentration seems implausible, at the deepest level it is the cause.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a smaller scale - how does a eukaryotic cell know when it is ready to divide? By the concentration of different cyclins and CDKs. They are produced all the time, in amounts dependent on the general availability of nutrients, but they are used at different times. Some are used during DNA synthesis, so that if they are present, the cell &quot;knows&quot; that there is not enough DNA to divide itself; others are used during cell division, so a freshly divided cell &quot;knows&quot; that there is a long period before next division. How do our hairs grow at seemingly same intervals? Because their location was decided on the basis of concentrations of certain proteins or small molecules when skin was just being formed (I don't have Developmental Biology right here, so no protein names, sorry).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The menstrual cycle is regulated by the concentration of the hormones and ovulation triggers changes leading to menstruation. That's why menstruation happens 14 days after ovulation and not just 28 days after the previous one - if a woman has a 30 day-long cycle, her ovulation will be on 16th day of the cycle. Menopause generally happens when the supply of eggs ends and they stop providing cues about the proper time for menstruation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cues about puberty and aging may be more subtle. One well-known cause of aging is the shrinking of the telomeres, the ends of the chromosomes. Cells with short telomeres can't divide. Too low of a &quot;concentration&quot; of these telomeres &quot;tells&quot; the cell that it is old.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another well known fact - malnourished girls don't go through puberty and malnourished women stop ovulating. Low food &quot;concentration&quot; is a sign of a bad time to burden your body with nourishing and feeding a baby.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Detailed mechanisms behind those processes are often different, but the general rule is the same: each process has threshold(s) for certain chemicals; if they are exceeded, the organism reacts.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastEditorUserId="57" LastEditDate="2012-09-21T02:38:52.727" LastActivityDate="2012-09-21T02:38:52.727" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3604" PostTypeId="2" ParentId="3601" CreationDate="2012-09-19T13:52:11.303" Score="4" Body="&lt;p&gt;Do you call ribosomal RNA non-coding? rRNA is spliced both in prokaryotes and eukaryotes.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastEditorUserId="43" LastEditDate="2012-09-19T13:56:06.523" LastActivityDate="2012-09-19T13:56:06.523" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3605" PostTypeId="1" CreationDate="2012-09-19T13:53:53.063" Score="6" ViewCount="3988" Body="&lt;p&gt;I've worked pretty frequently with genome and transcriptome data for several years now, but I'm still not 100% sure I understand the proper usage for certain terminology related to transcripts and transcriptomics. Let me give it my best shot.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;cDNA&lt;/strong&gt;: in general, this term corresponds to any DNA that is derived from an RNA template via reverse transcription (&lt;em&gt;complementary DNA&lt;/em&gt;); however, it is often used to refer to &lt;em&gt;full length cDNAs&lt;/em&gt;, DNA sequences that correspond to complete mRNA molecules&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;EST&lt;/strong&gt;: &lt;em&gt;expressed sequence tags&lt;/em&gt; correspond to cDNA (sub)sequences obtained from a single read of a cDNA sequencing experiment&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;RNA-seq&lt;/strong&gt;: this refers to the use of high-throughput sequencing technologies to characterize entire transcriptomes, such as by transcript assembly or expression analysis&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Here's my concern: I've seen ESTs described as &lt;a href=&quot;http://en.wikipedia.org/wiki/Expressed_sequence_tag&quot; rel=&quot;noreferrer&quot;&gt;&quot;one-shot&quot;&lt;/a&gt; or &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/dbEST/&quot; rel=&quot;noreferrer&quot;&gt;&quot;single-pass&quot;&lt;/a&gt; sequences, which I interpret to mean a single sequence read. However, they are also typically described as being hundreds of base pairs in length (Wikipedia claims about &lt;a href=&quot;http://en.wikipedia.org/wiki/Expressed_sequence_tag&quot; rel=&quot;noreferrer&quot;&gt;500-800bp in length max&lt;/a&gt;), which (currently) limits this definition to reads derived from Sanger-style sequencing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this mean that a short read derived from a high-throughput sequencing platform is &lt;em&gt;not&lt;/em&gt; an EST? Is this distinction based on read length? platform? throughput?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Due to technical limitations, short reads are often assembled before they are used for other downstream analysis. I have sometimes heard the contigs belonging to these assemblies as ESTs, but this doesn't seem to be consistent with the previous definitions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is our terminology becoming inconsistent due to the rapid improvements in sequencing technology, or am I missing or misinterpreting something?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-09-20T15:52:49.793" Title="Transcript(omics) terminology: cDNAs, ESTs, RNA-seq, etc" Tags="&lt;genomics&gt;&lt;terminology&gt;&lt;rna-sequencing&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3606" PostTypeId="2" ParentId="3601" CreationDate="2012-09-19T15:26:54.773" Score="4" Body="&lt;p&gt;Yes, check out &lt;a href=&quot;http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr12:54356096-54362515&amp;amp;hgsid=298485341&amp;amp;knownGene=pack&amp;amp;hgFind.matches=uc009zne.3,&quot; rel=&quot;nofollow&quot;&gt;HOTAIR&lt;/a&gt; (in human), as well as &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867411014504&quot; rel=&quot;nofollow&quot;&gt;cyrano and megamind&lt;/a&gt; in zebrafish -- they are all spliced.&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2012-09-19T15:26:54.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3607" PostTypeId="2" ParentId="3605" CreationDate="2012-09-19T16:21:56.657" Score="2" Body="&lt;p&gt;My 2 cents:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your main question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is our terminology becoming inconsistent due to the rapid improvements in sequencing technology, or am I missing or misinterpreting something?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think what you are witnessing (being subject to(?)) is, as you say, an inconsistency of terms due to the rapid improvements in the field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I put the caveat in that you are being subjected to this because I suspect the people referring to the &quot;things&quot; that a second-generation-sequencing protocol generates as &quot;ESTs&quot; are using a familiar word to describe something that might be unfamiliar to them.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Does this mean that a short read derived from a high-throughput sequencing platform is not an EST? Is this distinction based on read length? platform? throughput?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I guess it's (i) construction; (ii) platform; (iii) throughput; and (iv) relative &quot;quantitativeness&quot;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Due to technical limitations, short reads are often assembled before they are used for other downstream analysis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You lost me here with the word &quot;often&quot; -- are you talking about RNAseq now or is this an EST. If you have a reference genome, I think assembling RNAseq reads before downstream analysis (alignment(?)) is an exception instead of a rule ... which is why I'm lost.&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2012-09-19T16:21:56.657" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3608" PostTypeId="2" ParentId="3602" CreationDate="2012-09-19T18:16:19.737" Score="1" Body="&lt;p&gt;This isn't really a complete answer but I can't fit it into a comment.&lt;/p&gt;&#xA;&lt;p&gt;I've found that there is a large body of literature on seasonality of melatonin levels in various vertebrates, particularly livestock, because of its interaction with breeding patterns. Similar studies in humans are however, difficult to find, but the review paper cited below looks at a link between seasonal variations in melatonin levels and seasonal variations in immune system functions. It cites a few references that might be worth following up.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Srinivasan, V. &lt;em&gt;et al&lt;/em&gt;. (2008) Immunomodulation by melatonin: Its significance for seasonally occurring diseases. &lt;em&gt;Neuroimmunomodulation&lt;/em&gt; &lt;strong&gt;15&lt;/strong&gt;: 93-101 DOI: 10.1159/000148191&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Abstract&lt;/strong&gt;&#xA;Melatonin is not only synthesized by the pineal gland but also in many other organs and tissues of the body, particularly by lymphoid organs such as the bone marrow, thymus and lymphocytes. Melatonin participates in various functions of the body, among which its immunomodulatory role has assumed considerable significance in recent years. Melatonin has been shown to be involved in the regulation of both cellular and humoral immunity. Melatonin not only stimulates the production of natural killer cells, monocytes and leukocytes, but also alters the balance of T helper (Th)-1 and Th-2 cells mainly towards Th-1 responses and increas- es the production of relevant cytokines such as interleukin (IL)-2, IL-6, IL-12 and interferon-γ. The regulatory function of melatonin on immune mechanisms is seasonally dependent. This fact may in part account for the cyclic pattern of symptom expression shown by certain infectious diseases, which become more pronounced at particular times of the year. Moreover, melatonin-induced seasonal changes in immune function have also been implicated in the pathogenesis of seasonal affective disorder and rheumatoid arthritis. The clinical significance of the seasonally changing immunomodulatory role of melatonin is discussed in this review.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-09-19T18:16:19.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3609" PostTypeId="2" ParentId="3590" CreationDate="2012-09-19T18:57:55.363" Score="5" Body="&lt;p&gt;The short answer is: we do not know exactly, although we do have some insights.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will take the example of puberty.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although a clear definition of puberty is lacking, it is quite clear that it corresponds to a period where gonadal function starts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This, in turn, is derived from the activation of the gonadotropin system, which consists of two main cell types:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;a small number of neurons located in the preoptic area of the hypothalamus (a nucleus at the base of the brain) called the GnRH neurons. &lt;a href=&quot;http://en.wikipedia.org/wiki/Gonadotropin-releasing_hormone&quot; rel=&quot;nofollow noreferrer&quot;&gt;GnRH&lt;/a&gt; is the Gonadotropin-releasing hormone, a small peptide that stimulates the production of gonadotropins from the pituitary.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the &lt;a href=&quot;http://en.wikipedia.org/wiki/Gonadotroph&quot; rel=&quot;nofollow noreferrer&quot;&gt;gonadotrophs&lt;/a&gt;, a specialised group of cells in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Anterior_pituitary&quot; rel=&quot;nofollow noreferrer&quot;&gt;pituitary&lt;/a&gt; (a gland located underneath the brain) which produce two hormones, called luteinizing hormone (LH) and follicle-stimulating hormone (FSH) which stimulate the gonads to produce various hormones, such as estrogen.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In mammals, the secretion of GnRH, and thus LH/FSH varies during the course of the menstrual/estral cycle. This cyclicity lasts several days (4-5 days in rodents, ~1 month in humans) and entrains the cyclical secretion of estradiol (E2) from the gonads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that this is a sort of self-sustaining cycle, as cyclic levels of E2 will then allow for cyclic GnRH secretion and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, back to your question: how does the GnRH/LH/E2 system &quot;wake up&quot; at puberty?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact mechanism is still unknown, but recent work has found an important mediator, called kisspeptin, that is produced from two population of neurons in the hypothalamus, called the kisspeptin neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kisspeptin has been shown to be a very potent activator of GnRH neurons and work in the mouse has shown that these neurons appear at the time of puberty, their number increasing dramatically between 25 and 31 days (puberty is at around 30 days in mice).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/16959837&quot; rel=&quot;nofollow noreferrer&quot;&gt;Postnatal Development of Kisspeptin Neurons in Mouse Hypothalamus; Sexual Dimorphism and Projections to Gonadotropin-Releasing Hormone Neurons &lt;/a&gt; - Clarkson and Herbison - &lt;em&gt;Endocrinology&lt;/em&gt;, &lt;strong&gt;2006&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similar work exist in the monkey:&#xA;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/15684075&quot; rel=&quot;nofollow noreferrer&quot;&gt;Increased hypothalamic GPR54 signaling: A potential mechanism for initiation of puberty in primates&lt;/a&gt; - Shahab et al. - &lt;em&gt;PNAS&lt;/em&gt;, &lt;strong&gt;2005&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In humans mutations in either kisspeptin, or its cognate receptor &lt;a href=&quot;http://en.wikipedia.org/wiki/KiSS1-derived_peptide_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;GPR54&lt;/a&gt; results in disturbances of pubertal maturation because of underactivation of the system (hypogonadotropic hypogonadism) or hyperactivation (precocious puberty).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, now the question is shifted: why do kisspeptin neurons show up only at puberty? We don't know for sure, but it looks like increased levels of E2 could be important for this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, we get into a self-sustaining cycle. Growth of the body generates an increase in E2 production (possibly due to increased volume of the gonads?), which, when over a certain level permits the development of kisspeptin neurons, which will then stimulate the GnRH neurons, resulting in increased LH and E2. We then have more E2 and this makes kisspeptin neuron grow even more etc etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703539/bin/zee0070948160006.jpg&quot; alt=&quot;Kisspeptin system maturation&quot;&gt;&lt;br&gt;&#xA;From: &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/19299459&quot; rel=&quot;nofollow noreferrer&quot;&gt;Postnatal development of an estradiol-kisspeptin positive feedback mechanism implicated in puberty onset.&lt;/a&gt; - Clarkson et al. - &lt;em&gt;Endocrinology&lt;/em&gt;, &lt;strong&gt;2009&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.760" LastActivityDate="2012-09-19T20:57:21.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3610" PostTypeId="1" CreationDate="2012-09-19T19:02:34.020" Score="6" ViewCount="171" Body="&lt;p&gt;It seems that many nutrition experiments [directed at human diet] are carried on laboratory mice. Is there any justification that nutrition that is good or bad for laboratory mice will also be same way applicable to humans ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder because mice and humans, although both being mammals, are separated probably by tens millions years of separate evolution.  By the &quot;mammals&quot; logic, dolphins, cows, wolves, and goats, all being mammals, shall have same diet as mice ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes one man's food is another man's poison (lactose differences for example, due to genetic differences). That's man to man, same species. On what is &quot;transfer of nutritional information&quot; from species to species based ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Was it ever established, or the opposite, that all humans have same best diet. Other than known lactose metabolism difference.&lt;/p&gt;&#xA;" OwnerUserId="226" LastEditorUserId="226" LastEditDate="2012-09-19T19:30:51.043" LastActivityDate="2014-03-11T17:16:57.483" Title="laboratory mice, nutrition, and humans" Tags="&lt;nutrition&gt;&lt;mammals&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3611" PostTypeId="2" ParentId="3598" CreationDate="2012-09-19T19:52:50.527" Score="2" Body="&lt;p&gt;I'm no expert on the topic, but was about to find the following;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In mammals, the hippocampus region of the brain is one of only 2 regions with the capacity for lifelong neurogenesis (the creation of new neurons). This happens continuously with the creation of new memories and experiences (neurons are even created just to mark time passing - even if no memories are stored alongside - so that a perception of 10mins and 10secs is possible, even if nothing memorable happens). As new clusters of neurons are generated, they gradually differentiate and mature to become fully functional, and in this way time and memory are interlinked, and experiences are clustered together [&lt;a href=&quot;http://dx.doi.org/10.1038/nn1707&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a human study where individuals were asked to recall whether news events occurred within 1 week of each other (some related, some not), same-week and separation judgements were more far more accurate for related events. Unrelated events were essentially guesses, whereas deductions could be made about related events. [&lt;a href=&quot;http://dx.doi.org/10.3758/MC.38.8.1122&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]. This lends weight to the above argument that memories are clustered in the brain with temporal information embedded within.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hippocampus is also involved in imaging the future. (Inconsistent) findings suggest that activation of the hippocampus allows mammals to conceive a scenario constructed from previous memories and experiences, and to store these for later use [&lt;a href=&quot;http://dx.doi.org/10.3389/fnhum.2011.00173&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Refs&lt;/h3&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Aimone, J. B., Wiles, J., &amp;amp; Gage, F. H. (2006). Potential role for adult neurogenesis in the encoding of time in new memories. &lt;em&gt;Nature neuroscience&lt;/em&gt;, &lt;strong&gt;9&lt;/strong&gt;(6), 723-7. doi:&lt;a href=&quot;http://dx.doi.org/10.1038/nn1707&quot; rel=&quot;nofollow&quot;&gt;10.1038/nn1707&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Friedman, W. J., &amp;amp; Janssen, S. M. J. (2010). Do people remember the temporal proximity of unrelated events? &lt;em&gt;Memory &amp;amp; cognition&lt;/em&gt;, &lt;strong&gt;38&lt;/strong&gt;(8), 1122-36. doi:&lt;a href=&quot;http://dx.doi.org/10.3758/MC.38.8.1122&quot; rel=&quot;nofollow&quot;&gt;10.3758/MC.38.8.1122&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Addis, D. R., &amp;amp; Schacter, D. L. (2011). The hippocampus and imagining the future: where do we stand? &lt;em&gt;Frontiers in human neuroscience&lt;/em&gt;, &lt;strong&gt;5&lt;/strong&gt;, 173. doi:&lt;a href=&quot;http://dx.doi.org/10.3389/fnhum.2011.00173&quot; rel=&quot;nofollow&quot;&gt;10.3389/fnhum.2011.00173&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-09-19T19:52:50.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3612" PostTypeId="2" ParentId="3610" CreationDate="2012-09-19T19:55:47.990" Score="3" Body="&lt;p&gt;Whether using quantitative models, or &quot;animal models&quot;, I think this is a useful quote to keep in mind:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A model is a lie that helps you see the truth.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;-- &lt;a href=&quot;http://cancerres.aacrjournals.org/content/66/24/12035.full&quot; rel=&quot;nofollow&quot;&gt;Howard Skipper&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As for evidence that using mice models for human nutrition is justified -- I believe there has been a good deal of research that has provided useful insight on the influence of genetics on the susceptibility to diabetes in humans using mouse models, so ... yes?&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2012-09-19T19:55:47.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3613" PostTypeId="2" ParentId="3610" CreationDate="2012-09-19T21:04:03.337" Score="2" Body="&lt;p&gt;My impression is that the use of mice as human models for anything is primarily the result of historical precedent. A lot of work has been done to breed different lines of mice for particular purposes, and a lot of related methodology has therefore been established. Similarly, a lot of comparative genetic/genomic work has been done to characterize similarities between the mouse and human genomes. Developing similar methods and resources for another species could potentially require a huge investment of time and resources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additional reasons are purely technical and practical. Non-human primates are demonstrably more closely related to humans than mice, but breeding, storing, and working with these animals is a much more complicated issue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And, as @SteveLianoglou mentions, any model has to be taken with a healthy level of skepticism. I prefer the quote from &lt;a href=&quot;http://en.wikiquote.org/wiki/George_E._P._Box&quot; rel=&quot;nofollow&quot;&gt;G.E.P. Box&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Essentially, all models are wrong, but some are useful.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No model of human nutrition is going to be perfect, whether it was modeled in mice, primates, or even other humans (as you suggested). This does not mean, however, that we cannot gain insight from the models just because they are not perfect.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2012-09-19T21:04:03.337" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3614" PostTypeId="1" AcceptedAnswerId="3617" CreationDate="2012-09-19T22:14:17.170" Score="3" ViewCount="915" Body="&lt;p&gt;&lt;strong&gt;I'm wondering how it is possible to measure diurnal variations of melatonin levels in humans.&lt;/strong&gt; I keep reading that there should be a large difference in amplitude between melatonin levels measured at night and in the middle of the day.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have there been any studies of melatonin levels in humans where I can take a look at the methods they used for this kind of testing and/or see sample results?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="57" LastEditDate="2012-09-20T03:19:43.203" LastActivityDate="2012-09-20T06:48:55.657" Title="How are melatonin levels measured in humans?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3615" PostTypeId="1" CreationDate="2012-09-19T22:22:31.087" Score="8" ViewCount="4523" Body="&lt;p&gt;It is possible for a person to donate the harvestable organs (kidneys, eyes, and such) posthumously. Let's assume for a moment that the technology exists to kill rejection, and maintain the organ in excellent shape after it is harvested. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could the organ/s ( e.g. Eye ) (assuming a decent life-style) travel for centuries from one donor to yet another donee? What is the typical life-span of the various organs in the human body assuming a healthy, and low stress life?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;p.s. It's a curiosity question; my eyes even millenia after my death would continue to see.&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2013-06-20T05:36:50.833" LastActivityDate="2019-09-24T19:23:10.813" Title="What is the life-span of the various organs in the human body?" Tags="&lt;organs&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3616" PostTypeId="1" AcceptedAnswerId="3624" CreationDate="2012-09-20T06:36:00.063" Score="2" ViewCount="145" Body="&lt;p&gt;Here is what I know so far:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Multiple copies are present in prokaryotes, but according to a paper by Lukjancenko &lt;em&gt;el al.&lt;/em&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s00248-010-9717-3&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt; it is enough to select the most similar ones.&lt;/li&gt;&#xA;&lt;li&gt;There are &lt;em&gt;stem regions&lt;/em&gt; in the S16 which I suspect are much less variable than the loops.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;And here are my questions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About 1., it is this the usual procedure? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;About 2., do people use the loops or the stems to construct a phylogenetic tree? It they use stems, do they consider the coupling between stem bases? And, if they do so, where can I get a &quot;map&quot; of this coupling (preferably in a parseable form, not an image)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the other hand, is it correct to use a simpler nucleotide substitution model? which one?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance for any hints.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s00248-010-9717-3&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Lukjancenko O, Wassenaar TM, Ussery DW&lt;/strong&gt;. 2010. Comparison of 61 Sequenced &lt;em&gt;Escherichia coli&lt;/em&gt; Genomes. Microbial Ecology, 60:708-720, doi:10.1007/s00248-010-9717-3.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="117" LastEditorUserId="43" LastEditDate="2012-09-21T19:36:23.770" LastActivityDate="2012-09-22T00:03:09.337" Title="How to build S16 rRNAs phylogenetic trees?" Tags="&lt;bioinformatics&gt;&lt;phylogenetics&gt;&lt;rrna&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3617" PostTypeId="2" ParentId="3614" CreationDate="2012-09-20T06:48:55.657" Score="3" Body="&lt;p&gt;On the &lt;strong&gt;analytics of melatonin&lt;/strong&gt; I have here a german language text by the RKI with references. Translated quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Assay of melatonin is done by serum or sputum using RIA or ELISA.&#xA;  Alternatively, to infer the nightly amount of melatonin secretion it&#xA;  is possible to look for the melatonin catabolic metabolite 6-hydroxy&#xA;  melatonin sulfate (6-OHMS) in urine.[1,2] ... standardized&#xA;  conditions of sample taking are a must to get good results.[3,4]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Ref.:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11581093&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;P. Levallois, M. Dumont&lt;/strong&gt; et al: &lt;em&gt;Effects of electric and magnetic fields from high-power lines on female urinary excretion of 6-sulfatoxymelatonin.&lt;/em&gt; In: &lt;em&gt;American journal of epidemiology.&lt;/em&gt; 154, 7, October 2001, 601–609. PMID 11581093&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8912234&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;D. H. Pfluger, C. E. Minder&lt;/strong&gt;: &lt;em&gt;Effects of exposure to 16.7 Hz magnetic fields on urinary 6-hydroxymelatonin sulfate excretion of Swiss railway workers.&lt;/em&gt; In: &lt;em&gt;Journal of pineal research.&lt;/em&gt; 21, 2, September 1996, 91–100. PMID 8912234&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8825074&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;E. Gilad, N. Zisapel&lt;/strong&gt;: &lt;em&gt;High-affinity binding of melatonin to hemoglobin.&lt;/em&gt; In: &lt;em&gt;Biochemical and molecular medicine.&lt;/em&gt; 56, 2, December 1995, 115–120. PMID 8825074&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8439449&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;D. K. Lahiri, D. Davis&lt;/strong&gt; et al: &lt;em&gt;Factors that influence radioimmunoassay of human plasma melatonin: a modified column procedure to eliminate interference.&lt;/em&gt; In: &lt;em&gt;Biochemical medicine and metabolic biology.&lt;/em&gt; 49, 1, February 1993, 36–50. PMID 8439449&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-09-20T06:48:55.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3618" PostTypeId="1" AcceptedAnswerId="3620" CreationDate="2012-09-20T06:51:22.583" Score="4" ViewCount="127" Body="&lt;p&gt;The British government has announced that it plans a large-scale badger cull which they argue are implicated in the spread of &lt;em&gt;Mycobacterium bovis&lt;/em&gt; - so-called bovine tuberculosis. Any cattle that contract this disease need to be slaughtered under EU regulations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the link between badgers and cattle doesn't seem that clear to me. What is the evidence that badgers spread tuberculosis to cattle? Also, what is the evidence that badger culling will have a significant effect on the spread of the disease to cattle?&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-09-20T08:42:35.717" LastActivityDate="2012-09-20T10:31:34.990" Title="Does culling badgers restrict the spread of bovine tuberculosis?" Tags="&lt;zoology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3619" PostTypeId="1" AcceptedAnswerId="17851" CreationDate="2012-09-20T07:06:16.873" Score="9" ViewCount="2972" Body="&lt;p&gt;Now that we can compare whole microbiomes, has there been investigations on the effect of garlic (or diallyl disulfide, its main ingredient) on intestinal flora? From the proven antimicrobial activity, it should work like antibiotics. But does it leave &quot;good bacteria&quot; counts untouched?&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="16651" LastEditDate="2015-12-13T13:37:12.023" LastActivityDate="2015-12-13T13:37:12.023" Title="What is the effect of garlic on intestinal flora?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;gastroenterology&gt;&lt;microbiome&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3620" PostTypeId="2" ParentId="3618" CreationDate="2012-09-20T07:19:03.040" Score="4" Body="&lt;p&gt;This is apparently a debate since decades in the UK. As to the pathology:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Eurasian badgers (&lt;em&gt;Meles meles&lt;/em&gt;) are an important wildlife reservoir of&#xA;  tuberculosis (&lt;em&gt;Mycobacterium bovis&lt;/em&gt;) infection in Ireland and the United&#xA;  Kingdom. As part of national programmes to control tuberculosis in&#xA;  livestock, considerable effort has been devoted to studying the&#xA;  disease in badgers and this has lead to a rapid increase in our&#xA;  knowledge of tuberculosis in this host.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21131004&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;L. A. Corner, D. Murphy, E. Gormley&lt;/strong&gt;: &lt;em&gt;Mycobacterium bovis infection in the Eurasian badger (Meles meles): the disease, pathogenesis, epidemiology and control.'' In: ''Journal of comparative pathology.&lt;/em&gt; 144, 1, January 2011, 1–24. doi:10.1016/j.jcpa.2010.10.003. PMID 21131004. (Review).&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A summary of the pre-1997 debates is here:&#xA;&lt;a href=&quot;http://archive.defra.gov.uk/foodfarm/farmanimal/diseases/atoz/tb/publications/krebs.htm&quot; rel=&quot;nofollow&quot;&gt;http://archive.defra.gov.uk/foodfarm/farmanimal/diseases/atoz/tb/publications/krebs.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The up-to-date DEFRA informations are at:&#xA;&lt;a href=&quot;http://www.defra.gov.uk/animal-diseases/a-z/bovine-tb/&quot; rel=&quot;nofollow&quot;&gt;http://www.defra.gov.uk/animal-diseases/a-z/bovine-tb/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an alternative approach see:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19846226&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/19846226&lt;/a&gt; (in short: educate them not to piss everywhere)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been asked to give also a summary. Tuberculosis is probably one of the nastiest bacterial infections in existence. It is a prototype of those diseases which are called &lt;em&gt;latent&lt;/em&gt;: you can be infected for decades without symptoms, but when your immune system falters (or you have to take immune suppressants) it breaks out and kills you. &lt;strong&gt;One third of the human population&lt;/strong&gt; has such a latent infection with &lt;em&gt;Mycobacterium tuberculosis&lt;/em&gt;, and the HIV wave plus the high mycobacterial mutation rate with following extreme resistances make for interesting epidemiology. But this is also a result of our lifestyle, depending on huge cattle herds, as cattle can be cross-infected with human TB. In the west we have succeded to cut human infections by controlling cattle infection with human TB. Still, cattle can get bovine TB, and this may be economically disastrous. One of the pools of the infection is the badger population which can get bovine TB too and spread bacteria with their urine. It is unclear if protozoa may be an even more important pool. It is likewise unclear if culling of badgers would be successful for cattle TB control; the government bases its decision on a long-term study of regions where culling has happened. Alternative approaches include vaccination (which only affects uninfected animals), different cattle grazing regimes, habitat manipulations and badger latrine management. Physical exclusion of badgers from farm buildings is suggested as the simplest, and potentially most effective, method of reducing contact and opportunities for disease transmission between badgers and cattle. The government expert opinion clearly concluded that without such additional measures, culling won't be successful in reducing cattle TB.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-09-20T10:31:34.990" LastActivityDate="2012-09-20T10:31:34.990" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3621" PostTypeId="2" ParentId="3510" CreationDate="2012-09-20T11:49:54.167" Score="10" Body="&lt;p&gt;Yes, this is mostly about estrogen. Most breast cancers rely on endogenous estrogen to sustain proliferation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some general reading: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK13155/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cancer Medicine, Chapter 18&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More in-depth reading: &lt;a href=&quot;http://cancerres.aacrjournals.org/content/42/8/3232.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;Endogenous Hormones as a Major Factor in Human Cancer&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Requested summary of mentioned readings:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, there is an established link between breast cancer cell proliferation and concentration of estrogens and progesterone, which is logical, because normal breast cells divide in response to those hormones (e.g. puberty, pregnancy, even luteal phase of the menstrual cycle). Secondly, the incidence of breast cancer in women correlates with major changes in their hormonal profile - girls and elderly women (i.e. women with lower levels of sex hormones) don't get breast cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many factors, that influence the risk of developing breast cancer are in fact tightly connected to the hormones' levels. For example - early age of menarche (or, more importantly, first ovulation, because physical activity at young age disturbs ovulation AND is protective against breast cancer) and Hormone Replacement Therapy raise the risk, early age of first full-term pregnancy or any form of artificial menopause (such as preventive oophorectomy for women with mutations in BRCA1 or 2) reduce the risk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK13155/table/A5156/?report=objectonly&quot; rel=&quot;nofollow noreferrer&quot;&gt;The first table&lt;/a&gt; from the book chapter lists known risk and preventive factors. The review article explains the same ideas, but connects them to other types of cancer (e.g. ovarian cancer) and suggests mechanisms, which might be the cause of those risk changes.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastEditorUserId="5762" LastEditDate="2018-10-21T01:30:10.753" LastActivityDate="2018-10-21T01:30:10.753" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="3622" PostTypeId="1" AcceptedAnswerId="3623" CreationDate="2012-09-20T12:43:12.270" Score="6" ViewCount="1204" Body="&lt;p&gt;I was arguing with my colleague about this matter (I'm not going to mention which side I fall on).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would death be immediate in the vacuum of space? For example, if I was suddenly teleported into the vacuum of space would I die straight away? Or would I experience a suffocating sensation?&lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="43" LastEditDate="2012-09-20T13:17:37.233" LastActivityDate="2019-03-08T19:59:16.503" Title="In the vacuum of space would death be instantaneous?" Tags="&lt;human-biology&gt;&lt;death&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3623" PostTypeId="2" ParentId="3622" CreationDate="2012-09-20T13:38:54.610" Score="11" Body="&lt;p&gt;Nope, you wouldn't die &lt;em&gt;instantly&lt;/em&gt;. While explosive decompression has never been tested on humans (for obvious reasons), the dangers of a vacuum have mostly to do with the pressure differential between your body and the now pressure-less void around you. The most fragile parts of the biological system would be the lungs and ears, and the instantaneous transportation would cause a severe case of the Bends if you were rescued quickly enough. You would pass out within a few seconds &lt;a href=&quot;http://imagine.gsfc.nasa.gov/docs/ask_astro/answers/970603.html&quot;&gt;stated by NASA when an experiment went awry&lt;/a&gt;, and death might be from lack of oxygen to the brain, although after a few minutes everything bad starts to happen so nobody really knows what you would die of:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At NASA's Manned Spacecraft Center (now renamed Johnson Space Center) we had a test subject accidentally exposed to a near vacuum (less than 1 psi) in an incident involving a leaking space suit in a vacuum chamber back in '65. He remained conscious for about 14 seconds, which is about the time it takes for O2 deprived blood to go from the lungs to the brain. The suit probably did not reach a hard vacuum, and we began repressurizing the chamber within 15 seconds. The subject regained consciousness at around 15,000 feet equivalent altitude. The subject later reported that he could feel and hear the air leaking out, and his last conscious memory was of the water on his tongue beginning to boil. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-09-20T13:38:54.610" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3624" PostTypeId="2" ParentId="3616" CreationDate="2012-09-20T15:41:18.720" Score="6" Body="&lt;p&gt;OK, first of all do not use CLustalX to align the sequences. It is a very old algorithm and is outperformed by just about any modern aligner (including its descendent, &lt;a href=&quot;http://www.clustal.org/omega/&quot; rel=&quot;nofollow&quot;&gt;clustal omega&lt;/a&gt;, and &lt;a href=&quot;http://www.tcoffee.org/Projects/tcoffee/index.html&quot; rel=&quot;nofollow&quot;&gt;t-coffee&lt;/a&gt;, &lt;a href=&quot;http://mafft.cbrc.jp/alignment/software/&quot; rel=&quot;nofollow&quot;&gt;mafft&lt;/a&gt;, &lt;a href=&quot;http://www.ebi.ac.uk/Tools/msa/kalign/&quot; rel=&quot;nofollow&quot;&gt;kalign&lt;/a&gt; etc etc). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for 1) that depends on what you want to do, there is no perfect solution. What question are you trying to answer? If you want a tree with species-level resolution, use all sequences. If you don't need that high a resolution, choose a representative sequence from each order or genus or whatever. In all cases, remember to use a significantly different sequence as an outlier. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a general rule, I would use the entire sequence to build a tree, both the stems and the loops. To include structural information in your alignment you may want to check out &lt;a href=&quot;http://www.tcoffee.org/Projects/rcoffee/index.html&quot; rel=&quot;nofollow&quot;&gt;r-coffee&lt;/a&gt; from the t-coffee suite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, you don't really want to use a nucleotide substitution model. Most such models assume that the sequence codes for protein and are not suitable for non coding RNAs.  &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-09-22T00:03:09.337" LastActivityDate="2012-09-22T00:03:09.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3625" PostTypeId="2" ParentId="3605" CreationDate="2012-09-20T15:52:49.793" Score="3" Body="&lt;p&gt;The quick answer is that you are misinterpreting ESTs. EST stands for Expressed Sequence Tag. They are obtained by collecting and sequencing any &lt;em&gt;mature&lt;/em&gt; (i.e. poly-A) mRNAs found in a living cell. Well, it was living until the experiment was performed at any rate :).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term EST is not applicable to sequences derived from genomic data. It only applies to &lt;strong&gt;expressed&lt;/strong&gt; sequences. You do have ESTs that are derived from cDNA libraries but these are expressed cDNAs. Short reads are not ESTs because we have no information on whether that sequence is actually expressed in a living cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could apply the term to RNAseq reads (depending on the experimental procedure involved) but that is not what most people would understand by the term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, the operative term of EST is &quot;expressed&quot;. You cannot call anything an EST if you do not have evidence that it is actively expressed in a living cell.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2012-09-20T15:52:49.793" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3626" PostTypeId="2" ParentId="3491" CreationDate="2012-09-20T16:01:49.320" Score="4" Body="&lt;p&gt;Assuming that our emotions are the psychological manifestations of chemical changes in our bodies (an assumption I have no trouble with but one that others may take umbrage at), any emotion will be different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your brain can distinguish between two emotions, then the underlying chemistry through which these emotions are expressed will be different. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not to say that we, as scientists, can quantify this. Definitely not today at any rate. Simply that there will almost certainly be a physiological difference between any emotional state that can be differentiated by your brain. Otherwise the brain would not register different emotions. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;UPDATE:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human language has different words for different feelings. There is often a type of feeling &quot;continuum&quot; with different words representing different ranges on this scale. For example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adoration---&gt;Love--&gt;Infatuation--&gt;Affection--&gt;Indifference--&gt;Dislike--&gt;Hate&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How you decide to qualify an emotion you are feeling is more a question of semantics than biology. The point I am making here is that each point on that scale (and every point in between that we haven't explicitly assigned a word to) will represent a slightly different mix of various chemical signals in your body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your question is more about the English language words love and infatuation, their definition and distinguishing between them, try posting on &lt;a href=&quot;https://english.stackexchange.com/&quot;&gt;English.SE&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2017-04-13T12:38:11.520" LastActivityDate="2012-09-23T12:49:26.003" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3627" PostTypeId="2" ParentId="3601" CreationDate="2012-09-20T17:07:13.477" Score="9" Body="&lt;p&gt;You should check out &lt;a href=&quot;http://dx.doi.org/10.1101/gr.134478.111&quot;&gt;&lt;strong&gt;Howald C&lt;/strong&gt;, &lt;em&gt;et al&lt;/em&gt;&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt;.  This is one of the many recent papers tied to the &lt;a href=&quot;http://www.nature.com/encode/&quot;&gt;ENCODE data&lt;/a&gt;. They've used RT-PCR to amplify exon-exon junctions and then sequenced the results. Supplemental table 2 shows 3076 validated exon-exon junctions in putative processed transcripts which, in the main body of the paper may be sub-classified as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Non-coding, 3prime_overlapping_ncrna, Ambiguous_orf, Antisense,&#xA;  LincRNA, ncRNA_host, Retained_intron, Sense_intronic,&#xA;  Sense_overlapping, Processed transcript.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1101/gr.134478.111&quot;&gt;&lt;strong&gt;Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle S, Harrow J, Hubbard TJ, Guigó R, Reymond A&lt;/strong&gt;. 2012. Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Research, 22: 1698–1710, doi:10.1101/gr.134478.111&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1429" LastEditorUserId="43" LastEditDate="2012-09-20T17:59:21.373" LastActivityDate="2012-09-20T17:59:21.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3628" PostTypeId="1" AcceptedAnswerId="3629" CreationDate="2012-09-20T17:16:45.687" Score="3" ViewCount="128" Body="&lt;p&gt;Let consider two use cases :&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;I am the only farmer within a 200km radius. I first grow GMO plants. A few cycles later I decide to grow bio plants, so I uproot all of the GMO plants and plant fresh new bio plants.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I am surrounded with GMO plantations and I decide to grow bio plants.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In both cases, can we consider the plantation as bio or was it contaminated and how?&lt;/p&gt;&#xA;" OwnerUserId="1430" LastEditorUserId="57" LastEditDate="2012-09-21T02:40:17.763" LastActivityDate="2012-09-21T02:40:17.763" Title="How can GMO contaminate biologic plants?" Tags="&lt;genetics&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3629" PostTypeId="2" ParentId="3628" CreationDate="2012-09-20T17:49:56.683" Score="6" Body="&lt;p&gt;First let me say this: I am no gardener. Every plant that enters my home or yard dies a slow death of neglect. I do have some experience trying to remove weeds from other non-weeds, and there is a practical aspect of &quot;uproot every GMO plant&quot; that I think may be impossible, but this is speculation. Let's get into a literature review.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A frequently cited paper is Dröge, M., Pühler, A. &amp;amp; Selbitschka, W. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0168165698001059&quot;&gt;Horizontal gene transfer as a biosafety issue: A natural phenomenon of public concern&lt;/a&gt;. Journal of Biotechnology 64, 75–90 (1998). Table 3 contains the most relevant information about horizontal gene transfer between plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In situation number 1, consider that the rhizosphere (the area of soil around the root of a plant) is constantly populated with bacteria. These bacteria are shown to sometimes transfer genetic material to and from the plant, through the roots. Unless you somehow sterilize the soil after uprooting your previous crop, consider everything you plant in that field possibly contaminated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Situation 2 is less clear, but Monsanto does sue farmers found to be using their seeds without a contract, and &lt;a href=&quot;http://www.dailytech.com/Monsanto+Defeats+Small+Farmers+in+Critical+Bioethics+Class+Action+Suit/article24118.htmhttp://www.dailytech.com/Monsanto+Defeats+Small+Farmers+in+Critical+Bioethics+Class+Action+Suit/article24118.htm&quot;&gt;many farmers say this is because of cross-pollination&lt;/a&gt;. I think you should assume that your field will soon be contaminated.&lt;/p&gt;&#xA;" OwnerUserId="1429" LastActivityDate="2012-09-20T17:49:56.683" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3630" PostTypeId="2" ParentId="2883" CreationDate="2012-09-20T18:49:52.000" Score="3" Body="&lt;p&gt;You seem to be assuming that mutation rates are somehow constant over evolutionary time. They are not. Mutation rates will change according to the stresses a species is subjected to. If you take a bacterial population and place it in a stressful environment (high/low temperatures, oxidative stress, lack of nourishment or whatever) you are likely to see an increase in the mutation rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, this review and references therein might interest you:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2006.05150.x/full&quot; rel=&quot;nofollow&quot;&gt;E. Denamur and I. Matic,Evolution of mutation rates in bacteria,&lt;em&gt;Molecular Microbiology&lt;/em&gt; &lt;strong&gt;60&lt;/strong&gt;(4), pages 820–827, May 2006&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-11-11T02:00:37.173" LastActivityDate="2012-11-11T02:00:37.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3631" PostTypeId="2" ParentId="2883" CreationDate="2012-09-21T08:22:43.063" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;From my reading on M. tuberculosis, I know that this organism has a pretty high mutation rate&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Huh, that's news to me. In fact, Mtb has a rather low mutation rate and rather low genetic variance. See the paper by &lt;a href=&quot;http://www.nature.com/ng/journal/v43/n5/full/ng.815.html&quot; rel=&quot;nofollow&quot;&gt;Sherman &amp;amp; Gagneux&lt;/a&gt; in Nature genetics. The paper does state that mutation rate in latent infection is higher than expected or previously assumed, but that's a different story.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, mutation rate depends strongly on the genomic context. You can have mutator strains in &lt;em&gt;E. coli&lt;/em&gt; or other bacteria that exceed the mutation rates of other strains by orders of magnitude.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A clinical example of a bacterium with mutator strains that help in acquiring resistance is &lt;em&gt;Pseudomonas aeruginosa&lt;/em&gt;. More on that in the paper by &lt;a href=&quot;http://www.nature.com/ng/journal/v43/n5/full/ng.815.html&quot; rel=&quot;nofollow&quot;&gt;Ferroni et al.&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1435" LastActivityDate="2012-09-21T08:22:43.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3632" PostTypeId="2" ParentId="3591" CreationDate="2012-09-21T08:36:10.227" Score="19" Body="&lt;p&gt;The goal of the vaccine is to provoke an immune response, therefore some degree of inflammation is expected in order for the vaccine to work. As swbarnes2 says, vaccines contain adjuvants, pro-inflammatory molecules that produces local inflammation and recruits immune cells to the site of the inoculation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since you get the shot intramuscularily, intradermally or subcutaneously, it is local, and the inflammation does not spread. The reason why your whole arm seems to hurt (rather than the place where the vaccine was deposited) is, I think, that where you got your shot, you have not many pain receptors, and your brain is not able to determine the pain source very exactly.&lt;/p&gt;&#xA;" OwnerUserId="1435" LastEditorUserId="16651" LastEditDate="2015-12-17T05:10:57.780" LastActivityDate="2015-12-17T05:10:57.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3634" PostTypeId="1" CreationDate="2012-09-21T13:46:43.850" Score="4" ViewCount="791" Body="&lt;p&gt;I was under impression that data about &lt;a href=&quot;http://en.wikipedia.org/wiki/Tool_use_by_animals&quot; rel=&quot;nofollow&quot;&gt;quite a lot different species using different tools&lt;/a&gt; is a fairly modern phenomenon, i.e., all of the research is fairly recent. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Around 50 years ago it was widely believed, by scientists too, that it was only apes that are able to use tools. I was recently told that it's basically nonsense and scientists have been studying different tool-using animals since the beginning of the 20th century or earlier. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where could I get more info on research done in this area? I'd be especially thankful for those done in USSR, since it used to be my country and my knowledge on everything was basically limited by the Iron Curtain. However, I am also interested in research done worldwide as well. &lt;/p&gt;&#xA;" OwnerUserId="1436" LastEditorUserId="57" LastEditDate="2012-09-22T18:21:27.697" LastActivityDate="2012-09-22T18:21:27.697" Title="Tool use by animals: research history" Tags="&lt;history&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3635" PostTypeId="1" AcceptedAnswerId="3783" CreationDate="2012-09-21T15:18:42.800" Score="4" ViewCount="412" Body="&lt;p&gt;I've been thinking about this for a while and I can't figure out how a memory can be stored in the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that important memories are favourably retained, such as a near death experience, the birth of your child or your wedding day. But I cannot comprehend how this can be stored biologically in the brain. &lt;/p&gt;&#xA;" OwnerUserId="158" LastActivityDate="2013-07-11T18:28:16.513" Title="How are memories stored in the brain?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3636" PostTypeId="2" ParentId="3186" CreationDate="2012-09-21T18:07:22.003" Score="9" Body="&lt;p&gt;I might be taking a bit of a simplistic view on this, but I'm not sure what the confusion is.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ring of 10 c subunits constitute a motor which uses a proton gradient to drive the rotation of the FoFc synthase.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sN3pX.jpg&quot; alt=&quot;enter image description here&quot;&gt; (&lt;a href=&quot;http://www.life.illinois.edu/crofts/bioph354/lect10.html&quot; rel=&quot;noreferrer&quot;&gt;image reference is a nice lecture on ATP synthase&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The motor of c subunits has a 10 fold symmetry.  Each subunit releases a proton as it drives a 36 degree movement of the gamma subunit shaft.  The sixfold symmetry of the ATP FoF1 synthease is completely separate from this, and every 360 degree rotation, three ATPs are generated.  As long as the c motor keeps spinning more ATP is created. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question is similar to asking why the gear ratios of a bicycle or a car are 3:2 or 5:3.   The symmetry of the synthase and the c subunit are independent except that the torque generated by the c subunit motor needs to be enough to drive the ATP synthase.  If the proton gradient were stronger it could well be 7 protons per full rotation and not 10. Think of the two as gears and you might get the picture? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/G29hJ.gif&quot; alt=&quot;enter image description here&quot;&gt;  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-10-02T18:09:36.463" LastActivityDate="2014-10-02T18:09:36.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3637" PostTypeId="1" AcceptedAnswerId="3640" CreationDate="2012-09-21T21:45:44.400" Score="1" ViewCount="751" Body="&lt;p&gt;Being structurally composed of one or more cells, which are the basic units of life.&#xA;Yet within a cell, there seems to be the same behaviors that define life:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Regulation of the internal environment to maintain a constant state;&lt;/li&gt;&#xA;&lt;li&gt;Organization: Don't most cells have organs?&lt;/li&gt;&#xA;&lt;li&gt;Metabolism.&lt;/li&gt;&#xA;&lt;li&gt;Growth ~ not sure about this one.&lt;/li&gt;&#xA;&lt;li&gt;Adaption ~ Think this is accurate, but I'm not well versed in cellular biology at all.&lt;/li&gt;&#xA;&lt;li&gt;Response to stimuli. Cells interact with external whatnots.&lt;/li&gt;&#xA;&lt;li&gt;Reproduction - Cells do this, at least many of them.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;Most of what lead me to this question came from chapter 5 of Spontaneous Healing by Andrew Weil, M.D.. I'll type the parts relevant to the discussion below - in case he's wrong and I'm basing my thoughts on wrong information. bold sections indicate my interjection&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;DNA takes the same form in all organisms, from human beings to viruses - an enormous molecule with a double-helix structure made up of two chains of sugar molecules, with &amp;quot;rungs&amp;quot; linking the two chains. The rungs form between complementary pairs of nitrogen-containing subunits 'nucelotides', whose specific sequences differentiate the DNA of one organism from that of another. Only four different nucelotides occur in DNA; they are the &amp;quot;letters&amp;quot; of a genetic code spelling out &amp;quot;words&amp;quot; of information that direct the construction and operation of all forms of life. The so-called Central Dogma of modern molecular biology states that DNA replicates itself in order to pass its genetic information on from one cell to another and from one generation to the next &lt;strong&gt;reproduction&lt;/strong&gt;; DNA also transcribes its information into another macromelecule, RNA, that can travel out of the cell  nucleus; RNA, in turn, transslates this information into the manufacture of specific proteins that determine the structure and function of organisms. &lt;strong&gt;regulation?&lt;/strong&gt; These three processes - the replication, transcription, and translation of genetic information - are the most basic processes of life. They are also amazingly intricate and risky, because there are so many points at which things can go wrong.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Snipped for relevance.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Therefore, sophisticated mechanisms have evolved for the repair of this molecule in order to assure nearly error-free transmission of genetic information from one generation to the next, even in the simplest forms of life. &lt;strong&gt;organization, regulation, reproduction - evidence of response to stimuli?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;All of the mechanics of replication, transcription, and translation are directed by a special class of proteins called enzymes. A great deal of the genetic code specifies the manufacture of enzyme molecules, which, in turn, oversee the chemical reactions that develop the genetic code into biological reality. &lt;strong&gt;evidence of intelligence?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;much snipping.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In practical terms, they (enzymes) function as ingenious machines that alter the substrate molecules: cutting them apart, putting them back together, snipping particular pieces off them, adding others back, all with astonishing precision and speed.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;more snippage&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Therefore, polymerase I actually proofreads its own work, editing mistakes as it directs the synthesis of new copies of DNA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;He goes on to talk about plasma membranes, which seem to be how cells interact with the &amp;quot;outside&amp;quot; world..&lt;/p&gt;&#xA;" OwnerUserId="1432" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-09-24T11:54:59.360" Title="Is there sufficient evidence that human cells are not intelligent?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2012-09-24T11:56:08.290" ContentLicense="CC BY-SA 3.0" />
  <row Id="3638" PostTypeId="1" CreationDate="2012-09-21T21:50:37.590" Score="4" ViewCount="827" Body="&lt;p&gt;Is there any way in which uracil biosynthesis or metabolism could help cell in degradation of toxic levels of methionine?&lt;/p&gt;&#xA;" OwnerUserId="1437" LastActivityDate="2018-12-15T19:33:24.570" Title="Are there any intersections between the biochemical pathways of uracil biosynthesis (or metabolism) and methionine degradation in eukaryotes?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3640" PostTypeId="2" ParentId="3637" CreationDate="2012-09-21T22:19:50.940" Score="3" Body="&lt;p&gt;You seem to be asking if single mammalian cells are capable of intelligence. Yet, in your introduction, you mention that &lt;em&gt;within&lt;/em&gt; a cell there are these seven characteristics that are fundamental in defining life. Then, you target more of your supporting quotations and interjections toward the &lt;em&gt;definition of life&lt;/em&gt;. Of course cells are alive. You are alive, and so are the bacteria on your skin. Your title question is: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there sufficient evidence that human cells are not intelligent?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You have strayed from your question in your line of reasoning. Let's get back to answering the title question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there sufficient evidence that human cells are not intelligent? The definition of &quot;intelligence&quot; is controversial, but let's look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Intelligence&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Intelligence has been defined in many different ways including, but not limited to, abstract thought, understanding, self-awareness, communication, reasoning, learning, having emotional knowledge, retaining, planning, and problem solving.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Human (or any mammalian, fungal or bacterial) cells are able to &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0012160667900504&quot; rel=&quot;nofollow&quot;&gt;communicate&lt;/a&gt;, and &lt;a href=&quot;http://www.livescience.com/8035-slime-mold-beats-humans-perfecting-traffic-networks.html&quot; rel=&quot;nofollow&quot;&gt;solve problems&lt;/a&gt;, but most likely lack abstract thought, understanding, self-awareness, reasoning,  and emotion. Retaining and planning are somewhat more difficult.  Cells are able to retain information about a state of &quot;being&quot; and transmit that to progeny, a recent phenomenon known as &lt;a href=&quot;http://www.landesbioscience.com/journals/epigenetics/hollidayEPI1-2.pdf&quot; rel=&quot;nofollow&quot;&gt;epigenetics&lt;/a&gt;. Does this qualify as retaining and planning? I don't know. Cells also change based on environmental pressures through stochastic processes (a process known as evolution). Does this qualify as learning? Probably not, since the changes are usually pre-existing. The human equivalent would be finding out that you can swim by falling into water and not drowning. Did the person &quot;learn&quot; how to swim, or did they already possess an aptitude for it?&lt;/p&gt;&#xA;" OwnerUserId="1429" LastActivityDate="2012-09-21T22:19:50.940" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3641" PostTypeId="2" ParentId="3634" CreationDate="2012-09-21T22:32:34.143" Score="1" Body="&lt;p&gt;Best tip I can give you is buying a textbook or popular science book about &lt;strong&gt;ethology&lt;/strong&gt;. That should give you an overview about research done in the past decades. Konrad Lorenz was a pioneer of ethology, so a book should summarize his work, e.g. &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0226080900&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more current stuff look up some journals in this field:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.journals.elsevier.com/animal-behaviour/&quot; rel=&quot;nofollow&quot;&gt;Animal Behaviour&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.apa.org/pubs/journals/com/index.aspx&quot; rel=&quot;nofollow&quot;&gt;Journal of Comparative Psychology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Animals having a small brain compared to mammals but nevertheless showing very intelligent and reflective behaviour like &lt;a href=&quot;https://www.youtube.com/watch?v=riqtFvZg1mI&quot; rel=&quot;nofollow&quot;&gt;this rook&lt;/a&gt; are currently interesting research objects. This kind of research is not really tricky or expensive as you see, it just has to be done by a student :) But &lt;strong&gt;behaviorism&lt;/strong&gt; as the leading paradigm in the middle of the 20th century has probably made a lot of more fruitful research approaches impossible. &lt;/p&gt;&#xA;" OwnerUserId="45" LastActivityDate="2012-09-21T22:32:34.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3642" PostTypeId="1" CreationDate="2012-09-22T00:15:05.223" Score="2" ViewCount="571" Body="&lt;p&gt;I've been reading a few papers on &lt;code&gt;Melanopsin&lt;/code&gt; and &lt;code&gt;Suprachiasmatic Nucleus (SCN)&lt;/code&gt;, and see that the sleep/wake transition is influenced and entrained by &lt;strong&gt;visible light, particularly in the blue spectrum&lt;/strong&gt; that is registered by special cones in the eye and is transmitted to the SCN.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen a fleeting hypothesis/mention in two of these articles, that electromagnetic radiation may also play a part in the sleep/wake transition and melatonin release, on top of the blue light. It was some time after I read those articles that it dawned on me to ask this question, and I'm unable to find the exact lines where the mention was made. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Has there been any modern studies on the connection between electro-magnetic radiation (non-visible spectrum) and the human's circadian rhythm entrainment?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can humans be affected or feel the influence of electro magnetic radiation at all?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is a connection, what is the name of a process/organ/gland by which humans can be affected with electromagnetic radiation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your clarification!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-09-22T00:15:05.223" Title="Can the sleep/wake cycle be influenced by non-visible spectrum electro-magnetic radiation?" Tags="&lt;human-biology&gt;&lt;sleep&gt;&lt;circadian-rhythms&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3643" PostTypeId="1" CreationDate="2012-09-22T00:32:51.643" Score="2" ViewCount="73" Body="&lt;p&gt;I'm looking at inexpensive and un-intrusive ways to quantify the state of human body/mind . One of these is Actigraphy, which is a study of human motion over time. This can be done with an iPhone mounted on a wrist. There are algorithms that correlate actigraphy measurements to sleep and allow to calculate sleep onset latency, sleep efficiency, etc. I'm looking for additional metrics that may be added to actigraphy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recently, there has been a new iPhone app called &quot;heart rate&quot; which uses a camera to shine light through a finger, capture a series of images of the finger and count the heart rate based on the blood flowing in and out of a finger, changing the color of camera images. This is similar to pulse-oximetry derived heart rate, and maybe the technology would evolve sufficiently to give information about the blood oxygen content as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a sleep researcher, &lt;strong&gt;I'm wandering if there are any known algorithms or studies that relate heart rate (as beats per minute) and/or pulse oximetry to sleep or human's ability to fall asleep?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears to me that with a device like an iPhone measuring pulse at the same time of the day, it should be possible to create a history of heart rate, while accounting for the diurnal variation of heart rate. &lt;strong&gt;I'm wandering if there's anything biologically or medically relevant that can be glimpsed from such history of heart rate metric.&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-09-22T00:32:51.643" Title="Can we make any judgements about sleep or readiness to sleep from a heart rate metric and/or pulse oxymetry?" Tags="&lt;human-biology&gt;&lt;sleep&gt;&lt;cardiology&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3645" PostTypeId="1" AcceptedAnswerId="16595" CreationDate="2012-09-22T02:11:14.463" Score="18" ViewCount="73989" Body="&lt;p&gt;As far as I know, I've never seen anyone sneeze or cough while they're sleeping. Google wasn't very helpful either; a lot of contradicting claims.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the questions remains: do humans sneeze or cough in their sleep? (a few other things I've never seen with sleeping people are yawning and vomiting) If they don't, why?&lt;/p&gt;&#xA;" OwnerUserId="611" LastActivityDate="2018-07-24T09:03:48.227" Title="Do humans sneeze or cough in their sleep?" Tags="&lt;sleep&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3646" PostTypeId="1" CreationDate="2012-09-22T08:32:47.203" Score="8" ViewCount="1257" Body="&lt;p&gt;For the squid giant axon, the membrane potential computed by the Goldman equation is -60mV. And the Nernst potentials are (the differences between the K+ and the Na+'s Nernst potential and the membrane potential let the mechanism work):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;  K+ = -74mV&#xA;  Na+ = 55mV&#xA;  Cl- = -60mV&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I am wondering if the membrane potential is 0mV, whether the K+ and Na+ Nernst potentials still cause the mechanism to work, so can 0mV be a reasonable value? (That is, I think the value of potential is not important at all as long as the mechanism works well, is this true?)&lt;/p&gt;&#xA;" OwnerUserId="1439" LastEditorUserId="57" LastEditDate="2012-09-22T18:19:10.693" LastActivityDate="2014-04-09T21:40:29.307" Title="Why is membrane potential not zero at equilibrium?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3647" PostTypeId="1" CreationDate="2012-09-22T09:01:00.303" Score="7" ViewCount="66" Body="&lt;p&gt;In plasma and other body fluids, miRNAs can be found. They not only originate from dying cells but also from active secretion and are usually 'packed' into vesicles/lipo-proteic structures (i.e. &lt;a href=&quot;http://en.wikipedia.org/wiki/Exosome_%28vesicle%29&quot;&gt;exosomes&lt;/a&gt;) protecting them from the action of ribonucleases. Thus, miRNAs in plasma are very stable, offering diagnostic opportunities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is whether they may also have a functional role. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17486113&quot;&gt;Exosome transfer between cells&lt;/a&gt; has been demonstrated, so it is likely that miRNAs can be secreted by one source cell and reach a target cell, similarly to how hormones works. However, this has not been quantitatively assessed. Is the concentration of miRNAs in plasma known? Is it sufficient to hypothesize functional regulation of gene expression in target cells?  &lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="107" LastEditDate="2013-08-09T20:28:11.313" LastActivityDate="2013-08-09T20:28:11.313" Title="circulating microRNAs are functional?" Tags="&lt;molecular-biology&gt;&lt;endocrinology&gt;&lt;gene-expression&gt;&lt;rna&gt;&lt;microrna&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3648" PostTypeId="2" ParentId="3638" CreationDate="2012-09-22T17:56:38.877" Score="1" Body="&lt;p&gt;No, I don't think there are any intersections, and I can't see how uracil metabolism would have any influence upon methionine degradation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Methionine degradation is shown in Figure 1 below. The end product is succinyl CoA which is fed into the TCA cycle. The only obvious by-product is cysteine which doesn't have any connection with uracil biosynthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Uracil biosynthesis (as UMP) is shown in Figure 2: it is built from CO&lt;sub&gt;2&lt;/sub&gt; and NH&lt;sub&gt;3&lt;/sub&gt;. Uracil degradation produces CO&lt;sub&gt;2&lt;/sub&gt; NH&lt;sub&gt;3&lt;/sub&gt; and aspartate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are certainly no shared intermediates in these pathways, and I can't come up with any convincing indirect connections either. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Figure 1. Methionine degradation&lt;/strong&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/JQ3eU.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Figure 2. Uracil biosynthesis&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/poxda.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-09-22T17:56:38.877" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3649" PostTypeId="1" CreationDate="2012-09-22T18:22:25.247" Score="4" ViewCount="313" Body="&lt;p&gt;Given the human heart is autonomous, can a person die instantly from internal damage to the head/brain? I would expect the heart to continue to pulse until it ran out of energy ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My contention is whether brain-injury can cause death, albeit Memming raised a deeper question - What is the biological definition of death?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2012-09-23T02:04:56.653" LastActivityDate="2012-09-26T10:23:40.817" Title="Can a person die instantaneously from internal damage to the brain?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3650" PostTypeId="1" AcceptedAnswerId="3654" CreationDate="2012-09-22T20:17:51.220" Score="5" ViewCount="120" Body="&lt;p&gt;I guess that when there is surplus of methionine in the cell it is incorporated in the TCA cycle as a succinyl CoA, with cysteine as a by-product. But now the cell has the surplus of cysteine. What does it do with it? How does it remove excess sulphur from the cell? Would that process somehow influence NAD&lt;sup&gt;+&lt;/sup&gt;/NADH balance?&lt;/p&gt;&#xA;" OwnerUserId="1443" LastEditorUserId="1443" LastEditDate="2012-09-22T21:20:49.247" LastActivityDate="2014-10-31T13:19:17.677" Title="In which way would the yeast cell cope with the excess amount of methionine in the growth media? " Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3652" PostTypeId="1" AcceptedAnswerId="3666" CreationDate="2012-09-22T23:47:21.610" Score="11" ViewCount="741" Body="&lt;p&gt;I've been told that life on earth is &lt;a href=&quot;http://en.wikipedia.org/wiki/Carbon-based_life&quot;&gt;carbon-based&lt;/a&gt;, Then I got curious about one thing: What are the possible bases for life and under which circumstances could lifr based on other elements exist? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the existence of a silicon-based life is possible and if it is, under what temperature, pressure, etc?&lt;/p&gt;&#xA;" OwnerUserId="783" LastEditorUserId="3952" LastEditDate="2013-08-02T14:23:34.067" LastActivityDate="2013-08-02T14:23:34.067" Title="What elements are a possible basis for life?" Tags="&lt;abiogenesis&gt;&lt;speculative&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3653" PostTypeId="2" ParentId="3356" CreationDate="2012-09-23T06:01:43.070" Score="4" Body="&lt;p&gt;The anthropologist &lt;a href=&quot;http://en.wikipedia.org/wiki/Svante_P%C3%A4%C3%A4bo#Work&quot; rel=&quot;nofollow&quot;&gt;Svante Pääbo&lt;/a&gt; is more recently famous for trying to track down the 'language gene'.  There isn't a lot of reference to Chomsky in his work as I've noticed, but it is to me the same intriguing idea.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being that the chimpanzee and the bonobo have 99+% identical to human genome sequences and we also have data from human variations as well from a few thousand individuals.  Using this data you could try to evaluate a small list of differences which might have led to the inborn trait human beings have to acquire language.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pääbo's work focused on &lt;a href=&quot;http://en.wikipedia.org/wiki/FOXP2#Evolution&quot; rel=&quot;nofollow&quot;&gt;FOXP2&lt;/a&gt;, which leads to language disorders in humans when it is damaged in human beings.  On the other hand its also known that &lt;a href=&quot;http://en.wikipedia.org/wiki/Koko_%28gorilla%29&quot; rel=&quot;nofollow&quot;&gt;primates can learn to speak rather well&lt;/a&gt; if they are trained their entire lives by the right people.  They can even reflect on abstract ideas such as life after death.  This is a typical result when looking for a single gene that causes something- it rarely leads to a conclusive result as &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenotype#Difficulties_in_definition&quot; rel=&quot;nofollow&quot;&gt;a phenotype like verbality, or even height or body mass is the result of the action and fine tuning of many genes acting in concert&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is, if you introduced human FoxP2 into transgenic chimps its unlikely that they would be as verbal as human beings.  This &lt;a href=&quot;http://www.sciencedaily.com/releases/2012/09/120925142645.htm&quot; rel=&quot;nofollow&quot;&gt;current reference&lt;/a&gt; for instance talks about how important the slower development rate for human children is.  This is one of the most unusual thing about human beings - it takes 1/3 to 1/5 of the human lifetime before we are fully mature.  This phenotype is incredibly unlikely to be the result of FoxP2 alone, or any single gene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There has been recent work published (2012) &lt;a href=&quot;http://scienceblogs.com/notrocketscience/2009/05/29/scientists-humanise-foxp2-gene-in-mice-to-probe-origins-of-h/&quot; rel=&quot;nofollow&quot;&gt;where the unique human FOXP2 gene was put into transgenic mice&lt;/a&gt;.  They seem to have different sort of personality tendencies and are said to vocalize differently - &lt;a href=&quot;http://www.cell.com/retrieve/pii/S009286740900378X&quot; rel=&quot;nofollow&quot;&gt;brain activity profiles are also different&lt;/a&gt;.  Kinda exciting, but not the &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Secret_of_NIMH&quot; rel=&quot;nofollow&quot;&gt;Secret of NIMH yet&lt;/a&gt;....&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-11-02T05:39:42.493" LastActivityDate="2012-11-02T05:39:42.493" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3654" PostTypeId="2" ParentId="3650" CreationDate="2012-09-23T08:15:00.840" Score="3" Body="&lt;p&gt;In humans, cysteine first fills the glutathione pool (which itself is a reservoir for cysteine, apart from reduction equivalents and biotransformation). Excess cysteine can go three ways,&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&amp;amp;ID=1614645&quot; rel=&quot;nofollow&quot;&gt;oxidation to sulfoalanine and further hypotaurine and taurine&lt;/a&gt;, via still unknown enzyme(s)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&amp;amp;ID=1614591&quot; rel=&quot;nofollow&quot;&gt;degradation to lanthionine and toxic H&lt;sub&gt;2&lt;/sub&gt;S&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&amp;amp;ID=1614614&quot; rel=&quot;nofollow&quot;&gt;degradation to serine and toxic H&lt;sub&gt;2&lt;/sub&gt;S&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Since cystathionine gamma lyase which (its L-cysteine desulfhydrase activity) catalyses 2 and 3 has homologues in yeast, my guess is that H&lt;sub&gt;2&lt;/sub&gt;S is produced there too. &lt;a href=&quot;http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&amp;amp;FOCUS_SPECIES=Homo%20sapiens&amp;amp;ID=1614517&amp;amp;&quot; rel=&quot;nofollow&quot;&gt;Further oxidation of H&lt;sub&gt;2&lt;/sub&gt;S&lt;/a&gt; happens through an ancient mitochondrial pathway which is highly conserved as well, yielding sulfite and sulfate. Sulfate then makes for a bit acidic environment but else is non-toxic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have linked to reactome.org entries where you can find references. Filling up the yeast's glutathione pool (if it happens) would move the NAD&lt;sup&gt;+&lt;/sup&gt;/NADH balance to the NADH side, i.e., fill up reduction equivalents, too.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="3340" LastEditDate="2014-10-31T13:19:17.677" LastActivityDate="2014-10-31T13:19:17.677" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3656" PostTypeId="2" ParentId="3491" CreationDate="2012-09-23T23:15:44.823" Score="3" Body="&lt;p&gt;Using the &lt;a href=&quot;http://en.wikipedia.org/wiki/Triangular_theory_of_love&quot; rel=&quot;nofollow&quot;&gt;Triarchic Theory of Love&lt;/a&gt; proposed by Robert Sternberg, love is divided into three components:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Intimacy&lt;/li&gt;&#xA;&lt;li&gt;Passion&lt;/li&gt;&#xA;&lt;li&gt;Commitment&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Using the theory's particular &lt;em&gt;Infatuation&lt;/em&gt; is just the passion portion of love which is lacking in intimacy and commitment required for &lt;em&gt;Consummate Love&lt;/em&gt; or True Love.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Physiologically speaking, this is when a certain sense of dependency comes in and as we know from years of addiction research, there is a physiological difference between liking sex physically and liking sex with a particular person for non-physical reasons.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-09-23T23:15:44.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3657" PostTypeId="1" CreationDate="2012-09-24T13:59:00.983" Score="11" ViewCount="35441" Body="&lt;p&gt;Often when I sneeze, I smell flowers for a few seconds afterwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've done some searching on the internet, and apparently it's something that is at least not entirely uncommon, although the exact smell description seems to differ. It's sometimes also referred to as a 'honey sneeze'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just to be clear, there are no flowers anywhere in sight when I sneeze.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biology has never been a field of study of mine, but the scientist in me finds it fascinating. I've yet to come across any real explanation for this phenomenon, only guesses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know what causes this, or can you at least give a somewhat likely explanation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt;&#xA;When I sneeze through my mouth, I do not get the same smell sensation.&lt;/p&gt;&#xA;" OwnerUserId="1448" LastEditorUserId="1448" LastEditDate="2012-11-07T11:03:38.100" LastActivityDate="2018-10-12T22:22:47.983" Title="Why do I smell flowers after sneezing?" Tags="&lt;sensation&gt;" AnswerCount="3" CommentCount="5" ClosedDate="2015-09-02T05:15:25.967" ContentLicense="CC BY-SA 3.0" />
  <row Id="3658" PostTypeId="2" ParentId="3657" CreationDate="2012-09-24T15:16:31.820" Score="2" Body="&lt;p&gt;This will be a hypothetical answer for the moment, so take it with a grain of salt until I can find sources or someone else does:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My best (educated) guess would be that the smell is there all the time, and when you sneeze you reset what's currently being &quot;ignored&quot; (in that you are not aware of it, though it is being sensed) by your brain momentarily. The source of the smell may be up in the air - it could be cologne/perfume, fabric softener residue on your clothes, what you ate for breakfast and are currently digesting, the bar of soap in the kitchen, etc. - but I haven't heard of &quot;scent illusions&quot; before.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One very quirky way of possibly testing that out is to remove yourself from your regular environment, sniff some ground coffee beans for half a minute, and then re-enter your home or smell your clothes to see if any of the scents match up with what you do smell when you sneeze.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My apologies that this isn't a thoroughly-sourced answer, but hopefully it acts as a good starting point.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-09-24T15:16:31.820" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3659" PostTypeId="1" AcceptedAnswerId="5363" CreationDate="2012-09-24T19:04:39.570" Score="6" ViewCount="2090" Body="&lt;p&gt;Can female &lt;em&gt;Drosophila melanogaster&lt;/em&gt; lay egg without males? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I maintain our lab stock but find a line that seems to have all females (or all males). The flies have been in the vial for two weeks, but I don't see any eggs hatching or become larva. &lt;/p&gt;&#xA;" OwnerUserId="1141" LastEditorUserId="1590" LastEditDate="2016-08-20T08:15:57.907" LastActivityDate="2016-08-20T08:17:43.970" Title="Can female Drosophila melanogaster lay eggs without males?" Tags="&lt;zoology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3660" PostTypeId="1" AcceptedAnswerId="3672" CreationDate="2012-09-24T22:43:08.377" Score="6" ViewCount="1350" Body="&lt;p&gt;What makes mammals tend to evolve to have two testes?&lt;/p&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="57" LastEditDate="2012-09-24T23:22:27.797" LastActivityDate="2012-09-26T10:27:17.427" Title="Why did mammals evolve to have two testes?" Tags="&lt;evolution&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3661" PostTypeId="1" AcceptedAnswerId="3667" CreationDate="2012-09-24T23:08:19.003" Score="4" ViewCount="110" Body="&lt;p&gt;I have some RNA-Seq data and I'd like to align it to the physical genome and see which sections of chromatin are geometrically open and being transcribed.  The data are already sequence-aligned, and every Google search I do for tools that might help ends up sending me down a rabbit hole.  What computational tools have helped you?&lt;/p&gt;&#xA;" OwnerUserId="1387" LastEditorUserId="948" LastEditDate="2014-01-13T21:43:45.760" LastActivityDate="2014-01-13T21:43:45.760" Title="How can chromatin state be measured?" Tags="&lt;chromosome&gt;&lt;epigenetics&gt;&lt;rna-sequencing&gt;&lt;chromatin&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3662" PostTypeId="1" AcceptedAnswerId="3663" CreationDate="2012-09-24T23:22:07.390" Score="15" ViewCount="59024" Body="&lt;p&gt;Concerning medicine, what are the differences between antibiotics and antibacterials?&lt;/p&gt;&#xA;" OwnerUserId="262" LastEditorUserId="24354" LastEditorDisplayName="user4518" LastEditDate="2020-06-25T23:34:57.217" LastActivityDate="2020-06-25T23:34:57.217" Title="What is the difference between an antibiotic and an antibacterial?" Tags="&lt;bacteriology&gt;&lt;terminology&gt;&lt;antibiotics&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3663" PostTypeId="2" ParentId="3662" CreationDate="2012-09-24T23:51:21.680" Score="17" Body="&lt;p&gt;An antibacterial is any compound that will kill or at least slow down the growth of &lt;em&gt;strictly&lt;/em&gt; bacteria, a domain of prokaryotes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An antibiotic is often used synonymously, but denotes a compound that kills or slows down the growth of any &lt;em&gt;cellular&lt;/em&gt; pathogen, prokaryotic or eukaryotic. So, certain antibiotics can kill bacteria, fungi and parasites but antibiotics have no effect on viruses and &lt;a href=&quot;https://en.wikipedia.org/wiki/Prion&quot;&gt;prions&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="1306" LastEditDate="2012-09-25T14:19:16.597" LastActivityDate="2012-09-25T14:19:16.597" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3664" PostTypeId="1" AcceptedAnswerId="3670" CreationDate="2012-09-25T05:30:36.273" Score="1" ViewCount="2658" Body="&lt;p&gt;From wikipedia:&#xA;Biomagnetism is the phenomenon of magnetic fields produced by living organisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The present scientific definition took form in the 1970s, when an increasing number of researchers began to measure the magnetic fields produced by the human body. The first valid measurement was actually made in 1963,[1] but the field began to expand only after a low-noise technique was developed in 1970.[2] Today the community of biomagnetic researchers does not have a formal organization, but international conferences are held every two years, with about 600 attendees. Most conference activity centers around the MEG (magnetoencephalogram), the measurement of the magnetic field of the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do viruses produce such a field?&lt;/p&gt;&#xA;" OwnerUserId="1432" LastActivityDate="2012-09-27T06:06:12.407" Title="Do Viruses produce a biomagnetic field?" Tags="&lt;virology&gt;&lt;electrophysiology&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3665" PostTypeId="2" ParentId="3585" CreationDate="2012-09-25T07:29:51.040" Score="1" Body="&lt;p&gt;I think it could feasible to assemble complete synthetic cells in future. One of the first successes will probably be a simple bacteria. The synthetic genome is already on the road, so here, I'm pointing to other technologies that can be helpful. Feel free to add/edit/complete.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Inorganic chemistry.&lt;/strong&gt; &lt;a href=&quot;http://www.reportergene.com/2011/11/trends-in-synthetic-biology-2011.html&quot; rel=&quot;nofollow&quot;&gt;Self-replicating inorganic cells&lt;/a&gt; can be already obtained from polymer emulsions: optimistically, one may try in future to work with organic macromolecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;3D printing technology&lt;/strong&gt; may also evolve to the point that it will be possible to assemble cells by printing microscopic 'ink' molecules with the correct cellular organization. 3D printing works by serially printing one layer on the top of the other: to prevent molecular layers to mix, a technology to serially froze the printed layer will help in obtain a frozen synthetic cell.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-09-25T07:29:51.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3666" PostTypeId="2" ParentId="3652" CreationDate="2012-09-25T08:10:31.533" Score="6" Body="&lt;p&gt;This is an interesting question, particularly considered in the context that &lt;a href=&quot;http://www.cambridge.org/gb/knowledge/isbn/item5707777/?site_locale=en_GB&quot; rel=&quot;nofollow&quot;&gt;Cairns-Smith (1985)&lt;/a&gt; even suggested that clays (silicates in solution) may have had some sort of early selection acting on them due to their surface chemistries.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are a number of major problems with Silicon. Some are chemical and some are astrophysical in nature. For example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Silicon has a lower electronegativity than carbon and a longer bond length. Silicon &lt;em&gt;can&lt;/em&gt; polymerize, but many conformations (such as rings) are highly reactive or unstable.&lt;/li&gt;&#xA;&lt;li&gt;Silicon lacks chirality. Since biochemical reactions are very specific this may present a fundamental problem for alien biochemistries.&lt;/li&gt;&#xA;&lt;li&gt;We don't see silicon macromolecules in nature. Large carbon molecules are seen in space such a polycyclic aromatic hydrocarbon rings. The largest silicon molecule seen in space &lt;a href=&quot;http://dx.doi.org/10.1063/1.479694&quot; rel=&quot;nofollow&quot;&gt;is a chain of SiC_3&lt;/a&gt; (and maybe SiC_4).&lt;/li&gt;&#xA;&lt;li&gt;On reacting with oxygen (which it does readily) silicon likes to form solids like sand.&lt;/li&gt;&#xA;&lt;li&gt;Silicon is much less common than Carbon in the Universe. The Solar abundance of silicon is 1/10 that of carbon, and supernova yields suggest that the silicon abundance &lt;a href=&quot;http://adsabs.harvard.edu/abs/1995ApJS..101..181W&quot; rel=&quot;nofollow&quot;&gt;may be as low as 1/100 that of carbon during nucleosynthesis in low/intermediate mass stars.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;To form complex silicon molecules we would probably need to keep it in an oxygen-free environment and somehow maintain it in solution. One possibility would be to hold it at high pressure and temperature such as in the interiors of planets (think deep hot biosphere theory) but this presents another host of problems for conceivable biochmistries and is very speculative.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1063/1.479694&quot; rel=&quot;nofollow&quot;&gt;Apponi, A.J., McCarthy, M.C., Gottlieb, C.A., &amp;amp; Thaddeus, P. 1999, Journal of Chemical Physics, 111, 3911&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cairns-Smith, A. G. (1985) Seven Clues to the Origin of Life  Cambridge University Press, New York, ISBN 0-521-27522-9.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://adsabs.harvard.edu/abs/1995ApJS..101..181W&quot; rel=&quot;nofollow&quot;&gt;Woosley, S.E., &amp;amp; Weaver, T.A. 1995, Astrophysical Journal Supplement, 101, 181&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-09-29T02:12:14.700" LastActivityDate="2012-09-29T02:12:14.700" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3667" PostTypeId="2" ParentId="3661" CreationDate="2012-09-25T08:36:49.527" Score="2" Body="&lt;p&gt;Starting out with RNA data is great, since you already have fully spliced entities, despite  being in a different &lt;strong&gt;dynamic&lt;/strong&gt; regime.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the chromatin landscape itself is dynamic and High throughput data exploration has only begun in the last decade, consider the following tools and results with care...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may find the following &lt;strong&gt;tools helpful&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.acsu.buffalo.edu/~mjbuck/ArchAlign.html.&quot; rel=&quot;nofollow&quot;&gt;Archalign&lt;/a&gt; , &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21182771&quot; rel=&quot;nofollow&quot;&gt;Publication&lt;/a&gt; (didn't work well during my day of trials)&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Ensembl chromatin-state map data (See the &lt;a href=&quot;http://regulatorygenomics.upf.edu/Data/DGCR8/README&quot; rel=&quot;nofollow&quot;&gt;database layout&lt;/a&gt;, &lt;a href=&quot;http://ensembl.murdoch.edu.au/info/docs/funcgen/index.html&quot; rel=&quot;nofollow&quot;&gt;Regulatory Build&lt;/a&gt;, and the lincRNA&#xA;genes in the web-interface of the Ensembl databases)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://compbio.mit.edu/HaploReg&quot; rel=&quot;nofollow&quot;&gt;HaploReg&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245002/&quot; rel=&quot;nofollow&quot;&gt;Publication&lt;/a&gt; (the most recent)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1450" LastEditorUserId="1450" LastEditDate="2012-09-25T08:42:57.567" LastActivityDate="2012-09-25T08:42:57.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3668" PostTypeId="2" ParentId="3657" CreationDate="2012-09-25T09:00:02.593" Score="0" Body="&lt;p&gt;Another starting point (apologies if this has more considerations than a 'thoroughly-sourced answer') ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A sneeze is a violent, temporarily mechanically stressful event. See &lt;a href=&quot;http://uclue.com/?xq=1945&quot; rel=&quot;nofollow noreferrer&quot;&gt;How much force is generated by a sneeze?&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Temporary) mechanical stress on the brain can have many effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One point you should consider for your &lt;em&gt;Testing Hypothesis&lt;/em&gt;: If you sneeze through your mouth, do you still have this effect?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would also suggest looking into the interplay of short mechanical stress, serotonin, and the olfactory system...&lt;/p&gt;&#xA;" OwnerUserId="1450" LastEditorUserId="-1" LastEditDate="2018-10-12T22:22:47.983" LastActivityDate="2018-10-12T22:22:47.983" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="3669" PostTypeId="2" ParentId="3664" CreationDate="2012-09-25T10:05:09.413" Score="1" Body="&lt;p&gt;Every atom produces a magnetic field, so the formally correct answer would be &quot;yes&quot; (assuming that viruses belong to the tree of life, which is disputed -- otherwise, one would not use the prefix 'bio').&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, biomagnetism as a science (and not pseudoscience) is concerned with more measurable effects. The biomagnetism of a virus will be negligible compared to all the surrounding cells, and hardly measurable.&lt;/p&gt;&#xA;" OwnerUserId="1435" LastActivityDate="2012-09-25T10:05:09.413" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3670" PostTypeId="2" ParentId="3664" CreationDate="2012-09-25T12:35:26.440" Score="0" Body="&lt;p&gt;&lt;em&gt;Please excuse the phrasing, which is not scientifically rigorous&lt;/em&gt;. The post only serves as a starting point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any &lt;em&gt;electric current&lt;/em&gt; (the net movement of electrons) induces an magnetic field, and any magnetic field in turn induces an &lt;em&gt;electric field&lt;/em&gt;. Indeed, each other is just one side of the same coin. The first to join these two into what is known as &lt;em&gt;electromagnetism&lt;/em&gt; was JC Maxwell in his four fundamental equations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biomagnetism results from the flow of electricity within special functional tissues, located in organisms. (Some organisms have pure electrical junctions rather than 'interconnects' which rely on chemical messengers as vertebrae do. See this classical &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6129598&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt;, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_nervous_systems&quot; rel=&quot;nofollow&quot;&gt;Evolution of nervous systems&lt;/a&gt; )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Certain heavy atoms have asymptotic magnetic field effects (a thankful property for many  NMR structural biologists).&#xA;As such, even if a metalloprotein with such heavy metal-atoms were to move inside the virus, driven for instance by a chemical oscillator (which would eventually come to a standstill), the effect would really have to be theoretically predicted first, and &lt;strong&gt;then&lt;/strong&gt; empirically measured, rather than coincidentally just discovered (like say Penicillin). That is because it is very expensive to do science at such small scales, and the required hardware and human resources are in competition with projects that promise greater outlooks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Further Questions:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My &lt;strong&gt;answer&lt;/strong&gt; would be another question: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What sense would it make for a terrestrial virus to potentially benefit from producing an electric current inside, to motivate theoretical scientists to look into such a matter? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or, what virus features would account for the sufficient flow of electricity to be considered a mechanism ( - as the magnetism at these scales is just the 'side effect') ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Considerations:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;( During the life-cycle of a typical virus, the virus does produce a magnetic effect, as the information-carrier molecule is charged, and the production of a new virus requires the net transport of charged molecules. Note, that by convention viruses are not living entities. )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Afaik, the field of biomagnetism only really took off due to the invention and commercialization of the &lt;a href=&quot;http://en.wikipedia.org/wiki/SQUID&quot; rel=&quot;nofollow&quot;&gt;SQUID&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is just a starting point, motivated by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Mimivirus&quot; rel=&quot;nofollow&quot;&gt;challenged&lt;/a&gt; notion of viruses. Virologists have a much better and up-to date grasp on the matter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Killing a virus:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a less serious side-note, one way to kill any virus is to put it on a &lt;a href=&quot;http://en.wikipedia.org/wiki/Magnetar&quot; rel=&quot;nofollow&quot;&gt;Magnetar&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps as a starting point...&lt;/p&gt;&#xA;" OwnerUserId="1450" LastEditorUserId="1450" LastEditDate="2012-09-27T06:06:12.407" LastActivityDate="2012-09-27T06:06:12.407" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3671" PostTypeId="2" ParentId="3662" CreationDate="2012-09-25T12:54:12.960" Score="2" Body="&lt;p&gt;Antibiotics are a broader range of antimicrobial compounds which can act on fungi, bacteria, and other compounds. Although antibacterials come under antibiotics, antibacterials can kill only bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Penicillin was the first discovered by Alexander Fleming antibiotic and antibacterial.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are certian classes of compounds which are bacteriostatic, which will not allow bacteria to grow (Ampcillin kills dividing cells) in number.&lt;/p&gt;&#xA;" OwnerUserId="1452" LastEditorUserId="57" LastEditDate="2012-09-26T03:43:52.873" LastActivityDate="2012-09-26T03:43:52.873" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3672" PostTypeId="2" ParentId="3660" CreationDate="2012-09-25T13:00:25.103" Score="6" Body="&lt;p&gt;EvoDevo is not my field, but I will try to give you some pointers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mammals as vertebrates, start out as fertilized oocytes, transform into a rapidly dividing lump of cells with eventual polarity through numerous gradients of numerous chemical messengers, and form a neural tube.&#xA;The forming body is ever more segmented through the use of gradients and thresholds (see french flag model) and (dorsoventral) axial symmetry is maintained throughout development, and as such two testes represent the default development.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, it may be more interesting to ask for singular organs which require more information, and thus maintenance throughout evolution of this information. But when considering the energy requirements, the need for synchronization, the need for a separate blood supply and thus the introduction of additional faults, it is easy to see why we only have one heart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Hz3lI.png&quot; alt=&quot;Wikipedia; author: Zephyris&quot;&gt;&#xA;&lt;strong&gt;Wikipedia; author: Zephyris, title: &quot;The first few weeks of embryogenesis in humans&quot;, DOR: 25/09/2012&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Inversion_%28evolutionary_biology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;Inversion&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionary_developmental_biology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evolutionary developmental biology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I hope this helps as a starting point.&lt;/p&gt;&#xA;" OwnerUserId="1450" LastEditorUserId="69" LastEditDate="2012-09-26T10:27:17.427" LastActivityDate="2012-09-26T10:27:17.427" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3674" PostTypeId="2" ParentId="3649" CreationDate="2012-09-25T16:46:18.463" Score="3" Body="&lt;p&gt;Please consider this only as a starting point (although a lengthy one), and a race against an acute onset of  &lt;em&gt;tl:dr&lt;/em&gt; ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A person cannot die instantaneously from internal brain damage&lt;/strong&gt; (under everyday circumstances). The reason is the &lt;em&gt;non-centralized architecture&lt;/em&gt; of the brain and that consciousness is a global phenomenon which underlie the activity of many &lt;em&gt;brain structures&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These brain structures are themselves &lt;em&gt;comprised of a cellular hierarchy&lt;/em&gt;, with each cell being self-sufficient for at least a time regime in the order of minutes. As such the brain underlies to some extend the study of networks and robustness thereof. The brain also maintains a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20881595&quot; rel=&quot;nofollow noreferrer&quot;&gt;scale-free organization&lt;/a&gt; . Actual &lt;a href=&quot;http://en.wikipedia.org/wiki/Scale-free_network&quot; rel=&quot;nofollow noreferrer&quot;&gt;Scale free networks&lt;/a&gt; in nature are known to be robust.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Instantaneous&lt;/em&gt; in this context &lt;em&gt;means&lt;/em&gt; a consciously discernible difference in time, which is on the order of tens of &lt;em&gt;milliseconds&lt;/em&gt; (See: &lt;a href=&quot;http://en.wikipedia.org/wiki/Inspection_time&quot; rel=&quot;nofollow noreferrer&quot;&gt;Inspection time&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Mental_chronometry&quot; rel=&quot;nofollow noreferrer&quot;&gt;mental chronometry&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also I narrow the medical cause of death down to a &lt;em&gt;intracerebral haemorrhage&lt;/em&gt;, &lt;em&gt;systemic shock&lt;/em&gt; or &lt;em&gt;hypoxia&lt;/em&gt;. I definitely leave out all (rare) CNS-immunological phenomena (e.g. explosive brain death, Immune reconstitution inflammatory syndrome related,... )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;But&lt;/strong&gt;, effects that can mimmick instantaneous brain death are very plausible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notably, &lt;em&gt;this question can be answered&lt;/em&gt; despite there being no &lt;em&gt;rigorous consensus model of consciousness&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Consider the following just as pointers, but not as qualified, thoroughly sourced information, - contrary to a paper or review ( I will gladly include your resources, or turn this post into a community wiki if demand to do so exists):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;**** Consciousness**:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The brain weighs only 2% of the human body mass, yet consumes 20% of the total energy at rest. Crucially the brain can deplete oxygen at a great rate, which is proportional to the brain activity in various regions, giving rise to indirect measurements of brain topology and images like these:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/rA5w9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&quot;Visualization of a DTI measurement of a human brain&quot;-2006, &#xA;author: Thomas Schultz, DOR: 25/09/2012&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Humans have different states of consciousness which show different overall patterns of brain activity. As such the result a scientist would witness through an high-resolution fMRI/PET scanner in a stroking-individual would differ during sleep, sleep/wake transition or various levels of awareness during the days. Stroking and the effects on the brain is studied quite extensively with rats(See: &lt;em&gt;rat&lt;/em&gt;, &lt;em&gt;fMRI&lt;/em&gt;, &lt;em&gt;stroke&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover the brain activity, fine-anatomy and orchestration of brain utilization differs from individual to individual. In short the brain is what neurologists call &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Neuroplasticity&quot; rel=&quot;nofollow noreferrer&quot;&gt;plastic&lt;/a&gt;&quot; &lt;em&gt;Neuroplasticity is the change of entire brain structures, and the brain itself from experience and physical stress/trauma (on the brain).&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We are biologial enetities which have evolved to be in-sync with the planetary rotation and solar energy influx. As such brain activity changes during the day, in accordance with our circadian rythm or biorhythm, and if it weren't for artificial lightning brain activity would change over the seasons as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Connecting all the dots: &lt;strong&gt;Describing brain death in a seconds-regime comes down to which areas in an individual brain consume the most oxygen and &quot;shut down&quot; first, and which processes steer brain activity till organic shutdown.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since Stackexchange has a strong programmatic background, to put it in a somewhat &lt;strong&gt;programmatic analogy&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;The output of a memory dump and its analytic result depend on the hardware, the software and the state of the application. Unfortunately the software is spread across processors, has multiple threads and applies a genetic algorithm with dynamic recompilation.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Death Definitions:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The notion of instant death is a &lt;em&gt;cultural meme&lt;/em&gt; (which one can witness in child's play) and is further propagated in the media.  Additionally &quot;&lt;em&gt;death&lt;/em&gt;&quot; is a highly political matter...&lt;br&gt;&#xA;&quot;&lt;em&gt;Death&lt;/em&gt;&quot; has numerous legal definitions (throughout various cultures) &lt;a href=&quot;http://en.wikipedia.org/wiki/Clinical_death&quot; rel=&quot;nofollow noreferrer&quot;&gt;medical definitions&lt;/a&gt; and biological definitions depending on the context. Legal definitions depends on the culturally dependent legal corpus, medical definitions on the state of (pragmatic) technologies. The medical definition of human death is influenced by the legal definition. The legal definition in turn is influenced by politics.&#xA;The biological definition of death depends on the context and a threshold thereof, which in turn describes the level and and of hierarchical systems or one large system comprised out of systems such as organs. An organ is the collection of units in one structural one to serve a common purpose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally to answer more accurately, a person cannot (under everyday circumstances) shutdown brain activity within the time-interval of one reaction time-unit or 'cycle', but may transition between discernible states of global brain-activity. Such states may only be measurable with functional Imaging techniques and classifiable using computer algorithms.&lt;/p&gt;&#xA;" OwnerUserId="1450" LastEditorUserId="69" LastEditDate="2012-09-26T10:23:40.817" LastActivityDate="2012-09-26T10:23:40.817" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3676" PostTypeId="2" ParentId="1354" CreationDate="2012-09-25T19:22:16.330" Score="0" Body="&lt;p&gt;It is a filler/binding agent. Thus MC belongs in the context of a drug to the group of so called &lt;a href=&quot;http://en.wikipedia.org/wiki/Excipient&quot; rel=&quot;nofollow&quot;&gt;excipients&lt;/a&gt;. The study of the best suitable excipients (as a tradeoff of factors such as cost, and ease of approving the drug) is called &#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Galenic_formulation&quot; rel=&quot;nofollow&quot;&gt;galenics&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Methyl cellulose is also present in your toothpaste and some of the foods your eat and in the construction industry. It can be considered to be metabolically inert for humans, but can serve as a matrix for enhancing bacterial adhesion and biofilm formation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The gradual smudging and staining of your bathroom washbowl may be largely attributable to MC and bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;MC is a polymer that is sold as dry powder of various mean chain lengths. It is hydrophilic and can retain large volumes of water.&lt;/p&gt;&#xA;" OwnerUserId="1450" LastEditorUserId="69" LastEditDate="2012-09-26T10:38:49.477" LastActivityDate="2012-09-26T10:38:49.477" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3677" PostTypeId="2" ParentId="3664" CreationDate="2012-09-25T19:50:12.520" Score="1" Body="&lt;p&gt;Many living things have significant magnetic fields.  they are mostly the result of bacteria who assemble &lt;a href=&quot;http://en.wikipedia.org/wiki/Magnetotactic_bacteria&quot; rel=&quot;nofollow&quot;&gt;a tiny cluster of magentite within their cell bodies&lt;/a&gt;.  These tiny iron magnets are sensitive enough to respond to earth's magnetic field, which seems to be the best known function of the magnetic particle.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Symbiotic magentobacteria are one of the mechanisms of migratory bird's uncanny ability to find their way along their magnetic route. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't believe a virus has ever been a magnetic particle discovered in a virus, though you never say never in biology, esp with microlife.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other means by which electrical and magnetic fields may be sensed by living things, but the individual magnetic fields of typical atoms in biological samples are too weak to sense without &lt;a href=&quot;http://en.wikipedia.org/wiki/Magnetic_resonance_imaging#Magnetic_field&quot; rel=&quot;nofollow&quot;&gt;a big-ass magnet&lt;/a&gt;.  I don't know of any verified theory that gives any validity to this being important except maybe metal atoms inside proteins whos electromagnetic fields help guide ions and electrons along specific paths in the cell.  These are very local phenomena - spanning only 100 nm or so.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-09-25T19:50:12.520" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="3678" PostTypeId="1" CreationDate="2012-09-26T00:39:05.570" Score="15" ViewCount="814" Body="&lt;p&gt;I get conflicting answers.  One would think if it was true, it would be rather seminal and widely known.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are papers from Khorana&lt;a href=&quot;http://dx.doi.org/10.1016/0022-2836%2867%2990316-6&quot;&gt;&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt;, Holland&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC219759/&quot;&gt;&lt;sup&gt;[2]&lt;/sup&gt;&lt;/a&gt;, and Bretscher&lt;a href=&quot;http://dx.doi.org/10.1101/SQB.1969.034.01.075&quot;&gt;&lt;sup&gt;[3]&lt;/sup&gt;&lt;/a&gt; (late 60s) that suggest that it is quite easy in the presence of antibiotics like neomycin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But more recent papers like &lt;a href=&quot;http://dx.doi.org/10.1016/j.bbrc.2009.05.044&quot;&gt;this one&lt;sup&gt;[4]&lt;/sup&gt;&lt;/a&gt; still openly ask the question, and that the only thing we know is that the initial ribosome binding step is similar between RNA and DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't reconcile these papers.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/0022-2836%2867%2990316-6&quot;&gt;&lt;strong&gt;Morgan AR, Wells RD, Khorana HG&lt;/strong&gt;. 1967. Studies on polynucleotides. LXXIV. Direct translation in vitro of single-stranded DNA-like polymers with repeating nucleotide sequences in the presence of neomycin B. Journal of Molecular Biology, 26(3):477-497, doi:1016.10/0022-2836(67)90316-6.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC219759/&quot;&gt;&lt;strong&gt;McCarthy BJ, Holland JJ&lt;/strong&gt;. 1965. Denatured DNA as a direct template for in vitro protein synthesis. Proceedings of the National Academy of Sciences USA, 54(3):880-886.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1101/SQB.1969.034.01.075&quot;&gt;&lt;strong&gt;Bretscher MS&lt;/strong&gt;. 1969. Ribosome Initiation and the Mode of Action of Neomycin in the Direct Translation of Single-Stranded fd DNA. Cold Spring Harbor Symposia on Quantitative Biology, 34:653-651, doi:10.1101/SQB.1969.034.01.075.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.bbrc.2009.05.044&quot;&gt;&lt;strong&gt;Damiana L, Marty-Detravesa C, Winterhalterc M, Fourniera D, Paquereaua L&lt;/strong&gt;. 2009. Single-strand DNA translation initiation step analyzed by Isothermal Titration Calorimetry. Biochemical and Biophysical Research Communications, 385(3): 296-301, doi:10.1016/j.bbrc.2009.05.044.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1454" LastEditorUserId="43" LastEditDate="2012-09-26T10:58:02.753" LastActivityDate="2012-11-28T15:11:51.750" Title="Can DNA act as a translation substrate?" Tags="&lt;dna&gt;&lt;molecular-genetics&gt;&lt;rna&gt;&lt;translation&gt;&lt;ribosome&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3681" PostTypeId="1" AcceptedAnswerId="3683" CreationDate="2012-09-26T06:16:43.113" Score="8" ViewCount="10928" Body="&lt;p&gt;Reading a  &lt;a href=&quot;http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001284&quot;&gt;paper&lt;/a&gt; about gene evolution, I see that they do phylogenetic analysis for bacteria using protein sequences. They take the method from &lt;a href=&quot;http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0030130&quot;&gt;another paper&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can suspect that amino-acid sequences are more stable than nucleotide sequences, to the presence of synonymous substitutions.... but, is this stability required between closely related species? doesn't it make the analysis less powerful? does it make it more reliable? In other words, what's the advantage of using amino-acid sequences versus using nucleotide sequences for phylogenetic analysis?&lt;/p&gt;&#xA;" OwnerUserId="117" LastEditorUserId="112" LastEditDate="2012-09-26T07:10:59.480" LastActivityDate="2012-10-05T10:34:01.403" Title="Use of amino-acid sequences versus use of nucleotide sequences in phylogenetic analysis" Tags="&lt;bioinformatics&gt;&lt;phylogenetics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3682" PostTypeId="1" CreationDate="2012-09-26T06:38:11.473" Score="11" ViewCount="927" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Albatrosses, of the biological family Diomedeidae, are large seabirds allied to the procellariids, storm-petrels and diving-petrels in the order Procellariiformes. They range widely in the Southern Ocean and the North Pacific.&lt;br&gt;&#xA;  &lt;img src=&quot;https://i.stack.imgur.com/JJixs.jpg&quot; alt=&quot;albatross&quot;&gt;&lt;br&gt;&#xA;  Short tailed Albatross , Source: Wikipedia, DOR 16/09/2012&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I read that albatrosses can stay airborne for up to a decade and that they can cycle brain activity between hemispheres. How do they do this feat, and how did they evolve this ability?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Possible points to consider:&#xA;immune system, predation, cycling solar output, weather, seasons...&lt;/p&gt;&#xA;" OwnerUserId="1450" LastEditorUserId="43" LastEditDate="2012-09-26T12:27:11.430" LastActivityDate="2012-09-26T15:24:32.983" Title="How can an albatross stay airborne for months?" Tags="&lt;zoology&gt;&lt;physiology&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3683" PostTypeId="2" ParentId="3681" CreationDate="2012-09-26T07:33:00.513" Score="7" Body="&lt;p&gt;In general, many sequence alignment programs can use multiple &lt;a href=&quot;http://www.molecularevolution.org/resources/models&quot;&gt;substitution models&lt;/a&gt;, distinguishing between nucleotides, amino acids, and codons. A protein sequence has functional information that is not directly visible in the nucleotide sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The papers you link deal with horizontal gene transfer, where a gene is passed to more distant  organism. Different species have different codon usage biases, i.e. the translation efficiency is different for different codons. On one hand, this means that HGT is more likely to occur between &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113575/&quot;&gt;species of similar codon usage&lt;/a&gt;. On the other hand, &quot;&lt;a href=&quot;http://mbe.oxfordjournals.org/content/18/5/792.full&quot;&gt;codon usage of horizontally transferred genes approaches the host usage over time&lt;/a&gt;.&quot; Thus, on the nucleotide level, the phylogenetic signal will get lost due to the evolutionary pressure on translation efficiency, while on the protein level, there will be more conservation.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-09-26T07:33:00.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3684" PostTypeId="2" ParentId="1354" CreationDate="2012-09-26T08:15:32.297" Score="1" Body="&lt;p&gt;Like cellulose, it is not digestible, not toxic, and not an allergen. Bacteria cannot digest, methyl cellulose, so they cannot grow using MC as carbon source. It is artificially synthesized produced by heating cellulose with NaOH.&lt;/p&gt;&#xA;" OwnerUserId="1452" LastActivityDate="2012-09-26T08:15:32.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3685" PostTypeId="2" ParentId="3678" CreationDate="2012-09-26T12:09:01.090" Score="5" Body="&lt;p&gt;As far as I can tell from the paper you linked to (Damiana et al) it &lt;em&gt;is&lt;/em&gt; possible but inefficient:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Naturally, we tried to translate ssDNA, but as previously described&#xA;  elsewhere, direct DNA translation was not really efficient in absence&#xA;  of antibiotics such as neomycin [5] and [6]. It seemed that the&#xA;  elongation phase was the limiting step in the direct translation of&#xA;  single-stranded DNA. Whether direct participation of DNA in protein&#xA;  synthesis could play any role in vivo must be excluded, although such&#xA;  a role could be attractive for modelling the evolution of the earliest&#xA;  forms of life.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-11-28T15:11:51.750" LastActivityDate="2012-11-28T15:11:51.750" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3686" PostTypeId="1" AcceptedAnswerId="3727" CreationDate="2012-09-26T14:33:14.987" Score="7" ViewCount="141" Body="&lt;p&gt;What are the immediate challenges to break through in seeking a cure for mad cow disease?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that mad cow disease has no treatment as of yet.&lt;/p&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="3059" LastEditDate="2013-05-06T21:42:13.423" LastActivityDate="2017-03-01T11:22:06.213" Title="What are some of the immediate challenges to break through before finding a cure for mad cow disease?" Tags="&lt;pathology&gt;&lt;protein-folding&gt;&lt;neurodegenerative-disorders&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3688" PostTypeId="2" ParentId="3682" CreationDate="2012-09-26T15:24:32.983" Score="8" Body="&lt;p&gt;I'm not really inside the field but few weeks ago I noticed a Plos One article that was dealing with this. Indeed albatross can fly for thousands of miles and this is possible at no mechanical cost, because they use a dynamic way of flight that takes the energy from wind (dynamic soaring) (ref-1). Their muscle-skeletal system further evolved so that no energy is required to keep open the wing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, when foraging, they minimize diving and landing activities because they follow Killer Whales, so that food is always in proximity. (ref-2) Very smart birds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ref-1 &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0041449&quot;&gt;Sachs et al., Plos One 2012&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ref-2 &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0007322&quot;&gt;Sakamato et al., Plos One 2009&lt;/a&gt; both references are open access.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2012-09-26T15:24:32.983" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3689" PostTypeId="1" AcceptedAnswerId="3693" CreationDate="2012-09-26T19:10:07.937" Score="8" ViewCount="10520" Body="&lt;p&gt;I've heard both ways; people going to the doctor for a cold and then getting a prescription for antibiotics and those that go to the doctor and told they have ride it out because &lt;em&gt;it's a viral infection&lt;/em&gt;.  Do antibiotics really help in true cases of a viral cold?&lt;/p&gt;&#xA;" OwnerUserId="1459" LastActivityDate="2014-05-31T17:58:35.557" Title="Why are antibiotics prescribed with a viral infection like a cold?" Tags="&lt;pathology&gt;&lt;antibiotics&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3692" PostTypeId="2" ParentId="3647" CreationDate="2012-09-26T20:24:52.570" Score="2" Body="&lt;p&gt;See papers by D Bianchi for reports of miR levels in blood of pregnant humans, both of maternal and fetal origin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A review by Steer and Subramanian offers a number of examples pertaining to your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, Vickers, Palmisano, et al. (2011) show that some miRs are present in the HDL-cholesterol particle and that those levels differ between normal and familial hypercholesterolemia human subjects.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-09-26T20:24:52.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3693" PostTypeId="2" ParentId="3689" CreationDate="2012-09-27T03:39:25.140" Score="10" Body="&lt;p&gt;In general antibiotics don't help with viruses. However, sometimes a bacterial infection may follow a cold virus, so there might be some scenarios in which antibiotics would be needed. However in many cases it could be due to people demanding antibiotics from their doctor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read more here (CDC site): &lt;a href=&quot;http://www.cdc.gov/Features/getsmart/&quot;&gt;http://www.cdc.gov/Features/getsmart/&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2012-09-27T03:39:25.140" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3694" PostTypeId="1" CreationDate="2012-09-27T10:57:02.543" Score="5" ViewCount="2039" Body="&lt;p&gt;The carrots we buy from a supermarkets spoil very fast, albeit giving many consumers a false sense of preservability due to their structural rigidity. The answer extends to many other vegetables many of us eat:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gq1YK.jpg&quot; alt=&quot;carrots- wikimedia&quot;&gt;&lt;br&gt;&#xA; Larsinio (2006)- wikimedia, public domain, DOR 27/09/2012&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is, &lt;strong&gt;why do well aerated carrots spoil in the matter of days, at room temperature?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Things to consider&lt;/strong&gt;: a tuberous rhizome with rough and segmented skin / oxygen levels / levels of aeration / relatively high sugar content / differences in immediate microbiome / lack of possible synergies which the earth provides...the majority of antibiotics is extracted from soil microorganisms &lt;a href=&quot;https://i.stack.imgur.com/gq1YK.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;{1}&lt;/a&gt;,&lt;a href=&quot;http://benthamscience.com/open/tonutraj/articles/V005/107TONUTRAJ.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;{2}&lt;/a&gt;....&lt;/p&gt;&#xA;" OwnerUserId="1450" LastActivityDate="2016-01-18T14:18:21.603" Title="Why do carrots spoil so fast?" Tags="&lt;safety&gt;&lt;vegetable&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3695" PostTypeId="1" CreationDate="2012-09-27T11:48:54.923" Score="17" ViewCount="10629" Body="&lt;p&gt;I have just learnt about neurons. I wonder why neurons have only one axon. Can they transmit nerve impulses faster and more rapidly when they have more axons? Does having more axons help in coordination? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could anyone tell me why neurons have only one axon?&lt;/p&gt;&#xA;" OwnerUserId="1460" LastEditorUserId="9099" LastEditDate="2014-10-04T06:25:25.227" LastActivityDate="2014-10-04T06:25:25.227" Title="Why do neurons have only one axon?" Tags="&lt;neuroscience&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3696" PostTypeId="1" AcceptedAnswerId="3698" CreationDate="2012-09-27T12:28:40.833" Score="9" ViewCount="15193" Body="&lt;p&gt;There is plenty of anecdotal evidence (&quot;&lt;em&gt;beer after wine and you'll feel fine, wine after beer will make you feel queer&lt;/em&gt;&quot;) that mixing alcoholic drink types leads to a stronger effect, but I can't find any true studies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact the only studies I found are looking at mixing energy drinks and alcohol (mixing with energy drinks increases motivation for more alcohol (in college students) [&lt;a href=&quot;http://dx.doi.org/10.1111/j.1530-0277.2012.01868.x&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]), and discussed mixing caffeinated beverages with alcoholic ones [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22184486&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any studies specifically looking at mixing alcoholic drinks? They would have to compare people drinking the same amount of alcohol, but some people mixing, others drinking the same thing. Maybe even a cross-over study design? Same people do both, one after the other? The only way to get an unclouded answer!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am also interested in the follow-up &lt;em&gt;why&lt;/em&gt; question: Why does mixing some drinks make you more drunk? Presumably it is something in wine (for example) that interacts badly with something in beer at the chemical level (the metabolites maybe)?&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Marczinski CA, &lt;em&gt;et al&lt;/em&gt;, (2012). Mixing an Energy Drink with an Alcoholic Beverage Increases Motivation for More Alcohol in College Students. &lt;em&gt;Alcohol Clin Exp Res&lt;/em&gt;, epub. doi: &lt;a href=&quot;http://dx.doi.org/10.1111/j.1530-0277.2012.01868.x&quot; rel=&quot;nofollow&quot;&gt;10.1111/j.1530-0277.2012.01868.x&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Touyz LZ, (2011). Mixing drinks and concocting troubles. &lt;em&gt;Curr Oncology&lt;/em&gt;, &lt;strong&gt;18&lt;/strong&gt;(6):262-3. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22184486&quot; rel=&quot;nofollow&quot;&gt;PubMed&lt;/a&gt;; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224025/&quot; rel=&quot;nofollow&quot;&gt;FullText&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastEditorUserId="1590" LastEditDate="2015-07-14T14:57:55.223" LastActivityDate="2016-01-14T10:29:05.140" Title="Does mixing alcoholic drinks really make you more drunk?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;metabolism&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3697" PostTypeId="1" AcceptedAnswerId="3699" CreationDate="2012-09-27T12:38:36.500" Score="3" ViewCount="896" Body="&lt;p&gt;Looking around I see animals - ants, bees, birds, lizards, roaches all the way up to humans appear during a part of the day and not other parts. I would guess there is a sleep/recovery cycle involved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any multi-cellular organism with a nervous system, on record, that works without sleep/rest?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2012-09-27T18:08:55.073" LastActivityDate="2012-09-27T18:08:55.073" Title="Are there any multi-cellular organisms out there that do not sleep?" Tags="&lt;sleep&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3698" PostTypeId="2" ParentId="3696" CreationDate="2012-09-27T12:39:55.907" Score="11" Body="&lt;p&gt;There are some very general answers to your question.&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Definitely, there is a lot of magical thinking. We as humans are very prone to anecdotical evidence and extrapolations from incomplete data, even more so when we are drunk.&lt;/p&gt;&#xA;&lt;p&gt;As an interesting &amp;quot;proof&amp;quot; is the fact that the German counterpart of the saying &amp;quot;beer after wine and you'll feel fine, wine after beer will make you feel queer&amp;quot; is &amp;quot;Wein nach Bier, gönn' ich Dir, Bier nach Wein, lass es sein&amp;quot; -- which means the &lt;em&gt;exactly opposite&lt;/em&gt; of the English saying (beer after wine is bad, wine after beer is fine).&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Many kinds of alcohol contain unwelcome additional substances, for example fusel alcohols. Definitely, &amp;quot;mixing&amp;quot; broadens the range of these additions.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Mixing can lead to a misperception about the actual amount of alcohol that was taken in. Many people who would not drink a vodka and drive have no problem driving after a half a liter of beer (which contains same amount of alcohol two shots of vodka).&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1435" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-09-27T12:39:55.907" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3699" PostTypeId="2" ParentId="3697" CreationDate="2012-09-27T13:33:16.610" Score="9" Body="&lt;p&gt;Well, you may want to re-state your question. There are numerous multi-cellular organisms without a nervous system. So you could say that they never sleep: sponges, plants, mushrooms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://cache.orn.mpg.de/nwg/rattenb/Lesku2006a.pdf&quot;&gt;paper on the evolution of sleep&lt;/a&gt; concludes:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A phylogenetic evaluation of sleep demonstrates that all&#xA;  mammals, birds, and reptiles engage in sleep, and evidence&#xA;  for sleep in amphibians, ﬁshes, and invertebrates is strong if&#xA;  not certain.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So it seems that once you have a nervous system, you also have some rest periods. However, it may not be clear if the rest periods are dictated by the lifestyle (e.g. nocturnal foraging) or by a requirement to &quot;recharge&quot; the nervous system.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-09-27T13:33:16.610" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3700" PostTypeId="2" ParentId="3695" CreationDate="2012-09-27T15:31:30.013" Score="12" Body="&lt;p&gt;Neurons generally have one axon, because of the way it sums potentials from its dendrites. Right at the axon hillock (the little area where the axon protrudes from the soma), all the potentials are summed together. Now, you have to consider that what is actually summed here is dependent on the shape of the neuron, potentials lose amplitude as they travel towards the axon hillock. If there were multiple axons protruding from different sites, they would send out different signals and compromise the computational integrity of the neuron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead of having multiple axons, a neuron simply branches its axon with axon collaterals. This way, all post synaptic sites are receiving virtually the same message.&lt;/p&gt;&#xA;" OwnerUserId="510" LastActivityDate="2012-09-27T15:31:30.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3701" PostTypeId="2" ParentId="3561" CreationDate="2012-09-27T15:39:13.700" Score="0" Body="&lt;p&gt;Biological tissue by definition is tied to cellularity. To start this post, it might be useful to include important definitions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A definition from &lt;a href=&quot;http://en.wikipedia.org/wiki/Tissue_%28biology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Tissue is a cellular organizational level intermediate between cells&#xA;  and a complete organism. A tissue is an ensemble of similar cells and&#xA;  from the same origin, that together carry out a specific function&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The ECM or extracellular matrix, as the name suggest is a &lt;code&gt;matrix&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Matrix_%28biology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;WP&lt;/a&gt;: In biology, matrix (plural: matrices) is the material (or tissue)&#xA;  between animal or plant cells, in which more specialized structures&#xA;  are embedded, and a specific part of the mitochondrion that is the&#xA;  site of oxidation of organic molecules. The internal structure of&#xA;  connective tissues is an extracellular matrix.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Lastly,in chemistry, &lt;code&gt;matrix&lt;/code&gt; generally refers to any chemical species which is not of direct immediate regard to the context of the observer (e.g. a chemist), but may or may not have significant effect on the chemistry or chemical environment in question.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do the cellular organelles directly contribute to the tissue and organ's function?&lt;/strong&gt; &lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No, they do not &lt;em&gt;directly&lt;/em&gt; contribute to the tissue and organ's function but organelles contribute &lt;a href=&quot;http://universe-review.ca/F02-cosmicbg.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;indirectly&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There is a &lt;a href=&quot;http://www.isss.org/hierarchy.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;hierarchy&lt;/a&gt; of structure: Everything is composed of smaller&#xA;  things and is a part of something larger. The character of structures with different&#xA;  scale changes according to the interplay of various physical forces. Quantum&#xA;  phenomena control the small scales, while gravity dominates on large&#xA;  scales, and both come into play at the beginning of the universe.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(Source: The Little Book of the Big Bang: A Cosmic Primer, pg 6 By Craig J. Hogan).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematically the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hierarchy_problem&quot; rel=&quot;nofollow noreferrer&quot;&gt;matter of hierarchies&lt;/a&gt; in science is tractable through &lt;code&gt;renormalization&lt;/code&gt;. That isn't directly relatable to (structural) biology, but theoretical scientists have applied it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Or are they just there to maintain the cell itself?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Out of necessity, the cell's organelles take part in the function of the cell, yes. The reason is that the organelles are enclosed by the cell and as such all prerequisites for sourcing energy are &quot;enclosed by one additional level&quot; as well. That being said, the organelles must maintain themselves, structurally (referred to as &lt;code&gt;turnover&lt;/code&gt;) and information-wise. Information may not always be as accessible as through a designated external information carrier molecule, but may be a molecules properties or even another's  molecules properties, serving for instance as a &quot;nucleation template&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, the word &lt;code&gt;just&lt;/code&gt; in your question is not applicable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, I would like to give you a few pointers related to cellularity and the question of &quot;why&quot; in a context of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cellularity&lt;/strong&gt; may be a universal restriction that follows from the laws of thermodynamics. These laws are by consensus equally valid anywhere in the physically tractable universe.&lt;br&gt; To do any work you need to have a gradient of a physical property, which is relatable to an interconvertable form of energy. To do work in an open environment in a sustainable manner over a long-term period, it is good to have insulation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On this planet, inhabited by carbon-based lifeforms with evolution being confined to immediate (geo)chemistry**, that meant the use of lipids. Conveniently, lipids form micelles through intermolecular self-organization, in order to allow the system to reach a mimimum free energy state.&lt;br&gt;&#xA;Chemical systems with say ions too spontanously assemble given favorable energetic conditions,- all you have to do is let table-salt water evaporate, yielding you little salt-cubes which even shed a bit of insight into the underlying makeup of the crystal's &lt;a href=&quot;http://en.wikipedia.org/wiki/Crystal_structure&quot; rel=&quot;nofollow noreferrer&quot;&gt;unit cell&lt;/a&gt;. But the energies of bonds that make up the insulation layer must be in a reasonable vicinity of the &lt;a href=&quot;http://en.wikipedia.org/wiki/KT_%28energy%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;local thermal energy&lt;/a&gt; (&lt;code&gt;k*T&lt;/code&gt;), where k is the Boltzmann constant, and T the temperature in Kelvin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, chemical species where the weak London forces outweigh any other intermolecular forces, is ideal for self-assembly of an insulation layer in a biological context. It is not the only solution that evolved. But the insulation layer crucially determines your abilities and interactions as an unicellular or multicellular organism in the tempo-spatial regime. (How large can you get? How fast can you hunt? How fast can you bud something off or engulf? How flexible are you towards shifts in your environment? Those things...)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=tCB9IL8cEPo&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/r3G3s.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&#xA;&lt;br&gt;(Dileptus - a predatory protozoan - hunting, hiding, and playing around)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Self-organization can be observed across many hierarchies, serving the minimization (or optimization) of one or several properties.&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lipid membrane is ideal on a planet whose surface is covered by an extremely polar molecule. Insulation-wise lipids are impermeable to ions to allow the formation of an membrane potential. As electrical insulators lipids are excellent thermal insulators, locally confining electrons, and finally at providing mechanical insulation. Additionally lipids can serve as fuel, nutrients, signalling molecules, and many other tasks - which really just follows from or less local &lt;a href=&quot;http://en.wikipedia.org/wiki/Molecular_evolution&quot; rel=&quot;nofollow noreferrer&quot;&gt;molecular evolution&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Evolution:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Speaking of &lt;strong&gt;evolution&lt;/strong&gt;. Just like biology doesn't make sense without the context of evolution, evolution doesn't make sense without the context of energy.  For science, evolution starts at the earliest physically tractable point and transitions across many hierarchies. Matter itself is just another form of energy, and as poorly defined as space: as &quot;&lt;code&gt;anything that has mass and takes up space&lt;/code&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Concluding:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No-one can conclusively tell you what any given organelle is for (yet). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But science has furnished a comprehensive picture, by looking at the molecules that make up the organelle and tracing it back to genes to let scientists marvel at an organelles function from a bioinformatical perspective. What greatly helps the exploration of organelle function are many high-resolving imaging techniques, with a plethora of labeling techniques. This array of labeling methods was amassed over the course of a century. Recently imaging equipment has seen a rapid increase of better resolutions in the time domain, which is very important as each level of hierarchy has its own sort of &quot;time-signature&quot; - which is of course strongly influence by the masses (or inertial forces) involved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The entire picture of organelle function is however subject to a major revision-cycle with the ongoing efforts to map out entire cells at an atomic level, with large scale preparations already underway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This post isn't thoroughly sourced, and much of it is only a layman's perspective. Consider this only as a starting point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Disclaimer&lt;/strong&gt;: universe-review.ca has been around for almost a decade, despite an unclear author backing this project- for obvious copyright reasons of the textbook contents. it is scientifically sound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;***Immediate [geo]chemistry* would exclude anything from say Alpha Centauri, but not for instance &lt;a href=&quot;http://en.wikipedia.org/wiki/Kuiper_belt&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kiuper belt&lt;/a&gt; objects that may have had a significant role in the composition of earth's geochemistry. This subject is so far outside my field, I cannot give you any better information.  &lt;/p&gt;&#xA;" OwnerUserId="1450" LastEditorUserId="1450" LastEditDate="2012-09-27T15:52:43.890" LastActivityDate="2012-09-27T15:52:43.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3702" PostTypeId="1" CreationDate="2012-09-27T18:06:13.740" Score="11" ViewCount="2187" Body="&lt;p&gt;In the United States, &lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Anencephaly&quot; rel=&quot;noreferrer&quot;&gt;anencephaly&lt;/a&gt;&lt;/strong&gt; occurs in about &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0002547/&quot; rel=&quot;noreferrer&quot;&gt;1 out of every 10,000 births&lt;/a&gt;. There are several forms of this condition, wherein the forebrain is absent. The forebrain is host to most of the higher functional areas in the mammalian brain. In the most extreme case of anencephaly, the so called &lt;code&gt;holo&lt;/code&gt;-form, only the brain stem remains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;code&gt;MacLean's model&lt;/code&gt; of the brain, the term &lt;code&gt;brain stem&lt;/code&gt; is used interchangeably with the term reptilian brain, to designate the most primitive parts of the central nervous system. Many are taught this model.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/7uVh9.jpg&quot; rel=&quot;noreferrer&quot;&gt;An anencephalic newborn&lt;/a&gt; (warning: graphic content)&lt;br&gt;&#xA;  (&quot;An anencephalic newborn&quot;, wikimedia, author: Almazi, license: public domain, DOR 27/09/2012)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From my layman's perspective I can't help but notice a reptilian likeness of the anencephalic newborn. Whilst it goes without saying that correlation doesn't equal causation, I would like to know &lt;strong&gt;what is known so far about the cause of this condition to yield this particular morphology (as seen in the picture)?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps someone (eventually) has even some &lt;em&gt;evodevo&lt;/em&gt; insight to share as well?&lt;/p&gt;&#xA;" OwnerUserId="1450" LastEditorUserId="86" LastEditDate="2014-05-28T20:17:24.587" LastActivityDate="2014-05-28T20:17:24.587" Title="How are babies born without a brain?" Tags="&lt;brain&gt;&lt;embryology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3703" PostTypeId="1" CreationDate="2012-09-27T18:22:46.887" Score="6" ViewCount="2476" Body="&lt;p&gt;The title is pretty much what I seek to know.&#xA;Unless the other person is play-acting, one can often make out the eye of a living person has a shine-of-life to it; a cadaver does not. Similarly the gleam appears brighter when a person is feverish, or excited otherwise ... or has some infection in the eye itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What causes this gleam? Is it merely nervous electricity at work that disappears when the system is shutdown/crashed?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2012-09-27T20:37:37.417" Title="What causes the characteristic 'gleam' in the eye of a living being?" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3704" PostTypeId="1" CreationDate="2012-09-27T18:26:46.547" Score="10" ViewCount="390" Body="&lt;p&gt;Some shed tears of joy as the news about the successful landing of the Mars Rover &lt;strong&gt;Curiosity&lt;/strong&gt; came in. Then the &lt;a href=&quot;http://www.space.com/11781-3d-map-universe-photo-revealed.html&quot;&gt;most comprehensive 3D map&lt;/a&gt; of our observable universe was published. 2012 is literally an astronomical year.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an layman I would like to know about scientists &lt;strong&gt;current understanding about the frequency models that life forms on other planets&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;See also:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Drake_equation&quot;&gt;Drake equation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1450" LastActivityDate="2015-02-14T12:47:21.913" Title="Is there life on other planets and if so how frequent?" Tags="&lt;astrobiology&gt;&lt;life&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3705" PostTypeId="2" ParentId="3703" CreationDate="2012-09-27T20:37:37.417" Score="11" Body="&lt;p&gt;Not being an opthalmologist, if one happens along and gives a better/correct answer, listen to them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise, let's take a moment to look at the eye:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wUxGd.gif&quot; alt=&quot;Anatomy of the eye&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is not pictured here is the saline-like solution that keeps the conjuctiva moist. If we include the lubrication in all of the surfaces which interact with light, our list would look like this:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Lubrication&lt;/li&gt;&#xA;&lt;li&gt;Conjuctiva&lt;/li&gt;&#xA;&lt;li&gt;Cornea&lt;/li&gt;&#xA;&lt;li&gt;Anterior aqueous humour&lt;/li&gt;&#xA;&lt;li&gt;Iris&lt;/li&gt;&#xA;&lt;li&gt;Posterior aqueous humour&lt;/li&gt;&#xA;&lt;li&gt;Lens&lt;/li&gt;&#xA;&lt;li&gt;Vitreous humour&lt;/li&gt;&#xA;&lt;li&gt;Retina&lt;/li&gt;&#xA;&lt;li&gt;Fovea&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Out of that list, the &lt;em&gt;Iris&lt;/em&gt;, &lt;em&gt;Retina&lt;/em&gt;, and &lt;em&gt;Fovea&lt;/em&gt; are designed to absorb light; not reflect it. The &lt;em&gt;Vitreous humour&lt;/em&gt; merely serves as a medium for light to pass through and probably would not reflect light on its own. The same is true of both aqueous humours - they do not modify the light so much as serve the eye structurally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That leaves us with the Lubrication, Conjuctiva, Cornea, and Lens - surfaces which also interact with light, but act to some extent to reflect or modify it as well. The &lt;strong&gt;Cornea&lt;/strong&gt; is what's actually operated on when a person undergoes corrective surgery; a pattern is etched into the Cornea which redirects light similar to the person's previous prescription and giving them better vision.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, because you mention the difference between an excited person and presumably someone at their normal state, it's worth to note (when dealing specifically with the eye) a very common side-effect of psycho-active drugs and emotional states (particularly fear and interest/curiosity) is the change in pupil size when lighting conditions don't change:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yQWtP.jpg&quot; alt=&quot;Difference in pupil sizes.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reflection is different depending on the size of the pupil, and I would venture to guess the pupil size difference between someone who's excited or manic (whose system is flooded with endorphins) and the person at normality is part of what you define as 'gleam.'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other situation you draw a difference between is a dead person vs. a living person. Before &lt;em&gt;rigor mortis&lt;/em&gt; sets in, the relaxed state of the &lt;strong&gt;ciliary body&lt;/strong&gt; is to stress the &lt;strong&gt;suspensory ligaments&lt;/strong&gt; - resulting in pupil dilation. In addition, and I think this is the most important distinction: &lt;em&gt;dead people don't blink.&lt;/em&gt; The act of blinking spreads the &lt;strong&gt;lubrication&lt;/strong&gt; on the surface of the conjuctiva, and can be mimicked with tear-drops for people with dry eyes. Because the lubrication acts as another surface to reflect light (similar to having a thin layer of water on a surface), the dead person's eyes will have less of a &quot;gleam&quot; than a living person's.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So, to sum up:&lt;/strong&gt; The &quot;gleam&quot; in a person's eye is probably due to hydration and/or pupil dilation. Pupils will dilate at lower light levels, under the influence of certain drugs, or when showing interest. Hydration is constant, except when the lubrication is not produced in the quantities necessary or when the person is unable to blink ('dead' in your example).&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-09-27T20:37:37.417" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3708" PostTypeId="2" ParentId="3702" CreationDate="2012-09-28T02:10:58.570" Score="3" Body="&lt;p&gt;From what I've read and I know from my Biology classes, during the formation of the embryo a whole bunch of things may go wrong. In these cases, during the neurula stage, in which the brain is supposed to begin its development, something goes wrong while the neural tube is forming. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The causes? Some people argue that a lack of folic acid may lead to defective brain development. Studies seems to show that most factors don't affect the formation of the neural tube, which include age of the mother, occupation, and exposure to chemicals.&lt;/p&gt;&#xA;" OwnerUserId="1463" LastActivityDate="2012-09-28T02:10:58.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3709" PostTypeId="2" ParentId="3566" CreationDate="2012-09-28T06:13:43.003" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Although many studies have shown that there are trade-offs between&#xA;  longevity and reproduction, whether such trade-offs exist in humans&#xA;  has been a matter of debate [1,2]. In many species, including humans,&#xA;  males live shorter than females, which could be due to the action of&#xA;  male sex hormones. Castration, which removes the source of male sex&#xA;  hormones, prolongs male lifespan in many animals, but this issue has&#xA;  been debated in humans [3]. To examine the effects of castration on&#xA;  longevity, we analyzed the lifespan of historical Korean eunuchs.&#xA;  Korean eunuchs preserved their lineage by adopting castrated boys. We&#xA;  studied the genealogy records of Korean eunuchs and determined the&#xA;  lifespan of 81 eunuchs. The average lifespan of eunuchs was 70.0 ±&#xA;  1.76 years, which was 14.4–19.1 years longer than the lifespan of&#xA;  non-castrated men of similar socio-economic status. Our study supports&#xA;  the idea that &lt;strong&gt;male sex hormones decrease the lifespan of men&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Brand new article!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kyung-Jin Min, Cheol-Koo Lee, and Han-Nam Park: &lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822%2812%2900712-9&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;The lifespan of Korean eunuchs&lt;/em&gt;.&lt;/a&gt; In: &lt;em&gt;Current Biology&lt;/em&gt;, Volume 22, Issue 18, R792-R793, 25 September 2012&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-09-28T06:13:43.003" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="3710" PostTypeId="2" ParentId="3702" CreationDate="2012-09-28T06:23:52.200" Score="5" Body="&lt;p&gt;Know your databases! This is just the query fit for OMIM.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://omim.org/entry/206500&quot; rel=&quot;nofollow&quot;&gt;http://omim.org/entry/206500&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Anencephaly is considered an extreme form of neural tube defect&#xA;  (182940), which has been associated with variation in several genes.&#xA;  The entity described here is believed to show autosomal recessive&#xA;  inheritance.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The genes are those associated with neural tube effects, i.e., &lt;em&gt;VANGL1&lt;/em&gt;, &lt;em&gt;T&lt;/em&gt;, &lt;em&gt;CCL1&lt;/em&gt;, and &lt;em&gt;FUZ&lt;/em&gt;. See also folate-sensitive neural tube defects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://omim.org/entry/182940&quot; rel=&quot;nofollow&quot;&gt;http://omim.org/entry/182940&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The folate evidence was so convincing that the US/Canada in the 1990s introduced folate supplementation in all bread, flour, and cereal products. Today, US/Canada have a lower incidence of NTD (neural tube defects) than Europe, where folate supplementation is completely left to one's choice (and if women actually care they take it too late).&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-09-28T14:09:31.340" LastActivityDate="2012-09-28T14:09:31.340" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3711" PostTypeId="1" CreationDate="2012-09-28T12:55:10.287" Score="29" ViewCount="3038" Body="&lt;p&gt;It is commonly admitted that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The dose makes the poison&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;which means as a person, the more I take a substance, the more risk I take for my health.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is even an indicator called LD50 (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Median_lethal_dose&quot;&gt;Median Lethal Dose&lt;/a&gt;), which specifies the 'lethal dose' at which 50 percent of subjects will die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This might seems a stupid question but: &lt;em&gt;are there any substances for which it is more dangerous to take at low dose than at higher dose&lt;/em&gt;? For example, you have to ingest at least 1µg of XXX because if you ingest less you will have health problem...&lt;/p&gt;&#xA;" OwnerUserId="1430" LastEditorUserId="43" LastEditDate="2012-09-28T14:20:14.153" LastActivityDate="2012-10-30T08:26:08.690" Title="Are there any substance that are more dangerous at low dose than at higher dose?" Tags="&lt;human-biology&gt;&lt;toxicology&gt;" AnswerCount="5" CommentCount="6" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3712" PostTypeId="2" ParentId="3711" CreationDate="2012-09-28T17:14:26.090" Score="-2" Body="&lt;p&gt;First of all, that is an excellent question! Secondly, please excuse the lack of thorough sourcing for this post. I only like to share some pointers...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Q: &lt;strong&gt;Can substances do more harm in a mammal at a lower dose than at higher dose?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A: &lt;strong&gt;Yes.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some may know the example of the blood thinner, and widespread NSAID Acetyl-salicylic acid (Aspirin). I will use this example because Aspirin is one of the most known and used drugs in the world, with a long and &lt;a href=&quot;http://en.wikipedia.org/wiki/History_of_aspirin&quot; rel=&quot;nofollow&quot;&gt;interesting history&lt;/a&gt;. As being part of the class of nonsteroidal anti-inflammatory drugs (NSAIDs) it has recently gotten a bad wrap for blocking an enzyme which is crucial for prostaglandin synthesis and processes that maintain  a healthy stomach wall in the presence of an potentially harmful &lt;a href=&quot;http://en.wikipedia.org/wiki/Helicobacter_pylori#Pathophysiology&quot; rel=&quot;nofollow&quot;&gt;bacterial&lt;/a&gt; and chemical milieu. On a sidenote, as an acid, Aspirin actually hardly dissolves directly in the acidic stomach.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To quote &lt;a href=&quot;http://en.wikipedia.org/wiki/Aspirin#Pharmacokinetics&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; (DOR: 28/09/2012):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Salicylates are excreted mainly by the kidneys as salicyluric acid&#xA;  (75%), free salicylic acid (10%), salicylic phenol (10%), and acyl&#xA;  glucuronides (5%), gentisic acid (&amp;lt; 1%), and 2,3-dihydroxybenzoic&#xA;  acid.[148] When small doses (less than 250 mg in an adult) are&#xA;  ingested, all pathways proceed by first-order kinetics, with an&#xA;  elimination half-life of about 2.0 to 4.5 hours.[149][150] When higher&#xA;  doses of salicylate are ingested (more than 4 g), the half-life&#xA;  becomes much longer (15–30 hours),[151] because the biotransformation&#xA;  pathways concerned with the formation of salicyluric acid and salicyl&#xA;  phenolic glucuronide become saturated&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Aspirin can &lt;a href=&quot;http://www.drugs.com/drug-interactions/aspirin.html&quot; rel=&quot;nofollow&quot;&gt;interfere with a lot of drugs&lt;/a&gt;, including &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12533193&quot; rel=&quot;nofollow&quot;&gt;Ibuprofen&lt;/a&gt;. The known list of drugs is so high, in part due to the widespread application of aspirin, and in part due to the chemical composition of this very small drug with two functional groups. A functional group is a sort of chemical feature that determines how and with what probability a chemical interacts in a given milieu.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a certain metabolic degradation pathway may get saturated, other pathways can take over and lead to different potentially harmful metabolites resulting in damage to the excretion/clearance organs such as the liver (&lt;code&gt;hepatotoxic&lt;/code&gt;) and kidney (&lt;code&gt;nephrotoxic&lt;/code&gt;).&#xA;A &lt;code&gt;metabolite&lt;/code&gt; is the product of metabolism ( a weak back-referencing definition). &lt;code&gt;metabolic pathways&lt;/code&gt; are a sequence of chemical reactions within a cell, and metabolism is the entire set of metabolites and pathways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Liver/Kidney Toxicity is believed to result from an interplay of a) high concentrations of metabolites or direct toxins (=parent chemicals) within specialized high-concentration-forming cells, and b)  the non/covalent  binding of cellular macromolecules to interfere with their normal function and/or production of reactive oxygen species (ROS).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example (from memory) is the interaction pharmacokinetics of theobromine (from cacao) and other xanthines (unverified).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many more examples. I hope this example and mechanism serves you well as a starting point...&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;From a biochemical standpoint:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;In fact drugs may act differently at different concentration thresholds at different times at different places within an organism and its cells that make it up. Evolution exploited this very early on and used it for things like body segmentation along defined axis during development.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Drugs may interact with each other differently at different levels of concentrations, say as binary, ternary, and higher order complexes. The rate of formation of such complexes is denoted through the dissociation constant - which is a type of equilibrium constant such as pH is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The dissociation constant describes the propensity of a chemical species to separate reversibly and, - this is crucial! - is concentration dependent. This is accounted for by the use of so called &lt;code&gt;activities&lt;/code&gt; or the apparent concentrations, as a result of incomplete hydration of the chemical and other effects of a &quot;crowded environment&quot;. Now don't just think of chemicals, but macromolecules as well. In immunology for instance new molecular features can arise on the surface of a macromolecule, due to the association (complexation) with a small molecular drug. This in turn can lead to an immunological reaction, even anaphylaxis ( a so called Type I hypersensitivity reaction) and ultimately shock. Such drugs are classified as &lt;code&gt;haptens&lt;/code&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Important in an organisms sensitivity and susceptibility to drugs however, is the current &lt;a href=&quot;http://en.wikipedia.org/wiki/Allometry&quot; rel=&quot;nofollow&quot;&gt;allometric growth rate&lt;/a&gt; and types of organs and cells available. As such a fetus is more susceptible than an adult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope a simple &lt;strong&gt;yes&lt;/strong&gt; accompanied by this admittedly &lt;em&gt;to-long to really read&lt;/em&gt; post gave you some insight into what scientist across many, many fields are dealing with. Naturally, the issue is more complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally I believe the issue of dosing and drug reactions will improve significantly over the coming decade...&lt;/p&gt;&#xA;" OwnerUserId="1450" LastEditorUserId="1450" LastEditDate="2012-09-29T06:08:03.830" LastActivityDate="2012-09-29T06:08:03.830" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3713" PostTypeId="1" AcceptedAnswerId="3719" CreationDate="2012-09-28T19:04:59.917" Score="1" ViewCount="114" Body="&lt;p&gt;Just what the title states.&#xA;It stems from observation &amp;amp; personal experience that a person/dog/cat/monkey is more likely to relieve oneself immediately after it wakes up from the peak-sleep cycle of it's body-clock. Is this observation true? What causes this behaviour ?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2012-09-28T19:39:23.823" LastActivityDate="2012-10-01T06:10:49.263" Title="Are all healthy animals more likely to defecate near the end of a rest-cycle?" Tags="&lt;physiology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3714" PostTypeId="2" ParentId="3713" CreationDate="2012-09-28T19:30:18.147" Score="1" Body="&lt;p&gt;I'm prefixing this one by saying that I don't actually agree with you (also, I think the old nut that the plural of &quot;anecdote&quot; is not &quot;data&quot;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That having been said: wouldn't the simplest explanation just be &quot;because it was likely a long time since the animal's last 'relief'&quot; since it's been sleeping for XXX hours? Or would you argue that this observation is also true after, say, a 20 minute nap?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, what does this have to do with a nervous system?&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2012-09-28T19:30:18.147" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3715" PostTypeId="2" ParentId="3713" CreationDate="2012-09-28T19:32:29.797" Score="1" Body="&lt;p&gt;Digestion is an energy consuming process. It is, therefore, often followed by a period of rest. Animals will, consequently, often digest during sleep. It follows that they will eliminate the waste products of digestion upon awakening.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given the above, I doubt there is a causal link between sleep or rest and the need to commune with nature, water a tree, appease the porcelain god, or whatever your preferred euphemism happens to be, soon after awakening. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-09-28T23:12:03.610" LastActivityDate="2012-09-28T23:12:03.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3716" PostTypeId="2" ParentId="3566" CreationDate="2012-09-28T20:19:52.870" Score="8" Body="&lt;p&gt;In a study on longevity in 121 countries, women tended to outlive men by about 5 years [&lt;a href=&quot;http://dx.doi.org/10.1002/ajhb.20879&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]. The suggested causes for this are numerous, some of which are temporally, geographically, or culturally specific.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the terminology, &lt;strong&gt;sex&lt;/strong&gt; tends to refer to the absolute biological differences, whereas &lt;strong&gt;gender&lt;/strong&gt; relates more to differences in perception/lifestyle (for instance, socio-economic differences).&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Evidence&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;In a study on Greek centenarians the authors found that women outnumbered men (1.68:1), with men having a &lt;strong&gt;higher likelihood of smoking&lt;/strong&gt;, and thus are more at risk of smoking-related illness and mortality (historically this was more true than today) [&lt;a href=&quot;http://dx.doi.org/10.1186/1471-2318-11-87&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]. This is also true for alcohol consumption. The authors also report that having a first degree relative who was also a centenarian is associated with longevity (highlighting the importance of genetic factors in lifespan determination). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also evidence that the rate of telomere shortening (number of cell-divisions until cell-cycle arrest) is sex-specific [&lt;a href=&quot;http://dx.doi.org/10.1111/j.1474-9726.2011.00741.x&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;rwst cites an interesting paper, that presents evidence that suggests male hormones may decrease lifespan [&lt;a href=&quot;http://dx.doi.org/10.1016/j.cub.2012.06.036&quot; rel=&quot;nofollow&quot;&gt;4&lt;/a&gt;]. This may be due to differential onset of atherosclerosis and cardiovascular disease, caused by exposure to different sex hormones [&lt;a href=&quot;http://dx.doi.org/10.1177/1933719110367829&quot; rel=&quot;nofollow&quot;&gt;5&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a review on the brain/behaviour specific aspects of differential ageing between the sexes, the authors discuss differences in brain anatomy and cognitive (and emotional) functionality between the sexes [&lt;a href=&quot;http://dx.doi.org/10.1159/000323154&quot; rel=&quot;nofollow&quot;&gt;6&lt;/a&gt;]. &lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Remarks&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;This is by no means an exhaustive list of the reasons for differences in lifespan between the sexes in humans. There are likely to be many other causes, such as men tending to have more 'risky' behaviours, and possibly other unknown genetic effects, such as having 2 X chromosomes, vs. XY.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;References&lt;/h3&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Møller, A. P., &lt;em&gt;et al&lt;/em&gt; (2009). Why men have shorter lives than women: effects of resource availability, infectious disease, and senescence. &lt;em&gt;American journal of human biology : the official journal of the Human Biology Council&lt;/em&gt;, &lt;strong&gt;21&lt;/strong&gt;(3), 357-64. doi:&lt;a href=&quot;http://dx.doi.org/10.1002/ajhb.20879&quot; rel=&quot;nofollow&quot;&gt;10.1002/ajhb.20879&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Tigani, X., &lt;em&gt;et al&lt;/em&gt; (2011). Gender differences in Greek centenarians. A cross-sectional nation-wide study, examining multiple socio-demographic and personality factors and health locus of control. &lt;em&gt;BMC geriatrics&lt;/em&gt;, &lt;strong&gt;11&lt;/strong&gt;, 87. doi:&lt;a href=&quot;http://dx.doi.org/10.1186/1471-2318-11-87&quot; rel=&quot;nofollow&quot;&gt;10.1186/1471-2318-11-87&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Barrett, E. L. B., &amp;amp; Richardson, D. S. (2011). Sex differences in telomeres and lifespan. &lt;em&gt;Aging cell&lt;/em&gt;, &lt;strong&gt;10&lt;/strong&gt;(6), 913-21. doi:&lt;a href=&quot;http://dx.doi.org/10.1111/j.1474-9726.2011.00741.x&quot; rel=&quot;nofollow&quot;&gt;10.1111/j.1474-9726.2011.00741.x&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Min, K.-J., &lt;em&gt;et al&lt;/em&gt; (2012). The lifespan of Korean eunuchs. &lt;em&gt;Current Biology&lt;/em&gt;, *&lt;em&gt;22&lt;/em&gt;(18), R792-R793. doi:&lt;a href=&quot;http://dx.doi.org/10.1016/j.cub.2012.06.036&quot; rel=&quot;nofollow&quot;&gt;10.1016/j.cub.2012.06.036&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Pérez-López, F. R., &lt;em&gt;et al&lt;/em&gt; (2010). Gender differences in cardiovascular disease: hormonal and biochemical influences. &lt;em&gt;Reproductive sciences (Thousand Oaks, Calif.)&lt;/em&gt;, &lt;strong&gt;17&lt;/strong&gt;(6), 511-31. doi:&lt;a href=&quot;http://dx.doi.org/10.1177/1933719110367829&quot; rel=&quot;nofollow&quot;&gt;10.1177/1933719110367829&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Kryspin-Exner, I., &lt;em&gt;et al&lt;/em&gt; (2011). Geropsychology: the gender gap in human aging--a mini-review. &lt;em&gt;Gerontology&lt;/em&gt;, &lt;strong&gt;57&lt;/strong&gt;(6), 539-48. doi:&lt;a href=&quot;http://dx.doi.org/10.1159/000323154&quot; rel=&quot;nofollow&quot;&gt;10.1159/000323154&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Update&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Just been reading &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bies.201300021/full&quot; rel=&quot;nofollow&quot;&gt;this interesting paper&lt;/a&gt; by Maklakov, &lt;em&gt;et al&lt;/em&gt; (2013, BioEssays) titled &quot;Evolution of sex differences in lifespan and aging: Causes and constraints&quot;, which presents a more evolutionary/genetic argument for the differences.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Abstract&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Why do the two sexes have different lifespans and rates of aging? Two hypotheses based on asymmetric inheritance of sex chromosomes (“unguarded X”) or mitochondrial genomes (“mother's curse”) explain sex differences in lifespan as sex-specific maladaptation leading to increased mortality in the shorter-lived sex. While asymmetric inheritance hypotheses equate long life with high fitness, considerable empirical evidence suggests that sexes resolve the fundamental tradeoff between reproduction and survival differently resulting in sex-specific optima for lifespan. However, selection for sex-specific values in life-history traits is constrained by intersexual genetic correlations resulting in intra-locus sexual conflict over optimal lifespan. The available data suggest that the evolution of sexual dimorphism only partially resolves these conflicts. Sexual conflict over optimal trait values, which has been demonstrated in model organisms and in humans, is likely to play a key role in shaping the evolution of lifespan, as well as in maintaining genetic variation for sex-specific diseases.&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2013-06-06T10:34:11.117" LastActivityDate="2013-06-06T10:34:11.117" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3717" PostTypeId="2" ParentId="3566" CreationDate="2012-09-28T21:18:31.660" Score="1" Body="&lt;p&gt;The testosterone effect mentioned by @rwst is an exciting new discovery, but there may be a deeper answer which is an evolutionary adaptation.  There is a theory called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Grandmother_hypothesis#The_grandmother_effect_and_longevity&quot; rel=&quot;nofollow&quot;&gt;grandmother effect&lt;/a&gt; that tries to guess why women live often quite a long time after menopause. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Longevity in women doesn't make a great deal of sense from the standpoint of selection, since a lifespan past popping out the little ones wouldn't really increase fecundity.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you might guess, having a parent around for a long time after a human child is born might increase the number of offspring that reach the age.  The grandmother effect surmises that females have a stronger, more direct relationship with offspring and can contribute directly to the viability of her offspring even after she stops having children herself.  Grandfather's probably don't enjoy this benefit as much because they are thought to contribute less to the offspring.  You have to remember that over the length of human history men's tendency has been to be a little more distant because of the difference in parental certainty.  while it can be very low for fathers, it is pretty much zero for mothers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other adaptive arguments for human gender biases in longevity.  &lt;a href=&quot;http://www.immortalhumans.com/longevity-is-not-only-determined-by-%E2%80%9Cthe-grandmother-effect%E2%80%9D/&quot; rel=&quot;nofollow&quot;&gt;Men are going to try to contribute to their older age fertility&lt;/a&gt; by producing offspring later in life too.  Still, women do tend to live longer than men.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be surprising if the grandmother effect were the only reason women live longer then men, but it sounds like a stronger selective effect to me and men can probably evolve longer lives by taking an interest in their offspring longer.  This would have to be on an adaptive scale - over the entire population though.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Individual variations in longevity can of course be more important than these effects, but these theories try to explain the bias. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-09-28T21:18:31.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3718" PostTypeId="1" AcceptedAnswerId="3732" CreationDate="2012-09-28T22:53:04.443" Score="1" ViewCount="69" Body="&lt;p&gt;I'm looking for an Arabidopsis thaliana gene listed in RCSB with a clear mode of function and active site. In addition it needs to have an obvious phenotype when knocked out like severely retarded growth, lethal or near lethal. The gene also has to be exclusive to plants so RNA polymerase wouldn't work. &#xA;I found this paper in &lt;a href=&quot;http://www.plantphysiol.org/content/early/2012/01/13/pp.111.192393&quot; rel=&quot;nofollow&quot;&gt;plant physiology&lt;/a&gt; but I'm having trouble finding those genes with an obvious active site.&#xA;Thank you very much&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="3632" LastEditDate="2012-09-29T23:21:28.593" LastActivityDate="2012-09-30T15:51:42.343" Title="Arabidopsis thaliana RCSB active site gene mutant" Tags="&lt;plant-physiology&gt;&lt;molecular-genetics&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3719" PostTypeId="2" ParentId="3713" CreationDate="2012-09-29T07:08:11.763" Score="2" Body="&lt;p&gt;I think we can actually go farther than mere behavioral argumentation. The separation of the autonomous nervous system into parasympathetic and sympathetic is, one the one hand, associated with the sleep/wake cycle, on the other with parasympathetic/sympathetic activity (low/high epinephrine secretion). This duality certainly applies to all vertebrata (i.e. big animals), as fight &amp;amp; flight is associated with all vertebrata, see e.g.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fight_or_flight_response&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Fight_or_flight_response&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words: from the existence of fight or flight in all vertebrata I infer the existence of a dual autonomous nervous system (parasympathetic and sympathetic) in all vertebrata, although there may be other proof. Since in sleep the parasym. NS is active, the bowel moves. Conclusion: the bowel moves in the sleep of all vertebrata.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-10-01T06:10:49.263" LastActivityDate="2012-10-01T06:10:49.263" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3720" PostTypeId="1" CreationDate="2012-09-29T21:09:50.133" Score="2" ViewCount="2577" Body="&lt;p&gt;In the process of mitosis that starts from zygote, how do different cells appear? What happens that some cells become one type and some another? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, is there a cell that divides into a blood cell and a skin cell?&lt;/p&gt;&#xA;" OwnerUserId="1467" LastActivityDate="2013-05-12T17:06:22.270" Title="How are different types of cells created from zygote?" Tags="&lt;cell-biology&gt;&lt;mitosis&gt;&lt;stem-cells&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3721" PostTypeId="1" AcceptedAnswerId="3724" CreationDate="2012-09-29T23:54:30.397" Score="4" ViewCount="1102" Body="&lt;p&gt;If I insert a new gene with a yeast integrating plasmid and select with a drop out culture once, can I assume that the newly integrated gene will stay in the strain without putting selective pressure on it?  (i.e. can i use normal liquid culture and plates after getting the yeast with the newly integrated strain? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-09-30T15:33:15.360" LastActivityDate="2012-09-30T18:10:49.900" Title="Do Yeast Insertion constructs revert?" Tags="&lt;molecular-biology&gt;&lt;yeast&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3722" PostTypeId="1" CreationDate="2012-09-30T03:19:47.180" Score="7" ViewCount="12836" Body="&lt;p&gt;I tried an experiment. First, I placed grapes in pure water(hypotonic solution). The grapes burst because of endosmosis. Then, I placed new set of grapes in strong sugar solution(fully saturated) but they did not shrink. And then when I placed it in strong salt solution(fully saturated), they did shrink a little. Why does this occur?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is this possible?&lt;/p&gt;&#xA;" OwnerUserId="1428" LastEditorUserId="-1" LastEditDate="2018-07-23T06:32:56.990" LastActivityDate="2018-07-23T06:32:56.990" Title="Why do grapes not pea shrink when placed in strong sugar solution?" Tags="&lt;experimental&gt;&lt;cell-membrane&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="3723" PostTypeId="2" ParentId="3722" CreationDate="2012-09-30T04:10:08.543" Score="3" Body="&lt;p&gt;Well, without the details of your experiment to cross-check with the sugar and H&lt;sub&gt;2&lt;/sub&gt;O content of your average grape, I'd say the saturated solution probably approximated the natural molarity of sugar in the grape. At least to the point it didn't make any advese effects noticeably on your time scale.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That seems the most apparent solution to me. I suppose it's also possible (though I don't know the mechanics behind it) that hypertonic solution might have acted as a preservative - similar to jam. It's not just water which will attempt to reach an equilibrium, but all compounds that can pass through the membrane - perhaps sucrose/fructose/glucose can do so, maintaining the structural integrity of the grape.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both are guesses until you reveal more information, though.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="3340" LastEditDate="2014-10-31T12:39:54.920" LastActivityDate="2014-10-31T12:39:54.920" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3724" PostTypeId="2" ParentId="3721" CreationDate="2012-09-30T09:41:38.257" Score="4" Body="&lt;p&gt;It depends upon exactly what you have done.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The standard way of using a yeast intergrating plasmid (YIp) is for it to integrate into the genome by recombination between a piece of yeast DNA that the YIp carries and the same DNA in the genome. This is often, but not necessarily, the selectable marker. So for example a YIp carrying the &lt;em&gt;URA3&lt;/em&gt; gene as its only yeast DNA will integrate at the &lt;em&gt;URA3&lt;/em&gt; locus (probably mutant to allow selection for Ura&lt;sup&gt;+&lt;/sup&gt;, so more correctly &lt;em&gt;ura3&lt;/em&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the YIp is linearised by cutting at a site within the &lt;em&gt;URA3&lt;/em&gt; marker this will direct insertion and will increase the transformation efficiency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once insertion has taken place, the configuration at the integration site is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;chromosome...URA3...other YIp sequences...ura3...chromosome&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is inherently unstable because a looping-out event can take place &lt;em&gt;via&lt;/em&gt; recombination between the &lt;em&gt;URA3/ura3&lt;/em&gt; regions. So removing selection means that you run the risk of losing the insert. Furthermore, it is possible for looping out to occur leaving the &lt;em&gt;URA3&lt;/em&gt; allele behind instead of the &lt;em&gt;ura3&lt;/em&gt; allele. So you can lose the vector even when selection is maintained (but this will depend on the exact nature of the mutation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More complex configurations are possible where the targetting sequence is separate from the selectable marker, and where digestion removes a whole chunk of the targetting sequence before transformation. So for example if the &lt;em&gt;TRP1&lt;/em&gt; gene was used for targetting a plasmid with the &lt;em&gt;URA3&lt;/em&gt; marker in a &lt;em&gt;TRP1 ura3&lt;/em&gt; strain you would get:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;chromosome...TRP1 fragment A...URA3+other YIp sequences...TRP1 fragment B...chromosome&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the resulting transformant is now Ura&lt;sup&gt;+&lt;/sup&gt; because of the integrated &lt;em&gt;URA3&lt;/em&gt; plasmid, but some &lt;em&gt;TRP1&lt;/em&gt; DNA is now missing (the DNA that was excised when the plasmid was digested) so the strain is &lt;em&gt;trp1&lt;/em&gt;. The appearance of this Trp&lt;sup&gt;-&lt;/sup&gt; phenotype indicates that the transformation has probably occurred by the pathway described.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case the inserted plasmid is much more stable because those two remaining fragments of &lt;em&gt;TRP1&lt;/em&gt; DNA are not identical, so there is no possibility of looping out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, if your transformant has the insert carrying the &quot;new gene&quot; flanked by a repeating sequence then it is unstable, otherwise it is ok to remove selection. In the first case, if the new gene is at all deleterious then there will be a strong selective pressure in favour of cells which have lost the insert. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Addendum&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can avoid using YIp plasmids altogether by integrating your new gene at any locus using long targetting primers, as shown in the Figure below. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Design primers to amplify your gene as usual, but synthesise them with 40 bp 5' extensions corresponding to two sequences at the extreme ends of the integration site (&lt;em&gt;URA3&lt;/em&gt; used here for illustration purposes). The resulting fragment can then be used in a transformation and will integrate at the &lt;em&gt;URA3&lt;/em&gt; site by homologous recombination, replacing the resident DNA. The advantage of using &lt;em&gt;URA3&lt;/em&gt; for this is that you can select for integrants as Ura&lt;sup&gt;-&lt;/sup&gt; cells by resistance to fluoorotic acid (FOA). Although you can probably select directly for this, I have always co-transformed the fragment together with another selectable plasmid (&lt;em&gt;LEU2&lt;/em&gt;, &lt;em&gt;TRP1&lt;/em&gt; etc., but not a CEN plasmid) Then your e.g. Leu&lt;sup&gt;+&lt;/sup&gt; transformants can be screened for those that have also become FOA&lt;sup&gt;R&lt;/sup&gt;. This co-transformation happens at quite high frequency because the cells that do take up DNA take up a lot of it. Once you remove selection for the co-transforming plasmid it will soon get lost, leaving you with a clean non-reverting integrant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's been a while since I did this sort of thing - probably there are even smarter methods around now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/avG9U.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-09-30T18:10:49.900" LastActivityDate="2012-09-30T18:10:49.900" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3725" PostTypeId="2" ParentId="3721" CreationDate="2012-09-30T10:43:18.960" Score="3" Body="&lt;p&gt;Yeast integrating plasmids are known to be stable, even in absence of a selective medium but can revert like most homologous recombination plasmids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quoting from the book &lt;em&gt;Yeast Gene Analysis (pg476)&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;YIps are generally more stable than YRp or YEp plasmids. As a result&#xA;  it is safe to grow most YIp-bearing strains in rich media, although it&#xA;  is good practice to store them under selective conditions. The&#xA;  stability of YIp-bearing strains depends on the nature of the&#xA;  integration event. For example, if the YIp generates a tandem repeat&#xA;  upon integration into the genome, this can  revert to wild-type by an&#xA;  intramolecular homologous recombination event.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;-&gt; hence use markers regularly and frequently.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sources&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mick F. Tuite, Yeast Gene Analysis Vol 26 (Academic Press, 1998 ) p.476&lt;/p&gt;&#xA;" OwnerUserId="1450" LastActivityDate="2012-09-30T10:43:18.960" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3726" PostTypeId="2" ParentId="3720" CreationDate="2012-09-30T13:42:50.087" Score="2" Body="&lt;p&gt;I'm not sure about the first developmental stages but, given you already have hundreds of cells with slightly different physiology, the next developmental stages like dev. of neural tube happen through excretion of &lt;strong&gt;translation factors&lt;/strong&gt; and &lt;strong&gt;growth factors&lt;/strong&gt; in several cells. Each of those cells that are in a region where more than one excretion overlaps get a higher dose than the others. This is the signal for the cell to differentiate into another type, by changing its physiology. Such factor excretions are important events, and the genes encoding for the factors are evolutionally highly conserved (so called &lt;strong&gt;homeobox&lt;/strong&gt; proteins).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this has nothing to do with mitosis. The newly divided cell does not decide on its own but reacts to a stimulus, like skin cells develop into skin cells because they are on the outside of the cell ball. Excreted factors do the fine tuning.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-09-30T13:42:50.087" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3727" PostTypeId="2" ParentId="3686" CreationDate="2012-09-30T13:47:27.297" Score="8" Body="&lt;p&gt;The main problem is that Mad Cow disease is not caused by a &quot;normal&quot; pathogen but by a &lt;a href=&quot;http://en.wikipedia.org/wiki/Prion&quot; rel=&quot;noreferrer&quot;&gt;prion&lt;/a&gt;, a protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Traditionally, disease causing agents can be classified into viruses, bacteria, fungi, and parasites. Bacteria, fungi and parasites are all living organisms, alive in the traditional sense. It is, therefore, possible to design drugs that kill them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Viruses are trickier, while &lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=are-viruses-alive-2004&amp;amp;page=2&quot; rel=&quot;noreferrer&quot;&gt;not really alive&lt;/a&gt; in the traditional sense, they still have to make copies of their genetic material (DNA, or RNA in the case of &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_virus&quot; rel=&quot;noreferrer&quot;&gt;many viruses&lt;/a&gt;) in order to cause infection. Therefore, drugs like &lt;a href=&quot;http://en.wikipedia.org/wiki/Ganciclovir&quot; rel=&quot;noreferrer&quot;&gt;ganciclovir&lt;/a&gt; that stop the formation of viral DNA can be an effective treatment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prion based diseases such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Bovine_spongiform_encephalopathy&quot; rel=&quot;noreferrer&quot;&gt;Mad Cow disease&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Creutzfeldt%E2%80%93Jakob_disease&quot; rel=&quot;noreferrer&quot;&gt;Creutzfeldt–Jakob disease&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Kuru_%28disease%29&quot; rel=&quot;noreferrer&quot;&gt;Kuru&lt;/a&gt;, are not caused by a classical infectious agent but by a simple protein, a prion. Prions are misfolded versions of proteins already present in the host's body. When a prion interacts with the host protein, it causes this protein to adopt the same, misfolded, state as the prion. Protein function depends directly on the protein's structure, the way it is folded in three dimensional space. Therefore, the misfolded protein can no longer carry out its physiological role and disease symptoms occur. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, since the prion is just a protein, one single molecule, there is no essential life process that we can disrupt. We have to attack them using chemical agents that target the prion while not affecting the healthy, correctly folded, host protein. This is very hard to do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood%E2%80%93brain_barrier&quot; rel=&quot;noreferrer&quot;&gt;blood-brain barrier&lt;/a&gt; mentioned by Larry_Parnell is another problem. Briefly, the BBB, is a kind of fence that only allows certain of the various items circulating in the blood stream to enter the organism's brain. This is a wonderful defensive feature but it makes it much harder to design drugs that can enter the brain and target pathogens found there. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2012-09-30T13:47:27.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3729" PostTypeId="2" ParentId="3711" CreationDate="2012-09-30T14:26:26.663" Score="5" Body="&lt;p&gt;&lt;strong&gt;No.&lt;/strong&gt; The influence of &lt;a href=&quot;http://en.wikipedia.org/wiki/Dose%E2%80%93response_relationship&quot;&gt;dose–response relationship&lt;/a&gt; on toxicity is one of the fundamental properties of (bio)chemistry, and follows directly from the fact that concentration influences the &lt;a href=&quot;http://en.wikipedia.org/wiki/Reaction_rate&quot;&gt;reaction rate&lt;/a&gt;: a chemical reaction between two or more agents is a stochastic process where agents have a certain chance of interacting based on physical proximity (and other factors). The higher the dose, the higher the chance of two agents meeting, and a reaction taking place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has two interesting consequences:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Homeopathy doesn’t work.&lt;/li&gt;&#xA;&lt;li&gt;Although not all substances show a clear dose–response curve (simply because they are always reactive no matter their dose), toxicological studies which fail to show a dose–response relationship are met with scepticism. A recent example of this is &lt;a href=&quot;http://www.forbes.com/sites/henrymiller/2012/09/25/scientists-smell-a-rat-in-fraudulent-genetic-engineering-study/&quot;&gt;the GMO toxicity study undertaken by the French scientist Séralini&lt;/a&gt;. One of the many flaws in this paper cited by other scientists was precisely this lack of dose–response relationship.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="166" LastActivityDate="2012-09-30T14:26:26.663" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="3730" PostTypeId="1" AcceptedAnswerId="5201" CreationDate="2012-09-30T14:31:57.223" Score="2" ViewCount="203" Body="&lt;p&gt;For a head fixed animal, how stable is the current state-of-the-art whole cell recording from a cortical neuron? The animal's breathing, and heart beat must move the neuron relative to the recording device quite a bit, and I was wondering how stable the seal would be. How long can one hold a cell, and what is the typical quality of such recording?&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2012-11-11T17:47:24.297" Title="How stable is in vivo whole cell patch clamping?" Tags="&lt;neuroscience&gt;&lt;electrophysiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3731" PostTypeId="1" CreationDate="2012-09-30T15:38:41.347" Score="11" ViewCount="265" Body="&lt;p&gt;I've read about anecdotal evidence that human brain has a fairly good internal clock that can be used to judge the amount of time that has passed. &lt;strong&gt;I'm wandering if there are any mechanisms in the human brain by which the brain can make adjustments to biological processes, based on the expectation of getting so many hours of sleep in the upcoming night.&lt;/strong&gt; In this case, an alarm clock is not used.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, a person typically sleeps for 8 hours a night. On one day, that person realizes that he/she will sleep for only 5 hours that night, has there been any studies that demonstrate that the person's sleep would be &quot;different&quot; from the regular sleep? &lt;strong&gt;Will the person's sleep on that night be just a &quot;cut short&quot; version of regular sleep, or will the sleep be restructured to accomodate sleep time restriction?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example a person's normal sleep cycle is 90 minutes long, so in 8 hours there would be about 5 complete cycles. Would there be any observable adjustments to the sleep cycle length or the amount of deep/REM sleep within the cycle, if a person expects to sleep only 5-6 hours or 10+ hours?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-03-18T04:44:37.640" Title="Does sleep in humans re-structure based on the expected sleep time?" Tags="&lt;human-biology&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3732" PostTypeId="2" ParentId="3718" CreationDate="2012-09-30T15:45:23.177" Score="0" Body="&lt;p&gt;I can tell you generally how to go about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Go to table S2 from the paper and download the spreadsheet.  You can search RCSB for each gene symbol. There are 2400 individual genes and there are probably over 1000 alias genes, so that's a lot of searching.  You can do this en masse by using a python script and a library like BioPython, or you can put each symbol into the search box at RCSB.org and see if a structure comes up.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can and should look over that table for phenotypes you think you can actually work with.  Many of the phenotypes in the paper might require a microscope or a good deal of experience with arabidopsis.  E.g. &quot;Embryo defective; Preglobular / Globular&quot; what does that mean?  You can also write the authors for advice but they might be too busy to get back to you.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cutting down your search like this before you do it would be very helpful.  The number of genes with both an accessible phenotype and a structure will probably be a relatively small list (50?). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Relatively few arabidopsis protein structures are solved, so you will have to do homology modeling - aligning any protein structure sequence(s) you find with the A. thaliana sequence, and deciding where the active site or disruptive mutation would be in the plant gene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example: CHY1(CoA Ester Hydrolase) must be solved - searching for &quot;CoA Ester Hydrolase&quot; at rcsb I find a three structures.  the human structure 2DQZ has a lot of annotation associated with it.  This class of enzymes has been studied for a while, so the active site probably has been studied.  A pubmed search should give a lead on where the active site research has been done.  using BLAST to align the structures to the arabidopsis gene or to all other CoA Ester Hydrolases would be an important step to take too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-09-30T15:51:42.343" LastActivityDate="2012-09-30T15:51:42.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3734" PostTypeId="1" AcceptedAnswerId="3736" CreationDate="2012-09-30T17:43:50.247" Score="4" ViewCount="367" Body="&lt;p&gt;The potato appears to propagate by growing an 'eye'/'bud' which eventually grows into a new plant. So there would probably be single representative of the potato species in the world with all others being genetically identical. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet wikipedia indicates there are several closely related species of the potato; apparently as a result of selective breeding. To my understanding (which is probably wrong) there is only a single potato that grows the eyes without the need for a second parent - so there should probably only be the same genes repeated in each potato/plant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What am I missing here? Why are there multiple varieties of the potato? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2012-09-30T17:48:59.663" LastActivityDate="2012-10-03T09:59:01.547" Title="How are there multiple varieties of the potato?" Tags="&lt;genetics&gt;&lt;vegetable&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3736" PostTypeId="2" ParentId="3734" CreationDate="2012-09-30T23:34:47.830" Score="5" Body="&lt;p&gt;You're missing that potatoes also reproduce sexually. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They're flowering plants, and they produce seeds that are not genetically identical to their parent plants. &lt;/p&gt;&#xA;" OwnerUserId="1006" LastActivityDate="2012-09-30T23:34:47.830" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3737" PostTypeId="1" AcceptedAnswerId="3740" CreationDate="2012-10-01T00:31:21.097" Score="41" ViewCount="78316" Body="&lt;p&gt;I've read many years ago in books, that the brain has no nerves on it, and if someone was touching your brain, you couldn't feel a thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just two days before now, I had a very bad migraine, due to a cold. It's become better now, but when I had it I felt my head was going to literally split in half, as the pain was literally coming from my brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it lead me to the question: How come people can get headaches if the brain has no nerves?&lt;/p&gt;&#xA;" OwnerUserId="1470" LastEditorUserId="1470" LastEditDate="2012-10-02T00:30:24.007" LastActivityDate="2014-09-09T02:38:51.020" Title="If the brain has no pain receptors, how come you can get a headache?" Tags="&lt;neuroscience&gt;&lt;human-anatomy&gt;&lt;brain&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="3739" PostTypeId="1" AcceptedAnswerId="3779" CreationDate="2012-10-01T04:33:20.420" Score="9" ViewCount="293" Body="&lt;p&gt;People who are overweight and wish to lose weight, often do so because they are concerned about looking too big.  Their increased size is attributed to an increased volume of fat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When people try to lose weight however, they often quantify their goals in terms of weight, not volume.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is, is the &lt;strong&gt;volume&lt;/strong&gt; of an adipocyte cell always directly proportional to the &lt;strong&gt;weight&lt;/strong&gt; of the fat stored within the cell?   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, what factors would increase/decrease the size of the adipocyte cell for a given mass of stored fat?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2012-10-03T18:34:01.603" Title="Adipocyte Density" Tags="&lt;human-biology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3740" PostTypeId="2" ParentId="3737" CreationDate="2012-10-01T09:09:52.467" Score="35" Body="&lt;p&gt;Brain, indeed, cannot feel pain, as it lacks pain receptors (nociceptors). However, what you feel when you have a headache is not your brain hurting -- there are plenty of other areas in your head and neck that do have nociceptors which can perceive pain, and they literally cause the headaches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In especially, many types of headaches are generally thought to have a neurovascular background, and the responsible pain receptors are associated with blood vessels. However, the pathophysiology of migraines and headaches is still poorly understood.&lt;/p&gt;&#xA;" OwnerUserId="1435" LastActivityDate="2012-10-01T09:09:52.467" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3741" PostTypeId="1" AcceptedAnswerId="3744" CreationDate="2012-10-01T13:01:02.303" Score="7" ViewCount="1011" Body="&lt;p&gt;I have been reading about Townes and Holtfreter's work in 1955, in which cells are dissociated from a blastocyst in an alkaline solution then mixed together and spontaneously reaggregates based on type, so epidermal cells around the outside and neural plate cells in the middle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand enough about cell adhesion to understand why the cells will seem to attract cells of their own type, but would like to know how they can initially detect what to become and where they are needed in a specialised form, without something acting like a brain telling them what to become and where to go.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the selection from the available types is random, as I suspect, what happens to blastocysts with too much epidermal tissue or vice versa? I'm struggling to imagine how organisms like this can develop without something taking the lead and actively coordinating what goes where.&lt;/p&gt;&#xA;" OwnerUserId="1474" LastEditorUserId="22057" LastEditDate="2016-05-23T13:37:37.633" LastActivityDate="2016-05-23T17:45:40.070" Title="What determines the fate of a cell with respect to differentiation?" Tags="&lt;cell-biology&gt;&lt;development&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3742" PostTypeId="1" CreationDate="2012-10-01T14:40:46.220" Score="2" ViewCount="65" Body="&lt;p&gt;I would like to know what are currently used methods for targeted deletion of genomic regions in mammalian organisms or cell lines. I have heard of Zinc-Finger nucleases as a recent genetic engineering method, but I don't know if there are other methods, more efficient or better tailored, for the deletion of specific regions.&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2012-10-02T12:58:20.223" Title="methods for targetted deletion of genomic regions?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3743" PostTypeId="1" CreationDate="2012-10-01T15:39:42.177" Score="3" ViewCount="241" Body="&lt;p&gt;I'm not sure if this is the right place to ask this but Biology seemed to fit best.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm trying to find out what frequencies the brain responds to best while sleeping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for this is recently I attended a lecture where it was stated that the brain hears low frequencies/deep noises better, meaning fire alarms for example might not be as effective as we think.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However I remember there was an episode of The Big Bang Theory where they said high pitch noises are heard better while sleeping as a built in response to, for example, a baby crying. Now I know this is just a TV show but I presume they must have some basis for the remark since they do have science advisors, it also just seems to make more sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know which is correct or better yet can point me in the direction of some research to help.&lt;/p&gt;&#xA;" OwnerUserId="1476" LastActivityDate="2014-06-19T18:45:10.753" Title="Brain response frequencies while sleeping" Tags="&lt;brain&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3744" PostTypeId="2" ParentId="3741" CreationDate="2012-10-01T15:51:05.350" Score="7" Body="&lt;p&gt;Cell differentiation, cell fate and cell mapping is an interplay of accessible evolutionary strategies/programmes and responses to dynamic environmental cues such as specialized hormones (e.g. morphogens) and physical parameters and constraints. That is putting it very broadly. It is a complex issue, if L. Wolpert's PLOS assays are any indication. I compiled a few links to get you started.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, reappraising the topic of your cited classical experiment are &lt;em&gt;R.Moore et al&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The classical cell sorting experiments undertaken by Townes and&#xA;  Holtfreter described the intrinsic propensity of dissociated embryonic&#xA;  cells to self-organize and reconcile into their original embryonic&#xA;  germ layers with characteristic histotypic positioning. Steinberg&#xA;  presented the differential adhesion hypothesis to explain these&#xA;  patterning phenomena.....&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(Source: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755612/&quot;&gt;Robert Moore, Kathy Q. Cai, Diogo O. Escudero, Xiang-Xi Xu, &lt;em&gt;Cell Adhesive Affinity Does Not Dictate Primitive Endoderm Segregation and Positioning During Murine Embryoid Body Formation&lt;/em&gt;, Genesis. 2009 September; 47(9): 579–589&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding: &lt;strong&gt;...without something taking the lead and actively coordinating...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a hunch that you are not talking about complexity, attractors and polarity, I would like to share a few words. You may completely disregard them if you'd like.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My personal experience (from my country) is that few biologists delve into &quot;that&quot; branch of EvoDevo, because a profound understanding involves calculus, modeling and a knack for theoretical biology. Yet, afaik few struggled comprehending the evolutionary logic of making an organism based on &lt;em&gt;Albert's&lt;/em&gt; book chapters alone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;See&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Reaction-diffusion&quot;&gt;Reaction–diffusion system&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_fate_determination&quot;&gt;Cell fate determination&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fate_mapping&quot;&gt;Fate mapping&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Asymmetric_cell_division&quot;&gt;Asymmetric cell division&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Pattern_formation&quot;&gt;Pattern formation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Alberts Molecular Biology of the Cell describes this very well (can be accessed online for free)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I personally recommend &lt;em&gt;G.Müller's&lt;/em&gt; authored/coauthored papers:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(open access)&#xA;&lt;a href=&quot;http://homepage.univie.ac.at/gerhard.mueller/publications-papers.html&quot;&gt;http://homepage.univie.ac.at/gerhard.mueller/publications-papers.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Disclaimer&lt;/strong&gt;: I am not specialized in the field of EvoDevo or Theoretical Biology.&lt;br&gt;&#xA;Views expressed here are my own.&lt;/p&gt;&#xA;" OwnerUserId="1450" LastActivityDate="2012-10-01T15:51:05.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3745" PostTypeId="2" ParentId="3737" CreationDate="2012-10-01T16:07:07.753" Score="2" Body="&lt;p&gt;That the brain doesn't have pain receptors has somewhat drifted into the corpus of general knowledge, perpetuated by pamphlets, books and documentaries.&lt;br&gt;&#xA;Your question caused me to look up wikipedia. &lt;a href=&quot;http://en.wikipedia.org/wiki/Headache&quot; rel=&quot;nofollow&quot;&gt;Citing&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A headache or cephalalgia is pain anywhere in the region of the head&#xA;  or neck. It can be a symptom of a number of different conditions of&#xA;  the head and neck. The brain tissue itself is not sensitive to pain&#xA;  because it lacks pain receptors. Rather, the pain is caused by&#xA;  disturbance of the pain-sensitive structures around the brain. Nine&#xA;  areas of the head and neck have these pain-sensitive structures, which&#xA;  are the cranium (the periosteum of the skull), muscles, nerves,&#xA;  arteries and veins, subcutaneous tissues, eyes, ears, sinuses and&#xA;  mucous membranes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1450" LastActivityDate="2012-10-01T16:07:07.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3746" PostTypeId="1" CreationDate="2012-10-01T19:49:14.703" Score="5" ViewCount="348" Body="&lt;p&gt;As discussed in &lt;a href=&quot;https://biology.stackexchange.com/questions/935/why-is-polyploidy-lethal-for-some-organisms-while-for-others-is-not&quot;&gt;Why is polyploidy lethal for some organisms while for others is not?&lt;/a&gt;, polyploidy is normally lethal in mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, two species of Octodontidae (South American rodents), are tetraploid due to a recent doubling of all chromosomes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Plains_Viscacha_Rat&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Tympanoctomys barrerae&lt;/em&gt;&lt;/a&gt;: 4x = 102&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Golden_Vizcacha_Rat&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Pipanacoctomys aureus&lt;/em&gt;&lt;/a&gt;: 4x = 92 (apparently some chromosomes were lost after the polyploidy event)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://www.cricyt.edu.ar/institutos/iadiza/ojeda/grecia%202000.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;the paper discussing &lt;em&gt;T. barrerae&lt;/em&gt;&lt;/a&gt;, the first of these tetraploid rodents discovered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the Wikipedia article, both are believed descended from the same species, &lt;a href=&quot;http://en.wikipedia.org/wiki/Viscacha_rat&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Octomys mimax&lt;/em&gt;&lt;/a&gt; (or possibly now-extinct close relatives thereof), which has 2x = 2n = 56 chromosomes, half those of &lt;em&gt;T. barrerae&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What was special about &lt;em&gt;Octomys&lt;/em&gt; that allows it to survive polyploidy, unlike most mammals?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interesting:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The sperm head of Tympanoctomys is is by far the largest naturally occurring in mammals, and its size is causally related to the double genome size it has to accomodate.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1202" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2012-10-02T12:36:36.973" Title="Why was polyploidy not lethal in certain octodontid rodents?" Tags="&lt;evolution&gt;&lt;chromosome&gt;&lt;polyploidy&gt;&lt;rodents&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3748" PostTypeId="2" ParentId="3739" CreationDate="2012-10-02T00:19:08.107" Score="3" Body="&lt;p&gt;Adipocytes (fat cells) change in size quite a bit with nutrient and particularly fat uptake. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take a look at this &lt;a href=&quot;http://www.jlr.org/content/43/6/986.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper&lt;/a&gt; which is about identifying adipocyte sizes from histological slides.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rwIPb.gif&quot; alt=&quot;figure 1 shows how the rat fat cells were swollen after a high fat diet. &quot;&gt;  In the cross section they are sometimes 10+ times larger.  When you add depth to the equation there is quite a bit of range in the fat cell must be substantial.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, white fat cells do multiply and it is thought that when &lt;a href=&quot;http://www.imamu.edu.sa/Scientific_selections/abstracts/Biology/The%20biology%20of%20white%20adipocyte%20proliferation.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;fat cells are engorged, they secrete growth factors that encourage adipocyte division&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So its not just the adipocytes getting larger, but there are also more fat cells over time if there is extra fat storage needed.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its particularly of note that Insulin like growth factor 1 (IGF-1) is one of the factors identified that signals adipocytes to divide, coupling fat tissue multiplication with metabolic factors just as you might expect, possibly participating in the development of insulin resistance as the tissue expands.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-10-02T17:07:10.910" LastActivityDate="2012-10-02T17:07:10.910" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3749" PostTypeId="2" ParentId="3711" CreationDate="2012-10-02T03:47:59.273" Score="1" Body="&lt;p&gt;I think the best answer is right now would be &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Probably no, but we're not certain&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question of non-monotonic dose-response is still being discussed and debated. You will find a good example of this at &lt;a href=&quot;http://www.efsa.europa.eu/en/events/event/120614.htm&quot; rel=&quot;nofollow&quot;&gt;EFSA&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1006" LastActivityDate="2012-10-02T03:47:59.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3750" PostTypeId="2" ParentId="3746" CreationDate="2012-10-02T11:21:06.460" Score="2" Body="&lt;p&gt;Actually, that is not what is discussed in the question you linked to. The following is a quote from the very comprehensive accepted answer (emphasis mine):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Polyploidy arises easily in both animals and plants, but reproductive&#xA;  strategies might prevent it from propagating in certain circumstances,&#xA;  &lt;strong&gt;rather than any reduction in fitness resulting from the genome&#xA;  duplication&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In fact, try rereading that answer and the references therein, it answers your general question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a popular theory (mostly accepted) that there have been whole genome duplication events (WGDs) in the vertebrate ancestry. If true, it means that all mammals are the descendents of polyploid ancestors. For a very nice review of WGDs in vertebrate evolution, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov.gate1.inist.fr/pubmed/19652647&quot; rel=&quot;nofollow&quot;&gt;here [1]&lt;/a&gt;. Octomys is simply the only &lt;em&gt;known&lt;/em&gt; mammal with a more recent WGD event. As for what makes it special (taken from&lt;a href=&quot;http://www.ncbi.nlm.nih.gov.gate1.inist.fr/pubmed?term=18758856&quot; rel=&quot;nofollow&quot;&gt; [2]&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our data demonstrate that parental-specific silencing of at least one&#xA;  gene and normal X chromosomal dosage mechanism are conserved in the&#xA;  tetraploid genome. We hypothesize a concerted action of genetic and&#xA;  epigenetic mechanisms during the process of functional diploidization&#xA;  of this tetraploid genome.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov.gate1.inist.fr/pubmed/19652647&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;) Van de Peer Y, Maere S, Meyer A., The evolutionary significance of ancient genome duplications., &lt;em&gt;Nat Rev Genet.&lt;/em&gt; 2009 Oct;&lt;strong&gt;10&lt;/strong&gt;(10):725-32. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov.gate1.inist.fr/pubmed?term=18758856&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;) Bacquet C, &lt;em&gt;et al.&lt;/em&gt;, Epigenetic processes in a tetraploid mammal, &lt;em&gt;Mamm Genome&lt;/em&gt;. 2008 Jun;&lt;strong&gt;19&lt;/strong&gt;(6):439-47. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-10-02T12:36:36.973" LastActivityDate="2012-10-02T12:36:36.973" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3751" PostTypeId="2" ParentId="3742" CreationDate="2012-10-02T12:58:20.223" Score="4" Body="&lt;p&gt;I can only provide you with a few pointers from memory, as an ad hoc search for &quot;&lt;code&gt;review of dna cutting techniques&lt;/code&gt;&quot; was not prolific.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please consider the provided information with precaution and only for pointers to help you do literature research.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;cre/lox system and variants (best known), belong to SSRs (Site specific recombinases)&lt;/li&gt;&#xA;&lt;li&gt;various Restriction enzyme based systems (see Homing Endonucleases)&lt;/li&gt;&#xA;&lt;li&gt;meganuclease based tools&lt;/li&gt;&#xA;&lt;li&gt;aptamer based&lt;/li&gt;&#xA;&lt;li&gt;based on hybridizing n-mer probes which yields a reactive species nicking the DNA at the probe's-site when introduced to certain chemicals such as oxoacids&lt;/li&gt;&#xA;&lt;li&gt;light twizzers and lasers /purely proof of concept (perhaps already commercialized?)&lt;/li&gt;&#xA;&lt;li&gt;ZFNs and variants / protein based-probes . &lt;a href=&quot;http://en.wikipedia.org/wiki/Zinc_finger_nuclease&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Zinc_finger_nuclease&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are definitely published reviews on this exhaustive topic, notwithstanding the dozens of books. &lt;br&gt;&#xA;I would estimate that there are at least 10 commercial methods, and almost 100 methods in total when theoretical and proof-of concepts are included.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Naturally (literally!), the vast majority of methods will be based on the noncovalent interaction of an n-mer &quot;homing construct&quot;/probe a)attached to an nuclease or b)an&#xA;attachment site for a nuclease or c)participate in the reaction for the formation of a reactive chemical species to break the sugar-phosphate backbone.&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would speculate that most other methods are likely not practical in terms of either efficiency and/or affordability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To learn about the applicability of the respective methods relating to your field of research, and be provided with an overview of the pros and cons of the methods, you will still need to find a good review paper.&lt;/p&gt;&#xA;" OwnerUserId="1450" LastActivityDate="2012-10-02T12:58:20.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3753" PostTypeId="2" ParentId="3711" CreationDate="2012-10-02T15:36:34.950" Score="21" Body="&lt;p&gt;&lt;strong&gt;Yes.&lt;/strong&gt; Taking antibiotics (and by extension antivirals and antineoplastics) at low doses is dangerous, as this creates an evolutionary pressure to evolve antibiotic resistance (or rather, &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0017549&quot;&gt;incorporate through horizontal gene transfer&lt;/a&gt;). This is dangerous because an infection resulting from these bacteria will then be harder to treat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the paper &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1560030/&quot;&gt;Experimental evolution of resistance to an antimicrobial peptide&lt;/a&gt;&quot;, Perron et al. gave &lt;em&gt;E. coli&lt;/em&gt; the chance to evolve resistance against a novel antibiotic. When given a high dose initially, most bacteria died. When exposed to low doses, the bacteria evolved resistance in 600 to 700 generations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the same reason it is strongly advised to finish a course of antibiotics even after symptoms fade. &lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-10-02T15:36:34.950" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3754" PostTypeId="2" ParentId="3739" CreationDate="2012-10-02T16:28:24.687" Score="4" Body="&lt;p&gt;Is the volume of an adipocyte proportional to the mass of fat that it stores?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer is: yes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since fat is stored in a lipid droplet within the adipocyte, it is already in the densest form possible. In other words there is no way to make the stored fat more compact, so that a given mass of stored fat takes up less volume.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Response to comment from Chris:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think you are perhaps being a little pedantic here. Anyway the graph below conveys my view, together with your refinement. So yes, adipocyte volume changes in proportion to mass of fat stored. (The line on my graph should be at 45 degrees, but I drew it by hand so it may be a little out.) There is no way to escape the increase in volume when fat is stored.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Zt3EF.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-10-03T16:27:46.357" LastActivityDate="2012-10-03T16:27:46.357" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3755" PostTypeId="1" CreationDate="2012-10-02T17:30:34.740" Score="9" ViewCount="11782" Body="&lt;p&gt;This question arises because I saw that monocytes and leukocytes are commonly called 'mononuclear cells' in the scientific literature. The implication of course being that other immune sub-types are multi-nuclear!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know of granulocytes (e.g. neutrophils) that are classed as 'polymorphonuclear' because their nuclei are segmented, and can alter their shapes, and muscle cells that fuse together to form one long cell (muscle fiber) with multiple nuclei. What other examples of multi-nucleated cells are there?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am also interested in the advantages gained by cells having multiple (or segmented) nuclei?&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2018-12-08T14:02:44.810" Title="Multi-nucleated cells: advantages and examples?" Tags="&lt;cell-biology&gt;&lt;immunology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3757" PostTypeId="2" ParentId="3741" CreationDate="2012-10-02T23:12:50.443" Score="3" Body="&lt;p&gt;I would like to add to Lo Sauer's nice answer but give a slightly different perspective.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you referred to as the &quot;brain&quot; of the cell, is mostly its regulatory program. An abstract way to think about the regulatory program is like a computer, or mathematical function, which gets input (in the form of signal molecules inside and outside the cell) and calculates an output (behavior - which genes/proteins to activate, for example) based on this input. This is usually how cells make decisions, both in differentiation and when reacting to the environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course the really interesting part is how the regulatory program is implemented. It seems that most of it is encoded in the DNA, although there is also a significant role for epigenetics factors (non-DNA factors that are inherited from the zygotes). As you can imagine this regulatory program is highly complex and is being studied by many groups, mostly using genomic experimental and computational techniques. It is currently far from being understood at a comprehensive level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read about specific simple examples in some of the places Lo Sauer mentioned, for example Drosophila embryo segmentation/pattern formation.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2012-10-02T23:12:50.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3758" PostTypeId="1" AcceptedAnswerId="3759" CreationDate="2012-10-03T03:20:43.770" Score="10" ViewCount="919" Body="&lt;p&gt;A few years back when I was reading The Selfish Gene by Richard Dawkins, there's this short passage where he theorizes about a way to achieve an increased lifespan through controlled evolution.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The theory goes like this: we don't tend to have medical problems until after 30 because we all tend to reproduce before that age.  Thus, people who tended to die before 30 never passed on their dying-prone genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if you didn't let people reproduce before a age X (where X starts at 30) and then slowly move that age up, you could use evolution to increase lifespan.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ethical issues notwithstanding, is there any reason why this wouldn't work?  If it would work, how long do you think you would need to sit at each value of X?  How far apart do you think each value could be?  Finally, how many generations, using this technique, would it take before someone would live to be 1000 naturally?&lt;/p&gt;&#xA;" OwnerUserId="1480" LastActivityDate="2016-09-30T09:31:18.400" Title="Is it possible to increase lifespan through controlled evolution?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3759" PostTypeId="2" ParentId="3758" CreationDate="2012-10-03T03:46:16.357" Score="13" Body="&lt;p&gt;I think this would probably work.  The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745839/&quot; rel=&quot;noreferrer&quot;&gt;grandmother effect&lt;/a&gt;, which is one of the main theories for human longevity after fertility might indicate that human lifespan would increase if the children come later.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just have to disclaim here: We will never do this.  Many unthinkable consequences would result...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you simply forbid anyone to have children before they are 40 or 45 (fertility doesn't drop until age 35 or so), forbid invitro fertilization and medical assistance to conception we would probably be looking at a prolonged lifespan.  Infertility rates in women at age 40 are not clear, but one estimate is that &lt;a href=&quot;http://www.babycentre.co.uk/preconception/activelytrying/ageandfertility/&quot; rel=&quot;noreferrer&quot;&gt;40% of women can have children at 40 years of age&lt;/a&gt;.  If we want to seen an effect early, we would push the age up a year or two.  Forbidding in vitro fertilization and other medical assistance to offspring we could look like a 80-90% cut of people - lots of people would never have children.  This might make people unhappy an destabilize the social fabric.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its not clear how long this would take.  The generation time would go to 40 years from about 20 now - 40 to get to childbearing age, but results would take 80 years - when we find out how the children would fare.  Given the C elegans longevity experiments and the fact that we are starting with 8 billion people, we probably would find some great late age breeders who may also live long.  But for the longevity phenotype to set in it would take several generations as we are looking for an indirect effect: later breeding causing longevity.  The &lt;a href=&quot;http://en.wikipedia.org/wiki/Domesticated_silver_fox&quot; rel=&quot;noreferrer&quot;&gt;Belyaev experiments&lt;/a&gt; which produced domesticated foxes by strong selective breeding took some 30ish generations to complete though &lt;a href=&quot;http://cbsu.tc.cornell.edu/ccgr/behaviour/History.htm&quot; rel=&quot;noreferrer&quot;&gt;they saw a significant effect in just 10&lt;/a&gt;.  It could take a similar numbers of selection rounds in this cse.  4-500 years. Ethical issues aside, this is why most geneticists study flies.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There would also be a lot of other negative socioeconomic consequences to this thought experiment.  One good thing is that the population of the earth would plummet - many people would be eliminated from the gene pool, though eldercare would be a major part of the world workforce.  Lots of work, not clear who is going to pay for it, but low unemployment and low low wages may result.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XASqN.jpg&quot; alt=&quot;Why do I feel like this guy?&quot;&gt; &#xA;So you see Mister President, this is quite a distinct possibility, though some sacrifices would have to be made. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The science of human eugenics is not scientifically wrong, but selective animal breeding and lab experiments don't usually evaluate or care about the consequences of large peturbations in the gene pool. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You would also have a lot more autism and Downs syndrome and other congenital defects which tend to show up in offspring of older parents. These issues might improve with application of biotechnology which screens weak sperm and eggs without ruining the effect you are looking for, maybe not.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since we are selecting &lt;em&gt;against&lt;/em&gt; fecundity, the human race could be dogged by fertility problems or chronic genetic diseases which the genetic contribution of some of the more robust people in the gene pool being removed and the tendency to such age-related birth defects might not go away given the drastic selection pressure we are putting on the gene pool. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other consequences you might not expect; some physical traits associated with longevity and prolonged fertility would cause us to look more alike and not necessarily in a good way.   &lt;a href=&quot;http://www.cracked.com/article_19964_5-scientific-reasons-youre-better-off-being-unattractive.html&quot; rel=&quot;noreferrer&quot;&gt;Browse the internet&lt;/a&gt;; its probable that we would get shorter and possibly uglier?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many more direct ways to increase the human lifespan - better diet, exercise, the elimination of poverty, vaccinations, proper medical care, access to clean drinking water and a lower birth rate (fewer children not later) all are known to directly effect longevity, having more than doubled the human life expectancy in the past few hundred years. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-10-03T19:23:55.690" LastActivityDate="2012-10-03T19:23:55.690" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3761" PostTypeId="2" ParentId="3734" CreationDate="2012-10-03T09:28:08.623" Score="2" Body="&lt;p&gt;Well, &lt;strong&gt;uvesten&lt;/strong&gt; is correct in saying that potatoes are flowering plants and as such they can reproduce sexually. However, as &lt;strong&gt;everyone&lt;/strong&gt; mentions potatoes can, like many plants, reproduce asexually by putting out clones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since clones are (by definition) genetically identical to the parent plant, this would seem to rule out the possibility of producing different varieties (or even species) from clonal propagation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But! &lt;a href=&quot;http://dx.doi.org/10.1016/j.cub.2011.07.002&quot; rel=&quot;nofollow&quot;&gt;this very interesting study by Jiang et al.&lt;/a&gt; looked at &lt;em&gt;Arabidopsis&lt;/em&gt; lineages (Brassica family). They found:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;in vitro regeneration of Arabidopsis plants results in a high frequency of heritable phenotypic variation &quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That is, regenerant Arabidopsis plant lineages displayed extensive phenotypic somaclonal variation - the cloned &quot;offspring&quot; were &lt;em&gt;not genetically identical&lt;/em&gt;. They attributed most of this genetic variation to an increased base substitution frequency in the regenerant offspring but there may also be unknown epigentic factors as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Jiang et al. summarise:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... somatic mutation rates are characteristically higher than germline rates in multicellular organisms [26] and has important particular potential consequences for the evolution of plants, given that they frequently adopt life cycle strategies that involve regeneration from somatic tissues.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, perhaps some of the variation we see in plant species which commonly propagate asexually actually arose during this process and not via sexual reproduction ... ? This would be good news for houseplants which are nearly always propagated asexually.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I am not sure whether this extends to potatoes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.cub.2011.07.002&quot; rel=&quot;nofollow&quot;&gt;Jiang et al. 2011, Current Biology, 21, 1385, &lt;em&gt;Regenerant Arabidopsis Lineages Display a Distinct Genome-Wide Spectrum of Mutations Conferring Variant Phenotypes&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="81" LastEditDate="2012-10-03T09:59:01.547" LastActivityDate="2012-10-03T09:59:01.547" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3763" PostTypeId="1" AcceptedAnswerId="3766" CreationDate="2012-10-03T14:37:21.387" Score="5" ViewCount="706" Body="&lt;p&gt;I have a set of scaffolds from a genome assembly, and I want to align a collection of proteins from various species to it. I can do this using BLAST in two ways:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Create a BLAST database of the scaffolds, and run tblastn on it with&#xA;the proteins as the query.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Create a BLAST database of the proteins, and run blastx on it with&#xA;the scaffolds as the query.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Should both of these produce the exact same hits? Will there be any significant difference in running time between them? &lt;/p&gt;&#xA;" OwnerUserId="1481" LastActivityDate="2012-10-03T16:02:44.660" Title="Which way to run BLAST?" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3764" PostTypeId="1" CreationDate="2012-10-03T15:05:31.787" Score="3" ViewCount="83" Body="&lt;p&gt;&lt;strong&gt;Has the result of alpha-complementation ever happened via mutation through evolutionary time, and been preserved in modern day organisms?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, has a functional gene product ever been split or terminated by mutation, exhibit alpha-complementation, and has since been preserved as a quaternary protein? This could be found out by comparison of proteins in closely-related species, but don't know of any specific examples. Has such a thing ever happened?&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2019-07-10T15:21:21.113" Title="Preserved alpha complementation over evolutionary time?" Tags="&lt;evolution&gt;&lt;proteins&gt;&lt;protein-evolution&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3765" PostTypeId="1" CreationDate="2012-10-03T15:12:18.787" Score="4" ViewCount="63" Body="&lt;p&gt;A simple question that had occurred to me. Considering the small doubt of transcribed genes in both organelles, I would doubt it, but are there any known ribozymes strictly found in either mitochondria or chloroplasts?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;: Actually, I just thought of rRNA acting as a peptidyl transferase in mitochondrial ribosomes... Any other ideas?&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2014-10-21T05:10:01.497" Title="Are there any strictly chloroplast/mitochondrion-residing ribozymes?" Tags="&lt;rna&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3766" PostTypeId="2" ParentId="3763" CreationDate="2012-10-03T16:02:44.660" Score="4" Body="&lt;p&gt;Quick answer: use tblastn.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a general rule, when comparing two datasets using BLAST, it is recommended to use the larger of the two sets as the database and the smaller as queries. The main difference is one of computational time. Blast is optimized for large databases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are also likely to get different hits. Blast's e-value is calculated based on the size of the database, among other parameters. Roughly, the e-value answers the question: &quot;How many high scoring sequence pairs with X% of sequence identity and Y length would I expect to find in a database of size X by chance?&quot;. Your e-values could be artificially high if you use the protein sequences as a database. I am not sure about this, but there may also be differences in the way gap penalties are dealt with by tblastn and blastx. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, I would first try doing this using a tool specifically designed for the task. BLAST has no model for dealing with splicing and it is a pain to build gene models from BLAST results. To align protein sequences against genomic DNA I would use either &lt;a href=&quot;http://www.ebi.ac.uk/~guy/exonerate/&quot; rel=&quot;nofollow&quot;&gt;exonerate&lt;/a&gt; (with the p2g model) or &lt;a href=&quot;http://www.ebi.ac.uk/Tools/Wise2/&quot; rel=&quot;nofollow&quot;&gt;genewise&lt;/a&gt;. Both programs incorporate splicing models and will give you a decent prediction of the gene structure of your target genes. The following are extracts from each program's man page:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GENEWISE:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Genewise2 compares a protein sequence to a genomic DNA sequence,&#xA;  allowing for introns and frameshifting errors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;EXONERATE:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;exonerate is a general tool for sequence comparison.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;GAPPED ALIGNMENT OPTIONS&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;-m | --model &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;protein2genome&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This  model  allows  alignment of a protein sequence to genomic DNA.   This is similar to&#xA;                       the protein2dna model, with the addition of modelling of introns and intron phases.  This&#xA;                       model is simliar to those used by genewise.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In general, genewise gives slightly better results but is much slower and cannot deal with multi fasta files. It is best when you &lt;em&gt;know&lt;/em&gt; that your query protein will align against a specific nucleotide sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exonerate is &lt;strong&gt;fast&lt;/strong&gt; but uses some heuristics that &lt;em&gt;can&lt;/em&gt; give slightly worse results in some cases. Personally, I use exonerate to get my hits and then, if necessary, refine the gene model using genewise. In most cases, exonerate should be enough though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EXAMPLES:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;exonerate -m p2g -q proteins.fasta -t scaffolds.fasta &gt; output.txt&lt;/p&gt;&#xA;&#xA;&lt;p&gt;genewise -pretty -pep -gff single_prot.fasta single_scaff.fasta &gt; output.txt&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2012-10-03T16:02:44.660" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3767" PostTypeId="1" AcceptedAnswerId="3791" CreationDate="2012-10-03T16:09:35.740" Score="3" ViewCount="311" Body="&lt;p&gt;Is it right to assume that the first living organisms on earth had a linear genome? I base this on the fact that &lt;em&gt;linear&lt;/em&gt; &lt;strong&gt;macromolecules&lt;/strong&gt; &lt;em&gt;are clearly much more common in nature that circular ones&lt;/em&gt;. To be honest, I can't even think of any naturally-occurring circular macromolecules that aren't already a part of current living organisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Were the very first living organisms more likely to have linear genomes? If so, when during evolutionary time did circular chromosomes originate?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-10-03T21:15:07.280" LastActivityDate="2012-10-04T15:59:02.480" Title="Is it more likely that the very first living organisms had a linear genome?" Tags="&lt;chromosome&gt;&lt;abiogenesis&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3768" PostTypeId="1" CreationDate="2012-10-03T16:27:10.053" Score="2" ViewCount="739" Body="&lt;p&gt;Assuming the sequence shown is read left to right, what is the sequence of the protein produced? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;sequence: 5’-ATGTACTTCCATCTGGAATAG-3’&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MY ATTEMPT: I know RNA is synthesized 5 to 3.  This is throwing me off because if we read the above sequence from left to right then we are going to synthesize 3 to 5.  If I ignore this for now, I get an mRNA of 3'-UACAUGAAGGUAGACCUUAUC-5'  from this i could easily get the protein looking at a mRNA to protein chart.  Is this correct?&lt;/p&gt;&#xA;" OwnerUserId="558" LastActivityDate="2012-10-03T18:02:52.683" Title="Translate DNA to Protein" Tags="&lt;dna&gt;&lt;homework&gt;&lt;rna&gt;&lt;translation&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3769" PostTypeId="1" AcceptedAnswerId="3795" CreationDate="2012-10-03T16:30:38.257" Score="7" ViewCount="16556" Body="&lt;p&gt;The electron transport chains of both the light reactions of photosynthesis (in plants) and oxidative phosphorylation (in animals) &lt;em&gt;both contain 5 complexes&lt;/em&gt; including ATP synthase, as shown below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2mXZt.png&quot; alt=&quot;Oxidative phosphorylation&quot;&gt;&#xA;&lt;a href=&quot;http://prodomweb.univ-lyon1.fr/priam/REL_JUL03/RALSTO_ALL/PRIAM_REPLICON/RES_PRIAM/map00190_org.html&quot; rel=&quot;noreferrer&quot;&gt;Image Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UuhZi.png&quot; alt=&quot;Light Reaction&quot;&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/File:Thylakoid_membrane.png&quot; rel=&quot;noreferrer&quot;&gt;Image Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this coincidence, or does this possibly suggest that both chloroplast and mitochondrion precursors derived their energy-obtaining mechanisms via an ancient evolutionarily-related metabolic pathway which diverged?&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2020-01-25T17:15:53.533" Title="Is there an evolutionary reason for the 5 electron transport complexes in plants and animals?" Tags="&lt;evolution&gt;&lt;metabolism&gt;&lt;photosynthesis&gt;&lt;cellular-respiration&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3770" PostTypeId="1" AcceptedAnswerId="3775" CreationDate="2012-10-03T16:38:26.700" Score="2" ViewCount="71" Body="&lt;p&gt;Which of the following are usually identical between a lung cell and a brain cell, from the same person, assuming that they are normal (non-cancerous) cells?  Circle your choice(s).&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;a.  Size&#xA;b.  Shape&#xA;c.  Specific proteins found in the cell&#xA;d.  Specific genes in the cell’s genome&#xA;e.  Which genes are expressed&#xA;f.  Which parts of the DNA are methylated&#xA;g.  The specific DNA sequence of chromosome 12&#xA;h.  All of the above&#xA;i.  None of the above&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I said only D and G because all cells have the full genome.  The difference between cells is how the these genes are expressed.  All of the other options are results of different amound of gene expression.  Is this the correct thinking?&lt;/p&gt;&#xA;" OwnerUserId="558" LastActivityDate="2012-10-03T17:07:19.727" Title="Similarities Between Cells?" Tags="&lt;cell-biology&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3771" PostTypeId="1" CreationDate="2012-10-03T16:41:04.720" Score="4" ViewCount="222" Body="&lt;p&gt;I understand that evolution is constant process that acts on a population in successive generations. Thus, it is obvious that evolution &lt;em&gt;is happening&lt;/em&gt;. However, I'm curious as to the  &lt;em&gt;stricking examples&lt;/em&gt; of evolution that have occurred since Darwin's publication of the theory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially, &lt;em&gt;how different are we now from the humans at the time at which evolution was conceived?&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-10-04T12:10:41.343" Title="Since Darwinian times, has there been any striking/notable effects of evolution on humans?" Tags="&lt;evolution&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3772" PostTypeId="2" ParentId="3768" CreationDate="2012-10-03T16:45:41.670" Score="1" Body="&lt;p&gt;EMBOSS has a tool for doing this:&#xA;&lt;a href=&quot;http://www.ebi.ac.uk/Tools/st/emboss_transeq/&quot; rel=&quot;nofollow&quot;&gt;http://www.ebi.ac.uk/Tools/st/emboss_transeq/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="476" LastActivityDate="2012-10-03T16:45:41.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3773" PostTypeId="2" ParentId="3771" CreationDate="2012-10-03T16:57:15.353" Score="4" Body="&lt;p&gt;Well, &quot;On the origin of species&quot; was published in 1859. If we assume that for humans a generation is approximately 20 years, that means that there have been between seven and eight generations since 1859. That is nowehere near enough time to observe evolutionary changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in answer to your question, not very different at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think I need to clarify my answer. When we talk about a species evolving or a species being different today than it was X years ago, we are referring to the species as a whole. Of course evolution is an ongoing process, selective pressures are shaping our gene pool constantly. However, in order to say that humans are different today to those of 1859, we would need to show that the prevalence of particular genotypes has changed. That a specific trait (a gene or a mutation in a gene) has become &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fixation_%28population_genetics%29&quot; rel=&quot;nofollow&quot;&gt;fixed&lt;/a&gt;&quot;, or, at the very least, that it has spread to a significant percentage of the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;@niallhaslam's answer gives a link to a wired.com article about genetic resistance to HIV. This is not something that has recently evolved in response to HIV but is the result of an ancestral mutation. The article itself states that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Using formulas that estimate how long genetic mutations have been&#xA;  around, researchers have discovered that the mutation dates to the&#xA;  Middle Ages. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Granted, this could be a good example of selection in action. If, after &lt;em&gt;many&lt;/em&gt;, &lt;em&gt;many&lt;/em&gt; more generations, this mutation has spread to the majority, or a significant percentage, of the population, we could point to it as an example of how humans have changed under the selective pressure of HIV infection. In order for this to happen, HIV will have to become common enough that having a resistance to is beneficial to a very large subset of humanity. I would expect to see such selective pressure in, for example, countries like South Africa where &lt;a href=&quot;http://en.wikipedia.org/wiki/HIV/AIDS_in_South_Africa&quot; rel=&quot;nofollow&quot;&gt;12% of the population&lt;/a&gt; is HIV positive. Such pressure, however, will be negligible in countries with lower infection rates. In the US, for example, &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0017502&quot; rel=&quot;nofollow&quot;&gt;a recent study&lt;/a&gt; found HIV incidence among persons aged 13 years and older to be 42,200–54,000. Since the US has ~312 million people, 54,000 represents ~0.02% of the population. This will not provide enough of a selective pressure to observe differences in the &lt;em&gt;short term&lt;/em&gt; evolutionary scale. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We do not, in fact, &quot;evolve quickly in response to parasites viruses etc&quot;. Pathogens may apply selective pressure yes. But this is not a quick process. In any case, we do not evolve &lt;em&gt;in response&lt;/em&gt; to them. Mutations occur, randomly usually, and if they confer an advantage they may be selected for. Said advantage may be because they confer resistance to disease but even then, the original mutation was not &quot;in response&quot; to the pathogen, However, such selection happens over many successive generations and will spread relatively slowly (quickly by evolutionary standards perhaps, but still slow for us, and certainly slower than 7 generations) across the population. The same holds true of epigenetic changes. Even if they can (as now seems likely) be transmitted down the generations, any selective advantage they confer will still act at the generational level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, while we are, of course, constantly evolving, there are no significant differences between the humans of today and those of Darwin's times. Sure, some genotypes may exist today that did not then and vice versa. These, however, are not representative of the species' genome. They may become so after many generations but, even if they exist, they have not had time to propagate through the gene pool and cannot be taken as evidence that &lt;em&gt;H. sapiens&lt;/em&gt; as a species is &quot;different&quot; today.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-10-04T12:10:41.343" LastActivityDate="2012-10-04T12:10:41.343" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3774" PostTypeId="2" ParentId="3771" CreationDate="2012-10-03T17:06:49.413" Score="4" Body="&lt;p&gt;We're constantly evolving resistance to disease, &lt;a href=&quot;http://www.wired.com/medtech/health/news/2005/01/66198?currentPage=all&quot; rel=&quot;nofollow&quot;&gt;for example HIV&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's reasonably fair to say this is still a contentious issue, but I think the point is that we still evolve quite quickly in response to parasites, viruses etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another answer, though not strictly Darwinian is &lt;a href=&quot;http://www.time.com/time/health/article/0,8599,2016824,00.html&quot; rel=&quot;nofollow&quot;&gt;our epigenetic response to things&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="476" LastEditorUserId="307" LastEditDate="2012-10-03T21:14:14.970" LastActivityDate="2012-10-03T21:14:14.970" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3775" PostTypeId="2" ParentId="3770" CreationDate="2012-10-03T17:07:19.727" Score="0" Body="&lt;p&gt;I would also go for d and g. All the others may vary. Strictly speaking, you may even have random, point mutations that have changed the genomic sequence between two given cells so even d and g might not be true in some cases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would also like to point out that recent evidence implies that differential expression of non coding, regulatory RNA molecules may play as, or even more, important a role as differential expression of proteins. See the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22955616&quot; rel=&quot;nofollow&quot;&gt;ENCODE papers&lt;/a&gt; or &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23019584&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for a recent review.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2012-10-03T17:07:19.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3776" PostTypeId="2" ParentId="3768" CreationDate="2012-10-03T17:31:24.843" Score="4" Body="&lt;p&gt;Since the sequence starts with an initiation codon and ends with a stop codon I think it's safe to conclude that this is the coding strand.  The coding strand has the same sequence as the transcribed RNA (except T&gt;U). This is because it is the other strand of the DNA that is the template for the synthesis of an RNA. The RNA is indeed made 5'&gt;3', but the template it uses has to run in the opposite direction.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;5’-ATGTACTTCCATCTGGAATAG-3’&#xA;3'-TACATGAAGGTAGACCTTATC-5' template strand&#xA;&#xA;&#xA;5'-AUGUACUUCCAUCUGGAAUAG-3’ mRNA transcript&#xA;3'-TACATGAAGGTAGACCTTATC-5' template strand (read from left to right by the polymerase)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and the sequence of the protein is MetTyr...etc&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-10-03T18:02:52.683" LastActivityDate="2012-10-03T18:02:52.683" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3777" PostTypeId="1" CreationDate="2012-10-03T17:48:21.530" Score="3" ViewCount="73" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Are there any lectures available on Patch-Clamping? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Were can I find a mathematical model of Patch-Clamp? (that can be easily implemented in matlab).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I have found some step-by-step protocols on (Springer book site) but nothing to useful--I am setting up a new rig. Where can I find protocols that have worked and have been tested? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1482" LastEditorUserId="9943" LastEditDate="2014-12-25T13:17:02.197" LastActivityDate="2014-12-25T13:17:02.197" Title="Patch-Clamping Neurons Resources" Tags="&lt;biophysics&gt;&lt;electrophysiology&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ClosedDate="2014-12-26T04:09:40.557" ContentLicense="CC BY-SA 3.0" />
  <row Id="3778" PostTypeId="1" CreationDate="2012-10-03T18:29:42.413" Score="2" ViewCount="164" Body="&lt;p&gt;this may not be on topic but I'm hoping someone here can tell me the name/manufacturer of the connectors used with the thin teflon tubing in this picture:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VfbiS.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="46" LastActivityDate="2012-10-04T10:56:53.113" Title="Tubing connector identification request" Tags="&lt;cell-culture&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3779" PostTypeId="2" ParentId="3739" CreationDate="2012-10-03T18:34:01.603" Score="1" Body="&lt;p&gt;Chris asked, &quot;what factors would increase/decrease the size of the adipocyte cell for a given mass of stored fat?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an obese person, subcutaneous and visceral fat is composed of 40% immune cells, while that number is ~10% in lean individuals. There is much interplay between adipocytes and immune cells via adipokines and cytokines. Examples include ADIPOQ (adiponectin) and IL1 (interleukin 1). Thus, agents that reduce the inflammation state of the adipose tissue are also likely to have an effect on adipocyte size. This nonetheless is secondary to diet and diet composition as an adipocyte is nearly all lipid droplet and that lipid droplet stores fat - either from the diet directly or converted into fatty acid from simple carbohydrates in the diet.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-10-03T18:34:01.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3780" PostTypeId="1" CreationDate="2012-10-03T21:26:02.227" Score="6" ViewCount="140" Body="&lt;p&gt;Due to alternative RNA splicing, it isn't uncommon to ultimately find multiple gene products expressed from one gene in eukaryotes. I'm looking for a reference value for &lt;em&gt;the average number of final gene products expressed per gene&lt;/em&gt; for:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;... &lt;strong&gt;a particular eukaryote (preferably humans)&lt;/strong&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This can't be too hard to do for one species like humans. I would expect the following formula to provide me with a rough answer. Is this correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(number of distinct proteins + numbers of distinct non-translated RNAs) / number of genes&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;... &lt;strong&gt;all eukaryotes as a whole&lt;/strong&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This one is slightly more problematic.&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-10-05T14:50:25.403" Title="Average number of gene products in (a) eukaryote(s)" Tags="&lt;gene-expression&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3781" PostTypeId="1" AcceptedAnswerId="3782" CreationDate="2012-10-03T22:07:19.487" Score="2" ViewCount="63" Body="&lt;p&gt;I read somewhere that Darwin wrote a paper that dealt with cellular structure, but I've been unable to find the title or contents of the paper because Darwin wrote such a volume of material. What is the title of this paper or papers?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;http://www.google.co.uk/#hl=en&amp;amp;sclient=psy-ab&amp;amp;q=darwin+cell+structure&amp;amp;oq=darwin+cell+structure&amp;amp;gs_l=hp.3..0i30.945.4858.0.5009.31.17.5.6.7.2.229.1722.10j6j1.17.0.les%3B..1.0...1c.1.aF7QyE_Dwb4&amp;amp;pbx=1&amp;amp;bav=on.2,or.r_gc.r_pw.r_qf.&amp;amp;fp=86c0df5ee6ec5cdc&amp;amp;biw=1280&amp;amp;bih=931&quot; rel=&quot;nofollow&quot;&gt;google search&lt;/a&gt; does not turn up any helpful results, and a similar search in &lt;a href=&quot;http://scholar.google.co.uk/scholar?hl=en&amp;amp;q=darwin+cell+structure&amp;amp;btnG=&amp;amp;as_sdt=1%2C14&amp;amp;as_sdtp=&quot; rel=&quot;nofollow&quot;&gt;google scholar&lt;/a&gt; yields equally ambiguous results (at least to me, since I do not have a background in biology). &lt;/p&gt;&#xA;" OwnerUserId="777" LastEditorUserId="115" LastEditDate="2012-10-04T10:49:59.390" LastActivityDate="2012-10-04T10:49:59.390" Title="What is the title of Darwin's paper on cellular structure?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3782" PostTypeId="2" ParentId="3781" CreationDate="2012-10-03T22:38:10.880" Score="2" Body="&lt;p&gt;Darwin had written lots of papers which dealt with &lt;em&gt;fertilization&lt;/em&gt; (which involves single cells), as he primarily dealt with the reproduction, continuation and thus evolution of a species, but these did not deal with cell biology specifically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After a closer look at the &lt;a href=&quot;http://darwin-online.org.uk/contents.html&quot; rel=&quot;nofollow&quot;&gt;complete list of all his publications&lt;/a&gt;, I found that he did have two cell-related publishings, specifically about &lt;strong&gt;the size of cells&lt;/strong&gt;, one entitled &lt;a href=&quot;http://darwin-online.org.uk/converted/pdf/1862_jamaica_F1826_001.pdf&quot; rel=&quot;nofollow&quot;&gt;Bees in Jamaica increase the size and substance of their cells&lt;/a&gt;, and the other, &lt;a href=&quot;http://darwin-online.org.uk/converted/pdf/1862_beecells_F1824_001.pdf&quot; rel=&quot;nofollow&quot;&gt;Bee-cells in Jamaica not larger than in England&lt;/a&gt;, in which he retracts the statement he had made in the previous article.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultimately, to answer your question, it seems as though none of his works dealt with &lt;em&gt;cellular structures&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Charles Darwin&lt;/strong&gt;. &lt;em&gt;&quot;Bees in Jamaica increase the size and substance of their cells&quot;.&lt;/em&gt; Journal of Horticulture (15 July): 305.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Charles Darwin&lt;/strong&gt;. &lt;em&gt;&quot;Bee-cells in Jamaica not larger than in England.&quot;&lt;/em&gt; Journal of Horticulture (22 July): 323.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-10-03T22:38:10.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3783" PostTypeId="2" ParentId="3635" CreationDate="2012-10-04T01:16:32.837" Score="7" Body="&lt;p&gt;Firstly, I'd like to emphasize that &lt;em&gt;the understanding of memories and learning as we know it is still in its very early stages&lt;/em&gt;. In fact, the mechanisms behind short-term memory are still under intense debate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for long-term memory, it is essentially caused by chemical changes in synapses between neurons in the brain. When you sense stimuli from your environment, action potentials follow a specific trail of afferent neurons towards the central nervous system, which then sends a message back through efferent neurons to initiate a response. The high frequency of these action potentials from the same stimuli of whichever sense allows for the strengthening of specific connections between neurons, which is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Long-term_potentiation&quot;&gt;long-term potentiation&lt;/a&gt;. This phenomenon is one of the major components of &lt;a href=&quot;http://en.wikipedia.org/wiki/Synaptic_plasticity&quot;&gt;synaptic plasticity&lt;/a&gt;, which also applies to the weakening of synaptic connections between neurons due to lack of transmission, as well as the change in the number of connections the neurons are receiving and making. Synaptic plasticity is also influenced by the change in quantities of neurotransmitters being expulsed into the synaptic cleft, and how cells react to these neurotransmitters, which is highly regulated by calcium levels. Ultimately, synaptic plasticity in accordance with learning is referred to as &lt;a href=&quot;http://en.wikipedia.org/wiki/Hebbian_theory&quot;&gt;Hebbian theory&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We are still not exactly sure where memories are stored within the brain, but we do know that the hippocampus does play a big part. It definitely aids in the storing and structuring of memories in the form of these millions of synaptic changes. Finally, &lt;a href=&quot;http://en.wikipedia.org/wiki/Memory_consolidation&quot;&gt;memory consolidation&lt;/a&gt; occurring in others regions of the brain over longer periods of time is likely, but still debated by some. &lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-10-04T01:16:32.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3784" PostTypeId="1" CreationDate="2012-10-04T01:28:48.957" Score="2" ViewCount="69" Body="&lt;p&gt;In reading the &lt;a href=&quot;http://www.amazon.ca/The-Annotated-Origin-Facsimile-Edition/dp/0674032810&quot; rel=&quot;nofollow&quot;&gt;annotated Origin...&lt;/a&gt; I have come to the following note by Costa on p. 168:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Again, modern biologists would disagree with Darwin's idea that especially well-developed traits vary to a greater degree than expected simply because they have been varying and undergoing selection in the past (as evidence by their considerable development)...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am not sure I understand what the problem with Darwin's view is. From reading his work I understood that he, Darwin, is simply saying that traits that have been more recently acted on by natural selection would vary more than those that have been acted in the past and over a longer period of time (given that conditions remain relatively the same - I assume).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the modern view of biologists on this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. The excerpt to which this side note refers, follows:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In these remarks we have referred to special parts or organs being still variable, because they have recently varied and thus come to differ; but we have also seen in the second Chapter that the same principle applies to the whole individual; for in a district where many species of any genus are found - that is, where there has been much former variation and differentiation, or where the manufactory of new specific forms has been actively at work - there, on an average, we now find most varieties or incipient species.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1483" LastEditorUserId="1483" LastEditDate="2012-10-07T04:02:42.573" LastActivityDate="2012-10-07T04:02:42.573" Title="Biology view on trait variability" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3786" PostTypeId="2" ParentId="3771" CreationDate="2012-10-04T10:52:35.473" Score="1" Body="&lt;p&gt;In &lt;a href=&quot;http://www.plosbiology.org/article/info%3adoi/10.1371/journal.pbio.0040072&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; the authors identify many human genes that are under recent positive selection pressure, that is to say where natural selection is acting to promote the spread of certain genes.&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2012-10-04T10:52:35.473" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="3787" PostTypeId="2" ParentId="3778" CreationDate="2012-10-04T10:56:53.113" Score="1" Body="&lt;p&gt;Try looking for &quot;Luer valves&quot; or &quot;Luer fittings&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, we buy this kind of supplies &lt;a href=&quot;http://www.wpi-europe.com/en/products/laboratory_supplies/luervalve.shtml&quot; rel=&quot;nofollow&quot;&gt;from WPI&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-10-04T10:56:53.113" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3788" PostTypeId="2" ParentId="3767" CreationDate="2012-10-04T11:03:08.927" Score="3" Body="&lt;p&gt;It is hard to give an answer to this question that is not just speculation.  We can be reasonably confident that the most recent common ancestor of bacteria and archaea had circular genomes.  However, we currently have no way to get any conclusive evidence earlier than that.  3 billion year old DNA doesn't fossilize.  So it's just speculation what DNA looked like back then.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, my understanding is that most experts think that RNA genomes predated DNA genomes.  These RNA genomes would be linear.&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2012-10-04T11:03:08.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3789" PostTypeId="1" AcceptedAnswerId="3797" CreationDate="2012-10-04T13:07:24.843" Score="2" ViewCount="259" Body="&lt;p&gt;This is prompted by niallhaslam's answer to this question [&lt;a href=&quot;https://biology.stackexchange.com/questions/3771/since-darwinian-times-has-there-been-any-striking-notable-effects-of-evolution&quot;&gt;Since Darwinian times, has there been any striking/notable effects of evolution on humans?&lt;/a&gt;]. A comment by Alan Boyd asks whether epigenetic changes count as evolution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Transgenerational epigenetic inheritance can occur, and does increase the natural variation of a species (although this review is more about plants, this does apply to animals too) [&lt;a href=&quot;http://dx.doi.org/10.1016/j.pbi.2012.08.004&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;]. Based on this alone I'm inclined to say that epigenetics can affect the fitness of a species, and thus could contribute to evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested to know if, in practise, this does occur, and whether epigenetics have been shown to affect the reproductive success of a species? Because the changes are not permanent I could imagine that they actually have very little impact &quot;species-wide&quot;, as environmental effects (infections, toxic exposures) also affect epigenetics. So, is there any evidence for epigenetics affecting the reproductive success of a species? This also includes whether epigenetics can influence traits enough to create a new sub-species.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Becker, C., &amp;amp; Weigel, D. (2012). Epigenetic variation: origin and transgenerational inheritance. Current opinion in plant biology. doi:&lt;a href=&quot;http://dx.doi.org/10.1016/j.pbi.2012.08.004&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1016/j.pbi.2012.08.004&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2012-10-04T18:27:46.150" Title="Can epigenetic changes affect reproductive success?" Tags="&lt;evolution&gt;&lt;epigenetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3790" PostTypeId="2" ParentId="3764" CreationDate="2012-10-04T13:08:37.963" Score="4" Body="&lt;p&gt;Yes, there are cases where one gene has become two. Or, at least, where multiple  functions carried out by a single protein, the product of one gene, are carried out by distinct proteins, the products of different genes, in another species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One case I have personally worked with is the bacterial SelB protein. It is essential for &lt;a href=&quot;http://en.wikipedia.org/wiki/Selenoprotein&quot; rel=&quot;nofollow noreferrer&quot;&gt;selenoprotein&lt;/a&gt; biosynthesis and has a dual function as an elongation factor and RNA binding protein. In eukaryotes, these functions are split between two proteins coded for by different genes. The Sec specific elongation factor EfSec and the RNA binding protein SBP2. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12370018&quot; rel=&quot;nofollow noreferrer&quot;&gt;here [1]&lt;/a&gt; for more information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chimeric transcripts are also examples of this. One I happen to know of is the protein secp43 which in the mosquito &lt;em&gt;A. gambiae&lt;/em&gt; is encoded by genomic sequences found on two different chromosomes &lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002968&quot; rel=&quot;nofollow noreferrer&quot;&gt;[2]&lt;/a&gt;. Essentially, by two different genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem is that although we can easily find such cases of one protein's function being shared between multiple proteins in other species, or of one protein being coded for by multiple transcripts, it is hard to reconstruct the evolutionary history that gave rise to the current situation. So, whether the current situation has arisen because of alpha complementation or other causes is hard to know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;REFERENCES:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12370018&quot; rel=&quot;nofollow noreferrer&quot;&gt;1)&lt;/a&gt; Lescure A, Fagegaltier D, Carbon P, Krol A., Protein factors mediating selenoprotein synthesis. &lt;em&gt;Curr Protein Pept Sci.&lt;/em&gt; 2002 Feb;&lt;strong&gt;3&lt;/strong&gt;(1):143-51.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002968&quot; rel=&quot;nofollow noreferrer&quot;&gt;2)&lt;/a&gt; Chapple CE, Guigó R., Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes. &lt;em&gt;PLoS One&lt;/em&gt;, 2008, &lt;strong&gt;3&lt;/strong&gt;(8):e2968. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2019-07-10T15:21:21.113" LastActivityDate="2019-07-10T15:21:21.113" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="3791" PostTypeId="2" ParentId="3767" CreationDate="2012-10-04T13:31:42.660" Score="3" Body="&lt;p&gt;I would say this is a question that might not be resolved yet.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Going back to the earliest days of DNA - a billion years ago - its hard to imagine circular DNA being the first sort to show up.  Its speculated that in the transition from RNA world to DNA world, early on each gene had a separate piece of nucleic acid coding for it which would not have been circular.  &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_world_hypothesis#Further_developments&quot; rel=&quot;nofollow&quot;&gt;It's been proposed for example that RNA viruses might have been a next step to cellular life&lt;/a&gt;.  Although I can see an old electron microscopy reference, not it does not seem as if any RNA viruses with circular RNA have ever been found.  How the first DNA chromosomes came about and what they looked like seems unclear to me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, though not typical, its not unusual to find &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1974809/&quot; rel=&quot;nofollow&quot;&gt;linear chromosomes in prokaryotes&lt;/a&gt;.  I could not find reference to archaea with linear chromosomes, but in prokaryotes, the link above points to the observation that even close relatives can have linear or circular chromosomes.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A remarkable property of the 8.2-Mb chromosome of S. erythraea was that, contrary to the expectations and the earlier data (Reeves et al., 1998), it proved to be circular. The chromosomes of its close relatives, Streptomyces coelicolor and Streptomyces avermitilis, are both linear, as is the chromosome of Rhodococcus sp. strain RHA1. These chromosomes are the largest in actinobacteria (8.7, 9.0 and 7.8 Mb respectively) and comprise some of longest DNA molecules in the prokaryotic world. In contrast, the shorter chromosomes of other actinobacteria are all circular. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It seems that linear vs circular genomes are a 'lifestyle' choice or connected to selection critera we don't understand yet: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hence, it was tempting to speculate that the linearity of streptomycetal chromosomes was somehow linked to and perhaps beneficial for the maintenance of these extremely long DNA molecules, even though it resulted in the instability of their termini. This idea has been contradicted by the discovery of equally long but circular chromosomes in the acidobacterium Solibacter usitatus (9.97 Mb), δ-proteobacterium Myxococcus xanthus (9.1 Mb), cyanobacterium Trichodesmium erythraeum (7.8 Mb), and, now, in the actinobacterium S. erythraea.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I really doubt the instability of the chromosomal terminii is a real consideration - there must be genes that help maintain those, just as there are in eukaryotes.  S coelicolor is a soil bacterium that is so common most people can find it in the dirt right outside their door - its not hard to live with a linear chromosome as a bacterium. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-10-04T15:59:02.480" LastActivityDate="2012-10-04T15:59:02.480" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3792" PostTypeId="2" ParentId="3769" CreationDate="2012-10-04T14:03:34.850" Score="1" Body="&lt;p&gt;Well, according to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Endosymbiotic_theory&quot; rel=&quot;nofollow&quot;&gt;endosymbiosis theory&lt;/a&gt; both mitochondria and chloroplasts derive from ancestral bacteria that invaded/were phagocytosed (fancy word for eaten) by eukaryotic cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the electron transport chains of both mitochondria and chloroplasts would indeed share a common bacterial ancestor. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2012-10-04T14:03:34.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3793" PostTypeId="1" AcceptedAnswerId="3794" CreationDate="2012-10-04T15:27:17.670" Score="12" ViewCount="1965" Body="&lt;p&gt;As I understand it from my basic chemistry, there are some fundamental reactions that exist between any acid and other substances for example acid-base reactions that form a salt, and the existence of a state of equilibrium in water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do these reactions and equilibria occur to DNA (or, for that matter, RNA), which has only ever been described to me as an 'acid', and does this affect the processes DNA goes through, like replication and transcription?&lt;/p&gt;&#xA;" OwnerUserId="1474" LastActivityDate="2020-12-12T16:25:28.840" Title="Does DNA react in all of the ways most other acids do?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;nucleic-acids&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3794" PostTypeId="2" ParentId="3793" CreationDate="2012-10-04T16:05:48.290" Score="14" Body="&lt;p&gt;It may seem counterintuitive that deoxyribonucleic &lt;strong&gt;acid&lt;/strong&gt; has nitrogenous &lt;strong&gt;bases&lt;/strong&gt;. Nonetheless, nucleic acids (thus including RNA) were called that way because the phosphate backbone (linked by phosphodiester groups) is a derivative of phosphoric acid.&lt;/p&gt;&#xA;&lt;h2&gt;Phosphoric acid&lt;/h2&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pw98L.png&quot; alt=&quot;Phosphoric acid&quot; /&gt;&#xA;&lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/5/58/Phosphoric-acid-2D-dimensions.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;Image Source&lt;/a&gt;&lt;/p&gt;&#xA;&lt;h2&gt;Phosphodiester group&lt;/h2&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3hxhU.png&quot; alt=&quot;Phosphodiester group&quot; /&gt;&#xA;&lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/d/db/Phosphodiester-group.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;Image Source&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Note that the only difference between these two groups is that in the case of the phosphodiester, two O-H bonds are replaced by O-C bonds. This make the last remaining hydrogen atom quite acidic (can quickly be identified by how the conjugate base exhibits resonance). In fact, it is so acidic that at physiological pH, the phosphodiester group &lt;em&gt;is deprotonated&lt;/em&gt;, giving that nucleotide a &lt;strong&gt;negative charge&lt;/strong&gt;. This property does have a profound effect on DNA's structure and &amp;quot;behavior&amp;quot; in a cell, and is often exploited in genetics, such as in &lt;a href=&quot;http://en.wikipedia.org/wiki/Gel_electrophoresis_of_nucleic_acids&quot; rel=&quot;nofollow noreferrer&quot;&gt;gel electrophoresis&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;An interesting fact is that this acidity of the phosphodiester group actually &lt;em&gt;competes&lt;/em&gt; with the basicity of the nitrogenous bases. However, since most often DNA is double-stranded, individuals bases will hydrogen-bond with its partner to make base pairs, which stabilizes and thus reduces this basicity.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;TLDR:&lt;/strong&gt; Although different acids of different molecular composition can act in very different ways, the overall acid-base chemistry &lt;em&gt;is seen&lt;/em&gt; in nucleic acids.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="63085" LastEditDate="2020-12-12T16:25:28.840" LastActivityDate="2020-12-12T16:25:28.840" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="3795" PostTypeId="2" ParentId="3769" CreationDate="2012-10-04T17:10:51.440" Score="8" Body="&lt;p&gt;Your latter assumption is the best we have so far, to my understanding.&lt;/p&gt;&#xA;&lt;p&gt;Here are a few excerpts from &lt;a href=&quot;http://www.plantphysiol.org/content/154/2/434.full&quot; rel=&quot;noreferrer&quot;&gt;&amp;quot;Early Evolution of Photosynthesis&amp;quot;&lt;/a&gt; published in &lt;em&gt;Plant Physiology&lt;/em&gt;, October 2010 (emphasis mine):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;There is suggestive evidence that photosynthetic organisms were present &lt;strong&gt;approximately 3.2 to 3.5 billion years ago...&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Overwhelming evidence indicates that eukaryotic photosynthesis originated from endosymbiosis of &lt;strong&gt;cyanobacterial-like organisms&lt;/strong&gt;, which ultimately became chloroplasts (Margulis, 1992). So the evolutionary origin of photosynthesis is to be found in the bacterial domain.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;And then there's the abstract from this paper: &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/096800049090296N&quot; rel=&quot;noreferrer&quot;&gt;&amp;quot;Do photosynthetic and respiratory electron-transport chains share redox proteins?&amp;quot;&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In purple nonsulfur bacteria and cyanobacteria, &lt;strong&gt;there is close interaction between the photosynthetic and respiratory electron-transport chains, which share identical redox proteins.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Purple bacteria and cyanobacteria are some of the oldest known lineages (&amp;gt;3BY, whereas Mitochondria parallel Eukaryotic origins at about 1.4BY - and the endosymbiosis which created Chloroplasts probably came after [plants have &lt;em&gt;both&lt;/em&gt; Chloroplasts &lt;strong&gt;and&lt;/strong&gt; Mitochondria, whereas most Eukaryotes just have Mitochondria]), and since the respiratory chain and photosynthetic chain share identical proteins in cyanobacteria and purple bacteria it's not a huge leap to assume that - yup - the 5-protein structure is probably the template used by both Chloroplasts and Mitochondria because of a common source.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-10-04T17:10:51.440" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3796" PostTypeId="2" ParentId="3681" CreationDate="2012-10-04T17:40:27.833" Score="5" Body="&lt;p&gt;Due to the fact that several codons can code a same amino-acid, the amino-acid sequence is usually more conserved than the nucleotide sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For small scale studies, the higher variability of nucleotide data brings useful characters to establish relationships between closely related organisms that might not be differentiated at the amino-acid level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With long evolutionary distance, the nucleotide signal tends to become erased by multiple substitutions at a same site. A more annoying feature is that genomes tend to have a preferred nucleotide composition. A site undergoing substitutions will have an increased probability to display of the preferred nucleotide, particularly if the substitution has no effect at the amino-acid level (synonymous substitution). This mainly affects third codon positions, because, as you can see in the genetic code, this is where most codon families vary. It may happen that distant species share a same composition preference. The sites free to vary will then tend to display the same nucleotide in both species as the number of substitution increases. This can induce phylogeny reconstruction errors, especially if the models of nucleotide evolution are not sophisticated enough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The larger the evolutionary scale, the higher the chance that such misleading features will appear in the nucleotide data. This makes amino-acid more suited to large scale studies. But ultimately, one could hope that using better models will enable to use the signal present in the nucleotide data to its fullest without being too much mislead. Using amino-acid data amounts to discarding some of the information present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It should be noted that some methods use codon evolution models instead of nucleotide or amino-acid models: all the signal is kept, but it is possible to incorporate the knowledge that some codons are more likely to transform into one another, due to synonymy.&lt;/p&gt;&#xA;" OwnerUserId="1486" LastEditorUserId="1486" LastEditDate="2012-10-05T10:34:01.403" LastActivityDate="2012-10-05T10:34:01.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3797" PostTypeId="2" ParentId="3789" CreationDate="2012-10-04T18:27:46.150" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://rd.springer.com/static-content/0.5415/pdf/672/art%253A10.1186%252F1471-2164-13-59.pdf?token=1349547201563--df67f8e33c10393eeb2a5501673869cd27643eebc78b8e9ae9a8ba858d30b45062d36922685bb45cdc0fe9cfa3cbe814e638131409957240b1103900fa7df04a&amp;amp;doi=10.1186/1471-2164-13-59&amp;amp;contentType=article&quot; rel=&quot;nofollow noreferrer&quot;&gt;This article&lt;/a&gt; deals with the effect of phenotypic variation brought on by epigenetic patterns, and how these are inherited to the next generation. Their conclusions?&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Our results show that epigenetic variation is inherited in chickens, and we suggest that selection of&#xA;favourable epigenomes, either by selection of genotypes affecting epigenetic states, or by selection of methylation&#xA;states which are inherited independently of sequence differences, may have been an important aspect of chicken&#xA;domestication.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However, I personally prefer &lt;a href=&quot;http://www.cell.com/AJHG/abstract/S0002-9297%2812%2900410-7&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt;, as it has a more profound implication on reproductive success and addresses your question &lt;strong&gt;specifically&lt;/strong&gt;. They found the there is a species-level difference in DNA methylation between humans and chimps, but more importantly that &lt;em&gt;this difference is responsible for the causation of numerous lethal diseases/conditions&lt;/em&gt;, which has a direct impact of the fitness of the species as a whole.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Finally, we found that differentially methylated genes are strikingly enriched with loci associated with neurological disorders, psychological disorders, and cancers. Our results demonstrate that differential DNA methylation might be an important molecular mechanism driving gene-expression divergence between human and chimpanzee brains and might potentially contribute to the evolution of disease vulnerabilities. Thus, comparative studies of humans and chimpanzees stand to identify key epigenomic modifications underlying the evolution of human-specific traits.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;In summary, evidence has shown that epigenetics does seem to play an active role in the evolution of species, although the exact mode of inheritance of DNA methylation from generation to generation is unknown.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h1&gt;References&lt;/h1&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Nätt, Daniel, Carl-Johan Rubin, Dominic Wright, Martin Johnsson, Johan Beltéky, Leif Andersson, and Per Jensen.&lt;/strong&gt; &lt;em&gt;“Heritable Genome-wide Variation of Gene Expression and Promoter Methylation Between Wild and Domesticated Chickens.”&lt;/em&gt; BMC Genomics 13, no. 1 (February 4, 2012): 59.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Zeng, Jia, Genevieve Konopka, Brendan G. Hunt, Todd M. Preuss, Dan Geschwind, and Soojin V. Yi.&lt;/strong&gt; &lt;em&gt;“Divergent Whole-Genome Methylation Maps of Human and Chimpanzee Brains Reveal Epigenetic Basis of Human Regulatory Evolution.”&lt;/em&gt; The American Journal of Human Genetics 91, no. 3 (September 7, 2012): 455–465.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="307" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-10-04T18:27:46.150" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3798" PostTypeId="1" CreationDate="2012-10-04T19:40:11.253" Score="7" ViewCount="2487" Body="&lt;p&gt;This may be anecdotal; please feel free to vote to close.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After staying awake for an extended duration, I usually find myself having to take extra effort to focus my eyes on an object. Similarly after exerting myself to the extent of near total exhaustion I find it necessary to consciously focus to perform actions that would otherwise require little conscious effort (E.g. Writing a note). There're other similar symptoms almost all of which mandate 'conscious effort'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What really happens when a body is tired? &#xA;As a corollary, why does making conscious effort usually beat the initial error?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2012-10-18T12:26:32.627" Title="What really happens when a body is tired?" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3799" PostTypeId="2" ParentId="1375" CreationDate="2012-10-04T19:45:42.183" Score="3" Body="&lt;p&gt;From what I understand of the flight description you give, and given the size and habitat, I would suggest to have a look at woodpeckers. &lt;em&gt;Dryocopus martius&lt;/em&gt; is large and black.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another idea (my favourite, actually): a bird of the genus &lt;em&gt;Tetrao&lt;/em&gt;: they can be black and large, live in the forest, and the tail widens towards the end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other suggestions, but I really doubt it's relevant:&#xA;- cormoran (&lt;em&gt;Phalacrocorax&lt;/em&gt; for the size, dark color, and I've seen some perched in trees, and ther's a lake in Zürich);&#xA;- &lt;em&gt;Accipiter&lt;/em&gt; (for the flight and habitat):&#xA;- &lt;em&gt;Milvus&lt;/em&gt; (for the size, the tail, and the dark colour):&#xA;- cuckoo (&lt;em&gt;Cuculus canorus&lt;/em&gt;);&#xA;- magpie (&lt;em&gt;Pica pica&lt;/em&gt;, black, makes nests on top of high trees, but I suppose you would have recognised it without hesitation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The yellow stripe on the back matches none of the above suggestions.&lt;/p&gt;&#xA;" OwnerUserId="1486" LastActivityDate="2012-10-04T19:45:42.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3800" PostTypeId="1" CreationDate="2012-10-05T01:56:40.207" Score="0" ViewCount="1311" Body="&lt;p&gt;When identical twins marry identical twins, the children of the couples will be full genetic siblings but why are they not genetically identical?&lt;/p&gt;&#xA;" OwnerUserId="1488" LastEditorUserId="6" LastEditDate="2012-10-05T15:12:46.817" LastActivityDate="2018-10-01T16:21:45.907" Title="Why is offspring of identical twins not identical?" Tags="&lt;human-biology&gt;&lt;genetics&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3801" PostTypeId="1" CreationDate="2012-10-05T02:04:16.857" Score="9" ViewCount="1504" Body="&lt;p&gt;How does squinting alllow one to see clearer pictures? What are the harmful effects?&lt;/p&gt;&#xA;" OwnerUserId="1488" LastEditorUserId="460" LastEditDate="2014-02-21T23:22:37.383" LastActivityDate="2017-08-31T09:10:22.370" Title="Why does squinting allow you to see objects more clearly?" Tags="&lt;eyes&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3802" PostTypeId="2" ParentId="3800" CreationDate="2012-10-05T03:21:12.430" Score="9" Body="&lt;p&gt;They are not identical for the same reason full siblings are not identical.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A simplistic Mendelian setup would be the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;X1/X2 = Mothers&lt;br&gt;&#xA;X3/Y = Fathers&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That means the children could be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;X1/X3&lt;br&gt;&#xA;X1/Y&lt;br&gt;&#xA;X2/X3&lt;br&gt;&#xA;X2/Y  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So children born to two married couples composed of identical twins only have a 50/50 shot at being the same gender, much less have the exact same set of genes and express them in the same way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the simplistic view above only concerns 4 alleles - but the human genome is composed of thousands. By the end, the chances of genetically &lt;em&gt;identical&lt;/em&gt; offspring from a set of identical twins is still &lt;strong&gt;very, very low&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And you haven't even began to include epigenetic variations, which often arise as a response to the environment! One cousin might be shorter due to their diet as an infant, one might have allergies the other does not depending on if they played outside as a child, and for non-Mendelian traits (incomplete dominance, co-dominance, phenotypes that rely on more than one allele [especially hair, eye, and skin color]) there's even more opportunity to introduce differences!&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-10-05T03:21:12.430" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3803" PostTypeId="2" ParentId="3780" CreationDate="2012-10-05T05:18:35.760" Score="1" Body="&lt;p&gt;Well, there are a number of problems. First, the discovery of noncoding RNAs is relatively new and they are difficult to detect, so their number is unknown. In addition, it is unknown how many of them are functional. This has also made it very difficult to define what a gene is and thus made it difficult to count how many genes there are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Protein coding genes, however, are much easier to deal with, and if you like you can enter any public protein database (at NCBI, for example) and easily query the number of distinct proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, the last problem is that with an organism like human, experimental methods are generally limited by sensitivity (might not detect proteins/RNA at very low concentrations) and the fact that you can't measure all possible cell types/conditions (many gene products will be cell type/condition specific).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Who said life is easy? Somehow things are always complicated in biology...&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2012-10-05T05:18:35.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3804" PostTypeId="1" CreationDate="2012-10-05T07:11:34.780" Score="3" ViewCount="93" Body="&lt;p&gt;We would like to compare our simulation results with experimentation. When one wants to follow experimentally the dynamics (and possibly structure) of protein-protein or protein-ligand docking (involving both small and large conformational changes for the complex), which are the most useful hydrodynamic techniques? If not hydrodynamic, which others?&lt;/p&gt;&#xA;" OwnerUserId="551" LastActivityDate="2012-10-05T07:11:34.780" Title="Experimental techniques to measure protein-protein and protein-ligand structure and dynamics" Tags="&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;protein-binding&gt;&lt;protein-folding&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3806" PostTypeId="1" CreationDate="2012-10-05T11:36:01.323" Score="6" ViewCount="446" Body="&lt;p&gt;I have collected some data to compare the biodiversity of a field in which the plagioclimax is maintained by machine mowing with a field in which the plagioclimax is maintained by sheep grazing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I found was that there was a significant increase in floral biodiversity in the field which was managed by agricultural grazing when compared to the floral biodiversity of the machine-mown field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am trying to explain my findings, and I believe that it is due to the comparitively short amount of time that machine-mowing has been a grassland management technique, so there has been little time for natural selection to take place and for species to develop adaptations to machine-mowing (such as being low-lying, or extremely fast-growing). Whereas the field which is managed through sheep-grazing, contains multiple competing species which have adapted over time to grazing sheep, such as &lt;em&gt;Cirsium arvense&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, the field which is managed by grazing has nutrients returned to it through defecation of the grazing animals, allowing for more favourable conditions for growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is my explanation valid? Are there any other reasons why the floral biodiversity of a field managed by sheep grazing would be higher than one managed by machine-mowing?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance!&lt;/p&gt;&#xA;" OwnerUserId="1081" LastEditorUserId="3624" LastEditDate="2013-10-28T19:47:49.063" LastActivityDate="2014-10-09T14:40:27.997" Title="Why is the floral biodiversity of grazed grassland higher than that of mown grassland?" Tags="&lt;botany&gt;&lt;ecology&gt;&lt;adaptation&gt;&lt;biodiversity&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3807" PostTypeId="1" CreationDate="2012-10-05T12:47:52.677" Score="35" ViewCount="39863" Body="&lt;p&gt;Why does the left hemisphere control the right and the right hemisphere control the left? I googled it but didn't find a good answer regarding this. Could someone explain? &#xA;Does this adaptation help in the speed of transmission of nerve impulses?&lt;/p&gt;&#xA;" OwnerUserId="1460" LastEditorUserId="6" LastEditDate="2012-10-05T15:11:50.983" LastActivityDate="2018-07-31T04:52:11.750" Title="Why do the two hemispheres of the brain control the opposite sides of the body?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="6" CommentCount="3" FavoriteCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="3808" PostTypeId="2" ParentId="3801" CreationDate="2012-10-05T13:18:14.817" Score="9" Body="&lt;p&gt;This is an optical pinhole effect.  If the amount of light passed through the lens decreases, the sharper the image is at the focal point.  For a camera this is accomplished by increasing the f stop (f22 is a smaller aperture size than f6&amp;nbsp;— f-stop is an inverse number).  For the eye the iris will dilate (get larger) or contract to be smaller.  In very bright light, you can cut down on large amounts of light coming in by squinting, which creates a slit in front of the eye lens. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In photography this increases the &quot;depth of field&quot;. Which is to say that more objects are in focus and sharp.  It works the same for our eyes of course.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WFTH6.gif&quot; alt=&quot;aperture effect&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this image you can see as the aperture is smaller, any given point on the focal plane (right hand line) receives light from a smaller angle (i.e. from less of the image field).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not a physicist, but that's a first order explanation &#xA;@Luke reminds me that there was a question about whether squinting is harmful.  There is another reason that we squint.  If we are nearsighted or if we are getting older, we have a tendency to squint not because there is too much light coming into our eyes, but because our lenses are not focusing very well.  Is it harmful to strain our eyes?  Maybe, but it won't kill you.  Reading glasses won't either. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="5239" LastEditDate="2013-12-28T01:07:00.813" LastActivityDate="2013-12-28T01:07:00.813" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3809" PostTypeId="2" ParentId="3807" CreationDate="2012-10-05T14:33:37.347" Score="28" Body="&lt;p&gt;Just to get the ball rolling here.  This particular aspect of brain evolution is very old. The cross wiring of the hemispheres of the brain seems to be as old as the right and left hemispheres itself.  It &lt;a href=&quot;http://icb.oxfordjournals.org/content/42/4/743.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;predates lizards&lt;/a&gt; - i.e. hundreds of millions of years ago. It  possibly predates right/left dominance and the organ asymmetry which puts the heart on the left side of the body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Digging back deeper, we can see that &lt;a href=&quot;http://www.sfu.ca/biology/faculty/hutter/hutterlab/research/Ce_nervous_system.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;worms have bilateral brain structure&lt;/a&gt;, but as noted in the comments below, the nervous systems do not cross.  I would guess that this means that the phenomenon appears sometime before lizards - putting the development having been done by the early Carboniferous period when the first animals came to the land and the first reptiles appears, which is the perhaps 350 million years ago.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Echinoderms (like starfish) are 'missing links' in bilateral symmetry as their &lt;a href=&quot;http://en.wikipedia.org/wiki/Echinodermata#Larval_development&quot; rel=&quot;nofollow noreferrer&quot;&gt;larval stage has bilateral symmetry even though the adult has radial symmetry&lt;/a&gt;.  Such wiring may be so embedded in the way most animal body plans develop that it hasn't changed in evolutionary history. If that is related to other animals trait, it could be a billion years ago. Some argue this is not the case.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One might guess that the cross over of neurons in brain control is good for integrating the signals from both sides of the organism. &lt;a href=&quot;https://en.wikipedia.org/wiki/Contralateral_brain#Twist_theories&quot; rel=&quot;nofollow noreferrer&quot;&gt;There are quite a few theories&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2018-07-31T04:52:11.750" LastActivityDate="2018-07-31T04:52:11.750" CommentCount="6" ContentLicense="CC BY-SA 4.0" />
  <row Id="3810" PostTypeId="2" ParentId="3798" CreationDate="2012-10-05T14:38:02.490" Score="3" Body="&lt;p&gt;Its still not clear why we need to sleep (as distinguished from the question of why our body gets fatigued in physical exertion).  A popular idea is that the brain needs to 'catch up' and reorganize itself given all the stimulus it has had from the previous day.  This 2010 National Geographic article says it all:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I asked William Dement, the retired dean of sleep studies, a co-discoverer of REM sleep, and co-founder of the Stanford Sleep Medicine Center, to tell me what he knew, after 50 years of research, about the reason we sleep. “As far as I know,” he answered, “the only reason we need to sleep that is really, really solid is because we get sleepy.”&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is clear that we need sleep and that we become less reliable at tasks when we are sleep deprived.  eventually we become completely unable to function.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure anyone can answer the last question - why does conscious effort help us to perform tasks?  one would have to understand/define the neurology of consciousness to answer that question.  That is still a bigger question that remains open I think. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-10-18T12:26:32.627" LastActivityDate="2012-10-18T12:26:32.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3811" PostTypeId="2" ParentId="3780" CreationDate="2012-10-05T14:50:25.403" Score="4" Body="&lt;p&gt;One answer can be found in the UniProt FAQ:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What is the human complete proteome?&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In 2008, a draft of the complete human proteome was released from&#xA;  UniProtKB/Swiss-Prot: the approximately 20,000 putative human&#xA;  protein-coding genes were represented by one UniProtKB/Swiss-Prot&#xA;  entry, tagged with the keyword 'Complete proteome'. This&#xA;  UniProtKB/Swiss-Prot complete H. sapiens proteome (manually reviewed)&#xA;  can be considered as complete in the sense that it contains one&#xA;  representative (canonical) sequence for each currently known human&#xA;  gene. Close to 40% of these 20'000 entries contain manually annotated&#xA;  alternative isoforms representing over 15'000 additional sequences ...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.uniprot.org/faq/48&quot; rel=&quot;nofollow&quot;&gt;http://www.uniprot.org/faq/48&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, we have 20,000 genes and 35,000 products yielding about 1.75 gene products per gene. Alternatively, the 8,000 genes undergoing alternative splicing give about 2.88 proteins per gene.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-10-05T14:50:25.403" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3812" PostTypeId="2" ParentId="2750" CreationDate="2012-10-05T17:27:01.753" Score="6" Body="&lt;p&gt;There is a very simple experiment you can do that will demonstrate that animals prioritize. Give a dog two bones. Preferably one which is more tasty than the other. Say one has more meat on it. The dog cannot eat both at once and you will observe it choosing one over the other. This is a clear example of prioritization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again with a dog, try observing one greeting two people it is fond of. If you and a friend stand a few meters apart when the dog comes up to you, the animal will choose to greet one of the humans first. Prioritization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any animal, or plant, fungus, bacterium or archaeon for that matter, that is ever presented with a choice between two actions during its lifetime, will have to be able to prioritize in order to chose between them. Clearly they can as our world is not strewn with, for example, panicked, confused looking squirrels trying desperately to chose which tree to climb.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-11-12T02:36:26.927" LastActivityDate="2012-11-12T02:36:26.927" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3813" PostTypeId="1" AcceptedAnswerId="3879" CreationDate="2012-10-05T20:00:17.360" Score="2" ViewCount="90" Body="&lt;p&gt;Just what the title states. &#xA;I wonder whether it is possible to fire a chemical switch - sort-of like injecting adrenaline in a human, to accelerate a particular process in a plant. For example, transpiration.&lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2012-10-10T12:40:17.893" Title="Can a plant be induced to accelerate transpiration?" Tags="&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3814" PostTypeId="1" CreationDate="2012-10-05T20:11:56.580" Score="6" ViewCount="2374" Body="&lt;p&gt;During metaphase, the chromosomes are arranged on the equatorial plate and are attached to spindle fibres. After S phase, can the cell be said to attain the configuration of 4n?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, during metaphase, since two spindle fibres (one from say right centriole and other from say left centriole) are attached to one tetrad, so can it be said in a well defined pattern that for a human being, 46*2=92 spindle fibres are formed in order to proceed with mitosis? Also how would the number vary in case of Meiosis I and Meiosis II?&lt;/p&gt;&#xA;" OwnerUserId="1492" LastEditorUserId="43" LastEditDate="2012-10-06T14:14:07.033" LastActivityDate="2013-05-08T08:13:47.803" Title="Number of spindle fibres during Metaphase?" Tags="&lt;cell-biology&gt;&lt;chromosome&gt;&lt;meiosis&gt;&lt;mitosis&gt;&lt;cytogenetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3815" PostTypeId="1" CreationDate="2012-10-05T20:23:06.927" Score="2" ViewCount="11095" Body="&lt;p&gt;The chromosomal DNA is stacked with help of cohesin and condensin protein in which particular manner? Can cohesin be said to form kinetochore? How would they vary exactly?&#xA;The terms are so narrowly windowed that they squeeze my brain through...!!! thank you for your kind help ^_^&lt;/p&gt;&#xA;" OwnerUserId="1492" LastActivityDate="2014-07-29T14:36:47.710" Title="Difference between Condensin and Cohesin proteins?" Tags="&lt;proteins&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3817" PostTypeId="1" CreationDate="2012-10-06T01:12:25.103" Score="2" ViewCount="1281" Body="&lt;p&gt;Let's say, hypothetically, that you fell asleep at 10PM, and you were woken up by a noise at 1AM. If you went back to sleep immediately and woke up at 6AM, you will feel tired even though you had slept for 8 hours. However, if you sleep for 8 hours straight , your body will feel rejuvenated. Is it because of REM sleep being cut off and restarting again? &lt;/p&gt;&#xA;" OwnerUserId="1489" LastEditorUserId="307" LastEditDate="2012-10-06T02:07:13.563" LastActivityDate="2013-04-27T15:08:18.197" Title="Why does non-continuous sleep makes you feel tired?" Tags="&lt;sleep&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3818" PostTypeId="1" CreationDate="2012-10-06T06:02:31.343" Score="8" ViewCount="272" Body="&lt;p&gt;I heard that when people place goldfish in another tank, they just forget where they where previously? True or False ?&lt;/p&gt;&#xA;" OwnerUserId="1488" LastEditorUserId="81" LastEditDate="2012-10-06T08:19:54.057" LastActivityDate="2012-10-11T01:34:22.020" Title="Do goldfish really have a 5 second memory span?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3819" PostTypeId="1" CreationDate="2012-10-06T06:09:47.277" Score="3" ViewCount="960" Body="&lt;p&gt;Is it possible to completely cure myopia using natural methods (i.e. not with Lasik etc.)?.&lt;br&gt;&#xA;I have seen websites claiming that exercising the eyes will help improve eyesight. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this true?&lt;/p&gt;&#xA;" OwnerUserId="1488" LastEditorUserId="115" LastEditDate="2012-10-07T10:06:44.867" LastActivityDate="2012-10-07T10:06:44.867" Title="Can visual acuity be improved?" Tags="&lt;eyes&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3820" PostTypeId="1" CreationDate="2012-10-06T06:25:05.560" Score="2" ViewCount="4186" Body="&lt;p&gt;In addition, when do we know we stop growing taller? Or we keep growing taller? &#xA;To the first question:&#xA;Recently, I went to a doctor to have a check up, he said that my growth plates are closed and cannot grow taller anymore. True or false? Is it possible to have a second growth spurt. I am about 16.&lt;/p&gt;&#xA;" OwnerUserId="1488" LastEditorUserId="1590" LastEditDate="2015-07-12T10:15:08.437" LastActivityDate="2015-07-12T10:15:08.437" Title="Is it possible to still grow taller after growth plates have been closed?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3822" PostTypeId="2" ParentId="3820" CreationDate="2012-10-06T12:50:25.040" Score="2" Body="&lt;p&gt;No, because growth only occurs at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Epiphyseal_plate&quot; rel=&quot;nofollow&quot;&gt;epiphyseal plate&lt;/a&gt; or growth plate. In the picture &lt;a href=&quot;http://en.wikipedia.org/wiki/File%3aTib_fib_growth_plates.jpg&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, the epiphyseal plates are the two horizontal lines in the tibia and fibula, and bone growth occurs in the upward direction, or toward the middle (shaft) of the bone. Once the epiphyseal plates close, the bones can no longer elongate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's possible to have a second &quot;growth spurt,&quot; but it's only because the epiphyseal plates haven't closed. David Robinson, the basketball player, was 6'7&quot; as a senior in high school, but ended up being 7'1&quot;. The &quot;growth spurt&quot; is caused by the sex hormones, which is why a significant amount of growth occurs during puberty.&lt;/p&gt;&#xA;" OwnerUserId="1166" LastActivityDate="2012-10-06T12:50:25.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3824" PostTypeId="1" CreationDate="2012-10-06T20:14:37.780" Score="4" ViewCount="234" Body="&lt;p&gt;I recently took up the task of organizing the sequencing database for a research project. I am still quite unsure of which database type I should use for this. Some advices/recommendations would be wonderful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This research project is more like a class where students are taught how to sequence a piece of plasmid via Sanger sequencing method, with paired end primers. For each plasmid there will be two entries (~1kbp each). Then the students would BLAST the sequence, mostly to see if there is any close match with certain related organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main purpose of this database I'm creating is to monitor the sequencing progress, as well as to single out the samples that need to be redone. So far, the record-keeping is not exactly accessible, hence the need for re-organization. Additionally, the students would need to be able to view their own results and enter the BLAST results themselves. The last condition seems to necessitate a web-server type of thing that the student can connect to enter their information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The total number of bacteria clones containing plasmids are ~18k, which means there will be ~36k entries in this database. It would be great if there is anyway to manage the trace files of the entries, or if not, I think I can add a column for the file path.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there a database management program that is appropriate for organizing sequence and trace file, with easy access for data entry by multiple users?&lt;/strong&gt; It would also help if the program don't have a high maintenance need.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disclaimer: I have very limited knowledge with database structure, having only taken an online intro to database class. About programming language, I am still learning Python. This project is a way to force myself to learn more.&lt;/p&gt;&#xA;" OwnerUserId="1497" LastActivityDate="2012-10-07T07:03:53.457" Title="Organize sequence database" Tags="&lt;bioinformatics&gt;" AnswerCount="0" CommentCount="5" ClosedDate="2012-10-08T21:26:08.270" ContentLicense="CC BY-SA 3.0" />
  <row Id="3825" PostTypeId="2" ParentId="3784" CreationDate="2012-10-06T20:22:30.380" Score="2" Body="&lt;p&gt;The variance of a trait's allele frequency can follow different trends over time depending on several factors such as whether one or several of the alleles are consistently selected for or the population dynamics. For example &lt;a href=&quot;http://en.wikipedia.org/wiki/Disruptive_selection&quot; rel=&quot;nofollow&quot;&gt;Disruptive Selection&lt;/a&gt; will tend to increase the allele variance. On the other hand &lt;a href=&quot;http://en.wikipedia.org/wiki/Directional_selection&quot; rel=&quot;nofollow&quot;&gt;Directional selection&lt;/a&gt;, or Stabilizing selection will tend to decrease variance by driving the allele frequency to one side of the distribution (in the first case) or by &quot;cutting down&quot; its sides in the second case. It is true that stabilizing and directional selection processes are more common especially under relatively stable environments. Therefore for the majority of cases, during the first phase of selection for a trait variance will most commonly decrease . This, however, is not a rule. &#xA;There are additional, rare, but from an evolutionary point of view extremely important cases where allele frequency variance can see a sudden &quot;ballooning&quot;. Consider for example the case of selection processes after mass extinction events. Then, because of the sudden availability of previously occupied niches, genetic drift due to small population sizes as well as changed conditions the previously stabilized traits will start...well...drifting. The same is true for almost any circumstances that will destabilize equilibrium and lead to speciation.&lt;/p&gt;&#xA;" OwnerUserId="1498" LastActivityDate="2012-10-06T20:22:30.380" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3826" PostTypeId="2" ParentId="3169" CreationDate="2012-10-07T06:12:56.827" Score="3" Body="&lt;p&gt;H₂O is emitted through respiration and perspiration.&lt;/p&gt;&#xA;" OwnerUserId="1165" LastEditorUserId="3340" LastEditDate="2014-10-09T13:32:09.103" LastActivityDate="2014-10-09T13:32:09.103" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3828" PostTypeId="2" ParentId="3819" CreationDate="2012-10-07T07:51:03.473" Score="2" Body="&lt;p&gt;While there is no such thing as perfect vision, growing evidence from Asia shows that looking often at distant objects (which one does naturally when being outside) can stop myopia progression. Vice versa, progression appears to increase when myopic children mainly live indoors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D. J. Park, N. G. Congdon: &lt;em&gt;Evidence for an &quot;epidemic&quot; of myopia.&lt;/em&gt; In: &lt;em&gt;Annals of the Academy of Medicine, Singapore.&lt;/em&gt; 33, 1, Jan 2004, 21–26. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15008557&quot; rel=&quot;nofollow&quot;&gt;PMID 15008557.&lt;/a&gt; (Review).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;K. A. Rose, I. G. Morgan et al: &lt;em&gt;Outdoor activity reduces the prevalence of myopia in children.&lt;/em&gt; In: &lt;em&gt;Ophthalmology.&lt;/em&gt; 115, 8, Aug 2008, 1279–1285. DOI:10.1016/j.ophtha.2007.12.019. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18294691&quot; rel=&quot;nofollow&quot;&gt;PMID 18294691.&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-10-07T07:51:03.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3829" PostTypeId="1" CreationDate="2012-10-07T09:10:19.340" Score="6" ViewCount="135" Body="&lt;p&gt;What is the oldest sample of genetic material (presumably DNA) identified? What are the prospects of pushing back much further into the geologic record?&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="3059" LastEditDate="2013-05-06T21:41:15.310" LastActivityDate="2013-05-06T21:41:15.310" Title="What is the oldest example of DNA identified?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3830" PostTypeId="1" CreationDate="2012-10-07T09:55:41.963" Score="9" ViewCount="1805" Body="&lt;p&gt;When a person's arm is amputated, the arm will no longer be able to grow back. However, in salamanders, the arm actually grows back. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In comparison to a human, what is really happening to the cells in the wounded area in salamander ? &lt;/p&gt;&#xA;" OwnerUserId="1489" LastEditorUserId="57" LastEditDate="2012-10-08T08:18:04.783" LastActivityDate="2013-01-05T05:45:44.857" Title="Why can't a human regenerate limbs like some other species?" Tags="&lt;cell-biology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3831" PostTypeId="1" AcceptedAnswerId="3837" CreationDate="2012-10-07T10:19:25.927" Score="5" ViewCount="341" Body="&lt;p&gt;I just read &lt;a href=&quot;https://biology.stackexchange.com/questions/849/how-does-an-inhibitory-synapse-communicate-to-the-cell-body-of-a-neuron&quot;&gt;How does an inhibitory synapse communicate to the cell body of a neuron?&lt;/a&gt; and found myself asking this question ... hopefully I'm not asking the same thing&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any body possessed of a nervous system probably has hundreds of neurons. At one end of the neuron is the nervous system, at the other - the organ.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A neuron is connected to several others in the vicinity through it's dendrites. &#xA;When a 'signal' (for want of better word) is put on the system bus - how does a neuron know whether it has to act ( contract/relax it's associated muscle/organ ) on the signal, or pass it on ( forward ) after amplification of the signal, if necessary? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there something like a chemical protocol to identify the target neuron/group-of-neurons that form the destination?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2012-10-07T14:12:16.783" Title="What protocol does the nervous system use?" Tags="&lt;neuroscience&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3833" PostTypeId="1" CreationDate="2012-10-07T10:22:39.943" Score="10" ViewCount="1955" Body="&lt;p&gt;I have noticed that lizards feet can stick to walls but not to Teflon surfaces? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is that?&lt;/p&gt;&#xA;" OwnerUserId="1488" LastEditorUserId="115" LastEditDate="2012-10-07T11:48:40.153" LastActivityDate="2017-08-07T03:13:01.647" Title="Why do the feet of the Gecko Lizard not stick to Teflon surfaces?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3834" PostTypeId="1" AcceptedAnswerId="3844" CreationDate="2012-10-07T12:03:56.970" Score="10" ViewCount="57385" Body="&lt;p&gt;When I grew rabbits, I had a pair, one male and one female. And while the female's nipples were quite prominent, especially after giving birth, I don't remember the male having any nipples at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do males of other mammal species, have nipples like human males, or is it a trait that's unique to Humans?&lt;/p&gt;&#xA;" OwnerUserId="680" LastEditorUserId="22057" LastEditDate="2017-02-28T14:02:51.713" LastActivityDate="2019-02-14T09:20:00.470" Title="Do male mammals other than humans have nipples?" Tags="&lt;anatomy&gt;&lt;mammals&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3835" PostTypeId="2" ParentId="3807" CreationDate="2012-10-07T13:41:21.260" Score="25" Body="&lt;p&gt;When I was in school it was discussed as an evolutionary survival advantage... If you are attacked from the right side, the left side of the brain is less likely to be damaged and can use the right sided limbs to fend off the attack as opposed to the right side being damaged and less responsive..&lt;/p&gt;&#xA;" OwnerUserId="1501" LastActivityDate="2012-10-07T13:41:21.260" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3836" PostTypeId="1" CreationDate="2012-10-07T14:11:33.273" Score="3" ViewCount="84" Body="&lt;p&gt;There is a region that gets about 812mm of precipitation and is mildly hot all year long.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe this region is a tropical savanna, but I'm not 100% sure.  Is this correct? &lt;/p&gt;&#xA;" OwnerUserId="1502" LastEditorUserId="1502" LastEditDate="2012-10-08T20:01:40.047" LastActivityDate="2012-10-09T17:40:12.827" Title="What type of biome is this?" Tags="&lt;ecology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3837" PostTypeId="2" ParentId="3831" CreationDate="2012-10-07T14:12:16.783" Score="7" Body="&lt;p&gt;An analogy to a computer bus can easily mislead you. Neurons do not communicated via a multiplexed &quot;bus&quot; with different targets; rather the complex connectivity of the neurons itself works as a computing device as a whole. The area study for understanding the communication among neurons is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Neural_coding&quot;&gt;&quot;neural coding&quot;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are talking about just the motor and sensory peripheral nerves, they innervate specific targets.&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2012-10-07T14:12:16.783" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3838" PostTypeId="2" ParentId="3833" CreationDate="2012-10-07T15:30:12.583" Score="16" Body="&lt;p&gt;Gecko feet have been the focus of a lot of research over the past 10 years.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their ability to walk up vertical or even hanging from ceilings is attributed to tiny branching hairs growing from the pads of their feet.  The hairs branch down to the size of 100s of nanometers and its believed that this gives them large surfaces at the molecular scale, giving them a strong &lt;a href=&quot;https://en.wikipedia.org/wiki/Van_der_Waals_force&quot; rel=&quot;noreferrer&quot;&gt;van der Waals adhesion force&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4boYw.jpg&quot; alt=&quot;Micrograph of Gecko hairs from footpad&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Gecko#Adhesion_ability&quot; rel=&quot;noreferrer&quot;&gt;Teflon, being hydrocarbon chains covered with 'hard' electronegative flourine atoms doesn't provide the same attraction to the hairs&lt;/a&gt;, as van der Waals forces rely on mutual polarizability of atoms in close contact. That is to say, electronically fluffy atoms can stick together more readily.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="33358" LastEditDate="2017-08-07T03:13:01.647" LastActivityDate="2017-08-07T03:13:01.647" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3839" PostTypeId="1" AcceptedAnswerId="3842" CreationDate="2012-10-07T15:37:43.457" Score="3" ViewCount="189" Body="&lt;p&gt;I see that quite a lot of drugs and dietary supplements sold in the USA have -HCl(hydrochloride) added to their name. For example pyridoxine hydrochloride for Vitamin B6.  &lt;strong&gt;I'm interested in knowing where in the digestive system -HCl compounds are absorbed?&lt;/strong&gt; Is it in the stomach? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would also help if I get a rough idea of how long it takes for -HCl supplements to be absorbed. Is it an hour or more?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input! &lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="115" LastEditDate="2012-10-08T16:55:16.240" LastActivityDate="2012-10-08T16:55:16.240" Title="Where are -HCl supplements absorbed in the human digestive system?" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3840" PostTypeId="2" ParentId="165" CreationDate="2012-10-07T21:18:06.030" Score="-1" Body="&lt;p&gt;I am not sure I understand BLAST correctly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When using BLAST in DNA and protein, they are different. There is a threshold T in protein &quot;seeding&quot; step, which means the seeding sequence is not perfectly matched. However, it seems there is no T in seeding step and we are looking for perfect match and extend them to neighbouring sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if there is no word length 5 exact match between these 2 sequence, BLAST will fail. &lt;/p&gt;&#xA;" OwnerUserId="1503" LastEditorUserId="57" LastEditDate="2012-10-07T23:29:55.340" LastActivityDate="2012-10-07T23:29:55.340" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3841" PostTypeId="2" ParentId="3806" CreationDate="2012-10-07T21:51:36.567" Score="4" Body="&lt;p&gt;I think you may have covered the answer in your question... but here's my take;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The 'mowing' occurs at a distinct time-point and is highly destructive and uniform, so the selection pressure is very high and only highly competitive species that are fast to grow and reproduce will be successful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you point out, animals will defecate and naturally fertilize the land, thus favouring growth. Other favourable factors in an agricultural environment will be that the 'mowing' will be much less uniform; the animals may favour one plant over another - so a plant that is not eaten by the animals will continue to grow and reproduce, whereas in the mowing environment this plant would not succeed; this will allow various other species to succeed where they would not in the mown environment. Also, depending how many animals are in the area the height of the grass may be higher overall, so slower-growing plants could grow enough to reproduce. &lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-10-07T21:51:36.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3842" PostTypeId="2" ParentId="3839" CreationDate="2012-10-07T22:15:21.397" Score="8" Body="&lt;p&gt;The hydrochloride ions are not what facilitate their absorption into the body. The HCl notation is from organic chemical reactions of a weak base (usually amines are involved here) with HCl to form a salt. The salt is what gets purified as a powder (otherwise the chemical remains in solution and can't be made into a pill/supplement). The bottle may say: &quot;compound-HCl&quot; or &quot;compound HCl&quot; implying that the two are chemically bonded together, but that is incorrect. What actually happens is that the compound is an ionic salt, in the form [compound]H&lt;sup&gt;+&lt;/sup&gt; Cl&lt;sup&gt;-&lt;/sup&gt;. As far as absorption, that is entirely dependent on the compound(s) being absorbed. Once you swallow them, they dissociate back into the weak acid form and H&lt;sup&gt;+&lt;/sup&gt;,Cl&lt;sup&gt;-&lt;/sup&gt; ions.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-10-07T22:15:21.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3843" PostTypeId="2" ParentId="3755" CreationDate="2012-10-08T00:33:05.617" Score="3" Body="&lt;p&gt;Muscle cells are the only cells I know of that are polynuclear. With respect to monocytes, a concise review of their nomenclature can be found in &lt;a href=&quot;http://bloodjournal.hematologylibrary.org/content/116/16/e74.long&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; by L Ziegler-Heitbrock, P Ancuta, S Crowe, et al. (Blood, 2010). Apparently it has had quite a complex and confused biochemical characterization, but the article states the name indeed derived from its single lobed, mononuclear morphology. This is in distinction to other phagocytes which have multi-lobular nuclei (polymorphonuclear cells).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With respect to advantages, a multinucleated cell makes sense when the speed of intracellular signalling is important (e.g., calcium diffusion). It may also be useful in the case of cells when the cell needs to coordinate the synthesis of large amounts of protein.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-10-08T00:33:05.617" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3844" PostTypeId="2" ParentId="3834" CreationDate="2012-10-08T06:02:04.873" Score="9" Body="&lt;p&gt;At the very least, I know that male primates also have nipples like female, though they are very close relatives to human. On the other hand, in some of my dissection labs, I noticed that male pigs also have nipples just like the female ones. It seems to be the case that most male mammals have nipples, which probably has to do with mammals being breast-feeder and their developmental pattern.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a page on Wikipedia that I found about this topic:&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Nipple#In_male_mammals&quot;&gt;http://en.wikipedia.org/wiki/Nipple#In_male_mammals&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1497" LastActivityDate="2012-10-08T06:02:04.873" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3845" PostTypeId="2" ParentId="3830" CreationDate="2012-10-08T07:46:54.073" Score="-4" Body="&lt;p&gt;For salamanders, when they lose a limb, they have cells called fibroblasts that migrate to the wounded area. These cells are not differentiated and are able to be differentiated to whatever is necessary for regeneration. That sort of cellular differentiation for repair doesn't happen for us humans, yet. Give synthetic biology about 20 more years. :D&lt;/p&gt;&#xA;" OwnerUserId="1504" LastActivityDate="2012-10-08T07:46:54.073" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3846" PostTypeId="2" ParentId="3829" CreationDate="2012-10-08T07:51:56.780" Score="1" Body="&lt;p&gt;419 million year old DNA from halophilic bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://news.discovery.com/earth/oldest-dna-bacteria-discovered.html&quot; rel=&quot;nofollow&quot;&gt;http://news.discovery.com/earth/oldest-dna-bacteria-discovered.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1504" LastActivityDate="2012-10-08T07:51:56.780" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3847" PostTypeId="1" AcceptedAnswerId="3848" CreationDate="2012-10-08T11:29:50.190" Score="5" ViewCount="2076" Body="&lt;p&gt;These two concepts seem almost contradictory, proteins have a net negative charge due to the amino acids in them each having a small negative charge, yet membrane proteins are able to exist traversing the plasma membrane, which is impermeable to charged molecules (hence the need for membrane proteins).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do these two statements remain true simultaneously?&lt;/p&gt;&#xA;" OwnerUserId="1474" LastActivityDate="2012-10-08T11:44:24.557" Title="If proteins have an overall charge, how do membrane proteins traverse through the hydrophobic region of the plasma membrane?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3848" PostTypeId="2" ParentId="3847" CreationDate="2012-10-08T11:44:24.557" Score="8" Body="&lt;p&gt;Transmembrane proteins are inserted into the membrane in the ER in a rather complicated system, there is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26841/#A2216&quot;&gt;a whole chapter about translocation of proteins in &quot;Molecular Biology of the Cell&quot;&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The proteins are moved through an aqueous pore in the Sec61 complex, which explains how charged parts of a protein are moved across the membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The parts of a transmembrane protein that remain in the membrane are usually composed of hydrophobic amino acids that aren't charged.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I strongly recommend you to read up on the whole translocation stuff in a cell biology book like the Alberts I linked. There's a lot more to it than what I wrote here.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2012-10-08T11:44:24.557" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3849" PostTypeId="2" ParentId="3836" CreationDate="2012-10-08T16:25:30.833" Score="5" Body="&lt;p&gt;Well, first of all 812mm is a pretty precise value to be preceded by the word &quot;about&quot;. &quot;Mildly hot&quot;, on the other hand, is too vague a term for your question to be answerable. If you update your question with better parameters, you may get more helpful answers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, according to &lt;a href=&quot;https://php.radford.edu/~swoodwar/biomes/?page_id=105&quot; rel=&quot;nofollow&quot;&gt;this page&lt;/a&gt;, a tropical savanna has mean monthly temperatures at or above 64°F (~18°C), which may or may not qualify as &quot;mildly hot&quot; by your standards, and annual precipitation averages between 30 and 50 inches which means between 762mm and 1270mm.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I what you are describing &lt;em&gt;could be&lt;/em&gt; a tropical savanna, but as I said before, I can't tell unless you update your question with more information. Have a look at &lt;a href=&quot;http://www.climate-charts.com/World-Climate-Maps.html#rain&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt;, it may be of help.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-10-09T17:40:12.827" LastActivityDate="2012-10-09T17:40:12.827" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3851" PostTypeId="1" CreationDate="2012-10-07T10:20:05.177" Score="5" ViewCount="1849" Body="&lt;p&gt;Bone conduction, is it something different from the normal phenomena of listening through the ears. I checked on some literature . Is it so that Bone conduction has very less to do with the ears and more to do with vibrations of the bones in the skull. Maybe I am mistaken . Please anyone can present a simple picture here and maybe some text to refer .&#xA;Thanks !&lt;/p&gt;&#xA;" OwnerDisplayName="user12448" LastActivityDate="2013-01-02T08:43:40.040" Title="Bone conduction . Different from the normal hearing phenomena in humans?" Tags="&lt;biophysics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3852" PostTypeId="1" CreationDate="2012-10-08T18:11:09.933" Score="7" ViewCount="336" Body="&lt;p&gt;Just what the title states.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I recognize people around me by their facial appearance to begin with, then by their little idiosyncracies; this applies perhaps to most other humans too. We rely pretty heavily on vision - perhaps because we are a primarily diurnal species gifted with the ability to distinguish colour. But then, so are birds of prey e.g. eagle, kite ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do diurnal birds of prey identify each other by their appearance?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2012-10-11T04:04:15.100" Title="Do diurnal birds of prey recognize each other by their appearance?" Tags="&lt;ornithology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3853" PostTypeId="2" ParentId="3851" CreationDate="2012-10-08T18:18:16.997" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.physlink.com/education/askexperts/ae20.cfm&quot; rel=&quot;nofollow&quot;&gt;Sound travels faster through solid material than air.  It also travels more efficiently, the sound does not diminish as quickly over long distances as the molecules in the air do not collide as often and can cause the sound waves to decompose over time and distance&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is accentuated when the solid through which the sound is travelling is long in one dimension.  This is why old westerns have scouts listening to at railroad tracks to see if a train is coming.  Sound travels along the rails much further than we can hear through the air. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bone conduction uses this principle - you can touch a walking stick to your jaw bone and put the stick onto a wall and hear sound from the otherside of the wall more efficiently.  &lt;a href=&quot;http://www.hearingsparks.com/2011/01/another-update-hear-through-your.html&quot; rel=&quot;nofollow&quot;&gt;This cool hearing aid uses the jawbone and skull as a microphone to pick up sound waves&lt;/a&gt;.  I'm not advocating the product, but it demonstrates the idea - as microphones get smaller and smaller with shrinking hearing aids, it might make sense to use a different pick up for the sound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the bones of the middle ear use bone conduction to get the sound into the cochlea where the nerves actually pick up sound.  &lt;a href=&quot;http://www.medicalook.com/human_anatomy/organs/Middle_ear.html&quot; rel=&quot;nofollow&quot;&gt;This serves to isolate the delicate inner workings of the ear from the outside&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-10-08T18:18:16.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3854" PostTypeId="2" ParentId="3852" CreationDate="2012-10-08T18:20:52.957" Score="3" Body="&lt;p&gt;Having seen some nature documentaries about Penguins identifying their offspring using sound alone (even in flocks of hundreds of thousands of other birds), my immediate impression was that sound is likely to be more important with regard to recognizing individuals of the same species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is corroborated by Melissa Mayntz, a bird enthusiast, who has written a great account on birds use of their 5 senses (&lt;a href=&quot;http://birding.about.com/od/birdbehavior/a/Bird-Senses.htm&quot; rel=&quot;nofollow&quot;&gt;Understanding Bird Senses&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To summarize, she explains that whilst sight is a birds most important sense in terms of hunting and avoiding being hunted, their hearing is is their second most important sense and they use this to identify individuals;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Birds hear a smaller frequency range than humans, but they have much more acute sound recognition skills. Birds are especially sensitive to pitch, tone and rhythm changes and use those variations to recognize other individual birds, even in a noisy flock.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="740" LastActivityDate="2012-10-08T18:20:52.957" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3855" PostTypeId="1" AcceptedAnswerId="3857" CreationDate="2012-10-08T18:36:46.323" Score="4" ViewCount="806" Body="&lt;p&gt;In general does the pH effect the precipitation, e.g. would a pH of 6 cause less precipitation than pH 7.5. Or are they unrelated?&lt;/p&gt;&#xA;" OwnerUserId="571" LastActivityDate="2012-10-09T00:34:04.123" Title="Ammonium sulphate precipitation assay pH dependence" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3857" PostTypeId="2" ParentId="3855" CreationDate="2012-10-09T00:34:04.123" Score="4" Body="&lt;p&gt;I think it would affect some proteins, but ammonium sulfate precipitation usually requires such large amounts of salt, that you would have to add a &lt;em&gt;lot&lt;/em&gt; of base to adjust the pH.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I have done ammonium sulfate precipitation, its to take a rough cut of proteins out of a whole cell/whole organ lysate - its more like a hammer than a pair of tweezers as far as protein purification is concerned.  I would rather use a charged plastic resin or a sizing column if I were to care about the isoelectric purification. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-10-09T00:34:04.123" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="3858" PostTypeId="1" CreationDate="2012-10-09T01:01:04.633" Score="5" ViewCount="2134" Body="&lt;p&gt;During electroporation of bacterial cells (I work with &lt;em&gt;Mycobacterium tuberculosis&lt;/em&gt;, but I think this applies to &lt;em&gt;E. coli&lt;/em&gt; as well), sometimes I get sparking. I've read this is due to salts present, either in the DNA sample or the bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I use the Qiagen plasmid prep kit, which includes EB (Elution Buffer). This contains Tris-Cl. Could this be contributing to the sparking? Can you explain how this works? Does eluting with water instead of EB reduce chances of sparking?&lt;/p&gt;&#xA;" OwnerUserId="1509" LastEditorUserId="57" LastEditDate="2012-10-09T01:37:15.913" LastActivityDate="2013-08-26T22:11:50.653" Title="Sparking during electroporation of plasmid DNA into bacterial cells" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;transformation&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3861" PostTypeId="1" CreationDate="2012-10-09T11:01:54.083" Score="6" ViewCount="29696" Body="&lt;p&gt;In the morning, I went to the fridge to drink some chocolate milk. At night, when I took out the same carton of milk, the packaging seems expanded, like some kind of air is inside. Explain please !&lt;/p&gt;&#xA;" OwnerUserId="1488" LastEditorUserId="95" LastEditDate="2012-10-09T12:45:39.523" LastActivityDate="2018-06-25T10:26:16.173" Title="Why does milk contained in cartons of milk expand?" Tags="&lt;microbiology&gt;&lt;food&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3864" PostTypeId="1" CreationDate="2012-10-09T11:35:51.810" Score="10" ViewCount="59792" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Possible Duplicate:&lt;/strong&gt;&lt;br&gt;&#xA;  &lt;a href=&quot;https://biology.stackexchange.com/questions/3793/does-dna-react-in-all-of-the-ways-most-other-acids-do&quot;&gt;Does DNA react in all of the ways most other acids do?&lt;/a&gt;  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&#xA;&#xA;&lt;p&gt;Even if DNA is made up of nucleotide bases, it is said to be an acid. Why is this?&lt;/p&gt;&#xA;" OwnerUserId="1515" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2012-10-09T13:12:20.653" Title="DNA as an acid?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="5" ClosedDate="2012-10-11T08:55:16.413" ContentLicense="CC BY-SA 3.0" />
  <row Id="3866" PostTypeId="2" ParentId="3864" CreationDate="2012-10-09T12:56:36.967" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/DNA&quot; rel=&quot;nofollow&quot;&gt;DNA&lt;/a&gt; is made of three types of molecules in equal proportions - basic nucleotides, sugar deoxyribose and acidic phosphate groups. The bases are on the inside of the helix and partly hidden from the outside. Deoxyrybose and phopshates are on the outside, forming a backbone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though the proportions are equal, the nucleotides are weak bases, so the overall pH is acidic.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastActivityDate="2012-10-09T12:56:36.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3868" PostTypeId="2" ParentId="3864" CreationDate="2012-10-09T13:12:20.653" Score="16" Body="&lt;p&gt;First of all, DNA is &lt;em&gt;not&lt;/em&gt; made up of &quot;nucleotide bases&quot; but of &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleotide&quot; rel=&quot;noreferrer&quot;&gt;nucleotides&lt;/a&gt;. These consist of a sugar bound to one of the 4 nucleobases Adenine, Cytosine, Guanine or Thymine (Uracil in the case of RNA) and a &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphate&quot; rel=&quot;noreferrer&quot;&gt;phosphate group&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When these bases are bound to a sugar (2-deoxyribose for DNA), they form the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleoside&quot; rel=&quot;noreferrer&quot;&gt;nucleosides&lt;/a&gt; Adenosine, Cytidine, Guanosine or Thymidine respectively:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AiChU.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the nucleosides are bound to one or more phosphate groups, they become nucleotides. The general structure of a nucleotide is (&lt;a href=&quot;http://www.dnareplication.info/dnadoublehelix.php&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jD06h.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, nucleotides are joined together through their phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. This polymer is what we know of as DNA:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ObMgQ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, after this long introduction, the acidity of DNA is caused by the presence of the phosphate groups which are themselves acidic. You can see this by comparing the structure of DNA to that of Phosphoric acid:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/F6coz.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As explained very well &lt;a href=&quot;http://yearofchemistry.org.nz/more-stuff/ask-a-chemist-2/&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If you compare the structures of phosphoric acid (Figure 1) and a&#xA;  short strand of DNA (Figure 2), you’ll see that in the latter, two&#xA;  protons of phosphoric acid are replaced by carbon atoms either in, or&#xA;  attached to, the five-membered ring. In chemical terms, such a group&#xA;  is called a phosphate diester. The remaining proton is now quite&#xA;  acidic, and is relatively easily lost, thereby giving DNA its acidic&#xA;  character. Indeed, under neutral conditions, DNA is deprotonated at&#xA;  this site, and the oxygen atom bears a negative charge. Despite the&#xA;  fact that DNA does contain many basic groups, their basic properties&#xA;  are masked somewhat because of the fact that they hydrogen bond with&#xA;  each other to form base pairs. Hence it’s the acidic part of the&#xA;  molecule that dominates, and that is why we know DNA as an acid.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2012-10-09T13:12:20.653" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3869" PostTypeId="2" ParentId="3861" CreationDate="2012-10-09T13:35:15.220" Score="10" Body="&lt;p&gt;The likeliest culprit here is fermentation carried out by bacteria present in the milk. Fermentation of a sugar, for example glucose, releases carbon dioxide (a gas) : &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$C_{6}H_{12}O_{6} \rightarrow 2 C_{2}H_{5}OH + 2 CO_{2}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since this reaction produces a gas, the gas builds up in the milk carton causing it to bulge. This is not, generally, a good sign, make sure to smell the milk before drinking it! &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2015-07-22T12:01:48.737" LastActivityDate="2015-07-22T12:01:48.737" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3871" PostTypeId="1" AcceptedAnswerId="3877" CreationDate="2012-10-09T17:57:49.257" Score="9" ViewCount="55833" Body="&lt;p&gt;I'm trying to represent data graphically and am using a variation of hue/lightness to distinguish one data point from the next. I would like to use a color that would allow me to convey most information visually.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm interested in is which color I should use. &lt;strong&gt;I've read somewhere that humans are most capable of distinguishing shades of green, that is a human can differentiate more shades of green than any other color. Is it true?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has there been any studies to distinguish the number of shades that a typical westerner can distinguish? I'm looking for information like : ### shades of green, ### shades of red, ### shades of cyan, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cQlpU.jpg&quot; alt=&quot;Green color spectrum&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2014-05-07T08:06:56.757" Title="Which shades/hues of color are easiest to distinguish for humans?" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3872" PostTypeId="2" ParentId="3858" CreationDate="2012-10-09T18:10:47.943" Score="1" Body="&lt;p&gt;In my experience the elution buffer does not matter (both for E.coli and Mycobacteria). I have heard this before from co-workers, but it usually is based on superstition or anecdotal evidence. I have compared water/EB elution and never saw a difference in sparking (in fact, I usually get slightly more colonies with EB).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I get arcing (sparks), it's usually because I did not wash enough, have bubbles or have to many bacteria. Arcing is a collapse of resistance.&lt;/p&gt;&#xA;" OwnerUserId="867" LastActivityDate="2012-10-09T18:10:47.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3873" PostTypeId="1" CreationDate="2012-10-09T21:29:01.637" Score="6" ViewCount="754" Body="&lt;p&gt;Do all mushrooms have the same multicellular ancestor? Did that ancestor feature common mushroom elements such as cap, stem, sporofore, vulva, bulb, etc.&lt;/p&gt;&#xA;" OwnerUserId="408" LastActivityDate="2012-10-10T16:57:34.147" Title="Do all mushrooms have the same multicellular ancestor?" Tags="&lt;mycology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3874" PostTypeId="2" ParentId="3871" CreationDate="2012-10-10T01:58:09.587" Score="3" Body="&lt;p&gt;Light is either monochromatic, or a combination of different wavelength in different proportions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the eye, there're 4 types of sensor cells: one is greyscale-only, another 3 is for color vision. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Spectral_sensitivity&quot; rel=&quot;nofollow&quot;&gt;the graph here&lt;/a&gt; with the spectral sensitivity of the 3 color vision cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, for any giver hue, you have very wide possibility of the light spectrum that makes you see that hue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you see the yellow color from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sodium-vapor_lamp&quot; rel=&quot;nofollow&quot;&gt;sodium-vapor lamp&lt;/a&gt; you see almost monochromatic yellow light. When you see the photo of the lamp on your PC display, there’s no yellow light at all. Instead, you see some combination of red and green light produced by PC display which doesn’t have yellow subpixels, only red green and blue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's why there's no simple answer to your question. The answer depends not just on hue (which only exists inside our brain), but also on the spectrum of the light you see (which also exists in the real world).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. Even if you'll specify &quot;color on a PC display&quot;, the question is still vague: there're different types of displays with different spectral characteristics.&lt;/p&gt;&#xA;" OwnerUserId="1517" LastActivityDate="2012-10-10T01:58:09.587" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3875" PostTypeId="2" ParentId="3806" CreationDate="2012-10-10T02:21:55.183" Score="2" Body="&lt;p&gt;Other possible reasons except your and Luke's:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Different agriculture techniques. I could imagine machine-mowed grassland could be processed by different chemicals (fertilizers, insecticides). I could imagine machine-mowed grassland could be sown with different grass that grows faster but dies when trampled with hoofs.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Most agriculture machinery works on fossil fuel i.e. emits CO₂ and other compounds.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;You could also flip cause and effect. It could be that there're some reasons (dunno: soils, humidity, etc) why fields with lower biodiversity is more suitable for mowing.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1517" LastEditorUserId="3340" LastEditDate="2014-10-09T14:40:27.997" LastActivityDate="2014-10-09T14:40:27.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3876" PostTypeId="1" CreationDate="2012-10-10T02:44:51.270" Score="2" ViewCount="403" Body="&lt;p&gt;The question involves the &lt;a href=&quot;http://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_kinetics&quot; rel=&quot;nofollow&quot;&gt;Michaelis-Menten&lt;/a&gt; kinetics equation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is what I did: I took the Michaelis-Menten equation, replaced v with 0.4Vmax, canceled the Vmaxes (one on each side), and solved for [S].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I got -0.056 which is obviously wrong, because [S] cannot be negative.&lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="146" LastEditDate="2012-10-10T03:08:17.310" LastActivityDate="2012-10-10T07:55:05.347" Title="At what substrate concentration will an enzyme work at 40% of its maximum rate if its Km = 0.095M?" Tags="&lt;homework&gt;&lt;kinetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3877" PostTypeId="2" ParentId="3871" CreationDate="2012-10-10T03:10:39.030" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I've read somewhere that humans are most capable of distinguishing shades of green, that is a human can differentiate more shades of green than any other color. Is it true?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'd say it's &lt;strong&gt;plausible&lt;/strong&gt;, depending on your definition of &quot;Green.&quot; While your eyes do, indeed, have RGB receptors (cones) and Rods for grayscale - they don't perceive the Visible Spectrum equally. Here are a few graphs I found from Photo.net regarding the human eye and the sensitivity of the Cones (first and second) and Rods (third):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hnGdt.jpg&quot; alt=&quot;RGB cell detections&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rRu4N.jpg&quot; alt=&quot;Visible Wavelength sensitivity of the human eye&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you should be noticing above is not necessarily the Y axis, but the X axis - which represents the Wavelength, and amount of Wavelength our eyes are sensitive to each color. While our eyes perceives the most &lt;em&gt;Red&lt;/em&gt; wavelengths and the least &lt;em&gt;Blue&lt;/em&gt; wavelengths, &lt;em&gt;Green&lt;/em&gt; comes in just under Red's range for Wavelength coverage. However... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Kmtb2.jpg&quot; alt=&quot;Cone response of the human eye&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When combined with our Rod sensitivity, though, &lt;em&gt;Green&lt;/em&gt; wavelengths produce nearly double the sensitivity the &lt;em&gt;Red&lt;/em&gt; Wavelengths - and nearly quadruple the &lt;em&gt;Blue&lt;/em&gt; wavelengths. What that means is that in low-light situations when the Cones are unable to produce a precise color image, your Rods will be able to pick out &lt;em&gt;Green&lt;/em&gt; things (with a slightly loose definition of 'Green') more than other colors - which is perhaps the reason why night-vision goggles often use Green since they increase the &lt;strong&gt;Intensity&lt;/strong&gt; of the light, which presumably stimulates the Rods more (although not knowing precisely how the image is produced - if the green coloring is enhancing that particular bit of the spectrum of falsely colored - take this with a grain of salt).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does that explicitly prove you can see more &lt;em&gt;Green&lt;/em&gt; shades than others? &lt;strong&gt;No.&lt;/strong&gt; Your brain does &lt;em&gt;a lot&lt;/em&gt; of processing - the entire color Yellow is a construction of your brain, and Tetrachromats (people with 4 types of Cones) are real. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, like I said above, I'd say it's plausible. &lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-10-10T03:10:39.030" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3878" PostTypeId="2" ParentId="3876" CreationDate="2012-10-10T07:55:05.347" Score="5" Body="&lt;p&gt;To be honest I know very few about enzymes and absolutely nothing about Michaelis–Menten.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, when I &quot;took the Michaelis-Menten equation, replaced v with 0.4Vmax, canceled the Vmaxes (one on each side), and solved for [S]&quot;, my result is positive:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;0.4 * Vmax = S * Vmax / ( Km + S )&#xA;0.4 = S / ( Km + S )&#xA;S = 0.4 * Km + 0.4 * S&#xA;0.6 * S = 0.4 * Km&#xA;S = Km * 2 / 3.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="1517" LastActivityDate="2012-10-10T07:55:05.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3879" PostTypeId="2" ParentId="3813" CreationDate="2012-10-10T12:40:17.893" Score="1" Body="&lt;p&gt;With high(er) temperatures, especially in drier air with a bit of breeze, a plant will transpire more. While not a chemical solution, it is indeed a mechanism that serves to cool the plant.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-10-10T12:40:17.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3880" PostTypeId="2" ParentId="1145" CreationDate="2012-10-10T13:41:44.373" Score="3" Body="&lt;p&gt;Human embryogenesis is &lt;em&gt;much&lt;/em&gt; more complicated than the more general and simplified picture given in your 1st figure.&#xA;For details, please study &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_embryogenesis&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Human_embryogenesis&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To point out the most distinctive features which might have led to your confusion:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;em&gt;Before&lt;/em&gt; gastrulation, the blastocyst cavity is formed.&lt;/li&gt;&#xA;&lt;li&gt;Only the inner cell mass undergoes gastrulation.&lt;/li&gt;&#xA;&lt;li&gt;Mesoderm forms quiet late and spreads, thereby also forming the chorion as well as the amnion.&lt;/li&gt;&#xA;&lt;li&gt;The embryo itself is formed from a subset of all embryogenetic cells. This is shown in your 2nd figure, part C and D. Yet, tissues are still going to spread such that the final ectoderm as well as mouth and anus will be formed.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1518" LastActivityDate="2012-10-10T13:41:44.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3881" PostTypeId="2" ParentId="1145" CreationDate="2012-10-10T14:33:51.533" Score="0" Body="&lt;p&gt;The second picture does not show human &lt;em&gt;gastrulation&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your source talks about the development of yolk sac in human embryos, and does not claim it depicts gastrulation. In human embryos gastrulation happens about 7 days after fertilization and the development of membranes, as depicted in your second picture, begins about 15 days after fertilization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I highly recommend the part of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10052/&quot; rel=&quot;nofollow&quot;&gt;Chapter 11&lt;/a&gt; from &quot;The Developmental Biology&quot;, which deals with early mammal embryo development, from fertilization till formation of the body axes.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastActivityDate="2012-10-10T14:33:51.533" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3882" PostTypeId="2" ParentId="3873" CreationDate="2012-10-10T14:49:11.030" Score="5" Body="&lt;p&gt;All fungal species within the kingdom have the same common ancestor, which is &lt;strong&gt;unicellular&lt;/strong&gt; (thought to be protistan). This common ancestor is the point at which it is thought that animals diverged, as suggested by &lt;a href=&quot;http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/MulticellularityProject.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt;.&#xA;In their words:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is now well established that animals share a common single-celled ancestor with fungi, and that in the two sister lineages multicellularity arose independently&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A fungal phylogenetic tree is shown below, which originated from &lt;a href=&quot;http://www.biomedcentral.com/1471-2148/9/195&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Note: all colored areas represent different phyla of fungi.&lt;/em&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ikRZK.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will respond to a few questions addressed in the comments.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Is there a unique multicellular ancestor to all mushrooms?&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am rather sure (but can't explicitly confirm with a reference) that multicellularity in fungi only evolved &lt;strong&gt;once&lt;/strong&gt;. If this were true, I would also hypothesize that mushroom-like characteristics also evolved only once, thus indicating that there &lt;em&gt;is&lt;/em&gt; a multicellular ancestor to all mushrooms.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Are there multicellular fungi outside dikarya?&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No. One branch of dikarya seems to consist of only unicellular organisms, suggesting that multicellularity evolved at some point within organism under only one dikaryan branch.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Was the common ancestor of Dykarya multicellular?&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No. See previous answer.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Are those unicellular dykaria secondary unicellular or not? Given that the both branches of dykaria show similarities in fruiting bodies, it seems to be plausible that the common ancestors of dykaria had a similar structure.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am not exactly aware of the similarities in fruiting bodies in both branches, but if the physiology behind fruiting bodies are similar, it is &lt;strong&gt;very likely&lt;/strong&gt; because the dikaryan common ancestor had a similar mechanism.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2012-10-10T16:57:34.147" LastActivityDate="2012-10-10T16:57:34.147" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="3883" PostTypeId="1" AcceptedAnswerId="3885" CreationDate="2012-10-10T15:51:56.420" Score="9" ViewCount="5936" Body="&lt;p&gt;My 6 year old daughter asked me 2 biology-related questions yesterday and I tried my best to answer them with the aid of YouTube videos.  One of the questions (I may post the other one too) was&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How do we see colour?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I showed her a video on YouTube where it was explained that light hits an object and if that object is a tangerine then that object will absorb all colours except orange and will reflect orange and that's why we see it as being orange.  I then repeated this explanation and she said.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But how do we see different colours?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I then showed her a video describing corneas, vitreous humours, lenses, optical nerves and so on.  I think I lost her.  I got a bit lost too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now I have two problems, which I'd like to ask to you all as questions&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;I do not know how to explain to a 6 year old how we are able to perceive colour.  Does anyone know how this can be explained?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I have never quite understood this idea that an object has a colour depending on the light that hits it.  Okay, I understand that in low light objects have a different colour because there is a not much light hitting it and that different objects absorb different wavelengths of light and therefore appear as different colours.  What I don't understand is that if I place a bar of gold a bar of silver side by side in the same lighting conditions they do have different colours, so therefore there must be something inherent in these object that give them different colours.  What is that something?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1519" LastActivityDate="2019-01-23T21:01:54.903" Title="What gives things their colour?" Tags="&lt;vision&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3884" PostTypeId="1" CreationDate="2012-10-10T17:40:19.673" Score="3" ViewCount="2781" Body="&lt;p&gt;Why do some biologists refer to single-celled organisms such as Amoeba and Paramecium as &#xA;acellular (i.e., without cells) rather than unicellular (i.e., one cell)?&lt;/p&gt;&#xA;" OwnerUserId="1520" LastEditorUserId="1306" LastEditDate="2012-10-10T19:08:09.293" LastActivityDate="2012-10-11T13:35:42.953" Title="&quot;Acellular&quot; designation for organisms" Tags="&lt;cell-biology&gt;&lt;microbiology&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3885" PostTypeId="2" ParentId="3883" CreationDate="2012-10-10T21:37:55.223" Score="15" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I do not know how to explain to a 6 year old how we are able to perceive colour. Does anyone know how this can be explained?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, depending on the depth you want to introduce her to, it can be difficult to explain to &lt;em&gt;adults&lt;/em&gt; - much less children. You explained the basics well enough. Without going to the molecular mechanisms, here's a useful diagram:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2fgFZ.gif&quot; alt=&quot;Rods and Cones&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Light will pass through the eye and Retina until it hits the Cones and Rods. That produces a reaction (which I'll address next) - which then causes signals to either resume or cease (Rods are, ironically, shut off by light - not turned on). These signals pass through Ganglion cells, through the Optic Nerve, and interpreted by the brain. When some cells are switched on, like a 3-Way traffic stop, they will prevent the information from other cells being transmitted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;em&gt;simple&lt;/em&gt; way of explaining it might be that inside our eyes are millions of teeny-tiny molecules that act like light-switches, and the brightness and color of light determine which of the &quot;light-switches&quot; are on or off.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to go further into the actual mechanisms (or just have the background knowledge for future reference) the next diagram shows the mechanism itself (&lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/364/1531/2881/F1.large.jpg&quot; rel=&quot;noreferrer&quot;&gt;and the original in full-size since the one shown is squished if you prefer&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2OJLV.jpg&quot; alt=&quot;Protein conform mechanism&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The big things to note above is the change from &lt;em&gt;cis&lt;/em&gt;-Retinal to &lt;em&gt;trans&lt;/em&gt;-Retinal which occurs after a Photon is absorbed. This causes signaling molecules to go a bit wild, open ion channels, and the depolarization of the membrane propagates the charge down the cell - much like a neuron.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I have never quite understood this idea that an object has a colour depending on the light that hits it. Okay, I understand that in low light objects have a different colour because there is a not much light hitting it and that different objects absorb different wavelengths of light and therefore appear as different colours.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, let me stop you here. Low-light is a different situation than colored-light. Let's get the basics down:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photons are absorbed by the electrons of the atoms that compose the molecules of an object. Whatever &lt;em&gt;Wavelength&lt;/em&gt; of light is not absorbed by the electrons is &lt;strong&gt;reflected&lt;/strong&gt;, and it's this &lt;em&gt;Wavelength&lt;/em&gt; that we perceive as the color of the object as our Cones absorb the reflected light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photons can also be &lt;strong&gt;emitted&lt;/strong&gt; when an electron moves to a lower-energy state. The &lt;em&gt;Wavelength&lt;/em&gt; emitted by the electron is directly related to the difference between the High and Low energy states, as this diagram shows fairly well:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cn2SI.jpg&quot; alt=&quot;Photon emission&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;emitted&lt;/strong&gt; photons are the object's &quot;Incandescence&quot; - which is when an object produces a color of light by itself. The color you perceive is NOT going to change if the object emits incandescent light because the object is &lt;em&gt;generating&lt;/em&gt; its own light. Neon signs are a great example: The gases being subjected to a current &lt;em&gt;emit&lt;/em&gt; light, and will appear whatever color it's supposed to be whether or not it's a blue moon or sunset.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photons which are &lt;strong&gt;reflected&lt;/strong&gt; and not emitted - i.e. almost everything that doesn't have a power source - as I said above, are then absorbed by our Cones and our brain interprets the signals to produce a color.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason why objects that &lt;strong&gt;reflect&lt;/strong&gt; light can change color is because not all environmental light is the same. Red objects will appear Black under Blue light because Blue light &lt;em&gt;doesn't contain Red Wavelengths&lt;/em&gt; - there's nothing to reflect, so the object absorbs all of the available Wavelengths - the very definition of Black!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lot of our color perception depends on ambient light, and most of the time - thanks to the Sun - that is a full-spectrum white light. Which brings me to answer the last bit of your question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What I don't understand is that if I place a bar of gold a bar of silver side by side in the same lighting conditions they do have different colours, so therefore there must be something inherent in these object that give them different colours. What is that something?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, there definitely &lt;em&gt;is&lt;/em&gt; something inherent in both objects. That is: Their electron configurations absorb different chunks of the spectrum, and accordingly reflect different chunks of the spectrum. Although that's still a bit simplistic, since metals have some unique properties that other Elements do not. Their electrons exist in more of an &quot;ocean&quot; than around central atoms, but that's a whole other question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a fun bit of Trivia to impress your daughter when she's old enough, it's always a fun fact to know that the color &lt;strong&gt;Yellow&lt;/strong&gt; is &lt;em&gt;completely constructed in your head&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The human eye &lt;strong&gt;only&lt;/strong&gt; has Rho (Red), Gamma (Green), and Beta (Blue) color receptors which have the following absorption pattern (from photo.net):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DXGWy.jpg&quot; alt=&quot;Human Cone absorption spectrum&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What everybody sees as &quot;Yellow&quot; is actually when both the Green and Red receptors are activated at the Wavelength where they intercept above, which your brain interprets as &quot;Yellow&quot;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wlDyV.jpg&quot; alt=&quot;Color sensitivity&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because your brain does &lt;strong&gt;&lt;em&gt;a lot&lt;/em&gt;&lt;/strong&gt; of processing, despite having only three color receptors we can &lt;em&gt;perceive&lt;/em&gt; millions of colors (and shades/tones). Now for a while everywhere you look you'll be utterly amazed at what's going on, and you rightfully should be. ;-)&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-10-10T21:37:55.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3886" PostTypeId="2" ParentId="3884" CreationDate="2012-10-10T23:27:15.747" Score="3" Body="&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Non-cellular_life&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some biologists refer to wholly syncytial organisms as &quot;acellular&quot; because their bodies contain multiple nuclei which are not separated by cell walls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Albano pointed out, &quot;cell walls&quot; should probably be &quot;cell membranes&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Paramecium&quot; rel=&quot;nofollow&quot;&gt;Paramecium&lt;/a&gt; and some types of amoeba like the &lt;a href=&quot;http://en.wikipedia.org/wiki/Chaos_%28genus%29&quot; rel=&quot;nofollow&quot;&gt;Chaos genus&lt;/a&gt; have multiple nuclei so they fall under this definition.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2012-10-11T13:35:42.953" LastActivityDate="2012-10-11T13:35:42.953" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="3887" PostTypeId="2" ParentId="3818" CreationDate="2012-10-11T01:34:22.020" Score="4" Body="&lt;p&gt;My answer might sound unscientific, since I haven't had tanks filled with goldfish. However, I have had fish and other pets over the years, including cats, turtles and a very sick lizard. I have a scientific background, and on this strength, I will report based on personal observation, albeit with a small sample size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My fish always &quot;knew&quot; me. When I approached the tank, they knew it was their &quot;feeding person&quot;, and even when they were not getting fed, left what they were doing aside and came to the surface to &quot;greet&quot; me, or more likely, impending food. I even experimented by asking others to walk up to the tank and saw that most of them did not respond in a similar fashion, although sometimes they did. With me, I enticed the same reaction every time, even  after a new tank was populated or new additions were made. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This makes me conclude fish, and goldfish, which I did keep, have &quot;better than expected&quot; memory. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When they are put in a new tank - well, I suggest you move to a well crowded city that is new to you, and see how long it takes for you to get your orientation right. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope it helps. &lt;/p&gt;&#xA;" OwnerUserId="1521" LastActivityDate="2012-10-11T01:34:22.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3888" PostTypeId="1" AcceptedAnswerId="3896" CreationDate="2012-10-11T03:05:21.830" Score="6" ViewCount="17564" Body="&lt;p&gt;I recall a story from one of my Botany professors where he encountered a woman picking &lt;em&gt;Solanum dulcamara&lt;/em&gt; (nightshade) berries. When he asked her what she was doing with them, she responded that her husband had her make a pie from them every year. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As her husband was presumably still alive, and since I regard this particular professor as reliable, what would have removed enough solanine from the berries to avoid ill effects? Does the concentration decrease upon ripening, or would cooking destroy the toxin? Would that also be why we fry green tomatoes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(As a disclaimer, no-one should eat plants that are known to be poisonous. Even though some people don't react to poison ivy, it is still a bad idea to rub it all over your body.)&lt;/p&gt;&#xA;" OwnerUserId="1522" LastEditorUserId="3952" LastEditDate="2013-08-27T04:20:48.373" LastActivityDate="2020-08-17T16:27:05.117" Title="Does cooking or ripening reduce the concentration of solanine in nightshade?" Tags="&lt;botany&gt;&lt;toxicology&gt;&lt;ethnobiology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="3889" PostTypeId="1" AcceptedAnswerId="4941" CreationDate="2012-10-11T04:02:59.510" Score="3" ViewCount="72" Body="&lt;p&gt;I seem to recall from either reading or lecture that there have been instances of trees that are self-incompatible accumulating enough mutations in an axillary bud that the resulting branch was able to pollinate flowers on other parts of the tree. Unfortunately, I do not have a source for this information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there recorded instances of this happening, or is this a figment of my fevered brain?&lt;/p&gt;&#xA;" OwnerUserId="1522" LastEditorUserId="43" LastEditDate="2012-10-16T15:35:27.977" LastActivityDate="2012-10-16T15:35:27.977" Title="Mutation in axillary buds of trees overcoming self-incompatability?" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;reproduction&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3890" PostTypeId="2" ParentId="3852" CreationDate="2012-10-11T04:04:15.100" Score="2" Body="&lt;p&gt;Recent research has indicated that wild American crows (&lt;em&gt;Corvus brachyrhynchos&lt;/em&gt;) can recognize individual human faces &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0003347209005806&quot; rel=&quot;nofollow&quot;&gt;(Mazluff et al. 2010)&lt;/a&gt;.  If crows can recognize individual people, then it might not be too farfetched that other bird groups can recognize each other by appearance.&lt;/p&gt;&#xA;" OwnerUserId="1396" LastActivityDate="2012-10-11T04:04:15.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3891" PostTypeId="2" ParentId="450" CreationDate="2012-10-11T05:10:23.780" Score="15" Body="&lt;p&gt;There are two factors at play here. First is the balance between how much energy a plant can collect and how much it can use. It is not a problem of too much heat, but too many electrons. If it were a question of heat, a number of flowers selected for their black pigmentation would have their petals cooked off. ;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a plant does not have enough water, is too cold, is too hot, collects too much light, or has some other condition that prevents the electron transport chain from functioning properly, the electrons pile up in a process called &lt;a href=&quot;http://en.wikipedia.org/wiki/Photoinhibition&quot;&gt;photoinhibition&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These electrons are then transferred to molecules that they should not be transferred to, creating &lt;a href=&quot;http://en.wikipedia.org/wiki/Free_radicals&quot;&gt;free radicals&lt;/a&gt;, wreaking havok within the plant's cells. Fortunately, plants produce other compounds that prevent some of the damage by absorbing and passing around the electrons like hot potatos. These antioxidants are also beneficial to us when we eat them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This explains why plants collect the amount of light energy they do, but does not explain why they are green, and not grey or dark red. Surely there are other pigments that would be able to generate electrons for the electron transport chain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer to that is the same as why &lt;a href=&quot;http://en.wikipedia.org/wiki/Adenosine_triphosphate&quot;&gt;ATP&lt;/a&gt; is used as the main energy transport molecule in organisms rather than GTP or something else.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Chlorophyll&quot;&gt;Chlorophyll a and b&lt;/a&gt; were just the first things that came about that fulfilled the requirement. Certainly some other pigment could have collected the energy, but that region of parameter space never needed to be explored.&lt;/p&gt;&#xA;" OwnerUserId="1522" LastEditorUserId="1522" LastEditDate="2012-10-11T05:56:48.683" LastActivityDate="2012-10-11T05:56:48.683" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3892" PostTypeId="1" CreationDate="2012-10-11T09:34:04.620" Score="9" ViewCount="1288" Body="&lt;p&gt;From what I collected, coffee is a magical potion that lets you feel energetic, and essentially not-sleepy. But are there any tradeoffs? I mean, if it was so beneficial, wouldn't the human body produce caffeine naturally?&lt;/p&gt;&#xA;" OwnerUserId="1369" LastActivityDate="2019-12-22T16:40:08.773" Title="Does drinking coffee have negative effects?" Tags="&lt;biochemistry&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3893" PostTypeId="2" ParentId="3892" CreationDate="2012-10-11T10:39:56.477" Score="13" Body="&lt;p&gt;First of all, the fact that a substance is beneficial does not mean that our body will, perforce, produce it naturally. Think of oxygen and water for example&lt;sup&gt;1&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the negative effects of coffee drinking, yes there are many although coffee has both a positive and a detrimental effect on human health. The main active ingredient in coffee is caffeine which can have the following negative effects:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Caffeine can increase blood pressure in non-habitual consumers.&lt;/li&gt;&#xA;&lt;li&gt;High blood pressure is associated with an increase in strokes, and cerebral &#xA;vascular disease, which in turn increase the risk of multi-infarct dementia.&lt;/li&gt;&#xA;&lt;li&gt;Caffeine may reduce control of fine motor movements (e.g., producing shaky hands)&lt;/li&gt;&#xA;&lt;li&gt;Caffeine can stimulate urination.&lt;/li&gt;&#xA;&lt;li&gt;Caffeine can increase cortisol secretion, some tolerance is developed.&lt;/li&gt;&#xA;&lt;li&gt;Caffeine can contribute to increased insomnia and sleep latency.&lt;/li&gt;&#xA;&lt;li&gt;Caffeine withdrawal produces headache, fatigue and decreased alertness.&lt;/li&gt;&#xA;&lt;li&gt;Caffeine is addictive.&lt;/li&gt;&#xA;&lt;li&gt;High doses of caffeine (300 mg or higher) can cause anxiety.&lt;/li&gt;&#xA;&lt;li&gt;High caffeine consumption has been linked to an increase in the likelihood of experiencing auditory hallucinations. A study conducted by the La Trobe University School of Psychological Sciences revealed that as few as five cups of coffee a day could trigger the phenomenon.&lt;/li&gt;&#xA;&lt;li&gt;High caffeine consumption accelerates bone loss at the spine in elderly postmenopausal women.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The list above comes from the very comprehensive wikipedia page on the health effects of caffeine. In fact, wikipedia is particularly good on this subject, see the following pages:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Caffeine&quot;&gt;http://en.wikipedia.org/wiki/Caffeine&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Health_effects_of_caffeinehttp://&quot;&gt;http://en.wikipedia.org/wiki/Health_effects_of_caffeine&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Health_effects_of_coffee&quot;&gt;http://en.wikipedia.org/wiki/Health_effects_of_coffee&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt; Our bodies &lt;em&gt;do&lt;/em&gt; produce both Oxygen and water as byproducts of various reactions but nowhere near enough to satisfy our need for these substances. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-10-11T17:29:00.360" LastActivityDate="2012-10-11T17:29:00.360" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3894" PostTypeId="2" ParentId="1777" CreationDate="2012-10-11T11:58:44.107" Score="3" Body="&lt;p&gt;These two links go through the specifications required for the PDB format:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Link1: &lt;a href=&quot;http://deposit.rcsb.org/adit/docs/pdb_atom_format.html&quot; rel=&quot;nofollow&quot;&gt;http://deposit.rcsb.org/adit/docs/pdb_atom_format.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Link1 primarily goes through the specs. required if you say have a NMR file you would therefore require the &lt;code&gt;MODEL&lt;/code&gt; statement. It also goes through other statements such as when to use &lt;code&gt;TER&lt;/code&gt; and how each &lt;code&gt;ATOM&lt;/code&gt; line should look etc...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Link2: &lt;a href=&quot;http://www.wwpdb.org/documentation/format33/v3.3.html&quot; rel=&quot;nofollow&quot;&gt;http://www.wwpdb.org/documentation/format33/v3.3.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Link2 goes through the other statements such as &lt;code&gt;HEADER&lt;/code&gt;, &lt;code&gt;REMARKS&lt;/code&gt; and &lt;code&gt;TITLE&lt;/code&gt;&lt;/p&gt;&#xA;" OwnerUserId="158" LastActivityDate="2012-10-11T11:58:44.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3895" PostTypeId="1" CreationDate="2012-10-11T12:12:27.837" Score="4" ViewCount="8582" Body="&lt;p&gt;I had today an experiment that we put 95% alcohol to the blood which made it completely transparent so hemolysis must have occurred.&#xA;I started to think about the reasons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that this is because alcohol dissolved the lipid membrane of cells outside of the cell. &#xA;Alcohol molecule is also very small.&#xA;I think that I can go through the bilayer too.&#xA;So I started to think that the other possible reason was that alcohol went inside the cell so caused&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;dissolution of the membrane from the inner side&lt;/li&gt;&#xA;&lt;li&gt;increase in the volume of the cell so bursting&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the main reasons why Alcohol cause hemolysis to the red blood cell?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="69" LastEditDate="2013-01-02T13:37:06.693" LastActivityDate="2013-01-02T13:37:06.693" Title="Why does alcohol cause the hemolysis of RBC in a large proportion?" Tags="&lt;cell-biology&gt;&lt;alcohol&gt;&lt;red-blood-cell&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3896" PostTypeId="2" ParentId="3888" CreationDate="2012-10-11T14:40:04.213" Score="4" Body="&lt;p&gt;If you ask Dr. Duke's phytochemical database, by far the most solanine is found in green potatoe &lt;strong&gt;fruits (their skin)&lt;/strong&gt;, with much less in leaves and tissues. Similar values are seen in green tomatoes, with dozens of mg per 100g fruit. There is no value for &lt;em&gt;Solanum dulcamara&lt;/em&gt; (doesn't mean there is nothing in it) but it appears to have small quantities of atropine. Furthermore, Wikipedia gives for solanine a minimum toxically effective dose for humans of 200 mg---that's where dizzyness and dispnoe starts---, and gives for children a lethal amount of &lt;em&gt;S. dulcamara&lt;/em&gt; of 30-40 &lt;strong&gt;unripe&lt;/strong&gt; berries or less. The amount of solanine increases (in potato) when temperature goes up, because it is produced by plants as an antifungal against rot. Ripening in &lt;em&gt;S. dulcamara&lt;/em&gt; and, as we know all ourselves, potato and tomato, destroys solanine, so fully ripe berries seem to be okay. Solanine does &lt;em&gt;not&lt;/em&gt; degrade when cooked but is lost with the cooking water. For an account of solanine poisoning from potatoes see e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1597169/&quot; rel=&quot;noreferrer&quot;&gt;this free paper&lt;/a&gt;. Newer potato varieties have much less solanine than those from former times.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ars-grin.gov/duke/&quot; rel=&quot;noreferrer&quot;&gt;http://www.ars-grin.gov/duke/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://de.wikipedia.org/wiki/Solanin&quot; rel=&quot;noreferrer&quot;&gt;http://de.wikipedia.org/wiki/Solanin&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Know your databases!&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-10-11T14:40:04.213" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3897" PostTypeId="2" ParentId="3895" CreationDate="2012-10-11T14:54:44.320" Score="1" Body="&lt;p&gt;Ethanol, in less than 50% concentration, emulgates lipids and, through interference with hydrogen bonds, leads to conformational changes in proteins. Higher concentrations lead to denaturation of proteins and osmolysis of cells through small defects, so they finally burst, as ethanol forces a concentration equilibrium. This is why it's a good desinfection substance. But you could use any other small molecule polar solvent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ethanol#Antiseptic&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Ethanol#Antiseptic&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="43" LastEditDate="2012-10-11T15:28:09.287" LastActivityDate="2012-10-11T15:28:09.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3898" PostTypeId="1" AcceptedAnswerId="3900" CreationDate="2012-10-11T15:16:15.247" Score="7" ViewCount="734" Body="&lt;p&gt;I distinctly remember an episode of &lt;i&gt;NOVA&lt;/i&gt; from the early 1980&amp;rsquo;s that concerned itself with gold. One of the points that was made was that there are trace amounts of gold in the human body, specifically in the heart, and without this gold our hearts wouldn't beat. I've never been able to find another citation of this. Is this true?&lt;/p&gt;&#xA;" OwnerUserId="1523" LastActivityDate="2012-10-11T17:10:44.890" Title="Does the Heart Require Gold?" Tags="&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3899" PostTypeId="1" CreationDate="2012-10-11T16:30:31.030" Score="3" ViewCount="1577" Body="&lt;p&gt;I understand that it primarily enters the body through the nose by by &quot;feeding on the olfactory neurons in the nose&quot; as answered here in a &lt;a href=&quot;https://biology.stackexchange.com/q/820/1306&quot;&gt;different question&lt;/a&gt;. Would the nerve cells in the eyes present a similar entryway?&lt;/p&gt;&#xA;" OwnerUserId="1524" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-03-27T11:03:02.800" Title="Can Naegleria fowleri enter through the eyes ( example rinsing/splashing eyes with water)" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;parasitism&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3900" PostTypeId="2" ParentId="3898" CreationDate="2012-10-11T17:10:44.890" Score="6" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.webelements.com/gold/biology.html&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; source, gold is not a necessary trace element for living organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would have been cool, though...&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2012-10-11T17:10:44.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3901" PostTypeId="1" CreationDate="2012-10-11T18:13:24.453" Score="11" ViewCount="2290" Body="&lt;p&gt;I have a weight matrix of length 20 x 15 (amino acids x sequence positions). Each element of my weight matrix is a relative probability&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I have a sequence say &quot;AAPGTGASMHSGLLW&quot; how would I score it against the matrix? I tried taking the product of probabilities corresponding to the matrix, but I end up with a really small number&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any ideas?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider the simple matrix:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;    1    2   3     4&#xA;A 0.3 0.90 0.5 0.0001&#xA;B 0.2 0.05 0.4 0.2&#xA;C 0.5 0.05 0.1 0.8&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The best match is, with a score of:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;CAAC = 0.5 * 0.9 * 0.5 * 0.8 = 0.18&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;If you change the first letter to an B instead of C&lt;/p&gt;&#xA;&#xA;&lt;p&gt;you get a match, with a score of:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;BAAC = 0.2 * 0.9 * 0.5 * 0.8 = 0.072&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Which is a huge difference for such a small change...&#xA;This is even worse with my larger matrix since the score is easily affected by small probabilities &lt;/p&gt;&#xA;" OwnerUserId="1526" LastEditorUserId="1526" LastEditDate="2012-10-12T04:57:04.887" LastActivityDate="2014-08-15T19:07:35.277" Title="Scoring sequence against position weight matrix" Tags="&lt;bioinformatics&gt;&lt;mathematical-models&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3902" PostTypeId="2" ParentId="3895" CreationDate="2012-10-11T18:54:45.520" Score="4" Body="&lt;p&gt;Well, it turns out the situation is more complex. I had assumed the answer was what &lt;a href=&quot;https://biology.stackexchange.com/a/3897/1306&quot;&gt;rwst suggests&lt;/a&gt; or something to do with osmotic pressure. It seems that we don't really know that well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=1998708&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper from 1991&lt;/a&gt;, Chi and Wu suggest the following possible mechanisms :&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Membrane fusion during the shedding of exovesicles might produce a transient decrease of the permeability barrier. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Increase of lipid dynamics by the alcohol could decrease the packing of the&#xA;bilayer. The membrane barrier behaves like a soft polymer, which can sieve solutes. The meshes in the polymer might become larger if its packing density is&#xA;reduced. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Lateral phase separation of lipids could induce packing defects in the lipid domain. This has been observed for long chain alcohols and postulated to be responsible for the increase of membrane permeability by amphiphiles. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Increase of the dielectric constant of the membrane by the alcohol would also increase the partition of hydrophilic solutes into the membranes. Such an increase has been postulated to be responsible for the increase of the permeability by aliphatic alcohols.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Modification of the intrinsic membrane domain might follow modification of the membrane skeleton by the alcohol. Accordingly, aggregation of intrinsic proteins might cause membrane modification mentioned under point 2 to 4.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The authors state that it is not possible to decide between the&#xA;various possibilities, but they seem to prefer point 5:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Although it is not possible to decide between the various&#xA;  possibilities from the present data, we showed that the&#xA;  release of membrane fragments from ethanol-treated RBC was not a&#xA;  requirement for the creation of membrane pores since it occurred at a&#xA;  time much later than the detection of K ÷ leakage. In addition, we&#xA;  found that changes of membane rheological properties preceded the&#xA;  permeability increase. These properties have been related to&#xA;  the membrane skeletal protein spectrin. Moreover, ethanol has&#xA;  been shown to affect the skeleton. The processes leading to&#xA;  the formation of pores in ethanol-treated RBC may thus relate to a&#xA;  deranged cytoskeletal network, followed by the aforementioned&#xA;  alteration of membrane properties.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The plot thickens, apparently, low concentrations of alcohol protect erythrocytes from hemolysis while higher concentrations can cause it. The following are extracts from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=10446301&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tyulina &lt;em&gt;et al&lt;/em&gt;&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The seeming paradox between the direct haemolytic effect of ethanol on&#xA;  erythrocytes (Fig. 1) and the stabilizing effect of ethanol on&#xA;  erythrocytes undergoing NaOCl-induced haemolysis (Fig. 2) could be&#xA;  explained by the relatively small destabilizing effect of ethanol&#xA;  which is observed (&amp;lt;1% haemolysis) over 16 h. This effect would be&#xA;  negligible in the short time period (generally &amp;lt;10 min) assay for&#xA;  NaOCl-induced haemolysis where 100% of the cells are haemolysed. An&#xA;  alternative explanation for this paradox is that the mechanisms of&#xA;  haemolysis induced by ethanol and NaOCl are different. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It therefore appears that ethanol does not induce significant&#xA;  oxidative stress in the human erythrocyte, and these data are in&#xA;  agreement with previous studies (Seeman et al., 1971), in which it was&#xA;  found that low ethanol concentrations could protect erythrocytes&#xA;  against haemolysis. Although the mechanism for this protective effect&#xA;  is unknown, it has previously been suggested (Halliwell and&#xA;  Gutteridge, 1999) that ethanol can serve as a hydrogen donor in the&#xA;  elimination of the hydroxyl radical with formation of water and the&#xA;  2-hydroxyethyl radical. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors then state (emphasis mine):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In summary, we conclude that the damage to erythrocytes which occurs&#xA;  on in vitro exposure to ethanol &lt;strong&gt;may be caused, at least in part, by&#xA;  unmetabolized ethanol directly&lt;/strong&gt;, rather than by the oxidation of&#xA;  ethanol to acetaldehyde or its conversion to FAEE.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would guess this &quot;direct effect&quot; is something very much like what rwst suggested but the fact that the authors, who clearly work in this field, do not say so makes me think that the situation is more complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in conclusion, the exact details of alcohol's hemolytic properties don't seem to be understood in great detail. Admittedly, neither of these articles is very recent, if anyone can find a more up to date account I would love to read it.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;REFERENCES:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=1998708&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chi LM, Wu WG. Mechanism of hemolysis of red blood cell mediated by ethanol.&#xA;Biochim Biophys Acta. 1991 Feb 11;1062(1):46-50.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=10446301&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tyulina OV, Prokopieva VD, Dodd RD, Hawkins JR, Clay SW, Wilson DO, Boldyrev&#xA;AA, Johnson P. In vitro effects of ethanol, acetaldehyde and fatty acid ethyl&#xA;esters on human erythrocytes. &lt;em&gt;Alcohol Alcohol.&lt;/em&gt; 2002 Mar-Apr;&lt;strong&gt;37&lt;/strong&gt;(2):179-86.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=11912075&quot; rel=&quot;nofollow noreferrer&quot;&gt;Trandum C, Westh P, Jørgensen K, Mouritsen OG. Association of ethanol with&#xA;lipid membranes containing cholesterol, sphingomyelin and ganglioside: a&#xA;titration calorimetry study. &lt;em&gt;Biochim Biophys Acta.&lt;/em&gt; 1999 Aug 20;&lt;strong&gt;1420&lt;/strong&gt;(1-2):179-88.&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2012-10-11T18:54:45.520" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="3903" PostTypeId="1" CreationDate="2012-10-11T20:04:51.513" Score="2" ViewCount="25" Body="&lt;p&gt;This is a question that is a little bit hard to define for me. &lt;strong&gt;I'm interested in learning more about times of &quot;attractor/entrainment&quot; processes that may take place in the body/brain of mammals, and particularly humans.&lt;/strong&gt; I want to get a general idea of how long it takes for a mammal to switch into a new mode of operation, be it behavior or physiological change? Is it days, weeks or more?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, a polar circle animals may change the color of their fur in response to photoperiod changes. How quickly does the change get registered and take place? Is it days, weeks or months?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example might be a mating season of siberian hamster, where their testes weight changes in response to photoperiod duration. How long does it take for a behavior change like that to fully manifest?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've read that it takes ~21 days for a human to create a habit or break one. Is there any biological basis for this observation? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure how to search for information like that, as it seems to me such things might only be incidentally mentioned in scientific articles. Are there some keywords that may help me improve the search results?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for any input.&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-10-11T20:04:51.513" Title="How to seek information on the duration of biological entrainment processes in mammals?" Tags="&lt;human-biology&gt;&lt;photoperiod&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2014-06-11T09:06:35.653" ContentLicense="CC BY-SA 3.0" />
  <row Id="3904" PostTypeId="2" ParentId="3901" CreationDate="2012-10-11T20:35:47.093" Score="3" Body="&lt;p&gt;According to [this page][1], you should take the sum and not the product:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Once a Profile has been derived from a set of functionally related&#xA;  sites, the Profile can be used to scan a query sequence for the&#xA;  presence of potential sites. Usually you run a window the length of&#xA;  the matrix along the sequence, and sum the coefficients from the&#xA;  matrix corresponding to each nucleotide in each position on the window&#xA;  sequence. Formally, the score of a matrix M for a site s of length l&#xA;  (s = s1, ... , sl, and sk being one of {A, C, G, T}) is computed as&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;$m_s=\sum\limits_{j=1}^lM_{s_{lj}}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I highly recommend you read the rest of the page, the author, Roderic Guigó, is an authority on the subject. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="3340" LastEditDate="2014-08-15T19:07:35.277" LastActivityDate="2014-08-15T19:07:35.277" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3905" PostTypeId="1" AcceptedAnswerId="3908" CreationDate="2012-10-11T21:57:14.307" Score="6" ViewCount="3811" Body="&lt;p&gt;Do plants grow differently when given sun light, wolfram lamp, fluorescent light, LED light, infrared, ultraviolet, x-ray, unfocused laser and stroboscope?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2015-08-03T22:27:05.913" Title="Does the light color spectrum and frequency matter for photosynthesis?" Tags="&lt;photosynthesis&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3906" PostTypeId="2" ParentId="3901" CreationDate="2012-10-12T00:58:53.180" Score="12" Body="&lt;p&gt;The probabilities are correct. You must take the product (in log space this is equivalent to sum). The reason the probability looks small is just that you are perhaps thinking the score should be close to 1. However, this is not the case. To get a score of 1, you need the PWM to have 1/0/0/0 at all positions and get a perfect match.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what should you compare to? What people usually do is compare this to a background distribution, the easiest being uniform, so the PWM is 0.25 everywhere. For your example, the score in this case will be 0.25^4 = ~0.004 and this is what you should expect by random.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is why people usually look at the ratio between the score of the PWM relative to the score for the background model (and usually take the log2 of that), which in your case will be 0.18/0.004 = ~46 so the sequence you got is 46 times more than you would expect by random! And for your second example, 0.072/0.004 = ~18 times more than expected, so that is still high.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More conceptually, what you are doing is comparing two probabilistic models, your PWM and a background PWM, and comparing the probability to get your observed sequence according to each one of them. This is a common approach in general for comparing probabilistic models, even if they are more complicated.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2012-10-12T01:04:45.607" LastActivityDate="2012-10-12T01:04:45.607" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="3907" PostTypeId="1" CreationDate="2012-10-12T01:48:38.593" Score="7" ViewCount="100" Body="&lt;p&gt;I want to find which genes in the human genome can potentially be complementary to a transcript that could act as antisense transcript inhibtion? Are cis-NATs (naturally occuring anti-sense transcripts) considered different transcripts and named differently or do they have the same name as the sense transcript?&lt;/p&gt;&#xA;" OwnerUserId="601" LastEditorUserId="43" LastEditDate="2012-10-12T19:25:01.927" LastActivityDate="2012-11-30T15:44:26.600" Title="Do antisense transcripts have different names than their sense strand transcripts?" Tags="&lt;genetics&gt;&lt;genomics&gt;&lt;mrna&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3908" PostTypeId="2" ParentId="3905" CreationDate="2012-10-12T05:11:12.750" Score="6" Body="&lt;p&gt;It matters a lot.&#xA;Take a look at this graph:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/VYS0X.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This graph is for the &quot;normal&quot; plants containing &lt;a href=&quot;http://en.wikipedia.org/wiki/Chlorophyll&quot; rel=&quot;noreferrer&quot;&gt;chlorophyll&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There're also &quot;abnormal&quot; :-) ones, simple water plants and cyanobacteria, that contain various &lt;a href=&quot;http://en.wikipedia.org/wiki/Phycobilin&quot; rel=&quot;noreferrer&quot;&gt;phycobilins&lt;/a&gt; for photosynthesis instead of the chlorophyll.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your question is practical, I'd recommend using specialy-designed fluorescent lamps called &lt;a href=&quot;http://en.wikipedia.org/wiki/Grow_light&quot; rel=&quot;noreferrer&quot;&gt;grow light&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1517" LastActivityDate="2012-10-12T05:11:12.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3909" PostTypeId="1" AcceptedAnswerId="3910" CreationDate="2012-10-12T08:00:39.623" Score="23" ViewCount="8126" Body="&lt;p&gt;Why can't humans drink sea water?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would seem to be a huge evolutionary advantage for an animal to be able to drink sea water rather than have to rely on fresh water, and it's provably not impossible due to the existence of sea mammals that must filter the sea water somehow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could someone explain to me any likely reasons that this is the case?&lt;/p&gt;&#xA;" OwnerUserId="1529" LastActivityDate="2016-11-16T23:35:11.043" Title="Why can't humans drink sea water?" Tags="&lt;evolution&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3910" PostTypeId="2" ParentId="3909" CreationDate="2012-10-12T12:37:47.590" Score="29" Body="&lt;p&gt;For humans, our blood and other tissues have a salinity which is less than that of sea water. The &lt;a href=&quot;http://bionumbers.hms.harvard.edu/bionumber.aspx?&amp;amp;id=100803&amp;amp;ver=1&amp;amp;trm=osmolarity&quot;&gt;osmolarity of blood is 275-299mOsm/L&lt;/a&gt;, while the &lt;a href=&quot;http://bionumbers.hms.harvard.edu//bionumber.aspx?&amp;amp;id=100802&amp;amp;ver=5&quot;&gt;osmolarity of seawater is ~1000 mOsm/L&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The major reason we need to drink and excrete (sweat, breath and urine) water is to rid the system of waste- i.e. water soluble chemicals or heat we do not need.  The kidneys do a lot of this work and they need a reasonable osmotic potential to help them.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The osmotic potential is the tendency of molecules, for instance salts, to diffuse from one reservoir of liquid to another.  The kidneys burn metabolic energy (food) to create a slightly higher concentration of waste chemicals into the bladder/urine.  Other organs will fail or also work to maintain a local salt concentration (e.g. any nerve cell which depends on Na+/K+ concentrations to transmit their signals.  But the kidneys are the gatekeepers of salinity in the body.  They work hardest (and can get injured) when there is more salt in the water we drink. If you drink sea water you will quickly find your kidneys overworked and not really functioning.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's why salt water will tend to make you thirsty (if you can drink any at all). Most people will gag when they drink even a little sea water, much less a glassful. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.scientificamerican.com/article/how-can-sea-mammals-drink/&quot;&gt;Sea mammals actually eat their fresh water.&lt;/a&gt; They rely on the fluid they get from fish to keep their salt balance.  Its true that some animals like fish and molluscs etc have adapted other means of keeping their salt balance in check.  Its just also true that its a lot of work to keep this ability and when animals move away from the oceans, they quickly lose that ability.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="10456" LastEditDate="2015-07-23T05:59:03.477" LastActivityDate="2015-07-23T05:59:03.477" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="3911" PostTypeId="2" ParentId="3907" CreationDate="2012-10-12T13:56:01.143" Score="6" Body="&lt;p&gt;&lt;em&gt;If&lt;/em&gt; the anti-sense transcript is correctly annotated and in the databases (a very very big if), then it will have a different name. For example, the mouse Msx1 anti-sense transcript has the RefSeq accession &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/NR_027920?report=GenBank&quot; rel=&quot;nofollow&quot;&gt;NR_027920&lt;/a&gt; while the sense transcript of the same gene is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/NM_010835?report=GenBank&quot; rel=&quot;nofollow&quot;&gt;NM_010835&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, each transcript that is transcribed from a given locus has a different accession. The same is true for alternatively spliced transcripts. If a given gene has 4 AS transcripts, each of these transcripts will have a different, unique accession. The human insulin receptor gene, for example, has two protein coding transcripts, each with its own accession: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/NM_000208&quot; rel=&quot;nofollow&quot;&gt;NM_000208&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/NM_001079817&quot; rel=&quot;nofollow&quot;&gt;NM_001079817&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may be interested in a recent analysis of cis-NATs in 10 species&lt;a href=&quot;http://dx.doi.org/10.1534/genetics.106.069484&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt; and also in &lt;a href=&quot;http://natsdb.cbi.pku.edu.cn/&quot; rel=&quot;nofollow&quot;&gt;NATsDB&lt;/a&gt;: Natural Antisense Transcripts DataBase&lt;a href=&quot;http://dx.doi.org/10.1093/nar/gkn470&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[2]&lt;/sup&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://natsdb.cbi.pku.edu.cn/&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Osato N, Suzuki Y, Ikeo K, Gojobori T&lt;/strong&gt;. 2007. Transcriptional Interferences in &lt;em&gt;cis&lt;/em&gt; Natural Antisense Transcripts of Humans and Mice. Genetics, 176(2): 1299-1306, doi:10.1534/genetics.106.069484.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1093/nar/gkn470&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Li JT, Zhang Y, Kong L, Liu QR, Wei L&lt;/strong&gt;. 2008. &lt;em&gt;Trans&lt;/em&gt;-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Research, 36(15):4833-44, doi:10.1093/nar/gkn470.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="43" LastEditDate="2012-11-30T15:44:26.600" LastActivityDate="2012-11-30T15:44:26.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3913" PostTypeId="2" ParentId="3241" CreationDate="2012-10-12T19:56:05.130" Score="2" Body="&lt;p&gt;I thought this was an interesting subject and I had some time to do a little search around today.  I can't find anything better than the review you point out. All I can do is add a few interesting notes since 2001.  Nothing really turns over Rattenborg et al. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sleep is itself a poorly understood process and most of the theories of the necessity of sleep can teeter precariously with discoveries like this report that &lt;a href=&quot;http://www.bri.ucla.edu/bri_weekly/news_050714.asp&quot; rel=&quot;nofollow noreferrer&quot;&gt;baby dolphins and killer whales and their mothers simply don't sleep at all for the first few months of life&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Rattenborg review is only guessing, but I think its clear that there is a cost to unihemispheric sleep, even if we don't know what it is.  Cetaceans and birds and perhaps reptiles having unihemispheric sleep are all cases where there are perpetual and strong selection forces that maintain the ability in these animals.  Without &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0166432899000704&quot; rel=&quot;nofollow noreferrer&quot;&gt;constant predation experienced by tasty ducks&lt;/a&gt; or the vagaries of being an air-breathing underwater mammal, animals quickly lose their ability to sleep with one half their brain, one assumes because the ability to maintain it is particular and easily lost with variation.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22960411&quot; rel=&quot;nofollow noreferrer&quot;&gt;Modelling work of the hemispheres&lt;/a&gt; in sleep indicates that the connections between the hemispheres are modulated between the two modes of sleep - there may be advantages to such brain structures for instance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://takingapartcats.wordpress.com/2011/04/22/halfbrain/&quot; rel=&quot;nofollow noreferrer&quot;&gt;blog post&lt;/a&gt; is a good read though and a bit more recent, though most of the references are from before 2001. Dolphins do use both hemispheres to sleep, but just not very often (about 15% of the time), indicating there is some advantage even for these animals.  Seals may alternate between bi and uni-hemispheric sleep when they are on land and at sea. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you were wondering if there was something you were missing - I'd say no.  At the time of this writing &lt;a href=&quot;https://biology.stackexchange.com/questions/3241/disadvantages-of-unihemispheric-sleep&quot;&gt;THIS&lt;/a&gt; web page is the sixth hit on a google search for the term 'unihemispheric sleep'....&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2012-10-13T23:21:26.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3914" PostTypeId="1" AcceptedAnswerId="3917" CreationDate="2012-10-12T22:06:06.227" Score="3" ViewCount="3112" Body="&lt;p&gt;I was reading recently that the age of menarche has decreased in the last 150 years, and was wondering if the age of menopause in humans has also changed recently? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would there be selective pressure for it to increase currently, given that the average age of women having their first child is increasing in the West anyway?&lt;/p&gt;&#xA;" OwnerUserId="476" LastEditorUserId="57" LastEditDate="2012-10-13T11:02:24.337" LastActivityDate="2012-10-13T15:14:22.250" Title="Has the age at which menopause occurs changed throughout history?" Tags="&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3915" PostTypeId="1" CreationDate="2012-10-13T05:15:31.690" Score="15" ViewCount="315" Body="&lt;p&gt;Most (if not all) industrialized countries follow a 7-day work week now, such that we are bound to follow a certain weekly trend in matters such as pollution generation, where to go (e.g. stay in town during weekdays, more likely to go to parks during weekends), what to do (mow the lawn on weekends).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any evidence of any species evolving to adapt to the pace of the human 7-day week lifestyle?&lt;/p&gt;&#xA;" OwnerUserId="1114" LastActivityDate="2012-10-17T07:27:13.120" Title="Has the human 7-day week had any impact on the evolution of species?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="3917" PostTypeId="2" ParentId="3914" CreationDate="2012-10-13T15:02:38.940" Score="2" Body="&lt;p&gt;Quick answer: Yes, but not in the last 150 years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There seems to be no clear link between age at menarche and age at menopause (taken from [&lt;a href=&quot;http://www.e-pamj.com/pdf/PAMJ%20Articles/menopause%203.pdf&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;While earlier studies were able to establish an association between&#xA;  early age of menarche and later menopause (Frisch 1978; 1987), more&#xA;  modern studies have not been able to confirm this effect (Whelan et&#xA;  al., 1990; van Noord et al., 1997).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Aristotle's assessment was similar to those of Hippocrates and also&#xA;  Roman authors, so it seems that 2000 years ago most women entered the&#xA;  menopause in their early 40s. Mediaeval authors, however, gave the 50s&#xA;  as the age when menses ceased-much closer to the timing for twentieth&#xA;  century women.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Jean Ginsburg in [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov.gate1.inist.fr/pubmed/2059681&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;] states (emphasis mine):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the past 100 years data from schoolchildren have shown a steady&#xA;  fall in the age at menarche in industrialised communities. Has&#xA;  there been a corresponding change in the age at the menopause?&#xA;  Unfortunately, reported surveys of the menopause have suffered from&#xA;  methodological defects. [...] &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Nevertheless, those studies least subject to bias show a striking&#xA;  agreement that the median age at the menopause is currently around 50&#xA;  in Western industrialised societies. In Britain it is 50.78, in the&#xA;  United States 49.8 and in white South Africans 48.7 &lt;strong&gt;with little&#xA;  apparent change over the past century.&lt;/strong&gt; In non-European women, however,&#xA;  the menopause seems to occur earlier-in South Africa and the United&#xA;  States black women have an earlier menopause than white women.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, while early menarche is, apparently, irrelevant, age of onset of menopause has increased since antiquity but has remained relatively stable since the middle ages. Therefore, there have been no significant changes in the age of onset of menopause in the time frame you defined (150 years).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, Bengtsson &lt;em&gt;et al&lt;/em&gt; [&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0378512279900033&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;] state that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our study has, thus, not supported the view that the menopausal age is&#xA;  rapidly changing.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.e-pamj.com/pdf/PAMJ%20Articles/menopause%203.pdf&quot; rel=&quot;nofollow&quot;&gt;C. Keck, Predictive Factors to Determine Age of Onset of Menopause, &lt;em&gt;PAMJ&lt;/em&gt;&#xA;, &lt;strong&gt;3&lt;/strong&gt;, 2005&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov.gate1.inist.fr/pubmed/2059681&quot; rel=&quot;nofollow&quot;&gt;Ginsberg J. What determines the age at the menopause? BMJ. 1991 Jun&#xA;1;&lt;strong&gt;302&lt;/strong&gt;:1288-9.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0378512279900033&quot; rel=&quot;nofollow&quot;&gt;Calle Bengtsson, Olof Lindquist, Lasse Redvall, Is the menopausal age rapidly changing?, &lt;em&gt;Maturitas&lt;/em&gt;, &lt;strong&gt;1&lt;/strong&gt;(3), February 1979, Pages 159-164&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-10-13T15:14:22.250" LastActivityDate="2012-10-13T15:14:22.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3918" PostTypeId="1" AcceptedAnswerId="3923" CreationDate="2012-10-13T15:24:06.560" Score="2" ViewCount="3264" Body="&lt;p&gt;I was reading a &lt;em&gt;Scientific American&lt;/em&gt; story, “Controversial Spewed Iron Experiment Succeeds as Carbon Sink” (by David Biello), when I came across this sentence:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;“The problem for scientists is that oceanic waters tend to mix, which&#xA;  makes monitoring and &lt;em&gt;delineating an experiment&lt;/em&gt; in the ocean&#xA;  challenging.”&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm wondering what “&lt;strong&gt;delineate&lt;/strong&gt;” means in this context. I think I grasp the general idea of this sentence, but it is the exact meaning of the word that has been troubling me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could someone kindly enlighten me on this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="1533" LastEditorUserId="16866" LastEditDate="2020-04-16T04:57:07.190" LastActivityDate="2020-04-16T04:57:07.190" Title="What does &quot;delineate&quot; mean in this context?" Tags="&lt;terminology&gt;&lt;experimental&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3920" PostTypeId="1" AcceptedAnswerId="3921" CreationDate="2012-10-13T15:45:38.570" Score="2" ViewCount="564" Body="&lt;p&gt;I came across a confusing word when I was reading a &lt;em&gt;Scientific American&lt;/em&gt; &lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=fertilizing-ocean-with-iron-sequesters-co2&quot; rel=&quot;nofollow&quot;&gt;story&lt;/a&gt;, “Controversial Spewed Iron Experiment Succeeds as Carbon Sink” (by David Biello). It goes like this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;“One key to the whole experiment’s success turns out to be the&#xA;  specific diatoms involved, which use silicon to make their shells and&#xA;  tend to form long strands of cellular slime after their demise that&#xA;  falls quickly to the seafloor.”&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm wondering what “&lt;strong&gt;cellular&lt;/strong&gt;” means in this context. Does it mean “&lt;strong&gt;of (diatom) cells&lt;/strong&gt;” or “&lt;strong&gt;porous&lt;/strong&gt;”?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could someone kindly enlighten me on this?&lt;/p&gt;&#xA;" OwnerUserId="1533" LastEditorUserId="57" LastEditDate="2012-10-13T23:20:43.147" LastActivityDate="2015-10-26T02:28:47.317" Title="What does &quot;cellular&quot; mean in this context?" Tags="&lt;microbiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3921" PostTypeId="2" ParentId="3920" CreationDate="2012-10-13T15:51:53.077" Score="1" Body="&lt;p&gt;My understanding is that the slime in question is formed of the bodies (the cells) of the dead diatoms. Where does porous come into it? Is it mentioned in a previous sentence?&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2012-10-13T15:51:53.077" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="3922" PostTypeId="2" ParentId="3918" CreationDate="2012-10-13T15:59:25.377" Score="2" Body="&lt;p&gt;To delineate an experiment is to describe precisely the conditions and the states of all the parameters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in your sentence it probably means a scientist might struggle to keep track of all the confounding factors (changing salinity, composition, dissolved gases, particulates, pH, temp, etc.) which might affect an experiment in such a dynamic system as the ocean.&lt;/p&gt;&#xA;" OwnerUserId="430" LastActivityDate="2012-10-13T15:59:25.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="3923" PostTypeId="2" ParentId="3918" CreationDate="2012-10-13T17:30:35.773" Score="2" Body="&lt;p&gt;I think this would me more on topic at &lt;a href=&quot;https://english.stackexchange.com/&quot;&gt;English.SE&lt;/a&gt;, but (from Merriam-Webster):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Delineate:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;1&lt;/strong&gt; a : to indicate or represent by drawn or painted lines&lt;br&gt;&#xA;  &amp;nbsp; &amp;nbsp;           b : to mark the outline of &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;2&lt;/strong&gt; : to describe, portray, or set forth with accuracy or in detail   — de·lin·ea·tor  noun&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In this case, it could be either meaning that is used. Either 2, as Richard Smith said in his answer, to define the experiment's parameters in general, or 1b, to mark, limit a specific area of the ocean in which the experiment will be done. Obviously, delimiting an area in a body of liquid is not very easy.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2017-04-13T12:38:11.520" LastActivityDate="2012-10-13T17:30:35.773" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="4923" PostTypeId="2" ParentId="785" CreationDate="2012-10-13T20:07:06.957" Score="4" Body="&lt;p&gt;Agree that anaerobic &lt;strong&gt;respiration&lt;/strong&gt; involves the electron transport chain and alternative terminal electron acceptors such as nitrate. However, respiring cells (whether respiring aerobically or anaerobically) can run the Krebs cycle. As long as there is a terminal electron acceptor, the NADH/FADH2 generated by the Krebs cycle can be oxidized back to NAD+ or FAD.&lt;/p&gt;&#xA;" OwnerUserId="1535" LastEditorUserId="146" LastEditDate="2012-10-14T22:07:11.543" LastActivityDate="2012-10-14T22:07:11.543" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="4924" PostTypeId="1" AcceptedAnswerId="6857" CreationDate="2012-10-13T21:35:17.150" Score="5" ViewCount="101" Body="&lt;p&gt;I'm having problems with data analysis here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have flow cytometry data being collected on a Fortessa, and when I import them into FlowJo 8.7, all of my fluorescence values are systematically 10X lower than they are on the cytometer. No idea what's going on here, anybody can help? If you want screenshots and photos of the data, I'm happy to post them up.&lt;/p&gt;&#xA;" OwnerUserId="1536" LastEditorDisplayName="user560" LastEditDate="2012-10-22T06:57:10.113" LastActivityDate="2013-01-19T17:13:07.353" Title="Flow cytometry issues" Tags="&lt;bacteriology&gt;&lt;flow-cytometry&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4925" PostTypeId="1" AcceptedAnswerId="4927" CreationDate="2012-10-14T11:08:09.473" Score="3" ViewCount="801" Body="&lt;p&gt;If the provirus was not formed yet, can the virus make viral enzymes? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I know that it already has some, but supposing it doesn't)&lt;/p&gt;&#xA;" OwnerUserId="1537" LastEditorUserId="69" LastEditDate="2013-01-12T11:20:32.890" LastActivityDate="2018-07-04T22:48:40.203" Title="Can the RNA in the HIV virus make viral enzymes without entering the nucleus?" Tags="&lt;microbiology&gt;&lt;immunology&gt;&lt;hiv&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4926" PostTypeId="1" CreationDate="2012-10-14T12:00:12.263" Score="6" ViewCount="1623" Body="&lt;p&gt;&lt;em&gt;By &quot;children&quot; I mean young people at the age of 10 or lower.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that the adult brain cannot restore brain cells, but what about children? I mean, the brain must develop from a few cells to a 90 billion cells somehow, when do we lose this ability?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm also interested in cases when a child gets hit into the head (concussion). Can the damage  be fixed over time?&lt;/p&gt;&#xA;" OwnerUserId="1369" LastEditorUserId="69" LastEditDate="2012-12-02T15:49:25.527" LastActivityDate="2015-09-28T14:57:37.867" Title="Can children restore brain cells?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="4" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4927" PostTypeId="2" ParentId="4925" CreationDate="2012-10-14T13:21:34.643" Score="7" Body="&lt;p&gt;I am afraid your question is really not clear. You are asking one thing in the title of your question, another in the question body and a third in your comments. If you are asking (as you did in your comment above) what would happen if a virus with no enzymes were to infect a cell, see below. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of HIV (and other retroviruses) some of the most important enzymes contained in a normal viral particle are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A reverse transcriptase (RT): this enzyme reverse-transcribes the viral RNA genome to cDNA, &lt;/li&gt;&#xA;&lt;li&gt;An integrase: incorporates the cDNA produced by the RT into the host cell's DNA.&lt;/li&gt;&#xA;&lt;li&gt;A ribonuclease : an enzyme that can degrade (cut up) RNA. In the case of HIV this is the same protein as the RT.&lt;/li&gt;&#xA;&lt;li&gt;A protease: an enzyme that can degrade other proteins.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Viruses work by copying their genetic material (their DNA or RNA) into the host cell's genome and then hijacking the cell's replication machinery to make more copies of the virus. So, what would happen if these enzymes were absent? &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Without an integrase, the virus would not be able to insert its reverse transcribed DNA into the cell's genome.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Without an RT, the virus would not be able to copy its RNA into DNA. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The ribonuclease activity is also needed for successful reverse transcription to double stranded DNA (see [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21994660&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;] for a review and explanation of why.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The protease is necessary for the formation of new viral particles. Mutations in this enzyme result in aberrantly assembled virus particles with low infectivity [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=17210199&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;What you really must remember is that viruses are extremely streamlined. Everything they contain is essential. In some ways, you could say that viruses are the most highly evolved species (assuming they &lt;em&gt;are&lt;/em&gt; living species), they are the most highly specialized &quot;life forms&quot; we know of and they have managed to get rid of &lt;em&gt;all&lt;/em&gt; non-essential functions. The flip side of this is that everything that is left is essential, the virus cannot function without it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to answer your question, a virus without any enzymes is, essentially, not a virus. It would not work, would not successfully infect cells.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21994660&quot; rel=&quot;nofollow&quot;&gt;Greg L. Beilhartz and Matthias Götte, HIV-1 Ribonuclease H: Structure, Catalytic Mechanism and Inhibitors, &lt;em&gt;Viruses&lt;/em&gt; 2010, &lt;strong&gt;2&lt;/strong&gt;:900-926&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=17210199&quot; rel=&quot;nofollow&quot;&gt;Bukrinskaya A. HIV-1 matrix protein: a mysterious regulator of the viral life cycle. &lt;em&gt;Virus Res.&lt;/em&gt; 2007 &lt;strong&gt;124&lt;/strong&gt;(1-2):1-11.&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2015-10-05T02:05:48.307" LastActivityDate="2015-10-05T02:05:48.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4928" PostTypeId="2" ParentId="4926" CreationDate="2012-10-14T15:48:57.740" Score="3" Body="&lt;p&gt;I am not an expert in neurobiology, but this is what I have been able to find:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, the PNS (peripheral nervous system) does have remarkable &lt;a href=&quot;http://en.wikipedia.org/wiki/Neuroregeneration&quot; rel=&quot;nofollow&quot;&gt;neuroregeneration&lt;/a&gt; capabilities. However, the CNS (central nervous system), which includes the brain, has extremely limited neuroregeneration abilities. However, there are some interesting &lt;a href=&quot;http://blog.braininjury.com/tag/neuroregeneration/&quot; rel=&quot;nofollow&quot;&gt;examples&lt;/a&gt; of CNS recovery:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Children under six who undergo, unfortunately, a hemiectomy, whereby one half of their brain is taken out, are able to regain almost normal function because of the brain’s ability to rewire and literally take over the functions of the missing other half of the brain.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am guessing one thing that can explain this is that in children, the CNS is still developing, and so if there is damage, the CNS can just entirely replace damaged parts (this might be different than &quot;fixing&quot; which is required in adults). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, I am not an expert on this and would be glad to hear a neurobiologist's opinion.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="9943" LastEditDate="2015-09-28T14:00:06.053" LastActivityDate="2015-09-28T14:00:06.053" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="4929" PostTypeId="1" CreationDate="2012-10-14T18:37:42.247" Score="4" ViewCount="468" Body="&lt;p&gt;Finding numbers for the amount of neurons in the brain is quite easy. Finding them for other human organs is harder. How many neurons are there in the human heart?&lt;/p&gt;&#xA;" OwnerUserId="152" LastActivityDate="2012-10-14T18:48:31.280" Title="Amount of neurons in the heart" Tags="&lt;neurology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4930" PostTypeId="2" ParentId="4929" CreationDate="2012-10-14T18:48:31.280" Score="6" Body="&lt;p&gt;In terms of cell bodies? Zero.  There are autonomic &lt;em&gt;projections&lt;/em&gt; from the spinal cord (sympathetic) and vagus nerve (parasympathetic) to the &lt;a href=&quot;http://en.wikipedia.org/wiki/SA_node#Innervation&quot;&gt;sinoatrial node&lt;/a&gt;, the atrioventricular node, and at discrete points in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Autonomic_nervous_system#Circulatory_system&quot;&gt;atria and ventricles&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2012-10-14T18:48:31.280" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="4931" PostTypeId="2" ParentId="4924" CreationDate="2012-10-14T19:06:55.523" Score="1" Body="&lt;p&gt;I have this issue too with data from a Partec PAS III. I don't consider it a problem, as it's really just the x-axis which is one order of magnitude higher. At the end, all values coming from the machine are arbitrary values, so as long as the change is systematic, there's no problem.&lt;/p&gt;&#xA;" OwnerUserId="852" LastActivityDate="2012-10-14T19:06:55.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4932" PostTypeId="1" AcceptedAnswerId="4933" CreationDate="2012-10-15T13:59:13.427" Score="7" ViewCount="1273" Body="&lt;p&gt;What we know about our mammal ancestors that were alive (and survived) at the extinction event 65 million years ago?&lt;/p&gt;&#xA;" OwnerUserId="1086" LastActivityDate="2020-06-21T17:00:48.063" Title="What were the mammal ancestors like 65 million years ago?" Tags="&lt;palaeontology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4933" PostTypeId="2" ParentId="4932" CreationDate="2012-10-15T14:08:57.457" Score="11" Body="&lt;p&gt;Many of them looked like little rodents. However, several distinct mammalian lineages were already present, including &lt;a href=&quot;https://en.wikipedia.org/wiki/Monotreme&quot; rel=&quot;nofollow noreferrer&quot;&gt;Monotremes&lt;/a&gt;, marsupials and placental mammals. Throughout the whole Mesozoic era, mammals were already quite diversified! Also, even though most of the mammals that survived the &lt;a href=&quot;https://en.wikipedia.org/wiki/Cretaceous%E2%80%93Paleogene_boundary&quot; rel=&quot;nofollow noreferrer&quot;&gt;K/T boundary&lt;/a&gt; were rather small, there were already some larger mammals around in the Cretaceous.&lt;/p&gt;&#xA;&lt;p&gt;Here is a nice picture of a &lt;a href=&quot;http://www.cbc.ca/news/technology/story/2009/10/08/tech-biology-prehistoric-mammal.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;symmetrodont&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iPp1T.jpg&quot; alt=&quot;symmetrodont, prehistoric mammal&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;See a nice page on &lt;a href=&quot;http://dinosaurs.about.com/od/otherprehistoriclife/a/earlymammals.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;early mammals&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1435" LastEditorUserId="51661" LastEditDate="2020-06-21T17:00:48.063" LastActivityDate="2020-06-21T17:00:48.063" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="4935" PostTypeId="1" AcceptedAnswerId="4939" CreationDate="2012-10-15T20:20:09.857" Score="8" ViewCount="99" Body="&lt;p&gt;I have just read &lt;a href=&quot;https://biology.stackexchange.com/questions/3652/what-elements-are-a-possible-basis-for-life&quot;&gt;What elements are a possible basis for life?&lt;/a&gt; and I find myself wondering whether instead of seeking advanced life-forms at remote locales a La SETI, and perhaps fundamentally differently, we ought to be looking for similar microscopic life forms on comets that pass off-and-on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Granted, a comet may be near absolute 0 for a lot of the time, but microscopic life-forms are known to be capable of surviving lean periods by using a cyst, for instance. As far as the rest is concerned, comets probably contain some amount of ice, and hence water, too. Similarly a comet's sprint around the sun could provide some limited amount of gravity/mass too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, should we be looking for life on comets?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2012-10-16T18:34:15.947" Title="Should we be looking for extra-terrestrial life on comets?" Tags="&lt;biochemistry&gt;&lt;microbiology&gt;&lt;astrobiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4936" PostTypeId="1" CreationDate="2012-10-16T00:15:20.030" Score="4" ViewCount="4410" Body="&lt;p&gt;I'm wondering if someone out there has more information than me. Retinoids have well known metabolic pathways in vivo, and it's usually something like: &lt;code&gt;Retinyl Palmitate --&amp;gt; Retinol --&amp;gt; Retinaldehyde (Retinal) --&amp;gt; Retinoic Acid (Tretinoin)&lt;/code&gt; which is the biologically active form of the Retinoids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Retinoids are used in cosmetics all the time, and while Retinol is available OTC, Retinoic Acid (Tretinoin - a.k.a. &quot;Retin-A&quot; by brand) is available by prescription only since it is a 'stronger' version of Retinol. It's not difficult to find 1% Retinol creams or higher, but Retinoic Acid treatments top out at 0.1%. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I can't help but wonder 'why'? One study I was able to dig up was here: &lt;a href=&quot;http://www.fasebj.org/content/10/9/993.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Retinoic Acid Biosynthesis and Metabolism PDF&lt;/a&gt;. The table on page 5 shows Physiological Concentrations - starting at 50 microM for Retinol and ending at &quot;&amp;lt;50nM?&quot; suggesting an ultimate conversion rate of a little less than 10% which would make the 1% Retinol treatments roughly equivalent to a 0.1% Retinoic Acid treatment (and a 2% Retinol treatment to a 0.2% Retinoic Acid treatment - double what's available by prescription).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do other studies/other evidence support the rate of conversion of Retinol to Retinoic Acid to be roughly 10% or suggest than a 1% Retinol topical treatment is equivalent to a 0.1% Retinoic Acid topical treatment? Or are there some other interfering factors that reduce the utilization of Retinol to Retinoic Acid that I'm missing?&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="57" LastEditDate="2012-10-16T00:55:21.413" LastActivityDate="2012-11-13T21:06:19.267" Title="Conversion rate of topical Retinol to Retinoic Acid (Tretinoin)?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4937" PostTypeId="2" ParentId="4935" CreationDate="2012-10-16T00:46:55.780" Score="2" Body="&lt;p&gt;This is a cool idea and definitely we have found a lot of the chemicals important to life are associated with comets which have a lot of water too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another issue besides the v. low temperatures on comets, when they warm up to the sun are not long lived so I wonder if the &lt;a href=&quot;http://en.wikipedia.org/wiki/Comet#Fate_of_comets&quot; rel=&quot;nofollow&quot;&gt;a shorter lifespan would be an issue when they are seen&lt;/a&gt; in the temperate zones of the solar system.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still any cometary mission should try to do a biological survey when such things are more economical.  Right now even high profile missions like the current Mars missions are not spending any time looking for bacteria as we know it, but rather for other indications that life unlike our own might be there.  Its been very cautious going for xenobiologists so far. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-10-16T00:46:55.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4939" PostTypeId="2" ParentId="4935" CreationDate="2012-10-16T09:05:56.250" Score="4" Body="&lt;p&gt;Yes we should be and we are! Scientists have been analysing cometary material - but its a challenging task. The problem with looking at meteoritic material from comets on Earth is that it is generally contaminated with material &lt;em&gt;from&lt;/em&gt; Earth. In addition, meteorites get physically altered during their passage through the Earth's atmosphere due to the high temperatures of re-entry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the trick is to send missions to the comet. However, then the difficulty is in designing a mission that can analyse samples &lt;em&gt;in situ&lt;/em&gt;. &lt;a href=&quot;http://stardust.jpl.nasa.gov/home/index.html&quot; rel=&quot;nofollow&quot;&gt;NASA's Stardust mission&lt;/a&gt; got around this by sample return to Earth. The probe visited comet Wild-2 and found &lt;a href=&quot;http://adsabs.harvard.edu/abs/2009M&amp;amp;PS...44.1323E&quot; rel=&quot;nofollow&quot;&gt;the amino acid glycine&lt;/a&gt; among other interesting organic compounds. However, no evidence of life was found (metabolic products, organisms etc.) Further missions to comets (and asteroids) are planned, but they are not going to explicitly look for life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://adsabs.harvard.edu/abs/2009M&amp;amp;PS...44.1323E&quot; rel=&quot;nofollow&quot;&gt;Elsila, J.E., Glavin, D.P., &amp;amp; Dworkin, J.P. 2009, Meteoritics and Planetary Science, 44, 1323&lt;/a&gt;  &lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="1306" LastEditDate="2012-10-16T11:45:33.610" LastActivityDate="2012-10-16T11:45:33.610" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="4940" PostTypeId="2" ParentId="4936" CreationDate="2012-10-16T11:24:21.570" Score="1" Body="&lt;p&gt;My guess is that the effect you describe is due to compartmentalisation: both retinol and retinoate are practically lipophils and so will localize in membranes and other lipid &quot;pools&quot;, while both human retinal dehydrogenase enzymes are cytosolic. Probably the only occasion they have to get at their substrate is when it's bound to RBP. This however introduces another factor complicating the simple model.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-10-16T11:24:21.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4941" PostTypeId="2" ParentId="3889" CreationDate="2012-10-16T11:55:10.890" Score="2" Body="&lt;p&gt;Recently, samples from different parts of cottonwood trees have been sequenced (&lt;a href=&quot;http://www.nature.com/news/tree-s-leaves-genetically-different-from-its-roots-1.11156&quot; rel=&quot;nofollow&quot;&gt;Nature News&lt;/a&gt;). The conclusion:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;“The variation within a tree is as great as the variation across unrelated trees,” says Ken Paige, an evolutionary biologist at the University of Illinois at Urbana-Champaign, who led the team that made the discovery.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This doesn't say anything about overcoming self-incompatibility, and it probably depends on the mechanism of self-incompatibility if it can be overcome by accumulating mutations.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-10-16T11:55:10.890" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4942" PostTypeId="1" AcceptedAnswerId="4943" CreationDate="2012-10-16T13:45:54.997" Score="2" ViewCount="2479" Body="&lt;p&gt;I had today a class in microbiology and my teacher said that the Decolorizer component is the critical one and cannot be more than 30 seconds.&#xA;The decolorizer has alcohol in high concentration, my lecturer says 95%.&#xA;I know that alcohol dissolves the lipid membrane, more exactly &lt;a href=&quot;https://biology.stackexchange.com/questions/3895/why-does-alcohol-cause-the-hemolysis-of-rbc-in-a-large-proportion&quot;&gt;here&lt;/a&gt; for RBC which should be a similar situation here, not completely sure however.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What component is the critical one that you cannot keep alcohol on your bacteria samples more than 30 seconds?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-01-02T03:56:10.720" Title="Why must the alcohol decolorizer be used for 30 seconds or less for Gram staining?" Tags="&lt;alcohol&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="4943" PostTypeId="2" ParentId="4942" CreationDate="2012-10-16T15:25:42.587" Score="4" Body="&lt;p&gt;The crystal violet stain will be removed if the decolorizer is left on too long.  I'm assuming that the crystal violet complexes that are retained in the gram positive bacteria's peptidoglycan layers end up being washed away (perhaps from overdehydrtation).  &lt;/p&gt;&#xA;" OwnerUserId="12" LastEditorUserId="12" LastEditDate="2013-01-02T03:56:10.720" LastActivityDate="2013-01-02T03:56:10.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4944" PostTypeId="1" AcceptedAnswerId="4945" CreationDate="2012-10-16T18:20:42.937" Score="6" ViewCount="532" Body="&lt;p&gt;In order to put human DNA inside a bacteria in order to have it create Insulin, from what type of cell would you need to take the gene for insulin?&#xA;I thought it should be from any somatic cell, since the DNA is identical, but I'm told it should be only from the pancreas, why is that?&lt;/p&gt;&#xA;" OwnerUserId="1544" LastEditorUserId="24354" LastEditDate="2020-06-27T07:25:30.847" LastActivityDate="2020-06-27T07:25:30.847" Title="Genetic engineering for insulin production" Tags="&lt;genetics&gt;&lt;endocrinology&gt;&lt;insulin&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="4945" PostTypeId="2" ParentId="4944" CreationDate="2012-10-16T18:52:22.583" Score="11" Body="&lt;p&gt;In short, because the easiest way to get the protein coding sequence of the gene is to create cDNA based on the mRNA, and insulin mRNA is only expressed in pancreatic cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Insulin gene consists of two exons. That means, amplifying the genome will not give us a coding sequence -- two pieces of that sequence will be interrupted by a large, non-coding intron. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QJ3Lb.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the figure above, you see the translated (i.e., coding a protein) sequences represented as opaque boxes. They are linked by a slightly curving thin line -- this is a fragment of sequence that will get excised during mRNA maturation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To get the coding sequence in a straightforward manner, one can create cDNA from mRNA using a reverse transcriptase. Processed mRNA does not contain the intron. And clearly, pancreas cells express the insulin gene mRNA at very high levels, enabling such a procedure, whereas it is practically not expressed by other tissues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Since I see these comments upvoted, I need to debunk them here:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;There are introns and splicing in both, bacteria and archea. Both type I and type II introns are present in bacteria. See &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6976.2007.00068.x/full&quot; rel=&quot;noreferrer&quot;&gt;this review&lt;/a&gt; on bacterial type II introns. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Bacteria also have post-translational modifications, including glycosylation. Once thought to be rare, there is an increasing body of evidence that it plays a much more important role than previously thought. See a paper from a decade ago &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12821323&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1435" LastEditorUserId="1435" LastEditDate="2012-10-17T08:04:52.800" LastActivityDate="2012-10-17T08:04:52.800" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="4946" PostTypeId="1" AcceptedAnswerId="4947" CreationDate="2012-10-16T19:29:19.930" Score="4" ViewCount="174" Body="&lt;p&gt;I have found graphs for the light absorption of water, haemoglobin, lipids, melanin, etc., but I am having a hard time finding graphs about enzymes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any websites or other reference sources for this type of information?&lt;/p&gt;&#xA;" OwnerUserId="1537" LastEditorUserId="57" LastEditDate="2012-10-17T01:48:29.407" LastActivityDate="2012-10-17T01:48:29.407" Title="Are there any websites offering graphs for the light absorption of different enzymes?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4947" PostTypeId="2" ParentId="4946" CreationDate="2012-10-16T20:14:46.113" Score="2" Body="&lt;p&gt;It is not typical to investigate spectral absorption of compounds that are not useful for light absorption qualities, such as the compounds you've listed. Enzymes in particular will have less information because of the changes in binding partners our physical conformation to be enzymatically active. If you think there should be known info then I would try Google Scholar, Pubmed and a google search, in that order.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt;&#xA;The intended meaning of the question is related to spectroscopy and quantification of protein concentration. There are two common ways to determine protein concentration using optical methods (spectroscopy). The methods use colorimetric assays (colour intensity is proportional to protein concentration) or light absorbance at a reference wavelength. Both methods rely on light absorbance at a specific wavelength, but the former relies on an reagent that changes colour in response to protein quantity, and the latter depends on direct UV light absorbance. Here's a quick breakdown of each.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For both of these assays, to determine the quantity of a specific protein, they require a source of purified protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Colorimetric Assays:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are traditional biochemical assays, of which the most widely used are the: Bradford, BCA and Lowry protein assays. These assays rely on reduction-oxidation reactions between the key assay reagent (Bradford's reagent, bicinchonic acid, or Lowry's reagent) and protein. For example, the BCA reagent is reduced in the presence of protein, causing a chelated copper ion, Cu(II), to be reduced to Cu(I), and effecting a purple colour. This purple colour intensity, which read at a specific wavelength (~520 nm) will indicate the amount of protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Near-UV Absorbance:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This method relies on 280 nm (near-UV) absorbance. Usually absorbance at 260 nm is also used for a correction factor. Specifically, amino acids with aromatic rings (eg, tryptophan) cause absorption at 280 nm. Peptide bonds absorb at 200 nm, and various other bonds, pH, ionic conditions, all influence and absorb at various wavelengths.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These methods cannot be used with a protein sample alone, because there are a number of conditions that can affect readings. To correct for this, a protein standard is also used. A protein standard uses a series of known concentrations of a known protein. The common protein concentrations can range from 20-2000 &amp;micro;g/mL; the common protein standards are bovine serum albumin, chicken ovalbumin or purified IgG. The protein standard acts as a reference for protein concentrations that are valid for that experiment, under those specific conditions. A curve is fit to the readings of the protein standard, and the sample concentrations can be read off the standard curve by using the absorbance readings.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2012-10-16T23:36:21.217" LastActivityDate="2012-10-16T23:36:21.217" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="4948" PostTypeId="2" ParentId="2699" CreationDate="2012-10-17T01:04:55.860" Score="8" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;If streamlining makes movement/locomotion quicker and easier, why didn't the apes evolve into life-forms that had streamlined bodies (much like fish)?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As with &lt;strong&gt;everything&lt;/strong&gt; in Evolutionary Biology, you must ask yourself: &lt;strong&gt;&lt;em&gt;Gain vs. Cost?&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your specific case, the Gain is very little.  Air isn't nearly as dense as water, so a streamlined form won't show a major benefit unless the organism is traveling very, very quickly. This is why you see it in birds; raptors can travel over 100mph while diving, and at those speeds small changes in drag can mean the difference between dinner and starving. Smaller birds often make very quick turnabouts and changes in direction mid-flight where, again, small changes in efficiency can mean the difference between life and death. The cost was is worth it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For apes and monkeys, moving very quickly isn't a case of living or dying. That's what we evolved opposable thumbs and prehensile feet(/tails) for. You don't &lt;em&gt;need&lt;/em&gt; to run fast when you can climb a tree and simply get away from any predators on the ground. After we came down from the trees permanently, our larger brains allowed us to use tools to fend off predators - which, again, is much simpler than evolving an aerodynamic form that won't make a difference until you're running at the speed of a car.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in lieu of becoming a land-shark, we have hands that can use keyboards and minds that can invent the keyboard. Unfortunately, while the gains are many, the costs do include both a very long period of time where humans are helpless without parents, and an absolutely terrible form of locomotion with our upright stance on forward-pointing knees. Though you won't catch Cheetahs digging sewers anytime soon.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1306" LastEditDate="2012-10-24T12:55:53.287" LastActivityDate="2012-10-24T12:55:53.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4949" PostTypeId="2" ParentId="2750" CreationDate="2012-10-17T03:26:04.327" Score="2" Body="&lt;p&gt;All species of the genus Homo were able to plan stone tool manufacture in a way that suggests the ability to prioritize and follow steps to an envisioned end form.&lt;/p&gt;&#xA;" OwnerUserId="1545" LastEditorUserId="112" LastEditDate="2012-10-17T07:21:20.223" LastActivityDate="2012-10-17T07:21:20.223" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4950" PostTypeId="1" AcceptedAnswerId="4952" CreationDate="2012-10-17T07:24:22.527" Score="11" ViewCount="5026" Body="&lt;p&gt;The social insects consist of the ants, the bees, and the termites, which live in colonies rather than living solitary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I've heard that there are some species of bee which are solitary and don't live in colonies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there also any species anywhere of either ants or termites which are solitary?&lt;/p&gt;&#xA;" OwnerUserId="224" LastEditorUserId="69" LastEditDate="2013-02-21T01:20:16.337" LastActivityDate="2019-02-15T23:40:01.490" Title="Are there any solitary species of ant or termite?" Tags="&lt;entomology&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4951" PostTypeId="2" ParentId="3915" CreationDate="2012-10-17T07:27:13.120" Score="3" Body="&lt;p&gt;I have no clear evidence of a specific species, but two pieces of the puzzle:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;species can adapt to living in cities: birds living in cities are bolder (i.e. allow humans to come closer before flying away), and apparently even some &lt;a href=&quot;http://beheco.oxfordjournals.org/content/23/5/960.full&quot; rel=&quot;nofollow&quot;&gt;genetic changes can be detected&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;it may be possible for species to evolve a circaseptan rhythm: beach beetles may have a seven-day rhythm to accommodate for different heights of the tides (spring/neap tide). (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9949556&quot; rel=&quot;nofollow&quot;&gt;PubMed&lt;/a&gt; / &lt;a href=&quot;http://www.ane.pl/pdf/5834.pdf&quot; rel=&quot;nofollow&quot;&gt;PDF&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-10-17T07:27:13.120" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="4952" PostTypeId="2" ParentId="4950" CreationDate="2012-10-17T08:20:19.247" Score="8" Body="&lt;p&gt;I do not know of any solitary ants, but there are species that form very small colonies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One such species is &lt;a href=&quot;http://en.wikipedia.org/wiki/Harpegnathos_saltator&quot; rel=&quot;nofollow&quot;&gt;Jerdon's Jumping Ant (&lt;em&gt;Harpegnathos saltator&lt;/em&gt;)&lt;/a&gt;. They usually live in colonies &lt;a href=&quot;http://www.pnas.org/content/92/24/10977.full.pdf&quot; rel=&quot;nofollow&quot;&gt;smaller than 100 individuals&lt;/a&gt; and workers may reproduce, so the colony can survive after the queen's death.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastEditorUserId="1306" LastEditDate="2012-10-18T09:47:46.210" LastActivityDate="2012-10-18T09:47:46.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4954" PostTypeId="2" ParentId="2246" CreationDate="2012-10-17T16:18:20.693" Score="2" Body="&lt;p&gt;Just adding my 5 cents, there is a recent database called &lt;a href=&quot;http://orthology.phylomedb.org/&quot; rel=&quot;nofollow&quot;&gt;metaphors&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;MetaPhOrs is a public repository of phylogeny-based orthology and&#xA;  paralogy predictions that were computed using resources available in&#xA;  seven popular homology prediction services (PhylomeDB, EnsemblCompara,&#xA;  EggNOG, OrthoMCL, COG, Fungal Orthogroups, and TreeFam). Currently&#xA;  above 306 millions of unique homologous protein pairs are deposited in&#xA;  MetaPhOrs database. These predictions were retrieved from 705 123&#xA;  phylogenetic trees for 829 genomes. For each prediction, MetaPhOrs&#xA;  provides a Consistency Score and Evidence Level describing its&#xA;  goodness, together with number of trees and links to their source&#xA;  databases.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is particularly good because:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;It is the only homology database I know of that gives information on paralogy vs orthology.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It is linked to UniProt names&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It provides a pretty good python API for batch queries&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2012-10-17T16:18:20.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4957" PostTypeId="1" AcceptedAnswerId="4970" CreationDate="2012-10-18T06:56:51.577" Score="2" ViewCount="183" Body="&lt;p&gt;Is there any living organism that has the ability to remove and reattach body parts at will?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not talking about regeneration (like in starfish). Say I'm chasing prey, and I decide that my tail will be a hindrance. So I leave it behind, and reattach it after the hunt.&lt;/p&gt;&#xA;" OwnerUserId="1547" LastEditorUserId="1547" LastEditDate="2012-10-18T07:03:10.697" LastActivityDate="2012-10-19T21:28:34.650" Title="Reattaching body parts" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4958" PostTypeId="2" ParentId="4932" CreationDate="2012-10-18T09:13:39.627" Score="2" Body="&lt;p&gt;A recent genetic analysis suggests that they were probably bigger that we thought before :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.newscientist.com/article/dn22343-mammals-ancestor-was-not-as-puny-as-we-thought.html&quot; rel=&quot;nofollow&quot;&gt;http://www.newscientist.com/article/dn22343-mammals-ancestor-was-not-as-puny-as-we-thought.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1548" LastEditorUserId="1306" LastEditDate="2012-10-19T10:19:13.903" LastActivityDate="2012-10-19T10:19:13.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4959" PostTypeId="1" AcceptedAnswerId="4960" CreationDate="2012-10-18T09:52:33.870" Score="2" ViewCount="2240" Body="&lt;p&gt;This may be the wrong forum to ask. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance several people are known to have survived a direct lightning strike; albeit the number of fatalities are probably far larger. Anyway, I found myself wondering why high-voltage may shock a person and throw them off whereas &lt;strike&gt;high-current&lt;/strike&gt; even small current is, purportedly, a killer. &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2012-10-18T17:00:57.177" LastActivityDate="2012-10-18T17:24:55.347" Title="Why does high-voltage mostly shock a person, and even small current kill?" Tags="&lt;electrophysiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="4960" PostTypeId="2" ParentId="4959" CreationDate="2012-10-18T14:47:45.833" Score="3" Body="&lt;p&gt;These statements are not true, simply speaking. Currents as little as few microampers can kill a person if, for example, applied directly next to the heart. A few seconds of 220V can kill a person even if the current is in miliamper range (Biksom, cited below, mentions 4s at 120mA). However, it is true that it is not the voltage &lt;em&gt;alone&lt;/em&gt; that kills, that there are other factors (most importantly, the effective current, which, however, normally increases with voltage). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look, Ohms law states that R = V / I (resistance equals to voltage divided by current). Given a constant resistance, a higher voltage produces also a higher current, full stop. Given a voltage of, say, 24 V, and the resistance of our bodies being 1000 - 4000 Ohm, the current will not exceed 6 - 24 mA. Note that in case of 220V this largest current would be less than ten times these values, so well below 1A! Yet, this is sufficient to kill an adult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's more, extremely high voltage can actually break the skin and effectively &lt;em&gt;lower&lt;/em&gt; the skin resistance, which results in an even higher current (see formula above).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So where does this popular knowledge come from? Well, we know that things like electric sparks can have very high voltage, but are harmless. They are harmless not because the current is low, but because the &lt;em&gt;duration&lt;/em&gt; and the total energy is low, since the total energy is given by power (in watts) times seconds, and power P = V * I (voltage times current).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, it comes from anecdotical evidence, since being shocked by thousands of Volts and survive can make you famous... precisely because it is extremely rare to get into contact with a high voltage line which can supply a steady flow of the current and survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another reason became apparent in the comments: confusion between the &lt;em&gt;factual&lt;/em&gt; current of the jolt one is getting and the &lt;em&gt;nominal&lt;/em&gt; amps on the fuse. The former is given by the resistance and voltage; the higher the voltage, the higher the current. However, an 1A fuse is likely to blow quicker than a 10A fuse, thus cutting the line before the current penetrates our body to reach the heart and bring it into fibrillation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is a similar story with lightnings: duration is extremely short, but more importantly, in most of the cases the lightning did not run &lt;em&gt;through&lt;/em&gt; the person who survived -- because if it did, they would be dead (also, see &lt;a href=&quot;http://what-if.xkcd.com/&quot; rel=&quot;nofollow&quot;&gt;this fascinating bit&lt;/a&gt;). It either run over the skin, seeking the path of the lowest resistance, or through a material nearby.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, high frequency currents are less likely to penetrate the skin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Literature links:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bme.ccny.cuny.edu/faculty/mbikson/biksonmsafevoltagereview.pdf&quot; rel=&quot;nofollow&quot;&gt;Biksom, &quot;A review of hazards associated with exposure to low voltages&quot;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1435" LastEditorUserId="1435" LastEditDate="2012-10-18T17:24:55.347" LastActivityDate="2012-10-18T17:24:55.347" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="4961" PostTypeId="2" ParentId="2977" CreationDate="2012-10-18T15:24:43.123" Score="0" Body="&lt;p&gt;I would say not, though you might find occasional cases where it is important. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lamarckism could certainly apply to single celled organisms, but it would still tend to be associated with DNA.  As originally described by Lamarck, the traits cited would be retained through the offspring's lifetime, potentially being passed on to later generations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Protein half lives vary quite a bit, but usually in bacteria &lt;a href=&quot;http://www.jbc.org/content/246/22/6956.abstract&quot; rel=&quot;nofollow&quot;&gt;they are about an hour&lt;/a&gt; and can change &lt;a href=&quot;http://chaos.c.u-tokyo.ac.jp/papers/bio1/tsuru.pdf&quot; rel=&quot;nofollow&quot;&gt;faster than that&lt;/a&gt;.  The changes accorded to Lamarckism should at least persistant for most of a lifetime.  If this is Lamarckism then all embryonic stem cells have Larmarckian inheritance... at least for a few hours.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand... This &lt;em&gt;is&lt;/em&gt; Lamarckism in the sense that historically Lamarck was sometimes observing physiological adaptation.  One of his classic examples was how a blacksmith's muscles would become large from working hard.  The Blacksmith's children who also did this work would also become muscular.  That has little to do with inheritance though. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-10-18T20:54:55.827" LastActivityDate="2012-10-18T20:54:55.827" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4962" PostTypeId="1" AcceptedAnswerId="4964" CreationDate="2012-10-18T16:52:14.987" Score="43" ViewCount="157275" Body="&lt;p&gt;These three terms are often misused in the literature. Many researchers seem to treat them as synonyms. So, what is the definition of each of these terms and how do they differ from one another?&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-05-11T04:08:34.507" LastActivityDate="2016-06-17T23:03:08.160" Title="What is the difference between orthologs, paralogs and homologs?" Tags="&lt;evolution&gt;&lt;nomenclature&gt;&lt;phylogenetics&gt;" AnswerCount="3" CommentCount="7" FavoriteCount="24" ContentLicense="CC BY-SA 3.0" />
  <row Id="4963" PostTypeId="2" ParentId="4962" CreationDate="2012-10-18T16:57:14.167" Score="8" Body="&lt;p&gt;Both orthologs and paralogs are types of homologs, that is, they denote genes that derive from the same ancestral sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Orthologs are corresponding genes in different lineages and are a result of speciation, whereas paralogs result from a gene duplication. This often has important implications: while orthologs often fulfill the same role, paralogs tend to diverge in their function, so paralogy is a worse indicator of functional analogy than orthology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This, however, is only the tip of the iceberg, since the situation can be much more complex (see, for example, the hidden paralogy problem).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0168952500020059&quot;&gt;great article by Fitch&lt;/a&gt; on that subject.&lt;/p&gt;&#xA;" OwnerUserId="1435" LastEditorUserId="1306" LastEditDate="2012-10-18T18:30:42.200" LastActivityDate="2012-10-18T18:30:42.200" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4964" PostTypeId="2" ParentId="4962" CreationDate="2012-10-18T17:17:52.193" Score="45" Body="&lt;p&gt;First, a note on spelling. Both &quot;ortholog&quot; and &quot;orthologue&quot; are correct, one is the American and the other the British spelling. The same is true for homolog and paralog.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On to the biology. Homology is the blanket term, both ortho- and paralogs are homologs. &lt;strong&gt;So, when in doubt use &quot;homologs&quot;.&lt;/strong&gt; However:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Orthologs are homologous genes that are the result of a &lt;strong&gt;speciation event&lt;/strong&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Paralogs are homologous genes that are the result of a &lt;strong&gt;duplication event&lt;/strong&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The following image, adapted (slightly) from [&lt;a href=&quot;https://i.stack.imgur.com/vpbDk.png&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt;], illustrates the differences:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vpbDk.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Part &lt;strong&gt;(a)&lt;/strong&gt; of the diagram above shows a hypothetical evolutionary history of a gene. The ancestral genome had two copies of this gene (A and B) which were &lt;strong&gt;paralogs&lt;/strong&gt;. At some point, the ancestral species split into two daughter species, each of whose genome contains two copies of the ancestral duplicated gene (A1,A2 and B1,B2). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These genes are all homologous to one another but are they paralogs or orthologs? Since the duplication event that created genes A and B occurred before the speciation event that created species 1 and 2, A genes will be paralogs of B genes and 1 genes will be orthologs of 2 genes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A1 and B1 are &lt;strong&gt;paralogs&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;A1 and B2 are &lt;strong&gt;paralogs&lt;/strong&gt;.&lt;/li&gt;&#xA;&lt;li&gt;A2 and B1 are &lt;strong&gt;paralogs&lt;/strong&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A2 and B2 are &lt;strong&gt;paralogs&lt;/strong&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A1 and A2 are &lt;strong&gt;orthologs&lt;/strong&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;B1 and B2 are &lt;strong&gt;orthologs&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This however, is a very simple case. What happens when a duplication occurs &lt;em&gt;after&lt;/em&gt; a speciation event? In part &lt;strong&gt;(b)&lt;/strong&gt; of the above diagram, the ancestral gene was duplicated &lt;em&gt;only&lt;/em&gt; in species 2's lineage. Therefore, in &lt;strong&gt;(b)&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A2 and B2 are &lt;strong&gt;orthologs&lt;/strong&gt; of A1.&lt;/li&gt;&#xA;&lt;li&gt;A2 and B2 are &lt;strong&gt;paralogs&lt;/strong&gt; of each other.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;A common misconception is that paralogous genes are those homologous genes that are in the same genome while orthologous genes are those that are in different genomes. As you can see in the example above, this is absolutely not true. While it &lt;em&gt;can&lt;/em&gt; happen that way, ortho- vs paralogy depends exclusively on the evolutionary history of the genes involved. If you do not know whether a particular homology relationship is the result of a gene duplication or a speciation event, then you &lt;strong&gt;cannot know&lt;/strong&gt; if it is a case of paralogy or orthology. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;References&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC138949/&quot; rel=&quot;noreferrer&quot;&gt;R.A. Jensen, Orthologs and paralogs - we need to get it right, &lt;em&gt;Genome Biology&lt;/em&gt;, 2(8), 2001&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Suggested reading:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I highly recommend the Jensen article referenced above. I read it when I was first starting to work on comparative  genomics and evolution and it is a wonderfully clear and succinct explanation of the terms. Some of the articles referenced therein are also worth a read:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Koonin EV: An apology for orthologs - or brave new memes. &lt;em&gt;Genome Biol&lt;/em&gt;, 2001, &lt;strong&gt;2&lt;/strong&gt;:comment1005.1-1005.2.&lt;/li&gt;&#xA;&lt;li&gt;Petsko GA: Homologuephobia. &lt;em&gt;Genome Biol&lt;/em&gt; 2001, &lt;strong&gt;2&lt;/strong&gt;:comment1002.1-1002.2.&lt;/li&gt;&#xA;&lt;li&gt;Fitch WM: Distinguishing homologous from analogous proteins. &lt;em&gt;Syst Zool&lt;/em&gt; 1970, &lt;strong&gt;19&lt;/strong&gt;:99-113. (of historical interest, the terms were first used here)&lt;/li&gt;&#xA;&lt;li&gt;Fitch WM: Homology a personal view on some of the problems. &lt;em&gt;Trends Genet&lt;/em&gt;&#xA;2000, &lt;strong&gt;16&lt;/strong&gt;:227-31.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2016-06-17T23:03:08.160" LastActivityDate="2016-06-17T23:03:08.160" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="4965" PostTypeId="1" AcceptedAnswerId="5017" CreationDate="2012-10-19T04:05:18.617" Score="8" ViewCount="6628" Body="&lt;p&gt;Earlier this week I was looking at some bivalve shells that had ornate patterns which ranged in color from a light orange-pink to a deep orange-red. Here is an image I found online that seems to be of the same type of shell:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/y7knN.jpg&quot; alt=&quot;example clamshell&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The friend who was with me said, &quot;I wonder where the color comes from.&quot; We were trying to look for two shells with similar colors, patterns, and approximately equal sizes, and it was hard, even though we were looking through a large collection of similar shells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What determines this ornate pigmentation? Is it influenced by environmental factors such as the minerals in the water? Does it have anything to do with the age or health of the organism? Or is it purely genetic? Is this determined by the same basic biological principle that determines the color of human hair, or is there something different at work in shells?&lt;/p&gt;&#xA;" OwnerUserId="1550" LastEditorUserId="9906" LastEditDate="2016-10-10T21:02:20.870" LastActivityDate="2018-12-17T05:27:12.250" Title="What determines the colors and patterns of a clam shell?" Tags="&lt;genetics&gt;&lt;marine-biology&gt;&lt;pigmentation&gt;&lt;molluscs&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4966" PostTypeId="2" ParentId="4962" CreationDate="2012-10-19T06:10:55.600" Score="3" Body="&lt;p&gt;First, the definition: two genes are homologs if they derive from a common ancestor. Generally speaking, if two nucleotide sequences have at least 30% (or greater than 10% amino acid sequence) identity, they are likely to be from a common ancestry, however, they may not be homologous. Note the reverse does not apply: two genes can also be homologs if there is no similarity; this happens every time the drift was long enough (many genes are no longer similar---beyond random identity---after 1 billion years; only highly conserved genes keep some similarity).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to the other answers another diagram and further terms:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tItd1.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(after W. M. Fitch, Trends in Genetics, 16, 5, May 2000, p.228)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;B1 and C1 are &lt;strong&gt;(1:1) orthologs&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;B1, C2 and C3 are &lt;strong&gt;(1:n) orthologs&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;A1 and AB1 are &lt;strong&gt;xenologs&lt;/strong&gt; (horiz. gene transfer)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I &lt;em&gt;think&lt;/em&gt; (1:n) ortholog is a synonym for &lt;strong&gt;outparalog&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Klaus D. Grasser: Annual Plant Reviews, Regulation of Transcription in Plants (Volume 29). Wiley-Blackwell, ISBN 1-4051-4528-5, p. 37.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorDisplayName="user560" LastEditDate="2012-10-20T22:14:47.630" LastActivityDate="2012-10-20T22:14:47.630" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="4967" PostTypeId="1" CreationDate="2012-10-19T08:44:28.663" Score="1" ViewCount="2333" Body="&lt;p&gt;Hormones normally have short half-life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How is it possible that they have long-life in drugs?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-10-20T08:07:43.657" Title="Why do drugs which are hormones have long half-life?" Tags="&lt;endocrinology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4968" PostTypeId="1" CreationDate="2012-10-19T20:18:02.483" Score="7" ViewCount="638" Body="&lt;p&gt;How long ago can human genes be traced? Are there any genes that go back unchanged to the beginning of life on Earth? And if so, how many?&lt;/p&gt;&#xA;" OwnerUserId="1553" LastEditorUserId="307" LastEditDate="2012-10-19T21:33:30.870" LastActivityDate="2012-10-23T17:07:12.843" Title="Are there genes in humans from the common ancestor of all organisms?" Tags="&lt;evolution&gt;&lt;human-genetics&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="4969" PostTypeId="1" AcceptedAnswerId="4974" CreationDate="2012-10-19T20:20:07.737" Score="3" ViewCount="2532" Body="&lt;p&gt;Bats are known to navigate by using echo-location.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How far away can a bat detect an object by its sonar? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="57" LastEditDate="2012-10-20T08:43:06.113" LastActivityDate="2016-12-13T16:50:32.187" Title="What is the known maximum ranging distance of a bat's sonar?" Tags="&lt;zoology&gt;&lt;sensation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4970" PostTypeId="2" ParentId="4957" CreationDate="2012-10-19T21:28:34.650" Score="2" Body="&lt;p&gt;I dont think this would be possible from the simple idea that all cells need energy, and if there's no nutrient flow, then how would the cells inside the detached body part stay &quot;alive&quot;.  Doctors can currently reattach body parts right now if it's within a certain amount of time, but no animal yet can just reattach at will.&lt;/p&gt;&#xA;" OwnerUserId="1554" LastActivityDate="2012-10-19T21:28:34.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4971" PostTypeId="1" CreationDate="2012-10-19T21:30:53.540" Score="4" ViewCount="1124" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/4968/are-there-genes-in-humans-from-the-common-ancestor-of-all-organisms&quot;&gt;This question&lt;/a&gt; got me thinking about something. LUCA is the last universal common ancestor of all &lt;strong&gt;current&lt;/strong&gt; living organisms, which is a very different definition from the first-ever living organism. Is there any evidence that LUCA had evolved and diverged from a now-extinct, more primitive lifeform?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To rephrase, &lt;strong&gt;is there any evidence to suggest that at some point, the first-ever living organism(s) had diverged into two phylogenetic groups, one being now-extinct and the other describing all current life?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2019-05-26T08:37:16.037" Title="Were there lifeforms before LUCA?" Tags="&lt;evolution&gt;&lt;abiogenesis&gt;&lt;speciation&gt;" AnswerCount="3" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="4973" PostTypeId="2" ParentId="4968" CreationDate="2012-10-19T23:06:17.153" Score="7" Body="&lt;p&gt;Depends on what you mean by unchanged. If you mean a gene that maintained the same nucleotide sequence, then the answer is no.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you meant a gene that descends from a very ancient gene, i.e. one can find orthologs in very distant species, then the answer is yes. Many of the basic molecular systems are relatively conserved, including several metabolic paths and information processing machinery. This homology is one of the strongest molecular supports for evolution and also one of the reasons that genetic engineering works so nicely.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1306" LastEditDate="2012-10-20T10:55:12.573" LastActivityDate="2012-10-20T10:55:12.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4974" PostTypeId="2" ParentId="4969" CreationDate="2012-10-19T23:26:31.857" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0002036&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; paper finds some species can detect as far as 67 meters, but the range varies between species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the bats can actively change their range of detection and trade off range for resolution (low range with high speed resolution for hunting in closed, cluttered spaces or high range with low speed resolution for hunting in open spaces), as explained in Wikipedia's article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Animal_echolocation&quot; rel=&quot;nofollow&quot;&gt;Animal echolocation&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cool stuff.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1306" LastEditDate="2012-10-20T11:16:13.233" LastActivityDate="2012-10-20T11:16:13.233" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="4975" PostTypeId="2" ParentId="4971" CreationDate="2012-10-20T02:06:19.577" Score="7" Body="&lt;p&gt;Well, what you seem to be suggesting is &quot;Did life evolve twice on Earth?&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your original question has an answer: Probably yes. It's not unlikely to think that the original cell evolved into two different paths and then one went extinct. However, that doesn't address LUCA. If we found fossil evidence of what we &lt;em&gt;thought&lt;/em&gt; was LUCA, and then fossil evidence that LUCA had a genetic cousin - all that would do is push the application of the term &quot;LUCA&quot; on more evolutionary step backwards until both shared a common ancestor which would then be called LUCA. You can do this indefinitely until all life originates from a single cell, with countless offshoots which have gone extinct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you mean was there a &lt;em&gt;whole other type of life&lt;/em&gt; - one that did not originate from LUCA and existed - then the best answer we have right now is &quot;No.&quot; All life we know of, no matter how different and old, is still based on RNA/DNA and proteins. Fossil evidence supports this premise until about 3.5 BYA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there was an 'alternate' construction of life, we have not found the fossil evidence for it, and might not know what it was if we did. If the alternate form didn't utilize cells, we might not be aware we had it. If it did, but utilized different metabolisms or structures for proteins and storage - that evidence would be long gone by now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our best bet for answering if life can evolve differently than what we have today is out among the stars.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-10-20T02:06:19.577" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="4976" PostTypeId="2" ParentId="4967" CreationDate="2012-10-20T08:07:43.657" Score="1" Body="&lt;p&gt;The question is a bit vague, but in general a drug formulation is made of the active principle plus a series of other non-active compounds call excipients.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Excipients have multiple roles such as:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;They act as &lt;strong&gt;fillers&lt;/strong&gt; to add volume to the drug. Often only very small amounts of the active compound are present in each pill/capsule/etc. and it would be complicated for the patient to handle these very small amounts.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;They act as &lt;strong&gt;binders&lt;/strong&gt; to keep everything together and avoid the pill to crumble.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;They can modify the &lt;strong&gt;pharmacokinetics&lt;/strong&gt; of the active principle by speeding up or slowing down its release.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;(there are many more resons to add excipients, see the relevant &lt;a href=&quot;http://en.wikipedia.org/wiki/Excipient&quot; rel=&quot;nofollow&quot;&gt;Wikipedia page&lt;/a&gt; for a longer list)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This last point is what you are looking for. If the hormone (or any other molecule, it doesn't really matter) is complexed with excipients it will be released in the blood or metabolized slower/faster depending on the specific molecules/formulations/mode of administration.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2012-10-20T08:07:43.657" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="4978" PostTypeId="1" CreationDate="2012-10-20T17:24:46.073" Score="6" ViewCount="925" Body="&lt;p&gt;Humans have domesticated all manner of creatures during the course of their civilization - dogs, horses, several types of cattle, varieties of birds, and perhaps others too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A prerequisite for an animal to be domesticated, obviously, is that there be some return from the animal voluntarily, or otherwise. For instance, milk from cows/buffalos.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm looking for is an answer to the question what ... characteristics must an animal fulfil to be domesticated/trained. Docile is, perhaps, one characterstic. Amenable to training may be another. What other characteristics must be fulfilled before one would venture to consider training/domestication of another species?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="3952" LastEditDate="2013-08-08T00:14:58.230" LastActivityDate="2016-04-09T08:16:04.963" Title="What makes an animal/species suitable for domestication/training?" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;ethnobiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="4979" PostTypeId="2" ParentId="4968" CreationDate="2012-10-20T19:41:51.293" Score="8" Body="&lt;p&gt;I very much agree with bitwise's answer. I just want to point out that even in terms of nucleotide sequence there are some extremely conserved genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most highly conserved are ribosomal RNA genes. The image below shows the conservation of 16S rRNAs from archaea, bacteria, and eukaryotes (eukaryotes do not have 16S in their cellular genome but the gene is present in the DNA of mitochondria and chloroplasts). Residues in red are conserved across all domains of life (&lt;a href=&quot;http://www.rna.icmb.utexas.edu/SAE/2B/ConsStruc/&quot; rel=&quot;nofollow noreferrer&quot;&gt;image source&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/c8ZIv.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18853276&quot; rel=&quot;nofollow noreferrer&quot;&gt;very nice study from 2008&lt;/a&gt; [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18853276&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;] identified tRNA genes as the next most conserved and ABC transporter nucleotide binding domains (NBDs) after that. The alignment below (taken from the paper) shows the conservation of NBDs from various species. Note that they include eukaryotes, archaea and bacteria:&#xA;&lt;a href=&quot;http://aa.com&quot; rel=&quot;nofollow noreferrer&quot;&gt;[2]&lt;/a&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/6FjFk.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at orthologous genes in general, without specifying a specific level of sequence identity, then you can find various genes (notably those coding for the enzymes of the glycolysis pathway as mentioned in the comments) that are conserved across most, if not all, cellular life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to answer your question probably yes. At least, there are genes in humans today that can be found in all or almost all other life forms. Whether there were present in LUCA we cannot know for sure, it does seem likely however given how widespread they are today.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18853276&quot; rel=&quot;nofollow noreferrer&quot;&gt;Isenbarger T.A. &lt;em&gt;et al&lt;/em&gt;, The most conserved genome segments for life detection on Earth and other planets, &lt;em&gt;Orig Life Evol Biosph.&lt;/em&gt; 2008 Dec;&lt;strong&gt;38&lt;/strong&gt;(6):517-33.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1306" LastEditorDisplayName="user560" LastEditDate="2012-10-23T17:07:12.843" LastActivityDate="2012-10-23T17:07:12.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4980" PostTypeId="2" ParentId="4978" CreationDate="2012-10-21T13:52:54.427" Score="2" Body="&lt;p&gt;The ability of an animal to be trained or domesticated appears to be genetic. A quick Google search revealed this Review: &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/278/1722/3161.full.pdf&quot; rel=&quot;nofollow&quot;&gt;http://rspb.royalsocietypublishing.org/content/278/1722/3161.full.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="852" LastActivityDate="2012-10-21T13:52:54.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4981" PostTypeId="2" ParentId="2881" CreationDate="2012-10-21T13:58:39.753" Score="1" Body="&lt;p&gt;Coomassie blue fluoresces in infrared when bound to protein, so if your reader has the appropriate filter set, it should be possible.&lt;/p&gt;&#xA;" OwnerUserId="852" LastActivityDate="2012-10-21T13:58:39.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4982" PostTypeId="1" AcceptedAnswerId="4986" CreationDate="2012-10-21T15:13:13.717" Score="6" ViewCount="141" Body="&lt;p&gt;I've read a recent Nature Methods paper by Moon &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23041931&quot; rel=&quot;nofollow&quot;&gt;T.S. &lt;em&gt;et al&lt;/em&gt;&lt;/a&gt;, in which a synthetic genetic circuit consisting of layered logic gates was created. For example, the paper, a circuit is modelled in Figure 4a. How is this circuit computationally modelled? Can you refer me to any graduate level texts on the subject?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2012-10-23T17:36:53.790" LastActivityDate="2012-10-24T09:46:40.357" Title="How are Genetic Circuits Modelled?" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;synthetic-biology&gt;&lt;mathematical-models&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="4983" PostTypeId="1" CreationDate="2012-10-22T07:40:52.833" Score="3" ViewCount="200" Body="&lt;p&gt;Self-preservation, or preservation anyway, probably happens throughout the animal kingdom, and perhaps through the plant kingdom as well (some plants/trees, apparently, produce chemicals to repel bugs).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where does self-preservation stem from? Is it only about a biochemical imbalance? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="57" LastEditDate="2012-10-22T08:51:35.747" LastActivityDate="2012-10-23T22:36:39.510" Title="What does self-preservation stem from?" Tags="&lt;ecology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2012-10-23T23:10:14.963" ContentLicense="CC BY-SA 3.0" />
  <row Id="4984" PostTypeId="1" AcceptedAnswerId="4985" CreationDate="2012-10-22T11:30:08.470" Score="4" ViewCount="110" Body="&lt;p&gt;I'm trying to parse ATOM section of a PDB file. I'm using the &lt;code&gt;&lt;a href=&quot;http://www.salilab.org/~drussel/pdb/&quot; rel=&quot;nofollow&quot;&gt;dsr-pdb&lt;/a&gt;&lt;/code&gt; library for this purpose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've encountered a problem. This library interprets CD1 atom of ILE residue in the PDB file as AL_CD instead of AL_CD1*. Does it have a particular reason?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's maybe helpful that within the source code, in &lt;code&gt;Residue_data.cc&lt;/code&gt;, there is a mapping between atom lebels:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;Atom_fallback_data atom_fallback_data_[]=&#xA;      {{Residue::AL_CD1, Residue::AL_CD},&#xA;       {Residue::AL_1HA, Residue::AL_HA},&#xA;       {Residue::AL_1HB, Residue::AL_HB},&#xA;       {Residue::AL_1HD, Residue::AL_HD},&#xA;       {Residue::AL_1HE, Residue::AL_HE},&#xA;       {Residue::AL_1HZ, Residue::AL_HZ},&#xA;       //{Residue::AL_1HH, Residue::AL_HH},&#xA;       {Residue::AL_1HD1, Residue::AL_1HD},&#xA;       {Residue::AL_2HD1, Residue::AL_2HD},&#xA;       {Residue::AL_3HD1, Residue::AL_3HD},&#xA;       {Residue::AL_INVALID, Residue::AL_INVALID}};&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;It means that AL_CD1 is deliberately converted to AL_CD or for example AL_1HA to AL_HA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;In general, in dsr-pdb library, AL_X is the atom label of atom X.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1557" LastEditorUserId="112" LastEditDate="2012-10-22T11:49:38.037" LastActivityDate="2012-10-22T11:49:38.037" Title="Parse PDB using DSR-PDB Library" Tags="&lt;bioinformatics&gt;&lt;structural-biology&gt;&lt;pdb&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4985" PostTypeId="2" ParentId="4984" CreationDate="2012-10-22T11:49:20.410" Score="3" Body="&lt;p&gt;Isoleucine only has one delta carbon, which we can just call &lt;code&gt;CD&lt;/code&gt;. But it seems like some PDB files still name it &lt;code&gt;CD1&lt;/code&gt;, and hence programs map &lt;code&gt;CD1&lt;/code&gt; to &lt;code&gt;CD&lt;/code&gt; in this case. (E.g. see &lt;a href=&quot;http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node6.html&quot; rel=&quot;nofollow&quot;&gt;this tutorial&lt;/a&gt; where this practice is shown.)&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-10-22T11:49:20.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4986" PostTypeId="2" ParentId="4982" CreationDate="2012-10-22T16:44:03.897" Score="3" Body="&lt;p&gt;The following papers are a good starting point:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov.gate1.inist.fr/pubmed?term=4588055&quot; rel=&quot;nofollow&quot;&gt;René Thomas, Boolean formalization of genetic control circuits, &lt;em&gt;Journal of Theoretical Biology&lt;/em&gt;, Volume 42, Issue 3, December 1973, Pages 563-585&lt;/a&gt; &amp;lt;= A classic paper in the field. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17626067&quot; rel=&quot;nofollow&quot;&gt;Thieffry D. Dynamical roles of biological regulatory circuits. &lt;em&gt;Brief&#xA;Bioinform.&lt;/em&gt; 2007 Jul;8(4):220-5.&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18689829&quot; rel=&quot;nofollow&quot;&gt;Remy E, Ruet P. From minimal signed circuits to the dynamics of Boolean&#xA;regulatory networks. &lt;em&gt;Bioinformatics&lt;/em&gt;. 2008 Aug 15;24(16):i220-6&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;You can also have a look at &lt;a href=&quot;http://www.springerlink.com/index/10.1007/978-3-540-75140-3&quot; rel=&quot;nofollow&quot;&gt;Computational Methods in Systems Biology, International Conference CMSB 2007, Edinburgh, Scotland, September 20-21, 2007. Proceedings&lt;/a&gt;, specifically the chapter &quot;Decision diagrams for the representation and analysis of logical models of genetic networks&quot; by A. Naldi, D. Thieffry and C. Chaouiya,&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-10-22T16:55:55.817" LastActivityDate="2012-10-22T16:55:55.817" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4987" PostTypeId="1" CreationDate="2012-10-22T17:54:27.087" Score="5" ViewCount="2208" Body="&lt;p&gt;When applying this method we have a glass or plastic column of resin which is positively charged. Then we pour cell extract into the column in order to capture the negatively charged particles which include DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After that we gradually add salt which neutralizes the molecules. But it does this gradually so strongly attached DNA molecules fall last while RNA and proteins fall first. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is why does DNA have a greater negative charge than RNA ?&lt;/p&gt;&#xA;" OwnerUserId="1562" LastEditorUserId="389" LastEditDate="2012-10-24T09:47:53.787" LastActivityDate="2013-08-20T13:11:37.667" Title="Using ion-exchange chromatography to purify DNA from a cell extract - Is DNA more negatively charged then RNA?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;lab-techniques&gt;&lt;purification&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4988" PostTypeId="1" CreationDate="2012-10-22T18:19:23.777" Score="10" ViewCount="9493" Body="&lt;p&gt;If you cut open a pumpkin, the seeds are suspended inside the pumpkin by some fibrous, slimey strands. You can see them in the middle of this sliced-open pumpkin:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UVsha.jpg&quot; alt=&quot;Image of inside of a pumpkin&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm writing a post for the &lt;a href=&quot;http://cooking.blogoverflow.com&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cooking.SE blog&lt;/a&gt;, and am trying to find out the proper botanical term. Someone suggested that might be called the endocarp, but I want to make sure and also see if there is a more specific term.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Edit&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;In &quot;Morpho-Physiological Aspects of Productivity and Quality in Squash and Pumpkins (Cucurbita spp.)&quot; §C.1, I see this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the central portion of the fruit, a mass of tough fibers, together with vascular strands connected to the seeds, comprise the &lt;strong&gt;placental tissue.&lt;/strong&gt; The endocarp is made up of small, thin-walled cells that form a membranous tissue that adheres to seed, becoming a transparent skin on dried seeds. &lt;strong&gt;(emphasis added)&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Am I reading correctly that the name for this part of the pumpkin is &quot;placental tissue&quot;, and that the endocarp is just a thin layer on the seeds themselves? &lt;/p&gt;&#xA;" OwnerUserId="1563" LastEditorUserId="1563" LastEditDate="2012-10-25T22:07:57.483" LastActivityDate="2012-10-25T22:07:57.483" Title="What's the name of the fibrous strands that hold the seeds in a pumpkin?" Tags="&lt;botany&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="4990" PostTypeId="1" AcceptedAnswerId="5002" CreationDate="2012-10-22T20:23:58.340" Score="4" ViewCount="10750" Body="&lt;p&gt;In the biogas process you often measure Volatile solid and Total solids. Can any one explain these concepts more accurately and why it is interesting to look at these properties. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biogas process I refer to is a process of fermenting waste food materials and slaugther house waste in to bio fuels, consisting largely of methane. The fermentation is conducted in anaerobic milieu in large plants. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Total solids and Volatile solid are measurements on the sludge the currently fermented waste,(the gooey stuff that is in the bio-reactor).&lt;/p&gt;&#xA;" OwnerUserId="1565" LastEditorUserId="1565" LastEditDate="2012-10-23T05:57:37.060" LastActivityDate="2017-10-20T10:26:06.617" Title="What is the purpose of measuring both VS (volatile solid) and TS (total solid)?" Tags="&lt;homework&gt;&lt;biotechnology&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4991" PostTypeId="2" ParentId="2977" CreationDate="2012-10-22T23:52:20.637" Score="1" Body="&lt;p&gt;This phenomenon is well known and can be observed in several species. In fact, if you look at the time it takes for E. coli to change its transcription program in order to react to the environment (signal-&gt;transcription-&gt;translation), you will find it can be longer than its ~20 minute doubling time. You can indeed think of it as a form of Lamarckism. However, it is part of a field that has been booming in the last ~10 years, known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Epigenetics&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;epigenetics&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Epigenetics is a field of research that deals with hereditary information that is passed by non-genetic mechanisms, i.e. not in the DNA sequence. This includes several mechanisms including passing of proteins/RNA, chemical modifications of DNA (&lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_methylation&quot; rel=&quot;nofollow&quot;&gt;methylation&lt;/a&gt;) and chromatin (&lt;a href=&quot;http://en.wikipedia.org/wiki/Histone_modification&quot; rel=&quot;nofollow&quot;&gt;histone modification&lt;/a&gt;). It turns out that epigenetic effects can be observed in virtually all species (including human) and affected phenotypes can be significant (leading to disease, for example).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a very interesting field of research and is very wide, so I would recommend reading a bit. Specifically regarding protein/RNA passing, I believe this is somewhat less deeply studied, perhaps due to the fact that the effect decreases exponentially (due to dilution), can be limited by protein/RNA stability and some measurement difficulties. However, I think I recall mathematical treatment of this in Prof. Uri Alon's &lt;a href=&quot;http://www.weizmann.ac.il/mcb/UriAlon/bookUri.html&quot; rel=&quot;nofollow&quot;&gt;book&lt;/a&gt;. You can also catch his systems biology course online on &lt;a href=&quot;http://www.youtube.com/watch?v=Z__BHVFP0Lk&quot; rel=&quot;nofollow&quot;&gt;youtube&lt;/a&gt;, which I think touches on some of this material.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2012-10-23T03:17:08.347" LastActivityDate="2012-10-23T03:17:08.347" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4992" PostTypeId="1" CreationDate="2012-10-22T23:59:24.707" Score="2" ViewCount="330" Body="&lt;p&gt;Our waterways and oceans are showing increased levels of plastic contamination. These plastics are breaking down into smaller pieces. When one goes to the beach and plays in the surf they often swallow some seawater and thus some amounts of plastics, including Polyethylene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the biochemical pathways or effects of plastic, specifically Polyethylene, in the human body? I am looking for toxicity of both a large amount scenario (plastic bag milkshake) and a small amount (some in ocean water). &lt;/p&gt;&#xA;" OwnerUserId="238" LastActivityDate="2012-10-23T17:41:44.580" Title="What are the biochemical interactions between human body and Polyethylene?" Tags="&lt;biochemistry&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4994" PostTypeId="2" ParentId="4968" CreationDate="2012-10-23T06:31:03.750" Score="2" Body="&lt;p&gt;One thing still missing from the other answers: How many genes? One answer: about 6400, i.e. ~30% of all human genes can be traced back to LUCA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To come up with this number, I used the &lt;a href=&quot;http://eggnog.embl.de/&quot; rel=&quot;nofollow&quot;&gt;eggNOG database of orthologous groups&lt;/a&gt;. This database contains clusters of proteins that are probably homologous. So I checked how many human genes are in clusters that also contain bacterial genes. These are 6416 human genes, belonging to 1320 clusters. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Caveats: In some cases, the genes are too diverged and so their homology is missed. It is also possible that a protein evolved in bacteria after LUCA and then got transferred to eukaryotes, and vice versa. &lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-10-23T06:31:03.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="4995" PostTypeId="1" AcceptedAnswerId="4996" CreationDate="2012-10-23T12:34:39.647" Score="5" ViewCount="3258" Body="&lt;p&gt;I am currently reading &quot;&lt;a href=&quot;http://www.amazon.co.uk/Chemistry-Life-Penguin-Press-Science/dp/0140272739/ref=sr_1_1?ie=UTF8&amp;amp;qid=1350994643&amp;amp;sr=8-1&quot; rel=&quot;noreferrer&quot;&gt;The Chemistry of Life&lt;/a&gt;&quot; by Rose. It's a great book (to me as a lay reader at least) and an interesting topic so I am interested in pursuing some of the further reading he suggests. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first book he mentions in the bibliography is Alberts' &quot;&lt;a href=&quot;http://www.amazon.co.uk/Molecular-Biology-Cell-Bruce-Alberts/dp/0815341067/ref=sr_1_1?s=books&amp;amp;ie=UTF8&amp;amp;qid=1350994879&amp;amp;sr=1-1&quot; rel=&quot;noreferrer&quot;&gt;Molecular Biology of the Cell&lt;/a&gt;&quot;. Looking at the description and the reviews it seems that this is a pretty advanced bio-sciences graduate level text, and I am very much not that. I see that Alberts has also written &quot;&lt;a href=&quot;http://www.amazon.co.uk/Essential-Cell-Biology-Bruce-Alberts/dp/081534130X/ref=sr_1_2?s=books&amp;amp;ie=UTF8&amp;amp;qid=1350995133&amp;amp;sr=1-2&quot; rel=&quot;noreferrer&quot;&gt;Essential Cell Biology&lt;/a&gt;&quot; which looks more accessible. Before I buy this I wondered if anyone can explain the difference, which would be a better read for an enthusiastic amateur?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it helps at all I am a science grad and I typically read authors such as Dawkins and Matt Ridley, but I'm looking for something a little bit more rigorous to expand my knowledge in cell biology.&lt;/p&gt;&#xA;" OwnerUserId="1566" LastActivityDate="2013-02-17T19:40:01.057" Title="Advice on Cell Biology texts by Alberts" Tags="&lt;cell-biology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="4996" PostTypeId="2" ParentId="4995" CreationDate="2012-10-23T13:00:35.400" Score="7" Body="&lt;p&gt;Might as well make it into an answer. As I said in the comments, Albert's  &quot;Molecular Biology of the Cell&quot; is the classic textbook for Biology undergraduates. It has been so for decades now. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It starts from the basics and builds up. Anyone with a high-school science education and willingness to learn should be able to understand it. Just work your way through it :). &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2012-10-23T13:00:35.400" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="4997" PostTypeId="2" ParentId="4995" CreationDate="2012-10-23T13:39:21.220" Score="6" Body="&lt;p&gt;I've actually got a copy of Essential Cell Biology on my desk currently, it's one of our core textbooks.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When comparing with the &quot;look inside&quot; feature on Amazon for Molecular Biology of the Cell (remembering I only have access to the first few pages) I would suggest that Essential Cell Biology certainly takes a slower pace, but I wouldn't say that it was less detailed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It goes into great efforts to explain &lt;em&gt;how&lt;/em&gt; we know things experimentally, which I personally find quite helpful.  The pictures in Molecular Biology of the Cell look almost identical, however I would say they are more copiously used in essential cell biology.  Essential Cell Biology also comes with a DVD including very useful animations of cell processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Comparing the glossaries, I would still be inclined to say they are covering very similar levels of material, however Essential Cell Biology is using more 'entry level' language. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key difference between the two in my opinion is the copious use of images in Essential Cell Biology - it's almost half a picture/diagram book.  In your situation (pretty much identical to mine) I'd probably recommend Essential Cell Biology just as a start then move on to Molecular Biology of the Cell as everyone else rates it so highly.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, Essential Cell Biology certainly has &lt;em&gt;some&lt;/em&gt; kind of sense of humour:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6VGUF.png&quot; alt=&quot;Essential Cell Biology Back Cover&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Geek Spoiler:&lt;/p&gt;&#xA;&#xA;&lt;blockquote class=&quot;spoiler&quot;&gt;&#xA;  &lt;p&gt; The bottom line reads &lt;strong&gt;C A G T&lt;/strong&gt; whilst the top line reads &lt;strong&gt;G T C A&lt;/strong&gt; in semaphore, two complementary strands of DNA bases acted out for your amazement...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-10-23T13:39:21.220" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="4998" PostTypeId="2" ParentId="3478" CreationDate="2012-10-23T15:30:55.080" Score="6" Body="&lt;p&gt;Well, there are certain behaviors that may qualify. The clearest example I know of would be sexual cannibalism, and more specifically (&lt;a href=&quot;https://en.wikipedia.org/wiki/Latrodectus_hasselti#Reproduction&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The redback spider is one of only two animals to date where the male&#xA;  has been found to actively assist the female in sexual cannibalism. In&#xA;  the process of mating, the much smaller male somersaults to place his&#xA;  abdomen over the female's mouthparts. In about two of three cases, the&#xA;  female fully consumes the male while mating continues. Males which are&#xA;  not eaten die of their injuries soon after mating.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That sounds pretty suicidal to me...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A less flagrant but commoner example is that of mothers dying to nourish their offspring. Again often seen in spiders, the best example I know of is the giant pacific octopus (Enteroctopus dofleini). The female will chose a den and lay her eggs. She will then spend her last weeks tending her young, never leaving the lair to hunt. Eventually she dies of hunger and her body nourishes her young. My source here is the &lt;strong&gt;wonderful&lt;/strong&gt; &lt;a href=&quot;http://www.bbc.co.uk/nature/life/North_Pacific_Giant_Octopus&quot; rel=&quot;noreferrer&quot;&gt;BBC life&lt;/a&gt; documentary series. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neither of these are vertebrates of course but still, I thought the suicidal little spider was interesting. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-06-24T14:14:55.783" LastActivityDate="2013-06-24T14:14:55.783" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="4999" PostTypeId="1" AcceptedAnswerId="5005" CreationDate="2012-10-23T16:02:37.673" Score="9" ViewCount="638" Body="&lt;p&gt;I &lt;a href=&quot;http://en.wikipedia.org/wiki/Gal%C3%A1pagos_tortoise#Early_life_and_maturation&quot; rel=&quot;noreferrer&quot;&gt;read&lt;/a&gt; that they take up to 40 years (in the wild) to reach the age of reproduction and are thought to live over 100 years, with one in captivity reaching over 170 years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone explain in layman's terms how taking longer (especially spending years as a small tortoise) to reproduce was a winning trait, and how their biology delays the processes of senescence to the extent that it does compared to most other species?&lt;/p&gt;&#xA;" OwnerUserId="263" LastEditorUserId="3952" LastEditDate="2013-08-01T03:20:51.917" LastActivityDate="2013-08-01T03:20:51.917" Title="What evolutionary pressures pushed Galápagos tortoises to mature so slowly and live so long?" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;senescence&gt;&lt;life-history&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5000" PostTypeId="2" ParentId="4983" CreationDate="2012-10-23T16:14:12.093" Score="2" Body="&lt;p&gt;This is a prototypical case of evolution by natural selection. Any trait that prevents the organism from being eaten or destroyed will probably make that organism more likely to reproduce* than similar organisms that do not have that trait**. This results in self-preservation traits becoming more prevalent in the population and eventually ubiquitous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;* Or they reproduce more, or are able to provide for their offspring better, etc. Self-preservation behaviors that reduce reproductive success are not selected for and generally aren't common (unless they are a special case of some general trait that has a net reproductive benefit). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;** Assuming that the trait is reproductively favorable after considering any trade-offs such as increased energy expenditure. &lt;/p&gt;&#xA;" OwnerUserId="827" LastEditorUserId="827" LastEditDate="2012-10-23T22:36:39.510" LastActivityDate="2012-10-23T22:36:39.510" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5002" PostTypeId="2" ParentId="4990" CreationDate="2012-10-23T16:40:57.443" Score="4" Body="&lt;p&gt;Total solids (TS): The part of the sludge that remain after drying at 105$^{\circ}$C for 20 hours:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ TS(\%) = \frac{\textrm{weight dried at } 105^{\circ}C}{\textrm{wet weight} }\times 100 $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Volatile solids (VS): The part of the sludge that is combusted at 550$^{\circ}$C after 2 hours:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ VS(\% \textrm{ of TS}) = \frac{\textrm{dried weight at }105^{\circ}C -&#xA; \textrm{dried weight at }550^{\circ}C}{\textrm{dried weight at }105^{\circ}C}\times100$$&lt;/p&gt;&#xA;" OwnerUserId="1568" LastEditorUserId="36209" LastEditDate="2017-10-06T13:39:23.590" LastActivityDate="2017-10-06T13:39:23.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5003" PostTypeId="2" ParentId="4992" CreationDate="2012-10-23T17:41:44.580" Score="1" Body="&lt;p&gt;PE is not bothered by acids and there is no way humans have a pathway for it, except that for choking or being obstipated. But neither do bacteria or fungi make a dent in the molecule. That's why it's not degraded and collects in the oceans.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-10-23T17:41:44.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5004" PostTypeId="1" CreationDate="2012-10-23T21:30:30.460" Score="6" ViewCount="3702" Body="&lt;p&gt;What is the difference between $S_{0.5}$ values and $K_m$ values in enzyme kinetics?&lt;/p&gt;&#xA;" OwnerUserId="1569" LastEditorUserId="57" LastEditDate="2012-10-24T07:22:17.117" LastActivityDate="2012-11-04T09:03:08.287" Title="$S_{0.5}$ vs $K_m$ values in enzyme kinetics" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;&lt;kinetics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5005" PostTypeId="2" ParentId="4999" CreationDate="2012-10-24T00:34:40.193" Score="11" Body="&lt;p&gt;This isn't so precisely focused on tortoises, but a general theory in evolutionary biology for why some animals live longer is &lt;a href=&quot;http://en.wikipedia.org/wiki/R/K_selection_theory&quot; rel=&quot;noreferrer&quot;&gt;K vs r selection theory&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea here is that animals will make a sort of evolutionary 'choice' and configure themselves to breed as numerously and quickly as they can.  This is called 'r' selection, named after the constant that is proportional to the rate or speed of breeding.  r selected animals adapt quickly to a rapidly changing environment and their lives are pretty cheap.  Many insects that lay hundreds or thousands of eggs every few weeks are examples of r selection. They do not care for their offspring (and may even eat them!).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;K selected animals breed to be highly competitive in the environment.  They tend to be highly optimized for success and this often means they are larger, they live longer and require more investment as newborns. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By this theory the galapagos tortioises live longer because their environment changes very slowly and the tortoises are so optimized for that particular way of life that they have no predation or any competition at all.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Island_biogeography&quot; rel=&quot;noreferrer&quot;&gt;Islands like the Galapagos are studied in fact because they are so isolated by the water that new species rarely ever arrive.&lt;/a&gt;  Such new arrivals may cause drastic changes in their ecosystems because islands are stable environments because migration happens so rarely.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other theories that emphasize other factors in the evolution of larger, longer lived animals, but I think r/K selection may describe the environmental pressure on the Galapagos tortoise. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-10-24T22:13:37.217" LastActivityDate="2012-10-24T22:13:37.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5006" PostTypeId="2" ParentId="4982" CreationDate="2012-10-24T09:46:40.357" Score="3" Body="&lt;p&gt;I would also suggest Uri Alon's &lt;em&gt;&lt;a href=&quot;http://www.weizmann.ac.il/mcb/UriAlon/bookUri.html&quot; rel=&quot;nofollow&quot;&gt;An Introduction to Systems Biology&lt;/a&gt;&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally, I learned using JJ Tyson's body of work and I would particullary recommend &lt;em&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12648679&quot; rel=&quot;nofollow&quot;&gt;Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-10-24T09:46:40.357" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5007" PostTypeId="1" AcceptedAnswerId="5008" CreationDate="2012-10-24T11:32:20.520" Score="25" ViewCount="1969" Body="&lt;p&gt;I would like to know if evolution is continuing to happen in modern humans, assuming things like existence of the nuclear family structure, fidelity to one partner, etc. It seems to me the answer would be NO because evolution depends on differential reproductive rates, but in the modern world, all male humans have roughly 2.5 (or whatever the number) kids. Add in the process of culturally modified selection pressure, and it seems to me that even an &quot;unfit&quot; male would end up having a couple of offspring. The fittest male (or female) is no better off than his or her contemporaries because of this &quot;leveling&quot; effect. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the impression I get from the popular science media is that scientists think evolution is continuing to happen. I would like to know what the actual scientific consensus is, and why. Thanks. &lt;/p&gt;&#xA;" OwnerUserId="625" LastActivityDate="2016-04-19T08:22:01.610" Title="How is evolution possible in contemporary humans?" Tags="&lt;evolution&gt;" AnswerCount="6" CommentCount="6" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5008" PostTypeId="2" ParentId="5007" CreationDate="2012-10-24T12:20:56.900" Score="29" Body="&lt;p&gt;It is certainly not true that &quot;all male humans have roughly 2.5 (or whatever the number) kids&quot;. First of all, male and female humans have &lt;em&gt;exactly&lt;/em&gt; the same reproductive rate. For obvious reasons, every time a male has offspring, a female must have had also. Last I checked neither male nor female humans are capable of &lt;a href=&quot;https://en.wikipedia.org/wiki/Parthenogenesis&quot; rel=&quot;nofollow&quot;&gt;parthenogenesis&lt;/a&gt; (certain popular religious beliefs notwithstanding).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, let's assume that the 2.5 number is correct. That would be the &lt;em&gt;average&lt;/em&gt; number of children per couple. That does not mean that all couples will have 2.5, or even that &lt;em&gt;most&lt;/em&gt; couples will have 2.5. It just means that the &lt;em&gt;average&lt;/em&gt; will be 2.5. If, for example you have one couple with 6 children, one with 2 and two with 1, the average will be (6+2+1+1)/(1+1+2)= 2.5. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On to the main point. What does selection mean? In its simplest form, that the individual most likely to survive (the famous &quot;fittest&quot;) is also most likely to reproduce. This is a very simple concept, the longer you live the higher your chances of managing to have offspring. If you die two weeks after birth it is going to be hard to manage to reproduce yourself. This has not changed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what does &quot;fitness&quot; mean? It can mean many things. If you are a warm blooded creature at the beginning of an ice age for example, it could mean being better at regulating your temperature than your peers. If you are a 21st century human, it could mean being funnier on twitter than your peers. The two are not fundamentally different. They can both be selected for or against. As long as one mate is chosen over another, selection is happening and the &quot;fittest&quot; (in each particular context) is most often selected. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Add in the process of culturally modified selection pressure, and it&#xA;  seems to me that even an &quot;unfit&quot; male would end up having a couple of&#xA;  offspring. The fittest male (or female) is no better off than his or&#xA;  her contemporaries because of this &quot;leveling&quot; effect.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&quot;Culturally modified selection pressure&quot;, as you call it, is still selection pressure. Cultural factors can change what it means to be &quot;the fittest&quot; but there is no objective gold standard of &quot;fitness&quot;. While it may be true that in modern human society, different characteristics are selected for than was the case with early &lt;em&gt;Homo sapiens&lt;/em&gt;, this does not mean that &quot;evolution is not occurring&quot;. On the contrary, it is occurring but perhaps it is moving in a new direction. In fact, this is essentially a circular argument. By definition, &quot;fittest&quot; means most likely to survive and reproduce. It does not mean strongest or fastest or prettiest. It just means whoever is better at reproducing. If that happens to be those individuals who are best at square dancing, then it is they who are the fittest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take the example of a modern human with diabetes. Medicine allows diabetics to lead fully productive and largely normal lives. So, perhaps diabetes is no longer a selective criterion. This does not mean that the diabetic cannot be selected for or against based on their fitness on other scales. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whatever the selective pressure, whatever it may be that defines a &quot;good mate&quot;, if selection is present then so is evolution. The only way to remove a species from the process of selection would be to have &lt;em&gt;all&lt;/em&gt; (or none) individuals of each and every generation reproducing at the same rate. This is clearly not the case with humans. Surely not everyone around you has, or will have, children? There you go, selection!&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;UPDATE:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In answer to your comment, yes indeed, in order for a selective pressure to make itself felt and affect phenotype (at the species level), it needs to be constant across several generations. However, even the absence of selective pressure affects evolution. As others have mentioned below, active selection is not the only mechanism of evolution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your main question however seems to be the following: If modern society (medicine etc) allows individuals that would not survive in the wild to reproduce, how does that affect evolution? The main points in my answer, and all others here, are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Even if we accept that modern humans have removed themselves from the purely &quot;biological fitness&quot;-based selection pressure (an assumption I am not at all sure is true), and assuming that this removal is constant enough over many generations (again unclear), even if all this is true, evolution is most certainly still occurring. It may even be faster since genotypes that would not survive in the wild persist in the gene pool, thereby increasing its diversity.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;As you point out in your comment below, for such social pressure to make itself felt, it needs to be constant across many generations. We are probably not there yet.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Most importantly, as I said above, &lt;strong&gt;there is no such thing as an absolute biological fitness&lt;/strong&gt;. When the ecosystem changes, so does the definition of fitness. Modern humanity's ecosystem, our habitat, is intimately connected with our culture and society. If an individual is better at reproducing in that context, then that individual &lt;em&gt;is&lt;/em&gt; more fit. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2016-04-19T08:22:01.610" LastActivityDate="2016-04-19T08:22:01.610" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="5010" PostTypeId="1" AcceptedAnswerId="5012" CreationDate="2012-10-25T15:10:36.910" Score="8" ViewCount="177" Body="&lt;p&gt;I'm a mathematician trying to test some things on gene expression data, and I'm thus skimming over various articles such as &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=Sotiriou%20et.%20al.%2C%20Breast%20cancer%20classification%20and%20prognosis%20based%20on%20gene%20%20expression%20profiles%20from%20a%20population-based%20study.&quot; rel=&quot;nofollow&quot;&gt;Sotiriou et. al.&lt;/a&gt; to understand what is typically done with such data sets. Several things confuse me; in particular, a paragraph in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=Sotiriou%20et.%20al.%2C%20Breast%20cancer%20classification%20and%20prognosis%20based%20on%20gene%20%20expression%20profiles%20from%20a%20population-based%20study.&quot; rel=&quot;nofollow&quot;&gt;Sotiriou et. al.&lt;/a&gt; reads:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&quot;Clinical parameters such as ER status, [...] affect the behavior of breast &#xA;cancers. We asked whether these clinical/pathologic characteristics were &#xA;associated with differential gene expression. Parametric t tests identified 606 &#xA;probe elements of 7,650 elements represented in our array that could segregate &#xA;ER+ and ER- breast tumors (P &amp;lt; 0.001).&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As segregation of ER+/- based on gene expressions is one of several things I'm &#xA;interested in attempting to achieve through novel methods, I have been trying &#xA;to understand what precisely is meant with the above paragrah. To recap the &#xA;article, there are 99 patients with 7,650 probe expression values, and one &#xA;ER+/- value each. The article sets out to determine which of those 7,650 &#xA;probes successfully segregate the dataset into ER+ and ER-.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've run the above paragraph by a nearby statistician, and he could not for &#xA;the life of him figure out what was done, and had not even heard of such a &#xA;thing as a &quot;parametric t test&quot;. This leads me to suspect that the term is &#xA;specific to biology, so I ask: what is meant?  It is also unclear to me (and &#xA;him) what the P-value means in this context.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope the scope of this question isn't too broad. Of course I want to avoid &#xA;asking &quot;explain this article to me, the outsider, please&quot;; I do believe the &#xA;paragraph above is relatively self-contained in the context of gene &#xA;expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=Sotiriou%20et.%20al.%2C%20Breast%20cancer%20classification%20and%20prognosis%20based%20on%20gene%20%20expression%20profiles%20from%20a%20population-based%20study.&quot; rel=&quot;nofollow&quot;&gt;Sotiriou et. al., Breast cancer classification and prognosis based on gene &#xA;expression profiles from a population-based study.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1576" LastEditorDisplayName="user560" LastEditDate="2012-10-26T00:59:53.757" LastActivityDate="2012-10-26T00:59:53.757" Title="A mathematician's confusion regarding parametric $t$ tests for gene expression data" Tags="&lt;gene-expression&gt;&lt;statistics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5011" PostTypeId="2" ParentId="5010" CreationDate="2012-10-25T16:42:37.993" Score="3" Body="&lt;p&gt;This isn't the answer you're probably looking for, but I'd recommend not bothering with what they mean about their test in particular ... maybe they were really using a mann-whitney but their software (SPLUS) labeled it as a &quot;non-parametric t test&quot; for the non-formally-trained-statistical-end-user &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;[update]&lt;/strong&gt;: I misread the text and thought you (and the paper) wrote &quot;non-parameteric t-test&quot; which is why I suggested a possible mann-whitney -- mistake on my part, sorry. The second part below still stands &lt;strong&gt;[/update]&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, it has been nine years since that study has been published and the bioinformatics community has pretty much nailed down microarray analysis. Unless you have a specific reason not to, you should almost always prefer to use &lt;a href=&quot;http://www.bioconductor.org/packages/release/bioc/html/limma.html&quot; rel=&quot;nofollow&quot;&gt;limma&lt;/a&gt; first for your analysis of such data (gene-level expression data). It has an extremely thorough &lt;a href=&quot;http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf&quot; rel=&quot;nofollow&quot;&gt;user's guide&lt;/a&gt; to help you get started.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're looking for places to go to for follow up questions on your analysis, consider subscribing to the &lt;a href=&quot;https://stat.ethz.ch/mailman/listinfo/bioconductor&quot; rel=&quot;nofollow&quot;&gt;bioconductor mailing list&lt;/a&gt;, or head over to the &lt;a href=&quot;http://www.biostars.org/&quot; rel=&quot;nofollow&quot;&gt;biostars&lt;/a&gt; QA site.&lt;/p&gt;&#xA;" OwnerUserId="192" LastEditorUserId="192" LastEditDate="2012-10-25T18:10:59.220" LastActivityDate="2012-10-25T18:10:59.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5012" PostTypeId="2" ParentId="5010" CreationDate="2012-10-25T17:19:28.010" Score="8" Body="&lt;p&gt;I understand this in the following way:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For each probe you have two sets of measurements, one for ER+ and one for ER-. What you do is a T-test (to my understanding is that the &quot;parametric&quot; just emphasizes that T-test is a parametric test) on these two sets, testing if their mean is significantly different (they refer to this as &quot;separated&quot;). You repeat this test for all 7650 probes, and you get a set of 7650 p-values. You then do some multiple testing correction, such as a Bonferroni correction (I haven't checked in the paper if they did it, but they obviously should). Finally, they find that 606 of the p-values are significant (for some choice of threshold), suggesting that they can &quot;separate&quot; ER+ from ER-.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a computational biologist I would advise you to look specifically at bioinformatics papers if you are looking into developing new methods, since the analysis in &quot;pure biology&quot; papers can often be lacking and would not give you a good perspective of state-of-the-art analysis methods. Specifically for the question of separating groups from gene expression you should look into the field of Machine Learning, as it had been widely applied to this problem.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2012-10-25T17:19:28.010" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5013" PostTypeId="2" ParentId="4988" CreationDate="2012-10-25T19:04:51.157" Score="3" Body="&lt;p&gt;This part of the fruit is called &quot;Endocarp&quot;. It does not become more specific as that, as far as I know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fruit_anatomy&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Fruit_anatomy&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="852" LastActivityDate="2012-10-25T19:04:51.157" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="5017" PostTypeId="2" ParentId="4965" CreationDate="2012-10-26T03:15:18.987" Score="2" Body="&lt;p&gt;This post is pretty well written and seems to say that &lt;a href=&quot;http://www.conchologistsofamerica.org/articles/y1997/9703_Rosenberg.asp&quot; rel=&quot;nofollow&quot;&gt;the evolutionary forces that produce shell color like this is not known&lt;/a&gt;.  There are suggestions that the color is camoflage or the result of metabolic byproducts or that the pigments serve to strengthen the shell.  Its hard to believe some of these theories given that some shells do fine without coloring (at least that humans can see).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Structurally, shells are living things.  [They consist of many layers of thin irregular calcium carbonate hexagonal plates that make the mineral portion of the shell. The plates are held together by a protein glue and renewed by cellular action][3].  Whatever their evolutionary motivations, &lt;a href=&quot;http://en.wikipedia.org/wiki/Mollusc_shell#Structure&quot; rel=&quot;nofollow&quot;&gt;the colors are biomolecules which are in the biomatrix binding the plates together&lt;/a&gt;. This is a reason that shells that are left out to dry in the sun can become bleached and brittle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wish I had some better references about the shell structure, but I'm remembering a lot of this from a one afternoon book report given in a class, not from any intensive study on my part. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has influenced some ideas about things like tank armor, by the way.  At least there is funding for biomaterials research by agencies interested in tank armor.  Lamellar armor made of segmented plates can withstand tremendous impacts at a single point like a shell being dropped from a great height by a seabird or a shell hitting a tank. Plates just a few microns wide and a fraction of a micron deep shaped like irregular hexagons are hard to make if you aren't a mollusc so far though. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-10-30T16:41:12.667" LastActivityDate="2012-10-30T16:41:12.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5018" PostTypeId="1" CreationDate="2012-10-26T13:23:11.257" Score="6" ViewCount="1161" Body="&lt;p&gt;I have just taken some images with my light microscope at 400x of  (what I think is) some form of filamentous algae from a local pond. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I think I am looking at a single cell (centre) with some sort of arrangement of chloroplasts. Is this correct? Can anyone give me some more information on these structures?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also have included a higher-constrast image of the specimen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/p0UZJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lfHp9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="25568" LastEditDate="2016-09-08T13:42:25.880" LastActivityDate="2016-09-12T09:59:54.417" Title="Filamentous algae - what exactly am I looking at?" Tags="&lt;botany&gt;&lt;microbiology&gt;&lt;species-identification&gt;&lt;phycology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5019" PostTypeId="2" ParentId="5018" CreationDate="2012-10-26T13:52:21.080" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Spirogyra&quot; rel=&quot;nofollow&quot;&gt;Spirogyra&lt;/a&gt;. Apologies for the terse answer, but I think it does qualify.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-10-26T13:52:21.080" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5020" PostTypeId="2" ParentId="5004" CreationDate="2012-10-26T14:23:07.530" Score="2" Body="&lt;p&gt;This expands my comment on the question to an answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If an enzyme exhibits Michaelis-Menten kinetics, then it is valid to define a K&lt;sub&gt;M&lt;/sub&gt; and this equates to the substrate concentration when reaction velocity is 0.5 * V&lt;sub&gt;max&lt;/sub&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, many enzymes do not exhibit Michaelis-Menten kinetics. One example is when the enzyme shows a co-operative response to substrate concentration. In these circumstances the substrate concentration when reaction velocity is 0.5 * V&lt;sub&gt;max&lt;/sub&gt; is still a useful parameter, but there is no K&lt;sub&gt;M&lt;/sub&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://diabetes.diabetesjournals.org/content/47/3/307.full.pdf&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; for a discussion of the kinetic properties of the glucokinase of pancreatic &amp;beta; cells, which acts as the glucose sensor. This enzyme shows positive co-operativity with respect to its substrate glucose, and the authors develop a kinetic analysis in terms of various parameters. These include an S&lt;sub&gt;0.5&lt;/sub&gt; value for glucose, but a K&lt;sub&gt;M&lt;/sub&gt; value for ATP (presumably because the kinetics with respect to ATP are simple Michaelis-Menten).&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-11-04T09:03:08.287" LastActivityDate="2012-11-04T09:03:08.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5021" PostTypeId="1" AcceptedAnswerId="5022" CreationDate="2012-10-26T15:09:30.813" Score="9" ViewCount="2274" Body="&lt;p&gt;How quickly can the human heart rate rise and lower?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example lets say a human heart rate is rested and is at 60BPM and that person is suddenly scared to trigger their fight or flight reaction. Lets say their heart rate rises to double (120BPM).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the above example their rate has gone from 1000ms between beats to 500ms between beats. Can the human heart instantly in one heart beat go from the 1000ms to 500ms between beats or does it need to ramp up? If yes how quickly can the heart rate ramp up?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that each human heart is different, and that the speed increase and decrease will be different from person to person. What I'm looking for is a value that I can safely say the human heart won't exceed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly the same question goes to your heart going lower.&lt;/p&gt;&#xA;" OwnerUserId="1581" LastEditorUserId="3632" LastEditDate="2012-10-27T03:23:39.257" LastActivityDate="2012-10-27T03:23:39.257" Title="How quickly can the human heart rate rise and fall?" Tags="&lt;human-biology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5022" PostTypeId="2" ParentId="5021" CreationDate="2012-10-26T16:13:13.800" Score="8" Body="&lt;p&gt;According to the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Supraventricular_tachycardia&quot; rel=&quot;noreferrer&quot;&gt;&lt;strong&gt;&lt;em&gt;Supraventricular tachycardia&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt; the heart can go to a new faster rate in the space of a single beat, and then come down again just as quickly, as shown in this image taken from the Wikipedia page.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5wL7N.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-10-26T16:13:13.800" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5023" PostTypeId="2" ParentId="3711" CreationDate="2012-10-26T17:24:25.823" Score="8" Body="&lt;p&gt;This is a bit of a news flash - the answer is probably &lt;strong&gt;yes&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reading through recent Nature articles this one popped up: &lt;a href=&quot;http://www.nature.com/news/toxicology-the-learning-curve-1.11644&quot;&gt;Toxicology the learning curve&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where there are some intriguing examples of low concentration only toxic effects. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It might be worth a read. The preface gives a review of the idea, going back to the 16th century physician Paracelcius that the toxic properties of anything increases monotonically with dosage.  This is reflected in most of the answers and its one of the few things which toxicologists universally expect to see.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A research group at U Missouri-Columbia is claiming that endocrine disruptors have non-monotonic toxicology curves, meaning that toxic effects actually decrease with greater dosage.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/k6KGJ.jpg&quot; alt=&quot;non monotonic curves for endorcine disruptors&quot;&gt;&#xA;Nature is kind enough to allow access to this image.  The three curves on the right show a decline in drug effect as concentration increases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Endocrine hormones act at very low dosage - testosterone, estrogen, pituitary and thyroid hormones are some examples.  We'll probably be hearing more about this in the future, rather than less.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While this is still controversial, its made news because it is the sole class of compounds which really behave this way.  notably the first curve is for BPA (Bisphenol A) - the plastcizer which is common in pool toys and toy inflatable balls and drink bottles but the FDA has flagged for closer study. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-10-30T08:26:08.690" LastActivityDate="2012-10-30T08:26:08.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5025" PostTypeId="2" ParentId="5018" CreationDate="2012-10-26T22:35:18.520" Score="8" Body="&lt;p&gt;It looks indeed like a Spirogyra, or at least a member of the Zygnematales.&#xA;And yes, the green things are the chloroplasts (or one long chloroplast?), and they are arranged in spiral.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;empty&quot; space in the middle is likely the nucleus, and the darker circles within the chloroplast(s) could be the starch accumulated at the periphery of pyrenoids.&lt;/p&gt;&#xA;" OwnerUserId="1486" LastActivityDate="2012-10-26T22:35:18.520" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5026" PostTypeId="1" CreationDate="2012-10-27T00:40:12.583" Score="3" ViewCount="154" Body="&lt;p&gt;I am interested in the structural differences caused by benzopurines and benzopyrimidines at the oligonucleotide level between RNA and xRNA, both in single-stranded and double-stranded form. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am aware of RNA's tendency to be found in the A-form, of which the details are found &lt;a href=&quot;http://en.wikipedia.org/wiki/A-DNA#Comparison_Geometries_of_the_Most_Common_DNA_Forms&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. However, other than the obvious nucleobase expansion, I can't seem to find any details about xRNA's secondary structure.&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-10-27T09:11:41.847" Title="What are the distinctive structural features of single- or double-stranded xRNA, or where can I find them?" Tags="&lt;rna&gt;&lt;3d-structure&gt;&lt;nucleic-acids&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5027" PostTypeId="1" CreationDate="2012-10-27T00:47:09.360" Score="3" ViewCount="238" Body="&lt;p&gt;I am well-aware of the numbering system used for the traditional bases, as seen below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bGJty.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is &lt;strong&gt;how are the atoms in the size-expanded bases seen in xDNA and xRNA numbered&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bU8rL.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2017-11-19T18:52:04.767" Title="How are atoms in benzopyridines and benzopurines numbered?" Tags="&lt;dna&gt;&lt;rna&gt;&lt;nomenclature&gt;&lt;nucleic-acids&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5028" PostTypeId="1" CreationDate="2012-10-27T03:15:43.200" Score="4" ViewCount="4214" Body="&lt;p&gt;Why do slow oxidative muscle fibres contain more mitochondria compared to fast-glycolytic muscle fibres?&lt;/p&gt;&#xA;" OwnerUserId="1583" LastEditorDisplayName="user560" LastEditDate="2012-10-27T12:58:27.697" LastActivityDate="2012-10-27T12:58:27.697" Title="Slow-oxidative fibres vs fast-glycotic fibres" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;muscles&gt;&lt;mitochondria&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5029" PostTypeId="1" CreationDate="2012-10-27T06:39:17.323" Score="3" ViewCount="569" Body="&lt;p&gt;From what I read on the NatGeo app, it stated that the speed of the electrical impulses that are sent by a neurone will be approximately 332 kilometers per hour.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Will the speed of this electrical impulse decreases over the years as we age?&lt;/p&gt;&#xA;" OwnerUserId="1489" LastEditorUserId="69" LastEditDate="2012-11-27T12:19:36.327" LastActivityDate="2012-11-28T18:00:20.557" Title="Does the speed of electrical impulses through neurones decrease with age?" Tags="&lt;neuroscience&gt;&lt;senescence&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5030" PostTypeId="2" ParentId="5027" CreationDate="2012-10-27T08:40:29.510" Score="5" Body="&lt;p&gt;This is a question of chemical nomenclature and the principle source for this is the IUPAC (IUBMB in case of biological molecules; but not in this case). You can find all hetero-ring nomenclature references on the IUPAC web site:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.acdlabs.com/iupac/nomenclature/&quot;&gt;http://www.acdlabs.com/iupac/nomenclature/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.acdlabs.com/iupac/nomenclature/79/r79_702.htm&quot;&gt;http://www.acdlabs.com/iupac/nomenclature/79/r79_702.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I'm skipping the actual naming step)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Numbering is actually done according to&#xA;&lt;a href=&quot;http://www.acdlabs.com/iupac/nomenclature/79/r79_72.htm&quot;&gt;http://www.acdlabs.com/iupac/nomenclature/79/r79_72.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That means, if you take the skeleton without hetero atoms, you start&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;in a clockwise direction commencing with the carbon atom not engaged&#xA;  in ring-fusion in the most counter-clockwise position of the uppermost&#xA;  ring, or if there is a choice, of the uppermost ring farthest to the&#xA;  right, and omitting atoms common to two or more rings.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now, if there are more than one possibility due to symmetry, you chose the numbering that gives the heteros the smallest possible numbers (this means your purines would be actually wrongly numbered if they weren't an exception---see the List of retained names).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, we have finally in dxC and dxT the start at the lower nitrogen, going anti-clockwise (the other N at 3, methyl at 6, ribose at 8), and in dxA and dxG similarly the start at the lower right N, going anti-clockwise with other Ns at 3, 6, and 8, and ribose at 8, as well.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-10-27T08:40:29.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5031" PostTypeId="2" ParentId="5026" CreationDate="2012-10-27T08:51:01.303" Score="4" Body="&lt;p&gt;The only paper I found that examined the question is &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jp205122c&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;Structural, Dynamical, and Electronic Transport Properties of Modified DNA Duplexes Containing Size-Expanded Nucleobases&quot;&lt;/a&gt;. They state&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The results confirm that the structural and flexibility properties of&#xA;  the canonical DNA are globally little affected by the presence of&#xA;  benzo-fused bases. The most relevant differences are found in the&#xA;  enhanced size of the grooves, and the reduction in the twist.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They also have a picture comparing the structures of conventional DNA and xDNA:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/h1nXn.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So while the basic structure seems similar, the difference in diameter and twist look rather large to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is for xDNA, I would assume that xRNA behaves comparably if double-stranded. It would have to somehow fit the larger nucleobases into the helix like xDNA. And the structure of single-stranded RNA is variable, helical parts would probably look similar to xDNA, hard to say how the modified nucleobases would affect tertiary structure.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2012-10-27T09:11:41.847" LastActivityDate="2012-10-27T09:11:41.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5032" PostTypeId="2" ParentId="5028" CreationDate="2012-10-27T09:20:35.537" Score="4" Body="&lt;p&gt;This is well-explained at the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Skeletal_striated_muscle&quot; rel=&quot;nofollow&quot;&gt;skeletal striated muscle&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There are two principal ways to categorize muscle fibers: the type of&#xA;  myosin (fast or slow) present, and the degree of oxidative&#xA;  phosphorylation that the fiber undergoes. Skeletal muscle can thus be&#xA;  broken down into two broad categories: Type I and Type II. Type I&#xA;  fibers appear red due to the presence of the oxygen binding protein&#xA;  myoglobin. These fibers are suited for endurance and are slow to&#xA;  fatigue because they use oxidative metabolism to generate ATP. Type II&#xA;  fibers are white due to the absence of myoglobin and a reliance on&#xA;  glycolytic enzymes. These fibers are efficient for short bursts of&#xA;  speed and power and use both oxidative metabolism and anaerobic&#xA;  metabolism depending on the particular sub-type. These fibers are&#xA;  quicker to fatigue.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the terms used in the article, the Type II fibers rely on anaerobic, glycolytic metabolism, whereas the Type I fibers use oxidative metabolism which, of course, requires mitochondria for the TCA cycle and oxidative phosphorylation.The Type I fibers also contain myoglobin which promotes rapid movement of O&lt;sub&gt;2&lt;/sub&gt; through the cytosol to the mitochondrial ATP synthase.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-10-27T09:20:35.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5033" PostTypeId="1" AcceptedAnswerId="5054" CreationDate="2012-10-27T10:33:32.333" Score="5" ViewCount="273" Body="&lt;p&gt;My grandma is a great fan of mushrooms and knows quite a lot about them. About 10 years ago, she started throwing out mushroom remnants in one special place, in order to grow her own mushrooms. In fact, for last three years we found some parasol mushrooms (&lt;em&gt;Macrolepiota procera&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Today she found something, that nobody at home can classify. From what I searched, it might be  &lt;a href=&quot;http://www.grzyby.net/cortinarius-privignoides.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Cortinarius privignoides&lt;/em&gt;&lt;/a&gt;, but it is marked as almost extinct here in Poland, so I doubt this classification. Maybe you have seen this or know what it really is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Hkd8c.jpg&quot; alt=&quot;Strange mushroom&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hat is light brown with faint violet shades, the leg on the outside is partly violet too, but the inside is all white.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some more photos:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://hell.org.pl/~kamyk/mushroom/DSCN1448.JPG&quot; rel=&quot;nofollow noreferrer&quot;&gt;All three&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://hell.org.pl/~kamyk/mushroom/DSCN1450.JPG&quot; rel=&quot;nofollow noreferrer&quot;&gt;The gills&lt;/a&gt; are lighter brown, also with a violet tone&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://hell.org.pl/~kamyk/mushroom/DSCN1453.JPG&quot; rel=&quot;nofollow noreferrer&quot;&gt;The cut through the leg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://hell.org.pl/~kamyk/mushroom/DSCN1454.JPG&quot; rel=&quot;nofollow noreferrer&quot;&gt;The cut through the hat&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At my parents' house I found one more mushroom atlas, and a new candidate: Cortinarius traganus, but one thing is not right - the ones that I have don't have a smell and gassy webcap should smell and taste bad.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastEditorUserId="1427" LastEditDate="2012-10-28T18:45:39.490" LastActivityDate="2012-10-28T18:45:39.490" Title="An unexpected mushroom in my garden" Tags="&lt;taxonomy&gt;&lt;species-identification&gt;&lt;mycology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5034" PostTypeId="1" AcceptedAnswerId="5055" CreationDate="2012-10-27T15:14:41.800" Score="2" ViewCount="186" Body="&lt;p&gt;I have just an intuition that the carbohydrate part of glycoproteins help them to fulfil those tasks like in plasma membranes.&#xA;You can also get many more receptors if you can use carbohydrates too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, glycoproteins are necessary in recognising white blood cells. Antibodies are examples of glycoproteins. So they play a crucial role in our innate and adaptive immunity: MHC interaction with T cells in adaptive immunity.&#xA;Other examples: necessary in platelet aggregation and adherence, components of zona pellucida and connective tissue. Some hormones are also glycoproteins so necessary in humoral adaptive immunity: FSH, LH, TSH and EPO.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;But why glycoproteins are &quot;better&quot; than proteins without carbohydrates moiety in fulfilling biological tasks?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I still see that both are important, but why the one is better than the other one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words: &lt;strong&gt;Are there any biological tasks that only non-glycoproteins can fulfil, not glycoproteins?&lt;/strong&gt; Are non-glycoproteins necessary in some essential biological tasks?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the answer to the last two questions is &quot;yes&quot;, so why would one say that glycoproteins are better in fulfilling biological tasks than non-glycoproteins.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2012-10-29T02:14:18.043" Title="Why glycoproteins are better than non-glycoproteins in fulfilling biological tasks?" Tags="&lt;proteins&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5035" PostTypeId="2" ParentId="3445" CreationDate="2012-10-27T16:59:17.933" Score="4" Body="&lt;p&gt;We routinely use E. coli preps from 16-18h overnight cultures. The cultures don't show any overt signs of lysis (sometimes you can see cellular debris if the culture has indeed overgrown). I have also noticed inconsistent times when resuspending the pellet. For my own use, centrifuging at too great a g-force or for too long can increase the likelihood of making a difficult pellet. For example, I will typically spin a miniprep culture aliquot on a refrigerated table top centrifuge for 3 min @ 5,000 g.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I always vortex my bacterial pellet to resuspend and I have had great success with this method, though I'm well aware others will pipette up and down. What I normally do to increase the ease of resuspension is to add the buffer, and let the tubes sit in the fridge for 5-10 minutes. For whatever reason, letting the pellet literally chill makes resuspension very easy relative to immediate resuspension.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt; I have also observed strain-specific differences. JM109 seem a little stickier than DH5a and TOP10.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2014-08-30T13:48:47.423" LastActivityDate="2014-08-30T13:48:47.423" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5036" PostTypeId="1" CreationDate="2012-10-27T17:37:57.697" Score="3" ViewCount="83" Body="&lt;p&gt;I realize that there are many isolated efforts to sequence the genome of a particular endangered species such as the orangutan or the snow leopard. However is there a concerted effort to sequence the genomes of every species on the brink of extinction? Also, is there an effort to sequence the genetic diversity of the surviving populations, since it would be very difficult to re-create alleles that would be needed if the species were to ever be resurrected. &lt;/p&gt;&#xA;" OwnerUserId="146" LastActivityDate="2014-01-18T18:51:13.590" Title="Is There An Initiative To Sequence The Genomes Of Critically Endangered Species?" Tags="&lt;genomes&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5037" PostTypeId="1" CreationDate="2012-10-27T19:05:13.567" Score="2" ViewCount="62" Body="&lt;p&gt;It is impossible to breed a blue rose or a cat with a bulldog shape. This is because breeding is limited by gene variations in the population. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do breeders call this effect?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess this term is from medieval and/or handicraft breeders, not modern and hi-tech.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE 2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am speaking not about principal impossibility but just about observable or tangible barrier. We can be sure that it is possible to turn dog into cat in billion years, but it is much harder than turn German Shepherd to Yorkshire Terrier, which is possible for hundreds of years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, there are are two main types of changes, ones take hundreds of years, others take hundreds of millions of years. Former require genetic recombination while latter require genetic mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This barrier was felt by breeders in practice and caused some versions of anti-evolution beliefs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I need to know how this barrier is named.&lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="1584" LastEditDate="2012-10-29T19:22:07.270" LastActivityDate="2012-10-29T19:22:07.270" Title="What do breeders call the effect when a breed resists modification?" Tags="&lt;genetics&gt;&lt;zoology&gt;&lt;gene-expression&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5040" PostTypeId="2" ParentId="3657" CreationDate="2012-10-27T19:14:30.517" Score="0" Body="&lt;p&gt;You may have some liquid in your nose after sneeze. This liquid can contain microbial flora, which can have a smell, which is interpreted by you as of flowers. Check your health with a doctor to be on the safe side.&lt;/p&gt;&#xA;" OwnerUserId="1584" LastActivityDate="2012-10-27T19:14:30.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5042" PostTypeId="1" CreationDate="2012-10-27T23:07:13.123" Score="2" ViewCount="884" Body="&lt;p&gt;Do foods with preservatives stay digestible for longer in the gut by not rotting as much (producing less toxins)?&lt;/p&gt;&#xA;" OwnerUserId="1585" LastEditorUserId="1585" LastEditDate="2012-11-12T19:00:45.980" LastActivityDate="2012-11-12T19:04:50.980" Title="Do foods with preservatives become less toxic in the gut?" Tags="&lt;digestive-system&gt;&lt;food&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5043" PostTypeId="1" AcceptedAnswerId="5071" CreationDate="2012-10-28T01:59:42.087" Score="4" ViewCount="258" Body="&lt;p&gt;I'm wondering what produces the feeling of hunger in humans. Checking Wikipedia revealed that leptin and ghrelin are two hormones involved. I've also read that the digestive system produces its own melatonin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because melatonin is related to circadian rhythm and the biological clock,&lt;em&gt;Is melatonin involved in feeling hungry?&lt;/em&gt; &lt;strong&gt;Is there a circadian pattern to the levels of leptin and ghrelin in humans?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="57" LastEditDate="2012-10-28T03:03:54.490" LastActivityDate="2012-10-31T23:11:27.090" Title="Is there a circadian component to hunger?" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;&lt;circadian-rhythms&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5045" PostTypeId="2" ParentId="3165" CreationDate="2012-10-28T03:32:48.337" Score="-2" Body="&lt;p&gt;I don't think this will ever be answered, mostly because studying the long-term effects of athletic training is very difficult. People constantly change their training methods, habits, and schedule, so controls are nearly impossible to construct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My opinion, is that the nurture component is the strongest, because of the amazing plasticity of the body in response to stress: bones grow/reform differently, neural networks become trained, muscles change. Over many years these can be enormous. This is true of all humans, absent those with severe genetic faults.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetics probably has a stronger influence on the psychological traits which might induce someone to train so hard. Though parenting could certainly override this.&lt;/p&gt;&#xA;" OwnerUserId="1586" LastActivityDate="2012-10-28T03:32:48.337" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5046" PostTypeId="2" ParentId="3481" CreationDate="2012-10-28T03:45:43.570" Score="2" Body="&lt;p&gt;I think it would depend on the benefits you are looking for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you ate the same thing everyday, it's possible your intestinal flora, and the rest of your GI tract would optimize themselves for maximal nutritional extraction. It is known that the flora in you GI do affect nutrition. I recall reading about obese patients who had gut-bacteria which made more nutrients available.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if you were in an environment where your diet could change unexpectedly, this optimization could actually be detrimental, since you wouldn't be ready to switch foods when necessary.&lt;/p&gt;&#xA;" OwnerUserId="1586" LastActivityDate="2012-10-28T03:45:43.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5047" PostTypeId="2" ParentId="2250" CreationDate="2012-10-28T04:04:28.827" Score="17" Body="&lt;p&gt;I'm not sure why no one mentions this, but any food you eat would negate this effect entirely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming then, that you had no food, the lack of minerals in this pure water would simply be another deprivation for your body. The intestinal track actively reabsorbs ions, countering this. However, in this water-only deprivation, those mechanisms might fail as some are glucose dependent.&lt;/p&gt;&#xA;" OwnerUserId="1586" LastActivityDate="2012-10-28T04:04:28.827" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5048" PostTypeId="2" ParentId="5037" CreationDate="2012-10-28T04:09:37.100" Score="1" Body="&lt;p&gt;I'm honestly not sure if one exists. They simply lack the gene/allele - the only specific term I can think of when it comes to &lt;em&gt;lacking&lt;/em&gt; a gene is referencing &lt;strong&gt;Knockout&lt;/strong&gt; variations where a researcher purposefully removes a gene from a subject in order to observe the effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, &quot;Knockout Mice/etc.&quot; imply intent on behalf of the researcher, not a result of breeding or natural lack of an allele. Perhaps &quot;Genetically Incapable&quot; would be a phrase meaning the same thing - but I'm not aware of any 'official' shorthand for 'Cannot because it's not in their genes.'&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorDisplayName="user560" LastEditDate="2012-10-28T22:24:03.290" LastActivityDate="2012-10-28T22:24:03.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5049" PostTypeId="1" CreationDate="2012-10-28T04:20:32.500" Score="3" ViewCount="1649" Body="&lt;p&gt;While searching online I did not find any conclusive article on whether it is good or bad for one's eyesight to read on a computer screen in a dark room. Most mention that it will cause strain that will go away after some rest (sleep).&#xA;My question is does reading in dark room has any long term effect on one's eyesight and what screen brightness setting (low of high) should one prefer if trying to read in a dark room?&lt;/p&gt;&#xA;" OwnerUserId="1442" LastActivityDate="2012-10-28T16:08:20.640" Title="Screen brightness for reading in dark room" Tags="&lt;eyes&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2012-10-29T09:20:00.310" ContentLicense="CC BY-SA 3.0" />
  <row Id="5050" PostTypeId="2" ParentId="5042" CreationDate="2012-10-28T12:06:35.660" Score="2" Body="&lt;p&gt;&lt;strong&gt;Do foods with preservatives take longer to digest?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Food preservatives are either antimicrobials (e.g. sorbate, sulfite) or antioxidants (free radical scavengers such as butylated hydroxyanisole).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Digestion is initiated in the stomach by hydrochloric acid and pepsin. It continues in the small intestine with the action of numerous other enzymes including amylases, lipases and proteases. There is no obvious way that these digestive processes would be inhibited by preservatives.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-10-28T12:06:35.660" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="5051" PostTypeId="1" AcceptedAnswerId="5052" CreationDate="2012-10-28T15:31:30.733" Score="5" ViewCount="5569" Body="&lt;p&gt;Do all sea creatures that have scales have to have fins?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do we know of any sea creatures that have only scales without fins?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm especially interested in fish that have scales but no fins. &lt;/p&gt;&#xA;" OwnerUserId="1587" LastEditorUserId="57" LastEditDate="2012-10-28T16:10:10.203" LastActivityDate="2020-08-04T02:40:48.063" Title="Do all sea creatures that have scales have to have fins?" Tags="&lt;zoology&gt;&lt;marine-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5052" PostTypeId="2" ParentId="5051" CreationDate="2012-10-28T16:01:51.250" Score="5" Body="&lt;p&gt;How about marine reptiles? &lt;a href=&quot;http://en.wikipedia.org/wiki/Sea_snake&quot;&gt;Sea snakes&lt;/a&gt; have a paddle-like tail, so perhaps you would claim that as a fin, but maybe &lt;a href=&quot;http://en.wikipedia.org/wiki/Marine_iguana&quot;&gt;marine iguanas&lt;/a&gt; would qualify? And, of course, &lt;a href=&quot;http://en.wikipedia.org/wiki/Sea_turtle&quot;&gt;sea turtles&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-10-28T16:01:51.250" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5053" PostTypeId="2" ParentId="5049" CreationDate="2012-10-28T16:08:20.640" Score="0" Body="&lt;p&gt;Not an answer, but just a suggestion:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are in a position where you must read off of a computer monitor without ample ambient light, I'd suggest you try setting your monitor/reader/whatever to have a dark background and light/wight text so it doesn't feel like you're staring into the sun.&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2012-10-28T16:08:20.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5054" PostTypeId="2" ParentId="5033" CreationDate="2012-10-28T18:45:14.060" Score="1" Body="&lt;p&gt;Thanks to MCM's advice I know for almost-certain that this is &lt;a href=&quot;http://en.wikipedia.org/wiki/Lepista_personata&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Lepista personata&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastActivityDate="2012-10-28T18:45:14.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5055" PostTypeId="2" ParentId="5034" CreationDate="2012-10-29T02:14:18.043" Score="2" Body="&lt;p&gt;The central reasoning is flawed because it places some intrinsic value on glycoprotein modification. The general intuition is that, if the protein is glycosylated, then it's likely for a reason, whether it be to help fulfil antigen recognition, adopt a correct conformation, or help in molecular tethering. Beyond, that, many (perhaps a majority) of cellular proteins are not glycosylated. Two important examples of cell membrane proteins that are not glycosylated would be endoproteases (eg, furin) and chemical transporters.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-10-29T02:14:18.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5056" PostTypeId="1" AcceptedAnswerId="5070" CreationDate="2012-10-29T03:18:19.153" Score="12" ViewCount="607" Body="&lt;p&gt;I was just reading &lt;a href=&quot;http://www.slate.com/articles/health_and_science/human_evolution/2012/10/evolution_of_lactose_tolerance_why_do_humans_keep_drinking_milk.single.html&quot;&gt;Evolution of lactose tolerance&lt;/a&gt;, and in it one line says &quot;But there was a time in human history when our diet and environment conspired to create conditions that mimicked those of a disease epidemic&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something I've always wondered is rather than natural selection occurring and survival of the fittest and so on, is that a viral epidemic caused a mutation in the survivors, i.e. DNA was inserted from the virus that modified the survivors genome. There is some evidence that a significant percentage of the human genome comes from viruses. Probably a naive question - so is there any evidence that this has occurred? From my lay perspective this is what attempts at genetic engineering use, so it's possible nature already did this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's always seemed to me that natural selection and point mutations, and the chance meeting of two people with the same mutation would be too slow and viruses would be a more efficient method to evolve a large population at the same time. Things like punctuated evolution might support this? not really sure.&lt;/p&gt;&#xA;" OwnerUserId="1589" LastEditorDisplayName="user560" LastEditDate="2012-10-29T19:04:03.813" LastActivityDate="2012-10-30T19:28:13.887" Title="Is there any evidence that a virus can modify human evolution" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5057" PostTypeId="2" ParentId="5036" CreationDate="2012-10-29T08:13:31.900" Score="3" Body="&lt;p&gt;The seedbank terdon mentions is the Norwegian &lt;em&gt;Svalbard Global Seed Vault&lt;/em&gt; located at Spitsbergen island:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Svalbard_Global_Seed_Vault&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Svalbard_Global_Seed_Vault&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the closest thing to a concerted initiative for sequencing animals I know of is the Genome 10K project:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://genome10k.soe.ucsc.edu/&quot; rel=&quot;nofollow&quot;&gt;http://genome10k.soe.ucsc.edu/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their list of &lt;em&gt;first 101 vertebrata&lt;/em&gt; proposed for sequencing contains 29 species with status RED from the red list. Most of them are only proposed, but the sequencing of the following are already in progress:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;crested ibis&lt;/strong&gt; (&lt;em&gt;Nipponia nippon&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Amur tiger&lt;/strong&gt; (&lt;em&gt;Panthera tigris altaica&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;cheetah&lt;/strong&gt; (&lt;em&gt;Acynonyx jubatus&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;lion&lt;/strong&gt; (&lt;em&gt;Panthera leo&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;domestic yak&lt;/strong&gt; (&lt;em&gt;Bos grunniens&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;bactrian camel&lt;/strong&gt; (&lt;em&gt;Camelus bactrianus&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and that of the &lt;strong&gt;Chinese softshell turtle&lt;/strong&gt; (&lt;em&gt;Trionyx sinensis&lt;/em&gt;) has funding secured. Already complete are the &lt;strong&gt;giant panda&lt;/strong&gt;, the &lt;strong&gt;chiru&lt;/strong&gt;, and the &lt;strong&gt;polar bear&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And some surprising fact: where the funding is secured it is/was funded by the Beijing Genome Institute. A shame if this would remain the only one.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-10-29T08:23:30.967" LastActivityDate="2012-10-29T08:23:30.967" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5058" PostTypeId="2" ParentId="5007" CreationDate="2012-10-29T09:11:34.690" Score="4" Body="&lt;p&gt;Darwin used the term “&lt;em&gt;descent with modification&lt;/em&gt;” to describe evolution. That means &lt;strong&gt;a change between generations&lt;/strong&gt; in the characteristics, or traits, of a population. It is a process which occurs by four processes - mutation, migration, drift, and selection. The conditions for evolution are &lt;em&gt;i)&lt;/em&gt; a population must be able to reproduce, resulting in a descendant population, &lt;em&gt;ii)&lt;/em&gt; offspring must tend to resemble their parents and this occurs because traits are determined by heritable information, e.g. DNA, and &lt;em&gt;iii)&lt;/em&gt; that heritable information must have the potential to change from one generation to the next. &lt;strong&gt;It does not require selection&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/IZsJ4.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/IZsJ4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.huli.group.shef.ac.uk/Milot.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here is a paper about evolution and adaptation in humans:&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Despite popular misconceptions, natural selection does operate in&#xA;  modern human populations. New studies even show that changes&#xA;  associated with modernization are deeply reshaping selection pressures&#xA;  and, perhaps, bits of our biological nature.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Selection is still occurring in humans too&lt;/strong&gt;, &lt;a href=&quot;https://biology.stackexchange.com/questions/42050/if-evolution-is-not-about-improvement-why-is-there-so-much-improvement/42063#42063&quot;&gt;leading to further adaptation (a &lt;em&gt;subprocess&lt;/em&gt; of evolution)&lt;/a&gt; (e.g. &lt;a href=&quot;http://www.pnas.org/content/109/21/8044.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/nrg/journal/v11/n9/full/nrg2831.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;). Many people naively think and suggest that selection has been halted in humans, the fact is, it hasn't. &lt;strong&gt;We still have variance in reproductive success based upon the genes individuals possess&lt;/strong&gt;, e.g. some people die from genetic diseases before reproduction.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Here are some illustrations describing the &lt;strong&gt;mechanisms of evolution&lt;/strong&gt;. Note that drift and selection both cause variance in reproductive success among individuals in a population, for drift the variance is &lt;em&gt;independent&lt;/em&gt; of the genes, while for selection it is a tendency for the carriers of one allele to have higher reproductive output than another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Mutation:&lt;/strong&gt;&#xA;&lt;a href=&quot;https://i.stack.imgur.com/a3bvT.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/a3bvT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Migration:&lt;/strong&gt;&#xA;&lt;a href=&quot;https://i.stack.imgur.com/431yn.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/431yn.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Drift:&lt;/strong&gt;&#xA;&lt;a href=&quot;https://i.stack.imgur.com/BSffA.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/BSffA.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Selection:&lt;/strong&gt;&#xA;&lt;a href=&quot;https://i.stack.imgur.com/6XRIp.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/6XRIp.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2016-01-18T16:48:17.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5059" PostTypeId="1" AcceptedAnswerId="5061" CreationDate="2012-10-29T09:30:21.250" Score="5" ViewCount="1539" Body="&lt;p&gt;In protocols for minimal media for growing bacteria I often see that a vitamin mix or a mix of various trace metals is added. But at least for E. coli I know that those are not strictly necessary, they also grow in minimal medium without any of this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it make sense to add vitamins or trace elements when growing common E. coli for protein expression like BL21 (DE3) in minimal medium? Is there some literature data on how this can affect the growth of the bacteria?&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2018-06-01T13:31:32.900" Title="How useful are vitamin and trace element additions in E. coli culture medium?" Tags="&lt;ecoli&gt;&lt;growth-media&gt;&lt;protein-expression&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5060" PostTypeId="2" ParentId="5056" CreationDate="2012-10-29T10:28:04.890" Score="4" Body="&lt;p&gt;The simplest example, that I can recall are &lt;a href=&quot;http://en.wikipedia.org/wiki/Influenza_pandemic&quot; rel=&quot;nofollow&quot;&gt;the flu pandemics&lt;/a&gt;. The 1918 pandemic is the first to be described because of its severity, but quite possibly not the first in human history (see for example &lt;a href=&quot;http://en.wikipedia.org/wiki/Black_Death&quot; rel=&quot;nofollow&quot;&gt;the Black Death&lt;/a&gt; - &lt;em&gt;Yersinia pestis&lt;/em&gt; is a bacterium, but in the 15th century in just a few years it covered almost all of Europe, sometimes killing up to 40% of population in a given area).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Influenza pandemics appeared quite regularly during the 20th century, usually every 20 years and killed suspiciously many people compared to yearly influenza strains. Additionally, a person who survived one pandemic, was unaffected or only mildly affected by the next pandemic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All this suggests, that the pandemics &quot;clear&quot; the population from susceptible individuals, and regularity of pandemics (notice, that 20 years is more or less the time of one human generation!) assures that the new generations also go through this kind of selection. The surviving individuals are more resistant to all strains of influenza then those, who never suffered from a pandemic. Maybe the influenza didn't mutate our DNA, but it could be a major force of natural selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And one more note: did you notice the great noise in media every time a new potentially pandemic strain is discovered? Actually, it's not just hyperboly of the danger. Last pandemic was in the '70s, so it's high time for a new one. And, since the last one was  almost 40 years ago, the new one (&lt;em&gt;when&lt;/em&gt; it happens) will probably be very severe.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastActivityDate="2012-10-29T10:28:04.890" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5061" PostTypeId="2" ParentId="5059" CreationDate="2012-10-29T10:48:52.620" Score="3" Body="&lt;p&gt;Not sure that I have ever come across trace metals in recipes (I assume that you aren't referring to the Ca/Mg salts component of M9), but it is certainly the case that many K12 strains (e.g. C600, DH5&amp;alpha;) require thiamine because they are &lt;em&gt;thi&lt;/em&gt; mutants. This doesn't apply to BL21 since it is from a different lineage (it is a B strain). In a lab where several strains are being used it will always make sense to standardise on a universal recipe so that the medium available will suit all strains in use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a useful list of &lt;em&gt;E.coli&lt;/em&gt; genotypes &lt;a href=&quot;http://openwetware.org/wiki/E._coli_genotypes&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-10-29T10:48:52.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5062" PostTypeId="2" ParentId="1662" CreationDate="2012-10-29T15:43:36.607" Score="2" Body="&lt;p&gt;Trees that have been dormant over the winter exist on nutrients stored in their roots during fall. When a tree has been damaged or diseased, it may not have been able to store enough nutrients before winter, or may not have enough stored to heal the damage/disease. If the damaged/diseased tree has depleted its winter root stores, it must leaf out (earlier than others of its species) and resume photosynthesis in order to have enough energy to attempt healing itself.&lt;/p&gt;&#xA;" OwnerUserId="1591" LastActivityDate="2012-10-29T15:43:36.607" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5063" PostTypeId="1" AcceptedAnswerId="9981" CreationDate="2012-10-29T16:42:27.293" Score="3" ViewCount="169" Body="&lt;p&gt;Creativity, innovation and ideation. Is there something in the brain that makes the brain think that way, as opposed to &quot;normal baseline&quot;. &lt;strong&gt;What triggers creative thought in humans?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="577" LastEditDate="2012-11-19T03:55:25.223" LastActivityDate="2013-08-25T02:53:49.193" Title="What triggers creative thought in humans?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;neuromodulation&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="5064" PostTypeId="2" ParentId="5037" CreationDate="2012-10-29T17:28:49.547" Score="0" Body="&lt;p&gt;There must be a point where a desired trait cannot be obtained by selective breeding or by evolution at all!  Why can't there be viruses the size of houses or elephants as small as a flea?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Those may seem like absurd examples, but that's just to point out that not all traits can be obtained in less than infinite number of adaptive steps.  Jerry Fodor pointed this out (among other things) in his essay &lt;a href=&quot;http://www.lrb.co.uk/v29/n20/jerry-fodor/why-pigs-dont-have-wings&quot; rel=&quot;nofollow&quot;&gt;&quot;Why Pigs Don't Have Wings&quot;&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exactly what you can get and what you can't get is open to effort.  For instance I suppose you could turn a pig into a pigeon if you had a few million generations to do it - something similar to the evolutionary time back to the time they diverged.  That would be difficult, but you could basically run evolution for another billion years to get small hollow boned pigs with bats wings on their forearms.  you probably wouldn't recognize it as a pig, but then again youd be dead of old age several times over too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could you breed a human where bullets bounce off and they can fly?  not so sure of that. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-10-29T17:28:49.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5067" PostTypeId="2" ParentId="3052" CreationDate="2012-10-30T16:05:18.313" Score="4" Body="&lt;p&gt;I've recently seen this video: &lt;a href=&quot;http://www.ted.com/talks/juan_enriquez_will_our_kids_be_a_different_species.html&quot; rel=&quot;nofollow&quot;&gt;Juan Enriquez: Will our kids be a different species?&lt;/a&gt;, in which the speaker discusses differences between humans currently inhabiting the planet. At one point in the video,he does touch on the olympics and mention that a lot of the &lt;strong&gt;Olympic powerlifters have a certain gene expression.&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Power lifting is quite different from swimming, but from the top of my head, I can recall that people from east Africa excel at running. So &lt;strong&gt;the difference may be genetic&lt;/strong&gt;, at least on some level. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea of differences between races is very &quot;not politically correct&quot;, and as the speaker suggests, we still live int he world that remembers the Holocaust. &lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-10-30T16:05:18.313" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5069" PostTypeId="2" ParentId="5007" CreationDate="2012-10-30T17:58:45.853" Score="8" Body="&lt;p&gt;Evolution is defined as the change in the allele frequency of a population through time.  In other words a change in the genetic diversity of the population through time.  This change can be the result of 4 processes, known as the mechanisms of evolution:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) gene flow - this is the movement of individuals into or out of the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) genetic drift - this is the removal of individuals due to random events (such as accidents).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) mutation - this is the spontaneous change in the DNA, which instantly increases genetic diversity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) selection (natural, sexual or artificial) - this is the increase in the frequency of alleles (traits) that confer a fitness advantage (i.e., those with a given trait will leave more offspring). Most adaptive changes in gene frequency are the result of selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if one presumes that your analysis is correct and natural selection is no longer operating on modern humans (although this is suspect, as is pointed out by other answers), evolution would still be occurring due to mechanisms 1 - 3.  If we go further and consider the Earth's human population as a whole (eliminating gene flow as a mechanism) you would still have evolution via genetic drift and mutation.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, yes, evolution is not only possible but inevitable in modern human populations.&lt;/p&gt;&#xA;" OwnerUserId="137" LastEditorUserId="1590" LastEditDate="2012-10-31T00:00:03.637" LastActivityDate="2012-10-31T00:00:03.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5070" PostTypeId="2" ParentId="5056" CreationDate="2012-10-30T19:28:13.887" Score="4" Body="&lt;p&gt;There is some nice work from Pardis Sabeti in this broad area (not just viruses but pathogens in general). &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22357659&quot; rel=&quot;nofollow&quot;&gt;Her colleagues have found&lt;/a&gt; polymorphisms in SLC40A1, encoding an iron transport protein, that influence susceptibility to tuberculosis. She's also looked at human genetic variation and susceptibility to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22312054&quot; rel=&quot;nofollow&quot;&gt;Lassa fever&lt;/a&gt;. And this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19403559&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; talks about CD36 and malaria in sub-Saharan African populations (no association). Look at her work from 2009 onward, as there is a lot there. They're also looking at variation in the pathogen because it is a two-way interaction.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-10-30T19:28:13.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5071" PostTypeId="2" ParentId="5043" CreationDate="2012-10-30T22:22:46.593" Score="4" Body="&lt;p&gt;&lt;strong&gt;Yes&lt;/strong&gt;, absolutely. A major focus of understanding obesity, diabetes and other metabolic disorders are targeted to understanding the circadian (and other cyclical nature) systems in neurobiology and endocrinology. I can speak within the study of diabetes, there is an observed diabetic &quot;dawn effect&quot; in which there is an early morning (dawn) spike in blood glucose. The exact mechanism for this spike in blood glucose is not fully known, but the general circadian nature is intriguing and would suggest a dominant hormonal cause.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some other review articles may be found here. An overall &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18154499&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt; of homeostatic balance as it relates to the central nervous system and apetite regulation. The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19190620&quot; rel=&quot;nofollow&quot;&gt;second&lt;/a&gt; review more closely focuses on the biochemistry and endocrinology of central and peripheral regulation on food intake and physical activity.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18154499&quot; rel=&quot;nofollow&quot;&gt;Berthoud HR, Morrison C. The brain, appetite, and obesity. Annu Rev Psychol. 2008;59:55-92.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19190620&quot; rel=&quot;nofollow&quot;&gt;Lenard NR, Berthoud HR. Central and peripheral regulation of food intake and physical activity: pathways and genes. Obesity (Silver Spring). 2008 Dec;16 Suppl 3:S11-22.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-10-30T22:22:46.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5072" PostTypeId="2" ParentId="3280" CreationDate="2012-10-30T23:14:42.140" Score="2" Body="&lt;p&gt;I would suggest that the behaviour of the gazelles you are citing is perhaps over simplified. There will likely be temporal and spatial dynamics in their behaviour... Prey will probably spend more time concentrating on observation when they know there are predators around. There will also be likely peak times during which hunting occurs (in savannah systems it tends to be dawn and dusk) and prey would be more cautious at these times.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to me that the prey would not be judging the hunger of the predators but instead they learn the consistent patterns in the level of risk associated with being near predators. This could be genetic in its cause. If there is a gene (or genes) which determine when a prey individual is most likely to be out in the open grazing then the higher probability of predation at certain times would reduce the frequency of the genes which cause that choice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There could also be fluctuations over time as the predators learn that the prey have become less cautious, which then causes predators to take advantage of unsuspecting prey, which you might be interpreting as the &quot;faking&quot; behaviour... it is not a deliberate fake, more taking advantage of the risk taking behaviour of the prey (as time passes without attack they will become more brazen). To the best of my knowledge there are no examples of the deliberate fake but predator prey dynamics are not my specialism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall, I think you are asking a question based on learning and information use of repetitive patterns in behaviour of predators by prey, and have interpreted these behaviours in an over complex way (see Occams Razor).&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2012-10-30T23:14:42.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5073" PostTypeId="2" ParentId="5007" CreationDate="2012-10-31T02:11:51.107" Score="5" Body="&lt;p&gt;In the US, different races have &lt;a href=&quot;http://blogs.discovermagazine.com/gnxp/2010/09/which-american-racial-group-has-the-lowest-fertility/&quot; rel=&quot;nofollow&quot;&gt;significantly different birth rates&lt;/a&gt;.  Obviously race has a genetic component, though I'm guessing that the racial differences are mostly due to cultural and economic reasons.  Still in this sense, the US population is evolving: alleles associated with some populations (African Americans, Hispanics) are becoming more common, while those associated to other populations (white non-hispanic, etc) are becoming less common.  So the US is definitely evolving to become &quot;less white&quot;.  Note that this is true even though the overall birth rate reported in the study is not much above the minimal replacement rate of 2.0.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723861/&quot; rel=&quot;nofollow&quot;&gt;religiosity is associated with increased fertility&lt;/a&gt;, and there is some evidence that &lt;a href=&quot;http://marginalrevolution.com/marginalrevolution/2011/02/genetic-factors-and-the-religious-life.html&quot; rel=&quot;nofollow&quot;&gt;religiosity has a genetic component&lt;/a&gt;.  In that sense, the population may be evolving to be more religious over time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, there are &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetics_of_obesity&quot; rel=&quot;nofollow&quot;&gt;genetic factors to obesity&lt;/a&gt;, which has a &lt;a href=&quot;http://www.sciencedaily.com/releases/2007/03/070307075723.htm&quot; rel=&quot;nofollow&quot;&gt;negative effect on fertility&lt;/a&gt;.  These genes may even have been actively selected for in the past (the thrifty genome hypothesis), but are probably being selected against now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We are currently undergoing one of the biggest shifts in human fertility in the history of our species: in the past century, we've developed technologies which allow people to more carefully choose when to become pregnant (condoms, abortions, hormone birth control).  Any genetic factor which has an impact on use of birth control could lead to evolutionary changes: this could range anywhere from ethnicity associated with economic or religious status (poverty, Catholicism), impulse control, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is all somewhat speculative (except for the first example), but it's certainly possible for evolution to occur in modern human society, and it likely is occurring.&lt;/p&gt;&#xA;" OwnerUserId="1597" LastEditorUserId="69" LastEditDate="2012-10-31T21:56:17.690" LastActivityDate="2012-10-31T21:56:17.690" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5074" PostTypeId="1" AcceptedAnswerId="5080" CreationDate="2012-10-31T04:49:42.510" Score="5" ViewCount="345" Body="&lt;p&gt;The theory of natural selection has it that individuals with better genes tend to survive and reproduce, passing their genes to their offspring. This gradual process results in a population more adapted at survival. However, due to the advancement in medical science, humans with poorer genes tend to survive and reproduce just as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, in the past, many people, excluding those with natural immunity due to some genetic mutations, would have succumbed to illnesses such as malaria and typhoid. But with better hygiene and medical treatment, these patients tend to survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, imagine a future where all illnesses including cancer can be treated. How would it impact the survival of the human race? Would we become more and more vulnerable such that our survival hinges heavily on medical technology, analogous to how an astronaut's survival is dependent on his spacesuit?&lt;/p&gt;&#xA;" OwnerUserId="1283" LastActivityDate="2012-10-31T13:22:42.657" Title="Is better healthcare a bane to the long-term survival of the human race?" Tags="&lt;evolution&gt;&lt;human-genetics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5075" PostTypeId="2" ParentId="5074" CreationDate="2012-10-31T05:19:50.477" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;The theory of natural selection has it that individuals with better genes tend to survive and reproduce, passing their genes to their offspring.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, under &lt;strong&gt;selective pressure&lt;/strong&gt;, that is. The stronger the selective pressure, the more the population will change. Without a selective pressure, there isn't an impetus to change.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;However, due to the advancement in medical science, humans with poorer genes tend to survive and reproduce just as well.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You're making a mistake. &quot;Poor&quot; and &quot;Good&quot; are purely contextual. You might say that Sickle Cell Anemia is a poor lot to be stuck with... Unless, of course, you're in an area ravaged by Malaria. Then it's a boon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would be more accurate is that there aren't any strong forces acting upon humans that causes selective pressure and the proceeding adaptation. Of course, we are the result of such evolution, so by a basic standard all modern humans who reproduce are &lt;em&gt;fit&lt;/em&gt; in a Biological sense. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For example, in the past, many people, excluding those with natural immunity due to some genetic mutations, would have succumbed to illnesses such as malaria and typhoid. But with better hygiene and medical treatment, these patients tend to survive.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The brain is the one of the finest products of evolution. Because we're no longer dying en masse at the whims of bacteria or virii (usually) &lt;em&gt;does not mean we haven't adapted&lt;/em&gt;. Our ability to build advanced tools and perform science &lt;strong&gt;is&lt;/strong&gt; an adaptation. One for which we pay heavily; we're practically helpless until our teens.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Now, imagine a future where all illnesses including cancer can be treated. How would it impact the survival of the human race?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;We'd live longer, and assuming the rate of reproduction stays the same, there'd be a lot more of us.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Would we become more and more vulnerable such that our survival hinges heavily on medical technology, analogous to how an astronaut's survival is dependent on his spacesuit?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well... Vulnerable &lt;em&gt;to what&lt;/em&gt;? To disease? Probably not. Current Immunizations and treatments often utilize the body's own immune system; basically getting sick and all the benefits of encountering the disease without the side-effects of significant death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To genetic diseases? No. The human population has exploded in the last hundred or so years, and our genetic diversity has been greater than at any point in the last 40,000 years when a major bottlenecking event occurred. For a genetic disease to deal significant damage on a species, it would have to be suffuse throughout the population. That's not happening.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To a post-apocalyptic world where technology breaks down and suddenly we're facing off against parasites and predators? Well, if the event ever occurs, then a lot of us won't be ready, that's for sure. The stress such a life put on us in the past limited our lifespan to nearly half what it is now, but unless there's a complete lack of knowledge many basic safety habits should persist. Cooking, boiling water, dressing wounds, how illnesses spread - these are all things which dramatically increase quality of life when utilized correctly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Will we ever reach a point where we, quite literally, cannot live without technological intervention? No idea. Humans have very, &lt;em&gt;very&lt;/em&gt; strong reactions to things which aren't human but appear human (The &lt;strong&gt;Uncanny Valley&lt;/strong&gt; is a great example). It's just as possible that those instincts will prevent us from such a fate as the possibility that we'll be completely fine with becoming cyborgs. Nobody can even begin to give you a time-frame, though. As-is, there's no reason to become cyborgs (no &lt;em&gt;Selective Pressure&lt;/em&gt;), and won't be for the foreseeable future. &lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-10-31T05:19:50.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5076" PostTypeId="1" CreationDate="2012-10-31T06:14:10.573" Score="5" ViewCount="252" Body="&lt;p&gt;I have been reading through Peter Kropotkin's &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mutual_Aid%3a_A_Factor_of_Evolution&quot;&gt;Mutual Aid: A Factor of Evolution&lt;/a&gt;&lt;/em&gt; and he mentions a curious fact about bees (bolding by me for emphasis):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;predatory instincts and &lt;strong&gt;laziness continue to exist among the bees&lt;/strong&gt; as well, and reappear each. time that their growth is favoured by some circumstances. It is well known that there always are a &lt;strong&gt;number of bees which prefer a life of robbery to the laborious life of a worker&lt;/strong&gt;; and that &lt;strong&gt;both periods of scarcity and periods of an unusually rich &#xA;  supply of food&lt;/strong&gt; lead to an increase of the robbing class. When our crops are in and there remains but little to gather in our meadows and fields, robbing bees become of more frequent occurrence; while, on the other side, about the sugar plantations of the West Indies and the sugar refineries of Europe, robbery, laziness, and very often drunkenness become quite usual with the bees. We thus see that &lt;strong&gt;anti-social instincts continue to exist amidst the bees as well&lt;/strong&gt;;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;He does not provide a citation for this (and even if he did, it would be something from the late 1800s). &lt;strong&gt;Is there a good modern reference for the above behavior?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would in particular be interested in something like a graph of %-robber-bees vs. plentiness-of-food (in some abstract measure of the latter) so that I could intuitively see the increase in lazy/robber bees as the environment is low on food, or as it is overly abundant and compare it to 'typical levels'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Theories that explain this behavior are of interest, as well, but &lt;strong&gt;I am primarily after experimental measures/observations to support and quantify the above quote&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="3952" LastEditDate="2013-08-02T13:55:16.043" LastActivityDate="2013-09-17T19:01:09.367" Title="Modern reference for Kropotkin's lazy bees" Tags="&lt;entomology&gt;&lt;experimental&gt;&lt;literature&gt;&lt;collective-behaviour&gt;&lt;sociality&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5077" PostTypeId="1" AcceptedAnswerId="5083" CreationDate="2012-10-31T07:44:53.840" Score="11" ViewCount="1137" Body="&lt;p&gt;I'm trying to construct an anaerobic kitchen-waste digester at home.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The major output from the digester is methane - with a significant component of carbon dioxide. To scrub/reduce the CO2 I was thinking of passing the methane through a freshwater container charged with algae ... then it occurred to me to also think of introducing some bioluminescent algae to drive the photosynthesis &amp;amp; absorb some of the oxygen released by the other algae. Understandably this would be an unbalanced system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But ... can bioluminescence drive photosynthesis?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2020-09-15T10:14:42.870" Title="Can Bioluminescence drive photosynthesis?" Tags="&lt;photosynthesis&gt;&lt;bioluminescence&gt;" AnswerCount="2" CommentCount="10" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5079" PostTypeId="2" ParentId="932" CreationDate="2012-10-31T12:14:25.707" Score="1" Body="&lt;p&gt;I think there are two elements to this answer. To cut to the short answer skip to the &lt;strong&gt;bold&lt;/strong&gt; summary at the bottom...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, genetic variation &lt;strong&gt;exists&lt;/strong&gt; because of mutation. Genes get mutated every generation, the . Larger populations will have more mutants within them because: more individuals = more nucleotide base pairs (C's G's A's and T's) = more potential sites of mutation. However mutation is not likely to explain the &lt;strong&gt;persistence&lt;/strong&gt; of variation because mutation rates are very low (1 in 100,000 to 1,000,000 gametes have a newly mutated loci at any individual locus) and singleton alleles have only a 50% chance of reproduction (assuming no selection) so are likely to be lost by drift (Falconer &amp;amp; Mackay, Intro to Quantitative Genetics 1996).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You also talk about acne, which is likely to have a large component of environmental variance. Therefore you should remember that not all phenotypic variance is genetic its source and it is  highly likely that an individual trait has some degree of environmental variance component. Simplistically:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Phenotypic variance = genotypic variance + environmental variance&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So the bigger question is &lt;strong&gt;why does variation persist?&lt;/strong&gt; There are many potential causes of this which continue to be widely debated. Essentially it seems paradoxical because selection should reduce variation as it drives the fixation of all loci to the fittest allele. However, selection is transient, both spatially and temporally, and is not efficient against rare alleles (especially recessive alleles because they are hidden by dominant traits - e.g. disease &quot;carriers&quot;). Another important point is that some mutations will be neutral, therefore remain unaffected by selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the spatial context, this means that selection is not always favouring the same allele in all places a species inhabits. Selection might be different based on the where it is occurring (within a species, traits like fur would be beneficial to populations in cold climates but not to those in warmer climates - here I am assuming that the sole effect of fur is to improve the ability of retaining heat).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Temporally there are also key elements. Principally, over time selection changes. Again sticking with my fur example, climates change. Ice ages come and go bringing with them different selection coefficients for fur growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another variance in selection can be sexually antagonistic selection, where different alleles are favoured in either sex. In this case selection does not deplete variation but instead maintains it. It has recently been shown that sexual antagonism is prevalent throughout the genome.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the divergent reproductive strategies of the sexes could promote the&#xA;  maintenance of sexually-antagonistic variation (Sharp &amp;amp; Agrawal 2012... yesterday!)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Other hypotheses suggest mechanisms by with selection can maintain variation such as assortative mating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long story short, you stated that you expect variation to reduce as a consequence of selection. However genetic variation persists for many reasons, and can even be maintained by selection in several ways. Furthermore, phenotypic variation which is what you actually describe with your acne example (and I with my fur example) can be caused by non-genetic components of variation.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Suggested reading:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cox &amp;amp; Calsbeek 2009, Sexually Antagonistic Selection, Sexual Dimorphism, and the&#xA;Resolution of Intralocus Sexual Conflict.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Falconer &amp;amp; Mackay 1996, Introduction to Quantitative Genetics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Singh &amp;amp; Krimbas 2000, Evolutionary Genetics: from molecules to morphology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sharp &amp;amp; Agrawal 2012 (in press, accepted on-line version released yesterday, print may be 2013) Male-biased fitness effects of spontaneous mutations in Drosophila melanogaster, Evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Innocenti &amp;amp; Morrow 2011, The Sexually Antagonistic Genes of Drosophila melanogaster, PLoS Biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Arnqvist 2011 Assortative mating by fitness and sexually antagonistic genetic variation, Evolution. (also see his book sexual conflict).&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2012-10-31T12:14:25.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5080" PostTypeId="2" ParentId="5074" CreationDate="2012-10-31T13:22:42.657" Score="8" Body="&lt;p&gt;Gene frequencies (frequencies of each allele at a given loci) in populations are affected by many things divided in to systematic and dispersive processes. Systematic process (migration, mutation, selection) affect gene frequencies in an often quite predictable manner and strength. Dispersive process (Random drift, differentiation between sub-populations, uniformity within sub-populations, increased homozygosity) are random in their direction and only predictable in their amount. Your question focusses on the systematic process called selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a large population (if we ignore dispersive processes for the time being) the gene frequencies will reach an equilibrium called Hardy-Weinberg equilibrium. This means, with constant rates of the systematic processes, each locus will reach a point of stable equilibrium. Mutation and migration bringing more variation, and selection reduces it (over simplified - sometimes selection maintains variation, see my answer about why variation exists &lt;a href=&quot;https://biology.stackexchange.com/questions/932/why-does-so-much-variation-exist-within-species/5079#5079&quot;&gt;here&lt;/a&gt;). The frequency of each allele at equilibrium will be where these effects balance out. If selection becomes weaker against one allele it will become more frequent in the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By using medicine etc. to cure diseases we reduce the selection acting on a deleterious mutation thereby putting the gene frequencies in to a state of flux during which they move to new equilibrium points. So in short the answer is yes, modern medicine is decreasing our genetic fitness by allowing deleterious mutations to become more common.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I raise the question, will we ever be able to cure all genetically caused disease? In my reckoning, no, at least certainly not in our lifetimes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It only represents a real risk if we suddenly are unable to cure diseases. This would increase selection against that allele and the gene frequencies would move back towards the equilibrium point which existed before the selection was reduced. What this means for the population is the loss (death) of those with the low fitness genotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best reading you can do on this is the opening chapters of &lt;a href=&quot;http://www.amazon.co.uk/dp/0582243025/?tag=hydra0b-21&amp;amp;hvadid=11072782685&amp;amp;ref=asc_df_0582243025&quot; rel=&quot;nofollow noreferrer&quot;&gt;Falconer and Mackay's Introduction to Quantitative Genetics&lt;/a&gt;. Also read about Hardy-Weinberg equations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HTH&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2012-10-31T13:22:42.657" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5081" PostTypeId="1" AcceptedAnswerId="5082" CreationDate="2012-10-31T19:00:57.280" Score="14" ViewCount="856" Body="&lt;p&gt;If somehow a human could give a tumor unlimited resources, would the cancer grow forever?  It seems like it would until it gets so large that it physically affects vital organs.  Is what would likely happen?&lt;/p&gt;&#xA;" OwnerUserId="558" LastActivityDate="2012-11-01T15:56:03.193" Title="Can cancer grow forever if supplied with unlimited resources?" Tags="&lt;cancer&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5082" PostTypeId="2" ParentId="5081" CreationDate="2012-10-31T20:02:52.573" Score="17" Body="&lt;p&gt;Yes. The very first cells used to study cancer are still around (&lt;a href=&quot;http://en.wikipedia.org/wiki/HeLa&quot;&gt;HeLa Immortal Cells - Named for the subject Henrietta Lacks&lt;/a&gt;) and are basically immortal as long as they're fed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for tumors, whether cancerous or not they most definitely can continue to grow until they become a serious medical issue (&lt;a href=&quot;http://www.medicalopedia.org/2480/worlds-largest-tumors-the-top-three/&quot;&gt;WARNING: GRAPHIC - 3 Largest Tumors Recorded&lt;/a&gt;). One of the largest recorded tumors was 300lbs (~140kg) in a woman's abdomen that sprouted off of an ovary. They had to operate with her laying on her side, otherwise it would have crushed her abdomen and killed her.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all forms of cancer are immortal or produce large tumors (the 300lb tumor was benign), but it's definitely within the realm of plausibility.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1306" LastEditDate="2012-11-01T15:56:03.193" LastActivityDate="2012-11-01T15:56:03.193" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5083" PostTypeId="2" ParentId="5077" CreationDate="2012-10-31T21:29:53.467" Score="5" Body="&lt;p&gt;Yes and no. Yes as in the energetics do work out and you will be going down a small but non-trivial driving force as long as you continue to provide the luciferin to the algae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the wavelengths of light by which photosynthesis absorbs its energy are well defined and narrow. As a result, light sources for photosynthetic organisms have to be fairly strong and bright to cover the whole spectrum to provide the necessary light. As a result, your bioluminescent algae will also have to emit light at the desired wavelength to achieve a high photochemical efficiency and provide light to both Photosystem II and Photosystem I which have different wavelength requirements.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/bLKTs.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/bLKTs.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/biology/imgbio/pigabs.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;gsu.edu&lt;/a&gt;)&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="15950" LastEditDate="2019-02-19T00:00:28.013" LastActivityDate="2019-02-19T00:00:28.013" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="5084" PostTypeId="2" ParentId="5043" CreationDate="2012-10-31T23:11:27.090" Score="0" Body="&lt;p&gt;I found additional information on the subject. Apparently Serotonin is also involved in feeling hunger and the motivation to eat. It also follows a diurnal/circadian pattern as described below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Serotonin#Gauge_of_food_availability_.28appetite.29&quot; rel=&quot;nofollow&quot;&gt;Serotonin as as Gauge of food availability (appetite)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The expression of 5-HT2C receptors in the hippocampus follows a diurnal rhythm,[13] just as the serotonin release in the ventromedial&#xA;  nucleus, which is characterised by a peak at morning when the&#xA;  motivation to eat is strongest.[14]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-10-31T23:11:27.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5085" PostTypeId="1" CreationDate="2012-11-01T06:51:26.307" Score="2" ViewCount="92" Body="&lt;p&gt;I'm reading this paper, which discusses how Serotonin may be involved in motor functions of mammals: &lt;a href=&quot;http://www.princeton.edu/~sswang/awake_cerebellar_ms_refs/jacobs_fornal93_TINS.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;5-HT and motor control: a hypothesis&lt;/a&gt; .&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper includes the following diagram of the Dorsal Raphe Nuclei (DRN) firing pattern in a walking cat, and cat on a tredmill. Each step is associated with a distinct firing pattern. &lt;strong&gt;I'm wandering if the DRN firing pattern, in humans, changes in a similar way in response to voluntary breathing?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3GJ64.png&quot; alt=&quot;Dorsal Raphe Nuclei Firing pattern&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After searching wikipedia, I found a line that says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;REM sleep is turned on by acetylcholine secretion and is inhibited by&#xA;  neurons that secrete serotonin. (&lt;a href=&quot;http://en.wikipedia.org/wiki/Sleep_stages#Physiology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Psysiology of sleep stages&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm interested in dreaming, and at times have practiced entering dreams consciously, from the waking state after laying in bed for a long time. One of the obstacles to entring a dream was seizing control of breathing and starting to breathe voluntarily. This prevented me from entering dreams on a number of occasions, and appears to support the idea that voluntary breathing would affect the DRN. But I'm looking for a more scientifically-validated answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-11-01T06:51:26.307" Title="Does Dorsal Raphe Nuclei firing pattern change in response to voluntary breathing?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;sleep&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5087" PostTypeId="1" AcceptedAnswerId="5095" CreationDate="2012-11-01T16:29:40.667" Score="6" ViewCount="661" Body="&lt;p&gt;Well, most of us have experienced the wonderful feeling of the dreaded hangover. How does it work exactly? I imagine it has something to do with dehydration but what are the underlying mechanisms?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Extra points for explaining why mixing drinks makes it worse and why (or if) a hair of the dog (another drink) the next day can help. Someone once told me that hangovers are the first symptoms of withdrawal and if you drink (anecdotal evidence suggests that it should be the &lt;em&gt;same&lt;/em&gt; drink as the night before, but I doubt this is true) a small amount of alcohol, the symptoms are alleviated. I don't really see how that can be true.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-11-01T16:45:48.163" LastActivityDate="2012-11-02T07:33:27.227" Title="What is the molecular basis of hangovers?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5088" PostTypeId="1" CreationDate="2012-11-01T17:47:15.717" Score="13" ViewCount="39946" Body="&lt;p&gt;Due to high blood pressure, my doctor has recommended I go on a low-sodium diet.  So, that got me wondering what it is about sodium that drives this recommendation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does sodium do to a body that, by its presence or absence, affects blood pressure in humans?&lt;/p&gt;&#xA;" OwnerUserId="1602" LastActivityDate="2015-05-04T17:11:45.293" Title="How does sodium in one's diet affect blood pressure?" Tags="&lt;human-biology&gt;&lt;cardiology&gt;&lt;food&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5089" PostTypeId="1" CreationDate="2012-11-01T17:51:04.513" Score="2" ViewCount="3077" Body="&lt;p&gt;Do marine animals exhibit deep hibernation/aestivation as land-based creatures do? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, Why? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="57" LastEditDate="2012-11-01T19:42:04.973" LastActivityDate="2014-06-04T10:36:14.173" Title="What marine animals exhibit deep hibernation/aestivation?" Tags="&lt;zoology&gt;&lt;metabolism&gt;&lt;marine-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5090" PostTypeId="1" AcceptedAnswerId="5106" CreationDate="2012-11-01T19:54:57.120" Score="6" ViewCount="242" Body="&lt;p&gt;I'm wandering if mammals that can eat many different kinds of food &lt;strong&gt;(omnivores) vary their preference for food not only based on the availability, but also based on dietary needs?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking at this site &lt;a href=&quot;http://nutritiondata.self.com/&quot;&gt;Food nutritional content&lt;/a&gt; and see that &quot;not all foods are created equal&quot; - the vitamin/mineral and amino acid contents can vary dramatically. &lt;strong&gt;Is there some part of an omnivore brain/digestive system that &quot;monitors&quot; the micronutrient density of digested food and adjusts food preferences&lt;/strong&gt; towards foods that make the diet more complete?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-11-03T12:22:22.477" Title="Do omnivore mammals vary food preferences based on dietary needs?" Tags="&lt;digestive-system&gt;&lt;food&gt;&lt;nutrition&gt;&lt;mammals&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5092" PostTypeId="1" AcceptedAnswerId="5102" CreationDate="2012-11-02T05:53:23.827" Score="3" ViewCount="53" Body="&lt;p&gt;I am interested in a gene which is null lethal but I need to temporary induce diminished capacity. If a cell is homozygous is it possible to induce heterozygous phenotypes or a partial knockout from WT with siRNA or other molecular methods without virus vectors? I'm not interested in a medillian solution but an inducible molecular way.&#xA;Thank you&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to generate a heterozygous Sod2+/- like they do in this paper in mice and possibly human:&#xA;&lt;a href=&quot;http://physiolgenomics.physiology.org/content/16/1/29.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;http://physiolgenomics.physiology.org/content/16/1/29.full.pdf+html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2012-11-02T23:49:56.150" LastActivityDate="2012-11-03T00:43:44.843" Title="mutant down but not out" Tags="&lt;dna&gt;&lt;molecular-genetics&gt;&lt;mitochondria&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="5093" PostTypeId="2" ParentId="3030" CreationDate="2012-11-02T06:28:20.687" Score="0" Body="&lt;p&gt;I recalled a while ago that I saw a presentation on the concept of &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Flow_%28psychology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;Flow&lt;/a&gt;&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's an overview by the author :&lt;a href=&quot;http://www.ted.com/talks/mihaly_csikszentmihalyi_on_flow.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mihaly Csikszentmihalyi: Flow, the secret to happiness&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The kind of difference in cognitive capacity while engaged in such events can be described as flow. I'm still not certain as to what is causing the difference in the cognitive ability at these times, even in the same person.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KRRUB.png&quot; alt=&quot;flow image&quot;&gt; &lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-11-02T06:28:20.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5094" PostTypeId="2" ParentId="5090" CreationDate="2012-11-02T06:35:13.027" Score="0" Body="&lt;p&gt;I found that there are seasonal rhythms in the nutrient intake:&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/003193849190527U&quot; rel=&quot;nofollow&quot;&gt;Seasonal rhythms of human nutrient intake and meal pattern&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article's abstract mentions carbohydrates, while I'm more interested in the micronutrients, like amino acids and vitamins/minerals.&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-11-02T06:35:13.027" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5095" PostTypeId="2" ParentId="5087" CreationDate="2012-11-02T07:33:27.227" Score="10" Body="&lt;p&gt;First, the hormonal and hemodynamic changes seen in hangover are distinct from those seen in alcohol withdrawal, so the advice to drink more is not good, even if some symptoms are in fact improved. See tables 2/3 in the cited review.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears the molecular mechanism of &lt;strong&gt;veisalgia&lt;/strong&gt; (HA, a new word) is not well known.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1. acetaldehyde&lt;/strong&gt; Part of it may be attributed to acetaldehyde but there is clearly more to it. The liver enzyme alcohol dehydrogenase 1 (ADH1) produces acetaldehyde from ethanol, and aldehyde dehydrogenase 2 (ALDH2) makes acetate from that, so the aldehyde does not exist for a long time, and is rather responsible for short-term illnesses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. ADH and diuresis&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hangover severity is proportional to antidiuretic hormone&#xA;  concentration (46). Alcohol inhibits the effect of antidiuretic&#xA;  hormone on the kidneys, thereby inducing  diuresis that is out of&#xA;  proportion to the volume of fluid ingested. As blood alcohol&#xA;  concentration decreases and dehydration persists, the serum level of&#xA;  antidiuretic hormone increases, maintaining water retention in&#xA;  dehydrated patients with hangover. In our clinical experience,&#xA;  hydration attenuates but does not completely relieve hangover&#xA;  symptoms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;3. cytokines&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The constellation of hangover symptoms (nausea, headache, diarrhea)&#xA;  resembles that seen in conditions related to dysregulated cytokine&#xA;  pathways (for example, in viral infections and after administration of&#xA;  interferon-alpha). Alcohol alters cytokine production through a&#xA;  thromboxane pathway. Levels of thromboxane B2 are elevated during&#xA;  experimentally induced alcohol hangover (42), and the administration&#xA;  of tolfenamic acid, a prostaglandin inhibitor, at the time of alcohol&#xA;  consumption has a small prophylactic effect in reducing hangover&#xA;  severity (9).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;4. further substances&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Congeners, the byproducts of individual alcohol preparations (which&#xA;  are found primarily in brandy, wine, tequila, whiskey, and other dark&#xA;  liquors), increase the frequency and severity of hangover (24, 39,&#xA;  40). Clear liquors, such as rum, vodka, and gin, tend to cause&#xA;  hangover less frequently.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So there are factors that aren't even identified exactly, and these could fit the mixing of drinks observation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several reviews out there, just search for hangover at Google Scholar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wiese, Jeffrey G., Michael G. Shlipak, and Warren S. Browner. &quot;The alcohol hangover.&quot; Ann Intern Med 132.11 (2000): 897-902. Online at &lt;a href=&quot;http://dionysus.psych.wisc.edu/lit/topics/Hangover/WieseJ2000a.pdf&quot;&gt;http://dionysus.psych.wisc.edu/lit/topics/Hangover/WieseJ2000a.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastActivityDate="2012-11-02T07:33:27.227" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5096" PostTypeId="2" ParentId="5088" CreationDate="2012-11-02T16:11:19.530" Score="15" Body="&lt;p&gt;The basic reason is osmosis, the tendency of solutes to move from an area of high concentration to one of low concentration across a permeable barrier. So, ingesting large amounts of salt results in a high sodium concentration in the blood stream. This in turn causes water to enter the blood vessels by osmosis. More water in the blood means a greater volume of liquid and, therefore, higher blood pressure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This process occurs primarily in the kidneys, specifically in the part of the nephron called the loop of henle (the image below was taken from &lt;a href=&quot;https://en.wikipedia.org/wiki/Loop_of_Henle&quot;&gt;wikipedia&lt;/a&gt; and is originally from Grey's Anatomy):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With low salt concentrations, water exits the loop and is retained by the body. When sodium concentration is high, the opposite occurs, water enters the blood stream by osmosis and increases blood pressure.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-11-05T13:01:23.640" LastActivityDate="2012-11-05T13:01:23.640" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5097" PostTypeId="1" AcceptedAnswerId="5101" CreationDate="2012-11-02T20:34:05.827" Score="2" ViewCount="235" Body="&lt;p&gt;I'm reading about various parts of the human body and brain and started to wander if there's a branch of biology that deals with the entire human? I know that there are branches various -biologies, from neurobiology to something like heliobiology or chronobiology. All of them look at different organ systems or parts of an organism, but from different points of view.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there are sciences that deal with behavior and cognition of humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I read about these, I notice that there's quite a lot of overlap, particularly when neurotransmitters and hormones are involved. For example Melatonin, a hormone has functions in both the brain and the gut. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I'm wandering if there's some form of biology or science that deals with the entire organism, its behavior , as well as its parts?&lt;/strong&gt; Am I thinking about Biology or Medicine or something else?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="577" LastEditDate="2012-11-03T07:49:11.667" LastActivityDate="2012-11-03T07:49:11.667" Title="Is there some branch of biology that deals with the entire organism?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5098" PostTypeId="2" ParentId="3030" CreationDate="2012-11-02T20:53:43.533" Score="1" Body="&lt;p&gt;thinking and decision making under stress or pressure is significantly reduced.  its sometimes called the 'fight or flight' condition. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a pretty well established phenomenon.  Here's a great &lt;a href=&quot;http://www.radiolab.org/2007/apr/09/growing-up-is-awfuler-than-all-the-awful-things-that-ever-were/&quot; rel=&quot;nofollow&quot;&gt;radiolab segment on stress response&lt;/a&gt;.  Psychologist John Gottman notes how our ability to have a conversation where we can even listen to what someone else has to say is practically nil when we are emotionally saturated (frustrated or upset that is).  &lt;a href=&quot;http://www.cominghometopassion.com/articles_8.html&quot; rel=&quot;nofollow&quot;&gt;Even a mildly stressful conversation with your own spouse can shut down most rational processes&lt;/a&gt;.  Gottman can predict couples who overcome this problem which is highly corellated with divorce btw - but most of these couples remove stress in conversations rather than learn to work under pressure as it were. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Jonah Lehrer wrote about how &lt;a href=&quot;http://sports.espn.go.com/espn/print?id=6299428&amp;amp;type=story&quot; rel=&quot;nofollow&quot;&gt;tests to rank quarterbacks in their ability to respond on the gridiron are basically non correlated&lt;/a&gt;.  I know there have been criticisms of Lehrer, but this is a good piece and well grounded.  The point is that its hard to tell a-priori whether someone will perform under stress and given different sorts of stress.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the japanese space program they would screen candidates by making them do highly repetitive tasks &lt;a href=&quot;http://www.tofugu.com/2012/03/07/what-does-origami-have-to-do-with-space-travel/&quot; rel=&quot;nofollow&quot;&gt;like folding 1000 origami cranes&lt;/a&gt;.  NASA was just doing interviews with panels of psychologists.  &lt;a href=&quot;http://www.newscientist.com/article/dn11133-nasa-reviews-its-astronaut-screening-process.html&quot; rel=&quot;nofollow&quot;&gt;That wasn't infallible.&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such a test would be valuable for fighter pilots, astronauts, maybe presidents too! but it doesn't seem to really exist at this point. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the end you can winnow out those who break into a sweat in the interview, but to know who is going to really take the beach, I think that the only real answer is to see if they make it through a 'live fire' (or whatever) experience.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or as Clint Eastwood summed it up: &quot;A man's got to know his limitations.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(apologies to the ladies there - you can know your limitations too).&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorDisplayName="user560" LastEditDate="2012-11-02T21:30:32.930" LastActivityDate="2012-11-02T21:30:32.930" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5099" PostTypeId="1" CreationDate="2012-11-02T21:37:51.350" Score="10" ViewCount="3535" Body="&lt;p&gt;Melanin is a natural pigment that is categorized into two main forms, eumelanin and pheomelanin. It's well documented in the science literature that increased eumelanin levels reduces the risk of developing skin cancer, whereas it was recently reported in &lt;a href=&quot;http://www.nature.com/news/redhead-pigment-boosts-skin-cancer-risk-1.11711&quot;&gt;Nature&lt;/a&gt; that pheomelanin may itself be carcinogenic. So my question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does pheomelanin have a useful biological function?&lt;/p&gt;&#xA;" OwnerUserId="1607" LastEditorUserId="3971" LastEditDate="2013-08-29T16:04:14.567" LastActivityDate="2020-04-13T00:39:45.110" Title="Does pheomelanin have a useful biological function?" Tags="&lt;evolution&gt;&lt;cell-biology&gt;&lt;pigmentation&gt;" AnswerCount="4" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5100" PostTypeId="2" ParentId="5097" CreationDate="2012-11-02T22:49:26.530" Score="1" Body="&lt;p&gt;Medicine applies to healing illnesses of the body (with many subspecialties, including endocrinology which you may be interested in). Physiology is a branch of science which deals with the normal function of the body and its various parts. &lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-11-02T22:49:26.530" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5101" PostTypeId="2" ParentId="5097" CreationDate="2012-11-02T22:58:46.990" Score="2" Body="&lt;p&gt;I was thinking of &lt;a href=&quot;http://en.wikipedia.org/wiki/System_biology&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Systems/Integrative/Predictive Biology&lt;/em&gt;&lt;/a&gt; reading your question. Studying the wikipedia entry it looks like a research approach with many problems trying to understand organisms from a biochemical perspective, identifying control circuits and macro-quantities like temperature and its relation to such biochemical control circuits. Basically you have to give up reductionism and use holistic/systemic perspectives and methods. While physics was successful with such research approaches (climate simulation, many particle systems,...), biology is lacking very accurate and proven mathematical theories to implement and test reasonable models of an organism, not surprising when biological systems have so many degrees of freedom compared to something like a &lt;em&gt;ideal gas&lt;/em&gt; in physics. The wikipedia link doesn't show a lot of proven knowledge that this field/research approach has already created.&lt;/p&gt;&#xA;" OwnerUserId="45" LastActivityDate="2012-11-02T22:58:46.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5102" PostTypeId="2" ParentId="5092" CreationDate="2012-11-03T00:11:41.300" Score="1" Body="&lt;p&gt;Antisense, promoter replacement and when possible tetracycline allows one to titrate of gene expression&#xA;&lt;a href=&quot;http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-321-9_20#&quot; rel=&quot;nofollow&quot;&gt;http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-321-9_20#&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2012-11-03T00:43:44.843" LastActivityDate="2012-11-03T00:43:44.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5103" PostTypeId="1" AcceptedAnswerId="5114" CreationDate="2012-11-03T01:23:40.440" Score="2" ViewCount="57" Body="&lt;p&gt;I'd like to block a percentage of PGC-1β or Sod2 expression. According to the following paper's figure beta-blockers inhibit some expression of PGC-1α. Are there any medicines/chemicals which safely and temporarily block 50%-60% expression of PGC-1β or Sod2 in fully developed mice or humans? &#xA;Thank you&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jap.physiology.org/content/107/1/8.full&quot; rel=&quot;nofollow&quot;&gt;http://jap.physiology.org/content/107/1/8.full&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fig. 1.&#xA;Interactions of β-blockers and mitochondrial biogenesis. Aerobic exercise activates β2-adrenergic receptors (β-AR) on skeletal muscle and induces peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α) transcription, a regulator of mitochondrial biogenesis. Selective and nonselective β-blockers can blunt β2-AR signaling, which restricts the expected PGC-1α response following exercise and can impair adaptations to mitochondria and aerobic capacity. V̇O2max, maximum oxygen consumption.&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2012-11-03T02:02:30.000" LastActivityDate="2012-11-03T18:13:27.683" Title="PGC-1β Sod2 limiters/blockers" Tags="&lt;human-biology&gt;&lt;molecular-genetics&gt;&lt;human-genetics&gt;&lt;mitochondria&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5104" PostTypeId="1" AcceptedAnswerId="5113" CreationDate="2012-11-03T08:00:11.683" Score="6" ViewCount="439" Body="&lt;p&gt;As far as I can determine, lactose, and the monosaccharide galactose have few biological uses outside of mammalian lactation.  It not only required enzymes for its production, but enzymes in offspring for its digestion, suggesting that it serves some specific purpose.  Yet intuitively, it seems like it would have been significantly easier to just concentrate glucose from the blood or generate a disaccharide readily found in the diet like sucrose, for which digestive enzymes already existed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What drove the evolution of lactose in mammalian lactation?&lt;/p&gt;&#xA;" OwnerUserId="1597" LastActivityDate="2012-11-03T17:18:15.790" Title="What selective factors drove the evolution of lactose in lactation?" Tags="&lt;evolution&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5105" PostTypeId="1" AcceptedAnswerId="5109" CreationDate="2012-11-03T09:07:43.600" Score="4" ViewCount="512" Body="&lt;p&gt;I made a statement about tropical rainforests, and I want to know if it's somewhat true or not:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;The soil in tropical rainforests is not exceptionally fertile, because it contains few minerals. The reason that a tropical rainforest has a huge amount of vegetation is because of the quick mineralisation. If a dead leaf falls onto the ground, it immediately gets turned into minerals, which the plants immediately use for sustaining theirselves&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1609" LastActivityDate="2012-11-03T18:21:43.247" Title="Statement about Tropical Rainforests" Tags="&lt;ecology&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5106" PostTypeId="2" ParentId="5090" CreationDate="2012-11-03T10:07:22.430" Score="4" Body="&lt;p&gt;For what concerns amino acids, mice rapidly reject meals that are not balanced in essential amino acids and continue to look for other kind of foods. This behavior is called &lt;strong&gt;aversion response&lt;/strong&gt; and it is an adaptive phenomena that can be observed already 20 minutes after exposure to the unbalanced food. The mechanism involves brain sensing of uncharged tRNAs. The significance of the aversion response is to minimize depletion of essential amino acids that can not be directly synthethized but are required for protein synthesis. You can find good reviews in PubMed, for instance &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.nutr.27.061406.093726?journalCode=nutr&quot; rel=&quot;nofollow&quot;&gt;Gietzen et al. 2007&lt;/a&gt;, Annual Review of Nutrition, and &lt;a href=&quot;http://rd.springer.com/article/10.1007/s12035-012-8283-8&quot; rel=&quot;nofollow&quot;&gt;Gietzen and Aya 2012&lt;/a&gt;, Molecular Neurobiology.&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="444" LastEditDate="2012-11-03T12:22:22.477" LastActivityDate="2012-11-03T12:22:22.477" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5107" PostTypeId="1" AcceptedAnswerId="5110" CreationDate="2012-11-03T10:56:44.960" Score="15" ViewCount="1515" Body="&lt;p&gt;I have heard Sydney Brenner give a talk [0] on how the entire program of Systems Biology is suspect because, according to him, a chap named Hadamard showed that inverse problems are impossible to solve, or something to that effect. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I find it somewhat odd that no one seems to be paying any attention to this, and many are blithely carrying along trying to reverse-engineer biological organisms. I personally think that this reverse-engineering effort has its place, but Sydney Brenner doesn't seem to think so, and advocates tackling only the forward problem. Here's an excerpt from an abstract to a similar talk of his: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... This notion of computation is, in my opinion, the only valid approach to biological complexity and is opposed to many of the ideas underlying what has come to be called systems biology, which is very fashionable today. It will be shown that systems biology attempts to solve inverse problems — that is, obtain models of biological systems from observations of their behaviour — whereas, what I call computational biology, continues in the classical mode of discovering the machinery of the system and computing behaviour, solving a forward problem.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is Brenner simply wrong on this or is there something to his objections?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;[0] Sydney Brenner, &lt;a href=&quot;http://thesciencenetwork.org/programs/reading-the-human-genome-with-sydney-brenner/much-ado-about-nothing-systems-biology-and-inverse-problems&quot; rel=&quot;nofollow noreferrer&quot;&gt;Much ado about nothing: systems biology and inverse problems&lt;/a&gt;, 2009.&lt;/p&gt;&#xA;" OwnerUserId="625" LastEditorUserId="24354" LastEditDate="2018-05-07T11:11:37.717" LastActivityDate="2018-05-07T11:11:37.717" Title="Are the inverse problems of Systems Biology impossible to solve?" Tags="&lt;systems-biology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="7" ContentLicense="CC BY-SA 4.0" />
  <row Id="5108" PostTypeId="1" AcceptedAnswerId="5111" CreationDate="2012-11-03T12:34:15.910" Score="1" ViewCount="731" Body="&lt;p&gt;I am reading about the effect of extracellular potassium and chloride on the membrane potential, and now a question has come to my mind about what would happen if we added some molecules that have no charge to the extracellular? (consider that only K+ and Cl− can cross the membrane.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that membrane potential and volume does not change, but I'm not sure about that.&lt;/p&gt;&#xA;" OwnerUserId="1610" LastEditorUserId="69" LastEditDate="2012-11-03T16:32:40.820" LastActivityDate="2012-11-03T23:09:26.600" Title="Effect of extracellular molecules on membrane potential" Tags="&lt;cell-membrane&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5109" PostTypeId="2" ParentId="5105" CreationDate="2012-11-03T14:16:47.607" Score="6" Body="&lt;p&gt;There are many websites which describe this phenomenon. They all seem to confirm the basic premise of the question: in tropical rain forests most of the minerals are held in the biomass and rapid decomposition contributes to the recycling of these nutrients for new growth. One example is &lt;a href=&quot;http://www.marietta.edu/~biol/biomes/temprain.htm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Tropical rainforests are noted for the rapid nutrient cycling that occurs on the ground.  In the tropics, leaves fall and decompose rapidly.  The roots of the trees are on the surface of the soil, and form a thick mat which absorbs the nutrients before they reach the soil (or before the rain can carry them away).  The presence of roots on the surface is a common phenomenon in all mature forests; trees that come along later in succession win out in competition for nutrients by placing their roots over top of the competitors, and this pattern is seen in the temperate rainforest as well.  What does not occur in the temperate rainforest, however, is a rapid cycling of nutrients.  Because of the cold conditions and the acidity released by decomposing coniferous needles on the forest floor, decomposition is much slower.  More of the nutrients are found in the soil here than would be the case in a tropical forest, although like the tropical forest most of the nutrients are held in the plants and animals themselves.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I looked for actual evidence of these differences in rates of decomposition and I found this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Salinas, N. &lt;em&gt;et al&lt;/em&gt;. (2011) The sensitivity of tropical leaf litter decomposition to temperature: results from a large-scale leaf translocation experiment along an elevation gradient in Peruvian forests. New Phytologist 189: 967-977&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These authors reported a comparison of rates of decomposition at various elevations in Peruvian forest. The parameter k is the decay rate of dry mass, year&lt;sup&gt;-1&lt;/sup&gt;. The following data are taken from Table 3.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;site          elevation (m)   mean k (yr-1; 15 species)&#xA;Tambopata     210             1.753&#xA;Tono          1000            1.424&#xA;San Pedro     1500            0.968&#xA;Trocha Union  2720            0.546&#xA;Wayquecha     3025            0.424&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Jacob, M. et al. (2010) Leaf litter decomposition in temperate deciduous forest stands with a decreasing fraction of beech (Fagus sylvatica) Oecologia 164:1083–1094&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These authors studied leaf decomposition in a deciduous forest in Germany, with emphasis on the effect of proportion of beech trees upon overall rates of decomposition. Using data from Table 1 and Figure 2 (values converted from mg&lt;sup&gt;-1&lt;/sup&gt; g&lt;sup&gt;-1&lt;/sup&gt; day&lt;sup&gt;-1&lt;/sup&gt; to yr&lt;sup&gt;-1&lt;/sup&gt;) &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;% beech yr-1&#xA;  96    0.2555&#xA;  67    0.657&#xA;  21    1.022&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My Conclusion&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rates of decomposition can be much higher in tropical rainforest (k=1.753 yr&lt;sup&gt;-1&lt;/sup&gt; for the Tambopata site in Peru, k=0.256 yr&lt;sup&gt;-1&lt;/sup&gt; for a beech-rich forest in Germany). However, at higher elevations tropical rain forests are characterised by much lower rates of decomposition (Wayquecha k=0.424 yr&lt;sup&gt;-1&lt;/sup&gt;), comparable to those in deciduous forests.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are all measurements of loss of dry mass from leaf litter. This will be dominated by loss of carbon, and I would expect that minerals will leach from the decaying litter more rapidly than these values. Nevertheless it seems plausible that relative rates of mineral recycling will reflect these k values.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-11-03T18:21:43.247" LastActivityDate="2012-11-03T18:21:43.247" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5110" PostTypeId="2" ParentId="5107" CreationDate="2012-11-03T14:23:15.820" Score="16" Body="&lt;p&gt;The answer is mostly no, and this is not as disruptive a statement as it seems to be. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think Brenner has a point of course and he is not the only one who wonders whether the systems biology can create a holistic model of living things.  Still I wouldn't take this to mean we should stop doing systems biology research. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At 18:30 brenner illustrates the inverse problem with some examples 1) can you create a drum from only the sounds that come from the drum? (no he says). 2) can you solve the molecular structure of a molecule from a diffraction problem (no he says).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course we can do both of these, but the point is valid as we need to have an idea of what a drum looks like.  If we did have even a glance at a drum, this lets us build a model (cylinder of diameter d, height h and with a drum head of a tension t and material properties alpha beta, etc) from the sounds is a lot of work, but it could be done.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem of solving a molecular structure from diffraction intensities alone has also been solved for small molecules in the 60s I believe by so-called '&lt;a href=&quot;http://en.wikipedia.org/wiki/Direct_methods_%28crystallography%29&quot;&gt;direct methods&lt;/a&gt;' which don't work well or proteins and larger molecules.  Still the point is that you had to have a good mathematical model of molecules and diffraction to get to direct methods, &lt;a href=&quot;http://en.wikipedia.org/wiki/Multiple_isomorphous_replacement&quot;&gt;MIR&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Multi-wavelength_anomalous_dispersion&quot;&gt;MAD&lt;/a&gt; and other diffraction only methods. Sorry I can't go into details here...it might bore you to death if you don't care about crystallography. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In both cases the statement is that you need to have that model - what does a molecule look like, what does an x-ray do when it encounters a crystal? In order to get there.  Which makes total sense and I agree with.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wouldn't read too much into this though, because in practice this &lt;em&gt;has&lt;/em&gt; never been done, yet Bragg started with just the diffraction pattern and drew in models from other fields of study.  Given the nature of the proof described, no scientific discovery has ever happened in a mathematical vacuum and systems biology will not either. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rather I would read this talk as saying that the models we are using for action are not very good yet.  What is happening is that synthetic biology (engineering approaches), experimental observation, and intensive modeling (the 'inverse' and 'forward' approaches Brenner mentions) are all happening at once and are informing each other.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its hard to imagine that data from inverse approaches can't be an important part of any solution to biology.  Its also looking likelier that a mathematical model alone of biology will be difficult or impossible to find also.  What is currently (IMHO) working is a framework that is both conceptual (and not entirely quantitative) as well as analytical (mathematical) and data driven.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorDisplayName="user560" LastEditDate="2012-11-04T16:14:33.847" LastActivityDate="2012-11-04T16:14:33.847" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5111" PostTypeId="2" ParentId="5108" CreationDate="2012-11-03T16:33:13.090" Score="2" Body="&lt;p&gt;The absolute answer would depend on a lot of factors, but the basics of it would be that - &lt;strong&gt;Yes&lt;/strong&gt;, the volume does change and &lt;strong&gt;Yes&lt;/strong&gt;, it would have an affect on the membrane potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By adding mass to any liquid solution, you are changing the volume. Plain and simple. Liquids are not compressible, and the only way to maintain volume while adding mass would be to increase the density of the liquid. [Edit] I'm wondering if you don't mean increase the volume of the cell - in which case, in extreme conditions where the cell cannot maintain water and salt concentrations, the cell would lose volume as water and salts move out. In a hypotonic solution (much more water than solutes), the cell would lyse as osmotic pressure favors water moving into the cell&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The membrane potential would change, but how much depends on a lot of factors. It would most likely change due to the movement of ionic solvents down &lt;strong&gt;their&lt;/strong&gt; concentration gradients. Osmosis would move water out of the cell and into the extracellular environment, and ultimately reduce the membrane potential as more water outside the cell would essentially decrease the molarity of the solution. The cell would have to pump more ions out in order to regain the membrane potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exception might be if you added so many hydrophobic molecules outside the cell that you basically saturate the environment, which could prevent exchange of all charged or partially charged atoms and molecules.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2012-11-03T23:09:26.600" LastActivityDate="2012-11-03T23:09:26.600" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5112" PostTypeId="2" ParentId="5108" CreationDate="2012-11-03T16:39:57.727" Score="1" Body="&lt;p&gt;I'm no electrophysiologist, but I do know that the membrane potential is determined by the distribution of ions across the membrane: mostly Na&lt;sup&gt;+&lt;/sup&gt;, K&lt;sup&gt;+&lt;/sup&gt;, Ca&lt;sup&gt;2+&lt;/sup&gt; and Cl&lt;sup&gt;-&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An uncharged molecule will only influence membrane potential if it has an effect upon the distribution of these ions. One example of such a molecule is &lt;a href=&quot;http://en.wikipedia.org/wiki/Ouabain&quot; rel=&quot;nofollow&quot;&gt;valinomycin&lt;/a&gt;, a neutral ionophore which permeabilises membranes to K&lt;sup&gt;+&lt;/sup&gt; ions. Another example is &lt;a href=&quot;http://en.wikipedia.org/wiki/Ouabain&quot; rel=&quot;nofollow&quot;&gt;ouabain&lt;/a&gt; which inhibits the Na&lt;sup&gt;+&lt;/sup&gt;/K&lt;sup&gt;+&lt;/sup&gt; pump that is in part responsible for establishing resting membrane potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But in general the addition of uncharged molecules will have no direct effect upon membrane potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I expect that there will be someone along shortly to explain why it is much more complicated than this.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;edit: It turns out that MCM got here before me!&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-03T16:39:57.727" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5113" PostTypeId="2" ParentId="5104" CreationDate="2012-11-03T17:18:15.790" Score="4" Body="&lt;p&gt;As it happens someone has just &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22436215&quot; rel=&quot;nofollow&quot;&gt;published a theory&lt;/a&gt; about this. To save you following the link, I reproduce the abstract below. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I must admit that I had never realised that &lt;strong&gt;lactose is synthesised within the organelles of the secretory pathway&lt;/strong&gt; (β4-galactosyltransferase is a Golgi enzyme and α-lactalbumin is, of course, a whey protein, so is in transit through the pathway). This may go part of the way to answering your question: by having a disaccharide that is made within the Golgi, the cells of the mammary gland will effectively partition their glucose metabolism between the cytoplasm and that destined for secretion as lactose (transported into the Golgi lumen).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mammalian milk or colostrum contains up to 10% of carbohydrate, of which free lactose usually constitutes more than 80%. Lactose is synthesized within lactating mammary glands from uridine diphosphate galactose (UDP-Gal) and glucose by a transgalactosylation catalysed by a complex of β4-galactosyltransferase and α-lactalbumin (α-LA). α-LA is believed to have evolved from C-type lysozyme. Mammalian milk or colostrum usually contains a variety of oligosaccharides in addition to free lactose. Each oligosaccharide has a lactose unit at its reducing end; this unit acts as a precursor that is essential for its biosynthesis. It is generally believed that milk oligosaccharides act as prebiotics and also as receptor analogues that act as anti-infection factors. We propose the following hypothesis. The proto-lacteal secretions of the primitive mammary glands of the common ancestor of mammals contained fat and protein including lysozyme, but no lactose or oligosaccharides because of the absence of α-LA. When α-LA first appeared as a result of its evolution from lysozyme, its content within the lactating mammary glands was low and lactose was therefore synthesized at a slow rate. Because of the presence of glycosyltransferases, almost all of the nascent lactose was utilized for the biosynthesis of oligosaccharides. The predominant saccharides in the proto-lacteal secretions or primitive milk produced by this common ancestor were therefore oligosaccharides rather than free lactose. Subsequent to this initial period, the oligosaccharides began to serve as anti-infection factors. They were then recruited as a significant energy source for the neonate, which was achieved by an increase in the synthesis of α-LA. This produced a concomitant increase in the concentration of lactose in the milk, and lactose therefore became an important energy source for most eutherians, whereas oligosaccharides continued to serve mainly as anti-microbial agents. Lactose, in addition, began to act as an osmoregulatory molecule, controlling the milk volume. Studies on the chemical structures of the milk oligosaccharides of a variety of mammalian species suggest that human milk or colostrum is unique in that oligosaccharides containing lacto-N-biose I (LNB) (Gal(β1 → 3)GlcNAc, type I) predominate over those containing N-acetyllactosamine (Gal(β1 → 4)GlcNAc, type II), whereas in other species only type II oligosaccharides are found or else they predominate over type I oligosaccharides. It can be hypothesized that this feature may have a selective advantage in that it may promote the growth of beneficial colonic bacteria, Bifidobacteria, in the human infant colon.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-03T17:18:15.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5114" PostTypeId="2" ParentId="5103" CreationDate="2012-11-03T18:13:27.683" Score="0" Body="&lt;p&gt;Dexamethasone can be used to regulate PGC-1β &#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20647557&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/20647557&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2012-11-03T18:13:27.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5115" PostTypeId="1" AcceptedAnswerId="5120" CreationDate="2012-11-03T18:46:06.933" Score="10" ViewCount="2973" Body="&lt;p&gt;I'm reading an essay on the creating of the &lt;em&gt;Mammalia&lt;/em&gt; zoological classification (Londa Schiebinger, &lt;em&gt;The American Historical Review&lt;/em&gt;, Vol. 98, No. 2 (Apr., 1993), pp. 382-411).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It contains the statement (page 386)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;All mammals (including the whale) have hair, and it is still today considered a distinguishing characteristic of mammals. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is that statement correct? Do all known species of whale and dolphin have hair? If so, where is it? You can't see it on the surface of the animal, is it internal like we have nostril hair?&lt;/p&gt;&#xA;" OwnerUserId="1611" LastActivityDate="2018-11-05T23:59:03.847" Title="What hair do aquatic mammals have?" Tags="&lt;mammals&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5117" PostTypeId="1" AcceptedAnswerId="5118" CreationDate="2012-11-03T19:45:18.973" Score="4" ViewCount="842" Body="&lt;p&gt;Snails... We have some kind of huge garden snails appearing lately (read since the last 10 years or so). Try as one might, it's impossible to avoid them when driving. These snails do not appear to have red blood - I doubt they have blood at all. Wikipedia tells me blood's red colour is due to haemoglobin - which serves to transport oxygen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do snails (and any other animals that do not have red coloured blood) get oxygen? Or, do such animals need no oxygen at all?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1320" LastEditDate="2012-11-03T20:28:45.067" LastActivityDate="2012-11-03T20:28:45.067" Title="How does hemoglobin-free blood transport oxygen?" Tags="&lt;red-blood-cell&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5118" PostTypeId="2" ParentId="5117" CreationDate="2012-11-03T20:18:22.013" Score="9" Body="&lt;p&gt;Snails, like most molluscs, have a protein called hemocyanin dissolved directly in the hemolymph (&quot;blood&quot;). Hemocyanins are copper-containing metalloproteins: the binding site for a single O&lt;sub&gt;2&lt;/sub&gt; molecule contains two copper atoms. Unlike hemoglobin, where reversible oxygen binding is accomplished without a change in the oxidation state of the Fe(II) atoms in the heme prosthetic groups, in hemocyanin the copper undergoes a transition from colourless Cu(I) in the deoxygenated state to blue Cu(II) when oxygenated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incidentally, there are certain species of fish that manage with little or no hemoglobin - &lt;a href=&quot;http://en.wikipedia.org/wiki/Notothenioidei&quot;&gt;icefish&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-03T20:18:22.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5119" PostTypeId="1" AcceptedAnswerId="5122" CreationDate="2012-11-03T21:17:33.340" Score="2" ViewCount="72" Body="&lt;p&gt;Giving minimal credence to estimates in popular media of the average biomass of  insects/arachnids, etc. in an acre of land, it seems that a &quot;free-range&quot; cow (I don't mean to pick on cows) might be something of an omnivore. Is there any evidence that herbivores derive essential parts of their diet from sources other than cellulose? Or that they do not?&lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2012-11-04T10:15:38.813" Title="Diet of free-range herbivores" Tags="&lt;biochemistry&gt;&lt;zoology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="5120" PostTypeId="2" ParentId="5115" CreationDate="2012-11-03T23:32:34.297" Score="9" Body="&lt;p&gt;Well, technically yes, but &lt;a href=&quot;http://en.wikipedia.org/wiki/Dolphin&quot;&gt;most adult dolphins do not have hair&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Unlike most mammals, dolphins do not have hair, &lt;strong&gt;except for a few hairs around the tip of their rostrum (beak) which they lose shortly before or after birth.&lt;/strong&gt; The only exception to this is the Boto river dolphin, which has persistent small hairs on the rostrum.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Whales do, and depending on your definition of &quot;hair&quot; - that includes &lt;a href=&quot;http://en.wikipedia.org/wiki/Baleen&quot;&gt;Baleen - which is composed of fine keratin fibers, much like normal fur/hair&lt;/a&gt;, which is the distinguishing characteristic of &quot;Baleen whales&quot; (like the Blue Whale).&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-11-03T23:32:34.297" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5121" PostTypeId="1" AcceptedAnswerId="5787" CreationDate="2012-11-04T08:44:40.807" Score="6" ViewCount="142" Body="&lt;p&gt;I've been reading that over the course of the day, &lt;strong&gt;human body temperature follows diurnal rhythm&lt;/strong&gt; with the lowest body temperature observed some time close to the middle of the sleep episode, while the peak body temperature is observed some time close to sunset.&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Circadian_rhythm&quot; rel=&quot;nofollow&quot;&gt;Circadian rhythm on Wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested &lt;strong&gt;if humans have internal organ systems or brain &quot;sensors&quot; that &quot;read&quot; the body temperature as a part of synchronizing their own internal circadian clock to the master clock of the human body.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there are indeed such sensors, then I'm interested if they can be thrown &quot;off track&quot; by artificial heat sources, like hot food, drinks or showers. &lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="577" LastEditDate="2012-11-05T19:08:31.373" LastActivityDate="2013-01-13T21:27:35.960" Title="Does artificial heat (shower/tea) affect diurnal rhythms in humans?" Tags="&lt;human-biology&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5122" PostTypeId="2" ParentId="5119" CreationDate="2012-11-04T10:15:38.813" Score="3" Body="&lt;p&gt;One key nutrient worth thinking about in the context of this question is vitamin B&lt;sub&gt;12&lt;/sub&gt;. Herbivores such as cows and sheep will derive this directly from the bacteria in their rumen. Rabbits produce two types of feces - soft and hard - and they eat the soft variety, rich in gut bacteria, as a source of nutrients like vitamin B&lt;sub&gt;12&lt;/sub&gt;. Gorillas are primarily herbivores, but are thought to derive their vitamin B&lt;sub&gt;12&lt;/sub&gt; from insects, eaten purposefully or inadvertently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes, herbivores derive this particular nutrient from non-plant sources.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-04T10:15:38.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5123" PostTypeId="1" CreationDate="2012-11-04T10:57:54.927" Score="8" ViewCount="920" Body="&lt;p&gt;Yesterday my grandmother ate fresh tuna at a friend's party. She swears it was fresh and bought at a local fishmonger. The problem is, that we live in &lt;a href=&quot;https://maps.google.com/maps?q=Gda%C5%84sk,%20Polska&amp;amp;hl=pl&amp;amp;ie=UTF8&amp;amp;ll=56.559482,17.138672&amp;amp;spn=14.159361,40.561523&amp;amp;sll=54.361087,18.690027&amp;amp;sspn=0.233253,0.633774&amp;amp;oq=Gda%C5%84sk,&amp;amp;t=h&amp;amp;hnear=Gda%C5%84sk,%20pomorskie,%20Polska&amp;amp;z=5&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gdańsk&lt;/a&gt;, by the south-eastern side of the Baltic sea and I have never heard of tuna in the Baltic. I told her that the fish couldn't have been local and therefore couldn't have been fresh but frozen and thawed. But the thought still bothers me, maybe tuna fish can reach the Baltic?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did search a bit and found that tuna may be sometimes found in the Northern sea, so maybe it actually can travel so far east as to reach the Baltic? But the water in the Baltic is hardly saltwater (6-8‰), so would it be able to survive?&lt;/p&gt;&#xA;" OwnerUserId="1427" LastEditorUserId="3553" LastEditDate="2017-04-13T02:46:05.483" LastActivityDate="2017-04-13T02:46:05.483" Title="Are tuna fish present in the Baltic sea?" Tags="&lt;zoology&gt;&lt;ecology&gt;&lt;ichthyology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5124" PostTypeId="1" AcceptedAnswerId="5135" CreationDate="2012-11-04T16:47:41.603" Score="1" ViewCount="559" Body="&lt;p&gt;A follow-up to &lt;a href=&quot;https://biology.stackexchange.com/questions/5117/how-does-hemoglobin-free-blood-transport-oxygen&quot;&gt;How does hemoglobin-free blood transport oxygen?&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm unsure about the use of physiology/metabolism in the title there. The question in mind is whether this reversible binding makes an organism slower, or faster; perhaps more capable of surviving in rarefied atmosphere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&#xA;I apologize that my comment made it appear this question is only about the Icefish; it is not. There are still other species (for instance, molluscs, and arachnids) which acquire oxygen by means other than haemoglobin.&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-10-09T15:46:23.717" Title="What difference does it make in the organism's physiology/metabolism whether oxygen binds reversibly or not?" Tags="&lt;physiology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5125" PostTypeId="1" CreationDate="2012-11-04T18:03:14.137" Score="8" ViewCount="342" Body="&lt;p&gt;Anectodal. Feel free to shoot it down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Walking is an acquired skill; As far as I'm concerned exhaustion causes disorientation. Even after waking up it sometimes takes a second or so to get balanced. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is it sleepwalkers don't stumble around when walking? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="9943" LastEditDate="2015-05-22T01:53:02.157" LastActivityDate="2015-05-22T01:53:02.157" Title="How does one maintain balance sleepwalking?" Tags="&lt;physiology&gt;&lt;sleep&gt;&lt;balance&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5126" PostTypeId="2" ParentId="1157" CreationDate="2012-11-04T22:40:58.320" Score="-2" Body="&lt;p&gt;Apparently transfer between prokaryote and eukaryote (in both directions) has been detected:&#xA;&lt;a href=&quot;http://www.biomedcentral.com/1471-2148/11/276/abstract&quot; rel=&quot;nofollow&quot;&gt;http://www.biomedcentral.com/1471-2148/11/276/abstract&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0888754311001959&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0888754311001959&lt;/a&gt;&#xA;&lt;a href=&quot;http://genome.cshlp.org/content/19/8/1441.abstract&quot; rel=&quot;nofollow&quot;&gt;http://genome.cshlp.org/content/19/8/1441.abstract&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some numbers I'd like to know are the rate of pro&amp;lt;-&gt;eu HGT detection /versus the rate of looking for it/ (i.e. 3 confirmations in 300 attempts would be more impressive than 3 confirmations in 30,000 attempts).&lt;/p&gt;&#xA;" OwnerUserId="1616" LastEditorUserId="69" LastEditDate="2012-11-05T12:38:48.483" LastActivityDate="2012-11-05T12:38:48.483" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5127" PostTypeId="1" AcceptedAnswerId="5129" CreationDate="2012-11-05T03:42:20.900" Score="6" ViewCount="867" Body="&lt;p&gt;Birds from the family Columbidae (e.g., doves and pigeons) produce a fatty, milk-like substance in their crop.  The secretion is often referred to as &quot;crop milk.&quot;  They feed crop milk to their young through regurgitation.  Does anyone know of another bird or reptile group (or even mammals) that has evolved such a mechanism; not regurgitation but secretion of a milk-like substance for feeding young?  Also, both male and female doves produce crop milk; are there cases where males of a mammal species produce milk?&lt;/p&gt;&#xA;" OwnerUserId="1396" LastEditorUserId="3624" LastEditDate="2014-12-02T13:13:41.600" LastActivityDate="2014-12-02T13:13:41.600" Title="Do any birds beside the family Columbidae (or any reptile or mammal) feed their young &quot;Crop Milk&quot;" Tags="&lt;evolution&gt;&lt;ornithology&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5128" PostTypeId="1" AcceptedAnswerId="5136" CreationDate="2012-11-05T08:00:19.763" Score="9" ViewCount="9188" Body="&lt;p&gt;Our eyes are spherical, our retina is circular, but still our eyes can see more in the horizontal direction than in vertical direction. Why is it so, why is the preferred aspect ratio not square?     &lt;/p&gt;&#xA;" OwnerUserId="1110" LastEditorUserId="1320" LastEditDate="2012-11-05T19:06:07.550" LastActivityDate="2013-11-08T09:36:16.633" Title="Preferred Aspect Ratio for Human Eyes" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5129" PostTypeId="2" ParentId="5127" CreationDate="2012-11-05T09:46:02.410" Score="11" Body="&lt;p&gt;In mammals there are only two species (known, there may well be others) where males lactate. They are both species of bats and &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0169534708003467&quot;&gt;this paper&lt;/a&gt; discusses the evolutionary mechanisms that could underlie male lactation. I have ignored human cases because they are more of an unusual occurrence (often brought on by severe dietary stress) rather than an evolved mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other non-mammals include &lt;a href=&quot;http://www.stanford.edu/group/stanfordbirds/text/essays/Bird_Milk.html&quot;&gt;Flamingo and Penguins&lt;/a&gt;. There is also a species of fish, called a discus fish, which produces a mucus from its skin which the offspring feed on (&lt;a href=&quot;http://www.sciencedaily.com/releases/2010/10/101029104603.htm&quot;&gt;here&lt;/a&gt;). I would hypothesise that this evolved originally for different reasons (defence, scent communication, excretion...) but offspring &quot;discovered&quot; this was slightly nutritious so fed off it, those genetically predisposed to doing such things then had higher fitness and the trait spreads. Evolution of greater or more nutritious mucus production would be achieved because parents that produce more/better mucus would have more offspring that reach maturity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper by &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0169534708003467&quot;&gt;Kunz &amp;amp; Hosken&lt;/a&gt; is a good discussion on current evidence and the potential for evolution of male lactation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope that answers your question, happy reading!&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-12-28T01:56:20.687" LastActivityDate="2013-12-28T01:56:20.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5130" PostTypeId="1" CreationDate="2012-11-05T10:50:46.830" Score="11" ViewCount="440" Body="&lt;p&gt;Sorry  if this might appear funny. When I close my eyes for a longer time, and suddenly open  it, I see some twinkling white small circles, and when i concentrate on anyone of them it disappears, as if the image is falling on the blind spot. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This also happens when I am struck on my head sometimes accidentally. I would see thousands of tiny objects floating. What are these and why they appear shiny ?         &lt;/p&gt;&#xA;" OwnerUserId="1110" LastEditorUserId="460" LastEditDate="2012-11-14T23:02:11.363" LastActivityDate="2014-11-19T18:43:31.967" Title="What are the &quot;stars&quot; we see after a bump on the head?" Tags="&lt;neuroscience&gt;&lt;eyes&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5131" PostTypeId="2" ParentId="5123" CreationDate="2012-11-05T11:06:09.673" Score="1" Body="&lt;p&gt;Indeed tuna are present in the Baltic sea, and they can also grow in the Pacific and Indian oceans. A lot of the tuna we see in tuna cans in supermarkets comes from the stocks in the Indian ocean, but it is possible to have fresh tuna from the Baltic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry, I only found a French answer from a famous French news paper: &lt;a href=&quot;http://sante.lefigaro.fr/mieux-etre/nutrition-aliments/thon/dou-vient-thon&quot; rel=&quot;nofollow&quot;&gt;http://sante.lefigaro.fr/mieux-etre/nutrition-aliments/thon/dou-vient-thon&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1617" LastEditorUserId="658" LastEditDate="2012-11-09T14:22:12.923" LastActivityDate="2012-11-09T14:22:12.923" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5132" PostTypeId="2" ParentId="5124" CreationDate="2012-11-05T11:49:37.603" Score="2" Body="&lt;p&gt;I don't understand your question either, but my response is to the question in the title. Oxygen has low saturation in blood plasma, so humans require &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemoglobin&quot; rel=&quot;nofollow noreferrer&quot;&gt;hemoglobin&lt;/a&gt; to serve as a transport protein. Oxygen must bind reversibly, otherwise it gets stuck to hemoglobin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans actually have two proteins, hemoglobin and &lt;a href=&quot;http://en.wikipedia.org/wiki/Myoglobin&quot; rel=&quot;nofollow noreferrer&quot;&gt;myoglobin&lt;/a&gt;. Hemoglobin (HbA) circulates in the blood, whereas myoglobin is in the muscles. Myoglobin (Mb) has a higher affinity for oxygen than hemoglobin (see image). This makes sense, because the hemoglobin in the blood must unload oxygen at the muscles, and myoglobin must bind it. Hemoglobin's affinity for oxygen is regulated by 2,3-BPG, pH, and [CO₂] to ensure that it can unload oxygen at tissues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0RxCn.jpg&quot; alt=&quot;Oxygen saturation curves&quot;&gt;&#xA;(Curves to the left have higher affinity, meaning that they have a higher oxygen saturation for the same partial pressure of oxygen.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, humans have several types of hemoglobin. Fetal hemoglobin (HbF) has a higher affinity for oxygen than regular hemoglobin, ensuring that the fetus obtains the oxygen that it needs from the maternal blood.&lt;/p&gt;&#xA;" OwnerUserId="1166" LastEditorUserId="3340" LastEditDate="2014-10-09T15:46:23.717" LastActivityDate="2014-10-09T15:46:23.717" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5134" PostTypeId="2" ParentId="5124" CreationDate="2012-11-05T14:57:30.387" Score="6" Body="&lt;p&gt;I think I see where you are coming from.  There is a misunderstanding here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Channichthyidae#Hemoglobin&quot; rel=&quot;nofollow&quot;&gt;Ice-fish have relatively lost their hemoglobin gene over time&lt;/a&gt; because they have adapted such a slow metabolism in the cold water where the oxygen is richer (oxygen content in cold water is higher).  The don't need any binding of oxygen to a carrier protein like hemoglobin because enough oxygen diffuses in from the water for the needs of their tissue. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no binding - reversible or irreversible in their blood - that would imply that the oxygen is binding to a protein like hemoglobin or hemocyanin, which the fish does not have.   The oxygen is just diffusing into the fish from the water around it.  The circulatory system is helping by flushing the system out and keeping everything fresh as well.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-11-05T16:40:20.810" LastActivityDate="2012-11-05T16:40:20.810" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5135" PostTypeId="2" ParentId="5124" CreationDate="2012-11-05T16:05:49.333" Score="1" Body="&lt;p&gt;The classic example of a hemoglobin adaptation to high altitude is found in the case of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Bar-headed_goose&quot; rel=&quot;nofollow&quot;&gt;bar-headed goose&lt;/a&gt;, &lt;em&gt;Anser indicus&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This bird undertakes very high altitude migratory flight, crossing the Himalaya. It has a number of physiological adaptations that allow this, but it also has a novel form of hemoglobin with an unusually high affinity for O&lt;sub&gt;2&lt;/sub&gt;. A single mutation changes the co-operative oxygen-binding behaviour of the haemoglobin molecule. In terms of the diagram in jello's answer, this shifts the binding curve to the left (i.e. toward that of fetal haemoglobin). This, in turn, means that the molecule binds more oxygen in the lungs, but it also means that it doesn't release the oxygen as readily in the peripheral tissues. On balance the former effect dominates and the efficiency of oxygen delivery is improved.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-05T16:05:49.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5136" PostTypeId="2" ParentId="5128" CreationDate="2012-11-05T19:15:14.210" Score="8" Body="&lt;p&gt;I found the explanation given below &lt;a href=&quot;http://boards.straightdope.com/sdmb/showthread.php?t=300997&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; (my emphasis). It may not be authoritative, but it makes sense to me.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;You can determine the approximate shape of your visual field by looking straight ahead, and holding a hand out to each side and noticing where you can no longer see them. Do the same for above and below, and you'll see that your peripheral vision probably extends to about 180 degrees (or a little less) left and right, and about 100 degrees up and down. &lt;strong&gt;Your brow, nose, and cheeks narrow the vertical angle.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;So your visual field has a ratio of about 1 to 1.8.&lt;/p&gt;&#xA;&lt;p&gt;Interestingly, and not entirely coincidentally, ordinary films and wide-screen TVs have a ratio of 1.78 (16:9).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Another way to see this effect is to look at someone's head in profile and from directly above. In the former  case you have a clear view of their eyes, in the latter you don't. (Tested on a small sample - one 3 year old male, playing with an iPad).&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-11-05T19:24:36.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5137" PostTypeId="1" AcceptedAnswerId="8742" CreationDate="2012-11-05T19:50:26.860" Score="5" ViewCount="2089" Body="&lt;p&gt;What is the physical mechanism that causes temperature to rise during a fever? I know that somehow the hypothalamus &quot;orders&quot; to increase the standard body temperature regulation, and this should stimulate mitochondria to produce more ATP. Is that right? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this the only heating physical mechanism (through increasing production of ATP) that acts during a fever?&lt;/p&gt;&#xA;" OwnerUserId="1620" LastEditorUserId="57" LastEditDate="2012-11-06T00:05:17.557" LastActivityDate="2013-06-11T15:17:30.443" Title="How does fever physically work?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5138" PostTypeId="1" CreationDate="2012-11-05T19:54:50.557" Score="2" ViewCount="1901" Body="&lt;p&gt;If Humans are evolve from Monkeys, there must be stages in the evolution process, when it was 1% human and 99% monkey, 2% human and 98% monkey  and so on. This is because evolution was a very slow process that occurred in a span of thousands of years. So we expect there must be fossils of this intermediate stages under earth. These intermediate-stage fossils must be many times in no. as compared to 100% human or 100% monkey.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But why do we do not discover these intermediate fossils? &lt;/p&gt;&#xA;" OwnerUserId="1110" LastActivityDate="2012-11-05T20:34:22.113" Title="Fossils of intermediate stages?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5139" PostTypeId="2" ParentId="5138" CreationDate="2012-11-05T20:28:59.403" Score="13" Body="&lt;p&gt;We do, all the time. Here's a nice graphic from Dr. Douglas Theobald. (Images copyright 2000 Smithsonian Institution.):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zecLF.jpg&quot; alt=&quot;Hominid fossils&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's 14 Hominid species, ranging from about 4 M.Y. ago to a modern human skull (&quot;N&quot;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a nice genealogy as well (although these change frequently as more evidence is gathered):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/e87rq.jpg&quot; alt=&quot;Homo sapien geneology&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1320" LastEditDate="2012-11-05T20:34:22.113" LastActivityDate="2012-11-05T20:34:22.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5141" PostTypeId="1" AcceptedAnswerId="5142" CreationDate="2012-11-06T11:17:58.003" Score="6" ViewCount="2883" Body="&lt;p&gt;Giraffes, being one of the tallest mammals in the world, have a failsafe called rete mirabile to prevent them from dying from excessive blood pressure while lowering their head.[&lt;a href=&quot;http://en.wikipedia.org/wiki/Giraffe#Internal_systems&quot;&gt;1&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Due to their long necks, a formidable amount of blood pressure is needed (quoted from &lt;a href=&quot;http://animals.about.com/od/hoofedmammals/a/tenfactsgiraffes.htm&quot;&gt;animals.about.com&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A giraffe's heart has special adaptations to enable it to pump blood up the animal's long neck to its head.&#xA;  A giraffe's heart has the formidable task of pumping blood at high enough pressure so that it can flow up the giraffe's neck to the brain. &#xA;  To accomplish this, a giraffe's heart is specially adapted.&#xA;  It can weigh up to 10 kg (22 lb) and generates twice the blood pressure of other large mammals.&#xA;  Having enough blood pressure to pump blood to the brain when the giraffe's neck is extended upward is one challenge, but when the animal lowers its head it risks injury due to excessive blood pressure.&#xA;  To counter this, giraffes have a pressure-regulating system known as the rete mirabile which restricts the amount of blood that rushes towards the brain when the giraffe lowers its head.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;How did this evolve? I believe in evolution but I can't wrap my head around this. If an &quot;overload&quot; of blood would reach the giraffe's brain while it is, for instance, drinking water and either instantly killing the animal or severely wounding the animals mental and physical capabilities by rupturing the brain, how could a failsafe like this evolve? &lt;/p&gt;&#xA;" OwnerUserId="1624" OwnerDisplayName="Simon Carlson" LastActivityDate="2015-01-06T05:32:11.867" Title="How did giraffes develop their rete mirabile failsafe?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5142" PostTypeId="2" ParentId="5141" CreationDate="2012-11-06T14:50:46.420" Score="11" Body="&lt;p&gt;I think what leads to the confusion here is the assumption that the neck was evolved before the rete mirabile.  Giraffes evolved from creatures with shorter necks.  As evolution occurred nature was selecting for longer neck creatures (being able to eat more leaves) but at the same time creatures with longer necks had problems with blood pressure. &#xA;At this point this would also not be lethal because we are talking about animals with much shorter necks, just in some way disadvantageous to the animal.&#xA;So over time necks got bigger, blood pressure went up, and blood vessels developed that could better and better deal with the change of pressure. &lt;a href=&quot;http://en.wikipedia.org/wiki/Rete_mirabile&quot;&gt;Rete mirabile&lt;/a&gt; also occur in other animals, so they are not a rare evolutionary phenomenon of giraffes.&lt;/p&gt;&#xA;" OwnerUserId="1625" LastEditorUserId="112" LastEditDate="2012-11-06T15:37:11.560" LastActivityDate="2012-11-06T15:37:11.560" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5144" PostTypeId="1" AcceptedAnswerId="5146" CreationDate="2012-11-06T22:04:06.727" Score="3" ViewCount="1639" Body="&lt;p&gt;I'm thinking about neurons in the brain that are used for &quot;thinking&quot;. As I read about &lt;strong&gt;action potentials&lt;/strong&gt;, I see that an Axon is connected to a Dendrite of a neighboring cell and that there are &lt;a href=&quot;http://en.wikipedia.org/wiki/Nerve_impulse#Initiation&quot; rel=&quot;nofollow&quot;&gt;neurotransmitters involved in the signal propagation&lt;/a&gt; from cell to cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested in learning how action potential propagation gets terminated. Let's say a message from the brain region A to brain region B has been delivered through action potentials.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;How does the region B know &lt;strong&gt;not to &quot;route&quot;&lt;/strong&gt; the action potential further down the chain of neurons?&lt;/li&gt;&#xA;&lt;li&gt;How does the region A know that the message has been sent, to &lt;strong&gt;stop sending more&lt;/strong&gt; messages?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="577" LastActivityDate="2014-03-26T03:40:06.750" Title="How is propagation of action potentials terminated once the &quot;message&quot; has been sent/received?" Tags="&lt;neuroscience&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5145" PostTypeId="1" AcceptedAnswerId="7767" CreationDate="2012-11-07T01:56:36.173" Score="7" ViewCount="998" Body="&lt;p&gt;I'm going to undertake an siRNA experiment soon, but I have only read about them. I want to address the role an enzyme plays in processing a protein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I understand, I will need to pick two specific siRNA's from  a screen of multiple siRNA candidates. As a negative control, I should also make a non-sense scramble siRNA. Of course the specific siRNA should show a significant knock-down of the enzyme; the control should not affect expression. As well, there should also be a validated positive control (such as GAPDH) and a mock treated control.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this experimental design sufficient? What are some common things to keep in mind, or pitfalls to avoid when doing siRNA studies?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="757" LastEditDate="2012-12-09T02:06:32.787" LastActivityDate="2016-03-21T09:37:27.073" Title="How to Design an siRNA Experiment?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;experimental-design&gt;&lt;rna-interference&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5146" PostTypeId="2" ParentId="5144" CreationDate="2012-11-07T06:05:18.537" Score="1" Body="&lt;p&gt;I'm not a Neurologist or Neuroscientist, so I can only share what I know about the subject!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;TL:DR&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Cease sensation&lt;/li&gt;&#xA;&lt;li&gt;Neuronal recovery period prevents further signaling&lt;/li&gt;&#xA;&lt;li&gt;Neurotransmitter inhibition prevents ligands from binding to receptors (usually Feedback mechanisms)&lt;/li&gt;&#xA;&lt;li&gt;Neuronal hyperpolarization prevents signaling&lt;/li&gt;&#xA;&lt;li&gt;Creation of signal (can be &lt;em&gt;perceived&lt;/em&gt; as cessation of signal)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It's important to note, first and foremost, that a cessation of stimulation will result in a cessation of the propagation. This is one of the simplest ways that neurons can stop firing - you're no longer touching, tasting, hearing, seeing, smelling, or thinking of what you were previously. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of the way Neurons are constructed, and as far as I'm aware, signal propagation will persist as far down the line as possible. I don't believe there's a discrete point where an Axon will simply &lt;em&gt;not&lt;/em&gt; send a signal once a dendrite on the same neuron has received the order.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What &lt;strong&gt;can&lt;/strong&gt; happen is that a competing signal has exhausted the propagation potential for the next neuron in the chain (the neuron is still recovering), or a competing signal has released &lt;strong&gt;inhibitors&lt;/strong&gt; that prevents the neurotransmitters from another Axon from affecting the target neuron. Competing signals is particularly common in the neurons of your eye, since the Amacrine cells fire depending on the competitive input of the Cones if I'm remembering everything correctly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Qtl8t.jpg&quot; alt=&quot;from RadioFreethinker&amp;#39;s Wordpress&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there are also substances like Benzodiazepines which &lt;a href=&quot;http://en.wikipedia.org/wiki/Benzodiazepine#Mechanism_of_action&quot; rel=&quot;nofollow noreferrer&quot;&gt;block propagation by opening Cl- channels and &lt;em&gt;hyperpolarizing&lt;/em&gt; a neuron's membrane, which prevents it from firing.&lt;/a&gt; Only a subset of GABA receptors have sites for benzodiazepines, but it's one more way that signals will cease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way to cease a signal, or at least the &lt;em&gt;perception&lt;/em&gt; of a signal, is to actually induce propagation. The Rods in your eyes &lt;em&gt;only&lt;/em&gt; fire &lt;em&gt;below&lt;/em&gt; a certain lumination threshold. What you perceive as light is them &lt;em&gt;not&lt;/em&gt; firing, and darkness is what happens when Rods fire at full strength. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not the last word on neurobiology, but I hope I've given you a good start!&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1306" LastEditDate="2012-11-07T11:47:30.423" LastActivityDate="2012-11-07T11:47:30.423" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5147" PostTypeId="2" ParentId="973" CreationDate="2012-11-07T07:09:00.260" Score="3" Body="&lt;p&gt;We can keep extracted RNA in -80°C for a few weeks, but before the start of any experiments, it needs to be validated by gel electrophoresis.&lt;/p&gt;&#xA;" OwnerUserId="1627" LastEditorUserId="69" LastEditDate="2012-11-07T11:41:49.050" LastActivityDate="2012-11-07T11:41:49.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5148" PostTypeId="1" AcceptedAnswerId="5150" CreationDate="2012-11-07T08:29:04.933" Score="33" ViewCount="19105" Body="&lt;p&gt;If a hermaphrodite animal (like slug, snail, etc) finds a partner they can mate immediately.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If another animal with &quot;normal&quot; reproduction (lets say a mouse) finds a partner they can only mate if they are opposite genders.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it seems logical that the hermaphrodite way of reproduction is more successful than the &quot;normal&quot; way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But it is not, as far as I know all higher developed species are using, the standard way of reproduction (male and female).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why? What are the disadvantages of hermaphroditism?&lt;/p&gt;&#xA;" OwnerUserId="883" LastEditorUserId="57333" LastEditDate="2020-03-20T08:41:09.697" LastActivityDate="2021-05-19T12:43:44.250" Title="Why are not all species hermaphrodites?" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;sexual-selection&gt;" AnswerCount="7" CommentCount="2" FavoriteCount="7" ContentLicense="CC BY-SA 4.0" />
  <row Id="5150" PostTypeId="2" ParentId="5148" CreationDate="2012-11-07T09:57:50.967" Score="25" Body="&lt;p&gt;Firstly I'll clarify that you are talking about &lt;em&gt;simultaneous&lt;/em&gt; hermaphrodites rather than &lt;em&gt;sequential&lt;/em&gt; hermaphrodites (1st one sex, then the other e.g. the limpet Patella vulgata).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is perhaps easiest to address the question by countering it and asking why dioecy (2 sex systems/2 gonochoric types e.g. male and female) is better? As you have pointed out there are obvious advantages to being a hermaphroditic species such as more chance of mating - more likely to provide an advantage at very low population densities where interactions are infrequent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two key disadvantages of hermaphroditism which I will briefly cover but have been discussed in &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0022519377903630&quot; rel=&quot;noreferrer&quot;&gt;this paper&lt;/a&gt; and probably other costs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first is energy costs. Maintaining the capacity to produce male and female gametes will be more costly than maintaining one. This gives the hermaphrodite a fitness disadvantage because energy is rarely an infinite resource. Therefore at higher population densities, when mating opportunities are not rare, the gonochoric individuals will have a higher fitness because they have more energy. Monogamy is also analogous to rare encounters but true monogamy is rare (1 partner for life).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second disadvantage of hermaphroditism is self fertilisation. This will cause an increase in homozygosity and lead to inbreeding depression (reduced fitness).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you are right to some extent...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the hermaphrodite way of reproduction is more successful than the&#xA;  &quot;normal&quot; way.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;...but the conditions which give rise to an hermaphroditic advantage are restricting. Overall, the above costs, combined with the obvious complexity of evolving the ability to produce male and female gametes, the ability to both fertilise and be fertilised, pregnancy and birth, and mating systems, mean that it is often more beneficial to be a dioecious species. Thus dioecy evolves.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT: Question Raised by @Single_Digit&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I have been pondering this question for a while and I get what RG255&#xA;  is saying. I'm just not sure I entirely buy it. Take earthworms, for&#xA;  example. They are simultaneous true hermaphrodites (as far as I&#xA;  understand). The anatomy doesn't have to be that complex*. They simply&#xA;  have two genital openings (one for eggs and one for sperm) and they&#xA;  line up in a &quot;69&quot; (excuse the vulgarity) position. This should, in&#xA;  theory, minimize the inbreeding depression. However, it doesn't&#xA;  eliminate the maintenance of two sets of reproductive systems. But&#xA;  most organisms are not internally fertilized mammals with wildly&#xA;  complicated systems of internalized embryonic care. Most species lay a&#xA;  pile of eggs that a male squirts sperm on or squirt eggs while the&#xA;  male squirt sperm and then they hope for the best.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;I would think the advantages of simultaneous parenting (after all,&#xA;  many MANY species' males don't provide much in the way of child care)&#xA;  and its fitness advantage would vastly outweigh the burden of a second&#xA;  set of reproductive organs.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;With that said, I don't have a better explanation, but I find the&#xA;  question a very interesting one. The linked article is pay-walled,&#xA;  aside from the abstract, but I still disagree with some of its tenets.&#xA;  To me true hermaphroditism should be very common (I realize it isn't)&#xA;  in species that don't need two parents to raise offspring, but do&#xA;  benefit from some (as in one parent's) parental care. I recognize that&#xA;  it would do little to help species that merely dump gametes and leave&#xA;  because specialization of one reproductive system would likely do the&#xA;  job better and both genders equally contribute under that type of&#xA;  system.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;So, RG255 convince me! Clearly there are good reasons, since gender&#xA;  (or asexual repr) is the norm, but I need more/better evidence.&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;&lt;ul&gt;&#xA;  &lt;li&gt;Yes I realize they would need separate internal anatomies for each type of gamete, but still...&lt;/li&gt;&#xA;  &lt;/ul&gt;&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My response:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;You have presented one example of hermaphroditism and used that as&#xA;  evidence that all species should be hermaphrodites. Earthworms are&#xA;  small slow creatures living in soil, I don't imagine they have high&#xA;  rates of encounter, and therefore low rates of encountering the&#xA;  opposite sex, therefore hermaphroditism would be favoured as discussed&#xA;  above. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Further, you say most species are external fertilisers (do you&#xA;  have a reference for this?) and therefore it is not costly be a&#xA;  hermaphrodite. I don't see your logic there, the cost is not&#xA;  necessarily to do with the cost of bearing child, producing &amp;amp;&#xA;  maintaining the gonads and gametes is also a costly process. I would&#xA;  argue that this is extremely complex. This is not just on a&#xA;  morphological level but also physiological: in non-hermaphroditic&#xA;  species the sexes have very different, and often, conflicting gene&#xA;  expression and hormone production patterns. Hermaphrodites would not&#xA;  be able to optimize to the fulfilling both the male and female roles.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Finally, you pointed out that the worms do not inbreed. Inbreeding&#xA;  avoidance does not have to be the cause of the hermaphroditism&#xA;  persisting, if the environment/other factors favour hermaphroditism. I&#xA;  never said that both were simultaneously necessary. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;I hope this&#xA;  clarifies it for you, if not please expand as to why, I am on here&#xA;  because I want to help people understand biology properly!&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Further response from @single_digit:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Well fair enough about my external fertilizers comment. I don't have a&#xA;  reference, but I was thinking all multicellular life and I'd have to&#xA;  imagine that when you factor in plants, that external fertilization is&#xA;  relatively the norm (as is hermaphrodism (dioecy) for the plants). As&#xA;  to earthworms, I disagree about your description of them. Their&#xA;  densities are actually pretty high, so I'd wager they encounter each&#xA;  other frequently, so I'm not sure where that leaves them in terms of&#xA;  pressures for hermaphroditism. Your point on the physiologic/hormonal&#xA;  issues of maintaining the systems is one I haven't previously&#xA;  considered. I honestly don't have any clue as to how daunting (or&#xA;  simple) that is, but I'd imagine that the sophistication of the&#xA;  systems would play a pretty key role. Makes me wonder how much this&#xA;  has been researched in true hermaprhodites. I suppose the main thing I&#xA;  keep coming back to is the overwhelming disadvantage gender has in&#xA;  terms of potential to create offspring. Males in many (most?) species&#xA;  essentially act as little more than sperm donors, thus half the&#xA;  individuals have effectively zero fitness. That just seems like an&#xA;  overwhelming advantage for hermaphrodites.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My Response&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why do you consider half of the individuals to have zero fitness?&#xA;  Fitness is widely accepted as the number of offspring a parent&#xA;  produces because this is directly related to number of copies of their&#xA;  genes passed to the next generation. Sperm donor type males achieve&#xA;  increased fitness by mating as do females - with out the male they&#xA;  would never be fertilized. The key disadvantage of dioecy is the&#xA;  halved (assuming equal sex ratio) frequency of potential encounters&#xA;  that could lead to mating. The general disadvantages of&#xA;  hermaphroditism are inbreeding depression and high cost &amp;amp; complexity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Single_digit:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Zero fitness isn't exactly correct, but if we look at parental care as&#xA;  conveying a survival advantage for K selected species, and huge&#xA;  numbers of offspring conveying an advantage for r-selected species&#xA;  (obviously the type of env affects this) does a deadbeat dad really&#xA;  optimize for either of these? Passing on genes is fine, but if&#xA;  offspring survival is low, does it matter? Does it simply boil down to&#xA;  the maintenance of two repr systems plus decreased fitness from&#xA;  inbreeding vs the increased reproductive success from extra child&#xA;  care? Or is there more?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My response:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;r/K selection theory has generally been disregarded in the&#xA;  evolutionary biology community due to the substantial evidence against&#xA;  it so it is unhelpful to think of selection in this way. As long as&#xA;  the 2 sexes strategy is more successful at passing on genes than a&#xA;  hermaphroditic strategy it will (should) prevail. Dioecy will be more&#xA;  successful if the hermaphroditism introduces to much cost through&#xA;  production and maintenance of sexual organs/gamete and inbreeding&#xA;  whilst not attaining substantial gains from higher potential mating&#xA;  frequency.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;@Single_Digit&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Interesting about r/K selection. I hadn't heard that. Do you have any&#xA;  links? I'd be curious to learn more there. I incorrectly earlier made&#xA;  a comment about dioecy where I meant monecy. But this seems to beg the&#xA;  question, why is monecy/hermaphroditism so much more prevalent in&#xA;  plants? Obviously there are different survival pressures, but I'd&#xA;  think the same basic principles would apply as in animals, but the&#xA;  condition seems to be far more common than in animals.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My Response&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I seem to remeber there being a reason in plants, don't&#xA;  have time to look it up right now. The work about r/K selection was&#xA;  Reznick/Stearns/Charlesworth. Reznicks is the most recent and more&#xA;  overview type paper - best place to start:&#xA;  &lt;a href=&quot;http://www2.hawaii.edu/~taylor/z652/Reznicketal.pdf&quot; rel=&quot;noreferrer&quot;&gt;http://www2.hawaii.edu/~taylor/z652/Reznicketal.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-02-28T22:34:02.073" LastActivityDate="2016-02-28T22:34:02.073" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5151" PostTypeId="2" ParentId="1724" CreationDate="2012-11-07T14:32:17.180" Score="6" Body="&lt;p&gt;Prokaryotes can't have introns, because they have transcription coupled to translation. They don't have time/space for that, since intron splicing will stop the coupling. Eukaryotes evolved the nucleus, where splicing can be done. The ancestor of eukaryotes that developed the nucleus could afford more variability (because of introns) than species without it, so they had a greater fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria can't afford high complexity compartmentalization, a process that requires a lot of available energy per gene, a eukaryotic cell can have tens, hundreds or even thousands of mitochondria that have similar energy output to a bacterial cell, while having a genome about 100-500 times smaller (16 kb of a human mitochondria compared to 4.000 kb for a E. coli cell).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope that clarifies your doubts, and you can see that this is a debatable answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry for my bad English.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.molevol.de/publications/193.pdf&quot; rel=&quot;noreferrer&quot;&gt;Lane &amp;amp; Martin 2010&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biology-direct.com/content/pdf/1745-6150-6-36.pdf&quot; rel=&quot;noreferrer&quot;&gt;Martin 2011&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1631" LastEditorUserId="1306" LastEditDate="2012-11-07T15:25:41.080" LastActivityDate="2012-11-07T15:25:41.080" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5152" PostTypeId="1" AcceptedAnswerId="5154" CreationDate="2012-11-07T17:28:30.497" Score="10" ViewCount="14108" Body="&lt;p&gt;Why exactly is HDL-cholesterol good for us and LDL-cholesterol bad for us. It has been well-established that LDL-cholesterol is associated with atherosclerosis and that HDL-cholesterol helps remove excess LDL-cholesterol from the circulation. From a biochemical view, however, what is the difference between the molecules that causes this difference?&lt;/p&gt;&#xA;" OwnerUserId="1609" LastEditorUserId="16299" LastEditDate="2015-12-29T19:08:24.830" LastActivityDate="2016-04-30T08:10:38.080" Title="What is/are the molecular differences between HDL and LDL cholesterol?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;fat-metabolism&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5153" PostTypeId="2" ParentId="3369" CreationDate="2012-11-07T18:10:02.097" Score="2" Body="&lt;p&gt;While bobthejoe/leonardo's answers are correct, you also need to be aware of the quality and limitations of isotype controls. You need to pick your source very carefully, as extensive testing (at my former company) has shown that some isotypes stick non-specifically under certain conditions or with certain samples. For example, we found that one common isotype from a major manufacturer (I don't remember who, it might have been Jackson) stuck non-specifically to HeLa cells by immunofluorescence and flow cytometry (the chemistry in the two assays is very similar) when used with common IF and FC protocols. You should also run no-antibody and secondary-only controls to ensure that your samples are not auto-fluorescing and that the secondary antibody is not binding non-specifically to your sample. Finally, ensure that the control exactly matches the isotype of your primary - don't use a rabbit polyclonal isotype to control for a rabbit mono, don't mix IgG subtypes, etc. Good luck!&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2012-11-07T18:10:02.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5154" PostTypeId="2" ParentId="5152" CreationDate="2012-11-07T20:47:15.423" Score="16" Body="&lt;p&gt;First of all, we should specify that &lt;strong&gt;there is no such thing as &quot;HDL-cholesterols&quot; and &quot;LDL-cholesterols&quot;&lt;/strong&gt;. On the same note &lt;strong&gt;there is no such thing as &quot;good cholesterol&quot; and &quot;bad cholesterol&quot;&lt;/strong&gt;: cholesterol is just one molecule, with this chemical structure&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/9/9a/Cholesterol.svg/440px-Cholesterol.svg.png&quot; alt=&quot;Structure of cholesterol - from Wikipedia&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What blood tests generally report is HDL-C and LDL-C, that is the amount of cholesterol in HDL or LDL respectively (again, cholesterol is always the same molecule, whether in an HDL or in an LDL).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HDL (high density lipoprotein) and LDL (low density lipoprotein) are &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipoprotein&quot; rel=&quot;nofollow noreferrer&quot;&gt;lipoproteins&lt;/a&gt;, aggregates of proteins and lipids that can carry, amongst other things cholesterol.&#xA;There are 5 major types of lipoproteins, called &lt;a href=&quot;http://en.wikipedia.org/wiki/Chylomicron&quot; rel=&quot;nofollow noreferrer&quot;&gt;chylomicrons&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Very_low-density_lipoprotein&quot; rel=&quot;nofollow noreferrer&quot;&gt;VLDL&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Intermediate-density_lipoprotein&quot; rel=&quot;nofollow noreferrer&quot;&gt;IDL&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Low-density_lipoprotein&quot; rel=&quot;nofollow noreferrer&quot;&gt;LDL&lt;/a&gt;, and &lt;a href=&quot;http://en.wikipedia.org/wiki/High-density_lipoprotein&quot; rel=&quot;nofollow noreferrer&quot;&gt;HDL&lt;/a&gt; and are distinguished by their size, density and the proteins they are composed of.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main function of lipoproteins is that of carrying lipids (=fats) around the organism in the blood. The problem is that lipids are not soluble in water (try to pour some oil in a glass of water) and blood is mainly composed of water. Lipoproteins, on the other hand, have a hydrophilic (=&quot;water-loving&quot;) exterior and a lipophilic (=&quot;fat-loving&quot;) interior, like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/d/d1/Chylomicron.svg/500px-Chylomicron.svg.png&quot; alt=&quot;Structure of a chylomicron - from Wikipedia&quot;&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the picture, the &quot;balls&quot; represent proteins, called apoproteins, and the C represent cholesterol and T tryglicerids, which are both lipids.&#xA;As you can see, all the fats are inside the lipoprotein, but the exterior, being soluble in water can be easily dissolved in the blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biochemistry of lipoproteins is quite involved and I will not go into details here (but please leave a comment if you want further explanations) but, to simplify things:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;HDL bring lipids from the periphery back to the liver&lt;/li&gt;&#xA;&lt;li&gt;LDL bring lipids from the liver to the periphery&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It is very important, at this point, to note that lipids are a physiologically important part of our organisms. All the cells in our body contain lipids: the membrane of each cell in the body is made up of lipids (called phospholipids) and also contain cholesterol. In fact, &lt;strong&gt;cholesterol is extremely important for the correct functioning of the body&lt;/strong&gt; as, for instance, it is used as the base to make many hormones (the so-called steroid hormones, such as estrogen, progesterone, cortisol, testosterone etc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, too high levels of lipids, particularly cholesterol, are not beneficial, as high cholesterol levels have been in fact linked to many cardiovascular diseases, which we hear a lot about these days.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, because HDL tend to remove the lipids from the circulation and bring them back to the liver they can be considered as some sort of &quot;cleaners&quot;, that remove excess cholesterol from circulation.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.783" LastActivityDate="2012-11-07T20:47:15.423" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5155" PostTypeId="1" AcceptedAnswerId="5163" CreationDate="2012-11-08T00:17:57.203" Score="4" ViewCount="743" Body="&lt;p&gt;Quite simply, some organisms metabolize glucose under anaerobic conditions via Glucose-&gt;(2) Pyruvic Acid-&gt;(2)Ethyl Alcohol. Some organisms, however, metabolize to lactic acid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When did such a process (lactic acid) arise biochemically from its related (ethanol) fermentation, and how was it selected for? i.e What were the advantages?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;Also, can someone create the &lt;a href=&quot;/questions/tagged/glycolysis&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged 'glycolysis'&quot; rel=&quot;tag&quot;&gt;glycolysis&lt;/a&gt; or &lt;a href=&quot;/questions/tagged/fermentation&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged 'fermentation'&quot; rel=&quot;tag&quot;&gt;fermentation&lt;/a&gt; tag?&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="922" LastActivityDate="2015-10-09T18:30:57.270" Title="How was the diversity between ethanol fermentation and lactic acid fermentation evolved?" Tags="&lt;microbiology&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5156" PostTypeId="1" AcceptedAnswerId="5161" CreationDate="2012-11-08T00:45:59.703" Score="6" ViewCount="48530" Body="&lt;p&gt;While eating sour food or candy, I start to sweat if it's sour enough. My body feels much hotter although my actual temperature is the same, my forehead starts sweating a lot and I feel like it just got twice as hot wherever I am. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this a biological phenomena or is my DNA just stupid? Is it somehow related to the digestive system, that sour food is harder to digest?&lt;/p&gt;&#xA;" OwnerUserId="1624" LastActivityDate="2014-11-14T15:30:03.937" Title="Does sour food cause sweating?" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;&lt;food&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5159" PostTypeId="2" ParentId="5156" CreationDate="2012-11-08T03:38:27.330" Score="1" Body="&lt;p&gt;I don't think this is a normal physiological response, but I would seek medical advice to be sure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did a quick literature search with keywords &quot;sour&quot;, &quot;food&quot; and &quot;sweating&quot; and came up with one article about &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=sour%20food%20sweating&quot; rel=&quot;nofollow&quot;&gt;SUNCT syndrome&lt;/a&gt;. SUNCT syndrome is a short-lasting, unilateral, neuralgiform headache syndrome with autonomic phenomena on the symptomatic side. In other words, 3 patients of 6 studied, suffered headaches and sweating on one side of their forehead only. It seems to be predominant in males, with a mean age of onset around 50 years. The attacks are strictly unilateral, generally with the pain persistently confined to the ocular/periocular area. Most attacks are moderate to severe in intensity and burning, stabbing or electrical in character.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=sour%20food%20sweating&quot; rel=&quot;nofollow&quot;&gt;Kruszewski P, Zhao JM, Shen JM, Sjaastad O. SUNCT syndrome: forehead sweating pattern. Cephalalgia. 1993 Apr;13(2):108-13.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-11-08T03:38:27.330" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5161" PostTypeId="2" ParentId="5156" CreationDate="2012-11-08T08:23:32.603" Score="3" Body="&lt;p&gt;In general, sweating is caused by too much heat, even if you're not aware of the heat. This can happen if the bowel moves and so raises the core temperature. Such movement is often accompanied with sweating, and since you only feel the normal temperature on the skin, it is &lt;strong&gt;cold sweat&lt;/strong&gt;. But at the same time your core is hot so you think it's cold, but it will later mix to normal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, it points to unusual bowel movement. This can be due to food allergy or, in a milder form, in food intolerances which are quite common. When it comes to sour ingredients, they are often in fruits, so I'll make a shot in the blue and say that you have a food intolerance against some fruits. You can check this hypothesis by trying chemically pure acetic acid to sour your food. If that doesn't result in sweat/hotness then it's probably the fruits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Food_intolerance&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Food_intolerance&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Wikipedia points even directly to salicylate in fruits but I think you cannot exclude allergies against essential oils like limonene and such. Plants are really chemistry factories and not all is well that you can get with them.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-11-08T08:38:18.533" LastActivityDate="2012-11-08T08:38:18.533" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5162" PostTypeId="1" AcceptedAnswerId="5169" CreationDate="2012-11-08T08:56:22.373" Score="9" ViewCount="1141" Body="&lt;p&gt;ATP Synthase is ubiquitous throughout life on earth and so most probably evolved within the last universal common ancestor (LUCA) before that lineage diversified into the various kingdoms of life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is suggested that the functional domains comprising the ATP Synthase complex were cobbled together from pre-existing sub-units, each with with a related activity (e.g. the union of a proton motor with a DNA Helicase with ATPase activity), which seems reasonable, although a bit vague in the details. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fact that a primitive ATP Synthase arose in the first place suggests that ATP already had a central role in cellular metabolism and so begs the question, what preceded ATP Synthase in the role of generating ATP in the LUCA cell? &lt;/p&gt;&#xA;" OwnerUserId="1635" LastEditorUserId="22057" LastEditDate="2019-01-20T14:02:18.673" LastActivityDate="2019-01-21T08:46:40.363" Title="What preceded ATP synthase?" Tags="&lt;evolution&gt;&lt;metabolism&gt;&lt;cellular-respiration&gt;&lt;mitochondria&gt;&lt;protein-evolution&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="5163" PostTypeId="2" ParentId="5155" CreationDate="2012-11-08T09:30:20.610" Score="4" Body="&lt;p&gt;First, it is not clear from the physiology or biochemical information alone to determine what evolved from what. The intermediate pyruvate is always there, so &lt;strong&gt;lactose dehydrogenase&lt;/strong&gt; (LDH) and &lt;strong&gt;pyruvate decarboxylase&lt;/strong&gt; (PDC) could have each evolved anytime, and there are good reasons for both:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;LDH: the reaction pyruvate + NADH/H+ = lactate + NAD+ + 25 kJ/mol is highly exergonic, i.e. produces heat&lt;/li&gt;&#xA;&lt;li&gt;PDC: the reaction pyruvate = acetaldehyde + CO2 (and with ALD present) acetaldehyde + NADH/H+ = ethanol + NAD+ where ethanol is poisonous to other species&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Add to it that there are organisms like &lt;em&gt;Sch. pombe&lt;/em&gt; that have &lt;em&gt;both&lt;/em&gt; enzymes, so can do both reactions, your questions should be rather:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How has the enzyme LDH evolved?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The enzyme is similar to malate dehydrogenase, both form a family. They belong to a group of enzymes that all have a &lt;strong&gt;NAD(P) binding domain&lt;/strong&gt;, so it's not too far-fetched to state that LDH and MDH evolved from another enzyme with NAD(P) binding domain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ebi.ac.uk/interpro/IEntry?ac=IPR016040&quot; rel=&quot;nofollow&quot;&gt;http://www.ebi.ac.uk/interpro/IEntry?ac=IPR016040&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How has the enzyme PDC evolved?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Protein sequences of pyruvate decarboxylase (PDC) derived from cloned&#xA;  yeast (Saccharomyces cerevisiae) and bacterial (Zymomonas mobilis)&#xA;  genes were compared with each other and with sequence databases.&#xA;  Extensive sequence similarities were found between them and with two&#xA;  others: cytochrome-linked pyruvate oxidase from Escherichia coli and&#xA;  acetolactate synthase (ilvI in E. coli; ILV2 gene in S. cerevisiae).&#xA;  All catalyse decarboxylation of pyruvate using thiamine pyrophosphate&#xA;  (TPP) as cofactor. General overall similarity suggests common ancestry&#xA;  for these enzymes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;cited from abstract of&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Green, Jeremy. &quot;Pyruvate decarboxylase is like acetolactate synthase (&amp;lt; i&gt; ILV2) and not like the pyruvate dehydrogenase E1 subunit.&quot; FEBS letters 246.1 (1989): 1-5. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2651151?dopt=Abstract&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/2651151?dopt=Abstract&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-11-08T09:53:25.373" LastActivityDate="2012-11-08T09:53:25.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5164" PostTypeId="1" AcceptedAnswerId="5168" CreationDate="2012-11-08T09:33:53.280" Score="11" ViewCount="24316" Body="&lt;p&gt;Why did Darwin formulate his theory of evolution just after his visit to the Galápagos islands? Why were they so special from an evolutionary point of view?&lt;/p&gt;&#xA;" OwnerUserId="1061" LastEditorUserId="16651" LastEditDate="2016-01-16T17:59:49.973" LastActivityDate="2016-01-26T13:18:42.213" Title="Why are the Galápagos islands so special?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;history&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5165" PostTypeId="2" ParentId="3165" CreationDate="2012-11-08T09:34:47.063" Score="8" Body="&lt;p&gt;For all types of athlete, their ability is determined by both genetic and environmental factors (nature and nurture). The degree to which each contributes ultimately depends on the demands of the sport.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an example let's compare basketball and golf.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basketball is likely to have a strong genetic component because players tend to be exceptionally tall (average is &lt;a href=&quot;http://en.wikipedia.org/wiki/NBA_league_average_height,_weight,_age_and_playing_experience&quot; rel=&quot;nofollow&quot;&gt;over 2 metres&lt;/a&gt; and there are only a handful who have played NBA &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_shortest_players_in_National_Basketball_Association_history&quot; rel=&quot;nofollow&quot;&gt;under 1.75m&lt;/a&gt;). Because height is strongly genetically (but not entirely) determined by the genes, they have a big influence on whether someone can poses the physical qualities to play in the NBA. However, a large part of their technical capabilities are due to their environment. If you give a basketball to someone who has played 2 games a week their entire lives and ask them to take 10 shots it is likely they would score more than someone who has never seen a basketball!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Comparing basketball to golf, there are all sorts of body types within the PGA tour, and they is no/few obvious genetic traits which golfers tend to have over other people. This would suggest that golfing ability is more affected by environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So an easy way to get a rudimentary test of genetic contributions to sporting ability would be to compare frequency distributions of focal traits in the athletes to distributions of regular people. Obviously the phenotypic trait you measure has both genetic and environmental contributions (e.g. childhood diet) which could affect them but it would be a good starting indicator which could give some candidate traits to test. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a scientist I would also consider sequencing some athletes and some non athletes and seeing which genes the athletes have more often then the regular person's genome. However, such studies are likely to be complex - linking phenotypes (in polygenic traits) to the single allele variants relies on large sample sizes. Generally it will be more difficult if:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;There is large variance in the trait&lt;/li&gt;&#xA;&lt;li&gt;The gene has a small effect (see major and minor effect genes)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Both of these problems going to be positively correlated with the number of genes affecting a trait (how polygenic is it?) which for athletic ability is probably quite a substantial amount of genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt;  Here are some possible studies for your further exploration of the topic-&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://journals.lww.com/acsm-essr/Abstract/2001/01000/Specific_Genetic_Markers_of_Endurance_Performance.4.aspx&quot; rel=&quot;nofollow&quot;&gt;Candidate genes for Specific Genetic Markers of Endurance Performance and o2max&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/s004390050781?LI=true&quot; rel=&quot;nofollow&quot;&gt;Rowers have an excess of the ACE I allele&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22648472&quot; rel=&quot;nofollow&quot;&gt;Elite Italian footballers with &quot;explosive&quot; leg strength also reveal ACE and other genetic markers&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255226/&quot; rel=&quot;nofollow&quot;&gt;A precautionary tale about Genetic tests for athletic ability&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-02-06T10:57:22.180" LastActivityDate="2013-02-06T10:57:22.180" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5166" PostTypeId="1" AcceptedAnswerId="17018" CreationDate="2012-11-08T10:17:01.450" Score="4" ViewCount="498" Body="&lt;p&gt;The causes of sweating aside, i.e. I'm not interested in which and how nerve signals are transmitted to sweat glands. But I would like to read a detailed account on what a sweat gland consists of, what it does when not sweating, but esp. what happens when a sweat nerve signal arrives. Is there a good free review or can you give one?&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1306" LastEditDate="2012-11-08T16:01:25.717" LastActivityDate="2014-04-29T22:52:16.747" Title="what are the mechanics of sweating?" Tags="&lt;physiology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5167" PostTypeId="2" ParentId="5164" CreationDate="2012-11-08T10:48:51.717" Score="7" Body="&lt;p&gt;Galápagos islands are one of few islands with a unique fauna and flora. This can only happen when the distance to other land is great enough, and when the island exists long enough that flora and fauna could grow (volcano islands are sterile for a long time).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now Galápagos is even more unique because it is comprised of several islands that are distant enough that some animals cannot cross the distance like small birds. That leads to a unique fauna and flora that also differs between islands, so you can see differences just by visiting the next island. This made it practically a museum of evolution.&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorDisplayName="user560" LastEditDate="2012-11-08T12:37:31.390" LastActivityDate="2012-11-08T12:37:31.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5168" PostTypeId="2" ParentId="5164" CreationDate="2012-11-08T10:51:22.870" Score="14" Body="&lt;p&gt;Charles Darwin formulated his theory after travelling the world aboard the Beagle, here's &lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/4/42/Voyage_of_the_Beagle.jpg&quot; rel=&quot;nofollow&quot;&gt;the route&lt;/a&gt;. He found the Galapagos Islands particularly inspiring, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;'The natural history of this archipelago is very remarkable: it seems&#xA;  to be a little world within itself.'&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is a more detailed account of his relationship with the Galapagos islands, and there is also a book called &quot;Voyage of The Beagle&quot; (I think it is available as a free kindle download) which is basically his diary. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A big part of the reason it is so famous is because of &quot;Darwin's Finches,&quot; which are 12 species of finch on the island that have all evolved to specific niches. This is one of the classic examples of evolution. Darwin noted the differences between the birds, thinking they were of different families, but it was later discovered they were all finches and the differences had evolved because of factors like the food they eat (seed eaters had fatter beaks.. etc). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Galapagos islands offer opportunities to study evolution and adaptation because the islands are distant from the mainland, have differences between the islands, and migration between the islands is difficult. Studies like &lt;a href=&quot;http://www.jstor.org/stable/2460995?seq=1&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt; (which I happened to be reading at the time of the question being asked whilst writing a manuscript) are an example of how cool a place it is!&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="16651" LastEditDate="2016-01-16T17:51:51.890" LastActivityDate="2016-01-16T17:51:51.890" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5169" PostTypeId="2" ParentId="5162" CreationDate="2012-11-08T14:23:44.620" Score="9" Body="&lt;p&gt;There are metabolic processes in which ATP is synthesised without the involvement of ATP synthase. The best examples are, in fact, two steps in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Glycolysis&quot;&gt;glycolytic pathway&lt;/a&gt;, catalysed by phosphoglycerate kinase and pyruvate kinase. This is why, in the absence of any aerobic metabolism, many organisms (like yeast for example) can grow quite happily, producing two molecules of ATP for each molecule of glucose that is metabolised.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Presumably this process is what enabled ATP to gain its central role in energy metabolism without any need for an ATP synthase.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-08T14:23:44.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5170" PostTypeId="1" CreationDate="2012-11-08T17:03:38.013" Score="6" ViewCount="6262" Body="&lt;p&gt;What is the probability of conception in situations when sperm isn't directly ejaculated into the woman's vagina, like:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The man's or the woman's hands come into contact with sperm, for example when removing a condom. (Perhaps after washing them,) the hands later touch vagina, for example during foreplay to another intercourse.&lt;/li&gt;&#xA;&lt;li&gt;The man and the woman taking a bath together, the man ejaculates into the water.&lt;/li&gt;&#xA;&lt;li&gt;The man ejaculates on the woman's body, perhaps on or around vagina but not inside. (In this case it could also make a difference whether the woman has shaved pubic hair or not.)&lt;/li&gt;&#xA;&lt;li&gt;The man ejaculates during receiving oral sex, (perhaps the woman rinses her mouth), the couple kisses, the man performs oral sex to the woman.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In all these situations, it seems possible that a tiny amount of sperm is eventually transferred into vagina indirectly. And since just a single cell is enough to fertilize, it seems that there is non-zero probability of conceiving.&#xA;How much care need to be taken to prevent conception in such situations? Does simply washing sperm away with water (+ soap perhaps) eliminate it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;If you think of similar situations that are similar, please don't hesitate to add them.&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="1639" LastActivityDate="2020-12-27T15:23:19.400" Title="The probability of indirect human fertilization?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5171" PostTypeId="1" AcceptedAnswerId="5176" CreationDate="2012-11-08T17:06:02.673" Score="6" ViewCount="1093" Body="&lt;p&gt;A lot of people live in a 7 day cycle, where 5 days of work are followed by 2 days of &quot;rest&quot;. Vacations and holidays can increase the time available for resting. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any biological reason for humans to rest after x days of work?&lt;/strong&gt; Can this be explained by the buildup of by-products of metabolism, like &lt;a href=&quot;http://en.wikipedia.org/wiki/Homocysteine&quot;&gt;Homocysteine&lt;/a&gt;?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2021-02-18T11:54:28.753" Title="Is there any biological reason for humans to rest after x days of work?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5173" PostTypeId="2" ParentId="5144" CreationDate="2012-11-08T19:48:08.520" Score="1" Body="&lt;p&gt;The neuron doesn't need to know &quot;not to &quot;route&quot;&quot; an AP because this is not necessarily it's default response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Upon receiving an AP from another neuron (via either an a chemical synapse or a gap junction) the next neuron receives a signal. The nature of this signal depends on the nature of the connection between the two neurons - the proteins and neurotransmitters involved - and is therefore context specific. Also context specific is the sensitivity of the receiving cell. If the connection is strong and activating and the receiving neuron is sensitive, then it will fire and the AP would be &quot;routed&quot; as in your question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are other possibilities. For instance, the connection may too weak, such that it can only activate the receiving neuron given sustained activity, or in conjunction with another neuron (in effect forming an AND logic gate). The connection may also be inhibitory - meaning that it deactivates, rather than activates the neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Analogies between neurons and electronic systems are useful, but it's important to remember just how drastic a simplification they are. Individual synapses are complex. Cells have thousands of them, and a good deal of other moving parts besides.&lt;/p&gt;&#xA;" OwnerUserId="1640" LastEditorUserId="57" LastEditDate="2012-11-08T20:44:54.170" LastActivityDate="2012-11-08T20:44:54.170" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5174" PostTypeId="2" ParentId="5107" CreationDate="2012-11-08T21:03:10.840" Score="7" Body="&lt;p&gt;The article is well known and discussed amongst systems biologists. It makes a good point - high throughput, observational biology cannot substitute for mechanistic studies that provide causal information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But we know an awful lot about biological systems already. All systems biologists are using information from the forward approach implicitly when they formulate their models. More importantly however, most systems biologists combine the forward and inverse approach in their work. Models are tested and validated by perturbing the systems, and updated according to the results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Discussions of these kind often devolve into a debate over the semantics of systems biology, in which it's detractors attempt to define &quot;systems biology&quot; in the most unflattering terms possible.&lt;/p&gt;&#xA;" OwnerUserId="1640" LastActivityDate="2012-11-08T21:03:10.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5175" PostTypeId="2" ParentId="5170" CreationDate="2012-11-09T02:29:34.937" Score="6" Body="&lt;p&gt;I don't have answers to all of your questions, but here is one example of a highly unusual conception via the gastrointestinal tract: &lt;a href=&quot;http://blogs.discovermagazine.com/discoblog/2010/02/01/ncbi-rofl-thats-one-miraculous-conception/&quot; rel=&quot;nofollow&quot;&gt;http://blogs.discovermagazine.com/discoblog/2010/02/01/ncbi-rofl-thats-one-miraculous-conception/&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To cut a long story short, a woman born with a congenital defect that caused her to have no vagina was stabbed in the abdomen when her boyfriend found her performing fellatio on another man. She was taken to the hospital and patched up but a few months later:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Precisely 278 days later the patient was admitted again to hospital with acute, intermittent abdominal pain. Abdominal examination revealed a term pregnancy with a cephalic fetal presentation. The uterus was contracting regularly and the fetal heart was heard. Inspection of the vulva showed no vagina, only a shallow skin dimple was present below the external urethral meatus and between the labia minora. An emergency lower segment caesarean section was performed under spinal anaesthesia and a live male infant weighing 2800 g was born…&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The article concludes that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A plausible explanation for this pregnancy is that spermatozoa gained access to the reproductive organs via the injured gastrointestinal tract. It is known that spermatozoa do not survive long in an environment with a low pH (Jeffcoate1975), but it is also known that saliva has a high pH and that a starved person does not produce acid under normal circumstances (Bernards &amp;amp; Bouman 1976). It is likely that the patient became pregnant with her first or nearly first ovulation otherwise one would expect that inspissated blood in the uterus and salpinges would have made fertilization difficult. The fact that the son resembled the father excludes an even more miraculous conception.”&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="37" LastEditorUserId="1306" LastEditDate="2014-06-12T10:21:28.003" LastActivityDate="2014-06-12T10:21:28.003" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5176" PostTypeId="2" ParentId="5171" CreationDate="2012-11-09T08:29:37.543" Score="4" Body="&lt;p&gt;I think your main assumption is not true -- we do not really rest on weekends.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not know many people who only rest on weekends. Usually this is the time for socializing, doing home-related work, physical activity (sports, hiking), spending time with your kids, all of which is often almost the opposite of a rest.&lt;/p&gt;&#xA;" OwnerUserId="1435" LastActivityDate="2012-11-09T08:29:37.543" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5177" PostTypeId="2" ParentId="5170" CreationDate="2012-11-09T09:23:12.610" Score="5" Body="&lt;p&gt;Very very very very small. Next to impossible, millions of sperm cells start the journey and only a very small fraction of the sperm produced make it as far as the egg if &quot;inserted properly.&quot; The vagina is a very hostile environment - to prevent infection - and this means very few sperm make it far enough. We produce in the order of 200-300 million sperm and it estimated that less than 1000 make it, so that is a 0.000005 chance of each sperm cell making it far enough. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also a benefit to travelling in such large number (each sperm is less likely to be destroyed by dilution effects, one sperm cell vs the entire human reproductive tract stands no chance). The numbers I am giving may be a little out from the correct ones, it's a while since I did my undergraduate module in sperm biology... I'm sure more accurate numbers will be  in this &lt;a href=&quot;http://books.google.co.uk/books?hl=en&amp;amp;lr=&amp;amp;id=kctYNbO1fE0C&amp;amp;oi=fnd&amp;amp;pg=PP2&amp;amp;dq=sperm%20biology%20an%20evolutionary%20perspective&amp;amp;ots=N7OaUPi-iv&amp;amp;sig=OSvXTLM1Jk_AbgMuzyQj5XOGT1Y&quot;&gt;recommended reading&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further to this remember that not every attempt at fertilisation is successful even when doing it the right way, couples often try multiple times. If it takes 100 attempts to fertilise the egg just once the that is 1 in (100*200,000,000) sperm being successful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, if someone says they got pregnant sitting on a toilet seat that must have had sperm on it, or some other ridiculous claim, then simply don't believe them.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2012-11-09T09:23:12.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5178" PostTypeId="1" CreationDate="2012-11-09T09:23:39.977" Score="7" ViewCount="889" Body="&lt;p&gt;While peptide bonds usually adopt the &lt;em&gt;trans&lt;/em&gt; conformation, peptide bonds to proline can exist in either &lt;em&gt;cis&lt;/em&gt; or &lt;em&gt;trans&lt;/em&gt; conformation. The isomerization between &lt;em&gt;cis&lt;/em&gt; and &lt;em&gt;trans&lt;/em&gt; is slow, and has been shown to be the rate-limiting step in folding of certain proteins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What methods can be used to determine the conformation of a specific proline in a protein? &lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2012-11-09T12:19:28.637" Title="Determining if a specific proline is cis or trans in the protein?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5179" PostTypeId="1" AcceptedAnswerId="5200" CreationDate="2012-11-09T09:36:06.127" Score="3" ViewCount="3289" Body="&lt;p&gt;I've been reading about Dorsal Raphe Nucleus, a serotonin- rich part of the brain. I noticed mentioning of &quot;tonic activity&quot; - regular pulsing that releases neurotransmitters. On top of this &quot;tone&quot; the nucleus can fire bursts of spikes(action potentials?) that further increase neurotransmitter concentrations for a short time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is this kind of tonic firing common throughout the brain, or is it DRN specific?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-11-11T17:40:59.670" Title="Is &quot;tonic activity&quot; common for neurons firing in the brain?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5180" PostTypeId="1" CreationDate="2012-11-09T10:18:50.357" Score="4" ViewCount="364" Body="&lt;p&gt;Does anyone know where I can find a reliable list of virucides (not anti-virus) that can be used by humans? This virucide must be able to affect viruses that are already inside the cells. St John's Wort is considered a virucide along with it's other properties, for example.&lt;/p&gt;&#xA;" OwnerUserId="1643" LastActivityDate="2012-11-09T10:18:50.357" Title="Virucides - Herbal and otherwise, for HHV6 type virus or any inner-cell virus" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;virology&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5181" PostTypeId="2" ParentId="2905" CreationDate="2012-11-09T11:43:19.973" Score="3" Body="&lt;p&gt;I dont know about JMol, but this can be easily done with UCSF Chimera.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I loaded the 1a1x structure.&#xA;Then selected: Tools &gt; Structure Analysis &gt; FindHBond&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I kept the default values and selected &lt;code&gt;Write information to reply log&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then clicked &lt;code&gt;OK&lt;/code&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the structure the H Bonds will be identified with a coloured line.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To view which is the donor and acceptor go to: Favorites &gt; Reply log&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An output of the reply log is below:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):&#xA;ASP 12.A N    GLU 25.A OE2  no hydrogen  3.012  N/A&#xA;HIS 13.A N    GLU 25.A OE1  no hydrogen  3.338  N/A&#xA;HIS 13.A ND1  ASP 12.A OD2  no hydrogen  2.835  N/A&#xA;LEU 14.A N    TRP 70.A O    no hydrogen  2.934  N/A&#xA;TRP 15.A N    ARG 23.A O    no hydrogen  2.866  N/A&#xA;...&#xA;120 hydrogen bonds found&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;As you can see the donor and acceptor has been identified as defined in the header line.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you wish, the information can also be written to a file by selecteing &lt;code&gt;Write to text file&lt;/code&gt; in the &lt;code&gt;FindHBond&lt;/code&gt; window.&lt;/p&gt;&#xA;" OwnerUserId="158" LastActivityDate="2012-11-09T11:43:19.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5182" PostTypeId="2" ParentId="5007" CreationDate="2012-11-09T12:12:41.120" Score="1" Body="&lt;p&gt;Evolution is possible for the same reasons it has always been possible (and I'll let the other answers' details comment on the mechanics, as they have done already...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to offer a *slightly more philosophical point of view on the term, however.  I think that we have arrived at a point in our evolution where our prefrontal cortex is impeding our biologically driven urges, somewhat (which would have us evolving in similar ways to all the creatures less aware of the consequence of their actions).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it's impossible to say to what extent our evolution will now be driven by conscious choices we make about what traits we value vs. the traits that our biology drives us towards.  Certainly innate biological drivers are incredibly powerful, but as is evidenced by our desire to promote our intellect, and our progressive urge to help even the sickly and mentally challenged to get the most out of life (up to and including procreating), rather than to evaluate our potential partners purely based on physical traits and our brute strength, these purely biological imperatives are governing our reproductive choices less and less.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also much (reasonable) speculation as to what our new found understanding of genetics will allow us to artificially do to ourselves in the near future. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it's important to consider both these factors when speculating about how we're evolving, but I think it's not even slightly controversial to suggest that we're definitely evolving in a different way now than we were 500k years ago.  &lt;/p&gt;&#xA;" OwnerUserId="148" LastActivityDate="2012-11-09T12:12:41.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5183" PostTypeId="2" ParentId="5178" CreationDate="2012-11-09T12:19:28.637" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Sarkar et al.(2007) Proline cis-trans Isomerization Controls Autoinhibition of a Signaling Protein. &lt;em&gt;Molecular Cell&lt;/em&gt; &lt;strong&gt;25&lt;/strong&gt;, 413–426 (DOI 10.1016/j.molcel.2007.01.004), available &lt;a href=&quot;http://chem.rutgers.edu/~babis/Publications/Sarkar_Molcell.pdf&quot;&gt;here&lt;/a&gt;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors report on the interactions between two SH3 domains of the Crk adaptor protein. Basically they find that the linker which tethers these two domains contains a proline which interconverts between the &lt;em&gt;cis&lt;/em&gt; and &lt;em&gt;trans&lt;/em&gt; conformations, and that this interconversion determines the interaction between the two domains. They follow isomerisation by using &lt;a href=&quot;http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy_of_proteins&quot;&gt;NMR&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Cis-trans&lt;/em&gt; peptidyl-prolyl isomerization is a subtle change, and I don't think that you will find a way of following it in a specific protein that is simpler than this, unfortunately.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-09T12:19:28.637" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5184" PostTypeId="2" ParentId="457" CreationDate="2012-11-09T16:08:47.287" Score="3" Body="&lt;p&gt;To answer the question with a complicating question, suppose the anecdotal preference for &quot;tall&quot; men and &quot;short&quot; women is really just an urge toward the norm? Suppose that women seek taller men in proportion to their self-perception as &quot;shorter than average&quot;--the closer a woman is to average (female) height, the less likely she is to seek a mate who is markedly taller?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my unscientific experience, height matters less to people whose height is more or less normal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, with some assumptions about the heights of offspring of couples whose heights are different, the tendency might be toward a stable average. As noted in other answers, nutrition is probably a big factor in recent gains in Europe, Asia, and Africa. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This would be hard to model mathematically and I am not convinced the result would shed much light on the question, especially (as noted above) in light of the polygenetic nature of the trait.  &lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2012-11-09T16:08:47.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5185" PostTypeId="2" ParentId="3564" CreationDate="2012-11-09T19:26:40.170" Score="8" Body="&lt;p&gt;I worked for a long time at a leading high-quality antibody company, so I'll try and share some of my experiences with you. The process of making a highly specific antibody (I'll focus on monoclonals) has three important parts - antigen design and immunization, cloning and subcloning, and screening/validation. Each part is crucial on its own, and the better one is performed, the higher your chances of success downstream become.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order for an antibody to work, it needs to bind specifically to its target. I won't get into all the specifics here, as there is a good open literature on antigen design, but basically you need something that will promote a strong immune response in the host, give you a variety of clones to choose from, and be specific - it shouldn't bind other targets besides your protein of interest. There are lots of factors to consider, including antigenicity, solubility, ease of production (for immunizing and screening), steric considerations (does another protein or nucleic acid obscure the target site &lt;em&gt;in vivo&lt;/em&gt;?), and others. Antigens can be roughly divided into two types - peptides (typically less than 20 or 30 amino acids) and proteins or protein fragments. You will most likely want to try several antigens to maximize your probability of success. After the antigen is synthesized and purified, you need to come up with an immunization schedule for priming and boosting the animal(s), then determine when and how to test them (screening), and at what time and how to harvest it for the monoclonal process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cloning process then comes next. Clones can be generated by a variety of methods, some widely available, such as the various hybridoma methods, and some proprietary to individual companies. My former company employed a mix of both, depending on the species of animal, using some really cool in-house tech that was constantly being improved and expanded upon. These processes are very dependent on the quality of materials being used and the expertise of the cloners. The input B cells (which make the antibodies) need to have been harvested, treated, and stored according to a set of precise steps to allow for the highest number of viable clones. Once the immortalized cells have been obtained (after fusion with the myeloma partner cells in the hybridoma process, for example) they are diluted to a pre-determined cell count and plated in 96-well plates and allowed to recover and grow for a time, during which they are secreting antibodies into the medium. This media is then tested quickly (before the cells overgrow the well), and positive wells are diluted out to (hopefully) single-cell suspensions and subcloned, or frozen down for later. The first testing is frequently by ELISA using the immunizing antigen, although depending on your application of interest it may be by high-throughput screening via flow cytometry, immunohistochemistry, or immunofluorescence. After the initial testing, subsequent steps of subcloning and re-testing can occur at a more measured pace, as the cells can be frozen indefinitely after generating sufficient quantities of antibodies in the supernatant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is where the quality of your screening program comes in. Your assays need to be well-designed, robust, well-documented and performed, and have appropriate positive and negative controls so that you can truly tell whether a certain clone is of interest, or performs better than an existing product. This means controlled conditions, standardized reagents and protocols, and a high degree of repeatability from assay to assay. Also, the appropriateness of your controls cannot be emphasized enough. Do you have a knockout or non-expressing sample for comparison, or a way of looking at baseline vs. induced or inhibited activity? For ChIP, unless you have a good control antibody and primer pair for your gene of interest, how will you know if the assay works? You may get a great result doing a straight immunoprecipitation-Western blot, but still not pull down DNA-bound protein. If your ChIP method doesn't produce clean DNA, you may never get binding. And if you don't have appropriate data analysis protocols in place with multiple replicate wells, you may waste time chasing noise instead of specific signal. Additionally, along with testing all your clones, you also need to titrate them to determine the optimal working concentration. I've seen a lot of antibodies that look like crap when you first test the supe, but diluted 100 or 1000X they are clean, specific, and still strong. Be patient, testing is a lot of work and requires a ton of repetition to confirm your results, but it'll be well worth it in the end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, after all this is done, you hopefully have a great clone that does what you want it to do, and better than anything else out there. You now need to decide what you're going to do with it, because if you're an academic lab and publish with it, the world will come knocking at your door. Don't slack off at the end and decide 100 ml of supernatant will be enough to last forever - save the clones and put them in a cell bank, or try to get a commercialization deal with a manufacturing company so you don't have to do all the work!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps, please let me know if you have any additional questions or concerns.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2012-11-09T19:32:10.430" LastActivityDate="2012-11-09T19:32:10.430" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="5186" PostTypeId="1" AcceptedAnswerId="5187" CreationDate="2012-11-09T20:14:53.250" Score="7" ViewCount="74" Body="&lt;p&gt;I'm interested in learning if there's some way of quantifying the organism's metabolic efficiency associated with movement. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to me that some organisms would be more efficient than others at using energy. For mechanical systems, there are clear metrics of efficiency, for example &quot;miles per gallon&quot; or &quot;liters per 100km&quot;. &lt;strong&gt;Is there a similar metric that converts calories into how far an organism can go?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-11-09T21:17:13.293" Title="Is there such thing as &quot;meters per calorie&quot; for living organisms?" Tags="&lt;zoology&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5187" PostTypeId="2" ParentId="5186" CreationDate="2012-11-09T21:17:13.293" Score="9" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Halsey &amp;amp; White (2012) Comparative energetics of mammalian locomotion: Humans are not different. &lt;em&gt;Journal of Human Evolution&lt;/em&gt; &lt;strong&gt;63&lt;/strong&gt;:718–722&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This paper presents a comparison of the metabolic cost of walking and running in humans, &lt;em&gt;Australopithecus&lt;/em&gt; and other mammals.  They use a parameter NCOT (net cost of transport), whose units are ml O&lt;sub&gt;2&lt;/sub&gt; consumed m&lt;sup&gt;-1&lt;/sup&gt;. The inverse of this parameter would be related to your metres per calorie.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors quote an NCOT of 12.77 ml O&lt;sub&gt;2&lt;/sub&gt; m&lt;sup&gt;-1&lt;/sup&gt; for a walking human. Using a value of 4 kcal g&lt;sup&gt;-1&lt;/sup&gt; for glucose, I calculate that this NCOT is equivalent to 14.6 m kcal&lt;sup&gt;-1&lt;/sup&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.brianmac.co.uk/energyexp.htm&quot;&gt;Here&lt;/a&gt; I found an energy consumption value of 5.8 kcal min&lt;sup&gt;-1&lt;/sup&gt; (for a 73 kg man) walking at 6.4 km h&lt;sup&gt;-1&lt;/sup&gt;, which translates to 18.5 m kcal&lt;sup&gt;-1&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incidentally, according to the authors of the paper: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The predicted net cost of transport (NCOT, ml O&lt;sub&gt;2&lt;/sub&gt; m&lt;sup&gt;−1&lt;/sup&gt;) of mammals is related to mass (M, kg) according to 0.54M&lt;sup&gt;0.70&lt;/sup&gt;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-09T21:17:13.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5188" PostTypeId="1" AcceptedAnswerId="5189" CreationDate="2012-11-09T22:05:48.963" Score="6" ViewCount="354" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleic_acid_analogue#Base-pairing&quot;&gt;Wikipedia&lt;/a&gt; states that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;xDNA contains expanded bases, in which a benzene ring has been added, which may pair with canon bases, resulting in four possible base-pairs (8 bases:xA-T,xT-A,xC-G,xG-C, 16 bases if the unused arrangements are used). Another form of benzene added bases is yDNA, in which the base is widened by the benzene.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In this context, does widened and expanded refer to the same thing? If so, what would be the exact different between yDNA and xDNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;NOTE:&lt;/strong&gt; I am &lt;em&gt;not&lt;/em&gt; referring to the X and Y chromosomes.&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-11-10T12:34:06.167" Title="What is the difference between xDNA and yDNA?" Tags="&lt;genetics&gt;&lt;synthetic-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5189" PostTypeId="2" ParentId="5188" CreationDate="2012-11-10T09:13:32.723" Score="4" Body="&lt;p&gt;yDNA came first:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Lee &amp;amp; Kool (2005) A New Four-Base Genetic Helix, yDNA, Composed of Widened Benzopyrimidine−Purine Pairs. J Am Chem. Soc. 127: 3332-3338&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As seen in this Figure from the paper it is a DNA consisting of T and C substituted with yT and yC, widened analogues. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SJz1h.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;xDNA came next (also from the Kool lab.):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Lynch et al. (2006) Toward a Designed, Functioning Genetic System with Expanded-Size Base Pairs: Solution Structure of the Eight-Base xDNA Double Helix. J Am Chem. Soc. 128: 14704-14711&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As seen in this Figure from the paper, xDNA consists of an 8 base system A,C,G,T,xA,xC,xG,xT.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UYZIn.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This field is reviewed in:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The XNA world: progress towards replication and evolution of synthetic genetic polymers&#xA;  Pinheiro &amp;amp; Holliger (2012) The XNA world: progress towards replication and evolution of synthetic genetic polymers. &lt;em&gt;Current Opinion in Chemical Biology&lt;/em&gt; &lt;strong&gt;16&lt;/strong&gt;:245-252 &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-11-10T12:34:06.167" LastActivityDate="2012-11-10T12:34:06.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5191" PostTypeId="1" AcceptedAnswerId="5192" CreationDate="2012-11-10T15:29:47.540" Score="4" ViewCount="8695" Body="&lt;p&gt;What is the actual biological difference between mice and rats? Are they actually the same thing with two different names depending on appearance (are they all mice for instance and we call the larger ones rats or vice versa) or is there some fundamental difference in their genetics?&lt;/p&gt;&#xA;" OwnerUserId="1624" LastActivityDate="2018-06-12T01:04:23.977" Title="Difference between mice and rats" Tags="&lt;genetics&gt;&lt;zoology&gt;&lt;dna&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5192" PostTypeId="2" ParentId="5191" CreationDate="2012-11-10T15:51:46.843" Score="10" Body="&lt;p&gt;Mice (&lt;em&gt;Mus&lt;/em&gt;) and rats (&lt;em&gt;Rattus&lt;/em&gt;) are definitely separate species, by whichever &lt;a href=&quot;http://research.amnh.org/vz/ornithology/crossbills/species.html&quot; rel=&quot;noreferrer&quot;&gt;definition of species&lt;/a&gt; you choose to use. They are genetically distinct, and both genera are members of the clade Muridae, along with &lt;em&gt;Acomys&lt;/em&gt; (&quot;spiny mice&quot;) and &lt;em&gt;Gerbillus&lt;/em&gt; (&quot;gerbils&quot;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, what we call colloquially &quot;mice&quot; and &quot;rats&quot; encompass a great deal of variation within rodents. The genus &lt;em&gt;Mus&lt;/em&gt; is one of several subgenera with ~15 species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A recent phylogenetic study of rodents by &lt;a href=&quot;http://www.biomedcentral.com/1471-2148/9/71&quot; rel=&quot;noreferrer&quot;&gt;Blanga-Kanfi et al. (2009)&lt;/a&gt;, revealed that &lt;em&gt;Mus&lt;/em&gt; and &lt;em&gt;Rattus&lt;/em&gt; are sister groups, meaning that each is the other's closest relative. The image below from the paper above shows the complete tree. Muridae is about 2/3 of the way down in blue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gj2Jd.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-11-10T15:51:46.843" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5193" PostTypeId="2" ParentId="5191" CreationDate="2012-11-10T15:58:13.713" Score="5" Body="&lt;p&gt;True rats and mice are rodents that constitute part of the subfamily &lt;em&gt;Murinae&lt;/em&gt; in the family &lt;em&gt;Muridae&lt;/em&gt;. The Old World house mouse is &lt;em&gt;Mus musculus&lt;/em&gt;, the brown rat is &lt;em&gt;Rattus norvegicus&lt;/em&gt;, so they are members of two different genera in that family. It is estimated that they split from a common ancestor 12-24 million years ago. Just to put that in perspective, the rodent lineage (including rats and mice) and the primate lineage (apes, monkeys, humans) diverged about 80 million years ago. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read an &lt;a href=&quot;http://www.genome.gov/11511308&quot; rel=&quot;nofollow&quot;&gt;NIH News Release about the rat genome here&lt;/a&gt;, which is my source for these divergence times.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The names 'rat' and 'mouse' are also used in the names of many other, more distantly related, rodents such as mole rats and dormice. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Added later:&lt;/strong&gt;&#xA;Response to @rwst comment under the OP. Here is a relevant quotation from the NIH source that I cite above:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The new analysis also underscores the fact that while rats and mice look very similar to the human eye, there are significant genomic differences between the two types of rodents. For example, some aspects of genomic evolution in the rat appear to be accelerated when compared to the mouse. According to the new analysis, due to the unusually rapid expansion of selected gene families, rats possess some genes not found in the mouse, including genes involved in immunity, the production of pheromones (chemicals involved in sexual attraction), the breakdown of proteins and the detection and detoxification of chemicals.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-11-11T13:38:50.473" LastActivityDate="2012-11-11T13:38:50.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5194" PostTypeId="1" AcceptedAnswerId="5196" CreationDate="2012-11-10T19:05:28.410" Score="8" ViewCount="2407" Body="&lt;p&gt;I've heard that the brain consumes quite a lot of oxygen and energy, compared to the rest of the body. &lt;strong&gt;What I'm interested in is if this is the kind of energy and oxygen that the rest of the body competes for?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;For example, does running divert resources from the brain to the&#xA;muscles, leading to decreased cognitive performance?&lt;/li&gt;&#xA;&lt;li&gt;Does digesting food divert resources from the brain to the gut?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Does the heart rate or blood pressure have anything to do with how much resources, like oxygen and energy are available to neurons?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2016-10-19T04:39:15.983" Title="Does the brain and the body use the same energy source (glucose/ATP)?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5195" PostTypeId="2" ParentId="5194" CreationDate="2012-11-10T20:59:46.820" Score="3" Body="&lt;p&gt;While in general the answer is &quot;yes&quot;, the brain does use the same type of resources as other parts of the body, you cannot from that alone derive conclusions about the brain competing with other organs. Also, I think that cognitive performance is not a function of availability of resources. In fact, the moment that the brain lacks crucial resources like oxygen, it simply shuts down. But you don't faint when you start running (if you do, go see a doctor). &quot;Power-saving mode&quot; for the brain is not &quot;reduce IQ by 20 points&quot;, but &quot;just make sure the body is breathing and shut down everything else&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I do not think that digesting food requires any comparable amount of energy that it would require the brain to give up on some of the oxygen it needs.&lt;/p&gt;&#xA;" OwnerUserId="1435" LastActivityDate="2012-11-10T20:59:46.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5196" PostTypeId="2" ParentId="5194" CreationDate="2012-11-10T21:05:02.827" Score="5" Body="&lt;p&gt;You can grab any university level text on human physiology and you will find that the brain is a unique organ for cellular respiration. The brain is only capable of using two metabolic subtrates: glucose for oxidative phosphorylation (producing ATP) and ketone bodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exercise does indeed divert blood flow toward the muscles. After all, they are undergoing higher levels of respiration and need nourishment. Your body will always balance muscular needs and the needs of the brain and the rest of the body. Similarly, digesting food has a similar response, although this is more involved. Eating food has a autonomic reflex to increase blood flow to the stomach and digestive tract to facilitate the processing and distribution of nutrients.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-11-10T21:05:02.827" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5197" PostTypeId="1" CreationDate="2012-11-11T04:20:23.067" Score="7" ViewCount="445" Body="&lt;p&gt;If a protein is heterologously expressed in E. coli under the T7 promoter, what fraction of the total protein concentration in the cell is the heterologously expressed protein? What could be its concentration at most? Does it strongly depend on the size of the protein or are there certain size thresholds for low/high expression?&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2012-11-11T21:10:52.830" Title="Recombinant protein fraction in E. coli" Tags="&lt;proteins&gt;&lt;recombinant&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5198" PostTypeId="2" ParentId="5197" CreationDate="2012-11-11T09:52:59.283" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Miroux and Walker (1996) Over-production of Proteins in Escherichia coli: Mutant Hosts that Allow Synthesis of some Membrane Proteins and Globular Proteins at High Levels. J Mol Biol. 260: 289–298&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.fbs.leeds.ac.uk/staff/sab/Methods/Lab_Methods/Miroux.pdf&quot; rel=&quot;nofollow&quot;&gt;The authors report&lt;/a&gt; on problems of over-expressing membrane proteins in &lt;em&gt;E. coli&lt;/em&gt; using a T7 (pET) system. They isolate mutant strains which show improved levels of expression compared to the parent strain, BL21(DE3). In their Table 1 they document levels of expression of 17 proteins including, as a control, GFP. GFP was found as a combination of soluble and inclusion body protein at a level of 37 mg L&lt;sup&gt;-1&lt;/sup&gt; in BL21(DE3) and 140 mg L&lt;sup&gt;-1&lt;/sup&gt; in one of their mutant strains (C41(DE3)). The highest level of expression that they observed was 300 mg L&lt;sup&gt;-1&lt;/sup&gt; for bovine OSCP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately the authors document neither the total protein content, nor the cell density of the cultures that they analysed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's assume that the cultures were 10e9 cells mL&lt;sup&gt;-1&lt;/sup&gt; = 10e12 cells L&lt;sup&gt;-1&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://bionumbers.hms.harvard.edu/bionumber.aspx?&amp;amp;id=103905&amp;amp;ver=6&quot; rel=&quot;nofollow&quot;&gt;this source&lt;/a&gt; (citing Neidhardt F.C. Escherichia coli and Salmonella: Cellular and Molecular Biology. Vol 1. pp. 14, ASM Press 1996), the dry weight of an &lt;em&gt;E. coli&lt;/em&gt; cell is 2.8e-13 g&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The generally accepted figure for protein as a fraction of dry weight in &lt;em&gt;E. coli&lt;/em&gt; = 0.55&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I calculate from these numbers a value of 1540 mg protein L&lt;sup&gt;-1&lt;/sup&gt;. For the three protein expression levels described above this means:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GFP in BL21(DE3) = 2.4%&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GFP in C41(DE3) = 9.6%&lt;/p&gt;&#xA;&#xA;&lt;p&gt;bovine OSCP in C41(DE3) = 19.4%&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I conclude (from these numbers, and from personal experience) that overexpression levels are highly variable, and are going to be strain and protein-dependent. Values in the range of 1-20% total cell protein may be anticipated.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-11-11T21:10:52.830" LastActivityDate="2012-11-11T21:10:52.830" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5199" PostTypeId="1" CreationDate="2012-11-11T17:40:04.247" Score="3" ViewCount="182" Body="&lt;p&gt;I've recently been researching the subject of size-expanded nucleobases in alternative genetic sets. Many papers describe the, at least, partial success in replicating xDNA and yDNA, as well as transcribing them, as suggested &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152792/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At the same time, studies on polymerase replication and transcription of oligonucleotide sequences reveal that chemical entities other than the typical nucleoside triphosphates can be tolerated to varying degrees.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My question is &lt;strong&gt;can the cell's molecular machinery, including ribosomes and tRNA, possibly lead to translation of xRNA or yRNA? Would the translation product yield the traditional 20 amino acids? Have this ever been attempted?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;References to original papers would be appreciated. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-11-11T17:40:04.247" Title="Has anyone ever sucessfully translated xRNA or yRNA?" Tags="&lt;synthetic-biology&gt;&lt;translation&gt;&lt;polymerase&gt;" AnswerCount="0" CommentCount="0" ClosedDate="2015-03-30T19:35:53.587" ContentLicense="CC BY-SA 3.0" />
  <row Id="5200" PostTypeId="2" ParentId="5179" CreationDate="2012-11-11T17:40:59.670" Score="2" Body="&lt;p&gt;Most neurons that have been studied have spontaneous activity. Tonic firing is common in sensory neurons as well as cortical neurons. However, this could be very biased since it is difficult to study neurons that are silent in vivo. In vivo studies are &lt;strong&gt;blind&lt;/strong&gt;, meaning that we usually do not see which neurons we are recording from. This is known as the &quot;dark matter&quot; problem (ref 1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, it is known that there are homeostatic mechanism for maintaining average firing rate. Basically, if a neuron doesn't fire much, then the input sensitivity of the neuron increases to produce more activity (ref 2). But we don't know how widely this can be applied.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Shy Shoham, Daniel O’Connor, Ronen Segev. How silent is the brain: is there a &quot;dark matter&quot; problem in neuroscience? Journal of Comparative Physiology A: Neuroethology, Sensory, Neural, and Behavioral Physiology, Vol. 192, No. 8. (1 August 2006), pp. 777-784  &lt;a href=&quot;http://dx.doi.org/doi:10.1007/s00359-006-0117-6&quot; rel=&quot;nofollow&quot;&gt;doi:10.1007/s00359-006-0117-6&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Gina G. Turrigiano. Homeostatic plasticity in neuronal networks: the more things change, the more they stay the same. Trends in Neurosciences, Vol. 22, No. 5. (1 May 1999), pp. 221-227, &lt;a href=&quot;http://dx.doi.org/doi:10.1016/S0166-2236&quot; rel=&quot;nofollow&quot;&gt;doi:10.1016/S0166-2236&lt;/a&gt; (98)01341-1&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="460" LastActivityDate="2012-11-11T17:40:59.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5201" PostTypeId="2" ParentId="3730" CreationDate="2012-11-11T17:47:24.297" Score="1" Body="&lt;p&gt;After talking to a few electrophysiologists, I found out that they have very diverse opinions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that a common way of stabilizing the movement of the brain with respect to heart beat is to press the brain with some softish-rigid material like agar. Also, draining the CSF could help but then this cannot be done without sacrificing the animal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The quality of the patch degrades over time, and it could be held for an hour or more (anecdotal).&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2012-11-11T17:47:24.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5202" PostTypeId="1" AcceptedAnswerId="5209" CreationDate="2012-11-11T18:00:20.380" Score="3" ViewCount="1115" Body="&lt;p&gt;I've heard the following idea this morning: Before the introduction of contraception, humans conceived quite a lot of babies (there was little to do to avoid that), but the population was kept in check by very high childhood mortality rates. This mortality rate ensured that &lt;strong&gt;only the fittest survived.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea seems common sense, but I decided to investigate if this is really true. I know that for evolution, even 2000 years should be an instant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did some research, for example the worst &lt;a href=&quot;http://en.wikipedia.org/wiki/Infant_mortality#Global_trends&quot; rel=&quot;nofollow noreferrer&quot;&gt;childhood mortality&lt;/a&gt; rate currently in the world is around 17.5%, which is still about half of what it was in &quot;developed&quot; countries during the 1700s, according to the table below. But looking at the wikipedia map of childhood mortality, it seems that a baby nowadays has only around 1-3% chance of dying before adulthood, because even the weakest baby can be kept on life support long enough for the danger to pass. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the implications of reducing childhood mortality rates worldwide on human evolution?&lt;/strong&gt; Maybe evolution is a wrong term to use here. Would it be fitness as species? I'm particularly interested in how this relates to developmental defects and genetic disorders. &lt;strong&gt;Is there any evidence that people who lived in a world without contraception and with high childhood mortality rate were more physically or mentally fit?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's an paper that deals with the subject and the table is from the paper below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://shell.newpaltz.edu/jsec/articles/volume2/issue4/NEEPSvolkatkinson.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;IS CHILD DEATH THE CRUCIBLE OF HUMAN &#xA;EVOLUTION?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VtHB5.png&quot; alt=&quot;Childhood Mortality Rates&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2015-04-02T21:29:55.740" Title="What are evolutionary implications of contraception and reduced childhood mortality rates worldwide?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5203" PostTypeId="1" CreationDate="2012-11-11T17:19:37.263" Score="10" ViewCount="19005" Body="&lt;p&gt;I was watching a talk by Michio Kaku and he mentioned that crocodiles (or possibly alligators, I forget offhand) don't actually age -- they can die, but they essentially go through no aging process beyond adulthood&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone link me any sort of detailed information on this? &lt;/p&gt;&#xA;" OwnerDisplayName="sarah" LastEditorUserId="4101" LastEditDate="2013-10-31T01:30:12.227" LastActivityDate="2014-06-25T20:50:21.067" Title="Do crocodiles age?" Tags="&lt;senescence&gt;&lt;life-history&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5204" PostTypeId="1" CreationDate="2012-11-11T22:05:47.123" Score="1" ViewCount="1036" Body="&lt;p&gt;Using the Ames test, we add a mutagen to auxotrophic salmonella with mutations in the histidine pathway and rat liver extract to simulate metabolism.  How would we know if the carcinogen is a human carcinogen or not? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm guessing that if a mutagen showed no growth without the rat liver extract, but then growth with the rat liver extract this would mean that it is a human carcinogen. Is this true?&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="6" LastEditDate="2012-11-12T07:03:08.020" LastActivityDate="2012-11-12T08:16:37.207" Title="How can the Ames test detect a human carcinogen?" Tags="&lt;cancer&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5205" PostTypeId="1" AcceptedAnswerId="5212" CreationDate="2012-11-11T22:29:20.200" Score="6" ViewCount="446" Body="&lt;p&gt;Why do we think chronic inflammation can cause cancer? I know the pathway is not fully understood, but what makes scientists believe that inflammation causes cancer?&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="1122" LastEditDate="2012-11-12T07:29:30.427" LastActivityDate="2016-05-01T23:55:13.483" Title="Why do we think chronic inflammation can cause cancer?" Tags="&lt;cancer&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5206" PostTypeId="1" CreationDate="2012-11-11T22:43:28.873" Score="2" ViewCount="41" Body="&lt;p&gt;This is a dose-response experiment testing a new cancer drug.  the darker line represents cancer cells.  what range of dose should be used? I think it's 2-4 because this affects cancer cells only.  is this correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZB5Uu.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="558" LastActivityDate="2012-11-11T23:10:23.383" Title="What range of dose should be used?" Tags="&lt;homework&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5207" PostTypeId="2" ParentId="5206" CreationDate="2012-11-11T23:10:23.383" Score="3" Body="&lt;p&gt;In the most basic sense you want to kill the most cancerous cells whilst minimizing the regular somatic cell death. Almost all cancer medications affect regular cells, too - though the better ones do so at a minimum whilst being effective. In reality, it's also nearly impossible to kill &lt;em&gt;all&lt;/em&gt; of the cancerous cells. The goal is to bring them below detectable levels, which can allow the body to finish the job. Leaving significant amounts of cancerous cells alive won't do the patient any good - they'll just continue to proliferate and the patient will be back for more operations or treatments soon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, with the goal of minimizing benign cell cost and completely eradicating the cancerous line, on your crude chart that falls at about &lt;strong&gt;&quot;4&quot;&lt;/strong&gt;. &lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-11-11T23:10:23.383" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5208" PostTypeId="2" ParentId="5203" CreationDate="2012-11-11T23:30:05.417" Score="15" Body="&lt;p&gt;Well, this needs to be broken down into two parts. Do Crocodilians &lt;em&gt;age&lt;/em&gt; (undergo &lt;strong&gt;senescence&lt;/strong&gt;), and are Crocodilians &lt;em&gt;immortal&lt;/em&gt; (will only die of external causes)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are Crocodilians immortal?&lt;/strong&gt;&#xA; - &lt;a href=&quot;http://en.wikipedia.org/wiki/Crocodile#Age&quot;&gt;No&lt;/a&gt;. They appear to live about as long as humans before they die.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Measuring crocodile age is unreliable, although several techniques are used to derive a reasonable guess. The most common method is to measure lamellar growth rings in bones and teeth—each ring corresponds to a change in growth rate which typically occurs once a year between dry and wet seasons. Bearing these inaccuracies in mind, the oldest crocodilians appear to be the largest species. &lt;em&gt;C. porosus&lt;/em&gt; is estimated to live around &lt;strong&gt;70 years on average, with limited evidence of some individuals exceeding 100 years.&lt;/strong&gt; One of the oldest crocodiles recorded died in a zoo in Russia. A male freshwater crocodile at the Australia Zoo is estimated to be 130 years old. He was rescued from the wild by Bob Irwin and Steve Irwin after being shot twice by hunters. As a result of the shootings, this crocodile (known affectionately as &quot;Mr. Freshy&quot;) has lost his right eye.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do Crocodilians undergo senescence (show &lt;em&gt;signs&lt;/em&gt; of aging)?&lt;/strong&gt; Well, if &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7926857&quot;&gt;this study from &quot;Gerontology&quot;&lt;/a&gt; written by Patnaik BK in 1994 is to believed... &lt;em&gt;Maybe not&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Evidences and mechanisms of rapid or negligible senescence in reptiles are still fragmentary and unclear&lt;/strong&gt;... neither the increase in mortality rate and accumulation of lipofuscin nor the reproductive senility have been shown conclusively in ageing reptile populations. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, while Crocodiles and Alligators (both Crocodilians) definitely have a finite lifespan, because they just continue to grow it's hard to tell how long they have left until the day they die.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-11-11T23:30:05.417" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="5209" PostTypeId="2" ParentId="5202" CreationDate="2012-11-12T00:01:34.870" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Before the introduction of contraception, humans conceived quite a lot of babies (there was little to do to avoid that), but the population was kept in check by very high childhood mortality rates. &lt;strong&gt;This mortality rate ensured that only the fittest survived.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Woh! Let me stop you there. No, high rates of childhood mortality &lt;em&gt;do not&lt;/em&gt; ensure that whom Natural Selection is acting upon are the &quot;most fit.&quot; That title is given to individuals who are able to survive long enough &lt;strong&gt;to breed&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many, many conditions that affect humans do not interfere with a person's growth or ability to perform physical or intellectual feats - but can definitely reduce or completely eradicate a person's ability to reproduce. These individuals are evolutionary dead-ends, and thus - while they survive in the environment - are not &quot;fit&quot; in the context of this topic.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What are the implications of reducing childhood mortality rates worldwide on human evolution? Maybe evolution is a wrong term to use here. Would it be fitness as species?   &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What it means is that populations will rise. As populations rise and intermingle, alleles get spread around. Perhaps rarer alleles become more common, or more common alleles become rarer. We're talking about &lt;em&gt;Hardy-Weinberg&lt;/em&gt; equilibriums in the allele frequencies. However, with populations large enough true equilibriums are impractical to reach.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The more pragmatic explanation is that more mutations will arise, they'll be passed around, rare mutations will see more exposure, and humanity - &lt;strong&gt;in a very general sense&lt;/strong&gt; - becomes &lt;em&gt;more diverse&lt;/em&gt; genetically until a &lt;em&gt;Selective Pressure&lt;/em&gt; is applied. Until there's a detriment to having a particular gene, there isn't a need to eliminate it from the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your example is children who are too weak at birth to live outside of an NICU for their first few months - well, because we're capable of providing such care, until that care goes away it's not negatively affecting us. If it comes with an additional cost - say that, for whatever reason, premies can't digest mother's milk until the 8-month mark, then Natural Selection would pressure humans to evolve so that only 8+ month or older babies are born.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's no evidence of significant pressures in human populations at this time, though. At least not in politically stable and technologically apt countries, although in areas undergoing long-time drought or other dangers it is seen. &lt;strong&gt;Sickle-Cell Anemia&lt;/strong&gt; is though to be an adaptation to rising Malaria rates - which was quite fatal until medication was devised to treat it in the last 50 years or so (not even a blip in evolutionary terms).  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there any evidence that people who lived in a world without contraception and with high childhood mortality rate were more physically or mentally fit?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not that I can think of or find easily. While there are detriments &lt;em&gt;associated&lt;/em&gt; with being born prematurely, and some evidence that women waiting until they're late 30's and men until they're 60 or older can negatively affect their gametes and consequently the development of any children born from them - it's been such a short time since the introduction of hormonal contraception and modern medicine that we may not see results tangible results for hundreds of years. Although condoms have been around for several hundred years, and there's been no associations with condom use that I can think of.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the short term, what it has done is affect the ethnic diversity of countries. For the first time ever, Hispanic births have outnumbered Caucasian births in 2012 in the United States. Other countries, mostly European countries, are seeing declines in birth rates - which means their populations will decline with age or be compensated for by immigration. Higher birth rates, however, are associated with lower income brackets or very religious communities - both of which are associated with ethnic Minorities, at least in the United States. So while minority populations have more kids, they do so on fewer resources which may negatively affect their children in the long-term, whereas higher-earning segments of the population might have fewer children later in their lives, but can provide a much more stable environment and opportunities to continue that success.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One thing that hormone-centered birth control has done, however, is eliminate rape as a viable form of passing on one's genes. As gruesome as it might be to consider, pregnancies as a result of rape can produce &quot;fit&quot; offspring. It is a legitimate reproductive strategy in nature, and is in humans... &lt;em&gt;unless&lt;/em&gt; the woman is using contraception. In the long-term this will probably show some interesting results (nominally an enhanced &lt;strong&gt;&quot;Female Choice&quot;&lt;/strong&gt; effect - which is already evident in human evolution), but nothing right now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also worth considering the ability for humans' increasing abilities to manipulate our own genome. At this point, we're nearly able to remove detrimental genes at-will and replace them with more effective versions. Because of this bio-engineering ability, the generations after ours might never be susceptible to inherited diseases - or they might all hop on the trendy &quot;genes&quot; and end up completely identical to each other. That's part of the fun of being human, though; we're very messy when it comes to Evolution. We tend to muck things but up good. :)&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-11-12T00:01:34.870" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5210" PostTypeId="1" AcceptedAnswerId="5251" CreationDate="2012-11-12T01:55:43.533" Score="3" ViewCount="283" Body="&lt;p&gt;To my knowledge house cats (and likely other felines) are the only animal able to go into remission after onset of Type 2 diabetes mellitus. I don't have a reference, this has been by peers in my research institution and by a veterinarian. Has this mechanism been studied, and if so, what is it?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2012-11-16T19:44:11.867" LastActivityDate="2012-11-17T16:40:39.247" Title="By What Mechanism can Felines Reverse Diabetes?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5211" PostTypeId="1" CreationDate="2012-11-12T03:59:10.563" Score="2" ViewCount="200" Body="&lt;p&gt;I've been reading a curious paper about the use of cannabis, and one of the passages piqued my interest:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There’s also been a lot of work done on another constituent of&#xA;  marijuana, cannabinoid, which is not psychoactive by itself. A lot of&#xA;  research has shown that it’s a great &lt;strong&gt;anti-inflammatory&lt;/strong&gt;, it’s a&#xA;  neuro-protectant, and it &lt;strong&gt;may be what gives medical marijuana patients&#xA;  relief from things like epilepsy and anxiety&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Has there been any scientific evidence that links inflammation and anxiety?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&#xA;&lt;a href=&quot;https://www.erowid.org/plants/cannabis/cannabis_culture13.pdf&quot; rel=&quot;nofollow&quot;&gt;Cannabis, Forgetting, and the&#xA;The Botany of Desire&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="69" LastEditDate="2012-11-12T16:47:08.317" LastActivityDate="2013-12-21T16:18:07.193" Title="Are inflammation and anxiety connected?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5212" PostTypeId="2" ParentId="5205" CreationDate="2012-11-12T07:26:40.340" Score="5" Body="&lt;p&gt;There are good epidemiological data for this.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Links between cancer and inflammation were first made in the&#xA;nineteenth century, on the basis of observations that tumours often&#xA;arose at sites of chronic inflammation and that inflammatory cells&#xA;were present in biopsied samples from tumours.&lt;/p&gt;&#xA;&lt;p&gt;There are many triggers of chronic inflammation that increase the risk&#xA;of developing cancer. Such triggers include microbial infections (for&#xA;example, infection with Helicobacter pylori is associated with gastric&#xA;cancer and gastric mucosal lymphoma), autoimmune diseases (for&#xA;example, inflammatory bowel disease is associated with colon cancer)&#xA;and inflammatory conditions of unknown origin (for example,&#xA;prostatitis is associated with prostate cancer). Accordingly,&#xA;treatment with non-steroidal anti-inflammatory agents decreases the&#xA;incidence of, and the mortality that results from, several tumour&#xA;types.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Cited from Mantovani, Alberto, et al. &amp;quot;Cancer-related inflammation.&amp;quot; Nature 454.7203 (2008): 436-444.&#xA;&lt;a href=&quot;http://www.sld.cu/sitios/reumatologia/temas.php?idv=21500&quot; rel=&quot;noreferrer&quot;&gt;http://www.sld.cu/sitios/reumatologia/temas.php?idv=21500&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-11-12T07:26:40.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5213" PostTypeId="2" ParentId="5204" CreationDate="2012-11-12T08:16:37.207" Score="3" Body="&lt;p&gt;The Ames test aims to find out if a chemical (not yet known to be mutagen) is indeed a mutagen, either directly, or following treatment with liver enzymes (which may metabolise a chemical to mutagenic derivatives during &quot;detoxification&quot;). As you explain, the test involves looking for reversion of various histidine auxotrophic strains of &lt;em&gt;Salmonella&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the chemical is found to mutagenic in the Ames test then there is a good chance that it will be a carcinogen because of the link between mutagenesis and cancer. In practice further unrelated tests are needed to eliminate false positives.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this review of the method&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mortelmans &amp;amp; Zeiger (2000) The Ames Salmonella/microsome mutagenicity assay. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. 455: 29-60&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;the authors state that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...there is a high predictivity of a positive mutagenic response in the Ames test for rodent carcinogenicity...ranging from 90% to 77%...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-12T08:16:37.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5215" PostTypeId="2" ParentId="1910" CreationDate="2012-11-12T17:24:39.250" Score="1" Body="&lt;p&gt;there are of course foods for bodybuilders and for weightgainers and losers, never seen just one food containing all (and I activly searched for it) but you can create your own mix if you buy some protein suplements (that are usaly made from whey and other byproducts that have a good ratio of the various essencial aminoacids) or just soyabeans that also have good aminoacid ratios and is cheaper; some carb rich foods and those complete vitamin/mineral suplements + essencial fattyacids (ie: cods liver oil). only problem is finding a trully complete vitamin/mineral supplement. I've searched in vain thus far.&lt;/p&gt;&#xA;" OwnerUserId="1585" LastEditorUserId="1585" LastEditDate="2012-11-25T19:07:48.570" LastActivityDate="2012-11-25T19:07:48.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5217" PostTypeId="1" AcceptedAnswerId="5247" CreationDate="2012-11-12T18:42:24.797" Score="20" ViewCount="86739" Body="&lt;p&gt;Modern human beings, especially women, cut their armpit hair. It seems to me the armpit hair is trivial/useless. Shortly speaking, what is the armpit hair for?&lt;/p&gt;&#xA;" OwnerUserId="573" LastEditorUserId="1590" LastEditDate="2012-11-19T15:15:10.830" LastActivityDate="2014-02-12T08:38:55.127" Title="What is the armpit hair for?" Tags="&lt;human-biology&gt;" AnswerCount="4" CommentCount="4" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5219" PostTypeId="1" CreationDate="2012-11-12T19:31:25.050" Score="3" ViewCount="134" Body="&lt;p&gt;Evolution is traditionally spoken of as an inherited change over generations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does evolution happen one change at a time - or are there multiple changes occurring between two successive generations? Is there a known timeline for the frequency of such changes in any species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something like ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;20 Million years ago - Species X showed A, B, C.. Z characteristics &lt;/p&gt;&#xA;&#xA;&lt;p&gt;19 Million years ago - Species X following characteristics changed A'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;17 Million years ago - Species X following characteristics changed B', C', Q', M'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;16 Million years ago - Species X following characteristics changed A''&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2012-11-12T19:48:02.210" LastActivityDate="2012-11-13T17:14:39.700" Title="Is there a timeline for the frequency of evolution of any species?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5220" PostTypeId="2" ParentId="5219" CreationDate="2012-11-12T20:05:41.733" Score="3" Body="&lt;p&gt;There can be multiple changes at the DNA level generation after generation, however most of these changes are insignificant (doesn't contribute for any specific character). But rarely, there can be a significant trait/change gained by an individual because of such changes in DNA level. Unfortunately such changes gets 'lost', unless it is fixed in the population (i.e., the gained individual should be successful in breeding and passing the trait/change to large number of progenies. Those progenies should further continue to pass on the trait till about every one (or most of them) in the population has those trait/change). Only such changes contribute for the species development (continuous accumulation of such changes, over time will result in the novel population that is very different from the original population). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the timelines that we know are reconstructed from the DNA/protein sequences. Usually, DNA or protein sequences from the closely related species will be compared and looking at the differences they have, using suitable models, ancestral state of those sequences are determined. Once the sequence for the last common ancestor is known, mutational rate per unit time can be used to estimate the evolutionary time for those species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A simple example would be the blue eye color in humans: it occurred about 10,000 years ago and it is still not fixed in the population.&lt;/p&gt;&#xA;" OwnerUserId="1648" LastEditorUserId="1648" LastEditDate="2012-11-12T21:41:15.920" LastActivityDate="2012-11-12T21:41:15.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5221" PostTypeId="2" ParentId="5130" CreationDate="2012-11-12T20:19:58.283" Score="7" Body="&lt;p&gt;&quot;Seeing stars&quot;, or as it formally is called, &quot;phosphene&quot;, is caused by stimulation of the visual cortex or retina by causes other than light hitting the retina.&#xA;&lt;a href=&quot;http://www.oubliette.org.uk/Three.html&quot; rel=&quot;nofollow&quot;&gt;http://www.oubliette.org.uk/Three.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1585" LastEditorUserId="960" LastEditDate="2014-11-19T18:43:31.967" LastActivityDate="2014-11-19T18:43:31.967" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5222" PostTypeId="1" AcceptedAnswerId="5223" CreationDate="2012-11-13T00:27:54.723" Score="4" ViewCount="873" Body="&lt;p&gt;I've been reading about homeostatic nature of a lot of neurobiological processes - &lt;strong&gt;the brain is trying to maintain a balance&lt;/strong&gt; by desensitizing receptors, re-uptaking and breaking down neurotransmitters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With this in mind, I'm interested in what happens to the receptors in the brain with chronic use of caffeinated beverages.  Let's say an occasional caffeine drinker likes the cognitive boost of caffeine and starts to consume it habitually/chronically - every day. &lt;strong&gt;Will the caffeine drinker experience the same effects day after day, or will the effect change over time?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is a change in how the body responds to caffeine, are there any time frames that can be used to estimate when the change takes place - is it X days/weeks of habitual use?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-11-14T23:05:37.107" Title="Do effects of caffeine on human body change with habitual use?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5223" PostTypeId="2" ParentId="5222" CreationDate="2012-11-13T05:49:54.123" Score="5" Body="&lt;p&gt;I don't have any references off hand (though if you like, I will find them). The body acclimates to caffeine intake, becoming desensitized to chronic caffeine use, analogous to chronic narcotic use. Habitual coffee drinkers, soda drinkers, and so forth must achieve the same level of daily caffeine intake to maintain a normal state of being. Taking in less caffeine leads to withdrawal symptoms, and taking in more caffeine leads to the familiar stimulatory effects. As for time frame of addiction, this likely varies, but I hazard a guess it's on the order of a few days to a week. Fortunately, caffeine is not nearly as strong and addictive as narcotics, however it is the most widespread.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: Caffeine exerts high-affinity and low-specificity for adenosine receptors. This was a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11283304&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt; article I fould that may help you out. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11283304&quot; rel=&quot;nofollow&quot;&gt;Dunwiddie TV, Masino SA. The role and regulation of adenosine in the central nervous system. Annu Rev Neurosci. 2001;24:31-55.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2012-11-14T23:05:37.107" LastActivityDate="2012-11-14T23:05:37.107" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5224" PostTypeId="1" CreationDate="2012-11-13T13:36:19.533" Score="6" ViewCount="3286" Body="&lt;p&gt;I've noticed that in mammalian cell culture, there are often two types of DMEM available. High Glucose and Low Glucose. Does it matter which type I use for culturing of cells (e.g. Hela or HEK293)? Which is the type people normally use?&lt;/p&gt;&#xA;" OwnerUserId="1656" LastActivityDate="2017-03-21T22:45:15.180" Title="High Glucose vs Low Glucose DMEM for Cell Culture" Tags="&lt;molecular-biology&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5225" PostTypeId="2" ParentId="5217" CreationDate="2012-11-13T13:43:23.077" Score="3" Body="&lt;p&gt;The explanation I heard from the documentary called &quot;Curiosity: World's Dirtiest Man&quot; is that armpit hairs allows for the growth of microbes which allow for the production of smell. This smell is useful for the attraction of mates in primates (although this function is probably lost in humans as our society became more hygienic).&lt;/p&gt;&#xA;" OwnerUserId="1656" LastActivityDate="2012-11-13T13:43:23.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5226" PostTypeId="2" ParentId="2684" CreationDate="2012-11-13T13:57:50.483" Score="1" Body="&lt;p&gt;There is a phenomenon known as genomic imprinting where the allele of the gene would only get expressed if it is passed on from the father (e.g. IGF2). This means that although the same genes get passed on from both your father and mother, only the copy from your father will get expressed. Thus, although you get 50% of your DNA from your parent (and probablistically speaking 25% from your grandparent), the same gene can be deferentially expressed depending who you get them from).&lt;/p&gt;&#xA;" OwnerUserId="1656" LastActivityDate="2012-11-13T13:57:50.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5227" PostTypeId="2" ParentId="3564" CreationDate="2012-11-13T14:08:14.540" Score="1" Body="&lt;p&gt;Answering Konrad's comment, you produce the peptide or protein of interest using bacteria or chemically synthesize them (chemical synthesis generally only work for short peptide chains. After which, you get a lot of side products). This peptide or protein of your interest serves as your antigen. You inject this antigen into mouse or rabbit. The animal's immune system will naturally mount an immune response to produce antibodies against it. The B cells which are responsible for producing those antibodies can then be harvested. After which, you basically follow the protocol Matt stated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could, of course, also choose to just directly isolate the serum of the animal and purify it. However, this leads to the production of polyclonal antibodies which can be less specific than a monoclonal antibody.&lt;/p&gt;&#xA;" OwnerUserId="1656" LastEditorUserId="5239" LastEditDate="2013-12-28T00:58:14.997" LastActivityDate="2013-12-28T00:58:14.997" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5228" PostTypeId="2" ParentId="5219" CreationDate="2012-11-13T16:22:50.803" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Blount ZD, Barrick JE, Davidson CJ, Lenski RE. (2012) Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489:513-8. doi: 10.1038/nature11514&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Richard Lenski is conducting an experiment called the long-term evolution experiment (LTEE) in which twelve populations of &lt;em&gt;E. coli&lt;/em&gt; are grown in a glucose-limited minimal medium. This experiment has now been running for over 40,000 generations (&gt;20 years). If we take a human generation as being 25 years, this is equivalent to one million years of &lt;em&gt;Homo&lt;/em&gt; evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the diagnostic traits of the species &lt;em&gt;E. coli&lt;/em&gt; is the inability to grow aerobically on citrate. The medium that is used in the LTEE does however contain citrate as a chelating agent (probably to solubilise ferric ions, although I haven't been able to confirm this). The Lenski group have recently reported on the appearance of a novel citrate-utilising mutant in one of the populations. The Cit&lt;sup&gt;+&lt;/sup&gt; variant appeared at around 31000 generations, and became dominant after 33000 generations. Because the LTEE involves storing samples of each population every 500 generations it has been possible to analyse in detail the emergence of this new phenotypic trait, and indeed to replay it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The process that they describe has three phases:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Potentiation. This stage involved the appearance of mutations that were a necessary prerequisite for subsequent events. In this case it is thought that there were at least two potentiating mutations. These are as yet unidentified but their existence is inferred from replay experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Actualization. This is the emergence of the new trait, and in this case is the event that took place at 31,000 generations. This involved a tandem duplication event at the &lt;em&gt;citT&lt;/em&gt; locus, bringing &lt;em&gt;citT&lt;/em&gt; under control of a new promoter, belonging to the &lt;em&gt;rnk&lt;/em&gt; gene. The citT protein is a citrate transporter that is only expressed under anaerobic conditions in wild-type &lt;em&gt;E. coli&lt;/em&gt;. The gene duplication event led to the expression of the transporter under standard aerobic conditions, opening up the possibility of taking up citrate and metabolising it. Replay experiments indicate that this event originally conferred a very weak Cit&lt;sup&gt;+&lt;/sup&gt; phenotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Refinement. This involves changes that strengthen the Cit&lt;sup&gt;+&lt;/sup&gt; phenotype. In this case these seem to have been further gene duplications of the &lt;em&gt;rnk-citT&lt;/em&gt; module (with up to eight copies in one replay experiment). This eventually stabilised with the presence of four copies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This may be the nearest that we can hope to get to defining a timeline of evolution of a new characteristic.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-11-13T17:14:39.700" LastActivityDate="2012-11-13T17:14:39.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5231" PostTypeId="2" ParentId="2440" CreationDate="2012-11-13T21:27:46.377" Score="-2" Body="&lt;p&gt;The only reason why caffeine helps with migraine pain is because the pain is caused by expanded blood vessels and caffeine's effect is to narrow the blood vessels. &#xA;But how it helps with other types of pain I really  can't imagine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And it depends what you state as &quot;full dose&quot;. The dose that can harm your liver for adults is 4g per day, so if you have Paracetamol 500mg you would have to take 8 pills  to reach it. Would you possibly do it? If seeing pain doesn't go away after first pill .. ok, second one?&lt;/p&gt;&#xA;" OwnerUserId="1659" LastEditorUserId="1306" LastEditDate="2012-11-14T12:43:52.080" LastActivityDate="2012-11-14T12:43:52.080" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5233" PostTypeId="2" ParentId="1058" CreationDate="2012-11-13T22:43:34.803" Score="2" Body="&lt;p&gt;&lt;strong&gt;Why would it evolve?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No research (that I can find) is consistent with specific time of day mating across many species. I can't think of any reason why even just a few quite different mammals (e.g. mice, bats, lions, whales, and humans) would all find a fitness benefit of mating at the same specific time of day and therefore it is highly unlikely to evolve. I would suggest that if there are consistent patterns they are no reason other than coincidence (correlation over causality). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;For example, dawn and dusk peaks in activity...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have no references to back this idea up but lets see how this goes. The majority of mammals will be awake around dawn and dusk because there is likely an over lap between nocturnal and diurnal species at these times. Given that mating (normally) requires the participants to be awake then this would be a time when more animals are awake it is therefore a more likely time for mating to occur. But, as I already mentioned it would purely be because of the increased numbers awake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Simple statistical illustration of the dawn &amp;amp; dusk idea...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine a raffle with 2000 winning tickets. You buy 1000 and put 500 hundred of these in a box called nocturnal and the other 500 go in a box called diurnal. The raffle is drawn 24 times (perhaps every hour). The first 14 times it is drawn you can win if the ticket is from the nocturnal box, the latter 14 times you can instead check the diurnal box. This means during the first 10 draws you have a 25% chance of winning, and likewise in the latter 10 hours, but in the middle 4 hours there is a 50% chance every draw. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This comes down to a simple statistical phenomenon, &lt;em&gt;if you don't buy a ticket you can't win the raffle.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2012-11-13T22:43:34.803" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5234" PostTypeId="1" AcceptedAnswerId="5239" CreationDate="2012-11-14T16:53:48.923" Score="6" ViewCount="152" Body="&lt;p&gt;I am fusing a protein with a Dam enzyme (&lt;a href=&quot;http://en.wikipedia.org/wiki/Dam_%28methylase%29&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Dam_(methylase)&lt;/a&gt;).  The idea is that when the protein binds to the DNA, the Dam enzyme will start methylating nearby GATC sites, thus helping identify the protein binding region (using DpnI later on, and microarray technology).  However, I have no idea, in theory, how many (bps) will the enzyme traverse across the genome from its starting location.  I.e., how far (in terms of bp) from its starting location will the enzyme methylate the GATC sites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are methods for finding protein binding regions along the genome that use such technology, such example here: &lt;a href=&quot;http://www.nature.com/nbt/journal/v18/n4/abs/nbt0400_424.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nbt/journal/v18/n4/abs/nbt0400_424.html&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="1661" LastEditorUserId="1122" LastEditDate="2012-11-15T07:19:16.077" LastActivityDate="2012-11-15T10:06:20.710" Title="DAM enzyme distances move along the genome" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5235" PostTypeId="1" AcceptedAnswerId="5296" CreationDate="2012-11-14T21:47:14.377" Score="8" ViewCount="291" Body="&lt;p&gt;I've been looking around and cannot find a definite answer on what it is that tells trees to change their metabolism and drop leaves. I see that such activity is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Deciduous&quot; rel=&quot;nofollow&quot;&gt;Deciduous&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What interests me &lt;strong&gt;are the specific mechanisms by which a tree knows that it's time to drop leaves&lt;/strong&gt;. Is it photoperiod shortening (day duration?) Is it temperature changing metabolism? Is it build up of some toxic compound?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="3952" LastEditDate="2013-08-10T01:53:12.490" LastActivityDate="2013-08-10T01:53:12.490" Title="What mechanisms tell temperate trees when to drop leaves?" Tags="&lt;botany&gt;&lt;metabolism&gt;&lt;phenology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5236" PostTypeId="2" ParentId="5234" CreationDate="2012-11-14T22:56:41.913" Score="3" Body="&lt;p&gt;After re-reading your question, I suspect you are conflating DNA methylation and restriction digestion. For a more detailed overview of how these two relate to each other, please read the &lt;a href=&quot;http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/dam_dcm_cpg_methylation.asp#.UKQcV5swYYo&quot; rel=&quot;nofollow&quot;&gt;summary page&lt;/a&gt; at New England Biolab's website.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The crystal structures of common restriction enzymes do not suggest that they scan along the double-stranded DNA looking for a recognition site. Their reaction kinetics can be thought of as being a more random interaction, whereupon the enzyme comes into contact with a recognition site, then cleaves the DNA is and free to float around until the next reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA methylation comes in three common flavours: Dam (DNA adenine methylation), Dcm (DNA cytosine methylation) and CpG methylation. The addition of any of these methyl groups changes can interfere with enzyme recognition of the site. Many enzymes are partially or completely blocked by at least one kind of methylation, while other are completely uninhibited. This is due to the shape of the enzyme and of the DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now here is where I think you are conflating the two. &lt;a href=&quot;http://rebase.neb.com/rebase/&quot; rel=&quot;nofollow&quot;&gt;REbase&lt;/a&gt; (Restriction Enzyme database) is indeed the authoritative list on restriction enzyme. You mention Dam cuts at GATC. The sequence GATC is the canonical adenine &lt;em&gt;methylation&lt;/em&gt; (Dam) site. As you pointed out, no known restriction enzyme contains Dam. If we instead look up the recognition site, GATC will match with DpnI, a restriction enzyme that produced blunt ends. I think it is DpnI that you are speaking of, which preferentially cleaves Dam methylated DNA (hence why the recognition site GATC also matches Dam mythyltransferases). If the absense of methylated DNA (or if non-methylated DNA is more abundant), DpnI will also digest at GATC sites.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2012-11-15T01:50:57.400" LastActivityDate="2012-11-15T01:50:57.400" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5237" PostTypeId="1" AcceptedAnswerId="5240" CreationDate="2012-11-15T01:39:53.263" Score="17" ViewCount="2954" Body="&lt;p&gt;I suppose another way of looking at the question is: how important is gravity for the development of mammal fetuses?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if things would go wrong, what sort of things would they be, and what would be the result?&lt;/p&gt;&#xA;" OwnerUserId="1289" LastEditorUserId="1289" LastEditDate="2012-11-15T07:10:57.087" LastActivityDate="2016-06-16T06:16:34.607" Title="Could a fetus properly develop in micro/zero-gravity?" Tags="&lt;embryology&gt;&lt;development&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5239" PostTypeId="2" ParentId="5234" CreationDate="2012-11-15T10:06:20.710" Score="6" Body="&lt;p&gt;&lt;strong&gt;Dam methyltransferase methylates large DNA molecules in a processive manner, with an effective range of up to 7 kb on either side of an initial methylation reaction.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My answer is taken from this paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Urig, S. &lt;em&gt;et al&lt;/em&gt;. (2002) The &lt;em&gt;Escherichia coli&lt;/em&gt; Dam DNA Methyltransferase Modifies DNA in a Highly Processive Reaction J Mol Biol 319 1085-1096&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors report on a kinetic analysis of &lt;em&gt;E. coli&lt;/em&gt; dam methylase. For anyone using this system as described by the OP, this paper is essential reading. Their conclusion is that the methylation process is highly processive, which is to say that a single dam-DNA interaction leads to multiple methylations before the enzyme dissociates from the DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll restrict myself to describing just two of their experiments:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Figure 5&lt;/strong&gt;&#xA;In this experiment they analysed the time course of methylation of an end-labelled 879-mer with 4 GATC sites, using DpnI digestion to detect methylation. In this experiment all DNA was found to be either fully methylated or unmethylated - no evidence for the presence of partially methylated DNA molecules was detected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Figure 6&lt;/strong&gt;&#xA;In this experiment they analysed the methylation of &amp;lambda; DNA (48.5 kb) and were able to detect partially methylated molecules. A kinetic analysis of the data results in the following conclusions (MTase; methyltransferase):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;From these simulations, we [determine] a processivity of n&lt;sub&gt;av&lt;/sub&gt;=3000. This means that after binding to the λ-DNA and starting the one-dimensional diffusion process, one MTase on average meets 3000 dam sites before it dissociates from the DNA. Since the enzyme performs a random walk, it will hit many sites more often than only once and the effective range of processivity corresponds to the square root of n&lt;sub&gt;av&lt;/sub&gt;. Therefore, the dam MTase is able to methylate approximately 55 GATC sites on λ-DNA in a processive reaction in vitro. In this simulation, 4.6 associations of an MTase molecule to the same molecule of λ-DNA are required to obtain fully methylated DNA. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In a random DNA sequence GATC should occur on average every 4&lt;sup&gt;4&lt;/sup&gt; = 256 residues. This suggests an approximate range of (55/2)*256 = 7 kb on each side of an initial methylation reaction.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-15T10:06:20.710" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5240" PostTypeId="2" ParentId="5237" CreationDate="2012-11-15T12:00:37.433" Score="25" Body="&lt;p&gt;There is some evidence that fetal development under zero gravity conditions might be problematic.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Wakayama S, Kawahara Y, Li C, Yamagata K, Yuge L, et al. (2009) Detrimental Effects of Microgravity on Mouse Preimplantation Development In Vitro. &lt;em&gt;PLoS ONE 4&lt;/em&gt;(8): e6753. doi:10.1371/journal.pone.0006753&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The paper is &lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006753&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These authors studied aspects of reproduction of mice in a clinostat under 10&lt;sup&gt;-3&lt;/sup&gt;G. They found that fertilisation was unaffected, but that preimplantation development of the embryo was affected by the mG environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The introduction to the paper gives a good brief review of this area of research. Perhaps of particular relevance is this section:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the STS-80 space shuttle mission, mouse 2-cell embryos were collected on the ground, launched into space and cultured for four days in µG. The control embryos on Earth developed to normal blastocysts, but in the space flight group, none of the embryos showed any sign of development, and all degenerated (Schenker &amp;amp; Forkheim, 1998) . A more reliable experiment was done on the Cosmos 1129 mission in 1979, when mature male and female rats were sent into orbit and then allowed to intermingle in a common breeding chamber (Serova &amp;amp; Denisova, 1982). However, none of the females gave birth, although postflight examinations revealed that ovulation had occurred. Two of the females were reported to have achieved pregnancy, but the embryos appear to have been resorbed. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Schenker E, Forkheim K (1998) Mammalian mice embryo early development in weightlessness environment on STS 80 space flight. &lt;em&gt;Israel Aerospace Medicine Institute Report&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Serova LV, Denisova LA (1982) The effect of weightlessness on the reproductive function of mammals. &lt;em&gt;Physiologist 25&lt;/em&gt;: S9–12.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="24505" LastEditDate="2016-06-16T06:16:34.607" LastActivityDate="2016-06-16T06:16:34.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5241" PostTypeId="1" CreationDate="2012-11-15T17:11:47.517" Score="5" ViewCount="429" Body="&lt;p&gt;What is the mechanism of insulin stimulation in the human body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is leptin release stimulated by circulating insulin directly? Which other factors are involved in the level of insulin release? My goal is to identify nutrients that aid/trigger leptin production and release without causing undue inflammation or body-fat storage.&lt;/p&gt;&#xA;" OwnerUserId="1664" LastEditorUserId="1122" LastEditDate="2012-11-15T17:37:58.513" LastActivityDate="2012-11-26T16:40:04.997" Title="Is Leptin Stimulated by Insulin Alone?" Tags="&lt;endocrinology&gt;" AnswerCount="3" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="5242" PostTypeId="2" ParentId="5241" CreationDate="2012-11-15T17:51:28.043" Score="1" Body="&lt;p&gt;Leptin may not be as important as we think. A review in 2001 concludes:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Conversely, it is unlikely that leptin has evolved to prevent obesity&#xA;  when plenty of palatable foods are available because the elevated&#xA;  plasma leptin levels resulting from the increased adipose tissue mass&#xA;  do not prevent the development of obesity. In conclusion, in humans,&#xA;  the leptin signaling system appears to be mainly involved in&#xA;  maintenance of adequate energy stores for survival during periods of&#xA;  energy deficit. Its role in the etiology of human obesity is only&#xA;  demonstrated in the very rare situations of absence of the leptin&#xA;  signal (mutations of the leptin gene or of the leptin receptor gene),&#xA;  which produces an internal perception of starvation and results in a&#xA;  chronic stimulation of excessive food intake.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, in a newer review it looks as if leptin is involved in more processes than mere survival:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cloned in 1994, the ob gene encodes the protein hormone leptin, which&#xA;  is produced and secreted by white adipose tissue. Since its discovery,&#xA;  leptin has been found to have profound effects on behavior, metabolic&#xA;  rate, endocrine axes, and glucose fluxes. Leptin deficiency in mice&#xA;  and humans causes morbid obesity, diabetes, and various neuroendocrine&#xA;  anomalies, and replacement leads to decreased food intake, normalized&#xA;  glucose homeostasis, and increased energy expenditure. Here, we&#xA;  provide an update on the most current understanding of&#xA;  leptin-sensitive neural pathways in terms of both anatomical&#xA;  organization and physiological roles.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Jéquier, Eric. &quot;Leptin signaling, adiposity, and energy balance.&quot; Annals of the New York Academy of Sciences 967.1 (2002): 379-388.&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12079865&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/12079865&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gautron, Laurent, et al. &quot;Sixteen years and counting: an update on leptin in energy balance.&quot; The Journal of clinical investigation 121.6 (2011): 2087. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21633176/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21633176/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1122" LastEditorUserId="1122" LastEditDate="2012-11-15T18:12:46.637" LastActivityDate="2012-11-15T18:12:46.637" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5243" PostTypeId="2" ParentId="5217" CreationDate="2012-11-16T06:12:02.520" Score="9" Body="&lt;p&gt;It's not proper to think of evolution in teleological (purpose-driven) terms--armpit hair is probably a trait that was never eliminated because it is not harmful to the species, rather than a useful trait that was specifically &quot;selected for&quot;. &lt;/p&gt;&#xA;" OwnerUserId="1660" LastActivityDate="2012-11-16T06:12:02.520" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="5244" PostTypeId="1" AcceptedAnswerId="5246" CreationDate="2012-11-16T14:48:09.367" Score="2" ViewCount="221" Body="&lt;p&gt;I've read that there are several SNPs associated with increased risk of clinical or morbid obesity. I was wondering if there is any evidence that these are under positive selection. Would you expect them to be so? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess I'm interested to know if they would previously offered a selective advantage and only recently, say in the post-war period in the West morbid obesity become a problem due to differences in the diet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Related question:&#xA;&lt;a href=&quot;https://biology.stackexchange.com/questions/2179/obesity-risk-and-single-gene-polymorphisms&quot;&gt;How many, and how severe, are known single gene polymorphisms for obesity?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="476" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-07-30T15:22:57.173" Title="Are genes associated with obesity selected for?" Tags="&lt;evolution&gt;&lt;snp&gt;&lt;selection&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5245" PostTypeId="2" ParentId="5224" CreationDate="2012-11-16T20:37:06.990" Score="2" Body="&lt;p&gt;We typically use High Glucose as cells grow faster.  One caveat is that there are concerns that certain protein modifications (specifically OGlnAc-ylation) may be upregulated in non-physiological (25mM or high glucose) media.&lt;/p&gt;&#xA;" OwnerUserId="235" LastActivityDate="2012-11-16T20:37:06.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5246" PostTypeId="2" ParentId="5244" CreationDate="2012-11-16T21:00:56.577" Score="4" Body="&lt;p&gt;This is called the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Thrifty_gene_hypothesis&quot; rel=&quot;nofollow&quot;&gt;Thrifty Gene Hypothesis&lt;/a&gt;&quot; which was first used to explain why diabetes is so common. Basically it suggests that these alleles would have provided some kind of advantage, over the other possible alleles at that loci, until the environment changed. Then the environment changed and the allele became harmful. Environments are always changing and therefore favour different alleles (variant of a loci). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suggest the genes linked to obesity in the modern world would, if tested on the old world populations would have been linked to being of a healthy weight. Further, those without it may have been skinnier and more likely to suffer from the disadvantages of being in such condition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, &lt;a href=&quot;http://www.nature.com/ijo/journal/v32/n11/full/ijo2008161a.html&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; present some counter arguments to the thrifty gene hypothesis. Speakman suggests that the genes responsible spread via &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_drift&quot; rel=&quot;nofollow&quot;&gt;genetic (allelic) drift&lt;/a&gt; rather than by positive selection. It is worth remembering that drift is very poor at spreading new mutations through large populations so there are also weaknesses to his arguments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2011.02271.x/full&quot; rel=&quot;nofollow&quot;&gt;One example&lt;/a&gt; of a change in the favoured allele caused by an environmental shift is the DDT resistance gene in &lt;em&gt;Drosophila&lt;/em&gt; which was present in the population at very low levels for a long period of time. As an aside, it possibly remained this way because it was subject to sexually antagonistic selection - beneficial to females whilst detrimental to males. It then spread through the population when DDT pesticides were used because it obviously became highly beneficial.  Many other examples of environmental change leading to different selection are around, this is just one off the top of my head. Another is the &lt;a href=&quot;http://www.truthinscience.org.uk/tis2/index.php/component/content/article/53.html&quot; rel=&quot;nofollow&quot;&gt;Galapagos Finches in a drought in the late 20th century&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;HTH, if not please ask more and if it does then please accept it!&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2012-11-16T21:11:36.643" LastActivityDate="2012-11-16T21:11:36.643" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5247" PostTypeId="2" ParentId="5217" CreationDate="2012-11-17T08:31:22.717" Score="21" Body="&lt;p&gt;I have been trying to read up a bit on this. I started out looking on &lt;a href=&quot;http://en.wikipedia.org/wiki/Underarm_hair&quot;&gt;wikipedia&lt;/a&gt; and it seems there are three hypotheses which are not necessarily mutually exclusive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1.Aid the wicking of sweat away from the skin  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2.Reduce friction between the thorax and upper arm  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3.Facilitate the release of sex pheromones&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first would seem possible because it would help to prevent &lt;a href=&quot;http://www.medical-hypotheses.com/article/S0306-9877%2806%2900208-8/abstract&quot;&gt;over-heating of the lymph node&lt;/a&gt;s under the armpits and that also fits with the fact there are a lot of sweat glands there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second, I can't find any citations which support this but I understand that people who shave their armpits tend to suffer from dry underarms. This could be a result of increased friction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The third is apparently controversial although it seems perfectly reasonable and highly likely to me. There is &lt;a href=&quot;http://www.drjoebio.com/uploads/1/8/1/3/1813500/mhc_mate_preference_smell_t_shirts.pdf&quot;&gt;a famous experiment&lt;/a&gt; by Claus Wedekind who got men to wear a t-shirt for a few days. He then got women to choose a most preferred male purely by the scent of the t-shirt and found interesting results relating to the MHC profiles. The armpit hair could help to trap the odour produced by the sweat and help with mate attraction, like some kind of scent sponge. I don't understand why this is so controversial, loads of animals influence mate choice with scent - perhaps people don't like to think we are genetically attracted to each other by sweat because it seems animalistic and less romantic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, there is no sure answer and it could well be all of the above, or something entirely different.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2012-11-19T11:30:05.033" LastActivityDate="2012-11-19T11:30:05.033" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5248" PostTypeId="1" CreationDate="2012-11-17T13:30:38.947" Score="2" ViewCount="133" Body="&lt;p&gt;&lt;em&gt;Deinococcus radiodurans&lt;/em&gt; is an amazing bacterium with a fantastic survival rate. It can survive to high doses of radiation, in a complete vacuum and in hydrochloric acid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this bacterium manage to restore damaged chromosome?&#xA;It is polyploid with 4 to 10 copies of the genome which are packed in a highly ordered manner.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this imply that creating multiple copies of the genome or inceasing DNA base repair activity would increase life span?&#xA;Is that even conceivable on bigger life forms?&lt;/p&gt;&#xA;" OwnerUserId="1666" LastEditorUserId="115" LastEditDate="2012-11-18T09:22:14.320" LastActivityDate="2012-11-18T09:22:14.320" Title="Have there been any experiments that duplicate chromosome copies from 23*2 to 23*3 or 23*4?" Tags="&lt;genetics&gt;&lt;bacteriology&gt;&lt;human-genetics&gt;&lt;chromosome&gt;&lt;life&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5249" PostTypeId="1" AcceptedAnswerId="5250" CreationDate="2012-11-17T14:59:54.653" Score="7" ViewCount="122" Body="&lt;p&gt;In the normal function of the kidney, the bloodstream is near emptied of fluids as it moves through the glomerulus, in which glomerular filtrate is formed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As it proceeds through the Nephron, a significant amount of this material is returned to the bloodstream, and only a comparatively timy amount goes into the urine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why, in evoultionary terms, is it not more favourable energetically to remove only the small number of molecules, perhaph using specialised channels made of protein and activated only by a certain molecules which need removing, at a potentially huge energy saving?&lt;/p&gt;&#xA;" OwnerUserId="1474" LastActivityDate="2012-11-18T17:08:34.123" Title="What is the benefit of near-emptying the bloodstream in the mammalian kidney?" Tags="&lt;human-anatomy&gt;&lt;renal-physiology&gt;&lt;kidney&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5250" PostTypeId="2" ParentId="5249" CreationDate="2012-11-17T16:32:38.650" Score="9" Body="&lt;p&gt;Probably because it's easier to retain what the body &lt;em&gt;wants&lt;/em&gt; than get rid of what the body &lt;em&gt;doesn't want&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does your body want to &lt;strong&gt;keep&lt;/strong&gt; from your Urine? Pretty much water and selective ions (Cl-, K+, Na+, Ca+2, etc.). Maybe a few other things, depending on how healthy you are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, what does your body want to get &lt;em&gt;rid of&lt;/em&gt; in your Urine? Well, anything it can't get rid of in your solid waste. That includes pretty much anything water soluble that could harm you, whether it's Urea, chelating agents for heavy metals, ions your body doesn't want (excess minerals), excess vitamins, sugars (to maintain insulin levels), hormones, liver byproducts, and whatever dark horrors mother nature is concocting for us in the forms of virii or whatever else.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's just the beginning of the list, but already you should start to see the impracticality of having active transport or coupled transport for everything. The list of transmembrane proteins needed to ferry &lt;em&gt;all&lt;/em&gt; of the items your body wants to get rid of is &lt;strong&gt;a lot&lt;/strong&gt; longer than the list of transmembrane proteins needed to keep what the body needs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then you have the &quot;unknowns&quot; - whatever else your body hasn't encountered yet, but will still be water-soluble. If the body required some sort of transport across membranes for everything it &lt;em&gt;didn't&lt;/em&gt; want, then it would need to adapt to every single new compound it encounters. Given the relatively slow generation periods for humans, if a new compound turned out to be significantly fatal then the slow adaptation could spell disaster for any small populations and create serial bottlenecking events.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, while it may not be energetically favorable to let water and ions pass into the Nephron and subsequent tubules to be reclaimed, Evolutionarily speaking it's probably strongly selected for. We may expend a lot of energy reclaiming water against its concentration gradient, along with whatever else we want from Urine, but at the same time we get rid of everything else we don't &lt;em&gt;need&lt;/em&gt; that's filtered through the glomerulus. It doesn't matter what the &quot;everything else&quot; is - but we know we don't need it, and that's the big key.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With my current level of knowledge (B.S. - Biology) this is the best explanation I could think of, but I haven't read any specific papers nor heard any particular theories on why the kidney's components act as they do.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-11-17T16:32:38.650" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5251" PostTypeId="2" ParentId="5210" CreationDate="2012-11-17T16:40:39.247" Score="3" Body="&lt;p&gt;I spent a couple of years working in a diabetes research institute.  And you did hear right. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cats dogs monkeys all can be susceptible to diabetes, although rats and mice don't seem to have diabetes that behaves the same way as humans - I don't think a mouse has ever been observed to get diabetes without specific gene knockouts.  One could argue that mice simply do not get diabetes the way people do. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two causes of type 2 diabetes in the research world.  The first happens because the animal may have a genetic susceptibility and environmental conditions induce the disease (like most people).  The second happens because of mutations in one specific gene or another pretty much cause it to happen when the animal gets to a mature age (google term: mature onset diabetes in the young (MODY)).  MODY genes have not proven to be a great model for type 2 diabetes treatment in most people (&lt;a href=&quot;http://en.wikipedia.org/wiki/Maturity_onset_diabetes_of_the_young&quot; rel=&quot;nofollow&quot;&gt;about 1% of diabetics have a MODY diabetes though&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cats and dogs have been animals of interest as models of diabetes because their symptoms are human like and have shorter reproductive cycles.  &lt;a href=&quot;http://jn.nutrition.org/content/134/8/2072S.long&quot; rel=&quot;nofollow&quot;&gt;Some cats (like Burmese) clearly have a greater genetic predisposition to diabetes&lt;/a&gt;, but cats who are obese, have high glycemic diets, or who get little or no physical activity are more likely to develop diabetes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As with humans, the condition leads to the insulin secreting cells of of the pancreas to slowly degrade and if these cells are gone, there is no recovery from type 2 diabetes. All this given its likely that cats get diabetes that is similar to the human condition. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In treating cats its been shown that &lt;a href=&quot;http://www.vin.com/proceedings/Proceedings.plx?CID=WSAVA2002&amp;amp;Category=163&amp;amp;PID=812&amp;amp;O=Generic&quot; rel=&quot;nofollow&quot;&gt;such diabetes can be reversed&lt;/a&gt;.  The most important thing to do - common to all treatments - is to change the cat's diet - restrict calories if the cat is obese and change high glycemic food.  Additionally, insulin or drug treatments that reduce insulin resistance (such as are given to humans) can restart the islet cells that secrete insulin if the animal is lucky and don't always have to be lifetime prescriptions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reference I have does not give remission statistics, but it must work a reasonable amount of the time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I wouldn't want to leave you with the impression that cats are special.  It turns out that human diabetes type 2 is often reversible.  &lt;a href=&quot;http://www.diabetologia-journal.org/Lim.pdf&quot; rel=&quot;nofollow&quot;&gt;This reference&lt;/a&gt; estimates 80% of the time. This study mostly focuses on the same treatments - change of diet and some fasting, but no exercise regimin as the cats. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's probably nothing magical about cat diabetes 2... ;)&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-11-17T16:40:39.247" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5252" PostTypeId="1" CreationDate="2012-11-17T16:47:18.117" Score="3" ViewCount="1605" Body="&lt;p&gt;After using a binocular microscope recently for about 20 minutes, my vision went blurry and for an hour or so it was much harder to read small text. This occurs to a (far) lesser extent whenever I use it for a shorter time.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why does this occur?&lt;/li&gt;&#xA;&lt;li&gt;Which is the optimal microscope light intensity so this does not happen?&lt;/li&gt;&#xA;&lt;li&gt;What other variables should I beware of?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1667" LastEditorUserId="69" LastEditDate="2012-11-17T23:03:33.523" LastActivityDate="2012-11-17T23:03:33.523" Title="Why does vision go blurry after microscope use, and how to prevent it?" Tags="&lt;vision&gt;&lt;microscopy&gt;" AnswerCount="0" CommentCount="6" ClosedDate="2014-08-08T04:18:33.363" ContentLicense="CC BY-SA 3.0" />
  <row Id="5253" PostTypeId="2" ParentId="5248" CreationDate="2012-11-17T19:26:36.367" Score="1" Body="&lt;p&gt;&lt;strong&gt;It's an idea that doesn't hold much promise.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Individuals who show diploid/tetraploid mosaicism present &amp;quot;failure to thrive and multiple minor anomalies.&amp;quot; according to:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Alonso L et al (2002) Tetraploid/diploid mosaicism: case report and review of the literature. Annales de Genetique 45 177-180&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;On the other hand, complete tetraploidy is apparently lethal:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Nakamura, Y. et al. (2003) A Tetraploid Liveborn Neonate: Cytogenetic and Autopsy Findings. Archives of Pathology &amp;amp; Laboratory Medicine 127:1612-1614.&lt;/p&gt;&#xA;&lt;p&gt;Abstract&lt;/p&gt;&#xA;&lt;p&gt;Cytogenetic and autopsy findings of a nonmosaic tetraploid male neonate, alive until shortly after birth at 37 weeks' gestation, are described. Oligohydramnios, intrauterine growth retardation, cranial abnormalities, and Dandy-Walker malformation were noted prenatally. Autopsy findings included cleft lip and palate; overlapping fingers; low-set ears; simian creases; hypoplastic external genitalia with undescended testes; Dandy-Walker malformation; slightly dilated lateral and third ventricles; hypoplasia of the cerebrum, pons, medulla, pituitary gland, thymus, lung, adrenal gland, and kidney; large ventricular septal defect; and enteric cyst behind the urinary bladder. The placenta was hypoplastic and showed no remarkable abnormalities, except for mild syncytial knots. Chromosome analyses of amniotic fluid cells at 31 weeks' gestation and the umbilical cord blood cells at delivery revealed a 92,XXYY karyotype. G-, C-, Q-, and N-banding heteromorphic studies demonstrated duplication of paternal chromosomes 1, 3, and 15, and maternal chromosome 22. In addition, the results of an analysis with 16 CA repeat polymorphic markers were consistent with duplicated inheritance of 1 paternal and 1 maternal haploid sets to the tetraploid patient. Therefore, it is most likely that the tetraploidy was caused by a cytoplasmic cleavage failure at the first mitotic division.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;full text available &lt;a href=&quot;http://www.archivesofpathology.org/doi/pdf/10.1043/1543-2165%282003%29127%3C1612:ATLNCA%3E2.0.CO;2&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-11-17T19:55:02.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5254" PostTypeId="2" ParentId="5249" CreationDate="2012-11-18T17:08:34.123" Score="3" Body="&lt;p&gt;I would argue from an evolutionary perspective: not all kidneys are created equal. The mammalian kidney has a long evolutionary history and potentially a lot of phylogenetic inertia. Mammals do what they can with what they inherited from their ancestors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The metanephric kidney, which is what mammals have, is thought to have evolved with the first amniotes (terrestrial, cleidoic-egg-laying tetrapods). However, the metanephros, from when the definitive metanephric kidney evolved, was (is) present in most fishes as well as amphibians. These groups live all or part of their lives in fresh water, so their tissues are hyperosmotic relative to the water. Their problem is not retaining water, but getting rid of all the water that enters their tissues via osmosis. (Marine bony fish have small, aglomerular kidneys.) They produce large volumes of urine, and their kidneys are set up to reclaim essential minerals, etc., as @MCM describes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the first amniotes, although now living on land, had a kidney that had evolved in conditions where water was in excess. It evolved for filtering large volumes and reclaiming minerals. Amniotes simply adapted it for a water-poor environment. &lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2012-11-18T17:08:34.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5255" PostTypeId="1" AcceptedAnswerId="5257" CreationDate="2012-11-18T18:52:48.503" Score="3" ViewCount="2291" Body="&lt;p&gt;If a dopamine is released at T=0 and binds to receptor D2, what determines the time when the concentration of this neurotransmitter bound to the receptor reaches half of the original concentration? In other words, when will the effect of neurotransmitter on the intercell signalling fall in half?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any time estimate of how quickly the brain thinks that neurotransmitter has &quot;fulfilled its purpose&quot; and is to be re-uptaken?&lt;/strong&gt; Or is this process completely random?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="577" LastEditDate="2012-11-18T23:26:51.037" LastActivityDate="2019-07-13T20:30:38.573" Title="Is there such thing as &quot;half-life&quot; of dopamine?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;neurotransmitter&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5256" PostTypeId="2" ParentId="5255" CreationDate="2012-11-18T19:45:05.563" Score="5" Body="&lt;p&gt;Dopamine (DA) secreted by neurons is selectively reuptaken by the dopamine transporter (DAT), present on nerve terminals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/oKVAL.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/oKVAL.png&quot; alt=&quot;Monoamine reuptake&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://www.nature.com.gate1.inist.fr/nrn/journal/v4/n1/images/nrn1008-f1.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;inist.fr&lt;/a&gt;)&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image source: &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/12511858&quot; rel=&quot;nofollow noreferrer&quot;&gt;Plasma membrane monoamine transporters: structure, regulation and function&lt;/a&gt; - Torres et al. - &lt;em&gt;Nat Rev Neurosci.&lt;/em&gt;, &lt;strong&gt;2003&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DAT acts as a &lt;a href=&quot;https://en.wikipedia.org/wiki/Symporter&quot; rel=&quot;nofollow noreferrer&quot;&gt;symporter&lt;/a&gt;, using the Na&lt;sup&gt;+&lt;/sup&gt; and Cl&lt;sup&gt;-&lt;/sup&gt; gradients to generate the energy required to transport DA back in the cytosol.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanism of reuptake has been investigated &lt;em&gt;in vitro&lt;/em&gt; allowing the description of a model for DA reuptake by DAT.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, from the abstract of this paper:&#xA;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/1599505&quot; rel=&quot;nofollow noreferrer&quot;&gt;A multisubstrate mechanism of striatal dopamine uptake and its inhibition by cocaine.&lt;/a&gt; - McElvain and Schenk, &lt;em&gt;Biochem Pharmacol.&lt;/em&gt;, &lt;strong&gt;1992&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dopamine uptake was found to be &lt;strong&gt;first order in dopamine&lt;/strong&gt; with a Vmax of 582 pmol/sec/g wet weight and a Km of 1.2 μM. The results of experiments in which choline and isethionate were substituted for Na+ and Cl−, respectively, suggested that &lt;strong&gt;the uptake process is second order in Na+ and first order in Cl−&lt;/strong&gt;. Multisubstrate analyses of the initial velocities of uptake over the concentration range of 0.025 to 1.5 μM dopamine suggested that &lt;strong&gt;the mechanism of binding of dopamine to the uptake carrier is a partially random, sequential mechanism where dopamine or Na+ binds first with the uptake carrier and Cl− binds last.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A transport scheme is reported in:&#xA;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/10582600&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dopamine Neuronal Transport Kinetics and Effects of Amphetamine&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BJC2y.jpg&quot; alt=&quot;DAT schematics&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Scheme 1 is a kinetic scheme for a simple carrier adapted from that of Stein (1986) for the DAT. The subscripts o and i represent the outside and inside, respectively, of a DA neuron. Scheme 2 describes a possible mechanism for&#xA;  the cotransport of another species. All symbols are as in scheme 1 except that A corresponds to amphetamine.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From the text&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This scheme describes transport as a series of steps: the competition between binding and dissociation of the substrate to the transporter on the  extracellular side, a similar process on the cytoplasmic side, and an equilibrium between the unoccupied transporter facing toward the extracellular or cytoplasmic side. The driving force for inward transport arises from the cotransport of Na1 and Cl2 as well as the membrane potential difference&#xA;  (Stein, 1986; Sonders et al., 1997). Biochemical (Krueger, 1990) and electrophysiological (Sonders et al.,1997) studies have established that DA transport is accompanied by transport of at least two Na1 ions and one Cl2 ion and that DA transport can be bidirectional in isolated preparations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="115" LastEditorUserId="15950" LastEditDate="2019-07-13T20:30:38.573" LastActivityDate="2019-07-13T20:30:38.573" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="5257" PostTypeId="2" ParentId="5255" CreationDate="2012-11-18T20:14:03.803" Score="4" Body="&lt;p&gt;&lt;strong&gt;The half life of dopamine in the extracellular space is of the order of 200 milliseconds.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jneurosci.org/content/27/38/10196.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Yavich,L. (2007) Site-Specific Role of Catechol-O-Methyltransferase in Dopamine Overflow within Prefrontal Cortex and Dorsal Striatum. J. Neurosci. 27:10196-10202&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Figure 1 of this paper the authors present values for the half-life (&amp;tau;) of dopamine elimination from extracellular space in the caudate nucleus and prefrontal cortex of mice as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;caudate nucleus: 0.2 +/- 0.03 sec&lt;/p&gt;&#xA;&#xA;&lt;p&gt;prefrontal cortex: 1.92 +/- 0.22 sec&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently this is because dopamine is usually inactivated when the presynaptic cell takes it back up using the dopamine transporter, but in the prefrontal cortex uptake is instead via a lower affinity norepinephrine transporter on neighbouring neurones. Thus the value of 200 milliseconds seen in the caudate nucleus is probably more typical.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-18T20:14:03.803" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5258" PostTypeId="1" CreationDate="2012-11-19T09:36:09.837" Score="3" ViewCount="130" Body="&lt;p&gt;Here's an excerpt about Kimura's two-parameter model from Felsenstein's Inferring Phylogenies: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The model is symmetrical, and one can immediately see that, after&#xA;  enough time has elapsed, it will be equally likely for the base to be&#xA;  a purine or a pyrimidine.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think I understand the assumptions of the model but it's not obvious to me why the equilibrium frequencies are equal. Why is that so? &lt;/p&gt;&#xA;" OwnerUserId="9" LastEditorUserId="6" LastEditDate="2012-11-19T10:50:19.907" LastActivityDate="2012-11-19T10:50:19.907" Title="Nucleotide frequencies in Kimura's two-parameter model" Tags="&lt;evolution&gt;&lt;nucleic-acids&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5259" PostTypeId="2" ParentId="5258" CreationDate="2012-11-19T10:19:27.360" Score="2" Body="&lt;p&gt;If sufficient time has elapsed, there will be a large number of transversions present between the original base and the final state. The initial state will therefore not matter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Say, you flip (turn over, not toss) a coin at random intervals. For short time and few flips, the initial state will matter. But if you go on flipping it for millenia, the final state will be essentially random -- you will not be able to tell what was there in the beginning.&lt;/p&gt;&#xA;" OwnerUserId="1435" LastActivityDate="2012-11-19T10:19:27.360" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5260" PostTypeId="2" ParentId="2299" CreationDate="2012-11-19T17:01:30.993" Score="0" Body="&lt;p&gt;I've stumbled upon &lt;a href=&quot;http://www.psycheducation.org/mechanism/Clock.htm&quot; rel=&quot;nofollow&quot;&gt;a detailed explanation of the Biological clock&lt;/a&gt;. This one is broken into multiple steps and helped me better understand what PER and CRY are. I cannot vouch for the scientific accuracy of the diagrams, but they make sense when combined with text. &lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-11-19T17:01:30.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5261" PostTypeId="2" ParentId="5255" CreationDate="2012-11-19T18:42:45.627" Score="2" Body="&lt;p&gt;This is an attempt to illustrate how a system like this behaves kinetically, to help Alex visualise it. The model shown below contains external dopamine which can bind reversibly to a receptor. The unbound dopamine is subject to irreversible reuptake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0lsMa.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I built a quick simulation using &lt;a href=&quot;http://www.copasi.org/tiki-view_articles.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;Copasi&lt;/a&gt;. I haven't made any attempt to refine the parameters to fit the information in my previous answer - I'm just trying to illustrate qualitatively how the three different pools of dopamine (free external, bound external, internalised) behave in this kind of system. As @nico says, there is no question of extracting the receptor-bound dopamine - it will dissociate as the free dopamine concentration falls due to reuptake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GURx4.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/R6jA0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tDYYG.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-19T18:42:45.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5262" PostTypeId="1" CreationDate="2012-11-19T21:55:36.930" Score="1" ViewCount="195" Body="&lt;p&gt;For most SNPs identified in GWAS studies, is the underlying assumption that if it is indeed associated with a phenotype (and lets assume its associated because it affects protein function), that you don't need two knocked out copies of that gene for it to confer susceptibility risk to the individual? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, is my assumption that GWAS is likely uncovering alleles that confer risk in single copy, correct?&lt;/p&gt;&#xA;" OwnerUserId="1672" LastEditorUserId="1306" LastEditDate="2012-11-20T11:01:30.340" LastActivityDate="2012-11-20T11:12:08.083" Title="Interpreting SNP-in-gene associations from GWAS studies" Tags="&lt;human-genome&gt;&lt;gwas&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5263" PostTypeId="1" AcceptedAnswerId="5266" CreationDate="2012-11-19T23:09:17.320" Score="5" ViewCount="1807" Body="&lt;p&gt;Botulinum toxin (trade name Botox) inhibits acetylcholine release in neurons and causes botulism, an acute paralytic disease which leads to nerve degeneration and takes a long time to recover. I've read the statement that Botox is the most potent poison we know a few times now and was wondering &lt;em&gt;why exactly&lt;/em&gt; it is. All sources I've found only claim &lt;em&gt;that&lt;/em&gt; it is, without explanation.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-11-21T02:00:33.893" Title="Why is Botulinum toxin the most potent poison known?" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;&lt;toxicology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5266" PostTypeId="2" ParentId="5263" CreationDate="2012-11-20T02:13:26.797" Score="1" Body="&lt;p&gt;A quick search for a &lt;a href=&quot;http://en.wikipedia.org/wiki/Median_lethal_dose&quot; rel=&quot;nofollow&quot;&gt;list of LD50&lt;/a&gt; (median lethal dose; half of the people will die with that dosage) gave me 1 ng/kg for Botulinum toxin. This is pretty darn small amount, and in fact the smallest amount within that table.&lt;/p&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2012-11-20T02:20:08.223" LastActivityDate="2012-11-20T02:20:08.223" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5267" PostTypeId="1" CreationDate="2012-11-20T09:09:59.110" Score="4" ViewCount="3511" Body="&lt;p&gt;I'm having trouble aligning 3 sequences together - the total gene (~2500bp) and the forward and reverse sequences that are ~1000bp in length. Now I'm using Clustal X2, but the problem is that the program does complete alignment, which is useless for me right now.  Could anyone recommend or suggest any parameters or methods on how to align more that 2 sequences together, but that each sequence is aligned to the first one (the total gene)?&#xA;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="1673" LastActivityDate="2013-08-31T00:44:05.747" Title="Multiple sequence alignment - how to align everything to 1 gene sequence?" Tags="&lt;bioinformatics&gt;" AnswerCount="4" CommentCount="3" ClosedDate="2016-03-02T17:47:06.430" ContentLicense="CC BY-SA 3.0" />
  <row Id="5268" PostTypeId="1" AcceptedAnswerId="5272" CreationDate="2012-11-20T09:22:15.837" Score="0" ViewCount="2023" Body="&lt;p&gt;Why do living organisms spontaneously replicate itself or &quot;procreate&quot; (my understanding is that it does).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a uni-cellular and micro-organism point of view. Is there some sort of stimulant in the environment? A chemical reaction that causes it? Is is there a physical or emotional motivation? Is it by choice?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: I may have some terms used wrongly as I am not a biologist. In this question, I am interested at living organism nearer the forms of single smallest unit of life form.&lt;/p&gt;&#xA;" OwnerUserId="746" LastActivityDate="2015-02-11T20:56:16.797" Title="Why do living organisms replicate itself or procreate" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;abiogenesis&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5269" PostTypeId="2" ParentId="5262" CreationDate="2012-11-20T11:12:08.083" Score="1" Body="&lt;p&gt;In short, yes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a gwas study links a SNP to a particular phenotype then yes, it is an effect of a single copy. Bear in mind, however, that a SNP is not a knockout or even a knockdown. It &lt;em&gt;can&lt;/em&gt; be, but it is not always the case.  SNPs can produce a change in the protein sequence or in the regulation of the production of that protein. Both types of variation can result in a phenotypical change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, SNP information is always about a single allele, I imagine that you can find cases where a cell is homozygous for a particular SNP but is is not necessarily, or even often as far as I know, the case.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2012-11-20T11:12:08.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5270" PostTypeId="2" ParentId="5268" CreationDate="2012-11-20T11:39:18.097" Score="3" Body="&lt;p&gt;This is a very interesting question but the answer (or as much of the answer as is known) can fill a few books. There are many many signals that control cell division. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a horrible simplification, the cell can be compared to a car parked on a slope with a driver's foot on the brake. If she lifts her foot, the car will roll downhill. In the cell, there are various proteins (&lt;a href=&quot;https://en.wikipedia.org/wiki/P53&quot; rel=&quot;nofollow&quot;&gt;P53&lt;/a&gt; is the most famous) that have their metaphorical foot on the brake. Various external and internal stimuli can cause these proteins to stop suppressing replication and the cell will then continue its cycle and replicate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, a cell's &quot;natural state&quot; is to replicate, there is a complex network of interacting factors (primarily proteins) that actively block replication in resting cells. When the conditions are &quot;right&quot; (what that means depends on the cell in question) the block is removed and the cell replicates.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2015-02-11T20:56:16.797" LastActivityDate="2015-02-11T20:56:16.797" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5271" PostTypeId="1" CreationDate="2012-11-20T11:47:22.617" Score="7" ViewCount="123" Body="&lt;p&gt;&lt;a href=&quot;http://www.nature.com/bjc/journal/v105/n2s/full/bjc2011489a.html&quot;&gt;Alcohol consumption is known to be a risk factor for developing cancer&lt;/a&gt;. Compared to obvious causes like tobacco where one is exposed to known carcinogens, I don't see an obvious mechanism by which alcohol consumption would increase the risk of cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there anything known about the mechanisms by which alchohol consumption affects cancer risk?&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2013-04-15T00:02:58.993" Title="What are the biological mechanisms behind the increase in cancer risk and alcohol consumption?" Tags="&lt;cancer&gt;&lt;alcohol&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5272" PostTypeId="2" ParentId="5268" CreationDate="2012-11-20T13:26:21.150" Score="2" Body="&lt;p&gt;If there are enough nutrients, a unicellular organism will &quot;eat&quot; and grow until it reaches a certain size. Through different mechanisms, it can sense that it is large enough and has enough metabolites to divide. Then, the organism will duplicates its DNA, separate the duplicated DNA and divide. (This is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Fission_%28biology%29&quot; rel=&quot;nofollow&quot;&gt;fission&lt;/a&gt; for prokaryotes.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why does it happen? One of the characteristics of life is replication. In favorable conditions, the organism replicating the fastest will out-compete all other organisms. So there is no motivation or stimulus of some sort needed (or possible), by their very nature cells are made to divide as soon as feasible.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-11-20T13:26:21.150" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5273" PostTypeId="1" AcceptedAnswerId="5275" CreationDate="2012-11-20T15:14:55.310" Score="5" ViewCount="750" Body="&lt;p&gt;I'm testing out various phylogenetic libraries in Python. I want to read in a Newick tree, then, given a list of taxa, generate the smallest tree that contains them all. This task is quite simple and efficient in dendropy and ete2:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;newick = '((raccoon, bear),((sea_lion,seal),((monkey,cat), weasel)),dog);'&#xA;taxa = ['raccoon', 'sea_lion']&#xA;&#xA;import ete2&#xA;tree = ete2.Tree(newick)&#xA;pruned = tree.prune(taxa)&#xA;&#xA;import dendropy&#xA;tree = dendropy.Tree.get_from_string(newick, 'newick')&#xA;pruned = tree.prune_taxa_with_labels(taxa)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I'm trying but failing to find equivalent functionality in the Bio.Phylo package. Trees do have a &quot;prune&quot; method, but it prunes a single node from the tree.&lt;/p&gt;&#xA;" OwnerUserId="1675" LastActivityDate="2013-10-09T13:18:14.713" Title="How to get smallest subtree containing a set of nodes from BioPhylo?" Tags="&lt;evolution&gt;&lt;bioinformatics&gt;&lt;phylogenetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5274" PostTypeId="1" AcceptedAnswerId="5276" CreationDate="2012-11-20T15:40:55.977" Score="13" ViewCount="33712" Body="&lt;p&gt;Will a bone marrow transplant change one's blood type?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is the donor blood type matched with the person before transplant?&lt;/p&gt;&#xA;" OwnerUserId="238" LastActivityDate="2016-03-18T17:21:42.840" Title="Will a bone marrow transplant change one's blood type?" Tags="&lt;human-biology&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5275" PostTypeId="2" ParentId="5273" CreationDate="2012-11-20T16:14:44.490" Score="3" Body="&lt;p&gt;The &lt;a href=&quot;http://biopython.org/DIST/docs/api/Bio.Phylo.BaseTree.TreeMixin-class.html#common_ancestor&quot; rel=&quot;nofollow&quot;&gt;&lt;code&gt;common_ancestor&lt;/code&gt;&lt;/a&gt; function should give you the result you want: it gives you the tree (I think) that is the most recent common ancestor of all the given targets.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-11-20T16:14:44.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5276" PostTypeId="2" ParentId="5274" CreationDate="2012-11-20T16:40:22.237" Score="16" Body="&lt;p&gt;Bone Marrow transplants are extensively matched in order to prevent rejection. Current matching methodology is HLA matching: &lt;a href=&quot;http://www.lpch.org/DiseaseHealthInfo/HealthLibrary/hematology/bonetran.html&quot;&gt;Stanford Children's Hospital Guidelines&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;How are a donor and recipient matched?&lt;/strong&gt;&lt;br&gt;&#xA;  Matching involves typing human leukocyte antigen (HLA) tissue. The antigens on the surface of these special white blood cells determine the genetic make-up of a person's immune system. There are at least 100 HLA antigens; however, it is believed that there are a few major antigens that determine whether a donor and recipient match. The others are considered minor and their effect on a successful transplant is not as well defined.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Medical research is still investigating the role all antigens play in the process of a bone marrow transplant. The more antigens that match, the better the engraftment of donated marrow. Engraftment of the stem cells occurs when the donated cells make their way to the marrow and begin reproducing new blood cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, because the HLA matching &lt;em&gt;doesn't&lt;/em&gt; utilize blood-type and the recipient's marrow is destroyed in the process, then if the donor's marrow produces different red blood cells - &lt;a href=&quot;http://www.nationalcmlsociety.org/faq/stem-cellbone-marrow-transplant&quot;&gt;then so will the recipient&lt;/a&gt; with time:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Does my blood type change after SCT or [Bone Marrow Transplant]?&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Yes.  The recipients blood type eventually changes to the donor type.  That means if you had a blood type of A+ prior to transplant and your donor had a blood type of O, eventually your blood type would become O.  I may take several weeks, possibly months for your original blood type to disappear, but eventually it will.  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What's interesting is that blood-typing is not be expressly necessary with the modern bone marrow transplant process. The danger of mixing two antagonistic blood types &lt;em&gt;in vivo&lt;/em&gt; is that the recipient's immune system attacks the foreign red blood cells resulting in body-wide rejection. However, because the immune system's response capabilities are decimated by the destruction of the recipient's bone marrow (usually accomplished via chemotherapy or radiation), it can't mount much of an attack in the first place. That's not to say the body can't mount an attack, or that the donor's tissue can't mount an attack on the recipient (Graft-Versus-Host-Disease [GVHD]) - but the better the HLA match the less likely issues are to arise, which is why we do the more accurate and relevant HLA matching instead of blood-typing.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-11-20T16:40:22.237" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5277" PostTypeId="1" AcceptedAnswerId="5293" CreationDate="2012-11-20T20:41:50.720" Score="3" ViewCount="1742" Body="&lt;p&gt;Where does an organism store reserves of the amino acids it needs to build various proteins it needs:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;in the liver? &lt;/li&gt;&#xA;&lt;li&gt;in the blood? &lt;/li&gt;&#xA;&lt;li&gt;in every cell?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="226" LastEditorUserId="49230" LastEditDate="2019-03-12T10:53:49.017" LastActivityDate="2019-03-12T10:53:49.017" Title="Where does an organism store reserves of amino acids?" Tags="&lt;cell-biology&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="5278" PostTypeId="1" AcceptedAnswerId="5281" CreationDate="2012-11-20T22:24:35.083" Score="6" ViewCount="4618" Body="&lt;p&gt;Occasionally, after someone's been, there is an awful acrid smell lying about long after them. What causes this? The food that they've eaten? Urea less dilute due to dehydration?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it helps I've noticed it only with older males.&lt;/p&gt;&#xA;" OwnerUserId="1667" LastEditorUserId="1667" LastEditDate="2012-11-20T22:52:23.467" LastActivityDate="2013-09-04T19:43:19.767" Title="What makes urine smell acrid?" Tags="&lt;human-biology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5280" PostTypeId="2" ParentId="5267" CreationDate="2012-11-20T23:42:40.650" Score="4" Body="&lt;p&gt;Your question is not very clear, but I think what you are trying to do is align sequencing results to a reference gene sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your total gene sequence spans ~2500 bp. It sounds like you have a forward sequence at the start of gene, reading only about 1000 bp and the reverse strand reading in 1000 bp from the end (if this is Sanger sequencing, you likely only have 800-900 bp of accurate base reads by the way). Therefore, you have a gap of about 500 bp in the middle of your gene of interest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are (at least) two ways to do the alignment, and I would suggest the manual method if you are trying to verify gene sequencing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Manual Method:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;In a word processing document, paste in your gene-of-interest (or the recombinant gene you are trying to make), as well as the base reads from the forward strand, and the &lt;em&gt;reverse complement&lt;/em&gt;of your reverse strand. &lt;em&gt;Make sure you remove any whitespace like line breaks and spaces as this will disrupt the rest of the process.&lt;/em&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Manually select a small portion of your forward read (20-30 bp for example) and search for the same &quot;phrase&quot; in your gene-of-interest. If you find it, highlight it in both the sequence it came from and the gene-of-interest so that you know you have already matched them.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Carry on with adjacent bases for the forward strand. Repeat for the reverse complement of the reverse strand.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Semi-Automated Method:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Go to &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/&quot; rel=&quot;nofollow noreferrer&quot;&gt;NCBI Blast&lt;/a&gt;, and under the heading &lt;strong&gt;Basic Blast&lt;/strong&gt;, click &quot;nucleotide blast&quot;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Check &quot;Align 2 or more sequences.&quot;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Enter your &lt;strong&gt;Query Sequence&lt;/strong&gt; as your 1000 bp sequences, entered in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;FASTA format&lt;/a&gt;. FASTA format will allow you to enter multiple sequences, but if you just enter one at a time, that will work perfectly well. Results will only display one at a time anyway.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;For example:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt; sequence name here&#xA;ATCGATCGATCGATCGATCGATCG....&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;ol start=&quot;4&quot;&gt;&#xA;&lt;li&gt;&lt;p&gt;Enter your gene of interest as your &lt;strong&gt;Subject Sequence&lt;/strong&gt;. Format does not matter here, but for consistency, I use FASTA format.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Keep &quot;Highly similar sequences (megablast)&quot; selected. You shouldn't need to play with these parameters, they just change how the alignment method penalizes alignments for gaps and mismatches.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Hit &lt;strong&gt;BLAST&lt;/strong&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Interpret your results. I've included an example of BLAST results below.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mmzGs.png&quot; alt=&quot;BLAST example output aligning two sequences.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the top of this window is a schematic, showing exactly how much of the the query sequence aligns with the subject sequence. The longer the line, the more bases align. Similarly, the closer the colour of the line is to right of the scale (e.g., red), then the more continuous the segment is indicating a longer, continuous alignment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below the graphic is a table of results. Briefly, the table highlights all possible alignments that the BLAST algorithm has found, including how much coverage there was, confidence of the alignment and length of alignment coverage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below the results table, are the detailed results which were summarized in the table. This detailed report shows you exactly which bases align or mismatch, or any gaps. The top line is the subject sequence; the bottom is the query sequence. The other thing to keep in mind here is the &lt;strong&gt;Strand&lt;/strong&gt; line. In this case, it says &quot;&lt;strong&gt;Plus/Plus&lt;/strong&gt;, meaning that the aligned sequences were the forward sense, or plus strand, of each of subject and query sequence, respectively. If you entered a reverse complement sequence instead (such as the reverse sequencing results) then this would change to &lt;strong&gt;&quot;Plus/Minus&quot;&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From here, you will still need to manually line these results up to your gene of interest to determine exactly which portion of the gene is missing sequence coverage, as well as any mutations that may have cropped up in the cloning process.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-11-20T23:42:40.650" CommentCount="0" CommunityOwnedDate="2012-11-20T23:42:40.650" ContentLicense="CC BY-SA 3.0" />
  <row Id="5281" PostTypeId="2" ParentId="5278" CreationDate="2012-11-21T00:05:03.580" Score="4" Body="&lt;p&gt;The odor comes from &lt;a href=&quot;http://en.wikipedia.org/wiki/Urea&quot; rel=&quot;nofollow&quot;&gt;urea&lt;/a&gt;. Urea will slowly undergo displacement to become ammonia, but when it's fresh, it has a strong odor. Other odors do come from food, notably coffee and (in some of the population) asparagus.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2012-11-24T23:18:50.030" LastActivityDate="2012-11-24T23:18:50.030" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5282" PostTypeId="2" ParentId="5263" CreationDate="2012-11-21T02:00:33.893" Score="4" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Botulinum_toxin#Biochemical_mechanism_of_toxicity&quot; rel=&quot;nofollow&quot;&gt;biochemical mechanism&lt;/a&gt; of BT is pretty well laid out at Wikipedia already. The toxin is likely very potent because (1) it is targeted to neurons; (2) neurons endocytose BT; and (3) the BT light chain's protease activity is able to cleave a wide range of SNARE-complex proteins which effectively disrupt the neurons ability to secrete monoamine neurotransmitters, and peptide hormones. Basically, the neurons are completely inhibited from transmitting nerve impulses.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-11-21T02:00:33.893" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5283" PostTypeId="2" ParentId="5241" CreationDate="2012-11-21T02:22:39.790" Score="4" Body="&lt;p&gt;I have to say that this seems like a really odd approach to figuring out your diet.  The question of whether insulin increases satiety has been more specifically studied in the literature, as has the satiety generated by equicaloric portions of various kinds of foods, as have the actual effects of various specific diets in human feeding studies.  If you do a bit of digging, I'm sure you can find studies relating high/low GI diets to medically important outcomes (weight loss, blood lipids, fasting insulin levels, etc.), as opposed to their effect on one proposed satiety/fat regulation hormone (leptin).  Your approach also ignores leptin and insulin sensitivity, which might be as important as the levels themselves.  As someone concerned with which foods to actually eat, empirical studies of actual diets seem like the best place to look.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, here are a few relevant citations to help answer your question: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;This study found a increase in serum leptin levels in type I diabetic children who started insulin therapy:&lt;/strong&gt;&#xA;Flück CE, Kuhlmann BV, Mullis PE. &quot;Insulin increases serum leptin concentrations in children and adolescents with newly diagnosed type I diabetes mellitus with and without ketoacidosis.&quot; Diabetologia. 1999 Sep;42(9):1067-70.&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10447517&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/10447517&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A slightly smaller study asked the same question, and found no increase in leptin levels:&lt;/strong&gt;&#xA;McCormick KL, Mick GJ, Butterfield L, Ross H, Parton E, Totka J. &quot;Leptin in children with newly diagnosed type 1 diabetes: effect of insulin therapy.&quot; Int J Exp Diabetes Res. 2001;2(2):121-7. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12369715&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/12369715&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;An in vitro study of rat fat cells does indicate a direct increase in leptin secretion/production when given insulin:&lt;/strong&gt;&#xA;Barr VA, Malide D, Zarnowski MJ, Taylor SI, Cushman SW. &quot;Insulin stimulates both leptin secretion and production by rat white adipose tissue.&quot; Endocrinology. 1997 Oct;138(10):4463-72. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9322964&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/9322964&lt;/a&gt; http://endo.endojournals.org/content/138/10/4463.full&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;...and in human fat cells:&lt;/strong&gt;&#xA;Wabitsch M, Jensen PB, Blum WF, Christoffersen CT, Englaro P, Heinze E, Rascher W, Teller W, Tornqvist H, Hauner H. &quot;Insulin and cortisol promote leptin production in cultured human fat cells.&quot; Diabetes. 1996 Oct;45(10):1435-8. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8826983&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/8826983&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Leptin levels are positively correlated with insulin levels and BMI (presumably as a proxy for fat mass?):&lt;/strong&gt;&#xA;Lambrinoudaki I, Christodoulakos G, Panoulis C, Botsis D, Rizos D, Augoulea A, Creatsas G. &quot;Determinants of serum leptin levels in healthy postmenopausal women.&quot; J Endocrinol Invest. 2003 Dec;26(12):1225-30. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15055477&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/15055477&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thierry Thomas, Bartolome Burguera, L.Joseph Melton III, Elizabeth J. Atkinson, W.M. O'Fallon, B.Lawrence Riggs, Sundeep Khosla, &quot;Relationship of serum leptin levels with body composition and sex steroid and insulin levels in men and women&quot; Metabolism Volume 49, Issue 10, October 2000, Pages 1278–1284 &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S002604950041783X&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S002604950041783X&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;This study found a positive relationship between changes in insulin levels and leptin levels, though it sounds like only in women. (I don't have the full text to check, and the abstract was ambiguous):&lt;/strong&gt;&#xA;Widjaja A, Levy JC, Morris RJ, Frayn KN, Humphreys SM, Horn R, von zur Mühlen A, Turner RC, Brabant G. &quot;Determinants of within-subject variation of fasting serum leptin concentrations in healthy subjects.&quot; Exp Clin Endocrinol Diabetes. 2000;108(3):208-13.&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10926318&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/10926318&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So based on an incomplete and cursory literature search, it seems likely that injecting insulin increases leptin production, as do some other activities that tend to increase insulin.  The evidence for causation in humans is not totally clear cut, though suggestive.&lt;/p&gt;&#xA;" OwnerUserId="1597" LastActivityDate="2012-11-21T02:22:39.790" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5284" PostTypeId="1" CreationDate="2012-11-21T02:51:22.420" Score="2" ViewCount="178" Body="&lt;p&gt;I am slightly confused about the mechanisms that makes histone modifications associate with gene expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is, &lt;a href=&quot;http://en.wikipedia.org/wiki/Histone_code#Modifications&quot; rel=&quot;nofollow&quot;&gt;H3K36me3&lt;/a&gt; is believed to be present in actively transcribed genes, H3K27me3 in repressed regions, etc. What is the mechanism that makes the presence of H3K36me3 to be in active regions, etc.? Is it causal or just an association?&lt;/p&gt;&#xA;" OwnerUserId="1661" LastEditorUserId="948" LastEditDate="2014-01-13T21:36:10.267" LastActivityDate="2014-01-13T21:36:10.267" Title="Histone marks mechanism" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;epigenetics&gt;&lt;histone&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5285" PostTypeId="2" ParentId="5278" CreationDate="2012-11-21T03:40:14.307" Score="1" Body="&lt;p&gt;Urea could be one. Also, be aware that there are other sources of urine. Asparagus is a famous one. I am still amused because I once thought something was really off with me ( a male, not older yet) when my urine smelled. I panicked and then found out that it was because I had consumed asparagus in a prior meal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure if urine starts smelling differently in certain older males, but take diet into consideration. &lt;/p&gt;&#xA;" OwnerUserId="1521" LastActivityDate="2012-11-21T03:40:14.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5286" PostTypeId="1" AcceptedAnswerId="5310" CreationDate="2012-11-21T04:41:31.880" Score="1" ViewCount="105" Body="&lt;p&gt;I'm just curious which cells are largest/smallest in the human body other than sperm/ova. &lt;/p&gt;&#xA;" OwnerUserId="1677" LastEditorUserId="1677" LastEditDate="2012-11-21T17:08:04.173" LastActivityDate="2012-11-23T07:58:33.450" Title="In a human, what non-germline cells have the highest/lowest mass?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5287" PostTypeId="2" ParentId="942" CreationDate="2012-11-21T05:09:16.720" Score="1" Body="&lt;p&gt;It's not a totally answerable question, since some types of cells are going to divide more times than others.  But for an estimate, take as a starting proposition that there are 1 trillion cells in the adult human body. [1]  The average weight for a human is 62kg. [2] Average birth weight is about 3.4 kg.  [3]  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So that implies roughtly (3.4/62)* 1 trillion = 55 billion cells in a newborn.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You then take the log base 2 of 55 billion, which gives you the exponent you have to hang on 2 in order to get 55 billion, which is about 35.  Then add one for that additional cell division to get from one to two cells == 36 divisions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course I'm just using math, not biology, so your actual reality may vary.  Certainly some cells will reproduce more often than others, maybe cells actually grow in mass instead of dividing (i.e., baby cells might have less mass than adult cells) so the baby-cell-count could be off, lots of possible sources of error.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.nichd.nih.gov/publications/pubs/fragileX/sub3.cfm&quot; rel=&quot;nofollow&quot;&gt;http://www.nichd.nih.gov/publications/pubs/fragileX/sub3.cfm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] &lt;a href=&quot;http://en.wikipedia.org/wiki/Body_weight#Average_weight_around_the_world&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Body_weight#Average_weight_around_the_world&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[3] &lt;a href=&quot;http://en.wikipedia.org/wiki/Infant#Weight&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Infant#Weight&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1677" LastActivityDate="2012-11-21T05:09:16.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5288" PostTypeId="1" AcceptedAnswerId="5294" CreationDate="2012-11-21T05:12:05.153" Score="3" ViewCount="3638" Body="&lt;p&gt;I have a dim recollection of having heard that when humans gain weight, adipose cells just get larger, rather than dividing.  True?  &lt;/p&gt;&#xA;" OwnerUserId="1677" LastActivityDate="2017-01-27T19:49:30.773" Title="Do adipose cells divide in adults?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;eukaryotic-cells&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5289" PostTypeId="1" AcceptedAnswerId="5290" CreationDate="2012-11-21T05:17:12.870" Score="2" ViewCount="778" Body="&lt;p&gt;That is to say, are there cells that, between infancy and adulthood, get larger?  Or is all growth done entirely via cell division?  I'm wondering if it is safe to assume that the approximate number of cells per unit mass in a mammal will remain fairly constant throughout its lifespan.  &lt;/p&gt;&#xA;" OwnerUserId="1677" LastActivityDate="2012-11-21T15:31:24.807" Title="Do any cells change in size or mass as mammals grow?" Tags="&lt;zoology&gt;&lt;cell-biology&gt;&lt;mammals&gt;&lt;eukaryotic-cells&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5290" PostTypeId="2" ParentId="5289" CreationDate="2012-11-21T10:03:58.310" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I'm wondering if it is safe to assume that the approximate number of cells per unit mass in a mammal will remain fairly constant throughout its lifespan.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Not exactly.&lt;/em&gt;  When a tissue is put under stress, it can respond in four main ways:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Hypertrophy&lt;/strong&gt; - individual cells get larger.  &lt;em&gt;E.g. stressed muscle cells get bigger&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Atrophy&lt;/strong&gt; - invidivual cells get smaller.  &lt;em&gt;E.g. naturally in the thymus during development&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Hyperplasia&lt;/strong&gt; - increased cell division to produce more cells.  &lt;em&gt;E.g. mammary gland cells in pregnancy&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Metaplasia&lt;/strong&gt; - one type of specialised cell is replaced with another, usually more durable one, &lt;em&gt;E.g. columnar epithelium in the respiratory tract of a smoker being replaced with squamous epithelium&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The first three responses to stress can change both cell size (auxetic response) and number (multiplicative response), meaning you can't really say that cells per unit mass stays constant throughout life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Muscle tissue grows predominantly by hypertrophy, meaning that the muscle gains during puberty are likely to be more as a result of cells getting larger than the development of new ones. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both auxetic and multiplicative growth occurs as the body develops.  In addition to this, accretionary growth also occurs - where connective tissues such as bone and cartilage increase in size. &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2012-11-21T15:31:24.807" LastActivityDate="2012-11-21T15:31:24.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5291" PostTypeId="1" CreationDate="2012-11-21T11:15:44.603" Score="3" ViewCount="153" Body="&lt;p&gt;I have a list of candidate proteins as the result of my analysis. I am now trying to find various characteristics that they have in common. One of the things I would like to check is if my candidates are evolving faster or slower than the rest of the proteins in my dataset.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I know how to do this manually by building multi species alignments for each of my proteins and calculating ka/ks ratios for each set of alignments. This, however, is not a trivial process and I really do not want to do this manually for my ~1500 candidates. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone suggest a tool that will take two lists of proteins and return an estimate of evolutionary rate for each one?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am primarily interested in human but also mouse, yeast, fly and worm. Ideally, I would need a tool that can take a list of proteins, assign them to an orthologous group and return a value representing the rate of evolution for that group.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-11-22T11:37:48.410" LastActivityDate="2012-12-03T10:00:36.857" Title="How can I compare rates of evolution for two sets of proteins?" Tags="&lt;evolution&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5292" PostTypeId="2" ParentId="5289" CreationDate="2012-11-21T11:27:09.780" Score="3" Body="&lt;p&gt;This is not my field so I am sure there are other examples, but certain neurons will definitely be larger in adulthood than in infancy. There are motor neurons that connect the spine to, for example, the toes. These will grow in length as an animal grows. So, in a human infant they will be a few centimeters long and can reach lengths of over a meter in an adult.  &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2012-11-21T11:27:09.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5293" PostTypeId="2" ParentId="5277" CreationDate="2012-11-21T17:10:01.220" Score="7" Body="&lt;p&gt;In the sense that you have asked the question, humans have no stores of amino acids. Amino acids obtained from the diet are quickly incorporated into new proteins or are metabolised as fuel molecules. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Proteins are subject to continual turnover, and the amino acids that are released by degradation are either reused or metabolised in exactly the same way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is one of the reasons why the diet must contain appropriate levels of essential amino acids (those we cannot make for ourselves) since these are continually being released from proteins and used as fuel - we have no mechanism for storing them in case of future dietary deficiency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During starvation the protein turnover process releases amino acids from muscle and these are mainly used as fuel molecules. This is why muscle wasting occurs in starvation, although the mobilisation of fat reserves helps to delay this as long as possible as tissues, including brain, switch over to relying on ketones (derived from fat breakdown).&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-21T17:10:01.220" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5294" PostTypeId="2" ParentId="5288" CreationDate="2012-11-21T21:34:08.347" Score="4" Body="&lt;p&gt;My foray into the literature suggests that mature adipocytes do not divide. See, for example:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Lefterova, MI et al. (2009) New developments in adipogenesis. Trends in Endocrinology and Metabolism 20:107-114&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the context of looking at the possibility of stimulating the conversion of white adipose tissue to brown adipose tissue, the authors outline the way in which the expansion of adipose tissue occurs by a process in which fibroblast-like pre-adipocytes differentiate into cells capable of storing lipid droplets and responding to insulin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears therefore that expansion of adipose tissue occurs by the generation of new adipocytes. Thinking of the morphology of a fully-loaded adipocyte (a lipid droplet surrounded by a narrow band of cytoplasm) it seems rather unlikely that these cells would be capable of division. The Wikipedia citation linked to by QuietThud in the comments to the OP is to a popular book on nutrition, not an authoritative source.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-21T21:34:08.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5295" PostTypeId="1" CreationDate="2012-11-22T00:46:17.293" Score="4" ViewCount="291" Body="&lt;p&gt;Usually the protocol for preparing electrocompetent E. coli cells calls for growing the cells at 37deg and 225rpms until they reach OD of 0.3. I was wondering, is there any reason they should grow at optimal conditions for growth, instead of at suboptimal, for example at 30 degrees? Also, what is the physiological/epigenetic difference between a culture of OD 0.2 vs 03. vs 0.3? &lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2012-11-22T00:58:29.410" LastActivityDate="2018-06-11T18:18:26.457" Title="Cell growth conditions for preparing electrocompetent cells" Tags="&lt;protocol&gt;&lt;competent-cells&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5296" PostTypeId="2" ParentId="5235" CreationDate="2012-11-22T05:24:21.507" Score="1" Body="&lt;p&gt;Here is a good USDA link: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.usna.usda.gov/PhotoGallery/FallFoliage/ScienceFallColor.html&quot; rel=&quot;nofollow&quot;&gt;http://www.usna.usda.gov/PhotoGallery/FallFoliage/ScienceFallColor.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would appear that the shortening days are a main trigger, and there are other factors. I did a basic search using Google for &quot;what triggers leaf fall in deciduous trees?&quot;, since I always thought temperature and changing seasons were major triggers and wanted to double check. &lt;/p&gt;&#xA;" OwnerUserId="1521" LastActivityDate="2012-11-22T05:24:21.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5297" PostTypeId="1" AcceptedAnswerId="5303" CreationDate="2012-11-22T08:05:07.517" Score="8" ViewCount="5660" Body="&lt;p&gt;I am reading about transportation of ions in a cell. It is necessary to transport sodium back out and potassium back in, against their electrochemical gradient. This task is carried out by sodium-potassium pump, which transports three sodium ions out across the cell membrane for every two potassium ions carried inward. The source of energy for this transport process was hydrolysis of ATP.&#xA;My question is the order of the efficiency of a sodium-potassium pump.&lt;/p&gt;&#xA;" OwnerUserId="1610" LastEditorUserId="4562" LastEditDate="2014-03-23T18:00:37.640" LastActivityDate="2014-03-23T18:00:37.640" Title="How efficient is the sodium-potassium pump ?" Tags="&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5298" PostTypeId="1" AcceptedAnswerId="5309" CreationDate="2012-11-22T10:56:35.297" Score="5" ViewCount="1261" Body="&lt;p&gt;Many animals have red tongues, though not all of them - &lt;a href=&quot;http://en.wikipedia.org/wiki/Blue-tongued_skink&quot;&gt;blue-tongued skinks&lt;/a&gt; and &lt;a href=&quot;http://www.giraffeconservation.org/giraffe_facts.php?pgid=12&quot;&gt;giraffes&lt;/a&gt; come to mind. Are they red because of the blood (and therefore haemoglobin) in them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It sounds plausible, but it also sounds like a post-hoc explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd be especially curious about any other species having blue blood, like &lt;a href=&quot;http://en.wikipedia.org/wiki/Horseshoe_crab#Blood&quot;&gt;horseshoe crabs&lt;/a&gt;, but still having red tongues, unlike horseshoe crabs, which &lt;a href=&quot;http://uk.answers.yahoo.com/question/index?qid=20100120144643AAQ7ojt&quot;&gt;apparently&lt;/a&gt; don't even have tongues.&lt;/p&gt;&#xA;" OwnerUserId="576" LastEditorUserId="3971" LastEditDate="2013-08-29T16:15:03.413" LastActivityDate="2013-08-29T16:15:03.413" Title="Are tongues red because they contain blood?" Tags="&lt;zoology&gt;&lt;hematology&gt;&lt;pigmentation&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5300" PostTypeId="1" AcceptedAnswerId="5351" CreationDate="2012-11-22T12:12:06.460" Score="9" ViewCount="1558" Body="&lt;p&gt;I'm aware of measures like number of distinct cell types being used as a measurement of complexity in biology, for example in the G-value paradox. But this doesn't really help for unicellular organisms. Is it possible to define a unit of complexity to make comparisons between different organisms?&lt;/p&gt;&#xA;" OwnerUserId="476" LastActivityDate="2012-11-27T00:34:53.607" Title="What measures are commonly used for the complexity of an organism?" Tags="&lt;evolution&gt;&lt;complexity&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5301" PostTypeId="2" ParentId="5300" CreationDate="2012-11-22T13:00:48.147" Score="0" Body="&lt;p&gt;I don't know if it is helpful for your problem, but I measured complexity in gen regulatory networks by parsing them into boolean networks. Then you can initiate all nodes with a random boolean value and update the network until it reaches an attractor. For a hand full of initial states you can compute the average entropy and mutual information. Additionally the topology (scale free, small world [Barabasi]) and count of reached and cycle lengths as well as robustness (reaching same attractor by flipping a randomly chosen node in the trajectory) can give you information about the complexity. To compute all attractors by all possible initial states of the boolean network can be done with a sat solver [Dubrova].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;regards&lt;/p&gt;&#xA;" OwnerDisplayName="user1682" LastActivityDate="2012-11-22T13:00:48.147" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5302" PostTypeId="2" ParentId="5291" CreationDate="2012-11-22T14:26:14.570" Score="2" Body="&lt;p&gt;If protein alignments are sufficient for you, I suggest that you look at the &lt;a href=&quot;http://eggnog.embl.de&quot; rel=&quot;nofollow&quot;&gt;eggNOG database&lt;/a&gt;. There you can download mappings from proteins to protein families, and for the families you can also download pre-computed multiple (protein) sequence alignments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess depending on the type of analysis you want to do you would have to trim the alignments to get only homologous regions (for example, see this &lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0030288&quot; rel=&quot;nofollow&quot;&gt;recent paper&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0030288&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Wu M, Chatterji S, Eisen JA&lt;/strong&gt;. 2012. Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 7(1): e30288, doi:10.1371/journal.pone.0030288.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="112" LastEditorUserId="112" LastEditDate="2012-12-03T10:00:36.857" LastActivityDate="2012-12-03T10:00:36.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5303" PostTypeId="2" ParentId="5297" CreationDate="2012-11-22T16:01:44.023" Score="9" Body="&lt;p&gt;&lt;strong&gt;I couldn’t find a value for this but I have calculated an efficiency of 84 %.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Caution: this seems too high to me, so I show below my calculation, fully dissected, in case anyone can spot an error.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all the parameters. Ion concentrations are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;internal Na&lt;sup&gt;+&lt;/sup&gt;  = 12 mM;&#xA;external Na&lt;sup&gt;+&lt;/sup&gt; = 140 mM;&#xA;internal K&lt;sup&gt;+&lt;/sup&gt;   = 140 mM;&#xA;external K&lt;sup&gt;+&lt;/sup&gt;   = 5 mM;&#xA;and membrane potential = -60 mV (negative inside the cell)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I use these values for constants:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;gas constant R = 2 cal mol&lt;sup&gt;-1&lt;/sup&gt; K&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Faraday constant F= 23,062 cal mol&lt;sup&gt;-1&lt;/sup&gt; V&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and I’ll assume that the temperature, T, is 37℃ = 310 K&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Na&lt;sup&gt;+&lt;/sup&gt;/K&lt;sup&gt;+&lt;/sup&gt; pump uses 1 molecule of ATP to move 3 Na&lt;sup&gt;+&lt;/sup&gt; out of the cell and 2 K&lt;sup&gt;+&lt;/sup&gt; into the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The efficiency of the pump is therefore energy required to move these ions/energy released by ATP hydrolysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much energy is needed to move the ions? In each case there is a contribution from the fact that the ions are moved along a concentration gradient (the chemical component) and from the movement along a gradient of electrical potential (because of the membrane potential). In considering these components we have to think about whether energy needs to be used when the ions move, or whether it is released.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the chemical component we can use&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ΔG = RTln(ratio of concentration, inside and outside), where ln = natural logarithm&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sign of this ΔG will depend upon how the ratio is expressed (in/out or out/in) but the absolute value will be the same. So I calculate an absolute value and then deduce the sign of the free energy change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For Na&lt;sup&gt;+&lt;/sup&gt; ΔG = modulus(2 x 310 x ln(12/140)) = 1,523 cal mol&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since Na&lt;sup&gt;+&lt;/sup&gt; is being moved up a concentration gradient, work must be done so the free energy change is positive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Applying the same formula and logic for the movement of K&lt;sup&gt;+&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ΔG = 2,065 cal mol&lt;sup&gt;-1&lt;/sup&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(This value is greater than that for Na&lt;sup&gt;+&lt;/sup&gt; because the concentration gradient is steeper.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next I calculate the electrical components using:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ΔG = zFμ, where z is the charge on the ion = 1 in both cases, and μ is the membrane potential (in volts).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for both Na&lt;sup&gt;+&lt;/sup&gt; and K&lt;sup&gt;+&lt;/sup&gt; the absolute ΔG value is 1,383 cal mol&lt;sup&gt;-1&lt;/sup&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in this case Na&lt;sup&gt;+&lt;/sup&gt; is moving out, against the membrane potential while K&lt;sup&gt;+&lt;/sup&gt;  is moving in with the membrane potential. Thus the value of ΔG is positive for Na&lt;sup&gt;+&lt;/sup&gt; but negative for K&lt;sup&gt;+&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now I combine the chemical and electrical components to get the net free energy change per mole of ions moved:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Na&lt;sup&gt;+&lt;/sup&gt; ΔG = 1,523 + 1,383 = 2,906 cal mol&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;K&lt;sup&gt;+&lt;/sup&gt; ΔG = 2,065 -1,383 = 682 cal mol&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now I consider how to combine these two values. Each cycle of the pump uses 1 ATP to move 3 Na&lt;sup&gt;+&lt;/sup&gt; and 2 K&lt;sup&gt;+&lt;/sup&gt;. Therefore each mole of ATP moves 3 moles of Na&lt;sup&gt;+&lt;/sup&gt; and 2 moles of K&lt;sup&gt;+&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Energy from 1 mole ATP that is used to move ions = (3 x 2,906) + (2 x 682)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;= 10,082 cal &lt;/p&gt;&#xA;&#xA;&lt;p&gt;= 10.1 kcal&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much energy is released from hydrolysis of 1 mol of ATP? Estimates vary but a commonly accepted value seems to be 12 kcal mol&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus efficiency of the pump = 100*(10.1/12) = 84%.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the free energy of ATP hydrolysis depends on ATP concentration, pH, and the amount of Mg present. For a well-fed brain, this is around 14 kcal/mol (see Journal Of Physical Chemistry B, 114 (49), (2010). 16137-16146). This gives an efficiency of around 70%, still too high but better...&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2013-04-18T15:54:36.500" LastActivityDate="2013-04-18T15:54:36.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5304" PostTypeId="1" AcceptedAnswerId="5305" CreationDate="2012-11-22T16:41:21.773" Score="3" ViewCount="5228" Body="&lt;p&gt;Every time I get ill (cold, flu etc) I take a couple of these wonderful tablets for up to 4 times a day and I, eventually, get better.  What exactly is paracetamol?  Why is it so effective and is it really not harmful as my doctor would have me believe?&lt;/p&gt;&#xA;" OwnerUserId="1519" LastEditorUserId="69" LastEditDate="2012-12-02T15:51:13.870" LastActivityDate="2014-09-16T23:29:46.233" Title="Why is Paracetamol so great?" Tags="&lt;pharmacology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5305" PostTypeId="2" ParentId="5304" CreationDate="2012-11-22T17:07:12.343" Score="11" Body="&lt;p&gt;Paracetamol is a pain killer, it does not treat the cause of your illness, it only alleviates the symptoms. From its &lt;a href=&quot;http://en.wikipedia.org/wiki/Paracetamol&quot; rel=&quot;noreferrer&quot;&gt;wikipedia page&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Paracetamol [...], chemically named&#xA;N-acetyl-p-aminophenol, is a widely used over-the-counter analgesic&#xA;(pain reliever) and antipyretic (fever reducer).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So, &lt;strong&gt;paracetamol does not make you better&lt;/strong&gt;. Your immune system makes you better. Paracetamol just makes you &lt;em&gt;feel&lt;/em&gt; better while you are waiting for your immune system to get an infection under control.&lt;/p&gt;&#xA;&lt;p&gt;You should be aware that it is only safe in small doses and a toxic dose is not that much more than the recommended one (&lt;a href=&quot;http://www.patient.co.uk/doctor/Paracetamol-Poisoning.htm&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Risk of severe liver damage (ie a peak ALT more than 1000 IU/L)&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Based on the dose of paracetamol ingested (mg/kg body weight):&lt;/p&gt;&#xA;&lt;pre&gt;&lt;code&gt;Less than 150 mg/kg - unlikely&#xA;More than 250 mg/kg - likely&#xA;More than 12 g total - potentially fatal&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Again from wikipedia:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;While generally safe for use at recommended doses (1,000 mg per single&#xA;dose and up to 4,000 mg per day for adults),[6] acute overdoses of&#xA;paracetamol can cause potentially fatal liver damage and, in rare&#xA;individuals, a normal dose can do the same; the risk may be heightened&#xA;by chronic alcohol abuse, though it is lessened by contemporary&#xA;alcohol consumption. Paracetamol toxicity is the foremost cause of&#xA;acute liver failure in the Western world, and accounts for most drug&#xA;overdoses in the United States, the United Kingdom, Australia and New&#xA;Zealand.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I am sure someone else can explain the pharmacokinetics and details of action of paracetamol. I just wanted to point out that paracetamol &lt;em&gt;can&lt;/em&gt; be dangerous and should be treated with respect.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-11-22T19:11:13.260" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5306" PostTypeId="1" AcceptedAnswerId="5308" CreationDate="2012-11-22T18:53:48.533" Score="11" ViewCount="3959" Body="&lt;p&gt;I've been reading about brain plasticity and how the brain can &quot;rewire&quot; itself. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the things that is not clear to me - how neurons can establish new connections. &lt;strong&gt;Does this rewiring mean that neurons can &quot;disconnect&quot; from other neurons to reuse existing dendrites&lt;/strong&gt;?  Or do neurons grow new dendrites to make these new connections, adding to existing ones? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2017-09-14T18:55:11.907" Title="How do neurons form new connections in brain plasticity?" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5307" PostTypeId="2" ParentId="5217" CreationDate="2012-11-22T18:56:49.883" Score="5" Body="&lt;p&gt;Microbiome manipulation is a common theme in these answers/comments, and there are experimental methodologies for investigating such things. For example: &quot;Topographical and Temporal Diversity of the Human Skin Microbiome&quot; at &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805064&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805064&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One selection pressure that hasn't been mentioned is the reduction of harmful bacteria that occurs when providing a growth advantage to more benign bacteria. Many hairy areas are those where bacteria in general can live and prosper. Various ways hair could impact the microbioime are are easily imagined, for example greatly increased surface area should favor aerobic vs anaerobic bacteria. More specific host-bacteria interaction, e.g. specific bacteria being selected for due to the presence of certain hair surface proteins or the microstructure of the hairs surface might be harder to investigate. How hair surface varies in different location might be informative.&lt;/p&gt;&#xA;" OwnerUserId="1688" LastActivityDate="2012-11-22T18:56:49.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5308" PostTypeId="2" ParentId="5306" CreationDate="2012-11-22T19:41:26.287" Score="7" Body="&lt;p&gt;I haven't read anything particularly about dendrites being reshaped, though I would expect them to be as flexible as other parts of the cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The more commonly discussed topic (in my literary experience) is reshaping of the axon's branches before forming synaptic terminals. These branches are not fixed even in adults - neurons can grow new and retract old branches, attaching (synapsing) to other cells in new places and removing old connections (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Synaptogenesis&quot;&gt;Wikipedia: Synaptogenesis&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally to this actual change in the number of synapses, individual synapses can be regulated in their signal strength by adjusting the number of neurotransmitter receptors in the postsynaptic membrane (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20655734&quot;&gt;Gerrow&amp;amp;Triller, 2010&lt;/a&gt;, also see &lt;a href=&quot;http://en.wikipedia.org/wiki/Synaptic_plasticity&quot;&gt;Wikipedia: Synaptic plasticity&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-11-22T19:41:26.287" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5309" PostTypeId="2" ParentId="5298" CreationDate="2012-11-22T20:37:20.530" Score="6" Body="&lt;p&gt;Mammalian tongues are red because of haemoglobin. Blue/black colouration is due to the additional presence of melanin.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At the boundary between the epidermis and dermis are melanophores, cells that contain melanin. This brown pigment absorbs ultraviolet radiation from the sun that might otherwise damage the underlying dermal tissue. Melanin in the dark tongues of giraffes (Giraffa camelopardalis) protects the tissue from sunburn as the animals lift their heads into the top branches of trees to forage for leaves. In humans, synthesis of melanin increases upon exposure to sunlight and produces tanning. Extensions of melanophores reach into the epidermis where they inject their pigments into developing hair cells. In a few cases, such as the bright ischial callosities of baboons, pigmented patches of skin are used as visual signals. The blue and red coloration on the scrotum and perineal region of male vervets (Chlorocebus aethiops) is used in dominance displays.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From: Mammalogy: Adaptation, Diversity, Ecology by George A. Feldhamer, Lee C. Drickamer, Stephen H. Vessey and Joseph F. Merritt (2007) p 97 The Johns Hopkins University Press; 3rd edition edition &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-22T20:37:20.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5310" PostTypeId="2" ParentId="5286" CreationDate="2012-11-23T07:58:33.450" Score="2" Body="&lt;p&gt;Large cells: &lt;a href=&quot;http://en.wikipedia.org/wiki/Adipocyte&quot; rel=&quot;nofollow&quot;&gt;adipocytes&lt;/a&gt;, the cells that store fat are possible the largest in humans, because after puberty they rarely divide and just enlarge if a person gains weight. A typical adipocyte is about 0.1mm in diameter, but may be a lot larger. Another good candidate is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Megakaryocyte&quot; rel=&quot;nofollow&quot;&gt;megakaryocyte&lt;/a&gt;, which is a gigantic (up to 0.1mm), cell with multiple copies of its genome producing blood platelets. Depending on your definition of a single cell, also &lt;a href=&quot;http://en.wikipedia.org/wiki/Myocyte&quot; rel=&quot;nofollow&quot;&gt;myocytes&lt;/a&gt; may be considered large cells, because during development several cells fuse to form one muscular fibre. Additionally, myocytes gain weight if a person excersises and strengthens muscles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Small cells are more common, and it is difficult to point to some consistently smallest cells. The smallest kind-of-cells are definately &lt;a href=&quot;http://en.wikipedia.org/wiki/Thrombocytes&quot; rel=&quot;nofollow&quot;&gt;platelets&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Red_blood_cell&quot; rel=&quot;nofollow&quot;&gt;erythrocytes&lt;/a&gt; (red blood cells - they are anucleated, thus may not be considered &quot;real&quot; cells). Generally, the part that determines the minimum size of the cell is the nucleus, so any cells, that are more-or-less metabolically inactive may be just a tiny bit larger than the size of their nucleuses. These may be for example &lt;a href=&quot;http://en.wikipedia.org/wiki/Polar_body&quot; rel=&quot;nofollow&quot;&gt;polar cells&lt;/a&gt;, the tiny cells, that carry the excess of genome during meiosis in women and die soon afterwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in all kinds of strange cells inside yourself, you might start by browsing &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_distinct_cell_types_in_the_adult_human_body&quot; rel=&quot;nofollow&quot;&gt;this beautiful, though longish list&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastActivityDate="2012-11-23T07:58:33.450" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="5311" PostTypeId="1" CreationDate="2012-11-23T10:19:19.547" Score="8" ViewCount="324" Body="&lt;p&gt;Does the entire surface of the earth contain organisms?&#xA;My teacher mentioned that in some parts of the earth, there aren't any organism. Is this true?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="1460" LastActivityDate="2012-11-25T17:04:42.873" Title="Does the entire surface of the earth contain organisms?" Tags="&lt;ecology&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5312" PostTypeId="2" ParentId="5311" CreationDate="2012-11-23T11:57:43.870" Score="7" Body="&lt;p&gt;That will depend on many things. How do you define surface? Is one meter underground still &quot;surface&quot;? How about a kilometer?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, how large an area are we talking about? You could probably find a square millimeter in, for example, Antarctica that has no organisms. I don't think you would find a square kilometer with no organisms though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are organisms (called &lt;a href=&quot;http://en.wikipedia.org/wiki/Extremophile&quot; rel=&quot;nofollow noreferrer&quot;&gt;extremophiles&lt;/a&gt;) that thrive in the most hostile environments we know, they can survive extreme heat, cold, acidity, salinity etc. I found &lt;a href=&quot;http://nai.arc.nasa.gov/poster/poster_images/astrobioactivity1-studenthandout.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this very nice list&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Cold – The McMurdo Dry Valleys in Antarctica are some of the coldest, driest deserts on Earth, with average annual temperatures of&#xA;  -20oC (-4oF) and less than 10 centimeters (4 inches) of precipitation a year. Scientists have found bacteria in liquid water pockets&#xA;  embedded about twelve feet deep in “solid” lake ice. Some of these&#xA;  bacteria use chemical nutrients from particles of dirt in the ice and&#xA;  use energy from sunlight for photosynthesis.&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Hot – Large concentrations of microbes thrive in Yellowstone National Park’s Grand Prismatic Springs, a hot spring with water&#xA;  temperatures up to 90oC (188oF). Other hot springs in Yellowstone are&#xA;  extremely acidic, yet are home to many different kinds of bacteria and&#xA;  microbes. Many of these microbes use chemical nutrients in the waters&#xA;  and energy from sunlight for photosynthesis. Deep underground –&#xA;  Scientists have discovered bacteria living in ground- water 5&#xA;  kilometers below the surface in deep gold mines of the Witwatersrand&#xA;  Basin in South Africa. These microbes thrive in cavities and cracks in&#xA;  rocks. Scientists are also are investigating life within and below&#xA;  permafrost in north- ern Canada.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Bottom of the sea – Scientists have found abundant life clustered around hydro- thermal vents on the ocean floor, including bacteria,&#xA;  mussels, clams, shrimp, and giant tubeworms that can reach ten feet in&#xA;  length. Water pouring out of the vents in the complete darkness&#xA;  thousands of feet under the surface of the sea can reach temperatures&#xA;  of 113-120oC (235-248oF). The high pressures keep the water from&#xA;  boiling. Bacteria use chemicals in the vent’s water, primarily&#xA;  hydrogen sulfide, as their energy source instead of sunlight. Other&#xA;  creatures survive by eating the bacte- ria or each other.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;High Acidity – The water in the Rio Tinto in southwestern Spain is very acidic, a result of chemical reactions between the water, and&#xA;  iron and sulfur minerals in the ground. The river has a deep red&#xA;  color, like wine, because of iron dissolved in the water. Microbes&#xA;  living in the water use chemical reac- tions with iron and sulfur&#xA;  minerals to generate the energy they need. Products from these&#xA;  metabolic reactions contribute to the low pH in the environment. Many&#xA;  algae and fungi also live in the acidic waters.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As far as I know, there is no evidence of life in molten lava. Apart from that though, just about every habitat you can find on the earth has been colonized by life. Ask your teacher what parts of the earth she is talking about, and report back here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/a/5313/1306&quot;&gt;MCM's very interesting answer&lt;/a&gt; prompted me to do some more research. It seems that life has now been found even in the Atacama (taken from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov.gate1.inist.fr/pubmed/22819826&quot; rel=&quot;nofollow noreferrer&quot;&gt;Azua-Bustos&#xA;&lt;em&gt;et al&lt;/em&gt;&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For a long time it was thought that regions of the Atacama could not&#xA;  uphold any type of life forms. However, recent culture-independent&#xA;  methods (metagenomics, transcriptomics, in situ hybridization, etc.)&#xA;  have improved the sensitivity for life detection. Thus, microorganisms&#xA;  have been found even in the driest areas of this desert, which makes&#xA;  scientists wonder about the true limit of water availability needed to&#xA;  sustain life as we know it. In this review, we summarize the efforts&#xA;  devoted to the characterization of microbial life in the Atacama&#xA;  Desert.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, it seems that life can exist even in the Atacama. That leaves only molten lava...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov.gate1.inist.fr/pubmed/22819826&quot; rel=&quot;nofollow noreferrer&quot;&gt;Azua-Bustos &lt;em&gt;et al&lt;/em&gt;, Life at the dry edge: microorganisms of the Atacama Desert, &lt;em&gt;FEBS Lett.&lt;/em&gt; 2012 Aug 31;&lt;strong&gt;586&lt;/strong&gt;(18):2939-45&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2012-11-23T16:41:43.697" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5313" PostTypeId="2" ParentId="5311" CreationDate="2012-11-23T14:42:07.533" Score="5" Body="&lt;p&gt;Barring the very obvious surfaces (the pits of active volcanoes), the only place I'm aware of that might not contain life is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Atacama_Desert&quot;&gt;Atacama Desert&lt;/a&gt; near the Andes Mountains in Chile and Brazil. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whereas other places that seem inhospitable - Antarctic, Hot Springs, regular deserts, extremely high altitudes, etc. - the basic necessities for life still exist (carbon, water, nitrogen). In the Atacama, though:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The average rainfall in the Chilean region of Antofagasta is just 1 millimetre (0.04 in) per year. Some weather stations in the Atacama have &lt;strong&gt;never&lt;/strong&gt; received rain. Evidence suggests that the Atacama may not have had any significant rainfall from 1570 to 1971...  Studies by a group of British scientists have suggested that some river beds have been dry for 120,000 years.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's the driest place on the planet. It's drier than every other desert by a long shot, and is so dry that NASA occasionally uses it to simulate Mars.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In 2003, a team of researchers published a report in the journal &lt;strong&gt;Science&lt;/strong&gt; titled &lt;em&gt;&quot;Mars-like Soils in the Atacama Desert, Chile, and the Dry Limit of Microbial Life&quot;&lt;/em&gt; in which they duplicated the tests used by the Viking 1 and Viking 2 Mars landers to detect life, and were unable to detect any signs in Atacama Desert soil. The region may be unique on Earth in this regard and is being used by NASA to test instruments for future Mars missions. The team duplicated the Viking tests in Mars-like Earth environments and found that they missed present signs of life in soil samples from Antarctic dry valleys, the Atacama Desert of Chile and Peru, and other locales.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So while life &lt;em&gt;might&lt;/em&gt; exist in the Atacama (signs of life do not always point towards currently-existing life), it's hiding extremely well. Probably beneath the topsoil, where no multicellular organisms have ever been spotted and unicellular organisms may not exist at all. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultimately your teacher is correct, although whether they meant the Atacama or erroneously considered other places on the planet you'll have to ask them. &lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-11-23T14:42:07.533" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5314" PostTypeId="1" AcceptedAnswerId="5317" CreationDate="2012-11-23T23:35:47.600" Score="8" ViewCount="4847" Body="&lt;p&gt;If you have a single-stranded RNA that is complementary to a double-stranded DNA, how do they interact to form what my prof. calls a &quot;triplex structure&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;e.g.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;    UGCUGAUAGCUACG&#xA;ACGTACGACTA&#xA;TGCATGCTGAT&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I don't understand how the DNA can form 2 bonds there?&lt;/p&gt;&#xA;" OwnerUserId="1692" LastEditorUserId="1692" LastEditDate="2012-11-24T10:58:29.423" LastActivityDate="2012-11-24T13:14:01.117" Title="How does a single-stranded RNA bind to a double-stranded DNA to form a &quot;triplex structure&quot;?" Tags="&lt;rna&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5315" PostTypeId="1" CreationDate="2012-11-24T06:25:03.553" Score="5" ViewCount="596" Body="&lt;p&gt;What is a book that goes into reasonable detail (but isn't textbook-level technical) about the origin of earth and in particular the origin of life on earth? Something intended for a broad audience, but that still covers the biology/geology and does not completely gloss over the sicence.&lt;/p&gt;&#xA;" OwnerUserId="1693" LastEditorUserId="852" LastEditDate="2012-11-25T10:28:38.837" LastActivityDate="2012-11-26T10:32:08.800" Title="Good book on Origin of Life" Tags="&lt;evolution&gt;&lt;molecular-evolution&gt;&lt;book-recommendation&gt;&lt;literature&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="3" ClosedDate="2012-11-26T11:27:56.757" ContentLicense="CC BY-SA 3.0" />
  <row Id="5317" PostTypeId="2" ParentId="5314" CreationDate="2012-11-24T12:34:21.987" Score="7" Body="&lt;p&gt;DNA-RNA triplex formation is well-documented. It was originally analysed in simple model polynucleotides where the DNA has a polypurine strand and the RNA has a polypyrimidine, e.g.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;rCCCCCC&#xA;dGGGGGGGGGGGGGG   &#xA;dCCCCCCCCCCCCCC&#xA;&#xA;rUUUUUU&#xA;dAAAAAAAAAAAAA&#xA;dTTTTTTTTTTTTT&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;but it is now known to occur in more complex sequences. One of the best studied examples is in the promoter of the human DHFR gene: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Gee, J. E. et al.(1992) Triplex formation prevents Sp1 binding to the dihydrofolate reductase promoter. J. Biol. Chem. 267, 11163–11167&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IOyul.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this work the oligonucleotide GR19 was shown to bind in a triple helix to SpI binding site I in the DHFR promoter (CR19 was used as a control). Triplex formation was detected by gel shift, and the specificity was confirmed by DNase I footprinting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This effect is part  of the regulation of DHFR - the transcript from a minor upstream promoter binds to the major promoter, see:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Martianov, I. et al. (2007) Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445: 666-670&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The structure of these triple helices involves a combination of Watson-Crick base pairing in the DNA duplex together with &lt;a href=&quot;http://en.wikipedia.org/wiki/Hoogsteen_base_pair&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hoogsteen base pairing&lt;/a&gt; in the RNA-DNA interaction:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ahIEy.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure taken from:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Morgan, A. R. &amp;amp; Wells, R. D. (1968) Specificity of the three-stranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences. J. Mol. Biol. 37, 63–80&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-11-24T13:14:01.117" LastActivityDate="2012-11-24T13:14:01.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5318" PostTypeId="1" CreationDate="2012-11-24T14:05:21.003" Score="8" ViewCount="1267" Body="&lt;p&gt;This &lt;a href=&quot;http://www.ubergizmo.com/2011/07/worlds-strongest-magnet/&quot;&gt;article&lt;/a&gt; states of a 25T magnet, &quot;.. If are ever caught in one of these devices, let’s just say you probably won’t live to tell the tale.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the above statement in order? What effect would exposure to such a high magnetic field have on the exposed human?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="460" LastEditDate="2014-04-09T15:03:24.343" LastActivityDate="2014-04-09T15:03:24.343" Title="Would exposure to a strong magnetic field have deleterious effect on the human?" Tags="&lt;human-biology&gt;&lt;mri&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5319" PostTypeId="2" ParentId="5315" CreationDate="2012-11-24T14:22:04.537" Score="2" Body="&lt;p&gt;I think &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0198607865&quot; rel=&quot;nofollow&quot;&gt;this book&lt;/a&gt; (The Story of Life, Southwood) would be just what you are looking for - it was one of my modules during my undergrad in Evolution and I think it touches on the basic geology too. It is quite an easy ready but covers the material pretty well, it also has good reviews on Amazon etc.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2012-11-24T14:22:04.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5320" PostTypeId="2" ParentId="5315" CreationDate="2012-11-24T15:23:38.670" Score="5" Body="&lt;p&gt;I would recommend The selfish gene by Richard Dawkins. It is targeted at a scientifically interested audience, but well written and recognized by the scientific community.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://amzn.com/0199291152&quot;&gt;http://amzn.com/0199291152&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="852" LastActivityDate="2012-11-24T15:23:38.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5321" PostTypeId="2" ParentId="5318" CreationDate="2012-11-24T15:59:22.913" Score="9" Body="&lt;p&gt;First thing comes to my mind is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hall_effect&quot;&gt;Hall effect&lt;/a&gt;. Any directional ion or electron flow will experience a force (depending on the orientation with respect to the magnetic field). So if the magnet is very strong, I think some of the ion channels for action potential generation and propagation would malfunction. (11 mT stopped action potentials for a while but recovered in mouse as &lt;a href=&quot;http://dx.doi.org/10.1002/bem.2250160108&quot;&gt;reported here&lt;/a&gt;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, according to &lt;a href=&quot;http://www.biomedical-engineering-online.com/content/3/1/11&quot;&gt;these&lt;/a&gt; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0079610704001117&quot;&gt;papers&lt;/a&gt; static magnetic fields has little biological effect, and it seems to be reversible. But, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0079610704001178&quot;&gt;this&lt;/a&gt; reports genotoxicity in 4.5T (in vitro), and developmental disorders in 1.5T (in vivo, mouse). Contradictory reports indicate we do not know the full answer yet as usual.&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2012-11-24T15:59:22.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5322" PostTypeId="1" AcceptedAnswerId="5327" CreationDate="2012-11-24T19:26:51.270" Score="4" ViewCount="72" Body="&lt;p&gt;Is territoriality (recognizing a geographic location, and challenging another member of the same species and gender) only in the domain of the male of a species? Are there any species out there where the female of the species identifies, defines, and protects her territory? What about any species where territoriality is gender neutral (&lt;em&gt;tic&lt;/em&gt; humans excluded!)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought of bees, but that is a community affair - even if it is a matriarchial society.&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="3952" LastEditDate="2013-08-04T02:18:23.183" LastActivityDate="2013-08-04T05:49:23.243" Title="Is territoriality only the domain of the male of a species?" Tags="&lt;sociality&gt;&lt;territoriality&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5323" PostTypeId="2" ParentId="5311" CreationDate="2012-11-24T20:06:03.090" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;h1&gt;Sterile! Lake Vostok’s microbes elusive in first measurements of surface water&lt;/h1&gt;&#xA;  &#xA;  &lt;p&gt;A first analysis of the ice that froze onto the drillbit used in last&#xA;  February’s landmark drilling to a pristine Antarctic lake shows no&#xA;  native microbes came up with the lake water, according to Sergey Bulat&#xA;  of Petersburg Nuclear Physics Institute (Russia). The very uppermost&#xA;  layer of Lake Vostok appears to be “lifeless” so far, says Bulat, but&#xA;  that doesn’t mean the rest of it is.   Bulat reported what he calls&#xA;  his team’s “very preliminary results” on Tuesday, at the 12th European&#xA;  Workshop on Astrobiology (ENEA 2012), in Stockholm, Sweden, at the&#xA;  AlbaNova University Center. Bulat and his colleagues counted the&#xA;  microbes present in the ice sample and checked their genetic makeup to&#xA;  figure out the phylotypes. They counted fewer than 10 microbes/ml —&#xA;  about the same magnitude they would expect to find in the background&#xA;  in their clean room. And three of the four phylotypes they identified&#xA;  matched contaminants from the drilling oil, with the fourth unknown&#xA;  but also most likely from the lubricant.   Bulat hopes to get clean&#xA;  samples from the ice frozen in the borehole below where the drill bit&#xA;  stopped. That won’t be until next May (2013), if all goes well after&#xA;  the next Russian drilling expedition in December-January. Even if the&#xA;  top of the lake ends up being empty, Bulat suspects microbes will come&#xA;  from lower water depths, or from sediment samples at the bottom of the&#xA;  lake.   Lake Vostok is a stand-in for icy bodies that might harbor&#xA;  life, like Jupiter’s moon Europa. Gerda Horneck of the German&#xA;  Aerospace Center (DLR) said that any result from Lake Vostok is&#xA;  important for astrobiology, and the search for extremophiles that&#xA;  could give hints of what life could be like elsewhere. “Let’s see what&#xA;  comes out next round,” she told me at the end of the meeting on&#xA;  Wednesday.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.scoop.it/t/amazing-science/p/3031509753/sterile-lake-vostok-s-microbes-elusive-in-first-measurements-of-surface-water&quot; rel=&quot;nofollow&quot;&gt;http://www.scoop.it/t/amazing-science/p/3031509753/sterile-lake-vostok-s-microbes-elusive-in-first-measurements-of-surface-water&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;More info on Lake Vostok:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;http://earthsci.org/education/Lake_Vostok/vostok.html&quot; rel=&quot;nofollow&quot;&gt;http://earthsci.org/education/Lake_Vostok/vostok.html&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1697" LastEditorUserId="69" LastEditDate="2012-11-25T17:04:42.873" LastActivityDate="2012-11-25T17:04:42.873" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5324" PostTypeId="1" CreationDate="2012-11-23T23:19:00.897" Score="6" ViewCount="471" Body="&lt;p&gt;I was wondering if someone can compare the functionality of vitamin A, Bx (x means numbers, such as 1, 2, 3, ...), C, D, E, K in the skin?  They are used in cosmetics but what is their actual effect?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is some source that compares between them in particular, I think it will help me understand some important basics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some products:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.gnc.com/product/index.jsp?productId=2134133&quot; rel=&quot;nofollow&quot;&gt;GNC Vitamin C Moisturizing Cream&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.gnc.com/product/index.jsp?productId=2134134&quot; rel=&quot;nofollow&quot;&gt;GNC Vitamins E, A &amp;amp; D Moisturizing Cream&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.gnc.com/product/index.jsp?productId=2134011&quot; rel=&quot;nofollow&quot;&gt;Reviva™ Labs Alpha Lipoic Acid Vitamin C Ester &amp;amp; DMAE Cream&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.gnc.com/product/index.jsp?productId=2612785&quot; rel=&quot;nofollow&quot;&gt;Reviva™ Labs Vitamin K Cream&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="262" OwnerDisplayName="Tim" LastEditorUserId="262" LastEditDate="2012-12-26T03:50:26.470" LastActivityDate="2014-06-28T18:48:25.323" Title="Functionality of vitamin A, Bx, C, D, E, K as used in cosmetics for the skin?" Tags="&lt;human-biology&gt;&lt;vitamins&gt;&lt;skin&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5325" PostTypeId="1" CreationDate="2012-11-25T04:16:18.460" Score="3" ViewCount="1078" Body="&lt;p&gt;I think it's pith, but here (non-english country) many chef suggest orange's vascular veins which look &quot;fibrous&quot; and have similar translated word with &quot;fiber&quot; itself. &#xA;Please enlighten me which?&lt;/p&gt;&#xA;" OwnerUserId="1700" LastEditorUserId="69" LastEditDate="2012-11-25T17:06:47.627" LastActivityDate="2014-01-22T22:19:31.820" Title="Which part of oranges contain fiber?" Tags="&lt;nutrition&gt;&lt;fruit&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5326" PostTypeId="1" CreationDate="2012-11-25T04:30:12.317" Score="3" ViewCount="9431" Body="&lt;p&gt;Possibility also include &quot;adaptation mode&quot; if such exist. I don't discern whether autotrophic/heterotrophic part play only minor role either.&lt;/p&gt;&#xA;" OwnerUserId="1700" LastEditorUserId="1320" LastEditDate="2012-11-25T11:55:25.747" LastActivityDate="2014-10-23T00:18:51.913" Title="Is there any complex organism that is both autotroph and heterotroph?" Tags="&lt;evolution&gt;&lt;adaptation&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5327" PostTypeId="2" ParentId="5322" CreationDate="2012-11-25T05:27:18.087" Score="6" Body="&lt;p&gt;Absolutely not.  In many spiders and insects, the female holds the territory.  Many spiders for instance have much larger females than males - in these species the female can be &gt; 10x bigger than the male and the male may not even eat during its lifetime.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ordinary garden &lt;a href=&quot;http://en.wikipedia.org/wiki/Orb-weaver_spider&quot; rel=&quot;nofollow&quot;&gt;orb weaving spiders&lt;/a&gt; are this sort of animal.  Only the females even spin webs.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Redback_spider&quot; rel=&quot;nofollow&quot;&gt;Australian red back spider&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quite often males are the 'disposable sex'. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-08-04T05:49:23.243" LastActivityDate="2013-08-04T05:49:23.243" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5328" PostTypeId="1" CreationDate="2012-11-25T06:06:45.890" Score="3" ViewCount="115" Body="&lt;p&gt;I'm reading about &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemoreceptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;chemoreceptors on Wikipedia&lt;/a&gt;, and see that the typical ones are mentioned: taste, smell, CO₂.  I &lt;strong&gt;would like to learn more about the other kinds of chemoreceptors that humans may possess.&lt;/strong&gt; I'm particularly interested if these can detect chemical compounds, or lack of thereof in food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's an example:&#xA;&lt;a href=&quot;https://biology.stackexchange.com/questions/5090/do-omnivore-mammals-vary-food-preferences-based-on-dietary-needs&quot;&gt;Do omnivore mammals vary food preferences based on dietary needs?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There's &quot;rapid recognition of Indispensible Amino Acid(IAA) depletion in the rat brain's IAA chemosensor, the anterior piriform cortex (APC)&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Reading the article above, it appears that at least rats and birds can develop aversion to food that does not contain indispensable amino acids. This is done through chemosensors in the brain. Do humans possess any similar chemosensors?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-10-09T15:04:32.517" Title="Do humans have chemosensors for nutrients or chemicals?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;digestive-system&gt;&lt;sensation&gt;" AnswerCount="0" CommentCount="5" ClosedDate="2015-03-30T20:43:08.557" ContentLicense="CC BY-SA 3.0" />
  <row Id="5329" PostTypeId="1" AcceptedAnswerId="5340" CreationDate="2012-11-25T09:15:30.047" Score="2" ViewCount="45" Body="&lt;p&gt;A follow-up to &lt;a href=&quot;https://biology.stackexchange.com/questions/5322/is-territoriality-only-the-domain-of-the-male-of-a-species/5327&quot;&gt;Is territoriality only the domain of the male of a species?&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen a large butterfly chase a different kind of butterfly around - it may, or may not have been territoriality. Is there a minimum scale of size, sentience(?) an organism must attain to exhibit territoriality? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2012-11-26T02:18:13.430" Title="Is a minimum size/complexity necessary for an organism to exhibit territoriality?" Tags="&lt;territoriality&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5330" PostTypeId="2" ParentId="5326" CreationDate="2012-11-25T12:49:10.123" Score="6" Body="&lt;p&gt;For example &lt;a href=&quot;http://en.wikipedia.org/wiki/Drosera&quot;&gt;sundews&lt;/a&gt; are plants (so autotrophic), but they &quot;hunt&quot; for insects to get additional nutrients, e.g. nitrogen. As far as I remember the nitrogen is the main reason for eating other organisms but they also use other substances, including carbohydrates, from their prey.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastEditorUserId="1590" LastEditDate="2012-11-25T23:55:36.510" LastActivityDate="2012-11-25T23:55:36.510" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5331" PostTypeId="1" AcceptedAnswerId="5334" CreationDate="2012-11-25T14:13:24.263" Score="2" ViewCount="74" Body="&lt;p&gt;I have noticed that I rarely develop phlemmy throat-aches in the daytime, but often notice them after I have been sleeping.  Is this a recognised phenomenon?  Could it be because viruses or bacteria aren't being flushed out by food, water and vibration of the throat from speaking or that one's immune system is lower at night? If it is the latter, why is this?&lt;/p&gt;&#xA;" OwnerUserId="1667" LastEditorUserId="69" LastEditDate="2012-11-25T17:20:22.167" LastActivityDate="2012-11-25T17:51:58.560" Title="Is it more likely to develop a throat-ache at night?" Tags="&lt;human-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5332" PostTypeId="1" CreationDate="2012-11-25T14:46:19.083" Score="9" ViewCount="3117" Body="&lt;p&gt;What, physically, does the body do to measure it? I assume it's measured by how how turgid or plasmolysed certain 'sample cells' are, or water concentration in the blood,&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What &lt;em&gt;is&lt;/em&gt; the way they use to measure it?&lt;/li&gt;&#xA;&lt;li&gt;What do the receptor cells that do the measuring actually &lt;em&gt;do&lt;/em&gt; that is variable with water concentration, etc.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1667" LastEditorUserId="69" LastEditDate="2012-11-25T17:16:52.047" LastActivityDate="2013-09-04T20:08:59.043" Title="How does the body measure dehydration?" Tags="&lt;human-biology&gt;&lt;homeostasis&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5334" PostTypeId="2" ParentId="5331" CreationDate="2012-11-25T17:51:58.560" Score="2" Body="&lt;p&gt;It's because your mouth and tongue are stationary at night, so you don't move the slowly-drying saliva around to lubricate tissues. The mucous tissues dry out, resulting in greater friction with muscle movements (like swallowing), and your body is slightly dehydrated after 6-10 hours without water. If you've ever undergone surgery where they intubated you (stuck a tube down your throat to ensure air supply), afterwards it's a very similar feeling to waking up with a soar throat because your throat dries up and the anesthesia prevents muscle movements.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your immune system actually &lt;a href=&quot;http://health.usnews.com/health-news/family-health/sleep/articles/2008/12/15/immune-system-works-better-at-night&quot; rel=&quot;nofollow&quot;&gt;works better at night&lt;/a&gt; and &lt;a href=&quot;http://www.sciencedaily.com/releases/2008/09/080902075211.htm&quot; rel=&quot;nofollow&quot;&gt;requires rest to work efficiently&lt;/a&gt;. Bacteria and viruses don't really care about the time of day, although the muscles of the larynx do ensure that the mucous layer is continuously circulated. The continual circulation helps prevent debris and bacteria/virii from establishing themselves, although the magnitude of the effect isn't on the same scale of other tactics taken by your body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several factors can affect mucous/phlegm/saliva production - including infections, hydration levels, environmental temperature, smoking habits, diet, environmental humidity, and lots more. If it's a constant trouble, you can try drinking more water during the day, a steam humidifier, or talking to your doctor.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-11-25T17:51:58.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5337" PostTypeId="1" CreationDate="2012-11-25T22:38:54.120" Score="6" ViewCount="3983" Body="&lt;p&gt;I am trying to find 3D model of brains. I am particularly interested in adult-male -brains in Blender-model. I could find such 3D models of brains for sale &lt;a href=&quot;http://brain.turbosquid.com/3d-Models/3ds/max/xsi/c4d/obj&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; but because I am researching I would like to use some open-sourced candidate so anyone could preview things. So does there exist 3D models of brains in Blender?&lt;/p&gt;&#xA;" OwnerUserId="1705" LastEditorUserId="1705" LastEditDate="2012-12-01T22:01:48.430" LastActivityDate="2016-03-02T07:38:42.513" Title="3D models of adult male brain in the Blender software? Any open-sourced version for research?" Tags="&lt;human-anatomy&gt;&lt;brain&gt;&lt;software&gt;&lt;3d-structure&gt;&lt;visualization&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5338" PostTypeId="2" ParentId="2698" CreationDate="2012-11-26T00:02:30.037" Score="5" Body="&lt;p&gt;The Hoechst 33342 dye is similar to DAPI in that both are UV-excited, minor groove-binding, and emit signals proportional to total DNA content. Both are maximally excited around 355 nm and emit around 460 nm.  A UV light source is required, which may harm the cell. However, this is only a risk with Hoechst, as DAPI requires the cells to be fixed and/or permeabilized, which is incompatible with life. DAPI is more stable, but Hoechst is brighter. Both are subject to photo-bleaching after long exposure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is another newer DNA dye called DRAQ5 that makes up for all of the issues I mentioned earlier - it is bright, quite photo-stable, can be used in live cell imaging, and its excitation and emission wavelengths are in the far red end of the spectrum, meaning that no UV is needed. I found a good comparison chart at &lt;a href=&quot;http://www.biostatus.com/product/draq5/live_cell_comparison_chart/&quot; rel=&quot;nofollow&quot;&gt;http://www.biostatus.com/product/draq5/live_cell_comparison_chart/&lt;/a&gt; if you're interested. I have no connection to them, by the way, I've just used DRAQ5 a lot in the past.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2012-11-26T22:20:23.940" LastActivityDate="2012-11-26T22:20:23.940" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5339" PostTypeId="2" ParentId="1228" CreationDate="2012-11-26T01:02:54.017" Score="1" Body="&lt;p&gt;For one of the most comprehensive databases of protein post-translational modification (including phosphorylation, methylation, acetylation, ubiquitination, etc.), check out &lt;a href=&quot;http://www.phosphosite.org&quot; rel=&quot;nofollow&quot;&gt;PhosphoSite&lt;/a&gt;. You can find links to sequences, diseases, motifs, publications, antibodies, mass spec experiments, structures, you name it.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2012-11-26T01:02:54.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5340" PostTypeId="2" ParentId="5329" CreationDate="2012-11-26T02:18:13.430" Score="4" Body="&lt;p&gt;With some bacteria (e.g.. Bacillus subtilis) when food gets scarce they will start trying to kill their neighbors. (&lt;a href=&quot;http://arstechnica.com/science/2010/08/bacterial-cannibalism-factor-could-lead-to-new-antibiotics&quot; rel=&quot;nofollow&quot;&gt;See this arstechnica article&lt;/a&gt;) This appears to be a fight to the death between children and parents. That's a kind of territorial behavior, selectively applied only when there are not enough resources to go around. As there is no &quot;recognition&quot; of a specific territory being defended, just wherever the bacteria is currently, this might not meet a strict definition of territorial behavior. But the only thing simpler than bacteria are viruses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Come to think of it, I bet there are viruses that, once they infect a host cell, will change the cell's membrane or metabolism in a way that reduces its chance of being infected again by a similar virus. Such 'behavior' could be compared to defending a breeding ground. Can't find any examples though.&lt;/p&gt;&#xA;" OwnerUserId="1688" LastActivityDate="2012-11-26T02:18:13.430" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5341" PostTypeId="2" ParentId="5318" CreationDate="2012-11-26T02:46:44.340" Score="6" Body="&lt;p&gt;&quot;Strong&quot; is en entirely relative term, but given the number of MRI's performed, its pretty clear that fields several orders of magnitude larger than the Earth's background 0.5 gauss are at least &quot;mostly harmless&quot; with an exposure of limited duration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.fda.gov/Radiation-EmittingProducts/RadiationEmittingProductsandProcedures/MedicalImaging/ucm200086.htm&quot;&gt;an FDA publication regarding MRI scanners&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There are no known harmful side-effects associated with temporary exposure to the strong magnetic field used by MRI scanners. However, there are important safety concerns to consider before performing or undergoing an MRI scan.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jmri.22221/abstract&quot;&gt;This article&lt;/a&gt; describes human brain imaging with a 9.4T instrument, although this is about 10x larger than the strength of most MRIs. Note that &quot;no detrimental effects&quot; does not mean zero effects, but this is starting to get into the range of the 25T described above. There are 20T+ MRI machines avaialble, but I could not find an article describing use on live organisms. There is just this &lt;a href=&quot;http://precedings.nature.com/documents/3484/version/1&quot;&gt;one on dead mice parts&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1688" LastEditorUserId="1688" LastEditDate="2012-11-26T02:52:27.487" LastActivityDate="2012-11-26T02:52:27.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5342" PostTypeId="1" CreationDate="2012-11-26T04:06:52.247" Score="15" ViewCount="1403" Body="&lt;p&gt;As far as I know, this is one of the biggest questions in the epigenetic field: how are the epigenetic marks like histone modifications propagated through cell division? A lot is already known about DNA methylation (e.g. as in &lt;a href=&quot;https://biology.stackexchange.com/questions/3450/how-does-inheritance-of-methylation-of-dna-and-or-histones-work&quot;&gt;How does “inheritance of methylation” of DNA and/or histones work?&lt;/a&gt;), but very little about histone modifications. What is the current state of knowledge? &lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-01-13T21:38:10.277" Title="How are epigenetic marks transmitted during cell division?" Tags="&lt;genetics&gt;&lt;epigenetics&gt;&lt;histone&gt;&lt;histone-modifications&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5343" PostTypeId="2" ParentId="2698" CreationDate="2012-11-26T09:32:57.610" Score="5" Body="&lt;p&gt;DAPI and Hoechst 33342 (there are different Hoechst dyes, 33342 is one of the most commonly used) have very similar spectral characteristics. The only point is that DAPI is much better excited at 405 nm than Hoechst. Some microscopes and flow cytometers nowadays have 405 nm lasers or LEDs instead of UV sources, so this can become relevant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The main difference&lt;/strong&gt; and the main reason to choose either is that Hoechst can be used to stain living cells as it can pass the cell membrane, whereas DAPI can't. DAPI requires fixed and permeabilized cells.&lt;/p&gt;&#xA;" OwnerUserId="852" LastEditorUserId="852" LastEditDate="2012-11-26T09:58:51.597" LastActivityDate="2012-11-26T09:58:51.597" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5344" PostTypeId="2" ParentId="5315" CreationDate="2012-11-26T10:32:08.800" Score="0" Body="&lt;p&gt;This book by Steven Rose is supposed to be an update of the original for a modern audience:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.co.uk/Almost-Like-Whale-Species-Updated/dp/055299958X&quot; rel=&quot;nofollow&quot;&gt;http://www.amazon.co.uk/Almost-Like-Whale-Species-Updated/dp/055299958X&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="476" LastActivityDate="2012-11-26T10:32:08.800" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5347" PostTypeId="2" ParentId="5148" CreationDate="2012-11-26T16:20:14.830" Score="1" Body="&lt;p&gt;I have been pondering this question for a while and I get what RG255 is saying. I'm just not sure I entirely buy it. Take earthworms, for example. They are simultaneous true hermaphrodites (as far as I understand). The anatomy doesn't have to be &lt;em&gt;that&lt;/em&gt; complex*. They simply have two genital openings (one for eggs and one for sperm) and they line up in a &quot;69&quot; (excuse the vulgarity) position. This should, in theory, minimize the inbreeding depression. &#xA;However, it doesn't eliminate the maintenance of two sets of reproductive systems. But most organisms are not internally fertilized mammals with wildly complicated systems of internalized embryonic care. Most species lay a pile of eggs that a male squirts sperm on or squirt eggs while the male squirt sperm and then they hope for the best.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would think the advantages of simultaneous parenting (after all, many MANY species' males don't provide much in the way of child care) and its fitness advantage would vastly outweigh the burden of a second set of reproductive organs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With that said, I don't have a better explanation, but I find the question a very interesting one. The linked article is pay-walled, aside from the abstract, but I still disagree with &lt;em&gt;some&lt;/em&gt; of its tenets. To me true hermaphroditism should be very common (I realize it isn't) in species that don't need two parents to raise offspring, but &lt;strong&gt;do&lt;/strong&gt; benefit from some (as in one parent's) parental care. I recognize that it would do little to help species that merely dump gametes and leave because specialization of one reproductive system would likely do the job better and both genders equally contribute under that type of system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, RG255 convince me! Clearly there are good reasons, since gender (or asexual repr) is the norm, but I need more/better evidence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;* - Yes I realize they would need separate internal anatomies for each type of gamete, but still...&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Well fair enough about my external fertilizers comment. I don't have a reference, but I was thinking all multicellular life and I'd have to imagine that when you factor in plants, that external fertilization is relatively the norm (as is hermaphrodism (dioecy) for the plants).&#xA;As to earthworms, I disagree about your description of them. Their densities are actually &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0038071707001757&quot; rel=&quot;nofollow&quot;&gt;pretty high&lt;/a&gt;, so I'd wager they encounter each other frequently, so I'm not sure where that leaves them in terms of pressures for hermaphroditism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your point on the physiologic/hormonal issues of maintaining the systems is one I haven't previously considered. I honestly don't have any clue as to how daunting (or simple) that is, but I'd imagine that the sophistication of the systems would play a pretty key role. Makes me wonder how much this has been researched in true hermaprhodites. I suppose the main thing I keep coming back to is the overwhelming disadvantage gender has in terms of potential to create offspring. Males in many (most?) species essentially act as little more than sperm donors, thus half the individuals have effectively zero fitness. That just seems like an overwhelming advantage for hermaphrodites. &lt;/p&gt;&#xA;" OwnerUserId="1709" LastEditorUserId="69" LastEditDate="2012-11-27T12:09:58.927" LastActivityDate="2012-11-27T12:09:58.927" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="5348" PostTypeId="2" ParentId="5326" CreationDate="2012-11-26T16:38:31.430" Score="5" Body="&lt;p&gt;Just look up kleptoplasty&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Kleptoplasty&quot;&gt;http://en.wikipedia.org/wiki/Kleptoplasty&lt;/a&gt;&#xA;The slugs who most frequently employ it would fit your more restrictive definition. Now, if we're getting technical, they aren't born that way. They steal the chloroplasts, but you didn't say, so I guess you need to revise your expectations again. ;)&lt;/p&gt;&#xA;" OwnerUserId="1709" LastActivityDate="2012-11-26T16:38:31.430" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5349" PostTypeId="2" ParentId="5241" CreationDate="2012-11-26T16:40:04.997" Score="2" Body="&lt;p&gt;I agree - an odd approach to diet. Leptin does a lot and has several modes by which its expression is regulated. While the connections to insulin are well documented, I've brought to light here several other interesting characteristics of leptin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;LEP&lt;/em&gt; exerts its effects in the brain via the gene &lt;em&gt;MC4R&lt;/em&gt; - see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17932216&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HMGA1 strongly potentiates the capacity of the CEBPB (CCAAT/enhancer-binding protein beta) transcriptional factor to transactivate the LEP promoter (Esposito Fusco 2009 J Biol Chem 284:25998)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.fasebj.org/cgi/content/meeting_abstract/24/1_MeetingAbstracts/996.1&quot; rel=&quot;nofollow&quot;&gt;Subjects who watched a humorous video&lt;/a&gt; had changes in blood pressure and showed decreased levels of LEP as the level of GHRL increased, much like the acute effect of moderate physical exercise that is often associated with increased appetite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After adjustment for gender and age SERPINF1 SNP rs12603825 revealed significant association with MRI-derived total adipose tissue mass and fasting leptin concentrations, as well as nominal associations with bioelectrical impedance-derived percentage of body fat and clamp-derived insulin sensitivity in humans, thus contributing to overall body adiposity, obesity-related insulin resistance and circulating leptin levels (Böhm Ordelheide 2012 PLoS One 7:e34035).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Leptin influences the development of eyes and ears in zebrafish and was shown by knockout to affect eye and ear development in mice (Londraville 2012 General Comparative Endocrinology J). There are many connections between blood lipids, lipid homeostasis and eye health; many genes important to both blood lipids and eye health are shared.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, the LEP gene shows altered H3K9/K14 acetylation in response to hyperglycemia (Pirola Balcerczyk 2011 Genome Res).&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-11-26T16:40:04.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5351" PostTypeId="2" ParentId="5300" CreationDate="2012-11-27T00:34:53.607" Score="3" Body="&lt;p&gt;This is a very interesting question. Not sure if there is any way to answer without specifying a definition for complexity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is clear that everything is made of only the same few elements, so complexity must involve more than that. Do the number and position of identical molecules matter? If so, size matters and we would label a large jelly-fish as more complex than a cat and the air in a large hot-air ballon as more complex than any single living organism (assuming it is bigger).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it is clear that this is &lt;em&gt;not&lt;/em&gt; what is meant by biological complexity. Molecules acting identically should not count multiple times; the number of different molecules matters more than the mere number of molecules. But are immune cells really more complex simply because of a relatively minor difference that allows them to generate a wide variety of genetic variants?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about the variable coat color of a calico cat. Does the complex and non-repeatable (even with cloning) pattern mean it is complex, or does the fact that a simple genetic process underlies it mean it is simple.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The difference in complexity of different representation of the same thing is a classic problem in information theory (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Kolmogorov_complexity&quot; rel=&quot;nofollow&quot;&gt;Kolmogorov complexity&lt;/a&gt;). The ratio of the circumference of a circle to its diameter requires an infinite number of decimal digits to describe, but it is just a single geometric concept and it can be represented with one or two characters, as pi or &lt;strong&gt;π&lt;/strong&gt;. This applies to the problem of using phenotypes to measure complexity -- the language and definitions we use to describe or to differentiate phenotypes determines what is complex and what is simple.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moving beyond a simple static snapshot case, biological complexity involves time-dependent evolution. The &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Conway%27s_Game_of_Life&quot; rel=&quot;nofollow&quot;&gt;game of life&lt;/a&gt;&quot; demonstrates how simple rules + initial conditions yield apparent complex behaviors, and the beauty of fractals arises the same way. Many apparently complex organisms grow from small seeds plus time-evolved exposure to simple things like water and light and CO&lt;sub&gt;2&lt;/sub&gt;. Are trees only as complex as the seed they grow from?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, what about higher order complexity? One human brain is very similar in general makeup to another, but the concepts and memories stored seem complex and very different. Comparing the complexity of stored information between two people is the whole complexity problem over again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to me that complexity can only be cleanly measured within a specific context, and then only relatively. One can measure the &lt;em&gt;relative genomic complexity&lt;/em&gt; of two organism as the edit distance between the alphabetic sequences representing their genomes. The &lt;em&gt;relative regulatory complexity&lt;/em&gt; can be measured as mentioned above by @user1682. Each of these says something about an organisms complexity. But what if organism A has higher genomic complexity and organism B has higher regulatory complexity? It might be possible to derive something like a principle component &quot;basis set&quot; from several of these kinds of measurements using a training set and a list of organisms with predefined complexity values. Applying this &quot;standard&quot; scoring metric to another organism would allow ranking it on a &quot;standard&quot; scale, but it would be difficult to generate and obtain consensus on the initial &quot;expert&quot; ranked organism scale. Such a standard might have some value, but is not really theoretically satisfying in that it describe an organisms complexity in the same way that the average of a small sample describes the distribution of a large population.&lt;/p&gt;&#xA;" OwnerUserId="1688" LastActivityDate="2012-11-27T00:34:53.607" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5352" PostTypeId="1" AcceptedAnswerId="5370" CreationDate="2012-11-23T06:40:08.463" Score="2" ViewCount="352" Body="&lt;p&gt;This is a biology+physics question. Since there is no biology section, I am asking here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In brain, when a neuron reaches to threshold value, it fires an action potential. In most graphics, that is shown as 40 mV. An example is&#xA;&lt;img src=&quot;https://i.stack.imgur.com/m7alk.png&quot; alt=&quot;here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neuron's this potential reaches to all synapses where this neuron is connected to, and chemically transferred to other neuron and transformed into electric charge again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, because in artificial models not shown, if that whole 40 mV is distributed to those synapses according to synapse strengths, or do all synapses take a total 40 mV which is like creating a potential while it is not there?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another small question is if the collected potential is stored in neuron if it cannot reach to threshold value like a capacitor in circuit?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jVOVg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1713" OwnerDisplayName="tcak" LastEditorUserId="1713" LastEditDate="2012-11-28T18:17:17.273" LastActivityDate="2012-11-28T21:54:19.497" Title="Action Potential Distribution On Synapses" Tags="&lt;neuroscience&gt;&lt;biophysics&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5353" PostTypeId="2" ParentId="5352" CreationDate="2012-11-24T02:56:59.593" Score="1" Body="&lt;p&gt;Here is a pretty good animation of neurotransmission:&#xA;&lt;a href=&quot;http://www.mind.ilstu.edu/curriculum/neurons_intro/neurons_intro.php&quot; rel=&quot;nofollow&quot;&gt;google:Neurotransmitter action potential&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What they don't show there very well is that the action potential signal does not travel like a voltage on a wire, but as a propagating chemical condition. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the synapse, how strongly the connection is made to the next neuron is addressed in the &lt;a href=&quot;http://www.mind.ilstu.edu/curriculum/neurons_intro/flash_LTP.php?modGUI=232&amp;amp;compGUI=1828&amp;amp;itemGUI=3161&quot; rel=&quot;nofollow&quot;&gt;'long term potentiation'&lt;/a&gt; module. &lt;/p&gt;&#xA;" OwnerDisplayName="Bobbi Bennett" LastActivityDate="2012-11-24T02:56:59.593" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5356" PostTypeId="1" CreationDate="2012-11-27T16:38:48.443" Score="6" ViewCount="184" Body="&lt;p&gt;I am in the process of assembling and annotating the genome of a non-model organism, using almost exclusively short read (paired-end Illumina) data. Throughput is one obvious benefit of these data (high coverage for reasonable cost, error rates notwithstanding), but another benefit of RNA-seq data in particular is that they can be used in multiple ways. For example, I am mapping the RNA-seq reads to the genome to estimate transcript abundances and do some differential expression analysis, but I have also assembled the RNA-seq reads &lt;em&gt;de novo&lt;/em&gt; to use as evidence for genome annotation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are, however, limitations to using RNA-seq-derived transcripts for annotation. Full-length cDNAs would facilitate much more reliable annotation. However, I have no intuition for the relative cost, time commitment, or complexity of extracting and sequencing full-length cDNAs vs next-gen sequencing. Can anyone here comment on this?&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2015-10-19T03:56:59.787" Title="Comparative cost of RNA-seq vs sequencing full length cDNAs" Tags="&lt;molecular-genetics&gt;&lt;dna-sequencing&gt;&lt;genomics&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5357" PostTypeId="2" ParentId="1677" CreationDate="2012-11-27T17:32:15.027" Score="2" Body="&lt;p&gt;You also probobably need to check if your samples haven't been contaminated with PCR reaction inhibitors, which is very common if you first extract your mRNA, digest remaining DNA and then run a PCR with a less then 10-fold dilution. You need at least a 200 times dilution to get rid of all the artifacts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you've diluted your samples, place a repeats of successive dilutions of your target and baseline mRNA (200xdilution, 1000x dilution, 5000x dilution). Normally you will see a nice regular spacing between curves on your rtPCR plot. If you don't, something went wrong with the reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More generally rtPCR is a pretty tricky experience, and if you want it to be 100% reliable, you've got a certain number of controls to perform. You can find a good and comprehensive guideline over &lt;a href=&quot;http://www.primerdesign.co.uk/Download%20material/qPCRArticle_RoundTable.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="957" LastActivityDate="2012-11-27T17:32:15.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5358" PostTypeId="2" ParentId="5352" CreationDate="2012-11-27T19:43:40.703" Score="3" Body="&lt;p&gt;Action potentials are governed by the ion concentrations on different sides of the membranes. When an AP is triggered locally, it spreads because the ions which travel across the membrane during the AP spike diffuse to neighbouring regions and trigger the same response in the ion channels there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, it is irrelevant where an AP is, it is always the same voltage. The 40mV are not &quot;distributed&quot; at all - they diffuse and cause new depolarisations around them, triggering new 40mV potentials until they reach the neuron terminals. So in a way, yes, the AP propagates by &quot;creating a potential while it is not there&quot;. All terminals will have the same 40mV potential (the exact voltage of course may be different between cell types).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Potentials which do not reach the threshold value are stored to some extent. This is in the sense that potentials around neurons are always established by ion gradients - a potential in your sense means a change in concentrations from the resting state. Until the concentrations are normalised again by the various transport mechanisms for ions across the membrane, the potential across the membrane will remain changed and it may be closer or further away from the AP threshold.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-11-27T19:43:40.703" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="5359" PostTypeId="1" AcceptedAnswerId="5388" CreationDate="2012-11-27T21:03:07.423" Score="3" ViewCount="1580" Body="&lt;p&gt;I'm trying to get a list of unique soluble structured proteins that don't have a solved structure. That is, they aren't the usual membrane proteins or some derivative of another protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Things that I've been able to think of are low producing transcription factors and novel fusion proteins.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="3632" LastEditDate="2012-11-29T14:10:57.530" LastActivityDate="2012-11-30T18:28:59.567" Title="What is a good list of unsolved protein structures?" Tags="&lt;proteins&gt;&lt;structural-biology&gt;&lt;biophysics&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5360" PostTypeId="1" AcceptedAnswerId="5375" CreationDate="2012-11-27T21:06:40.180" Score="4" ViewCount="256" Body="&lt;p&gt;We're trying to do emulsion PCR using HA-coated polystyrene beads and we're noticing that the beads are seeing drastic issues with thermal degradation above 90C. As PCR has an unfortunate requirement of requiring a high temperature, I was curious about what options are out there to reduce the temperature during PCR denaturation or to stabilize the beads.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2017-09-21T09:35:35.253" Title="Low temperature PCR" Tags="&lt;pcr&gt;&lt;protocol&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5361" PostTypeId="1" AcceptedAnswerId="5368" CreationDate="2012-11-27T21:07:09.833" Score="12" ViewCount="7498" Body="&lt;p&gt;More specifically, is nicotine in the concentrations that smokers receive when smoking cigarettes toxic? I know that in great enough concentrations it can be toxic (but then, so can just about anything else, including oxygen) and I know that in plants it is used as a defense against insects and can even be used as an insecticide. However, it has always been my understanding that nicotine is irrelevant as far as the harmful effects of smoking go. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I recently had a conversation with another biologist who had just quit smoking and had done quite a bit of research on the subject. He said that nicotine itself is in fact bad for you and, therefore, that tobacco-less alternatives to cigarettes (such as electronic cigarettes) are still harmful &lt;strong&gt;because of the nicotine alone&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have any more information on this? Perhaps some references? Or, even better, a detailed explanation of the pathways involved? Again, I stress, not about nicotine's toxicity in general but about its harmful effects on vertebrates (preferably human) at the kinds of concentrations one could expect to ingest when smoking.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-11-28T18:40:08.073" LastActivityDate="2017-11-13T00:12:23.510" Title="Is nicotine toxic to humans?" Tags="&lt;human-biology&gt;&lt;toxicology&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5362" PostTypeId="2" ParentId="3659" CreationDate="2012-11-28T05:38:32.703" Score="2" Body="&lt;p&gt;Very old females (such as those in vials that have not been flipped for a long time) will often lay unfertilized eggs in the absence of males.&#xA;This happens to me occasionally when I am collecting virgins and then forget about them for a while.&lt;/p&gt;&#xA;" OwnerUserId="1389" LastActivityDate="2012-11-28T05:38:32.703" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5363" PostTypeId="2" ParentId="3659" CreationDate="2012-11-28T10:22:45.393" Score="4" Body="&lt;p&gt;Yes, I regularly have to collect female virgins (12500 of them in the last week). They will lay eggs especially when there is extra yeast available. It is actually a good way to check virginity (in case a fly hatched early and was already mature, or a male made it through sorting etc.) - put some extra yeast grains in the vial when you collect them, leave them for a few days and then check for larvae, if they are not virgins there will be eggs and larvae, if they are virgins there will only be eggs!&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-08-20T08:17:43.970" LastActivityDate="2016-08-20T08:17:43.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5364" PostTypeId="2" ParentId="5359" CreationDate="2012-11-28T13:42:25.437" Score="2" Body="&lt;p&gt;This is how I would do it:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Download the UniProt/SWISSPROT flat file for bacteria from &lt;a href=&quot;ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_bacteria.dat.gz&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;After decompressing the files, extract the E. coli protein IDs for which there is no PDB annotation in the file (I am giving you a command line that will work on *ix systems (Linux/Unix/OSX etc)):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;zcat uniprot_sprot_bacteria.dat.gz | gawk '{if($1~/ID/){if($2~/_ECOLI/){id=$2; frag=0; eco=1; want=1}else{eco=0}}  if($1~/DE/ &amp;amp;&amp;amp; $0~/Flags: Fragment/){frag=1;}if($1~/DR/ &amp;amp;&amp;amp; $2~/PDB/){want=0; } if($1~/\/\// &amp;amp;&amp;amp; want==1 &amp;amp;&amp;amp; eco==1 &amp;amp;&amp;amp; frag==0){print id}}' &amp;gt; no_pdbs.txt&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Explaining the details of this command line is clearly off topic here :). Suffice it to say that it will print those UniProt IDs from the flat file &#xA;whose name ends in _ECOLI and for which there is no PDB annotation in the file. It also ignores protein fragments. If you need help understanding it, let me know and we can chat or something. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The result of this quick and dirty analysis is &lt;a href=&quot;http://pastebin.com/uYRK9bzL&quot; rel=&quot;nofollow&quot;&gt;a list of 2694 &lt;em&gt;E.coli&lt;/em&gt; proteins&lt;/a&gt; with no PDB annotations in the UniProt flat files.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CAVEATS:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;These are only the curated SWISSPROT proteins, you may want to also get the UniProt/TrEMBL proteins from &lt;a href=&quot;ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_trembl_bacteria.dat.gz&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. I would recommend you stick to SWISSPROT though.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;As others have pointed out, you should filter this list for homology to other known structures.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The fact that there is no PDB annotation in the flat file does not necessarily mean that there is no known structure.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, this is not perfect but it should serve as a starting point. Good luck!&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-11-29T13:07:16.543" LastActivityDate="2012-11-29T13:07:16.543" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5365" PostTypeId="2" ParentId="5361" CreationDate="2012-11-28T17:33:16.343" Score="8" Body="&lt;p&gt;Nicotine acts as a ligand for nicotinic acetycholine receptors (nAChRs), which are ligand-gated ion channels normally activated by acetylcholine. This family of receptors is expressed in every mammalian cell (&lt;a href=&quot;http://dx.doi.org/10.1038/nrc2590&quot;&gt;Schuller, 2009&lt;/a&gt;). &lt;em&gt;A priori&lt;/em&gt;, at least to me, I'd suggest that it's a bad idea to chronically introduce a foreign substance that mimics the activity of an essential signaling molecule like acetylcholine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Directly to your question of toxicity, nicotine appears to be linked to many forms of cancer (&lt;a href=&quot;http://dx.doi.org/10.1038/nrc2590&quot;&gt;Schuller, 2009&lt;/a&gt;). Cancer promoting signaling pathways are stimulated as a result of calcium entry through nAChRs. Also, interactions of nAChRs with other signalling systems, such as those based on stress hormones, GABA, and dopamine, can lead to cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nicotine also has important effects in the brain. Chronic exposure to nicotine induces a homeostatic mechanism that upregulates nAChR expression in the brain to maintain responsiveness to endogenous acetylcholine. This effect partially underlies nicotine addiction (&lt;a href=&quot;http://dx.doi.org/10.1016/j.semcdb.2009.01.001&quot;&gt;Penton and Lester, 2009&lt;/a&gt;). As @Armatus notes, nicotine appears to have some neuroprotective properties against neurodegenerative diseases like Parkinson's (&lt;a href=&quot;http://dx.doi.org/10.1124/pr.110.003269&quot;&gt;Quik, M., Wonnacott, S., 2011&lt;/a&gt;) and Alzheimer's (&lt;a href=&quot;http://dx.doi.org/10.2741/367&quot;&gt;Mehta et al, 2012&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nrc2590&quot;&gt;Schuller, H.M., 2009.&lt;/a&gt; Is cancer triggered by altered signalling of nicotinic acetylcholine receptors? Nature Reviews Cancer 9, 195–205.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.semcdb.2009.01.001&quot;&gt;Penton, R.E., Lester, R.A.J., 2009.&lt;/a&gt; Cellular events in nicotine addiction. Seminars in Cell &amp;amp; Developmental Biology 20, 418–431.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1124/pr.110.003269&quot;&gt;Quik, M., Wonnacott, S., 2011.&lt;/a&gt; α6β2* and α4β2* nicotinic acetylcholine receptors as drug targets for Parkinson’s disease. Pharmacol. Rev. 63, 938–966.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.2741/367&quot;&gt;Mehta, M., Adem, A., Kahlon, M.S., Sabbagh, M.N., 2012.&lt;/a&gt; The nicotinic acetylcholine receptor: smoking and Alzheimer’s disease revisited. Front Biosci (Elite Ed) 4, 169–180.&lt;/p&gt;&#xA;" OwnerUserId="72" LastActivityDate="2012-11-28T17:33:16.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5366" PostTypeId="2" ParentId="5029" CreationDate="2012-11-28T17:53:04.210" Score="2" Body="&lt;p&gt;As @Armatus notes, it is now generally understood that age-related cognitive decline is related to loss of myelination and axon damage (see, for example, &lt;a href=&quot;http://dx.doi.org/10.1007/s11357-011-9357-7&quot; rel=&quot;nofollow&quot;&gt;Kohama et al, 2012&lt;/a&gt;). Myelin degeneration is also likely the cause of some age-related &lt;a href=&quot;http://en.wikipedia.org/wiki/Peripheral_neuropathy&quot; rel=&quot;nofollow&quot;&gt;peripheral neuropathies&lt;/a&gt;. Loss of myelination (due to inflammation) is also the mechanism behind multiple sclerosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Myelin allows for fast and reliable transmission of action potentials by a mechanism known as saltatory conduction. This is necessary to compensate for axons which have small diameters (unlike the squid giant axon) and travel long distances. Degraded myelin will reduce conduction velocity and can result in propogation failures. The links @nico provided in his comment above are useful references.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s11357-011-9357-7&quot; rel=&quot;nofollow&quot;&gt;Kohama, S.G., Rosene, D.L., Sherman, L.S., 2012&lt;/a&gt;. Age-related changes in human and non-human primate white matter: from myelination disturbances to cognitive decline. Age (Dordr) 34, 1093–1110.&lt;/p&gt;&#xA;" OwnerUserId="72" LastEditorUserId="72" LastEditDate="2012-11-28T18:00:20.557" LastActivityDate="2012-11-28T18:00:20.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5367" PostTypeId="1" AcceptedAnswerId="5369" CreationDate="2012-11-28T20:57:27.887" Score="4" ViewCount="953" Body="&lt;p&gt;A human, at some time in life or the other, must clear the auditory canal. This is usually achieved using soft-cotton buds, or such similar device. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where does this wax come from? What purpose does it serve? Is it really wax? Is it the inner fluid leaking out? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2012-11-28T21:10:31.830" Title="What is ear wax?" Tags="&lt;human-ear&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5368" PostTypeId="2" ParentId="5361" CreationDate="2012-11-28T20:57:55.457" Score="14" Body="&lt;p&gt;I think its useful to say that nicotine is not very toxic to humans - cells don't die or get sick for typical smoking habits.  Secondary health effects are possible, but here is a toxicological profiles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nicotine is a toxin in large enough quantities and nicotine has an LD50 (lethal dose for 50% of individuals) of &lt;a href=&quot;http://en.wikipedia.org/wiki/Nicotine_poisoning#Toxicology&quot;&gt;0.5-1 mg Nicotine / kg of body weight&lt;/a&gt;.  So even a small spill on your skin of the chemical can be life threatening, but for smokers the nicotine itself is not dangerous. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Individuals who smoke intake about 1 mg per cigarette smoked.  So a small adult (110 lbs) can smoke 25 cigarettes in a short period of time (or all at once!) and just barely get to the bottom end of that limit.  Nicotine is water soluble and clears out through the urine at a fast rate though - half of the nicotine from a cigarette is cleared from  your system within 2 hours, which means that 4-5 pack a day smokers are not really killing themselves (from nicotine).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, children are about 5-10 times more sensitive than adults, so even 5-6 cigarettes in an hour can be toxic.  That's quite a bit of smoking though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all animals have the same relationship to the nicotinic acetylcholine receptors as humans do.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Insecticide#Neonicotinoids&quot;&gt;Nicotine is toxic to insects and will kill an insect in a matter of minutes or hours&lt;/a&gt;. Rats are about 50x less sensitive than people.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think its comparable to the question of whether caffeine is harmful to people.  In the amount we consume it, sometimes up to grams a day, there is no obvious common side effect, but you figure that decades later it will show up as a problem - a difficult connection to prove.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-12-01T17:28:08.763" LastActivityDate="2012-12-01T17:28:08.763" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5369" PostTypeId="2" ParentId="5367" CreationDate="2012-11-28T21:10:31.830" Score="6" Body="&lt;p&gt;As quoted from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Ear_wax&quot;&gt;wikipedia page on Earwax&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cerumen [earwax] is produced in the outer third of the cartilaginous portion of&#xA;  the human ear canal. It is a mixture of viscous secretions from&#xA;  sebaceous glands and less-viscous ones from modified apocrine sweat&#xA;  glands. The primary components of earwax are shed layers of skin,&#xA;  with 60% of the earwax consisting of keratin, 12–20% saturated and&#xA;  unsaturated long-chain fatty acids, alcohols, squalene and 6–9%&#xA;  cholesterol.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's purpose -- further quoted -- is that it:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;protects the skin of the human ear canal, assists in cleaning and&#xA;  lubrication, and also provides some protection from bacteria, fungi,&#xA;  insects and water&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Some interesting (and stomach churning) earwax trivia:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;In medieval times earwax, and other substances such as urine, were&#xA;used to prepare pigments used by scribes to illustrate illuminated&#xA;manuscripts.&lt;/li&gt;&#xA;&lt;li&gt;The 1832 edition of the American Frugal Housewife&#xA;said that &quot;nothing was better than earwax to prevent the painful&#xA;effects resulting from a wound by a nail [or] skewer&quot;; and also&#xA;recommended earwax as a remedy for cracked lips.&lt;/li&gt;&#xA;&lt;li&gt;Before waxed thread was commonly available seamstresses would use their own earwax&#xA;to stop the cut ends of threads from fraying.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1249" LastActivityDate="2012-11-28T21:10:31.830" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5370" PostTypeId="2" ParentId="5352" CreationDate="2012-11-28T21:54:19.497" Score="5" Body="&lt;p&gt;I think you are really wondering how axonal morphology affects the voltage along the axon. The short answer to your question is that &lt;em&gt;each synaptic terminal sees the same voltage&lt;/em&gt; because that voltage is generated &quot;fresh&quot; at each site. This has &lt;em&gt;nothing to do with synaptic strength&lt;/em&gt;, which determines the amount of voltage deflection in the postsynaptic terminal but not in the presynaptic terminal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The axon has two major properties that allow for this even activation across its branches. First, as @Armatus said, the &lt;strong&gt;axon is an active structure&lt;/strong&gt;, meaning that the action potential (AP) regenerates as it travels along the axon. This means that there is essentially no decay of the voltage as the AP propagates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, the &lt;strong&gt;axonal geometry&lt;/strong&gt; appears to be carefully regulated. As you seem to have guessed, there has to be sufficient current flow to activate an action potential in the neighbouring patches of membrane or else there is a propagation failure and the AP stops. This is a problem at axonal branch points (see Box 1 in &lt;a href=&quot;http://dx.doi.org/10.1038/nrn1397&quot; rel=&quot;nofollow noreferrer&quot;&gt;Debanne, 2004&lt;/a&gt;), where the diameters of daughter branches have to be correctly sized so that there is little or no extra electrical load. (For instance, if one branch stays the same size as the mother, the other branch is an extra load that will &quot;steal&quot; current and leave less current travelling down the mother branch). Recent work using voltage-sensitive dyes have shown that in mammalian neurons, in practice, propagation failures are rare (&lt;a href=&quot;http://dx.doi.org/10.1523/JNEUROSCI.0552-10.2010&quot; rel=&quot;nofollow noreferrer&quot;&gt;Foust et al, 2010&lt;/a&gt;). This suggests that there is fine regulation to ensure that the geometry is &quot;just right.&quot; (Those &quot;just right&quot; rules are basically governed by cable theory, which I've &lt;a href=&quot;https://biology.stackexchange.com/a/852/72&quot;&gt;previously described here&lt;/a&gt;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To your last question, yes, &lt;em&gt;there is time-dependent decay of subthreshold potentials because the membrane is a capacitor&lt;/em&gt; (~1 uF / cm^2). I wouldn't call this &quot;storage&quot; exactly, but it does work just like a capacitor in a circuit. Many people think of the membrane as a capacitor and a resistor in parallel.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nrn1397&quot; rel=&quot;nofollow noreferrer&quot;&gt;Debanne, D., 2004.&lt;/a&gt; Information processing in the axon. Nature Reviews Neuroscience 5, 304–316.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1523/JNEUROSCI.0552-10.2010&quot; rel=&quot;nofollow noreferrer&quot;&gt;Foust, A., Popovic, M., Zecevic, D., McCormick, D.A., 2010.&lt;/a&gt; Action Potentials Initiate in the Axon Initial Segment and Propagate through Axon Collaterals Reliably in Cerebellar Purkinje Neurons. J. Neurosci. 30, 6891–6902.&lt;/p&gt;&#xA;" OwnerUserId="72" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2012-11-28T21:54:19.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5371" PostTypeId="2" ParentId="2311" CreationDate="2012-11-29T01:30:30.063" Score="2" Body="&lt;p&gt;These two papers&lt;sup&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/0092-8674%2889%2990062-7&quot; rel=&quot;nofollow&quot;&gt;[1]&lt;/a&gt; &lt;a href=&quot;http://www.bio.davidson.edu/COurses/Molbio/restricted/bcd/1989_bicoid.pdf&quot; rel=&quot;nofollow&quot;&gt;[2]&lt;/a&gt;&lt;/sup&gt; argue that &lt;em&gt;bcd&lt;/em&gt; is a direct activator of &lt;em&gt;hb&lt;/em&gt;, although be aware that this does not rule out downstream events feeding back to further activate  &lt;em&gt;hb&lt;/em&gt;. (In fact, given the complexity of the embryonic gene network, it is likely that both mechanisms have a role.)&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/0092-8674%2889%2990062-7&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Struhl G, Struhl K, Macdonald PM&lt;/strong&gt;. 1989. The gradient morphogen &lt;em&gt;bicoid&lt;/em&gt; is a concentration-dependent transcriptional activator. Cell, 57(7): 1259-1273, doi:10.1016/0092-8674(89)90062-7&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.bio.davidson.edu/COurses/Molbio/restricted/bcd/1989_bicoid.pdf&quot; rel=&quot;nofollow&quot;&gt;Driever W, Nüsslein-Volhard C. 1989. The bicoid protin is a positive regulator of &lt;em&gt;hunchback&lt;/em&gt; transcription in the early &lt;em&gt;Drosophila&lt;/em&gt; embryo. Nature, 337: 138-143.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1389" LastEditorUserId="43" LastEditDate="2012-11-29T15:45:18.127" LastActivityDate="2012-11-29T15:45:18.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5372" PostTypeId="1" CreationDate="2012-11-29T15:58:52.267" Score="0" ViewCount="539" Body="&lt;p&gt;Similar organisms generally have similar genome sizes. Given this, would two species of yeast have the same number of genes and chromosomes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: Fixed with thanks to @daniel-standage&lt;/p&gt;&#xA;" OwnerUserId="584" LastEditorUserId="584" LastEditDate="2012-11-29T16:21:03.107" LastActivityDate="2012-11-29T18:10:51.573" Title="Would two species of yeast with similar genome sizes have the same number of genes or chromosomes?" Tags="&lt;cell-biology&gt;&lt;microbiology&gt;&lt;chromosome&gt;&lt;genetics&gt;&lt;genomes&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5373" PostTypeId="2" ParentId="5372" CreationDate="2012-11-29T18:10:51.573" Score="3" Body="&lt;p&gt;This question appears to start from the premise that different species of yeast are closely related, but they aren't. &lt;em&gt;Saccharomyces cerevisae&lt;/em&gt; and &lt;em&gt;Schizosaccharomyces pombe&lt;/em&gt;, both Ascomycetes, are thought to have diverged at least 300 million years ago (c.f. the mammalian divergence from other vertebrates was about 200 million years ago).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.yeastgenome.org/cache/genomeSnapshot.html&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;S. cerevisiae&lt;/em&gt;&lt;/a&gt; has a genome size of 12.1 Mb, with 5821 protein coding genes (plus another 786 dubious ORFs) spread over 16 chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pombase.org/status/statistics&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;S. pombe&lt;/em&gt;&lt;/a&gt; has a genome size of 12.6 Mb with 5124 protein coding genes on just 3 chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Filamentous fungi have larger genomes and gene numbers. From memory, &lt;em&gt;Aspergillus nidulans&lt;/em&gt; has 8 chromosomes and over 9,000 protein coding genes. So, the similarity in gene numbers in the two yeasts probably reflects their broadly similar lifestyles.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-29T18:10:51.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5374" PostTypeId="2" ParentId="5359" CreationDate="2012-11-29T18:20:11.937" Score="2" Body="&lt;p&gt;Try looking at structure homology databases - the sequences that they have no annotation for are likely the kind of sequences that you are seeking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://supfam.cs.bris.ac.uk&quot; rel=&quot;nofollow&quot;&gt;SUPERFAMILY&lt;/a&gt; has a comprehensive annotation across almost 2500 fully sequenced cellular genomes. this would be a good place to start ...&lt;/p&gt;&#xA;" OwnerUserId="1719" LastEditorUserId="69" LastEditDate="2012-11-29T19:07:17.950" LastActivityDate="2012-11-29T19:07:17.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5375" PostTypeId="2" ParentId="5360" CreationDate="2012-11-29T19:10:02.750" Score="1" Body="&lt;p&gt;Perhaps isothermal amplification is possible (&lt;a href=&quot;http://en.wikipedia.org/wiki/NASBA_%28molecular_biology%29&quot; rel=&quot;nofollow&quot;&gt;NASBA&lt;/a&gt;)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Amplification of DNA also seems possible (&lt;a href=&quot;http://www.biomerieux-diagnostics.com/servlet/srt/bio/clinical-diagnostics/dynPage?node=NASBA_Technology&quot; rel=&quot;nofollow&quot;&gt;NASBA at biomerieux&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="867" LastActivityDate="2012-11-29T19:10:02.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5376" PostTypeId="1" CreationDate="2012-11-29T19:34:06.330" Score="1" ViewCount="119" Body="&lt;p&gt;Are there any living examples of cellular colonies demonstrating very primitive cellular specialization?  If so, what do we know about how they assimilate?  How independent are the individual cells and what do we know about their behavior (for example, do they, perhaps, migrate to different colonies in certain proximities)?&lt;/p&gt;&#xA;" OwnerUserId="1249" LastActivityDate="2012-11-29T20:13:09.333" Title="Colonial Cells Demonstrating Cell Specialization" Tags="&lt;evolution&gt;&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5377" PostTypeId="2" ParentId="5376" CreationDate="2012-11-29T20:13:09.333" Score="2" Body="&lt;p&gt;Probably not what you are looking for but the protozoan slime mold &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dictyostelium_discoideum&quot; rel=&quot;nofollow&quot;&gt;Dictyostelium discoideum&lt;/a&gt;&lt;/em&gt; lives as free amoebae which can coalesce into a multicellular migratory slug that eventually forms a fruiting body in which some cells form the stalk while others form spores.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Slug formation is by chemotactic signalling with cyclic AMP as the signal. I seem to remember that there is a predatory species of slime mold which uses cAMP to attract &lt;em&gt;D. discoideum&lt;/em&gt; as prey, but I can't bring the name to mind and have failed to find it online.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-29T20:13:09.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5378" PostTypeId="2" ParentId="5322" CreationDate="2012-11-29T21:02:47.697" Score="2" Body="&lt;p&gt;Both sexes of red squirrels defend exclusive year round territories.&#xA;See &lt;a href=&quot;http://www.jstor.org/stable/10.2307/1948536&quot; rel=&quot;nofollow&quot;&gt;Smith 1968&lt;/a&gt; or &lt;a href=&quot;http://www.jstor.org/stable/3504443&quot; rel=&quot;nofollow&quot;&gt;Steele 1998&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1720" LastActivityDate="2012-11-29T21:02:47.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5379" PostTypeId="2" ParentId="5322" CreationDate="2012-11-29T21:08:48.807" Score="0" Body="&lt;p&gt;The elephant matriarch (in Africa) leads her followers where they go for food and water.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-11-29T21:08:48.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5380" PostTypeId="1" AcceptedAnswerId="5412" CreationDate="2012-11-29T12:47:53.967" Score="4" ViewCount="1261" Body="&lt;p&gt;I know that &lt;a href=&quot;http://www.medicinenet.com/alcohol_and_nutrition/page4.htm&quot; rel=&quot;nofollow&quot;&gt;ethanol increases insulin secretion&lt;/a&gt;--could someone explain why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All I have found till now is experimental data analyses.  I am interested in mechanism of alcohol consumption.&lt;/p&gt;&#xA;" OwnerUserId="1281" OwnerDisplayName="Edward Ruchevits" LastEditorDisplayName="user560" LastEditDate="2012-12-03T12:52:13.193" LastActivityDate="2012-12-03T13:10:17.380" Title="How does ethanol interact with insulin?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5381" PostTypeId="1" CreationDate="2012-11-29T21:54:42.543" Score="1" ViewCount="201" Body="&lt;p&gt;I read somewhere that eating a lot of salt will raise blood pressure, which will in turn damage brain tissue. This is because water molecules gather around salt ions, thus making it harder for the body to remove the excess water from the blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this true? How much salt is actually dangerous?&lt;/p&gt;&#xA;" OwnerUserId="1369" LastEditorUserId="69" LastEditDate="2012-11-30T15:13:06.520" LastActivityDate="2013-09-03T00:30:31.070" Title="Is eating salt dangerous for the brain?" Tags="&lt;biochemistry&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5382" PostTypeId="2" ParentId="5360" CreationDate="2012-11-29T23:18:27.523" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://nar.oxfordjournals.org/content/29/11/2377.full&quot; rel=&quot;nofollow&quot;&gt;Look at chemical hydrogen bond breakers.&lt;/a&gt;  Guanadine hydrochloride is included in the buffer conventionally to compete with the the hydrogen bonds that form the double helix.  &lt;a href=&quot;http://nar.oxfordjournals.org/content/29/11/2377/T1.expansion.html&quot; rel=&quot;nofollow&quot;&gt;Other hydrogen bonders like Propionamide and 2-Pyrrolidone&lt;/a&gt; can weaken the helix and I would think lower the melting point of the bonds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much the Tm is affected would depend on the concentration of the breaker in the buffer.  It might not be possible to lower the temperature this much and you may loose specificity - you might be able to squeeze a few more degrees if the oligos can't get any shorter. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-11-29T23:18:27.523" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5383" PostTypeId="1" AcceptedAnswerId="5386" CreationDate="2012-11-30T00:13:22.687" Score="8" ViewCount="13079" Body="&lt;p&gt;In the University labs, we have used Beta-galactosidase as a reporter gene to quantify the expression initiated by the stress-response promoter in yeast. This was done by exposing one of the two groups to osmotic stress (high salt concentration) whilst the other was unstressed. Then the levels of beta-galactosidase were compared. &#xA;A question given to us afterwards asked to give advantages &amp;amp; disadvantages of using Beta-galactosidase compared to Luciferase as a reporter gene in this experiment. And which one would be, overall, more suitable?&lt;/p&gt;&#xA;" OwnerUserId="1721" LastEditorUserId="1590" LastEditDate="2012-11-30T22:26:06.930" LastActivityDate="2015-03-12T05:03:52.060" Title="What are the advantages and disadvantages of using beta-galactosidase compared to luciferase as a reporter gene?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;homework&gt;&lt;lab-techniques&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5384" PostTypeId="1" AcceptedAnswerId="5385" CreationDate="2012-11-30T12:21:15.507" Score="9" ViewCount="192" Body="&lt;p&gt;I think it happens for everyone that sometimes we go to a room and forget why we went there. Is there any research or article on this?&lt;/p&gt;&#xA;" OwnerUserId="1724" LastEditorUserId="1306" LastEditDate="2012-11-30T12:48:32.127" LastActivityDate="2012-11-30T12:48:32.127" Title="What happens when we know that there is something that we forgot but we can't remember what it was?" Tags="&lt;human-biology&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5385" PostTypeId="2" ParentId="5384" CreationDate="2012-11-30T12:47:01.617" Score="15" Body="&lt;p&gt;It is a phenomenon known as room amnesia, some research has shown that your brain may use physical barriers like the room and doorways as a way to compartmentalize thoughts.&#xA;One article summarizes it &lt;a href=&quot;http://www.scientificamerican.com/podcast/episode.cfm?id=doorway-to-blame-for-room-amnesia-11-11-30&quot;&gt;here&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The researchers say that when you pass through a doorway, your mind&#xA;  compartmentalizes your actions into separate episodes. Having moved&#xA;  into a new episode, the brain archives the previous one, making it&#xA;  less available for access. It’s as if you slam a mental door between&#xA;  what you knew and…what was I saying?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nd.edu/~memory/Reprints/Radvansky%20Krawietz%20&amp;amp;%20Tamplin%202011%20%28QJEP%29.pdf&quot;&gt;This is the research.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2012-11-30T12:47:01.617" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5386" PostTypeId="2" ParentId="5383" CreationDate="2012-11-30T13:23:45.430" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Beta-galactosidase&quot; rel=&quot;nofollow&quot;&gt;Beta-galactosidase&lt;/a&gt; (B-gal for short) is an enzyme that will process the substrate lactose. In applications using B-gal as a reporter (lacZ gene), two lactose analogues are commonly used: &lt;a href=&quot;http://en.wikipedia.org/wiki/X-gal&quot; rel=&quot;nofollow&quot;&gt;X-gal&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/Ortho-Nitrophenyl-%CE%B2-galactoside&quot; rel=&quot;nofollow&quot;&gt;ONPG&lt;/a&gt; (as pointed out by @Alan Boyd). Both substrates are colourless, becoming coloured once hydrolyzed by B-gal. The formation of this colour allows B-gal to be assayed by means of either visual inspection, or more accurate means by using a spectrophotometer or camera.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When X-Gal is hydrolyzed, an insoluble blue dye is formed. Evolution of blue colour is intensified as more substrate is hyrolyzed, allowing for quick blue/white screening by visual inspection in common applications of cloning and gene expression. Using the X-gal substrate, B-gal assays are more sensitive to gene expression (the dye precipitates out and retains colour very well), however X-gal is not quantitative (&lt;a href=&quot;http://www.biotechniques.com/multimedia/archive/00036/BTN_A_04365PT03_O_36496a.pdf&quot; rel=&quot;nofollow&quot;&gt;Möckli &amp;amp; Auerbach. BioTechniques 36:872-876 (May 2004)&lt;/a&gt;). In contrast, ONPG hydrolysis evolves a soluble yellow dye. This colour developement is quantitative, however is less senstive than X-gal because the linear relationship betwen light absorption (at 420 nm) and substrate concentration is small. Using ONPG as a B-gal substrate allows for quantitative measurement of B-gal activity (and therefore promoter activity). (Note that ONPG itself is not capable of inducing the lac promotor, unlike X-gal.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Luciferase reporters (there are actually a few different luc genes) operate in a similar fashion. The enzyme cleaves its substrate, however instead of yielding an insoluble blue dye, emits a characteristic photon. Luciferase activity must be measured using specialized camera hardware to detect and count photons emitted from your yeast clones. This assay will still answer yes/no reporter questions, but can also be quantified to look at how much the reporter was activated. Luciferase activity is a quantitative reporter while also yielding spatiotemporal information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The choice of reporters depends largely on the question you wish to answer. If promoter induction is relevant (eg, the stress-response promoter was activated), then luciferase or B-gal with X-gal are best suited for their higher sensitivity. Given that luciferase requires a special camera and optical filter (such as a gel documentation system), X-gal is ideal because it may be screened by eye. If promoter activity is being assayed, then B-gal+ONPG or luciferase will yield quantitative measurements of reporter gene activity, and require at least a spectrophotometer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given these are university labs, I assume that materials costs are to be minimized and ease of experimental protocol to be maximized, B-gal is the ideal reporter. Luciferase requires: more costly substrate; specialized equipment; careful handling of materials, and more time (as screening necessarily takes longer, therefore lower throughput for a lab demo setting).&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="1320" LastEditDate="2014-08-23T21:07:37.777" LastActivityDate="2014-08-23T21:07:37.777" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5387" PostTypeId="2" ParentId="5383" CreationDate="2012-11-30T17:21:49.470" Score="3" Body="&lt;p&gt;I think that @leonardo has this backwards. &amp;beta;-galactosidase can be assayed accurately and cheaply using &lt;a href=&quot;http://en.wikipedia.org/wiki/Ortho-Nitrophenyl-%CE%B2-galactoside&quot; rel=&quot;nofollow&quot;&gt;ONPG&lt;/a&gt; as a colorimetric substrate with no solubility problems. All that is needed is a spectrophotometer: my guess is that this is the assay the OP used in their experiment. So my answer is - use &amp;beta;-galactosidase for inexpensive quantitative analysis - no need to add luciferin and ATP or to worry about oxygen availability. I'm struggling to think of a disadvantage for &amp;beta;-galacosidase - maybe there are higher background levels from other cellular glycosidases, whereas there will be no background luciferase activity?&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-11-30T17:21:49.470" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5388" PostTypeId="2" ParentId="5359" CreationDate="2012-11-30T18:28:59.567" Score="3" Body="&lt;p&gt;There are some funded projects and analyses available just for this purpose.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Structural genomics or high throughput structure projects take all available peptide sequences group them into families and make sure sequence families pointing to most likely novel folds were available.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are the &lt;a href=&quot;http://www.jcsg.org/prod/newscripts/public_targets/selected.html&quot; rel=&quot;nofollow&quot;&gt;status and target list for the joint center for structural genomics&lt;/a&gt;. This list is filtered by species as well as by project status.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their analysis is availble for us to browse through.  &lt;a href=&quot;http://www1.jcsg.org/prod/newscripts/psca/help/document.cgi&quot; rel=&quot;nofollow&quot;&gt;http://www1.jcsg.org/prod/newscripts/psca/help/document.cgi&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry this isn't so thorough.  &lt;a href=&quot;http://sbkb.org/tt/centers.html&quot; rel=&quot;nofollow&quot;&gt;Nature also hosts Target Track, which allows several high throughput structure centers to coordinate their efforts.&lt;/a&gt;  Each might have resources which could do your work for you.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-11-30T18:28:59.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5389" PostTypeId="2" ParentId="5332" CreationDate="2012-11-30T19:10:53.803" Score="3" Body="&lt;p&gt;From Wikipedia &lt;a href=&quot;http://en.wikipedia.org/wiki/Thirst&quot; rel=&quot;nofollow&quot;&gt;entry on thirst&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the mammalian brain, the posterior surface of the hypothalamus&#xA;  forms the front wall of the third ventricle (a cerebrospinal&#xA;  fluid-filled cavity) and clusters of cells (osmoreceptors) on this&#xA;  surface, notably in the organum vasculosum of the lamina terminalis&#xA;  (OVLT) and subfornical organ (SFO), signal this cellular dehydration&#xA;  to other parts of the brain, and thirst is experienced. Destruction of&#xA;  this part of the hypothalamus in humans and other animals results in&#xA;  partial or total loss of desire to drink even with extremely high salt&#xA;  concentration in the extracellular fluids.&lt;a href=&quot;http://en.wikipedia.org/wiki/Osmoreceptor&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Osmoreceptor&quot; rel=&quot;nofollow&quot;&gt;entry on osmoreceptor&lt;/a&gt; says in part:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When the osmotic pressure of blood changes (i.e. it is more or less&#xA;  dilute), water diffusion into and out of the osmoreceptor cells&#xA;  changes. That is, they expand when the blood plasma is more dilute and&#xA;  contract with higher concentration.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It also describes how the kidney measures chlorine anion flow through some nephrons, which triggers a cascade of messenger molecules resulting in increased blood levels of the hormone angiotensin, which also results in thirst messages originating in the hypothalamus.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Thirst&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;Derek A. Denton (8 June 2006). The primordial emotions: the dawning of consciousness. Oxford University Press. pp. 118–19. ISBN 978-0-19-920314-7.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Osmoreceptor&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;Walter F., PhD. Boron (2005). Medical Physiology: A Cellular And Molecular Approach. Elsevier/Saunders. ISBN 1-4160-2328-3. Page 872&lt;/p&gt;&#xA;" OwnerUserId="1677" LastActivityDate="2012-11-30T19:10:53.803" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5391" PostTypeId="2" ParentId="5337" CreationDate="2012-11-30T22:30:17.663" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.turbosquid.com/3d-models/max-human-brain/580672&quot; rel=&quot;nofollow&quot;&gt;http://www.turbosquid.com/3d-models/max-human-brain/580672&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That one is only 30 which &lt;em&gt;really isn't&lt;/em&gt; bad for a model. You will have trouble finding an  anatomically correct model for free. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am curious, is the male brain that much different from the female brain? And do you want just the brain or a whole head with the skeleton and other anatomical features? And if you would like to elaborate, I am curious about what end product you are looking for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Side note: Autodesk has 'student' license version of software --in case you want to try learning Maya or 3Ds max, the latter has Retopology tools. &#xA;You can download from here:&#xA;&lt;a href=&quot;https://students.autodesk.com/?nd=download_center&quot; rel=&quot;nofollow&quot;&gt;https://students.autodesk.com/?nd=download_center&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ITKsnap is a program you could use to get 3d data from ct or mri scans &#xA;&lt;a href=&quot;http://www.itksnap.org/pmwiki/pmwiki.php?n=Main.Downloads&quot; rel=&quot;nofollow&quot;&gt;http://www.itksnap.org/pmwiki/pmwiki.php?n=Main.Downloads&lt;/a&gt;&#xA;MRI and CT data can be found here:&#xA;&lt;a href=&quot;http://www.osirix-viewer.com/Downloads.html&quot; rel=&quot;nofollow&quot;&gt;http://www.osirix-viewer.com/Downloads.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know you just wanted a free model, but the above are the steps to get to one at least.&lt;/p&gt;&#xA;" OwnerUserId="1726" LastEditorUserId="948" LastEditDate="2012-12-01T23:00:06.060" LastActivityDate="2012-12-01T23:00:06.060" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5392" PostTypeId="1" CreationDate="2012-12-01T06:42:45.193" Score="5" ViewCount="3075" Body="&lt;p&gt;Lysosomes are a bit like the &lt;em&gt;suicidal bags&lt;/em&gt; of cells. They help to clean cells, have an acidic pH and contain a large number of hydrolyzing enzymes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But why don't these hydrolyzing enzymes attack and destroy lysosomes' membranes?&lt;/p&gt;&#xA;" OwnerUserId="834" LastEditorUserId="1306" LastEditDate="2012-12-01T12:20:19.090" LastActivityDate="2012-12-01T15:02:44.607" Title="How are lysosome membranes protected from the attack of hydrolases?" Tags="&lt;cell-biology&gt;&lt;enzymes&gt;&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5393" PostTypeId="2" ParentId="3451" CreationDate="2012-12-01T13:17:29.070" Score="2" Body="&lt;p&gt;Senescence does not equal cell death, but is simply an arrested state in which the cell still remains viable (1). It has been shown throughout the literature that this state corresponds with an altered cell cycle profile different from contact inhibition or damage-induced arrest (2). This corresponds with an enlarged cell size, altered gene expression (3, 4), and the pH-dependent expression of β-galactosidase (5). This has been shown both in cultured cells and in animal models (6, 7). &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2204114&quot; rel=&quot;nofollow&quot;&gt;Goldstein, S. (1990) &lt;em&gt;Science&lt;/em&gt; 249, 1129-1133.&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3194411&quot; rel=&quot;nofollow&quot;&gt;Sherwood, S. W. et al. (1988) &lt;em&gt;Proc. Natl. Acad. Sci. , USA&lt;/em&gt; 85, 9086-9090.&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9673450&quot; rel=&quot;nofollow&quot;&gt;Cristofalo, V. J. et al. (1998) &lt;em&gt;Crit. Rev. Eukaryot Gene Expr.&lt;/em&gt; 8, 43-80.&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7667101&quot; rel=&quot;nofollow&quot;&gt;Linskens, M. H. et al. (1995) &lt;em&gt;Nucleic Acid Res.&lt;/em&gt; 23, 3244-3251.&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7568133&quot; rel=&quot;nofollow&quot;&gt;Dimri, G. et al. (1995) &lt;em&gt;Proc. Natl. Acad. Sci., USA&lt;/em&gt; 92, 9363-9367.&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18378907&quot; rel=&quot;nofollow&quot;&gt;Swarbrick, A. et al. (2008) &lt;em&gt;Proc. Natl. Acad. Sci., USA&lt;/em&gt; 105, 5402-7.&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19421407&quot; rel=&quot;nofollow&quot;&gt;Efeyan, A. et al. (2009) &lt;em&gt;PLoS One&lt;/em&gt; 4, e5475.&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="948" LastActivityDate="2012-12-01T13:17:29.070" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="5394" PostTypeId="2" ParentId="5392" CreationDate="2012-12-01T15:02:44.607" Score="5" Body="&lt;p&gt;Early histochemical work indicated that the internal surface of the lysosomal membrane has a &lt;em&gt;glycocalyx&lt;/em&gt; - a layer of polysaccharide, presumed to have a protective role.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Neiss, W. F. (1984) A coat of glycoconjugates on the inner surface of the lysosomal membrane in the rat kidney. Histochemistry 80, 603–608&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Subsequently it was found that major membrane proteins of the lysosomal membrane are protected from proteolysis by glycosylation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Kundra, R. and Kornfeld, S. (1999) Asparagine-linked oligosaccharides protect Lamp-1 and Lamp-2 from intracellular proteolysis. J. Biol. Chem. 274, 31039–31046&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;See this paper for a more recent study of another lysosomal membrane protein:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Schieweck O. et al. (2009) NCU-G1 is a highly glycosylated integral membrane protein of the lysosome. Biochem. J. 422: 83-90&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;NCU-G1 is the mouse orthologue of the human C1orf85 protein. The NCU-G1 gene encodes a 404 amino acid protein. This is a Type 1 transmembrane protein - i.e. the N terminal domain is directed to the extracytoplasmic surface of the membrane. In vivo the protein is detected in 70 kDa and 80 kDa forms. The discrepancy between the polypeptide size and the molecular mass is shown to be due to extensive glycosylation. The protein sequence includes 9 potential glycosylation sites. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-12-01T15:02:44.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5395" PostTypeId="1" AcceptedAnswerId="5415" CreationDate="2012-12-01T15:36:51.487" Score="11" ViewCount="11077" Body="&lt;p&gt;Microorganisms constitute the bulk of all the biomass on Earth. I weighed myself yesterday, and wondered how much less I would weigh if I were completely free of bacteria and microbes, inside and out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Approximately how much weight and volume do microbes occupy within the average human body? How were these values obtained?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="1306" LastEditDate="2012-12-02T22:44:58.720" LastActivityDate="2018-01-04T19:01:59.007" Title="How much weight/volume do microbes occupy within the human body?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5396" PostTypeId="1" CreationDate="2012-12-01T16:09:54.700" Score="5" ViewCount="196" Body="&lt;p&gt;I am curious as to the species or &quot;types&quot; of archaea that have been found to reside within animals symbiotically. One of the only ones I can think of off the top of my head are &lt;a href=&quot;http://en.wikipedia.org/wiki/Methanogen&quot;&gt;methanogens&lt;/a&gt;, which live in the gut of ruminants for example.&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2012-12-01T16:35:35.143" Title="What types of archaea have been found in animals?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5398" PostTypeId="2" ParentId="5396" CreationDate="2012-12-01T16:35:35.143" Score="7" Body="&lt;p&gt;Humans:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A pioneering study using 16S RNA primers found only &lt;em&gt;Methanobrevibacter smithii&lt;/em&gt; in the human intestine.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Eckburg PB &lt;em&gt;et al&lt;/em&gt;. (2005) Diversity of the human intestinal microbial flora. Science 308 1635-1638&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In a recent review there is a comprehensive Table of archaea found in humans (this includes non-intestinal flora):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dridi B &lt;em&gt;et al&lt;/em&gt;. (2011) Archea as emerging organisms in complex human microbiomes. Anaerob2 17: 56-63&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Much of the work that is catalogued by Dridi &lt;em&gt;et al&lt;/em&gt;. is repeated identifications of Methanobacteriales (&lt;em&gt;Methanobrevibacter smithii&lt;/em&gt;, &lt;em&gt;Methanosphaera stadtmanae&lt;/em&gt; and &lt;em&gt;Methanobrevibacter oralis&lt;/em&gt;), but there are others from the Thermoplasmateles, the Halobacteriales and the Sulfolobales, plus some that are thought to be members of unknown archaeal orders.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-12-01T16:35:35.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5399" PostTypeId="2" ParentId="5395" CreationDate="2012-12-01T18:52:13.817" Score="6" Body="&lt;p&gt;&lt;strong&gt;The bacterial flora weighs approximately 90 g and, assuming bacterial cell density is approximately 1 g ml&lt;sup&gt;-1&lt;/sup&gt;, occupies a volume of 90 ml.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Orders_of_magnitude_%28numbers%29#1012&quot;&gt;The human body has 10&lt;sup&gt;13&lt;/sup&gt; human cells and hosts 9x10&lt;sup&gt;13&lt;/sup&gt; bacterial cells.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bionumbers.hms.harvard.edu/bionumber.aspx?&amp;amp;id=103905&amp;amp;ver=6&quot;&gt;One &lt;em&gt;E. coli&lt;/em&gt; cell has a mass of 0.95×10&lt;sup&gt;−15&lt;/sup&gt; kg (wet weight).&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that &lt;em&gt;E. coli&lt;/em&gt; is typical with respect to mass of human microbial flora:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;mass of bacterial cells in one human body = (0.95×10&lt;sup&gt;−15&lt;/sup&gt; * 9x10&lt;sup&gt;13&lt;/sup&gt;) kg&#xA; = 0.0855 kg = 86 g&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-12-01T18:52:13.817" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5400" PostTypeId="1" CreationDate="2012-12-01T22:36:25.323" Score="13" ViewCount="9729" Body="&lt;p&gt;I have been reading the Wikipedia article about &lt;a href=&quot;http://en.wikipedia.org/wiki/Food_energy&quot;&gt;food energy&lt;/a&gt;, but as I'm not a biologist, I don't really understand it properly, so I came here to ask you guys.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: &lt;strong&gt;If a human body needs X kcal of energy and it's taking it from the stored fat, how much fat (weight/kg) does it need to burn?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that 1 gram of fat represents 9 kcal of energy, but according to the food energy article, the efficiency of getting that energy isn't 100%, so the formula might be a lot more difficult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure what is the real efficiency value here. The article mentions more values, ranging from 18% to 40%.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S.: If this belongs to Chemistry.stack, please, tell me or move it there.&lt;/p&gt;&#xA;" OwnerUserId="1727" LastEditorUserId="3632" LastEditDate="2012-12-01T22:58:09.603" LastActivityDate="2012-12-09T00:50:38.817" Title="How much energy does human body fat contain?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5401" PostTypeId="1" CreationDate="2012-12-02T00:35:54.270" Score="4" ViewCount="2697" Body="&lt;p&gt;I just accidentally pulled out, while playing, my cat's whisker entirely, follicle and all. I feel terrible as I know she is a kitten and whiskers are rooted deep in a place rich in nerves. I'm wondering if the whisker will grow back and if it will cause a lot of pain as it regrows.&lt;/p&gt;&#xA;" OwnerUserId="1728" LastEditorUserId="31230" LastEditDate="2018-04-08T01:27:25.917" LastActivityDate="2018-04-08T01:27:25.917" Title="Will a completely removed cat whisker grow back?" Tags="&lt;zoology&gt;&lt;sensation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5402" PostTypeId="1" AcceptedAnswerId="5404" CreationDate="2012-12-02T03:19:09.280" Score="4" ViewCount="1527" Body="&lt;p&gt;Both Coca-Cola and Pepsi add phosphoric acid $H_3PO_4$ to their colas to give them a signature &quot;bite&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The kidneys use a phosphoric acid/dihydrogen phosphate/hydrogen phosphate homeostasis as one mechanism to eliminate/excrete excess acid from the body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The issue of whether sodas containing phosphoric acid can exacerbate osteoporosis and related conditions has been explored &lt;a href=&quot;https://skeptics.stackexchange.com/questions/2139/does-pop-soda-pop-cause-osteoporosis&quot;&gt;here&lt;/a&gt; and in some detail on &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphoric_acid#Biological_effects_on_bone_calcium_and_kidney_health&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;, but I'm more interested in direct effects on the kidney.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested to know if the overall renal physiology is adversely affected by extra phosphoric acid that long-term moderate consumption (say a single 2L bottle per week for a year) of soda would introduce (including interrupting or saturating the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sodium/phosphate_cotransporter&quot; rel=&quot;nofollow noreferrer&quot;&gt;Na-Pi transporter&lt;/a&gt;)?&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2012-12-02T21:53:51.243" Title="Is the amount of phosphoric acid added to colas enough to disrupt the function of the kidney over the long term?" Tags="&lt;nutrition&gt;&lt;renal-physiology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5403" PostTypeId="1" AcceptedAnswerId="5407" CreationDate="2012-12-02T12:04:21.337" Score="4" ViewCount="4790" Body="&lt;p&gt;As written in my lecture handouts, there two main factors in the Geometric Growth Model of populations:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$R_{0}$ is the expected lifetime reproductive output. This way, for unicellulars, for example, when time between division represents life time, if there is no mortality, $R_{0}$ is calculated as $R_{0}=1*2$, where 1 is 100% and 2 is the amount of daughter cells expected to be produced as a result of the mother cell split. We also define that for this isolated incident, $B$, the amount of births is 2, while the mother cell &quot;dies&quot;, which leads to $D=1$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second factor is $\lambda$, which is the finite rate of increase, which in other words means that this is average per-capita multiplication factor per one time-step.&#xA;When we measure population growth in time-steps of 1 lifetime, we can conclude that $\lambda=R_0$. We actually look at $\lambda$ as at $\frac{N_{t+1}}{N_{t}}$, where $N_{t+1}=N_{t}+B-D$(1) and $N_t$ is the amount of individuals in the populations at time-step $t$. This way we define $\lambda$ using $b=\frac{B}{N_{t}}$ and $d=\frac{D}{N_{t}}$: $\lambda=\frac{N_{t+1}}{N_{t}}=\frac{N_{t}}{N_{t}}+\frac{B}{N_{t}}-\frac{D}{N_{t}}=1+b-d$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All fine when we deal with ideal conditions, where all mother cells divide and there are no mortalities or mutations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But suppose we're told that only 80% of the mother cells will divide, and the remaining 20% will die without division. In this case: $R_{0}=0.20*0+0.80*2$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm trying to understand, how will $\lambda$ be affected by this? Does $\lambda$ refers to ideal conditions only, or it depends on the natural situation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) We ignore Immigration and the Emigration at this point.&lt;/p&gt;&#xA;" OwnerUserId="246" LastEditorUserId="1320" LastEditDate="2012-12-02T16:56:28.580" LastActivityDate="2013-05-29T09:12:15.063" Title="Does finite rate of increase depend on mortality of individuals in a population?" Tags="&lt;ecology&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5404" PostTypeId="2" ParentId="5402" CreationDate="2012-12-02T21:53:51.243" Score="2" Body="&lt;p&gt;The phosphoric acid in cola will contribute to dietary intake of phosphate. I may be missing something, but, since the transporter functions to reabsorb phosphate that has been filtered out at the glomerulus, excess phosphate will spill over into the urine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dietary_Reference_Intake&quot; rel=&quot;nofollow&quot;&gt;According to Wikipedia&lt;/a&gt; the RDA for phosphorus is 700 mg and the tolerable upper intake level is 4000 mg. Coca cola contains 17 mg phosphorus (as phosphate) 100 ml&lt;sup&gt;-1&lt;/sup&gt; (which is 340 mg in 2 L)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.prosebeforehos.com/image-of-the-day/10/13/cocacola-consumption-per-capita/&quot; rel=&quot;nofollow&quot;&gt;this source&lt;/a&gt;, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;in the United States, an average person drinks 412 8-ounce drinks — or 3296 ounces — of Coke per year. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This works out at 9 oz per day = 266 ml = 45 mg phosphorus&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For comparison (from &lt;a href=&quot;http://apjcn.nhri.org.tw/server/info/books-phds/books/foodfacts/html/data/data5f.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;white flour contains 595 mg 100 g&lt;sup&gt;-1&lt;/sup&gt;&lt;/li&gt;&#xA;&lt;li&gt;one boiled egg contains 220 mg&lt;/li&gt;&#xA;&lt;li&gt;canned salmon contains 240 mg 100 g&lt;sup&gt;-1&lt;/sup&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-12-02T21:53:51.243" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5405" PostTypeId="1" AcceptedAnswerId="5408" CreationDate="2012-12-03T02:33:50.213" Score="10" ViewCount="2862" Body="&lt;p&gt;If it were possible to live forever, would our brains grow infinitely with the number of memories that we store? Or would we remove old memories as we create new ones?&lt;/p&gt;&#xA;" OwnerUserId="1569" LastActivityDate="2014-12-08T10:03:15.007" Title="Do memories have mass?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;brain&gt;&lt;neuroanatomy&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5406" PostTypeId="2" ParentId="5405" CreationDate="2012-12-03T03:40:30.530" Score="1" Body="&lt;p&gt;We already remove old ones and create new ones. I doubt you remember most of Geometry, for instance.&lt;/p&gt;&#xA;&lt;p&gt;As for capacity, &lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=what-is-the-memory-capacity&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article from Scientific American&lt;/a&gt; gives a good overview of what we can estimate with our current knowledge.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;For comparison, if your brain worked like a digital video recorder in a television, 2.5 petabytes would be enough to hold three million hours of TV shows. You would have to leave the TV running continuously for more than 300 years to use up all that storage.&lt;/p&gt;&#xA;&lt;p&gt;The brain’s exact storage capacity for memories is difficult to calculate. First, we do not know how to measure the size of a memory. Second, certain memories involve more details and thus take up more space; other memories are forgotten and thus free up space. Additionally, some information is just not worth remembering in the first place.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So, there is an upper limit. Where is it? Well, probably a bit longer than our reasonable lifespan at the moment.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-12-03T03:40:30.530" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="5407" PostTypeId="2" ParentId="5403" CreationDate="2012-12-03T04:13:26.753" Score="2" Body="&lt;p&gt;*It's been several years since I've worked with similar equations. The following reply is based on memory, and if anyone has a firmer grasp of the materials, please modify or answer as you see fit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would assume λ is under ideal conditions or as an average of whatever species you're working with. Your modified lifetime reproductive output still leaves out many variables which can affect λ. By your own words it leaves out mutations and daughter cells that are dead-on-arrival. There could also be predation or conditions where the Mother-cell produces more than one Daughter-cell, resulting in R = 3 instead of 2 and your subsequent λ also being 3. &lt;a href=&quot;http://newsroom.ucla.edu/portal/ucla/ucla-bioengineers-discover-confined-235851.aspx&quot; rel=&quot;nofollow&quot;&gt;UCLA Bioengineers have actually observed up to 5 daughter cells in cancer lines.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure what you mean by &quot;... or it depends on the natural situation?&quot;, but ultimately reality is always more complicated than basic equations usually describe. Either &lt;em&gt;B&lt;/em&gt; or &lt;em&gt;D&lt;/em&gt; can increase or decrease, depending on the species, environment, and how you define &lt;em&gt;t&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your equation still produces a population increase, just at a slower rate than your ideal conditions. If you're asking if there's a specific definition for &quot;λ&quot; referenced in your equation, I'm not aware of any specific definition for &quot;λ&quot; - it's not a Constant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your title question - does the rate of increase depend on mortality - is ultimately &quot;Yes.&quot; If mortality is higher than the birth rate, then you will see a decrease of the population until extinction is reached if there isn't an equilibrium or rebound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, &lt;strong&gt;most populations change at an &lt;em&gt;Exponential&lt;/em&gt; rate - NOT Geometric&lt;/strong&gt;. To that end, you might be interested in the &lt;a href=&quot;http://en.wikipedia.org/wiki/R/K_selection_theory&quot; rel=&quot;nofollow&quot;&gt;r/K Selection Theory&lt;/a&gt; and how they operate within Exponential equations (which are similar to your Geometric equations). In short, &lt;strong&gt;r-Selection&lt;/strong&gt; is the reproductive strategy of producing extraordinary amounts of offspring with a very, very low survival rate. However, because so many are produced you only need a small overall percentage of survival to maintain or increase populations. The tapeworm I mentioned above is one of the stereotypical examples. &lt;strong&gt;K-Selection&lt;/strong&gt; represents species that invest additional resources into raising &lt;em&gt;a few&lt;/em&gt; offspring, usually just a handful that are carefully watched over and raised by the parent(s) until they are capable of reproducing themselves. Humans, elephants, most birds, and larger animals in general are K-selected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For &lt;strong&gt;r-Selection&lt;/strong&gt; your &lt;em&gt;B&lt;/em&gt; and &lt;em&gt;D&lt;/em&gt; will both be very high, and for &lt;strong&gt;K-Selection&lt;/strong&gt; both &lt;em&gt;B&lt;/em&gt; and &lt;em&gt;D&lt;/em&gt; will be low. However, both will result in a positive λ simply because it's all about the ratios.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-12-03T04:13:26.753" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5408" PostTypeId="2" ParentId="5405" CreationDate="2012-12-03T06:52:04.793" Score="15" Body="&lt;p&gt;You would need to live a long, long, long, long time for this to become remotely problematic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question seems to suppose that a memory is &quot;stored&quot; by a neuron, and since neurons have mass, then the more memories we have the more our brains will weigh. Actually, &lt;a href=&quot;http://en.wikipedia.org/wiki/Neurogenesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;neurogenesis&lt;/a&gt; is pretty rare in the adult brain--most of the cortex is fixed, and new neurons do not grow. (The hippocampus is the best known counterexample, but it's important to note that contrary to lore, the hippocampus doesn't store memories &lt;em&gt;per sé&lt;/em&gt;, though it is involved in the formation and retrieval of memories).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Memories are represented in the brain as patterns of firing neurons. Let's say, for simplicity, that each neuron can either be on or off. Since there are &lt;a href=&quot;http://www.guardian.co.uk/science/blog/2012/feb/28/how-many-neurons-human-brain&quot; rel=&quot;nofollow noreferrer&quot;&gt;86 billion neurons in the brain&lt;/a&gt;, we can experience 2^86bn possible brain states. That's a lot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course there are a lot of simplifications here--most notably, there is a lot of structure to the brain, and so i'm not suggesting you can store 2^86bn memories--but the logic is the same. Even with only 1,000 neurons, we can store a ridiculous amount of information (2^1000).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to comment on &lt;a href=&quot;https://biology.stackexchange.com/a/5406/562&quot;&gt;MCM's answer&lt;/a&gt; as well, because I don't think it's true that we &quot;remove&quot; old memories. Or rather, the topic is still being debated in cognitive science today. For an old take on it, see renowned memory researcher Endel Tulving's (1974) article, in which he says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When we forget something we once knew, it does not necessarily mean that the memory trace has been lost; it may only be inaccessible&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The idea is that some memories are &lt;a href=&quot;http://en.wikipedia.org/wiki/Memory_inhibition&quot; rel=&quot;nofollow noreferrer&quot;&gt;suppressed&lt;/a&gt; (no, not &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Repressed_memory&quot; rel=&quot;nofollow noreferrer&quot;&gt;repressed&lt;/a&gt;&lt;/em&gt;), being rendered inaccessible. &lt;a href=&quot;http://en.wikipedia.org/wiki/Robert_Bjork&quot; rel=&quot;nofollow noreferrer&quot;&gt;Robert Bjork&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/John_Robert_Anderson_%28psychologist%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;John Anderson&lt;/a&gt; have (separately) done some nice work in this area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So before you worry about this becoming a problem, I suspect you need to work out the secret of immortality first.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Tulving, E. (1974). Cue-Dependent Forgetting: When we forget something&#xA;  we once knew, it does not necessarily mean that the memory trace has&#xA;  been lost; it may only be inaccessible. American Scientist, 74-82.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="562" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2012-12-04T04:39:14.387" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5409" PostTypeId="1" CreationDate="2012-12-03T06:55:25.297" Score="7" ViewCount="295" Body="&lt;p&gt;While for example a wolf pack provides protection to a sick wolf, increasing its chance of survival, there is a risk of infecting other members of the pack, decreasing their total chance of survival.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do animals have mechanisms for preventing that? For example the sick member leaving its group temporarily?&lt;/p&gt;&#xA;" OwnerUserId="1279" LastActivityDate="2016-08-18T20:27:41.957" Title="What mechanisms do animals living in groups (herds, packs, swarms) have against spreading contagious diseases?" Tags="&lt;pathology&gt;&lt;collective-behaviour&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5410" PostTypeId="2" ParentId="5409" CreationDate="2012-12-03T09:34:50.883" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Almberg ES, Mech LD, Smith DW, Sheldon JW, Crabtree RL (2009) A Serological Survey of Infectious Disease in Yellowstone National Park’s Canid Community. PLoS ONE 4(9): e7042. doi:10.1371/journal.pone.0007042&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors found that the majority of Yellowstone wolves had been exposed to a number of different viruses (evidence from antibodies in blood samples). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They also found evidence for historical outbreaks of canine distemper virus in wolves, coyotes and red foxes in 1999 and 2005. These outbreaks correlated with peaks in wolf pup mortality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This evidence suggests that wolves have no mechanisms for avoiding the spread of these viral diseases. Perhaps periodic episodes of increased mortality are the price that has to be paid for a longer-term 'herd immunity'?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit - in response to OP comment below:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The data indicate very high levels of seropositivity to the viruses. I would say that 'not 100% successful' is an understatement. But I must admit that I am way out of my area of expertise here!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We found high, constant exposure to canine parvovirus (wolf seroprevalence: 100%; coyote: 94%), canine adenovirus-1 (wolf pups [0.5-0.9 yr]: 91%, adults [&gt;or=1 yr]: 96%; coyote juveniles [0.5-1.5 yrs]: 18%, adults [&gt;or=1.6 yrs]: 83%), and canine herpesvirus (wolf: 87%; coyote juveniles: 23%, young adults [1.6-4.9 yrs]: 51%, old adults [&gt;or=5 yrs]: 87%) suggesting that these pathogens were enzootic within YNP wolves and coyotes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-12-03T10:16:44.610" LastActivityDate="2012-12-03T10:16:44.610" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5412" PostTypeId="2" ParentId="5380" CreationDate="2012-12-03T13:10:17.380" Score="5" Body="&lt;p&gt;Alcoholic beverages, ingested casually, deliver two main nutrients the body will metabolize: sugar and ethanol. The body's natural response to a rise in blood glucose will be stimulated secretion of insulin (from B cells of the pancreatic islets). Alcohol is metabolized primarily by the liver, being first converted to acetaldehyde by alohol dehydrogenase and a coezyme NAD+. Acetaldehyde metabolism quickly converts this to acetate. Acetate is then eventually metabolized elsewhere in the body to carbon dioxide and water. The interesting effects are mediated by acetaldehyde, which can accumulate to toxic levels in some people. This ties into insulin because &lt;a href=&quot;http://endo.endojournals.org/cgi/pmidlookup?view=long&amp;amp;pmid=17916634&quot;&gt;this article&lt;/a&gt; suggests that alcohol consumption changes blood flow from exocrine pancreas (responsible for digestive enzymes) to endocrine pancreas (responsible for secreting homrones, such as glucagon, insulin, somatostatin). Alcohol seems to modulate the late-phase of insulin secretion, increasing secretion, which leads to exaggerated glucose disposal and at least for diabetics causes hypoglycemia.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://endo.endojournals.org/cgi/pmidlookup?view=long&amp;amp;pmid=17916634&quot;&gt;Huang Z, Sjöholm A. Ethanol acutely stimulates islet blood flow, amplifies insulin secretion, and induces hypoglycemia via nitric oxide and vagally mediated mechanisms. Endocrinology. 2008 Jan;149(1):232-6. Epub 2007 Oct 4.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-12-03T13:10:17.380" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5413" PostTypeId="1" AcceptedAnswerId="5414" CreationDate="2012-12-03T14:54:53.387" Score="5" ViewCount="211" Body="&lt;p&gt;For some structural study I am looking for cyclodextrin strucutures (in 3D format such as pdb, mol2, etc) complexed with small molecule ligands, such as cholesterol and even smaller. Right now I could only find on the PDB database some proteins complexed with cyclodextrin, but no structure of cyclodextrin with small ligands, could you help me?&lt;/p&gt;&#xA;" OwnerUserId="551" LastActivityDate="2012-12-03T15:52:47.143" Title="Structures of cyclodextrin complexed with small ligands" Tags="&lt;structural-biology&gt;&lt;structure-prediction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5414" PostTypeId="2" ParentId="5413" CreationDate="2012-12-03T15:52:47.143" Score="7" Body="&lt;p&gt;I looked for relevant publications at Web of Science using 'structur* AND cyclodextrin' in the Title field. For the period 2011-2012 there were 56 hits including:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Racz et al (2012) Structure of the inclusion complex of beta-cyclodextrin with lipoic acid from laboratory powder diffraction data. Acta Crystallographica Section B 68: 164-170&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Ali et al (2012) Structure determination of fexofenadine-a-cyclodextrin complex by quantitative 2D ROESY analysis and molecular mechanics studies. Magnetic Resonance in Chemistry 50:299-304&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Lula et al (2012) Interaction between bradykinin potentiating nonapeptide (BPP9a) and beta-cyclodextrin: A structural and thermodynamic study. Materials Science &amp;amp; Engineering C 32: 244-253&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I looked at some of the papers but I didn't find any specific case where a structure has been deposited in a database. There were, however, several mentions of the &lt;a href=&quot;http://beta-www.ccdc.cam.ac.uk/pages/Home.aspx&quot;&gt;Cambridge Crystallographic Data Centre&lt;/a&gt;  as a source of small molecule structures.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-12-03T15:52:47.143" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5415" PostTypeId="2" ParentId="5395" CreationDate="2012-12-03T20:02:50.047" Score="7" Body="&lt;p&gt;@AlanBoyd's calculations are reasonable, I think the estimate is off though.  The human microbome includes other bacteria which are not necessarily E.coli equivalent.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nih.gov/news/health/jun2012/nhgri-13.htm&quot; rel=&quot;nofollow&quot;&gt;The human microbome projects give estimates that microbes are 1-3% total body mass&lt;/a&gt;.  i.e. several pounds of bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The GI tract alone has most of the microbome mass - &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_microbiome#Gut_flora&quot; rel=&quot;nofollow&quot;&gt;faeces is ~60% intestinal flora/fauna by dry weight&lt;/a&gt;, which for many adults alone must be hundreds of grams at any given moment. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-12-04T23:12:07.687" LastActivityDate="2012-12-04T23:12:07.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5416" PostTypeId="1" AcceptedAnswerId="5417" CreationDate="2012-12-04T18:40:02.703" Score="28" ViewCount="9009" Body="&lt;p&gt;When a human being exhales CO₂, what is, by the numbers, the main source of carbon atoms exiting the body in this way? I mean what class of cells, or which tissues are the biggest on a pie chart of where carbon atoms breathed out in the form of CO₂ molecules came from?&lt;/p&gt;&#xA;" OwnerUserId="263" LastEditorUserId="3340" LastEditDate="2014-10-09T13:33:49.150" LastActivityDate="2020-09-08T18:32:23.600" Title="Where does the 'C' in exhaled CO₂ mostly come from?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;cellular-respiration&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5417" PostTypeId="2" ParentId="5416" CreationDate="2012-12-04T19:36:02.933" Score="26" Body="&lt;p&gt;CO&lt;sub&gt;2&lt;/sub&gt; is a product of &lt;a href=&quot;http://en.wikipedia.org/wiki/Cellular_respiration&quot;&gt;Cellular Respiration&lt;/a&gt;, which generally takes Glucose and molecular Oxygen to produce Carbon Dioxide, water, heat, and allows ADP to be regenerated into ATP (or other various oxidation reactions). The &lt;strong&gt;Carbon&lt;/strong&gt; comes from wherever the acetyl-CoA used in the Citric Acid Cycle came from - either carboyhydrates or fatty-acids (saturated carbon chains).&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;Simplified reaction:   C&lt;sub&gt;6&lt;/sub&gt;H&lt;sub&gt;12&lt;/sub&gt;O&lt;sub&gt;6&lt;/sub&gt; (s) + 6 O&lt;sub&gt;2&lt;/sub&gt; (g) → 6 CO&lt;sub&gt;2&lt;/sub&gt; (g) + 6 H&lt;sub&gt;2&lt;/sub&gt;O (l) + heat&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So, you are correct. CO&lt;sub&gt;2&lt;/sub&gt; transferring out of the lungs is mostly the result of burning sugars (or fats) for energy (the regeneration of ADP/GDP with respect to human biology).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To that end, the tissues that produce the most CO&lt;sub&gt;2&lt;/sub&gt; will be the cell-types which constantly require energy. Nominally, &lt;em&gt;muscle tissues&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Per your comment, broken down fat, or rather, the process of &lt;a href=&quot;http://en.wikipedia.org/wiki/Fatty_acid_metabolism&quot;&gt;Fatty-Acid Catabolism&lt;/a&gt;, results in the production of &lt;strong&gt;acetyl-CoA&lt;/strong&gt;, which is a primary player in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Citric_acid_cycle&quot;&gt;Citric-Acid Cycle&lt;/a&gt;. The Citric Acid Cycle, which you should recognize as the Cycle that &lt;strong&gt;Pyruvate&lt;/strong&gt; - the end result of &lt;a href=&quot;http://en.wikipedia.org/wiki/Glycolysis&quot;&gt;Glycolysis&lt;/a&gt; (the breakdown of Glucose into 2x 3-Carbon Pyruvates) - also goes into after being converted into &lt;strong&gt;acetyl-CoA&lt;/strong&gt; by Pyruvate Dehydrogenase.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;The sum of all reactions in the citric acid cycle is:&#xA;Acetyl-CoA + 3 NAD&lt;sup&gt;+&lt;/sup&gt; + Q + GDP + Pi + 2 H&lt;sub&gt;2&lt;/sub&gt;O → CoA-SH + 3 NADH + 3 H&lt;sup&gt;+&lt;/sup&gt; + QH&lt;sub&gt;2&lt;/sub&gt; + GTP + 2 CO&lt;sub&gt;2&lt;/sub&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So, for a basic breakdown with respect to CO2:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Carbohydrates (Sugars, Starches) &lt;strong&gt;→&lt;/strong&gt; Glucose &lt;strong&gt;→ Pyruvate&lt;/strong&gt; + ATP + NADH&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Pyruvate → &lt;em&gt;Acetyl-CoA&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Lipids (fats) &lt;strong&gt;→&lt;/strong&gt; Lipolysis &lt;strong&gt;→ &lt;em&gt;Acetyl-CoA&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Acetyl-CoA&lt;/strong&gt; + ... + H&lt;sub&gt;2&lt;/sub&gt;0 &lt;strong&gt;→&lt;/strong&gt; ... + &lt;strong&gt;CO&lt;sub&gt;2&lt;/sub&gt;&lt;/strong&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="3340" LastEditDate="2014-10-31T12:57:32.473" LastActivityDate="2014-10-31T12:57:32.473" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5419" PostTypeId="1" CreationDate="2012-12-05T11:31:51.670" Score="10" ViewCount="322" Body="&lt;p&gt;We are running a gel on the products of a restriction digest to determine the size of an insert. We know the vector backbone size should be ~2.9kb; however, the standard appears to be running too quickly (or our samples too slowly), causing the backbone size to be about 4kb (which distorts our results for the insert size).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What could possibly cause this? Thank you.&lt;/p&gt;&#xA;" OwnerUserId="821" LastEditorUserId="6" LastEditDate="2012-12-05T12:13:36.283" LastActivityDate="2012-12-05T20:59:33.937" Title="When running a gel, what could cause a standard to run &quot;faster&quot; than usual?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;gel-electrophoresis&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5421" PostTypeId="1" AcceptedAnswerId="5424" CreationDate="2012-12-05T19:13:53.783" Score="8" ViewCount="6752" Body="&lt;p&gt;The title does, &lt;em&gt;prima facie&lt;/em&gt;, appear absurd.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Performing a swallowing action whilst pinching the nostrils shut gives the impression of listening through a bucket filled with water around the head; audible sound levels are perceptibly reduced. Some humans may encounter a similar sensation blowing their nose - hard.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This makes sense give the ears connect to the mouth/nose through the eustachian tubes. Can an odour make its way to the olfactory sensors through the ears?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="69" LastEditDate="2012-12-05T22:39:06.357" LastActivityDate="2012-12-06T18:36:03.007" Title="Can a human smell through the ears?" Tags="&lt;human-biology&gt;&lt;sensation&gt;&lt;human-ear&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5422" PostTypeId="2" ParentId="5421" CreationDate="2012-12-05T20:55:27.723" Score="-2" Body="&lt;p&gt;Modified 6 Dec 2012: One approach to this question is to perform a sequence similarity search for genes encoding genes with a functioning in sensing external stimuli, be they&#xA;olfactory receptor, taste receptor or other such genes that are expressed in cDNAs or RNA-Seq data from library preparations of the appropriate ear tissue. While there is not likely at this point in time to be much data available in RNA-Seq format, one might find cDNA libraries from cochlea or neighboring tissue. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &quot;hit,&quot; meaning there is evidence that, for example, an olfactory receptor gene is expressed in cochlea, &lt;em&gt;eg&lt;/em&gt;, only means that there is &lt;em&gt;potential&lt;/em&gt; to smell through the ears. Taste receptors are expressed throughout the alimentary canal in humans, but tasting the contents - food or other - is not readily perceived as de facto taste outside the oral cavity. Nonetheless, there is no reason not to expect such sensors are expressed to relay information to the brain as to what is or is not present. &quot;Smelling&quot; in/by the ear for the purpose of detecting the presence of a given entity or molecule could serve a similar function.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-12-06T18:36:03.007" LastActivityDate="2012-12-06T18:36:03.007" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5423" PostTypeId="2" ParentId="5419" CreationDate="2012-12-05T20:59:33.937" Score="3" Body="&lt;p&gt;If the salt content or pH is different than &quot;normal,&quot; run time can be affected. After all, you're applying an electric current to the sample(s) and ion concentrations and pH are sensitive to that current. Of these two, salt/ion levels are more likely to have an effect as your samples/markers are likely to be adequately buffered.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2012-12-05T20:59:33.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5424" PostTypeId="2" ParentId="5421" CreationDate="2012-12-05T21:39:53.437" Score="16" Body="&lt;p&gt;A quick diagram to point out to people who may not know what Eustachian tubes are (#2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uRzEC.gif&quot; alt=&quot;Anatomy of the Ear&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order for the aromatic molecule to reach the olfactory bulb, it would first have to get through the Tympanic Membrane (#22) [a.k.a. - Eardrum]. The Tympanic Membrane is water/airtight unless pierced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, while it's plausible that an aromatic molecule could travel through the Eustachian tubes and enter the pharynx areas, there isn't any way to get into the middle-ear in the first place unless the Tympanic Membrane has been compromised.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a healthy and intact individual, the answer should be &lt;strong&gt;No.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-12-05T21:39:53.437" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5425" PostTypeId="2" ParentId="5421" CreationDate="2012-12-06T00:46:32.523" Score="6" Body="&lt;p&gt;@MCM gave a succinct and accurate description of how a healthy and &quot;normal&quot; person will not be able to smell via olfactory sensing trough the Eustachian tube.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is an interesting concept in which the brain is able to confuse senses, or alternatively, use sensory input as a metaphor for interpretation via another sensory output. This is a condition known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Synesthesia&quot; rel=&quot;nofollow&quot;&gt;synesthesia&lt;/a&gt;. The majority of known synesthetes have cross-talk between audio-visual sensory pathways. That is, one may interpret sounds as shapes or colours, while another may interpret specific objects (or symbols) as colours or sounds. There were a handful of synesthetes studied in the late 1980's (referred to in this article by &lt;a href=&quot;http://www.theassc.org/files/assc/2358.pdf&quot; rel=&quot;nofollow&quot;&gt;Day S.&lt;/a&gt;) and one patient was able to interpret sounds as smells. In the review article, smell-interpretation of sound accounts for ~0.1% of known synesthetes, while sound-interpreting olfaction is more common at ~0.6% incidence. On some higher level, the neural information for two senses is confused, and synesthetes that may confuse smelling for some other sense, can not technically perceive scent (using olfactory receptors) through other sensory organs (like the eyes), so the answer is technically &lt;strong&gt;no&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.theassc.org/files/assc/2358.pdf&quot; rel=&quot;nofollow&quot;&gt;Day S. Psyche 1996, 2(32).&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2012-12-06T13:12:20.607" LastActivityDate="2012-12-06T13:12:20.607" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5426" PostTypeId="1" AcceptedAnswerId="7096" CreationDate="2012-12-06T05:24:46.013" Score="5" ViewCount="278" Body="&lt;p&gt;I have built an experimental portable batch biodigester to process organic garbage. A 50L drum filled half with garbage, half with water and with some cow dung added for inoculation, is connected from the top to a truck tire, boxed into another, larger drum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I consider filling the bin within a week, based on the amount of daily garbage my home is producing. After a week, the bin is filled in with water and inoculated, and connected to the gas-holder.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How long would the biodigestion take in average before I can disconnect the bin and use the remaining slurry?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have looked at existing information regarding the biodigestion process. The stages of biodigestion are explained in Chapter 4 of the Biogas Handbook sample I have:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Aerobic&lt;/strong&gt;&lt;br&gt;&#xA;  Oxygen will inevitably enter with the raw materials put into the generator, and so aerobic bacteria use this oxygen up,&#xA;  meanwhile doing what they can to break the materials down. CO&lt;sub&gt;2&lt;/sub&gt; is&#xA;  released, and some heat is generated.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Extracellular enzymes&lt;/strong&gt;&lt;br&gt;&#xA;  In this stage, anaerobic bacteria release enzymes that attack large molecules which are still outside their own&#xA;  bodies (extracellular), so these molecules will be broken down into&#xA;  “bite sizes.”&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Acid digestion&lt;/strong&gt;&lt;br&gt;&#xA;  The bite size molecules (still fairly large) are absorbed by the bacteria and digested. The main byproducts of this&#xA;  third process are simple molecules such as the short chain fatty&#xA;  acids, H&lt;sub&gt;2&lt;/sub&gt; and CO&lt;sub&gt;2&lt;/sub&gt;. (We’ll get into the short chain fatty acids soon.)&#xA;  It’s interesting to note that at this stage, hydrogen gas, an&#xA;  excellent fuel, is evolved. Hydrogen does not often show up in the&#xA;  final biogas apparently because it is used by the anaerobic bacteria&#xA;  (in the next stage) in making CH4, methane.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Gas digestion&lt;/strong&gt;&lt;br&gt;&#xA;  Now comes the part we’ve been waiting for. The fatty acids are now gobbled up by the last group of bacteria, who turn them&#xA;  into H&lt;sub&gt;2&lt;/sub&gt;O, CO&lt;sub&gt;2&lt;/sub&gt;, and best of all, CH&lt;sub&gt;4&lt;/sub&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Alas, the length of these stages is not explained. However, &lt;a href=&quot;http://biorealis.com/digester/digestion.html&quot; rel=&quot;nofollow&quot;&gt;Biorealis suggests&lt;/a&gt; the length of the Acid Digestion and Gas Digestion in a critique of conventional continuous-feed biodigesters vs. the two-phased biodigester it has developed:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Conventional single-stage digesters are not only unstable, they are&#xA;  also relatively inefficient. For example, if the system is operated at&#xA;  a hydraulic retention time (HRT) conducive to growth of acidogens (2-3&#xA;  days), any methanogens present will be washed out of the system faster&#xA;  than they can reproduce, preventing them from ever becoming&#xA;  established. On the other hand, if the system is operated at an HRT&#xA;  conducive to growth of methanogens (20-25days), the faster growing&#xA;  acidogens will be maintained at the low growth rates of the endogenous&#xA;  growth phase - essentially at starvation level.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;NB: I opted for a batch biodigestion system to avoid the complications mentioned by Biorealis here above and because Biorealis' two-phased biodigester is more expensive and less easy to build.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far I have a rough biodigestion calendar of:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;3 days of acid digestion&lt;/li&gt;&#xA;&lt;li&gt;20-25 days of gas &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;But I still lack some information on the stages:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;how about the length of the two previous stages&lt;/strong&gt; mentioned in the Biogas Handbook?&lt;/li&gt;&#xA;&lt;li&gt;on what do those stages depend and &lt;strong&gt;can I accelerate digestion&lt;/strong&gt; somehow? (I already know about heat at 21°C, how about water ratio or anything else?)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;how long does it take to digest a big chunk of food&lt;/strong&gt;, say a 27cm² bit of carrot? (Important because I hope the garbage is completely processed before I toss the slurry in the garden as fertilizer)&lt;/li&gt;&#xA;&lt;li&gt;in short &lt;strong&gt;after how much time can I confidently unplug the batch&lt;/strong&gt;, knowing the biodigestion is complete?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Could you help me shed some light on the length of biodigestion stages? Thanks. &lt;/p&gt;&#xA;" OwnerUserId="1749" OwnerDisplayName="Benjamin" LastEditorUserId="3340" LastEditDate="2014-10-31T13:10:03.767" LastActivityDate="2014-10-31T13:10:03.767" Title="What is the length of anaerobic biodigestion stages?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5427" PostTypeId="1" CreationDate="2012-12-06T10:15:47.740" Score="2" ViewCount="703" Body="&lt;p&gt;When producing insulin, the gene for its production is inserted into the plasmid of a bacterium that is allowed to replicate freely. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why can't the same thing be done with antibodies (as I understand it, currently cancer cells are fused with mammalian cells that produce these antibodies, and now the tumour is allowed to replicate, much like the bacterium, making more antibodies)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is different about these two proteins that means fairly distinct processes of production are required for each?&lt;/p&gt;&#xA;" OwnerUserId="1667" LastEditorUserId="1306" LastEditDate="2012-12-06T15:17:30.450" LastActivityDate="2012-12-06T15:47:25.920" Title="Insulin and monoclonal antibody production" Tags="&lt;immunology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5428" PostTypeId="2" ParentId="5427" CreationDate="2012-12-06T13:59:16.530" Score="3" Body="&lt;p&gt;I recommend that you take a look at this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Jeong KJ, Jang SH, Velmurugan N. (2011) Recombinant antibodies: engineering and production in yeast and bacterial hosts. Biotechnol J. 6:16-27.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This fairly recent view discusses the progress and prospects for producing functional antibodies in yeast and bacteria. As pointed out by @Nick in the comment to the OP, the main stumbling block in both cases is the engineering that would be necessary to ensure correct glycosylation in the heterologous expression systems. This quotation from the cited review sums up the situation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The &lt;em&gt;N&lt;/em&gt;-linked glycan structure in the Fc region of antibodies is indispensible for binding to receptors (FcγRs), but glycosylation has been one of the major limitations in choosing possible production hosts. Eukaryotic yeast as well as bacteria, including E. coli, have not been used as the main hosts for the production of recombinant antibodies (full-length IgG format) for use in humans because of glycosylation problems. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They do however go on to discuss some interesting developments such as the expression of a &lt;em&gt;Campylobacter&lt;/em&gt; N-glycosylation pathway in &lt;em&gt;E.coli,&lt;/em&gt; as well as strategies for the production of functional antibody fragments.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-12-06T15:47:25.920" LastActivityDate="2012-12-06T15:47:25.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5429" PostTypeId="2" ParentId="4926" CreationDate="2012-12-06T18:57:50.803" Score="3" Body="&lt;p&gt;Speaking to Artem Kaznatcheev's comment, it is not true that the adult brain is post-mitotic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dr Bernard &lt;a href=&quot;http://www.umbc.edu/psyc/faculty/rabin.html&quot; rel=&quot;nofollow&quot;&gt;Rabin&lt;/a&gt; has shown is his scientific research, often in collaboration with and funded by NASA, that the adult brain is not post-mitotic, meaning that cell growth and division does occur. The primary focus of his work is to examine the relationship between high-energy irradiation of the brain (such as on a long-term space mission, say to Mars) and normal aging, and how diet can affect that age-mimicking decline. A list of papers he has published in the field of the aging brain is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=rabin%20bm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="9943" LastEditDate="2015-09-28T14:51:26.777" LastActivityDate="2015-09-28T14:51:26.777" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5430" PostTypeId="1" AcceptedAnswerId="5431" CreationDate="2012-12-06T19:38:41.933" Score="14" ViewCount="85340" Body="&lt;p&gt;In order to survive, prokaryotes such as bacteria need to produce energy from food such as glucose. In eukaryotic cells, respiration is performed by mitochondria, but prokaryotic cells do not have membrane-enclosed organelles. How do prokaryotic cells respirate without mitochondria?&lt;/p&gt;&#xA;" OwnerUserId="1182" LastEditorUserId="1182" LastEditDate="2013-01-07T19:33:31.887" LastActivityDate="2018-04-17T18:11:24.557" Title="How do prokaryotes perform cellular respiration without membrane-bound organelles?" Tags="&lt;bacteriology&gt;&lt;cellular-respiration&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5431" PostTypeId="2" ParentId="5430" CreationDate="2012-12-06T19:48:20.917" Score="15" Body="&lt;p&gt;Mitochondria are very similar to bacteria and are thought to have originated from bacteria. This points you to the answer: bacteria produce ATPs the same way mitochondria do, with the oxidation machinery place in their plasma membrane (analogous to the mitochondrial membrane).&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2012-12-06T19:48:20.917" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5432" PostTypeId="2" ParentId="5304" CreationDate="2012-12-06T19:51:32.737" Score="1" Body="&lt;p&gt;Paracetamol, also known as acetominophen and Tylenol is a Non Steroidal Anti Inflammatory Drug (NSAID).  Other NSAIDs include aspirin and ibuprofen (Advil).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;NSAIDs all help with inflammation, reduce fever, but each has its own effect. Aspirin tends to thin the blood more than Paracetomol.  Paracetomol also has less effect on inflammation, but acts to reduce fever (antipyretic) and reduce pain (analgesic).  Your doctor has probably chosen this prescription because your needs fit better to this drug's properties. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ibuprofen for instance probably causes more problems more frequently when it's used frequently, one of the most common being ulcers because ibuprofen inhibits generation of stomach acid, &lt;a href=&quot;http://en.wikipedia.org/wiki/Ibuprofen#Adverse_effects&quot; rel=&quot;nofollow&quot;&gt;but cancer and a slew of other problems can crop up&lt;/a&gt;.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Paracetamol#Adverse_effects&quot; rel=&quot;nofollow&quot;&gt;While it is true that Paracetamol is the leading cause of pharmaceutical liver damage in North America, its toxicity as a drug is fairly moderate and the high number of cases is due to the fact that it is sold as an over the counter drug (with no prescription required) and is taken millions of times a day.&lt;/a&gt;  &lt;a href=&quot;http://www.drugs.com/paracetamol.html&quot; rel=&quot;nofollow&quot;&gt;The FDA has recently lowered the dose of Paracetamol to four 300 mg doses a day - but that's still 1.2 g a day&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its important to watch to see if you are one of those people who have an adverse reaction or if your liver is under stress.  You should not use this drug beyond its expiration date - it really does matter in this case.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still, all told, you probably could just take a handful of aspirin and feel just as good, but this prescription should get you feeling a little better a little faster, especially if you have pain or fever.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's true what @terdon says that acetominophen is not curing you, but drugs really mostly balance the body - healing never comes from pharmaceuticals, they often just let the body heal with fewer obstacles or discomfort.  I know I feel that when my fever comes down that I'm on the  mend - though thats not necessarily the case. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-12-07T00:07:27.017" LastActivityDate="2012-12-07T00:07:27.017" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5435" PostTypeId="1" AcceptedAnswerId="5440" CreationDate="2012-12-07T16:42:14.433" Score="4" ViewCount="465" Body="&lt;p&gt;Apparently there're species around as rely heavily on sonar to sense the world around them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.g. Bat, Dolphin, Whale ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The humans, and other terrestrial beings in a lighted world are capable of distinguishing colour in varying degrees of acuity. Is this ability to sense colour in our environment applicable to species (terrestrial, avian, and marine) that rely heavily on sonar? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="48636" LastEditDate="2019-02-11T13:55:29.497" LastActivityDate="2019-02-11T13:55:29.497" Title="Can animals that rely heavily on sonar sense colour?" Tags="&lt;zoology&gt;&lt;sensation&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5436" PostTypeId="1" AcceptedAnswerId="5437" CreationDate="2012-12-07T17:36:46.130" Score="3" ViewCount="1327" Body="&lt;p&gt;I've seen a patient who had a Vitrectomy (eye surgery) done on a single eye manifest massive swelling on both eyelids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That seems like having my left hand swell after punching a wall with my right one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this example in the eyes rare? How and why does it happen in the eyes? Does it happen anywhere else?&lt;/p&gt;&#xA;" OwnerUserId="1755" LastEditorUserId="1590" LastEditDate="2012-12-07T19:56:14.983" LastActivityDate="2012-12-09T04:56:29.080" Title="Eyelids interconnected?" Tags="&lt;eyes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5437" PostTypeId="2" ParentId="5436" CreationDate="2012-12-07T18:10:54.103" Score="5" Body="&lt;p&gt;I cannot obviously speak for the specific case you mention (and, anyway, I am not a medical doctor so I would not make a diagnosis in any case), but one thing that comes to mind is that eyes are part of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Immune_privilege&quot; rel=&quot;nofollow noreferrer&quot;&gt;immunologically privileged sites&lt;/a&gt; of the body. This means that an inflammatory response is not elicited in case of the introduction of an antigen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I quote from &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/books/NBK27174/#A1973&quot; rel=&quot;nofollow noreferrer&quot;&gt;Immunobiology by Charles Janeway&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Some body sites are immunologically privileged. Tissue grafts placed in these sites often last indefinitely, and antigens placed in these sites do not elicit destructive immune responses.&#xA;  Paradoxically, the antigens sequestered in immunologically privileged sites are often the targets of autoimmune attack; for example, brain autoantigens such as myelin basic protein are targeted in multiple sclerosis. It is therefore clear that this antigen does not induce tolerance due to clonal deletion of the self-reactive T cells. Mice only become diseased when they are deliberately immunized with myelin basic protein, in which case they become acutely sick, show severe infiltration of the brain with specific TH1 cells, and often die.&lt;br&gt;&#xA;  Thus, at least some antigens expressed in immunologically privileged sites induce neither tolerance nor activation, but if activation is induced elsewhere they can become targets for autoimmune attack (see Section 13-25). It seems plausible that T cells specific for antigens sequestered in immunologically privileged sites are more likely to remain in a state of immunological ignorance. Further evidence for this comes from the eye disease sympathetic ophthalmia (Fig. 13.36). If one eye is ruptured by a blow or other trauma, an autoimmune response to eye proteins can occur, although this happens only rarely. Once the response is induced, it often attacks both eyes. Immuno-suppression and removal of the damaged eye, the source of antigen, is frequently required to preserve vision in the undamaged eye. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://www.ncbi.nlm.nih.gov/books/NBK27174/bin/CH13F36.jpg&quot; alt=&quot;Figure 13.36&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.803" LastActivityDate="2012-12-09T04:56:29.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5438" PostTypeId="1" AcceptedAnswerId="5439" CreationDate="2012-12-07T20:34:24.783" Score="3" ViewCount="40128" Body="&lt;p&gt;What's the difference between an appendix and a cecum, and what are their functions?&lt;/p&gt;&#xA;" OwnerUserId="1609" LastActivityDate="2019-04-26T04:09:19.427" Title="Difference between Appendix and the Cecum?" Tags="&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5439" PostTypeId="2" ParentId="5438" CreationDate="2012-12-07T21:28:42.967" Score="6" Body="&lt;p&gt;In herbivores the &lt;strong&gt;&lt;em&gt;Cecum&lt;/em&gt;&lt;/strong&gt; is an area that stores plant matter and helps digest it via symbiotic bacteria. Carnivores have smaller Cecums because meat is easier to digest than plant matter. In humans the &lt;strong&gt;&lt;em&gt;Cecum&lt;/em&gt;&lt;/strong&gt; is also an anatomical landmark that delineates the change from small intestine (a digesting organ) to the large intestine (mostly a capacity/storage organ). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;&lt;em&gt;Appendix&lt;/em&gt;&lt;/strong&gt; is a small, previously thought &quot;superfluous&quot; fleshy worm-shaped organ at the junction between the small and large intestines. Recent research posits that the appendix is sort of a harbor for a person's gut flora that can re-populate the intestines should the existing bacteria die or get removed (diarrhea being the most common cause). It can also become infected, inflamed, and require surgery to remove (Appendicitis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9pRVz.png&quot; alt=&quot;Anatomic chart&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2014-09-21T19:16:50.633" LastActivityDate="2014-09-21T19:16:50.633" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5440" PostTypeId="2" ParentId="5435" CreationDate="2012-12-07T22:53:56.097" Score="5" Body="&lt;p&gt;Any animal using sound cannot sense color though sonar directly, though these animals are not entirely blind and &lt;a href=&quot;http://www.nhm.ac.uk/nature-online/life/mammals/bats/session3/index.html&quot; rel=&quot;noreferrer&quot;&gt;can probably see colors in the infrared we can't&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Even on the darkest night there is some light around and all bats use this. Old World fruit bats have colour vision, which is useful to them as they are often quite active in daytime, roosting on trees in exposed positions, rather than tucked away in dark crevices like most microbats, which can see only in black-and-white.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Dolphins have additional senses in addition to seeing they can &lt;a href=&quot;http://www.livescience.com/15240-dolphins-sense-electric-fields.html&quot; rel=&quot;noreferrer&quot;&gt;sense electrical fields&lt;/a&gt;.  So if an animal has its eyes covered, they will seem to be able to do things you would not expect.  Its not the same as seeing the color though.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such animals using sonar can additionally sense density and hardness as well as other material attributes which would cause the acoustic properties of the material as well as movement. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A hard-bodied insect produces a different quality of echo from one with a soft body, so bats can distinguish between some different groups of insects in this way. They can also determine the size of the object.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What's really interesting is that even human beings can experience this unusual sense.  &lt;a href=&quot;http://scienceblogs.com/neurophilosophy/2007/10/22/seeing-with-sound-the-boy-who/&quot; rel=&quot;noreferrer&quot;&gt;Blind people have learned to echolocate by making clicks with their mouth&lt;/a&gt;, and there is a movement to teach &lt;a href=&quot;http://science.slashdot.org/story/09/07/04/2246211/you-too-can-learn-echolocation&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; &lt;a href=&quot;http://science.slashdot.org/story/09/07/04/2246211/you-too-can-learn-echolocation&quot; rel=&quot;noreferrer&quot;&gt;skill&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://scienceblogs.com/neurophilosophy/2011/05/25/human-echolocation-activates-visual-parts-of-the-brain/&quot; rel=&quot;noreferrer&quot;&gt;Anyone can try it&lt;/a&gt;.  In just an hour or two I was able to tell how close I was to a wall, whether the wall was concrete.  I couldn't &lt;a href=&quot;http://www.youtube.com/watch?v=YBv79LKfMt4&quot; rel=&quot;noreferrer&quot;&gt;play video games (2:20 on the link)&lt;/a&gt; or see colors though.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-12-07T22:53:56.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5441" PostTypeId="1" CreationDate="2012-12-08T01:00:19.177" Score="3" ViewCount="272" Body="&lt;p&gt;I've seen a few talks on the subject. From a gene cluster, there is some decent ability to determine which domains contribute to certain functional groups in the final metabolites. It sounds like this is largely what Warp Drive Bio is trying to do. How realistic is this technology?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2012-12-10T19:54:49.080" Title="Can compounds be predicted from Polyketide synthases gene clusters?" Tags="&lt;biochemistry&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5442" PostTypeId="1" AcceptedAnswerId="5443" CreationDate="2012-12-08T08:03:38.507" Score="6" ViewCount="468" Body="&lt;p&gt;We know that we wash our hands because germs can get into our body through the nose, the mouth, the eyes, cuts, etc. But I doubt we can completely clean our hands of germs every time we wash them, down to the individual bacterium or virion, even if we use anti-septic soap. So chances are, even if we keep up with our hygiene, germs still get into our body, only in very very small quantities. So here are some questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;In theory, is there a dividing line where we can say &quot;ok, at this non-zero count of bacteria or virion, there is still (&lt;em&gt;an arbitrary probability&lt;/em&gt;) that a normal healthy person won't get sick&quot; &lt;strong&gt;for every germ known to man&lt;/strong&gt;? If not, are there germs that are known to cause havoc in a healthy person even if he comes into contact with a single individual bacterium or virion?&lt;/li&gt;&#xA;&lt;li&gt;Do we know a certain trend based on the classification of the germ?&lt;/li&gt;&#xA;&lt;li&gt;How about the most commonly found germs (whichever they are)?&lt;/li&gt;&#xA;&lt;li&gt;How about some of the most feared, but not so common, virii known to man, like HIV, ebola, SARS?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I think that without being able to answer some of these questions, especially #3, hygiene would be nothing but a ritual activity (because &quot;it just works&quot;).&lt;/p&gt;&#xA;" OwnerUserId="1114" LastEditorUserId="69" LastEditDate="2012-12-08T21:58:34.710" LastActivityDate="2013-01-30T20:01:58.623" Title="Are all known germs benign in small enough quantities? i.e. Why do we wash our hands?" Tags="&lt;microbiology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5443" PostTypeId="2" ParentId="5442" CreationDate="2012-12-08T13:11:23.967" Score="5" Body="&lt;p&gt;There is a Wikipedia page  which gives &lt;a href=&quot;http://en.wikipedia.org/wiki/Infectious_dose&quot;&gt;some typical values&lt;/a&gt; for infectious doses of bacteria. I suspect that lot of these have been taken from &lt;a href=&quot;http://www.fsis.usda.gov/PDF/Atlanta2010/Slides_FSEC_JGreig_Doses.pdf&quot;&gt;this slideshow&lt;/a&gt; which confirms the values on the Wikipedia page, gives more interesting details of how they have been arrived at, and also mentions a few viruses. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems from the slideshow that infectious dose isn't estimated in the way that the OP envisages - &lt;em&gt;&quot;What is the probability of infection if I ingest one cell?&quot;&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What &lt;strong&gt;is&lt;/strong&gt; clear is that the infectious doses for some bacteria can be less than 10 cells (e.g. &lt;em&gt;Shigella flexneri&lt;/em&gt;, &lt;em&gt;E. coli&lt;/em&gt; O157:H7). Conversely for many other pathogens such as other strains of &lt;em&gt;E. coli&lt;/em&gt; the estimate is &gt;10&lt;sup&gt;6&lt;/sup&gt; cells, so standard hygiene precautions will always offer some protection.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-12-08T13:11:23.967" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5444" PostTypeId="2" ParentId="5441" CreationDate="2012-12-08T17:41:51.327" Score="3" Body="&lt;p&gt;I would say that for type I polyketide synthases (PKS), this is possible. These proteins are variations on fatty acid synthases which have modules, each of which adds a two carbon unit as well as a chiral methyl group to an extending chain which may be reduced to give anything from a ketone, an alcohol to a completely reduced carbon chain.  In the illustration below you can see these 3 options, but double bonds are also possible.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DXsNF.gif&quot; alt=&quot;Type I modular PKS&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other sorts of PKS pathways (type II and III PKSs) have proteins which are harder to predict in terms of what they produce since a single protein does the extending of the polyketide chain to cyclize it, typically into an aromatic compound.  All this happens in a single protein site, so careful modelling would be required and I'd be suprised if this has been done accurately. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oEzhy.jpg&quot; alt=&quot;cycylization in a type II PKS&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note the last arrow there 'tailoring steps' - accompanying the PKS genes themselves are often a slew of acetyl and methyl transferases, additional reductases, coupling enzymes, even delivery proteins... the list goes on and on.  These steps would be hard to predict because the substrate for an o-methyl transferase isn't easily determined.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think there are several companies trying to leverage 'best guess' bioinformatics here.  They are likely to get a good idea of the backbone, but maybe won't place every methyl and acetyl group correctly.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are definitely people out there who think this could work to deliver diverse candidates to drug discovery.  see &lt;a href=&quot;http://www.radiantgenomics.com/?page_id=7&quot; rel=&quot;nofollow noreferrer&quot;&gt;Radiant Genomics&lt;/a&gt; as well.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-12-10T19:54:49.080" LastActivityDate="2012-12-10T19:54:49.080" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5445" PostTypeId="1" AcceptedAnswerId="5511" CreationDate="2012-12-08T21:44:49.707" Score="23" ViewCount="2572" Body="&lt;p&gt;From the moment we learn to communicate, we always get told, whether by our parents, or our teachers, or by anyone else, to avoid the cold, or to put a jacket on to avoid catching a cold, to dry our hair before we go outside, because we'll get sick otherwise, so on and so forth. I also was diagnosed with a pneumonia last year, while in Switzerland under chilly conditions ($-20^◦\text{C}$). This made me wonder, why does the cold make us sick? It doesn't seem logical to me that a viral infection like the common cold, or a viral/bacterial infection such as a pneumonia is more prevalent when it's colder outside. I always figured it was because our bodies are less 'effective' under cold temperatures, but this seems lacking to me. Can anyone explain? &lt;/p&gt;&#xA;" OwnerUserId="1609" LastEditorUserId="166" LastEditDate="2012-12-17T12:50:12.477" LastActivityDate="2018-03-14T11:21:36.160" Title="Why does the cold make us sick?" Tags="&lt;pathology&gt;" AnswerCount="5" CommentCount="7" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="5446" PostTypeId="1" AcceptedAnswerId="8510" CreationDate="2012-12-08T23:20:51.130" Score="13" ViewCount="333" Body="&lt;p&gt;More specifically, shampoo. What are the mechanics of detecting a noxious chemical stimulus in terms of which receptors recognise what, how do they do it, and how is this information relayed to the nerve cells? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is the pain (and so signal, I presume) larger if one is having a &lt;em&gt;hot&lt;/em&gt; shower at the time?&lt;/p&gt;&#xA;" OwnerUserId="1667" LastEditorUserId="57" LastEditDate="2012-12-09T02:15:25.370" LastActivityDate="2015-06-07T19:35:32.513" Title="Why does getting certain chemicals in cuts hurt?" Tags="&lt;biochemistry&gt;&lt;neuroscience&gt;&lt;sensation&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5447" PostTypeId="2" ParentId="5400" CreationDate="2012-12-09T00:50:38.817" Score="1" Body="&lt;p&gt;I am not sure if I am able to answer your question, but I will give it a try and hope that someone tells us if I'm wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biologists talk about different kinds of energy depending on where you measure it. The first measurement is the &lt;em&gt;gross energy&lt;/em&gt; (GE) which is measured through bomb calorimetry and is basically how much heat a substance gives off when completely burnt. I have recently read in a compendium that the GE value of fat is ~9,4 kcal/g.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The next stage is &lt;em&gt;digestible energy&lt;/em&gt; (DE), which is how much of the forage you actually can digest, which would exclude for example fibres. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next stage is the &lt;em&gt;metabolizable energy&lt;/em&gt; (ME), the energy which can be used in actual metabolism (DE - energy losses from transporting nutrients etc). This are the value you reported. (I don't have a source, but I've heard the same values from multiple recognized sources.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now is the part where it gets a bit trickier, as the final measurement of energy is the &lt;em&gt;net energy&lt;/em&gt; (NE). This is defined as the metabolic energy minus the heat increment, which could be simplified as the energy losses through the conversion between different types of energy (ie. from long carbohydrates into glucose etc.) within the body. Even more simplified it can be said to be the difference between the heat production in a fastened person and the heat production in a fed person, thus being the heat produced by eating, digesting, absorbing and transporting food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I argue that because the fat already is incorporated in the body it has a very efficient value, and very little transportation within the body is needed. And because the energy (ie, the fat) is internal, it is not accounted for in the heat increment and therefore the NE of internal fat is the same as ME. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And according to the wikipedia-article you linked to United Nations recommendation of the average minimum energy consumption per person is 1800 kcal/day. &lt;strong&gt;Thus the amount of fat required to meet the minimum &lt;em&gt;energy requirements&lt;/em&gt; of a person would be 1800/9=200g of fat per day.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to read more about the different energy-measurements and the heat increment here is a good &lt;a href=&quot;http://www.extension.org/pages/22405/energetics-for-the-practicing-nutritionist#ME_versus_NE_Systems&quot; rel=&quot;nofollow&quot;&gt;link.&lt;/a&gt; And don't forget that energy alone is not sufficient for a person as we need protein, vitamins, minerals etc...&lt;/p&gt;&#xA;" OwnerUserId="757" LastActivityDate="2012-12-09T00:50:38.817" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5449" PostTypeId="1" CreationDate="2012-12-09T14:20:35.957" Score="5" ViewCount="7032" Body="&lt;p&gt;Sweaty palms seems to be a reaction to stress, anxiety, etc. For our forest-inhabiting primate ancestors sweaty palms could cause unwanted side-effects such as slipping off tree branches under stressful conditions, like when being chased by a predator.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why did palm sweating became a reaction to fear, worry, anxiety etc in the course of human evolution? What is the benefit of sweaty palms?&lt;/p&gt;&#xA;" OwnerUserId="1200" LastEditorUserId="1231" LastEditDate="2012-12-09T23:37:33.860" LastActivityDate="2020-01-22T00:27:38.373" Title="What is the evolutionary rationale for palm sweating?" Tags="&lt;evolution&gt;" AnswerCount="5" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="5451" PostTypeId="1" AcceptedAnswerId="5454" CreationDate="2012-12-10T01:39:36.747" Score="8" ViewCount="6645" Body="&lt;p&gt;Can someone explain (or point me to an explanation of) exactly what is meant by all the different symbols I see used for writing genes and proteins?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think I know that for genes, we use an italic font and for proteins, we use a regular font.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think I've also learned that for human, all letters are in uppercase (eg. SHH) whereas for mouse, only the first letter is in uppercase and the remaining letters are in lowercase (Shh). (From &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene_nomenclature&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Gene_nomenclature&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I'm stumped with all the other &quot;tags&quot; (in quotes because that's how they seem to be used and I don't know how else to think of them) that I see floating around gene and protein symbols.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, Myc (MYC?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see these three articles in uniprot.org:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.uniprot.org/uniprot/Q99417&quot; rel=&quot;nofollow&quot;&gt;http://www.uniprot.org/uniprot/Q99417&lt;/a&gt; for C-Myc&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.uniprot.org/uniprot/P04198&quot; rel=&quot;nofollow&quot;&gt;http://www.uniprot.org/uniprot/P04198&lt;/a&gt; for N-myc&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.uniprot.org/uniprot/P12524&quot; rel=&quot;nofollow&quot;&gt;http://www.uniprot.org/uniprot/P12524&lt;/a&gt; for L-Myc&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These proteins are all in human, and yet their recommended names are not all caps; what's up with that? But even more confusing to me are the &quot;C-&quot;, &quot;N-&quot;, and &quot;L-&quot; letters prefixed to them. What in the world are those supposed to be indicating?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these all fundamentally different proteins (coded by different genes), but maybe related somehow to each other (thus the common three letters, 'myc' even if they are not all the same case and not all upper case as I thought was supposed to be the case in human), and they are just given these &quot;C-&quot;, &quot;N-&quot;, and &quot;L-&quot; tags to distinguish one from the other? Does one tag indicate an oncogene or a proto-oncogene? Why do I sometimes see &quot;c-Myc&quot; and other times, &quot;C-Myc&quot;? Does the case of the &quot;C-&quot; mean something? Is there some kind of key or legend I can look at to get answers to all these questions? I've found some explanations in Scott Gilbert's &lt;em&gt;Developmental Biology&lt;/em&gt; textbook, but it still doesn't give me all the answers I seek here&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just want to understand how these tags and symbols are being used because it seems to me that when I read research papers (of which I've read many), they are used by different authors in different papers in ways that are not consistent with each other. Either that, or else I'm missing something very basic, which is why I'm asking here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance for any help.&lt;/p&gt;&#xA;" OwnerUserId="1756" LastEditorUserId="43" LastEditDate="2012-12-10T18:06:54.033" LastActivityDate="2012-12-10T18:06:54.033" Title="Gene &amp; Protein nomenclature: N-Myc, c-Myc, et. al" Tags="&lt;proteins&gt;&lt;molecular-genetics&gt;&lt;genetics&gt;&lt;nomenclature&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5454" PostTypeId="2" ParentId="5451" CreationDate="2012-12-10T03:03:47.160" Score="3" Body="&lt;p&gt;That's a good question, and honestly, the nomenclature for genes and their coded proteins is somewhat abused in scientific literature. For example, when referring to microbes (like E. coli), gene names are all lowercase (eg, lacZ). The problem of protein names is compounded when the protein name is (often) an abbreviation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With respect to myc, it can refer to the family of MYC transcription factor proteins (of which, c-Myc, L-myc and N-myc are members). More commonly, myc refers to c-Myc, and is the name given to a 10-amino acid segment of human proto-oncogene myc (EQKLISEEDL) and is a common epitope added to recombinant DNA for making fusion proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I recall, the initial that precedes myc (in this instance) refers to what form of cancer that myc protein is associated with. I know c-myc comes from a mutation in wild-type myc that becomes constitutively expressed. Wikipedia tells me that N-myc is a neuroblastoma-associated myc transcription factor.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-12-10T03:03:47.160" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5456" PostTypeId="2" ParentId="5451" CreationDate="2012-12-10T07:56:18.747" Score="5" Body="&lt;p&gt;There is a useful set of links to nomenclature guidelines for all of the main genetic systems at &lt;a href=&quot;https://en.wikipedia.org/wiki/Gene_nomenclature#Human&quot; rel=&quot;nofollow&quot;&gt;this Wikipedia page&lt;/a&gt;. Personally, I think that &lt;a href=&quot;http://instruct.uwo.ca/biology/3596a/Saccharomyces_cerevisiae.pdf&quot; rel=&quot;nofollow&quot;&gt;the Saccharomyces cerevisiae system&lt;/a&gt; works best: it manages to cover dominant and recessive alleles of a gene, the name of the protein, how to refer to a related phenotype, and the use of a parallel convention for the designation of ORFs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately there is now no going back - there are many different systems and there is no hope of unifying them. When this plethora of naming conventions is combined with the reluctance of so many scientists to stick to the guidelines, we have a recipe for near anarchy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit - On the specific topic of MYC nomenclature:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The v- and c- prefixes come from the early days of oncogene research. Viral oncogenes such as myc and src were found to be related to (derived from?) similar genes in normal cells. Thus v- means viral and c- means cellular.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can be seen if you peruse the &lt;a href=&quot;http://www.genenames.org/&quot; rel=&quot;nofollow&quot;&gt;HUGO&lt;/a&gt; entries for the four MYC family members encoded in the human genome (extracts below). They all have an approved name which relates them back to a viral oncogene found in the genome of avian myelocyomatosis virus. This was the founder member of this gene family. Thus c-myc was the first myc-related gene found in the human genome, and is the one that is responsible for Burkitt's lymphoma. It is true, as @Leonardo says, that in tumours the expression of this this myc gene in lymphatic tissue changes due to chromosomal rearrangements, but this is not the origin of the designation c-myc.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;MYC&#xA;  &lt;br&gt;Approved Symbol:      MYC&#xA;  &lt;br&gt;Approved Name:   v-myc myelocytomatosis viral oncogene homolog (avian)&#xA;  &lt;br&gt;Previous Symbols &amp;amp; Names:   &quot;v-myc avian myelocytomatosis viral oncogene homolog&quot;&#xA;  &lt;br&gt;Synonyms:   bHLHe39, c-Myc&#xA;  &lt;br&gt;Chromosomal Location: 8q24&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;MYCL1&#xA;  &lt;br&gt;Approved Symbol:      MYCL1&#xA;  &lt;br&gt;Approved Name:   v-myc myelocytomatosis viral oncogene homolog 1, lung carcinoma derived (avian)&#xA;  &lt;br&gt;Previous Symbols &amp;amp; Names:   MYCL, &quot;v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived&quot;&#xA;  &lt;br&gt;Synonyms:   bHLHe38, &quot;l-myc protein&quot;, LMYC, &quot;myc-related gene from lung cancer&quot;, &quot;oncogene lmyc&quot;&#xA;  &lt;br&gt;Chromosomal Location: 1p34.3&#xA;   &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;MYCL2&#xA;  &lt;br&gt;Approved Symbol:      MYCL2&#xA;  &lt;br&gt;Approved Name:   v-myc myelocytomatosis viral oncogene homolog 2 (avian)&#xA;  &lt;br&gt;Previous Symbols &amp;amp; Names:   &quot;v-myc avian myelocytomatosis viral oncogene homolog 2&quot;&#xA;  &lt;br&gt;Synonyms:   bHLHe38&#xA;  &lt;br&gt;Chromosomal Location: Xq22-q28&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;MYCN&#xA;  &lt;br&gt;Approved Symbol:      MYCN&#xA;  &lt;br&gt;Approved Name:   v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)&#xA;  &lt;br&gt;Previous Symbols &amp;amp; Names:   NMYC, &quot;v-myc avian myelocytomatosis viral related oncogene, neuroblastoma derived&quot;&#xA;  &lt;br&gt;Synonyms:   bHLHe37, N-myc&#xA;  &lt;br&gt;Chromosomal Location: 2p24.3&#xA;   &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-12-10T15:33:53.777" LastActivityDate="2012-12-10T15:33:53.777" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5457" PostTypeId="1" AcceptedAnswerId="5465" CreationDate="2012-12-10T08:10:15.040" Score="15" ViewCount="183" Body="&lt;p&gt;I'm trying to figure out how should a vaccination model be built to correlate with population density, and I'm having problems to understand meanings of the results I receive when I apply theory on specific data I'm provided with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Theory&lt;/strong&gt;(i):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The initial phase of an outburst of a disease can be described by an exponential growth&#xA;model. The relevant equation is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$(1)\frac{dI}{dt}=\beta n(1-q)I-\mu I$ where:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$n$ = the population density. Let us measure it in units of $km^{-2}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$I$ = the density of already infected individuals in the population; measured in the&#xA;same units as $n$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$q$ = the fraction of the population that is immune to the disease, either naturally of&#xA;due to vaccination. Consequently, $1-q$ is the fraction of the population that is&#xA;susceptible, i.e., at risk of getting infected. $q$ is a pure number between $0$ and $1$,&#xA;and has no units.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\beta$ = is the transmission rate of the disease. It measures how easily and quickly&#xA;the disease can be transmitted from an infected individual to an non-infected&#xA;susceptible individual. $\beta$ includes within it both the rate at which encounter&#xA;between infected and non-infected individuals occur, and the probability that&#xA;such an encounter would result in actual transmission of the disease. $\beta$ has&#xA;dimensions of $\frac{1}{time\times density^{2}}$, so let us measure it in units of $week^{-1}km^{4}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\mu$ = the rate at which infected individuals are eliminated from the group of&#xA;infected individual, either because they recover, or because they die. $\frac{1}{\mu}$ is the average duration of the infection, i.e., the average time that an individual remains&#xA;infected before it either recovers or dies. Let us measure $\mu$ in units of $week^{-1}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This equation derives from the differential equation $(2) \frac{dN}{dt}=rN$ where $r$ is called instantaneous rate of increase. It is easy to see that $I$ from equation $(1)$ is equivalent to $N$ from equation $(2)$ and therefore, $r$ for equation $(1)$ will be $(3) r=\beta n(1-q)-\mu$. When we look at equation $(3)$, we see two factors:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\beta n(1-q)$ - A positive factor(ii)&#xA;$\mu$ - A negative factor&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Minding the above, when $r=0$, there is no increase in population(iii). From this, we can compute $q_{0}$ which is the minimum fraction of vaccinated/immune individuals in the population that is required in order to prevent the disease from spreading. From equation $(3)$ we can figure out that $q_{0}=1-\frac{\mu}{\beta n}$. Just as $q$, $q_{0}$ is a pure number between $0$ and $1$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Welcome to the desert of the real (my question)&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose we compare two countries with the following data:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Israel: $n=347km^{-2}$, $\beta=0.0015week^{-1}km^{4}$, $\mu=0.25week^{-1}$&lt;/li&gt;&#xA;&lt;li&gt;Finland: $n=16km^{-2}$, $\beta=0.0015week^{-1}km^{4}$, $\mu=0.25week^{-1}$&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;When we look for $q_{0}$ for Israel we see that $q_{0}(Israel)=1-\frac{0.25}{0.0015\times347}=0.52=52$% while for Finland we see that $q_{0}(Finland)=1-\frac{0.25}{0.0015\times16}=-9.42=-942$%. Assuming that we've got correct data in the first place, $q_{0}$ is a negative pure numbers which is not between $0$ and $1$.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Do such, and similar results make any sense at all? Especially when they are not between the defined boundaries of the variable.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If they do make sense, what does it mean getting a negative results? How should it affect my vaccination policy?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Footnotes&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(i) Taken from my Populations Ecology lecture slides&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(ii) Positive when looking at it from the epidemic point of view&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(iii) Of infected individuals&lt;/p&gt;&#xA;" OwnerUserId="246" LastEditorUserId="3340" LastEditDate="2014-10-20T09:39:47.320" LastActivityDate="2014-10-20T09:39:47.320" Title="Vaccination and population dynamics of an epidemic" Tags="&lt;ecology&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5458" PostTypeId="1" AcceptedAnswerId="5459" CreationDate="2012-12-10T09:44:40.607" Score="11" ViewCount="14097" Body="&lt;p&gt;Just had this thought occur to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If one were to take a DNA sample(or is it RNA?) of a caterpillar before it became a chrysalis, and attempt to match the sample against one taken after the chrysalis matured to a butterfly, would the two samples come up identical? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2012-12-10T18:35:31.663" LastActivityDate="2012-12-11T03:30:51.057" Title="Does the DNA sequence of a butterfly match that of the caterpillar it used to be?" Tags="&lt;genetics&gt;" AnswerCount="4" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5459" PostTypeId="2" ParentId="5458" CreationDate="2012-12-10T11:15:40.027" Score="13" Body="&lt;p&gt;The genome (entire DNA sequence) of the butterfly would be identical to that of the caterpillar in all somatic cells.  A caterpillar has the genes to produce wings, for example, however at that stage in it's development they are not 'switched on' to make the necessary proteins.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you were to sample the mRNA produced from transcription of the DNA in the caterpillar and butterfly stages, there are likely to be many differences.  As in the example I previously used, the mRNAs that are translated into wing-forming proteins are more likely to be apparent in the butterfly than the caterpillar.  When saying this, please be aware that I'm assuming that the regulation of these genes is pre-transcriptional - I'm not an expert of butterfly physiology!&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-12-10T11:15:40.027" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5460" PostTypeId="2" ParentId="5458" CreationDate="2012-12-10T15:44:44.747" Score="6" Body="&lt;p&gt;&lt;strong&gt;@Rory M&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Here is evidence for developmental genome rearrangements in &lt;em&gt;Hymenoptera&lt;/em&gt;. I have emphasised the relevant section of the Abstract. It is probably premature to assume that similar changes might not happen in somatic cells of some &lt;em&gt;Lepidoptera&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Bigot Y, Jegot G, Casteret S, Aupinel P, Tasei JN (2011) DNA modifications and genome rearrangements during the development and sex differentiation of the bumble bee Bombus terrestris. Insect Mol Biol. 20:165-75.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Abstract&lt;/strong&gt;&#xA;&lt;br&gt;Bombus terrestris is a bumble bee that, like most hymenopteran species, exhibits ploidy-specific sex determination controlled by a single sex gene. Depending on their ploidy and the queen pheromone repression, the imagoes differentiate into three castes: males, workers and queens. &lt;strong&gt;Here, we focus on the differences of genome organization that occur during development and sex differentiation.&lt;/strong&gt; We found that cytosine methylation is a significant epigenetic factor with profiles that can be correlated with both processes. &lt;em&gt;&lt;strong&gt;We also showed that two kinds of genomic rearrangement occur. The first consists of important DNA amplifications that have sequence profiles that differ in the different developmental instars and sexes. In the second kind, DNA losses also occur, at least involving the mosaic transposable element B. terrestris mosaic repeat 1 (BTMR1).&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-12-10T17:11:25.083" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5461" PostTypeId="2" ParentId="5458" CreationDate="2012-12-10T19:10:05.043" Score="3" Body="&lt;p&gt;I would like to expand on Rory's answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can think about the DNA like a very complex book of recipes (genes) for constructing cellular machinery (e.g. proteins). Every genome has a large repertoire of machines that it can construct. For a given organism, all its somatic cells will have the same DNA (more or less, but let's put that aside) since it starts out as a single cell. In spite of this, you can see that cells can have completely different shapes and functions. For example, look at how different a neuron is from a muscle cell or a blood cell in terms of shape and function. In addition, cells can change in reaction to their environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then how is the repertoire the same but the cells completely different?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The solution is &lt;strong&gt;choosing which genes to activate&lt;/strong&gt;. This is the called gene regulation and is an extremely complex system as you might guess. It is to some extent the &quot;brain&quot; of the cell, with which the cells can make decisions and gain its plasticity in biological function. This system operates on many levels, one of them being by controlling transcription, i.e. transcriptional regulation, which controls how much RNA to make from each gene, which will later translate into some level of activation (no RNA means the gene will not be active). This is why the RNA will probably vary widely according to the cell type and cellular state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, each species have a similar DNA sequence give or take some minor variations. The sequence of family members will be even more similar, and the sequence of clones (e.g. identical twins) will be virtually identical. This type of variation is random and thus will not be used as a control system. From this you can already guess that the change from caterpillar to butterfly will be controlled by its gene regulation program, as it is a developmental change, in the same way as a human grows from a single embryonic cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, it is always possible that some random changes occur somewhere along the way and would cause differences, as biology is stochastic. However, for these to be consistent between all cells in the organism, they would have to happen when the organism is a single cell, which is not the case when transitioning from caterpillar to butterfly.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2012-12-10T19:10:05.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5462" PostTypeId="2" ParentId="5458" CreationDate="2012-12-11T03:30:51.057" Score="1" Body="&lt;p&gt;Here's an interesting story from npr.org, &lt;a href=&quot;http://www.npr.org/blogs/krulwich/2012/08/01/157718428/are-butterflies-two-different-animals-in-one-the-death-and-resurrection-theory&quot; rel=&quot;nofollow&quot;&gt;Are Butterflies Two Different Animals in One? The Death And Resurrection Theory&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently some people are proposing a theory that says (heavily paraphrased) that a butterfly is actually two different ancestral species rolled into one. This is the relevant quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The old view was that over millions of years, animals evolved this habit of switching from one set of instructions to the other. The new view is that this is not one animal gradually changing shape, but rather instructions for two different animals sandwiched together and this change is so radical, says Bernd, &quot;with no continuity from one to the next, that the adult forms of these insets are actually new organisms.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Far out.&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2012-12-11T03:30:51.057" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5463" PostTypeId="2" ParentId="5449" CreationDate="2012-12-11T04:16:25.333" Score="4" Body="&lt;p&gt;There isn't necessarily a nice neat evolutionary rationale or advantage behind all of the observable traits found in all organisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's perhaps more likely that there simply was not enough selection pressure against having sweaty palms to eradicate it from the gene pool entirely.&lt;/p&gt;&#xA;" OwnerUserId="1763" LastActivityDate="2012-12-11T04:16:25.333" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5464" PostTypeId="2" ParentId="5449" CreationDate="2012-12-11T04:40:37.207" Score="8" Body="&lt;p&gt;As @Ben states, every theory of 'why' we evolve a trait is just a guess and never more than part of the story.   But there are theories.&lt;/p&gt;&#xA;&lt;p&gt;The palms of our hands are a major source of heat transfer out of our body.  For bears it is the nose and pads of their feet, for dogs it is their toungue, for us a major portal for heat out of our body is the palms of the hands.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Black bears are extremely well-insulated animals, equipped with a heavy coat of fur and a thick layer of subcutaneous fat that help them maintain their body temperature as they hibernate through winter. But once spring arrives and temperatures rise, these same bears face a greater risk of overheating than of hypothermia. How do they dump heat without changing insulation layers?&lt;/p&gt;&#xA;&lt;p&gt;Heller and Grahn discovered that bears and, in fact, nearly all mammals have built-in radiators: hairless areas of the body that feature extensive networks of veins very close to the surface of the skin.&lt;/p&gt;&#xA;&lt;p&gt;Rabbits have them in their ears, rats have them in their tails, dogs have them in their tongues. Heat transfer with the environment overwhelmingly occurs on these relatively small patches of skin. When you look at a thermal scan of a bear, the animal is mostly indistinguishable from the background. But the pads of the bear's feet and the tip of the nose look like they're on fire.&lt;/p&gt;&#xA;&lt;p&gt;These networks of veins, known as AVAs (arteriovenous anastomoses) seem exclusively devoted to rapid temperature management. They don't supply nutrition to the skin, and they have highly variable blood flow, ranging from negligible in cold weather to as much as 60 percent of total cardiac output during hot weather or exercise.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Given this, one could see how the palms of our hands are more likely to react to emotional situations where the heart rate elevates and sometimes we get hot under the collar.  The AVAs will&lt;/p&gt;&#xA;&lt;p&gt;I am not physiologist, but the quote above comes from an article &lt;a href=&quot;http://news.stanford.edu/news/2012/august/cooling-glove-research-082912.html&quot; rel=&quot;noreferrer&quot;&gt;I stumbled upon a few months ago&lt;/a&gt;.  They use the AVAs to reduce the swelling associated with exercise and got some amazing results.  I guess that's another story though.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-12-11T04:40:37.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5465" PostTypeId="2" ParentId="5457" CreationDate="2012-12-11T04:54:58.947" Score="8" Body="&lt;p&gt;I think it does make sense - with a population density for finland that is so low, the disease with such a low beta cannot communicate to enough people to propagate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The number of people who have this disease will be fewer each week.  I think this makes sense because at 16 / km^2, you can expect that practically nobody will ever see each other.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a flawed model though because it assumes that the mean density is uniform.  In a city like Helsinki (&lt;a href=&quot;http://www.hel.fi/hki/Helsinki/en/Information+on+Helsinki/Information+on+Helsinki&quot;&gt;2,800 / km^2&lt;/a&gt;) you would expect the disease to get caught by nearly everyone in just a week.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Helsinki: n = 94.5%&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Lapland (&lt;a href=&quot;http://en.wikipedia.org/wiki/Provinces_of_Finland#Provinces_of_Finland.2C_1997.E2.80.932009&quot;&gt;which has a population density of less than 2/km^2&lt;/a&gt;) , the transmission rate (beta) of 0.0015 translates to 0.003 incidents per week.  This is not a terribly catchy disease, you probably have to kiss someone, wear their clothes, or eat off their plate to get it. With only 2 people per km^2 the chances of this happening appear to be poor, though even here families tend to get the disease and the model breaks down. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to sum up, the model is consistent within itself, BUT it is a baby model and makes some broad assumptions that do not help it describe the dynamics of the disease in a national scope or in a highly detailed scope.  It probably describes the chances balls will collide in a box as well as disease spreading. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-12-11T05:01:04.653" LastActivityDate="2012-12-11T05:01:04.653" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5466" PostTypeId="1" CreationDate="2012-12-05T17:39:08.873" Score="4" ViewCount="29316" Body="&lt;p&gt;During inhalation, your alveoli expand, creating a pressure difference between the atmosphereic pressure and our lung sacks and therefore air will flow into the repspiratory airways. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am trying to find what the (I guess average) speed of this flow is, and therefore estimate the pressure difference. I have spent some time online trying to find this, but I have not got a definite number yet. It should be an order of magnitude of 1 m/s ?&lt;/p&gt;&#xA;" OwnerDisplayName="l3win" LastEditorUserId="69" LastEditDate="2012-12-11T13:34:46.087" LastActivityDate="2019-06-08T18:39:28.667" Title="What is the inlet/outlet speed of air going in/out of our mouth during inhalation/exhalation" Tags="&lt;human-biology&gt;&lt;breathing&gt;&lt;lungs&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5467" PostTypeId="2" ParentId="5466" CreationDate="2012-12-05T17:54:21.207" Score="1" Body="&lt;p&gt;I'm not sure this is a great answer, but since no-one else has stepped up: it will vary a great deal depending on what you're doing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Wikipedia the &lt;a href=&quot;http://en.wikipedia.org/wiki/Tidal_volume&quot; rel=&quot;nofollow&quot;&gt;tidal volume&lt;/a&gt; for a breath is typically about 500 cm$^3$, so you can work out the velocity from the time taken for a breath and the cross sectional area of the mouth. The trouble is that the breath rate varies enormously e.g. from resting to running a marathon. Also would you take the cross sectional area of the lips, or the larynx, or some other point in the respiratory tract?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case under most circumstances I doubt the limiting factor during an inhalation is the pressure difference. I suspect it's more likely to be how fast the ribs can expand. It seems to me that if I take a sudden breath and try to stop halfway through, the inhalation stops immediately. If the limiting factor were the pressure difference I'd expect the air to keep flowing in after I'd stopped trying to inhale.&lt;/p&gt;&#xA;" OwnerUserId="3220" OwnerDisplayName="John Rennie" LastActivityDate="2012-12-06T10:42:17.460" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5468" PostTypeId="2" ParentId="5466" CreationDate="2012-12-11T13:34:00.207" Score="4" Body="&lt;p&gt;Quick clarification firstly, the main change in thoracic volume that causes inspiration is &lt;strong&gt;not&lt;/strong&gt; as a result of the alveoli expanding - they have no smooth muscle lining therefore are unable to spontaneously contract.  They do have some elastic fascia however their expansion is passive. The change is mainly as a result of the diaphragm contracting to become flatter, increasing the space that the lungs can occupy.  The external intercostal muscles also raise the ribs (in adults) which further allows for inspiration.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ytl0k.jpg&quot; alt=&quot;Figure One: Inspiration and Expiration(1)&quot;&gt;&#xA;&lt;sup&gt;Figure One: Inspiration and Expiration&lt;sup&gt;(1)&lt;/sup&gt;.  &lt;em&gt;&quot;Rib muscles&quot; refers to the external intercostal muscles&lt;/em&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With that being said, the value I think you are looking for is &lt;strong&gt;peak expiratory flow&lt;/strong&gt;.  Peak flow is a common medical measurement that is often taken in the management of patients with respiratory conditions, either as part of their management plan or acute assessment.  Peak flow is a measurement of the maximum speed that a person can exhale at.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the comments on your question suggest, this varies &lt;em&gt;dramatically&lt;/em&gt; between person to person.  Ignoring any pathologies - such as asthma, chronic obstructive pulmonary diseases (COPD) or nerve damage to the diaphragm/intercostal muscles - peak expiratory flow varies primarily with &lt;strong&gt;age&lt;/strong&gt;, &lt;strong&gt;gender&lt;/strong&gt; and &lt;strong&gt;height&lt;/strong&gt;.  These variations are summarised in charts of expected peak flow that are used, amongst other things, to grade the severity of an asthma attack (and consequently how aggressively to manage it).  Charts resemble the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wnXqb.png&quot; alt=&quot;Image Two: Peak expiratory flow expected value chart using the EU Scale&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;Figure Two: Normal values for peak expiratory flow used in UK hospitals - The EU Scale &lt;sup&gt;(2)&lt;/sup&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if you pick the height, gender and age that you feel is appropriate for your question, you can then read off peak flow in litres per minute.  Then you would need, I think, to work out the area of the aperture (in your case the mouth) to get a speed in metres per second?  &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Medina B. Brenda's A&amp;amp;P eportfolio: objective 48 &amp;amp; 49: inhalation and exhalation [Online]. 2011 [accessed 2012 Dec 11]. Available from URL: &lt;a href=&quot;http://blm1128.blogspot.co.uk/2011/04/objective-49-contrast-inspiration-and.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://blm1128.blogspot.co.uk/2011/04/objective-49-contrast-inspiration-and.html&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Häggström M. File: normal values for peak expiratory flow - EU scale.png [Online]. 2009 [accessed 2012 Dec 11]. Available from URL: &lt;a href=&quot;http://en.wikipedia.org/wiki/File:Normal_values_for_peak_expiratory_flow_-_EU_scale.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/File:Normal_values_for_peak_expiratory_flow_-_EU_scale.png&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="69" LastActivityDate="2012-12-11T13:34:00.207" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5470" PostTypeId="1" CreationDate="2012-12-11T15:11:47.110" Score="11" ViewCount="1232" Body="&lt;p&gt;I am a science lover and want to buy a microscope to explore things around me. Like studying cell structures, microorganisms, blood and plants. It would be great if there is way to photograph slides. Just curious to know and explore things around me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know which features I should consider while buying it?&lt;/p&gt;&#xA;" OwnerUserId="1766" LastEditorUserId="69" LastEditDate="2012-12-12T15:45:24.717" LastActivityDate="2017-04-24T11:48:00.153" Title="What to look for when buying a light microscope?" Tags="&lt;microscopy&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5471" PostTypeId="1" AcceptedAnswerId="5472" CreationDate="2012-12-11T16:44:01.660" Score="9" ViewCount="952" Body="&lt;p&gt;Most plants require carbon dioxide for their photosynthesis, which Mars has in overabundance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would atmosphere composition (let's ignore temperatures for the purpose of this question) of Mars allow vegetation to grow?&lt;/p&gt;&#xA;" OwnerUserId="1086" LastEditorUserId="1320" LastEditDate="2012-12-11T21:36:10.427" LastActivityDate="2013-07-21T09:47:46.327" Title="What vegetation would thrive in the Martian atmosphere?" Tags="&lt;photosynthesis&gt;" AnswerCount="3" CommentCount="1" ClosedDate="2014-10-16T12:19:36.200" ContentLicense="CC BY-SA 3.0" />
  <row Id="5472" PostTypeId="2" ParentId="5471" CreationDate="2012-12-11T18:11:23.413" Score="5" Body="&lt;p&gt;This is not my field by a long shot, so take what I say with a grain of salt. However, this question is very hard to answer because whether or not a plant will grow depends on a great variety of factors. Even if we ignore the temperature as you say, there are other considerations. These include, but are not limited to:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Soil composition&lt;/strong&gt;, I doubt that Martian soil can support earth vegetation even if its atmosphere could. Plants need various nutrients, and specific pH ranges among other things.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Atmospheric pressure&lt;/strong&gt;, I am not at all sure that the Martian atmosphere (though it is, indeed rich in CO&lt;sub&gt;2&lt;/sub&gt;) would be enough to drive an earth plant's photosynthesis. Bear in mind that the atmospheric pressure on Mars averages 600 pascals (0.087 psi), about 0.6% of Earth's mean sea level pressure (&lt;a href=&quot;https://en.wikipedia.org/wiki/Atmosphere_of_Mars&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;). This makes it highly unlikely that unmodified earth plants would be able to thrive there.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Water&lt;/strong&gt; water water...&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Pollinating species&lt;/strong&gt;. Many many plants depend on other species (e.g. bees or hummingbirds) for their propagation. These would be hard to find on Mars. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Sunlight&lt;/strong&gt; I don't know if Mars receives enough sunlight at its distance from the sun to drive an unmodified plant's photosynthesis.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now, that said, it should &lt;em&gt;theoretically&lt;/em&gt; be possible to start with some extremophile archaea or bacteria that would over the course of many many many years (at least hundreds, thousands more probably) terraform Mars to make it suitable for human habitation. Specially engineered plants could play a role then but I find it very hard to believe that any existing, unmodified, multicellular plant life of earth origin could survive on Mars.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1320" LastEditDate="2012-12-12T20:14:03.060" LastActivityDate="2012-12-12T20:14:03.060" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5473" PostTypeId="2" ParentId="5471" CreationDate="2012-12-11T18:36:18.690" Score="10" Body="&lt;p&gt;&lt;strong&gt;I'll stick to considering the atmospheric composition, as referred to in the original question:&lt;/strong&gt; Although there may be some rare exceptions that I can't recall, under normal circumstances all green plants use aerobic respiration with O&lt;sub&gt;2&lt;/sub&gt; as final electron acceptor for energy production. This means that they require oxygen, which is essentially absent from the Martian atmosphere (0.13%). Even though our hypothetical Martian crop could produce oxygen as a byproduct of photosynthesis, that oxygen would be lost into the atmosphere, and would not be available for respiration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe that under waterlogged conditions some plants can switch temporarily to some sort of anaerobic metabolism as a stress response, but I don't know if this is just to survive or whether the plants can grow in this way - I suspect it is the former.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-12-11T18:36:18.690" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5474" PostTypeId="1" CreationDate="2012-12-11T18:51:13.363" Score="2" ViewCount="152" Body="&lt;p&gt;Does the term &lt;em&gt;in vitro&lt;/em&gt; necessarily imply that the organism/organs/cells of study are  &lt;em&gt;dead&lt;/em&gt;? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, is there an alternative latin term to refer to studies of &lt;em&gt;dead&lt;/em&gt; biological matter ? (e.g. in Connectomics where the tissue is biologically dead, and has been fixated and sectioned with a microtome)&lt;/p&gt;&#xA;" OwnerUserId="17" LastActivityDate="2012-12-11T19:57:48.253" Title="Experiments in vitro vs those with dead organisms and fixated tissue" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5475" PostTypeId="2" ParentId="5474" CreationDate="2012-12-11T19:57:48.253" Score="3" Body="&lt;p&gt;&lt;strong&gt;Does the term &lt;em&gt;in vitro&lt;/em&gt; necessarily imply that the organism/organs/cells of study are dead?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No, &lt;em&gt;in vitro&lt;/em&gt; studies are often carried out with living cells - just think of &lt;em&gt;in vitro&lt;/em&gt; fertilisation. The nearest I can come up with for what you want is &lt;strong&gt;histology&lt;/strong&gt;, but I think even this encompasses studies of living cells and tissues.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-12-11T19:57:48.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5477" PostTypeId="1" CreationDate="2012-12-12T01:59:43.227" Score="6" ViewCount="735" Body="&lt;p&gt;I'd think protozoans can be oligocellular, but I haven't found any examples, and I'm curious to know what is the minimum number of cells an organism can have other than a single cell.&lt;/p&gt;&#xA;" OwnerUserId="221" LastEditorUserId="1320" LastEditDate="2012-12-12T12:23:46.710" LastActivityDate="2012-12-12T12:23:46.710" Title="Are there oligocellular organisms in nature and, if so, what are they like?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5479" PostTypeId="2" ParentId="5477" CreationDate="2012-12-12T10:05:17.723" Score="6" Body="&lt;p&gt;Various colonial and multicellular forms of cyanobacterial species are reviewed in:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Beardall, J et al. (2009) Allometry and stoichiometry of unicellular, colonial and multicellular phytoplankton. New Phytologist 181: 295-309&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;Nostoc&lt;/em&gt; and &lt;em&gt;Volvox&lt;/em&gt; are some of the simplest true multicellular organisms known (usually 3-4 cell types), but in both cases the differentiated colonies (filaments in &lt;em&gt;Nostoc&lt;/em&gt;, spheres in &lt;em&gt;Volvox&lt;/em&gt;) typically consist of hundreds of cells.&lt;/p&gt;&#xA;&lt;p&gt;The paper below reports the emergence of a colonial form of a unicellular organism. Since there is no evidence that the individual cells within a colony have specialised functions this doesn't really count as 'oligocellular' but it is an interesting angle on the question nevertheless.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Boraas, ME et al. (1998)Phagotrophy by a flagellate selects for colonial prey: A possible origin of multicellularity. Evolutionary Ecology 12: 153-164&lt;/p&gt;&#xA;&lt;p&gt;Abstract: Predation was a powerful selective force promoting increased morphological complexity in a unicellular prey held in constant environmental conditions. The green alga, Chlorella vulgaris, is a well-studied eukaryote, which has retained its normal unicellular form in cultures in our laboratories for thousands of generations. For the experiments reported here, steady-state unicellular C. vulgaris continuous cultures were inoculated with the predator Ochromonas vallescia, a phagotrophic flagellated protist (&lt;span class=&quot;math-container&quot;&gt;`&lt;/span&gt;flagellate'). Within less than 100 generations of the prey, a multicellular Chlorella growth form became dominant in the culture (subsequently repeated in other cultures). The prey Chlorella first formed globose clusters of tens to hundreds of cells. After about 10-20 generations in the presence of the phagotroph, eight-celled colonies predominated. These colonies retained the eight-celled form indefinitely in continuous culture and when plated onto agar. These self-replicating, stable colonies were virtually immune to predation by the flagellate, but small enough that each Chlorella cell was exposed directly to the nutrient medium.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-12-12T11:10:55.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5480" PostTypeId="1" CreationDate="2012-12-12T14:03:05.463" Score="7" ViewCount="2681" Body="&lt;p&gt;I am trying to determine how quickly detergents act on bacterial cells (cell lysis). I would like to compare some detergents at difference concentrations for bacteriolytic activity. I don’t care about all metabolites inside the cells (proteins, DNA, etc…). Many publications suggest that often more complicated solutions are used. My first thought was to use a simple prepared detergent in PBS or saline for lysing the cells. Do I need a complex solution to lyse the cells?&#xA;Could someone please give me a suggestion? Thanks in advance. &lt;/p&gt;&#xA;" OwnerUserId="1771" LastEditorUserId="1320" LastEditDate="2012-12-12T17:00:39.473" LastActivityDate="2012-12-12T17:00:39.473" Title="Bacterial cell lysis - what solution to use?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5481" PostTypeId="2" ParentId="5480" CreationDate="2012-12-12T14:37:23.437" Score="4" Body="&lt;p&gt;What exactly is the purpose of lysing the cells? The &quot;complicated&quot; solutions, as you say, include a bunch of ingredients. The detergent is largely present to dissolve cell membranes (which are lipid-based) and allow for extraction of proteins or other biochemicals from within the cell (and organelles in eukaryotes). There are also two types of detergents: ionic and anionic. Both detergent types will dissolve membranes, but ionic detergents tend to be harsher of the two by strongly disrupting protein structures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If protein biochemistry is important, then the next most important ingredients will be specific inhibitors of proteases: enzymes which degrade proteins. There are many of these, but some examples include PMSF, EDTA, aprotinin, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes it is necessary to buffer the pH of lysis solution to monitor protein complexes, or keep a protein natured, or keep DNA in an optimal pH range. General solutions for lysis buffers include Tris-EDTA (TE), PBS, etc. This choice comes down to whether you want a buffer, and in which pH range you wish to keep your lysis solution. Common buffers like TE and PBS are made up for a pH range of between 7-8. There are other buffers that are used for low pH ranges (pH 4-6), but are usually less common.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, there are ways to lyse cells without using any kind of lysis buffer. One method is to use sonication, which uses directed pulses of high-frequency sound to lyse cells by mechanically shearing them. Another method is to repeatedly freeze-thaw cells from -80&amp;deg;C to 4&amp;deg;C (usually 3 times is sufficient). Lysis in this manner is accomplished by repeated formation of ice crystals which cut open cells, releasing their contents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have a more specific question, one of us can guide you further, but this provides a general overview of what is involved with cell lysis buffers.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-12-12T14:37:23.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5482" PostTypeId="2" ParentId="5480" CreationDate="2012-12-12T15:35:41.910" Score="2" Body="&lt;p&gt;I wonder how you plan to measure lysis? You will find that many lysis methods for &lt;em&gt;E. coli&lt;/em&gt; incorporate a treatment with lysozyme and EDTA. This is so that lipopolysaccharide (outer membrane) and peptidoglycan layers of the cell envelope can be breached before detergent (usually SDS or Triton X-100) is added to dissolve the inner or cytoplasmic membrane. I suspect that if you added detergent to intact cells it wouldn't be particularly effective, and any cells that were affected would remain as denatured cells which would, for example, still contribute to optical density.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since they are usually able to withstand bile salts in the small intestine, Gram-negative bacteria can be quite resistant to detergents. For example many &lt;em&gt;Enterobacteriaciae&lt;/em&gt; can grow in 5% SDS - see:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Rajagopal, S &lt;em&gt;et al&lt;/em&gt;. (2003) Eight Gram-negative bacteria are 10 000 times more sensitive to cationic detergents than to anionic detergents. Canad. J. Mic. 49:775-779&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-12-12T15:35:41.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5483" PostTypeId="2" ParentId="5416" CreationDate="2012-12-12T16:14:22.963" Score="3" Body="&lt;p&gt;The chemical formula for glucose is C&lt;sub&gt;6&lt;/sub&gt;H&lt;sub&gt;12&lt;/sub&gt;O&lt;sub&gt;6&lt;/sub&gt;. When the body needs energy, the glucose molecule is broken down to give CO&lt;sub&gt;2&lt;/sub&gt; and water:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$C_6H_{12}O_6 + 6O_2 =&amp;gt; 6CO_2 + 6H_2O$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, I think &quot;C&quot; comes mostly from glucose molecules.&lt;/p&gt;&#xA;" OwnerUserId="1765" LastEditorUserId="1320" LastEditDate="2012-12-15T14:49:54.397" LastActivityDate="2012-12-15T14:49:54.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5484" PostTypeId="1" AcceptedAnswerId="5485" CreationDate="2012-12-13T06:51:00.297" Score="12" ViewCount="84379" Body="&lt;p&gt;During DNA replication, RNA primase puts an RNA primer in the lagging strand. What is the function of this RNA primer? Why can't the enzymes put DNA fragments directly?&lt;/p&gt;&#xA;" OwnerUserId="1765" LastEditorUserId="1320" LastEditDate="2012-12-13T09:03:10.667" LastActivityDate="2015-05-08T07:57:42.633" Title="What is the function of the RNA primer in DNA replication?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;rna&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5485" PostTypeId="2" ParentId="5484" CreationDate="2012-12-13T07:57:38.643" Score="13" Body="&lt;p&gt;DNA polymerases need a primer oligonucleotide (RNA or DNA) - their substrates are an existing 3'-OH group and a dNTP. The primase however is a typical RNA polymerase, capable of initiating polynucleotide synthesis &lt;em&gt;de novo&lt;/em&gt; by positioning a complementary ribonucleoside 5'-triphosphate opposite its complementary DNA base. The primase makes an RNA primer that the DNA polymerase can then use for chain extension. The RNA primer is ultimately degraded and replaced by a DNA polymerase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rationale for this difference is that DNA polymerases have an active site that is geared towards proofreading and that primerless initiation would be an error-prone process. By having the primers 'tagged' by virtue of them being RNA, it is possible for the replication machinery to use them but then replace them with a high fidelity DNA copy of the template strand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit in response to OP comment:&lt;/strong&gt;&#xA;Synthesis of the leading strand consists of extending an existing DNA. However the leading strand is also originally initiated, at the ori element, with an RNA primer. Once that first initiation event has taken place the synthesis of the leading strand is simply a process of extending that original primer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some viruses employ ingenious variations on this theme such as using tRNA primers , or proteins - see &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_replication&quot;&gt;Wikipedia&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-12-13T13:18:08.680" LastActivityDate="2012-12-13T13:18:08.680" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5486" PostTypeId="1" CreationDate="2012-12-13T11:36:43.647" Score="3" ViewCount="217" Body="&lt;p&gt;I work with mice, and I want to see what happens to some specific proteins in the mouse brain after IL-1b injection (intracerebroventricular). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a problem: when I measure the mRNA and protein levels, I see that there are some differences between them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It can be like:  mRNA (upregulated)  Protein (no difference)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible that these proteins have a high turnover rate? If so, how can I prevent that? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can I (if it is possible) inject (intracerebroventricular) IL-1b mixed with protease inhibitors?&lt;/p&gt;&#xA;" OwnerUserId="1773" LastEditorUserId="57" LastEditDate="2012-12-14T02:31:50.147" LastActivityDate="2013-04-30T00:46:38.420" Title="High protein turnover rate and protease inhibitors?" Tags="&lt;molecular-biology&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5488" PostTypeId="1" AcceptedAnswerId="5494" CreationDate="2012-12-13T15:13:52.880" Score="8" ViewCount="539" Body="&lt;p&gt;Apparently all living humans are matrilineal descendants of a single woman who lived 200.000 years ago. She is called Mitochondrial Eve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But at the time she lived there was a different matrilineal ancestor that all living humans shared. And between then and now I imagine many other women have been Mitochondrial Eves of the human population that lived at a particular time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm wondering is what kinds of events would cause a different, more recent matrilineal ancestor to become the Mitochondrial Eve of all living humans?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One scenario I can image is that the human population is on the brink of extinction and literally only a few people survive. Because there are so few people alive, I imagine that the chance that they share a more recent matrilineal ancestor is high.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there other scenarios possible? Does the chance of a new Mitochondrial Eve emerging decrease if the human population is large (billions) instead of small (hundreds or thousands)? Suppose that the human population will not decrease, is it likely future human populations will ever have a different Mitochondrial Eve than the current population? Does it depend on the amount of people that migrate?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same questions could be posed for Y-Chromosomal Adam and the most recent common ancestor of all humans, I guess...&lt;/p&gt;&#xA;" OwnerUserId="1774" LastActivityDate="2017-05-10T13:49:54.393" Title="What kind of event would cause the current Mitochondrial Eve to be replaced by a new one?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;human-genetics&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5489" PostTypeId="1" CreationDate="2012-12-13T16:22:01.720" Score="7" ViewCount="1523" Body="&lt;p&gt;I am learning in Gene data lately so I apologize for the silly questions in advance. I read a paper for a cancer on human which found some important genes. For example, the paper listed one of genes in its name as    &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;gene1:    chromosome 12 open reading frame 52&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;May I know how I can find its corresponding gene symbol as     &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;C12orf52&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Is there a mapping table or  tool I can use ?     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you very much,&lt;/p&gt;&#xA;" OwnerUserId="1775" LastActivityDate="2012-12-19T12:46:41.760" Title="How to map the Gene name to its Gene Symbol?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;genomics&gt;&lt;gene-expression&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5490" PostTypeId="2" ParentId="5489" CreationDate="2012-12-13T17:40:47.203" Score="5" Body="&lt;p&gt;Unfortunately, protein and gene name mapping is one of the most annoying problems in modern computational biology. There is no surefire way of doing this. Especially from hopeless gene names as the one in the paper you cite. Here are a few services you can try though:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;General, text search, useful if you have a gene description (as in the case described in your question): &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/&quot; rel=&quot;nofollow&quot;&gt;NCBI Entrez,&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.uniprot.org&quot; rel=&quot;nofollow&quot;&gt;UniProt search&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Mapping servers, useful if you have an actual gene/protein symbol/name (e.g. P53_HUMAN, AF240684, NP_001119585 etc)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.uniprot.org&quot; rel=&quot;nofollow&quot;&gt;UniProt ID Mapping&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://david.abcc.ncifcrf.gov/conversion.jsp&quot; rel=&quot;nofollow&quot;&gt;DAVID Gene ID Conversion Tool&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2012-12-19T12:46:41.760" LastActivityDate="2012-12-19T12:46:41.760" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5491" PostTypeId="1" AcceptedAnswerId="5493" CreationDate="2012-12-13T17:55:50.800" Score="4" ViewCount="1116" Body="&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=3QJ4CjFsflA&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=3QJ4CjFsflA&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a link to Hershey and Chase experiment. According to this experiment, we conclude that DNA is the genetic material. But how do we conclude that DNA is the genetic material? They only proved that DNA of virus enters into the bacteria, not the protein coat of virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The DNA of the virus later destroys the bacteria because the virus reproduces inside them. Does this demonstrate that DNA is the genetic material?&lt;/p&gt;&#xA;" OwnerUserId="1765" LastEditorUserId="1320" LastEditDate="2012-12-13T18:30:42.667" LastActivityDate="2013-02-13T21:33:49.863" Title="Hershey and Chase experiment" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5492" PostTypeId="2" ParentId="5488" CreationDate="2012-12-13T17:58:08.187" Score="4" Body="&lt;p&gt;One possible scenario would be that a particular woman develops a mutation rendering her much more 'fit' (in the evolutionary sense) than her peers. For the sake of argument, lets take the very simplistic case of an X-linked recessive mutation causing the women who bear it to have say 10 children at each birth. If this mutation is then transferred to the offspring, it will very quickly spread across the entire population. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this continues for a few generations, the crushing majority of the earth's population will be the descendants of that one woman who carried the original mutation, she would be the new mitochondrial Eve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to stress that this is nothing but a very simplistic thought experiment. Such a mutation is i) very unlikely, probably impossible, ii) likely to render the carrying individual &lt;em&gt;less&lt;/em&gt; fit rather than more as each birth would be exhausting, increasing the chances of dying during child birth.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Update:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have specified that the mutation has to be X-linked and recessive. This means that it will only present a phenotype in women who are homozygous for it, women both of whose parents carried the mutation. This is because, as mgkrebbs very correctly pointed out in the comments below, otherwise her sons would mate with women who are not their sisters and &lt;em&gt;their&lt;/em&gt; children would have the mutation but not her mDNA. If the phenotype is only expressed when the mutation is homozygous, only women whose mother carried the mutation (and Eve's mDNA) would show it and only then would a new mEve arise. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2017-05-10T13:49:54.393" LastActivityDate="2017-05-10T13:49:54.393" CommentCount="16" ContentLicense="CC BY-SA 3.0" />
  <row Id="5493" PostTypeId="2" ParentId="5491" CreationDate="2012-12-13T18:04:40.427" Score="4" Body="&lt;p&gt;It is a matter of deduction. We know that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Viruses entering a cell are capable of making more copies of themselves.&lt;/li&gt;&#xA;&lt;li&gt;The &lt;em&gt;only&lt;/em&gt; part of a virus that actually enters the cell is its DNA (or RNA, depending on the virus in question).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Based on these two facts, we can conclude that the DNA ̣--since it is the only part of the virus to enter the cell-- somehow contains the information necessary to make new copies of the virus and is, therefore, the genetic material of the virus.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1320" LastEditDate="2013-02-13T21:33:49.863" LastActivityDate="2013-02-13T21:33:49.863" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5494" PostTypeId="2" ParentId="5488" CreationDate="2012-12-13T18:07:43.427" Score="1" Body="&lt;p&gt;The new mitochondrial eve is alive right now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When humans reproduce, mothers pass their mitochondria to their offspring without a contribution from the father.  As a result, each human can trace back their mitochondrial lineage as an unbroken chain to a single individual woman in the past.  Through random chance (genetic drift) or natural selection women in some mitochondrial lines will pass offspring to the next generation, while others will not.  If a woman fails to pass offspring to the next generation then she represents the end (i.e., extinction) of a particular mitochondrial lineage.  As time progresses more and more of the original mitochondrial lineages will go extinct until all humans represent one remaining linage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that this is a continual process since lineages accumulate differences through mutation of the mitochondrial DNA.  This mutation is the source of the different lineages that that will go forward.  Based on the estimated rate of mitochondrial DNA mutation we can estimate how long  it would take for extant mitochondria to have developed the genetic differences we now see. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you take a snapshot of this process at one point in time (e.g., contemporary humans), you can use this estimated time to say how long it would take to accumulate the present differences - that is when the line began.  Due to the continual extinction of extant mitochondrial lines, there is some point in the future where if we were to take the snapshot we would estimate that the mitochondrial eve was alive right now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt; based on comment:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rate that a new mitochondrial eve would be formed is based on the accumulation of mutations in non-coding regions of the mitochondrial DNA (i.e., the molecular clock) which is dependent on the population size only in so far as the probability that a given mitochondrial line will survive when all others go extinct is basically its initial frequency in the population. So in a large population with more initial diversity each line will have a lower probability of succeeding.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, if there is no selection for or against a given line then changes in frequency are due to chance (genetic drift). In a large population the effect of drift is smaller than it is on a small population.  So if the population size is small, then the likelihood that a mitochondrial line will go extinct is greater and the rate of a single mitochondrial line succeeding to be the mitochondrial eve is greater.&lt;/p&gt;&#xA;" OwnerUserId="137" LastEditorUserId="137" LastEditDate="2012-12-14T15:35:28.533" LastActivityDate="2012-12-14T15:35:28.533" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5495" PostTypeId="2" ParentId="5488" CreationDate="2012-12-13T18:45:50.023" Score="-1" Body="&lt;p&gt;What would need to happen for a single woman's mitochondrial genome to be in all living humans ?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All other women would &lt;em&gt;suddenly or gradually&lt;/em&gt; need to be eliminated from the gene pool.   No other woman could enter the gene pool of this future humanity.  So the most likely scenario is one where we would have to be reduced to a single woman at some point.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetic isolation was brought up, but the words 'all living humans' doesn't really say 'isolation'.  In isolation, there are other people still carrying on somewhere else.   Here we are talking about only isolation in the sense that the breeders are the only ones left to reproduce. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even so, any human woman will still be descended from MEve.  That original Eve would still be the mitochondrial Eve, though the genomic record pointing to her would have disappeared. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A completely New Eve could happen if there were a woman &lt;em&gt;unrelated to MEve&lt;/em&gt; were to come along, and her offspring were so much more successful than all other women that over time only this woman's daughters were chosen as mothers.  She would be incredibly successful- like all her children were 6'6&quot; and much smarter, attractive etc etc, then the rest of the gene pool could dwindle leaving only 'new Eve'.  This could happen say if we got some Neanderthals going.  &lt;a href=&quot;http://www.slate.com/articles/health_and_science/explainer/2012/10/neanderthal_vs_homo_sapiens_who_would_win_in_a_fight.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;They don't seem to be particularly likely to take over though&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is similar to the scenario where one female lineage simply out-competes all other female lineages to assume the mantle of M-Eve.  This seems less likely to me.  This lineage would have to enjoy an advantage would have to out-weigh all over variants that exist at the time and would ever emerge over the following generations before our new M-Eve's final domination. Given the number of genes and possible variants, in the entire genome, that is statistically really improbable. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as a new &lt;strong&gt;Y Adam&lt;/strong&gt;, this sort of thing nearly happened for men.  Just to remind, the Y chromosome is transmitted exclusively from father to son, so a Y Adam would be the only ancestor of all men on the face of the planet.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A national geographic sponsored survey of genomes found that in &lt;a href=&quot;http://news.nationalgeographic.com/news/2003/02/0214_030214_genghis_2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;central asia 8% of all men have the same Y chromosome&lt;/a&gt;.  &lt;a href=&quot;http://blogs.discovermagazine.com/gnxp/2010/08/1-in-200-men-direct-descendants-of-genghis-khan/#.UMogkG_A87k&quot; rel=&quot;nofollow noreferrer&quot;&gt;Over all humanity, 0.5% of all men have the same Y chromosome&lt;/a&gt;.  The genetics point to the Mongol Warrior King, Genghis Khan whose campaigns across Asia to the doorstep of Europe included him bedding with one or more different women from the conquered peoples every night, &lt;a href=&quot;http://en.wikipedia.org/wiki/Genghis_Khan#Death_and_burial&quot; rel=&quot;nofollow noreferrer&quot;&gt;one of whom is reputed to have killed him&lt;/a&gt;.  Not incidentally killing many men too, eliminating much future competition for his progeny.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still, all this is a mere fraction of the sort of effect you are talking about.  100% replacement by a single individuals descendants is hard to imagine in less than an extinction like scenario.  Or a new race of superbeings coming from a single individual.  Hard to imagine given the billions of people on the face of the planet now.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its a little easier to imagine in the case of a new Adam only because a one man can have hundreds or even thousands of offspring in his lifetime.  Even then, Male psychology &lt;a href=&quot;http://www.youtube.com/watch?v=gu9fESAlGc4&quot; rel=&quot;nofollow noreferrer&quot;&gt;seems to bring it up&lt;/a&gt; more than &lt;a href=&quot;http://www.youtube.com/watch?v=ybSzoLCCX-Y&quot; rel=&quot;nofollow noreferrer&quot;&gt;is rational&lt;/a&gt;. Its still extremely improbable (not going to happen). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cf1Sq.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its also worth noting that &lt;a href=&quot;http://www.time.com/time/photogallery/0,29307,1888702,00.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;few species have been able to come back from such a small gene pool and number&lt;/a&gt;... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a tree of human Y chromosomes. You can see that fat grey blob which are descendants of GK. &#xA;&lt;img src=&quot;https://i.stack.imgur.com/FQ2rK.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1306" LastEditDate="2012-12-19T12:57:21.633" LastActivityDate="2012-12-19T12:57:21.633" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="5496" PostTypeId="1" CreationDate="2012-12-13T22:11:54.877" Score="3" ViewCount="108" Body="&lt;p&gt;There is an area of where there is a distinct line of only trees on one side and only shrubs on the other (right next to each other). What could cause this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My attempt: I said there could be a difference in sunlight, but I'm not sure.&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="558" LastEditDate="2012-12-14T03:04:03.977" LastActivityDate="2013-03-25T01:00:53.640" Title="What causes tree lines?" Tags="&lt;homework&gt;&lt;ecology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5497" PostTypeId="1" AcceptedAnswerId="7169" CreationDate="2012-12-13T22:47:36.447" Score="6" ViewCount="114" Body="&lt;p&gt;I'm looking for some pointers to proteins that produce at really gigantic levels in E. coli and yeast (S. cerevisiae).  Can anyone point to some champion proteins?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even in inclusion bodies and non functional, just cases where the yield is very high - how much of a given protein can a liter of E. coli or S. cerevisiae make? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen bands on gels like this, but I've probably not seen the champions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zCmuB.jpg&quot; alt=&quot;random image from the web of an inclusion body&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be great if you could cite and discuss the plasmid/promoter used and whether codon optimization or other such tricks made a difference. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1320" LastEditDate="2012-12-15T15:26:27.810" LastActivityDate="2013-02-11T19:33:06.283" Title="Proteins that are strongly overproduced in E. coli and S. cerevisiae?" Tags="&lt;proteins&gt;&lt;bacteriology&gt;&lt;yeast&gt;&lt;recombinant&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5498" PostTypeId="2" ParentId="5445" CreationDate="2012-12-13T23:08:59.843" Score="-1" Body="&lt;p&gt;Most likely the energy to stay warm is not being used to fight infection. Also the virus is likely designed to operate with your respiratory system at a colder temperature more effective that the immune system is at that cooler temperature.&lt;/p&gt;&#xA;" OwnerUserId="1776" LastActivityDate="2012-12-13T23:08:59.843" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5499" PostTypeId="1" AcceptedAnswerId="5501" CreationDate="2012-12-14T00:00:01.317" Score="3" ViewCount="146" Body="&lt;p&gt;There is a flower population elevated 1000 meters above sea level.  If climate change causes a 12⁰C increase in temperature over the next 10 years, what will happen to the flowers?&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="3340" LastEditDate="2014-10-09T14:37:31.307" LastActivityDate="2014-10-09T14:37:31.307" Title="Will climate change affect flower population?" Tags="&lt;botany&gt;&lt;homework&gt;&lt;ecology&gt;&lt;climate-change&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5500" PostTypeId="2" ParentId="5491" CreationDate="2012-12-14T05:32:58.193" Score="4" Body="&lt;p&gt;This was an important experiment, but did not convince everyone.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not even Hershey and Chase claimed this conclusion, although it convinced many.  In most mol bio classes or when reading &quot;The Double Helix&quot; you can see how there were lots of facts pointing to DNA, but doubts lingered.  Some viruses contained RNA only and not DNA, but still replicated.  There was also a school of thought which felt that proteins could be the genetic material.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hershey%E2%80%93Chase_experiment#Discussion&quot; rel=&quot;nofollow&quot;&gt;It was Watson and Crick that finally convinced everyone that DNA was the medium of genetic inheritance&lt;/a&gt;.  The reasons for this are varied, one of them is probably that atomic structures are so clearly understandable and seem so uncomplicated compared to a wet lab experiment which is built upon so many other experiments.  Questions keep coming up:  &quot;how do you know you shook the flask long enough?&quot;, &quot;What if a small amount of residual viral protein got in?&quot;  For every revelation like Hershey and Chase, there are many cases where someone stopped an incubation too quickly or wrote down an illegible number and was found out after publishing.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And you can see how much the structure gave us in one fell swoop: the structure of DNA inspired a mechanism by which replication of the DNA could be produced with some error correction, the central dogma (DNA -&gt; RNA -&gt; protein).  There were several years more effort to demonstrate that the genetic code existed and then parsing out the exact codons and the fact that they were 3 bases long.  But all of this was predicted when the structure was found.  So much clearer as to what is going on. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-12-14T05:32:58.193" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5501" PostTypeId="2" ParentId="5499" CreationDate="2012-12-14T05:45:17.267" Score="3" Body="&lt;p&gt;Its really hard to say for any given field of flowers and its hard to separate temperature from so many other factors that are accompanying climate change. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, rainfall is changing as well as CO₂ levels.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Ocean_acidification&quot; rel=&quot;nofollow&quot;&gt;The pH of the rain may change because CO₂ becomes a mild acid when its absorbed into water.&lt;/a&gt;  &lt;a href=&quot;http://www.ext.colostate.edu/pubs/insect/05528.html&quot; rel=&quot;nofollow&quot;&gt;The speed at which the seasonal temperatures vary and how cold is the minimum temperature and how hot is the hottest day&lt;/a&gt; will cause parasites and infections which kill plants to appear.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be sure the heat is important, but the timing maybe just as important.  &lt;a href=&quot;http://www.livescience.com/19679-climate-change-seasons-shift-mismatch.html&quot; rel=&quot;nofollow&quot;&gt;The temperature is causing earlier blooms and later growing seasons.&lt;/a&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each different species is responding differently, but odds are that nearly any given field of flowers is going to feel it.  The temperature is important, but its sometimes hard to guess if its the specific culprit in changes. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3340" LastEditDate="2014-10-09T14:03:58.273" LastActivityDate="2014-10-09T14:03:58.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5502" PostTypeId="2" ParentId="5489" CreationDate="2012-12-14T08:29:50.727" Score="0" Body="&lt;p&gt;If the original source used the official human nomenclature, you can search the &lt;a href=&quot;http://www.genenames.org/cgi-bin/quick_search.pl?.cgifields=type&amp;amp;type=contains&amp;amp;num=50&amp;amp;search=chromosome%2012%20open%20reading%20frame%2052&amp;amp;submit=Submit&quot; rel=&quot;nofollow&quot;&gt;HGNC (HUGO Gene Nomenclature Committee) site&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2012-12-14T08:29:50.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5503" PostTypeId="1" AcceptedAnswerId="8100" CreationDate="2012-12-14T18:28:48.960" Score="15" ViewCount="2577" Body="&lt;p&gt;I'm interested in whether any studies have determined the &lt;strong&gt;intensity of light at eye level that starts melatonin release in humans&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;melatonin release is suppressed by blue light with peak suppression&#xA;occurring at 420-480nanometer range.&lt;/li&gt;&#xA;&lt;li&gt;This light is registered by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2376768/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Melanopsin, a photopigment in the&#xA;eye&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Melanopsin signals the Suprachiasmatic Nucleus, the master clock of the human body.&lt;/li&gt;&#xA;&lt;li&gt;The suprachiasmatic nucleus makes a decision to suppress melatonin&#xA;release in response to blue light observed.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;What I need to know is how much light is &quot;enough&quot; to trigger the suppression by the mechanism described above. I've seen a mention of as little as 200 lumens of white light, but do not have any reference to verify that. Additionally, the figure of 200 lumens was given for a typical smartphone screen, not necessarily translating to 200 lumens at eye level. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://endo.endojournals.org/content/149/12/6125.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;I'm aware of this experiment involving rats, where the light intensity at eye level was quantified&lt;/a&gt;. I'm looking for a similar measurement in humans.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/3599/what-light-intensity-determines-the-start-end-of-a-photoperiod-in-humans&quot;&gt;Here's my original question on the subject, but I've learned quite a lot since then to refine the question&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I appreciate your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-08-17T02:11:33.137" Title="What light intensity starts melatonin release in humans?" Tags="&lt;human-biology&gt;&lt;sleep&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5504" PostTypeId="2" ParentId="5416" CreationDate="2012-12-15T15:22:36.060" Score="8" Body="&lt;p&gt;&lt;strong&gt;At rest, the main sources of CO&lt;sub&gt;2&lt;/sub&gt; are the brain, liver and heart.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The original questions seems to me to be asking for information about which tissues or organs are responsible for producing most of the exhaled CO&lt;sub&gt;2&lt;/sub&gt;. As other answers have mentioned, CO&lt;sub&gt;2&lt;/sub&gt; production by cells reflects the amount of oxidative metabolism that is being carried out. This means that we can answer the question by simply asking - which tissues/organs are responsible for consuming the most O&lt;sub&gt;2&lt;/sub&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many sources of information about this, but the most succinct statement that I have found is &lt;a href=&quot;http://science.jrank.org/pages/856/Biochemical-Oxygen-Demand.html&quot;&gt;here&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The average human body of 139 lb (63 kg) consumes 250 ml of O&lt;sub&gt;2&lt;/sub&gt; each minute. The major single-organ oxygen consumers are the liver, brain, and heart (consuming 20.4%, 18.4%, and 11.6%, respectively), while the sum total of all the body's skeletal muscles consume about 20%. In addition, the kidneys use up about 7.2%, and the skin uses 4.8%. The rest of the body consumes the remaining 17.6% of the oxygen. Oxygen use can also be measured per 100 gm of an organ to indicate concentrations of use; as such, heart usage is highest, followed by the kidneys, then the brain, and then the liver. During exercise, the biochemical oxygen demand increases for active tissues including the heart and skeletal muscles.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Other sources are in broad agreement with this. Note however that these are values at rest. As the quotation states, during active exercise the skeletal muscle will become the major source of CO&lt;sub&gt;2&lt;/sub&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-12-15T15:22:36.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5505" PostTypeId="1" AcceptedAnswerId="5506" CreationDate="2012-12-15T19:52:48.737" Score="7" ViewCount="757" Body="&lt;p&gt;Why is the secondary antibody conjugated to the enzyme in ELISA, instead of the primary antibody? Wouldn't it be easier to conjugate the enzyme to the primary antibody?&lt;/p&gt;&#xA;" OwnerUserId="1609" LastEditorUserId="1609" LastEditDate="2012-12-19T20:05:01.067" LastActivityDate="2015-09-15T09:36:35.333" Title="Conjugate secondary antibody" Tags="&lt;immunology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5506" PostTypeId="2" ParentId="5505" CreationDate="2012-12-15T20:51:29.857" Score="7" Body="&lt;p&gt;Making an antibody-enzyme conjugate isn't trivial. By using a primary/secondary set-up you can use the same well-characterised conjugate in combination with many different primary antibodies (as long as these primaries are all raised in the same species). There is also the possibility of some amplification: for example, if the secondary is an anti-F&lt;sub&gt;ab&lt;/sub&gt; then two secondary Igs will bind to each primary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Response to OP comment&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most primary antibodies in common use are derived from rabbit or mouse, and most are IgG. So, for example, the secondary antibodies goat anti-rabbit IgG and goat anti-mouse IgG will cover most experiments.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-12-19T23:06:58.863" LastActivityDate="2012-12-19T23:06:58.863" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5507" PostTypeId="1" AcceptedAnswerId="5509" CreationDate="2012-12-15T22:40:18.083" Score="2" ViewCount="82" Body="&lt;p&gt;I wonder if Chili pepper's fruits which fall into the soil near the plant will harm it, since the peppers are so spicy for people.&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2012-12-16T12:21:40.280" Title="Is it ok for Chili pepper plant's fruits to fall into its soil?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5508" PostTypeId="1" CreationDate="2012-12-15T23:27:00.803" Score="2" ViewCount="34" Body="&lt;p&gt;Where might I find a list of all recorded instincts (possibly with all other attributes) by species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,&#xA;Chenz&lt;/p&gt;&#xA;" OwnerUserId="1783" LastEditorUserId="1320" LastEditDate="2012-12-15T23:36:04.383" LastActivityDate="2012-12-15T23:36:04.383" Title="Where might I find a list of all recorded instincts by species?" Tags="&lt;zoology&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2014-07-01T07:21:23.090" ContentLicense="CC BY-SA 3.0" />
  <row Id="5509" PostTypeId="2" ParentId="5507" CreationDate="2012-12-15T23:47:34.073" Score="2" Body="&lt;p&gt;As @MCM says, the capsaicin molecule isn't intrinsically damaging - its effect upon us is mediated through &lt;a href=&quot;http://en.wikipedia.org/wiki/TRPV&quot; rel=&quot;nofollow noreferrer&quot;&gt;the TRPV1 (Transient Receptor Potential Vanilloid 1) receptor&lt;/a&gt; in the membranes of cells whose function is to sense noxious stimuli such as heat. The binding of capsaicin to this protein causes transmembrane movement of Ca&lt;sup&gt;2+&lt;/sup&gt; ions which depolarises the membrane, triggering an action potential - a signal to the brain. Heat has the same effect on the TRPV1 protein. In this way the presence of capsaicin mimics the effects of heat, causing a painful sensation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a look at &lt;a href=&quot;https://biology.stackexchange.com/questions/371/how-is-temperature-sensed&quot;&gt;this SE.Biology question&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2012-12-16T12:21:40.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5511" PostTypeId="2" ParentId="5445" CreationDate="2012-12-16T02:41:27.093" Score="10" Body="&lt;p&gt;it does not, really. unless we're talking about things like frostbite or severe hypothermia.&lt;/p&gt;&#xA;&lt;p&gt;it's a myth that it does.&#xA;the virus is more stable in colder air, however.&lt;/p&gt;&#xA;&lt;p&gt;see more here:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nytimes.com/2007/12/05/health/research/05flu.html&quot; rel=&quot;noreferrer&quot;&gt;Study Shows Why the Flu Likes Winter&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.0030151&quot; rel=&quot;noreferrer&quot;&gt;Influenza Virus Transmission Is Dependent on Relative Humidity and Temperature&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Innate responses proved to be comparable between animals housed at 5 °C and 20 °C, suggesting that cold temperature (5 °C) does not impair the innate immune response in this system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1784" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-12-16T02:41:27.093" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5512" PostTypeId="1" CreationDate="2012-12-16T07:44:52.407" Score="5" ViewCount="902" Body="&lt;p&gt;A vague question, but let me try to explain. My friend explained to me that in females, some cells use one X chromosome, while all others use the other X chromosome. This can result in some differences of appearance of certain individuals. &lt;a href=&quot;http://en.wikipedia.org/wiki/X-inactivation&quot;&gt;The Wikipedia page on X-inactivation&lt;/a&gt; shows an example. There is a picture there that shows a cat with fur of two colors, each showing in seemingly random groups. My friend had explained that when one cell &quot;deactivates&quot; its X chromosome, all of its descendants have the same deactivated X chromosome, so it makes sense that the similar colors appear in groups on the cat's coat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But it seems &lt;a href=&quot;http://www.flickr.com/photos/capnkroaker/4661282992/&quot;&gt;tigers' coats&lt;/a&gt; are much more complicated than that. The pattern on a tiger's coat is not completely random. They make very discernible shapes. There are clear borders inside which only black fur grows, and outside of which only orange fur grows. How is this possible?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not suggesting that the patters on tigers' fur is in any way related to X-inactivation, since I know that only applies to female mammals. But X-inactivation seems like a &quot;natural&quot; phenomenon, while the stripes on a tiger (or other animals with complex patters) seem a bit more bizarre. How do the cells on a tiger's body know which color to show and still follow the pattern?&lt;/p&gt;&#xA;" OwnerUserId="970" LastActivityDate="2012-12-16T20:42:02.420" Title="How does a tiger have stripes?" Tags="&lt;genetics&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5513" PostTypeId="2" ParentId="2905" CreationDate="2012-12-16T10:46:28.010" Score="3" Body="&lt;p&gt;I also had to do the same using Jmol, and I figured it out how to get a list of all the hbonds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Step 1: Calculate the hbonds with or without RASMOL method. It's up to you, e.g.,&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;jmolScriptWait(&quot;select not hydrogen; set hbondsRasmol FALSE; calculate HBONDS&quot;)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Step 2: Only display the hbonds&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;jmolScriptWait(&quot;display connected(hbond)&quot;)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Step 3: Export the bonding info to JavaScript array&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;jmolGetPropertyAsArray(&quot;bondInfo&quot;)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;You will have an array of objects each will contain the atoms connected by this hbond and the bond length.&lt;/p&gt;&#xA;" OwnerUserId="1785" LastEditorUserId="57" LastEditDate="2012-12-16T15:14:16.747" LastActivityDate="2012-12-16T15:14:16.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5514" PostTypeId="1" CreationDate="2012-12-16T18:40:21.750" Score="3" ViewCount="623" Body="&lt;p&gt;Acuity of one's sight is rated on the 20/20 scale. An online search appeared to indicate there is no comparable 'standard' to rate olfactory acuity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is acuity of the olfactory system rated? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="69" LastEditDate="2012-12-17T17:04:38.880" LastActivityDate="2014-06-10T01:31:26.143" Title="How is olfactory acuity rated/measured?" Tags="&lt;physiology&gt;&lt;sensation&gt;&lt;olfaction&gt;&lt;odour&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5516" PostTypeId="1" AcceptedAnswerId="5625" CreationDate="2012-12-16T20:37:45.593" Score="7" ViewCount="1395" Body="&lt;p&gt;I understand that the atmospheric temperature is sensed relative to external body temperature. However, is the sensation of warmth registered linearly, or is it on a logarithmic scale, similar to sound that works on the Decibel scale? Or is it on another scale entirely?&lt;/p&gt;&#xA;" OwnerUserId="1787" LastEditorUserId="1787" LastEditDate="2012-12-16T21:18:49.380" LastActivityDate="2015-10-22T12:58:24.760" Title="Is warmth/temperature sensed linearly or on a different scale?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5517" PostTypeId="2" ParentId="5512" CreationDate="2012-12-16T20:42:02.420" Score="5" Body="&lt;p&gt;It turns out that this was a question that was answered by Alan Turing in the 1950s. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Turing hypothesized there would be two morphogens, an inhibitor/ activator pair, each of which would produce a one of two phenotypes by activation or suppression of a trait.  He hypothesized that this would produce a pattern like stripes or other patterns (e.g. black and orange stripes).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This year just such &lt;a href=&quot;http://phys.org/news/2012-02-alan-turing-1950s-tiger-stripe.html&quot; rel=&quot;nofollow&quot;&gt;inhibiting/activating pairs produce patterns like ridges in the top of the mouth&lt;/a&gt; of mice.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a broad way, this seems like X-inactivation, where there is an &lt;a href=&quot;http://en.wikipedia.org/wiki/X-inactivation#Selection_of_one_active_X_chromosome&quot; rel=&quot;nofollow&quot;&gt;X-inactivation center&lt;/a&gt; (XIC) that is inhibited or activated when the cell is created in mitosis.  &lt;a href=&quot;http://en.wikipedia.org/wiki/X-inactivation#Timing&quot; rel=&quot;nofollow&quot;&gt;XIC is still hypothetical and undiscovered, but it can create patterns and is non-random.&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I would say that this tiger stripes and X-inactivation may share Turing's mechanism, but the stripes, found in male and female tigers alike is not linked causally to X-inactivation. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-12-16T20:42:02.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5518" PostTypeId="1" CreationDate="2012-12-17T09:59:27.970" Score="3" ViewCount="78" Body="&lt;p&gt;Is there a term which can quantify how 'spread out' a particular character is on a tree? I want to distinguish between a character which is only restricted to a particular clade vs. a character that occurs all over the tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ETA: by 'all over' I meant it may be restricted to a few branches but those branches are spread out over the tree. It need not be ubiquitous. e.g. the character marked in blue on  compared with the case where these three branches are in a small clade.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MLvwF.gif&quot; alt=&quot;http://www.enchantedlearning.com/pgifs/Polyphyletic.GIF&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1789" LastEditorUserId="3632" LastEditDate="2013-01-24T14:06:43.007" LastActivityDate="2013-01-24T14:06:43.007" Title="Is there a term to quantify how spread a character is on a phylogenetic tree?" Tags="&lt;phylogenetics&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5519" PostTypeId="2" ParentId="5445" CreationDate="2012-12-17T13:45:35.803" Score="5" Body="&lt;p&gt;Cold weather makes your body use more energy for keeping warm and less energy for other activities. This is made at various levels: 1) modifications of the diameter of arteries changes the blood supply in specific regions&#xA;2) In the electron transport chain, that is a metabolic pathway involved in producing energy after glycolis and Krebs cycle there is a disjunction between the electron transport chain and the oxidative phosphorylation caused by the production of thermogenin. This causes a minor production of ATP (energy available for metabolic processes) and dissipation of energy as heat.&#xA;Moreover enzymes need a specific environment to work (ph and temperature). A cold weather can decrease the temperature of the body and reduce enzyme activity. When you are sick your body can use fever to stimulate enzymes and power immunitary system activity.&#xA;Moreover cold weather causes a reduction of the movements of the cilia of the trachea, so dust and bacteria can enter into the respiratory system more easily. These are just a few examples. There may be others. I'm available for further discussion. &lt;/p&gt;&#xA;" OwnerUserId="1790" LastActivityDate="2012-12-17T13:45:35.803" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5520" PostTypeId="2" ParentId="5489" CreationDate="2012-12-17T14:44:24.640" Score="0" Body="&lt;p&gt;Just use a genome database such as &lt;a href=&quot;http://www.ensembl.org/&quot; rel=&quot;nofollow&quot;&gt;Ensembl&lt;/a&gt;. Paste your gene name into the search box and &lt;a href=&quot;http://www.ensembl.org/Multi/Search/Results?species=homo;q=chromosome%2012%20open%20reading%20frame%2052&quot; rel=&quot;nofollow&quot;&gt;hit “Go”&lt;/a&gt;. The &lt;a href=&quot;http://www.ensembl.org/Homo_sapiens/Search/Details?idx=Gene;q=chromosome%2012%20open%20reading%20frame%2052&quot; rel=&quot;nofollow&quot;&gt;first hit&lt;/a&gt; in the result list is what you’re searching for.&lt;/p&gt;&#xA;" OwnerUserId="166" LastActivityDate="2012-12-17T14:44:24.640" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5522" PostTypeId="1" CreationDate="2012-12-17T18:32:43.810" Score="2" ViewCount="380" Body="&lt;p&gt;Instead of using  polymerase Vent  exo (-), can I go with the usual &lt;em&gt;Taq&lt;/em&gt; polymerase? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do the PCR conditions change (the temperature and master mix concentrations ) in the these two conditions? Do the primers (sequence and concentrations) change if we use vent exo instead of &lt;em&gt;Taq&lt;/em&gt; polymerase and vice versa? If the primers are designed specifically for Vent exo (-) how can I modify the PCR conditions so that I can use the same primers (meant for vent exo) using &lt;em&gt;Taq&lt;/em&gt; polymerase?&lt;/p&gt;&#xA;" OwnerUserId="1792" LastEditorUserId="57" LastEditDate="2012-12-18T00:14:53.623" LastActivityDate="2012-12-18T14:55:46.657" Title="Can Taq polymerase be used instead of polymerase Vent exo (-)?" Tags="&lt;molecular-biology&gt;&lt;pcr&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5523" PostTypeId="2" ParentId="5518" CreationDate="2012-12-17T19:11:10.357" Score="3" Body="&lt;p&gt;I agree with Terdon's terminology in the comment (&quot;ubiquitous&quot; or &quot;widespread&quot;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can use clade-specific or species-specific for a restricted character.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the characters that appear in all species of a branch and in a quantitative way you can also provide the estimated age of the last common ancestor to the branch featuring that character. This tool might help you: &lt;a href=&quot;http://www.timetree.org/&quot; rel=&quot;nofollow&quot;&gt;http://www.timetree.org/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1739" LastEditorUserId="57" LastEditDate="2012-12-18T00:17:11.317" LastActivityDate="2012-12-18T00:17:11.317" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5524" PostTypeId="1" AcceptedAnswerId="5526" CreationDate="2012-12-18T00:58:48.307" Score="27" ViewCount="55561" Body="&lt;p&gt;Imagine humans were to colonize a distant planet and it was a single one-way trip. How many people would they need to bring?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously 2 is the minimum, but that would result in a lot of inbreeding.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what number is the minimum number of people you can have in an isolated community and still maintain a healthy diversity?&lt;/p&gt;&#xA;" OwnerUserId="1480" LastActivityDate="2020-12-27T19:55:16.223" Title="How many people are required to maintain genetic diversity?" Tags="&lt;genetics&gt;&lt;human-genetics&gt;" AnswerCount="5" CommentCount="3" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5525" PostTypeId="2" ParentId="5522" CreationDate="2012-12-18T11:39:03.750" Score="2" Body="&lt;p&gt;I haven't done ARMS PCR myself, so my answer is based on theory and there might be other practical factors I overlooked.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The characteristic feature of the &lt;a href=&quot;http://www.neb.com/nebecomm/products/productm0257.asp&quot; rel=&quot;nofollow&quot;&gt;Vent exo(-) polymerase&lt;/a&gt; is the lack of exonuclease activity compared to the regular Vent polymerase. ARMS uses the fact that a mismatch at the 3' position prevents primer extension. For this to work it is important to use a polymerase without exonuclease activity, as such a polymerase could &quot;repair&quot; the mismatch and the whole method would not work. &lt;a href=&quot;http://www.neb.com/nebecomm/products/productm0273.asp&quot; rel=&quot;nofollow&quot;&gt;Taq polymerase&lt;/a&gt; also doesn't have any exonuclease activity, so in theory you should be able to use it for this experiment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The primers don't have to be changed for different polymerases, the polymerase buffer though is different and I wouldn't recommend using the wrong one.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2012-12-18T11:39:03.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5526" PostTypeId="2" ParentId="5524" CreationDate="2012-12-18T12:13:29.543" Score="25" Body="&lt;p&gt;Actually it is a very important question for laboratory animals (and, I imagine, endangered species) and was calculated to be 25 couples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With any number of animals (including humans), there is always some inbreeding happening, but you can reduce it with the number of breeding pairs and careful pairing. When you get to 25 pairs (50 animals) and have complete control over pairing, you can sustain the genetic diversity practically infinitely (especially if you take into account spontaneous mutations).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, such control over who can have children with who (plus whether one is at all allowed to procreate and what will be the sex of their children!) would be questionable morally, so in case of populating a distant planet, we would need a larger group, to provide for sexual preferences, fertility problems etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://isogenic.info/html/outbred_stocks.html#definition&quot;&gt;Some information on laboratory outbred stocks.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1427" LastEditorUserId="6" LastEditDate="2012-12-18T13:07:52.767" LastActivityDate="2012-12-18T13:07:52.767" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5528" PostTypeId="1" CreationDate="2012-12-18T19:07:29.187" Score="8" ViewCount="115" Body="&lt;p&gt;&lt;a href=&quot;http://www.nytimes.com/2009/12/15/health/15real.html&quot;&gt;http://www.nytimes.com/2009/12/15/health/15real.html&lt;/a&gt; seems to indicate for a surface, to serve as a medium, the following properties are relevant &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;animation &lt;/li&gt;&#xA;&lt;li&gt;humidity  &lt;/li&gt;&#xA;&lt;li&gt;temperature&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The article however does not elaborate on the properties a surface &lt;em&gt;must&lt;/em&gt; possess to serve as a medium - albeit i would figure it may vary from one virus/bacterium to another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same article also states &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;... when objects in a hotel room — light switches, telephones — were contaminated &#xA;with a  cold virus, 60 percent of healthy volunteers picked up the virus when they &#xA;touched one of the objects an hour later. Eighteen hours later, the transmission rate &#xA;was cut in half.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;When currency changes hands we rarely ever know whether it may , within a reasonable timespan, have passed through an agent/carrier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sir Dumpty loves to sneak off with a currency note to get me to chase him. He is protected; another member of his species may not be so protected. For that matter a person infected with, say, the common cold virus may have passed a note/coin/card to the vendor at the store within a minute of sneezing/coughing into his/her hand. What if the same person , instead, suffered from TB?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So ... can currency serve as a medium for transmission of pathogens?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2012-12-19T06:10:09.420" LastActivityDate="2016-06-07T10:01:05.460" Title="Can paper/plastic currency serve as a medium for pathogens?" Tags="&lt;pathology&gt;&lt;medium&gt;" AnswerCount="2" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5529" PostTypeId="1" AcceptedAnswerId="5530" CreationDate="2012-12-18T19:52:05.360" Score="15" ViewCount="915" Body="&lt;p&gt;I am confused, can evolution ( speciation ) really occur in such a short time ?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In 1971, biologists moved five adult pairs of Italian wall lizards from their home island of Pod Kopiste, in the South Adriatic Sea, to the neighboring island of Pod Mrcaru. Now, an international team of researchers has shown that introducing these small, green-backed lizards, &lt;em&gt;Podarcis sicula&lt;/em&gt;, to a new environment caused them to undergo rapid and large-scale evolutionary changes.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here is a &lt;a href=&quot;http://www.youtube.com/watch?v=G7SOPD8cG_M&quot; rel=&quot;nofollow noreferrer&quot;&gt;short video&lt;/a&gt; featuring the scientist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two related articles:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedaily.com/releases/2008/04/080417112433.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.sciencedaily.com/releases/2008/04/080417112433.htm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://news.nationalgeographic.com/news/2008/04/080421-lizard-evolution.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://news.nationalgeographic.com/news/2008/04/080421-lizard-evolution.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt; I asked a similar question previously about two people having 44 chromosomes and their possibility of creating a new species. You might like to read/answer that as well:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/1051/can-two-humans-with-44-chromosomes-produce-viable-offspring&quot;&gt;Can two humans with 44 chromosomes produce viable offspring?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="504" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-01-04T09:03:10.367" Title="Evolution in 37 years, is it possible?" Tags="&lt;evolution&gt;&lt;speciation&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5530" PostTypeId="2" ParentId="5529" CreationDate="2012-12-18T20:35:40.010" Score="17" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I am confused, can evolution ( speciation ) really occur in such a short time?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, &lt;strong&gt;Evolution&lt;/strong&gt; and &lt;em&gt;Speciation&lt;/em&gt; are not the same. &lt;strong&gt;Evolution&lt;/strong&gt; is the adaptation of an existing species to an environment over generations. &lt;em&gt;Speciation&lt;/em&gt; is the development of a new species, and the definition of &quot;species&quot; can vary depending on who you talk to - but a very commonly accepted one is that two individuals cannot produce fertile offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the answer is still &lt;strong&gt;&lt;em&gt;Yes&lt;/em&gt;&lt;/strong&gt;. Evolution can occur in as little as &lt;strong&gt;two&lt;/strong&gt; generations because that's all the time it takes for a change in the DNA to be exhibited in the newest generation. For instance, &lt;a href=&quot;http://en.wikipedia.org/wiki/Lactase_persistence&quot;&gt;Lactase Persistence&lt;/a&gt; - which allows the bearers to ingest dairy products without digestive stress into adulthood - has evolved at least twice in humans in separate groups. Both are the result of either one or two point mutations (single changes in a Nucleotide within the DNA). The result is that at one point in time for each appearance of lactase persistence, a child was born that could drink milk into adulthood while their parents and cousins could not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is evolution; the child was better adapted to the resources available, and because lactase persistence either...&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Provided a significant advantage over their kin in the environment (which is likely, as being able to digest milk in an agrarian society opens up a new source of energy)...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;or&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Didn't hinder the child's ability to grow and produce fertile offspring of their own...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;...it has persisted in the populations where it initially evolved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Speciation&lt;/em&gt; is a little trickier, but that's because there isn't a known qualitative way to differentiate species at the genetic level quite yet. It could be a few key gene changes, it could be a whole genome difference of 10%, or a million other factors. Practically speaking, though, &lt;em&gt;Speciation&lt;/em&gt; is simply the result of accumulated genome changes that at some point prevent the members of one group from producing fertile offspring with their ancestral group. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because we simply don't know &lt;em&gt;how much&lt;/em&gt; of or &lt;em&gt;where&lt;/em&gt; the genome has to change, it's certainly possible that speciation could occur in the same time period as it takes to evolve: &lt;strong&gt;Two generations&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since I'm doubting the wall lizards have a generational time of &gt;37 years (don't mistake it for lifespan, humans can reproduce in our teens - even if we live into our 80's), it's definitely possible that the wall lizards could evolve (and &lt;em&gt;potentially&lt;/em&gt; speciate) in such a short amount of time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With organisms that have a very, very short generational time - like E. coli or other bacteria - you can observe the Evolution of populations in days or hours.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2012-12-19T00:04:43.237" LastActivityDate="2012-12-19T00:04:43.237" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="5531" PostTypeId="1" AcceptedAnswerId="5544" CreationDate="2012-12-18T23:35:01.817" Score="2" ViewCount="143" Body="&lt;p&gt;Plants produce lots of compounds that inhibit (kill or irritate) microorganisms and insects.  They have defenses against plant viruses and infections.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What kinds of compounds or hormones to plants use to regulate the growth of other nearby plants?  I have hear of ethylene, but I would like to hear about more specific compounds that might be known that work against specific species or kinds of plants?&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1320" LastEditDate="2012-12-20T09:15:58.843" LastActivityDate="2013-07-05T17:51:03.127" Title="Do plant-plant interactions inhibit growth?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5532" PostTypeId="1" CreationDate="2012-12-19T08:50:20.107" Score="2" ViewCount="258" Body="&lt;p&gt;Just a pure curiosity: Does there exist a creature with an orthogonal view to the world instead of perspective? What would be an optical explanation for possibility/impossibility?&lt;/p&gt;&#xA;" OwnerDisplayName="Developer" LastActivityDate="2012-12-21T18:56:45.320" Title="Possibility of orthogonal view for a creature?" Tags="&lt;vision&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5533" PostTypeId="2" ParentId="5532" CreationDate="2012-12-19T10:47:47.180" Score="2" Body="&lt;p&gt;Many creatures have eyes on the sides of their head where they cannot have both eyes simultaneously look at the same target. For example whales. Chameleons are well known for having independently moving eyes (though they can align them for binocular vision)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/licns.jpg&quot; alt=&quot;Chameleon with eyes pointing akimbo&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since all the significant processing of vision occurs in the brain's occipital lobes there is no problem with optics.&lt;/p&gt;&#xA;" OwnerUserId="1642" OwnerDisplayName="RedGrittyBrick" LastActivityDate="2012-12-19T10:47:47.180" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5534" PostTypeId="2" ParentId="5529" CreationDate="2012-12-19T11:29:07.550" Score="8" Body="&lt;p&gt;&lt;strong&gt;Evolution can occur in just one full generation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Strong selection will rapidly reduce the gene frequencies of genes which cause negatively selected phenotypes. This reduces the likelihood of unfavourable genotypes occurring in the next generation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;(I regard generation here as the complete cycle of one individual being born to the point at which they successfully give birth/sire young).&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Population genetics explanation:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine a population in which LOC1 is a locus affecting a phenotypic marker allowing perfect identification of genotype at that locus. There are two alleles at LOC1, &lt;strong&gt;A&lt;/strong&gt; and &lt;strong&gt;a&lt;/strong&gt;. This gives rise to three different genotypes, &lt;strong&gt;AA, Aa&lt;/strong&gt; and &lt;strong&gt;aa&lt;/strong&gt;  which occur in the population in equal proportions. Those individuals with AA exhibit a certain trait, whilst Aa and aa individuals do not. If only the AA genotypes are allowed to mate then the following generation will only contain AA genotypes at LOC1 (assuming no mutation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more population genetics read &lt;a href=&quot;http://www.sinauer.com/detail.php?id=3082&quot; rel=&quot;nofollow&quot;&gt;Principles of Population Genetics&lt;/a&gt; and then &lt;a href=&quot;http://www.amazon.co.uk/Introduction-Quantitative-Genetics-Douglas-Falconer/dp/0582243025&quot; rel=&quot;nofollow&quot;&gt;Introduction to Quantitative Genetics.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Genetic drift caused by using 5 Pairs&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The new population was started with just 5 pairs of individuals. This means there is huge potential for fixation of alleles via drift with in the very first generation. I ran a (basic) &lt;a href=&quot;http://orgmode.org/worg/org-contrib/babel/examples/drift.html&quot; rel=&quot;nofollow&quot;&gt;genetic drift simulation&lt;/a&gt; in R just now. Out of 5000 replicates 4709 went to fixation (Single locus, two alleles, using 30 generations of 10 individuals).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Environmental change can cause hidden genetic variation to be exhibited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Molecular regulators which affect the expression of traits can respond differently depending on environmental influences. This point is summarized nicely by the opening lines of &lt;a href=&quot;http://service004.hpc.ncsu.edu/toxicology/websites/journalclub/linked_files/spring_06/Cowen_and_Lindquist_2005.pdf&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;- thanks to @leonardo for this point.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hsp90 is a molecular chaperone for many signal transducers and may&#xA;  influence evolution by releasing previously silent genetic variation&#xA;  in response to environmental change. In fungi separated by 800&#xA;  million years of evolution, Hsp90 potentiated the evolution of drug&#xA;  resistance in a different way, by enabling new mutations to have&#xA;  immediate phenotypic consequences.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Evolution and speciation are different things&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are just the simple wikipedia definitions, for better ones then consult the literature:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Evolution is the change in the inherited characteristics of biological&#xA;  populations over successive generations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For a good thorough introductory text on evolution I recommend &lt;a href=&quot;http://www.google.co.uk/products/catalog?q=ridley%20evolution&amp;amp;hl=en&amp;amp;safe=off&amp;amp;bav=on.2,or.r_gc.r_pw.r_cp.r_qf.&amp;amp;bvm=bv.1355534169,d.bGE&amp;amp;bpcl=40096503&amp;amp;biw=1280&amp;amp;bih=639&amp;amp;um=1&amp;amp;ie=UTF-8&amp;amp;cid=4423978030755146065&amp;amp;sa=X&amp;amp;ei=h5HXUOyFJ6T14QSMhYHoCw&amp;amp;ved=0CEwQ8wIwAA&quot; rel=&quot;nofollow&quot;&gt;Evolution&lt;/a&gt; by Mark Ridley (not to be confused with Matt Ridley - popular evolution science writer).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Speciation is the evolutionary process by which new biological species arise.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Speciation, thanks to a long fought debate over species concepts, is also an ambiguous process. What some species concepts would define as two distinct species, another would call one species, and another may call them 10 species! Seemingly everyone who specializes in the study of speciation would have there own twist on a species concept so don't expect that argument to resolve any time soon! It's not advanced much since Dobzhansky wrote &lt;a href=&quot;http://www.jstor.org/discover/10.2307/184528?uid=3738984&amp;amp;uid=2&amp;amp;uid=4&amp;amp;sid=21101588520797&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The species concept is one of the oldest and most fundamental in&#xA;  biology. And yet it is almost universally conceded that no&#xA;  satisfactory definition of what constitutes a species has ever been&#xA;  proposed.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;When does evolution occur? and when is change not evolution in such a short time?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've put this bit in because what I find is a strange, but common, question people ask is &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;species X has changed/adapted to novel selection very rapidly, has&#xA;  evolution really occurred?&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The way people ask this makes it sound like they want a certain amount of evolution to occur before we can say something has evolved. To me saying evolution has occurred means that some change has occurred, via any of the mechanisms of evolution, which results in one subset of individuals being different from another it is compared to (spatially or temporally separated). You could ask if such strong evolution can really occur over a short time period, but the answer is obvious - yes it can. If it has occurred then why do you think it is exceptional? what is your alternative explanation for the differences seen?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-01-04T09:03:10.367" LastActivityDate="2013-01-04T09:03:10.367" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5535" PostTypeId="1" AcceptedAnswerId="6971" CreationDate="2012-12-19T18:26:32.963" Score="6" ViewCount="1104" Body="&lt;p&gt;I'm looking for a graph or a curve that would show the &lt;strong&gt;typical concentration of melatonin in blood or saliva for humans over 24 hours&lt;/strong&gt;. It would be good to know the photoperiod for the same human as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that melatonin release is inhibited by blue light, perceived through the retina, with melanopsin being the photopigment that signals suprachiasmic nucleus to suppress melatonin release. This is why it would be great to see melatonin data alongside light exposure data. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for any hints on where I can find such information!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-01-30T02:09:34.390" Title="Is there a normal human melatonin concentration to light level curve?" Tags="&lt;human-biology&gt;&lt;sleep&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5536" PostTypeId="1" AcceptedAnswerId="5539" CreationDate="2012-12-19T20:29:36.370" Score="7" ViewCount="599" Body="&lt;p&gt;When you get sick, you generally don't contract enough bacteria at once for them to succeed in battling your immune system, right?  Their numbers must gradually increase in the host's body before they know that they can attack.  How does that work?&lt;/p&gt;&#xA;" OwnerUserId="1249" LastEditorUserId="22057" LastEditDate="2016-05-23T13:43:22.103" LastActivityDate="2016-05-23T13:43:22.103" Title="How do infectious bacteria determine when their numbers are high enough to attack a host?" Tags="&lt;immunology&gt;&lt;bacteriology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5537" PostTypeId="1" AcceptedAnswerId="5542" CreationDate="2012-12-19T20:35:50.443" Score="3" ViewCount="1319" Body="&lt;p&gt;I have recently peformed an ELISA (Enzyme-linked immunosorbent assay), but I still have some questions, let me first outline what I did:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;We had a number (20) of tubes containing fake 'bodily fluids' , namely saliva. One of these tubes contained the Epstein-Barr virus, which on its turn causes Pfeiffer's disease, aka the 'kissing disease' (so we basically conducted an experiment to see how fast the virus would spread within a class if everybody started kissing each other, if you don't mind the crudity).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Everybody mixed their saliva with the saliva of 3 other people, so at the end everybody had a tube with the saliva of 4 different people in it.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Since we worked in pairs of 2, every duo got a microtiter plate with 12 wells in it: 3 wells for a positive control, 3 wells for a negative control, 3 wells for the fluids of 1 of the duo and 3 wells for the fluids of the other one. You pippete in (is that correct?) the fluids accordingly. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;After a while you rinse and clean the wells with wash buffer.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Then you pippete in the primary antibody in each well.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;After a while you rinse and clean the wells with wash buffer.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Following this you pippete in the secondary antibody (conjugated with the enzyme HRP).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;After a while you rinse and clean the wells with wash buffer.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Finally, you add the enzyme substrate (TMB) to each well. This causes a blue color if when in contact with HRP. The positive controls must come out blue, the negative must come out colorless, and the other wells can go either way, depending if you have the virus.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I hope this is not to crudely explained, again. These are my questions concerning the experiment:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;What do the components of the acronym 'ELISA' actually stand for? Does immunosorbent refer to the binding of the antigens to the wells? My English isn't too good, and these acronyms and abbreviations often seem foreign to me (nevermind that they are foreign since I'm not English, you get the point I hope). &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When you pippete in the saliva in the wells, what actually sticks to the wells? All of the antigens in your saliva? Because it's hard to believe that they make special microtiter plates for every single antigen seperately. I assume it is only the antigens, since the primary antibodies attach to the antigens only, so there is no need for the microtiter plate itself to bind to antibodies. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How would we get the primary and secondary antibody? This is my assumption: The primary antibody we get is by injecting some antigens of the Epstein-Barr Virus into a human and then taking a serum. The secondary antibody could be gotten by injecting a random human primary antibody into ANY animal, irrelevant which anyimal, and then taking a serum. After that you conjugate an enzyme to the secondary antibody. Is this correct?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1609" LastEditorUserId="1609" LastEditDate="2012-12-19T21:25:46.480" LastActivityDate="2012-12-20T12:17:50.380" Title="Questions regarding ELISA" Tags="&lt;enzymes&gt;&lt;experimental&gt;&lt;antibody&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5538" PostTypeId="2" ParentId="5536" CreationDate="2012-12-19T20:59:15.737" Score="9" Body="&lt;p&gt;Infectious agents like bacteria, viruses, fungi, etc., don't &lt;em&gt;know&lt;/em&gt; when to &quot;attack&quot; or produce pathogenic substances, they just do it under their preferred conditions, and your body's immune system either succeeds in fighting them off immediately, or it doesn't and you get sick. Your body is constantly confronting and clearing potentially dangerous microorganisms without your ever being aware of it. Every breath of air, mouthful of food, or contact with your mucus membranes is a possible infection, if not for your &lt;a href=&quot;http://en.wikipedia.org/wiki/Innate_immune_system&quot; rel=&quot;nofollow&quot;&gt;innate immune system&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, sometimes pathogens get past the first line of defense, or are otherwise able to evade it, and in the time it takes for the &lt;a href=&quot;http://en.wikipedia.org/wiki/Adaptive_immune_system&quot; rel=&quot;nofollow&quot;&gt;adaptive immune system&lt;/a&gt; to engage they are building up their numbers and gradually getting to the point where you realize that you are sick or otherwise infected. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, many of the symptoms of sickness you often feel - being tired, feeling sore, having a fever or localized redness/inflammation - are actually caused by some of the effector chemicals or &lt;a href=&quot;http://en.wikipedia.org/wiki/Cytokine&quot; rel=&quot;nofollow&quot;&gt;cytokines&lt;/a&gt; released by your own immune system, and not by the infective agents themselves. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipopolysaccharide&quot; rel=&quot;nofollow&quot;&gt;lipopolysaccharide&lt;/a&gt; or LPS is a major component of the cell wall of &lt;a href=&quot;http://en.wikipedia.org/wiki/Gram-negative_bacteria&quot; rel=&quot;nofollow&quot;&gt;Gram-negative&lt;/a&gt; bacteria, including such pathogenic species as &lt;a href=&quot;http://en.wikipedia.org/wiki/Escherichia_coli&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;E. coli&lt;/em&gt;&lt;/a&gt; (food poisoning, urinary tract infections), &lt;em&gt;Neisseria&lt;/em&gt; species (&lt;a href=&quot;http://en.wikipedia.org/wiki/Neisseria_meningitidis&quot; rel=&quot;nofollow&quot;&gt;bacterial meningitis&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Neisseria_gonorrhoeae&quot; rel=&quot;nofollow&quot;&gt;gonorrhea&lt;/a&gt;), &lt;a href=&quot;http://en.wikipedia.org/wiki/Helicobacter_pylori&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;H. pylori&lt;/em&gt;&lt;/a&gt; (stomach ulcers), and &lt;em&gt;Salmonella&lt;/em&gt; species (&lt;a href=&quot;http://en.wikipedia.org/wiki/Salmonella#Enteritis_salmonellosis_or_food_poisoning_Salmonella&quot; rel=&quot;nofollow&quot;&gt;food poisoning&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Typhoid&quot; rel=&quot;nofollow&quot;&gt;typhoid fever&lt;/a&gt;). LPS on its own does not cause fever or inflammation, for example, but when bound by certain immune cells (&lt;a href=&quot;http://en.wikipedia.org/wiki/B_cell&quot; rel=&quot;nofollow&quot;&gt;B-cells&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Macrophage&quot; rel=&quot;nofollow&quot;&gt;macrophages&lt;/a&gt;, mostly) it rapidly and overwhelmingly promotes the generation and release of pro-inflammatory cytokines like &lt;a href=&quot;http://en.wikipedia.org/wiki/TNF-alpha&quot; rel=&quot;nofollow&quot;&gt;TNFα&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/IL-1beta&quot; rel=&quot;nofollow&quot;&gt;IL-1β&lt;/a&gt;. These proteins then act on target tissues to allow the &lt;a href=&quot;http://en.wikipedia.org/wiki/Inflammation&quot; rel=&quot;nofollow&quot;&gt;inflammatory response&lt;/a&gt; - swelling, pain, increased temperature, redness, etc. - and recruit immune cells to fight whatever invaders must be there.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2013-05-31T19:01:49.480" LastActivityDate="2013-05-31T19:01:49.480" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5539" PostTypeId="2" ParentId="5536" CreationDate="2012-12-20T00:32:20.900" Score="12" Body="&lt;p&gt;I think the current answer to this for bacterial infections is &lt;a href=&quot;http://en.wikipedia.org/wiki/Quorum_sensing&quot;&gt;quorum sensing&lt;/a&gt;.  Quorum sensing is a signalling pathway in bacteria which senses a molecule that the bacteria themselves secrete.  When the concentration of the quorum signal reaches a certain level, the bacteria interpret this as their population density reaching some threshhold.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria are always around - even infectious Staph, as described in the other answer, the bacteria are always being cleared out by the immune system, but when they find the right place where they can get critical mass, they dig in, form a biofilm and secrete toxins, which can help them divide more successfully.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a description of the process from a &lt;a href=&quot;http://www.jci.org/articles/view/20442&quot;&gt;paper on Staph infection&lt;/a&gt;, a common bacterial infection in humans.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;S. epidermidis is considered part of the of the normal human microbial flora, while S. aureus is usually regarded as a transient member. Colonization by either species usually does not lead to adverse events. However, when these organisms or their extracellular products are allowed to breach the epithelial layer, serious disease can result (1). S. aureus has many cell surface virulence factors (such as protein A and clumping factor) and secreted exotoxins and enzymes that allow strains to cause a myriad of infections. These diseases range from relatively benign furuncles and subcutaneous abscesses to scalded skin syndrome, sepsis, necrotizing pneumonia, and toxic shock syndrome (TSS). While no single cell surface virulence factor has been shown to be uniquely required for mucous membrane attachment, once colonization occurs, numerous secreted exotoxins, including the pyrogenic toxin superantigens and exfoliative toxins, definitively cause serious human disease. Other secreted exotoxins, such as the four hemolysins (α, β, δ, and γ) and Panton-Valentine leukocidin have also been suggested to contribute to significant illnesses. S. epidermidis does not possess the array of extracellular toxins that S. aureus does, and its primary virulence factor is considered to be its ability to form biofilms.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;To improve their ability to cause this variety of human disease and to occupy numerous niches within the host, staphylococci have developed quorum-sensing systems that enable cell-to-cell communication and regulation of numerous colonization and virulence factors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Viruses are typically simpler - as @MattDMo describes. They seem to rely on finding an environment where they can infect more cells at such a rate greater than the immune system can clear them out.  For influenza, this is more of a 'shock and awe' offense where they infect and multiply quickly, trying to outpace the immune system.  Another virus like HIV will actually multiply so slowly that the immune system can't find the host cells, allowing HIV to slowly spread over the host cell population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a bonus topic... When they were looking a cholera in the 1990s they found that V cholerae bacteria actually t&lt;a href=&quot;http://microbiology.ucsf.edu/micro/pathogenesis/course/05%20Lectures/MPDisc_0506_Waldor.pdf&quot;&gt;ake up phage with toxins in them that convert benign bacteria to virulent ones&lt;/a&gt; (that cause dysenteric cholera).  They do this by conveying both the pili that attach to human cells and the toxin that causes the violent G.I. reaction of dysentery.  I think this is not unusual for bacterial diseases.  (the reference is Science 272, 1910-14 BTW). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has lead to a suspicion that bacteria might be even &lt;a href=&quot;http://www.sciencedaily.com/releases/2012/12/121220195237.htm?utm_source=feedburner&amp;amp;utm_medium=feed&amp;amp;utm_campaign=Feed%3a%20sciencedaily/plants_animals%20%28ScienceDaily%3a%20Plants%20&amp;amp;%20Animals%20News%29&amp;amp;utm_content=My%20Yahoo&quot;&gt;adapting to infectious phenotypes through genomic changes&lt;/a&gt;.  This study had sequenced the genome of C difficile from 486 patients and found that relatively few of them really were capable of patient to patient infection:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The results of the study indicated that, although transmission between patients is likely to occur, it actually happens at relatively low frequency. In particular, concerns that healthcare teams were spreading infection between different hospitals seem to be misplaced. One exception to this general finding is that there were a large number of cases of infection from one particular strain that does appear to have been due to patient-to-patient transmission, emphasising the epidemic nature of this lineage. Notably, this strain has declined in UK hospitals in the last five years.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2012-12-23T00:37:08.283" LastActivityDate="2012-12-23T00:37:08.283" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5540" PostTypeId="1" AcceptedAnswerId="5549" CreationDate="2012-12-20T01:47:59.640" Score="2" ViewCount="89" Body="&lt;p&gt;An animal will stop foraging in a berry bush if the perceived cost of searching for berries remaining is greater than the cost of finding another bush which isn't as picked over. People do the same thing on websites. We'll stay on a website searching for our information berry if we feel it costs less than jumping to another website bush.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we had significant resources such that the cost of predatory/foraging behavior out-weighed the energy benefit from gaining more resources, would we stop? There seems to be a biological and cultural drive to keep getting more stuff. As people, could we ever reach a point where we're satisfied? The logic says yes, but common sense says we're hardwired to feel compelled to never stop gathering resources.&lt;/p&gt;&#xA;" OwnerUserId="1802" LastEditorUserId="1802" LastEditDate="2012-12-21T18:19:15.283" LastActivityDate="2012-12-21T18:19:15.283" Title="Are humans hardwired to continue gathering resources after the costs outweigh the benefits?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5541" PostTypeId="2" ParentId="5528" CreationDate="2012-12-20T03:02:16.667" Score="4" Body="&lt;p&gt;TB is an extremely poor example, because as has been mentioned, it usually requires prolonged contact.&lt;/p&gt;&#xA;&lt;p&gt;But lets go with something with a low required infectious dose, that's friendly to surface contamination, and persists in the environment: Norovirus.&lt;/p&gt;&#xA;&lt;p&gt;Can norovirus serve as a medium for pathogens? Absolutely. To be blunt, almost anything will serve as a medium for the right pathogen with some level of efficacy. This is a presentation from the &lt;a href=&quot;http://www.newyorkfed.org/newsevents/events/banking/2011/Currency_Health_Safety_Concerns.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;New York Federal Reserve&lt;/a&gt; on what contaminates money, but given the outlandish things that can be contaminated with infectious material, there's no reason to suspect money isn't among them.&lt;/p&gt;&#xA;&lt;p&gt;Wash your hands.&lt;/p&gt;&#xA;" OwnerUserId="67" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-12-20T03:02:16.667" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5542" PostTypeId="2" ParentId="5537" CreationDate="2012-12-20T09:12:43.247" Score="3" Body="&lt;p&gt;ELISA is Enzyme-Linked ImmunoSorbent Assay (capitalisation to point out source of acronym).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read about the various ways to do an ELISA &lt;a href=&quot;http://en.wikipedia.org/wiki/ELISA#Sandwich_ELISA&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your case this was probably an indirect ELISA. All ELISA techniques make use of the fact that proteins stick to plastic. In your case the protein components of the saliva, including the virus (the viral coat is proteinaceous) will stick to the wells. After rinsing out the sample the wells are treated with another protein (usually bovine serum albumin (BSA)) to completely block all available protein binding sites. At this stage these wells will no longer bind protein non-specifically, but will bind anti-EBV Ig because of the presence of the EBV particles bound to the plastic. This bound anti-EBV can then be detected with a secondary antibody. The protein complexes will build as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;plastic/EBV/rabbit anti-EBV/goat anti-rabbit IgG-HRP conjugate&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would also be possible to do this experiment as a sandwich ELISA. In this format the wells would have been pretreated with anti-EBV serum (or purified anti-EBV IgG) then blocked with BSA. At this stage these wells will no longer bind protein non-specifically, but will bind EBV because of the presence of the EBV-specific antibody. Once samples have been incubated in these wells (so that any EBV can bind to the antibody coating the wells) another antibody (raised in a different animal) is added, and this will bind to the EBV that has been captured by the original antibody that coats the wells. This latter antibody is then detected with a conjugate. The protein complexes will build as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;plastic/mouse anti-EBV/EBV/rabbit anti-EBV/goat anti-rabbit IgG-HRP conjugate&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your description of how to get the antibodies is basically correct, except that the primary antibody will probably have been raised in rabbits or mice, and certainly not in humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Added later:&lt;/strong&gt; I didn't read the first question carefully enough. An ELISA is an &lt;em&gt;assay&lt;/em&gt; because it measures something. It is based on a binding reaction mediated by an antibody-antigen interaction (&lt;em&gt;immunosorbent&lt;/em&gt;). It is &lt;em&gt;enzyme-linked&lt;/em&gt; because the secondary antibody is present as an antibody-enzyme conjugate. It is the amount of this conjugate that remains bound at the final step which is what is measured - the assay is set up so that the amount of this enzyme is a measure of the amount of the original molecule that is being assayed.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2012-12-20T12:17:50.380" LastActivityDate="2012-12-20T12:17:50.380" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5543" PostTypeId="1" CreationDate="2012-12-20T09:17:18.717" Score="-2" ViewCount="126" Body="&lt;p&gt;I like the development of biology.stackexchange.com, but it is still in an early stage and far from perfection. While we develop it further, could you guys help me finding places to ask questions related to health and biochemistry in general?&lt;/p&gt;&#xA;" OwnerUserId="1804" LastActivityDate="2012-12-20T09:30:44.840" Title="Good place to ask health based questions?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2012-12-20T14:06:44.390" ContentLicense="CC BY-SA 3.0" />
  <row Id="5544" PostTypeId="2" ParentId="5531" CreationDate="2012-12-20T09:28:54.240" Score="3" Body="&lt;p&gt;The phenomenon you are asking about is allelopathy.&lt;/p&gt;&#xA;&lt;p&gt;Remarkably, it has its own journal - Allelopathy Journal (ISSN:&#xA;0971-4693) published since 2009 and currently at volume 30, issue 1.&lt;/p&gt;&#xA;&lt;p&gt;Here are the titles of the papers from the most recent issue:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In-vitro assessment of allelopathic effects of wheat on potato.&lt;/p&gt;&#xA;&lt;p&gt;Allelopathic effects of sunflower on seed germination and seedling growth of &lt;em&gt;Trianthema portulacastrum&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Effects of simulated acid rain on the allelopathic potential of invasive weed &lt;em&gt;Wedelia trilobata&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Allelopathic effects of &lt;em&gt;Brachiaria ruziziensis&lt;/em&gt; and aconitic acid on &lt;em&gt;Ipomoea triloba&lt;/em&gt; weed.&lt;/p&gt;&#xA;&lt;p&gt;Effects of &lt;em&gt;Butia capitata&lt;/em&gt; pyrenes extracts on the germination of lettuce seeds.&lt;/p&gt;&#xA;&lt;p&gt;Effects of root exudates from crop plants on the growth of &lt;em&gt;Fusarium oxysporum f.sp. niveum&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So, if you have specific questions, this might be the place to look.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-12-20T09:28:54.240" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5545" PostTypeId="2" ParentId="5543" CreationDate="2012-12-20T09:30:44.840" Score="2" Body="&lt;p&gt;Health: &lt;a href=&quot;https://biology.stackexchange.com/faq#questions&quot;&gt;ask your doctor&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biochemistry: ask here, there are already &lt;a href=&quot;https://biology.stackexchange.com/questions/tagged/biochemistry&quot;&gt;&gt;100 biochemistry questions&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="112" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2012-12-20T09:30:44.840" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5549" PostTypeId="2" ParentId="5540" CreationDate="2012-12-20T17:27:35.093" Score="2" Body="&lt;p&gt;The answer to your question is very sensitive to the time frame you are interested in.  Assuming the costs and benefits you describe are referring to fitness (i.e., survival and reproduction), then the situation you are describing is one in which a particular behavior has lowered fitness (i.e., costs outweigh benefits). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several possible outcomes in this case.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Evolution. If the behavior is not plastic (i.e., it cannot change in a single individual), the there would be selection pressure against those individuals that exhibit the behavior.  If the behavior is heritable then evolution would cause a reduction in the frequency of the behavior over time.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Lowered Fitness. If you are not interested in evolutionary time scales but the behavior is not plastic, then the outcome would be no change in behavior but a reduction in the survival and reproduction success of individuals with the behavior.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Change in Behavior. If the behavior is plastic (i.e., it can be changed by a single human) and the current situation provides the appropriate information about the state of the behavior, then the behavior will change.  The key here (as with optimal foraging models) is that the appropriate cues have to be present to change the behavior.  Often organisms use proxy cues to trigger behavioral shifts.  For example certain caterpillars use day length to trigger shifts in developmental pathways (diapause vs pupation) when what really matters is temperature.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So the real answer to your question lies in the further questions of whether consumption is plastic (or hardwired as you say) and if it is, whether a situation provides the appropriate cues to indicate that we have acquired enough resources.  Those are rather complex questions that, as far as I know have not been answered definitively in the general sense that your question implies. &lt;/p&gt;&#xA;" OwnerUserId="137" LastActivityDate="2012-12-20T17:27:35.093" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5550" PostTypeId="1" AcceptedAnswerId="5594" CreationDate="2012-12-20T20:00:18.547" Score="3" ViewCount="163" Body="&lt;p&gt;As I just learned, allelopathy is the action by which plants regulate the growth of other nearby plants.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have hear of ethylene is a general signal for growth and fruit ripening in particular, but I would like to hear about more specific compounds or proteins that are known to be allelopathic agents and how specific can they be - lots of plants ignore each other and just grow over each other.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;@AlanBoyd &lt;a href=&quot;https://biology.stackexchange.com/questions/5531/do-plant-plant-interactions-inhibit-growth&quot;&gt;has pointed me to a journal&lt;/a&gt;, but as its not open content, I'm hoping for a next level review of the mechanisms and actors in this topic...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks in advance!&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-01-15T12:11:03.427" Title="What chemical or biochemical agents do plants use to inhibit each other's growth?" Tags="&lt;botany&gt;&lt;allelopathy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5552" PostTypeId="2" ParentId="1830" CreationDate="2012-12-21T01:57:03.890" Score="4" Body="&lt;p&gt;As you accurately stated, N bases in sequence data generally means the software is unable to identify the base. N bases may appear at the beginning of the sequence result for a number of reasons. One reason would be purification of the amplified product before electrophoresis. Salts in the sample or a poor purification could leave excess dyes in the sample and appear as &quot;dye blobs.&quot; Another reason is the software may have started analysis too soon before accurate sequence begins. Typically, quality sequence data begins 30 bases from the primer. N bases at end of the sequence simply could be the end of sequence data as stated earlier. Other reasons include hairpin loops and poly base regions that cause early termination. The best way to determine the cause is to look at the trace data.&lt;/p&gt;&#xA;" OwnerUserId="1808" LastActivityDate="2012-12-21T01:57:03.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5554" PostTypeId="1" AcceptedAnswerId="5581" CreationDate="2012-12-21T05:24:05.557" Score="4" ViewCount="247" Body="&lt;p&gt;I'm reading &lt;a href=&quot;http://en.wikipedia.org/wiki/Light_therapy#Light_boxes&quot; rel=&quot;nofollow&quot;&gt;this Wikipedia article on light therapy &lt;/a&gt; and noticed a peculiar statement:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The production of the hormone melatonin, a sleep regulator, is&#xA;  inhibited by light and permitted by darkness as registered by&#xA;  photosensitive ganglion cells in the retina. &lt;strong&gt;To some degree, the&#xA;  reverse is true for serotonin&lt;/strong&gt;, which has been linked to mood&#xA;  disorders.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If I read this correctly, when melatonin is suppressed, serotonin is released? This makes some sense. &lt;strong&gt;I'm interested if there is any scientific backing to serotonin being affected by light levels.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2012-12-25T16:02:47.060" Title="Are serotonin levels in humans affected by light?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;circadian-rhythms&gt;&lt;neurotransmitter&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5556" PostTypeId="2" ParentId="5532" CreationDate="2012-12-21T18:56:45.320" Score="1" Body="&lt;p&gt;The answer depends on the distance between eyes, and width of the objects you are viewing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The view of a separate object is close to the orthogonal view when the width of the object is equal to the distance between your eyes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence the creature that has variable distance between eyes, and has large maximum distance between eyes, has most possibilities to view objects in orthogonal view. Snail comes to mind when I try to think about animal with variable distance between eyes, but its maximum distance between eyes is not that large. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When object is narrower than distance between eyes, you see it in &quot;anti-panoramic view&quot;. You will see both left and right side of the object, which is impossible both in orthogonal view and in panoramic view.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Speaking about whole 180 degrees wide visble scene (wider for some animals), the answer is No. You cannot view the whole scene without perspective view, unless you have large number of &quot;eyes&quot; (sensors) that are spread over a large plane. There is no such animal, but you can artificially construct such &quot;perceptor plane&quot; using large number of photocameras.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When looking at the objects of width equal to distance between eyes, if your brain can direct eyes such that their viewing axes are parallel, and could integrated two pictures, then it would view perfectly orthogonal view. This is not what our brain normally does, though. But even with non-parallel view axes of eyes, what we eventually see when brain integrates different pictures the result is not par from orthogonal projection.&lt;/p&gt;&#xA;" OwnerUserId="226" LastActivityDate="2012-12-21T18:56:45.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5557" PostTypeId="1" AcceptedAnswerId="5559" CreationDate="2012-12-21T19:31:16.040" Score="2" ViewCount="194" Body="&lt;p&gt;Which enzymes are responsible for the biodegradation of the endogenous opioid peptide, beta-endorphin?&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2012-12-21T20:24:25.523" LastActivityDate="2012-12-21T20:24:25.523" Title="Which Enzymes are Responsible for the Biodegradation of Beta-endorphin?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;&lt;neurotransmitter&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5558" PostTypeId="1" CreationDate="2012-12-21T20:00:03.227" Score="5" ViewCount="3281" Body="&lt;p&gt;I read this article by Jeffrey Tomkins and Jerry Bergman claiming to debunk chromosome 2 fusion. Is there anything wrong with these conclusions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot; 1.The reputed fusion site is located in a peri-centric region with suppressed recombination and should exhibit a reasonable degree of tandem telomere motif conservation. Instead, the region is highly degenerate—a notable feature reported by a previous investigation.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;In a 30 kb region surrounding the fusion site, there exists a paucity of intact telomere motifs (forward and reverse) and very few of them are in tandem or in frame.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Telomere motifs, both forward and reverse (TTAGGG and CCTAAA), populate both sides of the purported fusion site. Forward motifs should only be found on the left side of the fusion site and reverse motifs on the right side&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The 798-base core fusion-site sequence is not unique to the purported fusion site, but found throughout the genome with 80% or greater identity internally on nearly every chromosome; indicating that it is some type of ubiquitous higher-order repeat.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;No evidence of synteny with chimp for the purported fusion site was found. The 798-base core fusion-site sequence does not align to its predicted orthologous telomeric regions in the chimp genome on chromsomes 2A and 2B.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Queries against the chimp genome with the human alphoid sequences found at the purported cryptic centromere site on human 2qfus produced no homologous hits using two different algorithms (BLAT and BLASTN).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Alphoid sequences at the putative cryptic centromere site are diverse, form three separate sub-groups in alignment analyses, and do not cluster with known functional human centromeric alphoid elements.&quot;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I've also heard them say that there has to be a fusion in every living thing that evolved or evolution isn't true.  Is that true or not?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article is here&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://creation.com/chromosome-2-fusion-1&quot; rel=&quot;nofollow&quot;&gt;Part one&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://creation.com/chromosome-2-fusion-2&quot; rel=&quot;nofollow&quot;&gt;Part two&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1814" LastEditorUserId="57" LastEditDate="2012-12-22T19:48:44.247" LastActivityDate="2015-10-02T11:05:34.427" Title="Chromosome 2 fusion?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;chromosome&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5559" PostTypeId="2" ParentId="5557" CreationDate="2012-12-21T20:19:50.233" Score="1" Body="&lt;p&gt;As far as I have been able to find out, there isn't a definitive answer to this question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;beta; endorphin is a peptide, and it would seem that there are numerous brain peptidase enzymes that are implicated in the hydrolysis of &amp;beta; endorphin and other peptide neurotransmitters. These include aminopeptidase N, membrane-dipeptidase A, angiotensin-converting enzyme and neutral endopeptidase (also called enkephalinase).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an early (1984) review of this topic see &lt;a href=&quot;http://igitur-archive.library.uu.nl/phar/2007-1214-203632/burbach_84_action%20of%20proteolytic%20enzymes%20on%20lipotropins.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;; there doesn't seem to be a more up-to-date review, but there is quite a bit of literature on the effects of inhibitors of these various enzymes.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-12-21T20:19:50.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5560" PostTypeId="1" CreationDate="2012-12-21T20:28:50.247" Score="2" ViewCount="82" Body="&lt;p&gt;Which enzymes degrade the CB&lt;sub&gt;1&lt;/sub&gt;-specific &lt;em&gt;endogenous cannabinoid&lt;/em&gt; &lt;strong&gt;2-arachidonyl glyceryl ether&lt;/strong&gt;? (Noladin ether)&lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2012-12-22T10:29:07.493" Title="Which Enzymes are Responsible for the Biodegradation of Noladin Ether?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;&lt;neurotransmitter&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5561" PostTypeId="2" ParentId="5560" CreationDate="2012-12-22T10:29:07.493" Score="1" Body="&lt;p&gt;Noladin is an endocannabinoid. The best-characterised members of this family of molecules are Arachidonoylethanolamine (AEA; anandamide) and 2-arachidonoylglycerol (2-AG). The degradation of these endocannabinoids is reviewed in:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pamplona, FA &lt;em&gt;et al&lt;/em&gt;. (2012) Psychopharmacology of the endocannabinoids: far beyond anandamide. Journal of Psychopharmacology 26:7-22&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These endocannabinoids are inactivated via a reuptake system that is present in both neuronal and glial cells, although the protein responsible has apparently not been identified.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AEA is then metabolised to arachidonic acid and ethanolamine by fatty acid amide hydrolase, while 2-AG is converted to arachidonic acid and glycerol by monoacylglycerol lipase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of its ether linkage, noladin cannot be a substrate for either of these enzymes. However the review also describes other possible pathways of endocannabinoid metabolism involving oxidation by cyclooxygenases, lipoxygenases and P450 cytochromes. These are the best candidates for the further metabolism of noladin, but there is apparently no direct evidence for this.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2012-12-22T10:29:07.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5562" PostTypeId="1" AcceptedAnswerId="5658" CreationDate="2012-12-22T16:16:36.717" Score="7" ViewCount="14112" Body="&lt;p&gt;Warm blooded animals like us keep their temperature constant irrespective of their surroundings. But how do they do that? Energy should be supplied from the inside. I assume that reactions like making ATP from glucose are exothermic. That means in winter our body reacts more. Water is absorbed by those reaction.We should need more water in winter. Which is contradictory with our real life experience.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand what prevents cold blooded animals from making heat? Don't they need ATP? Do they use different types of reactions to make energy? Do they have different evolutionary path? They don't seems very different from us.&lt;/p&gt;&#xA;" OwnerUserId="1870" OwnerDisplayName="Kazi arafat Ahmed" LastActivityDate="2014-05-05T21:32:55.100" Title="How do warm-blooded animals keep their temperatures constant?" Tags="&lt;thermodynamics&gt;&lt;biophysics&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5563" PostTypeId="2" ParentId="5562" CreationDate="2012-12-22T17:56:32.533" Score="2" Body="&lt;p&gt;Here answers a part of your question. Warm blood animal burns more food in the winter, so they can keep their body warm. They are not consuming much more ATP in the winter, just a bit more. Usually they have mechanism to reduce the heat loss, like growing hair. How do you know that you need to drink more water? You should know that you area also sweating less in the winter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cold blood animal has a mechanism encoded in their gene to prevent them keep warm in the winter. It is a evolution result so that they dont have to consume much foods and so ATP in the winter. It means that they belong to a different branch of phylogenetic tree thus has a different evolution path.&lt;/p&gt;&#xA;" OwnerUserId="4249" OwnerDisplayName="hwlau" LastActivityDate="2012-12-22T17:56:32.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5564" PostTypeId="1" CreationDate="2012-12-23T04:36:22.340" Score="8" ViewCount="311" Body="&lt;p&gt;The hiv antigens that are used in the oral rapid tests, are they infectious? The tests do not contain any actual virus but I am curious if the antigens themselves could somehow create the virus on their own if they get into the bloodstream? Like do they contain all of the parts needed for replication inside them? (Not the actual virus but the antigen).&lt;/p&gt;&#xA;" OwnerUserId="1820" LastEditorUserId="69" LastEditDate="2013-01-20T11:38:27.120" LastActivityDate="2015-04-08T06:29:59.627" Title="HIV Rapid Tests" Tags="&lt;microbiology&gt;&lt;hiv&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5565" PostTypeId="2" ParentId="5564" CreationDate="2012-12-23T06:30:24.883" Score="12" Body="&lt;p&gt;nope - &lt;a href=&quot;http://en.wikipedia.org/wiki/Diagnosis_of_HIV/AIDS#Antigen_tests&quot;&gt;the test contains antibodies to HIV protein&lt;/a&gt;s, but nothing from HIV itself.  &lt;a href=&quot;http://www.mayoclinic.com/health/hiv-aids/DS00005/DSECTION=tests-and-diagnosis&quot;&gt;The 'antigen test' tests &lt;em&gt;for&lt;/em&gt; antigens, it doesn't itself contain any antigens&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antibodies are proteins that animals (like humans) produce to fight of viral and bacterial infections, they don't come from viruses. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if the test did contain HIV proteins, it could not infect anyone.  You really have to have the HIV RNA, and almost certainly the rest of the virus too,  to cause any infection. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorDisplayName="user560" LastEditDate="2012-12-23T09:27:21.610" LastActivityDate="2012-12-23T09:27:21.610" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5566" PostTypeId="1" CreationDate="2012-12-23T14:22:07.870" Score="4" ViewCount="52" Body="&lt;p&gt;Does doxylamine have any affects on the monoaminergic system? Specifically I am interested in adrenergic or serotonergic activity but additional information on its dopaminergic activity won't hurt either.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2012-12-23T14:27:31.380" LastActivityDate="2012-12-23T14:27:31.380" Title="Does Doxylamine have any Influence on the Monoaminergic System?" Tags="&lt;biochemistry&gt;&lt;neurotransmitter&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5567" PostTypeId="2" ParentId="1051" CreationDate="2012-12-23T21:41:40.650" Score="3" Body="&lt;p&gt;I want to carry answers from soon-to-be-deleted forum to here (I also asked this in Coursera's Introduction to Evolution And Genetics), since I find them valuable. All of them belong to Andrew Wilmoth :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1st Answer:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The man has a Robertsonian whole-arm translocation which fuses&#xA;  chromosome 14 &amp;amp; chromosome 15. Essentially all of the genetic material&#xA;  is there, just packaged differently. He could have children whole are&#xA;  phenotypically normal regardless of whether his partner has a normal&#xA;  chromosome complement or a similar translocation.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;My Turkish is inadequate to understand the karotype of the woman in&#xA;  the other link.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Persons with translaocations are well known. It is rare but hardly&#xA;  unique. The odds of two such persons randomly meeting each other and&#xA;  mating are probably pretty low. Depending upon each partner's exact&#xA;  karotype there may be no difficulty producing healthy offspring with&#xA;  unusual chromosome complements.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&quot;If they will have make a new species, let's breed them!! Why doesn't&#xA;  science try that? :))&quot;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Because they are people and they might not want to have a child&#xA;  together? Experiments on humans require informed consent. I cannot&#xA;  imagine conducting any such experiment to satisfy scientific&#xA;  curiosity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;2nd answer:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A child born of such a voluntary mating would not by itself be enough&#xA;  to be considered a new species. There are a wide variety of&#xA;  chromosomal rearrangements that are known and there is no serious&#xA;  speculation that persons with such karotypes are members of a&#xA;  different species.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;It is quite possible that one of the many evolutionary changes that&#xA;  separate humans from chimpanzees evolutionarily is a translocation&#xA;  that fused chimpanzee ancestral chromosomes 2a and 2b to form human&#xA;  chromosome 2. There is strong genetic evidence for such a fusion.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;3rd Answer:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As you surmised, every possible combination of gametes with those two&#xA;  karotypes will result in an aneuploidy... unless there is a mutation&#xA;  which &quot;fixes&quot; the problem.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;But the gametes produced by these two individuals would not inherently&#xA;  be expected to result in a problem in an offspring. The F1 offspring&#xA;  would have only 44 chromosomes but likely be normal phenotypically.&#xA;  Any F2 generation produced by crossing two individuals from the F1&#xA;  would have a problem with possible trisomy 14 which would be expected&#xA;  to be fatal.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="504" LastActivityDate="2012-12-23T21:41:40.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5568" PostTypeId="2" ParentId="5558" CreationDate="2012-12-23T22:25:29.810" Score="7" Body="&lt;p&gt;Regarding the Papers referenced above: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the authors maintain that the evidence at the site of fusion is not clear and that explanations as to how this happened are flawed that is possibly concedable.   They would need to do more homework than these papers.  &lt;em&gt;The discussion of vestigial centromere sequences and telomere motifs being inverted is interesting, though contrary views have been &lt;a href=&quot;http://www.gate.net/~rwms/hum_ape_chrom.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;written up&lt;/a&gt; &lt;a href=&quot;http://www.indiana.edu/~ensiweb/lessons/c.fus.les.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;elsewhere&lt;/a&gt;.&lt;/em&gt;  I'm not going to review that evidence as I think its not primary to the question at hand...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would point out that the centromere and telomere sequences are highly repetitive - they are so repetitive that they are often associated with unreliable sequencing in a typical genome build.  While its possible some will be found in future builds of the human genome, such sequences are just as likely to have been excised during mitosis or by mutation.  There would be strong selection pressure for them to be excised quickly; having two centromeres on one chromosome would probably be a fatal trait and the same is probably true for telomerase susceptible sequences in the middle of a chromosomal arm is too.  A lot has happened at the point of fusion and &lt;a href=&quot;http://en.wikipedia.org/wiki/Chimpanzee_genome_project#Genes_of_the_Chromosome_2_fusion_site&quot; rel=&quot;nofollow noreferrer&quot;&gt;150 kB of DNA seems to have included itself which is not from the original Chr 2A or 2B&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think there is some confusion here: The fusion models examined do not predict the fusion from the local configuration of bases.  &lt;em&gt;The main evidence for fusion has always been the fact that the two pieces of human chromosome 2 are nearly identical to chromosomes 2A and 2B of apes - typically 96-98% identical.&lt;/em&gt;  The genes are almost entirely in the same order, the inter-genic regions are very similar All along the 2A/2B length - millions of bases.  The site of fusion ad models for its occurrence is merely confirming what we already - &lt;a href=&quot;http://www.evolutionpages.com/chromosome_2.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;there are two chromosomes somehow stuck together&lt;/a&gt;.  Since both papers focus on the site of combination and do not adequately address this primary piece of information, they seem to be missing this point. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The chances are infinitesimal that human chr 2 were to resemble those of other primates at random.   This is what you say in science when you mean 'impossible'.  One simply doesn't see a segment of DNA the size of Chr 2A and 2B being so similar for such a length when we look at rats, dogs, worms or any more distantly related living thing.  But for every primate the relationship corresponds to humans the same way.  In addition studies show that these &lt;a href=&quot;http://genome.cshlp.org/content/12/11/1651.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;highly similar blocks of DNA sit right next to the site of fusion&lt;/a&gt; and show a crossover where the fusion probably occurred.  Some recent hominids - Neanderthals and &lt;a href=&quot;http://biologos.org/blog/denisovans-humans-and-the-chromosome-2-fusion&quot; rel=&quot;nofollow noreferrer&quot;&gt;Denisovans&lt;/a&gt; had the chr 2 fusion as well.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have to say is that there's always a chance that chromosome 2 fusion did not happen though in my view &lt;a href=&quot;http://www.youtube.com/watch?v=KX5jNnDMfxA&quot; rel=&quot;nofollow noreferrer&quot;&gt;there's a tremendous amount of evidence that it did&lt;/a&gt;.  The second most likely explanation is that all the other apes had their chromosome 2 break into 2 pieces at some susceptible site. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I don't quite agree that chromosome 2 fusion is an indispensable or even leading piece of evidence that means that humans and the other primates are interrelated.&lt;/em&gt;  That question is a different kettle of fish and the relationship between Human chromosome 2 and the chromosomes of other primates is just one contributing point.  All the other chromosome sequences in primates are the same, and nearly every gene in human beings is closer to primates than to other animals.  If they had not found chromosome 2 fusion in the genome sequences few if anybody would have worried about it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to your last question - I don't know if its &lt;em&gt;necessary&lt;/em&gt; that chromosomal fusion must occur in every living thing, but it appears that it has.  In fact what we see as we look at all the diverse chromosomes being sequenced, is that &lt;em&gt;most chromosomes have been merged or rearranged over and over again.&lt;/em&gt;  Over long periods of evolutionary time, a typical chromosome looks like a patchwork quilt stitched up from pieces of other chromosomes.  These relationships are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Synteny&quot; rel=&quot;nofollow noreferrer&quot;&gt;synteny&lt;/a&gt;, which reaffirm the thesis that all living things came from a single point of origin, if you go back far enough.  Really, the fusion point of Chr2 is interesting because its a relatively new event; by picking through the pieces we might find some understanding of something that appears to be a common phenomenon in genome dynamics.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/X9xRl.jpg&quot; alt=&quot;Human Mouse synteny, Human Chr 7&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above image comes from a &lt;a href=&quot;http://genome.cshlp.org/content/13/1/1.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;review of methods to identify syntenic regions&lt;/a&gt;.  It identifies regions of human chromosome 7 and similar regions of mouse chromosomes, identifying regions on mouse chromosomes 6, 9, 11, and 12 with substantial similarities as well as a little bit of chr 2.  Hu chr 7 is 158 million bases long, so even a small band (&gt; 1/1000th of the full length) on this chart means 100,000s of bases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If all these syntenic relationships are considered together they can &lt;a href=&quot;http://genome.cshlp.org/content/13/1/37.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;construct chromosomal rearrangement events that compare with the phylogenetic tree&lt;/a&gt; and typically verify speciation events that separate the two organisms being compared.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whoops - just found this.  Take a look at this &lt;a href=&quot;https://biology.stackexchange.com/questions/1051/can-two-humans-with-44-chromosomes-produce-viable-offspring&quot;&gt;Biology.SE&lt;/a&gt; question: it refers to &lt;a href=&quot;http://en.wikipedia.org/wiki/Robertsonian_translocation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Robertsonian translocation&lt;/a&gt; where the long arms of several of the chromosomes chr 14, 15, 16, 21 and 22 are known to sometimes fuse, resulting in viability.  The answer there is useful - these variants don't tend to produce offspring, but it only takes one time.  Its only happened once in the past 5 million years or so.  So another point of view there. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;That should't discourage the authors from trying again.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All this being said, as a scientific question I'd rather have a discussion like this, based on evidence and facts that anyone can evaluate.  The authors did quite a bit of homework and read some of the literature that is out there.  This is the right direction some of the creationists are taking here and I personally hope that they keep at it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If science is to have any merit (or fun) at all, its because any idea can be called into question and be re-evaluated at any time by anyone.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2012-12-26T01:54:04.420" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5569" PostTypeId="1" CreationDate="2012-12-24T03:00:25.927" Score="3" ViewCount="3201" Body="&lt;p&gt;If I understand it correctly, levels of serotonin in the brain can indicate if a person is happy. What other physiological measures indicate happiness or well being for a humans?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for indicators which can be measured quantitatively but don't be very strictly correlated with 'happiness'. And on the flip-side is there physiological  indicators that a person is/not depressed?&lt;/p&gt;&#xA;" OwnerUserId="1822" LastEditorUserId="3053" LastEditDate="2013-02-23T00:51:46.880" LastActivityDate="2013-07-23T02:37:12.833" Title="Physiological indicators of happiness and well being" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;physiology&gt;&lt;neurotransmitter&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5570" PostTypeId="2" ParentId="5569" CreationDate="2012-12-24T03:18:22.410" Score="0" Body="&lt;p&gt;Facial Microexpressions can indicate happiness.  Not sure about depression, but sadness and other correlates might be useful there:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Microexpression&quot; rel=&quot;nofollow&quot;&gt;Microexpressions express the seven universal emotions: disgust, anger, fear, sadness, happiness, surprise, and contempt. Nevertheless, in the 1990s, Paul Ekman expanded his list of basic emotions, including a range of positive and negative emotions not all of which are encoded in facial muscles. These emotions are amusement, contempt, embarrassment, excitement, guilt, pride, relief, satisfaction, pleasure, and shame.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0730725X97000210&quot; rel=&quot;nofollow&quot;&gt;MRI seems to have some happiness metrics&lt;/a&gt; - though its not the easiest or cheapest method. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2012-12-24T03:18:22.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5571" PostTypeId="1" AcceptedAnswerId="5574" CreationDate="2012-12-24T05:35:15.813" Score="11" ViewCount="16105" Body="&lt;p&gt;It is a common observation that food is tasteless when we have a cold. Why is that so?&lt;br&gt;&#xA;&lt;strong&gt;What is the cause of inability to taste when we have a cold? Are the nose and ability to taste connected?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1809" LastEditorUserId="1590" LastEditDate="2012-12-24T11:11:59.693" LastActivityDate="2019-09-25T08:51:25.030" Title="Why can't you taste food when you have a cold?" Tags="&lt;human-biology&gt;&lt;food&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5572" PostTypeId="1" AcceptedAnswerId="17938" CreationDate="2012-12-24T12:00:47.787" Score="4" ViewCount="104" Body="&lt;p&gt;Are there any short or long term effects apparent in tissues if a zone (or the whole) of human body is scanned with ultrasonic waves often? &lt;/p&gt;&#xA;" OwnerUserId="1373" LastEditorUserId="69" LastEditDate="2012-12-25T12:58:09.787" LastActivityDate="2014-06-06T09:31:40.030" Title="Can frequent ultrasound diagnostics be harmful?" Tags="&lt;human-biology&gt;&lt;ultrasound&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5573" PostTypeId="2" ParentId="5571" CreationDate="2012-12-24T14:48:41.267" Score="4" Body="&lt;p&gt;There are many factors that contribute to the flavor of food - the five &quot;traditional&quot; tastes (sweet, sour, bitter, salty, umami), smell, texture, spiciness, &quot;coolness&quot; (like peppermint), temperature, etc. Smell and taste are detected in similar ways, by chemoreceptors expressed in taste pores by specialized cells of the lingual epithelium (tongue), and in the nose by the olfactory epithelium. Both are affected by upper respiratory tract infections like colds and the flu, leading to diminished senses of taste and smell, and a corresponding reduction in the overall flavor of food.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2012-12-24T14:48:41.267" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5574" PostTypeId="2" ParentId="5571" CreationDate="2012-12-24T20:25:12.903" Score="8" Body="&lt;p&gt;This &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=disturbances%20of%20taste%20and%20smell%20flu&quot;&gt;German review&lt;/a&gt; supports common wisdom that the sense of taste is predominantly informed by the sense of smell. For instance, common advice to children taking &quot;nasty&quot; tasting medicines is to plug one's nose. Any condition that blocks olfaction, such as sinusitis from flu or other sinus infections, or blocking nasal airflow, will decrease or block olfaction and as a result, the majority of taste.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=disturbances%20of%20taste%20and%20smell%20flu&quot;&gt;Hüttenbrink KB. [Disorders of the sense of smell and taste]. Ther Umsch. 1995 Nov;52(11):732-7. [Article in German]&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-12-24T20:25:12.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5575" PostTypeId="2" ParentId="5550" CreationDate="2012-12-25T01:54:17.720" Score="4" Body="&lt;p&gt;As with the massive variety of compounds that serve to protect plants against insect and animals, resulting in a wide range of poisons, antibiotics and other natural insecticides, allelopathic compounds are highly varied with different methods of action: some merely prevent germination while others are effectively herbicides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One example is &lt;em&gt;Alliolaria petiolata&lt;/em&gt;. In that species the allelopathic substance is not known, but is thought to ahve a fungicidal effect that &lt;a href=&quot;http://www.plosbiology.org/article/info%3adoi/10.1371/journal.pbio.0040140&quot; rel=&quot;nofollow&quot;&gt;impedes mycorrhizal development&lt;/a&gt;, which would seriously affect the development of many species.&lt;/p&gt;&#xA;" OwnerUserId="1826" LastActivityDate="2012-12-25T01:54:17.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5576" PostTypeId="1" AcceptedAnswerId="5580" CreationDate="2012-12-25T02:17:51.503" Score="10" ViewCount="1412" Body="&lt;p&gt;I've read that female mules can &lt;a href=&quot;http://www.seattlepi.com/national/article/Mule-does-impossible-Has-a-foal-1250061.php&quot;&gt;sometimes&lt;/a&gt; have offspring, but that male mules are incapable of doing so. Why is that the case? Is their sperm not capable of entering the egg or is their a genetic reason?&lt;/p&gt;&#xA;" OwnerUserId="1827" LastEditorUserId="3624" LastEditDate="2013-11-01T10:19:45.233" LastActivityDate="2016-09-04T22:13:37.887" Title="Why Can't A Male Mule Have Offspring?" Tags="&lt;genetics&gt;&lt;hybridization&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5577" PostTypeId="1" AcceptedAnswerId="20931" CreationDate="2012-12-24T21:14:07.190" Score="3" ViewCount="363" Body="&lt;p&gt;In training for scuba diving, they tell you that when you're bellow 100 ft or so you have to watch out for changes in mental state that resemble drunkenness. The cause of these mental disturbances is called nitrogen narcosis, and it has something to do with the increased pressure on the nitrogen component of the gas that you're breathing out of your tank. I just read &lt;a href=&quot;http://what-if.xkcd.com/14/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article from the what-if section of XKCD (halfway down the page, under the header about Michael Phelps) that mentioned a very similar sounding disorder called high pressure nervous syndrome. Are nitrogen narcosis and high pressure nervous syndrome related, or are the effects of high pressure nitrogen and high pressure by itself separable?&lt;/p&gt;&#xA;" OwnerUserId="784" OwnerDisplayName="tel" LastEditorUserId="3624" LastEditDate="2017-03-13T13:55:53.780" LastActivityDate="2017-03-30T20:28:45.527" Title="In scuba diving, are nitrogen narcosis and high pressure nervous syndrome the same thing?" Tags="&lt;neuroscience&gt;&lt;pathology&gt;&lt;human-physiology&gt;&lt;breathing&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5578" PostTypeId="1" AcceptedAnswerId="5579" CreationDate="2012-12-25T15:16:16.347" Score="0" ViewCount="221" Body="&lt;p&gt;Can gelatine cause blood thickening if digested?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2012-12-25T15:42:49.860" Title="Can gelatine digestion make blood more thick?" Tags="&lt;human-biology&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5579" PostTypeId="2" ParentId="5578" CreationDate="2012-12-25T15:42:49.860" Score="4" Body="&lt;p&gt;No, because gelatin is a mixture of collagen-derived peptides. When you eat them, they are first hydrolyzed by stomach acids into constituent amino acids. These amino acids are then absorbed from the small intestines as nutrients.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-12-25T15:42:49.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5580" PostTypeId="2" ParentId="5576" CreationDate="2012-12-25T15:51:08.043" Score="9" Body="&lt;p&gt;It's essentially genetic. The mule is a hybrid of a male donkey and female horse. A donkey has 62 chromosomes, a horse has 64 chromosomes, and a mule has 63 (mix of 62 and 64). There is a mismatch between both number and structure of the chromosomes and as a result, most mules are infertile.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-12-25T15:51:08.043" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5581" PostTypeId="2" ParentId="5554" CreationDate="2012-12-25T16:02:47.060" Score="1" Body="&lt;p&gt;I'm not sure about humans, but this is true of many vertebrate's retinas. There is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20504441&quot; rel=&quot;nofollow&quot;&gt;experimental evidence&lt;/a&gt; showing light-inhibited production of serotonin. This article reviews how serotonin is regulated in response to day lenght (as well as fasting/feeding cycles). The authors suggest a mechanism in which serotonin and ghrelin integrate signals from fasting/feeding and night/day together.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20504441&quot; rel=&quot;nofollow&quot;&gt;Nowak JZ, Z Urawska E, Zawilska J. Melatonin and its generating system in vertebrate retina: circadian rhythm, effect of environmental lighting and interaction with dopamine. Neurochem Int. 1989;14(4):397-406.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22974511&quot; rel=&quot;nofollow&quot;&gt;Kirsz K, Zieba DA. A review on the effect of the photoperiod and melatonin on interactions between ghrelin and serotonin. Gen Comp Endocrinol. 2012 Nov 1;179(2):248-53. doi: 10.1016/j.ygcen.2012.08.025. Epub 2012 Sep 5.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-12-25T16:02:47.060" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5584" PostTypeId="1" CreationDate="2012-12-14T10:45:24.073" Score="6" ViewCount="2070" Body="&lt;p&gt;Usually when left in hot temperature, the milk curdles (which I know when I boil it and it starts separating).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the re boiling does not curdle the milk, can that be taken as an indicator that the milk hasn't developed the bacteria (and their toxins)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the milk that I use.&lt;br&gt;&#xA;&lt;a href=&quot;http://www.amul.com/products/amul-taaza-info.php&quot; rel=&quot;nofollow&quot;&gt;http://www.amul.com/products/amul-taaza-info.php&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1809" OwnerDisplayName="Anisha Kaul" LastEditorDisplayName="user560" LastEditDate="2012-12-25T23:02:59.810" LastActivityDate="2013-01-25T00:02:40.670" Title="If re-boiling does not curdle the milk, can that be taken as an indicator that the milk hasn't developed the bacteria (and their toxins)?" Tags="&lt;microbiology&gt;&lt;food&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="5585" PostTypeId="2" ParentId="5584" CreationDate="2012-12-16T15:51:03.073" Score="1" Body="&lt;p&gt;Fresh milk does not separate when boiled. I use it in sauces and pan gravies and it always boils and never separates. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My suspicion is that you are separating it on purpose, for example to make cheese. In that case you have to add acid or rennet to separate it. If you then re-boil it to separate it again, you get very little solids. I have made cheese at home then tried to 'ricotta' the left over whey and all I get is a tiny bit of solids.&lt;/p&gt;&#xA;" OwnerDisplayName="Fladabosco" LastActivityDate="2012-12-16T15:51:03.073" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5586" PostTypeId="1" CreationDate="2012-12-26T05:44:09.583" Score="7" ViewCount="1253" Body="&lt;p&gt;I have seen some people &lt;strong&gt;&lt;em&gt;shivering&lt;/em&gt;&lt;/strong&gt; in the room temperature of 18°C while others of similar body structure do not feel that much amount of cold.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course the clothing of both people is similar if not same.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What can be the cause of such different body reactions?&lt;/p&gt;&#xA;" OwnerUserId="1809" LastEditorUserId="69" LastEditDate="2012-12-26T13:56:15.377" LastActivityDate="2014-12-28T14:55:57.487" Title="Why do people feel extreme cold at different temperatures compared to other people of same body structure?" Tags="&lt;human-biology&gt;&lt;homeostasis&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5587" PostTypeId="1" AcceptedAnswerId="10123" CreationDate="2012-12-26T08:03:07.867" Score="4" ViewCount="583" Body="&lt;p&gt;I wonder if there people who were cured of HIV only by means of highly active anti retro-viral therapy (HAART) or other drugs rather than by bone marrow transplant?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that HAART can suppress HIV below detectable level but are there people who stopped HAART and did not experience the HIV levels rising?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="69" LastEditDate="2012-12-26T13:49:16.420" LastActivityDate="2014-03-27T02:48:09.100" Title="Are there people cured of HIV by means of HAART?" Tags="&lt;virology&gt;&lt;hiv&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5588" PostTypeId="1" AcceptedAnswerId="5601" CreationDate="2012-12-26T08:10:44.667" Score="41" ViewCount="7394" Body="&lt;p&gt;Mammals, reptiles, arachnids, insects, etc are all as far as I am aware symmetrical in appearance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take a human for instance, make a line from the top of our head right down the middle. However, internally it is not the same. Our organs &lt;em&gt;excluding&lt;/em&gt; the kidneys, lungs, reproductive organs, etc are not symmetrically placed in our body.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why do we not have an even number of each organ so it can be placed symmetrically?&lt;/li&gt;&#xA;&lt;li&gt;If we have a single organ why is it not placed in the middle like the brain or bladder is for instance?&lt;/li&gt;&#xA;&lt;li&gt;Is there some evolutionary advantage that led to this setup?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1827" LastEditorUserId="69" LastEditDate="2012-12-27T21:09:05.137" LastActivityDate="2019-08-21T23:25:03.903" Title="Why Is Most Life Symmetrical Externally But Not Internally?" Tags="&lt;evolution&gt;&lt;anatomy&gt;&lt;organs&gt;" AnswerCount="5" CommentCount="6" FavoriteCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="5589" PostTypeId="1" AcceptedAnswerId="10513" CreationDate="2012-12-26T08:42:31.530" Score="5" ViewCount="235" Body="&lt;p&gt;From what I have read and understood telomeres cap off how many times a cell can divide before it can no longer divide and that is what causes aging.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;https://en.wikipedia.org/wiki/Arabidopsis_thaliana&quot; rel=&quot;nofollow&quot;&gt;thale cress plant&lt;/a&gt; apparently has a life cycle of 6 weeks before it dies, while the &lt;a href=&quot;https://en.wikipedia.org/wiki/Methuselah_%28tree%29&quot; rel=&quot;nofollow&quot;&gt;Methuselah tree&lt;/a&gt; has set the record at over 4,800+ years.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What is the difference between these two plants regarding their telomeres?&lt;/li&gt;&#xA;&lt;li&gt;Is the cell division rate different between both plants instead of a telomeres difference?&lt;/li&gt;&#xA;&lt;li&gt;If given ideal conditions what could the potential life-span of a Methuselah tree be?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Btw you don't have to answer all these. Just curious and looking for some insight into why the stark difference between both plants' aging.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1827" LastEditorUserId="1827" LastEditDate="2013-01-18T17:15:38.483" LastActivityDate="2013-09-20T14:51:18.033" Title="Difference In Telomeres Between A Thale Cress Plant And A Methuselah Tree" Tags="&lt;senescence&gt;&lt;mitosis&gt;&lt;telomere&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5590" PostTypeId="1" CreationDate="2012-12-26T15:43:57.087" Score="3" ViewCount="1012" Body="&lt;p&gt;I have given my high school biology students the thought experiment of &quot;What would happen if a researcher induced twinning of a female zygote and then replaced one of the X Chromosomes with a copy of the father's Y chromosome&quot;. In theory you should get what would be about as close as possible to male/female identical (monozygotic twins). However, I don't believe it would be possible for this to occur in nature (feel free to correct this if I am wrong). The closest I am familiar with is &quot;Semi-identical twins in which the egg is fertilized by two sperm and then twinning occurs. However this isn't really the same. &#xA;However, I realized that Androgen Insensitivity Syndrome, in which a mutation leads to the body not responding to masculinizing hormones, leads to a male developing as female. Is anyone aware of this ever happening? I realize it would need to occur after the zyote/morula split.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly if the SRY gene (essentially the master control switch for masculinizing an embryo) has ever been transferred on to an early embryo of a pair of female monozygotic twins, essentially inducing one twin to develop male. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In essence I'm asking for evidence of physical manifestations of (near)identical monozygotic twins. Has any of this ever been done in research on other species?&lt;/p&gt;&#xA;" OwnerUserId="1710" LastActivityDate="2020-08-24T11:52:22.307" Title="Are there records of monozygotic twins in which one experiences androgen insensitivity syndrome" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;endocrinology&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5591" PostTypeId="2" ParentId="5590" CreationDate="2012-12-26T17:46:35.823" Score="1" Body="&lt;p&gt;This is an important question to geneticists because monozygotic twins are the only ethically acceptable way to research genetically identical humans.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure the sort of non-symmetrical fission where specific DNA coding for genes are not present or are modified to completely different phenotype in the formation of the twins probably has happened, but it incredibly rare.  In stem cells, &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0050715&quot; rel=&quot;nofollow&quot;&gt;asymmetric division has been observed frequently (warning: google doesn't like PlosOne right now)&lt;/a&gt;.  In development, unless its actively been activated as an asymmetric division, this would be incredibly rare- this would be akin to a birth defect in a single fetus - how many cases of mixed male and female cells in a single baby. I can't even find a reference for such a thing.  Much more common are &lt;a href=&quot;http://en.wikipedia.org/wiki/Twin#Semi-identical_twins&quot; rel=&quot;nofollow&quot;&gt;semi-identical twins&lt;/a&gt;, where two different sperm fertilize a single egg which may have split.  Semi-twins are still vanishingly rare - the first &lt;a href=&quot;http://www.nature.com/news/2007/070326/full/news070326-1.html&quot; rel=&quot;nofollow&quot;&gt;report was in 2007&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Such twins are probably very rare. Their existence and discovery relies on three unusual, and possibly unlinked, events: first, that an egg fertilized by two sperm develops into a viable embryo; second, that this embryo splits to form twins; and third, that the children come to the attention of science.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This might be the case you are thinking of?  In one case reported there was a gender difference.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Souter and her colleagues investigated the twins' genetic makeup because one was born with ambiguous genitalia. This twin turned out to be a 'true hermaphrodite', with both ovarian and testicular tissue. The other twin is anatomically male.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They weren't monozygotic though.  Just others from the same mother ;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Monozygotic twins are not completely identical, &lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=identical-twins-genes-are-not-identical&quot; rel=&quot;nofollow&quot;&gt;epigenetic fingerprinting&lt;/a&gt; - including &lt;a href=&quot;http://www.pnas.org/content/102/30/10604.long&quot; rel=&quot;nofollow&quot;&gt;DNA methylation and chromatin DNA binding patterns (pnas - paywall)&lt;/a&gt; change while the fetus develops and as the child and adult age.  This can cause quite significant differences as the twins age. Epigenetic markers change the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22305529&quot; rel=&quot;nofollow&quot;&gt;dynamics of brain development&lt;/a&gt; and can make a difference in the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20060365&quot; rel=&quot;nofollow&quot;&gt;occurance of leukemia.&lt;/a&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also modifications to the DNA sequences of cells, &lt;a href=&quot;http://en.wikipedia.org/wiki/Copy-number_variation&quot; rel=&quot;nofollow&quot;&gt;copy number variations&lt;/a&gt; (CNVs) are multiple (sometimes hundreds or thousands of times over) repeats of short (2+ base pairs) DNA sequences.  These also occur as the cells differentiate and divide to form tissues and organs.  &lt;a href=&quot;http://www.sciencedaily.com/releases/2008/02/080215121214.htm&quot; rel=&quot;nofollow&quot;&gt;Twins show significant differences there too&lt;/a&gt; as this is not a deterministic mechanism in development. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't find any references to twins showing asymmetric &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK1429/&quot; rel=&quot;nofollow&quot;&gt;AIS&lt;/a&gt;. but the number of variants requiring this makes it sounds like its possible.  If you have a reference post it and I can have a look? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;note added: &lt;a href=&quot;http://genomebiology.com/2013/14/5/R44/abstract&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; shows that methylation profiles appear identical at least &lt;em&gt;in utero&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-06-11T23:36:05.113" LastActivityDate="2013-06-11T23:36:05.113" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5592" PostTypeId="1" CreationDate="2012-12-26T18:58:41.323" Score="1" ViewCount="46" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Possible Duplicate:&lt;/strong&gt;&lt;br&gt;&#xA;  &lt;a href=&quot;https://biology.stackexchange.com/questions/5564/hiv-rapid-tests&quot;&gt;HIV Rapid Tests&lt;/a&gt;  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&#xA;&#xA;&lt;p&gt;Can proteins found on the surface of RNA viruses cause infection without the presence of the actual RNA and other components used in the virus? &lt;/p&gt;&#xA;" OwnerUserId="1820" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2012-12-26T22:07:45.670" Title="Can viral proteins cause infection?" Tags="&lt;microbiology&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="0" ClosedDate="2012-12-27T13:12:47.860" ContentLicense="CC BY-SA 3.0" />
  <row Id="5593" PostTypeId="2" ParentId="5564" CreationDate="2012-12-26T22:07:45.670" Score="4" Body="&lt;p&gt;No, the protein components of viruses may be able to initiate the infectious process, i.e. injection, but if there is no RNA or DNA, there is no virus to inject into the target cell. Hence none of the viral genome's action such as replication or transcription will occur and the cell itself will remain unchanged.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, some effects of viral infection are actually part of an immune response of some kind, and these are often triggered by viral proteins themselves.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2012-12-26T22:07:45.670" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5594" PostTypeId="2" ParentId="5550" CreationDate="2012-12-26T22:23:32.610" Score="3" Body="&lt;p&gt;A classic example is juglone from Black Walnut tree roots. This &lt;a href=&quot;http://pubs.acs.org/doi/pdf/10.1021/ed050p782&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt; from 1973 discusses juglone and allelopathy, inhibiting growth of other trees. This 1961 &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14006337&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; describes juglone's effects as able to sedate or at depress movement of &lt;em&gt;Daphnia magna&lt;/em&gt;, leopard frogs, perch, catfish, goldfish, mice, rats and rabbits. That led to work testing juglone on cancer cells.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2012-12-27T13:40:59.813" LastActivityDate="2012-12-27T13:40:59.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5596" PostTypeId="1" CreationDate="2012-12-27T04:44:11.963" Score="11" ViewCount="293" Body="&lt;p&gt;Most of the things that come up in Google and Google Scholar for this question have a mostly/completely speculative tone, or at best use models instead of measurements. &lt;a href=&quot;http://www.e-library.lt/resursai/ES/Leidiniai/EEA_issue_reports/GMOsforwww.pdf&quot;&gt;This report&lt;/a&gt; describes some actual measurements in pollen transfer to neighboring fields from GM fields, though they all seem to have been one-off measurements at some unknown time after the GM plants appeared, rather than investigations on if the genes are &lt;em&gt;becoming more common over time&lt;/em&gt;, which might imply the ability to become unavoidably common in some environments or even a weed/pest/parasite. This doesn't seem like an obvious problem to me, because the traits associated with those genes are always meant for the context of being farmed or raised by humans and therefore probably wouldn't contribute more to fitness in wild populations relative to the wild alternatives of those genes, but a few counterexamples would smash that belief to bits.&lt;/p&gt;&#xA;" OwnerUserId="1836" LastEditorUserId="1836" LastEditDate="2013-01-19T01:52:25.957" LastActivityDate="2013-04-08T00:57:21.553" Title="Have any genetically altered organisms actually become abundant in a natural environment?" Tags="&lt;genetics&gt;&lt;environment&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5597" PostTypeId="1" AcceptedAnswerId="9011" CreationDate="2012-12-27T07:56:24.243" Score="5" ViewCount="7124" Body="&lt;p&gt;In the majority of human beings, the apex of the heart (left ventricle) points towards the left side of the body.  Sometimes however (approx. 1/12000 births), a person is born with a condition known as &quot;Dextrocardia&quot;, in which the apex of the heart points to the right side of the body instead.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there an evolutionary reason as to why the human heart usually points to the left side as opposed to the right side of the body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Note:  Please don't answer with, &quot;because there is a notch in the left lung&quot;, because I will simply reply with, &quot;is there an evolutionary reason for the apex of the heart AND the cardiac notch being on the left as opposed to the right side of the body&quot;).&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="16866" LastEditDate="2017-04-13T04:07:57.187" LastActivityDate="2017-04-13T04:07:57.187" Title="Why does the apex of the human heart usually point to the left?" Tags="&lt;evolution&gt;&lt;human-anatomy&gt;&lt;cardiology&gt;&lt;development&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5598" PostTypeId="1" AcceptedAnswerId="6952" CreationDate="2012-12-27T08:12:06.347" Score="2" ViewCount="3038" Body="&lt;p&gt;A humans body temperature averages at around &lt;code&gt;98.6°F&lt;/code&gt;&lt;br&gt;&#xA;A dog's body temperature averages at around &lt;code&gt;101.5°F&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;If the temperature outside is &lt;code&gt;45°F&lt;/code&gt; who would feel colder?&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The dog's temperature is higher than the human. So you would assume since its temperature is higher it would feel warmer than the human.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the temperature difference between the body and the external temperature is the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Difference in humans internal and ambient temperate: &lt;code&gt;52.6°F&lt;/code&gt;&lt;br&gt;&#xA;Difference in dog's internal and ambient temperate: &lt;code&gt;56.5°F&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like to know as I keep telling my mom that the dogs feel hot when she puts on doggy sweaters for them when its slightly cold for us humans.&lt;/p&gt;&#xA;" OwnerUserId="1827" LastActivityDate="2013-01-28T16:37:25.847" Title="Temperature Tolerance In Relationship To Body Temperature" Tags="&lt;temperature&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5599" PostTypeId="1" CreationDate="2012-12-27T12:11:46.830" Score="7" ViewCount="3048" Body="&lt;p&gt;If a human body were somehow to be kept at a cold temperature (say 30C) for the entire life of the given individual. And somehow the brain could be fooled into thinking that this 30C feels nice and warm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would that given individual live longer as a consequence?&#xA;What effect does a tempreature have on lifespan?&lt;/p&gt;&#xA;" OwnerUserId="542" LastEditorUserId="542" LastEditDate="2012-12-29T09:47:05.830" LastActivityDate="2020-02-10T15:14:39.823" Title="Does body temperature affect human lifespan?" Tags="&lt;temperature&gt;" AnswerCount="3" CommentCount="14" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5601" PostTypeId="2" ParentId="5588" CreationDate="2012-12-27T20:06:06.010" Score="26" Body="&lt;p&gt;First, I think it worthwhile considering 'Why would internal symmetry be beneficial?' Developmental simplicity jumps to mind immediately. You can also consider relationship to external organs; the stomach and esophagus are lined up with the mouth which is symmetrical about the sagittal plane. Or maybe even balance; the lungs are large organs and if put to one side would likely cause locomotive issues. (Perhaps this is even an interesting topic for another question.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, I feel, at it's core the evolutionary advantage which led to the lack of ubiquitous internal symmetry is &lt;strong&gt;space&lt;/strong&gt;. Simply put, there is only so much room inside an organism and every little counts. Thus, if there isn't a need for a particular organ to be mirrored about a plane then there &lt;em&gt;is&lt;/em&gt; a benefit in putting elsewhere: utilization of space.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think a fantastic example of this is the human digestive tract. The key factor in the shape of the intestines is utilization of space, which directly affects the point at which is connects to the stomach, itself contributing to the asymmetrical shape of the stomach. One could envision other configurations, sure, and nature has. However, this configuration works quite well and the extraordinary use of limited space seems to outweigh all benefits of symmetry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To directly respond to your questions above:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt; Why do we not have an even number of each organ so it can be placed symmetrically?&#xA;&lt;strong&gt;Response:&lt;/strong&gt; Each organ addresses (or addressed) a need of the organism. Addressing that need with multiple organs working in concert has benefits and consequences, as does addressing the need with a single organ alone. These benefits and consequences are balanced throughout the evolution of an organism.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt; If we have a single organ why is it not placed in the middle like the brain or bladder is for instance?&#xA;&lt;strong&gt;Response:&lt;/strong&gt; &lt;em&gt;I feel&lt;/em&gt; space. Again, there are benefits to symmetry but there are many other factors at play. Some of which, it seems, are more important than symmetry at times.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt; Is there some evolutionary advantage that led to this setup?&#xA;&lt;strong&gt;Response:&lt;/strong&gt; I hope this has been addressed - I don't claim to have 'answered' anything, this is a question for discussion.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other fuel for discussion:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In thinking through this question I found myself able to rationalize why internal symmetry isn't necessary. However, I'd be interested in seeing opinions on why, then, external symmetry is so prevalent.&lt;/p&gt;&#xA;" OwnerUserId="1838" LastEditorUserId="1838" LastEditDate="2012-12-27T20:11:32.893" LastActivityDate="2012-12-27T20:11:32.893" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5602" PostTypeId="1" CreationDate="2012-12-27T20:14:32.227" Score="2" ViewCount="114" Body="&lt;p&gt;I've long been interested in circadian rhythms and recently came across a variety of articles that appear to indicate that the following neurotransmitters, transferases and hormones are connected. There are mentions of some circadian rhythmicity and maintaining homeostasis for these compounds(&lt;a href=&quot;https://biology.stackexchange.com/questions/5554/are-serotonin-levels-in-humans-affected-by-light&quot;&gt;Are serotonin levels in humans affected by light?&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Serotonin#Gauge_of_social_situation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Serotonin&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dopamine#Functions_in_the_brain&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dopamine&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Melatonin#Circadian_rhythm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Melatonin&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;HIOMT, NAT&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ghrelin#Mechanism_of_action&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ghrelin&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Leptin#Function&quot; rel=&quot;nofollow noreferrer&quot;&gt;Leptin&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Additionally, their expression is related to &lt;a href=&quot;http://en.wikipedia.org/wiki/Suprachiasmatic_nucleus&quot; rel=&quot;nofollow noreferrer&quot;&gt;Suprachiasmatic Nucleus&lt;/a&gt; and light exposure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I'm interested if there's a good article or a talk that discusses the homeostatic system that those compounds are a part of.&lt;/strong&gt; I'm particularly interested in their effect on the feeling of well being.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to me that all these compounds are in some way related to moving and feeding. However, I cannot wrap my mind around multiple separate articles that describe how, and am looking for a single paper that may shed light on the connection between these compounds.&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2012-12-27T20:14:32.227" Title="Is there an entry-level circadian model of serotonin, ghrelin, dopamine and the sense of well being?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;circadian-rhythms&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5603" PostTypeId="1" CreationDate="2012-12-28T02:23:34.880" Score="1" ViewCount="211" Body="&lt;p&gt;I was reading Matt Ridley's &quot;Genome&quot; book. I am trying to understand the Interlocus Contest Evolution in his X-Y chapter. I do not understand why the X and Y chromosome would want to kill each other. Wouldn't that cause the death of the species (actually, have any species died that way?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone shed light on the issue?&lt;/p&gt;&#xA;" OwnerUserId="84" LastEditorUserId="1590" LastEditDate="2012-12-28T14:46:25.013" LastActivityDate="2015-05-09T01:19:02.450" Title="Interlocus Contest Evolution means suicide?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5604" PostTypeId="1" CreationDate="2012-12-28T02:29:50.433" Score="2" ViewCount="238" Body="&lt;p&gt;The major gene of the Y-chromosome is SRY. Would it be possible to get the X-chromosome and add SRY to create a &quot;fuller&quot; Y-chromosome? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What advantage does the skinny Y-chromosome give an individual anyway? Females only use one X-chromosome (via the Barr body) so they don't seem to gain as much from having the pair.&lt;/p&gt;&#xA;" OwnerUserId="84" LastEditorDisplayName="user560" LastEditDate="2012-12-28T03:24:06.690" LastActivityDate="2016-12-19T01:58:20.687" Title="Can a new Y-chromosome be created?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;chromosome&gt;&lt;human-genome&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5605" PostTypeId="1" AcceptedAnswerId="5607" CreationDate="2012-12-28T17:29:43.303" Score="1" ViewCount="745" Body="&lt;p&gt;Could someone explain the difference between Cine-MRI and MRI?  I am reading conflicting things online, such as Cine-MRI uses ECG-gating, or that Cine-MRI takes many images of the same position of the heart before stitching together the final result, and it is confusing me.  &lt;/p&gt;&#xA;" OwnerUserId="1841" LastEditorUserId="69" LastEditDate="2012-12-28T23:06:01.587" LastActivityDate="2012-12-28T23:24:03.957" Title="Cine-MRI versus MRI" Tags="&lt;imaging&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5606" PostTypeId="2" ParentId="5604" CreationDate="2012-12-28T20:26:29.390" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Would it be possible to get the X-chromosome and add SRY to create a &quot;fuller&quot; Y-chromosome? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Possible? Sure. You could sequence both chromosomes and then create some artificial DNA that included the combined sequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would it be viable? Probably not. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What advantage does the skinny Y-chromosome give an individual anyway?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If there is a genetic condition in the father's X-chromosome, the male child is spared from it.&lt;br&gt;&#xA;If there is a genetic condition in the mother's X-chromosome, the male child has a 50/50 shot at being spared from it.&lt;br&gt;&#xA;If the genetic condition requires two homogenous X-chromosomes, the male child is spared.&lt;br&gt;&#xA;If the genetic condition requires two heterozygous X-chromosomes, the male child is spared.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are all advantages of simply requiring a Y-Chromosome, and there are certainly disadvantages to having a Y-Chromosome as well; X-linked genetic disorders will &lt;em&gt;definitely&lt;/em&gt; affect any male heirs, unlike...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Females only use one X-chromosome (via the Barr body) so they don't seem to gain as much from having the pair.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;...Female offspring. Because women have two X-chromosomes they have redundancy. If there is a bad gene on the extra X-chromosome that is deactivated, then it doesn't matter - where for a man with the same X-chromosome it would definitely affect them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, because of the redundancy, what X-linked conditions do exist usually affect women less-so. If both X-chromosomes are utilized for a specific gene, then one bad protein product is partially made-up for with the one good protein product.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2012-12-28T20:26:29.390" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5607" PostTypeId="2" ParentId="5605" CreationDate="2012-12-28T23:24:03.957" Score="2" Body="&lt;p&gt;I'm not familiar with the technique, it is as I'm sure you already know very specialised and I've found it fairly difficult to find resources specific to cine-MRI.  At a glance at the wikipedia entry, however, there are a few differences that I can point out to you.&lt;/p&gt;&#xA;&lt;p&gt;A normal MRI will take a snapshot image of a section of the body in time, therefore can not be used to show motion of internal structures.  By contrast, cine-mri takes several snapshots at different times and stitches them together into an animation, allowing the physician to see movement.  For example, the technique is useful for imaging the beating heart and has also been used to examine the flow of cerebro-spinal fluid.&lt;/p&gt;&#xA;&lt;p&gt;ECG gating refers to how the images are collected when the scan is of the heart.  The timing of the scans matches up with the electrical activity in the heart measured with a surface ECG.  As a undoubtedly hugely oversimplified example, the scanner might take an image at P,Q,R,S and T on the ECG waveform before then stitching them together into an animation:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CMtfw.png&quot; alt=&quot;Sinus rhythm ecg trace&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-12-28T23:24:03.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5608" PostTypeId="1" CreationDate="2012-12-29T13:11:52.077" Score="6" ViewCount="577" Body="&lt;p&gt;When an antiserum is injected to a person to protect oneself from a certain disease, the antibodies in the antiserum come from another organism. The question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why don't the injected antibodies cause an immune response in the individual?&lt;/p&gt;&#xA;" OwnerUserId="1843" LastEditorDisplayName="user560" LastEditDate="2012-12-29T14:07:40.803" LastActivityDate="2013-01-15T23:42:21.417" Title="Why does not the host produce any immune response to antiserum antibodies?" Tags="&lt;molecular-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5609" PostTypeId="2" ParentId="5608" CreationDate="2012-12-29T16:54:39.917" Score="7" Body="&lt;p&gt;That's a good question - because its certainly possible to get antisera &lt;a href=&quot;http://www.abcam.com/human-IgG-Fab-fragment-antibody-4A11-ab771.html&quot; rel=&quot;nofollow&quot;&gt;against antibodies&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes antisera is actually &lt;a href=&quot;https://www.pediatriccareonline.org/pco/ub/citation/362528/Antiserum_treatment_of_gram_negative_bacteremia_?amod=aapea&amp;amp;login=true&amp;amp;nfstatus=401&amp;amp;nftoken=00000000-0000-0000-0000-000000000000&amp;amp;nfstatusdescription=ERROR%3a%20No%20local%20token&quot; rel=&quot;nofollow&quot;&gt;human antisera&lt;/a&gt;, so there would be no rejection at all.  But that is for extreme cases, e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9988160&quot; rel=&quot;nofollow&quot;&gt;serum transfusions from convalescent Ebola survivors to current Ebola patients&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One would expect that you could only give an antiserum once and then it would be less effective each time you get it.  Since antisera to snakebites is the most common application, where its quite possible to be exposed to multiple bites over one's lifetime.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found &lt;a href=&quot;http://emedicine.medscape.com/article/168828-treatment&quot; rel=&quot;nofollow&quot;&gt;one reference to a horse antiserum treatment&lt;/a&gt; that's being used. It makes reference to a source of antiserum which sounds like its been designed to reduce the antibody antibody immune reaction: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Horse-serum antivenin has been available since 1956; a purer antivenin with improved properties was released in 2000 (see Medication). With the &lt;em&gt;reduced side-effect&lt;/em&gt; profile of antigen-binding fragment antivenom (FabAV) and the improvement in tissue injury with antivenin administration, the threshold for dosing is lower.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Even before the availability of these new treatments, its probable that most patients can endure multiple anti serum treatments from the same source animal.  Even goat, horse and rabbit antibodies are pretty similar to ours and the reaction will not be as strong, in addition to which, the immune system will tend to clear out the antigen-xenoantibody complexes from the blood.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't find references, but my guess is there must have been some cases of rejection and reaction otherwise they would not have bothered to improve the serum treatment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update: just read this &lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=snake-scorpion-antivenoms-first-update-in-60-years&quot; rel=&quot;nofollow&quot;&gt;little blurb in scientific american&lt;/a&gt;, that describes how venom antisera will occasionally cause deadly reactions, while most of the time simply disarming the venom.  The new generations of antivenoms described have the Fc portion of the antibodies removed.  This eliminates the adverse immune reaction but I also think also eliminates any immune resistance the patient might get out of the antisera.  The Fc portion of the antibody is the part which our immune cells bind to.  In this case the new antivenoms aren't anti sera exactly, but they do use the antibodies to deactivate the venom toxins and crosslink them to make them less effective.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-01-15T23:42:21.417" LastActivityDate="2013-01-15T23:42:21.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5610" PostTypeId="1" AcceptedAnswerId="5611" CreationDate="2012-12-29T22:39:52.753" Score="3" ViewCount="131" Body="&lt;p&gt;It seems unlikely that an ovoviparous ancestor of mammals long ago could have had a viviparous offspring in a sharp one-generation dividing line, but what would be the gradual steps between egg birth and live birth? Are there any examples of answers to the first question today? It seems that marsupials are a different thing altogether, not something in between egg laying and live birth (no modern mammal's ancestors aren't believed to have marsupial-style birth in their evolutionary history, right?)?&lt;/p&gt;&#xA;" OwnerUserId="263" LastEditorUserId="263" LastEditDate="2012-12-30T03:34:51.810" LastActivityDate="2013-01-01T06:28:23.510" Title="Would ovoviparous to viviparous mutation have been gradual? How would that work?" Tags="&lt;evolution&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5611" PostTypeId="2" ParentId="5610" CreationDate="2012-12-30T04:42:55.813" Score="3" Body="&lt;p&gt;I happen to have seen a talk by an anthropologist who was working on this (i can't reference them here i'm sorry to say - forgotten her name).  I can only give an example from their work...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at old world and new world primates, &lt;a href=&quot;http://anthro.palomar.edu/primate/prim_1.htm&quot; rel=&quot;nofollow&quot;&gt;there is a large difference between the gestation time&lt;/a&gt;.  If you look at the table in the link, lemurs have half the gestation time that humans and gorillas have.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I can recall is that the lemurs placenta lacks many of the structures that primates have (see section 5).  The lemur placenta is supposed to be primitive and a lot more like an egg sac which was internalized as opposed to a more articulated womb that primates have.  So her thesis was that eggs would start out being internalized and subsisting only on their own internal structures, still isolated from the mother, then later placental structures would come about that nourish the fetus and enable it to enjoy longer gestation and better development pre-partum.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The stage I'm describing is only the divergence between primitive wombs and 'more advanced' wombs in the sense that they were capable of supporting the fetus for 9 months rather than just 4.  That development happened &lt;a href=&quot;http://newswatch.nationalgeographic.com/2010/08/05/old_world_monkeys_and_apes_diverged_later/&quot; rel=&quot;nofollow&quot;&gt;over about 30 million years&lt;/a&gt;.  The divergence of mammals is thought to have happened &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_mammals#Triassic_takeover&quot; rel=&quot;nofollow&quot;&gt;about 270 million years ago&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the rough answer would be hundreds of millions of years for the whole shebang, but internalized eggs and live birth would be a relatively smaller amount of time. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-01-01T06:28:23.510" LastActivityDate="2013-01-01T06:28:23.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5612" PostTypeId="1" AcceptedAnswerId="5622" CreationDate="2012-12-30T13:26:18.547" Score="3" ViewCount="22922" Body="&lt;p&gt;T-cells recognize the MHC molecules and body's own peptides. When it doesn't, it alarms the immune system. But do T-cells express MHC molecules ? If so, how are they using it? If not, what happens when a virus infects T-cells? (Yes, I am confused about HIV infection mechanism too. &lt;a href=&quot;http://www.mcb.uct.ac.za/cann/335/McMichael/McMichael.html&quot; rel=&quot;nofollow&quot;&gt;They escape from immune response by altering their genes and disrupting the MHC-peptide bonding&lt;/a&gt;. I can see that this can work in macrophages. But what is the situation in T-cells ?)&lt;/p&gt;&#xA;" OwnerUserId="1843" LastEditorUserId="4101" LastEditDate="2013-10-13T15:50:59.593" LastActivityDate="2017-11-08T08:20:16.523" Title="Do T-cells express MHC molecules?" Tags="&lt;immunology&gt;&lt;mhc&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5613" PostTypeId="1" AcceptedAnswerId="5614" CreationDate="2012-12-30T17:00:33.753" Score="3" ViewCount="1809" Body="&lt;p&gt;I'm currently reading a little about DNA replication, and have come accross the following statement;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Replication starts from a fixed point and is bi-directional ... In Eukaryotes, there are multiple replication forks, each progressing in a bi-directional fashion.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If there is a single, long strand of DNA in a Eukaryotic cell, I see potential problems with this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These forks involve opening up a section of double-stranded DNA, and each strand becoming a double strand in a newly synthesised piece of DNA. At some point, before any single fork has become two new double-stranded molecules, another fork could 'collide' with this, causing it to attempt to replicate the non-finished section. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Simply, how can one replication fork meet another without either exponentially increasing the number of strands being replicated?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, on a more general level, I would be quite interested to know the actual benefit of this, when, typically, only a single copy of the double-stranded molecule needs making.&lt;/p&gt;&#xA;" OwnerUserId="1474" LastActivityDate="2012-12-30T17:46:15.960" Title="How do multiple replication forks function without 'colliding', and what is the benefit of this method?" Tags="&lt;biochemistry&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5614" PostTypeId="2" ParentId="5613" CreationDate="2012-12-30T17:46:15.960" Score="2" Body="&lt;p&gt;To get to the exponentially increasing number of strands, the replication would have to be started on the already replicated strand, and not on the original strand. Replication in eukaryotes is tighly controlled and such an event is prevented by the regulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can the cell prevent re-replication of the strand that is currently synthesized? By timing the steps of the replication in strict order and preventing any replication outside of that order. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Replication starts at defined origins of replication. In the G1 phase, pre replication complexes (pre-RCs) are assembled at the origins of replications. At these pre-RCs the replication can be initiated, but pre-RCs itself cannot be assembled in the later phases of the cell cycle. When the replication starts, the pre-RC is converted to a post-RC which can't initiate the replication anymore, preventing re-replication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The benefit of multiple origins of replication is replication speed. Eukaryotic genomes can be much, much larger than those of simple bacteria. Replicating them using a single origin of replication would take a very long time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some further reading material:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21113/&quot; rel=&quot;nofollow&quot;&gt;Genomes, 2nd edition, chapter 13&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2292467/&quot; rel=&quot;nofollow&quot;&gt;Cell Cycle Regulation of DNA Replication&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6" LastActivityDate="2012-12-30T17:46:15.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5615" PostTypeId="1" AcceptedAnswerId="5628" CreationDate="2012-12-30T19:20:42.003" Score="5" ViewCount="7272" Body="&lt;p&gt;I have a question about the mechanics of human vision which may be as much of a physics question as it is a biology/physiology question. I noticed that if I try to imagine a clear blue daytime sky contrasted with a clear night sky and ask myself which of the two appears closer, my intuition says the daytime sky appears closer. My next thought was, given that a night sky is mostly black, visually the only difference between the two skies is their color. So why is that I want to &quot;blue&quot; is closer than &quot;black&quot;? And if the difference in color is truly what produces the difference in perceived depth, can similar effects be noticed with other color pairs at more familiar distance scales?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But then again, there are a couple of alternative explanations that seem more plausible to me on second thought. A black night sky could just as easily be called a dark sky, and the difference in perceived depth is really more a matter of shading. Then I remembered a night sky has stars of course, and it might be that my mind just wants to place the stars at normal &quot;sky depth&quot;, forcing the black backdrop to appear even further away.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Another related question I've been somewhat curious about: what precisely is the perceived &quot;distance to the sky&quot; as far as our intuitions are concerned?)&lt;/p&gt;&#xA;" OwnerUserId="1847" LastEditorUserId="69" LastEditDate="2013-01-01T22:51:07.947" LastActivityDate="2015-02-16T20:55:57.150" Title="Does coloring affect the perception of depth?" Tags="&lt;vision&gt;&lt;biophysics&gt;&lt;perception&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5617" PostTypeId="2" ParentId="5604" CreationDate="2012-12-30T22:58:31.357" Score="2" Body="&lt;p&gt;SRY translocation to the X chromosome clinically exists and characterizes the &lt;a href=&quot;http://en.wikipedia.org/wiki/XX_male_syndrome&quot; rel=&quot;nofollow&quot;&gt;De La Chapelle Syndrome&lt;/a&gt;. The phenotype associated to this syndrome demonstrates the necessity of other components on the Y chromosome to develop full masculine characteristics.&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="-1" LastEditDate="2013-05-06T09:51:02.200" LastActivityDate="2013-05-06T09:51:02.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5618" PostTypeId="1" AcceptedAnswerId="5637" CreationDate="2012-12-31T06:58:50.237" Score="4" ViewCount="141" Body="&lt;p&gt;Is there a way to generally characterize how species &quot;regrew&quot; after the various mass extinction events happening periodically from 450 Ma to 65 Ma.  Would the surviving species just start back where they had left off and evolve willy-nilly as if the destroyed 50% or 70% of biodiverse species had never existed?  Or would the biome in some way have the capacity to regrow something resembling the former order based just on the remaining species.  This is probably a whopper of a dumb question, my apologies in advance.&lt;/p&gt;&#xA;" OwnerUserId="1852" LastEditorUserId="3624" LastEditDate="2013-10-28T13:59:18.417" LastActivityDate="2013-10-28T13:59:18.417" Title="Historical recovery from mass extinction events" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;palaeontology&gt;&lt;extinction&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5619" PostTypeId="2" ParentId="5516" CreationDate="2012-12-31T10:07:31.020" Score="7" Body="&lt;p&gt;The human sensation of warmth is not the measurement of static temperature.  Humans detect the rate at which heat is leaving (or entering) their body.  For instance, if you are sitting in your 0 degree car in the morning, your hand in the open air will feels warmer than your hand touching the steering wheel, despite them both being at 0 degrees.&lt;/p&gt;&#xA;&lt;p&gt;The reason is that heat conduction from your hand to the steering wheel is much faster than convective heat transfer from the air.  So you feel &amp;quot;colder&amp;quot; touching the steering wheel, but it's really that you're losing heat faster.&lt;/p&gt;&#xA;&lt;p&gt;Scholarpedia's article on temperature receptors:&#xA;&lt;a href=&quot;http://www.scholarpedia.org/article/Thermal_touch#Temperature_receptors&quot; rel=&quot;noreferrer&quot;&gt;http://www.scholarpedia.org/article/Thermal_touch#Temperature_receptors&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;...Cold receptors respond to decreases in skin temperature over a range&#xA;of 5-43 °C...&lt;/p&gt;&#xA;&lt;p&gt;...In contrast, warm receptors signal that skin temperature has&#xA;increased...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1853" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2012-12-31T10:07:31.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5620" PostTypeId="1" AcceptedAnswerId="5727" CreationDate="2012-12-31T10:51:24.207" Score="7" ViewCount="12957" Body="&lt;p&gt;Is there any research showing how prolonged exposure to background noises, particularly high frequency noises, affect hearing abilities? Does constant high pitched noise cause damage even a low volumes? E.g an alarm sounding, noise of an air plane, or noise from road works and building sites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, what is the effect? and why does it happen?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-01-09T08:34:40.677" LastActivityDate="2019-06-09T21:06:53.977" Title="How does prolonged exposure to high frequency noise affect hearing?" Tags="&lt;human-biology&gt;&lt;hearing&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5621" PostTypeId="1" AcceptedAnswerId="5663" CreationDate="2012-12-31T13:06:48.793" Score="7" ViewCount="6738" Body="&lt;p&gt;Cows, camels, sheep, goats, etc being ruminants must chew their food repeatedly by regurgitating their food from their first stomach compartment and chewing their 'cud'. This then finer chewed material makes its way to the various stomach compartments to be digested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These animals are eating plant material, the same plant material animals such as elephants, horses and hippos eat as well. However, these animals only have one stomach compartment. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why does one need a multi-compartment stomach and one does not if they are all eating the same/similar food?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1827" LastActivityDate="2017-08-03T04:55:49.623" Title="Why Do Ruminants Require A Multi-Compartment Stomach To Digest Food?" Tags="&lt;digestive-system&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5622" PostTypeId="2" ParentId="5612" CreationDate="2012-12-31T15:18:46.260" Score="6" Body="&lt;p&gt;There are two types of MHC molecules:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;All nucleated cells express MHC class 1 proteins&lt;/strong&gt;.  A sample of all proteins produced within the cell are 'sliced' into their constituents which are then presented by MHC-I receptors.  This means that if a virus infects a cell, the foreign proteins the cell is induced to make are expressed on the cell membrane by MHC-I.  This is important as antibodies can not cross cell membranes, therefore this is the method by which a cell signals that it is infected by a virus.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;MHC II are the special molecules that are only expressed in antigen-presenting cells, which I think is what you are referring to.  As neither CD4 or CD8 T-cells present antigens, they do not express MHC-II themselves.  Instead CD4 have receptors for MHCII  (while CD8 have receptors for MHCI), allowing them to interact with antigens presented by other immune cells.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a virus infects T-cells, the viral proteins are sampled by the MHC-I pathway and presented via MHC-I on the surface of the infected T-Cell.  The immune response then progresses as for any other virally infected cell, destruction by CD8 T-Killers that destroy the cell by non-phagocytic means.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="-1" LastEditDate="2017-11-08T08:20:16.523" LastActivityDate="2017-11-08T08:20:16.523" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="5623" PostTypeId="1" CreationDate="2012-12-31T17:07:12.287" Score="4" ViewCount="305" Body="&lt;p&gt;Is every component of a virus absolutely essential for its infection and replication in a host cell? Or can you just have parts of it to cause infection? &lt;/p&gt;&#xA;" OwnerUserId="1820" LastEditorUserId="69" LastEditDate="2013-01-01T22:50:22.203" LastActivityDate="2013-01-01T22:50:22.203" Title="Is every part of a virus important for replication?" Tags="&lt;microbiology&gt;&lt;reproduction&gt;&lt;virology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5624" PostTypeId="2" ParentId="5623" CreationDate="2012-12-31T21:45:30.500" Score="1" Body="&lt;p&gt;Unless you have a specific virus in mind, I can speak generally about viruses. It seems that the viral genome is reduced to just essential genes. Many viruses segregate their genome into periods of expression: early, mid and late. The early proteins are so-called because they encode for proteins that help their entry into cells (what is called infection). Middle and late genes tend to help the virus co-opt cellular machinery to aid in viral replication. Late genes are then useful for final stages of viral assembly and ultimtely their exit from the cell (lysis) and the newly made viral particles can go on and infect more cells. When viewed in this manner, it follows that removing even one coding region from the viral genome would inhibit the overall infection/reproduction/assembly process. In fact, if you remove the gene encoding for a viral envelope protein, purified virus added to cells in culture are able to infect cells, but not produce complete and functional viral particles. In this sense, they are infection-competent, but reproduction-incompetent.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2012-12-31T21:45:30.500" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="5625" PostTypeId="2" ParentId="5516" CreationDate="2013-01-01T00:57:20.987" Score="5" Body="&lt;p&gt;A more general answer/comment is that technically almost nothing in biology is really linear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a linear relation, when one variable increases the other increases proportionally. In biological systems this typically cannot happen because of physical limits (such as the number of molecules), which tend to produce saturation at some level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, when a substance is &quot;sensed&quot; by the receptors of a cell, sensing would become saturated as the receptors approach maximal capacity. In a similar manner, heat sensing will be limited by a maximal capacity and saturation of the nervous system. This is of course not specific to sensing but is a general characteristic of biological systems, because they are ultimately made of a finite number of components.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, sometimes a linear-like relation is observed at a specific range of values. For example, this is a mathematical characteristic of a class of functions called logistic functions. At ranges that are far from saturation, these functions have approximately linear behavior.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the following example figure I marked (black box) the &quot;linear-like&quot; regime of a simple logistic function y=1/(1+100*exp(-x)):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cHqiJ.png&quot; alt=&quot;linear regime in logistic function&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2015-10-22T12:58:24.760" LastActivityDate="2015-10-22T12:58:24.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5626" PostTypeId="2" ParentId="5623" CreationDate="2013-01-01T12:26:00.233" Score="1" Body="&lt;p&gt;HIV has nine genes. According to the paper cited below, three of these genes (vpu, vpr and nef) are not required for replication in cultured cells. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Gibbs JS &lt;em&gt;et al&lt;/em&gt;. (1994) Construction and in vitro properties of HIV-1 mutants with deletions in &quot;nonessential&quot; genes. AIDS Res Hum Retroviruses 10: 343 - 50&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Abstract&lt;br&gt;&#xA;  Auxiliary genes that are not essential for viral replication in cell culture are found in all known lentiviruses. The &quot;nonessential&quot; auxiliary genes of HIV-1 are vif, vpr, vpu, and nef. Sequences within the upstream region of U3 in the LTR are also not required for virus replication in cell culture. We constructed a panel of 23 mutants with single and combination deletions in these regions in the wild-type HIV-1 infectious molecular clone NL4-3. Deletion of the vpu, vpr, and nef genes and the U3 upstream sequence (US), individually or in combinations, did not appreciably alter virus replication in either chimpanzee PBMCs, human PBMCs, or in the B/T cell hybrid line CEMx174. In contrast, deletion of the vif gene dramatically delayed virus replication in all three cell types. This collection of HIV-1 deletion mutants will be useful for elucidating the functions of these genes and for investigating antiviral immunity in animal models.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(PBMC = peripheral blood mononuclear cell)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As might be expected, none of these genes encodes a component of the virus - they are regulatory genes involved in co-ordinating the infective cycle of the virus. They are however implicated in HIV-associated disease symptoms. According to &lt;a href=&quot;http://www.hiv.lanl.gov/content/sequence/HIV/COMPENDIUM/2008/frontmatter.pdf&quot; rel=&quot;nofollow&quot;&gt;the Los Alamos National Laboratory HIV Sequence Compendium 2008&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;vpu is an integral membrane protein which promotes extracellular release of viral particles and degrades CD4 in the ER.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;vpr promotes nuclear localization of the preintegration complex, inhibits cell division, and arrests infected cells at G2/M&lt;/p&gt;&#xA;&#xA;&lt;p&gt;nef downregulates CD4 and class I MHC&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-01-01T12:26:00.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5627" PostTypeId="2" ParentId="3851" CreationDate="2013-01-01T13:22:56.417" Score="4" Body="&lt;p&gt;Prologue: Bone conducted signals are considered to be evoked by the perilymph fluid moving back and forth out of the cerebrospinal cavity, via the cochlear aqueduct, towards the scala tympani. And not by mechanical deformation of the cochlea. “the fact that the bone conduction phenomenon is actually the result of the push-pull movement of the perilymph fluid instead of the presumed deformation of the bony structures.” some text to refer: &#xA;&lt;a href=&quot;http://igitur-archive.library.uu.nl/med/2011-0204-200555/UUindex.html&quot; rel=&quot;nofollow&quot;&gt;Applying physics makes auditory sense&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am affiliated with this book. I am the co-author of the Appendices.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Year Article Author(s) Source &#xA;2010 1 Applying physics makes auditory sense : a new paradigm in hearing&#xA;Abstract  |  Full-text Heerens, W.C., Ru, J.A. de Medicine (2010), pp: 1-74 &lt;/p&gt;&#xA;&#xA;&lt;p&gt;pp: 13:&#xA;Objections against the existing bone conduction signal transfer hypothesis: The common model for the transfer of a bone conducted signal is based on the vibration of the temporal bone. However, both the material and the construction of this bony envelope are extremely rigid, while the cochlear shape of the cavity excludes the possibility that parts of this cavity can function as the hypothesized resonators. Therefore, sound stimuli cannot be transferred in such a manner. Certainly not the weak vibration signals with pressure variations of approximately 20 mPa, equal to a pressure variation of &#xA;0.2 x 10^-6 atmosphere that are generated by a normal sound stimulus of 60 dB SPL. Hence ‘bone conduction’ must have a cause other than the deformation of the rigid petrous bone that forms the cochlear bony envelope.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The physiological structure data: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;• The walls of the cochlear envelope are extremely rigid. Hardly compliant to not compliant at all. So bone conduction based on deformation of that envelope is not possible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume that it is clear, without further explanation that the petrous bone can be regarded as a non-deformable body when confronted with the extremely weak impact of acoustic signals.  We see that for a completely normal 60 dB SPL sound pressure signal, clearly showing that the vibrations of bone in the cochlea offer only extremely small, and therefore completely negligible contributions.  It means that we are talking about deformations which is therefore completely negligible as a possible mechanism for signal transfer. I dare say, no waving arm statements.  Contributions that all result in deformations comparable to an incredibly small fraction, are all leading to naught, one cannot escape the conclusion that there must be another cause for the phenomenon of bone conduction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bone conducted signals are considered to be evoked by the perilymph fluid moving back and forth out of the cerebrospinal cavity, via the cochlear aqueduct, towards the scala tympani. And not by mechanical deformation of the cochlea. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;pp: 47: It has been established that the rigid cochlear envelope is hardly deformable. This leads to the realistic hypothesis that the ‘bone conducted’ sound signals evoke stimuli by means of a similar process to those of the airborne sound stimuli, namely by means of a push-pull movement of the perilymph, in this case, out of the cerebrospinal cavity via the cochlear aqueduct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;pp: 19-21: Bone conduction: As the petrous bone is the toughest bone in the human body, it is practically impossible for deformation to occur through the vibrating movements that are caused by acoustic pressure changes. Therefore, there must be another means for this signal transfer. A bone conduction audiogram – apart from a reduced transfer of especially the higher frequencies – is not fundamentally different from a pure airborne tone threshold audiogram. It follows that the perilymph movement within the cochlea must somehow also generate the bone conducted signal transfer. And indeed there is such a possibility. The scala tympani is directly connected with the cerebrospinal cavity by means of the cochlear aqueduct, which has its opening in the vicinity of the round window. The cochlear aqueduct enables the perilymph to move backwards and forwards between the cranial cavity and the cochlear channels (scala tympani and scala vestibuli). The perilymph in this cranial cavity is exposed to the alternating pressures caused by the sound induced vibrations of the shell shaped cranial bones that are located in the front and the back of the skull. As a consequence of Newton’s fundamental law of motion we know that when a larger amount of fluid inside the skull must be brought into motion, the effect of these stimuli will be smaller for the higher frequency contributions than for those of the airborne stimuli for similar frequencies. Furthermore, the stapes introduces the airborne signal that results in a backwards and forwards motion of perilymph, in opposite phase to the back and forth motion of perilymph along the &#xA;basilar membrane, which is evoked by bone conduction. This results in a slight reduction of the airborne signal, which actually is the stronger of the two stimuli. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;pp: 19-21: The alternating movement of perilymph between the cerebrospinal cavity and the scala tympani via the cochlear aqueduct will also be partially directed towards the round window. This splitting up into two directions of the perilymph movement creates a reduced perilymph velocity in front of the basilar membrane, and finally results in a reduction of the bone conduction signal. The rate of reduction depends on the mobility ratio between the oval window and the round window. A further decrease in round window mobility, related to the mobility of the oval window, results in a higher perilymph &#xA;movement in front of the basilar membrane, which evokes a higher bone conduction signal, while an increase would result in a lower one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;pp: 19-21: This hypothesis that bone conduction consists entirely of the push-pull movement of perilymph from the cerebrospinal cavity via the cochlear aqueduct, and is evoked by the vibration of the shell shaped bones of the skull, while the rigid temporal bone does not deform at all, is just one logical step further than the functional possibilities indicated by others.&lt;/p&gt;&#xA;" OwnerUserId="1854" LastEditorUserId="1854" LastEditDate="2013-01-02T08:43:40.040" LastActivityDate="2013-01-02T08:43:40.040" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5628" PostTypeId="2" ParentId="5615" CreationDate="2013-01-01T15:16:37.473" Score="6" Body="&lt;p&gt;Yes, color and shading can certainly affect depth perception, as &lt;a href=&quot;http://en.wikipedia.org/wiki/Depth_perception&quot; rel=&quot;nofollow noreferrer&quot;&gt;explained by wikipedia:&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Aerial perspective&lt;/em&gt; – Due to light scattering by the atmosphere, &lt;strong&gt;objects that are a great distance away have lower luminance contrast and lower color saturation.&lt;/strong&gt; Due to this, images seem blurry the farther they are away from a person's point of view. In computer graphics, this is often called &quot;distance fog.&quot; The foreground has high contrast; the background has low contrast. &lt;strong&gt;Objects differing only in their contrast with a background appear to be at different depths. The color of distant objects are also shifted toward the blue end of the spectrum (e.g., distant mountains).&lt;/strong&gt; Some painters, notably Cézanne, employ &quot;warm&quot; pigments (red, yellow and orange) to bring features forward towards the viewer, and &quot;cool&quot; ones (blue, violet, and blue-green) to indicate the part of a form that curves away from the picture plane.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here are a few examples:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JgT9f.jpg&quot; alt=&quot;Manet&amp;#39;s &amp;quot;Luncheon on the Grass&amp;quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above is Manet's &quot;Luncheon on the Grass&quot; - and if you look at it briefly it seems the bathing woman is sort of hovering amidst the trio instead of rinsing herself off in the background. This is because the warmer colors flanked by more saturated greens in the grass around her &quot;pull&quot; her forward into the same space as the rest of the painting. Here, scale is one of the major cues that she should be in the background.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5W60c.jpg&quot; alt=&quot;Cezanne&amp;#39;s &amp;quot;The Bay&amp;quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Above is Cezanne's &quot;The Bay&quot; and is an excellent example of how warmer colors (reds, yellows, oranges) are used to add depth when contrasted with cool colors (blues, greens, violets). The image works very well, and that's partially because of the colors chosen. You can almost draw a diagonal line between the warm and cool portions of the painting.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I noticed that if I try to imagine a clear blue daytime sky contrasted with a clear night sky and ask myself which of the two appears closer, my intuition says the daytime sky appears closer. My next thought was, given that a night sky is mostly black, visually the only difference between the two skies is their color. So why is that I want to &quot;blue&quot; is closer than &quot;black&quot;? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, there are many differences between the two! The daytime sky has numerous reference points - the horizon, mountains, clouds, airplanes, nearby buildings, etc. I would bet the reference points are the number one reason you perceive the daytime sky to be closer, as our brain is constantly taking them into account without us thinking about it. There are other cues, too: The daytime sky has a gradient to it - that is, the blue of the sky differs due to the curve of the atmosphere, and gradients increase depth perception with more saturated colors being perceived as closer (as opposed to the edges of the daytime sky, which are often less saturated). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The night sky, on the other hand, is pretty much solid black (&lt;em&gt;if you live in suburban or urban areas&lt;/em&gt;). The lack of a gradient or other colors immediately robs the observer of some depth perception, and because of the inky blackness of night the other reference points - the horizon, nearby structures, airplanes, clouds, etc. - can practically disappear, robbing the observer of additional depth perception.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-01-01T15:16:37.473" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5629" PostTypeId="2" ParentId="5562" CreationDate="2013-01-02T02:51:11.557" Score="0" Body="&lt;p&gt;There's always shivering, and also the &lt;a href=&quot;http://en.wikipedia.org/wiki/Brown_adipose_tissue&quot; rel=&quot;nofollow&quot;&gt;brown adipose tissue&lt;/a&gt; that generates heat to keep the core temperature regulated. Extra mitochondria in brown adipose tissue can be used to generating heat without producing ATP. As @jackweirdy mentions, this is a negative feed back involving hypothalamus.&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2013-01-02T02:51:11.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5631" PostTypeId="1" CreationDate="2013-01-02T03:59:20.313" Score="3" ViewCount="588" Body="&lt;p&gt;The hypothalamus is known to be important in the regulation of body temperature, but I'm curious whether anyone knows about the neurocircuitry of perceived temperature. It seems like there could be a difference between how warm/cold someone feels and the temperature to which their body is trying to adjust. Intuitively, I'd imagine that any apparent difference in these  has to do with some sort of delayed feedback that is experienced before the autonomic nervous system can kick in. Does anyone know something more about this?&lt;/p&gt;&#xA;" OwnerUserId="1855" LastActivityDate="2013-01-03T17:29:52.560" Title="Neuroscience of temperature regulation and perception" Tags="&lt;neuroscience&gt;&lt;temperature&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5632" PostTypeId="1" AcceptedAnswerId="5633" CreationDate="2013-01-02T08:45:37.447" Score="3" ViewCount="202" Body="&lt;p&gt;I'm a computer programmer deeply interested in Biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wish to write a computer simulation for cell differentiation. I understand there will be seemingly impossible challenges in doing this. But first I am looking for  answers to some basic questions. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;I've learned that a zygote turns into 'embryonic stem cells' which results in the organism. How does the zygote turn into embryonic cells ?&lt;/li&gt;&#xA;&lt;li&gt;What are the factors that determine the specialization of embryonic stem cells into more specialized types of cells and how does this transformation take place physically ?&lt;/li&gt;&#xA;&lt;li&gt;Where is the data stored which acts as the &quot;guide&quot; for all these processes ? Is it stored in the DNA ? If it's stored in the DNA , is it known how the cells interpret the information in the DNA?&lt;/li&gt;&#xA;&lt;li&gt;What are some textbooks I should be referring for this project ?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;PS : Pardon my ignorance if these questions sound stupid, but I'm willing to commit time for learning anything needed to do this. Also , I understand all these questions cannot be answered in a few lines. Please provide references/pointers . Thanks !&lt;/p&gt;&#xA;" OwnerUserId="1816" LastEditorUserId="69" LastEditDate="2013-01-02T13:38:05.563" LastActivityDate="2013-01-02T15:46:52.130" Title="Simulating Cell differentiation" Tags="&lt;cell-biology&gt;&lt;dna&gt;&lt;embryology&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5633" PostTypeId="2" ParentId="5632" CreationDate="2013-01-02T11:17:22.673" Score="1" Body="&lt;p&gt;Trying to answer this question in a few lines is a tedious task. Mostly I'm not sure that as of today we know all there is to know about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll try to give you some hints though.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The process is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Embryogenesis&quot; rel=&quot;nofollow&quot;&gt;embryogenesis&lt;/a&gt;. The zygote (or &lt;em&gt;ovum&lt;/em&gt;) undergoes rapid mitotic divisions with no significant size growth which will lead to the development of an embryo. This process is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Cleavage_%28embryo%29&quot; rel=&quot;nofollow&quot;&gt;cleavage&lt;/a&gt;. Blastomeres are created during this process. On the third day - &lt;em&gt;time may vary but not significantly&lt;/em&gt; - &lt;strong&gt;cleavage&lt;/strong&gt; reaches the state of 16 cells. Cell divisions always occurs by parallel division (1 -&gt; 2, 2 -&gt; 4, 4 -&gt; 8, 8 -&gt; 16). Study the links I gave you and come back with more specific questions.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Again that's kind of impossible question to answer without explaining the entire process from fertilization to fetal development, because creation of tissues (cells) and organs happens along the way, not at once. However, it's documented.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Not sure.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Start with the wikipedia links and try to come back with more specific questions. I have a couple of text-books but I'm afraid they are not as detailed as you would want :-)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Good luck!&lt;/p&gt;&#xA;" OwnerUserId="1856" LastActivityDate="2013-01-02T11:17:22.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5634" PostTypeId="2" ParentId="5632" CreationDate="2013-01-02T14:56:14.460" Score="1" Body="&lt;p&gt;I would start with &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0878933840&quot; rel=&quot;nofollow&quot;&gt;Developmental Biology, 9th Ed.&lt;/a&gt; It's not up to the absolute cutting edge, as it was published in 2010, but it has a lot of good stuff in it. Wikipedia is a decent resource to get very brief overviews on certain subjects, but a lot of the life science articles I've read tend to be lacking, as opposed to the physics and math articles, for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for question 3, yes, the &quot;data&quot; is stored in DNA. For a thorough guide, one of my favorite books is &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0815341059&quot; rel=&quot;nofollow&quot;&gt;Molecular Biology of the Cell, 5th Ed.&lt;/a&gt;. It's a little dated now (published in 2007), but if you want to understand how DNA, RNA, and proteins work, it's a great overview text.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-01-02T14:56:14.460" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5635" PostTypeId="1" AcceptedAnswerId="5744" CreationDate="2013-01-02T15:23:29.153" Score="8" ViewCount="360" Body="&lt;p&gt;Algal blooms caused by man (harmful algal blooms) are a major ecological problem. An excessive amount of algae causes hypoxia and logically, most marine wildlife can't be sustained in hypoxic conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can't we use allelopathic plants to reduce the amount of algae significantly?&lt;/p&gt;&#xA;" OwnerUserId="1609" LastActivityDate="2013-01-15T20:51:07.500" Title="Can allelopathy succesfully be used against algal blooms?" Tags="&lt;ecology&gt;&lt;allelopathy&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5636" PostTypeId="2" ParentId="5632" CreationDate="2013-01-02T15:46:52.130" Score="1" Body="&lt;p&gt;The answers to most of your questions are under active research and there are many unknowns. Understanding this process is one of the main goals of developmental biology. So, try to set reasonable goals for your project, mainly by seeing where you have sufficient data to work with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would start with reading some basic textbook on developmental biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the flow of information: Remember that starting from the zygote and onwards to the whole organism, the DNA sequence is generally the same between all cells. As a computer scientist it might help you to think about it this way:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think of the DNA as a very complicated mathematical function $f()$ acting on cellular states. The current cellular state $S_i$ will be the total molecular components of the cell and will yield the biological function of the cell. So, you start with an initial cell state $S_0$ (could be a vector, for example) and then the daughter cells will be: $S_1=f(S_0)$, their daughter cells will be $S_2=f(S_1)$. This is not a perfect representation of the process (since at time point 2 you may actually have both $S_0$ and $S_1$ cells), but it emphasizes the point that although the DNA sequence &quot;computes&quot; the next step it is in fact constant, and the point that each cellular state dictates the next state. Seems to me like a Markov chain could be appropriate. Of course you can also try more sophisticated models - but it is better to start simple.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I would suggest starting with C. elegans as your modeled species. This is because the full differentiation fate of each of its 1031 somatic cells is known - a remarkable achievement and something you will not have in other species.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2013-01-02T15:46:52.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5637" PostTypeId="2" ParentId="5618" CreationDate="2013-01-02T17:49:44.333" Score="2" Body="&lt;p&gt;I think the concept of &lt;a href=&quot;https://en.wikipedia.org/wiki/Adaptive_radiation&quot; rel=&quot;nofollow&quot;&gt;adaptive radiation&lt;/a&gt; is what you may be thinking about, since adaptive radiations have been observed following historic mass extinctions.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When organisms are placed in environments with low diversity (either due to mass extinction or the recent creation of the environment) they can undergo adaptive radiation.  This generally occurs when there are lots of unoccupied niches in the environment - essentially there are lots of potential ways to make a living that are not being exploited by an existing organism.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this situation, any organism with a heritable trait that was able to utilize a niche better than other organisms would have a selective advantage and would increase in frequency.  Over time this process can result in new species of organisms.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is nothing really different about adaptive radiation and the normal process of evolution and speciation except that in an environment with lots of unoccupied niches, the probability of having a trait that gives you a selective advantage is greater so speciation occurs at a faster rate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is the normal processes of evolution and speciation that give the biome the capacity to increase diversity based on the remaining species.&lt;/p&gt;&#xA;" OwnerUserId="137" LastActivityDate="2013-01-02T17:49:44.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5638" PostTypeId="1" AcceptedAnswerId="5639" CreationDate="2013-01-02T19:43:04.530" Score="8" ViewCount="555" Body="&lt;p&gt;I was wondering if it's possible to gain more weight than the mass of the food you eat. At a first look, this is impossible because of the principle of mass conservation, but are there other things to take into consideration?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, fat contains carbon. Does the body use the carbon we breathe to produce the fat necessary to store any energy we don't use? And a relevant question: how efficient is human fat at storing energy, compared to what humans normally eat?&lt;/p&gt;&#xA;" OwnerUserId="1857" LastEditorUserId="16866" LastEditDate="2017-03-22T01:13:01.993" LastActivityDate="2017-03-22T01:13:01.993" Title="Possible to Gain More Weight than the Food You Eat" Tags="&lt;human-biology&gt;&lt;food&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5639" PostTypeId="2" ParentId="5638" CreationDate="2013-01-02T20:19:31.673" Score="7" Body="&lt;p&gt;No it is not possible.  Humans are heterotrophic organisms, which means that we use organic molecules (i.e., food) as a source of nutrients and energy.  We use the nutrients to add mass to our bodies.  These nutrients are the familiar carbohydrates, proteins, lipids (fats), etc...  During digestion food is broken down into simpler organic nutrient molecules that are then used to make our body tissues.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So even if we only used food for nutrients we could not gain more weight than the food we consume but note that the food is also used for energy. This means that some of the mass of the food that we eat is not used to add mass to the body but is &quot;burned&quot; as metabolic fuel.  The mass of the food used for energy is expelled from the body as waste in the $CO_2$ that we exhale and in the metabolic waste in the urine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The carbon in the air is mainly $CO_2$, which is an inorganic molecule.  Only autotrophic organisms like plants can use inorganic molecules as a source of nutrients.  Since inorganic molecules usually contain less potential energy than organic molecules autotrophic organisms need a different source of energy.  Plants use sunlight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, fat contains about &lt;a href=&quot;https://en.wikipedia.org/wiki/Food_energy&quot;&gt;9 Calories per gram&lt;/a&gt; whereas a Big Mac has about &lt;a href=&quot;http://www.wolframalpha.com/input/?i=big%20mac%20nutrition&quot;&gt;2.4 Calories per gram&lt;/a&gt; so fat has almost 4 times the energy of a Big Mac.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Calories are the amount of heat that is released if all of the energy in the organic molecules is released so it is an estimate of how much energy the body can get from food)   &lt;/p&gt;&#xA;" OwnerUserId="137" LastActivityDate="2013-01-02T20:19:31.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5640" PostTypeId="2" ParentId="1767" CreationDate="2013-01-02T21:10:30.657" Score="3" Body="&lt;p&gt;One significant point not considered in previous answers is the reproductive rate and environmental variability.  Larger animals have longer times between generations and generally reproduce less rapidly.  In a less stable environment, more rapid reproduction allows more rapidly adapting population to the availability of resources, providing a larger population so that random events are less likely to eliminate the entire species (genetic variation can be a factor here), and minimizes the absolute amount of resources needed for a stable population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are significant benefits to being larger.  In addition to interactions with other animals, a larger animal has lower surface area to mass ratio and so will lose less heat per unit mass (which might have been significant for ice-age mammals?).  A larger animal can also support larger organs (not just digestive tract as mentioned by Rosa Rubicondior, large brains would not be possible in small animals) or substantial-sized specialized features (where utility is not a linear function of size).&lt;/p&gt;&#xA;" OwnerUserId="1858" LastActivityDate="2013-01-02T21:10:30.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5642" PostTypeId="1" AcceptedAnswerId="5644" CreationDate="2013-01-02T21:45:47.763" Score="7" ViewCount="22356" Body="&lt;p&gt;When we breathe, our lungs absorb a portion of the oxygen in the air, and replace it with some amount of carbon dioxide and water vapor.  Typically, how much $O_2$ (in grams, milliliters, or moles for instance) is absorbed and how much $CO_2$ and $H_2O$ are released in one breath of a healthy adult?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, the exact amounts will vary from person to person and based on how deeply the person is breathing, lung health, etc.  I'm just looking for a ballpark figure.&lt;/p&gt;&#xA;" OwnerUserId="1859" LastActivityDate="2016-05-07T21:29:52.137" Title="How much gas is exchanged in one human breath?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;respiration&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5644" PostTypeId="2" ParentId="5642" CreationDate="2013-01-02T22:59:16.627" Score="8" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Tidal_volume&quot;&gt;Wikipedia&lt;/a&gt;  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;In a healthy, young adult, tidal volume is approximately 500 ml per inspiration...&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(tidal volume is the volume inspired/expired)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using this figure, together with values for gas composition also &lt;a href=&quot;http://en.wikipedia.org/wiki/Breathing#Breathing_in_gas&quot;&gt;taken from Wikipedia&lt;/a&gt;, I estimate that in each breath we take in 18 mg O&lt;sub&gt;2&lt;/sub&gt; (1.1 mmol) and we release 36 mg of CO&lt;sub&gt;2&lt;/sub&gt; (1.2 mmol) plus 20 mg H&lt;sub&gt;2&lt;/sub&gt;O (1.1 mmol). These are, as you say, ballpark figures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sample calculation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;O&lt;sub&gt;2&lt;/sub&gt; inspired = 21% by volume; O&lt;sub&gt;2&lt;/sub&gt; expired = 16% by volume&lt;/p&gt;&#xA;&#xA;&lt;p&gt;O&lt;sub&gt;2&lt;/sub&gt; change = 5% by volume = 5*500/100 = 25 mL&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1 mole gas = 22.4 L; 1 mmol gas = 22.4 mL&lt;/p&gt;&#xA;&#xA;&lt;p&gt;O&lt;sub&gt;2&lt;/sub&gt; change = 25/22.4 mmol = 1.1 mmol&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MW O&lt;sub&gt;2&lt;/sub&gt; = 16&lt;/p&gt;&#xA;&#xA;&lt;p&gt;O&lt;sub&gt;2&lt;/sub&gt; change = 17.6 mg&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The relative values are reassuringly close to what you might predict from the textbook equation for oxidation of carbohydrate: C&lt;sub&gt;6&lt;/sub&gt;H&lt;sub&gt;12&lt;/sub&gt;O&lt;sub&gt;6&lt;/sub&gt; + 6O&lt;sub&gt;2&lt;/sub&gt; -&gt; 6CO&lt;sub&gt;2&lt;/sub&gt; + 6H&lt;sub&gt;2&lt;/sub&gt;O&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-01-02T22:59:16.627" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5645" PostTypeId="1" CreationDate="2013-01-02T23:42:13.983" Score="3" ViewCount="73" Body="&lt;p&gt;What are the spatial (lateral and axional), and temporal resolutions that one is expected to get with the following optical imaging techniques?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Optical Bioluminiscence Imaging (BLI) &lt;/li&gt;&#xA;&lt;li&gt;Optical Fluorescence Imaging (FLI) &lt;/li&gt;&#xA;&lt;li&gt;Multiphoton Microscopy (e.g. 2-photon microscopy)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Are they any better than the  others in providing higher resolutions? &lt;/p&gt;&#xA;" OwnerUserId="17" LastEditorUserId="1320" LastEditDate="2013-01-03T08:57:56.697" LastActivityDate="2013-11-08T07:12:05.387" Title="Lateral, axional and temporal resolutions for imaging in vivo" Tags="&lt;microscopy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5646" PostTypeId="1" CreationDate="2013-01-02T23:45:33.687" Score="6" ViewCount="449" Body="&lt;p&gt;Are there any microscopy modalities or techniques for &lt;strong&gt;&lt;em&gt;in vivo&lt;/em&gt;&lt;/strong&gt; imaging at higher resolutions than the &lt;strong&gt;diffraction limit&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was looking at this list: &lt;a href=&quot;http://en.wikipedia.org/wiki/Super_resolution_microscopy&quot; rel=&quot;nofollow noreferrer&quot;&gt;Super resolution microscopy&lt;/a&gt;, but they don't talk about &lt;em&gt;in vivo&lt;/em&gt; imaging.&lt;/p&gt;&#xA;" OwnerUserId="17" LastEditorUserId="36209" LastEditDate="2018-01-21T07:31:51.417" LastActivityDate="2018-01-23T03:38:40.670" Title="Super-resolution imaging in vivo" Tags="&lt;microscopy&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5647" PostTypeId="1" AcceptedAnswerId="5648" CreationDate="2013-01-03T00:11:53.660" Score="4" ViewCount="337" Body="&lt;p&gt;What depth penetration can  one typically get with &lt;a href=&quot;http://en.wikipedia.org/wiki/Atomic_force_microscopy&quot; rel=&quot;nofollow&quot;&gt;atomic force microscopes&lt;/a&gt;? (i.e. how far into the tissue can one image?). I have found numbers on acquisition times (minutes) and spatial resolutions (~nm), but what about depth? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, what is the sensitivity of AFM? (e.g. in moles)&lt;/p&gt;&#xA;" OwnerUserId="17" LastActivityDate="2018-11-12T09:07:33.437" Title="Atomic force microscopy: depth penetration?" Tags="&lt;microscopy&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5648" PostTypeId="2" ParentId="5647" CreationDate="2013-01-03T01:24:44.403" Score="4" Body="&lt;p&gt;Taken right from the Wiki page you linked to:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AFM only images the surface of a specimen, to a maximum depth of 10-20 &amp;micro;m and a maximum scan area of 150 &amp;micro;m x 150 &amp;micro;m. Compared with scanning electron microscopy, SEM has a much larger depth of penetration and scanning area (~1 order of magnitude greater). AFM is also a much slower scanning method.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-01-03T01:24:44.403" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5649" PostTypeId="1" AcceptedAnswerId="5650" CreationDate="2013-01-03T09:23:51.823" Score="2" ViewCount="1650" Body="&lt;p&gt;I've read somewhere that after a person has a heart transplant, it is possible that his/her attitude, action or behavior would change slightly or significantly, as though he/she possesses some aspects of the organ donor's personality because he/she is using the donor's heart. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anything to support this phenomenon? Does it suggest that there are actually memories 'stored' in the heart and these memories may be retrieved by the person that owns the heart even if he/she is not the original owner?&lt;/p&gt;&#xA;" OwnerDisplayName="user661" LastEditorUserId="1320" LastEditDate="2013-01-03T10:42:40.997" LastActivityDate="2013-11-29T01:12:01.263" Title="Is it possible that the recipient of a heart transplant would display some of the donor's personality traits, as if the heart has memories?" Tags="&lt;behaviour&gt;&lt;memory&gt;&lt;cardiology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5650" PostTypeId="2" ParentId="5649" CreationDate="2013-01-03T10:40:33.177" Score="2" Body="&lt;p&gt;Although there is clearly no feasible mechanism for such a phenomenon, there is good evidence that transplant patients can &lt;strong&gt;believe&lt;/strong&gt; in some sort of transference of qualities from the donor. See for example (my emphasis):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Inspector, Y. &lt;em&gt;et al&lt;/em&gt;. (2004) Another Person's Heart: Magical and Rational Thinking in the Psychological Adaptation to Heart Transplantation. The Israel Journal of Psychiatry and Related Sciences 41: 161-73.&lt;/p&gt;&#xA;&lt;p&gt;Abstract&lt;/p&gt;&#xA;&lt;p&gt;The goal of this study was to examine heart transplant recipients' psychological adaptation to another person's heart, with particular emphasis on recipients' attitudes toward graft and donor.&#xA;Thirty-five male heart recipients were examined by: the Symptom Distress Checklist (revised) (SCL-90-R); the Depression Adjective Checklist (DACL); a Post-Traumatic Stress Disorder Questionnaire (PTSD-Q); a Heart Image Questionnaire (HIQ); and a Semi-Structured Interview (SSI), aimed at eliciting attitudes and fantasies regarding the transplanted heart.&#xA;All instruments indicated high levels of stress even several years after the transplant, but, simultaneously, 73% of recipients felt that acquiring a new heart had had a dramatic influence on their lives with a new appreciation of the preciousness of life and a shift of priorities, toward altruism and spirituality. Sixty percent returned to work after the transplant but some had to adapt to a changed attitude from those around them who regarded them as anything from mystical creatures to vulnerable or still-sick individuals. &lt;em&gt;&lt;strong&gt;While all recipients possessed a scientific knowledge of the anatomy and physiological significance of the heart (as revealed in the HIQ), many endorsed fantasies and displayed magical thinking: 46% of the recipients had fantasies about the donor's physical vigor and prowess, 40% expressed some guilt regarding the death of the donor, 34% entertained the possibility of acquiring qualities of the donor via the new heart.&lt;/strong&gt;&lt;/em&gt; When asked to choose a most and least preferred imagined donor, 49% constructed their choices according to prejudices, desires, or fears related to ethnic, racial or sexual traits attributed to the donor.&#xA;This study confirms the intuitive idea that heart transplant involves a stressful course of events that produces an amplified sense of the precariousness of existence. Simultaneously, it gives rise to rejoicing at having been granted a new lease on life and a clear sense of new priorities, especially with regard to relationships. Less expectedly, this study shows that, despite sophisticated knowledge of anatomy and physiology, almost half the heart recipients had an overt or covert notion of potentially acquiring some of the donor's personality characteristics along with the heart. The concomitance of the magical and the logical is not uncommon in many areas of human existence, and is probably enhanced by the symbolic nature of the heart, and maybe, also, by the persistent stress that requires an ongoing, emotionally intense, adaptation process.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Another study is reported in:&lt;/p&gt;&#xA;&lt;p&gt;Bunzel B, &lt;em&gt;et al&lt;/em&gt;. (1992) Does changing the heart mean changing personality? A retrospective inquiry on 47 heart transplant patients. Qual Life Res. 1:251-6.&lt;/p&gt;&#xA;&lt;p&gt;To actually investigate this further I suppose it would be necessary to set up experiments in which patients had transplant operations in which (unknown to the patient) no transplant actually took place, with the expectation that these individuals would display the same magical thinking. Grant application?&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-01-03T12:23:56.553" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5651" PostTypeId="2" ParentId="5621" CreationDate="2013-01-03T14:20:42.207" Score="0" Body="&lt;p&gt;They are not all eating the same/similar food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Elephants, horses and hippos are herbivores that have different diet to ruminants. Elephants, for example, have trunk to access fruits that is less difficult to digest. &lt;/p&gt;&#xA;" OwnerUserId="1795" LastEditorUserId="1795" LastEditDate="2013-01-03T15:55:35.813" LastActivityDate="2013-01-03T15:55:35.813" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5652" PostTypeId="2" ParentId="5646" CreationDate="2013-01-03T14:41:34.417" Score="3" Body="&lt;p&gt;Any superresolution techniques relying on stochastic sampling (e.g. PALM, STORM) is extremely difficult to accomplish &lt;em&gt;in vivo&lt;/em&gt;, as the tissue would be moving (e.g. due to respiration) and this would hinder a lot the reconstruction of the image.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently &lt;a href=&quot;http://optics.org/news/3/1/29&quot; rel=&quot;nofollow noreferrer&quot;&gt;it may be possible to do it with STED&lt;/a&gt; but I could not find the related paper*, although the same authors recently published some interesting &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0896627312007192&quot; rel=&quot;nofollow noreferrer&quot;&gt;work on living brain slices&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;*&lt;/sup&gt; Note that the images in that article come from &lt;a href=&quot;http://www.nature.com/nmeth/journal/v8/n7/full/nmeth.1624.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper&lt;/a&gt;, which is not done &lt;em&gt;in vivo&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks to @vkehayas for pointing out that in vivo STED has been done for instance here &lt;a href=&quot;http://www.sciencemag.org/cgi/doi/10.1126/science.1215369&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nanoscopy in a living mouse brain&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2018-01-23T03:38:40.670" LastActivityDate="2018-01-23T03:38:40.670" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5653" PostTypeId="2" ParentId="5631" CreationDate="2013-01-03T16:39:02.540" Score="3" Body="&lt;p&gt;I've found a good resource for this--an open-access review by Nakamura, &quot;&lt;a href=&quot;http://ajpregu.physiology.org.liboff.ohsu.edu/content/301/5/R1207.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Central Circuitries for Body Temperature Regulation and Fever&lt;/a&gt;.&quot; In it, the author provides a nice summary figure of the circuitry involved in temperature regulation (see below). As I suspected, the hypothalmus is pretty central to temperature regulation. I had forgotten about the involvement of the peripheral nervous system in responding to environmental temperatures, which, now that I think about it, makes some amount of sense, but is still pretty interesting. It appears that there's a difference in the specific circuitry and neurotransmitters used in responding to warm and cold temperature (especially GABA v. 5-HT), so I think a reasonable hypothesis regarding the basis of individual differences in the perceived temperature of an external environment might be differences in peripheral 5-HT systems (in addition to differences in body composition). Perhaps someone with a background in the peripheral nervous system could speak to this better than I can, but single nucleotide polymorphisms (SNPs) leading to differences in central 5-HT systems has been an active area of research in the neuroscience community of late (e.g., &lt;a href=&quot;http://www.biomedsearch.com/attachments/00/20/18/78/20187845/UPS-0300-9734-115-002.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nordquist &amp;amp; Oreland, 2010&lt;/a&gt;, &lt;a href=&quot;http://depressziostop.magtud.hu/rhimmer_zoltan/Gonda%20et%20al,%20Psychopharmacol%202010.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gonda et al., 2010&lt;/a&gt;), which I think lends some face validity to this idea.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/N18YC.png&quot; alt=&quot;Nakamura, 2011; Figure 1&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1855" LastEditorUserId="1855" LastEditDate="2013-01-03T17:29:52.560" LastActivityDate="2013-01-03T17:29:52.560" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5655" PostTypeId="2" ParentId="5587" CreationDate="2013-01-03T23:02:54.677" Score="3" Body="&lt;p&gt;While it's difficult to prove a negative, I know of no cases where a patient has been treated with HAART to the extent that their viral load never rises again. Keep in mind that, if nothing else, such a study would be extremely hard to do, as proving you've &quot;cured&quot; someone would require extremely long term followup.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HAART is however quite good at suppressing HIV, and there's currently no known upper bound on the lifespan of an HIV+ individual undergoing treatment. Compared to a 10 year post-infection life expectancy a decade or two ago, that's pretty darn good.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2013-01-03T23:02:54.677" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5656" PostTypeId="1" CreationDate="2013-01-04T00:02:20.033" Score="6" ViewCount="186" Body="&lt;p&gt;A more entertaining phrasing of the question would be &quot;what would a marine ecologist put into a perfect aquarium?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was reading about &lt;a href=&quot;http://en.wikipedia.org/wiki/Prochlorococcus&quot; rel=&quot;nofollow&quot;&gt;Prochlorococcus&lt;/a&gt;, among other photoautotrophs, and found that they seem to get their nitrogen from ammonia, which must be produced by some other organism. This set me off wondering what different species I would need in a hypothetical aquarium (how big that would have to be is another question, I guess), such that a sustainable ecological equilibrium occurs (one different from everybody dead, I guess), only requiring sunlight and air from the outside.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize that I'll have to put other components like iron etc in the water, but let's say I only put some fixed amount in during setup. What exactly that would have to be is probably another can of worms, so let's keep that out of this question as much as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has there been research towards such model ecosystems, and are there known minimum configurations?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's hard to give an authorative &quot;no&quot; to this answer. But maybe there's research that looked for such a system and failed, or maybe marine ecologists use model cultures in their labs that show instabilities (meaning the culture dies, you have to replace the water, or keep adding fertilizer, or keep removing some waste) which allow some generalizations.&lt;/p&gt;&#xA;" OwnerUserId="1864" LastEditorUserId="1864" LastEditDate="2013-01-04T12:58:46.120" LastActivityDate="2013-01-04T20:33:19.370" Title="Are there known minimal marine ecosystems that are stable?" Tags="&lt;ecology&gt;&lt;marine-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5658" PostTypeId="2" ParentId="5562" CreationDate="2013-01-04T06:03:14.597" Score="6" Body="&lt;p&gt;Since there seems to be several distinct sub-topics in your question, I will answer them one-by-one:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1). There are a variety of mechanisms that allow endothermic animals to maintain thermal homeostasis in a cold environment. The main ones are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a). The shivering response: When the core body temperature of a endotherm drops below a critical value (36.8C in humans), it causes the posterior hypothalamus to stimulate certain skeletal muscle groups (especially around vital organs) to start to &quot;shiver&quot; rapidly, generating heat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b). Compared to ectotherms, endotherms have more mitochondria per cell, thus allowing them to have a higher metabolism. Since metabolism always generates heat, an [general] increase in cellular metabolism will cause an increase in body heat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c). Many endotherms have layers of insulating matter, such as fur, blubber, feathers…etc, allowing them to preserve body heat. In addition, endotherms can also route blood away from  capillaries via vasoconstriction of arterioles, reducing the area in which heat can be lost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;d). As mentioned by Memming, brown adipose tissue also plays a role in temperature regulation. Thermoregulation-based metabolism in brown fat causes the P+ in the electron transport chain to go through thermogenin instead of ATP synthase. This process generates heat, but no ATP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;e). Some endotherms, such as penguins and arctic wolves have countercurrent exchange in their capillaries. This is when warm arterial blood &quot;passes&quot; some of its heat to cooler veinous blood. This feature allows some of the heat normally &quot;wasted&quot; into the air to be recycled back into the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: Though it is true that endotherms are able to keep their body temperature constant irrespective of their surroundings (ignoring extremes), they do this at a cost of requiring significant amounts sustenance. Most endotherms require much more sustenance than ectotherms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2). Your second sub-question is very interesting. Though it is true that generating heat will require substantial amounts of carbohydrates/fats/...etc, it does not necessarily mean that the net consumption of sustenance in cold environments is greater than that in normal environments. In most cases, endotherms in cold environments will have exhibit significantly less activity than when in an optimal environment. The decrease in activity when in a cold environment will likely balance out the increase in thermo-regulation based metabolism. This likely explains why people tend to drink equal or slightly less amounts of water when in cold environments. One more thing: some reactions heat-generating reactions (like the alternate ETC pathway) do not require water. Glycolysis and Krebs actually generates water (not to say that there is a net gain in the body :))&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3). In truth, nothing &quot;prevents&quot; ectotherms from generate heat. They simply do not have the cellular &quot;machinery&quot;. Ectotherms metabolize in ways very similar to other organisms, using molecules like ATP, glucose, fat…etc. Unlike endotherms however, they spend very little of their energy on temperature regulation. As a consequence, their overall metabolic rates are dependent on the external temperature. The point is this: A substantial portion of endotherm sustenance is used to generate heat. Only a small (if any) portion of ectotherm sustenance is used to regulate heat. As a result, endotherms require much more nourishment than ectotherms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4). I am not entirely certain what you mean by &quot;evolutionary path&quot;, but I will just say this: In many ways, endotherms and ectotherms are organisms that have found different ways to the same problem; how to regulate body heat for maximal survival and reproduction. Basically, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ectotherm- more dependent on environmental temperature, requires less sustenance&lt;/p&gt;&#xA;&#xA;&lt;p&gt;endotherm- less dependent on environmental temperature, requires more sustenance&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5). You are quite correct. The cellular and genetic components are very similar. Some morphological aspects seem to be shared as well.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sources: &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Cambell &amp;amp; Reece (2010) Biology (9th ed)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Swan, K. G.; R. E. Henshaw (March 1973), &quot;Lumbar sympathectomy and&#xA;  cold acclimatization by the arctic wolf&quot;, Analysis of Surgery 177 (3):&#xA;  286–292,&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Guyton &amp;amp; Hall (2006) Textbook of Medical Physiology. (11th ed)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Romanovsky AA. (2007). Thermoregulation: some concepts have changed.&#xA;  Functional architecture of the thermoregulatory system. Am J Physiol&#xA;  Regul Integr Comp Physiol. 292(1):R37-46.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1865" LastEditorUserId="69" LastEditDate="2013-01-04T11:00:27.960" LastActivityDate="2013-01-04T11:00:27.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5659" PostTypeId="1" CreationDate="2013-01-04T06:32:07.580" Score="2" ViewCount="83" Body="&lt;p&gt;Anecdotally, I have observed (myself included) that siblings tend to think that they look less similar to each other than an unrelated observer would say. Is there any experimental data to back this up, or am I completely wrong?&lt;/p&gt;&#xA;" OwnerUserId="1867" LastEditorUserId="69" LastEditDate="2013-01-04T11:02:11.393" LastActivityDate="2013-01-12T12:58:04.410" Title="Do siblings have a bias toward believing they look different from each other?" Tags="&lt;human-biology&gt;&lt;perception&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5660" PostTypeId="2" ParentId="5646" CreationDate="2013-01-04T07:38:35.340" Score="0" Body="&lt;p&gt;Yes. A decade ago I've been working on a software for microscope that does what you want.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amphoralabs.com/production/10404&quot; rel=&quot;nofollow&quot;&gt;Here's how the product looks after 12 years of development.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's optical, however it produces Z map instead if image, and has resolution is order of magnitudes below the diffraction limit:&#xA;&lt;a href=&quot;http://www.amphoralabs.com/production/10404/10708&quot; rel=&quot;nofollow&quot;&gt;http://www.amphoralabs.com/production/10404/10708&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1517" LastActivityDate="2013-01-04T07:38:35.340" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5662" PostTypeId="2" ParentId="5621" CreationDate="2013-01-04T08:19:29.410" Score="2" Body="&lt;p&gt;If you ever look at a huge pile of elephant/horse dung you will see it is full of poorly digested vegetation. I had an (unfortunate) 4 day project on a field trip in south africa which involved handling a lot of elephant s***, more than once I found whole amarula fruits!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think about this in comparison to ruminants which have a much better digested pile of dung, e.g. a cow-pat. The ruminant digestive system allows them to digest cellulose (found in plant material) much more efficiently than other vertebrates thanks to a specialized gut flora. You may want to look at &lt;a href=&quot;http://wiki.answers.com/Q/What_are_the_advantages_of_ruminant_digestion&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; and &lt;a href=&quot;http://www.vet.ed.ac.uk/clive/cal/rumencal/frames/frmrumen.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; for more details.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2013-01-04T08:19:29.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5663" PostTypeId="2" ParentId="5621" CreationDate="2013-01-04T10:55:25.853" Score="5" Body="&lt;p&gt;There is more difference than just the parts of plants that are eaten.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two of their stomachs - rumen and reticulum are not used for digesting food at all. Multiple rounds of chewing and mixing with saliva, wich result in very small particles of undigested food help the bacteria in those stomachs reach, digest and use that cellulose-rich plant material. Cows &quot;eat&quot; the bacteria from their stomachs and the grass is just food for these bacteria. You could say that cows are not herbivores but secondary consumers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look at this picture (from &lt;a href=&quot;http://en.wikipedia.org/wiki/Ruminant&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia article on ruminants&lt;/a&gt;, a good place to check all this in more detail but still simpler than most professional books):&#xA;&lt;img src=&quot;https://i.stack.imgur.com/DXgqL.jpg&quot; alt=&quot;ruminant digestion system versus single stomach animals&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See that the ruminants have the same second and third part of their digestive system (though the bacteria use up most of carbohydrates, so some difference in absorbed material), but have an additional part in the front - where the microbes digest and ferment the food, that the ruminant has provived them. The reticulorumen needs to be large in order to provide space for all that plant material and bacteria. &lt;/p&gt;&#xA;" OwnerUserId="1427" LastEditorUserId="1427" LastEditDate="2013-01-04T17:38:12.123" LastActivityDate="2013-01-04T17:38:12.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5664" PostTypeId="1" AcceptedAnswerId="5667" CreationDate="2013-01-04T11:32:14.783" Score="8" ViewCount="13952" Body="&lt;p&gt;I hope this is the right place to ask. I subscribe to several Stack Exchange threads, and regard them as the best internet forum for genuine and credible answers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I spent last evening talking to friend, at an Amateur Radio Club, who told me he has recently recovered from the norovirus. I was demonstrating an oscilloscope to him, and he also handled the handbook. All this is now in the holdall I used to carry it to the Club. I took all the precautions I could, like washing my hands and not getting them near my lips, nose etc. So, my question is: how long should I wait before opening my holdall, to be sure any infection there is dead?&lt;/p&gt;&#xA;" OwnerUserId="1868" LastActivityDate="2013-01-04T14:39:02.007" Title="How long will norovirus live?" Tags="&lt;virology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5665" PostTypeId="1" AcceptedAnswerId="7637" CreationDate="2013-01-04T13:09:24.027" Score="4" ViewCount="82" Body="&lt;p&gt;We cultivate a number of terrestrial organisms in greenhouses and stables where they live in completely artificial environments. This seems to extend far less to marine organisms, such as fish. Aquariums (especially the salt water variety) seem to be quite unstable and require a lot of maintenance, and commercial scale installations, like salmon farms, are set up in the ocean, rather than in a separate tank.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there inherent difficulties in cultivating marine organisms, or is it just that mankind has not tried as hard as with land species?&lt;/p&gt;&#xA;" OwnerUserId="1864" LastActivityDate="2016-01-10T23:20:51.133" Title="Are there inherent problems in simulating marine environments, as compared to terrestrial systems?" Tags="&lt;ecology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5666" PostTypeId="1" CreationDate="2013-01-04T13:51:08.003" Score="3" ViewCount="36" Body="&lt;p&gt;What are there the differences between these two modalities?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Diffuse_optical_imaging&quot; rel=&quot;nofollow&quot;&gt;Diffuse Optical Tomography (DOT)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Optical_Tomography&quot; rel=&quot;nofollow&quot;&gt;Optical Tomography (OT)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Are there forms of OT that are not DOT?&lt;/p&gt;&#xA;" OwnerUserId="17" LastActivityDate="2013-01-04T13:51:08.003" Title="Difference between Diffuse Optical Tomography and Optical Tomography" Tags="&lt;imaging&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5667" PostTypeId="2" ParentId="5664" CreationDate="2013-01-04T14:39:02.007" Score="6" Body="&lt;p&gt;Well, for him the virus is already likely at minimum levels within his body. If he's recovered (pass the fever phase) then his immune system has already dealt with the majority of the viral bodies in his system, since the peak of the immune response comes after the peak of the viral infection density (&lt;strong&gt;ignore B&lt;/strong&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZCfJi.jpg&quot; alt=&quot;graph from Nature Review: Immunology&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much of the virus was left in his system to actually spread is hard to guess. Sometimes infections never &lt;em&gt;truly&lt;/em&gt; go away, but merely become undetectable by conventional testing. However, if we're to assume that there's at least &lt;em&gt;some&lt;/em&gt; norovirus left to transfer to you then you should realize that the greatest chance for exposure has already come and gone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The moment you were in the same room together, talking in close proximity, shaking hands (if you did), or generally being &lt;em&gt;close&lt;/em&gt; is the most likely source of any infection you could have picked up. However, while most virii don't survive well outside of the body, the norovirus notably bucks that trend. &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;ved=0CDUQFjAA&amp;amp;url=http://hawaii.gov/health/environmental/sanitation/sanitationguidelines/norovirus.pdf&amp;amp;ei=5-XmUNGRHsGCrAGTs4EY&amp;amp;usg=AFQjCNEqsczlYE_k6RQO8EO1RGp9uD7kBw&amp;amp;bvm=bv.1355534169,d.aWM&quot; rel=&quot;noreferrer&quot;&gt;The Hawaiian Department of Health (PDF)&lt;/a&gt; notes that the virus can definitely survive outside the body for several days on hard surfaces (though it will &lt;em&gt;not&lt;/em&gt; grow), can survive being frozen, and that it only takes about 100 viral units to cause an infection (which could fit a few thousand times over on a grain of salt). &lt;a href=&quot;http://blogs.scientificamerican.com/artful-amoeba/2012/01/17/misery-inducing-norovirus-can-survive-for-months-perhaps-years-in-drinking-water/&quot; rel=&quot;noreferrer&quot;&gt;Scientific American&lt;/a&gt; also notes that norovirus can survive for &lt;em&gt;months or years&lt;/em&gt; in sources of drinking water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you've already done is pretty much what you should do to avoid infection. You've washed your hands, refraining from mucous membrane contact, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultimately how long you should wait depends on where the norovirus currently resides. A week should be sufficient if all of the norovirus is contained on the book or on other surfaces that you're not making contact with. However, if it's already had contact with your skin or mucous membrane, then you're either already fighting it off or you're about to become ill. Unfortunately it's a lot easier to expose yourself than contain something you can't see, as the &lt;a href=&quot;http://dsc.discovery.com/tv-shows/mythbusters/videos/flu-fiction-minimyth.htm&quot; rel=&quot;noreferrer&quot;&gt;Mythbusters have done a good job of showing (Video)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In all likelihood if he was still infected enough to transmit the virus to other people by the time you two started handling the same equipment and you didn't use gloves, you've probably been exposed. However, exposure doesn't automatically mean you get sick. If you're not sick within a week afterwards, you've successfully fought it off. So, congratulations, perhaps!&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-01-04T14:39:02.007" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5668" PostTypeId="1" CreationDate="2013-01-04T15:07:32.397" Score="8" ViewCount="196" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.nature.com/nature/journal/v460/n7255/full/nature08207.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this study&lt;/a&gt;, cited by &lt;a href=&quot;http://news.bbc.co.uk/2/hi/science/nature/8173384.stm&quot; rel=&quot;nofollow noreferrer&quot;&gt;many&lt;/a&gt; popular science magazines, jellyfish and other, smaller animals can contribute to the vertical ocean stir as much as currents do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Black Sea chemistry and biodiversity is highly coupled with the lack of vertical currents, present in oceans or bigger seas. Some of the effects are low salinity in the top layers - many ocean fish species cannot tolerate the Black Sea salinity, and limited space for life (below 50 meters there is no oxygen)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can the jellyfish population (which is exploding now) change the stratification of water layers enough that the highly saline waters from bottom go up, and oxygen goes to the deeper layers, allowing a completely new ecosystem here? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If yes, what are the outcomes of such prospects? Besides the potentially catastrophic &lt;a href=&quot;http://en.wikipedia.org/wiki/Black_Sea#cite_note-18&quot; rel=&quot;nofollow noreferrer&quot;&gt;release of hydrogen sulphide&lt;/a&gt; form the bottom, can it be an improvement for the biodiversity here?&lt;/p&gt;&#xA;" OwnerUserId="1869" LastEditorUserId="1869" LastEditDate="2017-08-27T19:24:52.537" LastActivityDate="2017-08-27T19:24:52.537" Title="Can jellyfish improve the Black Sea ecosystem?" Tags="&lt;biochemistry&gt;&lt;ecology&gt;&lt;marine-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5669" PostTypeId="2" ParentId="5621" CreationDate="2013-01-04T16:38:24.363" Score="3" Body="&lt;p&gt;It is not a biology question but simply a logistic problem. The digestion of cellulose just because of the presence of celluase producing microbes. Rumination itself, by the action of chewing, can enhance the cellulose digestion efficiency by incresing the surface area. Still nothing related to the multiple compartments of the ruminant stomach.&#xA;Actually, the multiple compartments allowed the anti-directional peristalysis and multi-tasking of the stomach. That is Ruminants need A Multi-Compartment Stomach to perform rumination for the reason of logistic.&lt;/p&gt;&#xA;" OwnerUserId="1871" LastActivityDate="2013-01-04T16:38:24.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5670" PostTypeId="1" AcceptedAnswerId="5671" CreationDate="2013-01-04T17:32:40.573" Score="14" ViewCount="90594" Body="&lt;p&gt;I overheard a rather heated argument about whether or not animal cells have vacuoles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One person said that they do, but they're much smaller than vacuoles in plant cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other person said they don't. While there is &lt;em&gt;something&lt;/em&gt; there that acts similar to a vacuole, it's slightly different. The person also noted that the only websites that say that &lt;em&gt;something&lt;/em&gt; as a vacuole aren't credible sites (ie. not University sites, etc...)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm really curious as to which it is: Do animal cells have vacuoles or not?&lt;/p&gt;&#xA;" OwnerUserId="1098" LastActivityDate="2017-04-11T05:58:36.173" Title="Do animal cells have vacuoles?" Tags="&lt;cell-biology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5671" PostTypeId="2" ParentId="5670" CreationDate="2013-01-04T17:54:23.213" Score="16" Body="&lt;p&gt;They are both right.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Animal cells do have vacuoles, but they are smaller, larger in number (plant cells usually have just one or a few large vacuoles) AND serve a somewhat different purpose than those of plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A vacuole is basically a membrane-covered compartment (vesicle) filled with molecules, that shouldn't, right now, be in the cytoplasm. For plants, this means long-term storage of water and waste products, which cannot be removed from the cell due to the cell wall. For animals it means mostly taking part in exocytosis and endocytosis - they are much more dynamic structures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And about some half-professional sources, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26844/#A2369&quot; rel=&quot;nofollow noreferrer&quot;&gt;here is a bit from Molecular Biology of the cell&lt;/a&gt; which in fact calls plant vacuoles &quot;a kind of specialized lysosome&quot;.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastEditorUserId="1098" LastEditDate="2017-04-11T05:58:36.173" LastActivityDate="2017-04-11T05:58:36.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5672" PostTypeId="1" CreationDate="2013-01-04T19:22:58.870" Score="1" ViewCount="90" Body="&lt;p&gt;I prefer answers, not just discussing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the mechanical part of the human eye the control system to protect for overload of the diaphragm in the iris with a strong coupling to the light intensity that falls on the retina has his place in the visual system as close as possible to the light source in the chain of control devices of the human visual system. The iris is disk-shaped and consists of two muscles. Like a diaphragm for light, the iris regulates how much light comes into our eyes. In bright conditions, the muscles of the iris limit how much light comes in. In lowlit conditions, the muscles of the iris increase the amount of light comming in. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basic hypotheses is that the protection device in mammalian human hearing system is based on similarity as in the visual system and therefore should well also be using similar protection tools as used in the visual system and should well also be placed in the chain of control devices as close as possible to the signal source, as an experienced system engineer will always place a protection device in the chain of control devices as close as possible to the signal source.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exists such an continuous functioning simalarity analogue in the protection system for sound signals ?&#xA;Both the iris in the eye (two muscles) and eardrum+ossicular chain in the ear (two muscles): in protection. &#xA;Exists that similarity ? &lt;/p&gt;&#xA;" OwnerUserId="1873" LastActivityDate="2015-07-23T14:04:42.733" Title="Hearing system as in visual system: exists well also - in protecting the inner mechanical parts of both sensing systems - a similarity?" Tags="&lt;hearing&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ClosedDate="2015-07-24T04:36:33.130" ContentLicense="CC BY-SA 3.0" />
  <row Id="5673" PostTypeId="2" ParentId="5656" CreationDate="2013-01-04T20:33:19.370" Score="5" Body="&lt;p&gt;This is the one I've heard of - Its a &lt;a href=&quot;http://www.kk.org/outofcontrol/ch8-b.html&quot; rel=&quot;noreferrer&quot;&gt;sealed acrylic globe that contains algae and brine shrimp&lt;/a&gt;.  There are quite a few references in the bibliography here to previous systems.&lt;/p&gt;&#xA;&lt;p&gt;Of course, it needs sunlight, but all the elements are recycled.  Its really closed and has reasonable endurance.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The basic commercial version of his closed world -- sold under the label of &amp;quot;Ecosphere&amp;quot; -- is a glass globe about the size of a large grapefruit. My world #58262 was one of these. Completely sealed inside the transparent ball were four tiny brine shrimp, a feathery mass of meadowgreen algae draped on a twig of coral, and microbes in the invisible millions. A bit of sand sat on the bottom. No air, water, or any other material entered or exited the globe. The thing ate only sunlight.&lt;/p&gt;&#xA;&lt;p&gt;The oldest living Hanson-world so far is ten years old; that's as long as they have been manufactured. That's surprising since the average life-span of the shrimp swimming inside was thought to be about five years. Getting them to reproduce in their closed world has been problematic, although researchers know of no reason why they could not go on replicating forever. Individual shrimp and algae cells die, of course. What &amp;quot;lives forever&amp;quot; is the collective life, the aggregate life of a community.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;All of this is a real subject of research for those interested in creating entirely useful ecosystems.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;It turns out that ecospheres scale up well. A huge commercial Ecosphere can weigh in at 200 liters. That's about the volume of a large garbage can -- so big you can't reach your arms around it. Inside a stunning 30-inch-diameter glass globe, shrimp paddle between fronds of algae. But instead of the usual three or four spore-eating shrimp, the giant Ecosphere holds 3,000. It's a tiny moon with its own inhabitants. Here, the law of large numbers takes hold; more is different. More individual lives make the ecosystem more resilient. The larger an Ecosphere is, the longer it takes to stabilize, and the harder it is to kill it. But once in gear, the collective give and take of a vivisystem takes root and persists.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Unfortunately larger systems that can support people have not been made yet.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Algae and man lasted a whole day. For about 24 hours, man breathed into algae and algae breathed into man. Then the staleness of the air drove Shepelev out. The oxygen content initially produced by the algae plummeted rapidly by the close of the first day. In the final hour when Shepelev cracked open the sealed door to clamber out, his colleagues were bowled over by the revolting stench in his cabin. Carbon dioxide and oxygen had traded harmoniously, but other gases, such as methane, hydrogen sulfide, and ammonia, given off by algae and Shepelev himself, had gradually fouled the air. Like the mythological happy frog in slowly boiling water, Shepelev had not noticed the stink.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Here is an &lt;a href=&quot;http://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1065&amp;amp;context=tnas&quot; rel=&quot;noreferrer&quot;&gt;academic reference&lt;/a&gt; you can use to start looking around if you like...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-01-04T20:33:19.370" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5674" PostTypeId="2" ParentId="5599" CreationDate="2013-01-04T21:29:18.063" Score="3" Body="&lt;p&gt;I am assuming that you are referring to a baseline human cooled to a core body temperature of 30C from birth. I am also assuming that you are ignoring the fact that the environmental temperature (and thus the temperature of the extremities) has to be much lower than 30C to cause a core temperature of 30C. Thus, I am ignoring hypothermia-based gangrene, necrosis, and extremity loss.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you had a normal human with a 30C core temperature starting at birth, I have doubts that it would live any longer than a human at 36.8C. Unlike flies, which are ectotherms, humans need to have a more or less constant temperature to successfully complete most of their metabolic processes efficiently. Since humans are not built to withstand extremely low temperatures, it is likely that lowering the core body temperature to 30C will cause it to have organ impairment, causing organ failure, followed by death. Though you might be able to &quot;fool&quot; the brain on thinking that 30C is normal, it is unlikely that the organ functions can follow. It could be possible to breed successive generations of humans in ever-lower temperatures, but it is unlikely for a baseline human to withstand such a large temperature drop. Sensory neuron adaptation =/= bodily adaption. However, lowering the core human body temperature by 1-2 degrees (typical of sleep) may have a chance of altering a human's lifespan in a more meaningful way. Though cooling may prolong the lifespan of temperature-conformers and single-celled animals, it is unlikely that the same can be said for endotherms. Endotherms have had biological processes that run on a fixed temperature for a long time already.  One more thing: @Hermann: Their core body temperature may not have been much lower than the baseline.&lt;/p&gt;&#xA;" OwnerUserId="1865" LastEditorUserId="1865" LastEditDate="2013-01-05T05:00:28.400" LastActivityDate="2013-01-05T05:00:28.400" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5675" PostTypeId="1" AcceptedAnswerId="5682" CreationDate="2013-01-04T22:55:57.483" Score="7" ViewCount="171" Body="&lt;p&gt;When tired and it was dark, I noticed that if I focused on a dim light source and moved my eyes fairly rapidly sideways, the resulting images that lingered for a short while were not smoothly blurred together, but were discrete.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume this is not due to the brain's inability to process the data fast enough or the retinas not repairing fast enough when light breaks part of them down, so I am lead to the conclusion that eyes (if not generally, sometimes) move in very small sudden jolts rather than smoothly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this correct? What is the reason for this (is it due to the eye muscles being unable to sustain motion for a long time, or something to do with the mechanics of the eye)? Was this result anomalous?&lt;/p&gt;&#xA;" OwnerUserId="1667" LastActivityDate="2015-01-20T11:02:22.670" Title="Is the eyes' movement discrete?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5676" PostTypeId="1" AcceptedAnswerId="13572" CreationDate="2013-01-04T23:09:53.043" Score="17" ViewCount="68993" Body="&lt;p&gt;Many people can grow extremely long head hair and facial hair. Are there evolutionary theories as to why this is the case? It seems like having long hair could be a disadvantage, and extremely long hair seems to be rare in other mammals.&lt;/p&gt;&#xA;" OwnerUserId="1874" LastActivityDate="2021-01-21T00:12:38.580" Title="Why does human facial and head hair continue to grow?" Tags="&lt;evolution&gt;&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5677" PostTypeId="2" ParentId="2229" CreationDate="2013-01-04T23:15:04.027" Score="2" Body="&lt;p&gt;Genotyping only tests for SNPs in predetermined locations. If you have SNPs in other places in your genome, genotyping won't tell you that, but whole genome sequencing will (by comparing your genome to a reference genome available at NCBI). Also, there are other variants such as copy number variations, repeats, insertions and deletions that genotyping can not capture, but all of those can contribute to disease.&lt;/p&gt;&#xA;" OwnerUserId="1875" LastActivityDate="2013-01-04T23:15:04.027" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5678" PostTypeId="2" ParentId="785" CreationDate="2013-01-04T23:25:14.413" Score="8" Body="&lt;p&gt;Your question is based on a bit of confusion about electron acceptors that is very common and that drives microbiologists crazy. Energy (as ATP) is generated when electrons are moved from an electron donor to an electron acceptor. In respiration, the electron acceptor is inorganic -- oxygen for aerobic respiration or an inorganic molecule such as sulfate or nitrate for anaerobic respiration. Use of an organic molecule such as pyruvate as an electron acceptor is properly called fermentation. Both anaerobic respiration and fermentation are termed anaerobic because they don't use oxygen. Any introductory microbiology textbook will cover these concepts in detail, because they are important to understanding the metabolic diversity of bacteria. Brock Biology of Microorganisms is a good text.&lt;/p&gt;&#xA;" OwnerUserId="1876" LastActivityDate="2013-01-04T23:25:14.413" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5679" PostTypeId="2" ParentId="5672" CreationDate="2013-01-04T23:52:14.220" Score="0" Body="&lt;p&gt;The cooperative functioning of the eardrum and ossicular chain attenuation can be regarded as in this &lt;a href=&quot;http://www.a3ccm-apmas-eakoh.be/figures/figures.htm&quot; rel=&quot;nofollow&quot;&gt;schematic drawing of the ear as an externally activated spring-mass system&lt;/a&gt;. Fig. 2. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ossicular chain and eardrum function, together operating as a continuous sound reduction mechanism for changes in the strength of the offered signal. The tympanic membrane and the ossicular chain can be seen as a spring-mass system with amplification facilities, like it is shown in this &lt;a href=&quot;http://www.a3ccm-apmas-eakoh.be/easms/easms.htm&quot; rel=&quot;nofollow&quot;&gt;figure&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The combined action of the ossicular chain and the eardrum is hypothesized to provide for both permanent volume control of the input sound and for overload protection. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Acoustic_reflex&quot; rel=&quot;nofollow&quot;&gt;stapedius reflex&lt;/a&gt;, evoked by sudden strong sound signal, cannot be seen as anything else than an extreme manifestation of the very mechanism that the schematic drawing of the ear as an externally activated spring-mass system propose. &lt;/p&gt;&#xA;" OwnerUserId="1854" LastActivityDate="2013-01-04T23:52:14.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5680" PostTypeId="1" CreationDate="2013-01-05T00:01:03.307" Score="4" ViewCount="1585" Body="&lt;p&gt;As in the subject line, what percentage of capillaries in a human (expressed in terms of total length, I suppose) are located in the skin, as opposed to internal organs?  Google scholar has not turned up anything obvious, but I'm an outsider so I may have missed the appropriate term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another followup question would be:  if we're considering the amount of energy expended by the heart in pumping blood throughout the body, what's the percentage of that energy that is devoted only to (1) transporting blood to the skin and (ii) circulating blood through the skin via capillaries?&lt;/p&gt;&#xA;" OwnerUserId="1877" LastActivityDate="2018-08-27T13:44:00.563" Title="What percentage of human capillaries are located in the skin?" Tags="&lt;cardiology&gt;&lt;skin&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5681" PostTypeId="2" ParentId="3830" CreationDate="2013-01-05T05:45:44.857" Score="4" Body="&lt;p&gt;After salamanders (or certain other amphibians) lose a limb, the epidermis migrates to cover the wound, forming a structure known as the apical epidermal cap. The underlying &quot;stump&quot; then generates a de-differentiated mass of cells from normal tissue. In most cases, these cells will express genes that are vital to the proper formation of limbs, such as HOX genes. This &quot;lump&quot; of cells at the stump of the wound are typically referred to as a blastema. Basically, the blastema continues to grow and regenerate the limb in a way similar to fetal growth. Though mammals (including humans) also have some regenerative capabilities, they are much more limited. In addition, many regenerated limbs will also be mildly deformed (square fingernails). In axolotl salamanders, it was found that certain retrotransposons, such as the LINE-1 element, were prevented from &quot;jumping&quot; around in the developing blastema during limb regeneration. The two active proteins PL1 and PL2 were responsible for inhibiting the activity of LINE-1 and other such retrotransposons. Active retrotransposons can potentially rearrange the genes in germ cells can be detrimental to the mechanisms that allow the blastema to replicate and differentiate, so the PL2 and PL1 proteins play a vital role in their regenerative capabilities. When the PL2 and PL1 proteins were &quot;switched off&quot; in certain axolotl salamanders, their regeneration was much less efficient. Since mammals lack the PL1 and PL2 proteins and have a different LINE-1 retrotransposon, they have reduced regenerative capabilities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wei Zhu, Dwight Kuo, Jason Nathanson, Akira Satoh, Gerald M. Pao, Gene W. Yeo, Susan V. Bryant, S. Randal Voss, David M. Gardiner, Tony Hunter. Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration. Development, Growth &amp;amp; Differentiation, 2012; 54 (7)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wei Zhu, Gerald M. Pao, Akira Satoh, Gillian Cummings, James R. Monaghan, Timothy T. Harkins, Susan V. Bryant, S. Randal Voss, David M. Gardiner, Tony Hunter. Activation of germline-specific genes is required for limb regeneration in the Mexican axolotl. Developmental Biology, 2012; 370 (1)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Odelberg SJ (August 2004). &quot;Unraveling the Molecular Basis for Regenerative Cellular Plasticity&quot;. PLoS Biology 2 (8)&lt;/p&gt;&#xA;" OwnerUserId="1865" LastActivityDate="2013-01-05T05:45:44.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5682" PostTypeId="2" ParentId="5675" CreationDate="2013-01-05T13:21:51.723" Score="6" Body="&lt;p&gt;There are two types of eye movement: &lt;a href=&quot;http://en.wikipedia.org/wiki/Smooth_pursuit&quot; rel=&quot;nofollow&quot;&gt;smooth pursuit&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Saccade&quot; rel=&quot;nofollow&quot;&gt;saccadic&lt;/a&gt;. As the name suggests the latter movement involves quick and discontinuous movements of the eyes. Saccadic movement is used most of the time as the eyes move around analysing the current scene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Wikipedia, these saccades are the fastest movements produced by the human body: peak angular speed of 900 degrees of rotation per second (this would be 2.5 full rotations of the eyeball per second, were such a thing possible).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The processing of information by the eye-brain system during a saccade is complex, and may be responsible for the effect that you report: it causes the phenomenon of saccadic masking explained in this quote from Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A person may observe the &lt;a href=&quot;http://en.wikipedia.org/wiki/Saccadic_masking&quot; rel=&quot;nofollow&quot;&gt;saccadic masking&lt;/a&gt; effect by standing in front of a mirror and looking from one eye to the next (and vice versa). The subject will not experience any movement of the eyes nor any evidence that the optic nerve has momentarily ceased transmitting. Due to saccadic masking, the eye/brain system not only hides the eye movements from the individual but also hides the evidence that anything has been hidden. Of course, a second observer watching the experiment will see the subject's eyes moving back and forth. The function's main purpose is to prevent smearing of the image.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="3624" LastEditDate="2015-01-20T11:02:22.670" LastActivityDate="2015-01-20T11:02:22.670" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5684" PostTypeId="1" CreationDate="2013-01-06T00:40:54.007" Score="18" ViewCount="30148" Body="&lt;p&gt;Are there any studies or general information on the composition of human feces?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd specifically like to know the percentage of carbohydrates and amino acids relative to the amount that was ingested in diets of various types and amounts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any additional facts are also welcome.&lt;/p&gt;&#xA;" OwnerUserId="1585" LastEditorUserId="57" LastEditDate="2013-01-06T02:16:55.153" LastActivityDate="2016-07-26T13:19:40.607" Title="What is the composition of human feces?" Tags="&lt;human-biology&gt;&lt;nutrition&gt;&lt;gastroenterology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5685" PostTypeId="1" CreationDate="2013-01-06T02:26:37.773" Score="5" ViewCount="107" Body="&lt;p&gt;Is it possible to select from colonies only cells which are at a certain stage in the cell cycle? E.g. if I was trying to analyse expression of a number of genes during different stages of the cell cycle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could imagine that if this is possible, the selection mechanism might target cyclins, or use an artificial gene cassette controlled by them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for example, a method may attach some gene to a certain cyclin which protects against a substance that otherwise destroys the cell. We could then use that substance to destroy all cells which were not in the cell cycle stage that we want to look at, wash away their nucleic acids, and then extract the mRNA from remaining cells to analyse expression levels at this particular stage in the cell cycle. If we repeat that for the different stages, we should be able to get a nice picture of what is expressed when. Does any method like this exist or is commonly used?&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-01-06T16:49:15.773" LastActivityDate="2016-05-25T16:40:38.037" Title="Cell cycle selection" Tags="&lt;cell-biology&gt;&lt;molecular-genetics&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5686" PostTypeId="2" ParentId="2688" CreationDate="2013-01-06T02:37:22.607" Score="1" Body="&lt;p&gt;I have found the answer to the purpose of the adrenal medulla to be &lt;em&gt;flexibility&lt;/em&gt;. Just like regulation for example of gene expression or metabolism occurs on many levels with different speeds and permanences of their effects, signalling needs to be available both quick and short-lived, and slower but with more long-lasting effects. The adrenal medulla provides exactly that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sympathetic adrenergic neurons are quick, but as quickly as they release their neurotransmitter, the effect is only of short duration and adrenalin is quickly cleared from the target area. Rather than giving off short bursts of adrenalin, the medulla maintains a constant systemic level of it and in response to stimulation raises or lowers that level. This response takes more time as blood circulates much slower than neurons respond, but its effects last longer.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-01-06T10:53:49.870" LastActivityDate="2013-01-06T10:53:49.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5687" PostTypeId="2" ParentId="2688" CreationDate="2013-01-06T05:19:38.767" Score="1" Body="&lt;p&gt;I would argue that the adrenal medulla is a real endocrine tissue for the following reasons. First and foremost, it fits the definition of an endocrine tissue, which is to produce and secrete hormones in a regulated manner. You've already highlighted the physiological effects of those hormones, and I would ad dopamine as the other major secretory hormone/neurotransmitter. Chromaffin cells are dervived from neurons, but the presence of a regulated secretory pathway is a hallmark of endocrine tissues. @Armatus answer of plasticity is on the mark, although I think a term that more readily describes the system's ability react over a greater time scale would be &lt;em&gt;impedence matching&lt;/em&gt;. Another differentiating characteristic is that the adrenal medulla is capable of sustained synthess and secretion in response to stimuli, whereas I don't think this is typical of most neurons which transmit a message only briefly.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-01-06T05:19:38.767" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5688" PostTypeId="1" AcceptedAnswerId="5695" CreationDate="2013-01-06T14:41:14.357" Score="4" ViewCount="143" Body="&lt;p&gt;I don't understand how to sum the changes in a phylogenetic tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here for example: &lt;a href=&quot;http://www.med.nyu.edu/rcr/rcr/course/phylo-cladistic.html&quot; rel=&quot;nofollow&quot;&gt;http://www.med.nyu.edu/rcr/rcr/course/phylo-cladistic.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do you end up with 8 for the first and 9 for the second ?&lt;/p&gt;&#xA;" OwnerUserId="1882" LastEditorUserId="806" LastEditDate="2013-01-06T15:47:40.950" LastActivityDate="2013-01-07T10:20:13.517" Title="Parsimony (cladistics)" Tags="&lt;homework&gt;&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5689" PostTypeId="2" ParentId="5685" CreationDate="2013-01-06T16:10:31.090" Score="0" Body="&lt;p&gt;You have correctly stated that we can monitor cell cycle stage by either monitoring protein (cyclin) levels or by following indirect methods such as green cassettes. One usually tries to monitor changing levels of:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;G1 cyclins (D cyclins)&lt;/li&gt;&#xA;&lt;li&gt;S-phase cyclins (cyclins E and A)&lt;/li&gt;&#xA;&lt;li&gt;Mitotic cyclins (B cyclins)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Or one might try to modify the gene where these proteins are produced so that one can observe some unique behavior that highlights that particular stage of cell cycle is going on. &lt;/p&gt;&#xA;" OwnerUserId="1878" LastActivityDate="2013-01-06T16:10:31.090" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5690" PostTypeId="1" CreationDate="2013-01-06T18:19:59.210" Score="1" ViewCount="33" Body="&lt;p&gt;Do heteroreceptors always suppress the release of the neurotransmitter they regulate upon their (the heteroreceptor's) activation? &lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-01-06T18:19:59.210" Title="Does regulate always mean suppress when it comes to heteroreceptors?" Tags="&lt;neurotransmitter&gt;&lt;receptor&gt;&lt;neuromodulation&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5691" PostTypeId="1" AcceptedAnswerId="5692" CreationDate="2013-01-07T03:04:38.723" Score="5" ViewCount="59761" Body="&lt;p&gt;As I understand it, the main difference between the Bacteria and the Eucaryota domains are that eukaryotes have a nucleus and bacteria don't. I understand that bacteria and archaebacteria have enough of a genetic difference to be separate kingdoms, but why are they separate domains?&lt;/p&gt;&#xA;" OwnerUserId="1182" LastEditorUserId="57" LastEditDate="2013-01-07T03:06:28.963" LastActivityDate="2016-09-22T01:08:50.337" Title="Why are bacteria and archaea in different domains?" Tags="&lt;bacteriology&gt;&lt;taxonomy&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5692" PostTypeId="2" ParentId="5691" CreationDate="2013-01-07T04:48:51.310" Score="11" Body="&lt;p&gt;The reason that Archaea were determined to be a separate (and only the third) kingdom so late (&lt;a href=&quot;http://www.ucmp.berkeley.edu/archaea/archaea.html&quot; rel=&quot;noreferrer&quot;&gt;1977 according to this reference&lt;/a&gt;) was because archaea often completely resemble eubacteria.  They are unicellular and have no organelles and appropriately they were grouped with other prokaryotes because of their morphology and cellular physiology.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But by the 1970s phylogeny becoming based on the sequence of DNA and RNA which were just becoming more available.  Based on a simple comparison of the sequences of 18S rRNA of 13 fungi, bacteria and archaea, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC432104/pdf/pnas00033-0388.pdf&quot; rel=&quot;noreferrer&quot;&gt;Woese and Fox showed that the bacteria and the archaea were about as different from the eukaryotes than from the bacteria&lt;/a&gt;.  (see table 1).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since then, the differences between bacteria and archaea have continued to be great.  The wikipedia diagram below is not to scale- the divergence of the three kingdoms is so far back that they pre-date the emergence of eukaryotes entirely. But you can see that fungi and other eukaryotes are more similar to archaea than the bacteria.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW, the idea that archaea are extremophiles is not entirely true - they are pretty much exclusively the only kingdom found in these conditions, but archaea have been found to coexist with bacteria and eukaryotes &lt;a href=&quot;http://www.biomedcentral.com/1471-2164/13/S7/S29&quot; rel=&quot;noreferrer&quot;&gt;in the open sea&lt;/a&gt; and their detection heretofore in most environments may be only due to the fact that archaea are difficult to grow in the lab.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just found this &lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=archaebacteria-the-third&amp;amp;WT.mc_id=SA_CAT_EVO_20130102&quot; rel=&quot;noreferrer&quot;&gt;retrospective from Woese himself&lt;/a&gt;, who passed away recently.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/J5LnS.png&quot; alt=&quot;phylogenetic trees of the 3 kingdoms&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-01-09T14:04:18.523" LastActivityDate="2013-01-09T14:04:18.523" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5693" PostTypeId="1" AcceptedAnswerId="5694" CreationDate="2013-01-07T06:24:16.860" Score="8" ViewCount="1127" Body="&lt;p&gt;Is there a reason as to why chickens lay &amp;quot;egg&amp;quot; shaped eggs, as opposed to spherically shaped eggs (or a random shape)?&lt;/p&gt;&#xA;&lt;p&gt;For extra points:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;why do plant seeds often come in this same &amp;quot;egg&amp;quot; shape (e.g. avocado&#xA;seeds), as opposed to a sphere?  Is it a coincidence that avocado&#xA;seeds and eggs are the same shape?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="60815" LastEditDate="2021-04-17T17:00:27.777" LastActivityDate="2021-04-17T17:00:27.777" Title="Why are eggs &quot;egg&quot; shaped?" Tags="&lt;evolution&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="5694" PostTypeId="2" ParentId="5693" CreationDate="2013-01-07T08:07:11.907" Score="11" Body="&lt;p&gt;There is variance in egg shape; sea-birds often use a more pear or conical shaped egg to prevent it from rolling off the cliff (where they nest) if it is disturbed. Some reptiles lay very spherical eggs (some turtles) whereas some reptiles lay very elongated ones (see black pine snake eggs).&lt;/p&gt;&#xA;&lt;p&gt;I imagine that we don't see square eggs because they would be difficult to shape and difficult to lay. Shape may also influence strength.&lt;/p&gt;&#xA;&lt;p&gt;Google your question (like I did after writing the above) and it will come up with &lt;a href=&quot;http://www.abc.net.au/science/articles/2012/05/01/3492086.htm&quot; rel=&quot;noreferrer&quot;&gt;this article&lt;/a&gt; which pretty much says what I just did. Here are some of the author's key points...&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&amp;quot;If eggs were rectangular little boxes, they would be very strong on the corners, but very weak in the middle of the straight walls.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;&amp;quot;The strongest shape of all is a ball, or sphere. But if you were to push or gently nudge a spherical egg, it would roll away downhill, never to be seen again.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;&amp;quot;So one reason that eggs have an asymmetric tapered oval shape is that if you nudge them, they'll come back to you. They'll sweep out a circle around the pointed end, and come to a stop with the pointed end facing uphill. In fact, the eggs of birds that have their nests on cliffs are more oval than the eggs of birds that nest on the ground. This means the 'more-oval' eggs of these cliff-nesting birds will roll in a very tight little circle, and be less likely to roll out of the nest — and off the cliff.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;&amp;quot;Another reason for eggs to be egg-shaped is that they fit together quite snugly in the nest, with only small air spaces between them. &amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;&amp;quot;Yet another reason that eggs are tapered is so that they can get pushed out of the hen.&amp;quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-01-07T09:08:54.870" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5695" PostTypeId="2" ParentId="5688" CreationDate="2013-01-07T10:20:13.517" Score="2" Body="&lt;p&gt;It seems to me that they are not summing the changes correctly in this page.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are summing the lengths of the paths to the root (and for the fig 2, they assume that the terminal branches, from left to right are of lengths 3, 2, 1 and 1). This doesn't make sense to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The correct way to count changes using parsimony is to consider each site in the alignment, and try to put the minimum number of mutations on the tree to explain the states observed at the terminal branches. Then, sum the number of mutations across alignment sites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here, for figure 1, I get:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;site 1: 1 mutation, either on the left (T-&gt;A) or on the right (A-&gt;T) internal branch.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;site 2: 1 mutation on the 4th terminal branch (T-&gt;C)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;site 3: 0 mutations (all terminals have C)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;site 4: 1 mutation on the 2nd terminal branch (G-&gt;C)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Total: 3&lt;/p&gt;&#xA;&#xA;&lt;p&gt;for figure 2:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;site 1: 1 mutation on the branch leading to the most recent common ancestor of the two right-most terminals (A-&gt;T)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;site 2: 1 mutation on the right-most terminal branch (T-&gt;C)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;site 3: 0 mutations (same reason as for figure 1)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;site 4: 1 mutation, either on the left-most branch (G-&gt;C) or on the branch leading to the most recent common ancestor of the 3 right-most terminals (C-&gt;G)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Total: 3&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The trees are equi-parsimonious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope I did not make any mistakes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There exist algorithms to do this. For instance, Wagner parsimony.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Don't trust a course on phylogeny that resides on a medical center web page.&lt;/p&gt;&#xA;" OwnerUserId="1486" LastActivityDate="2013-01-07T10:20:13.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5696" PostTypeId="1" AcceptedAnswerId="5701" CreationDate="2013-01-07T12:19:24.470" Score="7" ViewCount="14075" Body="&lt;p&gt;I've &lt;a href=&quot;http://en.wikipedia.org/wiki/Cephalopod_eye&quot; rel=&quot;nofollow noreferrer&quot;&gt;read&lt;/a&gt; that unlike humans, octopuses have eyes &quot;designed&quot; the &quot;right way&quot;, i.e. with the nerve fibers behind the retina, thus getting rid of the blind spot we humans have as well as theoretically improving eyesight. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have there been tests to compare octopus sight with that of humans, and do they indeed have better vision than us?&lt;/p&gt;&#xA;" OwnerUserId="1884" LastEditorUserId="16866" LastEditDate="2017-04-14T20:42:03.943" LastActivityDate="2020-04-03T20:57:46.507" Title="Do octopuses have better eyes than humans?" Tags="&lt;zoology&gt;&lt;vision&gt;&lt;eyes&gt;&lt;invertebrates&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5697" PostTypeId="1" AcceptedAnswerId="5698" CreationDate="2013-01-07T12:28:42.083" Score="1" ViewCount="3821" Body="&lt;p&gt;I often have to calculate the mass of peptide sequences using calculators such as &lt;a href=&quot;http://web.expasy.org/peptide_mass/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have the option of calculating the average and monoisotopic mass, but what is the difference?&lt;/p&gt;&#xA;" OwnerUserId="158" LastActivityDate="2013-01-07T12:56:27.447" Title="What is the difference between average and monoisotopic mass calculations of peptides?" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5698" PostTypeId="2" ParentId="5697" CreationDate="2013-01-07T12:33:52.313" Score="3" Body="&lt;p&gt;The elements that typically make up peptides and proteins can be present in different isotopes. For example, carbon is present to 98.9% as $\ce{^12C}$, and to 1.1% as $\ce{^13C}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The monoisotopic mass assumes that every element is present in the most abundant isotope, the average mass uses the actual distribution of the isotopes in nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have sufficient resolution in your mass spectrum you can see multiple signals corresponding to different isotope compositions of your molecule.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2013-01-07T12:56:27.447" LastActivityDate="2013-01-07T12:56:27.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5699" PostTypeId="1" AcceptedAnswerId="5700" CreationDate="2013-01-07T13:11:39.600" Score="9" ViewCount="41707" Body="&lt;p&gt;Can the combination of $+ve$ and $-ve$ blood groups of a couple be a cause of miscarriage in pregnancy?  &lt;/p&gt;&#xA;" OwnerUserId="1885" LastEditorUserId="22057" LastEditDate="2017-02-26T20:14:50.550" LastActivityDate="2017-11-21T17:39:07.893" Title="Can the mating of a couple with Rhesus positive and negative blood types result in miscarriage?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;&lt;hematology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5700" PostTypeId="2" ParentId="5699" CreationDate="2013-01-07T14:27:17.190" Score="10" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I want to know can +ve and -ve blood group of a couple could be a cause of miscarriage in pregnancy?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Yes.&lt;/strong&gt; In extreme cases, it can. You are talking about &lt;strong&gt;Rh Incompatibility&lt;/strong&gt;, and can become a big issue when the mother has Rh(-) blood and the father has Rh(+) blood (such as the case with your cousin and his wife).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What &lt;em&gt;could have&lt;/em&gt; happened (but definitely won't say for sure) is that your cousin's wife had a natural miscarriage which exposed her to the Rh proteins of the child, and then the subsequent pregnancy had complications due to the previous exposure and mother's development of antibodies which lead to the second miscarriage. However, &lt;strong&gt;I am not a licensed physician and you should consult a physician before pursuing any sort of treatments!!!&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rh factor is the presence of surface proteins on Erythrocytes (Red Blood Cells or &quot;RBC&quot;). If Leukocytes (White Blood Cells - most commonly reported as &quot;T-cells&quot;) encounter Erythrocytes that &lt;em&gt;do not share&lt;/em&gt; the Rh factor of their host, then they can develop &lt;em&gt;antibodies&lt;/em&gt; to it - which help identify Antigens (foreign proteins and molecules). Once the Antibodies have been generated the Immune System can attack any foreign Erythrocytes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this way, the mother's Immune System can actually attack the RBCs of her child.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find out more here: &lt;a href=&quot;http://kidshealth.org/parent/pregnancy_center/your_pregnancy/rh.html&quot;&gt;http://kidshealth.org/parent/pregnancy_center/your_pregnancy/rh.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And a few select quotations:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Rh incompatibility usually isn't a problem if it's the mother's &lt;strong&gt;first&lt;/strong&gt; pregnancy because, unless there's some sort of abnormality, the fetus's blood does not normally enter the mother's circulatory system during the course of the pregnancy...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;...Other ways Rh-negative pregnant women can be exposed to the Rh protein that might cause antibody production include blood transfusions with Rh-positive blood, &lt;strong&gt;miscarriage&lt;/strong&gt;, and ectopic pregnancy...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;...Rh antibodies are harmless until the mother's second or later pregnancies. If she is ever carrying another Rh-positive child, her Rh antibodies will recognize the Rh proteins on the surface of the baby's blood cells as foreign, and pass into the baby's bloodstream and attack those cells. &lt;strong&gt;This can lead to swelling and rupture of the baby's RBCs. A baby's blood count can get dangerously low when this condition, known as hemolytic or Rh disease of the newborn, occurs.*&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And you are correct that there is a treatment via injection, but the Doctor is also correct in that administering it past the first pregnancy does little for future fetuses:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Today, when a woman with the potential to develop Rh incompatibility is pregnant, doctors administer a series of two Rh immune-globulin shots during her first pregnancy. The first shot is given around the 28th week of pregnancy and the second within 72 hours after giving birth. Rh immune-globulin acts like a vaccine, preventing the mother's body from producing any potentially dangerous Rh antibodies that can cause serious complications in the newborn or complicate any future pregnancies.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And the ultimate effects of missing the shots and having very unfortunate luck:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Rh incompatibility rarely causes complications in a first pregnancy and does not affect the health of the mother. But Rh antibodies that develop during subsequent pregnancies can be potentially dangerous to mother and child. Rh disease can result in severe anemia, jaundice, brain damage, and heart failure in a newborn. &lt;strong&gt;In extreme cases, it can cause the death of the fetus because too many RBCs have been destroyed.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there a cure?&lt;/strong&gt; No. Once the antibodies have been developed, the Rh(+) protein is &lt;em&gt;known&lt;/em&gt; to the mother's Immune System. Nothing short of wiping out the mother's Immune System would act as a &lt;em&gt;cure&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in extreme cases, there are treatments:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If a doctor determines that a woman has already developed Rh antibodies, then the pregnancy will be closely monitored to make sure that those levels are not too high. In rare cases, if the incompatibility is severe and the baby is in danger, a series of special blood transfusions (called exchange transfusions) can be performed either while the baby is still in the uterus or after delivery.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;But don't fret yet!&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rh surface proteins are determined by genetics, and each time a child is conceived there is a chance that the Rh protein will be (-) if the exact genotype of the (+) parent allows it. So if your cousin's wife were to get pregnant again (and each time she does) it's a chance that the Rh Incompatibility (aka - &quot;Hemolytic Disease&quot;, aka - &quot;Rhesus Disease&quot;) won't show up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there are some reasons to stay positive.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1427" LastEditDate="2013-01-07T19:20:06.627" LastActivityDate="2013-01-07T19:20:06.627" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5701" PostTypeId="2" ParentId="5696" CreationDate="2013-01-07T17:39:00.307" Score="8" Body="&lt;p&gt;There are a couple of advantages and disadvantages of possessing the eyes of octopuses. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The first &lt;strong&gt;advantage&lt;/strong&gt; of the octopus eye is that it has no blind spot. This means that octopuses can see everything that is going on in their environment, and are more aware of predators and prey than some vertebrates. Also, they have many more photoreceptors than vertebrates, at roughly &lt;strong&gt;20,000-50,000/mm&lt;sup&gt;2&lt;/sup&gt;&lt;/strong&gt; which means that their vision is much better than that of any human. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The &lt;strong&gt;disadvantage&lt;/strong&gt; of the octopus eye is that it can not see in colour. The eyes possess no cones, only the invertebrate equivalent of rods. This means that  octopuses can only distinguish between light and dark.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1451" LastEditorUserId="1306" LastEditDate="2013-01-08T17:19:00.617" LastActivityDate="2013-01-08T17:19:00.617" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="5703" PostTypeId="1" AcceptedAnswerId="5757" CreationDate="2013-01-02T15:07:27.463" Score="4" ViewCount="233" Body="&lt;p&gt;The scientific consensus is that no one ever fills up their memory capacity by learning facts and so on, even in the information age.  My question is therefore, is there an evolutionary reason as to why we have evolved to have such large memory capacities, when we never come close to filling it up?&lt;/p&gt;&#xA;" OwnerUserId="1472" OwnerDisplayName="Chris" LastActivityDate="2020-12-08T15:54:42.713" Title="Evolutionary explanation to why we have such large memory capacities?" Tags="&lt;memory&gt;&lt;evolution&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5704" PostTypeId="2" ParentId="5684" CreationDate="2013-01-07T20:06:15.727" Score="9" Body="&lt;p&gt;This is a bit hard because the usual composition statements are a combination of different types of molecules. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of faeces are, by dry weight, bacteria (30%), undigested food and fiber (30%), fat (10%-20%), inorganic matter( 10-20%), other protein(2-3%). (&lt;a href=&quot;http://www.healthhype.com/feces-faeces-formation-composition-color-and-odor.html&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see the bacterial portion contains proteins (amino acids) and other types of molecules.  the inorganic matter includes bilins which are part of the used up hemoglobin from red blood cells which have been retired. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's also a lot of variation from one sample to the next - 10% seems pretty common here as you can imagine).  What makes faeces so dangerous is the bacterial portion, which can pose quite a health risk. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-01-07T20:06:15.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5705" PostTypeId="2" ParentId="5699" CreationDate="2013-01-07T20:08:33.733" Score="3" Body="&lt;p&gt;To add a more concise answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, the conflict between positive and negative Rh (Rhesus) blood groups can cause miscarriage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genetic makeup decides whether red blood cells (RBC) carry a specific surface protein known as Rhesus factor (Rh). If your own RBCs do not carry this protein (Rh-), your body will consider it (or RBC carrying it) a foreign substance and treat it like anything foreign - the immune system will respond and eliminate it, just like an infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a Rh- mother has a child whose RBC are Rh+ (which is possible even if only one parent was Rh+), the mother's body will develop an immune response against the baby's blood itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This includes the immune response's memory: just like it remembers the &quot;fake&quot; infection from a vaccine to protect against a real disease, the immune system will remember the Rhesus protein, so if future pregnancies develop babies with Rh+ blood, the reaction will be more severe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also &lt;a href=&quot;http://en.wikipedia.org/wiki/Rhesus_factor&quot; rel=&quot;nofollow&quot;&gt;Wikipedia on the Rh factor&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Rhesus_disease&quot; rel=&quot;nofollow&quot;&gt;Miscarriage due to Rh factor&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-01-08T10:29:56.183" LastActivityDate="2013-01-08T10:29:56.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5706" PostTypeId="1" CreationDate="2013-01-07T22:50:22.907" Score="4" ViewCount="245" Body="&lt;p&gt;I need to separate the antigens from several vaccines in order to use them for coating microplates to run an indirect ELISA. I at least need to remove the adjuvant from the vaccines. Is this possible to do and if yes, how do I go about it?&lt;/p&gt;&#xA;" OwnerUserId="1888" LastActivityDate="2013-01-08T17:24:03.817" Title="Is it possible to purify antigens from a vaccine and to separate them from the adjuvant?" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5707" PostTypeId="1" CreationDate="2013-01-08T03:20:18.023" Score="4" ViewCount="122" Body="&lt;p&gt;To what extent can humans, (mammals in general), theoretically regenerate, and is their a way to speed up and/or exceed this original extent.&lt;/p&gt;&#xA;" OwnerUserId="1889" LastActivityDate="2013-03-12T01:37:47.490" Title="Regeneration capabilities in humans?" Tags="&lt;human-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5708" PostTypeId="1" CreationDate="2013-01-08T05:43:11.713" Score="4" ViewCount="633" Body="&lt;p&gt;Recently, I was having an eye exam and admitted to squinting my eyes to sharpen blurred edges. Later, while waiting for the dilation to set in, my brother (a would-be pharmacist fresh off an anatomy course) was telling me about how vision works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a non-scientist, here's as much as I gathered:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The pupil allows light into our eyes.&lt;/li&gt;&#xA;&lt;li&gt;The lens bends and shifts to focus that light against our retina.&lt;/li&gt;&#xA;&lt;li&gt;The retina translates this light-information into signals via the optic nerve.&lt;/li&gt;&#xA;&lt;li&gt;Something about brains, and then &lt;em&gt;sight!&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, my question is, if the lens being bent and shifted inside of our eye by muscles is how our eyes focus, &lt;strong&gt;why do those of us with poor vision squint?&lt;/strong&gt; Surely it can't be that by narrowing my field of vision I'm consciously bending my lens.&lt;/p&gt;&#xA;" OwnerUserId="2" LastActivityDate="2013-01-08T05:53:45.280" Title="Why do we squint?" Tags="&lt;vision&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5709" PostTypeId="2" ParentId="5708" CreationDate="2013-01-08T05:53:45.280" Score="2" Body="&lt;p&gt;Actually it's a bit physics and biology, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It works, all right. In fact, the word &quot;&lt;strong&gt;myopia&lt;/strong&gt;&quot; (near-sightedness) comes from the Greek words myein (shut) and ops (eye). When you squint, it's like reducing the aperture of a camera lens: You reduce the diameter of your visual lens. This gives you a longer depth of focus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Shortly you can say, &lt;strong&gt;Yes&lt;/strong&gt; by squinting your eyes you actually bends the eye lens with the help of Ciliary Muscles present in your eyes which reduce it's focal length and helps you to see with a better vision&lt;/p&gt;&#xA;" OwnerUserId="1451" LastActivityDate="2013-01-08T05:53:45.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5710" PostTypeId="1" AcceptedAnswerId="5712" CreationDate="2013-01-08T13:30:28.993" Score="1" ViewCount="5219" Body="&lt;p&gt;Normal air consist of oxygen, CO₂ and nitrogen, with traces of water etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now imagine displacing all gasses except oxygen with water vapour. By water vapour I don't mean hot steam or fog. Just gaseous water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is would it be beneficial or harmful to human, and how much so?&#xA;And assuming it's not deadly, in which circumstances could it be useful?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One thing I am wondering in particular is deep dive and high altitude applications. Having no/low content of nitrogen in such an artificial air mixture would help to avoid decompression sickness. And one would think water vapour is at least cheaper than pure oxygen (also might be safer and have less side effects).&lt;/p&gt;&#xA;" OwnerUserId="1891" LastEditorUserId="3340" LastEditDate="2014-10-09T15:13:33.647" LastActivityDate="2014-10-09T15:13:33.647" Title="Breathing water vapour" Tags="&lt;breathing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5712" PostTypeId="2" ParentId="5710" CreationDate="2013-01-08T13:46:57.580" Score="3" Body="&lt;p&gt;Just because you have removed the Nitrogen and CO₂ won't help you keep a higher vapour pressure of H₂O in the air. You Could REMOVE all the other gasses and just have O₂ at its normal partial pressure at 1/5 bar total pressure and breath fine, but there would be a fire risk in this environment due to no non O₂ molecules to quench excited O₂.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only way to have a high enough vapour pressure of H₂O for something like diving would be to heat it, but I don't think a lungful of very hot water vapour would be terribly good for you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can't just pressurise water vapour to any pressure you feel like; it will condense fairly easily.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To avoid Nitrogen's toxic effects, divers often use Helium to replace it as pure Oxygen is deadly at high pressures.&lt;/p&gt;&#xA;" OwnerUserId="1300" LastEditorUserId="3340" LastEditDate="2014-10-09T15:04:11.043" LastActivityDate="2014-10-09T15:04:11.043" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="5713" PostTypeId="2" ParentId="5706" CreationDate="2013-01-08T16:26:59.107" Score="1" Body="&lt;p&gt;The major component of a vaccine is the adjuvant, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Immunologic_adjuvant&quot; rel=&quot;nofollow&quot;&gt;according to Wikipedia&lt;/a&gt; the most commonly used adjuvants in human vaccines are aluminium salts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here for example is the composition of Recombivax HB, a hepatitis B vaccine produced by Merck Frosst and used in Canada (source of information is &lt;a href=&quot;http://vran.org/ingredients-childhood-vaccines-in-canada/&quot; rel=&quot;nofollow&quot;&gt;a Canadian website&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;RECOMBIVAX HB ® [hepatitis B vaccine (recombinant)] is a non-infectious subunit viral vaccine consisting of surface antigen (HBsAg or Australia antigen) of hepatitis B virus produced in yeast cells. A portion of the hepatitis B virus gene, coding for HBsAg, is cloned into yeast and the vaccine for hepatitis B is produced from cultures of this recombinant yeast strain according to methods developed in the Merck Research Laboratories.&#xA;  Two formulations are available:&#xA;   •  10 µg/1.0 mL formulation: each 1.0 mL dose contains 10 µg of hepatitis B surface antigen adsorbed onto approximately 0.5 mg of amorphous aluminum hydroxyphosphate;&#xA;   •  40 µg/1.0 mL formulation: each 1.0 mL dose contains 40 µg of hepatitis B surface antigen adsorbed onto approximately 0.5 mg of amorphous aluminum hydroxyphosphate;&#xA;  Thimerosal (mercury derivative) 1:20,000 (50 µg/mL) has been added only to the preservative-containing formulations. All preparations have been treated with formaldehyde prior to adsorption onto amorphous aluminum hydroxyphosphate. The vaccine is of the adw subtype.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As explained in   Exley, C. &lt;em&gt;et al&lt;/em&gt;. (2010) The immunobiology of aluminium adjuvants: how do they really work? Trends in Immunology, 31:103-109:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The vaccine preparation is primarily micrometer-sized clusters of nano-sized primary particles of the aluminium salt with which the antigen is associated by adsorption and entrapment. The avidity with which the adjuvant associates with the antigen will depend upon multiple factors, including the form of aluminium salt (usually oxyhydroxide or hydroxyphosphate), the physico-chemical properties of the antigen (including its overall charge and molecular weight), the mode of preparation of the antigen-adjuvant complex (for example, ratio of adjuvant to antigen), and the final solution pH. The latter will usually be around neutral (pH 7.0 +/-0.5), and, along with the highly super-saturated state of the aluminium salt, this will ensure that the concentration of soluble aluminium in the vaccine preparation remains below ca 2 mM. Similarly, there will be a variable proportion of antigen, often &amp;lt;1% of the total antigen load, that is not associated directly with the adjuvant, and some of this ‘free’ antigen may also be in a complex with aluminium., what this means is that the protein antigen is not soluble in the vaccine, but rather is adsorbed and/or entrapped in the inorganic particulate material. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What this means is that the protein antigen is not soluble in the vaccine, but rather is adsorbed and/or entrapped in the inorganic particulate material. The antigen itself has of course already been extensively purified before being incorporated into the vaccine, so the task of purifying the antigen from the Recombivax vaccine is one of releasing it from the inorganic adjuvant. The obvious thing to try first would be to isolate the particulate material by centrifugation, and then attempt to release the antigen from this in a soluble form: things to try would be extremes of pH, high salt concentrations, and detergents. SDS-PAGE would be used to monitor how much was released by these treatments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the example that I gave above (Recombivax HB) is fairly straightforward because it contains a single protein antigen. Compare this to Pentacel, given as first vaccination to babies in Canada (same source as before). &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Act-HIB ® Reconstituted with QUADRACEL ®Haemophilus b Conjugate Vaccine (Tetanus Protein – Conjugate) Reconstituted with Component Pertussis Vaccine and Diphtheria and Tetanus Toxoids Adsorbed Combined with Inactivated Poliomyelitis Vaccine.&#xA;  Each single dose (approximately 0.5 mL) after reconstitution contains:&#xA;   •  purified polyribose ribitol phosphate capsular polysaccharide (PRP) of Haemophilus influenzae type b covalently bound to 20 µg of tetanus protein 10 µg&#xA;   •  pertussis toxoid (PT) 20 µg&#xA;   •  filamentous haemaglutinin (FHA) 20 µg&#xA;   •  fimbrial agglutinogens 2 + 3 (FIM) 5 µg&#xA;   •  pertactin (PRN) 3 µg&#xA;   •  diphtheria toxoid 15 Lf&#xA;   •  tetanus toxoid 5 Lf&#xA;   •  poliovirus type 1 (Mahoney) 40 D-antigen units&#xA;   •  poliovirus type 2 (MEF1) 8 D-antigen units&#xA;   •  poliovirus type 3 (Saukett) 32 D-antigen units&#xA;   •  aluminum phosphate 1.5 mg&#xA;   •  2-phenoxyethanol (not as a preservative) 0.6% v/v&#xA;   •  polysorbate 80 10 ppm (by calculation)&#xA;   •  bovine serum ≤50 ng&#xA;   •  trace amounts of formaldehyde&#xA;   •  trace amounts of polymyxin B and neomycin may be present from the cell growth medium&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This vaccine is clearly much more complex, so in this case, once the desired antigen(s) were freed from the adjuvant there would be a need to use standard protein purification techniques to separate the various contaminants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally it's worth pointing out that unless you have access to large amounts of vaccine, you are going to be starting with quite small amounts of antigen (see above) so it will probably be quite a challenging purification.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-01-08T17:24:03.817" LastActivityDate="2013-01-08T17:24:03.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5715" PostTypeId="2" ParentId="5342" CreationDate="2013-01-08T19:23:37.617" Score="3" Body="&lt;p&gt;I can get the ball rolling..&lt;/p&gt;&#xA;&lt;p&gt;Found a nice paper which looks at this phenomenon &lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028980&quot; rel=&quot;nofollow noreferrer&quot;&gt;in yeast&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;So as a primer, 8 histone proteins come together to make a spool of sorts which DNA wraps around:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pjs5a.png&quot; alt=&quot;the histone core from wikipedia&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Histone &lt;a href=&quot;http://en.wikipedia.org/wiki/Histone#Classes&quot; rel=&quot;nofollow noreferrer&quot;&gt;proteins have many sequence variants&lt;/a&gt;, and each one of them can be covalently modified with methyl, acyl, phospho, SUMO, adp and many other sorts of &lt;a href=&quot;http://en.wikipedia.org/wiki/Histone#Functions_of_histone_modifications&quot; rel=&quot;nofollow noreferrer&quot;&gt;chemical groups via a chemical bond&lt;/a&gt;.  Although its not yet clear exactly how it works its clear that these modifications can change the behavior of the histones which prevent transcription of the gene when they have the chromosomal DNA all wrapped up.&lt;/p&gt;&#xA;&lt;p&gt;So as to the question a pattern of inheritance of modified histone patterns is indeed seen and has epigenetic effects.  (that is, it modifies the genetic phenotype of daughter cells which retain the histone modifications of the parent cells).  In this paper, &lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028980&quot; rel=&quot;nofollow noreferrer&quot;&gt;newly synthesized (and labelled) yeast histone can be found incorporated into certain segments of the genome, which demonstrates that large segments of the histones are carried forward from the parent cell&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;They also found a particular case of histone epigenetic labeling carried forward through division:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Furthermore, if the heterochromatin-binding protein Sir3 is unavailable during DNA replication, histone H3-K4&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So there's evidence that histone configurations &lt;em&gt;are&lt;/em&gt; transmitted epigenetically, In this 2011 paper, the author support a 'conservative distribution model' and compare it to a 'semi-conservative' model:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The conservative distribution model proposes that newly synthesized histone molecules form nucleosomes that are randomly inserted among preexisting parental nucleosomes.&lt;/p&gt;&#xA;&lt;p&gt;The semi-conservative distribution model proposes that a hybrid nucleosome that contains both newly synthesized and parental histone H3-H4 dimers is formed, which facilitates the transmission of epigenetic information within the basic nucleosome unit.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;They go on to say that a conservative model of histone inheritance allows for strong epigenetic inheritance as the remaining parent histones will tend to attract similarly labelled histones as the new histones incorporate themselves among the parental histones on the daughter chromosome.&lt;/p&gt;&#xA;&lt;p&gt;Its still being worked out though...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-01-08T20:29:49.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5716" PostTypeId="1" CreationDate="2013-01-08T19:45:01.223" Score="2" ViewCount="48" Body="&lt;p&gt;I wanted to find out if anyone knows what stimulates histone methyltransferases to function?  I know that it is a process still trying to be understood, but I can't find anything that seems to direct the activity of the enzymes.  Additionally, where do the methyl groups come from that the enzymes transfer onto the histones?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="1892" LastEditorUserId="948" LastEditDate="2014-01-13T21:37:20.603" LastActivityDate="2014-01-13T21:37:20.603" Title="What signals histone methyl transferases to function?" Tags="&lt;histone&gt;&lt;histone-modifications&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5717" PostTypeId="2" ParentId="5716" CreationDate="2013-01-08T21:49:33.913" Score="1" Body="&lt;p&gt;Histone methylation is regulated by a variety of of events, including transcriptional activation and repression, relative location of the histone in the chromatin (pericentric or not, hetero- vs. euchromatin, etc.), X-inactivation, the cell's point in the cell cycle, and others. A variety of signaling pathways can lead to the (in)activation of HMTs. I found this &lt;a href=&quot;http://www.cellsignal.com/reference/pathway/histone_modification.html#methylation&quot; rel=&quot;nofollow&quot;&gt;table&lt;/a&gt; at cellsignal.com listing known methylation sites, along with literature references. Elsewhere on the site is &lt;a href=&quot;http://www.cellsignal.com/reference/pathway/Histone_Methylation.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; graphic, which shows some of the same info in a different way, and also has links to data at &lt;a href=&quot;http://www.phosphosite.org&quot; rel=&quot;nofollow&quot;&gt;PhosphoSitePlus&lt;/a&gt; with links to the protein of interest. If you dig around, you can find all sorts of pathway and experimental information. For example, if you look up &lt;a href=&quot;http://www.phosphosite.org/proteinAction.do?id=6954&quot; rel=&quot;nofollow&quot;&gt;PRMT1 (human)&lt;/a&gt;, you get a brief description of the protein and what pathways it's involved in, as well as links to all sorts of other info. On the histone side, a look at &lt;a href=&quot;http://www.phosphosite.org/proteinAction.do?id=984&amp;amp;showAllSites=true&quot; rel=&quot;nofollow&quot;&gt;Histone H4 (human)&lt;/a&gt; allows you to look at individual modified residues (I picked K21-m2) and find all sorts of literature links and information about experiments used to determine its function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: I'm not affiliated with Cell Signaling, I just think they have a ton of useful protein information, kind of like NEB for mol bio stuff...&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-01-08T21:49:33.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5718" PostTypeId="1" CreationDate="2013-01-08T22:27:58.477" Score="5" ViewCount="4065" Body="&lt;p&gt;What exactly is going on biologically at the molecular level with acne and causes breakouts? Hormonally, there is a lot going on but I'm curious about what is going on chemically.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2014-06-25T10:14:44.387" Title="What causes Acne?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5719" PostTypeId="2" ParentId="5718" CreationDate="2013-01-09T01:34:23.897" Score="3" Body="&lt;p&gt;Acne is caused by blockage of hair follicles by oils (&lt;em&gt;sebum&lt;/em&gt;) from your skin and dead skin cells. Hormonal changes in puberty cause your skin glands to produce a lot of oil.&#xA;Blocked follicles are visible as a small black dot (blackheads).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The recognizable pimples occurring during normal puberty acne form because of bacterial infection (the sebum/skin mix forms a good growth medium for bacteria). The immune system responds with inflammation (the red &quot;base&quot;). The pus (the white &quot;middle&quot;) is a dead bacteria, skin and white blood cell mix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most treatments for acne focus on either killing the bacteria or removing the dead skin or sebum. Professional medical treatments might also focus on altering hormonal levels. This is also why the COCP , the birth control pill, usually lessens acne in women. Popular over-the-counter remedies for acne (e.g. Clearasil) usually contain a lot of alcohol which both kills the bacteria and removes the sebum, but also makes the skin dry. This in turn causes the skin to produce more sebum thus making the problem worse.&lt;/p&gt;&#xA;" OwnerUserId="1893" LastEditorUserId="1893" LastEditDate="2014-06-25T10:14:44.387" LastActivityDate="2014-06-25T10:14:44.387" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5720" PostTypeId="1" AcceptedAnswerId="5724" CreationDate="2013-01-09T01:59:12.397" Score="25" ViewCount="34302" Body="&lt;p&gt;The ABO blood type divides each blood type according to whether they have the &quot;A&quot; and &quot;B&quot; antigen(s) (AB has both, O has none). People also have antibodies against the antigens they don't have (AB has none, O has both), even before they have ever come in contact with those antigens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do people have antibodies against these antigens they have never come in contact with? This isn't the normal situation for the immune system (e.g. for a virus or the blood type rhesus factor)&lt;/p&gt;&#xA;" OwnerUserId="1893" LastEditorUserId="69" LastEditDate="2013-01-09T11:38:49.153" LastActivityDate="2016-07-11T15:40:26.897" Title="Why do people have antibodies against other blood types?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;hematology&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5721" PostTypeId="1" AcceptedAnswerId="5722" CreationDate="2013-01-09T05:36:44.287" Score="4" ViewCount="63" Body="&lt;p&gt;I'd like to add a cell penetrating peptide to my custom peptide (30aa). Can I just add it to the end of the peptide sequence or does it have to be positioned on an outward facing external chain?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2013-02-08T17:20:42.670" Title="position of cell penetrating peptide" Tags="&lt;proteins&gt;&lt;protein-folding&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5722" PostTypeId="2" ParentId="5721" CreationDate="2013-01-09T05:52:54.523" Score="3" Body="&lt;p&gt;This papers tables shows that cell penetrating peptides are placed before their cargo peptide and do not need to be on a side chain.&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1576229/table/tbl1/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1576229/table/tbl1/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="1320" LastEditDate="2013-02-08T17:20:42.670" LastActivityDate="2013-02-08T17:20:42.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5723" PostTypeId="1" AcceptedAnswerId="19028" CreationDate="2013-01-09T08:24:32.133" Score="6" ViewCount="53727" Body="&lt;p&gt;A well known way to have a rest of mosquitoes during camping is to stand in the fire's smoke. Moreover, I learned recently that shepherds in certain regions of Africa use the same tactic for cattle. They make smoky fires and cattle gathers in smoke to get rid of mosquitoes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why humans and cattle can stand smoke, but mosquitoes can't? Does this technique work for other kinds of insects?&lt;/p&gt;&#xA;" OwnerUserId="1894" LastActivityDate="2014-06-10T23:25:06.203" Title="Why are mosquitoes repelled by smoke?" Tags="&lt;entomology&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5724" PostTypeId="2" ParentId="5720" CreationDate="2013-01-09T09:06:22.513" Score="21" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/ABO_blood_group_system#cite_note-13&quot;&gt;the Wikipedia entry for the ABO blood group system&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Anti-A antibodies are hypothesized to originate from immune response towards influenza virus, whose epitopes are similar enough to the α-D-N-galactosamine on the A glycoprotein to be able to elicit a cross-reaction. Anti-B antibodies are hypothesized to originate from antibodies produced against Gram-negative bacteria, such as E. coli, cross-reacting with the α-D-galactose on the B glycoprotein.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The cited reference is Van Oss, CJ (2004) Letter to the Editor: &quot;Natural versus Regular Antibodies The Protein Journal 23:357, available &lt;a href=&quot;http://resources.metapress.com/pdf-preview.axd?code=l2206u8gj73x3251&amp;amp;size=largest&quot;&gt;here&lt;/a&gt;. This source contains this statement:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...&quot;we have known for more than four decades that these bloodgroup (antibodies) arise out of minor infections occurring very early in life...&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The cited references are:&#xA;&lt;p&gt;Pettenkofer &lt;em&gt;et al&lt;/em&gt;. Z. ImmunForsch. 119: 415-429&#xA;&lt;p&gt;Springer, GF (1960) Klin. Wschr. 38: 513-514&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately I have access to neither of these articles, and besides they are presumably written in German.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-01-09T13:35:45.100" LastActivityDate="2013-01-09T13:35:45.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5727" PostTypeId="2" ParentId="5620" CreationDate="2013-01-09T18:34:14.253" Score="4" Body="&lt;p&gt;The ear uses a series of hairs to parse out sound frequency in the cochlea.  When the cochlear hairs die, we lose some frequency response.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As we get older, even without exposure to loud noises, the higher frequency responses tend to lose their response first.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Sensorineural_hearing_loss#Acquired&quot; rel=&quot;nofollow noreferrer&quot;&gt;But loud noises have been linked to hearing loss and high tones are often lost first&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hot off the presses: &lt;a href=&quot;http://medicalxpress.com/news/2013-01-sensory-hair-cells-regenerated-mammal.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;there's been some success in regenerating the cells which respond to sound in our ears&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to add @Armatus has a good point.  Ultrasonic sounds - above hearing range - seem to not adversely affect hearing at all.  &lt;a href=&quot;https://biology.stackexchange.com/questions/2077/will-humans-and-animals-be-harmed-by-frequencies-outside-their-hearing-range/7488#7488&quot;&gt;Will humans and animals be harmed by frequencies outside their hearing range? &lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-03-11T18:37:27.083" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5728" PostTypeId="1" AcceptedAnswerId="5731" CreationDate="2013-01-09T19:39:31.163" Score="7" ViewCount="1053" Body="&lt;p&gt;If I would show someone a yellow object and ask them, &quot;is this object yellow?&quot;&#xA; That person would say &quot;yes&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I could never know if my perception of the color yellow is the same as that other person's.&lt;br&gt;&#xA;Because he or she could actually be seeing, what I know to be the color green.&lt;br&gt;&#xA;But then tells me that its the color yellow because that has been taught to him or her from young age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how can you test if people are really seeing the same color?&lt;br&gt;&#xA;(originally posted this question on physics.stackexchange but was advised to try it here)&#xA;&lt;a href=&quot;https://physics.stackexchange.com/questions/48731/how-can-you-test-what-color-different-people-perceive&quot;&gt;https://physics.stackexchange.com/questions/48731/how-can-you-test-what-color-different-people-perceive&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1897" LastEditorUserId="-1" LastEditDate="2017-04-13T12:40:13.457" LastActivityDate="2014-01-07T12:04:32.013" Title="How can you test what color different people perceive?" Tags="&lt;perception&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="3" ClosedDate="2019-06-24T19:52:34.983" ContentLicense="CC BY-SA 3.0" />
  <row Id="5731" PostTypeId="2" ParentId="5728" CreationDate="2013-01-09T21:27:56.560" Score="6" Body="&lt;p&gt;One way we can get evidence &lt;a href=&quot;http://en.wikipedia.org/wiki/Qualia&quot;&gt;qualia&lt;/a&gt; are the same or very similar for different people is by reactions to it, beyond just the word. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, beyond the word &quot;pain&quot;, we have other strong reactions to pain. So nobody &#xA;suspects other people might experience pain as pleasure and vice versa. Obviously not!&#xA;There are no obvious signs for colour qualia, so it makes sense to suspect some people experience red as blue and vice versa. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still, there are weak reactions to colours, like sometimes certain colours are associated with certain emotions. But, this is very weak evidence and could easily mismeasured, or be bound up with culture rather than biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We could test it: take pairs of identical twins at birth (so that they haven't learned words for colours yet), re-wire optical nerves of one of each pair so that red and blue receptors were switched (and perform a placebo operation on the other one, so they don't know who is who), and see whether there is any statistically significant change in the attitudes to different colours or the like as they grow up. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The experiment has various technological and ethical problems :-) But it could be done in principle, so to me this shows the question isn't meaningless, just that it's hard to find the answer.&lt;/p&gt;&#xA;" OwnerUserId="1898" LastActivityDate="2013-01-09T21:27:56.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5732" PostTypeId="1" AcceptedAnswerId="7564" CreationDate="2013-01-09T21:50:54.287" Score="9" ViewCount="1522" Body="&lt;p&gt;I know that ingesting testosterone and other hormonal drugs may stimulate libido and increase sexual desire.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I wonder, if a man ingests female hormones such as estrogen, will he experience sexual desire towards other men or not? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, the other way around, whether a female ingesting male sexual hormones will experience desire towards other women?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is motivated by the interest to know whether transgender people, particularly, the MtF transsexuals engaged in prostitution experience genuine attraction to males.&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="408" LastEditDate="2013-03-18T22:17:00.363" LastActivityDate="2013-03-19T02:44:19.920" Title="Do hormone drugs affect whether a person feels sexual attraction to males or females?" Tags="&lt;human-biology&gt;&lt;pharmacology&gt;&lt;reproduction&gt;&lt;endocrinology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5733" PostTypeId="1" CreationDate="2013-01-09T21:54:47.227" Score="2" ViewCount="80" Body="&lt;p&gt;It is known that men in most countries live less than women. I wonder whether it is due to different life conditions or because male and female organisms differ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, I heard that testosterone may cause cardiovascular deceases. Is it true? Are there other biological mechanisms that can shorten men's lifespan?&lt;/p&gt;&#xA;" OwnerUserId="408" LastActivityDate="2013-01-09T22:43:46.567" Title="Does difference in expected life duration between men and women have biological nature?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5734" PostTypeId="2" ParentId="5733" CreationDate="2013-01-09T22:36:42.553" Score="2" Body="&lt;p&gt;There are several explanations. Probably these are all true to some degree and thus combine to give the general longer life expectancy of females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of these statistics are from &lt;a href=&quot;http://www.who.int/whr/2004/annex/topic/en/annex_2_en.pdf&quot; rel=&quot;nofollow&quot;&gt;Annex 2 of the WHO Health Report 2004&lt;/a&gt; (found through &lt;a href=&quot;http://en.wikipedia.org/wiki/Life_expectancy#Sex_differences&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Males are more likely to get lung cancer, liver damage and other drug-related illnesses (implied would be that males are more often alcohol/tobacco/drug users).&lt;/li&gt;&#xA;&lt;li&gt;Males also die more often as a result of work-related injury, especially as soldiers&lt;/li&gt;&#xA;&lt;li&gt;Males are usually larger. There seems to be a small inverse correlation between size and life expectancy&lt;/li&gt;&#xA;&lt;li&gt;Mitochondrial DNA is passes from mother to child. As such, &lt;a href=&quot;http://www.bbc.co.uk/news/health-19093442&quot; rel=&quot;nofollow&quot;&gt;mutations harmful for men are less effected by natural selection&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Men have one X chromosome, while women have 2. The y chromosome is very small and contains almost no genes. Thus if there is a genetic defect on the X chromosome the female might have a healthy X chromosome to compensate while the male does not have one. Among others this makes males more likely to have &lt;a href=&quot;http://www.cmu.edu/CSR/case_studies/women_live_longer.html&quot; rel=&quot;nofollow&quot;&gt;hemophilia or color blindness&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1893" LastEditorUserId="1893" LastEditDate="2013-01-09T22:43:46.567" LastActivityDate="2013-01-09T22:43:46.567" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5735" PostTypeId="2" ParentId="5728" CreationDate="2013-01-09T22:54:40.803" Score="3" Body="&lt;p&gt;I have often wondered this myself and have never found a way this could be asserted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact we know that not all people perceive color the same way: up to 5% of humans are colorblind and about 2-3% of the women are tetrachromates, they have an extra cone type in their eyes (usually somewhere near the red spectrum). So it would be logical to assume that those people perceive colors in a different way. We know this for a fact in colorblind people because we can create images which appear different to colorblind and non-colorblind people.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The evolutionary reason for the common prevalence of red-green color blindness might be because they are &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/248/1323/291.long&quot; rel=&quot;nofollow&quot;&gt;less affected by camouflage&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1893" LastActivityDate="2013-01-09T22:54:40.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5736" PostTypeId="2" ParentId="5732" CreationDate="2013-01-09T23:13:03.630" Score="3" Body="&lt;p&gt;People suspect that hormones for have an effect, but there are also genetic and biological factors. Hormones have caused some animals, such as frogs, to change sexes. Also, both genders have testosterone and estrogen in their bodies. Men just have more testosterone and women have more estrogen.&lt;/p&gt;&#xA;" OwnerUserId="1182" LastActivityDate="2013-01-09T23:13:03.630" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5737" PostTypeId="1" AcceptedAnswerId="5739" CreationDate="2013-01-10T00:07:09.180" Score="5" ViewCount="983" Body="&lt;p&gt;The equation for respiration is C&lt;sub&gt;6&lt;/sub&gt;H&lt;sub&gt;12&lt;/sub&gt;O&lt;sub&gt;6&lt;/sub&gt;+6O&lt;sub&gt;2&lt;/sub&gt;→6CO&lt;sub&gt;2&lt;/sub&gt;+6H&lt;sub&gt;2&lt;/sub&gt;O+36ATP. The chemical formula for ATP is C&lt;sub&gt;10&lt;/sub&gt;H&lt;sub&gt;16&lt;/sub&gt;N&lt;sub&gt;5&lt;/sub&gt;O&lt;sub&gt;13&lt;/sub&gt;P&lt;sub&gt;3&lt;/sub&gt;. How is this possible, since it violates the law of conservation of mass because it is unbalanced?&lt;/p&gt;&#xA;" OwnerUserId="1182" LastActivityDate="2016-02-24T17:49:38.853" Title="How is respiration an unbalanced equation" Tags="&lt;biochemistry&gt;&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5738" PostTypeId="2" ParentId="5723" CreationDate="2013-01-10T00:24:06.513" Score="-1" Body="&lt;p&gt;Mosquitoes aren't actually repelled by smoke. They are repelled by burning citronella oil. Citronella contains certain chemicals that naturally repel the dengue fever mosquito.&lt;/p&gt;&#xA;" OwnerUserId="1182" LastActivityDate="2013-01-10T00:24:06.513" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5739" PostTypeId="2" ParentId="5737" CreationDate="2013-01-10T00:32:00.630" Score="6" Body="&lt;p&gt;The ATP is not actually produced from the respiration. It comes from ADP and free phosphate ions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The production of ATP in cellular respiration happens in all parts of a series of chain reactions, and you can read more about those here: &lt;a href=&quot;https://en.wikipedia.org/wiki/Cellular_respiration#Aerobic_respiration&quot;&gt;https://en.wikipedia.org/wiki/Cellular_respiration#Aerobic_respiration&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1899" LastActivityDate="2013-01-10T00:32:00.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5740" PostTypeId="1" AcceptedAnswerId="6962" CreationDate="2013-01-10T00:37:16.690" Score="7" ViewCount="5114" Body="&lt;p&gt;As the old joke goes, &quot;God must have been a civil engineer. Who else would put a waste facility straight through a recreational area?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But maybe it wasn't God. Is there any evolutionary reason (or background for) having the urinary duct and reproductive organs right next to each other (in both humans and many other vertebrates)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be clear, I'm not asking why &lt;em&gt;isn't&lt;/em&gt; it elsewhere. I'm asking where the original &quot;design&quot; came from that spread everywhere.&lt;/p&gt;&#xA;" OwnerUserId="1899" LastEditorUserId="1899" LastEditDate="2013-01-29T14:03:23.460" LastActivityDate="2019-03-06T09:31:14.217" Title="What evolutionary reason is there for having the urinary duct and reproductive organs so close together?" Tags="&lt;evolution&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5741" PostTypeId="2" ParentId="5740" CreationDate="2013-01-10T00:57:38.667" Score="8" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there any evolutionary reason (or background for) having the urinary duct and reproductive organs right next to each other (in both humans and many other vertebrates)?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Because it works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution doesn't grow things or remove things because they might be funky or useful, Evolution is dictated by the survivability of organisms. If a change helps an organism survive to pass on its genes, it's kept. If it doesn't, it's eliminated from the gene pool over time. As long as a change doesn't significantly help or harm, it can be kept for hundreds, thousands, even millions of generations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolutionarily speaking they are where they are because we're mammals that were formally quadripeds that became bipeds. The stereotypical quadripedal design has the reproductive organs located near the pelvis. Probably because they're best protected there. Powerful hind limbs for kicking, and nasty teeth and claws up front. It also gives easy access for mating, which is pretty important if you want to continue the species. On quadripeds it could be pretty darn awkward if the genitalia were located near the ribcage&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Really, you could come up with a lot of reasons why the organs are located where they are. There are a lot of advantages, and a lot of disadvantages, but in the end the simplest explanation is going to be &quot;Because we can survive with them there.&quot; The advantages have outweighed the disadvantages for our species' history thus far, and until that changes they'll probably just stay where they are.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-01-10T00:57:38.667" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="5742" PostTypeId="2" ParentId="5740" CreationDate="2013-01-10T01:03:57.017" Score="-1" Body="&lt;p&gt;Human body has three channels for excretion of substances, one for each of the three physical phases of matter: lungs for gaseous substances, such as CO2, anus for solid substances such as feces and urinal channel for liquid substances.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It turned out that sperm is liquid, so it uses the same channel as liquid urine. &lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="408" LastEditDate="2013-01-15T02:47:19.410" LastActivityDate="2013-01-15T02:47:19.410" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="5743" PostTypeId="2" ParentId="5723" CreationDate="2013-01-10T01:46:41.080" Score="-3" Body="&lt;p&gt;All insects have a mortal fear of smoke because it is a harbinger of flames and flames - for an insect - means instant death. They have no mechanisms at all that are capable of regulating their body temperature sufficiently to survive direct flames.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Added:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider a population of mosquitoes (or any flying insect for that matter) that successfully develops a smoke-avoidance response. In an environment where forest fires are common and smoke is therefore a clear precursor - would this population have a better chance of survival than another that does not? I think you could only answer yes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It merely remains to prove that it is possible for a population I have described to develop. Well - the presence of this question on this board proves that it is possible. I realize this is a slightly weird form of proof by induction but you have to admit it works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry - no references or citations - just a &quot;because evolution&quot;.&lt;/p&gt;&#xA;" OwnerUserId="1156" LastEditorUserId="1156" LastEditDate="2013-01-12T23:14:43.447" LastActivityDate="2013-01-12T23:14:43.447" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="5744" PostTypeId="2" ParentId="5635" CreationDate="2013-01-10T03:46:25.220" Score="3" Body="&lt;p&gt;This has been tried and it sorta works. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.skepticalaquarist.com/algae-allelopathy&quot; rel=&quot;nofollow&quot;&gt;Algae in general seems to be inhibited by rotting barley straw in the water&lt;/a&gt;.&lt;br&gt;&#xA;There is also an observation (not universally accepted) that many plants in the water do not have as much algae.  This post is from April 2011, so it seems pretty current. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-01-10T03:46:25.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5745" PostTypeId="2" ParentId="5723" CreationDate="2013-01-10T13:50:39.193" Score="0" Body="&lt;p&gt;Mosquitoes have olfactory receptors. Certain chemicals acts as repellent.&#xA;See &lt;a href=&quot;http://en.wikipedia.org/wiki/DEET&quot; rel=&quot;nofollow&quot;&gt;this wikipedia page&lt;/a&gt; for an explanation about insects repellent mechanism.&lt;/p&gt;&#xA;" OwnerUserId="1902" LastEditorUserId="3632" LastEditDate="2014-06-10T21:05:19.427" LastActivityDate="2014-06-10T21:05:19.427" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5746" PostTypeId="2" ParentId="5685" CreationDate="2013-01-10T16:22:51.297" Score="1" Body="&lt;p&gt;Depending on the stage of cell-cycle you are interested in, people often use the size/morphology of the cell as an indicator. Then you select cells with a cell sorter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another option is to specifically tag some cellular molecule that can give an indication as to the relevant stage and then sort the cells based on the tag. This does not necessarily have to be cyclins - for example if you are only interested in S/G2 you could tag the DNA or maybe histones.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2013-01-10T17:25:36.723" LastActivityDate="2013-01-10T17:25:36.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5747" PostTypeId="1" CreationDate="2013-01-10T17:05:26.510" Score="2" ViewCount="49" Body="&lt;p&gt;Endocananbinoid = Endogenous Cannabinoid or CB&lt;sub&gt;1&lt;/sub&gt; and CB&lt;sub&gt;2&lt;/sub&gt; ligands. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm asking which endocannabinoid transporters exist and could the one answering show all the evidence for the existence of the transporters they mention. For instance anandamide is suspected to have a transporter and there is some evidence for its existence, and paracetamol's chief active metabolite, AM404, appears to work by inhibiting the actions of the anandamide transporter.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-01-11T19:33:48.993" LastActivityDate="2013-01-11T19:33:48.993" Title="Endocannabinoid Transporters - which ones are Likely to Exist and what is the Evidence for their Respective Existence?" Tags="&lt;proteins&gt;&lt;neuromodulation&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5748" PostTypeId="1" CreationDate="2013-01-10T18:37:41.577" Score="5" ViewCount="851" Body="&lt;p&gt;I was a fool and dissolved my antibiotic (Kanamycin) into Tris Buffer rather than H₂O. The Kanamycin still seems to be active but a fellow labmate mentioned that Tris messes around with the membrane permeability of cells. I was curious to what extent this actually influences experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC217144/&quot; rel=&quot;nofollow&quot;&gt;Tris(hydroxymethyl)aminomethane buffer modification of Escherichia coli outer membrane permeability.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="3340" LastEditDate="2014-10-10T10:27:00.817" LastActivityDate="2014-10-10T10:27:00.817" Title="What is the extent of the effect of Tris on E. coli?" Tags="&lt;molecular-biology&gt;&lt;ecoli&gt;&lt;lab-reagents&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5749" PostTypeId="1" CreationDate="2013-01-10T19:14:22.660" Score="6" ViewCount="184" Body="&lt;p&gt;While speaking with my co-workers, the topic of tumors growing things came up.  The examples were (and backed by images) of tumors growing a tooth, hair, and sometimes even more complex objects such as an eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, could a tumor reproduce something that isn't typically found in the human body?  Could it grow something that maybe a very distant ancestor would have had?&lt;/p&gt;&#xA;" OwnerUserId="1903" LastEditorUserId="69" LastEditDate="2013-01-11T18:21:04.627" LastActivityDate="2014-12-18T07:53:20.563" Title="Can a tumor produce something not currently found in our own bodies?" Tags="&lt;cancer&gt;" AnswerCount="4" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5750" PostTypeId="2" ParentId="5707" CreationDate="2013-01-10T23:53:26.547" Score="2" Body="&lt;p&gt;Regeneration - &lt;em&gt;or actions perceived as regeneration by popular culture&lt;/em&gt; - depend highly on age and specific type of cells (epithelial tissue cells are a fine example). But you can't regenerate a leg-bone once removed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But to get a more specific answer you to make a more specific question and define the terms you're using.&lt;/p&gt;&#xA;" OwnerUserId="1856" LastEditorDisplayName="user560" LastEditDate="2013-01-11T01:14:10.867" LastActivityDate="2013-01-11T01:14:10.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5751" PostTypeId="1" AcceptedAnswerId="5781" CreationDate="2013-01-11T01:47:28.710" Score="6" ViewCount="59843" Body="&lt;p&gt;Okay, I was learning about mitosis and meiosis in school and had a question. I know in Mitosis you first start off with a &lt;code&gt;Diploid (2N)&lt;/code&gt; cell and then end up with two daughter cells that are also &lt;code&gt;Diploid&lt;/code&gt;. However, in Meiosis, I know you end up with four &lt;code&gt;Haploid Cells (N)&lt;/code&gt;, but what exactly do you start off with? Is it like a single egg makes four more eggs or something? Or does it start off with a &lt;code&gt;Diploid Cell&lt;/code&gt; and then end up with the &lt;code&gt;Haploids&lt;/code&gt;? If so, what exactly is the starting cell called?&lt;/p&gt;&#xA;" OwnerUserId="1905" LastActivityDate="2015-04-16T00:48:43.553" Title="What type of cell do you start with in Meiosis?" Tags="&lt;cell-biology&gt;&lt;meiosis&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5752" PostTypeId="1" AcceptedAnswerId="6840" CreationDate="2013-01-11T02:14:24.717" Score="5" ViewCount="1195" Body="&lt;p&gt;The inbreeding coefficient of a sibling mating for a diploid organism is 0.25 (each allele has a 25% of being identical by descent in the offspring).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In haplodiploid organisms, males result from unfertilized eggs, so they don't have fathers (they get half of mom's diploid genome, and that's it). Females have both a mom and a dad, and are diploid in the standard way (dads give their daughters their entire genome).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the inbreeding coefficient for the daughter of a sib mating?&lt;/p&gt;&#xA;" OwnerUserId="1906" LastEditorUserId="107" LastEditDate="2013-01-11T13:54:00.693" LastActivityDate="2013-01-17T17:22:03.137" Title="What is the inbreeding coefficient for the female offspring of a sib-mating in a haplodiploid system?" Tags="&lt;genetics&gt;&lt;population-biology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5753" PostTypeId="2" ParentId="5751" CreationDate="2013-01-11T09:16:27.560" Score="1" Body="&lt;p&gt;During mitosis a diploid cell (2n = two copies of each chromosome, one from each parent) replicates its DNA so that it now has four copies of each chromosome. Then it divides, each daughter cell receives two copies of each chromosome and is again 2n. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In meiosis a diploid cell (2n) replicates its DNA so that it now has four copies of each chromosome. Then it divides, each daughter cell receives two copies of each chromosome and is again 2n. Then each of these divides once more &lt;strong&gt;without replicating DNA&lt;/strong&gt; so that there are now four cells each with one copy of each chromosome (1n).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might be tempted to think of a diploid cell which has replicated its DNA as tetraploid, but this word is not normally used in this context, since this is a transient 4n state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a very broad overview. Have a look at the Wikipedia entry for &lt;a href=&quot;http://en.wikipedia.org/wiki/Meiosis&quot; rel=&quot;nofollow&quot;&gt;meiosis&lt;/a&gt; to get a more detailed view and extended terminology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;@mgkrebbs (in comments)&lt;/strong&gt;:&#xA;&lt;p&gt;If we are considering the meiotic divisions that create gametes, then in spermatogenesis the cell which undergoes meiosis is a primary spermatocyte, and in oogenesis it is a primary oocyte. Primary spermatocytes and primary oocytes are both diploid cells which undergo DNA replication before entering meiosis I.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-01-12T22:24:50.047" LastActivityDate="2013-01-12T22:24:50.047" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5754" PostTypeId="2" ParentId="5748" CreationDate="2013-01-11T09:33:13.907" Score="5" Body="&lt;p&gt;The cited article describes effects of Tris on the outer membrane of &lt;em&gt;E. coli&lt;/em&gt;. Like all Gram negatives &lt;em&gt;E. coli&lt;/em&gt; has an inner (or cytoplasmic) membrane which is a typical phospholipid bilayer membrane containing many membrane proteins including transporters and, of course, an electron transport chain. Surrounding this there is a layer of peptidoglycan, and then the outer layer of the cell envelope is the outer membrane, which is a special (highly atypical) bilayer structure containing phospholipid and lipopolysaccharide as well as a number of proteins including the porins. The space between the two membranes is the periplasm, or periplasmic space which contains a number of small secreted proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The outer membrane is susceptible to disruption by a number of treatments including EDTA treatment. For example, many cell lysis procedures for &lt;em&gt;E. coli&lt;/em&gt; use EDTA to disrupt the outer membrane sufficiently to allow lysozyme to gain access to the peptidoglycan.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cells with destabilised outer membranes could display increased fragility, but in general I would imagine that this would not normally cause any specific problems: obviously this would depend upon exactly what your experiments are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally it is worth noting that the concentration of Tris that you will be adding with your kanamycin must be pretty low. Even if you have used 0.1 M Tris you are presumably using a 1000x stock, so the final concentration of Tris will only be 0.1 mM. The work in the cited paper looked at cells resuspended directly in 0.1 M Tris. I don't think that you need to worry about this at all. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-01-11T09:33:13.907" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5755" PostTypeId="1" CreationDate="2013-01-11T10:44:32.110" Score="0" ViewCount="4765" Body="&lt;p&gt;Some says that HIV &lt;a href=&quot;http://www.eurekalert.org/pub_releases/2012-07/uow-usd071112.php&quot; rel=&quot;nofollow&quot;&gt;destroy IRF3&lt;/a&gt;, and some says &lt;a href=&quot;http://answers.yahoo.com/question/index?qid=20090428223310AAjhNHy&quot; rel=&quot;nofollow&quot;&gt;HIV overruns T-cells&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1795" LastEditorUserId="806" LastEditDate="2018-09-17T12:01:08.683" LastActivityDate="2018-09-17T12:01:08.683" Title="Why human body cannot defend against HIV?" Tags="&lt;immunology&gt;&lt;hiv&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ClosedDate="2013-01-11T18:11:07.080" ContentLicense="CC BY-SA 3.0" />
  <row Id="5756" PostTypeId="2" ParentId="5755" CreationDate="2013-01-11T13:15:45.190" Score="3" Body="&lt;p&gt;For an understandable explanation: The human body &lt;em&gt;can&lt;/em&gt; defend against HIV - hence why an HIV infection does not immediately develop AIDS, and in fact for a long time the virus cannot be detected in blood. This is because the immune response is keeping them down, but slowly the virus works its way through the cells, proliferates and kills more and more T cells, until the immune response is too weak. That's when AIDS develops.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-01-11T13:15:45.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5757" PostTypeId="2" ParentId="5703" CreationDate="2013-01-11T14:25:19.023" Score="2" Body="&lt;p&gt;We don't have large memory capacities.&lt;/p&gt;&#xA;&lt;p&gt;If anything I would have asked the opposite, why is our memory so bad and unreliable considering how large our brains are. Even with this gigantic brain we struggle to remember a few phone numbers. Here's how our short term memory compares to monkeys: &lt;a href=&quot;https://www.youtube.com/watch?v=zsXP8qeFF6A&amp;amp;ab_channel=BBCEarth&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.youtube.com/watch?v=zsXP8qeFF6A&amp;amp;ab_channel=BBCEarth&lt;/a&gt; . I have no explanation as to why humans are so bad at this, this amount of data should be nothing for a brain of our size.&lt;/p&gt;&#xA;&lt;p&gt;As for long term memory, I'm not really convinced it is that large really, it seems to me people in general in ten years.. have forgotten pretty much everything. Occational glitch.. occational stuff, and even that is usually vague and full of wrongs.&#xA;And when people cram for exams.. take the best students ten years later and see how much they still remember, it will be just a tiny fraction.&lt;/p&gt;&#xA;&lt;p&gt;What do you mean by &amp;quot;filling up their memory capacity&amp;quot;?&#xA;Are you expecting some sort of a state where the persons hard disk is full and nothing.. &lt;i&gt;nothing&lt;/i&gt; new can be learned? That state doesn't make any sense, the brain is always deleting from memory plus it would make more sense to have the memory slowly deteriorate, rather than fall off a cliff into no functionality at all.&lt;/p&gt;&#xA;&lt;p&gt;We don't remember anything. We always feel like we are going to remember the now for so long and all but we don't. And we have this bias because we don't remember what we don't remember, which is nearly everything.&lt;/p&gt;&#xA;" OwnerUserId="542" LastEditorUserId="16459" LastEditDate="2020-12-08T15:54:42.713" LastActivityDate="2020-12-08T15:54:42.713" CommentCount="1" CommunityOwnedDate="2013-01-11T23:02:33.170" ContentLicense="CC BY-SA 4.0" />
  <row Id="5759" PostTypeId="2" ParentId="5755" CreationDate="2013-01-11T17:26:30.040" Score="4" Body="&lt;p&gt;There are two main components of the immune system that are involved: &lt;strong&gt;Antibodies&lt;/strong&gt; and &lt;strong&gt;T-cells&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;T-cells&lt;/strong&gt; are responsible for activating white blood cells to help fight off infection. These are the cells the HIV infects. Antibodies bond to the HIV virus and try to neutralize them before they can infect more cells. Unfortunately as the HIV virus replicates, there is too much virus and not enough antibodies to neutralize.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a T-cell becomes infected with HIV, the virus takes over and causes it to start replicating more HIV. This eventually causes the T-cell to die. So T-cells keep dying while HIV loads keep increasing. When enough T-cells die, the infected person is considered to have AIDS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is particularly difficult for the immune system to fight off HIV infection for a number of reasons, including the following:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;HIV attacks the immune system itself, weakening its ability to fight back.&lt;/li&gt;&#xA;&lt;li&gt;HIV replicates in large quantities that are more than the compromised immune system can handle. &lt;/li&gt;&#xA;&lt;li&gt;HIV has the ability to mutate (change itself) very quickly, making it more difficult for the body to fight the infection.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So conclusion, our bodies &lt;strong&gt;can&lt;/strong&gt; fight HIV for awhile. It's just a matter of time before the viral load outweighs the capabilities of our immune system.&lt;/p&gt;&#xA;" OwnerUserId="1451" LastActivityDate="2013-01-11T17:26:30.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5760" PostTypeId="2" ParentId="5588" CreationDate="2013-01-11T18:05:34.197" Score="10" Body="&lt;p&gt;Building on the answer given by Sean Connolly above, it would be very easy to imagine evolutionary scenarios where organs are more likely to develop asymmetrically than symmetrically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, imagine an organism that has a simple digestive system that consists only of a single undifferentiated intestine that runs directly from mouth to anus in a straight line, as in primitive annelids. Let's say that there is also only one enzyme present to break down the food particles, and that this is present throughout the intestine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, perhaps for space issues, or for reasons that are entirely unrelated to internal organs, the intestine itself becomes asymmetrical. This could be because a longer intestine is needed to dissolve and take up more of the food, but the organism cannot become longer (for instance, it might live in dead coral reefs, and the size of the hollows cannot be controlled by the organism itself, so there is an external limitation to how long the organism can become). One way to solve this would be to fold the intestine, which can make it asymmetrical.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, because food particles that enter the mouth are exposed to the single enzyme throughout the intestine, the gut fluid will be less and less nutritious the farther posterior it gets along the gut. Possibly, more anterior parts of the intestine will become specialized in breaking down and absorbing more frequent kinds of food, while more posterior parts will become specialized in less common foodstuffs. This could lead to differentiation of secretory organs along the intestine, and if this is already bent because of external selection pressures, it is not impossible that a given secretory organ will develop asymmetrically simply because the intestine at the point where the enzymes secreted by this organ are to be used is not near the mid-line of the body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, if we needed to absorb substance X from our food, but substance X only became abundant in the gut fluid at a distance from the mouth that corresponds to a place when our intestine is located on the left side of the body, it is not unreasonable that development of this excretory organ would develop on the left side of the body. This could then be self-reinforcing, as a more ready access to substance X may mean that this substance becomes more important for us, and the secretory organ may become larger and more dominant, and eventually we have a large organ that exists only on the left side of the body, without ever having existed in a symmetrical form.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is, of course, pure speculation, and I know of no example of this, but it is one that is not at odds with evolution in general, and could certainly be plausible. The same could occur if differentiation of enzyme secretion organs occur in a symmetrical gut, which later becomes asymmetrical and the whole secretory organ becomes displaced to one side. Retaining a symmetrical pair of secretory organs on each side of the body, but having the enzymes work on food only asymmetrically would imply that one of the secretory organs had a very long duct and the other had a very short one. It is reasonable to assume that over evolutionary time, the one with the long duct would become less important and may disappear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A similar reasoning could be applied to the blood circulation system and any organs relevant to that.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;There are many examples of external asymmetry throughout the animal kingdom. Many decapods, for instance, have asymmetrical claws that are used for different purposes (feeding in lobsters, for instance). Several genera of bird lice (e.g. &lt;em&gt;Struthiolipeurus, Bizarrifrons&lt;/em&gt;) have asymmetrical heads, which probably have something to do with how they attach to their hosts' feathers. I believe that many groups of sessile invertebrates have anal openings displaced to one side, but that may be caused by internal asymmetry or because it is less efficient to have our anus situated so that feces is filtered into your mouth again. &lt;/p&gt;&#xA;" OwnerUserId="1911" LastEditorUserId="1911" LastEditDate="2013-01-14T20:06:00.180" LastActivityDate="2013-01-14T20:06:00.180" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5761" PostTypeId="1" AcceptedAnswerId="5789" CreationDate="2013-01-11T20:01:07.717" Score="4" ViewCount="565" Body="&lt;p&gt;I am well aware of the phenomenon of neurogenesis induced by exercise, as well as the dopamine release that results from exercise. I am really interested in neuropsychology and the effects of exercise on personality. What are some other biological processes that are stimulated by exercise, does it activate our parasympathetic nervous system? Is there any cool research out there for me to read? I am grateful for any input. Any information about exercise and its effects on human biology is appreciated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;UPDATE&lt;/em&gt; &lt;br&gt;&#xA;While this answer was appreciated, i'm interested in other biological processes... What happens to stress and anxiety? Do our adrenal glands stop secreting as much corticosteroids? What effect does exercise have on circadian rhythms? With exercise, can you circumvent the problem of not getting enough light in the winter? What effect does exercise have on memory? It should probably help, since it would lead to decreased damage to the hippocampus. How does exercise effect sleep, learning, memory, metabolic processes??? I'm searching for the comprehensive list of different primary and secondary effects of exercise from a biological standpoint. I'm really interested in what the short term and long term effects of exercise are on the brain.&lt;/p&gt;&#xA;" OwnerUserId="1913" LastEditorUserId="1913" LastEditDate="2013-01-12T15:44:03.083" LastActivityDate="2013-01-13T22:25:34.210" Title="Effects of exercise on the brain" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;cell-biology&gt;&lt;general-biology&gt;&lt;neurology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5762" PostTypeId="1" CreationDate="2013-01-11T21:02:43.827" Score="3" ViewCount="332" Body="&lt;p&gt;&lt;em&gt;&quot;Is there a cannabinoid autoreceptor? And if so what is the cannabinoid autoreceptor?&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(i.e. &lt;em&gt;is the cannabinoid autoreceptor CB&lt;sub&gt;1&lt;/sub&gt;, CB&lt;sub&gt;2&lt;/sub&gt; or is it one of the G protein coupled receptors, GPR18, GPR55 or GPR119?&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;An autoreceptor is a receptor located presynaptically that sends back negative feedback that inhibits the synthesis of the neurotransmitter to which the autoreceptor belongs and this negative feedback also inhibits the release of the neurotransmitter from storage vesicles into the synaptic cleft. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The CB&lt;sub&gt;1&lt;/sub&gt; and CB&lt;sub&gt;2&lt;/sub&gt; receptors are respectively called the first and second cannabinoid receptors and are a pair of G protein coupled receptors.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;GPR18, GPR55 and GPR119 are G protein coupled receptors that are also activated by some lipid messengers including a few of the endocannabinoids and their related compounds.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="3632" LastEditDate="2013-01-12T15:59:53.247" LastActivityDate="2013-01-12T20:03:28.643" Title="What is the cannabinoid autoreceptor?" Tags="&lt;neurotransmitter&gt;&lt;receptor&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5764" PostTypeId="1" AcceptedAnswerId="5766" CreationDate="2013-01-11T22:55:16.710" Score="7" ViewCount="675" Body="&lt;p&gt;In a book about post-war Japan (Embracing Defeat, Dower) the author mentions a process for making sawdust at least partially edible, so it could be used in recipes in a 1:4 ratio with flour for cooking. The author says the sawdust was &quot;fermented,&quot; as I recall. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is whether this is anything more than marginally possible. After all, kimchee, yogurt, beer, and other fermented foods aren't necessarily easier to digest. Is there a fermentation process involving bacteria that break down cellulose that might make wood even slightly nutritious? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My impression is that in forests the process of breaking down wood does not initially involve bacteria but other microorganisms; on the other hand, ruminants such as cows use bacteria to help them metabolize. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any insight.  &lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2013-01-11T23:09:30.580" Title="Cooking with sawdust" Tags="&lt;metabolism&gt;&lt;digestive-system&gt;&lt;food&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5765" PostTypeId="2" ParentId="5752" CreationDate="2013-01-11T22:58:39.667" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Inbreeding&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Inbreeding&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm thinking that the answer is not defined as there is probably an explicit or implicit assumption about both parents having the same ploidy (brother (haploid) and sister (diploid) in your question) in both the path and tabular methods used for calculating inbreeding coefficient.&lt;/p&gt;&#xA;" OwnerUserId="1756" LastActivityDate="2013-01-11T22:58:39.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5766" PostTypeId="2" ParentId="5764" CreationDate="2013-01-11T23:09:30.580" Score="4" Body="&lt;p&gt;Yes. I think it would certainly be possible for raw sawdust to be made digestible by humans through some sort of fermentation process with some kind of microbe or another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pickling (as is done with kimchee and cucumbers and lots of other fruits) uses naturally occurring bacteria that are artificially selected for by using a strong brine solution so that most microbes die but the ones that naturally survive in strong brine also convert the organic materials they find (raw cucumber or cabbage) into different organic materials (pickled cucumber or pickled cabbage in the case of kimchee).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you could find a microbe that could digest wood (there are many I'm sure; the gut bacteria in termites provide evidence of at least one or some), and if you could find a way to select for that particular microbe, then fermenting sawdust for nutritious human consumption becomes feasible. The only remaining problem is finding that particular microbe whose excretions were digestible to humans.&lt;/p&gt;&#xA;" OwnerUserId="1756" LastActivityDate="2013-01-11T23:09:30.580" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5767" PostTypeId="2" ParentId="5749" CreationDate="2013-01-11T23:58:01.827" Score="4" Body="&lt;p&gt;If you look at a cancer textbook (eg. &lt;a href=&quot;http://www.garlandscience.com/product/isbn/9780815340782&quot; rel=&quot;nofollow&quot;&gt;Robert A. Weinberg's &lt;em&gt;The Biology of Cancer&lt;/em&gt;&lt;/a&gt;), you'll find that by definition, a tumor arises from tissues normally found in the patient's body. There's a great deal more to it than just that simple statement, but given the context of the question, I think that answer should suffice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In writing, &quot;...tumors growing a tooth, hair...&quot;, I think you're talking about &lt;a href=&quot;http://en.wikipedia.org/wiki/Teratoma&quot; rel=&quot;nofollow&quot;&gt;teratomas&lt;/a&gt;. These contain &quot;normal derivatives of all three germ layers&quot;. These arise naturally from cells &quot;...typically found in the human body...&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cancer is a process where mutations in a single cell transform that cell into something that is by definition not &quot;typically found in the human body.&quot; But a human cell transformed by mutation into a tumor (benign or malignant) is never (to the best of my knowledge) going to magically become a cell from another species or a very distant ancestor (ie. something that is not &quot;typically found in the human body.&quot;).&lt;/p&gt;&#xA;" OwnerUserId="1756" LastActivityDate="2013-01-11T23:58:01.827" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5769" PostTypeId="1" AcceptedAnswerId="5775" CreationDate="2013-01-12T02:42:03.977" Score="2" ViewCount="481" Body="&lt;p&gt;Say I was conducting an experiment for photosynthesis. If I moved light closer to the plant, what effect would this have on the process of photosynthesis?&lt;/p&gt;&#xA;" OwnerUserId="1914" LastEditorUserId="107" LastEditDate="2013-01-12T14:14:46.280" LastActivityDate="2013-01-12T17:04:25.180" Title="Photosynthesis - Light Intensity" Tags="&lt;photosynthesis&gt;&lt;botany&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5770" PostTypeId="2" ParentId="5749" CreationDate="2013-01-12T03:27:44.253" Score="0" Body="&lt;p&gt;Definitely NOT for cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you are speaking about are teratomas - results of incorrect development of stem cells. Stem cells are the type of cell that can become any other cell type. That way the growth of stem cell tissue may result in production of any organs.&lt;/p&gt;&#xA;" OwnerUserId="408" LastActivityDate="2013-01-12T03:27:44.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5771" PostTypeId="2" ParentId="5749" CreationDate="2013-01-12T04:39:38.300" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Teratoma&quot; rel=&quot;nofollow&quot;&gt;Teratomas&lt;/a&gt; are thought to be a particular type of cancer, present from early development.  As cells which are essentially developmental cells, they seem to have a fairly unique ability to develop hair follicles, teeth and even structures like organs. Indeed &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/001316.htm&quot; rel=&quot;nofollow&quot;&gt;malignant teratomas often require chemotherapy or radiation therapy&lt;/a&gt;.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this bizzarre quality of producing organs or hair etc, is the result of the fact that the origin cells are programmed to develop into these organs before they become tumorous.  Later in life, we have no developmental stem cells in the body which will differentiate into organs and so other sorts of teratomas would seem to be unique.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cancer cells are still cells programmed to perform the roles they started with, but they are usually not capable of generating whole functional tissue or organs. If they do they would normally be found amongst the tissue they would grow (e.g. liver cancer might produce tissue that looks like liver) so it would not have the unusual quality of teratomas of producing differentiated and specific tissues in isolation.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-01-12T04:39:38.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5772" PostTypeId="5" CreationDate="2013-01-12T11:21:34.530" Score="0" Body="&lt;p&gt;Questions should be about the biology of HIV, not seeking medical advice on the health aspects of HIV. Health questions are strictly off topic.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="1590" LastEditDate="2016-03-23T16:20:41.330" LastActivityDate="2016-03-23T16:20:41.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5773" PostTypeId="4" CreationDate="2013-01-12T11:21:34.530" Score="0" Body="The Human Immunodeficiency Virus (HIV) is a single-stranded RNA virus which reproduces in human CD4-positive cells, which are primarily T-helper lymphocytes and macrophages. HIV is the causative pathogen of Acquired Immunodeficiency Syndrome (AIDS)." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T18:00:08.960" LastActivityDate="2013-10-31T18:00:08.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5774" PostTypeId="2" ParentId="5752" CreationDate="2013-01-12T11:23:36.213" Score="1" Body="&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Inbreeding&quot; rel=&quot;nofollow noreferrer&quot;&gt;the same article on wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The inbreeding is computed as a percentage of chances for two alleles to be identical by descent. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now let's draw a family tree for such mating and sign chances for having each allele:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Zq70T.png&quot; alt=&quot;haplodiploid incest tree&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see, that the &quot;brother&quot; has a 50% chance of receiving A allele and the &quot;sister&quot; has a 50% chance of receiving A from their mother, but the &quot;brother&quot; will not have the C allele that the sister certainly has. Their daughter will have the allele from her father and one of mother's alleles. Therefore, her chances of having &lt;em&gt;a&lt;/em&gt; C allele are 50%, and for &lt;em&gt;a&lt;/em&gt; A or &lt;em&gt;a&lt;/em&gt; B allele each 75% (remember, she needs two copies, so we need to end up with 200%; furthermore, she may have two A alleles but not more than one C allele). Chances of her having two A or two B alleles are 56,25% $$0.75 * 0.75 = 0.5625$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now we have the &lt;em&gt;percentage of chances for two alleles to be identical by descent,&lt;/em&gt; her inbreeding coefficient is 56,25%.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The son will have only one allele, 50% for C, 25% for A and 25% for B. Because he does not have two alleles, by definition there is no inbreeding possible.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastActivityDate="2013-01-12T11:23:36.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5775" PostTypeId="2" ParentId="5769" CreationDate="2013-01-12T12:18:24.127" Score="1" Body="&lt;p&gt;The rate of photosynthesis varies from plant to plant. Some plants require more light and some require less. If you move light closer to the plant, in most scenarios the rate of photosynthesis is likely to be increased. For some plants a minimal light is enough for their photosynthesis, so for those plants, moving light source closer or further will have less effect.  &lt;/p&gt;&#xA;" OwnerUserId="1915" LastEditorUserId="1306" LastEditDate="2013-01-12T17:04:25.180" LastActivityDate="2013-01-12T17:04:25.180" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5776" PostTypeId="2" ParentId="5761" CreationDate="2013-01-12T12:39:09.007" Score="0" Body="&lt;p&gt;Exercise stimulates various hormones which have impact on brain as well as other parts of the body. In psychological perspective, endorphins and serotonin released during exercise, are responsible to feel good feeling or act as antidepressants. Endorphins are produced by pituitary gland in the brain. Serotonin is also produced in brain to some extent during exercise. An increased level of serotonin could lead to nausea and vomiting. The other hormone released significantly is dopamine which is responsible for increasing blood pressure but it also helps in focus, attention and increase memory. &lt;/p&gt;&#xA;" OwnerUserId="1915" LastActivityDate="2013-01-12T12:39:09.007" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5777" PostTypeId="2" ParentId="5659" CreationDate="2013-01-12T12:58:04.410" Score="2" Body="&lt;p&gt;You are not completely wrong but not completely right either. Some siblings tend to think they are less similar to each other, even twins. It may or may not have scientific reason, but it has sociological reason behind it. Every people in our society want to have their own separate identity and they do not want themselves to be compared with others even with their siblings.It might be also due to the result of fact that, siblings pass times with each other so often that they notice distinct differences in both their characteristics and look while ordinary people, looking at them for the first time, can not notice the differences. This is related to the reason why we can not sometime recognize people from any particular race or ethnicity at first look. &lt;/p&gt;&#xA;" OwnerUserId="1915" LastActivityDate="2013-01-12T12:58:04.410" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5778" PostTypeId="2" ParentId="5762" CreationDate="2013-01-12T15:54:32.237" Score="2" Body="&lt;p&gt;CB1 and CB2 are indeed particular genes which are present in neurons, but also liver and other tissues.  The HGNC website is a good resource for questions like this - HGNC is the international organization that tries to unify and track gene names.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The official gene names are &lt;a href=&quot;http://www.genenames.org/data/hgnc_data.php?hgnc_id=2159&quot; rel=&quot;nofollow&quot;&gt;CNR1&lt;/a&gt; and &lt;a href=&quot;http://www.genenames.org/data/hgnc_data.php?hgnc_id=2160&quot; rel=&quot;nofollow&quot;&gt;CNR2&lt;/a&gt; respectively.  Gene names are a bit of a mess, since many genes have been found by different experiments and so have many names. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;CNR1 has other aliases, I see:&#xA;CANN6, CB-R, CB1, CB1A, and CB1K5.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CNR2 has only the one alias: CB2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also searched the HGNC website for those alternate gene symbols and they appear to be different genes, although CB1 and CB2 are GPCR class receptors, humans have hundreds of these genes.  Most cell scientists would not be surprised if cannabinols bound other receptors - the fact is probably only that CB1 and CB2 bind strongest and were found first.  Often weak binding is important to specific pharma/neuro responses.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is to say there shouldn't be any single Cannabinoid receptor in the animal repetoire.  CB1 and CB2 almost certainly have a primary function other than cannibinol binding.  Primates evolved in the old world and cannabis is thought to have &lt;a href=&quot;http://en.wikipedia.org/wiki/Cannabis&quot; rel=&quot;nofollow&quot;&gt;originated in the Himalayan regions&lt;/a&gt;.  From an evolutionary standpoint, the activity of cannabinoids is as much coincidence as anything, so you would expect that a single receptor gene is unlikely. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-01-12T15:54:32.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5780" PostTypeId="2" ParentId="5740" CreationDate="2013-01-12T21:58:03.657" Score="9" Body="&lt;p&gt;The reason lies within our wormy chordate ancestors - an orifice used to eliminate waste can also function as an orifice to eject eggs. My vertebrate zoology is a little bit rusty so I would suggest picking up any first-course book on the subject, most of them cover the evolution of urinary/reproductive organs extensively.&lt;/p&gt;&#xA;" OwnerUserId="953" LastActivityDate="2013-01-12T21:58:03.657" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5781" PostTypeId="2" ParentId="5751" CreationDate="2013-01-12T23:08:42.670" Score="5" Body="&lt;p&gt;Meiosis starts with a diploid cell and produces four haploid cells.  In animals, the starting diploid cell is usually called a &lt;a href=&quot;http://en.wikipedia.org/wiki/Germ_cell&quot;&gt;&lt;em&gt;germ cell&lt;/em&gt;&lt;/a&gt; and the surviving haploid cells become &lt;a href=&quot;http://en.wikipedia.org/wiki/Gamete&quot;&gt;gametes&lt;/a&gt; (&lt;a href=&quot;http://en.wikipedia.org/wiki/Sperm&quot;&gt;sperm&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Ovum&quot;&gt;ova&lt;/a&gt;).  (In animals, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Oogenesis&quot;&gt;female mitotic sequence&lt;/a&gt; produces only one ovum; the other three haploid cells become &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Polar_body&quot;&gt;polar bodies&lt;/a&gt;&quot;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other organisms such as plants, the starting diploid cell is typically not called a &quot;germ cell&quot; as it is not distinguished early in the organism's life.  Instead the starting cell can be any undifferentiated diploid cell that finds itself in the appropriate location (e.g. in a flower) at the appropriate time. &lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2013-01-12T23:08:42.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5782" PostTypeId="1" CreationDate="2013-01-13T05:50:53.743" Score="16" ViewCount="57574" Body="&lt;p&gt;When babies are first born, they receive their antibodies from their mother (I assume because they do not yet have the capacity to synthesize their own).  So my question is, at what age do babies begin synthesizing their own antibodies?&lt;/p&gt;&#xA;" OwnerUserId="1919" LastEditorUserId="107" LastEditDate="2013-01-13T13:32:47.553" LastActivityDate="2015-07-25T23:03:20.680" Title="At what age do babies begin to synthesize their own antibodies?" Tags="&lt;human-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5783" PostTypeId="2" ParentId="5782" CreationDate="2013-01-13T12:31:26.850" Score="15" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nR7Qa.png&quot; alt=&quot;Graph of the progression of an infants antibody production&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the graph above the darker blue line refers to the antibodies the baby receives from the mother in utero, as you mentioned in your question.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, the red line indicates that babies begin to produce low levels of their own antibodies between 3 and 6 months before birth.  However, these are IgM antibodies, immature 'rough draft' versions.  These have much lower affinity for antigens then their mature IgG counterparts which are the classically thought of antibody.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Levels of an infant's own IgG start to rise after birth, however don't reach a reasonable level until after the child is roughly 1 year old.  Maternal antibodies start to tail off at around 3 months leaving a period highlighted in blue on the graph where infants are particularly prone to getting infections.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="5144" LastEditDate="2015-07-21T08:09:28.153" LastActivityDate="2015-07-21T08:09:28.153" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="5784" PostTypeId="1" CreationDate="2013-01-13T14:10:39.823" Score="1" ViewCount="71" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Possible Duplicate:&lt;/strong&gt;&lt;br&gt;&#xA;  &lt;a href=&quot;https://biology.stackexchange.com/questions/594/why-are-amino-acids-in-biology-homochiral&quot;&gt;Why are amino acids in biology homochiral?&lt;/a&gt;  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&#xA;&#xA;&lt;p&gt;Why are only L-amino acids used in protein construction, and not D-amino acids?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2013-01-13T15:25:24.043" Title="Why aren't D-amino acids used in proteins?" Tags="&lt;proteins&gt;&lt;amino-acids&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2013-01-13T16:49:26.260" ContentLicense="CC BY-SA 3.0" />
  <row Id="5786" PostTypeId="2" ParentId="5099" CreationDate="2013-01-13T19:33:11.107" Score="2" Body="&lt;p&gt;My understanding has been that it aids in sun absorption in the skin, specifically in low sunlight/overcast areas. I don't have source on hand, but that may steer you in the direction you are looking for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, consider that that pheomelanin, red hair specifically, may encourage breeding success, depending on where you are.&lt;/p&gt;&#xA;" OwnerUserId="1923" LastActivityDate="2013-01-13T19:33:11.107" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="5787" PostTypeId="2" ParentId="5121" CreationDate="2013-01-13T21:27:35.960" Score="3" Body="&lt;p&gt;Yes, the human body has thermoreceptors that &quot;sense&quot; the current temperature, but these merely help with regulation--you know, shivering to raise internal body temperature and sweating to cool via evaporation. The hypothalamus is primarily responsible for making sure that the circadian rhythm itinerary is adhered to reasonably well. So no, if the thermoreceptors detect that the body temperature is 97 deg F but it's 5 pm, the body will not &quot;get confused&quot; and decide that it is actually 4 am because a human body is about 97 deg F at 4 am. &lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2013-01-13T21:27:35.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5789" PostTypeId="2" ParentId="5761" CreationDate="2013-01-13T22:25:34.210" Score="1" Body="&lt;p&gt;Although current research has little to say about the effects of exercise on personality, there has been recent correlations demonstrated between personality and the &quot;drive&quot; to exercise--specifically, aggression as a personality trait has been linked to higher metabolic rate. See &lt;a href=&quot;http://phys.org/news206006380.html&quot; rel=&quot;nofollow&quot;&gt;http://phys.org/news206006380.html&lt;/a&gt; for more information about this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The causation in exercise-induced neurogenesis is not well understood. A correlation that has been found (in mice) is the presence of a hormone called beta-endorphin, which is attributed to positive affect (a boost in mood). Exercising mice that demonstrated the presence of beta-endorphin in their hippocampal region did experience exercise-induced neurogenesis, while those that naturally lacked beta-endorphin did not experience neurogenesis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The basic worth of circulation should not be overlooked, either. Anything that gets your blood pumping more efficiently means that the more distal parts of the body will appreciate an influx of nutrients. A smoker with poor circulation (as a result of lowered oxygen in the blood -- carbon monoxide competes for hemoglobin-binding) will have cold hands and brittle fingernails, and this is just a simple example of this phenomenon. The value of increased circulation to the brain shouldn't be overlooked -- the blood is our main transportation system, and the brain gets nothing that is not delivered via circulation. It's akin to watering a plant -- sure, it may grow it you give it 30 minutes of sunlight and 1/4 cup of water a day, but it will certainly grow to its full potential if it is fed as much as it needs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exercise is important, but it's easier to think about the questions you pose if you consider exercise more as a physiological stressor on the body. Muscle tissues are torn and damaged by exercise, but the body recognizes that it must need these resources (because of some present danger in the environment that caused you to run/strain yourself) so you begin to see the typical skeletal muscle hypertrophy. The heart is also made stronger through this strain, which is why regular exercisers have a lower resting heart rate -- it takes their heart less effort to pump the same amount of blood.   &lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2013-01-13T22:25:34.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5790" PostTypeId="1" CreationDate="2013-01-14T03:12:28.823" Score="4" ViewCount="192" Body="&lt;p&gt;I've been reading about the new phenomenon called &lt;strong&gt;&quot;arousal addiction&quot;&lt;/strong&gt;. The context in which this term is used is Internet, Porn and/or video game addiction(cummulatively &lt;strong&gt;Internet Addiction Disorder - IAD&lt;/strong&gt;). Dopamine and Dopamine receptor D2 are sometimes mentioned, as being affected by exposure to a new, novel stimuli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I'm interested if there are other forms of &quot;arousal&quot; that may involve more than just Dopamine.&lt;/strong&gt; For example, I know that there are 4 neuromodulators in the human brain: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Dopamine&lt;/li&gt;&#xA;&lt;li&gt;Serotonin&lt;/li&gt;&#xA;&lt;li&gt;Choline&lt;/li&gt;&#xA;&lt;li&gt;Noradrenaline&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For example, if a person likes horror movies to the point of addiction, is it Dopamine, or is it Noradrenaline that the person enjoys? If a person is addicted to comfort foods, is it Dopamine or Serotonin? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="577" LastEditDate="2013-01-15T22:59:23.810" LastActivityDate="2013-01-15T23:00:40.063" Title="What kinds of arousal can a human brain experience?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="5791" PostTypeId="2" ParentId="5790" CreationDate="2013-01-14T04:15:33.020" Score="3" Body="&lt;p&gt;Depends on what you mean by &quot;addiction&quot;: defined, addiction usually requires both psychological and physiological dependence, but conversationally we sometimes only talk about psychological dependence (as in here, your muscles won't cramp up if you NEED a horror flick).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a person enjoys horror movies, is it the suspense? Such a rush is caused by the well-known fight-or-flight catecholamine epinephrine (also known as adrenaline). This is the short-term stress response at play. Comfort foods are a whole other story, because it depends on the food as well. Carbohydrates can contribute to serotonin levels, yes, but I read a super-interesting study a couple years back about saturated fat causing a decrease in corticosteroid levels and this sought to explain why people eat fatty foods when they are stressed (I'll try to find this article for you). Tryptophan, an amino acid, is converted to serotonin, which is why turkey, milk, and other sources of trp can make one sleepy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Awesome question! I'm going to try to learn more about this and find that article for you. Dopamine is the primary player in most conventional addiction-talk, as it's crucial to the reward circuitry that is usually discussed.&lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2013-01-14T04:15:33.020" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="5792" PostTypeId="1" CreationDate="2013-01-14T06:40:22.070" Score="3" ViewCount="141" Body="&lt;p&gt;Assume that we planted floating solar cells on the ocean surfaces. Assume a 100km² solar cell field in the middle of the Pacific Ocean. All of the sunlight will be blocked by them. How would that affect the life in oceans?&lt;/p&gt;&#xA;" OwnerUserId="989" LastEditorUserId="3952" LastEditDate="2013-08-06T12:17:57.427" LastActivityDate="2013-08-06T12:17:57.427" Title="How would ecology be affected if 100km² of an ocean surface was covered by a floating object?" Tags="&lt;ecology&gt;&lt;speculative&gt;" AnswerCount="2" CommentCount="0" ClosedDate="2016-06-08T20:14:34.613" ContentLicense="CC BY-SA 3.0" />
  <row Id="6790" PostTypeId="1" AcceptedAnswerId="6791" CreationDate="2013-01-14T09:09:30.480" Score="3" ViewCount="261" Body="&lt;p&gt;In glycolysis, the conversion of glucose to pyruvate results in a net gain of 2 ATP molecules. In gluconeogenesis however, the conversion of pyruvate back to glucose requires 6 ATP molecules.  Why does there seem to be an apparent loss of energy?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="16299" LastEditDate="2015-11-27T03:16:44.620" LastActivityDate="2015-11-27T03:16:44.620" Title="ATP utilized in Glycolysis vs. Gluconeogenesis" Tags="&lt;metabolism&gt;&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6791" PostTypeId="2" ParentId="6790" CreationDate="2013-01-14T10:09:57.953" Score="3" Body="&lt;p&gt;This energy is not lost, it is dissipated as heat. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And this must happen because of thermodynamics -- the direction of the reaction is simply determined by the difference of energy between substrates and products, and it must be positive for the reaction to happen spontaneously. &lt;/p&gt;&#xA;" OwnerDisplayName="user59" LastActivityDate="2013-01-14T10:09:57.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6792" PostTypeId="2" ParentId="5792" CreationDate="2013-01-14T10:37:42.893" Score="3" Body="&lt;p&gt;The vast majority of light only penetrates the top 200 metres of the ocean, the &lt;a href=&quot;http://oceanservice.noaa.gov/facts/light_travel.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;euphotic&lt;/a&gt; zone, so your answer is roughly &amp;quot;what ever lives in the euphotic zone which requires light.&amp;quot; In all likelihood I would expect this to cause:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;anything  which is not highly mobile but, is dependent on sunlight (phytoplankton etc.), would die.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the more mobile (&amp;quot;free swimming&amp;quot;) which rely on either sunlight or the (now dead) slower resources would move out of the area.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;reduced flow of nutrients in to the lower parts of the ocean - biomass from the upper regions dies and sinks to the lower levels, if it no longer grows in the upper 200m then there will be less down flow after time.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;Overall, the impact would be low because the area of the pacific is &amp;gt;165,000,000 km2 so the density of biota would only increase marginally in the top 200 metres of the pacific (the sunlit water volume decreases from 33,040,000,000,000 cubic metres to 33,039,080,000,000 cub. metres). Also, if we assume that the platform is free floating that means it would drift thus only causing short term loss of sunlight for the less mobile organisms.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt;&#xA;Upon reading @Kotatsu's answer I feel they have made a very good point and I should add the following:&lt;/p&gt;&#xA;&lt;p&gt;By providing a solid surface it could also benefit oceanic life by increasing area available to live for sessile organisms (just like shipwrecks, oil rigs etc.). Further if the panels were broken up (I assume this would be the likely design because sitting a huge sheet across the ocean will leave it prone to twisting by wave motion) light would be able to pass between the gaps. I agree with @Kotatsu, and this &amp;quot;floating panel&amp;quot; could even be beneficial to the ocean ecosystem.&lt;/p&gt;&#xA;&lt;p&gt;&lt;br&gt;&lt;br&gt;&#xA;&lt;em&gt;note: I am not an expert on this so it is purely an application of logic and my best guess&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-01-14T18:40:59.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6794" PostTypeId="1" AcceptedAnswerId="6965" CreationDate="2013-01-14T12:53:30.213" Score="8" ViewCount="312" Body="&lt;p&gt;Suppose I have a nerve fiber consisting of several axons all running in parallel to each other.  When an action potential is generated in a certain axon, this will alter the concentration of sodium and potassium ions inside the axon, and in the extracellular fluid around that axon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is, will this change in ion concentration in the extracellular fluid, alter the threshold potential of an adjacent axon, which shares the same extracellular fluid?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2013-01-29T17:29:55.390" Title="Do adjacent axons in a nerve influence each other?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="6800" PostTypeId="2" ParentId="5792" CreationDate="2013-01-14T16:03:31.310" Score="3" Body="&lt;p&gt;It might, however, result in an increase of macrofauna, especially if the solar plates were anchored somehow at the bottom of the ocean. This may seem paradoxical, but for most groups of sessile macrofauna (cnidarians, tunicates, bryozoans, brachiopods, some molluscs, and so on), the limiting resource in the ocean is space, and any solid or semisolid surface is a good surface to live on, so &lt;em&gt;at least&lt;/em&gt; along the margins of the solar plates, we should expect to see enormous amounts of macrofauna, in the same way as we see lots of it on the keels of ships, on jetties, oilrigs, and all other man-made structures in the sea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would expect that once such a sessile community is established, it would be beneficial to other organisms as well. Many polychaetes, molluscs, arthropods, and other groups are predators of the sessile community, and as the larval stages are often planktonic, I would expect to see these established in this community as well, given time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This could in turn attract fish, especially if the platform is not too far from land, and is not cleaned, but the various shells and structures built by the sessile community is allowed to remain even after the actual organisms die off. The spaces between and inside dead sea shells are often very important places for egg deposition by fish, which may or may not remain in the area when they grow up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, if the solar plates were divided into smaller connected discs, so that there is sunlight reaching the water between the discs, this margin effect would be even more profound, I would expect, as there would be sessile macrofauna around all the margins, and if sunlight comes down between the discs, that would allow some primary production even within the solar field. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So while rg255's answer is certainly also correct, I do not think the situation is necessarily as bleak as depicted in that answer, however, it would all depend on how the structure is built and maintained. Dividing the solar panels into smaller, connected units would be much better than having one solid platform (I assume this would be true also for mechanical and engineering reasons, but I'm not an engineer...), and there are certainly other ways to reduce the impact of such a solar system platform. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would also guess that any platform placed in the middle of the ocean would have to include some system for keeping oceanic birds away.&lt;/p&gt;&#xA;" OwnerUserId="1911" LastActivityDate="2013-01-14T16:03:31.310" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6802" PostTypeId="7" CreationDate="2013-01-14T20:26:52.137" Score="0" Body="&lt;p&gt;&lt;ul&gt;&#xA;  &lt;li&gt;general questions about biological concepts&lt;/li&gt;&#xA;  &lt;li&gt;questions about the biological mechanisms behind medical conditions&lt;/li&gt;&#xA;  &lt;li&gt;questions about techniques in a biological or biochemical laboratory&lt;/li&gt;&#xA;  &lt;/ul&gt;&lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="111" LastEditDate="2013-01-14T20:26:52.137" LastActivityDate="2013-01-14T20:26:52.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6803" PostTypeId="7" CreationDate="2013-01-14T20:27:38.423" Score="0" Body="&lt;ul&gt;&#xA;    &lt;li&gt;Anything not directly related to biology, such as personal medical questions.&lt;/li&gt;&#xA;    &lt;li&gt;Philosophical or ethical questions related to biology&lt;/li&gt;&#xA;    &lt;li&gt;Questions that are primarily opinion-based&lt;/li&gt;&#xA;    &lt;li&gt;Questions with too many possible answers or that would require an extremely long answer&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="111" LastEditDate="2013-01-14T20:27:38.423" LastActivityDate="2013-01-14T20:27:38.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6804" PostTypeId="1" AcceptedAnswerId="6824" CreationDate="2013-01-15T00:50:11.053" Score="4" ViewCount="1489" Body="&lt;p&gt;Antibodies or immunoglobulins are proteins made ​​by the immune system in response to alien(!) molecules. Each antibody binds to its specific antigen. This great diversity and specificity is cause of diversity in Antigen Binding Site of heavy chain and light chain of antibody. Although other sections of Antibody are highly stable, Binding sites are very mutant. What is the reason for this difference in mutation rates in different parts of antibodies?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="1916" LastEditDate="2013-01-15T01:16:27.910" LastActivityDate="2013-01-17T14:20:47.503" Title="variation in antigen binding site of antibodies" Tags="&lt;immunology&gt;&lt;mutations&gt;&lt;antibody&gt;&lt;binding-sites&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6805" PostTypeId="1" AcceptedAnswerId="6809" CreationDate="2013-01-15T03:33:14.487" Score="6" ViewCount="122" Body="&lt;p&gt;Quantitative analysis of microscope images is essential for many types of studies, but the techniques used most often are very labor-intensive. I have been able to find some literature about using computers to perform the analysis, but do not have a good picture of the state of the art.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Is there a good literature review on the topic?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is there much use in practice which I have not yet seen?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="2928" LastEditorUserId="852" LastEditDate="2013-01-15T09:09:54.127" LastActivityDate="2013-01-15T17:42:50.973" Title="What is the state of automated quantitative analysis?" Tags="&lt;bioinformatics&gt;&lt;microscopy&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6807" PostTypeId="1" CreationDate="2013-01-15T06:45:24.777" Score="3" ViewCount="627" Body="&lt;p&gt;I am a student, and I have written a paper (in drug discovery) which I want to publish. While searching for possible journals I came across &lt;a href=&quot;http://www.webmedcentral.com&quot; rel=&quot;nofollow&quot;&gt;Webmedcentral&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is Webmedcentral a reputable scientific publisher?&#xA;What is the impact factor for this journal? &lt;/p&gt;&#xA;" OwnerUserId="834" LastEditorUserId="6" LastEditDate="2013-01-21T13:02:35.950" LastActivityDate="2013-01-21T13:02:35.950" Title="Is Webmedcentral a reputable scientific publisher?" Tags="&lt;literature&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6808" PostTypeId="2" ParentId="6805" CreationDate="2013-01-15T09:08:39.210" Score="4" Body="&lt;p&gt;The word to look for is 'Image segmentation'. But also here, it very much depends on what you're looking at. Segmentation and quantification of simple fluorescence images is relatively easy and widely used. It can get very complex depending on how complex the structure is you're looking at. There are machine-learning approaches which are able to distinguish complicated structures from each other, such as different mitosis states. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Segmenting Hematoxylin-Eosin (HE) stained specimens is subject of intensive bioinformatical research. One goal is to assist pathologists in grading tissue lesions, such as in prostate cancer, but this is as far as I know not used clinically yet. Whole-slide scans of histological specimens are becoming more widely used clinically. These images are very huge (1 GB per specimen), so a research focus is also to provide a large-scale analysis of these whole-slide scans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, take a look at CellProfiler (&lt;a href=&quot;http://www.cellprofiler.org&quot; rel=&quot;nofollow&quot;&gt;http://www.cellprofiler.org&lt;/a&gt;), this free open-source software saved my PhD project.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Literature I found:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tabesh, A., M. Teverovskiy, et al. (2007). &quot;Multifeature prostate cancer diagnosis and Gleason grading of histological images.&quot; IEEE Trans Med Imaging 26(10): 1366-1378.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Petushi, S., F. U. Garcia, et al. (2006). &quot;Large-scale computations on histology images reveal grade-differentiating parameters for breast cancer.&quot; BMC Med Imaging 6: 14. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1634843/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1634843/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I cannot provide you with a recent review, though...&lt;/p&gt;&#xA;" OwnerUserId="852" LastEditorUserId="1306" LastEditDate="2013-01-15T17:42:50.973" LastActivityDate="2013-01-15T17:42:50.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6809" PostTypeId="2" ParentId="6805" CreationDate="2013-01-15T12:08:42.737" Score="3" Body="&lt;p&gt;Nature Methods seems to publish quite a few methods that facilitate this kind of analysis. E.g.&#xA;&lt;a href=&quot;http://www.nature.com/nmeth/journal/v8/n3/full/nmeth.1558.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nmeth/journal/v8/n3/full/nmeth.1558.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And an editorial from them:&#xA;&lt;a href=&quot;http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2102.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2102.html&lt;/a&gt;&#xA;As part of a special issue on BioImage Informatics with some nice examples.&#xA;&lt;a href=&quot;http://www.nature.com/nmeth/journal/v9/n7/index.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nmeth/journal/v9/n7/index.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="476" LastActivityDate="2013-01-15T12:08:42.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6811" PostTypeId="2" ParentId="6807" CreationDate="2013-01-15T12:57:46.203" Score="2" Body="&lt;p&gt;I checked this site and its journals in Scopus.com based on its &quot;ISSN 2046-1690&quot; but nothing was there. they are fast in submitting and publishing but it is not some thing great by it self. I think maybe its better to find some where better to publish your article(s).&lt;/p&gt;&#xA;" OwnerUserId="1916" LastActivityDate="2013-01-15T12:57:46.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6812" PostTypeId="1" CreationDate="2013-01-15T13:43:03.723" Score="4" ViewCount="365" Body="&lt;p&gt;I am in the process of creating biological key software tool for use on android devices. I would like to know if there are any established file formats for storing biological key data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="2930" LastEditorUserId="112" LastEditDate="2013-02-22T09:02:49.687" LastActivityDate="2013-02-22T09:02:49.687" Title="Biological key file format" Tags="&lt;bioinformatics&gt;&lt;software&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="6813" PostTypeId="1" AcceptedAnswerId="6815" CreationDate="2013-01-15T15:06:04.657" Score="3" ViewCount="383" Body="&lt;p&gt;I'm trying to evaluate data taken from fluorescence microscopy with antibody staining, and am wondering whether there is any standard way to evaluate the specificity of the antibody for such measurements? In particular, I am interested in evaluating whether there is specific binding of the antibody to the cells in the experiment, or only unspecific binding.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By leaving out the primary antibody or taking a control antibody without specific binding, I can compare fluorescence intensity, and an increase in intensity in the actual experiment towards this control will indicate qualitatively that the antibody binds specifically. But I wonder whether there is a standard statistical test or something to get such a result in a more quantitative way?&lt;/p&gt;&#xA;" OwnerUserId="2931" LastActivityDate="2013-01-15T15:51:27.020" Title="How to evaluate the efficacy of an antibody for fluorescence microscopy?" Tags="&lt;immunology&gt;&lt;microscopy&gt;&lt;antibody&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6814" PostTypeId="1" CreationDate="2013-01-15T15:10:05.570" Score="3" ViewCount="95" Body="&lt;p&gt;I use to run a method to analyse all the amino-acids in a food sample. For that I have to hydrololyse the sample and in the last stage of the method I read the amino acids with a ion exchange chromatography.&#xA;However, when using this method, due to the hydrolysis, the glutamine transforms into glutamic acid, thus in my result I get a big peak for glutamic acid and I cannot read glutamine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is if there's a method to quantify glutamine in a food sample.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: it has been a while, thanks for the feedback! &#xA;In the kind of samples I have I need to measure the bound glutamine, not free glutamine. This imposes a problem during sample preparation when trying to separate the amino acids. I have made a few experiments and I have almost succeeded by using a 'enzyme cocktail' that does a total enzymatic hydrolysis. Next step will be to find out if I can quantify glutamine.&lt;/p&gt;&#xA;" OwnerUserId="31" LastEditorUserId="31" LastEditDate="2017-07-28T11:39:42.663" LastActivityDate="2017-07-28T11:39:42.663" Title="Glutamine analysis" Tags="&lt;biochemistry&gt;&lt;food&gt;&lt;organic-chemistry&gt;&lt;food-chemistry&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6815" PostTypeId="2" ParentId="6813" CreationDate="2013-01-15T15:51:27.020" Score="3" Body="&lt;p&gt;When testing an antibody for an imaging application, it is almost always a good idea to test it in another application like ELISA or Western blotting to see if it binds the target of interest. For example, try to find high- and low-expressing cell lines, load equal amounts, and see if there is a difference in signal at the expected molecular weight. Check the company's literature or contact their technical support to see if they have tested the antibody by immunofluorescence (IF), and if so what their results were and how they validated them. Check the literature to see if other people have published with this product. &lt;a href=&quot;http://highwire.stanford.edu&quot; rel=&quot;nofollow&quot;&gt;http://highwire.stanford.edu&lt;/a&gt; is a pretty good full-text search engine, but they don't have all journals in their database. Google Scholar can help, too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also use your high- and low-expressing cell lines to see if there is a stronger IF signal in the high-expressing line. Look at your images to see if the signal is localizing where you expect it to, and do co-staining with antibodies to other proteins that should co-localize with your target of interest. For example, if your target is expected to localize to mitochondria, co-stain with COX-IV. A quick Google search found this &lt;a href=&quot;http://www.cellsignal.com/products/4753.html&quot; rel=&quot;nofollow&quot;&gt;Cellular Localization IF Antibody Sampler Kit&lt;/a&gt; that has controls for several different organelles and other specific locations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Make sure you are following the manufacturer's recommended protocol. Don't crank the gain up too high on the scope, because non-specific background goes up, too. Look at the induction of signal between high- and low-expressing cell lines. Generally you would want at least a 2-3 fold shift, especially if you see a strong change in signal intensity by Western. Try using siRNA or similar silencing technology to knock down the signal in your cells, and validate using Western and IF.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultimately, you can never be absolutely 100% certain that an antibody is binding a certain target, and &lt;strong&gt;only&lt;/strong&gt; that target, but you can accumulate a lot of evidence to show that it is likely. Try to put yourself in the mindset of a reviewer, and objectively convince yourself that the signal is real. If you can't, then shop around and try something else. Good luck!&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-01-15T15:51:27.020" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="6816" PostTypeId="1" AcceptedAnswerId="6817" CreationDate="2013-01-15T16:40:57.760" Score="3" ViewCount="3100" Body="&lt;p&gt;When a person's glucose and glycogen stores are depleted, which can occur due to fasting or due to a diet consisting largely of fat (like eskimo diets), the body produces its energy by breaking down triglycerides into fatty acids.  Fatty acids can be then converted to Acetyl-CoA, which can consequently enter the citric acid cycle, generating ATP.*  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now normally when a cell does not receive sufficient oxygen to undergo its natural processes, it usually breaks down glucose anaerobically to generate ATP and lactic acid.  However, in the case where the body is running off fatty acids (e.g. fast, or fat/protein only diet), how does the body respond to such anaerobic situations?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;*&lt;em&gt;(Note:  In this situation many fatty acids are first taken up into the liver and converted to ketone bodies, which are subsequently converted to Acetyl-CoA after being taken up in the required tissues, hence causing &quot;ketosis&quot; as in the title)&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="1320" LastEditDate="2013-01-15T20:52:21.213" LastActivityDate="2018-11-06T01:31:58.773" Title="Is anaerobic activity during ketosis possible?" Tags="&lt;metabolism&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6817" PostTypeId="2" ParentId="6816" CreationDate="2013-01-15T17:39:16.480" Score="6" Body="&lt;p&gt;You are correct in thinking that fatty acids cannot be metabolised anaerobically. However, in the type of metabolic state that you are describing, blood glucose will be maintained by the liver to support tissues or cells which are more or less dependent upon anaerobic metabolism. The classic example of such a cell type is the red blood cell which as no mitochondria and so cannot use the TCA cycle. The brain is also heavily dependent upon glucose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The liver exports glucose that it has produced via gluconeogenesis from amino acid skeletons, as well as from glycerol produced as a result of fat metabolism.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-01-15T20:24:48.270" LastActivityDate="2013-01-15T20:24:48.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6818" PostTypeId="2" ParentId="5635" CreationDate="2013-01-15T18:25:30.077" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://qhxb.lib.tsinghua.edu.cn:8080/webpage/environment/chn/upload/Guide1_1.pdf&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a good review titled: &lt;em&gt;Use of allelopathy of aquatic macrophytes for algal-bloom control.&lt;/em&gt;&#xA;&lt;p&gt;Hu and Hung talked about Macrophyte species which have allelopathy effects on Algal-bloom.&#xA;This paper discussed the development and potential application of allelopathy of aquatic plants on algae, including the reported aquatic macrophytes having allelopathy on algae, their allelochemicals and potential modes of action on algae, possible ways for application and the prospect of using aquatic macrophytes to control algal bloom.&#xA;Plants which you want to use for allelopathy effects on algal bloom, must of course be marine.&#xA;But sometimes allelopathic agents of terresterial plants can be extracted and use for this purpose more commercial than marine planting.&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="1320" LastEditDate="2013-01-15T20:51:07.500" LastActivityDate="2013-01-15T20:51:07.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6819" PostTypeId="2" ParentId="6812" CreationDate="2013-01-15T18:56:10.093" Score="-1" Body="&lt;p&gt;If you mean some thing like .doc .txt .rar or etc. I think there is no special bioinformatics file formats like that, for example NCBI, EMBL, Expasy and others use this common formats in transfering sequence data. BUT there is some thing called file format for introducing data to this data banks for example FASTA file format:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&gt;gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]&#xA;  LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV&#xA;  EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG&#xA;  LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL&#xA;  GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX&#xA;  IENY&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As you see, a sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (&quot;&gt;&quot;) symbol in the first column. The word following the &quot;&gt;&quot; symbol is the identifier of the sequence, and the rest of the line is the description (both are optional). There should be no space between the &quot;&gt;&quot; and the first letter of the identifier. It is recommended that all lines of text be shorter than 80 characters. The sequence ends if another line starting with a &quot;&gt;&quot; appears; this indicates the start of another sequence.&#xA;you can learn more things about these bioinformatical formats &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/047172274X.app2/pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://rice.plantbiology.msu.edu/training/Childs_Data_Formats.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="1320" LastEditDate="2013-01-15T19:34:30.447" LastActivityDate="2013-01-15T19:34:30.447" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6820" PostTypeId="1" AcceptedAnswerId="6821" CreationDate="2013-01-15T19:01:11.817" Score="13" ViewCount="26861" Body="&lt;p&gt;How does the digestive acid (HCl) not burn the surrounding membrane of our stomach? It digests the majority of raw food we eat but how does it stay safely in our stomach? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, how does the stomach maintain the ability for a human body to retain HCl for all lifetime?&lt;/p&gt;&#xA;" OwnerUserId="1390" LastEditorUserId="-1" LastEditDate="2018-04-10T04:19:02.183" LastActivityDate="2020-01-18T03:22:08.943" Title="How does HCl not burn our stomach?" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6821" PostTypeId="2" ParentId="6820" CreationDate="2013-01-15T19:15:47.313" Score="18" Body="&lt;p&gt;Mucous-producing cells at the neck of the gastric pits create a layer of protective mucous covering the stomach lining. This mucous layer includes bicarbonate ions which act as a chemical barrier against the protons in gastric juice.  See &lt;a href=&quot;http://schulforschung.rub.de/gastricmuc.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for some evidence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The stomach lining stays protected because the mucous layer is continuously replenished.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="46609" LastEditDate="2020-01-18T03:22:08.943" LastActivityDate="2020-01-18T03:22:08.943" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="6823" PostTypeId="2" ParentId="6804" CreationDate="2013-01-15T21:14:28.400" Score="1" Body="&lt;p&gt;Antibody molecules or immunoglobulins (Ig) consist of heavy and light chains (e.g. two of each in IgG). Both heavy and light chains have variable domains at their N termini.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During development of the immune system the pro-B cells in the bone marrow undergo gene segment rearrangements, bringing V and J segments together for Ig light chain production, and V,D and J segments together for Ig heavy chain production. The V gene segments encode the variable domains at the N-terminus of light and heavy chains. There are a few tens of V gene segments in our genome - this is the first source of variability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second source of variability is the &quot;sloppy joining&quot; of the V (D) and J segments. This results in frame shifts together with short deletions and insertions. This V(D)J junction corresponds to the third hypervariable region of the variable domain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each immature B cell displays its antibody at the cell surface as a membrane-bound form of IgM. If an antigen binds to this antibody the cell is stimulated to divide (clonal selection). During the proliferation of the immature B cell it undergoes somatic mutation due to error-prone replication of the Ig loci. This allows for the production of Ig variants with improved binding affinities which are in turn stimulated to proliferate more rapidly, eventually maturing into antibody-producing plasma cells. This somatic mutation is the the third source of variability in the variable domains of Ig molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See any immunology textbook for details and diagrams.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-01-15T21:14:28.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6824" PostTypeId="2" ParentId="6804" CreationDate="2013-01-15T21:52:18.860" Score="3" Body="&lt;p&gt;The processes are called gene rearrangement and &lt;a href=&quot;http://en.wikipedia.org/wiki/Somatic_hypermutation&quot; rel=&quot;nofollow noreferrer&quot;&gt;somatic hypermutation&lt;/a&gt;, and are used by maturing B-cells to generate very (&lt;strong&gt;very&lt;/strong&gt;) large amounts of diversity in the antibody repertoire. If your institution has access, &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.immunol.26.021607.090236&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; great article in Annual Reviews in Immunology has all the details, or you can read about it in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK27140/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Janeway&lt;/a&gt; (slightly outdated edition). Essentially, the genes encoding the B-cell Receptor, or BCR, have many fragments of several different types in them, and through the process of gene rearrangement the final Complementarity Determining Regions, or CDRs (the antigen-binding sites), are generated into one mature sequence for each individual B-cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A mature IgG molecule (the soluble, secreted version of the BCR) contains four chains - 2 heavy (each of which are identical to each other) and 2 light (also identical). There are Constant or C regions in each chain that essentially don't vary much, and are not really involved in the process of antigen binding. On the &quot;business end&quot; are three regions (or types, from above) called V, D, and J in the heavy chain, while the light chain just has V and J. Those letters are from Variable, Diversity, and Joining, if you're interested.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wP63N.jpg&quot; alt=&quot;Janeway Figure 4.3&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 4.3 from Janeway shows the number of &quot;fragments&quot; or gene segments of each type in humans. So, when the heavy chain is being made, 1 fragment out of 65 Vs is picked, 1 of 27 Ds, and one of 6 Js, then each is joined together in a process that can also introduce an additional amount of randomness at the joins. Combine this with an only slightly less complex process in the light chain (as there is no D region), and the fact that a single insertion/deletion of a base pair can drastically effect the resulting protein sequence, and you get a protein with a huge number of possible sequences, potentially in the range of 10&lt;sup&gt;11&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This process of gene rearrangement typically generates immunoglobulins with relatively low affinity for their antigens. During affinity maturation, a process called somatic hypermutation randomly changes individual base pairs (translated to amino acids) in the CDR in cells that are descendents of, and bear the same base sequence as, the original. Cells expressing antigen receptors that are of higher affinity are then positively selected and clonally expanded by the immune system, allowing your body to tailor its response to an infection or other exposure to what it sees as foreign material.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2013-01-17T14:20:47.503" LastActivityDate="2013-01-17T14:20:47.503" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6825" PostTypeId="2" ParentId="6820" CreationDate="2013-01-15T22:02:10.133" Score="7" Body="&lt;p&gt;Cause of this secret are tight junctions and mucous.&#xA;As Wikipedia explains:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Tight junctions, or zonula occludens, are the closely associated areas of two cells whose membranes join together forming a virtually impermeable barrier to fluid. It is a type of junctional complex present only in vertebrates. The corresponding junctions that occur in invertebrates are septate junctions.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/R3Pbr.jpg&quot; alt=&quot;enter image tion here&quot;&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;They perform vital functions:They hold cells together.Barrier function, which can be further subdivided into protective barriers and functional barriers serving purposes such as material transport and maintenance of osmotic balance:They help to maintain the polarity of cells by preventing the lateral diffusion of integral membrane proteins between the apical and lateral/basal surfaces, allowing the specialized functions of each surface (for example receptor-mediated endocytosis at the apical surface and exocytosis at the basolateral surface) to be preserved. This aims to preserve the transcellular transport.They prevent the passage of molecules and ions through the space between cells. So materials must actually enter the cells (by diffusion or active transport) in order to pass through the tissue. This pathway provides control over what substances are allowed through. (Tight junctions play this role in maintaining the blood–brain barrier.) At the present time, it is still unclear whether the control is active or passive and how these pathways are formed. In one study for paracellular transport across the tight junction in kidney proximal tubule, a dual pathway model is proposed: large slit breaks formed by infrequent discontinuities in the TJ complex and numerous small circular pores.&lt;a href=&quot;https://i.stack.imgur.com/R3Pbr.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;In human physiology there are two main types of epithelia using distinct types of barrier mechanism. Dermal structures such as skin form a barrier from many layers of keratinised squamous cells. Internal epithelia on the other hand more often rely on tight cells junctions for their barrier function. This kind of barriers is mostly formed by only one or two layers of cells. Until recently it was not clear whether tight cell junctions also play any role in the barrier function of the skin and similar external epithelia, recent research suggests that this is indeed the case.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the next step mucous protect epithelial cells from released HCl.&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Tight_junction&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt;  you will find more things.&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="-1" LastEditDate="2018-05-04T01:54:22.530" LastActivityDate="2018-05-04T01:54:22.530" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="6827" PostTypeId="1" AcceptedAnswerId="6831" CreationDate="2013-01-16T04:31:56.733" Score="6" ViewCount="4890" Body="&lt;p&gt;Why did humans/animals evolve to become self-aware of their own thoughts.  That is, why don't humans act and compute like a machine, or walking zombie.  In my mind, such creatures would still be as smart and equally capable of surviving, the only difference being they don't experience the phenomenon of self-awareness. (To understand my question think: unconsciously sleep walking)&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="1590" LastEditDate="2013-01-16T08:38:24.440" LastActivityDate="2021-01-11T03:24:25.867" Title="Why have humans evolved conciousness?" Tags="&lt;evolution&gt;&lt;brain&gt;" AnswerCount="7" CommentCount="19" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6829" PostTypeId="1" AcceptedAnswerId="6930" CreationDate="2013-01-16T11:07:44.637" Score="21" ViewCount="990" Body="&lt;p&gt;When we eat, finally we feel full. I know which mechanism causes the sensation of being full. But when we sleep excessively we often still want more sleep. Why does this happen? Is there a mechanism underlying this?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="1590" LastEditDate="2013-01-16T11:42:28.623" LastActivityDate="2013-01-26T02:28:50.867" Title="Why do we feel tired if we sleep excessively?" Tags="&lt;biochemistry&gt;&lt;neuroscience&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="6830" PostTypeId="1" CreationDate="2013-01-16T13:14:40.883" Score="3" ViewCount="106" Body="&lt;p&gt;I'm currently writing a piece of work about telomeres and aging, and wondered if you could share some good papers you've either read or know of.&lt;/p&gt;&#xA;" OwnerUserId="2935" LastEditorUserId="1231" LastEditDate="2013-02-01T20:51:39.280" LastActivityDate="2013-02-01T20:51:39.280" Title="Papers linking telomeres and aging" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;senescence&gt;&lt;telomere&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2013-01-16T13:17:24.460" ContentLicense="CC BY-SA 3.0" />
  <row Id="6831" PostTypeId="2" ParentId="6827" CreationDate="2013-01-16T16:34:30.313" Score="9" Body="&lt;p&gt;There have been many proposals over the years as to why human consciousness has emerged and how, or even what it is.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of us will not be surprised to know that there is no consensus about an answer here.  Its hard to draw a trend from a single example.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a little survey of the one's I've heard. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;We are intelligent because we have opposable thumbs and can use tools, which evolved our brains.  This is an old one - maybe as old as Darwin's time.  I think its mostly ignored now because so many animals - including pandas and other non primates have opposable thumbs or use tools or both.  (monkeys and chimps use tools, and recently crows have also been observed to use tools.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;brain size.  We do have a large brain to body size ratio.  There are other animals with similar ratios and they don't have internets.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;We are 'self-aware'.  That is to say we recognize ourselves as an individual.  &lt;a href=&quot;http://psycnet.apa.org/journals/amp/32/5/329/&quot; rel=&quot;noreferrer&quot;&gt;It was proven that other primates can recognize themselves&lt;/a&gt; in mirrors (putting a red dot on their forehead. when they see their reflection, they touch their own forehead).  So that's not exclusive either.  its not a bad idea, but so far it doesn't seem to make the &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;'We ate something' I once read a discussion of &lt;a href=&quot;https://www.greenpassion.org/index.php?/topic/20997-humans-primates-psychedelics/&quot; rel=&quot;noreferrer&quot;&gt;how humans might have ingested psychotropic plants or fungi&lt;/a&gt;.  As you can see, this was 2010.  Its not the worst idea, but its hard to prove.  Lots of experiments on cats since the '60s have not produced cat's who care to tell us if they are intelligent.  Maybe they are just too smart in the first place.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;These theories, from when I was a student are so discounted now, you can't find too much record of anymore since they were pre-internet and also they seem so unlikely now.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More modern theories have locked onto &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_human_intelligence#Models&quot; rel=&quot;noreferrer&quot;&gt;social configurations of human societies which drive intelligent adaptations&lt;/a&gt;.  This is stemming from observations that human evolution (the rate at which genetic variants are retained in the gene pool) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/pmc2410101/&quot; rel=&quot;noreferrer&quot;&gt;are accelerating since humans have become social&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These new theories while standing on some amazing evidence are still feeling around in the dark - stuff about how social interactions have created a preference for intelligence-like traits. There is probably something to that - once intelligence gets a toehold it is a clear advantage.  But how did it show up only once and why us? I think that's the hard part that science has, for the moment, given a rest. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-01-16T16:34:30.313" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="6833" PostTypeId="2" ParentId="1808" CreationDate="2013-01-17T02:16:48.100" Score="4" Body="&lt;p&gt;This little dude is not a Caddisfly, but a true moth,  &lt;em&gt;Tinea pellionella&lt;/em&gt;, a case making clothing moth.  Confusing because they do resemble caddisfly larvae cocoons more so than those of their own family (Tineidae).  Sort blurb &lt;a href=&quot;http://waynesword.palomar.edu/redmite12.htm&quot; rel=&quot;noreferrer&quot;&gt;Here&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The brown-headed larva spins a silken case that is open at both ends. The case in the above image is covered with fine sand and debris, and superficially resembles a caddisfly case. The flattened case is about 10-11 mm long (3/8 to 1/2 inch). When crawling, the larva's head, thorax, and three pairs of legs protrude out of the case, and drag it along. According to Internet sources, the larva feeds on a variety of material, including hair, fur, silk, felt, feathers, woolen clothing, upholstered furniture and carpets. It apparently prefers darkness and soiled clothing, and is not fond of synthetic fabrics, such as nylon and polyesters.&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="2939" LastActivityDate="2013-01-17T02:16:48.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6834" PostTypeId="1" CreationDate="2013-01-17T08:52:56.883" Score="2" ViewCount="212" Body="&lt;p&gt;I'm not sure if this is actually a philosophical question, but I was reading a &lt;a href=&quot;http://en.wikipedia.org/wiki/Timeline_of_evolutionary_history_of_life&quot; rel=&quot;nofollow&quot;&gt;timeline of life on earth&lt;/a&gt; and I came to this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;4500-3500 Ma The earliest life appears, possibly at Alkaline vents&#xA;  with the creation of the Last Universal Common Ancestor, possibly&#xA;  derived from self-reproducing RNA molecules.[6][7] The replication of&#xA;  these organisms requires resources like energy, space, and smaller&#xA;  building blocks, which soon become limited, &lt;strong&gt;resulting in competition&lt;/strong&gt;,&#xA;  with natural selection favouring those molecules which are more&#xA;  efficient at replication. DNA molecules then take over as the main&#xA;  replicators and these archaic genomes soon develop inside enclosing&#xA;  membranes which provide a stable physical and chemical environment&#xA;  conducive to their replication: proto-cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;..and I thought to myself, are we still essentially doing that as we live our lives?  I think I'm trying to connect the idea of a human &quot;being competitive&quot; with &quot;evolution&quot;.. is there any truth to that?&lt;/p&gt;&#xA;" OwnerUserId="2940" LastEditorUserId="107" LastEditDate="2013-01-18T01:05:46.640" LastActivityDate="2018-03-26T14:23:32.450" Title="Are humans still competing in the same way now that the first life forms did?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6835" PostTypeId="2" ParentId="6834" CreationDate="2013-01-17T12:48:52.177" Score="0" Body="&lt;p&gt;Your question is a little vague, but if I understand it correctly yes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The crux of evolution is that in essence the resources we need to survive and reproduce are in lower supply than necessary for all to survive- therefore there is competition for such resources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Those who are more genetically adept to gain those resources are more likely to pass on their genetic material to the next generation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're speaking specifically about Humans there is of course still competition between individuals for resources (money being a primary one now). Competition is just an entirely different game now. Beyond that level of answer it's a philosophical can of worms I don't feel equipped to properly answer, and arguably it doesn't belong here but over in the &lt;a href=&quot;https://philosophy.stackexchange.com/&quot;&gt;philosophy stackoverflow&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps a bit...&lt;/p&gt;&#xA;" OwnerUserId="1763" LastEditorUserId="-1" LastEditDate="2017-04-13T12:42:22.377" LastActivityDate="2013-01-17T12:48:52.177" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6836" PostTypeId="1" AcceptedAnswerId="6837" CreationDate="2013-01-17T13:09:06.820" Score="8" ViewCount="1202" Body="&lt;p&gt;Food goes in, excrement come out. This seems obvious.&lt;br&gt;&#xA;But it seems like the mass of the excrement is less than the one of the food. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most people I asked answered: &quot;There's a difference because it's transformed into energy, like heat...&quot;. I think that's &lt;em&gt;bull-excrement&lt;/em&gt;. &#xA;There's still the law of conservation of mass: our body does no nuclear reactions, &lt;strong&gt;or does it?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example:&#xA;Someone's on a &quot;high protein / low carb&quot; diet, he may ingest like 1kg of food, he isn't really productive on the toilet (it's difficult to find any fibers in those diets), he loses 500g in a day... My question is: where does the 1.5kg of matter go?&lt;/p&gt;&#xA;" OwnerUserId="2942" LastEditorUserId="16866" LastEditDate="2017-04-03T17:20:41.587" LastActivityDate="2017-04-03T17:20:41.587" Title="Where does all the food go?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;food&gt;&lt;digestion&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6837" PostTypeId="2" ParentId="6836" CreationDate="2013-01-17T13:16:37.967" Score="5" Body="&lt;p&gt;Whatever the diet, the food intake contains macronutrients: carbohydrate, fat and protein. When they are metabolised all of these molecules will end up, for the most part, as carbon dioxide, water, and ammonia, unless they are incorporated into components of the body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These waste products are, of course, lost via breathing, and via the urine. That's where the &quot;missing mass&quot; goes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A related question is &lt;a href=&quot;https://biology.stackexchange.com/questions/5416/where-does-the-c-in-exhaled-co2-mostly-come-from/5504#5504&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2013-01-17T13:16:37.967" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="6838" PostTypeId="2" ParentId="6834" CreationDate="2013-01-17T13:58:01.117" Score="1" Body="&lt;p&gt;It's important to realise that evolutionatry competition and the common usage of the word competition do not mean quite the same thing. For example, you could talk about Usain Bolt competing in the 100m but this is only evolutionary competition with the other athletes in they are in competition in terms of evolutionary fitness. Evolutionary fitness encompasses ideas of survival, reproduction and the nurturing of offspring. The only thing that matters, from an evolutionary point of view, is how many successful offspring are produced&lt;sup&gt;1&lt;/sup&gt;. Where human competition does not relate to this, it is not related to competition in the evolutionary sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;People certainly do still compete in the evolutionary sense for mates, resources, etc. but in the West, in particular, much of human competition has become a very long way removed from anything that relates to evolutionary competition except in the most tangential of ways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1 - my favoured definition for fitness is number of grandchildren.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="2938" LastEditDate="2013-01-17T14:42:40.450" LastActivityDate="2013-01-17T14:42:40.450" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6839" PostTypeId="1" AcceptedAnswerId="6842" CreationDate="2013-01-17T17:08:25.637" Score="5" ViewCount="5604" Body="&lt;p&gt;I know that neurons communicate between each other by filling the junction between dendrites with neurotransmitters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What interests me is if a single neuron only works with one type of neurotransmitter(ex: serotonin), or if it can secrete/receive all of them (serotonin, dopamine, etc).&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a neuron can secrete all, then can all dendrites secrete and respond to all neurotransmitters, or is it one per dendrite (one branch only works with dopamine, another one with serotonin, etc)? &lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2015-09-07T04:38:45.217" Title="Do neurons secrete multiple neurotransmitters, or just one type?" Tags="&lt;neuroscience&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6840" PostTypeId="2" ParentId="5752" CreationDate="2013-01-17T17:22:03.137" Score="0" Body="&lt;p&gt;I think the answer is 0.25.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's how I arrived at it:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only way a daughter of a sib-mating can have an IBD (identical-by-decent) genotype is by being homozygous for one of the two alleles belonging to her grandmother (her mother and father's mother).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no way for her to be IBD for the allele that her grandfather has, because that allele can never end up in her father (who only gets an allele from his mother, because he's haploid).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's trace the path of an allele from the grandmother to the focal grand-daughter:&#xA;This allele has a 50% chance of being passed from the grandmother to mother, and another 50% chance of being passes from mother to focal. It has a 50% of being passed from grandmother to father, but then a 100% of being passed from father to focal (it's the only allele that father has to give). So, the probability that ALL of these things happen is 50%*50%&lt;em&gt;50%&lt;/em&gt;%100 or (1/2)^3 = 1/8 = 0.125 or 12.5%.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since this can happen for EITHER allele from the grandmother, this must be multiplied by 2, giving our final inbreeding coefficient of F=0.25 or 25%.&lt;/p&gt;&#xA;" OwnerUserId="1906" LastActivityDate="2013-01-17T17:22:03.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6842" PostTypeId="2" ParentId="6839" CreationDate="2013-01-17T22:56:20.860" Score="2" Body="&lt;p&gt;I've googled this for a biology class I taught, and the quick answer is that both possibilities happen in different instances.  Some specialized neurons secrete more than one type, even though the ruling concept used to be one neurotransmitter for one neuron.&lt;/p&gt;&#xA;" OwnerUserId="2944" LastActivityDate="2013-01-17T22:56:20.860" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6843" PostTypeId="1" CreationDate="2013-01-17T23:01:06.613" Score="2" ViewCount="67" Body="&lt;p&gt;I'm looking for a simple, inexpensive way to demonstrate that soil is not needed for plant growth to middle school students.  I plan to germinate bean seeds in cotton, but where do I take it from there?    &lt;/p&gt;&#xA;" OwnerUserId="2944" LastActivityDate="2013-02-17T00:22:07.473" Title="What's the simplest set-up to demonstrate soiless plant growth to middle school students?" Tags="&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6844" PostTypeId="2" ParentId="6843" CreationDate="2013-01-17T23:46:01.477" Score="2" Body="&lt;p&gt;You can take a glass mason jar, a bean seed, and a moist paper towel. Place the seed between the paper towel and the glass. If you press the paper towel so that it lines the inside of the glass jar, the seed with grow and the students can see this process through the glass.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-01-17T23:46:01.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6845" PostTypeId="1" AcceptedAnswerId="92898" CreationDate="2013-01-18T03:44:30.183" Score="2" ViewCount="184" Body="&lt;p&gt;Are there any mammals in which polyspermy produces viable zygotes? In &lt;a href=&quot;http://en.wikipedia.org/wiki/Polyspermy&quot; rel=&quot;nofollow&quot;&gt;the wikipedia page&lt;/a&gt; it is mentioned that there is a delicate equilibrium between female defenses against many sperms, which ocassionally results in low fertility rates (which in not all cases might be an evolutionary disadvantage, but i disgress)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is if there are cases where a ovum can be fertilized by several sperms, and the zygote somehow manages to select fairly between a subset of all chromosomes, avoiding polyploidy and producing a viable embryo.&lt;/p&gt;&#xA;" OwnerUserId="1086" LastEditorUserId="107" LastEditDate="2013-01-19T16:56:47.433" LastActivityDate="2020-04-22T17:17:15.463" Title="Are there any mammals in which polyspermy produces viable zygotes?" Tags="&lt;chromosome&gt;&lt;mammals&gt;&lt;sexual-selection&gt;&lt;polyploidy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6846" PostTypeId="1" AcceptedAnswerId="6848" CreationDate="2013-01-18T04:10:16.060" Score="4" ViewCount="171" Body="&lt;p&gt;There is a potential difference, but ions can not go through wires, right? Though there is a electric field, but there is no electron source, I am thinking the answer is no, or will there be some chemical reaction?&lt;/p&gt;&#xA;" OwnerUserId="2945" LastActivityDate="2018-11-23T17:03:39.650" Title="Connect the inner and outer space of cell with a wire, will there be electricity?" Tags="&lt;cell-biology&gt;&lt;electrophysiology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6848" PostTypeId="2" ParentId="6846" CreationDate="2013-01-18T13:14:08.110" Score="3" Body="&lt;p&gt;Let's start with the basics.  The inside of the cell contains predominantly positive potassium ions, and negative phosphate ions, and other negative ions (e.g. from amino acids).  The outside of the cell contains predominantly positive sodium ions, and negative chloride ions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cell however sets up a resting membrane potential, due to the cell's semi-permeable membrane, allowing predominantly only potassium to pass through the membrane.  This causes potassium to flow along its concentration gradient towards the outside of the cell, until it is balanced by the electric potential that is consequently set up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So we now have POSITIVE potassium ions on the outside of the cell and NEGATIVE phosphate ions (or other negative ions) on the inside of the cell, which aren't balanced.  Now as the wire is placed between the inside and the outside of the cell, electrons from the negative phosphate ions will travel through the wire, towards the positive potassium ions on the outside of the cell.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once this occurs, the potassium from the cell's interior can now continue to flow against its concentration gradient, because the previous potassium ions in the exterior no longer contribute to an opposing electric potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additional note:  As the K&lt;sup&gt;+&lt;/sup&gt; ion in the extra-cellular fluid gains electrons from the wire to form K, it will react almost immediately with water to form KOH and H&lt;sub&gt;2&lt;/sub&gt; (hydrogen gas).  The K and OH will be soluble in the extra-cellular fluid, forming K&lt;sup&gt;+&lt;/sup&gt; and OH&lt;sup&gt;-&lt;/sup&gt; ions.  Over time the K&lt;sup&gt;+&lt;/sup&gt; ions will be &quot;pumped&quot; back into the cell's cytoplasm.  (The left over OH&lt;sup&gt;-&lt;/sup&gt; ions will temporarily increase the flow of K&lt;sup&gt;+&lt;/sup&gt; down its concentration gradient, etc.)&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="3340" LastEditDate="2014-10-31T13:23:06.370" LastActivityDate="2014-10-31T13:23:06.370" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6849" PostTypeId="2" ParentId="2668" CreationDate="2013-01-19T09:01:56.373" Score="2" Body="&lt;p&gt;Although crossover events can be observed in mitosis (mitotic recombination), they most frequently occur in prophase I of meiosis (crossing over in bivalents). Circular chromosomes are common in prokaryotes, but eukaryotes have linear chromosomes. Remember what meiosis accomplishes and that prokaryotes reproduce asexually. Prokaryotes don't have a need for -- or engage in -- meiotic division, so crossover events in circular chromosomes can really only be observed in instances of mitotic recombination, and I don't know the frequency of this in prokaryotes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In prokaryote DNA replication, if any entangling of the two product circular chromosomes occurs, it is resolved by DNA topoisomerase. So perhaps a crossover would present a similar situation and the cell would resolve it by similar means.&lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2013-01-19T09:01:56.373" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="6850" PostTypeId="1" CreationDate="2013-01-19T13:16:33.803" Score="3" ViewCount="50" Body="&lt;p&gt;I know that Δ&lt;sup&gt;9&lt;/sup&gt;-tetrahydrocannabinol and other cannabinoids increase dopaminergic neurotransmission in the nucleus accumbens and that this is what results in the euphoria experienced by cannabis users. Other than this I do not know what effect cannabinoids have on monoaminergic neurotransmission. I would assume that it increases monoaminergic neurotransmission seeing how rimonabant $-$ a selective CB&lt;sub&gt;1&lt;/sub&gt; inverse agonist $-$ leads to depression and anxiety which according to the monoamine hypothesis can likely be linked to changes in the activity of monoaminergic pathways in the brain. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-01-20T00:35:46.137" LastActivityDate="2013-01-20T00:35:46.137" Title="What Effect Does the Endocannabinoid System have on Monoaminergic Neurotransmission?" Tags="&lt;neurotransmitter&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6851" PostTypeId="1" AcceptedAnswerId="6853" CreationDate="2013-01-19T15:18:22.017" Score="0" ViewCount="293" Body="&lt;p&gt;If you had an isolate bacteria sample how would you determine if they were nitrogen fixing?&lt;/p&gt;&#xA;" OwnerUserId="1763" LastActivityDate="2013-01-19T17:09:29.327" Title="How might one determine if bacteria are nitrogen fixing or not?" Tags="&lt;metabolism&gt;&lt;bacteriology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6852" PostTypeId="2" ParentId="6846" CreationDate="2013-01-19T15:21:01.520" Score="2" Body="&lt;p&gt;Just to clarify your ion/electron question - a neutral atom or molecule becomes &lt;em&gt;ionized&lt;/em&gt; when it either loses one or more electrons, becoming positively charged, or gains electron(s), becoming negatively charged. Since the negatively charged phosphate (&lt;strong&gt;PO&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;2-&lt;/sup&gt;&lt;/strong&gt;) ions have a surplus of electrons, they (the electrons) are free to flow &quot;up&quot; the wire and to the outside of the cell.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-01-19T15:21:01.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6853" PostTypeId="2" ParentId="6851" CreationDate="2013-01-19T15:22:43.577" Score="2" Body="&lt;p&gt;Never mind found the answer myself you can use the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC223907/&quot; rel=&quot;nofollow&quot;&gt;acetylene reduction assay&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1763" LastActivityDate="2013-01-19T15:22:43.577" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6854" PostTypeId="1" CreationDate="2013-01-19T15:53:45.887" Score="3" ViewCount="343" Body="&lt;p&gt;I have read that alcohol in general and wine in particular can have advantageous as well as detrimental effects on human health. Is this true? What are the physiological effects of consuming wine in moderate quantities?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="3952" LastEditDate="2013-08-05T06:16:09.610" LastActivityDate="2018-11-11T23:04:35.453" Title="What are the physiological effects of wine?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;food&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6856" PostTypeId="2" ParentId="6851" CreationDate="2013-01-19T17:09:29.327" Score="0" Body="&lt;p&gt;I'd suggest doing a bioinformatic search of the bacterial genomes first before doing the experiments. You should be able to find homologues of the &quot;nif&quot; (nitrogen fixation) genes there.&lt;/p&gt;&#xA;" OwnerUserId="1536" LastActivityDate="2013-01-19T17:09:29.327" CommentCount="1" CommunityOwnedDate="2013-01-19T17:09:29.327" ContentLicense="CC BY-SA 3.0" />
  <row Id="6857" PostTypeId="2" ParentId="4924" CreationDate="2013-01-19T17:13:07.353" Score="1" Body="&lt;p&gt;The answer I have come to is the difference between FCS2.0 and FCS3.0 files. The binning pattern is different, and as such FCS2.0 files arbitrarily lowered my flow cytometry values compared to what I saw on the FACS DiVa software.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the end, exporting with FCS3.0 was the way to go. If your software supports this, I'd highly recommend doing so!&lt;/p&gt;&#xA;" OwnerUserId="1536" LastActivityDate="2013-01-19T17:13:07.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6858" PostTypeId="1" AcceptedAnswerId="6898" CreationDate="2013-01-19T20:40:28.460" Score="13" ViewCount="14681" Body="&lt;p&gt;&lt;strong&gt;(1)&lt;/strong&gt;. Why does having cold hands create a painful sensation?&lt;/p&gt;&#xA;&lt;p&gt;Is it a physical effect, maybe a protection mechanism from evolution?&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;(2)&lt;/strong&gt;. Why, if one's hands are cold, does it feel as if they are more &lt;em&gt;susceptible&lt;/em&gt; to pain?&lt;/p&gt;&#xA;&lt;p&gt;Note: I have (2) as a separate question because the painful sensation in (1) refers to that from the coldness, whereas in (2), I mean that certain 'ordinary tasks' would feel painful, for example, holding a shopping bag.&lt;/p&gt;&#xA;" OwnerUserId="2952" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-01-23T21:59:04.843" Title="Why does having cold hands hurt?" Tags="&lt;physiology&gt;&lt;skin&gt;&lt;pain&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6860" PostTypeId="1" AcceptedAnswerId="6862" CreationDate="2013-01-20T01:15:27.067" Score="2" ViewCount="2594" Body="&lt;p&gt;I heard that the human heart had a surface area of 1000 square feet, and I thought that that cannot be true. So what &lt;em&gt;is&lt;/em&gt; the surface area of the human heart and what are the different ways it can be measured?&lt;/p&gt;&#xA;" OwnerUserId="101" LastActivityDate="2013-01-20T17:05:09.500" Title="What is the surface area of the human heart?" Tags="&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6861" PostTypeId="1" AcceptedAnswerId="6912" CreationDate="2013-01-20T04:34:47.050" Score="10" ViewCount="1000" Body="&lt;p&gt;I have been thinking a little about the origins of life, and was further inspired by this question: &lt;a href=&quot;https://biology.stackexchange.com/questions/2790/how-did-the-first-self-replicating-organism-come-into-existence&quot;&gt;How did the first self replicating organism come into existence?&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can accept that we don't quite know exactly how, but has any large-scale/long-term simulation been carried out? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been experiments but they seem to have been on a small scale. As an example, according to the Abiogenesis page on Wikipedia, some &lt;a href=&quot;http://en.wikipedia.org/wiki/Abiogenesis#Fox.27s_experiments&quot; rel=&quot;nofollow noreferrer&quot;&gt;experiment which spontaneously formed peptide structures&lt;/a&gt; was carried out by Sidney Fox during the 50s and 60s.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would be really interesting is if there had been some experiments or simulations carried out during a very long time, plausibly allowing for extremely low-probability structures to form. I doesn't matter whether this simulation/experiment has been carried out in a lab or as a computer simulation. There is of course the interesting but old &quot;Conway's Game of Life&quot; simulation, but according to my search efforts nobody has really tested it on a very large scale and in 3D.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, I'm looking for something extensive, like a decades-long single lab experiment or a simulation that has been run for years.&lt;/p&gt;&#xA;" OwnerUserId="2954" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-01-30T03:08:35.167" Title="Has any large-scale origin-of-life simulation/experiment been done?" Tags="&lt;bioinformatics&gt;&lt;abiogenesis&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="6862" PostTypeId="2" ParentId="6860" CreationDate="2013-01-20T05:17:50.850" Score="4" Body="&lt;p&gt;The number you are looking for might be quite large depending on the level of detail you demand for the measurement.  There is no single number for the area of most objects in fact. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The importance of fractals is much related to the question of what is the perimeter or surface area of something.  &lt;a href=&quot;http://en.wikipedia.org/wiki/How_Long_Is_the_Coast_of_Britain?_Statistical_Self-Similarity_and_Fractional_Dimension&quot; rel=&quot;nofollow noreferrer&quot;&gt;The classic example is trying to determine the length of Britain's coastline&lt;/a&gt;.  If you took a surveyors sight and set a point every 500 ft you would get a certain number, if you paced it out in strides you would end up taking more curves and turns and you would get a longer number.  If you took out a ruler and measured down to the inch you would get a still larger number.  In these two wikipedia pictures you would get a perimeter of 2400 km and 3400 km for points set every 200 and 50 km respectively:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jWZBl.png&quot; alt=&quot;Britain with 200 km points along the coast&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/MJamj.png&quot; alt=&quot;Britain with 50 km points along the coast.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see that makes a big difference.  So in the same thought organs also need to be measured using fractal sorts of measurements- depending on the level of detail desired. For a heart, if you were to cover the organ with a tight stretch of Saran wrap, you'd have maybe 1-2 square feet, but if you estimate the surface area for not only the inner chambers, but the blood vessels and capillaries, it would be &lt;em&gt;much&lt;/em&gt; larger.  The latter is probably relevant if you are a physiologist and want to know how much oxygen the heart is taking in as it beats.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't find a reference for a human heart, but fractal calculations for the human lungs tell me that 1000 sq ft seems reasonable.  &lt;a href=&quot;http://fractalfoundation.org/OFC/OFC-1-2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;If you take the oxygen accessible area of lungs, including every bronchial passage and aveoli, the answer is 50-100 m^2&lt;/a&gt;. This is about 538- 1,076 sq feet.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heart does not need to have as much surface area as the lung, but the capillaries and arteries that feed the heart need to be spaced a few millimeters apart to keep the tissue oxygen saturated.  1000 sq feet seems a possible range for the heart compared to the lung's surface area, maybe on the high end...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-01-20T17:05:09.500" LastActivityDate="2013-01-20T17:05:09.500" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6863" PostTypeId="1" AcceptedAnswerId="6867" CreationDate="2013-01-20T08:07:18.653" Score="5" ViewCount="16748" Body="&lt;p&gt;There is a question in my Biology textbook:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Which blood vessel in the human body carries most impure blood after&#xA;  few hours of meal.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The answer is given as &lt;em&gt;Renal artery&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I think the answer should be &lt;em&gt;Hepatic Vein&lt;/em&gt;, because the liver produces urea and other waste materials and then it pours it all in the right ventricle of the heart for oxygenation. And then the heart distributes the blood to various parts of the body. So the impure blood brought by the Hepatic Vein and other blood vessels gets distributed through the aorta. This will automatically imply that the Renal Artery will contain &lt;em&gt;lesser&lt;/em&gt; impure blood than the Hepatic Vein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Impure blood is the blood with urea, uric acid and other components of urine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be good if you give your opinion and also a reason for it.&lt;/p&gt;&#xA;" OwnerUserId="1428" LastEditorUserId="107" LastEditDate="2013-01-21T03:10:54.073" LastActivityDate="2018-07-03T03:20:29.070" Title="Which blood vessel carries the most impure blood?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;liver&gt;&lt;kidney&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6864" PostTypeId="1" AcceptedAnswerId="6868" CreationDate="2013-01-20T08:09:48.650" Score="6" ViewCount="1760" Body="&lt;p&gt;I have a book from &lt;em&gt;Dorling Kindersley&lt;/em&gt; called &lt;em&gt;Animal Encyclopedia&lt;/em&gt; (the German version that I have is called &lt;em&gt;Das große Tierlexikon&lt;/em&gt;) with images from animals.&lt;/p&gt;&#xA;&lt;p&gt;One is titled &lt;em&gt;Emperor Penguin&lt;/em&gt; (&lt;em&gt;Kaiserpinguin&lt;/em&gt;) which is in my opinion clearly recognizable as a &lt;em&gt;King Penguin&lt;/em&gt; (&lt;em&gt;Königspinguin&lt;/em&gt;).&lt;/p&gt;&#xA;&lt;p&gt;This is the image:&#xA;&lt;img src=&quot;https://i.imgur.com/oR00xds.jpg&quot; alt=&quot;Emperor or King&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;I wrote to Dorling Kindersley and they told my that their investigation revealed that it really is an &lt;em&gt;Emperor Penguin&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;p&gt;I am not a biologist nor a penguin expert, but from all the descriptions and images I could find (even in the same book on other pages!) I think the publishing company is wrong and just too lazy or arrogant to admit this error and too miserly to release a revised version of the book.&lt;/p&gt;&#xA;&lt;p&gt;Who is wrong? Me or &lt;em&gt;Dorling Kindersley&lt;/em&gt;? Emperor or King?&lt;/p&gt;&#xA;&lt;h2&gt;Update 2020&lt;/h2&gt;&#xA;&lt;p&gt;They seem to inherently admit it themselves, that the book was wrong (and that they lied to me), as they used the same picture on one of their &lt;a href=&quot;https://www.dkfindout.com/us/animals-and-nature/birds/penguins/&quot; rel=&quot;nofollow noreferrer&quot;&gt;websites&lt;/a&gt; and with &lt;strong&gt;king penguin&lt;/strong&gt; in the caption of the picture:&#xA;&lt;img src=&quot;https://i.imgur.com/YjQqWD9.jpg&quot; alt=&quot;image on the website of Dorling Kindersley / DK&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="2956" LastEditorUserId="2956" LastEditDate="2020-12-14T13:09:39.480" LastActivityDate="2020-12-14T13:09:39.480" Title="Is this an Emperor Penguin or a King Penguin?" Tags="&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="6865" PostTypeId="1" AcceptedAnswerId="6874" CreationDate="2013-01-20T08:23:58.097" Score="4" ViewCount="2546" Body="&lt;p&gt;I saw this refutation online of Darwin's Random Evolution Theory and cannot see any holes with the logic. Can anyone crack this simple refutation?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;h1&gt;Refutation of the Theory of Random Evolution&lt;/h1&gt;&#xA;  &#xA;  &lt;p&gt;As for the theory of evolution, which says that living things evolved progressively from&#xA;  mud - first organism - bacteria - fish - animals - humans through tiny&#xA;  random mutations which were advantageous and naturally selected;&#xA;  there's a lot to say on this. All currently living life forms appears&#xA;  to be highly related, sharing the same DNA system and cell structure.&#xA;  This would suggest a common first ancestor as the theory suggests (or&#xA;  better yet - one Designer), however, the most obvious flaw with the&#xA;  theory is that the first organism must have had highly sophisticated&#xA;  intelligent design. There is a minimum requirement for even the most&#xA;  primitive possible life form, without which it could not possibly&#xA;  survive.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Minimum Requirements for First Organism&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;&lt;p&gt;The first organism must have a system of producing and/or sourcing energy along with subsystems of distribution and management&#xA;  of that energy which interact and work together, otherwise it cannot&#xA;  power critical tasks such as reproduction.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;It must have a system of reproduction which necessitates pre-existing subsystems of information storage (DNA), information&#xA;  copying, and information reading/processing which interact with each&#xA;  other and work together. This reproductive system is dependent on a&#xA;  power source, so it must be coordinated with the power system. The&#xA;  reproductive system must also copy/rebuild all critical infrastructure&#xA;  such as the power system and the reproduction system along with the&#xA;  &quot;circuitry&quot; and feedback mechanisms between them, otherwise the child&#xA;  organism will be dead..&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;It must have a growth system, otherwise the organism will reduce itself every time it reproduces and vanish after a few generations.&#xA;  This growth system necessitates subsystems of ingestion of materials&#xA;  from the outside world, processing of those materials, distribution,&#xA;  and absorption of those materials to the proper place, building the&#xA;  right thing at the right place and in the right amount. It must also&#xA;  have an expulsion system for waste materials.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The growth system must also be coordinated with the reproduction system. Otherwise, if the reproduction trigger happens faster than the&#xA;  growth, it will reduce size faster than it grows in size and vanish&#xA;  after a few generations. The growth system also requires connection to&#xA;  the power infrastructure to perform its tasks.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;All the &quot;circuitry&quot;, signaling, and feedback infrastructure which allows the different systems and subsystems to coordinate&#xA;  together and work together must be in place before the organism can&#xA;  &quot;come alive&quot;. The reproduction system won't work without coordination&#xA;  with the growth and power systems. Likewise, the power system by&#xA;  itself is useless without the growth and reproduction systems and&#xA;  cannot survive. Only when all the &quot;circuitry&quot;, etc. is in place and&#xA;  the power is turned on is there hope for the hundreds of&#xA;  interdependent tasks to start working together. Otherwise, it is like&#xA;  turning on a computer which has no interconnections between the power&#xA;  supply, CPU, memory, hard drive, video, operating system, etc -&#xA;  nothing to write home about.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;We assume it originated in water since gas is too unstable and solid is too static. If so, the organism must be contained by some&#xA;  kind of membrane otherwise its precious contents will drift away in&#xA;  the water due to natural diffusion or drifting of water due to&#xA;  temperature variations in the water from sunlight, etc. or from heat&#xA;  generated through its own power, or wind, moon, etc. If so, this makes&#xA;  the assembly of such an organism more problematic, since it would need&#xA;  to be closed shut before it can build itself in a stable way. Yet, to&#xA;  build itself it would need to be open for a long time until all&#xA;  systems are built and interconnected.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;  &#xA;  &lt;p&gt;From the above minimum requirements it is clear that the simplest&#xA;  possible surviving organism is by no means simple. You would need&#xA;  thousands of different proteins/lipids etc., in the right proportions,&#xA;  all intricately folded and actively interacting with each other and&#xA;  with sophisticated organelles. Contemplate this and you will see the&#xA;  necessary complexity of this primitive organism is far more&#xA;  sophisticated than anything modern technology has ever produced. Even&#xA;  the most sophisticated Intel CPU is mere child's play compared with&#xA;  the design of such an organism.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="2957" LastEditorUserId="-1" LastEditDate="2014-01-09T11:29:59.840" LastActivityDate="2014-05-29T12:16:09.117" Title="Refutation of Darwin's Random Evolution Theory" Tags="&lt;evolution&gt;" AnswerCount="4" CommentCount="6" FavoriteCount="6" ClosedDate="2014-05-30T05:00:34.877" ContentLicense="CC BY-SA 3.0" />
  <row Id="6867" PostTypeId="2" ParentId="6863" CreationDate="2013-01-20T09:14:48.747" Score="9" Body="&lt;p&gt;It's the renal artery because it will contain everything from the liver as you describe &lt;em&gt;plus&lt;/em&gt; all waste accumulated on the way from the liver to the kidney. Here it gets filtered, so there cannot be a place after the kidney that is less &quot;pure&quot;.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="69" LastEditDate="2013-01-20T11:10:45.027" LastActivityDate="2013-01-20T11:10:45.027" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="6868" PostTypeId="2" ParentId="6864" CreationDate="2013-01-20T09:56:30.577" Score="6" Body="&lt;p&gt;Found this image &lt;a href=&quot;http://www.acuteaday.com/blog/tag/difference-between-emperor-and-king-penguin/&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;. I've also seen references to the &quot;closed orange ear patch&quot; of the King Penguin, which fits with the image. So my vote is for the DK image being a King Penguin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/f8rYC.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-01-20T09:56:30.577" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6869" PostTypeId="1" AcceptedAnswerId="6872" CreationDate="2013-01-20T10:10:30.380" Score="9" ViewCount="10621" Body="&lt;p&gt;When I yawn I can't hear anything happening around me. I also feel some kind of muscles inside my head contract and hear a faint hum, but it is not loud enough to explain not hearing other sounds. I can force those muscles to contract even without yawning and it produces the same effect of humming and no other sound, so I suppose they cause this effect, but how?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What really happens? What muscles do I feel?&lt;/p&gt;&#xA;" OwnerUserId="1427" LastEditorUserId="1320" LastEditDate="2013-01-20T13:59:20.300" LastActivityDate="2015-03-25T12:20:07.373" Title="Why does yawning impair hearing?" Tags="&lt;human-biology&gt;&lt;muscles&gt;&lt;human-ear&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6870" PostTypeId="2" ParentId="6865" CreationDate="2013-01-20T10:15:15.893" Score="15" Body="&lt;p&gt;(A few words about your source: it's little use to come a serious site about science and quote sources whose objective is to prove the existence of god. If you want to learn more about the beauty of life and the theory of evolution, I suggest you read the book &quot;The Blind Watchmaker&quot; by Richard Dawkins, it's an excellent introduction to the topic.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no such thing as &quot;Darwin's Random Evolution Theory&quot;. Further, Darwin put forward a theory of the origin of &lt;em&gt;species&lt;/em&gt; (which is the opposite of random!), not of the origin of life (I do believe he did not write anything at all about how life develops from &quot;mud&quot;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, there is nothing to &quot;crack&quot; in that &quot;logic&quot;, because the question is not valid in the first place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disregarding that the question is not valid in the first place, I think you're trying to refute the idea that self-replicating life-like things could emerge spontaneously. I'm not sure there is anything particularly random about how the world behaves, it's rather a label for what human imagination and ingenuity cannot predict. However, in the sense of random you are using, self-replicating patterns (I won't be the one to determine whether it passes as life) have been shown to be possible in a much simpler world than ours: Conway's Game of Life. A pattern that uses a kind of instruction tape, replicates and destroys its parent (repeating this every 34 million generations) was found in 2010 by Andrew J. Wade.&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Conway%27s_Game_of_Life#Self-replication&quot;&gt;http://en.wikipedia.org/wiki/Conway%27s_Game_of_Life#Self-replication&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this &lt;em&gt;can&lt;/em&gt; occur, although to a large part it was probably designed in this case, you cannot say it is impossible in a world on a &lt;em&gt;much&lt;/em&gt; larger scale and over eons of time (these kinds of time periods cannot easily be imagined - a good reason why we tend to believe it is very unlikely that something very improbable will happen during the period).&lt;/p&gt;&#xA;" OwnerUserId="2954" LastEditorUserId="2954" LastEditDate="2013-01-21T12:58:34.017" LastActivityDate="2013-01-21T12:58:34.017" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6871" PostTypeId="1" AcceptedAnswerId="6876" CreationDate="2013-01-20T10:57:11.507" Score="9" ViewCount="923" Body="&lt;p&gt;What is it in our brain that makes having such experiences possible? I assume other species don't have these. Sure there are instances in the natural world where you can see individuals of the species gather around the dead one. Sometime even the alpha male in the group allows the kin/relatives of the dead individual to approach it (for whatever reason).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The kind of thing I don't see in the wild-life kingdom is an individual becoming &quot;enlightened&quot; or the likes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sure our cerebrum is highly developed and all. But &quot;what&quot; is it in our brain that makes it capable for humans to have such experiences?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've read articles saying we have identified such regions in the brain. Just want to know what these structures are. Did such research establish that such structures also exist in other species too?&lt;/p&gt;&#xA;" OwnerUserId="2958" LastEditorUserId="1320" LastEditDate="2013-01-20T13:57:27.273" LastActivityDate="2015-12-23T08:15:03.377" Title="Why do humans alone have the capability to have religious/spiritual experiences?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;neuroanatomy&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="6872" PostTypeId="2" ParentId="6869" CreationDate="2013-01-20T14:30:08.080" Score="7" Body="&lt;p&gt;It is related to Eustachian tube. It links the back of throat and the middle ear and allows air pressure to equalize in the middle ear. When you yawn air pressure goes up in this and it bends the ear drum and causes impair hearing (notice, just impair and not stop).&#xA;Yawning also helps to open Eustachian tube.&lt;/p&gt;&#xA;" OwnerUserId="1916" LastActivityDate="2013-01-20T14:30:08.080" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6874" PostTypeId="2" ParentId="6865" CreationDate="2013-01-20T16:21:48.573" Score="12" Body="&lt;p&gt;I like @5th 's answer but I thought it might be worthwhile to clarify on some points and pull the logic out a bit more.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First there is some contesting the overall logic that it assumes all these &lt;em&gt;qualities of life are showing up at once&lt;/em&gt;.  If they had to, it probably is true that life could not evolve, but the general assumption is that there is a path to do so.  Let me try to be convincing of this.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dawkin's &lt;a href=&quot;http://old.richarddawkins.net/articles/642589-first-life-the-search-for-the-first-replicator&quot;&gt;theory of the replicator&lt;/a&gt; is axiomatic and not entirely helpful at this point, but it does have a lot to say.  Once you have self replicating systems, the rest of biology and evolution and selection does seem reasonable, even with the emergence of complicated structures like the &lt;a href=&quot;http://musingsofscience.wordpress.com/2010/11/27/the-evolutionary-massif-and-the-eyes-pinnacle-part-1/&quot;&gt;eye&lt;/a&gt;, the &lt;a href=&quot;http://www.detectingdesign.com/flagellum.html&quot;&gt;flageller motor&lt;/a&gt; and other seemingly unplausibly multi component systems seem to magically come together and do something new in the course of evolution.  Dawkins wrote a book on this topic &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Climbing_Mount_Improbable&quot;&gt;Climbing Mount Improbable&lt;/a&gt;&quot; on this topic which tries to answer this question for several cases.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To outline why biological systems can and do seem to leap to new abilities, organs and unprecedented assemblies. In fact the do not, but there are so many possible trials (quintillions? ) over the trillions of years, that eventually some adaptive path to these features, which has usually been found when we go looking for it.  As such there is no clear reason why new cases of this argument need to carry extra weight.   The argument of statistically improbable combinations has been tried and remains unconvincing with respect to evolution several times.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After this, I think it would be fair to say that the origins of life, although coming clear still has many details to be resolved, but progress is being made. &lt;a href=&quot;http://www.fossilmuseum.net/Paleobiology/Precambrian-Fossils.htm&quot;&gt;Precambrian evidence of primitive life&lt;/a&gt; was very different as seen in fossil records.  We can see that at one time there were only bacteria and single celled organisms.  There is evidence that at one time there appears to be only simple very large single celled organisms that lay in shallow water and soaked up the sunlight, growing and growing.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can see that going back about 1.2-2 billion years, life shows a pretty clear progression where selection and adaptation creates complexity in living things and transitions life from exclusively chemotrophs (metabolizing Sulfur from geological processes) to anoxic (no oxygen environment) photosynthesis, and then oxygen breathing organisms.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the precellular world, the RNA World hypothesis describes how all that life needed was one sort of molecule - RNA.  That is chemically a very simple replicator.  Evidence is pretty strong that RNA world was possible.  Many chemists are interested in proving that RNA can be created more or less spontaneously from early earth chemical environments and recent experiments show that spontaneous &lt;a href=&quot;http://www.nature.com/news/2009/090513/full/news.2009.471.html&quot;&gt;soups containing RNA are a reasonable picture of earth at one point&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All this being said its probably true that exactly what happened and how it happened will never be 100% known and the argument can be made that something unnatural happened at some point. But I hope you can also see that while the argument may still hold some water, the need for any magical interventions in the action of life is retreating to a point of origin - the beginning of time.  Scientific inquiry is very much focused on filling the picture of the origins of life on earth though and given the success of finding probable paths through to the origins of life, the odds actually are in favor for making a statement of the physical mechanisms of life's origins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just a couple of side notes.. (1) biologists are not stuck on &lt;a href=&quot;http://learn.genetics.utah.edu/content/epigenetics/inheritance/&quot;&gt;everything being random&lt;/a&gt;.  There is lots of work on mechanisms evolved to &lt;a href=&quot;http://learn.genetics.utah.edu/content/epigenetics/inheritance/&quot;&gt;adapt in non-random way&lt;/a&gt;s.&lt;br&gt;&#xA;(2) Darwin is not a sacred cow - just about any working biologist would love to show Darwin was wrong even in a little way.  The same is true for Einstein, Newton and the rest.  After a few years of trying though what one usually finds that its kinda difficult.  Its not a matter of who makes the argument or what it means, but it has to be convincing and that &lt;a href=&quot;http://www.gizmag.com/neutrinos-sub-light-speed/22876/&quot;&gt;turns out to be difficult&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-01-20T16:27:39.950" LastActivityDate="2013-01-20T16:27:39.950" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6875" PostTypeId="2" ParentId="6865" CreationDate="2013-01-20T16:26:50.907" Score="13" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I saw this refutation online of Darwin's Random Evolution Theory and cannot see any holes with the logic. Can anyone crack this simple refutation?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Certainly. First and foremost: The refutation is not simple. It is a complex argument that draws consistently on baseless assumptions and relies on the lack of education of the reader to get its point across. I do not mean that the reader is dumb, merely that the author's target audience is probably ill-informed about the details of Biology, Chemistry, Physics, and similar fields. The author relies on being long and convoluted, appealing to faulty logic, and a whole slew of fallacies that might be missed if the reader hadn't already encountered them in the context of Evolution.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As for the theory of evolution, which says that living things evolved progressively from mud...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, as 5th has already said, this is a bad start. The Theory of Evolution (via Natural Selection if we want to get the full name out there) says nothing about the &lt;strong&gt;beginnings&lt;/strong&gt; of life. That would be &lt;a href=&quot;http://en.wikipedia.org/wiki/Abiogenesis&quot;&gt;Abiogenesis&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Theory of Evolution merely dictates that subsequent generations adapt to their environment, and that those who have adapted best will pass their inheritable traits to the next generation.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;1. The first organism must have a system of producing and/or sourcing&#xA;  energy along with subsystems of distribution and management of that&#xA;  energy which interact and work together, otherwise it cannot power&#xA;  critical tasks such as reproduction.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This isn't a difficult task. Currently the most abundant source of energy on the planet is the Sun. It has been shining for billions of years before the Earth was formed, and will be shining for billions of years after you've read this paragraph.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we exclude sunlight for the LCA (Last Common Ancestor) of all life, then we're mostly talking about geothermal energy or chemical reactions. Ultimately, though, extant organisms store energy in chemical bonds. The primary &quot;Energy Carrier&quot; of the cell is ATP - Adenosine Tri-Phosphate, and it's the third of the three Phosphates that is often &quot;harvested&quot; for its energy - leaving ADP as a product of metabolic reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That a system of sourcing and managing energy distributions could arise from even simple situations is not so far fetched. Consider the Earth's atmosphere and weather patterns; initially they appear extremely complex and result in myriads of environments that even modern science cannot accurately predict more than a few days ahead.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the entire system is driven by the interaction of the planet's geography, the gases composing the atmosphere, and the Sun as it heats the system. Regulation is taken care of by Physics - hot air rises, cold air sinks, geographical location determines exposure to the energy source, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Power is not an issue. Basic regulation is not an issue. Once the basics are down, more complex forms can Evolve.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;2. It must have a system of reproduction which necessitates pre-existing subsystems of information storage (DNA), information copying, and information reading/processing which interact with each other and work together. This reproductive system is dependent on a power source, so it must be coordinated with the power system. The reproductive system must also copy/rebuild all critical infrastructure such as the power system and the reproduction system along with the &quot;circuitry&quot; and feedback mechanisms between them, otherwise the child organism will be dead..&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you're willing to accept that chemical reactions between amino acids and similar molecules can occur on primitive Earth, then the jump to this question isn't that hard.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, you should know that DNA almost certainly wasn't the initial genetic storage form. A commonly accepted and incredibly intriguing theory is the &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_world_hypothesis&quot;&gt;RNA World Hypothesis&lt;/a&gt;. RNA can &lt;em&gt;also&lt;/em&gt; store genetic information - albeit at a less accurate rate for a shorter amount of time. More importantly, RNA has also been observed &lt;em&gt;folding into itself to create proteins and catalysts&lt;/em&gt;. It's sort of a jack-of-all-trades, and since it's basic constituents have been discovered amongst the vacuum of spaces, all the pieces were here on Earth 4 B.Y.A. to make some of the first steps towards organic life. All that had to happen is that the right molecules had to come together, then physics takes over and you have some astonishing reactions. Given the right conditions and a few hundred million years, who's to say it isn't possible?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;3. It must have a growth system, otherwise the organism will reduce itself every time it reproduces and vanish after a few generations. This growth system necessitates subsystems of ingestion of materials from the outside world, processing of those materials, distribution, and absorption of those materials to the proper place, building the right thing at the right place and in the right amount. It must also have an expulsion system for waste materials.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Let me introduce you to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Micelle&quot;&gt;Micelle:&lt;/a&gt; A naturally occurring structure that looks an awful lot like today's cell membranes. It doesn't require exotic materials, it doesn't require fancy catalysts; it requires amphipathic molecules and that's about it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While complex organisms do require subsystems and various ways to ingest food to harness nutrition, for the most basic forms of life &quot;Digestion&quot; is little more than taking in outside material into the cell and then putting what's left back outside.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To that end, Micelles merge on their own when distance allows. The mechanism is powered by the entropy of the water molecules surrounding the micelle's structure and doesn't require any sort of metabolism or organic control to occur. In addition, hydrophobic molecules can slip through unhindered fairly easily (depending on size), and many of amino acids used to make proteins and micronutrients our current bodies require are hydrophobic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it's entirely possible to have a basic membrane that can &quot;eat&quot; other things without being strictly &lt;em&gt;alive&lt;/em&gt;. Everything after that is just added complexity that was retained due to improved functionality. It's important to remind yourself that we're talking of a span of &lt;strong&gt;hundreds of millions of years&lt;/strong&gt;. Almost &lt;em&gt;nothing&lt;/em&gt; currently living on the planet has gone more than a few hundred thousand or few million years without drastically changing how it looks. A hundred million years ago humans were little more than rats or furry lizards. Imagine what could happen with 5x that span!&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;4. All the &quot;circuitry&quot;, signaling, and feedback infrastructure which allows the different systems and subsystems to coordinate together and work together must be in place before the organism can &quot;come alive&quot;...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This very, very much depends on your definition of &lt;strong&gt;alive&lt;/strong&gt; - which is still difficult to define for Biologists to this day. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are viruses &lt;em&gt;alive&lt;/em&gt;? They certainly do not retain any reproductive ability of their own and must hijack the operations of a living cell to create the next generation - but they still have inheritable genetic material, they still create structures and adapt to their environment, and still - in an odd way - consume resources to reproduce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the difference between the spread of iron oxide (rust) -- which, you could argue, requires an interaction of existing elements to perpetuate and has built-in feedback (it is inhibited when there is a &lt;em&gt;lack&lt;/em&gt; of a substance - a completely viable and well-known trope of feedback mechanisms) -- and the spread of a fungus, which you could describe just as simply?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Defining &quot;Life&quot; by what exists today is a &lt;em&gt;mistake&lt;/em&gt;&lt;/strong&gt; often made by those who dispute the Theory of Evolution. Only the most basic assumptions and connections can be made between life as-it-exists and life-as-it-started. The planet is different, the air is different, &lt;em&gt;the Moon is significantly further away&lt;/em&gt;, and countless other things have occurred.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, we have definitely observed complex interactions of molecules and systems &lt;em&gt;in situ&lt;/em&gt; within conditions similar to those of early Earth. One of the most famous is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment&quot;&gt;Miller-Urey&lt;/a&gt; experiment. If you're asking why they didn't succeed in creating life, remember that it took about 500 million years for the LCA to spring into existence... &lt;strong&gt;And the LCA is not necessarily the first form of life, just the one that gave rise to all current forms.&lt;/strong&gt; Miller and Urey experimented for &lt;em&gt;two weeks&lt;/em&gt;, not 500 million years, but still made significant discoveries in that short a time-span.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;5. We assume it originated in water since gas is too unstable and solid is too static. If so, the organism must be contained by some kind of membrane otherwise its precious contents will drift away in the water due to natural diffusion or drifting of water due to temperature variations in the water from sunlight, etc. or from heat generated through its own power, or wind, moon, etc.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;We have already discussed the &lt;strong&gt;Micelle&lt;/strong&gt; above. &lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1306" LastEditDate="2013-01-21T19:18:30.630" LastActivityDate="2013-01-21T19:18:30.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6876" PostTypeId="2" ParentId="6871" CreationDate="2013-01-20T17:01:59.593" Score="18" Body="&lt;p&gt;Its not clear that this is true. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Working with animals has been a little disconcerting over the past 50-60 years.  In the distant past, I think most evolutionary anthropologists and their like bought into the idea that humans were completely uniquely intelligent and spiritual.  But the more we try to define human sensibilities apart from other animals, the more we find its difficult to see animals as being completely incapable of human feelings and even thoughts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I refer you to this question which describes the shift in intelligence theories over the years: &lt;a href=&quot;https://biology.stackexchange.com/questions/6827/why-have-humans-evolved-conciousness/6831#6831&quot;&gt;Why have humans evolved conciousness?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above reference is just to say that every definition of intelligence that is fairly broad has been overturned by animals (thumbs, socialization, tool use, self awareness, communication and language). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to say &lt;em&gt;'I know we're special, but I just can't say how'&lt;/em&gt; you are in lots of good company... it's become pretty hard to lay down a definition that includes all human beings and excludes animals.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lately it seems as if the definition of spiritual experience is similarly hard to define. What is your definition?  The &lt;em&gt;capacity to &lt;a href=&quot;http://www.huffingtonpost.com/2012/11/02/cat-adopts-hedgehog-babies_n_2066996.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;receive and reciprocate affection or love&lt;/a&gt;&lt;/em&gt; is almost never brought up - &lt;a href=&quot;http://weruletheinternet.com/2011/05/06/22-pictures-of-dogs-and-cats-sleeping-together/&quot; rel=&quot;nofollow noreferrer&quot;&gt;that seems to be half of the internet&lt;/a&gt;.  Yet, that's a common component to many ideas of spirituality.   It was found a while ago that &lt;em&gt;primates have some form of self-awareness&lt;/em&gt; to identify themselves as distinct from other individuals.  True this was only demonstrating that they &lt;a href=&quot;http://en.wikipedia.org/wiki/Mirror_test#Reactions_of_other_animals_to_mirrors&quot; rel=&quot;nofollow noreferrer&quot;&gt;know themselves in a mirror&lt;/a&gt;, but other experiments show it probably is deeper than just that.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the most confounding evidence is the work with animals who have been trained from infanthood to &lt;a href=&quot;http://www.cnn.com/2010/LIVING/wayoflife/05/14/mf.animals.that.could.talk/index.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;communicate to humans&lt;/a&gt; through sign language or symbols.  The most astounding example I know if is Koko the gorilla. She had the vocabulary of a 5 year old and the capacity to joke around, reason, and adopted pets as children including a cat called All Ball.  When All Ball who was killed by a car she &lt;em&gt;mourned and remembered&lt;/em&gt; her adopted cat for years.  This &lt;a href=&quot;http://www.animalliberationfront.com/Philosophy/Morality/Speciesism/Case4Personhood.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;page&lt;/a&gt; outlines all that, though there is a &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0307472205&quot; rel=&quot;nofollow noreferrer&quot;&gt;book&lt;/a&gt; that describes Koko's life.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The human staff sought to discover what Koko thought about death.  So they asked, “Where do gorillas go when they die?”  Koko answered, “Comfortable / hole / goodbye.”&#xA;  They asked, “When do gorillas die?”  Koko answered, “Trouble / old.”&#xA;  They asked, “How do gorillas feel when they die:  happy, sad, afraid?”  Koko answered, “Sleep.”&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So this has been taken as evidence that gorillas have a &lt;em&gt;concept of their own mortality&lt;/em&gt; or possibly even life after death.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what is left?  Not clear to me.  Any thoughts? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some regions of the brain and control of electrical activity in the brain have been associated with spiritual experiences or acts like prayer and meditation.  The temporal lobe is exciting because &lt;a href=&quot;http://www.bbc.co.uk/science/horizon/2003/godonbrain.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;magnetic stimulation of that region can create the sensation that there is a presence in the room with you&lt;/a&gt;. there appear to be many regions which are active in different instances though, which is something you might expect.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no evidence yet that animals do not experience similar effects in their brains, though primates have very much the same structures as we do.   Its too bad Koko has died - she might have told us.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-01-23T23:02:14.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6877" PostTypeId="1" CreationDate="2013-01-20T18:23:51.443" Score="1" ViewCount="1146" Body="&lt;p&gt;I heard people use silicone sheet for reducing raised scars (i.e., keloids). I was wondering what is the rational behind it, and whether it actually works.&lt;/p&gt;&#xA;" OwnerUserId="262" LastEditorUserId="107" LastEditDate="2013-01-21T02:30:29.160" LastActivityDate="2013-01-21T02:37:24.170" Title="Why can silicone reduce keloid?" Tags="&lt;skin&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6878" PostTypeId="1" AcceptedAnswerId="6882" CreationDate="2013-01-20T21:11:37.070" Score="5" ViewCount="1727" Body="&lt;p&gt;We just had a discussion about toluene abuse. It is known, that people inhaling toluene for a long time have significant brain damage, including  decreased intelligence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found that toluene is a lipid solvent, and that it can damage the myelin. However, myelin is only present in the white matter, but intelligence is related to the grey matter which does not contain myelin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any indirect damage, or did we miss some important point in this case? Second, how does toluene get to the brain? Is it able to infiltrate from the nose through the mucous membrane, or is it carried in the blood? I am just curious.&lt;/p&gt;&#xA;" OwnerUserId="2961" LastEditorUserId="1916" LastEditDate="2013-01-21T00:38:43.620" LastActivityDate="2015-02-23T13:31:21.320" Title="How does toluene inhalation damage the brain?" Tags="&lt;brain&gt;&lt;toxicology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="6879" PostTypeId="2" ParentId="6877" CreationDate="2013-01-21T00:16:44.703" Score="1" Body="&lt;p&gt;I cannot say the mechanism, but I can confirm it works, and can say that is generally accepted as working, not as some weird dubious treatment. I had surgery to install a rod in my leg after a broken bone. On the advice of my physical therapist, I purchased &quot;Scar Away&quot; brand silicone oil with roller applicator. Placing a thin layer and massaging with the applicator twice a day for four weeks turned my giant cheloids into small sections of skin which were distinguishable only by their smoothness and lack of hair, not color. He said he used to work for some basketball team and it was common practice to be used in professional basketball.&lt;/p&gt;&#xA;" OwnerUserId="2962" LastActivityDate="2013-01-21T00:16:44.703" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6881" PostTypeId="2" ParentId="6877" CreationDate="2013-01-21T02:37:24.170" Score="1" Body="&lt;p&gt;According to several papers (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1493533&quot; rel=&quot;nofollow&quot;&gt;Sawada and Sone, 1992&lt;/a&gt;; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8864367&quot; rel=&quot;nofollow&quot;&gt;Wong et al., 1996&lt;/a&gt;), increased hydration appears to be the main mechanism by which silicone oil acts on raised scars. Combined with an occlusive dressing, this preparation would increase hydration of the scar site. Sawada and Sone (1992) compared silicone oil treatment to vaseline treatment and found significantly improved healing with silicone oil, concluding that it was the hydrating action of silicone oil that led to improvement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sawada Y, Sone K. 1992. Hydration and occlusion treatment for hypertrophic scars and keloids. &lt;em&gt;Br J Plast Surg&lt;/em&gt; 45(8):599-603.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wong TW, Chiu HC, Chang CH, Lin LJ, Liu CC, Chen JS. 1996. Silicone cream occlusive dressing--a novel noninvasive regimen in the treatment of keloid.. &lt;em&gt;Dermatology&lt;/em&gt; 192(4):329-33.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-01-21T02:37:24.170" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6882" PostTypeId="2" ParentId="6878" CreationDate="2013-01-21T06:08:32.513" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;After crossing the blood-brain barrier, toluene, along with other volatile anesthetic agents, had been previously thought to inhibit neuronal transmission by causing a change in membrane or membrane protein conformation. Recent research has shown that interactions with several key brain neurotransmitters, mainly γ-aminobutyric acidA (GABA), to a lessor degree glycine, and possibly dopamine, are responsible for the clinical effects seen. Postmortem studies along with magnetic resonance imaging (MRI) findings have shown diffuse white matter demyelination and gliosis (solvent vapor/toluene leukoencephalopathy), which is postulated to be the end product by which chronic toxicity occurs, although the exact mechanism by which this occurs remains unclear &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(&lt;a href=&quot;http://emedicine.medscape.com/article/818939-overview#a0104&quot; rel=&quot;nofollow&quot;&gt;McKeown at al. Toluene Toxicity&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="1839" LastEditorUserId="1320" LastEditDate="2013-01-21T14:08:27.710" LastActivityDate="2013-01-21T14:08:27.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6883" PostTypeId="1" CreationDate="2013-01-21T21:51:49.467" Score="4" ViewCount="73" Body="&lt;p&gt;I want to compare the brain sizes of two populations of fish. However, all the samples I have were fixed in 95% ethanol. As far as I know, 4% formalin is the normal fixative for soft tissues. Can I conduct my study, or do I need to obtain samples in formalin? I've scoured the literature, and I can't find any useful recommendations. &lt;/p&gt;&#xA;" OwnerUserId="55" LastActivityDate="2014-10-04T00:31:15.980" Title="Effect of Ethanol on Brain Volume Measurements" Tags="&lt;brain&gt;&lt;lab-techniques&gt;&lt;ichthyology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6884" PostTypeId="1" AcceptedAnswerId="6887" CreationDate="2013-01-21T23:26:13.860" Score="26" ViewCount="10943" Body="&lt;p&gt;I have heard that the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hydra_%28genus%29&quot;&gt;&lt;em&gt;Hydra&lt;/em&gt;&lt;/a&gt; organism is &lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_immortality&quot;&gt;biologically immortal&lt;/a&gt; (later I found that there are more immortal organisms). Now I know that its immortality is related to its telomerase. The thing is that we all have telomerase, but we age and &lt;em&gt;Hydra&lt;/em&gt; don't. What are the proteins (especially telomerase) related to aging in humans and &lt;em&gt;Hydra&lt;/em&gt; and how do they work differently?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="2954" LastEditDate="2013-01-22T01:29:50.517" LastActivityDate="2018-06-14T07:15:20.917" Title="Why is the Hydra Biologically Immortal?" Tags="&lt;senescence&gt;&lt;telomere&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="6885" PostTypeId="1" AcceptedAnswerId="6890" CreationDate="2013-01-22T02:54:26.853" Score="3" ViewCount="361" Body="&lt;p&gt;I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a specific disease. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am confused about how people can determine whether a gene is down-regulated or up-regulated by its gene expression. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume we have a few samples of a gene: some of the samples are normal patients samples and rest of them are disease-infected samples. Do we determine the direction of regulation of a gene by the ratio of gene expression of normal/disease-infected samples? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, if the ratio of expressions is a negative value, do we say that the gene is a down-regulated gene, otherwise, it is a up-regulated gene ? &lt;/p&gt;&#xA;" OwnerUserId="1775" LastEditorUserId="6561" LastEditDate="2014-05-20T15:26:12.107" LastActivityDate="2014-05-20T15:26:12.107" Title="How to determine the direction of regulation of a gene by comparing gene expressions?" Tags="&lt;bioinformatics&gt;&lt;gene-expression&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6886" PostTypeId="1" AcceptedAnswerId="6888" CreationDate="2013-01-22T04:18:42.857" Score="7" ViewCount="4703" Body="&lt;p&gt;I was reading Watson and Crick’s original article on DNA structure in &lt;a href=&quot;https://www.nature.com/articles/171737a0&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Nature&lt;/em&gt; &lt;strong&gt;171&lt;/strong&gt;, 737–738 (1953)&lt;/a&gt;. The accompanying diagram (shown below) has something called the “fibre axis” going through the DNA. This axis isn’t shown in modern models of DNA, so what is it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/NL4v9.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/NL4v9.png&quot; alt=&quot;Watson and Crick Double Helix&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1182" LastEditorUserId="22057" LastEditDate="2019-03-04T23:24:38.883" LastActivityDate="2019-05-29T19:23:02.513" Title="What is the fibre axis in the Watson and Crick paper?" Tags="&lt;dna&gt;&lt;structural-biology&gt;&lt;3d-structure&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="6887" PostTypeId="2" ParentId="6884" CreationDate="2013-01-22T05:22:08.930" Score="17" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/atid9.jpg&quot; alt=&quot;a somewhat smaller picture of a Hydrae&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hydra are just one of the many organisms which are immortal.  That is to say all their cells divide forever - there is no senescence (planned cell death) in any of their cells. Interestingly Hydrae that reproduce sexually age and die, but asexual reproduction appear to be immortal.  Animals that are immortal more often reproduce asexually... this may only be because immortality became unpopular in evolution early on and may have not developed senescence in the way other animals have, or lost it when it was not so integral to life.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306686/&quot;&gt;Although immortal Hydra also appears to share the (TTAGGG)n telomere repeat, there is as yet no data on how or whether they avoid chromosome end depletion. These data suggest the possibility that senescence or death of asexual individuals and colonies may in part result from a failure to maintain chromosome ends that are restored by going through a sexually reproductive cycle .&lt;/a&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So its not clear if the telomeres are protected in hydrae and other immortal animals.  I would guess they probably don't have active telomerase if they are truly immortal, though its possible the telomeres are shortened and are repaired.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other factors which are supposed to be important for immortality.  Yeast and single eukaryotes are not individually immortal; an individual mother cell can only divide a limited number of times. While hydrae are not a popular focus of research, there has been a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2536486/&quot;&gt;concerted effort in trying to understand yeast mortality&lt;/a&gt; and there are more than one mechanism being pointed to. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since there is no germline in single celled organisms, (they only have one copy of their genome to reproduce from) telomeric shortening would not be a useful mechanism for aging; Calorie restriction has been shown to prolong fission and budding yeast by activating pathways which slow aging by protecting against stress, and slowing down reproduction.  All of these findings have strong parallels in work in aging in animals which is a hot topic now.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finding these pathways is encouraging strong thought that aging and senescence are an evolutionary adaptation rather than a biological necessity. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our current knowledge suggests that an apoptotic program has evolved in microorganisms as a survival strategy beneficial to the group. This program is dependent on cellular pathways like the Sch9, Tor1, and Ras/PKA pathways and its activation reduces cell protection and maintenance and raises the level of superoxide production, which in turn contributes to cell damage and death. Superoxide also elevates DNA damage and mutation frequency in the aging cultures ... Aging and apoptosis are intrinsically related in yeast and the mechanisms that cause them have just begun to be elucidated. ...  will provide important information to understand the fundamental biology of aging in other species and investigate the controversial hypothesis that an “aging program” might be conserved in higher eukaryotes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is an open question as to whether an immortal yeast could be &lt;em&gt;engineered&lt;/em&gt; to be immortal.  A team at Max Planck Institute did a lot of foot work and found a strain which they claim &lt;a href=&quot;http://dalje.com/en-lifestyle/finding-immortality-is-a-challenge-for-me/263225&quot;&gt;does not seem to experience individual mortality either&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So this does indicates that immortality might not be a necessity for any cell or maybe even for animals.  Occasionally, &lt;a href=&quot;http://en.wikipedia.org/wiki/Hayflick_limit&quot;&gt;even animal and human cells can be coaxed to revert to an immortalized state&lt;/a&gt;, though usually it is the result of &lt;a href=&quot;http://actu.epfl.ch/news/demystifying-the-immortality-of-cancer-cells/&quot;&gt;cancerous rearrangements of the genome&lt;/a&gt;.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a rich field and there are lots of &lt;a href=&quot;http://news.discovery.com/animals/immortal-animals-reveal-anti-aging-secrets-110421.htm&quot;&gt;telomerase focused ideas too&lt;/a&gt;.  Maybe someone can post something along those lines. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-02-04T18:16:12.487" LastActivityDate="2013-02-04T18:16:12.487" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="6888" PostTypeId="2" ParentId="6886" CreationDate="2013-01-22T07:21:29.653" Score="7" Body="&lt;p&gt;Short answer:&#xA;The term fiber axis is not in reference to the DNA model, it comes from the experiments that Watson and Crick referenced to guess their model (performed by Rosalind Franklin).   The fiber axis is the direction along the DNA strand.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Longer: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Watson and Crick created their model of DNA based on the esoteric experiment called X-ray &lt;a href=&quot;http://en.wikipedia.org/wiki/Fiber_diffraction&quot; rel=&quot;nofollow noreferrer&quot;&gt;fiber diffraction&lt;/a&gt;.  To collect fiber diffraction data ( gathered by Rosalind Franklin actually) DNA is pulled out of a cell lysate and washed with buffer.  It looks like a clear, &lt;a href=&quot;http://www.protocol-online.org/biology-forums/posts/40140.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;liquid, string of snot&lt;/a&gt; (a technical term that is).  Its stringy though because the long DNA molecules pull out and create viscous fluid where the DNA is pulled along the length of the snot fiber.  Because the DNA is ordered in this one dimension, if you shoot a beam of X-rays through it, it creates a pattern on film that looks like this: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CGbwq.jpg&quot; alt=&quot;fiber diffraction data by Rosalind Franklin&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see its got a nice X-shaped pattern.  The DNA in the fiber is mostly aligned along the fiber, in the up and down direction.  Because this is so, the spacings between the different layers is due to the spacings between the DNA bases and the x-pattern comes from the fact that DNA forms a double helix.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some misc details - you have to use X-rays because their wavelength is about the size of an atomic bond and this is the scale of model Watson and Crick and Franklin and Wilkinson were trying to find.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fiber axis is along the y axis (top to bottom) because the trail of DNA snot hangs down - it will sag if you hold it an angle.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rosalind Franklin was a great experimentalist and she realized that the DNA snot trail dries out over time as the experiment would go on for days.  She set up a moist stream of hydrogen gas blowing over the DNA strand during the X-ray experiment and so was the only experimentalist who obtained what we now know to be the true result - double helical DNA.  As it dries out, DNA interconverts to the Z-DNA form I believe, which does not have the x-pattern and also confuses things because the result is a smear of the DNA helix converting from one form to another.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Francis Crick had actually predicted the X-pattern for helices.  The structure actually required these two to come together to get the answer while the American genius Linus Pauling was working hard in California on the structure as well and would have won too if he understood how to keep his snot properly damp. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reference for nearly all of this is Watson's somewhat self-centered but historically accurate book &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/The_Double_Helix&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Double Helix&lt;/a&gt;&quot;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After some surprisingly difficult Googling, I can't found a picture of DNA fiber... picture below. You can make some yourself from the &lt;a href=&quot;http://www.instructables.com/id/5-minute-DNA-Extraction-in-a-Shot-Glass/&quot; rel=&quot;nofollow noreferrer&quot;&gt;protocol listed here&lt;/a&gt; and some saliva, soap and other common household items. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/179LT.jpg&quot; alt=&quot;DNA snot&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2019-05-29T19:23:02.513" LastActivityDate="2019-05-29T19:23:02.513" CommentCount="6" ContentLicense="CC BY-SA 4.0" />
  <row Id="6889" PostTypeId="1" CreationDate="2013-01-22T09:38:54.320" Score="6" ViewCount="485" Body="&lt;p&gt;The humans have been around for a few million years, other organisms longer yet. Changes that occur in the genome and propagate (may) eventually throw a new species ... or atleast branch off the old one. Are there any chromosomes out there that may be more susceptible to mutation than their neighbours? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2013-03-07T08:34:15.053" Title="Are all chromosomes equally susceptible to mutation?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6890" PostTypeId="2" ParentId="6885" CreationDate="2013-01-22T09:41:26.200" Score="3" Body="&lt;p&gt;If you have control expression values $c$ and e.g. disease expression values $d$, you take the ratio: $\frac{d}{c}$. If this is greater than one, it's up-regulated. Usually, the log-ratio is computed: $log\frac{d}{c}$. Now, if this is positive, the gene is up-regulated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gene expression values are usually measured genome-wide and then normalized before computing the ratios. So you rarely deal with individual raw expression values.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2013-01-22T09:41:26.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6891" PostTypeId="1" CreationDate="2013-01-22T10:28:00.030" Score="11" ViewCount="7150" Body="&lt;p&gt;So I am reading about muscles and I come across myoglobin. It has a much higher affinity for oxygen than haemoglobin. So why have animals evolved to have haemoglobin in red blood cells, rather than myoglobin, which would be much more advantageous?&lt;/p&gt;&#xA;" OwnerUserId="2967" LastEditorUserId="1320" LastEditDate="2013-01-26T17:15:50.910" LastActivityDate="2013-01-27T00:22:42.333" Title="Why do red blood cells contain haemoglobin and not myoglobin?" Tags="&lt;cell-biology&gt;&lt;cellular-respiration&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6892" PostTypeId="1" CreationDate="2013-01-22T11:45:46.697" Score="4" ViewCount="355" Body="&lt;p&gt;I use DNA green viewer in Lab to see DNA and RNA bands. Some peers told me it is carcinogenic and is not safe.&#xA;Is this correct? If yes, are there better choices to use in working with gel? &lt;/p&gt;&#xA;" OwnerDisplayName="user2968" LastEditorUserId="1855" LastEditDate="2013-01-22T20:06:56.200" LastActivityDate="2013-01-22T22:26:26.390" Title="Is DNA green viewer carcinogenic?" Tags="&lt;lab-techniques&gt;&lt;lab-reagents&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="6894" PostTypeId="2" ParentId="6891" CreationDate="2013-01-22T13:37:16.473" Score="3" Body="&lt;p&gt;Blood needs to be able to lose oxygen as well as capture it, the whole point is to take in oxygen in the lungs and then release it throughout the body. Blood that is simply really good at absorbing oxygen would only be an oxygen trap. Myoglobin, having more affinity for oxygen, can take oxygen from hemoglobin and store it in the muscle for the near future use.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="444" LastEditDate="2013-01-25T15:10:07.117" LastActivityDate="2013-01-25T15:10:07.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6895" PostTypeId="2" ParentId="6891" CreationDate="2013-01-22T14:16:26.287" Score="9" Body="&lt;p&gt;Just to expand slightly on the answer by Jack Aidley:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a look at &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK22596/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this section from Stryer's Biochemistry text book&lt;/a&gt;, particularly Fig 10.17, where you can see that haemoglobin has evolved to have a high affinity for oxygen at the O&lt;sub&gt;2&lt;/sub&gt; concentrations present in the lungs, but a low affinity at the O&lt;sub&gt;2&lt;/sub&gt; concentrations present in the peripheral tissues. This is achieved by binding oxygen co-operatively. This means that haemoglobin can release 60-70% of its bound oxygen. Under the same conditions myoglobin, were it be used in red blood cells as an oxygen carrier, would release much less.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incidentally the Figure linked to shows a comparison between haemoglobin and a hypothetical protein which shows 50% saturation at the same concentration of oxygen but which binds oxygen non-cooperatively (like myoglobin).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A more direct comparison of haemoglobin and myoglobin  - found &lt;a href=&quot;http://web.campbell.edu&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; -  is shown below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WQJe9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;edit added to respond to shigeta's response&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't understand some of the statements from shigeta so here are my views - if I am wrong, I would (genuinely) like to be corrected, since I have to teach this stuff.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...&quot;what is particularly useful about Hb's cooperativity is that the last oxygen is harder to pull off the Hb tetramer than the first.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This statement contradicts my understanding of the oxygen-binding behaviour of haemoglobin. In the deoxygenated state the protein is in the conformation known as the T (for &lt;em&gt;tense&lt;/em&gt;) state, and this is a low affinity state. The binding of an oxygen molecule to one of the haem groups in one of the globin subunits of the tetramer increases the affinity, so that subsequent binding of oxygen becomes easier. The details of how this happens are still debated, but I think what I have said so far is accepted by everyone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is an equation to represent the binding of the first oxygen molecule to the haemoglobin tetramer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;O&lt;sub&gt;2&lt;/sub&gt; + [Hb]&lt;sub&gt;4&lt;/sub&gt; &amp;lt;--&gt; [Hb&lt;sub&gt;4&lt;/sub&gt;]O&lt;sub&gt;2&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If deoxygenated Hb has a low affinity for oxygen then that equilibrium must lie to the left hand side - in other words the right to left reaction (release) is faster than the right to left reaction (binding). This is not consistent with the idea that haemoglobin hangs on to its last oxygen.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The heart, which is the first organ in the blood cycle after the lungs uses a lot of oxygen - if hemoglobin were not cooperative, it might take all the oxygen from hemoglobin just after the beat when it uses oxygen when in distress, creating a block of hemoglobin which is completely without bound oxygen.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is based on an erroneous view of the circulation - it implies that all of the blood passes through the coronary artery before getting to the rest of the body. Oxygenated blood leaves the heart via the aorta. Although it is true that the first branch off the aorta is the coronary artery, most of the blood doesn't enter this branch, but proceeds into the remainder of the circulation. In this sense the coronary circulation (by which I mean coronary artery&gt;coronary veins - the heart's own blood supply) is in parallel with the rest of the circulatory system, not in series with it. At rest, just 5% of the heart's output goes into the coronary circulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to this review, &lt;a href=&quot;http://physrev.physiology.org/content/88/3/1009.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Regulation of Coronary Blood Flow During Exercise&lt;/a&gt;, (I am simplifying a lot here, but this statement does appear in the review and is not taken out of context): &quot;Increased myocardial oxygen demands during exercise are met principally by augmenting coronary blood flow.&quot; At rest the heart is already extracting most of the oxygen from its blood supply (see &lt;a href=&quot;http://www.columbia.edu/~kj3/Chapter5.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for some interesting data) so again there is no question of the heart extracting much more - it simply needs more blood, and of course the increased heart rate will contribute to this. There is also scope for directing a greater proportion of heart output through the coronary circulation, but I have been unable to find any quantitative statements about that. Interestingly, if you take a look at the data in the 1st table of the data &lt;a href=&quot;http://www.columbia.edu/~kj3/Chapter5.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; you will see that, at rest, 22% of the heart's output goes into the renal circulation, but that much less oxygen is extracted from that blood (about one ninth of how much is extracted from the blood going through the cardiac circulation). This represents a source of potential increased blood to be diverted to the heart at the expense of a reduction in renal filtration.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Also - Hemoglobin is pretty clearly an evolutionary adaptation where four myoglobins came together to form a cooperative oxygen binder, so at one time probably myoglobin was the oxygen carrier. There are some primitive animals which have no distinct hemoglobin, just myoglobin like carriers.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I agree it is clear that haemoglobin and myoglobin evolved from a monomeric myoglobin-like ancestor, and that the appearance of a tetrameric molecule created the potential for co-operative oxygen binding. I am not as convinced by the rest of the sentence. I think we have to agree first on what we mean by an oxygen carrier. What &lt;strong&gt;I&lt;/strong&gt; mean is a protein that is a component of a circulatory system. I know of no evidence that a myoglobin like molecule could perform this function. This arises directly from the shape of a simple binding curve (a rectangular hyperbola). For the protein to be saturable at atmospheric oxygen concentrations it has to have a certain K&lt;sub&gt;d&lt;/sub&gt;, and this precludes significant release of oxygen at physiologically useful concentrations. You either have a protein which can unload effectively but will not ever become saturated with oxygen, or you have a molecule that is able to become saturated but cannot ever unload except at every low oxygen concentrations. That is the remarkable thing about haemoglobin - the appearance of cooperative binding allowed for a more switch-like interconversion between a high affinity state, for loading up, and a low-affinity state, for unloading.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, if you wish to include intracellular oxygen transport in your definition of &quot;carrier&quot; then we enter a whole other debate about the role of myoglobin, but I have gone on for far too long already, so I'll stop there.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-01-27T00:22:42.333" LastActivityDate="2013-01-27T00:22:42.333" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="6896" PostTypeId="1" AcceptedAnswerId="6897" CreationDate="2013-01-22T15:08:36.557" Score="2" ViewCount="1315" Body="&lt;p&gt;Assuming a 1% Agarose gel with TAE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Follow up questions:  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Is there a way to stain for it? &lt;/li&gt;&#xA;&lt;li&gt;Could the polymerase be captured and reused?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="96" LastActivityDate="2013-02-24T19:33:38.307" Title="Where does Taq polymerase migrate during electrophoresis?" Tags="&lt;gel-electrophoresis&gt;&lt;polymerase&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6897" PostTypeId="2" ParentId="6896" CreationDate="2013-01-22T15:28:19.750" Score="7" Body="&lt;p&gt;Unlike in an SDS-PAGE, where the SDS adds negative charges to all proteins, in a standard agarose gel for nucleic acids all proteins should move according to their own charge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can get a rough idea in which direction Taq would move by getting the amino acid sequence and calculating the isoelectric point at the pH you are running your get at. It might be that the protein isn't even negatively charged at this pH, then it would move in the opposite direction of the DNA out of the gel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An exact prediction is rather hard, as it depends on the shape and size of the protein, the pore size in the agarose gel and the exact charge. It is not as simple as for DNA. You would have to just try it out to get an accurate value.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can use any common method of staining proteins like Coomassie.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think reusing the Taq is very unrealistic. It is still pretty stable at higher temperatures, so it will probably survive the temperatures the gel is running at. I would guess that you lose so much during PCR, gel and purification that it would not be worth the effort. And you would need to purify it extremely well, unless you want to amplify the same DNA in all your future PCR reactions. Any DNA contamination left from your gel might interfere with your later reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you require a very large amount of Taq and want to cut costs, I'd rather try and produce and purify the enzyme yourself. That should save you a lot of money if you really use a lot of it, but it is likely not worth it on a small scale.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2013-02-24T19:33:38.307" LastActivityDate="2013-02-24T19:33:38.307" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6898" PostTypeId="2" ParentId="6858" CreationDate="2013-01-22T16:57:45.757" Score="11" Body="&lt;p&gt;For question 1 it's just a biochemical response from thermoreceptor nerves in the skin, temperatures that are likely to cause lasting damage from prolonged exposure cause a neurological response - in this case it's pain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In address to question 2 it is most likely down to the physiological response of vasoconstriction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the body is cold the body undergoes constriction of the blood vessels in the extremities to preserve core temperature where it is more essential for the proper functioning of vital organs. By constricting blood flow to the extremities (in this case the hands) there is less volume of blood present, because of this nerves present in the hand are closer to the surface and thus more sensitive to pain.&lt;/p&gt;&#xA;" OwnerUserId="1763" LastActivityDate="2013-01-22T16:57:45.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6899" PostTypeId="1" AcceptedAnswerId="6903" CreationDate="2013-01-22T17:17:37.917" Score="5" ViewCount="166" Body="&lt;p&gt;I am trying to find information on Prostaglandin F2-alpha, specificaly production in men. Could somebody explain how this prostaglandin is produced? What types of cells are producing it, production signaling? Any books on this subject?&lt;/p&gt;&#xA;" OwnerUserId="2969" LastActivityDate="2013-02-08T16:38:53.287" Title="Prostaglandin F2-alpha production in men" Tags="&lt;endocrinology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6900" PostTypeId="1" CreationDate="2013-01-22T17:34:03.437" Score="8" ViewCount="1665" Body="&lt;p&gt;This question may seem funny, but I think biology must have good answers.&#xA;I think no more explanation is needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I really thought about this and searched for an answer, but there is nothing yet.&#xA;If you know some thing about or have some thing which may lead to good answer(s) please express.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, do animals portray the same behavior in such situations?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="2989" LastEditDate="2013-01-27T13:05:30.827" LastActivityDate="2015-07-15T15:52:54.767" Title="Why people like to see pornographic scenes, but do not feel the same about eating scenes?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;behaviour&gt;" AnswerCount="4" CommentCount="8" FavoriteCount="2" ClosedDate="2015-07-15T18:18:26.787" ContentLicense="CC BY-SA 3.0" />
  <row Id="6901" PostTypeId="2" ParentId="6899" CreationDate="2013-01-22T18:39:38.057" Score="1" Body="&lt;p&gt;PubChem is a good resource for finding out more about compounds of pharmaceutical interest:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5280363&quot; rel=&quot;nofollow&quot;&gt;http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5280363&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="476" LastActivityDate="2013-01-22T18:39:38.057" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6903" PostTypeId="2" ParentId="6899" CreationDate="2013-01-22T19:23:58.333" Score="2" Body="&lt;p&gt;As I know:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the most important chemical mediators are prostaglandins that in vivo act on different cell receptors and have different effects on the body. Prostaglandins are twenty-carbon lipid molecules and structurally similar to cholesterol. Prostaglandins have different types, such as F2, E2 alpha, PGI2, and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A phospholipase enzyme converts phospholipids of cell membranes into arachidonic acid. The arachidonic acid within the cyclooxygenase enzyme or Cox (both type 1 and 2) can be converted to prostaglandins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PGF2alpha has functions in uterus contraction and bronchoconstriction, so I think both uterus and lung cells produce it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have no special information about production of PGF2alpha in men.&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="1320" LastEditDate="2013-02-08T16:38:53.287" LastActivityDate="2013-02-08T16:38:53.287" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6904" PostTypeId="2" ParentId="6858" CreationDate="2013-01-22T19:40:20.913" Score="3" Body="&lt;p&gt;It doesn't matter if its hand or any other human body organ, cold would hurt, the reason being that we humans being warm blooded animal require an optimal temperature-pressure balance to be maintained for our nervous system to work in its natural order.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when we have, in your case, cold hands its like a thermal shock to our hand as the above mentioned functional optimality is hampered, and just similar to a hot ceramic cracking due to cold water poured on it, our hand(would not crack, however might in extreme cases) reacts to  this with the sensation termed as Pain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a common answer to your questions, cold is directly proportional to pain being felt during our daily engagements(like holding a bag).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pressure plays a vital role in this too as when your hand is cold the pressure exerted to the epidermis is at a reduced rate, which is another reason for the same.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence commonly my conclusion would be the Temperature-Pressure Factor.&lt;/p&gt;&#xA;" OwnerUserId="2971" LastActivityDate="2013-01-22T19:40:20.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6905" PostTypeId="1" CreationDate="2013-01-22T20:29:59.700" Score="3" ViewCount="1601" Body="&lt;p&gt;Why do &lt;strong&gt;Marine&lt;/strong&gt; animals have &lt;strong&gt;fins&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="2973" LastEditorUserId="806" LastEditDate="2013-01-22T21:19:46.947" LastActivityDate="2017-02-22T23:13:42.523" Title="Why do marine animals have fins?" Tags="&lt;marine-biology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="6906" PostTypeId="2" ParentId="6892" CreationDate="2013-01-22T22:26:26.390" Score="2" Body="&lt;p&gt;SYBR green is designed to be &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20403457&quot; rel=&quot;nofollow&quot;&gt;much less carcinogenic than ethidium bromide (EtBr)&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All these gel dyes work by intercalating themselves into the DNA stack between the bases specifically which has a great potential for causing mutations and messing with the workings of the nucleus.  My remembrance is that the SYBR and GelGreen/Red etc dyes are large and relatively hydrophilic and can't find their way into the nucleus, greatly reducing their toxicity.  They also do not transfer energy to the DNA itself due to their structure and so also cause less DNA damage when being viewed on a transilluminator. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-01-22T22:26:26.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6907" PostTypeId="2" ParentId="6865" CreationDate="2013-01-22T23:37:15.773" Score="5" Body="&lt;p&gt;This refutation contains a fundamental error.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first living organism need not be anything complex, it just has to be&lt;br&gt;a molecule that creates copies of itself which inherit its characteristics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From there its population grows exponentially and evolution starts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore there is no need for any of those items he is listing as requirements for the first life.&lt;/p&gt;&#xA;" OwnerUserId="542" LastEditorUserId="542" LastEditDate="2014-05-29T12:16:09.117" LastActivityDate="2014-05-29T12:16:09.117" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="6908" PostTypeId="1" AcceptedAnswerId="6911" CreationDate="2013-01-23T00:33:50.990" Score="5" ViewCount="93" Body="&lt;p&gt;Is there any evidence showing that copy number variation changes over time? I'm wanting to model interactions in expression level as a dynamic bayesian network, but an assumption my approach will need to make is that it is static.&lt;/p&gt;&#xA;" OwnerUserId="1855" LastActivityDate="2013-01-23T13:48:09.327" Title="Is copy number variation dynamic?" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;&lt;copy-number-variation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6909" PostTypeId="1" AcceptedAnswerId="19201" CreationDate="2013-01-23T00:48:13.523" Score="6" ViewCount="393" Body="&lt;p&gt;According to one theory, ice cream headaches are caused by an increase in blood volume of the anterior cerebral artery:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Another theory into the cause of ice-cream headaches is explained by increased blood flow to the brain through the anterior cerebral artery, which supplies oxygenated blood to most medial portions of the frontal lobes and superior medial parietal lobes. This increase in blood volume and resulting increase in size in this artery is thought to bring on the pain associated with an ice-cream headache.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ice-cream_headache#Anterior_cerebral_artery_theory&quot; rel=&quot;noreferrer&quot;&gt;(from Wikipedia)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Does repeatedly experiencing this phenomenon put someone at higher risk for some sort of cerebral vascular accident, or is it not any more harmful than a small increase in blood pressure that one might experience under exertion, despite the painful nature of the headache?&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-06-19T15:02:50.633" Title="Long term effects of &quot;brain freeze&quot; on the cerebral vasculature" Tags="&lt;neuroanatomy&gt;&lt;neurology&gt;&lt;temperature&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6910" PostTypeId="2" ParentId="5596" CreationDate="2013-01-23T13:04:31.847" Score="3" Body="&lt;p&gt;Many organisms including plants, bacteria, insects, fishes and even mammals have been GMed. Most of them have experimental purposes, but GM crops have been released for commercial purposes. Maybe the most amazing between them is triticale, which is a hybrid of wheat (Triticum) and rye (Secale). Triticale, BT Potato, BT Tomato, BT Maize (I am not sure), BT and Golden Rice and lots of other GM crops have been released in almost all lands in world. Almost all these GM crops suppose to have higher yield and higher resistance to pathogens and physiological problems and as a result they have higher chance of surviving (specially in natural environment). &#xA;A &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11734853&quot; rel=&quot;nofollow&quot;&gt;study&lt;/a&gt; published in Nature in 2001 reported that Bt-containing maize genes were found in maize in its center of origin, Oaxaca, Mexico. In 2002 Nature &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11935145&quot; rel=&quot;nofollow&quot;&gt;concluded&lt;/a&gt; that the evidence available is not sufficient to justify the publication of the original paper.  A significant controversy happened over &lt;a href=&quot;http://www.pbs.org/now/science/genenature.html&quot; rel=&quot;nofollow&quot;&gt;the paper&lt;/a&gt; and &lt;a href=&quot;http://www.organicconsumers.org/articles/article_17133.cfm&quot; rel=&quot;nofollow&quot;&gt;Nature's unprecedented notice&lt;/a&gt;. Also there are safety concerns about modified gene transfer during pollination in GM Rice(s). Even some scientists think that that this would not be a problem because rice is a self-pollinating plant. Any way GM crops can become abundant and release their genes by themselves or through gene transfer to other organisms.&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="3632" LastEditDate="2013-01-25T17:00:28.377" LastActivityDate="2013-01-25T17:00:28.377" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="6911" PostTypeId="2" ParentId="6908" CreationDate="2013-01-23T13:48:09.327" Score="7" Body="&lt;p&gt;Your question could be phrased more specifically to avoid ambiguity, but rephrasing it the way that I suspect you mean it, (&quot;Is there any evidence showing that [the rate of] copy number variation changes over time?&quot;), then yes, there is indeed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rate depends on many factors including which mechanism and which organism and which region of the organism's genome and as @Michael wrote, also what scale (et. al.) is under consideration too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So your assumption that the rate is static should probably be stated explicitly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nrg2593&quot;&gt;Nature Reviews Genetics 10, 551-564 (August 2009) | doi:10.1038/nrg2593&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1756" LastActivityDate="2013-01-23T13:48:09.327" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6912" PostTypeId="2" ParentId="6861" CreationDate="2013-01-23T14:21:54.040" Score="8" Body="&lt;p&gt;What you are possibly thinking of is large versions of the &lt;a href=&quot;http://www.chem.duke.edu/~jds/cruise_chem/Exobiology/miller.html&quot; rel=&quot;nofollow&quot;&gt;Miller Urey Experiment&lt;/a&gt; where a mixture of reducing gasses carbon dioxide, ammonia, nitrogen and the like are subjected to electrical arcs in a closed flask reaction, resulting in some biological molecules being produced.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Opinions have changed - Miller Urey did get the atmosphere wrong and so their finding of amino acids is not necessarily, but variations of this experiment continue to be done, with different conditions in the reaction vessel which reflect typical or even unusual conditions.  I've found some nice &lt;a href=&quot;http://cshperspectives.cshlp.org/site/misc/the_origins_of_life.xhtml&quot; rel=&quot;nofollow&quot;&gt;collections&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828274/&quot; rel=&quot;nofollow&quot;&gt;reviews&lt;/a&gt;. There continues to be an enthusiastic effort even today.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking over several of these overviews, it's clear that many different conditions are being tried - reactions on mineral surfaces, examining chemicals on meteorites, near volcanic vents, different kinds of radiation.  What I don't see is anyone going to a huge tank.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that this might not have been tried (perhaps someone else will find a counter example), but if it were not me, I would probably not try longer experiments either. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's some good reasons for this, if true.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly all the published descendants of the Miller experiment have produced biologically relevant compounds after a few days.  Extending the experiment a few orders of magnitude may not prove anything new.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, the longer a reaction is run the more likely the sealed containers and heaters and other apparatus has to fail, causing you to restart or include contaminants that would ruin it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thirdly, one is not going to run an experiment that will ever come close to reproducing the time spans or volumes over which life emerged on earth - that was perhaps a few hundred million years over the area of the planet.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's not to say you won't find out something new - an extra week could produce a new set of compounds or even a replicating system - we don't know if we haven't done it, but the nature of science is that you have a little time and money for a project like this and you would like to prove feasibility  - 'it could have happened this way'.  By selecting the conditions and doing a series of modest experiments which allows some to fail so that you can find something new.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would say the observation of other planets and analysis of meteorites are getting closer to your idea - they are huge systems and been going for billions of years.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Titan_%28moon%29#Prebiotic_conditions_and_search_for_life&quot; rel=&quot;nofollow&quot;&gt;Titan is especially promising&lt;/a&gt;.  They just aren't the same conditions as Earth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In brief, nothing is both affordable and perfect in proto-biotic research. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-01-30T03:08:35.167" LastActivityDate="2013-01-30T03:08:35.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6913" PostTypeId="2" ParentId="1188" CreationDate="2013-01-23T14:36:23.763" Score="2" Body="&lt;p&gt;Astonishingly, if they are male you can take a pretty good punt at working out their surname and narrowing down exactly who they are. There was a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23329047&quot; rel=&quot;nofollow&quot;&gt;recent paper&lt;/a&gt; on doing this with anonymous genome data, discussed in a blog post &lt;a href=&quot;http://sickpapes.tumblr.com/day/2013/01/22&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; if you want a more accessible account.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-01-23T14:36:23.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6914" PostTypeId="2" ParentId="2874" CreationDate="2013-01-23T16:08:39.953" Score="15" Body="&lt;p&gt;A now deleted answer put this down to an argument based on amino-acid coding in codons but, as pointed out by Konrad Rudolph in a comment, arguments based on codons cannot be correct because the 4-base system likely pre-dates the evolution of protein translation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why four?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suggest that it comes from a combination of factors which make it a 'just right' fit for RNA-based replicators: more would be bad, and less would also be bad. The four bases are able to copy with high reliability because two features combine to exclude mis-pairings: there are two size classes - meaning any purine-purine or pyrimidine-pyrimidine pairing results in incorrect separation between the strands, excluding A-G and C-U bonds; and there are two classes based on number of OH-bonds - which limits the potential for A-C and G-U bonds. More bases must, inevitably, weaken the strength of these exclusionary approaches and increase the number of mispairings. RNA world replicators will have lacked the sophisticated repair and error checking mechanisms of modern lifeforms so this increase in mispairings would likely not be corrected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, a two base system would be even more capable of reducing errors. I suggest that the advantage of the four base system is that it allows for much more complex 3-dimensional structure to form in RNA and thus enabled a broader range of catalytic capabilities. I've only considered even-numbers because only even numbered systems could use the Watson-Crick style of base pairing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd also suggesting reading Eörs Szathmáry's &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14631359&quot; rel=&quot;noreferrer&quot;&gt;2003 paper&lt;/a&gt; on this very question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Addendum&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A group in California has just published a paper in which they successfully added a third base pair stably into DNA. I think this could shed some light on why four - you can read about it &lt;a href=&quot;http://loonylabs.org/2014/05/08/semi-synthetic-organism/&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; or get the full paper &lt;a href=&quot;http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13314.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; (Nature, so pay walled).&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="2938" LastEditDate="2014-05-10T11:09:37.197" LastActivityDate="2014-05-10T11:09:37.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6915" PostTypeId="1" AcceptedAnswerId="30657" CreationDate="2013-01-23T18:57:43.283" Score="40" ViewCount="53769" Body="&lt;p&gt;Obviously, the temperature of water does not affect its chemical composition. At least not in the ranges we are likely to drink it in. Yet it is clearly far more pleasant and refreshing to drink cool water than it is to drink tepid or warm water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there actually any difference to the organism or is this just a matter of perception? Is cool water somehow more efficient at rehydrating a cell? In any case, surely by the time water reaches individual cells it will have warmed up to body temperature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what, if any, is the difference between drinking cool and warm water in terms of its effect on the human (or other animal) body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Extra bonus for explaining why the &lt;em&gt;taste&lt;/em&gt; of water changes when it is cold.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-01-24T18:39:03.983" LastActivityDate="2016-03-19T23:34:57.027" Title="Why is cold water more refreshing than warm water?" Tags="&lt;human-biology&gt;&lt;hydration&gt;" AnswerCount="5" CommentCount="9" FavoriteCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="6916" PostTypeId="1" AcceptedAnswerId="7806" CreationDate="2013-01-23T20:26:24.830" Score="5" ViewCount="178" Body="&lt;p&gt;Can in the case of multiple sclerosis (MS),&#xA;a too high osmotic pressure in the nerve, &#xA;lead to a high intracellular concentration of potassium,&#xA;and also lead to 'pumping up' of nerve cells,&#xA;which then due to the strongly increased internal pressure, &#xA;the insulating myelin sheath can be pressed broken,&#xA;resulting in a lesion, &#xA;or a strong reduced transmission of stimuli ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If that were to happen, &#xA;one can expect in cerebrospinal fluid,&#xA;cytokines, which are normally also a component of the nerve cell contents, &#xA;and that it wrongly can be interpreted,&#xA;as inflammatory reaction to a potential autoimmune disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there research of this ?&lt;/p&gt;&#xA;" OwnerUserId="2975" LastActivityDate="2013-04-08T07:52:28.863" Title="Can in the case of multiple sclerosis (MS), a too high osmotic pressure in the nerve, lead to a high intracellular concentration of potassium?" Tags="&lt;cell-biology&gt;&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6918" PostTypeId="2" ParentId="6858" CreationDate="2013-01-23T21:59:04.843" Score="2" Body="&lt;p&gt;It has to do with the way that body parts are more rigid when it is cold. This makes them less flexible and more prone to superficial injury....even without frost nip setting in. In the event that actual frost nip set in, this would be even more sensitive, as you have tiny crystals beginning to form in your cells, like little shards of glass......and, smacking them, rubbing them, or scraping them would be like SMACKING, RUBBING, or SCRAPING your neutral temperature hand against shards of glass. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When it is cold, your nerves are very sensitive to the temperature, as it isn’t numb yet, and still....blood flow is slowed down tremendously. In fact, your body has begun &quot;vaso-constricting&quot; all blood flow away from your extremities, resulting in nerves being pressed upon by the less supple skin and vascular tissues.&lt;/p&gt;&#xA;" OwnerUserId="2977" LastActivityDate="2013-01-23T21:59:04.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6919" PostTypeId="1" CreationDate="2013-01-24T02:45:00.350" Score="5" ViewCount="1061" Body="&lt;p&gt;A Finnish firm Valkee sells light-ear-plugs against thing such as jetlag. I asked a researcher in Aalto university how do they really work and he responded &lt;code&gt;&quot;why would evolution have lead to photoreceptive cells in ears?&quot;&lt;/code&gt; -No direct answer. I asked a well-respected professor who said she did not know this area well enough. Now Valkee guided me to the publications such as &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/13946401&quot;&gt;Penetration of light into the brain of mammals (1963)&lt;/a&gt; and &lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00614615&quot;&gt;Spectral characteristics of visible radiation penetrating into the brain and stimulating extraretinal photoreceptors (1979)&lt;/a&gt;. Related to the first one, I found &lt;a href=&quot;https://ckm.osu.edu/sitetool/sites/neuroscience/documents/RandyPapers/1981/Nelson_1981_EOP.pdf&quot;&gt;this&lt;/a&gt; (1980) from the references:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;&quot;It  is  now  fully  accepted that  the  perception  of  light  by  &lt;strong&gt;extraocular  photoreceptors  plays  a  significant  role  in  synchronizing  endogenous  rhythms  with  the  environmental  light-dark cycle  in  non-mammalian  vertebrates&lt;/strong&gt;&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Things such as certain birds and lizards apparently have extraretinal photoreception aka photosensitive cells not in eyes (this is how I understand it). Now the publication continues&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;&quot;The  limited  number  of mammalian  species  tested  to &#xA;  date  and  the  near  exclusive  reliance  on  nocturnal  animals  leaves  &lt;strong&gt;open  the  possibility  of  extraocular  photoreception  in  some  adult  mammals&lt;/strong&gt;  (Rusak  &amp;amp;  Zucker, 1975;  1979).&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now according to a skeptical researcher in my university, there is only one paper supporting photosensitivity in mammals' brains: Wade et al (PNAS 85 (1988) 9322-9326 with rats. My professor in system sciences was extremely scornful when I even asked this question on a seminar course about brain -- he did not specify his reasons and pretty much labelled my thinking as inexperience. Now I am not sure whether researchers are even speaking about the same issues: too large disparities between opposing and proposing teams for the assumed effect apparently through the mechanism called &lt;em&gt;&quot;extraretinal photoreception in mammals&quot;&lt;/em&gt;. I am very curious. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Helper questions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;&lt;p&gt;What are the mechanisms by which a led in ear would affect a mammal such as a homo sapiens? You don't get D vitamin because of no UV light. You get very-very light heat because of tosslink connection. So it cannot sense the heat as antidote against things such as SAD and jetlag. Other mechanism?&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Is the &lt;em&gt;&quot;extraretinal photoreception in mammals&quot;&lt;/em&gt; just placebo or does there exist scientific proofs for it particularly with large mammals about the size of homo sapiens? &lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Why would evolution have lead to extraretinal photoreception in mammals?&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Do the terms &lt;em&gt;&quot;extraretinal photoreception&quot;&lt;/em&gt; and &lt;em&gt;&quot;non-eye photosensitive cells&quot;&lt;/em&gt; mean the same thing? Other terms for the same thing?&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Now eyes are developed very late in cell-division with mammals. Do born-blind mammals and later-blinded mammals experience extraretinal photoreception differently? If led-light (non-UV light) has an effect on large mammals, then I expect this may be possible to see by analyzing results of mammals with different-developed visual-cortexes. &lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Does this statement &lt;em&gt;&quot;Light penetrates deep brain areas, eye's receptors have developed from receptors of old CNS.&quot;&lt;/em&gt; by &lt;a href=&quot;https://twitter.com/HumanCharger/status/287158515011842049&quot;&gt;Humancharger&lt;/a&gt; justify the extraretinal photorecetpion?&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;P.s. I presupposed in this question that extraretinal photoreception is the effective mechanism by which light-in-ear would affect a mammal. It is also possible that there are other mechanisms -- I am not an expert with the terminology here, anatomically and physiologically challenging.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1705" LastEditorUserId="1705" LastEditDate="2013-01-24T03:00:56.463" LastActivityDate="2013-02-02T01:20:00.497" Title="Extraretinal photoreception in mammals?" Tags="&lt;evolution&gt;&lt;physiology&gt;&lt;human-anatomy&gt;&lt;neuroanatomy&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ClosedDate="2013-02-06T11:36:14.530" ContentLicense="CC BY-SA 3.0" />
  <row Id="6920" PostTypeId="2" ParentId="6919" CreationDate="2013-01-24T05:25:04.830" Score="3" Body="&lt;p&gt;Its pretty well established that there are photoreceptors in cells besides the cones and rods in the retina of the eye.  Humans and most animals have four light receptor genes known (so far).  In addition to Rhodopsin - there are the &lt;a href=&quot;http://en.wikipedia.org/wiki/Opsin&quot; rel=&quot;nofollow noreferrer&quot;&gt;short, med and long wavelength opsin genes&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While they are mostly expressed in the retina of the eye, they can be found in many other tissues as well. The first image from &lt;a href=&quot;http://www.geneatlas.org/gene/main.jsp&quot; rel=&quot;nofollow noreferrer&quot;&gt;GeneAtlas&lt;/a&gt; below shows the relative amount of RNA found for short wavelength opsin in a variety of tissues - its expressed in immune and nerve cells ( cyan and forest green respectively) relatively well too.   This might imply that neurons are light reactive.  Compare that to that of medium wavelength opsin, which is primarily much more common in the retina.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Q4Yx6.png&quot; alt=&quot;blue light opsin&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/lftqc.png&quot; alt=&quot;med wavelength opsin&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not a psychosomatic effect.  Light receptors in the skin are &lt;a href=&quot;http://www.ncpamd.com/seasonal.htm#Theories%20about%20how%20light%20affects%20mood%20and%20sleep&quot; rel=&quot;nofollow noreferrer&quot;&gt;known to help with seasonal affective disorder&lt;/a&gt; - shine a bright or blue light behind your knees.  These receptors are not connected to optical nerves, and so you don't get any image from them, but the information can affect your biochemistry anyway.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea of unconscious receptor inputs from other parts of the body probably applies to many sorts of receptors.  This last year there has been a great deal of interest in taste receptors which are expressed in the gut.  &lt;a href=&quot;http://www.nature.com/nature/journal/v486/n7403_supp/full/486S7a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;They can taste sweetness and other flavors a second time and register the gustatory response in the brain&lt;/a&gt;.  Its not a conscious input, but it registers in the brain in MRI.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why would evolution do this?  It seems to me that this is a new way of looking at the individual life of a cell and makes a good deal of sense.  If every cell has all the genes' DNA why wouldn't a little bit of receptor expression be found in any cell which could use the information?  The conscious processes of the brain probably only take in a small fraction of the information that is sent in and there maybe hundreds of other such senses from various parts of the body to integrate, only a fraction of which we are aware of.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, there are probably lots of cases where receptor signals are only used locally by cells that are sensing their local environment.  It really doesn't make sense that the individual cells must blind themselves.  Individual bacteria and fungi have scores of receptors.  It makes sense that cells that are part of an organism would have as many or more senses as well.   &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-01-24T05:31:55.510" LastActivityDate="2013-01-24T05:31:55.510" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6921" PostTypeId="2" ParentId="2874" CreationDate="2013-01-24T08:23:37.773" Score="1" Body="&lt;p&gt;The 4-bases DNA system with A-T bonds and C-G bonds is the one that evolved to be used by most living creatures on Earth, as mentioned in other answers, because it can encode a triplet table of bases for all aminoacids used, allowing for some aminoacids to have more than one triplet code. There are though slight variations of the system: even though the A-T and C-G bonds don't change, the nucleotides can be modified to mark areas of the genome in what is part of the epigenetic code. The most common modification is adding methyl and 5-hydroxymethyl molecules to the bases, although more modifications are still being discovered.&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="658" LastEditDate="2013-01-24T09:19:46.047" LastActivityDate="2013-01-24T09:19:46.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6922" PostTypeId="2" ParentId="6915" CreationDate="2013-01-24T10:48:37.367" Score="7" Body="&lt;p&gt;I think it's because we are more often thirsty in a warm/hot/dry environment.&lt;br&gt;&#xA;Since almost all of us have a house with a household furnace creating that warm/dry  environment.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus cold water would be more refreshing since it also cools us off a bit.&lt;br&gt;&#xA;I doubt that people that are on a north-pole expedition would still prefer that cold drink over a warm one. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This link contains a lot of information on this topic:&lt;br&gt;&#xA;&lt;a href=&quot;http://chestofbooks.com/health/nutrition/Dietetics-4/Temperature-And-Digestion.html&quot; rel=&quot;nofollow&quot;&gt;http://chestofbooks.com/health/nutrition/Dietetics-4/Temperature-And-Digestion.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1897" LastEditorUserId="5239" LastEditorDisplayName="user1897" LastEditDate="2013-12-28T01:00:39.413" LastActivityDate="2013-12-28T01:00:39.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6923" PostTypeId="1" AcceptedAnswerId="6924" CreationDate="2013-01-24T15:40:35.090" Score="5" ViewCount="128" Body="&lt;p&gt;I saw that cigarettes-smokers (more than 3 cigarettes per day) often have the skin of the face which is a little bit spoiled.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any scientific proof that cigarette smoke (or the nicotine inside it) is a damaging fator for face skin?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or it is just due to the skin-smoke interaction casued by the smoke that the person breaths out from the mouth?&lt;/p&gt;&#xA;" OwnerUserId="2982" LastEditorUserId="69" LastEditDate="2013-01-24T17:19:28.580" LastActivityDate="2013-01-24T19:06:46.230" Title="Is there a scientific proof that smoking spoils face skin?" Tags="&lt;skin&gt;&lt;smoking&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6924" PostTypeId="2" ParentId="6923" CreationDate="2013-01-24T19:06:46.230" Score="3" Body="&lt;p&gt;This &lt;a href=&quot;http://www.dermnetnz.org/reactions/smoking.html&quot; rel=&quot;nofollow&quot;&gt;page is pretty complete with examples and references&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary a lot of the evidence is empirical - you look at smokers and the quality of their skin and compare to non-smokers and the differences are statistically significant and reproducible.  It seems as if this is old work, dating from the 1970s. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in many cases these are only observed correlations.  But they are pretty strongly agreed upon by medical people.  Given the fact that we still don't know exactly what causes cancer, I think this is not an unusual level of explanation for medical conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see some theories would include direct effects of the smoke and some indirect effects.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is not certain exactly how smoking causes early ageing of the facial skin. Theories include:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Heat from the cigarette directly burning the skin &lt;/li&gt;&#xA;  &lt;li&gt;Changes in the elastic fibres of the skin &lt;/li&gt;&#xA;  &lt;li&gt;Narrowing of blood vessels (vasoconstriction), which reduces blood supply to the skin and can cause changes in skin elastic fibres and&#xA;  loss of collagen &lt;/li&gt;&#xA;  &lt;li&gt;Reducing Vitamin A levels and moisture of the skin&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-01-24T19:06:46.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6925" PostTypeId="2" ParentId="6905" CreationDate="2013-01-24T20:33:22.367" Score="2" Body="&lt;p&gt;It is more efficient to use fins than feet, hooves, or other similar body parts. It is the same reason that you can swim faster while wearing flippers. Having a larger surface area allows animals to push against more water, so that they have more force when swimming. &lt;a href=&quot;http://cetacea147.tripod.com/images/tursiopsflipper.gif&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a picture of the bones in a dolphin fin. They are extremely similar to the bones in a hand, because dolphins evolved from land animals that had individual fingers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Amphibians like frogs and salamanders have webbed feet, which is a &quot;compromise&quot; between feet and fins. These feet allow them to push against water with more power, since they have webbing instead is separate fingers. It also allows them to grip the ground on land, since their fingers can move independently of each other.&lt;/p&gt;&#xA;" OwnerUserId="1182" LastActivityDate="2013-01-24T20:33:22.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6926" PostTypeId="1" CreationDate="2013-01-24T21:17:03.637" Score="6" ViewCount="254" Body="&lt;p&gt;Nutritional and medical recommendations about cholesterol seem to focus exclusively on hypercholesterolemia, and as such, they provide only a maximum desirable level for LDL and a minimum for HDL. I've found a little bit of information about hypocholesterolemia caused by inadequate cholesterol in the body (due to overuse of statins, malnutrition, or other disorders), but not about cholesterol deficits due to lipoprotein levels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems like it should be theoretically possible to have so much HDL or so little LDL activity that organs don't maintain enough cholesterol to function properly, even if cholesterol synthesis is adequate. Obviously this might or might not ever occur in reality. Is there any research that has found an &lt;em&gt;upper&lt;/em&gt; bound on desirable HDL in humans, or a lower bound on desirable LDL or LDL:HDL ratio?&lt;/p&gt;&#xA;" OwnerUserId="827" LastActivityDate="2013-04-29T21:14:38.650" Title="functional hypocholesterolemia due to very high HDL or low LDL?" Tags="&lt;physiology&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6927" PostTypeId="2" ParentId="2874" CreationDate="2013-01-25T04:28:30.153" Score="11" Body="&lt;p&gt;There is a chemical dimension to this question too.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Base_pair&quot;&gt;Watson-Crick Base pairs&lt;/a&gt; you can see that there isn't a lot of wiggle room:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eMc8u.gif&quot; alt=&quot;Watson Crick Base Pairs&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nucleotide bases have 2 or 3 hydrogen bonds.  It's probably not sterically reasonable to have 4.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That means there are only a limited number of ways the base combinations can be complimentary and also specific as they form the double helix.  Since A-&gt;T and T-&gt;A hydrogen bond patterns take up both donor-receptor combinations there is one possible 2 H-bond pairing.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are 2 ways to configure the three hydrogen bond bases I think, so perhaps six is possible, but I'm guessing that if you expand the base pairing repetoire, one could start to lose specificity.  As it is, if you play with nucleotides enough, you can make non Watson-Crick base pairs and probably lose some of the confidence you have exact 1:1 matches between complimentary base pairings.   &lt;a href=&quot;http://en.wikipedia.org/wiki/Wobble_base_pair&quot;&gt;Wobble Base pairs&lt;/a&gt; in RNA and  &lt;a href=&quot;http://en.wikipedia.org/wiki/Hoogsteen_base_pair&quot;&gt;Hoogsteen Base Pairings&lt;/a&gt; can already be demonstrated to allow triple helixes and non-perfect match RNA helices.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CRMrG.png&quot; alt=&quot;non W-C base pairings&quot;&gt;  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-01-25T17:03:22.730" LastActivityDate="2013-01-25T17:03:22.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6928" PostTypeId="2" ParentId="6891" CreationDate="2013-01-25T19:00:41.880" Score="5" Body="&lt;p&gt;Just wanted to supplement to the other two answers... I was trying to use comments but ran out of space.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;@AlanBoyd s figure tells you a lot - you can see that myoglobin (Mb) has a much higher affinity for oxygen, so it will sit in the muscle and take the oxygen the tissue needs from the hemoglobin (Hb) as the blood flows through the tissue.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what is particularly useful about Hb's cooperativity is that the last oxygen is harder to pull off the Hb tetramer than the first. As a result, Hb will tend to hold onto some oxygen as it flows through the body, retaining some of its oxygen on each Hb molecule until later in the oxygenation cycle.  This keeps the oxygen concentration in the blood consistent.  The heart, which is the first organ in the blood cycle after the lungs uses a lot of oxygen - if hemoglobin were not cooperative, it might take all the oxygen from hemoglobin just after the beat when it uses oxygen when in distress, creating a block of hemoglobin which is completely without bound oxygen.  As this lot of hemoglobin circulates into the capillaries, you could get some parts of the body with no oxygen at all.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also - Hemoglobin is pretty clearly an evolutionary adaptation where four myoglobins came together to form a cooperative oxygen binder, so at one time probably myoglobin was the oxygen carrier.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemoglobin#Analogues_in_non-vertebrate_organisms&quot; rel=&quot;nofollow noreferrer&quot;&gt;There are some primitive animals which have no distinct hemoglobin, just myoglobin like carriers&lt;/a&gt;.  Also some hemoglobins are not tetrameric, but with many subunits, so the cooperativity curves have sometimes been tuned by evolution for different organisms.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yaShZ.jpg&quot; alt=&quot;myoglobin hemoglobin&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure above: &quot;Rendering of Hb tetramer and monomeric Mb. Hb is composed of four subunits, two α-subunits and two β-subunits, each highly homologous to Mb&quot; ( &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022283610000756&quot; rel=&quot;nofollow noreferrer&quot;&gt;from figure in reference&lt;/a&gt; )&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1320" LastEditDate="2013-01-25T19:35:39.953" LastActivityDate="2013-01-25T19:35:39.953" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6929" PostTypeId="1" CreationDate="2013-01-26T01:47:39.067" Score="15" ViewCount="1011" Body="&lt;p&gt;I'm reading a bit on the Fibonacci sequence in nature, be it the golden ratio or the golden spiral forming over and over again in biological structures, and then I came across &lt;a href=&quot;http://www.lhup.edu/~dsimanek/pseudo/fibonacc.htm&quot;&gt;this online article&lt;/a&gt; by Donald E. Simanek, refuting a lot of these observations as merely optimistic 'flim flam'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So which is true? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the Fibonacci sequence have a place in nature or is it all just a case of vigorously looking for anything that resembles a correlation?&lt;/p&gt;&#xA;" OwnerUserId="1763" LastActivityDate="2013-03-06T23:34:15.050" Title="Fibonacci sequence in nature, truth or just wishful thinking?" Tags="&lt;structural-biology&gt;&lt;development&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6930" PostTypeId="2" ParentId="6829" CreationDate="2013-01-26T02:28:50.867" Score="8" Body="&lt;p&gt;Studies have proven somewhat the opposite of what you're asking&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;For example a study from 2004 - &quot;&lt;a href=&quot;https://www.sciencedirect.com/science/article/pii/S1389945704001091&quot;&gt;The impact of extended sleep on daytime alertness, vigilance, and mood&lt;/a&gt;&quot; found that,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Average daily POMS vigor and fatigue scores also improved during the sleep extension period&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And thus concluded&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Extended sleep leads to substantial improvements in daytime alertness, reaction time, and mood.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Whilst an older study from '73 -&quot;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8986.1973.tb00805.x/abstract&quot;&gt;Performance and Mood Following Variations in the Length and Timing of Sleep&lt;/a&gt;&quot; found that,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Neither sleep duration, nor any other sleep parameter consistently correlated with the performance or mood measures.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The study does go on to state however,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Therefore, it seems reasonable to assume that the detrimental effects of acute changes in the length and/or timing of sleep were not directly related to any specific changes in the length or electrophysiological patterns of sleep, but to as yet unknown physiological changes resulting from the disruption of an established circadian rhythm of the sleep and wakefulness.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This perhaps suggests that the question which should be asked should not be why does oversleeping makes us feel tired, but &lt;em&gt;why does the disruption of normal sleeping patterns make us feel tired?&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1763" LastActivityDate="2013-01-26T02:28:50.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6931" PostTypeId="1" CreationDate="2013-01-26T06:57:26.817" Score="13" ViewCount="488" Body="&lt;p&gt;I know that &lt;em&gt;first generation&lt;/em&gt; H1 antagonists, commonly known as antihistamines have anticholinergic effects. Their sedative side effects go away due to tolerance, but as for their anticholinergic side effects well that's something that is unknown to me at least. You might say use &lt;strong&gt;second generation&lt;/strong&gt; H1 antagonists, but for this application the antiemetic effects that are unique to H1 antagonists that cross the BBB (i.e., &lt;strong&gt;first generation&lt;/strong&gt; H1 antagonists) are desired. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="107" LastEditDate="2013-01-27T17:13:26.787" LastActivityDate="2016-01-16T10:12:23.560" Title="Do mammals develop tolerance to anticholinergics?" Tags="&lt;neurotransmitter&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6932" PostTypeId="1" AcceptedAnswerId="7405" CreationDate="2013-01-26T08:01:50.600" Score="12" ViewCount="410" Body="&lt;p&gt;I'm familiar with the scenario of Rh- mother with Rh+ fetus having complications (more so after her first child), but that's not what I'm curious about. I want to know mechanistically why a pregnant woman's body does not display a reaction similar to what we see with rejection from a mismatched organ transplant. On the most basic level, I feel as though the fetus should be recognized as &quot;nonself&quot; due to paternal genetic contribution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I feel as though if this mechanism could be understood, it could be harnessed for other situations (e.g., organ transplants). &lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2013-03-02T01:44:41.910" Title="What prevents a pregnant woman's immune system from recognizing her fetus as nonself (and attacking)?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;development&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6933" PostTypeId="1" CreationDate="2013-01-26T11:55:48.270" Score="12" ViewCount="64364" Body="&lt;p&gt;DNA is made of 4 unique nucleotides. When coding for a protein, a sequence of 3 nucleotides is used to code for each amino acid. Why are codons 3 nucleotides in length?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A related question can be found here: &lt;a href=&quot;https://biology.stackexchange.com/questions/2874/why-are-there-exactly-four-nucleobases-in-dna&quot;&gt;why-are-there-exactly-four-nucleobases-in-dna&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2017-08-09T12:50:21.907" Title="Why are 3 nucleotides used as codons for amino-acid mapping in DNA?" Tags="&lt;dna&gt;&lt;proteins&gt;&lt;amino-acids&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6934" PostTypeId="2" ParentId="6933" CreationDate="2013-01-26T11:55:48.270" Score="10" Body="&lt;h3&gt;The central dogma of molecular biology: &lt;em&gt;DNA makes RNA makes Protein&lt;/em&gt;&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;DNA is a reference for proteins*, which are the functional molecules in cells. These are comprised of 20 unique amino acids, and each is coded for by a stretch of DNA known as a codon. Codons are always 3 base-pairs (nucleotides) in length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA is made of 4 unique nucleotides; (&lt;strong&gt;A&lt;/strong&gt;)denine, (&lt;strong&gt;G&lt;/strong&gt;)uanine, (&lt;strong&gt;C&lt;/strong&gt;)ytosine and (&lt;strong&gt;T&lt;/strong&gt;)hymine. This means that there are 64 unique codons that can be made with these 4 bases (4*4*4).&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Theory One - evolvability&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;If codons were only 2 bases in length then the variety of codons that could be created would be less (only 16 unique sequences if there are still 4 nucleotides). More unique nucleotides would be required to get enough unique sequences to code for the 20 amino acids (as well as the STOP codons). For instance, to get 64 unique sequences using a 2-bases-per-codon system there would need to be 8 unique nucleotides. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We cannot ever 'know' what happened in evolutionary terms, but it seems likely that the 3-base (nucleotide) codon system would have arisen after a period of a 2-base system, as the biological systems became more complex. This would have allowed a lot more variation in the amino-acids used, and thus more &quot;evolvability&quot;, which would have been very advantageous to early organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However as the 4-unique-nucleotide/3-codon system is ubiquitous to all life we have discovered on earth, it seems likely that, back at the start of DNA (in fact probably RNA), this was the system that worked, or at least, this is the one that survived (although as Kevin rightly points out, we don't know whether there ever were any other systems). Variations may have arisen over the years, but it is this 1 system that has prevailed here on Earth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this question for some more interesting info: &lt;a href=&quot;https://biology.stackexchange.com/questions/653/why-20-amino-acids-instead-of-64&quot;&gt;why-20-amino-acids-instead-of-64?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Theory Two - &quot;redundancy&quot; of codons conveys additional information&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;This theory is not mutually exclusive to the one described above. In a recent paper D'Onofrio and Abel [&lt;a href=&quot;http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00140/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;] state that ribosomes pause for different lengths of time at different codons (even if the codon codes for the same amino acid), and that this pausing affects the 3-dimensional structure of the final protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore the nucleotide sequence contains at least two &quot;layers&quot; of information: firstly which amino-acid should be added, and second the specific codon used for that amino acid can impact on the final structure of the protein. This could not be done with fewer nucleotides, but arguably even more control could be exerted with more nucleotides, but perhaps this comes back to my first point that this system evolved such a long time ago that more nucleotides were not necessary for life to &quot;work&quot; and proliferate into everything we see today.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;D'Onofrio and Abel, 2014. &lt;em&gt;Frontiers in Genetics&lt;/em&gt;. &lt;a href=&quot;http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00140/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Redundancy of the genetic code enables translational pausing&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;*only around 1% of our genome is actually protein-coding, and many non-protein-coding RNA products have very important functions, but I won't go into this here. Suffice it to say I am referring to the protein-coding regions of the DNA.&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-01-14T11:49:18.067" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="6935" PostTypeId="2" ParentId="2039" CreationDate="2013-01-26T19:11:37.450" Score="0" Body="&lt;p&gt;I think these answers have all missed the most likely explanation of the multiple bands in the uncut sample. I agree that you are likely to see supercoiled, linear and relaxed (open) circles in that order going up the gel. But then all of those higher forms are the same thing being repeated for dimers, trimers etc. formed by recombination between plasmid molecules. So, for example, I think the 10 kb band in the uncut lanes is a supercoiled dimer. I have a dim memory that you see more of this sort of thing if the DNA is prepared from a &lt;em&gt;recA&lt;/em&gt; strain of &lt;em&gt;E. coli&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;update&lt;/strong&gt;&#xA;&lt;a href=&quot;http://delliss.people.cofc.edu/virtuallabbook/LabReadings/Miniprep/MINIPREPARATION.pdf&quot; rel=&quot;nofollow&quot;&gt;Here is someone who I think would agree.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-01-26T19:11:37.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6936" PostTypeId="1" AcceptedAnswerId="8699" CreationDate="2013-01-26T22:11:39.743" Score="8" ViewCount="8804" Body="&lt;p&gt;Walking outside tonight in -15˚C I realized an interesting observation: While I felt cold on most part of my body, my face (although the only uncovered part) didn't really feel cold. It registered the temperature of course, but it wasn't a negative perception.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder, what is an explanation? Is it simply because our faces are used to the cold, because we almost never cover them? Or is it some evolutionary phenomenon?&lt;/p&gt;&#xA;" OwnerUserId="1279" LastActivityDate="2018-07-04T21:37:48.337" Title="Is human face more resistant to cold than other body parts?" Tags="&lt;human-biology&gt;&lt;temperature&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="6937" PostTypeId="1" CreationDate="2013-01-27T04:04:09.773" Score="24" ViewCount="18404" Body="&lt;p&gt;I've looked for some information on this, but couldn't find anything useful. Has there been any noteworthy attempt to estimate the sum amount of individuals of all species that have ever lived on Earth?&lt;/p&gt;&#xA;" OwnerUserId="2985" LastActivityDate="2015-04-16T11:43:48.223" Title="How many organisms have ever lived on Earth?" Tags="&lt;population-dynamics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="6938" PostTypeId="1" CreationDate="2013-01-27T05:27:28.567" Score="2" ViewCount="74" Body="&lt;p&gt;&lt;strong&gt;Neuromodulators:&lt;/strong&gt; acetylcholine, norepinephrine, epinephrine, vasopressin, histamine, arginine, serotonin, dopamine, autocrine agents, and $\beta$-endorphin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am aware that agonists of the $\alpha_7 $ nAChRs improve cognition in Schizophrenia, presumably by catalysing the release of histamine, norepinephrine and/or acetylcholine.&lt;sup&gt;1,2&lt;/sup&gt; I also know that $\alpha_7 $ nAChRs antagonists reduce $\Delta^9$-tetrahydrocannabinol (THC) self-administration in mice presumably by suppressing dopaminergic activity in the nucleus accumbens or by inhibiting the activity of the CB&lt;sub&gt;1&lt;/sub&gt; receptor.&lt;sup&gt;3&lt;/sup&gt; Selective CB&lt;sub&gt;1&lt;/sub&gt; antagonists also manage to reduce nicotine dependence.&lt;sup&gt;4&lt;/sup&gt; Also I know that the activation of the $ \alpha_3 \beta_4 $ nAChRs in the adrenal medulla catalyses an epinephrine and norepinephrine release.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Reference List (Oxford Style)&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;M Hajós, BN Rogers, '&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19909231&quot; rel=&quot;nofollow&quot;&gt;Targeting alpha7 nicotinic acetylcholine receptors in the treatment of schizophrenia.&lt;/a&gt;', &lt;em&gt;Current Pharmaceutical Design&lt;/em&gt;, 16/5 (2010), 538-554. &lt;/li&gt;&#xA;&lt;li&gt;LF Martin, WR Kem, R Freedman, '&lt;a href=&quot;http://link.springer.com/article/10.1007/s00213-003-1750-1?LI=true&quot; rel=&quot;nofollow&quot;&gt;Alpha-7 nicotinic receptor agonists: potential new candidates for the treatment of schizophrenia&lt;/a&gt;', &lt;em&gt;Psychopharmacology&lt;/em&gt;, 174/1 (2004), 54-64. &lt;/li&gt;&#xA;&lt;li&gt;M Solinas, M Scherma, L Fattore, J Stroik, C Wertheim, G Tanda, W Fratta, SR Goldberg, '&lt;a href=&quot;http://www.jneurosci.org/content/27/21/5615.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Nicotinic α7 Receptors as a New Target for Treatment of Cannabis Abuse&lt;/a&gt;', &lt;em&gt;The Journal of Neuroscience&lt;/em&gt;, 27/21 (2007), 5615-5620.&lt;/li&gt;&#xA;&lt;li&gt;C Cohen, E Kodas, G Griebel, '&lt;a href=&quot;http://ggriebel.perso.worldonline.fr/Pub87.pdf&quot; rel=&quot;nofollow&quot;&gt;CB&lt;sub&gt;1&lt;/sub&gt; receptor antagonists for the treatment of nicotine addiction.&lt;/a&gt;', &lt;em&gt;Pharmacology, Biochemistry and Behavior&lt;/em&gt;, 81/2 (2005), 387-395. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-01-27T05:27:28.567" Title="Which of the nicotinic acetylcholine receptors (nAChRs) catalyse the release of the neuromodulators mentioned below that's caused by nicotine?" Tags="&lt;neuromodulation&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6939" PostTypeId="1" AcceptedAnswerId="7929" CreationDate="2013-01-27T07:43:58.517" Score="17" ViewCount="3582" Body="&lt;p&gt;I'm a math undergrad looking for some papers on modelling the process of natural selection. The only paper I've been able to find is by the pre-eminent mathematician Herbert Wilf from 2010,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://arxiv.org/abs/1010.5178&quot;&gt;There's Plenty of Time for Evolution&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, Wilf's model is extremely simplistic - he calculates the number of 'generations' required to spell out a 'word', if we allow each letter to 'mutate' with certain probability every generation, and we stop mutating a letter once it is correct (this is the 'selective' feature of the model). So to spell the word 'Evolution' by randomly placing scrabble tiles would require 5.4 trillion generations, but if we keep the correctly placed letters each generation and only allow incorrect letters to 'mutate', Wilf calculates we'd only need about 57 generations on average.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wilf's model is a good first step towards modelling natural selection, but it's clearly only a first step. In particular, the fact that nature seems to know in advance exactly what letters it needs to keep in particular places and what it needs to throw out to construct a complex genetic 'word' is dubious at best.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a young maths student the idea of the incredible complexity and diversity of life developing by a directed stochastic process gets me shamelessly excited :) I have been very surprised at just how little mathematical literature there seems to be on this topic, as I say, Wilf's one super-simplistic model is all I've been able to find. Can someone direct me to any other theoretical analyses of the power of natural selection?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="2987" LastActivityDate="2013-04-16T09:36:48.470" Title="Mathematical Modelling of Natural Selection" Tags="&lt;evolution&gt;&lt;genetics&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="6940" PostTypeId="2" ParentId="6900" CreationDate="2013-01-27T12:02:25.043" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Why people like to see pornographic scenes, but do not feel the same about eating scenes?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, the whole point of watching porn is sexual arousal. (Or research for the curious, but that's another thing) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Watching someone eat delicious-looking food CAN make people feel hungry. I admit, I have a bad tendency of feeling hungry if I see good food, or if I see someone eating good food. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I don't get the point of the question. Are you wondering if most people feel this way about watching someone eat, or are you wondering if people are AROUSED by watching someone eat? Lol. Some clarification would be useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Ok, I think I get it now. You're wondering why aren't there any &quot;food scenes&quot; for food-loving people? Well, it's not as widely prevalent as porn, but it IS there for those who are into it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example: &lt;a href=&quot;http://foodporndaily.com/explore/food/&quot; rel=&quot;nofollow&quot;&gt;http://foodporndaily.com/explore/food/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;^ One of my favourite sites, actually. &lt;/p&gt;&#xA;" OwnerUserId="2988" LastEditorUserId="2988" LastEditDate="2013-01-27T12:12:13.713" LastActivityDate="2013-01-27T12:12:13.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6941" PostTypeId="2" ParentId="6939" CreationDate="2013-01-27T14:45:45.063" Score="11" Body="&lt;p&gt;Modeling evolutionary processes has a long history in evolutionary biology. Initially, these models were only theoretical or back-of-the-envelope quantitative (e.g., Simpson's &lt;a href=&quot;http://en.wikipedia.org/wiki/Tempo_and_Mode_in_Evolution&quot;&gt;Tempo and Mode in Evolution&lt;/a&gt;), but with the advent of cheap and accessible computing power, interest in stochastic models has greatly expanded.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The primary literature is vast, so I recommend a few books, which will give you a sampling of approaches and, more importantly, pointers to the relevant literature. If you are at a university, there is a good chance that your library will have one or more of these:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Otto SP and T Day. 2007. &lt;a href=&quot;http://press.princeton.edu/titles/8458.html&quot;&gt;A biologist's guide to mathematical modeling in ecology and evolution&lt;/a&gt;. Princeton University Press.&lt;/li&gt;&#xA;&lt;li&gt;Bolker BM. 2008. &lt;a href=&quot;http://press.princeton.edu/titles/8709.html&quot;&gt;Ecological models and data in R&lt;/a&gt;. Princeton University Press.&lt;/li&gt;&#xA;&lt;li&gt;Roff DA. 2010. &lt;a href=&quot;http://www.oup.com/us/catalog/general/subject/LifeSciences/EvolutionaryBiology/?view=usa&amp;amp;ci=9780199571147&quot;&gt;Modeling evolution: An introduction to numerical methods&lt;/a&gt;. Oxford University Press.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And want to try your own models and you use R, there is an entire page of evolutionary biology packages. Many of these have built-in functions to simulate evolutionary processes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://cran.r-project.org/web/views/Phylogenetics.html&quot;&gt;CRAN Task View: Phylogenetics, Especially Comparative Methods&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;One thing to keep in mind is that simple models, like the one by Wilf and Ewens, often encapsulate the question at hand very well. Even though relatively simple, they are nonetheless very powerful. Wilf and Ewens wanted to prove a point about mutation, and they do that very well. It's easy to imagine way to extend their model to be more realistic, but as a start this is a very sound approach.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A rule of thumb for modeling is to make the model as simple as possible at first, including only the essential process or processes. Then gradually add complexity.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-01-27T14:45:45.063" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="6942" PostTypeId="1" CreationDate="2013-01-27T14:46:24.577" Score="3" ViewCount="128" Body="&lt;p&gt;I've learned programming through great book recommendations; many from the Stack Exchange series of sites. I'm hoping to take this approach in order to gain a fundamental understanding of how fluorescence microscopy and sub-diffraction limit imaging tools work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What books or reviews do you recommend that offer both a conceptual explanation of imaging biological specimens and practical advice? I'd settle for either one if you find the author to be effective.&lt;/p&gt;&#xA;" OwnerUserId="2990" LastEditorUserId="6307" LastEditDate="2017-04-03T04:30:27.503" LastActivityDate="2017-04-03T04:30:27.503" Title="Microscopy Book Suggestions" Tags="&lt;cell-biology&gt;&lt;literature&gt;&lt;book-recommendation&gt;&lt;microscopy&gt;&lt;imaging&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="6943" PostTypeId="2" ParentId="6900" CreationDate="2013-01-27T16:25:43.757" Score="4" Body="&lt;p&gt;For these two phenomena to create the same feelings all of the time, the physiology that engenders these feelings would have to be the same.  All I can do is point out that these have been separate and distinct even in yeast and bacteria and invoke a likelihood argument. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The impulse for hunger is almost as old as living things.  In bacteria, &lt;a href=&quot;http://books.google.com/books?id=crAnYWLB09QC&amp;amp;pg=PA291&amp;amp;lpg=PA291&amp;amp;dq=cAMP%20hunger%20signal&amp;amp;source=bl&amp;amp;ots=BKL1r4wht8&amp;amp;sig=d5Mk5UL9fpyP0H4znt6D8ifJUTI&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=iVMFUe-oG8G1iwLTw4GgCQ&amp;amp;ved=0CEEQ6AEwAQ#v=onepage&amp;amp;q=cAMP%20hunger%20signal&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;cyclic Adenosine mono phosphate (cAMP) mediates hunger&lt;/a&gt;, though this &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/096800048590194X&quot; rel=&quot;nofollow&quot;&gt;does not appear to be universal&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sexual reproduction appeared much later - in the single celled eukaryotes mating factors for instance are mediated by &lt;a href=&quot;http://en.wikipedia.org/wiki/Mating_of_yeast&quot; rel=&quot;nofollow&quot;&gt;the MATa/alpha receptors&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In animals like C elegans the differences persist (&lt;a href=&quot;http://stke.sciencemag.org/cgi/content/abstract/genesdev;23/1/12&quot; rel=&quot;nofollow&quot;&gt;hunger&lt;/a&gt;, &lt;a href=&quot;http://www.nature.com/nature/journal/v454/n7208/full/nature07168.html&quot; rel=&quot;nofollow&quot;&gt;mating&lt;/a&gt;).  This is not a precise argument, but there is the entropy argument - the odds of these 2 signals evolving together biochemically or genetically is quite unlikely given how separate they have always been. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's not to say that eating food can't create a sexual arousal, but it does not do so all the time.  The sexual response appears to be plastic and &lt;a href=&quot;http://en.wikipedia.org/wiki/Sexual_fetishism#Psychological_origins_and_development&quot; rel=&quot;nofollow&quot;&gt;adaptable to nearly any sort of stimulus&lt;/a&gt;.  The fact that in primates and many other animals, the pleasure stimulus is related to both mating and eating might make them seem like similar impulses, but when you go deeper it doesn't seem plausible.  So the two could hypothetically create the same feeling, but if you are asking why doesn't it usually... then there are lots of reasons why.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I find it helpful to reverse the question and ask - what would happen to a species where you could suppress the mating impulse by eating?  Probably not an adaptation that would survive long.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-01-27T16:32:27.003" LastActivityDate="2013-01-27T16:32:27.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6945" PostTypeId="2" ParentId="6937" CreationDate="2013-01-27T23:00:39.203" Score="3" Body="&lt;p&gt;This is a hard problem - estimates of total living things in an given environment are usually created by looking at the number of species and individuals found in a sample area and extrapolating.  As far as estimating the number of living things in the world, there are still lots of species which are not known, making this number still unknown for the world today as it is.  Doing a similar survey into past ages adds another layer of problems to the estimate.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EO Wilson has, among others I'm sure, made a serious effort to understand how many species are currently alive on Earth.  Its pretty clear that currently we don't know how many species are currently alive - that would make it nearly impossible to answer your question historically. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://cmsdata.iucn.org/downloads/the_barometer_of_life_article.pdf&quot; rel=&quot;nofollow&quot;&gt;About 1.9 million species have been discovered and given scientific names, &lt;em&gt;though the actual number may exceed 10 million. Bacteria and archeans could comprise tens of millions species—once taxonomic units are precisely defined.&lt;/em&gt; Knowledge about species and extinction rates remains very poor, and &lt;em&gt;species disappear before we know they existed&lt;/em&gt;. We propose that, as scientists are better able to assess the conservation status of the species that compose an ecosystem, the more they will understand the health of that ecosystem. It is time to accelerate taxonomy and scientific natural history, two of the most vital but neglected disciplines of biology.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;from &quot;The barometer of Life&quot; Stuart, Wilson, McNeely, Mittermeier &amp;amp; Rodriguez, emphasis mine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see there are some important technical obstacles to even the question of how many species there are. Bacteria and free living eukaryotes have rules for speciation that are fairly difficult to define, esp since many can transfer just a few genes with many near relatives and do not require sexual reproduction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another obstacle is that the animal and plant surveys are not really done yet either.  Plants animals and insects are still being discovered in jungles, deep underwater and at &lt;a href=&quot;http://blogs.scientificamerican.com/guest-blog/2011/04/26/man-discovers-a-new-life-form-at-a-south-african-truck-stop/&quot; rel=&quot;nofollow&quot;&gt;rest stops&lt;/a&gt;.  As far as the microbial record goes, an average glass of water from a pond or river probably has undocumented species.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://eol.org/&quot; rel=&quot;nofollow&quot;&gt;encyclopedia of life&lt;/a&gt; is a resource worth mentioning here. It is self admittedly only a partial record. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For past speciation records, the geographical sampling is not strong - digging down in selected spots where fossil records remain is bound to miss many of the species which had existed.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In 1990, Peter Dodson wrote this &lt;a href=&quot;http://www.pnas.org/content/87/19/7608.full.pdf&quot; rel=&quot;nofollow&quot;&gt;review in PNAS&lt;/a&gt; holding forth on the taxonomical difficulties in estimating the number of dinosaur species which included a founding period which was as much circus as science as well as the incredibly sparse sampling of prehistoric surveys over time and history. &lt;a href=&quot;http://news.discovery.com/animals/dinosaurs/number-of-small-meat-eating-dinosaurs-triples-in-a-day-130124.htm&quot; rel=&quot;nofollow&quot;&gt;As recently as this year the count of dinosaurs has continued to vary wildly&lt;/a&gt;. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&amp;amp;from_uid=2217192&quot; rel=&quot;nofollow&quot;&gt;A pubmed citation list to Dodson's paper shows 7 citing works, mostly from the past 3 years&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-01-28T18:49:16.510" LastActivityDate="2013-01-28T18:49:16.510" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6947" PostTypeId="1" AcceptedAnswerId="54056" CreationDate="2013-01-28T11:39:59.710" Score="3" ViewCount="563" Body="&lt;p&gt;What effect do SSRIs have on the expression of the ligand-gated ion channel, the 5-HT&lt;sub&gt;3&lt;/sub&gt; receptor?&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-01-31T10:52:28.573" LastActivityDate="2016-12-06T03:40:23.080" Title="Do SSRIs downregulate or upregulate the 5-HT3 receptor?" Tags="&lt;neurotransmitter&gt;&lt;pharmacology&gt;&lt;receptor&gt;&lt;serotonin&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6948" PostTypeId="1" AcceptedAnswerId="20051" CreationDate="2013-01-28T12:57:11.113" Score="5" ViewCount="1475" Body="&lt;p&gt;How does the drug, modafinil (Provigil), exert its eugeroic (wakefulness-promoting) effects? I've read that it works by increasing dopamine and histamine concentrations in the CNS and by serving as a partial agonist at the dopamine D&lt;sub&gt;2&lt;/sub&gt; receptor. Perhaps by interfering with the function of orexin?&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="57" LastEditDate="2013-01-28T23:24:55.200" LastActivityDate="2019-07-05T09:14:04.223" Title="How does the eugeroic modafinil work?" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6949" PostTypeId="1" CreationDate="2013-01-28T12:59:35.320" Score="8" ViewCount="7632" Body="&lt;p&gt;Octopuses have 8 tentacles, spiders have 8 legs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there something special about 8? It seems like an animal that needs 360° mobility has 8 legs.&lt;/p&gt;&#xA;" OwnerUserId="2993" LastEditorUserId="1306" LastEditDate="2013-01-28T23:35:29.570" LastActivityDate="2015-10-20T00:48:02.500" Title="Why do some animals have 8 Limbs (e.g. Spiders, Octopuses)?" Tags="&lt;evolution&gt;&lt;zoology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6950" PostTypeId="1" CreationDate="2013-01-28T15:44:07.437" Score="2" ViewCount="210" Body="&lt;p&gt;I am looking for examples of colloids involved in digestion for a cross-curricular (bio-chem-physics) lesson plan.  Although I have found references implicating colloids in both lipid and protein digestion, I haven't been able to identify which colloids they are speaking of.  Can someone provide specific examples?&lt;/p&gt;&#xA;" OwnerUserId="2944" LastActivityDate="2013-01-28T17:19:38.787" Title="Colloids in digestion" Tags="&lt;digestive-system&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6951" PostTypeId="2" ParentId="6949" CreationDate="2013-01-28T16:29:02.157" Score="8" Body="&lt;p&gt;No, there is nothing special about eight legs. You have species with two legs (humans), four legs (most mammals), six legs (insects), eight legs (spiders), ten legs (lobsters), and many more legs (millipedes, centipedes). &lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2013-01-28T16:29:02.157" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="6952" PostTypeId="2" ParentId="5598" CreationDate="2013-01-28T16:37:25.847" Score="1" Body="&lt;p&gt;Things other than the temperature that could affect whether or not the coat is necessary: Is it raining? a wet dog will get cold quicker. How long/thick is the fur? thin coats of fur will be less efficient at keeping the dog warm than thick. Is it windy? Wind blows warm air out of the fur. How big is the dog? Size &amp;amp; body fat will affect the rate of heat loss. How active is the dog? A dog doing lots of fetching will keep warmer than a dog ambling along the pavement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clues as to whether the coats are necessary: Is the dog shivering? if yes, give it a coat. Is the dog panting? yes, take the coat off before you bake the thing!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;this probably does not fully answer the question &quot;If the temperature outside is 45°F who would feel colder?&quot; but as requested by the OP I have posted my comments as an answer. I would expect a dog without a &quot;doggy sweater&quot; to be better able to cope with the cold than a human not wearing a &quot;people sweater&quot; or any clothes, just like the dog, if you want to make it a fair test!&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2013-01-28T16:37:25.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6953" PostTypeId="2" ParentId="6950" CreationDate="2013-01-28T17:19:38.787" Score="2" Body="&lt;p&gt;Fat released from food will form macroscopic lipid droplets in the aqueous environment of the gut. In the small intestine, bile synthesised by the liver is secreted into the lumen via the bile duct. Bile contains &lt;a href=&quot;http://en.wikipedia.org/wiki/Bile_salts&quot; rel=&quot;nofollow&quot;&gt;bile salts&lt;/a&gt; which act as detergents to disperse the lipid droplets by forming &lt;a href=&quot;http://en.wikipedia.org/wiki/Micelle&quot; rel=&quot;nofollow&quot;&gt;micelles&lt;/a&gt;. I think this dispersion of micelles could be described as a colloid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have no idea what the reference to protein digestion could mean, although some hydrophobic proteins might become associated with the micelles that I've already described, and I imagine that bile salts might help to solubilise protein aggregates in the gut lumen by direct interaction - they, or their derivatives, are sometimes used by protein biochemists as detergents for protein solubilisation (e.g sodium deoxycholate.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-01-28T17:19:38.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6954" PostTypeId="1" CreationDate="2013-01-28T19:37:28.433" Score="4" ViewCount="73" Body="&lt;p&gt;How does serotonergic (5-HT2A specific) psychedelia work? I've read that there are some theories that it might involve the induction of a glutamate release in certain regions of the brain involved in perception. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="389" LastEditDate="2013-04-02T00:03:13.417" LastActivityDate="2013-05-02T00:10:30.403" Title="How does Serotonergic (5-HT2A mediated) Psychedelia work?" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6956" PostTypeId="1" CreationDate="2013-01-28T22:02:26.347" Score="2" ViewCount="207" Body="&lt;p&gt;I don't want to add much more about that. Since childhood I noticed a chilling effect, even when doing rollercoaster-type activities.&lt;/p&gt;&#xA;" OwnerUserId="2995" LastActivityDate="2013-01-28T22:17:37.120" Title="Why do genitals feel frozen when freefalling?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6957" PostTypeId="2" ParentId="6956" CreationDate="2013-01-28T22:11:34.917" Score="3" Body="&lt;p&gt;Probably because the blood would be forced, physically, that is, by inertia to move upwards during free-fall, thus causing the genital's blood supply to become obstructed thus reducing their temperature and thus leading to the sensation of them being frozen as you described. Plus you might feel cooler all over your body due to the air flow against it and since your genitals wouldn't be as biologically favoured when your body's survival instincts for low-temperature environments kicks in you're body would probably reduce the blood flow to your genitals and other extremities favouring your vital organs such as your heart, lungs, brain, etc. with a greater blood supply to keep them warm and working.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-01-28T22:17:37.120" LastActivityDate="2013-01-28T22:17:37.120" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="6958" PostTypeId="2" ParentId="6949" CreationDate="2013-01-28T23:41:18.617" Score="3" Body="&lt;p&gt;This is just a wild guess, but for movement on a surface in which legs are lifted from the surface, six legs might be sufficient to provide three points of support at all times (think three-legged stool) while allowing relatively rapid movement (legs on both sides can be moved simultaneously), but such might be both less stable and less friendly to variable direction of movement (since legs are in fixed locations and not evenly/radially distributed in animals with bilateral symmetry, having more legs would facilitate balance for different directions of movement).  Having eight legs allows well distributed support and might allow more simplified motor control.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having more than eight legs would tend to lengthen the body (for animals with bilateral symmetry) which might tend to bias movement direction (as well as possibly being wasteful of resources).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There might also be correlation of highly variable movement direction with requirements for greater stabilization.  E.g., eight legs might provide greater stability on a web (which surface might encourage more variable movement directions) and better support large claws (which might make sideways movement more useful in face-to-face encounters).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the above does not address non-walking animals nor animals with radial symmetry (For an animal with radial symmetry, six legs might be sufficient to provide support with three.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully, a better answer will be given, since I have not even paid attention to how spiders (or crabs) move.  (The manner of movement would give insight into how significant support/stability and motor control are.)&lt;/p&gt;&#xA;" OwnerUserId="1858" LastActivityDate="2013-01-28T23:41:18.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6959" PostTypeId="1" CreationDate="2013-01-29T08:21:50.673" Score="3" ViewCount="175" Body="&lt;p&gt;From what I've read the major receptor subtypes involved in the antidepressant effects of SSRIs are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;1A&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;2C&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;3&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;6&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Please cite journal articles to back up your claims, I don't want any piece of information to be unverifiable. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-01-31T10:51:29.933" LastActivityDate="2013-12-27T14:35:49.007" Title="Which Receptors are Involved in the antidepressant effects of SSRIs?" Tags="&lt;neuroscience&gt;&lt;receptor&gt;&lt;serotonin&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="6961" PostTypeId="1" AcceptedAnswerId="6963" CreationDate="2013-01-29T10:14:47.983" Score="8" ViewCount="272" Body="&lt;p&gt;Inspired by &lt;a href=&quot;https://biology.stackexchange.com/questions/653/why-20-amino-acids-instead-of-64&quot;&gt;this question&lt;/a&gt; among others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's widely suggested that the current 3-base codon system of encoding protein sequences in DNA evolved from an earlier 2-base codon system. This makes sense if you look at the coding sequences themselves but I fail to understand how it can evolve? Wouldn't any shift wreck the coding of all existing proteins?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps they could overlap, but wouldn't even that produce nonsense and how would it shift to non-overlapping codons? Perhaps both systems could run in parallel, but how would anything useful come from that in the short term? What selective of advantage of 3-base coding could be strong enough to overcome any disruption?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has anyone developed a coherent model of what intermediate stages might look like?&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-01-30T14:33:51.523" Title="How can a three-base codon evolve from a two-base codon?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;amino-acids&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6962" PostTypeId="2" ParentId="5740" CreationDate="2013-01-29T13:59:48.240" Score="7" Body="&lt;p&gt;Yes, there is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to reproduce, material has to leave one organism and enter another and, in species with internal fertilisation, the eggs need to leave later. Think back to a worm-like organism: it's basically a tube with an opening at either end, those two openings are the easy options for where you can locate your reproductive transfer (and possibly egg-laying). Positioning it at the head end has obvious drawbacks in terms of accidentally consumption, so that leaves positioning it at the excretion end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once evolved, there is no compelling reason to fundamentally alter this bodyplan, particularly as other animals show little or no sign of sharing our revulsion at bodily excretions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;: It's been a few years since I wrote this answer and I'm not really sure it is correct anymore. I've moved to working with &lt;em&gt;C. elegans&lt;/em&gt;, which is the kind of organism that would meet that &quot;worm-like organism&quot; idea I was talking about, but here's the thing: they don't have their reproductive opening near either gut opening, but with its own opening located half way down the organism. If extant organisms don't follow the bodyplan I suggested, does the argument really hold?&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="2938" LastEditDate="2019-03-06T09:31:14.217" LastActivityDate="2019-03-06T09:31:14.217" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="6963" PostTypeId="2" ParentId="6961" CreationDate="2013-01-29T14:26:51.293" Score="5" Body="&lt;p&gt;It is not suggesting a 2-base-&gt;3-base code in the way you are thinking, but of a non-coding, two-coding triplet pattern occurring first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means you would have 16 different coding sequences with 4 possible spacing bases in between.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Later, the spacing bases could become used as part of the code.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does that make more sense?&#xA;Instead of AA,CG becoming AAT,CGT; AAX,CGX becomes AAT,CGT etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its also likely that between 2 and 3 base codes a 2 base pyrimidine/purine system was used. Today the third base can often be switched for its pyrimidine/purine pair without changing the resulting amino acid.&lt;/p&gt;&#xA;" OwnerUserId="1300" LastEditorUserId="1300" LastEditDate="2013-01-29T14:59:09.903" LastActivityDate="2013-01-29T14:59:09.903" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6964" PostTypeId="1" CreationDate="2013-01-29T16:52:20.637" Score="4" ViewCount="869" Body="&lt;p&gt;I am making competent cells using DB3.1 &lt;em&gt;E. coli&lt;/em&gt; cells. Even after following the exact protocol (Inoue method for ultracompetent cells) given in 'Sambrook and Russel', I am not getting transformation efficiency of more than 10&lt;sup&gt;4&lt;/sup&gt;. I am using a 5.1kb plasmid for checking transformation efficiency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will be thankful if any of you can share your experience in this experiment. &lt;/p&gt;&#xA;" OwnerUserId="2998" LastEditorUserId="6" LastEditDate="2013-01-31T10:08:36.963" LastActivityDate="2013-01-31T19:27:51.643" Title="Why am I getting low transformation efficiency with DB3.1 E.coli cells?" Tags="&lt;molecular-biology&gt;&lt;competent-cells&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6965" PostTypeId="2" ParentId="6794" CreationDate="2013-01-29T17:14:15.903" Score="5" Body="&lt;p&gt;Yes, activity in other cells can affect the surrounding electric field and thereby influence the behavior of nearby neurons. This phenomenon, known as &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ephaptic_coupling&quot;&gt;ephatic coupling&lt;/a&gt;&lt;/em&gt;, can be important but is usually small.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For many cases, it is likely too small to be of physiological importance. Note that individual action potentials are quite transient and, especially in myelinated axons, the resulting currents are local and small. Therefore it's unlikely that a single neuron's activity will have a noticeable effect on nearby neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in unmyelinated axon tracts and/or when a larger group of neurons is active, ephatic coupling is more likely. In particular, it seems to play a role in synchronizing cell populations during oscillations. For example, Anastassiou et al (2011) found that firing of cortical neurons could be entrained by the extracellular field and affected the intracellular membrane potential by about 0.5 mV.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nn.2727&quot;&gt;Anastassiou, C.A., Perin, R., Markram, H., Koch, C., 2011.&lt;/a&gt; Ephaptic coupling of cortical neurons. Nature Neuroscience 14, 217–223.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, for reference:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://physrev.physiology.org/content/75/4/689.abstract&quot;&gt;Jefferys, J.G., 1995.&lt;/a&gt; Nonsynaptic modulation of neuronal activity in the brain: electric currents and extracellular ions. Physiol Rev 75, 689–723.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nrn3241&quot;&gt;Buzsáki, G., Anastassiou, C.A., Koch, C., 2012.&lt;/a&gt; The origin of extracellular fields and currents — EEG, ECoG, LFP and spikes. Nature Reviews Neuroscience 13, 407–420. &lt;em&gt;(see pages 411-412)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt;&#xA;For your particular case, action potential propagation in one axon is very unlikely to affect the other axons in any relevant way in a tract of myelinated axons. This is especially true because the initiation of action potentials does not occur along the axon itself, but where the axon is just branching from the cell body (the axon initial segment). Threshold is important at the initiation site, but is not really relevant in the tract itself, where the axon is just conducting the signal it receives from the initiation site.&lt;/p&gt;&#xA;" OwnerUserId="72" LastEditorUserId="72" LastEditDate="2013-01-29T17:29:55.390" LastActivityDate="2013-01-29T17:29:55.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6966" PostTypeId="1" CreationDate="2013-01-29T17:30:54.940" Score="13" ViewCount="6580" Body="&lt;p&gt;Why do antidepressants take so long to reach efficacy? I've read of theories about it perhaps being due to the strength of negative feedback via serotonergic and adrenergic autoreceptors during the first few weeks of treatment. What I'm looking for in an answer is the following:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The current theories regarding why currently-in-practise antidepressant regimens have a delayed onset of action.&lt;/li&gt;&#xA;&lt;li&gt;The evidence for these theories.&lt;/li&gt;&#xA;&lt;li&gt;How these theories fit in with the monoamine hypothesis or whether it is inconsistent with the monoamine hypothesis and how.&lt;/li&gt;&#xA;&lt;li&gt;Possible solutions to this problem of delayed responses to antidepressant therapy.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;All of this is strictly theoretical, there are no actual people involved here, this is simply a scientific inquiry. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2017-12-19T12:22:32.133" LastActivityDate="2017-12-19T12:22:32.133" Title="Why do antidepressants have a delayed onset of action?" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;&lt;neurophysiology&gt;&lt;neurotransmitter&gt;&lt;psychoneuropharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6967" PostTypeId="2" ParentId="6959" CreationDate="2013-01-29T17:47:30.060" Score="1" Body="&lt;p&gt;You're right, those are all important! There are several good reviews on the mechanism of action antidepressants. I like &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0071481273&quot; rel=&quot;nofollow&quot;&gt;Molecular Pharmacology&lt;/a&gt;, by Nestler, or even &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0838577016&quot; rel=&quot;nofollow&quot;&gt;Principles of Neural Science&lt;/a&gt;, by Kandel. I think a textbook is going to be your best bet, in terms of getting up to speed here, as this is largely an already-researched issue, but here are some good review articles as well:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://journals.lww.com/psychopharmacology/Abstract/1998/12000/Involvement_of_Serotonin_and_Dopamine_in_the.5.aspx&quot; rel=&quot;nofollow&quot;&gt;Bonhomme et al., 1988&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://archpsyc.jamanetwork.com/article.aspx?articleid=492650#qundefined&quot; rel=&quot;nofollow&quot;&gt;Charney et al., 1981&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://journals.lww.com/psychopharmacology/Abstract/1998/12000/Involvement_of_Serotonin_and_Dopamine_in_the.5.aspx&quot; rel=&quot;nofollow&quot;&gt;Norbert &amp;amp; Esposito, 1998&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2125.1977.tb05761.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Spencer, 2012&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;If you have a more specific question, let me know!&lt;/p&gt;&#xA;" OwnerUserId="1855" LastEditorUserId="1855" LastEditDate="2013-01-29T20:14:22.180" LastActivityDate="2013-01-29T20:14:22.180" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="6968" PostTypeId="1" CreationDate="2013-01-29T18:21:56.323" Score="7" ViewCount="103" Body="&lt;p&gt;I know that the 5-HT&lt;sub&gt;1A&lt;/sub&gt; and $\alpha$&lt;sub&gt;2&lt;/sub&gt; adrenoreceptors receptors serve as autoreceptors for serotonin (5-HT) and norepinephrine respectively and are down-regulated by repeat exposure to their respective ligands, it's believed that this is likely the cause for the therapeutic delay in the actions of antidepressants that target the serotonergic and noradrenergic systems.  My question is this: &quot;Is this the case for all autoreceptors? Are all autoreceptors down-regulated by the actions of their respective ligands?&quot;&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-01-31T15:25:18.413" LastActivityDate="2021-05-09T15:05:55.607" Title="Are all Autoreceptors Downregulated by their Respective Endogenous Ligands?" Tags="&lt;neurotransmitter&gt;&lt;receptor&gt;&lt;autoreceptor&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6969" PostTypeId="1" CreationDate="2013-01-29T20:15:17.077" Score="5" ViewCount="116" Body="&lt;p&gt;I'm looking for a resource that best surveys the anatomy and physiology of common genetic model organisms, and how their characteristics are particularly useful for biological experiments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;For example&lt;/em&gt;, I'm studying the eyeless Drosophila gene, but it would help to know that species' specific compound eye anatomy and normal development, so that I can weigh the pros and cons of using that particular model organism over another.&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2013-01-30T15:27:04.037" Title="Resource for model organism anatomy/physiology for biological experiments" Tags="&lt;experimental-design&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6970" PostTypeId="2" ParentId="175" CreationDate="2013-01-30T00:38:51.920" Score="2" Body="&lt;p&gt;I've worked with MIN6 cells in the past, and have found that they can take at least 12-24 hours to fully seed (if they are being cultured on polystyrine).  Depending on the specifics of your experiment, and whether doing so would complicate your controls, you might also want to try coating the surface you are attempting to seed on with laminin.  MIN6 cells seem to like growing on that over uncoated polystyrine and other ECM proteins.&lt;/p&gt;&#xA;" OwnerUserId="3000" LastActivityDate="2013-01-30T00:38:51.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6971" PostTypeId="2" ParentId="5535" CreationDate="2013-01-30T02:09:34.390" Score="2" Body="&lt;p&gt;Found a few samples here: &lt;a href=&quot;http://ars.els-cdn.com/content/image/1-s2.0-S0024320503008142-gr2.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://ars.els-cdn.com/content/image/1-s2.0-S0024320503008142-gr2.gif&lt;/a&gt; this shows the nocturnal melatonin peak, which is apparently very important for well being &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7fOMm.gif&quot; alt=&quot;melatonin concentration curve&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/urEHp.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-01-30T02:09:34.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6972" PostTypeId="1" CreationDate="2013-01-30T12:27:47.207" Score="3" ViewCount="188" Body="&lt;p&gt;I know that 5-HT&lt;sub&gt;2A&lt;/sub&gt; partial agonism is the key mechanism of action of serotonergic psychedelics but I also know that some research (e.g. the selective (no activity on any other known receptor sites) 5-HT&lt;sub&gt;2A&lt;/sub&gt; inverse agonist/antagonist eplivanserin was being investigated as a sedative) says that central blockade of the 5-HT&lt;sub&gt;2A&lt;/sub&gt; receptors induces sedation which is in opposition to the effect of 5-HT&lt;sub&gt;2A&lt;/sub&gt; partial agonists. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a partial answer to my question. I heard from LSD users that they find it regularly &lt;strong&gt;causes sleeplessness for the duration of its effects&lt;/strong&gt;, which is likely due to stimulant/wakefulness-promoting (eurogenic) effects. Albeit just because it is true for one serotonergic psychedelic doesn't necessarily mean it is true for all serotonergic psychedelics. Especially since LSD affects a wide range of serotonin and other receptor subtypes. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-12T04:04:02.513" LastActivityDate="2013-02-12T10:50:37.310" Title="Do serotonergic (5-HT2A-mediated) psychedelics elicit stimulant effects?" Tags="&lt;pharmacology&gt;&lt;neurotransmitter&gt;&lt;receptor&gt;&lt;serotonin&gt;&lt;hallucinogens&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6973" PostTypeId="2" ParentId="6961" CreationDate="2013-01-30T14:33:51.523" Score="1" Body="&lt;p&gt;Erives' paper is interesting:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21779963&quot; rel=&quot;nofollow&quot;&gt;A model of proto-anti-codon RNA enzymes requiring L-amino acid homochirality.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1210" LastActivityDate="2013-01-30T14:33:51.523" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6974" PostTypeId="2" ParentId="832" CreationDate="2013-01-30T15:05:45.700" Score="-1" Body="&lt;p&gt;I have mostly seen it used to mean &quot;possessing features that appeared most recently in the historical evolutionary record&quot;. Thus a human is considered more evolved than a chimp because our bipedality, hairlessness and large brain appeared more recently than the features of chimps, and a chimp is more evolved than a fish because fish very similar to ones alive today appear in the record before anything resembling an ape, and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it's pretty poor use of language, frankly, since it suggests linearity and ordering to evolution that is simply not there, conflates gross morphological change with change in general and incorrectly implies that stabilising selection is not evolution.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-01-30T15:05:45.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6975" PostTypeId="2" ParentId="6969" CreationDate="2013-01-30T15:27:04.037" Score="3" Body="&lt;p&gt;In the &lt;a href=&quot;http://bgee.unil.ch/bgee/bgee&quot; rel=&quot;nofollow&quot;&gt;Bgee database&lt;/a&gt;, you can look at gene expression and anatomy of various model species, e.g. &lt;a href=&quot;http://bgee.unil.ch/bgee/bgee?page=anatomy&amp;amp;action=organs&amp;amp;stage_children=on&amp;amp;species_id=7227&amp;amp;stage_id=FBdv:00005369&quot; rel=&quot;nofollow&quot;&gt;Drosophila&lt;/a&gt;. This doesn't give you the full anatomy, but at least an ontology of tissues and cell types.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2013-01-30T15:27:04.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6976" PostTypeId="2" ParentId="5442" CreationDate="2013-01-30T20:01:58.623" Score="4" Body="&lt;p&gt;Washing your hands is an exercise in probability rather than absolute values. An important thing to keep in mind is that not only is it very hard to kill all the bacteria on your hands, it's also not something you actually want to do.  Most of the bacteria we encounter day to day are either benign or beneficial to personal health. We know that gnotobiotic mice (sterile mice) exhibit impaired development, especially in the immune system.  We want to come into moderate contact with bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because it is a balancing act, I think hygiene needs to be reframed. For one things anti-septic soap should be reserved only for situations when it is absolutely necessary.  Anti-septic soap has a tendency to apply a selective pressure that encourages propagation of resistant strains.  Situations where it is worth using would include visiting an international transit center (airport), working in an Operating Room ward at a hospital, or going to a cafeteria during an epidemic.  In other situations, regular plain soap and water should be good enough to rub the majority of cells off your hands so that passive immunity has a good chance of eliminating any threats before they get to vulnerable parts of the body.  If you have the opportunity, paper towels are better for getting cells off your hands then blowers.&lt;/p&gt;&#xA;" OwnerUserId="3001" LastActivityDate="2013-01-30T20:01:58.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6977" PostTypeId="2" ParentId="6954" CreationDate="2013-01-30T21:46:53.867" Score="2" Body="&lt;p&gt;Brenton, the linked pdf is called &quot;Multiple receptors contribute to the behavioral effects of&#xA;indoleamine hallucinogens&quot;. It goes into detail on a a few basic behavioral responses.  I don't know what your background is so if you need help understanding parts point them out to me and I'll give it a go.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110631/pdf/nihms267079.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110631/pdf/nihms267079.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://docs.google.com/file/d/0B0JUrCVOms3MdzdlYmh0SnBmOHc/edit&quot; rel=&quot;nofollow&quot;&gt;https://docs.google.com/file/d/0B0JUrCVOms3MdzdlYmh0SnBmOHc/edit&lt;/a&gt; (I'm hosting the pdf on my Google Drive if you aren't able to see the link hosted by the NIH).&lt;/p&gt;&#xA;" OwnerUserId="3001" LastActivityDate="2013-01-30T21:46:53.867" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6978" PostTypeId="1" CreationDate="2013-01-31T01:30:30.777" Score="2" ViewCount="483" Body="&lt;p&gt;Given that bonobo chimps are more sexually active then humans, are the females almost always pregnant? if not how not?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;also are they so sexually active in the wild as well or is it just in captivity?&lt;/p&gt;&#xA;" OwnerUserId="1585" LastActivityDate="2013-01-31T13:54:52.890" Title="are female bonobos &quot;always&quot; pregnant?" Tags="&lt;ethology&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6979" PostTypeId="2" ParentId="6978" CreationDate="2013-01-31T10:08:37.270" Score="3" Body="&lt;p&gt;In most species, females are pregnant as often as they can be. Since the availability of sex is rarely a limiting factor, it seems likely that female bonobos are as &quot;always&quot; pregnant as other chimps and socially living primates. The actual rate of pregnancy will be hormonally limited by things such as reduced fertility during lactation and so on.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="2938" LastEditDate="2013-01-31T13:54:52.890" LastActivityDate="2013-01-31T13:54:52.890" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6981" PostTypeId="5" CreationDate="2013-01-31T10:49:57.363" Score="0" Body="&lt;p&gt;Serotonin is biosynthesised from the amino acid, tryptophan. It is the precursor compound to the sleep-modulating hormone, melatonin. It binds to, activates and serves as the endogenous ligand for the 5-HT family of receptors which includes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;5-HT&lt;sub&gt;1&lt;/sub&gt;&lt;/strong&gt; family:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;1A&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;1B&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;1D&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;1E&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;1F&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;5-HT&lt;sub&gt;2&lt;/sub&gt;&lt;/strong&gt; family:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;2A&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;2B&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;2C&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;3&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;4&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;5A&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;5B&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;6&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;5-HT&lt;sub&gt;7&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It plays a key role in mood regulation, sleep, anxiety, cognition and sensory perception.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VAKc0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Figure 1: Serotonin [Source: &lt;a href=&quot;http://www.chemspider.com/5013&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chemspider&lt;/a&gt;]&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/T4Tjv.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Figure 2: Trytophan [Source: &lt;a href=&quot;http://www.chemspider.com/Chemical-Structure.1116.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chemspider&lt;/a&gt;]&lt;/h2&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-01-31T13:20:57.813" LastActivityDate="2013-01-31T13:20:57.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6982" PostTypeId="4" CreationDate="2013-01-31T10:49:57.363" Score="0" Body="The monoamine neurotransmitter, serotonin, also referred to by its chemical name 5-hydroxytryptamine (5-HT). It binds to and activates the 5-HT family of receptors. " OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-01-31T13:08:10.327" LastActivityDate="2013-01-31T13:08:10.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6983" PostTypeId="5" CreationDate="2013-01-31T15:33:43.747" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-01-31T15:33:43.747" LastActivityDate="2013-01-31T15:33:43.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6984" PostTypeId="4" CreationDate="2013-01-31T15:33:43.747" Score="0" Body="Autoreceptors are receptors that are located presynaptically, on axon terminals that send negative feedback upon the actions of the neurotransmitter released from the axon terminal to prevent the further release of the neurotransmitter contained inside storage vesicles. " OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-01-31T16:47:49.737" LastActivityDate="2013-01-31T16:47:49.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6985" PostTypeId="2" ParentId="5445" CreationDate="2013-01-31T16:18:27.987" Score="2" Body="&lt;p&gt;I think this site best answers the question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dumbscientist.com/archives/cold-weather-can-make-you-sick&quot; rel=&quot;nofollow&quot;&gt;Cold Weather Can Make You Sick&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a part:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Professor Eccles explained this effect by saying that our bodies restrict blood flow to the extremities when we get cold to help conserve body heat for the torso and brain, which really need to be warm. Cutting off the blood flow reduces the supply of white blood cells which are the immune system’s primary weapon against germs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While his explanation makes sense, there may be a more general effect at work. The human body is a machine that accepts fuel in the form of food, and uses that fuel’s energy to keep us warm and to power our immune systems, muscles and brains. However, in frigid conditions our bodies have probably evolved to say “who cares if I might get sick a week later when I’m going to die of hypothermia in half an hour?”&quot;&lt;/p&gt;&#xA;" OwnerUserId="3003" LastActivityDate="2013-01-31T16:18:27.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6987" PostTypeId="2" ParentId="6964" CreationDate="2013-01-31T18:53:28.180" Score="1" Body="&lt;p&gt;How are you storing the cells?  Competent cells can be very finicky.  In my lab, we usually flash-freeze them with ethanol/dry-ice and store at -81 degrees (long-term use) or we store them surrounded by ice at 4 degrees (short-term use).&lt;/p&gt;&#xA;" OwnerUserId="3001" LastEditorUserId="3001" LastEditDate="2013-01-31T19:27:51.643" LastActivityDate="2013-01-31T19:27:51.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6988" PostTypeId="1" AcceptedAnswerId="7056" CreationDate="2013-01-31T19:50:37.577" Score="3" ViewCount="819" Body="&lt;p&gt;QSAR modelling in pharmacology basically hangs on using mathematical modelling to approximate the effects different molecules will have on various pharmacological targets. I would like to know what software is available to assist me in doing these studies. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="3553" LastEditDate="2017-04-03T03:04:15.253" LastActivityDate="2017-04-03T03:04:15.253" Title="What software is there available for quantitative structure–activity relationship (QSAR) pharmacological studies?" Tags="&lt;biochemistry&gt;&lt;bioinformatics&gt;&lt;pharmacology&gt;&lt;theoretical-biology&gt;&lt;medicinal-chemistry&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6989" PostTypeId="2" ParentId="2263" CreationDate="2013-01-31T19:51:22.500" Score="2" Body="&lt;p&gt;I think of &lt;em&gt;E. coli&lt;/em&gt; being more white than yellow.  When you compare &lt;em&gt;E. coli&lt;/em&gt; and &lt;em&gt;S. aureus&lt;/em&gt; on an agar plate, the &lt;em&gt;Staph&lt;/em&gt; colonies have a much more distinctive yellow tint.  The yellow tint in &lt;em&gt;Staph&lt;/em&gt; colonies is due to staphyloxanthin, a carotenoid pigment.&lt;/p&gt;&#xA;" OwnerUserId="3001" LastEditorUserId="115" LastEditDate="2013-01-31T22:53:04.320" LastActivityDate="2013-01-31T22:53:04.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6990" PostTypeId="1" AcceptedAnswerId="6993" CreationDate="2013-01-31T19:57:49.333" Score="3" ViewCount="161" Body="&lt;p&gt;My assumption is that dogs vary so much in size because of artificial selection pressures coming from human breeders, but are there genetic loci that roughly determine approximate size?  Do other feral species of animals exhibit such a wide range in sizes or is this something that only occurs when breeders intervene?&lt;/p&gt;&#xA;" OwnerUserId="3001" LastActivityDate="2013-01-31T23:26:00.677" Title="What accounts for size variation in breeds of dogs?" Tags="&lt;genetics&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="6991" PostTypeId="5" CreationDate="2013-01-31T19:59:14.720" Score="0" Body="&lt;p&gt;&lt;strong&gt;SAR&lt;/strong&gt; stands for &lt;strong&gt;Structure-Activity Relationship&lt;/strong&gt; (as this would exceed the amount of characters aloud for a tag). SAR is the relationship between the chemical structure of compounds and their biologic activity. SAR hangs on the theory that there is a relationship between the chemical structure of compounds and their respective biologic activity.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-01-31T20:17:57.670" LastActivityDate="2013-01-31T20:17:57.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6992" PostTypeId="4" CreationDate="2013-01-31T19:59:14.720" Score="0" Body="SAR stands for Structure-Activity Relationship. SAR is the relationship between the chemical structure of compounds and their biologic activity. " OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-01-31T20:17:51.400" LastActivityDate="2013-01-31T20:17:51.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6993" PostTypeId="2" ParentId="6990" CreationDate="2013-01-31T23:26:00.677" Score="3" Body="&lt;p&gt;This is a fascinating bit of genetics.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dogs are especially variable in size and many appearance, behavioral and temperamental phenotypes.  It was long expected that variations in developmental genes were the reason that dog breeds were responsible for the amazing flexibility of dog sizes.  One early locus found was &lt;a href=&quot;http://www.sciencemag.org/content/316/5821/112.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;IGF1&lt;/a&gt; (insulin like Growth Factor 1). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002316&quot; rel=&quot;nofollow noreferrer&quot;&gt;2011 PLOS paper&lt;/a&gt; actually review the specific genotypes of dog breeds and identifying loci that are strongly associated with breed phenotype supports this idea. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... (we scanned) the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for &lt;em&gt;developmental genes&lt;/em&gt;. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Emphasis added&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This theory has an intuitive appeal as well - no dog breeds (I think) are larger than the wolf, the stock from which all dog breeds are descended.  All such breeds being derived from earlier developmental stages of the wolf makes an intuitive, if imprecise description of the effect here.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regardless, dogs remain an important model organism for so many traits because relatively few genomic regions can cause so many important phenotypes, including size, but also behavioral and morphological variations.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the below figure you can see how few genomic regions are responsible for the 46 breeds &lt;a href=&quot;http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002316&quot; rel=&quot;nofollow noreferrer&quot;&gt;Vaysee et al.&lt;/a&gt; examined. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nsNyC.png&quot; alt=&quot;map of variation loci&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-01-31T23:26:00.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6994" PostTypeId="1" AcceptedAnswerId="6995" CreationDate="2013-01-31T23:47:06.580" Score="2" ViewCount="55" Body="&lt;p&gt;I'm reading &lt;a href=&quot;http://www.nature.com/nature/journal/v435/n7042/abs/nature03556.html&quot; rel=&quot;nofollow&quot;&gt;&quot;Highly efficient endogenous human gene correction using designed zinc finger nucleases&quot;&lt;/a&gt; by Urnov et al. They propose a way to use zinc finger proteins for gene therapy. They repeatedly claim their method is &quot;selection free&quot; and it seems they are claiming that as an advantage to their method. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why would selection free be an advantage? Wouldn't you have to select for the transformed cells anyway to be relevant in a clinical setting?&lt;/p&gt;&#xA;" OwnerUserId="524" LastEditorUserId="3632" LastEditDate="2013-02-01T02:22:23.623" LastActivityDate="2013-02-01T14:30:11.853" Title="What is the point of being selection-free?" Tags="&lt;genetics&gt;&lt;recombinant&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="6995" PostTypeId="2" ParentId="6994" CreationDate="2013-02-01T02:33:51.390" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v435/n7042/abs/nature03556.html&quot; rel=&quot;nofollow&quot;&gt;Urnov et al.&lt;/a&gt; are trying to effect gene therapy - where a mutation causing a genetic form of severe combined immunideficiency (SCID) (&lt;a href=&quot;http://www.scid.net/&quot; rel=&quot;nofollow&quot;&gt;also known as the bubble boy syndrome&lt;/a&gt;). Affected SCID patients can have little to no immunity to infection what so ever.  SCID in this case is caused by a single site mutation in the IL2R-gamma gene.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their method is to use a DNA binding protein (containing zinc finger domains that bind the DNA) which attracts a DNA repair enzyme.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The result is that 18% of the cells have the SCID gene repaired.  This would have been a trivial result if they had applied selection, which generally refers to any method which eliminates cells which were not affected (in this case having their DNA repaired) by a transformation like their treatment.  They claim that 18% of all the cells were repaired (I assume this is in a cell culture).  This implies that if their treatment were applied to living tissue, 18% of the cells would be repaired &lt;em&gt;in situ&lt;/em&gt;, which should be enough to restore immune function.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While its possible to apply a selection method to gene therapy, it would be far better if you did not.  Cancer chemotherapy for instance is a selection based treatment for instance, relying on toxins which kill fast dividing or growing cells preferentially, leaving the slower growing tissues relatively viable.   Still its quite toxic and disruptive to the patient.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-02-01T14:30:11.853" LastActivityDate="2013-02-01T14:30:11.853" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="6997" PostTypeId="2" ParentId="1495" CreationDate="2013-02-01T04:48:07.390" Score="3" Body="&lt;p&gt;From a systemic point of view, if we wish to evolutionarily induce our descendants (descendants of the current human race on the whole) to live longer lives, we would need to pro-create later.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the whole of human race enforced a statute that prohibits pro-creation before the age of 40, then two pronged dynamics would happen&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;only adults fit enough to pro-create after 40 would produce off-springs.&lt;/li&gt;&#xA;&lt;li&gt;only off-springs born to parents older than 40 who are fit enough would survive.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Since, there is a high tendency of abnormality and low survival of off-springs born to parents of older ages, absence of resource contention and genetic dynamics would encourage the initial propagation of the rare few fit off-springs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, unnatural &quot;natural selection&quot; would encourage the propagation of humans of longer life-spans. Perhaps, a natural disaster or viral outbreak could discourage humans from pro-creating before age 40. Perhaps, high rates of abortion. So long as the human race does not die out due to such restrictions. Perhaps, to the satisfaction of conspiracy lovers, a secretive organisation carries out a plan every 100K years to raise the bar for child-bearing age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, it might be less of a question of advantage and more of the effects of motivation. That current status where&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;high motivation for humans to pro-create early in life.&lt;/li&gt;&#xA;&lt;li&gt;low motivation for humans to have more children as they wise-up by being tired of raising kids too early.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Therefore, since no such secret organisation exists, there is infinitesimally little motivation for the existence of a &quot;super-virus&quot; type of humans to exist. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no motivation for super-humans to exist, because the distribution of life-spans have crowded out the food and survival resources of any possible primeval super-human.&lt;/p&gt;&#xA;" OwnerUserId="3004" LastEditorUserId="3004" LastEditDate="2013-02-01T04:54:52.210" LastActivityDate="2013-02-01T04:54:52.210" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7000" PostTypeId="1" AcceptedAnswerId="7001" CreationDate="2013-02-01T08:16:23.243" Score="3" ViewCount="680" Body="&lt;p&gt;I've heard of Henrietta Lacks. As a result of a genetic mutation, her cells never died. I've heard/read that overtime, our cells stop multiplying as much, (as an effect of aging). Why? Why do we age? Why do cells eventually die? What causes our bodies to degenerate? It is encoded for in our genes? If we treated our bodies in the highest regard, accounted for accurate diet and sleep, with the introduction of genetic engineering, could everlasting life be possible? &lt;/p&gt;&#xA;" OwnerUserId="1913" LastActivityDate="2013-02-01T08:26:43.737" Title="Why do cells have an average 'life span'" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7001" PostTypeId="2" ParentId="7000" CreationDate="2013-02-01T08:26:43.737" Score="2" Body="&lt;p&gt;We refer to the number of times the cells of an organism can possibly divide as the Hayflick limit for that organism. The Hayflick limit serves as a theoretical life span, because telomeres (on the ends of chromosomes) get slightly shorter with each round of division, until they are gone completely. Telomeres are put on the ends of chromosomes by the enzyme telomerase, which is abundant in infants (who are growing and undergoing rapid mitotic divisions) but bodily abundance of the enzyme quickly diminishes with age. Without telomeres, our actual chromosomes would shorten in length during each round of division -- essentially, this is what happens after the telomeres are eroded away at in the later years of life. The Hayflick limit for humans is given to be 120 years -- with perfect self-care, 120 years of life is possible.&lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2013-02-01T08:26:43.737" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7002" PostTypeId="1" AcceptedAnswerId="7003" CreationDate="2013-02-01T08:29:38.880" Score="3" ViewCount="773" Body="&lt;h3&gt;Question:&lt;/h3&gt;&#xA;&lt;p&gt;I know that experiments have been conducted to determine the importance of R.E.M. sleep in our sleep cycle. It is particularly important for &lt;em&gt;learning&lt;/em&gt;, &lt;em&gt;information synthesis&lt;/em&gt;, and &lt;em&gt;recovery from distress&lt;/em&gt;. Why else is R.E.M. sleep important? What experiments have been done/observations been made to determine the neurological mechanisms underlying R.E.M. sleep? I know that we exhibit high frequency &lt;span class=&quot;math-container&quot;&gt;$\alpha$&lt;/span&gt; waves, similar to the waves we experience during wakefulness.&lt;/p&gt;&#xA;&lt;h3&gt;Wiki:&lt;/h3&gt;&#xA;&lt;p&gt;&lt;em&gt;During REM sleep, high levels of acetylcholine in the hippocampus suppress feedback from hippocampus to the neocortex, and lower levels of acetylcholine and norepinephrine in the neocortex encourage the spread of associational activity within neocortical areas without control from the hippocampus. This is in contrast to waking consciousness, where higher levels of norepinephrine and acetylcholine inhibit recurrent connections in the neocortex. REM sleep through this process adds creativity by allowing &amp;quot;neocortical structures to reorganise associative hierarchies, in which information from the hippocampus would be reinterpreted in relation to previous semantic representations or nodes.&lt;/em&gt;&lt;br&gt;&lt;br&gt;&lt;/p&gt;&#xA;&lt;h3&gt;Do these reorganized neocortical hierarchies remain this way?&lt;/h3&gt;&#xA;&lt;h3&gt;Just HOW integral is R.E.M. sleep to our brain development?&lt;/h3&gt;&#xA;" OwnerUserId="1913" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-02-01T16:12:03.537" Title="The fundamental importance of R.E.M. Sleep. (Rapid Eye Movement)" Tags="&lt;human-biology&gt;&lt;sleep&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7003" PostTypeId="2" ParentId="7002" CreationDate="2013-02-01T08:34:20.180" Score="-1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;REM sleep stimulates the brain regions used in learning. This may be&#xA;  important for normal brain development during infancy, which would&#xA;  explain why infants spend much more time in REM sleep than adults (see&#xA;  Sleep: A Dynamic Activity ). Like deep sleep, REM sleep is associated&#xA;  with increased production of proteins. One study found that REM sleep&#xA;  affects learning of certain mental skills. People taught a skill and&#xA;  then deprived of non-REM sleep could recall what they had learned&#xA;  after sleeping, while people deprived of REM sleep could not.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Some scientists believe dreams are the cortex's attempt to find&#xA;  meaning in the random signals that it receives during REM sleep. The&#xA;  cortex is the part of the brain that interprets and organizes&#xA;  information from the environment during consciousness. It may be that,&#xA;  given random signals from the pons during REM sleep, the cortex tries&#xA;  to interpret these signals as well, creating a &quot;story&quot; out of&#xA;  fragmented brain activity. &lt;br&gt;&lt;br&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.ninds.nih.gov/disorders/brain_basics/understanding_sleep.htm#dreaming&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1917" LastEditorUserId="69" LastEditDate="2013-02-01T16:12:03.537" LastActivityDate="2013-02-01T16:12:03.537" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7005" PostTypeId="1" CreationDate="2013-02-01T16:25:27.567" Score="5" ViewCount="232" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/855&quot;&gt;I read another question, and its answers, about how vaccines work&lt;/a&gt;, but I don't see there, and and don't understand, why some infections can, seemingly, not be immunized against at all. For example, someone who gets the flu (or the flu vaccine) is immunized against that particular strain of flu for life (which was relevant, IIRC, when H1N1 came back a few years ago: many people above a certain age had immunity), whereas one person can get group-Α strep throat over and over again. Why is this?&lt;/p&gt;&#xA;" OwnerUserId="988" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-07-14T05:16:36.923" Title="Why don't we form immunity to some infections?" Tags="&lt;immunology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7006" PostTypeId="1" CreationDate="2013-02-01T17:42:57.380" Score="5" ViewCount="1003" Body="&lt;p&gt;I'm having trouble finding a method to find exons in the original DNA sequence used to create the mRNA, even given the sequence of the mRNA, as I cannot find a way to reliably identify the beginning and end of introns and exons. Is there an algorithm or method that I can use to do this? What information am I missing to be able to find the beginning and end of exons and introns?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance for answers.&lt;/p&gt;&#xA;" OwnerUserId="3006" LastActivityDate="2013-07-17T15:08:54.263" Title="How to find Exons in mRNA Computationally" Tags="&lt;dna&gt;&lt;rna-sequencing&gt;&lt;mrna&gt;&lt;introns&gt;&lt;exons&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7007" PostTypeId="2" ParentId="7006" CreationDate="2013-02-01T18:27:52.730" Score="2" Body="&lt;p&gt;You should ask this question over at &lt;a href=&quot;http://www.biostars.org&quot; rel=&quot;nofollow&quot;&gt;biostars.org&lt;/a&gt; -- and could use a bit more clarity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you actually have RNA-seq data that you want to use to find the exon/splicing structure of an mRNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First step would be to use a splicing-aware aligner. A few free ones are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bioinformatics.oxfordjournals.org/content/early/2012/10/25/bioinformatics.bts635.abstract&quot; rel=&quot;nofollow&quot;&gt;STAR&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://tophat.cbcb.umd.edu&quot; rel=&quot;nofollow&quot;&gt;TopHat&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://research-pub.gene.com/gmap/&quot; rel=&quot;nofollow&quot;&gt;GSNAP&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Let us know why that wouldn't do what you want when you re-ask this question over at biostar.&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2013-02-01T18:27:52.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7008" PostTypeId="2" ParentId="7005" CreationDate="2013-02-01T19:17:12.200" Score="9" Body="&lt;p&gt;The answer is sort of hidden behind the very first paragraph of your linked question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Vaccines work by introducing an attenuated strain of the pathogen (or alternatively the antigens that are normally present on the pathogens surface) into the body, whereupon the body mounts an immune response.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The body mounts an immune response based upon a particular epitope (molecule/protein chain) &lt;strong&gt;derived from the infection itself.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the bacteria/virus/parasite evolves so that the molecules/proteins on its surface change significantly, then the version stored in Memory Cells will no longer apply. There's &lt;em&gt;some&lt;/em&gt; wiggle room depending on epitope length and specificity of the Immune Response (highly specific MHC proteins will invoke a very strong, very &lt;em&gt;efficient&lt;/em&gt; response - while less specific [usually B-cell or early T-cell responses] will invoke a weaker, less effective response), but because pathogens can mutate so quickly it's not uncommon that you'll encounter a descendant of a virus you already encountered that has dramatically different characteristics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some pathogens are also just very &quot;clever&quot; at avoiding the immune system. Sometimes they can produce shells which can't be broken down to derive epitopes from, sometimes they live within host cells and simply hide (the most well known example being HIV), other times they can present the same &quot;I'm part of the body!&quot; MHC proteins that tells the immune system not to attack them, and they can even hide in parts of the body where the immune system rarely visits (eyes, brain, other very specialized tissues).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And at times the pathogen can be both very adaptive and very &quot;clever&quot;, as in the case for &lt;em&gt;Staphylococcus aureas&lt;/em&gt; - which &lt;a href=&quot;http://en.wikipedia.org/wiki/Staphylococcus_aureus&quot;&gt;can inactivate antibodies through surface proteins&lt;/a&gt; and has the ability to adapt to new antibodies very quickly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can think of it like a game of chess. If you play against the same person all the time you're going to learn their moves, their strategy, and be able to beat them very quickly. If you switch partners, or your regular partner learns new moves, you'll spend some time adapting to the new play style you've encountered before being able to win consistently again. Bacteria and virii are simply very, very good at coming up with new play styles.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2013-02-01T21:48:27.477" LastActivityDate="2013-02-01T21:48:27.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7009" PostTypeId="2" ParentId="6884" CreationDate="2013-02-01T20:15:22.673" Score="4" Body="&lt;p&gt;Actually, most adult cells do not express telomerase or express it only at a very low levels. &lt;a href=&quot;http://en.wikipedia.org/wiki/Telomerase&quot; rel=&quot;nofollow&quot;&gt;Telmoerase&lt;/a&gt; is highly expressed only in cells that need to divide (e.g. stem cells), thus &quot;immortalizing&quot; them.&#xA;In fact, human cell lines which scientists work with can be &quot;immortalized&quot; by activation of telomerase (along with other things).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you may ask yourself: why not have telomerase activated all the time in all cells? Well, allowing a cell to reproduce easily can be a pretty bad thing... that is exactly what cancer does. Indeed, one of the things a cancer has to do is to activate the telomerases in order to be able to grow. This is also why cancer cell lines are &quot;immortal&quot;. This also suggests a potential cancer therapy - targeting telomerase - which is currently being pursued experimentally.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2013-02-01T20:28:55.353" LastActivityDate="2013-02-01T20:28:55.353" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7010" PostTypeId="1" AcceptedAnswerId="8849" CreationDate="2013-02-01T20:41:47.907" Score="9" ViewCount="5625" Body="&lt;p&gt;I asked a question about &lt;a href=&quot;https://biology.stackexchange.com/questions/6884/why-is-the-hydra-biologically-immortal&quot;&gt;immortality of hydra&lt;/a&gt; and learned good things about senescence. Now I would like to know about immortality in plants, if there is some kind of immortality in plants and how this occurs - how does it protect itself from senescence? &lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-12-10T20:34:01.803" Title="Is there any kind of immortality in plants?" Tags="&lt;plant-physiology&gt;&lt;senescence&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7011" PostTypeId="1" CreationDate="2013-02-01T21:02:45.547" Score="4" ViewCount="234" Body="&lt;p&gt;I've read a new study which suggests that yawning may help you keep a cool head. Also, the findings might hold some hope for sufferers of insomnia, migraines, and even epilepsy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any conclusion about what the function of yawning is and why do we yawn?&lt;/p&gt;&#xA;" OwnerUserId="2974" LastActivityDate="2013-02-02T13:57:55.743" Title="Why do we yawn?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7013" PostTypeId="2" ParentId="6919" CreationDate="2013-02-02T00:31:29.117" Score="1" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Do born-blind mammals and later-blinded mammals experience extraretinal&#xA;photoreception differently?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This article in Scientific American &lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=ask-the-brains-do-blind-people&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; where they refer to &amp;quot;Circadian and vision neu­ro­scientist Russell G. Foster of the University of Oxford&amp;quot; outlines:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&amp;quot;&lt;em&gt;In 1999 we found that mice lacking rods and cones were nonetheless&#xA;able to synchronize their circadian rhythm to the light/dark cycle.&lt;/em&gt;&#xA;These observations led to the discovery of an additional&#xA;photo­receptor system in the retina of humans and other mammals&#xA;consisting  of a small number of photosensi­­tive retinal ganglion&#xA;cells (called pRGCs). These cells are &lt;em&gt;most sensitive to blue light&lt;/em&gt;,&#xA;and, significantly, blue light is most effective in alleviating the&#xA;symptoms of SAD.&amp;quot; (I added italics to interesting points)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://online.wsj.com/article/SB10001424127887323968304578249783750566070.html?mod=e2tw&quot; rel=&quot;nofollow noreferrer&quot;&gt;WSJ&lt;/a&gt; repeats the blue-light thing and recites:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&amp;quot;In 2002, German researchers isolated one from green algae—a class of proteins called channelrhodopsins—that responded only to blue light. -- Depending on just how researchers tailor the virus that carries the light-sensitive protein, they now can target almost any type of neuron they want to study.&amp;quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So differently in a way that they lack the cones/rods in retina and some links to visual-cortex but no in a way of SAD: evolution have apparently developed methods for blind-born mammals to survive and to sync their inner clock. This resonates with the earlier facts by shigeta but I don't know whether there is any other thing to light -- perhaps UV radiation -- that could tune the internal clock.&lt;/p&gt;&#xA;&lt;p&gt;It looks that they are trying to find ways to engineer bionic-visions things similar to dobelle without physical modification of skull. The viruses tries to propagate certain photo-receptive protein into some spot where they try to activate them though external radiation. This is called &lt;a href=&quot;http://www.youtube.com/watch?v=I64X7vHSHOE&quot; rel=&quot;nofollow noreferrer&quot;&gt;optogenetics&lt;/a&gt; where they are trying to control certain behavioral things with optics.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;New puzzles&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;why do they use protein? Why not other things?&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;do we have many kind of photoreceptivity? Certain muscles (requires protein) activated by EM radiation? What about other cells such as fat-cells?&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;P.s. this is pretty fruitless to advance unless someone provides precise power spectrum of Valkee (requires apparently spectrum-analyzer) and polarization experiments. WSJ referred to trials where they use monochromatic light and coherent light in testing while Valkee-light can be pretty much anything.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1705" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-02-02T01:20:00.497" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7014" PostTypeId="1" CreationDate="2013-02-02T01:00:43.790" Score="9" ViewCount="290" Body="&lt;p&gt;I live in a semi-rural area in Germany, close to a park which trains go through every 20 minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Today, I saw something that left me perplexed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a large population of birds that look like crows or ravens, yet fatter. They seem to be quite social and move around in large groups. Today, I spotted one carefully laying sticks from a nearby tree on the train track while the others seemed to spectate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What exactly was that bird doing? Is this common? Did it have a purpose, or was it just coincidental?&lt;/p&gt;&#xA;" OwnerUserId="3010" LastEditorUserId="69" LastEditDate="2014-08-01T15:47:41.020" LastActivityDate="2014-08-02T19:23:46.703" Title="Birds placing sticks on train tracks?" Tags="&lt;ethology&gt;&lt;ornithology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7015" PostTypeId="2" ParentId="7006" CreationDate="2013-02-02T02:26:07.773" Score="4" Body="&lt;p&gt;The only information you are missing is a way to identify the splice sites. There are many ways of doing what you need. The simplest, assuming you are sure of the origins of the mRNA, is to use a BLAST flavor, either plain &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&amp;amp;BLAST_PROGRAMS=megaBlast&amp;amp;PAGE_TYPE=BlastSearch&amp;amp;SHOW_DEFAULTS=on&amp;amp;LINK_LOC=blasthome&quot; rel=&quot;nofollow&quot;&gt;BLASTn&lt;/a&gt; or, even better, &lt;a href=&quot;http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&quot; rel=&quot;nofollow&quot;&gt;BLAT&lt;/a&gt;, to compare your mRNA sequence to the genome of interest. BLAT really should be all you need if the mRNA comes from the genome you are aligning it to. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;BLAT however, has no knowledge of splice sites and will simply cut your mRNA so as to maximize local alignment scores. If you need something more sophisticated than BLAT, use a specialized aligner as @SteveLianoglou suggested. These programs include a model of splice sites (both canonical and non) and will align exons correctly. My personal favorite is &lt;a href=&quot;http://www.ebi.ac.uk/~guy/exonerate/&quot; rel=&quot;nofollow&quot;&gt;exonerate&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming you are using Linux (which you should be if you are planning on doing a lot of this type of analyses), you can install it on a Debian based distribution (such as Ubuntu and its variants) with this command:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;sudo apt-get install exonerate&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Then, to align the mRNA to its gene do:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;exonerate -m est2genome -n 1 mrna.txt dna.txt &amp;gt; out.txt &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;code&gt;-m&lt;/code&gt; is the model that &lt;code&gt;exonerate&lt;/code&gt; will use to align your two sequences. Since the important thing in your case is to correctly model splice sites, you should use either &lt;code&gt;est2genome&lt;/code&gt; or, if you are comparing different species, &lt;code&gt;coding2genome&lt;/code&gt;, or if you have a full length cDNA including UTRs, &lt;code&gt;cdna2genome&lt;/code&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;code&gt;-n 1&lt;/code&gt; means find the best match only. Assuming you are aligning an mRNA to its coding gene, this is all you are interested in. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-07-17T15:08:54.263" LastActivityDate="2013-07-17T15:08:54.263" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7016" PostTypeId="1" AcceptedAnswerId="7021" CreationDate="2013-02-02T09:54:10.190" Score="11" ViewCount="15201" Body="&lt;p&gt;There's a &lt;a href=&quot;http://greenspaces.in/blog/ted09/&quot; rel=&quot;nofollow&quot;&gt;claim&lt;/a&gt; that &lt;em&gt;Sansevieria trifasciata&lt;/em&gt; (Mother-in-law’s Tongue) generates oxygen from carbon dioxide during the night.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This seems surprising to me: that process requires energy; plants generate &lt;strong&gt;O₂&lt;/strong&gt; from &lt;strong&gt;CO₂&lt;/strong&gt; through photosynthesis, requiring light. So not photosynthesis, and no &lt;strong&gt;CO₂&lt;/strong&gt; absorption, at night.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I missing something, or is this claim false?&lt;/p&gt;&#xA;" OwnerUserId="925" LastEditorUserId="3340" LastEditDate="2014-10-09T15:12:41.703" LastActivityDate="2018-06-12T07:12:15.017" Title="Does Sansevieria trifasciata really absorb Carbon Dioxide at night?" Tags="&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7017" PostTypeId="1" AcceptedAnswerId="7027" CreationDate="2013-02-02T10:59:21.797" Score="4" ViewCount="5187" Body="&lt;p&gt;I'm trying to find any information on sizes of the hippocampus?&#xA;Ideally in the average adult male &amp;amp; female brain&lt;/p&gt;&#xA;" OwnerUserId="3011" LastEditorUserId="1320" LastEditDate="2013-02-02T19:45:37.910" LastActivityDate="2013-02-02T19:45:37.910" Title="What is the average volume of the hippocampus?" Tags="&lt;brain&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7019" PostTypeId="1" AcceptedAnswerId="9143" CreationDate="2013-02-02T12:41:00.840" Score="16" ViewCount="49117" Body="&lt;p&gt;For instance, I realise being able to absorb simple sugars in the mouth is pivotal in the rapid action of oral glucose gel. Thus I was wondering what nutrients in general can be absorbed directly within the mouth, and &lt;em&gt;at what speed&lt;/em&gt;?&lt;/p&gt;&#xA;" OwnerUserId="3013" LastEditorUserId="1320" LastEditDate="2013-02-02T17:20:52.333" LastActivityDate="2014-07-11T17:13:21.557" Title="What nutrients can humans absorb in the mouth?" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;&lt;food&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7020" PostTypeId="2" ParentId="7011" CreationDate="2013-02-02T13:57:55.743" Score="2" Body="&lt;p&gt;In an abstract, &lt;a href=&quot;http://www.brown.edu/Departments/EEB/brainerd_lab/brainerd-sicb-2004.php&quot; rel=&quot;nofollow&quot;&gt;Brainerd at al. (2004)&lt;/a&gt; report the presence of yawn-like behaviors in &quot;cartilaginous and ray-finned fishes, a lungfish, salamanders, caecilians, mammals, turtles, lizards, an alligator and birds&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So clearly the motor patterns necessary for this behavior evolved before air breathing and apparently have been conserved for ~400 million years. They reject the increased oxygen delivery hypothesis and associate yawning with stretching:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Yawning also has been thought to serve a similar physiological&#xA;  function to stretching. We measured the stretching movements of fins&#xA;  and limbs in association with yawns, and found that they follow the&#xA;  same movement pattern as jaw opening and closing. This lends support&#xA;  to the existing hypothesis that yawning and stretching serve a similar&#xA;  function, but the detailed nature of this function remains unclear.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-02-02T13:57:55.743" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7021" PostTypeId="2" ParentId="7016" CreationDate="2013-02-02T15:30:03.987" Score="11" Body="&lt;p&gt;This is an interesting topic!  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Crassulacean_acid_metabolism&quot; rel=&quot;noreferrer&quot;&gt;Crassulacean acid metabolism&lt;/a&gt; is a second CO₂ fixation pathway where &lt;a href=&quot;http://en.wikipedia.org/wiki/Carbon_fixation#CAM_plants&quot; rel=&quot;noreferrer&quot;&gt;CO₂ is absorbed at night&lt;/a&gt;.  The CO₂ is fixed into &lt;a href=&quot;http://en.wikipedia.org/wiki/Malic_acid&quot; rel=&quot;noreferrer&quot;&gt;maleic acid&lt;/a&gt; HOOC-CH₂CH(OH)-COOH which stores some of the CO₂ in the form of carboxyl groups.  During the day carboxylases release the CO₂ for fixation during the day.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is an adaptation where the stomata open at night to take in the CO₂ and are closed during the day - the plants sort of 'hold their breath'.  The energy for this process is derived for glycolysis which were stored during the day (&lt;a href=&quot;http://jxb.oxfordjournals.org/content/53/369/569.full&quot; rel=&quot;noreferrer&quot;&gt;nice detailed review here&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper says that about 6% of plants (&lt;a href=&quot;http://en.wikipedia.org/wiki/Sansevieria#Air_purification&quot; rel=&quot;noreferrer&quot;&gt;including Mother-in-Laws Tongue&lt;/a&gt;) do this and you can imagine with night breathing how closing the stomata during the day would really help with dehydration.  Its interesting to note that this is found in a wide variety of plants &quot;CAM is found in five taxonomic classes, comprising monocots and dicots, encompassing 33 families and 328 genera&quot;.  That says that CAM is a pretty old development in plant evolution and not so expensive that it is easily lost.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3340" LastEditDate="2014-10-09T15:12:01.713" LastActivityDate="2014-10-09T15:12:01.713" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7022" PostTypeId="2" ParentId="7016" CreationDate="2013-02-02T15:46:45.127" Score="9" Body="&lt;p&gt;Shigeta submitted his answer as I was writing this!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sanseveria is one of a wide group of plants (mainly succulents) that adopt a photosynthetic strategy referred to as &lt;a href=&quot;http://en.wikipedia.org/wiki/CAM_photosynthesis&quot;&gt;crassulacean acid metabolism (CAM)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recall the basics of photosynthesis. The light-dependent reactions use energy from captured photons to generate ATP and NADPH, with the generation of O&lt;sub&gt;2&lt;/sub&gt;. In the light-independent reactions (the Calvin cycle) this ATP and NADPH is used to fix CO&lt;sub&gt;2&lt;/sub&gt; to form three carbon sugars, which can then enter standard metabolic pathways to produce other metabolites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to obtain CO&lt;sub&gt;2&lt;/sub&gt; for the fixation reactions plants have pores in their leaves called stomata to promote gas exchange (via diffusion). This presents a challenge for plants that grow in arid conditions: if they open their stomata during the day they lose water as water vapour. Many such plants use CAM to solve this problem. Basically what these plants do is to only open their stomata at night, capturing CO&lt;sub&gt;2&lt;/sub&gt; in the form of organic acids (oxaloacetate, malate, maleate) which are stored in vacuoles. Then, during the day, these acids can be metabolised to release the CO&lt;sub&gt;2&lt;/sub&gt; again for use in the photosynthetic reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notice that in this scheme the O&lt;sub&gt;2&lt;/sub&gt; will still be generated during the day. So when does it leave? Does it have to wait until the stomata open at night, or is it able to diffuse out through cells (recall that O&lt;sub&gt;2&lt;/sub&gt; readily diffuses through biological membranes)? I have been unable to find a definitive answer to this question so far (this is old literature), but my guess is that it is lost throughout the day.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-02-02T15:46:45.127" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7023" PostTypeId="1" AcceptedAnswerId="7026" CreationDate="2013-02-02T15:46:56.193" Score="3" ViewCount="171" Body="&lt;p&gt;The most &lt;a href=&quot;http://en.wikipedia.org/wiki/Transformation_%28genetics%29#Plants&quot; rel=&quot;nofollow&quot;&gt;common method to transform plants&lt;/a&gt; is by soaking plant tissue in cultures of agrobacteria (&lt;a href=&quot;http://en.wikipedia.org/wiki/Agrobacterium&quot; rel=&quot;nofollow&quot;&gt;this is not their current classification&lt;/a&gt;) which transfer DNA into the plants.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is lateral gene transfer ability like this found a lot in nature?  Is &lt;em&gt;agrobacterium tumificans&lt;/em&gt; especially good at this or is its use in plant genetics only because this strain is well studied?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is a method like this used for animal cells at all?  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3952" LastEditDate="2013-08-01T03:09:59.057" LastActivityDate="2013-08-01T03:09:59.057" Title="How common is bacterial mediated transformation? In plants? In animal cells?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;botany&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7025" PostTypeId="2" ParentId="7023" CreationDate="2013-02-02T16:31:15.217" Score="3" Body="&lt;p&gt;In animal cells the process is called &lt;em&gt;transfection&lt;/em&gt;, to differentiate from &lt;em&gt;transformation&lt;/em&gt; which is the process by which cells become immortalized (cancerous). I'm mainly familiar with mammalian cells, and in these systems some &lt;a href=&quot;http://en.wikipedia.org/wiki/Transfection&quot; rel=&quot;nofollow&quot; title=&quot;reaction&quot;&gt;reaction&lt;/a&gt; is required to open pores of some sort in the cell membrane to allow the genetic material to enter. Viruses can mediate cellular entry on their own, but I am unaware of any method that uses live bacteria (although this doesn't mean that some specialized method doesn't exist).&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-02-02T16:31:15.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7026" PostTypeId="2" ParentId="7023" CreationDate="2013-02-02T17:18:50.620" Score="3" Body="&lt;p&gt;An early report of conjugative transfer into mammalian cells (CHO cells) is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/ng779&quot; rel=&quot;nofollow&quot;&gt;Waters, VL (2001) Conjugation between bacterial and mammalian cells, Nat. Genet. 29: 375–376.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This work used the broad host range plasmid RK2 to mobilise shuttle vectors carrying selectable markers. To rule out transfection DNAse I was added (and in controls this was shown to block transfection by a large amount of vector DNA). In any case, the fact that the transfer of the vector required the presence of the mobilising plasmid is pretty strong evidence for a conjugative mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also more recent evidence for transfer into human cells via Type IV secretion systems: here is a recent example:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=21908662&quot; rel=&quot;nofollow&quot;&gt;Fernandez-Gonzalez et al. (2011),Transfer of R388 Derivatives by a Pathogenesis-Associated Type IV Secretion System into both Bacteria and Human Cells. J Bacteriol 193: 6257-6265&lt;/a&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And here is a recent review of the topic:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=22748513&quot; rel=&quot;nofollow&quot;&gt;Llosa et al. (2012) New perspectives into bacterial DNA transfer to human cells Trends in Microbiology 20: 355-359.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="948" LastEditDate="2013-02-03T02:22:08.167" LastActivityDate="2013-02-03T02:22:08.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7027" PostTypeId="2" ParentId="7017" CreationDate="2013-02-02T17:34:23.397" Score="4" Body="&lt;p&gt;The average values of right hippocampus were recorded as follows weight 4.11572 gm, length 6.996 cm, width 1.998,volume 13.978 and surface area11.839 cubic centimetre while left hippocampus mean values were weight 3.96458gms,length 6.995, width 1.998,volume 13.976 and surface area 11.713cc. &lt;a href=&quot;http://www.cibtech.org/J%20MEDICAL%20SCIENCES/PUBLICATIONS/2012/JMS-02-02/27-JMS%2039%20Adult%20morphometrice.pdf&quot; rel=&quot;nofollow&quot;&gt;B. Narasinga Rao, K.R.S. Prasad Rao, R. Ramana Rao. 2012. Morphometric study of hippocampus in adult human brains. &lt;em&gt;Int J Basic Appl Med Sci&lt;/em&gt; 2: 139-143.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Men and women had identical volumes of amygdala and hippocampus, as well as dorsal prefrontal cortex &lt;a href=&quot;http://cercor.oxfordjournals.org/content/12/9/998.full&quot; rel=&quot;nofollow&quot;&gt;Ruben C. Gur, Faith Gunning-Dixon, Warren B. Bilker, Raquel E. Gur. 2002. Sex Differences in Temporo-limbic and Frontal Brain Volumes of Healthy Adults. &lt;em&gt;Cerebral Cortex&lt;/em&gt; 12: 998-1003&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hippocampal volume change with age: Hippocampal volume diminished by 20% from 3,584 ± 136 mm3 at age 36 to 2,870 ± 220 mm3 at age of 85, corresponding to a volume loss of about 14.6 mm3/year (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2733348/&quot; rel=&quot;nofollow&quot;&gt;Schuff N., et al. 1999. Age-related metabolite changes and volume loss in the hippocampus by magnetic resonance spectroscopy and imaging. &lt;em&gt;Neurobiol Aging&lt;/em&gt; 20: 279–285&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="1839" LastEditorUserId="107" LastEditDate="2013-02-02T18:22:56.817" LastActivityDate="2013-02-02T18:22:56.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7028" PostTypeId="1" AcceptedAnswerId="7039" CreationDate="2013-02-02T19:51:44.607" Score="1" ViewCount="43" Body="&lt;p&gt;Do Fatty Acid Synthase (FAS) Inhibitors (e.g. cerulenin) selectively induce apoptosis in cancer cells without inducing the same in healthy human cells?&lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-02-02T22:12:23.667" Title="Do Fatty Acid Synthase Inhibitors Selectively induce Apoptosis in Cancer cells without inducing the same in healthy human cells?" Tags="&lt;cancer&gt;&lt;fatty-acid-synthase&gt;&lt;apoptosis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7029" PostTypeId="5" CreationDate="2013-02-02T19:55:54.147" Score="0" Body="&lt;p&gt;The chief enzyme involved in &lt;strong&gt;fatty acid biosynthesis&lt;/strong&gt;. Fatty acid synthase inhibitors such as &lt;strong&gt;cerulenin&lt;/strong&gt; (a natural product produced by the fungi &lt;em&gt;Sarocladium oryzae&lt;/em&gt;) have been found to have &lt;strong&gt;antineoplastic&lt;/strong&gt;, &lt;strong&gt;antibiotic&lt;/strong&gt;, &lt;strong&gt;antifungal&lt;/strong&gt; and &lt;strong&gt;antiparasitic&lt;/strong&gt; actions.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-02T20:13:28.287" LastActivityDate="2013-02-02T20:13:28.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7030" PostTypeId="4" CreationDate="2013-02-02T19:55:54.147" Score="0" Body="The chief enzyme involved in fatty acid biosynthesis. They include cerulenin, a natural products produced by the fungi Sarocladium oryzae." OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-02T20:13:21.000" LastActivityDate="2013-02-02T20:13:21.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7031" PostTypeId="5" CreationDate="2013-02-02T19:59:43.217" Score="0" Body="&lt;p&gt;Programmed cell death. It is designed to prevent old damaged cells from mutating into neoplastic (cancer) cells. Drugs that selectively induce apoptosis in cancer cells are pursued as antineoplastic (anti-cancer) agents. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-02T20:12:33.357" LastActivityDate="2013-02-02T20:12:33.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7032" PostTypeId="4" CreationDate="2013-02-02T19:59:43.217" Score="0" Body="A form of programmed cell death designed to remove old damaged cells.  This prevents them from mutating into neoplastic (cancer) cells, and also plays a role in control of viral infection. " OwnerUserId="1813" LastEditorUserId="24613" LastEditDate="2020-01-02T14:04:54.437" LastActivityDate="2020-01-02T14:04:54.437" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="7034" PostTypeId="5" CreationDate="2013-02-02T21:48:27.853" Score="0" Body="&lt;p&gt;&lt;strong&gt;Benzodiazepines&lt;/strong&gt; are a class of compounds that have &lt;strong&gt;two structural features&lt;/strong&gt; in common and &lt;strong&gt;one pharmacological action&lt;/strong&gt; in common. The structural features are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A diazepine group&lt;/li&gt;&#xA;&lt;li&gt;Two benzene rings&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;See figure below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pharmacological action they have in common is that they all serve as positive allosteric modulators at the GABA&lt;sub&gt;A&lt;/sub&gt; receptor. They do this by binding to the &lt;em&gt;benzodiazepine site&lt;/em&gt; on the the aforementioned receptor. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sTfNz.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="107" LastEditDate="2013-02-02T22:11:06.353" LastActivityDate="2013-02-02T22:11:06.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7035" PostTypeId="4" CreationDate="2013-02-02T21:48:27.853" Score="0" Body="Benzodiazepines are a class of compounds that have two structural features in common and they also serve as a positive allosteric modulator at the GABA-A receptor which inhibits CNS function. " OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-02T22:10:10.833" LastActivityDate="2013-02-02T22:10:10.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7036" PostTypeId="5" CreationDate="2013-02-02T21:54:54.200" Score="0" Body="&lt;p&gt;&lt;strong&gt;γ-Aminobutyric acid&lt;/strong&gt; (GABA for short) is the &lt;strong&gt;chief inhibitory neurotransmitter&lt;/strong&gt; in the mammalian &lt;strong&gt;central nervous system&lt;/strong&gt; (CNS). It is an amino acid that is synthesised in the mammals from &lt;strong&gt;glutamate&lt;/strong&gt; (the chief excitatory neurotransmitter in the mammalian CNS) which in itself is synthesised from &lt;strong&gt;L-glutamine&lt;/strong&gt;. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-02T23:24:37.767" LastActivityDate="2013-02-02T23:24:37.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7037" PostTypeId="4" CreationDate="2013-02-02T21:54:54.200" Score="0" Body="gamma-Aminobutyric acid (GABA for short) is the chief inhibitory neurotransmitter in the mammalian central nervous system.  " OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-02T23:24:47.580" LastActivityDate="2013-02-02T23:24:47.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7038" PostTypeId="1" CreationDate="2013-02-02T22:09:31.120" Score="2" ViewCount="72" Body="&lt;p&gt;Sulforaphane is a isothiocyanate found in cruciferous vegetables including broccoli and cauliflower. Its 2D structure is as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9eOiF.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's been found to serve as a &lt;strong&gt;histone deacetylase 6&lt;/strong&gt; (HDAC6) inhibitor and to inhibit androgen receptor expression in prostate cancer cells.&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2757849/pdf/zpq16663.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;&lt;/sup&gt; This caused me to become curious as to whether it would do the same in lower motor neuron cells and thus manage to prevent their polyglutamine-induced death and thus halt the progression of spinobulbar muscular atrophy (SBMA; Kennedy's disease).&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-02T22:53:58.417" LastActivityDate="2018-06-12T04:12:13.600" Title="What does effect would Sulforaphane have on Kennedy's Disease?" Tags="&lt;vegetable&gt;&lt;neurodegenerative-disorders&gt;&lt;histone-deacetylase&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7039" PostTypeId="2" ParentId="7028" CreationDate="2013-02-02T22:12:23.667" Score="1" Body="&lt;p&gt;I found this reference: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC490000/&quot; rel=&quot;nofollow&quot;&gt;&quot;Inhibition of fatty acid synthase (FAS) suppresses HER2/neu (erbB-2) oncogene overexpression in cancer cells&quot;&lt;/a&gt;.   Cerulenin is not a magic bullet, but in some cases it may help. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-02-02T22:12:23.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7040" PostTypeId="5" CreationDate="2013-02-02T22:21:59.383" Score="0" Body="&lt;p&gt;&lt;strong&gt;Histone deacetylase&lt;/strong&gt; (HDAC) is a family of enzymes (the known members of which are currently numbered 1-11) that play key roles in gene expression. They seem to play key roles in:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Tumorigenesis&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Various protein's expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The androgen receptor&lt;/li&gt;&#xA;&lt;li&gt;The glucocorticoid receptor&lt;/li&gt;&#xA;&lt;li&gt;Heat shock protein 90 (HSP90)&lt;/li&gt;&#xA;&lt;li&gt;α-Tubulin&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and many others&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;HIV latency&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and other processes of biologic significance. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-02T23:25:37.657" LastActivityDate="2013-02-02T23:25:37.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7041" PostTypeId="4" CreationDate="2013-02-02T22:21:59.383" Score="0" Body="Histone deacetylase (HDAC) is a family of enzymes that play key roles in gene expression." OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-02T23:49:36.920" LastActivityDate="2013-02-02T23:49:36.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7042" PostTypeId="5" CreationDate="2013-02-02T22:39:27.363" Score="0" Body="&lt;p&gt;Neurodegenerative disorders are disorders characterised by progressive neuronal cell death. Examples in humans include (but are &lt;strong&gt;not&lt;/strong&gt; limited to):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Progressive forms of dementia&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which include (but are &lt;strong&gt;not&lt;/strong&gt; limited to):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;AIDS dementia complex [which is caused, usually, by an uncontrolled HIV infection]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Alzheimer's disease (AD)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;Dementia with Lewy Bodies (DLB)&lt;/li&gt;&#xA;&lt;li&gt;Vascular dementia&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Huntington's disease&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Motor Neuron Diseases&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which include (but are &lt;strong&gt;not&lt;/strong&gt; limited to):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Amyotrophic lateral sclerosis (ALS; Lou Gehrig's disease)&lt;/li&gt;&#xA;&lt;li&gt;Primary lateral sclerosis (PLS)&lt;/li&gt;&#xA;&lt;li&gt;Progressive muscular atrophy (PMA)&lt;/li&gt;&#xA;&lt;li&gt;Spinal muscular atrophy (SMA)&lt;/li&gt;&#xA;&lt;li&gt;Spinobular muscular atrophy (SBMA; Kennedy's disease)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Multiple Sclerosis&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;Parkinson's disease&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Prion diseases&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which include (but are &lt;strong&gt;not&lt;/strong&gt; limited to):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Creutzfeldt-Jakob disease (CJD)&lt;/li&gt;&#xA;&lt;li&gt;Fatal familial insomnia (FFI)&lt;/li&gt;&#xA;&lt;li&gt;Gerstmann-Sträussler-Scheinker syndrome (GSSS)&lt;/li&gt;&#xA;&lt;li&gt;Kuru&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-02T23:20:27.410" LastActivityDate="2013-02-02T23:20:27.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7043" PostTypeId="4" CreationDate="2013-02-02T22:39:27.363" Score="0" Body="Neurodegenerative disorders are disorders characterised by progressive neuronal cell death. " OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-02T23:25:43.150" LastActivityDate="2013-02-02T23:25:43.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7044" PostTypeId="5" CreationDate="2013-02-02T22:48:55.687" Score="0" Body="&lt;p&gt;Analgesia is the medical term for pain relief. Some definitions require that analgesia and anaesthesia (impairment of consciousness that's precipitated by the use of drugs) be clearly distinct phenomena.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-02T23:19:45.070" LastActivityDate="2013-02-02T23:19:45.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7045" PostTypeId="4" CreationDate="2013-02-02T22:48:55.687" Score="0" Body="Analgesia is the medical term for pain relief." OwnerUserId="24354" LastEditorUserId="24354" LastEditDate="2020-07-07T02:38:43.197" LastActivityDate="2020-07-07T02:38:43.197" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="7046" PostTypeId="1" AcceptedAnswerId="7049" CreationDate="2013-02-03T03:21:45.480" Score="14" ViewCount="608" Body="&lt;p&gt;I've read that the eye color at birth for most humans and for cats may not always be the the true genetic color at first. This is due to the lack of melanin in the iris. This makes sense as there is no light in the womb to stimulate the production of melanin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question(s) though is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why does the lack of said melanin produce a blue/bluish colored iris?&lt;/li&gt;&#xA;&lt;li&gt;Why is it not say green, red, clear, etc?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1827" LastActivityDate="2019-10-25T01:33:30.137" Title="Why Do Most Humans &amp; Cats Have Blue/Bluish Eyes At Birth?" Tags="&lt;iris&gt;&lt;melanin&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7047" PostTypeId="1" AcceptedAnswerId="7769" CreationDate="2013-02-03T04:58:09.697" Score="6" ViewCount="11527" Body="&lt;p&gt;How does formaldehyde cause protein-DNA crosslinking?  I would guess it's because the strongly polar water molecule interacts strongly with polar residues on a protein-DNA complex, and adding a less polar solvent causes the DNA and protein to pull more tightly on each other than their pull on the solvent, but I haven't been able to find an answer online.&lt;/p&gt;&#xA;" OwnerUserId="1387" LastEditorUserId="1387" LastEditDate="2013-02-03T17:35:03.673" LastActivityDate="2013-04-05T14:55:51.317" Title="How does formaldehyde cause protein-DNA crosslinking?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;protein-binding&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7048" PostTypeId="2" ParentId="7046" CreationDate="2013-02-03T08:07:03.350" Score="17" Body="&lt;p&gt;The generation of iris color is quite complex and the exact color of the eyes depends upon many different factors, not just melanin. In fact, blue coloration does not depend on a specific chemical, but on the structure of the eye itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This very nice review (free) summarizes our current understanding:&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19619260&quot;&gt;Genetics of human iris colour and patterns&lt;/a&gt; - Sturm and Larsson, 2009&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the Introduction (bold is mine)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the brown iris there is an abundance of melanocytes and melanin in the  anterior border layer and stroma whereas in the blue iris these layers contain very little melanin. &lt;strong&gt;As light traverses these relatively melanin-free layers, collagen fibrils of the iris scatter the short blue wavelengths to the surface, thus a blue iris is a consequence of structure not of major differences in chemical composition&lt;/strong&gt;. Different shades of blue, and in irises with a limited amount of melanin, different shades of grey, green and hazel, are determined&#xA;  by the thickness and density of the iris itself and the extent of accumulation of white collagen fibres, as well as patches of tissue loss in the anterior border layer and stroma.&#xA;  However, a careful examination of people’s irises makes it clear that there are characteristics other than eye colour that present in the human iris. The iris has been analysed to show that it can display a degree of complexity encompassing over 240 degrees of freedom (Daugman, 2003).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="115" LastEditorUserId="1320" LastEditDate="2013-02-03T08:15:08.543" LastActivityDate="2013-02-03T08:15:08.543" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7049" PostTypeId="2" ParentId="7046" CreationDate="2013-02-03T08:13:58.747" Score="23" Body="&lt;p&gt;The blue colour is an example of &lt;a href=&quot;http://en.wikipedia.org/wiki/Structural_color&quot;&gt;&lt;strong&gt;structural colour&lt;/strong&gt;&lt;/a&gt;, caused by light interacting physically with something. Some examples of structural colour are the iridescence of insect wings and body surfaces (usually caused by repeating chitinous structures), and of certain birds feathers, as well as the non-iridescent colours of the blue and yellow macaw.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of the eye it is the stroma of the iris that is responsible. This is a network of fibrous tissue which scatters light. When light is scattered in this way (Rayleigh scattering) it is the short wavelengths which are most scattered. So when you look at the sky (away from the sun) you are seeing diffuse blue light created by this scattering in the atmosphere. In the case of the iris what you are seeing is light reflected from the eye being scattered within the iris, creating the diffuse blue colour. As you say in the question, everything else is down to melanin. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-02-03T08:13:58.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7051" PostTypeId="1" AcceptedAnswerId="7059" CreationDate="2013-02-03T10:23:42.130" Score="11" ViewCount="5096" Body="&lt;p&gt;Who has a more varied reproduction rate in modern western societies - men or women? The average rate is the same of course, but I wonder which sex have higher variance - higher variance means that reproduction is more concentrated in some subgroup of given sex so this subgroup transfer their genes at higher rates then average rate in whole population. The next question would be 'is that subgroup somehow homogeneous' ?&lt;/p&gt;&#xA;" OwnerUserId="3016" LastEditorUserId="3016" LastEditDate="2017-01-05T21:18:28.657" LastActivityDate="2017-01-05T21:18:28.657" Title="Which sex has higher variance of reproductive rate in modern societies - male or females?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7053" PostTypeId="1" CreationDate="2013-02-03T12:47:27.390" Score="14" ViewCount="13001" Body="&lt;p&gt;Sorry if this question seems strange, but in the recent time I have been interested in the question of what life is and how you can define life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question: &#xA;How long can individual cells live on a human body from the point the human dies? When a human dies, legally he is dead, but how is the medical explaination? Can a human be partly dead, that the heart and brain has stopped, but the cells on the body are still alive? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you talk about a human life, is it &lt;strong&gt;one life&lt;/strong&gt; or could you consider each cell on the body as a living piece and the whole human body itself including the consciousness is just a container for the cells?&lt;/p&gt;&#xA;" OwnerUserId="693" LastActivityDate="2015-03-05T12:36:44.723" Title="Can you consider a human as alive, or is it the cells on the body that are alive?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;life&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7054" PostTypeId="2" ParentId="7053" CreationDate="2013-02-03T18:28:25.200" Score="14" Body="&lt;p&gt;The definition of &lt;em&gt;life&lt;/em&gt; is the main issue here. That is one of the great philosophical questions in Biology (and not only Biology) and is way beyond the simple Q&amp;amp;A format of this site. However, most definitions of life can be boiled down to&lt;sup&gt;1&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A self replicating entity that interacts&lt;sup&gt;2&lt;/sup&gt; with its environment. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Or, even more simply&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21875147.1&quot; rel=&quot;noreferrer&quot;&gt; [1]&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Life is self-reproduction with variations&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In both cases, the answer to your question depends on which level you are focusing on, your &lt;em&gt;resolution&lt;/em&gt; if you like. If you take a human cell and apply either of the definitions above, it is alive. A cell is capable of autonomous reproduction, and metabolizes substances harvested from its environment. The same holds true of you look at the human body. However, the definition will not hold for a &lt;em&gt;part&lt;/em&gt; of the human body, for example an arm or kidney. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider also that a human cell is capable of making more copies of itself, more individual cells. A human body is also capable of making more copies of itself, more human bodies. They can, therefore, both be taken as alive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are even more complex examples like &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dictyostelium_discoideum&quot; rel=&quot;noreferrer&quot;&gt;Dictyostelium discoideum&lt;/a&gt;&lt;/em&gt; an amoeba that can exist (and be alive) either as a single cell or as a colony sporting different cell types and rudimentary organization. However, the organism is &lt;em&gt;alive&lt;/em&gt; in both of these stages. In one case, you would consider the cell to be the fundamental unit of &lt;em&gt;D. discoideum&lt;/em&gt; life, and in the other you could consider the &lt;em&gt;colony&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to answer your question &lt;em&gt;both&lt;/em&gt; a human cell (as long as it is alive, actively metabolising and capable of reproducing) and the entire human body can be taken as alive. That my cells are alive does not lessen the fact that I am too. It is just a matter of perspective.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21875147.1&quot; rel=&quot;noreferrer&quot;&gt;Trifonov EN., Vocabulary of definitions of life suggests a definition. &lt;em&gt;J Biomol Struct Dyn.&lt;/em&gt; 2011 Oct;29(&lt;strong&gt;2&lt;/strong&gt;):259-66.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt; Yes, I know this is a simplification, I just don't want to be drawn in to a long winded discussion on what the definition of life is. My answer is applicable to any of them really.&lt;br&gt;&#xA;&lt;sup&gt;2&lt;/sup&gt; Metabolism can be seen as a form of interaction.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2015-03-05T12:36:44.723" LastActivityDate="2015-03-05T12:36:44.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7055" PostTypeId="1" AcceptedAnswerId="7057" CreationDate="2013-02-03T22:10:17.587" Score="12" ViewCount="232" Body="&lt;p&gt;When analyzing data from cortex, we often try to understand what each neuron does in terms of its inputs from other neurons - a specific kind of a systems identification strategy. Most current approaches use generalized linear models for that purpose (&lt;a href=&quot;http://klab.smpp.northwestern.edu/wiki/images/0/0f/Stevenson_Infer_connect_btwn_neurons_2008.pdf&quot; rel=&quot;nofollow&quot;&gt;Review article&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For very small systems like the worm c.elegans it must be possible to record from all neurons at the same time, at least optically. How well can we understand the output of each neuron based on its inputs in such simple systems? What are the best databases to ask such questions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason I am asking this question now is because the &lt;a href=&quot;http://www.humanbrainproject.eu/&quot; rel=&quot;nofollow&quot;&gt;human brain project&lt;/a&gt; that just got roughly a billion dollars in funding basically needs such data for every cell in the whole brain.&lt;/p&gt;&#xA;" OwnerUserId="3020" LastEditorUserId="500" LastEditDate="2013-02-07T20:25:28.717" LastActivityDate="2013-02-07T20:25:28.717" Title="Systems identification in small neural network" Tags="&lt;neuroscience&gt;&lt;bioinformatics&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7056" PostTypeId="2" ParentId="6988" CreationDate="2013-02-04T01:15:40.513" Score="3" Body="&lt;p&gt;On the G6G Directory of OMICS and Intelligent software, I searched for &quot;QSAR Analysis, and received two product abstracts:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) SYBYL®-X Suite which contained:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;3D QSAR: use the power of industry leading CoMFA in a new way to&#xA;generate novel ideas for R-groups - predict the level of biological&#xA;activity or potency based on structure-activity data, Not just yes/No&#xA;activity predictions;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Cheminformatics: produce highly focused queries that avoid false&#xA;positives using a rich set of 3D queries; on-the-fly conformational&#xA;searching means you only store a single conformation of your&#xA;molecules, keeping database size small and very transportable; and...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Link to this abstract:&#xA;&lt;a href=&quot;http://g6g-softwaredirectory.com/bio/proteomics/structure-modeling/20710-Tripos-SYBYL-X-Suite.php&quot; rel=&quot;nofollow&quot;&gt;http://g6g-softwaredirectory.com/bio/proteomics/structure-modeling/20710-Tripos-SYBYL-X-Suite.php&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;2) Fujitsu GhostMiner &lt;/p&gt;&#xA;&#xA;&lt;p&gt;GhostMiner can be employed in a number of business intelligence areas and the following areas:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Bioinformatics - genetics, proteomics, Quantitative Structure&#xA;Activity Relationship (QSAR) modeling...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Link to this abstract:&#xA;&lt;a href=&quot;http://g6g-softwaredirectory.com/ai/neural-networks/20154-FQS-Poland-Fujitsu-GhostMiner.php&quot; rel=&quot;nofollow&quot;&gt;http://g6g-softwaredirectory.com/ai/neural-networks/20154-FQS-Poland-Fujitsu-GhostMiner.php&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Perhaps the above will help.&lt;/p&gt;&#xA;" OwnerUserId="3022" LastEditorUserId="107" LastEditDate="2013-02-04T03:39:45.023" LastActivityDate="2013-02-04T03:39:45.023" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7057" PostTypeId="2" ParentId="7055" CreationDate="2013-02-04T03:45:25.343" Score="15" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;For very small systems like the worm c.elegans it must be possible to record from all neurons at the same time, at least optically. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;While it is true that whole organism optical recording is technically possible in C. elegans, I'm not aware of any published work  where all neurons were identified and recorded from simultaneously and then combined with connectivity data in a systematic way. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I should note, that this isn't limited to C. elegans. Florian Engert's lab has published whole-organism recordings from zebrafish as well. At the moment, though, there are still technical challenges to work out before we get the input-output relationships you desire on a whole organism level. First off, the recordings aren't truly simultaneous, in the sense that it still takes time to build up 3D images from z-stacks. Second, the image processing to label neurons is not yet robust.  And finally, the most popular optical indicators  are based on calcium levels and thus provide only a proxy for membrane potential and furthermore they have limitations in time resolution, range and accuracy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The field, however, is progressing rapidly and I suspect that these challenges will be overcome in the next few years.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What are the best databases to ask such questions?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are no database yet for C. elegans neural activity,  likely because the number of groups publishing optical recordings in C. elegans is still fairly small. But as more labs pick up the technique, I think the value of a database will become more obvious to the community and the &lt;a href=&quot;http://www.openworm.org/&quot;&gt;OpenWorm project&lt;/a&gt; is providing some well-needed leadership in this area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, I should point out that in the end we may find that neural activity and connectivity provide only one part of the story. It is likely that in C. elegans neuromodulators and other &quot;unwired&quot; connections between neurons could play very important roles as well. &lt;/p&gt;&#xA;" OwnerUserId="3023" LastEditorUserId="3021" LastEditDate="2013-02-04T14:22:12.730" LastActivityDate="2013-02-04T14:22:12.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7058" PostTypeId="2" ParentId="6988" CreationDate="2013-02-04T07:31:43.197" Score="0" Body="&lt;p&gt;Click2drug is a good ressource for in silico studies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.click2drug.org/index.html#QSAR&quot; rel=&quot;nofollow&quot;&gt;See this link.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1902" LastActivityDate="2013-02-04T07:31:43.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7059" PostTypeId="2" ParentId="7051" CreationDate="2013-02-04T13:47:37.490" Score="11" Body="&lt;p&gt;&lt;strong&gt;Sperm are cheaper than eggs&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Bateman's Principle the males of a species are (typically) more able to produce a greater variance in the number of offspring. This is because generally the males can produce many gametes and achieve many matings whereas females are limited by the number of eggs, resources, and time lost to pregnancy. Therefore, just by simple logic, it would appear likely that males have greater variance in mating success (strong/attractive males would be able to mate with many females while weak/unattractive males would have little to no offspring). See &lt;a href=&quot;http://en.wikipedia.org/wiki/Bateman%27s_principle&quot;&gt;Wikipedia for an introduction to Bateman's Principle&lt;/a&gt;. Also see this paper about &lt;a href=&quot;http://www.jstor.org/stable/10.2307/2460741&quot;&gt;sexual selection and mating success variance&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;An Example&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An extreme example of &lt;a href=&quot;http://www.sfu.ca/biology/faculty/reynolds/The_Reynolds_Lab/Publications_files/Mackenzie%20et%20al.%20AN%2095.pdf&quot;&gt;higher variance in male mating success is that seen in lekking species&lt;/a&gt;. These species form groups of males called leks where females enter and choose mates. Often one/few males will sire the majority of offspring in the next generation. Fallow deer are one lekking species where &lt;a href=&quot;http://www.ivb.cz/folia/57/3/269_273.pdf&quot;&gt;males have higher mating success variation&lt;/a&gt; than expected by chance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In Humans&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a &lt;a href=&quot;http://dienekes.blogspot.se/2009/05/gender-differences-in-reproductive.html&quot;&gt;blog post&lt;/a&gt; discussing a paper which showed that males have greater reproductive success variance than females in humans. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3096780/&quot;&gt;In the paper&lt;/a&gt; see table 1 (Vm:Vf column) which indicates the majority, particularly those close to ancestral type lifestyles, have much greater variance in male reproductive success. Only one measured (Finland) is the reverse pattern.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2013-02-04T13:47:37.490" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7060" PostTypeId="1" CreationDate="2013-02-04T15:10:29.620" Score="4" ViewCount="230" Body="&lt;p&gt;So recently our commercial kitchen got some bunches of bananas with a curious feature. On the inside they were firm and delicious (no jokes, please), on the outside they looked incredibly sickly. Specifically, they had this grey/green/brownish yellow with lots of black spots, some of them with &lt;em&gt;depth&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Situational details: these are Cavendish bananas, and a weekend of ripening in the open air did nothing for them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This got us curious about the mechanisms of banana ripening - it's clearly not as closely related to how good the banana is to eat as we previously thought! Can someone explain it more?&lt;/p&gt;&#xA;" OwnerUserId="1226" LastEditorUserId="1226" LastEditDate="2013-02-04T23:17:46.793" LastActivityDate="2013-02-04T23:17:46.793" Title="What are the mechanisms that cause bananas to ripen? How is or isn't it related to the banana peel ripening?" Tags="&lt;food&gt;&lt;fruit&gt;" AnswerCount="0" CommentCount="9" ClosedDate="2013-02-05T12:43:40.047" ContentLicense="CC BY-SA 3.0" />
  <row Id="7061" PostTypeId="2" ParentId="2846" CreationDate="2013-02-04T16:49:17.077" Score="0" Body="&lt;p&gt;I've experienced migraines for 10 years, and now for the last 14 months that I've taken anti histamine medicine to see if there would be a benifit I've had good results. The frequency has dropped from approx 3 times a month to a migraine approx every 6-8 weeks. For me thats a sizeable drop. The other benifit is the severity is less intense.&#xA; Now I'm trying to find why my body produces too much histamine, so I hopefully can eliminate the anti histamine med's. &#xA; Recently I've greatly reduced foods with refined sugar, also processed foods, and added more whole foods, and I'm seeing excellent results.  &lt;/p&gt;&#xA;" OwnerUserId="3025" LastActivityDate="2013-02-04T16:49:17.077" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7063" PostTypeId="1" AcceptedAnswerId="7064" CreationDate="2013-02-04T19:30:00.903" Score="4" ViewCount="2567" Body="&lt;p&gt;Am I missing something very fundamental here for phosphoric acid's second pKa value?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I check the Wikipedia page and these are the values: (1) 2.148, &lt;strong&gt;(2) 7.198&lt;/strong&gt;, (3) 12.377&lt;/li&gt;&#xA;&lt;li&gt;Then I check Sigma-Aldrich website and it says: (1) 2.15, &lt;strong&gt;(2) 6.82&lt;/strong&gt;, (3) 12.38&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Why is the second pKa value different? Any ideas?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I need to prepare potassium phosphate buffer for my proteins and got stuck with this simple problem.&lt;/p&gt;&#xA;" OwnerUserId="1772" LastActivityDate="2013-02-04T21:03:27.727" Title="Why is second pKa value of phosphoric acid different across different sources?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7064" PostTypeId="2" ParentId="7063" CreationDate="2013-02-04T21:03:27.727" Score="3" Body="&lt;p&gt;Someone will probably come along and move this to &quot;chemistry&quot;, but here goes anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The answer is: it depends upon how you measure it&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Jungas, RL (2006) Best literature values for the pK of carbonic and phosphoric acid under physiological conditions. Analytical Biochemistry 349 1-15&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The author states that   &lt;em&gt;&quot;..the best value for the true thermodynamic second dissociation constant of phosphoric acid in pure water at 38&amp;deg;C is 7.180, rounded to the nearest 0.005.&quot;&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;He then goes on to re-analyse the data reported in:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cohn, EJ (1927) The activity coefficients of the ions in certain phosphate solutions: a contribution to the theory of buffer action. J Am Chem. Soc. 49 173-193&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and concludes that under physiological conditions of ionic strength and pH the best estimate is 6.795.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-02-04T21:03:27.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7065" PostTypeId="2" ParentId="6939" CreationDate="2013-02-04T23:19:40.960" Score="6" Body="&lt;p&gt;You might also have a look at some theoretical population genetics, which traditionally models selection as a diffusion process. The best introduction I know is chapter 15 of Karlin &amp;amp; Taylor's Second Course in Stochastic Processes (which, despite being only one chapter, makes up about half the book). From this, you can get results on hitting times, fixation times and other related distributions. Similar results are available in &lt;a href=&quot;http://www.springer.com/mathematics/probability/book/978-0-387-78168-6&quot; rel=&quot;noreferrer&quot; title=&quot;Durrett's book&quot;&gt;Durret's book&lt;/a&gt;, but he goes a bit deeper into the biological interpretations of his results.&lt;/p&gt;&#xA;" OwnerUserId="3029" LastActivityDate="2013-02-04T23:19:40.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7066" PostTypeId="2" ParentId="6929" CreationDate="2013-02-04T23:30:58.393" Score="3" Body="&lt;p&gt;As far as I remember, Fibonacci patterns emerge in plants from hormone gradients. I.e. an apical meristem forms a leaf where the auxin concentration is highest, and already existing leafs lower auxin concentration, leading to some negative feedback.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See e.g.&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1360138507000581&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S1360138507000581&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or &lt;a href=&quot;http://en.wikipedia.org/wiki/Phyllotaxis&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Phyllotaxis&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3029" LastActivityDate="2013-02-04T23:30:58.393" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7068" PostTypeId="2" ParentId="2505" CreationDate="2013-02-05T07:22:33.043" Score="1" Body="&lt;p&gt;There are lots of different overexpression vectors (usually they're promoters/regulatory elements upstream of the transfected gene). Here's an example of an overexpression vector (overexpression vector pCAMBIA1300S) that was used to overexpress a transcription factor called NAC in rice, resulting in large phenotypic changes (drought and salt tolerance): &lt;a href=&quot;http://www.ncgr.ac.cn/articles/2009ZhenXN_NAC.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.ncgr.ac.cn/articles/2009ZhenXN_NAC.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1906" LastEditorUserId="1906" LastEditDate="2013-02-05T08:07:20.723" LastActivityDate="2013-02-05T08:07:20.723" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7069" PostTypeId="2" ParentId="5603" CreationDate="2013-02-05T07:37:26.070" Score="2" Body="&lt;p&gt;X and Y chromosomes don't &quot;want&quot; anything-they are not conscious. I know that sounds obnoxious, but it's very important in evolutionary biology to understand that there is no agency and no intended final product for natural selection. I think the best way to think about it is like this: let's say there's a mutation on the X chromosome that happens to make females more fit at the expense of making males less fit. It seems possible that the evolutionary arms race that this establishes (i.e., males bearing a mutation that compensates or overcompensates for the new expense of the mutation that, say, their successful mom gave them, would then start to sweep to fixation in the population, and so on and so on) could result in population collapse. Apparently, there's theory out there that confirms this: &lt;a href=&quot;http://www.els.net/WileyCDA/ElsArticle/refId-a0003669.html&quot; rel=&quot;nofollow&quot;&gt;http://www.els.net/WileyCDA/ElsArticle/refId-a0003669.html&lt;/a&gt;. Also, I vaguely remember a paper about toxic sperm (vs. female mating behavior) in Drosophila melanogaster suggesting that populations could collapse. As Bonduriansky mentions in the link, though, one resolution to the arms race would be the evolution of genes that get expressed very differently between the sexes (i.e., a gene that is good for a female but terrible for a male would evolve to only be turned on when it's found in a female). I hope that helps?&lt;/p&gt;&#xA;" OwnerUserId="1906" LastActivityDate="2013-02-05T07:37:26.070" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7070" PostTypeId="2" ParentId="6889" CreationDate="2013-02-05T07:47:29.093" Score="3" Body="&lt;p&gt;terdon is spot on with the recombination hotspot comment. Mutations are often associated with recombination (information gets lost during crossing-over, so DNA repair is necessary, which of course can introduce mistakes/mutations). It's a fact that there areas in certain chromosomes where recombination happens much more often than other areas of the chromosome. So it follows that chromosomes with more hotspots would likely have higher mutation rates than other chromosomes, on average. This does raise the point, though, that perhaps it's not the mutation rate of the entire chromosome that matters-maybe mutation rates at a more-local level (such as near a hotspot or far away from a hotspot) are more worthy of consideration for your question.&#xA;Also, I imagine that sex chromosomes have much lower levels of polymorphism than autosomes. This doesn't have to be because of a lower mutation rate, though: another explanation would be that deleterious recessive mutations on the X chromosome would be purged more easily than on autosomes because their phenotype appears in males (who don't have a second allele because they don't have another X chromosome, so the deleterious phenotype can't be &quot;hidden&quot; like it would in a heterozygote).&lt;/p&gt;&#xA;" OwnerUserId="1906" LastActivityDate="2013-02-05T07:47:29.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7071" PostTypeId="1" AcceptedAnswerId="7073" CreationDate="2013-02-05T09:58:22.343" Score="7" ViewCount="14811" Body="&lt;p&gt;Are there some living things where the distinction between plant and animal is blurry or unclear?  I wouldn't know where to put something like yeast.  I also thought of photosynthesis, but then I heard that some salamanders have photosynthetic cells.  So, what's the difference between a plant and an animal, formally?  &lt;/p&gt;&#xA;" OwnerUserId="1203" LastActivityDate="2015-08-31T13:09:07.310" Title="What's the difference between a plant and an animal?" Tags="&lt;zoology&gt;&lt;botany&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7072" PostTypeId="1" AcceptedAnswerId="8741" CreationDate="2013-02-05T10:06:58.627" Score="8" ViewCount="919" Body="&lt;p&gt;I stacked my bike and split my head right open.  About three weeks later the scab falls off and the skin is sealed over, like magic!  How does it all work?  How does the brain know that part of the body is injured and needs repair, or does the brain know at all?  What kind of signals between brain/cells/body are involved.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry it's probably a basic question for a biologist, but I come from a different field and have always wondered about this amazing process.  It's also a very hard topic to google about, because most results are about spiritual healing, crystals, prayer and a lot of pseudoscience rubbish.  &lt;/p&gt;&#xA;" OwnerUserId="1203" LastEditorUserId="107" LastEditDate="2013-06-11T18:25:23.033" LastActivityDate="2020-01-02T14:48:45.720" Title="How does skin healing work?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;skin&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7073" PostTypeId="2" ParentId="7071" CreationDate="2013-02-05T11:15:43.860" Score="16" Body="&lt;p&gt;Yeast are neither plants nor animals; they are fungi. The old classification where things were lumped into only two buckets - plants or animals - has long since broken down. In fact, even things you might think of as plants, like algae or most seaweed are no longer classified as plants. Under the old system, plants and animals were considered kingdoms, and the latest classifications now divide the Eukaryotes into six kingdoms, but even this is poorly evidenced and facing challenge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best method of classification is probably &lt;a href=&quot;http://en.wikipedia.org/wiki/Cladistics&quot;&gt;cladistics&lt;/a&gt; which is based on the evolutionary history of organisms - but even it has problems when you start considering what to do with horizontal gene transfer and endosymbiosis. Because under a cladistic view, plants and animals are defined not by their features but by their ancestors your question becomes moot, I think.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-02-05T11:15:43.860" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7074" PostTypeId="1" AcceptedAnswerId="10818" CreationDate="2013-02-05T19:19:10.987" Score="18" ViewCount="66128" Body="&lt;p&gt;I had a hard climb a week ago. I got so tired then any time I closed my eyes I saw these lights inside my head. I see these lights almost every time that I run fast or some thing like that. What are they and where do they come from?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eN5bc.jpg&quot; alt=&quot;schematic representation&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a picture I drew using Photoshop ;)&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="3340" LastEditDate="2015-06-04T11:50:29.200" LastActivityDate="2016-08-17T18:19:28.720" Title="Why does strenous exercise cause vision of &quot;lights&quot;?" Tags="&lt;human-biology&gt;&lt;brain&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7075" PostTypeId="1" AcceptedAnswerId="7101" CreationDate="2013-02-05T19:55:57.450" Score="10" ViewCount="23672" Body="&lt;p&gt;I've started teaching myself about next-generation sequencing in preparation for a new job, and I'm wondering what the main differences are between the 454, SOLiD, and Illumina/Solexa machines, in terms of sample/library preparation and chemistry. How difficult is it for a protein veteran but next-gen newbie to get high-quality useful reads? I'm mainly going to be looking at antibody diversity, but consider this in general terms for any next-gen project.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand the basic theory of fluorescent chain-termination sequencing, but it's been a number of years since I last did it, and my career is now taking me back into the DNA realm.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2013-02-05T20:12:31.877" LastActivityDate="2013-02-09T21:20:51.373" Title="What is the difference between SOLiD, 454, and Illumina next-gen sequencing?" Tags="&lt;molecular-biology&gt;&lt;genomics&gt;&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7076" PostTypeId="1" AcceptedAnswerId="7080" CreationDate="2013-02-05T20:30:01.040" Score="6" ViewCount="21124" Body="&lt;p&gt;In explaining energy and work to an 8 year-old I said that all conversion of energy generates heat as a by-product.  For example, cars generate heat in their engines and running generates heat in our bodies.  Then the 8 year-old said, except for cold-blooded animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is, do cold-blooded animals generate any heat in their conversion of stored energy (food, fat, etc) into motion?  If they generate heat, why are they cold-blooded?&lt;/p&gt;&#xA;" OwnerUserId="3031" LastActivityDate="2013-02-06T05:59:46.090" Title="Do cold blooded animals generate any heat?" Tags="&lt;cellular-respiration&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7077" PostTypeId="2" ParentId="7076" CreationDate="2013-02-05T20:39:03.687" Score="1" Body="&lt;p&gt;I'm fairly certain that you were right in your initial hunch that heat is almost always a byproduct of metabolism (which is never 100% efficient). The difference between endothermic ('warm-blooded') and ectothermic ('cold-blooded') organisms is just where the primary source of body temperature regulation comes from (either from metabolic reactions in endotherms or from the environment in ectotherms).&lt;/p&gt;&#xA;" OwnerUserId="1906" LastEditorUserId="1906" LastEditDate="2013-02-06T00:08:50.050" LastActivityDate="2013-02-06T00:08:50.050" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7078" PostTypeId="2" ParentId="7071" CreationDate="2013-02-05T21:20:54.227" Score="1" Body="&lt;p&gt;Classification is not only based on one or a few features, but you have to consider lots of features in classification of livings. for example plant cells globally have chloroplast, cell wall, and vacuole and have not centrioles. Animals are different in all this features with plants. furtherly plants are autotroph and steady while animals are not. Other organisms are also different in these features or other features with plants and animals.&lt;/p&gt;&#xA;" OwnerUserId="1916" LastActivityDate="2013-02-05T21:20:54.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7079" PostTypeId="1" CreationDate="2013-02-05T21:21:17.207" Score="1" ViewCount="228" Body="&lt;p&gt;I was reading up on ethnic groups in which the women are naturally more hirsute (such as South Asian women) in the context of evolving standards of beauty. I came across this statement on a forum: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hirsutism is much more common in South Asian women (particularly North Indians such as Punjabi Sikhs) asymptomatically because they tend to have higher levels of circulating androgens than your typical [North or Western European ethnic group]. This is also true of Eastern European women to an extent.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Per &lt;a href=&quot;http://en.wikipedia.org/wiki/Androgen&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;, I learned:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Circulating levels of androgens can influence human behavior because some neurons are sensitive to steroid hormones. Androgen levels have been implicated in the regulation of human aggression and libido. Indeed, androgens are capable of altering the structure of the brain in several species, including mice, rats, and primates, producing sex differences.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So: do circulating androgens trigger higher testosterone production in some women? Is this what yields higher instances of &quot;hirsutism&quot; among certain populations? How are some women more prone to this than others? (That is, per the forum post, why are South Asian women more likely to have this than Western European women?)&lt;/p&gt;&#xA;" OwnerUserId="2" LastEditorUserId="1320" LastEditDate="2013-02-05T21:52:45.037" LastActivityDate="2013-02-09T23:54:40.443" Title="How do circulating androgens contribute to higher rates of hirsuteness in some women?" Tags="&lt;genetics&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7080" PostTypeId="2" ParentId="7076" CreationDate="2013-02-06T03:19:15.230" Score="11" Body="&lt;p&gt;They do generate heat. They just do not SPEND energy specifically on heating their bodies by raising their metabolisms. This is a form of energy conservation. The metabolic rate they need to live is not nearly enough to heat their bodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of spending energy to heat the body is seen in humans  shivering. Here muscle is activated not for its usual purpose, but to function as a furnace. &quot;Warm-blooded&quot; and &quot;cold-blooded&quot; is somewhat a misnomer. The correct way to think of it is...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Endotherm or ectotherm. Does the heat primarily come from within (endo) or from the surroundings (ecto). Endothermic animals include mammals. Most of their body heat is generated by their own metabolisms. Ectothermic animals include reptiles and insects. They absorb most of their body heat from the surroundings. This is not the same as saying they let their body temperature fluctuate with their surroundings, some avoid this by moving around to accomodate themselves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Homeotherm or poikilotherm. Homeotherms want to maintain homeostasis for their body temperatures. They don't want it to change. Poikilotherms do not exhibit this behaviour, instead their body temperatures vary greatly with the environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can have endotherm poikilotherms, such as squirrels, who let their body temperature drop while hibernating. Endotherm homeotherms, such as humans, where temperature is constant by means of complex thermoregulation. Ectotherm homeotherms, such as snakes (moving into shadow or into the sun to regulate temperature), and ectotherm poikilotherms, such as maggots.&lt;/p&gt;&#xA;" OwnerUserId="3032" LastActivityDate="2013-02-06T03:19:15.230" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7081" PostTypeId="2" ParentId="7076" CreationDate="2013-02-06T05:59:46.090" Score="2" Body="&lt;p&gt;As the others have said, animals and insects (and even plants) generate heat through metabolism and can regulate their temperature this way.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just wanted to add a third point that mammals have developed brown fat, &lt;a href=&quot;http://en.wikipedia.org/wiki/Brown_adipose_tissue&quot; rel=&quot;nofollow&quot;&gt;fat tissue which is dark with extra mitochondria which burn energy to generate heat&lt;/a&gt;.  These are rich with uncoupling protein (a particular uncoupling protein called &lt;a href=&quot;http://en.wikipedia.org/wiki/Thermogenin&quot; rel=&quot;nofollow&quot;&gt;thermogenin&lt;/a&gt;) which passes protons through the mitochondrial membrane to generate heat rather than generate ATP. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the heat generated by mammals is not from brown adipose tissue, but it is a particular adaptation to generate heat that &lt;a href=&quot;http://en.wikipedia.org/wiki/Endotherm&quot; rel=&quot;nofollow&quot;&gt;endotherms&lt;/a&gt; have evolved.  The brain alone is responsible for 16% of the heat generated by human bodies.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-02-06T05:59:46.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7082" PostTypeId="1" AcceptedAnswerId="92897" CreationDate="2013-02-06T08:16:53.733" Score="3" ViewCount="51" Body="&lt;p&gt;Do sulfate reducing bacteria help during the formation of the mineral dolomite in low temperature environments?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia &lt;a href=&quot;http://en.wikipedia.org/wiki/Dolomite#formation&quot; rel=&quot;nofollow&quot;&gt;says&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The actual role of bacteria in the low-temperature formation of&#xA;  dolomite remains to be demonstrated. The specific mechanism of&#xA;  dolomitization, involving sulfate-reducing bacteria, has not yet been&#xA;  demonstrated.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I wonder if someone has any updates on this. The reference given in the Wikipedia article is from 2000, from a source titled suspiciously &quot;Journal of Conference Abstracts&quot;. Now it's 2013 and maybe someone else has found out something new.&lt;/p&gt;&#xA;" OwnerUserId="349" LastActivityDate="2020-04-22T16:42:25.960" Title="Do sulfate reducing bacteria help during the formation of the mineral dolomite in low temperature environments?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7083" PostTypeId="2" ParentId="3165" CreationDate="2013-02-06T08:25:53.980" Score="3" Body="&lt;p&gt;Two hints:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Do a &lt;a href=&quot;https://www.google.com/search?name=f&amp;amp;hl=en&amp;amp;q=actn3&quot; rel=&quot;nofollow noreferrer&quot;&gt;google search for the ACTN3 gene&lt;/a&gt; (alpha-actinin-3)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Go to the fitness.stackexchange.com site and search for &lt;a href=&quot;https://fitness.stackexchange.com/search?q=fast%20twitch&quot;&gt;&quot;fast&#xA;twitch&quot;&lt;/a&gt; muscles, for example. There you'll find many similar questions&#xA;answered.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;You can get an answer for you personally by genetic testing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a quote from a genetic testing site 23andme.com (sorry it's behind a paywall). Note there are other companies who can do this equally well.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Genes vs. Environment&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Athletic performance has different estimates of heritability,&#xA;  depending on what aspect one examines. For example, differences in the&#xA;  relative proportion of fast-twitch and slow-twitch muscle fiber are&#xA;  thought to have a heritability of about 45%. Although it is not yet&#xA;  clear whether ACTN3 genotype affects this proportion, it has been&#xA;  shown that the SNP in ACTN3 that we report accounts for about 2.3% of&#xA;  the variation in sprinting performance. However, at the molecular&#xA;  level, whether you have 0, 1, or 2 working copies of alpha-actinin-3&#xA;  is highly heritable. Lastly, muscle fiber only contributes a small&#xA;  part to your overall athletic performance. Other physical&#xA;  characteristics, such as lung capacity, and behaviors, such as regular&#xA;  exercise, also make important contributions to your prowess in sports.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is considered &quot;&lt;a href=&quot;https://www.23andme.com/res/pdf/trmm3vmfI1BU5d3Qw_qlGg_23-03_Vetting_Genetic_Associations_2010_06.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;established research&lt;/a&gt; for 1 reported marker&quot;. It is still subject of much ongoing research, though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there you have it: around 2% of a difference in sprinting performance. For the general population this won't matter much. But for prospective professional athletes these 2.3% might matter a lot for developing the full potential of their athletic performance (assuming all other environmental factors, are of  equal top quality, e.g. technical equipment, coaching efficiency, etc)&lt;/p&gt;&#xA;" OwnerUserId="349" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:51.727" LastActivityDate="2013-02-06T09:16:12.493" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="7084" PostTypeId="1" AcceptedAnswerId="7099" CreationDate="2013-02-06T08:26:05.120" Score="0" ViewCount="60" Body="&lt;p&gt;I am tasked with designing an in vivo experiment in humans that requires manipulating the gut flora in one sample group to gauge its effect. Please suggest ways of doing this besides administering antibiotics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am of the view that antibiotics may have unintended consequences and may be unethical; explain any opposing view.&lt;/p&gt;&#xA;" OwnerUserId="3034" LastEditorUserId="107" LastEditDate="2013-02-06T13:30:34.910" LastActivityDate="2013-02-06T17:51:09.250" Title="Manipulating Gut flora in vivo" Tags="&lt;human-biology&gt;&lt;experimental-design&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7085" PostTypeId="1" CreationDate="2013-02-06T10:35:44.843" Score="1" ViewCount="2661" Body="&lt;p&gt;I am trying to self study BNDF a little bit when I found this article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Abstract Stress impacts multiple systems within the CNS, including the&#xA;  hippocampus. A key molecular mediator in hippocampal functions,&#xA;  including learning and memory, is brain-derived neurotrophic factor&#xA;  (BDNF). BDNF mRNA is reported to be decreased following chronic (every&#xA;  day) immobilization stress (CIS) in the rat, however the effect on&#xA;  protein is unknown. Utilizing a mouse model of CIS, the hypothesis&#xA;  that total hippocampal BDNF protein, in addition to BDNF mRNA, would&#xA;  be decreased was tested. The effects of intermittent (alternating day)&#xA;  immobilization and cold stress on hippocampal BDNF protein levels was&#xA;  also examined.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In this study it was demonstrated that CIS results in a small (8 per&#xA;  cent decrease relative to non-stressed controls), but significant (p =&#xA;  0.0013) decrease in the exon coding for mature BDNF (exon VI). In addition, there was a significant (34 per cent, p = 0.005) decrease in&#xA;  the mRNA coding for exon I in the stressed animals. Contrary to&#xA;  expectations, however, CIS resulted in a significant (116 per cent, p&#xA;  = 0.0087) increase in hippocampal BDNF protein levels. Furthermore, both intermittent immobilization and chronic cold stress both&#xA;  increased BDNF protein levels. Chronic stress, therefore,&#xA;  differentially regulates BDNF mRNA and protein levels in the&#xA;  hippocampus. Copyright © 2004 John Wiley &amp;amp; Sons, Ltd.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm really curious what they mean with CIS: Chronic immobilization stress.&#xA;I can't find anything on the internet that actually explains what this is.&lt;/p&gt;&#xA;" OwnerUserId="3035" LastActivityDate="2013-03-08T14:35:12.213" Title="What is Chronic immobilization stress (CIS)?" Tags="&lt;terminology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7086" PostTypeId="2" ParentId="7084" CreationDate="2013-02-06T10:43:44.063" Score="0" Body="&lt;p&gt;I'm no expert, but I read this, and I found it very intresting:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In its study, Henry Ford treated patients between May 2010 and June&#xA;  2012 with a therapy called intestinal microbiota transplantation&#xA;  (IMT), using donated stool from a healthy family member.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here are the results:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;“More than 90 percent of the patients in our study were cured of their&#xA;  C.diff infection,” says Dr. Ramesh. “This treatment is a viable option&#xA;  for patients who are not responding to conventional treatment and who&#xA;  want to avoid surgery.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.henryford.com/body.cfm?id=46335&amp;amp;action=detail&amp;amp;ref=1757&quot; rel=&quot;nofollow&quot;&gt;http://www.henryford.com/body.cfm?id=46335&amp;amp;action=detail&amp;amp;ref=1757&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3035" LastActivityDate="2013-02-06T10:43:44.063" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7087" PostTypeId="1" AcceptedAnswerId="7091" CreationDate="2013-02-06T10:58:02.473" Score="15" ViewCount="1400" Body="&lt;p&gt;Every now and then I got a glimpse of this bird which I'm pretty sure is not native to Northern Germany where I live. There are at least three of these birds around but I usually only see something quick and green somewhere in the trees. I finally managed to get some decent pictures so I'm hoping someone can tell me what kind of bird this is. I'm curious what biological niche this bird is likely to fill and which native species it might compete with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9ggwr.jpg&quot; alt=&quot;photo of strange bird&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/y4Pfn.jpg&quot; alt=&quot;detail of its head&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1711" LastEditorUserId="1590" LastEditDate="2015-06-16T18:03:48.550" LastActivityDate="2015-10-09T21:27:30.687" Title="What kind of bird species is this?" Tags="&lt;zoology&gt;&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7089" PostTypeId="5" CreationDate="2013-02-06T11:24:02.810" Score="0" Body="&lt;p&gt;Drugs that bind to the opioid receptors (mu, delta &amp;amp; kappa).&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-06T11:35:56.930" LastActivityDate="2013-02-06T11:35:56.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7090" PostTypeId="4" CreationDate="2013-02-06T11:24:02.810" Score="0" Body="Drugs that bind to the opioid receptors (mu, delta &amp; kappa)." OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-06T11:35:50.067" LastActivityDate="2013-02-06T11:35:50.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7091" PostTypeId="2" ParentId="7087" CreationDate="2013-02-06T12:14:13.897" Score="23" Body="&lt;p&gt;Almost definitely (I'm not a regular birder) &lt;a href=&quot;http://en.wikipedia.org/wiki/European_Green_Woodpecker&quot;&gt;&lt;strong&gt;European Green Woodpecker&lt;/strong&gt;&lt;/a&gt; (latin name: &lt;em&gt;&lt;a href=&quot;http://woodpeckersofeurope.info/?q=green_woodpecker&quot;&gt;Picus viridis&lt;/a&gt;&lt;/em&gt;) and it is native to your area according to its species &lt;a href=&quot;http://www.google.co.uk/imgres?imgurl=http://ichef.bbci.co.uk/naturelibrary/images/ic/464x261/g/gr/green_woodpecker/green_woodpecker_map.gif&amp;amp;imgrefurl=http://www.bbc.co.uk/nature/life/Green_Woodpecker&amp;amp;h=261&amp;amp;w=464&amp;amp;sz=13&amp;amp;tbnid=LFa5MpZdt_K1yM%3a&amp;amp;tbnh=90&amp;amp;tbnw=160&amp;amp;zoom=1&amp;amp;usg=__VQtoxUcuhOLx_cXGlr6TGxWC5bA=&amp;amp;docid=ZpZzRvSFjnpuLM&amp;amp;sa=X&amp;amp;ei=S5rSUc2sMMKDtAa40YC4BQ&amp;amp;ved=0CFMQ9QEwBA&amp;amp;dur=309&quot;&gt;distribution map&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Green woodpeckers are the largest and most colourful woodpeckers&#xA;  native to Britain. They are easily recognised by their laughing&#xA;  ‘yaffle’ call, which they use to demarcate their territory. They also&#xA;  drum on trees, though the sound is not as resonant as that made by the&#xA;  other two British species (the greater and lesser spotted&#xA;  woodpeckers). Green woodpeckers survive on a diet of insects and have&#xA;  a particular fondness for ants. They return day after day to their&#xA;  favourite ant hill to feed.&quot; - &lt;a href=&quot;http://www.bbc.co.uk/nature/life/Green_Woodpecker&quot;&gt;BBC nature&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-02T09:19:15.990" LastActivityDate="2013-07-02T09:19:15.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7092" PostTypeId="1" CreationDate="2013-02-06T13:00:52.683" Score="1" ViewCount="1351" Body="&lt;p&gt;Histamine is a neurotransmitter that also has peripheral functions such as the regulation of gastric acid secretions, allergic responses, etc. I know that opioids stimulate a release of histamine but I want to know how? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What exactly I would like answered is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Which of the opioid receptors are involved in the histamine release that opioids stimulate and to what extent are they?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How does the activation of the opioid receptors in question lead to a release of histamine?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are there any ways of suppressing the histamine release stimulated by opioids without compromising the analgesia they elicit?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I would like an answer, not just links. However I would like you to cite journal articles, although a formal reference list is not required so long as I can easily find the link to the abstract/full article. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1320" LastEditDate="2013-02-06T18:27:30.380" LastActivityDate="2013-02-06T18:27:30.380" Title="How do Opioids Stimulate a Histamine Release?" Tags="&lt;pharmacology&gt;&lt;opioid&gt;&lt;histamine&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7093" PostTypeId="5" CreationDate="2013-02-06T13:07:49.650" Score="0" Body="&lt;p&gt;Histamine is a neurotransmitter that plays a key role in allergenic responses, sleep, alertness, cognition and gastric acid synthesis and secretion. It binds primarily to the four types of histamine receptors:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;H&lt;sub&gt;1&lt;/sub&gt;&lt;/strong&gt;, responsible for alertness, cognition, allergenic responses.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;H&lt;sub&gt;2&lt;/sub&gt;&lt;/strong&gt;, responsible for gastric acid and intestinal excretions and motility in general.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;H&lt;sub&gt;3&lt;/sub&gt;&lt;/strong&gt;, which serves as the histamine autoreceptor.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;H&lt;sub&gt;4&lt;/sub&gt;&lt;/strong&gt;, which seems to play a role in immune function.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-06T13:37:31.317" LastActivityDate="2013-02-06T13:37:31.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7094" PostTypeId="4" CreationDate="2013-02-06T13:07:49.650" Score="0" Body="Histamine is a neurotransmitter that plays a key role in allergenic responses, sleep, alertness, cognition and gastric acid synthesis and secretion. It binds primarily to the four types of histamine receptors, H1 (responsible for alertness, cognition, allergenic responses), H2 (responsible for gastric acid synthesis and excretion), H3 (which serves as the histamine autoreceptor) and H4 which seems to play a role in immune function." OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-06T13:37:25.403" LastActivityDate="2013-02-06T13:37:25.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7095" PostTypeId="2" ParentId="7085" CreationDate="2013-02-06T13:41:56.323" Score="1" Body="&lt;p&gt;There are &gt;1200 articles tagged &quot;&lt;a href=&quot;http://ncbi.nlm.nih.gov/pubmed?term=chronic%20immobilization%20stress&quot; rel=&quot;nofollow&quot;&gt;chronic immobilization stress&lt;/a&gt;&quot; on pubmed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From Hennebelle et al. (2012):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Half of the 6-month old male rats from each dietary group were subjected to a validated chronic stress procedure (Buyntsky and Mostosky, 2009) based on a restraint stress procedure adapted from Veena et al, [32]. Rats were placed in wire mesh restrainers for 6 h a day (fom 10 am to 16 pm) for 21 days (5 days a week) over a period of 4 weeks. Unstressed rats were handled weekly. The unstressed and stressed animals were housed in different rooms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3408452/&quot; rel=&quot;nofollow&quot;&gt;Hennebelle, H., et al. 2012. Influence of Omega-3 Fatty Acid Status on the Way Rats Adapt to Chronic Restraint Stress. PLoSOne 7: e42142.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2013-02-06T13:47:15.110" LastActivityDate="2013-02-06T13:47:15.110" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7096" PostTypeId="2" ParentId="5426" CreationDate="2013-02-06T15:40:46.783" Score="2" Body="&lt;p&gt;To give timescales for the different processes is very difficult because the speed (in g/d product yield) depends greatly on the number of bacteria, so first you'd have to modl the bacteria growth. I assume you don't want to go that road.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also note that not all of the substrate is in the same state of fermentation at the same time, more so if you have bigger lumps. Like whole carrots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One industrial batch-style fermneter I know of uses total retention times of 3-4 weeks, and they mix half the digestate into the fermenter again to provide for inocculum.&lt;/p&gt;&#xA;" OwnerUserId="3037" LastActivityDate="2013-02-06T15:40:46.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7097" PostTypeId="2" ParentId="4990" CreationDate="2013-02-06T15:51:03.020" Score="3" Body="&lt;p&gt;For the definition, see Pelle's answer.&#xA;For the reasons, both are easy and cheap to measure and can tell you a lot about your material if you have similiar mterial to compare. TS is often used to asses howa material can be handled (pumpable, stackable)&#xA;In agricultural biogas applications for example, a sometimes used assumption is 1g COD = 1,6 g VS&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In AD, VS is broadly associated with digestible biomass, and depending on input one third to one half of VS will be converted to gas. In fact, gas yields are often given per mass of VS because of this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that solutes that are actually volatile, like alcohol, will be evaporated when testing for TS. Laso note that the points give na bove only work if you compare similiar materials.&lt;/p&gt;&#xA;" OwnerUserId="3037" LastActivityDate="2013-02-06T15:51:03.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7098" PostTypeId="2" ParentId="7075" CreationDate="2013-02-06T16:28:17.143" Score="-3" Body="&lt;p&gt;It's not easy to write down a comprehensive answer to your question, I would suggest you read this paper &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2011.03024.x/pdf&quot; rel=&quot;nofollow&quot;&gt;Field guide to next-generation DNA sequencers&lt;/a&gt;, which provide very good comparison of the NGS platforms&lt;/p&gt;&#xA;" OwnerUserId="3039" LastActivityDate="2013-02-06T16:28:17.143" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7099" PostTypeId="2" ParentId="7084" CreationDate="2013-02-06T17:51:09.250" Score="1" Body="&lt;p&gt;I can't think of any way to start with an intestinal &quot;blank slate&quot;, so to speak, except with antibiotics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps it's possible to at least partially homogenize/standardize a sample group's biota with probiotics?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it's ethics you're worried about, perhaps draw experimental subjects from a pool already being treated with antibiotics (although this, I suppose, introduces it's own biases?).&lt;/p&gt;&#xA;" OwnerUserId="1906" LastActivityDate="2013-02-06T17:51:09.250" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7100" PostTypeId="2" ParentId="5676" CreationDate="2013-02-06T19:22:56.197" Score="6" Body="&lt;p&gt;The hair doesn't keep growing!&lt;/p&gt;&#xA;&lt;p&gt;It's important to notice that there isn't a set point for the actual hair length. The hair doesn't know that it's been cut for example. Rather, there's a set point for time. A single strand of hair, in humans, on the scalp, will be in the growth phase for several years. The growth cessation takes a few weeks, and then the rest phase will last for another couple of months, until finally the hair strand is shed.&lt;/p&gt;&#xA;&lt;p&gt;I don't think there's a natural advantage for hair of as long a length as many humans can grow it, it may just be little or not at all disadvantageous. The selective advantage, if there is one, probably emanates from sexual selection, similar to why lions grow manes. A display of health and surplus of resources. Hair has a pretty central role in beauty ideals. In some cultures, women even cover up their hair.&lt;/p&gt;&#xA;&lt;p&gt;There are examples of traits that are disadvantageous to survival in the organism's environment, but shows advantages when it comes to reproduction, to a degree that the genes do not become extinct. I don't remember the name, so take it for what you will, but there's a fish species where the males are either small and stealthy, or they are very flashy. The females prefer the flashy males, but at the same time those males have a harder time avoiding getting eaten by other, larger fish. Thus both phenotypes are passed on to the next generation of fish.&lt;/p&gt;&#xA;" OwnerUserId="3032" LastEditorUserId="46609" LastEditDate="2021-01-21T00:12:38.580" LastActivityDate="2021-01-21T00:12:38.580" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="7101" PostTypeId="2" ParentId="7075" CreationDate="2013-02-06T19:31:35.520" Score="11" Body="&lt;p&gt;Here is a short summary of the sequencing technologies you listed. Illumina is the most frequently used one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Roche/454 FLX Pyrosequencer technology is based on pyrosequencing method, which utilizes the use of the enzymes ATP sulfurylase and luciferase. After the incorporation of each nucleotide by DNA polymerase, a pyrophosphate is released, which further takes part in downstream light-producing reactions. The amount of light is proportional to the incorporated number of nucleotides. The DNA is fragmented and adapters are ligated at both ends. The fragments are mixed with agarose beads, which carry adapters complementary to the library adapters, and thus each bead is associated with a unique DNA fragment. The beads and DNA fragments are isolated in individual micelles, where emulsion PCR takes place and million copies of the single fragments are amplified  onto the surface of each bead. Each bead is placed in a well of picotiter plate (PTP), as the wells have dimensions such that only one bead can fit per well. Enzymes are added to the beads and pure nucleotide solutions are added with an immediate imaging step. On one side of the array a CCD (charge-optic device) camera records the light emitted from each bead. The first four nucleotides (TCGA) are the same as the start of the adapter, which allows for the emitted light to be calibrated according to the type of nucleotide added. The major disadvantage of this method is the misinterpretation of homopolymers (consecutive nucleotides, e.g. AAA or CCC). Such areas are prone to insertions or deletions, as the length of the stretch can be inferred only by the intensity of the light emitted. On the other hand, substitution errors are very unlikely. The 454 FLX instrument generates ~400 000 reads per instrument-run, as the reads are 200-400bp. The greatest advantage of this platform is the read length, which is the longest of all second generation technologies. Although sequencing on 454 platform is more expensive than sequencing on Illumina platform (40USD per Mega base versus 2USD per Mega base), it could still be the best choice for de novo assembly or metagenomics applications. (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Illumina is the most frequently used one. The DNA to be sequenced is fragmented into about 200 base strands. Adapters are ligated onto the ends of the fragments and one of these adapters is hybridized on a flow cell. Illumina essentially utilizes a unique &quot;bridged&quot; amplification reaction that occurs on the surface of the flow cell. Localized PCR reaction is performed, and each of the hybridized pieces of DNA will get locally amplified to generate clusters which will have the exact same molecule. Subsequently, the DNA sequence is determined by adding a primer on one of the ends of the molecule. A mixture of modified nucleotides is added. Each one of them carries a base-specific fluorescent label attached to it. Also, each one has the 3' OH group blocked which ensures the incorporation of one nucleotide at a time.  The flow cell is placed under a microscope and when light is shined on its fluorescence, the emission light shows which base was incorporated on each one of those clusters. The Illumina read length is approximately 35 bases, but over billion reads are generated at a time. The major error type is substitution, rather than deletion or insertion (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The SOLiD platform utilizes the use of DNA fragmented library, which is flanked by ligated adapters. The fragments are attached to small paramagnetic beads and emulsion PCR is performed to amplify the fragments. In contrast to the other sequencing platforms, sequencing by synthesis is performed by utilizing DNA ligase, rather than polymerase. Each cycle of sequencing involves the ligation of a degenerate population of fluorescently labeled universal octamer primers. A specific position of the octamer (e.g., base 5) carries a fluorescent label. After ligation, images are acquired in four channels, followed by cleavage of the octamer between positions 5 and 6, removing the fluorescent label. After several rounds of octamer ligation, which enable sequencing of every 5th base (e.g., bases 5, 10, 15, and 20), the extended primer is denatured. Different primers can be used to examine the previous or next positions (e.g., base 3 or 6).  The platform can use primers which carry two adjacent correlated with label bases. This approach involves the examination of the bases twice in a cycle, which decreases the error rates. SOLiD read lengths are 25-35 bp, and each sequencing run yields 2–4 Gb of DNA sequence data (Mardis, E., 2008, Shendure, J. and Ji, H., 2008).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Mardis, E., &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18576944&quot;&gt;Next generation DNA sequencing methods.&lt;/a&gt; Ann. Rev. Genomics Hum. Genet, 9: 387-402 (2008). &lt;a href=&quot;http://dx.doi.org/10.1146/annurev.genom.9.081307.164359&quot;&gt;DOI 10.1146/annurev.genom.9.081307.164359&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Shendure, J. and Ji, H., &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18846087&quot;&gt;Next-generation DNA sequencing.&lt;/a&gt; Nat. Biotechnol., 26: 1135-1145 (2008). &lt;a href=&quot;http://dx.doi.org/10.1038/nbt1486&quot;&gt;DOI 10.1038/nbt1486&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="28" LastEditorUserId="948" LastEditDate="2013-02-09T21:20:51.373" LastActivityDate="2013-02-09T21:20:51.373" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="7102" PostTypeId="1" CreationDate="2013-02-06T20:01:09.043" Score="1" ViewCount="29" Body="&lt;p&gt;Which classes of drugs (filed by their binding sites) induce a release of β-endorphin? I know of agonists of the nAChRs and 5-HT&lt;sub&gt;1A&lt;/sub&gt; and ethanol. Are there any others? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Please cite journal articles with links to the respective articles&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="3340" LastEditDate="2014-12-08T05:23:00.380" LastActivityDate="2014-12-08T05:23:00.380" Title="Which classes of drugs (filed by their pharmacology) induce a release of β-endorphin?" Tags="&lt;pharmacology&gt;&lt;receptor&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7103" PostTypeId="1" AcceptedAnswerId="7107" CreationDate="2013-02-06T21:35:19.830" Score="4" ViewCount="724" Body="&lt;p&gt;My biology book says, that the equilibrium potential for an ion with a charge of +1 is: $$E_{ion}= 62mV \biggl(\log\frac{[ion]_{outside}}{[ion]_{inside}}\biggr)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where does the 62 mV come from? How was this value derived? I understand that it's the equilibrium voltage of $\ce{Na+}$.&lt;/p&gt;&#xA;" OwnerUserId="3032" LastActivityDate="2017-05-03T23:10:20.513" Title="Question about equilibrium potential formula" Tags="&lt;molecular-biology&gt;&lt;biophysics&gt;&lt;cell-membrane&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7104" PostTypeId="1" AcceptedAnswerId="7108" CreationDate="2013-02-06T22:09:30.113" Score="6" ViewCount="1463" Body="&lt;p&gt;How is the excretion of small kangaroos done when they are in the pouch of their mother, fastened onto her teat? My question is what happens with the products; do they accumulate in the pouch?&lt;/p&gt;&#xA;" OwnerUserId="1658" LastEditorUserId="107" LastEditDate="2013-02-07T01:09:12.523" LastActivityDate="2014-09-01T04:15:44.833" Title="Excretion of small kangaroos while in the pouch" Tags="&lt;zoology&gt;&lt;digestive-system&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7105" PostTypeId="1" AcceptedAnswerId="7151" CreationDate="2013-02-06T22:47:49.910" Score="2" ViewCount="694" Body="&lt;p&gt;Is it known exactly why the brain needs sleep? What's dropping low / going high when we experience mental fatigue? I can see why low glucose could result in mental fatigue, are other reasons known?&lt;/p&gt;&#xA;" OwnerUserId="3032" LastActivityDate="2015-08-28T14:54:16.183" Title="What is the biochemical reason for mental fatigue?" Tags="&lt;biochemistry&gt;&lt;neuroscience&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7107" PostTypeId="2" ParentId="7103" CreationDate="2013-02-07T00:18:56.263" Score="7" Body="&lt;p&gt;The System intracellular/membrane/extracellular space is well described by the model of a Concentration cell (see more on &lt;a href=&quot;http://en.wikipedia.org/wiki/Concentration_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;). The equation you mentioned is also called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nernst_equation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nernst equation&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;E_{ion}= 62mV \biggl(\log\frac{[ion]_{outside}}{[ion]_{inside}}\biggr)= \frac{k_\mathrm{B} T}{z \mathrm{e}} \biggl(\ln\frac{[ion]_{outside}}{[ion]_{inside}}\biggr)&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $k_\mathrm{B}$ is the Boltzmann constant, $T$ temperature (310 K), $\mathrm{e}$ elementary charge and $z$ the number of elementary charges per ion (1 in the case of Na+)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus the $62 mV$ come from $\frac{k_\mathrm{B} T}{\mathrm{e}}   ln(10)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, as the temperature increases, entropic effects gain strength and thus more ions move against the electric field, raising the membrane potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So your 62 mV are not only empirical but also based on a well defined physical model.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And the equilibrium voltage of Na+ is the same because at physiological conditons the intracellular concentration is ten times smaller than the extracellular. Thus $\log\frac{[ion]_{outside}}{[ion]_{inside}}$ equals to $log(10)$ which is $1$.&#xA;The total membrane reversal potential is well described by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Goldman_equation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Goldman Equation&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3042" LastEditorUserId="3042" LastEditDate="2017-05-03T23:10:20.513" LastActivityDate="2017-05-03T23:10:20.513" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7108" PostTypeId="2" ParentId="7104" CreationDate="2013-02-07T00:26:44.387" Score="9" Body="&lt;p&gt;Wow! What an interesting question! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did a bit of searching around, and here's what I found. It looks like the baby kangaroos, or joeys, do in fact produce excrement while in their mothers pouch. The mother kangaroo uses her tongue to clean her joey and her pouch. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this information in a couple of differently places by doing a google search for &quot;biology of marsupial reproduction pouch excrement.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the first sources I found was a New York Times article titled &quot;Marsupail Maintenance.&quot; You can find this article at this link:&#xA;&lt;a href=&quot;http://www.nytimes.com/2012/08/14/science/how-do-female-kangaroos-keep-their-pouches-clean.html?_r=0&quot; rel=&quot;nofollow&quot;&gt;http://www.nytimes.com/2012/08/14/science/how-do-female-kangaroos-keep-their-pouches-clean.html?_r=0&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article was published in a reputable news paper, and used an interview with a curator of mammals from the Bronx Zoo as a source. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another resource I found when researching this topic was an Australian wildlife sanctuary. This wildlife sanctuary has information web pages online to help visitors learn more about the animals that live in the sanctuary. You can find their entry on Eastern Grey Kangaroos at this link:&#xA;&lt;a href=&quot;http://billabongsanctuary.com.au/native-animals/mammals/eastern-grey-kangaroo/&quot; rel=&quot;nofollow&quot;&gt;http://billabongsanctuary.com.au/native-animals/mammals/eastern-grey-kangaroo/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This web pages gives a pretty detailed overview of the Eastern Grey Kangaroo. The information on joeys and pouch cleaning can be found in the section called &quot;Raising the Young.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this fully answered your question!&lt;/p&gt;&#xA;" OwnerUserId="3043" LastEditorUserId="9040" LastEditDate="2014-09-01T04:15:44.833" LastActivityDate="2014-09-01T04:15:44.833" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7110" PostTypeId="1" CreationDate="2013-02-07T01:33:51.317" Score="2" ViewCount="112" Body="&lt;p&gt;The majority of animals have two genders, and both are needed in reproduction. It seems like it would be more advantageous for creatures to be hermaphrodites, since they could mate with any member of their species instead of needing to find a partner of the opposite gender. Why did animals evolve to have genders instead of being hermaphrodites?&lt;/p&gt;&#xA;" OwnerUserId="1182" LastEditorUserId="5972" LastEditDate="2015-01-31T21:56:07.287" LastActivityDate="2015-01-31T21:56:07.287" Title="Why did animals evolve genders?" Tags="&lt;evolution&gt;&lt;sex&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2013-02-07T12:00:56.197" ContentLicense="CC BY-SA 3.0" />
  <row Id="7111" PostTypeId="2" ParentId="7103" CreationDate="2013-02-07T01:41:36.817" Score="9" Body="&lt;p&gt;That quasi-travesty is the &lt;em&gt;Nernst equation&lt;/em&gt; in $\log_{10}$ for a positive monovalent ion at physiological temperatures (37 degrees celsius), but they've hidden all that from you. Shame on them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The canonical form of the Nernst equation, for an ion $S$ is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;E_{S} = \frac{RT}{z_{S}F}\ln{\frac{[S]_{out}}{[S]_{in}}}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $R$ is the gas constant, $T$ is temperature expressed in Kelvin, $F$ is Faraday's constant, and $z_S$ is the charge of ion $S$. This is the actually useful form of the equation that can be used for any ion for any temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Nernst equation is a limiting case of the Goldman-Hodgkin-Katz equation for a single ion. The Nernst equation is useful for directly determining the &lt;em&gt;equilibrium potential&lt;/em&gt; of a single ionic species. The GHK equation is used for determining the &lt;em&gt;reversal potential&lt;/em&gt; of a membrane or channel in multi-ion cases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the terms &quot;reversal potential&quot; and &quot;equilibrium potential&quot; are not synonymous, except in the case of a single ion system. The reversal potential is where the direction of current switches. An equilibrium is when net ion flux is zero (although, in a living cell, it is more appropriate to call even this situation a &lt;em&gt;steady state&lt;/em&gt;). If membrane were only permeable to one ion, the reversal potential will be at the equilibrium potential (given by Nernst) for that single ion. However, when there are several permeant ions, usually none of the ions will be in equilibrium at the reversal potential--that is, all the ions will have a measurable flux across the membrane even though the sum of those fluxes (weighted by permeabilities) is zero at the reversal potential.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Converting natural log to log base 10, you can use the identity $\log_b{a} = \frac{\log_{10}{a}}{\log_{10}{b}}$, which gives&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;E_{S} = \frac{1}{\log_{10}{e}} \cdot \frac{RT}{z_{S}F}\log_{10}{\frac{[S]_{out}}{[S]_{in}}}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of sodium ions (Na+) at 37 degrees (physiological temperature), $T$ is 310 and $z_S$ is +1. Substituting in these values, we have&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;E_{S} = 2.303 \cdot \frac{(8.3145) (310)}{(+1) (96485) }\log_{10}{\frac{[S]_{out}}{[S]_{in}}} \\&#xA;E_{S} = 61.5 \text{ mV} \cdot\log_{10}{\frac{[S]_{out}}{[S]_{in}}}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;YAK uses a less common form of the Nernst equation in membrane physiology which uses the Boltzmann constant directly and deals with elementary charges instead of moles ($R = N_A k_B$). It is a wonderful exercise to derive the Nernst equation from the Boltzmann equation,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;\frac{p_2}{p_1} = \exp{(-\frac{u_2 - u_1}{k_BT})}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $p_i$ is the probability of a particle being in state $i$, and $u_i$ is the energy of state $i$. All it takes is some rearranging and keeping careful track of the units.&lt;/p&gt;&#xA;" OwnerUserId="72" LastEditorUserId="72" LastEditDate="2013-02-08T17:45:53.867" LastActivityDate="2013-02-08T17:45:53.867" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7112" PostTypeId="1" CreationDate="2013-02-07T08:06:26.837" Score="4" ViewCount="527" Body="&lt;p&gt;In my respiratory physiology lectures, my professor explained that hypoxia-induced hyperventilation occurs in 2 stages when people try to acclimate at high altitudes. &lt;strong&gt;My question is about the long-term 2nd stage, listed as #2 below:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;there's an immediate increase in alveolar ventilation triggered by peripheral chemoreceptors, but this only leads to a small increase, and also decreases levels of $p_{CO_2}$.&lt;/li&gt;&#xA;&lt;li&gt;over 8 hrs, there's a slow rise and 2 mechanisms are involved:&lt;br&gt;&#xA; a) bicarbonate ion ($HCO_3^-$) in cerebrospinal fluid is shuttled out and chemoreceptors increase their sensitivity to $p_{O_2}$&lt;br&gt;&#xA; b) kidneys excrete more $HCO_3^-$ to normalize blood pH&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I get that the $HCO_3^-$ and $H^+$ comes from $H_2CO_3$ being broken down through carbonic anhydrase. &lt;strong&gt;But she never mentioned where the $HCO_3^-$ is shuttled to or which chemoreceptors are increasing their sensitivity to $p_{O_2}$&lt;/strong&gt; (I assume peripheral since it's mentioning sensitivity to $O_2$). She then says that because of this $H^+$ and $CO_2$ levels increase, stimulating central chemoreceptors to increase ventilation to help decrease the acidity/$CO_2$ levels. &lt;strong&gt;I don't understand how $H^+$ and $CO_2$ levels are even rising because I don't know where the $HCO_3^-$ is even going and what it's role is.&lt;/strong&gt; This professor is terrible at explaining things, and I'm just so confused at this point! Any sort of direction would be so helpful! Thanks!&lt;/p&gt;&#xA;" OwnerUserId="3044" LastEditorUserId="112" LastEditDate="2013-02-07T14:49:33.377" LastActivityDate="2021-04-24T19:19:56.837" Title="What is the mechanism behind ventilatory acclimatization?" Tags="&lt;physiology&gt;&lt;respiration&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7113" PostTypeId="1" CreationDate="2013-02-07T14:47:35.560" Score="0" ViewCount="202" Body="&lt;p&gt;I'm not a biologist so bear with me. I know that the DNA molecule carries extremely large amounts of information. If the process of evolution is driven by completely random process .I think about it as the complex interactions between environment and random genetic mutations that leads to natural selection. &#xA;I've two questions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the probability of evolution of intelligent human beings within this scenario? I've heard that the probability of spontaneous generation of a good protein molecule should be nil in our universe: is this correct ? &lt;/p&gt;&#xA;" OwnerUserId="3047" LastEditorUserId="1320" LastEditDate="2013-02-07T18:12:07.390" LastActivityDate="2013-02-08T07:59:31.603" Title="A question regarding evolution" Tags="&lt;evolution&gt;&lt;protein-folding&gt;&lt;protein-evolution&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7114" PostTypeId="2" ParentId="7113" CreationDate="2013-02-07T15:10:48.033" Score="2" Body="&lt;p&gt;Exactly how genetic material changes from one generation to the next is a very complex subject. But essentially you are right. The change in genes from one generation to the next is not only mutations though. It is also mixing of the genes carried by the male and the genes carried by the female. The selection process is also very complex, and sexual selection is, for some species, a large part of it as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the probability of intelligent life emerging... Obviously, it's happened. The probability is at best extremely difficult to even provide an estimate of. How do you define a &quot;good&quot; protein molecule :-)?&lt;/p&gt;&#xA;" OwnerUserId="3032" LastActivityDate="2013-02-07T15:10:48.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7115" PostTypeId="1" AcceptedAnswerId="7116" CreationDate="2013-02-07T15:57:21.550" Score="3" ViewCount="2940" Body="&lt;p&gt;How do bats distinguish between day and night? Do they hunt at night - if yes, how they know that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are they afraid of sunlight?&lt;/p&gt;&#xA;" OwnerUserId="3048" LastEditorUserId="1320" LastEditDate="2013-02-07T18:10:06.177" LastActivityDate="2014-05-28T23:27:31.563" Title="How do bats distinguish between day and night?" Tags="&lt;eyes&gt;&lt;mammals&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7116" PostTypeId="2" ParentId="7115" CreationDate="2013-02-07T16:24:58.247" Score="4" Body="&lt;p&gt;Bats distinguish day and night the same way that other animals do, with an internal circadian clock and by environmental cues (dawn and dusk). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most bats (over 1000 different species total) are nocturnal, meaning that they are out of their roost and foraging at night. This includes that vast majority of bats, which also echolocate. Some bats, notably pteropodid &quot;Flying foxes&quot; are diurnal, meaning they are active during the day and sleep at night, like humans. These bats are typically fruit-eating. There are, of course, exceptions, but these general patterns hold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bat Conservation International has &lt;a href=&quot;http://www.batcon.org/index.php/all-about-bats/intro-to-bats.html&quot; rel=&quot;nofollow&quot;&gt;good educational information about bats&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-02-07T16:24:58.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7117" PostTypeId="1" AcceptedAnswerId="8459" CreationDate="2013-02-07T16:37:05.977" Score="2" ViewCount="63" Body="&lt;p&gt;If you are given an unlimited growth model in the form:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\frac {dP(t)}{dt} = k P(t)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously the population growth would never be unlimited, but let's presume for the moment that we are introducing a species into an environment where there is the possibility for unlimited growth, at least on for a given time -- i.e. invasive species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$k$ is some rate of growth of the population at time $t$, denoted by $P(t)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are some feasible values of $k$? In other words, if a number is way above or way below $k$, where would I know that the research I am reading is preposterously off-base?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am sure it is different for different types of animals, including mammals, birds, bacteria, etc.&lt;/p&gt;&#xA;" OwnerUserId="3049" LastEditorUserId="115" LastEditDate="2013-05-22T06:55:44.947" LastActivityDate="2013-05-22T06:55:44.947" Title="Range of feasible coefficients in an unlimited growth model" Tags="&lt;mathematical-models&gt;&lt;population-dynamics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7118" PostTypeId="1" AcceptedAnswerId="7123" CreationDate="2013-02-07T16:42:01.863" Score="4" ViewCount="2397" Body="&lt;p&gt;I've just finished a course of double antibiotics for &lt;em&gt;Helicobacter pylori&lt;/em&gt; in my stomach.  I looked up &lt;em&gt;H. pylori&lt;/em&gt; and found that it was a gram-negative bacterium.  I looked up gram-negative and didn't understand the definition.  I assume that if there are gram-negative bacteria then there are also gram-positive ones.  Can someone explain the terms gram-negative and gram-positive in basic, layman's terms?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sachin&lt;/p&gt;&#xA;" OwnerUserId="1519" LastEditorUserId="1320" LastEditDate="2013-02-07T18:08:06.837" LastActivityDate="2013-02-07T20:03:58.723" Title="What are gram negative and positive bacteria?" Tags="&lt;bacteriology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7120" PostTypeId="2" ParentId="7118" CreationDate="2013-02-07T17:03:02.167" Score="7" Body="&lt;p&gt;The Gram stain is one of a large number of techniques used to characterize bacteria. In particular, a bacterial species is usually either Gram-positive (purple when stained) or Gram-negative (pink when stained). In Gram-postive bacteria, the cell wall is thicker and has much more peptidoglycan compared to Gram-negative bacteria. The chemicals in the stain react with these molecules in the cell wall and result in the purple color. All of this information is well covered in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Gram_staining&quot;&gt;Wikipedia article&lt;/a&gt; on the subject.&lt;/p&gt;&#xA;" OwnerUserId="72" LastActivityDate="2013-02-07T17:03:02.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7121" PostTypeId="1" AcceptedAnswerId="10437" CreationDate="2013-02-07T18:30:19.623" Score="1" ViewCount="5354" Body="&lt;p&gt;When motor neurons are stimulated to trigger an action potential, this potential propagates down the spine, eventually reaching a neuromuscular junction, causing the release of acetylcholine (ACh).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ACh binds to nicotinic ACh receptors (nAChR) on the muscle fibers, leading to an action potential. The nAChR is a non-selective, ligand-gated ion channel, permeable to sodium-, potassium- and calcium ions. This means sodium ions will flow in, leading to depolarization, but potassium will flow out, working towards hyperpolarization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If enough of these channels are opened, the post-synaptic membrane potential will be drawn towards $E_{Na}$ enough to reach a threshold, so that voltage-gated sodium channels open on the post-synaptic membrane, causing a post-synaptic action potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This action potential travels down inward extrusions of the plasma membrane, called transverse (T) tubules. &lt;strong&gt;Is the membrane continuous along these tubules, or does the tubule just end somewhere inside the muscle fiber?&lt;/strong&gt; Anyway, the action potential comes in contact with the muscle fiber version of an endoplasmic reticulum: The sarcoplasmic reticulum (SR).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Upon contact with the action potential, the calcium ion channels in the SR open, causing calcium ions to flow into the cytosol. Here they bind to troponin complexes on the tropomyosin protein - a regulatory protein, that twists around the thin filaments of the muscle fiber. In short, when calcium ions bind to troponin, it reveals binding sites for myosin on the thin filaments, letting the muscle contraction cycle of the myosin heads proceed, and the muscle contracts!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the stimulus goes away, calcium ions are transported back into the SR, and myosin has nowhere to bind, thus the cycle is halted, and the muscle relaxes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;When the muscle is twitching...&lt;/strong&gt; is this neurological of nature, or is it related to a molecular cause in the muscle itself?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;When the muscle is cramping...&lt;/strong&gt; I'm almost certain this arises in the muscle. What causes it? A malfunction with regard to the calcium ions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, and on a slightly different subject, &lt;strong&gt;what are the microlesions in the muscles that occur during strength training, and what is the overcompensation that happens?&lt;/strong&gt; The basis of this might not be entirely on the molecular level I feel.&lt;/p&gt;&#xA;" OwnerUserId="3032" LastActivityDate="2013-09-15T01:43:45.937" Title="Molecular cause of cramps, spasms and strengthening in muscles? (incl. intro to muscle contraction)" Tags="&lt;molecular-biology&gt;&lt;neurotransmitter&gt;&lt;muscles&gt;&lt;receptor&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7122" PostTypeId="2" ParentId="7113" CreationDate="2013-02-07T18:55:21.867" Score="2" Body="&lt;p&gt;Since we only have one planet that we know of with life, it's a bit difficult to make good estimates on the probability of various events in the history of life.  To make a good estimate, you'd want to have thousands of planets very similar to earth to compare.  Since we don't have access to that kind of data, one proxy which you can look at is &lt;em&gt;how long&lt;/em&gt; did it take for some event to happen in earth's history.  In a vacuum you'd expect things that took longer to happen to be rarer.  From this point of view, it seems likely that the development of multi-cellular life from simpler life forms is a low probability event because it took 3 billion years of simpler life forms before it happened.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way to get information on probabilities is to look at widely separated branches of the tree of life.  Since wings evolved separately in birds, bats, insects, and pterosaurs, the probability of wings evolving in a planet with a similar atmosphere and multicellular animals is likely pretty high.  Similarly, you can argue that the development of human level intelligence is relatively low probability because it has only developed once in the history of the planet in one lineage that very nearly died out.  Dinosaurs never developed human level intelligence, nor did rodents, or mollusks, or arthropods.  On the other hand, it seems that a lower level of intelligence at say the dog level is relatively high probability (since it has evolved separately in mollusks, birds, mammals, etc.).&lt;/p&gt;&#xA;" OwnerUserId="997" LastActivityDate="2013-02-07T18:55:21.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7123" PostTypeId="2" ParentId="7118" CreationDate="2013-02-07T20:03:58.723" Score="7" Body="&lt;p&gt;@yamad is right on - Gram stain is a major way of categorizing bacteria. Its worth mentioning what the Gram stain color means.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While not failproof, the Gram stain test reflects a major division of the sorts of cells bacteria, helping to type the bacteria of interest &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gram stain reacts with the peptidogycan to create the purple color.  The &lt;a href=&quot;http://en.wikipedia.org/wiki/Peptidoglycan&quot; rel=&quot;noreferrer&quot;&gt;peptidoglycan&lt;/a&gt; is a mesh of carbohydrate (sugar) chains with short peptides attached to them that gives the bacterial wall mechanical strength against osmotic changes in the environment (e.g. large concentrations changes in sugars or salts) and mechanical stresses such as shearing from current.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DoZVu.png&quot; alt=&quot;peptidoglycan&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gram Negative bacteria have two lipid membranes with peptidoglycan sandwiched in between them while Gram positive bacteria have a single lipid membrane with the peptidoglycan mesh surrounding the membrane, forming an outer coat to the bacteria.  There is typically 5-10 times more peptidoglycan by weight in Gram Positive bacteria.  As such these two distinct categories of Bacteria is often the first determination used to characterize a bacterium.  Again while not without some error, Gram stains reflect a significant cell physiological division in bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RdSch.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-02-07T20:03:58.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7124" PostTypeId="1" AcceptedAnswerId="7125" CreationDate="2013-02-07T20:35:55.247" Score="6" ViewCount="2721" Body="&lt;p&gt;I have been measuring my protein solutions' concentrations by diluting them in water 20 fold with a final volume of 100 uL and then measuring the absorbances of these solutions in 96 well plates with plate reader. I don't remember having any problem up until today.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I used 20 mM phosphate buffer instead of water to dilute them today and measured the absorbances at 280 nm repeatedly three times and the absorbance for one of the solutions went up from 0.043 to 0.068 (absorbance of 20 mM phosphate buffer is 0.030 at 280 nM with same volume); I stopped measuring after third one but it would probably go higher as I measured until I hit a plateau.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I measured absorbances of two proteins and only one of them went up that much, other one went up from 0.071 to 0.088; if this were to be concentration dependent I would expect the second solution go even higher but it didn't happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know there may be differences in UV absorbances if protein is folded or unfolded; would it be that dramatic? What is the reason for that increase? I will be grateful for an explanation and a practical solution to the problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NOTE: I increased the total volume to 200 uL by simply adding 100 uL of 20 mM phosphate buffer into all wells and the signal increase slowed down a lot; there is still some increase though with 0.001-0.003 increments in each measurement.&lt;/p&gt;&#xA;" OwnerUserId="1772" LastEditorUserId="1772" LastEditDate="2013-02-07T20:48:30.853" LastActivityDate="2013-02-08T09:46:38.743" Title="Why is absorbance at 280 nm for protein solution going up when I measure repeatedly?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7125" PostTypeId="2" ParentId="7124" CreationDate="2013-02-07T21:43:46.843" Score="2" Body="&lt;p&gt;It looks like your protein concentrations are right on the limit of detection of the spectrophotometer, and changing the diluent buffer changed their concentrations. The samples may not have been thoroughly mixed after dilution and before measurement, so the varying measurements may simply be the solution coming to equilibrium. Temperature can also affect absorbance, so you should verify that your samples have equilibrated before drawing any conclusions. If the absorbance of your phosphate buffer is 0.03, I'd try to keep the sample absorbances above 0.075 or higher to avoid getting too close to the limit of detection. Also, make sure your buffer isn't too old or contaminated with something which could be affecting its absorbance characteristics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would suggest taking one or two protein samples and doing a dilution series (1:1, 1:5, 1:10, 1:20) in a large-ish volume (say 400 ul each, if you can spare it), vortex briefly to mix well, then measure triplicates of each dilution on your reader, along with appropriate blanks (buffer only). You will see differences between each measurement, but it should be quite small, depending on the accuracy and precision of your instrument. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Measured values will not be exactly the same from measurement to measurement, and it would take a lot more than three repetitions to determine if there was an actual drift trend occurring. Measure your sample plate every 5 minutes for an hour and plot the values (don't just eyeball them) to see if the machine may need to be serviced.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-02-07T21:43:46.843" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7127" PostTypeId="2" ParentId="7113" CreationDate="2013-02-08T07:59:31.603" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;If the process of evolution is driven by completely random process...&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's not.  The evolution of &quot;better&quot; protein (and other) molecules happens because of &lt;em&gt;selection&lt;/em&gt;, a very non-random process.  The repeated selection of better molecules, and then of the variants of the better molecules, repeated many times, will lead to &quot;good&quot; molecules (in the sense that they work better for their producers).&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2013-02-08T07:59:31.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7128" PostTypeId="1" AcceptedAnswerId="7135" CreationDate="2013-02-08T08:48:43.577" Score="5" ViewCount="2969" Body="&lt;p&gt;It's a pretty elementary concept, and when I first learned of it I don't think I had the foundations to even think of such a question, but I found myself the other day thinking about the amphipathic nature of the phospholipids in the plasma membrane and why it might be that lipid-soluble molecules don't stay in between the layers (of the bilayer). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that simple diffusion is a response to a concentration gradient, but consider a case where equilibrium is being restored and lipid-soluble molecules are diffusing from whatever extracellular matrix through the membrane and into the cytosol. Towards the end of this process, when equilibrium is nearly restored and the last few molecules are making their way into the cell, the rate of diffusion for these last couple molecules will be slower than those that diffused when the concentration difference was greater. Since the polar heads on the outside and inside of the bilayer are hydrophilic but the inner part, where the fatty acid tails are, is hydrophobic, what drives a molecule to leave the cozy, accepting, lipophilic environment of the middle (of the bilayer) to cross through the cytosolic-side rejecting polar heads and enter the cytosol?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that initially these molecules were moving into the cell in response to a difference in intracellular vs extracellular concentration, but I'm asking whether we would ever see a case where the gradient is nearly zero and a molecule in transit simply decides to reside in between the layers instead of crossing all the way into the cell; as if moving through the cytosolic polar head side is not worth the effort to reduce a nearly-zero gradient to zero.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please ask me if I can clarify my question in any way -- I'm finding it difficult to phrase. I asked my professor (who has her doctorate in toxicology &amp;amp; pharmacology) and she understood what I was asking but didn't have an answer.  &lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2013-02-09T05:59:20.147" Title="Simple diffusion of lipid-soluble molecules through phospholipid bilayer -- does anything get &quot;stuck&quot; in transit?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;cell-membrane&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7129" PostTypeId="1" AcceptedAnswerId="7131" CreationDate="2013-02-08T08:59:09.627" Score="4" ViewCount="537" Body="&lt;p&gt;I have wondered what actually happens in an allergic reaction that causes the symptoms such as pain, rash etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible that the human body actually kills its own cells in the process?&lt;/p&gt;&#xA;" OwnerUserId="3052" LastEditorUserId="107" LastEditDate="2013-02-08T13:15:30.693" LastActivityDate="2013-02-08T13:15:30.693" Title="Does an allergic reaction kill body cells?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7130" PostTypeId="2" ParentId="7124" CreationDate="2013-02-08T09:46:38.743" Score="0" Body="&lt;p&gt;Could be protein unfolding or changes in conformation. Absorbance at 280 nm is mainly due to the tryptophan residues, and can change substantially as these residues move from a more hydrophobic (buried inside the protein) to a more hydrophilic (exposed to the solvent) environment. Your protein may be reacting to the new buffer.&lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-02-08T09:46:38.743" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7131" PostTypeId="2" ParentId="7129" CreationDate="2013-02-08T13:03:12.377" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is it possible that the human body actually kills its own cells in the&#xA;  process?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes it is. It is happens not only as a result of allergic reactions (see comment of @terdon). But in case of allergy our body have 3 methods for killing own cells.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Cytotoxic, antibody-dependent (Type 2 hypersensitivity)&lt;/strong&gt; The antibodies produced by the immune response bind to antigens on the patient's own cell surfaces.These cells are recognized by macrophages or dendritic cells, which act as antigen-presenting cells. This causes a B cell response, wherein antibodies are produced against the foreign antigen.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Immune complex (Type 3 hypersensitivity)&lt;/strong&gt; Occurs when antigen-antibody complexes that are not adequately cleared by innate immune cells accumulate, giving rise to an inflammatory response and attraction of leukocytes&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Cell-mediated immune memory response (Type 4 hypersensitivity)&lt;/strong&gt; is an immune response that does not involve antibodies, but rather involves the activation of phagocytes, natural killer cells (NK), antigen-specific cytotoxic T-lymphocytes, and the release of various cytokines in response to an antigen.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;See Wiki about &lt;a href=&quot;http://en.wikipedia.org/wiki/Template%3aHypersensitivity_and_autoimmune_diseases&quot; rel=&quot;nofollow&quot;&gt;types and diseases&lt;/a&gt; and about Hypersensitivity&lt;/p&gt;&#xA;" OwnerUserId="1839" LastActivityDate="2013-02-08T13:03:12.377" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7132" PostTypeId="1" CreationDate="2013-02-08T14:54:34.387" Score="2" ViewCount="1677" Body="&lt;p&gt;Bacterial are a great group of organisms. They have circular genomes and never went toward linear genomes while other organisms show the opposite strategy and don't have circular genomes (disregarding their cytoplasmic genome). Why they have followed these different strategies?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="1320" LastEditDate="2013-02-08T15:32:44.137" LastActivityDate="2013-02-08T15:32:44.137" Title="What is the advantage of circular genomes for bacteria and linear genomes for other organisms?" Tags="&lt;chromosome&gt;&lt;genomes&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7133" PostTypeId="2" ParentId="7132" CreationDate="2013-02-08T15:17:48.500" Score="4" Body="&lt;p&gt;You can package linear genomes much more efficiently than circular genomes, and bacteria simply don't require the information density to be prosperous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be a bit more specific, it's the torque strain put on the double-helix while it's being wound that makes the difference. Linear genomes can be wound around Histones, and these Histones can be further formed into more complex and dense patterns so that the DNA of a linear genome is condensed to a mere fraction of the size it was before. The high density allows cell division to occur much, much easier than it would otherwise happen in Eukaryotic cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Circular genomes &lt;em&gt;cannot&lt;/em&gt; get rid of the torque stresses like linear genomes can. To attempt a similar packaging scheme as Eukaryotic cells would result in the DNA breaking apart at some point before you reached a high level of information density.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll look through my BioChem books again to find a reference later on, but hopefully you should have a solid idea of &quot;why&quot; from the above. For now you can do a little thought experiment: Think of all the ways you can wind a single piece of string or thread around things to make it as dense as possible. Then think of all the ways you can try to achieve the same density with a rubber band without breaking it. The string should win out in both the ease at which you can manipulate it, and the level of density you can achieve.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2013-02-08T15:23:51.947" LastActivityDate="2013-02-08T15:23:51.947" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="7134" PostTypeId="2" ParentId="7128" CreationDate="2013-02-08T15:55:17.930" Score="3" Body="&lt;p&gt;I interpret your question to refer to the movement of a lipid-soluble molecule that is therefore able to diffuse into cells down a concentration gradient. I think that you are asking whether as the gradient collapses, some of these molecules would &quot;stay in the bilayer&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are thinking about the diffusion process in the wrong way. There will always be a pool of these molecules in the bilayer, and these will be continually exchanging with molecules in the two aqueous phases on either side of the membrane. The net flux which results in diffusion in any particular direction will be the  movement that results from these equilibria. Diffusion isn't a directed process in the way you define your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JoxDB.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My diagram shows on the left the progress towards equilibrium and on the right the situation where it has been reached. Note that at equilibrium, because it is lipid soluble, the molecule is at a higher concentration (larger typeface) than it is in either aqueous phase. And - importantly, molecules will still be moving into and out of the bilayer at both faces.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Added later&lt;/strong&gt;:&#xA;A classic example of a lipid soluble molecule able to diffuse in this way is oxygen. According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1329181/?page=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper&lt;/a&gt;, at physiological temperatures, and at equilibrium, the concentration of oxygen in a bilayer will be approximately 3x that in the surrounding fluids. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-02-08T17:00:29.390" LastActivityDate="2013-02-08T17:00:29.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7135" PostTypeId="2" ParentId="7128" CreationDate="2013-02-08T16:27:29.720" Score="2" Body="&lt;p&gt;I think, given Alan's answer the question you might be asking is something like &#xA;'do compounds become concentrated in the lipid bilayer', as opposed to achieving high concentration inside the cell after diffusing through the membrane as he describes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This could certainly happen (if that's what you're thinking), but usually won't for I think two reasons. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first is that any molecule that would not soluble in the interior of the cell is going to have a correspondingly small not going to be found in the blood or lymph, tissue, ocean or other milieu the cell is living in, which will be mostly water.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might well ask whether there are cases where the compounds in question might be available in low concentrations around the cell and over time accumulate in the lipid bilayer. This slow concentration model probably happens, but there is a compensating mechanism - the lipid bilayer is taken into vescicles and degraded, to be replaced by newly synthesized such that membrane components renew themselves.  This process includes the cell engulfing by endocytosis and specifically turning over membrane proteins.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The turnover rate for most cells is on the order of days, some of the best numbers for this are behind a paywall, but a &lt;a href=&quot;http://onlinelibrary.wiley.com/store/10.1002/jnr.10352/asset/10352_ftp.pdf?v=1&amp;amp;t=hcxjfl94&amp;amp;s=86bb93d11604f951c0324fe568cd6e73034f1c61&quot; rel=&quot;nofollow&quot;&gt;reference to synaptic membrane turnover&lt;/a&gt; shows some components turn over varying between 6 and 24 days.  Different components such as cholesterol, phosphatidylcholine and phosphatidylethanolamine have differing rates of turnover.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So between these two effects, the concentration of '&lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_membrane#Permeability&quot; rel=&quot;nofollow&quot;&gt;permeant molecules&lt;/a&gt;' would be low for most cases.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-02-09T05:59:20.147" LastActivityDate="2013-02-09T05:59:20.147" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7136" PostTypeId="2" ParentId="1731" CreationDate="2013-02-08T17:19:20.200" Score="1" Body="&lt;p&gt;The answer is yes, not only meiotic, but any DNA double-strand breaks will be detected as long as they are processed by homologous recombination. This method (SSDS) is based on the detection of resected ssDNA ends at DSBs. The only difference for the mitotic breaks will be that you cannot use anti-DMC1 for ChIP. Instead, you should use either anti-Rad51 or anti-RPA in ChIP. &lt;/p&gt;&#xA;" OwnerUserId="3054" LastActivityDate="2013-02-08T17:19:20.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7137" PostTypeId="1" CreationDate="2013-02-08T17:42:10.337" Score="4" ViewCount="461" Body="&lt;p&gt;I have been working with GST tagged proteins for the last 4 years and after loading the cell lysate into the column I was washing it with 20-30 column volumes of PBS and sometimes my proteins were eluted very pure sometimes with a lot of impurities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few times I tried washing with NaCl gradient (0-400 mM) but later decided not to do that because it may denature the protein and some of my proteins may not refold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do you suggest for washing step?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: I don't have any UV detector to see the washouts/flowthroughs/elutions.&lt;/p&gt;&#xA;" OwnerUserId="1772" LastActivityDate="2014-05-11T10:01:21.803" Title="How to wash the column during protein purification with GST tag?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;protein-folding&gt;&lt;purification&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7139" PostTypeId="1" CreationDate="2013-02-08T22:04:25.187" Score="1" ViewCount="240" Body="&lt;p&gt;&lt;strong&gt;What Conditions must Drugs satisfy&lt;/strong&gt; for them to be Deliverable via the &lt;strong&gt;Transdermal route&lt;/strong&gt;? I assume a high $\log{P}$ (lipophilicity) would be one, are there any others? &lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-03-11T21:37:03.907" Title="What Conditions must Drugs satisfy for them to be Deliverable via the Transdermal route?" Tags="&lt;pharmacology&gt;&lt;transdermal&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7140" PostTypeId="5" CreationDate="2013-02-08T22:07:51.857" Score="0" Body="&lt;p&gt;The &lt;strong&gt;transdermal route&lt;/strong&gt; of &lt;strong&gt;administration&lt;/strong&gt; is a route of administration for drugs that entails them seeping through the site on the skin where they are applied, down into the bloodstream where they then gain access to the site(s) of action in the body.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-09T05:59:53.550" LastActivityDate="2013-02-09T05:59:53.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7141" PostTypeId="4" CreationDate="2013-02-08T22:07:51.857" Score="0" Body="The transdermal route of administration is a route of administration for drugs that entails them seeping through the site on the skin where they are applied, down into the bloodstream where they then gain access to the site(s) of action in the body." OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-09T06:00:09.623" LastActivityDate="2013-02-09T06:00:09.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7142" PostTypeId="1" CreationDate="2013-02-09T06:26:01.090" Score="9" ViewCount="105" Body="&lt;p&gt;I have been reading with fascination about the several molecular- and cellular-scale mechanisms and structural changes that underlie what we refer to as long-term plasticity. For instance, &lt;a href=&quot;https://biology.stackexchange.com/questions/5306/how-do-neurons-form-new-connections-in-brain-plasticity&quot;&gt;[1]&lt;/a&gt;, &lt;a href=&quot;https://biology.stackexchange.com/questions/8/under-what-conditions-do-dendritic-spines-form&quot;&gt;[2]&lt;/a&gt;, &lt;a href=&quot;https://biology.stackexchange.com/questions/1198/long-term-potentiation-and-memory-where-do-we-stand&quot;&gt;[3]&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, there seem to be at least: synaptic scaling, synaptic pruning, synaptogenesis, spinogenesis, neurogenesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;How do each of the above mechanisms/ events affect the classical extracellular single/ multi-unit spikes, postsynaptic potentials (LFPs), and local electric fields? Does a mechanistic forward model exist, which specifies the biophysical transformation from synapse-level changes to spikes and LFPs? Are there spike simulators out there that model these properties?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Using such a forward model, can we solve a statistical inverse problem to infer anything at all about these LTP/LTD-induced small-scale structural and functional changes? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;For instance, one metric of analysis could be: &lt;a href=&quot;http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.148.9372&amp;amp;rep=rep1&amp;amp;type=pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;post-spike-time filters&lt;/a&gt; (self-terms and cross-terms) inferred using statistical point-process models. Another could be the shape of the action potential itself, which is typically used only for spike sorting, and then discarded. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Has something along these lines been done? Or is it infeasible? If so, why?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Finally, If anyone could give a brief overview of the gamut of synapse-scale physiological/ imaging techniques used to characterize these mechanisms, I would be very grateful!&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3057" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-02-20T01:52:20.513" Title="Can we disambiguate competing molecular mechanisms of learning and plasticity by measuring electrical activity of neurons?" Tags="&lt;neuroscience&gt;&lt;statistics&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7143" PostTypeId="2" ParentId="7139" CreationDate="2013-02-09T07:03:19.203" Score="2" Body="&lt;p&gt;Whether a drug &lt;em&gt;can&lt;/em&gt; be delivered transdermally?  I think that carriers can be formulated to carry a small molecule through the skin into circulation, so I don't even know about lipophilicity. I believe if you spend enough money, you can overcome many of these problems.  I think that pharmacology might be just as important. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the first condition of a transdermal administration is that the drug cannot be effectively administered orally.  This is the most cost effective route go get a pharma compound into the body. It requires no devices, no fancy coatings or vaporizors.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reasons that a pill (or its less popular cousins the suppository and sublingual tablet) cannot be used as the delivery system for a drug include effect of pH and other degradation of the compound in the GI tract, absorption rate from the GI tract and other factors such as effect of food in the system, other drugs which might interact in the system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another advantage of absorption through the GI tract is that this is the physiological system which is meant to be ingested and introduced into the body - its relatively fault tolerant, even if less of the drug actually reaches the blood stream.  There's more, but that's not a bad outline.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After pills and the like, the second choice is intravenous administration, which puts 100% of the drug into the circulatory system.   This has its own disadvantages, requires a clinical setting and the needle and breaking of the skin are not ideal in many cases.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the drug needs continuous and non clinical administration there are &lt;a href=&quot;http://en.wikipedia.org/wiki/Route_of_administration#Application_location&quot; rel=&quot;nofollow&quot;&gt;many other means of drug delivery&lt;/a&gt;, including transdermal administration.  Differentiating these methods often includes making sure the drug is available specifically to the part of the body that needs it.  E.g. topical administration; putting on a medicated cream for a skin condition or use of an inhaler which delivers the drug directly to the lung for an asthmatic condition.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Transdermal administration has its own specific advantages; continuous distribution of the compound over long periods of time.  Disadvantages include: poor ADME properties for biologicals like antibodies and other proteins, low delivery concentrations where you need a large amount added (epinephrine, and maybe antibiotics come to mind).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples of successful transdermal delivery are testosterone gels and the nicotine patch.  Both of which apply continuous controlled low dosage that is important there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are &lt;a href=&quot;http://en.wikipedia.org/wiki/Transdermal#Transdermal_pathways&quot; rel=&quot;nofollow&quot;&gt;three typical routes of drug absorption in transdermal delivery&lt;/a&gt;.  The drugs can diffuse through the membranes of dead cells of the stratum corneum, which works if the drugs are lipophilic enough.  They can diffuse around these cells, through the intercellular spaces, which can work for more polar drugs although this path is not usually as efficient.  The most extreme means are patches which contain tiny needles that can deliver straight through the protective layer of the skin.  With enough economic investment probably any sort of compound could be introduced through a patch.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of this is just cribbing off the notes from this lecture on coursera: &lt;a href=&quot;https://class.coursera.org/pharm101-2012-001/lecture/3&quot; rel=&quot;nofollow&quot;&gt;Fundamentals of Pharmacology&lt;/a&gt;.  Its probably outlined on any pharmacology text.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-02-09T21:14:55.010" LastActivityDate="2013-02-09T21:14:55.010" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7145" PostTypeId="1" AcceptedAnswerId="7152" CreationDate="2013-02-09T15:52:08.623" Score="7" ViewCount="671" Body="&lt;p&gt;Dictyostelium is a slime mold which is well known for having a single cell free living phase and other some conditions (e.g. when food is scarce) for forming communal piles of cells called 'slugs' which migrate as a proto animal.  Eventually the slug can turn into a fruiting body with a stem and a nodule of spore forming cells at the top.  The spores can then be carried off by the air and seed dicty further away.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from being amazed at the seeming ability to form amoebic, animal, plant and seed like forms, there must be a lot decision making happening at the formation of the stalk and fruiting node at the top. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is: what is the current thought about how cells compete in the mexican hat and stalk formation to be at the top of the pile?  Its pretty altruistic of the cells in the stalk to do this - some web pages say they die, is that right?  Links to references after 2007 or so would be appreciated unless it's all been decided.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By analogy its always been pretty altruistic of 99% of our bodies to let our gonads reproduce, but we are (approximately) homogeneous genetically.  In the wild is slug formation heterogeneous?  How does genetic diversity influence slug and fruiting body formation? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JcMFA.png&quot; alt=&quot;dictystelium forming fruiting bodies&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="500" LastEditDate="2013-03-14T17:09:58.323" LastActivityDate="2013-03-14T18:15:33.363" Title="How selfish is Dictyostelium slug formation?" Tags="&lt;reproduction&gt;&lt;evolutionary-game-theory&gt;&lt;selection&gt;&lt;altruism&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7146" PostTypeId="1" CreationDate="2013-02-09T16:01:34.103" Score="3" ViewCount="113" Body="&lt;p&gt;I have been given mock results from a PCR test on blood samples taken from kidney recipient patients and their donors. The PCR reaction can detect single copies of viral DNA. I have been asked to determine whether 5 patients have been infected with &lt;strong&gt;either&lt;/strong&gt; human herpesvirus 6 (HHV6) or human cytomegalovirus (HCMV) following kidney transplants. I have results for patients pre-transplantation and 1/3 weeks post-transplantation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The results are as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Donors:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Donor for patient A = HCMV+ &lt;/li&gt;&#xA;&lt;li&gt;Donor for patient B = HCMV+ &amp;amp; HHV6+&lt;/li&gt;&#xA;&lt;li&gt;Donor for patient C = Neg for both viruses&lt;br&gt;&lt;/li&gt;&#xA;&lt;li&gt;Donor for patient D = HHV6+&lt;br&gt;&lt;/li&gt;&#xA;&lt;li&gt;Donor for patient E = HCMV+ &amp;amp; HHV6+&lt;br&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Recipients:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Patient A = HCMV+ before and 1 &amp;amp; 3 weeks post-transplant&lt;br&gt;&lt;/li&gt;&#xA;&lt;li&gt;Patient B = Neg for both viruses before, then HHV6+ at week 1 &amp;amp; HCMV+ at week 3 following transplantation but negative for HHV6.&lt;br&gt;&lt;/li&gt;&#xA;&lt;li&gt;Patient C = HHV6+ before and 1 &amp;amp; 3 weeks post-transplant.&lt;br&gt;&lt;/li&gt;&#xA;&lt;li&gt;Patient D = HCMV+ before and HCMV+ &amp;amp; HHV6+ 1 &amp;amp; 3 weeks  post-transplant&lt;br&gt;&lt;/li&gt;&#xA;&lt;li&gt;Patient E = HHV6+ before and HCMV+ &amp;amp; HHV6+ 1 &amp;amp; 3 weeks  post-transplant&lt;br&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Answers: I am guessing that Patient A was re-infected by donor A. Patient B was neg for both viruses, developed HHV6  week 1 but this test was neg week 3 &amp;amp; instead positive for HCMV – these viruses do not disappear, you either have it or don’t so assuming there is no contamination error then what virus did he develop post-transplant?? Patient C was HHV6+ prior to transplant but donor is neg for both, so what virus did he develop following transplant? I can see that Patient D was infected with HHV6 from donor post-transplant. Patient E was infected with HCMV from donor post-transplant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am struggling to determine what virus Patient A, B and C was infected with following transplant. Can anyone help? I know almost 100% of us are infected with both viruses but do not cause disease in healthy people, that both latent and active viruses show positive when in blood and that both viruses can re-activate under certain conditions such as via infected organ transplants and immunosuppression.  &lt;/p&gt;&#xA;" OwnerUserId="3058" LastEditorUserId="69" LastEditDate="2013-03-12T00:14:30.057" LastActivityDate="2016-07-13T11:11:07.670" Title="Does this patient have HHV6 or HCMV after transplant surgery?" Tags="&lt;homework&gt;&lt;virology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7147" PostTypeId="2" ParentId="7146" CreationDate="2013-02-09T16:49:41.533" Score="2" Body="&lt;p&gt;I get the feeling that there's something we should probably know from your textbook or notes that you have not included. As-is, here's my best shot:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;It is impossible to determine if &lt;strong&gt;Patient A&lt;/strong&gt; was infected by the transplant since the virus they had before the transplant is the same virus carried by the transplant itself. Without running further tests to separate the two lineages you can't tell. It's likely, though.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;While &lt;a href=&quot;http://www.virologyj.com/content/7/1/287&quot; rel=&quot;nofollow&quot;&gt;HHV6 has been known to precede HCMV in certain cases&lt;/a&gt; the conditions don't seem to apply here. My best guess, which is something I'm pretty loathe to say, is that if you're positive the tests are accurate then it's possible that &lt;strong&gt;Patient B&lt;/strong&gt;'s immune system alternately suppressed each virus below detectable levels. Since &lt;strong&gt;Patient B&lt;/strong&gt; is receiving donor tissue with both viruses, and transplant patients are put on immunosuppressants following surgery, it could simply be that at first the immune system was capable of dealing with HCMV for the first week, but not HHV6. Then as it adapted to HHV6, HCMV evolved to evade so it showed up on the assays. &lt;strong&gt;&lt;em&gt;That is entirely speculative&lt;/em&gt;&lt;/strong&gt;, though. Another explanation might be that the viral titers of HCMV were too low to detect at Week 1, but it had reproduced enough to show up at Week 3 while the immune system dealt with HHV6. There's a lot of information that's missing on how the virii behave, the characteristics of the immunosuppressants given to the patient, and so on.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Patient C&lt;/strong&gt; was clearly infected with &lt;em&gt;nothing&lt;/em&gt;. They already had HHV6, and that's what showed up post-op. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Patient D&lt;/strong&gt; was infected with HHV6. They had HCMV before, and both after.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Patient E&lt;/strong&gt; was infected with HCMV, although like Patient A they could have been infected with a different strain of HHV6 as well, but the tests probably aren't specific enough to determine viral lineages for the before and after strains.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-02-09T16:49:41.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7148" PostTypeId="1" AcceptedAnswerId="7149" CreationDate="2013-02-09T19:37:23.863" Score="2" ViewCount="89" Body="&lt;p&gt;Is there a proven way to trigger an allergic or allergic-like reaction in non-allergic people? I have wondered if this is possible, since allergies are basically just a form hypersensitivity - so could this be triggered somehow?&lt;/p&gt;&#xA;" OwnerUserId="3052" LastActivityDate="2013-02-09T23:14:18.037" Title="Trigger allergic reaction in non-allergic people?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7149" PostTypeId="2" ParentId="7148" CreationDate="2013-02-09T20:02:05.480" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there a proven way to trigger an allergic or allergic-like reaction in non-allergic people?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;No.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At least, not that I've ever heard of. Allergic reactions, as you point out, are an overactive immune system response to an &lt;strong&gt;allergen&lt;/strong&gt; (anything that causes the reaction). What determines who is allergic to what is &lt;a href=&quot;http://en.wikipedia.org/wiki/Allergy#Cause&quot; rel=&quot;nofollow&quot;&gt;a mix of genetic and environmental factors&lt;/a&gt;, and because an allergic reaction is categorized as an &lt;em&gt;error&lt;/em&gt; on the immune system's behalf, inducing an allergic reaction is essentially finding a way to force the immune system to make a very, &lt;strong&gt;very&lt;/strong&gt; specific error.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What can (and does) happen is the development of new allergies. Almost all allergies are acquired after birth, and repeated exposure to substances can lead to the appearance of new allergies - one case that stuck out in my head was &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12342487?dopt=Abstract&quot; rel=&quot;nofollow&quot;&gt;a woman developing an allergy to a copper IUD that she tolerated well when it was first put in place&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not aware of any ability to &lt;em&gt;predict&lt;/em&gt; what substances will cause the development of a new allergy. Both the unpredictability and inability to induce allergies comes down to how the immune system reacts to &lt;strong&gt;antigens&lt;/strong&gt; (foreign substances). The machinations of the immune system's response to an allergen or antigen is fairly complicated, and at any point in the chain of events the potential for an overreaction is there. That's probably another question, though, and a much longer answer.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2013-02-09T23:14:18.037" LastActivityDate="2013-02-09T23:14:18.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7150" PostTypeId="2" ParentId="7079" CreationDate="2013-02-09T23:54:40.443" Score="1" Body="&lt;p&gt;This review may be of interest:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sharma D, Shanker V, Tegta G, Gupta M, Verma GK. Clinico-investigative profile of patients of hirsutism in a tertiary level institution. Int J Trichol [serial online] 2012 [cited 2013 Feb 9];4:69-74. Available from: &lt;a href=&quot;http://www.ijtrichology.com/text.asp?2012/4/2/69/96904&quot; rel=&quot;nofollow&quot;&gt;http://www.ijtrichology.com/text.asp?2012/4/2/69/96904&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the genetic causes of hirsutism, researchers thought the number of CAG repeats in the androgen receptor gene might play a role, but there was no evidence to that effect, as of 2000.  I couldn't find any newer papers, but here you go: &lt;a href=&quot;http://jcem.endojournals.org/content/85/4/1735&quot; rel=&quot;nofollow&quot;&gt;http://jcem.endojournals.org/content/85/4/1735&lt;/a&gt;.&#xA;This paper was cited by the previous review, but Sharma et al didn't read more than the title, because they cited Calvo et al as evidence &lt;em&gt;for&lt;/em&gt; the role of CAG repeats in hirsutism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;tl;dr: read Sharma et al, and look up the references.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-02-09T23:54:40.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7151" PostTypeId="2" ParentId="7105" CreationDate="2013-02-10T05:35:57.150" Score="2" Body="&lt;p&gt;This is not the biochemistry, but the brain regions involved are described in this article about an fMRI study: &lt;a href=&quot;http://www.sciencedaily.com/releases/2012/12/121210101630.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedaily.com/releases/2012/12/121210101630.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I can tell, mental fatigue is attributed to low oxygenation levels.  Here's a study that examines the effect of creatine in preventing mental fatigue: &lt;a href=&quot;http://jtoomim.org/brain-training/watanabe2001-creatine-reduces-mentalfatigue.pdf&quot; rel=&quot;nofollow&quot;&gt;http://jtoomim.org/brain-training/watanabe2001-creatine-reduces-mentalfatigue.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-02-10T05:45:17.047" LastActivityDate="2013-02-10T05:45:17.047" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7152" PostTypeId="2" ParentId="7145" CreationDate="2013-02-10T06:13:13.530" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://wubio.wustl.edu/Strassmann&quot; rel=&quot;nofollow&quot;&gt;Joan Strassman&lt;/a&gt;'s work is probably the route to go for this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The short of your answer is that several things mediate who ends up where in the slug:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cheaters are limited from exploiting other&#xA;  clones by high relatedness, kin discrimination, pleiotropy, noble&#xA;  resistance, and lottery-like role assignment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here's the most relevant paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Strassmann, J. E., &amp;amp; Queller, D. C. (2011). Evolution of cooperation and control of cheating in a social microbe. Proceedings of the National Academy of Sciences, 108(Supplement 2), 10855-10862. [&lt;a href=&quot;http://www.pnas.org/content/early/2011/06/20/1102451108.full.pdf&quot; rel=&quot;nofollow&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&#xA;" OwnerUserId="1906" LastEditorUserId="500" LastEditDate="2013-03-14T18:15:33.363" LastActivityDate="2013-03-14T18:15:33.363" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7153" PostTypeId="1" CreationDate="2013-02-10T10:33:47.387" Score="9" ViewCount="2217" Body="&lt;p&gt;Benzodiazepines are a class of drugs that serve as positive allosteric modulators of the GABA&lt;sub&gt;A&lt;/sub&gt; receptor by binding to their own &quot;site&quot; on the aforementioned receptor. By doing this they produce euphoria and a wide range of effects characteristic of Central Nervous System (CNS) depression (e.g. anxiolysis, sedation, amnesia, mental confusion, muscle relaxant effects). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that an interaction with the mesolimbic dopamine (&quot;reward&quot;) pathway would have to come in somewhere but where? I also know that GABAergic neurons downregulate activity in the mesolimbic dopamine pathway and that this is how opioids and cannabinoids induce euphoria -- they inhibit the release of GABA from presynaptic neurons in the mesolimbic dopamine pathway. I just find that this would be confusing in the case of benzodiazepines since they increase GABA activity, presumably also in the mesolimbic dopamine pathway thus producing dysphoria and not euphoria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I just would like to know how they manage to induce euphoria in full (what they do to increase activity in the mesolimbic dopamine pathway that thus leads to euphoria)&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please cite journal articles to substantiate your claims. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-10T21:51:32.700" LastActivityDate="2014-06-07T00:57:12.740" Title="How do Benzodiazepines induce Rewarding (Euphoric) effects?" Tags="&lt;pharmacology&gt;&lt;benzodiazepine&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7154" PostTypeId="5" CreationDate="2013-02-10T10:58:46.730" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-02-10T10:58:46.730" LastActivityDate="2013-02-10T10:58:46.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7155" PostTypeId="4" CreationDate="2013-02-10T10:58:46.730" Score="0" Body="Euphoria is a sense of well-being and intense enjoyment/pleasure. It can be the result of various recreational drugs, or the result of various physical activities including orgasm, strenuous physical activity and social activity." OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-10T15:13:05.730" LastActivityDate="2013-02-10T15:13:05.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7156" PostTypeId="1" CreationDate="2013-02-10T16:40:47.127" Score="5" ViewCount="661" Body="&lt;p&gt;What I have read is that the contents of the unit cell affect the intensities, but how? I am also unclear on why you need to know the symmetry of the unit cell, what is that used for? &#xA;I understand segments of this topic (x-ray crystallography) but I am having trouble piecing all the segments together to make a complete picture. I've been spending hours every day on this on this, any help would be really appreciated! &lt;/p&gt;&#xA;" OwnerUserId="3062" LastActivityDate="2013-02-11T06:12:31.590" Title="In the diffraction pattern of a protein crystal what exactly determines the intensities of the spots?" Tags="&lt;xray-crystallography&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7157" PostTypeId="2" ParentId="7156" CreationDate="2013-02-10T18:05:57.840" Score="3" Body="&lt;p&gt;Two questions here: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) What does the symmetry of the crystal mean?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The symmetry of the unit cell is the symmetry of the crystal.  Its really useful thing to know about the crystal in practice.  You can always pretend that any crystal is space group P1 - with no internal symmetry.  This implies half of the diffraction data is needed to get a complete set.  Why half? The Laue symmetry of typical X-ray diffraction shows that the diffraction should be centrosymmetric  I(hkl) = I(-h,-k,-l).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you do this and the crystal has more symmetry than that you are collecting too many data.  Here I take the example of a 2-fold axis.  Along that axis the space group shows that the symmetry of the crystal should be 4 fold along the x axis (x axis is chosen by convention):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I(hkl) = I(-h,-k,-l) (as above) and I(hkl) = I(h,-k,-l) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This fact means we actually can collect less data and know the crystal diffraction pattern easily.  In practice we collect from more than just the unique data, but the more diffraction data we take it also means that we can assume equivalence and have taken more  measurements, giving us better experimental accuracy for the same effort. It also means that when we build a molecular model for structure in the crystal we have a simpler model - one only creates a model for the unique assymmetric unit of the crystal unit cell. Fewer atoms in the structure, fewer degrees of freedom and less error in our resulting model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's more... screw axes 2(1), 3(1) and non primitive lattices create systematic absences which helps us collect more accurate data and do refinement more easily in the same vein...  but maybe this gives you an idea...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) how does the unit cell contents reflect the diffraction intensities&lt;/p&gt;&#xA;&#xA;&lt;p&gt;X-ray scattering from crystals is the result of the photon causing an elastic scatter from atomic, inner shell electrons - Bragg scattering.  By considering the crystal as a series of slits in 3 dimensions, it can be shown that the average positions of atoms in the crystal reinforce each other to give the reciprocal lattice that is diffraction data in 3D.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nhCNY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the picture above from Wikipedia you can see a beautiful protein crystal diffraction pattern.  The rings of spots are a spherical section from a 3D orthorhombic lattice of spots.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rather than digress into the reason the diffraction appears this way, back to your question: what causes the intensities to vary from spot to spot and crystal to crystal.  The crystal lattice contains atoms which are in the same position in every unit cell which are creating the diffraction by Bragg scattering.  As such, &lt;em&gt;it is the positions, relative electrons in orbit that dictate the diffraction intensities measured&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The models built to model diffraction typically translate a set of atomic positions to the structure factors (square roots of the diffraction intensities), but this is an approximation that works pretty well - the full model is not atomic positions, but an electron density function in space.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other sorts of scattering methods, more that could be said about all these subjects, but I hope that gives you some help with your specific questions. If you want clarifications in this, I can edit the answer from comments...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-02-11T06:12:31.590" LastActivityDate="2013-02-11T06:12:31.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7158" PostTypeId="2" ParentId="7153" CreationDate="2013-02-10T19:45:06.387" Score="2" Body="&lt;p&gt;Okay, I read the question wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Benzodiazepines do not bind to GABA&lt;sub&gt;A&lt;/sub&gt; receptors universally. Thus the presumption that it inhibits the mesolimbic dopamine pathway may be wrong. They may not interact directly with said pathway at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many subtypes for the GABA&lt;sub&gt;A&lt;/sub&gt; receptor exist. The receptor consists of 5 subunits. The following subunits are known to exist: α1-6, β1-3 and γ1-3. The most common combination has two α, two β and one γ. You find ones with distinct compositions at distinct locations in the brain. All have two bindingsites for GABA, but only a subset has an additional binding site for benzodiazepines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The benzodiazepine binding site is at the interface of an α and a γ subunit, so receptors without this structure will show no affinity for benzodiazepines. Additionally the α subunit must contain a histidine residue, which is only true for α1, α2, α3 and α5. That is paraphrased from wikipedia, where you can find the sources as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I still think you need to consider the idea that benzodiazepines may not interact directly with the dopaminergic reward pathway, like opiates and cocaine does. I attribute the euphoria to be an indirect effect, resulting from the muscle relaxation (which will feel like you had a good massage), and the calmness of the mind.&lt;/p&gt;&#xA;" OwnerUserId="3032" LastEditorUserId="3032" LastEditDate="2013-02-11T17:25:24.840" LastActivityDate="2013-02-11T17:25:24.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7163" PostTypeId="1" CreationDate="2013-02-11T04:15:37.580" Score="0" ViewCount="1719" Body="&lt;p&gt;A compound's therapeutic index is defined as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$TI = \frac{LD_{50}}{ED_{50}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What range are the therapeutic indices of benzodiazepines in? For the method of administration I would prefer intravenous as with it one can estimate the therapeutic indices via other routes. Of course for humans it is difficult to find LD&lt;sub&gt;50&lt;/sub&gt;'s but a rat/mice LD&lt;sub&gt;50&lt;/sub&gt; will suffice provided the ED&lt;sub&gt;50&lt;/sub&gt; is for the same respective species. Such benzodiazepines I am interested in are (Although I will accept your answer if you just give me an estimate of the therapeutic indices of the drugs in bold, the others are just icing on the cake):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Alprazolam&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;Brotizolam&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Clonazepam&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;Clorazepate&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Diazepam&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;Estazolam&lt;/li&gt;&#xA;&lt;li&gt;Flurazepam&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Lorazepam&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;Lormetazepam&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Midazolam&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;Nitrazepam&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Temazepam&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-12T00:54:37.893" LastActivityDate="2013-02-12T00:54:37.893" Title="Which range are the Therapeutic Indices of Currently-Prescribed Benzodiazepines in?" Tags="&lt;pharmacology&gt;&lt;benzodiazepine&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7164" PostTypeId="2" ParentId="7163" CreationDate="2013-02-11T05:11:29.173" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Therapeutic_index&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; quoted &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1821133/&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; as a reference for its statement about alprazolam having a therapeutic index of 100:1, although I can't confirm that, since I can only read what's immediately available in that link. There's a figure saying less than 100:1 for diazepam though.&lt;/p&gt;&#xA;" OwnerUserId="3032" LastActivityDate="2013-02-11T05:11:29.173" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7165" PostTypeId="2" ParentId="7163" CreationDate="2013-02-11T06:24:59.067" Score="1" Body="&lt;p&gt;&lt;strong&gt;A first pass answer is 662-4342.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Therapeutic index is calculated from rat tolerances; LD50 is a rare number to see for human beings(!).  The toxic dose of a compound can vary widely over a class of compounds as well as does the Effective Dose (ED) midpoint (ED50).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I found this &lt;a href=&quot;http://books.google.com/books?id=pXvFGqz44pYC&amp;amp;pg=PA214&amp;amp;lpg=PA214&amp;amp;dq=benzodiazepine%20ld50&amp;amp;source=bl&amp;amp;ots=T0xS3yWuqs&amp;amp;sig=jrTSYnuIkyU2k0bZVmOLMSBaxfI&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=Q4wYUcqIDejhiwLJwYHQDA&amp;amp;ved=0CE4Q6AEwAg#v=onepage&amp;amp;q=benzodiazepine%20ld50&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;book reference&lt;/a&gt;:  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Benzodiazepines &lt;em&gt;have a wide margin of safety&lt;/em&gt; based on experimental studies in animals.  In the rat for example, the lethal dose of alprazolam is 331-2171 mg/kg. The effective therapeutic dose for alprazolam is 0.5 mg/kg which results in a therapeutic ratio of ... 662-4342.  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The page goes on to say, at rather great length, that human evidence is that despite the fact that this is a popular class of drugs to try to kill yourself with, there are relatively few human deaths, which is pretty ultimate a judge for toxicity, though you could look for FDA warnings on the class of drugs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would bet that you can find relatively toxic benzodiazepines, but for the ones that pass screening they seem pretty benign as a class.  There are other issues with these drugs rather than mere toxicity - they are quite addictive, so therapeutic index is not an ultimate judge of the adverse effects of a drug.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW taken literally, this is a hard question you ask.  If you are expecting a compiled list of all such drugs, cross referenced to their Therapeutic index, that is really more like the work for a paper rather than 25 points of stackexchange karma IMHO.  On the other hand maybe someone has this information at their fingertips...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-02-11T18:17:06.383" LastActivityDate="2013-02-11T18:17:06.383" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7166" PostTypeId="1" CreationDate="2013-02-11T06:32:59.127" Score="5" ViewCount="89" Body="&lt;p&gt;Just as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Waggle_dance&quot; rel=&quot;nofollow&quot;&gt;Bee dance&lt;/a&gt;, for a &quot;language&quot;, I mean that there are vocal pattens, or &quot;grammar&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the nature, there are many intelligent animals like human beings. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bird songs, whale songs, dogs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, bird vocalization includes both bird calls and bird songs. There are Parrots, hummingbirds and songbirds,... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wish to know the most well-understood vocal animal languages. Which species?&lt;/p&gt;&#xA;" OwnerUserId="3066" LastEditorUserId="3952" LastEditDate="2013-08-10T07:02:42.193" LastActivityDate="2013-08-10T07:02:42.193" Title="What are the most well-understood vocal animal languages?" Tags="&lt;ethology&gt;&lt;communication&gt;&lt;language&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="2" ClosedDate="2013-02-15T08:24:55.147" ContentLicense="CC BY-SA 3.0" />
  <row Id="7167" PostTypeId="2" ParentId="1362" CreationDate="2013-02-11T09:15:06.017" Score="6" Body="&lt;p&gt;Because of reflected pressure waves and the stiffness of the blood vessel.  The forward pressure wave from the heart travels much faster than the blood itself and is reflected at areas of tapering and branching.  This backward wave slows the forward flow of blood, and at the same time, when it meets the next forward pressure wave, that forward pressure wave is augmented...so higher pressures distally...And now you know, and knowing is half the battle... &lt;/p&gt;&#xA;" OwnerUserId="3068" LastActivityDate="2013-02-11T09:15:06.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7169" PostTypeId="2" ParentId="5497" CreationDate="2013-02-11T17:55:53.227" Score="2" Body="&lt;p&gt;Heat shock proteins - HSP70 and HSP30.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may also have ribosomal subunits as well.&lt;/p&gt;&#xA;" OwnerUserId="3072" LastEditorUserId="3072" LastEditDate="2013-02-11T19:33:06.283" LastActivityDate="2013-02-11T19:33:06.283" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7170" PostTypeId="1" AcceptedAnswerId="7171" CreationDate="2013-02-11T18:58:07.683" Score="2" ViewCount="74" Body="&lt;p&gt;First of all let me say that I'm not into Biology myself... but I have a question for those of you who are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I've read, cancer is caused by &lt;a href=&quot;http://www.foundationmedicine.com/patients-dna-cancer.php&quot; rel=&quot;nofollow&quot;&gt;'faulty' DNA that behaves abnormally&lt;/a&gt;. &lt;a href=&quot;http://learn.genetics.utah.edu/archive/sloozeworm/mutationbg.html&quot; rel=&quot;nofollow&quot;&gt;Mutations&lt;/a&gt; can occur for various reasons, ranging from simple 'copying errors' to &lt;a href=&quot;http://www.cancerresearchuk.org/cancer-info/cancerandresearch/all-about-cancer/what-is-cancer/what-causes-cancer/what-causes-cancer2&quot; rel=&quot;nofollow&quot;&gt;environmental factors&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was just wondering whether current research has dealt with storing DNA of people or animals (e.g. rodents) and observing how it changed, especially for cases where it eventually resulted in cancer. Something along the lines of &lt;a href=&quot;http://www.bbc.co.uk/news/health-20663090&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;, but I'd like to know what research has actually been done so far.&lt;/p&gt;&#xA;" OwnerUserId="3073" LastActivityDate="2013-02-11T19:39:02.140" Title="Studying changes in DNA for causes of cancer" Tags="&lt;dna&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7171" PostTypeId="2" ParentId="7170" CreationDate="2013-02-11T19:33:46.640" Score="3" Body="&lt;p&gt;I tried to comment but what I wrote is too long, so here it is as an answer of sorts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I understand the question, you are asking: has anyone done a prospective study where they store the DNA of individuals and then later, when some of these individuals get cancer, have a look for mutations that are associated with that cancer. In fact this is done all of the time, but it isn't necessary to store any DNA because the cancer patients will have the normal sequence in all of their non cancerous tissues - only the cancer cells will have the relevant mutations. See &lt;a href=&quot;http://www.sciencemag.org/content/early/2013/01/23/science.1229259&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for a recent example of this type of study that made the news. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your BBC link is to a story in which the genomes of people will be analysed to determine if there are genetic factors which predispose them to cancer (and other diseases), but these won't be the mutations that actually create the cancerous cells.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-02-11T19:33:46.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7172" PostTypeId="2" ParentId="7170" CreationDate="2013-02-11T19:39:02.140" Score="1" Body="&lt;p&gt;There is a tremendous amount of information relating to mutations of genes and how they produce cancer.  In fact, this is multi-billion area of research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is even more interesting, is the aneuploidy hypothesis of cancer, in which it is chromosomal abnormalities, rather than mutations in single genes, that lead to cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suggest reading about it, there was an article by Peter Deusberg in a 2007 Scientific American article.&lt;/p&gt;&#xA;" OwnerUserId="3072" LastActivityDate="2013-02-11T19:39:02.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7173" PostTypeId="1" CreationDate="2013-02-11T20:09:09.380" Score="6" ViewCount="507" Body="&lt;p&gt;I have a set of gene expression data downloaded from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo&quot;&gt;http://www.ncbi.nlm.nih.gov/geo&lt;/a&gt;. I have two sets of data, one is the raw probe intensity data set in the form of CEL files. Another is processed txt file.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a link for example&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7904&quot;&gt;http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7904&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know what kind of processing is done to generate the processed data from the raw CEL files. For example in the above link, I have processed data like &lt;/p&gt;&#xA;&#xA;&lt;p&gt;SOFT formatted family file(s)&#xA;MINiML formatted family file(s)&#xA;Series Matrix File(s)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know what sort of processing is done to generate those files. Any suggestions? I can read the raw CEL files in matlab but what sort of preprocessing am I supposed to do?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also want to map these probe its to gene ids and get the corresponding gene. How can I accomplish this? I know matlab. But I am bit confused about the terminology and all. Any suggestions?&lt;/p&gt;&#xA;" OwnerUserId="3074" LastActivityDate="2013-02-15T13:19:04.503" Title="Confusion related to gene expression" Tags="&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7174" PostTypeId="2" ParentId="7173" CreationDate="2013-02-11T21:45:38.717" Score="3" Body="&lt;p&gt;If you click through to some of the samples in the study, eg. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM194397&quot; rel=&quot;nofollow&quot;&gt;GSM194397&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM194398&quot; rel=&quot;nofollow&quot;&gt;GSM194398&lt;/a&gt;, etc. it mentions under the &quot;Data processing&quot; section that &quot;The data were analyzed with dchip with default normalization settings&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can learn more about dChip over at &lt;a href=&quot;http://www.hsph.harvard.edu/cli/complab/dchip/&quot; rel=&quot;nofollow&quot;&gt;the dChip website&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2013-02-11T21:45:38.717" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7175" PostTypeId="1" AcceptedAnswerId="7176" CreationDate="2013-02-11T23:52:08.627" Score="9" ViewCount="7750" Body="&lt;p&gt;Although pili have been observed in some species of Gram positive bacteria, the preliminary research that I have done indicates that pili are significantly more common in Gram negative bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this an accurate assessment of the current body of scientific knowledge? If so, do we know (or have any leading theories on) &lt;em&gt;why&lt;/em&gt; this is the case?&lt;/p&gt;&#xA;" OwnerUserId="145" LastActivityDate="2015-04-21T16:32:24.537" Title="Why are pili more common in Gram negative bacteria than in Gram positive?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7176" PostTypeId="2" ParentId="7175" CreationDate="2013-02-12T02:03:37.113" Score="6" Body="&lt;p&gt;Pili were at least discovered more recently in gram-positive bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pili are formed differently in gram-positive and gram-negative bacteria.  Here's a pretty good review on the differences: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18953686&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/18953686&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Researchers seem to think that pili might be involved in adhesion/formation of biofilms (adhesion is important for pathogenicity).  Certain types of pili are specifically involved in gene transfer. This is a good review on pili and pathogencity in gram-positive bacteria: &lt;a href=&quot;http://www.nature.com/nrmicro/journal/v4/n7/pdf/nrmicro1443.pdf&quot;&gt;http://www.nature.com/nrmicro/journal/v4/n7/pdf/nrmicro1443.pdf&lt;/a&gt;. If you can't access it, let me know, and I'll do my best to summarize.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Pilin&quot;&gt;Wikipedia entry for pilin&lt;/a&gt; interprets the second paper I linked as saying that pili &lt;em&gt;are&lt;/em&gt; more common in gram-negative bacteria and that pili are implicated in pathogenicity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Straight from the paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prevalence:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Over the past five decades, several distinct pilus types &#xA;  have been identified, most of which were described &#xA;  and characterized in Gram-negative bacteria.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Function:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A common feature of Gram-negative pili, however, is their role in adhesion to eukaryotic cells. It has been &#xA;  proposed that bacteria use these structures to form an &#xA;  initial association with host cells, which can then be &#xA;  followed by a more ‘intimate’ attachment that brings &#xA;  the bacterium into proximity to the host-cell surface.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pilus-like structures on the surface of Gram-positive &#xA;  bacteria were first detected in Corynebacterium renale, &#xA;  by electron microscopy. More recently, surface &#xA;  appendages were reported to be present in Actinomyces naeslundii&#xA;   and were subsequently found in other &#xA;  species, including Corynebacterium diphtheriae, Streptococcus parasanguis (Streptococcus parasanguinis), Streptococcus salivarius&#xA;   and Streptococcus sanguis (Streptococcus sanguinis). Finally, in the past &#xA;  year, pili were also characterized in all three of the &#xA;  principal streptococcal pathogens that cause invasive &#xA;  disease in humans — group A Streptococcus (GAS; that &#xA;  is, Streptococcus pyogenes), group B Streptococcus (GBS; &#xA;  that is, Streptococcus agalactiae) and Streptococcus &#xA;  pneumoniae — &lt;em&gt;&lt;strong&gt;in which they have been shown to &#xA;  have key roles in the adhesion and invasion process and &#xA;  in pathogenesis&lt;/strong&gt;&lt;/em&gt;. [emphasis added by me]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-02-15T01:21:31.350" LastActivityDate="2013-02-15T01:21:31.350" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7178" PostTypeId="1" CreationDate="2013-02-12T03:14:38.967" Score="3" ViewCount="332" Body="&lt;p&gt;What's the therapeutic index $\left(\frac{LD_{50}}{ED_{50}}\right)$ of Pethidine (Meperidine in the US) via the intravenous route for humans or whatever species you can find? The therapeutic window $\left(\frac{TD_{50}}{ED_{50}}\right)$ for humans will suffice if accompanied by the therapeutic index for pethidine via IV of another species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pethidine is an opioid painkiller with approximately $\frac{1}{7}-\frac{1}{8}$ the strength of morphine and a definite influence on monoaminergic neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I imagine it'd be in the neighbourhood of 30-100, like most opioids that have been implemented in medicine. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="69" LastEditDate="2013-02-14T16:31:32.643" LastActivityDate="2014-08-12T10:20:33.083" Title="What's the therapeutic index of Pethidine (Meperidine in the US)?" Tags="&lt;pharmacology&gt;&lt;opioid&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="7179" PostTypeId="1" AcceptedAnswerId="7182" CreationDate="2013-02-12T03:59:35.950" Score="1" ViewCount="625" Body="&lt;p&gt;Does the NMDA antagonist, Memantine that's used to prevent excitotoxicity in Alzheimer's disease (AD) and Dementia with Lewy Bodies (DLB) cause brain damage? I know that in rodents NMDA antagonists like ketamine and phencyclidine (PCP) cause a form of brain damage known as Olney's lesions. Despite Olney's lesions never being directly observed in primates like humans, permanent brain damage from chronic ketamine exposure has been observed in adolescent cynomolgus monkeys.&lt;sup&gt;1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Reference List&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Sun, Lin; Qi Li, Qing Li, Yuzhe Zhang, Dexiang Liu, Hong Jiang, Fang Pan, David T. Yew (2012). &quot;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/adb.12004/abstract&quot; rel=&quot;nofollow&quot;&gt;Chronic ketamine exposure induces permanent impairment of brain functions in adolescent cynomolgus monkeys&lt;/a&gt;&quot;. Addiction Biology. doi:&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/adb.12004/abstract&quot; rel=&quot;nofollow&quot;&gt;10.1111/adb.12004&lt;/a&gt;. PMID &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23145560&quot; rel=&quot;nofollow&quot;&gt;23145560&lt;/a&gt;. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-12T05:25:56.453" LastActivityDate="2013-02-12T05:25:56.453" Title="Does the NMDA antagonist, Memantine that's used to prevent Excitotoxicity cause brain damage?" Tags="&lt;pharmacology&gt;&lt;receptor&gt;&lt;hallucinogens&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7180" PostTypeId="5" CreationDate="2013-02-12T04:01:54.607" Score="0" Body="&lt;p&gt;Hallucinogens are compounds that induce hallucinations and often other psychotic phenomena. They include dissociatives (NMDA antagonists and kappa opioid agonists) and psychedelics (like LSD, psilocybin). &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-12T08:50:02.117" LastActivityDate="2013-02-12T08:50:02.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7181" PostTypeId="4" CreationDate="2013-02-12T04:01:54.607" Score="0" Body="Hallucinogens are compounds that induce hallucinations and often other psychotic phenomena. They include dissociatives (NMDA antagonists and kappa opioid agonists) and psychedelics (LSD and psilocybin). " OwnerUserId="1813" LastEditorUserId="4101" LastEditDate="2013-10-14T19:18:58.370" LastActivityDate="2013-10-14T19:18:58.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7182" PostTypeId="2" ParentId="7179" CreationDate="2013-02-12T05:04:19.863" Score="2" Body="&lt;p&gt;Yes, it does cause lesions in rats, although I don't think it's been observed to do so in humans. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See: &lt;a href=&quot;http://www.druglib.com/druginfo/namenda/description_pharmacology/&quot; rel=&quot;nofollow&quot;&gt;http://www.druglib.com/druginfo/namenda/description_pharmacology/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-02-12T05:04:19.863" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="7183" PostTypeId="2" ParentId="6972" CreationDate="2013-02-12T10:50:37.310" Score="1" Body="&lt;p&gt;I think you'll like &lt;a href=&quot;http://www.unc.edu/~dlinz/Papers/The%20effects%20of%20non-medically%20used%20psychoactive%20drugs%20on%20monoamine%20neurotransmission%20in%20rat%20brain.pdf&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;. It's on monoamine release / reuptake inhibition for a host of different psychedelic and empathogenic drugs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This wakefulness inducing effect you describe for LSD is widely reported for all common 5-HT2 mediated psychedelics.&lt;/p&gt;&#xA;" OwnerUserId="3032" LastActivityDate="2013-02-12T10:50:37.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7184" PostTypeId="1" AcceptedAnswerId="7188" CreationDate="2013-02-12T11:29:50.437" Score="6" ViewCount="579" Body="&lt;p&gt;I've read this question:&#xA;&lt;a href=&quot;https://biology.stackexchange.com/questions/5488/what-kind-of-event-would-cause-the-current-mitochondrial-eve-to-be-replaced-by-a&quot;&gt;What kind of event would cause the current Mitochondrial Eve to be replaced by a new one?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And the values in Wikipedia about &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitochondrial_Eve&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mitochondrial Eve&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Y-chromosomal_Adam&quot; rel=&quot;nofollow noreferrer&quot;&gt;Y-chromosomal Adam&lt;/a&gt; and I am not sure I understand the concept behind them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When talking about a maternal unbroken linage and a paternal unbroken linage, is the meaning that Mitochondrial Eve had a linage of only women reaching every person today, and the same with Y-chromosomal Adam and men? So that other humans that lived in their age, didn't have an unbroken line of linage consisting of only same sex descendants?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is the specific &quot;identity&quot; or time period of those persons is known, assuming that researchers didn't check the Mitochondrial DNA or Y-chromosome of every single living human being today, how can they know for sure that there aren't some tribes in the Amazons, which have a direct female linage to Mitochondrial Eve's sister?&lt;/p&gt;&#xA;" OwnerUserId="680" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-02-12T13:37:44.930" Title="What is a Mitochondrial Eve and Y-chromosomal Adam" Tags="&lt;human-genetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7185" PostTypeId="1" CreationDate="2013-02-12T11:55:19.433" Score="3" ViewCount="522" Body="&lt;p&gt;Do new beneficial mutation evolve simultaneously and independently with several individuals of the same specie or only with one specimen who then transfers it to all of the specie?&lt;/p&gt;&#xA;&lt;p&gt;In other words, when we talks about common ancestor we usually mean a specie, so for example, all earth dwelling reptiles, birds and mammals are the descendants of &lt;a href=&quot;http://en.wikipedia.org/wiki/Tiktaalik&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tiktaalik&lt;/a&gt; (to the best of my knowledge), and we know that Tiktaalik was the first (or one of the first) species to come to land, but was there a first individual Tiktaalik who went to the land, like Tim Minchin's &lt;a href=&quot;http://www.youtube.com/watch?v=3bwgp-JaTMA&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tony the fish&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Imagine being the first dude ever to have feet...&lt;/p&gt;&#xA;&lt;p&gt;Imagine you're a fish, and you are swimming in the ocean ... and suddenly out of nowhere Tony just goes &amp;quot;I'm getting out, I'm freezing, I'm just gonna pop out for a bit, maybe lie on my towel, I'll bring you an ice cream&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;-&amp;quot;Don't bother ,Tony, you are a freak! Tony is a freak, let's go, let's ostracize him for being different&amp;quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It seems to me that from the same species of ancestors there are several descending distinct species, so it seems to me that that that there was a species of reptiles that at some point some individual of that group developed Dinosaur features and traits and whose descendants became Dinosaurs and then Birds, and another individual of that specie or a descending specie (not necessarily at the same time) developed mammary glands whose descendants became mammals, and other individuals who didn't mate with those two whose descendants remained reptiles.&lt;/p&gt;&#xA;&lt;p&gt;Was there ever a first dinosaur with feathers who is the father or mother of all birds, or the first fish with lungs, the first monkey with opposable thumbs from whom all apes descend, or the first mammal that decided to go for a swim and all dolphins, whale and seals are his direct descendant of that first swimming mammal?&lt;/p&gt;&#xA;&lt;p&gt;And also for traits that don't lead to speciation, was there a first human who was lactose tolerant, and all the lactose tolerant people on the world are his/her descendants, or the first person with no wisdom teeth, the first person with slanted eyes, and the first person with red/blond hair?&lt;/p&gt;&#xA;&lt;p&gt;*- If there are gross inaccuracies and/or over-simplification in my understanding of the evolutionary process, this is because I'm not a biologist, and I would accept happily any correction.&lt;/p&gt;&#xA;" OwnerUserId="680" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-02-12T15:41:48.203" Title="Is there an &quot;Adam and Eve&quot; for each new trait during (not just human) evolution?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ClosedDate="2013-02-13T00:49:43.763" ContentLicense="CC BY-SA 3.0" />
  <row Id="7186" PostTypeId="1" CreationDate="2013-02-12T12:06:59.630" Score="1" ViewCount="309" Body="&lt;p&gt;Apart from pain when swallowing, there's also a persistent feeling of throat 'burning' in the same area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What causes it and why does it feel that way?&lt;/p&gt;&#xA;" OwnerUserId="3077" LastEditorUserId="3032" LastEditDate="2013-02-12T13:46:47.103" LastActivityDate="2013-02-14T09:22:59.863" Title="Why does throat 'burn' when you've got a common cold?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7187" PostTypeId="2" ParentId="7186" CreationDate="2013-02-12T12:47:29.003" Score="1" Body="&lt;p&gt;If you've been sneezing or coughing a lot it is probably micro abrasions in the throat. I don't recognize any other burning sensation.&lt;/p&gt;&#xA;" OwnerUserId="3032" LastEditorUserId="3032" LastEditDate="2013-02-12T13:10:42.197" LastActivityDate="2013-02-12T13:10:42.197" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7188" PostTypeId="2" ParentId="7184" CreationDate="2013-02-12T13:31:13.113" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;When talking about a maternal unbroken linage and a paternal unbroken linage, is the meaning that Mitochondrial Eve had a linage of only women reaching every person today, and the same with Y-chromosomal Adam and men?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Kind of, yes&lt;/strong&gt;. The concept behind &lt;em&gt;Mitochondrial Eve&lt;/em&gt; and &lt;em&gt;Y-Chromosomal Adam&lt;/em&gt; has to due with cell replication and basic genetics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;Mitochondria&lt;/strong&gt; (&quot;Power Generators&quot; of the cell) are &lt;em&gt;directly&lt;/em&gt; inherited from mother to daughter cell. That is, new cells do not start with 0 and are forced to make them &lt;em&gt;de novo&lt;/em&gt;. Some Mitochondria are replicated before division and some are 'given' to the daughter cell to start with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of the unique way that Mitochondria are inherited, when it comes to creating new humans it means that &lt;em&gt;only&lt;/em&gt; the Mother's Mitochondria are given to any children she gives birth to &lt;em&gt;regardless of the sex of the child&lt;/em&gt;. So I, being male, have my Mother's Mitochondria - which the same as my Grandmother's - and the same as my Great-Grandmother's - etc. etc. etc. until you can trace that line back to &lt;strong&gt;&quot;Mitochondrial Evel&quot;&lt;/strong&gt; whose Mitochondria are the origin for all humans on the planet and are inherited &lt;strong&gt;Maternally&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;em&gt;that&lt;/em&gt; sense it is an unbroken lineage of genetic information as inherited &lt;em&gt;from&lt;/em&gt; mothers, though not exclusive to women.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&quot;Y-Chromosomal Adam&quot;&lt;/strong&gt; is a similar concept - Women do not have a &quot;Y&quot;-Chromosome, so every Y-Chromosome men have today had to originate from somewhere. It's trickier to do than tracing Mitochondrial DNA because while Mitochondria are inherited &lt;em&gt;exclusively&lt;/em&gt; from mother to child, there could have been multiple Fathers to Mitochondrial Eve's children and other similar complications that muck things up.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How is the specific &quot;identity&quot; or time period of those persons is known, assuming that researchers didn't check the Mitochondrial DNA or Y-chromosome of every single living human being today?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For &lt;strong&gt;&quot;Y-Chromosome Adam&quot;&lt;/strong&gt; it's still more or less in the data-gathering phase as far as I was last aware. It's not as concrete as &quot;Mitochondrial Eve&quot;, which has a very solid body of work supporting her.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;identity&quot; is known because the more in common a person's genes have with the genes of another, the more closely they are related. The researchers took &lt;em&gt;a lot&lt;/em&gt; of genes from very divergent populations, and compared them. The researchers were then able to tell which portions were common among all of the Mitochondrial DNA, which had changed the most, and which had changed the least from each other. Using that data, you can construct a rough image of what the originator (or LCA - Last Common Ancestor) had for their own genetic makeup.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can construe a time period because portions of your DNA (either Mitochondrial or Nuclear) acquire/tolerate mutations at an &lt;em&gt;expected rate&lt;/em&gt; - say 1 mutation every 1.5 Million Years. So as long as you have a rough idea of what your LCA's genes looked like (see above), then a modern day sample with 5 mutations is 7.5 M.Y. away from the LCA.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;how can they know for sure that there aren't some tribes in the Amazons, which have a direct female linage to Mitochondrial Eve's sister?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They didn't when they started testing. That's part of the fun of the project.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.nature.com/scitable/content/out-of-africa-versus-the-multiregional-hypothesis-6391&quot; rel=&quot;noreferrer&quot;&gt;&quot;Out of Africa Hypothesis&quot;&lt;/a&gt; rose in prominence partially due to the findings of the research. It basically posits that the ancestors of humans evolved once in Africa, and then spread from Africa to the rest of the world. Because the Mitochondrial Eve research concludes that &quot;Eve&quot; was around before we spread throughout the rest of the world, it implies that every ancestor already had Eve's legacy when they started migrating into Europe, Asia, the Philippines, etc. Thus every human on Earth, no matter where they are today, shares traits with Mitochondrial Eve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the Amazonian tribes, they would have inherited it from their ancestors in North America, which were ancestors of tribes in Asia who crossed an ice bridge into North America, and the tribes in Asia came out of Africa.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2013-02-12T13:37:44.930" LastActivityDate="2013-02-12T13:37:44.930" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7189" PostTypeId="2" ParentId="7185" CreationDate="2013-02-12T15:41:48.203" Score="2" Body="&lt;p&gt;For most traits, there is no clear line where the trait is present or not. Exceptions are traits that occur with a single mutation, like lactose tolerance. So to pick one example, you had a population of fish that had a lung-like organ, and that by genetic drift that organ got more lung-like in a sub-population. So for most traits, you have a combination of mutations that lead to the traits, and these mutations need not occur in a direct line of ancestors. (I.e., a descendant will combine independent mutations from its parents.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there is no &quot;Adam and Eve&quot; in the sense that these are the only ancestors of all living individuals of a species. This would be a terrible genetic bottleneck! See this &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_evolutionary_genetics#Divergence_times_and_ancestral_effective_population_size&quot; rel=&quot;nofollow noreferrer&quot;&gt;illustration&lt;/a&gt;, which comes with the estimate that the population size of the chimp-human ancestor was around 100,000. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qyK58.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You ask for &quot;a first dinosaur with feathers who is the father or mother of all birds&quot;. It's possible that feathers arose multiple times from the same feather-like structures, or only once. But it is clear that this first dinosaur is only one of many dinosaurs that lived at the same time, and who are also ancestors of all birds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further reading: Lactose tolerance evolved several times independently (see &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17159977&quot; rel=&quot;nofollow noreferrer&quot;&gt;Convergent adaptation of human lactase persistence in Africa and Europe.&lt;/a&gt;&quot;). &lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2013-02-12T15:41:48.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7190" PostTypeId="1" AcceptedAnswerId="7192" CreationDate="2013-02-12T16:21:15.783" Score="9" ViewCount="1617" Body="&lt;p&gt;I have to do a task for a university task and I need to understand some things&#xA;before figuring out how to do it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The task is the following:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Find matches of known proteins (DNA-PolyI,II,III) to the specific E.Coli DNA, sequence.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I downloaded in &lt;a href=&quot;http://en.wikipedia.org/wiki/FASTA_format&quot; rel=&quot;nofollow&quot;&gt;FASTA&lt;/a&gt; format the protein sequence of &lt;s&gt;DNA-Poly3&lt;/s&gt; DNA-Poly1 of E.coli (strain K-12) and the entire DNA sequence&#xA;of the E.Coli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've studied a bit on-line and using the &lt;a href=&quot;http://bioruby.org/&quot; rel=&quot;nofollow&quot;&gt;BioRuby&lt;/a&gt; gem and the Ruby programming language I wrote a program that translates DNA to protein sequence.&#xA;Then I tried to match the known DNA-Poly3 sequence but it did not match. After searching a bit on-line again, I learned about &lt;a href=&quot;http://en.wikipedia.org/wiki/Open_reading_frame&quot; rel=&quot;nofollow&quot;&gt;ORF&lt;/a&gt; and&#xA;and the 6 possible reading ways of each frame. The longer, in terms of codons, ORF conformation is chosen but there's no way of telling for sure that the protein was made using&#xA;this frame.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then I've read about TATA boxes, but I can't use those since they can be found only in Eukaryotic and Archaea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how should I proceed in order to solve this problem: How can I &lt;em&gt;prove&lt;/em&gt; that the DNA-Poly3 gets produced by a specific area (gene) in the DNA sequence?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your time,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ps. Insights and hints are very much welcomed as this is just the tip of the iceberg for me and I'm very willing to study bioinformatics :-)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;: This is an update for info requested in relevant answer&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The files I have used are the following:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;➜  Bioinfo  ruby dogma.rb &#xA;----------------&#xA;DNA Length: 4639675&#xA;gi|48994873|gb|U00096.2| Escherichia coli str. K-12 substr. MG1655, complete genome&#xA;----------------&#xA;DNA Poly-1 sample: 928&#xA;gi|16131704|ref|NP_418300.1| fused DNA polymerase I 5'-&amp;gt;3' polymerase/3'-&amp;gt;5' exonuclease/5'-&amp;gt;3' exonuclease [Escherichia coli str. K-12 substr. MG1655]&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;You can download them here: &lt;a href=&quot;https://dl.dropbox.com/u/1184138/bio/e-coli-K12.fasta&quot; rel=&quot;nofollow&quot;&gt;E.Coli DNA&lt;/a&gt; and &lt;a href=&quot;https://dl.dropbox.com/u/1184138/bio/dna-polyI.e-coli.fasta&quot; rel=&quot;nofollow&quot;&gt;E.Coli DNA-Poly1&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;NOTE&lt;/strong&gt;: My sample protein is &lt;strong&gt;DNA Polymerase I&lt;/strong&gt; (and not 3). &lt;/p&gt;&#xA;" OwnerUserId="1856" LastEditorUserId="1856" LastEditDate="2013-02-13T10:11:03.370" LastActivityDate="2018-03-14T09:19:39.320" Title="Finding proteins in DNA sequence" Tags="&lt;dna-sequencing&gt;" AnswerCount="3" CommentCount="10" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7191" PostTypeId="1" AcceptedAnswerId="7195" CreationDate="2013-02-12T18:24:43.807" Score="4" ViewCount="626" Body="&lt;p&gt;Suppose a female &lt;em&gt;Anopheles&lt;/em&gt; infected with &lt;em&gt;Plasmodium&lt;/em&gt; bites someone and transmits Plasmodium to their body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can that person's immune system be strong enough that it can kill the &lt;em&gt;Plasmodium&lt;/em&gt; before it starts entering into red blood cells to rupture them?&lt;/p&gt;&#xA;" OwnerUserId="3055" LastEditorUserId="948" LastEditDate="2013-02-12T19:48:08.027" LastActivityDate="2013-02-13T02:01:56.713" Title="Can the immune system stop plasmodium from being active?" Tags="&lt;immunology&gt;&lt;malaria&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7192" PostTypeId="2" ParentId="7190" CreationDate="2013-02-12T18:36:27.620" Score="13" Body="&lt;p&gt;&lt;strong&gt;IMPORTANT EDIT :&lt;/strong&gt; In your particular case, if you are working with bacterial genes, splicing is not an issue since bacteria do not have introns. I am leaving the information here since it may be useful to someone else. However, I recommend you focus on the UTRs since they are probably what is causing you problems. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;There are three things that could be causing you problems. I will briefly touch on each one. I will talk about &lt;em&gt;all&lt;/em&gt; genes, bear in mind that bacteria have no introns so any discussion of splicing and/or introns and exons is not directly relevant to your problem.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;1. UTRs&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Untranslated_region&quot; rel=&quot;nofollow noreferrer&quot;&gt;Untranslated Regions (UTRs)&lt;/a&gt; are sequences at the beginning and end of a gene that are not translated into protein. UTRs are regions that are part of the original genomic sequence, they are also part of the mature mRNA (indeed, UTRs are sometimes modified by splicing events, they are exons not introns) &lt;em&gt;but&lt;/em&gt; they do not get translated into protein. To illustrate, have a look at this simplified representation of an mRNA molecule:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MtXrs.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Only the green exons will make it into the final protein. Introns are spliced out and UTRs are not translated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, if you translate the entire gene, you will not get the correct protein.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;2. Reading frames&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Genes are read in words of three letters (the codons). The sequence ATGTGTACCTGA has six possible reading frames (three on each strand) which can be read and translated as follows:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;5'3' Frame 1&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;    ATG TGT ACC TGA&#xA;     M   C   T  Stop&#xA;&lt;/code&gt;&lt;/pre&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;5'3' Frame 2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;    a TGT GTA CCT ga&#xA;       C   V   P    &#xA;&lt;/code&gt;&lt;/pre&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;5'3' Frame 3&lt;/strong&gt;    &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;    at GTG TAC CTG a&#xA;        V   Y   L    &#xA;&lt;/code&gt;&lt;/pre&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;3'5' Frame 1&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;TCA GGT ACA CAT&#xA; S   G   T   H  &#xA;&lt;/code&gt;&lt;/pre&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;3'5' Frame 2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;t CAG GTA CAC at&#xA;   Q   V   H    &#xA;&lt;/code&gt;&lt;/pre&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;3'5' Frame 3&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;tc AGG TAC ACA t&#xA;    R   Y   T    &#xA;&lt;/code&gt;&lt;/pre&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;DNA is double stranded. The sequence of one strand is complementary to that of the other, therefore if you have one strand you can infer the sequence of its complementary one. Genes can be found on either strand, the two are equivalent biologically. However, sequencing projects &lt;em&gt;choose&lt;/em&gt; one of the two strands (randomly) and call it the plus (+) strand and then save all sequences with respect to that strand. This means that sometimes the genomic sequence that you download from a database might be the complement of the actual sequence you are looking for. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;3. Names&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I once heard someone say in a conference that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Biologists would rather share a toothbrush than a gene name. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;While that might be a little exaggerated, naming conventions vary between research communities and species and databases. So, are you &lt;em&gt;sure&lt;/em&gt; that you have downloaded the correct gene? Where did you get it from? How did you identify it? Does the sequence also contain up/downstream regulatory regions, promoters, enhancers and the like? If you post the exact sequence you are attempting to use I can give you more specific help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, the first 20 hits when &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/?term=%28DNA%20Polymerase%203%29%20AND%20%22Escherichia%20coli%22%5Bporgn:__txid562%5D&quot; rel=&quot;nofollow noreferrer&quot;&gt;searching for the &lt;em&gt;E. coli&lt;/em&gt; &lt;code&gt;DNA Polymerase 3&lt;/code&gt; in ncbi's nucleotide database&lt;/a&gt;, are whole genome shotgun sequences. These do &lt;em&gt;not&lt;/em&gt; correspond to the gene sequence you are looking for. They are huge pieces of the genome (or even the entire genome) that will contain your gene and many others. Look at the Tools section below for suggestions on extracting your gene from the whole genome. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;4. Splicing (irrelevant to bacteria)&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Another possible problem is &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_splicing&quot; rel=&quot;nofollow noreferrer&quot;&gt;splicing&lt;/a&gt;. Lets start with the basics, the process of producing a eukaryotic (bacteria have no introns) protein from a genomic sequence is summarized in the image below (modified slightly from &lt;a href=&quot;http://err.bio.nyu.edu/courses/index.php/Griffin&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MZRny.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Transcription begins at the transcription start site (TSS) but not all the transcribed sequence is translated into protein. First, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Intron&quot; rel=&quot;nofollow noreferrer&quot;&gt;introns&lt;/a&gt; are spliced out of the mRNA to produce the &lt;em&gt;mature&lt;/em&gt; mRNA (other things like capping and poly-A addition also occur but are not relevant here). So,the mature mRNA contains the &lt;a href=&quot;http://en.wikipedia.org/wiki/Exon&quot; rel=&quot;nofollow noreferrer&quot;&gt;exons&lt;/a&gt; of the coding gene. This means that a linear translation of the gene's sequence will not correspond to the protein produced. You will need to take splicing into account. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, bear in mind that splicing will change the &lt;a href=&quot;http://en.wikipedia.org/wiki/Reading_frame&quot; rel=&quot;nofollow noreferrer&quot;&gt;reading frame&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, if the sequence &lt;code&gt;ATGT&lt;/code&gt; were spliced at, for example, &lt;code&gt;AT/gt&lt;/code&gt; (most splice events cut/join at GT/AG sites) and joined with the sequence &lt;code&gt;agATTATT&lt;/code&gt;, the resulting (spliced) sequence would be (the splicing process will remove the &lt;code&gt;gt&lt;/code&gt; from the first sequence and the &lt;code&gt;ag&lt;/code&gt; from the second):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ATATTATT&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;As you can see, the reading frame has now changed. Where before, in the first reading frame, we had the codon &lt;code&gt;ATG&lt;/code&gt;, the canonical translation initiation codon, we now have &lt;code&gt;ATA&lt;/code&gt; which codes for isoleucine (I). I hope that is clear,  the main point is that splicing can change the reading frame.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;5. Tools&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;OK, that was the background. Now, what you will need to do is use existing programs that model splice sites and can correctly align a protein sequence to genomic DNA. My personal favorites are &lt;a href=&quot;http://www.animalgenome.org/bioinfo/resources/manuals/exonerate/&quot; rel=&quot;nofollow noreferrer&quot;&gt;exonerate&lt;/a&gt; and &lt;a href=&quot;https://www.ebi.ac.uk/Tools/psa/genewise/&quot; rel=&quot;nofollow noreferrer&quot;&gt;genewise&lt;/a&gt;. On a Debian-based Linux distribution, you can install them with this command:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;sudo apt-get install exonerate wise&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Then, to align the protein to its gene do:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;exonerate -m protein2genome -n 1 prot.fa dna.fa &amp;gt; out.txt &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;or&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;genewise -pep -pretty -gff -cdna prot.fa dna.fa &amp;gt; out.txt &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;In my experience exonerate is (much) faster but genewise is a little more accurate. I usually use exonerate if I am dealing with a whole genome and genewise if I only have a few kilobases of sequence. Both are very good and both will be able to align a protein to its genome of origin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will not explain all these options because that is beyond the scope of this site. Have a look at their documentation (which is quite good and clear) and if you still have problems, you could ask a question on our sister site, &lt;a href=&quot;http://bioinformatics.stackexchange.com/&quot;&gt;Bioinformatics Stackexchange&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, you could link your web application to the &lt;a href=&quot;http://genome.ucsc.edu/cgi-bin/hgBlat&quot; rel=&quot;nofollow noreferrer&quot;&gt;ucsc genome browser&lt;/a&gt; BLAT service. Click &lt;a href=&quot;http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr17:7388084-7417493&amp;amp;db=hg19&amp;amp;ss=../trash/hgSs/hgSs_genome_56dd_a89560.pslx%20../trash/hgSs/hgSs_genome_56dd_a89560.fa&amp;amp;hgsid=325698025&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; to see the results when aligning the human &#xA;&lt;a href=&quot;http://www.uniprot.org/uniprot/P24928&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA-directed RNA polymerase II subunit RPB1 protein&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2018-03-14T09:19:39.320" LastActivityDate="2018-03-14T09:19:39.320" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="7193" PostTypeId="1" CreationDate="2013-02-12T22:30:07.933" Score="3" ViewCount="484" Body="&lt;p&gt;My experiment involves pulling down cells on to a filter plate for a variety of assays. However, I want to ensure that my cells are alive so I am trying to resuspend them so that I can do an accurate cell count. However, I am unable to close off the mass-balance which suggests that the cells are either getting through the membrane or getting stuck.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any suggestions on the appropriate way to fully resuspend cells? I'm currently using a P200 to mix the solution.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2013-02-12T22:30:07.933" Title="Resuspending Cells from a filter plate" Tags="&lt;cell-culture&gt;&lt;lab-techniques&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7194" PostTypeId="2" ParentId="2250" CreationDate="2013-02-13T00:01:01.080" Score="84" Body="&lt;p&gt;I'm extremely skeptical of @leonardo's answer.  I suspect that what would happen if you drank only distilled water is nothing perceptible.  The only place where concentrations of distilled water would ever be high enough to conceivably matter is in the tissues of the mouth and throat, and even there, the effect would be temporary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Compare drinking 8 glasses of either distilled or tap water every day.  &lt;a href=&quot;http://www.mgwater.com/mgrank.shtml&quot;&gt;With tap water&lt;/a&gt;, you're looking at less than 200 ppm of Mg, Na, K, and Ca combined.  That's less than 400mg of total mineral content per day.  Given that the combined RDA of all of those minerals is on the order of &lt;a href=&quot;http://www.iom.edu/Activities/Nutrition/SummaryDRIs/~/media/Files/Activity%20Files/Nutrition/DRIs/5_Summary%20Table%20Tables%201-4.pdf&quot;&gt;7g for an adult male&lt;/a&gt;, this is not &lt;em&gt;nothing&lt;/em&gt;, but it's certainly small.  Your dietary intake of these minerals probably varies by more than this daily, and your intestines, kidneys, sweat glands and mineral storage organs (like your bones and muscles) are constantly maintaining the mineral blood levels within a &lt;em&gt;very&lt;/em&gt; narrow range, despite handling a throughput of several pounds of water and food daily.  They might have to work slightly harder to manage this range if you drank nothing but distilled water, but in a healthy adult, normal intakes already vary by more than this amount without major problems.  For example, the average American &lt;a href=&quot;http://www.cdc.gov/features/dssodium/&quot;&gt;consumes more than 3.4 grams of sodium daily&lt;/a&gt;, while a &lt;a href=&quot;http://www.ucsfhealth.org/education/guidelines_for_a_low_sodium_diet/index.html&quot;&gt;low-sodium diet is on the order of 2g&lt;/a&gt;.  Low-sodium diets have been widely studied in the medical literature, and are considered safe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for pH, the lowered pH is caused by increased carbon-dioxide absorption to form carbonic acid.  Just as carbon dioxide is more soluble in distilled water, it is less soluble in stomach acid, and may be burped out.  Would you die of acidosis from drinking seltzer water all the time?  If that were the case, I'm sure there would be big health warnings about drinking soda, &lt;a href=&quot;http://www.popsci.com/scitech/article/2008-07/will-drinking-carbonated-beverages-weaken-my-bones&quot;&gt;while it seems relatively benign&lt;/a&gt;. Furthermore, your body produces and excretes (through the lungs) &lt;a href=&quot;http://en.wikipedia.org/wiki/Carbon_dioxide#Human_physiology&quot;&gt;around 1kg of CO2 daily&lt;/a&gt;, dwarfing any extra CO2 you might get by drinking distilled water.  If the small amounts of CO2 found in distilled water were dangerous, jogging would be invariably fatal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you were to drink nothing but distilled water, and eat no food, you probably would die of hyponatremia within a few weeks.  But you would also die of hyponatremia if you were to drink nothing but tap water, though perhaps slightly more slowly.&lt;/p&gt;&#xA;" OwnerUserId="1597" LastEditorUserId="1597" LastEditDate="2013-02-19T19:49:20.193" LastActivityDate="2013-02-19T19:49:20.193" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7195" PostTypeId="2" ParentId="7191" CreationDate="2013-02-13T02:01:56.713" Score="2" Body="&lt;p&gt;The experience of a former adviser of mine was that some people who are not taking anti-malarial medication can still resist infection with &lt;a href=&quot;http://en.wikipedia.org/wiki/Plasmodium_falciparum&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Plasmodium falciparum&lt;/em&gt;&lt;/a&gt;, one of the parasites responsible for &lt;a href=&quot;http://en.wikipedia.org/wiki/Malaria&quot; rel=&quot;nofollow noreferrer&quot;&gt;malaria&lt;/a&gt;. The parasite's life cycle includes stages inside the &lt;a href=&quot;http://en.wikipedia.org/wiki/Anopheles&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Anopheles sp.&lt;/em&gt;&lt;/a&gt; mosquito, and they are transmitted to human host via the female mosquito's saliva when she bites to have a blood meal:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PBQpK.jpg&quot; alt=&quot;Plasmodium life cycle&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(from &lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Plasmodium_lifecycle_PHIL_3405_lores.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikimedia&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is currently a great deal of research going on to understand the &lt;a href=&quot;http://en.wikipedia.org/wiki/Plasmodium_falciparum_biology&quot; rel=&quot;nofollow noreferrer&quot;&gt;biology&lt;/a&gt; of the parasite and how it typically evades the immune system so well. Proteins expressed by the parasite can undergo antigenic variation, meaning that different forms are expressed at different stages of the life cycle, and just as the immune system may be forming a response to one version, it is down-regulated and another takes its place. This is one reason why making a vaccine has proved to be so difficult, as unlike the influenza virus, for example, a single strain of &lt;em&gt;Plasmodium&lt;/em&gt; can alter its immunogenic appearance and escape &lt;a href=&quot;http://en.wikipedia.org/wiki/Adaptive_immune_response&quot; rel=&quot;nofollow noreferrer&quot;&gt;antigen-specific immune responses&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While malaria is responsible for a high degree of morbidity - sickness - it is not necessarily fatal except in some cases, frequently when the victims are young, already ill, or are otherwise immune-compromised, or when the infection moves to the central nervous system and the brain. I can't speak from personal experience (fortunately!), but I have been told by numerous friends that malaria is something you want to avoid at all costs. The sickness can last for weeks in some cases, and apparently is quite debilitating at its worst. Brain fever can be deadly, and in many third-world countries and among the poor the lack of good medical care can lead to complications. There is the additional factor that the family has to care for the sick, and if the ill person is a wage-earner that can mean the difference between food on the table and going hungry. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, your friends are not going to die (probably) if they don't take their tablets, but there is no reason &lt;strong&gt;not&lt;/strong&gt; to take them unless you have strong side-effects, and in that case the doctor may be able to find you another one. Other common-sense measures include always sleeping with a bed net, putting screens in windows, covering exposed skin during active mosquito hours, wearing repellant if available, and eliminating places where standing water can collect, stagnate, and provide a breeding area for mosquitoes.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-02-13T02:01:56.713" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7197" PostTypeId="2" ParentId="7190" CreationDate="2013-02-13T18:20:56.307" Score="5" Body="&lt;p&gt;For what its worth - I have replicated what you are trying to do using a Python script. This is not elegant, but I just wanted to check for you that it is possible, and that there really is a match.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;pseudocode is&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;take the genome sequence&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;make a reverse complement sequence&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;for each of the two DNA sequences, for each of three reading frames:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;translate the DNA into a single string of amino acids with &quot;*&quot; at stop codons&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;split the string at &quot;*&quot; characters, call these words&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;find the first Met residue in each word, the string from that Met to the end of the word is an ORF&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;if the ORF is &gt;99 (arbitrary cut off) put it in a big list of ORFs&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;now have a list of all ORFs in all 6 reading frames&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;search this list for a match to the polI sequence (I actually just looked for the first line in the fasta sequence).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The hit is identical to the entire polI sequence in a CLUSTAL alignment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that this algorithm does not detect any ORFs that cross the breakpoint in the linear sequence representing the circular genome of &lt;em&gt;E coli&lt;/em&gt;. Also assumes all initiator codons are ATG/Met but I seem to recall some &lt;em&gt;E.coli&lt;/em&gt; initiation codons are GTG/Val&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-02-13T18:59:14.557" LastActivityDate="2013-02-13T18:59:14.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7199" PostTypeId="1" AcceptedAnswerId="7239" CreationDate="2013-02-13T21:53:16.343" Score="6" ViewCount="457" Body="&lt;p&gt;I've just read an article &lt;a href=&quot;http://www.nature.com/ncb/journal/v15/n2/full/ncb2647.html&quot; rel=&quot;nofollow&quot;&gt;Rab10 GTPase regulates ER dynamics and morphology&lt;/a&gt; - Nature Cell Biology 15, 169–178 (2013) doi:&lt;a href=&quot;http://dx.doi.org/10.1038/ncb2647&quot; rel=&quot;nofollow&quot;&gt;10.1038/ncb2647&lt;/a&gt;. In this paper, to identify Rab proteins in ER, first they isolated ER vesicles. Then washed them to remove cytosolic proteins. After washing, these vesicles were solubilized by detergent. Then, it was loaded on to a GTP-agarose column (to bind GTP binding proteins to the column). In the last step GTP binding proteins were eluted with GTP and analysed by SDS-PAGE. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a control (before loading on to the column) they used GTP gamma S, because it prevents GTP-binding proteins from binding onto the column.&#xA;When I looked at their figure; on the control lane, there are lots of bands! So I'm confused :(If it prevents GTP-binding proteins from binding onto the column, after eluting from GTP agarose column why there are bands? And what can these bands be?)&lt;/p&gt;&#xA;" OwnerUserId="3082" LastEditorUserId="948" LastEditDate="2013-02-16T22:52:31.087" LastActivityDate="2013-02-17T17:48:10.327" Title="Does GTP-γS (GTP gamma S) bind all GTP-binding proteins?" Tags="&lt;cell-biology&gt;&lt;gel-electrophoresis&gt;&lt;eukaryotic-cells&gt;&lt;protein-binding&gt;&lt;sds-page&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7200" PostTypeId="1" CreationDate="2013-02-14T05:25:21.080" Score="1" ViewCount="104" Body="&lt;p&gt;Can I give a person an allergic reaction at a very specific spot in a tissue?&#xA;And if so, how accurate can i get? &lt;/p&gt;&#xA;" OwnerUserId="3085" LastEditorUserId="948" LastEditDate="2013-02-14T13:37:53.230" LastActivityDate="2013-02-14T13:37:53.230" Title="Is it possible to give a person an allergic reaction in a very specific place?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7201" PostTypeId="2" ParentId="7186" CreationDate="2013-02-14T09:22:59.863" Score="-1" Body="&lt;p&gt;I guess it is because the throat is sore, thus probably inflammated. Inflammations are hot. Though, I am not a doctor.&lt;/p&gt;&#xA;" OwnerUserId="3087" LastActivityDate="2013-02-14T09:22:59.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7202" PostTypeId="2" ParentId="7200" CreationDate="2013-02-14T10:05:24.297" Score="3" Body="&lt;p&gt;Depends on the kind of allergic reactions you want to create. If your target tissue is skin &lt;a href=&quot;http://en.wikipedia.org/wiki/Epithelium&quot; rel=&quot;nofollow&quot;&gt;epithelium&lt;/a&gt; sure you can.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's actually the way the &lt;a href=&quot;http://en.wikipedia.org/wiki/Skin_allergy_test&quot; rel=&quot;nofollow&quot;&gt;skin allergy test&lt;/a&gt; is all about: The physician tries a wide variety - &lt;em&gt;last time I did it were 28 well known kinds&lt;/em&gt; - of substances in liquid form (drops). If an allergic reaction is caused, the physician takes note. Even very small quantities can cause allergic reactions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These tests are usually made in a secured environment (physician's office, hospital, etc) at a very low level which most of the times, if result is positive will cause just an irritation. The level of irritation will be self-explanatory, so even a non trained patient can understand what is going on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not sure if &lt;em&gt;that&lt;/em&gt; what you were asking though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Best Regards,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;pa&lt;/p&gt;&#xA;" OwnerUserId="1856" LastActivityDate="2013-02-14T10:05:24.297" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7203" PostTypeId="2" ParentId="5646" CreationDate="2013-02-14T18:09:02.097" Score="3" Body="&lt;p&gt;There have been experiments with &lt;a href=&quot;http://www.nature.com/nmeth/journal/v8/n1/abs/nmeth0111-7b.html&quot; rel=&quot;nofollow&quot;&gt;Live-cell dSTORM with SNAP-tag fusion proteins&lt;/a&gt; in Markus Sauer's lab in Würzburg. If you are using the physiology definition of in-vivo, I'm pretty sure some of my co-workers have measured on live organisms. However, this is work in progress and not fully published; if you are interested, you should ask Markus Sauer directly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can use the dSTORM-like techniques (STORM, dSTORM, GSDIM, RPM, etc.) in live cells because the chemical environment in the cell is favourable and the redox system of the cell works for you. The key problem is to get the fluorophores into the cell, but SNAP-tags can help you to do it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As one of the co-authors, I can tell you that live cell was some pain, but considerably less than getting 3D localization microscopy to work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PALM is a different story because you generally have longer acquisition times. STED is difficult: If the cell wasn't dead before, the STED beam will ensure it is, either through the intensity or by unbalancing the chemical environment sufficiently. You might have your image before the cell dies, or maybe not.&lt;/p&gt;&#xA;" OwnerUserId="3088" LastActivityDate="2013-02-14T18:09:02.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7204" PostTypeId="2" ParentId="3704" CreationDate="2013-02-14T18:58:46.407" Score="8" Body="&lt;p&gt;OK, so we know a couple of things about life in the universe. Note, however, that this is not really an answer and is also not very biological in nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, we don't know how life began on the Earth. However, do know that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The probability of life evolving on a planet in the universe is &lt;strong&gt;non-zero&lt;/strong&gt; (since we exist) and, &lt;/li&gt;&#xA;&lt;li&gt;So far, we have &lt;strong&gt;not&lt;/strong&gt; found evidence for life elsewhere in the universe.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So this leaves us with two main possibilities:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Life is rare in the universe.&lt;/li&gt;&#xA;&lt;li&gt;Life is common in the universe but for some reason we do not detect it.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This latter possibility is basically a restatement of the &lt;em&gt;Fermi Paradox&lt;/em&gt; which says &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The universe is very big and there should be lots of alien life out&#xA;  there. Where is everybody?&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the case that life is common, we can speculate extensively on why we have not detected  it so far. For example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;We haven't been looking &lt;em&gt;long&lt;/em&gt; enough (SETI has been running for only a few decades)&lt;/li&gt;&#xA;&lt;li&gt;We haven't been looking &lt;em&gt;hard&lt;/em&gt; enough (the budget of SETI etc. is not large)&lt;/li&gt;&#xA;&lt;li&gt;We haven't been looking in the &lt;em&gt;right way&lt;/em&gt;. We are currently looking mainly in the radio regime, maybe aliens broadcast in &lt;em&gt;X&lt;/em&gt; (where &lt;em&gt;X&lt;/em&gt; is part of the E/M spectrum or something else entirely, e.g. gravity waves, tachyons)&lt;/li&gt;&#xA;&lt;li&gt;Life is common, but intelligent life is rare (this would be my guess) &lt;/li&gt;&#xA;&lt;li&gt;Life is common and intelligent, and doesn't want to answer (why? ask a xenopsychologist)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;OK, so these are just some examples of &quot;solutions&quot; to the Fermi Paradox. There are many more which are much more exotic. My personal favourite of these is that we live in a simulated universe and the coders have not included additional alien life in the simulation. It would explain some strange &quot;coincidences&quot; about fundamental physical constants, but what simulation, no matter how good, would ever come up with cauliflower cheese for example?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, until we actually detect life on another planet we will still be in the dark. The next generation of telescopes will be able to do this for nearby exoplanets if life is present on them and has affected the biosphere in a detectable way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Edit - You mention &quot;frequency models&quot;, but all we can currently say is that the probability of life on other planets is not zero - due to our existence - as I mentioned at the start&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some references:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://arxiv.org/abs/1111.6131&quot; rel=&quot;nofollow&quot;&gt;A joint analysis of the Drake equation and the Fermi paradox, 2012, arXiv, Prantzos, N.&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://arxiv.org/abs/1111.6131&quot; rel=&quot;nofollow&quot;&gt;The Fermi Paradox, Self-Replicating Probes, and the Interstellar Transportation Bandwidth, 2011, arXiv, Wiley, K.B.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://adsabs.harvard.edu/abs/1980Icar...41..193W&quot; rel=&quot;nofollow&quot;&gt;Interstellar colonization - A new parameter for the Drake equation, 1980, Icarus, vol. 41, 193, Walters, C., Hoover, R. A., Kotra, R. K.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="81" LastEditorUserId="231" LastEditDate="2015-02-13T20:39:07.973" LastActivityDate="2015-02-13T20:39:07.973" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7205" PostTypeId="1" CreationDate="2013-02-14T19:27:51.640" Score="5" ViewCount="1072" Body="&lt;p&gt;I am working with lungs from mice, and I want to do a western blot analysis to my samples.&#xA;I am having trouble with this because my images turn out very &quot;messy&quot;, with a high background.&#xA;Perhaps I should filter my samples following their homogenization? &#xA;Has anyone had this problem and knows how to avoid it? &#xA;What is the best method to homogenize the samples?&lt;/p&gt;&#xA;" OwnerUserId="3026" LastEditorUserId="6" LastEditDate="2013-02-15T08:18:19.223" LastActivityDate="2013-02-15T08:18:19.223" Title="How to do western analysis to lung tissue?" Tags="&lt;gel-electrophoresis&gt;&lt;western-blot&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7206" PostTypeId="1" CreationDate="2013-02-14T19:34:01.803" Score="5" ViewCount="5539" Body="&lt;p&gt;Our body does not produce two polyunsaturated fatty acids (PUFA): linoleic acid and alfa-linolenic acid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking reasons for it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Saturated fatty acids have more energy than unsaturated.&#xA;Saturated fatty acids do not need NADPH and some many other enzymes as unsaturated in beta oxidation.&#xA;This means that less storage places in the body needed to have energy in the form of saturated fatty acids such as for muscles and heart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are four main reasons why our body does not use PUFAs as the primary source of the energy but saturated:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;PUFAs lower metabolism and interfere with thyroid function&lt;/li&gt;&#xA;&lt;li&gt;PUFAs spontaneously oxidize, speed up the process of glycation, since too much glucose&lt;/li&gt;&#xA;&lt;li&gt;PUFAs decrease mitochondrial respiration - more oxygen and CO2, less lactate&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;where one reason is missing.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One complication of PUFA is&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;PUFAs promote diabetes, cancer, inflammation and biological stress&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which cannot be thought as a reason why our body does not use PUFAs as the primary source of the energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are positive sides of the PUFAs when they are used in other way.&#xA;- PUFAs replace trans fats and saturated fats in certain types of foods.&#xA;- PUFAs can help your body to eliminate high cholesterol levels&#xA;- PUFAs decrease the risk of heart disease&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also some types of essential fats that your body cannot produce on its own - omega-6 and omega-3 fatty acids.&#xA;PUFAs are used to create these.&#xA;You can get PUFAs from vegetable oil, fish and nuts for instance.&#xA;Balanced diet is essential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Normal lipid metabolism depends directly on food lipids.&#xA;Both the essential fatty acids and right amounts of PUFAs can be obtained from food.&#xA;Body converts the essential fatty acids to long PUFAs, which serve as the precursors of prostaglandins and leucotrienes for instance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are so many reasons why our body does not produce polyunsaturated fatty acids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why our body does not produce polyunsaturated fatty acids?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-08-03T08:35:47.080" LastActivityDate="2019-11-11T19:00:50.097" Title="Why our body does not produce polyunsaturated fatty acids?" Tags="&lt;metabolism&gt;&lt;fatty-acid-synthase&gt;&lt;lipids&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7207" PostTypeId="1" AcceptedAnswerId="7225" CreationDate="2013-02-14T22:01:03.460" Score="1" ViewCount="451" Body="&lt;p&gt;I have been looking at this antibiotic called doxycycline which is used mainly as an antibiotic. It has however some interesting anti-inflammatory properties. Does anyone know where these anti-inflammatory properties come from, chemically?&lt;/p&gt;&#xA;" OwnerUserId="3089" LastEditorUserId="69" LastEditDate="2013-02-15T00:01:58.700" LastActivityDate="2013-02-16T09:37:57.070" Title="Where are doxycycline's anti-inflammatory properties derived from?" Tags="&lt;pharmacology&gt;&lt;antibiotics&gt;&lt;organic-chemistry&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7208" PostTypeId="1" CreationDate="2013-02-14T23:19:54.533" Score="8" ViewCount="659" Body="&lt;p&gt;There are so many techniques/methodologies in the life sciences that we can use to interrogate interesting questions. The thing is, most of us are completely unaware of the &lt;em&gt;available&lt;/em&gt; methods we can employ. Rather, we go with the techniques we are familiar with or that are popular in our subdomains at the time. But that's pretty limiting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I'm wondering... we have databases for everything else... is there one for life sciences techniques/methods? Something like this could be immensely helpful in experimental planning. In particular, I think a comprehensive database would help scientists break outside of their spheres of familiarity and to employ less known (but potentially illuminating) methods to their questions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know there are journals that publish protocols and methods, but they are fragmented and don't encompass everything. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does what I'm looking for exist? If not, how might one go about creating such a tool? &lt;/p&gt;&#xA;" OwnerUserId="1909" LastActivityDate="2017-05-24T01:45:25.357" Title="Is there a comprehensive life science techniques/methods database?" Tags="&lt;lab-techniques&gt;&lt;experimental-design&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7209" PostTypeId="1" AcceptedAnswerId="7291" CreationDate="2013-02-15T00:04:08.727" Score="6" ViewCount="1237" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Topoisomerase II poisons represent some of the most important and&#xA;  widely prescribed anticancer drugs currently in clinical use. These&#xA;  drugs encompass a diverse group of natural and synthetic compounds&#xA;  that are commonly used to treat a variety of human malignancies. At&#xA;  the present time, six topoisomerase II-targeted anticancer agents are&#xA;  approved for use in the United States, and additional drugs are&#xA;  prescribed elsewhere in the world. These agents all act as traditional&#xA;  topoisomerase II poisons and function primarily by inhibiting&#xA;  enzyme-mediated DNA ligation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Briefly describe what TopoII does and how it works. Explain what &quot;inhibiting enzyme-mediated DNA ligation&quot; means.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My thoughts for the first question are Type II topoisomerases cut both strands of the DNA helix simultaneously in order to manage DNA tangles and &#xA;supercoils. They use the hydrolysis of ATP. It changes the linking number of circular DNA by ±2. After the ends are &#xA;cut, the ends of the DNA are separated and a second DNA duplex is passed through the break. The cut DNA is re-&#xA;ligated. This  allows the enzyme to increase or decrease the linking number of a DNA loop by 2 units.  It also &#xA;promotes chromosome disentanglement. Inhibiting enzyme-mediated DNA ligation means that it prevents the enzymes are not allowed to ligate. This is &#xA;prevented by not allowing the formation of a phosphodiester bond.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cancer cells grow much more rapidly than most cells in the body. What would be the consequence of &quot;inhibiting enzyme-mediated DNA ligation&quot; and why might this be particularly deleterious in cancer cells?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am really unsure on this one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have looked at the Wikipedia answers to this question and they are wrong. &lt;/p&gt;&#xA;" OwnerUserId="3090" LastEditorUserId="806" LastEditDate="2013-02-21T02:11:41.973" LastActivityDate="2013-02-21T02:36:21.610" Title="How does Topoisomerase II inhibition affect cancer cells?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;homework&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7210" PostTypeId="2" ParentId="7205" CreationDate="2013-02-15T02:24:25.830" Score="4" Body="&lt;p&gt;Doing westerns with primary tissue can be tough, especially because of the presence (sometimes at high levels) of extracellular matrix (ECM). This material can be quite resistant to homogenization and some lysis buffers. One method I have found to work is to snap-freeze the tissue in liquid nitrogen (not on dry ice or at -80&amp;deg;C) directly after removal from the animal, or after any sub-dissection you may wish to do. Then, when you are ready to prepare your sample, grind it thoroughly with a mortar and pestle in LN&lt;sub&gt;2&lt;/sub&gt;, collect the dust and add a good lysis buffer like &lt;a href=&quot;http://en.wikipedia.org/wiki/Radioimmunoprecipitation_assay_buffer&quot; rel=&quot;nofollow&quot;&gt;RIPA&lt;/a&gt; at 2-3X concentration, along with protease and phosphatase inhibitors, also at 2-3X. Then, instead of simply homogenizing, use a probe-tip sonicator (not a water bath one) and sonicate the lysate on ice with 8-10 pulses of perhaps 3-5 seconds each, ensuring that the lysate does not heat up too much, and making sure it does not froth up by getting the tip too close to the surface. &lt;a href=&quot;http://en.wikipedia.org/wiki/Sonication&quot; rel=&quot;nofollow&quot;&gt;Sonication&lt;/a&gt; sends very powerful shearing forces through liquid and is excellent at destroying membranes and breaking apart ECM. From here you can do your protein concentration assay (remember to use the same concentration of lysis buffer as your blank), aliquot the lysate and store at -80, or add SDS sample buffer and run your gel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I routinely use sonication on all of my western samples, regardless of whether it's tissue or cell lines I'm dealing with, and I almost never get smeared lanes anymore. Sonication reduces the viscosity or &quot;thickness&quot; of the lysate, allowing you to pipette it much more easily and accurately. It is also useful when your sample &quot;coagulates&quot; after adding SDS sample buffer, and in this instance it doesn't matter if the sample gets hot, as you'll just be boiling it anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps, please let me know if you're still having problems. I used to do troubleshooting like this for a living :)&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-02-15T02:24:25.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7211" PostTypeId="1" CreationDate="2013-02-15T02:58:13.593" Score="0" ViewCount="1397" Body="&lt;p&gt;I've been reading about &lt;a href=&quot;http://en.wikipedia.org/wiki/Prolactin&quot; rel=&quot;nofollow&quot;&gt;prolactin&lt;/a&gt;, a human hormone. Apparently it's levels within the brain can raise after exercise, although the mechanism is not clear to me. I'm interested of there is any connection between lactic acid build up in muscles during anaerobic exercise and prolactin levels in the days following exercise. Both of these sound similar, which may be a coincidence.&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-02-15T06:34:58.423" Title="Are lactic acid and prolactin rise after exercise connected?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7213" PostTypeId="2" ParentId="7211" CreationDate="2013-02-15T06:34:58.423" Score="3" Body="&lt;p&gt;Prolactin (PRL) is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Pleiotropy&quot; rel=&quot;nofollow&quot;&gt;pleiotropic&lt;/a&gt; hormone. More than 300 different functions have been described for it (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9626554&quot; rel=&quot;nofollow&quot;&gt;Bole-Feysot et al., 1998&lt;/a&gt;), although probably the most well known/studied&lt;sup&gt;1&lt;/sup&gt; is the maturation of the mammary gland during pregnancy and subsequent stimulation of milk production.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the fairly well known situations when PRL increases is after an acute stress (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/5529881&quot; rel=&quot;nofollow&quot;&gt;Neill, 1970&lt;/a&gt;; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1175088&quot; rel=&quot;nofollow&quot;&gt;Seggie and Brown, 1975&lt;/a&gt;; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6326176&quot; rel=&quot;nofollow&quot;&gt;Kant et al., 1983&lt;/a&gt;). Although the details of this are still a bit foggy, the reason seems to be connected to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Anxiolytic&quot; rel=&quot;nofollow&quot;&gt;anxiolytic&lt;/a&gt; properties of PRL (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11312305&quot; rel=&quot;nofollow&quot;&gt;Torner et al., 2001&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17432967&quot; rel=&quot;nofollow&quot;&gt;Donner et al., 2007&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anaerobic excercise is considered as a stressor, and therefore the PRL response may be important to avoid hyperactivation of the stress pathway. This has been suggested before (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16917019&quot; rel=&quot;nofollow&quot;&gt;Ohiwa et al., 2007&lt;/a&gt;) and the rise in PRL may be triggered by lactic acid, as administration of lactic acid alone can stimulate PRL secretion (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23053124&quot; rel=&quot;nofollow&quot;&gt;Sculthe et al., 2013&lt;/a&gt;).&lt;br&gt;&#xA;Note that this does not exclude that there may be other factors involved in this response. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt; at least in female mammals, but bear in mind that PRL is present in all vertebrates, males and females alike. &lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2013-02-15T06:34:58.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7214" PostTypeId="1" AcceptedAnswerId="7232" CreationDate="2013-02-15T07:08:56.443" Score="4" ViewCount="5610" Body="&lt;p&gt;I would like to be able to identify genera of fungi based on the shape, size, and colour of spores. So the requirements are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Must be able to view a 5 micrometre object clearly with reasonable resolution&lt;/li&gt;&#xA;&lt;li&gt;Must be true colour&lt;/li&gt;&#xA;&lt;li&gt;Must facilitate the measurement of an object within reasonable accuracy (500 nanometres would be nice)&lt;/li&gt;&#xA;&lt;li&gt;Should be inexpensive (\$100-\$400) &lt;sup&gt;&lt;em&gt;fingers crossed&lt;/em&gt;&lt;/sup&gt;&lt;/li&gt;&#xA;&lt;li&gt;Bonus: Be able to take photos&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;What type of microscope do I need? What magnification/resolution? Is there a good rule of thumb relating size of object with magnification?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do I find and purchase a decent microscope after defining my requirements? Any tips?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Blue light is ~450 nm, so does that mean I will not get very good resolution?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(For the sake of context: I have absolutely no formal experience in biology, but I have recently taken an amateur interest in mycology and might enrol in an undergraduate course as part of my degree at some point.)&lt;/p&gt;&#xA;" OwnerUserId="3091" LastEditorUserId="3091" LastEditDate="2013-02-15T08:01:44.047" LastActivityDate="2013-02-17T10:17:43.663" Title="What kind of microscope should be used to view biological structures (such as spores) roughly 5 µm in length?" Tags="&lt;mycology&gt;&lt;microscopy&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7215" PostTypeId="1" CreationDate="2013-02-15T11:29:39.867" Score="2" ViewCount="587" Body="&lt;p&gt;I have bakers asthma specifically to 'Sc' yeast, and know to avoid bakeries, breweries, etc...  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have figured out to not disturb rotting leaf piles, and fermenting bark mulch. Where else?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What percentage higher are concentrations in say Florida, as opposed to New York state?&lt;/p&gt;&#xA;" OwnerUserId="3096" LastEditorUserId="43" LastEditDate="2014-05-20T16:08:09.133" LastActivityDate="2014-05-20T16:08:09.133" Title="Where would Saccharomyces cerevisiae be found in highest concentrations in environment?" Tags="&lt;microbiology&gt;&lt;mycology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7216" PostTypeId="2" ParentId="7173" CreationDate="2013-02-15T13:19:04.503" Score="1" Body="&lt;p&gt;The methods used for the processign of the date should be mentioned in the Methods section of the paper the data come from (here it is Richardson AL, Wang ZC, De Nicolo A, Lu X et al. X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell 2006 Feb;9(2):121-32. PMID: 16473279). I quote from the paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;RNA extraction, cRNA synthesis, and hybridization to Affymetrix Human Genome U133 Plus 2.0 Arrays were performed as described previously (Signoretti et al., 2002 and Wang et al., 2004). Raw expression data obtained using Affymetrix GENECHIP software was normalized and analyzed using DNA-Chip Analyzer (dChip) custom software (W.H. Wong and C. Li, &lt;a href=&quot;http://www.dChip.org/&quot; rel=&quot;nofollow&quot;&gt;http://www.dChip.org/&lt;/a&gt;). Array probe data were normalized to the mean expression level of each probe across a sample set. Where indicated, tumors were classified as BLC or non-BLC on the basis of their expression array characteristics, using dChip hierarchical clustering analysis as previously described (Matros et al., 2005 and Wang et al., 2004). Comparisons between results obtained on BLC or BRCA1 tumors, non-BLC tumors, and normal breast samples were performed using the dChip “Compare Sample” function. A threshold of 1.2-fold overexpression in BLC and BRCA1 tumors was applied with 90% confidence. Of 1271 gene probes that map to the X chromosome, 60 satisfied these overexpression criteria with a range of fold difference from 1.35 to 5.11. The false discovery rate (number) of 1000 permutations was as follows: median, 0% (0); 90th percentile, 3.3% (2). Of the 60 probes, 19 were redundant (two or more probes mapping to the same gene) and excluded, leaving 41 gene-specific probes for use in the expression plot of Figure 5B. The complete gene expression array data set is available on the NCBI GEO database (accession no. GSE3744).&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since this is a standard Affymetrix human genome chip, it's CDF should either be embedded in most packages used to analyse this kind of data (limma is an industry gold standard example ;-), or downloaded from the Afymetrix website. Please note that the CDF itself may be quite old and it's annotation not always accurate any more (I have no experience with human data), so it's worth using an updated CDF (see Dai et al 2005).&lt;/p&gt;&#xA;" OwnerUserId="752" LastActivityDate="2013-02-15T13:19:04.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7217" PostTypeId="2" ParentId="7215" CreationDate="2013-02-15T14:45:38.390" Score="6" Body="&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com.ezproxy.liv.ac.uk/store/10.1111/j.1365-294X.2012.05732.x/asset/mec5732.pdf?v=1&amp;amp;t=hd7f4efn&amp;amp;s=d7918ad3c34791c5b30dc5f9c6750f46b0a990f4&quot;&gt;Here is a link to an interesting article&lt;/a&gt; which reports a survey of wild isolates of &lt;em&gt;Saccharomyces cerevisiae&lt;/em&gt; in China.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Wang, Qi-Ming, et al. (2012) Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity. Mol Ecol 21: 5404-5417&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A relevant quotation from the article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In addition to grapes and oak tree (Quercus spp.) bark, S. cerevisiae was successfully iso-lated from a variety of damaged fruit collected in orchards or markets in different provinces of China; from the bark of different deciduous trees; forest soil and rotten wood collected in primeval, original secondary and planted forests located in different regions covering temperate, subtropical and tropical climate zones from northern to southern China. Unexpectedly, the success rate of S. cerevisiae isolation from fruit samples (6.5%) was lower than that from tree bark (16.5%), soil (10.8%) and rotten wood (9.2%) samples. S. cerevisiae was more frequently isolated from forest soil samples (success rate 13.7%) than from orchard soil samples (success rate 9.1%). Among the fruits giving positive S. cerevisiae isolation, grape samples showed the lowest success rate.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Table S2 in the supplemental information records isolates as follows:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;climatic zone    sites   isolates&#xA;__________________________________&#xA;tropical           5       20&#xA;subtropical        2       14&#xA;temperate          13      51&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Superficially, from this it looks as if there would probably be little difference between New York state (&lt;a href=&quot;http://en.wikipedia.org/wiki/Climate_of_New_York&quot;&gt;humid, continental&lt;/a&gt;) and Florida (&lt;a href=&quot;http://en.wikipedia.org/wiki/Climate_of_Florida&quot;&gt;humid, subtropical&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-02-15T14:45:38.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7218" PostTypeId="1" CreationDate="2013-02-15T19:58:15.360" Score="3" ViewCount="5213" Body="&lt;p&gt;Say I'm designing a retrospective study (where I'd collect data from various schools for the last 5 years) to see if consuming milk can contribute to childhood obesity.  How do I decide on how many schools to visit? If I remember my stats correctly, in general, the goal is to achieve 95% confidence in our results, right?  So how many schools would I have to collect data from so that I will have 95% confidence in the outcome of the study?&lt;/p&gt;&#xA;" OwnerUserId="3097" LastActivityDate="2017-06-29T14:30:24.910" Title="What are the factors to consider when determining the sample size for a given study?" Tags="&lt;experimental-design&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="10" ClosedDate="2017-06-30T03:16:33.740" ContentLicense="CC BY-SA 3.0" />
  <row Id="7219" PostTypeId="1" CreationDate="2013-02-15T20:18:12.140" Score="1" ViewCount="978" Body="&lt;p&gt;According to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Gill&quot; rel=&quot;nofollow&quot;&gt;Wikipedia page on the design of gills&lt;/a&gt;, oxygen has a diffusion rate in air 10,000 times greater than in water. Is that true?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The WP entry refers to: M.B.V. Roberts, Michael Reiss, Grace Monger (2000). Advanced Biology. London, UK: Nelson. pp. 164–165.&lt;/p&gt;&#xA;" OwnerUserId="3098" LastEditorUserId="1320" LastEditDate="2013-02-16T07:20:31.373" LastActivityDate="2013-02-16T07:20:31.373" Title="Is it true that oxygen has a diffusion rate in air 10,000 times greater than in water?" Tags="&lt;aquatic-biology&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2013-02-15T23:39:32.633" ContentLicense="CC BY-SA 3.0" />
  <row Id="7220" PostTypeId="2" ParentId="7219" CreationDate="2013-02-15T21:17:28.347" Score="2" Body="&lt;p&gt;Yes, according to calculations presented &lt;a href=&quot;http://compost.css.cornell.edu/oxygen/oxygen.diff.water.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://compost.css.cornell.edu/oxygen/oxygen.diff.air.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; the conclusion is that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The O&lt;sub&gt;2&lt;/sub&gt; diffusion coefficient in saturated air (15% oxygen) is 5,700 to 10,800 times greater than in water (60°C and 20°C respectively). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And &lt;a href=&quot;http://jeb.biologists.org/content/203/16/2479.full.pdf&quot; rel=&quot;nofollow&quot;&gt;here is a paper&lt;/a&gt; using this difference to investigate the transfer of O&lt;sub&gt;2&lt;/sub&gt; through the tracheal system of a click beetle.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-02-15T21:17:28.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7221" PostTypeId="1" AcceptedAnswerId="7222" CreationDate="2013-02-15T21:43:40.370" Score="6" ViewCount="13562" Body="&lt;p&gt;I've gotten conflicting advice on this: some people believe one can remove RNase contamination simply by spraying the bench, pipettes, gloves, etc. with ethanol. Others think ethanol does not destroy RNase and special reagents are needed to prevent RNase contamination. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So does ethanol remove RNase contamination? If not, what reagent does?&lt;/p&gt;&#xA;" OwnerUserId="3053" LastEditorUserId="3053" LastEditDate="2013-02-16T11:29:11.217" LastActivityDate="2013-02-16T11:29:11.217" Title="Does ethanol destroy RNase?" Tags="&lt;biochemistry&gt;&lt;rna&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7222" PostTypeId="2" ParentId="7221" CreationDate="2013-02-16T00:31:29.467" Score="5" Body="&lt;p&gt;I think the protocols to clean glassware take no chances and just care about RNA degradation rather than targeting one class of enzymes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EtOH is supposed to denature RNAse and any other proteins on the surface.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other chemicals such as &lt;a href=&quot;http://www.invitrogen.com/site/us/en/home/References/Ambion-Tech-Support/nuclease-enzymes/general-articles/the-basics-rnase-control.html&quot; rel=&quot;nofollow&quot;&gt;Diethylpyrocarbonate  (DEPC) used to wash glassware kill all biochemical activity by reacting with nucleophilic moieties in the protein (-OH, -SH -NH(&lt;sub&gt;2/3&lt;/sub&gt;) )&lt;/a&gt;.   (See comments below for more.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These treatments are followed by heating at 300-450 F for 2-4 hours.  This is not a specific RNAse decontamination - all biological activity is killed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;RNAse activity is not assessed by specific detection of a particular enzyme, but rather judged by the degradation of an RNA sample in the lab environment.  So specific inhibition isn't worthwhile - any protein that might interact with and degrade RNA is called an RNAse in these protocols. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1320" LastEditDate="2013-02-16T08:00:22.757" LastActivityDate="2013-02-16T08:00:22.757" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7223" PostTypeId="2" ParentId="3731" CreationDate="2013-02-16T04:07:12.473" Score="2" Body="&lt;p&gt;I haven't heard of studies like the one you're proposing, but you can test this hypothesis on yourself &lt;a href=&quot;http://luciddreamingapp.com/android/help-how-to/detect-sleep-cycles/&quot; rel=&quot;nofollow&quot;&gt;with this app.&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Knowing you need to sleep less than your usual amount will probably affect the quantity and quality of your sleep, but not because of an &quot;internal clock&quot;. Most likely, &lt;strong&gt;whatever you need to wake up early for will cause you some anxiety, which will affect both sleep duration and quality.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-02-16T04:07:12.473" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7224" PostTypeId="2" ParentId="7221" CreationDate="2013-02-16T09:17:37.643" Score="4" Body="&lt;p&gt;You don't want to only inhibit or temporarily denature RNAses, if you work with RNA you have to permanently inactivate the RNAses. I work with RNA, and I haven't seen anyone use ethanol to remove RNAses, I would not trust it to work reliably. RNAses are really stable enzymes, they even survive autoclaving to some part, so I would not be suprised if they can refold after ethanol exposure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The usual methods to remove RNAses are&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Treatment with 0.1% DEPC (heat up to at least 60 °C, or autoclave if possible to remove residual DEPC later). Cannot be used with e.g. Tris buffer or anything else that reacts with it. DEPC is carcinogenic, so you should follow the proper safety procedures.&lt;/li&gt;&#xA;&lt;li&gt;Anything made of metal or glass, heat up to 250 °C for around 2 hours&lt;/li&gt;&#xA;&lt;li&gt;1M NaOH for at least 30 minutes (you need to wash thoroughly to remove the NaOH)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You should be aware that anything that destroys RNAses will likely do the same to your RNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Autoclaving does not protect completely against RNAses, &lt;a href=&quot;http://de-de.invitrogen.com/site/de/de/home/References/Ambion-Tech-Support/nuclease-enzymes/tech-notes/rnase-and-depc-treatment.html&quot; rel=&quot;nofollow&quot;&gt;but it still reduces RNAse activity significantly&lt;/a&gt;. So while you should not rely on autoclaving to get rid of RNAses, in my experience it is sufficient if you start from a source that is unlikely to contain a lot of RNAses. Pipette tips (not loose tips out of a bag, to minimize handling) and millipore-filtered water are pretty safe after they are autoclaved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also commercial RNAse inhibitors, but I've only used them in cases where I had to mix RNA and protein, and the protein wasn't completely RNAse-free. &lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2013-02-16T09:27:12.917" LastActivityDate="2013-02-16T09:27:12.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7225" PostTypeId="2" ParentId="7207" CreationDate="2013-02-16T09:37:57.070" Score="1" Body="&lt;p&gt;Doxycyline inhibits iNOS and TNF-alpha expression.   It also influences secretion of IL-1beta, IL-8, and TNF-alpha, as well as other inflammatory cytokines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[These are results collected from multiple systems.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For appropriate references, see: &lt;a href=&quot;http://link.springer.com/article/10.1007/s10787-011-0077-5/fulltext.html&quot; rel=&quot;nofollow&quot;&gt;Leite et al (2011). Anti-inflammatory properties of Doxycycline and Minocycline in experimental models: an in vivo and in vitro comparative study. Inflammopharmocology.&lt;/a&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the chemistry of how doxycycline accomplishes these things, I'm afraid I don't know the answer, but hopefully, this gives you a place to start.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-02-16T09:37:57.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7226" PostTypeId="1" CreationDate="2013-02-16T14:00:23.117" Score="7" ViewCount="201" Body="&lt;p&gt;Why and how does the proton travelling through the stalked particle in the inner mitochondrial membrane, cause a conformational change in the ATPase?&lt;/p&gt;&#xA;" OwnerUserId="3099" LastEditorUserId="22057" LastEditDate="2017-04-13T16:25:24.853" LastActivityDate="2017-04-13T16:25:24.853" Title="Cell Respiration and Oxidative Phosphorylation" Tags="&lt;cell-biology&gt;&lt;cellular-respiration&gt;&lt;mitochondria&gt;&lt;energy-metabolism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7227" PostTypeId="2" ParentId="7226" CreationDate="2013-02-16T14:47:17.400" Score="6" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XGaxF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The passage of protons through the F&lt;sub&gt;O&lt;/sub&gt; (membrane) portion of the molecule (driven by the electrochemical gradient of protons across the respiratory membrane) generates torque at the interface between the &lt;strong&gt;a&lt;/strong&gt; and &lt;strong&gt;c&lt;/strong&gt; subunits. This mean that the ring of 10 &lt;strong&gt;c&lt;/strong&gt; subunits rotates relative to the &lt;strong&gt;a&lt;/strong&gt; subunit. The &lt;strong&gt;&amp;gamma;&lt;/strong&gt; subunit in the stalk rotates along with the ring of &lt;strong&gt;c&lt;/strong&gt; subunits, while the ring of &lt;strong&gt;&amp;alpha;&lt;/strong&gt; and &lt;strong&gt;&amp;beta;&lt;/strong&gt; subunits in F&lt;sub&gt;1&lt;/sub&gt; is constrained to remain static with respect to the &lt;strong&gt;a&lt;/strong&gt; subunit because of the interaction with the &lt;strong&gt;&amp;delta;&lt;/strong&gt; and &lt;strong&gt;b&lt;/strong&gt; subunits (forming the peripheral stalk). So we have two portions of the molecule the &quot;static&quot; &lt;strong&gt;a-b&lt;sub&gt;2&lt;/sub&gt;-&amp;delta;-&amp;alpha;&lt;sub&gt;3&lt;/sub&gt;&amp;beta;&lt;sub&gt;3&lt;/sub&gt;&lt;/strong&gt; part and the rotating &lt;strong&gt;c&lt;sub&gt;10&lt;/sub&gt;-&amp;gamma;-&amp;epsilon;&lt;/strong&gt; part. The &lt;strong&gt;&amp;gamma;&lt;/strong&gt; subunit rotates within the &lt;strong&gt;&amp;alpha;&lt;sub&gt;3&lt;/sub&gt;&amp;beta;&lt;sub&gt;3&lt;/sub&gt;&lt;/strong&gt; part of F&lt;sub&gt;1&lt;/sub&gt; and drives a three-step cycle of conformational changes (via intersubunit interactions) which are linked to the phosphorylation of ADP. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a useful animation &lt;a href=&quot;http://en.wikipedia.org/wiki/ATP_synthase&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; illustrating the three step catalytic cycle being driven by the rotation of the &amp;gamma; subunit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(image from Aksimentiev &lt;em&gt;et al&lt;/em&gt;. (2004) &#xA;Insights into the molecular mechanism of rotation in the F&lt;sub&gt;O&lt;/sub&gt; sector of ATP synthase. Biophys J. 86:1332-44)&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-02-16T17:19:08.313" LastActivityDate="2013-02-16T17:19:08.313" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7228" PostTypeId="1" CreationDate="2013-02-16T16:19:39.603" Score="1" ViewCount="538" Body="&lt;p&gt;What factors must be taken into account for the maintenance of the immunogenicity of ovalbumin antigen? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the ovalbumin is aggregated, could we inject it for induction of immune reponse?&lt;/p&gt;&#xA;" OwnerUserId="3100" LastEditorUserId="1320" LastEditDate="2013-02-16T17:03:49.840" LastActivityDate="2013-02-19T09:04:57.147" Title="What factors must be taken into account for the maintenance of the immunogenicity of ovalbumin antigen?" Tags="&lt;immunology&gt;&lt;vaccination&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7229" PostTypeId="2" ParentId="7208" CreationDate="2013-02-16T20:08:26.763" Score="3" Body="&lt;p&gt;There's Benchfly, which is a video-based protocol library:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.benchfly.com/video-protocols.php&quot; rel=&quot;nofollow&quot;&gt;http://www.benchfly.com/video-protocols.php&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's also JOVE, which is a peer-reviewed video journal that sometimes covers protocols:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jove.com/&quot; rel=&quot;nofollow&quot;&gt;http://www.jove.com/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1906" LastActivityDate="2013-02-16T20:08:26.763" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7231" PostTypeId="2" ParentId="3704" CreationDate="2013-02-16T22:55:43.377" Score="3" Body="&lt;p&gt;According to &lt;a href=&quot;http://news.softpedia.com/news/Some-1-2-Percent-of-Milky-Way-Stars-Can-Support-Life-210871.shtml&quot; rel=&quot;nofollow&quot;&gt;this,&lt;/a&gt; 1.2% of stars have planets that can support life. According to Google, there are 300,000,000,000 stars in the Milky Way. That means 3,600,000 stars can support life. Each of these stars &lt;a href=&quot;http://www.fennzart.com/planetarysystems/drake_equation.html&quot; rel=&quot;nofollow&quot;&gt; is estimated to have 1-2 planets that can support life.&lt;/a&gt; For the sake of simplicity, I'll use 1.5 to represent this, since it is the average of 1 and 2. 1.5×3,600,000=5,400,000 planets capable of supporting life. Looking around the web, there are wildly different estimates of the odds of life evolving on one of these planets (from 1%-100%), but 100% seems like the most common. This means that, statistically, the odds of extraterrestrial life existing are extremely high.&lt;/p&gt;&#xA;" OwnerUserId="1182" LastActivityDate="2013-02-16T22:55:43.377" CommentCount="3" CommunityOwnedDate="2013-02-16T22:55:43.377" ContentLicense="CC BY-SA 3.0" />
  <row Id="7232" PostTypeId="2" ParentId="7214" CreationDate="2013-02-17T05:01:54.563" Score="4" Body="&lt;p&gt;I think you have a good question, but if you want to get a good understanding of the issues you raise with it, then you really ought to consider spending some time reading this &lt;a href=&quot;http://micro.magnet.fsu.edu/primer/&quot; rel=&quot;nofollow&quot;&gt;optical microscope primer&lt;/a&gt;. In my opinion, you need not bother with taking an undergraduate course at a physical university. As an intro to biology (which is not really necessary if all you want to do is look at small things in a microscope and understand what you're seeing), you might want to consider enrolling in &lt;a href=&quot;https://www.edx.org/press/eric-lander-secret-of-life&quot; rel=&quot;nofollow&quot;&gt;this free class&lt;/a&gt;, but if all you want to do is look at small things and have a basic understanding of what you're seeing, I think all you need to do is read the primer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it was me, I'd read at least some of the primer before investing the money in a microscope. Otherwise you're just taking a blind leap of faith from someone's (perhaps biased) suggestion.&lt;/p&gt;&#xA;" OwnerUserId="1756" LastActivityDate="2013-02-17T05:01:54.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7233" PostTypeId="2" ParentId="7214" CreationDate="2013-02-17T10:17:43.663" Score="3" Body="&lt;p&gt;I agree with Kevin F, if I was you, I'd take a bit of training before buying something or even trying. Biology teachers or staff from the university are usually happy to provide you with a microscope to test something, so just ask. If you want a resolution that high, there are a lot of adjustments to do, commonly referred to as &quot;Köhler illumination&quot;, because otherwise you won't get a nice picture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question, you can basically forget microscopes at that price range for this resolution, let alone the ability to take photos. You would have to spend &gt;$1000 to get something good enough. As in photography, this is largely due to the lenses. I don't have much experience with fungi, but you might want to have a phase contrast microscope to be able to see the specimens properly. You can buy microscopes with have a port for a DSLR camera, with which I've made good experiences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a 5 µm object, you could use a $60 \times$ lens (which, together with a $10 \times$ ocular makes a magnification of $600\times$), or even a $100 \times$ lens, when you want to resolve surface structures, but no idea, if the latter really works with your specimens, so you'd have to test that before buying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So: First, get a bit of formal training, as suggested by Kevin F. Then, try it yourself without buying, and try it with your own specimens! Then, save money and buy. :-)&lt;/p&gt;&#xA;" OwnerUserId="852" LastActivityDate="2013-02-17T10:17:43.663" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7234" PostTypeId="1" CreationDate="2013-02-17T14:20:10.103" Score="14" ViewCount="41872" Body="&lt;p&gt;I just learned that ATP can not be stored in excess and is only made by the body when it is needed. What makes ATP, like glucose and fat is what is stored under the skin or wherever. Now why cant the body just produce ATP and store it for heavy, heavy exercise when it would advantageous for it to be ready rather than it going through the production phase and then used. When I say ATP storage I mean in large amounts.&lt;/p&gt;&#xA;" OwnerUserId="2967" LastEditorUserId="3340" LastEditDate="2015-06-04T11:50:08.127" LastActivityDate="2021-02-25T07:19:07.253" Title="Why can ATP not be stored in excess?" Tags="&lt;bioenergetics&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7235" PostTypeId="2" ParentId="7234" CreationDate="2013-02-17T15:37:54.373" Score="8" Body="&lt;p&gt;Not a complete answer, but a few random thoughts to start off the conversation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) There is another molecule that is used as a fast access store, and that is phosphocreatine which can be used to very rapidly rephosphorylate ADP in muscle. In resting muscle it is present at about 5x the level of ATP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Levels of ATP are also used by cells as a regulatory input - in other words the fall in ATP levels with the onset of exercise triggers a response to replenish ATP through e.g. the breakdown of glycogen. In this view it is useful to have a final stage &quot;energy currency&quot; which can act directly as an enzyme substrate and whose level is a sensitive indicator of current energy demand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) ATP is also a substrate for RNA polymerase. If ATP was present at vastly higher levels than UTP, CTP and GTP it would probably cause errors in transcription, and might also interfere with the regulatory role of GTP binding proteins, since it would act as a competitor for binding at the GTP binding site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) In any case, if ATP was to be maintained at a much higher concentration for rapid use, presumably as soon as it began to be used the ATP generating systems would have to start up to try to replenish the pool. In other words things would really be no different from the way they are, but would simply operate at a higher resting level of ATP.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-02-17T15:37:54.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7236" PostTypeId="2" ParentId="7234" CreationDate="2013-02-17T15:39:02.003" Score="19" Body="&lt;p&gt;Let's compare ATP, glucose and fatty acids in terms of energy storage. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ATP has a molecular weight of 507 Da&lt;/li&gt;&#xA;&lt;li&gt;Glucose has a molecular weight of 180 Da, and contains the same amount of energy as 31 ATP molecules&lt;/li&gt;&#xA;&lt;li&gt;Fatty acids vary in size, but a gram of fat contains about twice as much energy as a gram of glucose (or glycogen)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The difference in energy density is huge, you would need enormous amounts of ATP to replace glucose/glycogen as energy storage mechanism, not to speak of fat. You can't put an arbitrary amount of ATP molecules into a cell, you 'll get into problems due to the osmotic pressure lots of molecules inside the cell would cause. Glucose is stored as glycogen in cells due to this effect, which makes one large glycogen molecule out of lots of glucose molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The energy density difference is even larger if you take into account that ATP and glucose bind water, while fat is stored without surrounding water. The actual difference in energy density of glycogen and fat is around 6 times.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ATP is also not as stable as fat, it can get hydrolized in water. This would be a problem for long-term storage of energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You'll find some more details in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26882/#ui-ncbiinpagenav-heading-12&quot;&gt;Albert's &quot;Molecular Biology of the Cell&quot;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2013-02-17T15:39:02.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7237" PostTypeId="1" AcceptedAnswerId="7241" CreationDate="2013-02-17T17:12:42.373" Score="4" ViewCount="550" Body="&lt;p&gt;I see some popular science articles on the plastic eating bacteria and fungi appearing on the web since 2009. Most of the articles praise discoveries, because such organisms promise to break down plastics which were previously thought to be indestructible. However, from the articles it is hard to understand the total number/names of promising organisms that can biodegrade plastic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, it's hard to gather from the dated articles if these plastic eating organisms have passed safety testing - for example that they don't break down plastic into something volatile and toxic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is - &lt;strong&gt;which organisms as of 2013 are seriously considered for solving the plastic in landfills problem?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2017-11-02T02:07:18.667" Title="What plastic eating organisms are there to help with plastic in landfills problem?" Tags="&lt;cell-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7238" PostTypeId="2" ParentId="7234" CreationDate="2013-02-17T17:27:31.627" Score="11" Body="&lt;p&gt;I think @AlanBoyd and @MadScientist have touched on the answer, fat is better suited by density for storing energy than ATP; ATP is optimal for quick conversion to bioenergy.  Look at the question in another way: ATP in bioenergy cycle is dynamic - its an energy flux from food and breath to bioenergy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biological energy is used at essentially the same rate at which we take it in.   The vast majority is used as soon as its available. If we were to try to store enough ATP for say an hour the costs would be large.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://books.google.com/books?id=iGPsen3fSOIC&amp;amp;pg=PA66&amp;amp;lpg=PA66&amp;amp;dq=g%20atp%20consumed%20in%20a%20day&amp;amp;source=bl&amp;amp;ots=P93ljrqW--&amp;amp;sig=s0inoHCZqwtqE3qYHzCadsWnNRo&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=BQ8hUbOFGMq0iQKImIGoDg&amp;amp;ved=0CDgQ6AEwAQ#v=onepage&quot;&gt;This back of the envelope calculation&lt;/a&gt; (see section 3.8) shows that &lt;strong&gt;1 day of ATP is 64.5kg for a 2800 kcal a day energy intake&lt;/strong&gt;.  Approximately equal to body weight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course ATP is stored in excess - just a few seconds worth though, &lt;a href=&quot;http://cyclistrules.blogspot.com/&quot;&gt;8 if you believe competitive cyclists&lt;/a&gt;.  ATP is a pretty small quantum of energy... Even an hour storage would add 12 pounds to an adult body weight.  That's a lot. And what advantage would this give us?  We might be able to engage in high energy activities (which use ATP faster than we can make it) for longer.  But up to now it looks as if improvements in efficiency in generating ATP have been adequate for animals to stay competitive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look at how evolution has dealt with the other component of bioenergy: oxygen. We can't hold our breath for more than a few minutes. &lt;a href=&quot;http://www.huffingtonpost.com/2012/11/16/breath-world-record-stig-severinsen_n_2144734.html&quot;&gt;22 minutes&lt;/a&gt; is the current human record; impressive but still not that long.  Oxygen is in plentiful supply brought in from outside and the adaptive costs to storing oxygen internally would simply not justify building up such a capacity for most of us. It seems even that aquatic mammals only hold their breath for a similar amount of time as we can if we practice.  &lt;a href=&quot;http://idw.org/html/dolphin_facts_1.html&quot;&gt;20 minutes for Orcas.&lt;/a&gt; &lt;a href=&quot;http://www.planet-science.com/categories/under-11s/our-world/2011/03/penguins---extreme-divers.aspx&quot;&gt;Penguins too&lt;/a&gt;.  This isn't meant to be a survey of all animals ability to store oxygen, the point being that storage of oxygen has an adaptive cost that is not trivial. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-02-17T18:19:54.953" LastActivityDate="2013-02-17T18:19:54.953" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7239" PostTypeId="2" ParentId="7199" CreationDate="2013-02-17T17:48:10.327" Score="5" Body="&lt;p&gt;This is the figure the question is about. On the right is the control experiment with GTP-γS, on the left without it: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sh0dJ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bands that are visible in both experiments are unspecific binding. If GTP-γS doesn't affect their presence, the mechanism by which they bind to the column can't be specific to the GTPase functionality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The proteins the authors were after are those that are present in the experiment without GTP-γS, but are not eluted in the experiment with GTP-γS. Those are binding via an GTPase functionality to the GTP on the column. They are marked with arrow heads in the figure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The general idea behind this control experiment is to distinguish specific binding from unspecific binding to the column. Being able to do that means that the authors had fewer proteins they needed to investigate further, saving them some work.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2013-02-17T17:48:10.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7241" PostTypeId="2" ParentId="7237" CreationDate="2013-02-18T03:27:58.087" Score="5" Body="&lt;p&gt;I remember this link - about &lt;a href=&quot;http://www.mnn.com/green-tech/research-innovations/blogs/boy-discovers-microbe-that-eats-plastic&quot; rel=&quot;nofollow&quot;&gt;a high school student who's science fair project&lt;/a&gt; was a basic but effective selection experiment.  He cut up plastic and put it in a yeast medium (growth medium for microorganisms) for a few weeks.  It says he tweaked the temperature and other incubation conditions for a few weeks and got a significant degradation of the plastic in the media.  The microorganisms in the media were not characterized.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That article is great because the bloggers compiled a list of similar work.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a couple of links that point to &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1389172303801767&quot; rel=&quot;nofollow&quot;&gt;styrene degradation&lt;/a&gt; by &lt;a href=&quot;http://mic.sgmjournals.org/content/147/4/973.full&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Pseudomonas putida&lt;/em&gt; variants&lt;/a&gt;.  &lt;em&gt;Pseudomonas putida&lt;/em&gt; is a likely candidate from bacteriology - it was first isolated near chemical and petroleum spills - they can degrade petrochemicals and organotoxics, so researchers might tend to start with this bacteria or an isolate of it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/es060408h&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; identifies &lt;em&gt;Phanerochaete chrysosporium&lt;/em&gt;, a white rot fungus as an organism that can degrade phenolic resins.  White rot fungi are found in wood rot and can degrade lignin which is derived from a poly-phenolic like biosynthesis pathway.  So this is also an interesting lead.  It doesn't always grow to industrial scale - I've known people working on this even in the early 80s. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it seems despite the fact that plastic never seems to go away, there are organisms in the wild that will chew away at the plastic, and with a little bit of selection work you can pick them out pretty easily.  This &lt;a href=&quot;http://www.nature.com/news/2011/110328/full/news.2011.191.html&quot; rel=&quot;nofollow&quot;&gt;survey of the plastic dump in the Pacific gyre&lt;/a&gt; found that there were marine microorgs that might be eating plastic there too.  They had a preliminary report: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So far, the DNA sequences obtained by her lab show that almost 25% of the bacteria on one polyethylene surface were vibrios&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://ecoprimate.wordpress.com/2012/02/03/the-biodegradation-of-plastic-by-fungi/&quot; rel=&quot;nofollow&quot;&gt;A survey of the tropical rainforest&lt;/a&gt; also found a collection of fungi that can subsist on polyurethane. These included Pestalotiopsis microspora which seems to be have the so far unique property of anaerobic degradation of polyurethane.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall it seems that finding organisms in the wild is of ongoing interest.  This may be because biodegradation of plastic tends to be slow, which makes sense because if it were quick there would be no problem with dumping it into the dirt of into the ocean, but it would also rot over time in the back yard or in your boat.  While its possible that more fishing trips may find the perfect plastic eater, its also possible that industrial processes for the bioremediation of plastics may have to wait for some engineered organisms.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-02-18T04:43:04.457" LastActivityDate="2013-02-18T04:43:04.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7242" PostTypeId="1" AcceptedAnswerId="7244" CreationDate="2013-02-18T05:11:51.780" Score="5" ViewCount="1079" Body="&lt;p&gt;I was walking through a park this afternoon and observed a few birds having fun flying around and it got me thinking why would natural selection favour birds with flesh at all if it hinders their flight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We started first with single-cell and micro-organisms flourishing the ponds and then they evolved into massive dinosaurs. It therefore seems, there are some unique reasons for growing to such a large size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I thought it's counter intuitive because the large body slows down locomotion, requires lots of food and energy upkeep, is a big flesh target for predators, makes hiding ineffective.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although it is obvious that the flesh protects the internal organs, but it seems like a chicken and egg problem because without a massive body, perhaps then there is no need for the internal organs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a different perspective, perhaps those animals that evolved without flesh are called plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That sums up my naive train of thoughts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, any expert can shed some light?&lt;/p&gt;&#xA;" OwnerUserId="746" LastActivityDate="2013-02-19T11:55:45.550" Title="How does natural selection favour large body mass and size (or so it seems)" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7243" PostTypeId="1" CreationDate="2013-02-18T05:36:25.360" Score="2" ViewCount="113" Body="&lt;p&gt;What's the Efficacy of Ampakines in the Treatment for ADHD? Ampakines are a class of drugs that serve as potentiators of the AMPA glutamate receptor. By so doing they serve as nootropic, anxiolytics and antidepressants. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1590" LastEditDate="2013-08-01T08:45:56.403" LastActivityDate="2013-08-01T08:45:56.403" Title="What's the Efficacy of Ampakines in the Treatment for ADHD?" Tags="&lt;pharmacology&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7244" PostTypeId="2" ParentId="7242" CreationDate="2013-02-18T06:54:26.963" Score="7" Body="&lt;p&gt;Well first of all I don't know if natural selection favors larger animals - most of the living things in the world are single celled.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still there are advantages to being larger.  I don't know if I can list them all!  In no particular order: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Living things that are large are &lt;a href=&quot;http://en.wikipedia.org/wiki/Kleiber%27s_law&quot;&gt;more metabolically efficient&lt;/a&gt;. The amount of food required goes as a 3/4 power of the size of the animal.  Thus a cat 100 times the mass of a mouse requires only 31 times more food.  I don't believe that it is not known how this works. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) &lt;a href=&quot;http://en.wikipedia.org/wiki/R/K_selection_theory#r-selection&quot;&gt;r vs K selection&lt;/a&gt;: larger animals have greater individual &quot;value&quot;.  Smaller animals tend to live by r-selection - they are cheap and reproduce in large amounts, then lead short and highly competitive lives where most offspring die without reproducing.  Larger animal tend to live longer and reproduce offspring with a greater chance of life. In the extreme case you can compare a cockaroach to an elephant here.  This is not a hard and fas rule, but cheap offspring do tend to be small.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I seem to remember that there are lots of other surveys done and body size correlates to life span and any number of other attributes, which I will try to add after I get some sleep unless someone slips in and lists them all. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) &lt;a href=&quot;http://en.wikipedia.org/wiki/Cope%27s_rule&quot;&gt;Cope's rule&lt;/a&gt; - an observation as much as a rule that size must convey some advantge because most animals become larger the longer they are around.  Not &lt;em&gt;always&lt;/em&gt; true, but there is a trend that the longer evolution works, the more likely a large animal will show up.  This might be because as niches for smaller animals are filled, niches for larger animals become more accessible? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-02-18T14:47:27.460" LastActivityDate="2013-02-18T14:47:27.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7245" PostTypeId="1" AcceptedAnswerId="7246" CreationDate="2013-02-18T09:37:56.167" Score="10" ViewCount="3627" Body="&lt;p&gt;My understanding, that may be wrong, is that cellulose/fibre has little nutritional value to many animals because it's hard to break down thus making consumption inefficient. However, &lt;a href=&quot;http://en.wikipedia.org/wiki/Ruminant&quot;&gt;Ruminating mammals&lt;/a&gt;, other mammals such as &lt;a href=&quot;http://www.cwf-fcf.org/en/resources/magazines/wild/wild-classes/grade-3/all-about-black-bears.html&quot;&gt;black bears&lt;/a&gt;, and many insects such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Grasshopper#Diet_and_digestion&quot;&gt;grasshoppers&lt;/a&gt; digest grasses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any birds with the gut flora to break down fibre? Or even some that eat grass but digest it in another way? &lt;/p&gt;&#xA;" OwnerUserId="3037" LastEditorUserId="1590" LastEditDate="2013-02-18T10:04:58.233" LastActivityDate="2015-03-05T01:28:39.927" Title="Are there grass or fiber eating birds?" Tags="&lt;bacteriology&gt;&lt;digestive-system&gt;&lt;ornithology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7246" PostTypeId="2" ParentId="7245" CreationDate="2013-02-18T10:33:57.337" Score="13" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Hoatzin#Feeding&quot;&gt;hoatzin&lt;/a&gt; has a digestive system that makes use of bacterial fermentation. Many other birds also consume grass, e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Ostrich#Feeding&quot;&gt;ostriches&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Duck#Feeding&quot;&gt;ducks&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Canada_Goose#Diet&quot;&gt;geese&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's also a &lt;a href=&quot;http://scholar.google.com/scholar?q=bird%20cellulose%20digestion&quot;&gt;large body of literature&lt;/a&gt; on how birds can digest cellulose.&lt;/p&gt;&#xA;" OwnerUserId="112" LastEditorUserId="1231" LastEditDate="2013-02-18T14:45:59.357" LastActivityDate="2013-02-18T14:45:59.357" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7247" PostTypeId="1" CreationDate="2013-02-18T12:22:29.177" Score="3" ViewCount="37" Body="&lt;p&gt;How long does it take for the Opioids listed in the Description to induce &lt;strong&gt;Analgesia&lt;/strong&gt; when Administered via IV? Now I don't mean how long it takes for euphoria to come on but &lt;em&gt;analgesia&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The opioids I would like to know this information to include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Buprenorphine&lt;/li&gt;&#xA;&lt;li&gt;Butorphanol&lt;/li&gt;&#xA;&lt;li&gt;Fentanyl&lt;/li&gt;&#xA;&lt;li&gt;Hydromorphone&lt;/li&gt;&#xA;&lt;li&gt;Methadone&lt;/li&gt;&#xA;&lt;li&gt;Morphine&lt;/li&gt;&#xA;&lt;li&gt;Oxycodone&lt;/li&gt;&#xA;&lt;li&gt;Pentazocine&lt;/li&gt;&#xA;&lt;li&gt;Pethidine (meperidine)&lt;/li&gt;&#xA;&lt;li&gt;Sufentanil&lt;/li&gt;&#xA;&lt;li&gt;Tramadol&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-07-23T23:30:55.810" Title="How long does it take for the Opioids listed in the Description to induce Analgesia when Administered via IV?" Tags="&lt;pharmacology&gt;&lt;analgesia&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7248" PostTypeId="1" CreationDate="2013-02-18T12:39:55.383" Score="6" ViewCount="714" Body="&lt;p&gt;My understanding is that there are two broad categories of cilia: motile and non-motile (also called primary. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples of the former include sperm flagella and the cilia of epithelial cells that line the airways. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples of the latter are mostly single cilia that protrude from the cell and act as an antenna, usually packed with certain receptors (HH pathway, Notch pathway etc.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the inner ear, a primary cilium called the kinocilium extends out of the center of the apical side of hair cells and migrates to the lateral side over the course of a few days. This cilium is non-motile, it is simply anchored to a basal body which is pulled to one side of the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know of another such example in any other tissue? A single non-motile primary cilium whose basal body migrates along the apical plane of the cell after docking with the cell cortex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="3111" LastEditorUserId="1590" LastEditDate="2013-02-18T13:31:45.023" LastActivityDate="2014-03-02T12:49:59.783" Title="Primary cilia: what cell types have non-motile cilia that migrate?" Tags="&lt;cell-biology&gt;&lt;development&gt;&lt;assay-development&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7249" PostTypeId="1" AcceptedAnswerId="7250" CreationDate="2013-02-18T13:06:02.413" Score="3" ViewCount="67679" Body="&lt;p&gt;I'm 20, in about 6 months I turn 21. For some time I've been wondering whether there are natural, non-surgical and non-pharmaceutical ways that humans can continue to grow after reaching adulthood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please answer only if you are certain about this or you can reference any&#xA;trustworthy source.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you a lot friends.&lt;/p&gt;&#xA;" OwnerUserId="3112" LastEditorUserId="630" LastEditDate="2019-06-25T19:19:48.270" LastActivityDate="2019-06-25T19:19:48.270" Title="I'm 20. Can I still grow taller?" Tags="&lt;human-anatomy&gt;&lt;growth&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ClosedDate="2013-02-18T17:30:18.037" ContentLicense="CC BY-SA 3.0" />
  <row Id="7250" PostTypeId="2" ParentId="7249" CreationDate="2013-02-18T15:03:45.740" Score="5" Body="&lt;p&gt;The answer is probably &lt;strong&gt;No.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Long&quot; bones - like the tibia, fibula, femur, humerus, etc. grow at the ends during childhood via a special formation called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Epiphyseal_plate&quot; rel=&quot;nofollow noreferrer&quot;&gt;Epiphyseal plate&lt;/a&gt; (also known as &quot;growth plates&quot;). The plates are composed of a special cartilage that grows, and slowly calcifies as a person reaches adulthood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the growth plates completely stop expanding &lt;a href=&quot;http://www.dukehealth.org/health_library/health_articles/your-growing-bones-all-about-growth-plates&quot; rel=&quot;nofollow noreferrer&quot;&gt;is left to genetics, but generally happens 2 years after puberty finishes - about 16 for women and 18 for men&lt;/a&gt;. So after those ages there's little, if any, significant growth - though it can happen in very rare cases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To date there aren't any exercises you can perform that will elongate bones. It doesn't make physiological sense; stretching puts stress on muscles and tendons - not bones. Weight lifting will compress bones, making them more dense and will make you shorter in the long run.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While there's been some success in getting chondrocytes to grow cartilage &lt;em&gt;in vitro&lt;/em&gt;, there has yet to be significant gains &lt;em&gt;in vivo&lt;/em&gt;, thus there aren't any medications available that would cause growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only widely practiced way of gaining height after adulthood is with very painful surgery that involves a lot of braces. The bones are systematically broken, held in place, and allowed to heal. The setup looks like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3krxV.jpg&quot; alt=&quot;Elongation setup.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While we get closer and closer to being able to control such things every day, for the time being (and I wouldn't count on this changing anytime soon) everybody is stuck with the height they were genetically programmed with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an aside: Being tall isn't all it's cracked up to be. At ~197cm I can tell you it is &lt;em&gt;hell&lt;/em&gt; finding pants that fit. &lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2013-02-18T15:23:47.330" LastActivityDate="2013-02-18T15:23:47.330" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7251" PostTypeId="1" CreationDate="2013-02-18T16:33:51.360" Score="6" ViewCount="137" Body="&lt;p&gt;A usual number for a healthy biogas fermenter is $10^9 - 10^{10}/mL$ Bacteria, 10-15% of which would be methanogenic archae. Exceptionally healthy fermenters have more total bacteria and up 25% archae. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mass of &lt;em&gt;E. coli&lt;/em&gt; is given with 670 femtograms. If &lt;em&gt;E. coli&lt;/em&gt; is representative for fermenting bacteria that would put us on the order of magnitude of 1 g/L living biomass.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This seems like much to me, though this is just a gut feeling. &#xA;As additional information, such a fermenter will have a total solids content of about 10%. A typical loading rate will be 4-5 g VS/d l *, two thirds of which get metabolized to gas. To put it another way: The amount of digested biomass per day would be the same order of magnitude as the living biomass. However, as anaerobic digestion is a multistage process, with at least three steps, each population will have a higher rate of digestion to mass.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are the numbers basically sound? Is &lt;em&gt;E. coli&lt;/em&gt; an exceptional bacterium in terms of mass? Are archae generally as massive as bacteria? What are bacteria counts for other fermentation processes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(*) g volatile solid per day and liter: for each liter fermenter volume, this many g potentially degradable matter are added per day&lt;/p&gt;&#xA;" OwnerUserId="3037" LastEditorUserId="3037" LastEditDate="2013-02-25T12:57:04.007" LastActivityDate="2013-12-26T15:35:30.697" Title="Is 1 g/l living biomass for a Biogas fermenter plausible?" Tags="&lt;bacteriology&gt;&lt;biotechnology&gt;&lt;fermentation&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7252" PostTypeId="1" CreationDate="2013-02-18T19:33:37.773" Score="3" ViewCount="37329" Body="&lt;p&gt;What factors determine the melting point of a fatty acid?&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Chain length &lt;/li&gt;&#xA;&lt;li&gt;The number of methylene group &lt;/li&gt;&#xA;&lt;li&gt;The ionized state of the fatty acid &lt;/li&gt;&#xA;&lt;li&gt;Its degree of saponification &lt;/li&gt;&#xA;&lt;li&gt;Its ability to alter the entropy of water &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3090" LastActivityDate="2016-09-16T02:06:49.627" Title="Melting point of a fatty acid?" Tags="&lt;biochemistry&gt;&lt;organic-chemistry&gt;&lt;lipids&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2016-09-16T04:52:54.467" ContentLicense="CC BY-SA 3.0" />
  <row Id="7253" PostTypeId="1" CreationDate="2013-02-18T20:13:11.027" Score="3" ViewCount="468" Body="&lt;p&gt;If I'm not told that they're non carriers, and if I don't have proof of their geneotype based off of progeny, when can I assume they're non carriers for a trait?&lt;/p&gt;&#xA;" OwnerUserId="3115" LastActivityDate="2013-02-22T23:35:26.463" Title="When can I assume individuals marrying into a pedigree are non-carriers?" Tags="&lt;genetics&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7254" PostTypeId="2" ParentId="7253" CreationDate="2013-02-18T20:26:49.157" Score="3" Body="&lt;p&gt;All the time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unless you are specifically told/shown they are carriers, they are assumed to be Wild Type and do not carry the mutation.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-02-18T20:26:49.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7255" PostTypeId="2" ParentId="7142" CreationDate="2013-02-18T20:58:49.570" Score="4" Body="&lt;p&gt;Just adding a little bit here. Estimating changes in connectivity based on STDP is hard&#xA;&lt;a href=&quot;http://klab.smpp.northwestern.edu/wiki/images/2/2b/Stevenson_Inferring_Plasticity_2011.pdf&quot; rel=&quot;nofollow&quot;&gt;http://klab.smpp.northwestern.edu/wiki/images/2/2b/Stevenson_Inferring_Plasticity_2011.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;but yes - these questions are enough to keep a big field busy for a &lt;em&gt;long&lt;/em&gt; time. &lt;/p&gt;&#xA;" OwnerUserId="3020" LastActivityDate="2013-02-18T20:58:49.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7256" PostTypeId="1" AcceptedAnswerId="7258" CreationDate="2013-02-18T23:28:08.630" Score="5" ViewCount="7278" Body="&lt;p&gt;As far as I know the fetus is fed by the umbilical cord which basically connects his/her circulatory system with the mother's in order to supply oxygen and nutrients. But how is this possible if they (the mother and the fetus) have different incompatible blood types?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible that the father has A blood type, the mother B and the child A and thus incompatible with the mother's.&lt;/p&gt;&#xA;" OwnerUserId="3116" LastActivityDate="2013-02-19T01:48:22.153" Title="How can the child and the mother have different blood types?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7257" PostTypeId="2" ParentId="7252" CreationDate="2013-02-19T00:47:05.703" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;(1) Chain Length&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Will definitely affect melting point, as &lt;a href=&quot;http://www.elmhurst.edu/~chm/vchembook/551fattyacids.html&quot;&gt;this website explains pretty well:&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;&quot;Melting point principle: as the molecular weight increases, the melting point increases.&quot;&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(2) Number of Methylene groups.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is another way of describing &lt;em&gt;unsaturated&lt;/em&gt; from &lt;em&gt;saturated&lt;/em&gt; fats. The more saturated a fat is, the straighter it is. Methylene groups cause kinks, which disrupts the Van der Waals forces along the rest of the carbon chain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As such, from the link above again:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&quot;On the other hand, the introduction of one or more double bonds in the hydrocarbon chain in unsaturated fatty acids results in one or more &quot;bends&quot; in the molecule. The geometry of the double bond is almost always a cis configuration in natural fatty acids. These molecules do not &quot;stack&quot; very well. The intermolecular interactions are much weaker than saturated molecules. &lt;strong&gt;As a result, the melting points are much lower for unsaturated fatty acids.&quot;&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(3) Ionized state of the fatty acid.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This will have a very minor affect. The fatty acid generally has an unpaired ester (-ate at the end) which can have a negative charge. However, from the link above &lt;em&gt;again&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;&quot;However, in fatty acids, the non-polar hydrocarbon chain gives the molecule a non- polar character.&quot;&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So even if the ester had a charge, the negative character is miniscule compared to the intermolecular forces exerted by the non-polar tail. Particularly since the charge can distribute amongst the two oxygen molecules which are conjugated, reducing the reactivity further.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(4) Degree of saponification.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm not super-familiar with the degree of saponification, but from a quick overview of the process I'd say this wouldn't affect melting point - counter to my comment. The process of making soap involves only the acidic portion of the fatty-acid triglycerides. That portion of the macromolecule is going to be pretty much the same regardless of the fatty acid, so it will have nearly the same reactivity regardless of its chain length and conjugation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What will not saponify are usually waxes - which are pretty much fully-saturated hydrocarbon chains with very few (if any) acidic sites. Parafin Wax, for instance, does not saponify, and has the formula ${C_{31}H_{64}}$.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(5) Ability to alter entropy of water.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Like the degree of saponification option above, the ability of a fatty acid to alter the entropy of water correlates to the number of reactive sites throughout the molecule. As-such, unsaturated fats (those with methylene groups) are going to be slightly more reactive as pi-bonds are more reactive than sigma bonds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, given that this answer relies on a previous option, it's probably better to go with the previous option.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultimately, if I were answering the question I'd choose &lt;strong&gt;1, 2&lt;/strong&gt; since the rest either depend on those two or are miniscule. However, beware that it's your question to answer and not mine.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-02-19T00:47:05.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7258" PostTypeId="2" ParentId="7256" CreationDate="2013-02-19T01:48:22.153" Score="10" Body="&lt;p&gt;The blood of the fetus does not mix with the blood of the mother.  Instead, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Placenta&quot;&gt;placenta&lt;/a&gt; provides a system where the two separate blood streams flow past each other with thin separation allowing nutrients to flow between the two streams but the not the blood cells and other large components. &lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2013-02-19T01:48:22.153" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7259" PostTypeId="1" AcceptedAnswerId="16907" CreationDate="2013-02-19T05:20:14.170" Score="21" ViewCount="130834" Body="&lt;p&gt;A &lt;a href=&quot;http://tvtropes.org/pmwiki/pmwiki.php/Main/TongueTrauma&quot;&gt;common trope&lt;/a&gt; in certain circles (like &lt;a href=&quot;http://www.kungfucinema.com/forums/showthread.php?t=18577&quot;&gt;Eastern martial fiction&lt;/a&gt;), is someone committing quick suicide by biting his or her tongue.  But is this really possible?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The internet turns up millions of pages of &lt;a href=&quot;http://answers.yahoo.com/question/index?qid=20071226130139AAqPpNb&quot;&gt;&lt;em&gt;speculation&lt;/em&gt;&lt;/a&gt;, but no &lt;a href=&quot;http://boards.straightdope.com/sdmb/archive/index.php/t-454918.html&quot;&gt;&lt;em&gt;Straight Dope&lt;/em&gt;&lt;/a&gt;.  People have been removing the tongues from mammals, and each other, throughout human history.  There has to be some scientific data on this somewhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Will an untreated, severe, lingual laceration, really result in bleed-out of an otherwise healthy human?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or will lingual trauma facilitate swallowing the tongue sufficiently to cause asphyxiation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does the science say?&lt;br&gt;&#xA;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="3117" LastEditorUserId="3117" LastEditDate="2015-07-11T07:39:40.923" LastActivityDate="2017-06-13T11:56:22.427" Title="Can a person really die quickly from biting their tongue?" Tags="&lt;human-biology&gt;&lt;mammals&gt;&lt;injury&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7261" PostTypeId="2" ParentId="7253" CreationDate="2013-02-19T08:31:46.460" Score="3" Body="&lt;p&gt;You can only rely on statistics in this case. Check the population the person is coming from for statistical probability to be carriers.&lt;/p&gt;&#xA;" OwnerUserId="3119" LastActivityDate="2013-02-19T08:31:46.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7262" PostTypeId="2" ParentId="7242" CreationDate="2013-02-19T08:40:06.873" Score="3" Body="&lt;p&gt;Another reason could be that bigger animals can better fight for resources like food or sex. Ususally it's the stronger (and often bigger) male that gets a chance to mate or defend their prey.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bigger animals are also harder to kill and therefore have to fear less predators.&lt;/p&gt;&#xA;" OwnerUserId="3119" LastActivityDate="2013-02-19T08:40:06.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7263" PostTypeId="1" AcceptedAnswerId="7266" CreationDate="2013-02-19T08:07:03.807" Score="8" ViewCount="1406" Body="&lt;p&gt;It is said that human eye can see light with wavelength approximately between 400nm and 700nm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these upper and lower bounds same for every human? If not, what are the means and standard deviations of these upper and lower wavelength values for human eyes?&lt;/p&gt;&#xA;" OwnerUserId="989" OwnerDisplayName="hkBattousai" LastEditorUserId="2938" LastEditDate="2013-02-19T11:48:25.253" LastActivityDate="2013-09-04T20:29:54.650" Title="Does every human eye see the same visible spectrum?" Tags="&lt;human-biology&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7264" PostTypeId="2" ParentId="7263" CreationDate="2013-02-19T08:16:40.860" Score="6" Body="&lt;p&gt;Human eyes all use the same optical pigment &lt;a href=&quot;http://en.wikipedia.org/wiki/Photopsin&quot;&gt;photopsin&lt;/a&gt;, so they all have the same basic frequency response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are differences. For example cataracts will change the sensitivity of the eye to colour, and people with colour blindness have various defect to cone cells that affect colour response. However these are secondary effects.&lt;/p&gt;&#xA;" OwnerUserId="3220" OwnerDisplayName="John Rennie" LastActivityDate="2013-02-19T08:16:40.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7265" PostTypeId="2" ParentId="7228" CreationDate="2013-02-19T09:04:57.147" Score="2" Body="&lt;p&gt;Ovalbumin is frequently used in immunology to induce an immune response (see some publications about mice and ovalbumin &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=%28ovalbumin%5BTitle%5D%29%20AND%20mice%5BTitle%5D&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&#xA;You usually inject it together with an adjuvans to enhance the reaction. The factors that must be taken into account for its maintainance are the same as for the other antigens, so you should boost this &quot;vaccination&quot; from time to time.&lt;/p&gt;&#xA;" OwnerUserId="3119" LastActivityDate="2013-02-19T09:04:57.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7266" PostTypeId="2" ParentId="7263" CreationDate="2013-02-19T09:15:47.123" Score="5" Body="&lt;p&gt;Basically every human sees the same spectrum as we all have the same four types of photoreceptors: rods and a cone for green, red, and one for blue light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In very rare cases there are women who have a duplication of one of their cone genes (usually the red one). If one of those duplicates mutates slightly, this results in a kind of fourth type of cone (see it mentioned here at &lt;a href=&quot;http://en.wikipedia.org/wiki/Colour_vision#Cone_cells_in_the_human_eye&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;), so they see a different spectrum.&lt;/p&gt;&#xA;" OwnerUserId="3119" LastEditorUserId="3119" LastEditDate="2013-09-04T20:29:54.650" LastActivityDate="2013-09-04T20:29:54.650" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7267" PostTypeId="1" AcceptedAnswerId="7278" CreationDate="2013-02-19T09:16:19.597" Score="14" ViewCount="20069" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Males do not show meiotic recombination, facilitating genetic studies.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For a while I have known that this phenomenon occurs, this quote comes from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Drosophila_melanogaster&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia page on &lt;em&gt;Drosophila melanogaster&lt;/em&gt;&lt;/a&gt;, and I frequently use this feature of &lt;em&gt;Drosophila&lt;/em&gt; in constructing hemiclones for my own research in quantitative genetics. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, until now, I have never asked &lt;strong&gt;&lt;em&gt;why&lt;/em&gt;&lt;/strong&gt; doesn't recombination happen? Why would this feature evolve? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further, why is the absence of recombination sex-limited to males, why do females have recombination?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-30T10:16:02.273" LastActivityDate="2017-07-16T21:44:46.077" Title="Why doesn't recombination occur in male Drosophila?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;meiosis&gt;&lt;drosophila&gt;&lt;recombination&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7268" PostTypeId="2" ParentId="7208" CreationDate="2013-02-19T09:20:07.417" Score="3" Body="&lt;p&gt;There is also &lt;a href=&quot;http://www.protocol-online.org/&quot; rel=&quot;nofollow&quot;&gt;protocol online&lt;/a&gt;, but without tags, only sorted by category. It could nevertheless be interesting.&lt;/p&gt;&#xA;" OwnerUserId="3119" LastActivityDate="2013-02-19T09:20:07.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7269" PostTypeId="1" AcceptedAnswerId="7272" CreationDate="2013-02-19T11:27:55.053" Score="7" ViewCount="1545" Body="&lt;p&gt;I'm reading the papers linked below and all three of them mention a 20% cut-off for buried/exposed residues, by calculating a relative solvent accessibility (RSA) value.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand how the RSA is calculated, by dividing the calculated solvent accessibility against its total solvent accessibility values from paper 4 table 2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RSA = calculated/total&lt;/p&gt;&#xA;&#xA;&lt;p&gt;e.g. if arginine is calculated to have a solvent accessibility of 55.43 and its total solvent accessibility is 241 then the RSA = 55.43/241 = 23%, so this arginine is considered exposed (see statement 1 below). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What leaves me confused is the definition or lack of the 20% method for defining an exposed or buried residue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am assuming it means one of the following:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;If an amino acids RSA is below 20% it is buried and above 20% it is exposed. So for an amino acid with an RSA of 21% is considered exposed, this value seems a little low for me. I think statement 2 would make for sense.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If an amino acids RSA is below 20% it is buried and above 80% it is exposed. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Which statement if any is correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1142490/&quot;&gt;Paper 1&lt;/a&gt; - see methods section first paragraph&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://biomine.ece.ualberta.ca/papers/PROTEINS-FlexibilitySolventAccessibility.pdf&quot;&gt;Paper 2&lt;/a&gt; - see figure 5 and table 3&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://crpit.com/abstracts/CRPITV29Chen.html&quot;&gt;Paper 3&lt;/a&gt; - see abstract and dataset&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0022283687900386&quot;&gt;Paper 4&lt;/a&gt; - see table 2 for total values&lt;/p&gt;&#xA;" OwnerUserId="158" LastActivityDate="2015-05-09T12:13:01.887" Title="Solvent Accessibility, the 20% cut-off method" Tags="&lt;proteins&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7270" PostTypeId="2" ParentId="7242" CreationDate="2013-02-19T11:55:45.550" Score="3" Body="&lt;p&gt;Unless you're living on an island! If you're reasonably large but got stuck on an island for a long time, you will get smaller. This phenomenon (which also goes the other way - if you're small you tend to get bigger if stuck on an island) is called insular dwarfism: &lt;a href=&quot;http://en.wikipedia.org/wiki/Island_dwarfism&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Island_dwarfism&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="752" LastActivityDate="2013-02-19T11:55:45.550" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7272" PostTypeId="2" ParentId="7269" CreationDate="2013-02-19T14:11:45.947" Score="5" Body="&lt;p&gt;Its 1.  Below cutoff, &lt;em&gt;buried&lt;/em&gt;, above cutoff &lt;em&gt;accessible&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Paper 1: &quot;A cutoff of 20% was used to define the two states, buried or exposed. With this definition, the dataset was, roughly, evenly split between the &lt;em&gt;two states&lt;/em&gt;.&quot;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Only two states are possible: solvent accessible and buried.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Paper 2: &quot;A given residue is defined as exposed (e) &lt;em&gt;if its RSA is larger than the cutoff&#xA;value, and otherwise it is defined as buried&lt;/em&gt; (b).&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abstract for Paper 3: a cutoff of 20% for &lt;em&gt;two-state&lt;/em&gt; definition of solvent accessibility.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it were def #2 it would be a three state definition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Paper 4: &quot;On average, 15% of residues in small proteins and 32% in larger ones may be classed as “buried residues”, having less than 5% of their surface accessible to the solvent...&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This paper, by the dean of structural analysis Cyrus Chothia, uses a 5% cutoff, not 20%...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The abstract goes on to say... &quot;The accessibilities of most other residues are evenly distributed in the range 5 to 50%.&quot;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This passage hints that SA doesn't even go up to 80%.  Just considering that you often won't get more than say 60% with this calculation.  I'm just guessing; but the thought being that unless you are at a terminus of the protein, which is often disordered and doesn't show up in a crystal structure, you will have two adjoining amino acids for each residue - just the solvent accesible area taken up by the contact with neighbors could easily be 20% of total.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-02-20T17:48:25.203" LastActivityDate="2013-02-20T17:48:25.203" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7273" PostTypeId="2" ParentId="2776" CreationDate="2013-02-19T14:13:38.777" Score="7" Body="&lt;p&gt;The Aquatic Ape theory has never gained wide acceptance. This is because it has never had strong evidential support.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The features supposedly supporting the hypothesis only do so under an extremely superficial analysis (e.g. the argument for bipedalism), frequently actually occur in other non-aquatic mammals (e.g. hairlessness in naked mole rats and rhinos, a descended larynx in red deer), show no sign of having arisen at similar times in the human evolutionary record (e.g. encephalisation evolved far later than bipedalism and bipedalism vastly predates hairlessness) and lack fossil evidence of having evolved near aquatic environments.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-02-19T14:13:38.777" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7275" PostTypeId="2" ParentId="7208" CreationDate="2013-02-19T15:09:17.847" Score="3" Body="&lt;p&gt;My personal favourite is &lt;a href=&quot;http://openwetware.org/&quot; rel=&quot;nofollow&quot;&gt;OpenWetWare&lt;/a&gt;. Think wikipedia for scientific protocols and an open access lab notebook.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's a problem with this things. Despite the common stereotype of scientist being open and good at sharing, my experience is the opposite. Many laboratories are not good at all in sharing their techniques/secrets. They will share the basic stuff that you can find online, no problem, but that's about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Seems they're afraid that everyone's else after them, trying to scoop them. I have suggested OpenWetWare to some other labs and they refused for that same reason. Even though some will use it to find protocols, they don't see a reason to share back.&lt;/p&gt;&#xA;" OwnerUserId="1303" LastActivityDate="2013-02-19T15:09:17.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7276" PostTypeId="2" ParentId="7267" CreationDate="2013-02-19T16:17:50.060" Score="4" Body="&lt;p&gt;To the best of my knowledge there is no strong evidence as to the reason why. The most reasonable explanation seems to be that it evolved as a crude mechanism for preventing recombination of the male sex-chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might then ask why a mechanism targeted to the sex-chromosome specifically (as in humans) did not evolve to which I'd suggest that evolution frequently continues with &quot;good enough&quot; solutions where the benefits of apparently better solutions are small or don't involve incremental benefits and note that there is some evidence that lower rates of recombination are beneficial in Drosophila (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1439-0469.1986.tb00628.x/abstract&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;]).&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-02-19T16:17:50.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7278" PostTypeId="2" ParentId="7267" CreationDate="2013-02-19T19:21:19.977" Score="12" Body="&lt;p&gt;This is a venerable fact.  &lt;a href=&quot;http://www.pnas.org/content/68/2/268.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Exceptions in &lt;em&gt;D. melanogaster&lt;/em&gt; strain Y-007 have been observed&lt;/a&gt; and &lt;em&gt;D. ananassae&lt;/em&gt; has consistent male cross-overs, but this work dates back to the 1970s.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/12225662&quot; rel=&quot;nofollow noreferrer&quot;&gt;Current Biology 2002 paper&lt;/a&gt; is not exactly new, but sheds some light on the issue in question. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In male &lt;em&gt;Drosophila melanogaster&lt;/em&gt;, meiosis occurs in the absence of recombination or a recognizable synaptonemal complex (SC). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors used a GFP-lac fusion to observe a series of sections of the male fly in meiosis with integrated lac - specific binding regions.  They see for the most part that the GFP bound segments of the DNA are not associated in cell division.  That is, homologous chromosomes physically associate during meiosis (via the SC) and in male drosophila, they do not.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems from &lt;a href=&quot;http://link.springer.com/article/10.1007/s00412-011-0314-0?LI=true&quot; rel=&quot;nofollow noreferrer&quot;&gt;more recent work&lt;/a&gt;, that the details of how this work is still being worked out but several gene regions and factors have been identified.  Suspected factors that help conspire to align the various homologous chromosomes are being looked into.  Take a look at the P.I.s &lt;a href=&quot;http://web.bio.utk.edu/bcmb/faculty/individual_faculty_pages/mckee_bruce/mckee_bruce.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;biblio&lt;/a&gt; for more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This isn't my main field, but as I understand it, many aspects of meiosis are still being mapped out.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the question of &lt;em&gt;how this evolved and why&lt;/em&gt;; its definitely strange. &#xA; It looks like there is a gender selected trait where the SC doesn't form in males.  Its easy to imagine a mutation that caused males only to lose recombination - the process is so complex its hard to imagine such a trait not showing up. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still it's surprising to think that the trait has not only survived but become dominant in &lt;em&gt;Drosophila&lt;/em&gt; all over the world.  To be a common traits to so many &lt;em&gt;Drosophila&lt;/em&gt; species, it must have happened more than 10 million years ago.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_sexual_reproduction#Deleterious_mutation_clearance&quot; rel=&quot;nofollow noreferrer&quot;&gt;Explanations of the advantages of sexual reproduction often include recombination&lt;/a&gt;.  Even the human Y chromosome has a &lt;a href=&quot;http://www.nature.com/nrg/journal/v4/n8/box/nrg1124_BX2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;self-recombination mechanism&lt;/a&gt; that reduces error in the coding regions.  As such, its hard to believe that this is not a huge disadvantage for the flies.  Still, if if it were such a big deal, you'd imagine Y-007 would have dominated and re-introduced the trait.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only theory I can think of might be called 'lazy males'; that the males got the females to do one more thing for the offspring and it somehow outcompetes the sperm of the recombining males.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Semen_analysis#Motility&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lots of sperm are non-motile&lt;/a&gt;; that's a fact for humans, I have no idea what its like for flies that recombine.  Take a look at the variance in morphology as well - sperm are really crazy ugly sometimes and a good deal of the mating process is to help weed out the defective ones.  Without recombination, might it be that males produce viable sperm at a greater rate, helping them in &lt;a href=&quot;http://en.wikipedia.org/wiki/Sperm_competition&quot; rel=&quot;nofollow noreferrer&quot;&gt;sperm competition&lt;/a&gt;, which I'm sure is the case for fly mating - Drosophila are not monogamous too I'd guess?  Anyway that's not a researched idea, just a guess on my part. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2017-07-16T21:44:46.077" LastActivityDate="2017-07-16T21:44:46.077" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7279" PostTypeId="1" CreationDate="2013-02-19T22:07:18.470" Score="6" ViewCount="6425" Body="&lt;p&gt;After my most recent RNA extraction, the RNA samples had very high 260/230 absorbance ratios, (ranging from 5 to 25). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've never gotten numbers like this and I know the ratio is supposed to be ~2 in general.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What could be the reason for such a high 260/230 absorbance?&lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2014-01-30T11:07:51.983" Title="Very high 260/230 absorbance ratio of an RNA sample" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;rna&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7280" PostTypeId="2" ParentId="7279" CreationDate="2013-02-19T22:57:54.397" Score="1" Body="&lt;p&gt;The 260/230 ratio gives you idea about the contaminants in your sample. Guanidine isothiocyanate, which is usually used for RNA isolation, absorbs at 230nm, so that might be what you see. But another explanation might be that your sample is very dilute (how much RNA did you get?), so that your A260 is also very low. Then it would be difficult to accurately measure A230, which will result in overestimated 260/230 ratios. &lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2013-02-19T22:57:54.397" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7281" PostTypeId="1" CreationDate="2013-02-20T01:42:26.247" Score="17" ViewCount="1584" Body="&lt;p&gt;There are examples of mathematics in nature such as Fibonacci number, fractals, etc.  Are there examples of encrypted information?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I am looking for is a pattern that seems random on the surface, but once you put it through a &quot;decryption&quot; process, it is actually something else.  Not patterns that seem random because they are complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One example that comes close is DNA.  But I see DNA as a form of &lt;em&gt;encoding&lt;/em&gt;, not &lt;em&gt;encryption&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3122" LastEditorUserId="9943" LastEditDate="2015-11-23T10:22:44.580" LastActivityDate="2018-10-27T15:00:05.347" Title="Are there examples of encryption in nature?" Tags="&lt;bioinformatics&gt;" AnswerCount="8" CommentCount="7" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7282" PostTypeId="2" ParentId="7142" CreationDate="2013-02-20T01:52:20.513" Score="0" Body="&lt;p&gt;Thanks! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was thinking along the following lines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) Write down the cable equations for neurons within a network, given: anatomical layout of the network, spatial distribution of dendrites, spines, synapses, and synaptic strengths (forward model).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) Acquire joint microscopy + electrophysiology dataset.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3) Invert the forward model with synaptic strengths as free parameters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(4) Track these inferred parameters over time or compare them between conditions.&lt;/p&gt;&#xA;" OwnerUserId="3057" LastActivityDate="2013-02-20T01:52:20.513" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7283" PostTypeId="2" ParentId="7281" CreationDate="2013-02-20T02:02:41.900" Score="8" Body="&lt;p&gt;One example is in the development of the immune system. V(D)J recombination, antibody production, and T-cell receptor production generates a specific &quot;key&quot; that, in most cases, can only be bypassed by that individual's molecular inventory. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In that sense, parasites, mutualists, and commensalists could be viewed as black, white, and grey hat hackers, respectively. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example is the organism-specific tRNA synthase inventory and the matching tRNAs. &lt;/p&gt;&#xA;" OwnerUserId="3061" LastActivityDate="2013-02-20T02:02:41.900" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7284" PostTypeId="2" ParentId="7281" CreationDate="2013-02-20T09:26:06.520" Score="2" Body="&lt;p&gt;Perhaps protein folding is an example of decryption? From a single primary sequence (i.e. the string of amino acids), it is impossible to guess the function of a protein. The folded protein is the functional unit (of course it might be further modified). &lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2013-02-20T09:26:06.520" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7286" PostTypeId="1" CreationDate="2013-02-20T12:11:29.037" Score="3" ViewCount="2694" Body="&lt;p&gt;I am working with a network object where the nodes are different events in molecular biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically;&#xA;Catalytic activity of X,&#xA;RNA expression of X,&#xA;GTP-bound activity of X,&#xA;Kinase activity of X,&#xA;Oxidoreductase activity of X,&#xA;Phosphatase axtivity of X,&#xA;Transcriptional activity of X,&#xA;Phosphorylation at residue Y.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the difference between RNA expression and Transcriptional activity? And which is the one that an Affymetrix microarray is measuring?&#xA;eg.;&#xA;transcriptional activity of KLF2, transcriptional activity of ATF2 RNA expression of HSPA1A RNA, and expression of CYP1B1&lt;/p&gt;&#xA;" OwnerUserId="3124" LastActivityDate="2013-02-20T14:46:36.460" Title="Difference between &quot;transcriptional activity&quot; and &quot;RNA expression&quot;" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;systems-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7287" PostTypeId="2" ParentId="7281" CreationDate="2013-02-20T13:39:03.587" Score="2" Body="&lt;p&gt;I would think that the Bacteria - Phage restriction enzyme and methylation enzyme race could be thought of as a form of encryption. If your DNA isn't &quot;signed&quot; with the appropriate methylation patterns then it gets chopped into pieces and destroyed. This is the signing/verifying side of encryption rather then the encrypt/decrypt side, however.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Restriction_modification_system&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Restriction_modification_system&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1300" LastActivityDate="2013-02-20T13:39:03.587" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7288" PostTypeId="1" CreationDate="2013-02-20T14:12:27.980" Score="3" ViewCount="111" Body="&lt;p&gt;I know that the human body can synthesise vitamin D from cholesterol, but can it do so from phytosterols?&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-20T15:38:57.723" LastActivityDate="2013-02-20T15:38:57.723" Title="Can the Human body Synthesise Vitamin D from Phytosterols?" Tags="&lt;vitamins&gt;&lt;biosynthesis&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7289" PostTypeId="2" ParentId="7286" CreationDate="2013-02-20T14:46:36.460" Score="4" Body="&lt;p&gt;In your case, RNA expression and transcriptional activity probably differ in the stage of processing. Transcriptional activity refers to the binding and processive activity of RNA polymerase. There are different ways to measure this experimentally, but with a microarray you are measuring the amount of actual transcripts relative to the control array.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RNA expression usually refers to the amount of mature transcripts but is often used interchangeably with transcriptional activity. The distinction is made at the sample extraction stage and whether or not the RNA was selectively recovered using poly-A selection or other methods that isolate mature transcripts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What your microarray will measure depends on the probe library constructed on the array and whether you are applying total RNA or selective RNA. Probes matching mature transcripts report for RNA expression. Probes matching immature or nascent transcripts can be used to measure transcriptional activity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Careful probe design is required to distinguish between the different levels of processing.   &lt;/p&gt;&#xA;" OwnerUserId="3061" LastActivityDate="2013-02-20T14:46:36.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7290" PostTypeId="1" AcceptedAnswerId="7295" CreationDate="2013-02-20T17:51:51.650" Score="6" ViewCount="398" Body="&lt;p&gt;I've heard about services like 23andme, which offer genetic testing to the general public. As a person who knows very little about genetics, I'm interested in the subject and would like to know what the modern &quot;commercial grade&quot; genotyping really does.  &lt;strong&gt;What are the limitations of commercial-grade &quot;genotyping&quot;?&lt;/strong&gt;  From what I've been reading, they test DNA against ~100 different markers, but do not really sequence it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I understand correctly, if DNA is sequenced, genetic markers and genes can be identified in it, including the newly discovered ones. However, (if I understand correctly) if DNA is genotyped, the genotyping is a one shot operation which states if some genetics markers are present in the DNA. To test against newly discovered markers, it would have to be genotyped again, right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for any clarifications!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-02-21T15:21:18.177" Title="What are the limitations of commercial-grade DNA genotyping compared to full sequencing?" Tags="&lt;human-biology&gt;&lt;dna&gt;&lt;dna-sequencing&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7291" PostTypeId="2" ParentId="7209" CreationDate="2013-02-20T19:01:17.460" Score="2" Body="&lt;p&gt;First question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, topoisomerases are enzymes that relieve supercoiling in DNA strands and tangling in chromosomes. Type II topoisomerases is special among eukaryotic topoisomerases, considering they use divalent metal ions and ATP hydrolysis in their active site. The enzyme cuts both strands of the DNA helix simultaneously (double strand break) in order to manage DNA tangles and supercoils. It changes the linking number of circular DNA by ±2. After the ends are cut, the ends of the DNA are separated and a second DNA duplex is passed through the break. The cut DNA is re- ligated. This allows the enzyme to increase or decrease the linking number of a DNA loop by 2 units. Inhibiting enzyme-mediated DNA ligation means that it prevents the enzyme to re-ligate the DNA strand after it is cut. In other words, the prevention of a phosphodeister bond between nucleotides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In normal cells, DNA topoisomerase II plays several vital roles, mainly to relieve DNA tangles and coiling. This is done by generating &quot;transient double strand breaks&quot; in the DNA strand, which can sometimes cause harmful translocations and damage. Damage of this type is linked to certain specific types of leukemia. This intrinsically &quot;harmful&quot; quality of DNA topoisomerase II can be exploited in cancer cells due to their high replication rate . Certain cancer drugs, such as etoposide, act by altering the active site of topoisomerase II, preventing (inhibiting) the enzyme from ligating cleaved DNA molecules, causing permanent DNA breaks (and inhibiting replication). The fast replication rate of cancer cells ensures that there are large amounts of the enzyme present in the cell, increasing the effectiveness of any Topoisomerase II poisons. However, this drug can also act against some other types of tissues with large amounts of Topoisomerase II, such as cardiac tissue. Also, cancer cells are constantly in a growing/replication cycle, so they exhibit large amounts of the isoform Topoisomerase IIa, the type that is most likely to produce permanent and detrimental DNA breaks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647315/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647315/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1865" LastEditorUserId="1865" LastEditDate="2013-02-21T02:36:21.610" LastActivityDate="2013-02-21T02:36:21.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7292" PostTypeId="1" CreationDate="2013-02-20T21:48:52.643" Score="1" ViewCount="204" Body="&lt;p&gt;What species of bird is depicted on this coin?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OxgXm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.artic.edu/aic/collections/citi/images/standard/WebLarge/WebImg_000100/139651_846511.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.artic.edu/aic/collections/citi/images/standard/WebLarge/WebImg_000100/139651_846511.jpg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance for your help!&lt;/p&gt;&#xA;" OwnerUserId="3125" LastEditorUserId="107" LastEditDate="2013-02-20T22:21:20.483" LastActivityDate="2019-02-06T05:10:45.813" Title="What species of bird is on this coin?" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2013-02-21T01:17:03.703" ContentLicense="CC BY-SA 3.0" />
  <row Id="7293" PostTypeId="2" ParentId="7292" CreationDate="2013-02-21T01:12:14.097" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://www.wildwinds.com/coins/greece/egypt/ptolemy_V/i.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;It said to be an eagle&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It looks like a Ptolemy V (204–181 BC): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bonanza.com/listings/-DD-G-068-Ptolomy-V-Octadrachm-COPY/16293418?gpid=21297750541&amp;amp;gpkwd=&amp;amp;goog_pla=1&amp;amp;gclid=CMWBpbOaxrUCFYx_Qgod6TsA9w&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.bonanza.com/listings/-DD-G-068-Ptolomy-V-Octadrachm-COPY/16293418?gpid=21297750541&amp;amp;gpkwd=&amp;amp;goog_pla=1&amp;amp;gclid=CMWBpbOaxrUCFYx_Qgod6TsA9w&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;it looks to be a pretty standard motif of that era:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0cFWK.jpg&quot; alt=&quot;Alexander III Great 336 BC Greek Coin&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From: &lt;a href=&quot;http://www.worthpoint.com/worthopedia/alexander-iii-great-336bc-greek-coin-150614256&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.worthpoint.com/worthopedia/alexander-iii-great-336bc-greek-coin-150614256&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I agree that this is not really a biology question.. but what the hey. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2019-02-06T05:10:45.813" LastActivityDate="2019-02-06T05:10:45.813" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="7294" PostTypeId="1" CreationDate="2013-02-21T01:44:12.740" Score="-1" ViewCount="214" Body="&lt;p&gt;What proportion of men who go through their whole lives and never find a mate at all, and what proportion of women do? And is the proportion of men greater than the proportion of women?&lt;/p&gt;&#xA;" OwnerUserId="3094" LastActivityDate="2013-02-22T19:04:09.770" Title="Do women have greater reproductive success than men?" Tags="&lt;psychology&gt;&lt;sexual-selection&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2013-02-23T00:34:05.867" ContentLicense="CC BY-SA 3.0" />
  <row Id="7295" PostTypeId="2" ParentId="7290" CreationDate="2013-02-21T01:50:05.017" Score="3" Body="&lt;p&gt;23andme briefly describes the technology they use &lt;a href=&quot;https://www.23andme.com/more/genotyping/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. They are testing the genotype of your DNA at roughly 1 million locations. The technology they use to do this is known as a &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_microarray&quot; rel=&quot;nofollow&quot;&gt;microarray&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The limitations of using a microarray, as compared to sequencing, is that you will only find what you are looking for -- people often describe the disadvantages of microarrays as compared to sequencing with &lt;a href=&quot;http://en.wikipedia.org/wiki/Streetlight_effect&quot; rel=&quot;nofollow&quot;&gt;the streetlight effect/metaphor&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Arrays can only measure regions of the genome that they were designed to probe. Technically, if they probe 1,000,000 million locations, and the human genome is roughly 3.4 billion bases ... you can do the math.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practice, SNPs tell you a bit more about just the nucleotide being interrogated, due to &lt;a href=&quot;http://en.wikipedia.org/wiki/Linkage_disequilibrium&quot; rel=&quot;nofollow&quot;&gt;linkage disequilibrium&lt;/a&gt; (cf. &lt;a href=&quot;http://en.wikipedia.org/wiki/Tag_SNP&quot; rel=&quot;nofollow&quot;&gt;tag/proxy SNPs&lt;/a&gt;), so the array might tell you more than you expect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, modulo sequencing errors, whole genome sequencing will tell you &quot;everything&quot; as far as recovering the NTs that make up your genome, but how much information that will provide you is another thing altogether (for now, that is).&lt;/p&gt;&#xA;" OwnerUserId="192" LastEditorUserId="192" LastEditDate="2013-02-21T15:21:18.177" LastActivityDate="2013-02-21T15:21:18.177" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7296" PostTypeId="2" ParentId="6812" CreationDate="2013-02-21T03:57:46.443" Score="2" Body="&lt;p&gt;I searched a bit and could not find any such format, but I am not a specialist in taxonomy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I understand, the structure you want is that of either a tree or a DAG (Directed Acyclic Graph). Both are straightforward to store in a variety of formats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One possibility is to use a format similar to other biological data that has a similar data structure. For example, Gene Ontology is a widely used dataset that has the structure of a DAG and has a number of formats including XML listing the parents and additional data of each node in the graph. See &lt;a href=&quot;http://www.geneontology.org/GO.format.shtml&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for their formats.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2013-02-21T03:57:46.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7297" PostTypeId="2" ParentId="7290" CreationDate="2013-02-21T04:16:57.577" Score="2" Body="&lt;p&gt;I want to give the OP a slight variation on Steve's answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important to note that most of the genome is the same between different people. That isn't surprising, since we belong to the same species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, it is estimated that there are about 10,000,000 SNPs (single basepair positions that may vary) in the human genome. So if you check 1,000,000 SNPs with a microarray (genotyping), you are covering ~10% of the possible differences. In addition, variation in some of the SNPs is very common while others are very rare, so if you check the most common 1,000,000 SNPs with a microarray, you might actually cover a very large portion of the differences. It is also possible that if you know in advance some general information about the person you are testing, such as ethnicity, you might be able to eliminate many uninformative SNPs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This of course only refers to variation in SNPs (but these are the most common variations).&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2013-02-21T04:16:57.577" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7298" PostTypeId="2" ParentId="7290" CreationDate="2013-02-21T04:47:01.880" Score="3" Body="&lt;p&gt;Just to be transparent, I work at a microarray company, but I've also attended high throughput sequencing workshops.  I think this is a pretty fair assessment, but leave me a comment if you see anything out of line...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As pointed out by @SteveLianoglou, Genotyping microarrays are best for revealing whether a particular variant (not only SNPs but short insertions and deletions, copy number variations (CNVs) reliably and cheaply.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;High Throughput DNA Sequencing has made great strides and the latest cost estimates are in the few thousands of dollars for a full human genome.  This is better for discovering new variants but currently its not a great way to do do say a medical test to see if you have a particular mutation.  The problem with sequencing right now is that &lt;a href=&quot;http://genomebiology.com/2009/10/3/R32&quot; rel=&quot;nofollow&quot;&gt;sequencers have systematic biases&lt;/a&gt; - the local sequence can give the same error over and over again.  It takes some significant effort to differentiate the error from the real variant data.  In the workshop I attended, the data consisted of &lt;a href=&quot;http://www.camda.info/&quot; rel=&quot;nofollow&quot;&gt;38 full human genomes at 30-40x coverage&lt;/a&gt;. Despite this deep level of sequencing, systematic errors were still obvious (the proceedings are in press now - reference should show up at the link provided soon).  So it can be fairly expensive when you have done all your data analysis and validation data to get the variants via sequencing.  All this could change very quickly, but I think this is accurate in the current state of things. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-02-21T04:47:01.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7299" PostTypeId="1" AcceptedAnswerId="7300" CreationDate="2013-02-21T13:36:25.810" Score="2" ViewCount="80" Body="&lt;p&gt;I am trying to use the DAVID tool to do some gene analysis. I have some probe set intensities for some cancer cell lines. I found this link in the DAVID tool &lt;a href=&quot;http://david.abcc.ncifcrf.gov/tools.jsp&quot; rel=&quot;nofollow&quot;&gt;http://david.abcc.ncifcrf.gov/tools.jsp&lt;/a&gt;. I am a bit confused with the terminology introduced here. It says gene list for the probe sets why is it so? I mean in the example you can see the probe sets like&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1007_s_at&#xA;1053_at&#xA;117_at&#xA;121_at&#xA;1255_g_at&#xA;1294_at&#xA;1316_at&#xA;1320_at&#xA;1405_i_at&#xA;1431_at&#xA;1438_at&#xA;1487_at&#xA;1494_f_at&#xA;1598_g_at&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Buy why are they called gene list not probe sets. Why?&lt;/p&gt;&#xA;" OwnerUserId="3074" LastEditorUserId="112" LastEditDate="2013-02-22T09:02:05.197" LastActivityDate="2013-02-22T09:02:05.197" Title="Confusion related to the DAVID tool" Tags="&lt;bioinformatics&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7300" PostTypeId="2" ParentId="7299" CreationDate="2013-02-21T14:59:26.473" Score="2" Body="&lt;p&gt;Its a bit confusing, but DAVID uses the term Gene List as a generic term.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at Step 2, you can submit many kinds of lists to DAVID, including actual gene symbols, Ensembl or RefSeq Accessions, etc... actually nearly 30 kinds of terms including 'not sure' which probably looks at your list and tries to guess.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Affymetrix or Illumina probe set IDs are each designed to measure a gene, ideally, though its not precisely a one Probe Set to one Gene relationship.  This is because when the array is designed there may be a partial transcript RNA records which turn out later to be parts of a single gene.  There are also probe sets which may turn out to hybridize to similar sequences in more than one gene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its messy, but its also true that often more than one gene symbol will appear for the same gene because of historical naming conventions...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-02-21T14:59:26.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7301" PostTypeId="2" ParentId="1136" CreationDate="2013-02-21T16:50:04.460" Score="3" Body="&lt;p&gt;I think &lt;strong&gt;&quot;tool use&quot;&lt;/strong&gt; could serve as a good term on it's own, don't you think?&lt;/p&gt;&#xA;" OwnerUserId="1224" LastActivityDate="2013-02-21T16:50:04.460" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7302" PostTypeId="1" AcceptedAnswerId="7303" CreationDate="2013-02-21T17:03:44.323" Score="34" ViewCount="2783" Body="&lt;p&gt;Plants and animals have the following distinct properties: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Plants live from solar energy by &lt;a href=&quot;http://en.wikipedia.org/wiki/Photosynthesis&quot; rel=&quot;noreferrer&quot;&gt;photosynthesis&lt;/a&gt;, they use solar energy to make sugar and oxygen out of carbon dioxide, which gives them energy. Animals live from the sugar and oxygen plants created and produce carbon dioxide for their energy.&lt;/li&gt;&#xA;&lt;li&gt;Animals can move across the planet while plants are tied to the ground.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Clearly, animals have a harder time to survive with no plants within their reach than plants have without animals coming close. This is logical because solar energy is always there while plants are not.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is: &lt;strong&gt;Are there animals that can do photosynthesis?&lt;/strong&gt; It's obvious that an animal with plant-like stateliness would be non-beneficial since it relies on eating other plants for it's energy and there may not always be plants within reach from it's spot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But &lt;em&gt;animals using the sun and carbon dioxide for energy production does not sound so stupid.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Night animals could also gather energy in their sleep.&lt;/li&gt;&#xA;&lt;li&gt;Much easier than plants, animals could make sure nothing blocks their sunlight.&lt;/li&gt;&#xA;&lt;li&gt;Many animals go through periods of hunger because food is scarce, for some of them this period is paired with high sunlight levels. (the dry season f.e.) (EDIT: This is just an idea, of course photosynthesis requires water, which is absent in the &lt;em&gt;dry season&lt;/em&gt;. But still, in warm period with enough water, there's sometimes too much animals to feed from the available vegeation.)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Some things I already took into consideration:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I know that plants, because they are small in mass (compared to the area with which they can collect sunlight) and static, don't need nearly as much energy as animals do. Is this the main reason?&lt;/li&gt;&#xA;&lt;li&gt;I know that f.e. reptiles, but in fact all cold-blooded animals, already use the sun's energy. But they only use the heat from the sun to warm their bodies, they don't photosynthesize.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1224" LastEditorUserId="46609" LastEditDate="2019-12-24T00:46:38.670" LastActivityDate="2019-12-24T00:46:38.670" Title="Can any animals photosynthesize?" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;zoology&gt;&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="6" ContentLicense="CC BY-SA 4.0" />
  <row Id="7303" PostTypeId="2" ParentId="7302" CreationDate="2013-02-21T17:11:02.347" Score="39" Body="&lt;p&gt;There are 5 answers, all &amp;quot;yes&amp;quot; (though the first one is disputable).&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;First: there exists at least one &lt;strong&gt;animal which &lt;a href=&quot;http://www.livescience.com/6030-surprising-sea-slug-plant-animal.html&quot; rel=&quot;noreferrer&quot;&gt;can produce its own chlorophyll&lt;/a&gt;&lt;/strong&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;A green sea slug appears to be part animal, part plant. It's the first critter discovered to produce the plant pigment chlorophyll.&lt;/p&gt;&#xA;&lt;p&gt;The sea slugs live in salt marshes in New England and Canada. In addition to burglarizing the genes needed to make the green pigment chlorophyll, the slugs also steal tiny cell parts called chloroplasts, which they use to conduct photosynthesis. The chloroplasts use the chlorophyl to convert sunlight into energy, just as plants do, eliminating the need to eat food to gain energy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The slug in the article appears to be &lt;a href=&quot;http://en.wikipedia.org/wiki/Elysia_chlorotica&quot; rel=&quot;noreferrer&quot;&gt;Elysia chlorotica&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Elysia chlorotica is one of the &amp;quot;solar-powered sea slugs&amp;quot;, utilizing solar energy via chloroplasts from its algal food. It lives in a subcellular endosymbiotic relationship with chloroplasts of the marine heterokont alga Vaucheria litorea.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;&lt;/em&gt;: As per @Teige's comment, this finding is somewhat disputable.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Second, animals need not produce their own Chlorophyll, and instead symbiotically host organisms that use Photosynthetis - e.g.  algae and cyanobacteria. This approach is called &lt;a href=&quot;http://jxb.oxfordjournals.org/content/59/5/1069&quot; rel=&quot;noreferrer&quot;&gt;&lt;strong&gt;Photosynthetic symbioses&lt;/strong&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Overall, 27 (49%) of the 55 eukaryotic groups identified by Baldauf (2003) have representatives which possess photosynthetic symbionts or their derivatives, the plastids. These include the three major groups of multicellular eukaryotes: the plants, which are derivatives of the most ancient symbiosis between eukaryotes and cyanobacteria; the fungi, many of which are lichenized with algae or cyanobacteria; and the animals. We, the authors, and probably many readers were taught that animals do not photosynthesize. This statement is true in the sense that the lineage giving rise to animals did not possess plastids, but false in the wider sense: many animals photosynthesize through symbiosis with algae or cyanobacteria.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Please note that while most organisms known for this are fungi, and some rare invertebrates (corals, clams, jellyfish, sponges, sea anemones), there is at least one example of vertebrate like this - &lt;a href=&quot;http://www.mnn.com/earth-matters/animals/stories/salamander-is-worlds-first-photosynthetic-vertebrate&quot; rel=&quot;noreferrer&quot;&gt;spotted salamander&lt;/a&gt; (Ambystoma maculatum)&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Non-chlorophyll synthesis&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;A 2010 &lt;a href=&quot;http://en.wikipedia.org/wiki/Photosynthesis#cite_note-40&quot; rel=&quot;noreferrer&quot;&gt;study&lt;/a&gt; by researchers at Tel Aviv University discovered that the Oriental hornet (Vespa orientalis) converts sunlight into electric power using a pigment called &lt;strong&gt;xanthopterin&lt;/strong&gt;. This is the first scientific evidence of a member of the animal kingdom engaging in photosynthesis, according to Wikipedia.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Another discovery from 2010 is &lt;a href=&quot;http://www.wired.com/wiredscience/2012/08/green-aphid-photosynthesis/&quot; rel=&quot;noreferrer&quot;&gt;possibly a second piece of evidence&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;University of Arizona biologists researcher Nancy Moran and Tyler Jarvik discovered that pea aphids can make their own carotenoids, like a plant. “What happened is a fungal gene got into an aphid and was copied,” said Moran in a press release.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Their research article is &lt;a href=&quot;http://www.sciencemag.org/content/328/5978/624&quot; rel=&quot;noreferrer&quot;&gt;http://www.sciencemag.org/content/328/5978/624&lt;/a&gt;, and they did not consider it conclusive:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The team warns that more research will be needed before we can be sure that aphids truly have photosynthesis-like abilities.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;hr /&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Third, depending on how you understand &lt;em&gt;Photosynthesis&lt;/em&gt;, &lt;strong&gt;you can include other chemical reactions converting sunlight energy&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;p&gt;If the answer is &amp;quot;usual 6H2O + 6CO2 ----------&amp;gt; C6H12O6+ 6O2 reaction done via chlorophyll&amp;quot;, then see answers #1,#2.&lt;/p&gt;&#xA;&lt;p&gt;But if you simply literally translate the term (synthesizing new molecules using light), then you can ALSO include the process of generating Vitamin D from exposure to sunlight that&#xA;humans do thanks to cholesterol (&lt;a href=&quot;http://dwb.unl.edu/teacher/nsf/c10/c10links/georgia.ncl.ac.uk/VitaminD/VitDBioch.html&quot; rel=&quot;noreferrer&quot;&gt;link&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Non-biological answer.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;As a side bonus, &lt;a href=&quot;http://en.wikipedia.org/wiki/Ophiocordyceps_sinensis&quot; rel=&quot;noreferrer&quot;&gt;Ophiocordyceps sinensis&lt;/a&gt; is referred to as half-animal half-plant (not very scientifically IMHO). But it doesn't do photosynthesis.&lt;/p&gt;&#xA;" OwnerUserId="185" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-19T14:29:53.650" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7304" PostTypeId="1" CreationDate="2013-02-21T18:35:43.103" Score="2" ViewCount="12445" Body="&lt;p&gt;I want to know how is inorganic phosphate able to inhibit alkaline phosphatase.&lt;/p&gt;&#xA;" OwnerUserId="3129" LastEditorUserId="69" LastEditDate="2013-02-22T08:22:03.830" LastActivityDate="2013-04-23T09:06:50.057" Title="How does inorganic phosphate inhibit alkaline phosphatase?" Tags="&lt;bioinorganic-chemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7306" PostTypeId="2" ParentId="7304" CreationDate="2013-02-21T19:22:41.100" Score="1" Body="&lt;p&gt;When alkaline phosphatase dephosphorylates a substrate one of the intermediates in the reaction pathway is a phosphorylated form of the enzyme in which the phosphate from the substrate has been transferred to the enzyme. This phosphate is subsequently lost by hydrolysis. Under certain conditions alkaline phosphatase will actually catalyse a reverse reaction - the addition of inorganic phosphate on to alcohol substrates, and this also proceeds via the phospho-enzyme intermediate, but proceeds in the opposite direction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that phosphate will inhibit the enzyme as a phosphatase via the formation of the phospho-enzyme, thus blocking the active site to substrates for dephosphorylation.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Reaction mechanism of alkaline phosphatase based on crystal structures: Two-metal ion catalysis&#xA;  Kim, EE &amp;amp;  Harold W. Wyckoff, HW 1991 Reaction mechanism of alkaline phosphatase based on crystal structures: Two-metal ion catalysis. J Mol Biol. 218: 449-464&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-02-21T19:50:00.000" LastActivityDate="2013-02-21T19:50:00.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7307" PostTypeId="1" AcceptedAnswerId="7315" CreationDate="2013-02-21T19:39:14.833" Score="10" ViewCount="7941" Body="&lt;p&gt;Plant &lt;a href=&quot;http://en.wikipedia.org/wiki/Grafting&quot;&gt;grafting&lt;/a&gt; is a process whereby a piece of one plant is inserted into another and results in a change of the original plant. For example, grafting a piece of a lemon tree into a bitter orange tree will cause that tree to produce lemons instead of oranges for the rest of its life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this work? I mean, at the genetic level. I guess the grafted plant is now a chimera of some sort but if so&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;How does the grafted DNA affect the host cells?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are all of the host's cells affected?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If we were to sequence the grafted tree which genome would we find?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is it perhaps that the host DNA is not affected at all and the effects come via a change in expression levels? If that is the case I would assume grafting will only work between very closely related species. Is that so?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Basically I know very little about plant genetics and physiology. I remember from my undergraduate days that plant genetics are just plain weird. Most, if not all, have various levels of polyploidy. Is that relevant?&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="3952" LastEditDate="2013-08-01T03:10:56.857" LastActivityDate="2015-12-09T09:42:51.347" Title="How does plant grafting work?" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;plant-physiology&gt;&lt;chimerism&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7308" PostTypeId="1" CreationDate="2013-02-21T21:43:42.507" Score="2" ViewCount="10071" Body="&lt;p&gt;As we all should know, abiogenesis and spontaneous generation are far from identical. For one, spontaneous generation was disproven with Pasteur, and abiogenesis seems to be a solid scientific theory. However, one can loosely summarize both as &quot;the emergence of life from non-living materials&quot; which, &lt;em&gt;at the very least&lt;/em&gt;, is confusing for the layman.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: &lt;strong&gt;What truly differentiates abiogenesis from spontaneous generation?&lt;/strong&gt; For example, if abiogenesis were to happen again, how would we differentiate the two terms? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is &lt;em&gt;time&lt;/em&gt; the most contributing factor (abiogenesis happened over hundreds of millions of years)? Or the fact that abiogenesis generates &quot;primitive organisms&quot;, while spontaneous generation assumes the generation of evolved, complex organisms?&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2020-10-10T13:51:11.707" Title="What is the difference between abiogenesis and spontaneous generation?" Tags="&lt;abiogenesis&gt;&lt;definitions&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7309" PostTypeId="1" AcceptedAnswerId="7501" CreationDate="2013-02-21T23:28:26.730" Score="8" ViewCount="1568" Body="&lt;p&gt;Humans take courses to learn how to assess the risk of avalanches and how to deal with it. Additionally, they often use special gear to survive avalanches if they got caught in the middle of one. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about animals that live in these areas like mountains with snow where avalanches occur (maybe wolves, deer, etc.)? Are they somehow aware of the risk? Do they handle it in any way (e.g. avoid especially steep regions) or able to manage getting out of it?&lt;/p&gt;&#xA;" OwnerDisplayName="user3130" LastEditorDisplayName="user3130" LastEditDate="2013-03-05T06:06:36.350" LastActivityDate="2013-03-11T20:36:02.177" Title="Are animals that live in areas where avalanches happen equipped to deal with that?" Tags="&lt;environment&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7310" PostTypeId="1" AcceptedAnswerId="7314" CreationDate="2013-02-21T23:59:19.897" Score="1" ViewCount="317" Body="&lt;p&gt;This is what a friend of mine said:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When there's human offspring, it will look a rough 'medium' between&#xA;  the two parents, with it sharing features from the two. well if the&#xA;  offspring of one set of parents has sex with the offspring of another&#xA;  set, the outcome becomes a 'medium' of those two. So the range from&#xA;  what we shall call 'completely average looks' (a hypothetical state of&#xA;  the average of everyone in the world, which is acceptable as we're&#xA;  looking at a process of millions of years) becomes less and less the&#xA;  further into the future we go. Eventually, there is almost no range&#xA;  between people and 'completely average looks'.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In summary: take the hypothetical average of everyone in the world, and because the offspring of two people is a slight mixture of those two people, they are a tiny bit closer to the hypothetical average of everyone in the world, which means that eventually people will be getting closer and closer to this average, so will one day look the same.&#xA;So he's suggesting that slowly people will become more and more similar.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My argument is that, although this baby may be that tiny bit closer to the overall average, they're new look has effectively altered the average, meaning that they aren't actually getting closer to the average. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like an opinion and flaw from some experts, such as yourselves, so please...&lt;/p&gt;&#xA;" OwnerUserId="839" LastEditorUserId="839" LastEditDate="2013-02-24T23:24:14.697" LastActivityDate="2013-03-23T05:40:25.790" Title="Can this theory on the evolution of human appearance be flawed?" Tags="&lt;evolution&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7311" PostTypeId="2" ParentId="7308" CreationDate="2013-02-22T01:46:00.263" Score="3" Body="&lt;p&gt;One important difference is that spontaneous generation is a form of &quot;mechanism&quot; by which a certain species is &quot;born&quot;, so it is repeated many times. For such complex organisms this would be part of their &quot;life cycle&quot;. It would also need to be a regulated, robust process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abiogenesis, on the other hand, would create an organism which from that point on does not rely on abiogenesis in any way, so it would be a unique event. Abiogenesis is highly probabilistic which is why it would result in very simple organisms.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2013-02-22T01:46:00.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7312" PostTypeId="1" AcceptedAnswerId="7316" CreationDate="2013-02-22T03:55:32.610" Score="4" ViewCount="176" Body="&lt;p&gt;I know that ants &lt;a href=&quot;http://en.wikipedia.org/wiki/Ant&quot; rel=&quot;nofollow&quot;&gt;communicate with pheromones&lt;/a&gt; but I am wondering if these pheromones can indicate in which direction to go. For example the ants leave pheromones to indicate a food source and when they find food they eventually create a &quot;highway&quot; of ants running to the food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I disturb the ants while they're going to the food source in such way that they don't know anymore in which direction is the food will they choose a direction randomly (nest or food) or will the pheromones also indicate in which way to go to get the food?&lt;/p&gt;&#xA;" OwnerUserId="3132" LastEditorUserId="55929" LastEditDate="2020-01-06T00:33:28.760" LastActivityDate="2020-01-06T00:33:28.760" Title="Do ant pheromones indicate the direction to go?" Tags="&lt;entomology&gt;&lt;ant&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7313" PostTypeId="1" CreationDate="2013-02-22T04:10:35.953" Score="4" ViewCount="1083" Body="&lt;p&gt;I'm looking at an output of a single dry sensor EEG headband with the sensor positioned above left eye. As a side effect of it's placement, the device picks up eye blinks, and some eye motion as changes in the amplitude of the raw output waveform. It is clearly visible, and I can probably detect it algorithmically. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is - &lt;strong&gt;does frequency of eye blinking (not controlled) reveal anything about the state of (autonomous?) nervous system, or processes that take place within the brain?&lt;/strong&gt; For example, what is the difference between blinking involuntary X times per minute versus Y times per minute for the same individual? Does blinking get suppressed in response to some stimuli, like loud noises, speech, etc?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I appreciate your input!&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2015-10-24T14:45:32.823" Title="Does frequency of eye blinking reveal anything about human biology/nervous system?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7314" PostTypeId="2" ParentId="7310" CreationDate="2013-02-22T07:41:32.567" Score="9" Body="&lt;p&gt;&lt;strong&gt;Quantitative genetics&lt;/strong&gt; is one reason why this doesn't happen. For example height is affected by many genetic loci, not just 1 gene, and we can for the sake of the following illustration call them Locus A through Locus J - 10 Loci. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now this is purely illustrative and hypothetical - in actuality there are some differences between this example and the real world, but nevertheless I shall plough on. Imagine everyone carries a basic set of genes which makes them 150cm tall. Loci A-J each have two alleles, either &lt;em&gt;T&lt;/em&gt; or &lt;em&gt;t&lt;/em&gt;, with one inherited from each parent. Each &lt;em&gt;T&lt;/em&gt; allele adds 2.5cm to the basic height per copy (each parent has two copies, one goes to the offspring) and &lt;em&gt;t&lt;/em&gt; has no effect. The parents are both heterozygous at each loci, that is they have one &lt;em&gt;T&lt;/em&gt; and one &lt;em&gt;t&lt;/em&gt; at each pair of loci. Therefore both parents are 175cm tall.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When these parents mate the offspring inherit one copy of each parent at random. As such the most likely single outcome is that the offspring will inherit 10 &lt;em&gt;T&lt;/em&gt;'s and 10 &lt;em&gt;t&lt;/em&gt;'s - roughly five of each from each parent. However, purely by chance they could receive 10 &lt;em&gt;T&lt;/em&gt; alleles from each parent, giving them a height of 150+(20*2.5) = 200cm. Likewise, a sibling could also inherit only &lt;em&gt;t&lt;/em&gt; alleles thus giving them a height of 150+(0*2.5)= 150cm. Thus variation can actually increase from one generation to the next.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other reasons why we do not regress to the mean as well, but I am writing a quick answer over breakfast, but I will be in the office soon where I can get some more thorough explanations from text books. E.g. &lt;strong&gt;(Dis)assortative mating, Mutation, Recombination, Environmental variance, Selection&lt;/strong&gt;. However, with the increase in global movement it has become easier for dominant alleles to spread which is why the number of blue eyed people in the US is decreasing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is an interesting article which backs up what I said about quantitative genetics, called &lt;a href=&quot;http://www.lifeslittlemysteries.com/2913-will-humans-eventually-all-look-like-brazilians.html&quot; rel=&quot;nofollow&quot;&gt;&quot;Will humans eventually all look like brazilians?&quot;&lt;/a&gt; Also for good quantitative genetics texts take &lt;a href=&quot;http://www.amazon.co.uk/Primer-Ecological-Genetics-Jeffrey-Conner/dp/087893202X/ref=sr_1_1?s=books&amp;amp;ie=UTF8&amp;amp;qid=1361518847&amp;amp;sr=1-1&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; as a basic intro and &lt;a href=&quot;http://www.amazon.co.uk/Introduction-Quantitative-Genetics-Douglas-Falconer/dp/0582243025&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; for further reading.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-02-23T14:14:10.803" LastActivityDate="2013-02-23T14:14:10.803" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7315" PostTypeId="2" ParentId="7307" CreationDate="2013-02-22T08:35:29.610" Score="4" Body="&lt;p&gt;This article analyses the exchange of DNA during the process of grafting&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencemag.org/content/324/5927/649.full&quot; rel=&quot;nofollow&quot;&gt;Exchange of Genetic Material Between Cells in Plant Tissue Grafts&lt;/a&gt; - Stegemann and Bock, Science 2009&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quoting from the article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Although the grafted tissues fuse and establish vascular connections,&#xA;  the stock (the lower part of the graft) and scion (the upper part,&#xA;  usually supplying solely aerial parts to the graft) are thought not to&#xA;  exchange their genetic materials. But grafting (whether natural or&#xA;  assisted) provides a path for horizontal gene transfer. Gene transfer&#xA;  is confined to the graft site and no long-distance transfer may occur.&#xA;  Analyzes indicating that large DNA pieces or even entire plastid&#xA;  genomes are transferred. Only plastid genes may be transferred, no&#xA;  transfer of nuclear genes occur. Plant cells are connected via&#xA;  plasmatic bridges called plasmodesmata, but the passage of large&#xA;  macromolecules requires the action of specific plasmodesmata-widening&#xA;  proteins. Whether large DNA pieces or even entire organelles can&#xA;  travel through plasmodesmata requires further investigation.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Finally, although our data demonstrate the exchange of genetic&#xA;  material between grafted plants, they do not lend support to the tenet&#xA;  of Lysenkoism that “graft hybridization” would be analogous to sexual&#xA;  hybridization. Instead, our finding that gene transfer is restricted&#xA;  to the contact zone between scion and stock indicates that the changes&#xA;  can become heritable only via lateral shoot formation from the graft&#xA;  site. However, there is some reported evidence for heritable&#xA;  alterations induced by grafting and, in light of our findings,&#xA;  these cases certainly warrant detailed molecular investigation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1839" LastEditorUserId="115" LastEditDate="2013-03-04T12:10:23.983" LastActivityDate="2013-03-04T12:10:23.983" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7316" PostTypeId="2" ParentId="7312" CreationDate="2013-02-22T09:18:51.487" Score="3" Body="&lt;p&gt;@shigeta is correct.  Trail disruption is actually a method of controlling ant populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an example, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20077128&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/20077128&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-02-22T09:18:51.487" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7317" PostTypeId="1" CreationDate="2013-02-22T09:33:27.833" Score="3" ViewCount="114" Body="&lt;p&gt;Which enzymes degrade dynorphins and what drugs are there available to inhibit said enzymes?&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="9943" LastEditDate="2015-06-10T11:32:48.890" LastActivityDate="2016-02-05T17:48:25.680" Title="Which enzymes degrade dynorphins and what drugs inhibit these enzymes?" Tags="&lt;pharmacology&gt;&lt;enzymes&gt;&lt;opioid&gt;&lt;dynorphin&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7318" PostTypeId="5" CreationDate="2013-02-22T10:52:42.010" Score="0" Body="&lt;p&gt;Dynorphins are endogenous opioid peptides that serve as selective kappa opioid receptor agonists. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-22T11:00:16.470" LastActivityDate="2013-02-22T11:00:16.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7319" PostTypeId="4" CreationDate="2013-02-22T10:52:42.010" Score="0" Body="Dynorphins are endogenous opioid peptides that serve as selective kappa opioid receptor agonists. " OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-02-22T11:00:19.467" LastActivityDate="2013-02-22T11:00:19.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7320" PostTypeId="2" ParentId="1116" CreationDate="2013-02-22T13:16:10.070" Score="1" Body="&lt;p&gt;Cats have different body structure than human beings. Its body-kinetics are quite different from us. Yes, muscles are quite strong, but this not the only reason. To know in-depth about the reasons behind the cats’ extreme jumping abilities, you can just refer this online article - &quot;The Glory of the Cat – adidarwinian&quot; at &lt;a href=&quot;http://adidarwinian.com/the-glory-of-the-cat&quot; rel=&quot;nofollow&quot;&gt;http://adidarwinian.com/the-glory-of-the-cat&lt;/a&gt;  Along with the flexible spine, strong muscles, flexible joints, they have a peculiar trait known as righting reflex. The same article has information on this peculiar trait. Due to the righting reflex instinct, cats can even survive falls from the high rise buildings.   &lt;/p&gt;&#xA;" OwnerUserId="3134" LastActivityDate="2013-02-22T13:16:10.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7322" PostTypeId="1" AcceptedAnswerId="7323" CreationDate="2013-02-22T17:24:30.463" Score="3" ViewCount="4486" Body="&lt;p&gt;I am a regular blood donor and I am also a skydiver.  We normally go to around 13,000 feet AGL (above ground level).  Depending on how high above sea level the ground is, altitudes could be as high as 15,000 MSL (mean sea level) before a jumper is required to use supplemental oxygen.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At those altitudes hemoglobin is less effective at carrying oxygen, which is why hypoxia is a risk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following chart taken from &lt;a href=&quot;http://www.avweb.com/news/aeromed/181893-1.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt; about aviation and the body shows how oxygen levels decrease as altitude increases:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oP67i.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I would like to know is if there is any research into the effect blood donation has on the blood stream's oxygen capacity?  Is it possible to say that x days after a donation, due to reduced hemoglobin levels, operating at 15,000 MSL would be equivalent to operating at 15,000 + x MSL without donation?&lt;/p&gt;&#xA;" OwnerUserId="3136" LastEditorUserId="3136" LastEditDate="2013-02-22T18:31:31.390" LastActivityDate="2013-02-23T07:04:08.843" Title="How much does donating blood affect the amount of oxygen in your blood stream at high altitude?" Tags="&lt;hematology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7323" PostTypeId="2" ParentId="7322" CreationDate="2013-02-22T18:20:43.463" Score="6" Body="&lt;p&gt;The oxygen-carrying capacity of the blood is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;amount of haemoglobin * % saturation&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The average blood donation is approximately 10% of total blood volume. . Since the donation will have no effect on the % saturation, the oxygen-carrying capacity at each altitude will go down by 10%.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By inspection of the graph in the question, the % saturation goes down by 10% at 10,000 feet. So I conclude that donating 10% of blood volume is equivalent to ascending to 10,000 feet in terms of the effect upon the blood's oxygen-carring capacity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Response to OP comments:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Anyone living at 5,000 feet will have adapted to that altitude in two ways. First of all the erythrocyte levels of 2,3 bisphosphoglycerate will be elevated to maintain unloading of oxygen from haemoglobin in the tissues. Secondly, the number of red cells per mL of blood will have increased, to restore oxygen delivery. Incidentally this increases blood viscosity which is deleterious in the long term. Tibetans living in the Himalaya have adapted genetically to prevent this effect on their blood viscosity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The effect of air pressure is already included in the graph, since it shows the actual degree of saturation of the blood. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-02-23T07:04:08.843" LastActivityDate="2013-02-23T07:04:08.843" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7324" PostTypeId="2" ParentId="7294" CreationDate="2013-02-22T19:04:09.770" Score="0" Body="&lt;p&gt;I think the answer runs along the same logic as this question: &lt;a href=&quot;https://biology.stackexchange.com/questions/7051/which-sex-has-higher-variance-of-reproductive-rate-in-modern-societies-male-or/7059#7059&quot;&gt;Which sex has higher variance of reproductive rate in modern societies - male or females?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because its easier for a male to have offspring with multiple partners, more women would typically produce offspring than men.  In polygamous cultures, &lt;a href=&quot;http://www.academicroom.com/article/wealth-status-and-reproductive-success-among-mukogodo-kenya&quot; rel=&quot;nofollow noreferrer&quot;&gt;it can lead to significant differences of reproductive success between the genders.&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-02-22T19:04:09.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7326" PostTypeId="2" ParentId="7313" CreationDate="2013-02-22T20:34:54.317" Score="1" Body="&lt;p&gt;People avoid looking at what they don't like thinking about.&#xA;A feared enemy, an individual whom you have something to hide from..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Avoidance of looking/excessive blinking is a sign of fear.&#xA;It's basically a sign that the individual is not having a good time looking at what he is looking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes people are lying and then they don't like looking at whom they are lying to... for them it would be nicer to look out the window or something that takes them away from their subject for a bit of time.&#xA;I would expect blinking to increase when lying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally I have noticed excessive durational closing of eyes (a second or so), exactly at the moment of stating their lie.&#xA;Those are off course people who are honest to themselves but are trying to be dishonest to you. But some people lie to themselves as well and they may be more difficult to detect.&lt;/p&gt;&#xA;" OwnerUserId="542" LastEditorUserId="542" LastEditDate="2013-02-22T21:11:37.763" LastActivityDate="2013-02-22T21:11:37.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7327" PostTypeId="2" ParentId="5569" CreationDate="2013-02-22T22:13:15.000" Score="1" Body="&lt;p&gt;There are beahvioral, physiological, and psychological indicators of happiness, and on the flipside of depression, all of which are quantitative. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Levels of the neurotransmitters serotonin and dopamine in the brain are a physiological indicator of depression. Higher levels of serotonin are correlated with increased happiness and decreased anxiety. Dopamine also contributes to good mood, and in addition causes an increase in activity and willpower. Both serotonin and dopamine show decreased levels in depression. However, it is important not just to look at general levels of the neurotransmitter, but to also consider &lt;strong&gt;which parts of the brain show decreased neurotransmitter levels. Depression correlates with decreased serotonin and dopamine levels in the amygdala, thalamus, and hyppocampus.&lt;/strong&gt; (&lt;a href=&quot;http://www.health.harvard.edu/newsweek/what-causes-depression.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.health.harvard.edu/newsweek/what-causes-depression.htm&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Behavioral tests of depression are used on laboratory animals. The most common tests are the forced swim test (in which scientists measure how long a mouse persists swimming in a water container before it gives up) and the tail suspension test (in which scientists measure how long a mouse struggles to free itself when suspended by its tail). (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3270071/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3270071/&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, self report questionnaires are designed to quantify depression in people. Some popular ones are the Beck Depression Inventory (BDI-II) (&lt;a href=&quot;http://en.wikipedia.org/wiki/Beck_Depression_Inventory&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Beck_Depression_Inventory&lt;/a&gt;) and the Beck Hopelessness scale (BHS) (&lt;a href=&quot;http://en.wikipedia.org/wiki/Beck_Hopelessness_Scale&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Beck_Hopelessness_Scale&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-02-22T22:13:15.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7328" PostTypeId="2" ParentId="2580" CreationDate="2013-02-22T23:20:34.443" Score="0" Body="&lt;p&gt;Many people switch to systems biology from a math/physics/computer science background and may need a cell biology textbook to update them on general biology knowledge. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;*&lt;em&gt;For molecular biology knowledge:&lt;/em&gt;*A comprehensive and reliable biology text on the graduate level is &quot;Molecular Biology of the Cell&quot; by Alberts:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0815341059&quot; rel=&quot;nofollow&quot;&gt;http://www.amazon.com/Molecular-Biology-Cell-Bruce-Alberts/dp/0815341059/ref=sr_1_1?ie=UTF8&amp;amp;qid=1361575051&amp;amp;sr=8-1&amp;amp;keywords=molecular+biology+of+the+cell&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*&lt;em&gt;For biochemistry knowledge, especially related to metabolic pathways:&lt;/em&gt;*A more Biochemistry focused textbook is the one by Voet&amp;amp;Voet, which is very comprehensive:&#xA;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0470570954&quot; rel=&quot;nofollow&quot;&gt;http://www.amazon.com/Biochemistry-BIOCHEMISTRY-VOET-Donald-Voet/dp/0470570954/ref=sr_1_1?s=books&amp;amp;ie=UTF8&amp;amp;qid=1361575189&amp;amp;sr=1-1&amp;amp;keywords=voet+biochemistry&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-02-22T23:20:34.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7329" PostTypeId="2" ParentId="3585" CreationDate="2013-02-22T23:31:31.800" Score="2" Body="&lt;p&gt;Many of the parts of a cell, which perform its basic functions, such as transcription, translation, DNA replication, etc. have been already isolated and successfully recreated in a test tube. So if we obtain a complete list of all the parts we need and know how to make those parts and mix them together, we can make a cell from scratch. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this will probably be very time-consuming and costly and will serve no other purpose than showing that it can be done. It is much more time- and cost-efficient to create a genome only, transplant it into an existing cell, and wait for the cell to replicate and synthesize new molecules until it changes in a way that completely fits the new genome. &lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-02-22T23:31:31.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7330" PostTypeId="2" ParentId="7253" CreationDate="2013-02-22T23:35:26.463" Score="0" Body="&lt;p&gt;Usually you assume neither situation. You are given some probability that they carry the trait based on measured allele frequency in the population. Then you use that probability in any downstream application, such as calculating the probability the children are carriers or affected with the genetic condition. &lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-02-22T23:35:26.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7331" PostTypeId="2" ParentId="7281" CreationDate="2013-02-23T00:28:55.703" Score="4" Body="&lt;p&gt;One example is sperm-egg attraction. Many species release their egg and sperm to be joined in water. The egg must try to avoid being fertilized by the sperm of a different species. So an egg secretes a special peptide which attracts the sperm to its location. The amino acid sequence of that peptide is unique for each species and sperm can only recognize the peptide secreted by the egg of their own species. To any other sperm, the peptide is just another molecule present in the water. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10010/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK10010/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-02-23T00:28:55.703" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7332" PostTypeId="2" ParentId="7310" CreationDate="2013-02-23T11:13:31.250" Score="4" Body="&lt;p&gt;The basic point your friend is missing is that offspring appearance is not &lt;em&gt;simply&lt;/em&gt; a mixture of their parents'. Each child also has individual characteristics which were not present in the parents. This is due to a variety of processes, the most important of which is &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosomal_crossover&quot; rel=&quot;nofollow&quot;&gt;chromosomal cross over&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each offspring will be a mixture of its parents &lt;em&gt;and&lt;/em&gt; its own individual characteristics. Therefore, your friend's argument does not stand because each generation causes novel characteristics to appear so each successive generation changes in unpredictable ways.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-02-23T11:13:31.250" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7333" PostTypeId="1" AcceptedAnswerId="7334" CreationDate="2013-02-23T12:50:00.583" Score="9" ViewCount="915" Body="&lt;p&gt;Seeing as ribosomes are what help perform the act of translation itself, and the blueprints for they themselves are in nucleotide sequences, how was the first ribosome theorized to have been made? Also, before there were any ribosome, how was translation theorized to have taken place?&lt;/p&gt;&#xA;" OwnerUserId="263" LastActivityDate="2013-02-23T17:46:25.717" Title="How was the first ribosome theorized to have been made?" Tags="&lt;cell-biology&gt;&lt;abiogenesis&gt;&lt;ribosome&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7334" PostTypeId="2" ParentId="7333" CreationDate="2013-02-23T17:46:25.717" Score="7" Body="&lt;p&gt;An interesting take on this question is addressed in &lt;strong&gt;Bokov and Steinberg's hypothesis&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They have proposed the ribosome has evolved from a short length (~110bp) of RNA that did not have the translational activity that we associate with ribosomes today. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead this short length of RNA carried out alternative functions on RNA in RNA based life. Then overtime the accumulation of mutations occurred, such as duplication events that allowed the RNA strands to fold around one another forming a larger unit. This larger unit may have been able to add building blocks together. Over time natural selection will have guided these strands to be more precise in their building actions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The details of course aren't entirely filled in yet (it's difficult to do because how long ribosomes have been a staple of life), but it's important to take any seemingly complex structure in organisms, and break them down into potentially useful intermediate evolutionary steps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some more reading on this subject here - &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://blogs.sciencemag.org/origins/2009/02/deconstructing-the-ribosome.html&quot;&gt;An article giving a background of Bokov and Steinberg&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v457/n7232/full/nature07749.html&quot;&gt;Bokov and Steinberg's 2009 paper (believe it's paywalled)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926754/&quot;&gt;Origin and Evolution of the Ribosome (paper)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1763" LastActivityDate="2013-02-23T17:46:25.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7335" PostTypeId="2" ParentId="7281" CreationDate="2013-02-23T19:56:49.427" Score="0" Body="&lt;p&gt;Not sure we can name it encryption, but&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a pattern that seems random in surface but once you put it through a&#xA;  decryption process, it is actually something else&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;reminds me about some forms of predatory camouflage. I'm talking from the perspective of the prey: the predator blends with the environment and what the prey perceives is just 'random' environment. When the prey 'decrypts' that there is actually something else, it is generally too late.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2013-02-23T19:56:49.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7336" PostTypeId="1" AcceptedAnswerId="7351" CreationDate="2013-02-23T22:57:42.610" Score="5" ViewCount="297" Body="&lt;p&gt;Is gas produced by bacteria always mainly methane? Or, are there bacteria out there that produce some biogas composed mainly of hydrogen, natural gas, propane, butane? &lt;/p&gt;&#xA;" OwnerUserId="3138" LastEditorUserId="1306" LastEditDate="2013-02-24T10:49:50.893" LastActivityDate="2016-03-21T19:07:53.377" Title="Gas from bacteria that's not methane" Tags="&lt;bacteriology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7337" PostTypeId="1" AcceptedAnswerId="7349" CreationDate="2013-02-24T02:08:05.940" Score="4" ViewCount="6480" Body="&lt;p&gt;Puffer fish is known for having a anti-predation defense mechanism of having toxin-exuding spikes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there predators which evolved specifically to prey on puffer fish? (presumably, by evolving immunity to the toxin)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that sharks eat them, but I doubt sharks evolved to be immune specifically to puffer fish toxin, since their evolutionary development preceded puffer fish's.&lt;/p&gt;&#xA;" OwnerUserId="185" LastActivityDate="2019-10-28T23:34:16.967" Title="Are there predators evolved to eat puffer fish?" Tags="&lt;ichthyology&gt;&lt;antipredator-adaptation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7338" PostTypeId="2" ParentId="7336" CreationDate="2013-02-24T04:29:56.523" Score="4" Body="&lt;p&gt;Well, some bacteria can produce Hydrogen Sulfide gas. For example, Proteus and Salmonella. The presence of $H_2S$ producing bacteria is actually clinically significant and we have a way to test for this, which is via the use of TSI (Triple Sugar Iron) media. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume you set up the test correctly, $H_2S$ producing bacteria will generate dark deposit within the media.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the clinical setting, there are other choices beside TSI, such as SIM media and API20E. &lt;/p&gt;&#xA;" OwnerUserId="3139" LastEditorUserId="1839" LastEditDate="2013-02-24T08:11:40.770" LastActivityDate="2013-02-24T08:11:40.770" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7340" PostTypeId="1" CreationDate="2013-02-24T04:37:10.577" Score="4" ViewCount="241" Body="&lt;p&gt;In a monochromatic spectrum, is the human eye equally able to distinguish between lighter colors just as it is in distinguishing between darker colors? I mean is there really a linear relationship between the Lightness property in the HSL color model and the perceived brightness?&lt;/p&gt;&#xA;" OwnerUserId="3140" LastActivityDate="2014-07-04T20:05:52.570" Title="HSL Lightness vs Eye sensitivity" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7341" PostTypeId="1" AcceptedAnswerId="7342" CreationDate="2013-02-24T08:23:05.310" Score="2" ViewCount="330" Body="&lt;p&gt;What nutrition is given to infants who are lactose intolerant? I understand, in today's day and that age we have non-lactose formula milk, but what happened, before lactose-free milk was created, to those who suffered from lactose intolerance (Native Americans, Asians, etc.)?&lt;/p&gt;&#xA;" OwnerUserId="3142" LastEditorUserId="3952" LastEditDate="2013-08-08T02:44:13.860" LastActivityDate="2013-08-08T02:44:13.860" Title="Lactose Intolerance" Tags="&lt;human-biology&gt;&lt;food&gt;&lt;ethnobiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7342" PostTypeId="2" ParentId="7341" CreationDate="2013-02-24T15:02:33.033" Score="4" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Lactose_intolerance&quot; rel=&quot;nofollow&quot;&gt;lactose intolerance&lt;/a&gt; Wikipedia page explains the problem fairly well, so I'll refer you to that for a more detailed explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Briefly, the most common cause of lactose intolerance is &lt;strong&gt;primary lactase deficiency&lt;/strong&gt;, which affects the majority of the world's population. This &lt;strong&gt;only affects adults&lt;/strong&gt;: the majority of people do not produce lactase as adults. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Congenital lactase deficiency, instead is a very rare, autosomal recessive genetic disorder that prevents lactase expression from birth.&lt;br&gt;&#xA;  [...]&lt;br&gt;&#xA;  Congenital lactase deficiency (CLD), where the production of lactase is inhibited from birth, can be dangerous in any society because of infants' nutritional reliance on human breast milk during their first months. &lt;em&gt;Before the 20th century, babies born with CLD often did not survive&lt;/em&gt;, but death rates decreased with soybean-derived infant formulas and manufactured lactose-free dairy products. Beyond infancy, individuals affected by CLD usually have the same nutritional concerns as any lactose-intolerant adult.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A couple of good references:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16951027&quot; rel=&quot;nofollow&quot;&gt;Lactose intolerance in infants, children, and adolescents.&lt;/a&gt; - Heyman, Pediatrics 2006&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14616060&quot; rel=&quot;nofollow&quot;&gt;Genetics of lactase persistence and lactose intolerance.&lt;/a&gt; - Swallow, Annu Rev Genet. 2003 &lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2013-02-24T15:02:33.033" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7343" PostTypeId="1" CreationDate="2013-02-24T17:51:55.247" Score="4" ViewCount="2792" Body="&lt;p&gt;What would cause a seed to not sprout despite showing signs of germination given excess water? Oxygen, temperature, and light were sufficient for germination and sprouting in seeds of a slightly lesser amount of water.&lt;/p&gt;&#xA;" OwnerUserId="584" LastActivityDate="2019-08-13T16:48:10.323" Title="Why seeds won't sprout given excess water?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7344" PostTypeId="1" CreationDate="2013-02-24T19:25:30.713" Score="12" ViewCount="664" Body="&lt;p&gt;With the recent rise in 3D printing, I keep hearing about more novel ways to use the technology: cell 3D printing, liquid aluminum or &lt;a href=&quot;http://www.digitalartsonline.co.uk/news/hacking-maker/3d-printer-pen-lets-you-draw-real-objects/&quot;&gt;plastic 3D printing&lt;/a&gt;. For example,   &lt;a href=&quot;http://www.ted.com/talks/anthony_atala_printing_a_human_kidney.html&quot;&gt;this Ted talk deals with printing a human kidney&lt;/a&gt;. What interests me is if the current technology can be adapted to print with spider silk. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Spider_silk&quot;&gt;silk has some amazing properties&lt;/a&gt;, and apparently there are multiple types of silk that spiders use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this project: &lt;a href=&quot;http://www.bnpeters.com/spiderbot.html&quot;&gt;Spiderbot 3D printer&lt;/a&gt;.  &lt;strong&gt;Can spider silk actually be synthesized in large enough amounts to enable 3D printing?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="16866" LastEditDate="2017-05-03T00:25:53.620" LastActivityDate="2017-07-11T21:39:41.143" Title="Can spider silk be synthesized to be used for 3D printing?" Tags="&lt;entomology&gt;&lt;synthetic-biology&gt;&lt;arachnology&gt;" AnswerCount="5" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7345" PostTypeId="2" ParentId="2263" CreationDate="2013-02-24T19:50:27.310" Score="1" Body="&lt;p&gt;You will be surprised that when describing the colonial morphology of E. coli on a Blood agar plate, the word choice for colour is &quot;grey&quot;. I believe that user leonardo up there had a very good explanation about this &quot;yellowish colour&quot; question.&lt;/p&gt;&#xA;" OwnerUserId="3139" LastActivityDate="2013-02-24T19:50:27.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7346" PostTypeId="2" ParentId="7344" CreationDate="2013-02-24T20:56:12.953" Score="6" Body="&lt;p&gt;The &quot;...in large enough amounts to enable 3D printing?&quot; part of your question is, I think, still unknown, but spider silk has been being synthesized in transgenic goat milk for quite a long time already, and I suspect that it's now just a matter of time before the answer to your question is an unqualified &quot;yes.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ma102291m&quot; rel=&quot;noreferrer&quot;&gt;Macromolecules, 2011, 44 (5), pp 1166–1176, doi:10.1021/ma102291m&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1756" LastEditorUserId="1756" LastEditDate="2013-02-24T21:18:24.550" LastActivityDate="2013-02-24T21:18:24.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7347" PostTypeId="2" ParentId="7343" CreationDate="2013-02-24T22:16:56.230" Score="5" Body="&lt;p&gt;You've stated in your question that oxygen was sufficient for germination, but if there's too much water this probably isn't the case. It's likely given excess water seeds will drown- that is they have not got access to sufficient oxygen to continue germination.&lt;/p&gt;&#xA;" OwnerUserId="1763" LastActivityDate="2013-02-24T22:16:56.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7348" PostTypeId="2" ParentId="3899" CreationDate="2013-02-25T04:27:36.753" Score="2" Body="&lt;p&gt;In a 1987 article &lt;a href=&quot;http://www.jstor.org/stable/pdfplus/4454035.pdf?acceptTC=true&quot; rel=&quot;nofollow&quot;&gt;&quot;Nonenteric Infections Acquired through Contact with Water&quot;&lt;/a&gt;, the author mentioned that &quot;Infection of the ears, throat, respiratory tract, and &lt;strong&gt;cornea&lt;/strong&gt; are also encountered&quot; by virulent strains of &lt;em&gt;Acanthamoeba&lt;/em&gt; and &lt;em&gt;Naegleria fowleri&lt;/em&gt;. The only reference that implicates Naegleria fowleri is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6617613&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt;, but it doesn't mention modes of infection.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The long and the short of it is that &lt;em&gt;Acanthamoeba&lt;/em&gt; infections can be acquired through contact with the cornea, but it's not clear whether &lt;em&gt;Naegleria&lt;/em&gt; infections can also be acquired in this way.&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;n.b. The first link takes you to the JSTOR page.  In the event you do not have access, here is the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3547578&quot; rel=&quot;nofollow&quot;&gt;PubMed page&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3139" LastEditorUserId="3059" LastEditDate="2013-03-27T11:03:02.800" LastActivityDate="2013-03-27T11:03:02.800" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7349" PostTypeId="2" ParentId="7337" CreationDate="2013-02-25T05:45:46.060" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Tetraodontidae#Natural_defenses&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; has some revealing information here: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Not all puffers are necessarily poisonous; Takifugu oblongus, for example, is a fugu puffer that is not poisonous, and &lt;em&gt;toxin level varies wildly even in fish that are&lt;/em&gt;. A puffer's neurotoxin is not necessarily as toxic to other animals as it is to humans, and puffers are eaten routinely by some species of fish, such as lizardfish and tiger sharks. Also, Japanese fish farmers have grown nonpoisonous puffers by controlling their diet.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It seems that susceptibility to tetrodotoxin varies a lot from one animal to another, and so some natural variation might allow a reasonable amount of predation to occur.  I also wonder whether the variation in the amount of toxin in the fish implies that the fish are often depleted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are cases of animals who have evolved a resistance to Tetrodotoxin, but for the most part its may the predators you are thinking of.  The toxin is synthesized by a symbiotic bacteria and is found not only in fugu but also blue-ringed octopus, rough-skinned newts and some sea slugs.  These animals probably all began with enough intrinsically low sensitivity to the toxin to take on the symbiont and probably evolved to be completely insensitive.  To find a predator that would have co-evolved a similar resistance you would look for a predator that particularly favors the envenomed animal.  In the case of the rough skinned newt, &lt;a href=&quot;http://news.stanford.edu/news/2008/march12/newts-031208.html&quot; rel=&quot;nofollow&quot;&gt;its suspected that the common garter snake is an example of such co-evolution&lt;/a&gt;. Others may be out there to discover - its probably difficult to watch marine animals to know what their typical predators are.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-02-25T12:53:17.643" LastActivityDate="2013-02-25T12:53:17.643" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7350" PostTypeId="1" AcceptedAnswerId="7353" CreationDate="2013-02-25T11:53:32.577" Score="13" ViewCount="4538" Body="&lt;p&gt;Sure it's &lt;em&gt;convenient&lt;/em&gt; to decide when to urinate but not &lt;em&gt;essential&lt;/em&gt; for survival or reproduction, as I understand. But just convenience is not a drive for evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the bladder serve any essential purpose? If not why did bladders evolve?&lt;/p&gt;&#xA;" OwnerUserId="3146" LastEditorUserId="107" LastEditDate="2013-02-26T00:02:05.047" LastActivityDate="2020-01-20T14:13:02.873" Title="Why did the urinary bladder evolve?" Tags="&lt;evolution&gt;" AnswerCount="3" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="7351" PostTypeId="2" ParentId="7336" CreationDate="2013-02-25T12:48:08.690" Score="7" Body="&lt;p&gt;Microbes can produce several gasses other than methane.  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;All microbes produce $CO_2$ through the oxidation of reduced carbon&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Additionally some metabolic pathways produce other gases.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Photosynthetic microbes produce $O_2$&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Sulfur reducing bacteria can produce $H_2S$ (as @ohcanada points out)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Denitrifying bacteria produce $NO$, $N_2O$, and $N_2$&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Fermenters produce $H_2$ (as @mart indicates) &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There may be others that I am not thinking of but these are some of the major players...&lt;/p&gt;&#xA;" OwnerUserId="137" LastEditorUserId="137" LastEditDate="2016-03-21T19:07:53.377" LastActivityDate="2016-03-21T19:07:53.377" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7352" PostTypeId="1" AcceptedAnswerId="7355" CreationDate="2013-02-25T14:18:38.533" Score="1" ViewCount="160" Body="&lt;p&gt;I am thinking Citric Acid cycle and activation of the end parts of Acetyl and alfa-ketoglutarate.&#xA;Let's consider only now Acetyl to make things simpler.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried to explain the thing by symmetry - phosphate tetrahedral, while coenzyme A seems to be mostly some V shaped. &#xA;However, it does not help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can human body use Acetyl Phosphate instead of Acetyl CoA in TCA in some situations?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that you can activate acetyl-CoA again by phosphate:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;acetyl-CoA + phosphate &amp;lt;-&amp;gt; CoA + acetyl phosphate&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1306" LastEditDate="2014-04-09T16:01:57.577" LastActivityDate="2014-04-09T16:01:57.577" Title="Can we use Acetyl Phosphate instead of Acetyl CoA in TCA?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7353" PostTypeId="2" ParentId="7350" CreationDate="2013-02-25T14:55:21.813" Score="18" Body="&lt;p&gt;Here are just a few points that might apply:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Urine is used for scent marking by some species, so the ability to store urine could be useful.  &lt;/li&gt;&#xA;&lt;li&gt;At the opposite side, controlling the release of a strong scent would help in stealth for both predators and prey.  (In addition, a single strong scent might temporarily overload a predator's sense of smell making tracking more subtle scents more difficult.)&lt;/li&gt;&#xA;&lt;li&gt;Flushing an excretion point (single point reduces opportunities for invasion) under some pressure could help avoid blockage and parasitic invasion/accumulation.  (Providing a tube from the extraction organ to the excretion point allows more flexible (and protected) placement of the organ, but also increasing the benefit of a flushing mechanism.)&lt;/li&gt;&#xA;&lt;li&gt;Flushing could also reduce contact with skin. Urine might act as an irritant and a nutrient source for parasites.&lt;/li&gt;&#xA;&lt;li&gt;Adding a buffer is a common technique for any pipelined operation to allow smaller resources to handle temporal variation in input and output rate.  Without a such a buffer, all stages have to be sized for the maximum utilization rather than something closer to average utilization.&lt;/li&gt;&#xA;&lt;li&gt;Avoiding potential contamination of food and water may also be a benefit of controlled urination (or excreting might have a fertilizing or pest-deterrent aspect for plants).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Since terrestrial animals presumably &lt;em&gt;retained&lt;/em&gt; urinary bladders developed by their marine ancestors, benefits associated with terrestrial lifestyle would only provide selective pressure to retain such a feature. However, if &lt;em&gt;somehow&lt;/em&gt; a line of terrestrial animals abandoned urinary bladders, it is not entirely implausible that even scent marking benefits could increase the selective pressure enough to overcome some peculiar opposing selective pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Initially, the animal might apply scents by scratching at an area of skin irritated by urine release against some surface. Then this scratching might be preferentially located (i.e., a scent marking behavior is developed). Having such a behavior would then obvious bring benefits to storing a significant amount of urine and eventually to being able to squirt the urine (allowing the scratching behavior to fall away).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above are just somewhat reasonable speculations about what selective pressures might encourage the development (and retention) of a urinary bladder.  Hopefully, someone with actual knowledge will provide a better answer documenting established theory and evidence for how urinary bladders actually developed.&lt;/p&gt;&#xA;" OwnerUserId="1858" LastEditorUserId="1858" LastEditDate="2013-08-15T20:28:17.740" LastActivityDate="2013-08-15T20:28:17.740" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7354" PostTypeId="1" CreationDate="2013-02-25T19:41:49.333" Score="4" ViewCount="336" Body="&lt;p&gt;I was doing some gene expression analysis using this tool &lt;a href=&quot;http://david.abcc.ncifcrf.gov/summary.jsp&quot; rel=&quot;nofollow&quot;&gt;http://david.abcc.ncifcrf.gov/summary.jsp&lt;/a&gt;. However, I have a confusion about what benjamini is. I fed it some gene list and it gave me some potential pathways the genes belong to(KEGG pathways). However, I have a confusion what this column called benjamini is. What does it denote? Any suggestions?&lt;/p&gt;&#xA;" OwnerUserId="3074" LastEditorUserId="57" LastEditDate="2013-02-26T06:17:39.307" LastActivityDate="2013-02-26T08:13:07.373" Title="What is benjamini" Tags="&lt;bioinformatics&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7355" PostTypeId="2" ParentId="7352" CreationDate="2013-02-25T21:35:30.443" Score="1" Body="&lt;p&gt;Enzymes are usually specific to a greater or lesser extent for their substrates. In this case we are looking at citrate synthase which catalyses a condensation reaction in which the acetyl group from acetyl-CoA is added to an oxaloacetate molecule to form citrate. This is the entry point for carbon into the TCA cycle for energy production. The condensation reaction follows an ordered pathway: oxalocatetate binds first and this results in a conformational change which increases the enzyme's affinity for acetyl-CoA by a factor of 20.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Citrate synthase is highly specific for acetyl-CoA as a substrate. The cited reference discusses several aspects of this specificity. The enzyme has a well-defined binding site for CoA, with contacts from both the small and large subunits. This includes the recognition of the adenylyl portion of the molecule. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A relevant quotation from the review:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Citrate synthase is highly specific towards its substrates. The condensation reaction occurs only with the physiological substrates oxaloacetate and acetyl-CoA.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, the answer is that citrate synthase cannot use acetyl-phosphate as a substrate because of its specificity for acetyl-CoA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wiegand,G and Remington, SJ (1986) Citrate Synthase: Structure, Control, and Mechanism. Ann. Rev. Biophys. 15: 97–117&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-02-25T21:35:30.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7356" PostTypeId="1" CreationDate="2013-02-25T23:27:54.340" Score="4" ViewCount="391" Body="&lt;p&gt;We ran PCR with a positive control and two lanes of sample. We used the same sample, but in one PCR mixture we used a total volume of 50&amp;mu;L (25&amp;mu;L Taq, 5&amp;mu;L forward&amp;amp;reverse primer each, 10&amp;mu;L sample, 5&amp;mu;L dH2O) while in the other we halved each volume to a total of 25&amp;mu;L. Pipetting was done by the same person.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The positive control and the 25&amp;mu;L total volume lane gave nice and clear bands, but the 50&amp;mu;L sample showed nothing. How could this be explained?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: We only ran one PCR with all the samples simultaneously, so no second thermocycler or different temperatures or anything. Didn't even consider that option!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit 2: In case it's relevant, we were using this: &lt;a href=&quot;http://www.chemheritage.org/discover/collections/collection-items/scientific-instruments/perkin-elmer-cetus-model-480-dna-thermal-cycler.aspx&quot; rel=&quot;nofollow&quot;&gt;http://www.chemheritage.org/discover/collections/collection-items/scientific-instruments/perkin-elmer-cetus-model-480-dna-thermal-cycler.aspx&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-02-26T15:08:01.757" LastActivityDate="2013-02-26T15:08:01.757" Title="Effect of doubling volumes of PCR reagents" Tags="&lt;gel-electrophoresis&gt;&lt;pcr&gt;&lt;diy-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7358" PostTypeId="2" ParentId="7356" CreationDate="2013-02-26T05:00:37.747" Score="2" Body="&lt;p&gt;The thermal cycler adjusts sample temperature based on the volume of the sample. So if you run samples of different volumes side by side, not all of them will cycle through the optimal temperatures of each step. If you were working with a &quot;hot start&quot; polymerase this is even more critical, as the Taq won't be able to amplify at all unless the sample is heated up to a specific temperature.&lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-02-26T05:00:37.747" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7359" PostTypeId="2" ParentId="7354" CreationDate="2013-02-26T05:06:31.900" Score="7" Body="&lt;p&gt;It is a &lt;a href=&quot;http://udel.edu/~mcdonald/statmultcomp.html&quot; rel=&quot;nofollow&quot;&gt;Benjamini-Hochberg q-value,&lt;/a&gt; similar to a p-value corrected for multiple hypothesis testing using the false discovery rate.&lt;/p&gt;&#xA;" OwnerUserId="3053" LastEditorUserId="112" LastEditDate="2013-02-26T08:13:07.373" LastActivityDate="2013-02-26T08:13:07.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7361" PostTypeId="2" ParentId="7341" CreationDate="2013-02-26T10:53:06.083" Score="7" Body="&lt;p&gt;In fact, being lactose &lt;em&gt;tolerant&lt;/em&gt; is the mutation. Adult mammals are normally not lactose tolerant, only the still milk drinking babies have the lactose gene activated. Humans developed this mutation earliest in the Neolithic.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Lactase persistence (LP), the dominant Mendelian trait conferring the ability to digest the milk sugar lactose in adults, has risen to high frequency in central and northern Europeans in the last 20,000 years. This trait is likely to have conferred a selective advantage in individuals who consume appreciable amounts of unfermented milk.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(citation from &lt;a href=&quot;http://www.pnas.org/content/104/10/3736.abstract&quot;&gt;Burger et al., PNAS, 2006&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in fact, people who are lactose intolerant are just plain normal. There is normally no reason to feed babies lactose-free milk. The rare cases where you need to do this are very well described in the post of nico.&lt;/p&gt;&#xA;" OwnerUserId="3119" LastActivityDate="2013-02-26T10:53:06.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7362" PostTypeId="5" CreationDate="2013-02-26T15:11:26.763" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-02-26T15:11:26.763" LastActivityDate="2013-02-26T15:11:26.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7363" PostTypeId="4" CreationDate="2013-02-26T15:11:26.763" Score="0" Body="DIY biology is a movement of hobby biologists practicing outside of mainstream labs. This means that budget, availability of technology, and possibly background knowledge may be minimal." OwnerUserId="806" LastEditorUserId="4101" LastEditDate="2013-10-31T18:23:37.323" LastActivityDate="2013-10-31T18:23:37.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7364" PostTypeId="1" AcceptedAnswerId="7369" CreationDate="2013-02-26T15:27:05.790" Score="3" ViewCount="3844" Body="&lt;p&gt;Spent a half hour googling this and the best I could find was this: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Now for some rhymes: Arginine = R. R we having fun yet?&#xA;  Asparagine = N The kNights of Ne say &quot;Ne&quot;.&#xA;  &lt;strong&gt;&lt;em&gt;Glutamine is a cute amine = Q&lt;/em&gt;&lt;/strong&gt;&#xA;  I say &quot;glutamate&quot;/a former vice president says &quot;glutEmate&quot; = E&#xA;  ditto with AsparDic acid = D&#xA;  Fenylalanine makes tasty italien sausage = F&#xA;  Theres are two rings in tryptophan, and there are two v's in W = W&#xA;  Tyrosine = Y, Y? Because we love biochemistry. Source: &lt;a href=&quot;http://wwwchem.csustan.edu/chem4400/code.htm&quot; rel=&quot;nofollow&quot;&gt;One letter codes, rhyme and reason&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="694" LastActivityDate="2013-02-26T18:45:20.080" Title="Why does Glutamine have the symbol Q?" Tags="&lt;biochemistry&gt;&lt;amino-acids&gt;&lt;nomenclature&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7366" PostTypeId="2" ParentId="7364" CreationDate="2013-02-26T18:18:48.250" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Initial letters of the names of the amino acids were chosen where&#xA;  there was no ambiguity. There are six such cases: cysteine, histidine.&#xA;  isoleucine, methionine, serine and valine. All the other amino acids&#xA;  share the initial letters A, G, L, P or T, so arbitrary assignments&#xA;  were made. These letters were assigned to the most frequently&#xA;  occurring and structurally most simple of the amino acids with these&#xA;  initials, alanine (A), glycine (G), leucine (L), proline (P) and&#xA;  threonine (T).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Other assignments were made on the basis of associations that might be&#xA;  helpful in remembering the code, e.g. the phonetic associations of F&#xA;  for phenylalanine and R for arginine. For tryptophan the double ring&#xA;  of the molecule is associated with the bulky letter W. The letters N&#xA;  and Q were assigned to asparagine and glutamine respectively; D and E&#xA;  to aspartic and glutamic acids respectively. K and Y were chosen for&#xA;  the two remaining amino acids, lysine and tyrosine, because, of the&#xA;  few remaining letters, they were close alphabetically to the initial&#xA;  letters of the names. U and O were avoided because U is easily&#xA;  confused with V in handwritten material, and O with G, Q, C and D in&#xA;  imperfect computer print-outs, and also with zero. J was avoided&#xA;  because it is absent from several languages.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Two other symbols are often necessary in partly determined sequences,&#xA;  so B was assigned to aspartic acid or asparagine when these have not&#xA;  been distinguished; Z was similarly assigned to glutamic acid or&#xA;  glutamine. X means that the identity of an amino acid is undetermined,&#xA;  or that the amino acid is atypical. &quot;&lt;a href=&quot;http://www.chem.qmul.ac.uk/iupac/AminoAcid/&quot;&gt;Nomenclature and Symbolism for Amino Acids and Peptides&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1839" LastActivityDate="2013-02-26T18:18:48.250" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7367" PostTypeId="2" ParentId="2580" CreationDate="2013-02-26T18:26:33.153" Score="2" Body="&lt;p&gt;I've been working to prepare a synthetic biology curriculum for non-biologist and have found a great resource in Prof. Scott Mohr's (BU, Chemistry) &quot;Primer for Synthetic Biology&quot; available here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://openwetware.org/images/3/3d/SB_Primer_100707.pdf&quot; rel=&quot;nofollow&quot;&gt;http://openwetware.org/images/3/3d/SB_Primer_100707.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3156" LastActivityDate="2013-02-26T18:26:33.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7368" PostTypeId="1" AcceptedAnswerId="7699" CreationDate="2013-02-26T18:31:24.567" Score="6" ViewCount="4378" Body="&lt;p&gt;I want to stock up on autoclaved disposables, such as Eppendorf tubes, pasteur pipettes etc., and some buffers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I don't open the container after autoclaving, how long can I store autoclaved materials and consider them still sterile? Does it make a difference if the material is dry or if it is a liquid?&lt;/p&gt;&#xA;" OwnerUserId="3053" LastEditorUserId="69" LastEditDate="2013-03-29T12:02:59.297" LastActivityDate="2013-03-30T14:35:00.573" Title="How long can I store autoclaved disposables and reagents?" Tags="&lt;lab-techniques&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7369" PostTypeId="2" ParentId="7364" CreationDate="2013-02-26T18:45:20.080" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.biology.arizona.edu/biochemistry/problem_sets/aa/Dayhoff.html&quot; rel=&quot;nofollow&quot;&gt;The Biology Project&lt;/a&gt; from the University of Arizona provides the best explanation of Dr. Margaret Oakley Dayhoff's logic for the non-obvious single letter AA abbreviations:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glutamine ~ &lt;strong&gt;Q&lt;/strong&gt;-tamine therefore, Q&lt;/p&gt;&#xA;" OwnerUserId="3156" LastActivityDate="2013-02-26T18:45:20.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7370" PostTypeId="1" CreationDate="2013-02-26T21:51:43.670" Score="3" ViewCount="1047" Body="&lt;p&gt;I have a problem with a molecular biology question; I don’t understand how DNA 3’ labelling works.&#xA;I took a diagram from my lesson and tried to understand with it; this is what I understood.&#xA;If I’m wrong, please tell me and correct me.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;We take a restriction enzyme which will cut both strands. The bottom strand will be a 5’ end. So, the top strand is shorter than the bottom strand.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;We will add a Klenow fragment which, with its polymerase activity, polymerizes in the 5’-&gt;3’ direction the missing part of the top strand, with dNTP α &lt;sup&gt;32&lt;/sup&gt;P (labelled by a radioactive phosphate in the alpha position).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;We get two strands which have the same size, of which one will be strongly labelled.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;We finish with a terminal transferase which will catalyse the addition of dNTP α &lt;sup&gt;32&lt;/sup&gt;P on the 3’OH ends of both DNA strands (in order to label these ends).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;But, if I’m right, could you explain the necessity of the last step; why label both ends since we have already labelled the top strand?&lt;/p&gt;&#xA;" OwnerUserId="3158" LastEditorUserId="1320" LastEditDate="2013-02-27T07:28:09.110" LastActivityDate="2013-10-16T18:40:03.857" Title="Why re-label the strand ends in 3' DNA labelling?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7372" PostTypeId="2" ParentId="2843" CreationDate="2013-02-26T23:38:28.433" Score="7" Body="&lt;p&gt;You are right - most jumping spiders have draglines they secure to the surface before they jump.  &lt;a href=&quot;http://books.google.com/books?id=JU0w9HVElf8C&amp;amp;pg=PT72&amp;amp;ei=iEUtUbH6N4zBiwKh_IGQAw&amp;amp;ved=0CFAQ6AEwBA#v=onepage&amp;amp;q&amp;amp;f=false&quot;&gt;They can't defy gravity, but they can recover from a miss if they do this&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Disturb a jumping spider on a wall, and watch it seemingly defy gravity: it will jump horizontally out into the air, then return to the wall.  This seems fantastic until you spot the major ampullate dragline.  It essentially becomes the bob at the end of a pendulum string. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;the book goes on to explain that the dragline is used as an airbrake and a spring to help the spider control the jump, which might make it seem to do unnatural things when jumping from a ceiling.  You might want to get a video of this if you can. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the &lt;a href=&quot;http://books.google.com/books?id=eKGk7jhOH20C&amp;amp;pg=PA158&amp;amp;#v=onepage&amp;amp;q&amp;amp;f=false&quot;&gt;references in another book here&lt;/a&gt;, point to other uses of draglines - the spiders can tell each other's species by them, attract a mate. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-02-26T23:38:28.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7373" PostTypeId="2" ParentId="7368" CreationDate="2013-02-27T01:32:10.873" Score="-1" Body="&lt;p&gt;If you work in a lab, there must be a SOP(Standard Operating Procedure) and you can (You should...) follow that. Each lab will have different standard so providing a single definitive answer here may not be beneficial. &lt;/p&gt;&#xA;" OwnerUserId="3139" LastActivityDate="2013-02-27T01:32:10.873" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7374" PostTypeId="1" CreationDate="2013-02-27T13:32:04.523" Score="-3" ViewCount="144" Body="&lt;p&gt;We are looking for an enzyme that appears in C. elegans but isn't common for: human, Drosophila or mouse.&#xA;We need it for a little research project, thanks for your help!&lt;/p&gt;&#xA;" OwnerUserId="3161" LastEditorUserId="1320" LastEditDate="2013-02-27T18:16:47.383" LastActivityDate="2013-03-21T00:58:08.960" Title="Specific enzyme for C. elegans" Tags="&lt;bioinformatics&gt;&lt;enzymes&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="0" ClosedDate="2013-03-21T19:25:19.967" ContentLicense="CC BY-SA 3.0" />
  <row Id="7375" PostTypeId="1" CreationDate="2013-02-27T16:34:52.000" Score="1" ViewCount="68" Body="&lt;p&gt;An often-used analysis of feedstocks for lifestocks is the Weender analysis, which basically divides the volatile solid content into fats, fibre and protein, as well as N-free matter. I found no English language article on the process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The individual values and how they are arrived at are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Fat: anything dissolvable in organic solvents;&lt;/li&gt;&#xA;&lt;li&gt;Fibre: anything not dissolvable in acids or bases;&lt;/li&gt;&#xA;&lt;li&gt;Protein: N-content times 6,25 or 6,38 for plants or protein (and the N-content in protein is most of the times close to 16%);&lt;/li&gt;&#xA;&lt;li&gt;N-free: the rest (sugars, starch, pectines, organic acids ...).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This data is often more readily available than a full chemical analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know the sulphur content - can I reliably say fats contain v mass-% sulphur, proteins x mass-% ... and so on?&#xA;If yes, would this be applicable to manure also?&lt;/p&gt;&#xA;" OwnerUserId="3037" LastEditorUserId="1320" LastEditDate="2013-02-27T18:14:57.413" LastActivityDate="2014-09-28T18:34:14.107" Title="Can the sulphur content of biological material be reliably calculated from fat, fibre and protein contents (Weender Analysis)?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7377" PostTypeId="1" AcceptedAnswerId="7382" CreationDate="2013-02-27T19:41:21.070" Score="2" ViewCount="652" Body="&lt;p&gt;Do invertebrates (like &lt;em&gt;Drosophila&lt;/em&gt; and &lt;em&gt;C.elegans&lt;/em&gt;) have a urea cycle?&lt;/p&gt;&#xA;" OwnerUserId="3163" LastEditorUserId="107" LastEditDate="2013-02-28T12:57:59.590" LastActivityDate="2013-02-28T21:58:52.337" Title="Does the Urea Cycle exist in invertebrates?" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7378" PostTypeId="1" CreationDate="2013-02-28T00:57:59.897" Score="7" ViewCount="1450" Body="&lt;p&gt;When I browsed NCBI I saw a pattern: even if the chromosome sizes, number of genes, and number of proteins are different, GC% in chromosomes tend to be similar. The examples are linked below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/genomes/15?details=on&amp;amp;&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yeast&lt;/a&gt;, &#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/genomes/33?details=on&amp;amp;&quot; rel=&quot;nofollow noreferrer&quot;&gt;Plasmodium falciparum&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you see Mitochondria genome it is not very similar to chromosome. Why all chromosomes tend adjust their GC% near to the average of total GC%&#xA;Is there a specific reason related to metaphase of meosis?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;to further clarify I have some images to help&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/i9PbC.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/6A3NH.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The chromosome size or genes in an organism are not adjusting near the average of their total but GC% does. It has only 3-2% (falciparum) or 3-4% (vivax) variation in GC%. It feel like its balancing like equalizer. Why?&lt;/p&gt;&#xA;" OwnerUserId="3164" LastEditorDisplayName="user560" LastEditDate="2013-03-12T22:16:33.723" LastActivityDate="2013-04-13T19:30:06.633" Title="Chromosomes are of different size but why do all chromosomes have similar GC percentage?" Tags="&lt;genetics&gt;&lt;chromosome&gt;&lt;genomes&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7379" PostTypeId="1" AcceptedAnswerId="7386" CreationDate="2013-02-28T09:44:53.447" Score="0" ViewCount="80" Body="&lt;p&gt;Is there a protein that catalyzes this or does it happen spontaneously?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In which part of the cell does this happen?&lt;/p&gt;&#xA;" OwnerUserId="1190" LastEditorUserId="1320" LastEditDate="2013-02-28T21:42:43.567" LastActivityDate="2013-03-01T02:15:11.220" Title="How do amino acids become attached to tRNA?" Tags="&lt;molecular-genetics&gt;&lt;rna&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7380" PostTypeId="1" CreationDate="2013-02-28T10:26:37.573" Score="1" ViewCount="100" Body="&lt;p&gt;Are there any studies of epigenetic difference between twins during their lifespan ? I ask because I wonder if there exist phases during lifespan, when environmental factors plays major role (expecially in early adulthood) - twins study should allow to distinguish between changes in epigenetic  profile caused by external factors and that from &quot;inner dynamics&quot; of organism.&lt;/p&gt;&#xA;" OwnerUserId="3016" LastActivityDate="2013-02-28T13:43:45.967" Title="Are there any studies of epigenetic difference between twins during their lifespan?" Tags="&lt;human-biology&gt;&lt;human-genetics&gt;&lt;epigenetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7381" PostTypeId="2" ParentId="7380" CreationDate="2013-02-28T13:43:45.967" Score="3" Body="&lt;p&gt;I would think there have to be, though do you mean collecting samples on a regular basis and plotting out the difference at each point? Or do you simply mean the total accumulated change. If it is the latter, the answer is certainly &quot;yes&quot;. You have probably seen the Nova documentary &quot;&lt;a href=&quot;http://www.youtube.com/watch?v=0o9f0VlyP5o&quot; rel=&quot;nofollow&quot;&gt;Ghost in Your Genes&lt;/a&gt;&quot; (The US, not BBC one). In it they show comparison of accumulated epigenetic change between a pair of identical twin Spanish women. I'm guessing you are more looking at measuring this change on a regular basis and looking for points of rapid divergence.... I don't know if this has been done for individuals, but it appears that it has been done for sample sets (see the same documentary). They discuss accumulated genetic change in younger twins vs older ones...&lt;/p&gt;&#xA;" OwnerUserId="1710" LastActivityDate="2013-02-28T13:43:45.967" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7382" PostTypeId="2" ParentId="7377" CreationDate="2013-02-28T13:50:55.623" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.genome.jp/kegg-bin/show_pathway?org_name=cel&amp;amp;mapno=00330&amp;amp;mapscale=&amp;amp;show_description=hide&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;C. elegans&lt;/em&gt; is missing all&lt;/a&gt; of the urea cycle enzymes. &lt;a href=&quot;http://www.genome.jp/kegg-bin/show_pathway?org_name=dme&amp;amp;mapno=00330&amp;amp;mapscale=&amp;amp;show_description=hide&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Drosophila&lt;/em&gt; is missing just one enzyme&lt;/a&gt;, but there's a shortcut which may enable it to nonetheless complete the cycle. (For comparison, here's the &lt;a href=&quot;http://www.genome.jp/kegg-bin/show_pathway?org_name=hsa&amp;amp;mapno=00330&amp;amp;mapscale=&amp;amp;show_description=hide&quot; rel=&quot;nofollow&quot;&gt;pathway map&lt;/a&gt; for human with the complete cycle.)&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2013-02-28T13:50:55.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7383" PostTypeId="2" ParentId="762" CreationDate="2013-02-28T14:08:59.790" Score="4" Body="&lt;p&gt;What you are talking about is genetic vs memetic evolution. While both are important in our species, the memetic evolution is responsible for the changes you are citing (mostly technological advancements and &quot;culture&quot;). There are some interesting situations where memetic evolution is actually &quot;cancelling out&quot; genetic evolution. For example medical technology has largely allowed many (at least in the developed world) to survive in spite of genetic handicaps (lack of resistance to a pathogen, insulin, glasses, etc). &#xA;Despite this I would argue we are still evolving rapidly in the genetic sense though not for the reasons you imply. In most vertebrates (any slow-reproducing creature), there is an ongoing selective pressure against pathogens. If their immune systems don't continually change (and antibiotics don't intervene), pathogens will wipe them out. While not as glorious as developing bipedalism, this is still evolution. We are also now a very transient species with people migrating extensively compared to the recent past. This leads to new genetic combinations and thus potential selection. &#xA;It could be argued (as others have) that the selective pressures for brain development (especially for language ala the FoxP2 gene) have brought about the rise of language, technology and culture. However I would argue that these evolutionary changes largely occurred, at minimum, the last few tens of thousands of years. &#xA;As others have also noted, crazy genius isn't &lt;strong&gt;THE&lt;/strong&gt; end goal of evolution, it is merely &lt;strong&gt;ONE&lt;/strong&gt; possible outcome. The real goal is genetic perpetuation (which we do seem to excel at) ;)&lt;/p&gt;&#xA;" OwnerUserId="1710" LastActivityDate="2013-02-28T14:08:59.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7384" PostTypeId="1" CreationDate="2013-02-28T14:26:33.893" Score="9" ViewCount="364" Body="&lt;p&gt;In light of the &lt;a href=&quot;http://www.washingtonpost.com/politics/supreme-court-weighs-dna-fingerprinting/2013/02/26/5eb3c5b6-804e-11e2-b99e-6baf4ebe42df_story.html&quot;&gt;current US supreme court case&lt;/a&gt;, I'm curious if enough information can be teased out of a DNA sample to get a &quot;reasonable&quot; approximation of the suspect (never mind the legality). I realize the term reasonable is subjective, so characteristics, such as skin color, hair color/texture, approx height, eye color, freckles, etc. I came across &lt;a href=&quot;http://www.wired.com/politics/law/magazine/16-01/ps_dna&quot;&gt;this&lt;/a&gt; article a few years ago, but the company that made the test went bust in 2009. It could detect race (how accurately?). I seem to recall reading an article a few years ago stating that &quot;soon&quot; we'd be able to get an approximation of appearance from a DNA sample that was better than a sketch artist could provide, though I can't recall now where I read it.&lt;/p&gt;&#xA;" OwnerUserId="1710" LastActivityDate="2014-11-03T05:28:47.303" Title="Can forensic DNA analysis be used to generate a visual approximation of a suspect?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;bioinformatics&gt;&lt;genomics&gt;&lt;biotechnology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7386" PostTypeId="2" ParentId="7379" CreationDate="2013-02-28T15:50:13.047" Score="4" Body="&lt;p&gt;The process to which you refer is called &lt;em&gt;tRNA charging&lt;/em&gt; and is catalyzed in the cytosol by a class of enzymes called &lt;a href=&quot;http://en.wikipedia.org/wiki/Aminoacyl_tRNA_synthetase&quot; rel=&quot;nofollow&quot;&gt;aminoacyl tRNA synthetases&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2013-03-01T02:15:11.220" LastActivityDate="2013-03-01T02:15:11.220" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7387" PostTypeId="1" AcceptedAnswerId="7389" CreationDate="2013-02-28T20:11:06.103" Score="1" ViewCount="62" Body="&lt;p&gt;I am not from the field, but have a question regarding modeling in biology:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;I know that some processes can be modeled with the mathematical multiplication operation, and wondered if anyone could give me an example (or examples).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Especially with regards to axonal growth and the chemical (de-)stabilization taking place which involve microtubuli and actin, I was wondering if these processes again could be formalized mathematically as multiplication of (several) variables.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I have looked through the internet but did not find anything so far,&#xA;any help is appreciated&lt;/p&gt;&#xA;" OwnerUserId="3169" LastActivityDate="2013-02-28T21:26:02.183" Title="Multiplication to formalize Microbiological Processes" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7388" PostTypeId="2" ParentId="7378" CreationDate="2013-02-28T20:16:18.147" Score="2" Body="&lt;p&gt;There is significant variation in genomic GC content, both between species and within an individual genome. An average GC content in the range of 35%-45% is common, although there are definitely organisms that fall outside this range. The plasmodium species you link to above is an example of extreme AT richness (low GC content), whereas some bacterial genomes have as much as 70% GC content or more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For eukaryotic genomes, nucleotide composition is not uniformly distributed. Just because a genome has an average GC content of 40% does not mean you can select any 10kb region in the genome and expect that region to have +/-40% GC content. Rather, eukaryotic genomes are a mosaic of large regions which internally have a very uniform composition, but whose composition is quite different from flanking regions (&lt;a href=&quot;http://en.wikipedia.org/wiki/Isochore_%28genetics%29&quot; rel=&quot;nofollow&quot;&gt;isochores&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So although all the chromosomes of a particular organism may have similar &lt;em&gt;average&lt;/em&gt; GC content, realize this is just an average and that nucleotide composition varies significantly throughout the genome.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2013-02-28T20:16:18.147" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7389" PostTypeId="2" ParentId="7387" CreationDate="2013-02-28T21:26:02.183" Score="0" Body="&lt;p&gt;Here's the quick answer you asked for, too big for comments so sorry if this is not a full answer either. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://arxiv.org/pdf/1212.0437v1.pdf&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; is an example of cytoskeletal modelling.  the equations are not simple products (that is to say they have exponentials, derivatives and other non- multiplication operations in them). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This example reference is a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1366631/&quot; rel=&quot;nofollow&quot;&gt;simple axonal growth model&lt;/a&gt;.  You will see derivatives being modeled as products.  Not sure if this is what you are looking for. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-02-28T21:26:02.183" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7390" PostTypeId="2" ParentId="7377" CreationDate="2013-02-28T21:58:52.337" Score="2" Body="&lt;p&gt;Perhaps worth adding that the role of the urea cycle in terrestrial vertebrates is the disposal of excess N derived from protein metabolism. Such animals are ureotelic. Arthropods, in contrast, are uricotelic, using uric acid for N disposal, so it would make no sense for them to have a functional urea cycle. (Nematodes - I don't know.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The importance of avoiding having a urea cycle when it is not needed is illustrated by the situation in yeast (&lt;em&gt;Saccharomyces cerevisiae&lt;/em&gt;). In yeast some of the enzymes that would be part of the urea cycle are used in degrading arginine, while others are used in the biosynthesis of arginine. Yeast cells will carry out one or the other of these processes depending upon their metabolic status. If both processes were to be active at the same time this would result in a urea cycle that would waste ATP. This is avoided by having a multienzyme complex consisting of arginase and ornithine transcarbamoylase (in the degradative and biosynthetic pathways respectively), allowing reciprocal regulation so that only one of these is active at any time. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-02-28T21:58:52.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7391" PostTypeId="2" ParentId="7384" CreationDate="2013-03-01T01:33:16.730" Score="7" Body="&lt;p&gt;In theory it's possible to have an approximation, but not to know with certainty. Identical twins have the same genomes and look very much alike. Whether it can be done in practice depends on how well we can model the relationship between genes and looks &lt;strong&gt;and&lt;/strong&gt; on how much information is necessary for a judge to permit arresting and questioning a suspect. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scientists know relatively little about &lt;strong&gt;how&lt;/strong&gt; genes influence physical appearance yet. The height of the suspect is controlled by hundreds of genes with complicated interplay between them, so I don't think it's possible to estimate it just yet. Eye color is more simple: it's controlled by only 3 genes. We know weight is partially controlled by genetics but exactly which genes are responsible is not clear. Age is impossible to tell by DNA alone. Skin color should be predictable, since it's caused by &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanin&quot;&gt;melanin&lt;/a&gt; production, and we know which genes are responsible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to sum up, DNA analysis can tell the gender, skin color, and eye color of the suspect, but very little about height and weight, and virtually nothing about age. That's not enough information to identify a suspect, although perhaps someone with legal knowledge could comment on this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But let's say in the future we know enough to determine all these traits. Then DNA analysis would be &lt;strong&gt;helpful&lt;/strong&gt; but never &lt;strong&gt;enough&lt;/strong&gt; to identify a suspect. The problem is that different cells in your body undergo different mutations in their DNA with time. That's how one gets cancer. Let's say there's a mutation in the eye color gene in skill cells from a murderer found on a victim's body. It won't affect the murderer's eye color but it will affect the forensic analysis. So it's impossible to know for sure what the suspect's appearance will be.&lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-03-01T01:33:16.730" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7392" PostTypeId="1" CreationDate="2013-03-01T03:37:55.460" Score="2" ViewCount="150" Body="&lt;p&gt;I have been intrigued by this question. Can palisade cells survive independently from its parent plant in a chemical environment? For example, if we were to separate a palisade cell from a plant and place it in sucrose solution, how long would it survive?&lt;/p&gt;&#xA;" OwnerUserId="3170" LastActivityDate="2013-03-01T18:08:27.873" Title="Can Palisade Cells Survive Independently?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7393" PostTypeId="1" AcceptedAnswerId="7398" CreationDate="2013-03-01T04:33:57.957" Score="6" ViewCount="1129" Body="&lt;p&gt;I am in an embryology course right now and we've just started covering cell-cell communication in development. We were talking about the roles of the various cadherins and their discoveries but we got to cell signaling pathways and in reading my textbook I'm finding myself confused by these pathways-- some of those that are mentioned include Notch, Wnt, FGF, TGF-beta, RTK, Jak-Stat, SMAD, integrins, PTHrP, Hedgehog, Discoidin domain receptors 1&amp;amp;2, and the unfolded protein response (UPR). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know the RTK pathway and I know the SMAD pathway, but the others just seem to be specific ligands that are using these pathways -- is this correct?&lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2013-03-01T18:18:53.553" Title="Question about cell signaling pathways (RTK, Jak-Stat, SMAD, etc)" Tags="&lt;development&gt;&lt;cell-signaling&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7394" PostTypeId="1" AcceptedAnswerId="7396" CreationDate="2013-03-01T08:23:54.090" Score="3" ViewCount="125" Body="&lt;p&gt;I am using Fermentase First strand cDNA synthesis kit but its buffer is over. I need to work today but I have not access to any sorce currently. I have PCR buffer in the lab. Can I use PCR buffer instead of cDNA synthesis buffer? What are your other suggestions? Thank you&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="3053" LastEditDate="2013-03-01T17:00:23.377" LastActivityDate="2013-03-01T17:00:23.377" Title="Can I use PCR buffer instead of cDNA synthesis buffer?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7395" PostTypeId="2" ParentId="7393" CreationDate="2013-03-01T14:47:53.787" Score="0" Body="&lt;p&gt;With the exception of Jak/Stat, all of the proteins you mentioned are ligands and/or receptors. When a &lt;em&gt;ligand&lt;/em&gt; binds to a &lt;em&gt;receptor&lt;/em&gt;, it induces one or more cell signaling &lt;em&gt;pathways&lt;/em&gt;, which are dependent on intracellular proteins being activated via association with the receptor, then going on to activate other proteins in a &lt;em&gt;signaling cascade&lt;/em&gt; that eventually results in the cell doing something - usually involving regulating gene transcription to make proteins that effect the change - such as altering the cell's developmental fate to become more specialized, for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Jak/Stat is an example of a cell signaling pathway, that is also fairly straightforward to understand. Various members of the &lt;em&gt;Jak&lt;/em&gt; family are loosely associated with a variety of receptor proteins. When those receptors are activated by a ligand binding to them, Jak becomes activated and recruits various members of the &lt;em&gt;Stat&lt;/em&gt; family of transcription factors. The Stats become activated and dimerize (form doublets), then translocate to the nucleus and bind specific promoter regions of DNA. They then recruit the rest of the DNA transcription machinery to transcribe these target genes. The gene products then help effect the cell's response to the original stimulation - the binding of the ligand to the receptor.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-03-01T14:47:53.787" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7396" PostTypeId="2" ParentId="7394" CreationDate="2013-03-01T15:47:30.847" Score="6" Body="&lt;p&gt;&lt;a href=&quot;http://www.enzymatics.com/product_p7040-l.htm&quot;&gt;This page&lt;/a&gt; has the recipe for 10X M-MuLV RT buffer:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;500 mM Tris-HCl &lt;/li&gt;&#xA;&lt;li&gt;750 mM KCl&lt;/li&gt;&#xA;&lt;li&gt;30 mM MgCl2&lt;/li&gt;&#xA;&lt;li&gt;100 mM DTT&lt;/li&gt;&#xA;&lt;li&gt;pH 8.3&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you have the basic reagents, I suggest making that. &lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-03-01T15:47:30.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7397" PostTypeId="2" ParentId="7392" CreationDate="2013-03-01T17:59:50.697" Score="2" Body="&lt;p&gt;Yes they can. In 1902 Haberlandt reported single palisade cell culture from leaves in knop’s salt solution. Now there are many different methods of plant tissue culture&lt;/p&gt;&#xA;&#xA;&lt;p&gt;for PLANT TISSUE CULTURE &lt;a href=&quot;http://www.liv.ac.uk/~sd21/tisscult/what.htm&quot; rel=&quot;nofollow&quot;&gt;see&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1839" LastEditorUserId="1839" LastEditDate="2013-03-01T18:08:27.873" LastActivityDate="2013-03-01T18:08:27.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7398" PostTypeId="2" ParentId="7393" CreationDate="2013-03-01T18:18:53.553" Score="3" Body="&lt;p&gt;@Alexandria Jak/Stat are two families of proteins which mediate signals through phosphotyrosines.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;JAK is a tyrosine kinase which binds to cell receptors and STAT is dimerized by JAK action.  JAK specificity seems to be your question.  A specific JAK protein (e.g. JAK1 or JAK2..) may mediate for &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1074552111000883&quot; rel=&quot;nofollow noreferrer&quot;&gt;different receptors in different cells&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There may be hetero- or homo-dimers of JAK, there may be more than one receptor in a cell using the same JAK enzyme, which may result in cross-talk between the two signals.  I think its a pathway dynamic that can vary quite a bit from one cell to another, depending on the receptor and cytokine environment the cell is seeing. JAK action can be modulated by any number of proteins which respond to other pathway signals or the cell state.  The diagram below from a &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S016372580800140X&quot; rel=&quot;nofollow noreferrer&quot;&gt;review of heart muscle cell JAK action&lt;/a&gt; is not unusual nor is it complete.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/A2wP1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-03-01T18:18:53.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7399" PostTypeId="2" ParentId="7378" CreationDate="2013-03-01T20:16:14.983" Score="1" Body="&lt;p&gt;Good answer from Daniel. I'd also add that there can be significant differences between chromosomal or nuclear DNA GC content and that of extra-chromosomal entities like mitochondrial and chloroplast genomes or (naturally occurring) plasmids. These DNAs have different constraints on them (replication, sub-cellular location, eg) and that may be reflected to some degree by a GC content different than that of the nuclear chromosomes.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2013-03-06T18:48:58.580" LastActivityDate="2013-03-06T18:48:58.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7400" PostTypeId="1" AcceptedAnswerId="7409" CreationDate="2013-03-01T20:22:40.513" Score="3" ViewCount="1116" Body="&lt;p&gt;I know from school, that all live on the Earth need &lt;strong&gt;bacteria&lt;/strong&gt; as low-level &quot;&lt;em&gt;machines&lt;/em&gt;&quot; that break down/extract/convert/produce chemical elements and combinations, other high-level organisms needed. But it is a natural way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But is it possible to have a world with plants (without mammals or microorganisms and &lt;strong&gt;without bacteria&lt;/strong&gt;) that could exist in the long term. Saying the atmosphere of these world has already enough nitrogen, oxygen and CO&lt;sub&gt;2&lt;/sub&gt;, and of course there is water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What could break this artificially created world with such conditions (say the world created not from low-level living structures)?&#xA;Could bacteria emerge in the world?&lt;/p&gt;&#xA;" OwnerUserId="3173" LastEditorUserId="1320" LastEditDate="2013-03-02T08:11:48.840" LastActivityDate="2016-12-28T17:15:00.950" Title="Plants without bacteria? is it theoretically possible?" Tags="&lt;evolution&gt;&lt;biochemistry&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;&lt;life&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7401" PostTypeId="1" CreationDate="2013-03-01T21:40:55.727" Score="10" ViewCount="13284" Body="&lt;p&gt;We all carry two copies of each gene (outside of male sex chromosomes).  If the two differ from each other often one is dominant and one recessive.  How does this mechanism work on a molecular level?  What mechanism determines which gene gets expressed?&lt;/p&gt;&#xA;" OwnerUserId="3174" LastEditorUserId="1320" LastEditDate="2013-03-02T08:13:34.520" LastActivityDate="2015-02-03T07:24:45.557" Title="What makes a gene dominant or recessive" Tags="&lt;genetics&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="5" ClosedDate="2015-02-03T07:28:05.080" ContentLicense="CC BY-SA 3.0" />
  <row Id="7402" PostTypeId="2" ParentId="7401" CreationDate="2013-03-01T22:02:37.587" Score="3" Body="&lt;p&gt;Generally if one of the genes' biochemical functions becomes knocked out completely, the other copy will fill in for it, making the trait &lt;em&gt;recessive&lt;/em&gt; - requiring both copies being knocked out.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of such a recessive trait is Albinism - &lt;a href=&quot;http://www.mayoclinic.com/health/albinism/DS00941/DSECTION=causes&quot; rel=&quot;nofollow&quot;&gt;if both copies of the enzyme participating in melanin biosynthesis are ineffective&lt;/a&gt;, the result is someone with no pigment.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Dominant&lt;/em&gt; genes are often variant genes which convey a new ability (phenotype) and as such the trait can show up with just one copy has this variant.  &lt;a href=&quot;http://www.britannica.com/EBchecked/topic/455706/phenylthiocarbamide-tasting&quot; rel=&quot;nofollow&quot;&gt;Phenylthiocarbamide tasting is an example of this dominance&lt;/a&gt;.  If both copies of the gene were the variant, the original ability might disappear - making the original trait dominant as well.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other sorts of dominance.  If a variant shows up that inhibits a the other copy this can cause dominance by a variant; it can remove or modulate a phenotype (trait) by turning off or turning down the other copy of the gene.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC276041/&quot; rel=&quot;nofollow&quot;&gt;This would be a case of &lt;em&gt;trans-dominance.&lt;/em&gt;&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure there are many other variants on these themes others could post.  Dominance and recessivity are relative and broad terms when you see how traits are inherited. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-03-01T22:02:37.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7403" PostTypeId="2" ParentId="7401" CreationDate="2013-03-01T22:12:59.607" Score="9" Body="&lt;p&gt;On the molecular level, genes most often encode proteins which perform some function for the cell: For example, they could be enzymes and catalyze chemical reactions. They could also have some structural function, such as make up the &quot;muscle&quot; part of your muscle cells... You get the idea. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the most simple case, the dominant allele encodes a protein that can perform its function. &lt;a href=&quot;http://ghr.nlm.nih.gov/condition/cystic-fibrosis&quot;&gt;For example, the dominant allele for the CFTR gene encodes a channel that can let chloride into and out of the cells.&lt;/a&gt; The recessive allele, on the other hand encodes a protein that cannot do its job correctly (this also called a loss-of-function mutation). So if you inherit a functional copy from one parent and a non-functional copy from the other parent, you will still have one copy of the protein that can do its job. &lt;strong&gt;Only&lt;/strong&gt; if you get a nonfunctional copy from both parents will you have a &lt;strong&gt;recessive&lt;/strong&gt; condition called cystic fybrosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the molecular level a gene can also encode a dominant-negative variant of a protein. In this case the protein cannot do its job &lt;strong&gt;and&lt;/strong&gt; also prevents the functional version of the protein to do its job too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A third way this could work is by a gain-of-function mutation. In this case, the gene encoding a protein acquires a mutation that gives a new function to the protein. For example, in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001775/&quot;&gt;Huntington's disease&lt;/a&gt;, the mutant Huntingtin protein acquires the ability to clump together in large plaques, which are poisonous to some neurons in the brain. Since it takes only one copy of the protein to perform the new function, the gain-of-function allele is a dominant one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are only a few examples that deal with simple dominant and recessive inheritance. Most often &lt;a href=&quot;http://en.wikipedia.org/wiki/Dominance_%28genetics%29&quot;&gt;there are more complex mechanisms of inheritance at play.&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-03-01T22:12:59.607" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7404" PostTypeId="1" AcceptedAnswerId="7406" CreationDate="2013-03-01T22:57:07.607" Score="1" ViewCount="694" Body="&lt;p&gt;I want to start learning Neuroscience. Can someone give me an advice about a nice textbook for beginners? I'm particularly interested in the application of Neuroscience in programming and AI development. Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="3175" LastActivityDate="2013-03-02T09:42:48.573" Title="A good textbook on Neuroscience" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2013-03-02T21:39:25.090" ContentLicense="CC BY-SA 3.0" />
  <row Id="7405" PostTypeId="2" ParentId="6932" CreationDate="2013-03-02T01:44:41.910" Score="6" Body="&lt;p&gt;Just so that someone answers this question so that the moderators have less work to do: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fundamental reason why embryos don't get massacred by the maternal immune system is because of the placenta and several of its functions. Three mechanisms are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Secretion of neurokinin B, which is also secreted by parasites to avoid detection of the host. &lt;br&gt;&#xA;2) The placenta has developed immunoevasive actions from a virus. It creates a syncytium to limit transaction of mobile immune cells. &lt;br&gt;&#xA;3)It only allows specific antibodies,(IgG) to enter and bind infection. (IgG being the only isotype here). &lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yay  for biology &lt;/p&gt;&#xA;" OwnerUserId="1913" LastActivityDate="2013-03-02T01:44:41.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7406" PostTypeId="2" ParentId="7404" CreationDate="2013-03-02T09:42:48.573" Score="0" Body="&lt;p&gt;If you are interested in computational neuroscience, I recommend Dayan and Abbott's book: &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0262541858&quot; rel=&quot;nofollow&quot;&gt;http://www.amazon.com/gp/aw/d/0262541858/ref=redir_mdp_mobile/181-1988504-8834745&lt;/a&gt;. This is not a book on neuroscience, not AI, although this particular book has more math than the other introductory neuroscience textbooks I've seen. &lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-03-02T09:42:48.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7407" PostTypeId="1" CreationDate="2013-03-02T10:18:10.643" Score="2" ViewCount="276" Body="&lt;p&gt;When the average person &lt;strong&gt;overeats&lt;/strong&gt;, how much food can he eat in a day? Which animal's average meal would that be equivalent to?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When documentaries are talking about animals feed, they usually say something like &quot;The fish can eat 500kg of prawns in a day!&quot; But when it comes to humans, they calculate in calories. Which animals are we closest to in terms of capacity?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: I think I can be slightly loose on the definition of overeating here. It can mean eating beyond the point of feeling full, or the human maximum stomach capacity.&lt;/p&gt;&#xA;" OwnerUserId="746" LastActivityDate="2013-03-02T17:25:39.847" Title="How much food can an average person eat, and which animal is that equivalent to?" Tags="&lt;food&gt;" AnswerCount="0" CommentCount="0" ClosedDate="2014-12-11T05:58:05.870" ContentLicense="CC BY-SA 3.0" />
  <row Id="7408" PostTypeId="1" AcceptedAnswerId="7434" CreationDate="2013-03-02T10:45:54.747" Score="2" ViewCount="1425" Body="&lt;p&gt;Could someone please explain the following process to me:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/91prk.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This process refers to carbon cycling in lakes and is described in the context of $CO_2$ flux from lakes into the atmosphere. GPP is &lt;a href=&quot;http://en.wikipedia.org/wiki/Primary_production#GPP_and_NPP&quot; rel=&quot;nofollow noreferrer&quot;&gt;gross primary production&lt;/a&gt;, $CO_2$ is carbon dioxide, R is respiration, and OM is &lt;a href=&quot;http://en.wikipedia.org/wiki/Organic_matter&quot; rel=&quot;nofollow noreferrer&quot;&gt;organic matter&lt;/a&gt;. I realize that this question may be rather simplistic to some but my basic knowledge of any biological/ecological processes is rather limited. So, basically what I am asking is&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;have I written this process correctly?&lt;/li&gt;&#xA;&lt;li&gt;how can this process be described?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3178" LastEditorUserId="137" LastEditDate="2013-03-04T19:57:53.850" LastActivityDate="2013-03-04T19:57:53.850" Title="How does this diagram illustrate carbon cycling in lakes?" Tags="&lt;photosynthesis&gt;&lt;respiration&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7409" PostTypeId="2" ParentId="7400" CreationDate="2013-03-02T16:20:17.980" Score="4" Body="&lt;p&gt;This is the sort of question that should be considered from more than one perspective.  Since this is speculation, take it as a given that there is a lot of 'what if' here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I doubt most animals and plants can do entirely without bacteria - as you say most of the essential nutrients come from bacteria, who fix &lt;a href=&quot;http://en.wikipedia.org/wiki/Nitrogen_fixation#Biological_nitrogen_fixation&quot; rel=&quot;nofollow&quot;&gt;nitrogen&lt;/a&gt;.  If only plants were left on earth, eventually the plants would use up all the nitrogen and they would have to find a way to fix more.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can bacteria emerge from just a world of plants?  I don't think viruses arise spontaneously, but since genomes often have viruses embedded in them, over the course of a billion years or so, its possible since bacteria and viruses continue to be impressed upon our genomes.  Would it happen in time?  Most would be skeptical whether that timing could work out.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practice it would be hard to create a world like this.  I would be interested to see whether you could sterilize the microorganisms off of seeds without killing the plant for instance.  If you're asking about a small sterile environment with only plants, you could do it by adding the nutrients the plants need and giving them sunlight.  Such self sustaining systems have been made with cyanobacteria and i'd be surprised if plants could not be included.  But these are closed systems and judged by limited amounts of time, so whether this is an answer to your question is not clear.  &lt;a href=&quot;http://www.biospheresystems.com/closedecosystems.html&quot; rel=&quot;nofollow&quot;&gt;Here it looks like some water plants and fish have been done.&lt;/a&gt;  If there was a plant that created CO₂ at an adequate rate its possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At one time there were no animals at all.  Its thought that for a while there might have only been photosynthetic structures that lay in the water and soaked up the rays.  Its not clear whether as some say there were &lt;a href=&quot;http://en.wikipedia.org/wiki/Stromatolite#Fossil_record&quot; rel=&quot;nofollow&quot;&gt;colony formations of cyanobacteria as we see today&lt;/a&gt;, or whether there may have been larger pre-cellular or proto-cellular structures.  But recovering the pre-cambrian configurations of genes from just plant genomes seems like a gambler's bet to me. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3340" LastEditDate="2014-10-09T15:03:23.387" LastActivityDate="2014-10-09T15:03:23.387" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7411" PostTypeId="1" AcceptedAnswerId="7422" CreationDate="2013-03-02T18:14:22.217" Score="2" ViewCount="196" Body="&lt;p&gt;Some of my family and friends seem to believe that vegetables/food should be subjected to as few freeze/thaw cycles as possible. The rationale put forward is that each such cycle reduces nutrition (sp. nutritive?) value, and accelerates rot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm skeptical; &lt;strong&gt;Do repeated (sp. repetitive?) freeze/thaw cycles strip nutrition from vegetables/food&lt;/strong&gt;? &lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="16866" LastEditDate="2017-04-03T17:30:32.073" LastActivityDate="2017-04-03T17:31:38.653" Title="Do repeated freeze-thaw strip nutrition from vegetables/food?" Tags="&lt;food&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7412" PostTypeId="1" AcceptedAnswerId="7413" CreationDate="2013-03-02T20:32:35.603" Score="8" ViewCount="333" Body="&lt;p&gt;It's obvious how a misdisjunction can result in klinefelter's syndrome (XXY) but I don't see how this can result in XYY syndrome. Your parents have a collective total of only one Y chromosome so how can any misdisjunction result in a child with two Y chromosomes?&lt;/p&gt;&#xA;" OwnerUserId="3180" LastActivityDate="2013-03-02T22:14:29.673" Title="What causes XYY Syndrome?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7413" PostTypeId="2" ParentId="7412" CreationDate="2013-03-02T22:14:29.673" Score="8" Body="&lt;p&gt;It comes from a Y nondisjunction in the father. Anaphase nondisjunction of the Y yields a YY, which goes with one X from the mother to give XYY.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-03-02T22:14:29.673" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7414" PostTypeId="1" AcceptedAnswerId="7415" CreationDate="2013-03-03T12:11:59.783" Score="3" ViewCount="129" Body="&lt;p&gt;I know you can purchase dog and cat breeds that are hypoallergenic so those who are prone to pet allergies will have reduced allergies or none at all. These breeds are specifically bred for that trait, and as a result are typically pricey compared to another breed. These breeds are not necessarily hairless or short-haired, so I do not think it has to do with the amount of fur shed.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What makes these animals different from other breeds in their inability to cause allergies?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1827" LastActivityDate="2013-03-03T17:37:19.060" Title="What Makes A Pet Hypoallergenic" Tags="&lt;allergies&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7415" PostTypeId="2" ParentId="7414" CreationDate="2013-03-03T13:42:36.543" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Pet allergy is an allergic reaction to proteins found not only in the&#xA;  animals' fur or hair but also in saliva, urine, mucous, and hair roots&#xA;  and in the dander sloughed from the animals' skin. Thus, the&#xA;  widespread idea that &quot;hypoallergenic pets&quot; are those that have less&#xA;  hair or shed less is a myth.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Most often, pet allergy is triggered by exposure to the dead flakes of&#xA;  skin (dander) a pet sheds. Any animal with fur can be a source of pet&#xA;  allergy, but pet allergies are most commonly associated with cats,&#xA;  dogs, rodents and horses.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Some dog breeds have been promoted as hypoallergenic because they do&#xA;  not shed their hair, shed very little, or have the same pH as human&#xA;  hair. However, no canine is known to be completely non-allergenic.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Some cat breeds, especially females are likely to have low levels of&#xA;  &lt;a href=&quot;http://en.wikipedia.org/wiki/Fel_d_1&quot; rel=&quot;nofollow&quot;&gt;Fel d 1&lt;/a&gt;, the main allergenic protein.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;There is only one known hypoallergenic horse breed. The Bashkir Curly&#xA;  horse has a uniquely textured coat that lacks the protein (present in&#xA;  all other horse fur) believed to be the source of allergic reactions&#xA;  to equines.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hypoallergenic&quot; rel=&quot;nofollow&quot;&gt;via&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1839" LastEditorUserId="69" LastEditDate="2013-03-03T17:37:19.060" LastActivityDate="2013-03-03T17:37:19.060" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7417" PostTypeId="1" AcceptedAnswerId="7420" CreationDate="2013-03-03T16:45:50.597" Score="1" ViewCount="1048" Body="&lt;p&gt;There are three mechanisms:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;prevention of the interaction between antibiotic and the target PBP;&lt;/li&gt;&#xA;  &lt;li&gt;modification of the binding of the antibiotic to the PBP;&lt;/li&gt;&#xA;  &lt;li&gt;hydrolysis of the antibiotic by a beta-lactamase.&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;  &#xA;  &lt;p&gt;&lt;em&gt;Medical Microbiology&lt;/em&gt;, 6e, p. 200, Murray&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;PBP: penicillin-binding protein&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It may be the case that the most common mechanism is not known.&#xA;It is just one of these three depending on the situation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the most common mechanism by which penicillin resistance develops in &lt;em&gt;S. pneumoniae?&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="57" LastEditDate="2013-03-03T20:26:37.237" LastActivityDate="2013-03-05T05:52:58.617" Title="By what mechanism does penicillin resistance usually develop in Streptococcus pneumoniae?" Tags="&lt;antibiotics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7418" PostTypeId="1" CreationDate="2013-03-03T19:05:02.643" Score="7" ViewCount="1430" Body="&lt;p&gt;A world class athlete spends a lot of time performing intense exercises.  Correct me if I'm wrong, but I assume that these intense exercises causes significant damage to the athlete's cells, but with proper nutrition, they are able replenish these cells with stronger ones.   This process of destroying and re-creating cells causes cell divisions to approach the Hayflick limit faster, and hence shorten the athlete's life expectancy.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also heard that caloric intake causes the number of cell divisions to approach the Hayflick limit faster.  World class athletes generally consume substantially more calories than the average individual, which also contributes to a shorter life expectancy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for this reason, is the life expectancy of world class athletes generally shorter than the average individual? And what about casual athletes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;&#xA;If world class athletes live longer lives than the average individual, why is this so despite performing activities that expedite the deterioration of telemeres, and hence, approach the Hayflick limit faster?&lt;/p&gt;&#xA;" OwnerUserId="3184" LastEditorUserId="3184" LastEditDate="2013-03-04T00:16:05.617" LastActivityDate="2013-05-10T15:47:27.033" Title="Exercise causes number of cell divisions to approach Hayflick limit faster? And hence shorten life expectancy?" Tags="&lt;senescence&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7419" PostTypeId="1" AcceptedAnswerId="7421" CreationDate="2013-03-03T20:19:51.167" Score="2" ViewCount="260" Body="&lt;p&gt;On extended bicycle trips I sometimes slept under a plastic sheet, which helped with mosquitoes on hot nights. But there was a noticeable build-up of ammonia which made this almost impossible for more than an hour or so at a time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Air is mostly nitrogen $(N_2)$ and there is always water (containing hydrogen) on a humid day. But I wonder about the mechanism for the formation of ammonia under these circumstances? There are (according to Wiki) trace amounts of methane and $H_2$ in the air. But methane and hydrogen (g) are I think pretty stable. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder if the presence of exhaled air (containing $CO_2)$ could be a factor?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any ideas.  &lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2015-09-23T18:16:21.070" Title="Formation of ammonia from air and moisture" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7420" PostTypeId="2" ParentId="7417" CreationDate="2013-03-03T20:57:08.700" Score="2" Body="&lt;p&gt;I think your guess is quite spot-on. According to this &lt;a href=&quot;http://genomebiology.com/2011/12/11/R115&quot; rel=&quot;nofollow&quot;&gt;scientific article&lt;/a&gt; I found online, They did a whole genome sequencing on penicillin-resistant &lt;em&gt;Streptococcus pneumoniae&lt;/em&gt; and their conclusion was&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;....is mediated by a mosaic of genes encoding altered&#xA;  penicillin-binding proteins (PBPs). Nonetheless, &lt;em&gt;S. pneumoniae&lt;/em&gt; has&#xA;  also developed non-PBP mechanisms implicated in penicillin resistance.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In clinical medical laboratory point of view, &lt;em&gt;S. pneumoniae&lt;/em&gt;'s AST is done with oxacillin instead of Penicillin because OXA gives better cut-off between Susceptible, Intermediate and Resistance. You may see a big zone of inhibition when you used PEN disk but that doesn't mean the isolate is susceptible to PEN. This may suggests that &quot;hydrolysis of the antibiotic by a beta-lactamase&quot; is less likely to be the main mechanism?&lt;/p&gt;&#xA;" OwnerUserId="3139" LastEditorUserId="107" LastEditDate="2013-03-04T01:19:23.153" LastActivityDate="2013-03-04T01:19:23.153" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7421" PostTypeId="2" ParentId="7419" CreationDate="2013-03-03T22:01:25.343" Score="5" Body="&lt;p&gt;If you're absolutely sure it's Ammonia ($NH_3$) you're smelling, it's probably from &lt;em&gt;you&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ammonia will not spontaneously form at any significant rate from the air. Molecular Nitrogen ($N_2$) is &lt;strong&gt;extremely&lt;/strong&gt; stable. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What &lt;em&gt;can&lt;/em&gt; happen is that during marathon-type activities, muscles turn from carbohydrates (which are later converted into glucose and enter into the Krebs Cycle) as an energy source to proteins themselves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Metabolic_waste&quot; rel=&quot;nofollow&quot;&gt;waste products of protein catabolism&lt;/a&gt; is Ammonia, which is excreted in your sweat if the body can't convert it into Urea ($CH_4N_2O$) quickly enough:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ammonia forms with the oxidation of amino groups (-NH&lt;sub&gt;2&lt;/sub&gt;), which are removed from the proteins when they convert into carbohydrates. It is a very toxic substance and only one nitrogen atom is removed with it. A lot of water is needed for the ammonia excretion.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1320" LastEditDate="2013-03-04T06:02:41.947" LastActivityDate="2013-03-04T06:02:41.947" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7422" PostTypeId="2" ParentId="7411" CreationDate="2013-03-04T01:25:34.937" Score="1" Body="&lt;p&gt;Repeated freeze-thaw has virtually no effect on macronutrients, such as proteins, lipids, and sugars, because these are broken down to their basic building blocks (such as amino acids and simple sugars) upon food digestion anyway. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.deepdyve.com/lp/american-association-for-clinical-chemistry/effect-of-repeated-freezing-and-thawing-on-vitamins-and-hormones-in-6b3T0n2R70&quot; rel=&quot;nofollow noreferrer&quot;&gt;According to this paper&lt;/a&gt; freeze-thaw has no effect on micronutrients, such as vitamins, as well.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What affects nutritious quality is the &lt;strong&gt;length&lt;/strong&gt; of time the food remains frozen. Most household freezers maintain a temperature of -20°C. At this temperature, the food doesn't get spoiled by bacteria, but degradation of vitamins still occurs, albeit at a slower rate. This is critical for some unstable vitamins, such as vitamin A and C. But elements such as iron, calcium, zinc, and phosphorus are not affected at all. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to prevent vitamin degradation for a very long time, you need a freezer that maintains food at -80°C. This is only if you want to keep the food frozen for many months though. &lt;/p&gt;&#xA;" OwnerUserId="3053" LastEditorUserId="16866" LastEditDate="2017-04-03T17:31:38.653" LastActivityDate="2017-04-03T17:31:38.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7423" PostTypeId="1" CreationDate="2013-03-04T08:04:10.457" Score="7" ViewCount="14730" Body="&lt;p&gt;When using a preculture with Ampicillin in my protein expression, I have to get rid of the preculture medium to avoid carrying over too much beta-lactamases that will destroy the ampicillin in the main culture. To do this I pellet the cells and resuspend.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which methods of resuspension are best suited if you need the bacteria alive afterwards? I'm not sure how much force I can apply without harming the bacteria, and resuspending very gently takes a very, very long time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which methods can be used to resuspend bacteria alive, and which ones are the fastest?&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2013-04-05T16:18:26.777" Title="How can I resuspend a cell pellet without harming the bacteria?" Tags="&lt;cell-culture&gt;&lt;lab-techniques&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7424" PostTypeId="1" CreationDate="2013-03-04T10:13:17.723" Score="1" ViewCount="90" Body="&lt;p&gt;Is it possible to do Chip-Seq on specific region of the genome. The idea is to enrich before the sequencing step to have more sensitivity.&lt;/p&gt;&#xA;" OwnerUserId="359" LastEditorUserId="948" LastEditDate="2014-04-20T04:17:38.630" LastActivityDate="2014-04-20T04:17:38.630" Title="Is it possible to do chip-seq on a specfic region?" Tags="&lt;epigenetics&gt;&lt;chip&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7425" PostTypeId="2" ParentId="7423" CreationDate="2013-03-04T10:45:26.230" Score="8" Body="&lt;p&gt;Assuming that you are talking about &lt;em&gt;E. coli&lt;/em&gt;: As long as you are resuspending the cells in a suitable liquid, e.g. fresh medium or buffer, then from my experience you don't have much to worry about - the cells are very robust. I've found that different strains and growth conditions give pellets with very different qualities - some will resuspend quite well with vortexing. If the pellet seems clumpy then trituration is something that I always found to work - pipette up and down until the pellet breaks up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you were going to do some kind of physiological measurement with the resuspended cells then it might require some checking, but if you only intend to regrow and induce expression I would say that giving the cells some time to recover in the new medium (check that absorbance is increasing) before inducing expression should be enough.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-03-04T10:45:26.230" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7426" PostTypeId="2" ParentId="7424" CreationDate="2013-03-04T13:33:42.343" Score="1" Body="&lt;p&gt;If the question here is to perform an assay that only sequences from a specific set of segments of the genome, you probably could, but it would be a lot of work and you'd need a good reason to want to go through that trouble.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not sure how you would limit the nucleotides you get back to a specific region of the genome say.  The entire point of a CHP-Seq experiment is to get as unbiased a set of nucleotides read and so using specific primers designed against only a specific set of the genome would be hard. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually CHP experiments focus the readout they are getting by only focusing on a specific transcription factor for instance.  The number of variants of short binding sequences that usually come out will easily be read by a sequencing lane.  You'd have to have a strong reason not to take all the data genome wide.  Generally the results for many such pulldown sequences are pretty short and frequently can't be found uniquely on the genome, esp if there are lots of binding sites for the protein to be found.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could speculate that you might synthesize labelled primers from random segments of a cut up library coming from a chromosomal segment you cloned somehow.  That again that seems like a lot of work to cut back on the data you get from the experiment without a big reason for doing this.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using a CHP-CHP experiment that only has specific regions tiled can make do something like this - this makes the chip itself more economical, making the experiment more accessible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-03-04T16:47:09.207" LastActivityDate="2013-03-04T16:47:09.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7427" PostTypeId="2" ParentId="7424" CreationDate="2013-03-04T15:49:12.613" Score="0" Body="&lt;p&gt;One way to increase power (if that is your goal) is to limit your mapping step: you only seek to map to a subset of the genome, e.g. promoters or transcribed regions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll post a link later, but the reference is Leuleu et al. 2010 doi: 10.1093/bfgp/elq022&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-03-04T15:49:12.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7429" PostTypeId="1" AcceptedAnswerId="7431" CreationDate="2013-03-04T17:56:39.370" Score="2" ViewCount="14720" Body="&lt;p&gt;My Psychology text book says Serotonin causes &quot;Sleep, arousal levels and emotion&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this really mean that when you are being aroused, Serotonin is released, which in turn makes you sleepy? If so, what evolutionary benefit would that have??&lt;/p&gt;&#xA;" OwnerUserId="3189" LastEditorUserId="1306" LastEditDate="2013-03-04T18:07:23.467" LastActivityDate="2018-11-11T04:09:24.993" Title="Serotonin - Does being aroused make you sleepy?" Tags="&lt;neuroscience&gt;&lt;sleep&gt;&lt;neurotransmitter&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7430" PostTypeId="1" CreationDate="2013-03-04T18:02:10.803" Score="2" ViewCount="2121" Body="&lt;p&gt;Nerve impulses of course go really fast, but the neurotransmitters have to travel through millions of nerves, so how can it go that fast?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it a sort of relay with lots of neurotransmitters taking over at each nerve cell, or do the neurotransmitters go all the way from A to B?&lt;/p&gt;&#xA;" OwnerUserId="3189" LastActivityDate="2013-03-04T18:29:25.667" Title="Does one neurotransmitter travel all the way through the nervous system?" Tags="&lt;neuroscience&gt;&lt;neurotransmitter&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7431" PostTypeId="2" ParentId="7429" CreationDate="2013-03-04T18:09:34.240" Score="1" Body="&lt;p&gt;According to &lt;a href=&quot;http://serendip.brynmawr.edu/exchange/node/1801&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt; [1], serotonin (5HT) inhibits sexual arousal:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Dopamine is generally facilitative to male sexual&#xA;behavior; however, 5-HT is regarded as inhibitory.&#xA;Antidepressants of the selective serotonin reuptake&#xA;inhibitor class (SSRIs, including Prozac and Zoloft)&#xA;impair ejaculatory/orgasmic function and frequently&#xA;inhibit erectile function and sexual interest as well.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However, serotonin can also facilitate erections:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Systemic administration of the 5-HT1B receptor agonist&#xA;anpirtoline impaired ejaculation in male rats. On the&#xA;other hand, stimulation of 5-HT2C receptors with mCPP&#xA;impaired ejaculation but facilitated erections in male&#xA;monkeys, suggesting an increase in parasympathetic&#xA;influence.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Serotonin release also causes sleepiness after ejaculation in males (&lt;a href=&quot;https://psy.fsu.edu/faculty/hull/DA&amp;amp;5HT_pdf.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;5-HT is released in the LHA at the&#xA;time of ejaculation and promotes sexual quiescence during&#xA;the postejaculatory interval&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;There are many signalling molecules used by the human body that have a different effect depending on the cell type they are detected by and the receptor type they activate.&lt;/p&gt;&#xA;&lt;p&gt;I would also like to touch on your question about evolutionary benefit. Evolution does not care about you &lt;em&gt;after&lt;/em&gt; you have reproduced. As long as an individual reproduces, evolution is &amp;quot;happy&amp;quot;. For example, you think falling asleep after sex is counterproductive on the evolutionary scale? What about Mantises where the female will sometimes eat the male during or immediately after copulation. Falling asleep seems like a pretty small thing compared to that (&lt;a href=&quot;http://serendip.brynmawr.edu/exchange/node/1801&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Although the praying mantis is known for its cannibalistic mating process in actuality it only occurs 5-31% of the time. Especially in laboratory conditions of bright lights and confinement, the female is more likely to eat the male as means of survival. &amp;quot;In nature, mating usually takes place under cover, so rather than leaning over the tank studying their every move, we left them alone and videotaped what happened. We were amazed at what we saw. Out of thirty matings, we didn't record one instance of cannibalism, and instead we saw an elaborate courtship display, with both sexes performing a ritual dance, stroking each other with their antennae before finally mating. It really was a lovely display&amp;quot;. (7) There is one species, however, the Mantis religiosa, in which it is necessary that the head be removed for the mating to take effect properly. (5) Sexual cannibalism occurs most often if the female is hungry. But eating the head does causes the body to ejaculate faster. (3)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Anything that makes an individual less likely to reproduce will be selected against. Things that happen &lt;em&gt;after&lt;/em&gt; reproduction do not affect the survival of the species and will not be subject to selective pressures.&lt;/p&gt;&#xA;&lt;h3&gt;References&lt;/h3&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;E. M. Hull, J. W. Muschamp, S. Sato, &lt;em&gt;Physiology &amp;amp; Behavior&lt;/em&gt; &lt;strong&gt;83&lt;/strong&gt; (2004) 291 – 307&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-11-27T12:36:01.797" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7432" PostTypeId="2" ParentId="7430" CreationDate="2013-03-04T18:22:07.013" Score="9" Body="&lt;p&gt;You've got a few things mixed up here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;strong&gt;signal&lt;/strong&gt; may travel down a pathway, passing through several &lt;a href=&quot;http://en.wikipedia.org/wiki/Neuron&quot;&gt;neurons&lt;/a&gt; (e.g. around 4-8). However, this signal is not always in the same form: From one end of a neuron to the other, it is merely an &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Electric_potential&quot;&gt;electric potential&lt;/a&gt;&lt;/em&gt; which travels down the neuron's &lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_membrane&quot;&gt;cell membrane&lt;/a&gt; (from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Dendrite&quot;&gt;dendrite&lt;/a&gt; to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Axon_hillock&quot;&gt;axon hillock&lt;/a&gt;, where the cell decides whether to carry the signal on; if yes, a new potential is sparked to travel down the &lt;a href=&quot;http://en.wikipedia.org/wiki/Axon&quot;&gt;axon&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the potential reaches the end of a neuron, i.e. an axon terminal, it causes &lt;a href=&quot;http://en.wikipedia.org/wiki/exocytosis&quot;&gt;exocytosis&lt;/a&gt; of &lt;a href=&quot;http://en.wikipedia.org/wiki/Neurotransmitter&quot;&gt;neurotransmitter&lt;/a&gt;. The signal has become &lt;em&gt;chemical&lt;/em&gt; now. This diffuses through the &lt;a href=&quot;http://en.wikipedia.org/wiki/Synapse&quot;&gt;synaptic cleft&lt;/a&gt; to the next neuron, where it acts on &lt;a href=&quot;http://en.wikipedia.org/wiki/Ion%20channel&quot;&gt;ion channels&lt;/a&gt; in the membrane to cause a new electric potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the actual distance a neurotransmitter travels is only the distance between the two membranes at the synapse, i.e. the synaptic cleft. This is only about 20-40 nm wide, so it's fairly rapid :)&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="1320" LastEditDate="2013-03-04T18:29:25.667" LastActivityDate="2013-03-04T18:29:25.667" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7433" PostTypeId="1" CreationDate="2013-03-04T19:10:04.377" Score="4" ViewCount="392" Body="&lt;p&gt;This question came to mind after reading this &lt;a href=&quot;http://www.patient.co.uk/health/sweat-test&quot; rel=&quot;nofollow noreferrer&quot;&gt;article&lt;/a&gt;. The article speaks of inducing sweating to determine, by a roundabout fashion, the amount of salt therein. I'm no medic but I find myself wondering whether sweat may be used directly to measure any other chemicals secreted by the body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;For instance&lt;/em&gt;: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If one's kidney/liver were to suffer some malady would the body attempt to discharge some additional waste through one's sweat&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What chemicals may be detected by analysing sweat?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="6307" LastEditDate="2017-04-03T04:27:36.077" LastActivityDate="2017-04-03T05:07:35.260" Title="What chemicals can be detected in sweat?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;physiology&gt;&lt;human-physiology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7434" PostTypeId="2" ParentId="7408" CreationDate="2013-03-04T19:43:48.347" Score="3" Body="&lt;p&gt;This shows the major biological transformations of carbon in any system (not just lakes).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;On the Left Side:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;$GPP$ (Gross Primary Production) is the total amount of $C$ from atmospheric $CO_2$&lt;sup&gt;&amp;dagger;&lt;/sup&gt; that is reduced into organic molecules during the calvin cycle of photosynthesis.  This is the process performed by photosynthetic organisms like green plants and algae. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&amp;dagger; atmospheric $CO_2$ diffuses into water and develops into several species of inorganic carbon molecules that plants and algae can use but in general you can think of this carbon as being very closely related to atmospheric $CO_2$&lt;/sub&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;$OM$ is a pool of organic matter, which is a general term for reduced carbon molecules.  $OM$ can be living organism tissues (e.g., a fish), dead tissues (e.g., senescent leaves) or biologically generated organic molecules (e.g., sugar that leached from a plant).  $OM$ is the principle pool of energy and raw materials for all living things on Earth so this is a really important pool of stuff. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Since $GPP$ is taking $CO_2$ and converting it to $OM$ as the left side progresses, the amount of $CO_2$ in the atmosphere goes down and the amount of $OM$ in the biosphere goes up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;On the Right Side:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;$R$ (respiration) is the oxidation of reduced carbon-containing molecules for the purpose of extracting usable energy.  This may be familiar as &quot;cellular respiration&quot; but there are other metabolic pathways that accomplish the same goal.  In the end when the $C$ in the $OM$ is oxidized and the energy released the $C$ that was in the $OM$ gets converted into $CO_2$.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Note that this is the opposite of the Left Side, so as this occurs, the amount of $OM$ in the biosphere goes down and the amount of $CO_2$ in the atmosphere goes up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the Left and Right sides are balanced, then there is no net change in the size of the $OM$ pool or the amount of $CO_2$ in the atmosphere.  However, note that over relatively short time scales these can be very out of balance.  Any time plants or algae are growing (i.e., gaining mass as $OM$) the Left Side &gt; the Right Side or $GPP$ &gt; $R$.  Once those plants die, they accumulate in the system as dead $OM$.  The decomposition of accumulated dead $OM$ by microbes will generally make the Right Side &gt; Left Side or $R$ &gt; $GPP$.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/File%3aCarbon_cycle.jpg&quot; rel=&quot;nofollow&quot;&gt;This picture from Wikicommons&lt;/a&gt; shows the same cycle in a more realistic setting.  &lt;/p&gt;&#xA;" OwnerUserId="137" LastEditorUserId="137" LastEditDate="2013-03-04T19:54:45.783" LastActivityDate="2013-03-04T19:54:45.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7435" PostTypeId="1" AcceptedAnswerId="8571" CreationDate="2013-03-04T23:32:00.797" Score="18" ViewCount="452627" Body="&lt;p&gt;I'm sure many of you have experienced this - you scratch your back or brush your hand over your arm and find a ridiculously long thin white hair, sometimes as long as 3 or 4 inches. I know a few people who get these quite frequently, and anecdotal evidence seems to suggest they almost grow almost overnight. A quick Google search for &quot;single long white hair&quot; throws up plenty of references to them, and various beauty advice, but I'd like to know the biology behind them.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What triggers abnormal body hair growth?&lt;/li&gt;&#xA;&lt;li&gt;What causes these hairs to grow so much longer than other &quot;normal&quot; body hairs in physical proximity?&lt;/li&gt;&#xA;&lt;li&gt;Why are they so thin and white compared to other body hair?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My primary hypothesis is that the hair cell grows rapidly in an uncontrolled manner, similar to how cancer might, and that the unusual appearance is due to the cells being starved of nutrients. I may be completely wrong, though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm mainly interested in humans here, but if more in-depth research is available on animals that'd be interesting too.&lt;/p&gt;&#xA;" OwnerUserId="172" LastActivityDate="2013-10-29T18:35:25.350" Title="What causes random long white body hairs?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;hair&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7436" PostTypeId="1" AcceptedAnswerId="7439" CreationDate="2013-03-04T23:49:56.997" Score="4" ViewCount="182" Body="&lt;p&gt;There's a &lt;a href=&quot;http://www.bloomberg.com/news/2013-03-03/hiv-infected-infant-cured-with-early-use-of-virus-blocking-drugs.html&quot; rel=&quot;nofollow&quot;&gt;story going round&lt;/a&gt; the news about a baby that was, apparently, cured of HIV using a cocktail of drugs at an early age. The story piqued my interest, but details seem scarce. One of the main things I've seen being refuted about it is the difficulty in proving that (a) the child actually had HIV in the first place, and (b) that the child is really fully cured.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen the following arguments:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Western Blot tests on young children are practically useless, since they test for antibodies. The child will likely have antibodies passed down by the HIV+ mother, regardless of whether the child has HIV. The test will show the antibodies, which may be mistaken for an active immune response from the child. As such, there will be a high false-positive rate on such tests.&lt;/li&gt;&#xA;&lt;li&gt;Using PCR to attempt to identify a lack of HIV is flawed, since it may lay dormant in a small colony of T-cells until a secondary immune response is triggered, causing a new outbreak. As such, it is very difficult to show that a patient is &quot;cured&quot;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Are these arguments valid? Are there any other reasons to be sceptical about the claims? Any other information that might be useful in understanding the case?&lt;/p&gt;&#xA;" OwnerUserId="172" LastActivityDate="2014-08-19T05:09:31.523" Title="Is there a strong reason to be sceptical about the &quot;cured HIV patient&quot; being reported by mainstream media?" Tags="&lt;immunology&gt;&lt;pcr&gt;&lt;hiv&gt;&lt;western-blot&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7437" PostTypeId="1" CreationDate="2013-03-05T00:31:44.543" Score="2" ViewCount="95" Body="&lt;p&gt;I'm reading into the basics of the nervous system, and am intrigued by neurotransmitters. I understand that certain neurotransmitters can trigger more than one neuron type, and may be used as inhibitors or regulators (antagonists). Conversely, are there any types of agonists that trigger excitation in all neurons, regardless of type? If so, what functions do these play?&lt;/p&gt;&#xA;" OwnerUserId="172" LastActivityDate="2013-04-08T09:10:29.063" Title="Are there any neurotransmitters that trigger all neurons?" Tags="&lt;neuroscience&gt;&lt;neurotransmitter&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7438" PostTypeId="2" ParentId="7436" CreationDate="2013-03-05T01:47:23.450" Score="2" Body="&lt;p&gt;The one that actually makes me skeptical of the &lt;em&gt;use&lt;/em&gt; of this is that this &quot;cure&quot; was primarily a massive dose of antiretrovirals used as catchup therapy because the infant's mother didn't have access to prophylactic treatments while she was pregnant and delivering.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, it's a cure that requires you to have access to antivirals very, very near the beginning of infection, and is largely a solution to a problem that is &quot;solved&quot; in the developed world (maternal transmission of HIV is very rare).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's not a cure that can be extended to the settings where a cure is most desperately needed. So while an excellent proof-of-concept, and a safety net for when someone is poorly served by the medical system? Sure, this is amazing. As some watershed moment in HIV research? Less convinced.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2013-03-05T01:47:23.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7439" PostTypeId="2" ParentId="7436" CreationDate="2013-03-05T01:49:07.143" Score="7" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Western Blot tests on young children are practically useless, since they test for antibodies. The child will likely have antibodies passed down by the HIV+ mother, regardless of whether the child has HIV. The test will show the antibodies, which may be mistaken for an active immune response from the child. As such, there will be a high false-positive rate on such tests.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nytimes.com/2009/02/03/health/research/03immu.html?_r=0&quot;&gt;The mother's T-cells are in the fetus anyways&lt;/a&gt; (15/18 Fetal lymph nodes contained T-reg cells). If the mother is infected and left untreated (as was the case with the Mississippi child), then the viral load is going to be high. The chances of it passing to the fetus are going to be high as a result.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Using PCR to attempt to identify a lack of HIV is flawed, since it may lay dormant in a small colony of T-cells until a secondary immune response is triggered, causing a new outbreak. As such, it is very difficult to show that a patient is &quot;cured&quot;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&quot;Flawed&quot; is the wrong word. The argument is built into the tests. The child was &lt;strong&gt;functionally cured&lt;/strong&gt; - which means &lt;em&gt;below detectable levels&lt;/em&gt; instead of &quot;completely nonexistent within the body.&quot; Yes, it's entirely possible that the HIV is hiding somewhere in the body and could make a reappearance, but at the moment it's not showing any significant titer in the blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think there's been a test developed that can assess the &lt;em&gt;entire&lt;/em&gt; body to find the lone viral capsid left.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;However&lt;/strong&gt; - that isn't to say that the &quot;cure&quot; has been found. So far it's a single person cured this way. One. That makes it a case study, not a therapy, treatment, vaccine, or even reasonable assessment that it's possible to do again.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-03-05T01:49:07.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7440" PostTypeId="1" AcceptedAnswerId="7441" CreationDate="2013-03-05T01:53:50.143" Score="2" ViewCount="8365" Body="&lt;p&gt;The best I've been able to find is that there's a feedback mechanism, but what is this feedback, and how does the mechanism work? If it's just that the concentration of thymidine is too high, why won't excess quantities of other nucleotides do the same thing? (Or do they, and I don't know about it?)&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2015-11-23T05:51:40.720" Title="How does a thymidine block halt DNA synthesis?" Tags="&lt;dna&gt;&lt;replication&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7441" PostTypeId="2" ParentId="7440" CreationDate="2013-03-05T03:16:19.523" Score="1" Body="&lt;p&gt;Excess thymidine in a mitotic cell generates negative feedback on the production of deoxycytidine triphosphate from cytidine-5'-phosphate. Excess quantities of deoxyadenosine and deoxyguanosine &lt;em&gt;also&lt;/em&gt; block progression through S-phase. However, as a reagent for the control of replication timing, thymidine has been found to work best as its blocking activity can be applied and reversed more consistently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/194682a0&quot; rel=&quot;nofollow&quot;&gt;Xeros N. (1962) &lt;em&gt;Deoxyriboside Control and Synchronization of Mitosis.&lt;/em&gt; Nature 194: 682-683.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3061" LastEditorUserId="6" LastEditDate="2013-03-05T09:41:30.383" LastActivityDate="2013-03-05T09:41:30.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7443" PostTypeId="2" ParentId="7417" CreationDate="2013-03-05T05:52:58.617" Score="0" Body="&lt;p&gt;Maybe you are asking where these genes came from and how they became so common?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It turns out that antibiotics are very common - many free living plants and microorganisms make antibiotics.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Penicillin&quot; rel=&quot;nofollow&quot;&gt;Penicillin&lt;/a&gt;, the first beta lactam antibiotic found is synthesized by a fairly common mold, they kill bacteria by inhibiting the synthesis of the cell wall.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All three of these classes of defense have evolved over the hundreds of millions of years of evolution since antibiotics like penicillin started showing up (probably more like billions of years).  They have all probably been with us for quite a long time.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beta-lactamases, which enzymatically neutralized the beta lactam ring of penicillins and related compounds &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9189640&quot; rel=&quot;nofollow&quot;&gt;seem to have evolved three times&lt;/a&gt; and its not hard to imagine why the genes have stuck around for so long.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/DD-transpeptidase&quot; rel=&quot;nofollow&quot;&gt;dd-transpeptidase&lt;/a&gt;, the 'penicillin binding protein' is actually an enzyme that helps to synthesize the peptidoglycan of the cell wall.  It can also mutate such that it tends not to bind penicillin so well, creating a second sort of penicillin resistant bacterium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other genes such as &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16313627&quot; rel=&quot;nofollow&quot;&gt;ABC drug transporters can kick out strange molecules before they can cause any damage&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These and all other sorts of mutants and genes that convey resistance, once created through selection are around in the huge bacterial gene pool.  Bacteria can pick them up through lateral gene transfer, plasmids (sex), phages and by taking in DNA from the environment.  Most of these genes and traits were sitting around for millions of years, but the increased use of antibiotics has increased the selection pressure to retain these traits in many more bacteria.  That's really where bacterial antibiotic resistance comes from. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-03-05T05:52:58.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7444" PostTypeId="2" ParentId="5720" CreationDate="2013-03-05T08:29:54.620" Score="9" Body="&lt;p&gt;We each inherit either A, B, AB or no antigens from our parents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The current thought is that when you're between 0-6 months old you are exposed to bacteria/viruses that contain very similar antigens (A or B). These antigens are similar enough to the A and B antigens found on red blood cells that any antibody created against these bacterial antigens would also react against the corresponding red blood cell antigen. Seeing as you can't produce an antibody against your own antigen (except in rare circumstances), you always produce the opposite antibody to what antigen you have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope some of that makes sense. Feel free to point out any glaring mistakes I've made, wouldn't be the first time! ;-)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: I'm a biomedical scientist.&lt;/p&gt;&#xA;" OwnerUserId="3196" LastEditorUserId="-1" LastEditDate="2015-10-27T02:53:09.320" LastActivityDate="2015-10-27T02:53:09.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7445" PostTypeId="1" AcceptedAnswerId="7448" CreationDate="2013-03-05T11:12:29.067" Score="5" ViewCount="2821" Body="&lt;p&gt;I noticed something strange a couple of years ago. I was walking down the street at night, when it struck me that the street lights were flickering. But, when I turned to take a direct look at the light source it did not flicker any more. In other words, when the light is not the main focus of your eye, it can flicker.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From then on, I started to focus on these flickerings and they are everywhere. Street lights, lights in a house, but also computer monitors or even projections on a screen. Again, the flickering only happens when you do not look directly at the source.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have an explanation for that? Is it the brain's fault, or the eye's?&lt;/p&gt;&#xA;" OwnerUserId="3198" LastActivityDate="2018-08-15T16:07:41.543" Title="Perception of artificial light - flickering" Tags="&lt;eyes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7446" PostTypeId="2" ParentId="7433" CreationDate="2013-03-05T12:50:11.940" Score="1" Body="&lt;p&gt;I can't provide any real technical details, but I recently watched a documentary in which a team demonstrated a new type of blood sugar sensor that could be simply swabbed against sweat. They were trialling it as a non-invasive option that paramedics could carry, for use on unconscious patients as a means of checking for signs of diabetic shock. They mentioned that it only required a minimal sample; a swab of the palm of the hand was sufficient to gain a decent reading.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm unsure as to the mechanism of the device - it could well have been direct measurements of sugars or sugar by-products in the sweat, or it could have been looking for other chemicals associated with abnormal blood sugar levels.&lt;/p&gt;&#xA;" OwnerUserId="172" LastActivityDate="2013-03-05T12:50:11.940" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7447" PostTypeId="1" AcceptedAnswerId="7449" CreationDate="2013-03-05T13:00:01.450" Score="11" ViewCount="35364" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Agar&quot;&gt;Agar&lt;/a&gt; is a relatively cheap substance from red algae.  And it contains a saccharide agarose as well as a small amount of pectin.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Agar is used for culture plates as is, but for DNA gels a grade of agarose, I guess with the pectin removed.  What happens when a gel is run in agar?  i.e. why remove the pectin?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you can guess, how is the pectin removed?  I know there are &lt;a href=&quot;http://en.wikipedia.org/wiki/Pectin_lyase&quot;&gt;enzymes&lt;/a&gt; that might do it, but not sure what's really used.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2018-09-27T05:21:04.783" Title="Agarose vs agar? Why do DNA gels use agarose only and how do you obtain agarose from agar?" Tags="&lt;molecular-biology&gt;&lt;lab-reagents&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7448" PostTypeId="2" ParentId="7445" CreationDate="2013-03-05T13:07:23.757" Score="8" Body="&lt;p&gt;It's difficult to give an exact answer without actually observing the light and performing measurements. I have a theory, though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your peripheral vision is hyper-sensitive to changes in light - an evolutionary trait that provided quicker reactions to predators sneaking up on you. As such, even the tiniest fluctuations in light can be registered with your peripheral vision; much more so than your primary field of vision. In this case, it may well have been that the light was flickering very subtly, or at a very high frequency, which your primary field of vision could not pick up. When your peripheral vision was in play, it immediately spotted the flicker.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is reliant on a principle called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Flicker_fusion_threshold&quot;&gt;flicker fusion threshold&lt;/a&gt;, which essentially states that there is a threshold of various light properties (including flicker frequency, colour, intensity, etc.) at which an eye begins to distinguish a steady light from a flickering one. Research has demonstrated that species who have high rod density are good at picking up flickering, whereas species with low rod densities have a much poorer threshold. Cone density doesn't seem to factor in very much, since flickering is primarily a change of intensity rather than hue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This transfers into the human eye, since we have a high rod density (and low cone density) at the edges of our retinas, i.e. in our peripheral vision. If you had the eyes of another species (as creepy as that would be) with a high rod density, you may well have been able to detect the flicker quite easily with your primary field of vision.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To directly answer your question - yes, I believe this is primarily the &quot;fault&quot; of the eye, rather than the brain. The brain has a role in identifying the flicker at a subconscious level, in terms of fight or flight response, but the eye is responsible for providing the elevated sensitivity at the peripheral.&lt;/p&gt;&#xA;" OwnerUserId="172" LastActivityDate="2013-03-05T13:07:23.757" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7449" PostTypeId="2" ParentId="7447" CreationDate="2013-03-05T15:51:57.373" Score="15" Body="&lt;p&gt;The answer to the first part of your question can be found on &lt;a href=&quot;http://en.wikipedia.org/wiki/Agar&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Agar is a heterogeneous mixture of two classes of polysaccharide:&#xA;  agaropectin and agarose. Although both polysaccharide classes&#xA;  share the same galactose-based backbone, agaropectin is heavily&#xA;  modified with acidic side-groups, such as sulfate and pyruvate. The&#xA;  neutral charge and lower degree of chemical complexity of agarose make&#xA;  it less likely to interact with biomolecules, and, therefore, agarose&#xA;  has become the preferred matrix for work with proteins and nucleic&#xA;  acids.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://citizensciencequarterly.com/2012/01/30/cheapass-science-comparison-of-agarose-agar-agar-and-cleaned-agar-agar-for-gel-electrophoresis-of-dna/&quot; rel=&quot;noreferrer&quot;&gt;page&lt;/a&gt; compares the result of using agar gels to that of using agarose:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/JXGtI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second part of your question: here's a &lt;a href=&quot;http://www.google.com/patents/US4990611&quot; rel=&quot;noreferrer&quot;&gt;patent&lt;/a&gt;, although I have no idea whether this method of agarose purification is widespread.  Propylene glycol purification of agarose does seem to pop up a lot.  I think people who  purify their own agarose use that method, but I am not sure if biotech companies have other methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: it's propylene glycol, followed by ethylene glycol, that is commonly used, but PEG has been used &lt;a href=&quot;http://deepblue.lib.umich.edu/bitstream/handle/2027.42/31965/0000007.pdf&quot; rel=&quot;noreferrer&quot;&gt;at least once&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-05-05T01:46:11.800" LastActivityDate="2013-05-05T01:46:11.800" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7450" PostTypeId="1" CreationDate="2013-03-05T17:54:46.157" Score="6" ViewCount="141" Body="&lt;p&gt;If I want to predict litterfall, what data do I need to collect, and what statistical model might I use?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, I might use the following coding to record phenological stage every other day, or perhaps once per week:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;|value| description&#xA;|-----|--------------&#xA;| 0   | all leaves fallen&#xA;| 0.5 | most leaves fallen&#xA;| 1   | no more green in canopy half of leaves have fallen&#xA;| 2   | most leaves yellow or red few leaves have fallen&#xA;| 3   | noticeable reddening or yellowing, green still present&#xA;| 4   | summer condition&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Once I have these data, I can also collect weather data. Now, say I want to predict the day on which each of the transitions ($4\rightarrow 3$, $3\rightarrow 2$, etc) occur. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many studies use a temperature metric of growing degree days $GDD = (T_{max}+T_{min})/2-T_{base}$, but I have also seen chiling days and photoperiod used to predict changes in phenological stage. I would like to develop a function (statistical model) $f$ that would allow me to predict a date of state change from environemental variables, such as $$D_{4\rightarrow 3} = f(GDD)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;what controls litterfall? Is it photoperiod, temperature, other? &lt;/li&gt;&#xA;&lt;li&gt;do the controls vary by species?&lt;/li&gt;&#xA;&lt;li&gt;is there a &quot;standard&quot; approach to modelling senescence? &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="154" LastEditorUserId="3952" LastEditDate="2013-08-02T14:36:18.290" LastActivityDate="2015-01-10T04:49:00.610" Title="What controls leaf senescence in deciduous tree species, and how can I predict it?" Tags="&lt;botany&gt;&lt;life-history&gt;&lt;phenology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7451" PostTypeId="2" ParentId="7433" CreationDate="2013-03-05T17:56:07.620" Score="3" Body="&lt;p&gt;Cystic fibrosis diagnosis. Here is a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22859523&quot; rel=&quot;nofollow noreferrer&quot;&gt;link to a paper&lt;/a&gt; describing the use of β-adrenergic sweat secretion as a diagnostic test for cystic fibrosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anti-cancer therapy and its effectiveness. This &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22004675&quot; rel=&quot;nofollow noreferrer&quot;&gt;report&lt;/a&gt; seeks to determine the levels of the anti-cancer drug sunitinib and its active metabolite N-desethylsunitinib in sweat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll add others later.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a 2004 &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17191896&quot; rel=&quot;nofollow noreferrer&quot;&gt;study&lt;/a&gt; looking at a particularly unpleasant sulfury compound produced by bacteria in contact with sweat. It's interesting that the enantiomer of the malodorous compound had a grapefruit-like smell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22305901&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper&lt;/a&gt; puts forth the idea that sweat, which contains lactate, lactic acid, urea (of course) and amino acids, can be used in forensics.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="3553" LastEditDate="2017-04-03T05:07:35.260" LastActivityDate="2017-04-03T05:07:35.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7452" PostTypeId="1" CreationDate="2013-03-05T19:02:40.803" Score="1" ViewCount="334" Body="&lt;p&gt;Just wondering ; I get the impression a large number of multicellular organisms are multi-lateral in their physical structure. Why would evolution/mutation have retained multi-lateral symmetry in an organism? What advantage/s does symmetry provide an organism?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: &#xA;By multi-lateral symmetry I mean at-least bi-lateral symmetry (as in the case of many beings such as elephants, crabs and fishes), but perhaps more than bi-lateral too (starfish come to mind)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;END EDIT:&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2013-03-06T03:06:10.393" LastActivityDate="2013-03-06T15:06:18.650" Title="Is there any evolutionary/physiological advantage to multi-lateral symmetry?" Tags="&lt;evolution&gt;&lt;physiology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7453" PostTypeId="1" AcceptedAnswerId="7456" CreationDate="2013-03-05T21:01:40.857" Score="1" ViewCount="5318" Body="&lt;p&gt;In class of molecular biology was posed this question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;How many reading frames start in sequence of nucleotides 5' ... ATATGAATGATGACAT... 3' ?&quot;&lt;/p&gt;&#xA;" OwnerUserId="3200" LastEditorUserId="3059" LastEditDate="2013-03-05T21:41:25.660" LastActivityDate="2013-12-01T23:52:36.233" Title="Number of reading frames in nucleotide sequence" Tags="&lt;homework&gt;&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7454" PostTypeId="2" ParentId="7452" CreationDate="2013-03-05T21:13:59.047" Score="4" Body="&lt;p&gt;Signs of symmetry are determined by the environment. Completely isotropic ecological niche corresponds to the maximum degree of symmetry of organisms (spherical symmetry). Asymmetrization on the axis &quot;up-down&quot; took place under the influence of gravity field and lead to radial symmetry. Bilateral symmetry of the multicellular animals arose with movement.&lt;/p&gt;&#xA;" OwnerUserId="1839" LastActivityDate="2013-03-05T21:13:59.047" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7456" PostTypeId="2" ParentId="7453" CreationDate="2013-03-05T23:23:37.797" Score="9" Body="&lt;p&gt;Every nucleotide sequence has six possible reading frames, because each codon (determining one amino acid) consists of a base triplet (3 frames), and there is a complementary strand which could be coding (3 reverse frames).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To find the possible open reading frames contained in your sequence, you have to look for start codons. That is: ATG. But, as said the complementary strand could be coding. So if your known sequence contains CAT, that would be ATG on the opposite strand and might also be an open reading frame.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Count them now and then read on to compare answers.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Your specific sequence contains four start codons (3x ATG and 1x CAT, which makes ATG on the complementary reverse).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5' ... AT &lt;strong&gt;ATG&lt;/strong&gt; A &lt;strong&gt;ATG ATG&lt;/strong&gt; A CAT ... 3'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3' ... TA TAC T TAC TAC T &lt;strong&gt;GTA&lt;/strong&gt; ... 5'&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-12-01T23:52:36.233" LastActivityDate="2013-12-01T23:52:36.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7457" PostTypeId="1" AcceptedAnswerId="7463" CreationDate="2013-03-06T00:01:54.810" Score="20" ViewCount="1344" Body="&lt;p&gt;I can't think of any reason why plants wouldn't be able to get cancer, but I've never heard of a plant growing a tumor. I've also never seen a plant with a noticeable abnormal growth. Can plants get cancer?&lt;/p&gt;&#xA;" OwnerUserId="1182" LastActivityDate="2014-05-24T22:22:24.717" Title="Can plants get cancer?" Tags="&lt;plant-physiology&gt;&lt;pathology&gt;&lt;cancer&gt;&lt;botany&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7459" PostTypeId="1" AcceptedAnswerId="7461" CreationDate="2013-03-06T00:45:50.287" Score="9" ViewCount="2023" Body="&lt;p&gt;If instincts are passed on through genetics, how is that information encoded in DNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, spiders instinctively know how to spin webs. Does that imply that the algorithm for web spinning is directly encoded in spider DNA? &lt;/p&gt;&#xA;" OwnerUserId="3204" LastActivityDate="2016-04-17T19:50:25.617" Title="How is instinctual information encoded?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7460" PostTypeId="1" CreationDate="2013-03-06T09:39:10.407" Score="4" ViewCount="301" Body="&lt;p&gt;Is there a database where I can find an affinity estimate if I provide a given antibody and a given antigen sequence ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Input : antibody + antigen sequence&#xA;Output : quantitative binding/affinity estimate&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many thanks.&lt;/p&gt;&#xA;" OwnerUserId="1020" LastEditorUserId="460" LastEditDate="2013-03-08T03:06:43.137" LastActivityDate="2013-03-08T16:04:19.237" Title="Antibody-antigen database" Tags="&lt;immunology&gt;&lt;database&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7461" PostTypeId="2" ParentId="7459" CreationDate="2013-03-06T09:40:39.380" Score="6" Body="&lt;p&gt;Web spinning in spiders is a complex behavior and probably involves a number of different factors, genetic and environmental. Genetically there are surely many different genomic regions underlying the development and expression of the behavior. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the algorithm for web spinning directly encoded in the DNA? Not directly. There is not a single region of contiguous DNA sequence that codes for all the steps involved in building a web. Instead, there is a sequential and parallel developmental process beginning at fertilization (earlier if you include parental epigenetic modifications) - encoded and regulated by the genome and its products - that, without too many errors, generates a viable and fertile web-spinning organism. But the DNA sequence involved in that algorithm is spread all over the genome and includes coding genes, non-coding (ncRNA) genes, and regulatory regions. And the genome alone will not carry out an effective algorithm without proper environmental inputs like nutrition and parental provisions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The act of constructing a web, when and where, and the design of the web is likely carried out via brain architecture and neuronal patterning, but of course these structures are built based on the DNA-based, developmental algorithm. In that sense, there are many nested levels of algorithms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the best models used for studying behavioral genetics is the fruit fly Drosophila. Many different behaviors have been studied at the genetic and molecular level in Drosophila including courtship, foraging, sleeping, and memory-related tasks. A popular science book on behavioral genetics worth checking out is &lt;em&gt;Time, Love, and Memory&lt;/em&gt; by Jonathan Weiner. It details the work of Seymour Benzer and provides a lot of background and easily understood explanations of how genes and their products can work together to exhibit complex phenotypes like sleeping patterns. It includes a detailed (though not up-to-date) description of circadian gene circuitry and how it develops.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the moment, the best that I can think of for an algorithm directly encoded for by DNA is the sequential activation of HOX genes for animal body plans. But even in this case DNA code does not progress through correct development without other factors.   &lt;/p&gt;&#xA;" OwnerUserId="3061" LastActivityDate="2013-03-06T09:40:39.380" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7462" PostTypeId="1" AcceptedAnswerId="7467" CreationDate="2013-03-06T11:25:14.413" Score="0" ViewCount="88" Body="&lt;p&gt;Does the Enzyme Monoamine Oxidase, Isoenzyme A (MAO-A) have an allosteric modulatory site? I ask because I would like to know if it is possible, in theory at least, for a positive allosteric modulator of MAO-A to be developed.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-03-06T18:05:36.253" Title="Does the Enzyme Monoamine Oxidase, Isoenzyme A have an allosteric modulatory site?" Tags="&lt;pharmacology&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7463" PostTypeId="2" ParentId="7457" CreationDate="2013-03-06T13:58:43.233" Score="17" Body="&lt;p&gt;Yes, plants of all sizes can have cancerous growths.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Agrobacterium tumifaciens&lt;/em&gt;, the causative agent of crown gall disease, produces what is called a tumor. See this &lt;a href=&quot;http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens&quot;&gt;link&lt;/a&gt; for detailed information on these growths. Alternatively, use a plant physiology textbook to look up the above terms. (Here, is where a textbook is better than a single abstract in PubMed.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am certain that you have seen such growths on trees, such as &lt;a href=&quot;http://www.motikon.com/curiosities/galls/&quot;&gt;this&lt;/a&gt;. Other smaller versions can occur on smaller plants - on stems and leaves, for example. The plant builds up tissue around the &lt;em&gt;A. tumifaciens&lt;/em&gt; infection in an effort to isolate and contain the infection and its effects.&lt;/p&gt;&#xA;" OwnerUserId="535" LastEditorUserId="535" LastEditDate="2013-03-06T18:52:33.923" LastActivityDate="2013-03-06T18:52:33.923" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7464" PostTypeId="2" ParentId="7452" CreationDate="2013-03-06T15:06:18.650" Score="0" Body="&lt;p&gt;Evolution works by tinkering, not engineering.  Gaining an evolutionary advantage in a simple way is rewarded, as is simplicity generally.  Symmetry allows for relatively greater simplicity at the genetic information level (modular body parts driven by repeated application of same genetic instructions).  Without symmetry, more genetic information would be needed to construct a similarly complex organism (symmetric like), with the concomitant exposure to increased genetic degradation.&lt;/p&gt;&#xA;" OwnerUserId="1068" LastActivityDate="2013-03-06T15:06:18.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7465" PostTypeId="1" AcceptedAnswerId="7466" CreationDate="2013-03-06T17:16:55.200" Score="3" ViewCount="73" Body="&lt;p&gt;I've been learning about the gene regulatory network (GRN) and protein-protein interaction network (PPI) recently.&#xA;I've found a huge amount of extremely interesting papers about how biological network data is accumulated and how it can be studied.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, what I haven't found is any examples where the network data was used to make a novel prediction which was later experimentally shown to actually exist.  What are some of the cases where this has happened?&lt;/p&gt;&#xA;" OwnerUserId="3208" LastActivityDate="2013-08-15T16:24:17.663" Title="Have novel interactions or pathways been predicted by GRN or PPI data and later confirmed by experiment?" Tags="&lt;proteins&gt;&lt;genetics&gt;&lt;network&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7466" PostTypeId="2" ParentId="7465" CreationDate="2013-03-06T17:42:14.523" Score="2" Body="&lt;p&gt;There is very interesting work in this regard done by Ed Marcotte. An overview of the &quot;machine&quot; and its conservation across species is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20637909&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. The point here is the machine or network is conserved, but used in different ways in different organisms. Hence, the phenotypes of mutants might be different, but they'd be consistent across many variants in the components of the machine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23268829&quot; rel=&quot;nofollow&quot;&gt;paper of his&lt;/a&gt; describes a tool, which uses well developed guilt-by-association principles upon a human gene network to identify associations of gene sets. This is available at www.functionalnet.org/RIDDLE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look at &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21536720&quot; rel=&quot;nofollow&quot;&gt;their approach&lt;/a&gt; to prioritizing candidate disease genes by network-based boosting of genome-wide association data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some specific examples of the conserved &quot;machine&quot; are given in this elegant &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20308572&quot; rel=&quot;nofollow&quot;&gt;PNAS paper&lt;/a&gt;. It is nice how they tested the genes in &lt;em&gt;Xenopus&lt;/em&gt; embryos.&lt;/p&gt;&#xA;" OwnerUserId="535" LastActivityDate="2013-03-06T17:42:14.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7467" PostTypeId="2" ParentId="7462" CreationDate="2013-03-06T18:05:36.253" Score="0" Body="&lt;p&gt;I think an allosteric modulatory site has already been found, but it's not specific to Isoenzyme A, if that's what you were looking for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See these papers:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1564771/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1564771/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jbc.org/content/270/17/9856.full&quot; rel=&quot;nofollow&quot;&gt;http://www.jbc.org/content/270/17/9856.full&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-03-06T18:05:36.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7468" PostTypeId="1" CreationDate="2013-03-06T18:24:52.207" Score="1" ViewCount="109" Body="&lt;p&gt;I have two related questions about soy allergies and possible reactions.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;What is it that are humans who have soy allergies actually allergic to? What is the allergen?&lt;/li&gt;&#xA;&lt;li&gt;If an animal eats soy, are those allergens broken down or retained? Can the consumption of that animal cause an allergic reaction similar to direct soy consumption?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3089" LastEditorUserId="107" LastEditDate="2013-03-06T23:10:48.713" LastActivityDate="2013-03-07T21:04:31.623" Title="What in soy are people allergic to and will these allergens be passed along if an animal that has eaten soy is consumed?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7469" PostTypeId="2" ParentId="7468" CreationDate="2013-03-06T23:14:05.173" Score="3" Body="&lt;p&gt;There are multiple soy protein allergens.  &lt;a href=&quot;http://jn.nutrition.org/content/134/5/1213S.full&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; has a pretty good review in the introduction.  &lt;a href=&quot;http://jn.nutrition.org/content/134/5/1213S/T3.expansion.html&quot; rel=&quot;nofollow&quot;&gt;Here is a list of some of the allergens&lt;/a&gt; (same paper).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chickens on soy diets do lay eggs with higher concentrations of soy isoflavones than chicken on non-soy diets. (Edit: higher concentrations of soy isoflavones are also found in chicken tissues -- see ref 4 below.) References (originally found &lt;a href=&quot;http://www.westonaprice.org/soy-alert/the-soy-ling-of-america-second-hand-soy-from-animal-feeds&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Saitoh, S.; Sato, T.; Harada, H.; Takita, T. Transfer of soy isoflavone into the egg yolk of chickens. Biosci. Biotechnol. , Biochem. 2001, 65, 2220-2225.&lt;/li&gt;&#xA;&lt;li&gt;Saitoh, S.; Sato, T.; Harada, H.; Matsuda, T. Biotransformation of soy isoflavone-glycosides in laying hens: intestinal absorption and preferential accumulation into egg yolk of equol, a more estrogenic metabolite of daidzein. Biochim. Biophys. Acta 2004, 1674 (2) 122-130.&lt;/li&gt;&#xA;&lt;li&gt;Lin, F.; Wu, J.; Abdelnabi, M.; Ottinger, M.; Giusti M.M. Effects of dose and glycosylation on the transfer of genistein into the eggs of the japanese quail (Coturnix japonica). J. Agric. Food Chem. 2004, 52, 2397-2403.&lt;/li&gt;&#xA;&lt;li&gt;Vargas Galdos, Dante Miguel Marcial. Quantification of Soy Isoflavones in commercial eggs and their transfer from poultry feed into eggs and tissues. Thesis. Ohio State University, Food Science and Technology Graduate Program, 2009; &lt;a href=&quot;http://etd.ohiolink.edu/send-pdf.cgi/Vargas%20Galdos%20Dante%20Miguel%20Marcial.pdf?osu1236706764&quot; rel=&quot;nofollow&quot;&gt;http://etd.ohiolink.edu/send-pdf.cgi/Vargas%20Galdos%20Dante%20Miguel%20Marcial.pdf?osu1236706764&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;However,&lt;/strong&gt; I do not know whether this is enough to cause an allergic reaction if consumed. (There's plenty of anecdotal evidence, but no clinical studies that I know of.)&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-03-07T21:04:31.623" LastActivityDate="2013-03-07T21:04:31.623" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7470" PostTypeId="2" ParentId="7378" CreationDate="2013-03-07T01:09:19.110" Score="1" Body="&lt;p&gt;To begin, one might ask &quot;What is the advantage of higher GC content?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Higher GC content is associated with higher stability of the DNA, and accordingly, people have suggested that this is important for protein-coding regions.  It has been found that there are quite a few protein-coding regions in GC-rich regions, but I am not sure whether the converse is true, which is the important part.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;If the converse is true&lt;/em&gt;, then one might look at the distribution of protein-coding regions across the chromosomes and correlate it with GC-content. If also the size of the protein-coding regions in a given chromosome is proportional to the size of the chromosome, then you would have a reason as to why the average GC content of each chromosome is similar. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I recognize that this is all very speculative.  Does anyone have better ideas? &lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-03-07T01:28:53.077" LastActivityDate="2013-03-07T01:28:53.077" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7472" PostTypeId="1" AcceptedAnswerId="7473" CreationDate="2013-03-07T12:03:23.967" Score="4" ViewCount="125" Body="&lt;p&gt;I currently have two sets of gene expression data. The first is a dataframe of genes identified by Annotation id CG numbers (for example &quot;CG10005&quot;) in one column and a numerical variable of interest associated with each of those genes in the other (the important part is that the genes are identified by the CG number). The second dataset is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17994089&quot; rel=&quot;nofollow&quot;&gt;this study&lt;/a&gt; from multiple species where genes are identified by &quot;GLEANR&quot; ID's like this one: &quot;dsim_GLEANR_10060&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to extract all of the values from this study for the D.melanogaster and D.simulans data, then link that to the Annotation ID's in the first dataset (to connect my variable of interest to the sex bias in expression for each species). The trouble I am having is connecting the orthologous genes within the second study to each other, and then connecting them to the CG identifiers in the first study.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have any suggestions on resources which can be used to get this all to link up?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="112" LastEditDate="2013-03-07T13:39:45.090" LastActivityDate="2013-03-07T19:36:46.010" Title="Combining gene expression data from two species" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;&lt;gene-expression&gt;&lt;gene-annotation&gt;&lt;drosophila&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7473" PostTypeId="2" ParentId="7472" CreationDate="2013-03-07T13:44:03.197" Score="2" Body="&lt;p&gt;This is the FlyBase page for the example gene: &lt;a href=&quot;http://flybase.org/reports/FBgn0181870.html&quot; rel=&quot;nofollow&quot;&gt;Dsim\GD10095&lt;/a&gt;. There, you have a section &quot;orthologs&quot;, linking to &lt;a href=&quot;http://cegg.unige.ch/OrthoDB6/results?searchtext=EOG65HSHC&quot; rel=&quot;nofollow&quot;&gt;OrthoDB&lt;/a&gt;. So my suggestion is: Find the list of synonyms for &lt;em&gt;D. simulans&lt;/em&gt; on FlyBase (&lt;a href=&quot;http://flybase.org/static_pages/docs/datafiles.html#gleanr_ids&quot; rel=&quot;nofollow&quot;&gt;perhaps here?&lt;/a&gt;), &lt;a href=&quot;ftp://cegg.unige.ch/OrthoDB6&quot; rel=&quot;nofollow&quot;&gt;download the Drosophila section of OrthoDB&lt;/a&gt;, and finally find the 1:1 orthologs. &lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2013-03-07T13:44:03.197" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7475" PostTypeId="2" ParentId="7472" CreationDate="2013-03-07T19:36:46.010" Score="0" Body="&lt;p&gt;You could also use &lt;a href=&quot;http://central.biomart.org&quot; rel=&quot;nofollow&quot;&gt;biomart&lt;/a&gt; for this purposes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Click on the &quot;ID Converter&quot; tab in the &quot;Tools&quot; section (on the left).&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2013-03-07T19:36:46.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7477" PostTypeId="1" AcceptedAnswerId="7478" CreationDate="2013-03-08T03:39:51.700" Score="1" ViewCount="151" Body="&lt;p&gt;Is trisomy mostly due to complications with fertilization?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, does in vitro fertilization reduce the probability of trisomy for the fetuses of older mothers?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, can zygotes be screened before in vitro fertilization?&lt;/p&gt;&#xA;" OwnerDisplayName="user3064" LastEditorUserId="3059" LastEditDate="2013-03-08T09:17:37.027" LastActivityDate="2013-03-08T09:17:37.027" Title="Can IVF decrease the probability of trisomy in the fetuses of older mothers?" Tags="&lt;dna&gt;&lt;chromosome&gt;&lt;meiosis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7478" PostTypeId="2" ParentId="7477" CreationDate="2013-03-08T03:46:38.640" Score="3" Body="&lt;p&gt;Trisomy is due to non-disjunction in meiosis (the process in which eggs and sperm are created). This happens before fertilization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trisomies are more frequently seen in children of older women.  It's not fully understood why this happens, but it is likely related to the fact that the oocytes do not complete meiosis (and become eggs) until ovulation.  Here's an interesting &lt;a href=&quot;http://www.plosgenetics.org/article/info%3adoi/10.1371/journal.pgen.1000033&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; that examines the physical causes of non-disjunction, but you might want to read up a bit more on meiosis (depending on your background) before tackling it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might screen for nondisjunction, but I don't think it's possible without killing the cells.  See the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Karyotype&quot; rel=&quot;nofollow&quot;&gt;karyotyping&lt;/a&gt;, which explains how an &lt;a href=&quot;http://en.wikipedia.org/wiki/Amniocentesis&quot; rel=&quot;nofollow&quot;&gt;amniocentesis&lt;/a&gt; might be used for a prenatal genetic diagnosis.  I don't know the regenerative capabilities of the human blastocyst, but if you had enough cells for a test, I don't think the blastocyst would develop normally.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-03-08T04:24:08.823" LastActivityDate="2013-03-08T04:24:08.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7479" PostTypeId="2" ParentId="7460" CreationDate="2013-03-08T13:32:37.547" Score="2" Body="&lt;p&gt;The binding constant of an antibody-antigen complex remains an empirical measurement. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been many efforts to solve this problem quantitatively and qualitatively over the years since the &lt;a href=&quot;http://www.rcsb.org/pdb/explore/explore.do?structureId=3HFM&quot; rel=&quot;nofollow&quot;&gt;original crystal structures of an lysozyme-Fab complex&lt;/a&gt; there are over 400 structures at the www.rcsb.org in a search for antibody antigen complexes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At this point the general methodology is to model the structure of the antibody-antigen complex.  Then from the complex a free energy of binding is estimated, or more reliably, variants which might bind more tightly can be modelled.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are tools available to do this work, but they are still far from perfect.  This &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0052613&quot; rel=&quot;nofollow&quot;&gt;2012 paper&lt;/a&gt; compares a new antibody-antigen crystal structure against the results of several modeling suites.  In Table 4 the authors show that the invariant parts of the structure as well as some of the hypervariable loops are really precisely modelled, but hypervariable region 3 was way off in this case (rms error of about 2 Angstroms).  Which is not precise enough to calculate actual free energy of binding. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Currently while free energies of binding and therefore estimates of binding constants are not reliably calculated from protein complex structures.  Such software is in practice used to rather compute the relative binding strength of two models (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/minf.201100135/full#sec3&quot; rel=&quot;nofollow&quot;&gt;see this 2012 example&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.ploscompbiol.org/article/info%3adoi/10.1371/journal.pcbi.1000644&quot; rel=&quot;nofollow&quot;&gt;2010 paper&lt;/a&gt; which describes SnugDock, a newer suite of software, outlines a state of the art antibody-antigen design process (emphasis added).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One could envision a complete computational antibody engineering pipeline starting from the antibody sequence and ending with accurate predictions for optimized antibody-antigen interactions. In this paper we have been successful in reaching the second step by computational docking using computational models of the monomer antibody. The next stages may be additionally challenging. High-resolution complex structures might next be used for computational alanine scanning, &lt;em&gt;computational affinity maturation or alteration of binding specificity&lt;/em&gt;. For antibody therapeutics, structures will help define drug mechanisms for regulatory approval, enable epitope mapping and humanize constructs. These applications require varying amounts of resolution and further testing will reveal the full utility of the SnugDock predictions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As you can see, the method recommended is to create a series of models to try to create tighter relative binding.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-03-08T16:04:19.237" LastActivityDate="2013-03-08T16:04:19.237" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7480" PostTypeId="1" AcceptedAnswerId="7482" CreationDate="2013-03-08T16:45:24.707" Score="2" ViewCount="1112" Body="&lt;p&gt;I would appreciate an answer specifically in the form of an exothermic chemical reaction. Namely, the one primarily responsible for generating heat in warm blooded animals that does not take place in cold blooded animals.&lt;/p&gt;&#xA;" OwnerUserId="263" LastActivityDate="2013-03-09T18:24:20.650" Title="What exothermic reaction distinguishes warm blooded animals?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7481" PostTypeId="2" ParentId="7480" CreationDate="2013-03-08T17:37:53.640" Score="0" Body="&lt;p&gt;While all animals and even plants generate heat from chemical reactions or mechanical motion of their tissues (like muscle tissues), warm blooded animals have brown fat which has the unusual ability to generate heat directly from metabolic energy.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The particular chemical process you are looking for is performed by &lt;a href=&quot;http://en.wikipedia.org/wiki/Uncoupling_protein&quot; rel=&quot;nofollow&quot;&gt;uncoupling proteins&lt;/a&gt; (UCPs).  They reside in the mitochondria and rather than use the proton gradient in the mitochondria to generate ATP, UCPs pass protons through the membrane and generate heat. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Brown_adipose_tissue&quot; rel=&quot;nofollow&quot;&gt;Brown fat&lt;/a&gt; is brown because of a relatively large iron content associated with many extra mitochondria (brown adipose tissue appears to be derived from muscle cells and not white adipose tissue).  Its a heat generating organ in humans, particularly infants.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-03-08T17:37:53.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7482" PostTypeId="2" ParentId="7480" CreationDate="2013-03-08T17:46:47.130" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Brown_adipose_tissue&quot; rel=&quot;nofollow noreferrer&quot;&gt;Brown adipose tissue&lt;/a&gt; or brown fat is one of the primary ways of generating body heat, and it is only found in warm-blooded animals. It is brown due to the high numbers of &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitochondria&quot; rel=&quot;nofollow noreferrer&quot;&gt;mitochondria&lt;/a&gt;, and heat is generated by uncoupling the &lt;a href=&quot;http://en.wikipedia.org/wiki/Electron_transport_chain&quot; rel=&quot;nofollow noreferrer&quot;&gt;electron transport chain&lt;/a&gt; from ATP synthesis by &lt;a href=&quot;http://en.wikipedia.org/wiki/Oxidative_phosphorylation&quot; rel=&quot;nofollow noreferrer&quot;&gt;oxidative phosphorylation&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the typical (ATP-producing) mitochondria, an energy gradient is formed by storing protons within the inter-membrane space, and these then flow through the &lt;a href=&quot;http://en.wikipedia.org/wiki/ATP_synthase&quot; rel=&quot;nofollow noreferrer&quot;&gt;ATP synthase&lt;/a&gt; to power the generation of ATP from ADP and phosphate. In brown fat mitochondria, Uncoupling Protein 1 (&lt;a href=&quot;http://en.wikipedia.org/wiki/Uncoupling_protein_1&quot; rel=&quot;nofollow noreferrer&quot;&gt;UCP1 or thermogenin&lt;/a&gt;) forms a pore in the inner membrane, allowing the proton/electron ratio to reach equilibrium and robbing ATP synthase of its motive power. This is what generates the heat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hC0Gg.png&quot; alt=&quot;Thermogenin pathway&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/File:ThermogeneseAdipozyten-en.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2013-03-09T18:24:20.650" LastActivityDate="2013-03-09T18:24:20.650" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7483" PostTypeId="1" CreationDate="2013-03-08T19:42:15.177" Score="0" ViewCount="2831" Body="&lt;p&gt;Blender companies state that a blender for smoothies should have speeds of at least 30000 rpm. They argue that only at 30000 rpm are cells of fruits and vegetables sheared enough to maximize nutrition and ease of digestion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would blending at lower speeds, such as 20000 rpm, be sufficient?&lt;/p&gt;&#xA;" OwnerUserId="3218" LastEditorUserId="3059" LastEditDate="2013-03-08T23:07:18.493" LastActivityDate="2014-12-09T18:34:26.033" Title="What is the appropriate blender speed to maximize nutrition and digestion of fruits and vegetables?" Tags="&lt;cell-biology&gt;&lt;fruit&gt;&lt;vegetable&gt;" AnswerCount="1" CommentCount="6" ClosedDate="2016-06-04T09:13:03.200" ContentLicense="CC BY-SA 3.0" />
  <row Id="7484" PostTypeId="1" CreationDate="2013-03-09T11:15:06.123" Score="4" ViewCount="63" Body="&lt;p&gt;We can't hear sounds outside the range of  20 Hz - 20 kHz. However, if an inaudible sound is played at high volume, will one's hearing be affected?&lt;/p&gt;&#xA;" OwnerDisplayName="Qwerty Uiopasd" LastEditorUserId="69" LastEditDate="2013-03-09T12:44:59.063" LastActivityDate="2013-03-09T12:44:59.063" Title="Can a sound frequency 'not' within human hearing (20 Hz - 20 kHz) damage hearing when it is of high volume?" Tags="&lt;human-biology&gt;&lt;hearing&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2013-03-09T12:45:10.967" ContentLicense="CC BY-SA 3.0" />
  <row Id="7487" PostTypeId="2" ParentId="7483" CreationDate="2013-03-09T21:03:26.827" Score="7" Body="&lt;p&gt;I'm guessing that what they mean by 'maximize nutrition' for digestion is that they are assuming that the cells are broken open.  This would make the co-factors we call vitamins, protein and sugars freely available to the digestive system and more easily absorbed.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it is a marketing literature claim, though the blender may have some valid advantages... details below. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stainless steel waring blenders used to be typical pieces of lab equipment which could be used to homogenize tissue to extract proteins or DNA from tissue.  These blenders would &lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_disruption#Rotor-stator_Processors_and_blenders&quot; rel=&quot;nofollow&quot;&gt;typically run from 10k-30k rpm&lt;/a&gt;.  The web search for 'cell lysis blender' gives lots of examples of prepping DNA from plants at these speeds, but they don't complain for speeds towards the lower end of the range.  A reputable looking example in my short search: This paper for &lt;a href=&quot;http://www.plantphysiol.org/content/91/3/816.full.pdf&quot; rel=&quot;nofollow&quot;&gt;tomato fruit cell wall preparations&lt;/a&gt; doesn't even give a speed the blender might have run at.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cell lysis in the literature is not precise - the cell toughness, the strength of the tissue around it and other such factors all come into play.  Putting woody stems into your blender and those cells won't really get opened up at all.  Also in the cell literature cell lysis buffers may have detergents or other chemicals (the reference above is done in 50% ethanol) to weaken the cell walls.  Not exactly what you'd want to use if you were making a health drink.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In experiments they have to contend with oxidation that happens when the cells are broken open with all the air whipping through the mixture.  This is one reason you don't see blenders in labs to much anymore - hydraulic presses, sonicators, and bead beaters have taken their place - they have less aeration in the mixture and also deliver more power so that they can break open yeast and bacteria, which blenders really can't.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there will be some vegetables where the cell walls won't break open and all the nutrients won't be so easily accessible.  It must help to be running at the top end of the range, but there will always be some vegetables which won't be broken open.  For most things like bananas and apples it sounds like you'll get similar benefit with other blenders too.  Just have to think about how much more are you paying for that extra 10k of rpm I guess. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a benefit to breaking open the cells and letting all the nutrients (as well as cell waste) break out into solution?  It might give you a quick pulse of nutrition when you drink, but I'm pretty sure all the cells of a piece of fruit or vegetable will be pretty much broken down and extracted by the end.  On the other hand, it sounds like it will save the digestive system some work...  So there's that question too. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-03-10T05:08:48.287" LastActivityDate="2013-03-10T05:08:48.287" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7488" PostTypeId="2" ParentId="2077" CreationDate="2013-03-09T21:13:47.430" Score="7" Body="&lt;p&gt;If you are talking about sound damaging the sound sensing organs in the ear, analogous to an ultrasonic heavy metal concert, I've found an interesting &lt;a href=&quot;http://www.hse.gov.uk/research/crr_pdf/2001/crr01343.pdf&quot; rel=&quot;noreferrer&quot;&gt;report just on this topic&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;For ultrasonic components above 20 kHz, the limits were set to avoid hearing damage in the audible (lower) frequencies. One-third-octave band levels of 105-115 dB were observed to produce &lt;em&gt;no temporary hearing loss, and were therefore judged non-hazardous in respect of permanent hearing damage.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Emphasis mine, from &amp;quot;Damage to human hearing by airborne sound of very high frequency or ultrasonic frequency&amp;quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;If you are talking about high frequency sound from a explosion, or some sort of sonic cutter with intensities of such a level of compression or a high decibel range that conveys enough energy to physically damage something of course the answer would be 'yes this would damage your ears and the rest of the body too.&lt;/p&gt;&#xA;&lt;p&gt;Operators of ultrasonic equipment with levels above 60 dB complained of headaches and fatigue, even nausea below 60 dB they felt no effect (reference table 7 in paper).  But they did not seem to have any hearing loss.&lt;/p&gt;&#xA;&lt;p&gt;One soviet experiment is both informative and maybe also entertaining to read about:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;An unspecified number of subjects were exposed for an hour to a tone of 20 kHz at 110 dB. Tests were made to examine shift of hearing threshold over the frequency range 250 Hz to 10 kHz. Pulse rate, body temperature and skin temperature were also monitored. These tests showed no appreciable effect, even when the Sound Pressure Level was increased to 115 dB. These same subjects were given a one hour exposure to a 5 kHz tone at 90 dB: a considerable TTS was found. The 5 kHz tone at 110 dB produced a powerful vascular response.&lt;/p&gt;&#xA;&lt;p&gt;...&lt;/p&gt;&#xA;&lt;p&gt;It seems safe to infer an underlying concept: A sound which does not produce temporary&#xA;dullness of hearing cannot produce a permanent noise-induced hearing loss.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-03-09T21:20:59.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7490" PostTypeId="1" AcceptedAnswerId="7497" CreationDate="2013-03-10T18:01:27.850" Score="2" ViewCount="391" Body="&lt;p&gt;I'd like to do chemical structure prediction using a known molecule formulas. I'm familiar with &lt;em&gt;de novo&lt;/em&gt; protein structure prediction, but are there any programs which will go from formula to structure with optimal geometry of random small chemicals (say 30 atoms)? I found &lt;a href=&quot;http://cccbdb.nist.gov/mdlmol1.asp&quot; rel=&quot;nofollow&quot;&gt;http://cccbdb.nist.gov/mdlmol1.asp&lt;/a&gt; but it selects mol files from a limited database. I need a command line UNIX program which computes mols from formulas. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Concise structural formulas popular during past ages are unable to describe every type of chemical structure like morphine. I found no software that supports csf (Smiles and inchi are popular but are encoded and not human readable). When the bonds of the structure are known geometric minimization (DG-AMMOS) orients the structure to a stable native like direction.&#xA;&lt;a href=&quot;http://www.mti.univ-paris-diderot.fr/fr/downloads.html&quot; rel=&quot;nofollow&quot;&gt;http://www.mti.univ-paris-diderot.fr/fr/downloads.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="43" LastEditDate="2013-04-30T15:22:27.193" LastActivityDate="2017-08-14T12:35:28.713" Title="Chemical structure prediction" Tags="&lt;biochemistry&gt;&lt;bioinformatics&gt;&lt;medicinal-chemistry&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7491" PostTypeId="1" AcceptedAnswerId="7519" CreationDate="2013-03-10T21:10:34.353" Score="6" ViewCount="29300" Body="&lt;p&gt;Speciation can occur by polyploidy. My understanding of the process is as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;'polyploidy is when the number of chromosomes in an organism's cell doubles. This means that the organism has more chromosomes than other individuals of the same species, meaning it cannot mate with other individuals. The polyploidy organism then evolves, eventually leading to it becoming a separate species'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realise this may not be exactly correct. Is someone able to provide a better description of speciation by polyploidy?&lt;/p&gt;&#xA;" OwnerUserId="1216" LastActivityDate="2015-08-24T22:53:17.583" Title="Speciation by polyploidy" Tags="&lt;polyploidy&gt;&lt;speciation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7492" PostTypeId="1" AcceptedAnswerId="7514" CreationDate="2013-03-11T06:10:04.417" Score="16" ViewCount="6173" Body="&lt;p&gt;I've been to local zoo the other day and one lizard caught my attention: its pupils are circular, which, I thought, is not usual for reptiles. Turns out it is, but now I can't find any explanation on why some animals have one kind of pupil and others have the other. Lizards can have both, and so can snakes. The only difference I have found is that circular pupil can't shrink quite as much as a cat's-eye pupil, but that hardly explains why circular pupil even evolved in the first place as I don't see any advantage to it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ideas?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P. S. Fish only have circular pupils so that shape is older, right?..&lt;/p&gt;&#xA;" OwnerUserId="3228" LastEditorUserId="3228" LastEditDate="2016-01-03T13:18:14.337" LastActivityDate="2016-01-03T23:42:47.137" Title="What is the difference between a circular and a cat's-eye (slit) pupil?" Tags="&lt;evolution&gt;&lt;eyes&gt;&lt;vision&gt;" AnswerCount="5" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7494" PostTypeId="1" AcceptedAnswerId="7495" CreationDate="2013-03-11T06:23:09.497" Score="-2" ViewCount="15176" Body="&lt;p&gt;As I know three nucleotide pairs (triplus) code one gene.  But I have found next information in  the &quot;Molecular biology of the cell&quot; by Bruce Alberts:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mycoplasma genitalium:  it has only about 480 genes in its genome of 580 070 nucleotide pairs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But 480 genes * 3 ~ 1500 nucleotide pairs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where I have made mistake ?&lt;/p&gt;&#xA;" OwnerUserId="3197" LastActivityDate="2021-05-20T01:15:51.403" Title="How many nucleotide pairs code one gene?" Tags="&lt;genetics&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7495" PostTypeId="2" ParentId="7494" CreationDate="2013-03-11T07:07:50.927" Score="10" Body="&lt;p&gt;You seem to have some confusion, so let's clear things up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A gene is a stretch of DNA (or RNA) that codes for a polypeptide (protein), that is a series of aminoacids bound together.&#xA;Each gene consists of nucleotides bound together, which are interpreted by the cellular machinery in groups of three, called &lt;em&gt;triplets&lt;/em&gt;.&#xA;DNA is first transcribed into messenger RNA (mRNA), which is then translated into proteins.&#xA;Each triplet codes for one &lt;strong&gt;aminoacid&lt;/strong&gt; not one gene! In fact genes are not &quot;coded&quot; by anything, they are the code!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, what I just wrote is extremely simplified, there are other important details that I omitted, but hopefully it cleared your doubt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To give you some further detail: not every single nucleotide in a gene will code for an aminoacid. There are regulatory elements such as the promoter of the gene, which allows the enzymes that transcribe the DNA to attach to the gene (essentialy it says: &quot;hey, start transcription right here!&quot;). Similarly, enhancers and silencers can tune up or down transcription of the gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In eukaryotes there are big stretches of DNA called &lt;em&gt;introns&lt;/em&gt; that are not coding for anything but have big importance for regulating transcription. In fact a single mRNA can be used to code more than one protein, using a process called &lt;a href=&quot;http://en.wikipedia.org/wiki/Alternative_splicing&quot;&gt;alternative splicing&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also regions of DNA that code for RNA sequences not translated into proteins at all, but which have &lt;a href=&quot;http://en.wikipedia.org/wiki/Non-coding_RNA&quot;&gt;all sorts of regulatory functions in the cell&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="1320" LastEditDate="2013-03-11T08:36:06.010" LastActivityDate="2013-03-11T08:36:06.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7496" PostTypeId="1" AcceptedAnswerId="7499" CreationDate="2013-03-11T12:32:17.447" Score="0" ViewCount="146" Body="&lt;p&gt;When a biologist is talking about a genetically engineered mouse strain which is a &quot;tool strain&quot;, what does that mean? What is the exact definition of a tool strain? What is the difference between a tool strain and any other mouse strain? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, how are tool strains connected to recombinase techniques? Does using a recombinase automatically create a tool strain? Or are the properties &quot;tool strain&quot; and &quot;recombinase containing strain&quot; independent from each other? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it is important, the context is mouse (and possibly other animal) strains used in cancer research. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would help if you could keep the explanation high-level. I only have high-school biology knowledge and I am trying to make sense of the requirements for a software application for use by biologists. &lt;/p&gt;&#xA;" OwnerUserId="1578" LastActivityDate="2013-03-11T17:11:36.090" Title="What is a &quot;tool strain&quot;?" Tags="&lt;cancer&gt;&lt;recombination&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7497" PostTypeId="2" ParentId="7490" CreationDate="2013-03-11T14:36:42.423" Score="3" Body="&lt;p&gt;Did you try to use &lt;a href=&quot;http://www.bioclipse.net/bioclipse-features&quot; rel=&quot;nofollow&quot;&gt;Bioclipse&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bioclipse is mainly based on the Chemistry Development Kit (CDK), and contains a framework for managing and analyzing chemical compounds. Bioclipse supports editing in 2D, processing large collections of molecules in tables, calculation of various types of properties, and much more cheminformatics functionality. The Jmol application is integrated in Bioclipse as an editor, and provides advanced interactive 3D visualizations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3230" LastEditorUserId="4101" LastEditDate="2013-10-03T21:02:38.633" LastActivityDate="2013-10-03T21:02:38.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7498" PostTypeId="2" ParentId="7496" CreationDate="2013-03-11T14:59:14.680" Score="1" Body="&lt;p&gt;Until a better answer shows up...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A tool strain appears to be a mouse strain that is useful for making recombinant mice.  It has genes inserted into its genome to make detection of your manipulations easier.  In &lt;a href=&quot;http://jaxmice.jax.org/strain/017596.html&quot; rel=&quot;nofollow&quot;&gt;this case&lt;/a&gt; several phenotypes (luciferase, human SMN) can be observed as well as a tetracenomycin resistance marker is in place so that offspring with the gene can be easily estimated.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These Tg(SMN2)89; Smn1+/-; Tg(SMNΔ7)4299; ROSA26rtTA; &quot;old&quot; Luci-TRE-SMN mice allow high levels of both luciferase and full-length human SMN expression to be regulated by the addition/removal of doxycycline. These may be useful as a fluorescent reporter and/or Tet-On/Tet-Off tool strain for doxycycline-inducible rescue of Type II (moderate) proximal spinal muscular atrophy (SMA).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-03-11T14:59:14.680" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7499" PostTypeId="2" ParentId="7496" CreationDate="2013-03-11T17:11:36.090" Score="1" Body="&lt;p&gt;In extension to shigeta's answer, I could well imagine &quot;tool strains&quot; and &quot;recombinase strains&quot; to be equivalent in the sense that they mean strains of mice whose genome you can easily manipulate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cre recombinase is an enzyme which can recombine (effectively insert) genes from a plasmid (which you somehow delivered to the cell) into the cell's genome, if Lox-sites are present (&lt;a href=&quot;http://en.wikipedia.org/wiki/Cre-Lox_recombination&quot; rel=&quot;nofollow&quot; title=&quot;Cre-Lox recombination&quot;&gt;Cre-Lox recombination&lt;/a&gt;). This is a very common method of integrating genes into eukaryotic model organisms (i.e. mice).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By tool/recombinase strains they could simply mean mice which express recombinase already, so that you can readily insert your genes into specific cells by delivering a plasmid with the genes on it, and then triggering Cre recombinase in the cells you want to modify in order to integrate the genes into those cells' genome.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-03-11T17:11:36.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7500" PostTypeId="2" ParentId="7492" CreationDate="2013-03-11T19:32:07.860" Score="3" Body="&lt;p&gt;Your mention of cats hinted that vertical pupils have to do with night vision, and &lt;a href=&quot;http://www.newscientist.com/article/mg16422167.600-the-last-word.html&quot; rel=&quot;nofollow&quot;&gt;indeed they do.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The retinas of cats and other nocturnal animals are very sensitive to even the tiniest amount of light. This can make their eyes hurt when exposed to bright sunlight. So their pupils have to shrink as much as possible in the sunlight, and, as you pointed out, vertical pupils can shrink more than circular ones. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: People pointed out in the comments that cats have vertical eye pupils only in bright sunlight. In low-light conditions, the pupils expand to a circle. &lt;/p&gt;&#xA;" OwnerUserId="3053" LastEditorUserId="3053" LastEditDate="2013-03-13T16:46:23.030" LastActivityDate="2013-03-13T16:46:23.030" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="7501" PostTypeId="2" ParentId="7309" CreationDate="2013-03-11T20:36:02.177" Score="3" Body="&lt;p&gt;Most animals are not well adapted to deal with avalanches. For example, more mountain goats are killed by rock slides than by predators. &lt;a href=&quot;http://www.nationalgeographic.com/lewisandclark/record_species_150_11_2.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nationalgeographic.com/lewisandclark/record_species_150_11_2.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Meanwhile, a mountain at risk of snow avalanche must be deep in snow, right? At that point, there is very little food to be found; it's all buried. So there won't be many animals on the surface. Most of them would leave for more hospitable locations, or hibernate.&lt;/p&gt;&#xA;" OwnerUserId="3231" LastActivityDate="2013-03-11T20:36:02.177" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7504" PostTypeId="1" AcceptedAnswerId="7512" CreationDate="2013-03-12T00:24:00.467" Score="1" ViewCount="2493" Body="&lt;p&gt;Does anyone know of tools to convert lists of miR names to their miRBase Accession IDs? I know they exist, but my search keeps pulling up gene ID converters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: both @rg255 and @shigeta have provided solutions to the underlying issue, but I am curious to know if something exists for miRNAs that is similar to a site like &lt;a href=&quot;http://idconverter.bioinfo.cnio.es/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT 2: miRNA names are of the form 'hsa-let-7a' and Accession IDs are of the form 'MI0000060'&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-03-13T07:45:28.033" LastActivityDate="2018-05-30T09:59:20.083" Title="Batch convert miRNA names to Accession IDs?" Tags="&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7505" PostTypeId="1" CreationDate="2013-03-12T02:24:53.273" Score="5" ViewCount="361" Body="&lt;p&gt;How does the biology community currently feel with regards to publishing descriptive and effect size statistics rather than significance stats?  Almost every journal article I read in the cell biology field almost always reports things like P values and stats tests to report statistical significance, but should effect sizes be more important to a biologist?  Do we even care if something is statistically significant if the effect size is negligible?  Rather than crunch for significance, could one get away with showing things like confidence intervals, eta^2, Cohen's d, and r values instead over P values?  P values tell you the odds that if you assume the null hypothesis is true, then the observation you're making are only 5%(assuming of course P&amp;lt;0.05).  However, this can lead to the logical fallacy as noted by Aristotle--theory A predicts that changing X will cause Y.  An experimenter thus performs experiments to manipulate X and sees changes in Y, therefore he/she concludes theory A is supported, which is however completely wrong.  Theories B, C, D, E....... could all also predict that X changes Y and may even be better at it.  Even if you conclude that your findings &quot;support&quot; theory A, it's still weak because you haven't ruled out all of the other possibilities.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in order to avoid statistical significance relative to null hypothesis that has all sorts of pitfalls, can one just use descriptive and effect size statistics just as effectively, if not more so?&lt;/p&gt;&#xA;" OwnerUserId="3232" LastEditorUserId="1320" LastEditDate="2013-03-12T07:57:33.643" LastActivityDate="2013-03-12T13:50:24.480" Title="Are descriptive statistics sometimes more useful than tests of significance?" Tags="&lt;biostatistics&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7506" PostTypeId="1" AcceptedAnswerId="30565" CreationDate="2013-03-12T05:05:53.543" Score="4" ViewCount="544" Body="&lt;p&gt;I noticed that every time I suffer temporary tinnitus after going to a very loud concert, the frequency I perceive is identical. I'd put it somewhere around 17 kHz, but it's difficult to pin down with any real accuracy due to the dulling effect it has on external sound sources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this frequency constant across all humans? If not, what determines the frequency? Note that I'm only interested in tinnitus caused by exposure to loud sounds, not other types of tinnitus such as idiopathic tinnitus or tinnitus caused as a side-effect of medication.&lt;/p&gt;&#xA;" OwnerUserId="172" LastEditorUserId="9943" LastEditDate="2015-03-19T12:22:36.743" LastActivityDate="2018-06-21T07:39:44.840" Title="What determines the perceived pitch (frequency) of tinnitus?" Tags="&lt;perception&gt;&lt;hearing&gt;&lt;psychophysics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7507" PostTypeId="1" AcceptedAnswerId="7509" CreationDate="2013-03-12T11:11:08.463" Score="9" ViewCount="5537" Body="&lt;p&gt;I very rarely sneeze just once, usually there's two coming in a row, and I've noticed the same thing in other people and even in animals.  Is there any reason for this?&lt;/p&gt;&#xA;" OwnerUserId="1203" LastActivityDate="2016-03-22T14:47:32.910" Title="Why do sneezes come in pairs or more?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7508" PostTypeId="2" ParentId="7505" CreationDate="2013-03-12T13:50:24.480" Score="1" Body="&lt;p&gt;I'm not a statistician, but I think the comments have got it right.  There is never a reason to omit P values, statistical power or some other measure that you have done something that is not a random outcome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the sake of reference lets define the terms you reference:&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Analysis_of_variance#Effect_size&quot; rel=&quot;nofollow&quot;&gt;Eta squared&lt;/a&gt; is a ratio of the variances of two sets of measurements&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Effect_size#Cohen.27s_d&quot; rel=&quot;nofollow&quot;&gt;Cohen's d&lt;/a&gt; is a measure of the difference between two means.&lt;br&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient&quot; rel=&quot;nofollow&quot;&gt;R value or Pearson Correlation&lt;/a&gt; describes the linearity of two numbers, usually one of them being a measurement and the second being an experimental variable.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These numbers as you say are descriptive, but they could be created by throwing coins and writing them up.  With small numbers of measurements, and a large enough range of possibilities, its possible to get terribly large numbers here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biology, medicine, social science and economics are really susceptible to this.  You go into the field and measure butterfly wings or do surveys of people's opinions, or try to guess who is going to win the election and its quite expensive to do more measurements.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are measuring something hard to determine because accuracy is important such as a close election race or that is really complicated such as which genes convey a susceptibility to type 2 diabetes (a problem which remains unsolved because so many genes play a role) you need large numbers of responses.  Yet each study that comes out gets some answer, but if you want to believe it these numbers should convince no one in most cases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Microarray data and RNASeq data analysis for instance often suffer from this problem.  The measurements are all statistically significant but each one costs hundreds or even thousands of dollars.  Most experiments do a minimal three measurements to understand the variance in each measurement and then do 2 to 8 actual measurements.  That's not going to so revealing when working with a system with thousands of genes in it. one bad sample with slightly different culture conditions can ruin the experiment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our butterfly biologist may measure 100 butterflies and stop when the P values are 0.05 or 0.001 - its a lot of work camping out and setting nets.  The truth is that 5% is a number that can happen at random a lot.  Even a 0.1% error will happen in one in ten such experiments.  In thousands of experiments published that means that 10% of them have a mistake.  Not so great. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It gets worse though - not only significance, but &lt;strong&gt;bias&lt;/strong&gt; needs consideration.  Because biologists and most other scientists don't understand statistics, the assumptions that we use when we calculate a P value are often inappropriate and don't give honest estimates of the chance that this is a random phenomenon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If good looking result is chosen specifically to show to prove the point or some data are thrown out because they simply don't look good, or if a hypothesis is chosen in a biased way simply to fit an unreliable set of data.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or the statistical assumptions of the calculation might simply be so inappropriate that to really cite them is an out and out lie. An everyday example of this is to do a BLAST search.  The E-value calculations, if read as a P value would be wrong, even though they are mathematically correct - two strings that show a 10% identity will have a small E value - 10^-8 for instance, but this is only the chance two strings of these lengths will have so many letters in common.  Anyone who plays with BLAST will quickly throw out anything that has less than 30% identity unless they are desperate, even though the E-values are infinitesimal.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;John Ioannidis has made this subject his focus and has published widely on this topic.  A good place to start is his commentary &lt;a href=&quot;http://www.plosmedicine.org/article/info%3adoi/10.1371/journal.pmed.0020124&quot; rel=&quot;nofollow&quot;&gt;&quot;Why Most Published Research Findings Are False&quot;&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field. In this framework, a research finding is less likely to be true when the studies conducted in a field are smaller; when effect sizes are smaller; when there is a greater number and lesser preselection of tested relationships; where there is greater flexibility in designs, definitions, outcomes, and analytical modes; when there is greater financial and other interest and prejudice; and when more teams are involved in a scientific field in chase of statistical significance. Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. Moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this essay, I discuss the implications of these problems for the conduct and interpretation of research.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-03-12T13:50:24.480" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7509" PostTypeId="2" ParentId="7507" CreationDate="2013-03-12T14:30:37.807" Score="4" Body="&lt;p&gt;The very simple answer is that the causal factor or trigger hasn't disappeared after the first sneeze. Sneezing is a reflex, partially autonomous, to clear the nasal cavity of particles that don't belong there. As long as the trigger is not removed, the reflex is repeated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is also one of the reasons that allergies that cause sneezing, such as hay fever, continue as long as the factor causing the allergy is present.&lt;/p&gt;&#xA;" OwnerUserId="138" LastActivityDate="2013-03-12T14:30:37.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7511" PostTypeId="2" ParentId="7504" CreationDate="2013-03-12T17:06:50.900" Score="1" Body="&lt;p&gt;If you want it all, download the mirRNA.xls.zip file from mirbase here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;ftp://mirbase.org/pub/mirbase/CURRENT/&quot; rel=&quot;nofollow&quot;&gt;ftp://mirbase.org/pub/mirbase/CURRENT/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;its a spreadsheet that includes these data as columns and also more information besides - for the entire database. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-03-12T17:06:50.900" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7512" PostTypeId="2" ParentId="7504" CreationDate="2013-03-12T22:10:12.470" Score="1" Body="&lt;p&gt;in what species? this website looks like it will have them mirbase.org/cgi-bin/browse.pl?org=hsa If you are trying to connect them to data I'd suggest you find the table you want, save it in to a .txt file and use R (using the merge() function - df=merge(df1,mirbase,by=&quot;miR_names&quot;) would be a rough guide) to match them up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a batch converter - &lt;a href=&quot;http://atlas.dmi.unict.it/mirandola/tools.php&quot; rel=&quot;nofollow&quot;&gt;http://atlas.dmi.unict.it/mirandola/tools.php&lt;/a&gt; - add the text list to box on the right and it produces a table.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-03-13T07:36:34.557" LastActivityDate="2013-03-13T07:36:34.557" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7513" PostTypeId="2" ParentId="7378" CreationDate="2013-03-13T02:44:58.067" Score="4" Body="&lt;p&gt;As @dd3 points out, average GC% indicates a need for stability and coding regions or structural regions of the genome may need to be more stable.  But the largest %GC in genomes are found in thermophiles - organisms which live in high temperature water - in hotsprings and undersea geothermal vents. &lt;a href=&quot;http://www.biomedcentral.com/content/pdf/gb-2004-5-10-117.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;This review&lt;/a&gt; mentions how some thermophiles can be found with 50% GC.  The extreme thermophile &lt;em&gt;&lt;a href=&quot;http://www.nature.com/nbt/journal/v22/n5/abs/nbt956.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Thermus thermophilus&lt;/a&gt;&lt;/em&gt; can have a GC% content of 69.4%.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But you are asking &lt;em&gt;how&lt;/em&gt; does GC content get averaged out over the length of a large genome.  The answer is variation and selection.  When a gene needs to be more stable because of genomic function or because its trying to live in a hotter environment mutations that convert A/T to G/C base pairs will convey an incremental advantage to survival and will tend to be retained in the gene pool as long as no greater disadvantage to the mutation results.  Over time and as the stability creates a greater advantage, GC % will migrate further and further away from the mean. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This works for both thermo-tolerance and because of the biofunctional constraints of being a telomere, centromere or a coding region - stability and coding constraints play against each other to converge on an optimal GC content in any given stretch of the genome.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conversely most genomes have a GC content below 50% are migrating there because too much stability can have a cost as well.  Breaking up the DNA helix for transcription and other cellular processes must go smoothly as well for example.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coding regions are significant for bacteria (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21120/#A5531&quot; rel=&quot;nofollow noreferrer&quot;&gt;E coli is 89% coding sequence&lt;/a&gt;).  For coding sequences, the genetic code is logically 50% GC on the average, but if you look at the actual codons in the diagram below you will see that except in the case of a single codon case (tryptophan, methionine) the third base always has a GC option, allowing for a GC content in the mid 60 percentiles.  The constraint of allowing coding sequences to freely vary is only an approximation - in some cases substitutions to amino acids with GC rich codons might move the cieling up a bit. And the more frequent amino acids have the possibility of making 2 or 3 bases of their codon GC bases.  Overall it would be remarkable to find a bacteria with GC% greater than 72%.  Mutations and the requirements of proteins being coded for would simply not allow it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2AMNW.jpg&quot; alt=&quot;genetic code&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So: over evolutionary periods these GC mutations accumulate where they are helpful, even to the extent of 2/3 of the genome being GC pairs.  The strongest selective force to accumulate a high average GC% for a genome is exposure of the genome itself to a high temperature environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that this thermo-stability argument doesn't count for many animals because they do regulate their body temperatures.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-04-13T19:30:06.633" LastActivityDate="2013-04-13T19:30:06.633" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7514" PostTypeId="2" ParentId="7492" CreationDate="2013-03-13T12:40:21.510" Score="12" Body="&lt;p&gt;Circular pupils are &lt;em&gt;always&lt;/em&gt; functionally superior to vertical pupils; a slit does not correctly focus light from all directions whereas a circular pupil does. If you observe cats when they're hunting at dawn and dusk*, they have big, circular pupils; it's only when they're in bright light that the pupil shrinks to a slit. So why have vertical pupils at all? Because, as you mention they're capable of letting a more controlled range of light into the eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus vertical slits let you be active in a wider range of light conditions at the cost of poorer vision in bright light; whilst circular pupils continue to function well in brighter light but at the cost of not allowing such a large range of control over the amount of light entering the eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is then easy to see why you get both kinds of pupil: circular pupils are favoured by animals that are typically active in bright light and need good vision under these circumstances; vertical pupils are favoured by animals that are primarily active in low light but need some ability to see in bright light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*- it's often stated that cats are nocturnal, this is untrue; cats are &lt;em&gt;crepuscular&lt;/em&gt; - that is they are most active at dawn and dusk.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-03-13T12:40:21.510" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7515" PostTypeId="1" CreationDate="2013-03-13T14:23:45.840" Score="4" ViewCount="298" Body="&lt;p&gt;I had a colleague ask me recently whether mRNAs could be sequenced directly. I found &lt;a href=&quot;http://dx.doi.org/10.1038/nature08390&quot; rel=&quot;nofollow&quot;&gt;this Nature paper&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt; published by Helicos in 2009, in which they describe their developments in the area. It's been several years since this was published, and yet RNAseq and most other transcriptomic analysis is still done by first reverse transcribing RNA into complementary DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the current state of RNA sequencing? Has Helicos failed to deliver on their technology? Have any other platforms risen to the challenge (or attempted to do so)? Or is the technology successfully in production and still simply overshadowed by the wide adoption of traditional cDNA-based sequencing methods?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nature08390&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Ozsolak F, Platt AR, Jones DR, Reifenberger JG, Sass LE, McInerney P, Thompson JF,  Bowers J, Jarosz M, Milos PM&lt;/strong&gt;. 2009. Direct RNA sequencing. Nature, 461, 814-818, doi:10.1038/nature08390.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="4101" LastEditDate="2013-11-02T00:26:45.777" LastActivityDate="2013-11-03T22:33:22.100" Title="Current state of direct RNA sequencing" Tags="&lt;rna&gt;&lt;rna-sequencing&gt;&lt;mrna&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7516" PostTypeId="1" CreationDate="2013-03-13T14:36:53.647" Score="1" ViewCount="98" Body="&lt;p&gt;Now that sequencing is becoming increasingly cheap, what is the value of recombination-based genetic mapping against the sequence-based genetic mapping?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that in the past recombination-based genetic maps were used as blueprints for sequencing projects. But since now the entire genome can be sequenced pretty cheaply both in time and money, what is the unique value of recombination-based genetic mapping?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One thing that comes to mind but I am not very sure. It might be suitable for mapping novel phenotypic markers e.g., unmapped diseases.&lt;/p&gt;&#xA;" OwnerUserId="3109" LastEditorUserId="948" LastEditDate="2013-03-13T16:16:27.963" LastActivityDate="2014-06-30T10:41:29.250" Title="Recombination-based vs. Sequence-based genetic mapping" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7517" PostTypeId="1" AcceptedAnswerId="7551" CreationDate="2013-03-13T22:47:51.450" Score="2" ViewCount="236" Body="&lt;p&gt;I've been curious as to which photosynthetic cycle St. John's wort uses to synthesise glucose and more complex carbohydrates. I know it probably won't be the crassulacean acid metabolism (CAM) cycle seeing how that applies mostly to plants that require a limited amount of water as opposed to St. John's wort which tends to prefer moisture. I suspect the answer to my question will be C3 seeing how they dominate in the plant kingdom and I know that St. John's wort requires relatively cool climates to grow successfully -- a trait characteristic of C3 plants seeing how high temperatures tend to cause excessive and wasteful photorespiration.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2014-10-09T13:35:37.930" Title="Is Hypericum Perforatum (St. John's wort) a C3 or C4 plant?" Tags="&lt;photosynthesis&gt;&lt;botany&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7518" PostTypeId="1" CreationDate="2013-03-13T23:27:16.870" Score="2" ViewCount="18145" Body="&lt;p&gt;In general, plants photosynthesize through their leaves and, to a much lesser extent, through their stems. Cacti, however, have no visible leaves, but instead spines. In what part of the cactus does the photosynthesis take place?&lt;/p&gt;&#xA;" OwnerUserId="3236" LastActivityDate="2016-01-13T07:22:23.397" Title="What part of the cactus photosynthesizes?" Tags="&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7519" PostTypeId="2" ParentId="7491" CreationDate="2013-03-13T23:39:06.867" Score="6" Body="&lt;p&gt;By definition, polyploidy just means that a cell or organism contains more than 2 pairs of homologous chromosomes (or is more than 2n). This is more common in plants than it is in animals. The plant, as shown below, undergoes failed meiosis, which means that the diploid (2n) cells never become haploid (n). As a result, a plant ends up with more than 2n when it self-polinates. The shown result is tetraploidy (4n), but there are other possible results (3n, 5n, etc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nrZX9.png&quot; alt=&quot;Polyploidization&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Multiple plants within a population can end up with the same polyploidy number. They can then reproduce with each other but not with the original plants or any other plants. As a result, they become biologically isolated from the original group of plants and are considered a different species. It is a type of sympatric speciation, which means that it occurs without geographic isolation.&lt;/p&gt;&#xA;" OwnerUserId="3236" LastActivityDate="2013-03-13T23:39:06.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7520" PostTypeId="2" ParentId="7518" CreationDate="2013-03-14T06:03:20.590" Score="1" Body="&lt;p&gt;In wiki there is a good answer for your question &lt;a href=&quot;http://en.wikipedia.org/wiki/Cactus#Leaves&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Cactus#Leaves&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In plants photosynthesis takes place in chloroplasts. Chloroplasts may be in the cells of fruits, stems, but most of all in leaves. In some succulents (such as cacti), the main photosynthetic activity is associated with a stem.&lt;/p&gt;&#xA;" OwnerUserId="1839" LastEditorUserId="1320" LastEditDate="2013-03-14T07:44:47.813" LastActivityDate="2013-03-14T07:44:47.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7521" PostTypeId="1" CreationDate="2013-03-14T10:13:25.893" Score="4" ViewCount="330" Body="&lt;p&gt;It was a question in one competition, but it remained unanswered and i am curious about an answer. &#xA;There was a hint: American bullfrog&#xA;but i can not find any example of this behaviour on the web.&lt;/p&gt;&#xA;" OwnerUserId="3239" LastEditorUserId="1590" LastEditDate="2013-03-14T14:12:11.317" LastActivityDate="2016-11-23T18:09:57.367" Title="Is there an animal which, when eaten by other animal, poisons the predator and gets out of it's stomach?" Tags="&lt;zoology&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7522" PostTypeId="1" CreationDate="2013-03-14T10:49:41.577" Score="6" ViewCount="237" Body="&lt;p&gt;Ophiocordyceps unilateralis is a parasitoidal fungus that alters the behavior of the infected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://en.wikipedia.org/wiki/Ophiocordyceps_unilateralis&quot; rel=&quot;noreferrer&quot;&gt;Wiki page&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is the fungus able to alter the behavior of the infected to such specfic commands?&lt;br&gt;&#xA;Does the fungus tap into the electrical signals of the brain directly or does it release some kind of hormone to alter the behavior?&lt;/p&gt;&#xA;" OwnerDisplayName="user1897" LastEditorDisplayName="user1897" LastEditDate="2013-03-18T12:08:28.213" LastActivityDate="2013-10-02T03:35:12.037" Title="Zombie Ant Fungus?" Tags="&lt;neuroscience&gt;&lt;mycology&gt;&lt;behaviour&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7523" PostTypeId="1" CreationDate="2013-03-14T11:48:39.857" Score="2" ViewCount="233" Body="&lt;p&gt;This question is motivated by a practical application in bread making.&#xA;While it is well known which are the optimal (highest reaction rate) temperatures for both alpha and beta amylase, I am not able to find any precise information concerning reaction rate as a function of temperature.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;How does alpha and beta amylase activity change when temperature decreases?&lt;/li&gt;&#xA;&lt;li&gt;At which temperatures does their activity stop?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3240" LastActivityDate="2013-03-14T11:48:39.857" Title="Cereal Alpha and Beta Amylase temperature range and reaction rate" Tags="&lt;enzymes&gt;&lt;temperature&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7525" PostTypeId="1" AcceptedAnswerId="8458" CreationDate="2013-03-14T12:38:48.310" Score="7" ViewCount="938" Body="&lt;p&gt;I'm trying to find out if a particular allele is in Hardy-Weinberg disequilibrium, but the data is poor. What's the minimum population number that you can use to get any sort of respectable conclusion?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've heard it's 5 individuals minimum for each genotype but can't find a source on that.&lt;/p&gt;&#xA;" OwnerUserId="1763" LastEditorUserId="3624" LastEditDate="2014-11-03T09:11:08.603" LastActivityDate="2014-11-03T09:11:08.603" Title="What is the minimum population size that Hardy-Weinberg calculations can be applied to?" Tags="&lt;genetics&gt;&lt;mathematical-models&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7527" PostTypeId="2" ParentId="7521" CreationDate="2013-03-14T13:04:15.783" Score="4" Body="&lt;p&gt;The closest I can think of with that hint is &lt;a href=&quot;https://blogs.discovermagazine.com/notrocketscience/2011/09/21/beetle-larva-lures-and-kills-frogs-while-the-adult-hunts-and-paralyses-them/#.UUHI6ldGxOI&quot; rel=&quot;nofollow&quot;&gt;a Middle Eastern beetle that hunts frogs and other amphibians&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In almost 400 face-offs, the amphibians only managed to get the larvae in their mouths seven times. Even then, they soon spat out the larvae, which quickly turned on them (first video below). One toad even managed to swallow a larva, which moved inside its stomach for two hours. For some reason, the toad eventually regurgitated its catch, and the larva, apparently unharmed, killed and ate the animal that had just eaten it (second video below).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, it's only a pseudo-fit to the clue. The beetle doesn't hunt American bullfrogs, but ones native to its area of the world.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-03-14T13:04:15.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7528" PostTypeId="1" CreationDate="2013-03-14T15:55:05.783" Score="4" ViewCount="4607" Body="&lt;p&gt;I want to know what are the effects of not using your teeth to grind foods but preparing it before eating with blending and grinding them into a liquid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here I am not talking about any weight loss or fitness industry prepared drinks. I mean the ordinary raw and cooked foods like meat, vegetables, cereals, and fruits that one would normally eat in classic meals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would this decrease of work done by teeth and digestion system have positive or negative health effects?&lt;/p&gt;&#xA;" OwnerUserId="3242" LastActivityDate="2014-07-24T00:39:34.797" Title="Long term liquid food diet by blending/grinding all quality foods one would normaly eat, not any weight loss or prepared drinks" Tags="&lt;digestive-system&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="7529" PostTypeId="1" CreationDate="2013-03-14T16:54:52.930" Score="10" ViewCount="1269" Body="&lt;p&gt;In &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionary_game_theory&quot;&gt;evolutionary game theory&lt;/a&gt;, it is typical to model organisms as having a base fitness that is modified slightly by the game interaction. The ratio of the game effect versus the base fitness determines the strength of selection, with &lt;em&gt;weak selection&lt;/em&gt; meaning the game modifies overall fitness only slightly, and &lt;em&gt;strong selection&lt;/em&gt; meaning that the game payoff is a big part of the overall fitness of the organism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most analytic models like to assume weak selection because it allows the authors to Taylor expand the selection function and linearize it by dropping terms that are higher order in the stength of selection. However, it is unclear that results derived for weak selection would necessarily hold under strong selection. &lt;strong&gt;Are there mathematical (or computational) models where weak and strong selection produce qualitatively different results? If not, is there an argument as to why weak and strong selection should produce the same results?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've also seen this discussion come up outside of evolutionary game theory, in a more general biological setting. In particular, with respect to inclusive fitness. The take away message I got was that in the regime of weak selection relatedness means what you expect it to mean, but for strong selection the concept becomes very slippery and counter-intuitive. &lt;strong&gt;What does inclusive fitness theory tell us about going from weak to strong selection?&lt;/strong&gt; Again, I prefer arguments supported by clean mathematical or computational models over ones based on intuition and words alone.&lt;/p&gt;&#xA;" OwnerUserId="500" LastActivityDate="2014-03-12T23:04:13.547" Title="When does weak selection produce qualitatively different results from strong selection?" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;population-dynamics&gt;&lt;theoretical-biology&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7530" PostTypeId="5" CreationDate="2013-03-14T17:20:12.430" Score="0" Body="&lt;p&gt;The application of dynamic systems and game theory to evolving populations in biology, economics, and social sciences. It is particularly well suited for studying social dilemmas like the evolution of cooperation. See also &lt;a href=&quot;/questions/tagged/altruism&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;altruism&amp;#39;&quot; rel=&quot;tag&quot;&gt;altruism&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="4101" LastEditDate="2013-10-31T18:16:12.923" LastActivityDate="2013-10-31T18:16:12.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7531" PostTypeId="4" CreationDate="2013-03-14T17:20:12.430" Score="0" Body="The application of dynamic systems and game theory to evolving populations in biology, economics, and social sciences. It is particularly well suited for studying social dilemmas like the evolution of cooperation and altruism." OwnerUserId="500" LastEditorUserId="4101" LastEditDate="2013-10-31T18:16:12.923" LastActivityDate="2013-10-31T18:16:12.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7533" PostTypeId="1" CreationDate="2013-03-14T18:29:05.693" Score="2" ViewCount="85" Body="&lt;p&gt;This is a hypothetical situation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Meningococcal polysaccharide vaccine (MPSV4) is a vaccine against Neisseria meningitidis. &#xA;MCV4 is a conjugate vaccine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know if the polysaccharide base could interact with the conjugate base.&#xA;I think they would not act like booster doses and that the efficacy of the conjugate vaccine would be decreased, due to the lifelong effects of MPSV4.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Might MPSV4's polysaccharide base interact with MCV4's conjugate base, and if so, what might be the mechanism?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="3059" LastEditDate="2013-03-15T01:26:21.983" LastActivityDate="2013-03-15T01:26:21.983" Title="Might a previously administered MPSV4 vaccine react with a newly administered MCV-4 vaccine?" Tags="&lt;vaccination&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7534" PostTypeId="1" AcceptedAnswerId="7536" CreationDate="2013-03-14T22:28:01.580" Score="6" ViewCount="363" Body="&lt;p&gt;On a random forum, a member speculated that their &lt;a href=&quot;http://en.wikipedia.org/wiki/Cirrhosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;cirrhosis&lt;/a&gt; was caused by wearing tight-fitting clothing such as a girdle or corset.  This leads me to the following question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;: Can cirrhosis be caused by physical compression of the body?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The list of causes on Wikipedia does not include this.  However, this may just be because the list is incomplete.  Alternatively, it may be because physical compression is unlikely to contribute to cirrhosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A plausible mechanism that springs to my mind is that physical compression leads to the constriction of hepatic veins, arteries and/or their tributaries.  But I suspect the rib cage would provide significant protection against this (see below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RxjF1.jpg&quot; alt=&quot;Image is on 100+ websites; I&amp;#39;ll assume it&amp;#39;s considered public domain.&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="203" LastActivityDate="2013-03-14T23:28:56.237" Title="Can cirrhosis be caused by physical compression of the body?" Tags="&lt;human-biology&gt;&lt;pathology&gt;&lt;liver&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7536" PostTypeId="2" ParentId="7534" CreationDate="2013-03-14T23:28:56.237" Score="9" Body="&lt;p&gt;There is the term “corset liver”. It describes changes (“grooves”) on the liver’s surface following external compression and subsequent local &lt;em&gt;atrophy&lt;/em&gt;, e.g. from wearing a corset for a long time. (see Dancygier: &lt;em&gt;Clinical Hepatology&lt;/em&gt;) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A paper from the 1980s describes &lt;em&gt;some abnormality&lt;/em&gt; in the histological findings of liver tissue of dogs after chronic abdominal compression but without providing any details in the abstract (I don’t have access to the full version). They measured an increased pressure in the Vena cava and the portal vein. (Ueyoshi, Shima: &lt;em&gt;Studies on spinal braces. With special reference to the effects of increased abdominal pressure.&lt;/em&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4093227&quot;&gt;PMID 4093227&lt;/a&gt;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A (chronic) Budd–Chiari syndrome can also cause liver necrosis and consequently cirrhosis and can be the result of venous compression from e.g. tumors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I doubt that a comparable chronic compression is possible from wearing clothing. Corsets are still used in orthopedic conditions. I have never heard about long-term side effects on liver tissue. The explanation for cirrhosis seems unlikely to me. &lt;/p&gt;&#xA;" OwnerUserId="3241" LastActivityDate="2013-03-14T23:28:56.237" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7537" PostTypeId="1" CreationDate="2013-03-15T02:05:29.077" Score="4" ViewCount="87" Body="&lt;p&gt;So I have a validated set of primers for rtPCR from Biorad that contains SYBR green.  If I do rtPCR, can I use the rtPCR product after purifying it with a Qiagen PCR purification kit?  Also, I'm under the impression that the sequencing company needs primers to do sequencing, do I just use the PCR primer or one of the &quot;universal&quot; primers the company has?  &lt;/p&gt;&#xA;" OwnerUserId="3232" LastActivityDate="2014-12-21T20:36:25.773" Title="Sequencing rtPCR product" Tags="&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7538" PostTypeId="1" AcceptedAnswerId="7540" CreationDate="2013-03-15T17:47:14.107" Score="-2" ViewCount="199" Body="&lt;p&gt;My bloodgroup for example is A+. How much information is knowing my bloodgroup? How much information can be known from a blood sample? I expect you to be able to clone if known a &lt;em&gt;complete&lt;/em&gt; DNA sequence but how much would I recognize myself from a clone you make from my DNA e.g. behaviour?&lt;/p&gt;&#xA;" OwnerUserId="3248" LastActivityDate="2013-03-15T20:28:28.930" Title="How much can be said about behaviour (future) based on bloodgroup?" Tags="&lt;human-biology&gt;&lt;dna&gt;&lt;cloning&gt;&lt;behaviour&gt;&lt;red-blood-cell&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7540" PostTypeId="2" ParentId="7538" CreationDate="2013-03-15T18:03:58.560" Score="1" Body="&lt;p&gt;The neurological basis of behavior is still unclear, and the genetic basis of behavior is even less clear.  What can be said is that genetics may predispose you to certain behaviors, but what the predisposing factors are, and how much they determine your behavior (and how much is due to environmental factors), is unclear.  And this varies for different behaviors -- if you want to read more about a particular behavior, you can try looking up the genetics of addiction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we want to examine the genetic basis of behavior, I don't think anyone would be looking at blood group, which is due to some physical characteristic that is not obviously linked with behavior (versus a differently structured neurotransmitter receptor, which is possibly more related). It's like using your height to explain your behavior.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: On cloning:&#xA;I should also mention that human reproductive cloning has not been successfully attempted, and if it were, you wouldn't get an exact copy of the donor of the genetic material (by the current technologies).  The most famous example of reproductive cloning, Dolly the sheep, required more than just nuclear DNA:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dolly or any other animal created using nuclear transfer technology is&#xA;  not truly an identical clone of the donor animal. Only the clone's&#xA;  chromosomal or nuclear DNA is the same as the donor. Some of the&#xA;  clone's genetic materials come from the mitochondria in the cytoplasm&#xA;  of the enucleated egg. Mitochondria, which are organelles that serve&#xA;  as power sources to the cell, contain their own short segments of DNA.&#xA;  Acquired mutations in mitochondrial DNA are believed to play an&#xA;  important role in the aging process.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The source also has more information about cloning: &lt;a href=&quot;http://www.ornl.gov/sci/techresources/Human_Genome/elsi/cloning.shtml&quot; rel=&quot;nofollow&quot;&gt;http://www.ornl.gov/sci/techresources/Human_Genome/elsi/cloning.shtml&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-03-15T20:28:28.930" LastActivityDate="2013-03-15T20:28:28.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7541" PostTypeId="1" AcceptedAnswerId="7542" CreationDate="2013-03-15T18:58:15.907" Score="12" ViewCount="3065" Body="&lt;p&gt;If fever is a natural defense against pathogens, why do sick people take NSAIDs to reduce the fever? &lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2019-03-02T04:37:25.060" Title="If fever is a natural immune defense, why do people take drugs to lower it?" Tags="&lt;human-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7542" PostTypeId="2" ParentId="7541" CreationDate="2013-03-15T21:11:12.960" Score="20" Body="&lt;p&gt;Personal comfort is the primary answer. Quite a bit of research has gone into fevers, and the current consensus is that &lt;a href=&quot;http://en.wikipedia.org/wiki/Hyperpyrexia#Management&quot; rel=&quot;noreferrer&quot;&gt;Fevers less than 105F (40.5C) shouldn't necessarily be treated&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The primary reason the body raises its temperature (via the Hypothalamus in this case) is that &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/003090.htm&quot; rel=&quot;noreferrer&quot;&gt;bacteria and viruses tend to optimally thrive at 98.6F&lt;/a&gt;, which is also your body's optimal operating temperature. By raising the body's temperature, the bacteria/viruses become less efficient, allowing your body to &quot;catch up&quot; since the body's immune response takes time to ramp up before it reaches its peak (which is a bit after peak viral/bacterial load). Here's an example for Hepatitis (HBxAg = the virus, Anti-HBx = antibodies against the virus):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/msbhR.jpg&quot; alt=&quot;Example of immune response kinetics&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Along with the Fever, joint inflammation (part of the Innate Immune system's primary response) is also a coinciding symptom. So when your body begins to fight an infection you get a fever (which can make the environment uncomfortably hot/cold) and the tissues around your joints swell (which makes movement and relaxation uncomfortable). NSAIDs like Ibuprofen reduce those symptoms, making the duration of the infection more bearable. They do not reduce the length of the infection by any measure (and &lt;em&gt;might&lt;/em&gt; increase it, though the research is not particularly conclusive), but can make the day go by better if you've used up all your sick days or have a child to take care of.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, people take NSAIDs to reduce fevers for the same reason most take any over-the-counter pain medications. To make life a little easier in the meantime.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1320" LastEditDate="2013-03-16T10:53:21.523" LastActivityDate="2013-03-16T10:53:21.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7543" PostTypeId="1" CreationDate="2013-03-16T01:21:10.793" Score="2" ViewCount="58" Body="&lt;p&gt;So I read a journal article entitled &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22612345&quot; rel=&quot;nofollow&quot;&gt;&quot;Maternal hypoxia and caffeine exposure depress fetal CV function during primary organogenesis&lt;/a&gt;&quot; (Momoi, et al., 2012) and in essence the article speaks of the period of time in embryological development when the cardiovascular system is developing as being the time when the fetus is most susceptible to epigenetic events, and how adenosine and its A2 receptor have a role in dilating coronary arteries in hypoxic conditions. It later goes on to say that since caffeine is an adenosine A2 receptor antagonist, mothers who consume caffeine regularly create a suboptimal environment for the fetus - this is referred to in the article as IUGR (intrauterine growth restriction).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: Are there any effects (or do you believe there could be effects) of this inhibition occurring during development that affect the fetus later in life? As in, do you think there would be adult phenotypic changes of any kind due to the regular inhibition of a receptor during development? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought about this for a while and all that was apparent to me is that if the mother was both consuming caffeine and hypoxic, then the fetus could experience myocardial damage because its coronary arteries wouldn't be receiving the signal to dilate and the heart might be &quot;starved&quot; of the proper oxygenation. But even so, the receptor would still be present in the adult. Do you think there could be a decrease in transcription of a receptor that is continuously blocked (you don't need to address this in your answer -- notice that I'm asking for an opinion, which you can choose to give or withhold)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;FYI: I'm writing a review on how maternal prenatal health contributes to the epigenetic profile of offspring and I'm actually focusing more on the epigenetic contributions to the adult hypertensive phenotype. I stumbled upon the CV/adenosine article and was curious about whether there could be any long-term changes, so I asked all you wise folk. It has been observed that mothers fed a low-protein diet give birth to children with reduced nephron count and glomerular hypertrophy -- my goal is to understand what the current state of knowledge of this mechanism is. So if you have any ideas about anything here, or you've got an awesome resource related to this material, I'd really appreciate hearing about it. &lt;/p&gt;&#xA;" OwnerUserId="1917" LastEditorUserId="69" LastEditDate="2013-03-16T12:38:16.883" LastActivityDate="2013-03-16T12:38:16.883" Title="If a receptor is inhibited throughout embryogenesis, could there be observable phenotypic differences in the adult?" Tags="&lt;epigenetics&gt;&lt;cardiology&gt;&lt;development&gt;&lt;receptor&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7544" PostTypeId="1" AcceptedAnswerId="7565" CreationDate="2013-03-16T03:18:31.437" Score="7" ViewCount="751" Body="&lt;p&gt;As far as I can tell, caffeine metabolism occurs primarily via the CYP1A2 enzyme. I am curious as to whether mutations in the CYP1A2 gene are associated with caffeine intolerance.  Some site that is not necessarily reputable suggested that caffeine intolerance is due to absence of the enzyme to metabolize caffeine. I am having difficulty finding evidence either supporting or contradicting this claim.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know if there is evidence that suggests mutations in CYP1A2 (and therefore inability to properly metabolize caffeine) are associated with caffeine intolerance, or if there is another proposed mechanism for caffeine intolerance?&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-03-16T07:32:39.630" LastActivityDate="2021-04-28T22:57:40.810" Title="What is the biological mechanism underlying caffeine intolerance? (CYP1A2 or other?)" Tags="&lt;genetics&gt;&lt;pharmacology&gt;&lt;metabolism&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7545" PostTypeId="1" AcceptedAnswerId="7555" CreationDate="2013-03-16T06:10:14.773" Score="2" ViewCount="355" Body="&lt;p&gt;My question was raised after receiving &lt;a href=&quot;https://biology.stackexchange.com/a/7542/69&quot;&gt;this information&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The primary reason the body raises its temperature (via the Hypothalamus in this case) is that bacteria and viruses tend to optimally thrive at 98.6F, which is also your body's optimal operating temperature. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am just wondering if there are any viruses or bacteria that have gained the ability to prosper under fever temperatures through evolution? If not, why not?  Is there any biological restriction stopping such viral evolution?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will try to explain my question.  As far as I know, evolution helps species to adapt to their environment.  For example, when people started using antibiotics we got new bacteria resistant to those antibiotics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If fever is part of the innate immune reaction to viruses and bacteria, why hasn't this resulted in selection for fever-resistant variants? Why has evolution apparently stopped in this case?&lt;/p&gt;&#xA;" OwnerUserId="3197" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-03-18T00:58:13.153" Title="Are there any viruses or bacteria which have evolved to withstand higher temperatures due to fever" Tags="&lt;human-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7547" PostTypeId="1" CreationDate="2013-03-16T14:41:52.933" Score="2" ViewCount="6442" Body="&lt;p&gt;I want to know this in particular about animals that no longer eat what they used to eat. The best example in my opinion are chickens. Chickens are often held to eat all kinds of food we would otherwise throw away. Most of this, they would never find in nature. &#xA;Chickens almost eat everything, but there are things they don't. Also, they often have a clear preference for some food. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can they differentiate this food? Do they use smell? Looks? How can they know smells of food they never had before? &lt;/p&gt;&#xA;" OwnerUserId="1224" LastActivityDate="2013-03-17T06:59:39.233" Title="How do animals decide what to eat and what not?" Tags="&lt;food&gt;&lt;chickens&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7548" PostTypeId="1" CreationDate="2013-03-16T17:02:55.073" Score="10" ViewCount="1408" Body="&lt;p&gt;After death which of our body's metabolic processes will continue functioning for the longest?&lt;/p&gt;&#xA;" OwnerUserId="1763" LastActivityDate="2014-10-09T15:44:22.063" Title="In humans what is the last metabolic process to cease after death?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;death&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7549" PostTypeId="2" ParentId="7547" CreationDate="2013-03-16T17:34:04.773" Score="1" Body="&lt;p&gt;To answer with a question: How do you decide what to eat (if you don't know whether something is edible)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All animals have evolved taste and smell (and I'm sure even prior to eyesight). The purpose of taste and smell in terms of nutrition is to determine if something is edible. If something tastes bitter or extremely sour, this is mostly a warning sign for toxins or advanced microbial degradation. The same accounts for smell: If you let raw meat foul, the smell is unbearable. Why? Because our brain is telling us not to eat this.&lt;/p&gt;&#xA;" OwnerUserId="852" LastActivityDate="2013-03-16T17:34:04.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7551" PostTypeId="2" ParentId="7517" CreationDate="2013-03-17T03:47:17.103" Score="2" Body="&lt;p&gt;It's C3, &lt;a href=&quot;http://www.fs.fed.us/ne/delaware/ilpin/1538.co&quot; rel=&quot;nofollow&quot;&gt;according to the Illinois plant information network&lt;/a&gt;.  (See CO₂ fixation on this page.) This is the best I could find.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3340" LastEditDate="2014-10-09T13:35:37.930" LastActivityDate="2014-10-09T13:35:37.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7552" PostTypeId="2" ParentId="7547" CreationDate="2013-03-17T06:59:39.233" Score="-2" Body="&lt;p&gt;Probably a lot of external and internal factors combined. But the most important would be the smell, eye sight and taste.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Smell&lt;/strong&gt; can be, I would say 60-70%. When some particles arrive to the smell receptors, htne on the cellular level the receptor gives a &quot;report&quot; to other parts of the bady, especially brain etc. E.g. some seabirds, like storm petrels, recognize the odor of a compound emitted by krill, their main fare.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Almost all birds have great &lt;strong&gt;eyes&lt;/strong&gt;, so this is a great long-distance food check.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But to be honest the &lt;strong&gt;taste&lt;/strong&gt; is also a big issue and I think that all birds go through a phase when they eat everything and after learning what tastes good and bad (with combination of how it look like before they eat it and how it smelled, the infomrmation is stored in the brain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even though the birds have problems with complicated thought processes in their brain, I think that they are more than capable of storing and reusing this &quot;good-bad-food&quot; information from their brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There could be other factors like e.g. some birds are allergic to some food (yes, animals can be allergic too, even though their immune system is much stronger then ours) and the body will store in the brain to not eat that in the future.&lt;/p&gt;&#xA;" OwnerUserId="3118" LastActivityDate="2013-03-17T06:59:39.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7553" PostTypeId="1" AcceptedAnswerId="7831" CreationDate="2013-03-17T07:16:51.473" Score="9" ViewCount="13427" Body="&lt;p&gt;Some human tissue can survive without oxygen a couple of minutes, even hours. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why are the neurons are so &quot;weak&quot; and depends so much on oxygen and other nutrients and cannot live without them for more than a few seconds or 1 or 2 minutes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are they missing some parts of their cells which can store nutrients for worse times in favor of their function or what is the case?&lt;/p&gt;&#xA;" OwnerUserId="3118" LastEditorUserId="6" LastEditDate="2013-03-17T08:31:09.323" LastActivityDate="2013-09-20T04:21:30.753" Title="Why do neurons die so fast without oxygen and nutrients?" Tags="&lt;neuroscience&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7554" PostTypeId="1" CreationDate="2013-03-17T13:39:31.413" Score="1" ViewCount="395" Body="&lt;p&gt;I'm undergraduate physics student, but I've always been interested in biology. So I have a couple of questions about an application of the evolutionary principles to practice.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Agony as the last stage of dying.&lt;/li&gt;&#xA;&lt;li&gt;Hydrophobia as symptom during &lt;a href=&quot;http://en.wikipedia.org/wiki/Rabies&quot; rel=&quot;nofollow&quot;&gt;Rabies&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Now I'm going to clarify what exactly I do not understand. In the first case it's not clear for me how this mechanism helps to survive, how it can help at all? In the second case it's not obvious why this virus causes such a symptom. As I think virus always create favorable environment for himselve (for reproduction). But how could water prevent it?&lt;/p&gt;&#xA;" OwnerUserId="3253" LastActivityDate="2015-02-02T15:13:40.200" Title="Agony, Hydrophobia and viruses in the light of evolutionary principles" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;virology&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7555" PostTypeId="2" ParentId="7545" CreationDate="2013-03-17T14:12:34.083" Score="3" Body="&lt;p&gt;Fever is just one of the many ways of the body's defense mechanism work. Under infection, human body can raise body temperature, release cytokins and activate white blood cells etc. Sometimes the bacteria can evade immune suppression or immune complement fixation so that they can stay inside a &quot;fever-ish&quot; body like they just don't care. Example: &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa#Pathogenesis&quot; rel=&quot;nofollow&quot;&gt;Pseudomonas aeruginosa&lt;/a&gt;&lt;/em&gt;. They can grow in 42 degree Celsius which surpass the normal fever temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My answer may not be the best for your question. All I'm trying to say is that fever acts as a supportive role during an infection. Human body relies on heavy artilleries such as white blood cells and cytokin to clear the infection. That's why it will be more beneficial for the bacteria to evolve abilities to evade immune suppression and immune complement fixation. And bacteria know how to do those.&lt;/p&gt;&#xA;" OwnerUserId="3139" LastEditorUserId="3139" LastEditDate="2013-03-18T00:58:13.153" LastActivityDate="2013-03-18T00:58:13.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7556" PostTypeId="1" AcceptedAnswerId="42340" CreationDate="2013-03-17T15:05:55.747" Score="19" ViewCount="267" Body="&lt;p&gt;I hope this is the right StackExchange forum for such a question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking for large data sets on world-wide ecology parameters, such as annual temperatures by latitude, annual rainfall, CO₂ and O₂ concentration in the atmosphere and in the oceans, data about the insect population, plants, algae, and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any research institute or NGO collecting such data and making it available to the public?&lt;/p&gt;&#xA;" OwnerUserId="3254" LastEditorUserId="16866" LastEditDate="2017-02-27T04:47:13.353" LastActivityDate="2018-12-01T04:40:04.983" Title="Where can I find historical data on world-wide ecology parameters?" Tags="&lt;botany&gt;&lt;entomology&gt;&lt;ecology&gt;&lt;database&gt;&lt;data&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="7557" PostTypeId="1" AcceptedAnswerId="7558" CreationDate="2013-03-17T19:33:36.440" Score="2" ViewCount="89" Body="&lt;p&gt;How are shrimp and other animals able to not be crushed by the 1000x greater pressure at the bottom on the Mariana trench?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wiki says the trench is home to &quot;large living creatures such as a sole or flounder about 30 cm (1 ft) long, and shrimp&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand natural selection, but what features has evolution &quot;selected&quot; that enable soft flesh and bones to not be instantly crushed like our own skulls would be at that depth?&lt;/p&gt;&#xA;" OwnerUserId="3255" LastActivityDate="2013-03-17T22:52:07.417" Title="Indestructible Super Shrimp" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7558" PostTypeId="2" ParentId="7557" CreationDate="2013-03-17T22:52:07.417" Score="4" Body="&lt;p&gt;Aquatic animals brethe the water around them and this equalizes their body pressure with that of the surrounding environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is how you can still find say a piece of pottery or a watch from a shipwreck... They are filled with water and don't experience the pressure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such pressures do affect humans because we breathe air and so we can't adapt to pressures underwater and we need a shell that allows the ship environment to be tolerable for humans beyond a couple of hundred feet or so. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the change of pressure would also affect fish or other animals If they dropped in depth too quickly.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-03-17T22:52:07.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7559" PostTypeId="1" CreationDate="2013-03-18T09:49:24.387" Score="3" ViewCount="268" Body="&lt;p&gt;I have noticed in a particular genome sequence of a prokaryote that various regions in a sequence share similarity which is high(&gt;80%) with known proteins. However, the start is not a methionine. Is this a dysfunctional 'protein' sequence? Or are there alternative codons which translate those regions without a Met or fMet for that matter?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Technically, do all annotations of proteins have to start with a methionine?&lt;/p&gt;&#xA;" OwnerUserId="95" LastActivityDate="2013-03-18T10:49:21.603" Title="High sequence similarity but start codon isn't methionine" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;proteins&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7560" PostTypeId="2" ParentId="7559" CreationDate="2013-03-18T10:44:32.620" Score="7" Body="&lt;p&gt;There are alternative start codons to AUG used in prokaryotes: GUG and UUG. Those still match the initiation tRNA and encode N-formylmethionine. The rare start codons are matched by wobble pairing.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2013-03-18T10:44:32.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7561" PostTypeId="2" ParentId="7559" CreationDate="2013-03-18T10:49:21.603" Score="2" Body="&lt;p&gt;As far as I know it is a universal rule that the initializing sequence codes the amino acid Methionine (or, as you mentioned fMet in prokaryotes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in very rare cases it is possible that Met is not coded by the expected sequence of &lt;strong&gt;AUG&lt;/strong&gt;. This happens more often in mitochondria and prokaryotes, for example &lt;em&gt;E. coli&lt;/em&gt; which uses &lt;strong&gt;GUG&lt;/strong&gt; quite frequent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an overview check &lt;a href=&quot;http://en.wikipedia.org/wiki/Start_codon&quot; rel=&quot;nofollow&quot;&gt;Wikipedia here&lt;/a&gt;. Papers to follow up are listed there.&lt;/p&gt;&#xA;" OwnerUserId="3258" LastActivityDate="2013-03-18T10:49:21.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7563" PostTypeId="2" ParentId="7522" CreationDate="2013-03-18T18:49:51.627" Score="5" Body="&lt;p&gt;The fungus releases toxins, but how exactly this alters behavior is unclear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read more &lt;a href=&quot;http://microbewiki.kenyon.edu/index.php/Ophiocordyceps_unilateralis&quot;&gt;here&lt;/a&gt;.  Pathogen manipulation of host behavior appears to have evolved a long time ago, and cordyceps is not the only pathogen that acts like this.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-03-18T18:49:51.627" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7564" PostTypeId="2" ParentId="5732" CreationDate="2013-03-18T22:12:58.300" Score="5" Body="&lt;p&gt;There is no evidence that postnatal hormone exposure can change the sexual sexual preference of an individual. However atypical hormonal stimulation of the fetus can induce homosexuality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Homosexuality does not develop without a variety of social factors which are up-to-date mostly unexplained. But can develop without hormonal stimulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As real life examples there are a androgen antagonists for the treatment of of prostate cancer, which reduce the testosterone level in males. Under treatment the men often turn softer and more emotional, as described by their wifes. And there is beer which contains oestrogens and can induce the growth of female breasts in men. But none of this mechanisms has been observed to turn males homosexual.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Further Reading (second text is free fulltext):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23397798&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/23397798&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] &lt;a href=&quot;http://endo.endojournals.org/content/152/8/2937.long&quot; rel=&quot;nofollow&quot;&gt;http://endo.endojournals.org/content/152/8/2937.long&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3262" LastEditorUserId="3263" LastEditDate="2013-03-19T02:44:19.920" LastActivityDate="2013-03-19T02:44:19.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7565" PostTypeId="2" ParentId="7544" CreationDate="2013-03-18T22:51:58.343" Score="4" Body="&lt;p&gt;I have found that caffeine is mostly metabolized over CYP1A2 (as we know), but also over CYP1A1, CYP2E1 and CYP3A4. The question is how much the individual can cope with this alternate pathways if he is a CYP1A2 poor metabolizer. [1]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly I found in my pharmaceutics textbook that CYP2A1 activity determination is indicated due to undesirable side effects to caffeine and theophyllin.[2]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE:&lt;/strong&gt; 19.03.2013 12:30 GMT+1&lt;/p&gt;&#xA;&#xA;&lt;p&gt;@dd3: To clarify the second statement: I used the approach that theophyllin and caffeine are similar xanthin derivates. Since theophyllin is used as therapeutic drug in respiratory diseases (COPD etc.), I thought that scientific interest would be greater. And yes CYP1A2 plays an important role in both theophyllin tolerance and intollerance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found some new sources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At first a study with CYP1A2 knock-out mice, which shows that the elimination of theophyllin takes 4-times longer in CYP1A2(-/-)mice. And they also assume that the same behaviour is also applicable to caffeine. [3]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also there are two clinical studies by Japanese and Turkish scientists. The Japanese conclude, that theophyllin should be used with care in CYP1A2 poor metabolizer (even in haplotype poor metabolizer), since theophyllin has a narrow therapeutic range.[4] But the Turkish scientist assume that according to their findings, theophyllin is also metabolized over alternative pathways such as CYP2A13, CYP1A1, CYP2E1, CYP2D6 and CYP3A4. And according to this the genetic status of CYP1A2 is not as important as expected. [&lt;a href=&quot;http://www.jbmb.or.kr/jbmb/pdf.php?data=MTEwODE5MDFAcGRmX3JhaW50cmFjZV9sZWV5c0AlNUI0My04JTVEMTAwODMwMTYxNV8xLSUyODUzMC01MzQlMjlCTUIzNjYlMjgxMC0wNjAlMjkucGRm&quot; rel=&quot;nofollow&quot; title=&quot;http://www.jbmb.or.kr&quot;&gt;5&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Conclusion:&lt;/strong&gt;&#xA;Assuming that theophyllin and caffeine are metabolized similarly, you can conclude that a mutation in CYP1A2 would lead to caffeine intolerance. In my experience people with caffeine intolerance describe severe nervousness after drinking a cup of coffee. Fatal cases I know were due to high consumption of energy drinks in children without or at least not known caffeine intolerance.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Sources&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;[1] &lt;a href=&quot;http://informahealthcare.com/doi/abs/10.1081/DMR-120001392&quot; rel=&quot;nofollow&quot;&gt;http://informahealthcare.com/doi/abs/10.1081/DMR-120001392&lt;/a&gt;    &lt;/li&gt;&#xA;&lt;li&gt;[2] german source: &lt;a href=&quot;http://www.medizinische-genetik.de/index.php?id=2642&quot; rel=&quot;nofollow&quot;&gt;http://www.medizinische-genetik.de/index.php?id=2642&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;[3] Derkenne S, Theophylline pharmacokinetics in mice: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15970798&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/15970798&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;[4] Obase Y, Polymorphisms in the CYP1A2 gene and theophylline metabolism in patients with asthma. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12732846&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/12732846&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;[&lt;a href=&quot;http://www.jbmb.or.kr/jbmb/pdf.php?data=MTEwODE5MDFAcGRmX3JhaW50cmFjZV9sZWV5c0AlNUI0My04JTVEMTAwODMwMTYxNV8xLSUyODUzMC01MzQlMjlCTUIzNjYlMjgxMC0wNjAlMjkucGRm&quot; rel=&quot;nofollow&quot; title=&quot;http://www.jbmb.or.kr&quot;&gt;5&lt;/a&gt;] Ahmet U, The effect of CYP1A2 gene polymorphisms on Theophylline metabolism and chronic obstructive pulmonary disease in Turkish patients &lt;a href=&quot;http://www.jbmb.or.kr/jbmb/pdf.php?data=MTEwODE5MDFAcGRmX3JhaW50cmFjZV9sZWV5c0AlNUI0My04JTVEMTAwODMwMTYxNV8xLSUyODUzMC01MzQlMjlCTUIzNjYlMjgxMC0wNjAlMjkucGRm&quot; rel=&quot;nofollow&quot; title=&quot;http://www.jbmb.or.kr&quot;&gt;http://www.jbmb.or.kr&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Further Reading:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Xanthines as therapeutic drugs: &lt;a href=&quot;http://web.carteret.edu/keoughp/LFreshwater/PHARM/NOTES/Xanthines.htm&quot; rel=&quot;nofollow&quot;&gt;http://web.carteret.edu/keoughp/LFreshwater/PHARM/NOTES/Xanthines.htm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3262" LastEditorUserId="3262" LastEditDate="2013-03-19T12:16:08.770" LastActivityDate="2013-03-19T12:16:08.770" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7566" PostTypeId="1" CreationDate="2013-03-18T23:23:56.040" Score="5" ViewCount="77" Body="&lt;p&gt;I'm looking for nutritional data, mostly vitamin and mineral contents of common fruits, such as apples, bananas, oranges, kiwis etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there scientific (published and peer-reviewed) sources that list or compare those? I spent an hour on Google Scholar but most of the sources there discuss only a small aspect (e.g. vitamin C content) or compare different states of fruits (frozen, fresh, canned). I'm not well educated in human nutritional aspects so I may overlook this one keyword to search for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm aware of tables on the Internet discussing these aspects but I need a solid scientific basis.&lt;/p&gt;&#xA;" OwnerUserId="3258" LastActivityDate="2015-01-09T10:25:16.797" Title="Vitamin and mineral contents of common fruits" Tags="&lt;nutrition&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7567" PostTypeId="2" ParentId="7554" CreationDate="2013-03-19T00:00:16.543" Score="4" Body="&lt;p&gt;The hydrophobia symptom is most likely a bi-product of the effects the virus has on the brain and not an evolutionarily derived strategy to create an appropriate environment to reproduce in. Just the same as other symptoms the infection causes, like fever for example, is a reaction the body has to the presence of the virus and not something the virus is doing on purpose to set up a better environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A bit old, but check out [1]: &quot;Hydrophobia may represent an exaggerated respiratory tract irritant reflex with associated arousal potentiated by the selective destruction of brain stem inhibitory systmes.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So basically the virus is indirectly causing a fear of water. The destruction of brain cells and inflammation caused by the presence of the virus in the central nervous system cause a reflex in the respiratory tract which manifests as muscle spasms and renders the patient, who is already pretty out of it at this stage, unable and very unwilling to drink any fluids [2].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://europepmc.org/abstract/MED/982512&quot; rel=&quot;noreferrer&quot;&gt;http://europepmc.org/abstract/MED/982512&lt;/a&gt; (Warrell DA, Transactions of the Royal Society of Tropical Medicine and Hygiene [1976, 70(3):188-195])&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] &lt;a href=&quot;http://publichealth.lacounty.gov/vet/rabiesmanual/clinical.htm&quot; rel=&quot;noreferrer&quot;&gt;http://publichealth.lacounty.gov/vet/rabiesmanual/clinical.htm&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3261" LastActivityDate="2013-03-19T00:00:16.543" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7568" PostTypeId="1" AcceptedAnswerId="9451" CreationDate="2013-03-19T03:43:36.703" Score="11" ViewCount="1229" Body="&lt;p&gt;I have a very raw understanding of sexual selection:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Say a group of females of a certain species &quot;like&quot; some feature of a certain groups of males; by &quot;like&quot; I mean some behaviour that makes this group of females tend to mate with males having this feature, then the females are selecting their genes which make them feel appealed to males with the feature, and then this process becomes exponent since the group of females becomes bigger and forces the population of males to have this feauture, until an equilibrium is reached. I know this also happens with the roles interchanged.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My first question is, why do females tend to like males that have high amounts of these features, more than the average in the population?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My second question is, why do the end products of these selections are such beautiful features? Perhaps this may sound a little arrogant but I don't understand how an animal can appreciate this beauty, I suppose this is to make some sort of selection of healthy males.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks &lt;/p&gt;&#xA;" OwnerUserId="3203" LastEditorUserId="3203" LastEditDate="2017-01-18T18:46:02.753" LastActivityDate="2017-01-18T18:46:02.753" Title="Why does sexual selection evolve beautiful features?" Tags="&lt;evolution&gt;&lt;sexual-selection&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7569" PostTypeId="1" AcceptedAnswerId="7571" CreationDate="2013-03-19T07:39:56.337" Score="1" ViewCount="2362" Body="&lt;p&gt;As we all know, cold weather will cause us to have goose bumps. I honestly don't know why (1), because our skin contracts?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from that something quite contradicting happened this morning. I was taking a hot shower and it was so hot that I suddenly felt that I had goose bumps. Not because it was cold, but because it was so hot. How can this happen? Because of a sudden change in temperature the skin goes haywire? Or aren't goose bumps related to temperature in a way, but is a sort of &lt;em&gt;safety reflex&lt;/em&gt;?&lt;/p&gt;&#xA;" OwnerUserId="3198" LastActivityDate="2016-01-07T04:22:34.490" Title="Relation between goose bumps and temperature" Tags="&lt;human-biology&gt;&lt;skin&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7570" PostTypeId="1" AcceptedAnswerId="24773" CreationDate="2013-03-19T10:57:59.057" Score="7" ViewCount="186" Body="&lt;p&gt;The Murray Microbiology book says that it is prefentially 10 years, similarly Estonian and Finnish health associations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, my professor says that it can be 5-7 years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I started to think if the age is affecting here to the result.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;When should you take booster vaccination of Pertussis if you are&lt;/strong&gt;&#xA;a) 25 years old,&#xA;b) 50 years old,&#xA;c) 70 years old, and&#xA;d) 90 years old?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My professor says that there is no significant studies about the efficacy of Pertussis booster vaccination among different age groups.&#xA;&lt;strong&gt;Is this true?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-12-10T22:22:01.007" Title="What is the efficacy of Pertussis booster vaccine among different age groups?" Tags="&lt;vaccination&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7571" PostTypeId="2" ParentId="7569" CreationDate="2013-03-19T14:24:14.233" Score="2" Body="&lt;p&gt;Goose Bumps (a.k.a. - Goose Pimples) are caused by the &lt;em&gt;Arrector Pili&lt;/em&gt; muscles in your skin:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8xrch.jpg&quot; alt=&quot;Skin diagram&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their purpose is to increase the distance from epidermis to the top of the follicle, and increase the area between follicles. This has the effect of increasing the amount of air trapped between the hair and surface of the skin. In other mammals the end-result is an increase in the &lt;strong&gt;&lt;em&gt;insulatory&lt;/em&gt;&lt;/strong&gt; properties of their fur, meaning they will stay warmer &lt;em&gt;or&lt;/em&gt; cooler depending on their current needs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another function in our mammalian cousins is to simply appear larger, and thus more of a &lt;em&gt;threat&lt;/em&gt; to any predators or dangerous animals. Much like the shoulder and lower back hair on this dog:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/L9BUs.jpg&quot; alt=&quot;Dog snarling&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thermoregulation in humans has evolved since our furrier ancestors; we &lt;em&gt;sweat&lt;/em&gt; to cool off, and &lt;em&gt;shiver&lt;/em&gt; to keep warm. We also use tools and weapons, can create fire, and have other ways to communicate our lethal capabilities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Goose Bumps are the human body utilizing old instinctual reflexes in the proper situations, but we lack the thick mattes of hair our ancestors had for the reflex to have any significant effect. They're a fun Easter-egg, a leftover that doesn't do us any harm and are an easy way to tell if someone is cold or scared - which might be useful under the proper circumstances.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-03-19T14:24:14.233" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7572" PostTypeId="1" AcceptedAnswerId="7617" CreationDate="2013-03-19T16:53:59.253" Score="2" ViewCount="649" Body="&lt;p&gt;I have been processing some ChIP-seq data with the R package &lt;a href=&quot;http://compbio.med.harvard.edu/Supplements/ChIP-seq/&quot; rel=&quot;nofollow&quot;&gt;spp&lt;/a&gt;. I looked through the literature (ENCODE uses it) and it seemed that spp is indicated as a good program to use.  I have found and adapted the two tutorials I found for using spp (&lt;a href=&quot;https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq&quot; rel=&quot;nofollow&quot;&gt;first&lt;/a&gt; and &lt;a href=&quot;http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html&quot; rel=&quot;nofollow&quot;&gt;second&lt;/a&gt;), and read the &lt;a href=&quot;http://ncbi.nlm.nih.gov/pubmed/19029915&quot; rel=&quot;nofollow&quot;&gt;original paper&lt;/a&gt;. I have also e-mailed Prof. Karchencko and posted on the bioconductor listserv - all with no response. My question is about the MSER and the predicted sequencing depth - additional output of spp. So what I think the MSER is, is the score value above which a peak is authoritatively determined? When I look at peaks above this score value they are very well defined. Also, is the predicted sequencing depth is a prediction of the number of additional &quot;tags&quot; necessary so that the MSER and the FDR value coincide? It is hard to find decent information about this program.  Any advice or additional information is greatly appreciated!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TIA&lt;/p&gt;&#xA;" OwnerUserId="3264" LastEditorUserId="948" LastEditDate="2014-04-20T04:02:34.013" LastActivityDate="2014-04-20T04:02:34.013" Title="ChIP-seq and the output of SPP" Tags="&lt;bioinformatics&gt;&lt;chip&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="7574" PostTypeId="1" CreationDate="2013-03-19T19:15:52.900" Score="3" ViewCount="422" Body="&lt;p&gt;Is there a species-agnostic metric for identifying plant maturity?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There seems to be plenty of literature defining life-history stages for specific crops, but it is not clear if there is a generic definition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the context of crops, I would like to be able to identify the stage at which plants are no longer exhibiting juvenile traits.&lt;/p&gt;&#xA;" OwnerUserId="154" LastEditorUserId="3952" LastEditDate="2013-08-02T14:37:20.450" LastActivityDate="2013-08-02T14:37:20.450" Title="Is there a standard definition for plant &quot;maturity&quot;?" Tags="&lt;plant-physiology&gt;&lt;life-history&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7575" PostTypeId="2" ParentId="1605" CreationDate="2013-03-19T20:12:27.487" Score="3" Body="&lt;p&gt;The Biological Species Concept is largely useful in looking at the &lt;em&gt;process&lt;/em&gt; of evolution. Since speciation isn't typically (though this isn't always true either!) an instantaneous process, it is useful to observe it in action. The BSC is the best way of approaching this (at least for sexually reproducing organisms). &#xA;Back to your original question. It might be useful for you to search &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ring_species&quot; rel=&quot;nofollow&quot;&gt;ring species&lt;/a&gt;&quot; as this is what you are talking about. The most famous example is the Ensantina salamander complex. They are essentially several species/one species depending on your perspective. It is more-or-less a spatial version of the hypothetical dog analogy, but it is also a natural phenomenon that occurs in many other species....&lt;/p&gt;&#xA;" OwnerUserId="1710" LastActivityDate="2013-03-19T20:12:27.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7576" PostTypeId="1" CreationDate="2013-03-19T20:16:51.340" Score="1" ViewCount="235" Body="&lt;p&gt;I had a student ask me about this and my google-fu let me down. He asked if individual nucleotides (not in a nucleic acid) base-pair with their complementary nucleotides, essentially forming many dinucleotides. I would think this would occur, but have no evidence one way or the other. If it does, how does this impact the usage of nucleotides in nucleic acid synthesis? I'd assume they have to be broken apart first...&lt;/p&gt;&#xA;" OwnerUserId="1710" LastActivityDate="2013-03-19T21:16:37.330" Title="Do individual (free) nucleotides base-pair with other free nucleotides?" Tags="&lt;dna&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7577" PostTypeId="2" ParentId="793" CreationDate="2013-03-19T20:51:20.903" Score="1" Body="&lt;p&gt;Not sure if the exome sequencing is the way to go for this kind of tasks, especially if you have an idea of the mutations you might be looking for. Current arrays are pretty performant and are much more rapid and cheap.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the data, you might consider having a look on &lt;a href=&quot;https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp&quot; rel=&quot;nofollow&quot;&gt;The Cancer Genome Atlas&lt;/a&gt;. Otherwise &lt;a href=&quot;http://biologicalnetworks.net&quot; rel=&quot;nofollow&quot;&gt;Biological Networks&lt;/a&gt; might provide you the API for you if you aren't afraid of doing a little bit of Java to interface it with R. &lt;/p&gt;&#xA;" OwnerUserId="957" LastActivityDate="2013-03-19T20:51:20.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7578" PostTypeId="2" ParentId="3291" CreationDate="2013-03-19T21:02:45.803" Score="1" Body="&lt;p&gt;I would advise you to use the SMBL for &lt;a href=&quot;http://www-bioeng.ucsd.edu/research/research_groups/gcrg/organisms/ecoli/ecoli_sbml.html&quot; rel=&quot;nofollow&quot;&gt;iAF1260 E. Coli&lt;/a&gt; with a &lt;a href=&quot;http://opencobra.sourceforge.net/openCOBRA/Welcome.html&quot; rel=&quot;nofollow&quot;&gt;COBRA toolbox&lt;/a&gt; on MATLAB. It has all the constants you are looking for optimized for the steady state and have been extensively tested for simulation of single and multiple genes deletion / mutation. Even if you want to stick with your model you will be able to copy the constants from there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However depending on what you are doing you might not be satisfied by the whole models, since the they are computationally too complicated to simulate and optimize and lead to computationally unstable results, especially when you try to simulate colony collaborative mechanisms.&lt;/p&gt;&#xA;" OwnerUserId="957" LastActivityDate="2013-03-19T21:02:45.803" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7579" PostTypeId="2" ParentId="7576" CreationDate="2013-03-19T21:04:30.550" Score="6" Body="&lt;p&gt;The base-pairing in solution only provides 2-3 hydrogen bonds, which the nucleotides could also form with water itself. There are no stacking interactions between bases in water like in a DNA helix. So I strongly doubt that the nucleotides would form a significant amount of dimers in water.&lt;/p&gt;&#xA;&lt;p&gt;I found a paper confirming my assumption:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Short nucleotide fragments such as mono- and dinucleotides are&#xA;generally unable to form stable hydrogen-bonded base pairs or duplexes&#xA;in water.&lt;/p&gt;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21378801&quot; rel=&quot;noreferrer&quot;&gt;Minimal nucleotide duplex formation in water through enclathration in self-assembled hosts.&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;An easy way to confirm this would be to observe the proton NMR spectra of free nucleotides. Base-pairing in nucleic acids shows characteristic signals in the imino proton region (around 10-15 ppm), which are not visible in unpaired nucleobases due to chemical exchange.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-03-19T21:04:30.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7580" PostTypeId="2" ParentId="7576" CreationDate="2013-03-19T21:16:37.330" Score="1" Body="&lt;p&gt;In a DNA strand, there are additional energetic advantages of the hydrophobic bases being internalized to the core the DNA double strand and the polar phosphate backbone being more uniformly exposed to solvent.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thermodynamically, the formation of the two individual molecules of base monomers forming a pair the solvent will still be exposed to the hydrophobic bases. So such a single base pair would be driven by the energy of the two or three hydrogen bonds in the base pair formed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is why you will not see such a complex forming in water; the hydrogen bonds with water are at least as strong as the hydrogen bonds with the bases. But such base pairings can in other circumstances be made to form. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there are no exchangeable protons for hydrogen bonding in the solvent itself, there will be an energetic advantage to the complex.  If there are no exchangeable protons (as with DMSO or carbon tetrachloride) &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S002228366680222X&quot; rel=&quot;nofollow&quot;&gt;such complexes can be detected by NMR&lt;/a&gt;.  Even in cases with single hydrogen bondable protons on the solvent, these bimolecular complexes are observed.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-03-19T21:16:37.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7581" PostTypeId="1" AcceptedAnswerId="9566" CreationDate="2013-03-19T21:17:50.663" Score="3" ViewCount="186" Body="&lt;p&gt;I'm interested in what kinds of nutrients mammals extract from food and would like to know &lt;strong&gt;how similar are the outputs of these systems.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, if it is possible to successfully replace one mammal's digestive system with another mammal's one (all the connections are correct). Would the recipient survive or experience some form of malnutrition resulting in death? &lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="3632" LastEditDate="2013-12-29T00:20:04.433" LastActivityDate="2014-04-28T02:52:36.217" Title="How compatible are mammalian digestive systems?" Tags="&lt;digestive-system&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7582" PostTypeId="1" AcceptedAnswerId="7595" CreationDate="2013-03-19T22:10:25.200" Score="2" ViewCount="147" Body="&lt;p&gt;(Exogenous) melatonin is administered at night for treatment of circadian rhythm disorders, but melatonin taken during the day is linked with depression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know if high blood levels of (endogenous) melatonin (at a steady state, throughout the day) might be linked with mood or sleep disorders (or have any effect at all), or if the body's response to melatonin adjusts accordingly.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the answer to &lt;a href=&quot;https://biology.stackexchange.com/questions/5535/is-there-a-normal-human-melatonin-concentration-to-light-level-curve&quot;&gt;this SE question&lt;/a&gt; is related, but I can't find the source using a reverse image search. &lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-03-20T23:50:08.877" Title="Are (baseline) high blood levels of melatonin associated with either circadian rhythm or mood disorders?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;sleep&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7583" PostTypeId="2" ParentId="7374" CreationDate="2013-03-19T22:56:30.903" Score="1" Body="&lt;p&gt;You might explore Li &lt;i&gt;et al&lt;/i&gt; (2004) &quot;Comparative genomics identifies a flagellar and basal body proteome that includes the &lt;i&gt;BBS5&lt;/i&gt; human disease gene&quot; &lt;i&gt;Cell&lt;/i&gt; &lt;b&gt;117&lt;/b&gt;: 541-552.  (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=Li+2004+Cell+BBS5&quot; rel=&quot;nofollow&quot;&gt;Pubmed Abstract&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Largely the authors focused on comparisons of Arabidopsis, Chlamydomonas and Human genomes, but they did also include &lt;i&gt;C. elegans&lt;/i&gt; for comparisons with at least Chlamydomonas (Summarized in Table 1).  Even if they do not give you exactly what you need, you could apply their methods for your particular project.&lt;/p&gt;&#xA;" OwnerUserId="3266" LastActivityDate="2013-03-19T22:56:30.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7584" PostTypeId="2" ParentId="5587" CreationDate="2013-03-20T00:00:20.477" Score="4" Body="&lt;p&gt;Since early March we know, that there is the first patient which has been cured by HAART. According to the paper it has been proven that the infant was infected with HIV. This was done by detecting the virus even after the first 48 hours, this rules out that the virus transmitted by the mother without infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The infant was first treated when it was 30 hours of age with a triple therapy (zidovudin, lamivudin and nevirapin). On the seventh day the therapy was changed to zidovudin, lamivudin and lopinavir/ritonavir. After one month of therapy no replicable virus particle could be found. The therapy was continued until the age of 18 months. The infant is now 26 months without a sign of a rebound of the HIV infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The approach was atypical, since they used a therapy scheme with not established high dosing of the antiretroviral drugs. They ruled out a innate HIV-immunity by certain HLA variants, since Mother and child had matching HLA-Haplotypes. But other genetic mutations are still possbile.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is scientific progress, the answer to your questions changes in only 2 months.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.retroconference.org/2013b/Abstracts/47897.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.retroconference.org/2013b/Abstracts/47897.htm&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3262" LastActivityDate="2013-03-20T00:00:20.477" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7586" PostTypeId="1" CreationDate="2013-03-20T03:55:18.150" Score="8" ViewCount="713" Body="&lt;p&gt;In my lab we've observed a phenomenon in which a culture of E. coli is found to shift from normal rod growth to filamentous growth and then back to normal rod growth again several times over the course of 400 hours. This was shown by an OD600 graph which oscillates from high values (~5) to low (~0.5) (the culture was also viewed directly).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The shift to filamentous growth is usually associated with an SOS response in E. coli and this makes sense (the media is M9 supplemented with 0.2% casamino acid and 0.1mM thiamine hydrochloride), however we don't know why it switches back from filamentous to normal growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has anyone observed a similar phenomenon? Does anyone have any suggestions why this might be happening?&lt;/p&gt;&#xA;" OwnerUserId="1051" LastActivityDate="2014-08-15T06:38:06.243" Title="What would cause E. coli to change from filamentous growth to normal growth?" Tags="&lt;bacteriology&gt;&lt;ecoli&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7588" PostTypeId="1" CreationDate="2013-03-20T08:55:57.550" Score="4" ViewCount="702" Body="&lt;p&gt;I am an engineering student studying how electric fields affect cells, specifically the phenomena of electroporation in living cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that electroporation is widely used for introducing genes into cells, but running a full transfection experiment is not so feasible in the lab I am working in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I want to demonstrate the principle of electroporation, i.e. that cells open up and intake substances from the environment, by using some kind of a dye which i can later visualize, what could be a good model for this type of experiment? Specifically - what dye, what cells could be used for this? &lt;/p&gt;&#xA;" OwnerUserId="3269" LastEditorUserId="3059" LastEditDate="2013-03-25T17:44:25.210" LastActivityDate="2013-03-25T17:44:25.210" Title="What is a simple protocol for staining cells in suspension?" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;microscopy&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7589" PostTypeId="1" AcceptedAnswerId="7598" CreationDate="2013-03-20T11:45:47.110" Score="0" ViewCount="654" Body="&lt;p&gt;I am using these terms because we can imagine them quite good, I guess ;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By &quot;anarchist&quot; I mean that the ape wants to live without the rule of others apes(same biological race or other) and he pursue his own goals (replication, getting food etc.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By &quot;communist&quot; I mean working together in groups because of the &quot;higher&quot;purpose (better chance to protect themselves, getting food easier, other benefits)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am particlarly interested in apes, excluding us, of course.&lt;/p&gt;&#xA;" OwnerUserId="3118" LastEditorUserId="3952" LastEditDate="2013-08-02T14:11:48.760" LastActivityDate="2013-08-02T14:11:48.760" Title="Are ape communities more &quot;anarchist&quot; or &quot;communist&quot; in structure?" Tags="&lt;zoology&gt;&lt;mammals&gt;&lt;behaviour&gt;&lt;sociality&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7591" PostTypeId="2" ParentId="7370" CreationDate="2013-03-20T14:24:30.017" Score="1" Body="&lt;p&gt;There are many ways to label nucleic acids for probes (&lt;a href=&quot;http://www.piercenet.com/browse.cfm?fldID=39047FFD-092E-4836-AD26-A99FAE51D9B2&quot; rel=&quot;nofollow&quot;&gt;Summary of Methods&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While there are cases where Klenow fragment-mediated fill-in should sufficiently label both strands of your probe, there are many others where this would not be enough.  Here are two illustrative, although somewhat contrived, examples:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Example 1: Double digest with 5' and 3' overhangs&lt;br&gt;&lt;br&gt;&#xA;  Imagine you did a double digest with &lt;i&gt;Bam&lt;/i&gt;HI and &lt;i&gt;Kpn&lt;/i&gt;I to release your probe sequence from the plasmid in which you propagate the sequence.  &lt;i&gt;Bam&lt;/i&gt;HI will give you a 5' overhang, but &lt;i&gt;Kpn&lt;/i&gt;I gives a 3' overhang.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;Resulting &lt;i&gt;Bam&lt;/i&gt;HI &amp; &lt;i&gt;Kpn&lt;/i&gt;I double digest fragment:&#xA;  5'-    GATCCNNNNNNNG      - 3'&#xA;             |||||||||&#xA;  3'-        GNNNNNNNCCATG  - 5'&#xA;&lt;/pre&gt;&#xA;  &#xA;  &lt;p&gt;Subsequent treatment with the Klenow fragment + $\alpha$P&lt;sup&gt;32&lt;/sup&gt;-dATP + cold dNTPs will both fill-in the 5'-overhang (Klenow's 5'-&gt;3' polymerase activity) and remove the 3' overhang (Klenow's 3'-&gt;5' exonuclease activity).&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;Post-Klenow reaction (bold = new bases, * = radio-labeled nucleotide):&#xA;  5'-    GATCCNNNNNNNG      - 3'&#xA;         |||||||||||||&#xA;  3'-    &lt;b&gt;CTAG&lt;/b&gt;GNNNNNNNC      - 5'&#xA;           *&#xA;&lt;/pre&gt;&#xA;  &#xA;  &lt;p&gt;At this point only one strand is radio-labeled so the terminal transferase step is needed to add a label to the top strand.&lt;br&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;When using $\alpha$P&lt;sup&gt;32&lt;/sup&gt;-dNTPs, you often pick only one base to be radioactive (eg dATP as above).  Sometimes you also just spike the reaction with radioactive dNTP leaving a population of cold dNTPs to be used most of the time.  In either case you now have the chance of not incorporating only non-radioactive bases.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Example 2: Fill-in reaction that fails to incorporate $\alpha$P&lt;sup&gt;32&lt;/sup&gt;-dATP:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Imagine a digest with &lt;i&gt;Psp&lt;/i&gt;I and want to fill-in the 5' overhangs using $\alpha$P&lt;sup&gt;32&lt;/sup&gt;-dATP + cold dNTPs.  &lt;i&gt;Psp&lt;/i&gt;I recognizes CCWGG sequences where W is either A or T so that some fill-ins will incorporate the $\alpha$P&lt;sup&gt;32&lt;/sup&gt;-dATP, but others will not.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;Possible digests and fill-in reactions:&#xA;   5'-  CCTGGNNNNNNNNNNCCTGG - 3'&#xA;        ||||||||||||||||||||&#xA;   3'-  GGACCNNNNNNNNNNGGACC - 5'&#xA;                 |&#xA;         Digest with &lt;i&gt;Psp&lt;/i&gt;I&#xA;                 |&#xA;                 V&#xA;   5'-  CCTGGNNNNNNNNNN      - 3'&#xA;             ||||||||||&#xA;   3'-       NNNNNNNNNNGGACC - 5'&#xA;                 |&#xA;        Fill-in with Klenow + hot dATP + cold dNTPs&#xA;                 |&#xA;                 V&#xA;   5'-  CCTGGNNNNNNNNNN&lt;b&gt;CCTGG&lt;/b&gt; - 3'&#xA;        ||||||||||||||||||||&#xA;   3'-  &lt;b&gt;GGACC&lt;/b&gt;NNNNNNNNNNGGACC - 5'&#xA;          *&#xA; &lt;/pre&gt;&#xA;  &#xA;  &lt;p&gt;Again you are left with only one strand being labeled (or no strand labeling if the sequence was 5'- CCAGGNNNNNCCTGG - 3') and a need for the terminal transferase step.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3266" LastActivityDate="2013-03-20T14:24:30.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7592" PostTypeId="1" CreationDate="2013-03-20T14:38:57.733" Score="12" ViewCount="19453" Body="&lt;p&gt;I had a question since I was a child. I was always curious about the fact that all animals can swim in water. They don't need any training or to learn swimming. But humans need to learn to swim. Why ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am a technical person and not in biology after my 10th year in school. Can anybody please shed some light on this question? &lt;/p&gt;&#xA;" OwnerUserId="3272" OwnerDisplayName="bill berlington" LastEditorUserId="5144" LastEditDate="2015-03-30T18:54:34.957" LastActivityDate="2015-03-30T18:54:34.957" Title="Why can all animals swim in water without learning to swim but humans cannot?" Tags="&lt;human-biology&gt;&lt;ethology&gt;&lt;learning&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7593" PostTypeId="1" CreationDate="2013-03-20T15:01:02.013" Score="0" ViewCount="238" Body="&lt;p&gt;I'm a molecular bio novice, and I'm trying to understand the differences between regular PCR and RACE PCR.  If it wanted to sequence my PCR product that might be hundreds, if not thousands of bps long, I should use RACE PCR correct?  My goal is to sequence the active site of some enzymes I'm interested in, but I'm not sure how to go about designing PCR primers for a specific site on my protein.  Additionally, the active site is over 100 amino acids long, which would imply that my PCR product has to be over 300 bps long.  Regular PCR amplicons have trouble amplifying long strands of DNA correct?  I was thnking about using RACE PCR to amplify my entire cDNA strand that is 4000 bps long and then just sequencing the RACE product.  Would RACE work for that many bps in my cDNA?&lt;/p&gt;&#xA;" OwnerUserId="3232" LastActivityDate="2013-03-21T22:51:31.267" Title="RACE pcr product" Tags="&lt;pcr&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7594" PostTypeId="2" ParentId="7588" CreationDate="2013-03-20T20:40:17.653" Score="1" Body="&lt;p&gt;&lt;strong&gt;You will get a lot of false-positives using the following method, and a real transfection of a fluorescent protein is always the way to go, because then you will prove that the transfection was really successful.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, you could try to use &lt;a href=&quot;http://en.wikipedia.org/wiki/DAPI&quot; rel=&quot;nofollow&quot;&gt;DAPI&lt;/a&gt;, followed by fluorescence microscopy or flow cytometry. DAPI is a very bright stain for DNA and cannot pass an intact cell membrane. If the cell membrane is disrupted, e. g. by necrosis, DAPI will enter the cell. I have never seen anyone trying to prove electroporation this way, but it will be worth a try. It could be that the time is too short for DAPI to enter the cell, so you'd need to tweak your setup.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd try the following: Prepare a cell solution with DAPI (something like 5 µM concentration should do). Split the solution into two electroporation cuvettes, perform the electroporation with one cuvette, leave the second one untouched as a control. After the electroporation, analyse the samples MOMENTARILY (means: within a few minutes) using a flow cytometer (if possible).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the cells, you could use anything. I suggest eukaryotic cells because they are more easy to visualize than bacteria. However, you would need a laminar flow hood for aseptic handling of cells. In theory you could also use bacteria, which are more easy to handle, but I'm not experienced with immunofluorescence in bacteria.&lt;/p&gt;&#xA;" OwnerUserId="852" LastEditorUserId="852" LastEditDate="2013-03-20T20:47:13.690" LastActivityDate="2013-03-20T20:47:13.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7595" PostTypeId="2" ParentId="7582" CreationDate="2013-03-20T23:37:44.810" Score="2" Body="&lt;p&gt;I found a recent PLoS article that said that none of hypochondriasis, depression, hysteria, psychopathic deviate, masculinity-femininity, psychasthenia, schizophrenia, or social intraversion (on the MMPI-2) &quot;were associated with any melatonin parameter.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it does appear that &quot;increases scores of Hypomania and Paranoia were associated with a shorter DLMO-DLMOff interval&quot; (duration of melatonin production).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only thing that concerns me are the significance and the effect size of the latter two results.  I can't tell whether they corrected for multiple comparisons or not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:  &lt;a href=&quot;http://ww.plosone.org/article/info%3adoi/10.1371/journal.pone.0003055&quot; rel=&quot;nofollow&quot;&gt;Burgess HJ, Fogg LF (2008) Individual Differences in the Amount and Timing of Salivary Melatonin Secretion. PLoS ONE 3(8): e3055. doi:10.1371/journal.pone.0003055&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-03-20T23:37:44.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7596" PostTypeId="1" CreationDate="2013-03-20T23:38:45.723" Score="8" ViewCount="732" Body="&lt;p&gt;The question pretty much explains itself. How do the two methods compare? I've always used Assembly PCR but the method is prone to mistakes and I'm curious how it compares to Ligase Chain Reaction (LCR).&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2016-03-02T16:45:22.903" Title="How does LCR compare to Assembly PCR" Tags="&lt;molecular-biology&gt;&lt;pcr&gt;&lt;cloning&gt;&lt;lcr&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7597" PostTypeId="1" CreationDate="2013-03-21T00:45:01.920" Score="3" ViewCount="3127" Body="&lt;p&gt;How can I improve my Gel Extraction yields. We use the standard protocol from Qiagen, gel extraction, dissolve in QG buffer at 42C and purify via anion exchange columns. However, with 500 ng we ultimately get 100 ng for a 20% yield. I was curious what else has been tried for gel extraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We also add IPA and NaOAc to the dissolved mixture prior to the column purification.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="3059" LastEditDate="2013-03-21T04:43:16.560" LastActivityDate="2013-03-25T22:14:20.240" Title="Improving Gel Extraction yields" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;cloning&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7598" PostTypeId="2" ParentId="7589" CreationDate="2013-03-21T00:51:01.470" Score="10" Body="&lt;p&gt;Among the great apes, chimpanzees and gorillas live in very hierarchical, male-dominated clans that are often in violent conflict with other clans. Bonobos, on the other hand, lead very peaceful lives, and are female-dominated, using sexual contact as a manner of communication to reduce tension within and between groups. Orangutans are largely solitary animals, with heavy parental investment (7 years, longest among non-human primates), wherein the mother lives separately with her child during the early years of development. Among the lesser apes, gibbons and siamangs are also highly territorial and pair-bonded, though notably, &lt;a href=&quot;http://www.aseanbiodiversity.info/Abstract/53005525.pdf&quot;&gt;polyandrous siamang groups&lt;/a&gt; have been shown to display higher degrees of cooperation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though Anarchism varies greatly between different definitions, the most popular form of contemporary Anarchism values non-hierarchical organization, centered around mutual aid, rather than the kind of isolated individualism that you seem to associate with the term. By this definition, bonobos would be more &quot;Anarchist&quot; than chimpanzees. By your definition, orangutans might be the most &quot;Anarchist.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your definition of &quot;Communism&quot; is closer to the contemporary definition of Anarchism above, due mainly to the historical trajectory of Communism, which in practice, did not work out so well, leaving contemporary utopian thinkers largely in the Anarchist camp. By your definition of &quot;Communism,&quot; bonobos may be the most &quot;Communist&quot;; however, if you mean the state-based gulag Communism of popular culture (ie portrayals of the Soviet Union), then you might say that chimps were more Communist. This is because individual chimps sacrifice individual goal attainment for group ends under the coercion of the alpha male chimp. Of course, some people may call that Fascism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may want to take a look at primatologist Franz De Waal's research on bonobos vs. chimpanzees. As a pacifist, he has a bit of an agenda, in terms of trying to prove that female-dominated bonobo &quot;societies&quot; are inherently more cooperative and less hierarchical. Another primatologist that agrees with this view is Harvard primatologist Richard Wrangham, who looks at hierarchical organization and violent behaviors in chimpanzees.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Robert Sapolsky's &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC387823/&quot;&gt;research on baboons&lt;/a&gt; may also be of interest to you. He found a clan of baboons, in which all the alpha males had died from tuberculosis due to exposure to an infected meat found in a neighboring human village. He noted, then, that the remaining baboons lived much more peaceably and cooperatively than other observed clans, and furthermore, that this clan retained its &quot;culture&quot; and passed on its more cooperative ways of behaving to new members in the clan, therefore demonstrating that perhaps baboons (and other primates) are capable of having and passing on &quot;culture.&quot; - Perhaps a more &quot;Anarchist&quot; culture than nature normally prescribes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, as a caveat, I must say: it is tenuous to make direct associations between ape behavior and human societies. Human culture, social intelligence, and symbolic reasoning facilitate human political systems. Though Sapolsky's work suggests primates may also be capable of some form of &quot;culture,&quot; biological descriptions of ape social organization is insufficient to explain human behavior.&lt;/p&gt;&#xA;" OwnerUserId="3271" LastEditorUserId="3271" LastEditDate="2013-03-21T00:56:13.707" LastActivityDate="2013-03-21T00:56:13.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7599" PostTypeId="2" ParentId="7374" CreationDate="2013-03-21T00:58:08.960" Score="1" Body="&lt;p&gt;One way to approach this is to use one of the protein database clusterings available.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Researchers have taken huge protein databases, like UniProt, which basically catalog all known protein sequences regardless of species and clustered the proteins by sequence. The results provide many interesting insights about protein families, but more importantly they are well-fitted for your problem. A cluster would be a set of sequences that are similar to each other but are relatively different from all other known proteins. So, essentially you would be interested in a cluster that is only has c elegans proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I went ahead and used &lt;a href=&quot;http://www.protonet.cs.huji.ac.il&quot; rel=&quot;nofollow&quot;&gt;ProtoNet&lt;/a&gt;, which is one such tool, and searched for such a c elegans cluster. I found two potential clusters: 4375747 and 4430980, which have mainly c elegans proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disclaimer: I have been involved in the past in the development of ProtoNet.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2013-03-21T00:58:08.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7600" PostTypeId="1" AcceptedAnswerId="7605" CreationDate="2013-03-21T01:43:21.600" Score="2" ViewCount="521" Body="&lt;p&gt;This is reference to a &lt;a href=&quot;http://dev.biologists.org/content/130/20/4761.full&quot; rel=&quot;nofollow&quot;&gt;review on C. elegans mosaic analysis by Yochem and Herman&lt;/a&gt;, in which the authors make a distinction between free chromosome fragments and extrachromosomal arrays.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the former, they reference &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1202392/pdf/165.pdf&quot; rel=&quot;nofollow&quot;&gt;Herman 1984&lt;/a&gt;.&#xA;For the latter, they reference &lt;a href=&quot;http://genesdev.cshlp.org/content/8/2/160.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;Lackner et al 1994&lt;/a&gt; and &lt;a href=&quot;http://www.genetics.org/content/143/3/1181.abstract?ijkey=875d37b16ef5604f0773d8266ba6e08b17dbde52&amp;amp;keytype2=tf_ipsecsha&quot; rel=&quot;nofollow&quot;&gt;Miller et al 1996&lt;/a&gt;, but these are studies that use extrachromosomal arrays, not papers defining them as a technique, per se.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am curious to know what the distinction is - I am under the impression that extrachromosomal arrays &lt;em&gt;are&lt;/em&gt; fragments with many copies of the gene of interest + a marker.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-03-21T20:18:10.397" Title="What's the difference between a free chromosome fragment and an extrachromosomal array?" Tags="&lt;genetics&gt;&lt;chromosome&gt;&lt;lab-techniques&gt;&lt;development&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7601" PostTypeId="2" ParentId="7592" CreationDate="2013-03-21T13:21:44.713" Score="13" Body="&lt;p&gt;While I am not sure I buy your assertion that all mammals know how to swim, I would say that humans are at least as good as dogs when swimming. If you drop a human in water we will instinctively flap around and try too keep our head out of the water in about as elegant a way as a dog. The main problem for humans is panicking. Someone who does not know how to swim is likely to panic and &lt;em&gt;not&lt;/em&gt; manage to keep their head out of the water. Remember that humans float in water, if you keep calm you should be able to keep your head above the water line easily enough.&lt;/p&gt;&#xA;&lt;p&gt;Dogs can't swim as such, they simply do the same motions in the water as they do on land. There is no different action happening, they don't instinctively do a breast stroke.&lt;/p&gt;&#xA;&lt;p&gt;In addition, human infants actually have a couple of instincts that make them &amp;quot;swim&amp;quot; (&lt;a href=&quot;http://www.livestrong.com/article/237480-can-newborn-babies-swim/&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;The Diving Reflex&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;The diving reflex, or bradycardic response, means that infants whose heads are submerged in water will naturally hold their breath. Their heart rate will also slow down while they are underwater. This reflex disappears after about six months of age.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;The Swimming Reflex&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Newborns placed stomach-side down in water will move their arms and&#xA;legs in a repetitive &amp;quot;swimming&amp;quot; motion. This is known as the swimming&#xA;reflex. This reflex, too, begins to fade at about the six-month mark.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;That is no better and no worse than any other non-aquatic mammal can do. Try dropping a cat in water* and telling me she is a graceful swimmer :).&lt;/p&gt;&#xA;&lt;p&gt;* Don't, that's not nice.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-03-21T14:06:35.953" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7602" PostTypeId="2" ParentId="7592" CreationDate="2013-03-21T13:26:24.217" Score="9" Body="&lt;p&gt;Unlike Terdon I think that you are generally correct in your assertion that animals can swim whereas humans can't (although I'm sure there are exceptions). However, I think his answer contains the real answer:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dogs can't swim as such, they simply do the same motions in the water as they do on land. There is no different action happening, they don't instinctively do a breast stroke.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Try making walking motions underwater, see how well they work for you. Whereas for a four legged animal their land based motions function as a passable swimming motion and the shape and weight distribution of their body means they can keep breathing simply by holding their heads up, humans need to learn a new skill in order to swim.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd note, however, that a human who has learnt to swim is much better at it than the natural swimming ability of a quadruped.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-03-21T13:26:24.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7604" PostTypeId="1" CreationDate="2013-03-21T16:18:55.330" Score="11" ViewCount="149" Body="&lt;p&gt;I have benthic samples that were collected with an Ekman dredge from some small ponds.  The samples contain quite a bit of coarse particulate organic matter (CPOM, basically dead leaves).  I would like to quantify the amount of CPOM in the samples but they were preserved with 70% ethanol in the field.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any evidence that ethanol preservation alters benthic CPOM mass?&lt;/p&gt;&#xA;" OwnerUserId="137" LastEditorUserId="16866" LastEditDate="2017-03-07T00:10:04.413" LastActivityDate="2018-11-18T18:42:02.407" Title="Does preservation in ethanol alter leaf litter mass?" Tags="&lt;botany&gt;&lt;ecology&gt;&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7605" PostTypeId="2" ParentId="7600" CreationDate="2013-03-21T20:18:10.397" Score="2" Body="&lt;p&gt;I asked my professor, and the answer appears to be differences in both the generation and the final product.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Free chromosome fragments are created through irradiation/other damage of the germline in one animal.  Through a series of crosses, it is possible to introduce individual fragments (containing a duplication of your gene of interest, as well as a marker) into a mutant background.  The extrachromosomal fragment will be lost during mitosis at various points in development, and in a mosaic analysis, you can look for the loss of your marker (and therefore the loss of the wildtype allele), and see if yfg product is required in certain cell types for a wildtype phenotype.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Extrachromosomal arrays are created by cloning, and you typically have many copies of both the gene and marker.  It's the same principle as free chromosomal fragments in terms of mosaic analysis, but it's very powerful, as you can easily clone individual genes (versus irradiating and hoping to discover yfg on a fragment) and markers (and now you can use non-endogenous markers like GFP).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even though extrachromosomal arrays are comparatively easier to generate, the problem is that you end up with many copies of the gene, which leads to non-endogenous dosage levels. Even if this doesn't cause a completely different mutant phenotype in the cells, it is possible that enough of these proteins could segregate at mitosis into the daughter cells, such that even if the fragment is lost, you could still have your gene product around in the daughter cells (if your marker protein didn't also segregate like this, you might draw erroneous conclusions about the necessity of yfg product in those particular cells).    &lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-03-21T20:18:10.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7606" PostTypeId="2" ParentId="7593" CreationDate="2013-03-21T22:51:31.267" Score="1" Body="&lt;p&gt;Judging by your post history, it seems like you may want to pick up an introductory book on molecular biology. This question is really asking a number of questions. I will attempt to answer the difference between PCR and RACE, and I would suggest asking the others as separate questions, as @dd3 has suggested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Polymerase Chain Reaction (PCR) is the basic method of amplifying a small amount of DNA (the template) into an exponentially large amount of DNA. This method assumes the knowledge of the sequence of (at least) the regions of DNA flanking what you wish to amplify. Using these flanking sequences, two short oligonucleotides (e.g., 18-24 nucleotides), called primers, are ordered such that one primer matches the 5' strand at the start of the sequence, while the other primer matches the 3' strand at the end of the sequence. When these primers are mixed together with the template DNA, and a DNA polymerase enzyme, and subjected to specific temperature cycles, amplification occurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RACE PCR is a specific type of PCR. RACE (Rapid Amplification of cDNA Ends) PCR is used when the template strand to be amplified is a specific mRNA message. In other words, this form of PCR produces a DNA copy of cDNA from an mRNA starting product. The exact details of RACE depends on which type you wish to use and can be looked up elsewhere.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-03-21T22:51:31.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7607" PostTypeId="2" ParentId="7568" CreationDate="2013-03-21T23:52:23.833" Score="1" Body="&lt;p&gt;&lt;em&gt;I'm not completely certain about the vocabulary used in this context so let me know if you wish clarification&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a few hypothesis why females care about the sexual features of males, the two most prominent are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The &lt;em&gt;sexy son&lt;/em&gt; hypothesis states that a sexually attractive male will have sexually attractive offspring which, in turn, is also more likely to mate. This way a female choses to maximize the chance to pass on it's genes to next generations.&lt;/li&gt;&#xA;&lt;li&gt;The &lt;em&gt;good genes&lt;/em&gt; hypothesis says that males who can afford to develop features that do not benefit their survival but are only for the purpose of sexual selection are healthy, strong and fit. If not, they would not spend resources on sexual attractiveness.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;But why are all these features &lt;em&gt;beautiful&lt;/em&gt;? Well, the purpose here is that they are beautiful, in terms of attractive, to the recipient of the message: the potential partner. We as humans may find these features also beautiful, as is most likely the case with the colourful feathers of the peafowl. But what about the antlers of deer? Beautiful, dangerous? This is subjective for us ..&lt;/p&gt;&#xA;" OwnerUserId="3258" LastActivityDate="2013-03-21T23:52:23.833" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7608" PostTypeId="1" AcceptedAnswerId="7639" CreationDate="2013-03-22T03:10:04.697" Score="1" ViewCount="192" Body="&lt;p&gt;I know of melanopsin, a photo pigment in mammal eye that helps regulate circadian rhythms. It responds most strongly to blue spectrum light. There have been experiments that demonstrated that intensity of light is proportional to the impact on circadian rhythm regulation/ melatonin suppression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is why &lt;strong&gt;I'm interested if there is some optimal illumination intensity that has been demonstrated to result in better health/cognition in humans.&lt;/strong&gt; I heard anecdotal reports of full spectrum lighting improving attention in classrooms, but is there some chart or figure which says how much is &quot;too much light&quot;.&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-03-24T13:55:03.853" Title="Is there an optimal illumination level for human habitats/workplaces?" Tags="&lt;human-biology&gt;&lt;vision&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7609" PostTypeId="1" AcceptedAnswerId="7611" CreationDate="2013-03-22T06:44:27.433" Score="4" ViewCount="128" Body="&lt;p&gt;When I saw a DNA molecule for the first time, it kinda reminded me of a hard drive. It consists of &lt;em&gt;slots&lt;/em&gt; and there are some possible combinations for each slot; in the hard drive these possible combinations would be 0's and 1's. In DNA, these &lt;em&gt;slots&lt;/em&gt; would be G's, A's, T's, C's.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, is there a way to measure the amount of bytes that are encoded in a DNA molecule? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've made this &lt;a href=&quot;http://www.scienceforums.net/topic/62128-dna-storage-capacity/#entry643821&quot; rel=&quot;nofollow&quot;&gt;question before&lt;/a&gt; in another forum, but the answerer provided me only with Shannon's theorem, which is $K=L-\frac{(1-q^L)^n}{q^L}$ and told me a little about genetic redundancy. I could only search for the ammount of &lt;em&gt;slots&lt;/em&gt; which are present in the DNA, but this genetic redundancy thing got me stuck.&lt;/p&gt;&#xA;" OwnerUserId="783" LastEditorUserId="476" LastEditDate="2013-03-22T16:02:23.440" LastActivityDate="2013-03-22T16:02:23.440" Title="Is there a way to measure the amount of bytes that are possible to encode in a DNA molecule?" Tags="&lt;dna&gt;&lt;complexity&gt;&lt;information-theory&gt;&lt;information&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7610" PostTypeId="2" ParentId="7609" CreationDate="2013-03-22T10:46:52.050" Score="2" Body="&lt;p&gt;You might also be interested in this paper from EMBL-EBI about storing data on DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v494/n7435/full/nature11875.html&quot; rel=&quot;nofollow&quot;&gt;Towards practical, high-capacity, low-maintenance information storage in synthesized DNA&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They show they can get 757,051 bytes or a Shannon information 10 of 5.2 × 106 bits onto 153,335 strings of DNA, each comprising 117 nucleotides (nt).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;George Church had a similar paper recently as well - &lt;a href=&quot;http://news.sciencemag.org/sciencenow/2012/08/written-in-dna-code.html?ref=hp&quot; rel=&quot;nofollow&quot;&gt;Science&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="476" LastActivityDate="2013-03-22T10:46:52.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7611" PostTypeId="2" ParentId="7609" CreationDate="2013-03-22T11:57:39.767" Score="4" Body="&lt;p&gt;Unfortunately the answer is highly dependent on what you mean. In the simplest terms, comparing it directly to how we measure data storage in digital media, the number of different states of a DNA string of length $n$ can have is simply $4^n$. A byte holds $2^8$ different states so the number of bytes in a DNA string of length $n$ is $\frac{n}{4}$. Of course, actually accessing this information would be more difficult than simply having it in a strand of DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA in real organisms is not random, however, so sequences are not randomly distributed meaning that you could compress that information down into less bits than that, Shannon information style.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, you can decently argue that this doesn't really tell us how much information is in real DNA because real DNA has structure that matters. It has exons and introns and promoter regions and so on. Meanwhile, the sequences in protein coding regions are a lot more important than sequences in non-coding regions for the most part. Large parts of the genome are functionally irrelevant but because of this they tend to be more random and thus have higher Shannon information.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-03-22T11:57:39.767" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7612" PostTypeId="2" ParentId="2033" CreationDate="2013-03-22T14:37:13.017" Score="2" Body="&lt;p&gt;I have used terrific broth to grow up transformed &lt;em&gt;E. coli&lt;/em&gt; so they grow faster.  Often people will conduct a transformation, screen the cells, and grow them up in broth for plasmid extraction.  This growth would be for 12-16 hours.  Instead a person could use terrific broth to grow up the cells and it would take may 6-8 hours for adequate cell density for plasmid extraction.  If you are trying to express a protein then I would go with LB.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I learned recently that terrific broth is also preferred over LB when needing to express proteins after transformation.&lt;/p&gt;&#xA;" OwnerUserId="3247" LastEditorUserId="3247" LastEditDate="2013-03-28T15:16:43.373" LastActivityDate="2013-03-28T15:16:43.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7614" PostTypeId="2" ParentId="7597" CreationDate="2013-03-22T15:00:21.987" Score="6" Body="&lt;p&gt;When I optimized gel extraction in my hands, two factors turned out to be critical in maximizing gel extraction yield:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pH of the eluting solution. I used to elute the final product with DEPC-treated water initially, but the yield would vary a lot as the pH of the water changed. Using buffer EB is better, since it maintains a stable pH 8. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most importantly, *&lt;em&gt;incubate the eluting solution with the column as long a possible (and also elute twice). *&lt;/em&gt; I incubate for about 10 min, which is longer than what they recommend but it works much better. &lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-03-22T15:00:21.987" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7615" PostTypeId="2" ParentId="7597" CreationDate="2013-03-22T15:42:50.560" Score="5" Body="&lt;p&gt;Try dissolving at 50C.  In the Qiagen gel extraction kit, it says to dissolve at 50C or until completely dissolved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The size of the gel is important too.  Make sure it is 1.5% or less, and the size of the gel needs to be less than 400 mg.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, pay attention to the first step.  If the liquid is not the same color as the color of the first QG buffer then there is a pH problem.&lt;/p&gt;&#xA;" OwnerUserId="3247" LastActivityDate="2013-03-22T15:42:50.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7616" PostTypeId="1" CreationDate="2013-03-22T16:07:27.990" Score="3" ViewCount="139" Body="&lt;p&gt;I have always wondered, if dolphins sleep with one eye opened, do they really sleep at all?&lt;br&gt;&#xA;According to &lt;a href=&quot;http://science.howstuffworks.com/zoology/mammals/question643.htm&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; dolphins indeed &lt;em&gt;shut down&lt;/em&gt; their brains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I already googled it. No help from &lt;a href=&quot;http://en.wikipedia.org/wiki/Unihemispheric_slow-wave_sleep&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; or other articles and publications found.&lt;/p&gt;&#xA;" OwnerUserId="3276" LastEditorUserId="115" LastEditDate="2013-03-23T08:51:39.883" LastActivityDate="2013-03-23T08:51:39.883" Title="Do dolphins really sleep?" Tags="&lt;sleep&gt;&lt;mammals&gt;&lt;aquatic-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7617" PostTypeId="2" ParentId="7572" CreationDate="2013-03-22T16:51:54.953" Score="0" Body="&lt;p&gt;I found the answer to this question and some more interesting details that people who stumble upon this might also need. First look at this paper, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3191340/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3191340/&lt;/a&gt; and especially this figure, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3191340/figure/F3/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3191340/figure/F3/&lt;/a&gt;. The MSER is a ratio of the fraction of discovered peaks to the fraction of the sampled reads to recapitulate them, so if you are able to return all of the peaks with a small sample of reads then you have excellent coverage. Now even though you have great and well defined peaks you need another sample to confirm that they are indeed significant, and you can do this with the IDR, see this website - &lt;a href=&quot;https://sites.google.com/site/anshulkundaje/projects/idr&quot; rel=&quot;nofollow&quot;&gt;https://sites.google.com/site/anshulkundaje/projects/idr&lt;/a&gt;. The IDR is laid out pretty well in the supplemental material for this ENCODE paper, &lt;a href=&quot;http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nature/journal/v489/n7414/full/nature11245.html&lt;/a&gt;. Beautiful!! &lt;/p&gt;&#xA;" OwnerUserId="3264" LastActivityDate="2013-03-22T16:51:54.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7618" PostTypeId="2" ParentId="7616" CreationDate="2013-03-22T19:56:41.113" Score="1" Body="&lt;p&gt;I suppose that it depends on how sleep is defined. If we define it a a mechanism by which the brain repairs itself in an altered state, then, yes they do indeed sleep. Just not with all of their brain at once.&lt;/p&gt;&#xA;" OwnerUserId="1906" LastActivityDate="2013-03-22T19:56:41.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7619" PostTypeId="1" AcceptedAnswerId="7620" CreationDate="2013-03-22T23:22:03.490" Score="0" ViewCount="98" Body="&lt;p&gt;Many papers I have seen describing transgenic rodent models (and presumably applicable to other model organisms) involve the knock-in, or modification to, a single gene, possibly two genes. With respect to recombineering techniques, what prevents targeting multiple genes in a single organism? For instance, if I wanted to simultaneously knock-in some genes and knock-out others within the same mouse, would I be forced to generate individually modified transgenic lines and then do some &quot;fancy&quot; breeding to generate the multiple-modified mice?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2015-08-30T05:13:26.267" Title="Complexity in creating transgenic animals (e.g., mice)" Tags="&lt;dna&gt;&lt;gene-expression&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7620" PostTypeId="2" ParentId="7619" CreationDate="2013-03-22T23:32:37.973" Score="3" Body="&lt;p&gt;One reason is the low likelihood of success. Modifying a gene almost always involves a recombination event of plasmid DNA with a target site in the genome (and I say almost just because there may be some method that I don't know about, but all the ones I'm familiar with do). The likelihood of that decreases &lt;strong&gt;exponentially&lt;/strong&gt; with the number of genes you're trying to modify. If you're trying to make several mutants of individual genes the likelihood of success decreases only linearly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another reason is having more knowledge and experimental power. You can learn little from a double mutant if you don't also have the individual mutants to compare. In fact, most reviewers would ask for individual mutant data if you've made a double mutant in your paper. This is especially true with flies and worms, as crosses take less time with them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, the more mutant genes you have, the weaker the animal. Your mutants may not be viable at all with too many mutations.&lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-03-22T23:32:37.973" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7623" PostTypeId="2" ParentId="7616" CreationDate="2013-03-23T05:23:33.870" Score="2" Body="&lt;p&gt;I'd say that &lt;a href=&quot;http://en.wikipedia.org/wiki/Unihemispheric_slow-wave_sleep#Surfacing_for_air_and_pod_cohesion_for_marine_mammals&quot; rel=&quot;nofollow&quot;&gt;unihemispheric sleep and adaptations like it&lt;/a&gt; really are sleep - the brain activity on one side of the brain gives a characteristic sleep pattern.  It certainly must satisfy the needs of an aquatic mammal like a dolphin or a whale since they have to be partially conscious to breathe by surfacing regularly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It does seem to affect the brain physiology, but is there a reason you would not call it sleep?&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-03-23T05:23:33.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7624" PostTypeId="2" ParentId="7310" CreationDate="2013-03-23T05:40:25.790" Score="1" Body="&lt;p&gt;Here's another take on it:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose, for starters that you have only one gene that is responsible for your trait. Say, having version 1 (denoted T) gives you +1 to height, and having version 2 (denoted t) gives you -1. Suppose further that each version occurs in half the population.  Now every individual has 2 copies of each gene, so that 1/4 of people has TT for +2, 1/4 has tt for -2 and 1/2 has Tt or tT for 0 change in height.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now suppose two people with Tt or tT mate. If traits followed simple averaging pattern your friend suggested we would get the average of 0 and 0, that is 0 - all the time. But in genetic model (which is what really happens)  1/4 of the ofspring will get TT for +2, 1/4 will get tt for -2 and only 1/2 will actually get tT ot Tt for 0. Note that the variance - amount of variation - increases (everyone was 0 before mating, but some of the offspring has +2 or -2), whereas with the &quot;mixing&quot; model this does not happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For another mating paring - TT with tT - 1/2 of offspring will have TT for +2 and 1/2 will have tT for 0, effectively replacing the parents, so that the amount of variation stays the same (since the mean of the population is 0 variance contribution of these two individuals is 2^2+0^2=4 in both parental and offspring populations). Note that the mixing model would have all offspring at +1, which decreases the amount of variation  (variance contribution going from 4 to 1^2+1^2=2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, the mixing model of mating always decreases variance - leading to the &quot;everyone looks average&quot; result in the long run, but the actual genetic mating keeps variance constant (unless another factor - like preferential mating, mutation, or environmental factors intervenes; this was pointed out in other answers). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same thing happens if the proportion of T and t are not 50-50. This is called the Hardy-Weinberg principle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, if there are many genes that contribute to height, the variance in a trait (like height) can be modeled as the sum of variances from each gene. Now if each one of the genes is inherited through the same genetic mechanism that preserves variance, the total variance will also be preserved. So we will not actually all become &quot;average&quot;. &lt;/p&gt;&#xA;" OwnerUserId="3284" LastActivityDate="2013-03-23T05:40:25.790" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7626" PostTypeId="1" AcceptedAnswerId="7638" CreationDate="2013-03-23T10:34:28.810" Score="5" ViewCount="902" Body="&lt;p&gt;I've made a photo using the reversed 58 mm lens and my cropped DSLR:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/EIAwT.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/EIAwT.jpg&quot; alt=&quot;Unknown caterpillar&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could you please help? I really don't know where this came from.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found it in Russia.&lt;/p&gt;&#xA;" OwnerUserId="3280" LastEditorUserId="16866" LastEditDate="2017-06-29T01:47:30.273" LastActivityDate="2017-06-29T01:47:30.273" Title="What kind of caterpillar type bug is this?" Tags="&lt;species-identification&gt;&lt;zoology&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7627" PostTypeId="1" AcceptedAnswerId="8073" CreationDate="2013-03-23T15:21:07.547" Score="8" ViewCount="9279" Body="&lt;p&gt;Paracetamol is used to reduce body temperature when it is to high. The high body temperature (fever) is known to be an indication that immune system fights against an infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this context I have two related questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Is high body temperature one of the mechanisms of immune system to suppress an infection or it is just a side effect?&lt;/li&gt;&#xA;&lt;li&gt;If it is just a side effect, does paracetamol remove it by decreasing the intensity with which immune system fights with an infection or not?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3282" LastEditorUserId="69" LastEditDate="2013-03-23T23:34:15.767" LastActivityDate="2013-04-24T20:26:30.340" Title="How does paracetamol interfere with immune system?" Tags="&lt;pharmacology&gt;&lt;immunology&gt;&lt;medicinal-chemistry&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7629" PostTypeId="1" AcceptedAnswerId="7632" CreationDate="2013-03-23T16:02:11.543" Score="2" ViewCount="1441" Body="&lt;p&gt;I am not a biology student, just a curious person. To be specific, I'm talking about female humans. I know that it might apply to other mammals.&lt;/p&gt;&#xA;&lt;p&gt;What controls the size of breasts?&lt;/p&gt;&#xA;&lt;p&gt;I have heard about progesterone hormone.&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Is it just progesterone?&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are there any other factors?&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I have seen &lt;a href=&quot;http://www.imdb.com/title/tt0315327&quot; rel=&quot;nofollow noreferrer&quot;&gt;a movie&lt;/a&gt; in which couple talks about breast size increases after sex. Is it true?&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Can somebody give more info on this?&lt;/p&gt;&#xA;" OwnerUserId="818" LastEditorUserId="5144" LastEditDate="2020-08-06T19:40:52.083" LastActivityDate="2020-08-06T21:19:44.260" Title="What controls the size of breasts?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="7630" PostTypeId="1" AcceptedAnswerId="7640" CreationDate="2013-03-23T16:07:07.047" Score="5" ViewCount="419" Body="&lt;p&gt;Ketone bodies are water-soluble and should pose no problem to the kidneys because of solubility. If the kidneys are able to utilize ketone bodies for energy, then they must express the enzyme 3-ketoacyl-CoA transferase, correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do the kidneys express the enzyme 3-ketoacyl-CoA transferase?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can kidneys use ketone bodies as fuel?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="16299" LastEditDate="2015-12-31T16:21:27.927" LastActivityDate="2015-12-31T16:21:27.927" Title="Can the kidneys utilize ketone bodies for energy?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;kidney&gt;&lt;renal-physiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7632" PostTypeId="2" ParentId="7629" CreationDate="2013-03-23T21:51:50.207" Score="5" Body="&lt;p&gt;The known factors seem to be mainly oestrogen and genetic (although I haven't been able whatsoever to find detail on &lt;em&gt;what&lt;/em&gt; genes):&lt;/p&gt;&#xA;&lt;p&gt;Manning et al (1997): &lt;a href=&quot;https://doi.org/10.1016/S0162-3095(97)00002-0&quot; rel=&quot;nofollow noreferrer&quot;&gt;Breast asymmetry and phenotypic quality in women&lt;/a&gt;. Evolution and Human Behavior, 17 (2): 129–143.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Our data support the thesis that mammotropic hormones, particularly estrogen, are harmful because they suppress the immune system. Heavy women with high levels of body fat produce more estrogen and, therefore, bigger breasts. However, more estrogen leads to an increase in breast asymmetry. Women with “good genes” are able to produce symmetric breasts despite the presence of large quantities of estrogen. Large and symmetric breasts are therefore honest signals of high phenotypic quality in women.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="806" LastEditorUserId="24354" LastEditDate="2020-08-06T21:19:44.260" LastActivityDate="2020-08-06T21:19:44.260" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="7633" PostTypeId="1" AcceptedAnswerId="7714" CreationDate="2013-03-23T23:09:55.410" Score="6" ViewCount="2713" Body="&lt;p&gt;I understand that organ function varies with the stages of development. Does a fetal liver EVER perform lipogenesis, gluconeogenesis, make bile, etc? Or does it only begin performing these actions postnatally? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have heard that a fetus delivered between 24-26 weeks can potentially be &quot;okay&quot; with proper care and monitoring in a hospital. I would assume (please correct me if I'm wrong) that this implies the fetus's liver has developed at this time. So in the case of a fetus that was not delivered at 24-26 weeks, does it spend the remainder of the pregnancy in a fully functioning state? Or at least, which functions does it begin to perform?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been trying to find an answer on Google, but one walks a fine line when searching for human development information -- either the results are oversimplified &quot;expecting mothers&quot; websites, or journal articles speculating about the effect of X on the development of Y in the mouse/chick/zebrafish/giraffe/et cetera other nonhuman model.&lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2013-03-30T22:32:48.193" Title="What metabolic activities are performed by a developing human fetus's liver?" Tags="&lt;physiology&gt;&lt;embryology&gt;&lt;development&gt;&lt;organs&gt;&lt;liver&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7637" PostTypeId="2" ParentId="5665" CreationDate="2013-03-24T13:16:21.120" Score="2" Body="&lt;p&gt;It probably depends on the type of marine organism you're referring to, some will be much more hardy than others and some will not be able to adapt to change at all. Due to the vast scale of the environment that marine fish come from it's likely that in their natural habitat the conditions they live in are not subject to drastic changes in water chemistry or temperature [1][2]. So recreating those exact conditions for them in man-made habitats, let alone maintaining them is going to be extrememly difficult.  Also, if you think about the conditions that most (there will be some exceptions) terrestrial animals and plants have to deal with on a day-to-day basis they have to be able to cope with some fluctuations in humidity, temperature, weather, light etc and therefore are highly adaptable by necessity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other issues can be supplying the correct feed. In artificial settings food may have to be a non-natural substitute and this will likely cause problems for species who require a highly specialised diet. The terrestrial animals we tend to cultivate extensively are omnivorous/herbivorous which are not difficult needs to meet. On the other hand a fish from the sea that requires a particular other kind of fish only found in a particular area and that needs very specific conditions to thrive is going to be problematic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check out this article &lt;a href=&quot;http://www.vliz.be/imisdocs/publications/301.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.vliz.be/imisdocs/publications/301.pdf&lt;/a&gt; , it might be for a specific fish but it highlights some of the general issues i think you are referring to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.bestfish.com/saltg.html&quot; rel=&quot;nofollow&quot;&gt;http://www.bestfish.com/saltg.html&lt;/a&gt;&#xA;[2] &lt;a href=&quot;http://www.aquaticcommunity.com/marineaquarium/&quot; rel=&quot;nofollow&quot;&gt;http://www.aquaticcommunity.com/marineaquarium/&lt;/a&gt;&#xA;(both general articles on keeping marine fish)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="3261" LastActivityDate="2013-03-24T13:16:21.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7638" PostTypeId="2" ParentId="7626" CreationDate="2013-03-24T13:27:42.477" Score="6" Body="&lt;p&gt;Likely to be a black carpet beetle larvae&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vidtF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ipm.ucdavis.edu/PMG/PESTNOTES/pn7436.html&quot;&gt;http://www.ipm.ucdavis.edu/PMG/PESTNOTES/pn7436.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more facts try: &lt;a href=&quot;http://www.ipm.ucdavis.edu/PMG/PESTNOTES/pn7436.html&quot;&gt;http://www.ipm.ucdavis.edu/PMG/PESTNOTES/pn7436.html&lt;/a&gt; &#xA;Don't worry though, they live everywhere!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia has some info on the family of beetles that they belong to (&lt;a href=&quot;http://en.wikipedia.org/wiki/Dermestidae&quot;&gt;http://en.wikipedia.org/wiki/Dermestidae&lt;/a&gt;). I don't think they really cause any harm, except in natural history museums where they tend to munch the collections of animals...although this can also be a good thing:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;'They are used in taxidermy and by natural history museums to clean animal skeletons' &lt;a href=&quot;https://i.stack.imgur.com/vidtF.jpg&quot;&gt;1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/vidtF.jpg&quot;&gt;1&lt;/a&gt; VanClay, Mary. &quot;Bitten By the Bug&quot;. www.johnsonstring.com. Retrieved November 10, 2012.&lt;/p&gt;&#xA;" OwnerUserId="3261" LastEditorUserId="3261" LastEditDate="2013-03-24T22:04:54.487" LastActivityDate="2013-03-24T22:04:54.487" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7639" PostTypeId="2" ParentId="7608" CreationDate="2013-03-24T13:55:03.853" Score="1" Body="&lt;p&gt;It seems there has been some work done on too much light affecting human health, but in regards to lack of darkness at night, rather than too much during the day. Without the appropriate amount of darkness at key times melatonin production and the major clock regulator or SCN can be disrupted and lose sync with the peripheral clocks. See here [1] for a comprehensive article with loads of information and other links to studies done on this topic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This part in particular illustrates some of the problems associated with too much light:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Overexposure to sun-mimicking light is also believed to play a role in the increase of insulin resistance, type 2 diabetes and obesity in developed countries (where round-the-clock illumination is more prevalent). Some research also shows that too much sun-mimicking light ups our craving for carbohydrates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before humans started cultivating grains, carbohydrate energy was available only from spring to fall. In response, our bodies evolved to stock up on carbohydrates during the growing season to prepare for winter, when no carbohydrates were available. In turn, we didn’t crave carbohydrates in the winter. All that changed with the light bulb, write T. S. Wiley and Bent Formby, PhD, in Lights Out: Sleep, Sugar and Survival (Atria, 2001)&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This might be a bit off topic but check out &lt;a href=&quot;http://www.lightingdeluxe.com/workplace-lighting-ergonomics.html&quot; rel=&quot;nofollow&quot;&gt;http://www.lightingdeluxe.com/workplace-lighting-ergonomics.html&lt;/a&gt; and the HSE has some info on what the required lighting conditons in the workplace should be [2]. They only mention lighting conditions with reference to reducing levels of stress in the workplace though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also not directly related but pretty cool; an article in Science from 1998 found that light shining on the back of the knees may be able to regulate circadian rhythms [3].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://experiencelife.com/article/light-rhythms/&quot; rel=&quot;nofollow&quot;&gt;http://experiencelife.com/article/light-rhythms/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] (scroll to the lighting section) &lt;a href=&quot;http://www.hse.gov.uk/humanfactors/topics/lighting.htm#lighting&quot; rel=&quot;nofollow&quot;&gt;http://www.hse.gov.uk/humanfactors/topics/lighting.htm#lighting&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[3] Wright, K.P. Jr. &amp;amp; C.A. Czeisler. Absence of circadian phase resetting in response to bright light behind the knees. Science 297, 571 (July 26, 2002).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or if you don't have access &lt;a href=&quot;http://www.genomenewsnetwork.org/articles/08_02/bright_knees.shtml&quot; rel=&quot;nofollow&quot;&gt;http://www.genomenewsnetwork.org/articles/08_02/bright_knees.shtml&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3261" LastActivityDate="2013-03-24T13:55:03.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7640" PostTypeId="2" ParentId="7630" CreationDate="2013-03-24T17:13:05.613" Score="0" Body="&lt;p&gt;Alexandria's answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This article's abstract says that 3-ketoacid-CoA transferase was found in the kidney: nature.com/pr/journal/v42/n4/abs/pr19972518a.html&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2013-03-24T17:13:05.613" CommentCount="0" CommunityOwnedDate="2013-03-24T17:13:05.613" ContentLicense="CC BY-SA 3.0" />
  <row Id="7642" PostTypeId="2" ParentId="5499" CreationDate="2013-03-25T00:44:17.350" Score="3" Body="&lt;p&gt;Making one change in an ecological system is much like eating one salted peanut.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A:  If you only assume a 12⁰ change (which is &lt;em&gt;really&lt;/em&gt; large) then the net effect is not only warmer but dryer. Higher temperatures mean faster evaporation, faster transpiration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B:  Warmer may also mean that some pest has a limiting factor removed. Look at the problem northern British Columbia has had with Mountain Pine Beatle. The pines are fine with the warmer winters.  But the lack of cold winters has allowed the beatle population to explode.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C:  Some plants are adapted to a large temperature range. Look at the range for dandelion. So warmer temps may make them grow faster and set seed sooner.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D:  Some plants are adapted to a narrow temp range, and will die out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the questions is, &quot;If the change is slow enough, won't they just move up the mountain. In some cases yes.  We can look at turn of the century (1900) photographs of mountains, and we can see the tree line -- both at the top, where it meets tundra, and at the bottom where it meets prairie -- has moved up the mountain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However it also depends on the soil. And soils neither move fast, nor are created fast.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example:  Lot of articles think Canada will win big with global warming, because more northerly land will be suitable for farming. Not so. Most of the land that has reasonable soil is already farmed. The soil north of that point tends to be mostly peat moss bogs, and glacial till. In addition over half that country is the Precambrian shield -- endless miles of granite under 2-3 inches of moss and gravel, with bogs and lakes between. The equivalent of a rural gravel road costs millions of dollars a mile to punch through this country.&lt;/p&gt;&#xA;" OwnerUserId="3287" LastEditorUserId="3340" LastEditDate="2014-10-09T14:04:18.380" LastActivityDate="2014-10-09T14:04:18.380" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7643" PostTypeId="2" ParentId="5496" CreationDate="2013-03-25T01:00:53.640" Score="3" Body="&lt;p&gt;There are a bunch of possible answers;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;On my own property I have such a line.  Turned out it was an old fence line.  One side was farmed intensely for 90 years, the other side left in bush.  The farmed soil is enough different that it doesn't grow good trees.  Even the grass is different.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Another place I have an abrupt line of willows.  That one turns out to be water level from the local creek.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A third one has an abrubt chaange in types of grass.  That one is caused by a clay seam coming to the surface.  Uphill the surface soil is sandy.  Water hits the clay, and moves downhill, coming out at the grass line.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I've seen another one, in the mountains, that I think is due to cold air drainage.  The valley floor and 20 feet up the sides are bush.  I think the cold air settles and kills young trees.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3287" LastActivityDate="2013-03-25T01:00:53.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7644" PostTypeId="1" AcceptedAnswerId="7645" CreationDate="2013-03-25T07:20:23.807" Score="10" ViewCount="6660" Body="&lt;p&gt;When a human stands in one place, he cannot stand still but we can see the body slightly swings. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this due to the Earth rotation or it has something with biology and muscles relaxations?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have not been able to find a concrete documents on this thing. &lt;/p&gt;&#xA;" OwnerUserId="3296" OwnerDisplayName="slone79" LastActivityDate="2013-03-25T08:27:50.870" Title="Why human cannot stand still in one place?" Tags="&lt;biophysics&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7645" PostTypeId="2" ParentId="7644" CreationDate="2013-03-25T07:52:03.307" Score="19" Body="&lt;p&gt;Although at first sight this might seem to be biology rather than physics, maintenance of human posture is an example of &lt;a href=&quot;http://en.wikipedia.org/wiki/Control_theory&quot;&gt;control theory&lt;/a&gt;. Indeed a quick Google will find many publications on it - I found a good review &lt;a href=&quot;http://www.cs.cmu.edu/~hgeyer/Teaching/R16-899B/Papers/Winter95Gait&amp;amp;Posture.pdf&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A standing human is a dynamical system that is not in equilibrium so it requires a (closed loop) feedback system to maintain it. This means sensors in your body detect deviations from your desired posture and muscles contract to return you to it. The problem is that there is a lower limit to the movements you can detect i.e. you body moves a certain distance before your muscles respond and move it back. The result is that even when we try to stand absolutely still we are actually continually moving then correcting that movement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some people are better at maintaining posture than others, so some people can stand stiller than others. Plus the ability declines with age, as I can testify from personal experience :-)&lt;/p&gt;&#xA;" OwnerUserId="3220" OwnerDisplayName="John Rennie" LastActivityDate="2013-03-25T07:52:03.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7646" PostTypeId="1" AcceptedAnswerId="7650" CreationDate="2013-03-25T08:30:31.573" Score="3" ViewCount="402" Body="&lt;p&gt;I am trying to convert a set of Affymetrix ID's, like this one 143053_at_3745, to Flybase Gene Numbers (FBgn) like this one FBgn0000015. I have downloaded the &lt;a href=&quot;http://flybase.org/static_pages/downloads/bulkdata7.html&quot; rel=&quot;nofollow&quot;&gt;Flybase file&lt;/a&gt; required to do so (as described &lt;a href=&quot;http://flybase.org/static_pages/docs/datafiles.html#exons_affy1_overlaps&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) but I have noticed that most of the FBgn's have more than one associated Affy id. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, how do I know which to assign to my data? From the list of affy-ids that I have, how do I label each one with the &lt;strong&gt;appropriate&lt;/strong&gt; FBgn? I am using data from the &lt;a href=&quot;http://www.nature.com/ng/journal/v41/n3/full/ng.332.html&quot; rel=&quot;nofollow&quot;&gt;Ayroles et al 2009 (DGRP)&lt;/a&gt; which has a column of AffyID which look similar to the ones in the Flybase file but shorter (1638273_at). Perhaps I don't grasp why there would be more than one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some have one affy id which is repeated across 15 columns in the file, whereas some seem to have several affy id's associated with them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Some questions this problem raises:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does a singular FBgn identifier have more than one associated affy identifier? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do some datasets, such as the dataset I have, have shorter versions of the affy identifier? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where can I find an up to date and appropriate list matching these Affy id's the FBgn identifiers correctly?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-03-25T12:28:57.487" LastActivityDate="2013-03-25T16:48:07.210" Title="One flybase gene number (FBgn), many Affymetrix Id's" Tags="&lt;bioinformatics&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7647" PostTypeId="1" CreationDate="2013-03-25T11:21:51.290" Score="4" ViewCount="643" Body="&lt;p&gt;Why do certain people (especially kids) find vegetables so &quot;repellent&quot; when evolutionarily they should find them an attractive and thus tasty food? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I ask this question because if Darwin's theory of evolution is true then foods like vegetables that us human beings have been eating and attaining better health from eating for millions of years should have a taste that accordingly attracts us to them.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="115" LastEditDate="2013-03-28T06:26:47.723" LastActivityDate="2014-12-20T23:09:12.870" Title="Why do some people find vegetables so repellent when evolutionarily they should find them an attractive and thus tasty food?" Tags="&lt;evolution&gt;&lt;food&gt;&lt;vegetable&gt;" AnswerCount="4" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7649" PostTypeId="2" ParentId="7647" CreationDate="2013-03-25T12:13:23.310" Score="10" Body="&lt;p&gt;Evolution is not that simple. There is no selective pressure for a feature if it does not ultimately in some way benefit reproduction or the offspring. Vegetables are healthy for us now because we live much longer than we used to in an environment not dominated by us, and they contain many nutrients which help to sustain a healthy body beyond, say, 50.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if you imagine an average life span of around 30, it becomes clearer why evolution would favour foods high in energy over foods containing high amounts of micronutrients. Over such a time span, the long-term effects of a diet rich in fat and sugar do not develop significantly, but the energy supply is exactly what is needed to sustain bare life to the reproductive age.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-03-25T12:13:23.310" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="7650" PostTypeId="2" ParentId="7646" CreationDate="2013-03-25T16:48:07.210" Score="3" Body="&lt;p&gt;I can answer this - I may not have time to dig though the file you are pointing to... but here's some explanation - lmk if you need more.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The shorter names (123456_at) are the original names for the probe sets that Affymetrix gave.  The file you area asking about has been extended for FlyBase's purpose and I'm only dimly aware of its existence. It looks like Flybase has tried to rename the probe set to a minimal gene list and create less ambiguous mappings.  I'm not familiar with it.  If I have time Ill try to look at it and put something here, but I'm fairly slammed this week. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general you should know, there is a many to many relationship between probe sets from arrays and genes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a few reasons for this.  The most common reasons: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;More than one probe set per gene&lt;/em&gt;&#xA;1) More than one start sequence per gene. The IVT arrays such as you are looking at read only the 3' end of the gene.  If there are  more than one such terminii, you will have more than one probe set. &#xA;2) Duplicate genes.  If the 3' end of the gene has been duplicated recently, then a probe set may read more than one gene and not be able to distinguish them, so it will have both gene references in its annotation files. &#xA;3) Duplicate probe sets. For older arrays, this did happen where the probes in two probe sets will be mostly or entirely the same. &#xA;4) formerly separate genes are now joined into a single gene.  This is similar to (1) above, but with the added reason that two neighboring transcripts seen separately at the time of the array design are currently known to be part of the same transcript.  This is something we often don't think about, but the array may have been designed before your current gene of interest had a full length sequence.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In several cases the transcription behavior of the two probe sets will be quite different and you can decide which one to take based on how it behaves experimentally.  for example one of the probe sets may never respond while another one may register large changes with biological sample conditions.  Sorry I can't be of more help here. There are too many possible scenarios to consider to write about cogently.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;More than one gene per probe set&lt;/em&gt; &#xA;1) a single stretch of DNA, even on the same strand, may simply be associated with more than one gene and the probe set will read both of them. &#xA;2) Even if they are not exactly the same, some genes resemble each other in nucleotide sequence that is impossible to choose probes which do not read both of them.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since they have similar read length to a probe set, all this is also true to some extent for short read NGS sequencers in RNASeq data. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can hopefully see, ambiguity is something you have to expect to some extent when deciding to work with a biological system.  In many cases (~ 80%) you will have a single gene read per probe set, but with those odds you'll be looking at the genome browser for a half dozen of your favorite experimental results.   &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-03-25T16:48:07.210" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7651" PostTypeId="1" AcceptedAnswerId="9983" CreationDate="2013-03-25T17:06:41.897" Score="1" ViewCount="79" Body="&lt;p&gt;The Marine Stewardship Council states that the cod fishery in the Eastern Baltic sea recovered well and issued it's MSC certificate to the Swedish cod fishery in 2011 for that region. (&lt;a href=&quot;http://www.msc.org/newsroom/news/first-swedish-cod-fishery-receives-msc-certification&quot; rel=&quot;nofollow&quot;&gt;MSC 2011&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Data downloaded from &lt;a href=&quot;http://epp.eurostat.ec.europa.eu/portal/page/portal/eurostat/home/&quot; rel=&quot;nofollow&quot;&gt;EUROSTAT&lt;/a&gt; shows that Portugal, a main importer of codfish and -products, imported less and less from Norway (besides Iceland and UK the main supplier) (&lt;a href=&quot;http://www.fao.org/fishery/culturedspecies/Gadus_morhua/en&quot; rel=&quot;nofollow&quot;&gt;FAO 2006&lt;/a&gt;); dropping from around 20,000 tons (2001) to &amp;lt; 1,000 tons (2011) and more and more from Sweden; &amp;lt; 5,000 tons until 2003 versus &gt; 30,000 in 2010 and 2011.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This trade data does not necessarily show the origin of a product but rather the country that is selling the fish. I wonder if either the Swedish cod fishery expanded in the past few (~ five) years; Portugal changed it's main supplier from Norway to Sweden for whatever reason; or Sweden buys cod from Norway and distributes it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending on this the answer may not be so closely related to biology but I hope to get an idea here.&lt;/p&gt;&#xA;" OwnerUserId="3258" LastEditorUserId="3952" LastEditDate="2013-08-25T08:21:29.053" LastActivityDate="2013-08-25T08:21:29.053" Title="Did the Swedish cod fishery expand in the past years?" Tags="&lt;marine-biology&gt;&lt;ichthyology&gt;&lt;ethnobiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7652" PostTypeId="1" AcceptedAnswerId="14665" CreationDate="2013-03-25T19:31:46.133" Score="15" ViewCount="195199" Body="&lt;p&gt;I have noticed that some of my sporadic gray hairs are gray at the tip side but oddly, not near the roots.  Some are even only gray in the middle.  I find all of this very counter intuitive, and I assure you nobody is secretly dying my hair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does the graying process work, and how is it that this can be happening?&lt;/p&gt;&#xA;" OwnerUserId="3292" LastEditorUserId="3292" LastEditDate="2013-03-25T21:11:49.073" LastActivityDate="2014-10-21T06:40:03.037" Title="What could cause hairs to gray at the tips but not the roots?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;human-anatomy&gt;&lt;hair&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7653" PostTypeId="2" ParentId="7652" CreationDate="2013-03-25T20:19:54.257" Score="1" Body="&lt;p&gt;Your hair grows out from the roots, and typically as you age, the pigments (melanin) that would normally keep your hair a certain colour are not produced anymore because the pigment producing cells (melanocytes) start to die. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They're likely different colours in the middle because that will be the result of a gradual dying off of the melanocytes at the base of that strand. As a result the root (newest part of the hair) will typically be gray when they have mostly all died off, the middle will have a bit of melanin because it was produced when there were still some functional melanocytes, and the tip (the oldest part of the hair) will still be full of melanin from when it was produced when the melanocytes were alive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for why this happens it's not fully understood why the melanocytes die as we age, but the gene Bcl-2 has been found to be essential for the maintenance of melanocytes. Mutations in this gene could be responsible for premature graying [1]. There is some literature on the role of Bcl2 family genes as regulators of cell death [2][3] but how these things are connected seems largely still unknown.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.nbcnews.com/id/6750793/ns/health-cancer/t/research-yields-clues-why-hair-turns-gray/#.UVCu21dONvJ&quot; rel=&quot;nofollow&quot;&gt;http://www.nbcnews.com/id/6750793/ns/health-cancer/t/research-yields-clues-why-hair-turns-gray/#.UVCu21dONvJ&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.immunol.16.1.395?journalCode=immunol&quot; rel=&quot;nofollow&quot;&gt;http://www.annualreviews.org/doi/abs/10.1146/annurev.immunol.16.1.395?journalCode=immunol&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[3] &lt;a href=&quot;http://genomics.senescence.info/genes/entry.php?hgnc=BCL2&quot; rel=&quot;nofollow&quot;&gt;http://genomics.senescence.info/genes/entry.php?hgnc=BCL2&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been some reports of people indicating that a change in lifestyle and/or diet have led to a decrease in gray hairs, or even that the hair begins to regain its colour leaving a gray section at the tip or in the middle. I've only found one relevant article which makes reference to some research into the restoration of hair growth and colour in mice[4]. An American group are studying the role of the Wnt signaling protein in controlling the activity of melanocytes. I'm just speculating here, but it could be that fluctuations in Wnt protein production (possibly influenced by diet and lifestyle and overall health) may switch melanocyte melanin production on and off. I haven't been able to find any literature to back up this hypothesis though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[4] &lt;a href=&quot;http://inventors.about.com/od/gstartinventions/a/Cure-For-Grey-Hair.htm&quot; rel=&quot;nofollow&quot;&gt;http://inventors.about.com/od/gstartinventions/a/Cure-For-Grey-Hair.htm&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3261" LastEditorUserId="3292" LastEditDate="2014-01-20T22:01:38.440" LastActivityDate="2014-01-20T22:01:38.440" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="7654" PostTypeId="1" AcceptedAnswerId="7655" CreationDate="2013-03-25T20:24:32.900" Score="1" ViewCount="4996" Body="&lt;p&gt;My coach says that I need to eat 1.2 - 1.5 grams of proteins per kilogram when I have a common cold and flu.&#xA;I normally eat one gram of proteins per kilogram, while double it when doing my exercise training.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He explained that the reason why you need to get more good proteins when you are sick is that the body is building antibodies by the adaptive immune system and later for innate immunity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think he can be right based only on my own experiences getting better from common cold with low protein diet - it just takes a lot of time, while under high protein diet, you get better faster.&#xA;I also think his explanation makes complete sense to me, since antibodies and antigens are proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why do you need more proteins when you are sick?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1306" LastEditDate="2013-03-25T20:43:50.427" LastActivityDate="2018-02-22T03:12:58.227" Title="More proteins from diet when common cold and flu?" Tags="&lt;proteins&gt;&lt;immunology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7655" PostTypeId="2" ParentId="7654" CreationDate="2013-03-25T20:38:53.213" Score="4" Body="&lt;p&gt;Your body needs more energy when you are ill to facilitate the recovery process which includes the production of white blood cells to help fight the infection. This shouldn't be limited to proteins though, carbs are also very important as they are provide high amounts of energy. Basically just making sure you eat a varied and balanced diet is more important when you are ill to make sure your body receives the nutrients it needs to fight infection and heal itself. As it is having to work harder when you are ill it makes sense to eat more high energy foods. Micronutrients are also very important!&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Minerals such as selenium and zinc work to keep the immune system strong. These minerals are found in protein rich foods such as beans, nuts, meat, and poultry. —&amp;nbsp;&lt;a href=&quot;http://www.webmd.com/cold-and-flu/flu-guide/what-to-eat-when-you-have-the-flu&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Although if your diet is varied you should be getting plenty of these anyway, without needing to take supplements.&lt;/p&gt;&#xA;" OwnerUserId="3261" LastEditorUserId="5239" LastEditDate="2013-12-28T01:01:10.680" LastActivityDate="2013-12-28T01:01:10.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7656" PostTypeId="2" ParentId="7597" CreationDate="2013-03-25T22:14:20.240" Score="1" Body="&lt;p&gt;Elute from the column with Elution Buffer that has been preheated to 50-60 degrees. I stick mine in the incubator for the duration of the extraction so it is warm when I come to elute. It seems to help yield.&lt;/p&gt;&#xA;" OwnerUserId="3261" LastActivityDate="2013-03-25T22:14:20.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7659" PostTypeId="1" AcceptedAnswerId="7660" CreationDate="2013-03-26T07:43:22.743" Score="5" ViewCount="826" Body="&lt;p&gt;The largest extant fish species is the whale shark (&lt;em&gt;Rhincodon typus&lt;/em&gt;). With a length of 13 meters and a mass of about 20-30 metric tons, the whale shark is relatively small compared to the largest mammals, blue whales (&lt;em&gt;Balaenoptera musculus&lt;/em&gt;, 180 tons) and fin whales (&lt;em&gt;Balaenoptera physalus&lt;/em&gt;, 120 tons).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a physical, physiological, or anatomical explanation why fish never reached the size of marine mammals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bigger isn't necessarily better, but I was wondering if there is a simple explanation why fish species are so much smaller than marine mammals.&lt;/p&gt;&#xA;" OwnerUserId="138" LastActivityDate="2013-03-26T08:10:51.003" Title="What limits the size of fish compared to marine mammals?" Tags="&lt;zoology&gt;&lt;physiology&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7660" PostTypeId="2" ParentId="7659" CreationDate="2013-03-26T08:10:51.003" Score="8" Body="&lt;p&gt;I'd suggest that one factor could be the difficulties of breathing water - it is highly inefficient. The following is a summary of &lt;a href=&quot;http://innri.unuftp.is/pauly/Geometrical%20constraints%20o.pdf&quot; rel=&quot;noreferrer&quot;&gt;this response&lt;/a&gt; to a TREE article.&lt;/p&gt;&#xA;&lt;p&gt;Fish spend 10-30% of their energy on breathing because it is so inefficient to use gills because diffusion rates are much slower and oxygen is less abundant. Gills grow in proportionate scales to body size, generally for every 100% increase in body size there is a 50-90% increase in gill size. Thus the larger fish species are working on a lesser body mass/gill size ratio so they can't take up oxygen very easily.&lt;/p&gt;&#xA;&lt;p&gt;From this I'd suggest it is difficult for fish to grow gill systems much larger than those of a whale shark as it would become to inefficient for them thrive. By comparison whales are air breathers so, despite &amp;quot;breathing&amp;quot; (collecting fresh air) less frequently they can get much more oxygen from it.&lt;/p&gt;&#xA;&lt;p&gt;I'm sure there is more to it but at least this is a starting idea. If anyone has more then feel free to add to/edit this answer, I merely suggest this as one possible theory and it is not my field.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-03-26T08:10:51.003" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7662" PostTypeId="2" ParentId="1580" CreationDate="2013-03-26T15:36:22.503" Score="3" Body="&lt;p&gt;Biological control does not have to be with an introduced species.  It can also be accomplished by either artificially inflating the number of existing predators.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.g.  Spruce bud worm has a natural predator in the form of a tiny wasp.  But budworm can spread through a stand faster than the wasp can.  By moving popluatins of the wasp to the forefront of the budworm advance, you get most of the 2nd generation budworms.  The trees have a bad needle year but aren't killed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It can also be done with habitat modification.  If you create conditions that favour the existing predator, then there are more predators in place.  E.g.  create places for ladybug overwintering to reduce aphid populations. (I have no idea if this would work.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anohter example -- although ecological controll may be better than biological -- I had a significant mosquito problem.  Lots of small puddles in spring.  I created a permanent pond.  This has resulted in much smaller mosquito population.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The pond is a local year round water supply for insectivorous birds.&lt;/li&gt;&#xA;&lt;li&gt;The pond is by far the largest water body around, so tends to get most of the mosquito eggs.&lt;/li&gt;&#xA;&lt;li&gt;The pond now has a permanent population of boreal and chorus frogs.  Tadpoles of these make it tough to be a mosquito larvae.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Is this species introduction?  Only if you consider immigrant species from neighborin populations to be introduction.&lt;/p&gt;&#xA;" OwnerUserId="3287" LastActivityDate="2013-03-26T15:36:22.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7663" PostTypeId="2" ParentId="7633" CreationDate="2013-03-26T16:23:12.703" Score="2" Body="&lt;p&gt;I found that a search through Google Books was helpful...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While without the excretion of feces, it might seem as if the liver would not be active, but the liver tissue is not only active in development and tissue generation but serves direct physiological function as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After initial phases of development, the liver &lt;a href=&quot;http://books.google.com/books?id=H85dwxYTKLwC&amp;amp;pg=PA150#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;produces fetal red blood cells&lt;/a&gt; which is normally a function carried out by specialized bone marrow hematopoietic cells. &#xA;Over the course of fetal development the liver &lt;a href=&quot;http://books.google.com/books?id=np9Ro-LzZQUC&amp;amp;pg=PA1306&quot; rel=&quot;nofollow&quot;&gt;develops its typical functions&lt;/a&gt;.  It breaks down old red blood cells and stores their iron, and pushes the waste bilins and other waste products to the umbilical cord to keep the fetus clean.  The liver also synthesizes and stores fats. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-03-26T16:23:12.703" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7664" PostTypeId="1" AcceptedAnswerId="7665" CreationDate="2013-03-26T19:32:35.793" Score="1" ViewCount="341" Body="&lt;p&gt;Most animals I see around seem to have two nostrils - humans, snakes, birds, fish .. and so on. From reading online I see that 2 nostrils provide a stereo olfactory effect. This stereo effect is caused by the difference in flow of air through the nostrils.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this stereo effect apply only to humans? Are there any animals that have a different number of nostrils? Say, more than 2, or less.&lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2013-03-26T23:34:29.180" Title="Is stereo olfactory ability restricted to humans?" Tags="&lt;physiology&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7665" PostTypeId="2" ParentId="7664" CreationDate="2013-03-26T20:01:37.357" Score="1" Body="&lt;p&gt;Moles and rats also smell in stereo (&lt;a href=&quot;http://www.nature.com/ncomms/journal/v4/n2/full/ncomms2444.html&quot; rel=&quot;nofollow&quot;&gt;Catania 2013&lt;/a&gt; and &lt;a href=&quot;http://www.sciencemag.org/content/311/5761/666.full?sid=fd5e85c4-e83a-400f-b1ac-e3f47854b686&quot; rel=&quot;nofollow&quot;&gt;Rajan et al 2006&lt;/a&gt;), as do desert ants (&lt;a href=&quot;http://www.mpg.de/623392/pressRelease201003103&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt;).  The latter is rather interesting, given that ants &quot;smell&quot; using their antennae, which suggests multiple sensory structures, not necessarily nostrils, are required for stereo olfactory ability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Hammerhead sharks have two nares and also stereo olfactory ability (&lt;a href=&quot;http://www.science.fau.edu/sharklab/pdfs/sm07.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;).  Dolphins have one spiracle, as do a number of other cetaceans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strike&gt;It's actually not clear whether humans have stereo olfactory ability,&lt;/strike&gt; &lt;strong&gt;(see edit below)&lt;/strong&gt;  as the &quot;stereo&quot; aspect derives from having nostrils that are sampling from different spatial locations.  However, the research in the eastern mole suggests that this is not so far-fetched an idea, as their nostrils are not so far apart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT of EDIT: I take that back about humans: &lt;a href=&quot;http://www.nature.com/neuro/journal/v10/n1/full/nn1819.html&quot; rel=&quot;nofollow&quot;&gt;we do appear to have stereo olfaction&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-03-26T23:34:29.180" LastActivityDate="2013-03-26T23:34:29.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7667" PostTypeId="1" AcceptedAnswerId="7672" CreationDate="2013-03-27T01:12:37.350" Score="6" ViewCount="4147" Body="&lt;p&gt;Is there a hormone or group of hormones that regulates when we feel sleepy late at night, or in the morning?  Or is sleepiness caused by some other non-hormonal mechanism?  (e.g. pure psychological, or neuronal.)&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="3059" LastEditDate="2013-03-27T02:18:14.630" LastActivityDate="2013-07-29T11:50:36.623" Title="What causes humans to be sleepy?" Tags="&lt;biochemistry&gt;&lt;endocrinology&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7669" PostTypeId="1" CreationDate="2013-03-27T02:17:16.330" Score="31" ViewCount="3897" Body="&lt;p&gt;I would imagine that the answer to this question would be population control, especially since even if one sibling is homosexual this does not necessarily mean that the other siblings will be too. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="3624" LastEditDate="2016-04-27T14:47:49.547" LastActivityDate="2018-10-25T10:14:29.413" Title="How can homosexuality evolve despite natural selection?" Tags="&lt;evolution&gt;&lt;sexual-selection&gt;&lt;homosexuality&gt;" AnswerCount="7" CommentCount="19" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="7670" PostTypeId="1" CreationDate="2013-03-27T03:30:08.617" Score="1" ViewCount="413" Body="&lt;p&gt;I'm reading a journal article about mitochondrial protein import and it mentions that one of the mutant proteins tested showed background binding with another protein. What the heck is background binding? &lt;/p&gt;&#xA;" OwnerUserId="496" LastEditorUserId="69" LastEditDate="2013-03-27T14:47:02.820" LastActivityDate="2013-03-27T16:55:35.303" Title="What is background binding?" Tags="&lt;cell-biology&gt;&lt;protein-binding&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7671" PostTypeId="1" AcceptedAnswerId="57785" CreationDate="2013-03-27T09:39:59.477" Score="4" ViewCount="78" Body="&lt;p&gt;Cell motility assessment is a branch of experimental biology or medical science. One example could be an assessment of treatment effects on sperm motility of an animal. The standard procedure involves taking film clips of sperm (or any other moving objects) through a microscope and measuring average linear velocity of particles on these film clips. The program used for measuring these linear velocities is important, and there are not too many choices to my knowledge. However, my knowledge might be limited.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have previously used &lt;a href=&quot;http://www.motionanalysis.com/html/microbiology/celltrak.html&quot; rel=&quot;noreferrer&quot;&gt;CellTrak&lt;/a&gt; for measuring sperm swimming speeds. The program works well, but lacks a batch processing function. As the assessment bases on a considerable number of replicates, I end up with 1000-2000 film clips to be analyzed and clicking my way through CellTrak is a tedious and irritating process. Also CellTrak licence costs a lot of money for such a poorly written program.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, my question is: Is someone aware of a similar program to CellTrak, which includes batch processing option, or even better, which works through command line and can be looped? Are there open source options or extensions to widely used open source programs (ImageJ, Bioconductor, etc.)? Please give a short tutorial/personal experience to the usage of the suggested program (if any).  &lt;/p&gt;&#xA;" OwnerUserId="3302" LastActivityDate="2017-03-29T08:24:33.787" Title="A program for cell motility assessment with a batch process function?" Tags="&lt;cell-biology&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7672" PostTypeId="2" ParentId="7667" CreationDate="2013-03-27T10:27:17.807" Score="5" Body="&lt;p&gt;The &lt;a href=&quot;http://www.sleepfoundation.org/article/sleep-topics/melatonin-and-sleep&quot; rel=&quot;nofollow&quot;&gt;release of the hormone melatonin is responsible for the feeling of sleepiness&lt;/a&gt;. It is released by the pineal gland and production starts when the light fades, as it's production is inhibited by light stimulation of the retina, the onset of the production is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Melatonin#Circadian_rhythm&quot; rel=&quot;nofollow&quot;&gt;dim-light melatonin onset.&lt;/a&gt; Artificial supplementation can increase sleep quality and regularity related to some sleep disorders and is often administered as pills or patches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adenosine is an inhibitory neuromodulator, ie it inhibits neural activity. Neural activity can be either excitatory or inhibitory and &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1087079201902011#&quot; rel=&quot;nofollow&quot;&gt;adenosine more strongly inhibits the excitatory neural activity&lt;/a&gt;. Thus, increased adenosine levels should decrease excitatory effect of nervous stimuli and make you feel more relaxed &amp;amp; sleepy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other hormones &amp;amp; neural pathways may be involved (serotonin and the serotonergic neural pathways for example) as well as other stimuli like other people's behaviours (yawning, stretching etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sleepfoundation.org/article/sleep-topics/melatonin-and-sleep&quot; rel=&quot;nofollow&quot;&gt;This page&lt;/a&gt; and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Melatonin&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt; entry on melatonin have much more information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sleepfoundation.org/article/sleep-topics/melatonin-and-sleep&quot; rel=&quot;nofollow&quot;&gt;From sleepfoundation&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Melatonin is a natural hormone made by your body's pineal gland - a&#xA;  pea-sized gland located just above the middle of the brain. During the&#xA;  day the pineal is inactive. When the sun goes down and darkness&#xA;  occurs, the pineal is &quot;turned on&quot; and begins to actively produce&#xA;  melatonin, which is released into the blood. Usually, this occurs&#xA;  around 9 p.m. As a result, melatonin levels in the blood rise sharply&#xA;  and you begin to feel less alert. Sleep becomes more inviting.&#xA;  Melatonin levels in the blood stay elevated for about 12 hours - all&#xA;  through the night - before the light of a new day when they fall back&#xA;  to low daytime levels by about 9 a.m. Daytime levels of melatonin are&#xA;  barely detectable.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-29T11:50:36.623" LastActivityDate="2013-07-29T11:50:36.623" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7673" PostTypeId="1" AcceptedAnswerId="10766" CreationDate="2013-03-27T11:23:18.133" Score="12" ViewCount="30347" Body="&lt;p&gt;Adenosine is an important hormone in sleep regulation.  It is postulated that when a person is awake, there is a build up of adenosine in the brain, which inhibits the neurons in the brain, and produces tiredness.  (See answer for more information:  &lt;a href=&quot;https://biology.stackexchange.com/questions/7667/what-causes-humans-to-be-sleepy&quot;&gt;What causes humans to be sleepy?&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I am wondering what specifically causes this adenosine build up.  I understand ATP (adenosine tri-phosphate) is broken down to ADP in the brain to produce energy.  I thought this ADP would then be used to re-generate ATP again etc, so I'm not sure how adenosine is built up in the brain over a day.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically I am unsure how Adenosine itself, as opposed to ATP or ADP, is produced during the waking state?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My theory is that during the high demand waking state there is insufficient energy to convert ADP back to ATP, and the excess ADP is broken down to adenosine somehow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would appreciate an explanation of how this build up occurs, and also an explanation of how this in turn how it induces sleepiness would be a plus.&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2017-01-18T04:54:21.133" Title="What causes adenosine build up in the brain when awake?" Tags="&lt;biochemistry&gt;&lt;sleep&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7674" PostTypeId="2" ParentId="7669" CreationDate="2013-03-27T11:23:21.693" Score="19" Body="&lt;p&gt;Obviously selection would appear to not favour being homosexual, in an evolutionary sense it represents somewhat of a decrease in fitness: Homosexuals fail to reproduce successfully due to the requirement of both male and female gametes and reproductive organs, therefore significantly fewer than the average heterosexual couple. Certainly I don't think it would have evolved as some kind of population control method - &lt;a href=&quot;http://en.wikipedia.org/wiki/Group_selection#Criticism&quot; rel=&quot;noreferrer&quot;&gt;group selection theory is generally discarded in favour of a gene-centred theory&lt;/a&gt; (see Dawkins for popular science literature)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is debate about whether someone can be biologically &quot;preprogrammed&quot; to be homosexual, this can occur &lt;strong&gt;genetically&lt;/strong&gt; or &lt;strong&gt;epigenetically&lt;/strong&gt;. Genetic models have used kin selection, overdominance, sexual antagonism in the past and are briefly discussed in the following article on epigenetics. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23397798&quot; rel=&quot;noreferrer&quot;&gt;Recent work&lt;/a&gt; has looked at possible models by which heritable homosexuality could arise by &lt;a href=&quot;http://en.wikipedia.org/wiki/Epigenetics&quot; rel=&quot;noreferrer&quot;&gt;&lt;strong&gt;epigenetic markers&lt;/strong&gt;&lt;/a&gt; and this was covered in a lot of mainstream media (&lt;a href=&quot;http://narth.com/2012/12/is-epigenetics-a-critical-factor-in-homosexuality/&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt;,&lt;a href=&quot;http://www.the-scientist.com/?articles.view/articleNo/33773/title/Can-Epigenetics-Explain-Homosexuality-/&quot; rel=&quot;noreferrer&quot;&gt;2&lt;/a&gt;.. just google epigenetics homosexuality). This quote is from their abstract and explains one reason it is difficult to pin down heritable causes of homosexuality:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pedigree and twin studies indicate that homosexuality has substantial&#xA;  heritability in both sexes, yet concordance between identical twins is&#xA;  low and molecular studies have failed to find associated DNA makers.&#xA;  This paradoxical pattern calls for an explanation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;By their readily testable model they have shown possible (&amp;amp; plausible) conditions under which the &quot;epi-marks&quot; which cause homosexuality could spread through populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ehbonline.org/article/S1090-5138%2808%2900068-8/abstract&quot; rel=&quot;noreferrer&quot;&gt;&lt;strong&gt;Genetic&lt;/strong&gt; studies of twins&lt;/a&gt; where one is homosexual have also revealed links between genes and a mating advantage. For example if in a pair of male identical twins one is homosexual, the other has a mating success greater than that of the average male. However, it could be that this link is found because of social reasons (perhaps someone who has grown up with a homosexual sibling may have a different mentality or lifestyle socially which could help them increase reproductive success).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Note: I have no problem with a person's sexual orientation &amp;amp; the rights/ethics of homosexuality is not the topic of this question &amp;amp; answer. This is purely an answer to the obvious &lt;strong&gt;evolutionary&lt;/strong&gt; conundrum.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-01-16T10:00:17.437" LastActivityDate="2016-01-16T10:00:17.437" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7675" PostTypeId="2" ParentId="7669" CreationDate="2013-03-27T13:06:26.017" Score="30" Body="&lt;p&gt;Several years back, results of a twin study (&lt;a href=&quot;http://dx.doi.org/10.1016/j.evolhumbehav.2008.07.002&quot;&gt;Zietsch, et al., 2008&lt;/a&gt;; &lt;a href=&quot;http://www.economist.com/node/12465295&quot;&gt;popular press in &lt;em&gt;The Economist&lt;/em&gt;&lt;/a&gt;) suggested that genes associated with homosexuality make heterosexuals who carry the same genes more reproductively successful. This would explain the observation that, for example, sisters of homosexual males have more offspring.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We show that psychologically masculine females and feminine men are&#xA;  (a) more likely to be nonheterosexual but (b), when heterosexual, have&#xA;  more opposite-sex sexual partners.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So if more sexual partners in heterosexuals is correlated with more offspring, then the genes associated with homosexuality may lead to more offspring in heterosexuals that carry them. So these &quot;homosexuality&quot; genes could easily be maintained in the population by conferring a reproductive advantage to siblings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors conclude:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Taken together, these results suggest that genes predisposing to&#xA;  homosexuality may confer a mating advantage in heterosexuals, which&#xA;  could help explain the evolution and maintenance of homosexuality in&#xA;  the population.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="107" LastEditorUserId="3340" LastEditDate="2015-12-16T08:15:56.363" LastActivityDate="2015-12-16T08:15:56.363" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7676" PostTypeId="1" CreationDate="2013-03-27T13:52:12.173" Score="2" ViewCount="158" Body="&lt;p&gt;I've recently read a couple articles dealing with long term data storage, and &lt;a href=&quot;http://blog.longnow.org/02012/08/16/storing-digital-data-in-dna/&quot; rel=&quot;nofollow&quot;&gt;DNA was suggested as one of the prime candidates for long term storage of digital data&lt;/a&gt; additionally, there is &lt;a href=&quot;http://blog.longnow.org/02012/10/12/decoding-long-term-data-storage/&quot; rel=&quot;nofollow&quot;&gt;this article which deals with decoding of long storage data&lt;/a&gt;. These popular articles, though simple do mention important concepts- how packets are stored in DNA use addressing schemes, redundancy of storage, writing for a recipient who may be using a different language, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This made me think - we have the SETI initiative which is looking for signs of (intelligent) life in the universe. That organization was created long time ago, and uses technologies of those days - radio waves. The modern science knows that we can store a lot of data in DNA, and that most organism DNA contains only a small fraction of protein coding sequences and a large amount of non-coding material. If I understand correctly, some of the non coding material is repetitive and highly preserved. &lt;strong&gt;Has anyone considered expanding the search for intelligent life to include examination of DNA for messages that might've been left by other intelligent species actually visiting earth?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-03-28T02:59:57.333" Title="Expanding the SETI initiative to seek intelligent data within DNA sequences?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7677" PostTypeId="5" CreationDate="2013-03-27T14:47:28.570" Score="0" Body="&lt;p&gt;Questions should be specific to biology, with discussion on the biological aspects of terminology and advice on specialist terminology. Some questions may be better suited for &lt;a href=&quot;http://english.stackexchange.com&quot;&gt;English Language and Usage&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="16866" LastEditDate="2019-12-13T04:26:41.750" LastActivityDate="2019-12-13T04:26:41.750" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="7678" PostTypeId="4" CreationDate="2013-03-27T14:47:28.570" Score="0" Body="How terms are used or the meaning of words as used in scientific literature.  Questions should ideally include a link or quote as context for where the term was encountered." OwnerUserId="69" LastEditorUserId="4101" LastEditDate="2013-10-31T00:48:08.527" LastActivityDate="2013-10-31T00:48:08.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7679" PostTypeId="2" ParentId="7670" CreationDate="2013-03-27T16:55:35.303" Score="2" Body="&lt;p&gt;Background binding in this case would be the extent to which two proteins associate together by chance.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A hypothetical example: you may have a mitochondrial protein import complex.  Usually cases there is a specific peptide sequence the import complex binds to , but proteins without an import peptide sequence will occasionally be bound to the import complex.  This is called the background binding for the protein complex.  The experimentalists might have measured this by cutting the import peptide sequence off a mitochondrial protein for instance.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any candidate would have to bind to the complex more than the background case to be considered a target for mitochondrial import.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-03-27T16:55:35.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7680" PostTypeId="1" AcceptedAnswerId="39833" CreationDate="2013-03-27T18:24:47.493" Score="7" ViewCount="1061" Body="&lt;p&gt;I have two proteins and I will be preparing a vector with both genes for stable transfection. Each protein will have their own promoter and I will use piggyBac vector to insert a single cassette with both genes in it into the chromosomes. My questions are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;If I use the same promoter (CMV, SV40 or an inducible one) for both genes how would this affect the expression levels? I read in some papers that one of the genes might get expressed lower than the other. If you have first-hand experience I will be grateful if you share it.&lt;/li&gt;&#xA;&lt;li&gt;If I use the same promoter for both, but put them far away (i.e. ends of the cassette) would the expression levels get affected again? It sounds simple enough but I think people would have published something if they had a good result with that.&lt;/li&gt;&#xA;&lt;li&gt;If I use different promoters for each gene (e.g. CMV for one and Tet-inducible for the other) how would it work? I couldn't find a paper which used this and I would like to continue with this approach; therefore, if you have any experience I will be really grateful for any help.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I don't want to use IRES or 2A-peptide. I would like to be able to control this experiment in transcription stage.&lt;/p&gt;&#xA;" OwnerUserId="1772" LastEditorUserId="1772" LastEditDate="2015-10-22T03:34:50.603" LastActivityDate="2015-10-22T03:39:26.417" Title="What is the best way to express two proteins in a mammalian cell?" Tags="&lt;gene-expression&gt;&lt;lab-techniques&gt;&lt;eukaryotic-cells&gt;&lt;protein-expression&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7681" PostTypeId="2" ParentId="7676" CreationDate="2013-03-27T20:45:23.993" Score="5" Body="&lt;p&gt;Let's extend your idea a bit... Ok, there are conserved sequences that we may not know what their function is. Let's assume that they are indeed not functional and are some kind of message left by an ancient form of intelligence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How would you go about detecting that? It is already given that they are highly non-random, but this is not surprising and many &quot;non-message&quot; sequences have this property. Also consider that these sequences are quite short, meaning that they will have low information content. This means that if you check enough conversion codes and use imagination, you would probably be able to find several &quot;messages&quot; which are &quot;hidden&quot; there (e.g. &quot;bible codes&quot; etc). In other words, as I am a scientist that deals with probability and pattern recognition frequently, you will have a very hard time trying to convince me that you found a real hidden message... Formally, you don't have a satisfying background model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main difference from SETI is that there they know that their background is essentially random noise, so it is much easier to detect &quot;intelligent&quot; messages.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2013-03-28T02:59:57.333" LastActivityDate="2013-03-28T02:59:57.333" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7682" PostTypeId="1" AcceptedAnswerId="7687" CreationDate="2013-03-27T22:40:15.910" Score="5" ViewCount="9174" Body="&lt;p&gt;I had never heard the term before today. From what I can tell, it's using antibodies to purify a cell population of interest. I would appreciate more details, especially in how it differs from &quot;immunoprecipitation&quot; of cells via cell surface markers, and FACS.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="69" LastEditDate="2013-03-27T23:15:08.020" LastActivityDate="2013-03-28T14:58:51.737" Title="What is immunopanning (vs. immunoprecipitation and FACS)?" Tags="&lt;proteins&gt;&lt;lab-techniques&gt;&lt;terminology&gt;&lt;antibody&gt;&lt;cell-sorting&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7683" PostTypeId="1" CreationDate="2013-03-28T04:59:40.673" Score="2" ViewCount="232" Body="&lt;p&gt;The conditions are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;As extensive and explanatory as &lt;em&gt;Goodman and Gilman's The Pharmacological Basis of Therapeutics, Twelfth Edition&lt;/em&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;With additional extensive and thoroughly explanatory information on drugs (e.g. flupirtine, piracetam, nefopam, etc.) that are used elsewhere in the developed/semi-developed (like Russia or China) world (e.g. European countries) but not in the US.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Additional information about the medically recognised (in some of the world at least) herbs &lt;em&gt;cannabis sativa&lt;/em&gt; and &lt;em&gt;hypericum perforatum&lt;/em&gt; (St. John's wort; recognised in Germany).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If there is no such book then the European (or a European, like for instance the British equivalent. So long as said equivalent comes in English) equivalent of Goodman and Gilman's will be accepted. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-03-28T05:09:36.250" LastActivityDate="2020-09-01T11:01:15.193" Title="Is there a Pharmacology Textbook that Satisfies the Conditions listed in the Body of this Question?" Tags="&lt;pharmacology&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ClosedDate="2020-09-02T12:37:42.893" ContentLicense="CC BY-SA 3.0" />
  <row Id="7684" PostTypeId="2" ParentId="7647" CreationDate="2013-03-28T05:52:51.660" Score="6" Body="&lt;p&gt;Vegetables provide calories and don't kill you. For a hunter-gatherer, that's reason enough to eat them even if you don't like the flavor a lot. Finding nourishing foods &quot;repellent&quot; is a modern luxury. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, the bitter flavors in vegetables may be less noticeable to people who were not raised from infancy with hyperpalatable, sugar-sweetened food.&lt;/p&gt;&#xA;" OwnerUserId="827" LastActivityDate="2013-03-28T05:52:51.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7685" PostTypeId="1" AcceptedAnswerId="7692" CreationDate="2013-03-28T13:47:38.600" Score="2" ViewCount="114" Body="&lt;p&gt;What does &quot;Psychomodulatory&quot; mean in the context of potentially psychoactive drugs? That is, in this journal article &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0028390812001931&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0028390812001931&lt;/a&gt; in the discussion (you will need special privileges to access the article via an institute or personal subscription or by paying for access) in the last sentence of the first paragraph it says&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;However, euphol even when given in very high doses, (up to 100 mg/kg)&#xA;  it did not show any evidence of psychomodulatory effects in the CNS&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="69" LastEditDate="2013-03-29T12:03:22.767" LastActivityDate="2013-03-29T12:03:22.767" Title="What does &quot;Psychomodulatory&quot; mean in the context of potentially psychoactive drugs?" Tags="&lt;pharmacology&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7686" PostTypeId="1" CreationDate="2013-03-28T14:25:17.730" Score="2" ViewCount="1093" Body="&lt;p&gt;Evolution naturally produces better features: stronger muscles, teeth and minds. Killing the weakest, evolution wipes defective genes out of populations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mutations are necessary for advance. However, they are random and, thus, mostly negative. Right? How does the nature eliminate them from the population? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see that one mechanism is polygamy: male have higher mutation rates. They tend to reproduce as much as possible. Female have lower mutation rates, they couple with only with best men and contribute much more to their offsprings. So, men generate as much random solutions as possible, whereas the role of female is to conserve the best of them. This means that the most of the male (bad mutations) die unreproduced. This eliminates the bad mutations and favours the progress of good qualities. The higher animals started to form harems and tournaments over their ownership. This further fosters the elimination of weak men and profileration of strong genes. However, human monogamy has disabled this selection mechanism. Best men are dedicated to only one woman. Other women cannot mix their genes with other good genes from previous generations. They are forced to look at the low quality men, who carry degenerate mutations. Might be it is monogamy that makes us human but it implies that all genes reproduce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet 100 years ago it was not a big deal since we still had another filter: our grandfathers were born in families that had normally 10 children (I am speaking about Russia) and only 2-3 survived until reproduction (the population increased really slowly). I bet that those who survived had really good health: thanks to the bad health and immense selection pressure, the negative mutants are eliminated immediately and population maintains a perfect genome (aka biologic health). Killing more weakest in the current generation improves the health of next generations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However everything has changed during the 20th century. The advances in economy and medicine have almost eliminated the selection. The selection pressure has relaxed to essentially zero so that everybody survives and leaves the same amount of offspring (and &lt;a href=&quot;https://en.wikipedia.org/wiki/Dysgenics&quot; rel=&quot;nofollow noreferrer&quot;&gt;some scientists are even concerned that degradatory individuals leave more offsprings than the prosperous ones&lt;/a&gt;). We have even eliminated the infant mortality. We use baby incubators so that the people with the weakest health could survive and reproduce as normal and we are proud of it. It may sound strange but the mutation rate has not changed at all. Does it mean that the human genome is in danger?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see the situation like you have inherited a perfect mechanism and decided not recovering it from the inevitably adverse action of entropy, that degrades it constantly. There is a constant chance, &lt;em&gt;d&lt;/em&gt;, that every good gene is affected by a mutation. It is a fraction of healthy genes that will fail passing to the next generation. This will leave only &lt;em&gt;(1-d)&lt;/em&gt; genes healthy in the next generation. The fraction of healthy genes will melt like &lt;em&gt;1&lt;/em&gt;, &lt;em&gt;(1-d)&lt;/em&gt;, &lt;em&gt;(1-d)²&lt;/em&gt;, &lt;em&gt;(1-d)³&lt;/em&gt;, an so on, with every generation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dxBYl.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You see the fraction that stays healthy over generations. It decays exponentially. Any utility turns into entropy (aka garbage) exponentially, if not protected. Is this model correct? How quickly does this dissipation go? What is &lt;em&gt;d&lt;/em&gt;? Let's assume absolute survival and equality in the reproduction rate among all groups people. How many generations is needed to lose 50% of good qualities?&lt;/p&gt;&#xA;" OwnerUserId="3310" LastEditorUserId="3310" LastEditDate="2013-12-04T14:00:06.163" LastActivityDate="2013-12-04T14:00:06.163" Title="Effect of zero selection (pressure) on the population health" Tags="&lt;evolution&gt;&lt;genomes&gt;&lt;selection&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7687" PostTypeId="2" ParentId="7682" CreationDate="2013-03-28T14:58:51.737" Score="5" Body="&lt;p&gt;Immunopanning is essentially an &lt;a href=&quot;http://en.wikipedia.org/wiki/Immunoprecipitation&quot; rel=&quot;noreferrer&quot;&gt;immunoprecipitation&lt;/a&gt; (IP) of cells using an &lt;a href=&quot;http://en.wikipedia.org/wiki/Antibody&quot; rel=&quot;noreferrer&quot;&gt;antibody&lt;/a&gt; immobilized to a solid surface, like a &lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_culture&quot; rel=&quot;noreferrer&quot;&gt;cell culture&lt;/a&gt; plate. Conventionally, an IP is performed using small agarose or magnetic beads (~50 to 150μm in size) conjugated to an antibody or &lt;a href=&quot;http://en.wikipedia.org/wiki/Protein_A/G&quot; rel=&quot;noreferrer&quot;&gt;Protein A/G&lt;/a&gt;, and can pull down individual proteins, protein complexes, and/or nucleic acid complexes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cells are much larger than protein complexes, obviously, and for the most part much smaller than beads, but they can be damaged during a traditional IP, so immunopanning utilizes a single solid surface coated with the specific antibody or cell-surface protein ligand of choice. In &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18701692?dopt=Abstract&quot; rel=&quot;noreferrer&quot;&gt;this article&lt;/a&gt; (free PDF &lt;a href=&quot;http://www.jneurosci.org/content/28/33/8294.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;), &lt;a href=&quot;http://en.wikipedia.org/wiki/Axoplasmic_transport#Retrograde_transport&quot; rel=&quot;noreferrer&quot;&gt;retrograde axonal transport&lt;/a&gt; was used to selectively label specific populations of neuronal cells with the extracellular portion of &lt;a href=&quot;http://en.wikipedia.org/wiki/Cholera_toxin&quot; rel=&quot;noreferrer&quot;&gt;cholera toxin β&lt;/a&gt; (CTB) adsorbed to fluorescent beads, then the cells were purified using an immobilized anti-CTB antibody.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fluorescence-activated_cell_sorting#Fluorescence-activated_cell_sorting_.28FACS.29&quot; rel=&quot;noreferrer&quot;&gt;Fluorescence-Activated Cell Sorting&lt;/a&gt; or FACS is another way to purify cell populations. Cells are labeled with a &lt;a href=&quot;http://en.wikipedia.org/wiki/Fluorophore&quot; rel=&quot;noreferrer&quot;&gt;fluorescent marker&lt;/a&gt; (either conjugated to an antibody specific to an extra-cellular &lt;a href=&quot;http://en.wikipedia.org/wiki/Epitope&quot; rel=&quot;noreferrer&quot;&gt;epitope&lt;/a&gt;, via absorption as in the example above, or by expression of a fluorescent &lt;a href=&quot;http://en.wikipedia.org/wiki/Transgene&quot; rel=&quot;noreferrer&quot;&gt;transgene&lt;/a&gt; like &lt;a href=&quot;http://en.wikipedia.org/wiki/Green_fluorescent_protein&quot; rel=&quot;noreferrer&quot;&gt;GFP&lt;/a&gt;), then scanned in a flow cytometer. Cells which match certain parameters or &quot;gates&quot; in the machine's software are then diverted into a separate collection chamber, allowing for the generation of a quite pure cell population. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, as the authors point out in their paper above, FACS requires an expensive piece of equipment (can be over US$100,000), can be harsh on the cells, and is dependent on the availability of an antibody to a cell surface marker specific to the desired population of cells. Immunopanning is much less expensive, is more gentle on the cells, and in the authors' case was really the only choice for purifying their cell population of interest, as no specific biomarkers were available. It certainly won't replace FACS in the long run, but is another tool for investigators to use when studying specific cell types.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-03-28T14:58:51.737" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7688" PostTypeId="2" ParentId="7686" CreationDate="2013-03-28T15:12:39.763" Score="2" Body="&lt;p&gt;Even if a species lives in abundance, there is still an evolutionary arms race: who reproduces the fastest? Even slight advantages in reproduction rate multiply over the generations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are, however, cases where selection pressures on specific traits have vanished. For example, for fish living in caves, there is not selection pressure to be able to see, and &lt;a href=&quot;http://www.sciencedaily.com/releases/2007/02/070215144258.htm&quot; rel=&quot;nofollow&quot;&gt;they lost  their eyes&lt;/a&gt;. A more complete discussion can be found in this paper: &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0169534709001505&quot; rel=&quot;nofollow&quot;&gt;&quot;Relaxed selection in the wild&quot;&lt;/a&gt; -- see also &lt;a href=&quot;http://www.sciencedaily.com/releases/2009/09/090908103904.htm&quot; rel=&quot;nofollow&quot;&gt;this summary&lt;/a&gt; with a funny cover image of a species living in abundance.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2013-03-28T15:12:39.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7689" PostTypeId="2" ParentId="7686" CreationDate="2013-03-28T15:13:54.160" Score="7" Body="&lt;p&gt;I need to point out one thing, natural selection does not bring species to perfection.  The best mutant may not be selected for many reasons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you have no selection pressure then you have &lt;a href=&quot;https://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution&quot; rel=&quot;nofollow&quot;&gt;neutral evolution&lt;/a&gt; concurring and what takes over instead of natural selection is &lt;a href=&quot;https://en.wikipedia.org/wiki/Genetic_drift&quot; rel=&quot;nofollow&quot;&gt;genetic drift&lt;/a&gt;.  Genetic drift is just sample error.  Say you have 1,000 individuals in a population and all of those individuals reproduce, in the next generation all the genotypes would be in the next population.  Now imagine if you only had 10 individuals in the population and only 5 of those individuals were randomly selected to produce 10 individuals in the next generation (the parents die every year).  There is no selection pressure but just by chance some individuals reproduce and some don't.  If you do this over and over again what you will see is that some genes become fixed in the population, meaning that there is no other genotype in the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;https://en.wikipedia.org/wiki/Fixation_%28population_genetics%29&quot; rel=&quot;nofollow&quot;&gt;fixation&lt;/a&gt; at small population sizes can occur with either beneficial or deleterious mutations.  Obviously if a mutation is very deleterious the individual will die but &lt;a href=&quot;https://en.wikipedia.org/wiki/Nearly_neutral_theory_of_molecular_evolution&quot; rel=&quot;nofollow&quot;&gt;slightly deleterious mutations&lt;/a&gt; can become fixed in the population as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an entire field of biology devoted to this study.  It is called &lt;a href=&quot;https://en.wikipedia.org/wiki/Population_genetics&quot; rel=&quot;nofollow&quot;&gt;population genetics&lt;/a&gt;.  The probability for fixation for an allele is its proportion in the population.  This proportion can be calculated by 1/2N, where N is the population size.&lt;/p&gt;&#xA;" OwnerUserId="3247" LastEditorUserId="3632" LastEditDate="2013-03-29T14:24:02.287" LastActivityDate="2013-03-29T14:24:02.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7691" PostTypeId="1" AcceptedAnswerId="8299" CreationDate="2013-03-28T21:57:52.280" Score="1" ViewCount="137" Body="&lt;p&gt;I was reading up on KCNQ1, which encodes a voltage-gated potassium channel, and I discovered that it happens to be only maternally expressed. This is regulated by KCNQ1OT1, a non-coding RNA, which is also epigenetically regulated (expressed only paternally). Mutations in KCNQ1OT1 are associated with Beckwith-Wiedemann Syndrome (BWS).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further reading led to the discovery that there are &lt;a href=&quot;http://humrep.oxfordjournals.org/content/18/12/2508.long&quot; rel=&quot;nofollow&quot;&gt;ART-related (assisted reproductive technology) cases of BWS due to loss of methylation at KCNQ1&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, &lt;a href=&quot;http://journals2005.pasteur.ac.ir/NG2005/NG37%286%29/585%20-%20587.pdf&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; found epigenetic stability of KCNQ1OT1 methylation in cultured human embryonic stem cells, which leads me to think that KCNQ1 might also have been properly methylated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what exactly are assisted reproductive technologies doing that can disrupt inheritance of epigenetic marks (that culturing hESCs doesn't do)? (Is this understood for any gene?)&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-03-28T23:35:32.113" LastActivityDate="2013-05-11T14:51:14.533" Title="How might IVF (and related technologies) alter epigenetic marks?" Tags="&lt;reproduction&gt;&lt;epigenetics&gt;&lt;stem-cells&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7692" PostTypeId="2" ParentId="7685" CreationDate="2013-03-29T01:45:50.257" Score="1" Body="&lt;p&gt;To me, &quot;psychomodulatory&quot; would mean &quot;eliciting a significant change (up &lt;em&gt;or&lt;/em&gt; down) relative to baseline or compared to a control, placebo, or carrier,&quot; here specifically in CNS function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This statement appears to refer to the results presented in section 3.8, &lt;em&gt;Effect of euphol in the cannabinoid tetrad tests&lt;/em&gt;. Across a range of doses (3-100 mg/kg) and across four different assessments of CNS function: locomotor activity (rotarod), catalepsy (time to move off of a suspended ring), analgesia (tail flick in response to thermal stress), and body temperature (self explanatory). The results of these four are summarized in the figure below. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JZP2N.jpg&quot; alt=&quot;Results of four tests of CNS function&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically the effects are not significantly different from each other between dosages or times. The lines sit more or less atop one another. Compare to this figure, where the differences are significant:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9eMaH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-03-29T01:45:50.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7693" PostTypeId="1" AcceptedAnswerId="7696" CreationDate="2013-03-29T02:24:04.950" Score="1" ViewCount="2168" Body="&lt;p&gt;Some say that smoking cigarettes will shorten lifespan. By how many years is the lifespan of a typical smoker shortened? What are the common cause(s) of death among smokers? Are there any known statistics for cigarette smoking and life expectancy? &lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="3059" LastEditDate="2013-03-29T07:07:39.463" LastActivityDate="2013-03-29T07:35:50.577" Title="What's the difference between life expectancy of cigarette smoker and general population?" Tags="&lt;epidemiology&gt;&lt;smoking&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7694" PostTypeId="1" CreationDate="2013-03-29T03:00:14.810" Score="1" ViewCount="63" Body="&lt;p&gt;As an example, this &lt;a href=&quot;http://blogs.scientificamerican.com/observations/2013/01/24/adaptation-to-starchy-diet-was-key-to-dog-domestication&quot; rel=&quot;nofollow&quot;&gt;Scientific American article&lt;/a&gt; describes a known area in the dog genome that metabolizes carbohydrates.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is it that researchers are able to determine specific functions such as this?&lt;/p&gt;&#xA;" OwnerUserId="3292" LastEditorUserId="3292" LastEditDate="2013-03-29T03:10:22.570" LastActivityDate="2013-03-29T06:00:35.330" Title="How are geneticists able to isolate gene functions?" Tags="&lt;genetics&gt;&lt;genomics&gt;&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7695" PostTypeId="2" ParentId="7694" CreationDate="2013-03-29T06:00:35.330" Score="3" Body="&lt;p&gt;@LanceLafontaine suggested a few ways above, but I would recommend reading &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26818/&quot; rel=&quot;nofollow&quot;&gt;this section&lt;/a&gt;&#xA;in Alberts' Molecular Biology of the Cell, which gives a more descriptive overview of some approaches, but even that is not exhaustive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An extremely simplistic and also not exhaustive summary:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;observe mutants, see what processes are disrupted, and map these back to particular mutations&lt;/li&gt;&#xA;&lt;li&gt;mutate a gene and see what processes are disrupted&lt;/li&gt;&#xA;&lt;li&gt;biochemical studies to see, for example, which proteins (which are gene products) interact &lt;em&gt;in vivo&lt;/em&gt; and things like where they're localized, which may hint at function.&lt;/li&gt;&#xA;&lt;li&gt;analyze structure of proteins, see &lt;a href=&quot;http://en.wikipedia.org/wiki/Homology_%28biology%29&quot; rel=&quot;nofollow&quot;&gt;how similar they are to other proteins&lt;/a&gt; with known function, and infer that the protein of interest probably has a similar function&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;EDIT: The link to Alberts is to the 2002 edition (which is free online; the latest edition of the textbook costs around $200), so things have come a long way since then, but the underlying approaches are still in use.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-03-29T06:00:35.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7696" PostTypeId="2" ParentId="7693" CreationDate="2013-03-29T06:27:19.487" Score="5" Body="&lt;p&gt;The difference in life expectancy between smokers and non-smokers appears to be at least 10 years on average, in a &lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMsa1211128&quot; rel=&quot;nofollow noreferrer&quot;&gt;survey of American adults between 1997 and 2004&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same paper lists causes of death (higher among smokers than non-smokers, as measured by hazard ratio), although this is not exhaustive: lung cancer, other cancers, ischemic heart disease, stroke, other vascular disease, and respiratory disease have an adjusted hazard ratio of 1.7 or more, with 94% of lung cancer deaths attributable to smoking among female smokers, and 93% to smoking among male smokers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have access, you will probably find Table 2 (hazard ratios) of interest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 2 shows the survival probability:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/8zwy6.jpg&quot; alt=&quot;Survival probabilities - smokers vs non smokers&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-03-29T07:35:50.577" LastActivityDate="2013-03-29T07:35:50.577" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="7697" PostTypeId="1" AcceptedAnswerId="7698" CreationDate="2013-03-29T12:24:02.463" Score="6" ViewCount="734" Body="&lt;p&gt;This may be a stupid question showing my lack of understanding of taxonomy, but I was wondering if the current classification system we use contains broad enough categories to include new life forms, if they are discovered on other planets?  Would this depend on whether or not the new organisms could be shown to be evolutionarily related (eg have DNA), or are the highest levels of organization independent of relatedness and more dependent on physical similarity?&lt;/p&gt;&#xA;" OwnerUserId="2944" LastEditorUserId="43" LastEditDate="2013-03-29T18:29:09.580" LastActivityDate="2013-03-31T12:57:46.847" Title="If life is discovered on another planet, will it likely be classified using the current domain/kingdom/phylum system?" Tags="&lt;taxonomy&gt;&lt;astrobiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7698" PostTypeId="2" ParentId="7697" CreationDate="2013-03-29T13:37:19.017" Score="11" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are basically three highest taxonomic levels: bacteria, archaea and eukaryotes. Many sources distinguish only prokaryotes and eukaryotes, subdividing prokaryotes into bacteria and archaea. Other sources posit archaea as a third domain on the highest level. That's a long debate though and fortunately not the topic here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By appearance, the dual-domain system makes more sense because archaea and bacteria look very much alike under a microscope, and can both be clearly distinguished from eukaryotes (which have membrane bound nuclei). At the same time, comparing genetic structure and the protein machinery that interacts with DNA, eukaryotes and archaea are very similar and bacteria are clearly different from both of them. This demonstrates how appearance and molecular organisation have been typical criteria for distinction between branches of the evolutionary tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are, however, many features that even those three most basic branches of life share, and they are in no way simple or few in number. For example, all extant life uses DNA to store genetic information and proteins for almost all processes governing the various reactions going on at any time in a cell. However, RNA for example is able to perform both the information storing function of DNA as well as the catalytic functions of protein. This just shows how the principles behind life are not unique to the molecules in use now, and extraterrestrial &quot;life&quot; may work by the same principles on an entirely different molecular basis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Extraterrestrial life&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to know whether life found on another planet could be fit into our current classification system, the answer would be: &lt;em&gt;No, most likely it will not be classified using the current domain/kingdom/phylum system&lt;/em&gt;. This is because our system describes evolutionary descendency, so unless this newly found life shares some common ancestor with an organism on earth, it would have to be classified in an entirely new system. (Of course this is subjective as you may find it more likely that it does share a common ancestor&lt;a href=&quot;http://en.wikipedia.org/wiki/Panspermia&quot; rel=&quot;nofollow&quot;&gt; [Panspermia]&lt;/a&gt;, while I personally find it more likely that life would have evolved entirely separated on this other planet seeing as we haven't heard of any life within reasonable distance.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it is possible that this new life will follow the same evolutionary rules such as natural selection, and similar evolutionary pressures may drive to evolve similar properties. It may then be possible to draw parallels to characteristics of the current classification system, especially based on molecular function, and possibly appearance (micro- and macroscopically).&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-03-31T12:57:46.847" LastActivityDate="2013-03-31T12:57:46.847" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7699" PostTypeId="2" ParentId="7368" CreationDate="2013-03-29T14:22:50.373" Score="3" Body="&lt;p&gt;Not really an answer I know, but too long for the comments...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is still too broad a question.  a well sealed, sterile plastic usually has a use by date, but can probably be used more than a year after you receive it.  But these cases are not usually the issue.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its sterile medium and chemicals, each of which needs to have their own due date.  LB can be used months after autoclaving, but antibiotics break down chemically in weeks (ampicillin 1000x stocks lose their potency in a month).  Even in the refrigerator Agar plates show colonies after a couple of months and dry out quickly.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So more details would be necessary and the case by case policy is the rule.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;added in response to comments&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its really a matter of how well they are sealed. An autoclaved bottle will stay sterile forever, until something gets into the bottle - it depends on how well you have sealed things up and the storage conditions.  For stuff sterilized in lab I would tend to use it within a couple of months. For eppendorfs we'd tend to sterilize a few hundred in a beaker and not worry about them... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our experiments were working with purified protein were only medium sensitive to bio-contamination; they would be done in a few hours and then sterile filtered again.  If you were purifying RNA for instance you would be much more paranoid I'm sure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you start to see contamination I would lower the use date and or improve your protocol.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plastics that come sterilized and sealed by the manufacturer in 3-5 mil plastic bags have really long use by dates and I've used them for up to a year after we received them.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-03-30T14:35:00.573" LastActivityDate="2013-03-30T14:35:00.573" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="7700" PostTypeId="1" CreationDate="2013-03-29T14:51:49.850" Score="2" ViewCount="228" Body="&lt;p&gt;Fasting and Intermittent Fasting (IF) have been proven to start autophagy (cellular self-digestion). How long does the average man and woman have to wait for autophagy to begin? Does diet prior to fasting effect the onset of autophagy? And lastly, does longer fasting produce more efficient autophagy than IF?&lt;/p&gt;&#xA;" OwnerUserId="3316" LastActivityDate="2018-11-12T21:00:54.767" Title="Onset of Autophagy" Tags="&lt;cell-biology&gt;" AnswerCount="0" CommentCount="5" ClosedDate="2018-11-21T09:28:51.713" ContentLicense="CC BY-SA 3.0" />
  <row Id="7701" PostTypeId="1" CreationDate="2013-03-29T18:24:35.707" Score="1" ViewCount="1595" Body="&lt;p&gt;I am performing a gel extraction to purify DNA after a double digest with EcoRI and BamHI.  After the gel extraction I need to complete a ligation step before bacterial transformation.  The problem I am having is that the DNA after the gel extraction have some kind of chemical contaminant that won't allow me to quantify the DNA using the Nanodrop spectrophotometer.  I am getting very low 260/230 ratios.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has anyone had some issues with this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am using the Qiagen Qiaquick Gel Extraction Kit.&lt;/p&gt;&#xA;" OwnerUserId="3247" LastActivityDate="2013-03-29T20:55:29.190" Title="DNA gel extraction: chemical contaminants" Tags="&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7703" PostTypeId="1" CreationDate="2013-03-29T19:53:10.723" Score="1" ViewCount="1353" Body="&lt;p&gt;There is a lot of talk about inhumane treatment of animals and how we don't kill them in the proper way. I wonder how much research is done on this subject. What is the overall least painful way for an animal to die? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also wonder if this would be the same for a human. It is often said that its least painful to die in ones sleep and i wonder if this is true. I wonder what is the most humane way to execute a capital punishment (if that is at all possible) &lt;/p&gt;&#xA;" OwnerUserId="3318" LastActivityDate="2013-03-29T21:49:31.203" Title="Least painful way to die" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7705" PostTypeId="2" ParentId="7701" CreationDate="2013-03-29T20:55:29.190" Score="3" Body="&lt;p&gt;Here are some possible reasons:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Your yield is very low, which you can infer from a low 260 absorbance. Either make sure your restriction digest is efficient or add more substrate to the digest reaction. &lt;/li&gt;&#xA;&lt;li&gt;Carbohydrate contamination, which will cause high 230 absorbance. Wash the column one more time with buffer QG (the step is described in the &lt;a href=&quot;http://www.qiagen.com/Products/Catalog/Sample-Technologies/DNA-Sample-Technologies/DNA-Cleanup/QIAquick-Gel-Extraction-Kit#resources&quot; rel=&quot;nofollow&quot;&gt;Qiagen gel extraction manual&lt;/a&gt;; if you're already doing a wash with buffer QG, do an extra one).&lt;/li&gt;&#xA;&lt;li&gt;You didn't dry the column enough and some ethanol from the wash remains in the sample. This can also cause high 230 absorbance and your sample with smell of ethanol. Place your column in an empty collection tube and spin it down for a long time (15-20 min). Don't worry, the DNA can withstand it. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-03-29T20:55:29.190" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7706" PostTypeId="1" CreationDate="2013-03-29T21:28:56.780" Score="3" ViewCount="302" Body="&lt;p&gt;Typically we determine the concentration of proteins using a 280 nm reading. However, it is reasonable to use 205 nm. I was curious about the effectiveness of this method.&lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="3059" LastEditDate="2013-03-29T22:05:14.090" LastActivityDate="2013-04-05T05:23:42.463" Title="205 nm UV-Vis readings" Tags="&lt;molecular-biology&gt;&lt;proteins&gt;&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7707" PostTypeId="2" ParentId="7703" CreationDate="2013-03-29T21:49:31.203" Score="6" Body="&lt;p&gt;The American Veterinary Medical Association (AVMA) has thought about humane methods of euthanasia quite a bit and has an extensive (102 p. PDF) set of &lt;a href=&quot;https://www.avma.org/KB/Policies/Pages/Euthanasia-Guidelines.aspx&quot;&gt;guidelines for the euthanasia of animals&lt;/a&gt;. The guidelines are not the same for all animals. Some examples:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Companion animals (e.g., dogs and cats): injected barbiturates are recommended&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Laboratory animals (e.g., mice and rats): injected barbiturates are acceptable as are inhaled agents (isoflurane, carbon dioxide).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for humans, you might look into the physician assisted suicide literature. I think that these generally use a sequence of drugs. As far as natural deaths, kidney failure is supposed to not be very painful.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-03-29T21:49:31.203" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7708" PostTypeId="1" AcceptedAnswerId="7713" CreationDate="2013-03-29T22:32:51.810" Score="3" ViewCount="601" Body="&lt;p&gt;The obvious answer for a gene cluster is gene duplication and mutation of one or both genes. But the genes in the lac operon seem not be so functionally/structurally similar (as compared to the Hox gene cluster, for example), so I was curious as to how they ended up physically associated in the first place.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-03-30T14:45:36.200" Title="How might gene clusters like the lac operon evolve?" Tags="&lt;evolution&gt;&lt;genomics&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7709" PostTypeId="2" ParentId="7706" CreationDate="2013-03-30T00:25:04.193" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.ruf.rice.edu/~bioslabs/methods/protein/abs205.html&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; may be what you are looking for. The conversion formula is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;\text{Protein concentration (mg/ml)} = \frac{ (\text{Absorbance at 205 nm})} {31}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first, &lt;a href=&quot;http://xa.yimg.com/kq/groups/14971503/107426481/name/9.pdf&quot; rel=&quot;nofollow&quot; title=&quot;Scopes, RK. Analytical Biochemistry 59: 277. 1974.&quot;&gt;Scopes&lt;/a&gt;, does indicate that nucleic acid contaminants will confounding 205 nm absorbance readings. It seems as though this spetrophotometic calculation is feasible for relatively pure protein species.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2013-03-30T20:00:13.100" LastActivityDate="2013-03-30T20:00:13.100" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7710" PostTypeId="1" AcceptedAnswerId="7711" CreationDate="2013-03-28T22:01:54.250" Score="1" ViewCount="921" Body="&lt;p&gt;Let's say there is a luminous light bulb that only emits blue light, and you (or a camera if you prefer) look at it from a close distance. Will the maximum brightness perceived not have any &quot;white&quot; to it? Because there is no white light if it's all blue. Probably the brightest it could be would be solid blue? Therefore, blue photons could produce a range of color of black to solid blue depending on the luminous or amount of photons hitting your eye per second? If that's the case then what happens if you raised the intensity of the bulb to an extreme? Is there a cut off point where even if you add more intensity to the bulb, you still see the same solid blue color?&lt;/p&gt;&#xA;" OwnerUserId="3331" OwnerDisplayName="Dan Webster" LastEditorUserId="69" LastEditDate="2013-03-30T12:27:20.990" LastActivityDate="2013-03-30T12:27:20.990" Title="What is the brightest color a light source that only emits blue frequency light can achieve?" Tags="&lt;vision&gt;&lt;perception&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="7711" PostTypeId="2" ParentId="7710" CreationDate="2013-03-29T00:44:02.790" Score="4" Body="&lt;p&gt;The color that human vision perceives for a specific frequency of light (prior to saturation of any cones) is derived from the relative responses of different cones.  For example, at about 480nm, the response of S and M cones are roughly equal.  However, the human eye is not able to distinguish pure colors (single wavelengths) from combinations of wavelengths which produce the same response in each of the three cone types.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible that a blue light source could appear white to the human eye, because the cones which inform our perception of color are not strictly monochromatic.  Rather, they have a range of sensitivity across the spectrum, and all cones are at least somewhat sensitive to blue light.  (See &lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/0/04/Cone-fundamentals-with-srgb-spectrum.svg&quot; rel=&quot;nofollow&quot;&gt;this diagram&lt;/a&gt;.)&#xA;If the blue light is so intense that it saturates all cones, S (blue), M (green), and L (red), then it will be perceived as white light.  However, in order to saturate the low-sensitivity M and L cones, the intensity of the light would be blindingly high.  Prior to this point, but after saturating the S cones, the apparent color of the light would shift toward green before eventually appearing white.  For intensities that are not saturating to any cones, the &lt;a href=&quot;http://en.wikipedia.org/wiki/HSL_and_HSV#Hue_and_chroma&quot; rel=&quot;nofollow&quot;&gt;hue&lt;/a&gt; of the color blue will remain constant, while it's value (or lightness) may change.&lt;/p&gt;&#xA;" OwnerDisplayName="KDN" LastActivityDate="2013-03-29T00:44:02.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7712" PostTypeId="2" ParentId="3328" CreationDate="2013-03-30T12:54:35.423" Score="4" Body="&lt;p&gt;This stuff is so interesting! The instinctive behaviour is also known as a fixed action pattern or FAP which is a collection of well-defined motor patterns that are activated in response to a stimulus, i.e. a group more eleborate reflexes [2]. FAPs allow the brain to concentrate on other things as they don't need require time or energy to be thought about. The theory is they've been selected for because they decrease choice and decision time, which can be particularly important to survival.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some cool examples here (&lt;a href=&quot;http://www.cerebromente.org.br/n09/fastfacts/comportold_i.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.cerebromente.org.br/n09/fastfacts/comportold_i.htm&lt;/a&gt;).&#xA;&lt;img src=&quot;https://i.stack.imgur.com/GTzhS.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the bird is continues to perform parental instinctive behaviour in the absence of a brood of chicks because the similar stimulus of hungry open-mouthed fish is present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another article draws comparisons between different animals as to how much of their behaviour is fixed/pre-determined [3]. There can be a correlation between the size of the cerebral cortex, used for thinking and problem solving, and the amount of innate behaviour (i.e. the bigger your cortex the less you need to rely on pre-determined behaviours in certain situations). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These patterns seem to be for the most part genetically determined, however some studies with song-birds in the 70's demonstrated that a learning aspect can modify the innate behviour. Birds which have been reared in an environemnt where they cannot hear other birds of the same species sing still sing their typical song, but when allowed to hear others sing the song becomes more complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Investigating the genetic basis behind innate behaviours involve searching for Quantitative Trait Loci (QTLs) or stretches of DNA that contain genes (complex traits require the concerted actions of multiple genes) or are linked to genes that are involved in determining a specifc trait (in this case a behaviour). Classically this involves crossing two animals that differ in the trait you're interested in and looking at the segregation patterns in the offspring to try and pinpoint the specifc region of DNA/collection of genes that control the trait. I think quite a lot of this has been done in insects and mice which have high breeding rates and can be studied easily in the lab. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;...at this risk of making this answer ridiculously long I've just included a snippet from another website on behavioural genetics which details the OMIM and some of the traits you can search for[4]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Online Mendelian Inheritance in Man (OMIM) is a large, searchable, up-to-date database of human genes, genetic traits, and disorders. Each OMIM record contains bibliographic references and a summary of the scientific literature describing what is known about a particular gene, trait, or disorder. The following behavioral traits are included in OMIM. The six-digit number MIM number is used to uniquely identify each record.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Hand skill, relative (handedness): (139900)&#xA;Hand clasping pattern: (139800)&#xA;Arm folding preference: (107850)&#xA;Ears, ability to move: (129100)&#xA;Tongue curling, folding, or rolling: (189300)&#xA;Musical perfect pitch: (159300) &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;[2] &lt;a href=&quot;http://books.google.co.uk/books?id=aQvGXLPjMPAC&amp;amp;pg=PA44&amp;amp;lpg=PA44&amp;amp;dq=fixed+action+patterns+difference+reflex&amp;amp;source=bl&amp;amp;ots=TxaSYeIpTs&amp;amp;sig=RfsmHLWVlNiF8B-dH928-F0I5M8&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=Bs1WUZeCFYiZtAbZ_IHYBw&amp;amp;ved=0CDcQ6AEwAA#v=onepage&amp;amp;q=fixed%20action%20patterns%20difference%20reflex&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://books.google.co.uk/books?id=aQvGXLPjMPAC&amp;amp;pg=PA44&amp;amp;lpg=PA44&amp;amp;dq=fixed+action+patterns+difference+reflex&amp;amp;source=bl&amp;amp;ots=TxaSYeIpTs&amp;amp;sig=RfsmHLWVlNiF8B-dH928-F0I5M8&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=Bs1WUZeCFYiZtAbZ_IHYBw&amp;amp;ved=0CDcQ6AEwAA#v=onepage&amp;amp;q=fixed%20action%20patterns%20difference%20reflex&amp;amp;f=false&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[3] &lt;a href=&quot;http://www.grandin.com/references/genetics.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.grandin.com/references/genetics.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[4] &lt;a href=&quot;http://www.ornl.gov/sci/techresources/Human_Genome/elsi/behavior.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ornl.gov/sci/techresources/Human_Genome/elsi/behavior.shtml&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3261" LastActivityDate="2013-03-30T12:54:35.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7713" PostTypeId="2" ParentId="7708" CreationDate="2013-03-30T14:33:39.780" Score="5" Body="&lt;p&gt;Operons, often but not always, contain clusters of genes (under the control of an operator region) which are involved in the same metabolic pathway. There have been several theories for how these groups of genes have arisen but the current feeling seems to be based around the regulation of the genes in question &lt;a href=&quot;https://i.stack.imgur.com/QisJq.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;. To facilitate co-ordinated gene regulation there may have been strong selection for physical clustering of genes involved in a particular process. By being physically clustered this also means that all the genes within a given operon are probably subject to the same chromatin remodelling and will then be more easily switched on and off under the appropriate conditions i.e. all turned on when they are needed and switched off when they are not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Operons with similarly arranged genes have been found in different micro-organisms, leading to the thought that the operon was an ancient and evolutionarily conserved arrangement [2]. The figure below from Fani et al. 2005 presents two possible ways of generating the current state of genome organisation for present day proteobacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QisJq.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the operon is an ancient arrangement we would predict high gene conservation within operons; but genome analysis of different micro-organisms shows this not to be the case (i.e. gene conservation is low and operons are pretty unstable). Accordingly, another author suggests that due to the lack of conservation, operon structure is pretty plastic and can change readily during evolution [3]. Indeed, Fari et al conclude in their paper that the histidine biosynthesis operon has been a construction or re-construction event from scattered genes and not from the descent of an ancient arrangement:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our model suggests that the his gene organization in the extant proteobacteria arose from a gene scattering in the genome of the proteobacterial ancestor. The model also predicts that all or most of the his genes (except for hisD) were monofunctional and that they underwent a progressive clustering and compacting which occurred together with gene overlapping and fusion events&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They found, as you suggested, evidence for several gene modifications which included elongation, duplication and gene fusions. As for what caused the progressive clustering, see reference &lt;a href=&quot;https://i.stack.imgur.com/QisJq.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt; again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously different operons are probably going to have formed in different ways in different organisms and I don't think we can rule out the 'ancient arrangement' argument completely. It's a pretty broad and confusing topic and there's a lot of literature, I hope the examples I picked and have listed are useful!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/QisJq.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt; Osbourn, A. and Field, B. Operons. Cell. Mol. Life Sci. (2009) 66:3755–3775&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] Fani et al. The Origin and Evolution of Operons: The Piecewise Building of theProteobacterial Histidine Operon. J Mol Evol (2005) 60:378–390&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[3] Itoh et al. Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol Biol Evol (1999) 16(3):332–346&lt;/p&gt;&#xA;" OwnerUserId="3261" LastEditorUserId="3261" LastEditDate="2013-03-30T14:45:36.200" LastActivityDate="2013-03-30T14:45:36.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7714" PostTypeId="2" ParentId="7633" CreationDate="2013-03-30T22:32:48.193" Score="4" Body="&lt;p&gt;It's old and I can't get access to &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/nyas.1963.111.issue-1/issuetoc&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; issue of the Annals of the New York Academy of Science, but it looks like it has some relevant information. Sifting through the abstracts it seems the vasculature of the fetal liver is completed at around &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1963.tb36952.x/abstract&quot; rel=&quot;nofollow&quot;&gt;8 weeks&lt;/a&gt; although is still different to the adult vasculature because of the umbilical vein. The growth of the organ itself goes through different stages with each lobe growing different amounts:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;They start the same size&lt;/li&gt;&#xA;&lt;li&gt;12 weeks the left lobe is twice as large as the right&lt;/li&gt;&#xA;&lt;li&gt;36 weeks the left is 10% larger than the right&lt;/li&gt;&#xA;&lt;li&gt;at birth they are the same size&lt;/li&gt;&#xA;&lt;li&gt;5days after birth the right is 10% larger&lt;/li&gt;&#xA;&lt;li&gt;adults, they are the same size&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And, studies have been conducted with dyes to look at liver function in both its capacity to concentrate the dyes and secrete it into the bile. The fetal liver &lt;em&gt;can&lt;/em&gt; carry out bile acid synthesis, despite lacking digestive purposes, from very early on (Suchy et al. 1987). The fetus does however require help in removing the toxic cholephilic organic anions (COAs), which is done via the placenta. &lt;a href=&quot;http://www.annalsofhepatology.com/PDF/vol4n2/Hp052-02.pdf&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; review describes more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1963.tb36958.x/abstract&quot; rel=&quot;nofollow&quot;&gt;evidence&lt;/a&gt; to suggest the newborn's liver is not performing all the usual metabolic processes of children or adults (from looking at drug toxicity and delays in excretion/detoxification), as would be expected. More &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10665839&quot; rel=&quot;nofollow&quot;&gt;recent literature&lt;/a&gt; notes the fetal liver lobes (right and left) as having differnt biochemical capacities and independent function due to the right one getting less oxygen. Also, a layer of drug metabolising enzymes normally present in adults is missing in the fetal liver, although its capacity for drug metabolism is still better than that of rodents.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the adult liver, there is a clear zonation of metabolism of carbohydrates, proteins, lipids, and bile salts. In the livers of fetal rats, mice, and humans, this heterogeneous distribution of enzymes and metabolic function does not exist initially. Towards the end of gestation, the adult pattern of heterogeneity for these processes begins to emerge, and after birth, the adult pattern is rapidly established (Ring &lt;em&gt;et al&lt;/em&gt;. 1999)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is in vitro evidence for the activity of glutathione S-transferase and sulfotransferases in the human fetal liver. Returning to the asymmetry of fetal liver function (albeit in sheep..) it was found that levels of malondialdehyde, an index of lipid peroxidation, oxygen consumption, and CYP levels (a family of oxidative enzymes), are higher in the left lobe than the right lobe of the fetal liver which evens out after birth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in conclusion, looks like a variety of metabolic enzymes are present in the human fetal liver from very early on after the organ is formed. We know a varitey of metabolic enzymes are present and the drug/dye metabolism studies show there is some fetal liver activity, albeit reduced from that of an adult or child. The limitation with many of the studies that have been done is that they have to use in vitro data and extrapolate to the in vivo situation, so I guess we still don't really know for sure how metabolically active it is. It is clear though that it remains inefficient and unable to carry out all the functions required of it during childhood/adulthood until after further development after birth when it has stopped growing and adapted to ex utero conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ring JA, Ghabrial H, Ching MS, Smallwood RA, Morgan DJ. Fetal hepatic drug elimination. Pharmacol Ther. 1999 Dec;84(3):429-45.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suchy FJ, Bucuvalas JC, Novak DA. Determinants of bile formation during development: Ontogeny of hepatic bile acid metabolism and transport. Semin Liver Dis 1987; 7(2): 77-84&lt;/p&gt;&#xA;" OwnerUserId="3261" LastActivityDate="2013-03-30T22:32:48.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7715" PostTypeId="2" ParentId="2588" CreationDate="2013-03-30T23:03:25.433" Score="5" Body="&lt;p&gt;The basal lamina, a specialised type of extracellular matrix (ECM) that differs between cell types, acts as a base for stratified epithelia cells to layer on top of and therefore has a supportive role as well as providing a base for attachment (for the layer of cells immediately on top of it) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773636/&quot;&gt;1&lt;/a&gt;. Layers of epithelial cells on top of further strata of similar cells with no differing tissue composition underneath would have no support and cell types would be able to mix freely within tissues. The different cell types within tissues are kept seperate by this ECM to maintain areas for specific functions. The importance of this can be seen through studying epithelial cancers, where the epithelial cell layer breaks through the entire basement membrance and invades the surrounding tissue. This can cause massive disruption of tissue function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, it seems that the layers of cells are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773636/&quot;&gt;attached&lt;/a&gt; by various junctional complexes, the desmosomes (maculae adherentes) being the most abundant for stratified epithelia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Referenes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773636/&quot;&gt;1&lt;/a&gt; &lt;a href=&quot;http://www.histology.leeds.ac.uk/tissue_types/connective/con_basal_lam.php&quot;&gt;http://www.histology.leeds.ac.uk/tissue_types/connective/con_basal_lam.php&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3261" LastActivityDate="2013-03-30T23:03:25.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7716" PostTypeId="1" AcceptedAnswerId="8036" CreationDate="2013-03-31T07:53:12.337" Score="0" ViewCount="230" Body="&lt;p&gt;If you would like more specifics seeing how I realise that this question is very broad and may be difficult to answer in general then hopefully the following will help you out:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;I am particularly interested in acetyl groups bound by carbon single bonds&lt;/li&gt;&#xA;&lt;li&gt;Drug metabolism in the liver particularly interests me&lt;/li&gt;&#xA;&lt;li&gt;The drug paracetamol's (acetaminophen) deacetylation to p-aminophenol is of particular interest to me.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-03-31T08:16:09.003" LastActivityDate="2013-04-23T04:11:36.947" Title="Which Enzymes Catalyse the Deacetylation of Drugs in the Human Body?" Tags="&lt;pharmacology&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7718" PostTypeId="1" AcceptedAnswerId="7724" CreationDate="2013-03-31T20:13:29.687" Score="8" ViewCount="679" Body="&lt;p&gt;I'm writing a little article and need any information about how human vision works and latest &#xA;technologies and discoveries around. Actually its not a professional article. Its for a group of my friends.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact I'm looking for any possible way to make someone ACTUALLY see when their eyes are closed. I don't know maybe convince some of brain cells that a real pulse is coming from eyes, but in reality its coming from a computer; or something like that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I call it a virtual vision, myself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you guys know if there's any professional article, discoveries or technologies available about this topic?&#xA;I'm very very interested in this topic by the way.&lt;/p&gt;&#xA;" OwnerUserId="3322" LastEditorUserId="69" LastEditDate="2013-03-31T23:29:38.130" LastActivityDate="2018-06-05T03:50:03.580" Title="Is it technically possible to make someone see something when their eyes are closed?" Tags="&lt;neuroscience&gt;&lt;eyes&gt;&lt;vision&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7719" PostTypeId="2" ParentId="7556" CreationDate="2013-03-31T23:40:10.920" Score="10" Body="&lt;p&gt;For climate related data you can start from &lt;a href=&quot;http://www.realclimate.org/&quot;&gt;Realclimate&lt;/a&gt; pages on data repository. For ecological data I always found less global data, but a good starting point may be the &lt;a href=&quot;http://data.esa.org/esa/style/skins/esa/index.jsp&quot;&gt;Ecological Society of America Data Registry&lt;/a&gt; page. An overview of repositories can be found the the Simmons University &lt;a href=&quot;http://oad.simmons.edu/oadwiki/Data_repositories&quot;&gt;Open Access Directory&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3323" LastEditorUserId="107" LastEditDate="2013-04-01T00:34:41.563" LastActivityDate="2013-04-01T00:34:41.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7720" PostTypeId="2" ParentId="2638" CreationDate="2013-04-01T00:11:10.363" Score="1" Body="&lt;p&gt;I may suggest to give a look to game theory based model and their generalization from homogenous spatial diatribution to network like model. An easy review can be found in Martin A. Nowak's &lt;em&gt;Evolutionary Dynamics&lt;/em&gt; (Harvard press 2006).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular you can see the classical Moran process as an evolutionary graph game going on a complete graph with identical weights. Changing the topology of the graph can give different results, though it is not necessary (and there're results showing in which case a graph behave just as a Moran process).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Graph related behaviour are, i.e., suppressing or amplifier of selection...&lt;/p&gt;&#xA;" OwnerUserId="3323" LastActivityDate="2013-04-01T00:11:10.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7721" PostTypeId="1" AcceptedAnswerId="10588" CreationDate="2013-04-01T01:37:13.263" Score="4" ViewCount="4977" Body="&lt;p&gt;First off, I don't know if this is a normal healthy thing to occur. There have been many times where I have an itch on say my arm and I scratch it, only to feel the scratching elsewhere on my body. I assume somewhere along the transit of the touch signals to my brain the signal gets mixed up and is processed incorrectly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my questions are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why does this mixup happen? &lt;em&gt;(chemical imbalance, damaged nerves, etc..)&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;How does my brain correspond the touch to somewhere else? &lt;em&gt;(what is the process behind it)&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1827" LastEditorUserId="3059" LastEditDate="2013-04-03T17:05:11.983" LastActivityDate="2018-12-29T11:01:20.123" Title="Why Do Nerve Signals Get Crossed?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;sensation&gt;&lt;pain&gt;" AnswerCount="2" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="7722" PostTypeId="2" ParentId="7718" CreationDate="2013-04-01T03:57:52.667" Score="0" Body="&lt;p&gt;I am not an expert on this subject, but essentially what you would need is to have a machine interface directly with neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neuro-mechanical interface is something which interests many scientists but unfortunately we are only at extremely early stages - even getting accurate readings from a single neuron in vivo is a very challenging task. To achieve virtual vision you would need both technology to accurately interface with many many neurons and to fully understand how the neurons encode visual information. I think these are huge challenges so it will probably take a while to get there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Until then I guess we will have to stick with VR glasses...&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2013-04-01T03:57:52.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7723" PostTypeId="1" AcceptedAnswerId="7725" CreationDate="2013-04-01T04:14:05.087" Score="0" ViewCount="51" Body="&lt;p&gt;I recall reading around one in four cancer patients will suffer a paraneoplastic syndrome during the course of their illness but I can't find where I read this and I can't find any reliable sources to back this up. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-04-01T15:38:10.257" Title="How Common are Paraneoplastic Syndromes in Cancer Patients?" Tags="&lt;cancer&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7724" PostTypeId="2" ParentId="7718" CreationDate="2013-04-01T12:03:27.223" Score="5" Body="&lt;p&gt;Yes, this is most certainly possible and already being done. As long as the visual cortex of the brain (in the occipital lobe, i.e. at the back of your head) is functional, the correct stimulation will produce visual perception.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In cases of blindness caused by malfunction of the retina, meaning that the rest of the visual pathway is functional, this is the most promising approach to restoring vision. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Visual_prosthesis&quot; rel=&quot;nofollow&quot;&gt;Visual prosthesis&lt;/a&gt; and the &lt;a href=&quot;http://www.ted.com/talks/sheila_nirenberg_a_prosthetic_eye_to_treat_blindness.html&quot; rel=&quot;nofollow&quot;&gt;TED talk on it&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Virtual vision&quot; as in projecting a whole field of vision (reflecting the real surroundings) is the big ideal target that this technology is aiming for. Of course as soon as they manage to make a working prosthesis for blind people, someone will probably try to make it non-invasive and easily usable for commercial exploitation.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-04-01T16:59:39.927" LastActivityDate="2013-04-01T16:59:39.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7725" PostTypeId="2" ParentId="7723" CreationDate="2013-04-01T15:38:10.257" Score="1" Body="&lt;p&gt;The incidence of paraneoplastic syndromes appears to be variable and dependent on the kind of cancer. Estimates by Baijens and Manni (2006; &lt;a href=&quot;http://link.springer.com/article/10.1007/s00405-005-0942-1&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Eur Arch Otorhinolaryngol&lt;/em&gt; 263: 32–36&lt;/a&gt;) are 1% to 7.4% of all cancer patients, however they are citing Gulya (1993; &lt;em&gt;Laryngoscope&lt;/em&gt; 103: 754–761) and Zuffa et al. (1984; &lt;em&gt;Neoplasma&lt;/em&gt; 31: 231–236) for the data. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pelosof and Gerber (2010; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2931619/&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Mayo Clin Proc&lt;/em&gt; 85: 838–854&lt;/a&gt;) make the particularly salient observation that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As patients with cancer live longer, and as diagnostic methods&#xA;  improve, this prevalence will likely increase.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-04-01T15:38:10.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7726" PostTypeId="1" CreationDate="2013-04-01T16:22:22.757" Score="4" ViewCount="66" Body="&lt;p&gt;I'm studying habitat use by Brent Goose in the UK, a species that feeds on maritime vegetation. It's main food types are &lt;em&gt;Zostera&lt;/em&gt; sp., &lt;em&gt;Ruppia&lt;/em&gt; sp., &lt;em&gt;Ulva&lt;/em&gt; / &lt;em&gt;Enteromorpha&lt;/em&gt; sp. and &lt;em&gt;Puccinellia&lt;/em&gt; sp. I plan to map these vegetation types on an inter-tidal mudflat in North-east England during the summer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to choose a month to map these vegetation types that will allow the most accurate mapping of their distribution of vegetation across the mudflat. I think there are two considerations 1. the month they easiest to identify 2. the month they are most visible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which month should I choose?&lt;/p&gt;&#xA;" OwnerUserId="1216" LastEditorUserId="107" LastEditDate="2013-04-01T17:50:58.547" LastActivityDate="2014-03-07T20:52:39.973" Title="In which month should I map maritime vegetation?" Tags="&lt;ecology&gt;&lt;vegetation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7727" PostTypeId="2" ParentId="7718" CreationDate="2013-04-01T16:54:12.047" Score="1" Body="&lt;p&gt;One of the things that you could also consider are the experiments done with LSD: if I recall correctly, LSD (or drugs coming from certain mushrooms) cross your neural circuits. You end up &quot;smelling what you see&quot;, and &quot;seeing what you smell&quot;, etc. In this sense, you would be able to see with your eyes closed, although this is a very particular (yet, interesting) case&lt;/p&gt;&#xA;" OwnerUserId="3324" LastActivityDate="2013-04-01T16:54:12.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7728" PostTypeId="1" AcceptedAnswerId="7730" CreationDate="2013-04-01T19:23:08.433" Score="18" ViewCount="2337" Body="&lt;p&gt;Every time I make fajitas, I cut into bell and chili peppers and notice how hollow they are.  I always think to myself: &lt;em&gt;what is the gas inside this pepper, and how does it get there?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps Capsicum peppers are porous.  I did a little kitchen experiment to try to find out.  (I'm afraid I don't know much about biology, so this &quot;experiment&quot; is likely to be flawed in at least one basic way, but I figured I should at least &lt;em&gt;try&lt;/em&gt; to figure it out myself before asking.)  Here's what I did:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I filled a small container with water and submerged an uncut Anaheim pepper.  It was quite buoyant!  I put the lid on the container so it would stay submerged.  It didn't seem to become any less buoyant, and its interior didn't seem to fill up with water.  No bubbles emerged from the pepper, as least as far as I could tell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So air doesn't seem to easily pass in or out of the pepper.  And of course they don't grow &lt;em&gt;around&lt;/em&gt; air, so how does the gas get in?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are my guesses:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The fruit &lt;em&gt;is&lt;/em&gt; porous to air, but the holes are small enough that, in my experiment, they were sealed by the surface tension of the water.&lt;/li&gt;&#xA;&lt;li&gt;The fully &lt;em&gt;isn't&lt;/em&gt; porous to air when fully grown, but it &lt;em&gt;is&lt;/em&gt; porous to air while it's still developing.&lt;/li&gt;&#xA;&lt;li&gt;The fruit does some amount of photosynthesis, and the air is waste oxygen.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user3325" LastActivityDate="2020-06-08T17:16:02.223" Title="What is the gas inside a Capsicum pepper, and how does it get there?" Tags="&lt;fruit&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7730" PostTypeId="2" ParentId="7728" CreationDate="2013-04-01T20:41:20.240" Score="13" Body="&lt;p&gt;To answer your question of what the gas is, how about the &lt;a href=&quot;http://www.youtube.com/watch?v=lohKLYbZp6Q&quot; rel=&quot;noreferrer&quot;&gt;glowing splint test&lt;/a&gt; for oxygen! I guess it might work with a recently snuffed out match too. Cut a plug in the the pepper but leave it in place until you have the glowing match ready, then quickly open the plug and hold the match into the opening. It should relight if it is oxygen and you may hear a popping noise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for whether the surface tension is preventing the flow of air, you could try adding some detergent (washing up liquid or soap) to the water to break the tension and see what happens. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I have found an article suggesting the environment is, compared to the standard atmospheric concentration anyway, low in O2 and high in CO2 in two different pepper cultivars.&lt;a href=&quot;http://www.youtube.com/watch?v=lohKLYbZp6Q&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Samples withdrawn from the fruit locule over time show that CO2 ranges between 0.5% and 3% (5000–30,000μmol·mol–1) (Fig. 2, top) while O2 ranges between 18% and 20% (Fig. 2, center), compared to the composition of standard atmosphere (400μmol·mol–1CO2; 21% O2)  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Rxeta.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=lohKLYbZp6Q&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt; Blasiak, J., Kuang, A., Farhangi, C.S., and Musgrave, M.E. Roles of Intra-fruit Oxygen and Carbon Dioxide in Controlling Pepper (Capsicum annuum L.) Seed Development and Storage Reserve Deposition. J. AMER. SOC. HORT. SCI. (2006) 131(1):164–173. &lt;/p&gt;&#xA;" OwnerUserId="3261" LastEditorUserId="3261" LastEditDate="2013-04-01T21:23:12.743" LastActivityDate="2013-04-01T21:23:12.743" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7731" PostTypeId="1" CreationDate="2013-04-02T01:34:08.030" Score="1" ViewCount="2440" Body="&lt;p&gt;I am currently taking a biology class. I do not understand this concept. I understand that the electrostatic repulsion of the negative charges, resonance stabilization and hydration stabilization all contribute. However, I do not understand why an increase in entropy would help. Wouldn't it be more favorable to have less entropy in a system?&lt;/p&gt;&#xA;" OwnerUserId="3090" LastEditorUserId="3059" LastEditDate="2013-04-02T04:19:52.830" LastActivityDate="2013-04-03T15:47:48.270" Title="Why does the hydrolysis of ATP increasing entropy increase the Phosphoryl-­‐transfer Potential?" Tags="&lt;molecular-biology&gt;&lt;metabolism&gt;&lt;thermodynamics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7732" PostTypeId="1" CreationDate="2013-04-02T05:00:42.953" Score="2" ViewCount="240" Body="&lt;p&gt;EGFR (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/1956&quot; rel=&quot;nofollow&quot;&gt;epidermal growth factor receptor&lt;/a&gt;) has been intensively studied in cancer and treatments have been developed to inhibit EGFR signaling.  Sialylation of EGFR is known to block dimerization  and down regulate signaling.  I just read this paper:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.1107385108&quot; rel=&quot;nofollow&quot;&gt;Liu et al. 2011. Sialylation and fucosylation of epidermal growth factor receptor suppress its dimerization and activation in lung cancer cells. PNAS 108: 11332–11337&lt;/a&gt;. (basically just read conclusion if you don't have time). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I don't understand is that the authors seem to say that increasing sialylation might be a good thing to prevent cancer progression since it inhibits EGFR dimerization.  However, wouldn't this go against almost 50 or 60 years of research that suggest that increased levels of sialic acid are one of the well known hallmarks of cancer that aid in its progression and metastasis?  What could explain this apparent discrepancy? &lt;/p&gt;&#xA;" OwnerUserId="3232" LastEditorUserId="107" LastEditDate="2013-04-02T12:52:09.093" LastActivityDate="2013-04-02T18:08:11.833" Title="EGFR, sialylation, and cancer progression" Tags="&lt;cancer&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7734" PostTypeId="1" CreationDate="2013-04-02T14:20:04.760" Score="6" ViewCount="1481" Body="&lt;p&gt;I am looking for studies on how many protein isoforms have different functions, preferably in human. We know that a great many, if not most, of human genes are alternatively spliced and that many produce different protein isoforms. Has anyone looked at how many of these isoforms have different cellular functions? If someone could point me to a published paper, that would be great.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If no such study has been made, can anyone recommend a database from which this information could be extracted? GeneOntology is gene based so the information cannot be found there. Genes will be annotated to specific terms, not their protein isoforms. Also, I would need to be able to do this in a high throughput manner, I am not interested in specific proteins but in what percentage of all isoforms have different functions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ideally, I would like to be able to extract, for every human gene, the list of the different protein isoforms it encodes and whether their functions differ, or at least what those functions are. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-07-26T00:42:09.247" Title="What percentage of protein isoforms have different functions?" Tags="&lt;bioinformatics&gt;&lt;isoforms&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7735" PostTypeId="1" CreationDate="2013-04-02T15:06:44.257" Score="5" ViewCount="1431" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/1724/why-do-eukaryotic-organisms-have-introns-in-their-dna&quot;&gt;This question on the function of introns in eukaryotic genes&lt;/a&gt; made me think: I know that more basal organisms have smaller introns and fewer alternatively spliced exons compared to mammals. But are there eukaryotes whose genomes have no introns at all? &lt;/p&gt;&#xA;" OwnerUserId="3053" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-04-04T19:23:03.110" Title="Are there eukaryotes without introns?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7736" PostTypeId="1" AcceptedAnswerId="7746" CreationDate="2013-04-02T15:09:10.733" Score="0" ViewCount="1404" Body="&lt;p&gt;Can some one give a simple explanation or definition on what a &lt;strong&gt;dye-reduction test&lt;/strong&gt; is.&lt;/p&gt;&#xA;" OwnerUserId="3329" LastEditorUserId="3059" LastEditDate="2013-04-02T20:23:04.683" LastActivityDate="2013-04-03T07:59:12.253" Title="Definition of Dye- Reduction Test?" Tags="&lt;biochemistry&gt;&lt;genetics&gt;&lt;pharmacology&gt;&lt;microbiology&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7737" PostTypeId="2" ParentId="7732" CreationDate="2013-04-02T18:08:11.833" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sialic_acid#Function&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; claims (without reference) that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Metastatic cancer cells often express a high density of sialic&#xA;  acid-rich glycoproteins. This overexpression of sialic acid on&#xA;  surfaces creates a negative charge on cell membranes. This creates&#xA;  repulsion between cells (cell opposition)[5] and helps these&#xA;  late-stage cancer cells enter the blood stream.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;so I assume this is a summary of the &quot;50 or 60 years of cancer research&quot; that you mentioned. I don't doubt you, I've just never read up on this particular aspect of cancer. Be that as it may, there is a difference between a cell's expressing high levels of sialoglycoproteins overall, and inducing high sialylation of one protein in particular, in this case EGFR. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you may be aware, &lt;a href=&quot;http://en.wikipedia.org/wiki/Epidermal_growth_factor_receptor#Function&quot; rel=&quot;nofollow&quot;&gt;EGFR dimerization&lt;/a&gt; induced by multiple methods, including EGF binding, overexpression, mutation, chemical or antibody crosslinking, etc. activates &lt;a href=&quot;http://en.wikipedia.org/wiki/Tyrosine_kinase&quot; rel=&quot;nofollow&quot;&gt;tyrosine kinase&lt;/a&gt; domains in its intracellular region to auto-&lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphorylation&quot; rel=&quot;nofollow&quot;&gt;phosphorylate&lt;/a&gt; specific Tyr residues in its tail, which then recruit adapter and scaffolding proteins which support downstream &lt;a href=&quot;http://en.wikipedia.org/wiki/Signal_transduction&quot; rel=&quot;nofollow&quot;&gt;signal transduction&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper you read shows how increasing sialylation of EGFR reduces its &lt;em&gt;trans&lt;/em&gt;-affinity for itself and inhibits dimerization, and hence the downstream signaling cascade. This is a good thing in certain types of cancer which are driven by aberrant EGFR signaling, whether through overexpression of EGF and/or EGFR, mutations in the kinase domains, mutations in the dimerization domains, or otherwise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This paper is also a great example of an apparent bad thing turning out to be good, when properly targeted and controlled. Excess sialylation of a cell may be bad, but specific over-sialylation of EGFR could turn out to be very useful, if we can learn how to modulate and target it. Another common example of this phenomenon is &lt;a href=&quot;http://en.wikipedia.org/wiki/Radiation_therapy&quot; rel=&quot;nofollow&quot;&gt;radiation therapy&lt;/a&gt;. Normally, high levels of radiation are bad for your body, and can actually cause cancer, among a range of other &lt;a href=&quot;http://en.wikipedia.org/wiki/Radiation_sickness&quot; rel=&quot;nofollow&quot;&gt;illnesses&lt;/a&gt;. But, there are many different ways of specifically targeting radiation to a tumor to kill it while sparing (to varying degrees) the surrounding tissue and the rest of the body. &lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-04-02T18:08:11.833" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7738" PostTypeId="2" ParentId="7734" CreationDate="2013-04-02T18:26:24.997" Score="0" Body="&lt;p&gt;I would take a look at &lt;a href=&quot;http://www.uniprot.org/&quot; rel=&quot;nofollow&quot;&gt;UniProt&lt;/a&gt; to begin with. It's my go-to whenever I need to look for isoforms or functional data, so it should help you as well. You could start by comparing the information in Swiss-Prot to TrEMBL, which are manually and automatically annotated, respectively. One issue that I've come across in my research on isoforms is that there often isn't a great deal known about them, as studies may have focused on just one or a few out of many possible. One way to get around this could be to use structure/function predictions based on sequence, then try to predict variations by looking at what's added or missing in the various isoforms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps...&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-04-02T18:26:24.997" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7739" PostTypeId="1" AcceptedAnswerId="7740" CreationDate="2013-04-02T19:07:32.040" Score="2" ViewCount="1470" Body="&lt;p&gt;I am conducting a mutagenesis on a gene in vivo of which I need to ligate into an expression vector.  The primers I have designed overlap restriction sites of which I plan to use to ligate into the expression vector.  The parts between the primers I will try to create mutants with error prone PCR.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My concern is the 3' A overhangs that are created from Taq polymerase.  How prevalent is this?  If it is highly common, what is the best way to account for these additions when trying to ligate my PCR product into the vector?&lt;/p&gt;&#xA;" OwnerUserId="3247" LastActivityDate="2013-04-03T22:03:32.790" Title="How prevalent is Taq polymerase in adding 3' A overhangs to the PCR product?" Tags="&lt;pcr&gt;&lt;experimental-design&gt;&lt;restriction-enzymes&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7740" PostTypeId="2" ParentId="7739" CreationDate="2013-04-02T20:19:08.460" Score="2" Body="&lt;p&gt;I am not sure of a case where Taq &lt;em&gt;doesn't&lt;/em&gt; add 3' A overhangs.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could use TA cloning to clone your PCR product.  The basic principle is to use a vector with 3' T overhangs.  If you have a vector without these overhangs, you can use a terminal transferase + dTTPs to create them (or even Taq, but this is not as great because it adds a purification step to isolate the vectors with overhangs; terminal transferase is much more efficient).  You can then ligate your PCR product that has a 3' overhang.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Protocols for adding the 3' T overhangs to your vector are given in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11464915&quot; rel=&quot;nofollow&quot;&gt;Zhou and Gomez-Sanchez 2000&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-03T22:03:32.790" LastActivityDate="2013-04-03T22:03:32.790" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7741" PostTypeId="1" AcceptedAnswerId="7744" CreationDate="2013-04-02T23:40:27.853" Score="1" ViewCount="371" Body="&lt;p&gt;The iris contracts automatically in the presence of bright light. This makes a flashlight appear bright in darkness, but outside in daylight you can't even see it's light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The iris is changing your sensitivity to the intenseness of light. But physically all is happening is the iris is getting smaller or larger. I can see how this allows less light to go in if it gets smaller, because it's less surface area. However, I would imagine this would change the field of view though if I didn't know any better. Why does it change the intenseness of light instead?&lt;/p&gt;&#xA;" OwnerUserId="3331" LastActivityDate="2013-04-03T00:29:31.230" Title="Why does contracting the iris allow less intense light to go in?" Tags="&lt;iris&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7742" PostTypeId="1" AcceptedAnswerId="7743" CreationDate="2013-04-02T23:41:00.157" Score="2" ViewCount="4887" Body="&lt;p&gt;Parthenogenesis is defined as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;A type of asexual reproduction in which egg develops without fertilization to form a new individual.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If parthenogenesis takes place in bees, a drone or male bee is produced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is that parthenogenesis is the development of EGG into new individual so, how can egg be developed into male because egg won't have that &quot;Y&quot; chromosome required for male offspring?&lt;/p&gt;&#xA;" OwnerUserId="1765" LastActivityDate="2018-04-12T15:13:57.073" Title="Parthenogenesis in Bees" Tags="&lt;reproduction&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7743" PostTypeId="2" ParentId="7742" CreationDate="2013-04-03T00:19:46.293" Score="5" Body="&lt;p&gt;Because the &quot;Y chromosome&quot; has nothing to do with sex determination in bees.  Instead, the number of X chromosomes determines the sex.  With only one X chromosome, the egg will develop into a male.  This is called a &lt;a href=&quot;http://en.wikipedia.org/wiki/Haplodiploidy&quot; rel=&quot;nofollow&quot;&gt;haplodiploid&lt;/a&gt; system of sex determination (the male bees are haploid, having only half the number of chromosomes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I should add that there are &lt;em&gt;many&lt;/em&gt; systems of sex determination, not just XY or the haplodiploid system.  See the &lt;a href=&quot;http://en.wikipedia.org/wiki/ZW_sex-determination_system&quot; rel=&quot;nofollow&quot;&gt;Z-W system&lt;/a&gt; (males are ZZ and females are ZW), the &lt;a href=&quot;http://en.wikipedia.org/wiki/X0_sex-determination_system&quot; rel=&quot;nofollow&quot;&gt;X0 system&lt;/a&gt; (the males are &lt;em&gt;diploid&lt;/em&gt; for all but the sex chromosome), and &lt;a href=&quot;http://en.wikipedia.org/wiki/Temperature-dependent_sex_determination&quot; rel=&quot;nofollow&quot;&gt;temperature-dependent system&lt;/a&gt; of sex determination. &lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-03T22:12:12.393" LastActivityDate="2013-04-03T22:12:12.393" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7744" PostTypeId="2" ParentId="7741" CreationDate="2013-04-03T00:29:31.230" Score="2" Body="&lt;p&gt;Imagine the iris like a shutter in front of a focussing lens (which, in fact, it is; see the &lt;a href=&quot;http://en.wikipedia.org/wiki/File:Schematic_diagram_of_the_human_eye_en.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;diagram&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yeqFP.png&quot; alt=&quot;Eye diagram&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that any light going through the iris will be focussed on a very small point on the retina, and your eye is wonderfully developed in a way that this exact spot is the &lt;em&gt;fovea&lt;/em&gt;, the only spot in the retina that allows you to see colour and high-resolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The iris does not modify the focussing function, it merely changes the amount of light going through into the lens to then be focussed onto the fovea. Imagine that every single object in your field of view reflects/radiates light in every possible direction - narrowing the shutter won't exclude parts of the field of vision, it will only exclude some of the rays coming in at very flat angles and thereby reduce intensity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Only if your lens is deformed, focussing (adaptation) will malfunction (directing the gathered light to the wrong spot; or focussing the incoming light in front of or behind the retina) and blur your vision.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-04-03T00:29:31.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7745" PostTypeId="2" ParentId="7739" CreationDate="2013-04-03T07:20:39.793" Score="1" Body="&lt;p&gt;Use &lt;a href=&quot;http://www.promega.com/~/media/Files/Resources/Protocols/Technical%20Manuals/0/pGEM-T%20and%20pGEM-T%20Easy%20Vector%20Systems%20Protocol.pdf&quot; rel=&quot;nofollow&quot;&gt;pGemT&lt;/a&gt; to clone your PCR product into. It is exactly designed to take products with 3' overhangs and features blue/white selection so is pretty easy to do! Then you would cut out of pGem with the restriction sites you added during your PCR and ligate it into your expression vector.&lt;/p&gt;&#xA;" OwnerUserId="3261" LastActivityDate="2013-04-03T07:20:39.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7746" PostTypeId="2" ParentId="7736" CreationDate="2013-04-03T07:59:12.253" Score="1" Body="&lt;p&gt;Dye reduction tests (and there seem to be loads of different ones) are simply assays in which a dye becomes decolourised to give you a visual indication of whether a certain process is occuring. &lt;a href=&quot;http://www.vet.cmu.ac.th/webmed/branch/web%20department/ck/mastitis/Milk%20quality/resazurin.pdf&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; you can find an example of a dye reduction test with Methylene Blue and Reazurin which indirectly measures the bacterial densities in milk and cream. See this &lt;a href=&quot;http://books.google.co.uk/books?id=f--1V1ftgtsC&amp;amp;pg=RA1-PA94&amp;amp;lpg=RA1-PA94&amp;amp;dq=Methylene%20Blue%20and%20Resazurin%20bacteria%20in%20milk&amp;amp;source=bl&amp;amp;ots=pYN6kN5Ivr&amp;amp;sig=87Ghg8hihFhdVHdTT-juL7R_2SE&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=6-BbUY2YIcrT0QXG-IGoDQ&amp;amp;ved=0CDkQ6AEwAQ#v=onepage&amp;amp;q=Methylene%20Blue%20and%20Resazurin%20bacteria%20in%20milk&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;google book&lt;/a&gt; for more info.&lt;/p&gt;&#xA;" OwnerUserId="3261" LastActivityDate="2013-04-03T07:59:12.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7748" PostTypeId="1" AcceptedAnswerId="8148" CreationDate="2013-04-03T10:46:54.927" Score="9" ViewCount="27027" Body="&lt;p&gt;It's not a particularly sad or painful thing to pluck a few nose hairs, but it's common for the tear ducts to wet up when doing this.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know the physiological reason for the correlation, how/why are the tear ducts and nose hairs related in the human body?&lt;/p&gt;&#xA;" OwnerUserId="1203" LastActivityDate="2016-12-28T21:23:29.177" Title="Why does plucking nose hair cause tears in the eyes?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7749" PostTypeId="2" ParentId="7731" CreationDate="2013-04-03T15:47:48.270" Score="1" Body="&lt;p&gt;The phosphoryl transfer potential is one way to think about the free energy available to do useful work when ATP is hydrolysed.&lt;/p&gt;&#xA;&lt;p&gt;As you can see from the free energy equation below, a positive change in entropy will help to decrease (i.e. make more negative) the free energy change.&lt;/p&gt;&#xA;&lt;p&gt;This is why an endothermic reaction can still occur spontaneously if the entropy change is big enough to create an entropy term that outweighs the enthalpy term in the Gibbs free energy equation.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;ΔG=ΔH - TΔS&lt;/p&gt;&#xA;&lt;p&gt;where:&lt;br /&gt;&#xA;T= temperature&lt;br /&gt;&#xA;G = Gibbs free energy&lt;br /&gt;&#xA;H = enthalpy&lt;br /&gt;&#xA;S = entropy&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-04-03T15:47:48.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7750" PostTypeId="2" ParentId="7548" CreationDate="2013-04-03T23:44:03.073" Score="4" Body="&lt;p&gt;My answer isn't researched; it is speculative. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I interpret &lt;em&gt;metabolic processes&lt;/em&gt; as anabolic or catabolic processes. I assert that only anaerobic processes can continue for a long time after vegetative death (the epithelia could house a counter-example of a post-mortem process, but I can't think of one), and I speculate that only catabolic processes are likely to have sufficient pools of reactants to continue after death. So we're looking for a catabolic process with a large reactant pool. Therefore I think that &lt;strong&gt;the action of digestive proteases will continue for the longest time&lt;/strong&gt;, because these enzymes are very stable and could have a lot of substrate around (including, at a very slow rate, cleaving each other.) The neutralization of stomach pH would inactivate this process...I don't know how long that takes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If something like blood clotting is considered a metabolic process, then probably that continues the longest. The binding of CO₂ by hemaglobin is probably faster than blood clotting. Again, I don't really consider those processes to be metabolic.&lt;/p&gt;&#xA;" OwnerUserId="3336" LastEditorUserId="3340" LastEditDate="2014-10-09T15:44:22.063" LastActivityDate="2014-10-09T15:44:22.063" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7751" PostTypeId="2" ParentId="1970" CreationDate="2013-04-03T23:48:00.533" Score="10" Body="&lt;p&gt;The switch from glucose to ketone bodies as the principal blood metabolite accompanies starvation. This prioritizes the heart, which preferentially uses ketone bodies as a fuel (update; actually it's fatty acids, but they're metabolically similar.) This de-prioritizes the brain, which preferentially uses glucose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[edit]&#xA;I was asked for a source. This is definitely in Voet, Voet &amp;amp; Pratt's &lt;em&gt;Fundamentals of Biochemistry&lt;/em&gt;, but I vouch for &lt;a href=&quot;https://en.wikipedia.org/wiki/Ketone_bodies#Uses_in_the_heart.2C_brain_and_muscle_.28but_not_the_liver.29&quot;&gt;Wikipedia's description.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3336" LastEditorUserId="13087" LastEditDate="2015-02-11T04:19:29.873" LastActivityDate="2015-02-11T04:19:29.873" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7753" PostTypeId="1" AcceptedAnswerId="7754" CreationDate="2013-04-04T00:16:50.990" Score="2" ViewCount="1546" Body="&lt;p&gt;I ran a PCR product of ~300 bp on a 2% TAE-agarose gel for 30 minutes. I used Sybr-safe as a DNA stain. Voltage was 80V.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I imaged the gel, the DNA on the bottom half of the gel, &lt;strong&gt;including the ladder&lt;/strong&gt; had disappeared (it showed no bands). The DNA in the top half looked-clear and well-separated, but the bands on the bottom were somehow missing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What could be the reason? I've never encountered this before.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know it's not due to gel overheating - I ran the gel in the cold room and when it was done it was cold to the touch. &lt;/p&gt;&#xA;" OwnerUserId="3053" LastEditorUserId="6" LastEditDate="2013-04-04T06:36:28.810" LastActivityDate="2016-10-03T22:12:07.517" Title="Strange behavior of a DNA gel" Tags="&lt;lab-techniques&gt;&lt;gel-electrophoresis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7754" PostTypeId="2" ParentId="7753" CreationDate="2013-04-04T06:30:40.087" Score="3" Body="&lt;p&gt;If you use pre-staining, the stain migrates as well in the electric field and this can lead to some parts of the gel being unstained. This would look pretty much like you describe, the ladder being invisible as well points strongly to that part of the gel just being no stained properly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It sounds a bit unlikely with your running parameters, I've only seen that with a very long running gel, but I also haven't used pre-staining for quite a while now. Ethidium bromide is positively charged and migrates in the opposite direction as the DNA, I have no experience with Sybr-Safe though and don't know if it behaves the same as EtBr in this regard.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2013-04-04T06:30:40.087" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7756" PostTypeId="1" AcceptedAnswerId="7775" CreationDate="2013-04-04T15:02:07.560" Score="3" ViewCount="847" Body="&lt;p&gt;What is the range of the number of individual organelles in a cell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not a biologist but I understand that there's one nucleus and sometimes lots of mitochondria, so I am after the total number.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that different types of cell will have a different number of Organelles in them, (e.g. there might be some very simple cells with 10 but there might be some with many more than that) but I am after the range with some examples. (I need references)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is for a computational model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks very much&lt;/p&gt;&#xA;" OwnerUserId="3338" LastActivityDate="2013-04-05T21:26:23.353" Title="What is range of the number of individual organelles in cells" Tags="&lt;cell-biology&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7757" PostTypeId="2" ParentId="7735" CreationDate="2013-04-04T18:38:44.150" Score="1" Body="&lt;p&gt;I don't believe so.  I have never come across a eukaryote that does not have introns although there are some genes that do not contain introns.  Some eukaryotes like ciliates actually contain other non-intronic intergenetic regions that seem to be nonfunctional.  These are called Internally Existed Sequences and are removed from the germ-line active micronucleus before going to form the transcriptionally active micronucleus.  Interestingly, introns are also present in these organisms and are present in both the micro and macronucleus.  These introns are spliced out in textbook fashion.  I believe one of the organisms where introns was discovered was in &lt;em&gt;Tetrahymena thermophila&lt;/em&gt; with the intron in the rDNA sequence.&lt;/p&gt;&#xA;" OwnerUserId="3247" LastEditorUserId="3247" LastEditDate="2013-04-04T19:23:03.110" LastActivityDate="2013-04-04T19:23:03.110" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7758" PostTypeId="1" AcceptedAnswerId="7759" CreationDate="2013-04-04T20:43:15.780" Score="5" ViewCount="2503" Body="&lt;p&gt;So I came across something terribly amazing today, that is, a video showing this species of peacock-spider, that literally, &lt;a href=&quot;http://www.youtube.com/watch?v=d_yYC5r8xMI&quot; rel=&quot;nofollow&quot;&gt;transforms into a human face waving his arms about&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What could have possibly given rise to this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can understand the arms waving around, but why the uncanny human-face template, complete with eyes, nose, mouth, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not believe this to be a case of anthropomorphism on my part, (seeing what I am familiar with), because I cannot imagine any other natural case where such symmetry in a pattern would closely resemble a human face. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would appreciate any explanation. Thanks! &lt;/p&gt;&#xA;" OwnerUserId="816" LastEditorUserId="1590" LastEditDate="2013-07-30T15:19:18.690" LastActivityDate="2015-12-07T20:47:43.610" Title="How did this spider evolve to mimic exactly a human face and arms?" Tags="&lt;evolution&gt;&lt;arachnology&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7759" PostTypeId="2" ParentId="7758" CreationDate="2013-04-04T21:11:03.283" Score="15" Body="&lt;p&gt;I think this really is just a case of what you refer to in your question as anthropomorphism. We are very, very good at seeing faces. &lt;a href=&quot;http://www.cracked.com/quick-fixes/the-3-most-terrifying-faces-drawn-by-nature/&quot;&gt;Here are some more examples&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Addendum&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mymodernmet.com/profiles/blogs/jurgen-otto-peacock-spider&quot;&gt;This site&lt;/a&gt; has pictures of quite a few peacock spiders, and as far as I can tell these are all the same species (The only peacock spider mentioned on Wikipedia is &lt;a href=&quot;http://en.wikipedia.org/wiki/Peacock_spider&quot;&gt;&lt;em&gt;Maratus volans&lt;/em&gt;&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The remarkable thing about these images is that individual spiders seem to have very different patterns on thorax and abdomen, and many of these are much less like human faces. This seems to me to weaken the case for some sort of mimicry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Interesting fact&lt;/strong&gt;: seeing faces and other forms where they do not exist is a psychological phenomenon called &lt;a href=&quot;http://en.wikipedia.org/wiki/Pareidolia&quot;&gt;pareidolia&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-04-05T19:03:32.080" LastActivityDate="2013-04-05T19:03:32.080" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="7761" PostTypeId="2" ParentId="7758" CreationDate="2013-04-04T21:23:57.243" Score="1" Body="&lt;p&gt;In part, the way the spider resembles a human face is due to &lt;a href=&quot;http://en.wikipedia.org/wiki/Symmetry_in_biology#Bilateral_symmetry&quot; rel=&quot;nofollow&quot;&gt;bilateral symmetry&lt;/a&gt; in the body shape and coloring of the spider. Bilateral symmetry evolved early in the animal kingdom to facilitate streamlining of the body (which makes it move faster in any fluid, including air and water), formation of a central nervous system and a head. Human faces (and bodies) are also bilaterally symmetric, hence the resemblance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another reason, as you note, is antropomorphism - the ability of humans to see a human face in many natural shapes and colorings. Other animals, including predators probably also have this ability to see faces in nature. This allowed the spider to evolve to imitate a scary face. This is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Mimicry&quot; rel=&quot;nofollow&quot;&gt;mimicry&lt;/a&gt; and it helps the spider ward off predators. &lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-04-04T21:23:57.243" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7762" PostTypeId="1" AcceptedAnswerId="7771" CreationDate="2013-04-04T21:44:14.267" Score="3" ViewCount="363" Body="&lt;p&gt;It is important to bear in mind that the distance between a neuron's axon terminal and its soma can be extensive, up to about 1m in the human body. The fastest transport along the axon is 400mm/day (For this purpose I suppose &lt;a href=&quot;http://en.wikipedia.org/wiki/Axoplasmic_transport&quot; rel=&quot;nofollow&quot;&gt;Source: Wikipedia&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course the axon terminals also need to be supplied with a steady stream of proteins to maintain normal turnover, for example the terminal may need enzymes which metabolise the neurotransmitter, membrane proteins for signalling, vesicle coating and membrane fusion proteins etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, sudden changes are possible in the level available of a certain protein. An example could be sudden depletion of SNAREs (required for vesicle fusion in neurotransmitter exocytosis) caused by botulinum toxin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, does the terminal somehow report back to the soma in any way if a certain protein needs to be made available more or less? And if so, how? Especially considering that retrograde transport, according to Wikipedia, gets up to 200mm/day only. If that was the mechanism for feedback, it would create a large discrepancy between signals received at the soma and the terminal's actual state.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-04-05T15:18:08.670" Title="How do axon terminals report to the soma?" Tags="&lt;neuroscience&gt;&lt;intracellular-transport&gt;&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7764" PostTypeId="2" ParentId="1909" CreationDate="2013-04-05T04:57:04.223" Score="0" Body="&lt;p&gt;I don't think SAS is a well-defined observable. (I like the work by &lt;a href=&quot;http://www.cmps.lu.se/bpc/people/bertil_halle/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bertil Halle&lt;/a&gt; on this and related problems.) You can measure &lt;em&gt;correlates&lt;/em&gt; to SAS that have been calculated according to known structures, using something like the rolling sphere algorithm that @shigeta describes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the best-parametrized approach would be differential scanning calorimetry. Because a lot of proteins have had their folding studied with this technique, a DSC curve can be directly converted into changes in polar and nonpolar SAS. The total SAS would be a sum of those two quantities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only ready reference I could find for this is here: &lt;a href=&quot;https://web.archive.org/web/20100228041032/https://www.bio.cmu.edu/courses/03438/LecS00/DSC.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://web.archive.org/web/20100228041032/https://www.bio.cmu.edu/courses/03438/LecS00/DSC.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think most of the analysis was worked out by Ernesto Freire. Basically, the idea is that surface accessible hydrophobic areas organize more solvent (and have a larger entropic footprint) than the polar areas. Since a DSC trace (for a two-state folder) can be deconvoluted into $\Delta$H and $\Delta$S components, it can be mapped onto $\Delta$ASA$_{folding}$. I wouldn't trust this for anything that was non-two-state or that bound cofactors.&lt;/p&gt;&#xA;" OwnerUserId="3336" LastEditorUserId="9686" LastEditDate="2018-06-28T05:50:51.537" LastActivityDate="2018-06-28T05:50:51.537" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="7765" PostTypeId="1" CreationDate="2013-04-05T05:22:10.523" Score="1" ViewCount="62" Body="&lt;p&gt;I have been working on lung samples to perform western blotting. I have two related questions about this:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;I get very nonspecific results: at times nothing at all, at times it glows on membrane but doesn't take up on x-ray film. What are the common causes of these errors and how might I avoid them?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I am interested in assaying GPCR expression. When I am assaying for GPCRs, do I need to prepare the lung samples in a specific way (that is different from sample preparation for Western blots of other proteins)?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3339" LastEditorUserId="57" LastEditDate="2013-04-05T08:31:52.247" LastActivityDate="2013-04-05T08:31:52.247" Title="Western blotting of lung samples" Tags="&lt;lab-techniques&gt;&lt;western-blot&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2014-08-05T18:48:21.387" ContentLicense="CC BY-SA 3.0" />
  <row Id="7766" PostTypeId="2" ParentId="7680" CreationDate="2013-04-05T12:57:31.510" Score="1" Body="&lt;p&gt;You can use a bidirectional promoter. The problem that you mentioned about proteins not expressed in same level happens because of competition for polymerase. But there are well optimized parts and also commercially available vectors that work fine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can clone genes in a serial order. It won't be a problem. Just leave a 100bp linker after the polyA signal of previous gene. If your cassette becomes too huge, then insertion becomes slightly difficult. That's why people use IRES or TA-peptides, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Retroviral based insertions work quite decently, but you can't control copy number variation between different cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can use two different promoters. The dynamics will depend on the promoter strength and concentration of inducer.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="107" LastEditDate="2013-05-06T02:52:26.333" LastActivityDate="2013-05-06T02:52:26.333" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7767" PostTypeId="2" ParentId="5145" CreationDate="2013-04-05T13:16:16.647" Score="3" Body="&lt;p&gt;First you should decide whether you want to design an shRNA or use siRNAs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to use shRNA you should look at the rules that &quot;Mad Scientist&quot; mentioned. You can insert mismatches but make sure not to disrupt the secondary structure. You can use RNAFold to verify. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;shRNA always has issues and you have to optimize your design, test it by realtime PCR or Northern blot etc to confirm the production and the concentration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can design siRNAs and there are online algorithms to help you design one. &#xA;You have to choose a sequence which is specific to your gene. This step is important for both shRNA and siRNAs in order to minimize/avoid off-targeting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A common practice is to use a pool of siRNAs for a single gene. Pooled siRNAs are commercially available for many genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the experimental controls you would need to do two experiments:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;mock siRNA treated; which wont affect any gene &lt;/li&gt;&#xA;&lt;li&gt;Your siRNA treated&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;then test for a reference gene such as GAPDH and your gene. A good reference gene should be the one which is not expected to change expression. GAPDH may not be a good reference always (for example in cases where metabolism is affected). The choice of reference gene is intuitive and depends on your prior knowledge of the system. Instead of GAPDH you can also transfect GFP and quantitate that as a control (spike in).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-03-21T09:37:27.073" LastActivityDate="2016-03-21T09:37:27.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7768" PostTypeId="2" ParentId="5271" CreationDate="2013-04-05T13:23:57.573" Score="2" Body="&lt;p&gt;There aren't many studies which associate between alcohol consumption and cancer to my knowledge. The association is more with metabolic diseases because the liver is affected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alcohol is oxidised to acetaldehyde by alcohol dehydrogenase. Acetaldehyde may also, in turn affect the cells by DNA damage if it is not metabolized quickly to acetyl-CoA (perhaps in a manner similar to formaldehyde or by formation of Schiff's base with nucleotides). The other way by which alcohol is metabolised is through cytochrome-p450 (CYP2E1) which produces ROS (Hydrogen Peroxide), that &lt;strong&gt;may&lt;/strong&gt; lead to carcinogenesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might want to check this &lt;a href=&quot;http://www.nature.com/nrc/journal/v7/n8/full/nrc2191.html&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3059" LastEditDate="2013-04-15T00:02:58.993" LastActivityDate="2013-04-15T00:02:58.993" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7769" PostTypeId="2" ParentId="7047" CreationDate="2013-04-05T14:06:05.207" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866014/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866014/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this work they find that formaldehyde crosslinking happens by formation of a methylol adduct (due to nucleophilic attack by N or S in case of proteins) in protein which then attacks the DNA or vice-versa.&#xA;The final crosslink is by a methylene bridge&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Formaldehyde can react to amino groups in nucleotides and proteins and form a schiff's base, but i dont have a clue how this is involved in crosslinking &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-05T14:55:51.317" LastActivityDate="2013-04-05T14:55:51.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7770" PostTypeId="1" CreationDate="2013-04-05T14:31:21.590" Score="1" ViewCount="829" Body="&lt;p&gt;I am somehow not convinced that biotic factors are solely responsible for creating 21% of atmosphere (around 40 million moles of oxygen). &#xA;There may be additional issues here. Since cyanobacteria produced oxygen, it should have developed antioxidant machineries. By the time cyanobacteria flourished, some dependent heterotrophs must have evolved and they also would need antioxidants, as they are expected to thrive in close proximity to the autotrophs. There is a likelihood that aerobic respiration co-evolved with biotic oxygenesis. This would have further delayed the build up of oxygen in the atmosphere. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Does anyone have an idea of what is the photosynthetic oxygen production rate per gram biomass of cyanobacteria?&lt;/strong&gt; Since photosynthesis must have happened mostly at the surface of the water (limnetic zone), the total biomass would be restricted. Then it might be possible to calculate the time required to achieve the oxygen levels of 21%. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This measure can indicate whether the current theory is plausible or not. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2016-05-09T11:36:45.460" Title="Cyanobacterial photosynthetic oxygen yield" Tags="&lt;evolution&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7771" PostTypeId="2" ParentId="7762" CreationDate="2013-04-05T15:18:08.670" Score="2" Body="&lt;p&gt;We can consider the classical example of Long Term Potentiation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;CREB is a transcription factor which is activated during LTP by phosphorylation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your reasoning about the delay between signal and transcriptional response is correct and thats why neurons have local translation factories near the dendritic spines and gene regulation (fast responses) is mostly post-transcriptional. (there is no article which says exactly so but you can refer so some articles  which report that miRNA-repressed genes are reactivated upon certain signals. They hint that post translational regulation is very important in neurons) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cell.com/neuron/abstract/S0896-6273%2809%2900939-8&quot; rel=&quot;nofollow&quot;&gt;http://www.cell.com/neuron/abstract/S0896-6273%2809%2900939-8&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://nar.oxfordjournals.org/content/40/11/5088&quot; rel=&quot;nofollow&quot;&gt;http://nar.oxfordjournals.org/content/40/11/5088&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-05T15:18:08.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7772" PostTypeId="1" AcceptedAnswerId="20366" CreationDate="2013-04-05T15:31:46.353" Score="7" ViewCount="193" Body="&lt;p&gt;Many willows (&lt;em&gt;Salix spp.&lt;/em&gt;) grow in northern states but do not grow in southern states, for example &lt;a href=&quot;http://plants.usda.gov/java/profile?symbol=SAVI2&quot;&gt;&lt;em&gt;Salix viminalis&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What mechanisms control the southern range of temperate hardwoods such as willow? Is it disease? Temperature sensitivity of respiration? Water use efficiency?&lt;/p&gt;&#xA;" OwnerUserId="154" LastActivityDate="2014-08-10T21:26:36.020" Title="What controls the southern range of willows?" Tags="&lt;plant-physiology&gt;&lt;ecology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7773" PostTypeId="2" ParentId="7423" CreationDate="2013-04-05T16:18:26.777" Score="0" Body="&lt;p&gt;Pipetting up and down GENTLY, the slower you pipet and the thicker the tip the more gentle it is, or vortexing SLOWLY, high vortexing speeds result in shear stress on the wall, just like fast pipetting with small tips&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacterias can take a lot, take more care with yeast and even more care with mammalian cells&lt;/p&gt;&#xA;" OwnerUserId="3342" LastActivityDate="2013-04-05T16:18:26.777" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7775" PostTypeId="2" ParentId="7756" CreationDate="2013-04-05T21:26:23.353" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://bionumbers.hms.harvard.edu/&quot; rel=&quot;nofollow&quot;&gt;BioNumbers&lt;/a&gt; is a database that contains exactly this sort of stuff.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, I took this from this site:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Number of mitochondria per cell:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yeast Cryptococcus neoformans cell: ~34&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human HELA cell: ~6000&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mouse L cell: ~1000&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2013-04-05T21:26:23.353" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7777" PostTypeId="1" AcceptedAnswerId="7811" CreationDate="2013-04-06T01:30:48.593" Score="5" ViewCount="735" Body="&lt;p&gt;I've heard that THC can cause permanent damage to brain cells. I've also heard this reffered to anti drug propaganda. Another theory i've read is that temporary effects reduce intelligence but long term results are not affected. If Marijuana does cause permanent brain damage how does it do so? How exactly does it kill the cell?&lt;/p&gt;&#xA;" OwnerUserId="1904" LastActivityDate="2013-04-08T18:53:45.767" Title="How exactly does marijuana damage brain cells?" Tags="&lt;biochemistry&gt;&lt;neuroscience&gt;&lt;cell-biology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7778" PostTypeId="1" CreationDate="2013-04-06T01:32:03.423" Score="4" ViewCount="1259" Body="&lt;p&gt;We're producing some membrane proteins and they aren't amenable to freeze thaws even when we add glycerol. The proteins are solubilized in detergent above the cmc so they should be in micelle form in solution. Currently, they are being held at 4C. I'm curious what is the best way to store them for long term use?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2015-07-04T18:18:40.613" Title="How do you store membrane proteins?" Tags="&lt;biochemistry&gt;&lt;lab-techniques&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7779" PostTypeId="1" AcceptedAnswerId="10725" CreationDate="2013-04-06T01:35:28.067" Score="1" ViewCount="293" Body="&lt;p&gt;I was reading &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2192750/&quot; rel=&quot;nofollow&quot;&gt;this paper by Cretekos et al (2008)&lt;/a&gt;, in which they state that wing development in the bat is not complete until after birth - the wing continues to elongate postnatally.  This would suggest that bats are unable to fly immediately after birth, and a brief web search confirms this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I would like to know:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;When is wing growth (by which I simply mean outward growth or extension) complete? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When are bats able to fly?  (Are there other developmental processes that take place after wing extension that delay this process?)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-10-05T13:20:14.587" Title="When is wing growth in the bat complete and how soon can bats fly after wing growth is complete?" Tags="&lt;zoology&gt;&lt;development&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7780" PostTypeId="1" AcceptedAnswerId="7802" CreationDate="2013-04-06T03:55:27.397" Score="4" ViewCount="219" Body="&lt;p&gt;There are several families of antibodies found in mammals.  They may have two or more antibody domains which contain heavy and light chains.  The variable regions of the light and heavy chains genes in the chromosome are spliced in antibody producing cells so that each cell produces a different antibody, with a unique sequence of amino acids in the variable regions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a cartoon:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/azXOu.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The variable regions are disproportionately large here, but it gives some idea...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm having trouble finding is how the DNA regions of these genes look in cells which don't produce antibodies.  Are they the same as that in the germline?  Do they undergo recombination but are not expressed? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help would be appreciated. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3340" LastEditDate="2013-04-09T10:23:49.290" LastActivityDate="2013-04-09T10:23:49.290" Title="How do the variable portions of antibody genes look in cells which don't produce antibodies?" Tags="&lt;immunology&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7782" PostTypeId="1" CreationDate="2013-04-06T12:42:21.720" Score="7" ViewCount="4801" Body="&lt;p&gt;I am fairly short-sighted and wear glasses pretty much all the time. Naively, I would expect that when I take my glasses off, the image I see should look very much the same as as a photograph that's out of focus, or an image to which someone has applied a Gaussian blur filter. In bright conditions this is mostly true, but at night if I look at distant point sources of light, the blurry halos around them appear to have quite a complex structure, and a fairly well-defined edge. Why is this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To make it clearer what I mean, and at the same time to make a hypothesis about the answer, here is a public domain image of some lights, taken with a camera out of focus:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ERRiY.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(&lt;a href=&quot;http://pixabay.com/en/bokeh-circles-background-light-69638/&quot; rel=&quot;noreferrer&quot;&gt;image source&lt;/a&gt;.) Notice that the image cast by each light is not simply a uniform circle. They are each slightly hexagonal; they are slightly brighter around the edge than in the middle; and there are distinct nonuniformities in the brightness in the interior of each shape.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I see is actually fairly similar to this but much more extreme. The shape formed by a light is much further from a circle, being very irregular in shape and distinctly elongated in one direction. (This latter is perhaps not surprising given that I have a strong &lt;a href=&quot;http://en.wikipedia.org/wiki/Astigmatism_%28eye%29&quot; rel=&quot;noreferrer&quot;&gt;astigmatism&lt;/a&gt;.) The bright edge to the shape, and the non-uniformities in its brightness, are much more pronounced than in the camera image.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, in the photograph I know that the hexagonal shape is due to the hexagonal aperture in the camera. This can be ruled out in my eyes because my pupils are definitely circular. (Unless some light also passes through parts of the iris?) I would guess that the bright edges are caused by &lt;a href=&quot;http://en.wikipedia.org/wiki/Diffraction&quot; rel=&quot;noreferrer&quot;&gt;diffraction&lt;/a&gt;, and that the nonuniformities are caused by defects in the lens and/or dirt on its surface. I suppose that diffraction and lens aberrations must be the causes of what I see when looking at distant lights without my glasses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in the end, my question is mostly just, am I right about this? Are the shapes I see the result of defects in my eye's optics, and which specific anatomical features of the eye are likely to be their main causes?&lt;/p&gt;&#xA;" OwnerUserId="3347" LastEditorUserId="3347" LastEditDate="2014-12-24T13:51:33.623" LastActivityDate="2020-12-01T08:24:28.263" Title="Perception of distant lights without glasses" Tags="&lt;human-biology&gt;&lt;vision&gt;&lt;perception&gt;" AnswerCount="1" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="7783" PostTypeId="2" ParentId="3048" CreationDate="2013-04-06T17:15:52.820" Score="1" Body="&lt;p&gt;In oviparous animals the egg retention phase in the uterus is brief. After fertilization eggshell mineralization is triggered but it seems the initial triggers of the pathway is not understood. The uterine fluid is rich in calcium and bicarbonates and calcium carbonate, in the form of calcite, precipitates around the egg. Shell mineralization is quite a rapid process and there are some specific proteins involved in this pathway. Have a look at these:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22201802&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/22201802&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://hera.ugr.es/doi/15773115&quot; rel=&quot;nofollow&quot;&gt;http://hera.ugr.es/doi/15773115&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In ovo-viviparous animals the egg is retained in the uterus for a longer time and embryo is quite developed when the egg is laid (happens in boas). You can call it a sort of &quot;pregnancy&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However &lt;a href=&quot;http://www.genome.jp/kegg-bin/show_pathway?category=Birds&amp;amp;mapno=04914&quot; rel=&quot;nofollow&quot;&gt;progesterone pathway&lt;/a&gt; exists in birds and is involved in oocyte maturation &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oxytocin pathways also exist in birds, acting through oxytocin homolog Mesotocin, and perhaps they cause development of maternal care as they do in mammals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12954415&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; talks about effects of oxytocin on birds but not exactly about its role in maternal care. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However i believe that the shell size and mineralization time shouldn't differ much between unfertilized and fertilized eggs in oviparous animals.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-05-03T06:40:57.977" LastActivityDate="2013-05-03T06:40:57.977" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7784" PostTypeId="2" ParentId="1937" CreationDate="2013-04-06T17:45:49.023" Score="1" Body="&lt;p&gt;it is highly variable even in a single cell type.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dont know for a human cell but this is the range for ecoli: 1500-11400&lt;/p&gt;&#xA;&#xA;&lt;p&gt;check this site out. got this number from there (its quite useful for questions like these):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bionumbers.hms.harvard.edu/bionumber.aspx?&amp;amp;id=101440&amp;amp;ver=3&amp;amp;trm=RNA%20polymerase&quot; rel=&quot;nofollow&quot;&gt;http://bionumbers.hms.harvard.edu/bionumber.aspx?&amp;amp;id=101440&amp;amp;ver=3&amp;amp;trm=RNA%20polymerase&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can estimate protein copy numbers and there are techniques available for doing so. One of such techniques:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mcponline.org/content/11/3/O111.009613.long&quot; rel=&quot;nofollow&quot;&gt;http://www.mcponline.org/content/11/3/O111.009613.long&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also calculate concentration using traditional techniques like western blot and elisa and calculate approximate copy-numbers (you have to also calculate average cell volume and number of cells for protein extraction. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-06T17:45:49.023" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7785" PostTypeId="1" CreationDate="2013-04-06T21:40:07.040" Score="11" ViewCount="65156" Body="&lt;p&gt;I am in a 300-level molecular biology class and am unclear about this concept and how to delineate motifs versus domains of proteins.  Any suggestions would be much obliged.&lt;/p&gt;&#xA;" OwnerUserId="3348" LastActivityDate="2018-04-30T12:12:11.043" Title="Differences Between Protein Motifs and Protein Domains?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;protein-folding&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7786" PostTypeId="2" ParentId="7785" CreationDate="2013-04-07T01:27:05.173" Score="2" Body="&lt;p&gt;The principal difference is that domains are independently stable, while motifs are not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a bit on motifs: &lt;a href=&quot;http://www.sinauer.com/pdf/nsp-protein-1-16.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.sinauer.com/pdf/nsp-protein-1-16.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A motif can be part of a domain.  From there:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The second, equally common, use of the term &lt;strong&gt;motif&lt;/strong&gt; refers to a set of&#xA;  contiguous secondary structure elements that either have a particular&#xA;  functional significance or &lt;strong&gt;define a portion of an independently folded&#xA;  domain&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-04-07T01:27:05.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7787" PostTypeId="1" CreationDate="2013-04-07T06:28:06.383" Score="0" ViewCount="261" Body="&lt;p&gt;I would imagine the answer to this question would be that religion tends to cause greater compliance of individuals within society, so it is pro-society. Plus these religions tend to incorporate some knowledge obtained by trial and error, an example of this is the fact that in Judaism the consumption of swine is forbidden which would be an evolutionary advantage seeing how swine is notorious for its parasitic constituents. Additionally religion offers an explanation for some of the phenomena that were once and still are poorly understood. Such things include near-death experiences. It also adds to motivation and tends to confer some other advantages such as a decreased rate of suicide due to the condemnation of suicide by the majority of religions. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-04-08T05:13:13.877" Title="What's the Evolutionary Purpose of Religion?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ClosedDate="2013-04-08T20:51:41.050" ContentLicense="CC BY-SA 3.0" />
  <row Id="7788" PostTypeId="2" ParentId="7787" CreationDate="2013-04-07T07:50:52.187" Score="7" Body="&lt;p&gt;In terms of genetic evolution, religion itself cannot really be considered to have an evolutionary advantage or disadvantage, as it is not anchored in any genes. This means that it is not an evolutionary trait and hence the principles of evolution do not apply to it. However, religion is a product of underlying capabilities of the brain (for example imaginative capacity?), and these are genetic and evolutionarily advantageous. Aside from this, asking for the 'evolutionary purpose' of anything is the wrong way to approach the topic, as things do not evolve to have a purpose but they simply evolve and stick around unless they produce a net disadvantage compared to a competing version of the same trait.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could look at religion from a memetic point of view however, i.e. as an idea which competes with other ideas. The idea of religion has many aspects to it that would help it to 'survive', i.e. not be forgotten. These include the drive to tell other people about it, ease of understanding, the claim of exclusivity, addressing many social cravings, and filling in gaps of knowledge for which explanations are desired.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-04-07T07:50:52.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7789" PostTypeId="1" AcceptedAnswerId="7793" CreationDate="2013-04-06T18:44:51.410" Score="3" ViewCount="698" Body="&lt;p&gt;Since &lt;a href=&quot;https://skeptics.stackexchange.com/questions/6375/do-bacteria-become-immune-to-antibiotics-if-you-dont-complete-your-course-of-th&quot;&gt;bacteria becomes resistant to antibiotics&lt;/a&gt; after an unfinished course, is it possible to do anything to be able to get treatment with the same antibiotic again, and reverse the resistance in the bacteria?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or, the bacteria with the resistance will stay resistant forever (until death)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some websites that are claiming that some natural remedies might be effective, like taking &quot;Honey&quot;, which doesn't seem to be medical facts.&lt;/p&gt;&#xA;" OwnerUserId="3350" OwnerDisplayName="sharp12345" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2013-04-09T18:25:04.343" Title="Is it possible to make bacteria vulnerable to antibiotics it's resistant to?" Tags="&lt;evolution&gt;" AnswerCount="3" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="7791" PostTypeId="2" ParentId="7785" CreationDate="2013-04-07T15:28:44.860" Score="13" Body="&lt;p&gt;These are completely different concepts, which sometimes may be connected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A motif in biology is a mathematical model, typically of a sequence, that predicts which sequences belong to some defined group. For example, a DNA sequence motif can characterize the binding site of a transcription factor, i.e. which sequences tend to be bound by this factor. For proteins, sequence motifs can characterize which proteins (protein sequences) belong to a given protein family. A simple motif could be, for example, some pattern which is strictly shared by all members of the group, e.g. WTRXEKXXY (where X stands for any amino acid). There are also more complex motif models.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Protein domains, on the other hand, are a structural entity, usually meaning a part of the protein structure which folds and functions independently. So, proteins are often constructed from different combinations of these domains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how are motifs and domains related? Well, when you think about protein families, it makes sense not only to look at the whole sequence but also to focus on individual domains. Since they are a elementary functional-structural units, it makes sense to find sequence motifs for individual domains. So, you often find that a protein contains multiple domains, each domain characterized by having a sequence that matches the motif of its family.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2018-04-30T06:36:40.800" LastActivityDate="2018-04-30T06:36:40.800" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7793" PostTypeId="2" ParentId="7789" CreationDate="2013-04-07T18:09:18.913" Score="5" Body="&lt;p&gt;Perhaps it is useful to first consider how resistance is gained:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you treat a population of bacteria with an antibiotic, some may die and some may live.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If none die, they are obviously resistant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If all of them die, then all of them were sensitive, meaning that the size of the population and the variation were not large enough in order for some of the bacteria to be resistant. One approach would be to try to get larger genetic variation by inducing mutations with some mutagen. In addition, you can take a larger population. This would in effect let you sample a larger part of the genetic space to see if you can find a resistant strain. Of course it is possible that this will not work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If some die and some are resistant, the situation is slightly more complicated. One possibility is that those which lived are genetically resistant (their DNA is different). To see if this is the case, you take those which lived and treat them again with the antibiotic. If they all live, they are resistant. Another possibility is that they are scholastically resistant. This phenomenon is known as bacterial persistence. What happens is that there is a genetic switch that randomly bestows resistance in some fraction of the population, let's say 10 percent. If you now take this population and reapply the antibiotic, only 10% of the population will survive. This interesting mechanism allows the bacteria adapt more quickly, since they do not have to make modifications to their DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am guessing that if the bacteria are genetically resistant, they will stay resistant. If the bacteria are scholastically resistant, it might be possible to affect the genetic switch which causes the persistence. This, in addition to reducing the size of the population, might cause a situation where none of the bacteria in the population are resistant long enough to survive.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2013-04-08T01:42:21.667" LastActivityDate="2013-04-08T01:42:21.667" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7794" PostTypeId="2" ParentId="7553" CreationDate="2013-04-07T19:16:17.103" Score="2" Body="&lt;p&gt;There are many factors contributing to neurons dying much faster than other cell types.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This website does not provide original references (for this question, it does for the rest of the article) but sounds trustworthy: &lt;a href=&quot;http://neuropathology-web.org/chapter2/chapter2aHIE.html&quot; rel=&quot;nofollow&quot;&gt;http://neuropathology-web.org/chapter2/chapter2aHIE.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some factors extracted from here are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Aside from small amounts in astrocytes, there is no glycogen storage in the brain.&lt;/li&gt;&#xA;&lt;li&gt;Fatty acids cannot cross the blood-brain barrier.&lt;/li&gt;&#xA;&lt;li&gt;Lack of a backup energy sources such as creatine phosphate in muscle cells.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Which leave the brain crucially dependent on oxydative phosphorylation, i.e. glucose and oxygen. Additionally of course, neurons are metabolically highly active and use up the small amounts of stored nutrients available at a faster rate than most cells. This is because they need to maintain strong ion gradients across their entire membrane, which spans a larger area than most other cell types due to extensive axonic and dendritic trees; not to mention constantly exocytosing neurotransmitters from the axon's numerous terminals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coupled with excitotoxicity as the actual mechanism inducing cell death as explained in the Quora answer linked above (&lt;a href=&quot;http://www.quora.com/Neuroscience-1/Why-do-neurons-die-so-quickly-when-deprived-of-oxygen&quot; rel=&quot;nofollow&quot;&gt;http://www.quora.com/Neuroscience-1/Why-do-neurons-die-so-quickly-when-deprived-of-oxygen&lt;/a&gt;), this seems to be a sufficient explanation.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-04-07T21:29:57.487" LastActivityDate="2013-04-07T21:29:57.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7795" PostTypeId="2" ParentId="7789" CreationDate="2013-04-07T19:17:21.033" Score="4" Body="&lt;p&gt;Bitwise has explained how antibiotic resistance develops in bacteria.  To address how it might go away: as long as the antibiotic is around, there is selective pressure on the bacteria to preserve the parts of their genome that confer antibiotic resistance.  If, for example, some bacteria developed mutations that made them no longer antibiotic-resistant, these bacteria would die, and thus, only the antibiotic-resistant bacteria would reproduce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For antibiotic-susceptible bacteria to develop and persist, you'd need to take away this selective pressure (no more of the antibiotic around to kill the antibiotic-susceptible bacteria) so that there would be no particular advantage to carrying non-mutated copies of the antibiotic-resistance gene(s). Of course, the natural rate of mutation is not that high, so I think it would take time for antibiotic-susceptible bacteria to reappear (unless there was a &lt;a href=&quot;http://en.wikipedia.org/wiki/Mutagen&quot; rel=&quot;nofollow&quot;&gt;mutagen&lt;/a&gt; around).   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: antibiotic-susceptible bacteria would become more prevalent if there was a way to select for them, over antibiotic-resistant bacteria. For example, if there were conditions under which maintaining antibiotic-resistance genes becomes &lt;em&gt;unfavorable&lt;/em&gt;, antibiotic-susceptible bacteria would reproduce more often/faster (see the term &lt;a href=&quot;http://en.wikipedia.org/wiki/Fitness_%28biology%29&quot; rel=&quot;nofollow&quot;&gt;fitness&lt;/a&gt;), and thus become more prevalent. However, this does &lt;em&gt;not&lt;/em&gt; change the mutation rate - only selects for things that have already evolved.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-09T14:45:15.623" LastActivityDate="2013-04-09T14:45:15.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7799" PostTypeId="2" ParentId="5596" CreationDate="2013-04-08T00:57:21.553" Score="1" Body="&lt;p&gt;I encountered &lt;a href=&quot;http://latimesblogs.latimes.com/greenspace/2010/11/ge-salmon-foes-cite-trojan-gene.html&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; discussing transgenic salmon, and it says that the modified genes don't find their way into nature because transgenic salmon are bad at the salmon mating ritual. It wasn't on purpose from what I can tell, but that's still a neat way to ensure modified organisms don't spread their genes into nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a relevant counterexample to what the question sought, but not a general argument against the possibility.&lt;/p&gt;&#xA;" OwnerUserId="1836" LastActivityDate="2013-04-08T00:57:21.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7800" PostTypeId="1" CreationDate="2013-04-08T02:19:23.603" Score="2" ViewCount="100" Body="&lt;p&gt;I was reading &lt;a href=&quot;http://www.nature.com/tpj/journal/v12/n5/full/tpj201135a.html&quot; rel=&quot;nofollow&quot;&gt;a paper&lt;/a&gt; related to bioinformatics where it uses the drug response on the cancer cells and the gene expression of the individual cells are studied to find any useful insights. Specially, using the gene expression of the cells a predictor of the drug response is created.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They have stated that just using the correlation between the gene expression and the drug response might not be a good predictor. But the genes interact through signaling pathways to drive a particular drug response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What these guys have done is like used PCA on the gene expressions of the cancer cells to use the components which preserve the greatest variance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually, I didn't get what they mean by probe-by-background interaction and how it is calculated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone please explain. I googled for a while but didn't get it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are some quotes from the paper where the term is used&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Towards this end, we have compared how well drug response can be&#xA;  predicted by simple statistical models, which either directly relate&#xA;  &lt;strong&gt;probe and background&lt;/strong&gt; networks to drug response or consider&#xA;  probe-by-background network interactions.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;To generalize this approach, the term ‘probe’ could be&#xA;  replaced by individual transcript expression levels measured through&#xA;  other gene expression methods. Similarly, ‘background networks’ and&#xA;  principal components are used interchangeably. Generally, ‘background&#xA;  networks’ could be represented by any data reduction method that&#xA;  summarizes the expression of a gene network. We demonstrate that&#xA;  &lt;strong&gt;probe-by-background&lt;/strong&gt; network interactions significantly enhance drug&#xA;  response predictions, over and above the predictive power garnered&#xA;  through utilizing individual probes and background networks alone.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3074" LastEditorUserId="3059" LastEditDate="2013-04-16T22:49:03.350" LastActivityDate="2013-04-16T22:49:03.350" Title="Confusion related to a term probe-by-background interaction" Tags="&lt;bioinformatics&gt;&lt;pharmacology&gt;&lt;gene-expression&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7802" PostTypeId="2" ParentId="7780" CreationDate="2013-04-08T04:42:26.263" Score="2" Body="&lt;p&gt;Perhaps you want to ask how VDJ recombination is regulated in non lymphoid cells.. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well even in immature lymphoid cells VDJ recombination is regulated. And also Ig genes are suppressed in T-cell and TCR genes are suppressed in B-cells.. &#xA;Also, the recombination of Ig is suppressed in T-cell and vice-versa. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;RAG-1,2(Recombination activating gene) downregulation partly does the job, but not fully. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Earlier reports say that transcription in the locus is essential and epigenetic regulation of transcription in turn regulates recombination. &#xA;But what it exactly means is that accessibility to the RSS (Recombination signal sequences) is limited in a repressed chromatin and recent reports say that nucleosomes are appropriately positioned over the RSS to control recombination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a look at these: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cell.com/abstract/S0092-8674%2802%2900675-X&quot; rel=&quot;nofollow&quot;&gt;http://www.cell.com/abstract/S0092-8674%2802%2900675-X&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0952791506000057&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0952791506000057&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC204470/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC204470/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-08T05:10:13.723" LastActivityDate="2013-04-08T05:10:13.723" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7803" PostTypeId="2" ParentId="4987" CreationDate="2013-04-08T05:26:01.797" Score="2" Body="&lt;p&gt;A longer or duplexed Nucleic acid will have more charge per mole of the molecule. But generally it is not the overall charge that matters in electrophoresis or MS or chromatography; it is the charge density and specific charge (z/m) that matters (charge density of a longer RNA will be almost same as smaller RNA. they will also have same specific charge)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The properties of stationary phase  is very important in controlling the separation process. Without knowing what resin is used, it will be difficult to comment about why RNA is not retained. &#xA;Sometimes the strong basicity of the stationary phase, such as in quaternary ammonium resins, degrades RNA by alkaline hydrolysis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If yours is a commercial resin then you will have a tough time finding out what exactly it is made of. Unless of course you break the column open and do a molecular analysis of the resin :P &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-08T05:56:26.470" LastActivityDate="2013-04-08T05:56:26.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7804" PostTypeId="2" ParentId="3814" CreationDate="2013-04-08T06:41:07.773" Score="3" Body="&lt;p&gt;The number of spindle fibres is actually more than total number of kinetochore pairs. The fibres attached to kinetochores are called K-fibres and the others are called polar fibres. I cant surely say that there is exactly one K-fibre per kinetochore but as per its definition and from the microscopic images you can conclude that there is one per kinetochore. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a normal mitotic metaphase there are 2n kinetochore pairs, and as you rightly calculated, there will be 96 K-fibres. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In meiosis-I there is a tetrad which has 2 kinetochore pairs but the ones in sister chromatids behave as a single unit. So there would be 23 fibres. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fusion of kinetochores of sister chromatids is relaxed in meiosis-II and again a separation would require 23 fibres.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please have a look at this article. Molecular biology of Meiosis nicely explained:&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867403000837&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0092867403000837&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More about K-fibre formation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/s00412-005-0028-2/fulltext.html&quot; rel=&quot;nofollow&quot;&gt;http://link.springer.com/article/10.1007/s00412-005-0028-2/fulltext.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-08T07:56:50.813" LastActivityDate="2013-04-08T07:56:50.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7805" PostTypeId="2" ParentId="2505" CreationDate="2013-04-08T07:25:17.263" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Which are the factors that modify the overall gene differential&#xA;  expression by introducing a vector for single-gene overexpression&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is a very relevant question and the field of experimental biology needs to revisit the experimental strategies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the explanations that you gave is correct- that the overexpressed protein might override the cellular processes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another problem that this practice gives rise to is incorrect inference. We are mostly interested in knowing what a protein does in a cell at general physiological conditions. If the stoichiometry is altered wrong results will definitely pop up.&#xA;For example in the case of a repressor/activator with multiple targets: At its general physiological concentration it may not really activate gene-X because of low affinity but in high concentrations it just may, and we end up concluding that gene-x is a target of repressor-1 by an OVEREXPRESSION experiment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A synthetic biological approach is very good in studying small signaling/transcriptional &lt;strong&gt;modules&lt;/strong&gt;. The entire module can be cloned and expressed in a cell under an inducible/constitutive promoter. This can be implemented in a heterologous cell also. A mathematical model generally helps in making certain predictions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other strategies which can be used instead of overexpression:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;using sensor constructs harboring a functional or non-functional&#xA;target sites instead of overexpressing the upstream protein&lt;/li&gt;&#xA;&lt;li&gt;downregulation experiments&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-08T07:25:17.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7806" PostTypeId="2" ParentId="6916" CreationDate="2013-04-08T07:52:28.863" Score="2" Body="&lt;p&gt;Firstly, demyelination has got nothing to do with membrane integrity of the neuron. Demyelination causes the current to &lt;strong&gt;&quot;leak&quot;&lt;/strong&gt; through the ion-channels and thus causing loss of signal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an old article which reports a study on membrane integrity of &lt;strong&gt;RBCs&lt;/strong&gt; of MS patients but there seems to be no connection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has been proven that neurons do secrete some cytokines such as IFNgamma but the signaling is mostly para/auto-crine and I dont think the cytokines will accumulate in CSF. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;MS is identified by the presence of anti-myelin antibodies, which might be the exact biomarker for the disease. A general neuroinflammation is not concluded as MS. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to answer your final question &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there research of this ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is none that exactly talks about neuron membrane dynamics in MS. The most parsimonious assumption is that there is no effect, but any hypothesis has to be proven. It might be experimentally difficult to address this question and how to design the experiment for this study would be an interesting question. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-08T07:52:28.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7807" PostTypeId="1" AcceptedAnswerId="7839" CreationDate="2013-04-08T08:00:03.290" Score="3" ViewCount="250" Body="&lt;p&gt;I wonder if it's possible to pet a domestic crow, or an owl. Do birds respond to grooming as cats or dogs, for example? If so, then how does one pet a bird?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2015-08-27T19:02:44.503" Title="Is it possible to pet/groom birds?" Tags="&lt;zoology&gt;&lt;ornithology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7808" PostTypeId="2" ParentId="7437" CreationDate="2013-04-08T09:10:29.063" Score="3" Body="&lt;p&gt;There is no such  &lt;em&gt;promiscuous&lt;/em&gt; neurotransmitter. There is always some difference between central and peripheral nervous system w.r.t neurotransmitter usage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glutamate is one neurotransmitter which acts as an excitatory agonist in most neurons (but still.. not ALL neurons)&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-08T09:10:29.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7809" PostTypeId="1" CreationDate="2013-04-08T09:19:46.880" Score="11" ViewCount="716" Body="&lt;p&gt;Some people have curly hair, as well as fur of some animals can be curly.&#xA;However, shapes which are curly are not &lt;a href=&quot;http://en.wikipedia.org/wiki/Chirality_%28mathematics%29&quot; rel=&quot;noreferrer&quot;&gt;mirror symmetric&lt;/a&gt;, much alike screws or chiral molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is whether curly hair in a given species (say, humans, but I don't stick to this example) are in the same proportion left-handed and right-handed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One can easily imagine that &lt;a href=&quot;http://en.wikipedia.org/wiki/Chirality_%28chemistry%29&quot; rel=&quot;noreferrer&quot;&gt;chirality of molecules&lt;/a&gt; (e.g. keratin) gives rise to macroscopic chirality of curly hair. However, it is far from obvious whether this effect is strong enough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested mostly in data. It might be easy (yet misleading) to convince oneself that there should (or there shouldn't) be relation of microscopic to macroscopic mirror symmetry (or lack of it).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(E.g. in some other cases there is such effect - e.g. with left/right orientation of body organs like heart, or asymmetry of left and right brain.)&lt;/p&gt;&#xA;" OwnerUserId="129" LastEditorUserId="129" LastEditDate="2013-04-10T08:12:23.477" LastActivityDate="2013-04-28T12:55:26.380" Title="Chiral (a)symmetry of curly hair (and fur)" Tags="&lt;hair&gt;&lt;chirality&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7810" PostTypeId="1" CreationDate="2013-04-08T14:51:54.240" Score="4" ViewCount="1127" Body="&lt;p&gt;I wonder if I can heat Trizol reagent for 30 min 65C. The goal is to disrupt protein-RNA complex while inhibiting nucleases. (I can't use RNasin cause it's inactivated in 65C, and can't use RVC cause reaction contains EDTA).&#xA;I realize that heating Trizol is not safe and its vapors are hazardous, but i can perform it in the hood.&lt;/p&gt;&#xA;" OwnerUserId="3358" LastEditorUserId="3340" LastEditDate="2014-01-18T06:49:10.977" LastActivityDate="2014-08-05T13:28:12.577" Title="Can I heat Trizol?" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;protocol&gt;&lt;lab-reagents&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7811" PostTypeId="2" ParentId="7777" CreationDate="2013-04-08T18:53:45.767" Score="7" Body="&lt;p&gt;There is &lt;strong&gt;no damage&lt;/strong&gt; of brain cells, as in the context of lesions in neurodegenerative disorders. There are, however, two mechanisms attributed to the memory loss associated with cannabis/marijuana and these are purely physiological responses.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867412001420&quot;&gt;Astrocyte mediated&lt;/a&gt;: CB1R (cannabinoid receptor) in astrocyte gets activated and promotes glutamate release. This glutamate induces &lt;strong&gt;Long Term Depression&lt;/strong&gt; in post synaptic neuron. &#xA;&lt;em&gt;Synaptic currents can cause both LTP and LTD. The properties of the synaptic current wave dictates the outcome. Please refer to review articles on LTP and LTD for more information.&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/neuro/journal/v12/n9/full/nn.2369.html&quot;&gt;GABAergic interneuron mediated&lt;/a&gt;: CB1R activation in GABAergic interneurons (inhibitory neurons) causes activation of mTOR pathway and promotes protein synthesis. CB1R activates mTOR through PI3K/Akt. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-08T18:53:45.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7812" PostTypeId="2" ParentId="7800" CreationDate="2013-04-09T03:14:13.413" Score="3" Body="&lt;p&gt;The &quot;probe by background&quot; interaction is the response of different probes as a function of background gene expression. For example, depending on which of the 6 backgrounds a probe is in, the drug response may go up or down. Probes as a function of background is probably easier to imagine than background as a function of probe (which is equally valid). For 39,115 probes and 6 background networks, there are 234,690 interactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a technical sense, &quot;probe by background&quot; is the interaction term in the linear model that the authors fit for each drug. The details of the analysis are in the supplemental methods. The model they fit is&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Drug_Response ~ Probe + Probe * Background + Background&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;which translates to &quot;Drug response is modeled by Probe, the interaction of Probe and Background, and Background&quot;. The middle term (with the &lt;code&gt;*&lt;/code&gt;) is the interaction term. &lt;a href=&quot;http://www.wilderdom.com/statistics/Interaction.html&quot; rel=&quot;nofollow&quot;&gt;Here is a page&lt;/a&gt; that helps to explain how to understand significant interaction terms in linear models.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-04-09T03:14:13.413" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7813" PostTypeId="5" CreationDate="2013-04-09T03:58:09.550" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;What questions should have this tag?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Questions related to principles of microscopy (not extending too much in the field of optics) &lt;/li&gt;&#xA;&lt;li&gt;Sample preparation for microscopy&lt;/li&gt;&#xA;&lt;li&gt;Technical queries regarding instrument settings&lt;/li&gt;&#xA;&lt;li&gt;Analysis of microscopic image data&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Some basic definitions&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Magnification: Ratio of the size of the image and the actual size of the object &lt;/li&gt;&#xA;&lt;li&gt;Focus: Actual or imaginary point of convergence of the rays refracted through the lens&lt;/li&gt;&#xA;&lt;li&gt;Numerical Aperture: The ability of an optical system to gather light and resolve two closely spaced objects. Defined by: NA = n*sinθ [where n is the refractive index of light and θ is the half-angle of the light cone formed between the object and the lens]&lt;/li&gt;&#xA;&lt;li&gt;Excitation and Emission (with respect to fluorescence microscopy): The wavelength of light absorbed or emitted by the major fluorophore, respectively.&lt;/li&gt;&#xA;&lt;li&gt;Quantum yield: Ratio of number of photons absorbed and number of photons emitted by a fluorophore&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="4101" LastEditDate="2013-10-31T16:46:51.523" LastActivityDate="2013-10-31T16:46:51.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7814" PostTypeId="4" CreationDate="2013-04-09T03:58:09.550" Score="0" Body="The technique of using microscopes to view objects that are otherwise too small to be easily seen by the naked eye." OwnerUserId="3340" LastEditorUserId="4101" LastEditDate="2013-10-31T16:46:51.523" LastActivityDate="2013-10-31T16:46:51.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7815" PostTypeId="5" CreationDate="2013-04-09T04:02:51.293" Score="0" Body="&lt;p&gt;Standard names should be used for all chemicals.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What questions should have this tag?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Questions related to usage, optimization and synthesis of chemicals required to perform laboratory experiments.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="4101" LastEditDate="2013-10-31T19:09:00.067" LastActivityDate="2013-10-31T19:09:00.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7816" PostTypeId="4" CreationDate="2013-04-09T04:02:51.293" Score="0" Body="Chemicals used in the lab for experiments." OwnerUserId="3340" LastEditorUserId="4101" LastEditDate="2013-10-31T19:09:00.067" LastActivityDate="2013-10-31T19:09:00.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7817" PostTypeId="5" CreationDate="2013-04-09T04:08:21.630" Score="0" Body="&lt;p&gt;A sub-discipline of evolutionary biology which involves the study of evolutionary relatedness between different organisms based on their molecular and morphological features.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-27T10:49:54.637" LastActivityDate="2017-03-27T10:49:54.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7818" PostTypeId="4" CreationDate="2013-04-09T04:08:21.630" Score="0" Body="A sub-discipline of evolutionary biology which involves the study of evolutionary relatedness between different organisms based on their molecular and morphological features." OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-09T04:18:32.460" LastActivityDate="2013-04-09T04:18:32.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7819" PostTypeId="5" CreationDate="2013-04-09T04:38:23.520" Score="0" Body="&lt;p&gt;In terms of humans, there is a strict definition of death, namely brain death:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brain death is defined as the absence of higher brain function or brain-stem reflexes, and when other factors that could mimic brain death, such as drugs or low blood pressure, have been ruled out (1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brain dead patients can be artificially maintained by means of life support that sustain blood flow and breathing. Still, they are clinically dead (1). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;(1): &lt;a href=&quot;http://www.webmd.com/brain/news/20140103/brain-dead-faq?page=2&quot; rel=&quot;nofollow&quot;&gt;WebMD&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="9943" LastEditDate="2016-02-22T13:42:00.920" LastActivityDate="2016-02-22T13:42:00.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7820" PostTypeId="4" CreationDate="2013-04-09T04:38:23.520" Score="0" Body="A state in which an organism or a cellular system, as defined by its full set of functionality, ceases to exist (i.e., most of the functions are irreversibly lost). " OwnerUserId="3340" LastEditorUserId="107" LastEditDate="2013-04-09T04:51:11.280" LastActivityDate="2013-04-09T04:51:11.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7823" PostTypeId="5" CreationDate="2013-04-09T08:04:15.753" Score="0" Body="&lt;p&gt;Classes of neurotransmitters include:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Amino acid and derivatives: Glutamate, Glycine, GABA, Epinephrine, Dopamine, Serotonin, etc.&lt;/li&gt;&#xA;&lt;li&gt;Acetylcholine &lt;/li&gt;&#xA;&lt;li&gt;Opioids: Endorphin, Enkephalin &lt;/li&gt;&#xA;&lt;li&gt;Peptides: Neuropeptide-Y, Oxytocin, Vasopressin, etc.&lt;/li&gt;&#xA;&lt;li&gt;Cannabinoid: Anandamide&lt;/li&gt;&#xA;&lt;li&gt;Gaseous: Nitric Oxide&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Neurotransmitters are not repressive or activating per-se as their effects on the postsynaptic cell are due to different receptors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neurotransmitter receptors are of two types:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Ionotropic: Ligand-gated ion channels that open up or close upon binding to neurotransmitter.&lt;/li&gt;&#xA;&lt;li&gt;Metabotropic: Receptors that transduce the signal through secondary messengers upon neurotransmitter binding&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="4101" LastEditDate="2013-10-31T01:03:18.527" LastActivityDate="2013-10-31T01:03:18.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7824" PostTypeId="4" CreationDate="2013-04-09T08:04:15.753" Score="0" Body="Small molecules involved in the propagation of a nerve signal across the synapses. " OwnerUserId="3340" LastEditorUserId="4101" LastEditDate="2013-10-31T01:03:18.527" LastActivityDate="2013-10-31T01:03:18.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7825" PostTypeId="1" AcceptedAnswerId="7864" CreationDate="2013-04-09T10:24:13.393" Score="2" ViewCount="1478" Body="&lt;p&gt;I have always faced a problem while analyzing small RNAseq data, at the step of adapter trimming.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Overview of small RNAseq (Illumina)&lt;/h3&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;RNA is size fractionated using columns or PAGE&lt;/li&gt;&#xA;&lt;li&gt;3' and 5' adapter ligation&lt;/li&gt;&#xA;&lt;li&gt;cDNA synthesis&lt;/li&gt;&#xA;&lt;li&gt;PCR amplification&lt;/li&gt;&#xA;&lt;li&gt;Sequencing &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The length of the reads is dependent on the machine and recent ones like HiSeq can provide ~200bp.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem, however, is with reads smaller than the max read length of the machine and this is common with small RNAs such as miRNAs (especially if the concatemer of smallRNA and the complete 3'adapter is bigger than the max read length).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first step of analysis is trimming of the 3' adapter (Illumina Truseq: TCGTATGCCGTCTTCTGCTTGT). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several algorithms are available to do this job and what they precisely do is to check for overlaps between the adapter sequence and 3'end of the reads and then clip the aligned region.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Now the problem is this&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;You can't be really sure of very small alignments because they may not really be originating from the adapters, which means that you should specify a lower limit of alignment for clipping. I usually set it as 5 (intuitively).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if a small piece of sequence really came from the adapter then it will remain and there is no way to clip it without any doubt. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The real problem comes during aligning the reads to the reference sequence. Aligners like bowtie (which i prefer to use), generally have user defined argument for number of allowed mismatches. Bowtie generally doesn't perform very well if you allow a lots of mismatches. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Subsequently, you might lose a really valuable read. &lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Alternative&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;To avoid this problem I sometimes trim the reads to around 25nt (for miRNA profiling). This creates a new problem:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can't really distinguish whether the read came from a pre-miRNA (a longer RNA) or from mature-miRNA (smaller RNA that arises by processing of pre-miRNA)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have an experience or an idea about how to solve this problem? &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="107" LastEditDate="2013-04-09T12:57:35.317" LastActivityDate="2013-04-11T08:50:41.973" Title="Problems with analysis of small RNAseq data - Adapter trimming" Tags="&lt;bioinformatics&gt;&lt;rna-sequencing&gt;&lt;small-rnaseq&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7827" PostTypeId="5" CreationDate="2013-04-09T10:45:30.697" Score="0" Body="&lt;p&gt;This technique is employed to detect and quantitate small RNAs such as miRNA, piRNA, endo-siRNA etc.&#xA;The basic process involves:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Enrichment of small RNAs using polyacylamide gel electrophoresis or RNA-binding columns&lt;/li&gt;&#xA;&lt;li&gt;Ligation of 3'and 5'adapters &lt;/li&gt;&#xA;&lt;li&gt;cDNA synthesis&lt;/li&gt;&#xA;&lt;li&gt;PCR amplification and library preparation&lt;/li&gt;&#xA;&lt;li&gt;Sequencing&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-09T12:51:43.850" LastActivityDate="2013-04-09T12:51:43.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7828" PostTypeId="4" CreationDate="2013-04-09T10:45:30.697" Score="0" Body="Next-Gen Sequencing of RNA sample enriched with small RNAs (~15-200nt) such as miRNA, piRNA  etc. " OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-09T12:51:39.477" LastActivityDate="2013-04-09T12:51:39.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7829" PostTypeId="1" AcceptedAnswerId="7830" CreationDate="2013-04-09T12:40:03.720" Score="2" ViewCount="1895" Body="&lt;p&gt;In my classes and on the internet, brittle nails and dry hair (or hair loss) are described as symptoms of iron deficiency anemia, but none explains the cause of such symptoms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have any clues or explanation of such symptoms?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Iron_deficiency_anemia#Signs_and_symptoms&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Iron_deficiency_anemia#Signs_and_symptoms&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3363" LastEditorUserId="3363" LastEditDate="2013-04-22T20:41:18.880" LastActivityDate="2018-09-11T15:58:01.710" Title="Iron deficiency anemia symptoms explanation" Tags="&lt;pathology&gt;&lt;hematology&gt;&lt;hair&gt;&lt;red-blood-cell&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7830" PostTypeId="2" ParentId="7829" CreationDate="2013-04-09T14:24:32.260" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/S1471-4914%2801%2901920-7&quot; rel=&quot;nofollow&quot;&gt;The molecular basis of copper-transport diseases&lt;/a&gt; in &lt;em&gt;Trends in Molecular Medicine&lt;/em&gt;, Volume 7, Issue 2, 1 February 2001, Pages 64–69, has a link to a 1973 paper by JM Gillespie entitled &quot;Keratin Structure and Changes with Copper Deficiency,&quot; stating&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Menkes patients are often diagnosed from their unusual hair structure – termed pili torti – also known as kinky or steely hair, caused by reduced keratin cross-linking, a process that is catalyzed by an uncharacterized copper oxidase.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I haven't been able to find anything further, but since iron and copper levels can both be affected in anemia, this may be the link you're looking for. There may also be other enzymes involved that use iron-mediated catalysis. Since there are so many different kinds of keratins (the major protein that makes up hair and nails, among diverse other functions in the body), there may easily be multiple cross-linking and assembly pathways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other websites I found have also claimed that anemia-associated pathologies with hair and/or nails may be related to reduced oxygenation as a result of low iron levels, but they don't give any citations, and given the nature of the sites (nail care, fashion, etc.) it may just be an educated guess.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2013-04-09T18:26:28.177" LastActivityDate="2013-04-09T18:26:28.177" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7831" PostTypeId="2" ParentId="7553" CreationDate="2013-04-09T15:04:05.987" Score="6" Body="&lt;p&gt;Neurons use lot of energy to maintain their polarized state, this is not required to other cells [1,2].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When O2 or blood flow (which is carrying the nutrients) is reduced, the neuronal ATP levels breaks down very fast, with 90% ATP depleted in less than 5 minutes. Without ATP, the neuron can not maintain the correct ion flux, so depolarization occurs causing glutamate excitotoxicity, cell swelling and finally cell death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1] &lt;a href=&quot;http://www.acnp.org/g4/gn401000064/ch064.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.acnp.org/g4/gn401000064/ch064.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2] &lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=why-does-the-brain-need-s&quot; rel=&quot;noreferrer&quot;&gt;http://www.scientificamerican.com/article.cfm?id=why-does-the-brain-need-s&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2013-04-09T15:04:05.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7832" PostTypeId="1" CreationDate="2013-04-09T18:20:27.253" Score="0" ViewCount="56" Body="&lt;p&gt;We usually thought that weightlifting is a tough game. It is only for great physique.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are 6 man in history who lifted  3 times their body weight. Check &lt;a href=&quot;http://www.chidlovski.net/liftup/a_club_3xbwt.asp&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3 of them are Bantamweight(56kg), 2 of them are Featherweight(60kg), and 1 is at Lightweight(67.5kg).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of them are light. Is there are fact that light weighted are more efficient in weight lifting?&lt;/p&gt;&#xA;" OwnerUserId="1870" LastActivityDate="2013-04-09T21:06:07.473" Title="Is there any relation between weight class and extreme lifting performance in O-lifting?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7833" PostTypeId="2" ParentId="7789" CreationDate="2013-04-09T18:25:04.343" Score="2" Body="&lt;p&gt;The other answers describe the situation well for an individual, however there have been cases in the past where antibiotic resistance has emerged and been outgunned by medical advances to overcome this specific resistance.  A good example of this &lt;em&gt;co-amoxyclav&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The original Amoxicillin, a  β-lactam antibiotic, was previously effective against a good range of bacteria.  However antibiotic resistance then developed when some bacteria began producing  β-lactamase, an enzyme which degraded the  β-lactam ring rendering the drug (and all within its class) useless against them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This resistance was then countered when a way to inhibit the β-lactamase the bacteria were producing was discovered.  Clavulanic acid does this, leading to the mixture of its potassium salt with Amoxicillin.  The mixture (coamoxyclav) allows the amoxicillin to still be effective against the previously resistant bacteria, as the resistance they have been developed is being inhibited in parallel.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For this reason in a hospital setting it is more common to prescribe Co-amoxyclav rather than a beta-lactam antibiotic in isolation.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2013-04-09T18:25:04.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7834" PostTypeId="2" ParentId="7832" CreationDate="2013-04-09T21:06:07.473" Score="1" Body="&lt;p&gt;I suspect that such might partially result from both an inherent advantage and a coincidental advantage of lower height.  The former would be an effect of strength being roughly proportional to the cross-sectional area of muscle (square of a linear measure) and mass being proportional to the body volume (cube of linear measure).  This would make a 182cm person 10% stronger by body weight than a 200cm person of the same build (when one might initially think that having the same build would imply the same strength per unit weight).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second advantage might be from taller individuals tending to have a more slender frame.  A more slender frame might be associated with lower muscle bulk (cross-sectional area) even with intensive training (more &quot;ectomorphic&quot;?).  Since there is a limit to thickness, to increase mass height must be increased, and if taller individuals tend to be more slender in build then as mass increases the build would tend to become more slender reducing muscle cross-sectional area (strength) in proportion to mass.&lt;/p&gt;&#xA;" OwnerUserId="1858" LastActivityDate="2013-04-09T21:06:07.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7835" PostTypeId="1" CreationDate="2013-04-09T22:23:56.757" Score="3" ViewCount="4655" Body="&lt;p&gt;As far as I know there is an optimum distance between a promoter and the gene for the best expression levels. What is that distance for common promoters like CMV, SV40? If you have a first hand experience about this (e.g. if you have cloned the gene way downstream of the promoter and didn't/did see expression) and share it I will be grateful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have comprehensive knowledge for other promoters please feel free to add them in the list too; they don't need to be common. I just want to hear people's experience on the subject.&lt;/p&gt;&#xA;" OwnerUserId="1772" LastActivityDate="2013-12-22T03:29:16.233" Title="Where to put the gene after eukaryotic promoter for best expression levels?" Tags="&lt;proteins&gt;&lt;gene-expression&gt;&lt;cell-culture&gt;&lt;experimental-design&gt;&lt;protein-expression&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7836" PostTypeId="1" CreationDate="2013-04-09T23:00:34.413" Score="3" ViewCount="593" Body="&lt;p&gt;When I express proteins in bacteria I put at least two stop codons at the end of the gene to increase the termination efficiency. Is this the case in eukaryotic cells too? If I put a single stop codon is there a risk for the ribosomal complex to readthrough and continue translation?&lt;/p&gt;&#xA;" OwnerUserId="1772" LastActivityDate="2013-12-30T00:39:37.007" Title="What is the translation termination efficiency in mammalian cells?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;translation&gt;&lt;protein-expression&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7837" PostTypeId="2" ParentId="7829" CreationDate="2013-04-10T00:31:18.997" Score="1" Body="&lt;p&gt;I did some searches on the relationship between iron deficiency anemia (IDA) and hair loss. Surprising, there are lots of debates about this and I don't think anyone has a solid reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If iron deficiency is related to hair loss then taking iron supplement may potentially reverse the effect. However, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0190962205047456&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; pointed out that:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;....there is insufficient evidence to recommend giving iron supplementation therapy to patients with hair loss and iron deficiency....&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding is, human body actually contains very little amount of iron. And most of the iron are involved in cellular respiration and oxygen exchange. Free floating iron is very toxic and bad for the body. Therefore most of the iron storage are in Hemoglobin (2/3), followed by ferritin+hemosiderin (about 1/3), some are utilized by the mitochondria (those awesome cytochromes and electron transport chains), lastly the transport vessel trans-ferritin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think Hair loss and brittle nail are just indirectly caused by IDA. Because most of the time IDA is cause by malnutrition. And usually the food sources that are contained the most iron are meat, poultry and egg. These food are also rich in protein. I think lack of meat protein-rich diet is the main reason of hair loss and brittle nail, and such diet leads to IDA. (Strict vegans, be careful about your food choices!)&lt;/p&gt;&#xA;" OwnerUserId="3139" LastActivityDate="2013-04-10T00:31:18.997" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7838" PostTypeId="2" ParentId="7809" CreationDate="2013-04-10T01:38:31.400" Score="0" Body="&lt;p&gt;Keratin's handedness does not &lt;em&gt;directly&lt;/em&gt; give rise to the curls of hair. One has to cross many many length scales to move from the keratin scale to the whole hair fiber. There's an animation &lt;a href=&quot;http://www.hair-science.com/_int/_en/topic/topic_sousrub.aspx?tc=ROOT-HAIR-SCIENCE%5EPORTRAIT-OF-AN-UNKNOWN-ELEMENT%5ESUPERB-CHEMISTRY&amp;amp;cur=SUPERB-CHEMISTRY&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; that shows those many length scales. But here are some other arguments if you're inclined...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the superhelicity of keratin effected the curling of hair, all hair would twist in the same direction, because the keratin superhelix always twists in the same (left-handed) direction (for the naturally occurring proteins.) But that isn't the case. At least not for my hair! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or you can ask, if the keratin superhelix gives rise to curly hair, then how is this effect mitigated in straight hair? The structure of keratin isn't &lt;em&gt;directly&lt;/em&gt; giving rise to the long-range patterns of hair. The keratin filaments are being arranged in particular ways, and the long-range behavior is independent of the short-range superhelicity.&lt;/p&gt;&#xA;" OwnerUserId="3336" LastEditorUserId="3059" LastEditDate="2013-04-10T02:17:17.767" LastActivityDate="2013-04-10T02:17:17.767" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7839" PostTypeId="2" ParentId="7807" CreationDate="2013-04-10T02:01:26.220" Score="5" Body="&lt;p&gt;Birds do groom, but not like mammals do. People tend to call their grooming behavior &lt;em&gt;preening&lt;/em&gt;. Preening removes dirt and parasites, arranges the feathers nicely, and distributes oils over the feather (very important for waterfowl.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question better, we need to look at the specific species. Lots of birds preen each other socially, so if you wanted to pet a bird (in a way it likes) it's good to know how the species behaves. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You mention crows and owls. Crows are social so they &lt;em&gt;may&lt;/em&gt; preen each other; they're also sophisticated (cultural) so it's hard to generalize. &lt;a href=&quot;https://www.youtube.com/watch?v=4KmDT6txbVA&quot;&gt;A 'bird nerd' on YouTube&lt;/a&gt; shows convincing footage of such behavior. I think family groups of crows preen each other, but I don't have a source. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Owls tend to be solitary and would not understand preening behavior from a human. A social species of owl might preen; I don't know. Of course, if you just &lt;a href=&quot;https://www.youtube.com/watch?v=KsVk6cYLwUw&quot;&gt;go ahead and pet your owl like a dog,&lt;/a&gt; it may appear to like it. It's hard to say if it does like it...it's easy to anthropomorphize a bird with binocular vision!&lt;/p&gt;&#xA;" OwnerUserId="3336" LastActivityDate="2013-04-10T02:01:26.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7840" PostTypeId="1" CreationDate="2013-04-10T02:52:09.733" Score="2" ViewCount="155" Body="&lt;p&gt;I am familiar with the &lt;a href=&quot;http://bioinformatics.org/firstglance/fgij/&quot; rel=&quot;nofollow&quot;&gt;Jmol&lt;/a&gt;, &lt;a href=&quot;http://rasmol.org/&quot; rel=&quot;nofollow&quot;&gt;Rasmol&lt;/a&gt; and &lt;a href=&quot;http://www.pymol.org/&quot; rel=&quot;nofollow&quot;&gt;PyMoL&lt;/a&gt; softwares, and was recently introduced to &lt;a href=&quot;http://bioblender.eu/&quot; rel=&quot;nofollow&quot;&gt;BioBlender&lt;/a&gt;. However, I am completely unaware if any of these programs (or others) are capable of loading a .pdb and allowing for the change in a particular amino acid, to ultimately visualize the change in tertiary structure caused by that substitution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are any programs capable of performing an amino acid substitution on a molecule loaded by .pdb and showing the change in tertiary structure?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="112" LastEditDate="2013-04-10T08:29:48.847" LastActivityDate="2013-04-27T07:17:35.307" Title="What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?" Tags="&lt;biochemistry&gt;&lt;bioinformatics&gt;&lt;proteins&gt;&lt;structural-biology&gt;&lt;software&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7841" PostTypeId="1" CreationDate="2013-04-10T02:58:22.753" Score="1" ViewCount="717" Body="&lt;p&gt;Surveys show that &lt;a href=&quot;http://www.niaid.nih.gov/topics/foodAllergy/understanding/Pages/quickFacts.aspx&quot; rel=&quot;nofollow&quot;&gt;0.6 percent of the US population has an allergic reaction to peanuts&lt;/a&gt;. This prevalent allergy has even prompted some to &lt;a href=&quot;http://shine.yahoo.com/parenting/pb-38-j-worst-weapon-kid-bring-school-215000284.html#!dmCXx&quot; rel=&quot;nofollow&quot;&gt;ban peanuts from schools altogether&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am completely unfamiliar with the topic, and can't seem to find any specifics in the literature. Thus my question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What specifically causes the the allergic reaction associated with peanut consumption, and why is it so prevalent in comparison to other foods?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="107" LastEditDate="2013-04-10T20:49:33.710" LastActivityDate="2013-04-11T03:51:19.083" Title="What causes peanut allergies?" Tags="&lt;immunology&gt;&lt;food&gt;&lt;allergies&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7842" PostTypeId="2" ParentId="2132" CreationDate="2013-04-10T03:10:12.923" Score="8" Body="&lt;p&gt;If you dissect striated muscle out of most-any organism, the actual contractile apparatus works over a wide range of temperatures. So that's at the single-muscle-fiber scale. The muscle itself continues to work at all (thawed) temperatures below body temperature -- the problem comes with its regulation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;https://en.wikipedia.org/wiki/Shivering&quot;&gt;shivering response&lt;/a&gt; -- a centrally controlled  involuntary contractile pattern -- overwhelms voluntary muscle control. So &lt;strong&gt;the mechanism behind loss of muscle coordination in hypothermia is the same as the shivering mechanism.&lt;/strong&gt; When the core temperature drops, the midbrain starts over-riding voluntary control of the muscles. When the core temperature drops far enough; &lt;a href=&quot;http://archive.rubicon-foundation.org/xmlui/bitstream/handle/123456789/5975/SPUMS_V28N3Supl_10.pdf?sequence=1&quot;&gt;around 32C&lt;/a&gt;, the shivering often slows down or stops. Voluntary movement becomes compromised probably because the brain simply isn't working; neuron firing rates are so slow that sensation, processing, and motor responses are all critically impaired. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;feeling&lt;/em&gt; of numbness does not actually directly accompany a loss of muscle contractility. You can walk pretty much indefinitely on frozen feet if you can keep your balance (and you keep your core temperature up.) Lots of people survive severe frostbite of their feet (their feet do not often survive, however.) The reason why it &lt;em&gt;seems&lt;/em&gt; your hands don't work when they get cold is that you can't feel what you're doing (note; your hands can be &lt;a href=&quot;http://www.ingentaconnect.com/content/asma/asem/2003/00000074/00000009/art00013&quot;&gt;much colder&lt;/a&gt; than your core body temperature.) But the muscles themselves work right up until they freeze solid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE:&#xA;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1192187/&quot;&gt; Here's a paper&lt;/a&gt; that directly addresses the scenario posed by OP -- the decrease in grip strength with temperature.   &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1192187/?page=3&quot;&gt;Figure 1 of that paper&lt;/a&gt; illustrates their experimental setup; they measure the contractile strength of the index finger while manipulating the temperature of the rest of the hand. They show that contractile function is impaired with temperature and look at temperatures as low as 12C. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They measure as much as a 50% impairment on twitch tension upon cooling to 12C. It's interesting that they review results suggesting that some of this effect is intrinsic to the muscle fiber (not neurological), showing that I should refine what is meant by &quot;continuing to work&quot; in my opening paragraph. (I meant having an ability to generate contractile force when equilibrated in solution containing sufficient ATP and Ca$^{2+}$, not the ability to contract optimally.) For fun, I linearly extrapolated the final arm of &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1192187/?page=9&quot;&gt;Figure 5&lt;/a&gt; and found that the 'voluntary tension' approached 25% at 5C. &lt;strong&gt;This suggests that total failure of the voluntary contraction happens somewhere below the freezing point of water&lt;/strong&gt; (muscle would freeze at a temperature lower than 0C because of colligative effects.) &lt;/p&gt;&#xA;" OwnerUserId="3336" LastEditorUserId="3336" LastEditDate="2013-04-12T23:08:19.630" LastActivityDate="2013-04-12T23:08:19.630" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7843" PostTypeId="1" CreationDate="2013-04-10T04:02:26.523" Score="2" ViewCount="86" Body="&lt;p&gt;I understand that mass spec is widely used to study PTMs like glycosylation of proteins, but how can mass spec determine correct PTM structure of say glycosylation if two glycan structures have the same mass but different arrangement (i.e. isobaric)? Also, how can mass spec determine the difference between structural isomers?  &lt;/p&gt;&#xA;" OwnerUserId="3232" LastEditorUserId="3059" LastEditDate="2013-04-10T10:51:57.433" LastActivityDate="2013-04-11T06:21:40.453" Title="PTMs of proteins via mass spec?" Tags="&lt;proteins&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7844" PostTypeId="2" ParentId="7843" CreationDate="2013-04-10T06:31:18.610" Score="1" Body="&lt;p&gt;I am not a MassSpec expert but this is what I understand from my spectroscopy basics: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In tandem MS (MS-MS), the ionized analyte generally undergoes or made to undergo fragmentation (breaking up into smaller ions). Fragmentation allows you to study finer details. It is also essential for de-novo peptide sequencing. Different fragmentation techniques, such as Collision Induced Dissociation (CID) or Photofragmentation, yield different kinds of secondary ions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can intuitively understand that Fragmentation of structural isomers will yield different kinds of secondary ions (using the same fragmentation technique). The choice of fragmentation technique depends on the molecular nature of the analyte. In the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2523269/&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; that I mentioned previously, they use laser induced photofragmentation to dissociate glycan-ions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even small molecules, which had been classically studied by MassSpec, undergo isomerization after ionization in order to stabilize the ion. Reactions such as reverse-Diels-Adler can also happen. The pattern of reactions would differ between structural isomers. For basics you can refer to a book on Spectroscopic techniques by &lt;a href=&quot;http://books.google.co.in/books/about/Spectrometric_identification_of_organic.html?id=3VJCAQAAIAAJ&quot; rel=&quot;nofollow&quot;&gt;Silverstein&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-11T06:21:40.453" LastActivityDate="2013-04-11T06:21:40.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7845" PostTypeId="2" ParentId="7840" CreationDate="2013-04-10T10:15:08.767" Score="1" Body="&lt;p&gt;Visualising the change induced by an amino acid on the 3D structure is part of an entire field of research call molecular modelling (&lt;a href=&quot;http://en.wikipedia.org/wiki/Molecular_modelling&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Molecular_modelling&lt;/a&gt;). There is a huge body of research available on the subject and I am not up-to-date anymore in this field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I used to do was simulating the optimal shape of a AA chain (~10) which was part of the bigger molecule. The technique consisted in using a Monte-Carlo procedure to simulate heating the molecule and cooling it down millions of time and checking for the stability of the resulting conformation using . I used Modeller, Procheck and Prosa. That was in 2000.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a wikipedia list of molecular mechanics modelling software here (&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="3364" LastActivityDate="2013-04-10T10:15:08.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7847" PostTypeId="1" AcceptedAnswerId="7859" CreationDate="2013-04-10T12:13:53.103" Score="12" ViewCount="49421" Body="&lt;p&gt;According to Wikipedia, muscle cramps are caused by the inability of myosin fibers to break free from the actin filaments during contraction, resulting in a prolonged contraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lack of ATP would obviously produce cramping, as myosin requires ATP to become free from actin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I have heard that potassium and sodium are useful for treating cramps and that their deficiencies can lead to cramping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, how does a deficiency in sodium or potassium result in the inability of myosin fibers to break free from the actin filaments during contraction?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="-1" LastEditDate="2017-11-11T15:50:38.263" LastActivityDate="2017-11-12T14:03:42.493" Title="What is the cause of muscle cramps?" Tags="&lt;physiology&gt;&lt;muscles&gt;" AnswerCount="6" CommentCount="1" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7848" PostTypeId="2" ParentId="7840" CreationDate="2013-04-10T13:06:15.307" Score="2" Body="&lt;p&gt;One application that I am aware of that will do this, as well as much else besides, is &lt;a href=&quot;http://spdbv.vital-it.ch&quot; rel=&quot;nofollow&quot;&gt;Swiss-PDB Viewer aka DeepView&lt;/a&gt;. If you go to the site and select User Guide in the left hand tabs you will see a subsection called mutations and following that will tell you what the application can do.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-04-10T16:04:16.013" LastActivityDate="2013-04-10T16:04:16.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7849" PostTypeId="1" AcceptedAnswerId="7855" CreationDate="2013-04-10T14:16:29.430" Score="0" ViewCount="957" Body="&lt;p&gt;I need to prepare YPD plates containing hygromycin, but I don't know which concentration I can use. I'll select transformants of &lt;em&gt;Hansenula polymorpha&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3082" LastEditorUserId="107" LastEditDate="2013-04-10T21:53:00.810" LastActivityDate="2013-04-10T21:53:00.810" Title="How the concentration of an antibiotic is chosen for YPD medium?" Tags="&lt;antibiotics&gt;&lt;yeast&gt;&lt;transformation&gt;&lt;medium&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7852" PostTypeId="1" AcceptedAnswerId="45086" CreationDate="2013-04-10T16:42:22.067" Score="5" ViewCount="401" Body="&lt;p&gt;I have heard that omega-3 fatty acids found in fish are a good way to prevent/reduce cholesterol problems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is how do omega-3 fatty acids do that: what are they doing on a chemical level to produce this effect? And is there any way to maximize this effect through other substances, that may work in concert with them?&lt;/p&gt;&#xA;" OwnerUserId="3366" LastEditorUserId="3366" LastEditDate="2013-04-10T18:16:55.873" LastActivityDate="2016-04-10T11:52:46.010" Title="How do omega-3 fatty acids reduce cholesterol at the molecular level?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7854" PostTypeId="1" CreationDate="2013-04-10T20:37:15.323" Score="3" ViewCount="12058" Body="&lt;p&gt;A plasmid is a small DNA molecule that is physically separate from, and can replicate independently of, chromosomal DNA within a cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, in eukaryotes, episomes are closed circular DNA molecules that are replicated in the nucleus. Viruses are the most common examples of this, such as herpesviruses, adenoviruses, and polyomaviruses. Episomes in eukaryotes behave similarly to plasmids in prokaryotes in that the DNA is stably maintained and replicated with the host cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Plasmid&quot; rel=&quot;nofollow&quot;&gt;Source is wikipedia.&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="3082" LastEditorUserId="3059" LastEditDate="2013-04-10T20:48:55.817" LastActivityDate="2015-05-23T17:05:05.067" Title="Is episome a plasmid or a virus?" Tags="&lt;dna&gt;&lt;bacteriology&gt;&lt;terminology&gt;&lt;eukaryotic-cells&gt;&lt;plasmids&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7855" PostTypeId="2" ParentId="7849" CreationDate="2013-04-10T21:40:22.410" Score="1" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.hygromycin.net/protocols.htm&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt;, &#xA;for yeast (I assume this means &lt;em&gt;Saccharomyces cerevisiae&lt;/em&gt;) you should use 50 µg/ml to 200 µg/ml; for fungi (!) use 100 µg/ml to 300 µg/ml. The site also stresses the importance of the pH of the medium.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that, unless a &lt;em&gt;Hansenula&lt;/em&gt; expert comes along,  you will have to try an initial experiment to measure the sensitivity of untransformed cells across the range indicated. Then you can try selecting resistant cells at a concentration somewhat higher than that which kills untransformed cells. Finally, you can check to see how resistant the transformants are, to enable you to decide on a useful concentration for routine selection of transformants. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-04-10T21:40:22.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7856" PostTypeId="1" CreationDate="2013-04-10T23:13:58.483" Score="1" ViewCount="1119" Body="&lt;p&gt;We're preparing for an experiment in our classroom and my teaching partner and I are at different points in the unit.  I am concerned that the experiment will be less successful because of the freshness of the eyes.  How long can they eyes be stored in the fridge before they have to be dissected and is freezing them an option?&lt;/p&gt;&#xA;" OwnerUserId="3369" LastActivityDate="2013-04-11T07:05:21.347" Title="How long can you keep sheep eyes in formaldehyde before dissecting?" Tags="&lt;zoology&gt;&lt;eyes&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7857" PostTypeId="2" ParentId="7856" CreationDate="2013-04-10T23:37:13.227" Score="2" Body="&lt;p&gt;Formaldehyde is a preservative, and is used to prevent decay. As long as the tissue is completely perfused (and there shouldn't be any issues with eyes that I'm aware of) it can be kept essentially forever. Have fun!&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-04-10T23:37:13.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7858" PostTypeId="2" ParentId="7841" CreationDate="2013-04-11T03:51:19.083" Score="4" Body="&lt;p&gt;Ara H 1, Ara H 2, and Ara H 3 are the three main peanut allergies. AH1 and AH2 are typically higher-acuity anaphylactic type reactions. The molecular cause for this is that some Immunoglobulin E develop a serum sensitivity and bind directly to vicilin and conglutin (the active proteins in AH1 and AH2). There are actually 7 or 8 Ara H complexes, but it is believed the remaining ones have a lesser affinity for IgE, reducing the frequency of allergic reactions and thus their availability for relevant studies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The prevalence of the allergy is generally attributed to a combination of exposure and genetics. Many people have a genetic predisposition to certain allergies, but to a certain extent the body must be exposed to the allergen before an allergy will develop. The high use of peanuts in the food industry, and even to a lesser degree in skin care products like lotions, can account for early exposure resulting in allergies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the other direction, some research suggests that early and frequent exposure from infancy through childhood (albeit the choking risk) can reduce the demographic prevalence of an allergy in a given population.&lt;/p&gt;&#xA;" OwnerUserId="3370" LastActivityDate="2013-04-11T03:51:19.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7859" PostTypeId="2" ParentId="7847" CreationDate="2013-04-11T04:08:47.390" Score="7" Body="&lt;p&gt;The quick and simple answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cramps of a hypokalemic origin are much more common than those of a hyponatremic origin because the Na-K pump is more effective at moving potassium in comparison to sodium.&#xA;At the onset of a muscle contraction, the presence of calcium triggers the opening of the Na-K channels in the membrane. Potassium is a calcium inhibitor, so as the potassium flows out of the cell, it eventually reduces the presence of calcium. This causes the closure of the Na-K channel (negative feedback mechanism). In a hypokalemic state, the lack of sufficient K doesn't inhibit the calcium channel, and in turn doesn't properly terminate the muscle contraction at the cellular level. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The continued presence of calcium, which has a lot to do with nerve impulses, means that the nerves keep firing, and in some cases such as a 'charlie horse', these impulses fire fast and continuously. The body at this point is reaching a small local state of metabolic acidosis resulting from the extremely high oxygen consumption, increasing levels of CO₂ (the acidosis component) and reducing blood partial oxygen levels. Since the oxygen is no longer as abundant as it was, it inhibits the bodies ability to locally produce the ribose and phosphate necessary for ATP. Less ATP = more myosin that can't be disconnected from actin = continued muscle cramp.&lt;/p&gt;&#xA;" OwnerUserId="3370" LastEditorUserId="3340" LastEditDate="2014-10-09T15:47:12.757" LastActivityDate="2014-10-09T15:47:12.757" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7860" PostTypeId="2" ParentId="7856" CreationDate="2013-04-11T07:05:21.347" Score="1" Body="&lt;p&gt;you can keep the samples in 4 degrees. Sometimes, in certain tissues, formaldehyde preservation makes them brittle. Or sometimes it makes certain slimy tissues easy to dissect. Nonetheless, it wont damage the morphology. And if you are not interested in protein/RNA isolation, then you can store the tissue as long as you want. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-11T07:05:21.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7861" PostTypeId="1" AcceptedAnswerId="7865" CreationDate="2013-04-11T07:37:49.137" Score="5" ViewCount="1246" Body="&lt;p&gt;I found it in Russia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZeCKJ.jpg&quot; alt=&quot;Insect in question&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where do they usually live? What do they eat?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Full length is approximately 2 cm.&lt;/p&gt;&#xA;" OwnerUserId="3280" LastEditorUserId="16866" LastEditDate="2017-06-29T02:14:23.677" LastActivityDate="2019-02-04T06:01:58.430" Title="What insect is this?" Tags="&lt;species-identification&gt;&lt;zoology&gt;&lt;entomology&gt;&lt;arthropod&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7862" PostTypeId="1" CreationDate="2013-04-11T07:51:44.840" Score="0" ViewCount="591" Body="&lt;p&gt;I know how it gets converted because PR is more stable and when there is neither red or far red light PFR naturally converts to PR. But what is the point of it? If PFR is the biologically active one why didn't evolution just make one pigment, PFR. At night neither is active so PR again has no point, in the morning PR gets converted to PFR. So why do we need a PR?&lt;/p&gt;&#xA;" OwnerUserId="3371" LastEditorUserId="3059" LastEditDate="2013-04-12T06:21:54.830" LastActivityDate="2013-04-12T18:28:22.050" Title="Why does the PR form of phytochrome exist?" Tags="&lt;evolution&gt;&lt;proteins&gt;&lt;plant-physiology&gt;&lt;botany&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7863" PostTypeId="2" ParentId="7854" CreationDate="2013-04-11T08:32:37.170" Score="3" Body="&lt;p&gt;(Reposting my comment as an answer since it seems to be what was required.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A DNA molecule that replicates independently of chromosomal DNA is an episome. By this definition a plasmid is (usually) an episome. If a plasmid integrates into a chromosome by some mechanism (as for example in Hfr strains of &lt;em&gt;E. coli&lt;/em&gt; where the F plasmid is integrated) the plasmid loses its episomal status. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term &quot;episome&quot; was first coined by Joshua Lederberg to describe the nature of &lt;a href=&quot;http://en.wikipedia.org/wiki/F_plasmid&quot; rel=&quot;nofollow&quot;&gt;the F element&lt;/a&gt; in &lt;em&gt;E. coli.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-04-11T08:32:37.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7864" PostTypeId="2" ParentId="7825" CreationDate="2013-04-11T08:50:41.973" Score="2" Body="&lt;p&gt;I would first recommend you ask this question &lt;a href=&quot;http://www.biostars.org&quot; rel=&quot;nofollow&quot;&gt;biostar&lt;/a&gt; as the subject matter you are inquiring about is much more relevant there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That having been said, you have another option which is to use an aligner that soft clips 3' ends of reads specifically to account for adapter (or polyA, or whatever) contamination that might have flew under your radar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://code.google.com/p/rna-star/&quot; rel=&quot;nofollow&quot;&gt;STAR&lt;/a&gt; is such an aligner. If you search their &lt;a href=&quot;https://groups.google.com/forum/#!forum/rna-star&quot; rel=&quot;nofollow&quot;&gt;mailing list&lt;/a&gt; archives for &quot;clip&quot;, you should find several posts related to your question.&lt;/p&gt;&#xA;" OwnerUserId="192" LastActivityDate="2013-04-11T08:50:41.973" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7865" PostTypeId="2" ParentId="7861" CreationDate="2013-04-11T11:45:24.430" Score="4" Body="&lt;p&gt;Seems to be it's a Woodlouse!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Woodlouse&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Woodlouse&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3280" LastActivityDate="2013-04-11T11:45:24.430" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7866" PostTypeId="1" CreationDate="2013-04-11T14:51:12.537" Score="1" ViewCount="183" Body="&lt;p&gt;My course book says about reproductive isolation that it does not allow the interbreeding among the individuals of different species. It also says that it is a cause of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is this cause of evolution? &lt;/p&gt;&#xA;" OwnerUserId="1765" LastActivityDate="2013-04-14T03:20:15.690" Title="Reproductive isolation causing evolution" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7867" PostTypeId="2" ParentId="7866" CreationDate="2013-04-11T16:07:40.640" Score="9" Body="&lt;p&gt;Reproductive isolation isn't exactly a cause of evolution, but rather a cause of &lt;strong&gt;speciation&lt;/strong&gt;. Reproductive isolation allows for two cohorts of one species to be reproductively separated. In this case, evolution via random mutation or mechanisms like genetic drift allows for the differentiation of the two groups, up to the point that the two cohorts and their respective gene pools have &lt;em&gt;evolved&lt;/em&gt; to be completely different species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Truly defining a species is still debatable (via the Biological species definition, Morphological, etc) but reproductive isolation is definitely a mechanism involved in speciation.&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2013-04-11T16:07:40.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7868" PostTypeId="1" AcceptedAnswerId="8336" CreationDate="2013-04-11T21:06:28.317" Score="2" ViewCount="3572" Body="&lt;p&gt;I have searched in the web for a detailed explanation of doing such validation experiment, but unfortunately couldn't find a satisfactory one. I came across the following sources:  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.piercenet.com/files/TR0058-Spike-and-Recovery.pdf&quot; rel=&quot;nofollow&quot;&gt;Thermo Scientific Tech tip #58&lt;/a&gt;: IMAHO, well written description, but still there are some issues  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Pros&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Clear on describing terms and straight forward calculations   &lt;/li&gt;&#xA;&lt;li&gt;Troubleshooting of the results is outlined    &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cons&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Not designed to be performed in one 96-well plate ELISA   &lt;/li&gt;&#xA;&lt;li&gt;No mention of any acceptable criteria for the both validation tests &lt;/li&gt;&#xA;&lt;li&gt;No mention of &lt;code&gt;blank&lt;/code&gt;  &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.quansysbio.com/recovery-and-linearity&quot; rel=&quot;nofollow&quot;&gt;Quansys Biosciences&lt;/a&gt;: a practical design to implement  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Pros&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Both spike-and-recovery and linearity-of-dilution experiments can be performed in one 96-well plate ELISA  &lt;/li&gt;&#xA;&lt;li&gt;Justified introduction of the &lt;code&gt;endogenous sample&lt;/code&gt;, which is diluted the same amount as the spiked sample   &lt;/li&gt;&#xA;&lt;li&gt;Addition of &lt;code&gt;blank&lt;/code&gt;  &lt;/li&gt;&#xA;&lt;li&gt;Mention of acceptance criteria for both types of experiments  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cons&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;No mention of troubleshooting  &lt;/li&gt;&#xA;&lt;li&gt;a little bit messy plate design &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.woongbee.com/0NewHome/RnD/ELISA/RnD_%20SPIKEandREC2006.pdf&quot; rel=&quot;nofollow&quot;&gt;R&amp;amp;D&lt;/a&gt; spike and recovery protocol: a brief one but useful  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Pros&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Clear on design  &lt;/li&gt;&#xA;&lt;li&gt;Mention of acceptable criteria at least for the spike recovery 80-120%     &lt;/li&gt;&#xA;&lt;li&gt;Mention of &lt;code&gt;blank&lt;/code&gt; &lt;/li&gt;&#xA;&lt;li&gt;Hint about possibility of using diluted neat sample until it gives reading  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cons&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;One sample was used for assessment and not averaging on 3 samples at least  &lt;/li&gt;&#xA;&lt;li&gt;No mention for any criteria for linearity of dilution    &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Issues/Questions&lt;/strong&gt;&lt;br&gt;&#xA;    - Q1: How can we combine the two experiments into one plate to spare samples, and materials?&lt;br&gt;&#xA;    - Q2: Can we dilute sample with assay diluent instead of sample diluent?&lt;br&gt;&#xA;    - Q3: In case low sample material is there, can we skip the neat sample and add 1:2 diluted one instead to spare material?&lt;br&gt;&#xA;    - Q4: In preparing spikes in Thermo Scientific tech#58, why was it 10µl spike stock solution added to 50µl sample? what governs this addition, is there any ratio to stick to here or arbitrary ratio? Can we add 90µl sample and 10µl stock solution? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please feel free to expand &lt;code&gt;sources&lt;/code&gt;, or &lt;code&gt;questions&lt;/code&gt;, and of course &lt;code&gt;answers&lt;/code&gt; are more than welcome to achieve the following aim:  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The best design for both validation tests (i.e., spike-and-recovery and linearity-of-dilution) in one 96-well plate ELISA that will use the minimum amount of sample material as possible with explanation of calculations based on averages and clear troubleshooting plan  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;PS: I am short of reputation to add important tags to enhance searching, e.g.: &lt;code&gt;ELISA&lt;/code&gt;, &lt;code&gt;validation&lt;/code&gt;   &lt;/p&gt;&#xA;" OwnerUserId="3320" LastEditorUserId="3059" LastEditDate="2013-04-30T03:52:35.513" LastActivityDate="2013-05-13T20:37:50.430" Title="What would be the best design for spike-and-recovery and linearity-of-dilution validation experiments in one 96-well ELISA plate?" Tags="&lt;human-biology&gt;&lt;assay-development&gt;&lt;elisa&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7869" PostTypeId="1" AcceptedAnswerId="7889" CreationDate="2013-04-11T21:13:22.353" Score="2" ViewCount="1343" Body="&lt;p&gt;Today, a presenter briefly mentioned that gene expression in sea urchins during development might be manipulated using VP16 and engrailed fusions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a slide, it said that expression might be increased by mRNA injection or &quot;VP16 fusion to binding domain of TF&quot; and decreased by antisense morpholinos or &quot;engrailed fusion to binding domain of TF&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand mRNA injection and antisense morpholinos, but I am unclear about the roles of VP16 and engrailed in this context. Can anyone clarify?&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-04-13T20:56:16.043" Title="Manipulation of gene expression using VP16 fusion and engrailed fusion to a transcription factor?" Tags="&lt;molecular-biology&gt;&lt;gene-expression&gt;&lt;development&gt;&lt;experimental-design&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7870" PostTypeId="1" CreationDate="2013-04-11T23:36:02.017" Score="1" ViewCount="498" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ob1V2.png&quot; alt=&quot;http://i.imgur.com/CVB3tUT.png&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Project 1 Base:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/syuvD.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone please help me understand what I need from Project 1 Base code to do questions 1 and 2 from the first image? I'm new to MATLAB so a thorough explanation would be great.&lt;/p&gt;&#xA;" OwnerUserId="3373" LastEditorUserId="107" LastEditDate="2013-04-11T23:40:51.023" LastActivityDate="2013-04-12T10:44:12.273" Title="Deterministic model of lambda-phage lysis/lysogeny [MATLAB]" Tags="&lt;bioinformatics&gt;&lt;homework&gt;&lt;mathematical-models&gt;" AnswerCount="2" CommentCount="1" ClosedDate="2014-07-31T11:46:34.233" ContentLicense="CC BY-SA 3.0" />
  <row Id="7871" PostTypeId="1" CreationDate="2013-04-12T00:48:43.963" Score="6" ViewCount="7515" Body="&lt;p&gt;I am familiar with the use of tag-SNPs in genome-wide association studies to identify gene loci involved in complex traits, but I keep seeing the term &quot;conditional analysis&quot; used without any explanation. Is it some sort of mathematical manipulation in which the significance of a tag-SNP is reduced to zero, to see if other SNPs are directly associated to the phenotype in question?&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2019-02-25T09:53:20.970" Title="What does conditional analysis of a SNP in a GWA study entail?" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;&lt;genomes&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="7872" PostTypeId="2" ParentId="7870" CreationDate="2013-04-12T02:13:50.450" Score="2" Body="&lt;p&gt;For homework questions, &lt;a href=&quot;https://biology.meta.stackexchange.com/a/267/3059&quot;&gt;the policy is to see some work from the poster&lt;/a&gt;.  Since you don't know programming, I've outlined what the code is doing, beyond the simple operations (+, -, /, *, ^), to get you started.  I think you should be able to implement the models with this information, and I'd be happy to confirm your own answers. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;So the best way to figure out what any line of code means, in any language, is to type it and see what happens. To help you get started with programming in MATLAB:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any text following a % (on the same line) is a comment: it does nothing in the program, and is only there for you to write notes to yourself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first two sections, Time-Related Constants and Simulation Constants, are just setting variables. It's like saying x = 3, so that later on you can do other operations with x.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The semicolon at the end of a line (in MATLAB) suppresses the output of the line. See what happens if you type &lt;code&gt;x = 3;&lt;/code&gt; versus &lt;code&gt;x = 3&lt;/code&gt; at the command prompt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In iteration constants, &lt;code&gt;length&lt;/code&gt; is just a function that tells you the length of the vector.  &lt;code&gt;X_rna_0&lt;/code&gt; was previously initialized to go from 0 to 1.4 in steps of 0.2: the syntax is vector_name = start:step:end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The simulation variables section is creating xyz-matrices, with all values initialized to zero.  The length in x is xr_max, and so on.  The idea is that, later on, at each step in Euler's method and each value of xr_max and xp_max, you'll save the value of X_rna.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The initial conditions are being set using &lt;code&gt;meshgrid&lt;/code&gt;, which is best explained &lt;a href=&quot;http://www.weizmann.ac.il/matlab/techdoc/ref/meshgrid.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.  The &lt;code&gt;:&lt;/code&gt; means all of the rows/columns, corresponding to position: say you had a 3 x 3 matrix called &lt;code&gt;apple&lt;/code&gt;.  &lt;code&gt;apple[:,1]&lt;/code&gt;  gives you all the first column (1) of all three rows.  &lt;code&gt;apple[1,:]&lt;/code&gt; gives you the first row (1) of all three columns. The .' means that the matrix is being transposed: again, the best way to see what's going on is to create a matrix of your own, perform the operation, and see if what you get is what you thought it would be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For loops, you can read about &lt;a href=&quot;http://www.cyclismo.org/tutorial/matlab/control.html#for&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;, for a start.  I do not think understanding this loop requires more information than that page.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dot before ^2 means that each element of the matrix is being squared; you are not multiplying the matrix by itself. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That should decipher most of the code for you.  If you have further questions, feel free to comment here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Question 2 asks you to make a plot.  A plot of y vs. x would be made by typing &lt;code&gt;plot(x,y)&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, help on a particular MATLAB function can be accessed by typing &lt;code&gt;help name_of_function&lt;/code&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="-1" LastEditDate="2017-03-16T15:49:46.677" LastActivityDate="2013-04-12T02:13:50.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7873" PostTypeId="2" ParentId="7862" CreationDate="2013-04-12T03:03:34.193" Score="2" Body="&lt;p&gt;First off, &amp;quot;evolution&amp;quot; doesn't necessarily lead the most efficient system for anything - it works with what we already have.  Once something has evolved, it might not go away, if there is no particular harm to having it around. You might take a look at the evolution tag, as other people have asked similar questions about the &amp;quot;usefulness&amp;quot; of biological mechanisms and molecules.&lt;/p&gt;&#xA;&lt;p&gt;Aside from that, having both isoforms is important for the detecting the color of light. When Pr absorbs red light, it gets converted to Pfr, and when Pfr absorbs far red light, it gets converted to Pr.  The ratios of Pr to Pfr allow plants to determine light levels and adjust their growth accordingly:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Sunlight has a R:FR ratio of 1.2&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Light under a canopy of leaves has a R:FR ratio of 0.13&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Light under 5 mm of soil has a R:FR ratio of 0.88&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A higher proportion of FR light allows plants to detect when they are&#xA;shaded. Plants adapted for growth in full sun will display greater&#xA;stem elongation when they are transferred to shade.  They also develop&#xA;smaller leaves and less branching.  This change is due to greater&#xA;proportion of Pr to Pfr.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Seeds of certain plants require red light for germination; FR light inhibits germination.  Many small seeds with low amounts of storage reserves (such as lettuce) show such a red light requirement.&#xA;If these seeds they are buried below the level of light penetration in the soil, they do not germinate.&#xA;If they are shaded by a leaf canopy, causing a high proportion of FR, germination is inhibited, [as] Pfr is required for germination.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mobot.org/jwcross/duckweed/phytochrome.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source: Missouri Botanical Garden&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-04-12T18:28:22.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7874" PostTypeId="2" ParentId="7870" CreationDate="2013-04-12T04:16:39.567" Score="1" Body="&lt;p&gt;This is a set of ordinary differential equations. Proceed like this&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Make a &lt;a href=&quot;http://www.mathworks.in/help/matlab/ref/function.html&quot; rel=&quot;nofollow&quot;&gt;matlab function&lt;/a&gt; for the ODEs that define the system (equations 1,2,3,4). The function should return a 4 dimensional vector which is basically the dy/dt (the rate equation) &lt;/li&gt;&#xA;&lt;li&gt;in the main program declare the initial values of different components. There is no absolute rule for what it should be and it is based on your prior knowledge of the system&lt;/li&gt;&#xA;&lt;li&gt;in the main program write a module to integrate the rate function over a time interval. there are several numerical algorithms to do it such as Euler, implicit euler, runge-kutta, polynomial interpolation- predictor corrector methods (Adam Bashworth) etc. If you want to improve your knowledge on the numerical methods then write your own code for any algorithm. A good book on basics of numerical methods can be referred. Otherwise, you can use inbuilt &lt;a href=&quot;http://www.mathworks.in/help/matlab/math/ordinary-differential-equations.html&quot; rel=&quot;nofollow&quot;&gt;ODE solvers in Matlab&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;A note on numerical methods for solving ODEs: what you precisely do is add-up and update the rate function in small intervals of time. The very basic method is euler in which you just implement this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;y = y + h*f(x,t)....... explicit/forward euler&#xA;y = y + h*f(x,t+h)...... implicit/backward euler&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;where &lt;code&gt;dy/dx =f(x,t)&lt;/code&gt; and &lt;code&gt;h&lt;/code&gt; is a small time interval &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what you have to do, exactly, is to run a loop which goes from &lt;code&gt;t=t_initial&lt;/code&gt; to &lt;code&gt;t=t_final&lt;/code&gt; with small increments of &lt;code&gt;h&lt;/code&gt;. You can use any basic loop such as &lt;code&gt;for&lt;/code&gt; loop or &lt;code&gt;while&lt;/code&gt; loop. &lt;code&gt;for&lt;/code&gt; loops are quite easy to implement. (the basic syntax is - for(initial;final condition; increment function) which in Matlab is as easy as &lt;code&gt;for t=t_initial:h:t_final&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within the loop you apply the integration operation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More advanced techniques use variable step size to improve the performance. You can use the inbuilt ODE solvers if you require better performance and accuracy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your homework.. You already have the code; just need to put the parameters. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-12T10:44:12.273" LastActivityDate="2013-04-12T10:44:12.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7875" PostTypeId="1" CreationDate="2013-04-12T12:45:12.363" Score="4" ViewCount="145" Body="&lt;p&gt;Do all human beings have a single oldest ancestor (a man and a woman), or were there were many ancestors at the same time at different places on earth? &#xA;&lt;a href=&quot;http://news.discovery.com/animals/dinosaurs/life-single-common-ancestor.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;This article&lt;/a&gt; sheds some light. Is there another authoritative report released more recently?      &lt;/p&gt;&#xA;" OwnerUserId="1110" LastEditorUserId="107" LastEditDate="2013-04-13T20:33:48.097" LastActivityDate="2013-04-23T04:35:55.203" Title="The oldest common ancesstor of all human beings" Tags="&lt;evolution&gt;&lt;palaeontology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7878" PostTypeId="1" CreationDate="2013-04-12T14:03:14.990" Score="3" ViewCount="343" Body="&lt;p&gt;If I cook some food, I get apparently several energetic advantages:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;thermal : the temperature of the food is closer or superior to the temperature of my body or internal organs, so I do not have to produce energy to warm it.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;chemical : the transformations of the organic compounds during cooking operations may store energy in a potential form: more energy will be released by the digestive process from these compounds than from the raw ones.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;mechanical : the food may become easier to chew, absorb, conduct in the digestive tract, leading to less muscular force used.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The cooking procedure may involve water immersion, and the water may penetrate the food and improve all three energetic aspects outline above.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;(I may have forgotten a few things)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what are the respective scale of these advantages, compared to the Joule intake of the raw food ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Focusing on meat, for instance, is there an optimal cooking duration/temperature and eating temperature for human eaters, independently of personal tastes, for say, beef or chicken meat ? &lt;/p&gt;&#xA;" OwnerUserId="207" LastActivityDate="2013-04-12T15:16:10.923" Title="What is the energy balance of cooking?" Tags="&lt;physiology&gt;&lt;digestive-system&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7879" PostTypeId="2" ParentId="7875" CreationDate="2013-04-12T14:53:28.990" Score="3" Body="&lt;p&gt;You are talking about the &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitochondrial_Eve&quot; rel=&quot;nofollow&quot;&gt;mitochondrial eve&lt;/a&gt; and the chromosome Y adam.  At some point there must be just one pair, though historically the evidence can be lost if there is a near complete extinction event.  Current evidence for eve points to SE Africa.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="107" LastEditDate="2013-04-23T04:35:55.203" LastActivityDate="2013-04-23T04:35:55.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7880" PostTypeId="2" ParentId="7878" CreationDate="2013-04-12T15:16:10.923" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;If I cook some food, I get apparently several energetic advantages...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Let's make things a little more explicit. If you are talking of &lt;em&gt;energy&lt;/em&gt; within the body, you are talking proteins, alcohols, fats, and sugars. You are &lt;strong&gt;not&lt;/strong&gt; talking Vitamins or Minerals or any of the unique compounds (like specific antioxidants) that are available in the food.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;thermal : the temperature of the food is closer or superior to the temperature of my body or internal organs, so I do not have to produce energy to warm it.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You cannot eat enough to significantly alter the temperature of your body. The average American will eat roughly &lt;a href=&quot;http://www.npr.org/blogs/thesalt/2011/12/31/144478009/the-average-american-ate-literally-a-ton-this-year&quot; rel=&quot;nofollow&quot;&gt;5.4lbs of food per day&lt;/a&gt; - or roughly 2lbs of food per meal. Given that even raw food is at room temperature, the metabolic requirements to warm food you've eaten is negligible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's important is acidity and exposure. Food is generally broken apart and utilized by catalysts and proteins which have specific operating boundaries - which is why your stomach contents is acidic. However, your normal meals will not significantly alter your digestive capabilities either via pKa values or thermoregulation requirements.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What cooking &lt;em&gt;can&lt;/em&gt; do is denature the raw food's proteins or compounds so as to make the usable energy sources more readily available. However, it can also just as easily destroy them (the 'char' on barbequed steaks is the meat exposed to high heat long enough to destroy almost everything but the carbon in the tissue). Whether a food gains or loses macronutrients depends upon the specific food and its preparation. A good example is potatoes, which are full of starch (sugars) in their natural state. However, french fries / frites / chips are often blanched before they're fried. The blanching dissolves much of the starch into water, leaving fewer sugars in the end product. However, the process of frying essentially adds fat to the food, and fats have a higher energy density than sugars so you have a net gain in caloric content.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;mechanical : the food may become easier to chew, absorb, conduct in the digestive tract, leading to less muscular force used.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For some foods, this is true. Steaming vegetables often makes them easier to chew/eat. The broth of stews and soups often contains micelles of fat and dissolved sugars, affording them greater and faster exposure to the digestive system. Keep in mind, you are &lt;strong&gt;not&lt;/strong&gt; getting a net gain of caloric content from food by doing so, but merely reducing the time to utilization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The calories saved by chewing less is going to be pathetically small, so to amend the previous paragraph: Yes, for some foods it's true that cooking will allow easier mastication and thus save energy. However, an extra chocolate chip or sip of spoon of rice could easily cover the energy spared. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The cooking procedure may involve water immersion, and the water may penetrate the food and improve all three energetic aspects outline above.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If the energy source is water-soluble (that is: &lt;em&gt;alcohols, ketones, and sugars&lt;/em&gt;) then water immersion - &lt;em&gt;assuming you are also digesting the water solution after&lt;/em&gt; - will offer &lt;strong&gt;faster&lt;/strong&gt; utilization, not necessarily more.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But what are the respective scale of these advantages, compared to the Joule intake of the raw food? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Negligible in almost all cases. What cooking does is make things more palatable, has the potential to make micronutrients/vitamins more available (&lt;em&gt;not&lt;/em&gt; macronutrients), and make the food edible in the first place as is the case with &lt;a href=&quot;http://en.wikipedia.org/wiki/Taro#Toxicity&quot; rel=&quot;nofollow&quot;&gt;Taro plants, whose roots must be cooked in order to eat.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Focusing on meat, for instance, is there an optimal cooking duration/temperature and eating temperature for human eaters, independently of personal tastes, for say, beef or chicken meat?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No. Cooking meat makes it &lt;em&gt;safer&lt;/em&gt; to eat (unless you end up overcooking the meat and end up with a bunch of charred bone) and more palatable. Properly cooked meat has a very low chance of passing on parasites or other harmful organisms. Beyond that, there aren't compelling reasons to expose meat to heat - although as someone who's picked up stomach flus in his travels, it is a &lt;strong&gt;very&lt;/strong&gt; compelling reason to do so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*The above is based mostly on sporadically gained knowledge. If there are studies indicating otherwise, please alert me to them and I will rectify my errors.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-04-12T15:16:10.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7881" PostTypeId="1" AcceptedAnswerId="7892" CreationDate="2013-04-12T15:29:28.860" Score="3" ViewCount="605" Body="&lt;p&gt;Bacteria produce something called a biofilm. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found a few definitions; some say it is a complex of live and dead bacteria and others say it is a layer on cell wall.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;What is it made of?&lt;/li&gt;&#xA;&lt;li&gt;What is its purpose?&lt;/li&gt;&#xA;&lt;li&gt;How do we combat biofilms when we encounter them?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="3059" LastEditDate="2013-04-12T18:27:32.500" LastActivityDate="2013-04-13T21:02:07.400" Title="What is a bacterial biofilm?" Tags="&lt;bacteriology&gt;&lt;terminology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7883" PostTypeId="2" ParentId="7881" CreationDate="2013-04-12T19:05:40.947" Score="4" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Biofilm&quot; rel=&quot;nofollow&quot;&gt;Bacterial biofilms&lt;/a&gt; are a bunch of bacteria that have attached themselves to a surface or to each other as a floating mat to form a solid phase community.  Its not seen in the lab so much, but they are common in nature.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bacteria not only adhere to the surface, but each other through a matrix of polymers they secrete.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bacteria in a biofilm are often resistant to chemicals, heat, acid and other changes in the environment.  Its a practically universal trait and its generally assumed that any bacteria can form a biofilm.  Dental Plaque is a biofilm. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Getting a biofilm eradicated can be a lot of work because the bacteria are sequestered in the matrix and somewhat protected.  Scrubbing or chemicals are usually used.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-04-12T19:05:40.947" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7885" PostTypeId="1" AcceptedAnswerId="7886" CreationDate="2013-04-12T20:09:36.023" Score="1" ViewCount="334" Body="&lt;p&gt;I study biology at school, and unfortunately for me, my program skips the muscles in humans chapter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know (and mainly, feel) that the movement in one direction isn't created by the same muscle as the movement in the opposite direction, e.g the Triceps (&quot;front&quot;) and Biceps (&quot;back&quot;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that the triceps straightens the elbow, while the biceps contracts the elbow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also know that, instead of &lt;em&gt;actually&lt;/em&gt; moving the arm, I can contract these two muscles (when I show off, for example...) without actually moving the arm. That area becomes hard. Both muscles, as I feel, are contracting. I cannot statically contract only one of them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is whether this action is something &quot;special&quot;, or simply both muscles working against each other, resulting in zero movement?&lt;/p&gt;&#xA;" OwnerUserId="951" LastEditorUserId="107" LastEditDate="2013-04-12T21:30:09.937" LastActivityDate="2013-04-12T21:37:06.260" Title="Contracting muscles in humans" Tags="&lt;human-anatomy&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7886" PostTypeId="2" ParentId="7885" CreationDate="2013-04-12T21:37:06.260" Score="3" Body="&lt;p&gt;The situation you are describing where muscles are situated on opposites sides of a joint and produce opposing movements is called &quot;antagonism.&quot; Most joints are set up where one or more muscles on either sides will produce such movements (e.g., flexors vs. extensors). &lt;a href=&quot;https://biology.stackexchange.com/questions/2373/skeletal-muscle-without-antagonist&quot;&gt;Here's a question about muscles without antagonists&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you contract all the muscles crossing a joint (i.e., when you are &quot;showing off&quot;), the muscles balance each other. If not, the bones would move and the joint angles would change. So taking the elbow as an example, in the image below, Arnold is contracting the elbow flexors (biceps brachii, brachialis) as well as the elbow extensors (triceps brachii). In order for the bones to remain static, the forces must be equal and opposite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZWRjy.jpg&quot; alt=&quot;Arnold&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-04-12T21:37:06.260" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7887" PostTypeId="1" CreationDate="2013-04-13T00:53:04.057" Score="8" ViewCount="1488" Body="&lt;p&gt;During transformation, a bacterium can take up DNA from its environment. A small fraction of bacterial species are known to be naturally competent, meaning that they can engage in this sort of horizontal gene transfer in their natural environments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I understand it, naturally competent bacteria carry genes that encode the machinery necessary to facilitate the transport of this DNA across the membrane and into the cell. The exogenous DNA binds to a receptor located on the surface of competent cells, gets fragmented into small pieces, and then one strand is degraded while the other strand is transported across the membrane into the cytoplasm with the aid of a DNA translocase enzyme. Ultimately, assuming a sufficient degree of homology, it incorporates into the host genome via recombination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During this process, however, the DNA has to be protected from degradative nucleases. I remember reading something about a transformation-specific DNA binding protein that coats the entire length of the DNA strand and prevents degradation. Is it the same translocase enzyme that facilitates movement across the membrane that is responsible for this? Or is there another protein involved?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And then, regardless of which protein is responsible in the case of natural competence, how does that protein get expressed and activated in the case of artificial competence? When we induce competence in the laboratory through one of various methods (e.g., electroporation), the DNA is essentially forced into the cell through openings in the membrane, so no transferase protein is needed. What signals the bacterium, then, to express the protective binding protein? What keeps the exogenous DNA from being readily degraded by endogenous nucleases? Whatever signals induced the expression of this protein in the case of natural competence would seem to be absent when competence is induced artificially, and it doesn't make any sense that the bacterium would constitutively express such a protein.&lt;/p&gt;&#xA;" OwnerUserId="145" LastActivityDate="2020-01-23T05:42:21.800" Title="How is the exogenous DNA protected from degradation during bacterial transformation?" Tags="&lt;genetics&gt;&lt;microbiology&gt;&lt;bacteriology&gt;&lt;molecular-genetics&gt;&lt;transformation&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7889" PostTypeId="2" ParentId="7869" CreationDate="2013-04-13T11:00:25.697" Score="1" Body="&lt;p&gt;VP16 is a herpesvirus derived protein transcription factor, which activates the early genes of the viral infection cycle. The activation domain (AD) which is formed by the 78-amino acids from the C-terminal, can be fused to DNA binding domain of other protein transcription factors, &lt;a href=&quot;http://www.jbc.org/content/271/9/4827.full&quot; rel=&quot;nofollow&quot;&gt;such as GAL4&lt;/a&gt;, to make a hybrid protein that constitutively and strongly activates transcription, without the requirement of any ligands. VP16-AD interacts with &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12297514&quot; rel=&quot;nofollow&quot;&gt;TBP, TFIID, SAGA histone acetyltransferase complex&lt;/a&gt;, and PC4 &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15654739&quot; rel=&quot;nofollow&quot;&gt;(transcriptional coactivator positive cofactor 4)&lt;/a&gt; to drive transcription. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;engrailed&lt;/em&gt; gene, from Drosophila, is a transcriptional repressor.  When the repressor domain is fused to transcription factors, the fusion results in &lt;a href=&quot;http://nar.oxfordjournals.org/content/30/21/4709&quot; rel=&quot;nofollow&quot;&gt;trans-dominant negative functions of the transcription factor (phenocopying loss of function mutations in the target genes).&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3059" LastEditDate="2013-04-13T20:56:16.043" LastActivityDate="2013-04-13T20:56:16.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7890" PostTypeId="2" ParentId="7887" CreationDate="2013-04-13T11:34:25.120" Score="2" Body="&lt;p&gt;Different bacteria have different modes of transformation and as I understand it is Haemophilus influenzae that takes up the single strand whereas ?Streptococcus &lt;em&gt;[i am not sure which bacteria it is]&lt;/em&gt; takes up dsDNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I intuitively think that DNAses are not that common like RNAses. Moreover, natural competence is associated with stress and is even &lt;a href=&quot;http://www.pnas.org/content/82/18/6201.short&quot; rel=&quot;nofollow&quot;&gt;triggered by DNA damage&lt;/a&gt;. Therefore we can speculate that DNA repair proteins will be prevalent and DNAses will be low in the cell, under these conditions. The chance of foreign DNA being damaged goes down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of artificial transformation, I guess the entire concept of heat shock is a way of providing stress. Moreover, the lab strains such as &lt;a href=&quot;http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cloning/competent-cells-for-transformation/Chemically-Competent/dh5alpha-genotypes.html&quot; rel=&quot;nofollow&quot;&gt;DH5alpha&lt;/a&gt; have certain mutations which disable them from recognizing a plasmid as &quot;foreign&quot;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-13T11:34:25.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7892" PostTypeId="2" ParentId="7881" CreationDate="2013-04-13T21:02:07.400" Score="6" Body="&lt;p&gt;Aside from the actual microbial cells themselves, biofilms are a slime matrix made of a variety of substances, including DNA, lipids, proteins, and other signaling molecules, but the major component is something called extracellular polymeric substance (EPS), also known as &lt;a href=&quot;https://en.wikipedia.org/wiki/Exopolysaccharide&quot; rel=&quot;nofollow noreferrer&quot;&gt;exopolysaccharides. &#xA;&lt;img src=&quot;https://i.stack.imgur.com/BN2Uc.png&quot; alt=&quot;Sinorhizobium meliloti monosuccinylated succinoglycan&quot;&gt;&lt;/a&gt;&#xA;Succinoglycan from &lt;em&gt;Sinorhizobium meliloti&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are high molecular weight extracellular (&lt;strong&gt;&lt;em&gt;exo&lt;/em&gt;&lt;/strong&gt;) polymers (&lt;strong&gt;&lt;em&gt;poly&lt;/em&gt;&lt;/strong&gt;) of sugars (&lt;strong&gt;&lt;em&gt;saccharides&lt;/em&gt;&lt;/strong&gt;) linked together into long linear or branched chains, which can be modified by moieties such as phosphate, sulfate, acetate, and succinate. As the biofilm forms (below), channels can form in the EPS to facilitate nutrient uptake and distribution, hydration, and inter-cellular signaling such as &lt;a href=&quot;https://en.wikipedia.org/wiki/Quorum_sensing&quot; rel=&quot;nofollow noreferrer&quot;&gt;quorum sensing&lt;/a&gt;. Biofilms are often composed of multiple species of microorganisms, from bacteria and archaea to fungi and algae, with the social (and physical) structure dependent on the &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6976.2008.00150.x/full&quot; rel=&quot;nofollow noreferrer&quot;&gt;species that compose it&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5TReh.jpg&quot; alt=&quot;Biofilm formation&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-04-13T21:02:07.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7894" PostTypeId="1" AcceptedAnswerId="7896" CreationDate="2013-04-14T11:19:48.170" Score="8" ViewCount="616" Body="&lt;p&gt;Put another way if the muscle is given everything it needs to contract and do work will it ever get tired or have a reduction in energy efficiency?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I understand muscles depend upon a blood supply delivering oxygen and nutrients (e.g. glucose and calcium) to effectively contract at its best level of performance. With the ability to work under anaerobic conditions if need be but producing lactic acid as a by-product which reduces the muscles ability to contract and therefore producing fatigue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also know that muscles are dependent upon temperature to work efficiently like the rest of the body. So, if the muscles temperature was able to be regulated well enough to maintain efficiency and aerobic conditions are met could fatigue be negated?&lt;/p&gt;&#xA;" OwnerUserId="342" LastActivityDate="2013-07-31T20:31:46.690" Title="Would muscle fatigue still occur if aerobic conditions for a working muscle is maintained?" Tags="&lt;physiology&gt;&lt;muscles&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7895" PostTypeId="1" AcceptedAnswerId="7898" CreationDate="2013-04-14T13:48:43.117" Score="2" ViewCount="310" Body="&lt;p&gt;I have the two differential equations:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{dN_1}{dt} = N_1(2 - N_1 - 2N_2)$$&#xA;$$\frac{dN_2}{dt} = N_2(3 - N_2 - 3N_1).$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I worked out the equilibrium points to be at $N_1 = 0, \frac{4}{5}$ and $N_2 = 0, \frac{3}{5}$. I then calculated all the Jacobi matrices and worked out the eigenvalues (and eigenvectors). I now have to classify these equilibria. How do I do that? Is there a set of rules I follow to classify them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, the next part says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sketch the phase portrait of this system in the biologically sensible region: draw the the null- clines of the system and determine the crude directions of trajectories in parts of the phase plane cut by the null clines, designate the equilibria in the phase plane, and sketch a few typical trajectories.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I can do the null - clines and I think once I have found out the stability of the equilibria, I can determine the directions of trajectories of the bits cut by the null -cline, but how would I sketch the trajectories of the equilibria?&lt;/p&gt;&#xA;" OwnerUserId="3385" LastActivityDate="2013-04-15T04:43:30.603" Title="How to classify equilibrium points" Tags="&lt;homework&gt;&lt;mathematical-models&gt;&lt;population-dynamics&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2013-04-16T00:16:38.337" ContentLicense="CC BY-SA 3.0" />
  <row Id="7896" PostTypeId="2" ParentId="7894" CreationDate="2013-04-14T14:31:32.393" Score="7" Body="&lt;p&gt;It seems that you are asking about activity significantly above basal metabolic rate. If aerobic conditions are maintained (and with appropriate training), muscles can operate more or less continuously for very long durations, days to weeks. In non-humans:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Godwits have been recorded &lt;a href=&quot;http://www.treehugger.com/slideshows/natural-sciences/nature-blows-my-mind-6-longest-bird-migrations/&quot;&gt;flying over 7000 miles&lt;/a&gt; (&gt;11000 km) without stopping for 9 days&lt;/li&gt;&#xA;&lt;li&gt;Arctic terms migrate 44000 miles (&gt;70000 km), albeit with stopovers&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedaily.com/releases/2007/04/070410091423.htm&quot;&gt;Humpback whales migrate 5000 miles&lt;/a&gt; (8000 km). Their muscles are probably operating close to continuously.&lt;/li&gt;&#xA;&lt;li&gt;Many (most?) species of sharks swim continuously.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are probably other examples as well (feel free to add). For humans, usually the limit to endurance is sleep. Two forms of racing push human endurance, but the longer races almost always require at least minimal sleep:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ultramarathon&quot;&gt;Ultramarathons&lt;/a&gt;, foot races of 50 mi (80 km), 100 mi (160 km) or more (e.g., 24 hours, multi-day).&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.raceacrossamerica.org/&quot;&gt;Race Across America&lt;/a&gt;, &lt;a href=&quot;http://rusa.org/pbp.html&quot;&gt;Paris-Brest-Paris&lt;/a&gt;, and similar endurance bicycle races. The RAAM has a &lt;a href=&quot;http://www.raceacrossamerica.org/raam/raam2.php?N_webcat_id=51&quot;&gt;record time&lt;/a&gt; of 3107 mi (4971 km) in 8 days, 9 hours for a mean velocity of 15.4 mi/hr (24.6 km/hr).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-04-14T14:31:32.393" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7898" PostTypeId="2" ParentId="7895" CreationDate="2013-04-14T18:38:53.410" Score="5" Body="&lt;p&gt;Classification of equilibrium points is done on the basis of the eigenvalues.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;If the two eigenvalues have no real parts, it is a hyperbolic fixed point and represents undamped oscillation.&lt;/li&gt;&#xA;&lt;li&gt;If both have a negative real part, it is a stable fixed point. If any of the eigenvalues has an imaginary part then it represents damped oscillations (in that case the equilibrium point is called a focus).&lt;/li&gt;&#xA;&lt;li&gt;If one or both eigenvalue have a positive real part, it is an unstable fixed point.&lt;/li&gt;&#xA;&lt;li&gt;If one eigenvalue has a positive real part and the other a negative real part, it is a saddle point.*&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You sketch the trajectories of the equilibria by starting a tiny distance away from the point (where it is not in equilibrium) and trace the quiver plot. Drawing trajectories around unstable points is tricky and you have to plot the function in negative time i.e. instead of plotting f(x1,x2,t), you plot -f(x1,x2,t).  &lt;a href=&quot;http://www.augustana.ualberta.ca/~hackw/mat332/exhibit/fxdpt2d.html&quot; rel=&quot;nofollow&quot;&gt;This page&lt;/a&gt; has representative trajectories for the different types of equilibrium points.  &lt;a href=&quot;http://www.scholarpedia.org/article/Equilibrium&quot; rel=&quot;nofollow&quot;&gt;This page&lt;/a&gt; has a more thorough explanation, generalized to multiple dimensions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*This classification appears to be slightly variable (more or less categories), on the basis of the two links I found.  I think the one I list is the simplest version, but any classification should suffice.  They are all based on the same principles. You can refer to some books on non-linear dynamics:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Nonlinear Systems by Hassan Khalil&lt;/li&gt;&#xA;&lt;li&gt;Nonlinear Dynamics and Chaos by Steven Strogatz&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-15T04:43:30.603" LastActivityDate="2013-04-15T04:43:30.603" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7899" PostTypeId="1" AcceptedAnswerId="7901" CreationDate="2013-04-14T20:15:22.103" Score="-3" ViewCount="192" Body="&lt;p&gt;Did anybody ever conduct experiments on fusing living brains?&lt;/p&gt;&#xA;" OwnerUserId="408" LastActivityDate="2013-04-14T21:32:12.550" Title="Were any brain fusion experiments ever conducted?" Tags="&lt;brain&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2013-04-17T14:32:18.310" ContentLicense="CC BY-SA 3.0" />
  <row Id="7900" PostTypeId="1" CreationDate="2013-04-14T21:29:01.877" Score="9" ViewCount="390" Body="&lt;p&gt;Whenever I look at discussions of &lt;a href=&quot;http://en.wikipedia.org/wiki/Fitness_landscape&quot;&gt;fitness landscapes&lt;/a&gt; (in particular, Kauffman's &lt;a href=&quot;http://en.wikipedia.org/wiki/NK_model&quot;&gt;NK model&lt;/a&gt;) the questions tend to resemble:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The population is at a local equilibrium, but another equilibrium of higher fitness exists, how will the population cross the fitness valley between these equilibria?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These sort of statements assume that the population has reached a local equilibrium. Although, the local equilibria must exist, &lt;strong&gt;why do the people working in this field believe that they can be found before environmental (or other external events) change the fitness function?&lt;/strong&gt; Are the timescales required to go from a random initial population to one that is at a local equilibrium compatible with the typical time-scales on which a fixed fitness landscape is an appropriate approximation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we switch to the polar opposite model of complete frequency-dependent selection (say replicator dynamics in evolutionary game theory) then limit-cycles (think rock-paper scissors game) and chaotic-attractors are common and it is possible for the population genetics to be constantly changing and never at equilibrium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In an experimental setting, it also seems like although beneficial point-mutations are much more rare than deleterious, they do exist. This would suggest that experimentally, organisms are not at a local equilibrium. &lt;strong&gt;Do model organisms tend to be at local fitness equilibria?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, &lt;strong&gt;is the local equilibrium assumption in fitness landscapes research a reasonable assumption?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="500" LastActivityDate="2013-08-19T10:02:47.077" Title="Is local equilibrium a reasonable assumption for evolutionary processes?" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7901" PostTypeId="2" ParentId="7899" CreationDate="2013-04-14T21:32:12.550" Score="7" Body="&lt;p&gt;The odds of that are really very slim. &quot;Growing brains&quot; in vitro is rather difficult, and it appears that no one has created the brain of a real organism, but &lt;a href=&quot;http://en.wikipedia.org/wiki/Isolated_brain#Growing_an_isolated_brain&quot;&gt;they have created &quot;brains&quot; from cultured dissociated neurons&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fusing brains is complicated by the fact that you need to make the appropriate synaptic connections between neurons, and what exactly are the appropriate connections is still being worked out.  As a side note, this is one of the goals of the &lt;a href=&quot;http://www.whitehouse.gov/infographics/brain-initiative&quot;&gt;BRAIN Initiative&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The closest I believe people have come to anything approaching fusion are brain transplants in non-human animals.  This might be the closest thing to an in vivo fusion, especially if it is only a partial brain transplant.  This is discussed a bit &lt;a href=&quot;http://en.wikipedia.org/wiki/Brain_transplant#Partial_brain_transplant&quot;&gt;here&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-04-14T21:32:12.550" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7902" PostTypeId="1" CreationDate="2013-04-15T02:06:37.447" Score="3" ViewCount="563" Body="&lt;p&gt;Has anyone ever conducted an evolution experiment and quantitatively compared it to theory?  For example, has anyone ever put bacteria in a million petri dishes filled with antibiotics and calculated the number of petri dishes that should develop drug-resistant bacteria, and then compared that calculation with the experiment?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I imagine that both the experiment and theoretical modeling would be very difficult, but maybe someone has been ambitious enough to try it.&lt;/p&gt;&#xA;" OwnerUserId="3227" LastEditorUserId="500" LastEditDate="2013-04-15T06:13:00.877" LastActivityDate="2016-05-05T23:48:31.640" Title="Are there natural selection experiments that quantitatively agree with theoretical modeling?" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;experimental&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ClosedDate="2016-05-10T03:06:54.873" ContentLicense="CC BY-SA 3.0" />
  <row Id="7903" PostTypeId="1" CreationDate="2013-04-15T02:49:58.553" Score="3" ViewCount="261" Body="&lt;p&gt;I am curious as to the processes and mechanisms involved in the extension of pseudopodia in amoeba. &lt;strong&gt;How does the cell know and control the direction and extent of pseudopodia formation at a molecular level?&lt;/strong&gt; I am not particularly interested in the taxes that amoeba recognize, but rather the mechanism of response to these taxes.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="57" LastEditDate="2013-04-15T04:18:26.833" LastActivityDate="2013-04-15T04:18:26.833" Title="What molecular processes are involved in pseudopodial extension?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;molecular-biology&gt;&lt;microbiology&gt;&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7904" PostTypeId="2" ParentId="7903" CreationDate="2013-04-15T03:57:08.817" Score="3" Body="&lt;p&gt;The extracellular cue signal must be relayed to the cell by Rho family of GTPases, like in the case of filopodia and lammelipodia. This causes local actin polymerization leading to extension of pseudopodium. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a casual reference you can check the &lt;a href=&quot;http://en.wikipedia.org/wiki/Rho_family_of_GTPases&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; page on Rho family of GTPases. Cell biology books like MBOTC also have information on mechanism of cytoskeletal dynamics. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-15T03:57:08.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7905" PostTypeId="1" AcceptedAnswerId="7910" CreationDate="2013-04-15T04:15:18.303" Score="13" ViewCount="2224" Body="&lt;p&gt;People often claim, in a colloquial sense, that they are &quot;allergic to everything&quot;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to have a full-fledged IgE mediated allergic response to very small molecules?  I was always under the impression that the smallest antigen was a oligopeptide, but is it possible for someone to be allergic to something like isopropanol, glucose, or another small organic molecule?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How about allergies to metals, as I know those are fairly common, would they be mediated through a similar mechanism?&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="3340" LastEditDate="2019-04-19T09:49:30.457" LastActivityDate="2019-04-19T09:49:30.457" Title="What is the smallest molecule that can present as an antigen to the immune system in the context of allergies?" Tags="&lt;immunology&gt;&lt;antigen&gt;&lt;allergies&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7906" PostTypeId="2" ParentId="7905" CreationDate="2013-04-15T08:16:54.837" Score="13" Body="&lt;p&gt;Small molecules do not have antigenic properties but they can elicit immune response by binding to a &quot;carrier&quot; protein. The small molecule is called a Hapten. An epitope forms at the protein-hapten binding interface. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15767020&quot;&gt;Nickel&lt;/a&gt;  acts like a hapten and elicits immune response by binding to proteins like transferrin, albumin etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other metals also cause allergy in a similar way.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-15T08:16:54.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7907" PostTypeId="5" CreationDate="2013-04-15T09:43:53.727" Score="0" Body="&lt;p&gt;Initially &lt;a href=&quot;http://www.nature.com/focus/rnai/index.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;RNAi&lt;/a&gt; was used to refer a process in which exogenous small(~22nt) RNAs (siRNA) silence expression of certain mRNAs which have regions complementary to the siRNA. This definition now also includes miRNA regulated pathway.&lt;/p&gt;&#xA;&lt;p&gt;The main catalytic component of RNAi is a ribo-endonuclease called &lt;a href=&quot;http://www.nature.com/nrm/journal/v9/n1/full/nrm2321.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Argonaute&lt;/a&gt; (Ago), which cleaves the target mRNAs. dsRNAs are cleaved by Dicer to give rise to siRNAs. Different species have different number of paralogous Argonaute proteins. In mammals only Ago2 has endonucleolytic activity.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nrg/journal/v9/n2/full/nrg2290.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;miRNAs&lt;/a&gt; are endogenous RNAs similar to siRNAs in function and biogenesis. However, miRNAs targets are usually localized in the 3'UTR of mRNAs and are usually not perfectly complementary to the miRNAs.  Moreover, the miRNA targets are not directly cleaved; degradation happens indirectly by decapping/deadenylation and subsequent exonucleolytic decay. Repression can also happen without degradation and in these cases the repressive effect is reversible.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="948" LastEditDate="2021-04-29T11:59:09.783" LastActivityDate="2021-04-29T11:59:09.783" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="7908" PostTypeId="4" CreationDate="2013-04-15T09:43:53.727" Score="0" Body="A post-transcriptional mechanism of gene-regulation/silencing mediated by small interfering RNAs (siRNA)" OwnerUserId="3340" LastEditorUserId="948" LastEditDate="2021-04-29T11:59:19.250" LastActivityDate="2021-04-29T11:59:19.250" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="7909" PostTypeId="1" AcceptedAnswerId="7917" CreationDate="2013-04-15T15:05:28.810" Score="4" ViewCount="697" Body="&lt;p&gt;How does your body know when it is infected with a virus or bacteria so it can invoke a fever or ramp up the immune system?&lt;/p&gt;&#xA;" OwnerDisplayName="user1897" LastActivityDate="2013-04-18T22:40:26.457" Title="How does your body know when it is infected so it can invoke a fever?" Tags="&lt;infection&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7910" PostTypeId="2" ParentId="7905" CreationDate="2013-04-15T15:17:49.977" Score="14" Body="&lt;p&gt;At one of my previous companies that raised antibodies to proteins and post-translational modifications, we found that 6-8 amino acids was generally the smallest peptide length required for an epitope. Anything much smaller than that won't induce the cross-linking or conformational changes required for signal transduction and an allergic response. As WYSIWYG notes, allergies to small molecules/atoms are formed via &lt;a href=&quot;http://en.wikipedia.org/wiki/Hapten&quot;&gt;hapten&lt;/a&gt;-carrier interactions. These can be covalent, as in the nickel-transferrin example, or as a result of denaturation/chemical modification, as likely happens with people who are allergic to things like isopropanol or bleach.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I very much doubt that there can be such a thing as a glucose allergy, as it is so ubiquitous in the body that such antibodies/T-cells would be &lt;a href=&quot;http://en.wikipedia.org/wiki/Negative_selection_%28immunology%29&quot;&gt;negatively selected&lt;/a&gt; long before they could do any damage.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-04-15T15:17:49.977" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7911" PostTypeId="1" CreationDate="2013-04-15T16:39:20.210" Score="3" ViewCount="337" Body="&lt;p&gt;Does anyone know how long it takes for a standard Lentivirus vector to express its genes (under a strong promoter such as CAG, CB7, etc.), after injection into the brain of a mouse?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By hearsay I think it's 2 weeks for full expression, is that true?&lt;/p&gt;&#xA;" OwnerUserId="3388" LastEditorUserId="3388" LastEditDate="2013-04-16T23:10:38.450" LastActivityDate="2017-03-18T03:03:46.633" Title="How long does Lentivirus take to express in vivo mouse neurons?" Tags="&lt;neuroscience&gt;&lt;lab-techniques&gt;&lt;virology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7912" PostTypeId="1" AcceptedAnswerId="24674" CreationDate="2013-04-15T16:45:34.923" Score="2" ViewCount="184" Body="&lt;p&gt;I'm wondering about the carrying capacity also referred to packaging capacity or loading capacity (how many base pairs can be packed efficiently into virions) of the pseudotyped rabies virus SAD-dG as described in the Wickersham, Callaway publications.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Wickersham, I. R., Finke, S., Conzelmann, K.-K., &amp;amp; Callaway, E. M.&#xA;(2006). Retrograde neuronal tracing with a deletion-mutant rabies&#xA;virus. Nature methods, 4(1), 47–49. doi:10.1038/nmeth999&lt;/p&gt;&#xA;&lt;p&gt;Wickersham, I. R., Lyon, D. C., Barnard, R. J. O., Mori, T., Finke,&#xA;S., Conzelmann, K.-K., et al. (2007). Monosynaptic Restriction of&#xA;Transsynaptic Tracing from Single, Genetically Targeted Neurons.&#xA;Neuron, 53(5), 639–647. doi:10.1016/j.neuron.2007.01.033&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3388" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-08T09:46:19.440" Title="Carrying or packaging capacity of SAD B19 dG rabies virus" Tags="&lt;neuroscience&gt;&lt;virology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7913" PostTypeId="1" CreationDate="2013-04-15T18:13:47.793" Score="3" ViewCount="150" Body="&lt;p&gt;I don't know much about medicine, and I know even less about microbiology, but I understand that there are organisms in the lower gastrointestinal tract (and in feces) of a human, like &lt;em&gt;Escherichia coli&lt;/em&gt;, that can cause dangerous disease if swallowed (or injected intravenously) by a human. So how did they get to the lower gastrointestinal tract in the first place? I assume either (or some combination of)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;its prevalence in feces is less than I'm led to believe, so my question as to how it got there doesn't arise;&lt;/li&gt;&#xA;&lt;li&gt;the percentage among cases of swallowed &lt;em&gt;E. coli&lt;/em&gt; of those that lead to disease is low; or&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;E. coli&lt;/em&gt;-caused disease is more common than I'm lead to believe.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Does anyone know which of these is true? Or is it something else? (Perhaps they enter the gastrointestinal tract from below and not via swallowing?)&lt;/p&gt;&#xA;" OwnerUserId="988" LastActivityDate="2018-04-18T00:52:50.267" Title="Whence fecal E. coli (et al.) if swallowing it is dangerous?" Tags="&lt;human-biology&gt;&lt;bacteriology&gt;&lt;pathology&gt;&lt;ecoli&gt;&lt;gastroenterology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7914" PostTypeId="1" CreationDate="2013-04-15T18:35:16.433" Score="3" ViewCount="76" Body="&lt;p&gt;I am studying horizontal transmission of primary symbionts in insect reproduction. This reminded me of &lt;a href=&quot;https://biology.stackexchange.com/questions/522/how-does-the-microbial-environment-in-your-gut-initiate&quot;&gt;an earlier question I had asked&lt;/a&gt;, in which I learned that humans analogously acquired their particular microbiomes. It is also known how the human gut can be stratified in microbial content along the digestive tract. My question is &lt;strong&gt;what mechanisms are employed in ensuring that organisms acquiring their microbiomes from outside sources via horizontal transmission acquire the correct microorganisms in the correct parts of the gut&lt;/strong&gt;? As the human gut metagenome does show &quot;homology&quot; between individuals, it can be safely assumed that the process &lt;em&gt;can't be due to random chance&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2020-05-13T19:44:59.643" Title="How is the appropriately-stratified gut microbiome acquired in organisms performing horizontal transmission?" Tags="&lt;microbiology&gt;&lt;digestive-system&gt;&lt;microbiome&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7915" PostTypeId="1" CreationDate="2013-04-15T18:52:59.367" Score="2" ViewCount="29" Body="&lt;p&gt;I am a software engineer and I am trying to develop a system to identify a deer by its photograph.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most deers lose their antlers every year. I would like to know if they re-grow in the same pattern next year and if yes, then what are the measurements that are of interest here?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any pointers for me? Any software that can help me in recognizing a deer?&lt;/p&gt;&#xA;" OwnerUserId="3389" LastActivityDate="2013-04-15T18:52:59.367" Title="Do the antlers re-grow in the same pattern every year?" Tags="&lt;zoology&gt;&lt;mathematical-models&gt;&lt;software&gt;&lt;imaging&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2013-04-15T23:10:23.890" ContentLicense="CC BY-SA 3.0" />
  <row Id="7916" PostTypeId="1" AcceptedAnswerId="7942" CreationDate="2013-04-15T18:59:10.913" Score="2" ViewCount="1451" Body="&lt;p&gt;I am trying to recognize a deer by its antlers or any other means. &#xA;Elaborating:&#xA;I was hoping to use their antlers to recognize them but I have heard that most deers shed their antlers every year so it would be difficult to recognize it from the last year's photo unless these antlers retain the same pattern every year. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not the antlers, what other characteristics should I be looking for?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any software that can help me in recognizing a deer?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ge3dA.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3389" LastEditorUserId="3389" LastEditDate="2013-04-15T21:42:44.057" LastActivityDate="2013-04-17T14:51:54.867" Title="What would it take to recognize a deer by its photo?" Tags="&lt;zoology&gt;&lt;mathematical-models&gt;&lt;software&gt;&lt;imaging&gt;" AnswerCount="2" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="7917" PostTypeId="2" ParentId="7909" CreationDate="2013-04-15T19:06:41.503" Score="3" Body="&lt;p&gt;During infection certain macromolecules present in the pathogens (pathogen associated molecular patterns) such as lipopolysaccharide launch the &lt;a href=&quot;http://en.wikipedia.org/wiki/Innate_immune_system&quot; rel=&quot;nofollow&quot;&gt;innate immune response&lt;/a&gt;, through toll like receptors. This leads to production of pro-inflammatory cytokines and also other inflammatory mediators like prostaglandins, thereby causing inflammation and fever.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-15T19:06:41.503" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7918" PostTypeId="2" ParentId="7916" CreationDate="2013-04-15T19:54:08.273" Score="1" Body="&lt;p&gt;The Open Source Computer Vision library &lt;a href=&quot;http://opencv.org/&quot; rel=&quot;nofollow&quot;&gt;OpenCV&lt;/a&gt; is pretty popular. I'm a Python guy, but it also has C, C++, and Java interfaces. The O'Reilly book &lt;a href=&quot;http://shop.oreilly.com/product/0636920022923.do&quot; rel=&quot;nofollow&quot;&gt;Programming Computer Vision with Python&lt;/a&gt; was pretty good, and their C-oriented &lt;a href=&quot;http://shop.oreilly.com/product/9780596516130.do&quot; rel=&quot;nofollow&quot;&gt;Learning OpenCV&lt;/a&gt; from 2008 is coming out with a &lt;a href=&quot;http://shop.oreilly.com/product/0636920022497.do&quot; rel=&quot;nofollow&quot;&gt;new C++ edition&lt;/a&gt; in July, supposedly. There are also the &lt;a href=&quot;http://opencv.org/documentation.html&quot; rel=&quot;nofollow&quot;&gt;OpenCV online docs&lt;/a&gt;, linking to the &lt;a href=&quot;http://docs.opencv.org/modules/refman.html&quot; rel=&quot;nofollow&quot;&gt;reference manual&lt;/a&gt;, &lt;a href=&quot;http://docs.opencv.org/doc/user_guide/user_guide.html&quot; rel=&quot;nofollow&quot;&gt;user guide&lt;/a&gt;, &lt;a href=&quot;http://docs.opencv.org/doc/tutorials/tutorials.html&quot; rel=&quot;nofollow&quot;&gt;tutorial&lt;/a&gt;, and &lt;a href=&quot;http://docs.opencv.org/java/&quot; rel=&quot;nofollow&quot;&gt;Java API&lt;/a&gt; for each release.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-04-15T19:54:08.273" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7919" PostTypeId="1" CreationDate="2013-04-15T21:10:32.553" Score="5" ViewCount="1269" Body="&lt;p&gt;I have a vector sequence and would like to find the following nucleotide sequence in it.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;AASYWSRA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This query sequence uses several degenerate symbols, defined as:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;S = C or G (&lt;strong&gt;S&lt;/strong&gt;trong)&lt;/li&gt;&#xA;&lt;li&gt;Y = C or T (p&lt;strong&gt;Y&lt;/strong&gt;rimidine)&lt;/li&gt;&#xA;&lt;li&gt;W = A or T (&lt;strong&gt;W&lt;/strong&gt;eak) &lt;/li&gt;&#xA;&lt;li&gt;R = A or G (pu&lt;strong&gt;R&lt;/strong&gt;ine)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;(See &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleotide#Abbreviation_codes_for_degenerate_bases&quot; rel=&quot;nofollow&quot;&gt;this page&lt;/a&gt; for a complete description of the IUPAC nucleotide codes.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a tool to align this sequence with the vector and find all the possible sites?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I found &lt;a href=&quot;http://www.expasy.org/genomics/sequence_alignment&quot; rel=&quot;nofollow&quot;&gt;this website&lt;/a&gt; but couldn't find any of the resources helpful. Maybe one of these will work but I found most of them too complicated. If you know which one will work and explain how to use it I will be grateful.&lt;/p&gt;&#xA;" OwnerUserId="1772" LastEditorUserId="43" LastEditDate="2013-04-30T21:11:04.120" LastActivityDate="2013-05-18T18:36:17.690" Title="Tool for nucleotide alignment with all nucleotide codes (e.g. R, Y, W, S, etc.)?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;nucleic-acids&gt;&lt;sequence-analysis&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7920" PostTypeId="2" ParentId="7913" CreationDate="2013-04-15T21:34:12.063" Score="5" Body="&lt;p&gt;&lt;em&gt;E. coli&lt;/em&gt; is mostly harmless; only a few strains are harmful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't believe the route by which gut biota is established has been entirely established for any species but, for example, koala feed their faeces to their offspring to help them establish biota capable of digesting eucalyptus. It seems that a small proportion of ingested bacteria somehow survive passage through the stomach to the gut and then begin multiplying and colonising the intestines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also important to realise that just because an organism is sometimes harmful doesn't mean it always is. There are many microorganisms that are pretty much ubiquitously found on or in your body which are capable of causing disease but only do so very rarely; usually when the body's defences have already been compromised (e.g. &lt;em&gt;Pseudomonas aeruginosa&lt;/em&gt;, &lt;em&gt;Candida albicans&lt;/em&gt; aka thrush, and so on).&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="145" LastEditDate="2013-04-16T09:06:52.533" LastActivityDate="2013-04-16T09:06:52.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7921" PostTypeId="2" ParentId="757" CreationDate="2013-04-15T21:48:17.627" Score="8" Body="&lt;p&gt;@kmm and @shigeta provided you with a nice observational account of sudden leaps in large organisms. However, if you want to look at where this is the norm and try to build a mathematical theory then you need to look at something much smaller; the prime candidate is &lt;a href=&quot;http://en.wikipedia.org/wiki/Affinity_maturation&quot; rel=&quot;nofollow noreferrer&quot;&gt;affinity maturation&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;In the human immune system, when exposed to an antigen B cells produce antibodies. If it is your first exposure to the antigen then the antibodies produced will probably have very low binding affinity. However, after some exposure time, your B cells will start to produce antibodies with much higher affinities for the antigen and thus you will be able to better fight off the disease. The cool part, is that &lt;strong&gt;the antigen produced is tuned via an evolutionary process&lt;/strong&gt;!&lt;/p&gt;&#xA;&lt;p&gt;There is differential survival, with only antibodies with the highest affinity being able to survive. Variability is introduced by a very high mutation rate in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Complementarity-determining_regions&quot; rel=&quot;nofollow noreferrer&quot;&gt;complementarity determing region&lt;/a&gt; (CDR). (Tonegawa, 1983). The length of this evolutionary process is very short, typically a local equilibrium is found after only 6-8 nucleotide changes in CDR (Crews et al., 1981; Tonegawa, 1983; Clark et al., 1985), so you need only a few point mutations to quickly develop a drastically better tuned antibody.&lt;/p&gt;&#xA;&lt;p&gt;The standard mathematical model for this is Kauffman's &lt;a href=&quot;http://en.wikipedia.org/wiki/NK_model&quot; rel=&quot;nofollow noreferrer&quot;&gt;NK model&lt;/a&gt;. With a protein sequence on &lt;span class=&quot;math-container&quot;&gt;$N$&lt;/span&gt; sites, we say that evolution is fast (and we have a sudden leap) if after our fitness landscape changes, we can get to a new local equilibrium in a number of generations that scales with &lt;span class=&quot;math-container&quot;&gt;$\log N$&lt;/span&gt;. Kauffman &amp;amp; Weinberger (1989) showed how this model can be used to study affinity maturation, and showed that to achieve a sudden leap we need high &lt;a href=&quot;http://en.wikipedia.org/wiki/Epistasis&quot; rel=&quot;nofollow noreferrer&quot;&gt;epistasis&lt;/a&gt; and low correlations between pointwise mutants. In particular, their model suggests that typical epistasis in the CDR is on the order of 40 proteins (out of the total 112 proteins in the CDR).&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&lt;p&gt;Clark, S.H., Huppi, K., Ruezinsky, D., Staudt, L., Gerhard, W., &amp;amp; Weigert, M. (1985). Inter- and intraclonal diversity in the antibody response to influenza hemagglutin. &lt;em&gt;J. Exp. Med.&lt;/em&gt; 161, 687.&lt;/p&gt;&#xA;&lt;p&gt;Crews, S., Griffin, J., Huang, H., Calame, K., &amp;amp; Hood, L. (1981). A single V gene segment encodes the immune response to phosphorylcholine: somatic mutation is correlated with the class of the antibody. &lt;em&gt;Cell&lt;/em&gt; 25, 59.&lt;/p&gt;&#xA;&lt;p&gt;Kauffman, S. and Weinberger, E. (1989) The NK Model of rugged fitness landscapes and its application to the maturation of the immune response. &lt;em&gt;Journal of Theoretical Biology&lt;/em&gt;, 141(2): 211-245&lt;/p&gt;&#xA;&lt;p&gt;Tonegawa, S. (1983). Somatic generation of antibody diversity. &lt;em&gt;Nature&lt;/em&gt; 302, 575.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="500" LastEditDate="2020-11-16T05:11:39.217" LastActivityDate="2020-11-16T05:11:39.217" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="7922" PostTypeId="1" AcceptedAnswerId="9851" CreationDate="2013-04-15T22:39:09.850" Score="13" ViewCount="1004" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/NK_model&quot; rel=&quot;noreferrer&quot;&gt;NK model of rugged fitness landscapes&lt;/a&gt; consists of &lt;span class=&quot;math-container&quot;&gt;$N$&lt;/span&gt; sites where fitness contribution of each site depends on its state &lt;span class=&quot;math-container&quot;&gt;$\{0,1\}$&lt;/span&gt; and is epistatically affected by &lt;span class=&quot;math-container&quot;&gt;$K$&lt;/span&gt; other sites. When defining the model, Kauffman &amp;amp; Weinberger (1989) stressed that:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The actual structure of [fitness] landscapes, although knowable is currently unknown&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;They then go on to assume either epistatic interactions are with adjacent sites in a linear ordering or at random, and that fitnesses are assigned to each of the &lt;span class=&quot;math-container&quot;&gt;$2^{K + 1}$&lt;/span&gt; epistatic combinations at each site uniformly at random in &lt;span class=&quot;math-container&quot;&gt;$[0,1]$&lt;/span&gt;. Although it is definitely possible to justify this random generation, it tends to produce a very structured fitness landscapes, that although rugged (for high &lt;span class=&quot;math-container&quot;&gt;$K$&lt;/span&gt;), has a very regular distribution of local fitness optima. As a computer scientist, this assumption of an arbitrary random distribution over possible NK landscapes seems very misguided. I would be more comfortable with a worst-case analysis on a &amp;quot;reasonable&amp;quot; (hopefully as determined by experiment) subset of possible NK landscapes.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;What is known about the typical structure of NK landscapes in biological domains?&lt;/strong&gt; Also, are there examples of biological papers that do a worst case instead of an arbitrary random analysis on some non-trivial subset of landscapes? The only example I am familiar with is the gadgets used by Weinberger (1996) to show that the unconstrained model is &lt;a href=&quot;http://en.wikipedia.org/wiki/NP-hard&quot; rel=&quot;noreferrer&quot;&gt;NP-hard&lt;/a&gt;, but that is a trivial subset (all possible landscapes) and not of biological interest.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&lt;p&gt;Kauffman, S. and Weinberger, E. (1989) The NK Model of rugged fitness landscapes and its application to the maturation of the immune response. &lt;em&gt;Journal of Theoretical Biology&lt;/em&gt;, 141(2): 211-245&lt;/p&gt;&#xA;&lt;p&gt;Weinberger, E. (1996). NP-completeness of Kauffman's N-k model, a Tuneable Rugged Fitness Landscape. &lt;em&gt;Santa Fe Institute Working Paper&lt;/em&gt;, 96-02-003.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-08-19T14:31:14.347" Title="Structure of fitness landscapes in the NK model" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;natural-selection&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7923" PostTypeId="2" ParentId="7919" CreationDate="2013-04-15T23:29:23.440" Score="0" Body="&lt;p&gt;I have used &lt;a href=&quot;http://meme.nbcr.net/meme/cgi-bin/mast.cgi&quot; rel=&quot;nofollow&quot;&gt;MAST&lt;/a&gt; to search for particular motifs in a sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the &lt;a href=&quot;http://meme.nbcr.net/meme/mast-intro.html&quot; rel=&quot;nofollow&quot;&gt;MAST intro page&lt;/a&gt;, it looks like you'll have to reformat your motif a little, but it should suffice for your purposes:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Motifs are represented as position-dependent scoring matrices that&#xA;  describe the score of each possible letter at each position in the&#xA;  pattern.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cbil.upenn.edu/EpoDB/release/version_2.2/meme/motif-format.html&quot; rel=&quot;nofollow&quot;&gt;Here is more info on formatting&lt;/a&gt;, which also indicates that the alphabet you use will be interpreted correctly.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-05-02T01:15:10.033" LastActivityDate="2013-05-02T01:15:10.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7924" PostTypeId="1" AcceptedAnswerId="7925" CreationDate="2013-04-15T23:41:35.753" Score="2" ViewCount="1283" Body="&lt;p&gt;I am not a biologist, but I know there exist three variants of photosynthesis, namely C3, C4 and CAM.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know what type is used by the ocean's phytoplankton? It might also be that different photosynthetic mechanisms are used by the bacteria vs. algae. I have searched the web, but the information I find is too broad.&lt;/p&gt;&#xA;" OwnerUserId="691" LastEditorUserId="3952" LastEditDate="2013-07-21T18:18:58.747" LastActivityDate="2014-10-09T15:41:31.127" Title="What type of photosynthesis is performed by phytoplankton?" Tags="&lt;microbiology&gt;&lt;photosynthesis&gt;&lt;marine-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7925" PostTypeId="2" ParentId="7924" CreationDate="2013-04-16T00:01:09.560" Score="4" Body="&lt;p&gt;I'm not sure that all phytoplankton perform the same type of photosynthesis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Originally, people thought that they all performed C4, on the basis of genome sequencing, which revealed the presence of genes important for C4 photosynthesis.  However, experiments on individual species seemed to indicate that the phytoplankton were performing multiple types of photosynthesis (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976569/&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: CAM is unlikely, as that is an adaptation for dry environments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT 2: and of course, some phytoplankton appear to have &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0037438&quot; rel=&quot;nofollow&quot;&gt;both C3 and C4 pathways&lt;/a&gt;. In short, you can't generalize. &lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-16T05:32:13.283" LastActivityDate="2013-04-16T05:32:13.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7926" PostTypeId="2" ParentId="3590" CreationDate="2013-04-16T01:38:56.980" Score="0" Body="&lt;p&gt;There has been some recent advancement answering this question, especially in terms of puberty. Here are some quotes from the news article about it.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The timing of puberty onset is highly variable and ultimately mysterious.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, our understanding is pretty limited.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Contrary to popular belief, however, puberty is not a simple developmental progression of maturation of the reproductive axis, as this system is fully mature long before puberty and, in fact, must be suppressed during a period called the juvenile hiatus. The key component of the axis is the gonadotropin-releasing hormone (GnRH) neuron.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But, how is GnRH controlled temporally?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The authors have thus established that epigenetic repression of at least Kiss1, and probably other genes, mediated indirectly through the PcG family of transcriptional repressors, is the brake on the hypothalamic-pituitary-gonadal axis that must be released for puberty to proceed. More importantly, an epigenetic regulator provides the perfect interface for coordinating the genetic and environmental influences that are known to buffet this process.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is just one piece of the puzzle as the title of the news article says, and there are still a lot of gaps in our understanding.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Lomniczi, A. et al. Epigenetic control of female puberty. Nat Neurosci 16, 281–289 (2013). &lt;a href=&quot;http://www.nature.com/neuro/journal/v16/n3/full/nn.3319.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/neuro/journal/v16/n3/full/nn.3319.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Margaret M McCarthy. A piece in the puzzle of puberty. Nature Neuroscience 16,&#xA;251–253 (2013) doi:10.1038/nn.3339 &lt;a href=&quot;http://www.nature.com/neuro/journal/v16/n3/full/nn.3339.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/neuro/journal/v16/n3/full/nn.3339.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="460" LastActivityDate="2013-04-16T01:38:56.980" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7927" PostTypeId="1" CreationDate="2013-04-16T07:06:42.270" Score="5" ViewCount="708" Body="&lt;p&gt;Is there any software that could be used to rapidly &lt;em&gt;(quicker than humans)&lt;/em&gt; count the eggs laid by &lt;em&gt;Drosophila&lt;/em&gt; on a substrate by placing them under a microscope with a camera attached? The eggs are laid on the surface of the food and have a fairly uniform shape - we regularly have to count the number of eggs in &gt;200 vials, which can take a over 4-5 hours per 100 vials. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder if there is some software which could be linked to a microscope with mounted camera connected to a computer, the software could then count from the live feed or a quickly taken photograph. It wouldn't have to be perfect but as long as it could be as accurate as humans (which is surprisingly low from our experience - we count up to a set amount then remove the rest, e.g. if I was aiming to leave 180 eggs I would be quite happy to get anywhere between 150-200 eggs). It would be using a stereo-microscope (aka dissection microscope) with a mounted camera.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The surface of the food with eggs looks something like this -&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/zXQZn.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;em&gt;purely for illustration, taken with iPhone - real images on microscope would be able to get closer (food surface could fill screen) and have more uniform lighting to give better contrast (this was taken to show in a talk so I wanted pretty rather than practical). The bottom two quarters of the food in this picture would be similar to the real result, just much closer...&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="112" LastEditDate="2013-04-16T10:00:44.407" LastActivityDate="2014-12-17T18:11:48.003" Title="Software for counting fly eggs" Tags="&lt;bioinformatics&gt;&lt;software&gt;&lt;microscopy&gt;&lt;imaging&gt;&lt;drosophila&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7928" PostTypeId="1" CreationDate="2013-04-16T08:41:56.153" Score="2" ViewCount="243" Body="&lt;p&gt;I've been reading through Paulsson (2002) and I am not sure what he means by &amp;quot;lineage selection&amp;quot; in the second to last section. The paper deals with &lt;a href=&quot;http://en.wikipedia.org/wiki/Plasmid&quot; rel=&quot;nofollow noreferrer&quot;&gt;plasmid&lt;/a&gt; replication, and mostly concentrates on the contrasting pressures from two levels of selection:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;em&gt;intracell selection&lt;/em&gt; - competition between plasmids in a single cell. A plasmid can undergo a cis-mutation and over-replicate, resulting in a higher intracell fitness than the focal plasmid. The plasmids reproduce.&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;intercell selection&lt;/em&gt; - competition between cells. Cells with a heavier load of plasmids will take longer to reproduce, and plasmids that produce a heavy load will have lower intercell fitness. The cells containing plasmids reproduce.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;In this context, &lt;strong&gt;what does the third level of selection -- lineage selection -- mean?&lt;/strong&gt; What reproduces? How do the lineages split or interact?&lt;/p&gt;&#xA;&lt;h3&gt;My guess&lt;/h3&gt;&#xA;&lt;p&gt;Does lineage selection simply mean group-selection on separate colonies of cells? In that case, how are new lineages formed? I would expect this group level to select for zero levels of plasmids (since they place no loads on the cells and thus these groups of cells will grow the fastest), but Paulsson (2002) suggests the opposite:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;lineage selection could favor plasmid traits that help the population of plasmid-containing cells to fight plasmid-free cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Is there a more detailed discussions of this available than the one section in Paulsson (2002)?&lt;/strong&gt; Neither the &lt;a href=&quot;http://en.wikipedia.org/wiki/Unit_of_selection&quot; rel=&quot;nofollow noreferrer&quot;&gt;unit of selection&lt;/a&gt; nor either the &lt;a href=&quot;http://en.wikipedia.org/wiki/Lineage_(evolution)&quot; rel=&quot;nofollow noreferrer&quot;&gt;evolutionary&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/Lineage_(genetic)&quot; rel=&quot;nofollow noreferrer&quot;&gt;genetic&lt;/a&gt; lineage Wikipedia articles address my question. The first only mentions lineage in passing, and the second two don't discuss models of selection.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h3&gt;References&lt;/h3&gt;&#xA;&lt;p&gt;Paulsson, J. (2002). Multileveled selection on plasmid replication. &lt;em&gt;Genetics&lt;/em&gt;, 161(4): 1373-1384.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-04-16T15:01:29.987" Title="Lineage selection in plasmid evolution" Tags="&lt;evolution&gt;&lt;microbiology&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7929" PostTypeId="2" ParentId="6939" CreationDate="2013-04-16T09:36:48.470" Score="15" Body="&lt;p&gt;Mathematical and computational modeling of evolution is a huge field. To start you off with some broad strokes, there are two main approaches to evolutionary modeling with their own communities: frequency-independent and frequency-dependent models. Of course, in a real biological setting, the truth lies somewhere in between, but models are idealizations of key principles, and so the two extremes are good to study.&lt;/p&gt;&#xA;&lt;p&gt;For frequency-independent selection, they key concept is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Fitness_landscape&quot; rel=&quot;noreferrer&quot;&gt;fitness landscape&lt;/a&gt; -- a way to map each genotype to a fitness. The population then lives in this landscape and agents with higher fitness reproduce better and so the population slowly movers over the lattice. Under reasonable &lt;a href=&quot;http://en.wikipedia.org/wiki/Macroevolution&quot; rel=&quot;noreferrer&quot;&gt;macroevolutionary&lt;/a&gt; assumptions such as very rare mutations and asexual populations, the population will tend to be homogenous and can be just modeled as a single point in the fitness landscape with &lt;a href=&quot;https://biology.stackexchange.com/q/2638/500&quot;&gt;properly chosen selective sweeps&lt;/a&gt; to move the point from vertex to vertx (Gillespie, 1983; 1984).&lt;/p&gt;&#xA;&lt;p&gt;The most popular concrete approach for frequency-independent selection is [Kauffman's NK model of rugged fitness landscapes] (Kauffman &amp;amp; Weinberger, 1989; Kauffman, 1993). Computer simulations tend to favor this sort of model. Wilf's model would be an NK model with K = 0, and fitness of 0 for incorrect letters and 1 for correct letters (to get the shorter walk). Related questions:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/7900/500&quot;&gt;Is local equilibrium a reasonable assumption for evolutionary processes?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/7922/500&quot;&gt;Structure of fitness landscapes in the NK model&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;The frequency-dependent selection approach is dominated by &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionary_game_theory&quot; rel=&quot;noreferrer&quot;&gt;evolutionary game theory&lt;/a&gt;. A typical question for this field is the &lt;a href=&quot;http://egtheory.wordpress.com/2012/10/28/evolving-cooperation/&quot; rel=&quot;noreferrer&quot;&gt;evolution of cooperation&lt;/a&gt;, and the most basic approach is to use &lt;a href=&quot;http://en.wikipedia.org/wiki/Replicator_equation&quot; rel=&quot;noreferrer&quot;&gt;replicator dynamics&lt;/a&gt; and look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionarily_stable_strategy&quot; rel=&quot;noreferrer&quot;&gt;evolutionary stable strategies&lt;/a&gt;. However, the field is in general saturated with all kinds of exciting models (both analytic and computational). A very friendly book-length intro is &lt;a href=&quot;http://egtheory.wordpress.com/2011/09/05/nowak-evolutionary-dynamics/&quot; rel=&quot;noreferrer&quot;&gt;Nowak's &lt;i&gt;Evolutionary Dynamics&lt;/i&gt;&lt;/a&gt;. For a genetle intro and connections to evolutionary psychology look at the &lt;a href=&quot;http://egtheory.wordpress.com/2012/11/18/psyc532-2012/&quot; rel=&quot;noreferrer&quot;&gt;slides in this post&lt;/a&gt;. A brief and sophisticated introduction aimed at mathematicians can be found in Hofbauer &amp;amp; Sigmund (2003). Related questions:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://cstheory.stackexchange.com/q/7286/1037&quot;&gt;Sources for Algorithmic Evolutionary Game Theory&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/2022/500&quot;&gt;Why is &amp;#39;Grudger&amp;#39; an evolutionary stable strategy?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/3487/500&quot;&gt;How exactly are game theoretical evolutionary models described during implementation for computer simulations?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/7529/500&quot;&gt;When does weak selection produce qualitatively different results from strong selection?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&lt;p&gt;Gillespie, J.H. (1983). A simple stochastic gene substitution model. &lt;em&gt;Theor. Pop. Biol.&lt;/em&gt; 23, 202.&lt;/p&gt;&#xA;&lt;p&gt;Gillespie, J.H. (1984). Molecular evolution over the mutational landscape. &lt;em&gt;Evolution&lt;/em&gt; 38, 1116.&lt;/p&gt;&#xA;&lt;p&gt;Hofbauer, J., &amp;amp; Sigmund, K. (2003). Evolutionary game dynamics. Bulletin of the American Mathematical Society, 40(4), 479-519.&lt;/p&gt;&#xA;&lt;p&gt;Kauffman, S. (1993). The origins of order: Self organization and selection in evolution. Oxford University Press, USA.&lt;/p&gt;&#xA;&lt;p&gt;Kauffman, S. &amp;amp; Weinberger, E. (1989) The NK Model of rugged fitness landscapes and its application to the maturation of the immune response. Journal of Theoretical Biology, 141(2): 211-245&lt;/p&gt;&#xA;&lt;p&gt;Nowak, M. A. (2006). Evolutionary dynamics: exploring the equations of life. Harvard University Press.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-04-16T09:36:48.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7930" PostTypeId="2" ParentId="7902" CreationDate="2013-04-16T11:00:30.493" Score="2" Body="&lt;p&gt;I think the closest example to this is Greg Lang's work at Princeton. His work will take a population of yeast and let it grow for 1000 generations. At each generation a sample will be kept allowing sequencing of the population at each generation.&#xA;His website is available here: &lt;a href=&quot;http://www.genomics.princeton.edu/glang/&quot; rel=&quot;nofollow&quot;&gt;http://www.genomics.princeton.edu/glang/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And some of his work has already been published here: &lt;a href=&quot;http://www.genomics.princeton.edu/glang/papers.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.genomics.princeton.edu/glang/papers.htm&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="476" LastActivityDate="2013-04-16T11:00:30.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7931" PostTypeId="2" ParentId="7928" CreationDate="2013-04-16T15:01:29.987" Score="3" Body="&lt;p&gt;He defines lineage selection as selection for traits which increase the fitness of a group of plasmids, rather than an individual plasmid with in a cell or a particular cell containing plasmids. He says that the unit of selection are &quot;plasmid-host clades&quot; : in other words the unit of selection is the group of closely related plasmids in separate cells. It is an example of a kin-selection though I haven't seen the specific terminology in widespread use. He likely doesn't use kin selection because the plasmids don't have well defined offspring, so he uses a broader term for kin--lineage. I might have preferred clade selection, but this term has its own baggage. I'm not sure (and neither is Paulsson) that kin selection is need to explain 'spitefully low loss' rates, since intra-cellular and inter-cellular selection both favor lower loss rates.&lt;/p&gt;&#xA;" OwnerUserId="3396" LastActivityDate="2013-04-16T15:01:29.987" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7932" PostTypeId="1" AcceptedAnswerId="7937" CreationDate="2013-04-16T15:05:08.750" Score="71" ViewCount="8177" Body="&lt;p&gt;In physics, &quot;almost everything is already discovered, and all that remains is to fill a few unimportant holes.&quot; (See &lt;a href=&quot;http://en.wikipedia.org/wiki/Philipp_von_Jolly&quot; rel=&quot;noreferrer&quot;&gt;Jolly&lt;/a&gt;.) Therefore, on Physics SE, people are veering off into different directions: &lt;em&gt;biology&lt;/em&gt;, for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, it happens that &lt;a href=&quot;https://physics.stackexchange.com/q/61174/17609&quot;&gt;a question about bicycles&lt;/a&gt; generates some discussion about evolution in biology and animals with wheels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Three explanations are offered for the apparent lack of wheely animals (also on &lt;a href=&quot;https://en.wikipedia.org/wiki/Rotating_locomotion_in_living_systems#Biological_barriers_to_wheeled_organisms&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt;, where, by the way, most Physics SE questions are answered perfectly).&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Evolutionary constraints: &quot;[A] complex structure or system will not evolve if its incomplete form provides no benefit to an organism.&quot;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Developmental and anatomical constraints.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wheels have significant disadvantages (e.g., when not on roads).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Now, I suggest that all three can be &quot;solved&quot;.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;With time.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;With a symbiotic relationship between a wheel-like animal and a &quot;driver&quot;-like animal, although this gets awfully close to a &lt;a href=&quot;https://www.youtube.com/watch?v=R8XAlSp838Y&quot; rel=&quot;noreferrer&quot;&gt;&quot;driver&quot;-animal&lt;/a&gt; to jump onto an actual (man-made) wheel. (So, perhaps, you can suggest a better loophole around this constraint.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Roads are presumably not the only ecological niche where animals with wheels could thrive. I'm thinking of frozen lakes, although there skates would be better than wheels.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What, therefore, is &lt;em&gt;the&lt;/em&gt; explanation for there not being any wheeled animals?&#xA;Please consider, in your answer, the counterfactual: What assumption of yours would be falsified once a wheely animal &lt;em&gt;is&lt;/em&gt; discovered?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user3395" LastEditorUserId="-1" LastEditDate="2017-04-13T12:40:13.457" LastActivityDate="2017-09-29T07:35:30.467" Title="Why are there no wheeled animals?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;speculative&gt;" AnswerCount="4" CommentCount="14" FavoriteCount="24" ContentLicense="CC BY-SA 3.0" />
  <row Id="7933" PostTypeId="2" ParentId="7900" CreationDate="2013-04-16T15:19:59.913" Score="4" Body="&lt;p&gt;Nothing is at a genome-wide local equilibrium. &lt;a href=&quot;http://biology.mcgill.ca/faculty/bell/publications.html&quot; rel=&quot;nofollow&quot;&gt;Graham Bell&lt;/a&gt; wrote fairly extensively on this (IIRC). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some loci&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;will be at what are likely global optimums (e.g. Cytochrome oxidase)&lt;/li&gt;&#xA;&lt;li&gt;will be at local but not global optimums (e.g. low-fitness malaria resistance vs. high fitness malaria resistance: for the extremely cool story check out &lt;a href=&quot;http://www.indiana.edu/~curtweb/L567/readings/Templeton.pdf&quot; rel=&quot;nofollow&quot;&gt;this page&lt;/a&gt;)  &lt;/li&gt;&#xA;&lt;li&gt;will not be at any optima because the environment shifts too quickly (e.g. loci clearly under frequency-dependent selection, such as MHC). &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, in general, it depends what you are trying to model. If you want to model a specific kind of evolutionary change, then model that kind of evolutionary change. If you want to model a different kind of change, then model that kind of evolutionary change. Natural populations will likely follow any model some of the time, but will probably never follow any model all of the time. &lt;/p&gt;&#xA;" OwnerUserId="3396" LastEditorUserId="500" LastEditDate="2013-04-17T01:21:30.027" LastActivityDate="2013-04-17T01:21:30.027" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="7934" PostTypeId="2" ParentId="7529" CreationDate="2013-04-16T15:53:24.990" Score="2" Body="&lt;p&gt;It has been shown that predictions based on weak selection can be different from that on strong selection.&#xA;In fact, for rare mutations, each strategy has stationary distribution at the mutation selection equilibrium. The rank of the component depicts the relative prevalence of the available strategies. Yet the rank of the components of this distribution can change with the selection intensity. Thus results obtained under weak selection can not generally carry over to strong selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more details, please refer to Fig. 1 in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22634207&quot; rel=&quot;nofollow&quot;&gt;[1]&lt;/a&gt; and Fig. 2 in the supplementary information of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17600218&quot; rel=&quot;nofollow&quot;&gt;[2]&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22634207&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt; Julián García and Arne Traulsen, (2012), Journal of Theoretical Biology, Leaving the loners alone: Evolution of cooperation in the presence of antisocial punishment&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17600218&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt; Christoph Hauert, Arne Traulsen, Hannelore Brandt, Martin A. Nowak and Karl Sigmund, (2007), Science, Via freedom to coercion: the emergence of costly punishment&lt;/p&gt;&#xA;" OwnerUserId="3397" LastEditorUserId="3059" LastEditDate="2013-04-16T17:32:38.747" LastActivityDate="2013-04-16T17:32:38.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7937" PostTypeId="2" ParentId="7932" CreationDate="2013-04-16T20:56:20.877" Score="79" Body="&lt;p&gt;Wheels are possible on the molecular level — bacterial flagella are rotating cores inside a molecular motor, but wheels larger than the flagellum have not really been found. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1YlbP.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A single animal with a wheel is an improbable* development that would require a single animal have two separable parts (axle/wheel and body).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[*read as: &lt;em&gt;pretty much impossible&lt;/em&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's hard to imagine how such a thing could evolve.  A wheel and axle would need to be made of living tissue, otherwise it would be vulnerable to wear and tear.  Wheels also have problems going over uneven terrain, which is really all terrain animals live in.  It's difficult to imagine what sort of selection conditions would be strong enough to push animals away from legs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you include driver-vehicle symbionts where the 'car' and 'wheel' are actually two animals, then they &lt;em&gt;have&lt;/em&gt; evolved. Parasites can have all sorts of symbiotic control over their victims including as means of transport. The Jewel Wasp is one which is the most suggestive of what you may be thinking. The wasp stings its victim (a cockroach) in the thorax to immobilize the animal and then again just behind its head.  After this, the wasp can ride the beetle, steering it by holding its antennae back to its nest where the roach is immobilized to feed the wasp larvae there.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.the-scientist.com/?articles.view/articleNo/31536/title/Animal-Mind-Control/&quot; rel=&quot;noreferrer&quot;&gt;(see section &quot;Pet cockaroaches&quot; in this reference.)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the three schools of thought you added to the question, I would probably rather say there were two strong arguments against.  The first is whether there is an evolutionary path to wheels (argument 1 in your question), which I doubt.  Given even a large amount of evolutionary time you will not see a naked human being able to fly on their own power.  Too many structural characteristics of the body plan have been made to all be reversed so that wings or other means of aerial conveyance will show up. The same can be said for wheels when the body plans have fins/legs/and wings already. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Argument 3, which I also tend to agree with, is perhaps more convincing.  By the time a pair of animals makes a symbiotic relationship to do this, or a single macroscopic animal evolves wheels, they will literally develop legs and walk away. When life came onto the land this happened, and since then it's happened several times.  It's sort of like saying that the random movement of water molecules might line up to run a stream uphill. There's just such a strong path downwards, that the statistical chances of you seeing it happen are nil.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a hypothetical case, but arguing this in a convincing way I think you would need to lay out:  a) an environment whose conditions created enough of a selective advantage for wheels to evolve over legs or other similar adaptations we already see. Perhaps based on the energy efficiency of wheels;   b) some sort of physiological model for the wheels that convey a reasonable lifestyle for the wheel. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are lots of questions that would need to be satisfied in our thought experiment.  Here are some: &quot;the symbiotic wheel would be spinning constantly; if it died the driver creature would be completely defenseless&quot;; &quot;if the ground were bumpy, all these wheeled animals would get eaten&quot;; &quot;the wheel symbiont — how would it eat while its spinning all the time? Only fed by the driver? Even symbionts such as barnacles or lampreys on the flanks of sharks still have their own ability to feed.&quot;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For many similar questions the same sort of discussion ensues where there are many disadvantages which outweigh advantages for animals. e.g.&#xA;&quot;why are all the flying animals and fish and plants even more similar to airplanes than helicopters?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry if I seem negative, but way back in grad school I actually did go over some of these angles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE: &lt;a href=&quot;http://www.popularmechanics.com/science/environment/the-first-gear-discovered-in-nature-15916433&quot; rel=&quot;noreferrer&quot;&gt;First Gear found in a Living Creature&lt;/a&gt;.&lt;/strong&gt; &#xA;A &lt;a href=&quot;http://www.sciencemag.org/content/341/6151/1254.full&quot; rel=&quot;noreferrer&quot;&gt;european plant hopper insect with one of the largest accelerations known in biology has been found to have gears&lt;/a&gt;!  (There's a movie on the article page.&#xA;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The little bug has gears in its exoskeleton that synchronize its two jumping legs.  Once again selection suprises. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The gears themselves are an oddity. With gear teeth shaped like&#xA;  cresting waves, they look nothing like what you'd find in your car or&#xA;  in a fancy watch.  There could be two&#xA;  reasons for this. Through a mathematical oddity, there is a limitless&#xA;  number of ways to design intermeshing gears. So, either nature evolved&#xA;  one solution at random, or, as Gregory Sutton, coauthor of the paper&#xA;  and insect researcher at the University of Bristol, suspects, the&#xA;  shape of the issus's gear is particularly apt for the job it does.&#xA;  It's built for &quot;high precision and speed in one direction,&quot; he says.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The gears do not rotate 360 degrees, but appear on the surface of two joints to synchronize them as they wind up like a circular spring.  The gear itself is not living tissue, so the big solves the problem of regenerating the gear by growing a new set when it molts (i.e. gears that continually regenerate and heal are still unknown).  It also does not keep its gears throughout its lifecycle.  So the arguments here still stand; the exception still supports the rule.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2017-09-29T07:35:30.467" LastActivityDate="2017-09-29T07:35:30.467" CommentCount="18" ContentLicense="CC BY-SA 3.0" />
  <row Id="7938" PostTypeId="2" ParentId="7932" CreationDate="2013-04-16T22:08:40.160" Score="15" Body="&lt;p&gt;Shigeta's molecular answer is spot on. However, at the large scale level I think the key problem with a biological wheel needs to be spelled out clearly: how does an organism with separate parts maintain these parts? Let's suppose that an organism evolves a fully rotational joint, how do they then provide nutrients to the tissue on the other side? If they don't provide nutrients how does self-repair in this tissue continue without nutrients?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mind you, I'm not sure that the biological problems with a wheel are the real answer. I'm not sure how a wheel evolves. What's the functional intermediate? How does a semi-connected wheel out-perform a limb? Remember than evolution is canalised by what has gone before.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-04-16T22:08:40.160" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="7939" PostTypeId="1" CreationDate="2013-04-16T22:18:18.877" Score="1" ViewCount="181" Body="&lt;p&gt;I was reading this &lt;a href=&quot;http://www.nature.com/tpj/journal/v12/n5/full/tpj201135a.html&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; related to use of gene expressions for predicting the drug response. I have this confusion, the paper has used PCA on the covariance matrix formed by the genes to get what is called the background network as they say.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know the essence of background in this case. I know PCA gives us components which preserves the greatest variance and used for dimension reduction. What they mean by background network. Is it pathways ?&lt;/p&gt;&#xA;" OwnerUserId="3074" LastActivityDate="2013-09-01T11:30:28.243" Title="Confusion related to the use of PCA to determine the background network" Tags="&lt;bioinformatics&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7941" PostTypeId="2" ParentId="7932" CreationDate="2013-04-17T06:14:37.070" Score="19" Body="&lt;p&gt;In your question, you mention frozen lakes and rightly say that skates would be far easier than wheels, but you could have used salt flats as an example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the reason there are no actual wheels is a mixture of ontogenetic and phylogentic barriers, maintenance (nutrition), lubrication and control (nerve connections). There would have to be severe and sustained evolutionary incentives to go from something simple, cheap and extant (legs) to something way more difficult and complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are several species of plants and animals that use rolling as a form of locomotion. Tumbleweeds are a good example of plants, and for animals, there are &lt;a href=&quot;https://www.youtube.com/watch?v=bzAF7WuXhKA&quot;&gt;spiders&lt;/a&gt;, &lt;a href=&quot;https://www.youtube.com/watch?v=HmLS2WXZQxU&quot;&gt;caterpillars and salamanders&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It only takes a small evolutionary development to take something like this from a passive motion (rolling down hill to escape predators) to active (perhaps creating waves of flexion to roll like... ahem, caterpillar tracks).&lt;/p&gt;&#xA;" OwnerUserId="3401" LastActivityDate="2013-04-17T06:14:37.070" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7942" PostTypeId="2" ParentId="7916" CreationDate="2013-04-17T08:08:23.990" Score="3" Body="&lt;p&gt;There is a lot of variation in how and when deer shed their antlers. In most arctic and temperate-zone species, antler growth and shedding is annual, and is controlled by the length of daylight. In tropical species, antlers may be shed at any time of year, and in some species such as the sambar, antlers last several years. Some equatorial deer never shed their antlers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The horns change every year and, especially, increase the number of branches (and consequently, change their shape). &lt;strong&gt;You can't recognize them by antlers, but by other features, such as color of the hair or the lineaments.&lt;/strong&gt; Like us, animals have individual morphological differences that are recognizable and listable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Biologists specializing in studies of particular animal species not only take photos, but also make drawings and write descriptions of behavior&lt;/strong&gt;, to identify individuals within herds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;An optical examination, however, of the subject through drawings and photos (and if possible, direct observation), is more useful than a PC program.&lt;/strong&gt; This involves identifying particular similarities and equalities that are not &quot;identical&quot;. This is possible to do visually on a large (but limited) number of specimens. The human eye is the best computer.&lt;/p&gt;&#xA;" OwnerUserId="3384" LastEditorUserId="3059" LastEditDate="2013-04-17T14:51:54.867" LastActivityDate="2013-04-17T14:51:54.867" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7943" PostTypeId="1" AcceptedAnswerId="7944" CreationDate="2013-04-17T11:13:14.467" Score="2" ViewCount="1977" Body="&lt;p&gt;Fungi and insects contain &lt;a href=&quot;http://en.wikipedia.org/wiki/Chitin&quot; rel=&quot;nofollow&quot;&gt;chitin&lt;/a&gt;, which is about 6% nitrogen.&#xA;Can an animal - like me - make use of this as a nitrogen source to build proteins?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any animals that can do this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there other uses an animal can put Nitrogen from this specific source to?&lt;/p&gt;&#xA;" OwnerUserId="3037" LastEditorUserId="6" LastEditDate="2013-04-17T11:45:00.103" LastActivityDate="2017-07-11T20:07:58.280" Title="Can animals use the nitrogen in chitin to build proteins?" Tags="&lt;digestive-system&gt;&lt;nutrition&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7944" PostTypeId="2" ParentId="7943" CreationDate="2013-04-17T12:29:46.353" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dietary_fiber&quot; rel=&quot;nofollow&quot;&gt;The first answer is that humans cannot.&lt;/a&gt;&#xA;Chitin is a major component of the exoskeleton of insects and other arthropods, the cell wall of fungi and bacteria, the perisarco of hydroids and is also present in the epidermal cuticle or other surface structures of many other invertebrates. After cellulose, chitin is the most abundant naturally occurring biopolymer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chitin is a polysaccharide consisting of multiple units of N-acetylglucosamine (N-acetyl-D-glucos-2-amine) linked together with a bond-type β-1, 4, of the same glucose units forming the cellulose. Therefore, the the chitin can be regarded as a cellulose in which the hydroxyl group on each monomer has been replaced a group of acetilammina.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pepsin in the stomach cleaves peptide bonds that bind together the amino acids of proteins, thus forming small peptides and amino fragments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;From the organoleptic point of view, chitin is considered a &lt;a href=&quot;http://en.wikipedia.org/wiki/Dietary_fiber&quot; rel=&quot;nofollow&quot;&gt;fiber&lt;/a&gt;, like cellulose and chitosans, suggesting it is indigestible.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some herbivores, such as goats and some ruminants can digest cellulose, breaking them down long chains of polysaccharides. &lt;strong&gt;Similarly, &lt;a href=&quot;https://it.wikipedia.org/wiki/Asteroidea&quot; rel=&quot;nofollow&quot;&gt;echinoderms&lt;/a&gt; can eat shellfish, sea urchins and mussels and digest chitin, breaking mechanically only ones with hard shells.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;However, hydrogen bonds between adjacent polymer guarantee the substance &lt;a href=&quot;http://en.wikipedia.org/wiki/Chitin&quot; rel=&quot;nofollow&quot;&gt;a remarkable hardness&lt;/a&gt;. This feature, combined with its flexibility and the fact that it is degradable by endogenous enzymes, &lt;strong&gt;chitin is an excellent material for the production of wires for surgical sutures, bandages and also synthetic leather. Chitin also has the unusual property of accelerating the healing of wounds in humans&lt;/strong&gt;, closely related to chitosan (a more water-soluble derivative of chitin) and to the immune system of plants and animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, @mart. Echinoderms use chitin for producing proteins, similar to how herbivores use plant cell walls, which consist mainly of polysaccharides (non-nitrogen compounds), to produce the proteins (nitrogen-containing compounds), that serve us also (since we are not able to digest the grass).&lt;/p&gt;&#xA;" OwnerUserId="3384" LastEditorUserId="3059" LastEditDate="2013-04-18T19:34:04.647" LastActivityDate="2013-04-18T19:34:04.647" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7945" PostTypeId="1" CreationDate="2013-04-17T17:38:00.007" Score="3" ViewCount="352" Body="&lt;p&gt;I have absolutely no idea as to how Levomepromazine elicits its analgesic effects so please do direct me to journal articles and other credible sources with you, the answerer, making a summary of Levomepromazine's mechanism of action in your answer.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2014-12-08T12:42:37.317" Title="What's the mechanism of action of Levomepromazine's analgesic effects?" Tags="&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7946" PostTypeId="1" CreationDate="2013-04-17T17:43:01.257" Score="2" ViewCount="89" Body="&lt;p&gt;I am trying to find the diagnosis figure for different bacteria where phases are illustrated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am using at the moment: 1) &lt;a href=&quot;http://www.mhprofessional.com/product.php?isbn=0071802320&amp;amp;cat=116&quot; rel=&quot;nofollow&quot;&gt;First Aid for the USMLE Step 1 2013&lt;/a&gt; and 2) &lt;a href=&quot;http://store.elsevier.com/Medical-Microbiology/Patrick-Murray/isbn-9780323086929/&quot; rel=&quot;nofollow&quot;&gt;Medical Microbiology by Murray et al, 7e&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is a good review source for basic microbiological diagnosis?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2013-04-18T06:30:54.363" LastActivityDate="2014-08-09T06:07:14.647" Title="What is a good review book/source for microbiological diagnosis?" Tags="&lt;microbiology&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7947" PostTypeId="1" AcceptedAnswerId="7952" CreationDate="2013-04-17T17:50:11.143" Score="4" ViewCount="846" Body="&lt;p&gt;Where is the line usually drawn between macroevolution and microevolution?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought that, although similar processes govern both, the line was at the species level, with macroevolution being changes at the above-species level and microevolution being changes within a species (something like changes in allele frequencies).  (So it's a question of timescales?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I heard someone talk about microevolution among &lt;em&gt;different species&lt;/em&gt; of &lt;em&gt;Drosophila&lt;/em&gt;, specifically referring to copy number variation.  Was the choice of &quot;microevolution&quot; to describe this process (more likely) due to the similarity between &lt;em&gt;Drosophila&lt;/em&gt; species or the type of change in the gene? Or at this level, is the distinction rather arbitrary?&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="6" LastEditDate="2014-01-16T08:22:36.793" LastActivityDate="2014-01-16T08:22:36.793" Title="Macroevolution vs. microevolution" Tags="&lt;evolution&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7948" PostTypeId="1" CreationDate="2013-04-17T18:17:43.360" Score="5" ViewCount="3544" Body="&lt;p&gt;I am learning about why it is important to measure Km and Vmax for each experimental setup because measuring the &quot;apparent&quot; Km and Vmax includes enzyme inhibitions of which one might not be aware.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, what if there are entire reactions going on that are consuming the product or substrate that are not known? Are these accurately aggregated into the Km and Vmax measurements?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are some of the links that I read through:&#xA;&lt;a href=&quot;http://www.bio.upenn.edu/media/pdf/courses/F02/BIOL202/Handouts/BIOL202.ApparentKmandVmax.pdf&quot; rel=&quot;noreferrer&quot;&gt;http://www.bio.upenn.edu/media/pdf/courses/F02/BIOL202/Handouts/BIOL202.ApparentKmandVmax.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Enzyme_inhibitor&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Enzyme_inhibitor&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3403" LastEditorUserId="3059" LastEditDate="2013-04-17T21:23:04.737" LastActivityDate="2017-07-29T06:17:49.527" Title="Michaelis-Menten Kinetics: Does measuring apparent Km and Vmax take into account competing reactions?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;&lt;mathematical-models&gt;&lt;kinetics&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7950" PostTypeId="1" CreationDate="2013-04-17T23:07:20.360" Score="2" ViewCount="1315" Body="&lt;p&gt;What's a good and reliable database for the pharmacodynamic and pharmacokinetic data of drugs both approved (in the US and elsewhere) and unapproved?&lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-04-19T20:27:18.487" Title="What's a good and reliable database on the pharmacodynamic and pharmacokinetic data of drugs both approved and unapproved?" Tags="&lt;pharmacology&gt;&lt;database&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7951" PostTypeId="2" ParentId="7950" CreationDate="2013-04-17T23:31:28.763" Score="2" Body="&lt;p&gt;For approved drugs, the &lt;strong&gt;Drugs @FDA&lt;/strong&gt; database at &lt;a href=&quot;http://www.accessdata.fda.gov/scripts/cder/drugsatfda/&quot; rel=&quot;nofollow&quot;&gt;CDER&lt;/a&gt; (Center for Drug Evaluation and Research) aggregates labeling information (which includes at least a cursory PD explanation and a listing of or reference to common PK data for the substance) for most modern drugs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unapproved drugs may be a bit trickier to find out about, but the FDA maintains a list of contract research organizations (CROs) who are running trials &lt;a href=&quot;http://www.fda.gov/Drugs/InformationOnDrugs/ucm135162.htm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, and the actual trials can be found on &lt;a href=&quot;http://www.clinicaltrials.gov/&quot; rel=&quot;nofollow&quot;&gt;http://www.clinicaltrials.gov/&lt;/a&gt;, which will have citations for the papers that have been published.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Drugs in their earliest stages of development, i.e., internal to a pharma company, are likely to be kept pretty tightly under wraps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know enough about the governing bodies in other countries to know where any international data would be, but I assume you can find published papers for substances in those countries as well.&lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2013-04-17T23:31:28.763" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="7952" PostTypeId="2" ParentId="7947" CreationDate="2013-04-18T00:44:12.137" Score="9" Body="&lt;p&gt;Let's start with a word of caution: on the internet, the terms macroevolution and microevolution (especially together) are usually used primarily in creationist rhetoric. As such, it is usually best to avoid them, especially when talking to a lay audience. The main mistake creationists perpetuate when thinking about micro-vs-macro evolution, is that the two are somehow different and distinct physical processes. This is simply not the case, they are both &lt;em&gt;just evolution&lt;/em&gt;. The scientific distinction between the terms, comes not from the physical world around us, but from how we choose to talk about it. When a biologist says &amp;quot;microevolution&amp;quot; or &amp;quot;macroevolution&amp;quot; they are actually signaling what kind of questions they are interested in asking, or what sort of tools they plan on using.&lt;/p&gt;&#xA;&lt;h2&gt;Verbal and empirical theories&lt;/h2&gt;&#xA;&lt;p&gt;In verbal and empirical theories, the micro-macro distinction is usually one of timescales. A person in the macroevolutionary paradigm, usually asks questions &lt;em&gt;above&lt;/em&gt; the level of individual species, as &lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/VIADefinition.shtml&quot; rel=&quot;noreferrer&quot;&gt;Evolution 101 writes&lt;/a&gt; (emphasis mine):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;instead of focusing on an individual beetle species, a macroevolutionary lens might require that we &lt;b&gt;zoom out on the tree of life&lt;/b&gt;, to assess the diversity of the &lt;b&gt;entire beetle clade&lt;/b&gt; and its position on the tree.&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Empirically, macroevolutionary answers to these sort of questions are usually ones that don't have access to detailed evolutionary histories or direct experiment. Instead, the method tends to be ones that use geology, fossils, and back-inferences from broad differences/similarities of existing species. As such, most macroevolutionary theories tend to be descriptive, instead of predictive. Most of paleontology can be classified under the macroevolutionary paradigm.&lt;/p&gt;&#xA;&lt;p&gt;If someone explicitly says that they are looking at microevolution then this usually refers to a contrasting methodology that tends to be heavy on direct experimental manipulation. Most importantly, microevolutionists tend to have access to rich and detailed evolutionary histories. As such, it is not surprising that you saw a study that identified itself as microevolutionary while looking at different species of &lt;em&gt;Drosophila&lt;/em&gt;. The fruit fly is one of the widest used model organisms, and as such the study you are referring to probably experimentally manipulated populations of fruit flies and collected a rich dataset of genetic changes in the generations of fruit flies that they studied.&lt;/p&gt;&#xA;&lt;p&gt;Of course, most studies are at intermittent levels, and no this isn't called meso-evolution (except by silly people). If you are not clearly using the macroevolutionary nor the microevolutionary &lt;em&gt;paradigm&lt;/em&gt; but still looking at evolution, you would just simply say 'evolutionary' without any prefix.&lt;/p&gt;&#xA;&lt;h2&gt;Formal and mathematical models&lt;/h2&gt;&#xA;&lt;p&gt;For formal and mathematical theories, the micro/macro distinction is also one of methods used by the theorist not of the underlying domain they are studying. &lt;a href=&quot;https://biology.stackexchange.com/a/7929/500&quot;&gt;Mathematical modeling of evolution falls into two broad categories: frequency-dependent and frequency-independent models&lt;/a&gt;. Frequency-dependent models almost never make the micro-macro distinction. Although you could argue that dynamic models in evolutionary game theory are micro, and static equilibrium concepts like &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionarily_stable_strategy&quot; rel=&quot;noreferrer&quot;&gt;ESS&lt;/a&gt; are macro, but I doubt theorists would endorse this view. As such, I will focus on the frequency-independent models.&lt;/p&gt;&#xA;&lt;p&gt;For frequency-independent models, they key concept is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Fitness_landscape&quot; rel=&quot;noreferrer&quot;&gt;fitness landscape&lt;/a&gt; -- a way to map each genotype to a fitness. If the model tracks a population (a distribution over vertices in the fitness graph) on a static fitness landscape, then it would typically be just called an evolutionary model (the word microevolutionary is seldom used explicitly in this field). However, if the authors assume that mutations are extremely rare and thus any mutant goes to fixation before a new one arises then they can use Gillespie (1983, 1984) to replace the population by a single &amp;quot;typical individual&amp;quot; occupying one vertex of the fitness graph. At this point, the model becomes macroevolutionary and the &lt;a href=&quot;https://biology.stackexchange.com/q/2638/500&quot;&gt;underlying rule for calculating fixation probabilities&lt;/a&gt; would be the microevolutionary component. This approach is often also coupled with an alternation of change in fitness landscape followed by mutations and a selective sweep. Fundamentally, though, macroevolutionary models are just convenient (or tractable) approximations to a real underlying evolutionary dynamics. This should &lt;em&gt;never&lt;/em&gt; be forgotten.&lt;/p&gt;&#xA;&lt;h2&gt;Strange example bridging the gaps&lt;/h2&gt;&#xA;&lt;p&gt;Finally, it is important to stress that the macro- and micro-evolutionary paradigms are not necessarily exclusive and &lt;strong&gt;do not&lt;/strong&gt; have to correspond to a difference in timescales! This is best done with an example of a respected theoretical study that mixes everything together. Kauffman &amp;amp; Weinberger (1989) used their newly developed &lt;a href=&quot;http://en.wikipedia.org/wiki/NK_model&quot; rel=&quot;noreferrer&quot;&gt;NK model or rugged fitness landscapes&lt;/a&gt; to study &lt;a href=&quot;http://en.wikipedia.org/wiki/Affinity_maturation&quot; rel=&quot;noreferrer&quot;&gt;maturation of the immune response&lt;/a&gt; (Tonegawa, 1983). The developed a macroevolutionary mathematical model because they used Gillespie's trick to replace a population by a typical individual by abstracting away from the underlying microevolutionary calculation of fixation probabilities. However, their model was studying evolutionary dynamics within the human immune system (so timescales of days to weeks) and was tuned by parameters gathered by empirical microevolutionary studies that tracked individual nucleotide changes (Crews et al., 1981; Tonegawa, 1983; Clark et al., 1985). Lastly, the study results can be used to inform a question typical of verbal macroevolutionary theory: &lt;a href=&quot;https://biology.stackexchange.com/a/7921/500&quot;&gt;Are there any examples of sudden leaps in evolution?&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;As such, the above study used a formal macroevolutionary model, informed by empirical microevolutionary work, to help us understand a question typical of verbal macroevolution while looking at a physical process that operated on the incredibly short timescale of days to weeks. No wonder people are so confused by the micro-macro &amp;quot;divide&amp;quot;!&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&lt;p&gt;Clark, S.H., Huppi, K., Ruezinsky, D., Staudt, L., Gerhard, W., &amp;amp; Weigert, M. (1985). Inter- and intraclonal diversity in the antibody response to influenza hemagglutin. &lt;em&gt;J. Exp. Med.&lt;/em&gt; 161, 687.&lt;/p&gt;&#xA;&lt;p&gt;Crews, S., Griffin, J., Huang, H., Calame, K., &amp;amp; Hood, L. (1981). A single V gene segment encodes the immune response to phosphorylcholine: somatic mutation is correlated with the class of the antibody. &lt;em&gt;Cell&lt;/em&gt; 25, 59.&lt;/p&gt;&#xA;&lt;p&gt;Gillespie, J.H. (1983). A simple stochastic gene substitution model. &lt;em&gt;Theor. Pop. Biol.&lt;/em&gt; 23, 202.&lt;/p&gt;&#xA;&lt;p&gt;Gillespie, J.H. (1984). Molecular evolution over the mutational landscape. &lt;em&gt;Evolution&lt;/em&gt; 38, 1116.&lt;/p&gt;&#xA;&lt;p&gt;Kauffman, S. and Weinberger, E. (1989) The NK Model of rugged fitness landscapes and its application to the maturation of the immune response. &lt;em&gt;Journal of Theoretical Biology&lt;/em&gt;, 141(2): 211-245&lt;/p&gt;&#xA;&lt;p&gt;Tonegawa, S. (1983). Somatic generation of antibody diversity. &lt;em&gt;Nature&lt;/em&gt; 302, 575.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-01-16T08:22:15.007" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7953" PostTypeId="1" CreationDate="2013-04-18T01:18:15.697" Score="3" ViewCount="81" Body="&lt;p&gt;&lt;em&gt;Drosophila&lt;/em&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/Polytene_chromosome&quot; rel=&quot;nofollow&quot;&gt;polytene chromosomes&lt;/a&gt; have been particularly useful in genetic research, as it made cytogenetic gene mapping possible with very little effort. This was primarily accomplished due to polytene bands, which are naturally-occuring (no stain) fixed bands seen along the chromosomes via microscopy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We have been exploiting these bands for decades, but it seems as though their function isn't quite clear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the cause of the visible polytene bands, and what function do they serve?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2013-04-18T01:23:57.953" LastActivityDate="2013-04-18T01:23:57.953" Title="What are polytene bands, and why are they there?" Tags="&lt;genetics&gt;&lt;cytogenetics&gt;&lt;drosophila&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7955" PostTypeId="2" ParentId="7948" CreationDate="2013-04-18T04:23:59.373" Score="6" Body="&lt;p&gt;Have you heard of something known as &quot;Occam's Razor&quot; ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It says when you have multiple possible explanations/hypotheses then select the one which is simplest (i.e least number of assumptions)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Same with mathematical models. Chemical kinetics models usually assume first order unless there is some evidence against it. Similarly, for enzyme kinetics, as long as you don't think there is something anomalous going on, use Michaelis-Menten model. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What if there are entire reactions going on that are consuming the&#xA;  product or substrate that are not known&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Many physiological enzyme catalysed reaction are &lt;strong&gt;not&lt;/strong&gt; Michaelis-Menten. If you happen to have an insight about it or if the simulations dont match the experimental data, you can revise the model. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, Michaelis-Menten model for for competitive inhibition exists, as you yourself indicate in the link.  &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-18T04:23:59.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7957" PostTypeId="2" ParentId="7948" CreationDate="2013-04-18T07:53:17.320" Score="1" Body="&lt;p&gt;The answer is no really, but some variants might allow you to study inhibition.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Michaelis Menten kinetics are experiments which try to characterize the catalysis characteristics of a reaction but to do so the numbers are obtained at concentrations of substrate that you dont find in a cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vmax is defined as the maximum rate at which the reaction is run in question.  To measure this the substrate concentration is also maximal - the binding sites of enzymes must be fully occupied during the entire experiment. So by definition there is no competitive reaction possible here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Km is a binding constant obtained where the reaction rate is found to be half Vmax.  This definition is free of any competing reactions.  You can use Michaelis Menten kinetics to study &lt;a href=&quot;http://en.wikipedia.org/wiki/Competitive_inhibition&quot; rel=&quot;nofollow&quot;&gt;competitive inhibition&lt;/a&gt; though and by comparing a reaction rate and comparing it to the reaction rate (called Vo) you can derive a Ki which gives you how much your inhibitor has affected substrate binding. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-04-18T07:53:17.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7958" PostTypeId="2" ParentId="7948" CreationDate="2013-04-18T08:09:34.527" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://www.kois.sk/bioorg/bioorganicka_chemia/BIOORG2/10%20prikazani.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;As Arthur Kornberg said&lt;/a&gt;: &quot;Don't waste clean thinking on dirty enzymes.&quot;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Discovering an assay for a biological event in a cell-free extract opens the way to its molecular resolution and reconstitution (Commandment I). Trying to devise a mechanism with a crude extract, even with ingenious experiments, is generally a waste of effort. An extract is too dirty; purification is the only way to go.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Added in response to a comment from Dexter:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jb.asm.org/content/182/13/3613#sec-4&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kornberg was quoting Efraim Racker.&lt;/a&gt; And in any case my original link is dead.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2017-07-29T06:17:49.527" LastActivityDate="2017-07-29T06:17:49.527" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7959" PostTypeId="5" CreationDate="2013-04-18T19:31:07.490" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-18T19:31:07.490" LastActivityDate="2013-04-18T19:31:07.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7960" PostTypeId="4" CreationDate="2013-04-18T19:31:07.490" Score="0" Body="Questions pertaining to periodic life cycle events, and how these are affected by the external environment, climatic variation and weather fluctiations." OwnerUserId="3059" LastEditorUserId="3624" LastEditDate="2015-03-12T13:24:54.087" LastActivityDate="2015-03-12T13:24:54.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7961" PostTypeId="5" CreationDate="2013-04-18T22:24:37.060" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-18T22:24:37.060" LastActivityDate="2013-04-18T22:24:37.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7962" PostTypeId="4" CreationDate="2013-04-18T22:24:37.060" Score="0" Body="Questions related to animal behaviour, in the lab or in their natural environments." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-18T22:39:27.867" LastActivityDate="2013-04-18T22:39:27.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7963" PostTypeId="2" ParentId="7909" CreationDate="2013-04-18T22:40:26.457" Score="-2" Body="&lt;p&gt;An opinion by non-technical observer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you know the function of a hive, you know that bees communicate with each other, touching and rubbing chemical information. In a few minutes the information reaches the center of the hive and returns to individuals which are caring of it. It is widely accepted that a hive is a unique individual, composed of thousands of insects each with its own function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe that we can make the observation reverse.&#xA;The man (and animals) are agglomerations of cells that pass chemically information to each other. Information reaches the central system, which responds by activating the necessary functions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case of infection, viral or bacterial, blood flow to the affected place very quickly, scrolling faster and thus raising the temperature. Similarly in the blood activates the necessary antibodies, which communicate with each other chemically referring where necessary. Pile up in the affected areas, resulting in swelling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other functions, such as sweating, vomiting or pus, are ways to excrete toxins (such should not be blocked). If we imagine the human body as a great hive where each cell is a member that transmits information and responds to stimulation of central system, acting in cooperation, the operation according to me is very clear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do the bees know that they are dying, if not passing to collecting companions honey too thick?&#xA;Sorry for non-technical opinion, if not useful delete it.&lt;/p&gt;&#xA;" OwnerUserId="3384" LastActivityDate="2013-04-18T22:40:26.457" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="7964" PostTypeId="1" CreationDate="2013-04-18T23:24:22.907" Score="4" ViewCount="11981" Body="&lt;p&gt;I know that the ascending loop of Henle is impermeable to water and ions, and, by end of the ascending limb, the osmolarity of the tubular fluid is very low due to the active transport of ions out (e.g, sodium, potassium, chloride). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, what if the person had to produce hypertonic urine due to dehydration or some other circumstance? Would the increase in osmolarity be done through a decrease in removal of ions in the descending limb, or has the distal tubule and collecting ducts got something to do with it?&lt;/p&gt;&#xA;" OwnerUserId="3382" LastEditorUserId="107" LastEditDate="2013-04-19T00:59:00.570" LastActivityDate="2018-05-18T05:21:25.617" Title="How is Hypertonic Urine Produced in a Mammalian Kidney?" Tags="&lt;physiology&gt;&lt;kidney&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7965" PostTypeId="5" CreationDate="2013-04-18T23:40:38.617" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-18T23:40:38.617" LastActivityDate="2013-04-18T23:40:38.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7966" PostTypeId="4" CreationDate="2013-04-18T23:40:38.617" Score="0" Body="Isoforms of proteins are differently spliced versions of a protein which are different in length. Isoforms can have different regulation and functions." OwnerUserId="3059" LastEditorUserId="5144" LastEditDate="2014-03-17T12:17:40.610" LastActivityDate="2014-03-17T12:17:40.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7967" PostTypeId="1" CreationDate="2013-04-19T02:07:08.147" Score="4" ViewCount="1018" Body="&lt;p&gt;&quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Huntington%27s_disease&quot; rel=&quot;nofollow noreferrer&quot;&gt;Huntington's disease&lt;/a&gt; (HD) is a neurodegenerative genetic disorder that affects muscle coordination and leads to cognitive decline and psychiatric problems.&quot; As we all know, this genetic disease exhibits a generally late age of onset. It has been shown that a increase in the number of CAG repeats in the hungtingtin gene is negatively correlated to the age of onset of the disease. However, patients having a  particular number of CAG repeats still have an &lt;strong&gt;extremely variable&lt;/strong&gt; age of onset, which leads to believe that &lt;em&gt;other factors&lt;/em&gt; are contributing to the Huntington phenotype.(&lt;a href=&quot;http://www.nature.com/ng/journal/v4/n4/abs/ng0893-398.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MwuaZ.png&quot; alt=&quot;enter image description here&quot;&gt; (&lt;a href=&quot;http://www.nature.com/ng/journal/v4/n4/abs/ng0893-398.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What other genetic or environmental factors have been shown to vary the age of onset of Huntington's disease?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Andrew, S. E. et al.&lt;/strong&gt; &lt;em&gt;The relationship between trinucleotide (CAG) repeat length and clinical features of Huntington’s disease.&lt;/em&gt; Nature Genetics 4, 398–403 (1993).&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2013-04-19T03:21:32.417" Title="What factors govern the variable age of onset in Huntington's Disease?" Tags="&lt;genetics&gt;&lt;pathology&gt;&lt;human-genetics&gt;&lt;neurodegenerative-disorders&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7968" PostTypeId="5" CreationDate="2013-04-19T02:52:41.640" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-19T02:52:41.640" LastActivityDate="2013-04-19T02:52:41.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7969" PostTypeId="4" CreationDate="2013-04-19T02:52:41.640" Score="0" Body="Questions relating to the separation of cells on the basis of physical properties." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T02:57:45.020" LastActivityDate="2013-04-19T02:57:45.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7970" PostTypeId="5" CreationDate="2013-04-19T02:54:50.743" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-19T02:54:50.743" LastActivityDate="2013-04-19T02:54:50.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7971" PostTypeId="4" CreationDate="2013-04-19T02:54:50.743" Score="0" Body="Questions pertaining to organized collections of biological data." OwnerUserId="3059" LastEditorUserId="4101" LastEditDate="2013-10-31T18:24:13.110" LastActivityDate="2013-10-31T18:24:13.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7972" PostTypeId="2" ParentId="7967" CreationDate="2013-04-19T03:11:59.097" Score="4" Body="&lt;p&gt;There is quite a bit of data available from Venezuelan HD families, but they haven't identified the factors themselves. From the abstract of the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14993615&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt;, emphasis mine:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Analysis of the 83 kindreds that comprise the Venezuelan HD kindreds&#xA;  demonstrates that residual variability in age of onset has &lt;strong&gt;both&#xA;  genetic and environmental components&lt;/strong&gt;. We created a residual age of&#xA;  onset phenotype from a regression analysis of the log of age of onset&#xA;  on repeat length. Familial correlations (correlation +/- SE) were&#xA;  estimated for sibling (0.40 +/- 0.09), parent-offspring (0.10 +/-&#xA;  0.11), avuncular (0.07 +/- 0.11), and cousin (0.15 +/- 0.10) pairs, &lt;strong&gt;suggesting a familial origin for the residual variance in onset*&lt;/strong&gt;. By&#xA;  using a variance-components approach with all available familial&#xA;  relationships, the additive genetic heritability of this residual age&#xA;  of onset trait is 38%. A model, including shared sibling environmental&#xA;  effects, estimated the components of additive genetic (0.37), shared&#xA;  environment (0.22), and nonshared environment (0.41) variances,&#xA;  &lt;strong&gt;&lt;em&gt;confirming that approximately 40% of the variance remaining in onset&#xA;  age is attributable to genes other than the HD gene and 60% is&#xA;  environmental&lt;/em&gt;&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;*&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11449389&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; also suggests the same, with a smaller (but different) samples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A recent study of an Italian sample suggests that &lt;a href=&quot;http://jnnp.bmj.com/content/83/Suppl_1/A20.3.short&quot; rel=&quot;nofollow&quot;&gt;a polymorphism in Atg7&lt;/a&gt; (autophagy-related gene) is a modifier of age-of-onset, but this result does not generalize to a European cohort.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;What is apparently &lt;em&gt;not&lt;/em&gt; linked to age of onset in HD? &lt;a href=&quot;http://iospress.metapress.com/content/p2271460602l7333/&quot; rel=&quot;nofollow&quot;&gt;β-defensin copy number variation&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, &lt;a href=&quot;http://jnnp.bmj.com/content/83/Suppl_1/A10.2.short&quot; rel=&quot;nofollow&quot;&gt;CTCF doesn't appear to be linked to the CAG repeat instability&lt;/a&gt; (mutations in CTCF have previously implicated in triplet repeat instability).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations in PGC-1α, mitochondrial regulator, were previously associated with age of onset, but a more recent study suggests that &lt;a href=&quot;http://link.springer.com/article/10.1007/s00439-012-1205-z&quot; rel=&quot;nofollow&quot;&gt;this might have been due to stratification of the sample&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, a polymorphism in HAP-1 was previously associated with age of onset, but a &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1353802012002088&quot; rel=&quot;nofollow&quot;&gt;subsequent study found no evidence of association&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Altogether, these results suggest that population stratification needs to be taken into account when evaluating associations between age of onset and genetic polymorphisms.  It is also possible that there are population-specific genetic factors that affect age of onset.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T03:21:32.417" LastActivityDate="2013-04-19T03:21:32.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7973" PostTypeId="5" CreationDate="2013-04-19T03:46:50.907" Score="0" Body="&lt;p&gt;Mammals are animals that nurse their young, have a neocortex, and three middle ear bones.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-29T12:19:53.740" LastActivityDate="2017-03-29T12:19:53.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7974" PostTypeId="4" CreationDate="2013-04-19T03:46:50.907" Score="0" Body="Questions related to mammals, animals that nurse their young, have a neocortex, and three middle ear bones." OwnerUserId="3059" LastEditorUserId="28834" LastEditDate="2017-03-29T16:44:11.287" LastActivityDate="2017-03-29T16:44:11.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7975" PostTypeId="5" CreationDate="2013-04-19T03:48:07.393" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-19T03:48:07.393" LastActivityDate="2013-04-19T03:48:07.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7976" PostTypeId="4" CreationDate="2013-04-19T03:48:07.393" Score="0" Body="Questions relating to the binding of proteins to each other and other molecules." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T07:52:01.800" LastActivityDate="2013-04-19T07:52:01.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7977" PostTypeId="1" CreationDate="2013-04-18T00:37:28.170" Score="1" ViewCount="362" Body="&lt;p&gt;I know that difference between different colors of light is difference between their wave length but I don't know what gives beautiful colors (like rainbow colors) to different wave length of observable light?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What makes our eyes to see different wavelengths of light as different colors?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Remark:&lt;/strong&gt;&#xA;I've meet someone which he was color blind, he was not able to see rainbow colors.&#xA;So the process that gives color to light must be in our eyes and brain.&lt;/p&gt;&#xA;" OwnerDisplayName="Achmet" LastEditorUserId="3340" LastEditDate="2013-04-19T11:36:04.957" LastActivityDate="2013-04-19T11:36:04.957" Title="What gives observable light its colors?" Tags="&lt;vision&gt;" AnswerCount="1" CommentCount="9" ClosedDate="2013-04-19T21:43:29.580" ContentLicense="CC BY-SA 3.0" />
  <row Id="7978" PostTypeId="2" ParentId="7977" CreationDate="2013-04-18T01:29:47.237" Score="2" Body="&lt;p&gt;Three different types of cones in the eye are sensitive to three different, contiguous and &lt;s&gt;slightly&lt;/s&gt; overlapping, sections of the visible spectrum. The nerve signals from these three different types of cones are interpreted by different sections of the brain as cyan, magenta, and yellow, from which all the discernible colours are composed. This forms the familiar Colour Triangle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sides of the Colour Triangle bulge slightly (I believe) because of the slight overlap in the sensitivity ranges of the three cone types.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Colour blindness occurs when someone is born with only two (or rarely one or none) different types of cones, instead of the usual three. This causes an inability to detect one of the thee sub-spectra.&lt;/p&gt;&#xA;" OwnerUserId="38417" OwnerDisplayName="Pieter Geerkens" LastActivityDate="2013-04-18T03:58:25.643" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="7980" PostTypeId="1" CreationDate="2013-04-19T11:27:05.183" Score="1" ViewCount="911" Body="&lt;p&gt;I am conducting a biochemistry-related experiment and I have been unable to understand a step which is commonly performed.&#xA;My aim in this step is to apply a PEG (Polyethylene glycol) silane layer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After immersing indium tin oxide (ITO) slides in a PEG-concentration, the slides are incubated for 18 hours at a temperature of 60 degrees Celsius.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you tell me why the incubation is performed? And why for 18 hours and at 60 degrees Celsius?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks a lot in advance!!&lt;/p&gt;&#xA;" OwnerUserId="3415" LastEditorUserId="3059" LastEditDate="2013-04-19T18:43:10.143" LastActivityDate="2013-05-13T06:42:53.280" Title="PEG-silane treatment: why incubate for 18 hours at 60 degrees Celsius?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;protocol&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7981" PostTypeId="1" CreationDate="2013-04-19T12:18:32.260" Score="2" ViewCount="748" Body="&lt;p&gt;For some reason the lab seems to have a problem with contamination every so often.  It's virtually impossible to prevent bacteria, viruses, fungi, etc. from getting into the incubator every time you open the door.  Our incubator is pretty old, we don't have one of the new fancier versions that's made with pure copper inside, which effectively kills microorganisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would it be a good idea to buy a copper plate and place it on the shelf, on which we could put our culture flasks?  Or would it disrupt the flow of heat/CO2 too much?  Would it be better to buy copper foil and wrap the shelves in it, then poke holes into it where all the holes are in the shelf?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We use good cell culturing practices; I don't contamination is happening because people don't know what they're doing.  It just happens over time with enough people working in a cell culture room.  Could copper in the incubator help?  We probably don't have the money to buy a brand new incubator that's made out of copper, so would this be a viable, economic alternative?&lt;/p&gt;&#xA;" OwnerUserId="3232" LastEditorUserId="3059" LastEditDate="2013-04-19T18:33:59.617" LastActivityDate="2013-04-19T18:33:59.617" Title="Copper for cell incubator to prevent contamination" Tags="&lt;lab-techniques&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7983" PostTypeId="2" ParentId="7980" CreationDate="2013-04-19T13:12:29.970" Score="3" Body="&lt;p&gt;The binding of proteins (and cells) to glass (or silicon) surfaces can be prevented by coating the glass with polyethylene glycol (PEG) groups. PEG-silane is a reagent used to create this coating.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;PEG-silane (the image shows a methoxy- version) (image taken from &lt;a href=&quot;http://www.laysanbio.com/index.php?src=directory&amp;amp;view=products&amp;amp;refno=303&amp;amp;srctype=products_detail&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;; no connection)  will coat glass surfaces because the silane portion (right hand end of the structure shown) will react with -OH groups on the glass surface.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't help with the part of the question about time and temperature of incubation, but it seems longer and hotter than protocols I have seen. Perhaps the indium tin oxide (ITO) coating on the slides has something to do with it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Bz3q5.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-04-19T13:12:29.970" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="7984" PostTypeId="2" ParentId="7981" CreationDate="2013-04-19T13:23:52.923" Score="4" Body="&lt;p&gt;First thing I'd do is replace the HEPA filter. A copper plate/foil may help, and it certainly won't disrupt the flow of heat, as copper is incredibly conductive (that's why they make electrical wires out of it), and poking holes would help with the airflow, but a new filter will probably make the most difference. I've never used a full-copper incubator, and the few serious contaminations I've had to deal with were related to the HEPA filter and poor TC practices.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you haven't already, I'd institute a good routine cleaning program as well. Change the water bath each week (make sure you're adding fungicide to the water), and wipe down the whole incubator with bleach followed by an alcohol rinse each month. Make &lt;strong&gt;sure&lt;/strong&gt; you clean all the bleach off, as it corrodes metal if left on very long. At the same time, clean and autoclave all of the removable components like shelves, rails, and water pans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good luck!&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-04-19T13:23:52.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7987" PostTypeId="5" CreationDate="2013-04-19T16:31:31.047" Score="0" Body="&lt;p&gt;GWAS test many individuals for associations of a genotype to a trait.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-08-01T13:48:24.257" LastActivityDate="2013-08-01T13:48:24.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7988" PostTypeId="4" CreationDate="2013-04-19T16:31:31.047" Score="0" Body="Questions pertaining to genome-wide association studies." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T16:37:33.697" LastActivityDate="2013-04-19T16:37:33.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7989" PostTypeId="5" CreationDate="2013-04-19T16:32:26.330" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-19T16:32:26.330" LastActivityDate="2013-04-19T16:32:26.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7990" PostTypeId="4" CreationDate="2013-04-19T16:32:26.330" Score="0" Body="Questions pertaining to the processes by which new species arise." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T16:37:42.090" LastActivityDate="2013-04-19T16:37:42.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7991" PostTypeId="5" CreationDate="2013-04-19T18:19:09.697" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-19T18:19:09.697" LastActivityDate="2013-04-19T18:19:09.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7992" PostTypeId="4" CreationDate="2013-04-19T18:19:09.697" Score="0" Body="Questions pertaining to the phenotype that results from the failure of neural tube closure." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T18:21:55.890" LastActivityDate="2013-04-19T18:21:55.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7993" PostTypeId="5" CreationDate="2013-04-19T18:20:17.013" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-19T18:20:17.013" LastActivityDate="2013-04-19T18:20:17.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7994" PostTypeId="4" CreationDate="2013-04-19T18:20:17.013" Score="0" Body="Questions pertaining to plants." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T18:22:03.127" LastActivityDate="2013-04-19T18:22:03.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7995" PostTypeId="5" CreationDate="2013-04-19T18:21:32.257" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-19T18:21:32.257" LastActivityDate="2013-04-19T18:21:32.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7996" PostTypeId="4" CreationDate="2013-04-19T18:21:32.257" Score="0" Body="Questions pertaining to the study of the digestive system." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T18:22:07.737" LastActivityDate="2013-04-19T18:22:07.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7997" PostTypeId="5" CreationDate="2013-04-19T18:23:56.907" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-19T18:23:56.907" LastActivityDate="2013-04-19T18:23:56.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7998" PostTypeId="4" CreationDate="2013-04-19T18:23:56.907" Score="0" Body="Questions pertaining to variation in the number of copies of a chromosomal region." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T18:24:41.857" LastActivityDate="2013-04-19T18:24:41.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="7999" PostTypeId="5" CreationDate="2013-04-19T18:30:44.677" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-19T18:30:44.677" LastActivityDate="2013-04-19T18:30:44.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8000" PostTypeId="4" CreationDate="2013-04-19T18:30:44.677" Score="0" Body="Questions pertaining to 1) the file format used for electron density information acquired by x-ray crystallography and cryo-electron microscopy, or 2) the project to develop software for x-ray crystallography" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T18:32:07.700" LastActivityDate="2013-04-19T18:32:07.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8001" PostTypeId="5" CreationDate="2013-04-19T18:32:31.640" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-19T18:32:31.640" LastActivityDate="2013-04-19T18:32:31.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8002" PostTypeId="4" CreationDate="2013-04-19T18:32:31.640" Score="0" Body="Questions pertaining to the graphics program used to develop macromolecular models from crystallography data" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T18:32:54.157" LastActivityDate="2013-04-19T18:32:54.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8003" PostTypeId="5" CreationDate="2013-04-19T18:53:03.303" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-19T18:53:03.303" LastActivityDate="2013-04-19T18:53:03.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8004" PostTypeId="4" CreationDate="2013-04-19T18:53:03.303" Score="0" Body="Questions pertaining to sodium dodecyl sulfate polyacrylamide gel electrophoresis, a technique used to separate proteins according to electrophoretic mobility" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T18:54:17.230" LastActivityDate="2013-04-19T18:54:17.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8005" PostTypeId="5" CreationDate="2013-04-19T18:54:27.047" Score="0" Body="&lt;p&gt;The conversion of sugar to ethanol, gas, or acids by bacteria or yeast.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-27T12:58:33.170" LastActivityDate="2017-03-27T12:58:33.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8006" PostTypeId="4" CreationDate="2013-04-19T18:54:27.047" Score="0" Body="Questions pertaining to the conversion of sugar to ethanol, gas, or acids by bacteria or yeast." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T19:18:57.000" LastActivityDate="2013-04-19T19:18:57.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8007" PostTypeId="5" CreationDate="2013-04-19T18:57:23.563" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-19T18:57:23.563" LastActivityDate="2013-04-19T18:57:23.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8008" PostTypeId="4" CreationDate="2013-04-19T18:57:23.563" Score="0" Body="Questions pertaining to the production of an immune response to self tissues/molecules." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-19T19:10:06.640" LastActivityDate="2013-04-19T19:10:06.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8009" PostTypeId="2" ParentId="7950" CreationDate="2013-04-19T20:19:11.527" Score="0" Body="&lt;p&gt;Before I asked this question I knew of a website that provides reliable (from the US government) pharmacodynamic and pharmacokinetic data for FDA-approved drugs: &lt;a href=&quot;http://dailymed.nlm.nih.gov/dailymed/about.cfm?&quot; rel=&quot;nofollow&quot;&gt;DailyMed&lt;/a&gt;. I didn't accept it as an answer because of the fact that it is just FDA-approved drugs but I'm interested in other drugs like moclobemide, tianeptine, piracetam, aniracetam, nefopam, flupirtine and levomepromazine too.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-04-19T20:27:18.487" LastActivityDate="2013-04-19T20:27:18.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8010" PostTypeId="5" CreationDate="2013-04-20T00:23:42.477" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-20T00:23:42.477" LastActivityDate="2013-04-20T00:23:42.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8011" PostTypeId="4" CreationDate="2013-04-20T00:23:42.477" Score="0" Body="Questions pertaining to fruit flies of the genus *Drosophila*." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-20T03:05:51.573" LastActivityDate="2013-04-20T03:05:51.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8012" PostTypeId="5" CreationDate="2013-04-20T00:26:17.413" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-20T00:26:17.413" LastActivityDate="2013-04-20T00:26:17.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8013" PostTypeId="4" CreationDate="2013-04-20T00:26:17.413" Score="0" Body="Questions pertaining to western blots, which are used for detecting specific proteins (sometimes called protein immunoblots)." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-20T03:05:59.170" LastActivityDate="2013-04-20T03:05:59.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8014" PostTypeId="5" CreationDate="2013-04-20T00:27:42.450" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-20T00:27:42.450" LastActivityDate="2013-04-20T00:27:42.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8015" PostTypeId="4" CreationDate="2013-04-20T00:27:42.450" Score="0" Body="Questions pertaining to the synthesis of DNA from RNA." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-20T03:05:45.717" LastActivityDate="2013-04-20T03:05:45.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8016" PostTypeId="1" AcceptedAnswerId="8017" CreationDate="2013-04-20T02:45:17.070" Score="11" ViewCount="369" Body="&lt;p&gt;The question &quot;why do we age&quot; has been asked numerous times. But why are we young? The cells of the adult human being are an age (time&gt;0), but how can old cells create new cells that are younger than themselves?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I.e, how are young people made from the cells of old people?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize that senescence, the act of a cell aging, has to do with the shortening of telomerase over time which puts a limit (the Hayflick limit) on the life of an autosomal cell. So in theory, because cells only make direct copies of themselves but the telomerase shortens with every division, each new daughter pair would be as old as the parent and would continue aging. But how come new people start senescence at time t=0?&lt;/p&gt;&#xA;" OwnerUserId="3419" LastEditorUserId="3340" LastEditDate="2014-07-02T05:23:09.180" LastActivityDate="2014-07-04T05:03:03.947" Title="How are new people created from the DNA of an aged person. i.e. Why are we young?" Tags="&lt;genetics&gt;&lt;senescence&gt;&lt;telomere&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8017" PostTypeId="2" ParentId="8016" CreationDate="2013-04-20T05:18:39.860" Score="10" Body="&lt;p&gt;Gametes (sperm and ovum), which fuse to form a zygote, arise from germ cells (spermatogonia and oogonia). Germ cells, like stem cells, are maintained carefully i.e the genome is preserved and transposition/recombination events are tightly controlled via different mechanisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So these germ cells don't have shortened telomeres. Also, during early embryonic development the future germ cells quickly migrate to an end of embryo and remain there while the rest of the body takes shape. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure if it has been demonstrated in an article or not but once I happened to talk to Dr Wakayama (who cloned a mouse frozen for 16 years) and got to know that animals cloned by the process of Somatic Cell Nuclear Transfer have reduced lifespan. (SCNT: the nucleus of a somatic cell is transferred to an ovum and triggered to form zygote). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to conclude, if germ cells were not protected from mutations and deleterious recombinations, lifespan would have been reduced with every generation.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-07-04T05:03:03.947" LastActivityDate="2014-07-04T05:03:03.947" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8021" PostTypeId="1" AcceptedAnswerId="8022" CreationDate="2013-04-21T15:40:08.140" Score="2" ViewCount="706" Body="&lt;p&gt;Two brown-haired people have two children, P and Q. P has blond hair. We therefore believe that each parent is heterozygous and that blond hair is a recessive trait.&#xA;Q has brown hair. What is the probability that Q is heterozygous?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My answer:  2/3.  There are four possibilities Bb, bB, BB,and bb. Before observing the color of Q's hair, we assign equal chance to each.  We eliminate bb as a possibility.  The chance that it is bB or Bb and not BB is 2/3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A Biology PhD disagrees with me and says that the probability is 1/2. Who is right?&lt;/p&gt;&#xA;" OwnerUserId="3425" LastEditorUserId="69" LastEditDate="2013-04-21T16:34:09.520" LastActivityDate="2013-04-21T17:00:01.007" Title="Two brown-haired people have two children, P and Q. P has blond hair. Q has brown hair. What is the probability that Q is heterozygous?" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8022" PostTypeId="2" ParentId="8021" CreationDate="2013-04-21T17:00:01.007" Score="7" Body="&lt;p&gt;&lt;strong&gt;Assumptions: &lt;em&gt;Blonde&lt;/em&gt; hair is &lt;em&gt;Homozygous Recessive&lt;/em&gt; and that the traits are strictly Mendelian.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The parental generation must be both heterozygotes as at least one child is Blonde (bb). So your cross is &lt;strong&gt;Bb&lt;/strong&gt; x &lt;strong&gt;Bb&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your square is going to look like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;           _B_            _b_&#xA;&#xA;_B_         BB           Bb&#xA;&#xA;&#xA;&#xA;_b_         bB           bb&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So of the question is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What is the probability that Q is heterozygous?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The PhD is &lt;strong&gt;INCORRECT&lt;/strong&gt;. They probably just made a simple Punnet Square in their head and forgot the caveat that you have to exclude &quot;&lt;strong&gt;bb&lt;/strong&gt;&quot; because Q is &lt;em&gt;not&lt;/em&gt; Blonde. The possible allele combinations for &lt;strong&gt;non-Blonde&lt;/strong&gt; offspring from a Heterozygotic cross are only &lt;strong&gt;BB, bB, Bb&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefor the probability that &lt;strong&gt;Q&lt;/strong&gt; is &lt;em&gt;Heterozygous&lt;/em&gt; is indeed 2/3 (&lt;strong&gt;bB, Bb&lt;/strong&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's not uncommon for PhD students - who are often deep into their own research - to gloss over details and possibly give incorrect answers because the information hasn't been relevant to them for years (most traits &lt;em&gt;aren't&lt;/em&gt; Mendelian, strictly recessive or dominant, and rarely involve a single allele), so give them some slack unless they were being a jerk about it. =)&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-04-21T17:00:01.007" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8023" PostTypeId="2" ParentId="1051" CreationDate="2013-04-21T22:03:29.453" Score="1" Body="&lt;p&gt;The man in China had both chromosomes 15 split and attached onto both chromosomes 14. If a male with 44 chromosomes wants to have children with a female with 46 chromosomes, this will not work. He won't be able to have viable offspring. During mitoses, he will have 22 chromatids and she will have 23. They will not match up and therefore no viable offspring. He'd have to meet someone who was his match and most likely that match is in his family, such as a sister or female cousin, who would have the same chromosomal arrangement as he has. In China, this man is from a family where a lot of miscarriages happened and other family members have variations on these fused chromosomes. They are very inbred for this to have happened. Only a close relative who matches identically to his arrangement would be able to have chromatids that could line up with his. His parents had chromosome abnormalities for this to have happened, so this is an inbred family. This family could go on to produce another species of humans with 44 chromosomes if they kept trying and future generations were stable with no odd arrangements that don't line up. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.asiahealthcareblog.com/2011/07/03/chinas-44-chromosome-man-may-be-missing-link-between-us-and-the-chimp/&quot; rel=&quot;nofollow&quot;&gt;http://www.asiahealthcareblog.com/2011/07/03/chinas-44-chromosome-man-may-be-missing-link-between-us-and-the-chimp/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3427" LastActivityDate="2013-04-21T22:03:29.453" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8024" PostTypeId="1" AcceptedAnswerId="8025" CreationDate="2013-04-22T00:50:46.127" Score="3" ViewCount="10750" Body="&lt;p&gt;My apologies if my question is too basic, and please point me to a more appropriate forum.  I am reading the textbook &quot;Essential Cell Biology&quot; by Alberts et al, and am consulting other sources as well.  I am reading Chapter 10 about DNA technology and have read how DNA is separated into strands of different lengths by restriction enzymes.  The different size strands can then by separated by Gel Electrophoresis.  I believe I understand these basics. My question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do all strands of the same length have the same sequence of base pairs?  I wouldn't think      so, and this would be a problem in the next step, determining the sequence of one size fragment by  using special base pairs that are lacking a hydroxyl group. Isn't it possible I could have two strands that are 50 base pairs long (for example) that have the same beginning and same end and are thus cut by the restriction enzymes to a length of 50, but are most assuredly not the same within their sequence&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The text says that once the different size strands are separated by electrophoresis, you can just cut out one of the bands and work with that.  That makes sense if you are guaranteed to only have 1 strand at that level of the gel agar or if the multiple strands are all the same exact sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you read this far, thank you.  I think more generally I need to know how many of these segments are produced when you use restriction enzymes and how long the average one is. And is there any guarantee for one chromosone (or all 46 chrmosones) having all the segments be unique sizes (I wouldn't think so)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And even more generally :), I need additional sources that explain DNA sequencing in simple to understand terms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dave&lt;/p&gt;&#xA;" OwnerUserId="3429" LastActivityDate="2014-09-25T01:10:01.850" Title="Separating DNA Fragments by Gel Electrophoresis. Are all the strands for one size the same?" Tags="&lt;dna&gt;&lt;dna-sequencing&gt;&lt;gel-electrophoresis&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8025" PostTypeId="2" ParentId="8024" CreationDate="2013-04-22T01:30:18.797" Score="2" Body="&lt;p&gt;You are correct: strands of the same length do &lt;em&gt;not&lt;/em&gt; necessarily have the same sequence. The separation of DNA in gel electrophoresis is purely based on the hydrodynamic size. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The number of fragments produced by restriction enzyme digestion depends on the number of sites for that particular enzyme in your input DNA.  Restriction enzymes only cut at specific nucleotide sequences.  There is no &quot;typical length&quot; of fragment produced for this reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea of separating DNA on the basis of an RE digest is that a mutation that changes the sequence &lt;em&gt;where the RE binds and cuts&lt;/em&gt; will reduce the number of fragments because the RE can no longer bind and cut at that site: 2 smaller fragments will now appear as one large fragment.  It will be visible on the gel because of the difference in number and size of fragments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Typically, when running a gel, you are using DNA that has been selectively amplified to bias the readout to a particular (known) region of the chromosome. This electrophoretic approach works because you're not looking at all 46 chromosomes at once.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as sequencing is concerned, I'd recommend starting with &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_sequencing&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;.  Sequencing techniques are changing rather rapidly, so there's not one good source of which I am aware. To begin with, you can read about Sanger sequencing method. If you understand PCR then you won't find it hard to understand. &lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-22T02:41:25.843" LastActivityDate="2013-04-22T02:41:25.843" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8026" PostTypeId="1" AcceptedAnswerId="8029" CreationDate="2013-04-22T06:04:09.260" Score="9" ViewCount="12602" Body="&lt;p&gt;In a neuroscience class I'm taking, it was explained that myelin covers axons in sections, the uncovered sections are called nodes of Ranvier, and signals propagate much faster in the covered sections.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if it is faster for signals to propagate along myelinated regions of the axon, why doesn't the entire axon get covered by myelin? Wouldn't that make it faster?&lt;/p&gt;&#xA;" OwnerUserId="3431" LastEditorUserId="107" LastEditDate="2013-04-23T04:33:27.913" LastActivityDate="2013-04-23T04:33:27.913" Title="What is the function of nodes of Ranvier in axons?" Tags="&lt;neuroscience&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8027" PostTypeId="2" ParentId="8026" CreationDate="2013-04-22T06:33:46.673" Score="4" Body="&lt;p&gt;Action potentials arise and propagate by membrane depolarization. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A myelin sheath is present in most neurons and is responsible for insulating the membrane against ions. The function of the myelin sheath is to prevent leakage of charge, by effectively restricting ion channels only at certain regions called &lt;strong&gt;Nodes of Ranvier&lt;/strong&gt;. This ensures that depolarization at one node is effectively equivalent to depolarization at another node, which initiates an action potential at the later node and as a result the action potential effectively &quot;jumps&quot; from node to node - this is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Saltatory_conduction&quot; rel=&quot;nofollow&quot;&gt;saltatory conduction&lt;/a&gt; and it speeds up the signals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In axons without a myelin sheath, the signal does (passively) travel the full length of the axon.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="107" LastEditDate="2013-04-22T12:51:37.410" LastActivityDate="2013-04-22T12:51:37.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8028" PostTypeId="1" AcceptedAnswerId="8039" CreationDate="2013-04-22T08:06:49.980" Score="4" ViewCount="717" Body="&lt;p&gt;How to know if a human female is fertile (can give birth to child in future) without making her pregnant? Any signs, tests?&lt;/p&gt;&#xA;" OwnerUserId="818" LastEditorUserId="115" LastEditDate="2013-04-22T14:26:08.170" LastActivityDate="2013-12-16T16:57:12.107" Title="How to know if a woman is fertile without actually making her pregnant?" Tags="&lt;human-biology&gt;&lt;zoology&gt;&lt;reproduction&gt;&lt;sex&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8029" PostTypeId="2" ParentId="8026" CreationDate="2013-04-22T08:15:29.927" Score="5" Body="&lt;p&gt;Every signal rapidly fades out with distance if it is not amplified. So if the whole axon were covered with myelin, action potentials wouldn't reach their target. Each Ranvier node can be seen as an active signal repeater.&lt;/p&gt;&#xA;" OwnerUserId="3394" LastActivityDate="2013-04-22T08:15:29.927" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8030" PostTypeId="1" CreationDate="2013-04-22T11:14:56.790" Score="1" ViewCount="246" Body="&lt;p&gt;I've seen many times how a person born in one place, goes to another country for a long time, and then they start looking more like the people there, but I never found out how it works. &#xA;&lt;a href=&quot;http://www.jstor.org/discover/10.2307/2332288?uid=3737496&amp;amp;uid=2&amp;amp;uid=4&amp;amp;sid=21101935763213&quot; rel=&quot;nofollow&quot;&gt;This report&lt;/a&gt; claims that second generation Japanese, born in the US are taller and heavier than those living in their native lands (there had been no intermingling of races).&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;To what extent do the genetic/environmental factors control human morphology ? &lt;/li&gt;&#xA;&lt;li&gt;What factors apart from the diet can bring about such morphological differences ? &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1373" LastEditorUserId="1590" LastEditDate="2016-01-30T09:59:15.940" LastActivityDate="2021-05-18T20:24:19.147" Title="How does geography affect morphological features of the human body" Tags="&lt;human-biology&gt;&lt;epigenetics&gt;&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8031" PostTypeId="2" ParentId="8024" CreationDate="2013-04-22T11:32:05.730" Score="4" Body="&lt;p&gt;The answer to the part of your question concerned with average lengths of restriction fragments is: if the DNA molecule being digested is of random sequence, and is 50% GC/ 50% AT, then the probability of finding any given short sequence at any position is 1/4&lt;sup&gt;N&lt;/sup&gt; where N is the length of the short sequence. So, for example for a restriction enzyme with a 4-base recognition sequence such as AluI (AGCT) the probability is 1/256 and so the average length of an AluI fragment would be 256 bp. For an enzyme with a 6-base recognition sequence such as HindIII (AAGCTT) the corresponding number is 4096 bp. Please note that this is the average length, and is not an 'expected' length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer to the part of your question about fragments of the same size co-migrating, how would you purify them on a gel for further analysis is trickier. I think the first thing to say is that you wouldn't do this for sequencing, and this is reflected in the various answers you have already received - sequencing no longer requires this sort of approach.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you were forced into this position for some reason then I can think of two things that could help: the first option would be to run the analysis on an acrylamide gel when you can get much better resolution of different fragments (all 50 bp fragments are not the same molecular weight), but this is really only useful for small fragments (100 bp or less). However the most likely way out of the co-migration problem would be to purify the two comigrating fragments as a mixture and then ligate them into a vector whereupon each recombinant would carry one or other of the two fragments. This is really going back to the original reason why molecular cloning revolutionised things - it allows the 'biological' purification of DNA fragments followed by production of these fragments in large amounts.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You mention &quot;&lt;em&gt;special base pairs that are lacking a hydroxyl group&lt;/em&gt;&quot; so clearly you are thinking in terms of Sanger (dideoxy-) sequencing, in which case you could clone directly into an M13 phage vector so that you could make ssDNA for direct sequencing. By sequencing a number of clones you would find two sequences, one for each fragment. You would still have to find a way to decide which one was the fragment that you were actually interested in, however.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like I say, things just aren't done in this way anymore. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-04-22T11:32:05.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8032" PostTypeId="2" ParentId="8028" CreationDate="2013-04-22T12:10:01.203" Score="6" Body="&lt;p&gt;Of course. There's several &lt;a href=&quot;http://en.wikipedia.org/wiki/Fertility_testing#Diagnosis_of_infertility&quot; rel=&quot;noreferrer&quot;&gt;fertility tests available&lt;/a&gt; to determine the quality and quantity of egg reserve, and whether or not the there are abnormalities in the uterus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, some of them are invasive procedures, and &lt;em&gt;all&lt;/em&gt; of them should be performed by a professional. I doubt the layperson would know what they're looking at on an Ovarian Ultrasound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're asking whether there's an &quot;easy&quot; way that doesn't involve a trip to a doctor - then I would say 'no.' Casual inspection would only reveal any abnormalities in the vagina and the opening of the cervix, and hormone tests are only partial indicators.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then again, if a woman has reached physical adulthood and is under the age of 38 then the chances of being infertile (or have difficulty conceiving) are quite low - about &lt;a href=&quot;http://en.wikipedia.org/wiki/Infertility&quot; rel=&quot;noreferrer&quot;&gt;3% to 10%&lt;/a&gt;. Infertility is usually much more of a concern to women who wait until after the age of 35 to have children, as there is a definite biological window (the number of eggs the woman was born with) to consider that starts to close as a woman nears her 40's.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also important to note that trouble conceiving can stem from either partner, and there's about a 40%-50% chance in a couple trying to conceive the male has an 'issue' and the woman is perfectly healthy.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2013-04-23T01:30:56.543" LastActivityDate="2013-04-23T01:30:56.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8033" PostTypeId="2" ParentId="8024" CreationDate="2013-04-22T13:20:44.357" Score="2" Body="&lt;p&gt;As I understand, you are confused how one would be sure that a band in a gel is the sequence one is looking for, seeing as sequences can be different and still have the same length (e.g. ACTTAT is the same length as GGCCGT but entirely different). So your actual question might rather be something like &quot;How does one ascertain that a gel band contains only the sequence one is looking for?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is true that in practice, restricting a long sequence can lead to similarly long segments which are not the same sequence. It is indeed possible to cut out a small square from the gel which contains the band, and then dissolve the gel and extract the genetic material. Sequencing the result would give you one of two outcomes: 1) If the band contained only your desired sequence, your sequencing technique should render exactly that sequence as a result. 2) If the band contained more than one different sequences of the same length, your sequencing method will probably leave you with ambiguous results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So sequencing would probably only confirm whether or not the band contained a single distinct sequence. It would not be useful as a method of separating the sequence you want for future experiments from any other sequence of the same length. One method to do this could be PCR (polymerase chain reaction), a procedure that produces vast numbers (billions) of copies of a specific target sequence. If a PCR was carried out to amplify the target sequence contained in the gel band, any other sequences of the same length would not have any copies produced. They would still be present, but being vastly outnumbered by the sequence relevant for your experiments should prevent the other sequences from having any significant effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, as dd3 noted, you would not normally run a the result of a restriction on a gel and then try to separate your target sequence from the rest. Rather, you would simply use the PCR method described above directly after using the restriction enzymes, and then run the result on a gel. You would then get a very strong band for the sequence you were looking for and much weaker bands for everything else.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-04-22T13:20:44.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8034" PostTypeId="1" CreationDate="2013-04-22T15:14:25.593" Score="2" ViewCount="93" Body="&lt;p&gt;I'm just curious as to whether crocodiles and if you require specifics, saltwater crocodiles, could eat bread as infants. I was watching Lake Placid and I was curious as to whether infant saltwater crocodiles could even digest bread.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-04-22T15:14:25.593" Title="Can Infant Crocodiles digest Bread?" Tags="&lt;reptile&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-12-11T06:03:40.870" ContentLicense="CC BY-SA 3.0" />
  <row Id="8035" PostTypeId="2" ParentId="809" CreationDate="2013-04-22T16:14:40.330" Score="1" Body="&lt;p&gt;Here is a definition taken from &lt;a href=&quot;http://www.scholarpedia.org/article/Computational_neuroanatomy#Potential_synaptic_connectivity_between_individual_cells&quot; rel=&quot;nofollow&quot;&gt;a Scholarpedia article on computational neuroanatomy&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The critical underlying question remains: how does the number of synapses between two neurons depend on the overlap between their dendritic and axonal trees? According to &quot;Peters rule&quot;, synaptic contacts occur where dendrites and axons happen to be in apposition. These &quot;potential synapses&quot; are required but not sufficient for an actual synapse formation; and the expected number of connections between two neurons is proportional to the product of their dendritic and axonal trees densities (e.g. Peters et al., 91).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This seems to be saying that there are really two pieces to Peter's rule-- first that &quot;synaptic contacts&quot; (potential synapses) actually occur where axons and dendrites share space, and secondly that the proportion of these contacts that are real synapses is proportional to tree density.&lt;/p&gt;&#xA;" OwnerUserId="3433" LastActivityDate="2013-04-22T16:14:40.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8036" PostTypeId="2" ParentId="7716" CreationDate="2013-04-22T18:20:51.950" Score="0" Body="&lt;p&gt;Acetyl esters can be deacetylated by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12773168&quot; rel=&quot;nofollow&quot;&gt;carboxylesterases&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case of an acyl/aryl group attached to acetate group (e.g., benzoate), I guess it will first undergo ring opening and then beta oxidation (as in case of tyrosine). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Paracetamol -&gt; p-aminophenol is a deamidation (I am not sure, but enzymes like ornithine decarboxylase can do that job... just a guess).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-23T04:11:36.947" LastActivityDate="2013-04-23T04:11:36.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8037" PostTypeId="2" ParentId="2909" CreationDate="2013-04-22T19:06:28.953" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Red_blood_cell#Nucleus&quot; rel=&quot;nofollow&quot;&gt;Red blood cells (RBCs) don't have nuclei in mammals&lt;/a&gt;, so they are usually considered to be pretty inert compared to other cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They do have some biochemical activity, and evidently there is some mechanism for cell death  in RBCs when they are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9813640&quot; rel=&quot;nofollow&quot;&gt;induced to degrade&lt;/a&gt; or &lt;a href=&quot;http://www.malariajournal.com/content/9/1/350&quot; rel=&quot;nofollow&quot;&gt;infected by pathogens&lt;/a&gt;.  I found this reference that shows &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11753567&quot; rel=&quot;nofollow&quot;&gt;caspases -8 and -3 are evident in mature RBCs&lt;/a&gt;.  Several other components of the cell death pathway are not evident. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At this time the authors speculate that they don't activate to induce cell death.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that over the broad field of disease research 'apoptosis' and 'cell death' are used equivalently even when the well known apoptosis pathway is not involved.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-04-22T19:06:28.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8039" PostTypeId="2" ParentId="8028" CreationDate="2013-04-22T19:34:52.367" Score="4" Body="&lt;p&gt;If you are talking potential for fertility. There are a few... &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Having regular periods&lt;/li&gt;&#xA;&lt;li&gt;Healthy weight. Extremely thin women tend to stop ovulating. Obesity also impairs fertility by altering hormone levels.&lt;/li&gt;&#xA;&lt;li&gt;Whether she has been using birth control (i.e., &quot;the pill&quot;) in the recent past. It takes a while for the body to get back to normal.&lt;/li&gt;&#xA;&lt;li&gt;Smoking impairs fertility&lt;/li&gt;&#xA;&lt;li&gt;stress&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://suite101.com/article/signs-of-fertility-a274354&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are talking about immediate fertility...&#xA;While I would not rely on them for the purposes of birth control there are several observable physiological changes that correlate with ovulation and fertility. These include&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;body temperature. There are patterns of elevated body temp associated with ovulation.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;cervical mucous. The mucous gets &quot;slippery and stretchy&quot;. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the cervix itself becomes less firm and slightly open during ovulation.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.fertilityuk.org/nfps25.html&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we are talking about anatomical cues that are proxy's for fertility, there are clues based on the concept of sexual selection.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Ample breasts. Indication of potential mammary tissue and ability to suckle child.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wider hips. Indication of ability to deliver child with minimal complications.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Note that these cues can be deceptive. Fat tissue may be deposited in both locations to imitate the fertility cues. &lt;a href=&quot;http://dieoff.com/_Biology/BeautyAndTheBeast.pdf&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1710" LastEditorUserId="107" LastEditDate="2013-04-23T01:47:04.517" LastActivityDate="2013-04-23T01:47:04.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8040" PostTypeId="1" AcceptedAnswerId="8042" CreationDate="2013-04-22T19:57:37.003" Score="2" ViewCount="5566" Body="&lt;p&gt;How long do melanocytes and melanosomes continue to protect DNA after UV exposure? Basically, if skin is tanned, then over the next month it is shed, will melanocytes continue to produce high levels of melanin to keep the new skin tanned without requiring more UV exposure? The cells react by producing more melanin after exposure but will they continue to do this in new skin cells? &lt;/p&gt;&#xA;" OwnerUserId="1904" LastActivityDate="2013-04-22T21:58:56.360" Title="How long does a tan last?" Tags="&lt;proteins&gt;&lt;skin&gt;&lt;melanin&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8042" PostTypeId="2" ParentId="8040" CreationDate="2013-04-22T20:46:24.527" Score="2" Body="&lt;p&gt;The tanning response to UV occurs in two phases:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The immediate response begins at exposure to UV-A, reaches a max at 1-2 hours, and fades between 3 and 24 hours.&#xA;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1751-1097.1996.tb02988.x/abstract;jsessionid=7D6945075A363E9069CD6969FE7E8864.d01t01&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; speculates that this is due to the redistribution of melanosomes rather than additional melanin production.&lt;/li&gt;&#xA;&lt;li&gt;The delayed response is more durable, occurring by repeated exposure to UV-B, as well as as UV-A and visible light. &quot;It is a gradual process in which the skin starts darkening 48–72 h after irradiation, reaches a maximum ∼3 wk after exposure, and the skin does not return to its original melanin content until ∼8–10 months later.&quot;&#xA;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1751-1097.1996.tb02988.x/abstract;jsessionid=7D6945075A363E9069CD6969FE7E8864.d01t01&quot; rel=&quot;nofollow&quot;&gt;This source&lt;/a&gt; says this is due to additional melanocytes, melanosomes, and more melanin, in general.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Both processes are influenced by genetic factors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.fasebj.org/content/21/4/976.full&quot; rel=&quot;nofollow&quot;&gt;Source for the initial points&lt;/a&gt;, which also contains interesting details on the enzymes involved in these processes.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-22T21:58:56.360" LastActivityDate="2013-04-22T21:58:56.360" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8043" PostTypeId="1" AcceptedAnswerId="8049" CreationDate="2013-04-22T21:04:47.617" Score="5" ViewCount="3249" Body="&lt;p&gt;I heard somewhere that as opposed to other cells, neurons do not use insulin to get their sugar supply.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the alternative mechanism? I assume sugar can't just enter the cell without some kind of help from a protein, is that true?&lt;/p&gt;&#xA;" OwnerUserId="1190" LastActivityDate="2013-04-23T04:19:21.673" Title="How does sugar enter neurons if they don't use insulin?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8046" PostTypeId="1" CreationDate="2013-04-23T02:13:00.557" Score="1" ViewCount="91" Body="&lt;p&gt;Animals spend a good portion of every day doing nothing, and it seems like that time could be better spent hunting, searching for mates, etc. Also, animals are not aware during sleep, so it would be easier for a predator to attack them. Why is sleep required for animals?&lt;/p&gt;&#xA;" OwnerUserId="1182" LastActivityDate="2013-04-23T02:13:00.557" Title="Why do animals sleep" Tags="&lt;behaviour&gt;&lt;ethology&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-08-08T05:00:33.470" ContentLicense="CC BY-SA 3.0" />
  <row Id="8048" PostTypeId="1" AcceptedAnswerId="8050" CreationDate="2013-04-23T04:00:33.663" Score="4" ViewCount="330" Body="&lt;p&gt;Is that correct that a complete DNA sequencing (the whole genome) need only to be done once (per person)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After that is done, it the complete genome can be stored and once the new genes (and their purposes are confirmed) are discovered, the scientist can simply go back to a previously sequenced data and to find it this particular person has this new gene or not.&lt;/p&gt;&#xA;" OwnerUserId="3440" LastEditorUserId="5144" LastEditDate="2014-11-05T13:25:11.373" LastActivityDate="2014-11-06T13:33:00.493" Title="Results of a complete DNA sequencing - are they 100% reusable?" Tags="&lt;genetics&gt;&lt;dna-sequencing&gt;&lt;genomics&gt;&lt;human-genome&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8049" PostTypeId="2" ParentId="8043" CreationDate="2013-04-23T04:19:21.673" Score="2" Body="&lt;p&gt;Insulin is not directly involved in sugar uptake. It accelerates sugar uptake by upregulating glucose transporters and activating glycogenesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neurons have many glucose transporters including &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19912819&quot; rel=&quot;nofollow&quot;&gt;GLUT1 and GLUT3&lt;/a&gt; which are responsible for glucose uptake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, insulin being an endocrine molecule has effects throughout the body &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0014488605004036&quot; rel=&quot;nofollow&quot;&gt;including neurons&lt;/a&gt;. So neurons need not secrete insulin. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-23T04:19:21.673" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8050" PostTypeId="2" ParentId="8048" CreationDate="2013-04-23T04:22:18.547" Score="5" Body="&lt;p&gt;A single run of sequencing won't cover the entire genome, in most cases. That's why they do multiple rounds in order to increase horizontal (covering more regions of genome) and vertical (a.k.a depth; more reads per locus so that you can be more confident) coverage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit by dd3:&#xA;In the cases where &quot;a new gene is discovered&quot;, i.e. genome reannotation, it is possible to go back and look at previously stored sequence data to find out what &lt;em&gt;alleles&lt;/em&gt; a person has (&lt;strong&gt;everyone has every gene&lt;/strong&gt;, unless they have a deletion that spans the full length of the gene). This is a bioinformatics project, and if you are interested in learning more, I would recommend searching for recent publications on genome reannotation and remapping of sequence reads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whole genome sequencing is generally not recommended for prognosis of a specific disease like breast cancer. The common approach is to do a PCR of the biomarker loci and if necessary do a Sanger sequencing. However, if you have the money you can get your whole genome sequencing done :P&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The number of runs required to increase the depth varies for different genomic regions. &lt;a href=&quot;http://www.nature.com/srep/2011/110805/srep00055/full/srep00055.html&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; says that CpG islands require more runs. According to &lt;a href=&quot;http://www.hindawi.com/journals/ijpg/2012/831460/&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;, the depth should be &gt;3 per genotype marker.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-24T19:16:19.807" LastActivityDate="2013-04-24T19:16:19.807" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="8051" PostTypeId="1" CreationDate="2013-04-23T06:58:21.453" Score="4" ViewCount="2537" Body="&lt;p&gt;I did a simulation of a protein-ligand complex, and it has stabilized after 5 ns. I have got the respective pdb files for every ns, but when I try to view in VMD (&lt;a href=&quot;https://www-s.ks.uiuc.edu/Research/vmd/&quot; rel=&quot;nofollow&quot;&gt;Visual Molecular Dynamics&lt;/a&gt;), I cannot see the ligand. How do I select the heteroatom in the graphical representation window? My complex has 1129 + 50(ligand atoms) but while loading it just shows the protein molecule(1129).&lt;/p&gt;&#xA;" OwnerUserId="3441" LastEditorUserId="43" LastEditDate="2013-04-24T17:54:47.160" LastActivityDate="2013-05-24T18:27:37.633" Title="How do I view the simulated protein structure along with ligand in VMD?" Tags="&lt;bioinformatics&gt;&lt;structural-biology&gt;&lt;software&gt;&lt;visualization&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8052" PostTypeId="1" AcceptedAnswerId="8062" CreationDate="2013-04-23T08:17:24.280" Score="19" ViewCount="1108" Body="&lt;p&gt;Why does yawning seems to be contagious?&lt;br&gt;&#xA;Is this similar to laughter being contagious or does it has a different reason? &lt;/p&gt;&#xA;" OwnerDisplayName="user1897" LastActivityDate="2013-04-30T02:02:46.317" Title="Why is yawning contagious?" Tags="&lt;behaviour&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8055" PostTypeId="1" AcceptedAnswerId="8069" CreationDate="2013-04-23T14:27:04.640" Score="2" ViewCount="892" Body="&lt;p&gt;I'm looking at melanopsin, &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanopsin#Mechanism&quot; rel=&quot;nofollow&quot;&gt;a photo pigment in the human eye.&lt;/a&gt; One of its actions is to trigger suprachiasmatic nuclei SCN to suppress &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanopsin#Mechanism&quot; rel=&quot;nofollow&quot;&gt;melatonin release&lt;/a&gt;. &lt;strong&gt;I'm interested in learning what is the exact mechanism that actually suppresses melatonin release.&lt;/strong&gt; Is it another hormone or some way of modulating the pineal gland function?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="3971" LastEditDate="2013-08-29T16:04:38.990" LastActivityDate="2013-08-29T16:04:38.990" Title="What mechanism suppresses melatonin release in humans?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;sleep&gt;&lt;pigmentation&gt;&lt;melatonin&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8056" PostTypeId="2" ParentId="8055" CreationDate="2013-04-23T19:05:29.727" Score="1" Body="&lt;p&gt;Take a look at this (especially page 938): &lt;a href=&quot;http://zcam.tsinghua.edu.cn/~jzlei/teaching/sysbio2009/Reppert_Nature_2002.pdf&quot; rel=&quot;nofollow&quot;&gt;Coordination of circadian timing in mammals by Steven M. Reppert &amp;amp; David R. Weaver Nature 418, 935-941 (29 August 2002) | doi:10.1038/nature00965&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sodium-dependent action potentials provide the primary means by which&#xA;  the SCN transmit circadian outputs to other brain areas and are&#xA;  essential to its role as a pacemaker1.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Signalling molecules from SCN efferents include neurotransmit- ters&#xA;  and &lt;strong&gt;secreted factors&lt;/strong&gt;. An output role for secreted factors comes from&#xA;  the results of SCN transplant studies that suggest that the&#xA;  alternating activity of SCN-derived ‘inhibitory’ and ‘activating’&#xA;  factors drives locomotor activity rhythms (and hence rest/activity and&#xA;  sleep/wake cycles) in rodents&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There was also a mention of per/cry gene expression.&lt;/p&gt;&#xA;" OwnerUserId="3444" LastEditorUserId="577" LastEditDate="2013-04-24T03:41:39.300" LastActivityDate="2013-04-24T03:41:39.300" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8057" PostTypeId="1" CreationDate="2013-04-23T20:53:04.857" Score="2" ViewCount="351" Body="&lt;p&gt;A classical liver lobule is made up of a central vein and the portal triads.  A typical human liver weighs around 3 lbs. , while a typical bovine liver weighs around 12 lbs.  I was wondering if anyone had a reference that might discuss the size of a bovine liver lobule vs. the size of a human liver lobule.  Specifically, is the bovine liver lobule also larger than a human liver lobule?&lt;/p&gt;&#xA;" OwnerUserId="3191" LastEditorUserId="20449" LastEditDate="2016-10-04T11:45:09.580" LastActivityDate="2016-10-04T11:45:09.580" Title="Size of classical liver lobule across species" Tags="&lt;human-anatomy&gt;&lt;literature&gt;&lt;histology&gt;&lt;liver&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8058" PostTypeId="5" CreationDate="2013-04-23T21:07:38.720" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-23T21:07:38.720" LastActivityDate="2013-04-23T21:07:38.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8059" PostTypeId="4" CreationDate="2013-04-23T21:07:38.720" Score="0" Body="Questions pertaining to populations of organisms." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-23T22:09:48.983" LastActivityDate="2013-04-23T22:09:48.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8060" PostTypeId="5" CreationDate="2013-04-23T21:10:03.043" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-04-23T21:10:03.043" LastActivityDate="2013-04-23T21:10:03.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8061" PostTypeId="4" CreationDate="2013-04-23T21:10:03.043" Score="0" Body="Questions pertaining to red blood cells, or erythrocytes, the most common type of blood cell that is responsible for delivering oxygen throughout the body." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-04-23T22:09:56.407" LastActivityDate="2013-04-23T22:09:56.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8062" PostTypeId="2" ParentId="8052" CreationDate="2013-04-23T23:26:27.417" Score="12" Body="&lt;p&gt;Yawning is contagious in humans, which means that, in general, it is more likely that a person yawning after perceived (by sight, hearing, or both directions) yawning issued by another person. The frequency of infection varies throughout the day, with a peak in early morning and late evening.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A recent study conducted by Ivan Norscia and Elisabetta Palagi (University of Pisa) has provided the first evidence that the behavioral contagion of yawning is associated with the empathic bond between people. The study showed that the infection follows the same gradient of empathy: is greatest in close relatives (parents / children / grandchildren, brothers, stable couples), decreases in friends, then acquaintances in (people connected only by a third, external, ie work or a friend in common) and reaches a minimum in the unknown.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Various studies of clinical, psychological and neurobiological suggest and support the link between the yawn contagion and empathy. For example, the infection begins to occur at 4-5 years of age, when children develop the ability to identify, in a proper way, the emotions of others. In addition, the infection is reduced or absent in people who have problems related to empathy, how people with autism, and is positively related to subjective scores of empathy based on tests of psychological type. Finally, the areas of the brain related to the emotional sphere overlap, in part, with those involved in the response to yawn, with a possible involvement of mirror neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yawning has been observed among various primates. In these cases the yawn is a threat gesture, a way of maintaining order in the primates' social structure. Specific studies were conducted on chimpanzees and stumptail macaques. A group of these animals was shown a video of other conspecifics yawning; both species yawned as well. This helps to partly confirm a yawn's &quot;contagiousness&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In animals, yawning can serve as a warning signal. For example, Charles Darwin, in his book The Expression of the Emotions in Man and Animals, mentioned that baboons yawn to threaten their enemies, possibly by displaying large canine teeth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Yawn&quot;&gt;see yawn&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Autism_spectrum_disorder&quot;&gt;autism&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gordon Gallup, who hypothesizes that yawning may be a means of keeping the brain cool, &lt;strong&gt;also hypothesizes that &quot;contagious&quot; yawning may be a survival instinct inherited from our evolutionary past&lt;/strong&gt;. &quot;During human evolutionary history, when we were subject to predation and attacks by other groups, &lt;strong&gt;if everybody yawns in response to seeing someone yawn the whole group becomes much more vigilant and much better at being able to detect danger.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally, I can make an observation. Cats yawn as specific means to calm people, and especially to reassure the other cats and the pups. In order, they stretch, yawn, lie down, half close theyr eyes as if they start to sleep. When the whole group repeats the gestures, the majority of them (now calm) actually falls asleep.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt; @kmm&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028472&quot;&gt;Norscia &amp;amp; Palagi&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;The Pisa Group in cooperation with CNR Consiglio Nazionale delle Ricerche =&#xA;&lt;a href=&quot;http://www.sciencedaily.com/releases/2011/12/111212092649.htm&quot;&gt;Friends and loved ones yawn together - Science Daily&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www-personal.umd.umich.edu/~fdolins/berenty/scientists/pisa_grp.html&quot;&gt;The Pisa Group/ Elisabetta Palagi, Ivan Norscia, and Daniela Antonacci - University of Michigan - Dearborny&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Gordon_G._Gallup&quot;&gt;Gordon G. Gallup&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3384" LastEditorUserId="3384" LastEditDate="2013-04-30T02:02:46.317" LastActivityDate="2013-04-30T02:02:46.317" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8063" PostTypeId="1" AcceptedAnswerId="8067" CreationDate="2013-04-23T23:56:03.897" Score="1" ViewCount="3543" Body="&lt;p&gt;I am trying to understand the assay for iPS cells in the &lt;a href=&quot;http://www.cell.com/abstract/S0092-8674%2806%2900976-7&quot; rel=&quot;nofollow&quot;&gt;Takahashi &amp;amp; Yamanaka 2006 paper&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They inserted a beta-geo cassette, which contains the neomycin resistance gene, into the &lt;em&gt;Fbx15&lt;/em&gt; gene.  The idea is that the beta-geo cassette will be expressed when &lt;em&gt;Fbx15&lt;/em&gt; will be expressed, thus conferring G418 resistance to only those cells expressing &lt;em&gt;Fbx15&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They say that &quot;Although specifically expressed in mouse ES cells and early embryos, Fbx15 is dispensable for the maintenance of pluripotency and mouse development.&quot;  Does this mean that &lt;em&gt;Fbx15&lt;/em&gt; will be expressed in induced pluripotent stem cells, and won't be expressed upon differentiation? (What is special about Fbx15 that will distinguish iPS cells from somatic cells, including those that might derive from iPS cells, as when pluripotency is not maintained?)&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-04-24T05:51:57.247" Title="Role of Fbx15 in ES cells and its use in assaying for iPS cells (Yamanaka paper and others)?" Tags="&lt;genetics&gt;&lt;experimental-design&gt;&lt;stem-cells&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8064" PostTypeId="2" ParentId="5665" CreationDate="2013-04-24T02:06:57.387" Score="2" Body="&lt;p&gt;Large numbers of marine animals are actually cultivated in large aquaria. They're just generally not as conspicuous as farms and farm animals and are often located in difficult to access areas around estuaries or close to ports. There are also a number of specialised journals that focus on aquaculture such as the journal &lt;a href=&quot;http://www.sciencedirect.com/science/journal/00448486&quot; rel=&quot;nofollow&quot;&gt;aquaculture&lt;/a&gt;. In addition to being cultivated in aquaria, large numbers of animals are also cultivated in more natural settings such as the salmon you mentioned or shrimp in shrimp ponds, which are widespread in countries such as Indonesia. A major problem in aquaculture is disease, although this can also be a problem with terrestrial livestock raised in high densities. If you're interested in marine aquaculture, I suggest you browse the various aquaculture journals to get an idea of what's going on.&lt;/p&gt;&#xA;" OwnerUserId="3445" LastEditorUserId="107" LastEditDate="2013-04-24T02:20:27.543" LastActivityDate="2013-04-24T02:20:27.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8065" PostTypeId="2" ParentId="8051" CreationDate="2013-04-24T02:15:46.860" Score="1" Body="&lt;p&gt;After you load the molecule in VMD, from the menu bar select Graphics-&gt;Representations... In the box labeled Selected Atoms, type &quot;hetero&quot; and hit enter. You should now see &lt;em&gt;only&lt;/em&gt; your ligand (and whatever other non-protein/DNA atoms that happen to be in your PDB file). Hit the Create Rep button, enter &quot;protein&quot; in the Selected Atoms box and hit enter (you can see a list of all the possible selection words in the Selections tab). You will now have a separate representation for your protein and your heteroatoms, and you can modify them with the other settings in the Graphical Representations dialog in order to make them visually distinct from one another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this doesn't fix your problem, open up your PDB file in a text editor and check to make sure that there are lines that start with ATOM or HETATM that correspond to the atoms in your ligand. If they aren't there, your problem isn't with VMD but with one of your prior manipulations.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2013-04-24T02:15:46.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8066" PostTypeId="1" AcceptedAnswerId="8070" CreationDate="2013-04-24T04:13:09.673" Score="4" ViewCount="598" Body="&lt;p&gt;As far as I know and could understand from reading about HIV, T helper cell is one of the main reasons to develop AIDS in patients infected with HIV virus, that because the absence of helper T cell suppresses the immune system because no T cell cytokines released to allow other white blood cells to attack or release antigens. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Q1&lt;/strong&gt;. Did I understand it correctly?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Q2&lt;/strong&gt;. Now if my understanding is correct, why don't scientists find a way to produce T cell cytokines in the lab? and then inject it to patients with HIV? wouldn't that in theory revive the immune system and perhaps heal them or at least make them live longer? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. My knowledge is close to nothing in this topic, so excuse me if the question itself is wrong :)&lt;/p&gt;&#xA;" OwnerDisplayName="user3130" LastEditorDisplayName="user3130" LastEditDate="2013-04-24T13:38:01.533" LastActivityDate="2015-09-12T04:28:36.280" Title="HIV and T helper cells" Tags="&lt;immunology&gt;&lt;hiv&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8067" PostTypeId="2" ParentId="8063" CreationDate="2013-04-24T05:13:12.910" Score="1" Body="&lt;p&gt;Another &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12665572&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; from Yamanaka's group explains Fbx15. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Inactivation of Oct3/4 in ES cells led to rapid extinction of Fbx15 expression. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Fbx15-null ES cells were normal in morphology, proliferation, and differentiation. These data demonstrate that Fbx15 is a novel target of Oct3/4 but is dispensable for ES cell self-renewal, development, and fertility.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So Fbx15 wont be expressed in &lt;strong&gt;Oct4⁻&lt;/strong&gt; cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't seen any paper describing the function of this gene but in the case of cassette insertions the locus would prove useful in expressing the inserts specifically in &lt;strong&gt;Oct3/4⁺&lt;/strong&gt; cells&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-24T05:51:57.247" LastActivityDate="2013-04-24T05:51:57.247" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="8068" PostTypeId="2" ParentId="8066" CreationDate="2013-04-24T05:28:12.690" Score="0" Body="&lt;ol&gt;&#xA;&lt;li&gt;yes&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;[Purely my guess]&lt;/em&gt; : &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I think it will be difficult when simultaneously several infections pop up. There is no antigen presentation (as there is no receiver); it will be difficult to manually deliver different kinds of responses by cytokine injection.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover most cytokines are paracrine i.e they act locally; injecting them would cause a systemic response which may be harmful. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plus, it might be expensive to perform a cytokine therapy. [interferons are used in certain viral infections and what I vaguely remember is that the therapy is expensive] &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-24T13:39:30.470" LastActivityDate="2013-04-24T13:39:30.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8069" PostTypeId="2" ParentId="8055" CreationDate="2013-04-24T07:48:32.090" Score="1" Body="&lt;p&gt;From Kalsbeek et al 1999 Neuroscience (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0306452298006356&quot; rel=&quot;nofollow&quot;&gt;link 1&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10366002&quot; rel=&quot;nofollow&quot;&gt;link 2&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;retina-mediated photic activation of suprachiasmatic nucleus neurons&#xA;  induces the release of GABA from efferent suprachiasmatic nucleus&#xA;  nerve terminals, resulting in an inhibition of melatonin release by&#xA;  the pineal gland.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So it appears that GABA is key. When the retina is stimulated by light it results in activation of the neurons within the SCN which then release GABA. There is much more detail within the article and this is not my field so you may get more from reading that rather than my summary attempts.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2013-04-24T07:48:32.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8070" PostTypeId="2" ParentId="8066" CreationDate="2013-04-24T09:31:56.123" Score="4" Body="&lt;p&gt;Q1: Partially. T cells are important for the immune response through pathways other than cytokine release. Being activated by contact with another immune cell presenting their corresponding antigen, T cells proliferate and themselves activate their compatible B cell counterpart. These then produce antibodies specific to that antigen, the basis of the adaptive immune response (see figure below, from Wikipedia). The important part here is that this mechanism requires cell-to-cell contact, not simply cytokines. Without it, any pathogen for which memory B cells do not exist yet will not produce an adaptive immune response - and will persist if the infection is not cleared by the innate immune response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/73osC.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Q2: I expect because merely injecting T cell cytokines would not be sufficient in order to replace the essential function of T cells. Aside from that, WYSIWYG's point about the general response is probably also true: the side effects would be horrendous.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-04-24T09:31:56.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8071" PostTypeId="2" ParentId="7919" CreationDate="2013-04-24T18:05:14.073" Score="0" Body="&lt;p&gt;I've never utilized the feature, but I know &lt;a href=&quot;http://www.vmatch.de/&quot; rel=&quot;nofollow&quot;&gt;Vmatch&lt;/a&gt; allows you to define your own alphabets and symbol mappings, which should allow you to handle the IUPAC ambiguous nucleotide symbols. The default alphabet/mapping may even include these symbols.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2013-04-24T18:05:14.073" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8072" PostTypeId="1" AcceptedAnswerId="8078" CreationDate="2013-04-24T20:11:25.970" Score="2" ViewCount="248" Body="&lt;p&gt;Where would I find an up to date (last 6-7 years max) review on B cells? I've tried searching through pubmed with filters, cochrane library, medline and various other resources including searching old questions. A textbook would be fine too, but I'm not sure which one would give me detailed information. I'm a BSc student studying immunology. I'm not trying to create a war of &quot;best&quot; answers, any answer that fits these criteria I will accept. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-08-10T18:54:56.153" Title="Up to date B cell review" Tags="&lt;cell-biology&gt;&lt;immunology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8073" PostTypeId="2" ParentId="7627" CreationDate="2013-04-24T20:26:30.340" Score="3" Body="&lt;p&gt;First question: Yes. The immune system releases pyrogenic cytokines such as IL-1. Bacteria aren't typically used to 37C, they prefer working at under that temperature to function in the environment. Our body however can take a few degrees here or there however this severely compromises the bacterial enzyme activity. The same is true for other pathogen enzymes. The body also increases copper concentrations in the blood for similar reasons. Problem is of course if the body goes into overdrive and raises our temperature too much, this compromises our own ability to fight the infection so in that case antipyretics like paracetamol can reduce fever. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second question. It isn't a side effect, however paracetamol works by blocking things like IL-1 that raise temperature. How IL-1 raises your temperature is quite interesting, it tells the hypothalamus (our thermostat) that it should be set higher. So we feel cold (so we try to keep ourselves warm) and the body thinks it's cold (so it increases the temperature by burning glucose mainly)&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-04-24T20:26:30.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8074" PostTypeId="2" ParentId="7654" CreationDate="2013-04-24T20:35:10.923" Score="1" Body="&lt;p&gt;Remember that your coach shouldn't give dietary advice unless he's trained as a dietician. Protein isn't as important as glucose really, that's the thing you burn the most. However you use everything: vitamins to tell the immune cells where to go, proteins to make antibodies, glucose to fuel millions and millions of neutrophils and other cells. Even fat stores may start to move in order to keep your glucose high but not too high. The excess protein is unlikely to do you harm, it'll just get urinated out typically. Minerals can be used by enzymes to make them active that are in charge of destroying bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So as a rough summary, eat healthily. Exactly how you should eat before getting ill to limit the duration or prevent symptoms in the first place. If you lack the minerals and vitamins during the time you're ill you probably lack them all the time round so don't change what you eat when you're ill, but change what you eat when you're well and then your body will have everything stocked up when you're ill and all you need to eat is glucose and drink plenty of fluids and if possible continue with the healthy stuff. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-04-24T20:35:10.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8075" PostTypeId="2" ParentId="2885" CreationDate="2013-04-24T20:44:25.567" Score="0" Body="&lt;p&gt;Different pathogens affect different organisms. We live longer because we have an advanced immune system far better than that of a cockroach and because of a hundred other reasons. A cockroach that were to keep itself well fed and clean would live longer, but they can't manage that as well as they could if they had a brain as powerful as ours. Furthermore they're evolutionary suited to live in the environment they do with less consequences than we would. But look at the opposite. A cockroach and a human are in identical locked rooms with a key on the floor. The rooms have no food or water. WHo dies first? The cockroach, because the human simply walks out. For those that will be brutal, the cockroach cannot get out unless it unlocks the door because it's a cockroach escape-proof room :P&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now for your cancer question. Cancer was much rarer in the human population hundreds of years ago than it is now. That's because it's a disease you get due to damage by radiation and other mutagens over time. Cockroaches don't live long enough. But radiation isn't the only mutagen, we could feed them something if we really wanted to give them cancer. As long as cells are dividing, cells can get cancer. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-04-24T20:44:25.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8076" PostTypeId="1" AcceptedAnswerId="8080" CreationDate="2013-04-24T23:11:14.957" Score="4" ViewCount="1076" Body="&lt;p&gt;I'm under the impression that most sloths exhibit this behavior, but why? They are slow moving and so have no way of escaping from predators when on the ground. Not to mention the energy they expire to break from their normally sedentary lifestyle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They may only have to defecate and urinate once a week, but it strikes me as an unnecessary risk.  Why not let gravity do all the hard work? &lt;/p&gt;&#xA;" OwnerUserId="3382" LastActivityDate="2013-04-29T01:53:06.433" Title="Why do sloths come down from the trees to defecate?" Tags="&lt;evolution&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8077" PostTypeId="2" ParentId="2885" CreationDate="2013-04-24T23:19:04.660" Score="1" Body="&lt;p&gt;AndroidPenguin, where did you read that our immune systems are far better than those of 'a cockroach'? This seems pretty strange to me, but I'd be interested in reading a study that compared human and cockroach immune systems if you can provide a reference. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Victor, with respect to cockroaches, there are numerous species of cockroaches. Here's a page about cockroaches with a link to publications on cockroaches and a phylogenetic tree of the families and subfamilies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bio.umass.edu/biology/kunkel/cockroach.html&quot; rel=&quot;nofollow&quot;&gt;http://www.bio.umass.edu/biology/kunkel/cockroach.html&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All those species tend to occupy distinct niches with distinct traits. With respect to cockroach evolution, sewers are too new a phenomenon to have had an influence on cockroaches. Rather cockroaches have been successful in adapting to this novel 'habitat'. The same holds for rats and other denizens of sewers. Sewers are a very nutrient rich environment, and as in many nutrient rich environments, a few species tend to possess the right traits (whatever those may be) to survive and out-compete other species. To take an example from coral reefs, when coral reefs suffer from eutrophication, this leads to a growth in phytoplankton and a reduction of the euphotic zone that can lead to the death of all but the most resistant corals. Likewise in the terrestrial environment, only the most tolerant or opportunistic species tend to survive in highly perturbed and nutrient rich environments like sewers. With respect to cockroaches getting cancer, I've never read anything about insect cancer, but I imagine in theory that they could get cancer. I'm not sure, however, of the impact given the much shorter life spans of insects. It's an interesting question though.&lt;/p&gt;&#xA;" OwnerUserId="3445" LastActivityDate="2013-04-24T23:19:04.660" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8078" PostTypeId="2" ParentId="8072" CreationDate="2013-04-24T23:41:36.863" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1437715281&quot; rel=&quot;nofollow&quot;&gt;Cellular and Molecular Immunology&lt;/a&gt; by Abul Abbas et al. is pretty good, and you can't beat Charlie Janeway's &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0815342438&quot; rel=&quot;nofollow&quot;&gt;Immunobiology&lt;/a&gt; either. Both will give a good introduction to B-cells, antibodies, BCR signaling, and how they fit in to the immune system's structure and function. I own earlier editions of both, and their different perspectives are good for getting a more holistic understanding of the field. Good luck in your studies, it's a fascinating subject!&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-04-24T23:41:36.863" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8079" PostTypeId="1" AcceptedAnswerId="27708" CreationDate="2013-04-24T23:45:19.057" Score="2" ViewCount="2938" Body="&lt;p&gt;Why is it that when secretory rate increases in the pancreas the concentration of chloride ions decreases, and the concentration of bicarbonate increases in the production of isotonic NaCl secretion?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The modification that goes on in the duct of the acinus is dependent on flow. If the flow is faster, then less ions can be reabsorbed from the primary secretion. In the pancreas, chloride ions are removed, so surely their concentration should go up as the flow increases?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bicarbonate on the other hand is added to the primary secretion in the duct. So shouldn't its concentration in the secretion stay the same or even increase as flow increases?&lt;img src=&quot;https://i.stack.imgur.com/vEMOh.png&quot; alt=&quot;This is an approximation of the graph given in our lecture notes; from Boron &amp;amp; Boulpaep, Medical Physiology, 1st Ed, p919 - Sorry for the bad quality reconstruction&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3382" LastEditorUserId="3382" LastEditDate="2013-04-25T09:07:41.717" LastActivityDate="2015-01-15T07:00:43.567" Title="Why do ion concentrations change with different secretion rates in pancreatic juice?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8080" PostTypeId="2" ParentId="8076" CreationDate="2013-04-25T00:51:38.700" Score="4" Body="&lt;p&gt;From Wikipedia: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sloths go to the ground to urinate and defecate about once a week, digging a hole and covering it afterwards. They go to the same spot each time and are vulnerable to predation while doing so. The reason for this risky behaviour is unknown, although some believe that it is to avoid making noise while defecating from up high that would attract predators. Consistent with this, they reportedly relieve themselves from their branches during storms in the rainy season. Another possible explanation is that the middens provide the sloths with one of their few methods of finding one another for breeding purposes, since their sense of smell is far more acute than their eyesight or hearing. It has also been pointed out that individual sloths tend to spend the bulk of their time feeding on a single &quot;modal&quot; tree; by burying their excreta near the trunk of that tree, they may help nourish it.&lt;a href=&quot;http://en.wikipedia.org/wiki/Sloth#Physiology&quot; rel=&quot;nofollow&quot;&gt; [Source]&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="107" LastEditDate="2013-04-29T01:53:06.433" LastActivityDate="2013-04-29T01:53:06.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8081" PostTypeId="1" AcceptedAnswerId="8082" CreationDate="2013-04-25T01:24:08.450" Score="2" ViewCount="1968" Body="&lt;p&gt;I heard that some monkeys can be homosexual? a friend of mine was saying that he saw a male monkey having sex with another male monkey in the zoo, I honestly didn't believe him, I think he just got confused or he made it up. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Could this be true? can monkeys become homosexuals? does homosexuality (other than human) exist in the animal kingdom?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user3130" LastEditorUserId="3624" LastEditDate="2016-05-10T14:23:43.090" LastActivityDate="2016-05-10T14:23:43.090" Title="Can animals, like monkeys, be homosexual?" Tags="&lt;sex&gt;&lt;homosexuality&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8082" PostTypeId="2" ParentId="8081" CreationDate="2013-04-25T07:01:31.443" Score="4" Body="&lt;p&gt;Cases of homosexuality have been described in numerous species, including primates, and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Homosexual_behavior_in_animals&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia link&lt;/a&gt; posted by @shigeta lists and describes some of them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It could be difficult to untangle the difference between &lt;strong&gt;an animal not being able to identify sexes very well, or, deliberately mating to anyone&lt;/strong&gt; and &lt;strong&gt;those actively making a choice to engage in intercourse with a same sex individual.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I there are some species where sexes are very difficult to tell apart so they may just go around having sex with anything that looks like the right species because the mating is relatively low cost so doesn't matter if the partner was male or female. This is one such example in sea snails:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;In a laboratory mate-choice experiment, male &lt;em&gt;N. radiata&lt;/em&gt; preferred to&#xA;  mate with females, indicating precopulatory sex identification. They&#xA;  copulated with males, however, at the frequency of 37%, perhaps&#xA;  because of sex misidentification.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Other likely candidates are those with little sexual dimorphism and those with sneaker males that mimic females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have also heard theoretical discussions (oh the joys of lunchtime in an evolutionary biology department!) which suggest it may be a way of individuals (particularly males) practising or keeping up fitness relating to sex or stimulating better sperm production etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you decide what constitutes &quot;a homosexual animal&quot; then it is perhaps easier to examine. I would say a homosexual animal is one that mates exclusively (or highly preferentially) with same sex individuals when given the choice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Models of genetic and epigenetic inheritance have been used to suggest just how homosexuality could evolve and you can read more about it in &lt;a href=&quot;https://biology.stackexchange.com/questions/7669/how-can-homosexuality-evolve-despite-natural-selection/7674#7674&quot;&gt;this Biology.Stackexchange post.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it seems that monkeys, and other animals, have been documented to exhibit homosexuality, reasons for them to do so could exist, and it could be a heritable trait which persists despite seemingly strong negative selection. &lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2013-08-01T02:28:29.177" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="8084" PostTypeId="1" AcceptedAnswerId="8085" CreationDate="2013-04-25T15:46:19.147" Score="10" ViewCount="4853" Body="&lt;p&gt;I read on &lt;a href=&quot;https://en.wikipedia.org/wiki/Dog#Smell&quot;&gt;Wikipedia&lt;/a&gt; that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The wet nose, or rhinarium, is essential for determining the direction of the air current containing the smell. Cold receptors in the skin are sensitive to the cooling of the skin by evaporation of the moisture by air currents.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That explains why their noses are wet. Why they're slightly moving them when smelling, like on &lt;a href=&quot;http://youtu.be/bJ2DgCCUstA&quot;&gt;this video&lt;/a&gt; (see the close-up in the second part)? Could this very little movement create enough air currents around the nose to determine what smells are coming from what directions? Or is there another reason?&lt;/p&gt;&#xA;" OwnerUserId="1279" LastActivityDate="2019-11-04T01:04:55.923" Title="Why dogs move their noses when smelling?" Tags="&lt;sensation&gt;&lt;olfaction&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8085" PostTypeId="2" ParentId="8084" CreationDate="2013-04-25T21:02:28.927" Score="6" Body="&lt;p&gt;The dog's ability to smell the world around him and to interpret these odors &lt;em&gt;depends on a complicated chemical sensory system&lt;/em&gt;. First of all, it possesses &lt;strong&gt;mobile nostrils&lt;/strong&gt;, &lt;em&gt;that help to determine the direction of the smell&lt;/em&gt;. Then comes &lt;strong&gt;sniffing&lt;/strong&gt;, the &lt;em&gt;ability to disrupt the air with a regular pattern of breathing&lt;/em&gt; that, through laboratory testing, &lt;strong&gt;is structured in a series of 3 to 7 snorts&lt;/strong&gt;. Most of the sensory organs of the dog's nose, the septal organ, are probably responsible for the outbreak of sniffing behavior.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The air is scented, it &lt;em&gt;passes over a bony structure called &quot;projection sub-ethmoid&quot;&lt;/em&gt;, that man does not possess, &lt;em&gt;and nasal membranes that cover it&lt;/em&gt;. The area above the protrusion is not sweep, when the dog exhales air and it allows olfactory molecules to settle and accumulate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a dog breathes normally, air is introduced into the nasal passages, it continues its way to the lungs. &lt;em&gt;The action of smell allows air to remain &quot;at rest&quot; in the nasal passages&lt;/em&gt;. &lt;em&gt;The intricate complex surrounds the maxillo-turbinate bones&lt;/em&gt; of the skeleton &lt;em&gt;provides that the nasal membranes are capable of creating models of air flows odors that lead content in the air to hit the regions of the olfactory receptors.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The odor molecules disintegrate and are concentrated in the nasal mucus that adheres to the receptor cells&lt;/strong&gt;. Once the mucus, load odor, adheres to the microscopic hairs of receptor cells, &lt;strong&gt;the chemical signal odor turns into an electric signal&lt;/strong&gt; and is sent to the cerebral cortex and the limbic system, ie, the part of the brain that regulate behaviors feeding, drinking and sex. &lt;strong&gt;Small molecules stimulate the olfactory nerve of smell&lt;/strong&gt;. &lt;strong&gt;Big odor molecules stimulate the trigeminal nerve&lt;/strong&gt;, one of the largest nerves of the skull, and the volatiles of sex hormones probably stimulate the vomeronasal organ, the other part of the anatomy of the dog that does not exist in primates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VqDYB.jpg&quot; alt=&quot;cranio&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Ps37w.jpg&quot; alt=&quot;cell&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ucsuggiatevedano.it/l-olfatto&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ucsuggiatevedano.it/l-olfatto&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt; @ kmm&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their &lt;strong&gt;nostrils can move&lt;/strong&gt;, like the eyes to focus and channel the light energy. Or the highly mobile ears of many predatory animals, including cats and owls, which can rotate, also independently one from the other, not only to improve the perception, but also to identify the direction of the sound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The principle is the same as the frontal binocular vision, which allows us to calculate the distance.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT II&lt;/strong&gt; @ terdon&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the dog sniffs, &quot;taste&quot; a smell with a series of inhalations shorter and faster than normal, as we do when we feel a bad smell, breathes quickly several times to understand what smell is that.&#xA;Of course we are well-educated people and we do not do this in public. But the gesture is the same. =-]&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT III&lt;/strong&gt; @Petr&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Smell is the ability to detect and discern the odorous emanations from the air. The snuff is the ability to intercept and discern the odorous emanations from the ground. They act with a pattern of regular breathing and is structured in a series of one / three smells accompanied by a series of three / seven snuffs.&#xA;The behavior is controlled by the organs of sense of smell nasal septum.&quot;&#xA;(Section 3.3.3.4.1 and the following) &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.fongaros.it/ana2.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.fongaros.it/ana2.pdf&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.cacciapassione.com/cani-e-cacciatori/1956-olfatto-del-cane-tutta-questione-di-naso.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.cacciapassione.com/cani-e-cacciatori/1956-olfatto-del-cane-tutta-questione-di-naso.html&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The dog is able to absorb the chemicals present in the air, thanks to the characteristics enjoyed by its olfactory cells. To further stimulate their sense of smell to the dog no choice but to expand with some emphasis their nostrils sneaking in a strong &quot;suction&quot; of odors. The air will be retained more or less long and the dog will recognize odors also very weak.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ucsuggiatevedano.it/l-olfatto&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ucsuggiatevedano.it/l-olfatto&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Olfaction&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Olfaction&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The nose of the dog is also called truffle, at its end there are the nostrils or the cavity, through which sucks air, and the vibrissae, equipped with sensory hairs. The dog's nose is particularly sensitive, is equipped on the inside of an organ said &quot;of Jacobson&quot;, which allows to perceive any kind of substance, able to distinguish between a million of specific molecules, over that of perceiving pheromones, i.e. substances that indicate important information about the physical and mental state of others like it.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.comeaddestrareuncane.com/blog/tag/cani-molecolari/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.comeaddestrareuncane.com/blog/tag/cani-molecolari/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In the dog, the surface of the olfactory mucosa varies between 70 and 150 cm2 - in this tissue the number of olfactory receptors varies from 250 to 280 million - In 1962, Becker et al. showed that dogs are able to recognize substances in dilutions from 1/100 to 1/10.000.000.&#xA;- &lt;a href=&quot;http://milano.corriere.it/milano/notizie/cronaca/12_febbraio_19/cani-olfatto-parere-esperto-1903358352720.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://milano.corriere.it/milano/notizie/cronaca/12_febbraio_19/cani-olfatto-parere-esperto-1903358352720.shtml&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have you noticed how a dog sniffs the urine of a female &quot;tasting it&quot;? It is the same action that makes the viper when it follows the track of the mouse: it evertes the tongue and carries on it the odorous particles in the buccal cavity, and this organ has a function in the middle between the olfactory and gustatory ones. &quot;Pointing dogs&quot; is as pointing &quot;the wild&quot; taste the smell.&#xA;&quot;Eat the scent&quot;, in the jargon, because savored, not only in terms of smell, the smell of the wild. &lt;strong&gt;The Jacobson's organ is then a second organ&lt;/strong&gt; capable of perceiving odors, &lt;strong&gt;the first we've said is represented ciliated epithelium of the mucous membrane of the nose&lt;/strong&gt;.&#xA;But there is &lt;strong&gt;a third organ called the &quot;Rodolfo-Masera&quot;&lt;/strong&gt; which also serves to sense the emanations chemical (not yet known which), that way you could explain a specialization of these organs to perceive certain groups of biochemicals than others.&#xA;- &lt;a href=&quot;http://www.laciotola.net/Cani/la-funzione-olfattiva-del-cane.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.laciotola.net/Cani/la-funzione-olfattiva-del-cane.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3384" LastEditorUserId="3384" LastEditDate="2013-05-02T00:04:08.043" LastActivityDate="2013-05-02T00:04:08.043" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8086" PostTypeId="2" ParentId="7734" CreationDate="2013-04-26T04:29:06.947" Score="1" Body="&lt;p&gt;It seems that most functional annotation these days is inferred from sequence similarity to previously annotated genes/proteins: this is certainly true of high-throughput functional annotation. It's hard to know how many layers of inference there are between your query sequence and an actual experiment verifying the (possibly tissue- or condition-specific) function of a gene/protein. But alas, I digress...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One confounding factor for is that alternatively spliced isoforms share a lot sequence in common, which means that they might share best hits when searching against a database of annotated transcripts and end up getting assigned the same GO terms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But as others have mentioned, I think the biggest limiting factor you will encounter is the low-throughput step: in many cases the experimental work required to characterize the functions of alternative isoforms simply has not yet been done.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2013-04-26T04:29:06.947" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8088" PostTypeId="1" CreationDate="2013-04-26T07:24:20.447" Score="2" ViewCount="178" Body="&lt;p&gt;I want to ask what is the reason that T315I type CML leukemia is currently untreatable. I have read quite a few papers in this subject. Why the current genetic oriented engineering drugs failed to stop the leukemia stem cell's expansion but can only slow the secondary leukemia stem cell's expansion? I found it to be utterly hopeless for a patient to be in such a position, as chemical therapy does not work well and radiation therapy can only target specific area. There are experimental drugs in the developmental stage but from what I know they are mostly unreliable. &lt;/p&gt;&#xA;" OwnerUserId="3450" LastEditorUserId="69" LastEditDate="2013-04-26T21:39:17.813" LastActivityDate="2013-04-26T21:39:17.813" Title="Why it is so difficult to treat leukemia?" Tags="&lt;human-biology&gt;&lt;cancer&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8090" PostTypeId="2" ParentId="3481" CreationDate="2013-04-26T08:41:09.523" Score="0" Body="&lt;p&gt;I've seen in a documentary that inuit, eating only seals for a longer period of time are some of the most healthy people on the planet.&lt;br&gt;&#xA;However I can't seem to find that documentary anymore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did found a wiki article about this subject:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Inuit_diet&quot; rel=&quot;nofollow&quot;&gt;Inuit diet Article&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1897" LastEditorDisplayName="user1897" LastEditDate="2013-04-26T12:49:54.443" LastActivityDate="2013-04-26T12:49:54.443" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8091" PostTypeId="1" AcceptedAnswerId="8093" CreationDate="2013-04-26T11:28:42.817" Score="3" ViewCount="170" Body="&lt;p&gt;I am looking at the &lt;a href=&quot;http://www.pharmgkb.org/index.jsp&quot; rel=&quot;nofollow&quot;&gt;PharmaPGKB&lt;/a&gt; database for SNPs and trying to understand what the following &lt;a href=&quot;http://www.pharmgkb.org/rsid/rs1801131&quot; rel=&quot;nofollow&quot;&gt;annotation&lt;/a&gt; means:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;rs1801131 at 1:11854475 in CLCN6, MTHFR (VIP)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Ok, the SNP identified by &lt;code&gt;rs1801131&lt;/code&gt; occurs in the first chromosome, at position &lt;code&gt;11854475&lt;/code&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, the two genes' identifiers come. The position &lt;code&gt;11854475&lt;/code&gt; is inside the gene &lt;code&gt;MTHFR&lt;/code&gt;. Why do they also annotate the SNP to the gene &lt;code&gt;CLCN6&lt;/code&gt; (which is a &quot;neighbour&quot; of &lt;code&gt;MTHFR&lt;/code&gt;) ?&lt;/p&gt;&#xA;" OwnerUserId="781" LastEditorUserId="1306" LastEditDate="2013-04-26T17:21:46.923" LastActivityDate="2013-04-26T17:21:46.923" Title="Understanding these SNP annotations" Tags="&lt;gene-annotation&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8093" PostTypeId="2" ParentId="8091" CreationDate="2013-04-26T17:17:56.157" Score="4" Body="&lt;p&gt;It is because the two genes overlap:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr1:11866207-11903201&amp;amp;hgsid=334433485&amp;amp;knownGene=pack&amp;amp;hgFind.matches=uc010oau.2,&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/kSJpf.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CLCN6 is on the plus strand and MTHFR is on the minus strand. The SNP is annotated to both because it falls in a region of the genome claimed by both genes. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-04-26T17:17:56.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8094" PostTypeId="1" CreationDate="2013-04-26T19:35:34.367" Score="8" ViewCount="4276" Body="&lt;p&gt;If you want a specific plant, let's say the snap peas I am growing that I bought at Agway. I noticed that they grow towards the light source through the nearby window. Also I think roots work the same way for water/minerals. also don't various kinds of ants find food conceptually identically?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How much of this is true? Please correct:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I think analogous to ant colonies, plants will attempt to grow every which way initially, and will only continue growing in directions that give the most/enough light/water/minerals. If a direction is or becomes unfruitful, that section withers. After the initial state the plant will start branching in directions off of locations on still growing sections of plants and that cycle continues until none of the plant can be supported and the whole thing withers (perennials) or slows its metabolism down to the point where it could survive those conditions until they picked up again (such as winter seasonal survival of tree species). Also, it is not as if they decide which direction to go in. that type of decision would forgo going in another direction. And not sure, but I don't think plants have decision capabilities anyways. they grow in directions they grow best.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3458" LastEditorUserId="3458" LastEditDate="2013-04-26T23:57:14.277" LastActivityDate="2015-05-11T04:56:29.357" Title="What chemicals and structures control the *direction* of plant growth in leaves, stems and roots?" Tags="&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8095" PostTypeId="2" ParentId="8088" CreationDate="2013-04-26T20:14:24.970" Score="2" Body="&lt;p&gt;The T315l mutation of BCR/ABL gene produce the complete resistance of CML leukemia to all currently available BCR/ABL inhibitors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a idea that is not yet tested for such patients - allogenic hematopoietic transplatation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More information: &#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20657522&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/20657522&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.ingentaconnect.com/content/maney/hem/pre-prints/1607845412Y.0000000050&quot; rel=&quot;nofollow&quot;&gt;http://www.ingentaconnect.com/content/maney/hem/pre-prints/1607845412Y.0000000050&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1668" LastActivityDate="2013-04-26T20:14:24.970" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8096" PostTypeId="2" ParentId="7734" CreationDate="2013-04-26T23:52:20.063" Score="0" Body="&lt;p&gt;I'd tend to agree there's very little data on this, esp given how many isoforms there are.  I believe that even some cases of pseudogenes may have function as a protein.  I'd bet that most of them have some unique functional aspects.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think we'd all agree we can't prove that they do in all cases, but let me sketch out how these different functions might arise or are known. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Protein_isoform&quot; rel=&quot;nofollow&quot;&gt;Protein Isoforms&lt;/a&gt; usually come from two causes.  The first being that there are two very similar copies of the same gene, from a gene duplication event.  The second coming from alternative splicing.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternative splice isoforms are often missing or adding a few amino acids - the sequence is different.  This can be from truncation of a large portion of the protein such as the leptin receptor. &lt;a href=&quot;http://diabetes.diabetesjournals.org/content/48/2/279.short&quot; rel=&quot;nofollow&quot;&gt;Leptin receptor has two full length variants that have different expression patterns at different temperatures and import leptin into the cell at different efficiencies&lt;/a&gt;.  &lt;a href=&quot;http://www.jbc.org/content/272/51/32686.short&quot; rel=&quot;nofollow&quot;&gt;Leptin also has several short isoforms, where only a short portion that faces the cell interior is produced.  These variants compete with the full receptor to modulate the cells sensitivity to leptin.&lt;/a&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can imagine, mapping all this out in just one case took years of work. Complete characterization of all human isoforms would take a long time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isoforms from gene duplication have many of the same properties as splice variant isoforms; they can have completely different regulatory machinery - popping up in different biological states than the main gene and they can vary in sequence a little bit or a lot.  It has been implied that these gene duplicates persist in the genome because they quickly find a new niche role.  This paper shows that 30% of 195 new genes that have shown up since two strains of fly have diverged are necessary for viability.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution doesn't let genes sit around because they are completely identical; they can be removed as easily as they show up, only differential function will keep an isoform in the mRNA repertoire for a prolonged time. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-04-26T23:52:20.063" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8097" PostTypeId="2" ParentId="8094" CreationDate="2013-04-27T00:56:58.660" Score="2" Body="&lt;p&gt;Your statement is partially correct, but not entirely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/aJYQp.jpg&quot; alt=&quot;struttura del seme&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an animal embryo, the seed, still closed, is already formed, with the distinction between root, stem and leaves. Tiny but already there are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All the rest of the seed (in this case two cotyledons) is a kind of food dough, and serves as a food reserve for the seedling, until the time of rooting and the achievement of energy independence.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;As animals, the plant seeks, first of all, water. The first need of water is determined by the need to break the skin that closes the seed. If there is no presence of water,  the seed dried and does not sprout.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it &quot;feel&quot; the water, the seed drinks, swells and the skin breaks down. At this stage we can also say that the seed is aware of where it can find water. I do not think that they have been studies done on the awareness of the high and low (orientation). On the edge of rivers and lakes the seed can also find favorable ground above itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The direction of the water determines an effort, which can also lead to the rotation of the seed in the right position to emit the radicle towards the water (and the earth). In this time the embryo &quot;eats&quot; the nutritional reserves contained in the seed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then precisely they decide which direction to go in. When the place and position are correct, the seed has open and the part to eat is almost eaten, then more light. The radicle grows to first, both in size and as the length. It hooks to the soil and establishes a firm basis. Starts to drink directly (and not by absorption of the tissues of the seed) and starts to push out the seedling, typically in the opposite direction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The seedling &quot;feel&quot; the light energy and go to that.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;If the plants have ability of decision or not, has not yet been established. But to me personally it seems that a functional DNA must be able to allow each subjet to handle each situation (consistent with its structure) in the best way to itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This seems to have been ascertained for the animals. A certain capacity of thought, namely to make decisions, is absolutely functional in a huge energy saving on the need for encoding and on the structure of DNA&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I know little about the life of the colonies of ants. But I know all about bees. A swarm that is detached from the hive to found a new colony, it also stops two or three times. Sends forward scouts, followed by architects and, if the place is right, the architects have a network, and bees wax begin to build.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your mention of the ants is not sufficient to me to find similarities.&lt;/p&gt;&#xA;" OwnerUserId="3384" LastActivityDate="2013-04-27T00:56:58.660" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8098" PostTypeId="1" AcceptedAnswerId="16471" CreationDate="2013-04-27T03:14:48.043" Score="1" ViewCount="306" Body="&lt;p&gt;I've been working a little with M. G. Bulmer's Principles of Statistics (Dover, 1979) and cannot see how to properly compute half of one question. This should be a basic probability computation, but I am not getting the same answer as the book's suggestion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the question (Chapter 2, Problem 2.4): If the three genotypes (i.e., AA, Aa, aa) are all distinguishable, find the probabilities that a) a pair of siblings and b) a pair of unrelated individuals will appear the same when p=q=.5.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The book offers .59 for a) and .38 for b). I can get b correctly, but I don't understand how to properly compute part a).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This does not seem like a complicated exercise! &lt;/p&gt;&#xA;" OwnerUserId="3461" LastEditorUserId="3340" LastEditDate="2013-04-28T05:46:05.410" LastActivityDate="2014-04-10T18:36:25.103" Title="Hardy-Weinberg Equilibrium: To compute probability of finding two siblings (random mating)" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;human-genetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8099" PostTypeId="1" CreationDate="2013-04-27T03:35:21.923" Score="1" ViewCount="1001" Body="&lt;p&gt;The question pretty much sums it up. How do animals/plants change for each: Spring, Summer, Autumn, and Winter? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A detailed explanation on distinct behaviour and appearance changes would be nice.&lt;/p&gt;&#xA;" OwnerUserId="3462" LastEditorUserId="3952" LastEditDate="2013-08-10T01:51:34.327" LastActivityDate="2017-03-06T10:09:52.663" Title="How do animals/plants change for each season?" Tags="&lt;zoology&gt;&lt;botany&gt;&lt;ethology&gt;&lt;life-history&gt;&lt;phenology&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2017-03-06T22:35:27.940" ContentLicense="CC BY-SA 3.0" />
  <row Id="8100" PostTypeId="2" ParentId="5503" CreationDate="2013-04-27T03:51:08.907" Score="7" Body="&lt;p&gt;The question piqued my interest, but after hunting through the literature for a bit, I hadn't found any direct answers.  Then I went back and read the mouse study you cited a bit more carefully. The mouse study only made a reference to mice being affected at 4 lux, ~100x more sensitive than humans.  However, for that number it cited a paper in Science that has a direct answer.  &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencemag.org/content/210/4475/1267&quot;&gt;http://www.sciencemag.org/content/210/4475/1267&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;blockquote&gt;&#xA;    &lt;p&gt;Melatonin concentrations decreased 10 to 20 minutes after the subjects were exposed to 2500-lux incandescent light and reached near-daytime levels within 1 hour (Fig. 1). After the subjects resumed sleeping in the dark, the melatonin concentrations increased immediately and within 40 minutes were at the levels measured before exposure. The fluorescent light (500 lux) did not reduce melatonin, and there was no change after the return to darkness. In the two subjects who were exposed to 1500-lux incandescent light, melatonin concentrations decreased to levels intermediate between those measured during exposure to 500 and 2500 lux (Fig. 2). The return to normal nighttime concentrations after subjects were exposed to 1500 lux was similar to that occurring after their exposure to 2500 lux. The concentration of melatonin in subjects awakened and exposed to 500-lux fluorescent light did not differ significantly from that measured while they were asleep in the dark.&lt;/p&gt;&#xA;  &lt;/blockquote&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Since that was the granddaddy study of the subject, I just checked the recent citation list on that page for modern articles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using pure blue LED lights at 446-477 nm wavelengths, West et al. measured light intensities necessary to induce melatonin suppression. Table 1 of that study converts LED irradiance/lux into retinal irradiance (uW/cm2) based on mean pupil size.  Figure 2 shows plasma melatonin falling (p&amp;lt;0.05) at 20 uW/cm2 of corneal irradiance (then curve fit to 14.19 uW/cm2). It's at least twice as powerful as white light, which didn't show significant suppression at 40 uW/cm2, but was &quot;numerically similar&quot; to 10 uW/cm2 exposure.  If I've got the conversions right, 20 uW/cm2 is about 136 lux, which is about the brightness of an overcast day or half the brightness of typical office lighting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jap.physiology.org/content/110/3/619.full&quot;&gt;http://jap.physiology.org/content/110/3/619.full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the discrepancy between the two studies (1500 lux vs. 136 lux), I would blame it mostly on technological advances since 1980.  The original study used gas chromatography. You can see the huge error bars and noisy data in the Figure.  The modern study uses a radioimmuno assay using antiserum, and is presumably far more sensitive. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I was also going to mention a nice review paper that summarizes more findings, but apparently I can only post 2 links as a new user.  So I'll just paste the abstract and citation.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;blockquote&gt;&#xA;    &lt;p&gt;Light is a potent stimulus for regulating the pineal gland's production of melatonin and the broader circadian system in humans. It initially was thought that only very bright photic stimuli (≥ 2500 lux) could suppress nocturnal melatonin secretion and induce other circadian responses. It is now known that markedly lower illuminances (≤ 200 lux) can acutely suppress melatonin or entrain and phase shift melatonin rhythms when exposure conditions are optimized. The elements for physical/biological stimulus processing that regulate photic influences on melatonin secretion include the physics of the light source, gaze behavior relative to the light source, and the transduction of light energy through the pupil and ocular media. Elements for sensory/neural signal processing become involved as photons are absorbed by retinal photopigments and neural signals are generated in the retinohypothalamic tract. Aspects of this physiology include the ability of the circadian system to integrate photic stimuli spatially and temporally as well as the wavelength sensitivity of the operative photoreceptors. Acute, light-induced suppression of melatonin is proving to be a powerful tool for clarifying how these elements of ocular and neural physiology influence the interaction between light and the secretion of melatonin from the human pineal gland.&lt;/p&gt;&#xA;  &lt;/blockquote&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Photic Regulation of Melatonin in Humans: Ocular and Neural Signal Transduction&#xA;Brainard, Rollag, and Hanifin&#xA;J Biol Rhythms December 1997 vol. 12 no. 6 537-546&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;If you need more information, I'd start by checking the papers cited by the second paper. Alternately, there's probably more historical information available by looking at papers which have cited the first one. &lt;/p&gt;&#xA;" OwnerUserId="3460" LastEditorUserId="3460" LastEditDate="2013-04-27T04:30:41.590" LastActivityDate="2013-04-27T04:30:41.590" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8101" PostTypeId="2" ParentId="8094" CreationDate="2013-04-27T05:02:00.960" Score="5" Body="&lt;p&gt;&lt;strong&gt;PART 1 : Phototropism&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The movement of plant shoot towards light is called phototropism. This process is mainly stimulated by the blue light. The photoreceptor involved is called &lt;em&gt;Phot1&lt;/em&gt; (Phototropin 1) or &lt;a href=&quot;http://www.rcsb.org/pdb/protein/O48963&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;JK244&lt;/em&gt;&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Auxins such as IAA (indole acetic acid) are plant hormones, expressed highly in meristem, which cause shoot growth. On illumination this phototropin, through currently unknown messengers, causes inhibition of polar &lt;strong&gt;Auxin&lt;/strong&gt; transport in the illuminated side. This causes the non-illuminated side to grow more and thus bending the plant towards light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bjH5P.jpg&quot; alt=&quot;Phototropism&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;The image represents an older model which proposed lateral movement of auxin. The mechanism mentioned in last paragraph is the currently accepted model. The below figure illustrates 'polar auxin transport'&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YiFdY.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For details refer to &lt;a href=&quot;http://www.plantcell.org/content/18/5/1110.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;this nice review on phototropism.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;PART 2 : Geotropism and Hydrotropism&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Geotropism or gravitropism is movement of roots towards earth (gravity) and hydrotropism is movement of roots towards water. Both phenomena interact with each other and share some common pathways. But hydrotropsim can inhibit geotropism and it is evident in conditions when root goes towards an adjacent water source.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ethylene and Auxin signaling is involved in root growth both in geotropism and hydrotropism. In geotropism the auxin is stimulated by statoliths (clustered and membrane bound grains of starch) in the amyloplasts- the organelles which store starch. The model suggests that amyloplst sediments under the influence of gravity and thereby affect auxin polar transport (the second figure co-incidentally illustrates polar auxin transport in geotropism). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact moisture sensor is unknown but Abscissic acid (ABA), which is well known for its involvement in drought tolerance, is known to affect hydrotropism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23263156&quot; rel=&quot;nofollow noreferrer&quot;&gt;MIZ1/2&lt;/a&gt; are some proteins uniquely involved in hyrdotropism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both pathways are dependent on Calcium as a secondary messenger.&#xA;To conclude, these pathways are not as clear as those of phototropism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.academicjournals.org/ajar/pdf/Pdf2006/Nov/Dexian%20and%20South.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.academicjournals.org/ajar/pdf/Pdf2006/Nov/Dexian%20and%20South.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1360138504002717&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.sciencedirect.com/science/article/pii/S1360138504002717&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plantphysiol.org/content/133/4/1677.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.plantphysiol.org/content/133/4/1677.full&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-05-11T04:56:29.357" LastActivityDate="2015-05-11T04:56:29.357" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8102" PostTypeId="2" ParentId="8098" CreationDate="2013-04-27T06:32:21.070" Score="1" Body="&lt;p&gt;Are you sure it is 0.59 because I am getting 0.5625 for part (a) and this is how I computed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To check genetic similarity of siblings we first have to pick up mating pairs. Six mating pairs possible with following offspring probabilities &lt;code&gt;(choice of first mate x choice of second mate x same offspring genotype freq)&lt;/code&gt;. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;AA x AA : will always give same type of offspring: &lt;code&gt;prob = 0.25x0.25x1&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;aa x aa : will always give same type of offspring: &lt;code&gt;prob = 0.25x0.25x1&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;AA x aa : will always give same type of offspring: &lt;code&gt;prob = 0.25x0.25x1&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;Aa x Aa : will give Aa in half the number of times: &lt;code&gt;prob = 0.5x0.5x0.5&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;Aa x AA : will give two types of similar offsprings, half the number of times - AA and Aa: &lt;code&gt;prob = 0.5x0.25x0.5x2&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;Aa x aa : will give two types of similar offsprings, half the number of times - aa and Aa: &lt;code&gt;prob = 0.5x0.25x0.5x2&lt;/code&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Total probability = &lt;code&gt;3x(0.5x0.5x0.5) + 3x(0.25x0.25) = 0.375+0.1875 = 0.5625&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assumptions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Population is infinite&lt;/li&gt;&#xA;&lt;li&gt;Population in equilibrium&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-27T08:55:10.523" LastActivityDate="2013-04-27T08:55:10.523" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8103" PostTypeId="2" ParentId="1795" CreationDate="2013-04-27T06:50:02.253" Score="3" Body="&lt;p&gt;I'm resurecting an old question, but I've heard this question from a few young bioinformaticians and had a couple more points to consider about compressing PDB files.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first is that many PDB files (including all PDBs hosted on the PDB site) have some 300-400 lines of meta data at the top of the file.  This accounts for about 10-20% of the total file size.  Also many PDBs have ANISOU records, but they're about as redundant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, even if you're dealing with raw coordinate data, I think you're underestimating just how well GZIP already does.  Let's just say half that column data is somehow completely redundant and we can just compress it all away. Next we'll encode the 5 numbers (x, y, z, q, b) in binary using 2 bytes for each number (which isn't even enough room for practical use, but we're optimistic here).  So we've compressed 80 columns to 10 columns, which is 12.5% of the original size. Running gzip on a couple simple pdbs (after grepping out just the ATOM records), it achieves 23.0% of the original size. If we really cared about file size, we could use bzip2 which gets to 16.4%.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our magical compression tool is only twice as good as gzip, which is nice, but gzip is already four times better than uncompressed pdbs.  If we cared enough, we'd just use bzip2, which is only 30% larger than this hypothetical minimum size. And once we got all the atom specifications back in there, I'm sure they'd be virtually identical.  The bottom line is that bzip2 is already very close to the maximal theoretical compression limit for many kinds of files, especially text files. For genome sequencing data, which is orders of magnitude larger and more redundant, people just made slight modifications of the underlying algorithm. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've downloaded and analyzed the entire PDB database (a little out of date, but it's 75K structures and 14GB, gzip compressed), and can appreciate wanting to shrink it down further, believe me.  At that level, compression makes a difference in analysis time just reading data off the hard disk (or an NFS server). Fortunately, many (if not most) pdb tools read gzip'd pdbs natively (sadly not the case for bzip'd files). Perl, Python, and every other major bioinformatics language have simple APIs for automatically decompressing gzip'd files as they're opened. Against the ubiquity of gzip, it's not really worth thinking about a small improvement in compression. Again, if we cared, we'd just make everything use bzip2 instead. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The future is more like PDBML, which I kind of despise.  But it's far more complete and easier to parse (given that XML parsers exist for every major language), even if the files themselves are an order of magnitude larger. I don't like them (and mostly XML in general) because they're not human readable in any practical sense. But at the same time I'm not suggesting we just move to a 120 column PDB format just to address PDB format limitations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using only dihedral angles would never work either, and not because of numerical precision. There is small but significant variance in bond lengths and angles that would cause coordinates to be off by angstroms by the end of the chain.  It wouldn't help with ANISOU, REMARK, and other records. And it would frankly be a huge pain to write new parsers for. &lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-04-27T06:50:02.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8104" PostTypeId="2" ParentId="7840" CreationDate="2013-04-27T07:17:35.307" Score="0" Body="&lt;p&gt;If I understand what you're attempting to accomplish, as David said, this is a vigorous area of study in structural biology. I'll start by saying that a single amino acid substitution will often make virtually no difference in a structure, but there are proteins where a couple substitutions will convert an all alpha-helical protein to all beta-sheet, so I'll leave it to you to judge what's worth trying. There are three routes you can take:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, for small changes, pymol does have a built in force field (&quot;molecular sculpting&quot;) and residue mutagenisis.  Chimera has a tool called &quot;minimize structure&quot; that are probably better developed. And VMD has the force field tool kit plugin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you expect larger changes, you might go with a full simulation package like NAMD or CHARMM.  They would take significant effort to get running, but they're there. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, you can just go with an empirical structure prediction server. All you do is open your sequence file, make your substituions there, upload it to the server, and wait for them to email you the results.  They'll do sequence alignments to find relevant PDB files and everything. I recommend the Robetta server (running David Baker's Rosetta). &lt;a href=&quot;http://robetta.bakerlab.org/&quot; rel=&quot;nofollow&quot;&gt;http://robetta.bakerlab.org/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-04-27T07:17:35.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8105" PostTypeId="2" ParentId="8099" CreationDate="2013-04-27T09:27:43.657" Score="3" Body="&lt;p&gt;There are various parameters that describe change of seasons such as day length, temperature, humidity. But it can be assumed that most of these parameters ultimately depend on one parameter- day length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The response of plants towards the length of day/night cycle is called photoperiodism (which dictates spring flowering).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencemag.org/content/303/5660/1003.long&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; article explains the effect of a gene called CONSTANS(CO) on spring flowering. CO is post transcriptionally regulated by cryptochromes and phyochromes.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The circadian rhythm in CO mRNA abundance was proposed to represent a photoperiod response rhythm, in which exposure to light coincides with CO expression only under LDs (Long Day) and thereby triggers flowering.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;......&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;We propose that early in the day phyB promotes the degradation of CO whereas in the evening cryptochromes and phyA antagonize this degradation and stabilize CO protein, &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, my knowledge of plant molecular biology is not that great and I would advise that you refer the mentioned article and the cross references cited in that.  &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-27T09:27:43.657" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8106" PostTypeId="2" ParentId="3290" CreationDate="2013-04-27T14:21:14.467" Score="0" Body="&lt;p&gt;Mitosis as a process does not have a verb form. However, as a process, there is an adjective; you could describe cells that undergo mitosis as mitotic. &lt;/p&gt;&#xA;" OwnerUserId="3464" LastActivityDate="2013-04-27T14:21:14.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8107" PostTypeId="2" ParentId="3817" CreationDate="2013-04-27T15:08:18.197" Score="3" Body="&lt;p&gt;Sleep is not homogenous - there are different phases of sleep - REM, NREM-1 to NREM-4. And these different stages may play different roles in 'rejuvenating' the body (as you put it).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you first fall asleep, you go into NREM-1 phase, which is the lightest sleep, and progresses into NREM-4, and for the first half of your sleep cycle, this cycles so you go from NREM-1 &gt; NREM-2 &gt; NREM-3 &gt; NREM-4 &gt; NREM-3 &gt; NREM-2 &gt; ....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the first half of your sleep cycle, the NREM3 and NREM4 phases dominates, only on latter half of your sleep cycle are REM phase observed and progressively dominate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending on how much you are waken up by, once you escape your sleep cycle, you may re-enter back at a different stage, which may mean you are no longer able to have much REM sleep. Subsequently, you will not have the rejuvenation that is associated with REM sleep and you feel tired.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interesting note: There are people who have tried a method called polyphasic sleep, where they nap/sleep periodically and regularly, instead of sleeping once a day for 8 hours, say. People who promote this says that people do not feel tired because as soon as they nap, they go in REM sleep, and so the amount of REM sleep you get per day will still be the same. I'll let you make your own mind up about this one.&lt;/p&gt;&#xA;" OwnerUserId="3465" LastActivityDate="2013-04-27T15:08:18.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8109" PostTypeId="2" ParentId="7809" CreationDate="2013-04-27T18:45:24.943" Score="1" Body="&lt;p&gt;Microscopic chirality is not at all necessary to explain curly hair (or other objects).  All that is required is flexibility. Once hair gets long enough, it collides with itself, and is pushed off to one side or another, forming a chiral curl. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For some anecdotal evidence against microscopic chirality, find someone with large diameter hanging curls in their hair. Those seem to often curl straight back on to themselves. A more compelling anecdote is that curled objects, including hair and telephone cords (if anyone still remembers those) can be pulled through themselves and chirally inverted. Sometimes there will be some resistance, but that could be the keratin or plastic or whatever having set in its shape over time, rather than being preferentially formed that way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are obviously both anecdotal though, and the idea that there is some slight chiral preference isn't ruled out. I'm not even opposed to the fundamental idea of transitive chirality through several orders of superhelicity (look at DNA), but it just hasn't been my empirical experience. As Ryan points out, if it were a strong effect, all hair would curl the same way, and straight hair wouldn't exist at all.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just to provide a bit of data, this paper demonstrates that hair curvature is based on the distribution of 4 different cell types in a follicle. The keratin (and many other proteins associated with) intermediate fibrils were associated with curvature, but only to the extend that their compositions were different in the 4 cell types. But the curvature was based on the distribution of the cells themselves.  Chirality wasn't specifically studied in the paper, but I think (given that they were staring at individual fibers with an electron microscope) that they would have noticed it had it existed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cortical cell types and intermediate filament arrangements correlate with fiber curvature in Japanese human hair&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1047847708002980&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S1047847708002980&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Naturally straight and curved human scalp hairs were examined using fluorescence and electron microscopy techniques to determine morphological and ultrastructural features contributing to single fiber curvature. The study excluded cuticle and medulla, which lack known bilateral structural asymmetry and therefore potential to form curved fibers. The cortex contained four classifiable cell types, two of which were always present in much greater abundance than the remaining two types. In straight hair, these cell types were arranged annularly and evenly within the cortex, implying that the averaging of differing structural features would maintain a straight fiber conformation. In curved fibers, the cell types were bilaterally distributed approximately perpendicular to fiber curvature direction with one dominant cell type predominantly located closest to the convex fiber side and the other, closest to the concave side. Electron tomography confirmed that the dominant cell type closest to the convex fiber side contained discrete macrofibrils composed of helically arranged intermediate filaments, while the dominant cell type closest to the concave side contained larger fused macrofibrils composed of intermediate filament arrangements varying from helical to hexagonal arrays approximately parallel to the longitudinal fiber axis. These findings concur with the current hypothesis of hair curvature formation and behavior.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3460" LastEditorUserId="107" LastEditDate="2013-04-28T12:55:26.380" LastActivityDate="2013-04-28T12:55:26.380" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8111" PostTypeId="1" CreationDate="2013-04-27T21:28:00.330" Score="-3" ViewCount="817" Body="&lt;p&gt;There are no good answers anywhere. so asking: this is not about days of survival without water. This is about &lt;strong&gt;long-term negative effects&lt;/strong&gt; induced from not drinking water for at least the mentioned days.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please link the most reliable link (has to be heavily-reviewed, meticulously-designed studies) that answers this question so I can look into it futher. Multiple studies are needed for it to be reliable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A related question is the same question for going without food, but with water (I'll ask this in a seperate question if the answer isn't already in the answer you provide).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is for modern human beings as it applies to the majority of people. Also you can comment with the most reliable resources on the topic so we can read into it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Important: NO comments without reliable &lt;strong&gt;scientific&lt;/strong&gt; sources are relevant or reliable (has to be heavily-reviewed, meticulously-designed studies) so we can look into it further by ourselves. &lt;strong&gt;Please don't comment/answer without one.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="3353" LastEditorUserId="69" LastEditDate="2013-04-27T22:06:38.627" LastActivityDate="2013-04-28T10:28:23.503" Title="What are the long-term negative effects of going without water/food for a period of time" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2013-04-30T16:28:03.937" ContentLicense="CC BY-SA 3.0" />
  <row Id="8112" PostTypeId="2" ParentId="8111" CreationDate="2013-04-28T01:33:17.203" Score="4" Body="&lt;p&gt;Besides its confrontational style, the way this question was asked suggests the author hasn't really looked into this or at least isn't clear on what questions they should be asking.  It is true that, in modern scientific culture, you cannot get approval to lock a bunch of college kids in a room for a week without food or water so you can check in with them years later and look for long term health effects.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But there are a &lt;em&gt;LOT&lt;/em&gt; of indirect ways to study this, either by studying populations that have suffered starvation (through famine or war) or brought it upon themselves (anorexia). Or you can look at animal studies, which might not give precise consequences for humans, but can be far better controlled (you can lock them up for a week and keep them around for a year). And they will have strong implications for humans, even if the results are numerically different. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Back at human population studies, you also don't need full starvation studies (X days without any food) to find that there are long term consequences, simple caloric restriction (CR) is well established as having long term negative consequences. I don't think it's a big stretch to assume that full starvation would (at the least) exacerbate these effects. On the other hand, there's a lot of recent age-related research showing controlled CR can extend lifespan from yeast up through mice. Though it's also well established that it can (for instance) reduce fertility at the same levels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll just give a couple links on population studies on starvation. Starvation is much easier to research because (as I recall) people can live for about a month without food or sleep, but a week without water and you're just dead. Population studies seem like the best way to get at the question you're asking (consequences of chronic starvation).  But as I said, these aren't controlled studies, you have to go out and find a relevant population and get what data you can. You're not going to just run across a dozen people who all went for exactly one week without food in 1943 and then went back to their normal lives. These are single study papers, but they each cite at least a dozen related papers (including reviews) and should be more than sufficient to nucleate further literature searches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Severe caloric restriction in young women during World War II and subsequent breast cancer risk&#xA;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1742-1241.2012.02966.x/full&quot; rel=&quot;nofollow&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1111/j.1742-1241.2012.02966.x/full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Comparison of metabolic profiles of acutely ill and short-term weight recovered patients with anorexia nervosa reveals alterations of 33 out of 163 metabolites&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022395612002488&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0022395612002488&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If these don't address what you're after, then please be more clear about what you actually need (and WHY this isn't it).  And, you know, this is a public forum that runs simply by the good graces of interested and knowledgable scientists. So please try and be a little nicer in how you phrase your questions.&lt;/p&gt;&#xA;" OwnerUserId="3460" LastEditorUserId="3460" LastEditDate="2013-04-28T10:28:23.503" LastActivityDate="2013-04-28T10:28:23.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8113" PostTypeId="1" CreationDate="2013-04-28T01:44:21.267" Score="0" ViewCount="234" Body="&lt;p&gt;Let's say there's a girl who carries a few masculine traits not normal in most girls, such as a high level of testosterone; we know there are countless reasons why something like this could happen, but could that girl have actually been concieved as a boy but modified before birth to become almost fully female, with only slight traces of male traits left? Is that possible through any sort of technology, or does biology even work that way?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, if a male baby was injected with high amounts of female hormones before his birth, or really, anything else that could alter his gender, in any case could he start morphing into a girl, even if not fully? (Say, to the extent where he became more of a girl but still possesed a few common but not very specific/clear/exclusively male traits such as excessive body hair, etc.?)  &lt;/p&gt;&#xA;" OwnerUserId="3469" LastEditorUserId="1231" LastEditDate="2013-04-28T02:17:55.903" LastActivityDate="2013-04-28T03:08:02.037" Title="Could a person become physically transgender through artificial means?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8114" PostTypeId="2" ParentId="8113" CreationDate="2013-04-28T03:08:02.037" Score="3" Body="&lt;p&gt;A &amp;quot;high level of testosterone&amp;quot; must be made within the context of a particular sex. Men tend to have much higher levels of testosterone than women, but the testosterone production and levels within women vary widely - just as many hormones. Genetics, environment, diet, drugs, and workout regimes can all affect testosterone levels. A qualified physician will be able to tell where a person is after a test.&lt;/p&gt;&#xA;&lt;p&gt;As for the rest... &lt;em&gt;&lt;strong&gt;Every&lt;/strong&gt;&lt;/em&gt; case of gender reassignment I've heard of and read about has occurred &lt;em&gt;after&lt;/em&gt; birth. Read through this &lt;a href=&quot;http://www.jhu.edu/jhumag/0900web/babes.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Johns Hopkins Magazine article from Sept. 2000&lt;/a&gt; to get a fairly good understanding of when gender reassignment occurs and how it's handled. Here's a quick rundown (summaries, NOT quotes from the article):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Inadequate exposure to Testosterone &lt;em&gt;in utero&lt;/em&gt; can result in &lt;strong&gt;ambiguous genitalia&lt;/strong&gt; or other conditions such as &lt;strong&gt;'micropenis'&lt;/strong&gt; for an XY fetus. Up until the 1990's, regardless of chromosomal gender, children with the conditions would be reassigned as 'female' and had reconstructive surgery very early on.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Androgen Insensitivity&lt;/strong&gt; is when an XY fetus is genetically &lt;em&gt;incapable&lt;/em&gt; of utilizing male hormones and can involve &lt;a href=&quot;http://en.wikipedia.org/wiki/Androgen_insensitivity_syndrome&quot; rel=&quot;nofollow noreferrer&quot;&gt;several levels of insensitivity from &amp;quot;Complete&amp;quot; to &amp;quot;Partial&amp;quot;&lt;/a&gt;. Complete insensitivity usually leads to fully feminine genitalia, while &amp;quot;Mild&amp;quot; or &amp;quot;Partial&amp;quot; can lead to partially or fully masculinized genitalia. Genitoplasty is an option for the latter cases.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;CAH&lt;/strong&gt; - congenital adrenal hyperplasia. This genetic disease causes the adrenal glands to produce excess androgens--the steroids that cause masculinization--a process that begins in the womb and can result in ambiguous genitals. However, CAH girls are generally more aggressive and display behavioral tendencies that more closely coincide with boys of the same age. &lt;strong&gt;Important to note: CAH children are genetically female (XX) and identify as female.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;An &lt;a href=&quot;http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1997-sex-reassignment.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;extensive review of gender reassignments in 1997&lt;/a&gt; had this to say about the consequences of surgically altering an infant's sex:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Considering this case follow-up, and as far as an extensive literature review can attest, there is no known case where a 46 chromosome, XY male, unequivocally so at birth, has ever easily and fully accepted an imposed life as an androphilic female regardless of the physical and medical intervention.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;HOWEVER&lt;/strong&gt; - as with all things scientific - there is dissent from the Johns Hopkins article above:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Preliminary analysis of the data, says Migeon, indicates that almost all of the patients are content with the gender in which they were raised. All but two showed a gender identity and gender role in accordance with their gender of rearing.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;There is significant divergence that has not been reconciled in any trustworthy article I could find. The modern practice is to raise the child as their genetic sex unless significantly afflicted.&lt;/p&gt;&#xA;&lt;p&gt;In adult transgender individuals, things like &lt;a href=&quot;http://en.wikipedia.org/wiki/Hormone_replacement_therapy_%28male-to-female%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hormone Replacement Therapy&lt;/a&gt; are part of a regime - along with surgery, acclimatization courses, and psychological evaluations - that can successfully result in a person presenting themselves and physically resembling another sex.&lt;/p&gt;&#xA;&lt;p&gt;With adequate surgery, hormone therapy, and proper treatment all-around, it is practically impossible to tell whether a person is transgender without getting invasive or performing genetic tests.&lt;/p&gt;&#xA;&lt;p&gt;As with all things that veer into a hazy area between medical knowledge (medical advice is &lt;em&gt;not&lt;/em&gt; allowed on this website) and human biology: &lt;em&gt;&lt;strong&gt;DO NOT&lt;/strong&gt; use the above information to diagnose yourself or anybody you know.&lt;/em&gt; &lt;em&gt;&lt;strong&gt;ONLY&lt;/strong&gt; a qualified medical professional can perform the necessary tests required and give a qualified interpretation of the results.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-04-28T03:08:02.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8115" PostTypeId="1" CreationDate="2013-04-28T04:14:58.300" Score="3" ViewCount="33022" Body="&lt;p&gt;The title is my question: what organs are absolutely needed (fatal if injured/removed) by the human body and perhaps animals in general?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not asking which organs are mechanically replaceable, but more what organs cannot be removed (and not replaced) in order to maintain human life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;--&lt;strong&gt;update&lt;/strong&gt;--&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To clarify the question, I'm wondering what organs when removed (and applied no medical intervention) would cause fatal effects in a short amount of time, or cause semi-fatal effects (ex. shortened lifespan). A list perhaps of importance, if possible, would be nice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;note: I have no medical knowledge so I'll leave 'short' open to interpretation.&lt;/p&gt;&#xA;" OwnerUserId="3462" LastEditorUserId="3462" LastEditDate="2013-04-30T00:39:44.253" LastActivityDate="2016-09-14T22:30:51.413" Title="What organs are absolutely needed by the human body?" Tags="&lt;human-biology&gt;&lt;zoology&gt;&lt;physiology&gt;" AnswerCount="3" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8118" PostTypeId="1" CreationDate="2013-04-28T08:12:07.473" Score="1" ViewCount="552" Body="&lt;p&gt;I understand that cone cells vary in the color they sense, is this because of wavelength, frequency, something else, or a combination of the previous? I also understand that tetrachromats can see an extended spectrum of color because they have four as opposed to three (for trichromats) color channels, hence, I believe, an extended variation of cone cells.&lt;/p&gt;&#xA;" OwnerUserId="3463" OwnerDisplayName="5ives" LastEditorUserId="3463" LastEditDate="2013-04-28T09:01:25.300" LastActivityDate="2013-06-27T12:43:08.103" Title="Why are trichromat cone cells unable to sense ultraviolet and infrared radiation?" Tags="&lt;vision&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8119" PostTypeId="2" ParentId="8118" CreationDate="2013-04-28T10:07:52.477" Score="1" Body="&lt;p&gt;The range of color perception in humans is primarily limited by the sensitivity of cone cells (specifically, the opsin proteins in cone cells) to various frequencies of light.  This sensitivity drops off at 700 nm on one side and 380 nm on the other, which is where infrared and ultraviolet begin, respectively.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even with hypothetical infrared or ultraviolet cones, we wouldn't necessarily be able to perceive color much further beyond our current range anyway.  The various parts of the eye (cornea, lens, and the liquid inside) block both ultraviolet (starting around 400 nm) and infrared (starting maybe at 1400 nm) beyond certain wavelenghts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Color_vision&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Color_vision&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tetrachromaticity, at least in humans, does NOT confer an extended spectrum of color perception.  Tetrachromaticity results from a mutation on one of the light sensing proteins, changing its peak sensitivity by a few nanometers. So a tetrachromat can't see beyond the normal color spectrum, but they can probably distinguish shades of green and blue more precisely than trichromats. This has been an area of active scientific research recently; I think most scientists didn't think they existed.  Now studies suggest they're 2-50% of the population.  Humans with 5+ cone types are also hypothesized, and with the ubiquity of genome sequencing I imagine we'll be learning a lot more about that soon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other species have more diverse color perception, with ultraviolet being especially common in insects and birds. The mantis shrimp has an astounding 16 different kinds of photo receptors, plus a few specialized eyes for detecting polarized light. For a loving account of mantis shrimp, I recommend this comic. &lt;a href=&quot;http://theoatmeal.com/comics/mantis_shrimp&quot; rel=&quot;nofollow&quot;&gt;http://theoatmeal.com/comics/mantis_shrimp&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3460" LastEditorUserId="3460" LastEditDate="2013-04-28T11:06:56.707" LastActivityDate="2013-04-28T11:06:56.707" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="8120" PostTypeId="2" ParentId="2893" CreationDate="2013-04-28T10:56:22.613" Score="4" Body="&lt;p&gt;This is almost more a philosophical question about how you would like to define helices and sheets, which I would argue is not so well defined.  shigeta mentions that they have well defined ramachandran coordinates, but that's for the central residues. Terminal residues are far more flexible. The more traditional definition is along the lines of the DSSP algorithm, i.e. what is their main-chain hydrogen bonding pattern. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The DSSP algorithm is a bit conservative about assignments, often leaving out the first and last residues in  both sheets and helices. In deposited structures, you can compare author annotations to DSSP and STRIDE and see the authors will often assign longer runs than either. And I have certainly seen structures where a residue is annotated as both, especially when it lies at the junction between two secondary structure elements. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at the structure, residues 254 and 255 are clearly hydrogen bonding into a beta-sheet on one side and an alpha helix on the other, so I see no reason they shouldn't be annotated into both.&lt;/p&gt;&#xA;" OwnerUserId="3460" LastEditorUserId="3460" LastEditDate="2013-04-30T00:03:48.943" LastActivityDate="2013-04-30T00:03:48.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8121" PostTypeId="2" ParentId="1602" CreationDate="2013-04-28T10:59:50.090" Score="1" Body="&lt;p&gt;You can try SB (sodium boric acid), LA (lithum acetate) or LB (lithium boric acid) buffers. Thex generate must less heat then TAE or TBE buffers and can be run on much higher voltages and are much cheaper than TAE or TBE. Also they do not interfere with standard applications such as band excision and they last longer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more info try this sites:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.fasterbettermedia.com/products.html&quot; rel=&quot;nofollow&quot;&gt;http://www.fasterbettermedia.com/products.html&lt;/a&gt;&#xA;&lt;a href=&quot;http://ddgehelp.blogspot.com/2008/01/alternative-electrophoresis-buffer-to.html&quot; rel=&quot;nofollow&quot;&gt;http://ddgehelp.blogspot.com/2008/01/alternative-electrophoresis-buffer-to.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1668" LastActivityDate="2013-04-28T10:59:50.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8122" PostTypeId="2" ParentId="1446" CreationDate="2013-04-28T11:35:26.357" Score="7" Body="&lt;p&gt;All of the above answers are great, and very informative.  But they are also &lt;em&gt;technically&lt;/em&gt; wrong, in certain conditions. Once you understand them, you'll be able to understand this explanation of why.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The canonical answer is that cones are used for color perception in bright light and rods are used in low light. But rods have a peak color sensitivity that is very distinct from the cones (see the chart posted above).  And more importantly, &lt;em&gt;there are light levels at which both rods and cones are equally functional for color perception&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is known as the &quot;Purkinje effect&quot; or &quot;Purkinje shift&quot;.  Basically, when light levels dim, your red color perception diminishes first, but your blue color perception is enhanced (or at least doesn't diminish nearly as fast).  The specific effect is that red objects get darker much faster than blue ones. But the brain isn't yet just perceiving the blue objects as a brighter gray, so it seems there is some color perception built into the brain based on the rods. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Purkinje_effect&quot;&gt;http://en.wikipedia.org/wiki/Purkinje_effect&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-04-28T11:35:26.357" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8123" PostTypeId="1" CreationDate="2013-04-28T16:07:50.667" Score="21" ViewCount="32437" Body="&lt;p&gt;It may seem obvious to us humans to hide our excreta, but this is not quite normal behavior for animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, dogs have the habit to pee all over the place. It's know that they do so to mark their territory. So when they want to mark their territory, why do they cover up their poop?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found an &lt;a href=&quot;http://hinessight.blogs.com/hinessight/2009/03/do-dogs-try-to-cover-or-spread-their-poop.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;old web article&lt;/a&gt; where someone asks the same question, without getting a credible answer. He quotes a Yahoo Answers &lt;a href=&quot;http://answers.yahoo.com/question/index?qid=20080424192530AAfTEcK&quot; rel=&quot;nofollow noreferrer&quot;&gt;answer&lt;/a&gt; making the following claim:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This behavior is natural in dogs. They cover up their &quot;waste&quot; so that&#xA;  an enemy does not find them, from the scent of the poop or pee. It is&#xA;  an instinct handed down from wolves, who hid their scent by covering&#xA;  up their feces in leaves, sticks, soil, or other nearby natural&#xA;  materials. They also rolled in animal carcasses to hide the scent of&#xA;  them. Your dog is just using her natural instinct to protect herself&#xA;  from predators.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Another things that dogs do, called marking, is when the dog pees in a&#xA;  certain area. They do not cover it up, as it is marking a territory as&#xA;  their own. Male dogs usually do this on trees, wooden posts,&#xA;  furniture, and other things. Female dogs do this in heat. Dogs do not&#xA;  poop to mark something, only pee. When you dog pees or poops and then&#xA;  covers it up, this does not mean she is marking her territory. Just&#xA;  wanted to add it so you don't get confused. :)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I find it hard to believe these two opposite claims. One time dogs want to mark their territory and the other time it's scared from predators. I know many dogs that do not cover their pee, but do cover their poop, sometimes even within the same walk (and so the same territory).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is true, why do dogs do both in the same walk? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On Wiki Answers I found &lt;a href=&quot;http://wiki.answers.com/Q/Why_do_dogs_cover_their_pee_and_poop&quot; rel=&quot;nofollow noreferrer&quot;&gt;this answer&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The animals are not actually covering up the pee or pooh but spreading&#xA;  their scent. This often happens with animals that are dominant (for&#xA;  instance show dogs).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's so that dogs never actually cover their poop anymore, they only perform some random scratches, throwing a little sand on the turd, sometimes even nothing. That fact makes this answer quite more likely than the previous one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another take that's similar to the previous one is &lt;a href=&quot;http://blogs.dogster.com/dog_tip_of_the_day/2008/10/21/dog-tip-why-do-dogs-scratch-the-ground-after-they-do-the-doo/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this one&lt;/a&gt; from Dogster:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So, why do dogs scratch with their hind legs after defecating? You&#xA;  might think the dog is trying to cover up his poop like a cat does,&#xA;  but it’s actually a way to mark territory, with the scratch marks in&#xA;  the ground pointing to the scent the dog has left.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I also found &lt;a href=&quot;http://www.ehow.com/about_6620614_do-scratch-ground-after-defecating_.html#ixzz2Rm5BDGql&quot; rel=&quot;nofollow noreferrer&quot;&gt;an eHow article&lt;/a&gt; on this subject. It seems to agree with the previous two explanations, but is more detailed.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is normal for dogs of both sexes to vigorously kick the ground with&#xA;  their hind legs after defecating. This is called scraping or peeling&#xA;  out. Some dogs will also do it after urinating. Dogs are descended&#xA;  from wolves, which also perform this behavior. It is not a bad habit,&#xA;  but a vital part of a dog leaving a visual message and scent message&#xA;  to any other dogs that happen to pass by.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They also say that the specific reason why they spread scent with their paws is because paws just contain a lot of scent.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dog paws contain scent glands. There are also glands in between the&#xA;  toes. The action of scraping the paws against the ground helps release&#xA;  the scent inside of the glands. Dogs scrape the ground in order to&#xA;  increase their scent on the area near the feces pile, according to&#xA;  veterinarian Dr. Justine Lee. Before domestication, dogs wandered in&#xA;  large territories. One vital way to communicate with other wandering&#xA;  dogs is through scent marking. This instinct has not been bred out of&#xA;  the domestic dog.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, which theory is the most valid? I tent to go for the scent one. Any additions?&lt;/p&gt;&#xA;" OwnerUserId="1224" LastEditorUserId="1224" LastEditDate="2017-06-24T14:52:19.113" LastActivityDate="2017-06-24T14:52:19.113" Title="Why do dogs try to cover their poop?" Tags="&lt;behaviour&gt;&lt;dogs&gt;&lt;excreta&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8124" PostTypeId="1" CreationDate="2013-04-28T16:08:42.270" Score="3" ViewCount="221" Body="&lt;p&gt;I'm reading this article on&lt;a href=&quot;http://med.stanford.edu/ism/2009/october/glucocorticoids.html&quot; rel=&quot;nofollow&quot;&gt;blood sugar and circadian rhythms&lt;/a&gt; and the following question popped into my head: a lot of articles mention various diurnal or circadian rhythmicity of biological processes. &lt;strong&gt;Is there a &quot;master&quot; list of hormones, gene expressions and other processes that the modern science recognizes as &quot;circadian&quot;?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, is there something that can give reader a clear picture of what's happening at a certain (biological)time for a human and is expected to happen tomorrow at similar time?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be great to take a look at such list and see what are the major processes that recur on a time-sensitive basis in humans.&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-04-29T01:09:37.203" Title="Is there a comprehensive list of human circadian-like processes, hormones or gene expressions?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8125" PostTypeId="2" ParentId="8081" CreationDate="2013-04-28T23:13:48.973" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.ted.com/talks/kees_moeliker_how_a_dead_duck_changed_my_life.html&quot; rel=&quot;nofollow&quot;&gt;Here's a Ted talk about a case of homosexual necrophilia in mallard duck&lt;/a&gt;. The speaker lists a few other examples of weird animal mating (frog with a fish). Apparently animals may have non-traditional preferences as well as humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The talk does not deal with whether this is a pathology or not, just lists a few weird examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, there's this section on &lt;a href=&quot;http://en.wikipedia.org/wiki/Hypothalamus#Sexual_dimorphism&quot; rel=&quot;nofollow&quot;&gt;sexual dimorphism of hypothalamus&lt;/a&gt;, which does mention pathology of hypothalamus. The statement below lacks a proper citation at the time of this writing, so it may be incorrect:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If a female rat is injected once with testosterone in the first few&#xA;  days of postnatal life (during the &quot;critical period&quot; of sex-steroid&#xA;  influence), the hypothalamus is irreversibly masculinized; the adult&#xA;  rat will be incapable of generating an LH surge in response to&#xA;  estrogen (a characteristic of females), but will be capable of&#xA;  exhibiting male sexual behaviors (mounting a sexually receptive female&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="577" LastEditorUserId="1590" LastEditDate="2013-07-31T07:43:50.500" LastActivityDate="2013-07-31T07:43:50.500" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8126" PostTypeId="2" ParentId="8124" CreationDate="2013-04-29T01:09:37.203" Score="2" Body="&lt;p&gt;There isn't a central/master website that I'm aware of, as it's still an area of active research.  I did a bit of work in the field about 10 years ago, and at that point we were still working out the circadian rhythms in the yeast mating cycle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since then, the field been enumerating more and more involved processes: mRNA expression, mRNA degradation, micro RNA, mRNA transport and translational regulation, then protein translation and protein regulation... Given that any single gene can be regulated at one or more of these points, and that there are at least a few different circadian cycles and they can even conflict... well, it's a bit of a mess.  Oh, and don't forget that different organs and cell types have different responses, so then you have to cross check 50 cell types. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd start with this review paper, which can give you an idea of what kinds of papers to search for.  If you decide you want to know about individual genes, a lot of scientists in the field have made their datasets available online in various gene expression databases.  There are several databases running currently, and maybe one of them will be specialized in circadian expression.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Circadian topology of metabolism&#xA;Joseph Bass&#xA;Nature 491, 348–356 (15 November 2012) doi:10.1038/nature11704&#xA;Published online 14 November 2012&#xA;&lt;a href=&quot;http://www.nature.com/nature/journal/v491/n7424/full/nature11704.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nature/journal/v491/n7424/full/nature11704.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-04-29T01:09:37.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8127" PostTypeId="1" AcceptedAnswerId="8131" CreationDate="2013-04-29T02:16:15.843" Score="5" ViewCount="973" Body="&lt;p&gt;It's my understanding that various hazards can damage the DNA in our cells, causing mutations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But whenever I picture this, I see the damage being done to one of our tissues (for example, our lungs due to smoking, or our skin due to UV rays).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I think about this, I see that... many cells in a smoker's lungs, or many cells on the back of a beach-goer's neck, may have mutations in their DNA. But &lt;em&gt;only&lt;/em&gt; the cells in that tissue have these mutations... the other cells in our body would not have the same mutations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, sperm and egg cells would not have the same mutations, so the mutations due to smoking and UV rays shouldn't pass on to children.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there instances where mutations that occur over the course of our life are spread to every cell, including sperm and egg cells, so that every cell reflects the mutation, and the mutation is passed onto our offspring?&lt;/p&gt;&#xA;" OwnerUserId="3474" LastActivityDate="2013-04-30T11:43:03.447" Title="How do mutations come to be shared by all cells?" Tags="&lt;genetics&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8128" PostTypeId="1" CreationDate="2013-04-28T17:12:17.000" Score="12" ViewCount="23192" Body="&lt;p&gt;I have always thought darker colors absorb more heat from the sun, so if you are wearing a white T-shirt you will be cooler under sun than wearing a darker T-shirt, or a black piece of steel will be hotter under the sun than a shiny silvery one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is true, then why is the same not applicable to skin color? It seems to me like the more sun in an area the darker the people's skin has become, isn't that the case? &lt;/p&gt;&#xA;" OwnerDisplayName="user893730" LastEditorUserId="3971" LastEditDate="2013-08-29T14:42:47.643" LastActivityDate="2019-04-24T10:37:26.013" Title="Does darker skin color make it easier to live under sun?" Tags="&lt;biophysics&gt;&lt;pigmentation&gt;" AnswerCount="5" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8129" PostTypeId="2" ParentId="8128" CreationDate="2013-04-28T20:29:50.870" Score="0" Body="&lt;p&gt;I think that you'll need a biologist to answer your question fully. However, I can try to explain what I can in terms of physics. Generally, the darker a material is, the greater the range of wavelengths of light it absorbs. With what is perceived as a perfectly black material by a human reflecting no wavelengths of the visible light spectrum of electromagnetic radiation at all. Therefore it would be logical that in cold climates humans would have darker skin colors in order to absorb a greater range of wavelengths of light. Although at first glance this seems the correct way for humans, and in fact all organisms to evolve, it's obviously not the case. There must be other underlying reasons that have caused organisms to evolve the way they do. An interesting example of how nature seems to defy this is leaves. One would think that the chloroplasts that make up leaves should be black in order to absorb sunlight as efficiently as possible. As we know, this isn't the case.&lt;/p&gt;&#xA;" OwnerDisplayName="Cheema" LastActivityDate="2013-04-28T20:29:50.870" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8130" PostTypeId="2" ParentId="8128" CreationDate="2013-04-29T08:00:25.920" Score="12" Body="&lt;p&gt;It isn't about heat but ultraviolet light. Melanin is the pigment that makes our skin colour whatever it is and in darker skin there's more melanin. Melanin dissipates UV, which otherwise would cause skin cancer as it introduces mutations into DNA. Melanin production is stimulated by UV so that's why tanning beds work, our body senses the danger and responds by making our skin darker. Yes this makes us hotter but that's a small price to pay, melanin needs to be dark to do its job well. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-04-29T08:00:25.920" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8131" PostTypeId="2" ParentId="8127" CreationDate="2013-04-29T08:20:03.447" Score="6" Body="&lt;p&gt;Goods question! Only mutations that occurred when we were in the early stages of development will affect all cells. That's why pregnant mothers shouldn't smoke. The reason for this is that one cell goes on to divide and become all our cells so any mutations in that cell are passed on to cells formed when it divides. That same principle explains your smoker example. In the lung we have two types of cells which are called Type 1 and Type 2. Type 1 cells are constantly dying as they get old and they get replaced by type 2 cells whose job it is to divide continuously to replace Type 1 cells. So we have lots of type 1 and few type 2. When type 2 divide they make one type 1 cell and one type 2 cell, so type 2 cells never run out. If smoke causes a mutation in type 1 cells generally they're okay because they'll die before enough mutations occur. Of course something that causes lots of mutations could make it cancerous before it dies but that's rare. Now if it occurs in Type 2 cells every subsequent type 1 or type 2 cell that cell makes is mutated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The last thing you mentioned are mutations that occur to eggs and sperm. When making sperm you have the same as above. One cell makes sperm and a sperm maker cell. The sperm is like type 1 cells and the sperm maker cell is like type 2. So mutations affect them as they do above, where a mutation in a sperm maker cell is way worse. As for eggs women are born with all the eggs they'll ever have and there's no egg maker cells. So mutations just occur, and the older women are the more mutations. That's why the older a mother is the much higher risk of genetic diseases like downs. But an older man only has a slight increase in risk. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations that affect eggs and sperm tend to be really harmful, as they affect every cell, so these cells or &quot;babies&quot; die before the mother even realises she's pregnant or as a miscarriage. I've not given the scientific names for things but if you request them, I'll give you the real names, but hope you enjoy the principles. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="806" LastEditDate="2013-04-30T11:43:03.447" LastActivityDate="2013-04-30T11:43:03.447" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8132" PostTypeId="2" ParentId="8115" CreationDate="2013-04-29T08:27:43.040" Score="7" Body="&lt;p&gt;You can't remove most organs. The heart, lungs and brain are the ones that without you'll die in seconds. The rest you'll live a few hours or more. All depends how long you wish to live. The best way to see which organs are most required is to look at the order organs are shut down when there isn't enough oxygen or blood. That tells you which area most and least important.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-04-29T08:27:43.040" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8133" PostTypeId="1" AcceptedAnswerId="8135" CreationDate="2013-04-29T09:07:42.233" Score="1" ViewCount="68" Body="&lt;p&gt;Is it possible to use a biologically active Telemorease Elongation Reverse Transcriptase (TERT) in the place of the Reverse Transcriptase (RT) for quantitative Reverse Transcriptase pcr (qRT-pcr)? Yes I do know that it would seemingly have no advantages. What kind of reverse transcriptase is used in qRT-pcr is there a standard like taq dna pol is used for qpcr?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2013-04-29T09:22:35.947" Title="qTERT-pcr like qRT-pcr" Tags="&lt;pcr&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8134" PostTypeId="2" ParentId="8115" CreationDate="2013-04-29T09:11:47.517" Score="3" Body="&lt;p&gt;There is a list of &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Organ_%28anatomy%29#Vital_organs&quot; rel=&quot;nofollow&quot;&gt;vital organs&lt;/a&gt;&quot; on which there is a consensus that if such organs are removed, the body dies within hours/minutes. Yet people can live long with only one lung or one kidney.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another list could include other organs that are semi-vital: we could live for a relatively long period without them, but their absence has to be compensated with a continuous treatment (pancreas, thyroid, etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In contrast, people can live in &quot;good health&quot; with non-vital organs removed such as legs, eyes, teeth...&lt;/p&gt;&#xA;" OwnerUserId="3394" LastActivityDate="2013-04-29T09:11:47.517" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8135" PostTypeId="2" ParentId="8133" CreationDate="2013-04-29T09:22:35.947" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;What kind of reverse transcriptase is used in qRT-pcr is there a standard like taq dna pol is used for qPCR&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;M-MuLV (Monoley murine leukemia virus) reverse transcriptase&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some RT enzymes are engineered to remove the RNAseH domain so that template RNA persists for more rounds of RT.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is it possible to use a biologically active Telemorease Elongation Reverse Transcriptase (TERT) in the place of the Reverse Transcriptase&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Perhaps it can catalyse an RT reaction in-vitro. But commercial enzymes need to be efficient and I think using TERT won't be that advantageous. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-29T09:22:35.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8136" PostTypeId="1" AcceptedAnswerId="8167" CreationDate="2013-04-29T12:25:51.210" Score="2" ViewCount="88" Body="&lt;p&gt;I am using PyMol to visualize .pdb protein structures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I show/hide representation a lot, and sometimes I get confused with what representations are currently displayed. So I end up with doing a lot of hides (basically trying to hide each representation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a command which shows me what representations are currently used.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance if I have used&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;show ribbon&#xA;show lines&#xA;show mesh&#xA;hide lines&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and than use some sort of &lt;code&gt;showRepresentation&lt;/code&gt;&#xA;it will return me &lt;code&gt;ribbon, mesh&lt;/code&gt;&lt;/p&gt;&#xA;" OwnerUserId="3476" LastEditorUserId="43" LastEditDate="2013-05-01T12:11:21.697" LastActivityDate="2013-05-01T12:11:21.697" Title="Is there a way to see what representations are currently displayed in PyMOL?" Tags="&lt;bioinformatics&gt;&lt;structural-biology&gt;&lt;pymol&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8137" PostTypeId="1" AcceptedAnswerId="8143" CreationDate="2013-04-29T12:42:53.113" Score="2" ViewCount="728" Body="&lt;p&gt;I've read multiple descriptions of biological/circadian clocks and they all mention PER, CRY and CLOCK genes. While I kinda get how they are connected, what interests me is how these actually regulate each other. &lt;strong&gt;Do these genes encode proteins that once created bind to the DNA and cover the transcription sites for other genes&lt;/strong&gt;(like PER protein covering the binding site of CRY)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lot of diagrams and descriptions of the process are very complex, and I would appreciate a simple answer (if it exists).&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-04-30T04:30:20.700" Title="What is the mechanism of regulation of PER /CRY genes?" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8139" PostTypeId="1" AcceptedAnswerId="8144" CreationDate="2013-04-29T14:53:34.910" Score="11" ViewCount="32446" Body="&lt;p&gt;They all seem to describe molecules of similar function and many people seem to use them interchangeably.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also please include any other similar molecules if I've forgotten any in the list above.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="3059" LastEditDate="2013-04-29T16:53:02.747" LastActivityDate="2015-07-14T20:35:58.877" Title="What is the distinction between chemokines, cytokines, interferons and interleukins?" Tags="&lt;cell-biology&gt;&lt;immunology&gt;&lt;terminology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8140" PostTypeId="1" AcceptedAnswerId="8168" CreationDate="2013-04-29T16:48:08.473" Score="2" ViewCount="1993" Body="&lt;p&gt;I've been tasked with using DTNB to find the number of thiol groups on a molecule of Bovine Serum albumin (BSA). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After measuring the absorbance, finding the concentration of TNB and calculating the concentration of the BSA, I've come out with a result of around 0.4 free thiol groups per molecule of BSA, which seems unlikely! There is either a free group or there isn't!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet, the implication from the demonstrator is that is is the correct result!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can this be? Is it possible to get a value of less than one in an experiment like this?&lt;/p&gt;&#xA;" OwnerUserId="1474" LastActivityDate="2015-11-06T21:09:22.513" Title="Using DTNP to find free thiol groups on a protein" Tags="&lt;proteins&gt;&lt;protocol&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8141" PostTypeId="1" AcceptedAnswerId="8156" CreationDate="2013-04-29T17:24:07.807" Score="2" ViewCount="880" Body="&lt;p&gt;If I stare at an object for a long time and close my eyes, at first I can still see the object with my eyes closed. But the image I see with my eyes closed is inverted: dark colors appear as light and light colors appear as dark. Why is that?&lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-04-30T11:06:06.823" Title="Why do I see an inverted image of an object when I close my eyes?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8142" PostTypeId="1" AcceptedAnswerId="8150" CreationDate="2013-04-29T18:17:15.990" Score="9" ViewCount="1951" Body="&lt;p&gt;Peach, pear, apple, cherry, and many other fruit trees seem to have flowers comprised of five petals. Assuming there is no evolutionary advantage to confusing students of trees, is there a plausible reason (evolutionary or otherwise) the morphology is so regimented? Are the trees related? Do they like the same pollinators? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any insight.  &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="-1" LastEditDate="2013-05-01T00:18:02.950" LastActivityDate="2016-05-08T14:29:32.773" Title="Why do many fruit trees have five-petaled flowers?" Tags="&lt;phylogenetics&gt;&lt;plant-anatomy&gt;&lt;botany&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8143" PostTypeId="2" ParentId="8137" CreationDate="2013-04-29T20:22:00.783" Score="2" Body="&lt;p&gt;Wikipedia gives a very good explanation of this, on the page for the suprachiasmatic nucleus.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For example, in the fruitfly Drosophila, the cellular circadian rhythm&#xA;  in neurons is controlled by two interlocked feedback loops.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In the first loop, the bHLH transcription factors clock (CLK) and&#xA;  cycle (CYC) drive the transcription of their own repressors period&#xA;  (PER) and timeless (TIM). PER and TIM proteins then accumulate in the&#xA;  cytoplasm, translocate into the nucleus at night, and turn off their&#xA;  own transcription, thereby setting up a 24-hour oscillation of&#xA;  transcription and translation. In the second loop, the transcription&#xA;  factors vrille (VRI) and Pdp1 are initiated by CLK/CYC. PDP1 acts&#xA;  positively on CLK transcription and negatively on VRI. These genes&#xA;  encode various transcription factors that trigger expression of other&#xA;  proteins. The products of clock and cycle, called CLK and CYC, belong&#xA;  to the PAS-containing subfamily of the basic helix-loop-helix (bHLH)&#xA;  family of transcription factors, and form a heterodimer. This&#xA;  heterodimer (CLK-CYC) initiates the transcription of PER and TIM,&#xA;  whose protein products dimerize and then inhibit their own expression&#xA;  by disrupting CLK-CYC-mediated transcription. This negative feedback&#xA;  mechanism gives a 24-hour rhythm in the expression of the clock genes.&#xA;  Many genes are suspected to be linked to circadian control by &quot;E-box&#xA;  elements&quot; in their promoters, as CLK-CYC and its homologs bind to&#xA;  these elements.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The 24-hr rhythm could be reset by light via the protein cryptochrome&#xA;  (CRY), which is involved in the circadian photoreception in&#xA;  Drosophila. CRY associates with TIM in a light-dependent manner that&#xA;  leads to the destruction of TIM. Without the presence of TIM for&#xA;  stabilization, PER is eventually destroyed during the day. As a&#xA;  result, the repression of CLK-CYC is reduced and the whole cycle&#xA;  reinitiates again. (&lt;a href=&quot;http://en.wikipedia.org/wiki/Suprachiasmatic_nucleus#Fruitfly&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Suprachiasmatic_nucleus#Fruitfly&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The suprachiasmatic nucleus (SCN) is a tiny part of our brain residing in the center. It maintains a biological clock through a gene expression cycle in the individual neurons. The mechanism for humans is very similar to the mechanism for fruit flies, as explained above, but to rehash a bit...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the fruit fly model there are five players: CLK, CYC, PER, TIM, CRY.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CLK and CYC are transcription factors for PER and TIM, and bind to their promoters in order to activate the expression of PER and TIM.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the expression level of PER and TIM gets very high, the PER and TIM proteins return to the nucleus, and inhibit their own transcription factors (CLK and CYC) through molecular interactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The CRY protein is light-sensitive, and so daylight (or artificial light) will cause CRY to destroy the TIM proteins. Without TIM, we no longer get the PER-TIM dimers that inhibit the CLK-CYC transcription factors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In humans and other mammals it's the same concept, but with slightly different players (e.g., homologous genes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's important here is that we have a biological clock on the cellular level. We haven't gone into how this clock is used yet... But, it's my understanding that the SCN uses the information to tell the pineal gland when to produce melatonin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The melatonin causes us to be drowsy, lowers our body temperatures, and causes us to fall asleep.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see another cycle at work here - our body temperature, which rises with wakefulness, and declines with sleep. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This gives a more general answer to how circadian rhythms are used to influence our sleep cycle. Your question was how the genes involved in circadian rhythms regulate each other. The answer is the transcription-translation negative feedback loop described above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps...&lt;/p&gt;&#xA;" OwnerUserId="3474" LastEditorUserId="3474" LastEditDate="2013-04-30T04:30:20.700" LastActivityDate="2013-04-30T04:30:20.700" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8144" PostTypeId="2" ParentId="8139" CreationDate="2013-04-29T20:41:07.250" Score="6" Body="&lt;p&gt;Cytokines is the general class of molecules to which chemokines, interferons, interleukins and others belong. Biologists dispute whether something is a hormone or a cytokine, but generally the consensus goes with if it's to do with immunology it's a cytokine or if the resting concentration is in the picomolar range, but that's a very rough distinction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chemokines are molecules that drive cellular chemotaxis. That means they make cells move towards a desired place. Generally chemokines refer to immune cells and there's loads and loads of them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interleukins are anything which are messenger molecules between immune cells (inter- means between and -leukins means leukocytes/white blood cells). They're typically denoted by IL + number. However the interferon and tumour necrosis families come under interleukins too in most people's opinion. The interferons are a special group that typically inhibit viruses by making cells non-permissible to viral replication. They also do a few other things like activate macrophages or promote Th1 response, which both also interfere with viruses but there is bacterial overlap. The TNF family is a bit weirder as some are interleukin-like but others aren't as much. TNF-alpha (the classic one) is involved in macrophage maturation. However not all interleukins are strictly between white blood cells, as IL1 acts on the hypothalamus among other leukocytes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See the problem is everything is a bit grey because most cytokines (if not all) have more than one role and there's never consensus in the world of immunology when it comes to cytokines because more and more keeps getting discovered. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1757" LastEditDate="2013-04-29T20:55:34.793" LastActivityDate="2013-04-29T20:55:34.793" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8145" PostTypeId="2" ParentId="2422" CreationDate="2013-04-29T21:05:18.223" Score="2" Body="&lt;p&gt;There's two phases of a menstrual cycle, before ovulation known as the follicular phase and after ovulation known as the luteal phase. The second phase is not very variable, it's the same length almost always as it is governed by how long the corpus luteum (remnants of the follicles after the ovum bursts out) survives. The first part is variable and is what causes periods to be irregular. In this phase the eggs mature. The body picks several eggs to mature but only one will &quot;win&quot;. However, how fast it wins changes. It all depends on how fast it grows and much it manages to suppress growth of the other eggs and that in turn depends on the quality of the egg. But then this also branches out, as it is controlled by levels of hormones this is heavily affected by stress and diet among other things. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's unfortunate that the first phase is variable otherwise knowing which day you were going to ovulate would be easy.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-04-29T21:05:18.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8146" PostTypeId="2" ParentId="6926" CreationDate="2013-04-29T21:14:38.650" Score="1" Body="&lt;p&gt;Upper bound of HDL doesn't really exist. The greeks are known for their incredibly high levels of HDL and the so called mediterranean diet/genetics combination that causes this is only beneficial to health (supposedly - although never been proven that incredibly high HDL levels are beneficial, they're just not harmful). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for too low LDL levels/cholesterol levels - that's interesting. Unfortunately it isn't possible because any mutations that caused this would be fatal, cholesterol makes up an essential part of cell membranes etc. That's why our body makes our own. A mutation preventing this would not even manifest. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-04-29T21:14:38.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8147" PostTypeId="2" ParentId="5125" CreationDate="2013-04-29T21:22:29.960" Score="3" Body="&lt;p&gt;Balance is mediated by 3 things: the cerebellum, vision and the ear via the semicircular canal + vestibular nerve (i.e. the ear).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sleepwalkers lack the visual feedback, but they have a functional cerebellum and semicircular system which is sufficient. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for waking up and feeling disorientated, if that's when you get up fast that's because your semicircular system hasn't yet reset (as well as your blood pressure has just dipped). &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-04-29T21:22:29.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8148" PostTypeId="2" ParentId="7748" CreationDate="2013-04-29T21:25:53.990" Score="3" Body="&lt;p&gt;Although I'm not sure, here's a working theory. The tear collection ducts feed into the nose. That's why when you cry you have a runny nose. When you pluck nose hairs you irritate the nasal mucosa, so that causes a reflex which attempts to flush out whatever might be causing a problem.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-04-29T21:25:53.990" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8150" PostTypeId="2" ParentId="8142" CreationDate="2013-04-29T22:01:49.993" Score="12" Body="&lt;p&gt;Peach, apricot, plum, pear, apple, cherry trees are plants of the same family, &lt;a href=&quot;https://en.wikipedia.org/wiki/Rosaceae&quot;&gt;Rosaceae&lt;/a&gt;, so they are closely related. They share many more aspects than the five petals. In fact, other plants in this family, and even many other dicots have five petal, simply because their share a common ancestry.&lt;/p&gt;&#xA;" OwnerUserId="3394" LastActivityDate="2013-04-29T22:01:49.993" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8152" PostTypeId="2" ParentId="5486" CreationDate="2013-04-30T00:46:38.420" Score="1" Body="&lt;p&gt;Scientists are recently finding (or coming to accept the notion) that, at least in eukaryotes, mRNA expression is poorly correlated to protein expression. There are several factors influencing translation regulation, such as siRNA or microRNAs, sequestering mRNAs while they are transported to various cell compartments, and others.  Even after the protein is made, there can be factors interfering with your expression reporter.  And as you mention, it may be degraded faster than you expect.  Cells try to keep proteins at certain expression levels, so if IL-1b is promoting expression without inhibiting the degradation pathway, degradation might kick into overdrive to bring the levels back down to normal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trying some protease inhibitors is worth a shot, since it's pretty simple by itself.  It should also increase your protein expression regardless of whether protein degradation is your limiting factor. If this doesn't work, or if it's prohibitively expensive to be sacrificing mice while you're working out a protocol (and is usually is), then I would turn to cell cultures and try and discern where you're getting blocked.  That kind of information will generally make a decent PNAS paper by itself. &lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-04-30T00:46:38.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8153" PostTypeId="1" AcceptedAnswerId="8157" CreationDate="2013-04-30T02:39:41.147" Score="5" ViewCount="260" Body="&lt;p&gt;I'm reading &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC509173/pdf/10111227.pdf&quot; rel=&quot;nofollow&quot;&gt;this fantastic article on estimating body time: Molecular-timetable methods for detection of body&#xA;time and rhythm disorders from single-time-point&#xA;genome-wide expression profiles&lt;/a&gt; and one of the things that is not very clear to me is how the researchers estimated which genes are expressed and which ones are not:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Total RNA was prepared by using Trizol reagent (GIBCOBRL). cDNA&#xA;  synthesis and cRNA labeling reactions were performed as described (5).&#xA;  Affymetrix high- density oligonucleotide arrays (Murine Genome Array&#xA;  U74A, Version 1.0, measuring 9,977 independent transcripts) were&#xA;  hybridized, stained, and washed according to the Technical Manual&#xA;  (Affymetrix). Affymetrix software was used to deter- mine the average&#xA;  difference (AD) between perfectly matched probes and&#xA;  single-base-pair-mismatched probes. The AD of each probe was then&#xA;  scaled globally so that the total AD of each microarray was equal. &lt;strong&gt;The&#xA;  resulting AD values reflect the abundance of a given mRNA relative to&#xA;  the total RNA popu- lation and were used in all subsequent analyses&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm not sure if I'm reading this correctly - did the researchers look at all RNA available in the cells and calculated the levels of messenger RNA produced by expressed genes? if not, how can the level of expression of a gene be estimated?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="3340" LastEditDate="2013-04-30T20:46:49.597" LastActivityDate="2013-04-30T23:27:49.960" Title="How is gene expression estimated?" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;experimental-design&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8154" PostTypeId="1" CreationDate="2013-04-30T02:56:03.797" Score="5" ViewCount="58" Body="&lt;p&gt;I found this article on &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC509173/pdf/10111227.pdf&quot;&gt;estimating body time using molecular timetable of 168 genes&lt;/a&gt;. researchers looked at gene expressions and plotted them to 24 hour cosines curve with some pretty spectacular results. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately the techniques discussed required sampling of liver cells, which may be invasive. &lt;strong&gt;Are there non- invasive methods of estimating body time/ biological clock/ circadian rhythm time?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of body time: at 8:00 real time, a mouse may exhibit gene expressions more appropriate for 9:30, so the body time of the mouse is 9:30.&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-09-29T15:33:39.463" Title="What non invasive methods of estimating Body Time are there?" Tags="&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8155" PostTypeId="1" CreationDate="2013-04-30T04:36:56.480" Score="2" ViewCount="427" Body="&lt;p&gt;It's embarrassing for me to ask this but well such is life. &lt;a href=&quot;http://pdsp.med.unc.edu/pdsp.php?&quot; rel=&quot;nofollow noreferrer&quot;&gt;NIMH Psychoactive Drug Screening Program (PDSP) Ki Database&lt;/a&gt; is mentioned as the source of the average binding affinity (K&lt;sub&gt;i&lt;/sub&gt;) values given in &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0071624422&quot; rel=&quot;nofollow noreferrer&quot;&gt;Goodman and Gilman&lt;/a&gt; but whenever I try to, in some way, confirm that these values are averages obtained from PDSP I get values that are way (up to 10,000 fold) off the values given in Goodman and Gilman. (ps. I am a mathematician too so I know how to take an average, $\bar{x} = \frac{\sum_i^n x_i}{n}$ so you don't need to hold my hand through the calculation with something as simple as the conventional definition of averages) Therefore I have reached the conclusion that I must be doing the calculations wrong. Please show me how to do them correctly. Here's a screenshot of exactly what Goodman and Gilman says that's confusing me:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OAjiS.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/zYSvF.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oh and yes I am using just the cloned human transporter values not just all the stuff that comes up. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-04-30T05:41:58.820" LastActivityDate="2013-06-12T07:30:02.437" Title="How do you average Ki values?" Tags="&lt;pharmacology&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8156" PostTypeId="2" ParentId="8141" CreationDate="2013-04-30T05:15:01.037" Score="2" Body="&lt;p&gt;I think it is because of &lt;a href=&quot;http://en.wikipedia.org/wiki/Adaptation_%28eye%29&quot; rel=&quot;nofollow&quot;&gt;light adaptation&lt;/a&gt;. The rods that are perceiving strong light, downregulate their response. But when the light is suddenly withdrawn then the rods that are adapted to perceive bright light cannot immediately sense dim light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two forms of adaptation- fast and slow. The fast one is Ca²⁺ dependent- decrease in Ca causes cGMP to increase which in turn depolarizes the cell. Calcium modulates this process by other means also. This &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11815664&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; suggests that slow adpatation is  because of an allosteric binding of cGMP on transducin-phosphodiesterase complex, which stabilizes this transition state and delays the signaling. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adaptation can also happen because of photobleaching of rhodopsin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know how an image &lt;strong&gt;&quot;remains&quot;&lt;/strong&gt; in the eye for a while. I believe it is because of asymmetric slow light adaptation between different spatially distributed rods(some rods take a while to readapt to dim conditions).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similar effect you can feel with colour vision also. You keep staring at green for a while, then when you see something else it appears reddish. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-04-30T11:06:06.823" LastActivityDate="2013-04-30T11:06:06.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8157" PostTypeId="2" ParentId="8153" CreationDate="2013-04-30T05:40:15.103" Score="7" Body="&lt;p&gt;The technique described here is called microarray. Your question has given me an opportunity to put forth one of my opinions about certain problems of gene expression studies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gene expression is a measure of the activity of any gene. If the gene performs its activity in the form of a protein, then its expression should be a measure of the protein. If a gene makes a non-coding RNA then its expression is a measure of the RNA concentration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;[You can omit the cases of post-translational modification because of signal transduction. They are highly expressed and transiently but frequently used. ]&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like your example there are many studies which use mRNA concentration as a proxy for protein activity. This proxy works in many cases because transcriptional gene regulation is more frequently used mechanism for imparting stable changes. But the best strategy would always be to measure the proteins also. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from microarray there are several techniques to measure RNA concentration:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;RNA sequencing (high throughput)&lt;/li&gt;&#xA;&lt;li&gt;Real-Time PCR (medium throughput)&lt;/li&gt;&#xA;&lt;li&gt;Northern Blotting (Low throughput, semi-quantitative)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Many techniques exist for measuring proteins also:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mass spectrometry (high throughput)&lt;/li&gt;&#xA;&lt;li&gt;ELISA (Low throughput, quantitative)&lt;/li&gt;&#xA;&lt;li&gt;Western blotting (Low throughput, semi-quantitative)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Usually the &lt;strong&gt;&quot;proxy method&quot;&lt;/strong&gt; is used because protein quantification is comparatively more difficult. Antibody based techniques like ELISA and Western blotting have problems of cross comparison of proteins because of the variability of the antibody binding efficiency. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-04-30T05:40:15.103" CommentCount="16" ContentLicense="CC BY-SA 3.0" />
  <row Id="8160" PostTypeId="1" AcceptedAnswerId="8162" CreationDate="2013-04-30T14:31:38.847" Score="9" ViewCount="3846" Body="&lt;p&gt;I have been trying to learn some basic DNA sequencing techniques and have been using &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/&quot; rel=&quot;nofollow noreferrer&quot;&gt;BLAST&lt;/a&gt; as a reference. I thought that I was starting to get it, but then I cam across this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ebhyr.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It looks like it's saying that the match starts at 10835 and ends at a smaller index (10714).&#xA;I tried clicking the link to view the full sequence, and I couldn't find the highlighted portion anywhere (not at 10835 or at 10776).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: Where (in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nucleotide/374429547?report=genbank&amp;amp;log$=nuclalign&amp;amp;blast_rank=1&amp;amp;RID=RZH41XEJ01R&quot; rel=&quot;nofollow noreferrer&quot;&gt;NR_046235.1&lt;/a&gt;) can I find the highlighted sequence? &#xA;And what does it mean to say that the &lt;code&gt;Sbjct&lt;/code&gt; starts at 10835 and ends at a lower index?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can post my query if necessary.&#xA;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="3484" LastEditorUserId="444" LastEditDate="2013-04-30T15:14:26.190" LastActivityDate="2013-04-30T16:58:44.123" Title="BLAST DNA Sequences Reversed" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8161" PostTypeId="2" ParentId="8160" CreationDate="2013-04-30T14:54:42.843" Score="6" Body="&lt;p&gt;Note that the query sequence you have provided matches the minus strand of your target sequence. That means not only that the target sequence will be reversed (as you have noted), but it will also be complemented as well. So in the GenBank record, you should not look for the sequence &lt;code&gt;CCGACCGA...&lt;/code&gt; starting at position 10835, you should look for the sequence &lt;code&gt;...TCGGTCGG&lt;/code&gt; ending at 10835.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ccgaccga...    minus strand&#xA;||||||||&#xA;bbɔʇbbɔʇ...    forward strand&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The sequence in the GenBank record contains spaces, so that complicates finding your sequence using the browser's &quot;Find&quot; function, but if you use the position indices at the beginning and end of each line of sequence, you will be able to find the reverse complement of the matched sequence reported in the BLAST results.&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2013-04-30T15:30:47.947" LastActivityDate="2013-04-30T15:30:47.947" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8162" PostTypeId="2" ParentId="8160" CreationDate="2013-04-30T16:58:44.123" Score="5" Body="&lt;p&gt;Just to flesh out Daniel Standage's answer a bit, remember that a genome is double stranded with one strand being complementary to the other. Genes can be found on either strand, the two are equivalent biologically. However, sequencing projects choose one of the two strands (randomly) and call it the plus (+) strand and then save all sequences with respect to that strand. This means that sometimes the genomic sequence that you download from a database might be the complement of the actual sequence you are looking for. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;BLAST and similar algorithms take this into account and will compare your query sequence to both strands. If your query hits the target sequence on the - strand, BLAST will give a a result like what you have obtained, where the start of the &lt;a href=&quot;http://genomevolution.org/wiki/index.php/High-scoring_segment_pair&quot; rel=&quot;nofollow noreferrer&quot;&gt;HSP&lt;/a&gt; is lower than the end. This is because RNA translation (though not DNA transcription) goes in a 5' to 3' direction, on both strands. We therefore &quot;read&quot; genes in that direction. The coordinates are always with respect to the + strand since we always consider DNA in a 5' to 3' direction, this means that its start position will appear to be after its end position. This is better explained using an image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wppqV.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the image above, the blue line represents your BLAST hit. It stretches from position 10 to position 40 (with respect to the + strand). However, since it is on the minus strand, BLAST will show it starting at position 40 and ending at position 10.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-04-30T16:58:44.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8163" PostTypeId="1" CreationDate="2013-04-30T23:08:52.253" Score="8" ViewCount="197" Body="&lt;p&gt;When a person is spying from around a corner with only one eye, it's rather easy to ignore the other eye's image, since it's probably much darker, because one usually spies around a corner standing close to a wall.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if both eyes get equally bright visual input, it takes some effort to try and stay focused on just one of them. What processes in human body allow such action?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastEditorUserId="9943" LastEditDate="2015-05-22T11:40:13.200" LastActivityDate="2015-05-22T11:40:13.200" Title="What processes are responsible for focusing on an image only seen by one of the eyes?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;vision&gt;&lt;human-eye&gt;&lt;visual-system&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8164" PostTypeId="2" ParentId="8153" CreationDate="2013-04-30T23:27:49.960" Score="2" Body="&lt;p&gt;Supplementary information from the Comments from the first answer: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have perhaps found @terdon's reference?  Not sure if this is it, but by measuring transcription events in individual cells, &lt;a href=&quot;http://www.sciencemag.org/content/329/5991/533.abstract&quot; rel=&quot;nofollow&quot;&gt;Taniguchi et al.&lt;/a&gt; certainly make the case that there is no correlation between protein and mRNA levels.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However microarray data (and &lt;em&gt;most&lt;/em&gt; rnaSeq and qPCR experiments) are ensemble measurements; they measure the average mRNA concentration in a sample of millions of cells.  In the aggregate, the paper also says that &lt;em&gt;in the aggregate&lt;/em&gt;, &lt;em&gt;the average mRNA correlates to the average protein product concentration&lt;/em&gt;.  See this &lt;a href=&quot;http://www.omespeak.com/blog/?p=216&quot; rel=&quot;nofollow&quot;&gt;nice writeup in the OmeSpeak blog&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall, what is happening microscopically: &lt;a href=&quot;http://www.sciencemag.org/content/297/5584/1183.full.html&quot; rel=&quot;nofollow&quot;&gt;translation is a somewhat stochastic process in the individual cell&lt;/a&gt; and events have to be modeled explicitly.  Biology in the aggregate (averaged case in a cell population) is often what we have to work with; single cell techniques are quite arduous.  (run a protein gel on a single cell!).  I think there is room for both sorts of information when investigating biology; certainly publication of work measured on more than one cell at a time will continue for some time.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All the work cited here is in E coli, but in Eukaryotes one assumes that this is not going to be any simpler.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-04-30T23:27:49.960" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8167" PostTypeId="2" ParentId="8136" CreationDate="2013-05-01T10:16:34.003" Score="5" Body="&lt;p&gt;You can use &quot;as&quot; to switch to a particular style (&lt;a href=&quot;http://pymolwiki.org/index.php/As&quot; rel=&quot;noreferrer&quot;&gt;http://pymolwiki.org/index.php/As&lt;/a&gt;&#xA;): &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;as cartooon, 11AS and chain a&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;You can also hide everything, to remove all representations (&lt;a href=&quot;http://pymolwiki.org/index.php/Hide&quot; rel=&quot;noreferrer&quot;&gt;http://pymolwiki.org/index.php/Hide&lt;/a&gt;): &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;hide every, 11AS and not (n. ca+c+n and resi 5-10)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I'm a fairly expert user of PyMOL and I've never seen an API exposed which will show you what representations are being used. That's not to say that it doesn't exist, there are a variety of undocumented features and commands still.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem is it isn't as simple as ribbon,mesh.  Every single atom can be displaying any combination of representations, so as an API call or command, it would have to return the status of every atom in your selection. If the displayed representations are exposed somewhere they're probably in a very low level format like that, and not of use unless you're a programmer. &lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-05-01T10:16:34.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8168" PostTypeId="2" ParentId="8140" CreationDate="2013-05-01T13:54:58.423" Score="3" Body="&lt;p&gt;This is a perfectly reasonable result. Remember that you are measuring an &lt;strong&gt;&lt;em&gt;average&lt;/em&gt;&lt;/strong&gt; value for a very large population of BSA molecules. Essentially what the 0.4 means is that at any one time, about 40% of the BSA molecules have a free thiol, while the rest of the cysteine residues are disulfide-bonded.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-05-01T13:54:58.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8169" PostTypeId="1" AcceptedAnswerId="8175" CreationDate="2013-05-01T20:33:14.437" Score="1" ViewCount="62" Body="&lt;p&gt;Similar to &lt;a href=&quot;https://biology.stackexchange.com/questions/551/a-good-book-for-history-of-biology-biotechnology-for-lay-people&quot;&gt;A good book for history of biology/biotechnology for lay people&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;but not for lay people.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone recommend an advanced dictionary of biotechnological engineering concepts in English (contemporary, not historical)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There doesn't seem to be anything adequate at my research institution nor even country.  I have been looking for PDF's and e-books since they can be previewed more easily than ISBN #'s, but any suggestions are welcome.&lt;/p&gt;&#xA;" OwnerUserId="3490" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-05-02T07:49:27.590" Title="glossary of biotechnological engineering" Tags="&lt;biotechnology&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8171" PostTypeId="1" AcceptedAnswerId="9396" CreationDate="2013-05-02T02:54:25.933" Score="20" ViewCount="1508" Body="&lt;p&gt;I've been reading a lot about circadian rhythms, when suddenly this question popped into my head: &lt;strong&gt;do circadian rhythms exist for deep sea organisms (3000 ft / 1000 meters+)?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For land mammals, the entrainment of circadian rhythms is done through exposure to light (retina or other photosensitive elements), but in the deep ocean there is no light. How are circadian rhythms maintained there - &lt;strong&gt;what acts as an entrainment signal?&lt;/strong&gt; Is it the moon, currents, etc.?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="107" LastEditDate="2013-05-02T14:34:53.557" LastActivityDate="2013-07-24T14:23:37.810" Title="Do marine deep sea life forms exhibit circadian rhythms? If so, what entrains them?" Tags="&lt;circadian-rhythms&gt;&lt;marine-biology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8172" PostTypeId="1" AcceptedAnswerId="8173" CreationDate="2013-05-02T03:05:54.213" Score="6" ViewCount="265" Body="&lt;p&gt;I'm approaching this question from the circadian rhythm perspective. A circadian rhythm is a 24 hour cycle. While doing research on deep sea circadian rhythms, I found this abstract which seemed to imply that there are some kinds of lunar rhythms (about a month long cycle). &lt;a href=&quot;http://intl-jbr.sagepub.com/content/26/1/82.abstract&quot;&gt;Lunar Rhythms in the Deep Sea: Evidence from the Reproductive Periodicity of Several Marine Invertebrates&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;While &lt;strong&gt;lunar rhythms are commonly documented in plants and animals&lt;/strong&gt;&#xA;  living in terrestrial and shallow-water environments, deep-sea&#xA;  organisms have essentially been overlooked in that respect.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What do the authors mean by the lunar rhythms? The roughly month long menstrual cycle, or &lt;strong&gt;are there other ways that the moon actually influences animal/human biology?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2016-11-04T09:55:20.463" Title="Do lunar rhythms have impact on human biology, if so, how?" Tags="&lt;human-biology&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8173" PostTypeId="2" ParentId="8172" CreationDate="2013-05-02T04:19:29.530" Score="1" Body="&lt;p&gt;The moon doesn't have a direct effect on metabolism. Nor does it affect menstruation (an archaic theory existed which claimed so!!). The lunar effects are due to its gravitational field which is known to affect tides (Spring tides and neap tides). &#xA;Even on a daily basis if you might have observed the sea advances into the beach in the night and recedes in the day. This effect is also because of the lunar gravity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The abstract of the article, that you mentioned, says that moonlight may have some effect on certain organisms; I am highly skeptical about that. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it is just the tidal patterns that might affect the behavior of marine/coastal organisms. I am also slightly skeptical about whether the currents produced by lunar gravitation would be deep enough to affect benthic life. In that case even the heating effect of the sun can produce sea currents. Perhaps it can also produce an upward current because of differential heating. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-05-02T04:44:18.280" LastActivityDate="2013-05-02T04:44:18.280" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8174" PostTypeId="1" CreationDate="2013-05-02T05:33:22.570" Score="0" ViewCount="275" Body="&lt;p&gt;In this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21208586&quot; rel=&quot;nofollow&quot;&gt;journal article&lt;/a&gt; certain symptoms are called &quot;activation&quot; in nature. I have never come across this term prior to coming across this article, so I would like to know quite simply what does it mean.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="107" LastEditDate="2013-05-02T14:21:52.190" LastActivityDate="2013-07-01T14:44:55.990" Title="What does &quot;Activation&quot; refer to in the context of the symptoms of Schizophrenia and Schizoaffective Disorder?" Tags="&lt;terminology&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8175" PostTypeId="2" ParentId="8169" CreationDate="2013-05-02T07:49:27.590" Score="1" Body="&lt;p&gt;I found &lt;a href=&quot;ftp://ftp.fao.org/docrep/fao/003/X3910E/X3910E00.pdf&quot; rel=&quot;nofollow&quot;&gt;this glossary of Biotechnology and Genetic Engineering&lt;/a&gt; off &lt;a href=&quot;http://en.wikipedia.org/wiki/Biotechnology&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;, what do you think?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or &lt;a href=&quot;http://www.bjcancer.org/_Library/UserFiles/pdf/The%20Facts%20On%20File%20DICTIONARY%20of%20BIOTECHNOLOGY%20and%20GENETIC%20ENGINEERING.pdf&quot; rel=&quot;nofollow&quot;&gt;The Facts On File&#xA;DICTIONARY of&#xA;BIOTECHNOLOGY&#xA;and&#xA;GENETIC&#xA;ENGINEERING&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What concepts are you necessarily hoping to include? I'm hoping someone actually experienced in this field can advise.&lt;/p&gt;&#xA;" OwnerUserId="3491" LastActivityDate="2013-05-02T07:49:27.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8176" PostTypeId="1" AcceptedAnswerId="8179" CreationDate="2013-05-02T11:41:00.487" Score="22" ViewCount="1194" Body="&lt;p&gt;Do organisms exist that are able to live indefinitely if they are not killed by external factors?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under external factors I would consider things like predators and natural disaster but not illness by bacteria for example.&lt;/p&gt;&#xA;" OwnerUserId="1224" LastEditorUserId="43480" LastEditDate="2019-02-28T19:55:58.850" LastActivityDate="2019-02-28T19:55:58.850" Title="Do immortal organisms exist?" Tags="&lt;zoology&gt;&lt;senescence&gt;&lt;life&gt;" AnswerCount="5" CommentCount="12" FavoriteCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="8177" PostTypeId="2" ParentId="6884" CreationDate="2013-05-02T13:59:10.457" Score="4" Body="&lt;p&gt;Telomerase activity is just one (probably minor) facet of aging.  It takes a lot more than just basic end repair of DNA to keep a complex organism alive, especially mammals.  Just a few issues off the top of my head:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;repairing oxidative stress to DNA and proteins&lt;/li&gt;&#xA;&lt;li&gt;repairing UV damage to DNA&lt;/li&gt;&#xA;&lt;li&gt;keeping cells clean of debris like protein aggregate buildup (think amyloid deposits like in Alzheimer's)&lt;/li&gt;&#xA;&lt;li&gt;replacing dead cells without compromising the tissue they're in&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For a solidly scientific, short, but very readable book on the subject, I personally liked &quot;Understanding Ageing&quot; by Robin Holliday.  For being published in 1995, it's still relevant. He had a later book that wasn't quite as good (Aging: The Paradox of Life: Why We Age, published in 2010). In large part it's because it was fairly redundant to the first one; we've known about these problems for a long time and have made fairly little progress on them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0521478022&quot; rel=&quot;nofollow&quot;&gt;http://www.amazon.com/gp/product/0521478022/ref=oh_details_o03_s00_i00?ie=UTF8&amp;amp;psc=1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Part of how hydra can get away with apparent immortality is their constant proliferation of stem cells and their ability to regenerate entire body parts. This circumvents a lot of the issues above (theoretically, but I'm not an expert on hydras). Many copies of the DNA are separately housed, so if a copy gets damaged irreversibly, it can just get trashed. Most (if not all) human organs have similar reserves of active stem cells. There isn't a single universal source (outside of the sperm and eggs), but this is less important so long as the entire stem cell supply isn't compromised by some gross organ damage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second part is much, much harder for humans though. While some tissues (say muscle) can easily replace dead cells, it's much harder in others, like the brain. You don't just have to replace a dead cell, but all of its connections to every other cell. And really, the brain is what this all comes down to, and an identity crisis in humans.  I don't care if you replace my liver and my left arm times, but how do you replace the brain?  I would speculate that we spend a lot more time keeping individual cells alive, because we can't replace them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you chop a starfish in half, you get two starfish, and would have trouble saying which was the original. &lt;a href=&quot;http://en.wikipedia.org/wiki/Ship_of_Theseus&quot; rel=&quot;nofollow&quot;&gt;Is it the same starfish if you've replaced the arms 3 times and the body twice?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you chopped a human in half down the center, and we could magically regenerate everything, you would get two very different people from each other and the original. The problem being that there's no way to reconstruct the connections; you'd just get a blank brain to fill up. &lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-05-02T13:59:10.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8178" PostTypeId="2" ParentId="8174" CreationDate="2013-05-02T14:22:16.253" Score="1" Body="&lt;p&gt;The authors use the Positive and Negative Syndrome Scale (PANSS) to assess symptoms.  One of its cluster scores is activation factor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Summary:&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Positive_and_Negative_Syndrome_Scale&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Positive_and_Negative_Syndrome_Scale&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Original publication of the article, which doesn't list activation factors:&#xA;&lt;a href=&quot;http://schizophreniabulletin.oxfordjournals.org/content/13/2/261.long&quot; rel=&quot;nofollow&quot;&gt;http://schizophreniabulletin.oxfordjournals.org/content/13/2/261.long&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Marketed currently here:&#xA;&lt;a href=&quot;http://www.mhs.com/product.aspx?gr=cli&amp;amp;id=overview&amp;amp;prod=panss&quot; rel=&quot;nofollow&quot;&gt;http://www.mhs.com/product.aspx?gr=cli&amp;amp;id=overview&amp;amp;prod=panss&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;None of the sources I saw specified what is meant by activation factor, and many didn't even mention it. It's possible that it's the hyperactivity mentioned in the original publication.  Also, it's possible that it's a modified category in the version sold at the last link. Hopefully this is enough information to get you started, if you want to hunt down the details.&lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-05-02T14:22:16.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8179" PostTypeId="2" ParentId="8176" CreationDate="2013-05-02T16:24:41.327" Score="15" Body="&lt;p&gt;I now found this Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_immortality&quot;&gt;biological immortality&lt;/a&gt;. It's pretty much what I was looking for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia describes the phenomenon as follows:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Biological immortality refers to a stable or decreasing rate of&#xA;  mortality from cellular senescence as a function of chronological age.&#xA;  Various unicellular and multicellular species may achieve this state&#xA;  either throughout their existence or after living long enough. A&#xA;  biologically immortal living thing can still die from means other than&#xA;  senescence, such as through injury or disease.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It has a list of &lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_immortality#Organisms&quot;&gt;such organisms&lt;/a&gt; as well, consisting of&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Tardigrades&quot;&gt;tardigrades&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hydra_%28genus%29&quot;&gt;hydras&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Turritopsis_nutricula&quot;&gt;turritopsis nutricula&lt;/a&gt;, some sort of jellyfish&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Lobster_longevity&quot;&gt;lobsters&lt;/a&gt;* &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Planarian&quot;&gt;planarian flatworms&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Addendum: This &lt;a href=&quot;http://neurodojo.blogspot.com/2013/05/all-lobsters-are-mortal.html&quot;&gt;blog post&lt;/a&gt; takes a good look into the myth of lobster immortality. It seems to be as much a myth as the result of any substantial observation.  &lt;/p&gt;&#xA;" OwnerUserId="1224" LastEditorUserId="3632" LastEditDate="2013-05-25T04:04:12.310" LastActivityDate="2013-05-25T04:04:12.310" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8180" PostTypeId="1" AcceptedAnswerId="8189" CreationDate="2013-05-02T23:08:24.147" Score="1" ViewCount="4452" Body="&lt;p&gt;One rate-limiting step of glycolysis is the conversion of Fructose-6-Phosphate (Fruc-6-P) to Fructose-1,6-Bisphosphate (Fruc-1,6-BP), catalysed by Phosphofructokinase 1 (PFK 1). The reaction involves hydrolysing one ATP to ADP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reverse reaction of gluconeogenesis is catalysed by Fructose-Bisphosphatase (FBP). This reaction uses 1 H&lt;sub&gt;2&lt;/sub&gt;O for hydrolysis and yields 1 phosphate (P&lt;sub&gt;i&lt;/sub&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One would expect the cell to be utilising only one of the two reactions at any one time, either to break down glucose or to generate it. However, the case is commonly that both reactions are taking place simultaneously in an equilibrium [ref 'Biochemistry', Voet &amp;amp; Voet, 4th ed., 628-629 (Section 17-4-F-f,g,h,(i))], cycling Fruc-1,6-BP to no apparent benefit, at the expense of valuable ATP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the purpose of such futile cycles?&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="51565" LastEditDate="2020-04-21T16:40:53.037" LastActivityDate="2020-04-21T16:40:53.037" Title="What is the use of futile reaction cycling such as Fruc-P to Fruc-BP?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;enzyme-kinetics&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="8181" PostTypeId="1" AcceptedAnswerId="8188" CreationDate="2013-05-03T01:31:51.673" Score="1" ViewCount="50" Body="&lt;p&gt;I am trying to calculate a titration amount for a molecule which I would like to use in my PCR samples. Different molecules have different densities so I would like to calculate the appropriate density of the titrated molecule. How many micrograms or microMolars of reverse transcriptase are used in qRT_PCR kits?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="43" LastEditDate="2013-05-03T12:33:13.630" LastActivityDate="2013-05-03T13:54:37.363" Title="Amount of reverse transcriptase in µg or mM for qRT-PCR" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;pcr&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8182" PostTypeId="1" AcceptedAnswerId="86398" CreationDate="2013-05-03T03:32:23.030" Score="4" ViewCount="186" Body="&lt;p&gt;I'm reading a text (&lt;a href=&quot;http://dx.doi.org/10.1534/genetics.107.074732&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wagner, 2007&lt;/a&gt;) on identifying positive selection. In the paper, the author says that low complexity regions are known to be associated with the relaxed selection. I'm trying to understand why this is true. I get that if the region is under relaxed selection then most mutations would be tolerated but why would that lead to low complexity (other than something like slippage during DNA replication)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's in the section: &quot;Little overlap between variation clusters and low complexity regions&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wagner A. 2007. Rapid Detection of Positive Selection in Genes and Genomes Through Variation Clusters. &lt;em&gt;Genetics&lt;/em&gt; 176(4): 2451–2463.&lt;/p&gt;&#xA;" OwnerUserId="3500" LastEditorUserId="3553" LastEditDate="2019-09-13T09:56:42.963" LastActivityDate="2019-09-13T09:56:42.963" Title="Why would low complexity regions be linked with relaxed selection?" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;natural-selection&gt;&lt;molecular-evolution&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="8183" PostTypeId="1" AcceptedAnswerId="14375" CreationDate="2013-05-03T08:07:14.940" Score="8" ViewCount="5848" Body="&lt;p&gt;How many species did Carl Linnaeus (senior) classify?&lt;/p&gt;&#xA;" OwnerUserId="320" LastEditorUserId="3952" LastEditDate="2014-01-09T15:30:21.103" LastActivityDate="2015-07-20T08:25:00.303" Title="How many species did Carl Linnaeus classify?" Tags="&lt;taxonomy&gt;&lt;history&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8184" PostTypeId="1" CreationDate="2013-05-03T08:31:13.943" Score="2" ViewCount="57" Body="&lt;p&gt;Most species complete mitosis, and in particular the process of chromosome condensation, rather quickly, in a matter of minutes. Are there any known species that undergo mitoses with substantially reduced kinetics (on the time scale of hours), particularly with respect to the processes of chromosome condensation (prophase through metaphase) or decondensation (anaphase through telophase)?&lt;/p&gt;&#xA;" OwnerUserId="3045" LastEditorUserId="43" LastEditDate="2013-05-03T12:28:55.097" LastActivityDate="2013-05-03T12:28:55.097" Title="Example(s) of reduced rate of mitotic progression?" Tags="&lt;cell-biology&gt;&lt;chromosome&gt;&lt;mitosis&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8185" PostTypeId="2" ParentId="752" CreationDate="2013-05-03T10:23:16.897" Score="3" Body="&lt;p&gt;As to your main question, I imagine the Paul Allan Brain Atlas has what you're looking for. In 3D even.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://human.brain-map.org/&quot; rel=&quot;nofollow&quot;&gt;Human Brain Map&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://human.brain-map.org/microarray/search/show?exact_match=false&amp;amp;search_term=drd1&amp;amp;search_type=gene&quot; rel=&quot;nofollow&quot;&gt;D1 Receptor&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://human.brain-map.org/microarray/search/show?exact_match=false&amp;amp;search_term=drd2&amp;amp;search_type=gene&amp;amp;page_num=0&quot; rel=&quot;nofollow&quot;&gt;D2 Receptor&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://mouse.brain-map.org/experiment/show/352&quot; rel=&quot;nofollow&quot;&gt;Also comes in mouse flavored.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Offhand, I cannot be of assistance for the second question.&lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-05-03T10:23:16.897" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8186" PostTypeId="5" CreationDate="2013-05-03T12:37:23.553" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-05-03T12:37:23.553" LastActivityDate="2013-05-03T12:37:23.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8187" PostTypeId="4" CreationDate="2013-05-03T12:37:23.553" Score="0" Body="The study of evolutionary mechanisms in operation at the molecular scale, primarily DNA, RNA, and proteins." OwnerUserId="43" LastEditorUserId="4101" LastEditDate="2013-10-31T19:29:03.393" LastActivityDate="2013-10-31T19:29:03.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8188" PostTypeId="2" ParentId="8181" CreationDate="2013-05-03T13:54:37.363" Score="1" Body="&lt;p&gt;Reverse transcriptase (and most other commercial enzymes these days) is made recombinantly, then purified to varying degrees, using varying methods, among different suppliers (and sometimes between different lots from the same supplier). Some enzymes actually have multiple functional units combined in a complex, others may require a post-translation activation step like phosphorylation by a separate kinase in order to be fully functional. All of these variables can yield preparations of different &lt;em&gt;molar concentration&lt;/em&gt;, but very similar &lt;em&gt;activity&lt;/em&gt;. Therefore, companies like New England Biolabs have &lt;a href=&quot;https://www.neb.com/products/m0368-protoscript-ii-reverse-transcriptase#pd-properties-usage&quot; rel=&quot;nofollow&quot;&gt;unit definitions&lt;/a&gt; for their various products based on activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having dealt with NEB in the past, I know that they generally have a concentration for their products as well, so if you're doing experiments like an enzyme inhibition assay, you can dose for concentration as well as activity. It will vary from enzyme to enzyme whether your inhibitor will even bind to any inactive protein that may be present, in which case activity would be the better attribute to use in your calculations.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-05-03T13:54:37.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8189" PostTypeId="2" ParentId="8180" CreationDate="2013-05-03T15:40:39.957" Score="2" Body="&lt;p&gt;As far as I am aware there are various regulatory mechanisms (allosteric regulation, hormonal control) in place to minimise futile cycling by ensuring that phosphofructokinase (glycolysis) and fructose 1,6 bisphosphatase (gluconeogenesis) are not both active at the same time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphofructokinase_1&quot; rel=&quot;nofollow&quot;&gt;this Wikipedia article&lt;/a&gt; for a starting point.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The precise regulation of PFK1 prevents glycolysis and gluconeogenesis from occurring simultaneously. However, there is substrate cycling between F6P and F-1,6-BP. Fructose-1,6-bisphosphatase (FBPase) catalyzes the hydrolysis of F-1,6-BP back to F6P, the reverse reaction catalyzed by PFK1. There is a small amount of FBPase activity during glycolysis and some PFK1 activity during gluconeogenesis. This cycle allows for the amplification of metabolic signals as well as the generation of heat by ATP hydrolysis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The last two sentences of the quotation are probably what you remember reading about. There is a theory that having some cycling provides an element of regulatory responsiveness. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16986621&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for example. I'm not enough of a mathematician to explain this idea well.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-05-05T11:12:25.143" LastActivityDate="2013-05-05T11:12:25.143" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8190" PostTypeId="1" AcceptedAnswerId="9216" CreationDate="2013-05-03T17:57:52.193" Score="1" ViewCount="181" Body="&lt;p&gt;I've been curious about a lot of vocabulary words in the world of botany. I've had quite a bit  of trouble finding somewhere online to help me out, but I'm having some trouble finding a resource like that. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Optimally, I'm looking for something with diagrams of anatomy, over the course of time, maybe some photo examples, and some sort of dictionary to accompany. Is there anything like this, online or offline that anyone knows about?&lt;/p&gt;&#xA;" OwnerUserId="3503" LastEditorUserId="3952" LastEditDate="2013-07-31T07:21:24.907" LastActivityDate="2013-07-31T07:21:24.907" Title="Resource plant anatomy/lifecycle vocabulary" Tags="&lt;botany&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8191" PostTypeId="2" ParentId="8183" CreationDate="2013-05-03T23:11:46.170" Score="4" Body="&lt;p&gt;Indeed this is a bit of interesting history.  &lt;a href=&quot;http://www.nhm.ac.uk/nature-online/science-of-natural-history/taxonomy-systematics/history-taxonomy/session1/&quot; rel=&quot;nofollow&quot;&gt;Linnaeus was not a modest man, but he was also a prodigious contributor to biology&lt;/a&gt;.  He made many editions of his two major works &lt;em&gt;Species Plantarum&lt;/em&gt; (1753) and &lt;em&gt;Systema Naturae&lt;/em&gt; published in 1759.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Systema_Naturae&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Systema Naturae&lt;/em&gt;&lt;/a&gt; covered both plants and animals and had 12 editions, eventually with 3 volumes in several parts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Linnaeus' sampling of species was not broad - &lt;a href=&quot;http://en.wikipedia.org/wiki/Carl_Linnaeus#Linnaean_collections&quot; rel=&quot;nofollow&quot;&gt;he traveled to Lapland France, and England&lt;/a&gt;.  His main experience was in botany and was able to look at samples in gardens which were a popular pursuit amongst wealthy hobbyists of the day and visited botanists in England and had samples from other continents.  He had heard about chimpanzees, but it doesn't seem as if he ever saw one.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Wikipedia gives a final count of nearly 10,000 species including over 7000 plants, from the entries in his works.&lt;/em&gt;  Linnaeus felt that there would be very few more to be discovered; he estimated 10,000 species of plants which turned out to be completely wrong.  The &lt;a href=&quot;http://eol.org/&quot; rel=&quot;nofollow&quot;&gt;Encyclopedia of Life&lt;/a&gt; has 1,316,775 entries today.  This was probably perpetuated by the influence of Aristotelian thought, which persisted through Darwin's life, &lt;a href=&quot;http://amazingdiscoveries.org/C-deception-evolution_Plato_Darwin&quot; rel=&quot;nofollow&quot;&gt;that species were only the result a higher reality creating animals&lt;/a&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/History_of_evolutionary_thought#Renaissance_and_Enlightenment&quot; rel=&quot;nofollow&quot;&gt;attuned to a local climate&lt;/a&gt; and geography and so the same species would in the mountains of Scandinavia would be the same as the alpine regions of India say.  But even Aristotelianism, which stood  for over a millenium the 19th Century and Darwin's work, was probably more the result of &lt;a href=&quot;http://en.wikipedia.org/wiki/Confirmation_bias&quot; rel=&quot;nofollow&quot;&gt;confirmation bias&lt;/a&gt; than any real proof. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-01-10T19:31:58.513" LastActivityDate="2014-01-10T19:31:58.513" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="8192" PostTypeId="2" ParentId="8182" CreationDate="2013-05-03T23:27:15.313" Score="5" Body="&lt;p&gt;Low complexity regions &lt;a href=&quot;http://www.broadinstitute.org/science/projects/fungal-genome-initiative/frequently-asked-questions#blast_lowcomplex&quot; rel=&quot;noreferrer&quot;&gt;have repeats in nucleotides&lt;/a&gt; ( or amino acids ).  E.g.  PPCDPPPPPKDKKKKDDGPP or AAATAAAAAAAATAAAAAAT.  This &lt;a href=&quot;http://gbe.oxfordjournals.org/content/3/539.full&quot; rel=&quot;noreferrer&quot;&gt;2011 article&lt;/a&gt; compares 14 individual Plasmodium falciparum genomes and finds that these repeats are highly variable between individuals - some may be short AAAATAAAA  others may be longer AAAATAAAAAAAAATAAAAAAATAAAATAAAA....AATAA even to scores of bases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think its not clear what these sequences do, but the mere fact that they can vary so much from one viable individual to another indicates that they are not strongly selective.  *If they were subject to selection, you would be able to see the difference in the variation in the health, fitness, and reproduction that these significant genetic changes have, but in this case the change in sequence would not change the properties of the sequence much if at all. * &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think these are also related to &lt;a href=&quot;http://en.wikipedia.org/wiki/Copy-number_variation&quot; rel=&quot;noreferrer&quot;&gt;copy number variable&lt;/a&gt; (CNV) regions.  which expand and contract in the genome easily &lt;a href=&quot;http://www.sciencedaily.com/releases/2008/02/080215121214.htm&quot; rel=&quot;noreferrer&quot;&gt;even between identical twins&lt;/a&gt;.  (sorry for the indirect reference - like many SDN stories, the reference is totally wrong), but I remember this work...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-06-05T13:41:31.117" LastActivityDate="2013-06-05T13:41:31.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8193" PostTypeId="1" AcceptedAnswerId="8208" CreationDate="2013-05-04T04:20:59.023" Score="4" ViewCount="460" Body="&lt;p&gt;I am trying to calculate a log-odds matrix for MAST input, from a position-specific probability matrix for the motif in which I am interested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know how MEME estimates the background frequency of nucleotides, as it does the conversion from position-specific probability matrices to log-odds matrices when you choose to run MAST on MEME output.  Is it simply counting frequencies in the sequences supplied, or is there some sort of modeling going on to correct for sample size and whatnot?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Another possibility that occurred to me is that MAST is capable of converting position-specific matrices to log-odds matrices.  I'd appreciate it if someone could clarify this point for me (and I'm still interested in how the background frequencies are calculated).  Also, I am specifically looking for answers with links to supporting documentation.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT 2 (05/07/13): Alexander has answered the original question.  Does anyone have an answer to the first edit (re: MAST)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT 3: MAST doesn't like PSPMs; it will accept the job but crash.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-05-10T05:33:03.003" LastActivityDate="2013-05-10T05:33:03.003" Title="How does MEME compute the background frequency of nucleotides?" Tags="&lt;bioinformatics&gt;&lt;software&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8195" PostTypeId="1" CreationDate="2013-05-04T07:17:19.663" Score="6" ViewCount="184" Body="&lt;p&gt;&lt;a href=&quot;http://blogs.smithsonianmag.com/artscience/2013/05/creepy-or-cool-portraits-derived-from-the-dna-in-hair-and-gum-found-in-public-places/?utm_source=plus.google.com&amp;amp;utm_medium=socialmedia&amp;amp;utm_campaign=20130503&amp;amp;utm_content=collageartdna&quot; rel=&quot;noreferrer&quot;&gt;http://blogs.smithsonianmag.com/artscience/2013/05/creepy-or-cool-portraits-derived-from-the-dna-in-hair-and-gum-found-in-public-places/?utm_source=plus.google.com&amp;amp;utm_medium=socialmedia&amp;amp;utm_campaign=20130503&amp;amp;utm_content=collageartdna&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can the face of a person be accurately rendered just from analysing a DNA sample of that individual?&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2015-03-04T01:17:59.337" Title="can the face of a person be accurately predicted from DNA information?" Tags="&lt;dna&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ClosedDate="2015-03-04T16:53:31.290" ContentLicense="CC BY-SA 3.0" />
  <row Id="8196" PostTypeId="2" ParentId="8195" CreationDate="2013-05-04T08:49:02.640" Score="6" Body="&lt;p&gt;Not accurately. Assuming the DNA information is the DNA sequence, you can't tell which genes are being expressed and which are being silenced. These are through chemical groups on the DNA which aren't generally picked up. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also there's the environment that grossly affects what you look like, how much you weigh, your skin colour and cosmetic surgery. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-04T08:49:02.640" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8197" PostTypeId="1" AcceptedAnswerId="8198" CreationDate="2013-05-04T19:10:04.893" Score="4" ViewCount="1128" Body="&lt;p&gt;When sun rays shoot through my house from a window, sometimes if the lighting is correct, it will reveal a huge amount of floating particles and dust.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these particles dangerous to humans if you live with them constantly?  &lt;/p&gt;&#xA;" OwnerUserId="3331" LastEditorUserId="3331" LastEditDate="2013-05-04T20:08:33.673" LastActivityDate="2013-05-06T09:22:26.553" Title="The effects of dust particles" Tags="&lt;breathing&gt;&lt;lungs&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8198" PostTypeId="2" ParentId="8197" CreationDate="2013-05-04T19:55:09.567" Score="2" Body="&lt;p&gt;You asked the single most difficult questions ever, so be proud of yourself! I've spent some time in the lab with a post doctorate trying to answer that particular question. It all is based on something called the hygiene hypothesis: the belief that as we are getting cleaner we are seeing less and less bacteria and so our immune system isn't working as it should so we get allergies. There's lot to this theory with regards to the different white blood cells in our body (specifically Th1, Th2 if you've ever heard of them). Of course there are reverse hypotheses, because we avoid eating stuff like peanuts, but minute amounts is found in dust, dust exposure (which also contains bacteria) makes us think peanuts are harmful so that's why we have allergies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Realistically a bit of dust to the most of us isn't harmful but if it contains things like dust mite poop which many people are allergic to, cat skin (another seriously common allergy) or is leaking from a place with mould... you should be okay :)&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-04T19:55:09.567" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8200" PostTypeId="1" AcceptedAnswerId="8217" CreationDate="2013-05-05T09:36:53.227" Score="1" ViewCount="111" Body="&lt;p&gt;I plan to measure the effects of &lt;a href=&quot;http://en.wikipedia.org/wiki/Tenofohttp://en.wikipedia.org/wiki/Tenofovirvir&quot; rel=&quot;nofollow&quot;&gt;Tenofovir&lt;/a&gt; a &lt;a href=&quot;http://en.wikipedia.org/wiki/Reverse-transcriptase_inhibitor&quot; rel=&quot;nofollow&quot;&gt;Nucleotide analog reverse-transcriptase inhibitors&lt;/a&gt; useing qrt-pcr with HIV-RT as the rt enzyme. Tenofovir causes early termination of the reverse transcriptase by binding to reads preventing the continuation of the chain process rather than stopping the action all together. How will qrt-pcr quantify the low molecular weight short incomplete fragments? I think since the areas complementary to the forward and reverse primers will rarely be on the same continuous double stranded dna expression will be decreased uniformly. Is this correct? Will I need to use absolute qrt-pcr since the changes will be the same for all genes?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2013-05-05T10:11:05.570" LastActivityDate="2013-05-06T09:09:03.613" Title="qrt-pcr and short fragments" Tags="&lt;pcr&gt;&lt;hiv&gt;&lt;reverse-transcription&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8202" PostTypeId="1" AcceptedAnswerId="8205" CreationDate="2013-05-05T14:17:08.197" Score="2" ViewCount="72" Body="&lt;p&gt;I once heard of this structure on the Discovery Science channel and have since forgotten the name. The details I remember about it were that it is the central time-keeping device for the brain located in the geographic center of the human brain. The DSC only mentioned it in passing to describe a person with an abnormality in this structure. Can someone post some reliable research links and a short description of it? I don't trust google much and am not good at using it, so thanks!&lt;/p&gt;&#xA;" OwnerUserId="3458" LastEditorUserId="107" LastEditDate="2013-05-06T02:50:29.090" LastActivityDate="2013-05-06T02:50:29.090" Title="I'd like to know the name and a few details of a certain time-keeping structure in the human brain" Tags="&lt;human-biology&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8203" PostTypeId="2" ParentId="8128" CreationDate="2013-05-05T15:23:53.733" Score="0" Body="&lt;p&gt;Yes, it is true that the hotter the sun, the darker people's skin becomes (in general) because of the evolutionary advantage conferred by having melanin to protect against UV light. The reason a dark object like an asphalt road gets hot quickly is that colors like black absorb most wavelengths of light, and therefore absorb more energy in the form of thermal energy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the same way, the melanin in your skin absorbs the UV from the sunlight because it is so dark, and protects your skin from it. &lt;/p&gt;&#xA;" OwnerUserId="3176" LastActivityDate="2013-05-05T15:23:53.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8204" PostTypeId="1" AcceptedAnswerId="8221" CreationDate="2013-05-05T15:27:53.890" Score="3" ViewCount="2587" Body="&lt;p&gt;I know that when RNA is transcribed from the original strand of DNA it contains introns and exons, and that the introns are spliced out of the strand to provide genetic diversity. However, what I don't understand is, how does whatever is doing this splicing know whether the section it is reading is an intron or an exon? Are there start and stop codes like there are for polypeptides, or is it determined by epigenetic factors like methyl markers? Or is it neither?&lt;/p&gt;&#xA;" OwnerUserId="3176" LastEditorUserId="3059" LastEditDate="2013-05-05T21:27:02.203" LastActivityDate="2013-05-06T13:07:07.283" Title="Detecting Introns and Exons" Tags="&lt;genetics&gt;&lt;rna&gt;&lt;introns&gt;&lt;exons&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8205" PostTypeId="2" ParentId="8202" CreationDate="2013-05-05T15:28:05.057" Score="4" Body="&lt;p&gt;You are probably referring to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Suprachiasmatic_nucleus&quot; rel=&quot;nofollow&quot;&gt;suprachiasmatic nucleus&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that, although this is the central clock, there are also so-called &quot;peripheral clocks&quot;, for instance in the liver, pituitary and other organs that can finely tune rhythms in the organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may also want to have a look at the Wikipedia page for &lt;a href=&quot;http://en.wikipedia.org/wiki/Circadian_clock&quot; rel=&quot;nofollow&quot;&gt;circadian clock&lt;/a&gt; and references therein.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2013-05-05T15:28:05.057" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8206" PostTypeId="1" CreationDate="2013-05-06T05:56:07.220" Score="8" ViewCount="11416" Body="&lt;p&gt;I understand that the imidazole ring in histidine is aromatic. I also realize that it retains it's aromaticity when protonated.&#xA;I am wondering why it is not mentioned at all in basic text books such as Lehninger? Also, across the web there are a number of places claiming that histidine isn't aromatic in all cases. &#xA;Another reason I am a little confused is, if protonation doesn't harm the aromatic nature, then why is histidine such a weak base?&#xA;Am I missing something?&lt;/p&gt;&#xA;" OwnerUserId="3026" LastActivityDate="2019-10-18T08:32:19.410" Title="Histidine aromaticity" Tags="&lt;biochemistry&gt;&lt;amino-acids&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8207" PostTypeId="1" AcceptedAnswerId="62892" CreationDate="2013-05-06T06:14:17.900" Score="4" ViewCount="737" Body="&lt;p&gt;A neurotropic virus is a virus which capable of infecting nerve cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Herpes simplex virus (HSV) has low neuroinvasivesess and high neurovirulence. HSV is transmitted in vesicle fluid, saliva and vaginal secretions. So the site of infection determines the disease - &quot;mixing and matching of mucous membranes&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: Murray 2013, Medical Microbiology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why is herpes virus neurotropic?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2017-07-21T15:43:40.483" Title="Why is herpes virus neurotropic?" Tags="&lt;virus&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8208" PostTypeId="2" ParentId="8193" CreationDate="2013-05-06T06:54:26.307" Score="3" Body="&lt;p&gt;At the &lt;a href=&quot;http://meme.nbcr.net/meme/cgi-bin/meme.cgi&quot; rel=&quot;nofollow&quot;&gt;MEME server page&lt;/a&gt;, there's a link to upload a customized &lt;a href=&quot;http://meme.nbcr.net/meme/meme-input.html#bfile&quot; rel=&quot;nofollow&quot;&gt;background markov model&lt;/a&gt; (using the command line interface, this is the -bfile option).  From there, there's a link to the &lt;a href=&quot;http://meme.nbcr.net/meme/doc/meme.html&quot; rel=&quot;nofollow&quot;&gt;MEME Man Page&lt;/a&gt;.  Under &quot;Objective Function&quot;, it specifies: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;blockquote&gt;&#xA;    &lt;p&gt;The background model is an n-order Markov model. By default, it is a 0-order model consisting of the frequencies of the letters in the training set.&lt;/p&gt;&#xA;  &lt;/blockquote&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So yes, it's basically the simplest possible correction: no accounting for pairwise frequencies, complements, motif width, etc.  I expect this is because MEME can be applied to essentially any dataset, such as phage display bindings from a &quot;truly&quot; random set of short oligos. In which case making higher order assumptions about the pairwise independence would be detrimental. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below that, I think it answers your question about the total log-odds calculation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;blockquote&gt;&#xA;    &lt;p&gt;The E-value reported by MEME is actually an approximation of the E-value of the log likelihood ratio. (An approximation is used because it is far more efficient to compute.) The approximation is based on the fact that the log likelihood ratio of a motif is the sum of the log likelihood ratios of each column of the motif. Instead of computing the statistical significance of this sum (its p-value), MEME computes the p-value of each column and then computes the significance of their product. Although not identical to the significance of the log likelihood ratio, this easier to compute objective function works very similarly in practice.&lt;/p&gt;&#xA;  &lt;/blockquote&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3460" LastEditorUserId="3460" LastEditDate="2013-05-06T07:00:41.053" LastActivityDate="2013-05-06T07:00:41.053" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8210" PostTypeId="1" AcceptedAnswerId="8214" CreationDate="2013-05-06T07:36:42.023" Score="4" ViewCount="95" Body="&lt;p&gt;In my lab we did a microarray to analyze differential gene expression in S. cerevisiae treated with UV irradiation. We are now analyzing the results and one of the up-regulated genes is labeled &quot;Alien4_60.&quot; I believe this is some kind of control, but I am having trouble understanding what it is. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would think that a probe labeled &quot;alien&quot; in a microarray would be some kind of negative control. The &lt;a href=&quot;http://www.microarrays.com/docs/SC4001-aros+ybox.zip&quot; rel=&quot;nofollow&quot;&gt;probe-list&lt;/a&gt; (excel file) says &quot;Control stringency: 60% identity to oligo Alien4&quot; as the description for this probe. What does this mean? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;..As you can imagine, searches for &quot;Alien4&quot; only brings up sci-fi movies! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;p.s. perhaps someone with enough rep could tag this question with more meaningful tags.&lt;/p&gt;&#xA;" OwnerUserId="3514" LastActivityDate="2013-05-13T07:16:22.010" Title="What is meant by &quot;alien&quot; probe in a microarray?" Tags="&lt;gene-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8211" PostTypeId="2" ParentId="8206" CreationDate="2013-05-06T07:57:08.183" Score="3" Body="&lt;p&gt;The imidazole ring in histidine is indeed aromatic. But an aromatic amino-acid is not usually defined as &quot;an amino-acid with an aromatic ring&quot;. Rather, they are usually defined by common chemical properties, such as high absorption at 280nm, or better their common metabolic pathway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Histidine as a stand-alone amino-acid is a weak base, but this is mainly due to the amino and acid groups shared with every amino-acid. The imidazole ring in itself has a neutral pKa. &lt;/p&gt;&#xA;" OwnerUserId="3394" LastActivityDate="2013-05-06T07:57:08.183" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8213" PostTypeId="2" ParentId="8206" CreationDate="2013-05-06T08:14:01.693" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I am wondering why it is not mentioned at all in basic text books such as Lehninger?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Books are not flawless.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Another reason I am a little confused is, if protonation doesn't harm the aromatic nature, then why is histidine such a weak base? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Pyrolles have a weak basicity because of delocalization of the electron lone pair of nitrogen. It is the lone pair of nitrogen, in amines, which gives it basicity (&lt;a href=&quot;http://en.wikipedia.org/wiki/Lewis_acids_and_bases&quot; rel=&quot;nofollow&quot;&gt;Check Lewis bases and acids&lt;/a&gt;) .&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In imidazole, the other nitrogen (N-2) has a free lone pair and does contribute to its basicity. As you pointed out before, imidazolium is a stable moiety and imidazole is much stronger base than pyridine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But compared to lysine &lt;code&gt;(pKb ≃ 10.5)&lt;/code&gt; and arginine &lt;code&gt;(pKb ≃ 12.48)&lt;/code&gt; it is a weaker base &lt;code&gt;(pKb ≃ 7)&lt;/code&gt;. Imines are generally weaker bases than amines because the &lt;code&gt;sp2&lt;/code&gt; hybridization of the former gives them a more &lt;code&gt;s&lt;/code&gt;-like  character; this makes the lone pair to be held more tightly to the nucleus thereby reducing the basicity. Also, the angle C-N(2)-C angle is constrained (small) because of the planar ring. This again leads to a higher &lt;code&gt;s&lt;/code&gt;-like character. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The strong basicity of arginine is because of the guanidium group. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-09-11T07:55:53.677" LastActivityDate="2015-09-11T07:55:53.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8214" PostTypeId="2" ParentId="8210" CreationDate="2013-05-06T08:37:22.213" Score="5" Body="&lt;p&gt;It's a probe to detect external 'Alien' RNA standard, a synthetic mRNA commercialized by Stratagene/Agilent.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Alien RNA transcript is a ~500-nt, polyadenylated RNA molecule that &#xA;  is synthesized by in vitro transcription. The Alien RNA transcript is &#xA;  nonhomologous to all known nucleic acid sequences currently in public &#xA;  databases, as determined by BLAST comparisons against NIH sequence &#xA;  databases. &lt;a href=&quot;https://www.chem.agilent.com/Library/usermanuals/Public/300602.pdf&quot; rel=&quot;nofollow&quot;&gt;https://www.chem.agilent.com/Library/usermanuals/Public/300602.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As any other external standard, you spike in the same amount of Alien RNA standard in your different reactions and then using the Alien probe you can normalize for extraction efficiencies etc. It works not only for microarrays, but also for qPCR, RNA-seq etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you didn't spike in any of it, I expect your probes giving very low signal that's probably why you thought about negative controls.&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="444" LastEditDate="2013-05-13T07:16:22.010" LastActivityDate="2013-05-13T07:16:22.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8215" PostTypeId="2" ParentId="8206" CreationDate="2013-05-06T08:40:31.130" Score="9" Body="&lt;p&gt;This is one of my favorite charts demonstrating the complexity of amino acid properties:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7IYf2.gif&quot; alt=&quot;Amino Acid Properties&quot;&gt;&#xA;&lt;a href=&quot;http://www.jalview.org/help/html/misc/aaproperties.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.jalview.org/help/html/misc/aaproperties.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Histidine is probably the most complicated amino acid in this regard (just compare how many circles it falls into).  But don't undersell Cysteine and Methionine; those sulfurs exhibit some surprising behavior, especially when coordinated properly.  Cysteine of course forming disulfide bonds, Methionine occasionally functioning as a methyl-transferase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biochemistry text books make some over simplifications because presenting the full messiness of these classifications is pretty confusing. Lehninger itself is the worst about this (and especially when presenting math).  Voet and Voet is probably the most reliable about presenting this complexity. I still think Lehninger is a better teaching textbook overall (I was first taught Biochemistry from the 3rd edition), but I also recall spending a week being confused about a topic before someone pointed me at V&amp;amp;V and I realized Lehninger was oversimplified to the point of being wrong, in that case.&lt;/p&gt;&#xA;" OwnerUserId="3460" LastEditorUserId="3340" LastEditDate="2014-07-03T09:20:40.593" LastActivityDate="2014-07-03T09:20:40.593" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8216" PostTypeId="2" ParentId="8204" CreationDate="2013-05-06T08:58:14.057" Score="2" Body="&lt;p&gt;There are some signature sequence which mark intron-exon boundaries. Usually introns start with a &lt;code&gt;GU&lt;/code&gt; and end with an &lt;code&gt;AG&lt;/code&gt;. But this feature per-se is not sufficient for splicing; there are other cis-elements such as &lt;code&gt;exon/intron splicing enhancers/silencers [ESE/ESS; ISE/ISS]&lt;/code&gt;. Refer &lt;a href=&quot;http://rnajournal.cshlp.org/content/14/5/802.full&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, there are protein regulators of splicing such as SR proteins; other proteins such as &lt;a href=&quot;http://genesdev.cshlp.org/content/22/18/2550.abstract&quot; rel=&quot;nofollow&quot;&gt;Fox-1/2&lt;/a&gt; can control alternate splicing events.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-05-06T08:58:14.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8217" PostTypeId="2" ParentId="8200" CreationDate="2013-05-06T09:09:03.613" Score="0" Body="&lt;p&gt;You have to design your primers properly. Usually, in real-time PCR, you don't choose a very long product. Ideal product size is 150-300. &#xA;Next, see what your NRTI is analogous to. For e.g. if I am using AZT (Azathymidie), I would place my reverse primer at or after the last &lt;code&gt;T&lt;/code&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are alternate techniques as well. You can use primer extension (radiolabeled) and then quantify different products by scanning the photograph. However, this technique won't be as  quantitative as real-time PCR. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-05-06T09:09:03.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8218" PostTypeId="2" ParentId="8197" CreationDate="2013-05-06T09:22:26.553" Score="0" Body="&lt;p&gt;Our basic defenses such as nasal hairs and mucus help in trapping the dust particles and other Suspended Particulate Matters (such as smoke etc). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if there is too much of dust inhalation then, as you suspect, it will be harmful. This can be seen in quarry workers who inhale a lot of dust- which causes &lt;a href=&quot;http://en.wikipedia.org/wiki/Silicosis&quot; rel=&quot;nofollow&quot;&gt;silicosis&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dust also instigates asthma. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You would feel much more comfortable in a dust free greenery but the mild dust which you would notice in your house wont be very hazardous in usual circumstances. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-05-06T09:22:26.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8220" PostTypeId="2" ParentId="8128" CreationDate="2013-05-06T10:15:35.540" Score="4" Body="&lt;p&gt;I agree with what has been said here about melanin and UV light, but I think there is a missing piece to fully understand the color variation in humans. Otherwise everyone would have just black skin and problem solved.&#xA;One of the counterparts appears to be the conversion of Vitamin D to an active form, that requires the action of sunlight. This trade-off explains the beautiful gradient of color in human populations *.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Native populations, not migrated populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm attaching and old but interesting article about this from scientific american 2002.&#xA;&lt;a href=&quot;http://www.direct-ms.org/pdf/VitDGenScience/Jablonski%202002%20Skin%20color.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.direct-ms.org/pdf/VitDGenScience/Jablonski%202002%20Skin%20color.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1739" LastActivityDate="2013-05-06T10:15:35.540" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8221" PostTypeId="2" ParentId="8204" CreationDate="2013-05-06T13:07:07.283" Score="3" Body="&lt;p&gt;Quick answer: we don't really know.&lt;/p&gt;&#xA;&lt;p&gt;As WYSIWYG said, splice sites &lt;em&gt;do&lt;/em&gt; have a sequence signature. The image below (taken from &lt;a href=&quot;http://dx.doi.org/10.1016/j.sbi.2004.05.007&quot; rel=&quot;nofollow noreferrer&quot;&gt;[1]&lt;/a&gt;) shows the consensus for human acceptor and donor sites:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mIy84.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;In the images above, the size of a nucleotide represents its frequency at that location. As you can see, there is a clear signal around the splice sites and this signal is used by various programs that do splice site prediction. What is not quite clear yet is how the cell recognizes these signals. Sometimes a &amp;quot;perfect&amp;quot; (identical to the consensus) splice site is ignored by the cell in preference to one that we would consider &amp;quot;worse&amp;quot;. This is further complicated by the presence of various downstream and upstream signals such as splicing &lt;a href=&quot;http://en.wikipedia.org/wiki/Exonic_splicing_enhancer&quot; rel=&quot;nofollow noreferrer&quot;&gt;enhancers&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Exonic_splicing_silencer&quot; rel=&quot;nofollow noreferrer&quot;&gt;silencers&lt;/a&gt; and structural elements (loops, hairpins etc) in the mRNA molecule.&lt;/p&gt;&#xA;&lt;p&gt;So, to answer your question yes there are start/end markers for introns/exons but they are far more complex than the simple START and STOP codons of transcription. We know know a lot about it but we still don't fully understand the details of splicing.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;References&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.sbi.2004.05.007&quot; rel=&quot;nofollow noreferrer&quot;&gt;Brent MR, Guigó R., Recent advances in gene structure prediction, Curr Opin Struct Biol. 2004 Jun;14(3):264-72.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-05-06T13:07:07.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8223" PostTypeId="1" AcceptedAnswerId="8224" CreationDate="2013-05-06T13:17:51.223" Score="3" ViewCount="292" Body="&lt;p&gt;So, there are numerous species of animals who use parthenogenesis, but to my knowledge the reproduction is clonal. That is, the offspring are identical to the mother. Are there any documented cases where a female goes through meiosis one to produce varied cells that are now diploid and these cells do not go through meiosis two, but rather develop in to a diploid organism? It would seem an effective reproductive strategy in that it generates genetic variation without a mate (at least more-so than strict asexual reproduction). Is my logic flawed in some way?&lt;/p&gt;&#xA;" OwnerUserId="1710" LastActivityDate="2013-05-06T21:03:00.880" Title="Are any organisms known to use meiosis I to create non-identical offspring asexually?" Tags="&lt;reproduction&gt;&lt;meiosis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8224" PostTypeId="2" ParentId="8223" CreationDate="2013-05-06T13:39:49.523" Score="4" Body="&lt;p&gt;In automixy the meiotic cells give rise to diploid offsprings. This can happen by diploidization of the haploid cell (&lt;code&gt;1n-&amp;gt;2n&lt;/code&gt;), which will produce homozygotes or endomitosis prior to meiosis (&lt;code&gt;4n-&amp;gt;2n&lt;/code&gt;) which produces heterozygotes. Examples:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jmor.1051330203/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Cnemidophorus uniparens&lt;/em&gt;&lt;/a&gt; : &lt;code&gt;4n-&amp;gt;2n&lt;/code&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://rsbl.royalsocietypublishing.org/content/3/4/425.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Sphyrna tiburo&lt;/em&gt;&lt;/a&gt;: &lt;code&gt;1n-&amp;gt;2n&lt;/code&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I don't know of any case where there is fusion of similar gametes to form a diploid cell. It is difficult for two ova to fuse in natural conditions because the vitelline membrane has to be dissolved. &#xA;Experimentally a haploid ES-cell can be fused to ovum to form a progeny. Haploid ES cells undergo diploidization and when injected in blastocyst, can develop properly (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21900896&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ref&lt;/a&gt;). In fact haploid androgenic-ES cell line had been made in &lt;a href=&quot;http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11435.html?WT.ec_id=NATURE-20121004&quot; rel=&quot;nofollow noreferrer&quot;&gt;this study&lt;/a&gt; by injecting sperm into an enucleated oocyte. These androgenic-haploid cell lines can be fused to ovum to give rise to viable offsprings. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also see &lt;a href=&quot;https://biology.stackexchange.com/questions/2853/is-ovum-ovum-fertilization-possible-for-human&quot;&gt;this question&lt;/a&gt;. &lt;em&gt;Similar topic&lt;/em&gt; &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-05-06T21:03:00.880" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8225" PostTypeId="2" ParentId="5099" CreationDate="2013-05-06T14:43:00.193" Score="1" Body="&lt;p&gt;Pheomelanin has it normal function in transforming radiant heat to energy but can't protect its host from ultra violet rays from the sun as UV will destroy melanin cells. &lt;/p&gt;&#xA;" OwnerUserId="3516" LastEditorUserId="3340" LastEditDate="2014-07-03T09:36:52.410" LastActivityDate="2014-07-03T09:36:52.410" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8226" PostTypeId="1" AcceptedAnswerId="8227" CreationDate="2013-05-06T18:18:38.887" Score="5" ViewCount="12667" Body="&lt;p&gt;In almost every movie scene when a character is shot in the chest area, some blood comes from his mouth or sometimes even coughs blood before he dies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these kind of scenes realistic/possible? If yes, why does blood come from mouth in this situation?&lt;/p&gt;&#xA;" OwnerUserId="989" LastActivityDate="2015-10-05T06:58:43.767" Title="Why does blood come from mouth when people are shot in the chest area?" Tags="&lt;hematology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8227" PostTypeId="2" ParentId="8226" CreationDate="2013-05-06T20:00:02.557" Score="10" Body="&lt;p&gt;Substances such as blood trigger the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cough_reflex&quot; rel=&quot;noreferrer&quot;&gt;Cough reflex&lt;/a&gt;, so if for any reason blood accumulates in the airways, it will be ejected this way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have a look at chest anatomy, you can see how this could be caused (look at Trachea down to the lungs, aorta and the carotid arteries above the heart). A shot through the chest can peforate many large blood vessels, along with the airways, and cause leakage inside.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would consider it quite hard to hit the aiways like that though, the bullet would have to enter the chest quite near the centre as the cough reflex is not triggered by substances in the lung itself, only in the airways. There may be other ways of blood getting into the airways, but I would assume that a scene with a shot near the breast and then blood coughing would be unrealistic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9ZBPa.jpg&quot; alt=&quot;Thorax anatomy&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image source: Micheau, A (2010) ANATOMY OF THE MEDIASTINUM: ILLUSTRATIONS AND CROSS-SECTIONS. From: &lt;a href=&quot;http://www.imaios.com/en/e-Anatomy/Thorax-Abdomen-Pelvis/Mediastinum-Illustrations&quot; rel=&quot;noreferrer&quot;&gt;http://www.imaios.com/en/e-Anatomy/Thorax-Abdomen-Pelvis/Mediastinum-Illustrations&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-05-08T16:09:29.723" LastActivityDate="2013-05-08T16:09:29.723" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8229" PostTypeId="5" CreationDate="2013-05-06T21:51:09.373" Score="0" Body="&lt;p&gt;See this &lt;a href=&quot;http://meta.biology.stackexchange.com/questions/414/why-is-there-an-untagged-tag&quot;&gt;meta post&lt;/a&gt; for an explanation.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-05-07T00:24:14.473" LastActivityDate="2013-05-07T00:24:14.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8230" PostTypeId="4" CreationDate="2013-05-06T21:51:09.373" Score="0" Body="Questions that were originally tagged with tags that no longer exist on Biology SE.  Please retag with existing tags.  " OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-05-07T00:24:10.473" LastActivityDate="2013-05-07T00:24:10.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8231" PostTypeId="1" AcceptedAnswerId="8232" CreationDate="2013-05-07T01:19:56.313" Score="3" ViewCount="151" Body="&lt;p&gt;In Saudi Arabia there are a lot of baboons in the mountain area. I would like to know what's the name of this specific baboons so I can read about them more:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FZ93o.jpg&quot; alt=&quot;baboons&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lD3bR.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user3130" LastActivityDate="2013-05-07T04:38:00.267" Title="What is the name of the baboons that live in Saudi Arabia" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8232" PostTypeId="2" ParentId="8231" CreationDate="2013-05-07T04:38:00.267" Score="2" Body="&lt;p&gt;These look like &lt;a href=&quot;http://en.wikipedia.org/wiki/Hamadryas_baboon&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hamadryas Baboons&lt;/a&gt; (&lt;em&gt;Papio hamadryas&lt;/em&gt;). They also fit the geographical location.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FkGLa.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2013-05-07T04:38:00.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8234" PostTypeId="2" ParentId="2414" CreationDate="2013-05-07T08:44:04.387" Score="0" Body="&lt;p&gt;I saw that some big dinosaurs got a second neuron group near their back legs to overcome some nerves signal delay problems. Not sure about that.&lt;/p&gt;&#xA;" OwnerUserId="1902" LastActivityDate="2013-05-07T08:44:04.387" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8235" PostTypeId="1" CreationDate="2013-05-07T10:16:39.460" Score="1" ViewCount="172" Body="&lt;p&gt;I extracted RNA from skin and quantified it in an Nanodrop machine. The 260/230 ratio was very low and two peaks appeared in the absorbance curve, but the RNA is ressuspended in RNAse free water. How can I clean it? &lt;/p&gt;&#xA;" OwnerUserId="3521" LastEditorUserId="6" LastEditDate="2013-05-07T10:31:04.350" LastActivityDate="2013-05-07T10:41:19.353" Title="How can I clean phenol extracted RNA?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8236" PostTypeId="1" AcceptedAnswerId="8239" CreationDate="2013-05-07T10:29:32.500" Score="2" ViewCount="358" Body="&lt;p&gt;I couldn't help but notice just how non-descriptive the gene names that modern genetics is using. Currently I'm reading &quot;The new science of Evo Devo&quot; by Sean B. Carroll and here are some examples of gene names used:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Fzrb&lt;/li&gt;&#xA;&lt;li&gt;Krox 20&lt;/li&gt;&#xA;&lt;li&gt;Hoxa2, Hoxb4&lt;/li&gt;&#xA;&lt;li&gt;ZPA&lt;/li&gt;&#xA;&lt;li&gt;FGF8&lt;/li&gt;&#xA;&lt;li&gt;sonic hedgehog&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;While these names identify genes uniquely, they do very little to express what and where the gene does, or how it is related to other genes (While FGF8 may be related to FGF7, it's relationship to XYZ10 is not obvious).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I get the need to uniquely identify genes , and &lt;strong&gt;the book is an example of just how hard it is to presently write about a lot of genes at once.&lt;/strong&gt; The author creates a picture of what's going on, but the gene names get in the way. Even in cases where a gene has a semi-descriptive name, like &quot;eyeless&quot;, the reader has to remember that it's actually the gene responsible for eye formation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are there are any efforts underway to systematize or name genes for a given organism in an expressive manner?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a programmer, I write code for a living, and having descriptive names makes it easier to look at someone else's code, read about code and even discuss it with novices. For example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;initializeDataModel&lt;/li&gt;&#xA;&lt;li&gt;createViewHierarchy&lt;/li&gt;&#xA;&lt;li&gt;userDidSelectLayerAtIndex&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Modern programming tools make using descriptive names easier, because of autocomplete - typing in the first few letters of a programming structure completes the rest. Even google has a list of autocomplete suggestions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We are all familiar with the Internet, where biology.stackexchange.com/questionname resolves into a specific page. Stackexchange is the site we are visiting, and Biology is a subset of that site. There are other biology websites, but biology.stackexchange.com uniquely identifies this site. The use of &quot;biology&quot; in the address gives readers a general idea of what the site is about and relates it to other biology sites. Our web browsers resolve the address into a proper string of bytes and get the right page. &lt;strong&gt;What if we name genes like like&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;com.drosophila.eyeformation&lt;/li&gt;&#xA;&lt;li&gt;com.chicken.limb.structure.ZPA&lt;/li&gt;&#xA;&lt;li&gt;com.human.development.geometry/XYZ10&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;,and whatever technology we use would actually resolve that descriptive name into a gene or a series of gene interactions? &lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="43" LastEditDate="2013-05-07T14:07:25.973" LastActivityDate="2013-05-07T14:07:25.973" Title="Are there more descriptive ways of naming genes and gene interactions?" Tags="&lt;genetics&gt;&lt;nomenclature&gt;&lt;evo-devo&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8237" PostTypeId="2" ParentId="8235" CreationDate="2013-05-07T10:30:17.830" Score="3" Body="&lt;p&gt;Phenol absorbs at 230 nm, this is the most likely contamination in your case. You should try to avoid pipetting from the phenol phase, or use a phase lock gel to make this easier. I assume you washed it a few times with pure chloroform after the phenol/chloroform mixture, that should help to get rid of the phenol.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I only precipitate my RNA with 1-1.5 volumes of isopropanol after the chloroform/phenol extraction, that should be sufficient for most uses. Just add the isopropanol, keep it at -20°C for 30 minutes and then centrifugate it at 9000 g for 20 minutes, redissolve the pellet in water.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2013-05-07T10:41:19.353" LastActivityDate="2013-05-07T10:41:19.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8238" PostTypeId="2" ParentId="8236" CreationDate="2013-05-07T10:46:37.317" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Are there are any efforts underway to systematize or name genes for a given organism in an expressive manner?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As you observed, the genes are named by their discoverers and some genes usually have anecdotes behind their names. Since gene names have to be small it is difficult to systematically describe them completely. But gene nomenclature can adopt a certain way of classification and it has been used extensively in yeast; genes are named by their chromosomal locations &lt;em&gt;(This was done in an age when cytogenetics was more developed than functional genetics. So you can understand why it so happened)&lt;/em&gt;. Some genes were named after the processes they are involved in. For example &lt;code&gt;cdc2, cdc48&lt;/code&gt; etc (cell cycle control)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check &lt;a href=&quot;http://www.genenames.org/guidelines.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; site: it has some guidelines for gene nomenclature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I completely agree with you that there should be a standard way of nomenclature. Perhaps it shall happen when functional genomics gets saturated. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-05-07T10:46:37.317" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8239" PostTypeId="2" ParentId="8236" CreationDate="2013-05-07T12:34:40.090" Score="4" Body="&lt;p&gt;Many gene names are descriptive, e.g. DRD1: dopamine receptor D1, TOP2A: DNA topoisomerase 2-alpha, or PTGS1: prostaglandin G/H synthase 1. These are examples of genes that have a clearly defined main function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genes you listed are involved in development, and there describing the function of a gene becomes much more difficult. E.g. sonic hedgehog is involved in patterning &lt;a href=&quot;http://en.wikipedia.org/wiki/Sonic_hedgehog#Function&quot; rel=&quot;nofollow&quot;&gt;many organs&lt;/a&gt;, from brain structures to teeth. How would you assign a descriptive name? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The analogy to (programming language) functions does not work for many genes, because they were not designed to fulfill one function, but evolved to do many different functions. For genes that have many functions, we just need a unique name. The multitude of functions is &lt;a href=&quot;http://amigo.geneontology.org/cgi-bin/amigo/gp-assoc.cgi?gp=UniProtKB%3aQ15465&quot; rel=&quot;nofollow&quot;&gt;catalogued elsewhere&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Bonus descriptive gene family name: &lt;a href=&quot;http://en.wikipedia.org/wiki/MAPKKK&quot; rel=&quot;nofollow&quot;&gt;MAPKKK&lt;/a&gt;: MAP kinase kinase kinase)&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2013-05-07T12:34:40.090" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8240" PostTypeId="2" ParentId="8236" CreationDate="2013-05-07T13:54:40.250" Score="1" Body="&lt;p&gt;I think it seems like a good idea at first but... &#xA;You have to take into account that as has been said genes might have multiple roles, sometimes very different and for most of them functions are still unknown.&#xA;So It's very difficult to classify a constatly changing promiscuous set of things. Even the gene concept is changing (Hello, ENCODE :)).&#xA;To me It's a lot easier to leave names as short as possible with some hints of they role (just the way they are) and if you're interested in the specific function, a very quick visit to a database and using the list as input will provide you with the current description and/or function of the gene.&lt;/p&gt;&#xA;" OwnerUserId="1739" LastActivityDate="2013-05-07T13:54:40.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8241" PostTypeId="2" ParentId="8236" CreationDate="2013-05-07T14:04:43.963" Score="3" Body="&lt;p&gt;In theory, your idea seems reasonable, but I can see at least to problems with implementing it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, the situation is complicated by the fact that &lt;strong&gt;genes often carry out multiple functions, and a single label is often insufficient to annotate the complete functional repertoire of a gene&lt;/strong&gt;. @MichaelKuhn made an excellent point with regards to the evolution of gene function. When one stops thinking about a gene (and its protein products) as something that was designed to fulfill a specific purpose, but rather as something that has been adapted (often serendipitously), for better and for worse, to fulfill a particular set of functions, the difficulty with annotating gene function is a lot clearer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, this idea is confounded by the fact that &lt;strong&gt;reliable functional annotations are &lt;em&gt;really, really rare&lt;/em&gt;&lt;/strong&gt;. Sure, lots of genes in human and yeast and &lt;em&gt;Drosophila&lt;/em&gt; have been extensively studied for decades, and many of their functions are well understood (at least we think they are). But for the vast majority of genes for the vast majority of organisms that have been studied, functional annotations are inferred from sequence similarity to previously annotated genes, without any additional experimental validation. Of course, every genome project would love to functionally classify all of the genes for their pet genome, but this is really expensive, time consuming, and low-throughput. For every extensively studied, well annotated gene, there are literally hundreds of analogous genes in other organisms that have been annotated solely based on sequence similarity to this gene. As disappointing as this is, it doesn't seem like it's going to change any time in the near future (unless there are some drastic improvements in the throughput of gene function annotation). So any proposed nomenclature convention that does not address this reality is quite inadequate in my opinion.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2013-05-07T14:04:43.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8243" PostTypeId="1" CreationDate="2013-05-07T17:20:45.987" Score="2" ViewCount="556" Body="&lt;p&gt;5,5'-dibromo-4,4'-dichloro-indigo is the product of X-gal cleavage, often used as a reporter with B-galactosidase. I've made the (unreferenced) observation that it seems as though the blue product slowly degrades over periods of time within the cell, allowing for cells to lose their blue coloration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What mechanisms can explain the degradation of 5,5'-dibromo-4,4'-dichloro-indigo within cells?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2013-05-07T17:20:45.987" Title="How do cells slowly degrade 5,5'-dibromo-4,4'-dichloro-indigo?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8244" PostTypeId="1" AcceptedAnswerId="8365" CreationDate="2013-05-07T21:55:14.820" Score="1" ViewCount="269" Body="&lt;p&gt;I'm a biotechnology student and I have to write a sort of non-experimental thesis (30 pages long) within the end of a three years study.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm very interested in the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Systems_biology&quot; rel=&quot;nofollow&quot;&gt;systems biology&lt;/a&gt;&quot; field and I'm searching good (innovative) and recent (max 3-4 years old) articles about this subject, but unfortunately I've found my research more difficult than I expected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like to focus on not immediate/easy articles and possibly containing new and promising approaches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anybody have suggestions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: it all started from &lt;a href=&quot;http://www.youtube.com/watch?v=Z__BHVFP0Lk&quot; rel=&quot;nofollow&quot;&gt;Uri Alon's great lessons on YouTube&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3523" LastEditorUserId="500" LastEditDate="2013-05-13T10:17:50.973" LastActivityDate="2013-05-15T13:14:41.483" Title="Recent and good quality articles on systems biology" Tags="&lt;homework&gt;&lt;systems-biology&gt;&lt;literature&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ClosedDate="2013-05-15T20:44:12.753" ContentLicense="CC BY-SA 3.0" />
  <row Id="8246" PostTypeId="1" CreationDate="2013-05-08T00:30:34.977" Score="5" ViewCount="3962" Body="&lt;p&gt;From the RNAseZap MSDS, it is an SDS at some unknown concentration, maybe with some NaOH?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some other links suggest there is some NaOH as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Ambion site states that RNAseZap destroys RNAse activity on contact, but they also instruct to rinse with water twice after wiping RNAseZap on the surface being cleaned.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, does RNAseZap actually destroy RNAse activity, or is it simply a &quot;good detergent&quot; to pick them up and rinse them away?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&#xA;Carmen&lt;/p&gt;&#xA;" OwnerUserId="3459" LastActivityDate="2014-10-31T12:58:32.607" Title="Is wiping with RNAse Zap enough to destroy RNAse activity?" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;rna&gt;&lt;lab-reagents&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8247" PostTypeId="1" CreationDate="2013-05-08T00:38:54.497" Score="5" ViewCount="2283" Body="&lt;p&gt;I am working with RNA samples, and I'm trying to be very careful about RNAse contamination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have some questions about bleach, though. Some people say that a solution of bleach is enough to destroy RNAse activity, but is it really? How does it do it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure if wiping the surface using a solution of bleach would be enough to kill RNAse activity, or if it is necessary to use products such as RNAseZap or RNAseAway.&lt;/p&gt;&#xA;" OwnerUserId="3459" LastEditorUserId="107" LastEditDate="2013-05-09T11:57:33.070" LastActivityDate="2013-10-28T20:53:14.270" Title="Does bleach destroy RNAse activity, and if so, how does it do it?" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;rna&gt;&lt;pcr&gt;&lt;nucleic-acids&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8249" PostTypeId="2" ParentId="8246" CreationDate="2013-05-08T02:49:33.570" Score="4" Body="&lt;p&gt;It's hard to know what RNaseZap does since the ingredients list is a trade secret.  However, I expect it is a lot more than just detergent.  RNaseA is extremely hard to destroy; moreover it can easily renature once the denaturant is removed. Therefore, very minute quantities are sufficient to annihilate RNA experiments.  The historical method of purification was to boil solutions of it until all other proteins denatured and could be easily separated. I can personally attest that you can precipitate it in pure alcohols and it will spontaneously refold as soon as it is rehydrated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would not trust a simple detergent to get rid of it; you'll need something more volatile to be reliable.  A lot of &quot;home made RNaseZap&quot; recipes on the internet include hydrogen peroxide, which causes a variety of covalent modifications to the protein.  It also has the advantage of cleaning itself up (eventually turning into H&lt;sub&gt;2&lt;/sub&gt;O).  The detergent is useful because you typically don't want any protein residue floating around your experiments, denatured or not.  If you have some dried RNaseA aggregates, it will also help break those up.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I work with RNaseA itself, so I can't personally vouch for the recipe below (since I'm not interested in destroying my sample), but it seems sound.  But if you have the cash to blow, just get the RNaseZap.  It's very widely used by RNA labs and you really don't want to chance a potentially expensive experiment on it.  Especially since you're constantly shedding tons of RNaseA from your skin, being sloppy will probably bite you eventually.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8405571&quot; rel=&quot;nofollow&quot;&gt;Mechanism of action for H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://forums.biotechniques.com/viewtopic.php?f=3&amp;amp;t=1515&quot; rel=&quot;nofollow&quot;&gt;plausible recipe&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3460" LastEditorUserId="3340" LastEditDate="2014-10-31T12:58:32.607" LastActivityDate="2014-10-31T12:58:32.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8250" PostTypeId="2" ParentId="3469" CreationDate="2013-05-08T03:28:39.567" Score="1" Body="&lt;p&gt;In case of normal, healthy person, no, I don't think so. In fact, retinal detachment could happen at anytime of the day. Main causes are diseases and illness, such as AIDS, diabetic retinopathy, cancer, or trauma such as post-cataract surgery and being hit/kicked hard on the eyes. &lt;/p&gt;&#xA;" OwnerUserId="3527" LastActivityDate="2013-05-08T03:28:39.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8252" PostTypeId="1" CreationDate="2013-05-08T11:21:36.293" Score="4" ViewCount="165" Body="&lt;p&gt;I'm looking at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Melatonin#Dreaming&quot; rel=&quot;nofollow&quot;&gt;wikipedia article on Melatonin&lt;/a&gt; and noticed that it mentions vivid dreaming caused by melatonin. I have the &quot;Melatonin and the Biological clock&quot; pamphlet referenced in the article, and it does not go into too much detail of how vivid dreaming is happening. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've personally experienced vivid dreaming side effects of melatonin today - dream after dream of profound intensity, but completely unrelated content. This makes me interested - &lt;strong&gt;how does melatonin influence the intensity of dreaming in humans?&lt;/strong&gt; Is it by interaction with Serotonin? Or does it get metabolized into something psychoactive?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-05-08T11:21:36.293" Title="What is the mechanism by which Melatonin increases dream vividness and intensity in humans?" Tags="&lt;endocrinology&gt;&lt;sleep&gt;&lt;dreaming&gt;&lt;melatonin&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8254" PostTypeId="1" AcceptedAnswerId="8256" CreationDate="2013-05-08T13:13:24.080" Score="10" ViewCount="2554" Body="&lt;p&gt;Certain &lt;a href=&quot;http://en.wikipedia.org/wiki/Aneuploidy&quot;&gt;aneuploidies&lt;/a&gt; such as trisomy-21 (Downs syndrome), trisomy-18 (Edward syndrome), Turner syndrome (XO) etc are more common than others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I had a vague thought that it is related to chromosome size: the chromosomes which are towards the extremes of size will be affected in an improper segregation event. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chromosomes 13, 18, 21 and Y are among the smaller chromosomes in humans, and are commonly associated with aneuploidy (but 22 which is also small is not affected). The larger ones are unaffected (X is an anomaly). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought that longer ones should be more affected because more &lt;a href=&quot;http://en.wikipedia.org/wiki/Cohesin&quot;&gt;cohesin&lt;/a&gt; bridges have to be broken, but it seems that is not the case.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Is there any association of chromosome size and frequency of aneuploidy? &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;EDIT&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;If the difference is because of differential lethalities then does the length correlation still hold true? Smaller the chromosomes, lesser the genes and hence lesser would be the effect of extra copy on the cellular biochemical networks. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-05-09T21:17:27.287" LastActivityDate="2013-05-09T21:17:27.287" Title="Why are certain aneuploidies more common?" Tags="&lt;cell-biology&gt;&lt;human-genetics&gt;&lt;cytogenetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8256" PostTypeId="2" ParentId="8254" CreationDate="2013-05-08T14:43:50.440" Score="12" Body="&lt;p&gt;I thought it was just that the other aneuploidies were fatal. They occur as often but miscarry earlier in the term therefore you don't see them. So basically there are only three that are viable 21,18 and the sex chromosome with a number of combinations: XO, XXY, XYY and XXX.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More information here:&#xA;&lt;a href=&quot;http://www.nature.com/scitable/topicpage/chromosomal-abnormalities-aneuploidies-290&quot;&gt;http://www.nature.com/scitable/topicpage/chromosomal-abnormalities-aneuploidies-290&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regard to the frequency for each chromosome:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For males (i.e., sperm; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11124518&quot;&gt;source&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The mean disomy frequency is 0.15% for each of the autosomes and 0.26%&#xA;  for the sex chromosomes. Most chromosomes analyzed have an equal&#xA;  distribution of disomy with the exception of chromosomes 14, 21, 22&#xA;  and the sex chromosomes, which display significantly higher disomy&#xA;  frequencies.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Size of the chromosome is frequently reported as a factor in the frequency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For females (i.e., eggs; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16192694&quot;&gt;source&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The data is obviously harder to attain. One study from IVF treatments&#xA;  show differences in the frequency of different chromosomes at&#xA;  different stages in meiosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="476" LastEditorUserId="107" LastEditDate="2013-05-09T12:11:10.647" LastActivityDate="2013-05-09T12:11:10.647" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8257" PostTypeId="1" CreationDate="2013-05-08T16:32:48.607" Score="3" ViewCount="288" Body="&lt;p&gt;If I understand correctly, &lt;a href=&quot;http://species-identification.org/species.php?species_group=zsao&amp;amp;id=1708&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Cenosphaera&lt;/em&gt; spp.&lt;/a&gt; is a type of &lt;a href=&quot;http://en.wikipedia.org/wiki/Radiolaria&quot; rel=&quot;nofollow noreferrer&quot;&gt;Radiolaria&lt;/a&gt;, which is a type of &lt;a href=&quot;http://en.wikipedia.org/wiki/Zooplankton&quot; rel=&quot;nofollow noreferrer&quot;&gt;zooplankton&lt;/a&gt;.  The following is an image of &lt;em&gt;Cenosphaera&lt;/em&gt; spp. is from the supplementary material (Figure S2) of the following paper: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;F. Lejzerowicz et al., &lt;a href=&quot;http://dx.doi.org/10.1098/rsbl.2013.0283&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ancient DNA complements microfossil record in deep-sea subsurface sediments&lt;/a&gt;, Biol. Lett. (9) 2013.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sD04i.png&quot; alt=&quot;Cenosphaera&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;: Does this image accurately depict the organism?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;More specifically, in other images of this organism, there are numerous thorns pointing outwards.  Is this thorn-less version a natural variation (or e.g. the result of the process of imaging the organism)?  Also, is it largely a sphere with a hollow inside?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors give the following description of the process involved in obtaining these images.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Eighteen sediment samples were wet washed over 63 μm and 20 μm sieves. The &gt;63 μm residua were dried and picked for radiolaria and foraminifera. From most samples all specimens were picked. Rich samples were divided with a dry microsplitter into fractions, from which at least 100 specimens were picked for each group. Specimens were arranged by taxa on micropaleontological slides. Radiolaria are classified on the generic level, according to the classification utilized by [8]. Foraminifera above the species level are classified according to [9]. In addition, for radiolaria, the 20-63 μm fractions were soaked in peroxide, then washed with tap water and propanol. For each sample, a few drops of suspended material was left on a glass to dry, covered with Durcupan ACM resin and a cover glass. The micropaleontological slides were analyzed under Olympus BX50 light microscope (electronic supplementary material, figures S2 and S3).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="203" LastEditorUserId="3632" LastEditDate="2013-06-10T17:03:07.413" LastActivityDate="2014-06-05T12:39:39.613" Title="Highly spherical Radiolaria; does this image accurately depict the organism?" Tags="&lt;microbiology&gt;&lt;marine-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8258" PostTypeId="2" ParentId="8207" CreationDate="2013-05-08T17:37:36.257" Score="6" Body="&lt;p&gt;Simply because it has neurotropic receptors. Why did acquiring these receptors seem evolutionarily advantageous? Well the immune system doesn't target nerve cells for destruction as well. There are few if any white blood cells in the CSF within which the neurones are bathed. The immune system is about protecting against damage, it doesn't care as much if a virus doesn't cause damage as it isn't geared to respond as well if that's the case. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-08T17:37:36.257" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8261" PostTypeId="1" AcceptedAnswerId="8292" CreationDate="2013-05-08T23:43:05.483" Score="1" ViewCount="99" Body="&lt;p&gt;I know that for a given mammal, half the chromosomes come from father and half from mother. This is typically denoted as x-y. I've recently read about &quot;toolkit&quot; genes that control how a cell develops into an embryo into an organism. &lt;strong&gt;I'm interested which set of chromosomes(x,y or both) contains these toolkit genes for development of an organism from a fertilized cell?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, does an X chromosome know how to build a female and Y chromosome how to build a male, or is it some &quot;overriding&quot; of developmental instructions that Takes place when Y is present?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-05-11T03:37:19.957" Title="Which X-Y chromosomes have the developmental genes for mammals?" Tags="&lt;genetics&gt;&lt;embryology&gt;&lt;evo-devo&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8262" PostTypeId="1" AcceptedAnswerId="8281" CreationDate="2013-05-09T00:59:18.387" Score="4" ViewCount="210" Body="&lt;p&gt;It is necessary to have extra source of CO&lt;sub&gt;2&lt;/sub&gt; i.e. from a nuclear reactor or factory chimney to produce bio-fuel by microalgae or is it able to do it with the normal CO&lt;sub&gt;2&lt;/sub&gt; density in the atmosphere?&lt;/p&gt;&#xA;" OwnerUserId="3533" LastEditorUserId="3340" LastEditDate="2015-06-04T11:49:44.253" LastActivityDate="2015-06-04T11:49:44.253" Title="Does biofuel production by microalgae need an extra source of CO₂?" Tags="&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="8263" PostTypeId="1" AcceptedAnswerId="8278" CreationDate="2013-05-09T02:09:22.320" Score="2" ViewCount="84" Body="&lt;p&gt;How do near sightedness, farsightedness, and normal sightedness work? If the eye is accustomed to one small focal point, how can it manage a wall of light? And also, how does it process the small pinpoint that it normally does? &lt;/p&gt;&#xA;" OwnerDisplayName="user3534" LastEditorUserId="107" LastEditDate="2013-05-09T02:51:41.843" LastActivityDate="2013-05-09T15:09:14.260" Title="The Eye, and Camera Lenses" Tags="&lt;vision&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8264" PostTypeId="1" CreationDate="2013-05-09T05:14:28.987" Score="3" ViewCount="2356" Body="&lt;p&gt;I have been trying to wrap my head around the concept of epistasis for a couple of days now, and I think I understand it, at least at a basic level, but I still don't understand some of the ways that the term is used. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does it mean if gene A is epistatic to gene B? Does this simply mean that gene A masks the phenotype of gene B when expressed? or is there more to it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, what does it mean when genes are in the same epistasis group? I am currently studying the transcriptional up-regulation of PSY3 in yeast as a result of UV treatment. PSY3 codes for a protein that forms the Shu complex along with 3 other proteins. One paper I am reading states that PSY3, is in the same epistasis group as the three other genes that code for these other proteins. What does this mean?&lt;/p&gt;&#xA;" OwnerUserId="3514" LastActivityDate="2013-05-10T23:38:55.990" Title="What is an epistasis group?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8265" PostTypeId="2" ParentId="8264" CreationDate="2013-05-09T05:28:55.083" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;What does it mean if gene A is epistatic to gene B? Does this simply mean that gene A masks the phenotype of gene B when expressed? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes.  Note that this does not say anything about mechanism. If A converts 1 to 2, and B converts 2 to 3, then &lt;strong&gt;A is epistatic to B, but A is also upstream of B&lt;/strong&gt;.  In a signaling pathway, say B inhibits A and prevents it from signaling. A mutation in B allows A to signal. A mutation in A means there is no signaling. Mutations in both A and B means there is no signaling: &lt;strong&gt;A is epistatic to B, but A is downstream of B&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An epistasis group is a group of genes in the same pathway.  Knocking out any combination of these genes will &lt;em&gt;not&lt;/em&gt; result in a more severe phenotype than knocking out the most &quot;sensitive&quot; of these genes (the single mutant with the most severe phenotype).&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-05-10T23:38:55.990" LastActivityDate="2013-05-10T23:38:55.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8266" PostTypeId="5" CreationDate="2013-05-09T05:41:32.980" Score="0" Body="&lt;p&gt;For questions about the skin, part of the integumentary system (skin, hair, feathers, nails, scales, hooves). The role of the system is to protect, detect, help regulate, and is a site of vitamin D synthesis.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-03-23T11:17:25.693" LastActivityDate="2016-03-23T11:17:25.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8267" PostTypeId="4" CreationDate="2013-05-09T05:41:32.980" Score="0" Body="The skin, part of the integumentary system." OwnerUserId="3059" LastEditorUserId="1590" LastEditDate="2016-03-23T11:17:28.523" LastActivityDate="2016-03-23T11:17:28.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8268" PostTypeId="5" CreationDate="2013-05-09T05:42:42.437" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-05-09T05:42:42.437" LastActivityDate="2013-05-09T05:42:42.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8269" PostTypeId="4" CreationDate="2013-05-09T05:42:42.437" Score="0" Body="Questions relating to representations of biological data." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-05-09T11:55:28.703" LastActivityDate="2013-05-09T11:55:28.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8270" PostTypeId="5" CreationDate="2013-05-09T05:43:54.693" Score="0" Body="&lt;p&gt;Imprecise questions on book recommendations tend to generate opinion-based answers. In order to not be considered opinion-based, and therefore closed, book recommendation questions must provide the following information:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Broad area of study (default)&lt;/li&gt;&#xA;&lt;li&gt;Scope of the book (i.e. what topics should it cover). This should be a detailed list of topics that the OP is interested to study.&lt;/li&gt;&#xA;&lt;li&gt;Level of the book (i.e. should it be a suitable/intended for beginners or should it have detailed information suited for an advanced reader)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Other useful information includes why some books are specifically not deemed suitable.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="16866" LastEditDate="2020-01-02T19:49:22.457" LastActivityDate="2020-01-02T19:49:22.457" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="8271" PostTypeId="4" CreationDate="2013-05-09T05:43:54.693" Score="0" Body="Questions relating to requests for basic reference materials on a broad area of study." OwnerUserId="3059" LastEditorUserId="3340" LastEditDate="2015-06-19T10:13:24.213" LastActivityDate="2015-06-19T10:13:24.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8272" PostTypeId="1" AcceptedAnswerId="14423" CreationDate="2013-05-09T05:48:27.913" Score="15" ViewCount="47357" Body="&lt;p&gt;How long can a naked human survive at the surface of the Mars planet?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, let's say a worker's base takes fire while he sleeps, the building is totally ablaze and he can do nothing but &lt;strong&gt;run to the emergency building 200 meters away&lt;/strong&gt; without any respiratory equipment, pressure suit, UV protections or anything.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe a human could survive for a rather long time, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Apnea&quot; rel=&quot;noreferrer&quot;&gt;apnea time&lt;/a&gt; is the real limiting factor?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Climate_of_Mars&quot; rel=&quot;noreferrer&quot;&gt;Climate&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Temperature: 27 °C to −50 °C (base is at a rather warm location, on Equator)&lt;/li&gt;&#xA;&lt;li&gt;Pressure: 0.006 bar (Earth: 1 bar)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3535" LastEditorUserId="3535" LastEditDate="2016-03-08T03:19:49.413" LastActivityDate="2016-03-08T03:19:49.413" Title="How long can a naked human survive on Mars?" Tags="&lt;human-biology&gt;&lt;death&gt;&lt;speculative&gt;" AnswerCount="4" CommentCount="7" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8273" PostTypeId="2" ParentId="8247" CreationDate="2013-05-09T10:39:55.240" Score="4" Body="&lt;p&gt;RNAses are enzymes, and there are various ways to inactivate them. Unfortunately, RNAses are rather stable proteins and autoclaving doesn't completely kill their activity. The common methods to inactivate are unspecific methods that will destroy any enzymes, either through covalent modification or degradation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most common methods for RNAse inactivation are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Treatment with DEPC. This covalently modifies histidine and a few other amino acids, which will inactivate RNAses. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Heating to 200-250 °C for at least an hour, this is most commonly used for metal and glass equipment&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Incubation with 1M NaOH for an hour at 37 °C, which will hydrolyze proteins&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Using bleach is not a method I've used, but it should work in principle &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1258487/?page=1&quot; rel=&quot;nofollow&quot;&gt;as hypochlorite will react with proteins&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2013-05-09T10:39:55.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8274" PostTypeId="2" ParentId="8272" CreationDate="2013-05-09T12:03:35.700" Score="5" Body="&lt;p&gt;Less then a minute breathing in the atmosphere (and a very painful death). &lt;a href=&quot;http://en.wikipedia.org/wiki/Atmosphere_of_Mars&quot; rel=&quot;noreferrer&quot;&gt;Mars' atmosphere&lt;/a&gt; is &gt;95% CO&lt;sub&gt;2&lt;/sub&gt; with only trivial O&lt;sub&gt;2&lt;/sub&gt;. These are atmospheric conditions similar to those used to euthanize laboratory animals. He probably wouldn't even make it 200 meters before suffocating.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-05-09T12:03:35.700" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="8275" PostTypeId="2" ParentId="8272" CreationDate="2013-05-09T13:01:31.367" Score="1" Body="&lt;p&gt;Coming up with the exact number is likely to be very difficult but i would put it in the range of 1-2 minutes to impossible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's ignore the lack of oxygen and assume you could hold your breath long enough to reach the safe haven.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The extreme cold would easily drop your core temperature to the realm of severe hypothermia within minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If that doesn't kill you first then the extreme cold has already caused your blood vessels to shrink before you can even take more than a few steps. On top of this the extreme cold is enough to freeze solid any muscles and other tissue, making movement painful / difficult / impossible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now lets assume that through some miracle none of that kills you and you make it to the safe haven. The distinct lack of a magnetic field around the planet exposes you to high levels of UV radiation. Being completely naked and having your entire body exposed to this level of UV is likely to cause lots of mutations throughout your cells. Which in itself will kill you. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So your chances aren't looking good for anything beyond a minute!&lt;/p&gt;&#xA;" OwnerDisplayName="user3393" LastActivityDate="2013-05-09T13:01:31.367" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="8276" PostTypeId="2" ParentId="2690" CreationDate="2013-05-09T13:11:20.383" Score="1" Body="&lt;p&gt;To calculate the charge at different pH:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At pH 3 K, R, H are + and D,E have no charge so add up all of the K,R,H in the sequence and that is your net charge at pH 3&#xA;At pH 6 K, R, H are + but now D,E are (-) so subtract one total from the other to figure if your net charge is + or -.&#xA;At pH 8 K and R are +, H has no charge and D,E are (-).&#xA;At pH 10 R is +, K, H have no charge and D,E are (-).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That can give you a general idea.  You can estimate the charge at pHs in between.  &lt;/p&gt;&#xA;" OwnerUserId="3536" LastActivityDate="2013-05-09T13:11:20.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8277" PostTypeId="1" CreationDate="2013-05-09T14:23:07.080" Score="1" ViewCount="74" Body="&lt;p&gt;I'm looking for a book that provides a good overview of primatology, one aimed more at researchers rather than a popular science book. Ideally, I'd like something with an ethology/ecology angle with an eye towards phylogeny. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My preference would be for an e-book.&lt;/p&gt;&#xA;" OwnerUserId="180" LastEditorUserId="180" LastEditDate="2013-05-11T01:15:37.490" LastActivityDate="2013-06-02T23:07:02.980" Title="Introductory text for primatology" Tags="&lt;ecology&gt;&lt;ethology&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8278" PostTypeId="2" ParentId="8263" CreationDate="2013-05-09T15:09:14.260" Score="1" Body="&lt;p&gt;I think I understand what your issue is here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Often, in diagrams of lens systems and eyes, the diagram will only show rays parallel to the optical axis (&lt;a href=&quot;http://en.wikipedia.org/wiki/Optical_axis&quot; rel=&quot;nofollow&quot;&gt;see here&lt;/a&gt;). Although many optical systems are designed so they are optimal for this axis, off axis rays respond in a fairly predictable way too. &lt;a href=&quot;http://en.wikipedia.org/wiki/File%3aLens3.svg&quot; rel=&quot;nofollow&quot;&gt;This figure&lt;/a&gt; shows an off-axis point source, which focuses at a corresponding off-axis point on the other side of the lens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, there is &quot;one focal point&quot;, as you say, for each position of the object relative to the optical axis. In optics we generally talk about a &lt;em&gt;focal plane&lt;/em&gt; rather than a point, as the focal point only refers to cases of idealized point sources, lasers etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the aperture (pupil) is a completely different matter. This provides a limit to how well an optical system can focus. When the aperture is small, it can focus really well, but not much light can get in. When it is large, the ability to focus is reduced but it allows one to see better in the dark (increasing the signal to noise ratio). Focusing requires all the rays from a source to end up at the same point on the retina/film, the aperture, when it is as small as possible &quot;selects&quot; only those rays that will end up focusing at exactly the right place (assuming the lens focuses to the right place, which it does not in the case of the short or long sighted). This selection cuts out a lot of the light, and often it is good to trade off the ability to focus for the amount of light. Without going into detail, this large aperture results in the focal ability of the optical being strongly dependent on how far away the object is (&lt;a href=&quot;http://en.wikipedia.org/wiki/Depth_of_field&quot; rel=&quot;nofollow&quot;&gt;see this&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question is rather open ended, but I hope this is what you were getting at.&lt;/p&gt;&#xA;" OwnerUserId="180" LastActivityDate="2013-05-09T15:09:14.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8279" PostTypeId="1" AcceptedAnswerId="8283" CreationDate="2013-05-09T17:05:26.883" Score="8" ViewCount="202972" Body="&lt;p&gt;Can humans live without eating food, just by drinking water?  How long can we survive just by drinking water everyday?&lt;/p&gt;&#xA;" OwnerUserId="3537" LastEditorUserId="4101" LastEditDate="2013-09-24T18:37:32.947" LastActivityDate="2014-02-05T14:15:56.893" Title="How long human can survive with just drinking water everyday" Tags="&lt;human-biology&gt;&lt;death&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8280" PostTypeId="2" ParentId="8279" CreationDate="2013-05-09T17:57:55.133" Score="6" Body="&lt;p&gt;This &lt;a href=&quot;http://mostextreme.org/longest_without_food.php&quot;&gt;would vary a LOT depending on the amount of stored fat, previous diet, the weather and even the water drunk&lt;/a&gt;.  Weeks though there is a good chance that a &lt;a href=&quot;http://en.wikipedia.org/wiki/Water_fasting&quot;&gt;loss of electrolytes can cause health problems&lt;/a&gt;.  (that's why I mention the water you drink, because many bottled water brands and wells have a bit of salt in them.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its hard to say from anecdotal experience. There are claims of 3 weeks being easy, but a medical study would be unethical because of the risks posed to the subjects.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-05-09T17:57:55.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8281" PostTypeId="2" ParentId="8262" CreationDate="2013-05-09T18:21:06.357" Score="4" Body="&lt;p&gt;Maybe this is easiest understood comparing to our current rate of CO2 consumption to the possible industrial CO2 absorption rate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.skepticalscience.com/human-co2-smaller-than-natural-emissions.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Human non biological CO2 production is 29 Gtons.  A little more than four tons of carbon per human being each year.  The natural carbon cycle on the planet through CO2 is otherwise about 788 Gtons&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JQpC8.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to grow enough algae to balance our current rate of industrial production? I think so - it would be an additional 2% of the current carbon cycle.  In a first pass, that implies turning 2% of the non-productive earth surface into an average patch of ocean or forest/jungle.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is possible, but it would be expensive.  we're talking about flooding a desert basin for algae production. (numbers are from google). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2% * (area of earth surface = 197million miles^2) = 3.9 M miles^2.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sounds doable, but remember that 70% of the earth's surface is already water and producing algae at a pretty good clip.  We'd be using ~6% of all the land for the algae farm:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.google.com/search?q=surface%20of%20the%20earth&amp;amp;ie=utf-8&amp;amp;oe=utf-8&amp;amp;aq=t&amp;amp;rls=org.mozilla:en-US:official&amp;amp;client=firefox-a&amp;amp;channel=fflb#safe=active&amp;amp;client=firefox-a&amp;amp;hs=s9B&amp;amp;rls=org.mozilla:en-US:official&amp;amp;channel=fflb&amp;amp;sclient=psy-ab&amp;amp;q=land%20area%20australia&amp;amp;oq=land%20area%20australia&amp;amp;gs_l=serp.3..0l4.55307.60301.1.60460.26.16.3.7.7.0.134.1501.10j6.16.0...0.0...1c.1.12.psy-ab.9AA7048KDE8&amp;amp;pbx=1&amp;amp;bav=on.2,or.r_cp.r_qf.&amp;amp;bvm=bv.46340616,d.cGE&amp;amp;fp=fd30d9debcc7a965&amp;amp;biw=1263&amp;amp;bih=842&quot; rel=&quot;nofollow noreferrer&quot;&gt;For comparison,  3.9M miles^2 is larger than the continent of Australia&lt;/a&gt;.  (2.97 Million miles ^2), and bigger than the Sahara desert (3.6 M miles^2).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;just to get into the questions raised in the comments.... To DEPLETE the CO2 level in the atmosphere, we'd have to produce more fuel from the algae than we use - which seems to be impractical from a market standpoint - the fuel would be sitting around in warehouses while the plants die.  I can't imagine anyone making any money from this, and it would be expensive... so it'd be a strange set of circumstances that would deplete the atmosphere from carbon dioxide.  Also more oxygen probably would encourage more combustion and more animals too... so hard to see this happening. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-05-26T04:32:03.640" LastActivityDate="2013-05-26T04:32:03.640" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8282" PostTypeId="1" AcceptedAnswerId="57622" CreationDate="2013-05-09T19:06:15.697" Score="28" ViewCount="30749" Body="&lt;p&gt;How does spacing apart sodium and potassium channels allow the action potential to travel faster down the axon? This is the reason always cited for saltatory conduction and myelination, but my mental model of conduction tells me that the density of ion gates along the axon should not affect the speed of the AP. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To illustrate, consider a myelinated axon. A wave of Na$^+$ from action potential site 1, a node of Ranvier, rushes into and quickly diffuses down the axon. (It travels in both directions, but backwards is still in the refractory period.) It diffuses through the myelinated region, its concentration always diminishing. Before it attenuates too much, however, it happens upon node of Ranvier 2, where it triggers another action potential. A new wave of Na$^+$ rushes in and the cycle repeats. This should be plain so far.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now imagine that there is actually a node of Ranvier halfway between node 1 and 2, called node 1.5. The wave of Na$^+$, on its way to node 2, happens to trigger an action potential at node 1.5, from which a wave of Na$^+$ pours in and either boosts the original wave or replaces it by taking its momentum. Now the reinforced wave proceeds to node 2 and triggers it just as soon as, perhaps even sooner than, if node 1.5 had not existed. Repeatedly insert nodes at higher densities until the situation is simply lack of myelination, and we conclude that unmyelinated axons can transmit an action-potential-triggering wave of Na+ as fast as or faster than a myelinated one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, my point of confusion is this: &lt;strong&gt;I cannot see how a higher density of gated channels can possibly slow down the wavefront of Na+ that triggers action potentials.&lt;/strong&gt; If anything, the additional influxes of Na+ should speed up the all-important wavefront, assuming that new waves really &quot;either boost the original wave or replace it by taking its momentum&quot;, and also assuming that the wavefront of Na$^+$ is really all-important for signal transmission, and also assuming that the mere presence of (voltage?) gated ion channels in the membrane does not significantly retard the wavefront.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the usual explanation for why saltatory conduction is faster than continuous conduction (a fact I hope is empirically and &lt;em&gt;unambiguously&lt;/em&gt; established) relies on &lt;strong&gt;the putative slowing effect of ion channels on the signal fore. Please explain this effect in more detail, if it is not a misconception.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="3538" LastEditorUserId="16866" LastEditDate="2017-03-24T17:01:54.830" LastActivityDate="2020-10-09T02:08:02.673" Title="Why is saltatory conduction in myelinated axons faster than continuous conduction in unmyelinated axons?" Tags="&lt;cell-biology&gt;&lt;neuroscience&gt;&lt;neurophysiology&gt;&lt;biophysics&gt;&lt;electrophysiology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="8283" PostTypeId="2" ParentId="8279" CreationDate="2013-05-10T01:07:13.227" Score="12" Body="&lt;p&gt;About 52 to 74 days according to &lt;a href=&quot;http://en.wikipedia.org/wiki/Hunger_strike#Medical_view&quot;&gt;&lt;code&gt;hunger strike&lt;/code&gt; wiki page&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This wiki page bases its data on &lt;a href=&quot;http://en.wikipedia.org/wiki/1981_Irish_hunger_strike#Participants_who_died_on_hunger_strike&quot;&gt;8 persons who died due to hunger strike&lt;/a&gt;:&lt;br&gt;&#xA;Days survived by each person: 66, 59, 61, 61, 61, 46, 71, 73, 62, 60.&lt;/p&gt;&#xA;" OwnerUserId="3533" LastEditorUserId="3535" LastEditDate="2013-05-10T02:25:36.317" LastActivityDate="2013-05-10T02:25:36.317" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8284" PostTypeId="2" ParentId="7418" CreationDate="2013-05-10T14:45:15.670" Score="3" Body="&lt;p&gt;Following damage to muscle (e.g., as a result of strenuous activity) the injured fibers are removed (by immune cells) and then replaced by new myofibers (individual muscle cells that join to create new muscle tissue). This is why for a few days after exercise your muscles can be sore - it is the tissues being initially cleared of damaged cells and repaired. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Muscles, like other tissues, have resident stem cell populations (&quot;satellite cells&quot;) that are used to replace damaged cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stem cells have potentially indefinite replicative potential, as they express telomerase and thus do not have a traditional Hayflick limit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KPy04.gif&quot; alt=&quot;Skeleteal Muscle Regeneration&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Volonte D, Liu Y, Galbiati F. &lt;a href=&quot;http://www.fasebj.org/content/early/2005/01/27/fj.04-2215fje.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;The modulation of caveolin-1 expression controls satellite cell activation during muscle repair&lt;/a&gt;. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 2005 Feb;19(2):237–9. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastEditorUserId="107" LastEditDate="2013-05-10T15:47:27.033" LastActivityDate="2013-05-10T15:47:27.033" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8285" PostTypeId="1" AcceptedAnswerId="8290" CreationDate="2013-05-10T18:31:42.207" Score="8" ViewCount="692" Body="&lt;p&gt;Is this due to pressure differentials in the surrounding tissue? (Is it possible to have a pinched nerve without compression of the surrounding tissues, and does this cause pain?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the molecules/cell types involved in this process? Is the pain dependent on the compression of axons from mechanosensitive or nociceptive neurons?&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-05-16T07:28:21.403" Title="How does a pinched nerve cause pain (at the molecular level)?" Tags="&lt;neuroscience&gt;&lt;pain&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8286" PostTypeId="1" CreationDate="2013-05-10T19:06:16.663" Score="4" ViewCount="99" Body="&lt;p&gt;I want to save my bacillus strains but I don't have access to a -80 degree freezer.  What are possible alternatives?&lt;/p&gt;&#xA;" OwnerUserId="3541" LastEditorUserId="3059" LastEditDate="2013-05-10T19:59:31.227" LastActivityDate="2013-06-14T12:01:02.177" Title="How can I save bacillus strains on filter paper without an -80 degree freezer?" Tags="&lt;molecular-biology&gt;&lt;bacteriology&gt;&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8287" PostTypeId="2" ParentId="8257" CreationDate="2013-05-10T22:21:33.930" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://species-identification.org/species.php?species_group=zsao&amp;amp;id=1708&quot; rel=&quot;nofollow&quot;&gt;According to the Marine Species Identification portal&lt;/a&gt;, the presence of these thorns is variable.  They also vary in size, shape, and the presence of polygonal frames.  I don't think there is anything about the imaging process described that would result in the uniform loss of spines (unless the sieve/microsplitter broke them all, but I think that would be a non-uniform loss).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Re: whether it's hollow or not, that appears to be variable too.  &lt;a href=&quot;http://www.radiolaria.org/species.htm?sp_id=492&amp;amp;division=13&quot; rel=&quot;nofollow&quot;&gt;One species is filled with oil&lt;/a&gt;, while &lt;a href=&quot;http://www.radiolaria.org/species.htm?sp_id=435&amp;amp;division=27&quot; rel=&quot;nofollow&quot;&gt;another appears to be hollow.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-05-11T08:18:09.130" LastActivityDate="2013-05-11T08:18:09.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8288" PostTypeId="1" CreationDate="2013-05-10T22:48:07.023" Score="4" ViewCount="55" Body="&lt;p&gt;Traditional methods of purifying polyhydroxyalkanoates (PHAs) and other bioplastics made by bacteria involve washing the cells with harsh chemicals or strong bases.I'm interested in maintaining the spatial position of the PHA globules relative to one another. Therefore, I'm hypothesizing that &lt;em&gt;by heating these cells extensively, I can lyse/degrade the cellular matter and be left with only PHAs&lt;/em&gt;, especially given that some PHAs have melting points up to 180 degrees.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is this approach to purifying PHAs plausible? Has it ever been done?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2013-05-15T03:02:03.833" LastActivityDate="2013-05-15T03:02:03.833" Title="Can I purify polyhydroxyalkanoates by heating the cells extensively?" Tags="&lt;lab-techniques&gt;&lt;biotechnology&gt;&lt;purification&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8289" PostTypeId="1" AcceptedAnswerId="8291" CreationDate="2013-05-10T23:25:48.963" Score="7" ViewCount="1725" Body="&lt;p&gt;An interesting tidbit floating around the internet these days is that &lt;a href=&quot;http://en.wikipedia.org/wiki/Duncan_MacDougall_%28doctor%29&quot;&gt;Dr. Duncan MacDougall&lt;/a&gt; apparently weighed people shortly before and after death, and found an average of a 21 gram discrepancy, to which he attributed to be the soul departing. As we all know, this certainly can't be the right explanation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Putting aside likely extreme bias and instrumental/experimental error, &lt;strong&gt;is there any bodily process at death that could potentially explain a small decrease in observed mass?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2017-06-03T19:38:37.470" Title="What could account for an apparent loss of mass at death?" Tags="&lt;human-biology&gt;&lt;death&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8290" PostTypeId="2" ParentId="8285" CreationDate="2013-05-10T23:42:07.637" Score="5" Body="&lt;p&gt;Typically nerve compression or a &quot;pinched&quot; nerve is due to inflammation in the tissue through which a nerve passes. The gap is already quite narrow so any inflammation is quite potent. Inflammation causes you to feel things as more painful (hyperalgesia). In a similar way to how of you burn your hand then poke it, it hurts, when cells are damaged the receptors surrounding them are sensitised to be more reactive. Binding of many ligands involved in inflammation leads to higher than normal sodium influxes which means you feel pain as this impulse is sent. I could be a lot more detailed but not sure what level you want, however for much more detail see this &lt;a href=&quot;http://bja.oxfordjournals.org/content/87/1/3.full&quot;&gt;review&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-10T23:42:07.637" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8291" PostTypeId="2" ParentId="8289" CreationDate="2013-05-11T00:11:14.313" Score="15" Body="&lt;p&gt;Snopes.com gives a &lt;a href=&quot;http://www.snopes.com/religion/soulweight.asp&quot; rel=&quot;noreferrer&quot;&gt;discussion of possible issues with the original experiment&lt;/a&gt;.  Evaporation or bowel or body movements for instance.  I think the biggest complaint about the experiment is that it has not been reproducible and that the original experiment was flawed.  MacDougall only took six measurements and he threw two of them out in his original work.  The Wikipedia link you give cites a paper where sheep were found to &lt;em&gt;gain weight&lt;/em&gt; at least for a time after death.  Dogs are found to have no weight change.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;MacDougall and his contemporaries were inclined to interpret their results such that animals simply do not have souls, or have different sorts of souls.  But if you look at an average of all experiments cited, it could also be said that the average weight loss up on death averages to zero.  3/4 of an ounce of a human being (or a sheep) over the course of something like a death is not an easy measurement.  You can't give them a drink of water, you worry that they are breathing too much and losing water.  Its not an easy experiment, at least for human beings where you can't control the circumstances of death so well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case this really needs to be measured better.  In 90 years it doesn't seem that there's been a real rush to do it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just stumbled across this blog post that talks about an effort to &lt;a href=&quot;http://blogs.discovermagazine.com/neuroskeptic/2013/05/21/a-machine-to-weigh-the-soul/&quot; rel=&quot;noreferrer&quot;&gt;measure a change in blood flow to the brain when in intense mental activity&lt;/a&gt; popularized in the late 19th century.  The investigator Mosso claimed he measured a difference, but the result is disputed today.  It could not have been more than a few grams. In any case a description of how difficult this measurement can be.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-05-22T12:41:13.920" LastActivityDate="2013-05-22T12:41:13.920" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8292" PostTypeId="2" ParentId="8261" CreationDate="2013-05-11T00:12:59.783" Score="2" Body="&lt;p&gt;First, while half the chromosomes come from each of the two parents, these two sets of chromosomes are &lt;em&gt;not&lt;/em&gt; termed X and Y (they would usually be called maternal and paternal).  The terms X and Y refer to potential members of just one pair of the 23 pairs (in humans) of chromosomes, and X chromosomes can come from either the mother or the father.  The presence or absence of a Y chromosome determines sex in mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Y chromosome contains one gene, SRY, which determines sex, and almost no nother genes.  SRY simply switches on the &quot;make a male&quot; program in the cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially all other genes, including any toolbox genes, come from both parents, one copy from each.  (An exception, in males, are those genes on the X chromosome, which in males are present in only one copy and which came from the mother.  Another exception is mitochondrial genes.)&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2013-05-11T00:12:59.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8294" PostTypeId="2" ParentId="8261" CreationDate="2013-05-11T03:37:19.957" Score="2" Body="&lt;p&gt;In addition to @mgkrebbs response, I'd add that many genes are controlled by epigenetic mechanisms &lt;a href=&quot;http://en.wikipedia.org/wiki/Genomic_imprinting#Imprinted_genes_in_mammals&quot; rel=&quot;nofollow&quot;&gt;which may mask one of the parental copies by methylation&lt;/a&gt;.  This can be a specific effect where, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2975825/&quot; rel=&quot;nofollow&quot;&gt;the active gene is specifically from either the father or the mother&lt;/a&gt;. Mosaicism, where one copy of gene is randomly inactivated in any given cell, is also possible.  The classic example of this is &lt;a href=&quot;http://www.vivo.colostate.edu/hbooks/genetics/medgen/chromo/mosaics.html&quot; rel=&quot;nofollow&quot;&gt;X chromosome mosaicism&lt;/a&gt;, where the entire X chromosome in each cell of a female is silenced. (At least in the case of humans and animals like humans)&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-05-11T03:37:19.957" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8295" PostTypeId="1" AcceptedAnswerId="8296" CreationDate="2013-05-11T08:22:29.967" Score="4" ViewCount="2111" Body="&lt;p&gt;By what mechanism does an obstructed bile duct (for example gallstones) cause steatorrhoea (excess fat in the stool)?&lt;/p&gt;&#xA;" OwnerUserId="1413" LastEditorUserId="948" LastEditDate="2013-05-11T14:12:30.277" LastActivityDate="2015-06-19T01:22:23.163" Title="By what mechanism does an obstructed bile duct cause excess fat in the stool?" Tags="&lt;digestive-system&gt;&lt;pathology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8296" PostTypeId="2" ParentId="8295" CreationDate="2013-05-11T10:02:05.003" Score="8" Body="&lt;p&gt;The function of bile produced by the liver and concentrated in the gall bladder is to aid in fat digestion.  Bile acts as an emulsifier to allow the fat to be packaged into small droplets, micelles.  The breakdown of fats into small micelles greatly increases the surface area for lipases produced by the pancreas have to act on.  These are then absorbed across the intestinal wall. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Uebdt.png&quot; alt=&quot;Breaking down of fats into micelles&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;Bile breaking down large fats into small micelles&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this first step of bile production and transport is lacking (due to liver dysfunction or obstruction anywhere in the biliary tree), the fats are not packaged into micelles and are consequently very hard to digest.  They pass through the entire alimentary canal virtually undigested causing steatorrhoea, fatty, bulky and foul smelling stool.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MxomR.jpg&quot; alt=&quot;The Biliary Tree&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;The Biliary Tree&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2013-05-11T10:02:05.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8297" PostTypeId="1" CreationDate="2013-05-11T11:39:32.420" Score="2" ViewCount="63" Body="&lt;p&gt;Stress echocardiography means a pair of cardiac ultrasound imaging examinations, before and after exercise. I assume that coronary blood flow is increased after exercise. Is cardiac ultrasound technology capable of showing this blood flow difference?&#xA;&lt;hr/&gt;&#xA;Update: I emphasize that my question concerns &lt;a href=&quot;https://en.wikipedia.org/wiki/Stress_echocardiography#Stress_echocardiography&quot; rel=&quot;nofollow&quot;&gt;stress echocardiography&lt;/a&gt;, i.e. two echocardiography sessions before and after exercise (or pharmacological stress test) - not simply echocardiography.&lt;/p&gt;&#xA;" OwnerUserId="1413" LastEditorUserId="1413" LastEditDate="2013-05-21T21:46:02.213" LastActivityDate="2013-05-21T22:01:49.023" Title="Can stress echocardiography show coronary blood flow difference before and after exercise?" Tags="&lt;cardiology&gt;&lt;imaging&gt;&lt;ultrasound&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8298" PostTypeId="1" CreationDate="2013-05-11T11:45:54.677" Score="2" ViewCount="550" Body="&lt;p&gt;Elevated homocysteine levels are listed among risk factors for angina. How is homocysteine related to the heart? Or the coronary arteries? How do these relationships make it a risk factor for angina? &#xA;&lt;img src=&quot;https://i.stack.imgur.com/WIITF.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1413" LastEditorUserId="1413" LastEditDate="2013-05-30T09:20:01.447" LastActivityDate="2013-05-30T09:20:01.447" Title="Why is elevated homocysteine considered a risk factor for angina?" Tags="&lt;cardiology&gt;&lt;homocysteine&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8299" PostTypeId="2" ParentId="7691" CreationDate="2013-05-11T14:51:14.533" Score="0" Body="&lt;p&gt;I was at a talk last year where some geneticists were starting to look at the effect of IVF techniques on genetic issues.  Because of the work being done and the inclinations of the clients involved, this has not been studied very much.  One presumes that since zygotes are still used, there will not be much epigenetic effects due to methylation patterns - its the same cell stocks being used in vitro and in vivo.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There may be an effect on genetics because the natural selection process.  Spermatogenesis and oogenesis is a highly selective process; only a small fraction of the ova generated by the ovaries ever mature and a large percentage of sperm generated are not motile or have other irregularities.  During fertilization, sperm competition obviously throws out all but &lt;a href=&quot;http://en.wikipedia.org/wiki/Semen_analysis#Total_sperm_count&quot; rel=&quot;nofollow&quot;&gt;one in 250 million&lt;/a&gt;.  It also appears that there are processes in the fallopian tubes that can store the &lt;a href=&quot;http://humupd.oxfordjournals.org/content/12/1/23.full&quot; rel=&quot;nofollow&quot;&gt;sperm for several (up to 5) days before fertilization&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So while its not strongly established one can see how various IVF processes vary from in vivo fertilization.  This could have an impact on epigenetic factors, although different sperm vary genetically due to Meiosis and this would be a big source of genetic variation in the outcome. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-05-11T14:51:14.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8300" PostTypeId="2" ParentId="8298" CreationDate="2013-05-11T16:05:05.353" Score="2" Body="&lt;p&gt;&lt;strong&gt;Homocysteine&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Causes endothelial dysfunction and damage&lt;/li&gt;&#xA;&lt;li&gt;Accelerates thrombin formation&lt;/li&gt;&#xA;&lt;li&gt;Inhibits native thrombolysis&lt;/li&gt;&#xA;&lt;li&gt;Promotes lipid peroxidation through free radical formation&lt;/li&gt;&#xA;&lt;li&gt;Induces vascular smooth muscle proliferation&lt;/li&gt;&#xA;&lt;li&gt;Promotes monocyte chemotaxis&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Many observational epidemiological studies indicate that individuals with higher &lt;strong&gt;Homocysteine&lt;/strong&gt; levels have increased risks of cardiovascular disease. &lt;/p&gt;&#xA;" OwnerUserId="3533" LastEditorUserId="1320" LastEditDate="2013-05-11T18:39:14.957" LastActivityDate="2013-05-11T18:39:14.957" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="8301" PostTypeId="2" ParentId="8297" CreationDate="2013-05-11T16:13:14.300" Score="1" Body="&lt;p&gt;No, echocardiography is not sensitive enough to do so. For tracing coronary arteries directly flow angiography is the choice.&lt;/p&gt;&#xA;" OwnerUserId="3533" LastEditorUserId="1413" LastEditDate="2013-05-17T12:24:19.760" LastActivityDate="2013-05-17T12:24:19.760" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8302" PostTypeId="1" CreationDate="2013-05-11T16:36:24.820" Score="20" ViewCount="13305" Body="&lt;p&gt;Almost all organs in the human body have a rather large threshold within which the organ or tissue is capable of repairing itself using materials supplied by the body, whether it's made from organic tissue or structural proteins. Wounds and minor damage to the skin or flesh for example heal by themselves, skin, nails and body hair can grow back if damaged or removed, even most bones can be repaired autonomously by a biological body. Cutting off a significant chunk from the human flesh or removing over 90% of a hair or a nail would cause no permanent injury, and the body is capable of repairing the damage over time with ease. The vast majority of the human body (not counting critical organs such as the heart or the brain) can be &quot;grown back&quot; to an extent by itself, because such parts have a rather large damage threshold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the contrary, teeth do not. There is a certain threshold in which tooth enamel can be supplied and &quot;repaired&quot; by the body to an minimal degree, but past that point virtually any damage caused to teeth are permanently irreparable by natural means. Which is quite strange, given how fragile a set of human teeth is, be it chemical or physical damage. Especially if you take more &quot;artificial&quot; causes into account. A moderately heavy object aimed towards a human mouth, for example, can easily render ten to fifteen teeth permanently damaged past the point of recovery within a heartbeat, also causing the said person's digestive process to be heavily impaired.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another strange fact worth noting, is that the human body is capable of producing two separate set of teeth due to biological growth and size differences, but not more than that. Wouldn't it be beneficial for a biological body to be able to supply new teeth in the place of ones that have been damaged or removed? One could argue that such an action would be too complex and impossible, similarly to growing back an entire limb or a spare heart, but given the material that makes up teeth and its fragile nature, it would be safe to assume that it is biologically possible, especially given the fact that the human body DOES produce two separate set of teeth over its lifespan.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, even stranger still, is that the only element capable of damaging or deteriorating  teeth by natural means, is the consumed &lt;em&gt;food&lt;/em&gt; itself, and the acidic bacteria found within. Several types of edible food consumable by human means are capable of damaging the enamel to critical levels within relatively short periods of time, even non-artificial ones. What happened before the invention of the toothbrush and various dental cleaning methods? Why haven't humans evolved in the past tens of thousands of years to the point where repairing or regrowing teeth by natural means is feasible? Simply put, why don't teeth grow back contrary to hair, nails or skin?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the biological and evolutionary reason behind teeth being so fragile and indisposable?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="3545" LastActivityDate="2019-08-27T05:06:47.037" Title="What is the evolutionary reason behind the fragility of teeth?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;human-anatomy&gt;&lt;protein-evolution&gt;&lt;teeth&gt;" AnswerCount="5" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8303" PostTypeId="1" AcceptedAnswerId="8306" CreationDate="2013-05-11T21:30:30.063" Score="4" ViewCount="1498" Body="&lt;p&gt;All of the references to this I can find refer to enzymes like Flippase making it 'easier' or 'more likely' that the translocation will occur, rather than actually make it possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following is from Alberts&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the ER, however, phospholipids equilibrate across the membrane within minutes, which is almost 100,000 times faster than can be accounted for by spontaneous “flip-flop.”&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Does this mean that left unattended, any phospholipid membrane will 'flip-flop' spontaneously, just very slowly, and can this be observed?&lt;/p&gt;&#xA;" OwnerUserId="1474" LastActivityDate="2016-11-16T01:52:16.493" Title="Will lipid molecules 'flip-flop' over a membrane without the use of an enzyme?" Tags="&lt;cell-biology&gt;&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8304" PostTypeId="2" ParentId="2874" CreationDate="2013-05-12T05:08:08.080" Score="11" Body="&lt;p&gt;Here is a possible answer given by this paper: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16794952&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/16794952&lt;/a&gt;&lt;br&gt;&#xA;or&#xA;&lt;a href=&quot;http://www.math.unl.edu/~bdeng1/Papers/DengDNAreplication.pdf&quot; rel=&quot;noreferrer&quot;&gt;http://www.math.unl.edu/~bdeng1/Papers/DengDNAreplication.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It gives a Darwinian explanation to the question. It approaches the problem from Claude Shannon's theory for communication. It treats DNA replication conceptually and mathematically the same as a data transmission. It concludes that the system of four bases, not two, not six, replicates the most genetic information at the shortest amount of time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The communicational analogy goes like this. If you have two data transmission systems, one can transmit, say, 1 MB per second, and the other can do 2 MB per second but cost less than twice as much. The answer is obvious you will buy the second service for a higher rate per cost. As a data service, it does not care what information you consume -- it can be spam, video, audio, etc. All that matters is the transmission rate. As for DNA replication, it is like a data transmission channel when one base is replicated a time along the mother DNA template. It too does not care whether the process is for a bacterium genome, or a plant, or an animal genome. The pay-off is in information and the cost is in time. Unlike your abiotic communication varieties, time is both the sender and the receiver of all messages of life, and different life forms or species are merely time's cell phones. So if one system can replicate more information in a unit time than another, the faster one will win the evolutionary arm race. A prey operating on a slow replicator system will not be able to compete with nor to adapt to a predator operating on a fast one. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now because the A-T pair has only two weak hydrogen bonds but the C-G pair has three, A and T take a shorter time to complete duplication than the C and G do. Although the replication time is short in some fraction of nano second, but the time adds up quickly for genomes with base pairs in the billions. So having the C-G pair may slow down the replication, but the gain is in information. One base pair gives you 1 bit per base information. Two pairs gives you 2 bits per base information. But, having more base pairs may eventually run into a diminished return in information replication rate if the new bases take too long a time to replicate. Hence the consideration for the optimal rate of replication measured in information bits per base per time. Without information there would be no diversity, no complexity. Without replication in information there would be no life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using a simple transmission/replication rate calculation by Shannon you can calculate the mean rate for the AT-system, the CG-system, the ATCG-system, and for some hypothetical 6-bases, 2n-bases system whose new bases take progressively longer time to replicate. The analysis shows the ATCG-system has the optimal replication rate if the CG bases take 1.65 to 3 times longer to replicate than the AT bases. That is, a base-2 system replicates its bases faster but does not carry more information to have a higher bit rate. Likewise, a base-6 system has a greater per-base information but replicate slower on average to end up with a suboptimal bit rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NLxOG.jpg&quot; alt=&quot;DNA Replication Rate&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to a comparison from the paper, the base-4 system is about 40% faster than the  A–T only system, and 133% faster than the G–C only system. Assume life on Earth started about 4 billion years ago, then the A-T only system would set back evolution by 1 billion years, the G–C system would do so by 2.3 billion years. For a hypothetical base-6 system, it would do so by 80 million years. In other words, life is where it should be because the base-4 system is able to transmit information through the time bottleneck at the optimal  bit rate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion, life is to replicate the most information with the shortest time, and the base-4 system does it the best. If ever there were other systems they would have lost the informatic competition to the base-4 system from the get-go. Darwin's principle works at life's most basic and most important level.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other explanations, all non-Darwinian. Most are based on the base's molecular structures. But these types of explanation border on circular argument -- using observations to explain themselves. They also face this catch-22 problem since there is no way to exhaust all possible bases for replication. However, such lines of exploration are fruitful regardless because more knowledge the better. But without taking information and its replication into consideration it is hard to imagine a sensible answer to the question.&lt;/p&gt;&#xA;" OwnerUserId="3548" LastEditorUserId="3548" LastEditDate="2013-05-14T17:57:25.910" LastActivityDate="2013-05-14T17:57:25.910" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8305" PostTypeId="1" AcceptedAnswerId="8321" CreationDate="2013-05-12T08:22:47.023" Score="3" ViewCount="766" Body="&lt;p&gt;I understand multiple origin bubbles; DNA polymerase only synthesizes DNA from 5' to 3' and all that. But what I don't understand is why it has to be in fragments. Yes, DNA is anti parallel, and so the DNA elongates in opposite directions, since DNA polymerase can only go one way. But why not go on just like the leading strand? Why not continue happily along the DNA template continuously but in fragments? &lt;/p&gt;&#xA;" OwnerUserId="3549" LastEditorUserId="107" LastEditDate="2013-05-13T00:07:35.223" LastActivityDate="2013-05-13T00:07:35.223" Title="DNA replication Okazaki fragments" Tags="&lt;genetics&gt;&lt;dna&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8306" PostTypeId="2" ParentId="8303" CreationDate="2013-05-12T11:11:34.103" Score="5" Body="&lt;p&gt;Bilayer components will 'flip-flop' at measurable rates, but these are very different for different lipid classes. Here are the results of an experiment using fluorescently-labelled analogues.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bai, JN and Pagano, RE (1997) Measurement of spontaneous transfer and transbilayer movement of BODIPY-labeled lipids in lipid vesicles. Biochemistry 36:8840-8848 &lt;a href=&quot;http://dx.doi.org/10.1021/bi970145r&quot; rel=&quot;nofollow&quot;&gt;DOI: 10.1021/bi970145r&lt;/a&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors followed the transbilayer (flip-flop) and interbilayer movement of fluorescently-labelled analogues of various membrane lipids: sphingomyelin (C-5-DMB-SM), ceramide (C-5-DMB-Cer), phosphatidylcholine (C-5-DMB-PC) and diacylglycerol (C-5-DMB-DAG) in a system of unilamellar vesicles consisting of 1-palmitoyl-2-oleoyl phosphatidylcholine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The results were analysed in terms of a model in which the labelled molecules could move between vesicles and between the two monolayers of the bilayer.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;half times:&#xA;            interbilayer    transbilayer (flip-flop)&#xA;C-5-DMB-SM  &amp;gt;21 s           3.3 h               &#xA;C-5-DMB-Cer 350 s           22 min&#xA;C-5-DMB-PC  400 s           7.5 h&#xA;C-5-DMB-DAG 100 h           70 ms&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So, for the phospholipid tested the half-time for flip-flop was 7.5 hours.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-05-12T12:09:42.163" LastActivityDate="2013-05-12T12:09:42.163" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8307" PostTypeId="1" AcceptedAnswerId="8311" CreationDate="2013-05-12T12:11:04.970" Score="3" ViewCount="249" Body="&lt;p&gt;According to this &lt;a href=&quot;http://www.foxnews.com/science/2013/02/06/3d-printed-human-embryonic-stem-cells/&quot; rel=&quot;nofollow&quot;&gt;news&lt;/a&gt;, scientists can use stem cells to print objects. So say theoretically, is there any possibility to print human beings? &lt;/p&gt;&#xA;" OwnerUserId="1011" OwnerDisplayName="Popopo" LastEditorUserId="948" LastEditDate="2013-05-12T14:01:45.900" LastActivityDate="2013-05-12T19:35:16.237" Title="Is it possible to print humans?" Tags="&lt;stem-cells&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8309" PostTypeId="2" ParentId="3720" CreationDate="2013-05-12T16:15:19.203" Score="2" Body="&lt;p&gt;The process of formation of different types of cells that differ in morphology and function is termed as cell differentiation. In multi-celled organism, each task of life is carried out by different types of  specialized cells say nerve cell for transmitting impulses, muscle cells for coordinating movement and these cells differ in their appearance and function, but originated from the same parental cell, the zygote. These specialized cells are formed by a process called differentiation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cell differentiation is the process by which genetically identical cells of an embryo become specialized. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;From a fertilized egg, at least 250 distinct types of differentiated cells are present in adults.&lt;/li&gt;&#xA;&lt;li&gt;Zygote-&gt;determination -&gt;differentiation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Cell specialization involves the preferential synthesis of some specific proteins like antibodies in plasma cells or Hb in erythrocytes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genome is the same in all cells of our body, but only certain genes are turned on and other genes are switched off and this lead to specialization. That is, genes active in the neurons may not be active in muscle cells. For instance, genes for actin and myosin filaments are present in all animal cells, but these genes are active only in muscle cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biologyexams4u.com/2012/08/cell-differentiation.html&quot; rel=&quot;nofollow&quot;&gt;http://www.biologyexams4u.com/2012/08/cell-differentiation.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3544" LastEditorUserId="69" LastEditDate="2013-05-12T17:06:22.270" LastActivityDate="2013-05-12T17:06:22.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8310" PostTypeId="1" AcceptedAnswerId="8315" CreationDate="2013-05-12T16:58:59.363" Score="2" ViewCount="1778" Body="&lt;p&gt;Is a light source giving off light composed of red, green and blue lights harmful to the eyes? Does it lack any important qualities that other artificial light sources, such incandescent lamps or white LEDs may have?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it alright to use RGB light panels in a room instead of the usual lighting?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2013-05-12T23:16:53.760" Title="Is RGB diode lighting okay for the eyes?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8311" PostTypeId="2" ParentId="8307" CreationDate="2013-05-12T17:57:04.430" Score="8" Body="&lt;p&gt;The easiest answer to this question is NO. We will not be able to print humans any time soon, if ever. Despite the potential of the technology, it will likely still make more sense to use stem cells to fight genetic diseases, create limited cellular masses such as hearts and other organs, and to do reconstructive surgeries such as skeletal repairs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reasons vary but will include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The human being is not just a single series of cells, we are a complex melange of integrated systems connected together in a predetermined manner by our genetic code.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The standard 3D printing process might be most effective for producing a single type of cells or a simple organ whose structure is simple and whose configuration could be managed with computer aided design to produce the cells needed at the time of the organ's creation. Even an organ such as a liver will need connective tissues, for blood to be provided for the organ and those cells would need to be integrated as well.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Brain tissue would be the most difficult part of this process. Even having the tissue matrix derived from stem cells would not give us the understanding of how to create an actual brain from a printing process, which uses a layering method to deliver the material into a 3D structure. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It is certain that some things we may do in the future may be done by printing output that resembles cellular matter, i.e. bone repair and restructuring.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;In the case of fixed materials such as bone, a 3D model could be taken and then replicated on a printer. The replicated material is then integrated into an area of the body and allowed to either grow in place or artificially stimulated to grow to replace the damaged area. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I use bones as an example since they have very limited purposes and once replicated artificially, would be relatively easy to put in place. This would certainly transform the dental industry, perhaps hip replacement surgeries. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If the technology could be applied internally to damaged tissues, perhaps spinal injuries could be repaired and with proper rehabilitation, a person who may have lost mobility due to an injury could have nervous tissue regrown and learn to walk again. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The potential for specific cellular development is outstanding but the method for growing complete humans has had millions of years evolution and not likely to be surpassed by Humanity in the next thirty to one hundred years unless we come to a far greater understanding of the human genome and the genetic/cellular relationships between systems in the human body as a collective whole.&lt;/p&gt;&#xA;" OwnerUserId="1099" LastActivityDate="2013-05-12T17:57:04.430" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8312" PostTypeId="1" AcceptedAnswerId="8316" CreationDate="2013-05-12T19:16:00.903" Score="1" ViewCount="77" Body="&lt;p&gt;I'm experimenting with a consumer-grade ElectroEncephaloGram (EEG) sensor and have created the image below using the device. Because the sensor on the device does not use a suction cup, there are a lot of motion artifacts when the headband contact is poor (during motion). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/p4Pb7.png&quot; alt=&quot;mindwave eeg motion artifact&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This got me thinking - neurons have mass and thus inertia, and they are not glued to each other.  When the person moves (actually rotates) the head around, forces of inertia are applied to neurons/axons. &lt;strong&gt;I'm interested if such motion produces any kind of firing artifacts within the brain or how the brain filters out such firing?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This reminded me of this article: (&lt;a href=&quot;http://www.princeton.edu/~sswang/awake_cerebellar_ms_refs/jacobs_fornal93_TINS.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;5-HT and motor control: a hypothesis&lt;/a&gt;). Could it be that some neurons stop firing in response to movement?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BBHKB.png&quot; alt=&quot;Cat neuronal firing change in response to movement&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-05-12T19:50:40.987" Title="Are there neuronal firing artifacts produced by head movement?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8313" PostTypeId="2" ParentId="8307" CreationDate="2013-05-12T19:35:16.237" Score="2" Body="&lt;p&gt;No.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason is that development is extremely important for getting tissue organized on the appropriate scale.  We can place groups of cells or a scaffold somewhere, but we can't assemble a working cell from component bits, much less make one that has one end in one's toe and the other in the spine (as is the case with sensory neurons for our legs).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So 3d printing of tissue is limited to tissues that have very simple or robustly automatic developmental processes.  This includes things like skin, liver, and bone; it does not include things like muscle, neurons, joints, or blood vessels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As technology and knowledge of developmental processes advances, we will be able to print more complex things, but it's not clear to me when or if we'll start running into physical limitations that mean that we basically just have to let things grow and develop the way they normally do.&lt;/p&gt;&#xA;" OwnerUserId="696" LastActivityDate="2013-05-12T19:35:16.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8314" PostTypeId="2" ParentId="8305" CreationDate="2013-05-12T19:40:33.357" Score="1" Body="&lt;p&gt;It's in fragments for efficiency.  Single-stranded DNA is not very stable without &lt;a href=&quot;http://en.wikipedia.org/wiki/Single-strand_binding_protein&quot; rel=&quot;nofollow&quot;&gt;proteins to stabilize it&lt;/a&gt;.  If you tried to replicate the entire strand in one go, you'd need to keep the entire strand in single-stranded form one way or another (e.g. start at both ends and meet in the middle would still leave each half as an old/new duplex, plus an old single-stranded copy waiting to be filled in from the other direction).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To avoid needing a chromosome or genome's worth of SSDNA binding proteins, it works in fragments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(That is: if you had organisms that had to produce that much SSDNA binding protein, they'd be out-competed by organisms that didn't have to.)&lt;/p&gt;&#xA;" OwnerUserId="696" LastActivityDate="2013-05-12T19:40:33.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8315" PostTypeId="2" ParentId="8310" CreationDate="2013-05-12T19:45:18.397" Score="5" Body="&lt;p&gt;At a fundamental level, no, we're fine with LED lighting.  The &lt;a href=&quot;http://en.wikipedia.org/wiki/Color_vision&quot; rel=&quot;nofollow&quot;&gt;absorption spectra of our cones are quite broad&lt;/a&gt;, and RGB LEDs are chosen to match our color sensitivity reasonably well.  That red+green looks the same to us as light that is actually yellow is because our eyes can't tell the difference since we don't have good enough spectral resolution in our vision.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There could be more subtle emotional or other complex effects, but to a good approximation, if it looks right it is right, and there aren't magical frequencies that we need to avoid e.g. retinal degeneration or something else awful.  (Well, large amounts of UV are bad, but RGB LEDs don't produce a significant amount of UV.)&lt;/p&gt;&#xA;" OwnerUserId="696" LastEditorUserId="696" LastEditDate="2013-05-12T23:16:53.760" LastActivityDate="2013-05-12T23:16:53.760" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8316" PostTypeId="2" ParentId="8312" CreationDate="2013-05-12T19:50:40.987" Score="5" Body="&lt;p&gt;There are certainly &lt;a href=&quot;http://en.wikipedia.org/wiki/Head_direction_cells&quot;&gt;head-orientation&lt;/a&gt; cells (e.g. in the hippocampus).  But neurons are reasonably immune to the kind of mild physical stresses that come from turning the head around; computing head orientation requires complex analysis of input from e.g. the visual system (optic flow) and vestibular system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the electrical activity of muscles tends to swamp that of (nearby) neurons, so various muscle-related artifacts are often visible in an EEG if not carefully filtered out.  And, of course, if the contact is poor you'll get artifacts from that: you're just measuring the variability in resistance between the sensor and your skin, not anything interesting about what faint potential changes are visible at your skin as a result of neuronal activity.&lt;/p&gt;&#xA;" OwnerUserId="696" LastActivityDate="2013-05-12T19:50:40.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8317" PostTypeId="1" AcceptedAnswerId="8320" CreationDate="2013-05-12T21:12:55.150" Score="9" ViewCount="14587" Body="&lt;p&gt;If a person contracts a virus, viral conjunctivitis for example, is it possible for the individual to become &quot;reinfected&quot; with the exact same strain of the virus once the person has it treated and the symptoms have gone away? I am a nursing student and am fascinated with virology, but my basic microbiology class did not go very in-depth on the subject. &lt;/p&gt;&#xA;" OwnerUserId="3554" LastActivityDate="2018-10-24T21:29:01.990" Title="Is it possible for a person to become &quot;reinfected&quot; with the same strain of a virus?" Tags="&lt;microbiology&gt;&lt;virology&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8318" PostTypeId="1" AcceptedAnswerId="8346" CreationDate="2013-05-12T21:21:56.290" Score="6" ViewCount="1043" Body="&lt;p&gt;With the osmolarity of the average vertebrate being around 300mOsml, and salt water having an osmolarity of 1000mOsml, why does the water from the shark not leave to the salt water around it? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I presume the scales must act as a barrier to stop water form leaving, but with the blood vessels being exposed to the saline water in the gills, why does water not leave the body?&lt;/p&gt;&#xA;" OwnerUserId="3382" LastActivityDate="2013-05-14T07:20:07.957" Title="How do sharks and other fish conserve and gain water in marine environments?" Tags="&lt;zoology&gt;&lt;marine-biology&gt;&lt;ichthyology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8319" PostTypeId="1" CreationDate="2013-05-12T22:25:50.473" Score="2" ViewCount="64" Body="&lt;p&gt;I am trying to view several data tracks in the modENCODE GBrowse genomic browser. However, the site is so slow, it is practically unworkable. Is there a faster way to explore the data?&lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2014-08-07T18:44:23.957" Title="How can I view modENCODE data faster?" Tags="&lt;bioinformatics&gt;&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8320" PostTypeId="2" ParentId="8317" CreationDate="2013-05-12T22:38:19.653" Score="9" Body="&lt;p&gt;The nature of infectious agents is that they transmit between organisms. This means that they have reservoirs outside a single host, and hence of course encountering the exact same strain twice is possible if this strain leaves the body and at a later stage is carried back to it. This could typically happen for example with influenza or common cold viruses, spreading from one child to other children at school and later being carried back to the original child through them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason why the child will not develop another illness when being exposed to the same virus again is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Adaptive_immune_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;adaptive immune response&lt;/a&gt;: After the first infection, immune cells specific to a pathogen will proliferate and differentiate both into effector cells to destroy the pathogen, and into memory cells. These can mount a much stronger immune response much faster when they come in contact with the same (or a structurally very similar) pathogen, meaning that a secondary exposure usually does not result in a proper infection and illness. Of course, this mechanism doesn't work properly for anyone with a compromised immune system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In most cases where a viral disease develops repeatedly, this is due to evasion mechanisms. For example in some viruses, those antigens which tend to be targeted by immune systems have high mutation rates. In this case the &quot;same&quot; virus is actually a mutated strain which causes the same illness, but &quot;looks&quot; different to the immune system, and so the memory cells don't respond. Again, influenza is a great example. The reason why we get flu again winter after winter, is because this virus tends to &lt;a href=&quot;https://www.cdc.gov/flu/about/viruses/change.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;mutate over the year&lt;/a&gt; with relatively low infection prevalence. Then during the winter, when the conditions are favourable for flu infections, typically only a small number of strains cause epidemics - because we were maybe immune to last year's influenza, but this year's has mutated antigens which our immune systems do not recognise yet.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2018-10-24T21:29:01.990" LastActivityDate="2018-10-24T21:29:01.990" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="8321" PostTypeId="2" ParentId="8305" CreationDate="2013-05-12T23:05:35.303" Score="3" Body="&lt;p&gt;I think you may have been misled by graphic representations of the process: The actual replication fork is very small as, like Rex Kerr mentions, it costs a lot of energy to keep DNA single stranded. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a watch of &lt;a href=&quot;https://www.youtube.com/watch?v=yqESR7E4b_8&quot; rel=&quot;nofollow&quot;&gt;https://www.youtube.com/watch?v=yqESR7E4b_8&lt;/a&gt; at minute 1:45, it contains a relatively realistic representation of the replication fork. Of course you have to imagine all of the space around the molecules in this video to be filled with other DNA, RNA, proteins and small molecules zipping about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On top of this, we like to think of DNA as a lone double strand where occasionally a protein might attach and do something. Realistically however, most of the DNA is constantly being manipulated by all sorts of proteins (mostly histones for compression, but also transcription factors, methylating and demethylating enzymes, DNA repair enzymes,...). DNA replication has to minimise the interruption it causes to all the mechanisms going on around it, and the most effective way to do this is by replicating the lagging strands in fragments which can be zipped up quickly and left to whatever other proteins might do to it.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-05-12T23:05:35.303" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8323" PostTypeId="1" CreationDate="2013-05-13T01:13:48.200" Score="1" ViewCount="112" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uzgcI.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know what this is a marsupial, but i'm not quite sure which one. Any thoughts? &lt;/p&gt;&#xA;" OwnerUserId="3382" LastEditorUserId="3059" LastEditDate="2013-05-13T03:41:43.727" LastActivityDate="2013-05-13T03:41:43.727" Title="Does anyone know what marsupial this is?" Tags="&lt;zoology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2013-05-13T10:14:02.513" ContentLicense="CC BY-SA 3.0" />
  <row Id="8324" PostTypeId="2" ParentId="8323" CreationDate="2013-05-13T01:23:05.137" Score="2" Body="&lt;p&gt;I've been told it is the marsupial 'Myrmecobius fasciatus' commonly known as the numbat. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Numbat&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Numbat&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3382" LastActivityDate="2013-05-13T01:23:05.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8325" PostTypeId="2" ParentId="8244" CreationDate="2013-05-13T06:23:44.593" Score="1" Body="&lt;p&gt;This question is extremely vague, and can't have any real answer without you specifying a question or at least focus. Keep in mind, there is no high-road to research, you will have to dig in and start reading papers to gain understanding of your field. If you want help from others, you should at least take time to list the papers that you have already read and why you liked them to give readers a flavor of your interests.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To start you off, consider this &lt;a href=&quot;http://scholar.google.ca/scholar?as_ylo=2009&amp;amp;q=Systems+biology&amp;amp;hl=en&amp;amp;as_sdt=0,5&quot; rel=&quot;nofollow&quot;&gt;Google Scholar query for systems biology since 2009&lt;/a&gt;. If you've read specific older papers that you've liked, for example this popular 2002 minu-survey:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kitano, H. (2002). Systems biology: a brief overview. &lt;i&gt;Science&lt;/i&gt;, 295(5560), 1662-1664.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then you can learn how the field has advanced since by &lt;a href=&quot;http://scholar.google.ca/scholar?cites=6041215083008231674&amp;amp;as_sdt=2005&amp;amp;sciodt=0,5&amp;amp;hl=en&quot; rel=&quot;nofollow&quot;&gt;doing a forward search in Scholar&lt;/a&gt; (and &lt;a href=&quot;http://scholar.google.ca/scholar?as_ylo=2009&amp;amp;hl=en&amp;amp;as_sdt=2005&amp;amp;sciodt=0,5&amp;amp;cites=6041215083008231674&amp;amp;scipsc=&quot; rel=&quot;nofollow&quot;&gt;restricted to 2009+&lt;/a&gt;). Hopefully this will provide you will some ideas so that you can ask a more precise question!&lt;/p&gt;&#xA;" OwnerUserId="500" LastActivityDate="2013-05-13T06:23:44.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8326" PostTypeId="2" ParentId="7980" CreationDate="2013-05-13T06:42:53.280" Score="1" Body="&lt;p&gt;please go through the journal: S. Jo, K. Park, Biomaterials 21 (2000) 605-616.&#xA;The time and temperature probably helps to hydrolyze, formation of hydrogen bond and covalent bond formation. Hope this paper will help you.&#xA;Good luck!&lt;/p&gt;&#xA;" OwnerUserId="3555" LastActivityDate="2013-05-13T06:42:53.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8327" PostTypeId="1" CreationDate="2013-05-13T10:42:33.680" Score="2" ViewCount="1353" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/a/8300/1413&quot;&gt;It has been stated&lt;/a&gt; that elevated homocysteine level causes endothelial dysfunction and damage. By what mechanism does this happen? Why is it the endothel where elevated homocysteine causes problems?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WIITF.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1413" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-07-21T04:59:37.543" Title="By what mechanism does elevated homocysteine level cause endothelial dysfunction and damage?" Tags="&lt;homocysteine&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8328" PostTypeId="1" AcceptedAnswerId="8333" CreationDate="2013-05-13T10:56:35.280" Score="1" ViewCount="1357" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/a/8300/1413&quot;&gt;It has been stated&lt;/a&gt; that elevated homocysteine level accelerates thrombin formation. By what mechanism does this happen?&lt;/p&gt;&#xA;" OwnerUserId="1413" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-05-13T15:39:40.097" Title="By what mechanism does elevated homocysteine level accelerate thrombin formation?" Tags="&lt;homocysteine&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8329" PostTypeId="1" CreationDate="2013-05-13T13:46:15.813" Score="1" ViewCount="60" Body="&lt;p&gt;I read on the text book:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The characteristic of &lt;em&gt;Dinemasporium&lt;/em&gt; are: superficial, cupulate to &lt;em&gt;Discoid conidiomata&lt;/em&gt; with brown satae, &lt;em&gt;Phialid conidiogenous&lt;/em&gt; cells that give rise to hyaline, &lt;strong&gt;oblong to &lt;em&gt;Allantoids&lt;/em&gt;&lt;/strong&gt;, and &lt;em&gt;Aseptate conidia&lt;/em&gt; with an appendage at each end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;the phrase &quot;oblong to &lt;em&gt;Allantoids&lt;/em&gt;&quot;; Is the word &lt;strong&gt;oblong&lt;/strong&gt; valid for this context? if not, what other word would associate?&lt;/p&gt;&#xA;" OwnerUserId="3558" LastEditorUserId="3558" LastEditDate="2013-05-13T14:10:15.747" LastActivityDate="2013-05-14T13:28:18.987" Title="&quot;Oblong to Allantoids&quot; .... Is it valid?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8330" PostTypeId="1" AcceptedAnswerId="8339" CreationDate="2013-05-13T14:05:46.543" Score="9" ViewCount="5714" Body="&lt;p&gt;I have noticed lately that if I go to sleep, when I have my radio running, it is on lowest volume, I still consider it kind of loud. &#xA;In the morning, when being on the edge of waking up, I hear the birds, and the tennis balls already being batted on the court nearby, but I do not hear my radio. If I wait a few more minutes, I start to hear the radio, with no changes in the sound levels outside.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that the human eye adapts to the light levels (aperture, what cells used), but is there something similar for sound sensitivity?&#xA;Note, the radio is on that occasion running all night long, with always the same sound level. &lt;/p&gt;&#xA;" OwnerUserId="3559" LastEditorUserId="57" LastEditDate="2014-07-20T01:48:44.300" LastActivityDate="2018-11-16T15:38:06.457" Title="Does the human ear adapt to noise levels?" Tags="&lt;physiology&gt;&lt;sensation&gt;&lt;hearing&gt;&lt;psychophysics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8331" PostTypeId="1" AcceptedAnswerId="8340" CreationDate="2013-05-13T14:29:47.930" Score="10" ViewCount="32087" Body="&lt;p&gt;In a lecture during  my undergraduate degree we were introduced to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1084159/&quot; rel=&quot;nofollow&quot;&gt;the race to complete the human genome&lt;/a&gt;. Celera were competing with Sanger and collaborators to sequence the human genome. Celera wanted to patent some sequences, whilst Sanger &lt;em&gt;et al.&lt;/em&gt; wanted to keep their findings in the public domain. Celera knew they couldn't compete with Sanger &lt;em&gt;et al.&lt;/em&gt; with conventional cloning techniques which required a lot of man-power, &lt;em&gt;&quot;so instead opted for &lt;a href=&quot;https://en.wikipedia.org/wiki/Shotgun_sequencing&quot; rel=&quot;nofollow&quot;&gt;shotgun sequencing&lt;/a&gt;&quot;&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To me it seems like both clone based sequencing and shotgun sequencing could have been used together, however the lecturers semantics were a bit vague (&lt;em&gt;...okay, I wasn't paying close enough attention!&lt;/em&gt;) and I didn't ask for clarification at the time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whilst I appreciate this is a large topic, what are the main differences between Celera's shotgun sequencing and Sanger's clone based sequencing during the late 1990s? Are &quot;shotgun cloning&quot; and &quot;clone based sequencing&quot; actually mutually exclusive terms?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2016-04-11T09:59:13.267" LastActivityDate="2019-04-02T08:08:51.087" Title="What's the difference between shotgun sequencing and clone based sequencing?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;dna-sequencing&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8332" PostTypeId="1" AcceptedAnswerId="8347" CreationDate="2013-05-13T14:59:29.657" Score="1" ViewCount="1191" Body="&lt;p&gt;During Illumina sequencing there is a step called bridge amplification by which DNA is amplified by isothermal enzymes. What is this stage, and how does it work?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastActivityDate="2013-05-14T07:21:42.213" Title="What is solid-phase bridge amplification?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8333" PostTypeId="2" ParentId="8328" CreationDate="2013-05-13T15:39:40.097" Score="2" Body="&lt;p&gt;According to a heavily-cited paper (below), homocysteine reduces the expression of thrombomodulin on the surface of endothelial cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thrombomodulin binds to thrombin, and the resulting complex does not promote coagulation, but instead activates protein C. Protein C has an anticoagulant effect. Thus reduced levels of thrombomodulin will result in increased levels of free thrombin (promoting coagulation) and in reduced levels of protein C (also promoting coagulation).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't found any evidence that homocysteine has an effect upon thrombin formation directly.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Lentz,SR and Sadler, JE (1991)Inhibition of thrombomodulin surface expression and protein-c activation by the thrombogenic agent homocysteine. J. Clin. Invest. 88:1906-1914&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Abstract&lt;/strong&gt; Elevated levels of plasma homocysteine are associated with both venous and arterial thrombosis. Homocysteine inhibits the function of thrombomodulin, an anticoagulant glycoprotein on the endothelial surface that serves as a cofactor for the activation of protein C by thrombin. The effects of homocysteine on thrombomodulin expression and protein C activation were investigated in cultured human umbilical vein endothelial cells and CV-1(18A) cells that express recombinant human thrombomodulin. Addition of 5 mM homocysteine to endothelial cells produced slight increases in thrombomodulin mRNA and thrombomodulin synthesis without affecting cell viability. In both cell types, thrombomodulin synthesized in the presence of homocysteine remained sensitive to digestion with endoglycosidase H and failed to appear on the cell surface, suggesting impaired transit along the secretory pathway. In a cell-free protein C activation assay, homocysteine irreversibly inactivated both thrombomodulin and protein C in a process that required free thiol groups and was inhibited by the oxidizing agents diamide or N-ethylmaleimide. By inhibiting both thrombomodulin surface expression and protein C activation, homocysteine may contribute to the development of thrombosis in patients with cystathionine beta-synthase deficiency.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-05-13T15:39:40.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8334" PostTypeId="1" AcceptedAnswerId="8345" CreationDate="2013-05-13T15:43:34.647" Score="5" ViewCount="3294" Body="&lt;p&gt;It has recently been brought to my attention that live laboratory mice with specific cancer strains can be readily purchased for medical research.  For example, &lt;a href=&quot;http://jaxmice.jax.org/cancer/featured.html&quot;&gt;the Jackson Laboratory&lt;/a&gt; sells mice with a wide range of strains of cancer (with price depending heavily on the type of cancer desired).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;: What is the general process behind breeding laboratory mice with specific cancers for medical research?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="203" LastActivityDate="2015-06-19T03:15:30.420" Title="Breeding laboratory mice with cancer; how does this work?" Tags="&lt;cancer&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8335" PostTypeId="2" ParentId="2079" CreationDate="2013-05-13T16:23:42.887" Score="2" Body="&lt;p&gt;N3 and P3 are different. N3 contain chaotropic agents. P3 does not.&#xA;Mainly there are two types of DNA purification kits on the market: silica membrane (glass fiber) based and DEAE anion exchange based. The silica membrane based method requires high concentration of chaotropic agents (salts that can change the water structure dramatically, GuHcl, GuSCN, NaI, are a few of them) present in the mixture before loading on to the spin column. DEAE based method, on the other hand, bind DNA based on the charge property on the DEAE resin which largely depends on the pH and ionic strength of the buffer. Chaotropic agents are not needed for DEAE based method.&#xA;In our lab we make our own kit using components and buffer recipe provided by Epoch Life Science for both mini prep and maxi prep. Their mini spin column and maxi DEAE column can be purchased without buffer. Their mini spin column also works perfectly with buffer from Qiagen and Lifetech. That's how we used up our leftover buffer from our old kits.&lt;/p&gt;&#xA;" OwnerUserId="3562" LastActivityDate="2013-05-13T16:23:42.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8336" PostTypeId="2" ParentId="7868" CreationDate="2013-05-13T16:40:56.223" Score="1" Body="&lt;p&gt;&lt;strong&gt;Background:&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;There are a lot of recipes to extract protein from human tissues out there, but all of them boil down to one thing; preserving the tissue proteins as much as possible while obtaining a reasonable yield for downstream applications, using extraction buffer, extra techniques, and by adding protease inhibitors  &lt;/li&gt;&#xA;&lt;li&gt;ELISA is one of the those downstream applications that you might be interested in, but one important question? is the sample matrix that you have already obtained valid for the ELISA assay? keep in mind, your sample is not serum, it is a mixture of tissue, extraction buffer, and protease inhibitors, and other things as well  &lt;/li&gt;&#xA;&lt;li&gt;Two known assays are usually performed to address the above question. These are, spike-and-recovery (SAR), and linearity-of-dilution (LOD), and these two assays are specific to the analyte that you want to measure in your samples, e.g., cytokines, factors, Igs, etc...and specific also to the tissue, and assay kit as well  &lt;/li&gt;&#xA;&lt;li&gt;Often times, you are interested in performing these two assays with minimum resources as much as possible, i.e., less time, less kit materials, and, most importantly, less sample material. This can be quite challenging and it depends on many issues that is out scope of this post to discuss them all  &lt;/li&gt;&#xA;&lt;li&gt;If you are interested in performing these two assays using only one 96-well ELISA plate and examine validity of different sample matrices, sample buffer (lysis buffer or sometimes called extraction buffer) for a certain analyte, say X, then this scheme below is for you:&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zThos.png&quot; alt=&quot;enter image description here&quot;&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Technical Notes:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;In this scheme, recovery is examined in 3 types of solutions; &lt;code&gt;assay buffer&lt;/code&gt;, &lt;code&gt;sample buffer&lt;/code&gt; and &lt;code&gt;samples&lt;/code&gt;. These are different in their complexity. Typically, the assay buffer is usually optimized to detect the standard protein provided with the commercial kit  &lt;/li&gt;&#xA;&lt;li&gt;The idea of &lt;code&gt;spike-and-recovery&lt;/code&gt; is that you add a certain amount from standard stock solution into the wells containing the solution to be tested (e.g., sample buffer or samples) and measure them, to see whether you can recover that amount again, and how much you can recover from it in %. If, for any reason, you couldn't recover that amount in comparison with a control well, where that same amount was added into assay buffer, then this means that something in the test solution is not in favor of the assay. The specific amount you add into the wells is called &lt;code&gt;spike&lt;/code&gt;, and it should be the same amount across all tested wells (try to be consistent). Make sure that the added amount when diluted in the well, its final concentration should still be measured by the assay and lie inside your standard curve. E.g., if your standard curve is from 4- 4500 pg/mL, and each well has 100µl of sample, if you want now to add spike into that sample well, you may add whatever amount you want that will still give you at the end a reading inside the standard curve, you may choose to add 10µl from the highest stock which is 500pg/mL, so you end up here with 1/10, that is 50pg/mL, which is fine as it lies inside the 4-500pg/mL range. Alternatively, you can add 50µl sample + 50µl spike (500pg/mL) and would end up with 1/2 dilution (which is the same in this scheme), that is 250pg/mL, which is also fine. So it is up to you to choose, keeping in mind the final concentration should lie inside your standard curve  &lt;/li&gt;&#xA;&lt;li&gt;For the &lt;code&gt;linearity-of-dilution&lt;/code&gt;, it is obvious that you need a high concentration solution that you can make two-fold (or whatever fold you like) serial dilution from and its reading should still lie inside the standard curve. The best candidate for this is the high spiked wells. The &lt;code&gt;LOD&lt;/code&gt; would tell you about the effect of different dilutions on the precision of the assay  &lt;/li&gt;&#xA;&lt;li&gt;For &lt;code&gt;SAR&lt;/code&gt; and &lt;code&gt;LOD&lt;/code&gt; you will get at the end an average percentage from 3 samples at least (calculation example will be provided later), I added a fourth sample, but this fourth can be a different sample type, say samples from tissue culture, so it is up to you to re-design this scheme and be innovative   &lt;/li&gt;&#xA;&lt;li&gt;Choosing the best dilution is not an easy task, it is not without compromises sometimes. For example, if you have a harsh sample buffer, you may not have good recovery at 1/2, 1/4, 1/8 dilutions of the &lt;code&gt;sample buffer&lt;/code&gt; in &lt;code&gt;assay buffer&lt;/code&gt;, whereas almost good recovery is achieved at 1/16, then this dilution factor is most probably the one you should go for in your assay. On the other hand, 1/16 might not be detected by your ELISA assay, which is limited by its sensitivity. Here, the &lt;code&gt;E&lt;/code&gt; wells can give you a clue whether you detect something in these unspiked samples or not, that's why I recommend you include at least one sample of high expected value of the analyte in question (this is not easy sometimes to predict) in this scheme, here this is sample 3. One more thing, if you get good recovery at 1/16 DO NOT go to 1/32 or 1/64, as it is obvious that with these higher dilutions you are reducing the chance of the analyte's detectability as it is limited by your assay's sensitivity  &lt;/li&gt;&#xA;&lt;li&gt;In most of the cases, you will see that the dilution factor of good recovery of the &lt;code&gt;sample buffer&lt;/code&gt; in columns 3 and 4, will coincide with that of the &lt;code&gt;spiked samples&lt;/code&gt; in columns 5, 7, and 9. This will give you the assurance that you are in the right direction. If sample 4 is extracted by a different &lt;code&gt;sample buffer&lt;/code&gt;, then it is clear that should not expect to end up with the same dilution factor (please, be more reasonable!)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3320" LastEditorUserId="3320" LastEditDate="2013-05-13T20:37:50.430" LastActivityDate="2013-05-13T20:37:50.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8337" PostTypeId="1" AcceptedAnswerId="8338" CreationDate="2013-05-13T18:06:26.690" Score="2" ViewCount="85" Body="&lt;p&gt;&lt;a href=&quot;http://www.thekitchn.com/how-to-store-apples-for-the-wi-68778&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; about storing apples for the winter says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;You do not want the apples' temperature to fall below 30°F (-1.1°C), however,&#xA;  because that will make them freeze and turn to mush when they're&#xA;  thawed. Their cell walls will all collapse.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Therefore, apples are best stored somewhere around 30-35°F (-1.1 to 1.6°C), in a humid environment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't understand why you should keep the apples below the freezing point of water. Why would damage only occur below 30°F (-1.1°C)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the article correct?&lt;/p&gt;&#xA;" OwnerUserId="3563" LastActivityDate="2013-05-13T18:35:11.597" Title="Storing Apples at 30F?" Tags="&lt;food&gt;&lt;temperature&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8338" PostTypeId="2" ParentId="8337" CreationDate="2013-05-13T18:35:11.597" Score="3" Body="&lt;p&gt;This temperature range would be a compromise between a very low temperature needed to limit natural decay or decay triggered by micro-organisms (the lower the temperature, the lesser the decay) and the formation of destructive ice crystals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Only pure water freezes at 0°C (32°F) under atmospheric pressure. But the content of apple cells and cell walls is a rather complex aqueous solution, containing many natural &lt;a href=&quot;http://en.wikipedia.org/wiki/Cryoprotectant&quot; rel=&quot;nofollow&quot;&gt;cryoprotectants&lt;/a&gt;, among which the fruit's sugars. Therefore, the freezing point of apples might be as low as 30°F.&lt;/p&gt;&#xA;" OwnerUserId="3394" LastActivityDate="2013-05-13T18:35:11.597" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8339" PostTypeId="2" ParentId="8330" CreationDate="2013-05-13T19:16:00.617" Score="9" Body="&lt;p&gt;In  this instance, I would say your attention has been adjusted, not your ear's ability to perceive sound. Our ears don't have a control setting or a means of adjusting incoming sound levels (though I'm certain when an ambulance with loud siren drives by, we all wish we did). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you are experiencing is a prioritization of the sound by your brain in relationship to other sounds.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;You put the sound on before you go to sleep. Your brain accepts that incoming sound as non-vital, non-threatening sound. (Radio, meant to soothe, supposed to be there, relegate this sound to innocuous)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Come dawn, new and novel sounds appear. For our brains, the new and novel could indicate a threat, so your brain prioritizes that sound over the known and considered innocuous sound (your radio) which it has heard all night. Birds, tennis balls on courts are distinctive enough your brain would prioritize them even though you know in your conscious mind neither is an actual threat.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;As you waken, your brain then reminds you there is still another sound in your environment which is not threatening and yet still prevalent (your radio) prompting you to decide if you want to do anything with the non-threatening sound.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Yes, this is an oversimplification of a very complex process of sound prioritization but most modern science bears this out. As a curiosity, our minds are predisposed to seek out information which may be vital to us, hence the reason conversations held by other people who are on the phone are so distracting because our brains dislike hearing things which may be necessary to our survival but only hearing half of the conversation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I was reminded there are some involuntary control elements built into the ear via:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;the &lt;a href=&quot;http://en.wikipedia.org/wiki/Tensor_tympani_muscle&quot;&gt;&lt;strong&gt;tensor tympani muscle&lt;/strong&gt;&lt;/a&gt; whose role is to dampen sounds (mainly internal ones such as chewing)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Stapedius_muscle&quot;&gt;&lt;strong&gt;stapedius muscle&lt;/strong&gt;&lt;/a&gt; which dampens the ability of the stapes vibration and protects the inner ear from high noise levels, primarily the volume of your own voice. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You can thank the stapedius muscle for making your voice sound so strange to you when you hear it on a recording. You have never truly heard your voice until you hear an external recording and playback of it!&lt;/p&gt;&#xA;" OwnerUserId="1099" LastEditorUserId="1099" LastEditDate="2013-05-14T00:21:25.453" LastActivityDate="2013-05-14T00:21:25.453" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8340" PostTypeId="2" ParentId="8331" CreationDate="2013-05-13T19:23:27.407" Score="7" Body="&lt;p&gt;The v short answer is that in shotgun sequencing, the sequencer is fed a set of random sequences from the target.  This can be done for instance by mechanically shearing DNA and then building a set of shotgun sequencing jobs which are then compiled back together by a genome assembler (i.e. in whole genome sequencing projects) into a full sequence.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In clone based sequencing, the DNA to be sequenced is specifically sectioned off into sequence copied into of plasmids (BACs - bacterial artificial chromosome) to divide the sequencing job into sections- a divide and conquer strategy.  BACs can be 150 kb long just to give you an idea. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.learner.org/courses/biology/textbook/genom/genom_2.html&quot;&gt;These are not mutually exclusive terms&lt;/a&gt;; clone-based sequencing projects usually use the large clone libraries to section the project into a set of shotgun sequencing projects. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-05-13T19:23:27.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8341" PostTypeId="1" AcceptedAnswerId="8342" CreationDate="2013-05-13T20:06:43.127" Score="0" ViewCount="127" Body="&lt;p&gt;Starting a new project on protein-protein interactions and SNP analysis tool development. I would like to ask how does SNPs is mapped into protein? What does mapping means? &lt;/p&gt;&#xA;" OwnerUserId="1715" LastEditorUserId="948" LastEditDate="2013-05-13T20:52:07.453" LastActivityDate="2013-05-13T20:52:07.453" Title="SNPs mapping into protein" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8342" PostTypeId="2" ParentId="8341" CreationDate="2013-05-13T20:49:45.837" Score="1" Body="&lt;p&gt;Well SNPs are &lt;a href=&quot;http://en.wikipedia.org/wiki/Single-nucleotide_polymorphism&quot; rel=&quot;nofollow&quot;&gt;single nucleotide polymorphisms&lt;/a&gt;. Some SNPs are in the coding regions of genes and they can result in changes in the resulting protein. For example, the SNP &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1801131&quot; rel=&quot;nofollow&quot;&gt;rs1801131&lt;/a&gt; is a human variation where some individuals have a G instead of an A at position &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/sites/nuccore/NM_005957.4?report=graph&amp;amp;v=1015:2015&amp;amp;content=5&amp;amp;m=1515!&amp;amp;mn=rs1801131&amp;amp;dispmax=1&amp;amp;currpage=1&quot; rel=&quot;nofollow&quot;&gt;1515&lt;/a&gt; of the gene &lt;a href=&quot;http://ghr.nlm.nih.gov/gene/MTHFR&quot; rel=&quot;nofollow&quot;&gt;MTHFR&lt;/a&gt;. When the gene is transcribed and then translated into protein, this variation (the presence of the G nucleotide) causes a Glutamate residue at position &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/sites/protein/NP_005948.3?report=graph&amp;amp;v=379:479&amp;amp;content=5&amp;amp;m=429!&amp;amp;mn=rs1801131&amp;amp;dispmax=1&amp;amp;currpage=1&quot; rel=&quot;nofollow&quot;&gt;429&lt;/a&gt; of the protein to be a Glycine instead. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, SNP rs1801131 maps to position 429 of the protein MTHFR.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-05-13T20:49:45.837" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8343" PostTypeId="1" AcceptedAnswerId="8348" CreationDate="2013-05-13T21:28:08.743" Score="2" ViewCount="2684" Body="&lt;p&gt;I am familiar with Sanger sequencing, but at the level of an undergraduate. A lecturer of mine tried to describe Sanger sequencing as losing the sequence information in noise when used to detect cancer. This paper also says &quot;lacks sufﬁcient sensitivity for detecting mutant alleles in tumor biopsies,&quot;(Thomas &lt;em&gt;et al.,&lt;/em&gt; 2006). What is it about Sanger that makes it too insensitive for SNP analysis?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thomas, R.,K., &lt;em&gt;et al.&lt;/em&gt; (2006) Sensitive mutation detection in heterogeneous cancer specimens &#xA;by massively parallel picoliter reactor sequencing. &lt;em&gt;Nat. Med.&lt;/em&gt; &lt;strong&gt;12&lt;/strong&gt;, 852–855&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="1320" LastEditDate="2013-05-14T11:58:11.653" LastActivityDate="2013-05-14T11:58:11.653" Title="Why is Sanger sequencing inferior for detecting SNPs in cancer cells?" Tags="&lt;molecular-biology&gt;&lt;dna-sequencing&gt;&lt;cancer&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8345" PostTypeId="2" ParentId="8334" CreationDate="2013-05-13T21:45:55.300" Score="4" Body="&lt;p&gt;Cancer is a highly genetic disease, and much is known about how different genetic mutations contribute to the generation, growth, proliferation, metastasis, and control of tumors. Jackson Labs (commonly known as Jax in the research community) provides literally &lt;em&gt;thousands&lt;/em&gt; of strains of mice, each bred/genetically engineered to have certain &lt;a href=&quot;http://en.wikipedia.org/wiki/Genotype&quot; rel=&quot;nofollow noreferrer&quot;&gt;genotypes&lt;/a&gt; and/or &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenotype&quot; rel=&quot;nofollow noreferrer&quot;&gt;phenotypes&lt;/a&gt;, a good proportion of which can be used for various purposes in cancer research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll take a very basic example to walk you through the creation of a &quot;cancer mouse.&quot; Say I've been doing research and have found through studying the DNA of many patients that the ABC123 gene seems to be associated with a certain type of cancer (skin, for example). I want to know more how ABC123 works, so one of the first things to do is to find out what (if anything) goes wrong when it isn't there - when it gets &quot;knocked out.&quot; Using genetic engineering techniques, I create a sequence of DNA (called a vector) that matches the &quot;wild-type&quot; (WT) or normal mouse ABC123 gene sequence at the ends, but in the middle has a certain selection gene called &lt;em&gt;Neo&lt;/em&gt; instead of the rest of the ABC123 sequence:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/XgpPd.png&quot; alt=&quot;from cellmigration.org&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Neo&lt;/em&gt; makes cells that it is in resistant to a certain antibiotic called &lt;a href=&quot;http://en.wikipedia.org/wiki/Neomycin&quot; rel=&quot;nofollow noreferrer&quot;&gt;Neomycin&lt;/a&gt; or Geneticin, also called G418. I take my targeting vector and &lt;a href=&quot;http://en.wikipedia.org/wiki/Electroporation&quot; rel=&quot;nofollow noreferrer&quot;&gt;electroporate&lt;/a&gt; it into mouse embryonic stem cells (ESCs) that, if implanted into an appropriately-prepared female mouse, could develop into a normal mouse embryo. I then culture these ESCs in the presence of neomycin, which will kill any cells that haven't taken up and incorporated the vector into the genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once I have some cells that I know have taken up the &lt;em&gt;Neo&lt;/em&gt; part &lt;strong&gt;and&lt;/strong&gt; are missing the targeted part of the gene (the &lt;a href=&quot;http://en.wikipedia.org/wiki/Exon&quot; rel=&quot;nofollow noreferrer&quot;&gt;exons&lt;/a&gt; marked 1, 2, and 3), I inject a few cells each into mouse &lt;a href=&quot;http://en.wikipedia.org/wiki/Blastocyst&quot; rel=&quot;nofollow noreferrer&quot;&gt;blastocysts&lt;/a&gt;, where they divide and differentiate to form various parts of the new mouse.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/JRHig.png&quot; alt=&quot;from Wikipedia&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Chimera_%28genetics%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;chimeric&lt;/a&gt; mouse, with different cells coming from different origins, either wild-type or ABC123-mutant. I try to generate a number of different chimeras to breed together in the hopes that at least some of my original injected mutant cells went on to form the gonads, and the mutant gene can be passed on to its offspring. I then breed the various chimeric mice to WT mates in hopes of producing heterozygous offspring, which have one copy of the WT-ABC123 gene (from one parent), and one copy of the mutant-ABC123 gene (from the other parent). &lt;strong&gt;These&lt;/strong&gt; mice can then be bred together to produce homozygous &quot;double-knockout&quot; mice, which I can then use to study my gene's effects and its possible relation to skin cancer. This is the type of animal typically sold by Jax, although this depends very strongly on the gene being studied.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Now, there are many issues that can arise along the way, such as the mutation being embryonic-lethal, causing sterility, or other defects that don't allow you to produce true knockout mice. Much can still be learned, though, and scientists have gotten very inventive in producing functional animal models of previously-difficult mutations. For example, it is possible to engineer a strain that only becomes a knockout when you feed it a certain chemical in its water, or is only knocked out in certain cell types or tissues. Some gene functions are only apparent when two (or more!) genes are knocked out at the same time. Genetics is incredibly complex, but fascinating, and more and more complex tools are being developed all the time to assist scientists in their research and ultimately help people overcome illness and disease.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-05-13T21:45:55.300" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8346" PostTypeId="2" ParentId="8318" CreationDate="2013-05-14T06:18:52.507" Score="4" Body="&lt;p&gt;The mechanisms of osmoregulation is different for sharks (and other &lt;a href=&quot;http://en.wikipedia.org/wiki/Elasmobranchii&quot; rel=&quot;nofollow noreferrer&quot;&gt;elasmobranch&lt;/a&gt; fishes) and &lt;a href=&quot;http://en.wikipedia.org/wiki/Teleost&quot; rel=&quot;nofollow noreferrer&quot;&gt;teleost&lt;/a&gt; fishes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In Elasmobranchs the body osmolarity is maintained equal to the seawater by Na⁺ Cl⁻ and urea.&lt;/strong&gt; Toxicity because of high concentrations of urea (strong chaotrope) is counteracted by high levels of trimethylamine oxide (TMAO). So, the elasmobranchs do not need to drink water to prevent dehydration. But sometimes they do drink water for adapting to different salinity levels [&lt;a href=&quot;http://jeb.biologists.org/content/205/8/1115.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Teleost fishes, however, need to drink water in order to prevent dehydration.&lt;/strong&gt; Initially Na⁺ and Cl⁻ are absorbed in the esophagus via cotransporters (Na-Cl/Na-K-Cl), thereby reducing the osmolarity of water. The cells that absorb Na⁺ maintain its low concentration by pumping extra Na⁺ in the Extracellular fluid, using Na⁺/K⁺-ATPase. Cl⁻ is also exchanged with Bicarbonate (HCO3⁻) via anion exchangers [&lt;a href=&quot;http://jeb.biologists.org/content/209/15/2813.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JNANI.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-05-14T07:20:07.957" LastActivityDate="2013-05-14T07:20:07.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8347" PostTypeId="2" ParentId="8332" CreationDate="2013-05-14T06:39:15.313" Score="1" Body="&lt;p&gt;This stage is after the adsorption of the adapter-ligated fragments on the flow cells. &#xA;The fragments are isothermally amplified to generate clusters [&lt;a href=&quot;https://ncifrederick.cancer.gov/atp/cms/wp-content/uploads/2010/08/CustomerIlluminaTechExplanation.pdf&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]. The exact nature of the enzyme mix that catalyses this step is not disclosed by Illumina. &lt;strong&gt;I assume&lt;/strong&gt; it must be similar to &lt;strong&gt;&lt;a href=&quot;http://www.nature.com/embor/journal/v5/n8/fig_tab/7400200_F1.html&quot; rel=&quot;nofollow&quot;&gt;Helicase mediated isothermal amplification&lt;/a&gt;&lt;/strong&gt;, which uses helicase and single strand-binding proteins (SSB) to denature the template. The polymerization is catalysed by a mesophilic DNA-Pol such as Klenow (&lt;em&gt;E.coli&lt;/em&gt;).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-05-14T07:21:42.213" LastActivityDate="2013-05-14T07:21:42.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8348" PostTypeId="2" ParentId="8343" CreationDate="2013-05-14T08:57:55.587" Score="3" Body="&lt;p&gt;In the Sanger approach, DNA would be isolated from the biopsy and would contain both normal alleles and mutant alleles of genes associated with the development of the tumour. If, for example, PCR amplification was then used to derive a sample of a target template region, this material would end up being sequenced as a mixed population: the derived sequence would be an average of that population of sequences, and rare alleles would be masked.&lt;/p&gt;&#xA;&lt;p&gt;The key difference in most next generation approaches is that the template DNA is &amp;quot;cloned&amp;quot; physically (e.g. by sequestering individual molecules into droplets, or by binding them to a surface) so that the sequences of these individual molecules can be determined in parallel. This approach would reveal tumour-associated polymorphisms when the sequences of the individual template molecules were compared.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Added later as supplementary information.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;I have now looked at the paper cited in the question. This quotation from the Introduction bears out my main point about sequencing a mixture of templates differing at just a few key positions.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Although commonly used in many clinical settings, dideoxynucleotide chain termination (or ‘Sanger’) sequencing of PCR products often lacks sufficient sensitivity for detecting mutant alleles in tumor biopsies, where the failure rate has reached 75% in some cases. Gain-of-function oncogenic mutations are frequently heterozygous events or may represent a single allele of an amplified gene; thus, the signal for mutated residues is typically reduced relative to neighboring bases. Moreover, the ability to detect single base mutations or small insertions or deletions in biopsy material by Sanger sequencing depends heavily on sample purity (for example, the extent of contaminating stromal DNA) and genomic DNA integrity. Furthermore, resistance to kinase inhibitors may correlate with low-frequency second-site mutations. These observations underscore the challenges for accurate mutation detection in cancer specimens.&lt;/p&gt;&#xA;&lt;p&gt;A massively parallel sequencing-by-synthesis approach, ‘picotiter plate pyrosequencing,’ provides a new alternative to Sanger sequencing. This approach relies on emulsion PCR-based clonal amplification of a DNA library adapted onto micron-sized beads and subsequent pyrosequencing-by-synthesis of each clonally amplified template in a picotiter plate, generating over 200,000 unique clonal sequencing reads per experiment. Sequence variants that represent a fraction of a complex sample can be vastly oversampled, thus enabling statistically meaningful quantification of low-abundance variants.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-05-14T11:44:03.097" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8349" PostTypeId="2" ParentId="8286" CreationDate="2013-05-14T10:11:25.317" Score="2" Body="&lt;p&gt;Use agar stubs: pour some Nutrient agar (or any suitable agar medium) in a test tube (~10% of the tube volume) and punch your inoculum halfway into it using a pipette tip or inoculation loop. Store it in 4⁰C.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glycerol stocks can be made and stored in -20⁰C also. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-05-14T10:11:25.317" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8350" PostTypeId="2" ParentId="8285" CreationDate="2013-05-14T10:47:09.873" Score="4" Body="&lt;p&gt;As AndroidPenguin described the nociceptive pathways are activated by inflammation or noxious chemicals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes pain can arise independent of active nociceptive pathways. Most evident in cases of &lt;a href=&quot;http://en.wikipedia.org/wiki/Neuralgia&quot; rel=&quot;nofollow&quot;&gt;Neuralgia&lt;/a&gt; and perhaps in case of &lt;a href=&quot;http://en.wikipedia.org/wiki/Traumatic_neuroma&quot; rel=&quot;nofollow&quot;&gt;Pseudoneuromas&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In certain cases the injured nerve causes disinhibition of the pain pathways arising from the dorsal horn of spinal cord. This disinhibition is because of loss of the nerve function. &#xA;Sometimes increased nociceptor drive can activate dorsal horn of spinal cord which will now respond to normal mechanosensation also [&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0140673699013070&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;1&lt;/strong&gt;&lt;/a&gt;]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phenotypic switching is also possible [&lt;a href=&quot;http://www.neurology.org/content/59/5_suppl_2/S2.short&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;2&lt;/strong&gt;&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: Both these articles are inaccessible to me at this moment. Refer them for more details. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-05-16T07:28:21.403" LastActivityDate="2013-05-16T07:28:21.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8352" PostTypeId="2" ParentId="8329" CreationDate="2013-05-14T13:28:18.987" Score="1" Body="&lt;p&gt;Oblong is probably correct in this context, but &quot;allantoids&quot; should probably be &quot;allantoid&quot; to be the adjective form. It's describing translucent (hyaline), oval (oblong) to sausage-shaped (allantoid), undivided (aseptate) spore.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-05-14T13:28:18.987" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8353" PostTypeId="1" AcceptedAnswerId="57289" CreationDate="2013-05-14T16:31:46.710" Score="9" ViewCount="632" Body="&lt;p&gt;A few days ago I observed a corridor built and used by ants that went over a path in fields:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JSMj4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do they build it? It seems it doesn't bring any considerable protection from the surrounding environment and it certainly costs them a lot of work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The picture was taken in the morning when the temperature was low so there is no ant activity visible.&lt;/p&gt;&#xA;" OwnerUserId="1279" LastEditorUserId="55929" LastEditDate="2020-01-04T21:54:37.370" LastActivityDate="2020-01-04T21:54:37.370" Title="Why do ants dig surface paths?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;ant&gt;&lt;sociality&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="8355" PostTypeId="1" CreationDate="2013-05-14T19:50:40.630" Score="8" ViewCount="1137" Body="&lt;p&gt;Natural selection is a central tenet of evolution. However, most biologists seem determined to prevent the extinction of the species that have been selected against. Why is this? Preservation of genetic diversity? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought evolution was supposed to create diversity not destroy it. What am I missing?&lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="3624" LastEditDate="2013-06-28T09:43:53.953" LastActivityDate="2015-02-06T02:57:04.257" Title="If Evolution Is In Progress, Why Fight Extinction?" Tags="&lt;evolution&gt;&lt;extinction&gt;&lt;conservation-biology&gt;" AnswerCount="4" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="8356" PostTypeId="1" AcceptedAnswerId="8377" CreationDate="2013-05-14T20:16:47.353" Score="6" ViewCount="6828" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Slow_worm&quot;&gt;Slow worms&lt;/a&gt; are considered lizards as opposed to snakes, both are &lt;a href=&quot;https://en.wikipedia.org/wiki/Reptile&quot;&gt;reptiles&lt;/a&gt;. Now I get that there are traits that distinguish them (eye lids, ears ...). But snake species themselves vary already quite a lot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;https://en.wikipedia.org/w/index.php?title=Snake&amp;amp;oldid=552637116#Evolution&quot;&gt;Wikipedia article on snakes&lt;/a&gt; states:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Based on comparative anatomy, there is consensus that snakes descended from lizards.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But how comes slow worms are considered lizards despite the loss of their limbs during evolution, whereas the same evidently has happened to snakes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the defining factor here? The time frame when it happened, that it happened independently (like the evolution of, say, an eye)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note:&lt;/strong&gt; I couldn't find any detailed descriptions about the alleged evolution of slow worms, whereas for snakes it is easy to find material.&lt;/p&gt;&#xA;" OwnerUserId="3315" LastEditorUserId="3624" LastEditDate="2015-05-04T13:33:52.740" LastActivityDate="2015-05-04T13:33:52.740" Title="Why is a slow worm not considered a snake?" Tags="&lt;evolution&gt;&lt;taxonomy&gt;&lt;phylogenetics&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8357" PostTypeId="1" AcceptedAnswerId="8373" CreationDate="2013-05-15T00:59:56.053" Score="4" ViewCount="486" Body="&lt;p&gt;I've seen that &lt;a href=&quot;http://en.wikipedia.org/wiki/Metabolic_theory_of_ecology&quot; rel=&quot;nofollow&quot;&gt;metabolic rate scales logarithmically&lt;/a&gt; as function of mass for many animals over an extremely large span of parameters. What other scaling laws exist at the individual level?&lt;/p&gt;&#xA;" OwnerUserId="822" LastEditorUserId="476" LastEditDate="2013-05-15T09:40:51.257" LastActivityDate="2013-05-16T01:22:07.143" Title="What are some examples of scaling laws in biology?" Tags="&lt;evolution&gt;&lt;physiology&gt;&lt;allometry&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8358" PostTypeId="1" CreationDate="2013-05-15T01:24:59.550" Score="3" ViewCount="1265" Body="&lt;p&gt;For further investigation into the progress of the blood pressure, we will measure a patient's blood pressure in the superior vena cava measured during inhalation and during an exhalation. His heart function remains the same during the measurements&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is this subject's blood pressure in the superior vena cava during inhalation less than during the exhalation?&lt;/p&gt;&#xA;" OwnerUserId="3569" LastEditorUserId="69" LastEditDate="2013-05-15T23:27:09.940" LastActivityDate="2013-05-16T19:55:06.297" Title="Why is the blood pressure in the superior vena cava during inhalation less than during the exhalation?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2015-01-26T17:02:01.003" ContentLicense="CC BY-SA 3.0" />
  <row Id="8360" PostTypeId="1" CreationDate="2013-05-15T05:22:56.583" Score="10" ViewCount="14180" Body="&lt;p&gt;I'm taking a 3-week Bio I summer course, and my textbook says the cell is the smallest/basic unit of life. I asked my professor why organelles aren't a living unit, and her reply was that they aren't self-sufficient. But it seems that cells in multi-cellular organisms need other cells with different specializations in order to survive. You can't just (or can't always) pluck a cell out of a larger organism and leave it to fend for itself outside of it. Same with an organelle. She said only the entire cell fits all the requirements for life, referring me to the textbook, but I couldn't find an actual description of these requirements. So, what is the relevant difference between an organelle and a cell such that only the entire cell is considered alive?&lt;/p&gt;&#xA;" OwnerUserId="3571" LastActivityDate="2017-05-11T23:07:11.617" Title="Why aren't organelles considered alive?" Tags="&lt;cell-biology&gt;&lt;life&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8361" PostTypeId="1" CreationDate="2013-05-15T10:35:35.653" Score="12" ViewCount="2787" Body="&lt;p&gt;Our senses are not as sensitive during sleep compared to wake. There is an arousal threshold during sleep that only when it is overcome will it wake a person up. My question is &lt;strong&gt;how&lt;/strong&gt; is this arousal threshold lowered as sleep progresses? And &lt;strong&gt;how&lt;/strong&gt; it is raised again during the latter stages of sleep?&lt;/p&gt;&#xA;" OwnerUserId="3465" LastEditorUserId="3952" LastEditDate="2013-07-21T18:18:41.150" LastActivityDate="2019-07-15T18:28:21.420" Title="How are our senses dimmed during sleep?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;sleep&gt;&lt;sensation&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8362" PostTypeId="2" ParentId="8360" CreationDate="2013-05-15T10:46:39.587" Score="12" Body="&lt;p&gt;The definition of life is a controversy in itself, and as it is simply a word that can be understood by everyone however they wish, there is no &quot;correct&quot; definition. It is thus not really possible to give a &quot;correct&quot; answer to your question, but here are a list of things you may want to consider:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Replication of DNA is probably the most agreed common feature to all life on earth. Most organelles do not contain their own DNA but are simply lipid and protein constructs.&lt;/li&gt;&#xA;&lt;li&gt;Independence is a difficult criterion of life, as parasites require a host for reproduction. However, while the organism may require a host, its cells individually can replicate without a host.&lt;/li&gt;&#xA;&lt;li&gt;Cells are able to replicate when removed from the body - under the right conditions. (We are getting better and better at culturing all sorts of cell types, for example to avoid having to use animals for research.) Most organelles are not able to replicate under any conditions.&lt;/li&gt;&#xA;&lt;li&gt;In nature, there are single living cells. In fact, the majority of organisms on earth consist of one cell only. There are no organelles living in nature.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Mitochondria and plastids make a complicated exception to these, as they are originally derived from bacteria themselves. It is indeed debatable whether they could be considered alive, as they possess DNA and it is replicated in order for them to divide, like individual cells do. However, the machinery required is not produced by themselves but rather by their &quot;host&quot; cell, making them subject of a similar argument as viruses.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-05-15T22:11:51.527" LastActivityDate="2013-05-15T22:11:51.527" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8364" PostTypeId="1" CreationDate="2013-05-15T11:30:02.007" Score="2" ViewCount="54" Body="&lt;p&gt;I'm looking for methodologies to compare the &lt;em&gt;costs&lt;/em&gt; a food production requires with the &lt;em&gt;gains&lt;/em&gt; it delivers (not in economic terms).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm aware of &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/EROEI&quot; rel=&quot;nofollow&quot;&gt;energy returned on investment&lt;/a&gt;&lt;/em&gt;. Are there other methods used in literature (also including qualitative approaches)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be a bit more precise (or rather unprecise?): &lt;em&gt;Costs&lt;/em&gt; may include the input of fuel, feed, energy in general or - for me most interesting - the environmental burden to our environment (for example the carbon footprint) while &lt;em&gt;gains&lt;/em&gt; should refer to the nutritional output of the product (energy, protein content, other (rare) nutrients).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The purpose is to link (or discuss) the burden of food production chains to their benefits but to find a unit that is quantitative comparable (except the pure energy content) doesn't seem so trivial - so I'm very happy with suggestions how to approach that - in the best case with a link to studies that employed the method.&lt;/p&gt;&#xA;" OwnerUserId="3258" LastEditorUserId="3340" LastEditDate="2015-06-04T11:49:28.647" LastActivityDate="2015-06-04T11:49:28.647" Title="What are ways to compare the &quot;costs&quot; and &quot;gains&quot; of food production systems?" Tags="&lt;food&gt;&lt;bioenergetics&gt;&lt;environment&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8365" PostTypeId="2" ParentId="8244" CreationDate="2013-05-15T13:14:41.483" Score="1" Body="&lt;p&gt;I'll have a go at a short list.  This is more of a highlight and primer sort of response to a somewhat subjective question so pardon if this isn't what you wanted. I don't have paper references for all this, but I'll try to come back and add some later - I usually only have half an hour or so to write an answer so bear with me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Synthetic biology as defined as the use of genes and promoters to engineer cells or even multicellular organisms like devices is a major category.  I like browsing the projects from the &lt;a href=&quot;http://www.igem.org/Main_Page&quot; rel=&quot;nofollow&quot;&gt;iGem Competitions&lt;/a&gt;.  A couple of outstanding efforts in this field are the use of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3053042/&quot; rel=&quot;nofollow&quot;&gt;photoreceptors to program E coli gene expression&lt;/a&gt; and the general effort to create logic and computational circuits in the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A major application in systems biology is engineering cells to produce new chemical compounds or to overproduce compounds.  A classic example (sort of old, but still pretty outstanding) is the &lt;a href=&quot;http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12051.html&quot; rel=&quot;nofollow&quot;&gt;engineering of E coli to produce the antimalarial drug artemisinin&lt;/a&gt; at levels which would enable world wide release of the drug.  This has inspired efforts to produce fuel from algae and bacteria as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you define Systems biology as being often concerned with modeling some or even all the biological processes of the cell, there are probably too many major efforts to cite, but this is just a list of some favorites. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are lots of papers focused on &lt;a href=&quot;http://en.wikipedia.org/wiki/Flux_balance_analysis&quot; rel=&quot;nofollow&quot;&gt;flux balance analysis&lt;/a&gt; which models how the metabolic machinery processes and synthesizes all the scores of chemical compounds that make up a cell.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another category of synbio tries to take the genes found in a genome and model the actions of all the genes.  One of the most exciting papers to come out in this sort of systems biology is the &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867412007763&quot; rel=&quot;nofollow&quot;&gt;whole cell model of Mycobacterium genetalium&lt;/a&gt;.  Using data from a massive effort to characterize every gene in this very small genome, the model consists of over 20 specific models which have combined to make a very impressive simulation of the entire cell dividing.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there is metagenomics, which looks at the different populations of microorganisms and tries to look at how they vary with different environmental conditions. A recent paper that's exciting is the review of &lt;a href=&quot;http://phenomena.nationalgeographic.com/2013/05/13/the-mucus-lover-that-stops-mice-from-getting-fat/&quot; rel=&quot;nofollow&quot;&gt;how different bacteria dominate in the gut of obese mice and people&lt;/a&gt; (several references in the link).  A tour de force in metagenomics was the &lt;a href=&quot;http://phylogenomics.wordpress.com/past-projects/sargasso-sea-and-global-ocean-survey-metagenomics/&quot; rel=&quot;nofollow&quot;&gt;global sea survey&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-05-15T13:14:41.483" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8366" PostTypeId="2" ParentId="8355" CreationDate="2013-05-15T16:45:51.680" Score="1" Body="&lt;p&gt;Good question.  Evolution will and does continue.  Mass extinctions have happened in the past and &lt;a href=&quot;http://ircamera.as.arizona.edu/NatSci102/NatSci102/lectures/intelligence.htm&quot; rel=&quot;nofollow&quot;&gt;in fact we are the product and beneficiaries of that process&lt;/a&gt;; when niches open up from extinctions, other species just move in and take over, eventually they will adapt to take the place of those who have left.  Of course that's a useful perspective since it &lt;em&gt;will&lt;/em&gt; happen.  A large number of animals and plants are endangered and while the impact overall can't be estimated since we have never counted all the animals and plants, much less microscopic species, an example of our dire straits can be gleaned from the fact that perhaps &lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=amphibian-ark&quot; rel=&quot;nofollow&quot;&gt;half of amphibians are endangered&lt;/a&gt;, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.earthwatch.org/aboutus/research/voices_of_science/future_life_interview_e_wilson/&quot; rel=&quot;nofollow&quot;&gt;There are various arguments that there is lost knowledge&lt;/a&gt; - when these animals and plants we have never even cataloged disappear we will lose hundreds of millions of years of biological 'experience', of lost knowledge as well as an aesthetic/ethical argument that this is clearly wrong somehow; like a mass murder of animals and plants. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that most people who have never seen these animals and plants, understood how wonderful and awe-inspiring they are, how many odd abilities that evolution has gifted them.  It seems like a nearly universal experience that those who have seen this are pretty strongly in favor of efforts to save them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But that's not the question at hand; really won't the ecosphere heal and eventually be okay?  Now that we have discovered life so far under the ocean and in the depths of the earth that even nuclear holocaust would probably not touch them.  The answer is yes.  The ecosphere and life will go on.  There are two other useful questions though:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) will we go on with it? Mass extinctions are the result of changes in the environment - all living things in that environment will sink or swim as it were and humans should not exclude ourselves.  Will the future human race deal with loss of oxygen content, the loss of fresh water and the misery of population explosion?  If the environment just keeps getting worse, will we do well?  We're all assuming that we will figure out how to feed ourselves, find drinking water when both food and water are not really growing to meet our growing population, not to mention the desertification of arable land and the rise in temperature that will impact human geography and economics over the next 100 years or so.  If the environment were to stabilize at least we would not be standing on shifting ground. If you are familiar with &lt;a href=&quot;http://en.wikipedia.org/wiki/Malthusian_catastrophe&quot; rel=&quot;nofollow&quot;&gt;Malthus' argument&lt;/a&gt;, when there is no food or land left to exploit nature will take its course with us - war, famine etc etc.  That is also a natural state, which we've managed to slowly eliminate.  We may be bringing it back in.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) How long do we want to wait for the ecosystem to heal? After the mass extinctions of the past, &lt;em&gt;hundreds of millions of years&lt;/em&gt; were needed for the species around to re-establish themselves as they are now.  Is that really a good trade off for a few decades of industrial-economic expansion? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Until then, the survivors are not necessarily the ones we'd prefer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I volunteered at a survey of shellfish in the San Franscisco Bay.  At one time the shellfish here were so plentiful that the natives piled giant shellmounds the size of small hills from their regular diets.  Now because of fertilizer runoff and pollution these shellfish are nearly gone - we didn't see one the entire day looking around the survey area.  Instead they nesting shells were covered with a slimy bunch of sea squirts -  plant-like animals which can grow quickly enough to absorb the nutrients and robust enough to ignore the pollution and chemicals.  I'd probably rather have a bay scallops on my plate rather than a salad of seq squirts.  The Bay is swimmable, but is plenty slimy.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Got to sign off now, but that's the outline of an answer...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-05-15T16:45:51.680" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="8368" PostTypeId="1" AcceptedAnswerId="8369" CreationDate="2013-05-15T19:22:30.490" Score="2" ViewCount="1448" Body="&lt;p&gt;I was reading page 92 of &lt;em&gt;Fundamentals of Microbiology, 4th edition&lt;/em&gt;, which states&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In &lt;strong&gt;facilitated diffusion,&lt;/strong&gt; the substance (glucose, for example) to be transported combines with a plasma membrane protein called a &lt;em&gt;transporter&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The section of text that says this is in a section describing prokaryotic cell anatomy. As far as I understand human biology, (just to use one example) that facilitated diffusion is regulated by insulin, which, to use less than perfect language simply to streamline my question, uses insulin to &quot;unlock&quot; the plasma membrane proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the difference when prokaryotic cells aren't dependent upon insulin to get glucose in?&lt;/p&gt;&#xA;" OwnerUserId="263" LastEditorUserId="1320" LastEditDate="2013-05-16T14:05:27.613" LastActivityDate="2013-05-16T14:05:27.613" Title="How is transport of glucose into prokaryotic cells different from transport into eukaryotic cells?" Tags="&lt;metabolism&gt;&lt;protein-binding&gt;&lt;glucose&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8369" PostTypeId="2" ParentId="8368" CreationDate="2013-05-15T20:08:12.183" Score="3" Body="&lt;p&gt;In prokaryotes the glucose transporter is always present in the cell membrane; in cells whose glucose uptake is insulin-regulated the transporter is only present in the plama membrane when hormone levels are high.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Glut4&quot; rel=&quot;nofollow&quot;&gt;GLUT4&lt;/a&gt; is the isulin-regulated glucose transporter found in muscle and adipose tissue. When insulin levels are low the GLUT4 protein is in the membrane of small vesicles inside the cell. The appearance of insulin signals the fusion of these vesicles with the plasma membrane. In this way the number of GLUT4 molecules in the plasma membrane is increased, raising the capacity of the cell for glucose transport. GLUT4 transports glucose into the cell by facilitated diffusion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More information about the GLUT family of glucose transporters can be found &lt;a href=&quot;http://en.wikipedia.org/wiki/Glucose_transporter&quot; rel=&quot;nofollow&quot;&gt;here.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-05-15T20:08:12.183" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8370" PostTypeId="2" ParentId="8358" CreationDate="2013-05-15T22:12:30.463" Score="1" Body="&lt;p&gt;The diaphragm moves down during inspiration. This leads to air being sucked in, due to the pressure difference created. The converse is true during expiration. As the thoracic space is where the SVC sits, it's pressure decreases during inspiration as it is subjected to the surrounding decrease in pressure. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1757" LastEditDate="2013-05-16T19:55:06.297" LastActivityDate="2013-05-16T19:55:06.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8371" PostTypeId="1" AcceptedAnswerId="8385" CreationDate="2013-05-15T22:19:29.850" Score="10" ViewCount="4488" Body="&lt;p&gt;I am not a biologist nor know much about biology (so please explain in layman's terms) however I have always been curious as to why this is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What causes the difference in pain between touching an open wound and pushing down on your skin? In both circumstances you are applying pressure to the nerves except one is a foreign object touching the nerve and the other is the nerve's natural surroundings in your body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is it that a foreign object causes so much more pain?&lt;/p&gt;&#xA;" OwnerUserId="3577" LastEditorUserId="9943" LastEditDate="2016-03-10T20:55:49.953" LastActivityDate="2019-03-31T08:51:57.660" Title="Why does it hurt more when you touch a nerve directly?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;physiology&gt;&lt;pain&gt;&lt;touch&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8372" PostTypeId="2" ParentId="8246" CreationDate="2013-05-15T23:49:42.067" Score="1" Body="&lt;p&gt;The Ambion's RNAseZAP is not a detergent but contains chemicals that denature RNAse, the step of rinsing with water is necessary in order to clean up the chemicals as well as the denatured proteins left.&#xA;It is highly recommended as it completely wipes out the RNAse and the experiment can be run safely. No need to risk time, money and samples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to sum up, it is not a detergent, but a solution that denatures proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good luck!&lt;/p&gt;&#xA;" OwnerUserId="3579" LastActivityDate="2013-05-15T23:49:42.067" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8373" PostTypeId="2" ParentId="8357" CreationDate="2013-05-15T23:53:54.637" Score="7" Body="&lt;p&gt;Here are some off the top of my head.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The height an animal can jump depends on the muscle cross-sectional area ($l^2$) and its mass ($l^3$). Mass grows faster with body size ($l$) so small animals can therefore jump higher relative to their body size ($l$) than large  animals. Very similar scaling exists for strength of limbs vs. mass, ability to fly vs. mass, etc.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In pinhole eyes (as found in clams and nautilus) sensitivity to light depends on the size of the pupil ($l^2$), the bigger the hole the more light gets in. However the ability to focus depends on the reciprocal of the size of the hole (but I don't know the scaling, so $l^{-n}$). Therefore there is a trade off between sensitivity and  ability to focus.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There are some recent models about foraging behaviour in a 2D terrestrial environment (with the front of the animal being a length  $l$) vs. foraging in a 3D marine environment (with the front of the animal being a surface $l^2$). The model predicts different behaviours for the size of prey animals should aim for.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The rate at which sound attenuates scales with the frequency of the sound as $1/f^2$. The frequency of a resonator scales with the reciprocal of volume $1/l^3$. So small animals make high pitched sounds which attenuate quickly and don't travel very far.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Finally, the properties of fluids change with size. The Reynolds number describes viscosity and is dependent on linear scale $l$. Therefore small animals experience fluids as viscous and can &quot;crawl&quot; through water whereas large animals have to &quot;swim&quot; through water.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;However, any directly physical or chemical-physical property of biology will experience scaling laws.&lt;/p&gt;&#xA;" OwnerUserId="3578" LastEditorUserId="107" LastEditDate="2013-05-16T01:22:07.143" LastActivityDate="2013-05-16T01:22:07.143" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8375" PostTypeId="1" AcceptedAnswerId="8493" CreationDate="2013-05-16T06:33:59.730" Score="5" ViewCount="242" Body="&lt;p&gt;I know that intestinal flora metabolising oligosaccharides, like those found in legumes, is the cause for the well known fact that legumes cause flatulence, but does an oligosaccharide-rich intestine change the composition (i.e. which specific bacteria make it up) of intestinal flora in humans?&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-05-19T07:24:32.410" LastActivityDate="2013-05-24T05:12:58.713" Title="What effect do oligosaccharides, like those found in legumes, have on the composition of intestinal flora in humans and if so how so?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;bacteriology&gt;&lt;diet&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8377" PostTypeId="2" ParentId="8356" CreationDate="2013-05-16T08:49:34.143" Score="13" Body="&lt;p&gt;You are correct that the reason is similar to that of convergent evolution of the eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both snakes and legless lizards are lizards (&lt;a href=&quot;http://en.wikipedia.org/wiki/Squamata&quot; rel=&quot;noreferrer&quot;&gt;Squamata&lt;/a&gt;) that have lost their legs. &lt;strong&gt;However they have done so entirely separately much as octopus and human eyes have evolved entirely separately.&lt;/strong&gt; An easier analogy is between whales and sea cows. Both are legless mammals but as they have evolved separately the must be given separate names.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately it seems that the exact position of the snakes in the tree is unknown which makes this explanation less clear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://tolweb.org/Squamata/14933&quot; rel=&quot;noreferrer&quot;&gt;http://tolweb.org/Squamata/14933&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the legless lizards (subfamily Anguinae) are within the family &lt;a href=&quot;http://en.wikipedia.org/wiki/Anguidae&quot; rel=&quot;noreferrer&quot;&gt;Anguidae&lt;/a&gt;, most of which have legs. This family is within the &lt;a href=&quot;http://en.wikipedia.org/wiki/Anguimorpha&quot; rel=&quot;noreferrer&quot;&gt;Anguimorpha&lt;/a&gt;, which includes even more species with legs. Just one small tip of the tree, with around 20 species is legless. On the other side of the tree, separated by many millions of years is the snakes (&lt;a href=&quot;http://en.wikipedia.org/wiki/Snake#Biology&quot; rel=&quot;noreferrer&quot;&gt;Serpentes&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A related question is why are snakes given their own name while legless lizards are just considered lizards without legs. This is partially due to the fact that there are so few species of legless lizard while there are thousands of species of snake. It is also probably due to cultural history. As snakes are dangerous to humans and prevalent in most inhabited areas of the world words for snakes are much older than the study of taxonomy. A western example is the snake in the garden of &lt;a href=&quot;http://en.wikipedia.org/wiki/Serpent_%28Bible%29&quot; rel=&quot;noreferrer&quot;&gt;Eden&lt;/a&gt;. It is also important in &lt;a href=&quot;http://en.wikipedia.org/wiki/Shesha&quot; rel=&quot;noreferrer&quot;&gt;Hinduism&lt;/a&gt;&#xA;and many other cultures/religions.&lt;/p&gt;&#xA;" OwnerUserId="3578" LastEditorUserId="3578" LastEditDate="2015-05-04T10:47:45.960" LastActivityDate="2015-05-04T10:47:45.960" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8378" PostTypeId="1" AcceptedAnswerId="8383" CreationDate="2013-05-16T11:30:19.573" Score="0" ViewCount="211" Body="&lt;p&gt;Is it true that we are more agressive during the night when there is a full moon?&lt;br&gt;&#xA;If true, could this be a remnant from times where we needed to hunt for our food and so could see more at night when there was a full moon?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source of question: &lt;a href=&quot;http://www.telegraph.co.uk/news/uknews/1553652/More-police-to-patrol-on-full-moons.html&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1897" LastEditorDisplayName="user1897" LastEditDate="2013-05-16T15:33:01.223" LastActivityDate="2013-05-16T16:18:52.100" Title="Are humans more aggressive during a full moon?" Tags="&lt;physiology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2013-05-16T18:41:27.470" ContentLicense="CC BY-SA 3.0" />
  <row Id="8379" PostTypeId="1" AcceptedAnswerId="8381" CreationDate="2013-05-16T12:50:05.350" Score="3" ViewCount="2211" Body="&lt;p&gt;I don't work at the wet lab and don't know all the details about the knockdown techniques.&lt;br&gt;&#xA;My question is:&lt;br&gt;&#xA;How lncRNA knockdown is done?&lt;br&gt;&#xA;For example - you have lncRNA that is &lt;strong&gt;functional in the nucleus&lt;/strong&gt;. How is it possible to do knockdown using iRNA if &lt;strong&gt;interference happens only in the cytoplasm&lt;/strong&gt;?&lt;br&gt;&#xA;Sorry if there is biology related misconception in my question.&lt;/p&gt;&#xA;" OwnerUserId="744" LastEditorUserId="1320" LastEditDate="2013-05-16T14:03:57.293" LastActivityDate="2013-05-19T11:32:38.967" Title="Knockdown of long noncoding RNA (lncRNA) - how is it done?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;rna&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8380" PostTypeId="2" ParentId="8379" CreationDate="2013-05-16T13:00:41.143" Score="1" Body="&lt;p&gt;Nuclear RNAi happens.. check these articles:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nrg/journal/v14/n2/execsumm/nrg3355.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nrg/journal/v14/n2/execsumm/nrg3355.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://nar.oxfordjournals.org/content/early/2011/11/07/nar.gkr891.full&quot; rel=&quot;nofollow&quot;&gt;http://nar.oxfordjournals.org/content/early/2011/11/07/nar.gkr891.full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also there is some &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23405074&quot; rel=&quot;nofollow&quot;&gt;evidence&lt;/a&gt; that Ago2 binds to lncRNAs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, you can employ other techniques to knock down lncRNAs for e.g. ribozymes. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-05-16T13:00:41.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8381" PostTypeId="2" ParentId="8379" CreationDate="2013-05-16T13:30:47.170" Score="2" Body="&lt;p&gt;Knockdown of lncRNA in mammals is not done via RNAi. Instead, one transfers antisense DNA oligos which bind to the RNA. This triggers the action of the &lt;a href=&quot;http://www.pnas.org/content/69/11/3360.full.pdf&quot; rel=&quot;nofollow&quot;&gt;RNase H&lt;/a&gt; enzyme, which degrades RNA-DNA duplexes. It degrades the lncRNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE: For reference, I learned about this from a seminar, and it is not very well documented, but after some literature search I found &lt;a href=&quot;http://mbio.asm.org/content/4/1/e00596-12.full&quot; rel=&quot;nofollow&quot;&gt;this paper to quote&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Although we (Fig. 3A) and others (42, 49) have used siRNA to knock down NEAT1 lncRNA and although the knockdown of strictly nuclear RNAs has been well described (53, 54), we remained concerned that because NEAT1 is mostly a nuclear RNA (55), it may not be very efficiently targeted by the RNAi machinery. Nuclear RNAs, however, are proficiently targeted using complementary antisense (AS) oligodeoxynucleotides that recruit nuclear RNase H activity to degrade the RNA (56). Hence, we also employed complementary AS oligodeoxynucleotides to knock down NEAT1 lncRNA in HIV-1 NL4-3-infected Jurkat cells (Fig. 4C, left). The AS approach reduced NEAT1 (Fig. 4C, left) and increased HIV-1 p24 production (Fig. 4C, right), providing results consistent with those from siRNA-mediated knockdown of NEAT1 (Fig. 4A and B).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3053" LastEditorUserId="3053" LastEditDate="2013-05-16T18:15:16.743" LastActivityDate="2013-05-16T18:15:16.743" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8382" PostTypeId="1" AcceptedAnswerId="8496" CreationDate="2013-05-16T15:29:47.397" Score="2" ViewCount="3974" Body="&lt;p&gt;I am very interested in zoology,and I want to study zoology in my spare time.&#xA;Any undergraduate level zoology text book recommendation?&lt;/p&gt;&#xA;" OwnerUserId="3179" LastEditorUserId="3059" LastEditDate="2013-05-16T16:16:27.257" LastActivityDate="2013-06-07T06:05:31.823" Title="General undergraduate zoology textbook recommendation?" Tags="&lt;zoology&gt;&lt;book-recommendation&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8383" PostTypeId="2" ParentId="8378" CreationDate="2013-05-16T16:18:52.100" Score="1" Body="&lt;p&gt;This seems to be a piece of &lt;em&gt;pseudoscience&lt;/em&gt; commonly seen these days. The truth is that &lt;em&gt;this effect has never been statistically observed&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the &lt;a href=&quot;https://skeptics.stackexchange.com/questions/948/are-more-crimes-committed-during-a-full-moon/949#949&quot;&gt;Skeptics Stack Exchange site&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ivan Kelly, James Rotton and Roger Culver (1996) examined over 100 studies on lunar effects and concluded that the studies have failed to show a reliable and significant correlation (i.e., one not likely due to chance) between the full moon, or any other phase of the moon, and each of the following: The homicide rate, traffic accidents, crisis calls to police or fire stations, domestic violence, assassinations, kidnappings, aggression by professional hockey players, violence in prisons, assaults, gunshot wounds, stabbings&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;... and many more seen &lt;a href=&quot;http://www.skepdic.com/fullmoon.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2013-05-16T16:18:52.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8384" PostTypeId="1" CreationDate="2013-05-16T17:45:46.747" Score="3" ViewCount="6488" Body="&lt;p&gt;Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the advantages of this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My take of this over having fully-complementary adapters (ADAPTER1 - - - - - ADAPTER1) is that:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-Upon primer annealing, the primer in turn would bind to the start AND end of the DNA fragment, and thus not allow synthesis to continue to until the end. Therefore, the next primer would not have a template to bind at the start of the fragment...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Y-shaped adapters also allow for paired-end sequencing. Fragments have a unique sequence on either end, which allows for the first &quot;run&quot; to sequence one side of all molecules, then synthesize the reverse and sequence that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I on the right track?&lt;/p&gt;&#xA;" OwnerUserId="3459" LastEditorUserId="1320" LastEditDate="2013-05-16T17:57:22.290" LastActivityDate="2013-10-02T16:23:47.427" Title="What is the purpose of Y-shaped adapters in Illumina sequencing?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;dna-sequencing&gt;&lt;pcr&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8385" PostTypeId="2" ParentId="8371" CreationDate="2013-05-16T18:37:48.923" Score="7" Body="&lt;p&gt;I answered the other question and it is similar. However, this one is different enough that I will give a slightly more simple explanation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nerves transmit messages using electrical current, more specifically the flow of sodium and potassium. Just remember that it's electricity. When you have any sort of cut or damage, your body recruits white blood cells which protect you from any bacteria that might enter. They also cause inflammation to prevent those bacteria from spreading (and to warn other cells that they may become infected). It is also important that we feel pain, so we know something is wrong (because we have the ability to do something about it). That's why inflammation causes pain. It does this by lowering our threshold so our nerves are more sensitive. In other words, it takes less damage, pressure etc. to cause our nerves to send the pain signal. Normally, it is set higher, so we don't suffer too much pain. Naturally if you want clarification on anything just ask.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="107" LastEditDate="2014-05-09T19:28:56.350" LastActivityDate="2014-05-09T19:28:56.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8386" PostTypeId="1" AcceptedAnswerId="8387" CreationDate="2013-05-16T20:39:07.000" Score="10" ViewCount="2463" Body="&lt;p&gt;When a neurone fires, it sends an electrical signal that jumps down the axon via the nodes of Ranvier very rapidly. At a synaptic junction, chemical Brownian diffusion signalling with receptor surface proteins is relatively slow and is often exploited by venoms and susceptible to toxins (on the plus side it's the reason a lot of medical drugs work). It seems flawed for evolution to have selected for this rather than some alternative quicker and more direct electrical interface.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question.&lt;/strong&gt; Why are chemical synaptic interfaces used in higher organisms at the synaptic junction?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2017-07-13T03:10:15.900" LastActivityDate="2017-07-14T23:14:16.323" Title="Why do neurones use chemical signalling at synaptic junctions?" Tags="&lt;biochemistry&gt;&lt;neuroscience&gt;&lt;molecular-biology&gt;&lt;molecular-evolution&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8387" PostTypeId="2" ParentId="8386" CreationDate="2013-05-16T21:47:38.240" Score="7" Body="&lt;p&gt;This is the coolest part. Those synapses are the reason the brain is so complex! Basically you've got the first part right, the neurones are quicker and they transmit messages from one end to the other. The other thing you have to do is analyse and calculate. Signals from multiple neurones feed into a single neurone using a chemical synapse. Similarly the converse is true, a single neurone can feed multiple synapses. So when we for example walk, receptors monitoring our balance can feed this to our conscious and unconscious mind, but I'm grossly simplifying this. What our brain does is take hundreds and thousands of ports of information, with where the chemical synapse is and the type of synapse and the receptors and a million other things just slightly changing the information until it's perfect and then send that information a million ways however it likes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most important thing is this allows inhibition. Most of the brain uses inhibitory GABA rather than activating signals. Furthermore, the system uses the delay created. Different transmitters act for different durations and send a different volume of signal. An impulse is all or nothing, it's of a fixed amplitude, however a chemical signal can be fine tuned. Neurones can not only interact to inhibit themselves or other neurones to increase the resolution of a signal etc. Conversely a system of just physical connections allows little regulation, in fact it'd be practically a seizure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does that make sense?&lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1757" LastEditDate="2013-05-17T02:08:05.547" LastActivityDate="2013-05-17T02:08:05.547" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8388" PostTypeId="2" ParentId="8386" CreationDate="2013-05-16T22:04:37.440" Score="7" Body="&lt;p&gt;There are both chemical and electrical synapses in many organisms.  The electrical synapses are called gap junctions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you point out, the primary advantage of gap junctions is their speed, and they are commonly used in systems involving defensive reflexes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, as AndroidPenguin indicates, chemical synapses allow for greater computational abilities (changing the gain, integrating multiple inputs, etc).  Gap junctions are also disadvantageous because they often (but not always) transmit signals in both directions; chemical synapses tend to be more unidirectional (of course, there's always &lt;a href=&quot;http://en.wikipedia.org/wiki/Neural_backpropagation&quot; rel=&quot;noreferrer&quot;&gt;backpropagation&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-05-16T23:26:39.120" LastActivityDate="2013-05-16T23:26:39.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8389" PostTypeId="1" CreationDate="2013-05-16T23:04:21.447" Score="2" ViewCount="3539" Body="&lt;p&gt;I'm trying to design a primer for &lt;a href=&quot;http://en.wikipedia.org/wiki/Gibson_assembly&quot; rel=&quot;nofollow&quot;&gt;Gibson assembly&lt;/a&gt;.  My gene of interest is on a plasmid, and I want to copy that gene, and put it into a different plasmid.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am unsure how to design my primers for PCR. I know that I need 2 sets of primers (4 total).  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Backward and forward primer to copy my gene out of the plasmid that holds it.&lt;/li&gt;&#xA;&lt;li&gt;Backward and forward primer to copy the plasmid.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I also know that I need to create complementary regions of overlap between my gene and the plasmid I want to put it in.  How do I do this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the plasmid and the gene. I want to place the gene in between the biobrick prefix and suffix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is what primers I think I need:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the plasmid I want to put the gene in, my primers should be&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Forward: &lt;code&gt;ATTCGCGGCCGCTTCTAGAG&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;Reverse: &lt;code&gt;CTGACGCGGCCGCTACTAGTA&lt;/code&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Primers to copy gene and add overlap&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Reverse: &lt;code&gt;ATCATTTCAAATTCGTCCATCTCTAGAAGCGGCCGCGAAT&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;Forward: &lt;code&gt;AATTAGAAAGAGATTATAATACTAGTAGCGGCCGCTGCA&lt;/code&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Here is the gene&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://docs.google.com/file/d/0B5gGZ4-SD7-ZalhLdG5PR3VvUVk/edit?usp=sharing&quot; rel=&quot;nofollow&quot;&gt;IodoY TyrRs&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://docs.google.com/file/d/0B5gGZ4-SD7-ZbUNld2FWel9SQTA/edit?usp=sharing&quot; rel=&quot;nofollow&quot;&gt;Here is the plasmid&lt;/a&gt; I want to put it in. I am using geneious, but I think for this purpose, word works just fine. &lt;/p&gt;&#xA;" OwnerUserId="3587" LastEditorUserId="1320" LastEditDate="2013-05-17T15:01:35.470" LastActivityDate="2013-06-18T16:57:10.167" Title="Primer design for Gibson assembly" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;experimental-design&gt;&lt;cloning&gt;&lt;plasmids&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8391" PostTypeId="2" ParentId="8389" CreationDate="2013-05-17T11:09:07.800" Score="2" Body="&lt;p&gt;Disclaimer: I haven't ever done a Gibson assembly, but here is my theoretical understanding of how to design your primers. You need four 40mers each consisting of 20 bp segments derived from the vector and the insert and corresponding to the junctions that you are trying to create. In the diagram below the dotted lines represent the junctions between the two 20 bp segments of each 40mer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jyqEH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-05-17T11:09:07.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8392" PostTypeId="1" CreationDate="2013-05-17T11:55:40.390" Score="1" ViewCount="134" Body="&lt;p&gt;What can be seen on the screen when stress echocardiography (a pair of heart ultrasounds before and after exercise) suggests ischaemia? Can this happen without chest pain?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Illustration from Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/t6SYp.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1413" LastEditorUserId="1413" LastEditDate="2013-06-06T20:13:31.477" LastActivityDate="2013-06-06T20:13:31.477" Title="What's seen when stress echocardiography shows ischaemia? Can this happen without angina?" Tags="&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8395" PostTypeId="1" CreationDate="2013-05-17T14:14:02.330" Score="1" ViewCount="7721" Body="&lt;p&gt;Considering that I am writing a paper for a journal, could the following phrase be understood? or should I put the 'step-by-step' way by giving numbers? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;PCR Amplification and sequencing&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PCR reaction for sequencing with universal primer  ITS5: F: (5’TCCTCCGCTTATTGATATGC3’ and ITS4:R: (5'TCCGTAGGTGAACCTGCG&#xA;C3'), including 5,8S rDNA region (White et al 1990). Amplification condition  was performed in a 25 ml reaction volume and consisting of 10 µL nuclease free water, 12.5 µL Tag green master mix, 0,5 µL forward primer, 0,5 µL reverse primer, 0,5 µLDMSO, 1 µL template. Mixture solution  was amplified by PCR machine (Biorad). Thermal cycle programmed for 90 seconds at 95°C as initial denaturation, followed by 35 cycles of 30 sec at 95°C for denaturation, 30 sec at 55 °C as annealing, 90 sec at 72 °C for extension, and final extension at 72 °C for 5 min. PCR products were examined by electrophoresis  at 100 V for 30 minutes in a 1% (w/v) agarose gel in 1 x TAE buffer. The marker used DNA ladder 1 kb.  Electrophoresis gel was soaked in ethidium bromide for 30 minutes then visualized in UV light.&lt;/p&gt;&#xA;" OwnerUserId="3558" LastEditorUserId="460" LastEditDate="2013-05-20T14:53:19.567" LastActivityDate="2013-07-19T16:29:55.050" Title="Writing methods section on PCR amplication in a paper" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="8396" PostTypeId="1" AcceptedAnswerId="8397" CreationDate="2013-05-17T15:01:17.063" Score="3" ViewCount="1265" Body="&lt;p&gt;&lt;em&gt;Streptococcus bovis&lt;/em&gt; bacteremia/endocarditis is considered a risk factor for colorectal cancer. What pathophysiological mechanism may link the two together?&lt;/p&gt;&#xA;" OwnerUserId="1413" LastEditorUserId="107" LastEditDate="2013-05-17T15:05:09.173" LastActivityDate="2013-05-17T16:11:02.950" Title="By what mechanism is Streptococcus bovis acting as a risk factor for colorectal cancer?" Tags="&lt;microbiology&gt;&lt;pathology&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8397" PostTypeId="2" ParentId="8396" CreationDate="2013-05-17T16:11:02.950" Score="2" Body="&lt;p&gt;As you probably know, there is a lot of literature on the correlation between &lt;em&gt;Streptococcus bovis&lt;/em&gt; and colorectal cancer, but very little on possible mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In an editorial (Streptococcus bovis: Causal or incidental involvement in cancer of the colon? in the International Journal of Cancer 119(9):xi-xii), Harald zur Hausen referring to this paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Biarc J, Nguyen IS, Pini A, Gosse F, Richert S, Thierse D, van Dorsselaer A, Leize-Wagner E, Raul F, Klein JP, Scholler-Guinard M. (2004) Carcinogenic properties of proteins with proinflammatory activity from Streptococcus infantarius (formerly S. bovis). Carcinogenesis 25: 1477–84.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;comments:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...used a partially purified S. bovis S300 fraction representing 12 different proteins and triggered the synthesis of proinflammatory proteins (human interleukin-8 and prostaglandin E2, correlated with the in vitro overexpression of cyclooxygenase-2 [Cox-2]) in human colon carcinoma cells (Caco-2) and in rat colonic mucosa. These data could point to a role of oxygen radicals in colon carcinogenesis induced by a chronic infection with S. bovis. The mechanism could be similar to the one suspected for the development of gastric carcinomas after persisting Helicobacter pylori infections. Presently it would still be important to know whether the increased presence of S. bovis in colonic cancers and polyps results from the preferential bacterial colonization of these cancers and their precursors or whether S. bovis represents a carcinogen that is causally involved in colon cancer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The last sentence summarises the ongoing debate: does the bacterium promote the cancer, or does the cancer promote the bacterial infection?&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-05-17T16:11:02.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8398" PostTypeId="1" CreationDate="2013-05-17T16:12:47.933" Score="1" ViewCount="89" Body="&lt;p&gt;Is chronic anticoagulation always given after pulmonary embolism?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the risks or disadvantages &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;if anticoagulation is not given? &lt;/li&gt;&#xA;&lt;li&gt;if terminated early?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1413" LastActivityDate="2013-05-17T16:51:58.087" Title="What is the disadvantage of having no anticoagulation after pulmonary embolism?" Tags="&lt;pharmacology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8399" PostTypeId="2" ParentId="8398" CreationDate="2013-05-17T16:51:58.087" Score="2" Body="&lt;p&gt;Not always, however typically it is given for at least a few months. Lack of anticoagulation therapy would greatly heighten the risk of having another PE or related cardiovascular events. At the worst side this could cause death or permanent disability, and PE related deaths are quite common. However this depends on the nature of the PE and risk factors. For example, obesity, cancer and the pill are all risk factors and if these were reduced then it is likely the person wouldn't have another PE despite not being on long term anticoagulation therapy. However, if there is an underlying cause even despite anticoagulation therapy a person may suffer a PE. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem with anticoagulation therapy is of course it stops your blood clotting. Thus haemorrhages are more common and also more severe. However in an individual receiving anticoagulation therapy, they typically have increased clotting so this may be balanced out by therapy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally anticoagulation therapy is typically warfarin in the long term. Warfarin interacts with so many drugs including even antibiotics, it is teratogenic and quite sensitive to diet (any changes in Vitamin K will directly affect the effectivity of warfarin) thus frequent monitoring is required. This is annoying for the patient as they have to report for frequent blood tests as well as watch their diet etc.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-17T16:51:58.087" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8400" PostTypeId="2" ParentId="8395" CreationDate="2013-05-17T18:39:09.007" Score="1" Body="&lt;p&gt;Here's my take, just a few minor changes which are shown in &lt;strong&gt;bold&lt;/strong&gt; (I have also changed &lt;code&gt;,&lt;/code&gt;to &lt;code&gt;.&lt;/code&gt; for decimal numbers and added a few spaces where needed):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;PCR Amplification and sequencing&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;A PCR reaction for sequencing was performed using universal primers ITS5: F:&#xA;  (5’TCCTCCGCTTATTGATATGC3’) and ITS4:R: (5'TCCGTAGGTGAACCTGCG C3'),&#xA;  including &lt;strong&gt;5.8 S rRNA&lt;/strong&gt; region (White &lt;strong&gt;&lt;em&gt;et al.&lt;/em&gt;&lt;/strong&gt; 1990). Amplification &lt;del&gt;&lt;strong&gt;condition&lt;/strong&gt;&lt;/del&gt;&#xA;  was performed in a 25 ml reaction volume and consisting of 10 µL&#xA;  nuclease free water, 12.5 µL Taq green master mix, 0.5 µL forward&#xA;  primer, 0.5 µL reverse primer, 0.5 µL DMSO, 1µL template. &lt;strong&gt;PCR was performed using a Biorad PCR machine&lt;/strong&gt;. The thermal cycle &lt;strong&gt;was&lt;/strong&gt;&#xA;  programmed for 90 &lt;strong&gt;s&lt;/strong&gt; at 95 °C &lt;strong&gt;for&lt;/strong&gt; initial denaturation, followed by&#xA;  35 cycles of 30 s at 95 °C for denaturation, 30 s at 55 °C &lt;strong&gt;for&lt;/strong&gt;&#xA;  annealing, 90 s at &lt;strong&gt;72 °C&lt;/strong&gt; for extension, and &lt;strong&gt;5 min at 72 °C for the final extension.&lt;/strong&gt;&#xA;  PCR products were examined by electrophoresis at 100 V for&#xA;  30 min in a 1% (w/v) agarose gel in 1 x TAE buffer. The marker&#xA;  used &lt;strong&gt;a 1 kb DNA ladder&lt;/strong&gt;. &lt;strong&gt;The&lt;/strong&gt; electrophoresis gel was soaked in ethidium&#xA;  bromide for 30 min then &lt;strong&gt;examined&lt;/strong&gt; in UV light.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-05-17T20:27:33.670" LastActivityDate="2013-05-17T20:27:33.670" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="8401" PostTypeId="1" AcceptedAnswerId="8402" CreationDate="2013-05-17T19:07:16.423" Score="2" ViewCount="307" Body="&lt;p&gt;We can cure many diseases nowadays, and thus the natural selection is very limited.&#xA;Plus, mankind spent the whole beginning of its existence in almost the same hostile environment, and that's where he evolved the most, whereas our environment is changing very quickly. So, can we say that mankind froze, if not stopped, its own evolution ?&lt;/p&gt;&#xA;" OwnerUserId="3575" LastEditorUserId="1320" LastEditDate="2013-05-17T19:48:30.687" LastActivityDate="2013-05-23T17:21:05.520" Title="Has medical progress stopped human evolution?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ClosedDate="2014-12-16T23:25:43.717" ContentLicense="CC BY-SA 3.0" />
  <row Id="8402" PostTypeId="2" ParentId="8401" CreationDate="2013-05-17T19:45:13.260" Score="3" Body="&lt;p&gt;Not at all. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mutations accumulate independent of medical progress. In fact harmful mutations which would otherwise cause an individual to die can now be &quot;cured&quot; thus if anything increasing the gene pool. &lt;/li&gt;&#xA;&lt;li&gt;Typically medical progress extends our lives when we are much older, thus we have already passed mutations on to our children before a bottleneck in evolution could occur&lt;/li&gt;&#xA;&lt;li&gt;We are getting taller, less hairy and women are getting more attractive which is another form of evolution&lt;/li&gt;&#xA;&lt;li&gt;As new diseases develop the selective pressures on humans are ever changing. HIV which was never as widespread is now pushing certain immunogenetic traits to be favourable, the same is true for malaria (HLA 5701) and many others&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In conclusion, whilst there are fewer and fewer strong selective pressures forcing extreme evolution, our bodies are designed to evolve slowly unlike viruses like HIV. Our mutation rates are around 1 in 10^9, allowing us to always slowly evolve as there will always be traits which are slightly more advantageous. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="3632" LastEditDate="2013-05-23T16:58:47.893" LastActivityDate="2013-05-23T16:58:47.893" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="8404" PostTypeId="1" CreationDate="2013-05-17T21:18:02.543" Score="4" ViewCount="11959" Body="&lt;p&gt;I know of Anfinsen's experiments and I'm aware that some denatured enzymes may regain their lost activity through the removal of the denaturant agent. What I'm unaware of is how rare is it for a protein to be able to renature? Can all proteins do that? If not all of them can do it then how rare or common is it to find a protein which can be renatured?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. To avoid answers like &quot;depend on your denaturation process&quot; let us assume that a protein can be renatured if it has been shown to renature in at least one experimental setup.&lt;/p&gt;&#xA;" OwnerUserId="3593" LastEditorUserId="948" LastEditDate="2013-05-17T23:06:49.083" LastActivityDate="2013-05-17T23:06:49.083" Title="How difficult is to renature a protein?" Tags="&lt;proteins&gt;&lt;protein-folding&gt;&lt;experimental&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8406" PostTypeId="2" ParentId="8404" CreationDate="2013-05-17T23:02:18.813" Score="4" Body="&lt;p&gt;The answer is more like &quot;It depends on the protein, and the renaturation (or refolding) process.&quot; There are a lot of factors that contribute to an individual protein's ability to refold, including size, sequence, secondary structure, amount and type of inter-amino acid links like disulfide bonds, number of subunits, the presence of chaperones/heat shock proteins, and, yes, how it was denatured in the first place (sorry, I couldn't resist). Smaller proteins will refold more easily than larger ones. Hydrophilic proteins tend to refold better than more hydrophobic ones, especially membrane-bound proteins. Multi-subunit proteins/complexes tend to need some help to properly reassemble. Adding in chaperones/heat shock proteins will almost certainly help the process along for all but the smallest and hardiest samples, and will give you better results than just dialyzing all the salts/detergents/chaotropic agents away into PBS. Finally, if you denature by boiling in &lt;a href=&quot;http://www.molecularstation.com/wiki/Laemmli_buffer&quot; rel=&quot;nofollow&quot;&gt;Laemmli buffer&lt;/a&gt;, you're going to have a very difficult time refolding most things, while going from Guanidine HCl to PBS isn't always that bad, depending on what you're looking at.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, unfortunately the answer is &quot;it depends.&quot; You have to remember that the intracellular environment is very complex, and is designed to correctly fold proteins after they're made, and break down misfolded proteins before they can aggregate or cause other damage. There are hundreds of thousands of proteins just in humans, so it is rather difficult to make blanket statements, but for the sake of resistance to damage, many smaller, single-subunit proteins can likely be at least partly to mostly refolded and regain some or all of their original activity. As complexity grows, however, the likelihood of successfully regaining function decreases.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-05-17T23:02:18.813" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8407" PostTypeId="1" AcceptedAnswerId="8409" CreationDate="2013-05-17T23:37:01.360" Score="3" ViewCount="495" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eMgX9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone identify this strange creature? I live in a very urban part of Montreal, Canada. It wasn't moving (seemed dead) and although the image is huge, it wasn't as big as it seems (a couple of centimeters).&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2013-10-07T07:19:50.593" Title="What kind of arthropod/animal is this?" Tags="&lt;zoology&gt;&lt;species-identification&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8409" PostTypeId="2" ParentId="8407" CreationDate="2013-05-18T07:18:37.747" Score="4" Body="&lt;p&gt;It's a type of centipede.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on the long legs, I would bet on something like that:&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Scutigera_coleoptrata&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Scutigera_coleoptrata&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or at least a Scutigeromorpha &lt;a href=&quot;http://en.wikipedia.org/wiki/Scutigeromorpha#Scutigeromorpha&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Scutigeromorpha#Scutigeromorpha&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1486" LastActivityDate="2013-05-18T07:18:37.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8412" PostTypeId="2" ParentId="7919" CreationDate="2013-05-18T18:36:17.690" Score="2" Body="&lt;p&gt;If you're looking for an exact match, you don't really need a complex aligner. Perl regular expressions are pretty powerful at string transformations or conditional matching of substrings. For example, to find all matches of &lt;code&gt;AASYWSRA&lt;/code&gt; in a nucleotide sequence &lt;code&gt;$seq&lt;/code&gt;, you can do:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;@matches = $seq =~ m/AA[CG][CT][AT][CG][AG]A/g;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The &lt;code&gt;[]&lt;/code&gt; brackets are known as Perl character classes, which allow different characters in a position.&lt;/p&gt;&#xA;" OwnerUserId="3597" LastActivityDate="2013-05-18T18:36:17.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8413" PostTypeId="1" CreationDate="2013-05-18T20:02:35.570" Score="2" ViewCount="78" Body="&lt;p&gt;&lt;strong&gt;Background:&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many methods to extract proteins form human tissues out there. The majority of them use an extraction buffer containing variable concentrations of detergents and protease inhibitors to preserve the extracted proteins as much as possible and keep them functional until being analyzed by downstream applications, like &lt;em&gt;western blot&lt;/em&gt;, &lt;em&gt;ELISA&lt;/em&gt;, etc. One drawback of this chemical extraction is the interaction of the buffer components with antigen-antibody binding in the analysis. The interaction is sometimes difficult to predict, therefore, validation of the sample matrix is &lt;em&gt;necessary&lt;/em&gt; before going into the real analysis, e.g., for ELISA, &lt;em&gt;spike-and-recovery&lt;/em&gt;, &lt;em&gt;linearity-of-dilution&lt;/em&gt; are two known validation assays to this effect. For more info about these two assay you may find this &lt;a href=&quot;https://biology.stackexchange.com/questions/7868/what-would-be-the-best-design-for-spike-and-recovery-and-linearity-of-dilution-v&quot;&gt;answer&lt;/a&gt; useful.&#xA;One optimal way would be to avoid such interaction by avoiding the use of extraction buffer altogether and using mechanical methods plus protease inhibitors, instead. I don't know the drawback of this method, but one may be it is not as effective to get cytokines out their vesicles to be accessible by assay analysis.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;How to use &lt;em&gt;Microstrainer&lt;/em&gt; as a mechanical substitute for protein extraction in human gastric tissue?&lt;/li&gt;&#xA;&lt;li&gt;What are the pros and cons of using the &lt;em&gt;Microstrainer&lt;/em&gt;?&lt;/li&gt;&#xA;&lt;li&gt;How effective is it to measure human cytokines from tissues?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3320" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-05-19T01:27:20.150" Title="How to use mechanical microstrainer to extract tissue proteins from human?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;proteins&gt;&lt;protocol&gt;&lt;elisa&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-12-11T09:12:40.760" ContentLicense="CC BY-SA 3.0" />
  <row Id="8415" PostTypeId="1" CreationDate="2013-05-18T22:07:46.003" Score="2" ViewCount="990" Body="&lt;p&gt;It's my first time posting to this forum but was looking for some help on the data aspects of this project. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My tools of choice would be in python/R .&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Goal:&lt;/strong&gt; I'm looking to create a disease specific profile of just SNPs and SNPs in miRNAs and miRNA target sites.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;PART 1: TCGA&lt;/strong&gt; &#xA;My first step is using TCGA data which lists a ton of harmful mutations in a LOH .txt format. I'd like to be able to map those mutations to SNPs or genes or miRNAs  (whatever entities they belong to). The TCGA datasheet is &lt;a href=&quot;https://tcga-data.nci.nih.gov/tcga/tcgaDataType.jsp&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&#xA;&lt;a href=&quot;http://mirdsnp.ccr.buffalo.edu/&quot; rel=&quot;nofollow&quot;&gt;Example data is here.&lt;/a&gt; for breast cancer. I guess I can use this miRNA and mRNA data as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Questions here:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;How to decipher the LOH data to figure out if it's meaningful and where it maps?&lt;/li&gt;&#xA;&lt;li&gt;Which Tools to use for mapping and what formats for final data ? Fasta ?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;miRNA/Targets and SNPs&lt;/strong&gt;&#xA;Next up is getting cancer specific miRNAs and mRNAs and mapping SNPs to them?&#xA;I'm assuming using dbSNP or Sanger miRNA databases to get miRNA/targets and seed sequences. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm a bit lost as how to combine all these pieces of information, what formats to use for output (linked to individual pieces) and which tools if any to use to gather all this data using python. This tool is useful tool &lt;a href=&quot;http://mirdsnp.ccr.buffalo.edu/&quot; rel=&quot;nofollow&quot;&gt;mirdsnp.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3599" LastEditorUserId="14852" LastEditDate="2015-04-24T04:48:53.300" LastActivityDate="2015-04-24T04:48:53.300" Title="TCGA data, and bioinformatics design questions for SNP/ mirna analysis" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;tcga&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8417" PostTypeId="2" ParentId="8415" CreationDate="2013-05-19T01:40:58.217" Score="2" Body="&lt;p&gt;You can take a look at &lt;a href=&quot;http://www.biostars.org/p/69222/&quot; rel=&quot;nofollow&quot;&gt;this tutorial&lt;/a&gt; to understand TCGA MAF files. And you can find a list of TCGA MAF files containing mutations mapped to genes and miRNA at &lt;a href=&quot;https://www.synapse.org/#!Search:syn1710680&quot; rel=&quot;nofollow&quot;&gt;https://www.synapse.org/#!Search:syn1710680&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3597" LastEditorUserId="3597" LastEditDate="2013-05-19T03:13:14.307" LastActivityDate="2013-05-19T03:13:14.307" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="8418" PostTypeId="2" ParentId="8379" CreationDate="2013-05-19T11:32:38.967" Score="0" Body="&lt;p&gt;This is controversial, but most groups in the field have concluded that RNAi does not work in the nucleus despite the presence of Ago.  When lncRNA have been KD'd with RNAi, they are usually shown to be present in both the nucleus and cytoplasm, and the KD is thought to occur in the cytoplasm, not nucleus.  Of course as always in biology it is possible that nuclear RNAi does occur in some cell types or under some special conditions.  Gapmer oligonucleotides acting via RNAseH are usually an excellent way to KD a nuclear lncRNA, but I would add that you should be prepared to test say 6 or more different oligos, as the efficacy is unpredictable, and in contrast to RNAi, there are no great generally available algorithms for antisense oligo design. &lt;/p&gt;&#xA;" OwnerUserId="3604" LastActivityDate="2013-05-19T11:32:38.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8420" PostTypeId="1" CreationDate="2013-05-19T14:59:37.447" Score="2" ViewCount="52" Body="&lt;p&gt;&quot;Thailand is considered as one of the areas containing a high percentage of unknown taxa of &lt;em&gt;Xylariaceae&lt;/em&gt; (Rogers 2000).  In Thailand, several studies on endophytic fungi have been documented, namely, from several bamboos (Luyong et al. 2000), banana (&lt;em&gt;Musa acuminata&lt;/em&gt;) (Photita et al. 2001), monkeypod/rain tree (&lt;em&gt;Samanea saman&lt;/em&gt;) (Chareprasert et al. 2006), and several xylariaceous endophytes were also reported from those plants.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Review quoted from Izumi okane, Prasert Srikitikulchai, Kyoko Toyama, Thomas Laessoe etc. Full Paper; Study of endophytic Xylariaceae in Thailand: diversity and taxonomy inferred from rDNA sequence analyses with saprobes forming fruit bodies in the field.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have any of you known the similar cases (the high percentage of Xylariaceae) in the USA, France, or UK, proved by reference(s)? &lt;/p&gt;&#xA;" OwnerUserId="3558" LastEditorUserId="3558" LastEditDate="2013-08-05T21:35:30.450" LastActivityDate="2013-08-05T21:35:30.450" Title="Endophytic Xylariaceae: diversity and taxonomy inferred from rDNA sequence analyses" Tags="&lt;microbiology&gt;&lt;mycology&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8422" PostTypeId="1" AcceptedAnswerId="8508" CreationDate="2013-05-19T19:46:14.563" Score="5" ViewCount="696" Body="&lt;p&gt;Recombinant technologies in micro-organisms being used to produce commercial and medically useful proteins like insulin are fairly common. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However some proteins are still produced commercially in genetically modified animals. Why are animals a better choice than microorganisms, and which are the most common proteins produced this way?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="444" LastEditDate="2013-05-24T14:58:38.577" LastActivityDate="2013-05-27T07:21:41.203" Title="What medical and commercial proteins are made using genetically modified animals?" Tags="&lt;zoology&gt;&lt;proteins&gt;&lt;biotechnology&gt;&lt;transformation&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8424" PostTypeId="2" ParentId="8422" CreationDate="2013-05-19T20:22:28.677" Score="7" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/ATryn&quot;&gt;ATryn&lt;/a&gt; is a human antithrombin produced in the milk of transgenic goats by GTC Biotherapeutics. It has FDA approval and I believe that it is available for prescription in the USA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Added later, after the emphasis of the question changed somewhat.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Proteins produced in a mammalian system are more likely to have post-translational modifications that are much closer to those found on the human protein. Antithrombin, for example, has four disulphide bonds and four glycosylation sites. Although it is reasonable to assume that the disulphide bonds would be correctly formed in a eukaryotic microorganism, the same isn't true of the glycosylation: microbial glycans differ from mammalian glycans, and these differences could affect the stability of the protein in the mammalian bloodstream, or the response of the mammalian immune system to the protein. Mammalian cells in culture could be used but are, of course, quite fastidious. So the holy grail of recombinant protein production has always been to get the protein secreted into an animal's milk, allowing the use of very cheap feedstocks and the easy harvest of the protein over a period of years, notwithstanding @shigeta's remarks.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-05-24T13:07:13.467" LastActivityDate="2013-05-24T13:07:13.467" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8425" PostTypeId="1" CreationDate="2013-05-19T22:29:04.760" Score="2" ViewCount="120" Body="&lt;p&gt;Would Schoon's Hard Shell muskmelon be considered a hybrid as I have read it was a cross between a Bender's Surprise and a Honey Rock.&lt;/p&gt;&#xA;" OwnerUserId="3606" LastEditorUserId="3952" LastEditDate="2013-08-30T05:50:56.230" LastActivityDate="2014-03-28T10:02:19.020" Title="Is Schoons Hard Shell muskmelon a hybrid?" Tags="&lt;botany&gt;&lt;food&gt;&lt;ethnobiology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8426" PostTypeId="1" AcceptedAnswerId="8427" CreationDate="2013-05-19T22:37:14.753" Score="2" ViewCount="1494" Body="&lt;p&gt;I got this question and don't really understand the difference between the answers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diffusion is (in cell membrane):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) passive by nature, no metabolic energy is needed&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) driven process by pressure or voltage&lt;/p&gt;&#xA;" OwnerUserId="3607" LastEditorUserId="1320" LastEditDate="2013-05-20T14:42:00.060" LastActivityDate="2013-05-20T14:42:00.060" Title="Diffusion across cell membranes" Tags="&lt;homework&gt;&lt;cell-membrane&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8427" PostTypeId="2" ParentId="8426" CreationDate="2013-05-19T23:02:10.977" Score="1" Body="&lt;p&gt;Diffusion is always a passive process that doesn't require energy.  Therefore it would seem that A is correct, B doesn't really make a whole lot of sense.  In the case of the cell membrane diffusion will often be in the form of 'facilitated diffusion' through carrier proteins, however the transport is still not active.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2013-05-19T23:02:10.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8429" PostTypeId="2" ParentId="8426" CreationDate="2013-05-20T13:41:21.893" Score="0" Body="&lt;p&gt;Diffusion relies on the fact particles move randomly in whatever they're in. If they are concentrated (I.e. there are lots of them in one place) they will fill out the whole place. With respect to cell membranes, anything that can diffuse freely will be the same concentration inside and outside the cell. It doesn't require metabolic energy as the cell doesn't need to do a thing. Thus the answer is A.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Facilitated diffusion is where the cell puts protein channels on its membrane to allow diffusion of things that can't pass through the cell membrane normally or do so really slowly. This can be driven by a voltage or by pressure, which &quot;facilitate&quot; or help the diffusion. Glucose for example moves like this into the cell. It uses the fact that there's a high concentration of sodium outside the cell that &quot;wants&quot; to move in because of the cell inside being negative and low concentration inside. So glucose hops onto a sodium ion whilst it is moving in. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-20T13:41:21.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8430" PostTypeId="2" ParentId="8426" CreationDate="2013-05-20T14:40:50.720" Score="0" Body="&lt;p&gt;AndroidPenguin's answer has really muddied the water, but I can't fit my response into a comment.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a glucose molecule moves from the blood into, for example, a muscle cell, it is indeed diffusing down a concentration gradient, and the GLUT transporter protein acts to facilitate this process by providing a route for the polar glucose molecule to get across the membrane. This is &lt;em&gt;facilitated diffusion&lt;/em&gt;. The movement of the glucose molecules requires no input of metabolic energy. That part of AP's answer is ok, and really that's all that the OP was about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In direct contrast to this, enterocytes can transport glucose from the gut lumen into their cytosol even though the gradient of glucose concentration is in the other direction. They do this by linking the inwards movement of the glucose molecule to the outwards movement of Na&lt;sup&gt;+&lt;/sup&gt; ions, down the electrochemical gradient for these ions. This Na&lt;sup&gt;+&lt;/sup&gt; gradient is, in turn, generated by a pump which uses ATP to move Na&lt;sup&gt;+&lt;/sup&gt; out and K&lt;sup&gt;+&lt;/sup&gt; in. So in this example the energy derived from ATP hydrolysis is 'stored' in a gradient of Na&lt;sup&gt;+&lt;/sup&gt; concentration, and this gradient is tapped as a source of energy to power movement of glucose. This is NOT an example of facilitated diffusion. The ATP-powered movement of ions is an example of &lt;em&gt;primary active transport&lt;/em&gt;, and the action of the Na&lt;sup&gt;+&lt;/sup&gt;/glucose transporter is an example of &lt;em&gt;secondary active transport&lt;/em&gt;. Note also that the glucose and the Na&lt;sup&gt;+&lt;/sup&gt; move in opposite directions (antiport) so there is no question of a direct interaction between the ion and the glucose.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-05-20T14:40:50.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8432" PostTypeId="1" AcceptedAnswerId="8434" CreationDate="2013-05-20T17:26:59.010" Score="4" ViewCount="95" Body="&lt;p&gt;I have learnt that our immune system distinguishes self from non-self by using MHC. So a mother during pregnancy should also develop antibodies against the fetus as it is also a genetically different individual. Answering by saying that antibodies won't cross the placental barrier seems wrong as there is so much research going on this thing that such a simple explanation wouldn't suffice.&#xA;Why doesn't the mother reject the baby?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1320" LastEditDate="2013-05-20T21:30:16.833" LastActivityDate="2013-05-20T21:33:43.003" Title="Immunity during pregnancy" Tags="&lt;physiology&gt;&lt;immunology&gt;&lt;autoimmune&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8433" PostTypeId="1" AcceptedAnswerId="8435" CreationDate="2013-05-20T18:23:47.280" Score="5" ViewCount="4699" Body="&lt;p&gt;I am trying to learn about basic cell biology, and have what is probably an extremely simple question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So this is how I understand it so far:&#xA;Proteins are made from amino acids. This process is called protein biosynthesis, which is carried out by the ribosomes. So proteins are made by the ribosomes in every single cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So are the proteins made by the ribosomes to stay in the cell? Or can a protein move to other cells, and if so, what's the reason behind it?&lt;/p&gt;&#xA;" OwnerUserId="3614" LastEditorUserId="1320" LastEditDate="2013-05-20T21:21:35.707" LastActivityDate="2013-06-09T18:16:31.743" Title="Can proteins move outside cells?" Tags="&lt;cell-biology&gt;&lt;proteins&gt;&lt;amino-acids&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8434" PostTypeId="2" ParentId="8432" CreationDate="2013-05-20T20:17:52.807" Score="2" Body="&lt;p&gt;Awesome question! The immune system detects the presence of non-self using MHC and T cells and the lack of self using NK cells. The placenta first of all doesn't display MHC so T cells can't detect it, and expresses NK inhibitory receptors which stop NK cells killing it. Furthermore, the immune system isn't able to get to the foetus so it isn't able to activate against these antigens nor produce the antibodies which require T cells to be activated first, which then activate B cells. This is because the placenta is a syncitium, thus no spaces between cells for immune cells to slip through (a mechanism used by viruses). The placenta also secretes Neurokinin B, this makes it hard for the immune system to see the baby, and is a mechanism used by parasites. There are T reg cells which act to supress an immune response. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1320" LastEditDate="2013-05-20T21:33:43.003" LastActivityDate="2013-05-20T21:33:43.003" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8435" PostTypeId="2" ParentId="8433" CreationDate="2013-05-20T20:23:18.750" Score="10" Body="&lt;p&gt;Yes. All proteins actually begin to get synthesized on cytoplasmic ribosomes but if they are going to be used for extracellular purposes, they are tagged and whole ribosome is taken to ER where protein synthesis is completed. The proteins are exocytosed with help of Golgi body, the post office tagging and packaging organelle (the Golgi body packages these proteins into the vesicles that fuse with the plasma membrane).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples of this process are: the pancreas secreting insulin for blood sugar control, digestive enzymes for digestion, the immune system telling the body there's a bacterium we must fight it and calls more immune cells (cytokines). Most proteins of course stay in the cell, and are necessary to make the cell or carry out metabolism or DNA transcription. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="3059" LastEditDate="2013-05-21T17:05:13.677" LastActivityDate="2013-05-21T17:05:13.677" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8436" PostTypeId="2" ParentId="8392" CreationDate="2013-05-20T20:31:27.890" Score="1" Body="&lt;p&gt;A number of things can be seen. Ischaemia is typically caused by the narrowing of blood vessels that prevents perfusion (blood flow) to the heart or other organs. When the heart muscle doesn't get enough oxygen, the walls of the heart might not &quot;beat&quot; (i.e. contract) properly. We observe this and thus can tell if a coronary artery is reduced or blocked or fine. It doesn't give absolute numbers of how blocked it is, although observation of the way the muscle moves can give some indication. Contrast can further allow us to visualise the wall with more detail, giving a clearer indication of coronary artery disease in the vessels that supply this part of the heart. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pain is caused when the heart muscle is really suffering, which doesn't occur unless the vessels are seriously blocked. They're so great that even if about 70% of the artery is blocked there is almost no effect including chest pain. In fact it is silent, which is quite worrying also. However, when the heart is most stressed, we can potentially detect decrease in perfusion from small changes in the contraction of the heart.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1757" LastEditDate="2013-05-21T17:36:07.397" LastActivityDate="2013-05-21T17:36:07.397" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8437" PostTypeId="1" CreationDate="2013-05-20T20:59:00.167" Score="2" ViewCount="80" Body="&lt;p&gt;During the autologous transplantation of stems cells from bone marrow to produce new blood cells why all the other stem cells other than the one obtained are destroyed?&lt;/p&gt;&#xA;" OwnerUserId="3617" LastEditorUserId="1320" LastEditDate="2013-05-20T22:06:16.757" LastActivityDate="2018-09-11T18:09:06.423" Title="Transplantation of stem cells" Tags="&lt;cell-biology&gt;&lt;stem-cells&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8438" PostTypeId="2" ParentId="8437" CreationDate="2013-05-20T21:07:19.997" Score="2" Body="&lt;p&gt;Autologous stem cell transplants are used to treat individuals who have had their bone marrow destroyed or damaged by diseases such as lymphomas or by irradiation or cancer treatments. As they are damaged and potentially cancerous, they are removed. They are then replaced in the transplant. The whole idea is to destroy all the cells before transplanting the marrow back. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1320" LastEditDate="2013-05-20T21:28:28.513" LastActivityDate="2013-05-20T21:28:28.513" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8439" PostTypeId="1" AcceptedAnswerId="8440" CreationDate="2013-05-21T01:05:10.803" Score="8" ViewCount="14899" Body="&lt;p&gt;My kids sweat plenty in this hot heat, but they don't smell afterward. I on the other hand need all kinds of deodorant. Why doesn't kid sweat smell?&lt;/p&gt;&#xA;" OwnerUserId="933" LastEditorUserId="107" LastEditDate="2013-05-21T01:54:23.880" LastActivityDate="2015-05-21T18:56:59.210" Title="Why does the sweat of children not smell like adults?" Tags="&lt;human-anatomy&gt;&lt;skin&gt;&lt;odour&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8440" PostTypeId="2" ParentId="8439" CreationDate="2013-05-21T01:53:54.973" Score="15" Body="&lt;p&gt;There are two types of sweat glands: (1) eccrine sweat glands and (2) apocrine sweat glands.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Eccrine sweat glands are present from birth in humans and secrete sweat that is mostly water and functions in evaporative cooling.&lt;/li&gt;&#xA;&lt;li&gt;Apocrine sweat glands are found in the armpits and groin regions and become active in humans at puberty (although the distribution appears to be broader fetally). These sweat glands secrete an oily substance containing lipids and proteins that through interactions with bacteria on the skin (e.g., bacteria digesting lipids), lead to the &quot;smelliness&quot; of adults (including body odor).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So it's not really the sweat that smells, it's the action of bacteria on apocrine sweat that becomes prevalent after puberty.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-05-21T01:53:54.973" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8441" PostTypeId="1" CreationDate="2013-05-21T03:04:38.547" Score="2" ViewCount="111" Body="&lt;p&gt;One way to assemble fragments produced by DNA sequencing (often called reads) is to seek for the shortest common superstring that contains all the reads of a given set of reads. One model for this problem is the reconstruction model, which calculates the minimal edit distance between a possible superstring (that contains all fragments) and each one of the fragments. What I don't understand yet is the fact that when calculating the edit distance for a given fragment, it's necessary to calculate the edit distance for the reverse complement of that fragment.&lt;br/&gt; An example of a fragment and its reverse complement could be:&lt;br/&gt;&lt;br/&gt;&#xA; ACTGTCC fragment&lt;br/&gt;&#xA; TGACAGG complement (the complementary strand as we know)&lt;br/&gt;&#xA; GGACAGT reverse complement&lt;br/&gt;&lt;br/&gt;&#xA;According to the book I'm reading the ideia behind it is to find a superstring as short as possible that either the given fragment or its reverse complement must be an approximate substring of the superstring. I know that many mathematical/computational models don't have a biological sense for their way of soluting a biological problem, but this recontruction model I could think it's biologically reasonable to find a string that contains all the fragments of a certain region of a DNA sequence, and all the complement fragments, after all when assembling we can find both strand sequence. But a reverse complement is not something that exist for a given sequence, unless it has suffered some kind of break-recombination event, which is something not expected, mainly when talking about conserved regions. Do you any idea why this model takes into account the reverse complements ? Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="3609" LastActivityDate="2013-05-21T03:04:38.547" Title="Reverse complement of reconstruction model for assembling reads" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;mathematical-models&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8443" PostTypeId="2" ParentId="8389" CreationDate="2013-05-21T06:03:53.243" Score="1" Body="&lt;p&gt;Here is a good overview of primer design considerations when using Gibson assembly.&#xA;&lt;a href=&quot;http://j5.jbei.org/j5manual/pages/22.html&quot; rel=&quot;nofollow&quot;&gt;http://j5.jbei.org/j5manual/pages/22.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3619" LastActivityDate="2013-05-21T06:03:53.243" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8445" PostTypeId="2" ParentId="8407" CreationDate="2013-05-21T07:37:53.053" Score="2" Body="&lt;p&gt;I live in Japan and here they are called &quot;gejigeji&quot;. As mentioned, they are a member of the centipede family and are as creepy as hell. I live in a newly-built house, so thankfully there are no cockroaches, but every now and again one of these little blighters will scurry across my floor in my peripheral vision and scare the bejesus out of me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are not dangerous (at least not to humans). I have been told they eat the larvae of other insects, like cockroaches so they are not so bad really. Also, and I assume this is just a Japanese myth, but it's said they hunt in pairs.&lt;/p&gt;&#xA;" OwnerUserId="3401" LastActivityDate="2013-05-21T07:37:53.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8448" PostTypeId="1" AcceptedAnswerId="8452" CreationDate="2013-05-21T12:35:32.367" Score="7" ViewCount="1549" Body="&lt;p&gt;&lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=why-do-cats-purr&quot;&gt;http://www.scientificamerican.com/article.cfm?id=why-do-cats-purr&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article above says that cats purr mostly when they're wounded or under duress. They hypothesis that cats purring leads to increases in bone density and bone healing. How is this possible? What are some physiological possibilities for something like this to occur? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't see any journal articles backing up any of these claims. Is it similar to how ultrasound in clinical trials works? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the cat purring affect formation of osteoblasts? What is possibly happening microscopically? &lt;/p&gt;&#xA;" OwnerUserId="3622" LastEditorUserId="107" LastEditDate="2013-05-22T14:33:02.810" LastActivityDate="2013-05-22T14:33:02.810" Title="Cat purring: What are some possible underlying mechanisms behind purring and bone remodeling and formation?" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;ethology&gt;&lt;cell-signaling&gt;&lt;bone-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8449" PostTypeId="1" AcceptedAnswerId="9963" CreationDate="2013-05-21T15:40:58.937" Score="4" ViewCount="461" Body="&lt;p&gt;I have learned that first a protocell came to exist and its characteristics came to be passed on by genetic material. So how come genes for all the activities come to incorporate into genetic material? Did genetic material come first and random sequences made random proteins that were used to make cells ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1320" LastEditDate="2013-05-21T20:12:18.593" LastActivityDate="2013-08-25T08:30:50.600" Title="How did the activities of protocells become inheritable?" Tags="&lt;evolution&gt;&lt;genetics&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8450" PostTypeId="2" ParentId="8297" CreationDate="2013-05-21T17:46:26.563" Score="1" Body="&lt;p&gt;Coronary artery disease thickens the wall. Flow is dramatically affected by thickness (radius to the fourth power). In an echo you observe the heart muscle i.e. does it contract normally using the surrounding muscle and baseline as a comparison. If the wall is thickened, this will cause a decrease in perfusion which will result in the heart muscle contracting abnormally. Xaqron is right, it doesn't show you flow directly, but what it does show you is a quick and cheap way to estimate if the artery is blocked enough that it will cause a noticeable difference. If the heart muscle doesn't beat that means it really isn't getting oxygen (but could be because of abnormal conduction), and if it beats suboptimally it is getting less oxygen than it requires. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1757" LastEditDate="2013-05-21T22:01:49.023" LastActivityDate="2013-05-21T22:01:49.023" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8451" PostTypeId="2" ParentId="8449" CreationDate="2013-05-21T17:52:04.443" Score="0" Body="&lt;p&gt;The general theory is RNA came first, then DNA. Both are able to replicate with simple changes in temperature (see polymerase chain reaction). So if we imagine a world with nucleotides making RNA, the idea is the survival of the fittest RNA. RNA for example that also had enzymatic activity was &quot;fitter&quot; than RNA that did not. Then go further down the line where RNA that made a certain protein was more &quot;fitter&quot; as thus it's concentration increased. Keep going down the line as this continues, whatever was favourable in the surrounding environment increased until we have what we have today. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course this is widely disputed. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-21T17:52:04.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8452" PostTypeId="2" ParentId="8448" CreationDate="2013-05-21T20:46:17.350" Score="8" Body="&lt;p&gt;The author is likely referring to the mechanosensory behavior of bone (reviewed in &lt;a href=&quot;http://www.fasebj.org/content/24/10/3625.short&quot;&gt;Huang and Ogawa, 2010&lt;/a&gt;; &lt;a href=&quot;http://scholar.google.com/scholar?hl=en&amp;amp;q=mechanotransduction%20bone&quot;&gt;lots of Google Scholar citations&lt;/a&gt;). Bone loading produces very tiny mechanical deflections (strain) which are translated into biochemical signals that promote bone growth through the action of osteoblasts. &lt;a href=&quot;http://www.fasebj.org/content/13/9001/S101.short&quot;&gt;Burger and Klein-Nuland (1999)&lt;/a&gt; review possible mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The low frequency soundwaves produced during purring overlap the frequencies that have been shown experimentally to induce bone formation (1-50Hz; e.g., &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S8756328206004455&quot;&gt;Castillo et al., 2006&lt;/a&gt;; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S8756328206005199&quot;&gt;Xie at al. 2006&lt;/a&gt;). Although an interesting hypothesis, I don't think that osteogenesis in response to purring has ever been experimentally shown in cats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Huang C, Ogawa R. 2010 FASEB J. 2010 Mechanotransduction in bone repair and regeneration. 24(10):3625-3632.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Burger EH, Klein-Nulend. 1999. Mechanotransduction in bone--role of the lacuno-canalicular network. FASEB J 13(Suppl):S101-S112.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Castillo AB, et al. 2006 Low-amplitude, broad-frequency vibration effects on cortical bone formation in mice. Bone 39:1087-1096.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Xie L, et al. 2006. Low-level mechanical vibrations can influence bone resorption and bone formation in the growing skeleton. Bone 39:1059-1066.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-05-21T20:46:17.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8453" PostTypeId="2" ParentId="8449" CreationDate="2013-05-21T20:59:52.450" Score="1" Body="&lt;p&gt;The sequence is believed to be opposite of that implied by the phrasing of the question: the inheritance of structures supporting inheritance came before protocells.  The important point is that you need a system of reproduction before building more complicated structures (such as a cell).  Without replication (reproduction), a cell would be little more than a soap bubble, and would disappear without a trace before long.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The initial (or very early) form of replication is thought to be based on a simple form of RNA. The reason for this is that (1) RNA does encode genetic information in a way that is replicatable, and (2) RNA can take on shapes and chemical structures that act as an enzyme (called a ribozyme) that catalyze chemical reactions.  The hypothesis is that an RNA molecule formed that catalyzed assembly of copies of RNA chains, including itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After such replication was established, probably some kind of enclosure like the cell membrane evolved to contain the chemicals, making the reactions more efficient.  After (or maybe before) this, RNA catalyzing assembly of simple protein-like molecules whose sequence was encoded by RNA sequences evolved, leading to protein-based cellular machinery.  This mechanism is still evident in life today in that protein assembly uses a ribozyme-based molecule assembly (the ribosome) to translate messenger-RNA into proteins.&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2013-05-21T20:59:52.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8454" PostTypeId="1" CreationDate="2013-05-21T21:13:02.680" Score="1" ViewCount="364" Body="&lt;p&gt;I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ssm is in the following format:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;['Gene name', 'Ensembl Gene ID', 'Chromosome', 'Chromosome start', 'Cancer Type']&#xA;['NTRK1', 'ENSG00000198400', '1','156849827', 'Prostate Adenocarcinoma (TCGA, US)']&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;From there I would like to grab each mutation and :&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Map the chromosomal position to a known SNP (rs something output). &lt;/li&gt;&#xA;&lt;li&gt;See if this snp is found in a 3'UTR&lt;/li&gt;&#xA;&lt;li&gt;See if this snp is found in a miRNA &lt;/li&gt;&#xA;&lt;li&gt;Missense or sense mutation&lt;/li&gt;&#xA;&lt;li&gt;Any relevant genbank etc.. ids &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I'd like to do this Python (I think BioPython is suited for this) for downstream applications. &lt;/p&gt;&#xA;" OwnerUserId="3599" LastEditorUserId="14852" LastEditDate="2015-04-24T04:48:22.803" LastActivityDate="2015-04-24T04:48:22.803" Title="Mapping a mutation to known SNP, 3' UTR, miR" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;snp&gt;&lt;tcga&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8455" PostTypeId="1" AcceptedAnswerId="8530" CreationDate="2013-05-21T22:00:28.983" Score="1" ViewCount="37" Body="&lt;p&gt;I'm generating random molecules I would like to know if they are able to pass through the cell membrane. Are there any ways (preferably computational) to predict cellular uptake of an organic molecule which is about 55 atoms?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2013-05-22T01:56:51.940" LastActivityDate="2013-05-26T14:10:06.493" Title="cell uptake prediction" Tags="&lt;cell-membrane&gt;&lt;organic-chemistry&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8456" PostTypeId="2" ParentId="8454" CreationDate="2013-05-21T23:52:40.220" Score="1" Body="&lt;p&gt;In order:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Unfortunately, there's no easy way to batch query with only location. You could look up SNPs within genes &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK44464/#Search.can_you_tell_me_how_to_find_the_2&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.  (You could find the gene a SNP is located in by searching an annotated human genome file for the position.)&lt;/li&gt;&#xA;&lt;li&gt;You can figure out whether it's in 3'UTR by comparing to a list of human 3' UTRs. The UCSC genome browser page here will &lt;a href=&quot;http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=336773187&amp;amp;clade=mammal&amp;amp;org=Human&amp;amp;db=hg19&amp;amp;hgta_group=genes&amp;amp;hgta_track=knownGene&amp;amp;hgta_table=0&quot; rel=&quot;nofollow&quot;&gt;help&lt;/a&gt;: change the region to &quot;genome&quot;, output format to &quot;BED&quot;, click &quot;get output&quot;, and then filter for 3' UTRs.&lt;/li&gt;&#xA;&lt;li&gt;You can figure out if it's in a miRNA by comparing chr/start positions to the database available &lt;a href=&quot;ftp://mirbase.org/pub/mirbase/CURRENT/genomes/hsa.gff3&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;You could use the chromosomal locations and compare to the human genome sequence.  There is probably a better way to do this, but the FASTA for each chromosome is available &lt;a href=&quot;ftp://ftp.ensembl.org/pub/release-71/fasta/homo_sapiens/dna/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;You could use the SNP IDs to map to Genbank accessions, as per the instructions &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK44453/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;You don't need BioPython for the first three steps, since it's just parsing each line and comparing values. BioPython is useful for working with FASTA files (so part 4).  All in all, this is mostly reduced to a programming question with all of these resources (basically, you need split each string to get the appropriate numbers/IDs and then compare).&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-05-22T00:36:55.897" LastActivityDate="2013-05-22T00:36:55.897" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8457" PostTypeId="1" AcceptedAnswerId="8462" CreationDate="2013-05-22T00:25:37.300" Score="1" ViewCount="119" Body="&lt;p&gt;I've been watching a &lt;em&gt;The Crocodile Hunter&lt;/em&gt; episode about Komodo dragons, and Steve Irwin kept speaking about the animals being in &quot;food mode&quot;, in which they apparently change their behavior to one of a killing machine. He said if bark falls of a tree when they're in food mode, they'll snap it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it for real? I googled &quot;food mode&quot; but nothing interesting came up. Which animals have a food mode like this? Is it restricted to reptiles? Does it have a scientific name? Can I read about it somewhere?&lt;/p&gt;&#xA;" OwnerUserId="1278" LastEditorUserId="16866" LastEditDate="2017-04-03T17:18:17.910" LastActivityDate="2017-04-03T17:18:17.910" Title="What's food mode?" Tags="&lt;zoology&gt;&lt;food&gt;&lt;ethology&gt;&lt;reptile&gt;&lt;herpetology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8458" PostTypeId="2" ParentId="7525" CreationDate="2013-05-22T01:17:14.353" Score="8" Body="&lt;p&gt;You can use &lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Statistical_power&quot;&gt;power analysis&lt;/a&gt;&lt;/strong&gt; to work out answers depending on the specifics of your data. The things you need to consider are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;The power of the test&lt;/strong&gt;. This is the probability that the test will&#xA;fail to reject the null hypothesis even if in truth it is false&#xA;(Type II error). If the population is not in equilibrium, what is&#xA;the probability that the test will fail to detect this? This will largely depend on the costs of a Type II error. If the experiment is expensive in terms of time/money/animals used etc. you would want to make sure it will give a sold answer at the end.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;The significance level&lt;/strong&gt;. 0.05 is commonly used. The probability that&#xA;the null hypothesis is rejected even though it is true (Type I&#xA;error). If the population is in equilibrium, what is the probability&#xA;that the test will erroneously say it is in disequilibrium.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;The degrees of freedom&lt;/strong&gt;. The number of alleles.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;The effect size&lt;/strong&gt;. This is how far away from equilibrium you expect&#xA;your samples to be. The largest effect size would be extinction of&#xA;one allele. However, if two alleles are in a ratio of 100:101 across&#xA;the full population, this is a small effect size.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;For the &lt;strong&gt;Pearson's Chi-squared test&lt;/strong&gt; we can use (in R)&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;library(pwr)&#xA;pwr.chisq.test(w = 0.3, N = 40, df = 4, sig.level = 0.05 ) &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;A rough guide for effect size (&lt;code&gt;w&lt;/code&gt;) is 0.1, 0.3, and 0.5 for small, medium, and large effect sizes. There is more detail &lt;a href=&quot;http://www.statmethods.net/stats/power.html&quot;&gt;here&lt;/a&gt;. &lt;code&gt;N&lt;/code&gt; is the total number of data points, &lt;code&gt;df&lt;/code&gt; is the number of alleles. This function will give us a value for 1 minus the power of our test. A value of 0.9 means there is a 10% chance of failing to detect an effect that truly exists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we want to work out a suitable number of data points to collect we must decide what power we want. Say we decide that a 0.01 chance of doing the test, but failing to detect disequilibrium if it exists is acceptable.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;pwr.chisq.test(w = 0.3, df = 4, sig.level = 0.05, power=0.99 ) &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;tells us that 280 data points are needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Without estimates of effect size or a number of genotypes it is hard to give a straight answer to your question, but 5 per genotype seems very small.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have only two genotypes, you might choose to use the &lt;strong&gt;Fisher Exact Test&lt;/strong&gt; in which case you can use &lt;code&gt;power.fisher.test()&lt;/code&gt; in the &lt;code&gt;statmod&lt;/code&gt; package. The definitions of effect size and degrees of freedom are slightly different but the idea is the same.&lt;/p&gt;&#xA;" OwnerUserId="3578" LastActivityDate="2013-05-22T01:17:14.353" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8459" PostTypeId="2" ParentId="7117" CreationDate="2013-05-22T01:48:53.003" Score="4" Body="&lt;p&gt;&lt;strong&gt;A solid limit&lt;/strong&gt;: k must be greater than zero. Unless you're talking about some cannibalistic species or something that isn't suited to the model at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As long as the &lt;strong&gt;species is productive&lt;/strong&gt; in the new environment: k is greater than 1. The population is probably growing or again you probably won't be using an exponential growth model. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As mentioned before you would need to know the species for more information. But if you look at generation times and litter sizes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Some &lt;strong&gt;bacterial&lt;/strong&gt; generation times (from &lt;a href=&quot;http://textbookofbacteriology.net/growth_3.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) range from 10 to&#xA;2000 minutes (33 hours). So that is $k=2$ per generation time. Per&#xA;day you're looking at a lower bound of 2 per day and an upper bound&#xA;of $k=2^{14}=10^{43}$ per day.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Mice&lt;/strong&gt; are something like 12 week generation time and a litter of 10&#xA;giving something like $k=10^{10}$ per year.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Elephants&lt;/strong&gt; are one young every 25 years. So $k=16$ per century or so.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Of course this is all based on gross assumptions. But you're looking for guidelines for a unrealistic model so hopefully they'll do.&lt;/p&gt;&#xA;" OwnerUserId="3578" LastActivityDate="2013-05-22T01:48:53.003" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8460" PostTypeId="2" ParentId="5284" CreationDate="2013-05-22T03:47:48.993" Score="1" Body="&lt;p&gt;First we must remember what a nucleosome is: a segment of DNA packed with proteins called histones. This is the initial step to turn the DNA a more compact structure. Citing the advantages of an extremely compact but flexible structure like chromosomes would make this answer a little longer (if you want, I can add them later), and to answer your question faster, we'd better keep moving on the discussion. &lt;br/&gt;Epigenetics and gene expression are so beautiful that they have many mechanisms to regulate or change gene expression, and you mention one, which is done by reversible covalent modifications on histones. Such modifications are executed by especific proteins, that can do methylation, acetylation, phosphorilation in some aminoacids of histones. &lt;br/&gt;When an aminoacid of a histone is linked with charged groups (e.g: methyl, acetyl) its charge is altered, and depending of the resulting charge (negative or positive), it can reduce or increase the afinity between the histone tail and the adjacent nucleosomes, and therefore, make the nucleosome more compact and less accessible or less compact and more accessible, respectively. &lt;br/&gt;But the main effect of these covalent modifications on histones is that the groups added to the aminoacids act like markers indicating for proteins involved in expression (like transcriptional factors and RNA polymerase) that some genes are switched on or switched off. The patterns of this modifications (which one repress or estimulate gene expression) is not completely understood yet.&lt;br/&gt;An example of how a certain region is chosen to be marked for expression or repression: &lt;br/&gt;Consider an organism that has received a repressed gene related to obesity from its parents and this organism is lazy, eats a lot, has a sedentary life. As a result of all this stimulation, the proteins responsible for altering the histones of the gene related to obesity can be activated or recruited by others proteins, and make covalent modifications in a way that the histones of that gene now are marked for it to be expressed. This organism can pass the new mark to the its children and they will have propensity to obesity due to the activated gene. (This final example was an experiment of epigenetics using rats, I saw a long time ago, so I can't remember the reference).&lt;br/&gt;And about if it's casual or not, the marks of regulation in a sequence of DNA can't be casual. For each one or two modifications of histones there is an enzyme that will only do its function if some event is already triggered or if it's triggered during the cell life depending on the environment the cell is exposed to. So millions of cells of a same tissue that have the same function would not have the same pattern of expression for the main genes related with that function by chance. Therefore, regulation of gene expression is very refined and histone marks are one of the many mechanisms that together dictate if a gene is repressed or expressed.&lt;/p&gt;&#xA;" OwnerUserId="3609" LastEditorUserId="3609" LastEditDate="2013-05-22T10:24:11.270" LastActivityDate="2013-05-22T10:24:11.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8461" PostTypeId="1" AcceptedAnswerId="8466" CreationDate="2013-05-22T09:03:57.170" Score="0" ViewCount="879" Body="&lt;p&gt;I know there is a difference between digestive and metabolic waste, but which one is called excretion? And what's the other one called? Thanks!&lt;/p&gt;&#xA;" OwnerUserId="3627" LastEditorUserId="69" LastEditDate="2013-05-22T09:24:41.567" LastActivityDate="2013-05-22T14:25:55.670" Title="Excretion and metabolic waste?" Tags="&lt;terminology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8462" PostTypeId="2" ParentId="8457" CreationDate="2013-05-22T09:51:47.810" Score="2" Body="&lt;p&gt;I suspect he just meant &quot;when they are hungry&quot; and likely was playing it up for TV.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the San Diego Zoo, they only manage to eat about once a month, and spend a few days digesting their prey. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Adults spend an average of 26 days searching for prey. 10-20 minutes eating. (A 50 kg female was observed to swallow a 31 kg boar in 17 minutes). 3-6 days is spent in digestive pause.&lt;/li&gt;&#xA;&lt;li&gt;Ingestion rate may be as much as 2.5 kg/min - higher than any other predator except large snakes.&lt;/li&gt;&#xA;&lt;li&gt;High digestive efficiency (70-90%) Time is dependent upon temperature (about 26 hours at normal body temperature) Cool nights can delay to almost 5 days. Stress can slow or even stop digestion (defecation of partially digested prey may occur)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://library.sandiegozoo.org/factsheets/komodo_dragon/komodo.htm&quot; rel=&quot;nofollow&quot;&gt;http://library.sandiegozoo.org/factsheets/komodo_dragon/komodo.htm&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-05-22T09:51:47.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8463" PostTypeId="1" AcceptedAnswerId="8467" CreationDate="2013-05-22T11:48:32.077" Score="1" ViewCount="162" Body="&lt;p&gt;I Always thought that copper was toxic to the human body.&lt;br&gt;&#xA;So how can it be safe to place a copper object (birth control spiral) into a uterus for a duration of 5 years?&lt;/p&gt;&#xA;" OwnerDisplayName="user1897" LastActivityDate="2013-05-22T14:30:12.380" Title="copper spiral birth control not toxic?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8466" PostTypeId="2" ParentId="8461" CreationDate="2013-05-22T14:25:55.670" Score="1" Body="&lt;p&gt;Egestion is the expulsion of undigested food which occurs typically via the anus. Although, interestingly or maybe just gross, flatworms must use their mouth has they have no anus. This is the non-metabolised material. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Excretion is the transfer of any metabolised material to the environment, including urine or carbon dioxide. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-22T14:25:55.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8467" PostTypeId="2" ParentId="8463" CreationDate="2013-05-22T14:30:12.380" Score="1" Body="&lt;p&gt;Copper is toxic, however from a copper device insufficient levels enter the bloodstream to cause any harm. The released copper is however toxic to sperm. Nevertheless at the site of insertion, they can cause inflammation (especially in the first 21 days and during menstruation) and thus they also recruit white blood cells and the increase in levels of prostaglandins. However, this isn't that common. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-22T14:30:12.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8469" PostTypeId="1" AcceptedAnswerId="8474" CreationDate="2013-05-22T16:52:47.393" Score="4" ViewCount="1234" Body="&lt;p&gt;Therapeutic antibodies, for example Rituximab which recognises CD20 on B lymphoma cells, can cause adverse effects (e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19399690&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/19399690&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One reason behind these adverse effects could of course be an over-response of immune cells stimulated by the Fc region of antibodies attached to lymphona cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it could also be thinkable that the immune system launches a response against the antibody itself, recognising it as foreign. Does this occur? If so, what part of the injected antibody acts as the epitope recognised by immune cells as foreign?&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-05-23T04:30:20.400" Title="How does the immune system distinguish own and foreign antibodies?" Tags="&lt;immunology&gt;&lt;antibody&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8470" PostTypeId="2" ParentId="7019" CreationDate="2013-05-22T18:00:04.463" Score="-2" Body="&lt;p&gt;Many vitamins are absorbed in mouth. Even spraying vitamins will help you overcome vitamin deficiency.&#xA;Even some drugs can be absorbed directly into mouth.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-05-23T16:48:23.290" LastActivityDate="2013-05-23T16:48:23.290" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8471" PostTypeId="1" CreationDate="2013-05-22T18:11:08.060" Score="4" ViewCount="188" Body="&lt;p&gt;I only know the vasovagal reflex. I would really appreciate if someone could inform me about the other ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About the pathologies, I already know the effects of direct nerve damage. I am talking about more sparse and indirect ones, for example so far I found Roemheld syndrome, which is a gastrocardiac syndrome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually, any subtle clinical presentation including the vagus nerve could be really helpful!&lt;/p&gt;&#xA;" OwnerUserId="3630" LastEditorUserId="107" LastEditDate="2013-05-22T20:12:04.397" LastActivityDate="2013-09-10T06:23:26.523" Title="Reflexes &amp; Pathologies including the Vagus Nerve" Tags="&lt;neurology&gt;&lt;cranial-nerves&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8473" PostTypeId="1" CreationDate="2013-05-22T19:20:50.723" Score="4" ViewCount="250" Body="&lt;p&gt;On sites like SNPedia, some pages contain the frequency of the SNP in question in different populations, based on published research. I'm trying to write a script that takes 23andme data and compares it with SNP frequency to find rare SNPs that the user possesses. I'm thinking that the only way to do this might be to scrape it from a SNP database. Is there anywhere you know of that makes this information available in a more accessible format, ideally preformatted for parsing?&lt;/p&gt;&#xA;" OwnerUserId="3308" LastActivityDate="2013-06-14T22:38:23.467" Title="Is there any source for raw data of SNP genotype frequency?" Tags="&lt;genetics&gt;&lt;snp&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8474" PostTypeId="2" ParentId="8469" CreationDate="2013-05-22T19:46:40.183" Score="3" Body="&lt;p&gt;The short answer is that antibodies are proteins like any other, and if an antibody from a foreign source is injected it can result in an immune response. This is, of course, exploited in the production of secondary antibodies for use in research (e.g. goat anti-rabbit IgG is a goat  antibody that recognises rabbit IgG).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of this, therapeutic antibodies are &quot;humanised&quot; and this is the case with &lt;a href=&quot;http://www.drugbank.ca/drugs/DB00073&quot; rel=&quot;nofollow&quot;&gt;Rituximab which is derived from a mouse monoclonal IgG&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Rituxan is a genetically engineered chimeric murine/human monoclonal antibody directed against the CD20 antigen found on the surface of normal and malignant B lymphocytes. The antibody is an IgG1 kappa immunoglobulin containing murine light- and heavy-chain variable region sequences and human constant region sequences. Rituximab is composed of two heavy chains of 451 amino acids and two light chains of 213 amino acids&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Presumably it would be possible for the remaining mouse-derived variable regions to be recognised as foreign by the human immune system, and this possibility is hinted at in the abstract of an early paper on rituximab (McLaughlin et al. (1998) Rituximab chimeric anti-CD20 monoclonal antibody therapy for relapsed indolent lymphoma: half of patients respond to a four-dose treatment program. J Clin Oncol.16:2825-33.) My emphasis...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A chimeric monoclonal antibody more effectively mediates host effector functions and is itself &lt;strong&gt;less immunogenic&lt;/strong&gt; than are murine antibodies.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, I'm not aware of any evidence that simple immune responses to Rituximab actually occur.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-05-22T19:46:40.183" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8475" PostTypeId="2" ParentId="8473" CreationDate="2013-05-22T20:16:38.850" Score="1" Body="&lt;p&gt;You might be able to get some raw data on SNP frequency by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/SNP/batchquery.html&quot; rel=&quot;nofollow&quot;&gt;batch querying the dbSNP database&lt;/a&gt;.  I have not used it myself, though.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-05-22T20:16:38.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8476" PostTypeId="1" AcceptedAnswerId="8483" CreationDate="2013-05-22T21:31:13.193" Score="4" ViewCount="1381" Body="&lt;p&gt;Is active transport required for all living cells to function?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was under the impression that if a cell doesn't have active transport, it either would lose molecules through the membrane and not be able to maintain a proper gradient, or molecules would be trapped inside the membrane (waste) or outside the membrane (food).&lt;/p&gt;&#xA;" OwnerUserId="866" LastActivityDate="2013-05-23T07:21:19.273" Title="Is Active Transport Required For Life?" Tags="&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8477" PostTypeId="1" AcceptedAnswerId="8487" CreationDate="2013-05-22T22:20:09.770" Score="3" ViewCount="80" Body="&lt;p&gt;Can someone explain exactly what &quot;rapamycin-sensitive oncogenic transformation&quot; is? I get that it's a drug that suppresses the immune system but what does it have to do with oncogenic transformation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the article where they talk about it:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/104/13/5569.full&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/104/13/5569.full&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3500" LastEditorUserId="6" LastEditDate="2013-05-23T12:48:04.800" LastActivityDate="2013-05-23T14:19:49.260" Title="What does &quot;rapamycin-sensitive oncogenic transformation&quot; mean?" Tags="&lt;biochemistry&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8478" PostTypeId="2" ParentId="8356" CreationDate="2013-05-22T23:40:29.140" Score="3" Body="&lt;p&gt;Slow worms share many characteristics with other lizards, such as the presence of eyelids, which no snake has. Leglessness in slow worms evolved separately than in snakes, as can be seen by the fact that other lizards in the same family, &lt;a href=&quot;https://en.wikipedia.org/wiki/Anguidae&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Anguidae&lt;/em&gt;&lt;/a&gt; (and therefore, more closely related to them than snakes) possess legs (see &lt;a href=&quot;https://en.wikipedia.org/wiki/Gerrhonotus&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Gerrohonotus&lt;/em&gt;&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Abronia_%28animal%29&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Abronia&lt;/em&gt;&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Things are complicated a bit because work by &lt;a href=&quot;http://www.venomdoc.com/venomdoc/Reptiles_files/2006_BGF_Nature_squamate_venom.pdf&quot; rel=&quot;nofollow&quot;&gt;Fry &lt;em&gt;et al.&lt;/em&gt; (2006)&lt;/a&gt; shows that the Anguimorpha (slow worms), along with Varanids (monitor lizards), Iguanids (iguanas), Helodermatids (gila monsters and beaded lizards) and snakes form an evolutionarily related clade, since all of these possess some or all of the components of snake venom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, for anatomical and phylogenetic reasons, it is clear that the slow worm is more closely related to other lizards than it is to snakes.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastActivityDate="2013-05-22T23:40:29.140" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8479" PostTypeId="2" ParentId="8473" CreationDate="2013-05-23T00:03:43.700" Score="0" Body="&lt;p&gt;This is one of the reasons the &lt;a href=&quot;http://www.1000genomes.org/data&quot; rel=&quot;nofollow&quot;&gt;1000 genomes project&lt;/a&gt; was created.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-05-23T00:03:43.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8481" PostTypeId="2" ParentId="8469" CreationDate="2013-05-23T04:30:20.400" Score="1" Body="&lt;p&gt;It is unlikely that an antibody would bind another antibody within just the human species. Human antibodies which bind to the human Fc portion cannot exist as they would be filtered by self tolerance mechanisms (as these B cells would be chronically activated or would the T cells that would be required for costimulatory help allowing the B cells to class switch and make the antibodies). Antibodies that bind to other portions are possible but unlikely because they wouldn't be pathogenic thus wouldn't cause an inflammatory response so wouldn't be presented with the relevant danger signals to instruct T cells and B cells to respond. If they were CD8 T cells would rapidly destroy these B cells by binding to these B cells so again, no B cell antibodies recognising self antibodies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There must be mechanisms to prevent this as if there weren't as B cell survival is dependent on its cognate antigen, if its cognate antigen were itself or other antibodies we would be in for deep trouble: namely a lymphoproliferative disorder is assume. But all this is off the top of my head, so guys correct me if I'm wrong. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't say there aren't B cells that can recognise antibodies, I just say they'll be deleted. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-23T04:30:20.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8482" PostTypeId="2" ParentId="2909" CreationDate="2013-05-23T04:37:40.520" Score="1" Body="&lt;p&gt;Senescent red blood cells are cleared by macrophages in a process called eryptosis or is better known as erythrocyte programmed cell death or apoptosis. The mechanism is excellently reviewed &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/m/pubmed/16910766/&quot; rel=&quot;nofollow&quot; title=&quot;here&quot;&gt;here&lt;/a&gt;. In summary it is mediated by caspases, phospholipase A and prostaglandin E.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-23T04:37:40.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8483" PostTypeId="2" ParentId="8476" CreationDate="2013-05-23T07:21:19.273" Score="5" Body="&lt;p&gt;For an organism (think single-celled) living in &lt;em&gt;just&lt;/em&gt; the right kind of environment, it &lt;em&gt;might&lt;/em&gt; just be possible to survive using only &lt;a href=&quot;https://en.wikipedia.org/wiki/Facilitated_diffusion&quot;&gt;facilitated diffusion&lt;/a&gt;, at least as far as small molecules are concerned. This kind of organism would have to maintain exactly the right concentration of the molecules it wants to keep or get rid of, based on the external concentration of those molecules. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, if an organism was living in a glucose-rich environment, it might be able to fulfill its glucose requirements by (1) making the membrane itself tightly impermeable to glucose and (2) tightly controlling the number of passive glucose transporters. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;It would be nigh-impossible to achieve this for every solute in the environment, especially those that are able to permeate the membrane.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there were such a thing, it might be found in organisms that live in very low energy aquatic regimes such as &lt;a href=&quot;https://en.wikipedia.org/wiki/Anaerobic_oxidation_of_methane&quot;&gt;anaerobic methane oxidizers&lt;/a&gt;, where the solute concentration in the environment doesn't really change in small time scales.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even in such environments, the number of small ions in the environment is likely to be high enough that &lt;em&gt;some&lt;/em&gt; active transport would be required to maintain the osmotic balance within the cell.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastActivityDate="2013-05-23T07:21:19.273" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8485" PostTypeId="1" CreationDate="2013-05-23T09:14:12.457" Score="4" ViewCount="932" Body="&lt;p&gt;I was searching what are the animals I frequently saw in the north of Ethiopia. I took some bad quality pictures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For me it looked like a large squirrel, local people called it a rat, and on the internet I find rock hyraxes are quite frequent in the region, but they appear not to have a long tail like the animals I saw, and they don't have the white lateral line &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FU9jH.jpg&quot; alt=&quot;Mammal 1&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/4hTMD.jpg&quot; alt=&quot;Mammal 2&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3635" LastEditorUserId="3635" LastEditDate="2013-05-23T14:06:24.633" LastActivityDate="2013-05-24T08:23:46.620" Title="What is this marmot-like animal (Tigray, Ethiopia)?" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8487" PostTypeId="2" ParentId="8477" CreationDate="2013-05-23T14:19:49.260" Score="4" Body="&lt;p&gt;The mammalian target of &lt;a href=&quot;http://en.wikipedia.org/wiki/Rapamycin&quot; rel=&quot;nofollow&quot;&gt;rapamycin&lt;/a&gt; (&lt;a href=&quot;http://en.wikipedia.org/wiki/MTOR&quot; rel=&quot;nofollow&quot;&gt;mTOR&lt;/a&gt;) is a Ser/Thr &lt;a href=&quot;http://en.wikipedia.org/wiki/Protein_kinase&quot; rel=&quot;nofollow&quot;&gt;protein kinase&lt;/a&gt; that functions as an ATP and amino acid sensor to balance nutrient availability and cell growth. When sufficient nutrients are available, mTOR responds to a &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphatidic_acid&quot; rel=&quot;nofollow&quot;&gt;phosphatidic acid&lt;/a&gt;-mediated signal to transmit a positive signal to &lt;a href=&quot;http://en.wikipedia.org/wiki/P70S6_kinase&quot; rel=&quot;nofollow&quot;&gt;p70 S6 kinase&lt;/a&gt; and participate in the inactivation of the &lt;a href=&quot;http://en.wikipedia.org/wiki/EIF4E&quot; rel=&quot;nofollow&quot;&gt;eIF4E&lt;/a&gt; inhibitor, &lt;a href=&quot;http://en.wikipedia.org/wiki/EIF4EBP1&quot; rel=&quot;nofollow&quot;&gt;4E-BP1&lt;/a&gt;. These events result in the translation of specific mRNA subpopulations. mTOR is phosphorylated via the &lt;a href=&quot;http://www.cellsignal.com/pathways/akt-signaling.jsp&quot; rel=&quot;nofollow&quot;&gt;PI3 kinase/Akt signaling pathway&lt;/a&gt; and also autophosphorylates under translationally repressive conditions. mTOR plays a key role in cell growth and homeostasis and may be abnormally regulated in tumors. It is currently under investigation as a potential target for anti-cancer therapy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.cellsignal.com/pathways/translational-control.jsp?pathway=trans-mtor&quot; rel=&quot;nofollow&quot;&gt;mTOR signaling pathway&lt;/a&gt; shows how mTOR is involved in numerous cell processes that can be dysregulated in cancer, including cell growth, proliferation, angiogenesis, &lt;a href=&quot;http://en.wikipedia.org/wiki/Autophagy&quot; rel=&quot;nofollow&quot;&gt;autophagy&lt;/a&gt;, and various kinds of metabolism. &quot;&lt;em&gt;Rapamycin-sensitive oncogenic transformation&lt;/em&gt;&quot; therefore means that the transformed cells still have intact &quot;wild-type&quot; mTOR complexes that can be down-regulated by the tumor-specific administration of rapamycin analogues, hence inhibiting the above-mentioned processes and arresting or killing the cells.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-05-23T14:19:49.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8489" PostTypeId="1" CreationDate="2013-05-23T14:36:55.207" Score="0" ViewCount="41" Body="&lt;p&gt;&quot;The researchers found that a single type of fungus, belonging to the genus Malassezia, is predominant on the head and trunk. Hands, which harbor a great diversity of bacteria, are home for relatively few types of fungi. In contrast, feet, including toenails, heels and toe webs contain tremendous diversity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Applying DNA sequencing to a study of the skin's fungi is the natural progression in understanding microbial life that co-exists on our bodies,&quot; said NHGRI Scientific Director Daniel Kastner, M.D., Ph.D. &quot;Along with recent genome sequencing to define bacterial diversity, this analysis of fungal diversity provides a more complete human microbiome picture.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Fungal communities occupy complex niches, even on the human body,&quot; said Heidi Kong, M.D., co-senior author and an investigator in the dermatology branch of NCI's Center for Cancer Research. &quot;By gaining a more complete awareness of the fungal and bacterial ecosystems, we can better address associated skin diseases, including skin conditions which can be related to cancer treatments.&quot;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://phys.org/news/2013-05-genomic-survey-human-skin-fungal.html&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there another reference for this research please?&lt;/p&gt;&#xA;" OwnerUserId="3558" LastEditorUserId="3558" LastEditDate="2013-05-23T15:41:31.693" LastActivityDate="2013-05-23T15:53:30.530" Title="First genomic survey of human skin fungal diversity" Tags="&lt;microbiology&gt;&lt;mycology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8490" PostTypeId="2" ParentId="8485" CreationDate="2013-05-23T14:58:03.817" Score="4" Body="&lt;p&gt;This looks like some sort of ground squirrel. Especially in the second picture, the posture is  very characteristic of squirrels in general. The tail also looks very squirrel-like to my eyes. My best guess, without better pictures, is the &lt;a href=&quot;https://en.wikipedia.org/wiki/Xerus_erythropus&quot; rel=&quot;nofollow&quot;&gt;Striped Ground Squirrel (&lt;em&gt;Xerus erythropus&lt;/em&gt;)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See the images at:&#xA;&lt;a href=&quot;http://www.flickriver.com/photos/8834404@N02/2902284598/&quot; rel=&quot;nofollow&quot;&gt;http://www.flickriver.com/photos/8834404@N02/2902284598/&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.flickriver.com/photos/kpzaremba/5094580855/&quot; rel=&quot;nofollow&quot;&gt;http://www.flickriver.com/photos/kpzaremba/5094580855/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3631" LastEditorUserId="3631" LastEditDate="2013-05-24T08:23:46.620" LastActivityDate="2013-05-24T08:23:46.620" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8491" PostTypeId="2" ParentId="8489" CreationDate="2013-05-23T15:53:30.530" Score="2" Body="&lt;p&gt;The link is given at bottom of the article that you linked to. &lt;a href=&quot;http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12171.html&quot; rel=&quot;nofollow&quot;&gt;It's a Nature paper&lt;/a&gt; so you need to have access rights.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-05-23T15:53:30.530" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8492" PostTypeId="1" AcceptedAnswerId="14084" CreationDate="2013-05-23T16:41:22.313" Score="4" ViewCount="7268" Body="&lt;p&gt;What exactly does urea do that harms our body? Does it interfere with our cellular processes or disturbs the colloidal onchotic pressure of our blood? &#xA;I have heard that NH&lt;sub&gt;3&lt;/sub&gt; damages the brain. What does it actually do?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3340" LastEditDate="2014-10-31T12:18:47.637" LastActivityDate="2017-07-04T12:51:52.170" Title="Ill effects of urea and NH₃ on metabolism" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8493" PostTypeId="2" ParentId="8375" CreationDate="2013-05-23T17:19:12.740" Score="2" Body="&lt;p&gt;The answer to this is fairly complex, and it depends on whether you are talking about short-term or long-term changes to the microbiota. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When talking about short-term changes, the answer is almost certainly a resounding yes. Any ingested nutrient will lead to an increase in the growth rates of bacteria capable of metabolising that nutrient, and will therefore lead to a change in the composition of the intestinal microbiota. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is, unfortunately, difficult to observe, as most studies of the intestinal microbiota use fecal samples to look at intestinal microbial composition. Since stool represents an average of what happens between two bowel movements, it is difficult to draw inferences about short-term changes in the microbial composition of the bowel. However, there is &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/20520652&quot; rel=&quot;nofollow&quot;&gt;evidence&lt;/a&gt; from Pythons that suggests extensive remodelling of the microbial composition does indeed occur, at least in animals with less regular feeding schedules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of long-term changes, there is strong evidence that specific oligosaccharides contained in human milk &lt;a href=&quot;http://www.pnas.org/content/105/48/18964.short&quot; rel=&quot;nofollow&quot;&gt;specifically select&lt;/a&gt; for certain strains of &lt;em&gt;Bifidobacterium&lt;/em&gt; and &lt;em&gt;Lactobacillus&lt;/em&gt;. Apart from this very specific set of oligosaccharides however, there is a paucity of studies dealing with the effects of diet on the gut microbiota, and even fewer looking at specific nutrients. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The premise that long-term changes to the gut microbiota can be made with diets is the foundation on which the entire &lt;a href=&quot;https://en.wikipedia.org/wiki/Prebiotic_%28nutrition%29&quot; rel=&quot;nofollow&quot;&gt;prebiotics&lt;/a&gt; industry is built. The most popular prebiotics are fructo-oligosaccharide, inulin, galacto-oligosaccharide and lactulose. These are said to encourage the growth of beneficial strains of &lt;em&gt;Bifidobacterium&lt;/em&gt; and &lt;em&gt;Lactobacillus&lt;/em&gt;. However, there is currently no consensus on the long-term effects of these oligosaccharides on the microbiota.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastEditorUserId="3631" LastEditDate="2013-05-24T05:12:58.713" LastActivityDate="2013-05-24T05:12:58.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8494" PostTypeId="2" ParentId="8401" CreationDate="2013-05-23T17:21:05.520" Score="1" Body="&lt;p&gt;Keep in mind that most people live in environments where antibiotics are of limited availability and hygiene is not as rigorous as in the &quot;western&quot; world. Combine this with high population densities and you get, if anything, more natural selection due to the spread/proliferation of pathogens and the subsequent mortality of the patient.&#xA;Also, don't confuse natural selection for evolution. Natural selection is one of only five causes of (micro-) evolution. Mutations will continue to occur. Sexual selection continues unabated, and migration is more important now than ever. The only evolutionary factor I'd argue is being diminished is genetic drift since there are so many people today.&lt;/p&gt;&#xA;" OwnerUserId="1710" LastActivityDate="2013-05-23T17:21:05.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8496" PostTypeId="2" ParentId="8382" CreationDate="2013-05-23T18:34:51.600" Score="2" Body="&lt;p&gt;I used &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0073524174&quot; rel=&quot;nofollow&quot;&gt;Zoology by Miller and Harley&lt;/a&gt; in my undergraduate years and I found it to be an engaging, informative text book. &lt;/p&gt;&#xA;" OwnerUserId="3631" LastActivityDate="2013-05-23T18:34:51.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8497" PostTypeId="1" AcceptedAnswerId="8503" CreationDate="2013-05-24T02:55:59.290" Score="1" ViewCount="1503" Body="&lt;p&gt;Does having gecko lizards living in your house pose any health risk?&lt;/p&gt;&#xA;" OwnerUserId="3647" LastEditorUserId="3624" LastEditDate="2014-03-27T14:06:18.847" LastActivityDate="2017-01-20T03:01:47.673" Title="How do pet gecko lizards pose a health risk?" Tags="&lt;zoology&gt;&lt;pathology&gt;&lt;herpetology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8498" PostTypeId="1" AcceptedAnswerId="8627" CreationDate="2013-05-24T03:01:11.213" Score="4" ViewCount="211" Body="&lt;p&gt;I recently witnessed a cockroach eat its shell after it moulted. Do cockroaches always do this?&lt;/p&gt;&#xA;" OwnerUserId="3647" LastActivityDate="2013-06-02T21:47:33.640" Title="Do cockroaches eat their shells after moulting?" Tags="&lt;zoology&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8499" PostTypeId="1" AcceptedAnswerId="10023" CreationDate="2013-05-24T03:23:12.317" Score="1" ViewCount="2194" Body="&lt;p&gt;I have this equation:&#xA;Corresponds to HW in equilibria with three alleles:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$(p+q+r)^2=1$    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Expanding the square results:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$p^2+2pq+r^2+2pr+q^2+2qr = 1$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I need to separate homozygous and heterozygous, that means:&#xA;$2pq+2pr+2qr=1-p^2-q^2-r^2$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How I can use a equivalence similar to $(p=1-q) or (q=1-p)$ in two alleles to resolve the last equation?&lt;/p&gt;&#xA;" OwnerUserId="923" LastActivityDate="2014-02-08T05:27:37.860" Title="Hardy-Weinberg applied to three alleles and stimation of allele frequencies" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;population-biology&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="8500" PostTypeId="1" CreationDate="2013-05-24T03:34:25.067" Score="2" ViewCount="1248" Body="&lt;p&gt;What chemical aspect of amino acids results in their having different properties such that the chemical and physical properties of polypeptides vary with both amino acid content and amino acid order? &lt;/p&gt;&#xA;" OwnerUserId="3648" LastEditorUserId="3059" LastEditDate="2013-05-24T17:00:47.140" LastActivityDate="2014-12-04T01:04:06.163" Title="Amino acid characteristics that determine their chemical properties?" Tags="&lt;biochemistry&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8501" PostTypeId="1" AcceptedAnswerId="8509" CreationDate="2013-05-24T04:22:22.117" Score="2" ViewCount="86" Body="&lt;p&gt;I need to express a protein in vitro but I don't know where to start.  I will likely do a  &lt;a href=&quot;http://openwetware.org/wiki/Sauer%3aIn_vitro_transcription_with_T7_RNA_polymerase&quot; rel=&quot;nofollow&quot;&gt;T7 transcription protocol&lt;/a&gt; but for translation I am not sure what to do.  Are there any good kits?&lt;/p&gt;&#xA;" OwnerUserId="3247" LastEditorUserId="3059" LastEditDate="2013-05-24T17:00:16.027" LastActivityDate="2013-05-24T17:00:16.027" Title="In vitro enzyme production" Tags="&lt;molecular-biology&gt;&lt;protocol&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8503" PostTypeId="2" ParentId="8497" CreationDate="2013-05-24T08:16:16.690" Score="3" Body="&lt;p&gt;If you're referring to keeping geckos as pets, like all reptiles, amphibians and birds, they come with a small but finite risk of contracting &lt;a href=&quot;http://www.cdc.gov/features/salmonellafrogturtle/&quot; rel=&quot;nofollow&quot;&gt;salmonellosis&lt;/a&gt;. Having said this, the infection is easy to avoid if you maintain basic hygiene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a personal note, I know dozens (perhaps hundreds) of people who keep or have kept reptiles as pets and have yet to meet anyone who contracted salmonellosis. Basically, if you wash your hands after touching the gecko, keep it away from food preparation areas and don't put the lizard in your mouth, you should be fine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're talking about geckos living free in your home, as is common in many tropical places, I have never heard of any health risks associated with them. If anything, I would think that the geckos would &lt;em&gt;reduce&lt;/em&gt; health risks by eating insects such as cockroaches and mosquitoes that are prominent disease carriers.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastActivityDate="2013-05-24T08:16:16.690" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8504" PostTypeId="1" AcceptedAnswerId="8544" CreationDate="2013-05-24T09:59:41.857" Score="4" ViewCount="521" Body="&lt;p&gt;I have always wondered how cells are modified to give them a specific shape. On what specific part of a cell does gene regulation act  for giving the shape ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-06-26T07:42:14.047" Title="Reason behind formation of different shapes of cell" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8505" PostTypeId="1" AcceptedAnswerId="8506" CreationDate="2013-05-24T13:59:09.847" Score="2" ViewCount="5844" Body="&lt;p&gt;Do male marsupials have a pouch, or is it a female organ only (like the womb)?&lt;/p&gt;&#xA;" OwnerUserId="680" LastActivityDate="2013-05-24T14:42:43.497" Title="Do male marsupials have a pouch?" Tags="&lt;zoology&gt;&lt;marsupials&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8506" PostTypeId="2" ParentId="8505" CreationDate="2013-05-24T14:42:43.497" Score="5" Body="&lt;p&gt;In most marsupials, only the females have a pouch. However, males of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Water_opossum&quot;&gt;water opossum&lt;/a&gt; and the extinct &lt;a href=&quot;https://en.wikipedia.org/wiki/Thylacine&quot;&gt;tasmanian tiger (or thylacine)&lt;/a&gt; also have a pouch.  The males of both the thylacine and water opposum used/use their pouch to keep their genitalia from getting entangled in vegetation.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastActivityDate="2013-05-24T14:42:43.497" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8507" PostTypeId="2" ParentId="8500" CreationDate="2013-05-24T14:54:25.070" Score="3" Body="&lt;p&gt;Sounds seriously like your homework, so it'd be better if you researched. However as a starting point amino acids can be polar and non-polar. These properties cause varying forces of attraction between amino acids and their surrounding environment. The location changes the way they can interact. Ask if you are unsure about something :)&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-24T14:54:25.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8508" PostTypeId="2" ParentId="8422" CreationDate="2013-05-24T14:58:07.573" Score="6" Body="&lt;p&gt;&lt;strong&gt;The rationale&lt;/strong&gt; for the choice of higher organisms as the producing source is based on costs and biological activity.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Biological activity&lt;/em&gt;. In their active forms, various proteins have&#xA;post-translational modifications (i.e. glycosylation) which are&#xA;difficult to reproduce in bacteria. Alan's answer is already&#xA;exhaustive.&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Costs&lt;/em&gt;. Mammalian cell lines are easier to generate and maintain but&#xA;suffer from genetic and epigenetic instability (the transgene can be&#xA;lost or inactivated). Contrarywise, transgenic animals require more&#xA;investment but once established that the transgene is present in the&#xA;germline and breed through, the protein can be produced in larger&#xA;quantities with ~1/10 of the costs required to setup a&#xA;GMP-bioreactor. This is particularly appealing for small&#xA;pharmaceutical niches, i.e. drugs targeting rare diseases: if the&#xA;market is small, farming few goats can be more profitable than&#xA;building and maintaining sterile bioreactors. Downstream purification&#xA;facilities are however required for both cellular and animal farms.&#xA;That's why animal models that produce high levels of the therapeutic&#xA;protein in secreted matrices (i.e. milk, egg white) are preferred:&#xA;this facilitates bulk storage of unpurified protein prior to&#xA;purification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good and recent review comparing models and strategies is from Wang&#xA;et al., Expression Systems and Species Used for Transgenic Animal&#xA;Bioreactors (&lt;a href=&quot;http://dx.doi.org/10.1155/2013/580463&quot; rel=&quot;nofollow&quot;&gt;doi:10.1155/2013/580463&lt;/a&gt;).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;To stay updated on &lt;strong&gt;recombinant proteins from transgenic farms entering the market&lt;/strong&gt;, the official reference would probably be the &lt;a href=&quot;http://www.fda.gov/BiologicsBloodVaccines/ResourcesforYou/Industry/default.htm&quot; rel=&quot;nofollow&quot;&gt;FDA section on Biologics&lt;/a&gt;. Two companies actively working on transgenic farms are GTC Biotherapeutics and Synageva.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;GTC Biotherapeutics produces &lt;em&gt;human antithrombin alfa&lt;/em&gt; (ATryn) in the milk of transgenic goats, for use in patients with hereditary antithrombin deficiency (HD). Quoting the &lt;a href=&quot;http://www.fda.gov/downloads/BiologicsBloodVaccines/BloodBloodProducts/ApprovedProducts/LicensedProductsBLAs/FractionatedPlasmaProducts/UCM226514.pdf&quot; rel=&quot;nofollow&quot;&gt;ATryn executive report&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Antithrombin III (recombinant) is a highly purified, well&#xA;  characterized recombinant glycoprotein consisting of432 amino acids, 3&#xA;  disulphide bridges between cysteine residues and 4-N linked&#xA;  glycosylation sites, identical to human plasma-derived antithrombin.&#xA;  Recombinant human antithrombin is produced in the milk of transgenic&#xA;  goats. For expression of rhAT, the DNA construct contained a goat beta&#xA;  casein promoter with the cDNA coding region for human antithrombin&#xA;  (hAT). The DNA construct was microinjected into fertilized one-cell&#xA;  goat embryos, which were transFerred to female recipients. Kids born&#xA;  from the recipients were tested for presence of the transgene and&#xA;  expression of the human protein. A founder transgenic goat was&#xA;  selected from which subsequent offspring were generated by natural&#xA;  breeding to give rise to a production herd of hAT transgenic goats,&#xA;  which are milked to provide the source material for downstream&#xA;  purification.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Synageva produces &lt;em&gt;Sebelipase alfa (SBC-102)&lt;/em&gt; in the egg white of transgenic hens, for use as an enzyme replacement for Lysosomal Acid &#xA;Lipase (LAL) Deficiency. I think they are in clinical phase 2/3 (not &#xA;yet on the market). According to their &lt;a href=&quot;http://www.synageva.com/Collateral/Documents/English-US/Revised%204%2024%2013%20BIOPHARMA%20CORP_BMK.pdf&quot; rel=&quot;nofollow&quot;&gt;2012 Annual Report&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our proprietary vectors allow incorporation of the gene of interest&#xA;  into the genome of normal cells of an avian (Gallus) with selective&#xA;  expression of the resulting protein in the oviduct tissues and&#xA;  secretion into EW. The importance of this cellular environment for&#xA;  therapeutic protein expression is highlighted by the tight consistency&#xA;  of post-translational modification, including glycosylation, seen in&#xA;  proteins manufactured using our platform compared to cell culture&#xA;  produced material. Furthermore, our expression system yields&#xA;  consistent expression levels and quality of protein within production&#xA;  lines and through multiple generations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="444" LastEditorUserId="444" LastEditDate="2013-05-27T07:21:41.203" LastActivityDate="2013-05-27T07:21:41.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8509" PostTypeId="2" ParentId="8501" CreationDate="2013-05-24T15:05:01.057" Score="1" Body="&lt;p&gt;New England Biolabs, which has an excellent reputation for well-tested, well-documented, and robust products, has a line of &lt;a href=&quot;https://www.neb.com/products/protein-expression-and-purification-technologies/protein-expression-and-purification-technologies&quot; rel=&quot;nofollow noreferrer&quot;&gt;protein expression and purification products&lt;/a&gt; that I'd definitely take a look at. I've used the pMAL system for expression of fusion proteins in &lt;em&gt;E. coli&lt;/em&gt;, and the PURExpress system looks just like what you're looking for. I have a personal (but not financial) connection with them, and I can vouch for their quality and technical support.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.piercenet.com/browse.cfm?fldID=0F2CFDF7-D2CA-1B1D-A941-0C88DC305129&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pierce/Thermo&lt;/a&gt; is generally a good place to look when dealing with protein stuff. I've had good results with lots of their stuff, but I haven't done &lt;em&gt;in vitro&lt;/em&gt; expression in ages, so I can't remember what I used. (BTW, I have no connection with them, I just tend to like their products.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Alan Boyd &lt;a href=&quot;https://biology.stackexchange.com/questions/8501/in-vitro-enzyme-production#comment10849_8501&quot;&gt;mentioned&lt;/a&gt;, lots of companies like Life Technologies, Promega, Qiagen, and Sigma have &lt;em&gt;in vitro&lt;/em&gt; expression kits. Which one you pick will ultimately be influenced by what exactly you need your protein to do, the desired scale of expression, the type of tag(s) you want to put on it, what equipment and expertise you have in your lab, and how much time and money you want to invest.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-05-24T15:05:01.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8510" PostTypeId="2" ParentId="5446" CreationDate="2013-05-24T17:24:08.740" Score="11" Body="&lt;p&gt;Shampoo contains &lt;a href=&quot;https://en.wikipedia.org/wiki/Surfactant&quot;&gt;surfactants&lt;/a&gt;, chemicals which cause lipids to emulsify. The &lt;a href=&quot;https://en.wikipedia.org/wiki/Cell_membrane&quot;&gt;cell membrane&lt;/a&gt; is composed primarily of phospholipids, which are vulnerable to action by surfactants. In fact, &lt;a href=&quot;https://en.wikipedia.org/wiki/Sodium_dodecyl_sulfate&quot;&gt;sodium dodecyl sulphate&lt;/a&gt; (SDS, often labelled SLS on shampoo bottles), an integral component of many shampoos is also used in the lab (albeit at substantially higher concentration) to achieve &lt;a href=&quot;https://en.wikipedia.org/wiki/Lysis&quot;&gt;cell lysis&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The outer layer of skin is composed largely of a very tough type of cells called &lt;a href=&quot;https://en.wikipedia.org/wiki/Keratinocytes&quot;&gt;keratinocytes&lt;/a&gt;, which form an impenetrable barrier to potentially harmful chemicals like surfactants. Once the skin is ruptured, the surfactant can act on cells that don't have the protection of &lt;a href=&quot;https://en.wikipedia.org/wiki/Keratin&quot;&gt;keratin&lt;/a&gt;, causing damage to cell membranes, and perhaps even cell death. This will obviously lead to an immune response and inflammation, which is likely to be the source of the burning sensation/pain that one feels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The inflammatory process involves various immune system-related mediators such as &lt;a href=&quot;https://en.wikipedia.org/wiki/Bradykinin&quot;&gt;bradykinin&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Prostaglandin&quot;&gt;prostaglandins&lt;/a&gt;, which act to increase the sensitivity of neurons to pain.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With other chemicals that cause a burning sensation, the mechanism of cell injury might be different, but ultimately, the immune mechanisms kick in, causing inflammation and pain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bja.oxfordjournals.org/content/87/1/3.full&quot;&gt;Kid &amp;amp; Urban (2001)&lt;/a&gt; reviews the processes that cause inflammatory pain in great detail (full text is available for free).&lt;/p&gt;&#xA;" OwnerUserId="3631" LastEditorUserId="3631" LastEditDate="2013-05-27T15:59:32.390" LastActivityDate="2013-05-27T15:59:32.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8511" PostTypeId="1" CreationDate="2013-05-24T19:51:43.123" Score="8" ViewCount="728" Body="&lt;p&gt;In &lt;em&gt;the Selfish Gene&lt;/em&gt;, Dawkins makes the argument that a better  view of evolution (i.e. more in accordance with experiment) is obtained if you view the basic unit of evolution to be the gene rather than the group. Having read the book, I am convinced (inasmuch as a layperson can be convinced) that group selection comes up with &lt;em&gt;incorrect&lt;/em&gt; predictions about evolution, so is a fallacious interpretation of evolution (is this a correct interpretation of the book and is this conclusion common opinion among biologists?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have heard that historically, his book was part of a backlash against the then prevalent viw of group selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;TL;DR&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, is there an experimental way to prove whether the gene-selection or individual-selection interpretation of evolution is more correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope my question is not ill-defined whilst leaving 'unit of evolution' vaguely defined.&lt;/p&gt;&#xA;" OwnerUserId="1667" LastActivityDate="2013-05-26T19:37:50.573" Title="Experimental evidence for the selfish gene vs. the selfish individual" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8512" PostTypeId="1" CreationDate="2013-05-25T01:12:24.660" Score="5" ViewCount="1349" Body="&lt;p&gt;I'm reading this article on &lt;a href=&quot;http://www.kurzweilai.net/growing-new-brains-with-infrared-light&quot; rel=&quot;noreferrer&quot;&gt;guiding axon growth using temperature gradient&lt;/a&gt;, and it mentions that the trajectory of growth of neuron connections can be influenced by temperature gradients as little as 0.1C.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This got me thinking - &lt;strong&gt;does thinking generate heat or increases blood flow enough to create heat gradients within the brain?&lt;/strong&gt; If so, this may explain how the brain rewires itself.&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-05-25T01:12:24.660" Title="Does brain activity generate heat gradients in the brain?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;neuroanatomy&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8513" PostTypeId="1" AcceptedAnswerId="8515" CreationDate="2013-05-25T01:21:10.533" Score="3" ViewCount="6144" Body="&lt;p&gt;When neuron animations are displayed, there are frequently seen neurons, axons arranged in a lattice with a lot of empty space between. I'm interested if there is indeed empty space in the brain, or if it is filled with some sort of fluid? I've checked an article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Cerebrospinal_fluid&quot; rel=&quot;nofollow&quot;&gt;cerebrospinal fluid&lt;/a&gt; but am not sure that it is present all throughout the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason I'm asking is that I'm thinking of neurotransmitters- they are released in synapses, but I'm not sure how they stay there - are they suspended in some liquid as well?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="1320" LastEditDate="2013-05-25T05:24:45.757" LastActivityDate="2018-11-14T18:26:10.180" Title="What is in the space between neurons in a brain?" Tags="&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8514" PostTypeId="2" ParentId="8513" CreationDate="2013-05-25T04:09:53.007" Score="3" Body="&lt;p&gt;Apologies for just referencing Wikipedia, but this is a very old bit of science.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The neuron gap junction - the point where the axon touches the next cell over - &lt;a href=&quot;http://en.wikipedia.org/wiki/Gap_junction#Structure&quot; rel=&quot;nofollow&quot;&gt;is 4 nanometers&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is actually a controlled channel where the neuro transmitter molecules are transferred from one cell interior to another - its a controlled cellular - cellular channel so they really are as close to touching as they could be. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-05-25T04:09:53.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8515" PostTypeId="2" ParentId="8513" CreationDate="2013-05-25T06:03:10.453" Score="7" Body="&lt;p&gt;Not so empty, actually.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The human brain has a mass of ~1.5kg, and volume ~1200cc (a little bigger for men, a little smaller for women). So is heavier than water by a good margin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While it has Cerebrospinal fluid, that only occupies the subarachnoid space (the space below the skull and above the cortex, contained between two layers: pia matter and arachnoid membrane) and the ventricular system (several spaces inside the brain, remnants of the embryological development of the brain).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neuron density may vary widely, depending mainly on the particular characteristics of neuron cell types and their interconnections. But besides neurons, there's a lot of infrastructure inside the brain. For example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Astroglia: They are a type of glial cells which participate in the formation of the blood-brain barrier (supporting the endothelial cells), nourishing of neurons, maintenance of ion and neurotransmitter concentrations, among others. They also keep in place most of the tissue.&lt;/li&gt;&#xA;&lt;li&gt;Microglia: Small cells with immune (phagocitic) functions inside the brain.&lt;/li&gt;&#xA;&lt;li&gt;Radial glia: A more specialized precursor cell, that also participates in neuronal migration in the brain.&lt;/li&gt;&#xA;&lt;li&gt;Oligodendrocites: Cells responsible for the insulation (myelination) of axons.&lt;/li&gt;&#xA;&lt;li&gt;Neuroepithelial cells: The stem cells in the brain.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Neuroglia, which includes the first four cell types above, accounts for ~90% of tissue in human brain (&lt;a href=&quot;http://classes.biology.ucsd.edu/bipn140.WI13/documents/Gliamorethanjustbrainglue.pdf&quot;&gt;http://classes.biology.ucsd.edu/bipn140.WI13/documents/Gliamorethanjustbrainglue.pdf&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, when you collect some billions of axons, they can be quite representative in terms of mass and volume. The ratio between white matter and gray matter is close to one for humans, but lower for smaller mammals (&lt;a href=&quot;http://www.pnas.org/content/97/10/5621.full.pdf&quot;&gt;http://www.pnas.org/content/97/10/5621.full.pdf&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About the last part of your question, the synaptic cleft (the space between pre-synaptic and post-synaptic neurons) is a salty solution: water with high concentration of sodium and chloride ions (and also calcium ions, neurotransmitters and a lot more). These ion concentrations are fundamental to the generation of action potentials, neural signaling, and the general dynamics of the brain.&lt;/p&gt;&#xA;" OwnerUserId="3570" LastEditorUserId="3570" LastEditDate="2013-05-25T06:09:59.380" LastActivityDate="2013-05-25T06:09:59.380" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8517" PostTypeId="2" ParentId="8511" CreationDate="2013-05-25T15:09:20.363" Score="8" Body="&lt;p&gt;My understanding of this is that the complete reference for molecular centralized evolution is The Selfish Gene itself.  I'm going to cite &lt;a href=&quot;http://en.wikipedia.org/wiki/Richard_Dawkins%3a_How_a_Scientist_Changed_the_Way_We_Think&quot;&gt;Alan Grafen's essay here&lt;/a&gt;, &#xA;Richard Dawkins, proposes that the logical, fundamental unit of evolution is the &lt;a href=&quot;http://www.stephenjaygould.org/library/dawkins_replicators.html&quot;&gt;replicator&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The replicator is the fundamental unit of reproduction - whether these replicators survive or do not defines the properties of the biological system they reside in.  These words were chosen carefully because DNA sequences themselves are not replicators exactly - many individual copies make up the animals in a gene pool and the replication of one copy or another doesn't matter.  The distinction between a physical strand of DNA and the replicator is the bulk of more than one of Dawkins book.  It shows why the life of an individual means nothing to biology or evolution, how the boundaries of genes as transcriptional elements do not define the replicon (commonly misunderstood by molecular biologists).  The replicon (a genetic unit of replication) manifests a behavior or phenotype in the organism that helps it reproduce and is reproduced.  This can be cooperation with other members of your species or egg rolling or killing other sperm and is usually the result of many individual mRNA transcripts working in concert.  A given gene as defined by mRNA transcription commonly participates in multiple replicon type behaviors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But DNA is in the mind of the molecular biology camp highly intertwined as a replicator because it is the physical medium through which the replicator is passed from one generation to another.  Without DNA, meiosis and the rest there are no replicons.  The earliest replicators were possibly simple transcripts which self replicated and not much more, but over time they have become a network of intertwined molecules working in a system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To my understanding this is axiom more than proof.  It does not need to be proven because the physical transmission of DNA replication over time is the minimal necessary scenario to picture biology and evolution as we understand it.  The selection amongst groups of genes or groups of cells or groups of individual multicellular animals seem unnecessary given the physical framework of DNA replication.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Certainly that these connections have been shown.  The inspiration for The Selfish Gene is the confirmation of &lt;a href=&quot;http://en.wikipedia.org/wiki/Robert_Trivers#Influence&quot;&gt;Robert Triver's&lt;/a&gt; Selfish Gene hypothesis with the discovery of &lt;em&gt;t&lt;/em&gt; a terribly selfish gene which takes up the better part of chromosome in drosophila and increases its chances of showing up in the next generation by showing up in sperm more than half the time.  There are lots of other examples in the Selfish Gene and &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Extended_Phenotype&quot;&gt;the Extended Phenotype&lt;/a&gt;, which answers many of the common questions about this thesis.  The literature since has been pretty productive. That being understood, its one thing to prove that something is true in biology, and another thing to prove that all other similar mechanisms are simply not true.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet even in Dawkins essays we see that the replicator is a bit of an abstraction some practically indefinable group of genes. Even as they each compete against each other, they create phenotypes collectively and the replicon becomes abstracted from the fundamental mechanism of replication.  The most popular example of replication Dawkins creates - the meme - has no relationship to DNA at all - a sticky idea that spreads socially and replicates in the minds of individuals.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When we look at terribly complicated but obviously advantageous behaviors, the connection between the replicator and the competition of individual genes gets muddy.  EO Wilson, having discovered pheromones and started ecology and sociobiology as disciplines still publishes &lt;a href=&quot;http://www.nature.com/nature/journal/v466/n7310/full/nature09205.html&quot;&gt;group selection arguments&lt;/a&gt;.  Having studied social behavior in insects over his career and &lt;a href=&quot;http://www.hup.harvard.edu/catalog.php?isbn=9780674040755&quot;&gt;co-authored one of the most complete compendiums on the subject&lt;/a&gt;, he has put forth consistant arguments &lt;a href=&quot;http://www.jstor.org/discover/10.2307/1296775?uid=3739560&amp;amp;uid=2&amp;amp;uid=4&amp;amp;uid=3739256&amp;amp;sid=21102256660201&quot;&gt;since the 70s&lt;/a&gt; that group selection &lt;a href=&quot;http://socialresearch.metapress.com/app/home/contribution.asp?referrer=parent&amp;amp;backto=issue,12,13;journal,31,43;linkingpublicationresults,1:119739,1&quot;&gt;still has a place in evolution&lt;/a&gt;. Unlike others, Wilson has I think always kept the conversation scientific and isn't jumping off any ideological cliffs (though responses say differently, the whole conversation is still published).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't see how an unbiased forum can ignore the fact that the editors of Nature still call this an open discussion.  Some may object, but calling the subject closed is overreaching I feel. There are others besides Wilson; I'm not familiar enough with the whole discussion to go into David Sloane Wilson and the rest, though they publish in &lt;a href=&quot;http://www.pnas.org/content/72/1/143.full.pdf&quot;&gt;reputable places&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've started in this post since the question has been sitting around for a while. I expect others will post their corrections/objections/views - please do!  Whenever group selection is mentioned it often happens that someone will pop up and say 'this is not appropriate for a scientific discussion of biology here' but never any justification of disqualifying questions - I think that's not really scientific.  The fundamental attraction to academic thought to me is that minority voices that have legitimate observations are tolerated and often result in scientific revolutions, after which they are venerated for their persistence.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a good place to tell us why some questions are beneath discussion in biology.  I personally do not agree; even if a position is intertwined by politics and religion, its the scientific value that should be judged, not by the company it keeps - lest science become just another intolerant clot, not driven by logic, observation and facts.  I ask you, why bother then? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-05-26T19:37:50.573" LastActivityDate="2013-05-26T19:37:50.573" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8518" PostTypeId="1" AcceptedAnswerId="8524" CreationDate="2013-05-25T15:16:36.027" Score="10" ViewCount="1021" Body="&lt;p&gt;Is there a small chance that in sexual reproduction a new allele forms in the off-spring that was not present in either of the parents, or are the alleles in the offspring always from at least one of the parents?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is new genetic information ever created during sexual reproduction, or only through mutations during an organisms life time?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="3624" LastEditDate="2016-01-21T15:51:26.527" LastActivityDate="2016-01-21T15:51:26.527" Title="Can sexual reproduction create new genetic information?" Tags="&lt;genetics&gt;&lt;allele&gt;&lt;sexual-reproduction&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8520" PostTypeId="2" ParentId="8518" CreationDate="2013-05-25T19:14:30.800" Score="3" Body="&lt;p&gt;Many mutations occur during DNA replication (or when a mutagen is around, but that also largely affects replication).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations occurring &quot;during sexual reproduction&quot; might occur during gametogenesis, when the eggs and sperm are developing in the parents. If a mutation were to occur during these processes, it could be that the alleles in the offspring are different from that of both parents.  Alternatively, an intragenic crossover during synapsis might produce new alleles (if the parent is heterozygous).&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-05-25T19:14:30.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8522" PostTypeId="2" ParentId="8518" CreationDate="2013-05-25T21:31:00.620" Score="3" Body="&lt;p&gt;An interesting question! During homologous recombinations many mutations are actually fixed (here meaning that those that have accumulated over time can be restored) as both chromosomes are condensed and can be compared by the DNA repair enzymes. However additionally mutations can occur and be passed on. As gametocytes primarily do not have to do much more than housekeeping (energy metabolism, basic cellular processes etc) genes they do not rely on can mutate and become dysfunctional. This frequently causes miscarriages, if you check the chromosomes there can be massive errors due to deletions or translocations in miscarried fetuses. Specifically the ova, as these are made before the female is born and then are &quot;revived&quot; as needed they carry the burden of mutations throughout life and this causes the increased rate of genetic diseases (particularly Down's syndrome) observed in later pregnancies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;tl;dr&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations can continue if they're not deleterious. Those that are particularly common that lie in &quot;functional&quot; genes are the ones that lie in HLA. These genes are involved in the immune system, and differences across generations are frequently observed. This is because there are many and if one fails, another can take its place. Mutations that are neutral occur the most frequently (i.e. don't affect offspring at all). But new alleles can most definitely be generated, and is the whole basis of evolution. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1757" LastEditDate="2013-05-26T16:25:08.560" LastActivityDate="2013-05-26T16:25:08.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8523" PostTypeId="2" ParentId="8331" CreationDate="2013-05-25T23:20:05.613" Score="2" Body="&lt;p&gt;In short: the basis of the process is the same in both, the difference relies that in the clone based sequencing you make DNA library of the pieces of DNA clones you got from the sequence you used in first place. Like that, data management and the mounting of DNA contigs will be a lot easier computationally speaking.&#xA;In shotgun sequencing the same is done but without the cloning and libraries, you directly mount contigs from sequenced sequence pieces, thus better computers are needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also I think your terminology is wrong: shotgun strictly means the sequencing based on the random shearing and consecutive construction of contigs. I think you better mean &lt;strong&gt;whole genome shotgun sequencing&lt;/strong&gt; with &quot;shotgun sequencing&quot;(as the clone based sequencing also is a shotgun sequencing method).&lt;/p&gt;&#xA;" OwnerUserId="3657" LastActivityDate="2013-05-25T23:20:05.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8524" PostTypeId="2" ParentId="8518" CreationDate="2013-05-26T00:00:44.187" Score="7" Body="&lt;p&gt;Homologous Recombination not only shuffles different mutations together, but similar sequences near each other from gene duplication events and from regions with highly repetitive sequences can r&lt;a href=&quot;http://en.wikipedia.org/wiki/Non_allelic_homologous_recombination&quot;&gt;ecombine and cause gross changes in the sequence of the genome in hot spots&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-05-26T00:00:44.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8527" PostTypeId="2" ParentId="8518" CreationDate="2013-05-26T08:10:32.223" Score="1" Body="&lt;p&gt;Biological information has several hierarchies is ambiguous between syntactic information in a hierarchical modular system, and functional information, without a particular context[1]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Out of necessity the DNA is sequence is generally highly conserved, but small changes can easily lead to gross changes in folding, function and the minimum energy states of the protein. (Proteins are ultimately dynamic systems, with many constantly sampling their minimum energy conformation structures - the static pictures on magazine and book covers are misleading)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally an allele, by definition, is a gene variant that occurs in at least 1% of the population - by consensus (and and sufficient statistical power). As such the term is part of population genetics. For instance, for a 400AA long protein, that would mean that a particular homologous recombination event has to occur very frequently and be favored by at least one of many (known) mechanisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is new genetic information ever created during sexual reproduction, or only through mutations during an organisms life time?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes. Recombination has several mechanisms, is not a perfect event, and shows different efficiencies depending on the type of mechanism and &quot;helpers&quot;/helper-types as well as helper concentrations involved, - notwithstanding cofactor-concentrations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1]John Collier, Hierarchical Dynamical Information Systems With a Focus on&#xA;Biology, Entropy 2003, 5, pg. 100-124&lt;/p&gt;&#xA;" OwnerUserId="1450" LastEditorUserId="1450" LastEditDate="2013-05-26T08:27:11.500" LastActivityDate="2013-05-26T08:27:11.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8529" PostTypeId="1" CreationDate="2013-05-26T13:45:10.573" Score="0" ViewCount="1717" Body="&lt;p&gt;If I recall correctly, nails (finger nails or toe nails) grow by adding matter at its base. So for instance, if you would draw a dot at the very bottom of your nail, it would end at the top in a couple of weeks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering how this works with hair. Is new hair added at the bottom and the old hair 'pushed' away? Or does hair consist of layers that always try to get further and further (that would mean longer hair is thicker than shorter hair). And is this wayof growth similar to how grass grows?&lt;/p&gt;&#xA;" OwnerUserId="3198" LastActivityDate="2013-07-12T05:53:01.897" Title="How does hair grow and is it similar to how grass grows?" Tags="&lt;development&gt;&lt;hair&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8530" PostTypeId="2" ParentId="8455" CreationDate="2013-05-26T14:10:06.493" Score="0" Body="&lt;p&gt;Absorption, distribution, metabolism, excretion, and toxicity ADMET can be somewhat computationally defined but is largely secretive due to the money involved in drug discovery. &lt;a href=&quot;http://www.biomedcentral.com/1471-2105/9/396&quot; rel=&quot;nofollow&quot;&gt;FAF-Drugs2&lt;/a&gt; will do basic ADMET. The &lt;a href=&quot;http://www.schrodinger.com/productpage/14/17/&quot; rel=&quot;nofollow&quot;&gt;Schordinger Suit&lt;/a&gt; provides a more indepth ADMET for a fee.&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2013-05-26T14:10:06.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8531" PostTypeId="1" AcceptedAnswerId="8542" CreationDate="2013-05-26T14:14:01.423" Score="6" ViewCount="610" Body="&lt;p&gt;I've gathered that a centromere is a a region*  where the DNA is bundles up even tighter (around &lt;a href=&quot;http://en.wikipedia.org/wiki/Centromere#Structure&quot; rel=&quot;nofollow&quot;&gt;protein&lt;/a&gt; different to Histone) and chromatids are 'joined'. However I'm still mostly in the dark regarding its physical structure and functioning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At what point during DNA replication is the centromere created, and how is it created? How does it hold the chromatids together (what are its components)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When it is being created (presumably during cell division) how is the positioning  of the centromere controlled? Which flags are used by the enzymes in the process of making the centromere to tell them that it is the right spot: a section of DNA that 'says' &quot;&lt;em&gt;Right part of centromere, to be attached to left part&lt;/em&gt;&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, after their condensation into chromosomes (e.g. during prophase), are the sister chromatids physically intertwined around each other** for the purpose of joining, or are they simply adjacent?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Is there a 'loop' in the centromere slung over the adjacent chromatids to join them?&lt;/li&gt;&#xA;&lt;li&gt;If they are intertwined, how is this achieved during DNA replication, whilst the non-centromere parts of the sister chromatids are not intertwined?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;How does the centromere break down to allow the chromatids to separate (e.g. during meoisis 2 and anaphase)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a somewhat unrelated note, what in the centromeres do the spindle fibres attach to, and how do the tips of the growing fibres notice it to head it its general direction?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;*(i.e. there is not a separate physical object dubbed 'the centromere', rather it is a collection of objects in a region)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;**(That is, considering no other molecules than the chromatids, if you were to pinch the top and bottom ends of the left and right chromatids and pull them apart, could you separate them without them locking together (basically, do they intersect &lt;a href=&quot;http://en.wikipedia.org/wiki/Knot_%28mathematics%29&quot; rel=&quot;nofollow&quot;&gt;knot&lt;/a&gt;-theoretically)?)&lt;/p&gt;&#xA;" OwnerUserId="1667" LastEditorUserId="948" LastEditDate="2014-01-13T21:41:28.373" LastActivityDate="2016-12-19T01:10:44.697" Title="What are centromeres *really*?" Tags="&lt;molecular-biology&gt;&lt;chromosome&gt;&lt;meiosis&gt;&lt;mitosis&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8533" PostTypeId="1" AcceptedAnswerId="8551" CreationDate="2013-05-26T19:22:24.523" Score="2" ViewCount="392" Body="&lt;p&gt;I've found it in my kitchen. It seems to be that he flew through the window from the street.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The country is Russia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TVGP5.jpg&quot; alt=&quot;Unknown flyting beetle. Top side&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/1lKu8.jpg&quot; alt=&quot;Unknown flyting beetle. Bottom side&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3280" LastEditorUserId="3624" LastEditDate="2013-06-15T23:09:34.063" LastActivityDate="2013-06-15T23:09:34.063" Title="What beetle is this?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8534" PostTypeId="2" ParentId="8533" CreationDate="2013-05-26T19:30:54.623" Score="4" Body="&lt;p&gt;I am not an entomologist, I just happen to have worked on the genome of the red flour beetle, &lt;em&gt;Tribolium castaneum&lt;/em&gt; and this looks very similar. A quick &lt;a href=&quot;http://en.wikipedia.org/wiki/Confused_flour_beetle&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia search&lt;/a&gt; turned up the amusingly named &quot;confused flour beetle&quot;, &lt;em&gt;Tribolium confusa&lt;/em&gt;, which looks almost exactly like what you have photographed:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ui9XJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I would &lt;em&gt;guess&lt;/em&gt; (I stress that I don't really know) that this is some sort of Tribolium species and, by now, is thoroughly confused even if it was not to begin with.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1320" LastEditDate="2013-05-26T21:35:07.150" LastActivityDate="2013-05-26T21:35:07.150" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8535" PostTypeId="1" AcceptedAnswerId="19834" CreationDate="2013-05-26T21:39:37.293" Score="4" ViewCount="3713" Body="&lt;p&gt;A woman I know has been losing height at a rate of few cm a year following a severe spinal injury. How is this possible? What kind of injury could cause such progressive loss of height? Could this be a genetic defect? Are there any disorders that cause this type of shrinking?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case it could be relevant, her brothers are very tall.&lt;/p&gt;&#xA;" OwnerUserId="3664" LastEditorUserId="3664" LastEditDate="2014-07-22T13:40:12.200" LastActivityDate="2014-07-22T13:40:12.200" Title="Would a spinal injury decrease human height?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;human-genetics&gt;&lt;auxology&gt;" AnswerCount="1" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="8537" PostTypeId="1" AcceptedAnswerId="8549" CreationDate="2013-05-26T22:02:57.513" Score="4" ViewCount="5872" Body="&lt;p&gt;Metastasis to the liver and lungs are the main causes of death in colorectal cancer.(1)&#xA;I understand that colorectal cancer may have metastases. But how do these metastases cause death?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) A. Bolocan, D. Ion, D.N. Ciocan, D.N Paduraru. &lt;em&gt;Chirurgia&lt;/em&gt; (2012) 107:555-563. Introduction.&lt;/p&gt;&#xA;" OwnerUserId="1413" LastActivityDate="2016-12-11T14:17:53.593" Title="How do liver and lung metastases cause death?" Tags="&lt;pathology&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8538" PostTypeId="1" AcceptedAnswerId="17689" CreationDate="2013-05-26T22:14:28.563" Score="2" ViewCount="150" Body="&lt;p&gt;&lt;em&gt;tumour budding, lymphocytic infiltration and resection margins are established factors that influence the outcome of colorectal cancer&lt;/em&gt; (1)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this context what does &quot;tumour budding&quot; mean?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) A. Bolocan, D. Ion, D.N. Ciocan, D.N Paduraru. &lt;em&gt;Chirurgia&lt;/em&gt; (2012) 107:555-563. Introduction/0&lt;/p&gt;&#xA;" OwnerUserId="1413" LastActivityDate="2014-05-27T11:04:51.850" Title="What does &quot;tumour budding&quot; mean?" Tags="&lt;cancer&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8539" PostTypeId="1" AcceptedAnswerId="24752" CreationDate="2013-05-26T23:02:32.973" Score="2" ViewCount="469" Body="&lt;p&gt;&lt;strong&gt;Magic bullets&lt;/strong&gt; are drugs that can be administered on a micro local scale. In this context administration/binding would occur in or near the tumour by exploiting the different surface antigens that cancers expose. Basic lectures teach that a &quot;magic bullt&quot; drug could attach via an mAb (attached to the pro-drug) and then a conjugated enzyme cleaves or converts the pro drug to a drug. This would eliminate a lot of side effects from chemotherapy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Use in clinical trials.&lt;/strong&gt; Some mAbs have started to be used in clinical trials, almost 40 years after they were first proposed. My question is simply; have there been any cases of mAbs being used as a successful treatment for any disease? If not, what makes the R&amp;amp;D of this drug type so difficult?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2014-12-09T22:29:06.817" LastActivityDate="2014-12-10T02:14:25.300" Title="Are there any examples where 'magic bullet' drugs have worked in cancer treatment?" Tags="&lt;pharmacology&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8540" PostTypeId="1" AcceptedAnswerId="10080" CreationDate="2013-05-26T23:07:50.510" Score="1" ViewCount="868" Body="&lt;p&gt;The drug development industry is a multi-billion dollar economy powered by a multitude of research bodies from industry and academia. A big risk is that drug development costs are in &lt;a href=&quot;https://en.wikipedia.org/wiki/Cost_of_drug_development&quot; rel=&quot;nofollow noreferrer&quot;&gt;the tens of millions of dollars when looking at the most successful drugs&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally speaking, what makes a good drug for research for those researchers working on these projects? Why are some potential drug pursued and others not? What traits, according to the experts, justifies such a vast investment?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2018-02-07T17:25:20.887" LastActivityDate="2018-02-07T17:25:20.887" Title="What are the characteristics of a promising drug?" Tags="&lt;proteins&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8542" PostTypeId="2" ParentId="8531" CreationDate="2013-05-27T06:06:37.220" Score="2" Body="&lt;p&gt;There are many questions in your &lt;em&gt;question&lt;/em&gt;. I'll try to answer each question pointwise.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Which flags are used by the enzymes in the process of making the&#xA;  centromere to tell them that it is the right spot&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are some centromere associated repeats in the DNA which mark the site for centromere assembly. There is no particular consensus sequence of this repeat. However, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15998740&quot; rel=&quot;nofollow noreferrer&quot;&gt;this study&lt;/a&gt; says that in certain cases stable chromosomes are formed in the absence of centromeric repeats.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;are the sister chromatids physically intertwined around each other for&#xA;  the purpose of joining, or are they simply adjacent?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They are joined by proteins called &lt;strong&gt;cohesins&lt;/strong&gt;. Cohesins looks like rings which form around the sister chromatids. During anaphase, the anaphase promoting complex (APC) activates an enzyme called &lt;strong&gt;separase&lt;/strong&gt;, which in turn degrades cohesin. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;what in the centromeres do the spindle fibres attach to, and how do&#xA;  the tips of the growing fibres notice it to head it its general&#xA;  direction?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Centromeres serve as a site for the assembly of &lt;strong&gt;kinetochore&lt;/strong&gt;. Kinetochore is a multi-protein complex which forms contact with the spindle fibres (specifically, K-fibres. Refer this &lt;a href=&quot;https://biology.stackexchange.com/questions/3814/number-of-spindle-fibres-during-metaphase&quot;&gt;previous post&lt;/a&gt;). An essential component of kinetochore is the motor protein &lt;strong&gt;dynein&lt;/strong&gt; which makes the kitetochore to crawl along the spindle fibres, towards the pole. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Kinetochore&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia article&lt;/a&gt; on kinetochore is quite descriptive and you can refer that for details. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-05-27T06:12:30.170" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8543" PostTypeId="2" ParentId="8529" CreationDate="2013-05-27T06:28:12.280" Score="2" Body="&lt;p&gt;In hair and nail growth new cells are added to the bottom. These cells are produced at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hair_follicle&quot; rel=&quot;nofollow&quot;&gt;follicle&lt;/a&gt;. There are three stages called:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Anagen : active growth&lt;/li&gt;&#xA;&lt;li&gt;Catagen : end of active growth&lt;/li&gt;&#xA;&lt;li&gt;Telogen : total stop of follicular growth&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I don't know what you mean by &lt;em&gt;like grass&lt;/em&gt; but both nails and hair have a first in first out order. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Feathers present a contrasting case: the outermost portion is the most recent. Feather growth is relatively more complex. &lt;a href=&quot;http://www.yale.edu/eeb/prum/pdf/Prum_1999_MDE.pdf&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; is a nice read on feathers.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-05-27T06:28:12.280" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8544" PostTypeId="2" ParentId="8504" CreationDate="2013-05-27T06:37:46.687" Score="3" Body="&lt;p&gt;Cell shape is dictated by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cytoskeleton&quot; rel=&quot;nofollow&quot;&gt;cytoskeletal&lt;/a&gt; arrangement. There are both intrinsic and extrinsic factors that control cell shape. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Extrinsic factors consist of environmental factors such as extracellular matrix. Rho-GTPases relay the environmental signal to the cells to cause cytoskeletal rearrangement. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intrinsic factors are basically the stable transcriptomic identity (a gene regulatory programme) which determine a cell shape. I personally don't have an idea about what genes give an intrinsic cell shape. For e.g. why does hela cell look different from HEK cell in the same type of cell culture plate under same conditions (even at low densities where there is no &lt;em&gt;neighbor effect&lt;/em&gt;). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-05-27T07:10:24.180" LastActivityDate="2013-05-27T07:10:24.180" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8545" PostTypeId="1" AcceptedAnswerId="8558" CreationDate="2013-05-27T08:37:42.693" Score="8" ViewCount="1905" Body="&lt;p&gt;Does the colony collapse? Do workers keep following the last orders? Or can future queens replace the dead one? I'm guessing this might also depend on each specific sub-species.&lt;/p&gt;&#xA;" OwnerUserId="3668" LastEditorUserId="55929" LastEditDate="2020-01-06T00:33:34.353" LastActivityDate="2020-01-06T00:33:34.353" Title="What happens to an ant colony when the queen dies?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;ethology&gt;&lt;ant&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8546" PostTypeId="2" ParentId="7556" CreationDate="2013-05-27T10:44:38.750" Score="10" Body="&lt;p&gt;For species occurance data the &lt;em&gt;Global Biodiversity Information Facility&lt;/em&gt; (&lt;a href=&quot;http://www.gbif.org/&quot;&gt;http://www.gbif.org/&lt;/a&gt;) database should be an obvious choice. It contains both historical records from museums etc and information from more recent surveys and inventories. Note that the occurrence data can both come from standardized inventories and observational records from specialists and amateurs (Citizen science data).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2013-05-27T10:44:38.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8548" PostTypeId="2" ParentId="8355" CreationDate="2013-05-27T13:50:39.143" Score="13" Body="&lt;p&gt;First, a shorthand definition of Evolution is heritable change and not 'progress' (which is a rather loaded word). Also, evolution is not 'supposed' to do anything, and can lead to both an increase or a decrease in diversity, since (local) diversity is simply the net result of speciation rate and extinction rate (if we exclude colonization of new species from other areas). Therefore, I think the question is framed in the wrong way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, there are many reasons why biologists might want to halt species extinctions, as hinted in the other comments and answers. Most obviously, conservation biologists want to prevent man-made extinctions which are due to how we have influenced/modified/destroyed the natural environments. I don't think conservation biologists in general are determined to halt all 'natural' extinction. However, most of the time it is really hard to pinpoint what would be a 'natural' extinction. Either way, the current rates of extinction, which have been estimated to lie 100-1000 times (&lt;a href=&quot;http://www.iucn.org/knowledge/news/?81/Extinction-crisis-escalates-Red-List-shows-apes-corals-vultures-dolphins-all-in-danger&quot; rel=&quot;nofollow&quot; title=&quot;IUCN. 2007. Extinction crisis escalates: Red List shows apes, corals, vultures, dolphins all in danger.&quot;&gt;IUCN, 2007&lt;/a&gt;) above &lt;a href=&quot;http://en.wikipedia.org/wiki/Background_extinction_rate&quot; rel=&quot;nofollow&quot;&gt;background rates&lt;/a&gt; (some say it's closer to 10000 times higher), indicate that most extinctions are man-made. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rationales people use for preserving biodiversity can however differ. Three distinct categories are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) For human survival and/or economy, e.g. through ecosystem services or resources we rely on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) For human welfare, e.g. recreation or esthetical reasons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Ethical considerations, e.g. inherent value of species or to preserve the unique evolutionary history of the system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way to structure these is to label 1) &amp;amp; 2) as instrumental values and 3) as inherent values. The instrumental values can then be subcategorized as services, goods/resources, information (e.g. genetic to be used in medical research), and esthetical/spiritual values.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the direct value of individual species are often (usually) uncertain (irrespectivly of the direct rationales used) the precautionary principle is often invoked to justify species conservation. Also, numerous examples exist of how aspects of biodiversity are related to human values (some recent examples are &lt;a href=&quot;http://www.sciencemag.org/content/339/6127/1608.abstract&quot; rel=&quot;nofollow&quot; title=&quot;Garibaldi et al. 2013. Wild Pollinators Enhance Fruit Set of Crops Regardless of Honey Bee Abundance. Science 139(6): 1608-1611.&quot;&gt;Garibaldi et al. 2013&lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/ncomms/journal/v4/n1/full/ncomms2328.html&quot; rel=&quot;nofollow&quot; title=&quot;Gamfeldt et al. 2013. Higher levels of multiple ecosystem services are found in forests with more tree species. Nature communications 4(1340).&quot;&gt;Gamfeldt et al. 2013&lt;/a&gt;), such as production or services, which can also be used to justify both conserving biodiversity or individual species. However, other aspects of biodiversity are &lt;em&gt;functional diversity&lt;/em&gt;, which focus on preserving functional groups of species, or &lt;em&gt;phylogenetic diversity&lt;/em&gt;, focusing on taxonomic coverage and uniqueness (evolutionary history), instead of 'overall' biodiversity (see e.g. &lt;a href=&quot;http://www.esajournals.org/doi/abs/10.1890/10-1245.1&quot; rel=&quot;nofollow&quot; title=&quot;Flynn et al. 2011. Functional and phylogenetic diversity as predictors of biodiversity–ecosystem-function relationships. Ecology 92(8)&quot;&gt;Flynn et al, 2011&lt;/a&gt; for a discussion of these concepts). Under these perspectives less focus is placed on individual species. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-10-30T23:53:01.050" LastActivityDate="2014-10-30T23:53:01.050" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8549" PostTypeId="2" ParentId="8537" CreationDate="2013-05-27T14:04:19.833" Score="4" Body="&lt;p&gt;Metastasis is the spreading of cancerous cells to a new site within the body where they form a secondary tumour.  There is nothing special about how these metastases cause death, they do so in the same ways as the primary cancer eventually might:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Replacing functional cells with non-functional cancerous cells&lt;/li&gt;&#xA;&lt;li&gt;Eroding into other tissues and disrupting normal body architecture &lt;/li&gt;&#xA;&lt;li&gt;Causing haemorrhage &lt;/li&gt;&#xA;&lt;li&gt;Putting pressure onto other structures&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If we apply those principles to lung and liver secondary tumours, it is easy to see why they are likely to contribute significantly to mortality.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cancerous masses in the lungs reduce the surface area available for gas exchange, reducing oxygen saturation of the patient.  The tumour may also erode into a primary bronchus, which if obstructed would cause lung collapse, or into the mediastinum.  If the mediastinum is involved then the great vessels or heart may be invaded into with significant consequences.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Liver metastases are more likely to cause problems due to the reduction of liver function as the cancer grows. This causes a plethora of problems as the liver is involved in so many pathways within the body.  Examples of serious effects would include the patient becoming coagulopathic due to a reduction in production of clotting factors, making bleeding much more severe.  The liver can begin to fail to clear toxins from the blood, leading to the risk of acidosis or hepatic encephalopathy (leading to coma and eventual death).  If the tumour were to invade the portal vein, this can cause portal hypertension, which in turn shunts pressure into the systemic venous system.  This can cause oesophageal varices which are prone to spontaneous and catastrophic bleeding. Similarly a tumour invading the common bile duct (or other part of the biliary tree) can cause obstructive jaundice and associated problems. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason your quote suggests that most deaths are from metastases than the primary tumour is probably because tumours in these locations have greater negative effects at a smaller size because they are in crucial tissues.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There may be another contributing factor in the form of data interpretation, however.  Tumours are often 'staged' via the &lt;a href=&quot;http://www.cancerresearchuk.org/cancer-help/type/bowel-cancer/treatment/tnm-and-number-stages-of-bowel-cancer&quot; rel=&quot;nofollow&quot;&gt;TNM staging system&lt;/a&gt;, the last component of which is the presence of metastases.  The presence of distal metastases automatically makes colorectal cancer Stage 4.  This is often considered not to be curable, meaning a move to more palliative treatment options.  This may affect the survival curves for those with distal metastases and those without.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="1858" LastEditDate="2013-05-27T20:09:31.083" LastActivityDate="2013-05-27T20:09:31.083" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8550" PostTypeId="1" CreationDate="2013-05-27T15:34:22.013" Score="9" ViewCount="112" Body="&lt;p&gt;To what extent is the number of immature eggs from dissected, newly emerged individuals a reasonable approximation for maximum/potential fecundity in insects (more specifically beetles)? I know that many species must feed for the eggs to become mature and viable. However, can a comparison between species on immature eggs still be used to capture the range of maximum fecundity between species or to accurately rank species from low---high fecundity? &lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2014-11-25T10:25:58.247" Title="To what extent is immature eggs in insects (beetles) a good approximation for maximum fecundity?" Tags="&lt;ecology&gt;&lt;entomology&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8551" PostTypeId="2" ParentId="8533" CreationDate="2013-05-27T16:04:07.553" Score="7" Body="&lt;p&gt;This is &lt;strong&gt;Mealworm beetle&lt;/strong&gt;, &lt;em&gt;Tenebrio molitor&lt;/em&gt;, a species of darkling beetle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mealworm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Mealworm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/4/4c/Tenebrio_molitor_MHNT.jpg/240px-Tenebrio_molitor_MHNT.jpg&quot; alt=&quot;Tenebrio molitor&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you @terdon for help!&lt;/p&gt;&#xA;" OwnerUserId="3280" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.820" LastActivityDate="2013-05-27T16:04:07.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8552" PostTypeId="1" CreationDate="2013-05-27T22:02:36.910" Score="2" ViewCount="95" Body="&lt;p&gt;Most trees I know that have their flowers in groups hang these groups down. I noticed, however, that conker flowers grow upwards!&#xA;I guess that growing against gravity requires special effort, so conker may benefit somehow from growing the flowers upwards. Is this true? What's the benefit?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SGlGc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1413" LastEditorUserId="1413" LastEditDate="2013-05-27T22:13:41.457" LastActivityDate="2013-05-27T22:13:41.457" Title="Why do conker flowers grow upwards?" Tags="&lt;plant-anatomy&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8553" PostTypeId="1" CreationDate="2013-05-27T23:51:07.910" Score="4" ViewCount="318" Body="&lt;p&gt;I found groups of these growing in the &lt;a href=&quot;http://www.fs.usda.gov/lassen&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lassen National Forest&lt;/a&gt; (Susanville, CA, USA). It looks like some sort of mushroom. I have Googled extensively, but can't seem to find a match.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bwOOa.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3672" LastEditorUserId="3624" LastEditDate="2013-05-28T13:00:30.770" LastActivityDate="2013-05-28T13:00:30.770" Title="What kind of mushroom(?) is this?" Tags="&lt;botany&gt;&lt;species-identification&gt;&lt;parasitism&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8554" PostTypeId="1" CreationDate="2013-05-28T01:48:12.840" Score="5" ViewCount="919" Body="&lt;p&gt;Although skeletal muscle fatigues fairly rapidly, clams have a protein called paramyosin that allows them to sustain contractions for up to a month. What might be the role of paramyosin at the molecular or cellular level, which results in this peculiarity?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-09-23T21:29:43.137" LastActivityDate="2013-09-23T21:29:43.137" Title="Skeletal muscles in clam" Tags="&lt;physiology&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8555" PostTypeId="2" ParentId="8553" CreationDate="2013-05-28T02:43:06.880" Score="7" Body="&lt;p&gt;Found it. It's a Sarcodes or snow plant:&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sarcodes&quot;&gt;http://en.wikipedia.org/wiki/Sarcodes&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3672" LastActivityDate="2013-05-28T02:43:06.880" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8556" PostTypeId="1" AcceptedAnswerId="8776" CreationDate="2013-05-28T06:49:13.737" Score="3" ViewCount="1390" Body="&lt;p&gt;What happens to blood pressure when we exercise? Does it increase, decrease, or remain the same? If it does increase, why are patients with high blood pressure recommended to exercise?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2013-10-09T13:58:38.907" LastActivityDate="2013-10-09T13:58:38.907" Title="Blood pressure during exercise" Tags="&lt;human-biology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8557" PostTypeId="2" ParentId="8556" CreationDate="2013-05-28T07:57:41.297" Score="1" Body="&lt;p&gt;Increases during exercise, but as we get fitter it decreases. Vessels become more optimal, they grow to supply muscles better, the heart beats less as it becomes more efficient. However this goes beyond that, hypertensive patients are at risk of stroke and heart attacks. Exercise reduces many risk factors: stress, obesity and coronary artery disease and many others. Thus exercise is really helpful. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-28T07:57:41.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8558" PostTypeId="2" ParentId="8545" CreationDate="2013-05-28T08:38:14.447" Score="3" Body="&lt;p&gt;Not really my field, but I can point to this review which discusses a couple of different ways in which ants organize their communities:&#xA;&lt;a href=&quot;http://myrmecologicalnews.org/cms/images/pdf/volume11/mn11_9-20_printable.pdf&quot; rel=&quot;nofollow&quot;&gt;Heinze. 2008. The demise of the standard ant (Hymenoptera: Formicidae)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that in some species there can be several queens per colony (so more robust to queen deaths). In many species, workers can start laying eggs if the queen dies, but these will develop as males (since they are unfertilized). However, in some species (e.g. &lt;em&gt;Platythyrea punctata&lt;/em&gt;) the workers can reproduce by parthenogenesis which can stabilize the colony to some extent after the queen dies. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2013-05-28T08:38:14.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8560" PostTypeId="1" CreationDate="2013-05-28T09:53:08.323" Score="6" ViewCount="1224" Body="&lt;p&gt;This may be a strange question, but does anyone know what kind of tree this could be?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EY5bR.png&quot; alt=&quot;XKCD tree&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know, it's just a comic, but these trees, at “walking distance” within that comic &lt;em&gt;are&lt;/em&gt; easily identifiable as Grandidier's Baobabs:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SPMwP.png&quot; alt=&quot;Gradidier&amp;#39;s Baobab&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(That might indicate, of course, that the above tree also occurs on Madagascar, but it's a comic, so all bets are off.  And yes, we know, there are no squirrels on Madagascar.)&lt;/p&gt;&#xA;" OwnerUserId="3677" LastEditorUserId="107" LastEditDate="2013-05-28T13:16:15.310" LastActivityDate="2019-04-10T14:08:59.043" Title="What kind of tree could this be?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="4" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8564" PostTypeId="2" ParentId="5403" CreationDate="2013-05-28T15:21:49.340" Score="0" Body="&lt;p&gt;The same relationship still holds, and $\lambda$ just describes the finite population growth rate under a particular set of conditions. 'Ideal' conditions (whatever that means) are not implied. Generally you can write: $\lambda = e^r = R_0^{1/G}$, where $G$ is the (average) generation time. However, $r$ (the instantaneous/intrinsic rate of increase) is not really relevant for an organism with discrete reproductive events (i.e. geometric growth)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for your second example where $R_0$=1.6, assuming that $G$=3 timesteps, $\lambda$= 1.169. However, as hinted above an exponential model is generally a better fit for unicellular organisms.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-05-29T09:12:15.063" LastActivityDate="2013-05-29T09:12:15.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8565" PostTypeId="1" AcceptedAnswerId="8592" CreationDate="2013-05-28T19:34:06.263" Score="1" ViewCount="472" Body="&lt;p&gt;The wikipedia article on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Dopamine_transporter&quot; rel=&quot;nofollow&quot;&gt;dopamine transporter&lt;/a&gt; gives examples of some drugs whose effects are mediated by the inhibition of the dopamine transporter, such as cocaine and amphetamines.  Are there any drugs or substances whose mechanism of action involves increasing the activity of the dopamine transporter, i.e., a &quot;DAT releaser?&quot;&lt;/p&gt;&#xA;" OwnerUserId="3683" LastEditorUserId="107" LastEditDate="2013-05-28T19:51:45.380" LastActivityDate="2013-09-03T00:44:58.890" Title="Inverse of dopamine reuptake inhibitor?" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;&lt;neurotransmitter&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8566" PostTypeId="1" CreationDate="2013-05-28T19:40:55.127" Score="4" ViewCount="1020" Body="&lt;p&gt;There are a lot of food allergies, but for some reason not to meat (mammalian meat or poultry) or mushrooms. I've googled a bit, and now I know that one can actually have a meat or mushroom allergy, although the odds of that are very-very small. Why is it so?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it because both meat and mushrooms are usually cooked and that kills potential allergens? What about undercooked or raw food like portobellos or carpaccio and steaks?&#xA;Or is it because animal tissues are so similar to ours and so are better digested? What about mushrooms then?&#xA;Is it something else?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, are there any data of what types of meat and mushrooms are most allergic?&lt;/p&gt;&#xA;" OwnerUserId="3625" LastEditorUserId="3625" LastEditDate="2013-05-28T20:24:45.297" LastActivityDate="2013-05-30T10:51:33.693" Title="Meat and mushroom allergies, why are they so rare?" Tags="&lt;food&gt;&lt;allergies&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="8569" PostTypeId="1" CreationDate="2013-05-29T02:37:18.437" Score="1" ViewCount="427" Body="&lt;p&gt;Using the tool &lt;a href=&quot;http://berry.engin.umich.edu/gene2oligo/index.html&quot; rel=&quot;nofollow&quot;&gt;Gene2Oligo&lt;/a&gt; I have a set of DNA oligonucleotides to synthesize a gene using ligase chain reaction (LCR).  The average melting temperature is 72 degrees Celsius.  I am going to use a the thermostable Taq ligase enzyme for the LCR reaction but I am unsure of the annealing temperature to use.  Should I use the standard recommendation as in PCR of 5 degrees less than the melting temperature or should I use another tool?  Taq ligase has a cutoff in activity at 65C so that is the highest I can use.&lt;/p&gt;&#xA;" OwnerUserId="3247" LastEditorUserId="3059" LastEditDate="2013-06-23T02:16:34.330" LastActivityDate="2013-06-23T02:16:34.330" Title="Ligase Chain Reaction: Determining the annealing temperature for gene synthesis" Tags="&lt;protocol&gt;&lt;gene-synthesis&gt;&lt;lcr&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8571" PostTypeId="2" ParentId="7435" CreationDate="2013-05-29T08:55:07.240" Score="8" Body="&lt;p&gt;Since it's been so long, I guess a rushed speculative answer might be at least an idea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA gets damaged randomly all the time, and repair mechanisms are in place to fix it. When the damage is too large or of a very complex kind, permanent mutations can develop, and cause disorders such as cells proliferating without control - i.e. tumours.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could imagine that the same mechanism could result in cells which overproduce keratin (hair) without melanin (pigment), if the associated genes are affected. Considering that trichocytes and melanocytes, the two cell populations at the base of the hair responsible for production, are among the most rapidly proliferating cell types in humans, an increased risk for mutation would not surprise me. I was able to find a few papers on keratin-associated gene clusters by a quick search, but they all seemed to be related to production of fragile hair rather than excessive length.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-05-29T14:06:22.463" LastActivityDate="2013-05-29T14:06:22.463" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8573" PostTypeId="2" ParentId="5484" CreationDate="2013-05-29T10:16:48.900" Score="8" Body="&lt;p&gt;In simple terms:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Function of the RNA primer&lt;/strong&gt;: DNA polymerases need a double-stranded DNA region to which they can attach in order to begin copying the rest of the DNA strand. In order to provide this double-stranded attachment site, RNA primers are added by primase, an RNA polymerase which does not require such an attachment site itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When DNA replication starts, one primer is needed at the start of the leading strand. The lagging strand will need new primers regularly, and they mark the start of the stretches known as Okazaki fragments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why is RNA used instead of DNA?&lt;/strong&gt;: Adding primers is an error-prone process, and DNA replication must copy the original strand with as high fidelity as possible. Using RNA for primers and then copying the original using DNA means that there is &quot;memory&quot; of which bits of the new strand were originally primers and hence more likely to contain errors (any RNA in the copy must have been primers). This allows removing them, in order to then replace them with proper high-fidelity DNA copies. When this happens, there is double-stranded DNA around the sites where primers were located, allowing DNA polymerases to attach there and fill in the gaps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aside from this, I would guess using RNA for priming may be more energy-efficient as RNA is more reactive than DNA.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-05-29T10:16:48.900" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8574" PostTypeId="1" CreationDate="2013-05-29T13:11:39.680" Score="3" ViewCount="560" Body="&lt;p&gt;When you use cultures e.g. insect cells, which are infected with virus one way to clean the (plastics) shake flasks is with virkon. Which is the most effective way to clean your flasks in order to extinguish the virus? &#xA;Also, is it effective to use SDS in order to denatured the virus proteins?&lt;/p&gt;&#xA;" OwnerUserId="1304" LastEditorUserId="3624" LastEditDate="2013-05-29T14:29:09.550" LastActivityDate="2013-08-27T21:18:08.873" Title="What is the best way to clean plastic flasks that have been used for cell cultures - is virkon a good idea?" Tags="&lt;virology&gt;&lt;cell-culture&gt;&lt;lab-reagents&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8575" PostTypeId="1" AcceptedAnswerId="8578" CreationDate="2013-05-29T13:20:16.977" Score="2" ViewCount="10597" Body="&lt;p&gt;After exercising vigorously one can sometimes smell ammonia and it feels like it's coming from within the nose actually. There is no indication that others can smell it when I do (i.e. seems to be internal rather than external). I know I'm not the only one experiencing this, but I was wondering what the physiological processes are that are responsible for that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also: is this merely a perceived smell or is there actually ammonia in/on my body after the exercise.&lt;/p&gt;&#xA;" OwnerUserId="3315" LastEditorUserId="3315" LastEditDate="2013-05-29T14:20:36.827" LastActivityDate="2013-05-29T17:53:22.630" Title="Ammonia smell after physical exercise? What is the explanation?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2014-05-12T12:46:42.457" ContentLicense="CC BY-SA 3.0" />
  <row Id="8576" PostTypeId="2" ParentId="8355" CreationDate="2013-05-29T14:57:21.110" Score="3" Body="&lt;p&gt;Evolution is simply a change in the allele frequency of a population over time.  It is not progressive nor does it have to create diversity.  Some of the mechanisms of evolution such as genetic drift and stabilizing selection tend to reduce the genetic diversity of populations.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore evolution and extinction are two independent processes.  Extinction is the complete loss of a unit of genetic diversity (e.g., a species) from the planet.  Evolution and extinction are linked because extinction eliminates a particular evolutionary history that cannot be recovered, but the two processes are affected by different factors within the environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clarifying these definitions we can see that both evolution and extinction are value neutral from the perspective of the biosphere.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans tend to ascribe value to biodiversity based on aesthetics, ecosystem services, ethics, etc... and thus we may strive to preserve it for these reasons but this is unrelated to the biological function of evolution and extinction.&lt;/p&gt;&#xA;" OwnerUserId="137" LastActivityDate="2013-05-29T14:57:21.110" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8577" PostTypeId="1" AcceptedAnswerId="24784" CreationDate="2013-05-29T16:22:36.017" Score="6" ViewCount="1659" Body="&lt;p&gt;I've wondered about this for a long time, and hopefully someone here has a reasonable answer. I'm a cell and molecular biologist, and much of my time at the bench is spent wearing (usually nitrile) gloves. I've noticed that if I wear them for longer than 10 or 15 minutes they start accumulating sweat. However, my hands aren't clammy or damp when I'm not wearing gloves, so my question is whether my hands are always sweating at approximately the same rate, and the impermeable barrier of the gloves just traps the moisture, or does the enclosed environment inside the gloves promote sweating? My hands don't seem particularly hot when I have the gloves on, and the gloves themselves are pretty thin, although they do have some insulating properties, as I can handle items taken from a -80°C more easily gloved than bare-handed. What causes this diaphoresis?&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2018-08-07T14:17:36.897" Title="Would my hands sweat this much if I wasn't wearing gloves?" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8578" PostTypeId="2" ParentId="8575" CreationDate="2013-05-29T17:53:22.630" Score="4" Body="&lt;p&gt;There are two explanations which come to mind answering your question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I asked if you eat a lot of protein, because the amount of protein which some body builders consume leads to renal failure. And one sign of renal failure is the smell of ammonia. It's a quite common problem. But I don't think this applies to you. Your protein intake shouldn't exceed 2g per kg of body weight per day, some body builder eat up 4g per kg. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ammonia is normally linked to your protein metabolism, which is higher during and after sport. The smell of Ammonia can occur when your carbohydrate reservoir is depleted and the body is mainly using protein as fuel. This effect also occurs when fasting or in patients with diabetes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Try to keep your blood sugar level raised during exercise by eating something, like a banana, powerbars (also known as high energy bar) or directly dextrose. Or eat more long-chain carbohydrates. And this always depending the form of sport you are practicing. Just like the pasta party prior to marathons.&lt;/p&gt;&#xA;" OwnerUserId="3262" LastActivityDate="2013-05-29T17:53:22.630" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8579" PostTypeId="2" ParentId="8574" CreationDate="2013-05-29T20:28:40.127" Score="1" Body="&lt;p&gt;I use virkon for cell cultures, but for viruses I tended to use standard bleach during the time I worked in a virology lab. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-29T20:28:40.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8580" PostTypeId="1" CreationDate="2013-05-30T02:45:27.187" Score="7" ViewCount="461" Body="&lt;p&gt;The brain is separated into different regions, and different regions perform different tasks. Well, what are the differences between these regions on the cellular/systemic level. The brain is made up of neurons and other cells, but how come one part is used to process sound and another is used to process, say, smell? Are they like different computer circuit boards - using the same components but are wired differently?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And anyways, why did evolution not come up with a brain that uses the entire brain to process something, would that not be more efficient?&lt;/p&gt;&#xA;" OwnerUserId="3465" LastActivityDate="2019-05-16T05:00:18.040" Title="What is the difference between different brain regions" Tags="&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8582" PostTypeId="2" ParentId="8580" CreationDate="2013-05-30T10:29:29.747" Score="2" Body="&lt;p&gt;The wiring is different as you mentioned. However, perhaps the most important is the brain knows where it's input is coming from. The brain knows where each fibre innervates and thus can compile and present this data to our conscious mind. We show if we stimulate the brain directly, than we feel a sensation in the part of the body that portion of the brain is responsible for. Plasticity means our brain can change what feeds into where, this is most commonly where we learn a motor skill. If we play the piano for example the part of the cortex feeding to this area increases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way is the type of chemical transmitter and receptor. Dopamine is primarily used for things that cause us pleasure for example. However dopamine can affect our movement if it is secreted in from the substantia nigra, as this feeds into the motor cortex. Furthermore, neurotransmitters can be excitatory or inhibitory and this is an analogue rather than binary signal. All of these fine tune, and the position at which they inhibit and the location and the feedback from which they obtain their signal all indicates from where the brain is getting the information or to what it is responding to. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary it is wiring, signalling and location. However the components are incredibly similar but it isn't the small differences that have a profound effect.  &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-30T10:29:29.747" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8583" PostTypeId="2" ParentId="8560" CreationDate="2013-05-30T10:45:06.713" Score="-1" Body="&lt;p&gt;It looks like a pine to me. Might be close to &lt;em&gt;Pinus pinaster&lt;/em&gt; but take into account that&#xA;a) I'm not a botanist. &#xA;b) I'm only familiar with pines that grow in my area (Catalonia).&lt;/p&gt;&#xA;" OwnerUserId="1739" LastActivityDate="2013-05-30T10:45:06.713" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8584" PostTypeId="2" ParentId="8566" CreationDate="2013-05-30T10:51:33.693" Score="2" Body="&lt;p&gt;Whilst it is true that animal cells are more like our own, I'm not sure that would be the reason for non-allergic responses. If we take xenografts (transplanting pig organs for example) we see a profound response. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The latter theory of it having a higher mortality is more closer to the truth. Typically we observe that things we are given from childhood causes induction of tolerance (T reg cells). However this occurs best at a young age and if given orally. Peanut allergies for example are incredibly infrequent in Japan for example. Meat is given typically from a young age. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However what about the vegetarian converts or exposure to new foods as you grow older. Well the theory suggested for this are some antigens act to signal the immune system. These proteins are similar to the cell signals our body uses to tell the body there's a fight on, we are being invaded by something dangerous. This causes an immune system reaction to build up, specfically IgE antibodies. Thus on subsequent exposure, the response is stronger due to a preformed response. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although these are they hypotheses, they're being actively investigated because frankly they can't be that simple. And of course there is conflicting evidence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, I've met a person with mushroom allergy. It does occur. Maybe polymorphisms (slight genetic differences) means someone responds to antigens others don't?&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-05-30T10:51:33.693" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8586" PostTypeId="1" AcceptedAnswerId="8589" CreationDate="2013-05-30T15:43:03.277" Score="5" ViewCount="536" Body="&lt;p&gt;If antibodies are produced against other blood groups' red blood cells, why can't antibodies form against white blood cells, of any blood group? (even the same one, as MHC will be different in almost all individuals)&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-13T15:41:26.900" LastActivityDate="2015-09-25T14:15:39.853" Title="Can antibodies be formed against white blood cells after blood transfusion?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;hematology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8588" PostTypeId="1" CreationDate="2013-05-30T16:44:50.883" Score="9" ViewCount="1437" Body="&lt;p&gt;And how do we know whether they do or not?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;§&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If sleep is a physiological need, it seems weird that we become unable to fulfill on demand even in the absence of any obvious physical issues. We would all probably would like to be able to fall asleep on demand on a long flight and we all know this can be hard even when we are tired.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, my question is whether this is a mostly human dysfunction or a common animal property.&lt;/p&gt;&#xA;" OwnerUserId="29" LastEditorUserId="69" LastEditDate="2013-05-30T17:26:57.993" LastActivityDate="2014-08-10T17:18:04.880" Title="Do non-human animals suffer from insomnia?" Tags="&lt;zoology&gt;&lt;sleep&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8589" PostTypeId="2" ParentId="8586" CreationDate="2013-05-30T17:50:13.193" Score="8" Body="&lt;p&gt;Antibodies and other immune responses do indeed occur against the donor's white blood cells. However, white blood cells are present in relatively tiny quantities (&lt;a href=&quot;https://www.mayoclinic.com/health/complete-blood-count/MY00476/DSECTION=results&quot;&gt;3-10 million WBCs per ml of blood vs 4-6 &lt;em&gt;billion&lt;/em&gt; cells per ml&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the number of WBCs is so low, the immune reaction to them is also proportionally lower, with fever being a typical (and minor) complication of the reaction to WBCs. Some blood banks remove WBCs from blood to prevent these reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information on the possible types of reactions to blood transfusions, see &lt;a href=&quot;https://en.wikipedia.org/wiki/Blood_transfusion#Adverse_effects&quot;&gt;Wikipedia&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Even in cases where the transfusion does not produce any symptoms, an immune reaction is most assuredly happening. In those cases, the immune system is simply killing off the foreign WBCs without any fuss.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastEditorUserId="3631" LastEditDate="2013-05-30T19:17:21.687" LastActivityDate="2013-05-30T19:17:21.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8590" PostTypeId="1" CreationDate="2013-05-29T18:22:18.440" Score="6" ViewCount="394" Body="&lt;p&gt;Scientists have found mammoth blood, and are planning to &lt;a href=&quot;http://www.inquisitr.com/680125/mammoth-blood-found-cloning-extinct-species-may-soon-be-possible/&quot; rel=&quot;nofollow&quot;&gt;clone a mammoth.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does one go from having its blood to a full blown living mammoth? Is it possible?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does it matter if the blood is frozen or not? Suppose one found dinosaur blood, could one clone a dinsosaur (as in say 'Jurassic Park')?   &lt;/p&gt;&#xA;" OwnerDisplayName="anon" LastEditorUserId="107" LastEditorDisplayName="anon" LastEditDate="2013-06-29T04:51:10.003" LastActivityDate="2013-07-03T10:48:19.827" Title="Can extinct animals be cloned?" Tags="&lt;genetics&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8591" PostTypeId="2" ParentId="8590" CreationDate="2013-05-30T07:51:21.490" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;How does one go from having its blood to a full blown living mammoth?&#xA;  Is it possible?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is possible, but it is really hard with the current technology. The DNA in the frozen mammoth blood is heavily degraded, but with enough degraded DNA samples you can create a DNA sequence. After that you can compare it with elephant DNA, and you can genetically alter an elephant zygote. You can synthesize the whole genome too, but it's much harder.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why does it matter if the blood is frozen or not?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The DNA degrades slower when the blood is frozen.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Suppose one found dinosaur blood, could one clone a dinsosaur (as in&#xA;  say 'Jurrasic Park')?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You will never find dinosaur blood, fossils are just rock, nothing more.&lt;/p&gt;&#xA;" OwnerUserId="3703" OwnerDisplayName="inf3rno" LastActivityDate="2013-05-30T08:00:35.537" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="8592" PostTypeId="2" ParentId="8565" CreationDate="2013-05-30T22:14:19.037" Score="2" Body="&lt;p&gt;It's important to note the difference in mechanism between cocaine and meth. While cocaine blocks reuptake, meth makes VMAT - vesicular monoamine transport - leaky and actually reverses the transportation of dopamine, so that instead of transporting dopamine into the axon terminal, it actually transports dopamine out as it leaks from the vesicle that carry it. This is what is meant when referring to 'reverse transport' of dopamine through DAT. Feel free to read this abstract and the sources it cites (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631950/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631950/&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the possibility of a DAT agonist of sorts, looks like current research has identified some potential targets. One of which seems to be luteolin and its derivatives (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20971650&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/20971650&lt;/a&gt;). Current studies find new derivatives and test the EC50 to assess pharmacological efficacy.&lt;/p&gt;&#xA;" OwnerUserId="3695" LastEditorUserId="107" LastEditDate="2013-05-30T23:07:20.837" LastActivityDate="2013-05-30T23:07:20.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8593" PostTypeId="1" CreationDate="2013-05-30T23:36:06.077" Score="5" ViewCount="1165" Body="&lt;p&gt;I'm currently working on a synthetic biology project which involves working with lots of different parts. I would ultimately like to integrate these genes by transforming a single plasmid. I've heard (casually) that 9-10 foreign genes on a transformed plasmid is often the practical upper limit for these types of experiments, without a real explanation other than &quot;beyond that, it just doesn't work&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there a practical upper limit to size of amount of genes in a transformed plasmid, assuming all need to be expressible? What causes this upper limit?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2013-05-31T14:36:27.967" LastActivityDate="2013-05-31T16:22:53.923" Title="Is there a practical upper limit to amount of nucleotides or genes in a transformed plasmid?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;molecular-genetics&gt;&lt;synthetic-biology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8600" PostTypeId="1" AcceptedAnswerId="8645" CreationDate="2013-05-31T05:50:16.650" Score="3" ViewCount="178" Body="&lt;p&gt;I've been unable to find anything on the Google resembling this bird. I took the photo in Virginia Beach, VA around 2010, October, I think...&#xA;It appears to be between winter and summer plumage but I'm not sure. I tried looking on whatbird.com but couldn't find anything that really seemed to match up well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've added some more photos since people seem to question whether or not the white is snow, for some reason. Also note that most seem to have a red bill with a black tip, while the one with more white on its breast has a largely black bill with just a red band. Do bills change colors when plumage does, is that a thing, or perhaps it's just an anomaly or a gender trait?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KoHE4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/GqlFR.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/IMyeY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3700" LastEditorUserId="3700" LastEditDate="2013-06-01T23:45:53.317" LastActivityDate="2013-06-04T03:29:09.227" Title="Identify this waterfowl species?" Tags="&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8601" PostTypeId="1" CreationDate="2013-05-31T06:46:27.487" Score="2" ViewCount="917" Body="&lt;p&gt;I know that a minority of plants are fully dioecious, with adult plants producing either only male or only female flowers. When is this sexual differentiation determined? Is the seed of such a plant already male or female? Is it a simple genetic difference?&lt;/p&gt;&#xA;" OwnerUserId="3501" LastActivityDate="2013-05-31T19:11:54.553" Title="How do fully dioecious plants determine sex?" Tags="&lt;botany&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8603" PostTypeId="2" ParentId="8601" CreationDate="2013-05-31T07:41:04.740" Score="2" Body="&lt;p&gt;The short answer is that in dioecious plants the sex of an individual plant is determined by its chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several familiar crop plants are dioecious: asparagus, kiwi, hop, papaya, spinach and yam. The evidence indicates that dioecy has evolved independently in different plant families. I refer you to &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Matsunuga &amp;amp; Kawano (2001) Sex determination by sex chromosomes in dioecius plants. Plant Biol 3: 481-488. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I have summarised below some of the introductory information in this review.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First some background for context: In mammals there is an XY system in which maleness is determined by an active Y chromosome i.e. the Y chromosome carries male sex determination gene(s). Males are said to be heterogametic. In Drosophila there is also an XY system, with heterogametic males, but in this case what determines sex is the ratio of X chromosomes to autosomes. This ratio exerts its effects through the Sxl gene. In this system the Y chromosome does not carry male-determining genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In flowering plants, in dioecious species, the usual situation is that males are heterogametic. However, there is variability in the underlying mechanism of sex determination.  So for example in hop (&lt;em&gt;Humulus lupulus&lt;/em&gt;) there is a pair of sex chromosomes that can be distinguished by their appearance. However there is no active male determination but rather the X to autosomal ratio determines sex (as in Drosophila). Conversely, in asparagus (&lt;em&gt;Asparagus officinalis&lt;/em&gt;), sex is determined by a pair of chromosomes designated pair 5. The two chromosomes are morphologically indistinguishable but genetic evidence indicates that there is active sex determination in this species - one member of pair 5 acts like the mammalian Y chromosome.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-05-31T19:11:54.553" LastActivityDate="2013-05-31T19:11:54.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8604" PostTypeId="1" AcceptedAnswerId="8610" CreationDate="2013-05-31T09:10:14.727" Score="0" ViewCount="140" Body="&lt;p&gt;I am looking review articles for Physiology.&#xA;For instance, Physiological explanation of steps of measurement of the metabolism by Douglas-Haldane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no section for Physiology or metabolism in Advanced Search of Nature Review.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is a good review article source of Physiology?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2013-06-01T15:24:17.273" Title="What is a good review article source for Physiology?" Tags="&lt;physiology&gt;&lt;review&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8605" PostTypeId="2" ParentId="8593" CreationDate="2013-05-31T13:53:59.640" Score="4" Body="&lt;p&gt;From my experience in the mammalian world (and this may apply to bacterial systems as well), it's not so much the number of genes in the plasmid as its actual size. The larger the construct is, the more difficult it will be to get it into your target cells in one piece, without degradation or shearing. Since the transformation efficiency is lower, you are getting fewer whole constructs per cell, so depending on how you've set up your promoters, the overall expression level can be significantly lower. The trouble with splitting your genes amongst two or more plasmids is that each will have different transformation efficiencies, and there will be a certain (perhaps large) number of cells that don't get the full complement of genes, interfering with phenotype analysis. And again, you'll also have to consider differential expression rates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, once you get your vector into the cells in one piece, theoretically they should all get expressed at approximately equal levels (assuming identical promoters). It's possible that steric hindrance among multiple transcription complexes may occur - I just don't know enough about bacterial transcription and the effects of circular plasmids to say.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One way to get around many of these factors would be to use a &lt;a href=&quot;http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome&quot; rel=&quot;nofollow&quot;&gt;bacterial artificial chromosome&lt;/a&gt; or BAC. BACs are 7-10 kb vectors that can have inserts of up to 1 million bp cloned into them and are then &lt;a href=&quot;http://en.wikipedia.org/wiki/Electroporation&quot; rel=&quot;nofollow&quot;&gt;electroporated&lt;/a&gt; into cells. One of (the many) cool things about them is they control their own duplication and partitioning at cell division, so succeeding generations should have essentially the same copy number as the original. They were heavily used during the Human Genome Project to amplify large sections of DNA for sequencing, but they are also used in many other studies, including synthetic biology. &lt;a href=&quot;http://openwetware.org/wiki/Bacterial_artificial_chromosomes&quot; rel=&quot;nofollow&quot;&gt;OpenWetWare&lt;/a&gt; has a list of some common ones, and NEB sells &lt;a href=&quot;https://www.neb.com/search?q=pBeloBAC11&quot; rel=&quot;nofollow&quot;&gt;pBeloBAC11&lt;/a&gt; systems.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="1320" LastEditDate="2013-05-31T16:22:53.923" LastActivityDate="2013-05-31T16:22:53.923" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8607" PostTypeId="1" CreationDate="2013-06-01T00:10:23.277" Score="2" ViewCount="93" Body="&lt;p&gt;We have a few Strep-tactin columns that had some growth in them and we would like to regenerate the columns back since the resin is quite expensive. Basic goal: remove the brown stuff.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far, I've killed whatever living material there is with 20% EtOH and 0.5 N NaOH. After cleaning out the columns with Tris Buffer, I've tried regenerating the columns with Buffer with HABA and the resin is a bit redder than before (typical reflection of good regeneration). However, rinsing out the columns again still leaves behind a brownish color. There is also a good deal of black particulate in the resin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm curious what methods exists to clean out a contaminated column.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2013-06-01T00:10:23.277" Title="Removing bacterial contaminants from resin" Tags="&lt;protocol&gt;&lt;purification&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8608" PostTypeId="2" ParentId="8590" CreationDate="2013-06-01T11:27:28.820" Score="4" Body="&lt;p&gt;DNA degradation half-lifetime within fossilized/frozen species is ~ &lt;a href=&quot;http://www.nature.com/news/dna-has-a-521-year-half-life-1.11555&quot; rel=&quot;nofollow&quot;&gt;500 years.&lt;/a&gt;, even when the conditions are perfect for preservation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, in theory, if we could sequence anything that is less then 13 000 years old (expected length of preserved nucleotide sequences ~30 bp, which is just enough to stitch together two unique regions). If we have several copies of DNA (several cells), we can go a little bit further by sequencing same reads several times. If we assume an average cell is 30 um in diameter, we have ~40 000 cells in a cubic mm of tissue samle. this will allow us to extend the sequencing horizon by another 8000 years. With a cubic sample of intact, perfectly preserved tissue (this is REALLY A LOT and REALLY RARE) we could get an additional 5000 years, limiting our possibility to know the genome, let alone reproduce it to 26-30 000 years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By using a couple of sequence assembly tricks, such as existence of reference genomes of closely related species, we could either decrease the amount of tissue sames or allow the DNA to get a little bit more degraded. However, even with a cubic centimeter of tissue we won't be able to go beyond 50-100 000 years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The furthest we have gotten now is a &lt;a href=&quot;http://www.eva.mpg.de/neandertal/index.html&quot; rel=&quot;nofollow&quot;&gt;Neanderthal sequence&lt;/a&gt; (~30 000 years) and it was already tough. It would be impossible to get a hand on dinasaurus DNA sequence, let alone trying to clone it. Mammoth, Saber-tooth Tiger and Dodo should be ok, provided we can find their remainders.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, Once you get the raw DNA sequence, you have to get the epigenetic code right, find a compatible egg of a related spicies (that is quite hard), inject your DNA into it, and hopefully, with lots of ifs you can get your clone and hope it survives. However the part about getting the epigenetic code right and finding a compatible egg is really not easy. Personally, I won't parry on anything that doesn't have close related species still living.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE: as of June 2013 a genome of a wild horse 700 000 years old have been sequenced, which is the furthers we could get so far.&lt;/p&gt;&#xA;" OwnerUserId="957" LastEditorUserId="957" LastEditDate="2013-06-28T22:38:38.217" LastActivityDate="2013-06-28T22:38:38.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8609" PostTypeId="2" ParentId="8590" CreationDate="2013-06-01T13:11:43.050" Score="3" Body="&lt;p&gt;I'll just add that projects to clone a mammoth have been &lt;a href=&quot;http://discovermagazine.com/1999/apr/cover&quot; rel=&quot;nofollow&quot;&gt;active for over a decade&lt;/a&gt; and &lt;a href=&quot;http://blogs.discovermagazine.com/notrocketscience/2012/06/06/will-we-ever-clone-a-mammoth/&quot; rel=&quot;nofollow&quot;&gt;privately funded projects are also underway&lt;/a&gt;.  While the precedent has not been set by actually doing this, the technology of reproductive cloning of animals is still very new and each new case is its own problems to solve but there's reason to believe that the technical difficulties can be overcome as new animals are &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_animals_that_have_been_cloned&quot; rel=&quot;nofollow&quot;&gt;constantly being added to the list.&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance lots of hybrid experiments are underway where a modern animal's genome is used as a scaffold in which extinct animals genes are inserted, just as was suggested in Jurassic Park.  Its not clear how far this can go, but there's reason to be quite optimistic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, &lt;a href=&quot;http://discovermagazine.com/1999/apr/cover&quot; rel=&quot;nofollow&quot;&gt;Ed Yong's blog post&lt;/a&gt; is a great place to start for a discussion of the details of inseminating an elephant successfully. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1590" LastEditDate="2013-07-03T10:48:19.827" LastActivityDate="2013-07-03T10:48:19.827" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8610" PostTypeId="2" ParentId="8604" CreationDate="2013-06-01T15:24:17.273" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291469-7793&quot; rel=&quot;nofollow&quot;&gt;The Journal of Physiology&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.annualreviews.org/journal/physiol&quot; rel=&quot;nofollow&quot;&gt;Annual Reviews Physiology&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.physiology.org/&quot; rel=&quot;nofollow&quot;&gt;Journals from American Physiological Society&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.frontiersin.org/physiology&quot; rel=&quot;nofollow&quot;&gt;Frontiers in Physiology&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://journals.cambridge.org/action/displayJournal?jid=EPH&quot; rel=&quot;nofollow&quot;&gt;Experimental Physiology&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Often, notable research papers are published in journals with high impact factors, although being published in a journal with high impact factor does not mean the research is better over research in smaller journals. But it can be a rough indication.&lt;/p&gt;&#xA;" OwnerUserId="3465" LastActivityDate="2013-06-01T15:24:17.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8611" PostTypeId="1" AcceptedAnswerId="8638" CreationDate="2013-06-01T17:07:07.940" Score="13" ViewCount="9355" Body="&lt;p&gt;There is an specific angle of the bond between oxygen and hemoglobin in lungs, which I don't know, but what interests me more is the question, why is it specific?&lt;/p&gt;&#xA;" OwnerDisplayName="user3711" LastActivityDate="2017-09-18T15:40:41.207" Title="Why does oxygen bind to hemoglobin in an specific angle?" Tags="&lt;hematology&gt;&lt;lungs&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8612" PostTypeId="1" AcceptedAnswerId="8621" CreationDate="2013-06-01T17:14:29.527" Score="3" ViewCount="1870" Body="&lt;p&gt;I'm just introduced to the optogenetics method and am having some trouble grasping the &lt;em&gt;genetics&lt;/em&gt; (of the optogenteics) part of things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So we have Retinal and Opsin that form Rhodopsin molecule that serves as a light-gated ion channel (which is, needless to say, very cool). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the process in which a cell population is targeted and implanted with these Rhodopsins?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And where does the microbial opsin gets into picture? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My main resource, so far, was - &lt;a href=&quot;http://www.stanford.edu/group/dlab/papers/deisserothnature2010.pdf&quot; rel=&quot;nofollow&quot;&gt;Optogenetics - Method of the year/Nature&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="3712" LastActivityDate="2013-06-02T17:05:19.883" Title="Optogenetics - How do microbial opsins work?" Tags="&lt;neuroscience&gt;&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8613" PostTypeId="1" AcceptedAnswerId="8626" CreationDate="2013-06-01T22:28:55.720" Score="4" ViewCount="158" Body="&lt;p&gt;Certain creatures that are considered carnivores are non-obligate carnivores and are technically omnivores (such as wolves/dogs).  How different is the potential digestive ability of these species compared to humans?  If they theoretically developed sapience and the intelligence for agriculture, would they be able to survive on the same wide variety of plant foods that we do (i.e. could wolves survive on wheat, rice, etc)&lt;/p&gt;&#xA;" OwnerUserId="3713" LastEditorUserId="3465" LastEditDate="2013-06-02T14:50:45.470" LastActivityDate="2013-06-02T19:05:41.793" Title="Would non-human carnivores be able to survive on farmed foods?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;digestive-system&gt;&lt;food&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8614" PostTypeId="1" AcceptedAnswerId="8617" CreationDate="2013-06-01T23:45:24.047" Score="1" ViewCount="1281" Body="&lt;p&gt;I wonder why most of us find senior people lovely and charming. Is it because to love grandpa and granny is vital to our survival as a species, in the same way as we love babies? If so, it would mean that we are either aging slower with time, or being selected somehow to love senior people despite their physical appearance, while they are aging at the same rate but living longer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say every common characteristic among individuals of the same specie is product of evolution.&#xA;Many caracteristics are passed by the individuals to their offspring, but only those that were advantageous in some way or another allowed the offsring to survive and pass that caracteristic to their decendants in turn.&#xA;Our love for babies and elders is one of those caracteristics that we as indivudials of  a species have in common.&#xA;That make us to want our elders to be with us as much time as posible, just becouse our affinity with them.&#xA;This love for the elder have to be an advantaje that worthed to be selected by the evolutionary process, and this caracteristic is reflected in the tendency of the life expectancy to increase generation after generation.&#xA;One could say, that those elders that age slower would be more likely to benefit from the love of their offspring, than those that age faster.&#xA;On the other hand, to age slower may not make a difference at all, just because we love our elders despicte their physical appearance.&#xA;I'm considering the cultural and technological advantages that allow our elders to live longer to be a product of evolution too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So my question is wheter we are evolving to age slower, or to live longer aging at the same rate?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note, we are becoming more like what they call a super-organism, as most of os can only benefit of a longer life spam by living in society. Just like an anthill or a beehive. If that is true, we are not evolving to age slower.&lt;/p&gt;&#xA;" OwnerUserId="1862" LastEditorUserId="1862" LastEditDate="2013-06-04T20:13:27.313" LastActivityDate="2013-06-04T22:38:17.230" Title="Are we evolving to age slower, or to live longer aging at the same rate?" Tags="&lt;human-biology&gt;&lt;evolution&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8616" PostTypeId="2" ParentId="7758" CreationDate="2013-06-02T02:42:05.057" Score="5" Body="&lt;p&gt;Peacock spiders certainly aren't mimicking human faces, and I strongly doubt they're mimicking anything at all. As others have noted, it's the combination of a fluke, and some anthropomorphising on your part (easy to do!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The stunning colours and 'dancing' are actually part of a courtship display, and are most likely under strong &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025390&quot;&gt;sexual selection&lt;/a&gt;, rather than selection for any anti-predator function. The male-limited colours are only on display during courtship, and are otherwise flattened along the abdomen. It's also worth remembering that these spiders are tiny (&amp;lt; 5 mm), so the only other animals that are likely to be able to resolve those patterns in any detail are similarly sized organisms with decent eyesight (i.e. female peacock spiders).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://nature.berkeley.edu/~maddiegirard34/menu.html&quot;&gt;Madeline Girard&lt;/a&gt; is in the latter-stages of her PhD on these guys, I'd recommend shooting her an e-mail if you're really interested.&lt;/p&gt;&#xA;" OwnerUserId="3589" LastActivityDate="2013-06-02T02:42:05.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8617" PostTypeId="2" ParentId="8614" CreationDate="2013-06-02T03:59:55.913" Score="3" Body="&lt;p&gt;The question has a more or less official scientific name - &lt;a href=&quot;http://www.nature.com/nature/journal/v428/n6979/full/428128a.html&quot; rel=&quot;nofollow&quot;&gt;the grandmother effect&lt;/a&gt; (or hypothesis).   In the rational world of evolutionary biology, children love their parents for the same sort of reason - the parents give them resources to gather their strength and develop as adults so they can have their own children with the most advantage that they possibly can.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans are off the charts in the amount of resources we invest in our children - our lives are 1/4 to 1/3 over before we sometimes leave our parents household (in some societies of course they never leave the house, but step into an extended family).  This may be one of the reasons we are so successful as a species - we live in practically every place we possibly could and have no danger of competition from any other living thing excepting ourselves.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The grandmother effect is essentially the idea that if women, who are more attached to the offspring in more cases than fathers, continue to live and help support the grandchildren and make them more successful, then this will allow post menopausal women to have a longer lifespan (which they do). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The evolutionary biologist Sara Hrdy, emeritus UC Davis, has written quite a bit about the nuances of the evolution of the role of motherhood - reading some of &lt;a href=&quot;http://www.americanscientist.org/bookshelf/pub/with-a-little-help-from-my-friends&quot; rel=&quot;nofollow&quot;&gt;her articles&lt;/a&gt; or &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0345408934&quot; rel=&quot;nofollow&quot;&gt;books&lt;/a&gt; might give you a deeper sense of how profoundly filial love has shaped human beings. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;--- more answer this stuff may or may not be worth reading depending on how broadly you want to understand this question...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its important to say that many of the expansions of human average human lifespan have not been genetic.  Its commonly cited that sewer systems, clean water, antibiotics and plentiful food are the three most important factors in human lifespan - and before modern developed world nations, the average lifespan of human beings was somewhere in the 30s.  And there are significant lifespan differences in regions where these factors and others (education of women, access to prenatal and early care etc) are available.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Studies continue to be published that examine environmental and lifestyle factors compared to genetics and it seems that &lt;a href=&quot;http://www.nytimes.com/2012/10/28/magazine/the-island-where-people-forget-to-die.html?pagewanted=all&amp;amp;_r=0&quot; rel=&quot;nofollow&quot;&gt;environment and lifestyle can make an astounding difference&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But genetics undoubtedly has a role to play here too.  &lt;a href=&quot;http://www.plosgenetics.org/article/info%3adoi/10.1371/journal.pgen.0030125&quot; rel=&quot;nofollow&quot;&gt;There are probably some individual humans and animals which have evolved to live longer&lt;/a&gt;.  This has been found to be genetically related in some humans by demographics and family lines.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still there are genetic factors that are being identified.  I think its a common misconception that evolution changes the entire species, but its not really true.  There are some who have that tendency and others who do not - at times there will be more of say shorter lived people and other times longer lived individuals will be more common.  It depends upon whether the living conditions of the population really favor one tendency over another.  Usually shorter lived individuals can assume to have other advantages, say the ability to store energy more efficiently.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-06-02T03:59:55.913" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8618" PostTypeId="1" CreationDate="2013-06-02T09:41:33.363" Score="4" ViewCount="688" Body="&lt;p&gt;&lt;a href=&quot;https://www.mayoclinic.org/tests-procedures/allergy-shots/about/pac-20392876&quot; rel=&quot;nofollow noreferrer&quot;&gt;Allergy shots&lt;/a&gt; (aka. &lt;a href=&quot;https://www.aaaai.org/conditions-and-treatments/library/allergy-library/allergy-shots-(immunotherapy)&quot; rel=&quot;nofollow noreferrer&quot;&gt;allergen immunotherapy&lt;/a&gt;) help people adapt to allergens by injecting a gradually increasing doses of one or more allergens. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this procedure tell the body that this allergen is safe and there is no need to mount a response to it? In other words, does this mean that there will be no reaction at all rather than just a reduction in the allergic reaction.&lt;/p&gt;&#xA;" OwnerUserId="3465" LastEditorUserId="46609" LastEditDate="2020-03-19T22:36:54.440" LastActivityDate="2020-03-19T22:36:54.440" Title="How does injecting low doses of allergens cure allergies?" Tags="&lt;immunology&gt;&lt;vaccination&gt;&lt;allergies&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="8619" PostTypeId="1" CreationDate="2013-06-02T09:51:46.977" Score="7" ViewCount="178" Body="&lt;p&gt;We often see videos of octopuses and chameleons changing their color to suit their surroundings. If it was a simple color change from white to red, it'd be understandable, but some of these animals can change colors while incorporating a lot of detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do they process so much information and mimic it. Is this a subconscious action, or do they actually draw a picture in their head and then 'print' it on their bodies? Does this ability come from birth or does it get better over time?&lt;/p&gt;&#xA;" OwnerUserId="3465" LastEditorUserId="3971" LastEditDate="2013-08-29T15:51:04.807" LastActivityDate="2014-05-27T05:54:58.597" Title="How do animals perform detailed active camouflage?" Tags="&lt;pigmentation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8620" PostTypeId="2" ParentId="5125" CreationDate="2013-06-02T10:18:00.687" Score="-2" Body="&lt;p&gt;The part of the brain that maintains balance acts subconsciously, and so while you are sleeping in the behavioral sense, you part of your brain (the cerebellum) do not necessarily have to be asleep. And so it can still maintain balance.&lt;/p&gt;&#xA;" OwnerUserId="3465" LastActivityDate="2013-06-02T10:18:00.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8621" PostTypeId="2" ParentId="8612" CreationDate="2013-06-02T12:52:01.693" Score="2" Body="&lt;p&gt;There is nothing special about the use of rhodopsin when compared to making a cell express any transgene. This question can then be read as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What is the process in which a cell population is targeted and implanted with a gene of interest?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are many ways, which depend on the specific cell type and on whether you want to do it &lt;em&gt;in vitro&lt;/em&gt;, &lt;em&gt;in vivo&lt;/em&gt; and in which species, and it would be very complex to explain them all in detail here, so I will limit myself to two approaches that are popular when doing optogenetics in rodents: viral infection and transgenesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Viral infection&lt;/strong&gt; uses an inactivated virus to deliver the transgene. Essentially you engineer a piece of DNA with the gene for the bacterial opsin of interest and you put it in a &lt;em&gt;viral envelope&lt;/em&gt;, that is a series of proteins that form the &quot;body&quot; of the virus and that contain its genetic material.&lt;br&gt;&#xA;You then inject the virus in the desired zone (e.g. in a specific brain nucleus) and wait for it to infect the cells around the injection site. A week later those cells will express the transgene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For (at least, I think) historical reasons the first type of viruses used for this approach were lentiviruses. These, however, are a tad more complex to handle (especially as they require specialised rooms where they can be handled safely) so adeno-associated viruses (AAV) are becoming more and more popular.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the virus is inactivated, that is, it cannot replicate, just infect the cells around the infection site, but it will not be able to spread around. This is both for safety reasons and because you want the infection to be confined to the specific region where you injected the virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I was saying before, instead of putting a bacterial opsin you can put whatever gene of interest, the procedure is the same. As for the opsins, the first two that were used were the channelrhodopsin-2 (&lt;em&gt;ChR2&lt;/em&gt;), a channel sensitive to blue light and that can be used to depolarize (=excite) the cells and the halorhodopsin (&lt;em&gt;NpHR&lt;/em&gt;), a chloride pump sensitive to yellow light that will, conversely, hyperpolarize (=inhibit) the cells.&lt;br&gt;&#xA;There are nowadays tens of variants of these and other opsins that can be used to drive cell activity with lights. Many of these are described in this (beware! Quite technical) review:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21745635&quot; rel=&quot;nofollow noreferrer&quot;&gt;Optogenetics in neural systems&lt;/a&gt; - Yizhar et al., Neuron 2011&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Transgenesis&lt;/strong&gt; works instead by generating an animal that carries the opsin (or any other gene) in its DNA. This can be done in various way, such as by microinjection of embryonic stem cells carrying the transgene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find a fairly detailed explanation of the process here: &lt;a href=&quot;http://9e.devbio.com/article.php?id=290&amp;amp;iact=hc&amp;amp;vpx=1198&amp;amp;vpy=115&amp;amp;dur=615&amp;amp;hovh=245&amp;amp;hovw=205&amp;amp;tx=184&amp;amp;ty=108&amp;amp;ei=zjirUebAJ46BhQf4qoC4Ag&amp;amp;page=2&amp;amp;tbnh=137&amp;amp;tbnw=115&amp;amp;start=25&amp;amp;ndsp=32&amp;amp;ved=1t:429,r:32,s:0,i:186&quot; rel=&quot;nofollow noreferrer&quot;&gt;Transgenic Cells and Gene Knock-outs&lt;/a&gt;, well summed up by this figure (taken by the same page):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://9e.devbio.com/images/ch02/wt020302-2.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Transgenic mice generation http://9e.devbio.com/images/ch02/wt020302-2.jpg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But how do you get &lt;strong&gt;cell-type selectivity&lt;/strong&gt;?&lt;br&gt;&#xA;In front of the gene for the opsin you also will have to put another sequence, called promoter. The promoter is a sequence that is specific to each gene and that is used to determine which genes a cell will or will not transcribe. For instance, the promoter for the gene coding for a protein only present in muscles will be used by muscle cells but not by neurons. You can even get more specific, for instance by using promoters that are typical of a subset of cells and not other (e.g. glutamatergic neurons use a different set of promoters than GABAergic neurons, although these two sets will -at least in part- overlap). However, this means that if you want to change the cell type you are working on you will have to change the DNA vector you are using.&lt;br&gt;&#xA;A commonly used approach to avoid this is that of using &lt;strong&gt;Cre-dependent vectors&lt;/strong&gt; (note that this can be used both for viral infections or for transgenic animals).&lt;br&gt;&#xA;Essentially you will have a mouse line which expresses a protein derived from the &lt;a href=&quot;https://en.wikipedia.org/wiki/P1_phage&quot; rel=&quot;nofollow noreferrer&quot;&gt;P1 phage&lt;/a&gt;, called &lt;strong&gt;Cre recombinase&lt;/strong&gt;, only in the cell type of interest (again, using a specific promoter). Cre has the property of cutting DNA next to specific 34 base-pair-long sequences called &lt;strong&gt;loxP&lt;/strong&gt; (with sequence &lt;code&gt;ATAACTTCGTATAGCATACATTATACGAAGTTAT&lt;/code&gt;). Essentially, if you have &lt;code&gt;loxP-[some sequence in the middle]-loxP&lt;/code&gt; and Cre recombinase is around, it will cut away the sequence in the middle, leaving only a loxP sequence.&lt;br&gt;&#xA;Hundreds of different Cre-expressing mouse lines are commercially available nowadays, to target many different cell types in different organs.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, you just need a construct that allows you to express the opsin in a Cre-dependent manner. This is what was done by the group of Hongkui Zeng, and reported in this paper:&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22446880&quot; rel=&quot;nofollow noreferrer&quot;&gt;A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing.&lt;/a&gt; - Madisen et al., Nat. Neurosci. 2012&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Without going into too much details, the idea is to flank a &lt;em&gt;STOP sequence&lt;/em&gt; with two loxP sites. This will block transcription (that is what a STOP sequence does) unless Cre-recombinase is present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YCmDF.jpg&quot; alt=&quot;Cre-dependent expression of opsins&quot;&gt;&lt;br&gt;&#xA;&lt;em&gt;Source&lt;/em&gt;: myself, &lt;a href=&quot;http://creativecommons.org/licenses/by-sa/3.0/deed.en_GB&quot; rel=&quot;nofollow noreferrer&quot;&gt;CC-by-sa licensed&lt;/a&gt;, feel free to reuse it&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that in the scheme, ROSA26 is an ubiquitous promoter, that is, a promoter used by all cells, so in this case the specificity is given by expression of Cre recombinase and not by the promoter of this construct. Also, a fluorescent reporter (e.g. &lt;a href=&quot;https://en.wikipedia.org/wiki/Green_fluorescent_protein&quot; rel=&quot;nofollow noreferrer&quot;&gt;GFP&lt;/a&gt;) is inserted to be able to visualize where the opsin is expressed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By breeding these mice with the Cre-line(s) of your choice you can then express the opsins in the cell type of your interest.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2013-06-02T17:05:19.883" LastActivityDate="2013-06-02T17:05:19.883" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8623" PostTypeId="2" ParentId="832" CreationDate="2013-06-02T17:02:55.060" Score="8" Body="&lt;p&gt;There is no such thing as more or less evolved. At least not outside popular media. The only reasonable comparison one can make is comparing generation numbers. You &lt;em&gt;could&lt;/em&gt; say that a species that has undergone X generations is less evolved than one that has undergone X*2 generations. It just doesn't mean much. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolved is not a quantitative term, you cannot really be more or less evolved than something else. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2015-06-26T21:30:36.683" LastActivityDate="2015-06-26T21:30:36.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8624" PostTypeId="1" AcceptedAnswerId="8634" CreationDate="2013-06-02T18:29:53.320" Score="5" ViewCount="1730" Body="&lt;p&gt;These photographs were taken today in Marseille, in the Mediterranean coast of France. My French friends inform me that these beasties are called &lt;em&gt;cousins&lt;/em&gt; because they are &quot;cousins&quot; of mosquitoes (whatever that means). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thing is, we are absolutely infested by them. They seem to be more active at dawn and dusk (like mosquitoes) but we have dozens flying around the house every evening. I would like to know the species' name to see if I can learn anything about them. Do they have cycles like cicadas? Are they linked to stagnant waters like mosquitoes? Why are there so many of them this year?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tWoub.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's one with my hand next to it to give you an indication of their size:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iCSxO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-06-02T18:41:33.967" LastActivityDate="2013-06-05T07:47:21.053" Title="What is this insect?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8625" PostTypeId="1" CreationDate="2013-06-02T18:43:03.447" Score="4" ViewCount="102" Body="&lt;p&gt;Logically speaking, if a hummingbird drinks too much nectar, it will be temporarily overweight and less able or unable to fly to escape danger. However if the same hummingbird doesn't drink enough nectar, it will suffer the same problem of not being able to flee danger, but for the different reason of it wouldn't have enough energy to do so. Hummingbirds are incredibly small, so I would assume they would have the most problem with this issue due to the fact it would have very little margin for error. I am not sure how much that margin is though or the marginal percent of body weight, so I'll ask that question too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What mechanisms do (humming)birds have to regulate and control their body weight and their energy needs and scouting and timing the acquisition of their next potential food source? What is their margin for error and how do they meet it and how did they meet it in the past?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I want a more concise question, so hopefully this is answerable:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively and optionally, Can you describe to  me a general day in the life of a Hummingbird? I want to know what good decisions it makes over the course of its &quot;perfectly average&quot; day to survive. Such things as what it does to avoid dangers, and how it finds its time to eat and how much it eats and at what intervals, and what it does with the rest of its time?&lt;/p&gt;&#xA;" OwnerUserId="3458" LastEditorUserId="3458" LastEditDate="2013-06-06T01:08:24.087" LastActivityDate="2013-06-06T01:08:24.087" Title="Food Intake versus ability to flee among birds, particularly the hummingbird?" Tags="&lt;metabolism&gt;&lt;ecology&gt;&lt;ornithology&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8626" PostTypeId="2" ParentId="8613" CreationDate="2013-06-02T18:55:31.070" Score="3" Body="&lt;p&gt;The foods people in the developed world typically feed their carnivorous pets (including dogs and cats) are not made primarily from meat.  Instead, they are made from plants, specifically grains, such as corn, rice and wheat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to get our pets to eat foods that are so different from the meat-rich diets of their ancestors, we add flavors to the food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check out this episode on the making of pet foods from the television series &quot;How Its Made&quot;, &lt;a href=&quot;http://www.youtube.com/watch?v=220PSFJWHao&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=220PSFJWHao&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to answer your question directly-- yes, in places like the USA, domestic dogs and cats are already living on a diet that is almost entirely plant-based.&lt;/p&gt;&#xA;" OwnerUserId="3718" LastEditorUserId="3718" LastEditDate="2013-06-02T19:05:41.793" LastActivityDate="2013-06-02T19:05:41.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8627" PostTypeId="2" ParentId="8498" CreationDate="2013-06-02T21:47:33.640" Score="4" Body="&lt;p&gt;Yes, it's fairly common for insects to eat their egg casings, shed skin etc. where possible. In a similar vein, as Alex Stone mentions, &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jez.1401760302/abstract&quot; rel=&quot;nofollow&quot;&gt;spiders often eat their webs&lt;/a&gt; too. There's generally plenty of valuable protein and nutrients tied up in there, so why not recycle? &lt;/p&gt;&#xA;" OwnerUserId="3589" LastActivityDate="2013-06-02T21:47:33.640" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8628" PostTypeId="1" CreationDate="2013-06-02T22:08:33.037" Score="6" ViewCount="107" Body="&lt;p&gt;The most distinctive characteristic of a human is it's face - it is unique among each individual (with the exception of identical twins). It is uncertain to me if whether we best identify other humans by their face due to special brain parts developed for this (there are people with disease that cannot recognize faces) or for actual very distinctive physical face forms; maybe it is a combination of this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, the question is about evolution. Why would distinct faces (or ability to recognize distinct faces) be something useful that would be retained by evolution? How is this better at survival?&lt;/p&gt;&#xA;" OwnerUserId="3116" LastActivityDate="2013-06-05T17:52:16.467" Title="What determined the evolution of different faces in humans?" Tags="&lt;evolution&gt;&lt;perception&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8629" PostTypeId="2" ParentId="8277" CreationDate="2013-06-02T23:07:02.980" Score="1" Body="&lt;p&gt;I've had some experience with Karen Strier's 'Primate Behavioural Ecology', and it's solid. It's a nice overview with (obviously) a strong ecology/ethology bent. I don't think it comes in ebook though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0205790178&quot; rel=&quot;nofollow&quot;&gt;Amazon link&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3589" LastActivityDate="2013-06-02T23:07:02.980" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8630" PostTypeId="1" AcceptedAnswerId="8637" CreationDate="2013-06-03T01:20:52.793" Score="11" ViewCount="500" Body="&lt;p&gt;I've done some research and it appears that dogs are the most diverse looking single species of mammals. The questions that interest me is - are dogs special in respect to genes/gene activation mechanisms related to appearance? Or does this dramatic difference in appearance have something to do with dog anatomy and how they give birth?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If dogs are not special, this makes me interested &lt;strong&gt;if other species of mammals can also be bred selectively (or genetically engineered) to produce such dramatic variation?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="26292" LastEditDate="2017-06-15T14:30:04.767" LastActivityDate="2018-03-17T12:10:52.537" Title="Can any species be bred selectively/engineered to become as diverse looking as dogs?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;zoology&gt;&lt;dogs&gt;&lt;morphology&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8633" PostTypeId="1" CreationDate="2013-06-03T07:15:14.263" Score="2" ViewCount="1507" Body="&lt;p&gt;I have been checking my sample for Hydroxyl radical scavenging activity. I have dissolved Hydrogen peroxide in Phosphate buffer. My sample is clear and reagent is also clear but when I have mixed my sample extract with Hydrogen peroxide reagent a precipitant is formed. Control is very less than solution that is kept for reaction to proceed. So I am getting an answer in negatives (230 nm). Is that formation of precipitate affect the absorbance of the solution? Does precipitation increase the OD value compare to clear solution?&#xA; Mine is mushroom powder. It is extracted with Ethanol. Extract is dried and finally it is dissolved with solvent above said. That has been used for Hydroxyl radical scavenging activity. Hydrogen peroxide 0.01 milli molar reagent is prepared with Phosphate buffer. First i have taken reading for H2O2 and added extract kept for ten mins and took reading. in 230 nm..&lt;/p&gt;&#xA;" OwnerUserId="3720" LastEditorUserId="3720" LastEditDate="2013-06-03T15:14:38.407" LastActivityDate="2013-06-03T15:14:38.407" Title="Does precipitation influence the UV spec reading?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="8634" PostTypeId="2" ParentId="8624" CreationDate="2013-06-03T11:22:15.573" Score="9" Body="&lt;p&gt;It is indeed a &lt;a href=&quot;http://en.wikipedia.org/wiki/Crane_fly&quot;&gt;Crane fly&lt;/a&gt;, superfamily &lt;a href=&quot;http://en.wikipedia.org/wiki/Tipuloidea&quot;&gt;Tipuloidea&lt;/a&gt;, which is part of two-winged insects (Diptera). There are &gt;15000 species worldwide. Their systematics is somewhat uncertain (used to be a single family, now a superfamily). They are placed in the same suborder as mosquitoes (&lt;a href=&quot;http://en.wikipedia.org/wiki/Nematocera&quot;&gt;Nematocera&lt;/a&gt;). The adults feed on nectar or not at all (they do not prey on mosquitoes), and the larvae usually feeds on litter, roots, fungi etc, but some aquatic species are predatory. Larvae of some species develop in soil and others in water. Adults of many species are attracted by light, which is why you often find them inside houses. I dont know why you find so many this year where you live, but winter conditions affecting survival is a possible explanation. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-06-05T07:47:21.053" LastActivityDate="2013-06-05T07:47:21.053" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8635" PostTypeId="2" ParentId="8633" CreationDate="2013-06-03T11:42:30.133" Score="2" Body="&lt;p&gt;The answer to the question as asked is that yes, any precipitate will affect the value that you are reading in your spectrophotometer. The basis of spectrophotometry is that light passes through a sample, and less light emerges than the amount which entered. The amount of light that has &quot;disappeared&quot; is used to deduce something about the solution in the cuvette. Light can be absorbed by chemical groups (this is the basis for e.g. DNA having an absorbance value) or it can be scattered by particulate material (this is the basis for measuring the cell density of a bacterial culture). If you are trying to make a measurement of the first type (absorbance) and you get a precipitate your reading will be distorted by the light scattering effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Precipitates are incompatible with spectrophotometry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the comments have noted: if you give more details of your protocol someone may be able to help. Phosphates are, of course, notorious for generating unwanted precipitates.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-06-03T11:42:30.133" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8636" PostTypeId="1" CreationDate="2013-06-03T15:28:36.727" Score="3" ViewCount="137" Body="&lt;p&gt;I have a series of protein models with DNA docked. I now want to superpose the DNA on a reference DNA molecule and extract the translational distance applied and the rotation angle used.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can superpose DNA molecules with Chimera, but I can't extract the translational distance and the rotational angle that was applied to superpose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have also had a look at MODELLER but it seems MODELLER cannot not superpose DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know of software/code by which I can extract the information I want?&lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="3059" LastEditDate="2013-06-03T20:02:10.303" LastActivityDate="2013-09-25T10:33:24.330" Title="Superposing DNA" Tags="&lt;bioinformatics&gt;&lt;dna&gt;&lt;proteins&gt;&lt;software&gt;&lt;visualization&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8637" PostTypeId="2" ParentId="8630" CreationDate="2013-06-03T15:32:53.700" Score="12" Body="&lt;p&gt;Dogs have a &lt;a href=&quot;http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000451&quot; rel=&quot;nofollow noreferrer&quot;&gt;genomic structure that allows breeding with high variation&lt;/a&gt; in size, shape, coat quality, color and &lt;a href=&quot;http://dogcare.dailypuppy.com/criteria-show-dog-judging-3605.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;other qualities&lt;/a&gt; &lt;a href=&quot;http://www.westminsterkennelclub.org/dogshows/aboutdogshows.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;particular to each breed as well&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other domesticated animals can be &lt;a href=&quot;http://en.wikipedia.org/wiki/Cattle_judging#Judging_cattle&quot; rel=&quot;nofollow noreferrer&quot;&gt;bred for as many qualities&lt;/a&gt;, but dogs in particular show a wide level of morphological traits - varying in size from just over a pound to the size of a wolf, from which dogs are derived and genetically are still compatible.  But more interesting than just size or coat color/texture and even their intelligence and personalities, &lt;a href=&quot;http://www.justdogbreeds.com/all-dog-breeds.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;the proportions of their bodies, of their skull length and breadth, are remarkable&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are over 160 registered breeds of dogs, but this is only a measure of how much time people have put into them.  I think its possible to get nearly anything you want with animals, if you are patient enough - its not clear what is and is not possible with enough genetic manipulating. For instance, horses can be bred over nearly &lt;a href=&quot;http://smallesthorse.com/shgpicks/breeders.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;as great a size&lt;/a&gt; &lt;a href=&quot;http://animals.pawnation.com/largest-horse-alive-4369.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;range&lt;/a&gt; for instance (the miniature horse the size of a large dog, the Shire is 3,300 pounds), but it would not be as easy to get both the size and muscularity and shape of a bulldog in a horse.  Breeding &lt;a href=&quot;http://www.thenationalmouseclub.co.uk/breeds.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;a mouse of various colors can be done&lt;/a&gt;, and so can interesting behaviors, but body shape seems to be harder: a &lt;a href=&quot;http://en.wikipedia.org/wiki/Weimaraner&quot; rel=&quot;nofollow noreferrer&quot;&gt;Weimaraner&lt;/a&gt; mouse could take a tremendous amount of time and animals.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2017-01-23T00:44:34.043" LastActivityDate="2017-01-23T00:44:34.043" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="8638" PostTypeId="2" ParentId="8611" CreationDate="2013-06-03T17:24:04.430" Score="15" Body="&lt;p&gt;summary: &#xA;O2 could form a linear complex with the Fe atom, but then it would start to look more like a mineral Fe=O...O bond - a linear bond would be like a transition state to an iron oxide (rust).   An Fe-O-O bent bond preserves more of the electronic character of the O2 molecule and promotes strong but reversible binding to Hemoglobin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The oxygen molecule forms a partial covalent bond with the iron in the heme (the ringlike molecule in the picture below &lt;img src=&quot;https://i.stack.imgur.com/1ovXx.jpg&quot; alt=&quot;nice picture from Rice Univ Biotechnology intro class&quot;&gt; ).  The lone pair of electrons of the oxygen atom which forms the bond to the iron has a 120 degree angle with respect to the oxygen molecule itself.  In chemistry we say it is sp2 hybridized.  This implies a slightly greater than 120 degree angle between the Fe-O and the O-O axis would be energetically preferred in oxygen binding. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see on the other end of the oxygen, there is a histidine sidechain nitrogen which interacts in a similar way - crooked at a similar angle to the oxygen molecule. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As @MattDMo points out in the comments, it would not be 120 degrees exactly in fact even freshman chemistry molecular orbital theory would say that the double bond would take up more 'space' than the sp2 orbitals, widening out the angle Fe-O=O angle to be greater than 120 degrees.  Then the protein has its own geometry - the histidine and the heme iron are fixed in space and probably have their own location, so this is just an approximate, qualitative bond angle..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The claims of &lt;a href=&quot;http://www.pnas.org/content/67/4/1846.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;superoxide formation&lt;/a&gt; is because the oxygen is diamagnetic the iron and he oxygen, which are both paramagnetic, somehow pair to eliminate their magnetic moment.  The PNAS paper cited here goes in depth on this issue.  The article curiously just says the highly reactive superoxide is kept from being chemically consumed by the hydrophobic pocket around it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The oxygen almost makes a superoxygen the iron sort of oxidizes but doesn't quite. Its also due to the peroxide like character of the oxygen molecule, partially bonded at both ends.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still the point is that hemoglobin holds onto the oxygen by making a partial covalent bond.  After all when the O2 unbinds, its just O2 again.  A &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC392294/pdf/pnas00024-0012.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;later study&lt;/a&gt; does detect some paramagnetism at low temperatures. In the last word on this that I could find, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC431209/pdf/pnas00029-0024.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pauling does a review&lt;/a&gt; and concludes that the electronic state of the heme iron and oxygen complex is a combination of three different electronic states - partly superoxygen, partly oxy-iron and molecular oxygen.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reference also gives the Fe-O-O angle as 117 degrees.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[Just a note that the &lt;a href=&quot;http://www.bioc.rice.edu/bios576/proteng/protengsite.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference page I got the picture from&lt;/a&gt; refers to &lt;em&gt;rational design&lt;/em&gt; of the hemoglobin molecule...in this case they are engineers talking about how they could change the amino acids in the protein to get other properties out of the hemoglobin system - rationally.]&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-10-03T01:32:25.123" LastActivityDate="2013-10-03T01:32:25.123" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8639" PostTypeId="2" ParentId="8630" CreationDate="2013-06-03T17:36:20.650" Score="6" Body="&lt;p&gt;Rabbits have been bred domestically since at least ancient egypt.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rabbits vary in size from &gt; 15 kg (35lb) for &lt;a href=&quot;http://www.rabbitwelfare.co.uk/pdfs/GiantRabbitCareGuidelines.pdf&quot; rel=&quot;noreferrer&quot;&gt;a Continental Giant&lt;/a&gt; to .5kg(1lb) for A small &lt;a href=&quot;http://en.wikipedia.org/wiki/Netherland_Dwarf&quot; rel=&quot;noreferrer&quot;&gt;Netherland Dwarf&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The American Rabbit Breeders Association &lt;a href=&quot;https://www.arba.net/breeds.htm&quot; rel=&quot;noreferrer&quot;&gt;recognizes 47 different breeds&lt;/a&gt; of rabbit for shows and there are a number of breeds that are either not recognized or are being developed for acceptance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Breeders break the rabbits down by type of body, size, fur, and ear type.  Each breed is then broken down into Groups and Varieties.  It may be hard to believe but each of these rabbits share the same basic DNA.  Though interestingly some breeds will express the genes in manners that are often not the same visually.  &lt;/p&gt;&#xA;" OwnerUserId="3721" LastActivityDate="2013-06-03T17:36:20.650" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8640" PostTypeId="1" AcceptedAnswerId="8644" CreationDate="2013-06-03T20:03:34.787" Score="2" ViewCount="190" Body="&lt;p&gt;My understanding of evolution is that genetic mutation occurs in individual members of a species, and they become a new species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isn't a definition of species a group of genetically similar organisms that are pretty much exclusive in breeding ability?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wouldn't there have to be a male and female with the same genetic divergence at the same time to make a new species?  What is the popularly accepted mechanism for the splitting into a new species in organisms that require sexual reproduction?&lt;/p&gt;&#xA;" OwnerUserId="3722" LastActivityDate="2013-06-06T13:20:45.437" Title="Evolution after the development of sexual reproduction" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;reproduction&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8641" PostTypeId="1" AcceptedAnswerId="8642" CreationDate="2013-06-03T22:50:05.950" Score="1" ViewCount="332" Body="&lt;p&gt;I learned that the adrenal medulla releases epinephrine, which is a vasodilator of the vessels that lead to the skeletal muscle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also learned that somatic nervous system only uses Achetycholine as its hormone (not epinephrine).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also learned that the somatic nervous system controls skeletal muscle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, why is epinephrine not considered a part of the somatic nervous system hormones, if it is controlling the skeletal muscle? What is wrong here?&lt;/p&gt;&#xA;" OwnerUserId="3725" LastEditorUserId="806" LastEditDate="2013-06-03T23:30:38.890" LastActivityDate="2013-06-03T23:30:38.890" Title="Why is epinephrine not part of the somatic nervous system?" Tags="&lt;endocrinology&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8642" PostTypeId="2" ParentId="8641" CreationDate="2013-06-03T23:10:38.993" Score="2" Body="&lt;p&gt;You are confusing different functional systems. Epinephrine released by the adrenal medulla circulates in the blood and indeed dilates the blood vessels in skeletal muscle. This ensures that enough oxygen and nutrients are available for the muscles to perform in a fight/flight response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The somatic nervous system utilises acetylcholine not as a hormone but as a neurotransmitter. It is not released into the blood but only into the tiny (about 10nm wide) gap (synapse) between the nerve cell's axon terminal and the next nerve cell or muscle cell respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This release by the somatic nerve cells causes an electrical potential in the muscle which makes it contract.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In summary&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The somatic nervous system &lt;em&gt;controls&lt;/em&gt; the muscles because it stimulates the contraction which makes e.g. your arm move. Epinephrine released into the blood by the adrenal medulla serves to ensure the muscles have the blood supply they need in a stress response (e.g. a dangerous situation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Along with muscular blood vessel dilation, epinephrine in the blood for example also stimulates the heart to beat faster and stronger, and dampens down mechanisms involved in digestion - essentially it does everything necessary to allow a quick escape or a strong fight.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-06-03T23:10:38.993" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8644" PostTypeId="2" ParentId="8640" CreationDate="2013-06-04T02:42:29.447" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;My understanding of evolution is that genetic mutation occurs in individual members of a species, and they become a new species.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Isn't a definition of species a group of genetically similar organisms that are pretty much exclusive in breeding ability?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, &lt;strong&gt;no&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are correct in that the origin for any new species lies in mutations which occur in individuals and are then passed down through DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are misunderstanding that simply because a mutation &lt;em&gt;exists&lt;/em&gt; in an individual that they become a new species. Take &lt;a href=&quot;http://en.wikipedia.org/wiki/Lactose_intolerance#Lactase_persistence&quot; rel=&quot;nofollow&quot;&gt;Lactase Persistence&lt;/a&gt; as a widely studied example in humans. The majority of the world is lactose intolerant after they stop drinking their mother's milk, but a single point mutation results in the ability to consume dairy products into adulthood. It does not make people who are lactose tolerant a new &lt;em&gt;species&lt;/em&gt;, but it does open up a potential new nutrient source, which benefits the people who have it and thus it was passed down successfully over other variations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to that example, the definition of &quot;Species&quot; is &lt;strong&gt;NOT&lt;/strong&gt; exactly defined. There are many variations, including (but not limited to):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) A group of organisms that cannot interbreed &lt;em&gt;in the wild&lt;/em&gt;.&lt;br&gt;&#xA;2) A group of organisms with significantly different phenotypes (appearances).&lt;br&gt;&#xA;3) A group of organisms with sufficient* genetic divergence.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;*There is absolutely &lt;em&gt;no&lt;/em&gt; scientific consensus on how much genetic divergence is necessary to create a new species. We share &gt;95% of our genetics with Chimpanzees, so it's not much - it could be as little as a few key genes out of the entire genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So where you define the boundaries of species is up for grabs to some extent, but the most &lt;em&gt;common&lt;/em&gt; is what you delineated - when a member of one group cannot interbreed with another group.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Wouldn't there have to be a male and female with the same genetic divergence at the same time to make a new species?  What is the popularly accepted mechanism for the splitting into a new species in organisms that require sexual reproduction?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Nope. Assuming everything necessary for the gametes to produce fertile offspring is present (aka - the chromosomes aren't significantly altered and the gametes are compatible) then a new species emerges through successive generations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One mother or father gives their mutation to their children, which pass it on to their children, which pass it on to their children, etc. If the mutation is significantly advantageous it will allow the children with the mutation to better survive in the environment, and over time it could become the dominant phenotype that could lead to the creation of a new species as further mutations build in the new group - further differing the generations of the mother/father from the original group the mother/father were born into. Good examples are the &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_accelerated_regions&quot; rel=&quot;nofollow&quot;&gt;HAR - Human Accelerated Regions&lt;/a&gt; which are sets of genes that are pretty much the same throughout all other vertebrates, but startlingly different in humans. The HAR did not &lt;em&gt;create&lt;/em&gt; humans, but it's thought the mutations contributed greatly to our intelligence - which allowed &lt;em&gt;other&lt;/em&gt; mutations to be taken advantage of (like the humble opposable thumb) as our lifestyle changed due to the increased intelligence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all mutations need to be advantageous, though. There's lots of fuzzy areas. If a mutation isn't beneficial, but also isn't that detrimental, it can also stick around in a population. These mutations might not lead to the creation of new species, but can certainly contribute to genetic divergence.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-06-04T02:42:29.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8645" PostTypeId="2" ParentId="8600" CreationDate="2013-06-04T03:07:09.150" Score="6" Body="&lt;p&gt;I am not an ornithologist, but using identify.whatbird.com and a simple google search, this appears to be a Muscovy Duck. Try a google image search for yourself! Some of the birds pictured have more ostentatiously red or larger caruncles, but some look very similar to the birds you photographed. For example: &lt;a href=&quot;http://www.birdinginformation.com/birds/ducks/muskovy-duck/&quot;&gt;http://www.birdinginformation.com/birds/ducks/muskovy-duck/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From muscovyduckcentral.com and identify.whatbird.com:&#xA;The domestic breeds can come in a variety of colors, but are primarily black and white with red and white bills. The males are larger than the females -- around 15 lbs for a male and only 8 lbs for a female. Females are duller colored than the males. Muscovy ducks are indigenous to Mexico, Central and South America, but are now raised in many different locations. They are considered a good duck stock because they are large, breed quickly, provide good pest control, and are quieter than many other duck breeds.&lt;/p&gt;&#xA;" OwnerUserId="3723" LastEditorUserId="3723" LastEditDate="2013-06-04T03:29:09.227" LastActivityDate="2013-06-04T03:29:09.227" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8646" PostTypeId="1" CreationDate="2013-06-04T08:32:20.420" Score="2" ViewCount="1099" Body="&lt;p&gt;What would be effect on weight of individuals if we bring a fully adapted (to cold climate ) human individual and a fully adapted to very hot climate individual to a moderate climate region?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="806" LastEditDate="2013-06-05T10:57:27.853" LastActivityDate="2013-06-05T12:46:29.793" Title="How do changes in temperature affect body weight in humans?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8648" PostTypeId="1" AcceptedAnswerId="20090" CreationDate="2013-06-04T16:13:28.890" Score="7" ViewCount="252" Body="&lt;p&gt;I have heard that sharks excrete $\ce{Na+}$ and $\ce{Cl-}$ by their gill surfaces but divalent ions like magnesium are excreted through feces. What could be the reason behind this?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="6" LastEditDate="2013-06-05T16:31:42.167" LastActivityDate="2014-07-30T20:46:46.073" Title="Excretion of monovalent and divalent ions in sharks" Tags="&lt;biochemistry&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8649" PostTypeId="1" CreationDate="2013-06-04T17:23:52.893" Score="5" ViewCount="3411" Body="&lt;p&gt;I'm developing a cell-based assay in 96-well plates that requires adherent cells, as they need to be washed at least twice during the protocol. I'm using in-house strains of &lt;a href=&quot;https://www.atcc.org/Products/All/CCL-121.aspx&quot; rel=&quot;nofollow&quot;&gt;HT1080&lt;/a&gt; cells (some overexpressing a certain protein of interest) that unfortunately have been selected for suspension growth in chemically-defined media (50/50 &lt;a href=&quot;http://products.invitrogen.com/ivgn/product/10743011?ICID=search-product&quot; rel=&quot;nofollow&quot;&gt;CD-CHO&lt;/a&gt;/&lt;a href=&quot;https://products.invitrogen.com/ivgn/product/11913019?ICID=search-product&quot; rel=&quot;nofollow&quot;&gt;CD-293&lt;/a&gt;). I can convince them to adhere by culturing in &lt;a href=&quot;http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cell-Culture/Mammalian-Cell-Culture/Classical_Media/dmem.html&quot; rel=&quot;nofollow&quot;&gt;DMEM&lt;/a&gt; with 10% &lt;a href=&quot;http://products.invitrogen.com/ivgn/product/16000036?ICID=search-product&quot; rel=&quot;nofollow&quot;&gt;FBS&lt;/a&gt; and growing them in &lt;a href=&quot;http://www.corning.com/lifesciences/us_canada/en/technical_resources/surfaces/culture/corning_cellbind_polystyrene.aspx&quot; rel=&quot;nofollow&quot;&gt;CELLBind&lt;/a&gt; flasks, but they still tend to pull away if there is very much shearing force, such as during the wash steps, or when they're in PBS during the assay wash and incubation steps (maybe 2 hours total for now, I'm still optimizing that).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, the parameters of my experiments don't allow me to keep the cells in serum-containing media during the assay, as it would interfere with the uptake of my drug. Like I've said, when in PBS they start detaching, and I would assume the same in HBSS, which I don't really want to use anyway due to its low buffering capacity in CO&lt;sub&gt;2&lt;/sub&gt; incubators. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Might DMEM alone (without FBS) provide a little more impetus to stay attached during the assay? What would the effect be of increasing the amount of FBS to say 15 or 20% during culturing - would that promote stronger attachment? I'm a little hesitant to coat the wells with poly-&lt;em&gt;D&lt;/em&gt;-lysine, as my readout is on a fluorescent imager, and I'm worried it would substantially increase background. I don't really have enough time to re-select the cells for adherent growth (although if I'd known about these issues from my predecessor 3 or 4 months ago I would have started right away...), so are there any other tricks I can try in the meantime? Are there any media supplements I could use to promote adherin expression or something like that? Any tips or advice at all would be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2013-06-05T15:12:54.167" LastActivityDate="2014-05-05T14:53:29.203" Title="How to convince suspension cells to adhere more tightly?" Tags="&lt;cell-biology&gt;&lt;cell-culture&gt;&lt;fluorescent-microscopy&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8651" PostTypeId="1" AcceptedAnswerId="8654" CreationDate="2013-06-04T22:22:16.543" Score="4" ViewCount="230" Body="&lt;p&gt;I would like to grow mushrooms on oak trees I can harvest from my property.  I've read that the best results will be when the sap is rising but the tree hasn't budded yet.  The mycelium feeds on the sugars in the logs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would love to be able to measure the sugar content so I could accurately asses the sugar content.  Here in Southern Oregon the winters are mild and the leafing out of the oaks varies quite a bit from year to year.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can I measure sugar content of the sap in a tree?&lt;/p&gt;&#xA;" OwnerUserId="3731" LastActivityDate="2013-06-06T06:42:47.487" Title="Measuring sugar content of a tree" Tags="&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="8652" PostTypeId="2" ParentId="8649" CreationDate="2013-06-04T22:39:14.967" Score="3" Body="&lt;p&gt;My main concern here is why you are using suspension-culture selected cells for an adherent cell-based assay? Is it possible to obtain a clone of adherent HT1080? Depending on what you are assaying with your protein of interest, the cell biology may be altered changing from suspension/adherent culture systems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are my experiences using PC12 cells in culture, which are weakly adherent cells, with a preference to grow in clumps, rather than monolayers. I have found that these cells have a preference for specific tissue plastic; (without mentioning names), these cells will adhere on some poly-D-lysine coated plates while they won't adhere on others. I routinely perform immunofluorescence microscopy with these cells, and grow them on glass cover slips which I have skim-coated with rat tail type I collagen. This coating provides minor background in the green range and only when imaging close to the glass. With a bright fluorophore (e.g., AlexaFluor or cyanin dyes for fixed cell; enhanced GFP for live cells), this backgorund is not a problem for quantitative microscopy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, for secretion assays we use high-glucose DMEM supplemented with 1% dialyzed FBS. If memory serves, this retains all serum components less than ~15 kDa, which includes various growth factors. I have observed these cells continue to live for up to one day (and maybe longer?) in supplemented medium, while they die after a few hours without. This may also help with non-specific binding you may be worried about with drug addition.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-06-04T22:39:14.967" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8653" PostTypeId="1" CreationDate="2013-06-05T01:47:44.357" Score="1" ViewCount="481" Body="&lt;p&gt;I'm reading this &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood_pressure#Physiology&quot; rel=&quot;nofollow&quot;&gt;Wikipedia  article on blood pressure and its regulation&lt;/a&gt;, and it mentions that medulla is involved. however, I vaguely remember reading another article on Wikipedia and it mentioned that hypothalamus or hippocampus could be involved. So my question is - what other parts of the brain or neurotransmitters have significant effect on blood pressure regulation?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-06-05T01:47:44.357" Title="What parts of the brain are involved in regulating blood pressure in mammals?" Tags="&lt;human-biology&gt;&lt;circulatory-system&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8654" PostTypeId="2" ParentId="8651" CreationDate="2013-06-05T07:19:57.220" Score="2" Body="&lt;p&gt;The difficult step will be getting samples of sap: have a look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Maple_syrup&quot; rel=&quot;nofollow&quot;&gt;the WP page for maple syrup&lt;/a&gt; for ideas about methods of tapping into the xylem of your trees. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will then need to assay sucrose in the sample of sap. There are many commercial assay kits available (Google: sucrose assay), which rely on an enzyme, invertase, to convert the sucrose to glucose + fructose. The released glucose is then measured by a glucose oxidase assay. You would need some kind of colorimeter/spectrophotometer for quantitative results but there is a visible color change, so you could probably get a rough idea of what is going on by visual comparison with a set of glucose standards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Supplementary&lt;/strong&gt;&lt;br&gt;&#xA;An alternative would be to measure sugar concentration by refractometry: see &lt;a href=&quot;http://maple.dnr.cornell.edu/kids/refractometer.htm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/B000K312Q8&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-06-06T06:42:47.487" LastActivityDate="2013-06-06T06:42:47.487" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8655" PostTypeId="2" ParentId="8646" CreationDate="2013-06-05T12:46:29.793" Score="3" Body="&lt;p&gt;You would see moderate weight gain in &lt;em&gt;both&lt;/em&gt; subjects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since humans thermoregulate and aren't terribly &quot;adapted&quot; to any extreme for either very hot or very cold climates, anything outside of short range of temperatures will cause us to either sweat or shiver.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sweating or shivering will cost kcals (&quot;Calories&quot;, &quot;Joules&quot;), and the extra energy expenditure will keep the subjects' weights lower than they would otherwise be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once the subjects enter an environment where they no longer need to sweat, shiver, or basically maintain a wide gap between the outside temperature and their body temperatures (which is the real driver here - the difference between the two), they will no longer expend as much energy maintaining human body temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much energy are they saving? Not much. I wish I could find the article again, but you're talking an extra 50kcal or so an hour saved - or a few pounds until the energy required to maintain the extra weight reaches equilibrium with the energy saved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a few assumptions built into the above, which sees the question as more of a physics-oriented hypothetical than real-world example. In reality you have some large complications - getting anything done in cold temperatures is going to require a much larger energy expenditure, as you're usually carrying 30-50lbs of gear to not freeze to death, for example. A person used to wearing a dozen kilograms of animal furs during their weekly routine would gain a lot more weight than hypothesized above if they suddenly entered a mild climate with similar food intake, but without the constant load on their muscles.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-06-05T12:46:29.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8656" PostTypeId="1" AcceptedAnswerId="8668" CreationDate="2013-06-05T15:36:40.493" Score="3" ViewCount="305" Body="&lt;p&gt;In response to my &lt;a href=&quot;https://biology.stackexchange.com/q/8649/948&quot;&gt;previous question&lt;/a&gt;, I've been reading up a little bit on poly-&lt;em&gt;D&lt;/em&gt;-lysine, Collagen I, Collagen IV, laminin, and other tissue culture coatings that promote cell adhesion. I've always assumed that anything other than standard TC-treated plastic or glass would significantly increase background, but perhaps my views on background fluorescence are a little outdated. Does anybody have experience with these in a fluorescent microscopy/high-throughput screening environment?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically in my case, I'm looking at &lt;a href=&quot;http://en.wikipedia.org/wiki/Endocytosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;endocytosis&lt;/a&gt; and trafficking of a labeled protein into the &lt;a href=&quot;http://en.wikipedia.org/wiki/Lysosome&quot; rel=&quot;nofollow noreferrer&quot;&gt;lysosome&lt;/a&gt;. I'm labeling the protein with the pH-dependent dye &lt;a href=&quot;http://www.invitrogen.com/site/us/en/home/brands/Molecular-Probes/Key-Molecular-Probes-Products/pHrodo-indicators.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;pHrodo&lt;sup&gt;TM&lt;/sup&gt;&lt;/a&gt; from Molecular Probes, which supposedly has very little fluorescence at neutral pH, but becomes very bright as the pH drops when endocytic vesicles become lysosomes. This theoretically means that a final wash step is not needed, but with a matrix coating on the plates I'm worried about background.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what is the current thinking as far as background fluorescence of the various TC matrices is concerned? Does the background come from the matrix itself, or by the fluorescent dye becoming adsorbed to it? Is it wavelength-dependent? Fortunately I may not be stuck with my poorly-adhering cells, and I may not need supplemental matrix at all in the end, but I still want a better understanding of how it works.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2013-06-06T16:13:16.410" Title="How do different tissue culture matrices affect background in fluorescent microscopy?" Tags="&lt;cell-biology&gt;&lt;lab-techniques&gt;&lt;cell-culture&gt;&lt;lab-reagents&gt;&lt;fluorescent-microscopy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8657" PostTypeId="2" ParentId="8628" CreationDate="2013-06-05T17:52:16.467" Score="2" Body="&lt;p&gt;Given the prevalance of myopia in humans I would have thought that facial recognition was secondary to other indicators such as gait recognition which is also unique to individuals though can be copied to an extent. Voice and shape are also used to identify people. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Being able to recognise individuals would allow the formation of groups, allow for structures of trust, reciprocal altruism to develop as well as punishing transgressors. Repeat interactions with other people require some kind of identification, but I dunno if facial recognition is the only/primary one. &lt;/p&gt;&#xA;" OwnerUserId="476" LastActivityDate="2013-06-05T17:52:16.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8659" PostTypeId="1" AcceptedAnswerId="8662" CreationDate="2013-06-05T19:40:07.500" Score="4" ViewCount="3187" Body="&lt;p&gt;One lab I was in was paranoid about keeping it in a foil-wrapped conical tube; my current lab leaves it out on the bench (and it works fine for staining gels). It's the same company/concentration in both cases, but this second lab uses it up much faster.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-06-09T07:30:56.410" Title="Just how light-sensitive is ethidium bromide?" Tags="&lt;molecular-biology&gt;&lt;gel-electrophoresis&gt;&lt;lab-reagents&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8660" PostTypeId="1" CreationDate="2013-06-05T21:33:33.503" Score="2" ViewCount="95" Body="&lt;p&gt;I want to experimentally look at the behavior of antibodies. To do so, I need to be able to bind these antibodies to a substrate.&lt;/p&gt;&#xA;&lt;p&gt;Eventually, I want to study the specificity of antibodies to know to what substrates they bind. After that, I want to study the biological activity of the antibody over time.&lt;/p&gt;&#xA;&lt;p&gt;But my question is more basic, namely: to what material do antibodies bind non-specifically? It's not about antigens at this stage, it's just about non-specific binding of antibodies to a carrier material. Also of interest would be howw to get the antibodies of that carrier again.&lt;/p&gt;&#xA;" OwnerUserId="3737" LastEditorUserId="9943" LastEditDate="2020-08-27T10:01:15.827" LastActivityDate="2020-08-27T10:01:15.827" Title="How to bind antibodies to study their properties?" Tags="&lt;proteins&gt;&lt;protein-binding&gt;&lt;antibody&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="8661" PostTypeId="2" ParentId="8618" CreationDate="2013-06-05T23:39:15.050" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;But are there ways to tell the body that this allergy is safe and there is no need to amount a response to it?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, that's what allergy shots (Exposure Therapy) does. Exposure Therapy is an effective, albeit sometimes imperfect, method of letting the body know that a substance is common and that it shouldn't mount a response to it. Over time the body re-calibrates itself to accept the allergen, although in some cases it's never fully accepted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A complete &quot;cure&quot; can be attained via allergy shots, but the extent of the therapy's success will rely almost exclusively on the individual's immune system. Some people can be cured completely, others will never be cured.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If not, why not?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There will probably not be a general &quot;allergy&quot; cure anytime soon because we're still not 100% sure why the body responds in such an overprotective matter sometimes and not others. Even if we fully understood at some point, there are many ways which the immune system can go awry that result in allergies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There isn't a single, double, or triple point of failure along the line - just about any immune cell, whether Mast, Eisonophile, T-Cell, T-Reg, B-Cell, etc. can misidentify a substance and contribute to an allergic reaction (although some are more likely candidates than others). More than that, just about &lt;strong&gt;any&lt;/strong&gt; substance can become an allergen for people. There's a well-studied case of a woman who became allergic to Copper because of repeated exposure via an early version of IUD that she had implanted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So with nearly every immune cell capable of mounting a response, and nearly anything in the world capable of provoking a response, the best route - at least thus far - has been repeated, increasing exposures to teach the body what is &quot;OK&quot; and what isn't. The absolute best way to avoid allergies later in life is to simply promote outdoor playtime and a widely variable diet to children while the immune system is operating at peak efficiency and learning capability. &lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-06-05T23:39:15.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8662" PostTypeId="2" ParentId="8659" CreationDate="2013-06-05T23:44:50.283" Score="3" Body="&lt;p&gt;Good question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this reference in &quot;&lt;a href=&quot;http://books.google.com/books?id=PND76ZPTuXUC&amp;amp;pg=PA85&amp;amp;lpg=PA85&amp;amp;dq=ethidium%20bromide%20photobleaching&amp;amp;source=bl&amp;amp;ots=rz8SAHMknF&amp;amp;sig=m-kJFB5HJ1GNBIffBZYvLG1NTWU&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=xMmvUYuiBpHxiQLqhoBA&amp;amp;ved=0CGgQ6AEwBg#v=onepage&amp;amp;q=ethidium%20bromide%20photobleaching&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Molecular Biology: A Project Approach&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A phenomenon called photobleaching occurs when ethidium bromide (EtBr) -stained DNA is illuminated by ultraviolet light.... This decreased fluorescence is presumably due to the dissociation of ethidium bromide from the DNA. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ethidium_bromide#Structure.2C_chemistry.2C_fluorescence&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ethidium bromide fluoresces when it is in a hydrophobic environment&lt;/a&gt;, such as when its stuck between two base pair stacks in DNA- water quenches its fluorescence.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also found &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0920586107004099&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt; citing the fact that sunlight can break down EtBr but only when a catalyst of iron and titanium dioxide is there to catalyze the reaction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lot of the original characterization of EtBr as a stain is very old, so I couldn't access it directly online... It looks like the compound itself is pretty stable, but UV can, somehow interact with it when its bound to DNA to bleach it out.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PkkuT.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-06-06T05:22:51.290" LastActivityDate="2013-06-06T05:22:51.290" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8663" PostTypeId="1" CreationDate="2013-06-06T07:53:23.750" Score="3" ViewCount="176" Body="&lt;p&gt;Recent results from J Lee Nelson and colleagues (&lt;a href=&quot;http://www.sciamdigital.com/index.cfm?fa=Products.ViewIssuePreview&amp;amp;ARTICLEID_CHAR=6AB777F9-3048-8A5E-10312400AC68A14A&quot; rel=&quot;nofollow&quot;&gt;Sci Am. 2008 Feb;298(2):64-71&lt;/a&gt;; available as full text through Google) show that cells from the mother were found in a person aged 46. Logically, these cells should be stem cells, as any other cells would die in such a long period of time.&#xA;So, what stem cells could be transferred from mother to fetus?&#xA;Why doesn't the immune system reject those cells?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="69" LastEditDate="2013-06-06T18:51:55.867" LastActivityDate="2018-02-25T10:55:59.650" Title="Movement of stem cells from mother to fetus" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;stem-cells&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="8664" PostTypeId="2" ParentId="8660" CreationDate="2013-06-06T09:23:12.663" Score="3" Body="&lt;p&gt;Like any other protein, antibodies will aspecifically bind nitrocellulose or PVDF membranes, but any other protein present in your antibody preparation will also do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending on the antibody class, more specific binding can be obtained with protein A or protein G, that recognize the Fc domain. It's usual to have protein A/G immobilized on a stationary phase like agarose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you know the antigen used to develop the antibody, you can also use the immunizing peptide crosslinked to CnBr activated sepharose as a probe to bind your antibodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Knowing something more about your antibody preparation and what exactly is the 'behavior' your want to study could help obtain better answers.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2013-06-06T09:23:12.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8665" PostTypeId="2" ParentId="239" CreationDate="2013-06-06T11:21:11.270" Score="5" Body="&lt;p&gt;Relating to your last comment on random fluctuations in survival, a recent theoretical paper by &lt;a href=&quot;http://www.jstor.org/stable/10.1086/658344&quot;&gt;Lee et al. 2011&lt;/a&gt; studies the effect of mating systems on demographic stochasticity in small population. No empirical data there though. Their main conclusion is that polygyny (in relation with sex ratio) can lead to high demographic variance, therefore lowering stochastic population growth rate and increasing extinction risk. The general effect is known as &lt;em&gt;demographic stochasticity&lt;/em&gt;, a sampling effect leading to random variation in realized demographic rates due to small population size.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2013-06-06T11:21:11.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8666" PostTypeId="2" ParentId="8640" CreationDate="2013-06-06T11:49:02.820" Score="2" Body="&lt;p&gt;It should also be added that &lt;a href=&quot;https://en.wikipedia.org/wiki/Allopatric_speciation&quot; rel=&quot;nofollow&quot;&gt;allopatric speciation&lt;/a&gt; is arguably the most common form of speciation (compared to &lt;a href=&quot;https://en.wikipedia.org/wiki/Sympatric_speciation&quot; rel=&quot;nofollow&quot;&gt;sympatric speciation&lt;/a&gt;). This means that, often, the only thing needed for speciation is lack of gene flow, time and genetic drift. Add to that the different selection pressures at different locations. However, the different mechanisms of allopatric, sympatric and parapatric speciation are probably better seen as a continuum (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18522915&quot; rel=&quot;nofollow&quot; title=&quot;Butlin RK, Galindo J, Grahame JW.. 2008. Sympatric, parapatric or allopatric: the most important way to classify speciation? Phil. Trans. R. Soc. B 363(1506): 2997-3007&quot;&gt;Butlin et al. 2008&lt;/a&gt;). Generally, speciation is a gradual and incremental process, even though distinct mutations can sometimes surely be important. For a review on the genetics of speciation see &lt;a href=&quot;http://www.nature.com/nrg/journal/v7/n11/full/nrg1968.html&quot; rel=&quot;nofollow&quot; title=&quot;Mohamed Noor &amp;amp; Jeffrey L. Feder. 2006. Speciation genetics: evolving approaches. Nature Reviews Genetics 7: 851-861&quot;&gt;Noor &amp;amp; Feder (2006)&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-06-06T13:20:45.437" LastActivityDate="2013-06-06T13:20:45.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8667" PostTypeId="1" AcceptedAnswerId="8678" CreationDate="2013-06-06T14:45:02.573" Score="2" ViewCount="146" Body="&lt;p&gt;This is for a short story idea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to modify the DNA of a child to make their metabolism more susceptible (physical response, addiction, etc) to a certain type of chemical i.e. a chemical present in a fictional food. The idea being that their DNA is modified when in the womb (or before) and when they grow older (think teenager) they become addicted to said product.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This could be before conception, during pregnancy or after birth. What ways, in the future, could we go about doing this? Maybe chemical mutagens (&lt;a href=&quot;http://en.wikipedia.org/wiki/Mutagen&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Mutagen&lt;/a&gt;) or site-directed mutagenesis (&lt;a href=&quot;http://en.wikipedia.org/wiki/Site-directed_mutagenesis&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Site-directed_mutagenesis&lt;/a&gt;)? Gene therapy?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is there a way to alter the regulation of the physiological processes in the human body to make someone become easily addicted to a particular product?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking to have this aspect of the story as scientifically accurate as possible so I can examine the ethical questions around it within the story.&lt;/p&gt;&#xA;" OwnerUserId="3743" LastEditorUserId="1590" LastEditDate="2013-07-16T13:16:30.897" LastActivityDate="2016-10-12T07:41:29.240" Title="Prenatal Marketing" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;molecular-genetics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8668" PostTypeId="2" ParentId="8656" CreationDate="2013-06-06T16:13:16.410" Score="3" Body="&lt;p&gt;Extracellular matrix (ECM) fluoresces, especially Collagen and Laminin. The maximum is in the DAPI and FITC channels and the fluorescence becomes weaker towards longer wavelengths. However, since the coat on the TC flasks is very thin, I would not expect this to be a problem. The best thing is just to try it. There is also a quite famous document available which might be of help:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.uhnresearch.ca/facilities/wcif/PDF/Autofluorescence.pdf&quot; rel=&quot;nofollow&quot;&gt;Autofluorescence: Causes and Cures&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="852" LastActivityDate="2013-06-06T16:13:16.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8670" PostTypeId="2" ParentId="8364" CreationDate="2013-06-06T16:47:21.737" Score="2" Body="&lt;p&gt;Calories and dollars are the most obvious and straightforward, but including additional variables complicates the accounting. . A great paper that used &lt;a href=&quot;http://dx.doi.org/10.1126/science.184.4134.307&quot; rel=&quot;nofollow&quot;&gt;energy&lt;/a&gt; has been updated in a &lt;a href=&quot;http://dusp.mit.edu/sites/all/files/attachments/project/Energy_in_Food_System.pdf&quot; rel=&quot;nofollow&quot;&gt;more recent publication&lt;/a&gt;. &lt;a href=&quot;http://en.wikipedia.org/wiki/Emergy&quot; rel=&quot;nofollow&quot;&gt;Emergy&lt;/a&gt; is an interesting alternative. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Current work includes the &lt;a href=&quot;http://www.naturalcapitalproject.org/&quot; rel=&quot;nofollow&quot;&gt;Natural Captial project&lt;/a&gt; that &quot;aims to integrate the values of nature into all major decisions affecting the environment and human well-being&quot;. Of course, this approach exchanges a simple currency for a more comprehensive one. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nclimate/journal/v2/n3/full/nclimate1346.html&quot; rel=&quot;nofollow&quot;&gt;Climate regulating value&lt;/a&gt; is also a relatively straightforward and relevant currency that can be used to compare the value of food production systems.&lt;/p&gt;&#xA;" OwnerUserId="222" LastActivityDate="2013-06-06T16:47:21.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8672" PostTypeId="1" AcceptedAnswerId="8676" CreationDate="2013-06-06T21:58:23.643" Score="7" ViewCount="98" Body="&lt;p&gt;I know that lipids are carried around the body in the blood either as micelles or by lipid-binding proteins which allow them to be solved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lipids can't always be integrated in a membrane though, the phospholipids used in membranes have to be synthesised somewhere from a precursor which will also by hydrophobic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consequently, at some point there will have to be transport of lipids within the cell where the lipids will need to be in solution. How is this facilitated?&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-06-07T06:33:03.660" Title="Intracellular lipid transport" Tags="&lt;cell-biology&gt;&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8674" PostTypeId="2" ParentId="8667" CreationDate="2013-06-07T05:36:51.913" Score="4" Body="&lt;p&gt;As fiction this is a reasonable premise, but at this point you are talking about what is called Gene Therapy - intentionally modifying or adding the sequence of a functional gene to change a deficiency of the subject. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gene therapy is a persistent goal of research, but it has only recent been executed - changing the DNA of cells in a living human being.  There have been some scary and unpredictable side effects of gene therapy.  In the &lt;a href=&quot;http://www.nytimes.com/1999/11/28/magazine/the-biotech-death-of-jesse-gelsinger.html?pagewanted=all&amp;amp;src=pm&quot; rel=&quot;nofollow&quot;&gt;mid 1990s an 18 year old boy&lt;/a&gt; developed multiple organ failure as the result of gene therapy to cure a genetic digestive deficiency. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJM200301163480314&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; describes a retrovirally mediated gene therapy to treat X-linked severe combined immunodeficiency (SCID) in 2003.   SCID patients (also known as bubble boy disease) have a single defective gene (yc) on their one X chromosome and the varicella–zoster virus infection inserted a functional copy into the patients.  Three of the four subjects responded well and at 3 years seemed to be effectively cured, but a fourth developed acute lymphocytic leukemia.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the gene therapy projects continue to happen in mice, &lt;a href=&quot;http://www.nature.com/news/2011/110824/full/news.2011.500.html&quot; rel=&quot;nofollow&quot;&gt;but there has been&lt;/a&gt; some &lt;a href=&quot;http://blogs.nature.com/news/2011/12/gene_therapy_success_for_haemo.html&quot; rel=&quot;nofollow&quot;&gt;encouraging progress recently&lt;/a&gt;, the devil is in the details as to how gene therapy would work. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedaily.com/news/health_medicine/gene_therapy/&quot; rel=&quot;nofollow&quot;&gt;Here is a decent feed&lt;/a&gt; of gene therapy goings on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If and when gene therapy is safe and precise enough to use, then it could change a lot of characteristics in human beings - just about anything that genes do could be modified or modulated. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-06-07T05:36:51.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8675" PostTypeId="2" ParentId="8382" CreationDate="2013-06-07T06:05:31.823" Score="2" Body="&lt;p&gt;LIFE : The Science of Biology by Sadava &amp;amp; Hills &amp;amp; Hellar &amp;amp; Berenbaum&lt;/p&gt;&#xA;" OwnerUserId="3665" LastActivityDate="2013-06-07T06:05:31.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8676" PostTypeId="2" ParentId="8672" CreationDate="2013-06-07T06:33:03.660" Score="5" Body="&lt;p&gt;Like in the blood, intracellular lipid trafficking is facilitated by vesicular transport and lipid carriers like &lt;a href=&quot;http://en.wikipedia.org/wiki/Fatty_acid-binding_protein&quot;&gt;fatty acid binding proteins&lt;/a&gt;. In addition, intracellular membranes are densely packed and they can exchange lipids by collision and transient hemifusion. If you have access to Cell, a good review is from &lt;a href=&quot;http://dx.doi.org/10.1016/j.cell.2010.11.031&quot;&gt;Prinz W. 2010 Lipid Trafficking sans vesicles, Where, Why, How?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2013-06-07T06:33:03.660" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8678" PostTypeId="2" ParentId="8667" CreationDate="2013-06-07T09:09:14.560" Score="1" Body="&lt;p&gt;To extend with a theoretical way such a method might be possible (though I really hope this will never work or be done!) This is essentially a gene-therapy approach.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Are you talking about psychological addiction (needing it to avoid running crazy), or physical dependence (needing it to avoid health complications)? The latter could be achieved in a cruel way for example by engineering vital genes of enzymes involved in cell metabolism in such a way that they require your substance of choice as a cofactor to work. The former would first require the identification of some genetic basis of psychological addiction. Though for science fiction you could stay vague (because scientific knowledge is vague) and say that the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22640768&quot; rel=&quot;nofollow&quot;&gt;metabolism of their substance&lt;/a&gt; is genetically modified in such a way that it overstimulates reward pathways. This would not make them addicted, but rather susceptible to addiction after little exposure.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;One of these methods will require altering an existing gene, the other may require inserting a new gene for a new enzyme, or altering the gene of an existing enzyme. The modification will have to be made at the very earliest stages of embryonic development to ensure that all cells carry the modification later. If &lt;a href=&quot;http://en.wikipedia.org/wiki/In_vitro_fertilisation&quot; rel=&quot;nofollow&quot;&gt;in-vitro fertilisation&lt;/a&gt; is performed, this can be done before inserting the embryo into the mother's womb. In a normal pergnancy, there is a problem as the developing embryo does not become accessible from the mother's blood vessels until several days into development, when there is already a considerable number of cells. You could claim that a virus was modified in a way that it would be able to cross endometrial tissue and enter the embryo. If you want to go more &quot;fancy&quot; high-tech (even though successfully engineering such a virus would already be very high-tech), they could use a &lt;a href=&quot;http://en.wikipedia.org/wiki/Nanoparticle&quot; rel=&quot;nofollow&quot;&gt;nanoparticle&lt;/a&gt;, for example made of silicon, gold, or pure &lt;a href=&quot;https://en.wikipedia.org/wiki/Fullerene&quot; rel=&quot;nofollow&quot;&gt;carbon&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Whichever method you choose, they could use said delivery method to carry a short stretch of DNA with the desired gene and machinery to &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_recombination&quot; rel=&quot;nofollow&quot;&gt;recombine&lt;/a&gt; it into the embryonic cells' genomes, either exchanging the old gene for a new, engineered one, or simple inserting their own gene.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;As for how they manufactured their own new gene or version of a gene, this could be achieved by site-directed mutagenesis&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-06-07T13:07:24.617" LastActivityDate="2013-06-07T13:07:24.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8679" PostTypeId="1" CreationDate="2013-06-07T12:36:51.143" Score="2" ViewCount="2105" Body="&lt;p&gt;I've been asked: how does BLAST improve dynamic programming accuracy?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do know that BLAST is based on heuristic approach that approximates the Smith-Waterman algorithm and that the Smith-Waterman is too slow for large databases but more accurate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone settle my conflict?&lt;/p&gt;&#xA;" OwnerUserId="3739" LastEditorUserId="107" LastEditDate="2013-06-07T13:36:06.950" LastActivityDate="2013-06-08T20:18:59.500" Title="Comparing BLAST and the Smith-Waterman algorithm" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8680" PostTypeId="1" CreationDate="2013-06-07T13:10:11.543" Score="5" ViewCount="84" Body="&lt;p&gt;Alternative splicing can shuffle the exon order and select from the exon sequence of a single gene site to provide a combinatorial selection of possible transcription products from the one gene. Can intergenic trans splicing can do this starting from multiple gene sites?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What regulates these two &quot;non linear&quot; gene combination, transcript-splicing processes?&lt;/p&gt;&#xA;" OwnerUserId="3749" LastEditorUserId="107" LastEditDate="2013-06-07T13:34:58.930" LastActivityDate="2013-06-10T07:45:40.947" Title="What regulates these two methods of splicing?" Tags="&lt;gene-regulation&gt;&lt;splicing&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8682" PostTypeId="1" CreationDate="2013-06-07T15:07:08.843" Score="3" ViewCount="4216" Body="&lt;p&gt;&lt;strong&gt;As far as we know Ape Men or the Neanderthal Man was the first to bury its dead&lt;/strong&gt;. My question is why.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think they practiced religion or believed in spirits or faith or stuff like that. Therefore what was their main reason to bury their dead in the first place?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Also correct me if I'm wrong but i think that religion only emerged after &lt;em&gt;Homo sapiens&lt;/em&gt; came to be.)&lt;/p&gt;&#xA;" OwnerUserId="3660" LastEditorUserId="107" LastEditDate="2013-06-08T16:06:17.810" LastActivityDate="2016-01-18T08:51:08.053" Title="Why do humans bury their dead?" Tags="&lt;evolution&gt;&lt;death&gt;&lt;anthropology&gt;" AnswerCount="2" CommentCount="5" ClosedDate="2016-01-19T17:12:20.147" ContentLicense="CC BY-SA 3.0" />
  <row Id="8684" PostTypeId="1" AcceptedAnswerId="8691" CreationDate="2013-06-08T03:42:58.450" Score="6" ViewCount="1158" Body="&lt;p&gt;I always wonder about the capability of diversity of our antibodies. Do we have enough antibodies to fit to every kind of molecule? Wont't it be easier if our antibodies are like clay and can be molded to any form by antigens? Why to waste energy producing so many types of antibodies? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If some pathogen makes its antigens just like antibodies of our body, (I think) they won't ever be detected. So what would our body do?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2013-06-08T20:34:55.450" LastActivityDate="2014-02-12T14:28:43.750" Title="Do we have enough diversity of antibodies to overcome almost any antigen?" Tags="&lt;immunology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8685" PostTypeId="1" AcceptedAnswerId="8693" CreationDate="2013-06-08T04:16:25.390" Score="4" ViewCount="1378" Body="&lt;p&gt;What decides whether an activated B cell will get converted to plasma cell or memory B cell? Is it necessary that out of a mitotic division one will convert to memory B cell and the other to plasma cell?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2013-06-08T20:38:38.777" LastActivityDate="2013-06-08T20:38:38.777" Title="Plasma cells and memory cells" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8686" PostTypeId="2" ParentId="8684" CreationDate="2013-06-08T04:18:20.267" Score="2" Body="&lt;p&gt;The structure of a protein is largely dependent on what it is supposed to do. There is a little bit of wiggle room, but essentially, major changes in structure will also change the function of the protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is why it would be difficult (though not entirely impossible) for a pathogen to successfully change all its surface antigens into close-enough mimics of the host antigens that the host immune response is completely evaded. Antibody &lt;a href=&quot;https://en.wikipedia.org/wiki/Complementarity_determining_region&quot; rel=&quot;nofollow&quot;&gt;CDRs&lt;/a&gt; are extremely sensitive, and a change in even a single amino acid of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Epitope&quot; rel=&quot;nofollow&quot;&gt;epitope&lt;/a&gt; is often sufficient to trigger a full-blown immune response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, antibodies are only one of the many mechanisms (albeit a very important one) by which the immune system detects and eliminates invading pathogens, so even in the case of failure of the antibody system, T-cells and the innate immune system &lt;em&gt;should&lt;/em&gt; generally be sufficient to initiate an immune response. &lt;/p&gt;&#xA;" OwnerUserId="3631" LastActivityDate="2013-06-08T04:18:20.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8687" PostTypeId="1" CreationDate="2013-06-08T08:04:36.347" Score="5" ViewCount="4232" Body="&lt;p&gt;I do combat sports, and in these sports there are a lot of hits that can cause bruising.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've found that, over time, physical conditioning can reduce and/or eliminate the bruising to the point where even after hard impacts, there is no residual bruising.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I was under the impression that it is not possible to &quot;condition&quot; for reduced bruising since bruising is the result of ruptured capillaries, and you can't condition to not rupture blood vessels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone offer an explanation to why, with conditioning, it is possible to reduce/eliminate bruising?&lt;/p&gt;&#xA;" OwnerUserId="3750" LastActivityDate="2019-12-19T00:05:38.300" Title="Is it possible to condition the body to reduce bruising?" Tags="&lt;hematology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8688" PostTypeId="1" AcceptedAnswerId="8715" CreationDate="2013-06-08T08:50:09.720" Score="1" ViewCount="58" Body="&lt;p&gt;I would like to learn about how the process of cloning works in nature - how are twins &quot;created&quot; after fertilization what genetic changes can occur in each of the twins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where should I start? What are some interesting books on the topic, as well as recent research papers (or just the most important research topics that I could use to start looking for more information)?&lt;/p&gt;&#xA;" OwnerUserId="3751" LastActivityDate="2013-07-10T00:56:33.257" Title="How can I learn about how cloning works in nature (twins)?" Tags="&lt;cloning&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8689" PostTypeId="1" AcceptedAnswerId="8690" CreationDate="2013-06-08T09:13:24.087" Score="7" ViewCount="230" Body="&lt;p&gt;I was watching a lecture by Richard Dawkins earlier today and he mentioned that “Your 185th million grandfather was a fish.” I started wondering about the following question,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is it true that my 185th million grandfather is the same as your 185th million grandfather?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I fully recognize that there are more generations in my family tree than in yours or vice-versa so the 185 million may not match up exactly. This is not the point of the question. Do Humans share a common ancestor substantially after the origin of life?&lt;/p&gt;&#xA;" OwnerUserId="3752" LastEditorDisplayName="user560" LastEditDate="2013-06-08T12:15:25.830" LastActivityDate="2013-06-08T12:15:25.830" Title="Same 185th million grandfather?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8690" PostTypeId="2" ParentId="8689" CreationDate="2013-06-08T11:36:48.617" Score="6" Body="&lt;p&gt;All currently existent forms of life (and all their ancestors) are thought to be descended from a single life form known as &lt;a href=&quot;https://en.wikipedia.org/wiki/Last_universal_ancestor&quot;&gt;LUCA&lt;/a&gt; (Last Universal Common Ancestor). Within those organisms, all organisms that share a common ancestor more recent than LUCA are said to be &lt;a href=&quot;https://en.wikipedia.org/wiki/Phylogenetics&quot;&gt;phylogenetically&lt;/a&gt; related. These organisms are (ideally - see note) grouped together by &lt;a href=&quot;https://en.wikipedia.org/wiki/Taxonomy&quot;&gt;scientists&lt;/a&gt; into &lt;a href=&quot;https://en.wikipedia.org/wiki/Monophyletic&quot;&gt;monophyletic&lt;/a&gt; &lt;a href=&quot;https://en.wikipedia.org/wiki/Taxon&quot;&gt;taxa&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, ideally, each taxon represents a group of organisms that have descended from a single common ancestor, not shared by any other taxon. Taxa are defined at various levels including, but not limited to, &lt;em&gt;Kingdom&lt;/em&gt;, &lt;em&gt;Phylum&lt;/em&gt;, &lt;em&gt;Class&lt;/em&gt;, &lt;em&gt;Order&lt;/em&gt;, &lt;em&gt;Family&lt;/em&gt;, &lt;em&gt;Genus&lt;/em&gt; and &lt;em&gt;Species&lt;/em&gt;, with organisms at each level having a more recent common ancestor than the ones preceding it. For example, for humans, a superficial phylogenetic classification would look somewhat like this:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Kingdom: &lt;em&gt;Animalia&lt;/em&gt; (shares a common ancestor with all multicellular, eukaryotic, heterotrphic, motile organisms)&lt;/li&gt;&#xA;&lt;li&gt;Phylum: &lt;em&gt;Chordata&lt;/em&gt; (shares a common ancestor with all animals that possess a spinal cord)&lt;/li&gt;&#xA;&lt;li&gt;Class: &lt;em&gt;Mammalia&lt;/em&gt; (shares a common ancestor with all chordates that produce milk and are warm-blooded)&lt;/li&gt;&#xA;&lt;li&gt;Order: &lt;em&gt;Primates&lt;/em&gt; (shares a common ancestor with all monkey-like mammals)&lt;/li&gt;&#xA;&lt;li&gt;Family: &lt;em&gt;Hominidae&lt;/em&gt; (shares a common ancestor with all the great apes)&lt;/li&gt;&#xA;&lt;li&gt;Genus: &lt;em&gt;Homo&lt;/em&gt; (shares a common ancestor with relatively recent humanoid species)&lt;/li&gt;&#xA;&lt;li&gt;Species: &lt;em&gt;sapiens&lt;/em&gt; (shares a common ancestor with all humans)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;As you can see, this means that all humans share a common ancestor with all other humans, but going further back, they also share a common ancestor with all primates, all mammmals and all vertebrates. Eventually, all animals share a common ancestor, and if you go as far back as LUCA, so does all life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note on taxonomy and phylogenetics:&lt;/strong&gt; Many modern taxa are (to the best of our knowledge) &lt;a href=&quot;https://en.wikipedia.org/wiki/Monophyletic&quot;&gt;monophyletic&lt;/a&gt;, meaning &lt;em&gt;all&lt;/em&gt; organisms in a given taxon share a &lt;em&gt;unique&lt;/em&gt; common ancestor. However, there remain several taxa that are &lt;a href=&quot;https://en.wikipedia.org/wiki/Paraphyly&quot;&gt;paraphyletic&lt;/a&gt;, because they were described before modern genetic methods became available, or because no one has got down to reclassifying them or (in at least one case, reptiles and birds), because they are so widely used that changing the classification could (and probably would) cause a lot of confusion. So, when using taxonomic classifications to deduce phylogenetic relationships, a bit of caution must be exercised to ensure that the taxon one is talking about is indeed monophyletic.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastEditorUserId="3631" LastEditDate="2013-06-08T12:02:23.100" LastActivityDate="2013-06-08T12:02:23.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8691" PostTypeId="2" ParentId="8684" CreationDate="2013-06-08T13:18:44.493" Score="6" Body="&lt;p&gt;As my answer is quite big I've highlighted the different regions I answer your question.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Intro and basic info&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I take it you know how antibodies are made, but as a quick recap they're made by VDJ recombination of a limited but still quite numerous pool of genes which are recombined randomly, and then further recombination occurs by hypermutation of certain segments particularly in the regions that identify antigens. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;What is Hypermutation?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Hypermutation&lt;/strong&gt; occurs after the original antibody is made in order to perfect it. The same mechanism I talk about in moulding antigens below. It is exactly what it says: a high rate of mutation compared to that of the low rate in cells normally. When B cells are activated because they've met their antigen to which they respond (&lt;strong&gt;cognate antigen&lt;/strong&gt;), they undergo somatic hypermutation. While the B cells undergo somatic hypermutation, the genes which code for the antibody are mutated so that the antibody binds to its cognate antigen with a different specificity. If it binds better the B cell gets to live, if it doesn't bind or it is worse then the B cell dies.   &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Moulding antigens&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;What we cannot do is the other way around. We can't recognise an antigen and then make an antibody to it, because recognising the antigen requires an antibody. What we can do is once we've recognised the antigen, then mould the antibody so it is a better fit. How we do this is by B cells mutating their antibodies and competing which binds better. However, B cells just don't have the knowledge to see an antigen and think a tyrosine residue at this position will be perfect to change my shape to this configuration - that's really complex stuff!&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Do antibodies recognise every molecule?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Antibodies are made to essentially every antigen which is very costly in terms of energy as you mentioned. In fact, the number of genes that make antibodies are thought to be the perfect amount as to protect us without being too numerous so that it is not only too costly, but we have so many different antibodies the chance of ever finding the right B cell is so low we die before we manage. This is because of the way antibodies are mass produced, in the typical pathway of new antigens, firstly a T cell must recognise the antigen then B cells that produce an antibody that binds to the antigen (rarely in the same region, and may not even be to a protein antigen). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So these two paragraphs highlight the limitations and answer your first question. Antibodies are so diverse that we can expect quite a few to recognise every pathogen, but not every single possible antigen will have a cognate antibody. Diversity without so much diversity that it becomes redundant. The second limitation is that antibodies will ideally not form if they recognise self (our own proteins etc.) Which leads on to your next question. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;What if a pathogen makes antigens that look like our own proteins?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Autoantibodies are made but are typically non-pathogenic (i.e., they don't cause harm). Certain HLA/MHC polymorphisms that make us likely to form autoreactive T cells, also make us make autoreactive antibodies. Interestingly, this increases our risk of autoimmune diabetes but ALSO makes us more resistant to infection by HIV. This can be practically seen in the DQ8 polymorphism. This is a perfect example to illustrate the answer to your second question. Ideally, pathogens which have antigens similar to our own would not be detected. HIV wraps itself with an envelope of our own lipid membrane for this purpose, and the best neutralising antibodies are often self-reactive and therefore are those that failed elimination. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However even these pathogens are going to do something or make something that isn't something our cells usually do. This is how the body finds and targets cancer cells (in a way), they do things our own cells won't typically do like make the wrong proteins or wrong amounts etc. Thus cancer cells and pathogens can be targeted by our cells that find something that isn't self (CD8 cytotoxic/killer T cells). As for pathogens, we all make MHC/HLA which is unique to us and pathogens could never manage to invade and make the specific HLA/MHC that we do, so our body also targets missing HLA/MHC. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="5427" LastEditDate="2014-02-12T14:28:43.750" LastActivityDate="2014-02-12T14:28:43.750" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="8692" PostTypeId="2" ParentId="8682" CreationDate="2013-06-08T13:24:13.657" Score="1" Body="&lt;p&gt;Some theories:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Dead bodies died of something. In the earliest ages these were generally infection. Burying them protected us from something that could kill us too. This is also why we would be evolutionarily programmed against cannibalism&lt;/li&gt;&#xA;&lt;li&gt;They make great fertiliser. Burying waste, dead animals etc resulted in the growth of plants etc which not only food we could eat but animals that would then eat the plants we could kill and eat. &lt;/li&gt;&#xA;&lt;li&gt;Dead bodies are unpleasant. They stink and so we would want to get rid of them. Also they would attract carnivores which are likely to target humans too&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;All these would be evolutionarily advantageous so any cultures practising burial would be likely to survive and pass on those customs. Whether this is genetic, that's open to debate because I'm not sure.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-06-08T13:24:13.657" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8693" PostTypeId="2" ParentId="8685" CreationDate="2013-06-08T17:19:06.823" Score="3" Body="&lt;p&gt;A summary of what we know so far includes that for B cells to become plasma cells they need BLIMP-1. For memory cells CD40 engaging with CD40L on B cells is required. CD40 is expressed on Th cells and thus they are also necessary for memory cell development. Problem is though, it's really damn confusing after that. It really isn't known but if you're interested in this stuff consider reading this &lt;a href=&quot;http://www.jmordoh.com.ar/clases/LTyLBmemoria.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;review&lt;/a&gt; which talks about memory cell differentiation and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19846886&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; which discusses plasma cell differentiation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image below helps (taken from &lt;a href=&quot;http://www.jmordoh.com.ar/clases/LTyLBmemoria.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; review)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PC = Plasma Cell, MBC = Memory B cell&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CuguP.png&quot; alt=&quot;B cell Differentiation&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-06-08T17:19:06.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8694" PostTypeId="2" ParentId="8679" CreationDate="2013-06-08T18:18:15.593" Score="1" Body="&lt;p&gt;So I got this answer from my lecturer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since Smith-Waterman algorithm is based on DP, we will get the best performance on accuracy, but there is a change that the homologous sequence is not with the highest probability (so better matching sequences will be &quot;hidden&quot; behind worse ones).&#xA;Since blast is based on the heuristic approach, it overcomes the disadvantage described above, by adding biological information, and therefore make it more accurate from biologist's perspective.&lt;/p&gt;&#xA;" OwnerUserId="3739" LastEditorUserId="3739" LastEditDate="2013-06-08T20:18:59.500" LastActivityDate="2013-06-08T20:18:59.500" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8695" PostTypeId="1" AcceptedAnswerId="8714" CreationDate="2013-06-09T01:15:07.400" Score="1" ViewCount="158" Body="&lt;p&gt;What is autophagy? How and under which circumstances is it used by the cell? I believe The reason for autophagy is some kind of recycling, am I right? But why does it occur in infections?&lt;/p&gt;&#xA;" OwnerUserId="3262" LastActivityDate="2013-06-10T00:37:23.773" Title="Autophagy in eukaryotic cells" Tags="&lt;cell-biology&gt;&lt;immunology&gt;&lt;cell-signaling&gt;&lt;autophagy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8696" PostTypeId="2" ParentId="8659" CreationDate="2013-06-09T07:30:56.410" Score="1" Body="&lt;p&gt;In my current lab we just leave the bottle out (but use it up pretty quickly as we have 20+ people). But we do buy 5 bottles at a time and leave them in the same spot as the bottle that is in use (inside a hood, with the light always turned on) and we've never had a problem with degradation/expiration&lt;/p&gt;&#xA;" OwnerUserId="3758" LastActivityDate="2013-06-09T07:30:56.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8697" PostTypeId="2" ParentId="8302" CreationDate="2013-06-09T11:04:30.803" Score="2" Body="&lt;p&gt;Human teeth are strongly attached to a socket, which is not true for many other animals. Our teeth are designed to last our lifetime (specifically up until the point we pass on our genes). Most people's teeth last until they are in their 50s, when the majority of people have passed their genes on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for food attacking our teeth, this would be fruit juice, sugar etc. These were not the diet of people years ago, in fact refining sugar is more of a recent discovery. And since that time we have been plagued with bad teeth. I think it was queen Victoria that was first introduced to refined sugar and suffered deleterious consequences quite rapidly. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="3624" LastEditDate="2013-06-10T11:09:24.697" LastActivityDate="2013-06-10T11:09:24.697" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8698" PostTypeId="2" ParentId="2031" CreationDate="2013-06-09T11:10:02.610" Score="1" Body="&lt;p&gt;Muscle is heavier than fat so actually it does. Muscle growth directly increases angiogenesis. Particularly the mechanism relies on hypoxia, any tissue with less than adequate blood supply secretes factors which result in angiogenesis. This is seen frequently when muscle is bulking as this increases the oxygen requirement but is also seen in heart muscle where subsequent to a heart attack tissue which isn't dead but mildly suffering caused new blood vessels to grow to supply this tissue (as the other ones are blocked which was the cause of the heart attack in most cases).&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-06-09T11:10:02.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8699" PostTypeId="2" ParentId="6936" CreationDate="2013-06-09T11:19:00.660" Score="4" Body="&lt;p&gt;In response to cold your body causes blood supply to the skin to drop in the whole body. This is to conserve heat, but results in us feeling really cold. Exercising reverses this, resulting in an increased blood supply to the skin in order to remove excess heat and in this case we feel hot. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As mentioned, the head receives a large blood supply, and continues to do so despite other tissues being restricted. This is particularly as a result of the brain requiring a lot of oxygen and glucose. This keeps our head warm. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This phenomenon is why hats keep us warm and are important in cold weather, we lose a lot of heat from our head.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also likely that the skin on our head contains less cold receptors, as these aren't likely to be required. However the other parts of our body, particularly the soles of our feet and anterior surface of our hands have many sensory receptors. They are likely to make first contact with anything that may be harmfully cold. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-06-09T11:19:00.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8700" PostTypeId="1" AcceptedAnswerId="8705" CreationDate="2013-06-09T13:03:30.640" Score="1" ViewCount="267" Body="&lt;p&gt;I think the question is very broad and cannot find precise mechanisms.&#xA;I am not sure about the precise mechanisms of the regulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think they are at least Vitamin D, diffusion and specific calcium channels: calbindins. &#xA;More specifically, calbindin-D9K and the basolateral calcium pump transport calcium from cell interior to extracellular space.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The calcium gradient should also be free, -2-6 mmol/l, in the lumen to allow diffusional calcium absorption from the interstitial space. &#xA;Similarly, free calcium concentration in the extracellular fluid of the lamina propria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that the most important mechanism for this absorption is the electrochemical gradient of sodium across the epithelial cell boundary of the lumen, similarly as for carbohydrates.&#xA;To keep the extracellular space free from calcium, the NA/K-ATPase i.e. sodium pump has to work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did not find any hormones that affect the intestinal calcium absorption.&#xA;&lt;strong&gt;Which factors affect calcium absorption and its regulation?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1306" LastEditDate="2014-04-09T16:02:35.913" LastActivityDate="2014-04-09T16:02:35.913" Title="Which hormones/factors affect Calcium absorption in the small intestine and its regulation?" Tags="&lt;endocrinology&gt;&lt;calcium&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8701" PostTypeId="1" CreationDate="2013-06-09T13:34:44.743" Score="3" ViewCount="598" Body="&lt;p&gt;Let's think about the slash and burn method and its effects on the ecosystem.&#xA;Cutting down trees that rise all the way up to the canopy would expose the plants at ground level to more light, so would change an abiotic factor so changes the conditions required for survival. These plants are not adapted to the high light intensity so would find it hard to survive and compete, through inter-species competition, with newly arrived plant species that are much more adapted to the extra light intensity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously this would cause a dramatic reduction in the numbers of the previous plant species and would result in migration of the animals due to lack of food, assuming they can't feed on the newly arrived plants, and a change in the food chain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In what ways do this affect the local and regional ecosystem, and what problems could it produce (both from an ecosystem and human perspective)? These types of land-use changes are often seen as problematic in conservation biology (as &quot;...a bad thing&quot;). Wouldn't the new plant species bring in new animals that do feed on them and a new equilibrium be reached just with different species? Is it to do with the reduced biodiversity or danger of extinction of indigenous organisms?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you have probably realized I don't exactly understand this topic perfectly and would appreciate any amendments or extra information to the paragraphs above.&#xA;Thanks in advance. &lt;/p&gt;&#xA;" OwnerUserId="3760" LastEditorUserId="3952" LastEditDate="2013-08-25T23:37:32.537" LastActivityDate="2013-08-26T00:50:16.627" Title="Change in conditions of an ecosystem lead to change in organisms" Tags="&lt;botany&gt;&lt;ecology&gt;&lt;ethnobiology&gt;&lt;extinction&gt;&lt;conservation-biology&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8702" PostTypeId="1" AcceptedAnswerId="8703" CreationDate="2013-06-09T13:56:13.693" Score="3" ViewCount="1042" Body="&lt;p&gt;A silly question. A few days ago I observed a very vocal bird with impressive vocal variety. It was rapidly switching from one tune to the next. After sometime I realized that the bird might be mimicking the 6-8 tone car alarm (the one that rapidly changes). Is this my imagination, or are birds really know to mimic/compete with car alarms?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-06-09T14:04:10.103" Title="Can songbirds mimic car alarm sounds?" Tags="&lt;zoology&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8703" PostTypeId="2" ParentId="8702" CreationDate="2013-06-09T14:04:10.103" Score="6" Body="&lt;p&gt;You would be amazed at the vocal abilities of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Lyrebird&quot;&gt;lyrebird&lt;/a&gt;.  A car alarm is easy for them; they can mimic much more complicated sounds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=VjE0Kdfos4Y&quot;&gt;Here&lt;/a&gt;'s a snippet from a David Attenborough BBC documentary on YouTube (which includes the car alarm example, among others).  They are so skilled, it's hard not to think this video is fake.&lt;/p&gt;&#xA;" OwnerUserId="203" LastActivityDate="2013-06-09T14:04:10.103" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8704" PostTypeId="1" AcceptedAnswerId="8706" CreationDate="2013-06-09T14:52:26.820" Score="2" ViewCount="277" Body="&lt;p&gt;I think the answer is no, but I am not 100% sure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it was yes, then the dendrite of the nerve cell should each time receive a stimulus causing Na+ channels to open, when the contraction happen. &#xA;Also, then it would mean that outside events could alter the function of hearth, which would be dangerous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heart has a special excitatory system and a contractile system - Sinoatrial node and Pacemaker cells, which control the action potentials in different portions of the heart.&#xA;So heart and primarily myocardium i.e. cardiac muscle can depolarise without any external influence with a slow, positive increase in voltage across the cell's membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do nerve cells cause action potential in cardiac muscle?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="6" LastEditDate="2013-06-09T20:45:47.463" LastActivityDate="2016-10-09T05:01:14.097" Title="Do nerve cells cause action potential in cardiac muscle?" Tags="&lt;neuroscience&gt;&lt;cardiology&gt;&lt;action-potential&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8705" PostTypeId="2" ParentId="8700" CreationDate="2013-06-09T14:54:29.423" Score="1" Body="&lt;p&gt;Parathyroid hormone increases intestinal calcium absorption by increasing production of vitamin D, which in turn uses calbindin. It also enhances calcium reabsorption from the kidney and the release of calcium from bone. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-06-09T14:54:29.423" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8706" PostTypeId="2" ParentId="8704" CreationDate="2013-06-09T15:01:18.367" Score="1" Body="&lt;p&gt;The vagus nerve controls heart rate. This is the best example of a direct nerve action potential impacting cardiac muscle, although one could argue the adrenaline system to be an indirect mechanism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The vagus nerve is part of the parasympathetic system, it acts to decrease heart rate. Resting heart rate is maintained by permanent vagal stimulation/tone by the release of acetylcholine. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-06-09T15:01:18.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8707" PostTypeId="1" AcceptedAnswerId="8723" CreationDate="2013-06-09T15:19:51.023" Score="0" ViewCount="94" Body="&lt;p&gt;What are the evolution operators, meaning allowed actions on the DNA sequence that encodes a protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume all evolution of genes is a result of duplication errors. So an answer could look somewhat like this: duplication of gene into two identical ones, omitting of nucleotide, addition of nucleotide and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And some followup questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Does this mean that originally there were very few genes and they were very short?&lt;/li&gt;&#xA;&lt;li&gt;If so - how few? How short?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1190" LastEditorUserId="6" LastEditDate="2013-06-09T20:44:27.190" LastActivityDate="2013-06-10T10:34:23.483" Title="What are the allowed evolution operators (on protein encoding sequences)?" Tags="&lt;evolution&gt;&lt;genetics&gt;" AnswerCount="3" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="8708" PostTypeId="1" AcceptedAnswerId="8709" CreationDate="2013-06-09T16:27:39.870" Score="2" ViewCount="302" Body="&lt;p&gt;Is CoA-S-R the same as CoA-R, and is CH&lt;sub&gt;3&lt;/sub&gt;C(=O)CoA the same as CH&lt;sub&gt;3&lt;/sub&gt;C(=O)SCoA? Eg. Above is the compound on the right just coenzyme A or is it actually another compound and not just notation?&lt;/p&gt;&#xA;" OwnerUserId="3761" LastEditorUserId="948" LastEditDate="2013-06-09T17:01:13.570" LastActivityDate="2013-06-10T09:27:06.723" Title="Are CoA and CoAS the same thing in a compound?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8709" PostTypeId="2" ParentId="8708" CreationDate="2013-06-09T16:40:13.937" Score="2" Body="&lt;p&gt;To understand the nomenclature here it is very helpful to think about how Coenzyme A works. It has a thiol group (-SH) which can form a thioester bond to an acyl group. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the sulphur in &quot;CoA-S-R&quot; is part of the CoA, and in &quot;CoA-R&quot; the sulfur is just not explicitly named. Those two mean exactly the same thing: Coenzyme A linked to R via a thioester on the thiol group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One specific variant that is very important in biology is acetyl CoA. The chemical formula you mentioned (CH&lt;sub&gt;3&lt;/sub&gt;C(=O)CoA) is acetyl CoA, and here the same as above applies and the sulphur is explicitly mentioned in the second one and implied in the first one.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="1320" LastEditDate="2013-06-10T09:27:06.723" LastActivityDate="2013-06-10T09:27:06.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8710" PostTypeId="2" ParentId="8433" CreationDate="2013-06-09T18:16:31.743" Score="1" Body="&lt;p&gt;I would like to complement dd3's answer a bit. It is about bacteria&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Bacteria secret enzymes outside. The bacterial membrane has import size limits and it is necessary for them to chop the big molecule into smaller pieces before import. Examples are glycoside hydrolases and protease. Bacteria take part in the clean-up after the annual algal and jellyfish bloom. It is especially important for the jellyfish because they have few predators and if it were not for the bacteria, their gelatinous body will pile up at our sea bottoms.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Bacteria release protein toxin, either to defend, or use to recognize the host if they are symbionts.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Gram-positive bacteria use peptide as autoinducer to do quorum sensing.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Last but not least, bacteria sometimes form aggregates. The glue among them is chemically very complex (in other words, we don't know exactly what it is). It is believed sugars are there and, proteins too.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3762" LastActivityDate="2013-06-09T18:16:31.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8711" PostTypeId="1" AcceptedAnswerId="8721" CreationDate="2013-06-09T18:43:26.867" Score="4" ViewCount="164" Body="&lt;p&gt;Given a fix volume of water saturated with dissolved oxygen through aeration. Suppose that ammonium, &lt;em&gt;Nitrosomonas&lt;/em&gt;, and &lt;em&gt;Nitrobacter&lt;/em&gt; are always available in the water. We know that some of the ammonium will eventually be oxidized, by the bacteria, to nitrate. We also know that under anaerobic condition, some of the nitrate, through many steps, will be broken down into Nitrogen by denitrifying bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Question: Are there any bacteria, in our environment, able to break down nitrate under aerobic conditions? If there aren't, will the nitrate continue to accumulate?&lt;/p&gt;&#xA;" OwnerUserId="3763" LastEditorUserId="107" LastEditDate="2013-06-11T01:07:59.017" LastActivityDate="2013-06-11T01:07:59.017" Title="Are there any bacteria, in our environment, able to break down nitrate under aerobic conditions?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8712" PostTypeId="2" ParentId="8707" CreationDate="2013-06-09T21:18:28.297" Score="0" Body="&lt;p&gt;I'm assuming your question is about how proteins have evolved from their earliest forms into those that are found today. As has been stated in the comments, changes in protein primary structure occur as a consequence of changes in the nucleotide sequences of the genes that encode them. Such changes may be caused by &lt;em&gt;mutation&lt;/em&gt; or &lt;em&gt;recombination&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations are changes in the nucleotide sequence that can be spontaneous, caused by errors in replication or DNA repair, or induced by mutagens such as radiation or chemicals. Recombination (non-meiotic) is the breaking and joining of different DNA strand, producing new strands with new combinations of alleles. Both these processes could result in changes in the amino acid sequence of proteins, affecting its tertiary structure and thus function. Through these processes, evolution has selected for nucleotide sequences carrying mutations that have caused beneficial changes in protein structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your follow-ups, I don't think there is an absolute answer. What is certain is that genetic complexity has increased through time, so the earliest genes that were part of a system in which a genetic code could be translated into protein are likely to have been both fewer and shorter.&lt;/p&gt;&#xA;" OwnerUserId="3674" LastActivityDate="2013-06-09T21:18:28.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8713" PostTypeId="2" ParentId="8707" CreationDate="2013-06-09T21:51:18.003" Score="1" Body="&lt;p&gt;The most frequent mechanisms are &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Intragenic mutations: when existing genes mutate modifying gene function. &lt;/li&gt;&#xA;&lt;li&gt;Gene duplication: leads to related genes in a single cell. A gene duplicates and then as two copies are available, one is free to change&lt;/li&gt;&#xA;&lt;li&gt;Segment shuffling: leads to hybridisation of different DNA segments. &lt;/li&gt;&#xA;&lt;li&gt;Horizontal transfer is transfer of DNA from one cell to another&lt;/li&gt;&#xA;&lt;li&gt;Transduction: infection of cells by viruses or other intracellular pathogens where their DNA can integrate into the genome&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You are incorrect to say all evolution occurs due to duplication. Your follow up questions are too vague. Genes can become larger or smaller, but yes as they increase so does their diversity. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-06-09T21:51:18.003" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8714" PostTypeId="2" ParentId="8695" CreationDate="2013-06-10T00:37:23.773" Score="1" Body="&lt;p&gt;Autophagy is a cellular process that is occurring all the time, but it can be elevated during times of need (see below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In autophagy, cargo (can be anything - mostly macromolecules but also bacteria/viruses etc) is taken up by a lipid membrane which folds on itself to form an autophagosome, which is like a vesicle but have markers on it that makes it specialized in carrying out autophagy. These autophagosomes are then transported to, and merge with, lysosomes, releasing the cargo into the lysosome to be degraded. The broken down materials are then released back into the cytosol, where other processes can make use of them. That is the &quot;some kind of recycling&quot; you are referring to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two types of autophagy - selective and general. In selective autophagy, receptors on the membrane of the autophagosome specifically selects for ligands (e.g. p62, ndp52 selects for ubiquinylated substrates, which usually marks molecules for degradation). In general autophagy, the uptake into the autophagosome is random.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, you can think of general autophagy as maintaining a basic level of turnover - to ensure everything in the cell is not worn out; and selective autophagy as a response to specific ligands that needs to be degraded.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By this logic, autophagy activity increases during infection because those infectious agents, once gaining entry into the cell (either through phagocytosis or by forced entry), will need the autophagy machinery to transport it to the lysosome to be degraded. Interestingly, some bacteria actualy hi-jacks this process to ensure its survival in the cell. Here's a good &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/cmi.12063/abstract&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt; to get you started if you are interested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the proteasome also recycles macromolecules, although the things it can recycle is limited by size.&lt;/p&gt;&#xA;" OwnerUserId="3465" LastActivityDate="2013-06-10T00:37:23.773" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8715" PostTypeId="2" ParentId="8688" CreationDate="2013-06-10T00:49:06.613" Score="1" Body="&lt;p&gt;To learn about the process of how cloning works, you need to appreciate the underlying principles. A general bio textbook should suffice (most popular one is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21054/&quot; rel=&quot;nofollow&quot;&gt;Alberts&lt;/a&gt;, where you should focus on chapter 21, but maybe read other chapters for background)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/scitable&quot; rel=&quot;nofollow&quot;&gt;Nature Scitable&lt;/a&gt; is also a good source.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd discourage reading research papers at this stage, primary research paper are often very specialized, and reviews are aimed at other researchers in the field, that is unless you find one that is focused on communicating science to the public.&lt;/p&gt;&#xA;" OwnerUserId="3465" LastActivityDate="2013-06-10T00:49:06.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8719" PostTypeId="1" AcceptedAnswerId="8726" CreationDate="2013-06-10T07:10:13.823" Score="5" ViewCount="2527" Body="&lt;p&gt;Once clonal selection is done, B cells would start dividing and producing antibodies. So, after an antigen is eliminated, what stops the division of B cells and antibody production?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2013-08-08T19:48:12.867" LastActivityDate="2013-08-08T19:48:12.867" Title="How is antibody production stopped?" Tags="&lt;immunology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8720" PostTypeId="2" ParentId="8680" CreationDate="2013-06-10T07:45:40.947" Score="1" Body="&lt;p&gt;As Alan Boyd said, this process is called trans splicing where exons of different RNAs are joined together. Physical proximity is conducive for trans-splicing. This &lt;a href=&quot;http://rnajournal.cshlp.org/content/14/6/1081.full&quot; rel=&quot;nofollow&quot;&gt;study&lt;/a&gt; shows that trans-splicing frequency is higher if the genes are proximal. Proximity not only means closer in the genome but also the 3D proximity governed by chromosomal interactions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, what factors  &lt;strong&gt;promote&lt;/strong&gt; trans splicing is not properly understood. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-06-10T07:45:40.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8721" PostTypeId="2" ParentId="8711" CreationDate="2013-06-10T08:11:27.307" Score="4" Body="&lt;p&gt;My initial reaction upon reading this question was to think that the answer was: no, denitrification is a process in which nitrate is used in the absence of oxygen as an alternative electron acceptor. However I decided to check the literature, and I have discovered that there is, in fact, a lot of new evidence that many bacterial species may be able to use both of these electron acceptors simultaneously. This article is a good place to start if you want to find out more:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Chen &amp;amp; Strous (2013) Denitrification and aerobic respiration, hybrid electron transport chains and co-evolution. BBA Bioenergetics 1827: 136-144  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is a review which summarises the area from the point of view of bioenergetics, but most importantly for this question, includes a Table summarising the experimental evidence for the phenomenon.  Referring to this Table, they state:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It appears that in most cases, the evidence presented is not sufficient to support the conclusion that denitrification really proceeded in the presence of excess oxygen. It should be noted that the aerobic denitrification rates were much lower than the anaerobic denitrification rates measured for the same strain while aerobic respiration rates remain high. This implies that the major electron flow in the respiratory chain is towards complex IV rather than the NOx reductases, and that aerobic respiration is still the preferred pathway for growth. Apparently aerobic denitrification can be an auxiliary pathway next to aerobic respiration.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The last sentence answers the OP question.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-06-10T08:11:27.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8722" PostTypeId="2" ParentId="8719" CreationDate="2013-06-10T10:29:00.603" Score="1" Body="&lt;p&gt;My understanding of this question is: Antibodies are produced by plasma cells which are terminally-differentiated B cells. Maturation of B cells to plasma cells is stimulated by the presence of antigen (T cells, cytokines, etc. etc).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the absence of antigen the existing plasma cells undergo apoptosis, and the maturation of the cognate B cells will not be stimulated, so no more plasma cells will be produced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found it surprisingly difficult to find references in support of these statements, although there is a large literature on the suppression of apoptosis in memory B cells.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-06-10T10:29:00.603" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8723" PostTypeId="2" ParentId="8707" CreationDate="2013-06-10T10:34:23.483" Score="1" Body="&lt;p&gt;An old microbial geneticists' adage is: anything that can happen will happen, and you just need to find a way to select for what you are seeking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Mutation&quot; rel=&quot;nofollow&quot;&gt;the Wikipedia page on mutation&lt;/a&gt; might be instructive.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-06-10T10:34:23.483" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8724" PostTypeId="1" AcceptedAnswerId="8786" CreationDate="2013-06-10T11:09:34.150" Score="0" ViewCount="316" Body="&lt;p&gt;The volume of blood coursing the blood circulation is approximately five litres. A typical vein will stretch about eight times as much as corresponding artery. Because veins have high capacitance, large changes in blood volume have little effect on arterial blood pressure.&#xA;If the volume rise or falls, the elastic walls stretch or recoil, changing the volume of blood thus blood pressure in the nervous system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What else tissues can we consider?&lt;/strong&gt;&#xA;I am interested in blood circulation and blood pressures in different tissues.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2013-06-26T12:21:10.680" Title="Blood circulation and blood pressure in different tissues" Tags="&lt;blood-circulation&gt;&lt;blood-pressure&gt;&lt;tissue&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="0" ClosedDate="2013-06-26T16:00:58.547" ContentLicense="CC BY-SA 3.0" />
  <row Id="8726" PostTypeId="2" ParentId="8719" CreationDate="2013-06-10T14:47:08.897" Score="4" Body="&lt;p&gt;Upon activation plasma B cells upregulate death receptors as part of being activated. Presence of the antigen overcomes the death signal, thus the cell survives. When antigen is lost, the death signals overcome the survival signals as there is no antigen, so the B cell dies via apoptosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Memory B cells don't do this. They survive and continue to produce antibodies for years, although this slowly wanes. Antibodies have to be produced as antibody mediated immune mechanisms are extremely important for memory and the reason why a subsequent infection is cleared so rapidly. Furthermore for the example of HPV, antibodies induced by the vaccine prevent the virus even infecting cells (so called neutralising antibodies).&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-06-10T14:47:08.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8727" PostTypeId="1" CreationDate="2013-06-10T15:06:52.657" Score="1" ViewCount="4316" Body="&lt;p&gt;The distinction between Gram-positive and Gram-negative bacteria is based upon the &lt;a href=&quot;http://en.wikipedia.org/wiki/Gram_staining&quot; rel=&quot;nofollow&quot; title=&quot;Gram staining&quot;&gt;&lt;strong&gt;Gram staining&lt;/strong&gt;&lt;/a&gt; method, that reflects the bacterial wall physical properties.&#xA;However, this classification involves also a large number of differences between them. For example, the endospore formation usually occurs in Gram-positive bacteria and also the &lt;em&gt;quorum sensing&lt;/em&gt; mechanism is different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what are those differences? Which of them are due to the cell wall thickness and membrane(s) composition and which instead to evolutionary divergences?&lt;/p&gt;&#xA;" OwnerUserId="3523" LastEditorUserId="4101" LastEditDate="2013-10-31T01:42:58.660" LastActivityDate="2014-01-28T12:52:56.560" Title="What are the differences between G+ and G- bacteria?" Tags="&lt;evolution&gt;&lt;microbiology&gt;&lt;bacteriology&gt;&lt;quorum-sensing&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8728" PostTypeId="1" AcceptedAnswerId="8733" CreationDate="2013-06-10T16:02:18.047" Score="1" ViewCount="325" Body="&lt;p&gt;In terms of the reactions they undergo are they roughly equivalent groups?&lt;/p&gt;&#xA;" OwnerUserId="3761" LastActivityDate="2013-06-10T19:50:42.120" Title="Do Acyl Carrier Proteins and Conenzyme A have similar reactivity?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8729" PostTypeId="2" ParentId="8727" CreationDate="2013-06-10T16:12:47.837" Score="4" Body="&lt;p&gt;I didn't know there were distinct differences between gram-positive and gram-negative bacteria when it came to quorum sensing, but it seems as though there are:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In gram negative bacteria, acyl-homoserine lactone type molecules serve as the main signalling molecules while lipid, peptide, and amino acid based signalling molecules infrequently serve as signalling molecules. Furthermore, in gram-negative bacteria, there is one well conserved mechanism for controlling quorum response. Gram-positive bacteria, on the other hand, use peptides or modified peptides as the primary means of signaling; and also differing from gram-negative bacteria, there are several different mechanisms found within the class which are used to gain quorum responses.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.bio.cmu.edu/courses/03441/TermPapers/99TermPapers/Quorum/mechanisms.htm&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In G&lt;sup&gt;+&lt;/sup&gt; bacteria, the two main quorum sensing mechanisms are apparently as follows:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Two-component signal transduction, in which the peptide signal works by binding to a sensor protein, histidine kinase, located in the cell membrane of the bacterium. The activation of the histidine kinase leads to phosphorylation of response-regulating protein, and interaction with another regulatory protein facilitates transcriptional activation.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Internalization, in which the signal molecules are transported into the responder cell to interact with intracellular effectors.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;G&lt;sup&gt;-&lt;/sup&gt; bacteria on the other hand, synthesize autoinducers, effector molecules that can diffuse freely through the cell membrane and trigger cell response when a certain concentration threshold is reached. I do not know how or if these differences are related to cell wall structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When it comes to endospore formation, all I know of the difference between the two is that this is by far most common in gram-positive bacteria.&lt;/p&gt;&#xA;" OwnerUserId="3674" LastEditorUserId="3674" LastEditDate="2014-01-28T12:52:56.560" LastActivityDate="2014-01-28T12:52:56.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8730" PostTypeId="1" CreationDate="2013-06-10T18:15:33.257" Score="4" ViewCount="6894" Body="&lt;p&gt;When the virus integrates its DNA with the hosts and enters the lytic pathway, do the viral proteins that produced destroy the cells DNA? Do they deactivate it? Also does the cell function in the same way as before?&lt;/p&gt;&#xA;" OwnerUserId="3760" LastActivityDate="2013-06-10T19:51:16.093" Title="How does a virus take control over the host cell?" Tags="&lt;virus&gt;&lt;infection&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8731" PostTypeId="1" AcceptedAnswerId="8735" CreationDate="2013-06-10T19:29:03.897" Score="5" ViewCount="395" Body="&lt;p&gt;We adopted a dog at the age of two. Our vet said it was a mix of an Australian Shepherd and Border Collie, which we've told everyone. Based on markings, I think it's likely. I am wondering, however, if there are any tests or other ways to know the mix of a dog if you don't know the specific parentage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does each dog breed have specific genetic markers that can be used to identify the breed? If so, has a dog breed test been developed or is there no commercial demand for such a test?&lt;/p&gt;&#xA;" OwnerUserId="3770" LastEditorUserId="1320" LastEditDate="2013-06-10T20:42:05.090" LastActivityDate="2013-06-10T20:42:05.090" Title="Is there a DNA test to identify dog mixes?" Tags="&lt;zoology&gt;&lt;dna&gt;&lt;dogs&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8733" PostTypeId="2" ParentId="8728" CreationDate="2013-06-10T19:50:42.120" Score="2" Body="&lt;p&gt;The acyl groups ligated to CoA and to acyl carrier proteins are actually attached to the same group (a phosphopantetheine group) as shown below, and so have very similar reactivities (i.e. group transfer potentials).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GNlLN.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-06-10T19:50:42.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8734" PostTypeId="2" ParentId="8730" CreationDate="2013-06-10T19:51:16.093" Score="5" Body="&lt;p&gt;A virus does not typically destroy its host's DNA. Rather, the virus makes the host cell express viral proteins at an elevated rate compared to the host's own proteins. This is usually achieved because the viral genome contains a strong &lt;a href=&quot;https://en.wikipedia.org/wiki/Promoter_%28genetics%29&quot;&gt;constitutive promoter&lt;/a&gt;, possibly coupled to an &lt;a href=&quot;https://en.wikipedia.org/wiki/Enhancer_%28genetics%29&quot;&gt;enhancer&lt;/a&gt; sequence. The virus may also preferentially insert itself into transcriptionally active sections of the host DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I said earlier, expression of the host's own genes as a whole is not directly regulated by the virus, though specific genes may be up- or down-regulated (immune-system related genes are often primary targets). However, the host's genes will usually be expressed at a reduced level because of the resources being diverted to make virions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remember however, that the virus relies totally on the host's machinery to make viral proteins. So, anything that kills the cell before sufficient viral particles are assembled is going to be selected against. This doesn't mean that the cell is healthy though. A significant chunk of the cell's resources have been hijacked by the virus, and a virus infected cell is typically just limping along, clinging to life, as it were.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending on the virus, once sufficient virions have been assembled inside the cell, the virus may enter a lytic phase, where the cell literally bursts to release the virions into the surrounding environment to infect new cells. At this point, the cell is obviously dead.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastActivityDate="2013-06-10T19:51:16.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8735" PostTypeId="2" ParentId="8731" CreationDate="2013-06-10T20:24:28.517" Score="6" Body="&lt;p&gt;There are many commercially available mixed breed ID tests, as a quick Google search will tell you.  However, I cannot vouch for their accuracy: &lt;a href=&quot;http://www.mnn.com/family/pets/blogs/dog-breed-tests-do-they-really-work&quot;&gt;this news article may be of interest&lt;/a&gt;. Also &lt;a href=&quot;http://news.vin.com/VINNews.aspx?articleId=23206&quot;&gt;this&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genetic markers used to identify breeds in a mixed-breed are microsatellite markers (sometimes SNPs): you can read more &lt;a href=&quot;http://www.sciencemag.org/content/304/5674/1160.abstract&quot;&gt;here&lt;/a&gt;, but from the abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We used molecular markers to study genetic relationships in a diverse collection of 85 domestic dog breeds. Differences among breeds accounted for ∼30% of genetic variation. Microsatellite genotypes were used to correctly assign 99% of individual dogs to breeds.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you're interested in dog genetics, I encourage you to check out Elaine Ostrander's work.  She's written at least one book for laypeople, in addition to her numerous journal publications.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-06-10T20:24:28.517" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8737" PostTypeId="2" ParentId="8139" CreationDate="2013-06-10T23:56:39.653" Score="0" Body="&lt;p&gt;In short, this is my understanding following my immunology course (which is mostly identical to AndroidPenguin's answer):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Chemokines: Produce cell movement, i.e. act as chemoattractants. Typically these are used to recruit more immune cells to a site of infection. (Name origin says it all: &quot;chemotactic cytokine = chemokine...)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Cytokines: Produce an inflammatory response by altering transcription (via surface receptor signal cascades). These often act on non-immune cells.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Interferons: A type of cytokine. Secreted by virtually every cell in response to being infected by a virus. Produce an 'anti-viral' state in other cells, through MANY mechanisms. Causes the typical flu-like symptoms.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Tumor necrosis factors (specifically TNF alpha): A type of cytokine. Prepares endothelium (blood vessel walls) to support an inflammatory response by vasodilation, increased adhesion and increased permeability.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Interleukins: Some are chemokines (e.g. secreted by macrophages and dendritic cells upon activation to recruit further phagocytes and adaptive immune cells), others are cytokines (e.g. activating B cells to differentiate into plasma and memory cells after T cell contact).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-06-12T01:03:51.730" LastActivityDate="2013-06-12T01:03:51.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8738" PostTypeId="1" AcceptedAnswerId="14124" CreationDate="2013-06-11T08:30:12.080" Score="1" ViewCount="5000" Body="&lt;p&gt;I am not sure this question belongs in biology, but I can't find a more suitable stack exchange site, feel free to delete it if this doesn't fit here.&lt;/p&gt;&#xA;&lt;p&gt;Also, this question is going to be slightly gross, just a warning, but I promise it comes to a point.&lt;/p&gt;&#xA;&lt;p&gt;I have read that the adenoids have a texture to them but, unlike say the palatine tonsils, they don't have crypts.&lt;/p&gt;&#xA;&lt;p&gt;Last year my palatine tonsils became fairly badly infected and had to be removed over the summer. Before the surgery, I discovered I could reach back to the tonsils with my tongue, enabling me to remove the tonsil stones that built up. Gross, I know, but I believe it actually did make the infection noticeably better. After the surgery, and after the area had healed, I resumed discovering the back of my throat and, eventually, up the nasal cavity, all the way to the back of the nasal septum, which means I can reach the Eustachian tubes, adenoids, and posterior nares. If that sounds impossible, I assure you, it is perfectly achievable, and only mildly uncomfortable. With my tongue I can feel the texture of the adenoids but, more toward the posterior nares, this texture changes and resembles folds or crypts like I remember the texture of the palatine tonsils. Three times, always in the morning after waking up, I have discovered debris in this region strongly resembling tonsil stones but green instead of off white. The mucus, however, is always clear.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;My question has several parts:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;What are these crypts? Are they even crypts at all? Are they part of the adenoids?&lt;/li&gt;&#xA;&lt;li&gt;Why can I not find mention to these structures in any diagrams or medical articles?&lt;/li&gt;&#xA;&lt;li&gt;Why can I not find mention to tonsil stone like debris except in the palatine tonsils? I am quite convinced that, if these are not tonsil stones of a sort, they are closely related.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The proportions of diagrams and cross sections of the nasal cavity all seem wildly different. Some of them are just blatantly wrong, depicting, for example, the Eustachian tubes coming from the roof of the nasal cavity instead of the sides. It has been very difficult to find good information on any of this. I am not even sure if I am referring to the region correctly. By nasal cavity, I mean everything between the back of the throat and the posterior nares, although I am aware the nasal cavity includes the region all the way up to the anterior nares as well.&lt;/p&gt;&#xA;&lt;p&gt;This is the only picture I can find that shows the nasal septum.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/I5SqJ.jpg&quot; alt=&quot;Nasal Septum&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;This is a better diagram of the rest of the structures. The pharyngeal tonsils are the adenoids.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/SiheP.jpg&quot; alt=&quot;Adenoids&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="1123" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-03-12T00:49:46.127" Title="Structure of adenoids" Tags="&lt;human-biology&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8739" PostTypeId="2" ParentId="5137" CreationDate="2013-06-11T13:23:55.393" Score="1" Body="&lt;p&gt;Cytokine production in the body resets the thermoregulatory centre in the hypothalamus to a higher temperature. As a result, your muscles begin to contract violently (rigors) to generate more heat until you equilibrate to the new setpoint. Hope this helps. &lt;/p&gt;&#xA;" OwnerUserId="3773" LastEditorUserId="3773" LastEditDate="2013-06-11T14:34:02.397" LastActivityDate="2013-06-11T14:34:02.397" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8741" PostTypeId="2" ParentId="7072" CreationDate="2013-06-11T14:44:28.003" Score="3" Body="&lt;p&gt;Healing in the body is normally independent of the brain. Following an injury, a process of inflammation attracts lots of cells to the site of the injury (including platelets, white blood cells, clotting factors). There's also vasoconstriction (tightening of your blood vessels) to reduce blood loss from the injury site. Your skin cells continue to divide rapidly until new skin replaces the damaged one which later falls off. This is a highly simplified version of the process but hope it makes sense. So in summary, healing takes place by cell division (also known as mitosis).   &lt;/p&gt;&#xA;" OwnerUserId="3773" LastEditorUserId="3773" LastEditDate="2013-06-11T14:52:49.493" LastActivityDate="2013-06-11T14:52:49.493" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8742" PostTypeId="2" ParentId="5137" CreationDate="2013-06-11T15:17:30.443" Score="6" Body="&lt;p&gt;As John mentioned, pyrokines such as IL1 and TNF affect the hypothalamus. Your hypothalamus is a thermostat, similar to central heating for example. So when you set your core temperature higher, your body thinks it is cold. To warm up it does several things:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Vasoconstriction directs blood to the core body and prevents heat&#xA;loss &lt;/li&gt;&#xA;&lt;li&gt;Brown fat break down in infants makes heat &lt;/li&gt;&#xA;&lt;li&gt;Shivering which requires respiration which produces a lot of heat. Metabolism also&#xA;increases in other ways - this is why it is commonly advised to&#xA;increase food consumption during illness &lt;/li&gt;&#xA;&lt;li&gt;We wrap up warm - an often overlooked mechanism that is incredibly important.  &lt;/li&gt;&#xA;&lt;li&gt;Limited piloerection: if we are hairy our hair will stand up attempting to&#xA;create a barrier for heat loss &lt;/li&gt;&#xA;&lt;li&gt;We stop sweating (breaking of a fever or when the hypothalamus is reset to normal causes us to sweat)&lt;/li&gt;&#xA;&lt;li&gt;Hormonal regulation via (nor)adrenaline/epinephrine, thyroxine - these are related to the increased metabolism.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-06-11T15:17:30.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8743" PostTypeId="1" AcceptedAnswerId="8751" CreationDate="2013-06-11T15:35:59.430" Score="3" ViewCount="1232" Body="&lt;p&gt;I have noticed that some TF binding sites are located in the introns of the genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am puzzled about whether the TF only binds to DNA in the initiation stage of transcription and will detach during transcription. (I am thinking if the TF bind to the sense strand, it will block the PoLII for transcription, thus they should be removed.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="3775" LastEditorUserId="3059" LastEditDate="2013-06-11T22:28:57.687" LastActivityDate="2013-06-12T04:38:40.313" Title="Transcription factor binding site located in intron" Tags="&lt;dna&gt;&lt;genetics&gt;&lt;transcription&gt;&lt;introns&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8744" PostTypeId="2" ParentId="8743" CreationDate="2013-06-11T15:51:33.247" Score="1" Body="&lt;p&gt;Even in a quiescent state, DNA is bound to a &lt;em&gt;lot&lt;/em&gt; of proteins. It is not a lone double-helix of DNA with an occasional protein attaching here or there. Rather, it is tightly wrapped around histones, which themselves have other proteins attaching and detaching constantly. Repair enzymes are always whizzing about and fixing the random damage that occurs in DNA naturally, and transcription factors may be sitting on the DNA for a while and then diffusing away again without doing anything. There are probably more proteins around that I've forgotten.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, the nucleus, DNA and in general the cell interior are extremely crowded spaces, and for transcription to happen it takes more than just removing some TFs attached to intronic sequences. Histones need to be modified to repel each other and make space. Ultimately, all proteins will need to detach for a short time when RNA polymerase comes through. If they don't, polymerase will stall until they move away, or it may simply fall off, producing an incomplete RNA fragment which will be degraded quickly. Another polymerase will come along soon enough and produce a new transcript if the promotor is still in a permissive state.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-06-11T15:51:33.247" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8745" PostTypeId="1" AcceptedAnswerId="9148" CreationDate="2013-06-11T16:19:04.713" Score="6" ViewCount="4496" Body="&lt;p&gt;To me, the phenomenon of polymorphism in cnidarians is particularly troubling. I gather that it essentially refers to existence of various different &lt;strong&gt;&lt;em&gt;forms&lt;/em&gt;&lt;/strong&gt; or  &lt;strong&gt;&lt;em&gt;kinds&lt;/em&gt;&lt;/strong&gt; of individuals, i.e. zooids and polyps in one species. But when we refer to the cnidarian &lt;em&gt;Physalia&lt;/em&gt;, as an animal, aren't we actually referring to a colony of individuals? &lt;em&gt;Physalia&lt;/em&gt; consists of several &quot;entities&quot; including &lt;em&gt;gastrozooids&lt;/em&gt;, &lt;em&gt;dactylozooids&lt;/em&gt;, and the &lt;em&gt;float&lt;/em&gt;, and since each of these is a distinct &quot;organism&quot;, therefore is what we refer to by saying &lt;em&gt;Physalia&lt;/em&gt; is actually a colony of phenotypically distinct forms of the same species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, can &quot;animals&quot; like &lt;em&gt;Physalia&lt;/em&gt; or &lt;em&gt;Gorgonia&lt;/em&gt; or &lt;em&gt;Pennatula&lt;/em&gt; be thought of actually as &quot;colony-beings&quot; which always contain several individuals in group?&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3952" LastEditDate="2013-08-06T00:40:56.337" LastActivityDate="2014-05-08T16:34:19.100" Title="Polymorphism in cnidarians?" Tags="&lt;zoology&gt;&lt;taxonomy&gt;&lt;nomenclature&gt;&lt;sociality&gt;&lt;definitions&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8747" PostTypeId="2" ParentId="8471" CreationDate="2013-06-11T17:16:06.437" Score="2" Body="&lt;p&gt;One pathology affecting the vagus nerve is autonomic neuropathy which can be secondary to several causes-one of the most commonly acquired cause is diabetes mellitus. It can manifest with various symptoms such as resting tachycardia (heart beating fast without exercise), exercise intolerance, orthostatic hypotension, constipation, gastroparesis (delayed gastric emptying), etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you'd like to read more-&lt;a href=&quot;http://care.diabetesjournals.org/content/26/5/1553.full&quot; rel=&quot;nofollow&quot;&gt;http://care.diabetesjournals.org/content/26/5/1553.full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope its helpful.&lt;/p&gt;&#xA;" OwnerUserId="3773" LastActivityDate="2013-06-11T17:16:06.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8748" PostTypeId="1" AcceptedAnswerId="8749" CreationDate="2013-06-11T20:15:52.427" Score="3" ViewCount="670" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/goTGI.jpg&quot; alt=&quot;Unknown insect in Russia&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/pI1x0.jpg&quot; alt=&quot;Unknown insect in Russia&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Found in Russia. Approx. 7 cm.&lt;/p&gt;&#xA;" OwnerUserId="3280" LastEditorUserId="3624" LastEditDate="2013-06-15T23:10:12.627" LastActivityDate="2013-06-15T23:10:12.627" Title="What flying insect is this?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8749" PostTypeId="2" ParentId="8748" CreationDate="2013-06-11T21:38:02.810" Score="9" Body="&lt;p&gt;This is &lt;a href=&quot;http://en.wikipedia.org/wiki/Crane_fly&quot;&gt;Crane fly&lt;/a&gt;, of the Tipulidae family. They don't bite humans, adults feed on nectar. Larvae prefer moist environments such as wet soil or decomposing vegetable matter and can consume roots and vegetation, damaging plants. Among others, bats and some Coleoptera are its predators.&#xA;Further informations can be found in the Wikipedia article linked above.&lt;/p&gt;&#xA;" OwnerUserId="3523" LastActivityDate="2013-06-11T21:38:02.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8750" PostTypeId="1" AcceptedAnswerId="8867" CreationDate="2013-06-12T02:32:45.217" Score="0" ViewCount="158" Body="&lt;p&gt;[This is one more post in my &lt;a href=&quot;https://stats.stackexchange.com/q/61303/4769&quot;&gt;growing&lt;/a&gt; &quot;X for dummies/idiots/morons/etc.&quot; series.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been enjoying Provine's &lt;em&gt;The origins of theoretical population genetics&lt;/em&gt; for the last couple of days, but I must confess that I find his description (on pp 127-8) of the &lt;em&gt;logic&lt;/em&gt; behind Sewall Wright's (and W. Castle's) selection experiments with &quot;hooded rats&quot; about as clear as if it had been chiseled in Linear A...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which is really bumming me out, because I'd love to understand these experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know where I can find a description of these experiments aimed at those with only a very limited grasp of classical genetics?  (I took a graduate-level genetics class a billion years ago, and I did not find it easy.)&lt;/p&gt;&#xA;" OwnerUserId="3778" LastEditorUserId="-1" LastEditDate="2017-04-13T12:44:17.897" LastActivityDate="2013-07-03T14:36:42.407" Title="Sewall Wright for dunces" Tags="&lt;genetics&gt;&lt;history&gt;&lt;literature&gt;&lt;selection&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8751" PostTypeId="2" ParentId="8743" CreationDate="2013-06-12T04:38:40.313" Score="1" Body="&lt;p&gt;As Armatus said TF can remain bound without an effect. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some alternative explanations:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Promoters need not be always upstream to the Transcription Start Site (TSS). There are promoters called Downstream Promoter Elements that are actually downstream to TSS. &lt;/li&gt;&#xA;&lt;li&gt;There can be alternate TSS within the introns&lt;/li&gt;&#xA;&lt;li&gt;TF bound to intron may regulate elongation or splicing rather than initiation. [Elongation can also be regulated especially when a gene is &lt;em&gt;poised&lt;/em&gt; for expression. RNApolymerase stalling is a well known phenomenon and is affected by epigenetic marks. Since splicing happens co-transcriptionally there can be DNA marks that affect the process. Although it has not been shown whether such a thing happens, but Intron-Exon boundaries are known to have a distinct nucleosomal pattern.{&lt;a href=&quot;http://genome.cshlp.org/content/early/2009/08/17/gr.092353.109.abstract&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;http://www.nature.com/nsmb/journal/v16/n9/full/nsmb.1658.html&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;, &lt;a href=&quot;http://www.landesbioscience.com/journals/6/article/9916/&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;}]&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-06-12T04:38:40.313" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8752" PostTypeId="2" ParentId="8471" CreationDate="2013-06-12T05:25:11.890" Score="1" Body="&lt;p&gt;I know the vagus nerve is linked to ulcerative colitis, which could have serious effects on the brain due to body-wide inflammation. You could probably search &quot;vagus nerve&quot; &quot;colitis&quot; and &quot;neuroinflammation&quot; and get some good papers on pubmed. &lt;/p&gt;&#xA;" OwnerUserId="3758" LastActivityDate="2013-06-12T05:25:11.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8753" PostTypeId="2" ParentId="8155" CreationDate="2013-06-12T07:30:02.437" Score="1" Body="&lt;p&gt;Since I asked this question I found out what I was doing wrong in searching for K&lt;sub&gt;i&lt;/sub&gt; (i.e. I thought the K&lt;sub&gt;i&lt;/sub&gt; ID was the &lt;em&gt;test ligand&lt;/em&gt; and hence I was searching for drugs the wrong way) values but also how, &lt;strong&gt;I think&lt;/strong&gt; Goodman and Gilman got its K&lt;sub&gt;i&lt;/sub&gt; values. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think what they did was they searched for the &lt;strong&gt;hot ligand&lt;/strong&gt; that gave the most &lt;strong&gt;consistent&lt;/strong&gt; and &lt;strong&gt;numerous&lt;/strong&gt; K&lt;sub&gt;i&lt;/sub&gt; values and took the average of the consistent K&lt;sub&gt;i&lt;/sub&gt; values (with an relative tolerance of ~100% between results). Additionally since I knew the data, as is stated in the page displayed above, was taken 30 June 2009 I was able to eliminate some sources that were probably not available on PDSP at the time. Using this I was able to get consistent averaged K&lt;sub&gt;i&lt;/sub&gt; values in the vast majority of cases (with like, at most a small handful of exceptions). &lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-06-12T07:30:02.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8754" PostTypeId="2" ParentId="8748" CreationDate="2013-06-12T08:05:08.040" Score="2" Body="&lt;p&gt;As a complement to Mattia Rovetta's answer, notice that this insect has only 2 wings, while insects typically have four.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like flies and mosquitoes, these are Diptera: the hind wings have evolved into a stucture called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Haltere&quot; rel=&quot;nofollow&quot;&gt;Haltere&lt;/a&gt;&quot;, and one of these small halteres can be seen on your upper photo.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The wikipedia page about halters is illustrated by a Crane Fly photo (as of June 2013), which is quite similar to your insect, but might be of a different species, if I judge by the fact that yours has a dark spot on the wing.&lt;/p&gt;&#xA;" OwnerUserId="1486" LastEditorUserId="1306" LastEditDate="2013-06-13T02:03:38.527" LastActivityDate="2013-06-13T02:03:38.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8755" PostTypeId="2" ParentId="8750" CreationDate="2013-06-12T08:21:41.310" Score="2" Body="&lt;p&gt;I don't have access to Provine's book, and I can't describe the details of the hooded rat experiments, but here is an attempt to explain the importance of the work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Darwin published “Origin of Species” in 1859. He proposed that modern species were all descended from ancestral species, and that evolution proceeded by natural selection. He believed that evolution proceeded gradually by an accretion of small changes (gradualism). The origins of hereditary change were, of course, unknown to Darwin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mendel’s work (published in 1865) was rediscovered in 1900, and gave rise to a school of thought referred to as mutationism.  Mutationist theories emphasised the importance of single factor changes with large effects, and placed these “leaps forward” at the centre of the mechanism for the generation of new species. This was in contrast to the biometricians who argued, in the Darwinian tradition, that natural selection acted on populations in which there was continuous variation. Extreme mutationists believed that continuous variation within a species had no relevance to the evolution of new species. Their view was that within a species most genes were fixed (100% wild-type allele), and that only mutations could create new species (‘hopeful monsters’). T.H. Morgan, for example, was a strong proponent of the mutationist theory, so this wasn't some minor controversy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sewall Wright joined the laboratory of W.E.Castle as an assistant in 1912, when he was 23. Starting with black and white hooded rats (white rats with black ‘hoods’) they instigated breeding programmes and showed that they could progress gradually, through a number of generations, towards all white or all black rats. The importance of this work was that it demonstrated that there was underlying genetic variation within this strain of rats that could be acted upon by selection (selective breeding) resulting in  gradual changes in coat colour. This provided strong evidence for the gradualist school.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the 1930s the modern synthesis began to emerge, which combined mutationist and gradualist ideas: natural selection acts upon populations (gene frequencies etc.) but mutation provides the raw material that creates new variations in the population. Key to the acceptance of the modern synthesis was the development of a mathematical treatment of population genetics. This led to the current view of phenotypic  traits influenced by multiple loci, with natural populations harbouring genetic variability which can be acted upon by selective forces. We have all accepted this and so of course it is difficult to think ourselves into the controversies that existed in genetics at the beginning of the twentieth century.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.animal-science.org/content/46/5/1192.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Here is an article&lt;/a&gt; in which Sewall Wright refers briefly to his work with Castle, placing it in historical context. It also describes subsequent work with guinea pigs. This is a quotation from the article which underscores what I have written:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;From assisting Prof. Castle, I learned at firsthand the efficacy of mass selection in changing permanently a character subject merely to quantitative variability. Because of this and a distaste for miracles in science, I started with full acceptance of Darwin's contention that evolution depends mainly on quantitative variability rather than on favorable major mutations. Thus, I have assumed that species are typically heteroallelic in tens of thousands of loci in which the leading alleles differ only slightly in effect, a situation that is maintained in a continually shifting state of near-equilibrium by the opposing pressures of recurrent mutation, diffusion and weak selection. Only a few loci at any time can show fairly rapid changes in allelic frequencies from strong selection.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-06-12T09:08:12.807" LastActivityDate="2013-06-12T09:08:12.807" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8756" PostTypeId="1" AcceptedAnswerId="8757" CreationDate="2013-06-12T12:42:28.820" Score="1" ViewCount="752" Body="&lt;p&gt;I am looking for a online atlas for Bacteriology, the cost does not matter.&#xA;I have been searching SpringerLink, and Amazon but no good online version found.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is a good atlas for Bacteriology as a online version?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2013-06-12T13:20:45.420" Title="What is a good Microbiology atlas for Bacteriology as online version?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8757" PostTypeId="2" ParentId="8756" CreationDate="2013-06-12T13:20:45.420" Score="1" Body="&lt;p&gt;Not sure what you are exactly looking for? If you change the question or comment I can update my answer...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/&quot; rel=&quot;nofollow&quot;&gt;NCBI's taxonomy site&lt;/a&gt; has a listing of bacteria.  &lt;a href=&quot;http://eol.org/&quot; rel=&quot;nofollow&quot;&gt;Encyclopedia of life&lt;/a&gt; is also great. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there's &lt;a href=&quot;http://microbes.ucsc.edu/&quot; rel=&quot;nofollow&quot;&gt;UCSC's microbial genome browser&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://biocyc.org/&quot; rel=&quot;nofollow&quot;&gt;Biocyc&lt;/a&gt; is  great reference for bacterial genes.  to get into E coli, which is the model bacterium there's &lt;a href=&quot;http://porteco.org/&quot; rel=&quot;nofollow&quot;&gt;Port Eco&lt;/a&gt; featuring 130 E coli genomes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am Soc Micro has an excellent &lt;a href=&quot;http://ecosal.org/&quot; rel=&quot;nofollow&quot;&gt;E coli/ Salmonella site based on their classic reference&lt;/a&gt; - you have to pay for access though. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-06-12T13:20:45.420" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8758" PostTypeId="2" ParentId="8748" CreationDate="2013-06-12T13:25:04.643" Score="1" Body="&lt;p&gt;It is indeed a crane fly and there are &gt;15000 species worldwide. Also see answers to this question: &lt;a href=&quot;https://biology.stackexchange.com/questions/8624/what-is-this-insect/8634#8634&quot;&gt;What is this insect?&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-06-12T13:25:04.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8759" PostTypeId="1" AcceptedAnswerId="8765" CreationDate="2013-06-12T17:09:41.517" Score="9" ViewCount="326" Body="&lt;p&gt;The male to female ratio in autism spectrum disorder is around 4:1. However it seems ASD is not a simple X-linked disorder. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then how is it possible males are more susceptible than females, if the causal genes are located in autosomes? &lt;/p&gt;&#xA;" OwnerUserId="3775" LastEditorUserId="3059" LastEditDate="2013-06-12T19:07:58.537" LastActivityDate="2018-12-20T07:21:17.470" Title="Why are males more likely than females to have autism spectrum disorder?" Tags="&lt;genetics&gt;&lt;brain&gt;&lt;human-genetics&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8760" PostTypeId="1" AcceptedAnswerId="8763" CreationDate="2013-06-12T17:18:07.840" Score="1" ViewCount="78" Body="&lt;p&gt;There is a question I encountered. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is fat harder to digest ?&#xA;A) It has ester bonds.&#xA;B) It is not easily soluble in water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which is the most appropriate answer?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3059" LastEditDate="2013-06-12T18:32:32.170" LastActivityDate="2013-06-12T20:31:46.190" Title="Breaking of fats" Tags="&lt;biochemistry&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8761" PostTypeId="2" ParentId="8759" CreationDate="2013-06-12T19:06:50.747" Score="3" Body="&lt;p&gt;Males are more likely to develop ASD, but affected females tend to be more severely impaired. Why this occurs is an area of active research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, to address your question, there is a &lt;a href=&quot;http://stm.sciencemag.org/content/2/49/49ra68.abstract&quot; rel=&quot;nofollow&quot;&gt;study suggesting that mutations on the X-chromosome account for about 1% of ASD and intellectual disability cases&lt;/a&gt;.  This clearly doesn't explain everything, but it's a start.  It might suggest that there are other X-linked loci involved. IIRC, ASD is one of those disorders that can be caused by many different combinations of (relatively rare) mutations, so it's hard to identify the genetic causes by GWAS.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-06-12T19:06:50.747" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8762" PostTypeId="1" CreationDate="2013-06-12T19:34:14.817" Score="2" ViewCount="4299" Body="&lt;p&gt;As viroids are simply non-encapsidated non-coding RNA molecules, it is difficult to imagine a mechanism for their continual infection, other than &lt;a href=&quot;http://en.wikipedia.org/wiki/Horizontal_gene_transfer&quot; rel=&quot;nofollow&quot;&gt;horizontal transfer&lt;/a&gt; which doesn't seem to be the case. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a working theory on &lt;strong&gt;how viroids propagate and continually infect hosts&lt;/strong&gt;?&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2017-04-19T19:54:30.097" Title="How do viroids propagate to other hosts?" Tags="&lt;molecular-biology&gt;&lt;virology&gt;&lt;infection&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8763" PostTypeId="2" ParentId="8760" CreationDate="2013-06-12T20:31:46.190" Score="3" Body="&lt;p&gt;I think that the main reason (but probably &lt;em&gt;not&lt;/em&gt; the only one) is because &lt;strong&gt;fats are hydrophobic&lt;/strong&gt;, while the environment of the digestive tract is aqueous. Most of the fats in the diet are triglyceride and in hydrophilic environment they form globules. Triglycerides must be hydrolysed to be absorbed by the duodenum and this work is done by &lt;a href=&quot;https://en.wikipedia.org/wiki/Pancreatic_lipase&quot; rel=&quot;nofollow&quot;&gt;pancreatic lipase&lt;/a&gt;, that is a water soluble enzyme and can only hydrolyse the esteric bonds at the surface of fat globules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, during the digestion amphipathic molecules such as bile salts and phospholipids emulsify those droplets in smaller ones, increasing the surface area where lipases, together with &lt;a href=&quot;https://en.wikipedia.org/wiki/Colipase&quot; rel=&quot;nofollow&quot;&gt;colipase&lt;/a&gt; can digest.&lt;/p&gt;&#xA;" OwnerUserId="3523" LastActivityDate="2013-06-12T20:31:46.190" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8764" PostTypeId="2" ParentId="8762" CreationDate="2013-06-12T23:11:19.913" Score="2" Body="&lt;p&gt;Viroids are commonly thought of as remnants from the &quot;RNA world&quot; since they are composed of only RNA and have &lt;a href=&quot;http://en.wikipedia.org/wiki/Ribozyme&quot; rel=&quot;nofollow noreferrer&quot;&gt;ribozyme&lt;/a&gt; activity.&#xA;Viroids can be considered as plant parasites of the transcriptional machinery of the organelles (nucleus or chloroplast), since they are non-coding and they replicate by RNA–RNA transcription (in a &lt;a href=&quot;https://en.wikipedia.org/wiki/Rolling_circle_replication&quot; rel=&quot;nofollow noreferrer&quot;&gt;rolling cycle mode&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Viroids infect the epidermis of their hosts after mechanical damage of the plant cell wall. After entry to the first cell layers, viroids initiate replication in the nucleus or in the chloroplast and then are transported to neighbouring cells, reaching the vascular tissues and virtually all plant tissues.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/tG2EQ.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The transmission of viroids is both &quot;natural&quot; and human-driven. Viroids are mostly transmitted via mechanical methods by contaminated machinery and tools, pruning, and other mechanic argricultural techniques. Transmission also occurs through infected seed and pollen, they don't have important natural vectors from the animal kingdom. Also contact between adjacent plants can be another (inefficient) way to transmit viriods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found a reference &lt;a href=&quot;http://www.publish.csiro.au/pid/3163.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for further informations. It isn't open access but it is possible to watch an abundant Google preview.&lt;/p&gt;&#xA;" OwnerUserId="3523" LastActivityDate="2013-06-12T23:11:19.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8765" PostTypeId="2" ParentId="8759" CreationDate="2013-06-12T23:19:19.303" Score="9" Body="&lt;p&gt;As the father of two sons with diagnoses of ASD, I think that it is best to think in terms of an extended spectrum which encompasses 'normal' people. We are all somewhere on this spectrum, but there is a threshold zone around where we cross from &quot;normal&quot; to &quot;diagnosable as ASD&quot;. Now, if the distribution of spectral position for males is displaced towards the ASD end of the spectrum relative to females (because of some aspect underlying &quot;normal' maleness, such as testosterone levels) then any genetic variation which pushes someone towards the ASD end of the spectrum by some fixed amount will tend to push more males over the threshold than females. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-06-12T23:19:19.303" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8766" PostTypeId="1" AcceptedAnswerId="8779" CreationDate="2013-06-13T00:21:56.673" Score="1" ViewCount="92" Body="&lt;p&gt;I'm looking at services like 23andme, and see that they identify a wide variety of genetic-based risks, like predisposition to diseases, hair loss, cancer, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are there a more &quot;positive&quot; DNA analysis outcomes out there?&lt;/strong&gt; Like increased strength, cheerfulness(resistance to depression), etc?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-06-13T15:36:06.017" Title="Are there beneficial genetic mutations identified by consumer DNA genotyping?" Tags="&lt;dna&gt;&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8767" PostTypeId="1" CreationDate="2013-06-13T01:19:05.570" Score="5" ViewCount="319" Body="&lt;p&gt;Could the brain be working without consciousness? Does the brain interact with consciousness? Alternately, is it that consciousness can't really control the brain, and you only have the impression that you make the decisions, but your brain does.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the answer to the last question is yes, it is impossible to know if someone else has a consciousness? Even if he doesn't, he'll say he does, because the brain thinks he does.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can't be made only from matter. If we would, we'd be a mix of chemicals interacting with each other. What makes us be aware of our feelings, what we think, and our 5 senses?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When and how is consciousnesses created?&lt;/p&gt;&#xA;" OwnerUserId="3782" LastEditorUserId="107" LastEditDate="2013-06-13T13:09:51.917" LastActivityDate="2013-06-14T09:01:24.640" Title="How is consciousness linked to the brain?" Tags="&lt;brain&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8769" PostTypeId="1" CreationDate="2013-06-13T05:12:14.393" Score="2" ViewCount="347" Body="&lt;p&gt;Are there good texts to study the evolution, how it works, and how mutations and changes lead to evolution of the organism ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And how does the information increase through the long time using mutations and other mechanisms?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you recommend specific texts? &lt;/p&gt;&#xA;" OwnerUserId="3784" LastEditorUserId="107" LastEditDate="2013-06-13T13:06:42.690" LastActivityDate="2013-06-14T09:06:27.253" Title="Which texts are good for beginners to understand evolution on the genetic scope?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;literature&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8771" PostTypeId="2" ParentId="8769" CreationDate="2013-06-13T07:39:38.903" Score="1" Body="&lt;p&gt;&lt;strong&gt;Books on my shelf right now (I'm an evolutionary genetics grad student)...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Entry level:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution - Mark Ridley (not Matt Ridley)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A primer of ecological genetics - Connor &amp;amp; Hartl&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Intermediate:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Elements of evolutionary genetics -  Charlesworth &amp;amp; Charlesworth&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Advanced:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Principles of Population genetics - Hartl &amp;amp; Clark&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Introduction to quantitative genetics - Falconer &amp;amp; Mackay&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Further basic/popular-science books include R Dawkins' Selfish Gene/The Extended Phenotype/The Greatest Show on Earth and of course The Origin of Species by Darwin&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-06-13T07:51:41.030" LastActivityDate="2013-06-13T07:51:41.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8772" PostTypeId="2" ParentId="8556" CreationDate="2013-06-13T09:56:16.603" Score="4" Body="&lt;p&gt;Blood pressure increases during exercise as shown &lt;a href=&quot;http://jama.jamanetwork.com/article.aspx?articleid=368206&quot; rel=&quot;nofollow&quot;&gt;in this paper&lt;/a&gt;, but the reason that experts recommend exercise for &lt;a href=&quot;http://en.wikipedia.org/wiki/Hypertension&quot; rel=&quot;nofollow&quot;&gt;hypertensive&lt;/a&gt; patients is that &lt;strong&gt;increases in fitness decrease blood pressure&lt;/strong&gt; (demonstrated nicely in &lt;a href=&quot;http://hyper.ahajournals.org/content/9/2/188.short&quot; rel=&quot;nofollow&quot;&gt;this study&lt;/a&gt; of &gt;2000 children, measuring fitness and blood pressure changes over 12 months). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a way, the doctors aren't saying that &lt;em&gt;exercise itself&lt;/em&gt; will decrease blood pressure, more: &lt;strong&gt;&quot;increasing fitness will decrease blood pressure, fitness will increase with regular exercise, therefore you should exercise more.&quot;&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bloodpressureuk.org/BloodPressureandyou/Yourlifestyle/Beingactive&quot; rel=&quot;nofollow&quot;&gt;Caution should be used though for taking up new exercise regimes and doctors should be consulted.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are of course other &lt;a href=&quot;http://www.nhs.uk/Livewell/fitness/Pages/Whybeactive.aspx&quot; rel=&quot;nofollow&quot;&gt;well documented benefits to regular exercise&lt;/a&gt; and personally I find it is great stress relief which could indirectly aid lowering of blood pressure (&lt;a href=&quot;http://www.heart.org/HEARTORG/Conditions/HighBloodPressure/PreventionTreatmentofHighBloodPressure/Stress-and-Blood-Pressure_UCM_301883_Article.jsp&quot; rel=&quot;nofollow&quot;&gt;stress increases blood pressure&lt;/a&gt;, mine is 80/50 - very low - and I would describe myself as quite easy going :D).&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2013-06-13T09:56:16.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8773" PostTypeId="2" ParentId="8769" CreationDate="2013-06-13T10:15:56.657" Score="1" Body="&lt;p&gt;Adding to previous answers. For basic textbooks I've been happy with (earlier editions of):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1605351156&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Evolution&lt;/em&gt;, Futuyma&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/007352526X&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Genetics: From Genes to Genomes&lt;/em&gt;, Hartwell et al.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;EDIT:&#xA;I should also mention the free pdf book &lt;a href=&quot;http://evolution.genetics.washington.edu/pgbook/pgbook.html&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Theoretical Evolutionary Genetics&lt;/em&gt; by Joe Felsenstein&lt;/a&gt;, with latest update from 2013. He uses it for a course in population gentics. So far, I have only browsed it myself. It is fairly math-heavy, but I thought that it could be of general interest. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-06-14T09:06:27.253" LastActivityDate="2013-06-14T09:06:27.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8774" PostTypeId="5" CreationDate="2013-06-13T11:50:21.753" Score="0" Body="&lt;p&gt;Extinction is sometimes also used to refer to local extinction, where a species disappears from a particular area but still exists in other places.  &lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="4101" LastEditDate="2013-10-31T19:28:00.527" LastActivityDate="2013-10-31T19:28:00.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8775" PostTypeId="4" CreationDate="2013-06-13T11:50:21.753" Score="0" Body="Extinction refers to the global disappearance of a taxon, caused by the death of the last individual member. Extinction can be used on many different levels and may relate to populations, groups of populations, species or higher taxa (such as families)." OwnerUserId="3624" LastEditorUserId="4101" LastEditDate="2013-10-31T19:28:00.527" LastActivityDate="2013-10-31T19:28:00.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8776" PostTypeId="2" ParentId="8556" CreationDate="2013-06-13T12:56:08.963" Score="5" Body="&lt;p&gt;As pointed out in the answers above, your blood pressure increases transiently as you exercise because more oxygen and nutrients are consumed by your muscles. However, regular exercise increases your &quot;cardiovascular reserve&quot;-this means your body will be able to function well at lower blood pressures. However, caution must be taken in hypertensive patients whose blood pressures are already up the roof. In these patients, gentle exercise and life style modifications (diet, stopping smoking, weight loss etc) may reduce their blood pressures over time. This will also reduce their risk of cardiovascular catastrophes in the future.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So whilst exercise will reduce blood pressure, it is not recommended as a first line of life style modification in hypertensive patients because exercise itself is stressful initially and stress is also bad for a hypertensive patient. Hence, exercise is good but gentle exercise is recommended for hypertensive patients. But again I doubt gentle exercise will do maximum good to your cardiovascular system because the type of exercise that helps lower your blood pressure is one that makes you sweat (e.g tread mill, etc). But once the blood pressure of a hypertensive patient is under control, then they can safely exercise and this should help lower their blood pressure long term. I hope this makes sense.&lt;/p&gt;&#xA;" OwnerUserId="3773" LastActivityDate="2013-06-13T12:56:08.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8777" PostTypeId="2" ParentId="8767" CreationDate="2013-06-13T14:06:41.753" Score="2" Body="&lt;p&gt;This question is difficult to answer and in the end, we'll just have to accept that we don't really know (at least for now). My own understanding is that what we call our consciousness is an emergent phenomenon, arising from the extraordinarily complex network of billions of neurons interacting with each other within the brain. Perhaps the rest of the cells in the body - everything that is interconnected - should also be included. This would mean that we are, indeed, &quot;a mix of chemicals interacting with each other&quot;, but in my opinion, that does not make being any less meaningful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note, although this seems to imply determinism, the future behaviour of complex systems such as our brain, or better yet, the entire universe, is impossible to predict accurately with any computing device. We, as well as the universe, are the best simulators of ourselves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it is really difficult to handle questions like this. To start with, how do you even define &quot;consciousness&quot;? Also, I don't think that such a discussion belongs to philosophy; surely any plausible explanation of conciousness must be rooted within the framework of science.&lt;/p&gt;&#xA;" OwnerUserId="3674" LastActivityDate="2013-06-13T14:06:41.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8778" PostTypeId="1" CreationDate="2013-06-13T14:46:44.123" Score="3" ViewCount="31512" Body="&lt;p&gt;I heard that drinking too much mineral (bottled) water could lead to problems such as kidney stones because of the high amount of minerals in it. Is it true? If so, what is considered to be excessive?&lt;/p&gt;&#xA;" OwnerUserId="3788" LastEditorUserId="69" LastEditDate="2013-08-31T13:25:51.910" LastActivityDate="2018-10-11T07:10:02.930" Title="Can the excessive consumption of mineral water lead to kidney stones or other health issues?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;kidney&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8779" PostTypeId="2" ParentId="8766" CreationDate="2013-06-13T15:22:07.327" Score="3" Body="&lt;p&gt;First of all, I think it is, to a large extent, the way you perceive it. Instead of cancer-causing allele and hair-loss allele, you can think of them as cancer-protection and great-hair alleles. If you don't have disease alleles, that means that in some sense you have &quot;life-extending&quot; genes! Sounds much better, doesn't it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second of all, most funding for research is directed at disease so it is not surprising that most of the scientific knowledge is regarding this type of genetic variation.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2013-06-13T15:22:07.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8780" PostTypeId="2" ParentId="8766" CreationDate="2013-06-13T15:36:06.017" Score="1" Body="&lt;p&gt;Lactase persistence is a recent mutation which enables the people who have it to drink and digest milk as adults, while the default state has people unable to digest milk after childhood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also a loci for muscle performance. People either have fast-twitch or slow-twitch preference, which affects your sprinting vs long-distance ability. Which one is &quot;better&quot;? It depends!&lt;/p&gt;&#xA;" OwnerUserId="1300" LastActivityDate="2013-06-13T15:36:06.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8782" PostTypeId="1" AcceptedAnswerId="8783" CreationDate="2013-06-13T15:45:37.000" Score="2" ViewCount="71" Body="&lt;p&gt;Mammals like seals often dive and can remain under water for more than 70 minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do seals know when is it the time to come up?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="115" LastEditDate="2013-06-13T15:49:31.037" LastActivityDate="2013-06-13T16:27:40.430" Title="Deep diving in mammals" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8783" PostTypeId="2" ParentId="8782" CreationDate="2013-06-13T16:27:40.430" Score="2" Body="&lt;p&gt;I imagine that their breathing is controlled in the same way as ours. During a dive, oxygen will be used up and carbon dioxide will be produced, dissolving in the blood as bicarbonate and tending to decrease the pH of the blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Peripheral_chemoreceptors&quot; rel=&quot;nofollow&quot;&gt;Peripheral chemoreceptors&lt;/a&gt; in the circulatory system detect all of these changes and &lt;a href=&quot;http://en.wikipedia.org/wiki/Control_of_respiration&quot; rel=&quot;nofollow&quot;&gt;signal the need to breathe&lt;/a&gt;. This would tell the seal that it is time to head for the surface.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diving mammals have various adaptations for prolonged diving, most importantly large reservoirs of blood containing haemoglobin which is oxygenated before a dive, as well as high concentrations of myoglobin in muscle which can also act as an oxygen reservoir.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-06-13T16:27:40.430" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8784" PostTypeId="1" CreationDate="2013-06-13T16:57:05.577" Score="2" ViewCount="126" Body="&lt;p&gt;There has been a warning about E. coli contaminated water in South Florida. Now I'm wondering are there empirical data or historic cases which show a correlation between E.coli levels in tap water and risk of infection in the population drinking this water. Which pathogens, that could be transmitted through tap water, are common in this area?&lt;/p&gt;&#xA;" OwnerUserId="3627" LastEditorUserId="3262" LastEditDate="2013-06-15T14:32:13.043" LastActivityDate="2013-06-15T14:32:13.043" Title="E. coli, risk of infection?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;digestive-system&gt;&lt;ecoli&gt;&lt;infection&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8785" PostTypeId="2" ParentId="8778" CreationDate="2013-06-13T17:03:39.730" Score="1" Body="&lt;p&gt;It is unlikely that drinking too much mineral water will cause kidney stones. One of the chief causes of kidney stones is dehydration. I can't imagine the calcium content of mineral water could be that high as to cause kidney stones (please correct me if I'm wrong) unless you drink ridiculous amount by which stage you will probably start to have electrolyte abnormalities and perhaps seizures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consumption of excessive amount of water can cause various health issues (even life threatening). These include seizures, rhythm disturbances in the heart (all usually secondary to acute electrolyte imbalance in the blood).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've never come across drinking too much mineral water as a cause for kidney stones-most people who get kidney stones usually aren't drinking enough water. The more water you take (in moderation), the less the likelihood for stone formation in your kidneys. &lt;/p&gt;&#xA;" OwnerUserId="3773" LastActivityDate="2013-06-13T17:03:39.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8786" PostTypeId="2" ParentId="8724" CreationDate="2013-06-13T17:37:02.283" Score="1" Body="&lt;p&gt;I'm not sure I understand your question very well-maybe try and rephrase it? As another example, low blood pressure in the kidneys is sensed by the juxtaglomerular apparatus which secretes renin into the circulation. Renin converts angiotensinogen (released by the liver) into angiotensin I. Angiotensin I is then converted into angiotensin II by angiotensin converting enzyme (this is the target of anti-hypertensives called ACE inhibitors) secreted by the lungs. Angiotensin II is a potent vasoconstrictor which directly increases the blood pressure (and hence glomerular filtration rate).  Angiotensin II also causes the release of aldosterone which acts on the kidneys to re-absorb salt and water again all facilitating an increase in blood pressure. I hope I've answered your question, if not please edit the question so it very clear. &lt;/p&gt;&#xA;" OwnerUserId="3773" LastActivityDate="2013-06-13T17:37:02.283" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8788" PostTypeId="1" AcceptedAnswerId="8789" CreationDate="2013-06-14T07:52:06.323" Score="4" ViewCount="3005" Body="&lt;p&gt;Some background - Some recent research has strongly suggested that UVA penetration into the skin is far more dangerous than UVB, a very good example is &lt;a href=&quot;http://www.pnas.org/content/101/14/4954.short&quot; rel=&quot;nofollow&quot;&gt;this paper by Agar et al. (2004)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My query is, is there a measure that relates the UV wavelength with the penetration depth into human skin?  Related, is the answer to this related to skin types?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I understand that this may be migrated to Biology.SE).&lt;/p&gt;&#xA;" OwnerDisplayName="user9474" LastActivityDate="2013-06-15T05:14:44.067" Title="What is the relationship between UV wavelength and penetration depth into human skin?" Tags="&lt;biophysics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8789" PostTypeId="2" ParentId="8788" CreationDate="2013-06-14T10:10:23.467" Score="6" Body="&lt;p&gt;Solar UV radiation is broadly classified as UV- A,B and C (&lt;a href=&quot;http://www.americanairandwater.com/uv-facts/uv-types.htm&quot; rel=&quot;nofollow&quot;&gt;Decreasing order&lt;/a&gt; of wavelengths). Penetrating ability of UV is a not a direct function of its wavelength; lesser the wavelength lesser is the penetrating ability (But higher is the energy: a direct function of wavelength). Penetration ability is dependent on scattering and absorption. Most biomolecules in the skin, including melanin and proteins absorb at around 220-300nm range. Plus, scattering (esp Rayleigh scattering) is inversely proportional to wavelength. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since UV B has higher energy compared to UV A, the former is more toxic to the cells. But a little UV B also does some good; conversion 7-dehydrocholesterol to Vitamin D. UV A doesn't have sufficient energy to directly cause DNA damage  but it can give rise to free radicals and cause DNA damage indirectly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper that you mentioned says that the tissue that they studied has more of UV A mediated lesions. This could be because of higher availability of UV A to the cells. Ozone filters out a major chunk of UV B and C and melanin does little more. If these mechanisms didn't exist then high energy UVs would have burnt us. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To summarize, the inherent order of toxicity is &lt;code&gt;C &amp;gt; B &amp;gt; A&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.uio.no/studier/emner/matnat/fys/FYS3610/h04/undervisningsmateriale/Moan7.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.uio.no/studier/emner/matnat/fys/FYS3610/h04/undervisningsmateriale/Moan7.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/jid/journal/v77/n1/abs/5615637a.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/jid/journal/v77/n1/abs/5615637a.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-06-15T05:14:44.067" LastActivityDate="2013-06-15T05:14:44.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8791" PostTypeId="2" ParentId="8784" CreationDate="2013-06-14T13:05:00.873" Score="1" Body="&lt;p&gt;The maximum temperature for &lt;em&gt;E. coli&lt;/em&gt; to survive is dependent on the strain. &lt;em&gt;E. coli&lt;/em&gt; from warm areas can easily survive 45 °C and more. The minimum number of &lt;em&gt;E. coli&lt;/em&gt; to ingest in order to become ill is also dependent on the strain. Whether you become ill at all is also dependent on the strain. You harbor many billions of &lt;em&gt;E. coli&lt;/em&gt; in your digestive tract without becoming ill, so without further information on the released strain, it's really hard to tell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the suggestions from the &lt;a href=&quot;http://www.who.int/water_sanitation_health/dwq/guidelines/en/&quot; rel=&quot;nofollow&quot;&gt;WHO Guidelines for drinking water quality&lt;/a&gt; is to boil the water in order to desinfect it.&lt;/p&gt;&#xA;" OwnerUserId="852" LastEditorUserId="852" LastEditDate="2013-06-14T13:13:16.817" LastActivityDate="2013-06-14T13:13:16.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8792" PostTypeId="2" ParentId="8784" CreationDate="2013-06-14T15:22:57.913" Score="1" Body="&lt;p&gt;One &lt;a href=&quot;http://www.textbookofbacteriology.net/e.coli_4.html&quot; rel=&quot;nofollow&quot;&gt;textbook of microbiology&lt;/a&gt; suggests that the infectious dose of a specific strain of enterotoxigenic &lt;em&gt;E. coli&lt;/em&gt; in adults would be $10^{8}$ cells. Keep in mind that infective dose will vary with species and strain, as well as the health, age and immune-status of the individual ingesting the bacteria. Children, elderly and ill people will generally be affected by a lower infective dose. This does also not consider how well the bacteria can colonize the gastrointestinal system. It is possible for minimal numbers of pathogenic &lt;em&gt;E. coli&lt;/em&gt; to colonize in the gut, and only after growing to a infectious level, being to exert pathogenic effects.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2013-06-14T17:39:47.130" LastActivityDate="2013-06-14T17:39:47.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8793" PostTypeId="1" AcceptedAnswerId="8794" CreationDate="2013-06-14T17:13:21.563" Score="5" ViewCount="120" Body="&lt;p&gt;I read about the regulation of Calvin cycle by thioredoxin which activates key enzymes essentially by converting disulphide linkages on inactive enzymes into sulfhydryls. Another regulatory mechanism is the pH control. The enzymes work at a slightly alkaline pH which is established as soon as the proton gradient is set up by the light reactions. But aren't these two mechanisms contradictory: at alkaline pH, the sulfhydryls $-SH$ groups, being acidic, will dissociate by giving up a proton and will be more stable in the dissociated form.&lt;br&gt;&#xA;In general I fail to understand how pH will decide which bio-compounds will dissociate into proton or hydroxyl.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="1320" LastEditDate="2013-06-14T19:07:18.943" LastActivityDate="2013-06-14T19:59:05.930" Title="Photosynthesis regulation" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;plant-physiology&gt;&lt;enzymes&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8794" PostTypeId="2" ParentId="8793" CreationDate="2013-06-14T19:20:33.440" Score="4" Body="&lt;p&gt;Your question conflates two separable events, a redox process and an acid-base dissociation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The interconversion between disulfides and free sulfhydryls is a redox reaction, governed by the redox potential of the surroundings. The importance of redox potential to the -S-S- &amp;lt;&gt; -SH equilibrium is illustrated by the difference between the cytosol and the lumen of the endoplasmic reticulum (ER). The cytosol is reducing and so free thiols are prevalent (there are usually no disulfide bonds in cytosolic proteins) whereas the ER lumen is oxidising, and the formation of disulfides in secreted proteins is promoted. The redox potentials of the two compartments is set primarily by the ratio between oxidised glutathione and reduced glutathione.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thiol group in cysteine residues of proteins typically has a pK&lt;sub&gt;a&lt;/sub&gt; of around 7, so it will indeed have some acidic character at slightly alkaline pH, dissociating to form a thiolate group. This doesn't however promote the reformation of disulfides, and in any case if it is important for a protein to have an undissociated thiol, then the environment of the specific cysteine residue can be adapted to raise its pK&lt;sub&gt;a&lt;/sub&gt;. Note however that it is also possible that the thiolate form may be compatible with (or even required for) the function of the enzyme.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-06-14T19:59:05.930" LastActivityDate="2013-06-14T19:59:05.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8795" PostTypeId="2" ParentId="8473" CreationDate="2013-06-14T22:38:23.467" Score="0" Body="&lt;p&gt;Have you looked at ALFRED (The ALlele FREquency Database)?  The data is from 2011, but seems extensive and has downloadable zip files at &lt;a href=&quot;http://alfred.med.yale.edu/alfred/alfredDataDownload.asp&quot; rel=&quot;nofollow&quot;&gt;http://alfred.med.yale.edu/alfred/alfredDataDownload.asp&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2013-06-14T22:38:23.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8796" PostTypeId="1" AcceptedAnswerId="8905" CreationDate="2013-06-15T04:16:13.520" Score="3" ViewCount="238" Body="&lt;p&gt;&lt;a href=&quot;http://research.eeescience.utoledo.edu/lees/papers_PDF/PhotosynRes_73_2002/Anderson_2002_PhotosynRes.pdf&quot; rel=&quot;nofollow&quot;&gt;See paper for distribution of PS-I and PS-II within grana&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As explained in the above paper, the PS-I complex is primarily located within non-appressed thylakoid region and stroma lamella, while PS-II in the appressed regions. Now since non-cyclic electron transfer (non-cyclic photophosphorylation) requires both the photosystems, wouldn't their distribution within grana far from one another hamper their ability to carry out non-cyclic electron transport. Although there are mobile untis to account for the electron transport between marginal PS-I and the PS-II immediately below, but the electron transport to the PS-II units deep in the granal core would still be unaccounted for.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2013-06-23T09:28:22.137" LastActivityDate="2013-06-23T11:55:29.857" Title="Electron transport in granal stacks" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8798" PostTypeId="1" AcceptedAnswerId="8820" CreationDate="2013-06-15T07:03:33.937" Score="4" ViewCount="161" Body="&lt;p&gt;It is reasonably well known that many species, such as bees and some types of birds as examples can see into the ultraviolet (UV).  How is the structure of their eye different to humans to allow this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, how are they shielded from some of the harmful effects of ocular UV exposure?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2018-10-29T16:37:20.500" Title="Animal UV vision" Tags="&lt;vision&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8799" PostTypeId="1" AcceptedAnswerId="8801" CreationDate="2013-06-15T10:22:32.193" Score="0" ViewCount="81" Body="&lt;p&gt;I would like to know if every cell is competent or if there are any cells that are not competent.&lt;/p&gt;&#xA;" OwnerUserId="3751" LastEditorUserId="1320" LastEditDate="2013-06-15T21:47:07.943" LastActivityDate="2013-06-15T21:47:07.943" Title="Is every cell competent?" Tags="&lt;cell-biology&gt;&lt;competent-cells&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8800" PostTypeId="1" CreationDate="2013-06-15T11:16:40.233" Score="4" ViewCount="179" Body="&lt;p&gt;I am trying to find a model to link the phenotype eye color to its genotypes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that there exists a simple model from Davenport, which explains &lt;em&gt;{brown,blue}&lt;/em&gt; eyes. Further, there is an extended model for &lt;em&gt;{brown,green,blue,gray}&lt;/em&gt; eyes, based on the two genes &lt;em&gt;bey2&lt;/em&gt; and &lt;em&gt;gey&lt;/em&gt;. There are plenty of articles suggesting further genes which may or may not have certain impacts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a model which is more precise than the above mentioned, but which is well applicable (i.e. does not introduce excessive complexity and has greater accuracy)? I am trying to come up with some probabilistic calculations, and could well handle one or two further genes. It would also be interesting to know about the accuracy of the model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many thanks!&lt;/p&gt;&#xA;" OwnerUserId="3801" LastActivityDate="2013-06-15T11:16:40.233" Title="Eye color genetics" Tags="&lt;genetics&gt;&lt;eyes&gt;&lt;mathematical-models&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8801" PostTypeId="2" ParentId="8799" CreationDate="2013-06-15T11:22:03.017" Score="1" Body="&lt;p&gt;Assuming that you are asking about &lt;em&gt;E.coli&lt;/em&gt; cells being made competent for transformation using plasmid DNA, an answer is cached &lt;a href=&quot;http://scholar.googleusercontent.com/scholar?q=cache%3atBaJCHM2y-MJ%3ascholar.google.com/&amp;amp;hl=en&amp;amp;as_sdt=0,5&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; from this source:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hanahan, D. &amp;amp; Bloom, F.R. (1996). Mechanisms of DNA transformation. In F.C. Neidhardt (ed.). Escherichia coli and Salmonella : Cellular and Molecular Biology. (pp. 2449-2459). Washington D.C., United States: ASM Press. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The source (and it is perhaps worth emphasising that Hanahan is/was a transformation guru) states that treatment with divalent cations can achieve 10% of cells rendered competent, whereas treatment for electroporation can achieve transfer into 95% of cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This information was, of course, published in 1996 so it is conceivable that advances have been made in the case of the former method.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-06-15T11:22:03.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8802" PostTypeId="1" CreationDate="2013-06-15T11:24:08.917" Score="13" ViewCount="5846" Body="&lt;p&gt;I have always been told to watch to see if ant-hole mounds are built up as a sign of imminent rainfall.  My questions are, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;if what I have always been told is true, then by what mechanism do ants 'sense' the imminent rainfall?  Is it a case of sensing air pressure drop, increasing humidity or both?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="55929" LastEditDate="2020-01-06T00:33:19.927" LastActivityDate="2020-11-29T15:28:34.200" Title="How do ants sense imminent rainfall?" Tags="&lt;entomology&gt;&lt;sensation&gt;&lt;ant&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8803" PostTypeId="2" ParentId="8386" CreationDate="2013-06-15T12:38:28.163" Score="7" Body="&lt;p&gt;There are indeed 'gap junctions' which pass current directly from one cell to the next. So what advantages do we get out of chemical synapses that gap junctions do not provide? &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Asymmetry&lt;/strong&gt;. Synapses do not operate in reverse, thus the postsynaptic cell cannot generate currents in the presynaptic terminal (although there are secondary forms of communication which may operate in the reverse direction). &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Ion Selectivity&lt;/strong&gt;. A synapse allows one set of ionic currents to be transformed into any other set. Thus sodium and calcium influx at the presynaptic terminal might translate to chloride influx to make the synapse inhibitory. Furthermore, the ability of the postsynaptic cell to control calcium levels is critical for plasticity mechanisms.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Insulation&lt;/strong&gt;. Gap junctions increase the conductance of the cell membrane, which can reduce the fidelity of signals as they propagate along the dendrite. In contrast, an inactive synapse might have virtually no effect on the postsynaptic cell--it does not pass currents.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Kinetics&lt;/strong&gt;. Because chemical synapses generate their own ionic currents, they are also free to modify the &lt;em&gt;speed&lt;/em&gt; of those currents (how quickly they rise and fall). This is much more difficult to achieve with gap junctions.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;There is a very long list of functionality provided only by synapses which I have not listed here, but I think most of those are things which could, in principle, also be achieved with gap junctions (for example: amplitude control, metabolic responses, short- and long-term plasticity). &lt;/p&gt;&#xA;" OwnerUserId="1248" LastEditorUserId="1248" LastEditDate="2017-07-14T23:14:16.323" LastActivityDate="2017-07-14T23:14:16.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8804" PostTypeId="2" ParentId="8282" CreationDate="2013-06-15T13:21:23.797" Score="17" Body="&lt;p&gt;There are two factors that need to be taken into account here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1. Myelination decreases membrance capacitance.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rate at which sodium influx through a node can depolarize the axon at the next node is related to both the &lt;em&gt;current&lt;/em&gt; and &lt;em&gt;capacitance&lt;/em&gt; across the membrane (in addition to a few other factors). So while adding a new node to the axon would indeed increase its ability to generate sodium current, it would also increase the capacitance and thus diminish the effectiveness of other nearby nodes. So it doesn't help to move the nodes closer together. What if instead we &lt;em&gt;increase&lt;/em&gt; the distance between nodes? In that case, the trade-off is reversed and conduction velocity is again decreased. So there is some optimal internodal distance at which conduction velocity is maximized, and it turns out most axons happen to have just that geometry. [See: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov.libproxy.lib.unc.edu/pubmed/6245357&quot;&gt;Waxman, SG. 1980&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. Action potentials are metabolically expensive.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The brain uses a lot of energy (about 20% of the body's metabolism at rest)! Maintaining the proper balance of ions inside the neuron is the major reason for this energy usage. Every action potential incurs metabolic cost and if we double the number of nodes along an axon, we (nearly) double the metabolic cost of propagating spikes down that axon. So although conduction velocity appears to be the primary determinant in the choice of internodal distance, it is important to remember that it is not the only factor the organism must take into account.&lt;/p&gt;&#xA;" OwnerUserId="1248" LastActivityDate="2013-06-15T13:21:23.797" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8806" PostTypeId="1" CreationDate="2013-06-15T18:32:34.583" Score="8" ViewCount="6538" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;Lactulose is also used to reduce the amount of ammonia in the blood of patients with liver disease. It works by drawing ammonia from the blood into the colon where it is removed from the body.&#xA;[&lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/druginfo/meds/a682338.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;How is ammonia removed from the colon?&lt;/p&gt;&#xA;&lt;p&gt;From the quote above it sounds like ammonia removal must be some other mechanism than absorbing it into the blood, correct?&lt;/p&gt;&#xA;" OwnerUserId="1413" LastEditorUserId="24354" LastEditDate="2020-06-27T08:42:52.840" LastActivityDate="2020-07-27T20:12:53.217" Title="How does lactulose cause the removal of ammonia from the colon?" Tags="&lt;physiology&gt;&lt;metabolism&gt;&lt;pharmacology&gt;&lt;digestive-system&gt;&lt;gastroenterology&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="8807" PostTypeId="1" AcceptedAnswerId="9619" CreationDate="2013-06-15T18:47:44.180" Score="0" ViewCount="3142" Body="&lt;p&gt;“&lt;em&gt;Before taking lactulose, tell your doctor and pharmacist what prescription and nonprescription medications you are taking, especially &lt;strong&gt;antacids&lt;/strong&gt;, antibiotics including neomycin (Mycifradin), and other laxatives.&lt;/em&gt;” (Quote from &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/druginfo/meds/a682338.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do antacids have a special importance when taking lactulose?&lt;/p&gt;&#xA;" OwnerUserId="1413" LastEditorUserId="69" LastEditDate="2013-06-18T15:16:16.963" LastActivityDate="2018-01-25T19:54:05.177" Title="Why do antacids have a special importance when taking lactulose?" Tags="&lt;pharmacology&gt;&lt;digestive-system&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8808" PostTypeId="1" CreationDate="2013-06-15T18:56:15.953" Score="2" ViewCount="4260" Body="&lt;p&gt;“&lt;em&gt;Before taking lactulose, tell your doctor and pharmacist what prescription and nonprescription medications you are taking, especially antacids, &lt;strong&gt;antibiotics including neomycin (Mycifradin)&lt;/strong&gt;, and other laxatives.&lt;/em&gt;” (Quote from &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/druginfo/meds/a682338.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do antibiotics have a special importance when taking lactulose?&#xA;Why is neomycin (Mycifradin) mentioned separately?&lt;/p&gt;&#xA;" OwnerUserId="1413" LastActivityDate="2013-06-17T20:23:41.733" Title="Why do antibiotics have a special importance when taking lactulose?" Tags="&lt;digestive-system&gt;&lt;antibiotics&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8809" PostTypeId="1" CreationDate="2013-06-15T19:27:06.777" Score="1" ViewCount="402" Body="&lt;p&gt;What is neutral genetic differentiation? Presumably it's a measure of the distance between organisms in terms of their genetics, but what does 'neutral' refer to?&lt;/p&gt;&#xA;" OwnerUserId="1216" LastActivityDate="2020-09-21T18:03:10.303" Title="What is neutral genetic differentiation?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8810" PostTypeId="2" ParentId="8808" CreationDate="2013-06-16T01:42:53.273" Score="3" Body="&lt;p&gt;From the &lt;a href=&quot;http://en.wikipedia.org/wiki/Lactulose&quot; rel=&quot;nofollow&quot;&gt;Wikipedia article&lt;/a&gt; (I'm sure there's a scholarly reference, but I think this is well-known):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Lactulose works by relieving constipation through a number of different methods. Lactulose is made up of sugar molecules and is partly broken down by the bacteria that live in the lower part of the gut. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, certain antibiotics affect (and reduce) the intestinal flora (and neomycin especially so, which is I believe the reason why it is mainly used in ointments), leaving the lactulose undigested and not as effective in forcing the body to retain water in the colon, which is the mechanism through which the drug acts.&lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2013-06-16T01:42:53.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8811" PostTypeId="1" AcceptedAnswerId="8859" CreationDate="2013-06-16T03:29:56.950" Score="7" ViewCount="5305" Body="&lt;p&gt;Neurons expend the majority of their energy powering ion pumps to maintain the chemical gradients that power their electrical activity. To have a negative resting potential, neurons leak potassium across the membrane, which seems like a terrible waste of energy to me. I would like to know what benefit a neuron receives in exchange for this seemingly unnecessary metabolic load. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not asking &lt;em&gt;how&lt;/em&gt; the resting potential is achieved. I am also not interested in the trivial answer: that the voltage-gated channels are configured to require a transition across the -40mV or so threshold in order to fire an action potential. It seems to me that this threshold is arbitrary; if there was no advantage to maintaining this gradient then neurons would have evolved to avoid it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any ideas? Or better yet, pointers to places where this has already been answered? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My best guess so far looks like this: The total range of available voltages is more-or-less fixed from -90 to +50mV. We want to avoid getting too close to either end, since the channels become less effective near their reversal potentials, so maybe the effective range is more like -70 to +30 (to go outside that range, we must sacrifice speed). Within that 100mV range, we leave the bottom 30mV or so for EPSP integration, and the other 60mV for action potentials.  Now, if the resting potential was 0mV, the available dynamic range for integration and spiking would be much smaller which probably translates to making the output noisier. &lt;/p&gt;&#xA;" OwnerUserId="1248" LastActivityDate="2013-06-19T22:25:46.777" Title="Why do neurons have a negative resting potential?" Tags="&lt;neuroscience&gt;&lt;electrophysiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8812" PostTypeId="1" AcceptedAnswerId="8818" CreationDate="2013-06-16T03:54:00.700" Score="3" ViewCount="1289" Body="&lt;p&gt;What is the main difference between a precursor miRNA and a mature miRNA? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is often the case that we have more than one precursor miRNA but only one mature miRNA.  The miRNA-seq data contains only precursor miRNAs, so I was wondering if we could use the expression of the precursor miRNA as the expression of the mature product or not?&lt;/p&gt;&#xA;" OwnerUserId="3806" LastEditorUserId="3059" LastEditDate="2013-06-16T18:20:37.697" LastActivityDate="2013-06-17T13:13:21.693" Title="Precursor miRNA and a mature miRNA" Tags="&lt;genetics&gt;&lt;rna&gt;&lt;small-rnaseq&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8813" PostTypeId="1" CreationDate="2013-06-16T10:24:58.810" Score="3" ViewCount="1484" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Coeliac_Disease#Signs_and_symptoms&quot; rel=&quot;nofollow&quot;&gt;Wikipedia states&lt;/a&gt; that “&lt;em&gt;Severe coeliac disease leads to the characteristic symptoms of pale, loose and greasy stool (steatorrhoea)&lt;/em&gt;”. However thumbing through the causes and the pathophysiology it did not become clear to me what leads to this key symptom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By what mechanism does coeliac disease cause excess fat in the feces?&lt;/p&gt;&#xA;" OwnerUserId="1413" LastEditorUserId="1413" LastEditDate="2013-08-08T13:26:20.947" LastActivityDate="2013-08-08T13:26:20.947" Title="By what mechanism does coeliac disease cause excess fat in the feces?" Tags="&lt;digestive-system&gt;&lt;pathology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8814" PostTypeId="2" ParentId="8813" CreationDate="2013-06-16T11:53:11.270" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Coeliac_disease&quot;&gt;Coeliac disease&lt;/a&gt; is an immune disorder resulting from a reaction to ingested gluten (a protein found in wheat, barley and rye). It is associated with inflammation of the small intestine resulting in a generalised reduction in the capacity for digestion and absorption. According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10570344&quot;&gt;this paper&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Celiac disease is associated with pancreatico-biliary disease. Postulated mechanisms include reduced gallbladder emptying due to impaired cholecystokinin release and pancreatitis due to malnutrition.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Cholecystokinin is a peptide hormone that is produced by specialised cells in the small intestine and which stimulates the production and release of pancreatic enzymes and bile. Digestion of fat is critically dependent upon the emulsifying properties of bile salts in bile, together with pancreatic lipase. Any breakdown in this stimulatory pathway would result in reduced capacity for digestion of dietary fat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Failure to digest fat results in fatty stools (steatorrhoea) which is one of the classic symptoms of the disorder.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-06-16T11:53:11.270" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8815" PostTypeId="2" ParentId="8813" CreationDate="2013-06-16T12:07:52.170" Score="2" Body="&lt;p&gt;Alan has covered some of it, but to add an illustration of the malabsorption piece of it, below left you can see a &quot;normal&quot; slice of small intestine, where the villi (finger like projections) are covered in enterocytes (the purple &quot;bricks&quot; along the border of the finger), which are responsible for the uptake of lipids (and their eventual &quot;packaging&quot;) after they have been emulsified with bile salts in the intestinal lumen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The offending gluten causes an autoimmune reaction over time that damages these villi as well as the enterocytes (as seen on the right side of the diagram), leaving a flattened area (hence far less surface area for absorption), and disrupted lipid packaging, so the unabsorbed lipids continue through the intestine into the stool.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/T6oKS.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;from &lt;a href=&quot;http://medcell.med.yale.edu/systems_cell_biology/gi/celiac_sprue.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cell Biology at Yale&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2013-06-16T12:07:52.170" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8816" PostTypeId="1" AcceptedAnswerId="8827" CreationDate="2013-06-16T14:11:44.493" Score="3" ViewCount="1693" Body="&lt;p&gt;I'm looking at this &lt;a href=&quot;http://www.ted.com/talks/manal_al_sharif_a_saudi_woman_who_dared_to_drive.html&quot; rel=&quot;nofollow&quot;&gt;Ted talk about a Saudi Arabia woman who dared to drive a car in the last few years&lt;/a&gt;. This reminds me that until the last century or so, women (all over the world?) enjoyed less rights and might've been pigeonholed into roles predetermined by society. Those roles might've encouraged certain traits, and discouraged others. Those who did not conform might've been punished, like the woman in the talk above received death threats and was jailed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This sounds to me like selective pressure, did it really exist, and did it have any effect on the genetics/traits of modern women?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This makes me interested in the question - &lt;strong&gt;compared to other species, are men and women more genetically different because of selective pressure put on women to conform to male-dominated world&lt;/strong&gt; for thousands of years before 19th century?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-06-18T05:56:27.723" Title="Are human males and females more genetically different than members of other species?" Tags="&lt;human-genetics&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8817" PostTypeId="1" CreationDate="2013-06-16T14:58:19.080" Score="3" ViewCount="698" Body="&lt;p&gt;Evolution is often described as a fact, and a theory. Evolution is a heavily overloaded term, with one definition being the fact that, &amp;quot;changes in the frequency of alleles in populations of organisms from generation to generation.&amp;quot; This is a measurable fact, but not the usage of the word evolution that I am in interested in.&lt;/p&gt;&#xA;&lt;p&gt;Wikipedia has several quotes on the matter, including the Webaters definition used in this questions title, but also includes clearly observational facts like the Earth revolves around the sun.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;A fact is a hypothesis that is so firmly supported by evidence that we assume it is true, and act as if it were true. —&lt;em&gt;Douglas Futuyma&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;There is no sharp line between speculation, hypothesis, theory, principle, and fact, but only a difference along a sliding scale, in the degree of probability of the idea. When we say a thing is a fact, then, we only mean that its probability is an extremely high one: so high that we are not bothered by doubt about it and are ready to act accordingly. Now in this use of the term fact, the only proper one, evolution is a fact. —&lt;em&gt;H. J. Muller&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;Scientists most often use the word &amp;quot;fact&amp;quot; to describe an observation. But scientists can also use fact to mean something that has been tested or observed so many times that there is no longer a compelling reason to keep testing or looking for examples. The occurrence of evolution in this sense is fact. Scientists no longer question whether descent with modification occurred because the evidence is so strong. —&lt;em&gt;National Academy of Science&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Do scientists refer to any theories for which there is overwhelming evidence as a &amp;quot;scientific fact&amp;quot;, other than in biological sciences?&lt;/p&gt;&#xA;&lt;p&gt;Note: Good answers will include quotes from scientific organizations or prominent scientists using the term &lt;strong&gt;fact&lt;/strong&gt; to describe the theory, and will include references to the theory itself.&lt;/p&gt;&#xA;" OwnerUserId="3807" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-07-01T22:07:03.877" Title="Is a &quot;Fact&quot; any theory for which there is overwhelming evidence in any field other than biology?" Tags="&lt;evolution&gt;&lt;terminology&gt;&lt;philosophy-of-science&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8818" PostTypeId="2" ParentId="8812" CreationDate="2013-06-16T16:22:03.363" Score="4" Body="&lt;p&gt;precursor miRNA is ~70mer RNA with a stem loop structure. It is cleaved by dicer to generate one or two mature miRNAs (from one or both the 'arms' of the stem ; called 3p and 5p which are ~22nt long). Refer to &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867404000455&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; review. (It is an old one and some facts might have changed, but the basics are there.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, there can be different precursors giving rise to same mature form. There are a few cases like that (check for entries like mir-x-y [where y can be 1,2,3,...], in miRbase). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually pre-miRNA is shortlived and is immediately converted to mature form. Therefore, in small RNAseq data, most miRNA reads (more than 90% [at least that's what I get]) come from mature form (pre reads would be longer [after adapter removal] and will contain sequences not retained in mature form). Most algorithms select for the mature reads. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is difficult to determine which precursor gave rise to a certain mature miRNA, using an RNAseq data. The usual practice is to assign the average read count to each locus. E.g., for a mature form that has 3 precursors, each precursor is assigned 1/3 of the total mature reads. However, in most RNAseq experiments, the objective is to obtain the mature miRNA profile and which precursor gives rise to it becomes immaterial.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="107" LastEditDate="2013-06-17T13:13:21.693" LastActivityDate="2013-06-17T13:13:21.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8819" PostTypeId="2" ParentId="8817" CreationDate="2013-06-16T16:30:22.360" Score="3" Body="&lt;p&gt;Your question really applies to any scientific theory, not just evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem is that, outside of the scientific world, a theory is often thought as something unproven, an unproven guess if you wish. This is not true for scientific theories, which, instead are confirmed by experimental data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The OED defines &lt;strong&gt;theory&lt;/strong&gt; as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A scheme or system of ideas or statements held as an explanation or account of a group of facts or phenomena; a hypothesis that has been confirmed or established by observation or experiment, and is propounded or accepted as accounting for the known facts; a statement of what are held to be the general laws, principles, or causes of something known or observed. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and &lt;strong&gt;fact&lt;/strong&gt; as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Something that has really occurred or is actually the case; something certainly known to be of this character; hence, a particular truth known by actual observation or authentic testimony, as opposed to what is merely inferred, or to a conjecture or fiction; a datum of experience, as distinguished from the conclusions that may be based upon it.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, essentially we start with an unproven idea, we corroborate it with facts (=experimental data) and we define our theory accordingly to facts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, why don't we say that evolution is true or that it is a dogma or that it is a fact?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well, that is not how science work. Evolution is a scientific theory, and it always will be. Maybe (hopefully, dare I say) in 50 years from now new evidence will have make us change the theory of evolution, at least some bits of it.&lt;br&gt;&#xA;Luckily evolutionary biology is not stuck at the time of Darwin and genetics is not stuck at the time of Mendel. Many new pieces of evidence have made us &lt;strong&gt;improve&lt;/strong&gt; the theories that they initially defined. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does that mean they were bad scientist or that they experiments were faked? Not at all!  Simply as their knowledge was more restricted than ours, they could not formulate a more advanced theory. Mendel's experiments still hold true, but now we know that transmissions of characters is not as simple. He was just looking at &lt;em&gt;a special case&lt;/em&gt;. And his experiments still fit in our current theory, and will have to fit in any future one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A scientific theory is defined by its falsifiability, that is &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the trait of a statement, hypothesis, or theory whereby it could be shown to be false if some conceivable observation were true. In this sense, falsify is synonymous with nullify, meaning not &quot;to commit fraud&quot; but &quot;show to be false&quot;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The famous black swan example by Karl Popper (see e.g. &lt;a href=&quot;http://books.google.no/books?id=IENmxiVBaSoC&amp;amp;lpg=PP1&amp;amp;dq=Conjectures%20and%20Refutations%3A%20The%20Growth%20of%20Scientific%20Knowledge&amp;amp;pg=PP1#v=onepage&amp;amp;q=Conjectures%20and%20Refutations%3a%20The%20Growth%20of%20Scientific%20Knowledge&amp;amp;f=false&quot; rel=&quot;nofollow&quot; title=&quot;Karl Popper. 2002 .  Conjectures and refutations: the growth of scientific knowledge (original ed. 1963). London: Routledge&quot;&gt;&lt;em&gt;Conjectures and refutations&lt;/em&gt;, 1963, chapter 11.6&lt;/a&gt;), can be exemplified by (source: &lt;a href=&quot;http://en.wikipedia.org/wiki/Falsifiability&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One notices a white swan. From this one can conclude:&lt;br&gt;&#xA;      At least one swan is white.&lt;br&gt;&#xA;  From this, one may wish to conjecture:&lt;br&gt;&#xA;      All swans are white.&lt;br&gt;&#xA;  It is impractical to observe all the swans in the world to verify that they are all white.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Even so, the statement all swans are white is testable by being falsifiable. For, if in testing many swans, the researcher finds a single black swan, then the statement all swans are white would be falsified by the counterexample of the single black swan.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, our theory of the white swan is accepted as &quot;temporary true&quot;, as long as a black swan is not found. Obviously the more white swans we count (i.e. the more experimental evidence we have), the stronger our theory will be. But it will never be true.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to finish quoting Richard Feynman:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is scientific only to say what is more likely and what less likely, and not to be proving all the time the possible and impossible. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We never are right, we can only be sure we're wrong&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I suggest to watch the full video of his fantastic lecture on scientific method &lt;a href=&quot;http://youtu.be/EYPapE-3FRw&quot; rel=&quot;nofollow&quot;&gt;on YouTube&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2013-07-01T22:07:03.877" LastActivityDate="2013-07-01T22:07:03.877" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="8820" PostTypeId="2" ParentId="8798" CreationDate="2013-06-16T16:53:11.957" Score="2" Body="&lt;p&gt;Firstly most UV perceiving organisms only perceive far UV (~300-400nm) which is less damaging. There are different &lt;a href=&quot;http://en.wikipedia.org/wiki/Photopsin&quot; rel=&quot;nofollow noreferrer&quot;&gt;opsins&lt;/a&gt;, which get activated by different wavelengths. Like other light UV is perceived by opsins sensitive to UV wavelength [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17251489&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref&lt;/a&gt;]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure about this but opsin sensitivity to UV must be high so that low irradiation is sufficient for perception and excess is filtered off.&#xA;UV filter mechanism in reported for &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21873681&quot; rel=&quot;nofollow noreferrer&quot;&gt;human&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16297909&quot; rel=&quot;nofollow noreferrer&quot;&gt;squirrel&lt;/a&gt; eye; mostly uses kynurenine derivaties. May be similar mechanism is present in other organisms too.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2018-10-29T16:37:20.500" LastActivityDate="2018-10-29T16:37:20.500" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="8821" PostTypeId="1" CreationDate="2013-06-16T22:28:46.677" Score="9" ViewCount="7410" Body="&lt;p&gt;Specifically the part of the brain that does depth perception based on binocular vision. I have searched all over the web and have turned up nothing. Is it the same part of the brain that processes all images from the retina?&lt;/p&gt;&#xA;" OwnerUserId="3809" LastActivityDate="2016-11-01T16:53:22.483" Title="What part of the brain controls depth perception?" Tags="&lt;neuroscience&gt;&lt;perception&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8822" PostTypeId="2" ParentId="8816" CreationDate="2013-06-17T06:20:14.437" Score="4" Body="&lt;p&gt;Essentially, what makes a (mammalian) man a man is a small region on the Y-chromosome called SRY. If this region is deleted, a female phenotype having XY-chromosomes develops. If this region is translocated to an X-chromosome, a male phenotype with two X-chromosomes develops. Other than that, the Y-chromosome does not carry a lot of genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So apart from the Y chromosome, males and females are genetically very similar and more similar compared to other species.&lt;/p&gt;&#xA;" OwnerUserId="852" LastActivityDate="2013-06-17T06:20:14.437" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8823" PostTypeId="2" ParentId="8821" CreationDate="2013-06-17T06:52:02.823" Score="3" Body="&lt;p&gt;According to &lt;a href=&quot;http://machineslikeus.com/news/scientists-uncover-second-depth-perception-method-brain&quot; rel=&quot;nofollow&quot;&gt;the article: Scientists uncover second depth-perception method in the brain&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the neurons in the middle temporal area of the brain are combining visual information and physical movement to extract depth information&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=two-eyes-two-views&quot; rel=&quot;nofollow&quot;&gt;This Scientific American article&lt;/a&gt; states that there is a process involved:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Visual-image processing from the eye to the brain happens in stages. Rudimentary features such as the orientation of edges, direction of motion, color, and so on are extracted early on in areas called V1 and V2 before reaching the next stages in the visual-processing hierarchy for a progressively more refined analysis. This stage-by-stage description is a caricature; many pathways go “back” from stage to stage—allowing the brain to play a kind of 20-questions game to arrive at a solution after successive iterations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This process is discussed further in &lt;a href=&quot;http://cns.bu.edu/~steve/FanGro2007FromStereoSV.pdf&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; with what is known as the Laminart model.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-06-17T06:52:02.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8824" PostTypeId="1" CreationDate="2013-06-17T09:41:14.847" Score="1" ViewCount="73" Body="&lt;p&gt;Gene : HBA2? hemoglobin alpha 2 (&lt;em&gt;Homo sapiens&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't find any tissues (or organs) in which the expression of this gene is strongest? What is the size of the gene (promoter off) encoding this sequence?&lt;/p&gt;&#xA;" OwnerUserId="3813" LastEditorUserId="107" LastEditDate="2013-06-17T13:15:25.593" LastActivityDate="2013-07-17T16:21:52.250" Title="Information Gene HBA2" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="8825" PostTypeId="1" AcceptedAnswerId="8826" CreationDate="2013-06-17T09:49:07.287" Score="11" ViewCount="4684" Body="&lt;p&gt;According to the information from &lt;a href=&quot;http://www.abc.net.au/science/slab/shorter/story.htm&quot; rel=&quot;noreferrer&quot;&gt;this article&lt;/a&gt;, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;People and other primates are exquisitely sensitive to funnel web venom but, intriguingly, other mammals such as mice, rabbits, guineapigs, dogs and cats are relatively immune and often survive 100 times the human lethal dosage.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why is the funnel web spider venom so much more lethal for humans and primates than other mammals?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="1590" LastEditDate="2013-07-30T15:19:36.613" LastActivityDate="2018-10-18T22:15:15.197" Title="Why is funnel web spider venom so lethal to humans and not so much for other mammals?" Tags="&lt;biochemistry&gt;&lt;toxicology&gt;&lt;arachnology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8826" PostTypeId="2" ParentId="8825" CreationDate="2013-06-17T12:54:24.160" Score="20" Body="&lt;p&gt;First, we need to understand that neurons have special proteins embedded in their membranes called ion channels. These allow dissolved ions such as sodium, potassium, and calcium to pass from one side of the membrane to the other. Neurons use these channels to control their electrical activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Peptide neurotoxins such as the one produced by funnel spiders (robustoxin) work by having a shape and charge configuration that is complementary to ion channels, and thus they will bind to these channels and affect the way they operate (often by simply blocking the channel). Robustoxin seems to operate by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9560455&quot;&gt;removing sodium-channel inactivation&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a bit more information about the primary toxin on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Delta_atracotoxin&quot;&gt;Wikipedia page for delta atracotoxin&lt;/a&gt;. The intended target of this toxin seems to be insects, where it interferes with potassium and calcium channels. In mammals it interferes with sodium channels, but it seems to be particularly potent in primates. Why are some species affected more than others? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all ion channels are built the same. From species to species, we see a huge array of genetic differences that affect both the shape and functional properties of these proteins. Ion channels which happen to have a shape and charge configuration that is highly complementary to robustoxin will adhere to it more firmly, and thus be more affected by it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So did we just get unlucky and happen to have sodium channels that perfectly fit robustoxin? That seems to be the most likely answer, given that Australia probably has no native spider-consuming primates. Perhaps someone else can suggest other arachnid predators that might be an intended target for robustoxin?&lt;/p&gt;&#xA;" OwnerUserId="1248" LastActivityDate="2013-06-17T12:54:24.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8827" PostTypeId="2" ParentId="8816" CreationDate="2013-06-17T13:10:48.367" Score="7" Body="&lt;p&gt;I'm not sure I buy your premise: firstly, the degree and form of male-female differentiation in social roles has varied widely across time and culture in human history so I doubt it forms a uniform evolutionary driver such as you describe. Secondly, the degree of male-female differentiation appears to me to be much greater in species such as gorillas, lions and peacocks than it does in humans so I'm not convinced that humans would stand out on this front as a species we'd expect to have greater genetic differences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even so, the only genetic difference between male and female humans is the Y-chromosome. The X appears in both males and females and doesn't have exclusively female lineage so it can't acquire separate genes for male and female. The Y chromosome contains very few genes so its not capable of manifesting a major genetic gap and because there is no recombination in the Y chromosome it is not a fertile ground for new genes anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So males and females have essentially the same genes. However, this isn't the whole story because &lt;em&gt;how&lt;/em&gt;, &lt;em&gt;when&lt;/em&gt; and &lt;em&gt;whether&lt;/em&gt; genes are expressed is about as important as &lt;em&gt;what&lt;/em&gt; genes are encoded anyway. It is these differences that enable big differences between the sexes not actual coding differences. &lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="2938" LastEditDate="2013-06-18T05:56:27.723" LastActivityDate="2013-06-18T05:56:27.723" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8828" PostTypeId="2" ParentId="3012" CreationDate="2013-06-17T14:59:04.570" Score="1" Body="&lt;p&gt;There can be other modifications resulting from DNA damage (oxidising agents etc). Those may include Xanthine and Hypoxanthine (caused by chemical deamination of guanine and adenine).&#xA;There are no other known modifications resulting because of a physiological process. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-06-17T14:59:04.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8829" PostTypeId="2" ParentId="8824" CreationDate="2013-06-17T15:55:54.747" Score="2" Body="&lt;p&gt;You mention that you &quot;started in bioinformatics&quot;, so perhaps you might feel more comfortable taking such an approach to better characterize where the promoter for HBA2 might be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As @Bitwise mentioned in his comment, &quot;the promoter&quot; is not a well defined region. Often times &quot;we&quot; take the promoter of a gene to be some arbitrary (2-4) kilobytes upstream from the TSS. With more high throughput data coming online (especially from &lt;a href=&quot;http://genome.ucsc.edu/ENCODE/&quot; rel=&quot;nofollow&quot;&gt;ENCODE&lt;/a&gt;), we are starting to get a better picture of where the &lt;em&gt;functional&lt;/em&gt; regulatory elements of genes might be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By combining data from several different high-throughput assays across a variety of cell types, the human genome has been &lt;a href=&quot;http://uswest.ensembl.org/info/docs/funcgen/regulatory_segmentation.html&quot; rel=&quot;nofollow&quot;&gt;segmented&lt;/a&gt; into broad regions of interest. You might start by looking for where the &quot;Predicted promoter region including transcription start site&quot; segment is for HBA2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd also take a closer look at the &lt;a href=&quot;http://en.wikipedia.org/wiki/DNase-Seq&quot; rel=&quot;nofollow&quot;&gt;DNase-seq data&lt;/a&gt; in this &quot;promoter region&quot; across as many cell lines as they have processed for you to look for regions that are differentially occupied in hopes of identifying more precisely which parts in the promoter region might be important for the gene's expression (this would, of course, require you to connect DNAseq data with gene expression (RNA-seq) data).&lt;/p&gt;&#xA;" OwnerUserId="192" LastEditorUserId="192" LastEditDate="2013-06-17T16:03:22.677" LastActivityDate="2013-06-17T16:03:22.677" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8830" PostTypeId="2" ParentId="8808" CreationDate="2013-06-17T20:23:41.733" Score="0" Body="&lt;p&gt;Lactulose is an osmotic laxative. This means it works by drawing water into the colon (i.e. it retains a lot of water with it) and hence softens your stool in cases of constipation. As you can imagine, this interferes with absorption of most drugs including antibiotics and even food. Neomycin is especially toxic to gut flora (as mentioned above) and if taken with lactulose, it will linger in your GI tract for even longer and kill more gut flora. Your gut flora is important in protecting you against other harmful bacteria through competition for food, nutrients, etc. If you kill your flora, you are allowing other harmful organisms a field day in your intestine and they will grow and cause a condition known as pseudomembranous colitis (commonly caused by clostridium difficile infection). Also neomycin is mentioned separately because it has been associated with this condition which can sometimes be fatal (toxic megacolon, GI perforation, severe diarrhoea, etc) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, you shouldn't be taking other medication whilst you're constipated anyway (especially when taking lactulose) because they won't get absorbed and may make the constipation worse.&lt;/p&gt;&#xA;" OwnerUserId="3773" LastActivityDate="2013-06-17T20:23:41.733" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="8834" PostTypeId="1" CreationDate="2013-06-18T08:46:03.970" Score="3" ViewCount="139" Body="&lt;p&gt;&lt;em&gt;I understand this is not a biological question but this is often a problem whenever I look for literature.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How to look for a reference for some fact based on keywords. For instance you know about a fact such as - Cell signaling responses are faster but short lived compared to transcriptional responses. How to find the literature which actually says this. I often end up getting irrelevant results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, how to represent a fact using appropriate keywords. Is there an algorithm which can generate synonymous statements [like MeSH terms in pubmed] and search for those. &#xA;Or is there any way of setting up a hierarchical search. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: If someone finds a reference for &quot;&lt;em&gt;Cell signaling responses are faster but short lived compared to transcriptional responses&lt;/em&gt;&quot; then please let me know&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-06-18T12:54:03.417" LastActivityDate="2014-07-09T04:08:40.367" Title="Keyword based literature search" Tags="&lt;literature&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2014-12-05T00:02:43.813" ContentLicense="CC BY-SA 3.0" />
  <row Id="8835" PostTypeId="1" AcceptedAnswerId="8856" CreationDate="2013-06-18T15:46:32.740" Score="1" ViewCount="102" Body="&lt;p&gt;What nutritious insects exist to farm that require the least attention? I'm looking to automate simply, in a self regulating way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: To add detail, I imagine the insects would live densely in a large tank and be isolated from the outside. They would be able to breed and would co-exist with a plant that is also able to propagate, that could if needs be even be an air plant, that is eaten by the insects, dead insects either return to nourish the plant, or leave through a funnel, water also evaporates and falls as rain inside the tank.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea is to produce food without human effort. This could be in the form of a very cheap to use coin operated vending machine. The insects could be compressed and dry fried into a block to be dispensed, maybe like a bar, the machine could be solar powered.&lt;/p&gt;&#xA;" OwnerUserId="843" LastEditorUserId="1005" LastEditDate="2013-06-20T05:42:33.947" LastActivityDate="2013-06-20T05:42:33.947" Title="What nutritious insects exist to farm that require the least attention?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;entomology&gt;&lt;food&gt;&lt;nutrition&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8837" PostTypeId="1" AcceptedAnswerId="8838" CreationDate="2013-06-18T17:01:22.363" Score="5" ViewCount="5946" Body="&lt;p&gt;For what reason(s) is allolactose, instead of lactose, the &quot;natural&quot; inducer of &lt;em&gt;lac&lt;/em&gt; operon repressor?&lt;/p&gt;&#xA;" OwnerUserId="3523" LastActivityDate="2013-06-18T18:13:04.917" Title="Why is allolactose the LacI inducer?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8838" PostTypeId="2" ParentId="8837" CreationDate="2013-06-18T18:13:04.917" Score="4" Body="&lt;p&gt;When lactose is present in a cell, some of it is enzymatically converted by $\beta$-galactosidase from the $\beta(1,4)$ linkage (typical of lactose) to the $\beta(1,6)$ glycosidic linkage (becoming allolactose). Allolactose and other analogues can then bind LacI to induce the appropriate conformational change and unbind the &lt;em&gt;lac&lt;/em&gt; operator (one such &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=23011886&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt; here).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does allolactose act as a signal of lactose presence instead of just lactose? From the perspective of the lac operon, there is no operational difference between lactose and allolactose -- either way one molecule binds LacI and cannot be metabolized while bound. The full paradox is explained by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=3072716&quot; rel=&quot;nofollow&quot;&gt;Edgel&lt;/a&gt; and summarized by well-known biochemistry textbook author and scientist, Larry Moran, on his &lt;a href=&quot;http://sandwalk.blogspot.ca/2008/10/lactose-paradox.html&quot; rel=&quot;nofollow&quot;&gt;personal blog&lt;/a&gt;. The short version is that neither allolactose nor lactose are the intended substrates for $\beta$-gal and instead a different sugar entirely is the &quot;natural&quot; inducer and substrate.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=23011886&quot; rel=&quot;nofollow&quot;&gt;Juers DH, Matthews BW, Huber RE. LacZ β-galactosidase: structure and function of an enzyme of historical and molecular biological importance. Protein Sci. 2012 1792-807.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=3072716&quot; rel=&quot;nofollow&quot;&gt;Egel R. The 'lac' operon: an irrelevant paradox? Trends Genet. 1988 Feb;4(2):31.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-06-18T18:13:04.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8845" PostTypeId="2" ParentId="7010" CreationDate="2013-06-18T21:07:06.370" Score="1" Body="&lt;p&gt;Since meristems (the parts of plants from which growth happens) are constantly creating new stem cells, plants have a theoretical capacity for immortality. Of course, in practice, the vast majority of plants still senesce and die. But there are some notable exceptions such as bristlecone pines and quaking aspens which live for thousands of years. If you consider new individuals produced through clonal reproduction to be extensions of the original individual, then even more plants could be seen as immortal.&lt;/p&gt;&#xA;" OwnerUserId="3824" LastActivityDate="2013-06-18T21:07:06.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8846" PostTypeId="2" ParentId="8835" CreationDate="2013-06-18T21:33:32.340" Score="1" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Bombyx_mori&quot; rel=&quot;nofollow&quot;&gt;silkworm &lt;em&gt;Bombyx mori&lt;/em&gt;&lt;/a&gt; is farmed for silk, but the pupae are also eaten across the Far East. Since these insects (larvae) have been domesticated for centuries there are well-established procedures for growing them. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-06-18T21:33:32.340" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8847" PostTypeId="1" CreationDate="2013-06-18T23:40:55.693" Score="3" ViewCount="57" Body="&lt;p&gt;Can the ingestion of vitamin B6 upset the stomach, and if so by what mechanism? &lt;/p&gt;&#xA;" OwnerUserId="3825" LastEditorUserId="69" LastEditDate="2013-06-19T13:31:43.813" LastActivityDate="2013-06-19T13:31:43.813" Title="Can ingestion of B6 cause gastrointestinal disturbance?" Tags="&lt;pharmacology&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-12-09T10:08:25.093" ContentLicense="CC BY-SA 3.0" />
  <row Id="8848" PostTypeId="2" ParentId="3615" CreationDate="2013-06-18T23:47:00.770" Score="3" Body="&lt;p&gt;Perhaps you can infer relative lifespan from the age at which organs start declining in someone of average health.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Skin, muscles, bones, eyes, and ears start to visibly decline around age 40.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kidneys become smaller and their ability to filter blood starts to decline around age 30. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brain function begins to decline around 70, even in the absence of neurodegenerative diseases such as Alzheimers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think any organs can be passed through people for centuries, since decline of virtually every organ is observed even in individuals in perfect health. There may be two exceptions: The digestive tract and liver seem to be the most long-lived and are very little affected in healthy elders, probably because they regenerate their cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.merckmanuals.com/home/older_peoples_health_issues/the_aging_body/changes_in_the_body_with_aging.html&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-06-18T23:47:00.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8849" PostTypeId="2" ParentId="7010" CreationDate="2013-06-19T08:28:25.193" Score="8" Body="&lt;p&gt;I can find no examples of immortal plants, but then again &lt;strong&gt;immortality is rather hard to prove&lt;/strong&gt;, it's rather like trying to prove that space will never turn in to a pony - as long as time exists it could still occur, only if you go beyond the end of all time would you be able to say that it has or has not happened but then time would no longer exist and nor would space/the pony. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, for examples of &lt;strong&gt;long lived plants&lt;/strong&gt; it is perhaps best to look at trees - there are some species that live a long time and they can easily be aged. Here is a list of &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_oldest_trees&quot; rel=&quot;nofollow noreferrer&quot;&gt;oldest known trees&lt;/a&gt;. It is difficult to tell how old these trees can become, and thus whether they are &quot;immortal&quot;, because anything that lives that long is likely to encounter sources of extrinsic mortality during it's lifetime - predation, deforestation, extreme weather, erosion, natural disasters, contaminants, humans, disease, parasites etc. (rather than intrinsic dying of old age).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lot of plants go through some kind of apoptosis, where cells are programmed to die. Plants such as annuals, biennials etc. die after a few months or years in a programmed way. It is difficult to say whether long lived species of trees would do the same after a few thousand years of life, because we just don't get to see many reach that stage of life, or if the mechanisms causing it have been suppressed (which could explain their long life).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Luke has posted a very thorough answer on the cellular and genetic aging of plants &lt;a href=&quot;https://biology.stackexchange.com/questions/2055/do-trees-age-on-a-microscopic-level/&quot;&gt;here&lt;/a&gt;. And to quote him:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;...it seems to me likely that plants may also have enhanced maintenance&#xA;  against other cellular stresses than DNA damage, such as build-ups of&#xA;  aberrant proteins. It therefore appears that in a protected&#xA;  environment some plants could live indefinitely&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Wikipedia has some very good pages on the evolution of &lt;a href=&quot;http://en.wikipedia.org/wiki/Senescence&quot; rel=&quot;nofollow noreferrer&quot;&gt;senescence&lt;/a&gt; &amp;amp; &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_ageing&quot; rel=&quot;nofollow noreferrer&quot;&gt;aging&lt;/a&gt;. &lt;strong&gt;&lt;a href=&quot;http://www.pnas.org/content/95/19/11034.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;This article has also a good section on plant aging&lt;/a&gt; and I hope you can access it.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;and finally, if you want to have a laugh,&lt;/strong&gt; take a look at this entry on plant immortality and aging from &lt;a href=&quot;http://creationwiki.org/Immortality&quot; rel=&quot;nofollow noreferrer&quot;&gt;creationwiki.org&lt;/a&gt;...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Plants are actually or potentially immortal organisms that will live&#xA;  indefinitely provided their environmental requirements are met. In&#xA;  striking contrast to plants, humans and animals have a maximum life&#xA;  expectancy regardless of whether their needs are fulfilled. Although&#xA;  it is true that some plants grow as annuals, all plants are actually&#xA;  perennials by nature, and have adapted to a programmed life cycle in&#xA;  some instances to match growing seasons. Otherwise, plants only die&#xA;  because of biochemical starvation or disease. If their physical&#xA;  requirements are met, plants will grow indefinitely.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Some great clear science there, well done creationists... but it's just &lt;a href=&quot;https://en.wikipedia.org/wiki/Annual_plant&quot; rel=&quot;nofollow noreferrer&quot;&gt;plain wrong.&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-06-19T08:42:41.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8851" PostTypeId="1" AcceptedAnswerId="8853" CreationDate="2013-06-19T13:50:12.457" Score="4" ViewCount="4394" Body="&lt;p&gt;So, for a project I've been working on (different story), I've been looking at the HapMap Project, and their free online files. In their README file, they talk about how for each legend file for each chromosome/region, there is an rs id, an alelle coded 0, 1, and a base pair position.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now it's fairly obvious after staring at this for a while that base pair position means where each nucleotide is located along the genetic sequence... is this correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And what do rs id, and the other words mean? Any help would be greatly appreciated!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the link to the README file, in that same directory are the files about the participants, only including SNPs (snips!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2006-07_phaseII/00README.txt&quot; rel=&quot;nofollow&quot;&gt;HapMap Project README file link&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2006-07_phaseII/&quot; rel=&quot;nofollow&quot;&gt;HapMap Project sequence data link (phase 2)&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3829" LastEditorUserId="1320" LastEditDate="2013-06-19T14:24:34.690" LastActivityDate="2013-06-19T18:45:19.637" Title="What do rs id, allele coded 0 and allele coded 1 mean?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;bioinformatics&gt;&lt;human-genetics&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8853" PostTypeId="2" ParentId="8851" CreationDate="2013-06-19T14:22:59.933" Score="6" Body="&lt;p&gt;rs id is &lt;em&gt;reference SNP cluster ID&lt;/em&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/SNP/get_html.cgi?whichHtml=how_to_submit#REFSNP&quot; rel=&quot;nofollow&quot;&gt;see here&lt;/a&gt;. It's basically a unique identifier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This table is taken from your link:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;rs              position        0       1&#xA;rs11089130      14431347        C       G  &#xA;rs738829        14432618        A       G  &#xA;rs915674        14433624        A       G&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The allele codes are the 3rd and 4th columns. An SNP is  site where a different base is found in different versions of the same gene (different versions of genes are alleles). For a given SNP the different alleles are referred to as the &lt;strong&gt;0&lt;/strong&gt; or the &lt;strong&gt;1&lt;/strong&gt; allele. So in the table the first SNP, rs11089130,  has two alleles: allele &lt;strong&gt;0&lt;/strong&gt; has a C at the SNP position (14431347) whereas  allele &lt;strong&gt;1&lt;/strong&gt; has a G at that position. The allele code does not imply any biological significance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure what would happen if there were three alleles at an SNP, but presumably there would then also be an SNP coded as &lt;strong&gt;2&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt;&#xA;Allele 0 is the residue from the reference genome. Allele 1 is the residue being studied, the SNP.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="3829" LastEditDate="2013-06-19T18:45:19.637" LastActivityDate="2013-06-19T18:45:19.637" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8856" PostTypeId="2" ParentId="8835" CreationDate="2013-06-19T17:07:12.117" Score="1" Body="&lt;p&gt;The leaf cutter ant &lt;em&gt;Atta laevigata&lt;/em&gt; is a popular delicacy in Colombia where it is known as &lt;em&gt;hormiga culona&lt;/em&gt; (big-ass ant). The ants are usually salted and fried and play a similar culinary role (I am told) as pop corn (&lt;a href=&quot;http://www.restlessadventurer.net/travel/comidas-tipicas/hormigas-culonas/hormigas-culonas.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;image source)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OVCO7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't testify as to how hard it is to cultivate them, but one difficulty will be chosing the edible ones. Apparently, &lt;a href=&quot;http://en.wikipedia.org/wiki/Atta_laevigata&quot; rel=&quot;nofollow noreferrer&quot;&gt;only the queens are edible&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-06-19T17:07:12.117" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="8857" PostTypeId="1" AcceptedAnswerId="8858" CreationDate="2013-06-19T19:14:12.480" Score="6" ViewCount="333" Body="&lt;p&gt;I understand that there would have to be a portion of liver present to regrow from, so how much liver would the minimum to be able to regrow?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By what mechanism does regrowth occur?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-06-19T19:52:47.660" Title="How does the human liver regrow?" Tags="&lt;liver&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8858" PostTypeId="2" ParentId="8857" CreationDate="2013-06-19T19:52:47.660" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://books.google.com/books?id=RJEg-p-9iqsC&amp;amp;pg=PA1#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;noreferrer&quot;&gt;At least 25%&lt;/a&gt; of the original liver seems to be the minimum for regrowth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The initial regrowth is due to proliferation of hepatocytes: they exit G0 and enter mitosis. The ECM dissolves and is remodeled; the cholangiocytes and SECs also divide. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to read more, you can visit the Google books link above, and the preview lets you read several pages on liver regeneration in rodents.  (If it doesn't work, try changing the URL to your current location: books.google.com is US, books.google.ca is Canada, etc.)&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-06-19T19:52:47.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8859" PostTypeId="2" ParentId="8811" CreationDate="2013-06-19T22:25:46.777" Score="4" Body="&lt;p&gt;Essentially all animal cells maintain an ionic balance causing a resting potential of about -70 mV in order to maintain their internal environment including pH, ion concentrations, osmotic pressure and volume. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21627/&quot; rel=&quot;nofollow&quot;&gt;Lodish, &lt;em&gt;Molecular Cell Biology&lt;/em&gt;&lt;/a&gt;)  Neurons developed from existing types of cells and it's unlikely that the cost of maintaining resting potential in the neuron could have driven evolution of an entire alternative system to provide the homeostasis supported by the existing system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the depolarization of the membrane at any particular place during an impulse is very short so the impact of the ion flows have only limited effect on the cell's overall internal environment beyond requiring adjustment by ion pumps for the losses involved.  It also is not obvious how the wave-like characteristic of a nerve impulse could be generated if the membrane did not carry a nonzero potential; there would be no stored energy (in the form of ion gradients) available to make the pulse swiftly spread across the membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another point to consider is that the perhaps 15% of a neuron's energy spent on replacing leaking ions may have some hidden usefulness.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23479331?dopt=Abstract&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; suggests that neurons may actually be set up to leak at a rate higher than they would if it were minimized.&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2013-06-19T22:25:46.777" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8860" PostTypeId="1" AcceptedAnswerId="8868" CreationDate="2013-06-19T22:28:04.107" Score="4" ViewCount="95" Body="&lt;p&gt;I'm researching the genetics of brain cancer, and finding a huge number of mutations in voltage-gated channels.  It stands to reason that some of this DNA damage is due to the DNA being transcribed heavily, or in an open chromatin conformation more often, leading to more breakage and damage due to environmental stress.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, those are just guesses.  Does anyone know of any research papers in the area?&lt;/p&gt;&#xA;" OwnerUserId="1387" LastEditorUserId="948" LastEditDate="2014-01-13T21:44:24.217" LastActivityDate="2014-01-13T21:44:24.217" Title="Transcriptionally-mediated DNA damage" Tags="&lt;genetics&gt;&lt;cancer&gt;&lt;transcription&gt;&lt;mutations&gt;&lt;chromatin&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8861" PostTypeId="2" ParentId="5148" CreationDate="2013-06-19T23:07:32.770" Score="0" Body="&lt;p&gt;This is a bit expressed in an unclear way but I think it solves the problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the reason is simply that if you have all the hermaphrodites being difficult about their mates they will evolve fast because the best mates will mate more and the worst won't mate a lot. But if the hermaphrodite individual is hard to get, it also  won't be motivated to pursue sex and it will be hard for the 'best' individuals to mate more cause they will be too hard to get.  So the requirement to impress while also being hard to get are contradictory in non differentiated individuals. In most animals, the difference in libido of the female versus that of the male can solve this paradox. One has to show they have good genetic material (the male) and the other just have to be hard to get. This is pretty shitty for females, but nature often is. I think the fitness of this difference almost disappears in monogamous species where both have an advantage if they are hard to get. So we can hope hermaphroditism is not an advantage only for an intermediary stage of evolution but can become one again in higher species. This would alleviate some of the sexual conflict.&lt;/p&gt;&#xA;" OwnerUserId="3835" LastEditorUserId="1590" LastEditDate="2013-06-20T12:02:04.627" LastActivityDate="2013-06-20T12:02:04.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8862" PostTypeId="1" AcceptedAnswerId="8863" CreationDate="2013-06-20T07:59:28.987" Score="9" ViewCount="9096" Body="&lt;p&gt;As far as I know, just leg bones produce red blood cells. So, how people who lost their both legs produce red blood cells?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="1590" LastEditDate="2013-06-20T09:31:12.860" LastActivityDate="2016-03-04T19:33:06.443" Title="How do people who have lost both of their legs produce red blood cells?" Tags="&lt;human-biology&gt;&lt;red-blood-cell&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8863" PostTypeId="2" ParentId="8862" CreationDate="2013-06-20T09:29:37.933" Score="18" Body="&lt;p&gt;Red blood cells are produced in the red marrow which...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;is found mainly in the flat bones, such as the pelvis, sternum,&#xA;  cranium, ribs, vertebrae and scapulae, and in the cancellous&#xA;  (&quot;spongy&quot;) material at the epiphyseal ends of long bones such as the&#xA;  femur and humerus.&quot; - &lt;a href=&quot;http://en.wikipedia.org/wiki/Red_bone_marrow&quot;&gt;Wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So you are partly right; the femur &lt;em&gt;is&lt;/em&gt; associated with red blood cell production, or Erythropoiesis to give it it's technical name, &lt;strong&gt;but there are other bones within the human body that also do this job.&lt;/strong&gt; The process of erythropoiesis is stimulated when the kidneys detect low levels of oxygen in the blood stream and stimulate production of the hormone erythropoietin. Further, the role of the tibia and femur in erythropoiesis also decreases with age whereas...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;the vertebrae, sternum, pelvis and ribs, and cranial bones continue&#xA;  to produce red blood cells throughout life.&quot; - again from the wiki page&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So I'd suggest it is unlikely that loss of the legs would have a major impact on the production of red blood cells in adults. I imagine that with the loss of legs comes some reduction in functionality of erythropoiesis but also a lower requirement of red blood cell production (less blood capacity = less blood cells needed = less blood cells need to be produced). I can't find any studies which explore the ability or needs of amputees and non-amputees with regards to red blood cell production.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2013-06-20T09:29:37.933" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8864" PostTypeId="1" AcceptedAnswerId="8865" CreationDate="2013-06-20T11:34:28.360" Score="2" ViewCount="111" Body="&lt;p&gt;I need enzyme concentration and metabolites concentration values to en-corporate these values in my model and do some simulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I searched through some database  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;yeast metabolome database &lt;a href=&quot;http://www.ymdb.ca/&quot; rel=&quot;nofollow&quot;&gt;http://www.ymdb.ca/&lt;/a&gt;&#xA;brenda and other enzyme databases for enzmye conc&#xA;and also did some literature search&lt;/p&gt;&#xA;&#xA;&lt;p&gt;but couldn't find much of data&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where possibly i can get these data ??&#xA;is there any other way to do simulation without data.&lt;/p&gt;&#xA;" OwnerUserId="3841" LastActivityDate="2013-06-21T06:26:57.410" Title="Modeling yeast biochemical pathway using enzyme kinetics" Tags="&lt;bioinformatics&gt;&lt;mathematical-models&gt;&lt;database&gt;&lt;enzyme-kinetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8865" PostTypeId="2" ParentId="8864" CreationDate="2013-06-20T12:09:30.620" Score="1" Body="&lt;p&gt;You should take a look at SGD (the &lt;a href=&quot;http://www.yeastgenome.org/&quot; rel=&quot;nofollow&quot;&gt;Saccharomyces Genome Database&lt;/a&gt;), and in particular &lt;a href=&quot;http://pathway.yeastgenome.org/overviewsWeb/celOv.shtml&quot; rel=&quot;nofollow&quot;&gt;YeastCyc&lt;/a&gt;. Some protein information pages at SGD give estimates of molecules per cell taken from &lt;a href=&quot;http://www.nature.com/nature/journal/v425/n6959/pdf/nature02046.pdf&quot; rel=&quot;nofollow&quot;&gt;this Nature paper&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;Added later in response to some comments:&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question asks about levels of metabolites and of enzymes, not of transcripts. Microarray data can be, at best, only a guide to levels of proteins. Estimating the levels of metabolites from microarray data is a complete non-starter since there are entire layers of regulation that will be ignored. Just to give one example of a pitfall in this approach: you could have high levels of transcript from which you could you could infer high levels of enzyme, but that enzyme could be inactivated by a post-translational modification.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-06-21T06:26:57.410" LastActivityDate="2013-06-21T06:26:57.410" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8866" PostTypeId="2" ParentId="7669" CreationDate="2013-06-20T12:27:18.707" Score="10" Body="&lt;p&gt;This is not a subject I know well, but I can point to several recent textbooks on homosexuality in animals, all with an evolutionary perspective. I remember that Bagemihl's book got good reviews when it was published. In general, I think it is important to acknowledge that homosexuality is common in many animal species and not just humans:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/031225377X&quot;&gt;Bagemihl. 2000. Biological Exuberance: Animal Homosexuality and Natural Diversity&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.cambridge.org/us/knowledge/isbn/item5708830/?site_locale=en_US&quot;&gt;Sommer &amp;amp; Vasey (eds). 2006. Homosexual Behaviour in Animals: An Evolutionary Perspective&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0520260120&quot;&gt;Roughgarden. 2009. Evolution's Rainbow: Diversity, Gender, and Sexuality in Nature and People&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.cambridge.org/us/knowledge/isbn/item5706975/?site_locale=en_US&quot;&gt;Poiani. 2010. Animal Homosexuality: A Biosocial Perspective&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2013-06-20T12:27:18.707" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8867" PostTypeId="2" ParentId="8750" CreationDate="2013-06-20T13:08:45.707" Score="2" Body="&lt;p&gt;I think there might be several places to read a description of these experiments, but they are discussed extensively in a book by historian-philosopher Lindley Darden, entitled &quot;Theory Change in Science: Strategies from Mendelian Genetics&quot;, parts of which are &lt;a href=&quot;http://books.google.com/books?id=O_-jPuVdo08C&quot; rel=&quot;nofollow&quot;&gt;available online&lt;/a&gt;.  See p. 112 of Darden's book for references to other accounts of these experiments by historians E.A. Carlson (1966) and W. Provine (1988). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Everyone knows what Castle &lt;strong&gt;did&lt;/strong&gt; but his aims have been obscured by &quot;Synthesis Historiography&quot; (i.e. making things turn out right for Ernst Mayr and his homies).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What Castle did was to breed rats in the laboratory and implement selection on coat patterns, with such success that he has able to get a large seemingly continuous range of forms. Imagine breeding oreos, with one line of selection of darker forms, and one of lighter, and achieving the success of getting both pure-black or pure-white oreos, and then lining up all the oreos from black to white to show the continuous range of forms.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The story that we hear from people like Wright and Provine is that this proved that selection can work on continuous variation, an idea that the &quot;mutationists&quot; allegedly rejected, paving the way for acceptance of Darwinism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet, while the experiments may have helped one version of Darwinism, they also represented the dying gasps of another form of Darwinism-- the form that Darwin proposed and Castle was (partially) defending. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can get an inkling of this from p. 143 of Provine's book, where you will find a curious confession, made in passing.  Provine is explaining why Pearson did not want to publish Fisher's famous 1918 paper.  He writes &quot;Pearson claimed, and Darwin would probably have agreed, that the continuous variations in a pure line were heritable and that continued selection in a pure line should be effective.&quot;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why would Pearson believe-- 17 years &lt;strong&gt;after&lt;/strong&gt; the rediscovery of Mendelian inheritance-- that the environmental variations in Johannsen's pure lines were suitable material for selection?  The reason is that this is what Darwin believed, and Pearson was a follower of Darwin.  Darwin's &quot;indefinite variability&quot;, the fuel for modification in his theory of &quot;natural selection&quot;, described in Ch. 1 of the OOS, is clearly a description of environmental variation-- it is always present and emerges anew every generation in response to &quot;conditions of life&quot; (see Winther, 2000).  Darwin knew about &quot;definite&quot; single variations or &quot;sports&quot;, which could be inherited perfectly (whereas indefinite variations were inherited by blending), but he didn't think they were important for evolution.  Darwin bet on the wrong horse, as Johannsen showed in 1903.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pearson, Castle, and others defended Darwin's original view well into the 20th century.  They were not satisfied with the idea that selection merely sorted out stable Mendelian factors that undergo rare mutations.  Instead, they held out hope that there was some other form of heredity, or that the Mendelian units were squishy and underwent continuous shifts in potency under conditions of selection.  Thus Castle and Phillips in 1914 argued that &quot;the unit character for hooded pattern is itself variable&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Muller, Sturtevant and others from Morgan's lab disagreed, arguing instead that there were simply various Mendelian modifying factors in the background affecting coat color.  There was a long-running dispute over the proper genetic interpretation of Castle's results.  If you want a very clear statement of the dispute, go to a &lt;a href=&quot;http://books.google.com/books?id=2rhMAAAAYAAJ&amp;amp;pg=PA287#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;1916 article by Jennings&lt;/a&gt;, p. 287: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Castle finds that in rats he can, by selection, gradually increase&#xA;  of decrease the amount of colour in the coat, passing by continuous&#xA;  stages from one extreme to the other.  As to this, he holds two main&#xA;  points: &lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;&lt;p&gt;The change is an actual change in the hereditary characteristics of the stock; not a mere result of the recombination of Mendelian&#xA;  factors.  This is the general and fundamental point at issue.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;More specifically, he holds it to be an actual change in a single unit factor; this single factor changes its grade in a continuous and&#xA;  quantitative manner.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;  &#xA;  &lt;p&gt;On the other side, the critics of these views&#xA;  maintain that the changes shown are not actual alterations in the&#xA;  hereditary constitution at all, but are mere results of recombinations&#xA;  of Mendelian factors.  And specifically, they find a complete&#xA;  explanation of such results as those of Castle in the hypothesis of&#xA;  multiple modifying factors.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A few years later in 1919, Castle recanted his earlier view and accepted the multifactorial theory (the development of which is described by Kyung-Man Kim, cited below). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And finally, the idea that the &quot;mutationists&quot; rejected selection on quantitative variation is mistaken.  What the mutationists rejected was selection on non-heritable environmental variations.  Johannsen's 1903 results were revolutionary because scientists at the time understood that they refuted Darwin's theory.  We don't &quot;get&quot; this today because &quot;Darwinism&quot; has been redefined to disentangle &quot;natural selection&quot; from Darwin's errant views of heredity-- see Jean Gayon's &quot;Darwinism's Struggle for Survival&quot; for more explanation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kim K-M. 1994. Explaining scientific consensus : the case of Mendelian genetics New York: Guilford Press. xxiv, 239 p. p.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gayon J. 1998. Darwinism's Struggle for Survival: Heredity andthe Hypothesis of Natural Selection Cambridge, UK: Cambridge University Press.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Winther RG. 2000. Darwin on Variation and Heredity. Journal of the History of Biology 33:425-55.&lt;/p&gt;&#xA;" OwnerUserId="3842" LastEditorUserId="3842" LastEditDate="2013-07-03T14:36:42.407" LastActivityDate="2013-07-03T14:36:42.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8868" PostTypeId="2" ParentId="8860" CreationDate="2013-06-20T14:40:57.980" Score="4" Body="&lt;p&gt;There seems to be some solid evidence that transcription promotes mutation because the untranscribed strand is able to form secondary structures which expose bases to chemical mutagenesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a recent paper about transcription-associated mutagenesis:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20479947&quot; rel=&quot;nofollow&quot;&gt;Kim H &lt;em&gt;et al.&lt;/em&gt;(2010)&lt;/a&gt; Transcription-associated mutagenesis increases protein sequence diversity more effectively than does random mutagenesis in Escherichia coli. PLoS One 5(5):e10567. doi: 10.1371/journal.pone.0010567.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;During transcription, the nontranscribed DNA strand becomes single-stranded DNA (ssDNA), which can form secondary structures. Unpaired bases in the ssDNA are less protected from mutagens and hence experience more mutations than do paired bases. These mutations are called transcription-associated mutations. Transcription-associated mutagenesis is increased under stress and depends on the DNA sequence. Therefore, selection might significantly influence protein-coding sequences in terms of the transcription-associated mutability per transcription event under stress to improve the survival of Escherichia coli.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors cite a number of papers in their introduction which document the phenomenon that you could follow up. Just in case the focus on a bacterial system puts you off, the Kim &lt;em&gt;et al.&lt;/em&gt; paper has in turn been cited in:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21803733&quot; rel=&quot;nofollow&quot;&gt;Wright &lt;em&gt;et al.&lt;/em&gt; (2011)&lt;/a&gt; The roles of transcription and genotoxins underlying p53 mutagenesis in vivo. CARCINOGENESIS 32:1559-1567&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abstract in full: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Transcription drives supercoiling which forms and stabilizes single-stranded (ss) DNA secondary structures with loops exposing G and C bases that are intrinsically mutable and vulnerable to non-enzymatic hydrolytic reactions. Since many studies in prokaryotes have shown direct correlations between the frequencies of transcription and mutation, we conducted in silico analyses using the computer program, mfg, which simulates transcription and predicts the location of known mutable bases in loops of high-stability secondary structures. Mfg analyses of the p53 tumor suppressor gene predicted the location of mutable bases and mutation frequencies correlated with the extent to which these mutable bases were exposed in secondary structures. In vitro analyses have now confirmed that the 12 most mutable bases in p53 are in fact located in predicted ssDNA loops of these structures. Data show that genotoxins have two independent effects on mutagenesis and the incidence of cancer: Firstly, they activate p53 transcription, which increases the number of exposed mutable bases and also increases mutation frequency. Secondly, genotoxins increase the frequency of G-to-T transversions resulting in a decrease in G-to-A and C mutations. This precise compensatory shift in the 'fate' of G mutations has no impact on mutation frequency. Moreover, it is consistent with our proposed mechanism of mutagenesis in which the frequency of G exposure in ssDNA via transcription is rate limiting for mutation frequency in vivo.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="948" LastEditDate="2013-06-21T01:30:47.950" LastActivityDate="2013-06-21T01:30:47.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8871" PostTypeId="1" AcceptedAnswerId="8879" CreationDate="2013-06-20T19:41:08.603" Score="1" ViewCount="150" Body="&lt;p&gt;I’m new to the field of protein folding. I’ve been searching and came across some books for predicting structures (&lt;a href=&quot;http://www.wiley.com/WileyCDA/WileyTitle/productCd-0470470593.html&quot; rel=&quot;nofollow&quot;&gt;Introduction to Protein Structure Prediction: Methods and Algorithms&lt;/a&gt;). Does anyone know whether I can find some code (say in C++, Java, or R) related to the prediction of protein structures? Or, do you know other good articles or books related to the statistics of the protein folding problem?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for the help.&lt;/p&gt;&#xA;" OwnerUserId="3845" LastEditorUserId="1320" LastEditDate="2013-06-20T19:51:58.460" LastActivityDate="2013-06-21T13:38:44.900" Title="Statistical Analysis of Protein Folding Problem" Tags="&lt;software&gt;&lt;book-recommendation&gt;&lt;protein-folding&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2013-06-24T11:37:15.513" ContentLicense="CC BY-SA 3.0" />
  <row Id="8872" PostTypeId="1" CreationDate="2013-06-20T20:11:48.753" Score="9" ViewCount="4275" Body="&lt;p&gt;For example, outside of humans, do other species of animals engage in oral sex, or any oral stimulation of others' genitals purely for pleasure, not any cleansing habits, etc.?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, what I am saying is, is it true that oral sex, like in humans, exists in non-human animals?&lt;/p&gt;&#xA;" OwnerDisplayName="user3846" LastActivityDate="2015-04-12T01:29:49.940" Title="Is it true that oral sex exists in non-human animals?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8873" PostTypeId="2" ParentId="8872" CreationDate="2013-06-20T21:59:22.623" Score="10" Body="&lt;p&gt;Yes, it is true. Have a look at this post:&lt;a href=&quot;http://www.thefrisky.com/2013-04-04/9-animals-who-are-into-oral-sex/&quot;&gt;9 Animals Who Are Into Oral Sex&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A recent study of fruit bats found cunnilingus to be a major part of their repertoire. While following a colony of 420 bats roosting in a fig tree over the course of 13 months, researchers witnessed 57 incidences of sex — both oral and intercourse. The female bats who received oral sex before intercourse were found to last longer during copulation. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The paper they cite is &lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059743&quot;&gt;this one&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5evEx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3848" LastEditorUserId="3059" LastEditDate="2013-06-20T22:34:56.490" LastActivityDate="2013-06-20T22:34:56.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8875" PostTypeId="1" CreationDate="2013-06-21T04:33:23.227" Score="2" ViewCount="108" Body="&lt;p&gt;If our eyes are separated by some kind of full proof barrier/isolation, is it possible that our brain can picture/visualize two different pictures at a time?&#xA;How the brain will function in this situation?&#xA;which are the books to read to understand in depth brain behavior?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried to isolate my eyes with hands/paper but i am not able to do it.&lt;/p&gt;&#xA;" OwnerUserId="3850" LastEditorUserId="948" LastEditDate="2013-06-21T11:14:07.343" LastActivityDate="2013-07-21T18:34:32.350" Title="Eye Brain Mapping" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8879" PostTypeId="2" ParentId="8871" CreationDate="2013-06-21T13:38:44.900" Score="4" Body="&lt;p&gt;One of the quickest ways to get oriented on what is going in the world of protein folding and modeling is to look at the proceedings of the &lt;a href=&quot;http://www.predictioncenter.org/casp10/&quot; rel=&quot;nofollow&quot;&gt;Critical Assessment of Structure Prediction&lt;/a&gt; (CASP).  CASP is basically a contest, held every 2 years where anyone can use their algorithm to predict the 3D structure of a protein whose structure is known, but not publicly available.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its been a few years since I reviewed them results much - it looks like this year was interesting, but a perennial winner has been &lt;a href=&quot;http://rosettadesigngroup.com/blog/865/a-plos-one-rosetta-collection/&quot; rel=&quot;nofollow&quot;&gt;Rosetta&lt;/a&gt;, which has turned into an edifice of many suites of software which each execute different tasks in protein folding and modeling.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Open source software is pretty hard to find in this field.  The software is complex.  It usually includes components of machine and statistical learning, molecular dynamics, specialized algorithms that build up the protein one residue at a time, others which manipulate blocks of the protein structure around in space, electrostatic calculations, you name it.  In addition, the software, once it gives some sort of result is quite valuable.  I don't think any of these suites has really been released.  I know that &lt;a href=&quot;https://www.rosettacommons.org/&quot; rel=&quot;nofollow&quot;&gt;Rosetta&lt;/a&gt; is available to use as a web service, but you have to apply for access to the source.  I don't think its an easy thing to get. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the most complicated components are available open source.  Molecular modeling and molecular dynamics &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling&quot; rel=&quot;nofollow&quot;&gt;open source software&lt;/a&gt; is quite sophisticated.  I think we need an open source protein folding suite open source.  I think &lt;a href=&quot;http://pmcb.jhu.edu/faculty/shortle-profile.html&quot; rel=&quot;nofollow&quot;&gt;David Shortle's algorithms&lt;/a&gt; might be a candidate for such a suite as its not so complicated and it works in some cases.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This field is pretty obscure and difficult to get around in.  There aren't any easy introductions that I know of.  Protein structures are computationally expensive and painful to work with in terms of writing software.  On the other hand protein folding that really works is a revolutionary breakthrough, at least equal to the impact of the development of computers as a technology. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-06-21T13:38:44.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8880" PostTypeId="1" AcceptedAnswerId="9607" CreationDate="2013-06-21T16:16:51.273" Score="11" ViewCount="1088" Body="&lt;p&gt;You can't plant the leaves, you can't plant the fruit, but, if you plant the part where leaves and fruit &lt;em&gt;meet&lt;/em&gt; you will grow a whole pineapple plant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The part of the pineapple where the leaves meet the stem is the point from which the whole plant &lt;em&gt;seems&lt;/em&gt; to form. Cells below seem to become fruit and fruit skin, cells above seem to become leaves. If you look at a cross-section of this part of the plant you can see the way that the cells seem to move outward from this point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://travellingartist.files.wordpress.com/2012/06/pineapple-2.jpg?w=383&amp;amp;h=511&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1)But is that really how it grows? Are the new cells added from the center or do new cells get added to the leaves at the tips and in the middle of the leaves?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2)I know some orchid roots grow from the tip... but is this the case for all roots?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3)I noticed that some lemongrass in my worm compost bin has grown roots! So, I transplanted it outside. Maybe I can grow lemongrass. Again, it was the part of the plant where the roots met the leaves that still had life in it.  This seems like a very powerful part of the plant. Is there a name for the part of a plant from which everything else grows?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE: &lt;a href=&quot;http://en.wikipedia.org/wiki/Meristem&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Meristem&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is what the regions is called! But I still want to know if the plant &quot;pushes&quot; out the leaves from this central point or not... and are all root like orchid roots that grow from the tips?&lt;/p&gt;&#xA;" OwnerUserId="301" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.833" LastActivityDate="2013-08-03T03:53:19.020" Title="How do pineapples and lemongrass grow?" Tags="&lt;plant-physiology&gt;&lt;botany&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8881" PostTypeId="2" ParentId="1640" CreationDate="2013-06-21T17:31:43.303" Score="3" Body="&lt;p&gt;Bigger pumpkins have more seeds than smaller pumpkins. When they get ideal nutrition the plant tries to make as many seeds as it can to take advantage of the windfall. Many of these vines with big fruit potential grow in compost and rotting material. So they are more opportunistic a pumpkin seed &quot;in the wild&quot; could land in a barren area or in a heap of rotting material-- if it hits the jackpot it meeds to quickly use those nutrients to make more seeds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PLants with more consistent fruit sizes don't respond as well to &quot;jack pot&quot; levels of rotting material-- they like more consistent nourishment. I think this is another difference. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also one large pumpkin is a more efficient way to enclose seeds than lots of little pumpkins. &lt;/p&gt;&#xA;" OwnerUserId="301" LastActivityDate="2013-06-21T17:31:43.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8882" PostTypeId="2" ParentId="8875" CreationDate="2013-06-21T17:41:22.840" Score="1" Body="&lt;p&gt;First off, I should note that binocular vision is important for depth perception. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The phenomenon in which you are interested is called binocular rivalry (distinct images are presented to each eye).  You typically switch between the images, and sometimes, both at once (superimposed; this is called binocular transparency) or an averaged picture (binocular fusion). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find some good links at the &lt;a href=&quot;https://en.wikipedia.org/wiki/Binocular_rivalry&quot; rel=&quot;nofollow&quot;&gt;Wikipedia page&lt;/a&gt;.  The &lt;a href=&quot;http://www.scholarpedia.org/article/Binocular_rivalry&quot; rel=&quot;nofollow&quot;&gt;Scholarpedia page&lt;/a&gt; is even better.  If you don't find what you're looking for, I think searching for papers on &quot;binocular rivalry&quot; will give you the best result. &lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-06-21T17:47:18.090" LastActivityDate="2013-06-21T17:47:18.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8883" PostTypeId="1" AcceptedAnswerId="8889" CreationDate="2013-06-21T21:18:05.537" Score="3" ViewCount="170" Body="&lt;p&gt;As the title asks, what are the longterm effects of pancreatitis?  Having one event, is the person more susceptible to have a recurrence, or are they at higher risk of other conditions such as diabetes?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="1306" LastEditDate="2014-04-09T16:02:51.700" LastActivityDate="2014-04-09T16:02:51.700" Title="What are the longterm effects of pancreatitis?" Tags="&lt;medicine&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8884" PostTypeId="1" CreationDate="2013-06-22T08:13:16.153" Score="3" ViewCount="338" Body="&lt;p&gt;I want to buy a model of Human skull for education purpose. However, I really want a very accurate model and at a decent price. I got the info that many of the available skulls in the market are not accurate.  Can anyone suggest me one? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also I want to know is there any regulatory body that certifies such&lt;br&gt;&#xA;educational models regarding the accuracy etc.? If not then what is the way I can ensure that I am buying an accurate (or most accurate) model.  &lt;/p&gt;&#xA;" OwnerUserId="1110" LastActivityDate="2014-07-30T18:19:48.243" Title="Accurate Human Skull Model for Educational Purpose" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="8889" PostTypeId="2" ParentId="8883" CreationDate="2013-06-22T21:03:57.607" Score="1" Body="&lt;p&gt;Pancreatitis may cause a condition called ''systemic inflammatory response syndrome'', a immune system reaction affecting the whole body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, more frequently, pancreatitis is linked with steatorrhea, which means oily fat, and it may cause malnutrition and weight loss, due to restriction of secretions containing digestive enzymes. Longer term inflammations of pancreas may cause fibrosis (scar tissue) in the organ, therefore restricting the endocrine functions including insulin secretion, so acquired diabetes is another risk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obstruction of the bile duct and jaundice, leading to possible liver damage is another complication of pancreatitis.&lt;/p&gt;&#xA;" OwnerUserId="3859" LastActivityDate="2013-06-22T21:03:57.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8890" PostTypeId="1" AcceptedAnswerId="8891" CreationDate="2013-06-22T21:14:20.103" Score="5" ViewCount="100" Body="&lt;p&gt;Is there a medical condition that affects the long term memory, but leaves the short-term and working memories totally or fairly intact?&lt;/p&gt;&#xA;" OwnerUserId="3859" LastEditorUserId="25231" LastEditDate="2018-04-27T15:48:06.687" LastActivityDate="2018-04-27T15:48:06.687" Title="Is there a type of amnesia that separately affects long-term memory?" Tags="&lt;neuroscience&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8891" PostTypeId="2" ParentId="8890" CreationDate="2013-06-22T21:56:04.833" Score="3" Body="&lt;p&gt;If I understand your question correctly, what you are describing is &lt;a href=&quot;http://www.human-memory.net/disorders_retrograde.html&quot; rel=&quot;nofollow&quot;&gt;retrograde amnesia&lt;/a&gt;.  This is further subdivided into pure, focal and isolated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the site:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Typically, episodic memory is more severely affected than semantic memory, so that the patient may remember words and general knowledge (such as who their country’s leader is, how everyday objects work, colours, etc) but not specific events in their lives. Procedural memories (memory of skills, habits and how to perform everyday fucntions) are typically not affected at all. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-06-22T21:56:04.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8893" PostTypeId="1" AcceptedAnswerId="20157" CreationDate="2013-06-22T23:05:56.320" Score="5" ViewCount="149" Body="&lt;p&gt;I heard that Actinia Equina normally eats what it can catch, but this clownfish here doesn't care much about that:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=Ughm4mnZ1ls&quot;&gt;https://www.youtube.com/watch?v=Ughm4mnZ1ls&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the actinia obviously can't hold the clownfish, clownfish does whatever it wants with actinia swimming all over it. Is the clownfish having some sort of fish fun, or is there a purpose behind this playing with actinia?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2014-08-02T08:15:22.000" Title="Why is clownfish attracted to actinia?" Tags="&lt;ichthyology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8894" PostTypeId="1" AcceptedAnswerId="8900" CreationDate="2013-06-23T01:35:07.520" Score="13" ViewCount="451" Body="&lt;p&gt;Could cancer be in itself a evolutionary process? Maybe in some way could it be a process of variation? Or would this idea be completely without support, if so, why? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't mean that each case would lead to evolution, but that within an entire group of organisms, it could lead to case of of individuals developing ways to resist what caused the cancer, maybe in cases of individuals beating the cancer or in cases of successive generations of off spring from individuals with cancer? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could it be possible that in rare cases it could lead to the development of new organs or specialized cells?&lt;/p&gt;&#xA;" OwnerUserId="3860" LastEditorDisplayName="user3795" LastEditDate="2013-06-23T01:54:29.310" LastActivityDate="2015-04-16T11:32:01.200" Title="Could cancer be in itself a evolutionary process?" Tags="&lt;evolution&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8895" PostTypeId="1" CreationDate="2013-06-23T01:45:24.383" Score="-3" ViewCount="248" Body="&lt;p&gt;We know that a person can be infected with HIV viruses when he/she has sexual relationship with those having HIV viruses (and very, very, very rarely, urine/defecation-related transmission) - but I wonder if there are other sources of HIV transmission - so for example, let's say during sexual relationship, some cuts on body (for example, inside vagina) occurred. Then even if the partner did not have HIV viruses, and a person afterwards does not sex with partners with HIV viruses, is there a chance that he/she may get HIV viruses, still?&lt;/p&gt;&#xA;" OwnerUserId="3861" LastActivityDate="2014-04-29T17:29:24.293" Title="Can a person be infected with HIV viruses without contacting them by person-related stuffs?" Tags="&lt;hiv&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ClosedDate="2014-05-01T12:53:29.050" ContentLicense="CC BY-SA 3.0" />
  <row Id="8896" PostTypeId="2" ParentId="8894" CreationDate="2013-06-23T01:54:46.200" Score="7" Body="&lt;p&gt;This very interesting question has been explored in a paper, linked this &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/news/071001_cancer&quot;&gt;Berkeley page : &quot;Another perspective on cancer: Evolution within&quot;&lt;/a&gt; (the paper is at the bottom of the page).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the site:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If one of those mutations (or a series of mutations) allows its bearer to evade cell death and reproduce more prolifically than others, it will pass that mutation on to its daughter cells, and cells bearing that mutation will increase in frequency over time. Like organisms in an ecosystem, cell lineages within one's own body compete for resources. A cell lineage that gains an advantage in that competition, accumulating mutations that allow it to grab extra resources and escape the body's control mechanisms, will proliferate and may evolve into a cancerous tumor. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The researchers also state that looking at cancer through the 'lens' of cellular evolution could be a major reason why a 'cure' eludes us.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further, in this article &lt;a href=&quot;http://www.news-medical.net/news/2007/04/17/23697.aspx&quot;&gt;&quot;Connection between cancer development and Darwinian evolution explored&quot;&lt;/a&gt;, the authors state that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;He believes that many of our genes are constructed such that they protect against cancer in the first part of our lives, but that they are programmed for destruction as we get older.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Essentially, the article asserts that as we get better at prolonging our lives, that cancer is a means to shut down the body over a period of time.  My understanding is (and I could be wrong) is that the increase in cancer incidents are an evolutionary way to put the brakes on the increasing human life span.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorDisplayName="user3795" LastEditDate="2013-06-23T02:30:52.070" LastActivityDate="2013-06-23T02:30:52.070" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8897" PostTypeId="1" CreationDate="2013-06-23T07:23:50.770" Score="3" ViewCount="314" Body="&lt;p&gt;By &quot;dream&quot;, I mean:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Dreaming while sleeping.&lt;/li&gt;&#xA;&lt;li&gt;Dreaming about their future life while being awake.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance.&lt;/p&gt;&#xA;" OwnerUserId="3839" LastActivityDate="2015-03-27T10:37:22.547" Title="Do animals also dream?" Tags="&lt;ethology&gt;&lt;dreaming&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8898" PostTypeId="1" CreationDate="2013-06-23T07:40:35.000" Score="1" ViewCount="319" Body="&lt;p&gt;Sometimes I have many consecutive &quot;dreamfull&quot; nights but sometimes there is no dream during week. Why? What determines whether I will have any dream or not?&lt;/p&gt;&#xA;" OwnerUserId="3839" LastActivityDate="2013-06-23T12:05:09.807" Title="What determines whether I will have any dream or not?" Tags="&lt;dreaming&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8899" PostTypeId="1" CreationDate="2013-06-23T07:47:29.610" Score="0" ViewCount="90" Body="&lt;p&gt;Is it possible to completely realize that I am only dreaming and to completely manage my dream?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="3839" LastActivityDate="2013-06-23T11:35:16.163" Title="Can I control my dreams?" Tags="&lt;dreaming&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8900" PostTypeId="2" ParentId="8894" CreationDate="2013-06-23T08:19:13.867" Score="13" Body="&lt;p&gt;Interesting question. I believe it definitely is an evolutionary process. unicellularity breaking away from a multicellular life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two examples that I can think of, which can support this argument:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Hela cells: Hela cells have been classified as a different organism because they have the ability to grow outside the host indefinitely and their genome is different from Homo sapiens. Hela cells also have a new scientific name- &lt;a href=&quot;http://en.wikipedia.org/wiki/HeLa&quot;&gt;Helacyton gartleri&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Transmissible tumors: two tumors have been known to infect other hosts and therefore can be called obligate pathogenic lifeforms. One is &lt;a href=&quot;http://en.wikipedia.org/wiki/Devil_facial_tumour_disease&quot;&gt;Devil Facial Tumor Disease&lt;/a&gt; which infects Tasmanian devils and gets transmitted by biting. Another is &lt;a href=&quot;http://en.wikipedia.org/wiki/Canine_transmissible_venereal_tumor&quot;&gt;Canine Transmissible Venereal Tumor&lt;/a&gt; which infects dogs and spreads via sexual route. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Could it be possible that in rare cases it could lead to the development of new organs or specialized cells?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Cancer as of now has a pathogenic identity. It is a simplistic process which in a thermodynamic point of view can be described as maximization of entropy(disorder) and thereby increasing the stability [like the way solutes diffuse]. If a cancer has to give rise to a new functional organ then it has to be supportive of the ordered lifestyle which it is trying to break away from in the first place. It may adopt a pathogenic lifestyle initially and then may redevelop order. I don't know of any such evolutionary event but it may nonetheless be possible. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-04-16T11:32:01.200" LastActivityDate="2015-04-16T11:32:01.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8901" PostTypeId="1" AcceptedAnswerId="8902" CreationDate="2013-06-23T09:27:42.760" Score="7" ViewCount="1298" Body="&lt;p&gt;Is there any exact definition of vegetable and fruit? How can new plant be classified? &lt;/p&gt;&#xA;" OwnerUserId="3839" LastActivityDate="2017-03-14T22:35:54.070" Title="What is the difference between vegetable and fruit?" Tags="&lt;fruit&gt;&lt;vegetable&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8902" PostTypeId="2" ParentId="8901" CreationDate="2013-06-23T09:35:13.080" Score="8" Body="&lt;p&gt;A true fruit is a ripened ovary that usually starts ripening when it is fertilized. And vegetable is any vegetative part of the plant which is edible and contains stored food probably in the form of starch.&lt;br&gt;&#xA;These definitions are not exact as there are a lot of fruits which are fruits but do not strictly follow the given definition. See Syconus, Composite fruits, Sorosis.etc&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Classification is based on several different criteria, for example the mode of reproduction, arrangement and design of flowering parts and flowers and also on the basis of habitat and habit.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2013-06-23T09:35:13.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8903" PostTypeId="2" ParentId="8897" CreationDate="2013-06-23T11:25:58.423" Score="4" Body="&lt;p&gt;According to this &lt;a href=&quot;http://www.psychologytoday.com/blog/animal-emotions/201212/do-animals-dream-science-shows-course-they-do-rats-too&quot; rel=&quot;nofollow&quot;&gt;Psychology Today blogpost&lt;/a&gt;, it is quite likely that animals can dream.  Particularly mammals that according to the blogpost:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;All mammals share the same neural structures that are important in sleeping and dreaming.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, for your second question, I do not think it is at all possible to know what they are dreaming about (if they indeed do dream).&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-06-23T11:25:58.423" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8904" PostTypeId="2" ParentId="8899" CreationDate="2013-06-23T11:35:16.163" Score="2" Body="&lt;p&gt;According to &lt;a href=&quot;http://psychoanalysis101.org/dreams/frequently-asked-questions/#5&quot; rel=&quot;nofollow&quot;&gt;Psychoanalysis101.org&lt;/a&gt;, it is quite rare to be able to control dreams, though apparently it can happen 9according to the article.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Lucid_dream&quot; rel=&quot;nofollow&quot;&gt;Lucid dreaming&lt;/a&gt; is the term to describe when the person is aware that they are dreaming, further research and scepticism of lucid dreaming are outlined &lt;a href=&quot;http://en.wikipedia.org/wiki/Lucid_dream#Research_and_clinical_applications&quot; rel=&quot;nofollow&quot;&gt;in this section of the article.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-06-23T11:35:16.163" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8905" PostTypeId="2" ParentId="8796" CreationDate="2013-06-23T11:55:29.857" Score="2" Body="&lt;p&gt;First a clarification: the mobile units are no so &quot;mobile&quot;. Due to (1) the high protein:lipid ratio of the thylakoid membrane and (2) the packing of protein complexes, the rapid diffusion of components along the membrane is hindered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has been proposed the existence of small local PQ diffusion microdomains, based upon the percolation theory:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;From the percolation theory, above a critical density, immobile or slowly moving transmembrane proteins are, indeed, expected to form flexible 2D networks of closed compartments preventing long range movement of small molecules. (&lt;a href=&quot;http://www.psi.cz/ftp/publications/others/david/Kirchhoff2000.pdf&quot; rel=&quot;nofollow&quot;&gt;Kirchhoff, H &lt;em&gt;et al.&lt;/em&gt; (2000) &lt;em&gt;Biochim. Biophys. Acta&lt;/em&gt; 1459, 148–168&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For this reason the PQ are confined, on a short time scale, within these domains, preventing their &quot;dispersion&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition of the low diffusion of mobile carriers, the geometry of the granal stacks mantains the contact area between the PSII of the appressed grana and the PSI in the margin annulus domains relatively large, enabling effective linear electron transport in microdomains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 2b of the paper cited below shows the geometrical organization of the stacked grana and its description says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The circular border between the appressed domain and the margin annulus (ring) allows a large contact area between the PSII and the PSI domains and efficient linear electron transport from PSII via plastoquinone (PQ), plastocyanin and cytochrome b6f to PSI at a short distance of ~30–60 nm in local domain.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Further informations can be found in &lt;a href=&quot;http://www.thylabisco.com/pdf/albertsson_2001.pdf&quot; rel=&quot;nofollow&quot;&gt;Albertsson, P-Å. (2001) &lt;em&gt;Trends Plant Sci.&lt;/em&gt; 6, 349–354&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3523" LastActivityDate="2013-06-23T11:55:29.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8906" PostTypeId="2" ParentId="8898" CreationDate="2013-06-23T12:05:09.807" Score="2" Body="&lt;p&gt;According to the &lt;a href=&quot;http://www2.ucsc.edu/dreams/FAQ/&quot; rel=&quot;nofollow&quot;&gt;DreamResearch.net of UCSC&lt;/a&gt;, typically, we dream up to 10 times a night (sometimes more, sometimes less), and it is likely that on those nights when you feel that you have not dreamt, you may have forgotten the dream.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dream amnesia is very common, where we forget most of the dreams (an any instances of sleep walking etc), this article &lt;a href=&quot;http://munshi.4t.com/wbt/stickgold.html&quot; rel=&quot;nofollow&quot;&gt;Dreaming: A Neurocognitive Approach&lt;/a&gt; has more of the study.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-06-23T12:05:09.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8907" PostTypeId="1" AcceptedAnswerId="8913" CreationDate="2013-06-23T13:27:36.227" Score="6" ViewCount="24609" Body="&lt;p&gt;Often an activity to do at a party, breath in helium and speak like one of the chipmunks. But, I am wondering, would infrequent inhalation of helium cause long term harm to the throat? in particular, the vocal cords?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="69" LastEditDate="2013-06-24T09:04:36.593" LastActivityDate="2018-09-16T15:45:14.100" Title="Can breathing in helium (from balloons for example) cause damage to the throat in the long term?" Tags="&lt;breathing&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8908" PostTypeId="1" CreationDate="2013-06-23T14:07:19.657" Score="9" ViewCount="6525" Body="&lt;p&gt;Some time ago I tasted ostrich meat, and what was amazing to me was that the meat very much resembled beef, much more than it resembled chicken, turkey or duck meat. And even more than lamb and pork resemble beef.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The resemblance is both in look, both raw and grilled, and in taste (only tried grilled). I would have thought that the meat of related animals would have similar taste. Why is it that the meat of an ostrich, which is a bird, doesn't taste like that of other birds?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Warning&lt;/strong&gt;, the following links are to pictures of meats!&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://shop.ayrshirefarm.com/images/P/BeefSampler.gif&quot; rel=&quot;noreferrer&quot;&gt;A picture of beef&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://cdn.cobone.com/deals/egypt/bonnyretaurant/bonny-ostrich-meat/bigostrich-meat.jpg?v=11&quot; rel=&quot;noreferrer&quot;&gt;A picture of ostrich meat&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://images.sciencedaily.com/2009/05/090527175333-large.jpg&quot; rel=&quot;noreferrer&quot;&gt;A picture of chicken meat&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="680" LastEditorUserId="3952" LastEditDate="2013-08-01T10:05:15.293" LastActivityDate="2013-08-01T10:05:15.293" Title="Why does ostrich meat look and taste more like beef than chicken?" Tags="&lt;zoology&gt;&lt;food&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8909" PostTypeId="1" CreationDate="2013-06-23T14:33:52.913" Score="3" ViewCount="741" Body="&lt;p&gt;Are there any articles reporting any significant differences in behavior, attitudes, intelligence, appearance, etc., between right and left handed people?&lt;/p&gt;&#xA;" OwnerUserId="3839" LastEditorUserId="107" LastEditDate="2013-06-23T15:57:07.660" LastActivityDate="2016-08-26T13:29:14.663" Title="Differences between right and left handed people" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8910" PostTypeId="2" ParentId="8908" CreationDate="2013-06-23T14:42:07.733" Score="7" Body="&lt;p&gt;There is a very plausible explanation &lt;a href=&quot;http://science.howstuffworks.com/zoology/birds/ostrich-meat1.htm&quot;&gt;here&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, it explains that meat colour is due to the protein myoglobin (a haem-containing protein related to haemoglobin). There are two types of skeletal muscle: &lt;a href=&quot;http://en.wikipedia.org/wiki/Muscle&quot;&gt;fast-twitch and slow-twitch&lt;/a&gt; (Wikipedia). Slow-twitch muscle is red muscle because it contains lots of myoglobin. Fast-twitch muscle is white muscle, containing less myoglobin. The Wikipedia link explains a little more about these muscle types and their functional differences. Evidently the lifestyle of the ostrich dictates that it have more fast-twitch muscle, and so it has red meat. It isn't unique in this: duck and goose are classified as red meat too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incidentally the role of myoglobin is to improve the rate of diffusion of oxygen from the haemoglobin in the capillaries through the cytoplasm of the myocytes to the mitochondria. It has also been suggested that it acts as an oxygen storage mechanism in diving mammals which have very high levels of myoglobin in their muscles, but this storage function is unlikely to be important in other mammals, despite what you may read in textbooks.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="680" LastEditDate="2013-06-23T15:56:27.800" LastActivityDate="2013-06-23T15:56:27.800" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8911" PostTypeId="1" CreationDate="2013-06-23T15:05:39.647" Score="2" ViewCount="90" Body="&lt;p&gt;I've been averaging K&lt;sub&gt;i&lt;/sub&gt; values from the PDSP K&lt;sub&gt;i&lt;/sub&gt; Database, and I can't help but to wonder: how I can determine p values for the binding affinities, so I can exclude anomalies in the data if need be?&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="107" LastEditDate="2013-06-23T15:57:57.350" LastActivityDate="2014-04-20T05:07:14.970" Title="What type of distribution should binding affinities fit?" Tags="&lt;statistics&gt;&lt;protein-binding&gt;&lt;database&gt;&lt;dissociation-constant&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8912" PostTypeId="2" ParentId="8909" CreationDate="2013-06-23T15:15:52.753" Score="4" Body="&lt;p&gt;According to this &lt;a href=&quot;http://www.psychologytoday.com/blog/brain-myths/201303/three-myths-and-three-facts-about-left-handers&quot; rel=&quot;nofollow&quot;&gt;Psychology Today article: 3 Myths and 3 Facts about Left-Handers&lt;/a&gt; (with numerous links to many papers throughout the article), there are no particular difference between left and right handed people in terms of intelligence, personality, creativity or mortality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There seems to be a noticeable difference in the number of people having the language centre being in the left hemisphere of the brain (95% for right handed people vs 70% for left handed people).&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-06-23T15:15:52.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8913" PostTypeId="2" ParentId="8907" CreationDate="2013-06-23T17:21:36.927" Score="7" Body="&lt;p&gt;When we speak, our vocal cords vibrate to the air. Helium makes them vibrate a lot faster (that's what makes the funny sound of your voice after inhaling helium), because its atoms are a lot lighter than nitrogen and oxygen atoms. Obviously, lighter atoms, can travel faster. This faster vibrations are unusual to the cords and they can cause sore throat or even strong throat ache. After you stop inhaling the gas, things should get back to normal, especially if the inhalation really is infrequent. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Breathing helium balloons at parties is a very dangerous fun activity, because it replaces the oxygen and this could lead to hypoxia - a condition when tissues can't get enough oxygen one reason or another. In some cases, this could even be fatal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even though inhaling of pure helium is dangerous, in submarines, divers breathe a mixture of nitrogen, oxygen and helium as helium is better under higher pressures. At these depths the low density of helium is found to considerably reduce the effort of breathing. Divers often have problems with dry throat and constant thirst due to the need of more oxygen. At least, inhaling helium, when it's mixed with oxygen, is far less harmful than breathing it directly from a balloon. &lt;/p&gt;&#xA;" OwnerUserId="3864" LastEditorUserId="1320" LastEditDate="2013-06-23T18:49:03.090" LastActivityDate="2013-06-23T18:49:03.090" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8915" PostTypeId="1" CreationDate="2013-06-23T20:28:35.087" Score="2" ViewCount="127" Body="&lt;p&gt;Can humans' ability to dive with only breathing modifications tell us anything about our evolution?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, it is possible to imagine a human anatomy that would be destroyed by the pressure of a few meters of water, and yet humans can, with scuba apparatus dive to several hundred meters.&lt;/p&gt;&#xA;" OwnerUserId="3867" LastActivityDate="2013-06-24T03:15:25.083" Title="Can humans' ability to dive with only breathing modifications tell us anything about our evolution?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8916" PostTypeId="2" ParentId="8915" CreationDate="2013-06-23T21:31:56.733" Score="-4" Body="&lt;p&gt;Actually, there was a very interesting Animal planet episode (&lt;a href=&quot;http://www.youtube.com/watch?v=Cm3XdC-p8_I&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=Cm3XdC-p8_I&lt;/a&gt;) on the recent news about the probable discovery of a mermaid body. In the show, scientists suggest that may be our evolution has had some roots under water. First, our body structure is far more plastic and ergonomic than the structure of a monkey. We are great swimmers in our movements and as you mentioned - our ability to hold our breaths under water for a very long time - the record is about 20 minutes! We can easily control our breathing which is something usually connected with marine mammals. In difference of other animals, we are almost hairless. Just like other marine mammals, we are born with insulating fat distributed throughout our bodies. This keeps us warm in water. All this takes place in the &quot;Aquatic ape hypothesis&quot;. This view claims that our alleged ancestors went through a watery stage in our evolutionary development. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, although all those facts connect very conveniently, the theory has not been proven yet by experiments and is so far just an idea that should be considered and investigated more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, some people still have marks from gills as an atavism.&lt;/p&gt;&#xA;" OwnerUserId="3864" LastActivityDate="2013-06-23T21:31:56.733" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8917" PostTypeId="2" ParentId="8895" CreationDate="2013-06-23T21:39:39.583" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;let's say during sexual relationship, some cuts on body (for example, inside vagina) occurred. Then even if the partner did not have HIV viruses, and a person afterwards does not sex with partners with HIV viruses, is there a chance that he/she may get HIV viruses, still?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No, because there is no virus present in any of the people involved to be transmitted in this scenario.  HIV doesn't spontaneously occur in people.  It should also be noted that HIV is also highly transmissible in the blood.&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2013-06-23T21:39:39.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8918" PostTypeId="2" ParentId="8911" CreationDate="2013-06-24T01:20:34.130" Score="1" Body="&lt;p&gt;P-values reflect how well the data fits some background model. This background model should reflect some assumptions you make about the data. What assumptions do you think would be reasonable in this case? For example, do you assume high values are more likely to be incorrect?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Throwing away outliers like kmm suggested is probably not a good idea, because it means you will remove $K_i$ values which are very high or very low. It is not clear there is much biological justification for that, since we know some $K_i$s can be low and some can be high, but it doesn't tell us they are wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bottom line is that without making some assumption about what the values should look like, you can't identify what incorrect values look like.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2013-06-24T01:20:34.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8919" PostTypeId="2" ParentId="8915" CreationDate="2013-06-24T03:15:25.083" Score="1" Body="&lt;p&gt;This is not a complete answer to your question, but your question prompted me to research the &lt;a href=&quot;http://dujs.dartmouth.edu/winter-2012/the-mammalian-diving-reflex&quot; rel=&quot;nofollow&quot;&gt;Mammalian Diving Reflex&lt;/a&gt;, which is used, according to the article, as a survival mechanism rather than assisting us in day to day functioning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at the evolution of the diving reflex, and how it appears in varying degrees in all mammals, suggest that it has been around for a long time, &lt;a href=&quot;http://evolvify.com/superhuman-tricks-mammalian-diving-reflex/&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; suggests for over 125 million years.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-06-24T03:15:25.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8921" PostTypeId="1" AcceptedAnswerId="8943" CreationDate="2013-06-24T07:25:52.237" Score="12" ViewCount="55412" Body="&lt;p&gt;E.g. you can see a lot of videos where cats are smashing some mouse or spider on an ipad, but I have never seen it with a dog. I have a dog myself and I know that he sometimes responds to the sounds from the TV, but not to the images.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is that?&lt;/p&gt;&#xA;" OwnerUserId="3118" LastEditorUserId="5005" LastEditDate="2013-12-17T02:22:20.547" LastActivityDate="2017-06-13T08:11:05.410" Title="Why can cats interpret things on a monitor/tv, but dogs cannot?" Tags="&lt;eyes&gt;&lt;ethology&gt;&lt;behaviour&gt;&lt;sensation&gt;&lt;pets&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8922" PostTypeId="1" CreationDate="2013-06-24T07:43:25.413" Score="5" ViewCount="1638" Body="&lt;p&gt;For example, animals that live only a few days or a few years are often not very intelligent. In contrast, the most intelligent animals seem to live longer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this true? Are there any studies to prove or disprove this statement?&lt;/p&gt;&#xA;" OwnerUserId="3118" LastEditorUserId="3624" LastEditDate="2013-08-09T12:34:10.990" LastActivityDate="2013-09-21T18:27:41.783" Title="Is life expectancy linked to intelligence in animals?" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;life-history&gt;&lt;intelligence&gt;&lt;cognition&gt;" AnswerCount="2" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8923" PostTypeId="1" AcceptedAnswerId="9879" CreationDate="2013-06-24T08:03:34.227" Score="10" ViewCount="2575" Body="&lt;p&gt;Could a cavity in a human tooth &quot;heal over&quot; or possibly fill back in?&lt;/p&gt;&#xA;" OwnerUserId="3869" LastEditorUserId="69" LastEditDate="2013-06-24T09:03:50.953" LastActivityDate="2013-08-20T19:16:32.850" Title="Do teeth have the capacity to heal?" Tags="&lt;human-biology&gt;&lt;teeth&gt;&lt;healing&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8928" PostTypeId="1" CreationDate="2013-06-24T13:33:09.703" Score="2" ViewCount="761" Body="&lt;p&gt;I know that PLINK and HapMap files show the same information, but can you give a thorough explanation of how exactly they differ.&lt;/p&gt;&#xA;" OwnerUserId="3829" LastActivityDate="2013-06-25T14:48:19.597" Title="How do PLINK files and HapMap Phased files differ?" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8929" PostTypeId="2" ParentId="8923" CreationDate="2013-06-24T14:10:54.257" Score="6" Body="&lt;p&gt;Yes, it can be done to a certain degree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cementum&lt;/strong&gt; is capable of repairing itself to a limited degree and is not resorbed under normal conditions. Some root resorption of the apical portion of the root may occur, however, if orthodontic pressures are excessive and movement is too fast. Some experts also agree on a third type of cementum, afibrillar cementum, which sometimes extends onto the enamel of the tooth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cementum is produced by cells called cementoblasts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;more here:&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cementum&quot;&gt;http://en.wikipedia.org/wiki/Cementum&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3118" LastActivityDate="2013-06-24T14:10:54.257" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8931" PostTypeId="2" ParentId="3478" CreationDate="2013-06-24T14:32:17.893" Score="4" Body="&lt;p&gt;The problem is that committing suicide, using the commonplace definition of it, would require an understanding of death. I am sure that an animal can have a basic understanding of the death of others, so far as they realise the difference between a living companion and it's dead body. But if they understand that this lifeless body will never go &quot;back to normal&quot; again and that there is also future death for themselves, I am not convinced.&#xA;So, without the understanding of the own, irreversible death, there is (following the definition) no suicide.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-06-24T14:32:17.893" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8932" PostTypeId="2" ParentId="3478" CreationDate="2013-06-24T14:33:12.450" Score="3" Body="&lt;p&gt;According to this &lt;a href=&quot;http://news.discovery.com/animals/zoo-animals/animal-suicide-behavior.htm&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; whales could kill themselves by swimming to the beach and even when pushed back to the water, they return or dogs can drown in the water when suffer a lot.&lt;/p&gt;&#xA;" OwnerUserId="3118" LastActivityDate="2013-06-24T14:33:12.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8934" PostTypeId="2" ParentId="8759" CreationDate="2013-06-24T19:00:41.383" Score="2" Body="&lt;p&gt;I'm not expert on the topic, but whenever males more predominately have a condition than females, it might point to a sex-linked (recessive) trait. Males have one X chromosome, while females have two. This means that a male only needs one copy of a gene to have a condition (inherited from their mother), while females need two X chromosomes to be inherited to have the condition (mother and father).&lt;/p&gt;&#xA;" OwnerUserId="3829" LastActivityDate="2013-06-24T19:00:41.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8935" PostTypeId="1" AcceptedAnswerId="8993" CreationDate="2013-06-24T19:32:13.277" Score="0" ViewCount="65" Body="&lt;p&gt;In an attempts to eat my veggies for the day in one shot, I blended together a bag of salad with some water. The mixture separated by density, a thick top layer containing the bits of leaves, and a bottom layer of just juice. My question is: how many vitamins and nutrients are actually found in the top layer compared to the bottom, and how efficiently would the body process them? &lt;/p&gt;&#xA;" OwnerUserId="3627" LastEditorUserId="3059" LastEditDate="2013-06-27T22:48:55.930" LastActivityDate="2013-06-27T22:48:55.930" Title="Distribution of nutrients throuought a drink made of plants?" Tags="&lt;human-biology&gt;&lt;nutrition&gt;&lt;botany&gt;&lt;vitamins&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8936" PostTypeId="1" CreationDate="2013-06-24T19:40:44.207" Score="6" ViewCount="116" Body="&lt;p&gt;I had read about science working towards the creation of artificial wombs however I wonder how compatible are mammal wombs and connected systems to develop fetuses. What species are so compatible that they would be able to surrogate the embryos and fetuses of another species? &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2013-06-25T18:21:06.017" LastActivityDate="2013-09-29T21:34:40.450" Title="How compatible are mammal wombs?" Tags="&lt;embryology&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8937" PostTypeId="1" AcceptedAnswerId="9956" CreationDate="2013-06-24T20:07:07.913" Score="7" ViewCount="2497" Body="&lt;p&gt;If you grow a plant from seed in your nice warm house, then plant it out in your temperate garden, it will stop growing for a while, possibly die, and if not, subsequently resume growth. Standard gardening practice is to 'harden off' plants, moving them to an area of intermediate temperature for a while before planting them out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does this happen? What is the difference between a plant adapted to a warm environment and one adapted to a cold environment?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Expression of cold-tolerance genes? Levels of some secondary metabolite? Thickness of cell walls? Density of root hairs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An &lt;a href=&quot;http://apps.rhs.org.uk/advicesearch/profile.aspx?PID=386&quot;&gt;unidentified author on the Royal Horticultural Society website&lt;/a&gt; states that&#xA;&quot;The effect of hardening off is to thicken and alter the plant's leaf structure and increase leaf waxiness&quot;, which is not quite detailed enough to satisfy.&lt;/p&gt;&#xA;" OwnerUserId="3871" LastActivityDate="2013-11-24T23:15:13.030" Title="How do individual plants adapt to changes in temperature?" Tags="&lt;botany&gt;&lt;temperature&gt;&lt;adaptation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8938" PostTypeId="2" ParentId="8922" CreationDate="2013-06-24T20:27:08.130" Score="1" Body="&lt;p&gt;This is too long to be a comment. Life expectancy is apparently affected the size of an animal, and this is especially evident in mammals and supported by the heartbeat hypothesis. This hypothesis says that all mammals have a similar number of heartbeats, and that the larger an animal is, the less heart beats it has per minute. Therefore, the larger an animal, the longer it lives. A larger size is also associated with a larger brain (which is associated with higher intelligence, although this is not true in all cases since for example some dinosaurs were very large but had very tiny brains). All I'm saying is that any correlation between intelligence and life expectancy may not necessarily be brought about directly by intelligence, but by the size of the animal. Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="3627" LastEditorUserId="3627" LastEditDate="2013-06-25T08:41:00.013" LastActivityDate="2013-06-25T08:41:00.013" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8939" PostTypeId="1" CreationDate="2013-06-24T21:37:05.443" Score="14" ViewCount="2416" Body="&lt;p&gt;I have seen fake wasp nests sold as a deterrent against wasps and similar insects. Do they really work? Is there some scientific evidence for it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A related link: &lt;a href=&quot;http://www.scienceworld.ca/do-fake-wasp-nests-fool-wasps&quot;&gt;http://www.scienceworld.ca/do-fake-wasp-nests-fool-wasps&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1279" LastEditorUserId="69" LastEditDate="2013-08-13T10:21:24.953" LastActivityDate="2014-07-22T13:24:35.867" Title="Do fake wasp nests actually fool wasps?" Tags="&lt;entomology&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8940" PostTypeId="1" CreationDate="2013-06-24T22:38:30.317" Score="4" ViewCount="160" Body="&lt;p&gt;I've recently read a book on evolutionary-developmental biology for laymen, and it described how a fetus is progressively divided into more refined zones of genetic activity. These zones, kinda like GPS coordinates define which genes will be activated at which time and at which location.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What interests me is - &lt;strong&gt;after development to maturity, what defines how animals maintain their body shape?&lt;/strong&gt; Is it the same &quot;GPS&quot; system that defines boundaries of an organism? Or is it something else within the specialized cells that tells them to grow in certain directions and avoid others?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To clarify the question with an example - lets take blood vessels - what prevents blood vessel lining from growing forever in all directions, taking up all available internal cavity space?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="577" LastEditDate="2013-06-26T01:05:44.003" LastActivityDate="2013-10-02T20:07:01.053" Title="How animals maintain their body shape after development to maturity?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;development&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8942" PostTypeId="1" AcceptedAnswerId="8945" CreationDate="2013-06-25T03:35:37.417" Score="1" ViewCount="73" Body="&lt;p&gt;I have heard here and there that instead of consuming 3 largish meals (the traditional 3 meals a day), that consuming several smaller meals throughout the day is beneficial for health (and weight loss).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How true is this statement?  What are the biological advantages, if any, of such a diet?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-06-25T08:31:23.847" Title="What are the biological and nutritional benefits of having numerous smaller meals a day?" Tags="&lt;human-biology&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8943" PostTypeId="2" ParentId="8921" CreationDate="2013-06-25T07:06:32.820" Score="21" Body="&lt;p&gt;&lt;strong&gt;Cats and dogs can both view tv screens &amp;amp; monitors&lt;/strong&gt; ... though their viewing experience is a little different to ours thanks to differences in cone structure leaving them &lt;a href=&quot;http://i.stuff.co.nz/life-style/blogs/four-legs-good/2604288/What-your-pets-really-see-on-TV&quot;&gt;color blind and giving low acuity&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both species have lower levels of color vision than humans. Cats see slightly more color &lt;a href=&quot;http://i.stuff.co.nz/life-style/blogs/four-legs-good/2604288/What-your-pets-really-see-on-TV&quot;&gt;(in the blue green and yellow end of the spectrum)&lt;/a&gt; than dogs do so they may get more of an immersive experience from watching TV. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further, cats and dogs need a higher frame rate than humans to make it appear as a smooth film, a phenomenon known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Flicker_fusion_threshold&quot;&gt;flicker fusion&lt;/a&gt;, in humans &lt;a href=&quot;http://sciencenordic.com/do-dogs-see-what%E2%80%99s-happening-tv&quot;&gt;we require 15-20 frames per second, dogs require 70fps&lt;/a&gt; and &lt;a href=&quot;http://i.stuff.co.nz/life-style/blogs/four-legs-good/2604288/What-your-pets-really-see-on-TV&quot;&gt;cats about 100&lt;/a&gt;. Before the frame rate of televisions increased in recent years it would appeared to them to be flashing images, similar to when you &lt;a href=&quot;http://electronics.howstuffworks.com/question336.htm&quot;&gt;point a digital camera at a screen&lt;/a&gt; which may explain why the dog is not interested in the TV, it'd be like staring at a strobe for hours on end. Here is &lt;a href=&quot;http://www.daisypeel.com/wp-content/uploads/2013/01/dog-vision-miller-murphy.pdf&quot;&gt;a paper which discusses flicker rates and color vision in dogs&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To summarize there are several factors which influence the &quot;enjoyment&quot; an animal can take from watching a TV - &lt;strong&gt;their response to TV imagery will depend on the frames per second, colors, contrast, clarity, movement, subject matter, and (perhaps most importantly in my opinion) the temperament of the animal, for all of which there are difference between the species.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From sciencenordic.com:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;We humans need about 16 to 20 images a second to perceive what we see&#xA;  as continuous film, whereas dogs need about 70 images per second.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;So a few years ago, Fido was probably confounded by his master's&#xA;  behaviour of sitting for hours staring at a flashing succession of&#xA;  images. With modern resolution and quicker imaging, dogs have become&#xA;  potential television viewers.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This has not gone unrecognised in the USA, for example, where hopeful&#xA;  TV producers have started special TV channels for dogs.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;If you have other pets, however, you need to think twice before&#xA;  placing them in front of the TV.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Birds need at least 100 frames per second to see TV images as a moving&#xA;  picture. Having a bird in the same room as a TV with a lower frame&#xA;  rate than that will be very stressful for the creature.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-06-25T09:24:38.587" LastActivityDate="2013-06-25T09:24:38.587" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8944" PostTypeId="2" ParentId="8928" CreationDate="2013-06-25T07:55:48.927" Score="2" Body="&lt;p&gt;According to &lt;a href=&quot;http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped&quot; rel=&quot;nofollow&quot;&gt;http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; Family ID&#xA; Individual ID&#xA; Paternal ID&#xA; Maternal ID&#xA; Sex (1=male; 2=female; other=unknown)&#xA; Phenotype&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;  &#xA;  &lt;p&gt;[...]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Genotypes (column 7 onwards) should also be white-space delimited; they can be any character (e.g. 1,2,3,4 or A,C,G,T or anything else) except 0 which is, by default, the missing genotype character. All markers should be biallelic. All SNPs (whether haploid or not) must have two alleles specified. Either Both alleles should be missing (i.e. 0) or neither. No header row should be given. For example, here are two individuals typed for 3 SNPs (one row = one person):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; FAM001  1  0 0  1  2  A A  G G  A C &#xA; FAM001  2  0 0  1  2  A A  A G  0 0 &#xA; ...&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And here is what I find in the begining of a HapMap .ped file I got a few years ago (hapmap3_r2_b36_fwd.YRI.qc.poly.ped):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;&lt;pre&gt;&lt;code&gt; Y001    NA18488 0       0       2       -9      C C     T T     ...&#xA; Y014    NA18519 0       0       1       -9      C C     T T     ...&#xA; ...&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So far, it seems to me than this is plain .ped format: the number of &quot;header&quot; columns is the same, and seems to conform to the specifications given in the above-mentioned web page.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now let's have a look at the .map files.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;By default, each line of the MAP file describes a single marker and must contain exactly 4 columns:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; chromosome (1-22, X, Y or 0 if unplaced)&#xA; rs# or snp identifier&#xA; Genetic distance (morgans)&#xA; Base-pair position (bp units)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;  &#xA;  &lt;p&gt;[...]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Note: Most analyses do not require a genetic map to be specified in any case; specifying a genetic (cM) map is most crucial for a set of analyses that look for shared segments between individuals. For basic association testing, the genetic distance column can be set at 0. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;[...]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The autosomes should be coded 1 through 22. The following other codes can be used to specify other chromosome types:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; X    X chromosome                    -&amp;gt; 23&#xA; Y    Y chromosome                    -&amp;gt; 24&#xA; XY   Pseudo-autosomal region of X    -&amp;gt; 25&#xA; MT   Mitochondrial                   -&amp;gt; 26&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;  &#xA;  &lt;p&gt;The numbers on the right represent PLINK's internal numeric coding of these chromosomes: these will appear in all output rather than the original chromosome codes. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here we have something that may be different.&#xA;The end of the .map file corresponding to the HapMap .ped file looks like this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;&lt;pre&gt;&lt;code&gt; 26      rs28357376      0       15825&#xA; 26      rs2853510       0       15925&#xA; 26      rs2854125       0       16149&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The HapMap .map file uses &quot;plink's internal numeric coding&quot; for the chromosome instead of the letter code (MT).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise, it looks a pretty standard .map file, with no genetic distance indicated.&lt;/p&gt;&#xA;" OwnerUserId="1486" LastEditorUserId="3829" LastEditDate="2013-06-25T14:48:19.597" LastActivityDate="2013-06-25T14:48:19.597" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8945" PostTypeId="2" ParentId="8942" CreationDate="2013-06-25T08:31:23.847" Score="2" Body="&lt;p&gt;One rationale is that smaller meals will cause less insulin secretion compared to a larger meal. With less circulating insulin over the time, insulin will be under the threshold required to activate the adipogenic program in the white adipose tissue. So, you will burn ingested carbohydrates instead of converting them in fat despite the same caloric intake. See for instance &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0038632&quot; rel=&quot;nofollow&quot;&gt;Munster and Saris, Plos One 2012&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2013-06-25T08:31:23.847" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8946" PostTypeId="1" CreationDate="2013-06-25T10:13:14.643" Score="9" ViewCount="1201" Body="&lt;p&gt;Im trying to find out what this is, see image below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Im thinking these are either some insect eggs or some sort of mosslike plant.&lt;br&gt;&#xA;The substance is stuck to a steel pillar, outside, about 5 feet above the ground.&lt;br&gt;&#xA;The substance is found in the Netherlands in a wet meadow area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The substance has multiple tiny cells or eggs, seems to be only 1 layer thick and has a soft/smooth feel to it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wjzgz.jpg&quot; alt=&quot;unknown organism&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Excuse me for the bad picture, my camera would not focus better because of the reflective surface of the pillar.&lt;/p&gt;&#xA;" OwnerDisplayName="user1897" LastEditorDisplayName="user1897" LastEditDate="2013-06-25T11:21:00.470" LastActivityDate="2019-05-06T20:44:43.497" Title="Organism identification, what is this?" Tags="&lt;species-identification&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8947" PostTypeId="1" CreationDate="2013-06-25T10:34:56.427" Score="1" ViewCount="155" Body="&lt;p&gt;In Estonia, the product bought from the shop lasts about 2-3 days, in Finland 3-5 days and In Oslo Norway 7 days.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The better infrastructure of transportation explains some for Finland and Norway.&#xA;But how on earth so big difference between Norway and Finland?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I heard today that some countries are fluoridating milk.&#xA;Ii is not in Finland and Norway.&#xA;However, it may be the case that some minerals are existing naturally more in Norway than in Finland. Also, more rain dissolves more minerals in Norway than in Finland.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can pasteurized milk last 7 days?&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1590" LastEditDate="2013-06-25T10:55:01.280" LastActivityDate="2013-06-25T15:23:39.387" Title="How can pasteurized milk last 7 days?" Tags="&lt;milk&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8948" PostTypeId="2" ParentId="8947" CreationDate="2013-06-25T11:14:29.547" Score="3" Body="&lt;p&gt;I would rather think about regulatory differences instead of biological ones. (Edit, as also Rory M highlighted in a comment)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Extended shelf life can be obtained through microbial ultrafiltration. However in Europe, ultrafiltration labelling is not mandatory, so it is difficult to distinguish if a milk product was simply pasteurized or also ultrafiltrated. The converse case, biologically speaking, two milk products could be generally the same but one country could be more stricter than the other on shelf-life legislation. (The shelf-life relates more to the unsuitability for sale rather than for consumption).&lt;/p&gt;&#xA;" OwnerUserId="444" LastActivityDate="2013-06-25T11:14:29.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8949" PostTypeId="2" ParentId="8947" CreationDate="2013-06-25T14:03:20.673" Score="1" Body="&lt;p&gt;Evidently the shelf-life of pasteurised milk is very dependent upon post-pasteurisation temperature of storage. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20492183&quot; rel=&quot;nofollow&quot;&gt;Here is a paper&lt;/a&gt; in which the effect of temperature on shelf-life has been analysed. A sentence from the abstract says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The microbiological stability for pasteurized milk packaged in HDPE bottle and stored at 2, 4, 9, 14, and 16 degrees C was estimated at 43, 36, 8, 5, and 3 d, respectively.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think that you would need to know exactly how the milk had been handled from pasteurisation plant to retail outlet before you could make any valid comparisons. Any period out of cold storage could clearly have a big impact.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="107" LastEditDate="2013-06-25T15:23:39.387" LastActivityDate="2013-06-25T15:23:39.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8950" PostTypeId="1" AcceptedAnswerId="8951" CreationDate="2013-06-25T14:59:53.630" Score="1" ViewCount="353" Body="&lt;p&gt;When a bacteria A divides it produces two cells A', A''. Each of them receives a copy of the chromosome/plasmids. Now, DNA replication occurs way before division in a semiconservative manner. That is, each new chromosome has an 'old' strand and a 'new' strand. Since the polymerase is error prone, my belief is that both genomes can potentially have mutations. Now when people refer to the mutation rate/genome/replication, e.g. 3x10-4 , Does this mean that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Only one of the resulting genomes have this mutation rate? (according to me not likely).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The mutation rate takes into account the total number of mutations in both new genomes.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Each of the genomes can potentially have independently as many mutations as the mutation rate specifies.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="233" LastEditorUserId="107" LastEditDate="2013-06-25T15:16:14.000" LastActivityDate="2013-06-25T21:07:29.400" Title="Bacterial division and mutation rate" Tags="&lt;mutations&gt;&lt;genomes&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8951" PostTypeId="2" ParentId="8950" CreationDate="2013-06-25T16:08:39.473" Score="2" Body="&lt;p&gt;Your question comes down to the definition of the units you state in your question - mutations genome&lt;sup&gt;-1&lt;/sup&gt; generation&lt;sup&gt;-1&lt;/sup&gt;. In my opinion the answer is your choice (2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How are mutation frequencies measured? Usually it is a case of scoring the appearance of a mutant phenotype as an indicator of underlying mutational events (see &lt;a href=&quot;http://www.pnas.org/content/88/16/7160.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;Drake,JW (1991)A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. USA 88:7160-7164&lt;/a&gt; for a detailed explanation.) Since, as you say, DNA replication is semi-conservative, the two daughter cells of a bacterial cell division each inherit one old DNA strand and one new DNA strand and so have the same probability of sustaining a given mutation. The overall mutational frequency has to be an aggregate of what has happened in both of them (and in all other cells in the population) since there is no way of distinguishing between them. In terms of your question the answer is (2) and this is why the mutation rate is normalised per genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practice this figure is arrived at as follows. Suppose that you study a 1 kb gene, gene X, and measure the rate of spontaneous mutation in that gene (by some convenient assay) as 1 mutation per 10&lt;sup&gt;7&lt;/sup&gt; cell divisions (again see the Drake reference for details). Assume also that the bacteria have a genome size of 2 x 10&lt;sup&gt;6&lt;/sup&gt; bp.  Since each cell division equates to the creation of one new genome we get:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;mutations per gene X per generation = 1 x 10&lt;sup&gt;-7&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;mutations per bp per generation  = 1 x 10&lt;sup&gt;-7&lt;/sup&gt;/1000 (because it is a 1000 bp gene)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;mutations per genome per generation = 1 x 10&lt;sup&gt;-7&lt;/sup&gt; * 2 x 10&lt;sup&gt;6&lt;/sup&gt;/1000&lt;/p&gt;&#xA;&#xA;&lt;p&gt;mutations per genome per generation = 0.0002&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now this is an underestimate because not all mutations will create a detectable change in phenotype. Drake uses a correction factor of 3.12 for this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;true mutations per genome per generation = 0.0002 * 3.12 = 0.0006 or 6 x 10&lt;sup&gt;-4&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These were made-up numbers. See review in &lt;a href=&quot;http://www.genetics.org/content/148/4/1667.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;Drake JW &lt;em&gt;et al&lt;/em&gt;.(1998) Rates of spontaneous mutation. Genetics 148: 1667-1686&lt;/a&gt; for real examples.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-06-25T21:07:29.400" LastActivityDate="2013-06-25T21:07:29.400" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8952" PostTypeId="1" AcceptedAnswerId="8957" CreationDate="2013-06-25T16:12:54.970" Score="2" ViewCount="469" Body="&lt;p&gt;I was recently bitten by a tick. After having removed it from my body, I put it in a glass. By now, it has stopped moving, so I put it under a microscope and looked at it. I was surprised about being unable to get a sharp image of its body (upper part in the images) – what could that be? And can someone help me identify it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found a picture of a tick with a somewhat transparent thing around its back &lt;a href=&quot;http://en.wikipedia.org/wiki/File:Ixodes_hexagonus_%28aka%29.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; – maybe that's what made it hard for me to get a clear focus on the back? And maybe it's related to this one?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BzPEq.jpg&quot; alt=&quot;thing that bit me 1&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was found in Oldenburg, Lower Saxony, Germany. Its length is between 1.2mm and 1.4mm (I don't have anything that's very usable for precise measurement of such small lengths).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If clearer focus on a particular part of that thing is needed for identification, please tell me.&lt;/p&gt;&#xA;" OwnerUserId="585" LastEditorUserId="1590" LastEditDate="2013-07-30T09:30:28.550" LastActivityDate="2013-07-30T09:30:28.550" Title="Which kind of tick is this and what is that thing around its back?" Tags="&lt;species-identification&gt;&lt;arachnology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8953" PostTypeId="1" AcceptedAnswerId="8954" CreationDate="2013-06-25T16:46:47.640" Score="1" ViewCount="161" Body="&lt;p&gt;I am writing a report on how Single Nucleotide Polymorphisms occurring in each of these regions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Transcription factor (TF) binding sites &lt;/li&gt;&#xA;&lt;li&gt;Epigentic signals&lt;/li&gt;&#xA;&lt;li&gt;Splicing variants&lt;/li&gt;&#xA;&lt;li&gt;MicroRNA binding sites&lt;/li&gt;&#xA;&lt;li&gt;Coding regions&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;can cause diseases.   Related literature suggestion from you or just informations that you know would be grateful&lt;/p&gt;&#xA;" OwnerUserId="1715" LastEditorUserId="3059" LastEditDate="2013-06-25T22:58:43.937" LastActivityDate="2013-06-25T22:58:43.937" Title="Single Nucleotide Polymorphisms and diseases" Tags="&lt;bioinformatics&gt;&lt;homework&gt;&lt;snp&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8954" PostTypeId="2" ParentId="8953" CreationDate="2013-06-25T19:43:56.933" Score="2" Body="&lt;p&gt;SNPs in all these regions will modify the DNA sequence. Effects will depend on where exactly the SNP is. I'll summarize the conditions in which effects can be maximum&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Transcription Factors (TFs) binding sites: SNP in the nucleotide positions that bind to the recognition amino acids in the TF&lt;/li&gt;&#xA;&lt;li&gt;Epigentic signals: C-&gt;X [x: A,G,T] SNPs can disrupt DNA methylation hotspots&lt;/li&gt;&#xA;&lt;li&gt;Splicing variants: SNPs at splice donor/acceptor sites can cause intron retention&lt;/li&gt;&#xA;&lt;li&gt;microRNA binding sites: SNP in seed region can abolish miRNA targeting&lt;/li&gt;&#xA;&lt;li&gt;Coding regions: certain SNPs can create premature stop codons for e.g. CAG (Gln) -&gt; UAG (stop)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;there is a lot of work on SNPs. If you search in pubmed for all these categories, you'll get many research articles as well as reviews. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-06-25T19:43:56.933" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8957" PostTypeId="2" ParentId="8952" CreationDate="2013-06-25T21:45:06.890" Score="5" Body="&lt;p&gt;As your link suggests, it looks like a female tick of the genus &lt;em&gt;Ixodus&lt;/em&gt;. It is likely female because the scutum or shield only covers part of the dorsal surface. E.g.,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tfVl7.png&quot; alt=&quot;Female Ixodus&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;which comes from &lt;a href=&quot;http://bristoltickid.blogs.ilrt.org/key-to-genera/ixodes/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bristol University Tick ID&lt;/a&gt;. The translucent posterior portion may just be from light passing through.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are able to zoom in closer on different parts, you can &lt;a href=&quot;http://bristoltickid.blogs.ilrt.org/key-to-genera/ixodes/ixodes-female-key/&quot; rel=&quot;nofollow noreferrer&quot;&gt;key out what species it is&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-06-25T21:45:06.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8958" PostTypeId="5" CreationDate="2013-06-25T22:01:22.537" Score="0" Body="&lt;p&gt;Reference request questions should address the following points:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A clear description of the scientific question (also include relevant subject tag)&lt;/li&gt;&#xA;&lt;li&gt;The kind of information that is needed and specific details that the reference should provide (if any)&lt;/li&gt;&#xA;&lt;li&gt;Type of reference needed: research article/review/book; for books also include &lt;a href=&quot;/questions/tagged/book-recommendation&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;book-recommendation&amp;#39;&quot; rel=&quot;tag&quot;&gt;book-recommendation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Publication date (a broad range) can also be included if necessary.&lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="3340" LastEditDate="2016-03-23T16:38:58.630" LastActivityDate="2016-03-23T16:38:58.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8959" PostTypeId="4" CreationDate="2013-06-25T22:01:22.537" Score="0" Body="Questions requesting a reference (book, journal article, etc) for a specific topic/finding." OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2013-06-25T22:03:34.803" LastActivityDate="2013-06-25T22:03:34.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8960" PostTypeId="1" AcceptedAnswerId="8973" CreationDate="2013-06-26T01:09:48.267" Score="7" ViewCount="1148" Body="&lt;p&gt;In this &lt;a href=&quot;http://www.youtube.com/watch?v=cG1wzGbBnsg&quot;&gt;short clip&lt;/a&gt;, you can see the mantis shrimp using some sort of feathery arm/claw to rub its eyes. Looking at a diagram &lt;a href=&quot;http://4.bp.blogspot.com/_82GUbxEh8kI/TSWY6qkab_I/AAAAAAAAACU/qSjy1DsmwgI/s1600/Alek4.png&quot;&gt;here&lt;/a&gt;, it appears possibly that it's using maxillipeds. Someone with knowledge of crustaceans (the behavior is probably not unique to mantis shrimp) would be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="1728" LastActivityDate="2013-06-26T21:56:18.987" Title="What is the name of the appendage that mantis shrimp use to rub their eyes?" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8961" PostTypeId="2" ParentId="7447" CreationDate="2013-06-26T07:18:41.003" Score="1" Body="&lt;p&gt;Using DMSO (dimethyl sulfoxide), agarose can be separated. After heating and stirring around 2 hrs you will get a yellow stiff gel of agarose by filtering.&lt;/p&gt;&#xA;" OwnerUserId="3879" LastEditorUserId="444" LastEditDate="2013-06-26T09:12:14.743" LastActivityDate="2013-06-26T09:12:14.743" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8962" PostTypeId="1" CreationDate="2013-06-26T08:15:46.020" Score="3" ViewCount="758" Body="&lt;p&gt;I've been physically carrying out serial  tenfold dilutions on samples of Ureaplasma to work out the color-changing units (CCU). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a definition, the CCU is the highest dilution at which there is a color change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the highest dilution is 10^3, apparently that means that there are 10^3 cells per ml in the original sample. But this is what I do not understand. How are we sure of this? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I feel like there is a lot that I am missing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help would be greatly appreciated.&lt;/p&gt;&#xA;" OwnerUserId="3880" LastActivityDate="2013-06-26T08:15:46.020" Title="Can someone explain the color-changing unit (CCU) to me?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;microbiology&gt;&lt;growth-media&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8963" PostTypeId="2" ParentId="1799" CreationDate="2013-06-26T09:59:36.677" Score="5" Body="&lt;p&gt;No. No other group found in the fossil record after the K-T boundary (the extinction &quot;event&quot;) descends from dinosaurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is likely that the extinction event was not itself instantaneous so if you wanted to be extremely picky you could argue that small numbers of individuals survived the K-T boundary but, apart from birds, none of these survivors went on to form long lasting lineages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Non-avian dinosaurs that survived the extinction event are referred to as &quot;palaeocene dinosaurs&quot;, there are some links on &lt;a href=&quot;http://en.wikipedia.org/wiki/Paleocene_dinosaurs&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; that might interest you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see a diagram linking vertebrate groups &lt;a href=&quot;http://www.dinosaur-world.com/milestones_of_evolution/images/milestones426-fullsize.jpg&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, similar diagrams can be found in most evolution texts.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="2938" LastEditDate="2013-06-26T13:58:03.910" LastActivityDate="2013-06-26T13:58:03.910" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8964" PostTypeId="1" CreationDate="2013-06-26T12:12:09.923" Score="4" ViewCount="313" Body="&lt;p&gt;I am planning to utilize a new system in our lab, in which I will co-culture cancer cells from different tissues with fibroblasts. &#xA;I have the option to receive skin-derived primary fibroblasts. I have been told the normal fibroblasts are very similar all over the body. Is this really true? I assume that fibroblasts secrete factors, for example, that are tissue specific. The question is, how quickly do they adapt to a new environment? For example if I take these skin-derived fibroblasts and co-culture them with breast cancer cells, how long will it take the fibroblasts, if any, to become more like fibroblasts derived from the breast?&lt;/p&gt;&#xA;" OwnerUserId="3026" LastActivityDate="2014-07-29T12:36:10.923" Title="How different are tissue-specific fibroblasts from each other?" Tags="&lt;biochemistry&gt;&lt;cell-culture&gt;&lt;tissue&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8965" PostTypeId="2" ParentId="8724" CreationDate="2013-06-26T12:21:10.680" Score="0" Body="&lt;p&gt;The diameter of the blood vessel affects the speed of the flow of blood. Blood flow slows down as it moves from arteries to arterioles and subsequently to the capillaries because the cross-sectional area in the capillary beds is much bigger than the arteries or any part of the circulatory system. Use this &lt;a href=&quot;http://forum.internationaldrugmart.com/&quot; rel=&quot;nofollow&quot;&gt;drug awareness&lt;/a&gt; forum to know more about this. &lt;/p&gt;&#xA;" OwnerUserId="3883" LastActivityDate="2013-06-26T12:21:10.680" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8966" PostTypeId="1" AcceptedAnswerId="8970" CreationDate="2013-06-26T13:16:05.110" Score="5" ViewCount="1234" Body="&lt;p&gt;As stated &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19252842&quot;&gt;here&lt;/a&gt; it is possible to produce fragments of antibodies in bacteria and harvest them (from the medium, I guess, but I don't have access to the full article).&#xA;As it is possible to design antibodies, would it be possible and feasible to produce important antibodies large scale through bacteria like it is done for example with insulin?&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-06-26T18:17:09.133" Title="Possibility and feasibility of producing designed antibodies with bacteria" Tags="&lt;immunology&gt;&lt;bacteriology&gt;&lt;antibody&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8967" PostTypeId="1" AcceptedAnswerId="8969" CreationDate="2013-06-26T16:04:28.557" Score="15" ViewCount="2145" Body="&lt;p&gt;In some cases two species can hybridize. For example, Tigers and lions can hybridize to produce &quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/Liger&quot;&gt;Ligers&lt;/a&gt;&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would it also be possible for humans and chimpanzees (or any other species) to hybridize ?&#xA;If not, what would be the likely cause of failure?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do some hybridization matings produce offspring, like the Liger, and some not? What mechanisms prevent hybridizations?&lt;/p&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="3624" LastEditDate="2013-10-28T15:08:48.010" LastActivityDate="2018-03-05T00:43:03.717" Title="Could humans and chimpanzees hybridize?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;reproduction&gt;&lt;human-genetics&gt;&lt;hybridization&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8969" PostTypeId="2" ParentId="8967" CreationDate="2013-06-26T16:32:55.830" Score="12" Body="&lt;p&gt;The concept of a human/chimp hybrid is called a &lt;a href=&quot;http://en.wikipedia.org/wiki/Humanzee&quot; rel=&quot;nofollow noreferrer&quot;&gt;humanzee&lt;/a&gt;. No humanzees have ever been recorded despite the fact that sexual intercourse between humans and chimps have been recorded on several occasions. This suggests that male-human/female-chimpanzee is not capable of producing viable offspring, at the very least.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to why, several reasons will contribute: humans and chimps have a different number of chromosomes, making cross-fertility unlikely (although animals with different chromosome numbers can and do breed so this isn't absolute). Humans and chimps are anisomorphically quite different (i.e. the ratios of limbs are different and so on) so it's quite plausible that the growth patterns are not compatible. I'm not aware of any exhaustive studies into reasons why cross-breeding is impossible but it's also quite plausible that there are changes in the chemistry of fertilisation, etc. that will limit cross-breeding.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd note, finally, that there's evidence from the X chromosome that the human line continued to have some level of interbreeding with chimps for some million years after the initial split (&lt;a href=&quot;http://dx.doi.org/10.1038/nature04789&quot; rel=&quot;nofollow noreferrer&quot;&gt;Patterson et al, 2005&lt;/a&gt;&lt;sup&gt;&amp;dagger;&lt;/sup&gt;).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&amp;dagger;&lt;/sup&gt;  &lt;sub&gt;I see that there are some later publications that have disputed the claims made in that paper. So I'll leave you to judge the merits of the arguments. &lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="4108" LastEditDate="2018-03-05T00:43:03.717" LastActivityDate="2018-03-05T00:43:03.717" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="8970" PostTypeId="2" ParentId="8966" CreationDate="2013-06-26T17:45:03.363" Score="3" Body="&lt;p&gt;I'll preface this by saying that I'm talking about antibodies of mammalian/human origin, consisting of two identical heavy and two identical light chains disulfide-bonded into the classic antibody structure:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Liacj.png&quot; alt=&quot;structure of IgG, from en.wikipedia.org/wiki/File:Antibody_IgG2.png&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible to produce antibody-like molecules known as single-chain antibodies, including &lt;a href=&quot;http://en.wikipedia.org/wiki/Single-chain_variable_fragment&quot; rel=&quot;nofollow noreferrer&quot;&gt;single-chain variable fragments&lt;/a&gt; (scFv) in bacteria and viruses, where it is also known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Phage_display&quot; rel=&quot;nofollow noreferrer&quot;&gt;phage display&lt;/a&gt;. These hosts can also produce a modified &lt;a href=&quot;http://en.wikipedia.org/wiki/Fab_fragment&quot; rel=&quot;nofollow noreferrer&quot;&gt;F&lt;sub&gt;ab&lt;/sub&gt; fragment&lt;/a&gt; that is engineered as a single polypeptide chain, and multiple other single-chain antibody-like molecules as shown below. In the past, this has primarily been done in &lt;em&gt;E. coli&lt;/em&gt;, as they are a common tool used in protein expression, and have many advantages as an experimental system in general. However, single-chain antibody production in &lt;em&gt;E. coli&lt;/em&gt; is hampered by the fact that these exogenous proteins tend to form &lt;a href=&quot;http://en.wikipedia.org/wiki/Inclusion_body&quot; rel=&quot;nofollow noreferrer&quot;&gt;inclusion bodies&lt;/a&gt; instead of being secreted into the medium, where they can be collected and purified much more easily, without the need for lysing the host cells. The paper you linked to describes a method for producing scFvs in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Gram_positive&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gram-positive&lt;/a&gt; bacterium &lt;a href=&quot;http://en.wikipedia.org/wiki/Bacillus_megaterium&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Bacillus megaterium&lt;/em&gt;&lt;/a&gt;, which is becoming more common for the production of recombinant proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/l2ona.png&quot; alt=&quot;engineered antibodies, from en.wikipedia.org/wiki/File:Engineered_monoclonal_antibodies.svg&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, it is possible to produce antibody-like molecules in bacteria. However, unlike insulin, full-length antibodies are made up of multiple polypeptide chains, and are both &lt;a href=&quot;http://en.wikipedia.org/wiki/Glycosylation&quot; rel=&quot;nofollow noreferrer&quot;&gt;glycosylated&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Disulfide_bond&quot; rel=&quot;nofollow noreferrer&quot;&gt;disulfide-bonded&lt;/a&gt;. While there is evidence that bacteria can accomplish both of these biochemical tasks, the processes seem to require additional chaperone, trafficking, and regulatory proteins that bacteria do not possess, and as far as I know scientists have so far not been successful in producing full &quot;proper&quot; antibody molecules in prokaryotes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are many mammalian/human expression systems for producing fully functional recombinant antibodies in very high yield, and a number of &lt;a href=&quot;http://en.wikipedia.org/wiki/Monoclonal_antibody_therapy#FDA_approved_therapeutic_antibodies&quot; rel=&quot;nofollow noreferrer&quot;&gt;FDA-approved monoclonal antibody drugs&lt;/a&gt; are now on the market, with many more in various stages of development and clinical trials.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2013-06-26T18:17:09.133" LastActivityDate="2013-06-26T18:17:09.133" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8971" PostTypeId="2" ParentId="8966" CreationDate="2013-06-26T18:02:10.073" Score="1" Body="&lt;p&gt;@MattDMo hit the highlights, but I wanted to comment on the creation of libraries of anbitodies for screening in bacatera.  But there has been interest in &lt;a href=&quot;http://www.ablynx.com/en/research-development/nanobody-technology/understanding-nanobodies/&quot; rel=&quot;nofollow&quot;&gt;nanobodies&lt;/a&gt; - the antibodies of camelids  (llamas and camels) have only one chain, which makes the idea of heterologous expression in bacteria even simpler.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-06-26T18:02:10.073" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8972" PostTypeId="1" CreationDate="2013-06-26T19:14:13.573" Score="9" ViewCount="237" Body="&lt;p&gt;I have seen many articles that talk about a star's &quot;habitable zone&quot; as the ring around it which is just the right temperature for planets to have liquid water, which is necessary for life. My question is, why does a planet need to have liquid water in order to sustain life? Who says that extraterrestrial life can't live off of some other kind of sustenance?&lt;/p&gt;&#xA;" OwnerUserId="3885" LastActivityDate="2013-06-26T20:45:02.733" Title="Why must a planet be in a star's &quot;habitable zone&quot; to have life?" Tags="&lt;astrobiology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8973" PostTypeId="2" ParentId="8960" CreationDate="2013-06-26T20:02:48.307" Score="5" Body="&lt;p&gt;Mantis shrimp use their first maxillipeds for grooming (&lt;a href=&quot;https://en.wikipedia.org/wiki/Appendage&quot;&gt;maxilliped=modified appendage&lt;/a&gt;), which is &lt;a href=&quot;http://arthropoda.southernfriedscience.com/?p=3526&quot;&gt;specialized for this purpose&lt;/a&gt;. Details and a picture of the organ can be found in the link. The second maxilliped is their famous specialized organ for &lt;a href=&quot;http://www.youtube.com/watch?v=i-ahuZEvWH8&quot;&gt;striking or spearing prey with enormous force&lt;/a&gt;. More about their &lt;a href=&quot;http://arthropoda.southernfriedscience.com/?p=801&quot;&gt;raptoral appendage&lt;/a&gt;, with links to further references. Mantis shrimp also have very complex eyes, described as &lt;a href=&quot;http://www.popsci.com/scitech/article/2008-03/eye-mantis-shrimp&quot;&gt;&quot;...the most complicated visual system of any animal on Earth&quot;&lt;/a&gt;. Their eyes can see a range from ultraviolet to infra-red and has specialized regions for observing motion, form, depth, and color. More on Mantis shrimp eyes can be found in &lt;a href=&quot;http://www.nature.com/nature/journal/v401/n6756/full/401873a0.html&quot;&gt;Marshall &amp;amp; Oberwinkler (1999)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-06-26T21:56:18.987" LastActivityDate="2013-06-26T21:56:18.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8974" PostTypeId="2" ParentId="8972" CreationDate="2013-06-26T20:26:36.240" Score="4" Body="&lt;p&gt;Your question is not complete. I would suggest to slightly change the title to something like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Why must a planet be in a star's “habitable zone” to have life &lt;strong&gt;as we know it from our experience&lt;/strong&gt;?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are right, when you are assuming that there could be another than carbon based life as we know it from our planet Earth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many hypotheses that life could be based on &lt;a href=&quot;https://en.wikipedia.org/wiki/Silicon&quot; rel=&quot;nofollow&quot;&gt;Si&lt;/a&gt; or other elements. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But carbon is still the easiest element to create bounds with other&#xA;elements and carbon too. Why? Here is the answer from wikipedia &lt;a href=&quot;http://en.wikipedia.org/wiki/Carbon-based_life&quot; rel=&quot;nofollow&quot;&gt;Carbon-based life&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There are not many&#xA;  other elements which even appear to be promising candidates for&#xA;  supporting life - for example, processes such as metabolism - but the&#xA;  most frequently suggested alternative is silicon.&lt;a href=&quot;https://en.wikipedia.org/wiki/Brian_Cox_%28physicist%29&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt; This is in the&#xA;  same group in the Periodic Table of elements and therefore also has&#xA;  four valence bonds. It also bonds to itself, but generally in the form&#xA;  of crystal lattices rather than long chains. Silicon compounds are&#xA;  generally stable but do not support the ability readily to re-combine&#xA;  in different permutations in a manner that would plausibly support&#xA;  lifelike processes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is a great documentary from a physicist &lt;a href=&quot;https://en.wikipedia.org/wiki/Brian_Cox_%28physicist%29&quot; rel=&quot;nofollow&quot;&gt;Brian Cox&lt;/a&gt; published by BBC this year called &lt;a href=&quot;http://en.wikipedia.org/wiki/Wonders_of_Life_%28TV_series%29&quot; rel=&quot;nofollow&quot;&gt;Wonders Of Life&lt;/a&gt; which deals with the basic questions how carbon based creatures were &quot;born&quot; on this planet ;) + other interesting things about life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brian talks there why the first organisms were created probably in water and how it could be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why water?&lt;/strong&gt; &#xA;&lt;a href=&quot;http://www.pbs.org/wgbh/nova/evolution/liquid-of-life.html&quot; rel=&quot;nofollow&quot;&gt;http://www.pbs.org/wgbh/nova/evolution/liquid-of-life.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;And why is water the best liquid to do the job? For one thing, it&#xA;  dissolves just about anything. &quot;Water is probably the best solvent in&#xA;  the universe,&quot; says Jeffrey Bada, a planetary scientist at the Scripps&#xA;  Institution of Oceanography in La Jolla, Calif. &quot;Everything is soluble&#xA;  in water to some degree.&quot; Even gold is somewhat soluble in seawater.&#xA;  (Before you get any ideas about extracting gold from the oceans, I&#xA;  should add that, according to Bada, the value of dissolved gold in a&#xA;  metric ton of seawater comes to about $0.0000004).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you take a route that there could be a different form of life outside of habitable zone, then many things are possible. E.g. life on asteroids, ouside of solar systems, life in other dimensions, life based on silicon or some other elements, energy based life? Or even dark matter and dark energy based life or gods/God-like creatures and all kinds of sci-fi ideas ;).&lt;/p&gt;&#xA;" OwnerUserId="3118" LastEditorUserId="3118" LastEditDate="2013-06-26T20:45:02.733" LastActivityDate="2013-06-26T20:45:02.733" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="8976" PostTypeId="1" CreationDate="2013-06-26T20:45:17.903" Score="1" ViewCount="92" Body="&lt;p&gt;Let's say a Lysosome that bonds to a hazardous material to neutralize it has all bonding sites used up. would it be more safe / efficient to excrete the entire Lysosome / hazardous material molecule or to bring it to a certain organelle / organ to unbind the material and send it for excretion and then have the Lysosome available for use again? In which way do Lysosomes in nature commonly handle this problem?&lt;/p&gt;&#xA;" OwnerUserId="3458" LastEditorUserId="3458" LastEditDate="2013-06-27T18:29:06.640" LastActivityDate="2013-06-27T18:29:06.640" Title="When a Lysosome's bonding sites all get bonded to, what is the most resource and energy efficient way to handle the used Lysosome?" Tags="&lt;biochemistry&gt;&lt;thermodynamics&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8977" PostTypeId="1" CreationDate="2013-06-26T20:55:14.947" Score="11" ViewCount="286" Body="&lt;p&gt;Inspired by an &lt;a href=&quot;https://biology.stackexchange.com/questions/8972/why-must-a-planet-be-in-a-stars-habitable-zone-to-have-life&quot;&gt;answer to a previous question.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's hypothesized that extraterrestrial life could be based on silicon rather than carbon as its main structural element.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there similar theories about an alternative &quot;life solvent&quot; rather than water? &lt;/p&gt;&#xA;" OwnerUserId="3053" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-08-02T14:20:30.413" Title="Can life subsist on anything else but water?" Tags="&lt;astrobiology&gt;&lt;speculative&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="8978" PostTypeId="2" ParentId="8977" CreationDate="2013-06-26T21:35:49.173" Score="5" Body="&lt;p&gt;This may not completely answer your question, but provide some information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at this Wikipedia outline &lt;a href=&quot;https://en.wikipedia.org/wiki/Hypothetical_types_of_biochemistry#Non-water_solvents&quot;&gt;Non water solvents&lt;/a&gt;, other possible candidates are ammonia, hydrocarbons even hydrogen fluoride.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Digging a little deeper, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15253836&quot;&gt;this abstract of the article: &quot;Many chemistries could be used to build living systems.&quot;&lt;/a&gt; (Abstract only) describes the possibilities of ammonia and liquid nitrogen as being potential suitable solvents.  Page 678 onwards of the article: &lt;a href=&quot;http://westheimerinstitute.org/pubs/Is%20there%20a%20common%20chemical%20model%20for%20life%20in%20the%20universe?.pdf&quot;&gt;&quot;Is there a common chemical model for life in the universe?&quot;&lt;/a&gt; also describes other solvents such as ammonia (I should say that there quite a lot of Star Trek references in that paper).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this goes part of the way to help.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-06-26T21:35:49.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8979" PostTypeId="1" AcceptedAnswerId="8984" CreationDate="2013-06-26T23:59:55.690" Score="8" ViewCount="11042" Body="&lt;p&gt;Genetics aside, what are the biochemical reasons for the different colours of human irises?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, related, how does eye colour change, particularly in childhood?  (example:  my eyes used to be blue, but are now greenish-hazel).&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="6307" LastEditDate="2017-03-25T20:13:09.873" LastActivityDate="2017-03-25T20:13:09.873" Title="What causes the colors we see in eyes?" Tags="&lt;human-biology&gt;&lt;molecular-biology&gt;&lt;eyes&gt;&lt;pigmentation&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8980" PostTypeId="2" ParentId="8977" CreationDate="2013-06-27T04:40:44.837" Score="5" Body="&lt;p&gt;This is not a definitive answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The solvent closest to water in its properties such as dielectric constant, melting/boiling points, etc are formamide and sulphuric acid. &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;                        F       S       W&#xA;Melting point (⁰C)      2       10      0&#xA;Boiling point (⁰C)      210     337     100&#xA;Dielectric Const        109     84–100  80&#xA;Specific gravity        1.133   1.94    1&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;But water is the simplest i.e made up of only two types of atoms (Which are decently abundant).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding silicon: even though silicon can undergo some level of catenation (silanes) it is not comparable to carbon. Silicon can form polymers like silicone (poly-siloxanes). But I think carbon seems to be more versatile. It is also more abundant (check &lt;a href=&quot;http://www.periodictable.com/Properties/A/UniverseAbundance.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; out. A nice representation of abundance of different elements in the universe)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also check &lt;a href=&quot;http://www.sciencemag.org/content/340/6132/577.full&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; out: it is about exoplanet habitability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since certain elements are more abundant than others, the likelihood of them giving rise to life is higher. Therefore water seemingly emerges as the life solvent. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[&lt;em&gt;still most times we see everything in an earth point of view&lt;/em&gt;]&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-06-28T09:44:01.303" LastActivityDate="2013-06-28T09:44:01.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8981" PostTypeId="2" ParentId="8636" CreationDate="2013-06-27T09:43:08.003" Score="1" Body="&lt;p&gt;Try this out with BioPython:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;from Bio.PDB.PDBSuperimposer import PDBSuperimposer as superimposer&#xA;from Bio.PDB.PDBParser import PDBParser&#xA;&#xA;parser = PDBParser()&#xA;sup = superimposer()&#xA;struct_1 = parser.get_structure(&quot;XXXX&quot;,&quot;first_pdb&quot;)&#xA;struct_2 = parser.get_structure(&quot;XXXX&quot;,&quot;second_pdb&quot;)&#xA;&#xA;atoms1 = struct_1.get_atoms()&#xA;atoms2 = struct_2.get_atoms()&#xA;sup.set_atoms(atoms1,atoms2)&#xA;&#xA;print sup.rotrans #print the rotation translation matrix from the SVD&#xA;&#xA;#then to complete the alignment&#xA;sup.apply()  &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;You can look here for further details. &lt;a href=&quot;http://biopython.org/DIST/docs/api/Bio.PDB.Superimposer%27-pysrc.html#Superimposer&quot; rel=&quot;nofollow&quot;&gt;SuperPoser&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="3887" LastActivityDate="2013-06-27T09:43:08.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8982" PostTypeId="1" AcceptedAnswerId="8983" CreationDate="2013-06-27T09:56:52.767" Score="3" ViewCount="313" Body="&lt;p&gt;I am reading a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23233545&quot; rel=&quot;nofollow&quot;&gt;paper &lt;/a&gt; which discusses a complex (MSL-DCC) involved in dosage compensation of the drosophila X-chromosome. Descriptions of the complex's structure and function are given in the papers introduction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To start with, could someone explain what is chromatin shearing? what is happening during the process?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, the authors then say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Our data suggest that the complex is particularly sensitive to shear&#xA;  forces on transcribed chromatin so that only the direct interactions&#xA;  on MSL-3 with nucleosomes are retained&quot; - discussion section (subheading: interaction of the MSL-DCC with target gene bodies)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Could someone explain what is meant by 'particularly sensitive to shear forces'? In comparison to what? And what are the consequences of it being more sensitive?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="948" LastEditDate="2014-01-13T21:44:00.730" LastActivityDate="2014-01-13T21:44:00.730" Title="Chromatin shearing: what is it and what are the effects of high-sensitivity?" Tags="&lt;genetics&gt;&lt;chromatin&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8983" PostTypeId="2" ParentId="8982" CreationDate="2013-06-27T11:32:56.237" Score="2" Body="&lt;p&gt;Shear forces are experienced by all molecules, and molecular complexes when they are treated roughly. So, for example, if you have a solution of high molecular weight DNA it will be very viscous, but if you treat it roughly by pipetting up and down through a narrow aperture the DNA strands will suffer shear forces strong enough to break covalent bonds and the solution will become less viscous. &lt;s&gt;Another example of the use of shear forces in biology is lysis of yeast cells using small glass beads. As the slurry of beads and cells is vortexes the cells experience intense shearing forces (forces tending to pull different parts of the cell in different directions) and they break open. They are not being physically ground by the beads.&lt;/s&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the specific case that you quote, you apparently have a multimolecular complex (MSL-DCC) held together by weak (non-covalent) interactions and interacting with the nucleosomes through a component called MSL-3. Without looking at the paper, it seems that this complex is prone to falling apart (during isolation?) as a result of shear forces strong enough to overcome the non-covalent binding interactions. Think of a helicopter with a man hanging on to the undercarriage with both hands. Then imagine a second man hanging on to the first man's boot lace with his thumb and finger. Who will fall off first due to the shearing forces experienced as they are buffeted by the wind?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The helicopter is the nucleosome, the first man is MSL-3 and the second man is the rest of the complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;added later in response to MattDMo&lt;/strong&gt;&#xA;looks &lt;a href=&quot;http://www.embl.de/pepcore/pepcore_services/protein_purification/extraction_clarification/cell_lysates_yeast/&quot; rel=&quot;nofollow&quot;&gt;from this&lt;/a&gt; that I was wrong - it's actually a French press and other homogenizers that generate shear forces. I don't think I made the glass bead story up, but I can't remember who told me. The BeadBeater people also refer to &quot;cell cracking&quot; not shear. Apologies everyone, I think the rest of the post still holds up, and thanks to MattDMo for the challenge.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-06-27T17:02:06.777" LastActivityDate="2013-06-27T17:02:06.777" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="8984" PostTypeId="2" ParentId="8979" CreationDate="2013-06-27T14:00:09.433" Score="11" Body="&lt;p&gt;The colour of human eyes is determined by the &lt;a href=&quot;https://en.wikipedia.org/wiki/Eye_color&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;pigmentation&lt;/strong&gt; present and the &lt;strong&gt;scattering of light&lt;/strong&gt;.&lt;/a&gt; Variance in the colour and density of the pigments affects how light is absorbed and reflected causing the different iris colours we see. Wiki has a fairly comprehensive coverage on the topic so,I'll use a few of the wikipedia examples to explain how the pigmentation and scattering of light interact to give colours:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Blue eye colour&lt;/strong&gt; is the result of pigment in low concentration and Rayleigh scattering (or Tyndall effect) of the short &lt;a href=&quot;http://en.wikipedia.org/wiki/File:EM_spectrum.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;light wavelengths (blue is short, red is long)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;There is no blue pigmentation either in the iris or in the ocular&#xA;  fluid. Dissection reveals that the iris pigment epithelium is brownish&#xA;  black due to the presence of melanin. Unlike brown eyes, blue eyes&#xA;  have low concentrations of melanin in the stroma of the iris, which&#xA;  lies in front of the dark epithelium. Longer wavelengths of light tend&#xA;  to be absorbed by the dark underlying epithelium, while shorter&#xA;  wavelengths are reflected and undergo Rayleigh scattering in the&#xA;  turbid medium of the stroma. This is the same frequency-dependence&#xA;  of scattering that accounts for the blue appearance of the sky.&#xA;  The result is a &quot;Tyndall blue&quot; structural color that varies with&#xA;  external lighting conditions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Brown eyes&lt;/strong&gt; are the result of higher melanin concentrations which absorbs more of the light, reducing the amount of light being reflected.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;In humans, brown eyes result from a relatively high concentration of&#xA;  melanin in the stroma of the iris, which causes light of both shorter&#xA;  and longer wavelengths to be absorbed.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Green eyes&lt;/strong&gt; appear to be mid-ground between blue and brown, they have more pigment than blue but less than brown.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;As in the case of blue eyes, the color of green eyes does not result&#xA;  simply from the pigmentation of the iris. Rather, its appearance is&#xA;  caused by the combination of an amber or light brown pigmentation of&#xA;  the stroma, given by a low or moderate concentration of melanin, with&#xA;  the blue tone imparted by the Rayleigh scattering of the reflected&#xA;  light.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;More can be read on this in these two studies: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9778410&quot; rel=&quot;nofollow noreferrer&quot;&gt;study 1&lt;/a&gt; &amp;amp; &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0749.2005.00268.x/full&quot; rel=&quot;nofollow noreferrer&quot;&gt;study 2&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is Rayleigh scattering / the Tyndall effect and why do they turn eyes blue?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I shall refer to this as the &lt;a href=&quot;https://en.wikipedia.org/wiki/Tyndall_effect&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tyndall effect&lt;/a&gt; but in the literature both Rayleigh and Tyndall are used because they are apparently very similar though Tyndall occurs with much larger particles. The Tyndall effect is caused by the variable scattering of light by particles depending on the wavelength of the light and relative size of the particles. Shorter wavelength lights are scattered more than the longer ones (so more red light is absorb than blue) which means more blue light is reflected. When more melanin is present in the iris it will better absorb the short wavelength light than when there is little melanin, therefore, people with low melanin levels appear to have blue eyes.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;An analogy to this wavelength dependency is that longwave electromagnetic waves such as radio waves are able to pass through the walls of buildings, while shortwave electromagnetic waves such as light waves are stopped and reflected by the walls.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why do eye colours change?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, wikipedia has a fairly thorough section on this and I will just summarise and directly quote it. Eye colour can change because the melanocytes responsible for the pigments have to continually produce pigment and, just like those causing colour in hair, they can become less productive (&lt;a href=&quot;https://biology.stackexchange.com/questions/2756/why-does-hair-turn-grey-or-white-and-why-does-it-happen-later-for-some&quot;&gt;which is why we have grey hair&lt;/a&gt;) and this happens more with age. Infants often have blue eyes that turn dark, just like yours did, because the melanin is gradually accumulated - it just takes time for enough pigment to build up and allow the eye colour to match it's genetic determinants:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Most babies who have European ancestry have light-colored eyes before the age of one. As the child develops, melanocytes (cells found within the iris of human eyes, as well as skin and hair follicles) slowly begin to produce melanin. Because melanocyte cells continually produce pigment, in theory eye color can be changed. Most eye changes happen when the infant is around one year old, although it can happen up to three years of age. Observing the iris of an infant from the side using only transmitted light with no reflection from the back of the iris, it is possible to detect the presence or absence of low levels of melanin. An iris that appears blue under this method of observation is more likely to remain blue as the infant ages. An iris that appears golden contains some melanin even at this early age and is likely to turn green or brown as the infant ages.&#xA;  Changes (lightening or darkening) of eye colors during puberty, early childhood, pregnancy, and sometimes after serious trauma (like heterochromia) do represent cause for plausible argument to state that some eyes can or do change, based on chemical reactions and hormonal changes within the body.&#xA;  ... eye color over time can be subject to change, and major demelanization of the iris may also be genetically determined.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://archopht.jamanetwork.com/article.aspx?articleid=642125&quot; rel=&quot;nofollow noreferrer&quot;&gt;In this study&lt;/a&gt; 10-15% of those studied had changes in eye colour beyond childhood so, al though colour is generally stable past childhood, it is not uncommon for eyes to change, and this is likely due to changes in melanin composition. &lt;a href=&quot;http://www.usask.ca/biology/bortolotti/pubs/pbz-76-99-104.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;This study&lt;/a&gt; is an example of clour change in birds too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A side note: Animals with other colours&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is common for animals to have other eye colours, for example Blackbirds (&lt;em&gt;Turdus merula&lt;/em&gt;) have an Orange eye, which is caused by Carotenoid pigments, rather than melanin as in humans. The reason they have this could be as an indicator of quality in courtship - carotenoids are hard to get, males with bright orange eyes therefore have access to good food resources, and female blackbirds find that attractive. (This section is all from my memory after a talk with a tutor on my undergrad field course in the Isles of Scilly). &lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-06-29T08:17:19.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8985" PostTypeId="1" AcceptedAnswerId="8986" CreationDate="2013-06-27T14:13:04.927" Score="4" ViewCount="207" Body="&lt;p&gt;Ostensibly, in people with sickle cell trait, half of the hemoglobin in their body would be defective. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it actually the case that sickle cell hemoglobin is produced in equal amounts?&#xA;If not, how is that regulated? If so, how does that still not cause anemia?&lt;/p&gt;&#xA;" OwnerUserId="3888" LastEditorUserId="69" LastEditDate="2013-06-27T19:12:13.890" LastActivityDate="2013-06-27T19:12:13.890" Title="Why don't individuals with sickle cell trait suffer from sickle cell anemia?" Tags="&lt;hematology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8986" PostTypeId="2" ParentId="8985" CreationDate="2013-06-27T14:36:19.853" Score="6" Body="&lt;p&gt;This could be a very long answer, but I'll try to keep it brief. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first thing to understand is what causes the anaemia. I'm going to refer to defective haemoglobin found in a sickle cell patient as HbS and normal haemoglobin as HbA. Under certain circumstances (low O&lt;sub&gt;2&lt;/sub&gt; concentrations) the HbS protein is prone to aggregating into long filaments. Here is an image of a lysed erythrocyte releasing some of these filaments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4Y8Ud.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The presence of these filaments in the erythrocytes causes them to become misshapen (sickle-shaped) and this in turn causes them to get filtered out for destruction in the spleen which is continuously monitoring for defective erythrocytes (which could cause blockages in the circulation). This causes the anaemia (specifically a haemolytic anaemia, due to erythrocyte destruction, and nothing to do with a lack of iron).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The appearance of the ability to form filaments is due to a single Glu&gt;Val mutation in the two &amp;beta; subunits of the haemoglobin tetramer. The new amino acid can fit into a pre-existing hydrophobic pocket on the surface of another subunit and so the molecules can daisy-chain to form the filaments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The normal HbA can also bind on to a growing filament (it has the binding pocket) but that terminates the filament (because HbA doesn't have the Val residue).&lt;/strong&gt; In this way people with sickle cell trait are protected from the anaemia by their normal haemoglobin.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="3059" LastEditDate="2013-06-27T17:15:25.767" LastActivityDate="2013-06-27T17:15:25.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8989" PostTypeId="2" ParentId="7586" CreationDate="2013-06-27T15:27:52.327" Score="3" Body="&lt;p&gt;Expression of sfiA (sulA) causes filamentation during the SOS response, so presumably sfiA is induced, as part of SOS, in response to some sort of DNA damage. Once the DNA damage is repaired the SOS genes, including sfiA, will be repressed again and normal growth will resume.   &lt;/p&gt;&#xA;" OwnerUserId="3890" LastActivityDate="2013-06-27T15:27:52.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8991" PostTypeId="1" AcceptedAnswerId="8992" CreationDate="2013-06-27T16:09:36.710" Score="2" ViewCount="16758" Body="&lt;p&gt;I saw this article &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16710314&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/16710314&lt;/a&gt; and it mentioned pA(2) values and I had no idea what they were. What are they? What do they mean? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If possible it'd be just dandy if you could cite some journal articles/books/other reliable sources for me to dig up. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="69" LastEditDate="2013-06-27T19:12:59.707" LastActivityDate="2015-03-20T01:36:25.020" Title="What is a pA(2) value?" Tags="&lt;pharmacology&gt;&lt;terminology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="8992" PostTypeId="2" ParentId="8991" CreationDate="2013-06-27T16:25:38.907" Score="3" Body="&lt;p&gt;Digging around a bit, I found a few resources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10219974&quot; rel=&quot;nofollow&quot;&gt;Design and models for estimating antagonist potency (pA2, Kd and IC50) following the detection of antagonism observed in the presence of intrinsic activity.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and &lt;a href=&quot;http://www.ctf.edu.tr/farma/cihatkucukhuseyin/Ing/03_Pharmacodinamics.pdf&quot; rel=&quot;nofollow&quot;&gt;PHARMACODINAMIC&lt;/a&gt; on page 30, describes pA2 as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;indicates affinity of antagonist for receptors&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(as Alan Boyd just commented on)&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-06-27T16:25:38.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8993" PostTypeId="2" ParentId="8935" CreationDate="2013-06-27T19:43:38.883" Score="1" Body="&lt;p&gt;If we assume the drink was very well blended most of the water-soluble vitamis (B and C) as well sugars could dissolve in the juice. Fiber would mostly remain in the plant debris. Oils and fat-soluble vitamins (A, D, E, K) would form their own oily layer or be found in an emulsion with the fruit juice.&lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-06-27T19:43:38.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8994" PostTypeId="1" AcceptedAnswerId="9006" CreationDate="2013-06-27T21:09:41.013" Score="2" ViewCount="6342" Body="&lt;p&gt;I am interested in fibroblast cells in human arteries. Here are the things that I am not clear at the moment and I could not find any answer from the literature:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;What are the dimensions of these fibroblast cells? How big are they in terms of diameter and thickness? How big are they if they are comparing with the collagen fibers in the artery?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I think they have to attach themselves to the fibers in order to proliferate or differentiate. However, I do not know, do one fibroblast cell attach itself to one fiber and then &quot;crawl&quot; to another? Or do they &quot;sit&quot; on a network of fibers?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I will appreciate your help on this and will be even more grateful if you could provide me with some literature that I could find the answer to these questions.&lt;/p&gt;&#xA;" OwnerUserId="3892" LastEditorUserId="3892" LastEditDate="2013-06-28T08:47:13.630" LastActivityDate="2013-06-28T12:14:42.660" Title="fibroblast cells and fibers" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;physiology&gt;&lt;cell-culture&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8995" PostTypeId="1" AcceptedAnswerId="16999" CreationDate="2013-06-27T21:10:40.480" Score="19" ViewCount="837" Body="&lt;p&gt;I know that some birds and marine animals can continue complicated activity (swimming, flying?) while one hemisphere of their brain is asleep.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested if human brain has some parts of it that can be asleep while others are awake? In other words, &lt;strong&gt;can a human brain be only partially asleep while experiencing insomnia or similar sleep disturbances?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If human brain can have different parts &quot;sleeping&quot; independently of each other, &lt;strong&gt;is it possible that the times to &quot;fall asleep&quot; vary between these different parts of the brain?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would appreciate research articles on the topic or just the names of brain regions that may exhibit behavior described above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt;: I've taken a look at R&amp;amp;K &quot;principles and practice of sleep medicine&quot;' and it mentions the following parts as involved in sleep:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Medulla, preoptic area, hypothalamus, thalamus, entire neocortex involved in NREM.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neurotransmitter systems: histaminergic, orexinergic, serotonergic, noradrinergic&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sleep factors: adenosine, interleukin-1 and other cytokines, prostaglandin D2, growth hormone releasing hormone, nitric oxide, all promote sleep in or around preoptic area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This makes me hypothesize that drugs that modify the effects of these systems (ex- caffeine affecting adenosine) could result in sleep- related disturbances in these systems, potentially causing them to fall asleep later that usual. But I'm looking for more info to fihre out if this is true&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="577" LastEditDate="2013-06-30T23:58:29.153" LastActivityDate="2016-06-29T20:11:38.200" Title="Can parts of a human brain be asleep independently of each other, or vary in the times required for them to fall asleep?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;endocrinology&gt;&lt;brain&gt;&lt;sleep&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="8996" PostTypeId="1" CreationDate="2013-06-27T21:17:01.467" Score="12" ViewCount="339" Body="&lt;p&gt;We all know that DNA acts as a genetic molecule. Does DNA have any other function in the cell other than being a genetic material and carrier of information?&lt;/p&gt;&#xA;" OwnerUserId="3893" LastEditorUserId="3059" LastEditDate="2013-06-27T21:21:04.403" LastActivityDate="2016-05-06T12:36:13.060" Title="Is there any other function of DNA?" Tags="&lt;genetics&gt;&lt;dna&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8997" PostTypeId="1" CreationDate="2013-06-27T23:23:08.153" Score="6" ViewCount="6806" Body="&lt;p&gt;Do animals suffer from tooth decay, such as cavities? Is it to the same extent as in humans, or do animal teeth decay more or less? If teeth decay in animals as well, are there natural strategies animals use to heal it? And, lastly, how do animals take care of their teeth?&lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2018-06-29T05:03:16.607" Title="What is dental health like in animals?" Tags="&lt;zoology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="8998" PostTypeId="2" ParentId="8996" CreationDate="2013-06-27T23:39:34.227" Score="10" Body="&lt;p&gt;In &lt;a href=&quot;http://en.wikipedia.org/wiki/Eukaryote&quot;&gt;eukaryotes&lt;/a&gt; DNA has a structural as well coding function. Parts of chromosomes called &lt;a href=&quot;http://en.wikipedia.org/wiki/Centromere&quot;&gt;centromeres&lt;/a&gt; bind to proteins and form a scaffold which helps chromosomes attach to each other and correctly segregate during division. Technically this is still related to the transmission of genetic information though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since RNA can act as an enzyme (the so-called &lt;a href=&quot;http://en.wikipedia.org/wiki/Ribozyme&quot;&gt;ribozymes&lt;/a&gt;), scientists have hypothesized that DNA can also have an enzymatic function, but no such function has been found in nature. Artificial DNA enzymes (deoxiribozymes) have been designed to cleave DNA, covalently modify proteins, ligate RNA molecules, and even catalyze reactions between small molecules. &lt;a href=&quot;http://www.scs.illinois.edu/silverman/research/index.html&quot;&gt;See this lab's website.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3053" LastActivityDate="2013-06-27T23:39:34.227" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9000" PostTypeId="1" AcceptedAnswerId="24692" CreationDate="2013-06-28T01:00:30.570" Score="3" ViewCount="800" Body="&lt;p&gt;My cat was licking my arm with his sandpaper like tongue. It hurt and the area he was licking was slightly smarting afterwards. However, when he licks the palm of my hand the feeling is rather ticklish and results in no pain during or after. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can pick up sharp, prickly, abrasive objects with our hands (palms/fingers) and even rub against them and have little to no damage incurred. However, if we do the same with say the back of our hand we are more likely to be injured.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought maybe the skin is thicker in our palms and that is resulting in our palms being more resilient. But, our palms are so sensitive to touch that it makes me think the skin is thinner to allow the nerves closer access to our environment.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why is there such a stark difference in different areas of skin on our body when it comes to feeling pain and being susceptible to injury from scrapes, bruises, cuts, etc?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1827" LastActivityDate="2014-12-08T15:05:27.190" Title="Why Is The Toughness Of Skin Different On Different Parts Of The Body?" Tags="&lt;organs&gt;&lt;skin&gt;&lt;pain&gt;&lt;injury&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9001" PostTypeId="1" CreationDate="2013-06-28T02:28:45.333" Score="3" ViewCount="164" Body="&lt;p&gt;As I know, $Cu(OH)_2$ $+$ Protein $\rightarrow$ Purple. So why not use $Cu(OH)_2$ as dye in protein electrophoresis?&lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="107" LastEditDate="2013-06-28T02:36:37.223" LastActivityDate="2013-12-08T23:58:17.313" Title="Why not use Cu(OH)2 as a dye for protein electrophoresis?" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9003" PostTypeId="1" CreationDate="2013-06-28T08:25:33.037" Score="0" ViewCount="774" Body="&lt;p&gt;I want to know how to make plastic containers free of DNA &amp;amp; RNA? this is just for knowledge&lt;/p&gt;&#xA;" OwnerUserId="3895" LastEditorUserId="1590" LastEditDate="2013-06-28T09:28:53.603" LastActivityDate="2013-06-28T09:28:53.603" Title="How do you remove DNA/RNA from plastics?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9004" PostTypeId="2" ParentId="8701" CreationDate="2013-06-28T08:27:35.127" Score="1" Body="&lt;p&gt;I will try to provide a general answer, starting point and overview to this question, even though it is rather wide ranging and vague.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;The biological process&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;If we start with your description of the process; you are correct that such a dramatic change in the environment as slash-and-burn agriculture will drastically change the living environments on the canopy floor (well, in the entire ecosystem).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To name a few, there will be changes in:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Light conditions&lt;/strong&gt;, which will alter the competitive balance between plant species, where ones adapted to a closed canopy will disappear.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Moisture&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Temperature&lt;/strong&gt; (maximum, minimum and variance in temperature) &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Nutrients&lt;/strong&gt; The point of slash-and-burn agriculture is to provide a boost of nutrients for farming. However, the boost is short-lived and transient. Afterwards, you are usually left with a very nutrient poor soil, which is common in tropical forests. Tropical forests (where slash-and-burn is often used) are high in biomass, but most if it is &lt;a href=&quot;http://www.globalchange.umich.edu/globalchange1/current/lectures/kling/rainforest/rainforest.html&quot; rel=&quot;nofollow&quot; title=&quot;The Tropical Rain Forest&quot;&gt;bound in the standing biomass&lt;/a&gt;. When this is removed by clear-cutting, the natural cycling of nutrients is disrupted, and excess nutrients are leached out of the soil (&lt;a href=&quot;http://bcs.whfreeman.com/ricklefs6e/default.asp?s=&amp;amp;n=&amp;amp;i=&amp;amp;v=&amp;amp;o=&amp;amp;ns=0&amp;amp;uid=0&amp;amp;rau=0&quot; rel=&quot;nofollow&quot; title=&quot;Ricklefs. 2001. The economy of nature. W.H. Freeman and company. New York&quot;&gt;Ricklefs, 2001&lt;/a&gt;). &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Loss of host species&lt;/strong&gt; This will lead to loss of primary consumers (specialists &amp;amp; generalists) feeding on them, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Cascade_effect_%28ecology%29&quot; rel=&quot;nofollow&quot;&gt;cascading effects&lt;/a&gt; into the ecosystem that depends on these.  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;All these changes and several others will dramatically modify the niche spaces and the competition between species in the forest patch, and most previous species will probably not be able to persist locally. New species will move in to fill the open niches, and over a (long) period of &lt;a href=&quot;https://en.wikipedia.org/wiki/Ecological_succession&quot; rel=&quot;nofollow&quot;&gt;succession&lt;/a&gt; a new quasi-stable community will emerge. Due to the extremely high biodiversity in tropical forests it will almost certainly contain fewer species than the original community.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question of whether the community will eventually return to its previous state (even if that will take an extremely long time), is a relatively open question, and also depends on the conditions at the specific site and if the spatial scale of the disturbance. The biggest issue for conservation biology is that these land-use changes generally happen at a large scale, so &lt;a href=&quot;http://en.wikipedia.org/wiki/Habitat_fragmentation&quot; rel=&quot;nofollow&quot;&gt;fragmentation of species habitats&lt;/a&gt; can lead to regional and even global extinction. Since many tropical species have small ranges and are not adapted to fragmented landscapes, many run the risk of going extinct. Therefore, even if the overall appearance of the original forest will return, it will contain a very different set of species. Land-use changes, even in the form of temporary slash-and-burn agriculture, also generally leads to continued/secondary exploitation of the area and seldom to restoration/regrowth (&lt;a href=&quot;http://books.google.no/books/about/Principles_of_Conservation_Biology.html?id=MUljQgAACAAJ&amp;amp;redir_esc=y&quot; rel=&quot;nofollow&quot; title=&quot;Meffe &amp;amp; Carroll (ed). 1997. Principles of conservation biology. Sinauer. Sunderland USA&quot;&gt;Meffe &amp;amp; Carroll, 1997&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also want to point out that you are indirectly referring (&quot;...new equilibrium be reached...&quot;) to the idea of a &lt;a href=&quot;https://en.wikipedia.org/wiki/Balance_of_nature&quot; rel=&quot;nofollow&quot;&gt;Balance of nature&lt;/a&gt; in ecosystems, which is largely seen as obsolete and incorrect. However, as shorthand or when referring to a dynamical equilibrium between multiple populations (with ongoing evolutionary change) it can be meaningful.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;The philosophical issue&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The question of whether an ecosystem change or extinction of species is &quot;&lt;em&gt;...a bad thing&lt;/em&gt;&quot; is inherently philosophical and depends on human judgement. The philosophical foundations for conservation biology can be divided into instrumental values and intrinsic/inherent values. &lt;strong&gt;Instrumental values&lt;/strong&gt; can then be subcategorized as &lt;em&gt;services&lt;/em&gt; (pollination, water regulation), &lt;em&gt;goods/resources&lt;/em&gt;, &lt;em&gt;information&lt;/em&gt; (e.g. genetical info to be used in medical research), and &lt;em&gt;esthetic/spiritual values&lt;/em&gt;. &lt;strong&gt;Intrinsic values&lt;/strong&gt; refers to a specific value placed on species, ecosystems or evolutionary history due to its uniqueness and it is seen as independent of human needs and wants (although some argue that values independent of humans are impossible). &lt;a href=&quot;http://en.wikipedia.org/wiki/Intrinsic_value_%28animal_ethics%29&quot; rel=&quot;nofollow&quot;&gt;Intrinsic values&lt;/a&gt; are also connected to the acknowledgement that organisms have interests and wants themselves (their own 'good'). Different people naturally weight these issues in different ways, and for some the short-term economical gains will weigh heavier. The long-term economic costs are potentially large, but less certain. From a strict biodiversity perspective (i.e. a species counting perspective), the change will certainly be negative, since the change in land-use will decrease diversity and probably lead to more 'trivial' species moving in. From the perspective of the original ecosystem (if it has a say) the change is per definition negative, since it will disappear. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The direct intrumental value of individual species are usually uncertain (irrespectivly of the direct rationales used), so the precautionary principle is often invoked to justify species conservation. Also, numerous examples exist of how aspects of biodiversity are related to human values (some recent examples are &lt;a href=&quot;http://www.sciencemag.org/content/339/6127/1608.abstract&quot; rel=&quot;nofollow&quot; title=&quot;Garibaldi et al. 2013. Wild Pollinators Enhance Fruit Set of Crops Regardless of Honey Bee Abundance. Science 139(6): 1608-1611.&quot;&gt;Garibaldi et al. 2013&lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/ncomms/journal/v4/n1/full/ncomms2328.html&quot; rel=&quot;nofollow&quot; title=&quot;Gamfeldt et al. 2013. Higher levels of multiple ecosystem services are found in forests with more tree species. Nature communications 4(1340).&quot;&gt;Gamfeldt et al. 2013&lt;/a&gt;), such as production or services, which can also be used to justify both conserving biodiversity or individual species. An example of ecosystem services from tropical environements can be seen in &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1523-1739.2004.00227.x/abstract&quot; rel=&quot;nofollow&quot; title=&quot;Ricketts. 2004. Tropical Forest Fragments Enhance Pollinator Activity in Nearby Coffee Crops. Conservation biology 18(5): 1262–1271&quot;&gt;Ricketts (2004)&lt;/a&gt;. However, sometimes functional diversity is emphasized which focus on preserving functional groups of species instead of 'general' biodiversity (i.e. specific species). &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3952" LastEditDate="2013-08-25T23:54:06.983" LastActivityDate="2013-08-25T23:54:06.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9005" PostTypeId="2" ParentId="9003" CreationDate="2013-06-28T09:10:40.213" Score="1" Body="&lt;p&gt;Lab cleaning solutions can be bought which remove/destroy nucleic acids such as &lt;a href=&quot;http://www.mobio.com/lab-accessories/ultraclean-lab-cleaner.html&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt;. UV is another &lt;a href=&quot;http://discoveryscientific.com/products-by-area/thermal-cycling/UV-sterilization-cabinets-DNA-PCR-decontamination-workstations-amplification&quot; rel=&quot;nofollow&quot;&gt;technique for destroying DNA&lt;/a&gt;. And bleach is used to remove contaminant DNA in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16182949&quot; rel=&quot;nofollow&quot;&gt;ancient DNA studies&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Searching for a DNA/RNA lab cleaning protocol would be a good idea to - &lt;a href=&quot;http://www.bowserlab.org/benthic_ecology/molececol/godliness.htm&quot; rel=&quot;nofollow&quot;&gt;something like this&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-06-28T09:26:34.873" LastActivityDate="2013-06-28T09:26:34.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9006" PostTypeId="2" ParentId="8994" CreationDate="2013-06-28T09:37:26.803" Score="2" Body="&lt;p&gt;Regarding dimensions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8B38B.jpg&quot; alt=&quot;Cultured fibroblasts&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As per this image the length and breadth seems to be ~30-50 μm (area should be roughly around 900 μm²). The third dimension (thickness) as per &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9737542&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; article can be assumed to be around 3-7 μm. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding cell attachment:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cells attach to extracellular matrix via integrins, which attach to ECM proteins like collagen and fibronectin. The matrix is a net of fibres and the cell is not specifically attached to a single fibre but rather &quot;sits&quot;(as you said) on the matrix [see the below image]. A single cell also simultaneously interacts with two different types of ECM proteins such as fibronectin and collagen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7sirE.jpg&quot; alt=&quot;ECM&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During migration they move along the matrix using lammelipodia (actin filament polymerization in the direction of motion).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fibroblast express ICAM1/VCAM1 (Inter/Vascular Cell Adhesion Molecules) under &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16303942&quot; rel=&quot;nofollow noreferrer&quot;&gt;certain conditions such as inflammation&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10464130&quot; rel=&quot;nofollow noreferrer&quot;&gt;bind to T-cells&lt;/a&gt; and endothelial cells. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-06-28T12:14:42.660" LastActivityDate="2013-06-28T12:14:42.660" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9007" PostTypeId="1" AcceptedAnswerId="9028" CreationDate="2013-06-28T10:03:09.113" Score="3" ViewCount="2570" Body="&lt;p&gt;I know it's a type of capillary electrophoresis, but I don't get how does the separation happen exactly. &lt;/p&gt;&#xA;" OwnerUserId="3864" LastActivityDate="2013-06-29T21:36:35.897" Title="What is the exact principle of capillary isotachophoresis?" Tags="&lt;molecular-biology&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9008" PostTypeId="1" AcceptedAnswerId="9009" CreationDate="2013-06-28T10:48:52.190" Score="2" ViewCount="115" Body="&lt;p&gt;I have just been reading &lt;a href=&quot;https://biology.stackexchange.com/questions/108/how-do-cockroaches-resist-the-effects-of-ionizing-radiation&quot;&gt;this excellent question and answer about cockroaches ability to withstand ionizing radiation&lt;/a&gt;.  My question is an extension of that question: aside from insects, which other animals (if any) have an increased defence against ionizing radiation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there species of plants, fungi, and bacteria also &quot;immune&quot;?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2013-06-29T04:50:18.890" Title="Aside from cockroaches and other insects, which species (of all kinds) are 'immune' to ionizing radiation?" Tags="&lt;zoology&gt;&lt;botany&gt;&lt;bacteriology&gt;&lt;mycology&gt;&lt;radiation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9009" PostTypeId="2" ParentId="9008" CreationDate="2013-06-28T17:22:27.713" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://hopedance.org/other-news/1971-myco-remediation-of-the-japanese-landscape-after-radioactive-fallout-&quot; rel=&quot;nofollow&quot;&gt;According to Paul Stamets&lt;/a&gt;, &lt;em&gt;Gomphidius glutinosus&lt;/em&gt; is especially well suited to collecting Cesium-137:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;G. glutinosus&lt;/em&gt; has been reported to absorb – via the mycelium – and&#xA;  concentrate radioactive Cesium 137 more than 10,000-fold over ambient&#xA;  background levels.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That article and Stamets' book &lt;em&gt;Mycelium Running&lt;/em&gt; have more details on other species.&lt;/p&gt;&#xA;" OwnerUserId="3731" LastEditorUserId="107" LastEditDate="2013-06-29T04:50:18.890" LastActivityDate="2013-06-29T04:50:18.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9010" PostTypeId="2" ParentId="5597" CreationDate="2013-06-28T18:28:03.327" Score="-1" Body="&lt;p&gt;I think it is because of the reason that the left ventricle pumps blood throughout body, thus is bigger than the right ventricle. So, actually, the human heart is along the center septum, but seems just a bit to the right. 1.5 cm to be precise.&lt;/p&gt;&#xA;" OwnerUserId="3897" LastEditorDisplayName="user3795" LastEditDate="2013-06-28T19:39:20.920" LastActivityDate="2013-06-28T19:39:20.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9011" PostTypeId="2" ParentId="5597" CreationDate="2013-06-28T19:08:27.480" Score="5" Body="&lt;p&gt;From a quick look at the paper @ChinmayKanchi links to (&lt;a href=&quot;https://www.sciencemag.org/content/306/5697/828.full&quot; rel=&quot;noreferrer&quot; title=&quot;Palmer. 2004. Symmetry Breaking and the Evolution of Development. Science 306&quot;&gt;Palmer, 2004&lt;/a&gt;) it seems that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;All living vertebrates possess a heart that is conspicuously asymmetrical and normally displaced toward the left (&lt;a href=&quot;http://dev.biologists.org/content/124/11/2099.abstract?ijkey=98ffa089b81e8ed19fd71a9f7d8a9521e2a20e18&amp;amp;keytype2=tf_ipsecsha&quot; rel=&quot;noreferrer&quot; title=&quot;Fishman &amp;amp; Chien. 1997. Fashioning the vertebrate heart: earliest embryonic decisions. Development 124: 2099-2117.&quot;&gt;Fishman &amp;amp; Chien, 1997&lt;/a&gt;). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So the heart orientation seems to be evolutionary conserved in vertebrates (as are many fundamental traits), and no specific explanation is needed for humans. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is said with the reservation that human anatomy is not my subject field, and the refered paper also digs deeper into the molecular basis for the orientation/symmetry of organisms. For instance, it also says that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Second, the molecular pathway directing hearts leftward—the nodal cascade—varies considerably among vertebrates (homology of form does not require homology of development) and was possibly co-opted from a preexisting asymmetrical chordate organ system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;so the molecular mechanisms governing this seems to differ between species. This &lt;em&gt;could&lt;/em&gt; indicate that there is a selective pressure molding species into the same heart orientation. This is pure speculation on my part though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also want to mention that evolutionary outcomes doesn't have to have a &quot;reason&quot; (i.e. a selective advantage). Much depends on chance events and evolution can only act on what is present at the moment (i.e. is restricted by earlier evolutionary history).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-06-29T12:21:57.783" LastActivityDate="2013-06-29T12:21:57.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9012" PostTypeId="1" CreationDate="2013-06-28T19:59:28.747" Score="0" ViewCount="887" Body="&lt;p&gt;Can I have a list of suggestions, such as the mutated allele, other allele, etc. ? Are there any blatantly missing ones on my short list?&lt;/p&gt;&#xA;" OwnerUserId="3829" LastEditorUserId="3059" LastEditDate="2013-06-28T20:08:02.217" LastActivityDate="2013-07-10T15:19:17.327" Title="What do you call the non-Wild Type allele?" Tags="&lt;genetics&gt;&lt;terminology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9013" PostTypeId="2" ParentId="9012" CreationDate="2013-06-28T20:22:43.237" Score="3" Body="&lt;p&gt;Usually its &lt;em&gt;major allele and minor allele&lt;/em&gt;.  When you hear this language, you feel that the major allele is the 'wild' type, but its more precise to avoid 'wild'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This language avoids the question of which one is 'wild' since different populations may have different ratios of the two. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-06-28T20:22:43.237" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9014" PostTypeId="1" CreationDate="2013-06-28T20:45:56.757" Score="1" ViewCount="440" Body="&lt;p&gt;Is it possible to ligate a small DNA molecule to mRNA?  I was reading a protocol from Current Protocols in Molecular Biology and one of the procedures involve ligating a DNA molecule to mRNA using a DNA splint that overlaps between the 5' of the DNA molecule and the 3' of the mRNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would a reaction like the following work?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5'-phosphorylated DNA linker&#xA;mRNA library&#xA;DNA splint&#xA;T4 DNA ligase + buffer&lt;/p&gt;&#xA;" OwnerUserId="3247" LastActivityDate="2013-06-28T20:45:56.757" Title="How to ligate DNA to an RNA molecule" Tags="&lt;ligation&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9015" PostTypeId="1" AcceptedAnswerId="9391" CreationDate="2013-06-28T22:46:18.047" Score="7" ViewCount="109659" Body="&lt;p&gt;In Skeptics.SE, a question regarding the skulls of children arose. Depicting a scary skull where the permenent teeth are &quot;hidden&quot; inside the jaws and the milk teeth are in the their place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After all milk teeth fall out, and the permanent teeth &quot;rise&quot;, do the holes left by them filled up, or do we go around with holes in our jaws?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://skeptics.stackexchange.com/questions/9541/is-this-scary-looking-image-about-child-teeth-development-accurate&quot;&gt;The question on Skeptics&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The picture:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/35njF.jpg&quot; alt=&quot;picture&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="680" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2020-03-17T10:09:30.313" Title="What happens to the holes in the skull where teeth were developing?" Tags="&lt;human-biology&gt;&lt;teeth&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9016" PostTypeId="1" CreationDate="2013-06-29T04:35:00.013" Score="4" ViewCount="795" Body="&lt;p&gt;What is exactly coiling of chromosomes?&#xA;I just heard about the names i.e paranemic, plectonemic, orthostichious, anorthospiral.&#xA;I have ecaxtly no idea of what phenomenon is this.&#xA;Also what type of coiling occurs during meiosis and mytosis type of cell division.&#xA;Could it be explained in detail....?&lt;/p&gt;&#xA;" OwnerDisplayName="user3800" LastEditorDisplayName="user3800" LastEditDate="2013-07-08T04:51:01.577" LastActivityDate="2013-07-08T04:51:01.577" Title="Coiling of chromatids during cell division" Tags="&lt;cell-biology&gt;&lt;chromosome&gt;&lt;meiosis&gt;&lt;mitosis&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="0" ClosedDate="2015-03-30T20:44:26.447" ContentLicense="CC BY-SA 3.0" />
  <row Id="9017" PostTypeId="1" AcceptedAnswerId="9041" CreationDate="2013-06-29T05:05:45.993" Score="2" ViewCount="242" Body="&lt;p&gt;The Australian platypus, is a marsupial with a unique feature - in that the males of the species have venom sacs around their hind-claws. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding is that this venom is not lethal to humans, however, how potent is this venom to other animals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, how does the platypus 'manufacture' this venom?  &lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="1590" LastEditDate="2013-07-30T09:27:07.973" LastActivityDate="2013-07-30T09:27:07.973" Title="How potent is the venom from the Australian platypus?" Tags="&lt;toxicology&gt;&lt;marsupials&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9018" PostTypeId="1" AcceptedAnswerId="9023" CreationDate="2013-06-29T09:54:33.807" Score="0" ViewCount="190" Body="&lt;p&gt;I know that DNA molecules or proteins can be separated in electrophoresis because the electrical charge is used to pull the DNA through the gel. So instead of using electrical, can I using physical impact like pumping ?&lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="3624" LastEditDate="2013-07-01T18:07:58.280" LastActivityDate="2013-07-01T18:07:58.280" Title="Pump to separate protein/DNA instead of electrophoresis?" Tags="&lt;molecular-biology&gt;&lt;gel-electrophoresis&gt;&lt;diy-biology&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9019" PostTypeId="2" ParentId="9018" CreationDate="2013-06-29T11:37:45.317" Score="0" Body="&lt;p&gt;No, you can't use mechanical pumping for gel electrophoresis. The nature of electrophoresis is the create a uniform electric field through the gel, and this electric field stimulates motion from the charged DNA/protein.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-06-29T11:37:45.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9020" PostTypeId="2" ParentId="5597" CreationDate="2013-06-29T16:47:27.807" Score="0" Body="&lt;p&gt;I think this deals with the steps of Heart development during organogenesis, together with the influence of external factors (such as the lung development and the hemodynamics), which by nature would lead heart to occupy the optimal positions for it and for those interrelated organs. Basically, the organs tend to develop on the midline, or symmetrically to the midline, but due to cardiac tube contortion during the development, it changes the position.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can check the details on wiki (&lt;a href=&quot;https://en.wikipedia.org/wiki/Heart_development&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Heart_development&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerDisplayName="user3854" LastEditorUserId="3059" LastEditDate="2013-06-29T17:40:26.807" LastActivityDate="2013-06-29T17:40:26.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9022" PostTypeId="2" ParentId="1343" CreationDate="2013-06-29T17:06:58.317" Score="-2" Body="&lt;p&gt;According to me animals use these teeth to chew meat particles etc. So because they don't brush these food particles get exposed to bacterial agents which in turn causes corrosion of teeth. As we see the structure of the animal teeth the food particles are trapped in between resulting into high bacterial corrosive activity. But in humans, regular maintenance and high use of water it decreases the acidity caused by the food in our mouth this prevents excessive corrosion and bacterial activity and growth. On the other hand canines have an initial use of tearing so the usually are not much affected by the food particles and also because of their protruding shape.&#xA;The exposure of air and light increase the bacterial activity.&lt;/p&gt;&#xA;" OwnerUserId="3900" LastEditorUserId="107" LastEditDate="2013-06-30T03:02:34.640" LastActivityDate="2013-06-30T03:02:34.640" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9023" PostTypeId="2" ParentId="9018" CreationDate="2013-06-29T17:57:14.720" Score="3" Body="&lt;p&gt;If you tried to set up a system in which movement of DNA molecules through a gel matrix was driven by pumping buffer, the gel would become compressed. I am old enough to remember running vertical agarose gel electrophoresis overnight, and these gels would collapse under normal pressure to about 2/3rds of their initial height. A gel porous enough to give useful separation of DNA molecules just isn't strong enough to withstand pumping.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-06-29T17:57:14.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9024" PostTypeId="1" AcceptedAnswerId="9029" CreationDate="2013-06-29T20:26:09.120" Score="6" ViewCount="2127" Body="&lt;p&gt;Suppose I'm using 200 nmoles of enzyme and 2 mmoles of substrate. The enzyme should be saturated but if I use 50 mmoles of substrate, the reaction will be faster. Why?&#xA;I just can't get it! Even at lower concentration of substrate the enzyme is saturated (all enzyme molecules are engaged in the reaction) but still the reaction rate is lower.&lt;/p&gt;&#xA;" OwnerUserId="3901" LastEditorUserId="1320" LastEditDate="2013-06-30T18:56:57.987" LastActivityDate="2013-06-30T18:56:57.987" Title="Why are enzyme-catalysed reactions slower at lower substrate concentration?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;&lt;kinetics&gt;&lt;enzyme-kinetics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9025" PostTypeId="2" ParentId="9024" CreationDate="2013-06-29T20:50:08.823" Score="3" Body="&lt;p&gt;In terms of Michaelis-Menten kinetics, the rate never reaches the maximum rate:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$v = V_{max} \times \frac{S}{K_m + S}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $S$ is substrate concentration. Notice that however large $S$ is, the term on the bottom line ($K_m + S$) will be larger than $S$, so $v$ will be less than $V_{max}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can think about this in terms of the binding equilibrium between the enzyme and the substrate:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$E + S \leftrightarrow ES$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since it is an equilibrium, it can never lie completely over to the right hand side.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is why $V_{max}$ is always determined by extrapolation. In practice of course, at very high substrate:enzyme concentrations your measurements would have to be very accurate to see the difference: if $S$ is $100 \times K_m$ you are looking at a 1% difference. In your hypothetical example you don't mention what the value of $K_m$ is. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="107" LastEditDate="2013-06-30T00:51:55.060" LastActivityDate="2013-06-30T00:51:55.060" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9026" PostTypeId="1" AcceptedAnswerId="9034" CreationDate="2013-06-29T21:00:35.197" Score="4" ViewCount="51542" Body="&lt;p&gt;My textbook doesn't do a very good job of pointing out what the differences between the two are. It basically mentions axons only in the same breath as the synapse (that synapses are the endings/tips of axons). &lt;/p&gt;&#xA;" OwnerUserId="3903" LastEditorUserId="9943" LastEditDate="2015-07-14T14:05:57.487" LastActivityDate="2015-07-15T02:42:40.223" Title="What are the functions and differences between axons and dendrites?" Tags="&lt;neuroscience&gt;&lt;terminology&gt;&lt;neurophysiology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9027" PostTypeId="1" AcceptedAnswerId="9030" CreationDate="2013-06-29T21:27:42.790" Score="2" ViewCount="2242" Body="&lt;p&gt;Assume that we have a semi-permeable membrane with water on both sides. First, straightforward, case: On the right side, we have a concentration of the substance A, and on the left side, we have pure water. Obvious effect: water flows from left to right. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, imagine we have a second case. We have the same membrane, and a water solution of A to the right. To the left, we have a water solution of a different substance, let's call it B. Now, what happens? I can imagine a few possibilities: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the system behaves exactly as in the first case, because the substances have no influence on each other &lt;/li&gt;&#xA;&lt;li&gt;the system behaves as if it was a solution of A on both sides, with water flowing in the direction of higher concentration (because it only matters if there is something dispersed between the water molecules, but it does not matter what) &lt;/li&gt;&#xA;&lt;li&gt;some interesting cross-influence effect happens &lt;/li&gt;&#xA;&lt;li&gt;either one of the three things above can happen, depending on the particular combination of substances A and B&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Which one is the true effect? What happens, and why? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you need an example of the actual substances, let B be thiamine and A be plain sodium chloride, but I am interested in the general case. &lt;/p&gt;&#xA;" OwnerUserId="1578" LastActivityDate="2013-07-31T04:11:50.857" Title="Does osmosis occur when we have two different substances?" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9028" PostTypeId="2" ParentId="9007" CreationDate="2013-06-29T21:36:35.897" Score="2" Body="&lt;p&gt;Many of us are using isotachophoresis all the time without even realising it. The explanation that follows may not be exact, but I hope that it helps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, think about a simple electrophoresis set-up - in agarose electrophoresis of DNA we have a uniformly distributed buffer such as Tris-borate. The current is carried by the borate ions and the DNA molecules run through the &lt;strong&gt;homogeneous&lt;/strong&gt; electric field towards the anode. They separate by size because of the sieving effect of the agarose matrix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now let's think about what is happening in an SDS-PAGE separation (a Laemmli gel). Just to remind you:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The running (or reservoir)  buffer is Tris-glycine pH 8.3&lt;br&gt;&#xA;The stacking gel is in Tris.HCl pH 6.8&lt;br&gt;&#xA;The separating gel is in Tris.HCl pH 8.8&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the power supply is turned on, the glycinate ion in the top reservoir begins to move into the stacking gel. When it hits the zone of pH = 6.8 it is much closer to its pK&lt;sub&gt;a&lt;/sub&gt; and so is now only weakly charged. Consequently it slows down. Meanwhile the chloride ions in the stacking gel have begun to move rapidly down through the stacking gel (towards the anode). This creates a &lt;strong&gt;discontinuous&lt;/strong&gt; electric field: the chloride zone has a lower resistance than the glycinate zone so the field strength in the chloride zone is weaker than the field strength in the glycinate zone. This is a stable situation because the ions cannot stray into each other's zones: if a glycinate ion happens to diffuse forwards into the chloride zone it will experience a weaker field and slow down, whereas if a chloride ion diffuses back into the glycinate zone it will hit the stronger field and quickly move ahead again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about the SDS-protein complexes that were in the well? (I'll just refer to these as proteins from now on.) Their ionic properties lie between the glycinate and the chloride, and so they eventually end up moving through the stacking gel between the trailing zone of glycinate and the leading zone of chloride. Any protein that finds itself in the glycinate zone will move quickly forward (due to the higher field strength) and any protein that moves ahead by chance into the chloride zone will slow down due to the weak field strength, falling back into the protein zone. And in this way these zones move in a procession through the stacking gel, with the proteins being focussed into a very narrow region in the middle. The glycinate, the proteins and the chloride are all moving at the same speed, and so this is an example of isotachophoresis (isotacho- = &quot;same speed&quot;). The polyacrylamide gel matrix in the stacking gel has no separating function - its role is simply to stabilise against convective effects. The proteins can reach very high local concentrations in the stacking gel, and if you look carefully you will often see refractive effects as your sample runs through the stacking gel. In this way the protein sample is &quot;applied&quot; to the separating gel in a very tight band, perfect for achieving high resolution separation (bands broaden by diffusion in the separating gel so the tighter the bands ar eat the point of loading, the better the final result.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once the sample hits the separating gel, all of this breaks down: the pH is now 8.8 so the glycinate becomes strongly charged and zooms off ahead with the chloride through the gel, leaving the proteins to move more slowly due to the sieving effect of the polyacrylamide matrix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible to set up an isotachophoresis as described above in isolation. Individual proteins will have slightly different ionic properties and will line up in the region between the two buffer ions, allowing for their separation. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-06-29T21:36:35.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9029" PostTypeId="2" ParentId="9024" CreationDate="2013-06-29T22:05:34.807" Score="4" Body="&lt;p&gt;Alan Boyd's &lt;a href=&quot;https://biology.stackexchange.com/a/9025/948&quot;&gt;answer&lt;/a&gt; covers the mechanistic aspects quite well, but there is another aspect he didn't quite touch on - what's going on at the molecular level. To understand this, you need to think about the actual conditions of the reaction: unless it's taking place inside a cell, which straight biochemical reactions of the kind you're talking about almost never are, then the enzyme, substrate, and product are all floating around at a certain concentration. The enzymatic reaction is proceeding nicely, and as the substrate binding pocket is freed as product dissociates from the enzyme and diffuses away, allowing another substrate molecule to take its place and the next reaction to occur. This is the situation at your 2 mmol [substrate] level. At 50 mmol, the concentration of substrate is much higher, and so even though the actual catalytic portion of the enzymatic reaction is taking place at essentially the same speed, the rate of substrate diffusing into the active pocket is somewhat higher because the local concentration of substrate is higher, allowing for an apparently slightly faster reaction rate.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-06-30T00:14:14.103" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9030" PostTypeId="2" ParentId="9027" CreationDate="2013-06-29T22:06:55.073" Score="3" Body="&lt;p&gt;If A and B are at the same concentration there will be no net movement of water. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Everything is down to diffusion. In your example of solution A/pure water, water molecules on both sides of the membrane are diffusing through the membrane to the other compartment. However the &quot;concentration&quot; of water is less in solution A, so the rate of movement is less from solution A to water than it is from water to solution A. Water will continue to move into the solution until another force, such as hydrostatic pressure, counteracts the &quot;osmotic pressure&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If solution A and solution B have solute at the same concentration then the rate of movement of water will be the same in both directions, so no net movement will occur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(In a typical experimental set up using dialysis membrane none of this would apply with the solutes that you mention since they would also be able to move through the pores and you would end up with perfect mixing. You would have to use macromolecular solutes.)&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-06-30T16:37:09.807" LastActivityDate="2013-06-30T16:37:09.807" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9032" PostTypeId="1" AcceptedAnswerId="9043" CreationDate="2013-06-29T22:49:04.443" Score="2" ViewCount="190" Body="&lt;p&gt;I've always thought that the majority of the &quot;work&quot; in a cell is protein production, until I read the following.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Wikipedia article on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology&quot; rel=&quot;nofollow&quot;&gt;central dogma of molecular biology&lt;/a&gt; states this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;80% of the human genome is transcribed even though only 1% codes for&#xA;  proteins.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Current research focuses on investigating the function of non-coding&#xA;  RNA, that is, RNA that does not follow the dogma trend and does not&#xA;  code for polypeptides.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If 99% of what's transcribed isn't used for creating proteins, what is it used for?  If it's not known - are there any hypotheses?  &lt;/p&gt;&#xA;" OwnerUserId="3906" LastActivityDate="2013-08-08T00:21:25.097" Title="What do cells do when they aren't creating proteins?" Tags="&lt;cell-biology&gt;&lt;proteins&gt;&lt;rrna&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9033" PostTypeId="2" ParentId="1515" CreationDate="2013-06-29T22:54:45.853" Score="-4" Body="&lt;p&gt;It's my opinion the rh antigen developed from toxoplasmosis infection. I only recently learned that this protozoan can actually insert its genes into a host's genome. Once it's in the genes, it can be passed in the germline. Toxoplasmosis can infect all primates, human and otherwise. Monkeys get it, and so do humans living in toxoplasmosis endemic places. The life cycle of toxoplasmosis is connected with mice and cats as an evolved survival strategy for the toxoplasmosis protozoan. There never were cats in northwest Europe, and that would explain why the people with ancestry from that area were never exposed to toxoplasmosis. I look for the rational biological explaination. One great clue to my thinking is I found a term used in some research writings, the text read &quot;RH strain of toxoplasmosis&quot;. Yes they seemed to be doing experiments with the toxoplasmosis found in rhesus monkey.&lt;/p&gt;&#xA;" OwnerUserId="3907" LastEditorUserId="107" LastEditDate="2013-06-29T23:25:51.780" LastActivityDate="2013-06-29T23:25:51.780" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9034" PostTypeId="2" ParentId="9026" CreationDate="2013-06-30T00:12:34.063" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.gwinnett.k12.ga.us/LilburnES/PromoteGA/biochemistry/Neuron_a_and_d.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;This reference&lt;/a&gt; is a bit basic, but lists the functions and differences between axons and dendrites.  Specifically, dendrites receive signals from other neurons, to the cell body; whereas, axons take signals away from the cell body (essentially 'input-output').  A diagram of the parts and the processes is below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pX1sj.jpg&quot; alt=&quot;Neuron&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(&lt;a href=&quot;http://www.appsychology.com/Book/Biological/neuroscience.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Image source with additional information)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=86EBfEz6CYA&quot; rel=&quot;nofollow noreferrer&quot;&gt;This Youtube tutorial&lt;/a&gt; is a nice visual description of both, and how they function within a neuron.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="9943" LastEditorDisplayName="user3795" LastEditDate="2015-07-15T02:42:40.223" LastActivityDate="2015-07-15T02:42:40.223" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9035" PostTypeId="1" CreationDate="2013-06-30T03:44:00.163" Score="5" ViewCount="187" Body="&lt;p&gt;I'm an information technology engineer. I love biology so I research biological topics and have an interest in PCR. That's why I have decided to create a PCR machine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Everything is done now and I want to do my first experiment to see if it works or not. I would be very happy if someone could give me any suggestions for testing it at home. Which oligo should I use for testing in the easiest way? I mean a template DNA for testing that is easy to find and extract. &lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="3624" LastEditDate="2013-06-30T17:13:26.663" LastActivityDate="2013-07-01T07:22:43.217" Title="Finding a template/oligo combination for my first PCR experiment" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;diy-biology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9036" PostTypeId="1" CreationDate="2013-06-30T03:58:24.783" Score="2" ViewCount="1435" Body="&lt;p&gt;i'm working as a diy bio. I'm finding a way to create a micro glass capillary for picking up single cells. I see this video on youtube and would like to know what is the minimum I/O diameter if I &lt;a href=&quot;http://www.youtube.com/watch?v=2yKHvKCatmM&quot; rel=&quot;nofollow&quot;&gt;pull a capillary like this&lt;/a&gt;.&#xA;Can it be 10-50 µm at least ?&lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="3624" LastEditDate="2013-06-30T17:13:07.117" LastActivityDate="2015-11-20T11:03:59.437" Title="How can I create a microcapillary for manipulation of single cells?" Tags="&lt;cell-biology&gt;&lt;diy-biology&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9037" PostTypeId="2" ParentId="9035" CreationDate="2013-06-30T11:26:28.587" Score="3" Body="&lt;p&gt;You need a genome that isn't too complex, which suggests something microbial. You also need a genome that is well-characterised : either fully- sequenced, or with lots of sequenced genes to allow you to design primers. And finally you need a readily accessible source of material for DNA extraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would suggest either dried yeast, as a source of &lt;em&gt;Saccharomyces cerevisiae&lt;/em&gt; DNA, or live yoghurt as a source of DNA from Lactobacilli. You could even try culturing something from yoghurt to get pure bacterial colonies: since these would be from a food source there should be minimal risk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might be tempted by one of the traditional plant sources of DNA (e.g. onions) , but it can be tricky to avoid copurifying polysaccharides which inhibit DNA-related enzymes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, if you do culture some bacteria, or even if you use dried yeast, you probably wouldn't need to actually prepare DNA at all. PCR direct from bacterial cells is widely used - the 95 C step will release sufficient DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;added later in response to comment by OP&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I chose to follow up on &lt;em&gt;Lactobacillus delbrueckii subsp. bulgaricus&lt;/em&gt; because I found this coming up over and over again with reference to yoghurt. If you were to test a range of yoghurts I think you could be fairly confident that this would be present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/?term=bulgaricus&quot; rel=&quot;nofollow&quot;&gt;There are 5 published genomes for different strains of the species &lt;em&gt;Lactobacillus delbrueckii&lt;/em&gt;&lt;/a&gt; including subspecies &lt;em&gt;bulgaricus&lt;/em&gt; (various strains) and &lt;em&gt;lactis&lt;/em&gt;. How different are they? I decided to look at one gene, and lactate dehydrogenase seemed like a logical choice (it produces the lactic acid).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The complete nucleotide sequence for the lactate dehydrogenase gene from &lt;em&gt;Lactobacillus delbrueckii subsp. bulgaricus&lt;/em&gt; ATCC 11842 is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/NC_008054.1?report=fasta&amp;amp;from=99766&amp;amp;to=100965&amp;amp;strand=true&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. If you run a BLAST from that page limiting the search to Lactobacilli (taxid 1578) you do indeed find hits to the gene from several other genomes. Here is a representative selection from the sequence alignment to the least similar of the hits:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Query  99766   CCTTCCACGCTTCTGGAGGTACTGAATTCGCCCTGGCTCAACTGGGCAACGATGCCGGTA  99825&#xA;               ||||||||||||||| ||||||||||||||||||||| ||||||||||||||||||||||&#xA;Sbjct  90616   CCTTCCACGCTTCTGAAGGTACTGAATTCGCCCTGGCCCAACTGGGCAACGATGCCGGTA  90675&#xA;&#xA;Query  99826   TGTACGGTGCCGTTAAGATGGTTCTGTAATTTTGAATGTAAAAAAGCACCAGGCTTTTAA  99885&#xA;               ||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||&#xA;Sbjct  90676   TGTACGGTGCCGTTAAGATGGTTCTGTAATTTTGAATATAAAAAAGCACCAGACTTTTAA  90735&#xA;&#xA;Query  99886   AGTCTGGTGCtttttttGTTTATCCTAAAGAGTCCAGGGTTGCCTTTATCGTCGCGGCTG  99945&#xA;               |||||||||||| |||||||||| |||||||||||||||||||||| |||||||||||||&#xA;Sbjct  90736   AGTCTGGTGCTTATTTTGTTTATTCTAAAGAGTCCAGGGTTGCCTTCATCGTCGCGGCTG  90795&#xA;&#xA;Query  99946   AGGCCCGCATCTTGGCCAATTCGCTGTCATTTAACGGCAATTCCAGTACGTGGCTGATCC  100005&#xA;               ||||| |||||||||||||||||||||||||||||||||||||||| ||||||||||| |&#xA;Sbjct  90796   AGGCCTGCATCTTGGCCAATTCGCTGTCATTTAACGGCAATTCCAGCACGTGGCTGATTC  90855&#xA;&#xA;Query  100006  CTTGTCCGTTGATGATGGCCAGGGTGCCCAGGTAGATCTCATCCTTGATCCCGTATTCCC  100065&#xA;               |||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||&#xA;Sbjct  90856   CTTGCCCGTTGATGATGGCCAGGGTGCCCAGATAGATCTCATCCTTGATCCCGTATTCCC  90915&#xA;&#xA;Query  100066  CGTGCAATGGTGCGGAAAGAGGCAGGGCCAGGTCGTTGTTTTCCAAAATGGCCGTCACGA  100125&#xA;               |||||||||| ||||||||||||||||||||||||||||||||||||||||||| |||||&#xA;Sbjct  90916   CGTGCAATGGCGCGGAAAGAGGCAGGGCCAGGTCGTTGTTTTCCAAAATGGCCGCCACGA  90975&#xA;&#xA;Query  100126  TCTTGGCCAGCATCATGGCCACGCCATAGTAGGTTGCGCCCTTTTTGACGATAATCTCGC  100185&#xA;               |||||||||||||||||||||||||||||||||| |||||||||||| |||| |||||||&#xA;Sbjct  90976   TCTTGGCCAGCATCATGGCCACGCCATAGTAGGTCGCGCCCTTTTTGCCGATGATCTCGC  91035&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;As you can see, there are some differences, but there should be no problem designing primers matching both (again - this is just one part of the gene). Obviously you might wish to make an alignment for all 5 sequences, but I got the impression that at least some of the others were identical to the query, even though they are from different subspecies. These are very closely-related organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of your experiment, I suggest that you plan to use a range of yoghurts and/or starters as the source of template. You could even mix them, if there are constraints on your set-up.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-07-01T07:22:43.217" LastActivityDate="2013-07-01T07:22:43.217" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9039" PostTypeId="2" ParentId="9036" CreationDate="2013-06-30T13:54:56.680" Score="4" Body="&lt;p&gt;It is very difficult to establish what kind of tip you will get from pulling a capillary on a Bunsen burner. &#xA;There are many variables to consider, including the glass you are using, the temperature you reach before pulling, the pulling strenght, speed and time, whether you pull once or make multiple pulls etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you do not want to invest into a micropipette puller (they are indeed VERY expensive) you could at least build some mechanism to obtain a constant pull in terms of time and force.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following paper may be of help:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://pbl.gatech.edu/publications/journal/forest_auto_pipette_puller.pdf&quot; rel=&quot;nofollow&quot;&gt;An Instrument for Controlled, Automated Production of Micrometer Scale Fused Silica Pipettes&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems you would need a fairly high speed (0.8-1 m/s) to get a tip size of &amp;lt;50um.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could not really find a specific reference for pulling over a Bunsen.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2013-06-30T13:54:56.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9040" PostTypeId="2" ParentId="9035" CreationDate="2013-06-30T14:07:25.160" Score="2" Body="&lt;p&gt;Nice project. How does your machine compare with this &lt;a href=&quot;http://openpcr.org/&quot; rel=&quot;nofollow&quot;&gt;open source thermocycler&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since you are probably ordering a couple of oligonucleotide DNA (primers), I would order a couple more DNA oligos that will work as your template.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;oligo 1, primer forward. 5'-AAAAAAAAAAA-3'-&amp;gt;&#xA;oligo 2, template        3'-TTTTTTTTTTTNNNNNNN[...]NNNNNNNNNNCCCCCCCCCC-5'&#xA;oligo 3, template        5'-AAAAAAAAAAANNNNNNN[...]NNNNNNNNNNGGGGGGGGGG-3'&#xA;oligo 4, primer reverse                                &amp;lt;--3'-CCCCCCCCCC-5'&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This is just to give you the idea, the actual sequences should be longer, have similar GC% content, and similar t-melting. The advantage is that you reduce complexity and you are virtually void of PCR inhibitors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will also need some DNA polymerase. Perhaps you can borrow an aliquot from someone working in a biology lab.&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="444" LastEditDate="2013-06-30T17:38:33.247" LastActivityDate="2013-06-30T17:38:33.247" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="9041" PostTypeId="2" ParentId="9017" CreationDate="2013-06-30T22:27:26.717" Score="3" Body="&lt;p&gt;The Internet says that platypus venom can kill small animals, but I haven't come up with a definitive source for this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an informative Wikipedia page about the venom &lt;a href=&quot;http://en.wikipedia.org/wiki/Platypus_venom&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. Basically the venom contains a number of toxic peptides including a family of C-type natriuretic peptides, some defensin-like peptides and nerve growth factor. Defensins are very widely-distributed in nature but typically are used by cells as antimicrobials. Natriuretic peptides have a range of effects upon fluid balance and blood pressure control - these are the best-characterized components of platypus venom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These peptides are all genetically-encoded, so they are made as segments of precursor polypeptides. Intriguingly some of the the C-type natriuretic peptides contain a D-Leu residue. (All of the amino acids used in protein synthesis are the L stereoisomeric forms.) The presence of a D-amino acid in a peptide derived from a genetically-encoded molecule suggest that there must be a specific isomerase present, and evidence for this isomerase in the venom has indeed been found as reported in Torres &lt;em&gt;et al&lt;/em&gt;. (2006) Mammalian L-to-D-amino-acid-residue isomerase from platypus venom. FEBS Lett.580:1587–1591. The introduction to this article states:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Platypus venom contains many non-protein and protein components...whose roles are yet to be established. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-06-30T22:27:26.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9042" PostTypeId="2" ParentId="9018" CreationDate="2013-07-01T01:43:46.353" Score="2" Body="&lt;p&gt;not from gels but physical force can be used to separate molecules.. e.g. density centrifugation, filtration. Closest to what you are asking is size exclusion chromatography in HPLC where molecules are separated based on size and high pressure is maintained in order to &lt;em&gt;pump&lt;/em&gt; the solution (containing the analytes) through the stationary phase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Alan Boyd mentioned, the gels cannot withstand high pressure. In HPLC silica beads are used (sometimes coated with specific resins for e.g. in ion-exchange chromatography).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The principal differences between electrophoresis and HPLC (chromatogrphy) are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;HPLC relies on differential interaction of the molecules with the stationary phase (i.e beads) whereas electrophoresis is purely based on the hydrodynamic size of the molecules.&lt;/li&gt;&#xA;&lt;li&gt;HPLC uses pressure to keep the entire mobile phase (solution) pumping through the stationary phase, whereas electrophoresis uses electric field to move the molecules.&lt;/li&gt;&#xA;&lt;li&gt;HPLC can also be used for uncharged molecules&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Size exclusion and gel-filtration chromatographies resolve the molecules based on size as in the case of electrophoresis but as I previously mentioned, the molecules need not be charged. The techniques used for analysis of molecules in both techniques can be similar. For e.g UV absorption/fluorescence. An advantage of HPLC is that it can be connected to other analyzers like Mass Spectrometer, Flame Photometer etc.  &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-07-01T10:06:51.760" LastActivityDate="2013-07-01T10:06:51.760" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9043" PostTypeId="2" ParentId="9032" CreationDate="2013-07-01T02:10:47.763" Score="4" Body="&lt;p&gt;As indicated in the comments there are several non-coding (untranslated) RNAs, that the cell produces. Most of these perform gene regulatory functions.&#xA;However, widespread transcription is known to take place throughout the genome (&lt;a href=&quot;http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000625&quot; rel=&quot;nofollow&quot;&gt;pervasive transcription&lt;/a&gt;), but the functions of these RNAs are not clearly understood. It has been suggested that in certain cases the event of transcription, rather than its product, is responsible for chromatin regulation.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-07-01T02:10:47.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9044" PostTypeId="2" ParentId="9035" CreationDate="2013-07-01T02:39:32.470" Score="2" Body="&lt;p&gt;You are anyways going to get primers and enzymes from somewhere. &#xA;The best option would be to get a plasmid from any biolab. Most of the plasmids have specific sequences like &lt;strong&gt;M13 promoter sequence&lt;/strong&gt;, &lt;strong&gt;T7 terminator/promoter sequence&lt;/strong&gt; etc. These are standard sequences derived form viruses, that are commonly used for primer binding sites for sequencing. Also, these primers are pretty standard and optimized for easy PCR and you can get them quite easily.  &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-07-01T02:39:32.470" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9045" PostTypeId="1" CreationDate="2013-07-01T07:45:26.583" Score="6" ViewCount="33615" Body="&lt;p&gt;I found this today in the library while studying. I am very curious to know whether this particular insect has a name that I can look up and find more information about:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tx71c.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Full length is almost one centimeter. It doesn't bite or anything. It has lots of small hairs in its back (similar to cockroaches and ants) and has a tail that a white sticky substance comes out from.&lt;/p&gt;&#xA;" OwnerUserId="3910" LastEditorUserId="3624" LastEditDate="2013-07-01T13:31:49.467" LastActivityDate="2018-10-29T01:25:23.230" Title="What insect is this? (Black body two orange lines in its back and six legs)" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9046" PostTypeId="2" ParentId="9045" CreationDate="2013-07-01T08:14:26.597" Score="16" Body="&lt;p&gt;It's a &lt;a href=&quot;http://www.brisbaneinsects.com/brisbane_ladybirds/&quot;&gt;larvae from a ladybird (or ladybug)&lt;/a&gt;.  Judging by the stripe pattern it is a &lt;a href=&quot;http://www.brisbaneinsects.com/brisbane_ladybirds/CommonSpotted.htm&quot;&gt;Common Spotted Ladybird&lt;/a&gt; (wiki: &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Harmonia_conformis&quot;&gt;Harmonia conformis&lt;/a&gt;&lt;/em&gt;) and from the body shape &amp;amp; size I'd also say &lt;a href=&quot;http://www.flickr.com/photos/burtonandy/4628261516/&quot;&gt;3rd instar&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The one you have photographed, and the one on &lt;a href=&quot;http://www.flickr.com/photos/burtonandy/4628261516/&quot;&gt;flickr&lt;/a&gt;, are larval forms of the ladybug, just like when a catepillar becomes a butterfly, the ladybugs also have a &lt;a href=&quot;http://www.enchantedlearning.com/subjects/insects/Ladybug.shtml&quot;&gt;larval stage in their life cycle&lt;/a&gt; which crawl around and look very different to the adult form.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-01T08:29:50.367" LastActivityDate="2013-07-01T08:29:50.367" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9047" PostTypeId="1" AcceptedAnswerId="9048" CreationDate="2013-07-01T10:54:18.137" Score="11" ViewCount="571" Body="&lt;p&gt;I'm trying to understand why are bacteria &quot;equipped&quot; with magnetosomes (&lt;a href=&quot;https://www.boundless.com/microbiology/textbooks/boundless-microbiology-textbook/cell-structure-of-bacteria-archaea-and-eukaryotes-4/specialized-internal-structures-of-prokaryotes-36/magnetosomes-269-7642/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;intracellular organelles in magnetotactic bacteria that allow them to sense and align themselves along a magnetic field&quot;&lt;/a&gt;) and why and for what do they need such organelles.&lt;/p&gt;&#xA;" OwnerUserId="3751" LastEditorUserId="21009" LastEditDate="2017-01-02T04:51:52.747" LastActivityDate="2017-01-02T04:51:52.747" Title="What are the functions of magnetic bacteria?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9048" PostTypeId="2" ParentId="9047" CreationDate="2013-07-01T11:22:50.340" Score="15" Body="&lt;p&gt;You can find a detailed discussion of this topic &lt;a href=&quot;http://www.calpoly.edu/~rfrankel/magbac101.html&quot;&gt;here.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Magnetic bacteria contain chains of magnetic crystals (magnetite or greigite) which cause the cells to be oriented in a magnetic field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was originally proposed that magnetic bacteria use their magnetosomes to ensure that they swim downwards into the sediment (everywhere on earth, except at the equator, these lines of force have a downward component vector.) However, the current view is more complex than this: magnetic bacteria are microaerophilic and occur in stratified aquatic environments (i.e. ones where there are zones of oxygen concentration at different depths). In this view the magnetic &quot;sense&quot; is not a true taxis, but rather is used to keep the cells oriented in the magnetic field while they adjust their position by sensing oxygen (aerotaxis). As you may be aware, the standard way that Gram-negative bacteria operate is to perform a biassed random walk in three dimensions. The alignment of cells with the magetic field will reduce the dimensionality of the movement, which is more efficient.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-07-01T16:32:55.197" LastActivityDate="2013-07-01T16:32:55.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9049" PostTypeId="1" AcceptedAnswerId="9050" CreationDate="2013-07-01T12:41:41.663" Score="8" ViewCount="3906" Body="&lt;p&gt;Spiders fascinate me, but what intrigues me the most is just how big some spiders can get, which leads me to my question. What biological constraints (if any) would limit how large a spider could grow, given ample food and no predators?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="30491" LastEditDate="2017-03-16T23:15:59.597" LastActivityDate="2017-03-16T23:15:59.597" Title="What biological constraints are there on how large a spider can grow?" Tags="&lt;physiology&gt;&lt;arachnology&gt;&lt;invertebrates&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9050" PostTypeId="2" ParentId="9049" CreationDate="2013-07-01T13:06:57.133" Score="11" Body="&lt;p&gt;The standard view on this is that the size of terrestrial arthropods like insects and spiders  is limited by the atmospheric concentration of oxygen. This is because they rely upon diffusuion of oxygen into the 'blood' or haemolymph via a system of tubes called trachea that open on to the body surface at the spiracles. As the body grows larger the proportion that has to be taken up by the trachea gets larger. Consistent with this is the presence of fossil giant dragonflies, &lt;em&gt;Meganeura&lt;/em&gt; dating from the Carboniferous era when oxygen levels were at an all time high. However you will find that if you go to &lt;a href=&quot;http://en.wikipedia.org/wiki/Meganeura&quot;&gt;the Wikipedia page for Meganeura&lt;/a&gt; that this idea has been disputed, so the answer may be that no-one really knows. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In relation to alternative explanations; a recent paper by &lt;a href=&quot;http://www.pnas.org/content/109/27/10927.abstract&quot;&gt;Clapham &amp;amp; Karr (2012)&lt;/a&gt; compares fossil insect wing lengths and oxygen concentrations to study the historical drivers of evolution of body size. They conclude that oxygen seems to be the main driver until the end of the Jurassic, but after that biotic interactions (such as bird predation) could be more important.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-07-01T14:28:09.700" LastActivityDate="2013-07-01T14:28:09.700" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9051" PostTypeId="1" AcceptedAnswerId="17677" CreationDate="2013-07-01T15:29:08.997" Score="6" ViewCount="279" Body="&lt;p&gt;I'm looking for an inducer that strongly activates the androgen receptor, but not the glucocorticoid receptor that is not DEA regulated. I know that SARMS (Selective Androgen Receptor Modulators) are something of a hot topic in some corners of some fields, but I'm having some trouble in my laboratory finding one. My research necessitates the independent induction of AR (Androgen Receptor). Does anyone know how to go about this search or know of some chemical?&lt;/p&gt;&#xA;" OwnerUserId="1504" LastEditorUserId="78" LastEditDate="2013-07-02T21:10:22.493" LastActivityDate="2014-05-27T02:48:59.647" Title="Selective Androgen Receptor Agonist" Tags="&lt;proteins&gt;&lt;pharmacology&gt;&lt;metabolism&gt;&lt;protein-binding&gt;&lt;chemical-communication&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9052" PostTypeId="2" ParentId="9032" CreationDate="2013-07-01T17:19:32.810" Score="2" Body="&lt;p&gt;Untranslated RNA is incredibly important. As mentioned it regulates gene control, siRNA or miRNA for example can cut up mRNA preventing it being translated. Others can cause an increase in expression like enhancer RNA. Then RNA can act as tRNA or ribosomal RNA in protein translation. RNA can be enzymatically active, RNA also acts as a primer for initiation of replication. Then theres retroviruses that have inserted into our genome but have lost the ability to exit and are now part of our genome: the endogenous viruses. There are genes that are redundant duplications of functional genes that are free to evolve. As mutations occur silent parts may regain the ability to be transcribed. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-07-01T17:19:32.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9053" PostTypeId="1" CreationDate="2013-07-01T20:19:23.960" Score="5" ViewCount="3253" Body="&lt;p&gt;Misfolded proteins are tagged by ubiquitin and then are destroyed by proteasomes. How does ubiquitin know which protein to tag?&lt;/p&gt;&#xA;" OwnerUserId="3893" LastEditorUserId="107" LastEditDate="2013-07-02T00:56:05.010" LastActivityDate="2013-07-06T00:42:11.917" Title="How does ubiquitin recognize misfolded proteins?" Tags="&lt;cell-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9054" PostTypeId="1" CreationDate="2013-07-01T20:46:28.003" Score="1" ViewCount="949" Body="&lt;p&gt;I should be clear in saying that this question is &lt;strong&gt;NOT&lt;/strong&gt; intended for personal medical advice. Rather what I am looking for is journal articles and/or books that touch on this subject because I think it would be quite an intriguing topic to probe. I am unaware of any interaction between the endocannabinoid system and the formation of haem and porphyrins in general. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2016-05-05T11:37:38.137" Title="What Effect would Cannabinoids have on the Acute Porphyrias?" Tags="&lt;pharmacology&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9056" PostTypeId="1" CreationDate="2013-07-02T00:29:29.683" Score="1" ViewCount="207" Body="&lt;p&gt;I have heard of &lt;a href=&quot;http://en.wikipedia.org/wiki/Extremophile&quot; rel=&quot;nofollow&quot;&gt;'extremophiles'&lt;/a&gt;, lifeforms that naturally thrive in all sorts of extreme environments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any evidence to suggest that lifeforms are adapting to the extreme environments (such as in mining waste, nuclear waste etc) that result from human activity?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-07-02T00:29:29.683" Title="Which are the most extreme artificial environments that lifeforms/ecosystems have adapted to?" Tags="&lt;adaptation&gt;&lt;extremophiles&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9060" PostTypeId="1" AcceptedAnswerId="9065" CreationDate="2013-07-02T03:24:48.273" Score="3" ViewCount="505" Body="&lt;p&gt;Can I recognize the age of a firebug from the pattern on its back?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If yes, what pattern shows what age/stage?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below is what I extrapolated from &lt;a href=&quot;http://en.wikipedia.org/wiki/Firebug&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;, but is there a more precise scale with more steps? (I could not find more than this with google).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nymph:&lt;img src=&quot;https://i.stack.imgur.com/eGuU0.jpg&quot; alt=&quot;enter image description here&quot;&gt; Adults:&lt;img src=&quot;https://i.stack.imgur.com/pWoag.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3535" LastEditorUserId="1590" LastEditDate="2013-07-02T22:09:22.243" LastActivityDate="2013-08-28T11:21:14.400" Title="Method to recognize the age of a firebug from the pattern on its back" Tags="&lt;entomology&gt;&lt;development&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9061" PostTypeId="1" AcceptedAnswerId="9064" CreationDate="2013-07-02T03:48:30.830" Score="1" ViewCount="2024" Body="&lt;p&gt;During 24 hours there is a time in i.e. twilight when plants neither give oxygen nor carbon dioxide why is it so?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This also suggests that neither of the two vital processes i.e. respiration or photosynthesis is being carried out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well, &#xA;during twilight there is not enough sunlight so photosynthesis may  slow down or even cease but what about respiration?&lt;/p&gt;&#xA;" OwnerDisplayName="user3800" LastActivityDate="2013-07-02T10:16:27.317" Title="Confusion regarding photosynthesis and respiration in plants" Tags="&lt;plant-physiology&gt;&lt;photosynthesis&gt;&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9063" PostTypeId="1" AcceptedAnswerId="9067" CreationDate="2013-07-02T07:56:20.947" Score="3" ViewCount="1230" Body="&lt;p&gt;DNA consists of deoxyribonucleotides, RNA consists of ribonucleotides. They differ mainly (apart from the uracil / thymine difference) in the sugar part, the deoxyribose and the ribose. Those two molecules differ in the hydroxy group in the ribose which is only a single proton in the deoxyribose. This part of the sugar molecule is not directly involved in binding reactions, nevertheless it causes the whole difference in RNA and DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder: could a dNTP be used in an RNA strand (or vice versa)? Is it chemically possible that we have a RNA molecule that contains a dNTP next to its NTPs?&lt;/p&gt;&#xA;" OwnerUserId="3119" LastEditorUserId="1320" LastEditDate="2013-07-02T08:25:47.140" LastActivityDate="2013-07-02T08:43:16.887" Title="Can a dNTP be built into a RNA strand?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;rna&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9064" PostTypeId="2" ParentId="9061" CreationDate="2013-07-02T08:16:42.083" Score="5" Body="&lt;p&gt;You haven't directed us to any evidence for your assertion, so it is difficult to evaluate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not a plant physiologist, so I will argue from first principles:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;photosynthesis&lt;/strong&gt; consumes CO&lt;sub&gt;2&lt;/sub&gt; and produces O&lt;sub&gt;2&lt;/sub&gt;:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;6CO&lt;sub&gt;2&lt;/sub&gt; +6H&lt;sub&gt;2&lt;/sub&gt;O -&gt; C&lt;sub&gt;6&lt;/sub&gt;H&lt;sub&gt;12&lt;/sub&gt;O&lt;sub&gt;6&lt;/sub&gt; + 6O&lt;sub&gt;2&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;respiration&lt;/strong&gt; consumes O&lt;sub&gt;2&lt;/sub&gt; and produces CO&lt;sub&gt;2&lt;/sub&gt;:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;C&lt;sub&gt;6&lt;/sub&gt;H&lt;sub&gt;12&lt;/sub&gt;O&lt;sub&gt;6&lt;/sub&gt; + 6O&lt;sub&gt;2&lt;/sub&gt; -&gt; 6CO&lt;sub&gt;2&lt;/sub&gt; +6H&lt;sub&gt;2&lt;/sub&gt;O&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants do both of these things at the same time for at least part of the day. During the day, in a growing plant, photosynthesis will exceed respiration: a lot of the fixed carbon is fed into anabolic processes to produce &quot;plant stuff&quot;; polysaccharides, proteins, nucleic acids. This means that the plant will be a net producer of O&lt;sub&gt;2&lt;/sub&gt; and a net consumer of CO&lt;sub&gt;2&lt;/sub&gt;. At night there is, of course, no photosynthesis and respiration will dominate and the plant will be a net producer of CO&lt;sub&gt;2&lt;/sub&gt; and a net consumer of O&lt;sub&gt;2&lt;/sub&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At certain times of the day, twilight for example, there will be a transition between these two states, and the plant will pass through a state where there will be no net flux in either of the gases.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-07-02T10:16:27.317" LastActivityDate="2013-07-02T10:16:27.317" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9065" PostTypeId="2" ParentId="9060" CreationDate="2013-07-02T08:23:51.133" Score="7" Body="&lt;p&gt;The answer is more or less yes. Normally Firebugs (&lt;em&gt;Pyrrhocoris apterus&lt;/em&gt;) go through 5 nymph instar stages (as do most &lt;a href=&quot;https://en.wikipedia.org/wiki/Hemiptera&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hemiptera&lt;/a&gt;), where they resemble the adults more and more as they grow. Only adults are winged and have have functional reproductive organs. This type of metamorphosis is called &lt;a href=&quot;https://en.wikipedia.org/wiki/Hemimetabolous&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;hemimetabolous&lt;/em&gt;&lt;/a&gt; or simple metamorphosis (in contrast to &lt;a href=&quot;https://en.wikipedia.org/wiki/Holometabolous&quot; rel=&quot;nofollow noreferrer&quot;&gt;Holometabolism or complete metamorphosis&lt;/a&gt;). However, I cannot find a good overview of the instar stages of Firebugs to link to.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A generic overview of Heteroptera (True Bugs) can bee seen here &#xA;(from &lt;a href=&quot;http://www.amnh.org/learn/biodiversity_counts/ident_help/Parts_Arthropods/metamorphosis.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;www.amnh.org/learn/biodiversity_counts&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4eKd9.gif&quot; alt=&quot;development of Heteroptera (True Bugs)&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This picture shows (at least) three instars + adults of Pyrrhocoris apterus (from &lt;a href=&quot;http://www.projectnoah.org/spottings/17248017&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.projectnoah.org/spottings/17248017&lt;/a&gt;). The large nymph with 3 dots along the midline is the final 5th instar nymph:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4Ke7l.jpg&quot; alt=&quot;Pyrrhocoris apterus instars + adults&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, due to hormonal disruptions there have been cases with even more nymph stages (6th and 7th instars with adult characteristics), but this is under unnatural laboratory conditions (e.g. &lt;a href=&quot;http://www.pnas.org/content/54/2/411.full.pdf&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Slama &amp;amp; Williams. 1965. Juvenile hormone activity for the bug Pyrrhocoris apterus. Proceedings of the National Academy of Sciences 54(2): 411–414.&quot;&gt;Slama &amp;amp; Williams 1965&lt;/a&gt; and &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028728&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Konopova, Smykal &amp;amp; Jindra. 2011. Common and Distinct Roles of Juvenile Hormone Signaling Genes in Metamorphosis of Holometabolous and Hemimetabolous Insects . PLOS ONE 6(12): e28728. doi:10.1371/journal.pone.0028728&quot;&gt;Konopova et al. 2011&lt;/a&gt;). Konopova et al (2011) also has pictures of instar stages 4 &amp;amp; 5 (along with gene knowdown versions).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-08-28T11:21:14.400" LastActivityDate="2013-08-28T11:21:14.400" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9066" PostTypeId="2" ParentId="9063" CreationDate="2013-07-02T08:24:20.947" Score="2" Body="&lt;p&gt;All DNA polymerases use an RNA primer during DNA replication - they cannot begin a DNA molecule &lt;em&gt;de novo&lt;/em&gt;. Before the primer is removed the newly synthesised strand is an RNA-DNA hybrid. The first deoxynucleotide to be incorporated into the new DNA is added to the 3'-OH of an RNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this count?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Added later&lt;/strong&gt;:&#xA;&lt;a href=&quot;http://www.pnas.org/content/94/5/1619.full.pdf&quot; rel=&quot;nofollow&quot;&gt;this looks like a place to start reading&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-07-02T08:43:16.887" LastActivityDate="2013-07-02T08:43:16.887" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9067" PostTypeId="2" ParentId="9063" CreationDate="2013-07-02T08:30:09.613" Score="4" Body="&lt;p&gt;This is rather easy to do if you synthesize oligonucleotides chemically and not enzymatically. This is typically done using &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleoside_phosphoramidite&quot; rel=&quot;nofollow&quot;&gt;phosphoramidite chemistry&lt;/a&gt;, and it allows for the synthesis of chimeric RNA/DNA oligos. You can even incorporate modified nucleosides like 2'-O-Me or LNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is typically done if you want to change the properties of an oligo, e.g. if you want to make it resistant to degradation by enzymes.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2013-07-02T08:30:09.613" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9068" PostTypeId="1" CreationDate="2013-07-02T09:38:01.313" Score="6" ViewCount="637" Body="&lt;p&gt;Does it matter if I replace the PCR tube (usually made of plastic) with another material like aluminum, glass, or something similar? &lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="3624" LastEditDate="2013-07-02T10:18:37.500" LastActivityDate="2016-08-17T08:49:56.220" Title="Can PCR tubes be made of different materials than plastic?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;diy-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9069" PostTypeId="2" ParentId="9053" CreationDate="2013-07-02T09:38:18.043" Score="2" Body="&lt;p&gt;Ubiquitin is active as part of a complex of proteins. Other elements of the complex recognise the proteins to be degraded. These recognition or specificity proteins are responsible for targetting proteins for ubiquitination. They are called &lt;a href=&quot;https://en.wikipedia.org/wiki/Ubiquitin_ligase&quot; rel=&quot;nofollow&quot;&gt;ubiquitin ligases&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="476" LastEditorUserId="3624" LastEditDate="2013-07-03T09:14:39.850" LastActivityDate="2013-07-03T09:14:39.850" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9070" PostTypeId="2" ParentId="9068" CreationDate="2013-07-02T10:14:00.293" Score="5" Body="&lt;p&gt;The key property would seem to be, at first glance, thermal conductivity. According to &lt;a href=&quot;http://www.engineeringtoolbox.com/thermal-conductivity-metals-d_858.html&quot;&gt;this table&lt;/a&gt; copper wins. But then, what about chemical reactivity? Maybe gold is a better choice. And that brings us to cost and disposability. These factors make the choice of a metal problematic. That leaves plastic and glass. Glass has better thermal conductivity, but clearly it has other drawbacks.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-07-02T10:14:00.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9071" PostTypeId="1" AcceptedAnswerId="9073" CreationDate="2013-07-02T11:04:41.343" Score="1" ViewCount="105" Body="&lt;p&gt;Does Budding Yeast Sacchromyces cerevisiae produces significant amount of carotenoids?&#xA;Have anybody estimated the ratio of flux going in branches 1. Cholesterol synthesis(via squalene)&#xA;2. Coenzyme Q6 and 3. Dolichols Glycoprotein and others from the branch point of Farnesyl diphosphate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the kegg pathway &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.genome.jp/kegg-bin/show_pathway?map00900&quot; rel=&quot;nofollow&quot;&gt;http://www.genome.jp/kegg-bin/show_pathway?map00900&lt;/a&gt;&#xA;I also have pathway formatted but couldn't upload.&lt;/p&gt;&#xA;" OwnerUserId="3841" LastEditorUserId="1590" LastEditDate="2013-07-02T22:07:38.550" LastActivityDate="2013-07-02T22:07:38.550" Title="Carotenoid biosynthesis in yeast" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;enzymes&gt;&lt;yeast&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9072" PostTypeId="1" CreationDate="2013-07-02T11:29:13.870" Score="4" ViewCount="654" Body="&lt;p&gt;How is an introverts brain wired differently than an extroverts? Just to give you an example. On an average, the processing that goes on in an introverts brain is greater than in an extroverts [&lt;em&gt;citation needed&lt;/em&gt;]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What part of the brain affects personality traits such how introverted someone is? How is this part of the brain different in either it's physical entity or it's activity between extroverts and introverts?&lt;/p&gt;&#xA;" OwnerUserId="3918" LastEditorUserId="1590" LastEditDate="2013-07-02T11:35:12.337" LastActivityDate="2013-07-03T05:28:19.963" Title="How different is an introverts brain different from an extroverts?" Tags="&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9073" PostTypeId="2" ParentId="9071" CreationDate="2013-07-02T11:38:03.310" Score="1" Body="&lt;p&gt;The enzyme phytoene synthase is the first committed step in carotenoid biosynthesis. &lt;em&gt;Saccharomyces cerevisiae&lt;/em&gt; doesn't have this enzyme, nor does it have the rest of the relevant pathway. Other yeasts such as &lt;em&gt;Rhodotorula spp&lt;/em&gt; and &lt;em&gt;Phaffia rhodozyma&lt;/em&gt; can make carotenoids.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21573686&quot; rel=&quot;nofollow&quot;&gt;carotenoid biosynthesis has been engineered into &lt;em&gt;S. cerevisiae&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-07-02T13:46:18.873" LastActivityDate="2013-07-02T13:46:18.873" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9074" PostTypeId="2" ParentId="9068" CreationDate="2013-07-02T11:55:40.467" Score="4" Body="&lt;p&gt;Next to the cost for aluminium or any other metal, a lot of metal ions have chemical functions that makes them not suitable to do chemical reactions in tubes of that material. Copper, for example, reacts with oxygen and can therefore affect the reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biotechniques.com/BiotechniquesJournal/2008/April/Plastic-versus-glass-capillaries-for-rapid-cycle-PCR/biotechniques-44804.html&quot; rel=&quot;nofollow&quot;&gt;The article&lt;/a&gt; that rg255 posted in a comment says clearly that glass tubes have advantages compared to plastic tubes: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Heat transfer into plastic capillaries was slowed by thicker walls, lower thermal conductivity, and a lower surface area—to-volume ratio than glass capillaries. Whereas the denaturation and annealing target temperatures were reached by samples in glass capillaries, samples in plastic capillaries fell short of these target temperatures by 6°–7°C.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Nevertheless glass might have a big disadvantage: it breaks much easier than plastic. When you handle the tubes in the lab and don't pay enough attention you might lose your samples, and if you want to freeze some tubes and they are pretty full the glass might break due to the bigger volume of the frozen probe.&lt;/p&gt;&#xA;" OwnerUserId="3119" LastEditorUserId="1590" LastEditDate="2016-08-17T08:49:56.220" LastActivityDate="2016-08-17T08:49:56.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9075" PostTypeId="1" AcceptedAnswerId="11342" CreationDate="2013-07-02T15:34:06.840" Score="7" ViewCount="9821" Body="&lt;p&gt;Sometimes while tasting a very sour thing (like tamarind, lemon etc.) our eyes squint immediately and involuntarily for a second, but a little later becomes normal again. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why, and how, does this reflexive movement occur?&lt;/p&gt;&#xA;" OwnerUserId="3881" LastEditorUserId="1590" LastEditDate="2013-07-02T22:05:58.763" LastActivityDate="2015-03-23T12:56:37.577" Title="Why do we squint when tasting very sour things?" Tags="&lt;homework&gt;&lt;sensation&gt;&lt;reflexes&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9076" PostTypeId="1" CreationDate="2013-07-02T16:34:53.450" Score="0" ViewCount="103" Body="&lt;p&gt;I'm planning to order oligo, polymerase, nucleotide, buffer for my first diy PCR experiment (now I have nothing), so I have some questions.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;How and how long I can storage them?  I have only a fridge that can freeze to -10 -&gt; -20C.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I see the size/concentration of polymerase is 400 units and 25 nmole of oligo. So what can I do with 25 nmole oligo and 400 units of polymerase? How many PCR experiment I can do with 400 units of polymerase, and how many PCR experiment I can do with 25 nmole of oligo?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If I have a HPLC machine, can I reuse the polymerase by purify it after reaction?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="107" LastEditDate="2013-07-02T17:06:02.777" LastActivityDate="2017-10-25T23:40:27.773" Title="Some question about materials for PCR" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;diy-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9077" PostTypeId="2" ParentId="9076" CreationDate="2013-07-02T17:01:31.173" Score="2" Body="&lt;p&gt;The manufacturers of each component should have information available on their website regarding storage temperatures, along with recommended protocols on how much of each component to add to the PCR reaction. I would not try to reuse the polymerase, as depending on the kind you buy it may be a complex of proteins, and it may not be functional after purification. However, you're welcome to experiment all you want, it's your stuff!&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-07-02T17:01:31.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9079" PostTypeId="2" ParentId="9075" CreationDate="2013-07-02T17:28:23.730" Score="-2" Body="&lt;p&gt;Squinting is the organism's way to warn us that we are eating something that could eventually be dangerous, acidic or toxic. It's a reflex, developed many many years ago when the ancient people did not know much about the safety of plants, roots and other foods. They used to try them and decide if the object is eatable or not according to its taste. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, our tongue has very sensitive papilla, which react to sourness and make the muscles contract. &lt;/p&gt;&#xA;" OwnerUserId="3864" LastActivityDate="2013-07-02T17:28:23.730" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9084" PostTypeId="1" AcceptedAnswerId="9088" CreationDate="2013-07-02T21:41:54.590" Score="1" ViewCount="338" Body="&lt;p&gt;Can polyA tails occur within (rather than at the end) of a sequenced tag? Consider, for example the following two sequences from NCBI:&#xA;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/nucest/DY008075&quot; rel=&quot;nofollow&quot;&gt;DY008075&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt;gi|119423037|gb|DY008075.1|DY008075 19ACACYS_UP_022_A11_29OCT2004_095 Brassica napus 19ACACYS Brassica napus cDNA 5', mRNA sequence&#xA;TGGTACGGTCAGATGCTTGCTAAAGGAGAAATAAATAGAGACATGGGTGATAGTATAAGCGGAAAGGGAA&#xA;TGATTCAGGGTGTTTCTGCAGTGGGAGCGTTTTACCAACTGCTTAGTCAGTCCAGCCTAAGTATATTGCA&#xA;TTCTGAAGAGAAGAAACCTGTGGCTCCGGTTGAATCATGTCCTATTTTGAAAACACTCTACAAGATACTC&#xA;ATCACAAGAGAACAATCAACACAAGCGATTCTGCAAGCATTAAGGGATGAAACACTGAATGACCCAAGAG&#xA;ACAGGATTGAGATTGCACAGAGCCATGCATTCTACAGGCCTTCCCTTCTAGATCAGCCTTGATTAGTCTG&#xA;TCATGGCTCATAATCCGAACTTCTAAGATCTTACTTGTGCAAACTGCAGATTCTGCTATGTTAAACATCA&#xA;TGTCTTAAAATTGATTGTTGTTCAGCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACATGTC&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;or &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/nucest/126492146?report=est&quot; rel=&quot;nofollow&quot;&gt;EE485195&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt;gi|126492146|gb|EE485195.1|EE485195 DHBN8DCT_UP_012_C05_25FEB2005_043 BRASSICA NAPUS SEEDS BNDH8DCT Brassica napus cDNA 5', mRNA sequence&#xA;GTTACAGCTGGTTGAGAACAGTGACAATTCCCGGTTGAGCAAAGAAATTGCAGACAAGAGCCACCAACTA&#xA;AGGCAAATGAGAGGAGAGGAACTTCAAGGACTTAACATAGAAGAGCTGCAACAGCTGGAAAAGGCCCTTG&#xA;AAGCTGGTTTGACGCGCGTGATTGAAACAAAGAGTGAGAAGATTATGAGTGAGATCAGTGACCTTCAAAG&#xA;AAAGGGAATGAAATTGATGGATGAGAACAAGCGGCTAAGGCAGCATGGAACACAACTAACAGAAGAGAAC&#xA;GAGCGACTAGGCAAGCAAATATATAATAATATGCATGAAAGATACGGTGGTGTTGAGTCGGAGAAGACCG&#xA;CCGTGTACGAGGAAGGGCAGTCGTCAGAGTCCATTACTAACGCCGGAAACTCCACCGGCGCTCCTGTTGA&#xA;CTCCGAGAGCTCCGATACCTCTCTTAGGCTCGGCTTACCGTATGGCGGTTAGAGATGGAACCATACAAAG&#xA;AAGTTCATGGAGTGAGGAGATGCTCTGTAGTAACAAGTGGCAATGTAGTAATTTCTCTTGTTTGATGTAA&#xA;GTTTTTGTCTGAGGAAGAGGTTTTCCTTTTATGTTCTCTTTGATATTATTATCTTTCTTCACTGCAAAAA&#xA;AAAAAAAAAAAAAAAAAAAAAAAACATGTC&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;It seems to me that both the polyA sequences at the end are some sort of tail rather than actual coding for poly lysines. If we BLAST either of the sequences, the polyA part doesn't align with any reliable nucleotide or protein (i.e., with the NCBI non-redundant databases). I can give more examples and show their best alignments to nr-Sequences but it will make the question too long.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cross posted to &lt;a href=&quot;http://seqanswers.com/forums/showthread.php?p=109334&quot; rel=&quot;nofollow&quot;&gt;SeqAnswers&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3922" LastEditorUserId="3922" LastEditDate="2013-07-02T22:09:30.883" LastActivityDate="2013-07-03T11:03:01.493" Title="Can PolyA tails be within Expressed Sequence Tags?" Tags="&lt;rna-sequencing&gt;&lt;sequence-analysis&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9085" PostTypeId="1" CreationDate="2013-07-02T22:17:58.540" Score="8" ViewCount="777" Body="&lt;p&gt;First of all I am &lt;strong&gt;not&lt;/strong&gt; endorsing &lt;a href=&quot;http://en.wikipedia.org/wiki/Intelligent_design&quot; rel=&quot;noreferrer&quot;&gt;Intelligent Design (Wikipedia link)&lt;/a&gt;; I'm asking this because I (someone who does not have a background in biology, organic chemistry, or philosophy) got into a conversation with someone who does endorse it, and I'm trying to see his point of view as far as rationality can allow. Second of all, I apologize for any vagueness; Intelligent Design isn't well enough defined as a theory for me to help that. I also apologize if this is rehashing content already plentiful on the Internet, but for my purposes I can't simply depend on the likes of Wikipedia or Talk Origins, &lt;strong&gt;so what I'm looking for here instead&lt;/strong&gt; is to take the opposite approach and see, based on your informed minds, if there &lt;strong&gt;could possibly&lt;/strong&gt; be any reasonable likelihood of an ideal ID theory being adopted.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I'm looking for the most favorable consideration for what ID might be&#xA;  if it were best developed as a viable hypothesis or theory to get an&#xA;  idea of how far such a discussion is worth taking. An unbiased,&#xA;  informed Devil's advocate, if you will.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My cursory investigation of what &lt;a href=&quot;http://www.youtube.com/watch?v=NbluTDb1Nfs&quot; rel=&quot;noreferrer&quot;&gt;Stephen Meyers (video link)&lt;/a&gt; and &lt;a href=&quot;http://www.youtube.com/watch?v=V_XN8s-zXx4&quot; rel=&quot;noreferrer&quot;&gt;Michael Behe (video link)&lt;/a&gt; say (correct me if I'm wrong) seems to be that either the first cell was likely designed intelligently judging by the complex code of DNA and that evolution took course from there, or that the first cells were made and many instances of evolution were from some kind of intelligently guided mutations as was needed to make &quot;irreducibly complex&quot; cells or body functions (whether the guidance stops after the Cambrian or continued even to the point of making different types of new bacteria and different types of apes/humans or whether every single mutation and adaptive ability is being guided, I'm not sure if they're at any consensus, and that's why I don't know if I should stop my question at abiogenesis or include evolution). The person I spoke with also brought up some specific claims (everything looks designed, DNA has ordered, complex information, blood clotting is irreducibly complex, ID can and has make predictions like decades ago that &quot;Junk DNA&quot; wasn't junk) that I don't need you to debunk (I have Google).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if there could be any possible support or truth to any of the above, I would appreciate knowing about that. (Again, Devil's advocate so I can be informed and understand where the points come from.) Reading an ID book alone, it would be in places hard to know where they differ from actual scientific conclusions. After all, when someone who &lt;em&gt;seems&lt;/em&gt; to know what they're talking about and can explain something in technical detail says that something is impossible or extremely unlikely, it's hard for me to know why they would be wrong (are they ignoring other possibilities? misrepresenting facts? are they really right and just getting the cold shoulder from an atheistic scientific community because it implies a deity?). So I focus on mainstream sources, even if they don't bother entertaining ID and leave me ignorant of its possible virtues. And thus I'm hoping someone from this informed community might enlighten me to what those possible virtues might be.&lt;/p&gt;&#xA;" OwnerUserId="3920" LastEditorUserId="3920" LastEditDate="2013-07-19T01:57:41.407" LastActivityDate="2015-03-11T03:19:31.820" Title="What is the viability of Intelligent Design as a supplement to chemical abiogenesis and Darwinian Evolution?" Tags="&lt;evolution&gt;&lt;abiogenesis&gt;&lt;molecular-evolution&gt;" AnswerCount="4" CommentCount="11" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9086" PostTypeId="2" ParentId="9072" CreationDate="2013-07-03T05:28:19.963" Score="4" Body="&lt;p&gt;I am not sure if this answers your question, but according to the article &quot;&lt;a href=&quot;http://www.psychologytoday.com/articles/199907/the-difference-between-introverts-and-extroverts&quot; rel=&quot;nofollow&quot;&gt;The Difference Between Introverts and Extroverts&lt;/a&gt;&quot; (Gallagher, 1999), the main differences between introverts and extraverts are where the main brain activity occurs (as seen by positron emission tomography (PET) measurements).  The full PET study is in the article &quot;&lt;a href=&quot;http://ajp.psychiatryonline.org/article.aspx?articleID=173270&amp;amp;RelatedWidgetArticles=true&quot; rel=&quot;nofollow&quot;&gt;Cerebral Blood Flow and Personality: A Positron Emission Tomography Study &lt;/a&gt;&quot; (Johnson et al. 1999).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The conclusion of the Johnson et al. paper states:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This study revealed a pattern of increased blood flow in the frontal lobes associated with introversion. ... in the present study, there were more cortical regions associated with introversion than with extraversion. ...in the present study, extraverts did show lower blood flow in several regions in the behavioral inhibition system, namely, the frontal lobes and the hippocampus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Some images of brain activity is included in a more recent article &quot;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0168010211020967&quot; rel=&quot;nofollow&quot;&gt;Differences in regional brain volume related to the extraversion–introversion dimension—A voxel based morphometry study&lt;/a&gt;&quot; (Forsman et al. 2012).  Forsman's article looks at activity in  the white and grey matter of the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-07-03T05:28:19.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9088" PostTypeId="2" ParentId="9084" CreationDate="2013-07-03T11:03:01.493" Score="2" Body="&lt;p&gt;The CATGTC sequence at the end of the poly A tail is an artefact of the method used in constructing the original cDNA library.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/nucest/EE485195.1&quot; rel=&quot;nofollow&quot;&gt;https://www.ncbi.nlm.nih.gov/nucest/EE485195.1&lt;/a&gt; this EST comes from a library constructed in the Clontech vector pDNR-LIB&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Clontech SMART cDNA cloning system manuals are linked to &lt;a href=&quot;http://www.clontech.com/GB/Products/cDNA_Synthesis_and_Library_Construction/cDNA_Library_Construction/Library_Construction_Kits?sitex=10030:22372%3aUS&amp;amp;PROD=DgtuTHcwAnX2qGdN3ZKA0w1p%3aS&amp;amp;PROD_pses=ZGAF0D666B4D4595A682BFD6DF8058E0ED507B9F5B3DC8F392B52FC05E5DB00A12DA6356462F7CF745EAB550720A975EEC5B75A6E19984F82F&quot; rel=&quot;nofollow&quot;&gt;from here&lt;/a&gt;&#xA;and the general manual descibes the use of a primer for 1st strand synthesis:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;CDS III/3' PCR Primer  5'-ATTCTAGAGGCCGAGGCGGCCGACATG-d(T)&lt;sub&gt;30&lt;/sub&gt;N&lt;sub&gt;-1&lt;/sub&gt;N-3'&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(N = A, G, C, or T; N&lt;sub&gt;-1&lt;/sub&gt; = A, G, or C)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you look carefully at the primer you will see that the oligo dT portion, designed to anneal to the poly-A tail of the mRNA is preceded by the sequence GACATG and a SfiI site that is used in some clever cloning strategy that I don't fully understand. What is clear however is that the use of this primer will put CATGTC immediately after the poly A in the cDNA:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;           .....SfiI....&#xA;5'-ATTCTAGAGGCCGAGGCGGCCGACATGTTTTTTTTTTTTTTTTTTT...&#xA;   TAAGATCTCCGGCTCCGCCGGCTGTACAAAAAAAAAAAAAAAAAAA...5'&#xA;&#xA;&amp;gt;&amp;gt;&amp;gt; turning bottom strand around -  5' ...AAAAAAACATGTC&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-07-03T11:03:01.493" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9089" PostTypeId="1" CreationDate="2013-07-03T12:58:08.640" Score="1" ViewCount="1191" Body="&lt;p&gt;What is the recommended DIY way of extracting and long term storing of human DNA samples to store at home and send for sequencing in years time? Considerations:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Sample material: cheek swab, hair, blood?&lt;/li&gt;&#xA;&lt;li&gt;Extraction: which detergent, alcohol?&lt;/li&gt;&#xA;&lt;li&gt;Storage: freezer? what temperature?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Any ideas?&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="658" LastEditDate="2013-07-03T14:12:18.603" LastActivityDate="2014-12-11T18:31:02.313" Title="DIY extraction and long term storage of human DNA sample?" Tags="&lt;dna&gt;&lt;diy-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9091" PostTypeId="1" AcceptedAnswerId="9096" CreationDate="2013-07-03T14:37:33.250" Score="2" ViewCount="9657" Body="&lt;p&gt;Are bioscience and lifescience the same things? I am a little bit confused about it. If not, then what is the difference between the two?&lt;/p&gt;&#xA;" OwnerUserId="3881" LastEditorUserId="3059" LastEditDate="2013-07-03T17:15:14.263" LastActivityDate="2018-10-10T18:13:16.347" Title="Difference between Bioscience and Lifescience" Tags="&lt;terminology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9093" PostTypeId="1" CreationDate="2013-07-03T18:13:27.887" Score="5" ViewCount="840" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Thymine&quot;&gt;Wikipedia&lt;/a&gt; says that &quot;in RNA, thymine is replaced with uracil in most cases.&quot;  I'm curious what are the cases when this does not happen?  Does this ever occur in normal functioning, or is it an error?  Do T and U ever appear in the same strands of RNA together, or does a single strand just use T or just use U?&lt;/p&gt;&#xA;" OwnerUserId="3927" LastActivityDate="2019-02-04T20:53:02.173" Title="Do thymine and uracil ever appear in the same strand of RNA?" Tags="&lt;dna&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9094" PostTypeId="2" ParentId="9093" CreationDate="2013-07-03T19:09:03.800" Score="6" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Transfer_RNA&quot;&gt;tRNA molecules contain a T in the &lt;em&gt;T arm&lt;/em&gt;&lt;/a&gt;. I believe that this results from post-transcriptional modification of a U by uridine methylase.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-07-03T19:28:38.437" LastActivityDate="2013-07-03T19:28:38.437" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9095" PostTypeId="1" AcceptedAnswerId="9099" CreationDate="2013-07-03T20:48:26.993" Score="9" ViewCount="2617" Body="&lt;p&gt;Firstly I could do with a brief description of mitochondrial DNA. How does the structure of DNA in mitochondria compare to animal DNA (for the sake of simplicity let's say human - some animals might have unusual DNA structure) and what living organism is the mitochondrial genome most akin to? (Circular like bacteria maybe?) and are the mitochondria within a single human homogenous?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, and most importantly to my aim, does the mitochondrial genome recombine in anyway? Is the process of recombination affected by its structure? Are there any patterns/rules in mitochondrial recombination? Is there DNA transfer between mitochondria which could have a similar effect?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am trying to think about how male deleterious alleles can spread differently in diverged populations given potential recombination to female beneficial (or recombination away from female deleterious mutations). &lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-04T06:04:46.760" LastActivityDate="2015-12-12T14:56:34.717" Title="Mitochondrial DNA and recombination" Tags="&lt;dna&gt;&lt;mitochondria&gt;&lt;recombination&gt;" AnswerCount="4" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9096" PostTypeId="2" ParentId="9091" CreationDate="2013-07-03T22:33:27.837" Score="3" Body="&lt;p&gt;I agree with the comments and largely see them as the same thing, and many dictionaries would probably agree with this. However, in practical use (from my experience) &lt;strong&gt;Life science&lt;/strong&gt; is used somewhat more broadly (everything from ecology and agricultural science to genomics and biochemisty), while &lt;strong&gt;Bioscience&lt;/strong&gt; is more often applied to &quot;whiter&quot; lab-based biology and more technical applications (biotechnology, genetics, etc.). Personally, I would feel comfortable to label my research as &lt;em&gt;life science&lt;/em&gt; but a bit more uneasy with &lt;em&gt;bioscience&lt;/em&gt;. However, the terms are so vague that I wouldn't pass judgement on the content of research just based on these labels. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-07-03T22:40:28.553" LastActivityDate="2013-07-03T22:40:28.553" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9097" PostTypeId="1" CreationDate="2013-07-04T03:46:04.530" Score="10" ViewCount="22758" Body="&lt;p&gt;In my basic science classes in high school, I have learned that during photosynthesis, plants absorb sunlight and produce food by converting carbon dioxide and water into sugar and starch. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To me, this seems similar to the analogy of solar cells that convert sunlight into electricity. When sunlight falls directly on the solar cell, it produces electricity, but even when it is cloudy with no direct sunlight available, electricity is produced, but with less efficiency. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So can photosynthesis occur in plants only when they are in direct sunlight or does photosynthesis also occur during cloudy weather when the light is diffuse or indirect?&lt;/p&gt;&#xA;" OwnerUserId="3918" LastEditorUserId="16651" LastEditorDisplayName="user3795" LastEditDate="2015-12-13T03:55:03.277" LastActivityDate="2015-12-13T03:55:03.277" Title="Does photosynthesis occur on cloudy days or does it require direct sunlight?" Tags="&lt;photosynthesis&gt;&lt;botany&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9098" PostTypeId="2" ParentId="9097" CreationDate="2013-07-04T04:47:44.423" Score="6" Body="&lt;p&gt;Yes, photosynthesis does occur on cloudy days where the light exposure is &lt;em&gt;diffuse&lt;/em&gt; - but the overall picture is not as simple as your solar cell analogy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider one of the findings of the following article: &quot;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2435.2011.01934.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Impact of clear and cloudy sky conditions on the vertical distribution of photosynthetic CO₂ uptake within a spruce canopy&lt;/a&gt;&quot; (Urban et al. 2011), where one of the findings is that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;that shoots from deep within the canopy contribute substantially to the overall carbon balance during cloudy days. But, although shade-adapted shoots had a markedly positive carbon balance over a 24-h period on cloudy days, their performance was impaired on sunny days contributing only a marginal or even negative carbon balance from the middle and shaded parts of the canopy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, while leaves at the top of the canopy have a reduced rate of photosynthesis on cloudy days, leaves within the canopy and those that are shade-adapted, still photosynthesised.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps a bit.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="3340" LastEditDate="2014-10-09T15:04:56.420" LastActivityDate="2014-10-09T15:04:56.420" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9099" PostTypeId="2" ParentId="9095" CreationDate="2013-07-04T08:58:44.560" Score="4" Body="&lt;p&gt;Mitochondrial DNA is circular, like bacterial DNA, and around 16.6 Kb long. It codes for 37 genes in total but the majority of these are simply the machinery for gene expression (curiously, mitochondria have a slightly different codon-&gt;amino acid translation 'table' to nuclear DNA) and so just 13 code for proteins. Single mitochondria usually have multiple copies of the DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mitochondria are thought to be most closely related to the bacteria &lt;em&gt;Rickettsia&lt;/em&gt;, an obligate intracellular parasite that causes typhus. Mitochondria are so degenerate, however, that they've lost nearly all the genes that normal bacteria have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While there is some small level of heterogeneity in mitochondria in a single person because mitochondria are exclusively transmitted down the female line most people typically only start with a single clonal population of mitochondria. Because of this, there is no other mitochondrial population present that the mitochondrial DNA could undergo recombination with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mitochondrial DNA does undergo recombination with nuclear DNA, however, in that genes can be transfered from the mitochondria to the nuclear DNA and because of this the majority of genes necessary for mitochondrial function are now coded not on the mitochondrial DNA but on the nuclear DNA and their protein products transported into the mitochondria after translation.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="112" LastEditDate="2013-07-04T09:03:47.573" LastActivityDate="2013-07-04T09:03:47.573" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9100" PostTypeId="1" AcceptedAnswerId="9105" CreationDate="2013-07-04T12:02:27.163" Score="3" ViewCount="445" Body="&lt;p&gt;From what I have read, outer hair cells in the human ear amplify incoming signals and inner hair cells &quot;pick-up&quot; the signals and generate action potential. However, neurons have refractory periods during which they cannot fire again. Does this mean that the human ear has a &quot;sampling period&quot; within which it cannot &quot;pick-up&quot; sounds?&lt;/p&gt;&#xA;" OwnerUserId="3932" LastEditorUserId="460" LastEditDate="2013-07-04T14:17:00.520" LastActivityDate="2013-07-04T14:26:58.287" Title="Hearing and neurons- do ears have a sampling period?" Tags="&lt;neuroscience&gt;&lt;human-ear&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9101" PostTypeId="1" CreationDate="2013-07-04T12:24:14.810" Score="9" ViewCount="532" Body="&lt;p&gt;I was reading about a few studies on estimating functional connectivity between brain areas using fMRI signals. However, as far as I know that fMRI has a very poor time resolution, roughly in the order of 1 second. Individual neurons communicate with delay less than 100 ms, and many brain functions happen within a second, in which case fMRI wouldn't have enough time resolution to determine if things happened simultaneously, or in a sequence at all. This problem would be even greater for causality analysis such as Granger causality framework.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is, what is the theoretical, and practical limit of time resolution in fMRI on human?&lt;/p&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2013-09-09T13:48:35.940" LastActivityDate="2018-12-22T23:10:58.590" Title="What is the limit of time resolution in fMRI?" Tags="&lt;neuroscience&gt;&lt;mri&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9102" PostTypeId="1" CreationDate="2013-07-04T13:01:21.270" Score="8" ViewCount="2189" Body="&lt;p&gt;Do you have any suggestions on a suitable introductory text on bioinformatics for a computer scientist? Any recommendations with pros and cons of different books would be appreciated. I'm mainly looking for a brief introduction since I'm a novice to this field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found some books like &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;em&gt;Systems Biology&lt;/em&gt; by Edda Klipp,&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Introduction to Bioinformatics&lt;/em&gt;  by Arthur Lesk&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Bioinformatics For Dummies&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Bioinformatics and Functional Genomics&lt;/em&gt; by Jonathan Pevsner&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;An Introduction to Bioinformatics Algorithms&lt;/em&gt; by Neil C. Jones and Pavel A. Pevzner&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I would like to develop software related to sequencing applications, so any suggestions should ideally aid in this goal.&lt;/p&gt;&#xA;" OwnerUserId="3930" LastEditorUserId="107" LastEditDate="2013-07-14T15:53:11.847" LastActivityDate="2013-08-13T20:21:47.017" Title="Suitable introductory book on Bioinformatics for a computer scientist?" Tags="&lt;bioinformatics&gt;&lt;book-recommendation&gt;" AnswerCount="4" CommentCount="10" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9104" PostTypeId="1" CreationDate="2013-07-04T13:24:25.587" Score="3" ViewCount="166" Body="&lt;p&gt;I am aligning a large number of ESTs. It seems poly-A tails show in many different ways. In addition to occurring at the very end, they can be flanked by the cloning sequence one one end, or have mismatches/errors. What is a good rule or available tools that will handle the usual cases?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few examples of the non-trivial cases I found, with their Genbank Accs:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt;EE409337&#xA;... AAAAAAAAAAAAAAAAAAAAAAAAAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTTGTC&#xA;&amp;gt;EE409340&#xA;... TTTCTACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACTTGTC&#xA;&amp;gt;EE409361&#xA;... TTGTTAAACTGAAAAAAAAAAAAAAAAAAAAAAAAAAAACCATGTCGGC&#xA;TTACTGAATTGAA&#xA;&amp;gt;EE420306&#xA;.... AAAAAAAGTTATGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGAAAAAAA&#xA;AAAAAAAAAAAAAAAAA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Cross-posted on &lt;a href=&quot;http://seqanswers.com/forums/showthread.php?t=31628&quot; rel=&quot;nofollow&quot;&gt;SeqAnswers&lt;/a&gt;,&lt;a href=&quot;http://www.biostars.org/p/76043&quot; rel=&quot;nofollow&quot;&gt;Biostars&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3922" LastEditorUserId="3922" LastEditDate="2013-07-05T23:01:03.927" LastActivityDate="2013-07-10T18:57:07.623" Title="Good poly-A filtering rules or tools" Tags="&lt;bioinformatics&gt;&lt;rna-sequencing&gt;&lt;sequence-analysis&gt;" AnswerCount="0" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="9105" PostTypeId="2" ParentId="9100" CreationDate="2013-07-04T14:05:46.803" Score="1" Body="&lt;p&gt;Inner hair cells (IHC) do not fire action potentials themselves. It's the auditory-nerve that synapses with IHC that generates action potentials. The firing rate of the auditory nerve can be as high as few hundred Hz with a refractory period as short as 1 ms or so (depends on the animal).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it is important to note that the signal is not sampled at this rate. As you may know, the auditory signal is first transformed to the &quot;frequency&quot; domain through the physical structure of cochlea. Each inner hair cell therefore is roughly only encoding the relative strength of a frequency band. There are presumably inner hair cells in the human cochlea that correspond to a range centered around 18 kHz for example, but neither the neurotransmitters of the corresponding IHC nor the auditory nerve can fire at 18 kHz. Nevertheless, the amplitude modulation at this high frequency is what is transmitted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, thinking of neural firing as a &quot;&lt;em&gt;sampling period&lt;/em&gt;&quot; is not always a good analogy. There are debates about this, but it could be that precise timing of action potential carries large amount of information about the stimulus (perhaps not so much so in early auditory system.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to see some computational modeling work for inner ear, IHC, and auditory nerve, I recommend the Meddis IHC model:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;C. J. Sumner, E. A. Lopez-Poveda, L. P. O'Mard, R. Meddis. A revised model of the inner-hair cell and auditory-nerve complex, J. Acoust. Soc. Am. 111 (5) 2002&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="460" LastEditorUserId="107" LastEditDate="2013-07-04T14:26:58.287" LastActivityDate="2013-07-04T14:26:58.287" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9106" PostTypeId="2" ParentId="9095" CreationDate="2013-07-04T14:36:59.367" Score="0" Body="&lt;p&gt;Addition to Jack Adley's answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolutionarily, mitochondria are thought to be descended from α-proteobacterium (&lt;em&gt;Rickettsia&lt;/em&gt; are also descendants of this bacterium). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are evidences that &lt;a href=&quot;http://www.nature.com/nature/journal/v492/n7427/pdf/nature11681.pdf&quot; rel=&quot;nofollow&quot;&gt;nuclear genes have also been imported to organellar minigenome&lt;/a&gt;. This can also happen because of recombination. I am not sure about the case of mitochondria, though. Since the current hypothesis is that organeller DNA that got leaked because of organeller damage, got incorporated in the nuclear genome, there not much of a likelihood that active recombination takes place between the two. However inter-mitochondrial recombinations have been &lt;a href=&quot;http://www.uam.es/personal_pdi/ciencias/genhum/biblioparte2/recombinacenmitocond.pdf&quot; rel=&quot;nofollow&quot;&gt;reported&lt;/a&gt;, which perhaps happen during mitochondrial fusions. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-07-04T14:36:59.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9107" PostTypeId="1" AcceptedAnswerId="9166" CreationDate="2013-07-04T20:24:46.727" Score="7" ViewCount="513" Body="&lt;p&gt;What causes autism? &#xA;By this &lt;strong&gt;I don't mean what is to blame&lt;/strong&gt; i.e. Vaccines, Gluten or Pharmaceuticals etc.. I mean &lt;strong&gt;what exactly is happening in the brain&lt;/strong&gt; to cause the autistic behaviors such as little to no communication skills, regression of skills around age 3, hand flapping etc..&#xA;I see a lot of research looking for something to blame however I see little to no research on identifying the physical causes or links (maybe I'm not using the correct search terms).&lt;/p&gt;&#xA;" OwnerUserId="3935" LastEditorUserId="1590" LastEditDate="2013-07-08T11:30:14.877" LastActivityDate="2018-11-27T11:27:25.690" Title="What causes autism?" Tags="&lt;brain&gt;&lt;neurodegenerative-disorders&gt;" AnswerCount="5" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9108" PostTypeId="2" ParentId="9107" CreationDate="2013-07-04T20:56:05.923" Score="4" Body="&lt;p&gt;While still not entirely clear as to what causes autism, there is a growing body of research (as jonsca said), and a model is being developed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A suggested explanation from &lt;a href=&quot;http://www.autism.net.au/Autism_causes.htm&quot; rel=&quot;nofollow&quot;&gt;&quot;Causes of Autism Spectrum Disorders&quot;&lt;/a&gt;, that the disorder may begin in utero, with the interaction of genes and nutrients. However, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;recent research suggests that Autism may result when a child with a genetic susceptibility and/ or abnormal Omega-3 fatty acid profile in cell membranes is exposed to one or more environmental insults (heavy metal exposure, virus or bacteria) resulting in malfunctioning cells (often in the gut and brain). This can happen “in utero” (during pregnancy) or after birth (post-partum).&#xA;  (from the first link).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Genes seem to certainly play a role, as in the article &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16252243&quot; rel=&quot;nofollow&quot;&gt;&quot;Support for the homeobox transcription factor gene ENGRAILED 2 as an autism spectrum disorder susceptibility locus.&quot;&lt;/a&gt; (Benayed et al. 2005), the homeodomain transcription gene EN2 are associated with Autism, associated with about 40% of the people they tested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disorders in the serotonergic system have also been found to be a mechanism of autism, according to &lt;a href=&quot;http://journals.lww.com/psychgenetics/Abstract/2009/06000/Serotonin_transporter_genotype_and_neuroanatomy_in.6.aspx&quot; rel=&quot;nofollow&quot;&gt;&quot;Serotonin transporter genotype and neuroanatomy in autism spectrum disorders&quot;&lt;/a&gt; (Raznahan et al. 2009).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this goes part of the way in answering your question.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-07-04T20:56:05.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9109" PostTypeId="2" ParentId="9095" CreationDate="2013-07-04T21:03:01.487" Score="0" Body="&lt;p&gt;Mitochondrial chromosomes do not undergo recombination. They replicate their DNA in an asexual manner, producing identical copies (except for the occasional mutation).  Mitochondria do not exchange or transfer DNA between themselves as they have no mechanism for that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Very rarely a piece of DNA might get out of a mitochondrion and into another or into the cell's nucleus.  The latter type of transfer is believed have happened multiple times in the more than a billion years eukaryotic cells have existed.  Most of the genes needed for  mitochondrial functioning are located in the nucleus, not in the mitochondria, and many of those genes probably had such a mitochondrial source. Having mitochondrial genes in the nuclear genome is advantageous, exactly because it allows them to undergo recombination and thereby allows improvements to spread through a population of organisms.  &lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2013-07-04T21:03:01.487" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9110" PostTypeId="1" CreationDate="2013-07-04T21:11:56.917" Score="2" ViewCount="50" Body="&lt;p&gt;Antibiotic peptides are present in almost all multicellular eukaryotes. So can they be called antibiotics ? ( which are usually defined only for fungi and bacteria )&lt;/p&gt;&#xA;" OwnerUserId="3936" LastActivityDate="2013-07-05T05:14:14.753" Title="Can antimicrobial peptides be called antibiotics?" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9111" PostTypeId="1" CreationDate="2013-07-04T22:25:41.373" Score="2" ViewCount="313" Body="&lt;p&gt;I just wanted to understand the basic steps behind the replication of the lagging strand of DNA:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Have helicase unwind it first&lt;/li&gt;&#xA;&lt;li&gt;DNA Primase lays down RNA primers in fragments, called Okazaki fragments&lt;/li&gt;&#xA;&lt;li&gt;DNA polymerase III goes through and corrects all the mistakes (essentially replace the Uracil with Thymine)&lt;/li&gt;&#xA;&lt;li&gt;DNA polymerase I goes through and removes RNA primer&lt;/li&gt;&#xA;&lt;li&gt;DNA ligase hooks up each of the 5' to 3' end fragments&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Is this the correct order of steps? If so, does the leading strand need any RNA primer or does the DNA polymerase just start and go to the end without any help?&#xA;Thanks&lt;/p&gt;&#xA;" OwnerUserId="3937" LastActivityDate="2013-07-05T09:04:54.343" Title="DNA Replication" Tags="&lt;dna&gt;&lt;proteins&gt;&lt;rna&gt;&lt;polymerase&gt;&lt;replication&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9113" PostTypeId="2" ParentId="9085" CreationDate="2013-07-05T00:16:48.743" Score="14" Body="&lt;p&gt;I think the issue with Intelligent Design is not so much that its patently proven wrong.  On the contrary, the problem is that it not a scientific hypothesis and so it really isn't a scientific question.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I may, the basis of the scientific method, as formulated by Karl Popper, but commonly in use today, is that science is the putting forth of theories of cause and effect which are &lt;a href=&quot;http://en.wikipedia.org/wiki/Testability&quot; rel=&quot;nofollow&quot;&gt;testable&lt;/a&gt; (or if we are being precise, &lt;a href=&quot;http://en.wikipedia.org/wiki/Falsifiability&quot; rel=&quot;nofollow&quot;&gt;falsifiable&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is to say, you put forth a theory such as 'God/some diety figure made all living things' and then you perform an experiment which can differentiate whether the hypothesis or its null version (i.e. 'no intelligence is the source of life / biology is the result of accidents') is more likely true.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question will not be testable in a way to answer enough of the reasonable skeptical questions ( or at least so far it has not).  Experiments have been tried, but they are often not acceptable to everyone.  For instance the idea that some biological structures such as the eye or the flagellar motor are too complex to have evolved through a typical Darwinian process which involves a series of small changes are almost biological theology - one can always hypothesize a more inhuman God (probably appropriate) who acts and 'thinks' in such an inhuman manner that anything you see could be created/inspired.  While I think you should feel free to believe either way, I also believe that this is not an argument that can be won or lost.  The tendency for any experiment to confirm both the hypothesis and its inverse seem inescapable.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is to say, that biology and physics will ultimately fail where philosophy and logic also did in proving the existence of God, besides the less interesting truism that if God does exist, the deity is consistently elusive to proof.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other side of the coin, the proof that life has emerged from naturally occurring phenomena such as lighting strikes in a prebiotic environment are interesting since it shows that nucleotides and amino acids might have been available without metabolic pathways to synthesize them.  In its way, the molecular origins of life on earth is a question which is really testable only in theory.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyone who thinks they are going to re-create the event of the beginning of life itself is scientifically on thin ice - the prebiotic environment may have extended to the entire surface and atmosphere of the earth as well as down into mud and bodies of water and sat incubating for maybe hundreds of millions of years.  The idea that the fundamental moment of life generation is just going to show up on a well chosen set of conditions in a 500 ml flasks with some electrodes attached is an idea that workers in the field don't even entertain.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Until such an experiment produces life, the work will have to rely upon the idea that there was a moment in time where the necessary elements came together.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This being said, cosmology, biogenesis work has approached the moment of the genesis of life asymptotically with amazing clarity.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://exploringorigins.org/ribozymes.html&quot; rel=&quot;nofollow&quot;&gt;RNAWorld&lt;/a&gt; hypothesis strongly supports the idea that an early biotic system might have been very simple - maybe only RNA and its four nucleotides.  Clearly after what Dawkins calls a replicator exists, then the pathway to living things as we know them is pretty easy to envision.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I should add that I'm not one of those people who think that science is everything - the trend that is impoverishing some humanities program is alarming to me.  Its just that some things are not science. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2015-03-11T03:19:31.820" LastActivityDate="2015-03-11T03:19:31.820" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9115" PostTypeId="2" ParentId="8946" CreationDate="2013-07-05T01:20:25.640" Score="4" Body="&lt;p&gt;What we have here appears to be clustered insect eggs, and examples such as this tend to have some type of moth or butterfly as the culprit. It appears similar to moth eggs that I have observed on surfaces. See &lt;a href=&quot;http://www.learnaboutbutterflies.com/Lifecycle.htm&quot; rel=&quot;nofollow&quot;&gt;this page&lt;/a&gt; with information and &lt;a href=&quot;http://entnemdept.ufl.edu/creatures/veg/leaf/saltmarsh_caterpillar.htm&quot; rel=&quot;nofollow&quot;&gt;this page&lt;/a&gt; with an example that look vaguely similar to your photograph. You would need an expert to identify a specific species though, if it's possible.&lt;/p&gt;&#xA;" OwnerUserId="3920" LastActivityDate="2013-07-05T01:20:25.640" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9117" PostTypeId="2" ParentId="9110" CreationDate="2013-07-05T05:14:14.753" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1383011&quot; rel=&quot;nofollow&quot;&gt;Antibiotic peptides are definitely antibiotics&lt;/a&gt;.  They are often referred to more specifically as peptides because the fact implies that they are less toxic and conveys some important understanding of how they work.  Not sure if they all form pores in the target cell, but that's how magainins work.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-07-05T05:14:14.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9118" PostTypeId="2" ParentId="9111" CreationDate="2013-07-05T09:04:54.343" Score="1" Body="&lt;p&gt;I think that you have a couple of points wrong. Since your question is asked using bacterial terminology, I'll stick to that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The leading strand, the one that is initiated at the origin of replication, is synthesised by pol III which is a highly processive polymerase, i.e. it keeps on going for long periods, making very long products. In principle a single pol III molecule could produce the entire leading strand copy of the template.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lagging strand is, as you say, initiated at multiple RNA primers. The enzyme that extends these primers is pol I. As polI  extends a primer it creates an Okazaki fragment (i.e. this is not an alternative name for the primer itself). Eventually the pol I will encounter the 5' end of another RNA primer. At this point the 5'&gt;3' exonuclease activity of the pol I comes into play and removes the primer, replacing it with DNA. The pol I will probably also degrade some of the DNA that has been added to that primer by another pol I, resynthesising it as it goes. This is so-called &quot;nick tranlation&quot; since as the pol I moves along the template it moves a nick in the new strand as it goes. pol I is not a very processive enzyme however and will fall off, leaving the nick to be sealed by DNA  ligase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The leading strand does require a primer, and in most cases this is an RNA laid down by the initiation complex at the origin of replication. In some cases, a protein provides an -OH  group for DNA polymerase to initiate at. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-07-05T09:04:54.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9119" PostTypeId="1" AcceptedAnswerId="9123" CreationDate="2013-07-05T10:32:43.673" Score="2" ViewCount="5888" Body="&lt;p&gt;I've recently read a little on Wikipedia about genetics, but I can't find a direct answer to this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My rough understanding is this:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Both males and females have pairs of chromosomes, one copy from each parent&lt;/li&gt;&#xA;&lt;li&gt;Both produce gametes (eggs in females, sperm in males)&lt;/li&gt;&#xA;&lt;li&gt;The gamete is produced during something called 'meiosis' to take only one set of genes&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;What I can't find an answer to though is whether that selection is completely random, such that every chromosome in a gamete has an equally likely chance of being taken from the male parent set and the female parent set.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way of putting it, perhaps: Would the range of 100% male parent to 100% female parent chromosome selection in the gamete be a binomial distribution?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My background is computing, so please assume very little knowledge of biology.&lt;/p&gt;&#xA;" OwnerUserId="3939" LastActivityDate="2014-07-15T16:13:01.950" Title="Are chromosomes from each parent split between gametes with equal probability (esp. in humans)?" Tags="&lt;genetics&gt;&lt;reproduction&gt;" AnswerCount="4" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9120" PostTypeId="1" AcceptedAnswerId="9133" CreationDate="2013-07-05T10:47:37.167" Score="7" ViewCount="1013" Body="&lt;p&gt;DNA replication is more accurate than transcription (or RNA replication) because mechanisms exist for proof-reading and repair of DNA, but not for RNA.&#xA;Consider a segment of a DNA strand, AGTC. Its complement is GACT. Now suppose its complement is mutated to TACT — the DNA repair system will replace the wrong T by G. Why isn’t A in the original strand replaced by C? How does the system determine that the first strand is correct and its complement is incorrect? &lt;/p&gt;&#xA;" OwnerUserId="1011" LastEditorUserId="22057" LastEditDate="2016-06-25T12:03:17.820" LastActivityDate="2016-08-31T11:48:44.840" Title="In DNA repair, how is it determined which strand contains the error?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;molecular-genetics&gt;&lt;dna-repair&gt;" AnswerCount="4" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9121" PostTypeId="2" ParentId="9119" CreationDate="2013-07-05T10:49:32.503" Score="0" Body="&lt;p&gt;Yes, every chromosome in gamete has an equal probability of being taken from the male parent set and the female set.&lt;/p&gt;&#xA;" OwnerUserId="3940" LastActivityDate="2013-07-05T10:49:32.503" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9122" PostTypeId="2" ParentId="9119" CreationDate="2013-07-05T10:53:41.410" Score="1" Body="&lt;p&gt;Yes, for all intents and purposes, the assorting of chromosomes during meiosis is random. In fact, it's difficult to imagine a mechanism by which the chromosomes would assort in any &lt;em&gt;non-random&lt;/em&gt; manner (i.e., how would the maternal chromosomes &quot;identify&quot; each other so as to assort together during meiosis?)&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastActivityDate="2013-07-05T10:53:41.410" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9123" PostTypeId="2" ParentId="9119" CreationDate="2013-07-05T10:58:27.417" Score="6" Body="&lt;p&gt;Other answers are correct in their own terms, but because of homologous recombination during meiosis, the idea of maternal and paternal chromosomes becomes meaningless. Any chromosome in a gamete will be a mosaic of the maternal and paternal versions. In this sense the chromosome is not the unit of inheritance.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-07-05T10:58:27.417" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9124" PostTypeId="2" ParentId="9120" CreationDate="2013-07-05T11:03:17.683" Score="1" Body="&lt;p&gt;Your specific scenario is not realistic, thymine is a pyrimidine base while guanine is a purine base. They are very different chemically and can't spontaneously convert into each other. So this is a type of damage that only occurs during the replication of DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The typical damage that occurs and can be repaired is oxidation, methylation and hydrolysis of DNA. This kind of damage results in modified or missing bases and can be detected due to that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might also be interested in &lt;a href=&quot;https://biology.stackexchange.com/a/172/6&quot;&gt;why thymine is used in DNA instead of uracil&lt;/a&gt;, as uracil can be easily damaged in a way that would not be detectable.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2013-07-05T11:03:17.683" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9125" PostTypeId="1" AcceptedAnswerId="14770" CreationDate="2013-07-05T11:17:18.757" Score="6" ViewCount="554" Body="&lt;p&gt;From my limited knowledge of science, I know transformation can be one of the hardest step in cloning, and that a large amount of research/trial and error has been done to improve on this step. I've heard electroporation is the most efficient technique, though I have no reference, and of course the cell, media and duration all have vital parts to play in the process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I've never heard of supercoiling as an important factor. Size of the plasmid plays a large part in transformation, so intuitively it makes me think supercoiling the plasmid prior to transformation would improve the efficiency. I thought transformation was simply DNA diffusing through holes, but are parts of the plasmid required to bind/interact with the host?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why aren't we suggested we supercoil prior to transformation? I have several thoughts but I'm just guessing:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Is it because gyrase can disrupt the integrity of DNA?&lt;/li&gt;&#xA;&lt;li&gt;Or is it that it's just an expensive enzyme and the gain isn't worth it?&lt;/li&gt;&#xA;&lt;li&gt;Or perhaps supercoiling reduces efficiency of subsequent plasmid preps/transcription (though wouldn't the host's natural enzymes supercoil anyway?)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3942" LastEditorUserId="16460" LastEditDate="2017-04-01T08:13:43.397" LastActivityDate="2017-04-01T08:13:43.397" Title="Improving transformation efficiencies- induce supercoiling?" Tags="&lt;cell-biology&gt;&lt;transformation&gt;&lt;supercoiling&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9126" PostTypeId="1" AcceptedAnswerId="9127" CreationDate="2013-07-05T12:45:10.627" Score="2" ViewCount="130" Body="&lt;p&gt;Could an ant colony have 2 or more &quot;branches&quot; located far from each other (i.e. physically separated but interconnected nests) ? If so, how far is the limit?&lt;/p&gt;&#xA;" OwnerUserId="3141" LastEditorUserId="3624" LastEditDate="2013-07-05T14:45:04.430" LastActivityDate="2013-07-05T14:45:04.430" Title="Can ant colonies have two &quot;branches&quot;?" Tags="&lt;entomology&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9127" PostTypeId="2" ParentId="9126" CreationDate="2013-07-05T13:24:00.650" Score="7" Body="&lt;p&gt;Yes, sub- or satellite colonies are common in many species (see e.g. &lt;a href=&quot;http://books.google.no/books/about/The_Ants.html?id=ljxV4h61vhUC&amp;amp;redir_esc=y&quot;&gt;Hölldobler &amp;amp; Wilson, 1990&lt;/a&gt;; &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2007.00728.x/pdf&quot;&gt;Debout et al. 2007&lt;/a&gt;), and these are then labelled as polydomous species. Subcolonies can either contain extra queens, but sometimes only contain foraging workers. The purpose can be both to expand foraging grounds or as a pre-stage for colony budding. The distance between colonies can differ dramatically between species, but there are cases of &lt;a href=&quot;http://sciencenordic.com/ants-supercolonies-defy-evolution&quot;&gt;supercolonies&lt;/a&gt; (especially in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Argentine_ant&quot;&gt;Argentine ant&lt;/a&gt;) streching over hundreds of square kilometers (&lt;a href=&quot;http://beheco.oxfordjournals.org/content/early/2012/04/13/beheco.ars043.full?sid=8eb4e726-93bc-48a9-ad8f-bd8c423b0278&quot;&gt;Moffett 2012&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Satellite colonies are also common in e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Carpenter_ant&quot;&gt;Carpenter ants (&lt;em&gt;Camponotus&lt;/em&gt;)&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Formica_rufa&quot;&gt;wood ants (e.g. &lt;em&gt;Formica rufa&lt;/em&gt;)&lt;/a&gt;, and when colonies are found inside a house there is often a primary colony somewhere outside the building (see e.g. &lt;a href=&quot;http://www.ext.colostate.edu/pubs/insect/05518.html&quot;&gt;Ants in the home&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-07-05T13:57:52.113" LastActivityDate="2013-07-05T13:57:52.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9128" PostTypeId="2" ParentId="9102" CreationDate="2013-07-05T13:29:51.510" Score="3" Body="&lt;p&gt;Systems biology and bioinformatics are quite diverse subjects, but here are some options:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Biological Sequence Analysis&lt;/strong&gt; by Durbin et al.: the classic bioinformatics text for people with a CS background. Does not deal with networks.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;An Introduction to Systems Biology&lt;/strong&gt; by Uri Alon: A physicist's view of systems biology, focusing on design principles and networks. Interesting concepts and some math (no algorithms). Doesn't really deal with methodology.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Physical Biology of the Cell&lt;/strong&gt; by Phillips et al.: Nice introduction to biophysics and quantitative biology (no algorithms). Many parts are relevant for systems biology.&lt;/li&gt;&#xA;&lt;li&gt;Any diverse Machine Learning text will be relevant and many have examples from biology/bioinformatics.&lt;/li&gt;&#xA;&lt;li&gt;Probabilistic Graphical Models are also quite popular in bioinformatics (e.g. Hidden Markov Models, Expectation-Maximization, Bayesian Networks). &lt;strong&gt;Probabilistic Graphical Models&lt;/strong&gt; by Koller et al. is a very comprehensive CS book on the subject.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Another suggestion is to look for primers/reviews in relevant journals. This is important because the field is new, so once a new technology is developed, it takes time until the appropriate computational methodology is developed enough to make it into a text book. Also, they can point you to relevant research papers. For example, PLoS Computational Biology has an &lt;a href=&quot;http://www.ploscollections.org/article/browse/issue/info%3adoi/10.1371/issue.pcol.v03.i02&quot; rel=&quot;nofollow&quot;&gt;Education Collection&lt;/a&gt; which features a large variety of such reviews.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2013-07-07T17:55:50.200" LastActivityDate="2013-07-07T17:55:50.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9130" PostTypeId="1" CreationDate="2013-07-05T15:21:56.477" Score="2" ViewCount="37" Body="&lt;p&gt;Is there any example of currently living organisms that shows close resemblance to both being a plant and an animal?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the plant with the closest possible resemblance to animals, and&#xA;What is the animal with the closest possible resemblance to plants?&lt;/p&gt;&#xA;" OwnerUserId="3350" LastActivityDate="2013-07-05T15:21:56.477" Title="Living organisms with properties similar to both plants and animals?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;botany&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2013-07-05T15:44:11.223" ContentLicense="CC BY-SA 3.0" />
  <row Id="9131" PostTypeId="2" ParentId="7302" CreationDate="2013-07-05T16:07:10.197" Score="8" Body="&lt;p&gt;I was all set to answer anothervquestion which has now been marked as a duplicate of this one. My answer adds new information relevant to the accepted answer here, so I have decided to post it here..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One longstanding candidate for something approaching this idea is the green sea slug &lt;em&gt;Elysia chlorotica&lt;/em&gt; which uses chloroplasts derived from the alga &lt;em&gt;Vaucheria litorea&lt;/em&gt;. Various pieces of evidence have indicated that the longevity of these chloroplasts in cells of the sea slug's digestive tract is explained by the presence of algal genes that have been transferred to the mollusc genome. However the most recent analysis of germline DNA  in the sea slug has revealed no evidence for such horizontal gene transfer. It seems that all of the evidence for algal genes and algal gene expression in the sea slug must now be explained in terms of somatically-acquired algal DNA.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://mbe.oxfordjournals.org/content/early/2013/05/02/molbev.mst084&quot; rel=&quot;noreferrer&quot;&gt;Bhattacharya &lt;em&gt;et al.&lt;/em&gt; (2013) Genome Analysis of Elysia chlorotica Egg DNA Provides No Evidence for Horizontal Gene Transfer into the Germ Line of This Kleptoplastic Mollusc. &#xA;  Mol. Biol. Evol. epub ahead of print&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="10456" LastEditDate="2015-03-19T19:20:25.923" LastActivityDate="2015-03-19T19:20:25.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9133" PostTypeId="2" ParentId="9120" CreationDate="2013-07-05T18:04:34.650" Score="3" Body="&lt;p&gt;The reason the fact it isn't realistic is important. DNA repair machinery works by repairing common errors that occur due to common mutational pathways. The enzymes are specific for this, for example one particular enzyme targets mutations caused by UV and itself is activated by sunlight thus it's specificity makes it repair the correct chain. Also during replication, newly synthesised DNA lacks methylation. The repair enzymes thus know which chain is correct. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-07-05T18:04:34.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9134" PostTypeId="1" AcceptedAnswerId="9142" CreationDate="2013-07-05T18:11:25.547" Score="9" ViewCount="2979" Body="&lt;p&gt;I found this wonderful creature in my yard (I live in the south of France) last night:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jiKdD.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jKdQn.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was about 2-3cm long, with a hard carapace and wings. It also made loud hissing noises when agitated. I am curious as to what species this is, I'm quite surprised I'd never seen it before cause the beastie is quite large and last night I found it because of the &lt;em&gt;noise&lt;/em&gt; it was making. It was upside down and hissing like a kettle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More than the specific species' name, I am curious as to what the large antennae are for. Does their shape and size somehow increase the beetle's sensitivity to whatever stimuli these are atuned to? &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Alan Boyd's comment below helped me along a bit. I seem to have found a close relative of the ten-lined June beetle (Polyphylla decemlineata) pictured below (image &lt;a href=&quot;http://waynesword.palomar.edu/ww0502.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AtaM7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2015-06-17T14:57:10.260" LastActivityDate="2015-06-17T14:57:10.260" Title="What is this beetle and what are the strange antennae for?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9136" PostTypeId="2" ParentId="9053" CreationDate="2013-07-05T21:41:20.017" Score="3" Body="&lt;h2&gt;Ubiquitin and the UPS&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The ubiquitin proteasomal system (UPS) is a common method of regulation for many proteins in the cell. The modification is actually generated by E3 ubiquitin ligase, of which there are ~400-800 in the mammalian cell and the main source of specificity in the UPS (E2 ~40 and only 1 or 2 E1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ubiquitin gets its name from ubiquitous, meaning found everywhere. It's a 76 amino acid molecule that modifies proteins at lysine residues. Monoubiquitination can act as a signalling molecule whereas polyubiquitination leads to degradation. Ubiquitin is first activated via an ATP-dependent pathway to create a high energy thioester with E1. This is transthiolated to E2 and finally E3 allows the addition to the target protein. So really, your question is how E3 ubiquitin ligase recognises its target. &lt;a href=&quot;http://jcs.biologists.org/content/125/3/531.full&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;E3 ligases&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There are 3 classes of &lt;a href=&quot;http://www.chem.qmul.ac.uk/iubmb/enzyme/EC6/3/2/19.html&quot; rel=&quot;nofollow&quot;&gt;E3 ligases&lt;/a&gt;, according to whether they contain a RING, U-box or HECT domain. These domains are responsible for either directly catalysing the addition of ubiquitin or simply facilitating another E3 ligase to do so. RING and RING-like domains are by far the most common (&amp;lt;600). Exactly how these domains mediate the transmission of ubiquitin is not clear, but it can be via an E3-Ub intermediate or directly from E2 to the target. The domains are relatively standardised, due to the fact they bind to E2 proteins, which contain less diversity than target proteins. However, it's the combination of the E2 and substrate binding domains that generates the selection. &lt;a href=&quot;http://essays.biochemistry.org/bsessays/041/0015/bse0410015.htm&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Target recognition&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;So how does the target come into all of this? Each E3 ligase recognises a specific sequence on the target protein due to it's own conformation and signal sequence creating a unique interface full of intermolecular interactions- just like any protein recognises any other protein. However, although individual cases vary, the tight control primarily comes from post translational modifications on the target. Phosphorylation in particular is common in signalling and may allow E3 to bind, inducing degradation of the target. I'll use some examples to demonstrate this point, but note that every case will be different.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S009286740000057X&quot; rel=&quot;nofollow&quot;&gt;c-Cbl&lt;/a&gt; (E3) recognises activated receptor tyrosine kinases and ZAP 70/Syk kinases (target) by binding a phosphotyrosine sequence through its tyrosine kinase binding domain (containing SH2 domain). The phosphorylation is controlled by other cellular signals&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v418/n6896/full/nature00890.html&quot; rel=&quot;nofollow&quot;&gt;Glycosylation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencemag.org/content/292/5516/464&quot; rel=&quot;nofollow&quot;&gt;Proline hydroxylation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jbc.org/content/282/47/34176&quot; rel=&quot;nofollow&quot;&gt;Sumoylation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Other regulations of the process that are linked but perhaps outside the scope of your question include E3 post translational modifications (eg. autoubiquitination), sequestration of E3 via binding partners (Cand1 and Roc1), pseudosubstrates and substrate competition. &lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.biochem.78.101807.093809&quot; rel=&quot;nofollow&quot;&gt;7&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Misfolded protein degradation&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Making protein is a large investment for the cell and so there are several protective measures to prevent misfolding/aggregation. Whilst there are many different types, chaperones generally work by isolating the misfolded protein and undergoing a series of binding release steps, triggered by hydrolysis of ATP. The protein can still be released unfolded, and the cell will continually try to isolate it for refolding. However, certain chaperones form a complex with the proteasome, and can recruit other UPS components. The choice to give up on refolding appears to be a stochastic process, and will depend on the concentration of the appropriate chaperones. Misfolded proteins tend to have significant regions of exposed hydrophobic residues, and E3 ligases are therefore likely to recognise this less specifically than the degradation pathway described above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Relevant sources include &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039444/&quot; rel=&quot;nofollow&quot;&gt;endoplasmic reticulum associated degradation&lt;/a&gt; and &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022282812003641&quot; rel=&quot;nofollow&quot;&gt;chaperones&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Summary&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The answer to your question is that there is no standard recognition sequence in E3 to know which protein to target, the binding needs to be diverse in order to give the control the cell needs. That means it could be anything, but each E3 is likely to be relatively specific for its target, and is often controlled by other post translation modifications on the substrate. Misfolded proteins can be recognised and degraded due to the association of the UPS with chaperones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're really interested, you can download &lt;a href=&quot;http://www.rcsb.org/pdb/explore/explore.do?structureId=3RTR&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; file and open it in something like &lt;a href=&quot;http://www.pymol.org/&quot; rel=&quot;nofollow&quot;&gt;PyMol&lt;/a&gt; to actually see the ligase ready to transfer ubiquitin.&lt;/p&gt;&#xA;" OwnerUserId="3942" LastEditorUserId="3942" LastEditDate="2013-07-06T00:42:11.917" LastActivityDate="2013-07-06T00:42:11.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9138" PostTypeId="1" CreationDate="2013-07-06T00:32:14.263" Score="5" ViewCount="3090" Body="&lt;p&gt;Last night I came across this spider outside my house (costal Southern California). It was bigger than any I'd seen before, about 2.5 or maybe 3 inch legspan, maybe just under an inch for the body length. It is a brown-gray color, the cephalothorax has two dark brown stripes, and some mean looking fangs. Can anyone identify it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WO721.jpg&quot; alt=&quot;Head on view&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/mYeK8.jpg&quot; alt=&quot;back view&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/GHeju.jpg&quot; alt=&quot;back view with flash&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3920" LastEditorUserId="1590" LastEditDate="2013-07-30T14:05:12.913" LastActivityDate="2017-11-27T20:49:48.493" Title="What species is this large-ish spider?" Tags="&lt;species-identification&gt;&lt;arachnology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9139" PostTypeId="2" ParentId="8745" CreationDate="2013-07-06T04:31:40.707" Score="-1" Body="&lt;p&gt;While refering to an animal say &lt;em&gt;Physalia&lt;/em&gt;, we refer to its massive type colony, containing many zooids. Among the zooids, a large cup shaped float is seen, which is bright blue in color and remains above sea water normally. On the undersurface of float many gastroaooids, gonozooids and dactylozooids are present. The colony thus shows a high degree of polymorphism.&#xA;This is all I know and thus the reasoning seems to be absolutely correct...&lt;/p&gt;&#xA;" OwnerUserId="3949" LastEditorUserId="107" LastEditDate="2013-07-07T17:36:54.090" LastActivityDate="2013-07-07T17:36:54.090" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9141" PostTypeId="2" ParentId="9138" CreationDate="2013-07-06T06:40:06.937" Score="7" Body="&lt;p&gt;Looking at this reference &lt;a href=&quot;http://nature.berkeley.edu/~callobius/cbcstuff/common_spiders/big_spi_quilt.html&quot; rel=&quot;noreferrer&quot;&gt;&quot;Frequently synanthropic spiders of Southern California&quot;&lt;/a&gt;, I would have to say that it is possibly a &lt;a href=&quot;http://en.wikipedia.org/wiki/Grass_spider&quot; rel=&quot;noreferrer&quot;&gt;grass spider&lt;/a&gt;. (Please someone correct me if I am wrong).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beautiful looking specimen!&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-07-06T06:40:06.937" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9142" PostTypeId="2" ParentId="9134" CreationDate="2013-07-06T12:56:17.033" Score="12" Body="&lt;p&gt;From the pattern on the elytra (hard upper wings), it looks like you might have a beautiful male &lt;em&gt;Polyphylla fullo&lt;/em&gt;. Compare your photos with the &lt;em&gt;P. fullo&lt;/em&gt; in &lt;a href=&quot;http://www.biodiversitylibrary.org/page/27416209#page/617/mode/1up&quot; rel=&quot;noreferrer&quot;&gt;this illustration&lt;/a&gt;, or photos on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Polyphylla_fullo&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia page&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;edit to fully respond to the comments:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect you're right that the antennae plates in your picture are just tightly closed up, giving a different appearance. Here's a photo I took of a related species where you can see both appearances of the antennae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And I think that Alan Boyd is correct about the antennae being used as chemoreceptors to locate females. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Ten-lined_June_beetle&quot; rel=&quot;noreferrer&quot;&gt;wikipedia page on the Ten-Lined June Bug&lt;/a&gt; also mentions both of these points.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sGcun.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-07-06T14:54:24.797" LastActivityDate="2013-07-06T14:54:24.797" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="9143" PostTypeId="2" ParentId="7019" CreationDate="2013-07-06T13:33:39.693" Score="10" Body="&lt;p&gt;Quite a bit can be absorbed through the mouth. Most commonly, starches are broken down to maltose (two glucose molecules formed by a condensation reaction) and are easily absorbed by the bloodstream. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lot of other factors balance into this, ie pH, lipid solubility, and molecular weight. Generally, if a substance is easily dissolved in saliva, it can be administered buccally or sublingually because the only remaining step is the diffusion into the subepithelial capillaries. In regards to speed, anything properly absorbed via buccal or sublingual administration goes to work much faster than a standard oral medication, and with a higher availability in the bloodstream. You are taking first pass metabolism and enzyme breakdown in the stomach out of the equation by diffusing the drug directly into the bloodstream.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is quite a laundry list of medications that can be administered transbucally or sublingually, just a few of these:&#xA;Nitroglycerin&#xA;Acetylsalicylic acid (aspirin)&#xA;Glucose gel (as you mentioned)&#xA;Fentanyl (a narcotic painkiller)&#xA;buprenorphine (for opioid dependency)&#xA;Benzodiazepines (alprazolam, clonazepam)&lt;/p&gt;&#xA;" OwnerUserId="3370" LastActivityDate="2013-07-06T13:33:39.693" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9144" PostTypeId="1" AcceptedAnswerId="9145" CreationDate="2013-07-06T15:15:26.213" Score="1" ViewCount="41" Body="&lt;p&gt;I have came to know that taking a lot of stress increases the risk of Diabetes, and patients of Diabetes are adviced not to take too much stress, am i correct? if yes then I am unable to understand that how stress affects the level of glucose in our blood?&lt;/p&gt;&#xA;" OwnerUserId="3881" LastActivityDate="2013-07-06T15:27:27.483" Title="Preventing Diabetes by preventing stress?" Tags="&lt;pathology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9145" PostTypeId="2" ParentId="9144" CreationDate="2013-07-06T15:27:27.483" Score="3" Body="&lt;p&gt;Prolonged stress leads to elevated levels of &lt;a href=&quot;https://en.wikipedia.org/wiki/Cortisol&quot; rel=&quot;nofollow&quot;&gt;cortisol&lt;/a&gt;. Cortisol interacts with insulin action and blood glucose levels in various ways, essentially promoting hyperglycaemia. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-07-06T15:27:27.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9148" PostTypeId="2" ParentId="8745" CreationDate="2013-07-06T23:47:03.037" Score="6" Body="&lt;p&gt;It seems like your question might contain two separate and linked issues, both of which are perhaps equally confusing and equally interesting. They're both really discussion questions in a sense, but they've also both been dealt with in the literature in thoughtful ways, so here's a stab at an &quot;answer&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Issue One:&lt;/strong&gt; how does your &lt;strong&gt;species concept&lt;/strong&gt; deal with polymorphism?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This may depend on &lt;em&gt;which&lt;/em&gt; species concept you're using. And, to some extent, the choice of which species concept you use depends on what kind of organism you're dealing with (for instance, organisms that reproduce asexually have a whole different set of issues and challenge several species concepts). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Various papers by Kevin de Queiroz deal very well with species concepts. In '&lt;a href=&quot;http://si-pddr.si.edu/jspui/bitstream/10088/4652/1/VZ_1998deQueirozEndlessForms.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;The General Lineage Concept of Species&lt;/a&gt;'  (which is also summarized &lt;a href=&quot;http://evobiojournalclub.wordpress.com/2013/01/30/paper-summary-de-queiroz-1998/&quot; rel=&quot;nofollow noreferrer&quot;&gt;on this page&lt;/a&gt;), he argues that although there are many different species concepts that can be better applied to different situations, they all share the basic tenet of defining a &quot;segment of a population-level lineage&quot;. In other words, each concept is attempting to put a continuum into slightly different categorical bins, but they all recognize the existence of the same continuum (the lineage). (Also see his &lt;a href=&quot;http://sysbio.oxfordjournals.org/content/56/6/879.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;'Species Concepts and Species Delimitation'&lt;/a&gt;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think most species concepts have no trouble dealing with polymorphism because the different morphs are all part of the same &lt;em&gt;lineage&lt;/em&gt;, that is, &quot;a series of entities forming a single line of direct ancestry and descent&quot; (de Queiroz 1999).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Issue Two:&lt;/strong&gt; how does your &lt;strong&gt;concept of the individual organism&lt;/strong&gt; deal with colonialism?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://www.eebweb.arizona.edu/grads/mherron/publications/BR_08.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;'Does Biology Need an Organism Concept?'&lt;/a&gt;  Pepper and Herron make a similar point to that of de Queiroz. They argue that multiple definitions (concepts) exist, and that these concepts all attempt to categorically bin what is in fact a continuum. Like de Quieroz, they argue that most definitions recognize the same underlying continuum, and that the difference is in the categorical bins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of the organism concept, this continuum is based on two criteria: increasing &lt;strong&gt;genetic homogeneity&lt;/strong&gt;, and increasing &lt;strong&gt;physiological integration&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, for instance you could have two organism concepts (in the picture below, lighter yellow and darker yellow) that agree that &lt;em&gt;Physalia&lt;/em&gt; falls in the same location along these axes, but disagree on exactly where to draw the boundary between their &quot;multiple organisms / colony&quot; zone (yellow), and their &quot;individual organism&quot; zone (white).&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ZeESC.jpg&quot; alt=&quot;after Pepper and Herron&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll finally get to my point, paraphrasing both de Queiroz and Pepper and Herron. For both concepts of the species and of the organism, arguing about whether one concept is better than another is endless (especially on a site that aims at answers rather than discussion). However, recognizing that there &lt;em&gt;are&lt;/em&gt; different concepts, understanding that what these concepts do is to bin the same continuum in different ways, and being &lt;strong&gt;clear about which concept you decide to use&lt;/strong&gt; is very useful.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-05-08T16:34:19.100" LastActivityDate="2014-05-08T16:34:19.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9149" PostTypeId="2" ParentId="9102" CreationDate="2013-07-07T03:01:35.280" Score="1" Body="&lt;p&gt;For my bioinformatics class a few years ago, we used these:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;b&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0805346333&quot; rel=&quot;nofollow&quot;&gt;Fundamental Concepts of Bioinformatics&lt;/a&gt;&lt;/b&gt; - Krane and Raymer&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Was excellent as an intro text. Explained a lot of the biological concepts while it was teaching you the methods. Useful either for biologists or computer scientists bridging into bioinformatics. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;b&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1441923020&quot; rel=&quot;nofollow&quot;&gt;Statistical Methods in Bioinformatics&lt;/a&gt;&lt;/b&gt; - Ewens and Grant&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The go to book for more comprehensive coverage of algorithms and applications. Did a good job covering the details of a method, like dynamic programming, from start to finish.  Much more computer science oriented.&lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-07-07T03:01:35.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9152" PostTypeId="1" CreationDate="2013-07-07T10:34:30.317" Score="2" ViewCount="1381" Body="&lt;p&gt;Have anyone used realtime PCR, is that the plate for realtime PCR is one-time using or not ? Otherwise how to clean the plate after reaction to prevent wrong result in next time using ? &lt;/p&gt;&#xA;" OwnerUserId="3894" LastActivityDate="2014-08-18T13:09:02.927" Title="Realtime PCR plate cleaning" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9153" PostTypeId="1" AcceptedAnswerId="9164" CreationDate="2013-07-07T12:20:29.310" Score="1" ViewCount="131" Body="&lt;p&gt;I always hear the pseudo-evolutionary claim &quot;plants are green because they need to use red and blue light&quot;.  If this premise to my question is true,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What (if any) other functional relationship occur between the color of the blossom of the flower or the color of the leaves in the fall, and the spectrum of the sun.  Could it be said that plants are actively absorbing a particular spectrum for a particular purpose by expressing particular colors other than green?&lt;/p&gt;&#xA;" OwnerUserId="1853" LastEditorUserId="3971" LastEditDate="2013-08-29T14:21:23.357" LastActivityDate="2013-08-29T14:21:23.357" Title="Do non-green flower colors have any functional interactions with the sun?" Tags="&lt;botany&gt;&lt;pigmentation&gt;&lt;light&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9154" PostTypeId="1" AcceptedAnswerId="9158" CreationDate="2013-07-07T14:36:49.763" Score="4" ViewCount="2991" Body="&lt;p&gt;A person wih blood group O is called a Universal Donor. Well, his plasma contains antibodies A and B. During blood donation, if blood group O is given to a person with blood group A (since blood group O can be donated to all the blood groups) then wouldn't the antibodies of the donor with blood group O harm the recipient?&#xA;Although nowadays doctors prefer giving blood having 100 percent compatibility...&lt;/p&gt;&#xA;" OwnerDisplayName="user3800" LastEditorDisplayName="user3800" LastEditDate="2013-07-07T15:47:45.343" LastActivityDate="2014-09-14T14:39:45.940" Title="Antigen Antibody reactions during blood donation" Tags="&lt;hematology&gt;&lt;antibody&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9155" PostTypeId="1" CreationDate="2013-07-07T16:00:56.060" Score="2" ViewCount="97" Body="&lt;p&gt;When I searched HIV on NCBI gene bank, I found 2 results from 1997: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/?term=HIV&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/genome/?term=HIV&lt;/a&gt;. HIV can change every day, so I think the sequence from 1997 is not useful. Is it?&lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="107" LastEditDate="2013-07-07T17:35:27.443" LastActivityDate="2014-02-10T09:22:17.610" Title="Should I design a primer to detect virus based on NCBI genebank?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="9156" PostTypeId="1" AcceptedAnswerId="9162" CreationDate="2013-07-07T16:25:36.300" Score="2" ViewCount="4608" Body="&lt;p&gt;I am confused regarding the presence of valves in the superior vena cava.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The superior vena cava does not possess valves unlike inferior vena cava, which possesses Eustachian Valve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then where are Haversian valves present?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aren't they present at the opening of caval i.e., superior vena cava. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then why is it said that there is absence of valves in superior vena cava?&lt;/p&gt;&#xA;" OwnerDisplayName="user3800" LastEditorUserId="107" LastEditDate="2013-07-07T17:52:48.597" LastActivityDate="2014-02-03T06:39:05.457" Title="Valves in the heart" Tags="&lt;cardiology&gt;&lt;circulatory-system&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9157" PostTypeId="2" ParentId="9154" CreationDate="2013-07-07T16:26:59.413" Score="-1" Body="&lt;p&gt;Since a person with blood group O does not express the A and B antigens, his blood does not contain antibodies to A and B. Therefore, it is safe to transfuse into someone with type A, B, AB, or O blood.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-07-07T16:26:59.413" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9158" PostTypeId="2" ParentId="9154" CreationDate="2013-07-07T17:13:55.443" Score="9" Body="&lt;p&gt;The key feature of type O blood as &quot;universal donor&quot; is that the incoming red blood cells have neither A nor B antigens and so the resident antibodies (anti-A , anti-B) will not react with them. Since transfusions are carried out with packed red blood cells the plasma antibodies of the donor don't matter - they will not be introduced into the recipient.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-07-07T17:13:55.443" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9162" PostTypeId="2" ParentId="9156" CreationDate="2013-07-08T03:19:13.153" Score="4" Body="&lt;p&gt;The purpose of valves is to maintain blood pressure &lt;em&gt;against gravity&lt;/em&gt; until it reaches the heart. The Superior Vena Cava (SVC) inlets exist above the heart, and any valves would only prevent gravity from &lt;em&gt;helping&lt;/em&gt; bloodflow. The Tricuspid prevents blood from the SVC from just directly flowing into the Right Ventricle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a note: The Eustachian Valve &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC140300/&quot; rel=&quot;nofollow&quot;&gt;either isn't present, or is very small in most individuals&lt;/a&gt; as it's only used during development. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Haversian Valves are also found in development, if I remember correctly, and exist when the two vena cavas have yet to separate and mediate bloodflow into the Right Auricle.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-07-08T03:19:13.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9164" PostTypeId="2" ParentId="9153" CreationDate="2013-07-08T06:15:47.843" Score="4" Body="&lt;p&gt;Some functions of non-green flower colors:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;#1: plant-animal interaction&lt;/strong&gt;. Flower colors act as signals received by animals with eyes (e.g., pollinators, which many plants need to attract in order to reproduce).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it sounds from your question as if you're looking for other physiological effects. Two that come to mind are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;#2: heat&lt;/strong&gt;. Flower color and opacity have a great effect on flower temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can be especially important for arctic and alpine flowers. Many of these are not only shaped like satellite dishes, but even pivot to follow the sun. This creates a warmer micro-environment which can be important to attracting pollinators and to increasing/speeding seed production. (See, e.g. &lt;a href=&quot;http://www.jstor.org/discover/10.2307/1551519&quot; rel=&quot;nofollow&quot;&gt;Mølgaard 1989&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;#3: UV protection&lt;/strong&gt;. Certain pigments can be more effective at filtering UV.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I work in the alpine and occasionally encounter &quot;glasshouse&quot; plants, which have translucent floral parts that act to create warmer microenvironments, with the same effects as above. In addition, these floral parts have been shown to be more effective at UV filtering than green floral parts (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12884050&quot; rel=&quot;nofollow&quot;&gt;Tsukaya 2002&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*edit: as these papers are behind paywalls, I'll also point out that the Wikipedia pages on &lt;a href=&quot;http://en.wikipedia.org/wiki/Heliotropism&quot; rel=&quot;nofollow&quot;&gt;Heliotropism&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Noble_rhubarb&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Rheum nobile&lt;/em&gt;&lt;/a&gt; contain similar information.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.2307/1551519&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Mølgaard P&lt;/strong&gt;. 1989. Temperature Relations of Yellow and White Flowered &lt;em&gt;Papaver radicatum&lt;/em&gt; in North Greenland. Arctic and Alpine Research 21: 83–90.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s102650200009&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Tsukaya H&lt;/strong&gt;. 2002. Optical and anatomical characteristics of bracts from the Chinese “glasshouse” plant, &lt;em&gt;Rheum alexandrae&lt;/em&gt; Batalin (Polygonaceae), in Yunnan, China. J Plant Res 115: 59–63.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-07-08T14:20:03.460" LastActivityDate="2013-07-08T14:20:03.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9165" PostTypeId="1" AcceptedAnswerId="80421" CreationDate="2013-07-08T07:54:02.993" Score="8" ViewCount="156" Body="&lt;p&gt;I did an expression profiling from publicly available RNAseq data for mouse tissues. While for liver and testes I am getting expected proteins in the top highly expressed mRNAs, for &lt;strong&gt;brain&lt;/strong&gt; I am getting &lt;strong&gt;ferritin&lt;/strong&gt; (Ferritin heavy chain 1: &lt;em&gt;Fth1&lt;/em&gt;) as the top expressed mRNA!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a few studies which report elevated ferritin and iron in neurodegenerative diseases while some others have implicated its role in ageing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't come across any study on iron metabolism in the normal brain. Does iron metabolism play an important role in the function of the brain? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS : &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The data that I am talking about, has the SRA accession number- &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/sra/?term=SRR652247&quot; rel=&quot;noreferrer&quot;&gt;SRR652247&lt;/a&gt; &lt;em&gt;(I tried all three runs submitted in SRA)&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;The mice used in the experiment were 11 weeks old&lt;/li&gt;&#xA;&lt;li&gt;I used bowtie -&gt; eXpress for quantification of RNAseq reads.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-07-08T12:45:00.587" LastActivityDate="2019-01-10T02:14:48.423" Title="Iron metabolism in the brain" Tags="&lt;metabolism&gt;&lt;brain&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9166" PostTypeId="2" ParentId="9107" CreationDate="2013-07-08T11:25:51.310" Score="7" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fragile_X_syndrome&quot; rel=&quot;noreferrer&quot;&gt;Fragile X syndrome&lt;/a&gt; is a genetic disorder which is highly &lt;a href=&quot;http://dept.wofford.edu/neuroscience/neuroseminar/pdfFall2011/5-fragileX-autism.pdf&quot; rel=&quot;noreferrer&quot;&gt;related to autism&lt;/a&gt; and is considered to be the most common single gene association with autism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Establishing what actually happens in autistic people is difficult because it is hard to quantify someone as being autistic or not - it is common for some people to show some signs of autistic type behaviour and some people are more extreme than others - plus the symptoms are numerous:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Clinically, autism is defined by a “triad” of deficits comprising&#xA;  impaired social interaction, impaired communication, restricted&#xA;  interests, and repetitive behaviors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Wikipedia splits the mechanisms in to two key groups, &lt;a href=&quot;http://en.wikipedia.org/wiki/Autism#Pathophysiology&quot; rel=&quot;noreferrer&quot;&gt;pathophysiology&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Autism#Neuropsychology&quot; rel=&quot;noreferrer&quot;&gt;neuropsychology&lt;/a&gt;. The pathophysiological aspects are perhaps better documented and some known correlates to autism are listed:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cesa7.org/wspei/documents/EricCourchesne.pdf&quot; rel=&quot;noreferrer&quot;&gt;Excess of neurons in key brain regions&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17971078&quot; rel=&quot;noreferrer&quot;&gt;Disturbed neuronal migration during early gestation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0166223606001111&quot; rel=&quot;noreferrer&quot;&gt;Unbalanced excitatory–inhibitory networks&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0166223606001111&quot; rel=&quot;noreferrer&quot;&gt;Abnormal formation of synapses and dendritic spines&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Our understanding of the mechanisms causing autistic behaviours does not go much beyond this. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0736574804001364&quot; rel=&quot;noreferrer&quot;&gt;This paper is a review&lt;/a&gt; of the neuroanatomic associations with autism which could, at least in part, help you to identify the physical differences linked to autism.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2013-07-08T11:25:51.310" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9168" PostTypeId="2" ParentId="8176" CreationDate="2013-07-08T14:08:06.453" Score="13" Body="&lt;p&gt;Yes. The Bristlecone Pine, &lt;em&gt;Pinus longaeva&lt;/em&gt;, is one example. This species boasts the oldest individual living organisms, and also has been convincingly argued by &lt;a href=&quot;http://dx.doi.org/10.1016/S0531-5565%2800%2900234-5&quot;&gt;Lanner and Connor (2001)&lt;/a&gt; to show no evidence of senescence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the Wikipedia page on Biological Immortality (as of June 2013) unfortunately ignores plants, the pages on &lt;a href=&quot;http://en.wikipedia.org/wiki/Negligible_senescence&quot;&gt;Negligible Senescence&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_long-living_organisms&quot;&gt;Longest-lived Organisms&lt;/a&gt; list many plant seeds, clonal groups, and individuals.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/S0531-5565%2800%2900234-5&quot;&gt; &lt;strong&gt;Lanner R, Connor KF&lt;/strong&gt;. 2001. Does bristlecone pine senesce? Experimental Gerontology 36: 675–685.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-05-15T22:04:51.767" LastActivityDate="2014-05-15T22:04:51.767" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9169" PostTypeId="1" CreationDate="2013-07-08T16:11:40.820" Score="9" ViewCount="12993" Body="&lt;p&gt;It's been recurrent when I hear people saying that AIDS doesn't exist. When I ask why, they give weird reasons like HIV is a virus created to control economy and to develop medicine, etc. Also when I try to watch videos on youtube about people that are infected with this virus, I see a lot of comments saying that AIDS is a lie and some of them base their opinions on a documentary called House of Numbers. So I would like to know scientific reasons if this a myth, or why this is true.&lt;/p&gt;&#xA;" OwnerUserId="3966" LastEditorUserId="1590" LastEditDate="2013-07-09T11:43:36.447" LastActivityDate="2014-11-01T19:01:46.313" Title="Reasons why people say that AIDS/HIV doesn't exist" Tags="&lt;immunology&gt;&lt;pathology&gt;&lt;hiv&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9171" PostTypeId="2" ParentId="9169" CreationDate="2013-07-08T19:17:49.577" Score="17" Body="&lt;p&gt;I think no one can really deny the existence of HIV or AIDS, just a search on google scholar will show &lt;a href=&quot;http://scholar.google.se/scholar?q=HIV&amp;amp;btnG=&amp;amp;hl=en&amp;amp;as_sdt=0,5&quot;&gt;&gt;1,500,000 hits&lt;/a&gt; for each of those terms, and ask (hopefully any) doctor and they will say it does, though AIDS denialists do debate whether HIV causes AIDS. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S030698770400012X&quot;&gt;This paper explains the process of HIV causing AIDS&lt;/a&gt;. Further, AIDS denialists have not offered up well supported alternatives as to how AIDS arises without HIV being involved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think however that there is more debate fuelled by conspiracy theorists as to &lt;strong&gt;how the disease came about&lt;/strong&gt;. This article from &lt;a href=&quot;http://www.time.com/time/specials/packages/article/0,28804,1860871_1860876_1861031,00.html&quot;&gt;TIME magazine&lt;/a&gt; on conspiracy theories is a short piece about it, there are two main conspiracy theories:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) The west invented the disease to &lt;a href=&quot;http://en.wikipedia.org/wiki/Wangari_Maathai&quot;&gt;&quot;decimate the African population.&quot;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The US government invented the disease in the 70's and injected gay men to stop the spread of homosexuality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should read &lt;a href=&quot;http://en.wikipedia.org/wiki/House_of_Numbers_%282009_film%29#Critical_reception&quot;&gt;this section on the critical response&lt;/a&gt; to the film House of Numbers, it seems to be thought that the film was driven by funding wishing to promote conspiracy theory and interviews were edited in such a way as to help portray that message.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Caution, the following is my own personal opinion ;)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To most these seem like pretty outlandish claims and most people do ignore them - apart from anything, placing blame on someone won't stop the continuing spread of this horrendously devastating disease so the conspiracies are quite pointless. I personally think these conspiracies are driven by the uneducated, the scared, and those who want to &quot;bring down the man &amp;amp; corporate/capitalist western society led by a powerful minority&quot; etc..&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Back to the science:&lt;/em&gt; The people who discovered the disease (Dr. Robert Gallo of the National Cancer Institute and Dr. Luc Montagnier of the Pasteur Institute in Paris) along with the majority of the scientific community say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;the virus jumped from monkeys to humans some time during the 1930s&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Molecular analysis of the genetic sequence for the virus supports the theory that &lt;a href=&quot;http://www.fasebj.org/content/15/2/276.full&quot;&gt;the jump from apes to humans was around 1920-1930&lt;/a&gt;. Some other studies support the jump being made around this time though some estimate it to be a little earlier, this is due to estimated rates of mutation being used to calibrate molecular clocks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I recommend taking a look at &lt;a href=&quot;http://www.aidstruth.org/denialism/myths&quot;&gt;AIDStruth.org&lt;/a&gt; and more specifically start with &lt;a href=&quot;http://www.aidstruth.org/features/2009/real-answers-fake-questions-%E2%80%9Chouse-numbers%E2%80%9D&quot;&gt;this page&lt;/a&gt; (thanks for the link @MattDMo) if you have watched House of Numbers.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-08T21:31:01.540" LastActivityDate="2013-07-08T21:31:01.540" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9172" PostTypeId="1" AcceptedAnswerId="9174" CreationDate="2013-07-08T21:35:54.503" Score="23" ViewCount="34668" Body="&lt;p&gt;I made an answer on the Scifi.SE that can be read &lt;a href=&quot;https://scifi.stackexchange.com/questions/37780/how-did-they-clone-other-breeds-of-dinosaur-other-than-the-one-in-the-blood-of-t/37806#37806&quot;&gt;here&lt;/a&gt;. It is about how the characters in the story Jurassic Park might have gotten DNA for all the species shown.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my answer, I said this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Apes and Humans, for example, share over 99% of their genes. That means the difference between our species is less than 1% of our genes. In fact, all life on Earth shares about 50% of it's genes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;but in the original posting (before someone edited it) I chose to use the word DNA instead of genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He left this comment in the section to explain the edit:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sorry, I'm a biologist, I can't help it. Humans and apes share 99% similarity in the coding sequences of their DNA, the ~5% that codes for genes, not on all the DNA. I simplified this to genes for the answer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I have a basic high school understanding of DNA and genes, so I'm afraid I fail to see the difference between using &quot;DNA&quot; or using &quot;genes&quot; in my statement. I understand that genes are specific sequences of DNA that are used by the cell in some way. I understand that DNA is more generic, including all of the strands, whether they are used or not, whether they seem to code for something or not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So is it wrong then to say that apes and humans share 99% of their DNA or is it equally correct to say &quot;genes&quot;?&lt;/p&gt;&#xA;" OwnerUserId="3970" LastEditorUserId="-1" LastEditDate="2017-04-13T12:43:38.097" LastActivityDate="2019-08-06T22:05:59.343" Title="Do apes and humans share 99% of DNA or 99% of genes? What is the difference?" Tags="&lt;dna&gt;&lt;genetics&gt;&lt;definitions&gt;" AnswerCount="6" CommentCount="2" FavoriteCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="9173" PostTypeId="2" ParentId="9172" CreationDate="2013-07-08T21:50:46.780" Score="7" Body="&lt;p&gt;Just to clarify definitions, your &lt;a href=&quot;http://en.wikipedia.org/wiki/Genome&quot; rel=&quot;noreferrer&quot;&gt;genome&lt;/a&gt; is made up of sequences of DNA. DNA is constructed pairs of four nucleic acids, or nucleotides (A,G,T,C). That DNA has many &lt;a href=&quot;http://en.wikipedia.org/wiki/Locus_%28genetics%29&quot; rel=&quot;noreferrer&quot;&gt;loci&lt;/a&gt; within it, each codes for a gene. Loci are given gene names such as SHH (sonic hedgehog) which is part of a discipline called &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene_nomenclature&quot; rel=&quot;noreferrer&quot;&gt;gene nomenclature&lt;/a&gt;. Humans have two versions of each gene, one from each parent. These genes, such as SHH, have different variants called &lt;a href=&quot;http://en.wikipedia.org/wiki/Allele&quot; rel=&quot;noreferrer&quot;&gt;alleles&lt;/a&gt;. This is where you may have heard the terms homozygote and heterozygote, when a person has two copies of the same allele or two different ones respectively. You may remember talking about &lt;a href=&quot;http://circuitsurfersdotcom.files.wordpress.com/2011/08/sickle-cell.jpg&quot; rel=&quot;noreferrer&quot;&gt;sickle cell anemia in high school.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;So is it wrong then to say that apes and humans share 99% of their DNA or is it equally correct to say &amp;quot;genes&amp;quot;?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Well the similarity between humans and chimps in terms of known DNA sequence is about 98.8%, there is fairly low sequence divergence, so in my opinion you are right to say that they share 99% of their DNA. This means that in 100 nucleotides there is roughly one difference e.g. (showing 90 bases, made using random sample of four letters in R):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Human DNA strand:&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;atgactgtagcccatga &lt;strong&gt;t&lt;/strong&gt;&#xA;gtaaacgtaccaagcctcctcggctgtcccgaaatagatacgcctggtagacgtattaatagtgagtaa...cgt&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Chimpanzee:&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;atgactgtagcccatga &lt;strong&gt;c&lt;/strong&gt; gtaaacgtaccaagcctcctcggctgtcccgaaatagatacgcctggtagacgtattaatagtgagtaa...cgt&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Having said that, given that there is &lt;a href=&quot;http://www.genome.gov/11006943&quot; rel=&quot;noreferrer&quot;&gt;&amp;gt;3,000,000,000 base pairs in the human genome&lt;/a&gt; (the sequence of 4 nucleotides that make up the DNA) that equates to ~36,000,000 different base pairs (bnetween humans and chimps) which likely equates to a large difference. Sometimes even a single nucleotide polymorphism (SNP, pronounced snip), a change in just one base pair, can bring about quantifiable changes:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;a single base mutation in the APOE (apolipoprotein E) gene is&#xA;associated with a higher risk for Alzheimer disease.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Here is a little &lt;a href=&quot;http://www.amnh.org/exhibitions/past-exhibitions/human-origins/understanding-our-past/dna-comparing-humans-and-chimps&quot; rel=&quot;noreferrer&quot;&gt;reading on the humans vs chimp&lt;/a&gt;. You may also wish to see this similar post on &lt;a href=&quot;https://biology.stackexchange.com/questions/1981/how-many-genes-do-we-share-with-our-mother&quot;&gt;biology SE&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;But the editor of your original post is right... only the Euchromatic region has been sequenced.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&amp;quot;Humans and apes share 99% similarity in the &lt;strong&gt;coding sequences&lt;/strong&gt; of their DNA&amp;quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The euchromatic region is often thought of as the protein coding part of the DNA, and makes up &lt;a href=&quot;http://www.nature.com/nature/journal/v431/n7011/full/nature03001.html&quot; rel=&quot;noreferrer&quot;&gt;92% of the genome&lt;/a&gt; (I think this is perhaps 92% of genes, but only a small part of the physical DNA).&lt;/p&gt;&#xA;&lt;p&gt;The rest, the heterochromatin, contains non-sequenced information and could harbour some of the DNA variation between the two species. Some work has suggested that the heterochromatin, previously labelled as Junk DNA, actually has some effect on traits. For example in &lt;em&gt;Drosophila&lt;/em&gt; there has been studies which show &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18174442&quot; rel=&quot;noreferrer&quot;&gt;effects of the Y chromosome&lt;/a&gt; on traits despite the Y chromosome being mainly heterochromatic.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;Further: I think a common source of confusion comes from the use of the word gene. It is often used interchangeably to mean either &lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Allele&quot; rel=&quot;noreferrer&quot;&gt;Allele&lt;/a&gt;&lt;/strong&gt; or &lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Locus_%28genetics%29&quot; rel=&quot;noreferrer&quot;&gt;Genetic Locus&lt;/a&gt;&lt;/strong&gt;. When someone says that humans and apes share 99% of their genes they mean they share 99% of their genetic loci. When someone says that a person shares 50% of their genes with a parent they mean that they share half of their alleles with that parent (it is only roughly half due to recombination and mutation). An individual has all (barring genetic defects &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18157829&quot; rel=&quot;noreferrer&quot;&gt;such as deletions&lt;/a&gt;) the same loci as their parent.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-07-09T11:32:44.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9174" PostTypeId="2" ParentId="9172" CreationDate="2013-07-08T21:58:42.487" Score="22" Body="&lt;p&gt;So, a quick molecular biology lesson. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Proteins&lt;/strong&gt; are the things that make up a good percentage of our cells (which make up a good percentage of &lt;em&gt;us&lt;/em&gt;), and are the things that do the work of the cells - many are catalysts and are known as &quot;enzymes&quot;. &lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Proteins are encoded by &lt;strong&gt;genes&lt;/strong&gt; - while the statement that one gene&#xA;codes for one protein is not quite correct (one gene can code for&#xA;different variations of the same basic protein), it's a good way to&#xA;think about things in this context.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Genes are made up of &lt;strong&gt;DNA&lt;/strong&gt;, a polymeric molecule that constitutes our chromosomes, the informational portion of which resides four “letters” (chemical bases).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;However, now we get to the key part — although &lt;em&gt;all genes are made of DNA,&#xA;not all the DNA of chromosomes makes up genes&lt;/em&gt;. In fact, as @terdon    mentioned in a comment, only about 5% (or less) of the 4 billion letters in the total DNA — the &lt;strong&gt;genome&lt;/strong&gt; — constitute genes - those sequences that&lt;br&gt;&#xA;directly code for protein. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The function of the rest of the genome is not entirely clear. Some is regulatory, some may be structural, and may be “junk DNA”. However it’s stuck      around for millions of years, so it we assume it must have some purpose. This non-coding DNA differs between species to a greater extent than the genes themselves do, so perhaps it somehow contributes to the differences between organisms.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;https://biology.stackexchange.com/users/1757/androidpenguin&quot;&gt;AndroidPenguin&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are the links to a paper about the function of &quot;junk&quot; DNA from 2013. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?pagewanted=all&quot; rel=&quot;nofollow noreferrer&quot;&gt;Summary in NY Times&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v489/n7414/full/489045a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Abstract in Nature&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/encode/#/threads&quot; rel=&quot;nofollow noreferrer&quot;&gt;ENCODE threads on nature.com&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="948" LastEditorUserId="22057" LastEditDate="2019-08-06T22:05:59.343" LastActivityDate="2019-08-06T22:05:59.343" CommentCount="7" ContentLicense="CC BY-SA 4.0" />
  <row Id="9176" PostTypeId="1" AcceptedAnswerId="9178" CreationDate="2013-07-09T00:14:19.647" Score="6" ViewCount="1787" Body="&lt;p&gt;I found a a few of these guys on my composter, so they could have easily been eating bugs or decaying organics (or both):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Xp9Ke.jpg&quot; alt=&quot;Image 1&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/08hBR.jpg&quot; alt=&quot;Image 2&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To me it looks like a stink bug with oversized legs, not like the ones I'm used to seeing. His body measures just under 3cm, and I haven't pulled on his legs to get a measurement (I haven't pulled on it at all).  The legs seem to be at least 1.5 times the body length as do the antenna.  The body is grayish brown and the antenna and parts of the leg seem reddish brown.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm a microbiologist, so things big enough to see in a jar are not really my specialty.  That said, here's info that I've been trying to use ID it:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wingless Normal compound forelimbs (don't seem to have any kind of   prey modification)  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Segments filiform antenna (I think) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2 Tarsomeres (I think) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the middle of South East US &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have had (unusually) heavy rains &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Underside of the limbs and antenna seem red, but to seems gray&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've never seen it before! (and I usually notice such things).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update: Despite my 4 year old putting other bugs and some leaves in with it, the bug died.  I took the opportunity to get some much better photos, and low and behold when I started manipulating it I was able to pull out a substantial rostrum that I missed!  These guys are good at hiding those.  So going back to assassin bugs, can anyone id which assassin bug it is?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More photos: [I would add more but I think this should be plenty]&#xA;&lt;img src=&quot;https://i.stack.imgur.com/CopKO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/lzt3b.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ESqjy.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/uZ0zC.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I at least think it's quite a pretty specimen (to betray my mammalian aversion to bugs).&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="16866" LastEditDate="2019-11-30T22:42:56.737" LastActivityDate="2019-11-30T22:42:56.737" Title="Identification of an Insect (Hemiptera)" Tags="&lt;species-identification&gt;&lt;entomology&gt;&lt;hemiptera&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9178" PostTypeId="2" ParentId="9176" CreationDate="2013-07-09T01:04:13.610" Score="5" Body="&lt;p&gt;&lt;strong&gt;species ID&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I feel reasonably confident this is a late-instar &lt;em&gt;Acanthocephala declivis&lt;/em&gt; nymph (that is, almost-but-not-quite-adult).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Compare your pictures with those on bugguide of a &lt;a href=&quot;http://bugguide.net/node/view/37387&quot; rel=&quot;nofollow&quot;&gt;similarly-aged individual,&lt;/a&gt; or the bugguide &lt;a href=&quot;http://bugguide.net/node/view/2718#id&quot; rel=&quot;nofollow&quot;&gt;ID page&lt;/a&gt;. Also see the key &lt;a href=&quot;http://entomology.ifas.ufl.edu/choate/insectclass/beyond_family.htm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;; which gives three characters for &lt;em&gt;declivis&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Humeral angles of pronotum broadly expanded, extending laterally well beyond maximum lateral abdominal margin. Distal dilation of hind tibia broad until apex, then curving in at right angles to tibial shaft. Anterior pronotal lobe with 2 small shining blunt tubercles along midline&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you look at your pictures, you'll see that you're three for three here: the broad 'shoulders' (pronotum), the right-angle in the leg flange (dilated tibia) just above the the 'ankle', and the two rounded bumps on the pronotum (visible in photos 1 and 3).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;original answer / working towards the ID&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You're right on track, it definitely looks like a true bug (Hemiptera/Heteroptera). Possibly immature if it looks wingless. Maybe some kind of Assassin Bug (Reduviidae)? They don't all have burly forelimbs. You might also want to consider Coreidae, for instance the genus &lt;em&gt;Leptoglossus&lt;/em&gt; (&lt;a href=&quot;http://www.ent.uga.edu/veg/solanaceous/leaffoot.pdf&quot; rel=&quot;nofollow&quot;&gt;pdf on &lt;em&gt;Leptoglossus&lt;/em&gt; in Georgia&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could try &lt;a href=&quot;http://entnemdept.ufl.edu/choate/heteroptera_new1.pdf&quot; rel=&quot;nofollow&quot;&gt;this key&lt;/a&gt; to Florida bug families, it looks pretty user-friendly.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-07-10T02:39:21.977" LastActivityDate="2013-07-10T02:39:21.977" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="9179" PostTypeId="2" ParentId="9169" CreationDate="2013-07-09T03:16:20.183" Score="10" Body="&lt;p&gt;I'm not sure if I should be posting this as an answer, but I think a very approachable and accurate account of the history of HIV can be found from &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848574/#!po=10.6061&quot;&gt;Dinis de Sousa et al.&lt;/a&gt;.  I agree with what has been posted above.  On the theory that a picture is worth a thousands words, you might also introduce skeptics to the cryo-electron microscopy images of the virus (searching cryo-EM HIV will pull up plenty).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, hard skeptics would likely want discount the thousands of publications, studies, and plain old researchers who have studied the virus (myself included).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, for the record, viruses that are &quot;created&quot; by humans artificially in a lab do exist, practically by definition.  I, &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/?term=fluorescent%20virus&quot;&gt;and a great many others&lt;/a&gt;, make viruses with markers that make them easier to measure or see (such as fluorescent proteins).  But given the time that HIV entered humanity, it seems highly unlikely that anyone had the technology, let alone the will, to engineer the virus as a bioweapon.  Certainly SIV predates HIV, but the technology to make such modifications (or even of the basic players and genetics) to make a recombinant/chimeric virus simply didn't exist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is the unfortunate truth that viruses have been used as weapons of terror and warfare against various populations (I could get into examples but that seems off topic).  But the historical examples we have of this are all surrounding existing viruses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To the question of people made to make money (not withstanding all of the above), it is certainly not for lack of trying that we don't have an vaccine for HIV.  There are a lot of complications (extremely rapid mutation and escape mutants, reservoirs of virus, direct infection of cells from your immune system, etc etc).  And it shouldn't be seen as though HIV is the long lasting human virus we need a vaccine for (Herpes and RSV just two good examples).  You would stand to make a lot of money if you could successfully make a vaccine to any of the pathogens.  And a LOT of people are &lt;a href=&quot;http://www.hvtn.org/about/index.html&quot;&gt;trying&lt;/a&gt;.  The US government alone is spending a &lt;a href=&quot;http://aids.gov/federal-resources/funding-opportunities/how-were-spending/&quot;&gt;lot of money on HIV/AIDS&lt;/a&gt;.  Having a successful vaccine could actually SAVE a good deal of money.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2013-07-09T18:29:47.113" LastActivityDate="2013-07-09T18:29:47.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9180" PostTypeId="1" AcceptedAnswerId="9181" CreationDate="2013-07-09T03:17:59.033" Score="1" ViewCount="1855" Body="&lt;p&gt;Would anyone know how to go about obtaining samples of Salmonella or E. coli for purely educational purposes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note:&lt;/strong&gt; I just want to look at the stuff under a microscope. &lt;/p&gt;&#xA;" OwnerUserId="3972" LastEditorUserId="1320" LastEditDate="2013-07-12T12:49:05.290" LastActivityDate="2013-09-09T13:14:26.083" Title="How to obtain bacteria samples?" Tags="&lt;microbiology&gt;&lt;ecoli&gt;" AnswerCount="1" CommentCount="17" ContentLicense="CC BY-SA 3.0" />
  <row Id="9181" PostTypeId="2" ParentId="9180" CreationDate="2013-07-09T03:48:16.863" Score="7" Body="&lt;p&gt;To be honest, you really shouldn't be buying such things if you're not prepared to handle them properly.  If you work with a proper lab, you will be inindated with vendors trying to sell you these and many others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But to answer your question, if you are looking to purchase many such items &lt;a href=&quot;http://www.atcc.org/&quot; rel=&quot;nofollow&quot;&gt;ATCC&lt;/a&gt; is an excellent resource.  Not only will you have to meet regulatory requirements, but you will also have to deal with a great many MTA's depending on what you are trying to get. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In response to edit: Salmonella is actually not normally a &lt;a href=&quot;https://www.nlm.nih.gov/medlineplus/ency/article/000294.htm&quot; rel=&quot;nofollow&quot;&gt;serious&lt;/a&gt; pathogen to a healthy adult.  It is, however, still a human pathogen and should be handled under BSL2 conditions.  So if you have the funds and time to setup a BSL2 lab at your house, by all means go to town.  And I hope you don't live with any children, the elderly, or otherwise immunocompromised individuals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In response to further edits: &#xA;If you just want to look at things under the scope, then I suggest you get started by making your own homemade culture plates.  If you can get your hands on some &lt;a href=&quot;https://en.wikipedia.org/wiki/Lysogeny_broth&quot; rel=&quot;nofollow&quot;&gt;Lysogeny Broth&lt;/a&gt; (LB), agar, and petri dishes then you can make lb plates like a researcher in a real lab (minus an autoclave but you could use a pressure cooker).  These are items the public could get, but might be harder to come by.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I however will assume that you want to make your own plates from common household ingredients (I used to do this a lot as kid, whatever that says about me).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;**&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Making your own culture dishes:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;**&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) The &quot;plates&quot; themselves.  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I recommend getting the smallest Tupperware like&#xA;containers your can find that are microwave safe, dishwasher safe, and&#xA;really make a good seal (water tight at the least).  They really&#xA;don't have to be big, and you will make your life easier if you buy a&#xA;bunch to match.&lt;/li&gt;&#xA;&lt;li&gt;They need to be super clean.  After running them through your&#xA;dishwasher at home, put them all in a boiling pot of water until you&#xA;are ready to pour in your &quot;media.&quot; A mid-low simmer will work&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Note that you won't probably be able to have perfect sterile technique at your house, but you should try to do what you can.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Your &quot;Media&quot; or Broth&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;I highly recommend using pectin as your gelling agent if you can't&#xA;get your hands on some agar.  After that comes plain unflavored&#xA;gelatin, but I recommend pectin.  You can get it at almost any&#xA;grocery store and my recipe is made assuming that.  You can determine&#xA;how much you want to make, just scale up the ratios.  I'm going to&#xA;list things as rough volume by volume so you won't need a scale.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;i) Make the powder first:&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;45mL of pectin;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;4 bouillon cubes ground as finely as you can (you can get different&#xA;types and results depending on if you start with vegetable, beef, or&#xA;chicken.  I recommend starting with vegetable.);&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;125mL of refined white sugar; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Additives (more on this later)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;ii) Mix the powder into 500mL of water&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Before you mix in the powder, hear the water to 50-75oC (mid low&#xA;heat), but not boiling.  Mix the powder in while stirring until&#xA;dissolved.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;iii) &lt;em&gt;Bring the mixture up to a boil.&lt;/em&gt;&lt;br&gt;&#xA;Let it boil for about 2 min, stirring all the while.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;iv) &lt;em&gt;Cover the pot and let it cool for 4-5 min.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You by no means want it cool down to room temperature, you just want to get it a little below boiling.  If you are at 55oC or bellow it's definitely time move on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;v) &lt;em&gt;Dip/fill your &quot;plates&quot; 1/3 full of media using clean/sterile utensils and seal while hot but not boiling.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may have noticed this seems an awful lot like canning, and that's because it is.  Again you want to be as clean as possible in this step and of course try not to burn yourself on anything.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;vi) &lt;em&gt;Let your media plates set and chill over night in the refrigerator.&lt;/em&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You really probably only have to wait a few hours if you are anxious to get going.  You are going to want to store the plates that you are not using in the refrigerator anyway.  Also if you made a bunch of plates, let the cool on a counter before you put them in the fridge so that you don't raise the temp of your fridge too much.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remember the thing about additives?  You can play around with adding different amounts and different types of salts, vitamins, food, or other items to see how they effect the cultures you get to grow.  All kinds of fun there.  First go round, leave them all out.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Now you have your own home made culture plates!&lt;/strong&gt;  The above recipe was empirically tested by my childhood, and repeated by my son's.  Not all pectin from the store may be equal, this is with Ball Classic (I have no relation to the company).  I'd love to know people's results in trying it, because I might need to re-think how/what I'm doing to get it to work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Go around your house swabbing things with sterile swabs (you can get these at a drug store), and then streak them out on plate.  While it will be a little different with a swab and homemade plate, the idea is similar to what is done &lt;a href=&quot;https://www.youtube.com/watch?v=DAm21yPGMRo&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Leave your plate in a warm wet place, but not in direct sunlight.  Ideal temp is going to be around 37, but you can leave them above and below that and still get things to grow.  On top of our dryer is where I leave.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After a day or so you should have colonies you can streak out on a slide and look under a scope.  You will find all kinds of things this way.  If you want a more formal way to put things on a slide, you can check out dry and wet mounting from a Google search.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are actually quite likely to run into E.coli if you sample enough &quot;areas&quot; this way.  Obviously don't eat or huff the stuff that ends up growing.  Maybe you can post some fun pictures of this if you try it.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2013-07-13T02:44:14.350" LastActivityDate="2013-07-13T02:44:14.350" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9183" PostTypeId="1" AcceptedAnswerId="9184" CreationDate="2013-07-09T09:58:05.747" Score="6" ViewCount="215" Body="&lt;p&gt;I'm thinking here about environmental disturbance or like climate change-driven warming. It seems as if there are two macroevolutionary ways to deal with environmental change:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Have short generation times, and evolve fast. For instance, the mosquito &lt;em&gt;Wyeomyia smithii&lt;/em&gt; is under selection by the warming climate in North America and it has shown an evolutionary repsonse. The response is &quot;detectable over a time interval as short as 5 years&quot; (&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.241391498&quot; rel=&quot;noreferrer&quot;&gt;Bradshaw and Holzapfel 2001&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Be hardy, and 'try' to wait out changes. No real-world example to cite, but imagine a long-lived tree growing in an area that has become to warm for its seeds to effectively produce seedlings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems intuitively like strategy 1 is better in the case of ongoing climate warming. However, we could easily imagine a 5-year hot spell followed by a return to the normal as part of natural weather variation. Perhaps in this situation strategy 2 is better.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially, having a longevity/generation time/hardiness that matches the time-scale of the disturbance would be important – if the disturbance is long (or unidirectional) compared to your lifespan, evolving fast seems best; if the disturbance is short compared to your life, it seems best to wait it out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the question is, is there theory that deals with this? I suspect that I just need to hit the population genetics books again or something; or perhaps there's a massive tome by Gould I should be reading?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.241391498&quot; rel=&quot;noreferrer&quot;&gt; &lt;strong&gt;Bradshaw WE, Holzapfel CM&lt;/strong&gt;. 2001. Genetic shift in photoperiodic response correlated with global warming. PNAS 98: 14509–14511.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-08-21T03:55:16.143" LastActivityDate="2013-12-28T01:34:06.723" Title="Is there theory that connects longevity, time-scale of environmental disturbance, and adaptation?" Tags="&lt;evolution&gt;&lt;ecology&gt;&lt;life-history&gt;&lt;adaptation&gt;&lt;climate-change&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9184" PostTypeId="2" ParentId="9183" CreationDate="2013-07-09T10:21:41.097" Score="3" Body="&lt;p&gt;If the disturbance is short compared to a species' lifespan, then it's would be difficult for any adaptations to that disturbance to become fixed. Say an individual with a novel mutation is born during the disturbance that would impart some benefit under such conditions; since the species lifespan is much longer than that disturbance, by the time the individual reproduces, the disturbance will no longer be in effect and thus that allele will no longer be beneficial. In fact, this is seen in the &lt;a href=&quot;https://en.wikipedia.org/wiki/Thrifty_phenotype&quot; rel=&quot;nofollow&quot;&gt;thrifty phenotype&lt;/a&gt; in humans. When the mother experiences a period of duress during her pregnancy (say, the &lt;a href=&quot;https://en.wikipedia.org/wiki/Dutch_hunger_winter&quot; rel=&quot;nofollow&quot;&gt;Dutch Hunger Winter&lt;/a&gt; of 1944), the fetus will undergo epigenetic changes that signal, in effect, that food is scarce and resources should be used sparingly. When those children grow up, they find themselves no longer under harsh conditions and this thrifty phenotype &lt;a href=&quot;http://www.pnas.org/content/107/39/16757.long&quot; rel=&quot;nofollow&quot;&gt;becomes a disadvantage&lt;/a&gt;, causing diabetes, obesity and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the disturbance is on the order of the lifespan of the species or slightly larger and especially if it is cyclic, &lt;a href=&quot;https://en.wikipedia.org/wiki/Polyphenism&quot; rel=&quot;nofollow&quot;&gt;polyphenism&lt;/a&gt; would be advantageous. This might also impart some resistance against long-term change, at least up to a certain point. For example, the butterfly &lt;em&gt;Bycyclus anynana&lt;/em&gt; shows marked differences when born in the cool, dry season versus the warm, wet season: different body mass, different resting metabolic rate, different wing patterns and so on. This is controlled by &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/20826484&quot; rel=&quot;nofollow&quot;&gt;hormonal switches in response primarily to temperature&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that the best strategy in the face of long-term change would be gradual evolution due to progressive selection on traits that impart resistance to the disruption, at the cost of being vulnerable to future reversions in the conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But of course, none of this can be &quot;planned for&quot; by the species. In the face of a new change in environmental conditions, be it gradual or sudden, the species can only work from its current genetic background. So whether there is a specific theory that deals with this (aside from the examples given above) is not clear. I would think that what we will see with strong-but-gradual climate change is a progressive loss of biodiversity (due to the inability to adapt in time) followed by rapid expansion to fill newly opened niches. To that end, I guess Gould's &quot;Wonderful Life&quot; would be appropriate to read. Any book on Evo Devo would lend insight into understanding how species might be able to rapidly adapt to a slowly changing environment, albeit in an indirect/abstract manner (i.e. &quot;food for thought&quot;); I like Sean B. Carroll's &quot;Endless Forms Most Beautiful&quot;.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorDisplayName="user3934" LastEditDate="2013-07-09T11:25:24.573" LastActivityDate="2013-07-09T11:25:24.573" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9185" PostTypeId="1" CreationDate="2013-07-09T10:26:45.080" Score="1" ViewCount="141" Body="&lt;p&gt;I know that neurons can exhibit tonic and phasic firing, and also that a neuron is sometimes called an integrator. This makes me interested to know &lt;strong&gt;if there are activities in the brain that depend on two or more signals of different frequency occurring at the same time.&lt;/strong&gt; For example, in a telephone system, &lt;a href=&quot;http://en.wikipedia.org/wiki/Dual-tone_multi-frequency_signaling&quot; rel=&quot;nofollow&quot;&gt;two signals with a different frequencies at once(DTMF)&lt;/a&gt; are interpreted as 1. Is there anything similar in the human brain?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="57" LastEditDate="2013-07-09T13:03:11.653" LastActivityDate="2013-07-11T12:33:01.400" Title="Are there &quot;multi-frequency&quot; signals within a human brain?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9187" PostTypeId="1" AcceptedAnswerId="9194" CreationDate="2013-07-09T11:19:49.397" Score="5" ViewCount="2064" Body="&lt;p&gt;(sorry, I couldn't resist the rhyming, silly title)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I find it facinating that humans can suffer from an amoeba infestation. Amoeba must reproduce far more slowly than bacteria. In size, they seem to be approximately the same size as the various leukocyte cell types (I see estimates ranging from 10μm to 30μm in diameter). I would assume that they are slow-moving, or, at least no more motile than a leukocyte. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is it, then, that a population of amoeba can take up residence (and a particularly dangerous one, at that) in a human body without them being wiped out by the immune system? Do we know much about the pathology of such an infection? Do the amoeba actually consume the leukocytes by phagocytosis before they can be consumed themselves?&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorUserId="1306" LastEditDate="2013-07-09T18:19:19.637" LastActivityDate="2018-03-04T14:58:31.983" Title="Who would win in a fight: an amoeba or a leukocyte?" Tags="&lt;immunology&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9188" PostTypeId="1" AcceptedAnswerId="9192" CreationDate="2013-07-09T13:30:35.287" Score="3" ViewCount="1956" Body="&lt;p&gt;This question is out of curiosity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The life expectancy of a red blood cell (RBC) is approximately 3 months, and then RBCs are disposed of. Why does the body opt to build new red blood cells rather than using the existing ones? Do RBCs lose functionality/efficiency as they get older?&lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="1320" LastEditDate="2013-07-12T11:47:42.607" LastActivityDate="2013-07-12T11:48:38.800" Title="Why does the body not recycle red blood cells?" Tags="&lt;red-blood-cell&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9189" PostTypeId="2" ParentId="9185" CreationDate="2013-07-09T15:26:29.270" Score="2" Body="&lt;p&gt;Remembering that neurons don't generate sinusoids, just spikes (mostly)....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It depends on exactly how you want to define &quot;depend on&quot;.  For instance, a downstream neuron receiving inputs from two neurons will be more likely to fire as it &lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/0/0a/Temporal_summation.JPG&quot; rel=&quot;nofollow&quot;&gt;spatially/temporally sums&lt;/a&gt; the inputs from the two neurons.  Regardless of their specific rates, if their interaction is such that an impulse from each neuron arrives within a certain timing of the other, it may be sufficient to cause the downstream neuron to spike.  In this case, particular sets of frequencies of the two upstream neurons would be more likely to activate the downstream neuron and would do so at a particular rate for the downstream neuron.  Of course, the phase delay between the two neurons would be important too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a more general sense, one might consider the &lt;a href=&quot;http://www.springerreference.com/docs/html/chapterdbid/114175.html&quot; rel=&quot;nofollow&quot;&gt;binding problem&lt;/a&gt;, by which many sensory inputs are bound into a single, higher level experience, such as an object or a biographical memory, which can then later be recalled (and thus activate all the lower sensory regions that encoded the memory in the first place, nearly recreating the experience).&lt;/p&gt;&#xA;" OwnerUserId="1853" LastActivityDate="2013-07-09T15:26:29.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9191" PostTypeId="1" AcceptedAnswerId="9195" CreationDate="2013-07-09T16:11:20.980" Score="1" ViewCount="365" Body="&lt;p&gt;I was reading &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs10508-008-9386-1&quot; rel=&quot;nofollow&quot;&gt;this study on sexual behavior&lt;/a&gt; and they refer to both terms without clarification. Does 'unique environmental factors' refer only to the prenatal environment or does it include individual experiences with, say, illness as well? Would friends be considered a 'shared environment factor' or an 'individual environment factor?'&lt;/p&gt;&#xA;" OwnerUserId="3980" LastEditorUserId="107" LastEditDate="2013-07-09T18:24:30.563" LastActivityDate="2013-07-09T18:24:30.563" Title="In the context of twin studies, what do 'unique environmental factors' and 'shared environmental factors' refer to?" Tags="&lt;behaviour&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9192" PostTypeId="2" ParentId="9188" CreationDate="2013-07-09T16:37:22.010" Score="6" Body="&lt;p&gt;They are recycled, the iron and other components are broken down and then absorbed. Adaptations of the RBC prevent the same RBC being used. They lack a nucleus to make them highly efficient oxygen carriers (pack as much haemoglobin as possible). Without a nucleus and other organelles they're unable to synthesise the stuff they'd need for renewal. There's a lot of wear and tear that occurs as they're constantly flowing in tiny blood vessels and getting damaged or affected by substances in the blood. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1320" LastEditDate="2013-07-12T11:48:38.800" LastActivityDate="2013-07-12T11:48:38.800" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9193" PostTypeId="2" ParentId="7939" CreationDate="2013-07-09T16:46:36.290" Score="1" Body="&lt;p&gt;I am by far not an expert, but I read the paper and maybe I can help clarifing things a bit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's start with the simplest answer to your question:&#xA;In the last paragraph of the Introduction paper the authors say &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;&quot;Throughout this manuscript [...]'background networks' and principle components are used interchangeably.&quot;&lt;/em&gt; ([1] Torkamani and Schork, Genetic background and drug response, The Pharmacogenomics Journal (2012) 12, 446-452; doi:10.1038/tpj.2011.35)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So they did not &quot;use&quot; PCA to get the background networks, they just call the PCs background models to indicate how they interpret it: As stated earlier in the introduction&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;&quot;...interacting networks cannot be expected to correlate strongly with drug response, as their influence may only be observed when the major determinant of drug response and the interacting network complement one another or are both at a synergistic state. A major problem with identifying these interaction partners [...] is the extremely large number of possible partners [...] and [...] that individual genes are unlikely to accurately represent the overall state of a biological network.&quot;&lt;/em&gt; [1]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As far as I understand the article, they suggest PCA as a kind of compromise: Ignoring interactions would miss associations of all networks lacking a single gene representing the network's state accurate enough. Including all interactions is infeasable due to the huge number of gene-pairs. By PCA, the number of interactions can be decreased by orders of magnitude while keeping a maximum on information (as in variation): Instead of using the interaction (as in product) of all probes with all probes, they only consider those of all probes with the first six PCs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think, in this context 'background' is not used in the meaning of 'background noise' but of 'cultural background' - instead of assesing individual interactions, genes are assigned a 'background'. Since this corresponds to a) the biological network(s) they belong to and b) the principle components(s) they contribute to, those two ideas are used synonymously by calling PCs 'background networks'.&lt;/p&gt;&#xA;" OwnerUserId="3973" LastEditorUserId="3973" LastEditDate="2013-09-01T11:30:28.243" LastActivityDate="2013-09-01T11:30:28.243" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9194" PostTypeId="2" ParentId="9187" CreationDate="2013-07-09T16:58:30.127" Score="3" Body="&lt;p&gt;Assuming you don't mean a single leukocyte as I doubt That a lone leukocyte could do much. Macrophages and neutrophils can release their lytic/degrading enzymes spewing them on to the amoeba. Antibodies produced by BCells, particularly the IgE type can coat amoeba and cause histamine release from mast cells recruiting more neutrophils and macrophages. Eosinophils are also important. Finally one must not forget the complement system, a series of proteins that could kill by making pores in the amoeba membrane. Amoeba have however developed many techniques for immune evasion, such as diverting the immune system via cell signalling (cytokines) such as IL10 which dampens the immune system or coating themselves or activating the &quot;wrong&quot; immune system. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-07-09T16:58:30.127" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9195" PostTypeId="2" ParentId="9191" CreationDate="2013-07-09T17:08:51.097" Score="2" Body="&lt;p&gt;Shared environmental factors are those shared by the twins: uterine/prenatal environment and then the home environment and other environments both twins are raised in or remain in together. Unique environments are any environment not shared by the twins - they generally appear later in age. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-07-09T17:08:51.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9196" PostTypeId="2" ParentId="9102" CreationDate="2013-07-09T17:49:14.790" Score="2" Body="&lt;p&gt;I second these two I used both and liked them overall:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Bioinformatics and Functional Genomics&lt;/em&gt; by Jonathan Pevsner&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;An Introduction to Bioinformatics Algorithms&lt;/em&gt; by Neil C. Jones and Pavel A. Pevzner&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3981" LastEditorUserId="107" LastEditDate="2013-08-13T20:21:47.017" LastActivityDate="2013-08-13T20:21:47.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9197" PostTypeId="1" AcceptedAnswerId="9217" CreationDate="2013-07-09T17:59:04.450" Score="10" ViewCount="115602" Body="&lt;p&gt;What is the name of a phenomenon where one of the human eyes is seeing brighter/more saturated color than the other? I can observe the same object from the same position while alternating which eye is closed, and there's a visible difference in the saturation of color. Like one color is more pale than the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's an example of what the difference looks like between image perceived by two eyes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/j3YKk.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/FeeTe.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="24354" LastEditDate="2017-12-08T22:30:23.050" LastActivityDate="2017-12-08T22:30:23.050" Title="What is it called when one human eye is seeing brighter color than the other?" Tags="&lt;human-biology&gt;&lt;terminology&gt;&lt;vision&gt;&lt;human-eye&gt;&lt;perception&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9198" PostTypeId="1" CreationDate="2013-07-09T18:07:48.667" Score="2" ViewCount="3819" Body="&lt;p&gt;I did a little research to lead me to finding the general range of width for human hair, which is anywhere from around 30µm to 180µm... approximately.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm trying to compare this to the width of cat hair, since I have been told (and it does seem a bit evident) that cat hair is much thinner than human hair in general.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't seem to find any information on this.  Does anybody have any answers? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note:  I apologize if this isn't the right Stack Exchange forum for this question.  I wasn't sure where to put it, so I did an SE site search for 'cat' and this one seemed to be the most appropriate.&lt;/p&gt;&#xA;" OwnerUserId="3982" LastActivityDate="2013-07-09T19:57:18.377" Title="Approximately how thick is a single strand of cat (domestic housecat) hair?" Tags="&lt;hair&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9199" PostTypeId="2" ParentId="9198" CreationDate="2013-07-09T18:57:26.740" Score="3" Body="&lt;p&gt;There are a few different types of hair on a cat.  But I think you are referring to the down hair on the cat.  It will also vary on the breed of domestic cat.  As a general statement, you can find a lot of quirky characteristics of mammals by looking at early genetics papers where people where trying to find genetic elements to obvious phenotypes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the down hairs, you can see &lt;a href=&quot;http://www.snugglebugs.dk/genetics.html&quot; rel=&quot;nofollow&quot;&gt;&quot;The ‘rex’ type of coat in the domestic cat.&quot;&lt;/a&gt;&#xA;Journal of Genetics [0022-1333] Searle, A G and Jude, A C yr:1956 vol:54 iss:3 pg:506&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Table 3. Thickness in µ of normal and rex down-hairs&#xA;&#xA;[Type of Cat][Diameter in um][SE of Mean]&#xA;&#xA;Normal          25.8;   1·32;&#xA;&#xA;English rex     16·2;   0·54;&#xA;&#xA;German rex      17·0;   0·50;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3059" LastEditDate="2013-07-09T19:57:18.377" LastActivityDate="2013-07-09T19:57:18.377" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9200" PostTypeId="2" ParentId="8142" CreationDate="2013-07-09T19:00:49.063" Score="2" Body="&lt;p&gt;It is hard finding answers to this question, which also interests me a lot. The most satisfying answer I have found is detailed in this paper &lt;a href=&quot;http://www.ijpam.eu/contents/2012-78-3/6/6.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.ijpam.eu/contents/2012-78-3/6/6.pdf&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the abstract : &quot;This article examines why many flowers are five-petaled through the use of a five-petal model that draws insight from the location of cell clusters at a shoot apex, rather than from concepts such as the Fibonacci sequence or the Golden ratio which have been referred to in the past. The conclusions drawn are that flowers are most likely to be five-petaled, followed by six-petaled flowers, and that four petals are unstable and almost no flower can be seven-petaled.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the alternative theory alluded to at the end of this abstract, you may want to check out the work of mathematician Michael S. Schneider (Master's Degree in Mathematics Education from University of Florida). His answer revolves around this idea where, much like what Plato proposed, geometry is seen as the fundamental building block of the universe and where geometric patterns (therefore numbers) are given different meanings based on observational data. In this theory the number five is seen as the &quot;flag of life&quot; if you will. Look-up an image of a DNA strand viewed along axis, I find it interesting that it's mostly in series of five. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, the article I linked certaintly contains a more satisfying answer to your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helped. &lt;/p&gt;&#xA;" OwnerUserId="3983" LastEditorUserId="3983" LastEditDate="2013-07-10T06:45:03.537" LastActivityDate="2013-07-10T06:45:03.537" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9201" PostTypeId="1" CreationDate="2013-07-09T19:27:12.807" Score="2" ViewCount="1553" Body="&lt;p&gt;I'm currently working on extracting some features of the leaf architecture based on their images (like L:W ratio, laminar shape, ...). I use the &lt;em&gt;Manual of Leaf Architecture&lt;/em&gt; as the reference. It is really great in mathematically describing the features and how to calculate them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, the problem is I am not able to find a source (a book, or a data set) to have this architecture of different leaves (plants). For example, whether the &lt;em&gt;Acer&lt;/em&gt; genus has leaves with a certain (or a range of) L:W ratio or the laminar shape for this species is mainly ovate,....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anybody know any source of this kind? &lt;/p&gt;&#xA;" OwnerUserId="1467" LastEditorUserId="3952" LastEditDate="2013-07-10T03:52:12.840" LastActivityDate="2013-07-10T13:59:44.003" Title="A source for leaf architecture of different plant species/genus?" Tags="&lt;botany&gt;&lt;plant-anatomy&gt;&lt;literature&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9202" PostTypeId="1" CreationDate="2013-07-09T19:51:28.513" Score="2" ViewCount="453" Body="&lt;p&gt;I am trying to clone a PCR product that was amplified using Pfx polymerase into pGemT vector. I had to A-tail the PCR product using Taq polymerase since Pfx only generates blunt end products. My ligation reaction was successful, however when I got the sequences, there is an extra T between the 3'end-T of pGem and the start codon of my product. It only happens in the 3' end of pGemT (or 5' end of my product). Can Pfx polymerase generates PCR products with just one 3'end overhang? or Can Taq polymerase add two consecutive dATP during the A-tailing?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please write me your thoughts ASAP, it has happened twice and it's a pain already :(&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GGC CGC GGG A-&lt;strong&gt;T-T&lt;/strong&gt;-&lt;em&gt;T&lt;/em&gt;-G ATG GGA AGC ATG AAG&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two Ts in Bold belong to pGemT, the T Italic is the extra T I've got from the sequencing reaction. After the T in Italic you may find the 5'end of my insert. The second T (in bold) from pGemT is the one that ligates with the overhang A added through the A-tailing protocol.&lt;/p&gt;&#xA;" OwnerUserId="3987" LastEditorUserId="3987" LastEditDate="2013-07-10T12:41:04.323" LastActivityDate="2013-07-10T12:41:04.323" Title="Can Pfx polymerase add only one 3' A overhang?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;dna-sequencing&gt;&lt;cloning&gt;" AnswerCount="0" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="9203" PostTypeId="2" ParentId="9201" CreationDate="2013-07-10T05:21:35.587" Score="5" Body="&lt;p&gt;Quantitative descriptions of leaf shape used as diagnostics are hard to come by. There are numerous qualitative descriptions (lyrate, cordate, acicular, etc.), and I think this fits within the example you give that &quot;the laminar shape for this species is mainly ovate.&quot; But actual quantitative ranges as you mention (e.g., that the L:W ratio of Acer lies within a certain range) are much more difficult to come by. Also, there are ways of quantifying leaves using all the shape variance present in their outlines, and I describe some of these methods below. By using quantitative methods such as these, you can avoid the trap of a subjective criteria that arbitrarily distinguishes leaf morphs by a particular feature. Plus, you won't be biased by using a particular shape attribute, as you will be measuring the entirety of shape. Use of these various methods though depends on the species you are studying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oreotrephes I think is on track saying that, if possible, you should build your own diagnostic criteria for whatever system you are working in. You mentioned certain &quot;ranges&quot; that can diagnose a species ... this is a critical question. Measuring intra-genotype/individual variance in shape for your system is critical. Which leaf to measure for a species? ... i.e., shoot position, developmental age of the leaf, if working with compound leaves, the placement of the leaflet along the proximal distal axis of the leaf, what about heteroblasty (changes in leaf form at different nodes), leaves from lateral vs. main branches, environmental effects on leaves (e.g. sun vs. shade leaves)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For tomato, I measure shape quantitatively using Elliptical Fourier Descriptors, which reduces the shape of an object to a series approximation and explains variance with a Principal Component Analysis. I use the resulting Principal Component values of leaves as a trait and explain shape quantitatively that way. A very useful program to perform Elliptical Fourier Descriptors is described in &lt;a href=&quot;http://dx.doi.org/10.1093/jhered/93.5.384&quot; rel=&quot;nofollow&quot;&gt;Iwata &amp;amp; Ukai 2002&lt;/a&gt; and can be downloaded &lt;a href=&quot;http://lbm.ab.a.u-tokyo.ac.jp/~iwata/shape/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. In &lt;a href=&quot;http://dx.doi.org/10.1104/pp.111.192518&quot; rel=&quot;nofollow&quot;&gt;Chitwood et al 2012&lt;/a&gt;, I describe how to perform shape analysis on tomato leaves, separating components of shape based on genotype (e.g., by species), by position in the leaf series (heteroblasty), the ontogentic age of the leaf, and placement of leaflets along the proximal-distal axis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other easy ways to measure shape: Circularity, solidity, L:W ratio (or aspect ratio) as you mentioned. All very easy to measure in ImageJ!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You mentioned Acer leaves, which piqued my interest because I study differences in the shape of grape leaves. But like grape, many Acer leaves are palmately lobed. If every one of your samples has certain features (e.g. 5 lobes and 5 sinuses as in Acer, including petiolar sinus) then you can perform a landmark analysis using a Generalized Procrustes Analysis (The &quot;Shapes&quot; package in R is useful for this analysis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using global methods to describe shape, that is, methods to quantify the totality of shape variance, are critical to distinguish leaves. It may very well be that two leaves are so similar from different species that they are not statistically separable by shape! Be creative in the ways you measure shape, and if need be, create your own system for doing so!&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1104/pp.111.192518&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Chitwood DHD, Headland LRL, Kumar RR, Peng JJ, Maloof JNJ, Sinha NRN&lt;/strong&gt;. 2012. The developmental trajectory of leaflet morphology in wild tomato species. Annu Rev Plant Physiol 158: 1230–1240.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1093/jhered/93.5.384&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Iwata H, Ukai Y&lt;/strong&gt;. 2002. SHAPE: a computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors. Journal of Heredity 93: 384–385.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3990" LastEditorUserId="3952" LastEditDate="2013-07-10T06:49:36.447" LastActivityDate="2013-07-10T06:49:36.447" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9204" PostTypeId="1" CreationDate="2013-07-10T05:53:18.557" Score="0" ViewCount="326" Body="&lt;p&gt;Is Hydrogen gas present in biogas? As it is highly inflammable, may it ignite the other gases like methane?&lt;/p&gt;&#xA;" OwnerUserId="3991" LastEditorUserId="3952" LastEditDate="2013-07-10T07:50:13.053" LastActivityDate="2013-07-10T23:03:02.750" Title="Is Hydrogen gas present in biogas, and does it spontaneously ignite?" Tags="&lt;biochemistry&gt;&lt;organic-chemistry&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9205" PostTypeId="2" ParentId="1290" CreationDate="2013-07-10T06:11:57.257" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://firstpeoples.org/wp/maple-syrup-threatened-by-climate-change/&quot; rel=&quot;nofollow noreferrer&quot;&gt;This article&lt;/a&gt; has a clear explanation (backed up by good links) of the effects of climate change on maple sap production, including the following:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Maple trees produce the best sap on cool days preceded by freezing nights – the cold weather causes the sap in the tree to freeze, creating a low-pressure vacuum that draws more sap up from the roots. When temperatures rise the next day, the sap melts and oozes through the tree, making for easy collection. When temperatures stay abnormally warm, as they have been lately, this process does not occur.&lt;/p&gt;&#xA;&lt;p&gt;Additionally, the warm weather causes the trees to begin to bud.  The hormones that trigger budding also decrease the sap’s sugar content and spoil its taste. This means that it takes much larger quantities of sap to boil down to a gallon of syrup.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-07-10T14:00:47.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9206" PostTypeId="1" AcceptedAnswerId="9539" CreationDate="2013-07-10T07:52:20.160" Score="1" ViewCount="322" Body="&lt;p&gt;Eusociality, particularly focusing on the presence of certain altruistic sterile organisms within the social set-up creates questions as to why would the process of natural selection have favoured the persistence of such genes especially in hymenopteric species. One explanation (provided &lt;em&gt;probably&lt;/em&gt; by Hamilton) pertains to very similar genetic constitutions of females of such species (owing to haploid nature of males), which increases genetic similarity between the female members of the social group. Thus it would be more &quot;beneficial&quot; (i.e., favourable for the persistence of similar genetic builds) for a female worker to help the fellow siblings, to which it bears greater genetic similarity, than its own offspring to which it bears a lesser genetic similarity. This might in a deeper way explain altruism in case of hymenopterans where the male is a parthenogenetic haploid and the female is diploid.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But why would the sterile condition of the workers in case of almost all eusocial groups be favoured by natural selection on grounds that it improves the 'fitness' of the 'genetic build' of the workers and ultimately the sterile altruists benefit the persistence of its genetic traits? Moreover the altruistic nature of the haploid males also goes unexplained.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3952" LastEditDate="2013-08-02T14:06:08.240" LastActivityDate="2013-10-31T23:55:01.147" Title="Eusociality and Natural selection?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;entomology&gt;&lt;natural-selection&gt;&lt;sociality&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9207" PostTypeId="2" ParentId="9204" CreationDate="2013-07-10T07:56:35.353" Score="3" Body="&lt;p&gt;The constitution of the biogas depends greatly on its source and the fermenting microbe. But in general, it does contain hydrogen about 0-1%. Even if it did contain large amounts, the mixture would be inflammable, but it would not burst into flames without any external igniter, which could be any small fluctuation of heat if the mixture is too unstable. But in general, an inflammable gas doesn't start burning on its own.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="107" LastEditDate="2013-07-10T07:58:34.363" LastActivityDate="2013-07-10T07:58:34.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9208" PostTypeId="2" ParentId="9201" CreationDate="2013-07-10T12:11:06.657" Score="1" Body="&lt;p&gt;For qualitative features, you could try essentially any flora. Most of these will have descriptions like this one in &lt;a href=&quot;http://efloras.org/browse.aspx?flora_id=2&quot; rel=&quot;nofollow&quot;&gt;Flora of China&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;Acer ....&#xA;  Leaves mostly simple and palmately lobed or at least palmately veined, in a few species pinnately veined and entire or toothed, or pinnately or palmately 3-5-foliolate.&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The problem with using florae is that a) they're limited in geographical scope and b) they're  usually just blocks of text (not databased or usually even XML tagged). However, a big flora like FoC will have plenty of genera for you to work with, and it should be easy to manually look up the information you want for a few genera, and possible for you to automate the information retrieval with online florae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Florae can be a pain to use for non-botanists, but I think the FoC site is pretty explanatory – you can navigate from the &lt;a href=&quot;http://efloras.org/browse.aspx?flora_id=2&quot; rel=&quot;nofollow&quot;&gt;family list&lt;/a&gt; to any family, and then down at the bottom will be a link called &quot;list of lower taxa&quot; (or just a list, if it's a small family) where you'll seelinks to each of the genera in the family. Then you'll see the genus description page, for instance, for &lt;em&gt;Acer&lt;/em&gt; as quoted above.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-07-10T13:59:44.003" LastActivityDate="2013-07-10T13:59:44.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9209" PostTypeId="1" AcceptedAnswerId="9210" CreationDate="2013-07-10T13:44:36.720" Score="2" ViewCount="1872" Body="&lt;p&gt;This is the first time I do a centrifuge experiment with my own centrifuge machine, it's just simple made by a rotor that can rotate the tube at high speed. As I know a centrifuge machine can be using for separate biology samples like bacteria, cells, molecules ... But I need some advice to understanding more how to working with it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/9035/finding-a-template-oligo-combination-for-my-first-pcr-experiment/9037#comment11975_9037&quot;&gt;As the suggestion from Alan Boyd&lt;/a&gt;, I'm planning to separate &lt;em&gt;Lactobacillus&lt;/em&gt; from diluted yogurt. How do I know where the bacteria will be located in the tube after centrifugation (is it usually in bottom ?) and how do I  calculate the RPM that is suitable ? And any other interesting diy experiment to do with it ?&lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-07-13T02:24:21.980" Title="Beginning with centrifuge experiment" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;diy-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9210" PostTypeId="2" ParentId="9209" CreationDate="2013-07-10T14:40:10.723" Score="2" Body="&lt;p&gt;It would be interesting to see a picture of your centrifuge, which you appear to have built in a few days.&lt;/p&gt;&#xA;&lt;p&gt;Centrifugation simply accentuates the effects of gravity, and since bacteria are denser than aqueous solutions they will move to the bottom of the sample to form a fairly tight pellet.&lt;/p&gt;&#xA;&lt;p&gt;The conditions for your centrifugation will depend very much on the design of the centrifuge since as well as the rotational velocity, the radius of rotation is also important.&lt;/p&gt;&#xA;&lt;p&gt;I found a suggestion on the internet to use a relative centrifugal force (RCF) of 12000 g for 2 minutes (I must admit that from memory I always spun slower and for longer than this suggests). Anyway...&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;using RCF = 1.12 * 10&lt;sup&gt;-5&lt;/sup&gt; * r *N&lt;sup&gt;2&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;p&gt;r = radius of rotation&lt;br /&gt;&#xA;N is revolutions per minute&lt;/p&gt;&#xA;&lt;p&gt;and plugging 12000 g into that, for a rotational radius of 10 cm, I get 3300 rpm.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Don't know if you can manage that with your machine, but as I say, a lower RCF with a longer spin will probably be ok as long as you can dilute the yoghurt sufficiently to reduce viscous drag. Of course if you have access to any microbiological growth media you could grow a standard liquid culture by inoculating some sort of broth with a small amount of yoghurt.&lt;/p&gt;&#xA;&lt;p&gt;Try a Google image search for &lt;em&gt;hand powered centrifuge&lt;/em&gt; to get an idea of what has been used in the past.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;after comment from Mad Scientist&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mseuk.co.uk/Products/Centrifuges/NonRefrigerated/Centaur_2/Default.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;see here for a typical large table top centrifuge&lt;/a&gt; maximum RCF is 3120 g at 4600 rpm. You can certainly pellet bacteria in something like this in tens of minutes.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-07-10T15:34:22.217" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9211" PostTypeId="2" ParentId="9012" CreationDate="2013-07-10T15:19:17.327" Score="2" Body="&lt;p&gt;Wild type refers to the phenotype of the typical form. Normally it is wild type is being compared to a mutant allele because the allele is not longer typical. So the answer would an allele that is not typical which, in most cases is a mutated allele.&lt;/p&gt;&#xA;" OwnerUserId="3981" LastActivityDate="2013-07-10T15:19:17.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9212" PostTypeId="2" ParentId="9209" CreationDate="2013-07-10T16:53:28.270" Score="2" Body="&lt;p&gt;I certainly don't want to discourage experimentation and self-learning, but please be extremely careful. A centrifuge has to be perfectly balanced at high speed to stay stable. As an example, one of the table-top centrifuges I use has a steel jacket that's perhaps 1 cm thick or more surrounding the rotor, just in case there is a balance issue or the rotor breaks from mechanical stress. A Google image search for &lt;a href=&quot;http://google.com/search?q=centrifuge+accident&amp;amp;tbm=isch&quot; rel=&quot;nofollow&quot;&gt;centrifuge accident&lt;/a&gt; shows what mechanical stress can do when an improper rotor was used on a high-speed centrifuge for just a few hours. Keep in mind that &lt;a href=&quot;https://en.wikipedia.org/wiki/Angular_momentum&quot; rel=&quot;nofollow&quot;&gt;angular momentum&lt;/a&gt; increases both with the mass of the object being rotated, and with the &lt;a href=&quot;https://en.wikipedia.org/wiki/Moment_of_inertia&quot; rel=&quot;nofollow&quot;&gt;moment of inertia&lt;/a&gt;, which increases as the radius of the object being rotated increases. In other words, if you tie a ball to a short piece of string (say 0.5m) and swing it around your head, you can feel a certain amount of force. Take that same ball and tie it to a 2m piece of string, and at the same number of rotations per minute the force will increase substantially. All this means is that as the radius of the rotation increases, the amount of &lt;em&gt;g&lt;/em&gt; force increases as well, but the stress on the machine also increases, especially if the balance is off.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, good luck with your experiments, just remember that safety always comes first. You can replace samples, and you can replace equipment, but you can't replace you. Even simple precautions like always wearing goggles or protective safety glasses should always be followed. Don't work alone, or in a situation where there is no one to call for help if you get hurt. If something doesn't feel right, don't do it.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-07-10T16:53:28.270" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9214" PostTypeId="2" ParentId="9185" CreationDate="2013-07-10T22:25:06.343" Score="1" Body="&lt;p&gt;There is a somewhat-hypothetical phenomenon called cross-frequency coupling which has generated some interest recently. This has mostly been described in the hippocampus and in interactions between the hippocampus and neocortex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cell.com/neuron/abstract/S0896-6273(13)00231-6&quot; rel=&quot;nofollow&quot;&gt;http://www.cell.com/neuron/abstract/S0896-6273(13)00231-6&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bio.brandeis.edu/lismanlab/theta.html&quot; rel=&quot;nofollow&quot;&gt;http://www.bio.brandeis.edu/lismanlab/theta.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1248" LastActivityDate="2013-07-10T22:25:06.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9215" PostTypeId="2" ParentId="9204" CreationDate="2013-07-10T23:03:02.750" Score="1" Body="&lt;p&gt;The auto ignition temperature of a combustible mixture of hydrogen in air is 500 degrees C &lt;a href=&quot;http://en.wikipedia.org/wiki/Hydrogen&quot; rel=&quot;nofollow&quot;&gt;source - Wikipedia&lt;/a&gt;. It will not spontaneously ignite, some part of it must first reach that temperature through a spark, flame, or other heat source.  Once it ignites, the methane of course will burn too.&lt;/p&gt;&#xA;" OwnerUserId="1165" LastActivityDate="2013-07-10T23:03:02.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9216" PostTypeId="2" ParentId="8190" CreationDate="2013-07-11T01:57:35.967" Score="1" Body="&lt;p&gt;&lt;strong&gt;specifically development-focused&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;An Introduction to Plant Structure and Development&lt;/em&gt; by Beck looks comprehensive and has been well-reviewed. It has both photos and diagrams, and sections certainly deal specifically with growth/lifecycle. It's &lt;a href=&quot;http://books.google.com/books?id=zSK1BuxMh9cC&amp;amp;printsec=frontcover#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;available to preview or purchase as an ebook on Google Play&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;more general plant anatomy vocabulary resources&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In print, &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0964022168&quot; rel=&quot;nofollow&quot;&gt;Plant Identification Terminology: an illustrated glossary&lt;/a&gt; by Harris and Harris is a fairly standard reference, and I've found it very useful both for looking up terms and for just flipping through.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Online, but with fewer diagrams, you could try the Glossary page on the &lt;a href=&quot;http://www.mobot.org/MOBOT/research/APweb/&quot; rel=&quot;nofollow&quot;&gt;Angiosperm Phylogeny Website&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This might sound silly, but if you're looking for more of a course on the fundamentals rather than a dictionary of the specifics, the &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0064603024&quot; rel=&quot;nofollow&quot;&gt;Botany Coloring Book&lt;/a&gt; is actually a great, seriously useful work.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-07-11T23:49:07.597" LastActivityDate="2013-07-11T23:49:07.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9217" PostTypeId="2" ParentId="9197" CreationDate="2013-07-11T05:09:53.323" Score="6" Body="&lt;p&gt;here is &lt;a href=&quot;http://photo.net/casual-conversations-forum/00R4Vd?start=10&quot; rel=&quot;noreferrer&quot;&gt;forum discussing similar effect&lt;/a&gt; ,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where as similar problem which leads to double vision is single eye is called monocular Diplopia. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two possible causes discussed in that forum. One is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Cataract&quot; rel=&quot;noreferrer&quot;&gt;cataract&lt;/a&gt; or an early indication of a cataract, for which a vision specialist visit is recommended.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another solution is much simpler one of the pupils is more dilated than the other:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The way your eyes see colors changes throughout the day, not dependent&#xA;  only on external conditions. Try this: gently press the palm of your&#xA;  hand against one eye (closed), for about a minute; leave the other eye&#xA;  open during this time (feel free to blink, of course...). Now, look at&#xA;  the world with one eye covered (for a couple of seconds), then the&#xA;  other — the eye you help closed will see things as quite more&#xA;  saturated, partly because you've fostered its pupil to dilate in the&#xA;  time during which it was shut. I recall being confused by this when I&#xA;  first started noticing that, &lt;strong&gt;upon awaking&lt;/strong&gt;, either eye would see colors&#xA;  differently from the other; simply, &lt;strong&gt;the eye rested on the mattress&#xA;  would be seeing colors with greater saturation.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3841" LastEditorUserId="577" LastEditDate="2013-07-11T22:07:41.190" LastActivityDate="2013-07-11T22:07:41.190" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9219" PostTypeId="1" AcceptedAnswerId="9220" CreationDate="2013-07-11T09:20:41.817" Score="1" ViewCount="266" Body="&lt;p&gt;I want to measure OD to know the concentration of dNTP. Any idea for dyeing dNTP at cheapest price and easiest way ? &lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="948" LastEditDate="2013-07-13T02:24:07.793" LastActivityDate="2013-07-13T02:24:07.793" Title="Finding a easy and cheap method for dyeing dNTP" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;diy-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9220" PostTypeId="2" ParentId="9219" CreationDate="2013-07-11T10:14:58.630" Score="4" Body="&lt;p&gt;There may be such a dye, but I'm not aware of it.  The standard way to measure dNTPs, and nucleic acids in general is by absorbance at 260 nm. &lt;a href=&quot;http://webdoc.nyumc.org/nyumc/files/sun-lab/attachments/MBPS.Ch10.pdf&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; has a table of molar extinction coefficients for dNTPs (Table 10.2). They are  &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;        wavelength      molar extinction coefficient&#xA;dATP    259 nm          15,200&#xA;dCTP    280 nm          13,100&#xA;dGTP    253 nm          13,700&#xA;dTTP    267 nm           9,600&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;In practice for routine work with DNA you can use 260 nm and assume that an absorbance of 1 corresponds to [DNA] = 50 &amp;micro;g ml&lt;sup&gt;-1&lt;/sup&gt;. Using an average of the values in the Table, and disregarding the fact that these are actually at different wavelengths, and using an approximate average dNTP MW of 500, I calculate an absorbance for a 50 &amp;micro;g ml&lt;sup&gt;-1&lt;/sup&gt; solution of all 4 dNTPs as 1.3, so that's a reasonable agreement given all of the assumptions I've made.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are fluorescent dyes that can be used to measure DNA, but these rely upon the presence of stacked bases, so are not useful for free dNTPs.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, bad news if you don't have a UV spectrophotometer. There are plans available for construction of simple spectrophotometers using Lego and a few optoelectronic components. These tend to use LEDs as a light source, but I don't know if UV LEDs are available.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-07-11T10:33:56.757" LastActivityDate="2013-07-11T10:33:56.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9221" PostTypeId="2" ParentId="9185" CreationDate="2013-07-11T12:33:01.400" Score="1" Body="&lt;p&gt;In general, drawing analogies of how the brain might work from engineered telecommunication/computing system can be quite misleading.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just wanted to add Izhikevich's FM modulation theory of communication, but I would say it is controversial.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Izhikevich E.M. (1999) Weakly Pulse-Coupled Oscillators, FM Interactions, Synchronization, and Oscillatory Associative Memory. IEEE Transactions On Neural Networks, 10:508-526&lt;/li&gt;&#xA;&lt;li&gt;Hoppensteadt F.C. and Izhikevich E.M. (1998) Thalamo-Cortical Interactions Modeled by Weakly Connected Oscillators: Could Brain Use FM Radio Principles? BioSystems, 48:85-94&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="460" LastActivityDate="2013-07-11T12:33:01.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9222" PostTypeId="2" ParentId="9219" CreationDate="2013-07-11T13:10:09.803" Score="2" Body="&lt;p&gt;It will be difficult to achieve the level of wavelength resolution required to differentiate dNTPs, considering that you are doing a DIY experiment. Only very precise spectrophotometers can achieve it and they are expensive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another technique you can try is &lt;a href=&quot;http://en.wikipedia.org/wiki/Thin_layer_chromatography&quot; rel=&quot;nofollow&quot;&gt;thin layer chromatography(TLC)&lt;/a&gt;. It is cheap and you can easily do a DIY. But you need standards in order to differentiate NTP, NDP and NMP; the latter two might arise because of degradation during the experiment. People generally use a cocktail of anti-oxidants and protectants to minimize the degradation of nucleotides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A strategy to go about this is to remove the phosphate using phosphatase and then do a TLC with Nucleosides (which are quite stable). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can check this &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/anie.196204351/abstract&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt; on nucleic acid TLC. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-07-11T17:41:47.393" LastActivityDate="2013-07-11T17:41:47.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9223" PostTypeId="1" AcceptedAnswerId="11085" CreationDate="2013-07-11T13:14:33.307" Score="2" ViewCount="94" Body="&lt;p&gt;Are there words that categorize latin specific epithets by how they're derived? Specifically, I was wondering if there exist adjectives to refer to:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Person-derived species names as in &lt;em&gt;Nothura darwini&lt;/em&gt; (these could be &quot;eponymic&quot; or &quot;eponymous&quot; perhaps, but that seems grammatically wrong )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Place-derived species names as in &lt;em&gt;Amolops hongkongensis&lt;/em&gt; (would these be &quot;toponmyous&quot;, or maybe &quot;loconymous&quot;?)&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-10-25T00:34:19.527" Title="How to refer to person-derived and place-derived species names" Tags="&lt;nomenclature&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9225" PostTypeId="1" AcceptedAnswerId="9235" CreationDate="2013-07-11T15:11:51.820" Score="4" ViewCount="694" Body="&lt;p&gt;I've started a hobby machine vision project (and posted some questions to this end on other SE sites) and on a side track, also been looking at relevant research in human vision (and partly, hearing).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I came across the work of one &quot;James T Fulton&quot; through an excerpt of a book which claims to have &quot;revolutionised&quot; our understanding of human vision and hearing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are the respective links:&#xA;&lt;br/&gt;&#xA;&lt;a href=&quot;http://neuronresearch.net/vision/&quot;&gt;http://neuronresearch.net/vision/&lt;/a&gt;&#xA;&lt;br/&gt;&#xA;&lt;a href=&quot;http://www.neuronresearch.net/hearing/&quot;&gt;http://www.neuronresearch.net/hearing/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried cross-verifying these claims via Google, but nothing turned up on searching either for the author or the book (apart from some Amazon links and very obscure references).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering the controversial natural of the claims made here, I would have imagined some level of debate, but the silence I found on the Internet is puzzling. Puzzling, because the sheer level of DETAIL in these books, prevents me from dismissing the claims altogether as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone validate some of the content from these books so I can get an idea of the overall legitimacy of the work (and decide if I should continue reading, or not). Below might be a good link to start from:&#xA;&lt;a href=&quot;http://neuronresearch.net/vision/pdf/11Biophenom.pdf&quot;&gt;http://neuronresearch.net/vision/pdf/11Biophenom.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adding a few examples:&#xA;&lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The simplest one - is that the Principle of Univariance is not entirely correct. This is examined on pages 15 through 17 at this link (where I read it):&#xA;&lt;a href=&quot;http://neuronresearch.net/vision/pdf/11Biophenom.pdf&quot;&gt;http://neuronresearch.net/vision/pdf/11Biophenom.pdf&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There is this claim quoted verbatim from the site:&lt;br/&gt;&#xA;&quot;The theory shows that the ARCHITECTURE OF ALL VISION IS TETRACHROMATIC. Although traditionally called trichromats, it is shown that HUMANS ARE BLOCKED TETRACHROMATS&quot;&#xA;&lt;br/&gt;&lt;br/&gt;Caps in original. I just pasted it here to give an idea of the tone of some of the text.&#xA;This specific claim is &quot;proven&quot; here (in short):&lt;br/&gt;&#xA;&lt;a href=&quot;http://neuronresearch.net/vision/files/tetracomparison.htm&quot;&gt;http://neuronresearch.net/vision/files/tetracomparison.htm&lt;/a&gt;&#xA;&lt;br/&gt;&#xA;And a longer form of the text is linked in the same page&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There is also a theory proposed on why cochlea are coiled:&#xA;&lt;a href=&quot;http://neuronresearch.net/hearing/pdf/coiledcochlea.pdf&quot;&gt;http://neuronresearch.net/hearing/pdf/coiledcochlea.pdf&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="3998" LastEditorUserId="3998" LastEditDate="2013-07-11T17:45:30.080" LastActivityDate="2014-08-04T15:46:07.823" Title="Are these claims of &quot;revolutionising&quot; understanding of human vision and hearing valid?" Tags="&lt;neuroscience&gt;&lt;vision&gt;&lt;eyes&gt;&lt;hearing&gt;&lt;human-ear&gt;" AnswerCount="1" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="9226" PostTypeId="2" ParentId="9172" CreationDate="2013-07-11T16:16:48.807" Score="17" Body="&lt;p&gt;Since it was my edit of your question that started all this, I may as well weigh in. I will give a &lt;strong&gt;simplified&lt;/strong&gt; version of genes and gene transcription, there are various details that make the process much more complicated than what I will describe but they are not relevant to the basic question here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, as others have mentioned, genes are specific sequences of DNA. A gene's job is to &quot;code for&quot; a protein (first big simplification). However, not &lt;em&gt;all&lt;/em&gt; of the gene codes for protein, only those parts of it called &lt;a href=&quot;http://en.wikipedia.org/wiki/Exon&quot; rel=&quot;noreferrer&quot;&gt;exons&lt;/a&gt; (image modified slightly from &lt;a href=&quot;http://err.bio.nyu.edu/courses/index.php/Griffin&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MZRny.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The take home message from the image above is that the red bits (the &lt;a href=&quot;http://en.wikipedia.org/wiki/Intron&quot; rel=&quot;noreferrer&quot;&gt;introns&lt;/a&gt;) are removed and do not affect the final protein product. So, only &lt;em&gt;part&lt;/em&gt; of the gene codes for the protein. Introns tend to be far less conserved between different species than exons. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not only does the entire gene not code for protein but most of the genome does not contain genes. In fact, in humans, genes represent ~5% of the total DNA and &lt;em&gt;exons&lt;/em&gt; represent ~2%. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another confounding factor are the sequences called &lt;em&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Repeated_sequence_%28DNA%29&quot; rel=&quot;noreferrer&quot;&gt;repetitive elements&lt;/a&gt;&lt;/em&gt;. These are various types of usually shortish sequences that exist in many copies in genomes, In the human genome ~41% &lt;a href=&quot;http://www.ncbi.nlm.nih.gov.gate1.inist.fr/pubmed/8994846&quot; rel=&quot;noreferrer&quot;&gt;consists of repetitive elements&lt;/a&gt; of various types, and ~10% represents copies of a single such element (Alu), that's twice as many as genes. Such repetitive elements are usually not considered when calculating whole genome similarity rates. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of their &lt;em&gt;entire&lt;/em&gt; genome, human and chimp are very very similar. However, the exact percentages vary (I've seen estimates from ~85 to ~90something) depending on the way the sequences are studied. To be on the safe side, you should say that they share 99% similarity &lt;em&gt;at the gene level&lt;/em&gt; and leave it at that.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-10-11T15:04:03.150" LastActivityDate="2013-10-11T15:04:03.150" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9232" PostTypeId="1" CreationDate="2013-07-11T20:10:29.827" Score="0" ViewCount="18425" Body="&lt;p&gt;What does &quot;fit&quot; mean in &quot;survival of the fittest&quot;? &lt;/p&gt;&#xA;" OwnerUserId="4003" LastEditorUserId="3952" LastEditDate="2013-07-12T00:22:13.670" LastActivityDate="2013-07-12T23:18:55.883" Title="What does &quot;fit&quot; mean in &quot;survival of the fittest&quot;?" Tags="&lt;evolution&gt;" AnswerCount="6" CommentCount="1" ClosedDate="2013-07-14T13:06:34.447" ContentLicense="CC BY-SA 3.0" />
  <row Id="9233" PostTypeId="2" ParentId="9232" CreationDate="2013-07-11T20:38:41.077" Score="1" Body="&lt;p&gt;It might sound tautological, but fitness is pretty much defined as 'being more likely to survive - and reproduce'; fitness is surviving and survival goes to the fittest.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a trite way of citing Richard Dawkins' &lt;a href=&quot;http://www.stephenjaygould.org/library/dawkins_replicators.html&quot; rel=&quot;nofollow&quot;&gt;theory of the replicator&lt;/a&gt; to describe fitness.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fitness is a property of being able to carry one's genes to a later generation.  Fitness is result of the individual properties and how well the individual can get along in the environment that it finds itself, in comparison to other individuals who might be competing for resources in that environment.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no concrete definition of fitness.  Fitness can mean size and strength, or lightness and resilience, short or long life.  There is no &lt;em&gt;a priori&lt;/em&gt; way of looking at two individuals you know nothing about and deciding which is going to be more successful at reproducing.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;not sure this is better, but there's definitely more of it...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-07-12T17:33:46.770" LastActivityDate="2013-07-12T17:33:46.770" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9234" PostTypeId="2" ParentId="9232" CreationDate="2013-07-11T21:16:31.197" Score="1" Body="&lt;p&gt;Rather than &quot;fitter&quot;, I'd say &quot;better&quot;. Better at hunting, gathering food, surviving predators, surviving weather conditions or other kinds of population pressures. The better a population gets at the above things, the more (and fitter/better) offspring it is likely to have and the pyramid goes on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In some cases, mutations might simply confer a &quot;new&quot; advantage that there was no prior pressure in the system for. For example, I can easily imagine a bird population where one of them evolves a plumage/pigment mutation that gives it a selection advantage and it quickly becomes the norm. This mutation could have - theoretically, and in my view - evolved even in the ABSENCE of a sexual selection pressure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's just that natural selection (in my simplistic interpretation) &quot;favors&quot; any improvements in organisms in a really simple, statistical way.&lt;/p&gt;&#xA;" OwnerUserId="3998" LastActivityDate="2013-07-11T21:16:31.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9235" PostTypeId="2" ParentId="9225" CreationDate="2013-07-11T21:16:48.597" Score="10" Body="&lt;p&gt;OK, I'll field this one. I'll ignore any of the tell-tale signs of hokum such as writing in ALL CAPS. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nevertheless, it's a lot of hokum. It's true that he goes into a lot of detail and I'm sure his math looks nice but the fact is that it's not grounded in reality. I would consider myself to be something of an expert (in training) in the field of phototransduction, so I'll focus on claims related to it. However, if he's as sloppy with the rest of the visual process as he is with phototransduction, then his claims are entirely bogus.  I'll just be working from the Synopsis section.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where to start...How about the first sentence of the &quot;Background&quot; section:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This work originated in the 1960's with the realization that rhodopsin, as then defined, did not meet the requirements for being a chromophore.  It was particularly deficient in the structural characteristics required of a good chromophore.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;FALSE. Rhodopsin is not a chromophore and, to my knowledge no one has ever claimed it to be a chromophore. Rhodopsin is a protein. It is &lt;em&gt;coupled&lt;/em&gt; with a chromophore, retinal, a form of vitamin A. OK, so if this is the foundation of his research, he is off to a bad start.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The basic assumption had been that the residues of a destructive process could be easily returned to their original state and that state was a simple chemical bond involving only two components in a single molecule...It was assumed that one of the residues was the alcohol or aldehyde of Vitamin A. The other residue was assumed to be a protein and was given the name opsin. Valiant, but unsuccessful, efforts were made to define the nature of the molecule and achieve the formation of rhodopsin in the laboratory. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It absolutely is possible to reconstitute rhodopsin with the chromophore in the lab. This has been going on since &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/6224755&quot;&gt;at least 1983&lt;/a&gt;. Also, the crystal structure of rhodopsin, including the chromophore, &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/10926528&quot;&gt;was resolved in 2000&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A new class of retinoids was defined by the author at that time, the Rhodonines. This class met the requirements of physical chemistry and photochemistry for a high performance chromophore. However, it was difficult to obtain acceptance of the Rhodonines as a replacement for Rhodopsin within the vision research community.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I have never heard of Rhodonines and web searches only result in his page. Due to his confusion of terminology, I don't know if he is proposing them to be proteins (&quot;replacement for Rhodopsin&quot;) or simple chemical molecules (&quot;a high performance chromophore&quot;). If it were the former, one would wonder why Rhodonines were not identified &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/22108793&quot;&gt;in a comprehensive proteomics assay of the rod outer segment&lt;/a&gt;. One would also wonder why rhodopsin is so highly expressed in the outer segment (on the order of 1e8 molecules in mammals and 1e9 molecules in amphibians, more than any other protein in that compartment). If it were the former, one would wonder why there is an &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/15177205&quot;&gt;entire biochemical cycle dedicated to recycling retinal&lt;/a&gt; that takes place just outside the outer segment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll ignore whatever physical state these Rhodonines are supposedly in since they don't exist. I'll also ignore this &quot;Activa&quot; thing. He owns a patent on it, which doesn't bode well for its existence in nature.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The visual system is a very sophisticated system. It uses many of the most sophisticated methodologies known to man at the start of the 21st Century. Failure to recognize these mechanisms and methodologies leads to an inadequate understanding of the overall process. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'll agree there, with the exception of the use of the word &quot;methodologies&quot;! This isn't engineering, this is biology.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The visual system employs a number of time related processes that have not previously been addressed in the literature. To understand these processes, it is necessary to employ &quot;complex algebra&quot; in the differential equations arena. Employing these techniques provides the complete solution to the overall photoexcitation/de-excitation process within the Outer Segment of the photoreceptor&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Phototransduction has a rich history of mathematical modeling. And yes, they involve &quot;complex algebra in the differential equations arena.&quot; An excellent review of the first few decades of it can be found in the bible: &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1383812100800081&quot;&gt;Phototransduction in vertebrate rods and cones: molecular mechanisms of amplification, recovery and light adaptation&lt;/a&gt;. Since that publication, there have been two very nice lineages of models: one comprehensive one that focuses on the proteins (&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/16212700&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/19756313&quot;&gt;2&lt;/a&gt;, &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/23693153&quot;&gt;3&lt;/a&gt;) and one that focuses on spatial accuracy and stochastic interactions and gives more attention to second messengers (&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/16986276&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/18400950&quot;&gt;2&lt;/a&gt;, &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/20001089&quot;&gt;3&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It has also been compounded by the historically poor preparation of the researchers in the field of mathematics.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I challenge him to read one of DiBenedetto's modeling papers and not glow in admiration of his mathematical prowess.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The goal has been to present an overall view of the visual system in a defendable mathematical context and a global scientific framework. This goal has required the introduction of techniques and mechanisms not normally found in the literature of vision. This has been particularly true in two areas, the definition and detailing of the initial photodetection process and a similar detailing of the mechanisms of neural signal transmission. In both cases, the dominance of chemically based concepts is shown to have impeded progress. The description of the visual system, including the neural system, as an entirely electronic, more precisely electrolytic, based system leads to much greater insight into the operation of the visual system than any chemically based theory can offer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I had to quote in full here. This is entirely bogus. The &quot;initial photodetection process&quot; (phototransduction) is &lt;em&gt;entirely&lt;/em&gt; chemical in nature. All of the main players in the process are known and their interactions are largely well understood. Viewing the system as entirely &quot;electronic&quot; ignores the mountains of evidence of all of the proteins participating in it.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Probably the most venerable is that of a dichotomy between types of photoreceptors, the rods and cones. The theory demonstrates in excruciating detail that there is only one functional type of photoreceptor cell and that it is associated with one of four types of chromophore. These chromophores are sensitive in the ultraviolet, the short, the medium and the long wavelength portions of the visual spectrum of light.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The problem with this is that if you look at a retina, you can see rods and cones. You can generate knock-out animals that have only one or the other. Those with only rods cannot handle bright visual stimulii, those with only cones cannot see in the dark. More damning is that you have two distinct phototransduction cascades, separated by evolution dating back to the origins of vertebrates. They share only a few proteins in common and otherwise have unique paralogs performing similar duties. You can isolate individual rod cells and, if you're clever and you have the right species, individual cone cells (they're much smaller and harder to harvest in animals like mice or cows). You can measure their electrophysiological characteristics and find that they are extremely different: cone responses are &lt;em&gt;fast&lt;/em&gt; while rods can respond to a single photon of light. Their morphologies are completely different: the rod outer segment is filled with lipid bilayer disks, while that of the cone has a series of in-folds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the whole tetrachromat thing, well, again I have to assume that he's referring to opsins when he talks about chromophores. Thanks to genomics, we can be confident that there are only three cone opsin varieties in old world apes (and one rod opsin). The rest of mammals only have two. If you get into other vertebrates, you'll find more...if you get into invertebrates, you'll find ridiculous numbers. There's not much to say here. A fourth cone opsin protein simply does not exist in the human genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, that's just a quick overview. Do not worry about this guy's research. It is unsubstantiated and exists in a vacuum outside of the rest of the vision research world. I do wish that there were a way for him to work with others. I do wish there were a way for him to integrate current knowledge into his work. But the problem is that his work as it stands simply seems to ignore the wealth of data generated on the visual system and instead treats it as some theoretical circuit.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorDisplayName="user3934" LastEditDate="2013-07-11T21:36:56.807" LastActivityDate="2013-07-11T21:36:56.807" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="9236" PostTypeId="2" ParentId="9232" CreationDate="2013-07-11T21:28:55.000" Score="2" Body="&lt;p&gt;Simply put, &quot;fit&quot; refers to being adept at finding and utilizing resources, evading predation and producing offspring.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastActivityDate="2013-07-11T21:28:55.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9237" PostTypeId="2" ParentId="9232" CreationDate="2013-07-11T21:39:45.710" Score="1" Body="&lt;p&gt;Often it is re-phrased &quot;Survival of the Most Adapted.&quot;  Fittest might make you think of the strongest or the fastest, but suppose in extreme famine, those who had better regulation of muscle growth could have more surviving generations.  In an over abundance of resources the reverse could be true.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultimately in natural selection, it's all about getting your genetic information to as many surviving copies or permutations as you can. Many organisms use DNA to hold the information, but there are other options (RNA viruses for example).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Getting back to the phrase:&lt;/em&gt; It's saying that the fittest is the one who &lt;em&gt;continually&lt;/em&gt; replicates well in the current environment/surroundings.  Ecosystems are often changing, thus who has the best fitness will change as the ecosystems changes.  When an ecosystem is stable for a long period of time, you will find highly adapted organisms to that ecosystem.  This is because the selection towards &quot;fittest&quot; has been applied to many, many generations.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2013-07-11T21:39:45.710" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9238" PostTypeId="2" ParentId="9232" CreationDate="2013-07-11T22:47:12.867" Score="4" Body="&lt;p&gt;'Survival of the fittest' has never really made sense, because it confuses the scientific (evo. biological) and colloquial definitions of the word - which some of the previous posters have also done. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biological fitness simply refers to an individuals genetic contribution to the following generation. That is, a 'fitter' individual, in an evolutionary sense, is one whose genetic material is proportionally overrepresented in the next generation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;mechanism&lt;/em&gt; by which an individual achieves this may include out-surviving competitors, but it's certainly not the only way to increase fitness. Two individuals may live for the same length of time, but one may successfully court more females, or out-compete the other for food resources, for example. So when we refer to a 'fitter' individual (or individuals), we're saying nothing about &lt;em&gt;why&lt;/em&gt; they are so. It's not a comment on their 'fitness' in the human sense of the word (bigger, stronger, longer-living), it simply refers to how well they pass on their genetic material.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you can see why the phrase is nonsense. If we're being precise, then 'survival of the fittest' translates to 'survival of the individual who is better able to pass on their genetic material to the next generation' - which is meaningless because it tangles up these different concepts.   &lt;/p&gt;&#xA;" OwnerUserId="3589" LastEditorUserId="3059" LastEditDate="2013-07-12T23:18:55.883" LastActivityDate="2013-07-12T23:18:55.883" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9239" PostTypeId="2" ParentId="9188" CreationDate="2013-07-12T00:19:04.170" Score="0" Body="&lt;p&gt;RBCs do lose their functionality as they get older. In addition to the free radical damage they receive, the cells also become smaller over time which increases the effective concentration of the haemoglobin which causes other problems like hemolysis or rigidity. &lt;/p&gt;&#xA;" OwnerUserId="389" LastEditorUserId="1320" LastEditDate="2013-07-12T11:46:28.460" LastActivityDate="2013-07-12T11:46:28.460" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9240" PostTypeId="1" AcceptedAnswerId="9241" CreationDate="2013-07-12T03:04:25.427" Score="2" ViewCount="404" Body="&lt;p&gt;I noticed several of these guys outside, all in a vertical position clinging to a wall. I didn't come to them too closely, but my immediate reaction was that they are scorpions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://imgur.com/U641JBm&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.imgur.com/U641JBm.jpg&quot; title=&quot;Hosted by imgur.com&quot; /&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought that maybe it's a curled-up scorpion, or maybe there's some kind of particular scorpion that is this circular in shape? These are probably silly conclusions, but I'm not an expert in this field. I would really appreciate the insight of a professional!  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks very much.  &lt;/p&gt;&#xA;" OwnerUserId="3997" LastEditorUserId="16866" LastEditDate="2021-05-14T04:53:18.323" LastActivityDate="2021-05-16T21:05:26.993" Title="Identification of this humpbacked, brown, clawed insect climbing up my wall?" Tags="&lt;species-identification&gt;&lt;zoology&gt;&lt;entomology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="9241" PostTypeId="2" ParentId="9240" CreationDate="2013-07-12T04:49:51.567" Score="8" Body="&lt;p&gt;That's the exoskeleton (shed outer shell) of a young cicada, left behind when it emerged as an adult and (we can imagine) flew off somewhere to sing, and find a mate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://earthsky.org/todays-image/hail-the-17-year-cicada-hatch-of-2013&quot; rel=&quot;noreferrer&quot;&gt;This article on EarthSky&lt;/a&gt; has a nice description of the big cicada hatch this summer (2013), and also a great picture of an adult cicada emerging from the exoskeleton. However, this article and other recent news about cicadas mostly deals with the Eastern US genus &lt;em&gt;Magicicada&lt;/em&gt;, and it's likely that in Arizona you're seeing a different genus (that is, a different type of cicada).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You'd probably have to find an adult in order to identify exactly what genus and species of cicada you've got. Alternatively, you could listen for their songs – &lt;a href=&quot;http://www.insectsingers.com/100th_meridian_cicadas/western_species.html&quot; rel=&quot;noreferrer&quot;&gt;this site&lt;/a&gt; has examples of calls from many Western US species, including the Apache Cicada &lt;em&gt;Diceroprocta apache&lt;/em&gt;, which seems to be a common cicada in your area.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-07-12T05:10:40.203" LastActivityDate="2013-07-12T05:10:40.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9242" PostTypeId="1" AcceptedAnswerId="9254" CreationDate="2013-07-12T07:09:47.613" Score="1" ViewCount="221" Body="&lt;p&gt;i don't need Taq polymerase. Just need normal DNA polymerase. So the main idea is preparation polymerase directly from Lactobacillus without using cloned vector. My idea is electrophoresis using agarose gel and calculating the isoelectric point of Polymerase based on protein sequence to know where they will migrate after electrophoresis. Is it possible for this idea ? &lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="948" LastEditDate="2013-07-13T02:23:27.290" LastActivityDate="2013-07-13T02:23:27.290" Title="Preparation of normal DNA polymerase" Tags="&lt;molecular-biology&gt;&lt;diy-biology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9243" PostTypeId="1" AcceptedAnswerId="9245" CreationDate="2013-07-12T07:33:11.803" Score="2" ViewCount="542" Body="&lt;p&gt;I'm currently an undergraduate math student and researching on the internet I discover that exists an area called &quot;biomathematics&quot;. Looks so interesting. They use the graph theory and topology to describe the cells and DNA structure. Was love at first sight, because I really love maths and biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm reading the book &quot;Clinically Oriented Anatomy&quot; of Keith L. Moore and &quot;Essential Cells Biology&quot; of Bruce Alberts, but I don't know if I'm doing right. If anyone know how to start to learn this science I would really appreciate it.&lt;/p&gt;&#xA;" OwnerUserId="4006" LastEditorUserId="3952" LastEditDate="2013-07-12T08:54:16.823" LastActivityDate="2013-07-14T05:44:57.533" Title="How to learn biomathematics?" Tags="&lt;microbiology&gt;&lt;book-recommendation&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9244" PostTypeId="1" AcceptedAnswerId="9255" CreationDate="2013-07-12T08:43:59.983" Score="6" ViewCount="1212" Body="&lt;p&gt;Neural receptive fields map the spatial or temporal distribution of the data to individual neuron excitation, if I understand correctly, but I do not understand if receptive fields (especially in the higher cognitive areas such as the various layers of the visual cortex, etc.) are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Actual &lt;em&gt;structural&lt;/em&gt; distributions of neurons that help map specific spatial or temporal properties of stimuli (such as concentric arrangement for contrast detection, rectangular arrangement for orientation detection, or movement detection, etc.), or,&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Merely a &lt;em&gt;mapping&lt;/em&gt; of the structure of the &lt;em&gt;stimuli&lt;/em&gt; that can excite specific neurons.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;If it's the latter, isn't it basically as simple as a pattern/feature/vector that individual neurons are sensitive to?&lt;/p&gt;&#xA;" OwnerUserId="3998" LastEditorUserId="9943" LastEditDate="2016-03-10T21:11:50.497" LastActivityDate="2016-03-10T21:11:50.497" Title="What exactly is the neural receptive field?" Tags="&lt;neuroscience&gt;&lt;vision&gt;&lt;neuroanatomy&gt;&lt;touch&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9245" PostTypeId="2" ParentId="9243" CreationDate="2013-07-12T09:03:13.283" Score="4" Body="&lt;p&gt;MathsBio is quite a large field. It is an interdisciplinary branch having utility in a lot of branches in biology like biophysics, biomedical, genetics and molecular biology. Applied  Mathematics is generally used in modelling and understanding biological phenomena where we have to deal with large amount of data, for example the use of graph theory for analysing biochemical networks. Systems biology is an emerging field which uses a lot of mathematics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should pick a book depending on the field in which you want to use mathematics, though having knowledge of elementary biology is necessary. I am suggesting some books which cover wide application of mathematics in biology. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematical Biology: I. An Introduction by JD Murray  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For systems biology:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematical Modelling in Systems Biology: An Introduction by Brian Ingalls&lt;/p&gt;&#xA;" OwnerUserId="3841" LastEditorUserId="1320" LastEditDate="2013-07-12T11:43:16.823" LastActivityDate="2013-07-12T11:43:16.823" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9246" PostTypeId="2" ParentId="675" CreationDate="2013-07-12T09:24:47.553" Score="1" Body="&lt;p&gt;Judging from your response to Gurav in the comments, it sounds like introductory zoology and plant biology texts would fit the bill. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For zoology, we teach from Hickman et al's &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0073040509&quot; rel=&quot;nofollow&quot;&gt;Integrated Principles of Zoology&lt;/a&gt;. It outlines the major phyla, their defining characteristics, with plenty of specific examples scattered throughout. There are nice little problem sets throughout, and it goes into a solid amount of detail for a first or second year zoology course.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For plants, I've used Graham et al's &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0131469061&quot; rel=&quot;nofollow&quot;&gt;Plant Biology&lt;/a&gt;, which takes a similar general approach. Though it's perhaps a bit broader, and less species-focused.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both of these books outline the major relevant groups, and use 'representative' species to illustrate various biological points throughout. They might be a good place to start!&lt;/p&gt;&#xA;" OwnerUserId="3589" LastActivityDate="2013-07-12T09:24:47.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9247" PostTypeId="1" CreationDate="2013-07-12T09:50:41.937" Score="2" ViewCount="499" Body="&lt;p&gt;As far as I know, humans can distinguish between 5 basic tastes based on various molecules in food and their interactions. There's a level to all 5 so there can be an endless variety of tastes, and we can recognize them with some precision. What surprises me is that we can often distinguish the original flavors in a mix - for example in a salad or even more so in a blended juice. Shouldn't we perceive an entirely new flavor having the average of each basic taste?&#xA;Not entirely sure this belongs on a biology forum, but I hope someone can explain :)&lt;/p&gt;&#xA;" OwnerUserId="4007" LastActivityDate="2013-10-01T16:37:33.270" Title="How can we distinguish blended flavors?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9248" PostTypeId="2" ParentId="9232" CreationDate="2013-07-12T10:42:36.910" Score="1" Body="&lt;p&gt;While, as others point out, &quot;survival of the fittest&quot; is a pithy description of the theory rather than an actual serious statement I think it can be converted to a useful definition relatively easily.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is substantial debate about how, exactly, fitness should be defined. I'm not enough of an expert to want to try and lay out the complications here but I will give my preferred definition:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The fitness of an organism is defined as the number of its&#xA;  grandchildren that make it to adulthood (or that number divided by two&#xA;  for sexual organisms).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This has the advantage of being amenable to experimental investigation and intuitively simple while complex enough to avoid simple problems arising from the differences in offspring number and the question of infertile offspring.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-07-12T10:42:36.910" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9249" PostTypeId="1" AcceptedAnswerId="9251" CreationDate="2013-07-12T12:47:06.340" Score="1" ViewCount="84" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;E. coli&lt;/em&gt; is prevalent everywhere but only some strains produce toxins harmful to humans, such as &lt;em&gt;E. coli&lt;/em&gt; O157:H7. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Would anyone know if these strains are always producing this toxin or is it only under certain conditions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Is it the toxin itself that makes people sick and not the presence of the bacteria?&lt;/p&gt;&#xA;" OwnerUserId="3972" LastEditorUserId="1320" LastEditDate="2013-07-12T12:50:20.670" LastActivityDate="2013-07-12T13:44:45.930" Title="Do toxin producing strains of E. coli constantly produce toxin or only under certain conditions?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9251" PostTypeId="2" ParentId="9249" CreationDate="2013-07-12T13:44:45.930" Score="2" Body="&lt;p&gt;1) That depends on the fact, if the protein in the bacterium is regulated somehow or it is constantly expressed. That could be different for different toxins and even for the same toxins in different strains, so there is no  plain answer for all strains and toxins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) That, I guess, also depends on the toxin. There are some that are basically toxins, but do not make people sick. Sometimes, the toxin is produced by the bacterium, but never secreted. Sometimes it is secreted, but has no influence on the host. Sometimes the host does react to a toxin. But the human immune system can also react to the bacteria before they start producing toxin (if it is somehow regulated) or before the toxin concentration secreted by the bacteria starts to be harmful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of E. coli O157:H7, &lt;a href=&quot;http://dnaresearch.oxfordjournals.org/content/8/1/11.abstract&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper states it produces two different Shigatoxins (that were supposedly causing its pathogeny), but also some other toxins/toxin-like proteins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have studied some E.coli genomes previously, some non-pathogenic had several toxin-related genes, some pathogenic had actually none at all (at least none that could be annotated).&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-07-12T13:44:45.930" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9252" PostTypeId="1" CreationDate="2013-07-12T16:07:17.133" Score="6" ViewCount="141" Body="&lt;p&gt;Is it possible to have both type-1 (insulin-dependent) and type-2 (non-insulin-dependent) diabetes mellitus? That is, to have both insulin resistance and zero (or negligible) insulin production? If not, why not? And if so, then how common is this (among humans with each type of diabetes)? Any information on why the comorbidity may be high or low is also most welcome.&lt;/p&gt;&#xA;" OwnerUserId="988" LastActivityDate="2018-03-29T09:53:40.860" Title="Diabetes-diabetes comorbidity" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9254" PostTypeId="2" ParentId="9242" CreationDate="2013-07-12T20:31:55.507" Score="3" Body="&lt;p&gt;This is a very ambitious project for a DIY-er. To explain why, I'm going to use the example of DNA polymerase I from &lt;em&gt;E. coli&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA polymerase I is the most abundant DNA polymerase in the &lt;em&gt;E. coli&lt;/em&gt; cell, but nevertheless is still only present at around 300 copies per cell    &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.biomedcentral.com/1471-2164/9/102&quot; rel=&quot;nofollow&quot;&gt;Ishihama Y &lt;em&gt;et al&lt;/em&gt;. (2008) Protein abundance profiling of the &lt;em&gt;Escherichia coli&lt;/em&gt; cytosol. BMC Genomics. 9:102&lt;/a&gt;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This was the first DNA polymerase that was ever purified, in the laboratory of Arthur Kornberg    &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(&lt;a href=&quot;http://www.jbc.org/content/233/1/163.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Enzymatic Synthesis of Deoxyribonucleic Acid : I. PREPARATION OF SUBSTRATES AND PARTIAL PURIFICATION OF AN ENZYME FROM ESCHERICHIA COLI Lehman, MJ &lt;em&gt;et al&lt;/em&gt;. (1958) J. Biol. Chem. 33:163-170.&lt;/a&gt;). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In this paper a method of purification is described that starts with 60 litres of culture. There is also this statement:    &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;One kilo of &lt;em&gt;E. coli&lt;/em&gt; yields less than 10 mg of the purified enzyme.&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm guessing that you have no experience of protein purification, so I'll just tell you that this is very discouraging: these days, with overexpression, people expect to get mg quantities of their protein from just a few grams of bacterial cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a clear illustration of why it is pretty much unthinkable for you to set out to purify an enzyme like this using small-scale methods, and explains why techniques of overexpression and the use of affinity tags have revolutionised protein purification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And it gets worse: even if you did manage to purify some DNA polymerase I from a bacterial source you would find that it is actually not very good at making DNA. This is because as well as extending primers in a 5'&gt;3' direction, it is is very good at degrading DNA in the same direction. In other words as the enzyme moves along a template molecule, copying it, it will degrade any existing DNA that it meets &quot;ahead&quot; of its direction of travel. This is why the most commonly-used form of this enzyme in research is the &quot;Klenow fragment&quot;, a fragment of the polymerase that lacks the 5'&gt;3' exonuclease activity. This fragment was originally made by treating DNA polymerase I with the protease subtilisin, but it is now expressed from an engineered polA gene. Klenow fragment polymerase was used in the original PCR experiments (it had to be added afresh at every cycle).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know how much money you have to spend on your projects, but in fact these enzymes can now be bought relatively cheaply.  I don't think that you can expect to make them for yourself, without this becoming the actual project.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, if you can get hold of a strain of &lt;em&gt;E. coli&lt;/em&gt; with an expression plasmid for Taq polymerase then you really could make your own very easily - I've done this myself (but I no longer have the strain) and the heat stability of the enzyme makes the purification trivial. It would be much easier to use your own Taq with a heated water bath than to try to make DNA polymerase I. But obviously it depends upon what you are trying to do: Taq polymerase may be unsuitable for other reasons.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-07-12T20:31:55.507" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9255" PostTypeId="2" ParentId="9244" CreationDate="2013-07-12T23:35:41.643" Score="2" Body="&lt;p&gt;No, it is not 1. the structural distribution of the neurons themselves.  If by mapping you mean a kind of function that maps real space to cognitive space (or such) then it is not that either (at least, not explicitly/directly).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;receptive field&lt;/strong&gt; is the region of 3D space in which sensory neurons can make their relevant detection.  It's not a pattern/feature/vector, just the coordinates defining some spatial region itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For &lt;strong&gt;example&lt;/strong&gt;, take the neurons making up your audio sensory system.  If an object is making noise and you can hear it, then that object is within the receptive field of the hair cells responsible for the audible frequencies.  That is, the object's physical location is within the spatial coordinates that define your audio system's perceptive field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fun fact&lt;/strong&gt;: for two sounds of the same amplitude, lower frequency detecting hair cells tend to have a larger receptive field since lower frequency signals travel farther.  In other words, the receptive field is somewhat dependent on the quality of the source of perception, not just the sensory neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's strange terminology coming from physics, because we generally define &quot;fields&quot; by sources, not by receivers.  An audio source has an unambiguous &quot;field&quot; of acoustic radiation.  A receiver does not generate a field but is sensitive to a certain threshold of field quantity.  So to define the field as something coming from the receivers (the sensory neurons) is an unintuitive idea.&lt;/p&gt;&#xA;" OwnerUserId="1853" LastEditorUserId="107" LastEditDate="2013-07-14T13:12:34.470" LastActivityDate="2013-07-14T13:12:34.470" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9256" PostTypeId="2" ParentId="9252" CreationDate="2013-07-13T01:55:54.400" Score="2" Body="&lt;p&gt;Yes you could think of an individual as &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/22109281&quot; rel=&quot;nofollow&quot;&gt;having both&lt;/a&gt;(1).  A good place to start looking at &quot;newer&quot; diabetes other than the classic 1 and 2 is latent autoimmune diabetes (LADA).  Though, I don't know if one would say you had &lt;em&gt;no&lt;/em&gt; insulin production.  It would seem as though patients exhibit some characteristics of &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/dmrr.2411/abstract;jsessionid=912BFAAC8657AAB17875BD1C28FA1E24.d02t04&quot; rel=&quot;nofollow&quot;&gt;both types&lt;/a&gt;(2), and indeed there maybe a &lt;a href=&quot;http://www.cmj.org/ch/reader/view_abstract.aspx?volume=126&amp;amp;issue=4&amp;amp;start_page=783&quot; rel=&quot;nofollow&quot;&gt;continuum possible&lt;/a&gt;(3) between ether &quot;pure&quot; type on each extreme.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) The type 2 diabetes-associated variant in TCF7L2 is associated with latent autoimmune diabetes in adult Europeans and the gene effect is modified by obesity: a meta-analysis and an individual study. Diabetologia. 2012 Mar;55(3):689-93. doi: 10.1007/s00125-011-2378-z. Epub 2011 Nov 23.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) Latent autoimmune diabetes (LADA) is perched between type 1 and type 2: evidence from adults in one region of Spain. Diabetes/Metabolism Research and Reviews 2013; 1520-7560.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3) Latent autoimmune diabetes in adults: evidences for diabetes spectrum?.Chin Med J 2013;126:783-788&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2013-07-13T02:25:43.727" LastActivityDate="2013-07-13T02:25:43.727" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9257" PostTypeId="2" ParentId="3646" CreationDate="2013-07-13T02:27:16.043" Score="3" Body="&lt;p&gt;The value of the membrane potential does not affect the location of the resting potential.  The membrane potential affects only the fraction of channels that are open, thus allowing net current to change, which allows for the depolarization and repolarization of the membrane (the action potential).  During the action potential, the resting potential does not change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The value of the resting potential is governed only by the distribution of ions (how many are on one side of the membrane vs. how many are on the other).  This is relatively constant even as ions cross the membrane for the action potential; it is really not a very large fraction of ions moving at all compared to the reservoir they are in, so the reversal potentials are preserved over time. &lt;/p&gt;&#xA;" OwnerUserId="1853" LastEditorUserId="1853" LastEditDate="2013-07-13T11:47:08.313" LastActivityDate="2013-07-13T11:47:08.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9259" PostTypeId="1" CreationDate="2013-07-13T06:46:56.783" Score="0" ViewCount="42" Body="&lt;p&gt;I am searching for image and information, like distribution etc of the genus Acesina. The Taxonomic tree is:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Kingdom:        Animalia&#xA;Phylum:         Arthropoda&#xA;Class:          Insecta&#xA;Order:          Lepidoptera&#xA;Superfamily:    Papilionoidea&#xA;Family:         Lycaenidae&#xA;Genus:          Acesina&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.catalogueoflife.org/col/browse/tree&quot; rel=&quot;nofollow&quot;&gt;Catalogue of Life&lt;/a&gt; this genus has the 4 species. I haven't found any information by searching web, even the species are extinct or not! Any pointer would be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="4012" LastActivityDate="2013-07-15T18:57:31.803" Title="Information and image of Genus Acesina" Tags="&lt;zoology&gt;&lt;taxonomy&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9260" PostTypeId="1" AcceptedAnswerId="9263" CreationDate="2013-07-13T16:15:29.597" Score="0" ViewCount="763" Body="&lt;p&gt;As i know, Taq Polymerase can be found in Thermus aquaticus, so i do a search for protein list of Thermus aquaticus and have this : &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/proteins/1724?project_id=55053&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/genome/proteins/1724?project_id=55053&lt;/a&gt; . After filter for 'polymerase' i found a lot of protein named polymerase :&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;DNA polymerase beta domain protein region&lt;/li&gt;&#xA;&lt;li&gt;DNA polymerase I&lt;/li&gt;&#xA;&lt;li&gt;DNA polymerase III, alpha subunit&lt;/li&gt;&#xA;&lt;li&gt;DNA polymerase III, beta subunit&lt;/li&gt;&#xA;&lt;li&gt;DNA polymerase III, delta subunit&lt;/li&gt;&#xA;&lt;li&gt;DNA-directed DNA polymerase&#xA;-.....&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I don't know what they mean and which is the protein i'm looking for ?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;After click on one of them i have the sequence not in A-T-G-X format :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ORIGIN&lt;br&gt;&#xA;        1 msgvdallll gvelsraiit aysvyaivli lggflarlpt rweervealg gsfylagvil&#xA;       61 wryyaggday dldlflrasg mallvlprlv rvvlreyggg r&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does it mean and how to working with it ?&lt;/p&gt;&#xA;" OwnerUserId="3894" LastActivityDate="2013-07-14T04:50:23.943" Title="Problem on finding sequence of Taq polymerase" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9261" PostTypeId="1" CreationDate="2013-07-13T16:44:34.363" Score="6" ViewCount="23045" Body="&lt;p&gt;Many cells have a cell membrane composed of two layers of lipids. Why is it that they have two layers and not just one? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What purpose do this arrangement serve?&lt;/p&gt;&#xA;" OwnerUserId="4013" LastEditorUserId="3340" LastEditDate="2016-06-09T13:31:20.333" LastActivityDate="2016-06-09T13:50:08.807" Title="Why do cell membranes have a lipid bilayer instead of a monolayer?" Tags="&lt;cell-biology&gt;&lt;microbiology&gt;&lt;cell-membrane&gt;&lt;lipids&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9263" PostTypeId="2" ParentId="9260" CreationDate="2013-07-13T17:33:05.397" Score="3" Body="&lt;p&gt;According to &lt;a href=&quot;http://talon.niagara.edu/~mgallo/391s08web/papers/taq-isolation.pdf&quot; rel=&quot;nofollow&quot;&gt;the paper here&lt;/a&gt; &quot;Taq polymerase&quot; is the DNA polymerase I from &lt;em&gt;Thermus aquaticus&lt;/em&gt;. (Incidentally the paper has the complete sequence of the gene in question.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find a protein sequence entry at NCBI &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/protein/507891?report=genbank&amp;amp;log%24=protalign&amp;amp;blast_rank=9&amp;amp;RID=Y334H3GW014&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. This shows the sequence of amino acids in the protein, not the DNA sequence of the gene. Several lines from the top you will see:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;DBSOURCE    locus TTHDNAP accession D32013.1&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;with the last word highlighted as a link. Follow that link to the DNA sequence. That entry includes the line:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;CDS             1..2499&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;which tells you that the initiator ATG of the gene is right at the start of the sequence shown, but that the 3026 bp sequence includes a lot of downstream DNA. If you click on CDS on that line it will highlight the coding sequence in the DNA.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A very cursory comparison of this sequence with the one in the paper that I linked to suggests that this is the same gene.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-07-13T17:33:05.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9265" PostTypeId="1" AcceptedAnswerId="19775" CreationDate="2013-07-13T20:09:04.357" Score="6" ViewCount="20094" Body="&lt;p&gt;Kefir is a fermented milk drink made with kefir grains. It usually is prepared by inoculating cow, goat or sheep milk with kefir grains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to prepare the drink with soy milk, which worked fine for some months. Then the kefir grain stagnated in its growth. I use bottled soy milk from the supermarket. I do not produce the soy milk by myself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &quot;real&quot; milk the kefir grains never stop growing (and dividing), but in soy milk they apparently do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do the kefir grains stop growing in soy milk? Are they lacking a specific nutrient that is only contained in milk from animals?&lt;/p&gt;&#xA;" OwnerUserId="4014" LastEditorUserId="107" LastEditDate="2013-07-14T15:54:21.897" LastActivityDate="2018-03-05T11:25:58.103" Title="Why do kefir grains stop growing in soy milk?" Tags="&lt;microbiology&gt;&lt;ecology&gt;&lt;food&gt;&lt;milk&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9266" PostTypeId="1" AcceptedAnswerId="14298" CreationDate="2013-07-14T02:41:32.323" Score="5" ViewCount="1442" Body="&lt;p&gt;Does anyone know an effective buffer mix to use for high current Western transfers?  We are successfully using the vendor's premixed buffer to transfer a wide range of protein sizes to PVDF membranes at 1A/25V for 10 min.  We get great results with the vendor's expensive buffer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't been able to find a non-proprietary recipe that works.  The best ones we have hold the 25V, but then have a decrease in conductivity (increase in resistance) where they will start at 1A, but drop to 0.4A by the end of the 10 min.  The vendor's buffer seems to hold the high current and results in better transfers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know if it will be helpful to list all the variations I've tried in detail, but they have revolved around modifying a traditional Towbin buffer plus SDS, more glycine/Tris, or MgCl2.  These were all various suggestions from people around the department, but I haven't found much published evidence for a buffer under these conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize 1A (and no I don't mean 1mA) is a lot of current, but the vendor's system works really well.  Any pointers on what I might try/add would be appreciated even if you don't have a worked out protocol.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: Info from the MSDS indicates it has 3 reagents:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Listing of dangerous and non-hazardous components:&#xA;Proprietary Reagent K&#xA;10-20%&#xA;Proprietary Reagent EB II&#xA;5-10%&#xA;Proprietary Reagent S&#xA;1.0-2.5%&#xA;7732-18-5 water&#xA;50-100%&#xA;·&#xA;.....&#xA;Solvent content:&#xA;Organic solvents:&#xA;0.0 %&#xA;Water:&#xA;74.8 %&#xA;Solids content:&#xA;25.2 %&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;[I'm not sure if this MSDS info should be put here, just because I'm looking for someone who has already used a high current buffer they know the formulation for, not a guess to what I have.]&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2013-07-16T23:59:26.340" LastActivityDate="2017-02-08T12:58:35.783" Title="High Current (Speed) Transfer Buffer Recipe" Tags="&lt;lab-techniques&gt;&lt;protocol&gt;&lt;western-blot&gt;" AnswerCount="2" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="9267" PostTypeId="2" ParentId="9260" CreationDate="2013-07-14T04:50:23.943" Score="0" Body="&lt;p&gt;Thank Alan Boyd so much, below is the answer for these protein code mean:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;    A  alanine               P  proline       &#xA;    B  aspartate/asparagine  Q  glutamine      &#xA;    C  cystine               R  arginine      &#xA;    D  aspartate             S  serine      &#xA;    E  glutamate             T  threonine      &#xA;    F  phenylalanine         U  selenocysteine      &#xA;    G  glycine               V  valine        &#xA;    H  histidine             W  tryptophan        &#xA;    I  isoleucine            Y  tyrosine&#xA;    K  lysine                Z  glutamate/glutamine&#xA;    L  leucine               X  any&#xA;    M  methionine            *  translation stop&#xA;    N  asparagine            -  gap of indeterminate length&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Source from NCBI : &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3894" LastActivityDate="2013-07-14T04:50:23.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9268" PostTypeId="2" ParentId="7005" CreationDate="2013-07-14T05:16:36.923" Score="1" Body="&lt;p&gt;MCM's answer is quite correct. There are quite a few specific ways various pathogens escape &quot;immunity&quot; (long term, often not truly life-long, protection).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To quickly restate what he has said:&#xA;First the pathogen can mutate to be different enough that your body won't recognize it (ie different strains of flu or HIV), it can hide in cells or immunoprivileged areas of the body, it can actually shut your immune system down, actively combat your immune system, or prevent an immune response from being mounted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And just a few more thoughts:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are certain pathogens we are still trying to figure out how they avoid the immune system (the technical quality is &lt;a href=&quot;https://en.wikipedia.org/wiki/Immunogenicity&quot; rel=&quot;nofollow&quot;&gt;immunogenicity&lt;/a&gt;).  A good example human respiratory syncytial virus (RSV).  Again this is actually an active field of study for a great many pathogens.  When we test many of these &quot;tricky&quot; pathogens in animal models, we find that they often can gain immunity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;+1 @MCM, I was trying to cram this into a comment, but I didn't think I could.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some interesting areas to read up on if you are interested in the subject are immune avoidance/evasion and forward genetics.  You will more often hear about reverse genetics, but forward genetic experiments can allow us to see how the &quot;chess game&quot; will be played out by the pathogens in new situations.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2013-07-14T05:16:36.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9269" PostTypeId="2" ParentId="9243" CreationDate="2013-07-14T05:44:57.533" Score="1" Body="&lt;p&gt;I really like &lt;a href=&quot;http://press.princeton.edu/titles/8458.html&quot; rel=&quot;nofollow&quot;&gt;&quot;A Biologist's Guide to Mathematical Modeling in Ecology and Evolution&quot;&lt;/a&gt; by&#xA;Sarah P. Otto &amp;amp; Troy Day, although it's more specific to Biology and Evolution - which may have been the first field in biology to use mathematics.&lt;/p&gt;&#xA;" OwnerUserId="4015" LastActivityDate="2013-07-14T05:44:57.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9270" PostTypeId="2" ParentId="9265" CreationDate="2013-07-14T06:57:08.813" Score="8" Body="&lt;p&gt;Yes, they are behaving differently because of the lack of nutrients, including lactose, and possibly because of the presence of other chemicals in soy milk that aren't in dairy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kefir grains are a complex community of different types of lactic acid bacteria and yeasts which metabolize (eat) various nutrients/chemicals in their environment. Because soy milk is a chemically different environment than dairy milk, these communities function in different ways. Over repeated propagations in soy milk, you probably have cultivated a very different community in regards to species diversity and the chemical products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Liu and Lin describe &lt;a href=&quot;http://dx.doi.org/10.1111/j.1365-2621.2000.tb16078.x&quot;&gt;here&lt;/a&gt;&#xA;, the &lt;strong&gt;kefir community members in dairy milk are eating mainly lactose, whereas in soymilk they are eating sucrose, raffinose and stachyose&lt;/strong&gt;. As a result, the reproduction of the bacteria and the yeasts differs, as did the alcohol and lactic-acid contents of the end-product.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because your question is a practical one, you might be interested to know that in that paper, the authors found that adding 1% sucrose (table sugar) or 1% glucose to the soymilk produced an end-product that more closely mimicked that of dairy milk. You could give that a try and see if it improves your kefir growth.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1111/j.1365-2621.2000.tb16078.x&quot;&gt; &lt;strong&gt;Liu JR, Lin CW&lt;/strong&gt;. 2000. Production of kefir from soymilk with or without added glucose, lactose, or sucrose. Journal of Food Science 65: 716–719.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-07-14T23:07:25.190" LastActivityDate="2013-07-14T23:07:25.190" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9271" PostTypeId="1" AcceptedAnswerId="9280" CreationDate="2013-07-14T07:09:25.087" Score="7" ViewCount="10319" Body="&lt;p&gt;I remember that in Michael Crichton's novel &lt;a href=&quot;http://en.wikipedia.org/wiki/Jurassic_Park_%28novel%29&quot;&gt;Jurassic Park&lt;/a&gt;, Tyrannosaurus Rex was supposed to have movement based vision. (Of course, that is a novel and not a scientific text.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have also noticed while feeding chickens, that they behave differently when they see me adding the food for them into the container as opposed to leaving it there for them when they cannot see me. (But this can be explained easily by different reasons, for example they are used to human as a source of their food, so they naturally go close to them.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are there some kinds of animals who have primarily movement based vision? If yes, which animals are examples for this?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The Michael Crichton's novel has been widely discussed online, I found for example &lt;a href=&quot;http://jurassicpark.wikia.com/wiki/Tyrannosaurus_rex#Eyesight_Debate&quot;&gt;this&lt;/a&gt; and several answers at &lt;a href=&quot;http://answers.yahoo.com/question/index?qid=20061217193648AASG0Fp&quot;&gt;Yahoo Answers&lt;/a&gt;. Frogs and reptiles are mentioned there. &lt;/p&gt;&#xA;" OwnerUserId="3956" LastEditorUserId="3952" LastEditDate="2013-07-14T07:38:49.210" LastActivityDate="2013-07-16T13:15:42.090" Title="Are there animals which can see movements better than shapes or colors?" Tags="&lt;zoology&gt;&lt;vision&gt;" AnswerCount="4" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9272" PostTypeId="1" AcceptedAnswerId="9273" CreationDate="2013-07-14T10:53:18.140" Score="0" ViewCount="745" Body="&lt;p&gt;Recently, I have been researching about DNA and I know the most popular method for detecting viruses is based on DNA. After learning about proteins, I wonder why we do not detect viruses based on virus proteins? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it becomes true we can save a lot of money, instead of doing a PCR reaction, we can detect more than one disease in a single reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, when I have the sequence of a virus from NCBI Genebank, I can know how many proteins the target organism produces and I can calculate the molecular weight of each protein. Then running it in a SDS-PAGE gel to see what the bands look like, may be that I can know the target organism is present or not?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, HIV produces 9 proteins and the molecular weight of each protein is different.&#xA;So after doing electrophoresis, I have 9 bands. Based on the distance between each band and based on the molecular weight, it's possible to know HIV is present or not? &lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="948" LastEditDate="2013-07-15T14:16:26.007" LastActivityDate="2013-07-15T14:16:26.007" Title="Why not use SDS-PAGE as a method to detect viruses?" Tags="&lt;molecular-biology&gt;&lt;virology&gt;&lt;sds-page&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9273" PostTypeId="2" ParentId="9272" CreationDate="2013-07-14T11:34:58.907" Score="5" Body="&lt;p&gt;Put simply, the answer is that you &lt;strong&gt;could&lt;/strong&gt; seek to detect viral proteins, but because these proteins would be very minor components of your sample, you would have to use an immunoblotting technique to detect a specific viral protein. While immunoblotting is quite a sensitive technique, I think its fair to say that it can be technically demanding. In contrast a PCR reaction is exquisitely sensitive and is fairly robust. PCR is also technically more staightfoward because DNA is generally easier to work with than are proteins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before the advent of PCR, immunoblotting would have been the method of choice.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-07-14T11:34:58.907" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9274" PostTypeId="2" ParentId="9259" CreationDate="2013-07-14T13:09:20.770" Score="1" Body="&lt;p&gt;The genus &lt;em&gt;Acesina&lt;/em&gt; has been revised and is now part of the genus &lt;em&gt;&lt;a href=&quot;http://tolweb.org/Arhopala/112304&quot; rel=&quot;nofollow&quot;&gt;Arhopala&lt;/a&gt;&lt;/em&gt;. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Arhopala&quot; rel=&quot;nofollow&quot;&gt;wikipedia page for &lt;em&gt;Arhopala&lt;/em&gt;&lt;/a&gt; has some additional information on this genus.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2013-07-15T18:57:31.803" LastActivityDate="2013-07-15T18:57:31.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9275" PostTypeId="2" ParentId="9271" CreationDate="2013-07-14T14:56:38.893" Score="1" Body="&lt;p&gt;There certainly are many adaptations in the light receptors in the eyes that enhance &lt;a href=&quot;http://www.springerreference.com/docs/html/chapterdbid/318221.html&quot; rel=&quot;nofollow&quot;&gt;contrast, color sensing, color discrimination as well as feature and movement sensitivity&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In school we usually learn about the cone and rod cells which are color and contrast sensitive in humans.  Humans have only 3 types of cone receptors, &lt;a href=&quot;http://wildthings.sarahzielinski.com/blog/what-the-oatmeal-might-have-gotten-wrong-about-mantis-shrimp/&quot; rel=&quot;nofollow&quot;&gt;the record may be 16 types of cone receptors&lt;/a&gt;.  Many animals have no cone receptors and don't see color.  The highly polychromatic mantis shrimp with 16 color receptors mentioned here may devote most of its brain power to motion sensing and little to color or feature parsing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Motion sensing is not only wired in the brain, but the neural layers within the retina &lt;a href=&quot;http://www.bcs.rochester.edu/courses/crsinf/504/ARCHIVES/F03/calkins.cones01.pdf&quot; rel=&quot;nofollow&quot;&gt;also generate neural signals when motion happens in the eye&lt;/a&gt;.  In the case of human beings the rod cells generate motion sensitivity..  Individual cell groups can cue to motion in a specific direction before passing off to the brain, which really helps with the reflex time.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All this takes a lot of brain power and the density of the cone cell density is highest in &lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/vision/rodcone.html&quot; rel=&quot;nofollow&quot;&gt;the center of your field of vision&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The density and the neural structure of the retina is highly flexible, adaptable to many configurations.  Humans have a circular patch of high density cone receptors, cheetah have a long vertical streak of them which help them track prey when running at speeds over 60 miles per hour. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All this being said, its unlikely that an animal would only see movement, especially a larger on. In Jurassic park, the tyrannosaurus motion only eyes was a dramatic twist - its hard to imagine an animal having such a huge blindspot.  &lt;a href=&quot;http://jurassicpark.wikia.com/wiki/Tyrannosaurus_rex&quot; rel=&quot;nofollow&quot;&gt;Indeed this specific theory is now mostly discounted&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-07-15T17:14:14.587" LastActivityDate="2013-07-15T17:14:14.587" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9276" PostTypeId="1" AcceptedAnswerId="24022" CreationDate="2013-07-14T15:07:12.500" Score="5" ViewCount="1587" Body="&lt;p&gt;I would like to understand which mechanism triggers the first cell differentiation after &lt;em&gt;n&lt;/em&gt; divisions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read &lt;a href=&quot;https://biology.stackexchange.com/questions/3720/how-are-different-types-of-cells-created-from-zygote/8309#8309&quot;&gt;previous&lt;/a&gt; &lt;a href=&quot;https://biology.stackexchange.com/questions/3741/how-do-cells-know-what-type-to-differentiate-into&quot;&gt;articles&lt;/a&gt; on SE and Wikipedia articles on &lt;a href=&quot;http://en.wikipedia.org/wiki/Cellular_differentiation&quot; rel=&quot;nofollow noreferrer&quot;&gt;cellular differentiation&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Embryogenesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;embryogenesis&lt;/a&gt; but still fail to understand what exactly makes it so that starting from a given division cells suddenly start to be different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia claims that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the first hours after fertilization, this cell divides into&#xA;  identical cells. In humans, approximately four days after&#xA;  fertilization and after several cycles of cell division, these cells&#xA;  begin to specialize, forming a hollow sphere of cells, called a&#xA;  blastocyst&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;but do not explain &lt;strong&gt;&lt;em&gt;why&lt;/em&gt;&lt;/strong&gt; they begin to specialize.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could imagine &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;that a cell has a &quot;counter&quot; on the number of divisions which triggers differentiation after a given amount of divisions &lt;/li&gt;&#xA;&lt;li&gt;or a chemical substance (either cell-borne or external) forces a change in the division&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;but why some cells would become &quot;cell A&quot; and some others &quot;cell B&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am fairly sure that the biochemical mechanisms which regulate the life of a grown up mechanism can explain cellular differentiation (through hormones for instance) -- I am however interested by this specific moment, this &lt;em&gt;n-th&lt;/em&gt; division where identical cells become differentiated.&lt;/p&gt;&#xA;" OwnerUserId="4016" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2017-10-29T22:53:17.983" Title="which exact mechanism triggers the first cell differentiation after n divisions?" Tags="&lt;cell-biology&gt;&lt;gene-expression&gt;&lt;development&gt;&lt;embryology&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9277" PostTypeId="1" CreationDate="2013-07-14T16:43:20.053" Score="1" ViewCount="246" Body="&lt;p&gt;Definitely anecdotal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This friend is hypermetropic, and uses reading glasses. He doesn't have major issues facing car headlights, or using a torch (the one with a bulb - not a white LED). Yet place him in front of a TV/Computer screen, and he'll develop an ache in the eye sockets in no time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand an electric torch, an incandescent bulb, a car lamp are all DC types, whereas a TV/Computer screen is fast changing AC.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are human eyes equally sensitive to light from an AC, and a DC lamp?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2014-08-02T11:05:07.313" Title="Are human eyes equally sensitive to AC, and DC lamps?" Tags="&lt;eyes&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9278" PostTypeId="2" ParentId="9244" CreationDate="2013-07-14T17:45:45.440" Score="3" Body="&lt;p&gt;I think is closer to 2. It is the &lt;strong&gt;subset&lt;/strong&gt; of &lt;strong&gt;sensory space&lt;/strong&gt; that elicits a &lt;strong&gt;reaction&lt;/strong&gt; in a given &lt;strong&gt;neural population&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you should:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Pick your &lt;strong&gt;neural population&lt;/strong&gt;. Usually it is a single neuron (but can be easily extrapolated to bigger populations). It may be a sensory neuron, or a neuron in a higher processing region.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Determine your &lt;strong&gt;sensory space&lt;/strong&gt;. That is, you should decide the kind of stimuli you'll be dealing with. For example, not only &quot;visual stimuli&quot;, but you should identify the parameters, or independent variables, you will vary in your experiment.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Define a criterion to discriminate between &lt;strong&gt;reaction&lt;/strong&gt; and non-reaction. This implies to choose what is the dependent variable in your study (for example neuron firing rate). Then you could define what features in the relation $\frac{dependent\:variables}{independent\:variables}$ you will search for. That is the tuning curve (which well may be a high dimensional curve).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Perform your experiment and analyze your curve. The region of parameters (independent variables) whose reaction goes above threshold according to your criterion is the &lt;strong&gt;receptive field&lt;/strong&gt;. Sometimes is not trivial to define such a criterion (see: &lt;a href=&quot;http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0040092&quot; rel=&quot;nofollow&quot;&gt;http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0040092&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;A good general reference is the article in Scholarpedia: &lt;a href=&quot;http://www.scholarpedia.org/article/Receptive_field&quot; rel=&quot;nofollow&quot;&gt;http://www.scholarpedia.org/article/Receptive_field&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This type of analysis is very useful for position coding, that is, when you expect that the activation of a specific region in the brain correlates to stimuli in a region of sensory space. But sometimes things are more complicated (e.g Olfactory coding &lt;a href=&quot;http://www.jneurosci.org/content/30/27/9017.full&quot; rel=&quot;nofollow&quot;&gt;http://www.jneurosci.org/content/30/27/9017.full&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="3570" LastEditorUserId="3570" LastEditDate="2013-07-14T18:03:45.700" LastActivityDate="2013-07-14T18:03:45.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9279" PostTypeId="1" CreationDate="2013-07-14T20:45:36.990" Score="2" ViewCount="6744" Body="&lt;p&gt;Squirrels have the ability to eat toxic mushrooms as described below. Are there any mushrooms that they can't eat without dying? &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;According to Dr. John Rippon, an IMA member and world expert on fungal diseases, squirrels have an interesting adaptation that allows them to eat mushrooms containing deadly amanita-toxins without being affected. There are three important chemicals in the amanitas. Two will knock you right off, but are destroyed in cooking. The third one is the interesting one: it consists of the second amanitin, bound tightly to a glycoprotein molecule. When we digest the mushroom, the enzymes in our gut break the bond between the toxin and the glycoprotein, leaving the toxin free to enter our bloodstream, while the glycoprotein is excreted (a glycoprotein is a [protein containing sugar molecules and accounts for the viscous properties of mucus], in case you don't know). What the squirrels have done is line their gut with a toxin-compatible glycoprotein, so that as soon as it gets split from its original glycoprotein molecule, it gets rebound to the squirrel glycoprotein, and excreted along with it. Obviously, the squirrels don't cook their food to destroy the first two molecules, but presumably those get bound in exactly the same way. Thus, squirrels and a few other animals (guinea pigs also, I believe) can eat mushrooms that are highly toxic to other animals with no ill effects.  &lt;a href=&quot;http://www.mushroomthejournal.com/greatlakesdata/Terms/squir27.html&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="146" LastEditorUserId="1590" LastEditDate="2013-07-30T09:34:08.583" LastActivityDate="2013-07-30T09:34:08.583" Title="Can Squirrels Eat Every Mushroom?" Tags="&lt;mammals&gt;&lt;toxicology&gt;&lt;mushroom&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2014-12-11T11:02:41.163" ContentLicense="CC BY-SA 3.0" />
  <row Id="9280" PostTypeId="2" ParentId="9271" CreationDate="2013-07-14T22:58:27.543" Score="5" Body="&lt;p&gt;I think &quot;movement-based vision&quot; is perhaps a bit of a misnomer. Ultimately, all vision is &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/21092350&quot; rel=&quot;nofollow&quot;&gt;contrast-based, depending on integrating signals from ON and OFF bipolar cells&lt;/a&gt;. It seems that this notion of so-called &quot;movement-based vision&quot; is derived from work on toad vision and &lt;a href=&quot;https://en.wikipedia.org/wiki/Feature_detection_%28nervous_system%29#Feature_detection_in_toad_vision&quot; rel=&quot;nofollow&quot;&gt;feature detection&lt;/a&gt;. In this case, it's more the downstream processing that results in different behavior based on the shape of the stimulus and the direction that it moves. The simple sensing of visual stimuli does not seem to be motion-based. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, aside from evolutionary inference, we would have no way of knowing whether Tyranassaurus rex had such behavior. As for the chickens, it's possible but I would be skeptical of such a system discriminating between immobile food and hand pouring food. I would chalk that up to a simple behavior of associating seeing you with getting food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One interesting note: many, many species have reflexive responses to moving visual stimuli. The first is called the &lt;a href=&quot;https://en.wikipedia.org/wiki/Optokinetic_reflex&quot; rel=&quot;nofollow&quot;&gt;optokinetic reflex&lt;/a&gt;, in which the eyes reflexively track contrast-based movement; and the second is the &lt;a href=&quot;https://en.wikipedia.org/wiki/Optomotor_response&quot; rel=&quot;nofollow&quot;&gt;optomotor response&lt;/a&gt;, in which the head or even the whole body move in response to a moving stimulus. Thus it &lt;em&gt;is&lt;/em&gt; safe to say that for many (most?) species, motion detection has a strong influence on the visual response...but again, I remain hesitant to use the phrase &quot;motion-based vision&quot;.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorDisplayName="user3934" LastEditDate="2013-07-16T12:05:10.550" LastActivityDate="2013-07-16T12:05:10.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9281" PostTypeId="1" AcceptedAnswerId="9282" CreationDate="2013-07-15T00:26:12.910" Score="6" ViewCount="241" Body="&lt;p&gt;This is growing in the woods near my house in the Butler, Pennsylvania (USA) area. I have not seen it around before, and I have no idea what is it. What is it? Is it poisonous to pets (or little kids)?&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Zxj5f.jpg&quot; alt=&quot;Unknown Plant&quot; /&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/fBnXx.jpg&quot; alt=&quot;Unknown Plant&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="4019" LastEditorUserId="16866" LastEditDate="2021-05-16T03:56:00.833" LastActivityDate="2021-05-17T20:20:22.317" Title="What is this plant in the Butler, Pennsylvania area?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="9282" PostTypeId="2" ParentId="9281" CreationDate="2013-07-15T01:05:16.797" Score="3" Body="&lt;p&gt;That looks like a bit like a Smilax to me, possibly &lt;a href=&quot;http://www.efloras.org/florataxon.aspx?flora_id=1&amp;amp;taxon_id=242101932&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Smilax herbacea&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Make sure you have a positive ID on any wild plant before you eat it, but if this is &lt;em&gt;Smilax&lt;/em&gt; it looks like you don't have to worry about it being poisonous: from &lt;a href=&quot;http://www.efloras.org/florataxon.aspx?flora_id=1&amp;amp;taxon_id=130567&quot; rel=&quot;nofollow&quot;&gt;Flora of North America entry on the genus &lt;em&gt;Smilax&lt;/em&gt;:&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Smilax has numerous uses. Sarsaparilla, a beverage and medicinal used&#xA;  against rheumatism, is obtained from the rhizomes of various species... All species of Smilax are excellent wildlife food and are also browsed, or the rhizomes dug&#xA;  and eaten, by domestic stock.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For you, or for other Pennsylvania people, note that the &lt;a href=&quot;http://www.paflora.org/&quot; rel=&quot;nofollow&quot;&gt;Pennsylvania Flora Project of the  Morris Aboretum&lt;/a&gt; is a great resource. You can download species lists by county, and just that and some google image searches can often substitute for a field-guide of your county.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to identify plants the hard way, and are willing to deal with special botanical vocabulary, the Flora of North America that I linked to above is the definitive resource.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-07-16T23:51:17.770" LastActivityDate="2013-07-16T23:51:17.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9283" PostTypeId="1" AcceptedAnswerId="9284" CreationDate="2013-07-15T04:16:52.153" Score="15" ViewCount="16084" Body="&lt;p&gt;As the &lt;a href=&quot;https://biology.stackexchange.com/q/9180/948&quot;&gt;original question&lt;/a&gt; went from hold to closed, I thought I would write up a more appropriate question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How should one go about getting bacterial samples to look at under a microscope at home?  How do professionals do it?  What if I want to look at cool pathogenic species like Salmonella bongori, Escherichia coli, or Bacillus anthracis?&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2017-04-17T10:39:25.593" Title="How to obtain bacteria samples at home?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;species-identification&gt;&lt;diy-biology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9284" PostTypeId="2" ParentId="9283" CreationDate="2013-07-15T04:16:52.153" Score="25" Body="&lt;p&gt;First, and I cannot stress this enough, you should not go seeking out human pathogens if you don't have the appropriate equipment to handle it at the right &lt;a href=&quot;https://en.wikipedia.org/wiki/Biosafety_level&quot; rel=&quot;noreferrer&quot;&gt;safety level&lt;/a&gt;.  That goes for all pathogens, even ones you might find around your house.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a professional lab, you might get samples from collaborators, clinical samples, vendor, or really an number of other professional resources.  A well respected vendor as an example is &lt;a href=&quot;http://www.atcc.org/&quot; rel=&quot;noreferrer&quot;&gt;ATCC&lt;/a&gt;, but the general public wouldn't be able to &quot;shop&quot; there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But you really don't need to go far to get a whole host of microbes to study, you can grow them all at your house.  The basics of bacteria culturing can really be broken down to three steps: (1) get a source of bacteria, (2) put some of the bacteria in an environment where they can grow easily, and (3) harvest them to do something useful with them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) Is fairly easy, bacteria are everywhere.  You can swab nearly any surface of anything in your house and come up with microbes (note you might also get some mold/fungi).  In this case (3) is easy as well.  Once you have culture you can streak it across a slide to view it under a microscope (you could also use several proper mounting techniques).  After all, looking at microbes under a microscope is the real goal here!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only part of this plan that will take some real elbow grease is making your own culture dishes at home, but it's not as hard as you might think.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Making your own culture dishes:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) The &quot;plates&quot; themselves.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I recommend getting the smallest Tupperware like containers your can&#xA;  find that are microwave safe, dishwasher safe, and really make a good&#xA;  seal (water tight at the least). They really don't have to be big, and&#xA;  you will make your life easier if you buy a bunch to match. They need&#xA;  to be super clean. After running them through your dishwasher at home,&#xA;  put them all in a boiling pot of water until you are ready to pour in&#xA;  your &quot;medium.&quot; A mid-low simmer will work&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Note that you won't probably be able to have perfect sterile technique at your house, but you should try to do what you can.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Your &quot;Medium&quot; or Broth&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I highly recommend using pectin as your gelling agent if you can't get&#xA;  your hands on some agar. After that comes plain unflavored gelatin,&#xA;  but I recommend pectin. You can get it at almost any grocery store and&#xA;  my recipe is made assuming that. You can determine how much you want&#xA;  to make, just scale up the ratios. I'm going to list things as rough&#xA;  volume by volume so you won't need a scale.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;i) Make the powder first:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;&lt;p&gt;45mL of pectin;&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;4 bouillon cubes ground as finely as you can (you can get different&#xA;  types and results depending on if you start with vegetable, beef, or&#xA;  chicken. I recommend starting with vegetable.);&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;125mL of refined white sugar;&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Additives (more on this later)&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;  &#xA;  &lt;p&gt;ii) Mix the powder into 500mL of water.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Before you mix in the powder, heat the water to 50-75&lt;sup&gt;o&lt;/sup&gt;C (mid low heat), but not boiling. Mix the powder in while stirring until&#xA;  dissolved.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;iii) Bring the mixture up to a boil. Let it boil for about 2 min,&#xA;  stirring all the while.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;iv) Cover the pot and let it cool for 4-5 min.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;You by no means want it to cool down to room temperature, you just want&#xA;  to get it a little below boiling. If you are at 55&lt;sup&gt;o&lt;/sup&gt;C or below it's&#xA;  definitely time move on.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;v) Dip/fill your &quot;plates&quot; 1/3 full of media using clean/sterile&#xA;  utensils and seal while hot but not boiling.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;You may have noticed this seems an awful lot like canning, and that's&#xA;  because it is. Again you want to be as clean as possible in this step&#xA;  and of course try not to burn yourself on anything.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;vi) Let your media plates set and chill over night in the&#xA;  refrigerator.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;You really probably only have to wait a few hours if you are anxious&#xA;  to get going. You are going to want to store the plates that you are&#xA;  not using in the refrigerator anyway. Also if you made a bunch of&#xA;  plates, let the cool on a counter before you put them in the fridge so&#xA;  that you don't raise the temp of your fridge too much.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Remember the thing about additives? You can play around with adding&#xA;  different amounts and different types of salts, vitamins, food, or&#xA;  other items to see how they affect the cultures you get to grow. All&#xA;  kinds of fun there. First go round, leave them all out.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Now you have your own home made culture plates! The above recipe was empirically tested by my childhood, and repeated by my son's. Not all pectin from the store may be equal, this is with Ball Classic (I have no relation to the company). I'd love to know people's results in trying it, because I might need to re-think how/what I'm doing to get it to work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Go around your house swabbing things with sterile swabs (you can get these at a drug store), and then streak them out on plate. While it will be a little different with a swab and homemade plate, the idea is similar to what is done &lt;a href=&quot;https://www.youtube.com/watch?v=DAm21yPGMRo&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Leave your plate in a warm wet place, but not in direct sunlight. Ideal temp is going to be around 37, but you can leave them above and below that and still get things to grow. On top of our dryer is where I leave them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After a day or so you should have colonies you can streak out on a slide and look under a scope. You will find all kinds of things this way. If you want a more formal way to put things on a slide, you can check out dry and wet mounting from a Google search.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are actually quite likely to run into E.coli if you sample enough &quot;areas&quot; this way. Obviously don't eat or huff the stuff that ends up growing. Maybe you can post some fun pictures of this if you try it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As pointed out in the comments, if you successfully get bacteria to grow, then you will need to successfully get rid of them.  I should point that a good set of rubber gloves (that you can bleach and wash after use), or disposable gloves are a really good idea when handling plates that have grown bacteria.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Clean Up&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;First off, I want to clearly say that this stuff can clog a pipe.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you tried to grow something on a plate, and you didn't get a colony that you can see with the naked eye (note some microbes might make CLEAR growths) you can &lt;em&gt;probably&lt;/em&gt; just scoop the gel into the trash.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that I said &lt;em&gt;probably&lt;/em&gt;.  If you swapped any part of your body, waste, or that of an animal you &lt;strong&gt;must&lt;/strong&gt; decontaminate even if you didn't see anything grow.  On the plus side decontamination is easy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;If you did see something grow, or you otherwise need decontamination:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First make a 20% bleach solution in a large Tupperware like container (probably don't want to do this is a nice metal pot, but could do it in a junk one).  You can go as low as 10% bleach solution if you sure your bleach is NOT a cheap already watered down brand (like something bought at dollar store).  But just to be sure, I recommend 200mL of bleach in 800mL of plain tap water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Drop your plates and lids into the bath (with the lid off) and let it sit for 10-15 min.  Then, working under/in the bleach solution with your gloves on, use a fork/spoon to get out the medium (it will be like thick jello).  Do this for all your plates, and you can do more than one at a time this way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you have all the medium out and floating in the bleach, take the plates out and put them in the dishwasher.  Strain out the bleach/medium/funkiness you grew through a cheap colander (I recommend dishwasher safe plastic like PP).  Put what get's caught in the colander in the trash and take the trash out.  Wash the plates, lids, colander, and large container you used for the beach bath.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Slides&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Slides present extra caution because they can break or shatter to create sharp edges.  For the most part, if you cover your sample with a cover slip, and seal it with nail polish, you can actually keep your slides indefinitely with little risk.  If you do decide to dispose of them, they should first go into a thick Ziploc bag (use an expensive freezer guard type bag for this) or into a Tupperware you don't mind throwing away.  If you never sealed your sample to your slide, you should also decontaminate the slide in bleach first (as above, with extra caution to not cut yourself).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are sophisticated enough to get microscopic photos of the microbes you see, by all means post them up and we'll try to ID them as best we can (many look very similar, and we use genetic or protein markers to get a true ID).&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2016-03-17T13:25:10.943" LastActivityDate="2016-03-17T13:25:10.943" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="9286" PostTypeId="5" CreationDate="2013-07-15T14:27:05.327" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-07-15T14:27:05.327" LastActivityDate="2013-07-15T14:27:05.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9287" PostTypeId="4" CreationDate="2013-07-15T14:27:05.327" Score="0" Body="A virus is a small infectious agent that can replicate only inside the living cells of an organism. Virology is the study of viruses." OwnerUserId="948" LastEditorUserId="948" LastEditDate="2013-07-15T15:20:40.177" LastActivityDate="2013-07-15T15:20:40.177" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9288" PostTypeId="1" AcceptedAnswerId="9290" CreationDate="2013-07-15T16:15:07.210" Score="10" ViewCount="434" Body="&lt;p&gt;Osmosis seems very counter-intuitive to me. I will try to explain my doubt with the following thought experiment:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider a huge container divided into two by a semi-permeable membrane. We add equal levels of water on both sides. On one side, dissolve some sugar. After some time, there will be a net movement of water to the sugar containing side of the container. This will increase the level of water on one side and decrease it on the other. If we create a huge hole in the membrane (large enough for both water and sugar molecules), then water will rush from one side to the other, equalizing the levels. If we were to somehow place a turbine at this hole, we could generate quite a bit of energy. Where did this energy come from? &lt;/p&gt;&#xA;" OwnerUserId="4013" LastEditorUserId="3059" LastEditDate="2013-07-15T18:34:12.497" LastActivityDate="2013-07-15T18:34:12.497" Title="Doesn't osmosis violate the law of conservation of energy?" Tags="&lt;thermodynamics&gt;&lt;general-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9289" PostTypeId="1" CreationDate="2013-07-15T16:46:02.640" Score="2" ViewCount="73" Body="&lt;p&gt;I am currently building a synthetic system in E.coli, and am often faced with the need to use genes from other distant prokaryotes. I know that myself and most of my colleagues resort to an educated trial and error approach. Besides the obvious (elimination of introns from eukaryotes, codon optimization, genetic relatedness), &lt;strong&gt;is there any predictable or semi-rational way of knowing if a transgene for a different organism will function properly in any given organism?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2013-07-16T04:29:13.233" LastActivityDate="2013-07-16T13:53:43.107" Title="How can I accurately predict proper transgenic protein function/structure from different species?" Tags="&lt;synthetic-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9290" PostTypeId="2" ParentId="9288" CreationDate="2013-07-15T17:37:07.267" Score="10" Body="&lt;p&gt;I'm no thermodynamics expert, but Ill have a go at this.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The energy comes from the original set up, in which you have created a low entropy state. As the diffusion of water molecules equalises their concentration across the membrane so the entropy of the system will increase. This translates to a negative free energy change. That manifests as potential energy stored in the hydrostatic pressure resulting from the changes in volume, which in turn is available to turn the turbine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in the case of an experiment of the type described, the energy is derived from the experimenter who sets up the experimental situation in the first place.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-07-15T17:45:04.867" LastActivityDate="2013-07-15T17:45:04.867" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9291" PostTypeId="1" CreationDate="2013-07-15T05:06:46.900" Score="3" ViewCount="794" Body="&lt;p&gt;Does flash UHTP homogenision and pasteurisation change significantly the extent of maillard reaction in milk compared with traditional batch pasteurisation? If this is significant does this effect the nutritional value of the milk? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Initial research; i have found via my wikisearch  &lt;a href=&quot;http://www.food-info.net/uk/colour/maillard.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.food-info.net/uk/colour/maillard.htm&lt;/a&gt; and on pub med an abstract: J Nutr Sci Vitaminol (Tokyo). 1990;36 Suppl 1:S57-69.Influence of processing on protein quality.&#xA;Mauron J.&#xA;Source University of Fribourg, Switzerland.  i dont have full access to pubmed papers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;background to question.I have developed a sensitivity or intolerance to UHT and typical homogenised and pasteurised milk in the supermarket and any products with milk solids. I can consume non homogenised batch pasteurised milk from the specialty organic store, thus the curious chemist in me was alert. Either my body doesn't produce sufficient of the necessary enzymes ,ruled out by the latter scenario,  or the composition of the milk has changed in modern high throughput pasteurisation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Flash pasturisation we have P.T and V all being varied to increase proximity and likelyhood of collisions of reactants as well as temporary emulsification. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is another term AGE see &lt;a href=&quot;http://agefoundation.com&quot; rel=&quot;nofollow&quot;&gt;http://agefoundation.com&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4070" OwnerDisplayName="Analogue girl" LastEditorUserId="4070" LastEditDate="2013-07-31T14:09:02.713" LastActivityDate="2013-10-29T14:45:43.460" Title="What is the effect of flash pasteurisation on Maillard reactions or production of AGEs in milk?" Tags="&lt;organic-chemistry&gt;&lt;milk&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9292" PostTypeId="2" ParentId="9271" CreationDate="2013-07-15T20:47:40.107" Score="2" Body="&lt;p&gt;Nocturnal owls may present a good example of an animal with greater sensitivity to movement than color. While they also rely heavily on good hearing, many owls like the Scops Owl referenced in the link below (time~ 5m 58s), rely heavily on detecting movement rather than color. Other nocturnal predators that rely on vision, such as many felids (e.g. ocelot), may provide further examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=ShPhYUQmRN8#t=05m58s&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=ShPhYUQmRN8#t=05m58s&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1060" LastActivityDate="2013-07-15T20:47:40.107" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9294" PostTypeId="2" ParentId="2075" CreationDate="2013-07-15T22:28:05.270" Score="1" Body="&lt;p&gt;Yes red light is useful IF and only if &gt;650 nm. Some of the answers above are close, but they miss the issue because they used the same scale for rods and cones which they are not on. Rods are several orders of magnitude more sensitive than cones and hence why the graphs above make it look like they have no sensitivity out to 700nm, they actually do, just not nearly as much.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look up photochromatic step. It explains why &gt;650nm works and it is well documented.&lt;/p&gt;&#xA;" OwnerUserId="4021" LastActivityDate="2013-07-15T22:28:05.270" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9295" PostTypeId="1" AcceptedAnswerId="9296" CreationDate="2013-07-16T03:30:32.197" Score="1" ViewCount="91" Body="&lt;p&gt;Isoprenoid  Diphosphate(IPP) is an important metabolites which is precursor in lot of secondary metabolites like Dolichol diphosphate, ubiquinone, prenylated proteins and carotenoid (not synthesized in s cerevisiae).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the average concentration of IPP present in yeast per gm ? &lt;/p&gt;&#xA;" OwnerUserId="3841" LastEditorUserId="3841" LastEditDate="2013-12-01T07:27:35.790" LastActivityDate="2013-12-01T07:27:35.790" Title="Isoprenoid Diphosphate Concentration in Yeast saccharomyces cerevisiae" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;metabolism&gt;&lt;yeast&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9296" PostTypeId="2" ParentId="9295" CreationDate="2013-07-16T09:21:44.993" Score="1" Body="&lt;p&gt;Although this information doesn't provide a direct answer to your question, I hope that it sets the scene for what is achievable in metabolic engineering from IPP. It should also provide a jumping off point for further literature research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a fairly recent review of metabolic engineering of relevant pathways in various microbial systems, including &lt;em&gt;Saccaharmoyes&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ajikumar  PK &lt;em&gt;et al&lt;/em&gt;. (2008)  Terpenoids: Opportunities for Biosynthesis of Natural Product Drugs Using Engineered Microorganisms. Molecular Pharmaceutics 5:167–190&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The review refers to:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ro, D. &lt;em&gt;et al.&lt;/em&gt; (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440, 940–943.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In this work, the introduction of a pathway-specific gene led to the production of 4.4 mg L&lt;sup&gt;-1&lt;/sup&gt; of product. This was increased to 153 mg L&lt;sup&gt;-1&lt;/sup&gt; by several manipulations including:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Increasing flux through the pathway by expressing a modified HMG CoA reductase&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Decreasing flux into sterol synthesis by downregulation of the &lt;em&gt;ERG9&lt;/em&gt; gene combined with expression of a dominant negative allele of the transcription factor Upc2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After posting my answer I found this paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Huang, B. &lt;em&gt;et al&lt;/em&gt;. (2011) Metabolite target analysis of isoprenoid pathway in Saccharomyces cerevisiae in response to genetic modification by GC-SIM-MS coupled with chemometrics. Metabolomics 7:134–146&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The paper includes a detailed discussion of methodologies, which I won't go into here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although there are no measurements of IPP, in Table 7 they present this result: geranyl pyrophosphate 32 ng ml&lt;sup&gt;-1&lt;/sup&gt; in a 48 h culture, A&lt;sub&gt;600&lt;/sub&gt; ~ 2.3. &lt;em&gt;ERG9&lt;/em&gt; disruption increased this to 56 ng ml&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I can tell these values are presented as ng ml&lt;sup&gt;-1&lt;/sup&gt; original culture. Using 1 U of OD600 corresponds to 0.41 g of dry cells liter−1 taken from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC404389/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; I calculate a value for GPP of 34 &amp;micro;g g&lt;sup&gt;-1&lt;/sup&gt; dry weight in the wild-type strain.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-07-16T10:11:16.503" LastActivityDate="2013-07-16T10:11:16.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9297" PostTypeId="1" CreationDate="2013-07-16T11:32:46.240" Score="5" ViewCount="868" Body="&lt;p&gt;I've been looking at this &lt;a href=&quot;http://www.ted.com/talks/the_interspecies_internet_an_idea_in_progress.html&quot;&gt;Ted talk on interspecies internet&lt;/a&gt;, and it appears that they have selected a small number of species of animals (dolphin, elephant, and some ape(?)) and are intent on developing interfaces for these animals to be able to connect with other animals over the internet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the talk, it appeared as if one of the criteria for animal selection was whether or not an animal recognizes itself in the mirror. This got me thinking - there are many more &lt;a href=&quot;http://www.youtube.com/watch?v=Tq0gwLY4yQE&amp;amp;noredirect=1&quot;&gt;cats that have access to technology like the internet or TV&lt;/a&gt; or &lt;a href=&quot;http://www.youtube.com/watch?v=H9fwmG-oue8&quot;&gt;cats that have been interacting with touch screen displays&lt;/a&gt;. Yet apparently cats cant recognize their own reflection as themselves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is so special about being able to recognize one's own reflection?&lt;/strong&gt; Is it a true measure of self awareness? Does it only appear in animals with larger brains?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2014-11-30T06:32:04.273" Title="Is recognizing one's own mirror reflection a valid test of animal intelligence/self awareness?" Tags="&lt;zoology&gt;&lt;behaviour&gt;&lt;intelligence&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9298" PostTypeId="2" ParentId="9297" CreationDate="2013-07-16T12:59:12.193" Score="5" Body="&lt;p&gt;I think it is a necessary test of self-awareness. In order to make the connection that &quot;I am the being in the mirror&quot; and that every action I do will be reflected in the mirror (or, &lt;em&gt;vice versa&lt;/em&gt;, every action I see the being in the mirror take is a reflection of my own action), one must first have a concept of self. One requires a constant present-tense (at least) story of oneself: &quot;I am doing this. Now I am doing that. Oh look, I am doing this and that guy is doing the exact same thing.&quot; And then there's the ultimate realization, &quot;Ah ha! That's me!&quot;. That realization would make no sense if the individual has no sense of &quot;me&quot;! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[speculation] On the other hand, perhaps it is too strict. It seems that it would unfairly favor social species, since it requires not only recognizing another member of the species (and being able to associate the anatomy of another member of the species with one's own anatomy), but it may also require the recognition of intent. That latter requirement is complicated by differentiating between intent and compulsion: at some point, one must realize that the being in the mirror isn't trying to copy but rather it always, inevitibly reflects one's motions. So, perhaps a cat is self-aware, in a sense that it has a constant story in its head of what it is doing and what it intends to do, but it cannot easily ascribe intent to other members of the species and thus cannot figure out that the cat in the mirror is automatically mirroring all of its movements. [/speculation] &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Herein lies the rub: there is no perfect test for self-awareness; we can cast doubt on any outcome. The best would be if these animals could communicate with us by language. In lieu of that, we have to think of such tests that demonstrate with reasonable confidence that the species carries all of the characteristics that we attribute to self-awareness. I think another good test would be determining whether the species can plan individual actions in the future; in order to say, &quot;first I will do this, then that; finally, that will allow me to do that&quot;, it seems like it would reasonably require an understanding of self and the consequences of one's actions. An example would be &lt;a href=&quot;https://www.youtube.com/watch?v=ZE4BT8QSgZk&quot; rel=&quot;nofollow&quot;&gt;birds solving sequential puzzles&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorDisplayName="user3934" LastEditDate="2013-07-17T07:02:11.983" LastActivityDate="2013-07-17T07:02:11.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9299" PostTypeId="2" ParentId="9271" CreationDate="2013-07-16T13:15:42.090" Score="1" Body="&lt;p&gt;Even for humans, without saccades we do not have visual perception. Visual system easily adapts to things that do not change. There have been several experiments with human that shows this. Microsaccades are essential. I am busy at a conference now, but if nobody else answers in detail, I'll expand this answer in a couple of weeks with proper references.&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2013-07-16T13:15:42.090" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9300" PostTypeId="2" ParentId="9289" CreationDate="2013-07-16T13:53:43.107" Score="5" Body="&lt;p&gt;By looking at the sequence only?  This is an unsolved problem.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its not clear to me exactly what you are looking for, but here are some thoughts...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a relatively narrow question as to whether any gene you plug into a bacterium, yeast, mouse, goat or other transgenic organism - the rna may not translate into protein in detectable levels or at high enough levels to get the desired result.  changing the sequence of the DNA of the gene for better transcription/translation is a common necessary experimental.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the broader systems biology level, other cofactors, substrates that are necessary for the function of the gene may have to be engineered in the host organism. That is also an open question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All this is assuming the gene in question codes for an enzyme to make a new or different amount of the metabolic product from the host organism, a commmon synthetic biology target.  If you are adding signaling pathway components, tinkering with a more specific mechanism in the cell, getting the function you desire could be a lot of work.  E.g. if you were inserting a new ribosomal component or a gene related to mitosis, that would be hard to imagine a priori how it would function in the new cell or if it would just kill it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, &lt;a href=&quot;http://reducio.princeton.edu/cm/node/13&quot;&gt;Olga Troyanskaya&lt;/a&gt; at Princeton CS is working on the related problem of finding the function of a gene by looking at its sequence and cross referencing to other known data. Electronic functional inference is difficult, esp when we have no complete gene functional description of any living organism to start with. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-07-16T13:53:43.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9301" PostTypeId="1" CreationDate="2013-07-16T17:11:48.993" Score="2" ViewCount="274" Body="&lt;p&gt;Over the last year or so, I've been observing &lt;a href=&quot;http://en.wikipedia.org/wiki/Sparrow&quot; rel=&quot;nofollow&quot;&gt;house sparrows&lt;/a&gt;, because they are so prevalent in the northeast US cities. I noticed that a lot of sparrows, even in different cities seem to have very similar body language for communicating. I learned 3 expressions&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's an &lt;a href=&quot;http://youtu.be/qGnRTvSHzXs&quot; rel=&quot;nofollow&quot;&gt;example of a sparrow feeding their young&lt;/a&gt;. The young bird opens month and flickers its wings in what I can only describe as impatiently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A sparrow swipes its beak along a surface at its feet - something food related?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A sparrow fluffs its feathers, turning into something like a tennis ball made of feathers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://youtu.be/XjEfqoufozA&quot; rel=&quot;nofollow&quot;&gt;I'm looking at this video of a sparrow raised in captivity&lt;/a&gt;, and it does 2 out of 3 expressions described here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What interests me is if expressions like these are &quot;local dialects&quot; or universal, thus found across different geographies and times?&lt;/strong&gt; for example, do sparrows in northeast US use the same expressions as sparrows in Australia? What about sparrows in the United Kingdom in the 1950s? &lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="3952" LastEditDate="2013-08-02T13:58:58.433" LastActivityDate="2013-08-02T13:58:58.433" Title="Is there an instinct-driven body language for birds?" Tags="&lt;zoology&gt;&lt;behaviour&gt;&lt;ornithology&gt;&lt;sociality&gt;&lt;communication&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9304" PostTypeId="1" CreationDate="2013-07-16T19:59:17.763" Score="6" ViewCount="146" Body="&lt;p&gt;I am working on a project in which an XOR gate is being built by having two hammerhead ribozymes simultaneously cleave each other when both are expressed, but have these ribozymes cleave a target transcript when expressed alone. &lt;strong&gt;Has it ever been shown in the literature that a hammerhead ribozyme was able to cleave the flanking arms of another ribozyme?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2013-07-17T02:23:29.910" LastActivityDate="2014-03-21T11:15:56.310" Title="Can two hammerhead ribozymes simultaneously cleave each other?" Tags="&lt;rna&gt;&lt;synthetic-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9305" PostTypeId="2" ParentId="9266" CreationDate="2013-07-16T23:09:59.880" Score="0" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/SB_buffer&quot; rel=&quot;nofollow&quot;&gt;SB buffer&lt;/a&gt; has been around for quite a while, and I definitely have used it successfully before for both agarose and PAGE gel buffers for some time. The only thing is that you have to run the gel in a cold room (high voltage equals high temperature) and that you have to optimize the timing and conditions so that your samples don't run off the gel.&lt;/p&gt;&#xA;" OwnerUserId="4026" LastActivityDate="2013-07-16T23:09:59.880" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="9307" PostTypeId="1" AcceptedAnswerId="9308" CreationDate="2013-07-17T04:31:01.113" Score="0" ViewCount="174" Body="&lt;p&gt;The picture below shows what I am talking about. Each flower has one and I am just wondering what they are?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VGxiL.jpg&quot; alt=&quot;plant image&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3989" LastEditorUserId="948" LastEditDate="2013-07-17T14:42:31.197" LastActivityDate="2013-07-18T01:42:13.997" Title="Plant anatomy, what are these stem like filaments growing under the flower" Tags="&lt;botany&gt;&lt;anatomy&gt;&lt;plant-anatomy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9308" PostTypeId="2" ParentId="9307" CreationDate="2013-07-17T06:28:16.690" Score="1" Body="&lt;p&gt;Looking at &lt;a href=&quot;http://www.orchidireland.ie/images/previews/Orchid_Spur_types.jpg&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;, it looks like a spur. A quite overbreed one, though. &lt;/p&gt;&#xA;" OwnerUserId="3827" LastEditorUserId="948" LastEditDate="2013-07-17T14:42:47.637" LastActivityDate="2013-07-17T14:42:47.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9309" PostTypeId="2" ParentId="9291" CreationDate="2013-07-17T07:18:04.407" Score="2" Body="&lt;p&gt;This is only an partial answer, as I do not have the time now to look for other references.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the chapter about milk, Harold McGee's beautiful book &quot;On Food &amp;amp; Cooking&quot; says (pg. 21 of the 2004 edition, bold is mine):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Flavors from cooking&lt;/strong&gt;&lt;br&gt;&#xA;  Low-temperature pasteurization slightly modifies milk flavor by driving off some of the more delicate aromas, but stabilizes it by inactivating enzymes and bacteria, and adds slightly sulfury and green-leaf notes (dimethyl sulfide, hexanal). High-temperature pasteurization or brief cooking - heating milk above 170°F/76°C - generates traces of many flavorful substances, including those characteristic of vanilla, almonds and cultured butter, as well as hydrogen sulfide. &lt;strong&gt;Prolonged boiling encourages browning or Maillard reactions between lactose and milk proteins&lt;/strong&gt;, and generates molecules that combine to give the flavor of butterscotch.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;He continues by speaking about the different types of pasteurization, and says (pg.22-23)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The third method of pasteurizing milk is the &lt;em&gt;ultra-high temperature&lt;/em&gt; (UHT) method which involves heating milk at 265-300°F/130-150°C either instantaneously or for 1 to 3 seconds, and produces milk that, if packaged under strictly sterile conditions can be stored for months without refrigeration. The longer UHT treatment imparts a cooked flavor and slightly brown color to milk; cream contains less lactose and protein, so its color and flavor are less affected.&lt;br&gt;&#xA;  Sterilized milk has been heated at 230-250°F/110-121°C for 8 to 30 minutes; it is even darker and stronger in flavor, and keeps indefinitely at room temperature.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, it appears as if indeed there may be some Maillard reaction going on in UHT, although it is probably minor (otherwise the milk would be much darker in color, as it is the case for sterilized milk).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The book also speaks about homogenization, but it does not mention anything specific about Maillard reaction there (homogenization is not carried on at high temperatures, so it does makes sense not to have it).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Does this effect the nutritional value of the milk? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, according to this presentation (but, be warned, it does not cite any reference!) it seems that it does, although I don't think the Maillard reaction is specially involved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.slideshare.net/Aslal_saja/effect-of-uht-treatment&quot; rel=&quot;nofollow&quot;&gt;http://www.slideshare.net/Aslal_saja/effect-of-uht-treatment&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically it says that the irreversible changes that occur are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Whey protein denaturation (35 to 100% of denaturation of $\beta$-lactoglobulin)  &lt;/li&gt;&#xA;&lt;li&gt;Slight increase in the size of casein micelles  &lt;/li&gt;&#xA;&lt;li&gt;Whey protein-casein micelle interaction&lt;/li&gt;&#xA;&lt;li&gt;Maillard reactions&lt;/li&gt;&#xA;&lt;li&gt;Fat globule composition changes (although no changes in nutritional value of milk fat)&lt;/li&gt;&#xA;&lt;li&gt;Vitamin content changes (20-30% loss in vitamin B1 and B12. Markedly reduced content in vitamin C and folic acid if high level of oxygen were present during the treatment, no changes in vitamins A, D, E and beta-carotene). &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It also says that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Biological value and net protein utilization of UHT milk were lower for stored milk than directly used milk. Lysine loss during UHT is high but not significant to affect milk nutritional values.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I don't know whether the fact that you have problems when drinking UHT milk has anything to do with Maillard reaction or any of the other modifications brought by UHT treatment, and I will not venture in there, as I am not an MD and prefer not to give any sort of medical advice.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2013-07-17T07:18:04.407" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9310" PostTypeId="1" CreationDate="2013-07-17T08:06:14.740" Score="3" ViewCount="257" Body="&lt;p&gt;I want to align WGS data from several mammals to one reference such as the human genome sequence. Since in most cases exons should be conserved and spliced in the same way and introns should vary, I want to use a tool that is aware of the annotation of exon and intron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is to say that matches in an exon region should have be given a higher weighting than matches in intronic regions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, when a read pair maps to 2 exons, the insert size should be more flexible as the intron length can be vary among different mammals. Since the library insert is less than 2kb for short libraries, the more common situation should be one read on exon and another on intron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is different from RNA-seq as I am using WGS data of a whole genome, so both exons and introns are in the reads. And I want to align them to a human reference sequence.&lt;/p&gt;&#xA;" OwnerUserId="4028" LastEditorUserId="1320" LastEditDate="2013-07-17T13:09:57.527" LastActivityDate="2015-03-29T10:26:37.790" Title="Any tool to align whole genome sequence data to another genome and give exon regions a higher mark?" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;sequence-analysis&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9311" PostTypeId="2" ParentId="9310" CreationDate="2013-07-17T15:11:42.807" Score="4" Body="&lt;p&gt;If you are not trying to assemble but just to align each read to the genome, you can use &lt;a href=&quot;http://www.animalgenome.org/bioinfo/resources/manuals/exonerate/&quot; rel=&quot;nofollow&quot;&gt;&lt;code&gt;exonerate&lt;/code&gt;&lt;/a&gt;. On a Unix/Linux platform, once you have installed it run something like:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;exonerate -m genome2genome WGS.fasta genome.fasta &amp;gt; out.txt &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;From the &lt;code&gt;exonerate&lt;/code&gt; manual:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;          genome2genome&#xA;                 This  model  is  similar  to  the  cod‐&#xA;                 ing2coding  model,  except  introns are&#xA;                 modelled on both sequences.  (not work‐&#xA;                 ing well yet)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;What I would recommend though, is to align against a reference cDNA dataset, not the whole genome. In that case, you should use this instead:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;exonerate -m cdna2genome genome_cdna.fasta WGS.fasta &amp;gt; out.txt &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;From the exonerate manual:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;          cdna2genome&#xA;                 This   combines   properties   of   the&#xA;                 est2genome and coding2genome models, to&#xA;                 allow modeling of an whole cDNA where a&#xA;                 central coding region can be flanked by&#xA;                 non-coding UTRs.  When  the  CDS  start&#xA;                 and  end  is  known it may be specified&#xA;                 using  the  --annotation  option   (see&#xA;                 below)  to permit only the correct cod‐&#xA;                 ing region to appear in the alignemnt.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-07-17T15:11:42.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9312" PostTypeId="1" AcceptedAnswerId="9313" CreationDate="2013-07-17T16:51:22.693" Score="2" ViewCount="2451" Body="&lt;p&gt;I will be beginning a science project about sustaining life on space stations. I already know that pure oxygen is harmful for humans but would $O_2$ + $CO_2$ be enough for humans to breathe in or do humans need other gases as well?&lt;/p&gt;&#xA;" OwnerUserId="4031" LastEditorUserId="57" LastEditDate="2013-07-17T21:08:13.483" LastActivityDate="2013-07-17T21:08:45.143" Title="What gases are needed for humans to breathe?" Tags="&lt;physiology&gt;&lt;respiration&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9313" PostTypeId="2" ParentId="9312" CreationDate="2013-07-17T19:41:34.517" Score="4" Body="&lt;p&gt;Why not look at the existing space station as an example.  The International Space Station (ISS), a starting article is &lt;a href=&quot;http://science1.nasa.gov/science-news/science-at-nasa/2000/ast13nov_1/&quot; rel=&quot;nofollow&quot;&gt;&quot;Breathing easy on the space station&quot;&lt;/a&gt; (NASA), while this article does not discuss the amounts of various chemicals, it looks at the process about how the chemical balance is maintained - an important point related to your question is that carbon dioxide is filtered away.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second article &lt;a href=&quot;http://www.e-missions.net/ssa/CH4-breathingonthespacestation.htm&quot; rel=&quot;nofollow&quot;&gt;&quot;Breathing on the Space Station&quot;&lt;/a&gt; (e-missions), discusses the actual percentages of each component.  It states that the chemical composition of the space station air is ideally similar to Earth's atmosphere.  With 78% nitrogen, 21% oxygen and 1% water vapour on the space station (Argon is in the Earth's atmosphere, but appears to be unnecessary on the space station).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-07-17T19:41:34.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9315" PostTypeId="1" AcceptedAnswerId="9317" CreationDate="2013-07-17T20:56:47.523" Score="8" ViewCount="305" Body="&lt;p&gt;I was reading &lt;a href=&quot;http://www.frontiersin.org/Human_Neuroscience/10.3389/fnhum.2013.00245/abstract&quot; rel=&quot;nofollow&quot;&gt;this(1)&lt;/a&gt; and it led me back to ask a very basic question (I'm not a neuroscientist).  All the way back to undergrad anthropology and neuroscience courses I remember being taught the general rule of relative intelligence was that one looked at the ratio of the brain mass over the total mass of the animal (or the estimations therein from let's say fossils).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know a lot of the interesting neuroscience research going on these days does looks into bird brains, particularly within &lt;em&gt;Corvidae&lt;/em&gt;.  It would seem that birds are often much more efficient in the abilities they seem to show with considerably less brain mass.  I do realize that birds often weigh very little as well, so perhaps the ratio is preserved?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also realize that within birds, they see better ratios in more intelligent birds.  But what about the comparison from mammals to birds?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dinosaurs are often predicted to &lt;strong&gt;not&lt;/strong&gt; be intelligent because of the enormous body size and small cavities for a brain.  Now I realize that some dinosaurs were actually quite tiny, but this is just an example.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given birds' close genetic link to dinosaurs, could it simply be that they were just doing more with less?  The mammalian brain is a huge caloric burden, so perhaps this would show an efficiency that could be selected for?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus as the title suggests, my main question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the ratio of brain mass to body mass still considered to be a valid indication of intelligence of a species in modern (current) neuroscience?  Certainly there are exceptions, but is it still considered the rule of thumb?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I also wanted to point out the &lt;a href=&quot;http://www.karger.com/Article/FullText/102973&quot; rel=&quot;nofollow&quot;&gt;first article(2)&lt;/a&gt; I started to read after formulating the question.  It made me question the usefulness of encephalization in addressing this issue at all, but I don't/didn't feel adequately trained to evaluate the conclusions of the meta study.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, this still leaves us comparing within primates, which still leaves me feeling that &lt;em&gt;Corvidae&lt;/em&gt; have some really impressive efficiency going on with their overall brain mass.  Which then leads to hope that some dinosaurs could be at least equally intelligent, if not more so (noted that this is complete conjecture).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;(1) Front Hum Neurosci. 2013 Jun 6;7:245. doi:&lt;a href=&quot;http://dx.doi.org/10.3389/fnhum.2013.00245&quot; rel=&quot;nofollow&quot;&gt;10.3389/fnhum.2013.00245&lt;/a&gt;. Print 2013.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) Brain Behav Evol. 2007;70(2):115-24. Epub 2007 May 18.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="9943" LastEditDate="2017-03-29T08:01:23.833" LastActivityDate="2017-03-29T08:01:49.490" Title="Is the ratio Brain Mass/Total Mass still considered a valid indicator of intelligence?" Tags="&lt;evolution&gt;&lt;neuroscience&gt;&lt;anthropology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9316" PostTypeId="2" ParentId="5267" CreationDate="2013-07-18T00:46:22.670" Score="2" Body="&lt;p&gt;Multiple sequence alignment is a common bioinformatics problem and there are many tools available to solve it.&lt;br&gt;&#xA;This paper provides a good comparison of the following tools: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0018093&quot; rel=&quot;nofollow&quot;&gt;Thompson, et al.  A comprehensive benchmark study of multiple&#xA;  sequence alignment methods: a current challenge and future&#xA;  perspectives&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The paper addresses the following methods:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ClustalW&lt;/li&gt;&#xA;&lt;li&gt;MUSCLE&lt;/li&gt;&#xA;&lt;li&gt;DIALIGN-TX&lt;/li&gt;&#xA;&lt;li&gt;KALIGN&lt;/li&gt;&#xA;&lt;li&gt;ProbCons&lt;/li&gt;&#xA;&lt;li&gt;MAFFT&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4033" LastEditorUserId="3059" LastEditDate="2013-07-18T01:20:30.617" LastActivityDate="2013-07-18T01:20:30.617" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9317" PostTypeId="2" ParentId="9315" CreationDate="2013-07-18T01:23:20.600" Score="10" Body="&lt;p&gt;I don't know about brain mass to body size, but ratio of neocortex to brain volume is correlated with primate evolution (Figure 3, &lt;a href=&quot;http://www.nature.com/nature/journal/v411/n6834/full/411189a0.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;). If you subscribe to the view that humans and more closely related primates are more intelligent than more distantly related primates, then that is an important correlate.&lt;/p&gt;&#xA;&lt;p&gt;I think the issue with this question is that we're still having trouble defining intelligence.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-07-18T01:23:20.600" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9318" PostTypeId="2" ParentId="9307" CreationDate="2013-07-18T01:42:13.997" Score="2" Body="&lt;p&gt;These are &quot;floral spurs&quot; – they usually contain nectar, and are part of the variety of complex flower shapes that orchids and other flowers, like columbines, have co-evolved with their pollinators.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially, in order for the pollinator to reach the nectar down in the base of the spur, it must move into a position where pollen is deposited onto it; then when it moves to another flower, it can transfer that pollen and the plant is able to reproduce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, long tongues are good at getting nectar from long-spurred flowers, so there is both species filtering for long-tongued species, and presumably also selective pressure within a species for long-tongued individuals. This, in turn, drives selective pressure on the spurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Spurs are a classic example of a &quot;key innovation&quot;: they have evolved separately in different types of flowers, and when they evolve, they often lead to rapid speciation (because a small change in spur architecture can constitute a barrier to reproduction). (See, for example, &lt;a href=&quot;http://www.eemb.ucsb.edu/people/faculty/hodges&quot; rel=&quot;nofollow&quot;&gt;publications of Scott Hodges&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-07-18T01:42:13.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9319" PostTypeId="2" ParentId="9301" CreationDate="2013-07-18T02:45:51.683" Score="1" Body="&lt;p&gt;In general, &lt;strong&gt;animal communication contains both &quot;cultural&quot; aspects and genetic components&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you suggest, the cultural aspects vary more across geographies and times. The genetic components might vary as well, with genetic differences among different populations, but you'd expect them to be more conservative than the cultural aspects. To make the matter even more complex, if the communication behaviors affect mating; they could in turn have an effect on the genetic components!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://acp.eugraph.com/birds/index.html&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; describes birds raised in captivity that had &quot;maladjusted&quot; songs (which would support both genetic and cultural components), and North Carolina cowbirds raised by Texas parents who grew up with a Texas birdsong dialect (evidence for cultural components). Although the piece is mostly focused on song, I imagine the mechanisms would be similar for body language.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-07-18T14:34:09.917" LastActivityDate="2013-07-18T14:34:09.917" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9320" PostTypeId="1" AcceptedAnswerId="9321" CreationDate="2013-07-18T11:17:39.793" Score="17" ViewCount="2269" Body="&lt;p&gt;I recently finished reading Contact by Carl Sagan. In the book they talk about a pattern in the transcendental number like pi or e, and comment that it is found in base 10 or however many fingers the race has to count with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When in the end they find a pattern in pi it is in base 11, which I found a strange choice since I can't think of an animal that has an uneven total number of fingers, and I would think that most evolution would result in a somewhat symmetrical design.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do any animal exist that has an uneven total number of fingers or equal lim, excluding polydactyly and oligodactyly?&lt;/p&gt;&#xA;" OwnerUserId="4037" LastEditorUserId="107" LastEditDate="2013-07-18T18:54:57.117" LastActivityDate="2013-07-19T09:36:27.363" Title="Do animals exist with an uneven total number of digits?" Tags="&lt;evolution&gt;&lt;physiology&gt;&lt;morphology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9321" PostTypeId="2" ParentId="9320" CreationDate="2013-07-18T12:01:06.660" Score="24" Body="&lt;p&gt;Your conclusion relies on the supposition that all beings must count using their finger tips (or the most paralogous, &quot;finger-like&quot; limb). In fact, even within humans this is not necessarily true: the Yuki native people of California count in base 8 by &lt;a href=&quot;http://www.jstor.org/stable/2686959?seq=1&quot;&gt;counting the spaces between their fingers&lt;/a&gt;; meanwhile the Oksapmin people of Papua New Guinea count in base 27 (an odd number!) via &lt;a href=&quot;http://www.jstor.org/discover/10.2307/1129012?uid=39929&amp;amp;uid=3737952&amp;amp;uid=2&amp;amp;uid=3&amp;amp;uid=67&amp;amp;uid=39928&amp;amp;uid=5909704&amp;amp;uid=62&amp;amp;sid=21102543550487&quot;&gt;counting a range of different body parts&lt;/a&gt;. One can easily imagine counting in base 20 by counting on fingers and toes. Heck, the &lt;a href=&quot;https://en.wikipedia.org/wiki/Base_60&quot;&gt;Sumerians used base 60&lt;/a&gt;. And &lt;a href=&quot;https://en.wikipedia.org/wiki/File%3aHexadecimal-counting.jpg&quot;&gt;here's a scheme for counting in base 16 on your fingers&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, it's entirely plausible to count in base 11, even when assuming morphological symmetry. The beings just need to settle on precisely which 11 parts of their anatomy to count.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your actual question, I am unaware of any species with an uneven total number of fingers and I would be surprised if we found one, based on an argument of developmental symmetry and overall (coarse-grained) evolutionarily conserved development plans within major clades of extant animals.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorUserId="1306" LastEditDate="2013-07-18T15:47:34.540" LastActivityDate="2013-07-18T15:47:34.540" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9322" PostTypeId="2" ParentId="9320" CreationDate="2013-07-18T14:01:13.583" Score="27" Body="&lt;p&gt;&lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Coscinasterias_calamaria&quot; rel=&quot;noreferrer&quot;&gt;Coscinasterias calamaria&lt;/a&gt;&lt;/em&gt;, the Eleven-Armed Sea Star! (Although I doubt it has much to do with pi)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mp1KF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/File:Eleven-Armed_Sea_Star.jpg&quot; rel=&quot;noreferrer&quot;&gt;Image from Wikimedia Commons&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="6" LastEditDate="2013-07-18T18:20:09.480" LastActivityDate="2013-07-18T18:20:09.480" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="9323" PostTypeId="1" CreationDate="2013-07-18T17:34:38.477" Score="5" ViewCount="107" Body="&lt;p&gt;As far as I know, there are no specific eukaryotic or prokaryotic factors that aid in RNA folding other than cellular environment (salt and ion concentrations, dissolved molecules, etc). Are there any factors to consider when introducing eukaryotic RNA in prokaryotes? Is it possible to predict the proper shape and folding upon introduction to a prokaryotic cell?&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="5144" LastEditDate="2014-11-12T14:31:42.773" LastActivityDate="2014-11-12T14:31:42.773" Title="Will eukaryotic RNA fold in the same way in prokaryotes?" Tags="&lt;molecular-biology&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9324" PostTypeId="1" AcceptedAnswerId="9325" CreationDate="2013-07-18T17:38:29.780" Score="1" ViewCount="162" Body="&lt;p&gt;I've been thinking about this lately.  Would it be possible for a type of spider to gain the ability to fly freely by weaving its web between it's legs and creating wings much like those of a bat?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there anything like that in nature currently?&#xA;Is it plausible at all?&lt;/p&gt;&#xA;" OwnerUserId="4048" LastEditorUserId="1590" LastEditDate="2013-07-30T15:20:32.913" LastActivityDate="2013-07-30T15:20:32.913" Title="Would it be possible/plausible for a type of spider to fly by weaving web between it's legs to create bat-like wings?" Tags="&lt;evolution&gt;&lt;theoretical-biology&gt;&lt;arachnology&gt;&lt;flight&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9325" PostTypeId="2" ParentId="9324" CreationDate="2013-07-18T18:00:40.143" Score="2" Body="&lt;p&gt;It takes more than wings to fly, just look at the poor penguins. The first problem is that simply weaving webs between a spider's legs would probably not generate enough lift to keep her airborne. Flying creatures have a specific body plan that allows them to fly, if you just add a couple of wings to a hippopotamus it won't be able to fly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On top of that, the spider would not have the necessary muscles to enable it to flap these wings even if they were capable of producing sufficient lift.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While it is theoretically possible (I stress theoretically) for a spider species to adapt over time (long long time) into a flying form, then it would no longer be a spider. So, in answer to your question, no, it is not possible.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-07-18T18:00:40.143" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9326" PostTypeId="1" AcceptedAnswerId="9327" CreationDate="2013-07-18T18:42:07.663" Score="7" ViewCount="12420" Body="&lt;p&gt;What does phasing mean in genetics/informatics? I've heard that a phased file is a file that has genes separated by chromosome, but can someone give a concrete definition of what phasing actually means?&lt;/p&gt;&#xA;" OwnerUserId="3829" LastActivityDate="2018-06-12T16:31:18.990" Title="What does phasing mean?" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9327" PostTypeId="2" ParentId="9326" CreationDate="2013-07-18T19:19:05.503" Score="9" Body="&lt;p&gt;This refers to &lt;a href=&quot;http://en.wikipedia.org/wiki/Haplotype&quot;&gt;haplotype&lt;/a&gt; phase (aka &lt;a href=&quot;http://en.wikipedia.org/wiki/Gametic_phase&quot;&gt;gametic phase&lt;/a&gt;). This essentially means knowing which allele belongs to which copy of the chromosome, or alternatively, which alleles appear together on the same chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short-read sequencing, for example, it is difficult to resolve the haplotype of two heterozygous SNPs if they have not been covered by the same read. If you observe A/a and B/b, you do not know whether you have AB + ab or aB + Ab. So you would say you do not know the phasing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See the Wikipedia links for more information.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2013-07-18T19:19:05.503" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9329" PostTypeId="2" ParentId="9324" CreationDate="2013-07-18T23:39:00.717" Score="0" Body="&lt;p&gt;Very unlikely as spiders don't have direct muscle/exoskeleton connections like insects, it would be a more complicated mechanism for powered flight...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;imagine replacing a radial engine in an airplane with and engine that powers a hydraulic pump that then has a mechanism that converts that force to a force usable for flight.&lt;/p&gt;&#xA;" OwnerUserId="4054" LastActivityDate="2013-07-18T23:39:00.717" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9330" PostTypeId="2" ParentId="9324" CreationDate="2013-07-18T23:41:57.793" Score="0" Body="&lt;p&gt;probably permitted by the laws of physics and biology...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;almost anything is possible, jumping spiders move extremely quickly for their scale, and you could easily imagine an evolutionary pathway... spiders already use parachutes: the parachute gets bigger, the line get shorter and controlled by the rear most legs... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;maybe it has already happened, there likely wouldn't be any fossil record of it, and spiders have been around for a long time (compared to apes).&lt;/p&gt;&#xA;" OwnerUserId="4054" LastActivityDate="2013-07-18T23:41:57.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9331" PostTypeId="1" CreationDate="2013-07-19T03:40:17.617" Score="1" ViewCount="94" Body="&lt;p&gt;I am completely a noob to biology and DNAs, but recently I am looking into EM-algorithm used in the case of re-constructing haplotypes from genotype data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am just wondering what exactly in the process of DNA data collection prevents us from observing haplotypes directly.&lt;/p&gt;&#xA;" OwnerUserId="4057" LastEditorUserId="107" LastEditDate="2013-07-19T12:36:23.157" LastActivityDate="2013-09-29T19:33:52.800" Title="Why can't we observe haplotypes directly?" Tags="&lt;dna&gt;&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9332" PostTypeId="1" AcceptedAnswerId="9333" CreationDate="2013-07-19T06:59:10.740" Score="2" ViewCount="3780" Body="&lt;p&gt;We know that most of the so called &quot;Advanced&quot; organisms are deuterostomes (i.e., development of gut starts from anus). Is there any evolutionary advantage of that? If not, why and how did it evolve?&lt;/p&gt;&#xA;" OwnerUserId="4058" LastEditorUserId="107" LastEditDate="2013-07-19T12:34:39.290" LastActivityDate="2014-04-23T17:38:15.563" Title="Advantage of being deuterostome" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9333" PostTypeId="2" ParentId="9332" CreationDate="2013-07-19T07:28:50.940" Score="2" Body="&lt;p&gt;I would speculate that there is no direct advantage imparted by the deuterostomic development process over that of protostomes with regards to the evolution of more complex species. Instead, I would guess that sometime after that split, a series of novel alleles arose in various genes which were eventually fixed and laid the groundwork for future increased complexity. Given the trait in question (increased organismal complexity), I would be certain that these alleles were in mostly unrelated genes and were selected for some other function (in other words, there is no gene encoding a protein that imparts organismal complexity; that trait is, by definition, a complex one!). Perhaps the genes involved in the deuterostome/protostome split were part of this groundwork, given their activity at the base of development, however it would be very difficult to know at this point.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I don't know why I didn't think about this before, but the more likely explanation for the difference in complexity between deuterostomes and protostomes is actually unrelated to that difference. Most of the complex deuterostomes that you're probably thinking of are vertebrates. Vertebrates went through &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/8486346&quot; rel=&quot;nofollow&quot;&gt;a couple of rounds of&lt;/a&gt; &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/19267631&quot; rel=&quot;nofollow&quot;&gt;genome doublings (tetraploidizations)&lt;/a&gt; during their early divergence. The extra copies of all the genes provided fertile ground for evolutionary novelties that seems to have led to some wonderfully complex creatures. It's still possible that the tissue groundwork laid out by the deuterostome developmental process somehow contributes to that complexity, but it would be rather indirect, I think.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorDisplayName="user3934" LastEditDate="2013-07-19T13:31:47.733" LastActivityDate="2013-07-19T13:31:47.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9334" PostTypeId="2" ParentId="9320" CreationDate="2013-07-19T09:09:29.860" Score="1" Body="&lt;p&gt;I just wanted to say that I believe you're seeing it from a quite anthropocentric standpoint. It doesn't make much sense to search for patterns like even or odd numbers of fingers or limbs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If evolutionary tends to result in bilateral symmetry, there is no reason at all why the symmetry should be inconsistent - like 4 fingers on one hand and 5 on the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consistent bilateral symmetry will always result in even numbers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;4 fingers x2 = 8&lt;/li&gt;&#xA;&lt;li&gt;7 ribs x2 = 14&lt;/li&gt;&#xA;&lt;li&gt;5 toes x2 = 10&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The Eleven Armed Sea Star in @Oreotrephes' answer isn't much of an exception to the rule of symmetry, it's just radially symmetric.&lt;/p&gt;&#xA;" OwnerUserId="4059" LastEditorUserId="3952" LastEditDate="2013-07-19T09:36:27.363" LastActivityDate="2013-07-19T09:36:27.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9336" PostTypeId="2" ParentId="8327" CreationDate="2013-07-19T09:39:04.507" Score="1" Body="&lt;p&gt;&lt;strong&gt;Short answer: homocysteine promotes elevated levels of reactive oxygen species which interfere with signalling via nitric oxide.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an extensive literature on this topic: a Web of Science search using [TITLE: endotheli* AND homocysteine] produces 567 hits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The prevailing view seems to be that homocysteine causes oxidative stress in cells because autooxidation of the sulphydryl group of homocysteine promotes the production of reactive oxygen species (ROS): superoxide, hydrogen peroxide and hydroxide radical. There is also evidence for decreased levels of glutathione (GSH) and glutathione peroxidase (GPX) (McCully, 2009). The classical pathway for dealing with ROS is conversion of the primary species,superoxide, to hydrogen peroxide (by superoxide dismutase) followed by reduction of peroxide to water by GPX using GSH as a reductant. This pathway rapidly destroys ROS and importantly avoids the generation of the damaging hydroxide radical. Reduced glutathione is regenerated at the expense of NADPH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Endothelial cells use nitric oxide (NO) to signal to surrounding smooth muscle, resulting in vasodilation. ROS react with NO, inactivating it. There is also evidence that NO production by epithial nitric oxide synthase (eNOS) is affected, and Leung &lt;em&gt;et al&lt;/em&gt;., 2013 present data indicating that the phosphorylation level of eNOS is reduced by homocysteine. Phosphorylation is a key regulator of eNOS activity (Mount et al., 2007).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Leung SB &lt;em&gt;et al&lt;/em&gt;. (2013) Salidroside Improves Homocysteine-Induced Endothelial Dysfunction by Reducing Oxidative Stress. Evidence-Based Complementary and Alternative Medicine 20: Article ID 679635&lt;/p&gt;&#xA;&#xA;&lt;p&gt;McCully, KS (2009) Chemical Pathology of Homocysteine. IV. Excitotoxicity, Oxidative Stress, Endothelial Dysfunction, and Inflammation. Annals Clin. Lab. Sci. 39:219-232&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mount, PF &lt;em&gt;et al&lt;/em&gt;. (2007) Regulation of endothelial and myocardial NO synthesis by multi-site eNOS phosphorylation. J Molec. Cell. Cardiology 42: 271-279&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-07-19T09:39:04.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9337" PostTypeId="1" CreationDate="2013-07-19T13:50:20.463" Score="2" ViewCount="1255" Body="&lt;p&gt;I'm doing some sleep research and would like to compare a human sleep pattern as recorded by a wrist-based actigraph with a &quot;natural&quot; sleep pattern, such as from apes. In an experiment like that, a human wears an activity monitor on a non-dominant arm over multiple days. The monitor analyzes activity pattern and can detect when the user is asleep versus active.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone suggest a research article or a website that did &lt;strong&gt;a sleep study of primates&lt;/strong&gt; (monkeys/apes) either in captivity or natural habitat over multiple days? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm particularly interested in how consistent their bedtimes are - &lt;strong&gt;do primates go to sleep in the evening whenever they feel like, or do they stick to a more consistent sleep schedule?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="3952" LastEditDate="2013-07-20T02:03:02.220" LastActivityDate="2013-09-24T19:54:29.823" Title="Do primates other than humans have a consistent sleep schedule?" Tags="&lt;zoology&gt;&lt;sleep&gt;&lt;literature&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9338" PostTypeId="1" CreationDate="2013-07-19T15:08:19.937" Score="2" ViewCount="293" Body="&lt;p&gt;I have a set of questions actually, it will be very helpful if you answer them in order.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Where does the HIV virus hide (during incubation period)? Let answer be X cell.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is X cell in the bloodstream?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What parts of the HIV are constant for all its version? (I suspect it's Reverse Transcription Protein, Glycoprotein 120 and 41) Let answer be Y.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is there a chemical that can destroy Y?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is Y present in the normal Human body?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If Answer to question 2 is yes and that to question 5 is no can we inject the said drug into the bloodstream so that it can wipe out the virus? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3660" LastEditorUserId="806" LastEditDate="2013-10-01T10:04:28.507" LastActivityDate="2013-12-17T09:32:52.703" Title="Is this a valid principle of curing HIV?" Tags="&lt;virology&gt;&lt;hiv&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9339" PostTypeId="1" CreationDate="2013-07-19T15:14:05.967" Score="1" ViewCount="170" Body="&lt;p&gt;How do the B-cells and T-cells recognize or distinguish a body cell from a foreign particle?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect something to do with this causes Auto Immune Disorders. &lt;/p&gt;&#xA;" OwnerUserId="3660" LastActivityDate="2013-08-08T23:37:49.053" Title="Cell identification by Body Cells" Tags="&lt;immunology&gt;&lt;autoimmune&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9340" PostTypeId="1" CreationDate="2013-07-19T15:28:32.540" Score="3" ViewCount="1480" Body="&lt;p&gt;I was discussing sauerkraut recipes with someone on IRC a minute ago, and they warned me not to use iodised salt in the process. My first (and so far, the only successful) batch is one I made with iodised salt - I think it's pretty much the default here. Searching the Internet shows roughly equal numbers of answers going either way, from &quot;it doesn't matter&quot; to &quot;it discolours the vegetables&quot; to &quot;it kills the bacteria you want&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clearly elemental iodine is nasty, as are any of the halogens. But is the iodide ion similarly harmful to the bacteria (and yeasts?) involved in lactofermentation, in the low quantities in which it's present in supermarket salt?&lt;/p&gt;&#xA;" OwnerUserId="3046" LastEditorUserId="3059" LastEditDate="2013-07-19T22:16:07.927" LastActivityDate="2019-10-26T20:42:03.427" Title="Is iodised salt harmful to the lactofermentation process?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;food&gt;&lt;fermentation&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9342" PostTypeId="1" AcceptedAnswerId="15669" CreationDate="2013-07-19T16:39:08.907" Score="2" ViewCount="196" Body="&lt;p&gt;Assuming the current model of human evolution to be correct, approximately when did the earliest ancestor of humans live, who was intelligent enough, that if raised from a young enough age, could learn the necessary skills to live in today's society:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;learn a modern language&lt;/li&gt;&#xA;&lt;li&gt;learn to read and write&lt;/li&gt;&#xA;&lt;li&gt;learn to use most common tools and household items&lt;/li&gt;&#xA;&lt;li&gt;learn to drive a car, use a telephone, a computer, have an average job.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3798" LastEditorUserId="948" LastEditDate="2013-07-19T18:41:54.997" LastActivityDate="2016-12-26T05:46:30.360" Title="Earliest ancestor of humans who could integrate into modern society" Tags="&lt;evolution&gt;&lt;anthropology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9343" PostTypeId="1" CreationDate="2013-07-19T18:52:30.613" Score="5" ViewCount="1367" Body="&lt;p&gt;I've been reading some articles on the internet about dangers of Teflon and aluminium to the body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My family say I'm just exaggerating the situation, and maybe I am, though I'm not sure because not everything on the internet is true. They always tell me that if aluminium were dangerous then why would the government allow the use of aluminium bottles in drinks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there strong references and facts to support dangers associated with aluminium or Teflon cookware? If aluminium or other chemicals enter the body from cookware, are they naturally eliminated, or do they remain in the body?&lt;/p&gt;&#xA;" OwnerUserId="3966" LastEditorUserId="3952" LastEditDate="2013-07-22T08:24:09.390" LastActivityDate="2014-09-01T09:02:19.413" Title="Are there dangers to Teflon and aluminium cookware?" Tags="&lt;biochemistry&gt;&lt;pharmacology&gt;&lt;toxicology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9344" PostTypeId="2" ParentId="9340" CreationDate="2013-07-19T19:08:44.503" Score="1" Body="&lt;p&gt;from &lt;a href=&quot;http://en.wikipedia.org/wiki/Iodised_salt&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;No-additive salts for canning and pickling&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;In contrast to table salt, which often has iodide as well as&#xA;anticaking ingredients,&#xA;special canning and pickling salt is made for producing the brine to&#xA;be used in pickling vegetables and other food-stuffs. This salt has no&#xA;iodine added because the iodide can be oxidised by the foods and&#xA;darken them—a harmless but aesthetically undesirable effect.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I have been looking for a concentration, but I suspect it is below the threshold that would harm microflora, as it typically has to be visibly yellow (~6ppm if i remember correctly) to be effective as a contact antimicrobial agent...&lt;/p&gt;&#xA;" OwnerUserId="4054" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-07-19T19:08:44.503" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9345" PostTypeId="1" AcceptedAnswerId="9346" CreationDate="2013-07-19T19:48:52.247" Score="9" ViewCount="2957" Body="&lt;p&gt;The human body can synthesize vitamin D in the skin from cholesterol, when sun exposure is adequate. But how can haired mammals do it? Do not they need it?&lt;/p&gt;&#xA;" OwnerUserId="4064" LastEditorUserId="107" LastEditDate="2013-07-19T20:24:52.210" LastActivityDate="2016-10-10T00:15:51.713" Title="How can haired mammals synthesize vitamin D?" Tags="&lt;metabolism&gt;&lt;skin&gt;&lt;vitamins&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9346" PostTypeId="2" ParentId="9345" CreationDate="2013-07-19T21:59:18.450" Score="7" Body="&lt;p&gt;According to &lt;a href=&quot;http://faculty.massasoit.mass.edu/whanna/201/201_assets/pl_melanocytebiology.pdf&quot;&gt;&quot;Melanocyte biology and skin pigmentation&quot;&lt;/a&gt; (Yin and Fisher, 2007), the exposed parts of mammal bodies, such as their noses have melanocytes that can be locations of vitamin D production. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Vitamin_D#Industrial_production&quot;&gt;this Wikipedia article&lt;/a&gt;, the secretions in woolly animals also produce vitamin D. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is further explored in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20412916&quot;&gt;&quot;Vitamin D(3) synthesis in the entire skin surface of dairy cows despite hair coverage.&quot;&lt;/a&gt; (Hymoller and Jensen, 2010), where they found that cows synthesise vitamin D all over their body, where they dispute an idea that vitamin D is manufactured in the fur secretions, and ingested via grooming.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-07-19T21:59:18.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9347" PostTypeId="2" ParentId="9337" CreationDate="2013-07-19T23:12:47.863" Score="1" Body="&lt;p&gt;This is only a partial answer, but a reasonable starting point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a blog-article &lt;a href=&quot;http://theadvancedapes.com/20121016the-evolution-of-primate-sleep/&quot; rel=&quot;nofollow&quot;&gt;&quot;The Evolution of Primate Sleep&quot;&lt;/a&gt;, the author identified 3 main patterns - the third pattern seems most relevant to your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What he found was that there are 2 divisions of sleep patterns - several primates, such as some species of lemurs are nocturnally active, whereas apes, gorillas etc tend not to be active at night.  Seemingly adapting to the diurnal cycle.  In the article &lt;a href=&quot;http://www.ploscompbiol.org/article/info%3adoi/10.1371/journal.pcbi.1000826&quot; rel=&quot;nofollow&quot;&gt;&quot;Mammalian Sleep Dynamics: How Diverse Features Arise from a Common Physiological Framework &quot;&lt;/a&gt; (Phillips et al.), primates uniquely undergo monophasic sleep.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-07-19T23:12:47.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9349" PostTypeId="1" CreationDate="2013-07-20T01:30:31.240" Score="4" ViewCount="2118" Body="&lt;p&gt;How do mosquitoes find and get their food? For how much time can they survive without food? &lt;/p&gt;&#xA;" OwnerUserId="4066" LastEditorUserId="16866" LastEditDate="2017-04-03T17:19:09.593" LastActivityDate="2018-06-29T16:16:50.370" Title="How mosquitoes get their food and survive?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;ecology&gt;&lt;food&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9350" PostTypeId="2" ParentId="9349" CreationDate="2013-07-20T03:09:04.707" Score="1" Body="&lt;p&gt;Only female mosquitos (of some, but not all species) need blood to reproduce, they find it by following cues that lead them to warm blooded animals. These include gradients of heat and CO₂. Pretty much all mosquitos feed on nectar and plants while they are adults...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for how long they could survive without food, I don't know, but no longer than their normal lifespans of a few days to a couple of months as adult.&lt;/p&gt;&#xA;" OwnerUserId="4054" LastEditorUserId="3340" LastEditDate="2014-10-09T15:01:29.520" LastActivityDate="2014-10-09T15:01:29.520" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9351" PostTypeId="1" CreationDate="2013-07-20T10:23:39.887" Score="2" ViewCount="3065" Body="&lt;p&gt;Ants have something like a single fertile female to several males. The same applies to bees, and larger animals - elephants too. Is the sex ratio universally skewed in favour of the female? What animal species exhibit this ?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2013-07-20T12:58:42.903" LastActivityDate="2017-01-17T08:08:34.380" Title="In what animal species is the sex ratio skewed in favour of the fertile female?" Tags="&lt;reproduction&gt;&lt;sexual-selection&gt;&lt;sex-ratio&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9352" PostTypeId="1" AcceptedAnswerId="9354" CreationDate="2013-07-20T12:56:12.750" Score="5" ViewCount="333" Body="&lt;p&gt;Just what the title states. The thought came from reading &lt;a href=&quot;https://biology.stackexchange.com/questions/2705/when-has-an-organism-evolved-enough-to-be-called-a-new-species&quot;&gt;When has an organism evolved enough to be called a new species?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm probably wrong but I understand new species happen sporadically rather than in whole-sale lot during breeding season. Is the new species capable of breeding with members of its parent species? How does a new species survive inbreeding initially?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-04-02T13:35:05.170" Title="How does a new species survive without suffering inbreeding?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9353" PostTypeId="2" ParentId="9351" CreationDate="2013-07-20T14:27:12.017" Score="4" Body="&lt;p&gt;It is advantageous to have a skew towards more males. Males can be expendable as they are only required briefly for impregnation and can then focus on providing resources for the mother and young and protection. This breaks down when this is no longer the case, for example in humans we are closer to a 50/50 divide. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jstor.org/discover/10.2307/2389787?uid=3738032&amp;amp;uid=2&amp;amp;uid=4&amp;amp;sid=21102169440673&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; notes that in aphids, there are twice as many females as males, the same is true for daphnia. I don't think the reason behind this is known. In reptiles, the female to male ratio can depend on temperature of incubation thus this can lead to strong fluctuations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An interesting principle is Fisher's principle:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fisher’s principle explains why for most species, the sex ratio is&#xA;  approximately 1:1. Bill Hamilton expounded Fisher’s argument in his&#xA;  1967 paper on “Extraordinary sex ratios” as follows, given the&#xA;  assumption of equal parental expenditure on offspring of both sexes.&#xA;  Suppose male births are less common than female. A newborn male then&#xA;  has better mating prospects than a newborn female, and therefore can&#xA;  expect to have more offspring. Therefore parents genetically disposed&#xA;  to produce males tend to have more than average numbers of&#xA;  grandchildren born to them. Therefore the genes for male-producing&#xA;  tendencies spread, and male births become more common. As the 1:1 sex&#xA;  ratio is approached, the advantage associated with producing males&#xA;  dies away. The same reasoning holds if females are substituted for&#xA;  males throughout. Therefore 1:1 is the equilibrium ratio.&#xA;  &lt;a href=&quot;http://en.wikipedia.org/wiki/Sex_ratio&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-07-20T14:27:12.017" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9354" PostTypeId="2" ParentId="9352" CreationDate="2013-07-20T14:34:14.253" Score="7" Body="&lt;p&gt;Well, speciation is a process, not a single event thing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually what happens initially is geographic isolation of some members of a species, so in that sense the inbreeding is something that is influencing and you can also think of it as causing the speciation process. The presence of special harmless or semi-harmless disadvantagious mutations - which increases in frequency from this isolation - influences how the species is going to evolve, but eventually shapes this species to better cope adapt to some environment, or evolves the new species out of existence.&lt;/p&gt;&#xA;" OwnerUserId="4036" LastActivityDate="2013-07-20T14:34:14.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9355" PostTypeId="2" ParentId="9338" CreationDate="2013-07-20T14:41:58.017" Score="8" Body="&lt;p&gt;HIV hides in a number of known cells and unknown cells. Although most of the damage of HIV is caused by its infection of shorter lived cells, long lived cells which it infects includes anything with adequate receptors including memory T cells, dendritic cells, macrophages and some glial cells too. These cells are found widespread in the body from tissues to the blood stream. HIV also infects an as of yet unknown pool, which is thought to be the cause of rebound after HART (Highly Active Retroviral Therapy) is stopped. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The constant parts are not exactly there. Every part of HIV can essentially mutate and does. In functional HIV particles (which surprisingly make up a tiny proportion of total HIV particles in an infected individual), the epitopes you mentioned are mostly constant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Destroying them is impossible as of yet and hence no cure for HIV. It is hard to destroy a particular protein. We could make HIV that doesn't make these proteins (it would then rapidly mutate until it did, or be non-functional to the point it was an awful vaccine not inducing a particularly adept CD8 response). Otherwise we could block either these proteins themselves or that which they bind. There is a group of individuals with the delta 32 mutation which blocks CCR5 preventing infection, however this is rare. For the most part most individuals are susceptible as CD4 and CCR5 are highly conserved amongst humans. We would benefit therefore from inhibitors of these proteins themselves, however due to glycosylation generally our antibodies are terrible at inhibiting the glycoproteins. Reverse transcriptase inhibitors exist and are in fact very important as part of HART.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HIV came from chimpanzees. In their natural host the HIV equivalent (SIV) doesn't cause immunosuppression. HIV doesn't infect quite a few primates due to restriction factors which do not exist in humans or do not target the same things. Then of course there's the matter of the lack of the correct receptors. There's ongoing research if there's a chemical that does cure HIV however there isn't a subset of individuals where this occurs to study. HIV resistance is normally due to elite control of the virus due to specific genetic features that make the immune system target the best least variable, most deleterious (if HIV mutates them to escape) epitopes. If we could get everyone to respond to these epitopes that would be great (see a billion vaccine trials for HIV) otherwise if we could flush out the cells where it hides latently integrated (our current therapy and the immune system can only target cells where HIV is constantly replicating). &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1757" LastEditDate="2013-07-20T15:03:02.200" LastActivityDate="2013-07-20T15:03:02.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9356" PostTypeId="2" ParentId="9339" CreationDate="2013-07-20T14:57:11.300" Score="2" Body="&lt;p&gt;Broad question. Summary:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The innate immune system processes everything. When it senses that something is dangerous it tells the adaptive immune system, that is T and B cells, that this thing I'm holding is dangerous (via coreceptors and cytokines). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;T and B cells that are specific for this dangerous protein (or sometimes non-protein) are activated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ideally T and B cells that react to self proteins are deleted. These are from central tolerance mechanisms when the cells are developing (T and B cells are tested against self proteins; if they react they die) and in the periphery (once they're mature) by them only getting activated by the innate immune system and other mechanisms. There's also T regs which regulate the immune system by preventing any cells that react to self proteins from being activated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Autoimmune disorders are caused by a break down of these mechanisms.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-07-20T14:57:11.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9358" PostTypeId="1" AcceptedAnswerId="9360" CreationDate="2013-07-20T16:50:44.657" Score="4" ViewCount="103" Body="&lt;p&gt;I was reading about the necessity of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21519242&quot; rel=&quot;nofollow&quot;&gt;niche formations to adequate development of blood progenitors&lt;/a&gt; and this idea reminded me of the &lt;a href=&quot;http://www.nature.com/scitable/topicpage/x-chromosome-x-inactivation-323&quot; rel=&quot;nofollow&quot;&gt;patchy inactivation of the X chromosome&lt;/a&gt; which followed that maybe, if some of these pathways passed through X coded proteins, this might make women have different niches, that could account for the seemingly greater occurrence of auto-immune diseases in women. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any sense to this idea? Was this ever researched? &lt;/p&gt;&#xA;" OwnerUserId="4036" LastEditorUserId="1320" LastEditDate="2013-07-22T13:34:34.233" LastActivityDate="2013-07-22T13:34:34.233" Title="Is there a link between autoimmune diseases and X-chromosome inactivation?" Tags="&lt;immunology&gt;&lt;chromosome&gt;&lt;autoimmune&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9359" PostTypeId="1" AcceptedAnswerId="9372" CreationDate="2013-07-20T18:02:31.127" Score="11" ViewCount="345" Body="&lt;p&gt;Have we as a species faced extinction in the past? Resulting in a 'population bottleneck'?  If so, what genetic evidence is there of this occurring?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-07-22T13:26:47.997" Title="Is there any evidence that humans have faced extinction before?" Tags="&lt;human-genetics&gt;&lt;extinction&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9360" PostTypeId="2" ParentId="9358" CreationDate="2013-07-20T20:25:51.630" Score="4" Body="&lt;p&gt;Yes, here is an article on it: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC17816/&quot;&gt;&quot;The role of X-chromosome inactivation in female predisposition to autoimmunity&quot;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below see the method and results summarised. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Using a DNA methylation assay, we have examined the X-chromosome&#xA;  inactivation patterns in peripheral blood from normal females (n =&#xA;  30), female patients with a variety of autoimmune diseases (n = 167).&#xA;  No differences between patients and controls were observed. However,&#xA;  locally skewed X-chromsome inactivation may exist in the thymus, and&#xA;  therefore the underlying hypothesis remains to be disproved.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-07-20T20:25:51.630" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9361" PostTypeId="1" CreationDate="2013-07-21T01:15:24.320" Score="4" ViewCount="461" Body="&lt;p&gt;I've seen a &lt;a href=&quot;http://www.ted.com/talks/craig_venter_unveils_synthetic_life.html&quot; rel=&quot;nofollow&quot;&gt;Ted.com talk where the speaker suggests that modern science can create new micro organisms&lt;/a&gt;, like bacteria with a pre- defined new set of traits. But has anyone create a new species of plants or animals using synthetic DNA yet? If so, what are their names?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2016-09-12T13:39:05.863" Title="Has synthetic biology created new plants or animals as of 2013?" Tags="&lt;zoology&gt;&lt;botany&gt;&lt;synthetic-biology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9362" PostTypeId="1" AcceptedAnswerId="9366" CreationDate="2013-07-21T02:02:02.540" Score="3" ViewCount="119" Body="&lt;p&gt;If osteoarthritis (osteoarthrosis) is a degenerative condition, where the cartilage in joints wears down, what causes the joints to become inflamed? I'm reading through a book called Understanding Disease: Arthritis by Steven Tiger, and it mentions that Heberden's nodes are caused by osteoarthrosis. if things inside the joint are wearing down, why does it get bigger? &lt;/p&gt;&#xA;" OwnerUserId="4068" LastActivityDate="2013-07-21T19:07:48.663" Title="Enlargement of joints in osteoarthrosis" Tags="&lt;pathology&gt;&lt;joints&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9363" PostTypeId="2" ParentId="5471" CreationDate="2013-07-21T09:47:46.327" Score="3" Body="&lt;p&gt;I work on photosynthesis in algae, blue-green algae and anoxygenic photosynthetic bacteria.  All would more or less be able to live on Mars in a blow up tent equipped with a simple blow compressor (like some tennis courts in cold climates).  This could be used to raise the air pressure up enough (say 100 millibars) for water to exist in liquid form over a reasonable range of temperatures (Mars atmosphere is about 10 mB, Earth about 1000 mB).  The tent material could be made of UV opague material.  Besides many algae are quite resistant to UV anyway. The light intensity on Mars is no problem.  Most earth plants saturate photosynthesis at about 30% of full sunlight anyway.   Keeping the inside warm enough would not be a huge problem because the Mars atmosphere is essentially a near vacuum and so is a very poor conductor of heat. I do not think it would be all that hard. Low O2 is no problem for many algae. You could grow many higher plants quite easily if the O2 level was resonable.&lt;/p&gt;&#xA;" OwnerUserId="4069" LastActivityDate="2013-07-21T09:47:46.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9364" PostTypeId="2" ParentId="7924" CreationDate="2013-07-21T10:03:59.477" Score="2" Body="&lt;p&gt;Some wires crossed here.  Most algae are C3, in other words they use the Calvin cycle to fix CO₂. Another way of saying it is that RUBISCO (Ribulose bisphosphate carboxylase) is dorectly responsible for CO₂ fixation.  There is some evidence (disputed) that some diatoms use a form of the C4 pathway in which CO₂ is initially fixed as a 4-carbon compound (CO₂+C3 → C4).  The C4 compound formed is often malic acid.&#xA;Trying to establish if the C4 pathway is functional for carbon fixation is not easy.  Genomics can be misleading. Practically all photosynthetic organisms have the genes required for the C4 pathway but whether they are expressed is another matter (look at KEGG).  C4 photosynthesis usually requires complex anatomy because it is essentially a CO₂ supercharger mechanism because the C4 carbon form is then decarboxylated in a special location to provide RUBISCO with a very high CO₂ environment to finally fix CO₂ a 2nd time and pass the two C3 carbon compounds formed from CO₂ plus Ribulose Bisphosphate into the Calvin cycle.&lt;/p&gt;&#xA;" OwnerUserId="4069" LastEditorUserId="3340" LastEditDate="2014-10-09T15:41:31.127" LastActivityDate="2014-10-09T15:41:31.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9365" PostTypeId="1" AcceptedAnswerId="9371" CreationDate="2013-07-21T14:12:50.520" Score="3" ViewCount="197" Body="&lt;p&gt;It is often said &quot;You don't need to outrun the cheetah, just the other gazelles&quot;, thus emphasizing that greater part of the adaptation pressure comes from competing with other individuals of the same species and not directly from predators/parasites (which are seen as more indirect forces similar to the living conditions imposed by the environment (climate, geophysical factors, etc.))&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isn't there a difference between competing with other individuals of the same species for food, habitats (i.e. resources) and competing with them in avoiding being eaten?&lt;/p&gt;&#xA;" OwnerUserId="4071" LastActivityDate="2013-07-22T10:18:26.370" Title="Competition with other individuals of the same species vs. adaptation pressure from predators" Tags="&lt;adaptation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9366" PostTypeId="2" ParentId="9362" CreationDate="2013-07-21T19:07:48.663" Score="1" Body="&lt;p&gt;Osteoarthritis results from the gradual degradation of articular cartilage. When the cartilage is damaged extensively, e.g., all the way through the cartilage and into the bone, an inflammatory response ensues in the bone. This often happens when bone is rubbing against bone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of bone's responses to injury and inflammation is the production of new bone. In this case, the bone, called &lt;a href=&quot;http://www.mayoclinic.com/health/bone-spurs/DS00627&quot; rel=&quot;nofollow&quot;&gt;osteophytes&lt;/a&gt; or bone spurs, is produced pathologically (i.e., not like the bone laid down normally during growth). Heberden's nodes are the names given to these osteophytes at the distal interphalangeal joints, but the process is basically the same at other joints in the digits, ankle, etc.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-07-21T19:07:48.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9370" PostTypeId="2" ParentId="9349" CreationDate="2013-07-22T01:11:26.137" Score="1" Body="&lt;p&gt;Both Male and Female Mosquitoes feeds nectar and plant juice. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Only Female Mosquitoes feeds blood from Vertebrates. They find Lipid, protein from blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lipid and Protein will help in nourishing egg nutrients. Their breeding proportionately increases with the amount of blood meal they intake. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure about their life expectancy without food. &lt;/p&gt;&#xA;" OwnerUserId="4076" LastEditorUserId="4076" LastEditDate="2015-09-11T03:25:12.590" LastActivityDate="2015-09-11T03:25:12.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9371" PostTypeId="2" ParentId="9365" CreationDate="2013-07-22T07:10:09.973" Score="2" Body="&lt;p&gt;The correct answer is, &quot;it depends.&quot;  The traits that will be under the strongest selective pressure will be those related to survival in the face of the most common causes of death for that species. If food is abundant but so are predators, then clearly predator evasion will be of supreme importance. If food is scarce, then perhaps metabolism-related traits will be under strong selective pressure. But it's important to remember that just because one selective pressure is stronger doesn't mean that the rest disappear. Thus, the individual's survival is dependent upon really a composite fitness that depends on a countless array of selective pressures, some of which may be larger components than others. The competition between individuals of the same species is really a complex interplay of fitness effects, then.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;As for the maxim about outrunning a cheetah, what it's illustrating is that the gazelles are not competing with the cheetah for survival. They're competing with each other. If you want, you could expand it to say &quot;...just the other gazelles and the rest of the herbivores in the environment&quot;. If a herd of gazelles and a herd of some slower animal are nearby and a cheetah attacks, one of the individuals from the slower species will probably get caught and all the gazelles will get away. The point is that the gazelles and the cheetahs fill very different niches in the environment, so they don't really compete for the same resources (as a matter of fact, one is the primary resource of the other). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When it comes to determining survival, one talks about fitness only within the context of the population (or, if you want, between species directly competing for the same niche). The less fit members of the population do not survive. Thus, the less fit ones that fail to evade the predator are simply doing a worse job evading the predator than the other members of the population. But it's not only the relative fitness that is important. Imagine that a new predator migrates into the environment, for which none of the prey has any evasive adaptation. Even though there may be a relative fitness between them regarding evading this predator, if even the best individual is not good enough to evade it, they would all have an absolute fitness that is too low to ensure survival. Then the saying breaks down, since none of the gazelles can out-run each other with respect to evading this new predator.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, this idiom falls apart when you start talking about asocial species, since there aren't any other individuals around to out-run.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorDisplayName="user3934" LastEditDate="2013-07-22T10:18:26.370" LastActivityDate="2013-07-22T10:18:26.370" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9372" PostTypeId="2" ParentId="9359" CreationDate="2013-07-22T07:20:22.257" Score="15" Body="&lt;p&gt;There is ample genetic evidence for a &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/12433581&quot;&gt;population bottleneck following the out-of-Africa migration&lt;/a&gt;. This would account for the reduced genetic diversity found in non-African populations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is further evidence for an &lt;a href=&quot;http://www.nature.com/nature/journal/v475/n7357/full/nature10231.html&quot;&gt;earlier major bottleneck&lt;/a&gt; that reduced the human population to around 10,000 individuals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These kinds of studies are typically done now via &lt;a href=&quot;https://en.wikipedia.org/wiki/Coalescent_theory&quot;&gt;Coalescent theory&lt;/a&gt; using whole-genome sequences.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I just found this nice &lt;a href=&quot;https://whyevolutionistrue.wordpress.com/2011/09/18/how-big-was-the-human-population-bottleneck-not-anything-close-to-2/&quot;&gt;blog post&lt;/a&gt; summarizing the Nature paper I linked to.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorDisplayName="user3934" LastEditDate="2013-07-22T13:26:47.997" LastActivityDate="2013-07-22T13:26:47.997" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9373" PostTypeId="2" ParentId="9343" CreationDate="2013-07-22T08:05:49.187" Score="5" Body="&lt;p&gt;The US Department of Health and Human Services has a nice set of &lt;a href=&quot;http://www.atsdr.cdc.gov/substances/toxsubstance.asp?toxid=34&quot; rel=&quot;nofollow&quot;&gt;factsheets on aluminum&lt;/a&gt;. In brief, and to specifically answer your questions, they point out that:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Aluminum occurs naturally in air, water, soil, and plants.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The amounts of aluminum that we encounter in pots and pans are considered to be safe for healthy people. Cooking acidic foods in aluminum pots increases the amount ingested, but is still considered to be safe; and it still represents many times less aluminum than in over-the-counter antacids, which are also considered safe.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;Much of the aluminum we ingest leaves ones body naturally through the digestive system (that is, feces), and is not taken up into the bloodstream. The small amount of aluminum that makes it to our bloodstream is mostly quickly eliminated in urine. Those with kindey problems may not process this bloodstream aluminum as quickly.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Nonstick pan coatings are a little more difficult, probably because they're so diverse. Cookware isn't even mentioned as a source on the &lt;a href=&quot;http://www.atsdr.cdc.gov/substances/toxsubstance.asp?toxid=237&quot; rel=&quot;nofollow&quot;&gt;factsheet for perflouroalkyls&lt;/a&gt;, the chemical which has been mentioned in connection with nonstick pan health issues. The &lt;a href=&quot;http://www.epa.gov/oppt/pfoa/pubs/faq.html#consumers&quot; rel=&quot;nofollow&quot;&gt;US Environmental Protection Agency FAQ&lt;/a&gt; says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Consumer products made with perfluorochemicals include some non-stick cookware ... Consumer products made with fluoropolymers and fluorinated telomers, such as Teflon and other trademark products, are not PFOA. PFOA is used as a processing aid in the manufacture of fluoropolymers and can be also be produced by the breakdown of some fluorinated telomers [NB. I assume they mean overheating nonstick pans]. The information that EPA has available does not indicate that the routine use of consumer products poses a concern.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-10-04T19:31:21.013" LastActivityDate="2013-10-04T19:31:21.013" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9374" PostTypeId="1" CreationDate="2013-07-22T09:37:13.483" Score="2" ViewCount="899" Body="&lt;p&gt;I'm planning to build an inverted microscope and I am not sure if I can use a plane achromatic objective of a normal microscope for the inverted microscope as well. Are there any specific needs for the objective of an inverted microscope? &lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="5762" LastEditDate="2014-06-04T06:56:45.753" LastActivityDate="2014-07-04T07:19:11.807" Title="Any difference between inverted microscope objective vs normal microscope objective?" Tags="&lt;microscopy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9375" PostTypeId="1" AcceptedAnswerId="9376" CreationDate="2013-07-22T09:39:54.573" Score="1" ViewCount="570" Body="&lt;p&gt;Is chlorophyll living or non living, and after boiling the water out of a chlorophyll extract would it still live, as in would it still maintain its properties after re-adding liquid to the dried chlorophyll?    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for any help.&lt;/p&gt;&#xA;" OwnerUserId="4031" LastEditorUserId="3952" LastEditDate="2013-07-31T07:28:37.390" LastActivityDate="2016-03-01T15:38:33.170" Title="Is chlorophyll living or non living?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9376" PostTypeId="2" ParentId="9375" CreationDate="2013-07-22T10:26:01.480" Score="3" Body="&lt;p&gt;Chlorophyll is &lt;a href=&quot;https://en.wikipedia.org/wiki/Organic_compound&quot; rel=&quot;nofollow&quot;&gt;organic&lt;/a&gt;, not living, which is a fancy way of saying that it contains carbon. As for your question about boiling, it depends on whether or not the heat from boiling will disrupt the chemical bonds and destroy the molecule. According to &lt;a href=&quot;https://en.wikipedia.org/wiki/Chlorophyll_a&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;, chlorophyll a will melt at around 117°C (I'll assume that chlorophyll b is similar), which is higher than the boiling point of water, so if the temperature is strictly maintained, the chemical should stay intact.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorDisplayName="user3934" LastEditDate="2013-07-22T14:12:50.610" LastActivityDate="2013-07-22T14:12:50.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9377" PostTypeId="1" AcceptedAnswerId="9378" CreationDate="2013-07-22T11:24:36.957" Score="2" ViewCount="3253" Body="&lt;p&gt;In the beginning of meiosis, there is one cell. During meiosis, 1 cell divides into 4 cells. Does each of these 4 cells divide each into 4 more cells?&lt;/p&gt;&#xA;" OwnerUserId="4079" LastEditorUserId="1320" LastEditDate="2013-07-22T13:31:27.940" LastActivityDate="2013-07-26T13:22:47.983" Title="Do the four cells produced by meiosis each divide into four cells again?" Tags="&lt;meiosis&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9378" PostTypeId="2" ParentId="9377" CreationDate="2013-07-22T12:10:24.577" Score="3" Body="&lt;p&gt;No, meiosis is not a cycle like mitosis. In mitosis, haploid or diploid cells divide to create two genetically identical cells, and this process can go on and on. On the other hand, meiosis results in 4 genetically unique daughter cells which are also haploid. If a haploid cell was to try to undergo meiosis, there would not be enough genetic material and you would end up with half-chromatids.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2013-07-22T16:27:47.003" LastActivityDate="2013-07-22T16:27:47.003" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9379" PostTypeId="1" AcceptedAnswerId="9385" CreationDate="2013-07-22T13:16:30.817" Score="3" ViewCount="148" Body="&lt;p&gt;When we see something, how and where in the brain do we remember it and are able to recognize it later? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens in the brain that makes this possible?&lt;/p&gt;&#xA;" OwnerUserId="4080" LastEditorDisplayName="user3795" LastEditDate="2013-07-22T19:54:20.733" LastActivityDate="2013-07-22T22:53:54.013" Title="How do we memorize something?" Tags="&lt;brain&gt;&lt;memory&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9380" PostTypeId="1" CreationDate="2013-07-22T14:05:38.500" Score="1" ViewCount="623" Body="&lt;p&gt;To detect the deamidation from Glutamine to Glutamate in a protein, normal practise seems to be a mass spec, where it is claimed there is a change of 1 dalton.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EG &lt;a href=&quot;http://www.ionsource.com/Card/Deamidation/mono0001.htm&quot; rel=&quot;nofollow&quot;&gt;It is claimed&lt;/a&gt; that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Deamidation of an Asn to Asp/IsoAsp results in an increase in mass of a single dalton.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But when I look at their table, they are using Glutamic Acid as being 1 Dalton heavier than Glutamate, but at pH 7 the Glutamic Acid will be deprotonated to Glutamate. Do they  put the sample in pH 4 to protonate the Glutamate first? But then you are risking catalysing the hydrolysis of Glutamine anyway, rendering your results useless!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There should be a charge difference though, as you are going from neutral to a negative charge, so that would show up in a change in mass/charge on the mass spec, rather than a mass change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help would be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="1300" LastEditorUserId="1300" LastEditDate="2013-07-22T21:30:12.307" LastActivityDate="2013-07-22T21:30:12.307" Title="Mass change in deamidation from Glutamine to Glutamate" Tags="&lt;mass-spec&gt;" AnswerCount="0" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="9381" PostTypeId="2" ParentId="1415" CreationDate="2013-07-22T14:23:50.143" Score="8" Body="&lt;p&gt;There are many different kinds of plants that have independently evolved this sort of variegation (non-green areas) in the leaves. However, the mechanisms by which they effect this vary between species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some have little or no chlorophyll in the non-green areas, but many others have changed the architecture of their leaf cell layers in the non-green areas, creating &lt;strong&gt;refraction effects that make the leaves appear white, but &lt;em&gt;don't&lt;/em&gt; significantly change their photosynthetic efficiency&lt;/strong&gt; (&lt;a href=&quot;http://dx.doi.org/10.1093/aob/mcs025&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sheue et al.&lt;/a&gt;) In fact, &lt;em&gt;Arum italicum&lt;/em&gt; white areas actually have &lt;em&gt;higher&lt;/em&gt; efficiency in certain light conditions! (&lt;a href=&quot;http://dx.doi.org/10.1016/j.plaphy.2011.09.009&quot; rel=&quot;nofollow noreferrer&quot;&gt;La Rocca et al.&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't find any information on which type of variegation &lt;em&gt;Caladium&lt;/em&gt; shows. The genus &lt;em&gt;Caladium&lt;/em&gt; is related to the &lt;em&gt;Arum&lt;/em&gt; I mentioned above which uses the &quot;architecture&quot; method, but it's also related to &lt;em&gt;Epipremnum&lt;/em&gt;, which seems to use the &quot;no-cholorophyl&quot; method.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1093/aob/mcs025&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sheue et al.&lt;/a&gt; mention that with some species that use the architecture method, using transmitted light instead of reflected light reveals that the white spots are actually green; while in no-chlorophyll plants the spots remain white. If you have a &lt;em&gt;Caladium&lt;/em&gt; around, you could try holding its leaf up to a bright light, and see!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to answer your question: if &lt;em&gt;Caladium&lt;/em&gt; is an 'architecture-variegation' plant, its white areas perform photosynthesis at or near the efficiency of the green areas of the leaf. If it's a 'no-chlorophyll-variegation' plant, it would have reduced efficiency, but might make up for this with strategies including:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Having a larger total leaf area (&lt;a href=&quot;http://dx.doi.org/10.1016/j.plaphy.2011.09.009&quot; rel=&quot;nofollow noreferrer&quot;&gt;La Rocca et al.&lt;/a&gt; and also see &lt;a href=&quot;https://biology.stackexchange.com/questions/1762/why-do-plants-leaves-become-enlarged-in-low-light-areas?rq=1&quot;&gt;this question&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Only developing large white areas if there's plenty of light as they grow (&lt;a href=&quot;http://horttech.ashspublications.org/content/20/5/929.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Garland et al.&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Increasing the mitochondrial activity in its white areas, which could lead to other energy efficiencies (&lt;a href=&quot;http://dx.doi.org/10.1007/s00709-011-0325-y&quot; rel=&quot;nofollow noreferrer&quot;&gt;Toshoji et al.&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Using &lt;em&gt;Homo sapiens&lt;/em&gt; to help it reproduce and provide plenty of light for it. Many of these extreme variegation patterns are found in horticulturally bred varieties!&lt;/li&gt;&#xA;&lt;li&gt;Just using its green areas for photosynthesis, and &quot;accepting&quot; the fact that the white areas are not producing energy. In natural populations, you often don't find varieties as completely white as in that picture: they usually show white spots and plenty of green. This is true of &lt;em&gt;Caladium&lt;/em&gt; species in the wild, which may use the variegation to mimic and to prevent herbivory: potential pests think the leaves are already infested, and avoid them (&lt;a href=&quot;http://dx.doi.org/10.1007/s10682-008-9248-2&quot; rel=&quot;nofollow noreferrer&quot;&gt;Soltau et al.&lt;/a&gt;). In other words, even if the white patches represent decreased photosynthesis efficiency, it could be a trade-off in order to achieve less herbivory.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://horttech.ashspublications.org/content/20/5/929.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Garland KF, Burnett SE, Stack LB, Zhang D&lt;/strong&gt;. 2010. Minimum Daily Light Integral for Growing High-quality Coleus. HortTechnology 20: 929–933.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.plaphy.2011.09.009&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;La Rocca NN, Rascio NN, Pupillo PP&lt;/strong&gt;. 2011. Variegation in Arum italicum leaves. A structural-functional study. Plant Physiol Biochem 49: 1392–1398.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1093/aob/mcs025&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Sheue C-RC, Pao S-HS, Chien L-FL, Chesson PP, Peng C-IC&lt;/strong&gt;. 2012. Natural foliar variegation without costs? The case of Begonia. Ann Bot 109: 1065–1074.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s10682-008-9248-2&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Soltau U, Dötterl S, Liede-Schumann S&lt;/strong&gt;. 2009. Leaf variegation in Caladium steudneriifolium (Araceae): a case of mimicry? Evolutionary Ecology 23: 503–512.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s00709-011-0325-y&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Toshoji HH, Katsumata TT, Takusagawa MM, Yusa YY, Sakai AA&lt;/strong&gt;. 2012. Effects of chloroplast dysfunction on mitochondria: white sectors in variegated leaves have higher mitochondrial DNA levels and lower dark respiration rates than green sectors. Protoplasma 249: 805–817.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-05-20T14:41:13.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9382" PostTypeId="1" AcceptedAnswerId="9383" CreationDate="2013-07-22T14:42:41.103" Score="3" ViewCount="464" Body="&lt;p&gt;Found in Russia, in the kitchen. It is about 1–2 cm length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/gc5QK.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/gc5QK.jpg&quot; alt=&quot;unknown insect&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/pcc8P.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/pcc8P.jpg&quot; alt=&quot;unknown insect&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3280" LastEditorUserId="16866" LastEditDate="2019-11-30T22:43:42.003" LastActivityDate="2019-11-30T22:43:42.003" Title="What insect is in this photo?" Tags="&lt;species-identification&gt;&lt;zoology&gt;&lt;entomology&gt;&lt;hemiptera&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9383" PostTypeId="2" ParentId="9382" CreationDate="2013-07-22T14:58:01.297" Score="9" Body="&lt;p&gt;This is an immature &quot;True Bug&quot;, order Hemiptera. You can tell this from the general shape of the wings, and from the big &quot;beak&quot;, a feature of the Hemiptera.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within Hemiptera, it's possible that with those enlarged front legs, it could be an Assassin Bug, family Reduviidae.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-07-22T14:58:01.297" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9385" PostTypeId="2" ParentId="9379" CreationDate="2013-07-22T21:37:00.567" Score="6" Body="&lt;p&gt;The current working theory (note this is still an open question, but there are many leads being followed):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sensory systems receive a combination of signals from an event, which are initially &lt;a href=&quot;http://psych.colorado.edu/~oreilly/papers/ceroreillyip.pdf&quot;&gt;bound to the hippocampus&lt;/a&gt; (this is called episodic memory).  Then, typically during sleep, the &lt;a href=&quot;http://www.sciencemag.org/content/287/5451/248.short&quot;&gt;memories are consolidated&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A simplified view is that consolidation basically consists of communication between the neocortex and the hippocampus, and the memories are thought to be &quot;saved&quot; in the neocortex.  Thus, amnesia patients with hippocampal damage still have all their long-term memories, they just can't create new memories (because their old memories were already consolidated to neocortex).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your neocortex has many subregions with many functions.  One is the temporal lobe, where semantic memory seems to be stored.  So your episodic memory may record several interactions apples and, over time, your semantic memory will be updated (as memory consolidation occurs) to &quot;consolidate&quot; your concept of &quot;apple&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The temporal lobe is highly connected with the occipital lobe (where visual information is processed) and the two likely work together to identify objects using the consolidated information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the molecular level, how the memories are actually stored.  The most well known concept is &lt;a href=&quot;https://en.wikipedia.org/wiki/Connectionism#Neural_networks&quot;&gt;connectionism&lt;/a&gt;: different connection strengths between neurons carry different information.  But there's also genetic expression going on, and there was recently some research on &lt;a href=&quot;http://www.sciencedaily.com/releases/2012/01/120127162409.htm&quot;&gt;prion-like proteins contributing to memory&lt;/a&gt; as well as &lt;a href=&quot;http://www.nature.com/nature/journal/v463/n7278/edsumm/e100114-12.html&quot;&gt;astrocytes&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Realize, of course, that a lot of this is cutting edge research... and therefore could be wrong or contain numerous oversights and simplifications.&lt;/p&gt;&#xA;" OwnerUserId="1853" LastEditorUserId="1853" LastEditDate="2013-07-22T22:53:54.013" LastActivityDate="2013-07-22T22:53:54.013" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9386" PostTypeId="1" AcceptedAnswerId="9475" CreationDate="2013-07-23T00:25:50.183" Score="9" ViewCount="19707" Body="&lt;p&gt;How would you begin to estimate the world population of the European Honeybee (&lt;em&gt;Apis mellifera&lt;/em&gt;)? Would recent colony collapse disorder show up as a blip? How about the spread of &lt;em&gt;A. mellifera&lt;/em&gt; from Europe to Asia and the New World?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ideally, I'd love to see a chart with estimates of the kept and feral populations of &lt;em&gt;A. mellifera&lt;/em&gt; across time. I realize that this is a tall order; but given that we have available to us:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;the complete genome,&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;current data from agricultural organizations, and&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;historical and archaeological records,&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;it seeems that with a combination of genetic and historical methods this shouldn't be impossible. Or is it? There seem to be plenty of articles arguing about &lt;em&gt;A. mellifera&lt;/em&gt;'s African or European origin, but none that I see that mention actual population sizes.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-08-21T04:19:11.683" LastActivityDate="2017-02-21T16:52:45.470" Title="How many honeybees are there, and how has the number changed across time?" Tags="&lt;entomology&gt;&lt;food&gt;&lt;population-biology&gt;&lt;ethnobiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9387" PostTypeId="1" AcceptedAnswerId="9404" CreationDate="2013-07-23T00:51:10.610" Score="4" ViewCount="142" Body="&lt;p&gt;I've asked &lt;a href=&quot;https://biology.stackexchange.com/questions/8630/can-any-species-be-bred-selectively-engineered-to-become-as-diverse-looking-as-d&quot;&gt;this question about dogs&lt;/a&gt; not so long ago, and the short answer was - &lt;strong&gt;&lt;em&gt;dogs are the most diverse looking species of mammals&lt;/em&gt;&lt;/strong&gt; because they got a small number of genes that have a big impact on appearance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to ask a follow up question- differences in appearance are easy to notice, and I would like to learn about other traits that might be genetically based.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are there other major differences between dog breeds, like longevity, cognitive performance, friendliness, etc?&lt;/strong&gt; Or are all dogs more or less the same in traits other than appearance? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there plots of traits like these among different dog breeds that identify outliers?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-08-23T08:15:10.637" Title="How diverse are dogs in their traits other than appearance?" Tags="&lt;genetics&gt;&lt;zoology&gt;&lt;dogs&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9388" PostTypeId="1" AcceptedAnswerId="9390" CreationDate="2013-07-23T09:09:49.913" Score="2" ViewCount="300" Body="&lt;p&gt;Tired of hearing of these urban legends and popular opinions, I ask this question here to see if there really is scientific merit to this belief. My questions is, is it really &quot;harmful&quot; for a person to reproduce with his/her own first cousin? Everyone, at least in America, seems to think that this is incest which I completely dismiss because incest is purely a religious concept. The next argument I get is that we want more genetic diversity and having offspring with a first cousin is detrimental to our survival as a species. If you have any genetic weaknesses then your cousin is likely to be carrying them as well and then the chances of your offspring carrying them increase and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't really believe any of this. It is rather well known (or may be not so well known) that only a very small percentage of a human individual is different from another human individual's genome. Differences due to skin color, race, ethnicity, and such are literally skin deep. So one reproducing with her cousin or someone half way across the globe is only negligibly different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Forgetting about religion, has this been scientifically systematically tested and/or proven? Has any research been done on this? Is it true one way or the other? I don't mean to spark any debates here. Opinions are of course welcome. But if anyone can point me to any reputable sources or published results/references, that would be ideal.&lt;/p&gt;&#xA;" OwnerUserId="4053" LastEditorUserId="1590" LastEditDate="2013-07-31T14:10:03.457" LastActivityDate="2013-07-31T14:10:03.457" Title="Is it really detrimental to humans as a species to reproduce with one's own first cousin?" Tags="&lt;reproduction&gt;&lt;human-genetics&gt;&lt;human-genome&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9389" PostTypeId="1" AcceptedAnswerId="9395" CreationDate="2013-07-23T09:21:33.937" Score="1" ViewCount="186" Body="&lt;p&gt;Verging on the realm of science fiction, my question is that is there any theoretically possible way, biologically/chemically, with which the entire human race can be killed without affecting the rest of the biosphere at all? I am only curious about theoretically possible no matter how unlikely. If we encounter a sufficiently advanced alien civilization bent on our destruction, would it be possible for them to make sure all humans die without harming any other living organism on our planet?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there anything biological/chemical which makes us unique or different than other lifeforms on Earth? Something which can be used against us? Or are we just so similar with a bunch of other species that we cannot be wiped out without other lifeforms getting harmed or our destruction cannot be ensured? Is it possible to artificially make humans extinct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks you.&lt;/p&gt;&#xA;" OwnerUserId="4053" LastActivityDate="2013-07-31T13:07:37.407" Title="Is it possible to make humans extinct artificially?" Tags="&lt;human-biology&gt;&lt;extinction&gt;" AnswerCount="3" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9390" PostTypeId="2" ParentId="9388" CreationDate="2013-07-23T09:57:27.307" Score="12" Body="&lt;p&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/19834483&quot;&gt;Inbreeding depression&lt;/a&gt;, &quot;the reduced survival and fertility of offspring of related individuals&quot; (quoting the linked article), is a well-known and well-understood biological effect. It does, indeed, affect humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem is that recessive mutations become more likely to affect the survival of the offspring of relatives. Imagine that you have a mutation affecting, say, some gene that's critical to your metabolism, which is entirely possible. But, since you have two copies of the gene and only one of them is faulty, you are not affected by this. Nevertheless, you, by chance, pass the non-functional one on to a couple of your kids, who are also not affected due to only having one copy as well. They, in turn, pass it on to one or more of their kids. Now, two of them, cousins, have a kid. The kid gets both copies and can no longer properly metabolize something due to having two faulty copies of the gene. This can prove to be fatal or at least severely debilitating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, lest you think this is improbable, there are on average &lt;a href=&quot;http://sandwalk.blogspot.com.es/2013/03/estimating-human-mutation-rate-direct.html&quot;&gt;70-something mutations per generation&lt;/a&gt;. Some of those will be neutral in effect, others will be detrimental. Once an offspring gets two copies of those detrimental alleles, then there could be serious health effects. The likelihood of an offspring getting two copies decreases as the relatedness of its parents decreases. So, sibling or parent/child pairings would be the most likely to produce offspring with the problems. Pairing between 3rd generation (First-cousins) or any pairings between them and their siblings, parents, aunts/uncles or grand-parents would be the next most likely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes, first-cousins marrying and having kids is a bad idea for very basic scientific reasons. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I missed the &quot;as a species&quot; part of your question. Inbreeding will only likely have an effect within small, closed populations, though it will continue to have a lasting effect even as those populations grow and open up. Two textbook examples are &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/16143014&quot;&gt;French Canadians&lt;/a&gt; and &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/15516842&quot;&gt;Ashkenazi Jews&lt;/a&gt;. Even now, there is continued elevated risk of certain rare genetic diseases in these populations. As for the species as a whole, it is likely to be really detrimental only if the effective population size of the species becomes really low: a general rule of thumb used by conservation biologists is that the &lt;a href=&quot;https://en.wikipedia.org/wiki/Effective_population_size&quot;&gt;effective population size&lt;/a&gt; should be at least 50 to avoid the effects of inbreeding (and 500 to avoid the effects of genetic drift) (&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/?term=50%2F500+rule&quot;&gt;50/500 rule&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry about the confusion. &lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorDisplayName="user3934" LastEditDate="2013-07-23T12:09:41.970" LastActivityDate="2013-07-23T12:09:41.970" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="9391" PostTypeId="2" ParentId="9015" CreationDate="2013-07-23T11:14:48.080" Score="9" Body="&lt;p&gt;Bone growth continues in the human body for quite awhile after permanent teeth come in. Generally, the complete closure of all growth plates doesn't occur until the mid 20s.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the top and bottom primary teeth come in, the empty space left behind is gradually filled by growth of the maxilla and mandible, respectively. During the time period when teeth are actively coming in, teeth can displace into the empty space left by other permanent teeth that are no longer there, resulting in crooked teeth. &lt;/p&gt;&#xA;" OwnerUserId="3370" LastActivityDate="2013-07-23T11:14:48.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9392" PostTypeId="2" ParentId="1133" CreationDate="2013-07-23T13:50:02.487" Score="11" Body="&lt;p&gt;From the Smithsonian website:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans are the only mammal that cannot breathe and swallow at the same time, and we are the only species that can choke on its own food. The reason? The lowering of the voice box in our throats (during infancy) enables us to create the enormous range of sounds used in producing language; but this lowering of the voice box comes at a big cost in adulthood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://newsdesk.si.edu/factsheets/did-you-know-human-origins-facts&quot;&gt;http://newsdesk.si.edu/factsheets/did-you-know-human-origins-facts&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4086" LastActivityDate="2013-07-23T13:50:02.487" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9393" PostTypeId="1" CreationDate="2013-07-23T16:07:54.713" Score="1" ViewCount="51" Body="&lt;p&gt;I read that NASA looks for water on Mars or other planets as a sign of a life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder why scientists look for water as proof of a life? isn't there any animal that drinks another liquid like alcohol or something?&lt;/p&gt;&#xA;" OwnerUserId="4087" LastActivityDate="2013-07-23T16:07:54.713" Title="why water is a proof of a life?" Tags="&lt;zoology&gt;&lt;life&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2013-07-23T16:48:43.387" ContentLicense="CC BY-SA 3.0" />
  <row Id="9395" PostTypeId="2" ParentId="9389" CreationDate="2013-07-23T21:24:36.963" Score="3" Body="&lt;p&gt;Infectious diseases is probably the only way I can think of. Viruses for example may have tropisms based on receptors to which they attach. These receptors may be and often are unique to a species, and thus an infection could target humans very specifically. Differences between humans and animals present the weaknesses and resistances we would have to such an infection. As an international species, spread of the disease can be quite rapid. However, our increased intelligence means we could given time, understand the threat and combat it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If an infectious disease killed rapidly enough that development of a cure or administration of one was not easily possible, the disease itself would be wiped out by quarantine measures (theoretically). For an infection it is not wise to kill the host too quickly as this prevents survival of the infection which is dependent on its host. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus we want an infection that is non-pathological at first then rapidly pathological but affected the whole world as a whole. This infection would need to spread to every individual so would have to be incredibly infectious and for no individuals to have any resistance to it and also ideally to kill everyone at roughly the same time or at least quickly enough to prevent us having time to come up with a cure. The only way I can think of that would fulfil all of those conditions is if the infection on it's own was non-pathological but then a novel secondary universal factor made this infection pathological. This factor would have to be in low levels prior to infection but then rapidly escalate to worldwide distribution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disclaimer: Obviously this is theoretical and probably not at all possible. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-07-23T21:24:36.963" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9396" PostTypeId="2" ParentId="8171" CreationDate="2013-07-23T23:12:11.433" Score="5" Body="&lt;p&gt;A research paper that recently came out suggests that deep-sea life does have a circadian rhythm, but it is regulated much differently than it is by us surface dwellers. We see light, we eat and digest, and the suprachiasmatic nucleus in the brain (our &quot;biological&quot; clock) keeps track of it and eventually establishes a rhythm of the circadian variety.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most living things at the surface have some sort of circadian rhythm - the mechanisms vary, but they are present and can be readily observed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the deep sea, the mechanisms are quite different since they can't see any light, but the rhythm is still established. When these animals (squid in the research) eat a certain type of bacteria containing a light organ, the presence of certain proteins within that organ actually trigger a change in the gene transcription responsible for encoding the protein controlling the circadian rhythm. Thus, when the squid eats, it ultimately determines what the rhythm will be. The entrainment itself actually happens by means of the light organs consumed in the bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as where the bacteria ultimately get there bioluminescence, there is still research to be done, although I would presume there is a mixture of downward bacterial migration and chemical generation contributing to this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Link to the article: &lt;a href=&quot;http://mbio.asm.org/content/4/2/e00167-13&quot; rel=&quot;nofollow&quot;&gt;http://mbio.asm.org/content/4/2/e00167-13&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3370" LastEditorUserId="3370" LastEditDate="2013-07-24T14:23:37.810" LastActivityDate="2013-07-24T14:23:37.810" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9397" PostTypeId="2" ParentId="7247" CreationDate="2013-07-23T23:30:55.810" Score="1" Body="&lt;p&gt;These are 'peak' values when administered via IV, with the exception of oxycodone. There will be some variation person to person depending on their opioid tolerance and any concomitantly administered medications.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Buprenorphine: 60m&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Butorphanol: 5m&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fentanyl: 5m&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hydromorphone: 30-90m&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Methadone: 1-2h&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Morphine: 20m&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oxycodone: Not administered intravenously&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pentazocine: 15m&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sufentanil: 3m&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tramadol: 2h&lt;/p&gt;&#xA;" OwnerUserId="3370" LastActivityDate="2013-07-23T23:30:55.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9398" PostTypeId="1" CreationDate="2013-07-24T02:01:12.543" Score="4" ViewCount="952" Body="&lt;p&gt;There have been demonstrations of ecomorphs in different taxa, where each morphology type is associated to a single environment. I know that it happens because special morphological characters increase the fitness and therefore will be positive selected.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is; if we find similar places (talking about natural pressures and climatic conditions) on earth and given enough time, can we expect to see more or less the same ecomorphs living in different places? Also, assuming that, could evolution be a regarded a non-stochastic process?&lt;/p&gt;&#xA;" OwnerUserId="4089" LastEditorUserId="1590" LastEditDate="2013-07-24T07:16:46.820" LastActivityDate="2013-07-24T09:59:27.620" Title="Ecomorphs as evolutionary definitions" Tags="&lt;evolution&gt;&lt;ecology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9399" PostTypeId="1" CreationDate="2013-07-24T03:38:48.707" Score="5" ViewCount="99" Body="&lt;p&gt;Question is rather self-explanatory. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Putting aside other post-transcriptional factors like rate of degradation of transcript, what is the smallest gene ever reported to have successfully been transcribed in &lt;em&gt;E. coli&lt;/em&gt; or other similar prokaryotic systems? Why couldn't this gene be any smaller? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that in the context of this question, I am disregarding factors like promoters, operators and terminators. Also note that this gene does not necessarily need to code for a protein.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="5144" LastEditDate="2014-11-05T06:47:28.440" LastActivityDate="2014-11-05T06:47:28.440" Title="Is there are practical lower limit to gene length in E. coli?" Tags="&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;genetics&gt;&lt;ecoli&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9400" PostTypeId="2" ParentId="7785" CreationDate="2013-07-24T05:15:12.317" Score="0" Body="&lt;p&gt;After the peptide chain of a protein has been organised into successive stretches of secondary elements, combinations of such elements are first arranged into distinctive groups called super secondary motifs. Several neighbouring secondary elements and supersecondary motifs are folded and twisted further into compact globular cluster called a domain.&lt;/p&gt;&#xA;" OwnerUserId="4090" LastEditorDisplayName="user3795" LastEditDate="2013-07-24T09:28:37.430" LastActivityDate="2013-07-24T09:28:37.430" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9401" PostTypeId="2" ParentId="9398" CreationDate="2013-07-24T07:05:11.413" Score="2" Body="&lt;p&gt;If you have two similar environments and you allow the organisms to evolve indefinitely, then you would, indeed, expect to see &lt;a href=&quot;https://en.wikipedia.org/wiki/Convergent_evolution&quot; rel=&quot;nofollow&quot;&gt;convergent evolution&lt;/a&gt;, in which different species evolve to have very similar adaptations. However, because the species in the two environments have different genetic backgrounds, they would most likely arrive at these these traits through distinct genetic adaptations (see: &lt;a href=&quot;https://en.wikipedia.org/wiki/Analogy_%28biology%29&quot; rel=&quot;nofollow&quot;&gt;analogous traits&lt;/a&gt;). Thus, they might look similar but not exactly the same (think: bird wings vs. bat wings vs. insect wings). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that this should still be the case even if you take a population of some species, split it in two and put one half in the one environment and the other half in the other environment. Over time, there will begin to be novel traits popping up only in one of the linneages, resulting in the accumulation of genetic differences despite their initial shared history. It's probably that, in the evolution of some new trait, these two populations will have attained it through distinct genetic routes: either through mutations on distinct genes (or their regulatory mechanisms), or through distinct mutations within the same genes (not to mention other mechanisms such as gene duplication).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your other question, it's important to remember that evolution by natural selection is a &lt;em&gt;deterministic&lt;/em&gt; (non-stochastic) process! All else being equal, the most fit individuals will survive. However, the &quot;raw material&quot; that determines the fitness of individuals, such as mutations and recombination, are &lt;em&gt;stochastic&lt;/em&gt;. There is also a stochastic evulotionary process, namely &lt;a href=&quot;https://en.wikipedia.org/wiki/Genetic_drift&quot; rel=&quot;nofollow&quot;&gt;genetic drift&lt;/a&gt;, however the actual process of evolution by natural selection is entirely deterministic. So, that's why you would see convergent evolution: species will develop similar adaptations because they deterministically give advantages under certain environmental conditions, but the adaptations will not be exactly the same owing to the stochastic manner in which mutations arose to give rise to those adaptations.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorDisplayName="user3934" LastEditDate="2013-07-24T08:00:22.410" LastActivityDate="2013-07-24T08:00:22.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9403" PostTypeId="2" ParentId="9389" CreationDate="2013-07-24T07:17:01.347" Score="4" Body="&lt;p&gt;Trick question. By driving humans to extinction, you almost certainly will be driving all human-specific parasites and pathogens to extinction as well.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastActivityDate="2013-07-24T07:17:01.347" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9404" PostTypeId="2" ParentId="9387" CreationDate="2013-07-24T07:26:21.987" Score="2" Body="&lt;p&gt;Dogs are highly diverse in their patterns of &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/22138850&quot; rel=&quot;nofollow&quot;&gt;copy number variation&lt;/a&gt; (variation in the number of copies of different genes). This has been shown to be probably related to the diversity in morphology. It would thus presumably also affect other traits such as those that you list, and it seems to at least have been shown for disease susceptibility. Interestingly, wolves have less copy number variation on average than dogs (&lt;a href=&quot;http://genomebiology.com/content/13/8/R73&quot; rel=&quot;nofollow&quot;&gt;citation&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastActivityDate="2013-07-24T07:26:21.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9405" PostTypeId="2" ParentId="9398" CreationDate="2013-07-24T07:38:17.033" Score="4" Body="&lt;p&gt;The phenomenon you describe, where the same result comes about in more than one time/location via evolution, is called &lt;a href=&quot;http://www.mapoflife.org/topics/topic_337_Anolis-lizard-ecomorphs/&quot; rel=&quot;nofollow&quot;&gt;&quot;convergent evolution.&lt;/a&gt;&quot; It is when the same character, or trait, evolve independently of one another. One example is the wing, it has evolved (at least) several times independently, in bats, birds, and insects. Parallels can also be drawn with &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_examples_of_convergent_evolution&quot; rel=&quot;nofollow&quot;&gt;other traits&lt;/a&gt; like dispersion methods of seeds, or the evolution of fins in fish, dolphins, and whales. &lt;a href=&quot;http://www.anoleannals.org/wp-content/uploads/2011/08/williams-1972.pdf&quot; rel=&quot;nofollow&quot;&gt;Here is a classic paper by Ernest Williams&lt;/a&gt; from 1972 which describes one of the earliest examples given of ecomorphs, the anolis lizard, also talked about &lt;a href=&quot;http://www.mapoflife.org/topics/topic_337_Anolis-lizard-ecomorphs/&quot; rel=&quot;nofollow&quot;&gt;on this site&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is from a &lt;a href=&quot;http://www.newscientist.com/article/dn13698-evolution-myths-evolution-is-random.html#.Ue-D143vh8E&quot; rel=&quot;nofollow&quot;&gt;good article on the new scientist&lt;/a&gt; website that would be worth reading:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Evolutionary convergence occurs at every level, from proteins to&#xA;  societies. An unusual antibody once thought to be unique to camels has&#xA;  a close equivalent in sharks, for instance, while naked mole rats form&#xA;  social colonies like those of ants and bees.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&quot;What this means is that if we could wind the clock back and let life&#xA;  evolve all over again, life might take very different paths but still&#xA;  produce organisms that, in some ways, resemble the organisms alive&#xA;  today.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&quot;There would almost certainly be streamlined swimmers in the oceans and&#xA;  winged creatures in the skies. In fact, some argue that the evolution&#xA;  of intelligence is also virtually inevitable, though intelligent&#xA;  organisms could be very different from us.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The answer to your question is yes, with enough time and the same selection effects we would not be surprised if there was a similar pair of independently evolved characters. However, selection acts on random mutations which is not a directed process, therefore for the same characters to evolve you would need mutations to occur that had similar effects. This is why &lt;em&gt;given enough time&lt;/em&gt; we can see the same responses. Despite the non-random effect of selection, we could consider evolution to be a stochastic process, it only arrives at the same converged point by chance. This is because selection (the main driver of evolution) acts on randomly generated genetic variation thus the direction of the evolutionary trajectory is random.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;..often used to represent the evolution of some random value, or&#xA;  system, over time. This is the probabilistic counterpart to a&#xA;  deterministic process (or deterministic system). Instead of describing&#xA;  a process which can only evolve in one way (as in the case, for&#xA;  example, of solutions of an ordinary differential equation), in a&#xA;  stochastic or random process there is some indeterminacy: even if the&#xA;  initial condition (or starting point) is known, there are several&#xA;  (often infinitely many) directions in which the process may evolve.&quot; -&#xA;  &lt;a href=&quot;https://en.wikipedia.org/wiki/Stochastic_process&quot; rel=&quot;nofollow&quot;&gt;wikipedia entry on Stochastic Processes&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Following the quote above it may seem that evolution is a directed process, i.e. selection is aiming for a specific target. It is not, selection can only weed out the least fit genotypes and increase the frequency of the better ones, selection has no goal or pre-existing aim. Thus, when discussing stochasticity in evolutionary terms it is perhaps better to use &lt;strong&gt;evolutionary trajectories, to describe the randomly created paths they move along, instead of &quot;directions.&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;As an example of convergent evolution we could use the peppered moth and a little imagination because this is purely a hypothetical illustration I am making up on the spot&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Peppered_moth#Evolution&quot; rel=&quot;nofollow&quot;&gt;The peppered moth is famous for once being a white moth that turned dark&lt;/a&gt; during the industrial revolution, when towns and cities grew and pollution killed the light coloured lichens that helped the light morph hide. This meant, rather suddenly by evolutionary time-scales, the white morph of the moth was not very well camouflaged against the dark bark of the trees. This created a positive selection for darker morphs, as such, alleles which made for dark moths would have spread rapidly in the population. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using a little imagination we can think about two different parts of the world where this same event occurred independently - e.g. &lt;a href=&quot;http://www.theglasgowstory.com/storyc.php&quot; rel=&quot;nofollow&quot;&gt;Glasgow&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/History_of_Plymouth&quot; rel=&quot;nofollow&quot;&gt;Plymouth&lt;/a&gt; in Britain which are quite far apart but both grew expansively during the industrial revolution. In both of these locations we would have seen a simultaneous rapid loss of lichens and increase in the dark moth ecomorph. This would have been convergent evolution because it is likely that they were independent of each other, i.e. the dark moth probably did not evolve in Glasgow and then fly itself down to Plymouth.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-24T09:59:27.620" LastActivityDate="2013-07-24T09:59:27.620" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="9406" PostTypeId="1" AcceptedAnswerId="9421" CreationDate="2013-07-24T08:14:11.237" Score="9" ViewCount="654" Body="&lt;p&gt;I found this in Russia. It is approximately 2cm long.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/QXtQy.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/QXtQy.jpg&quot; alt=&quot;unidentified insect photo 1&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/5vTrV.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/5vTrV.jpg&quot; alt=&quot;unidentified insect photo 2&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3280" LastEditorUserId="239" LastEditDate="2015-08-17T22:41:47.967" LastActivityDate="2015-08-18T17:24:49.117" Title="What is this insect I found in Russia?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9407" PostTypeId="2" ParentId="9399" CreationDate="2013-07-24T08:34:36.057" Score="2" Body="&lt;p&gt;In terms of naturally-occurring &quot;genes&quot; I think that the record is probably held by the &lt;strong&gt;attenuator peptides&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In bacteria, the regulatory mechanism known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Attenuator_%28genetics%29#Protein-mediated_attenuation&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;transcription attenuation&lt;/em&gt;&lt;/a&gt; involves the ribosomal biosynthesis of very short peptides. In the &lt;a href=&quot;http://en.wikipedia.org/wiki/Trp_operon&quot; rel=&quot;nofollow&quot;&gt;trp operon&lt;/a&gt;, where the phenomenon was first &lt;a href=&quot;http://jb.asm.org/content/182/1/1.full&quot; rel=&quot;nofollow&quot;&gt;described by Yanofsky's group&lt;/a&gt;, the peptide, MKAIFVLKGWWRTS, consists of just 14 amino acids. Other examples, described subsequently, are of comparable size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now that I have written this answer, I have reread your question and I see that you are really interested in transcripts. In the case of the attenuators, the peptides are encoded by the 5' end of a much larger transcript, so they probably don't count for you.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-07-24T08:34:36.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9412" PostTypeId="1" CreationDate="2013-07-24T17:31:57.800" Score="1" ViewCount="101" Body="&lt;p&gt;Imagine that complexity is measured by a positive number $f_n$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If one has no prior knowledge about the positive number $f_n$ then from Bayesian theory one can assign $\log f_n$ an &quot;improper&quot; uniform prior over the range $-\infty$ to $\infty$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A random mutation might increase or decrease the complexity of the offspring $f_{n+1}$. If we assume the offspring's complexity is likely to be close to the parent then we could simply model the random change in complexity by:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$log f_{n+1} = log f_n + \Delta\ \ \ \ \  \hbox{with probability 0.5}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$log f_{n+1} = log f_n - \Delta\ \ \ \ \  \hbox{with probability 0.5}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $\Delta$ is some small number.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such a random evolution will lead to the log of the complexity performing a random walk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But now add sex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume the complexity of a sexual organism is the average of the complexities of its parents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$f_{child} = \frac{f_{male} + f_{female}}{2}.$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If one evolves the simple model now one finds that the complexity of the population grows exponentially.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this idea interesting or not? :)&lt;/p&gt;&#xA;" OwnerUserId="4095" LastEditorUserId="4095" LastEditDate="2013-07-25T15:03:48.373" LastActivityDate="2013-07-25T15:18:07.247" Title="Could sex alone drive complexity?" Tags="&lt;evolution&gt;&lt;theoretical-biology&gt;&lt;evolutionary-game-theory&gt;&lt;information-theory&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9413" PostTypeId="2" ParentId="9412" CreationDate="2013-07-24T18:11:38.820" Score="5" Body="&lt;p&gt;Replace the word &quot;complexity&quot; with any other word...&quot;height&quot;, &quot;weight&quot;, &quot;resting metabolic rate&quot;, etc. and the model would still be solvable in a mathematical sense and it would read the same way. So, it's hard for me to accept the model as relevant to the evolution of complexity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think you need to make the model have a more robust definition of complexity (as mentioned in the comments) but you also need to consider the costs and benefits of complexity in your model, which will greatly affect the dynamics and actually carry biological relevance.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastActivityDate="2013-07-24T18:11:38.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9414" PostTypeId="1" CreationDate="2013-07-24T21:18:25.920" Score="1" ViewCount="293" Body="&lt;p&gt;I have seen a paper in which deuterated water was used to follow dividing cells. The assumption was that deuterated water will be incorporated into newly synthesized DNA molecules. Is there any direct incorporation of water in the replication process? Is there any proton exchange?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper describing the method can be found here:&#xA;&lt;a href=&quot;http://www.pnas.org/content/105/16/6115.full.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/105/16/6115.full.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4099" LastEditorUserId="4099" LastEditDate="2013-07-25T09:03:07.533" LastActivityDate="2014-04-06T01:43:28.220" Title="What is the mechanism of labeling a DNA molecule with deuterated water?" Tags="&lt;dna&gt;&lt;replication&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9415" PostTypeId="1" CreationDate="2013-07-24T21:25:35.880" Score="0" ViewCount="1364" Body="&lt;p&gt;I'm curious if NGF, or Neurotrophins in general is available commercially. Can I order it online? If not, what are the medical/biological reasons. Does it breakdown quickly after synthesis/capture? Is it a regulated protein?&lt;/p&gt;&#xA;" OwnerUserId="1086" LastActivityDate="2019-04-23T17:54:52.897" Title="Is Nerve Growth Factor (NGF) commercially available?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9416" PostTypeId="2" ParentId="9412" CreationDate="2013-07-24T21:36:30.940" Score="2" Body="&lt;p&gt;Is it interesting?  Perhaps, but &quot;complexity&quot; is a vague notion.  If you want to simplify and just say &quot;variation&quot; then sure, sex increases variation.  But so does that random mutation you brought in.  Really, all you need for increased variability is some difference between generations and genetic Drift will take care of the rest.  Mutation is enough, which is clear from asexual organisms.  Sexual reproduction tends to increase diversity, but that has nothing to do with &quot;complexity.&quot;  The environment, in particular interaction with other organisms, drives complexity more than anything.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-07-24T21:36:30.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9417" PostTypeId="1" CreationDate="2013-07-24T22:07:05.610" Score="4" ViewCount="368" Body="&lt;p&gt;I want to clone two fluorescent proteins both driven by different promoters in a plasmid to be used to transform &lt;em&gt;B. subtilis&lt;/em&gt; at the amyE locus. For this I want to use plasmid pSG1729 (Lewis and Marston, 1999), because this plasmid can be used for homologous recombination at this specific locus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the problem is, because of a few reasons (i.e., the locations of the restriction sites, keeping the spc resistance gene and deleting the current GFP gene), if I want to clone two genes into this plasmid, they will be very close to each other (~10bp). Will this be a problem either technically or biologically after transformation? I don't think that possible read-through will be bad, as I want one of the fluorescent proteins (pHluorin) to be continuously expressed. Maybe an option would be to clone the two genes in opposite directions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the current genotype of the plasmid:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Ori amyE5' currentGFP Spc amyE3' bla&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="4098" LastEditorUserId="107" LastEditDate="2013-07-24T23:29:32.173" LastActivityDate="2013-10-23T01:58:42.060" Title="Cloning two fluorescent proteins with different promoters in the same plasmid?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;plasmids&gt;&lt;transformation&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9418" PostTypeId="1" CreationDate="2013-07-25T01:25:01.590" Score="0" ViewCount="264" Body="&lt;p&gt;I'm fairly new learning about protein. As I know protein can be synthesis by condensation reaction. And the current method to produce protein is purify them from an organism. So why not produce protein based on condensation reaction instead of purifying it from an organism?&lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="107" LastEditDate="2013-07-25T01:33:22.370" LastActivityDate="2013-07-31T03:41:39.040" Title="Why not produce protein based on condensation reaction?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9419" PostTypeId="1" AcceptedAnswerId="9420" CreationDate="2013-07-25T02:44:03.033" Score="53" ViewCount="13858" Body="&lt;p&gt;Reading this question, &lt;a href=&quot;https://biology.stackexchange.com/questions/7932/why-are-there-no-wheeled-animals&quot;&gt;Why are there no wheeled animals?&lt;/a&gt;, I wondered why &lt;strong&gt;no organisms seem to make use of the tensile and other strengths of metal&lt;/strong&gt;, as we do in metal tools and constructions. I am obviously not talking about the microscopic uses of metal, as in human blood etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why are there no plants with metal thorns? No trees with &quot;reinforced&quot; wood? No metal-plated sloths? No beetles with metal-tipped drills? Or are there?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can think of some &lt;strong&gt;potential factors&lt;/strong&gt; why there are none (or few), but I do not know whether they are true:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Is metal too &lt;strong&gt;scarce&lt;/strong&gt; near the surface?&lt;/li&gt;&#xA;&lt;li&gt;Are there certain chemical properties that make metal &lt;strong&gt;hard to extract and accumulate in larger quantities&lt;/strong&gt;?&lt;/li&gt;&#xA;&lt;li&gt;Is metal &lt;strong&gt;too heavy&lt;/strong&gt; to carry around, even in a thin layer or mesh or tip?&lt;/li&gt;&#xA;&lt;li&gt;Can metal of high (tensile etc.) strength only be forged under &lt;strong&gt;temperatures too high&lt;/strong&gt; to sustain inside (or touching) organic tissue, and is &lt;strong&gt;crystallised metal too weak&lt;/strong&gt;?&lt;/li&gt;&#xA;&lt;li&gt;Are functionally comparable organic materials like horn, bone, wood, etc. in fact &lt;strong&gt;better at their tasks than metal&lt;/strong&gt;, and do we humans only use metal because we are not good enough at using e.g. horn to make armour or chitin to make drills?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;As a predator, I would like to eat a lot of vertebrates and save up the metal from their blood to reinforce my fangs...&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;A bonus question: are there any organisms that use the high &lt;strong&gt;electric conductivity&lt;/strong&gt; of metal? Animals depend upon electric signals for their nervous system, but I do not think nerves contain much metal. The same applies to the few animals that use electricity as a weapon.&lt;/p&gt;&#xA;" OwnerUserId="1070" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2019-06-19T11:50:04.493" Title="Why are there no organisms with metal body parts, like weapons, bones, and armour? (Or are there?)" Tags="&lt;evolution&gt;&lt;biochemistry&gt;&lt;physiology&gt;&lt;speculative&gt;&lt;bioinorganic-chemistry&gt;" AnswerCount="10" CommentCount="22" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="9420" PostTypeId="2" ParentId="9419" CreationDate="2013-07-25T05:50:50.293" Score="55" Body="&lt;p&gt;There are some cases, as hinted at by the comments. But these are relatively small amount of metal.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its not that there is no metal available, but I can think of several reasons you don't see iron exoskeletons on animals all the time.  Firstly, fully reduced (oxidation state 0) metal has a high energetic cost to create in reduced form.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Iron is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Abundance_of_elements_in_Earth%27s_crust&quot;&gt;second most common metal after aluminum on the earth's crust&lt;/a&gt; but its almost entirely present in oxidized states - that's to say: as rust.  Most biological iron functions in the +2/+3 oxidation state, which is rust or closer to it than metal.  &lt;a href=&quot;http://rcsb.org/pdb/101/motm.do?momID=82&amp;amp;evtc=Suggest&amp;amp;evta=Moleculeof%20the%20Month&amp;amp;evtl=OtherOptions&quot;&gt;Cytochromes&lt;/a&gt; and &lt;a href=&quot;http://rcsb.org/pdb/101/motm.do?momID=41&quot;&gt;haemoglobin&lt;/a&gt; are examples of how iron is more valuable as a chemically active biological agent than a structural agent, using oxidized iron ions as they do. &lt;a href=&quot;http://www.siliconfareast.com/ox_potential.htm&quot;&gt;Aluminium, the most common metal on earth has relatively little biological activity one might assume because its redox costs are even higher than iron&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there are some reasons why reduced biometal doesn't show up very often, inability of biological systems to deposit reduced (metallic) metals is &lt;em&gt;not&lt;/em&gt; one of them.  Bone and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17950376&quot;&gt;shell&lt;/a&gt; are examples of biomineralization where the proteins depositing the calcium carbonate or other oxides in the material are structured by the proteins to be stronger than they would be as a simple crystal.  There are cases of admittedly small pieces of reduced metal being produced by biological systems. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Magnetotactic_bacteria#Magnetosomes&quot;&gt;Magnetosomes&lt;/a&gt; in magnetotactic bacteria are mentioned, but there are also cases of &lt;a href=&quot;http://www.nature.com/nature/journal/v495/n7440_supp/full/495S12a.html&quot;&gt;reduced gold being accumulated by microorganisms&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would say that while iron skeletons might seem to be an advantage, they are electrochemically unstable - oxygen and water will tend to oxidize (rust) them quickly and the organism would have to spend a lot of energy keeping it in working form.  Electrical conductivity sounds useful, but the nervous system favors exquisite levels of control over bulk current flow, even in cases like electric eels, &lt;a href=&quot;http://www.pnas.org/content/70/9/2473.full.pdf&quot;&gt;whose current is produced by gradients from acetylcholine&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's more, it is a fact that biological materials actually perform as well as or better than metal when they need to.  Spider silk has a greater tensile strength than steel (along the direction of the thread). Mollusc shells are models for tank armor - they are remarkably resistant to puncture and breakage.  The time it would take for metalized structures to evolve biologically might be too long - by the time the metalized version of an organ or skeleton got started, the bones, shells and fibers we know probably have a big lead and selective advantage. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2016-03-06T05:35:26.160" LastActivityDate="2016-03-06T05:35:26.160" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="9421" PostTypeId="2" ParentId="9406" CreationDate="2013-07-25T06:50:55.037" Score="8" Body="&lt;p&gt;This is a wasp, (see that nice slim &quot;wasp waist&quot; it's got?), which means taxonomically that it is in the order Hymenoptera (which it shares with bees and ants).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within Hymenoptera, wasps are diverse and often difficult to ID, but it's possible that this is a Braconid or Ichneumon (family Braconidae or Ichneumonidae). If you take a good closeup of its wing veins, chances are an expert (not me) could ID it.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-07-25T06:50:55.037" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9422" PostTypeId="1" AcceptedAnswerId="9423" CreationDate="2013-07-25T09:32:40.500" Score="-3" ViewCount="45469" Body="&lt;p&gt;Differentiate between the following:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Ureter and Urethra&lt;/li&gt;&#xA;&lt;li&gt;Renal papilla and Renal pelvis&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;It is not given in my book.&#xA;Please help.&lt;/p&gt;&#xA;" OwnerUserId="4079" LastEditorUserId="1590" LastEditDate="2013-07-25T11:08:24.587" LastActivityDate="2014-05-09T15:12:58.060" Title="What is the difference between the Ureter and Urethra? also between the Renal papilla and Renal pelvis?" Tags="&lt;homework&gt;&lt;kidney&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2014-05-09T21:39:27.950" ContentLicense="CC BY-SA 3.0" />
  <row Id="9423" PostTypeId="2" ParentId="9422" CreationDate="2013-07-25T11:00:36.787" Score="5" Body="&lt;p&gt;The ureters run from the kidneys to the bladder whilst the urethra runs from the bladder to exit the body:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ddoyQ.png&quot; alt=&quot;Schematic of urethra and ureters&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The renal papillae are the site where urine drains into one of the minor calyxes of the kidney.   Multiple minor calyxes join together into a major calyx, and multiple major calyxes join together to form the renal pelvis which then drains into the ureter.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6eP0g.jpg&quot; alt=&quot;Kidney&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2013-07-25T11:00:36.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9424" PostTypeId="1" AcceptedAnswerId="9751" CreationDate="2013-07-25T12:28:04.743" Score="1" ViewCount="2279" Body="&lt;p&gt;I'm looking at different &lt;a href=&quot;http://opensnp.org/&quot; rel=&quot;nofollow&quot;&gt;genotyping profiles available at opensnp.org&lt;/a&gt; and am &lt;strong&gt;trying to compare profiles for people with different phenotypes&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, given 10 profiles of people who can roll their tongue and those who cannot, I am trying to identify what is different between these people and what's similar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A typical record is in this format:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Rsid, chromosome, Position on chromosome, actual 2 letter mutation&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;How can such records be compared to identify similarities for a given phenotype? &lt;strong&gt;Does RSID uniquely identify a mutation, or is it a combination of rsid and position?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, if one user has rsid 123 at position 555 and another one has rsid 123 at position 666, and the mutation is the same, is this a similarity, or does position matter?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="577" LastEditDate="2013-07-25T20:59:02.457" LastActivityDate="2013-08-13T16:11:20.237" Title="How to compare SNP from genotyping results for multiple people with a known phenotype?" Tags="&lt;genetics&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9425" PostTypeId="1" CreationDate="2013-07-25T13:14:17.717" Score="4" ViewCount="340" Body="&lt;p&gt;I can't use HRP since my substrates interfere with it and I need a real-time method because I want to measure kinetic parameters of some oxidases.&lt;/p&gt;&#xA;" OwnerUserId="3901" LastEditorUserId="3901" LastEditDate="2013-07-29T05:57:12.250" LastActivityDate="2013-07-31T10:55:23.443" Title="Are there any methods to quantify H2O2 (hydrogen peroxide) which don't rely on horseradish peroxidase?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;&lt;enzyme-kinetics&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9426" PostTypeId="2" ParentId="9419" CreationDate="2013-07-25T14:09:49.830" Score="20" Body="&lt;p&gt;A few minor points to add to shigeta's excellent answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biological enzymes don't work well on metals.  Some often incorporate metals (see &lt;a href=&quot;https://en.wikipedia.org/wiki/Chelation&quot;&gt;chelation&lt;/a&gt;) but elemental atoms aren't easy to process.  For one, a large molecule would be identical everywhere, so cleavage, for example, would be indiscriminate and just leave a bunch of tiny tiny atoms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More to the point, once an organism incorporates metal there certainly isn't a lot it can do about that.  A lot of shell-based organisms swap out their shells because of the inflexibility of those designs, and metal would be no different.  It's difficult to grow when you're encased in a self-made iron maiden.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-07-25T14:09:49.830" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9427" PostTypeId="1" AcceptedAnswerId="9428" CreationDate="2013-07-25T14:15:00.033" Score="9" ViewCount="206" Body="&lt;p&gt;I'm working on a piece of &lt;a href=&quot;http://www.ebi.ac.uk/compneur-srv/melting/&quot;&gt;software&lt;/a&gt; that computes melting temperatures for nucleic acid duplexes, and I'm about to add support for 5-methylcytosine as a nucleotide base.  At the moment, the bases accepted by the program are adenine, cytosine, guanine, thymine and uracil, with their standard letters A,C,G,T,U.  Is there a standard letter for 5-methylcytosine?  The only example I've found is this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1945840&quot;&gt;paper&lt;/a&gt;, which uses an italic &lt;em&gt;C&lt;/em&gt; for 5mc, but I want a distinct letter.  The three candidates I've thought of are: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;5&lt;/strong&gt; - for '5-methylcytosine'&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;M&lt;/strong&gt; - for 'methyl'&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;B&lt;/strong&gt; - Since methylation of &lt;strong&gt;U&lt;/strong&gt; gives you &lt;strong&gt;T&lt;/strong&gt;, which is one place earlier in the alphabet, so methylation of &lt;strong&gt;C&lt;/strong&gt; gives &lt;strong&gt;B&lt;/strong&gt;.  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4104" LastEditorUserId="4101" LastEditDate="2013-11-02T00:24:57.923" LastActivityDate="2013-11-14T12:19:02.390" Title="Standard letter for 5-methylcytosine" Tags="&lt;bioinformatics&gt;&lt;epigenetics&gt;&lt;nucleic-acids&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9428" PostTypeId="2" ParentId="9427" CreationDate="2013-07-25T14:36:55.047" Score="11" Body="&lt;p&gt;Well, don't use &lt;strong&gt;M&lt;/strong&gt; or &lt;strong&gt;B&lt;/strong&gt;, those are already taken (&lt;strong&gt;C&lt;/strong&gt; or &lt;strong&gt;A&lt;/strong&gt;, and &lt;strong&gt;not A&lt;/strong&gt;, respectively).  You can see the full list here: &lt;a href=&quot;http://www.dna.affrc.go.jp/misc/MPsrch/InfoIUPAC.html&quot; rel=&quot;nofollow&quot;&gt;http://www.dna.affrc.go.jp/misc/MPsrch/InfoIUPAC.html&lt;/a&gt; (The enWiki article on &lt;a href=&quot;https://en.wikipedia.org/wiki/Nucleobase&quot; rel=&quot;nofollow&quot;&gt;Nucleobases&lt;/a&gt; lists a few others but I would ignore those as 1. D is present in both and 2. they are rare and inapplicable)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5-methylcytosine isn't on there.  If you want to be pedantic about it, 5-methylcytosine is an epigenetic marker and as such is by definition &lt;em&gt;not&lt;/em&gt; a genetic sequence; that remains simply a C and, genetically, the &lt;em&gt;sequence&lt;/em&gt; is the same, despite the fact that it may indeed make a difference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the time people use m&lt;sup&gt;5&lt;/sup&gt;C, so I'd go with &lt;strong&gt;5&lt;/strong&gt; if I were you.  That certainly isn't used for anything else and if you must use a single character most anybody will know what you are talking about.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-07-25T20:45:05.030" LastActivityDate="2013-07-25T20:45:05.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9429" PostTypeId="2" ParentId="9412" CreationDate="2013-07-25T15:18:07.247" Score="1" Body="&lt;p&gt;A concrete theoretical version of my model could be a population of random computer programs or Turing machines. I would define the complexity of a computer program as its run time not the size of its code.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutating programs will have varying run times whose logs just perform a random walk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if you allow pairs of those programs to occasionally combine in such a way that they generate a child program with a run time that is the average of their own then the run times of the population will grow. &lt;/p&gt;&#xA;" OwnerUserId="4095" LastActivityDate="2013-07-25T15:18:07.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9430" PostTypeId="1" CreationDate="2013-07-25T15:53:04.860" Score="2" ViewCount="68" Body="&lt;p&gt;E.g. in a MASCOT search, the accuracy of the fragment ions in a ms/ms spectrum does not have any influence on the scores of identified proteins (unless the fragment ions are out of the set ms/ms tolerance of course).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know other search algorithms that do include the fragment mass accuracy in the protein identification scores.&#xA;Also, if the protein scores are not influenced, i would like to know in which way other evaluation values of MASCOT or SEQUEST results are influenced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your time.&lt;/p&gt;&#xA;" OwnerUserId="4106" LastActivityDate="2013-07-25T15:53:04.860" Title="Which mass spectrometry database search algorithms include the fragment mass accuracy in the calculation of protein scores?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;mass-spec&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9431" PostTypeId="1" AcceptedAnswerId="9444" CreationDate="2013-07-25T19:58:05.267" Score="0" ViewCount="40" Body="&lt;p&gt;I'm guessing it &lt;strong&gt;&lt;em&gt;is&lt;/em&gt;&lt;/strong&gt; important,  but just to be a little more precise, &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;What would be the maximum amount of calories above which it is just a waste (or even harmful)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How much does the metabolism raise during the illness?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;More carbs or more proteins? (or less?)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3141" LastActivityDate="2013-08-25T11:16:51.010" Title="To what extent is eating and nutrition important in recovery from minor illness like viral fever?" Tags="&lt;pathology&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9432" PostTypeId="1" AcceptedAnswerId="9433" CreationDate="2013-07-25T20:10:13.820" Score="2" ViewCount="88" Body="&lt;p&gt;I'm wondering what makes cells to divide (and stop) in such a way that they make our hands the shape that our hands are...&lt;/p&gt;&#xA;" OwnerUserId="3141" LastActivityDate="2013-07-25T20:44:05.140" Title="How do cells figure out the big-picture shape?" Tags="&lt;molecular-biology&gt;&lt;human-anatomy&gt;&lt;development&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9433" PostTypeId="2" ParentId="9432" CreationDate="2013-07-25T20:44:05.140" Score="3" Body="&lt;p&gt;Hands are complicated and the genetic machinery behind their shape doubly so. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's easier to figure out worm segments first, and then work up from there. An egg has head/tail information encoded in it even before fertilization: &lt;a href=&quot;http://www.biologie.uni-regensburg.de/Zellbiologie/Sprunck/Research/Establishment/Polarity%20egg%20cell.png&quot; rel=&quot;nofollow&quot;&gt;see here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can imagine the first or second cell division would give a 'head' cell with higher concentration of head polarity transcription factors. These transcription factors switch on other regulatory genes, and the complexity works upwards from there. For more information about how worms and other segmented animals work out what goes where see &lt;a href=&quot;http://en.wikipedia.org/wiki/Hox_gene&quot; rel=&quot;nofollow&quot;&gt;Hox genes.&lt;/a&gt; The sad truth is that most of how this is done is unknown or not well understood.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2013-07-25T20:44:05.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9434" PostTypeId="1" AcceptedAnswerId="9488" CreationDate="2013-07-25T20:57:32.743" Score="1" ViewCount="200" Body="&lt;p&gt;When looking broadly at the tree of life, my feeling is that, after a divergence there is almost systematically one taxon that speciates way more than the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(There will have some approximations below it is not really the point of my question to discuss whether the urochordata is a sister group to the vertebrates or not.) Let's look at the kingdom Animalia for example:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Chaonflagellata vs &quot;the others&quot;&lt;/li&gt;&#xA;&lt;li&gt;Sponges vs &quot;the others&quot;&lt;/li&gt;&#xA;&lt;li&gt;Cnidaire and cténaire vs &quot;the others&quot;&lt;/li&gt;&#xA;&lt;li&gt;Protostomia vs Deuterostomia (both are fairly equally diverse diverse! Some might not be happy with this claim!)...let's continue with the Deuterostomata&lt;/li&gt;&#xA;&lt;li&gt;echinodermata vs chordata&lt;/li&gt;&#xA;&lt;li&gt;cephalocordata vs vertebrata&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;etc ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Is there really a systematic difference in diversity between the branches?&lt;/li&gt;&#xA;&lt;li&gt;Is this difference can be explained by chance?&lt;/li&gt;&#xA;&lt;li&gt;Is it only a bias due to out ability to recognize more species in animals that look more like us (or a bias due to something else)?&lt;/li&gt;&#xA;&lt;li&gt;Does it make sense to say: the more diverse is a taxon, the more likely it is that it gets even more diverse (because each species might have an equal chance to speciate or something like this)?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="107" LastEditDate="2013-07-26T00:14:33.453" LastActivityDate="2013-07-29T04:37:37.697" Title="Systematic difference of diversity between sister taxa?" Tags="&lt;evolution&gt;&lt;speciation&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9435" PostTypeId="2" ParentId="2965" CreationDate="2013-07-25T21:15:44.897" Score="1" Body="&lt;p&gt;@gkadam is correct and quite exhaustive. There are a lot of things that can affect protein binding, and many of them have little to do with the protein itself, but instead where it is and what else it is doing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;All other things being equal,&lt;/em&gt; smaller proteins will form networks more quickly than larger ones for kinetic reasons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Size differences don't affect how likely two proteins are to interact by itself. Big proteins and little ones interact all the time.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="107" LastEditDate="2013-07-26T00:16:10.177" LastActivityDate="2013-07-26T00:16:10.177" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9437" PostTypeId="1" AcceptedAnswerId="9443" CreationDate="2013-07-26T03:38:22.237" Score="36" ViewCount="14784" Body="&lt;p&gt;It's bothered me for a while now. I understand why a parasitoid would do this, as it only temporarily requires the host, and that not all parasites kill their hosts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There seems to be no evolutionary advantage in killing a host, because the parasite relies on the host for resources. Yet some organisms, usually microscopic pathogens, seem to fatally damage the host with no immediate benefit to themselves. Why is this? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know this is asking for a broad soft answer, but I don't want the question to get bogged down by a specific species, although bonus points for using examples.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="107" LastEditDate="2013-07-26T13:58:41.233" LastActivityDate="2019-03-26T20:01:04.847" Title="Why do parasites sometimes kill their hosts?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;parasitology&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9438" PostTypeId="1" AcceptedAnswerId="9455" CreationDate="2013-07-26T03:43:00.910" Score="54" ViewCount="10056" Body="&lt;p&gt;The recent &lt;a href=&quot;http://www.the-scientist.com/?articles.view/articleNo/36624/title/New-Giant-Viruses-Break-Records/&quot;&gt;news&lt;/a&gt; about a new supermassive virus being discovered got me thinking about how we define viruses as non-living organisms whilst they are bigger than bacteria, and much more complex than we first gave them credit for. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What biological differences between viruses and cellular organisms have made viruses be deemed non-living?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2016-04-22T03:06:47.513" LastActivityDate="2020-06-17T09:05:21.913" Title="Why isn't a virus &quot;alive&quot;?" Tags="&lt;virology&gt;&lt;taxonomy&gt;&lt;virus&gt;&lt;nomenclature&gt;" AnswerCount="7" CommentCount="1" FavoriteCount="20" ContentLicense="CC BY-SA 3.0" />
  <row Id="9439" PostTypeId="2" ParentId="9438" CreationDate="2013-07-26T06:25:42.447" Score="15" Body="&lt;p&gt;There are quite some different definitions of being &quot;alive&quot;, but a common one includes the need to have responsiveness, growth, metabolism, energy transformation, and reproduction (found from the &lt;a href=&quot;http://www.britannica.com/EBchecked/topic/340003/life&quot;&gt;Encyclopedia Britannica&lt;/a&gt;). Viruses depend on host cells to do all this, so seen alone as a virus outside a host cell, they are not alive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's &lt;a href=&quot;http://www.virology.ws/2004/06/09/are-viruses-living/&quot;&gt;another&lt;/a&gt; short, but to the point blog entry about this.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-07-26T06:25:42.447" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9441" PostTypeId="2" ParentId="9437" CreationDate="2013-07-26T10:24:18.250" Score="10" Body="&lt;p&gt;Some parasites aren't natural hosts of humans, instead we are an accidental host in which they cannot replicate. Zoonoses such as this can be quite fatal as the parasite is not adapted to us. Although viruses are often separated, they are parasites and you can see just in influenza that the animal derived flus are more fatal than those that are well adapted to humans. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise because there is no need for the host they can be fatal. If they have finished their round of replication or require death of the host to be able to spread. Still this is less common than simply a badly adapted parasite. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;HPV causes cervical cancers. It is adapted to increase replication of its host cell which is obviously beneficial, but this also kills the host in the long term. Thus some viruses are not yet adapted to the new longer lives we live, but may never do so due to less of a survival pressure hence vaccines. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please feel free to ask questions. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-07-26T10:24:18.250" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9442" PostTypeId="2" ParentId="9419" CreationDate="2013-07-26T10:25:26.753" Score="16" Body="&lt;p&gt;There are good reasons why tissues/structures with a very high metal content might cause problems (I defer to the other answers here).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I am aware of one other example: some &lt;a href=&quot;http://researchrepository.murdoch.edu.au/1728/1/radula_synthesis.pdf&quot;&gt;molluscs&lt;/a&gt; incorporate high concentrations of iron into the points of the radula (basically a ribbon of teeth, used for grazing). This is especially important for grazing molluscs, as they essentially make a living by scraping a thin layer of microalgae directly off the rock surface.&lt;/p&gt;&#xA;" OwnerUserId="4116" LastActivityDate="2013-07-26T10:25:26.753" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9443" PostTypeId="2" ParentId="9437" CreationDate="2013-07-26T10:35:19.693" Score="32" Body="&lt;p&gt;I can think of several (non-exclusive and probably non-exhaustive) hypotheses:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Maladaptive&lt;/strong&gt;. It is maladaptive. Maybe because it is a virus coming from another species (e.g. SIV and HIV) or because it is not adapted to our modern lifespan.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Benefit of the host immune system to the parasite&lt;/strong&gt;. Some parasites might benefit from host immune defence (e.g. sneezing helps bacteria to spread) and death is a consequence of the selection for increasing disease symptoms to the host.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Pathogen's and host's fate&lt;/strong&gt;. The pathogen's fate is not linked to the host's fate. This is especially true if the pathogens spread well (easily jump from one host to another) I guess or for parasitoïd because the pathogen leaves its parasitic life after the death of its single host.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;intra- and inter-host selection&lt;/strong&gt;. Among hosts, there might have a selection for reducing resource consumptions and therefore for decreasing the probability for the host to die. But within a host (among individuals of a parasite population or even among parasite species), it is a &lt;a href=&quot;https://en.wikipedia.org/wiki/Prisoner%27s_dilemma&quot; rel=&quot;nofollow noreferrer&quot;&gt;prisoner's dilemma (tragedy of the commons)&lt;/a&gt;. The more you invest in foraging, the more competitive you are. This might not be adaptative at the population level but it is at the individual level. We might think of this prisoner's dilemma happening among individuals of a single parasite species or among several parasite species. You may want to have a look at the work of Martin Nowak on the subject incl. Consider for example his book; &lt;a href=&quot;https://www.amazon.ca/Evolutionary-Dynamics-Exploring-Equations-Life/dp/0674023382/ref=sr_1_1?ie=UTF8&amp;amp;qid=1491419447&amp;amp;sr=8-1&amp;amp;keywords=martin%20nowak%20dynamic&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evolutionary Dynamics&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Consequence of harming on trade-offs&lt;/strong&gt;. Harming an individual will cause him not to spend energy into reproduction in order that more energy is available for the pathogen use. Moreover, by causing symptoms, the infected individual will be sexually less attractive and will again have less opportunity to spend energy into reproduction.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;The pathogen does not mean much harm&lt;/strong&gt;. When fighting pathogens, many of the symptoms we experience (such as fever typically) are actually caused by the immune system and not the pathogen itself. A maladaptive overreaction of the immune system can cause our death.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The book &lt;em&gt;&lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0679746749&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Why we get sick&lt;/a&gt;&lt;/em&gt; by Randolph Nesse and George Williams, will probably interest you.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2019-03-26T20:01:04.847" LastActivityDate="2019-03-26T20:01:04.847" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="9444" PostTypeId="2" ParentId="9431" CreationDate="2013-07-26T10:38:16.157" Score="1" Body="&lt;p&gt;During infection a body has to produce absolute masses of immune cells, raise your temperature via increased metabolism, repair tissue damage, migrate components of the immune system including proteins and cells, produce masses of antibodies and probably lot's more. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lot of protein components need to be made which require protein synthesis and energy. Metabolism of fats and carbs goes up too. Also, importantly, vitamins are a key part of the immune system serving to migrate the immune system  such as vitamin D aids migration of cells to the skin. Vitamin C is required for collagen synthesis in repair. Minerals are required for the metalloenzymes. However your dependency on each component depends on the type of infection, your immune response, your natural state including your reserves of everything. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How important is it? Very. I've listed what the things are needed for which gives an indication of how important they are. If starved, the body will do the best it can by focussing its resources on the thing it deems most important.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-07-26T10:38:16.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9445" PostTypeId="2" ParentId="9438" CreationDate="2013-07-26T11:12:32.503" Score="25" Body="&lt;p&gt;It is only a question of definition. You can set the boundaries between living things and not living things anywhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some philosophers have argued that using a clear boundary between living and non-living things is not such a good solution. In nature, there would rather be a continuum from a stone to a bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is true that in thinking of viruses such as Lausannevirus or Marseillevirus we might be willing to integrate them in the category of living things. These viruses are giant, and even can be parasitized by other viruses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Viruses are made of proteins and contain nucleic acids (RNA or DNA). If you consider that they are alive, what would you say about viroids? A viroid is just a nucleic acid that is able to infect a host and cause the replication of itself. What about a prion? A prion is a protein that, roughly speaking, has the same consequences as that of a viroid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think (one should check the literature, I might be mistaken) that there is a species of parasitoid wasp that produces out of its own genomes, viruses that reduce the host immune system in order to make the caterpillar a suitable habitat for the egg. Is this virus alive? Isn't it just a toxin of the wasp?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess one reason for considering viruses as non-living is that we do not know how to branch them in the tree of life! Some might argue by the way that viruses would not at all form a monophyletic group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several people tackling the question of &quot;what is alive&quot;. Unfortunately, the best book I know on the subject comes from the French literature; it is &lt;a href=&quot;https://www.amazon.fr/Comment-d%C3%A9finir-vie-Hugues-Bersini/dp/2711748650/ref=sr_1_1?ie=UTF8&amp;amp;qid=1461354538&amp;amp;sr=8-1&amp;amp;keywords=comment%20definir%20la%20vie&quot; rel=&quot;nofollow noreferrer&quot;&gt;Comment définir la vie? by Bersini and Reisse&lt;/a&gt;. In this field, the most popular authors are Varella and Maturana. Again, if I'm not mistaken, the definitions of life are quite different among philosophers, people having an interest in the origin of life, and people seeking a definition suitable for extra-terrestrial life.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-27T20:38:26.733" LastActivityDate="2019-03-27T20:38:26.733" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="9446" PostTypeId="2" ParentId="9438" CreationDate="2013-07-26T12:58:30.777" Score="18" Body="&lt;p&gt;I agree with the answers already given, these are the reasons that viruses are not considered alive. I want to point out though that this isn't an area you find 100% agreement on; there is a decent subset of biologists who &lt;em&gt;do&lt;/em&gt; consider viruses alive. I would say - completely on the basis of personal observation - that virologists themselves are the group most likely to claim that viruses are alive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837877/&quot;&gt;This paper&lt;/a&gt; and &lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=are-viruses-alive-2004&quot;&gt;this article&lt;/a&gt; from the Scientific American have some coverage of the debate if you want to read more.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="2938" LastEditDate="2013-07-28T11:58:55.810" LastActivityDate="2013-07-28T11:58:55.810" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9447" PostTypeId="1" AcceptedAnswerId="9453" CreationDate="2013-07-26T13:00:58.283" Score="1" ViewCount="167" Body="&lt;p&gt;(Kinda &lt;a href=&quot;https://biology.stackexchange.com/questions/9126/can-ant-colonies-have-two-branches&quot;&gt;follow-up to this&lt;/a&gt;.…)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've heard before that if you put 2 ant colonies side by side they're going to attack each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But then from the previous question, there could be &quot;sister&quot; ant colonies which (assumingly) don't harm one another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can probably see that generation-by-generation colonies would just naturally be either too far apart in space, (or too close in &quot;generation&quot;), to have any fights. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what actually makes ants decide whether to fight or to not? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And whatever it is, is it a spectrum or a limit..? (i.e would there be a case in which &lt;em&gt;some ants&lt;/em&gt; of a colony will fight and some wont?)&lt;/p&gt;&#xA;" OwnerUserId="3141" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-08-25T17:17:08.173" Title="How far do 2 ant colonies of same heritage have to be in space (and generation) in order to fight?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9448" PostTypeId="2" ParentId="9427" CreationDate="2013-07-26T13:08:18.637" Score="2" Body="&lt;p&gt;As Amory suggests the IUPAC &quot;Recommendations on Organic &amp;amp; Biochemical Nomenclature, Symbols &amp;amp; Terminology etc.&quot; (&lt;a href=&quot;http://www.chem.qmul.ac.uk/iupac/&quot; rel=&quot;nofollow&quot;&gt;http://www.chem.qmul.ac.uk/iupac/&lt;/a&gt;) are probably the best place to start. From a quick scan the obviously relevant documents would be:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents&quot;&lt;/li&gt;&#xA;&lt;li&gt;&quot;Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences&quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;These provide the complete description of the commonly used IUPAC nucleic acid codes, including both the one letter and three letter variants.&lt;/p&gt;&#xA;" OwnerUserId="4117" LastActivityDate="2013-07-26T13:08:18.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9449" PostTypeId="2" ParentId="9377" CreationDate="2013-07-26T13:22:47.983" Score="1" Body="&lt;p&gt;In species where an individual can be haploid (for example in &lt;a href=&quot;http://en.wikipedia.org/wiki/Haplodiploid&quot; rel=&quot;nofollow&quot;&gt;haplodiploidy&lt;/a&gt;) then cells produced by meiosis do multiply by mitosis in order for the individual to grow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a brief scan the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Ploidy&quot; rel=&quot;nofollow&quot;&gt;ploidy&lt;/a&gt; nicely summarises the various possibilities.&lt;/p&gt;&#xA;" OwnerUserId="4117" LastActivityDate="2013-07-26T13:22:47.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9451" PostTypeId="2" ParentId="7568" CreationDate="2013-07-26T14:37:54.990" Score="10" Body="&lt;p&gt;I think I can expand on the answer by @boo2060.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The evolution of female mate choice depends on females achieving higher fitness by choosing certain males over others. At the broadest scale, there are two mechanisms by which this can occur, direct benefits, and indirect benefits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Direct benefits&lt;/strong&gt;&#xA;These are material things that (surprise) directly benefit the female. This might be the provision of food by the preferred male, access to a good territory or shelter that is under the control of the preferred male, protection by the preferred male, that sort of thing. Females will accordingly favour male traits that advertise potential direct benefits. These might include male size/condition/colouration, or even built structures like those of the &lt;a href=&quot;http://cdn2.arkive.org/media/BA/BAB5B8BC-85EE-46AF-B8FB-EDF58DE63597/Presentation.Large/Decorated-bower-of-Vogelkop-bowerbird.jpg&quot;&gt;bowerbirds&lt;/a&gt;. Basically, these traits show that the male knows how to look after himself, and by extension, he knows how to look after her (as males in good condition generally inhabit the best habitats and will offer the best protection and parenting).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Indirect benefits&lt;/strong&gt;&#xA;These don't do much for the female, but they increase the genetic quality (and thus potential fitness) of her offspring. This is a much more complicated area of mate choice, and can be split into a bunch of (non-exclusive) hypotheses (below). And of course, attractive males may well offer both direct and indirect benefits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Sensory bias:&lt;/em&gt; Males may, by chance, possess a trait that holds intrinsic appeal for a female. The best explanation might be that it mimics the colour or shape of a food source (e.g. fruit) that the animal eats, and thus the animal has pre-evolved preference for that colour or shape (e.g. red patches). From that point, males with more of that trait, whatever it is, will tend to be more attractive, for no rational reason. This hypothesis is sound, but is currently lacking good empirical evidence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Fisherian sexy sons:&lt;/em&gt; This can in fact lead on from an initial sensory bias. Females may choose males that they find 'sexy', because their offspring will also be sexy, and thus be successfull in reproduction. This can lead to 'runaway' selection for sexier and sexier sons, at considerable survival cost for males. In this case, natural selection and sexual selection work in opposing directions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Indicator mechanisms:&lt;/em&gt; This is the handicap principle or 'good genes' principle. If a structure is costly to produce or maintain, or increases the risk of predation, and yet the male possessing it is still alive, he must have good genes to have withstood such a handicap. It may also advertise that the male is not infested with parasites. The extravagant plumes of birds may be largely explained by this one, but also sexy sons and sensory bias.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Genetic compatibility:&lt;/em&gt; Individuals seek partners that are genetically compatible. A certain proportion of the fitness of the offspring depends on the specific combination of genes (i.e. it's not additive), and individuals that can signal or detect signals in such a way that they can choose compatible partners will have an evolutionary advantage. The best example is scent (e.g. preference for dissimilar MHC immune genes - see the human t-shirt experiment).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These mechanisms are well known in theory, but not always well-supported by evidence (yet). &lt;a href=&quot;http://www.reed.edu/biology/professors/srenn/pages/teaching/2010_syllabus/2010_readings/Anderson-Simmons_2006.pdf&quot;&gt;This is probably the best reference&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4116" LastEditorUserId="4116" LastEditDate="2013-07-26T14:51:33.437" LastActivityDate="2013-07-26T14:51:33.437" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9452" PostTypeId="2" ParentId="9438" CreationDate="2013-07-26T15:35:32.683" Score="3" Body="&lt;p&gt;In addition to the good answers given here, I would like to propose a more intuitive argument against viruses being alive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Viruses are, at one point of their &quot;life&quot;, simply a piece of DNA (or RNA). Would you consider a piece of DNA to be alive? If so, then are transposons alive? Are chromosomes alive? How about synthesizing a piece of DNA - is that creating life? The answer will probably be &quot;no&quot; for most people.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2013-07-26T23:12:33.427" LastActivityDate="2013-07-26T23:12:33.427" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="9453" PostTypeId="2" ParentId="9447" CreationDate="2013-07-26T16:45:26.533" Score="3" Body="&lt;p&gt;Space and generation don't directly affect whether ants fight, that's all regulated with pheromones. Some ant species are more tolerant of different smells than others (see the argentine supercolonies mentioned above) while some species of ant have 'rival' nests that they are particularly aggressive to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I guess the answer is 'it depends'. On pheromones produced by the queen, and species. And probably diet/weather/local food availability/ some other things I haven't thought of.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think it's possible for some ants of a colony to fight and others not to, but I don't have any evidence to back that up specifically.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2013-07-26T16:45:26.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9454" PostTypeId="2" ParentId="9437" CreationDate="2013-07-26T18:11:18.397" Score="8" Body="&lt;p&gt;This is related to Remi.b's answer, but a common reason is that sometimes parasites/pathogens actually need to kill the host to spread.  A lot of viruses, in particular phages, are only released from their host by bursting out of the cell.  If the parasite can't leave the host, there's no point in any of it, and death may be a good way to achieve that.  A number of diarrheal diseases in humans cause death because massive diarrhea (aka water loss) is how they spread.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-07-26T18:11:18.397" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9455" PostTypeId="2" ParentId="9438" CreationDate="2013-07-26T19:20:14.423" Score="72" Body="&lt;p&gt;If this is a topic that really interests you, I'd suggest searching for papers/reviews/opinions written by &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/?term=Didier+Raoult+mimivirus&quot;&gt;Didier Raoult.&lt;/a&gt;  Raoult is one of the original discoverers of the massive &lt;a href=&quot;https://en.wikipedia.org/wiki/Mimivirus&quot;&gt;Mimivirus&lt;/a&gt; and his work will lead you to some truly fascinating discussions that I couldn't hope to reproduce here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main argument for why viruses aren't living is basically what has been said already.  Viruses are obligate parasites, and while plenty of parasites are indeed living what sets viruses apart is that they always rely on the host for the &lt;em&gt;machinery&lt;/em&gt; with which to replicate.  A parasitic worm may need the host to survive, using the host as a source for energy, but the worm produces and synthesizes its own proteins using its own ribosomes and associated complexes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's basically what it boils down to.  No ribosomes?  Not living.   One advantage of this definition, for example, is that it is a positive selection (everyone &quot;alive&quot; has got ribosomes) which eliminates things like mitochondria that are sort of near the boundary of other definitions.  There are examples on either side of something that breaks every other rule but not this one.  Another common rule is metabolism and while that suffices for most cases some living parasites have lost metabolic activity, relying on their host for energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However (and this is the really interesting part) even the ribosome definition is a bit shaky, especially as viruses have been found encoding things like their own tRNAs.  Here are a few points to think about:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;We have ribosome encoding organisms (REOs), so why can't we define viruses as capsid encoding organisms (CEOs)?&lt;/li&gt;&#xA;&lt;li&gt;Comparing viruses to a living organism such as a human is absurd, given the massive differences in complexity.  A virus, really, is just a vehicle or genetic material, and would be more rightly compared to a sperm cell.  Is a sperm cell alive, or is it a package for genetic material that is &lt;em&gt;capable&lt;/em&gt; of life once it has infected/fertilized another cell?&lt;/li&gt;&#xA;&lt;li&gt;The really large DNA viruses often create cytoplasmic features called virus factories.  These look an awful lot like a nucleus.  What is a nucleus anyway?  Maybe it's just a very successful DNA virus that never left.&lt;/li&gt;&#xA;&lt;li&gt;Viruses can get &lt;a href=&quot;https://en.wikipedia.org/wiki/Sputnik_virophage&quot;&gt;viruses&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I'll wind down here, but suffice to say that while our current definition may have sufficed for a while, and still does, it is no longer quite solid.  In particular, there is a theory alluded to above that eukaryotic life itself actually formed &lt;em&gt;because&lt;/em&gt; of viruses.  I can expand on this if you like, but here are some great sources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Boyer, M., Yutin, N., Pagnier, I., et al.  2009.  Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms.  &lt;em&gt;PNAS&lt;/em&gt;.  106(51):21848-21853 (&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0911354106&quot;&gt;http://dx.doi.org/10.1073/pnas.0911354106&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Claverie, JM.  Viruses take center stage in cellular evolution.  2006.  &lt;em&gt;Genome Biology&lt;/em&gt;.  7:110. (&lt;a href=&quot;http://dx.doi.org/10.1186/gb-2006-7-6-110&quot;&gt;http://dx.doi.org/10.1186/gb-2006-7-6-110&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ogata, H., Ray, J., Toyoda, K., et al.  2011.  Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment.  &lt;em&gt;The ISME Journal&lt;/em&gt;.  5:1143-1151 (&lt;a href=&quot;http://dx.doi.org/10.1038/ismej.2010.210&quot;&gt;http://dx.doi.org/10.1038/ismej.2010.210&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Raoult, D. and Forterre, P.  2008.  Redefining viruses: lessons from Mimivirus.  &lt;em&gt;Nature Reviews Microbiology&lt;/em&gt;. 6:315-319. (&lt;a href=&quot;http://dx.doi.org/10.1038/nrmicro1858&quot;&gt;http://dx.doi.org/10.1038/nrmicro1858&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scola, B., Desnues, C., Pagnier, I., et al.  The virophage as a unique parasite of the giant mimivirus.  2008.  &lt;em&gt;Nature&lt;/em&gt;.  455:100-104 (&lt;a href=&quot;http://dx.doi.org/10.1038/nature07218&quot;&gt;http://dx.doi.org/10.1038/nature07218&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2015-11-26T16:43:52.670" LastActivityDate="2015-11-26T16:43:52.670" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9460" PostTypeId="1" AcceptedAnswerId="9461" CreationDate="2013-07-27T01:57:23.777" Score="1" ViewCount="291" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UKoWW.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In shotgun sequencing method or some related method that DNA is break up into random fragment. The fragment that have about 3kb in size is inserted into plasmid by enzyme ligase and then plasmid transform to E.coli using electroporator. As i understand, the goal is amplify the fragment to be sequencing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At this time, i have a question :&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;After the e.coli growth up, we have too many different type of miscellaneous DNA strand with same size in a colony. How to purify a type of fragment to be sequencing ? &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For example, i have 20.000 different DNA strand with the same 3kb in size after break up into random fragment :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-- AAAAAAAAAAAAAAAAAAAA...AAAAAAAAAAAAAAAAATTTTTTT -- (3kb fragment of chromosome 1)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-- GGGGXXXXXAAAAAAAAAAA...AAAAAAAAAAAAAAAAAAAAAAAA -- (3kb fragment of chromosome 2)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-- 19998 DNA fragment left ............................. -- (3kb fragment of random chromosome)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So after amplify them i have :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1000000x of -- AAAAAAAAAAAAAAAAAAAA...AAAAAAAAAAAAAAAAATTTTTTT --&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1000000x of -- GGGGXXXXXAAAAAAAAAAA...AAAAAAAAAAAAAAAAAAAAAAAA --&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1000000x of -- 19998 DNA fragment left........................ --&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These DNA strand is mixed together in a colony. We cannot run sequencing them together as mixed, so how to have the only one for sequencing :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1000000x of -- AAAAAAAAAAAAAAAAAAAA...AAAAAAAAAAAAAAAAATTTTTTT --&lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="3894" LastEditDate="2013-07-27T02:51:00.420" LastActivityDate="2013-07-27T03:34:33.907" Title="DNA preparation for sequencing" Tags="&lt;molecular-biology&gt;&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9461" PostTypeId="2" ParentId="9460" CreationDate="2013-07-27T03:34:33.907" Score="2" Body="&lt;p&gt;I hope I understood your question correctly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think what you are missing is that after you break up the DNA, you dilute the concentration so that each bacteria will incorporate ~1 DNA molecule. Then, you dilute the bacteria on a plate and spread it so that they each single bacteria is far from other bacteria. Finally, after they grow you get one genetically identical colony per DNA fragment.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2013-07-27T03:34:33.907" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9464" PostTypeId="1" AcceptedAnswerId="9468" CreationDate="2013-07-27T08:26:22.963" Score="0" ViewCount="36" Body="&lt;p&gt;Many hormones released by endocrine organs travel down in the blood and bind to specific receptors on the target cells. What then breaks that binding of the molecule with the receptor ? ( thus inactivating further stimulation of the target cell )&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-07-27T11:40:48.577" Title="Stopping the effect of hormone" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9465" PostTypeId="1" AcceptedAnswerId="9469" CreationDate="2013-07-27T09:05:58.677" Score="4" ViewCount="377" Body="&lt;p&gt;We spotted this thing crawling around a (thankfully empty) bowl in our apartment in Barcelona, Spain. I have never seen anything like it. It appears to be some kind of caterpillar-like insect, but it is inside a flat, leaf-like shell. It can only move by sticking its head out a hole in the tip of the shell and it has to pull itself by its front legs (no legs under the shell). But it can actually pop out of &lt;em&gt;either&lt;/em&gt; end of the shell! When it's threatened, it just hides inside the shell completely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm completely flummoxed as to what this thing is. Does anyone have any clue?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(click the images for full-size)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://invergo.net/img/IMG_4796.JPG&quot; rel=&quot;nofollow noreferrer&quot;&gt;&#xA;    &lt;img src=&quot;https://i.stack.imgur.com/4OErB.jpg&quot;&gt;&#xA;&lt;/a&gt;&#xA;&lt;a href=&quot;http://invergo.net/img/IMG_4797.JPG&quot; rel=&quot;nofollow noreferrer&quot;&gt;&#xA;    &lt;img src=&quot;https://i.stack.imgur.com/ghorB.jpg&quot;&gt;&#xA;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://invergo.net/img/IMG_4800.JPG&quot; rel=&quot;nofollow noreferrer&quot;&gt;&#xA;    &lt;img src=&quot;https://i.stack.imgur.com/QxEbO.jpg&quot;&gt;&#xA;&lt;/a&gt;&#xA;&lt;a href=&quot;http://invergo.net/img/IMG_4801.JPG&quot; rel=&quot;nofollow noreferrer&quot;&gt;&#xA;    &lt;img src=&quot;https://i.stack.imgur.com/Q4CxI.jpg&quot;&gt;&#xA;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorUserId="15950" LastEditorDisplayName="user3934" LastEditDate="2018-12-31T03:40:42.250" LastActivityDate="2021-04-12T13:30:55.433" Title="What in the world is this critter?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="9466" PostTypeId="1" AcceptedAnswerId="14182" CreationDate="2013-07-27T11:06:34.777" Score="13" ViewCount="28498" Body="&lt;p&gt;As the title suggests, I've noticed that my fingernail grow much faster than my toenails. For instance, I usually trim my fingernails every two week or so, but for toenails the number would be about 6 to 8 weeks.&lt;/p&gt;&#xA;&lt;p&gt;A bit of research revealed this &lt;a href=&quot;http://en.wikipedia.org/wiki/Nail_%28anatomy%29&quot; rel=&quot;noreferrer&quot;&gt;wikipedia article&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In mammals, the length and growth rate of nails is related to the length of the terminal phalanges (outermost finger bones). Thus, in humans, the nail of the index finger grows faster than that of the little finger; and fingernails grow up to four times faster than toenails. [12]&lt;/p&gt;&#xA;&lt;p&gt;In humans, nails grow at an average rate of 3 mm (0.12 in) a month.[13] Fingernails require three to six months to regrow completely, and toenails require 12 to 18 months. Actual growth rate is dependent upon age, sex, season, exercise level, diet, and hereditary factors. Nails grow faster in the summer than in any other season.[14]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;But &lt;a href=&quot;http://en.wikipedia.org/wiki/Correlation_does_not_imply_causation&quot; rel=&quot;noreferrer&quot;&gt;correlation does not imply causation&lt;/a&gt;, so why should the growth rate of nails depend on the  length of the terminal phalanges? Then why do babies grow nail much faster? I wasn't satisfied by its answer, so I looked a bit more where I found &lt;a href=&quot;http://www-scf.usc.edu/%7Euscience/nail_growth.html&quot; rel=&quot;noreferrer&quot;&gt;this other article&lt;/a&gt;. They had two possible candidates:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;because hands are physically closer to the heart than are feet, fingers get better blood circulation and consequently better access to oxygen and nutrients.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Fingernails experience almost constant trauma through tapping, typing, bumping, and other seemingly insignificant actions. These persistent minor traumas stimulate fingernail growth. Toes, on the other hand, are not exposed to nearly as much trauma as they are usually bundled up safely inside socks and shoes. Similarly, fingernails on a person's right hand grow faster in right-handed people than on their left hand and vice-versa.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However they don't give actual experimental results. So my question is which of the above is the real cause of this difference in the growth rate of nails; or simply why toenails grow much slower than fingernails?&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;strong&gt;P.S.&lt;/strong&gt; The season dependence and the lefthand-righthand asymmetry were news to me; it would be really nice if the answer explains them as well.&lt;/p&gt;&#xA;" OwnerUserId="4041" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-08-02T19:39:58.180" Title="Why do toenails grow much slower than fingernails?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9467" PostTypeId="1" CreationDate="2013-07-27T11:18:03.763" Score="1" ViewCount="264" Body="&lt;p&gt;Pardon my ignorance ... A lip is apparently a very sensitive tactile device - as it at-least serves to warn it's owner they may just be about to consume something that could cause injury. Primates (including humans), dogs, cats, sheep, buffalo, elephants, some fish, octopodes - to name a few, have a lip. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How have lips evolved to be nearly ubiquitous across animals? Why have they evolved into a beak/bill in some birds &amp;amp; fish? What niche/purpose do they fulfill?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2014-03-26T09:05:25.483" Title="What use a pair of lips?" Tags="&lt;physiology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9468" PostTypeId="2" ParentId="9464" CreationDate="2013-07-27T11:40:48.577" Score="2" Body="&lt;p&gt;The binding is reversible typically; part of the potency of a drug is ow well and for how long it binds to its target. There's a natural equilibrium of binding and dissociation. Many drugs, once bound to their cognate receptor, cause a down regulation of their cognate receptor on the target cell. The bound/activated downstream signalling pathways may be inhibited by ubiquitination of the downstream signals themselves or upregulation of antagonists etc. The hormone itself has a half life, which is very important, thus levels naturally decrease and for some hormones this is incredibly rapid. Levels may decrease due to breakdown or excretion. Increase of binding hormones may decrease free hormone thus it's effect also. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-07-27T11:40:48.577" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9469" PostTypeId="2" ParentId="9465" CreationDate="2013-07-27T12:59:15.847" Score="5" Body="&lt;p&gt;Found it. It's a &lt;a href=&quot;http://www.whatsthatbug.com/2007/04/10/case-bearing-moth-larva/&quot;&gt;case-bearing moth larva&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerDisplayName="user3934" LastEditorDisplayName="user3934" LastEditDate="2013-07-27T13:07:24.597" LastActivityDate="2013-07-27T13:07:24.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9470" PostTypeId="2" ParentId="9425" CreationDate="2013-07-27T15:26:23.117" Score="1" Body="&lt;p&gt;For a purely chemical assay, &lt;a href=&quot;http://depts.washington.edu/chem/facilserv/lecturedemo/DecompositionofH2O2withMnO2-UWDept.ofChemistry.html&quot; rel=&quot;nofollow&quot;&gt;Manganese dioxide (MnO2) will react to produce oxygen from hydrogen peroxide&lt;/a&gt;, which can be detected spectroscopically or by means of direct chemical analysis.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the enzymatic assay is less environmentally challenging and produces colorometric results directly, which is probably why it is ubiquitous. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-07-27T15:26:23.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9471" PostTypeId="2" ParentId="9467" CreationDate="2013-07-27T16:00:06.593" Score="1" Body="&lt;p&gt;I think what you are looking for can be found &lt;a href=&quot;https://en.wikipedia.org/wiki/Lips#Functions_of_the_lips&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Lips#Functions_of_the_lips&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Beak#Functions&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Beak#Functions&lt;/a&gt; pretty easily.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To summarize, lips:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mainly useful in mammals&lt;/li&gt;&#xA;&lt;li&gt;Food intake&lt;/li&gt;&#xA;&lt;li&gt;Articulation&lt;/li&gt;&#xA;&lt;li&gt;Tactile organ&lt;/li&gt;&#xA;&lt;li&gt;Erogenous zone&lt;/li&gt;&#xA;&lt;li&gt;Facial expressions&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Beaks:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Found in birds&lt;/li&gt;&#xA;&lt;li&gt;Feeding&lt;/li&gt;&#xA;&lt;li&gt;Defense&lt;/li&gt;&#xA;&lt;li&gt;Manipulation of objects&lt;/li&gt;&#xA;&lt;li&gt;Communication&lt;/li&gt;&#xA;&lt;li&gt;Heat exchange&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-07-27T16:00:06.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9473" PostTypeId="1" AcceptedAnswerId="9575" CreationDate="2013-07-27T21:05:05.477" Score="1" ViewCount="353" Body="&lt;p&gt;During fertilization, the nuclear membrane of the pro-nucleus of the ovum and sperm degenerate. Is the cell is stage called a zygote?&#xA;After the dissolution, mitosis occurs and two cells are formed.Or is the cell is stage called a zygote?&#xA;I'm confused as i knew a zygote was single-celled.&lt;/p&gt;&#xA;" OwnerUserId="4128" LastActivityDate="2013-08-01T06:08:35.270" Title="What is a zygote?" Tags="&lt;embryology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9474" PostTypeId="2" ParentId="9425" CreationDate="2013-07-27T23:58:21.163" Score="2" Body="&lt;p&gt;Amperometric detection of H2O2 can be performed without HRP, and gives high-resolution real-time readings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will find many different type of electrodes that are used in the literature to detect H2O2, including for instance &lt;a href=&quot;http://pubs.rsc.org/en/Content/ArticleLanding/1997/AN/a701723e&quot; rel=&quot;nofollow&quot;&gt;MnO2-coated carbon paste microelectrodes&lt;/a&gt; or &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1359511312001328&quot; rel=&quot;nofollow&quot;&gt;gold electrodes derivatized with cytochrome c&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Commercial electrodes also exists. For instance &lt;a href=&quot;http://www.wpiinc.com/index.php?submenu=phybiohypxsen&amp;amp;class0_0=31&amp;amp;class1_0=323&amp;amp;class2_0=&amp;amp;class3_0=&amp;amp;class4_0=&amp;amp;submit=Filter&amp;amp;xsearch_id=products_type_search&amp;amp;src=directory&amp;amp;srctype=products_lister&amp;amp;view=products&quot; rel=&quot;nofollow&quot;&gt;these from WPI&lt;/a&gt; are based on derivatized carbon fibers (although they do not specify with what, so I would not exclude HRP...)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another option is that of using the H2O2-sensitive dye H2DCF (dihydro-dichlorofluorescein).&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2013-07-27T23:58:21.163" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9475" PostTypeId="2" ParentId="9386" CreationDate="2013-07-28T00:46:52.643" Score="14" Body="&lt;p&gt;&lt;strong&gt;1 billion hives&lt;/strong&gt;&#xA;(at 10,000-50,000 bees/hive this is 10-50 trillion bees)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Managed: 100 million hives&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on country-level &lt;a href=&quot;http://faostat.fao.org/&quot;&gt;data from FAO&lt;/a&gt;, supplemented  for a few countries with &lt;a href=&quot;http://www.beekeeping.org/&quot;&gt;Apiservices&lt;/a&gt;, in 2011 there were about 80 million managed hives. Because FAO lacks any data for some countries, and other countries under-report (for instance US figures don't include hives kept for pollination service and hives kept by small-scale operators) a reasonable round estimate of managed hives in the world is 100 million. (This implies a 128% correction to the FAO numbers). (&lt;a href=&quot;http://dx.doi.org/10.1016/j.cub.2009.03.071&quot;&gt;Aizen and Harder 2009&lt;/a&gt; give context on FAO figures).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Wild/Feral: 900 million hives&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wild/feral hives of &lt;em&gt;Apis mellifera&lt;/em&gt; are difficult to count via direct observation. &lt;a href=&quot;http://dx.doi.org/10.1111/j.1523-1739.2009.01331.x&quot;&gt;Jaffe et al 2010&lt;/a&gt; use a genetic sampling method, and also report a reasonably strong correlation between the total number of hives (managed and wild) per square kilometer and the mean annual temperature of the area.&#xA;I used the best fit line from their data to estimate the &quot;hive-carrying-capacity&quot; by country using (the admittedly very general) &lt;a href=&quot;http://data.worldbank.org/indicator/AG.LND.TOTL.K2&quot;&gt;land area&lt;/a&gt; and &lt;a href=&quot;http://www.cru.uea.ac.uk/~timm/cty/obs/TYN_CY_1_1.html&quot;&gt;mean annual temperature&lt;/a&gt;. Then I subtracted the number of managed hives from the carrying capacity to estimate wild hives.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although this formula probably overestimates large, cold countries and underestimates Africa (the formula gives 211 million feral hives in Africa when literature suggests closer to 300 million), in general, it seems to give not unreasonable estimates in comparison to the literature. Globally, this formula gives an estimate of 984 million wild hives. Given that land area included desert and other unsuitable habitat, it seemed reasonable to round down, and I took 900 million as my estimate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Historical Populations&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KuyLe.jpg&quot; alt=&quot;Hives of *Apis mellifera* over time.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1961-2011&lt;/strong&gt; &#xA;FAO statistics date to 1961. I plotted their numbers, with the 128% correction for each year. I assumed that during this time the number of wild bees has remained virtually unchanged, at 900 million, because it was defined by mean temperature and land area, which have not changed.*&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1650-1961&lt;/strong&gt;&#xA;This period represents the globalization of &lt;em&gt;Apis mellifera&lt;/em&gt;. Before 1600, there were no European honey bees beyond their native range (Western Eurasia and Africa). However, once established in new areas (the usually cited first beehive in the USA in 1622), &lt;em&gt;Apis mellifera&lt;/em&gt; rapidly spread in both managed and feral populations, in North America (17th c), South America (18th c), Australia (19th c) and East Asia (20th c) &lt;a href=&quot;http://books.google.com/books?id=ANTSvKj1AZEC&amp;amp;pg=PA91&amp;amp;source=gbs_toc_r&amp;amp;cad=4#v=onepage&amp;amp;q&amp;amp;f=false&quot;&gt;(Crane 1999)&lt;/a&gt;&#xA;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I used carrying capacity of native range countries (just about 35% of the carrying capacity of the globe, or 350 million hives) as a before-1650 estimate,  and then assumed a geometric increase of about 2% per decade in available land area (ALA), as &lt;em&gt;Apis mellifera&lt;/em&gt; bees and beekeeping made their way around the globe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To estimate the number of managed bees during this period, I assumed a human:hive ratio of 35:1**, and modelled hives based on historical estimates of human population, multiplied by the ALA for the decade. The 1650 estimate was 5 million managed hives.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;*Although diseases, pests, and pesticides have been reported to affect feral populations, I didn't find any solid information on this. For instance, feral populations of &lt;em&gt;Apis mellifera mellifera&lt;/em&gt; and &lt;em&gt;A. m ligustica&lt;/em&gt; have been widely reported to be in decline in the USA, but at the same time, feral populations of Africanized honeybees (&lt;em&gt;Apis mellifera&lt;/em&gt; hybrids) have been rapidly spreading. Even with 90% losses in the USA, Canada, Japan, and Europe (areas affected by varroa) my estimates would only be decreased about 10%. However, it's also possible that land-use change has greatly affected feral bee populations &lt;a href=&quot;http://dx.doi.org/10.1007/s10841-006-9054-5&quot;&gt;(Moritz et al 2007)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;**This wasn't a totally wild guess. I first calculated the human:hive ratio for 1961-2011. This ratio was increasing - there were 71 people / hive in 2011, and 47 in 1961. Initially, I assumed the rate of change in the ratio to be constant, but this led to unrealistically large estimates for historically managed hives. However, the rate was clearly increasing (just, perhaps in a nonlinear way I didn't want to estimate), so I decided instead to compromise on a number less than 47 and greater than 4. I decided on 35, as it produced what seemed like a realistic estimate of 5 million hives in 1650, compared to around 20 million today for Eurasia and North Africa (excluding sub-saharan Africa where wild-harvest remains important and likely was even more so in the past).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.cub.2009.03.071&quot;&gt; &lt;strong&gt;Aizen MA, Harder LD&lt;/strong&gt;. 2009. The Global Stock of Domesticated Honey Bees Is Growing Slower Than Agricultural Demand for Pollination. Current Biology 19: 4–4.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://books.google.com/books?id=ANTSvKj1AZEC&amp;amp;pg=PA91&amp;amp;source=gbs_toc_r&amp;amp;cad=4#v=onepage&amp;amp;q&amp;amp;f=false&quot;&gt; &lt;strong&gt;Crane E&lt;/strong&gt;. 1999. The World History of Beekeeping and Honey Hunting. Taylor &amp;amp; Francis. (Chapter 12).&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1111/j.1523-1739.2009.01331.x&quot;&gt; &lt;strong&gt;Jaffé RR, Dietemann VV, Allsopp MHM, Costa CC, Crewe RMR, Dall'olio RR, Rúa PPDL, El-Niweiri MAAM, Fries II, Kezic NN, et al.&lt;/strong&gt;. 2010. Estimating the density of honeybee colonies across their natural range to fill the gap in pollinator decline censuses. Conservation Biology 24: 583–593.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s10841-006-9054-5&quot;&gt;&lt;strong&gt;Moritz R, Kraus FB, Kryger P, Crewe RM&lt;/strong&gt;. 2007. The size of wild honeybee populations (Apis mellifera) and its implications for the conservation of honeybees. Journal of Insect Conservation&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2015-04-19T13:48:54.417" LastActivityDate="2015-04-19T13:48:54.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9476" PostTypeId="2" ParentId="9415" CreationDate="2013-07-28T01:23:04.823" Score="3" Body="&lt;p&gt;recombinant human NGF is available for purchase.  You might not be able to buy it without some sort of a research lab affiliation.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://products.creative-biolabs.com/symbolsearch_NGF_1.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://products.creative-biolabs.com/symbolsearch_NGF_1.htm&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2019-04-23T17:54:52.897" LastActivityDate="2019-04-23T17:54:52.897" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="9477" PostTypeId="1" AcceptedAnswerId="9499" CreationDate="2013-07-28T02:27:14.037" Score="2" ViewCount="335" Body="&lt;p&gt;When humans give birth, more than often medical assistance is needed. Others gather around and frantically look for any way to help. But when an animal gives birth, it is usually seen as a moment where you give the female its space and let the birth occur naturally and without any assistance. The animal is of course in serious pain just as a female human but this is more than often not taken into account. Why is it that animal births are not taken as seriously?&lt;/p&gt;&#xA;" OwnerUserId="4130" LastActivityDate="2013-07-29T23:41:27.010" Title="Why are animal births not taken as seriously as human births?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9478" PostTypeId="2" ParentId="5076" CreationDate="2013-07-28T03:07:17.833" Score="4" Body="&lt;p&gt;The quote refers to 'robber' bees, but in today's terminology, there are actually three separate phenomena. &quot;Cheating&quot; in bees and other social animals refers to the exploitation of a social contract for one's own benefit. Example: bee workers lay their own eggs rather than tending those of the queen. &quot;Laziness&quot; or &quot;inactivity&quot; of bee or other social insect workers is incredibly widespread, but it is not clear that it is selfish: it may be a side-effect of imperfect task allocation, or those individuals may be a reserve work force. &quot;Robbing&quot; in bees usually refers to removal of nectar or pollen from flowers without pollinating them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Cheating&quot; associated with illicit reproduction is widespread in social insects, including in bees, and there's a broad literature on it (search terms &quot;anarchist&quot; &quot;queenright&quot;, &quot;policing&quot;) but it sounds like your question concerns differential effort and environmental resources specifically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Differential effort in labor (&quot;laziness vs. busynesss&quot;) has been seen in many social animals. The way you frame the question seems to be in terms of:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;how many lazy individuals can a society tolerate given environmental&#xA;  conditions?&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Most observational/experimental studies seem to have approached the question in terms of:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;how can what appears to be cheating actually be adaptive?&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For instance, &lt;a href=&quot;http://dx.doi.org/10.1007%2Fs001140050528&quot; rel=&quot;nofollow&quot;&gt;Kukuk et al.&lt;/a&gt; suggest that in Halictine bees, lazy bees who avoid the high-mortality-risk foraging tasks are actually acting as caretakers and orphan-rearers for the brood of the foraging busy bees. It's also been proposed that apparently lazy insects act as a &quot;defensive reserve&quot; for the nest, although at least in &lt;em&gt;Bombus impatiens&lt;/em&gt;, experiments show no evidence that lazy bees defend any more than busy bees (&lt;a href=&quot;https://docs.google.com/viewer?a=v&amp;amp;pid=sites&amp;amp;srcid=ZW1haWwuYXJpem9uYS5lZHV8ZHItamFuZHR8Z3g6NmY0Y2JmYWM1NjU2ZDk4ZQ&quot; rel=&quot;nofollow&quot;&gt;Jandt et al.&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lazy individuals could also be acting a labor reserve (&quot;substitute helpers&quot;), in case of food or colony depletion. To me, this scenario is the closest to what you mention – the idea that lazy individuals become busier, either voluntarily or through coercion, in time of need. &lt;a href=&quot;http://dx.doi.org/10.1098/rspb.2010.0745&quot; rel=&quot;nofollow&quot;&gt;Baglione et al.&lt;/a&gt; show that this is the case for carrion crows, and quantify it to some degree along the terms you suggest. On the other hand, &lt;a href=&quot;http://dx.doi.org.ezproxy.umsl.edu/10.1016/S0003-3472%2805%2980757-2&quot; rel=&quot;nofollow&quot;&gt;Cartar&lt;/a&gt; (&lt;a href=&quot;https://docs.google.com/viewer?a=v&amp;amp;pid=sites&amp;amp;srcid=ZW1haWwuYXJpem9uYS5lZHV8ZHItamFuZHR8Z3g6M2JkNTE2Njg3Mjg4ZGI1Yg&quot; rel=&quot;nofollow&quot;&gt;cited in Jandt and Dornhaus&lt;/a&gt;) shows that for a number of bumblebee species, it was more likely that busy bees would work harder or switch tasks than it was that the lazy bees would become busy!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In sum, what you/Kropotkin suggest exists in all social insects, although the mechanisms of sociality and of laziness are diverse and various among species.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1098/rspb.2010.0745&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Baglione V, Canestrari D, Chiarati E, Vera R, Marcos JM&lt;/strong&gt;. 2010. Lazy group members are substitute helpers in carrion crows. Proc Biol Sci 277: 3275–3282.&lt;/a&gt; (free)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org.ezproxy.umsl.edu/10.1016/S0003-3472%2805%2980757-2&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Cartar RV&lt;/strong&gt;. 1992. Adjustment of foraging effort and task switching in energy-manipulated wild bumblebee colonies. Animal Behaviour.&lt;/a&gt; (full text not online?)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.anbehav.2008.11.019&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Jandt JM, Robins NS, Moore RE, Dornhaus A&lt;/strong&gt;. 2012. Individual bumblebees vary in response to disturbance: a test of the defensive reserve hypothesis. Insectes sociaux.&lt;/a&gt; (behind paywall, buy Jandt kindly has uploaded &lt;a href=&quot;https://docs.google.com/viewer?a=v&amp;amp;pid=sites&amp;amp;srcid=ZW1haWwuYXJpem9uYS5lZHV8ZHItamFuZHR8Z3g6NmY0Y2JmYWM1NjU2ZDk4ZQ&quot; rel=&quot;nofollow&quot;&gt;for free on her site&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.anbehav.2008.11.019&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Jandt, Dornhaus&lt;/strong&gt;. 2009. Spatial organization and division of labour in the bumblebee Bombus impatiens. Animal Behaviour 77: 11–11.&lt;/a&gt; (behind paywall, but also &lt;a href=&quot;https://docs.google.com/viewer?a=v&amp;amp;pid=sites&amp;amp;srcid=ZW1haWwuYXJpem9uYS5lZHV8ZHItamFuZHR8Z3g6M2JkNTE2Njg3Mjg4ZGI1Yg&quot; rel=&quot;nofollow&quot;&gt;free on Jandt's site&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1007%2Fs001140050528&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Kukuk PF, Ward SA, Jozwiak A&lt;/strong&gt;. 1998. Mutualistic benefits generate an unequal distribution of risky activities among unrelated group members. Naturwissenschaften.&lt;/a&gt; (Behind paywall, but &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC355920/?report=classic&quot; rel=&quot;nofollow&quot;&gt;this free article by Forbes et al.&lt;/a&gt; reports similar information)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Also see:&#xA;Jandt JM, Dornhaus A 2011 ‘Competition and cooperation: bumblebee spatial organization and division of labor may affect worker reproduction late in life’, Behavioral Ecology and Sociobiology 65: 2341-2349. &#xA;- shows that selfishness/cheating may actually play a role&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dornhaus A, Holley J-A, Pook VG, Worswick G, Franks NR 2008 'Why do not all workers work? Colony size and workload during emigrations in the ant Temnothorax albipennis' Behavioral Ecology and Sociobiology 63: 43-51 &#xA;- this paper reviews other literature about how many bees/ants in a colony are lazy; up to 75% or even more at a time!&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2013-09-17T19:01:09.367" LastActivityDate="2013-09-17T19:01:09.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9480" PostTypeId="2" ParentId="9477" CreationDate="2013-07-28T07:56:59.840" Score="2" Body="&lt;p&gt;And, if your question pertains to &quot;seen by animals of the same species&quot;, there are at least anecdotal accounts of animal-assisted births, as in &lt;a href=&quot;http://io9.com/5983426/zoologists-watch-as-monkey-midwife-delivers-baby&quot; rel=&quot;nofollow&quot;&gt;this case of a &quot;monkey midwife&quot;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The linked article also mentions another feature of &quot;social&quot; births, which is that it can might help juvenile females learn.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-07-28T07:56:59.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9481" PostTypeId="1" CreationDate="2013-07-28T10:43:58.703" Score="4" ViewCount="994" Body="&lt;p&gt;The lining of the blood vessel as an interface and boundary layer is of existential necessity to the life-support of mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is:&lt;br&gt;&#xA;&lt;strong&gt;How are major blood vessels and the blood vessel lining affected by sun-irradiation in humans, when exposed through equal or less than a millimeter of skin in total (including subcutaneous fatty tissue)?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Information regarding infrared exposure is welcome too.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ahiLZ.png&quot; alt=&quot;Penetration of UV radiation into skin&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.dermatology.ucsf.edu/skincancer/General/prevention/UV_Radiation.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.dermatology.ucsf.edu/skincancer/General/prevention/UV_Radiation.aspx&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="1450" LastActivityDate="2013-10-11T16:52:02.657" Title="How are blood vessels affected by UV and infrared radiation?" Tags="&lt;mammals&gt;&lt;skin&gt;&lt;blood-circulation&gt;&lt;tissue-repair&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9482" PostTypeId="1" AcceptedAnswerId="9483" CreationDate="2013-07-28T14:42:40.813" Score="4" ViewCount="100" Body="&lt;p&gt;I know that ssRNA molecule can fold over itself (e.g. in t-RNA). Can DNA do the same? Is there any example of this in nature?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is this phenomenon more common in RNA than in DNA?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="6" LastEditDate="2013-07-28T15:32:38.773" LastActivityDate="2013-07-28T20:44:21.710" Title="Self pairing in DNA" Tags="&lt;molecular-biology&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9483" PostTypeId="2" ParentId="9482" CreationDate="2013-07-28T15:30:02.403" Score="7" Body="&lt;p&gt;DNA can adopt secondary structures like RNA, the main difference is that DNA is usually present as double-stranded DNA while RNA is in most cases present as single-stranded RNA. Double-stranded DNA won't easily adopt any other conformation than the well-known double helix as this one is more stable than possible structures each single strand could adopt on its own.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One example that occurs in nature are &lt;a href=&quot;http://en.wikipedia.org/wiki/G-quadruplex&quot;&gt;G-Quadruplexes&lt;/a&gt; which for example occur in telomeres. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also artificially created &lt;a href=&quot;http://en.wikipedia.org/wiki/Deoxyribozyme&quot;&gt;DNA enzymes (also called DNAzymes or deoxyribozymes)&lt;/a&gt; that adopt tertiary structures like ribozymes do. But there are no known DNA enzymes that occur in nature as far as I know.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2013-07-28T15:40:30.177" LastActivityDate="2013-07-28T15:40:30.177" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9484" PostTypeId="2" ParentId="801" CreationDate="2013-07-28T17:08:59.867" Score="0" Body="&lt;p&gt;NADPH is found in the cytosol and stroma (chloroplast) of eukaryotes. NADH is more ubiquitous, but mostly found in bacteria and in mitichondria, possibly evidence for the endosymbosis of bacteria in eukaryotes. Neither can pass easily through a membrane. &lt;/p&gt;&#xA;" OwnerUserId="4132" LastActivityDate="2013-07-28T17:08:59.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9486" PostTypeId="2" ParentId="9438" CreationDate="2013-07-28T21:41:59.103" Score="9" Body="&lt;p&gt;Despite great answers from Amory and Remi.b, I want to emphasize this: there is continual debate about the definition of life because &lt;em&gt;&quot;life&quot; is not something that exists in the real world&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;People seek a definition of life that satisfies an intuitive notion of what alive should mean.  They feel that, say, &lt;a href=&quot;https://en.wikipedia.org/wiki/Intracellular_parasite&quot;&gt;intracellular parasites&lt;/a&gt; should be considered alive, but (say) only if they have an enclosing membrane, like &lt;a href=&quot;https://en.wikipedia.org/wiki/Rickettsia&quot;&gt;Rickettsia&lt;/a&gt;, and not if they are just a virus, or just an RNA molecule like a &lt;a href=&quot;https://en.wikipedia.org/wiki/Viroid&quot;&gt;viroid&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While people have a built-in intuition that, for example, reliably categorizes a tiger as alive and a rock as not alive, that intuition can't be precisely bounded by a definition such that everyone is satisfied by the boundary.  There are arrangements of matter in the physical world that fall outside the clear region of the intuitive concept of life, and this leads to continual, unresolvable, argument on what a precise definition of life should be, and what it should include.&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2013-07-28T21:41:59.103" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9487" PostTypeId="1" AcceptedAnswerId="13710" CreationDate="2013-07-29T03:50:13.587" Score="6" ViewCount="94612" Body="&lt;p&gt;Why are my faeces black in colour the morning after I eat some &lt;strong&gt;Oreos&lt;/strong&gt;? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Day 1&lt;/strong&gt; : Eat a handful of Oreos &amp;amp; the next morning your stool is black.&lt;br&gt;&#xA;&lt;strong&gt;Day 3&lt;/strong&gt; : Eat a handful of cocoa flavored biscuits &amp;amp; the next morning your stool is normal.&lt;br&gt;&#xA;&lt;strong&gt;Day 5&lt;/strong&gt; : Eat a handful of Chocolates &amp;amp; the next morning your stool is normal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.thenakedscientists.com/HTML/questions/question/2494/&quot; rel=&quot;nofollow noreferrer&quot;&gt;I'm aware of the beetroot digestion story&lt;/a&gt;, and how it doesn't happen to everyone. What is surprising in the case of Oreos is that it just takes a &#xA;handful of Oreos to turn the stool black. But with any other biscuits or chocolates, my faeces are normal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't have anything other than anecdotal evidence but a lot (&lt;strong&gt;NOT ALL&lt;/strong&gt;) of my friends have had similar experience. Just Googling &quot;&lt;strong&gt;&lt;a href=&quot;http://www.google.com/search?q=Black+stool+after+eating+Oreos&quot; rel=&quot;nofollow noreferrer&quot;&gt;Black stool after eating Oreos&lt;/a&gt;&lt;/strong&gt;&quot; &amp;amp; I see a lot of people (not all) having similar experience. Do note that to my knowledge it doesn't affect my body in any way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is that the case? Why doesn't it happen to everybody?&#xA;What ingredient in Oreos makes it happen? What is the physiological underpinning? &#xA;Asking this question with curiosity than caution. Looking for biological/biochemical perspective.&lt;/p&gt;&#xA;" OwnerUserId="3918" LastEditorUserId="22057" LastEditDate="2017-05-23T18:43:22.783" LastActivityDate="2017-06-28T17:59:08.073" Title="Why are my faeces black in color after eating Oreos" Tags="&lt;metabolism&gt;&lt;food&gt;&lt;digestive-system&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9488" PostTypeId="2" ParentId="9434" CreationDate="2013-07-29T04:37:37.697" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.botany.wisc.edu/courses/botany_940/03KeyInnovations/papers/Bond1998.pdf&quot; rel=&quot;nofollow&quot;&gt;Bond and Oppell&lt;/a&gt; address your question points one, two and three empirically by looking for what they call &quot;unbalanced bifurcations&quot; as a sign of adaptive radiations in a well-resolved phylogenetic tree (spiders), and find that &lt;strong&gt;the number of unbalanced bifurcations does indeed exceed what they would expect to occur by chance&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you mention and as I suggested in the comment, there are some serious problems that arise in trying to answer your question. Many of these are well presented in &lt;a href=&quot;http://research.amnh.org/vz/ornithology/pdfs/1990b.Key%20Innovations%20Novelties.pdf&quot; rel=&quot;nofollow&quot;&gt;Cracraft&lt;/a&gt;, including assuming that higher taxa are comparable with one another, making arbitrary choices about what rank of taxa to compare, ignoring counterexamples, and qualifying rather than quantifying diversity. I think that &lt;a href=&quot;http://www.botany.wisc.edu/courses/botany_940/03KeyInnovations/papers/Bond1998.pdf&quot; rel=&quot;nofollow&quot;&gt;Bond and Oppell&lt;/a&gt; effectively address most of these problems through rigorous, apriori definitions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;There's a diversity of opinions and evidence from biological systems on your fourth question point&lt;/strong&gt;. &lt;a href=&quot;http://www.botany.wisc.edu/courses/botany_940/03KeyInnovations/papers/Bond1998.pdf&quot; rel=&quot;nofollow&quot;&gt;Bond and Oppell&lt;/a&gt; connect these significantly unbalanced bifurcations to key traits (like orb-weaving) that open up new adaptive zones. I suppose therefore they might say that there's a fundamental factor (a key trait, and therefore open adaptive zones) driving diversification, and therefore might not agree with you that diversification would necessarily beget more diversification (at least, not in the absence of open adaptive zones). For instance, in Hawaiian tetragnathid spiders, ecomorph niches on an island are filled either through immigration from another island or through adaptive diversification &lt;a href=&quot;http://nature.berkeley.edu/~gillespie/Science.pdf&quot; rel=&quot;nofollow&quot;&gt;(Gillespie)&lt;/a&gt;. No ecomorph is represented by two sympatric species, so a niche filled by immigration will presumably not spur adaptive radiation. However, species radiations in Andean lupines &lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0601928103&quot; rel=&quot;nofollow&quot;&gt;(Hughes and Eastwood)&lt;/a&gt; and plethodontid salamanders &lt;a href=&quot;http://dx.doi.org/10.1098/rspb.2005.3326&quot; rel=&quot;nofollow&quot;&gt;(Kozak et al)&lt;/a&gt; seem not to have been accompanied by any key traits or particular ecological opportunity, and could theoretically be driven by the self-reinforcing mechanism you propose. As a related point, I suppose more diverse lineages could be less likely to go extinct; which could support diverse lineages becoming more diverse.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.2307/2411077&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Bond JE, Opell BD&lt;/strong&gt;. 1998. Testing adaptive radiation and key innovation hypotheses in spiders. Evolution 52: 403–415.&lt;/a&gt; (Behind paywall, &lt;a href=&quot;http://www.botany.wisc.edu/courses/botany_940/03KeyInnovations/papers/Bond1998.pdf&quot; rel=&quot;nofollow&quot;&gt;free pdf here&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1126/science.1091875&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Gillespie R&lt;/strong&gt;. 2004. Community assembly through adaptive radiation in Hawaiian spiders. Science 303: 356–359.&lt;/a&gt; (Behind paywall, &lt;a href=&quot;http://nature.berkeley.edu/~gillespie/Science.pdf&quot; rel=&quot;nofollow&quot;&gt;free pdf here&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://research.amnh.org/vz/ornithology/pdfs/1990b.Key%20Innovations%20Novelties.pdf&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Cracraft J&lt;/strong&gt;. 1990. Origin of evolutionary novelties: pattern and process at different hierarchical levels. p. 21-44 in Evolutionary Innovations, ed. M. Nitecki, U Chicago Press.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0601928103&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Hughes C, Eastwood R&lt;/strong&gt;. 2006. Island radiation on a continental scale: exceptional rates of plant diversification after uplift of the Andes.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1098/rspb.2005.3326&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Kozak KH, Weisrock DW, Larson A&lt;/strong&gt;. 2006. Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon). Proceedings of the Royal Society B: Biological Sciences 273: 539–546.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-07-29T04:37:37.697" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9489" PostTypeId="1" AcceptedAnswerId="9501" CreationDate="2013-07-29T08:34:46.210" Score="4" ViewCount="213" Body="&lt;p&gt;I am wondering, out of pure curiosity, whether with current medical &amp;amp; biological science, (or indeed with accepted probable future developments in those areas), in theory, would it be possible to create an injection of vitamins, minerals, sugars etc so that eating was no longer necessary, and in fact, an average life with average energy usage could be continued?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not a biological professional nor academic, so apologies if this is on the wrong Stack Exchange site, however I thought this was closest to the mark. If there is somewhere more appropriate please direct me, and I shall delete the question and post it there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, if no, would there be certain parts that you couldn't replicate in an injection or something of the like?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NB: This doesn't have to be an injection, any simple method of ingesting or attaining everything the body needs. This could be a pill, or anything. I simply used an injection as an example. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank-you very much.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&#xA;Having found this question,&#xA;&lt;a href=&quot;https://biology.stackexchange.com/questions/1910/has-there-ever-been-an-attempt-to-create-nutritionally-tailored-food-for-adult-h&quot;&gt;Has there ever been an attempt to create nutritionally tailored food for adult human consumption?&lt;/a&gt;&#xA;I would like clarify. This has given me a lot of information, however, I am looking for any method APART from food. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="4134" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-07-29T18:23:47.467" Title="In theory, would it be possible to create an injection of Vitamins, Minerals, sugars etc so that eating was no longer necessary?" Tags="&lt;human-biology&gt;&lt;nutrition&gt;&lt;vitamins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9490" PostTypeId="1" CreationDate="2013-07-29T09:49:47.283" Score="5" ViewCount="12316" Body="&lt;p&gt;There is a light pollution movement that says lighting at night obstructs melatonin production. They say: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What makes you fall asleep are changes in the level of the hormone&#xA;  melatonin circulating in your body. During the day, light stimulates a&#xA;  part of the brain. This brain part (known as the suprachiasmatic&#xA;  nucleus) tells the pineal gland to decrease the melatonin level when&#xA;  it is light out and to increase it when it is dark. The brighter the&#xA;  light, the bigger the decrease and the darker the dark, the bigger the&#xA;  increase of melatonin. By making your days lighter and your nights&#xA;  darker, you can improve both the quality of your sleep and the amount&#xA;  of time it takes you to fall asleep.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and recommend all kind of protection against the light, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dark Nights: Make your nights as dark as possible. Draw the curtains,&#xA;  close the shades and keep the lights off. Try a sleep mask if you&#xA;  can’t get eliminate enough light. The darker your night, the quicker&#xA;  you will fall asleep.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Do I sense the light by the whole skin surface or only open eyes? If you sense by eyes, which are closed during the sleep, then what is the problem?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, the question is: is the sleep mask sufficient for melatonin secretion or you need to cover the skin?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;update&lt;/strong&gt; What if I close only one eye? I tend to do this when the blinding sun shines. Does such light eject melatonin?&lt;/p&gt;&#xA;" OwnerUserId="3310" LastEditorUserId="3310" LastEditDate="2013-08-04T14:16:58.057" LastActivityDate="2013-08-04T14:16:58.057" Title="Why do you need you room dark for melatonin release?" Tags="&lt;human-biology&gt;&lt;sleep&gt;&lt;melatonin&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9491" PostTypeId="2" ParentId="9490" CreationDate="2013-07-29T11:22:53.820" Score="2" Body="&lt;p&gt;The release of the hormone melatonin is responsible for the feeling of sleepiness. It is released by the pineal gland and production starts when the light fades, as it's &lt;strong&gt;production is inhibited by light stimulation of the retina&lt;/strong&gt;, the onset of the production is called dim-light melatonin onset. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Read more about this at this &lt;a href=&quot;https://biology.stackexchange.com/questions/7667/what-causes-humans-to-be-sleepy/7672#7672&quot;&gt;previous answer&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jcem.endojournals.org/content/82/11/3763.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;This study on blind people&lt;/a&gt; will show you that the light entering the eyes is the (main at least) regulator of melatonin rhythms. They took blind people, 19 of whom could perceive light and 30 who could not, and showed that 14 of 19 light perceivers had normal melatonin rhythms while 23 of the light-blind people had abnormal or unclassifiable rhythms.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-07-29T14:33:31.640" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9492" PostTypeId="1" AcceptedAnswerId="9497" CreationDate="2013-07-29T11:31:30.687" Score="1" ViewCount="246" Body="&lt;p&gt;An American is staying in my house for the summer and claims that food (specifically, bread and milk) spoils a lot faster here than at home in California. Is there a significant difference in chemical content (preservatives etc.), or other factors, that might explain this? &lt;/p&gt;&#xA;" OwnerUserId="4107" LastActivityDate="2013-07-29T15:58:04.070" Title="Why might food spoil faster in Ireland than the US?" Tags="&lt;food&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9493" PostTypeId="1" CreationDate="2013-07-29T12:15:05.467" Score="2" ViewCount="252" Body="&lt;p&gt;Is it possible to transplant a brain and would it keep the memory? If not, what would be the prerequisite to transplant one?&lt;/p&gt;&#xA;" OwnerUserId="883" LastActivityDate="2021-01-31T18:59:21.243" Title="Can a brain be transplanted?" Tags="&lt;brain&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9494" PostTypeId="2" ParentId="9493" CreationDate="2013-07-29T12:47:18.950" Score="4" Body="&lt;p&gt;&quot;Is it possible&quot; has a carefully conditional &quot;yes&quot;.  Do we have the expertise or technology to do it now? No.  One of the biggest difficulties is that nerve tissues (the connections between brain and rest of body) will take time to heal... time during which the brain cannot sufficiently give commands to the rest of the body to keep autonomic functions running.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Head transplants, however, have been &quot;successfully&quot; completed using monkeys.  The monkey lived for sometime after the transplant, but eventually died.  China has also been known to do a similar procedure with dogs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Caution, this may be too explicit for some; I'm not sure ethics boards would allow it nowadays:&#xA;&lt;a href=&quot;http://www.youtube.com/watch?v=TGpmTf2kOc0&quot; rel=&quot;nofollow&quot;&gt;Monkey Head Transplant&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1853" LastActivityDate="2013-07-29T12:47:18.950" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9495" PostTypeId="2" ParentId="9492" CreationDate="2013-07-29T14:27:03.900" Score="2" Body="&lt;p&gt;There are more factors than we can ever consider.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as region: does California represent all of the US? What part of California?  What part of Ireland?  What's the humidity and average temperature of each region?  What are the agricultural regulations?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as cultural/methodical differences: how do you store the food in your homes? The quality of your cooling method? The way people in the household handle the food?&lt;/p&gt;&#xA;" OwnerUserId="1853" LastActivityDate="2013-07-29T14:27:03.900" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9496" PostTypeId="1" AcceptedAnswerId="9525" CreationDate="2013-07-29T15:52:00.953" Score="2" ViewCount="1987" Body="&lt;p&gt;The concept of water potential in plants tries (and succeeds) to explain various movement and transports in plants. I have learnt that it can be though of being composed of various components like the solute (osmotic) potential, Matric potential, gravitational potential and the pressure potential. I know how to quantitatively determine the osmotic pressure and have worked with the chemical potential of water in solution and pure state. Can someone help me develop an intuitive understanding of all these components quantitatively? I am comfortable with basic thermodynamic treatments of chemical potential and already have an intuition of the osmotic component. &lt;a href=&quot;http://jxb.oxfordjournals.org/content/24/5/816.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Here is the basic definition regarding water potential&lt;/a&gt;. (Since this pdf is quite old, I am not sure whether the same definitions operate or rather are used now.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:- As an example, we can derive the lowering of chemical potential of pure water on addition of solute and for the ideal case, the lowering turns out to be $RTln(X_a)$ (where $x_a$ is the mole-fraction of solute, $R$ is the gas constant and $T$ the absolute temperature) and this is defined as the osmotic potential or the solute potential. Next, the gravimetric component. We can intuitively understand that the water must flow from higher gravitational potential to lower and hence flow downwards. But I want to understand how can we assign a quantitative basis to our arguments in terms of chemical potential for differenf heights. Same way, how can we ascribe a mathematical (or chemical) basis to all the components of water potential including the turgor pressure and the matric components.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2013-07-30T15:41:07.627" LastActivityDate="2013-07-30T20:57:48.717" Title="Water potential in plants?" Tags="&lt;biochemistry&gt;&lt;plant-physiology&gt;&lt;intracellular-transport&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9497" PostTypeId="2" ParentId="9492" CreationDate="2013-07-29T15:58:04.070" Score="6" Body="&lt;p&gt;I would think added preservatives are the most likely candidate, for example, Azodicarbonamide is frequently added to bread in the US, but banned in Ireland and most of the rest of the EU. Since it has a preservative effect it is a reasonable candidate for a specific causal factor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But as Keegan points out there are an awful lot of possible factors so it's impossible for us to say with any certainty.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-07-29T15:58:04.070" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9498" PostTypeId="1" AcceptedAnswerId="9511" CreationDate="2013-07-29T16:18:58.197" Score="1" ViewCount="3253" Body="&lt;p&gt;I've recently heard about experiments with brain tissue, where a virus is introduced in a rats brain, causing a &quot;glow when electric charge is present&quot; protein to be created. This protein then helps to study the brain using optical techniques to detect this glow. As far as I understand, not all cells in the brain were affected by this virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems like this kind of &quot;virus operation&quot; on DNA is pretty powerful, so my question is : &lt;strong&gt;at which point in an organism's life can a virus operation be done in such a way as to affect the entire organism for the rest of its life?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, will a virus is introduced into a young embryo(or sperm), affect all cells and stay with an organism until death? Can it be introduced later and still have &quot;complete effect&quot;?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-08-29T10:55:31.510" Title="When can a virus modify DNA in every cell of a living organism?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;development&gt;&lt;embryology&gt;&lt;virus&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9499" PostTypeId="2" ParentId="9477" CreationDate="2013-07-29T16:38:08.770" Score="6" Body="&lt;p&gt;Our heads are bigger.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's &lt;a href=&quot;http://www.pnas.org/content/106/23/9125.extract&quot; rel=&quot;nofollow&quot;&gt;some&lt;/a&gt; &lt;a href=&quot;http://www.sciencedaily.com/releases/2012/08/120827152037.htm&quot; rel=&quot;nofollow&quot;&gt;debate&lt;/a&gt; on the issue, but in essence, human brains, and therefore heads, are very large relative to our body size.  This is handy for all the intelligent things we like to do, but can be rather painful during birth.  Because we walk upright, the size of a newborn's head is actually a non-trivial fact during the birthing process.  There are two major implications.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first is that human birth &lt;strong&gt;hurts&lt;/strong&gt;.  You can watch the birth of other animals and they seem to brush it off, but for humans, forcing that huge head through a relatively small birth canal is difficult.  Evolution has (supposedly) limited the size of the hips because, while that would allow an easier birthing process, it would negatively impact our ability to walk.  As such, it has to hurt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, in order to make the process easier, humans rotate during birth.  The end result is that, unlike even other closely related primates, humans come out backward in a way that is very difficult for a birthing female to attend to.  This almost requires having another person or two on hand to help out.  This would, of course, be a huge reinforcement for social connections.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few books I know of touch on this.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Up_From_Dragons&quot; rel=&quot;nofollow&quot;&gt;Up From Dragons&lt;/a&gt; deals with the brain size/hip size issue and &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1598743902&quot; rel=&quot;nofollow&quot;&gt;The Invisible Sex&lt;/a&gt; talks about rotation during the birthing process and the social implications.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="3952" LastEditDate="2013-07-29T23:41:27.010" LastActivityDate="2013-07-29T23:41:27.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9500" PostTypeId="1" AcceptedAnswerId="9503" CreationDate="2013-07-29T17:30:41.380" Score="5" ViewCount="9965" Body="&lt;p&gt;If we somehow remove pheromones, &lt;strong&gt;do animals experience a phenomenon similar to human &quot;visual beauty&quot; when looking at members of the opposite sex?&lt;/strong&gt; For example, given a set of 20 female ducks observed through a glass panel, would male ducks attempt to court/mate with a small subset of female ducks first(more attractive ones), or is it based on some other criteria (most receptive, random, closest, fittest, pheromones, etc?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is some &quot;visual attractiveness selection criteria&quot;, &lt;strong&gt;is there a requirement of certain complexity of the brain and/or visual system for an animal before this phenomenon starts to occur?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm aware of the existence of this question: &lt;a href=&quot;https://biology.stackexchange.com/questions/7568/why-does-sexual-selection-evolve-beautiful-features&quot;&gt;Why does sexual selection evolve beautiful features?&lt;/a&gt;, and my question deals with the members of the same generation, not long-term evolution. &lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2016-04-27T14:34:47.767" Title="Do male animals visually perceive females as more/less attractive?" Tags="&lt;zoology&gt;&lt;perception&gt;&lt;sexual-selection&gt;" AnswerCount="5" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9501" PostTypeId="2" ParentId="9489" CreationDate="2013-07-29T18:23:47.467" Score="6" Body="&lt;p&gt;The quantity of nutrients the body requires takes much more physical space than can be included in a simple pill or injection (used only a few times a day).  But nutrition can be provided by IV (&lt;a href=&quot;http://en.wikipedia.org/wiki/Intravenous_therapy&quot;&gt;intravenous administration&lt;/a&gt;), and it is used today for some medical conditions.  When the IV completely substitutes for normal digestion, it is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Parenteral_nutrition&quot;&gt;total parenteral nutrition&lt;/a&gt; (or TPN).  The procedure is simple and reliable enough that it can sometimes be used outside of a hospital setting and be self-administered by users at home.&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2013-07-29T18:23:47.467" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9502" PostTypeId="2" ParentId="9500" CreationDate="2013-07-29T22:56:46.603" Score="5" Body="&lt;p&gt;Absolutely.  Quality by appearance is sometimes a big part of mate selection and sometimes it is not.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The size and cognitive capacity brain is probably important but not always. Primates are closest to us and have most similar tastes to us, &lt;a href=&quot;http://www.hup.harvard.edu/catalog.php?isbn=9780674955394&quot;&gt;have varying levels of interest in mate appearance&lt;/a&gt;.  Most primates have a troupe dominance where a dominant male mates with &lt;em&gt;all&lt;/em&gt; the females and sires as many offspring as he can before he loses his place on top.  Many smaller primates rely more on sperm competition and the females mate with all the males they can when they are in estrus - the offspring just emerge from the most competitive sperm.  Note I studied Sarah Hrdy a while ago.  I hear &lt;a href=&quot;http://en.wikipedia.org/wiki/Robert_Sapolsky&quot;&gt;Robert Sapolsky&lt;/a&gt; is another great source of insight on primate/human behavior. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neither of these modes are quite so focused on visual beauty as our culture is.  Other cultures are also not selective based on appearance, e.g. cultures where marriages are arranged would often consider the social and economic relationships between the families more than we do.  This is a broad generalization, but just to point out that just looking at someone to decide mate choice isn't as dominant as sometimes it feels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But to look at some tiny brains I know that snakes often mate in gigantic balls of snake and mate choice is pretty indiscriminate, on the other hand, &lt;a href=&quot;http://beheco.oxfordjournals.org/content/9/1/33.abstract&quot;&gt;spiders where female choice is dominant, males will experience rejection&lt;/a&gt;.  This is a bummer for the males because they only often live long enough to offer to one mate.  Its probable that the females are not hungry or have recently mated with another male, but just an example to demonstrate that even small brained animals can be discriminating.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-07-29T22:56:46.603" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9503" PostTypeId="2" ParentId="9500" CreationDate="2013-07-30T08:22:52.863" Score="8" Body="&lt;p&gt;There are numerous examples of visual attraction in animals. An absolute classic of an experiment, taught to most/all evolutionary biology students, is the &lt;a href=&quot;http://www.treknature.com/gallery/photo139613.htm&quot; rel=&quot;nofollow&quot;&gt;widowbird&lt;/a&gt; tail length &lt;a href=&quot;http://www.nature.com/nature/journal/v299/n5886/abs/299818a0.html&quot; rel=&quot;nofollow&quot;&gt;experiment by Andersson&lt;/a&gt;. He experimentally manipulated the tail lengths of male widowbirds at random. Some tails were made longer and some shorter. From this experiment Andersson showed that females choose males with longer tails more preferentially. Another classic example is the &lt;a href=&quot;https://en.wikipedia.org/wiki/Lek_mating&quot; rel=&quot;nofollow&quot;&gt;lek mating system&lt;/a&gt; where there is a bias in reproductive success towards attractive males, in some cases &lt;a href=&quot;http://www.sfu.ca/biology/faculty/reynolds/The_Reynolds_Lab/Publications_files/Mackenzie%20et%20al.%20AN%2095.pdf&quot; rel=&quot;nofollow&quot;&gt;10-20% of the males get 70-80% of the matings&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A lek is an aggregation of males that gather to engage in competitive&#xA;  displays that may entice visiting females who are surveying&#xA;  prospective partners for copulation. Leks are commonly formed&#xA;  before or during the breeding season. A lekking species is defined by&#xA;  the following characteristics: male displays, &lt;strong&gt;strong female mate&#xA;  choice&lt;/strong&gt;, and the conferring of male indirect benefits. Although&#xA;  lekking is most prevalent among avian species, lekking behavior is&#xA;  found in a variety of animals such as insects, amphibians, and&#xA;  mammals&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mate_choice#Indicator_traits&quot; rel=&quot;nofollow&quot;&gt;Beauty could be a an example of a an indicator trait&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Indicator traits&lt;/strong&gt; are those that &lt;strong&gt;signal good overall quality of the&#xA;  individual&lt;/strong&gt;. Traits that are perceived as attractive must reliably&#xA;  indicate broad genetic quality in order for selection to favor them&#xA;  and for preference to evolve.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm sure there are some studies in fish, likely guppies or zebra fish, which gave individual fish the opportunity to visually assess potential mates (placing tanks next to each other and observing courtship) which would be very similar to your hypothetical duck example. &lt;a href=&quot;http://www.jstor.org/sici?sici=0014-3820%281982%2936:1%3C1:SSATEO%3E2.0.CO;2-9&amp;amp;origin=ISI&quot; rel=&quot;nofollow&quot;&gt;Despite often being a paradox, female mate choice is well documented.&lt;/a&gt; Further, &lt;a href=&quot;http://en.wikipedia.org/wiki/Mate_choice#Male_mate_choice.2FSex_role_reversal&quot; rel=&quot;nofollow&quot;&gt;male mate choice&lt;/a&gt; is now coming to light, &lt;a href=&quot;http://bonduriansky.net/BR-2001.pdf&quot; rel=&quot;nofollow&quot;&gt;even in species where female mate choice and male-male competition exists&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think selection on &quot;beauty&quot; would require some kind of particularly special neural system, obviously some visual capacity is necessary for visual attraction and some basic neural pathways linked to that. I have done experiments myself in &lt;em&gt;Drosophila simulans&lt;/em&gt; which looked at good gene benefits of mating with attractive males (indirect genetic benefits of female mate choice) and another which assessed precopulatory selection (female mate choice) for a secondary sexual character in the same species. Even in such a small-brained species there appears to be some degree of (partially visual) mate choice going on.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="577" LastEditDate="2014-10-24T17:09:13.070" LastActivityDate="2014-10-24T17:09:13.070" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9504" PostTypeId="5" CreationDate="2013-07-30T08:50:14.383" Score="0" Body="&lt;p&gt;This field is focussed on learning how to monitor biodiversity, prevent extinction of species, and prevent changes in, or loss of, ecosystems and habitats. It involves the development of techniques for restoration, conservation planning, and understanding how economics and law affect conservation policy.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="69" LastEditDate="2013-07-30T12:06:56.810" LastActivityDate="2013-07-30T12:06:56.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9505" PostTypeId="4" CreationDate="2013-07-30T08:50:14.383" Score="0" Body="The study of biodiversity with the applied goal of learning how to protect species, habitats, and ecosystems from change, particularly that caused by non-natural effects.&#xD;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-30T12:07:03.060" LastActivityDate="2013-07-30T12:07:03.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9506" PostTypeId="1" AcceptedAnswerId="9565" CreationDate="2013-07-30T08:54:14.650" Score="9" ViewCount="25780" Body="&lt;p&gt;I have heard that &quot;The animals who have their 'EARS' outside their body give birth to their young ones and the animals who have their 'EARS' inside their body lay eggs.&quot; Is this true? Are there counterexamples?&lt;/p&gt;&#xA;" OwnerUserId="3055" LastEditorUserId="3952" LastEditDate="2013-07-30T13:47:17.383" LastActivityDate="2017-05-02T09:13:02.437" Title="Laying eggs vs giving birth: is there a connection with internal vs. external ears?" Tags="&lt;zoology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9507" PostTypeId="2" ParentId="8560" CreationDate="2013-07-30T08:57:47.247" Score="5" Body="&lt;p&gt;As @fileunderwater suggested, this looks like an Acacia. Like many others with OSX, I have this incuded picture of an acacia as one of my screensaver rotations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It looks very similar in bauplan to the illustration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/imGW2.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-08-14T15:55:21.247" LastActivityDate="2013-08-14T15:55:21.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9508" PostTypeId="2" ParentId="9506" CreationDate="2013-07-30T09:11:32.957" Score="16" Body="&lt;p&gt;You are quoting from Imam Ali, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The animals who have their 'EARS' outside their body give birth to&#xA;  their young ones and the animals who have their 'EARS' inside their&#xA;  body lay eggs.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And in short the answer is that is wrong. Giving birth to live young is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Vivipary&quot;&gt;vivipary&lt;/a&gt;. When a species lays eggs it is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Oviparity&quot;&gt;oviparity&lt;/a&gt;. There are other mechanisms too.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ovuliparity: fecundation is external (in arthropods and fishes, most&#xA;  of frogs) &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Oviparity: fecundation is internal, the female lays zygotes&#xA;  as eggs with important vitellus (typically birds) &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Ovo-viviparity: or&#xA;  oviparity with retention of zygotes in the female’s body or in the&#xA;  male’s body, but there are no trophic interactions between zygote and&#xA;  parents. (Anguis fragilis is an example of ovo-viviparity.) In the sea&#xA;  horse, zygotes are retained in the male’s ventral &quot;marsupium&quot;. In the&#xA;  frog Rhinoderma darwinii, the zygotes developed in the vocal sac. In&#xA;  the frog Rheobatrachus, zygotes developed in the stomach. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Histotrophic&#xA;  viviparity: the zygotes developed in the female’s oviducts, but find&#xA;  their nutriments by oophagy or adelphophagy (intra-uterine cannibalism&#xA;  in some sharks or in the black salamander Salamandra atra).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Hemotrophic viviparity: nutriments are provided by the female, often&#xA;  through placenta. In the frog Gastrotheca ovifera, embryos are fed by&#xA;  the mother through specialized gills. &lt;strong&gt;The lizard Pseudomoia&#xA;  pagenstecheri and most mammals exhibit a hemotrophic viviparity.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Though it is true that most &lt;strong&gt;typically we would associate egg laying with animals with ears &quot;inside&quot; such as birds and snakes, there are some examples that are not this way&lt;/strong&gt;. Boa constrictors are one species which &lt;a href=&quot;https://en.wikipedia.org/wiki/Boa_constrictor#Reproduction_and_development&quot;&gt;gives birth to live young rather than laying an egg&lt;/a&gt; and being a snake their ears are 'inside their body'. However I should point out that this is Ovoviviparity, not viviparity. For an example of a lizard with viviparity see the &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Pseudemoia_entrecasteauxii&quot;&gt;Pseudomoia&lt;/a&gt;&lt;/em&gt; lizard genus.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-30T09:22:48.190" LastActivityDate="2013-07-30T09:22:48.190" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9509" PostTypeId="5" CreationDate="2013-07-30T09:33:08.983" Score="0" Body="&lt;p&gt;Arachnology is the scientific study of arachnids. It can  include the study of ticks and mites which is sometimes also called acarology.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-30T12:07:09.563" LastActivityDate="2013-07-30T12:07:09.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9510" PostTypeId="4" CreationDate="2013-07-30T09:33:08.983" Score="0" Body="Arachnology is the scientific study of spiders and related animals such as scorpions, pseudoscorpions, harvestmen, collectively called arachnids. It can include the study of ticks and mites which is sometimes also called acarology." OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-30T12:07:20.203" LastActivityDate="2013-07-30T12:07:20.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9511" PostTypeId="2" ParentId="9498" CreationDate="2013-07-30T09:52:52.060" Score="3" Body="&lt;p&gt;The answer depends on two factors:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The type of vector (virus) you are using&lt;/li&gt;&#xA;&lt;li&gt;How well your vector can be integrated. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The bottom-line is that there is no guarantee the vector will work even if you start from the embyro. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I know, the problem of using vectors in general is that the vector you are using might not be integrated into the genome of the host. (Not necessarily get into the DNA, but just keep replicating during each S phase.) Therefore doing it earlier gives you a better chance to actually get them in the organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, there is a linear vector used in &lt;em&gt;C. elegans&lt;/em&gt; that was injected into the oocyte even before fertilization. The cell later treats the vectors as broken DNAs and linages them so they could be pull to one side of the cell during mitosis. However, the huge chunk of vector DNA is mosaic. (i.e. only some of the cells in that worm have the vectors.) Other vectors like engineered HIV have better chance to integrate themselves.&lt;/p&gt;&#xA;" OwnerUserId="4136" LastEditorUserId="1306" LastEditDate="2013-08-29T10:55:31.510" LastActivityDate="2013-08-29T10:55:31.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9512" PostTypeId="1" AcceptedAnswerId="9523" CreationDate="2013-07-30T13:26:40.683" Score="2" ViewCount="4812" Body="&lt;p&gt;I have read about cortical circuits in the context of connectomics (e.g. any example &lt;a href=&quot;https://www.google.com/search?q=cortical%20circuits%20connectomics#sclient=psy-ab&amp;amp;q=%22cortical%20circuits%22%20%20connectomics&amp;amp;oq=%22cortical%20circuits%22%20%20connectomics&amp;amp;gs_l=serp.3...5544.7332.0.7501.3.3.0.0.0.0.64.167.3.3.0....0.0..1c.1.20.psy-ab.AAgDLCcYx5k&amp;amp;pbx=1&amp;amp;bav=on.2,or.r_cp.r_qf.&amp;amp;bvm=bv.49967636,d.dmg,pv.xjs.s.en_US.jOYpRJj4zMA.O&amp;amp;fp=332b6c997d1bae1d&amp;amp;biw=1200&amp;amp;bih=1754&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) and computational neuroscience (e.g. any example &lt;a href=&quot;https://www.google.com/search?q=computational%20neuroscience#sclient=psy-ab&amp;amp;q=computational%20neuroscience%20%22cortical%20circuits%22%20&amp;amp;oq=computational%20neuroscience%20%22cortical%20circuits%22%20&amp;amp;gs_l=serp.3...7052.7052.0.7472.1.1.0.0.0.0.57.57.1.1.0....0.0..1c.1.20.psy-ab.T0CItQP16pQ&amp;amp;pbx=1&amp;amp;bav=on.2,or.r_cp.r_qf.&amp;amp;fp=332b6c997d1bae1d&amp;amp;biw=1200&amp;amp;bih=1754&amp;amp;bvm=pv.xjs.s.en_US.jOYpRJj4zMA.O&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;), but a simple Google/Wikipedia does search not show an exact definition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What exactly is a cortical circuit?&lt;/p&gt;&#xA;" OwnerUserId="17" LastEditorUserId="17" LastEditDate="2013-07-30T18:08:57.320" LastActivityDate="2013-07-31T00:13:48.703" Title="What is a cortical circuit?" Tags="&lt;neuroscience&gt;&lt;definitions&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9513" PostTypeId="5" CreationDate="2013-07-30T13:49:54.350" Score="0" Body="&lt;p&gt;This tag is for questions relating to SNPs (single nucleotide polymorphisms), which are individual nucleotide differences between two sequences, which may be found comparing paired chromosomes within a species, or sequences between species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following two sequences contain an example SNP, in bold: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A C G T &lt;strong&gt;G&lt;/strong&gt; T G C C A  ...&lt;br&gt;&#xA;A C G T &lt;strong&gt;C&lt;/strong&gt; T G C C A  ...&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="4101" LastEditDate="2013-10-31T18:12:39.687" LastActivityDate="2013-10-31T18:12:39.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9514" PostTypeId="4" CreationDate="2013-07-30T13:49:54.350" Score="0" Body="Single nucleotide polymorphisms, or SNPs, are differences between two sequences of DNA at one individual nucleotide location." OwnerUserId="1590" LastEditorUserId="4101" LastEditDate="2013-10-31T18:11:49.590" LastActivityDate="2013-10-31T18:11:49.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9515" PostTypeId="5" CreationDate="2013-07-30T14:02:33.887" Score="0" Body="&lt;p&gt;Sex is when two gametes, such as an egg and a sperm, fuse to form one individual cell. Each gamete contains genetic material that will form half the genetic make-up of the offspring. Sex evolved around 1 billion years ago, though the causes for its initial evolution remain open to much debate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Differences can occur between the sexes, such as behaviour or morphology, which is called sexual dimorphism. Even the gametes often show differences in what is called anisogamy, which is the presence of male and female specific gametes, i.e. the sperm and the egg. Males by definition produce small motile gametes and females a larger non-motile gamete containing nutrients.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sex-determination occurs in a number of different patterns: the XY system, where females are XX and males are XY, is found mainly in mammals; the ZW system, mainly found in birds, has ZW females and ZZ males; and the single-chromosome X0 system, mainly in insects, where females are XX and males are merely X.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="4101" LastEditDate="2013-10-31T16:57:34.133" LastActivityDate="2013-10-31T16:57:34.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9516" PostTypeId="4" CreationDate="2013-07-30T14:02:33.887" Score="0" Body="Questions involving the study of sex and reproduction, mating systems, sexuality, sex determination, gender, the evolution of sex, and other topics in the context of sex." OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-30T15:20:27.377" LastActivityDate="2013-07-30T15:20:27.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9517" PostTypeId="1" AcceptedAnswerId="9522" CreationDate="2013-07-30T14:11:55.457" Score="15" ViewCount="589" Body="&lt;p&gt;Reading &lt;a href=&quot;https://biology.stackexchange.com/questions/9017/how-potent-is-the-venom-from-the-australian-platypus&quot;&gt;this question&lt;/a&gt;, I wondered why is it that we associate vertebrate venoms so often with snakes and fish, and more rarely with lizards, amphibians, mammals, and birds (apparently never, in birds?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are venoms more advantageous for snakes and fish, or more expensive or dangerous to produce for the other taxa? Or is it connected to evolutionary history – is venom somehow more 'evolvable' for snake and fish lineages?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or, perhaps, is it just chance?&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2021-05-20T11:38:02.177" Title="Why is venom more common in fish and snakes than other vertebrates?" Tags="&lt;evolution&gt;&lt;toxicology&gt;&lt;vertebrates&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9519" PostTypeId="5" CreationDate="2013-07-30T15:16:08.207" Score="0" Body="&lt;p&gt;Vertebrata is a Subphylum within the Chordata Phylum, and Animalia Kingdom. Vertebrates are animals with backbones and consist of 4% of the described animal species, and include mammals, birds, amphibians, reptiles, and several Classes of fish.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-30T15:23:46.390" LastActivityDate="2013-07-30T15:23:46.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9520" PostTypeId="4" CreationDate="2013-07-30T15:16:08.207" Score="0" Body="Question specifically regards vertebrates. Vertebrata is a Subphylum within the Chordata Phylum, and Animalia Kingdom. Vertebrates are animals with backbones and consist of 4% of the described animal species, and include mammals, birds, amphibians, reptiles, and several Classes of fish." OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-30T17:12:58.857" LastActivityDate="2013-07-30T17:12:58.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9521" PostTypeId="1" CreationDate="2013-07-30T15:19:44.263" Score="3" ViewCount="950" Body="&lt;p&gt;Sometimes in synthetic biology, we need to know rates of transcription of one promoter in relation to others (particularly inducible vs constitutive) in order to perform tasks like balancing transcription products and ensuring an excess of one product over another. As far as I know, there is no standard method of characterizing promoter strengths in relation to one another. However, a logical unit for transcription rate made (by organism or &lt;em&gt;in vitro&lt;/em&gt;) could look something like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;Promoter Strength&lt;/strong&gt; = number of transcript made / (concentration of RNA polymerase) (length of transcript) (unit of time).&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why hasn't this been done yet? What other factors could contribute to rate of expression in a particular organism? Is there another system for comparing promoter strengths?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: a similar system could be used for strength of repression. &lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2013-07-30T15:32:52.847" LastActivityDate="2020-02-11T20:23:04.600" Title="Why isn't there a standard unit of promoter strength?" Tags="&lt;synthetic-biology&gt;&lt;transcription&gt;" AnswerCount="4" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9522" PostTypeId="2" ParentId="9517" CreationDate="2013-07-30T15:29:13.303" Score="13" Body="&lt;p&gt;&lt;a href=&quot;http://phenomena.nationalgeographic.com/2013/01/09/on-the-origin-of-venom/&quot; rel=&quot;nofollow noreferrer&quot;&gt;This write up by Carl Zimmer&lt;/a&gt; basically covers anything I could have said.  He links to a number of resources, in particular &lt;a href=&quot;https://doi.org/10.1016/j.tree.2012.10.020&quot; rel=&quot;nofollow noreferrer&quot;&gt;Casewell et. al. 2013&lt;/a&gt;, which at a cursory glance looks utterly fascinating and very well done.  Zimmer recapitulates figure 1, which sums it all up, or to quote Carl:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&amp;quot;Each lineage of venomous animals became deadly on its own, independent of all the others. And yet, in the end, their venoms echo each other&lt;b&gt;...&lt;/b&gt; These results show that there are a limited number of ways to kill your victim quickly. No matter what genes you borrow for the evolution of venom, they will end up very similar to other venoms.&amp;quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nytimes.com/2005/11/22/science/22venom.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Another Zimmer piece&lt;/a&gt; specifically points out research purporting to show that snake venom genes are much older than snakes, maybe 200 million years old.  That gets around but doesn't quite answer your question.  &lt;a href=&quot;https://www.sciencedirect.com/science/article/pii/016372589290009O&quot; rel=&quot;nofollow noreferrer&quot;&gt;An older review&lt;/a&gt; tried to coalesce things (as best as he could in '92), spending time focusing on insectivora and dealing with mammals.  The theory is that while venom is an excellent advantage, it requires a significant investment and is often slow-working.  In a world with sharp teeth capable of tearing, venom may not be necessary.  Mammals, for example, might evolve to &lt;em&gt;not&lt;/em&gt; use venom, as it may not be suitable for their high daily energy demands.  The pdf linked above briefly touches on the concept of &amp;quot;reverse recruitment,&amp;quot; where venom genes may be usefully re-purposed for other biological processes.&lt;/p&gt;&#xA;&lt;h2&gt;Reference:&lt;/h2&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://doi.org/10.1016/j.tree.2012.10.020&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nicholas R. Casewell, Wolfgang Wüster, Freek J. Vonk, Robert A. Harrison, Bryan G. Fry. Complex cocktails: the evolutionary novelty of venoms. Trends in Ecology &amp;amp; Evolution&#xA;Volume 28, Issue 4, April 2013, Pages 219-229&#xA;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2021-05-20T11:38:02.177" LastActivityDate="2021-05-20T11:38:02.177" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="9523" PostTypeId="2" ParentId="9512" CreationDate="2013-07-30T16:03:26.557" Score="2" Body="&lt;p&gt;I may be simplifying this, but I think it's just a fancy schmancy way of referring to the electrical &quot;circuits&quot; found in the brain, in this case the cortex (overall, or more specifically motor, visual, etc., as the case may be).  &lt;a href=&quot;https://en.wikipedia.org/wiki/Connectomics&quot; rel=&quot;nofollow&quot;&gt;Connectomics&lt;/a&gt; tries to map the connections between neurons, mainly in the brain, building what is, in some sense, a circuit.  For some sentences in context:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jneurosci.org/content/32/31/10562.short&quot; rel=&quot;nofollow&quot;&gt;http://www.jneurosci.org/content/32/31/10562.short&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These results indicate a tight correlation between the effects of sensory drive and maturation on cortical neurons and provide a new set of cellular mechanisms engaged in the postnatal refinement of cortical circuits.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jneurosci.org/content/32/32/10982.short&quot; rel=&quot;nofollow&quot;&gt;http://www.jneurosci.org/content/32/32/10982.short&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...spontaneous cortical activity provides a recurring template of functional cortical circuits within the developing cortex and could contribute to the maturation of integrative connections between sensory and motor cortices.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-07-30T16:03:26.557" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9524" PostTypeId="1" AcceptedAnswerId="9532" CreationDate="2013-07-30T17:37:52.340" Score="3" ViewCount="224" Body="&lt;p&gt;Can the lipid-soluble hormones (like steroid hormones) go inside every cell, as their particular receptors are located in the cytoplasm or nucleus of the target cells? Is there anything special on the membrane of the target cells which enables the steroid hormone to know that it has to enter that particular type of cells and avoid others? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Peptide hormones function through cognate receptors located on the cell membrane of the target cell.)&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorDisplayName="user560" LastEditDate="2013-07-30T23:23:22.170" LastActivityDate="2013-07-30T23:42:33.587" Title="Steroid Hormone Signalling" Tags="&lt;endocrinology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9525" PostTypeId="2" ParentId="9496" CreationDate="2013-07-30T17:45:32.340" Score="0" Body="&lt;p&gt;Ok let me try to tackle this one - still could be off - let me know. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://lawr.ucdavis.edu/classes/ssc107/SSC107Syllabus/chapter2-00.pdf&quot; rel=&quot;nofollow&quot;&gt;book Chapter from UCDavis&lt;/a&gt; that is linked from your wikipedia page is a good reference I think. Overall the term 'water potential' will try to estimate an energy function that describes the behavior of water in a chemo-mechanical sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\Psi_{total} = \Psi_{reference} + \Psi_{solute} + \Psi_{pressure} + \Psi_{gravitational} + \Psi_{humidity} + \Psi_{matrix}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It looks a lot like a Hamiltonian expression of total energy that tries to see the water as a fluid.  The water potential is not the same as an energy equation for &lt;a href=&quot;http://en.wikipedia.org/wiki/Hamiltonian_fluid_mechanics&quot; rel=&quot;nofollow&quot;&gt;fluid dynamics&lt;/a&gt; which tries to understand the motion of a body of liquid and does not typically take into consideration chemical changes like solute in the behavior. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So first we are looking at a set of behaviors that the fluid experiences.  some of them treat the fluid as a body ( pressure, gravitational) others look at the potential for evaporation or diffusion (solute and humidity to some degree).  wetting of surfaces and surface tension (matrix).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The water potential is an equation broken down into a set of measurable or approximately measurable energy terms.  But like a lot of Energy equations, when  you are looking at a biological system, it is more often qualitative than a quantitated entity.  The general observation that surface tension decreases when temperature goes up, or when the solutes have higher concentration is used to make arguments of the mechanism of say physiology &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally speaking looking at the magnitudes of the various terms you can see how influential they are and then try to focus the hypothesis into a test that can make a distinction about the mechanism with specific measurements.  The actual overall measurement of a water potential or &lt;em&gt;any&lt;/em&gt; total energy is almost always intractable.  The difference in energy is what you might be able to measure, but in the case of the water potential, the measurement will usually be an observation, with some uncertainty that water is moving from point A to B and not elsewhere.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take a look at &lt;a href=&quot;http://www.plantphysiol.org/content/154/3/1254.full&quot; rel=&quot;nofollow&quot;&gt;this paper describing Drought Stress in Arabidopsis&lt;/a&gt;.  The water potential is cited as a critical element of drought response - and of course it should be.  But all this work here, with all the proteins acting to change the physiology of the cell, adjust the chemical potential (and therefore the osmotic potential) of the cell membrane, its hard to imagine how measuring a root system at all points would be possible. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Physical properties of the cell wall play a crucial role in the response of plants to water deficit (Bacon, 1999). Transcriptome analysis of pDr showed the repression of many expansin genes (Bray, 2004), while mild osmotic stress revealed the induction of expansin genes (Skirycz et al., 2010). Cell expansion in response to drought was characterized in the maize (Zea mays) root system as an adaptation to low water potential (Wu and Cosgrove, 2000). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="107" LastEditDate="2013-07-30T20:57:48.717" LastActivityDate="2013-07-30T20:57:48.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9526" PostTypeId="1" CreationDate="2013-07-30T17:46:47.917" Score="1" ViewCount="345" Body="&lt;p&gt;I've been debating this topic with a friend of mine and we can't get to a common answer. She argues that we don't descend from any Chimpanzee or Orangutan because, if we did, they would also have the cognitive thinking ability that we have. I am arguing that a high protein diet allowed the first humans to have the possibility to develop a higher memory, intelligence and other mental procedures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But after all, what would be the real origin of the intelligence? And if animals do have intelligence too, why isn't theirs as advanced as us.&lt;/p&gt;&#xA;" OwnerUserId="4138" LastEditorUserId="107" LastEditDate="2013-07-30T18:13:01.800" LastActivityDate="2015-12-27T02:20:48.017" Title="Origin of human intelligence and thought" Tags="&lt;evolution&gt;&lt;intelligence&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9527" PostTypeId="2" ParentId="9521" CreationDate="2013-07-30T21:47:19.390" Score="3" Body="&lt;p&gt;Transcription rates are &lt;em&gt;very&lt;/em&gt; context dependent. This shouldn't surprise you, since the same genes aren't expressed in your lungs and your eyes. They're also very environment dependent, this shouldn't surprise you either, since it's pretty obvious every organism is going to respond to temperature, their current nutritional state and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in order to define promoter strength, you'd first need to define the exact conditions under which you're measuring it, including the exact strain you're measuring it in. Because if you get any of those even slightly different you're going to get a different answer. Doing this might get you a consistent number but you're abstracting away the most important parts of differences in transcription anyway: how it varies between cells and contexts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, even if got past these hurdles you'd not have a particularly useful answer anyway since the rate of transcription is only a small part of the whole process. Why not consider mRNA durability, or rates of translation, or protein durability? What matters very much depends on what you're considering.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-07-30T21:47:19.390" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9529" PostTypeId="2" ParentId="9517" CreationDate="2013-07-30T22:04:38.217" Score="5" Body="&lt;p&gt;Old answer:&lt;/p&gt;&#xA;&lt;p&gt;Venom production is a &amp;quot;hard&amp;quot; adaptation to achieve**. So it is conceivable that simpler organisms had enough evolutionary time to get the adequate mutations for this to happen, which would explain why venom is almost absent (I know only of a platypus as being poisonous) in mammals and birds, and seemingly abundant in fishes, amphibians (such dart frogs) or reptilians.&lt;/p&gt;&#xA;&lt;p&gt;Also, as I understand there should be great selective pressure and mutation in simpler organisms is more likely to produce viable offspring than in more complex ones, which can be a contributing factor.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;**UPDATE:&lt;/p&gt;&#xA;&lt;p&gt;It has come to my attention that the answer I gave is not exactly correct. Upon investigating venomous mammals many more came up (not only platypus - male platypus to be more precise),  such as vampire bats, solenodons, many types of shrews (thanks @releseabe), moles and even primates (the slow loris , being the possible single candidate)&lt;/p&gt;&#xA;&lt;p&gt;There are no birds know to be venomous, but some (such as the &lt;a href=&quot;https://www.birdsofeden.co.za/meet-pitohui-ifrita-and-rufous-the-most-poisonous-birds-on-earth_article_op_view_id_706&quot; rel=&quot;nofollow noreferrer&quot;&gt;pitohui, the ifrita and the roufous&lt;/a&gt;) can be toxic to eat.&lt;/p&gt;&#xA;&lt;p&gt;My initial belief that toxicity is hard to achieve (this is hardly my area of expertise, and perhaps I should have refrained from answering something incomplete), does not seem to be really substantiated by literature, where lots of different organisms seem to have developed toxic/venomous adaptations.&lt;/p&gt;&#xA;&lt;p&gt;Maybe it should be noted that many of these animals have evolved poisonous glands from salivary glands/sudoriferous glands and that they are described as presenting convergent evolution. Another caveat is also that most(all?) poisonous birds have Batrachotoxins that comes from their diet (which they concentrate on their skin and feathers), not something they produce themselves and are not as potent as the ones produced by dart-frogs. In this sense they are maybe less toxic than other animals, and the intensity of this effect may be related to co-evolution of those organisms and their prey/predators.&lt;/p&gt;&#xA;&lt;p&gt;It's also worth mentioning that the slow loris, while considered venomous, has the poison from its gland that resembles a cat salivary allergen, and maybe would be better described as allergy inducing, rather than a poison, or perhaps cats could be considered venomous (my opinion, hardly worth anything). Another possibility is that the substances used in marking territory are the same and eliciting allergy is an unintended consequence (from the paper: &amp;quot;Rather than possessing a brachial gland like the loris, small cats directly add salivary allergen proteins to inanimate objects (... ) The idea that species recognition systems share a close relationship with immune recognition&amp;quot;).&lt;/p&gt;&#xA;&lt;p&gt;My opinions about toxic and venomous animals changed as I was reviewing this subject and, as I view it now, it is a property that is ubiquitous on many different branches of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Arrow_poison&quot; rel=&quot;nofollow noreferrer&quot;&gt;tree of life&lt;/a&gt; .&lt;/p&gt;&#xA;&lt;p&gt;Wikipedia link about venomous mammals. it is not very good to reference because people may change it at some point and the information to which I am refering would no longer be there, but it is strongly peer reviewed &lt;a href=&quot;https://en.wikipedia.org/wiki/Venomous_mammal&quot; rel=&quot;nofollow noreferrer&quot;&gt;see here&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;shamelessly stolen from wikipedia about slow loris venom characterisation &lt;a href=&quot;https://www.webcitation.org/5ve55eWIW?url=http://www.venomdoc.com/venomdoc/Mammals_files/slow%20loris%20chapter.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Talking Defensively: A Dual Usefor the Brachial Gland Exudate of Slowand Pygmy LorisesLee R. Hagey, Bryan G. Fry, and Helena Fitch-Snyder&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;pitohui: &lt;a href=&quot;https://science.sciencemag.org/content/258/5083/799&quot; rel=&quot;nofollow noreferrer&quot;&gt;    JP Dumbacher, BM Beehler, TF Spande, HM Garraffo, JW Daly. Homobatrachotoxin in the genus Pitohui: chemical defense in birds?&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;slow loris paper: &lt;a href=&quot;https://jvat.biomedcentral.com/articles/10.1186/1678-9199-19-21&quot; rel=&quot;nofollow noreferrer&quot;&gt; Nekaris, K. Anne-Isola, Richard S. Moore, E. Johanna Rode, and Bryan G. Fry. 2013. “Mad, Bad and Dangerous to Know: The Biochemistry, Ecology and Evolution of Slow Loris Venom.” Journal of Venomous Animals and Toxins Including Tropical Diseases 19 (1): 21. https://doi.org/10.1186/1678-9199-19-21.&#xA;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4036" LastEditorUserId="4036" LastEditDate="2020-07-10T17:00:11.200" LastActivityDate="2020-07-10T17:00:11.200" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="9531" PostTypeId="2" ParentId="8449" CreationDate="2013-07-30T22:26:28.977" Score="0" Body="&lt;p&gt;AndroidPenguin and mgkrebbs both gave excellent answers to this. There are currently several ideas about the first life on Earth. Data for these methods are pretty useless because we can argue for what is the most probable and what can be modeled in the lab, but we can't (as yet) look for any fossil remains of molecules to see what really happened.&#xA;One of the most satisfying hypotheses is that protocells and self-replicating molecules (like RNA) probably came about independently, but in the same location. If the self-replicating molecule found a way to hide out in the protocell, this might be the beginning of something like what we call life.&#xA;A good talk on this topic is &lt;a href=&quot;http://www.ted.com/talks/martin_hanczyc_the_line_between_life_and_not_life.html&quot; rel=&quot;nofollow&quot;&gt;Martin Hanczyc's TED talk&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4139" LastActivityDate="2013-07-30T22:26:28.977" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9532" PostTypeId="2" ParentId="9524" CreationDate="2013-07-30T23:42:33.587" Score="4" Body="&lt;p&gt;Note: Since my area of expertise is with peptide hormones, I will offer a partial answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Steroid hormones are carried through the circulation by binding to globular proteins. When these hormones are released from binding proteins, the classical route of action is by free diffusion through the cell membrane. This diffusion is due to their aromatic structure. You rightly point out that the classical receptors of these hormones are found in the cytoplasm or nucleus. For example, &lt;a href=&quot;http://mend.endojournals.org/content/19/4/833.full&quot; rel=&quot;nofollow&quot;&gt;estrogen signalling&lt;/a&gt; as a classic signalling template which has genomic (DNA) and non-genomic (protein) targets to exert its effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Non-canonical signalling can occur through at least one G-protein coupled receptor (GPCR). Unlike most GPCR's which are localized to the cell membrane, &lt;a href=&quot;http://www.nature.com/nrd/journal/v3/n1/full/nrd1283.html&quot; rel=&quot;nofollow&quot;&gt;GPR30&lt;/a&gt; appears to be localized to the endoplasmic reticulum, which means steroid signalling still occurs through canonical means and also this newer pathway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then again, there are also steroid effects that modulate ion channels, for example GABA receptors. These are not specific receptors where only a steroid hormone can have an effect, yet they can activate or inhibit the effects (along with other drugs).&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-07-30T23:42:33.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9533" PostTypeId="2" ParentId="9512" CreationDate="2013-07-31T00:13:48.703" Score="4" Body="&lt;p&gt;The term &quot;cortical circuit&quot; refers to the generalization that the neocortex is a uniform structure. For the most part, the outer sheet of the brain (the neocortex) is the same structure of neurons all the way around the brain.  It consists of the canonical &lt;a href=&quot;http://en.wikipedia.org/wiki/Cerebral_cortex#Layered_structure&quot; rel=&quot;nofollow&quot;&gt;six layers&lt;/a&gt; and it generally looks something like &lt;a href=&quot;http://origin-ars.els-cdn.com/content/image/1-s2.0-S095943881100081X-gr2.jpg&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;.  Different research will emphasize different aspects of the circuit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, it's quite an interesting evolutionary step for mammals.  The neocortex.. or &quot;associative cortex&quot; as it's sometimes called... is a very dexterous structure.  Someone born without sight will still make use of their occipital lobe to process nonvisual sensations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, as a I qualified above, it's not strictly true that the neocortex is uniform all the way around; there are exceptions.&lt;/p&gt;&#xA;" OwnerUserId="1853" LastActivityDate="2013-07-31T00:13:48.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9534" PostTypeId="2" ParentId="8425" CreationDate="2013-07-31T02:05:49.547" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://books.google.com/books?id=xqG22Ah3Hx4C&amp;amp;lpg=PA76&amp;amp;dq=%22Schoon%27s%20Hard%20Shell%22&amp;amp;pg=PA76#v=onepage&amp;amp;q=%22Schoon%27s%20Hard%20Shell%22&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Goldman surmises&lt;/a&gt; that Schoon's Hard Shell is a variant of the Bender, so would have been bred from the Surprise, Irondequoit, and Tip Top, all of which were from the Sill's Hybrid.&lt;/p&gt;&#xA;&lt;p&gt;In that sense, I suppose it's a hybrid. I'm guessing that you're asking because you want to know if you can save the seed; that is, if Schoon's Hard Shell will breed true or will lose its characters in subsequent generations.&lt;/p&gt;&#xA;&lt;p&gt;I can't find any specific detail on that, but given that &lt;a href=&quot;http://www.seedsavers.org/onlinestore/melon/Melon-Schoons-Hard-Shell.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;it's sold by Seed Savers Exchange&lt;/a&gt;, I'd guess that it is a good candidate for seed saving, as long as you make sure it's not crossing with related species in your garden. &lt;a href=&quot;http://books.google.com/books?id=N08guuBXT5gC&amp;amp;lpg=PP1&amp;amp;dq=%22seed%20to%20seed%22&amp;amp;pg=PA103#v=onepage&amp;amp;q=%22cucumis%22&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Seed to Seed&lt;/a&gt; has detailed info on melon seed saving.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://books.google.com/books?id=xqG22Ah3Hx4C&amp;amp;lpg=PA76&amp;amp;dq=%22Schoon%27s%20Hard%20Shell%22&amp;amp;pg=PA76#v=onepage&amp;amp;q=%22Schoon%27s%20Hard%20Shell%22&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Goldman A&lt;/strong&gt;. 2002. Melons. Artisan Books (p. 76)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://books.google.com/books?id=N08guuBXT5gC&amp;amp;lpg=PP1&amp;amp;dq=%22seed%20to%20seed%22&amp;amp;pg=PA103#v=onepage&amp;amp;q=%22cucumis%22&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Whealy K&lt;/strong&gt;. 2012. Seed to Seed. Chelsea Green Publishing (p. 103)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-08-30T05:50:44.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9535" PostTypeId="2" ParentId="9526" CreationDate="2013-07-31T02:48:41.200" Score="1" Body="&lt;p&gt;How is &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;we don't descend from any Chimpanzee or Orangutan because, if we did, they would also have the cognitive thinking ability that we have&quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;not equivalent to&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;We are not related to the chimpanzee or orangutan because, if we did, they would also have [the same amount of body hair]/[the same sized mouths]/[the same muscular strength] that we have&quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any related species are going to differ in some respects (otherwise they would not be different species, after all), and it is plain to see that intelligence is one of the ways in which species can differ.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Regardless of that&lt;/strong&gt; (if your friend thinks intelligence is special in a way that hairiness is not), you can make your argument even while sticking to talking about intelligence, and there is &lt;em&gt;no need to go into the reasons for changes&lt;/em&gt; (increases) in intelligence to see that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To make the point with your friend, it might be best to point to two different animals that&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;she recognizes as related, and that&lt;/li&gt;&#xA;&lt;li&gt;she &lt;em&gt;also&lt;/em&gt; recognizes as having different levels of &quot;cognitive thinking ability&quot;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In light of such an example, her argument falls flat (unless she further considers only &lt;em&gt;human&lt;/em&gt; thinking ability special, in which case you will have a harder time!)&lt;/p&gt;&#xA;" OwnerUserId="3986" LastEditorUserId="3986" LastEditDate="2013-07-31T02:59:26.310" LastActivityDate="2013-07-31T02:59:26.310" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="9536" PostTypeId="2" ParentId="9418" CreationDate="2013-07-31T03:41:39.040" Score="1" Body="&lt;p&gt;It is important to first remember that to do anything useful, the sequence of the amino acids in the protein must be exact. For example, sickle-cell anaemia is caused because one amino acid in a haemoglobin protein is incorrect. Because of this, peptide synthesis involves rather complex chemistry in order to ensure that amino acids are added in the correct order and number, and is only effect up to a chain of a few dozen amino acids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now it is possible to produce peptides of various lengths in a cell-free extract, which basically involves taking the cytosol out of cells (with all the ribosomes, tRNA's, and other factors therein) and adding the mRNA template to be translated and an ATP source. This way, a peptide can be prepared by using the cell's own machinery for protein synthesis without actually needing a viable cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remember also that even if it were possible to chemically synthesize a correct peptide sequence, the protein would still need to fold into a correct 3-dimensional structure to work properly, which in some cases is impossible for any artificial method currently available.&lt;/p&gt;&#xA;" OwnerUserId="4140" LastActivityDate="2013-07-31T03:41:39.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9537" PostTypeId="1" CreationDate="2013-07-31T03:56:34.713" Score="2" ViewCount="53" Body="&lt;p&gt;I am interested in using the CI and Mnt proteins as well as their respective promoters (pR and Pmnt) within the same synthetic system, but am concerned as to their similarity and potential crosstalk. A quick search of the literature yielded no results and a Multalin did show some significant sequence homology (although Mnt forms a homodimer while CI does not).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/M6kGK.png&quot; alt=&quot;CI and Mnt Multalin&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Boeio.png&quot; alt=&quot;pR and Pmnt Multalin&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sequences: &lt;a href=&quot;http://parts.igem.org/wiki/index.php?title=Part:BBa_K228003&quot; rel=&quot;nofollow noreferrer&quot;&gt;CI and pR&lt;/a&gt;, &lt;a href=&quot;http://parts.igem.org/Part:BBa_C0072&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mnt repressor&lt;/a&gt; and &lt;a href=&quot;http://parts.igem.org/Part:BBa_R0073&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mnt promoter&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Has it ever been reported that the CI or Mnt repressor exhibit crosstalk on the pR and Pmnt promoters?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2014-11-20T14:13:39.847" Title="Do the phage repressors CI and Mnt exhibit crosstalk?" Tags="&lt;gene-expression&gt;&lt;synthetic-biology&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9538" PostTypeId="2" ParentId="9027" CreationDate="2013-07-31T04:11:50.857" Score="2" Body="&lt;p&gt;Actually, the so-called osmolarity of a solution is only determined by the concentration and number of dissociating species in the solute, and is irrespective of the chemical composition of the solute. This is an example of what is known as a &lt;em&gt;colligative property&lt;/em&gt; in chemistry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The van't Hoff equation gives the osmotic pressure exhibited by a solution:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P = icRT&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where P is the osmotic pressure, i is the coefficient associated with the number of dissociating units in the solute, c is the molar concentration of the solute, R is the universal gas constant, and T is the absolute temperature. A nonionic species, such as glucose, would have a value of 'i' close to one as the molecule does not dissociate in solution, while NaCl in relatively dilute concentrations should have an 'i' value close to 2, as it dissociates into sodium and chloride ions in solution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus in the case of the two solutions on opposite sides of the semipermeable membrane as you described, water would flow from the region of lower osmolarity to the region of higher osmolarity, until the osmotic pressure on both sides of the membrane come to equilibrium (due to the changes in concentration of the solutes by the net water movement).&lt;/p&gt;&#xA;" OwnerUserId="4140" LastActivityDate="2013-07-31T04:11:50.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9539" PostTypeId="2" ParentId="9206" CreationDate="2013-07-31T06:55:36.253" Score="2" Body="&lt;p&gt;I hope I've interpreted your question properly... It's an interesting question, but I think it's important to remember that evolution doesn't act on the two sexes separately. Sterile males might evolve and be maintained simply because they're good for their sisters or mothers. Sometimes genes that are advantageous for one sex are linked with genes that are disadvantageous for the other sex, leading to maladaptative traits in one sex. And of course, individuals don't necessarily forego opportunities willingly. If subordinates that attempt to mate are killed by the dominant individuals, then that trait is not advantageous. They'd be better advised to be altruistic and help their relatives, rather than be selfish and be killed (thereby depriving their colony of a worker). This would lead to selection for sterility.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also worth noting that while haploidy makes it easier for kin selection to evolve by increasing relatedness, it's not crucial. It all depends on the relative costs and benefits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In these eusocial situations, nothing really makes sense until you summed the fitness of the whole lineage, not just one caste or one sex or one individual.&lt;/p&gt;&#xA;" OwnerUserId="4116" LastActivityDate="2013-07-31T06:55:36.253" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="9540" PostTypeId="5" CreationDate="2013-07-31T08:45:00.893" Score="0" Body="&lt;p&gt;Trait adaptations contribute to the fitness and survival of individuals and develop in response to the current environment an individual finds itself within.  It is important to remember that not all traits are adaptive. Users may wish to see the question &lt;a href=&quot;http://biology.stackexchange.com/questions/35532/why-do-some-bad-traits-evolve-and-good-ones-dont&quot;&gt;&lt;em&gt;Why do some bad traits evolve, and good ones don't?&lt;/em&gt;&lt;/a&gt; and meta before asking their question.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-03-23T11:16:23.797" LastActivityDate="2016-03-23T11:16:23.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9541" PostTypeId="4" CreationDate="2013-07-31T08:45:00.893" Score="0" Body="Adaptation refers to both the current state of being adapted and to the dynamic evolutionary process that leads to the adaptation." OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-31T13:10:53.867" LastActivityDate="2013-07-31T13:10:53.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9542" PostTypeId="5" CreationDate="2013-07-31T08:47:24.467" Score="0" Body="&lt;p&gt;Altruism refers to behaviour by an individual that increases the fitness of another individual while decreasing the fitness of the actor. Possible explanations for altruism have been suggested (but continue to be highly debated) and include group selection, kin selection, vested interests, and reciprocity.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-31T13:10:56.337" LastActivityDate="2013-07-31T13:10:56.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9543" PostTypeId="4" CreationDate="2013-07-31T08:47:24.467" Score="0" Body="Altruism refers to behaviour by an individual that increases the fitness of another individual while decreasing the fitness of the actor." OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-31T13:10:28.453" LastActivityDate="2013-07-31T13:10:28.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9544" PostTypeId="5" CreationDate="2013-07-31T08:51:13.530" Score="0" Body="&lt;p&gt;The science of humanity. It examines the biological and social factors that have affected the evolution of humans and other primates, and that generate, maintain or change contemporary genetic and physiological variation.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-31T13:10:13.193" LastActivityDate="2013-07-31T13:10:13.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9545" PostTypeId="4" CreationDate="2013-07-31T08:51:13.530" Score="0" Body="The science of humanity. In a biological sense anthropology focusses on humans and non-human primates, and their evolutionary, biological, and demographic attributes." OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-31T13:10:33.913" LastActivityDate="2013-07-31T13:10:33.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9546" PostTypeId="5" CreationDate="2013-07-31T08:52:58.600" Score="0" Body="" OwnerUserId="1590" LastEditorUserId="4101" LastEditDate="2013-10-31T19:26:08.110" LastActivityDate="2013-10-31T19:26:08.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9547" PostTypeId="4" CreationDate="2013-07-31T08:52:58.600" Score="0" Body="Questions looking for clarifications or definitions of biological terminology." OwnerUserId="1590" LastEditorUserId="4101" LastEditDate="2013-10-31T19:26:08.110" LastActivityDate="2013-10-31T19:26:08.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9548" PostTypeId="5" CreationDate="2013-07-31T08:56:29.490" Score="0" Body="&lt;p&gt;This field studies the evolution of developmental processes of different organisms by studying the ancestral relationship between them. Focusses include the origin and evolution of embryonic development, how modifications of development and developmental processes lead to the production of novel features, the role of developmental plasticity in evolution and, how ecology impacts development and evolutionary change.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-31T13:10:59.043" LastActivityDate="2013-07-31T13:10:59.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9549" PostTypeId="4" CreationDate="2013-07-31T08:56:29.490" Score="0" Body="The study of evolutionary developmental biology." OwnerUserId="1590" LastEditorUserId="107" LastEditDate="2013-07-31T13:10:49.597" LastActivityDate="2013-07-31T13:10:49.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9550" PostTypeId="1" CreationDate="2013-07-31T10:52:17.507" Score="1" ViewCount="103" Body="&lt;p&gt;I'm learning about antibodies. As I understand it, antibodies detect stranger cells/bacterial/viruses by the molecules present in their membranes. In cancer cells, the cancer cell have produce some unknown protein, so why antibody cannot detect that molecule and kill them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it that the cancer cell is surrounded by a normal cell? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is the protein it produces is not obvious in the cell membrane? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or that the protein can bypass antibody? if so, why? &lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="948" LastEditDate="2013-07-31T14:34:56.430" LastActivityDate="2013-07-31T14:34:56.430" Title="The role of antibodies interacting with cancer" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;cancer&gt;&lt;antibody&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9551" PostTypeId="2" ParentId="9425" CreationDate="2013-07-31T10:55:23.443" Score="0" Body="&lt;p&gt;To measure the kinetic parameters of oxidases you could also look into measuring the oxygen concentration directly. Oxygen sensors are much more common than H2O2 sensors, and I know small setups (1 ml samples) based on a fluorescent dye based probe are available. &lt;/p&gt;&#xA;" OwnerUserId="4142" LastActivityDate="2013-07-31T10:55:23.443" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9552" PostTypeId="2" ParentId="9550" CreationDate="2013-07-31T11:27:12.877" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.research.uky.edu/odyssey/fall99/cancerkllers.html&quot; rel=&quot;nofollow&quot;&gt;This article on the University of Kentucky website&lt;/a&gt; is pretty good, it seems the cancer cells hide because they do not express CD80, a co-stimulating molecule. Co-stimulating molecules are often necessary for an effective immune response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a big part of the article and I think they do a good job of explaining it so I'll just quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;People once thought that cancer occurred because of a weakness in the&#xA;  body's immune system,&quot; says Yannelli, &quot;but we have known for years&#xA;  that overall that is not the case. The immune system in cancer&#xA;  patients actually works quite well. Otherwise, they could not survive&#xA;  the disease for long periods of time nor could they fight off other&#xA;  viruses, which they routinely do. The problem is not that the immune&#xA;  system doesn't work; it is that the immune system doesn't recognize&#xA;  the tumor.&quot;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;According to Yannelli, for the body's defense system to work properly,&#xA;  key antigens must be presented in a specific way to lymphocytes, the&#xA;  cellular mediators of the immune system, which then kill the cancerous&#xA;  cells. Normally, antigens are tipped off by co-stimulating molecules.&#xA;  When the co-stimulating molecules are not present, the immune system&#xA;  does not &quot;see&quot; the cancer cell, and therefore does not act to destroy&#xA;  it.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Scientists have discovered that lymphocytes have very narrow job&#xA;  descriptions, each one designed to attack only a specific molecule.&#xA;  The researchers have also discovered a wide range of co-stimulating&#xA;  molecules. A critical co-simulating molecule is CD80. Because cancer&#xA;  cells do not express CD80, they are invisible to the lymphocytes&#xA;  responsible for destroying them.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8702435&quot; rel=&quot;nofollow&quot;&gt;This paper has more on the function and mechanism of CD80.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks to @Nico for pointing out that not all cancers are the same so the generalization discussed in this answer may not be true of all cancers.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-07-31T12:10:41.823" LastActivityDate="2013-07-31T12:10:41.823" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9553" PostTypeId="2" ParentId="9550" CreationDate="2013-07-31T12:20:35.077" Score="1" Body="&lt;p&gt;In general the immune system sees the world in very simplistic terms: Self vs Non-Self. Ideally, threats to the health of the animal are all non-self and can be attacked strongly. Whereas self cells and proteins are tolerated - effectively invisible to the immune system. Cancer is a particularly insidious disease because it arises, not from the outside world, but from subtle changes within the host's own cells. Therefore, cancer cells are starting as 100% self, but can adopt changes that make them more different over time.&#xA;A good review of this interaction between cancer cells and the immune system can be found &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23577028&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. &#xA;A second aspect of your question that is important is how antibodies are made and what they are capable of 'seeing'. I wrote a short essay about B cells, the cells that produce antibodies, and how they are activated on &lt;a href=&quot;http://downhousesoftware.wordpress.com/2013/05/12/b-cell-activation-the-basics/&quot; rel=&quot;nofollow&quot;&gt;my blog&lt;/a&gt;. That might be a good resource to check for you - I also link to one or two other articles there. Briefly, B cells can only 'see' cellular antigens that are either expressed on the cell surface or secreted. Although some cancer cells alter these types of molecules, many more are part of the internal workings of the cell and therefore invisible to antibodies. For this reason, many oncologists focus on T cell responses, which are capable of detecting non-native internal antigens.&lt;/p&gt;&#xA;" OwnerUserId="4139" LastActivityDate="2013-07-31T12:20:35.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9554" PostTypeId="2" ParentId="9500" CreationDate="2013-07-31T12:26:32.310" Score="3" Body="&lt;p&gt;In addition to the answers stated here, it is also important to remember that we, humans, are more guided by vision than many other animals. Therefore, the idea of separating an animal from a potential mate with glass would also inhibit other important mate selection criteria that other organisms use (calls, pheromones, nest tending, etc.).&lt;/p&gt;&#xA;" OwnerUserId="4139" LastActivityDate="2013-07-31T12:26:32.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9555" PostTypeId="2" ParentId="9389" CreationDate="2013-07-31T13:07:37.407" Score="2" Body="&lt;p&gt;This answer is building on the &lt;a href=&quot;https://biology.stackexchange.com/questions/9389/is-it-possible-to-make-humans-extinct-artificially/9403#9403&quot;&gt;answer&lt;/a&gt; by @BrandonInvergo and focusing on the &quot;..possible way...the entire human race can be killed without affecting the rest of the biosphere...&quot; part of your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No, it is impossible to remove humans without affecting the biosphere (barring some extremely made-up scifi scenario) because many species are adapted to us. It doesn't stop with the parasites and pathogens in Brandon's answer. Most obviously, the majority of all domesticated animals and plants will go extinct, and these number ~750 species (&lt;a href=&quot;http://www.soest.hawaii.edu/oceanography/zij/education/ocn201/fisheries.pdf&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Duarte et al. 2007. Rapid Domestication of Marine Species. Science 316(5823): 382-383&quot;&gt;Duarte et al 2007&lt;/a&gt;). A large number of other species (e.g. plants, insects, birds) are also adapted to man-made environments and many are likely to go extinct if humans disappear, and these effects will cascade into their respective ecosystems. Just look at what is happening to species adapted to traditional low-intensive pasturelands in e.g. Europe. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-07-31T13:07:37.407" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9556" PostTypeId="1" AcceptedAnswerId="16703" CreationDate="2013-07-31T14:50:15.560" Score="3" ViewCount="234" Body="&lt;p&gt;When recording change in allele frequency in diploid, bi-allelic, infinite and panmixic population we usually use this kind of equation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\delta_p = \frac{p * q *( p (w11 - w12) + q * (w12 - w22))}{\bar{w}}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\bar{w} = p^2 * w11 + 2*p*q*w12+q^2*w22$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\delta_p$ = change of $p$ (frequency of one of the allele) from one time step to another&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w11$ is the mean fitness of individuals of genotype 11. $p$ and $q$ are the allele frequencies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The only indicators for the fitness distribution is the arithmetic mean. Why don't we include other indicator of the probability distribution of fitness? The skew, the sd, the median for examples. Could you argue why we don't need to care about the probability distribution of fitness of individuals with genotypes 11 (for example)? In other words, why is the mean fitness (=w11) a sufficient statistics?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wouldn't be able to answer if one asks me:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Why don't you take the median instead of the arithmetic mean?&quot;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Why don't you care about the variance, the skew (or any other moment) of your distribution?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What if the traits were not countinuous but discrete (sex is a discrete trait for example)?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-07-31T16:52:53.497" LastActivityDate="2014-04-20T04:07:41.620" Title="Population genetics and the fitness probability distribution. Why is the arithmetic mean all we need?" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="9557" PostTypeId="2" ParentId="457" CreationDate="2013-07-31T15:12:51.013" Score="3" Body="&lt;p&gt;The tendency for mean height to be pushed upward is natural when you consider two facts&lt;br&gt;&#xA;(that so far have been left out here):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;With the higher costs to females in general for reproducing, they are the &quot;choosier&quot; gender, so &lt;strong&gt;when it comes to mate selection, females' preferences matter more&lt;/strong&gt;.  Therefore, a tendency for males to prefer shorter females (if that is even true) would not have an equal and opposite effect.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There is not a 1:1 ratio between males and females who pass on their genes.  The standard deviation on number of children is higher for males, and &lt;strong&gt;a higher proportion of males than females produce 0 offspring&lt;/strong&gt;, thus &quot;truncating part of the normal distribution&quot;, every generation, more for males than for females.  Again, even if there were just as much preference for short females by males as there is preference for tall males by females, there would &lt;em&gt;still&lt;/em&gt; be a trend upward in mean height.  This fact has more to do with the speed of the change rather than whether or not the change will happen, though.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Two facts that have been discussed already but not widely acknowledged here should be explicitly mentioned again:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Male and female height each influence height in both male and female offspring.  This matters because even if there were preference not for the male to be &lt;em&gt;too&lt;/em&gt; much taller than the female, this would not stop the trend upward in height because females would be constantly be trending upward in height.  Thus, &lt;strong&gt;females would not serve as any kind of &quot;anchor&quot; for height&lt;/strong&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Height changes are due to more than just genes (whose effects could &quot;top out&quot; in the absence of mutation, as kmm mentioned), but in any case mutation is not negligible for human height (as Marta Cz-C mentioned), so &lt;strong&gt;a lack of possible genotypes for the extreme height we are talking about is not an issue&lt;/strong&gt;.  Actually, this is obvious from the fact that there already are (fertile) people taller than the threshold mentioned in this question.&lt;br&gt;&#xA;(The only &lt;em&gt;real&lt;/em&gt; reasons for an upper limit on human height, which have not be brought up here, are nicely presented in this video: &lt;a href=&quot;http://www.youtube.com/watch?v=DkzQxw16G9w&quot; rel=&quot;nofollow&quot;&gt;How big can a person get?&lt;/a&gt;, and &lt;em&gt;those&lt;/em&gt; lead to a maximum height somewhere above the 213 cm (7 feet) we are talking about.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Some things that have been mentioned here, though true or possibly true, are not really relevant to the question:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;A limit on &lt;em&gt;how much&lt;/em&gt; taller the father is than the mother for the typical child (imposed by female or male preference) does not change the answer to the main question (direction of mean height change, if any), only the speed (&quot;in 'hundreds of years'&quot;).  (This follows from the &quot;anchor&quot; comment above.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The fact that there are many other factors than height for mate selection, and even that many of these factors are more important than height, also does not change the answer to the main question.  (That is unless the other factors which correlate with lower height put downward pressure on it.  I don't think anyone would argue this, but I will provide an example because I think it is interesting:  If shorter males were, on average, more intelligent than taller males, then even if females preferred taller males (intelligence being equal), if they also preferred more intelligent males then human height &lt;em&gt;could&lt;/em&gt; go down (while mean human intelligence goes up).)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Of course, generalizing all of this to humans in the present and in the future (switching language from &quot;males&quot; and &quot;females&quot; to &quot;men&quot; and &quot;women&quot;) is predicated on some assumptions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;that women, &lt;em&gt;particularly the ones who have children&lt;/em&gt;, do prefer and &lt;em&gt;get&lt;/em&gt; taller men.  This could fail to be the case in the face of competition from women who also prefer taller men but do not have children.  This could also change due to reversal of the preference for height &lt;em&gt;or&lt;/em&gt; due to increased preference for &lt;em&gt;other&lt;/em&gt; factors that correlate with lower height combined with a reduction in the lustre of male height for females.  As one example, the ever-decreasing importance of physical competition between males and the ever-increasing level of safety from unarmed attack in the modern world means that height (and other measures of strength) matters less and less.  As another example, the reduction in face-to-face workplace settings, which are no doubt at least partially responsible for taller men being paid more than shorter men, should lead to wealth (which is a factor on its own) being less of a correlate with height and therefore reduce selection for height.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;that the preferences of women will &lt;em&gt;continue&lt;/em&gt; to matter more than the preferences of men, for mate selection.  If women and men were completely rational actors, this one could &lt;em&gt;already&lt;/em&gt; have changed due to recent &lt;strong&gt;decreases in reproduction costs for females&lt;/strong&gt; (mostly due to &lt;strong&gt;medical&lt;/strong&gt; changes, such as lower death rate associated with pregnancy) and &lt;strong&gt;increases in reproduction costs for males&lt;/strong&gt; (mostly due to &lt;strong&gt;legal&lt;/strong&gt; changes, possibly to the point where the costs for males are &lt;em&gt;higher&lt;/em&gt; than for females).  The way women and men think and feel with regard to mate selection is very strongly biased toward the normal conditions in our evolutionary history, though (higher female investment), and are hard to act against.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3986" LastActivityDate="2013-07-31T15:12:51.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9558" PostTypeId="1" AcceptedAnswerId="9560" CreationDate="2013-07-31T17:28:10.667" Score="2" ViewCount="138" Body="&lt;p&gt;Is there a term I can use to refer collectively to both exons and introns? By collectively, I don't mean ligated as with an unprocessed transcription product. I'm just writing about exons and introns and getting frustrated that I keep on having to write &quot;exons and introns&quot;, wishing there was a more concise term I can use in the place of that phrase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, the term I am looking for would fill in the following blank perfectly.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The gene has 5 exons and 4 introns, so it has 9 &lt;strong&gt;&lt;em&gt;_&lt;/em&gt;____&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2013-08-01T01:57:54.260" LastActivityDate="2013-08-01T01:57:54.260" Title="Collective term for both exons and introns" Tags="&lt;molecular-genetics&gt;&lt;terminology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9560" PostTypeId="2" ParentId="9558" CreationDate="2013-07-31T18:16:25.570" Score="6" Body="&lt;p&gt;How about &quot;splicing fragments&quot;? It might be easier to refer to them according to the mechanism of production.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2013-07-31T18:16:25.570" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="9561" PostTypeId="2" ParentId="9331" CreationDate="2013-07-31T18:17:38.497" Score="0" Body="&lt;p&gt;Are you asking why it is difficult to tell whether a cell is homozygous or heterozygous? If so, this is usually a combination of sensitivity of the assay (rtPCR can be optimized for this purpose - at least, I've heard of people doing it). Another aspect of this is that even if the alleles code for different things (eye pigment or something), much of the gene may be similar enough that PCR primers are difficult to construct in a way that they distinguish between the two alleles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then again, sometimes you get lucky and there's an EcoRI site right in the middle of one allele, but not the other.&lt;/p&gt;&#xA;" OwnerUserId="4139" LastActivityDate="2013-07-31T18:17:38.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9562" PostTypeId="2" ParentId="1762" CreationDate="2013-07-31T18:28:13.787" Score="3" Body="&lt;p&gt;The main factors that affect leaf shape are water and light needs. The plant needs a certain area of leaf to provide enough energy to live, so smaller leaves means more leaves(grasses), as opposed to one enormous leaf like a lilypad. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally, as light intensity increases water needs increase along with it. A thicker stem with a smaller leaf can support enough water flux to keep a grass blade hydrated in full sun, whereas a big tropical plant in high humidity has low water needs and can therefore use a thin stem to support a big leaf.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would hypothesize that self-regulatory systems that affect leaf development as a function of available water and sunlight needs are responsible for the effect.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2013-07-31T18:28:13.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9563" PostTypeId="2" ParentId="9331" CreationDate="2013-07-31T18:42:56.620" Score="1" Body="&lt;p&gt;The difficulty of reading haplotypes 'directly' lies in the difficulty of reading any long sequence of DNA, and this is for technical reasons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Short DNA fragments are sequenced using &lt;a href=&quot;https://en.wikipedia.org/wiki/DNA_sequencing#Chain-termination_methods&quot; rel=&quot;nofollow&quot;&gt;a variety of methods&lt;/a&gt;. Gel electrophoresis can pull these fragments apart by length, but all the fragments have to be relatively close in size to get the accuracy needed to tell fragments that differ by one base pair apart. It's easy to separate a 16-bp segment from a 17bp segment easily, but it's much harder with a 516bp segment and a 517bp segment. Modern sequencing can sequence reads up to about 5kbp in length at a time. The 'reads' are then reassembled.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are next-generation methods(&lt;a href=&quot;https://en.wikipedia.org/wiki/Pyrosequencing&quot; rel=&quot;nofollow&quot;&gt;pyrosequencing&lt;/a&gt;, etc) that can read a long dna molecule one base at a time, but for practical reasons sequencing an entire chromosome this way is cost and time prohibitive. As a result, there are always going to be fragments that you need to reassemble computationally, no matter how the sequencing is done.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2013-07-31T18:42:56.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9564" PostTypeId="2" ParentId="9558" CreationDate="2013-07-31T19:22:28.977" Score="1" Body="&lt;p&gt;I think your best bet would be &lt;em&gt;transcript&lt;/em&gt;. &lt;em&gt;Gene&lt;/em&gt; is actually quite close but most of the current definitions include the promoter sequence in the gene so that is not restricted to introns and exons. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Transcripts, on the other hand, are all of a gene's sequence that is transcribed and consist exclusively of introns and exons (UTRs are also exons and are actually spliced in some cases). Note that I am using &lt;em&gt;transcript&lt;/em&gt; and not &lt;em&gt;mRNA&lt;/em&gt; since mature mRNAs do not of course contain introns. Immature ones do and transcript can apply.  &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-07-31T19:22:28.977" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9565" PostTypeId="2" ParentId="9506" CreationDate="2013-07-31T19:50:36.320" Score="14" Body="&lt;p&gt;Just to expand on @rg255's very good answer, you could make the same sort of claim using just about any characteristic that is more commonly found in mammals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Giving birth to live young is a characteristic of most (see the platypus below), if not all, mammals. Therefore, you could make the statement about external ears (also more common to mammals) using any other mammal specific body plan. For example:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The animals who have their 'TESTICLES' outside their body give birth to their young ones and the animals who have their 'TESTICLES' inside their body lay eggs.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am pretty sure you will find that this is as true as the statement about ears. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As in all other debates about this kind of thing, the &lt;a href=&quot;https://en.wikipedia.org/wiki/Platypus&quot; rel=&quot;nofollow noreferrer&quot;&gt;platypus&lt;/a&gt; comes along and complicates things. This beastie has no external ears (or external testicles for that matter), it has tiny ear slits instead and it lays eggs. So, even this extreme weirdo seems to follow the ears (or testicles) on the inside means eggs rule. However, it is a mammal, it produces milk that it will feed to its newly hatched young like all mammals (well, almost, it doesn't have teats and instead the young suck up their mother's milk through her spongy belly).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A more straightforward and well known example that directly contradicts the ears claim is the dolphin. Dolphin ears are small holes on the sides of their heads but they give birth to live young as do all sea mammals. In fact, I am pretty sure that all sea mammals lack external ears (and cetaceans at least also lack external testicles) but give birth to live young. So seals, sea lions, walruses etc also contradict the ears rule.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion, no it is not true that all animals with internal ears lay eggs.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2017-05-02T09:13:02.437" LastActivityDate="2017-05-02T09:13:02.437" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9566" PostTypeId="2" ParentId="7581" CreationDate="2013-07-31T20:13:16.277" Score="3" Body="&lt;p&gt;I think this would depend entirely on the diet of the host and donor mammal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming they are of similar size and diet, I don't see any reason why this wouldn't work. The gut tends to absorb more or less everything in the food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the diet of the two mammals differed significantly, I could see some problems with eating the correct foods. Herbivores with the significantly shorter carnivore gut would have trouble killing and eating things without carnivore teeth/claws/what have you, and the plants would not provide enough nutrition on their own. Rabbits, for instance, have a two-pass digestive system, so in order to use a rabbit gut the mammal would have to eat their own feces regularly. (Rabbits have digestive bacteria in their colon, but grass has to travel to the colon and then back 'upstream' to the absorptive part of the gut. So this is achieved by going around again.)&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2013-07-31T20:13:16.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9567" PostTypeId="2" ParentId="8936" CreationDate="2013-07-31T20:17:54.387" Score="1" Body="&lt;p&gt;In short: Not completely, but more than you would expect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The project to clone a mammoth considered using an adult female elephant as a surrogate mother, so in theory closely related species can do this.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2013-07-31T20:17:54.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9568" PostTypeId="2" ParentId="2919" CreationDate="2013-07-31T20:28:19.240" Score="4" Body="&lt;p&gt;The heart does have stem cells in it, and there is cell turnover in the heart, of about 1% per year. Which is much slower than your skin, but not nothing. This allows your heart to grow during your life, and remodel itself slightly to become stronger/more efficient when you get in shape.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heart can repair itself, when damaged it doesn't simply stay damaged. Unfortunately, the 'repair' leaves particularly useless scar tissue. After a heart attack, the dead muscle does repair itself, but very poorly. This 'scar' barely contracts, and isn't as strong as the heart wall around it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is mostly a function of the very specialized heart myocytes, and the evolutionary (relative) uselessness of being able to regenerate your heart after injury. In the wild, if your heart was injured, you were probably dead. &lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2013-07-31T20:28:19.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9569" PostTypeId="2" ParentId="7894" CreationDate="2013-07-31T20:31:46.690" Score="2" Body="&lt;p&gt;If the muscle is provided with adequate food and oxygen, the muscle can theoretically work indefinitely. However, microtearing when a muscle is stressed more than usual can over time damage the muscle. This is the mechanism by which you get larger, stronger muscles. Without rest, it's theoretically possible to simply destroy the muscle faster than it can be repaired.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2013-07-31T20:31:46.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9570" PostTypeId="1" AcceptedAnswerId="9571" CreationDate="2013-07-31T21:04:30.180" Score="7" ViewCount="4785" Body="&lt;p&gt;Given that mitochondria are evolutionarily closely related to bacteria, and antibiotics kill bacteria, why don't antibiotics also kill mitochondria?&lt;/p&gt;&#xA;" OwnerUserId="37" LastActivityDate="2013-07-31T22:11:43.630" Title="Why don't antibiotics affect mitochondria?" Tags="&lt;mitochondria&gt;&lt;antibiotics&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9571" PostTypeId="2" ParentId="9570" CreationDate="2013-07-31T22:11:43.630" Score="7" Body="&lt;p&gt;The short answer is, as you found, that mitochondria are wrapped in a double membrane and are thus harder to penetrate with antibiotics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The long answer is some of them do.  Good antibiotics target structures widely found on and conserved in bacteria that are not found in human bodies.  Some antibiotics are a little less specific and can indeed interact with other molecules.  The allergy to penicillin, for example, is caused by the immune system reacting to a &quot;novel&quot; protein formed when penicillin binds to the surface of red blood cells.  Some antibiotics can indeed harm mitochondria, but we tend not to use those and in fact wouldn't even call most of them antibiotics since we wouldn't use them because of their harmful effects.  &lt;a href=&quot;http://stm.sciencemag.org/content/5/192/192ra85&quot;&gt;Here&lt;/a&gt; is a very recent report looking at some of the anti-mitochondrial effects of some antibiotics.  To quote from the abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We show that clinically relevant doses of bactericidal antibiotics—quinolones, aminoglycosides, and β-lactams—cause mitochondrial dysfunction and ROS [reactive oxygen species] overproduction in mammalian cells. We demonstrate that these bactericidal antibiotic–induced effects lead to oxidative damage to DNA, proteins, and membrane lipids.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-07-31T22:11:43.630" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9572" PostTypeId="1" CreationDate="2013-07-31T23:15:02.433" Score="3" ViewCount="1654" Body="&lt;p&gt;This question is not for the squeamish. I was told that non-Kosher animals like pigs have a different anatomy in their neck compared to kosher animals like cows such that the &lt;a href=&quot;http://en.wikipedia.org/wiki/Shechita&quot; rel=&quot;nofollow&quot;&gt;Shechita method of religious slaughter&lt;/a&gt; (a very sharp knife held on the neck only by the weight of gravity rapidly going back and forth in a single cut that drains blood and results in an &quot;instant&quot; drop in blood pressure in the brain), while causing pain in the non-Kosher animals, doesn't cause pain in the Kosher animals. Is there such an anatomical difference and thus difference in pain?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(If this would be more on-topic at Skeptics.SE, let me know.)&lt;/p&gt;&#xA;" OwnerUserId="3920" LastEditorUserId="69" LastEditDate="2013-08-01T10:06:28.530" LastActivityDate="2013-11-21T03:43:22.333" Title="Is there a difference between pig and cow anatomy that makes religious slaughter of the latter less painful?" Tags="&lt;zoology&gt;&lt;mammals&gt;&lt;anatomy&gt;&lt;pain&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9573" PostTypeId="5" CreationDate="2013-08-01T03:17:24.650" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-08-01T03:17:24.650" LastActivityDate="2013-08-01T03:17:24.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9574" PostTypeId="4" CreationDate="2013-08-01T03:17:24.650" Score="0" Body="The timing of key events in an organism's lifetime, including development, reproduction and death." OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-08-01T07:00:04.797" LastActivityDate="2013-08-01T07:00:04.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9575" PostTypeId="2" ParentId="9473" CreationDate="2013-08-01T06:08:35.270" Score="1" Body="&lt;p&gt;Conventionally, a zygote is considered to be formed the moment that a spermatozoum, penetrates the cell membrane of the ovum and yields its genetic material into the ovum. Effectually, however, there is a lag between the instant of fertilization and the fusion of the male and female pronuclei. In mammals, the duration of this lag period is ~12 hours. There are also additional actions that must be completed before the first mitosis as in most mammals, including humans, the ovum is actually in the second metaphase of meiosis at the time of fertilization. &lt;/p&gt;&#xA;" OwnerUserId="4140" LastActivityDate="2013-08-01T06:08:35.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9576" PostTypeId="1" CreationDate="2013-08-01T07:21:54.010" Score="8" ViewCount="877" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1hKI1.jpg&quot; alt=&quot;Fearless goats&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you see in the picture goats (not only wild goats) are so fearless, but I never saw any sheep do this. What is the source of this difference in behavior? &lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="3952" LastEditDate="2013-08-02T13:57:54.833" LastActivityDate="2017-06-16T16:43:51.830" Title="Goats are so fearless but sheep are not. Is there any genetic difference responsible?" Tags="&lt;zoology&gt;&lt;taxonomy&gt;&lt;mammals&gt;&lt;behaviour&gt;&lt;phylogenetics&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9577" PostTypeId="2" ParentId="9576" CreationDate="2013-08-01T07:45:56.947" Score="30" Body="&lt;p&gt;&lt;strong&gt;1. Sheep &lt;em&gt;are&lt;/em&gt; fearless&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3SjWw.jpg&quot; alt=&quot;Bighorn Sheep by TwelveX&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. English common names are misleading when it comes to the genetic differences between goats and sheep&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You posted a picture of Mountain Goats (&lt;em&gt;Oreamnos americanus&lt;/em&gt;), which are a different genus than Domestic Goats (&lt;em&gt;Capra aegagrus&lt;/em&gt;). Both &lt;em&gt;Capra&lt;/em&gt; and &lt;em&gt;Oreamnos&lt;/em&gt; are members of the Subfamily Caprinae, as are Domestic Sheep (&lt;em&gt;Ovis aries&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within Caprinae, &lt;em&gt;Capra&lt;/em&gt; and &lt;em&gt;Ovis&lt;/em&gt; are actually &lt;strong&gt;more related to each other&lt;/strong&gt; than either one is to &lt;em&gt;Oreamnos&lt;/em&gt;, despite the confusing way that we parcel out English common names. &lt;em&gt;Oreamnos&lt;/em&gt; is, in fact, more closely related to the Musk Ox! (Here's &lt;a href=&quot;http://tolweb.org/Caprinae/51161&quot; rel=&quot;nofollow noreferrer&quot;&gt;the Tree of Life page that shows the phylogeny of Caprinae&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Domestic Sheep genus &lt;em&gt;Ovis&lt;/em&gt; also includes mountain species such as the Bighorn Sheep &lt;em&gt;Ovis canadensis&lt;/em&gt;, which is plenty fearless. See the Bighorn Sheep above, and in &lt;a href=&quot;http://www.robertweselmann.com/sheep_7989.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this incredible photo&lt;/a&gt;. For what it's worth, the Domestic Goat genus &lt;em&gt;Capra&lt;/em&gt; also includes cool mountain species, such as the Ibex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: the differences in behaviour between the domestic goat and sheep would be a combination of the initial differences between wild &lt;em&gt;Ovis&lt;/em&gt; and &lt;em&gt;Capra&lt;/em&gt; and the coevolutionary process of domestication; where humans shape niches to fit animals and animals to fit niches. It's possible that there has been more &lt;a href=&quot;https://books.google.com/books?id=wKO6GFaVpRAC&amp;amp;pg=PA78#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;neotenization in the domestication of sheep&lt;/a&gt;, in which individuals who show immature characteristics are successfully selected for. See also &lt;a href=&quot;https://biology.stackexchange.com/questions/1435/what-are-the-evolutionary-niches-differentiating-an-apple-from-a-pear&quot;&gt;this other question on apple and pear domestication&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;(Bighorn Sheep photo by &lt;a href=&quot;http://www.flickr.com/photos/twelvex/&quot; rel=&quot;nofollow noreferrer&quot;&gt;TwelveX&lt;/a&gt;, used under CC BY-NC-SA license.)&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2017-06-16T16:43:51.830" LastActivityDate="2017-06-16T16:43:51.830" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9578" PostTypeId="1" AcceptedAnswerId="9652" CreationDate="2013-08-01T10:57:36.857" Score="9" ViewCount="848" Body="&lt;p&gt;I am curious to learn what are the biological mechanisms that cause leaves of deciduous plants to change colour? What happens to the chlorophyll?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What environmental phenomena (temperature/air pressure/length of sunlight) are they responding to? &lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="3971" LastEditDate="2013-08-29T16:04:56.133" LastActivityDate="2013-08-29T16:04:56.133" Title="What biological processes cause leaves to change colours in Autumn?" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;life-history&gt;&lt;pigmentation&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9580" PostTypeId="1" AcceptedAnswerId="9581" CreationDate="2013-08-01T15:36:47.833" Score="1" ViewCount="686" Body="&lt;p&gt;Recently I found out that the common houseplant Pothos (Epipremnum aureum) is toxic to cats and dogs due to the presence of &quot;insoluble raphides.&quot; I have a lot of these plants around my house and my cat drinks water from the vase that they are in (I put drinking water into the vase that he always drinks from). He doesn't chew the Pothos leaves, he only drinks the water, is it still dangerous? I tried several times to give him water in an ordinary bowl, but he prefers the water that's associated with the Pothos plant, so I thought that maybe the roots of the plant excrete something nutritious (but I guess that's not the case, apparently...). &#xA;Is it harmful for an animal (cat) to drink water that has a Pothos plant immersed in it? &#xA;Also, my other cat &lt;em&gt;does&lt;/em&gt; chew on the Pothos leaves (he goes crazy for them). Is it possible to have immunity and not be affected by the toxic chemicals? I read that chewing is supposed to provoke stomach irritation, but I would think that if the cat that chews the leaves suffered from irritation he wouldn't keep getting excited about chewing the leaves...&lt;br&gt;&#xA;So what is going on? Many thanks!&lt;/p&gt;&#xA;" OwnerUserId="4150" LastEditorUserId="3952" LastEditDate="2013-08-01T15:57:13.573" LastActivityDate="2018-06-13T14:14:46.227" Title="Raphide toxicity in Pothos plant" Tags="&lt;biochemistry&gt;&lt;zoology&gt;&lt;nutrition&gt;&lt;botany&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9581" PostTypeId="2" ParentId="9580" CreationDate="2013-08-01T15:56:50.600" Score="2" Body="&lt;p&gt;Perhaps someone else can answer this with more certainty, but I'd guess that because raphides are essentially sharp crystals that cause irritation-related symptoms, rather than toxic chemicals in the way one might usually think of them, that drinking the water wouldn't pose a problem (actually, I suppose the word &quot;insoluble&quot; might be a clue here). Raphides are defence against herbivory, and &lt;em&gt;chewing&lt;/em&gt; raphide-containing leaves is what you want not to do (or not let your pets do).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://books.google.com/books?id=NgMX__L3q40C&amp;amp;lpg=PA881&amp;amp;ots=wryz4qWl8d&amp;amp;dq=%22insoluble%20raphides%22&amp;amp;pg=PA889#v=onepage&amp;amp;q=raphides&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Veterinary Toxicology p. 889&lt;/a&gt; has more info.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-08-01T16:02:17.953" LastActivityDate="2013-08-01T16:02:17.953" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9582" PostTypeId="2" ParentId="9576" CreationDate="2013-08-01T16:51:58.830" Score="12" Body="&lt;p&gt;You should also bear in mind that the fact that they are great climbers does not make them fearless. For example, if I were to find myself floating 500 meters above the ground, I would be terrified. The fact that birds do not appear to be scared in the same situation does not make them fearless, it just makes them fliers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, I am sure a fish would be terrified if forced to spend half an hour in a beach bar. I, on the other hand, would find it enjoyable and not scary at all. It does not mean I am fearless or brave. You can only be brave when you ignore your fears not when you have none. Since mountain goats are exquisitely suited to jumping around on sheer mountain cliffs, it probably causes them no more fear than visiting a beach bar would cause me. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-08-01T16:51:58.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9583" PostTypeId="1" AcceptedAnswerId="9585" CreationDate="2013-08-01T16:57:57.317" Score="3" ViewCount="606" Body="&lt;p&gt;I understand that DNA fragmentation is a molecular indicator of apoptosis. What distinguishes this as a hallmark of programmed cell death, versus one of necrosis?&lt;/p&gt;&#xA;" OwnerUserId="4151" LastEditorUserId="4151" LastEditDate="2013-08-01T17:13:24.690" LastActivityDate="2013-08-01T17:26:00.723" Title="molecular indicators of apoptosis: clarification needed" Tags="&lt;death&gt;&lt;apoptosis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9584" PostTypeId="2" ParentId="9500" CreationDate="2013-08-01T17:06:25.960" Score="3" Body="&lt;p&gt;You seem to be dissociating physical beauty from fitness. In fact, beauty &lt;em&gt;can&lt;/em&gt; be taken as a measure of biological fitness. For a classic, if simplistic example, many male humans find large breasts attractive and beautiful, however, large mammary glands are also an indication of fertility and robustness that would imply the prospective mate would be a good mother.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anything that we consider beautiful in a prospective mate can be interpreted in terms of fitness. Another classic example is symmetry. Humans are attracted to symmetrical faces and bodies. Since we are a symmetrical species, symmetry is an indication of fitness. In other words, lack of symmetry may indicate a developmental problem and by extension decreased fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There isn't really a qualitative difference between the way we define attraction and the way other animals do. In both cases we have instinctive attractions to healthy and fit (in the evolutionary sense) mates. It is simply that our complex society has marked these choices as &quot;aesthetics&quot; while we call them &quot;instincts&quot; in other animals.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-10-24T21:18:55.453" LastActivityDate="2014-10-24T21:18:55.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9585" PostTypeId="2" ParentId="9583" CreationDate="2013-08-01T17:26:00.723" Score="5" Body="&lt;p&gt;Although both involve DNA fragmentation, the pattern produced is very different.  During apoptosis, DNA fragmentation is done in a regular, controlled pattern, which if run on a gel produces a characteristic &quot;ladder&quot; pattern.  Necrosis, on the other hand, is a more stochastic process, and will produce a smear.  &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/18228342&quot; rel=&quot;nofollow noreferrer&quot;&gt;This&lt;/a&gt; details the difference rather nicely, including different ways to assay for either one in table 18.3.1 such as morphological staining or flow cytometry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a nifty image from the link.  Figure 18.3.2.  M is the marker, and in panel A, a conventional gel, lane 1 is apoptotic DNA, lane 2 is unprocessed DNA, and lane 3 is necrotic DNA.  In panel B, a pulsed-field gel, lanes 1 2 and 3 are untreated, apoptotic, and necrotic, respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0Dgqg.gif&quot; alt=&quot;Here&amp;#39;s a nifty image from the paper&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-01T17:26:00.723" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9586" PostTypeId="1" AcceptedAnswerId="9831" CreationDate="2013-08-02T06:53:38.750" Score="3" ViewCount="123" Body="&lt;p&gt;I need information on the disease frequency distribution among age groups for an Android app I'm building... Hopefully I've come to the right place. Is there a good data source for this? Like a bioinformatics database? &lt;/p&gt;&#xA;" OwnerUserId="4155" LastEditorUserId="3952" LastEditDate="2013-08-02T10:21:11.413" LastActivityDate="2013-08-18T01:19:58.310" Title="What is a good source for info on disease frequency distribution among age groups?" Tags="&lt;bioinformatics&gt;&lt;statistics&gt;&lt;database&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9587" PostTypeId="1" CreationDate="2013-08-02T12:46:45.347" Score="1" ViewCount="2162" Body="&lt;p&gt;I hold to the truth of Evolution, but I've encountered several problems with it, that I can't answer, and I can't find an answer for, despite much research. If would be great if anyone can answer these supposedly fatal problems for Biological Evolution, since I find it troubling that there appears to be no answer for these.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Problem/Question #1:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first one is called the mutation protection paradox. Simply put, Evolution has evolved mechanisms to protect itself from mutations, that if left unchecked, would build up and wreck the biological system, yet the mutation repair and protection mechanisms guard and stop the very changes that allow Evolution to occur, which is mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there an answer to this paradox?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Problem/Question #2:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem of genetic entropy. John Sanford has supposedly shown in his book Genetic Entropy and the mystery of the genome, that the human genome is degrading so quickly, that we could not have evolved from ape like creatures over millions of years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem is supposedly that we have 100-300 more mutations than either of our parents. This is supposed to mean that 100-300 new mutations accumulate in every person, in every single generation. Then it's said that these mutations are so small they cannot be gotten rid of by natural selection, and that the vast majority are harmful to the human genotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the mutations are unselectable, they are left to build up in all people until the entire human race becomes extinct, and it is estimated that this should have occurred in less than 80,000 years. So if Evolution were true, we wouldn't be here to talk about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The person presenting this problem gave answers to two responses. He gave a response to the Evolutionist retort that most mutations are not harmful but neutral by saying &quot;most mutations are neutral from the perspective of the organism’s physical fitness (phenotype), but all mutations must have effect on the genetic content (genotype). In no way are mutations truly neutral – they all must have effect on the genotype, even if they only affect the efficiency of transferRNA production. And as pointed out above, most are harmful.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then he gave a response to the Evolutionist retort that -almost all of the unselectable mutations will occur in non-coding regions of the DNA (the so-called, Junk DNA), and therefore have no effect. Thus, the individual will not die and the population will not become extinct- by saying quote: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Non-coding DNA does not code for proteins and scientists have previously thought it is largely useless. But mutations in the non-coding DNA won’t make them without effect since non-coding DNA helps during embryonic development and can be a part of many diseases. The idea that non-coding DNA absorbs mutations, thereby making them neutral, is false and is merely an argument from ignorance.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there an answer to this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Problem/Question #3:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can be called the meta-informaton paradox. How it goes is that you have two types of dynamics. Primary DNA which tells what proteins to make, and meta-information which tells the cell how to maintain the primary DNA. So it is said that primary DNA and meta-information are completely dependent on one another. If they become unrelated to each other, both become unusable and the animal would die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem is that mutations are random, and thus completely independent events, and this means primary DNA and meta-information would evolve by completely random and independent events and thus would not be able to stay relevant and related to one another, which then creates a barrier stopping microbes to man evolution from taking place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Problem/Question #4:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The person claims his calculations show that there is 1 chance in 10 to the 150 billion, that all species have evolved, each from a previous species. Here's how his calculation works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He says he is being as generous as possible with Evolution, and has five assumptions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Assumption 1&lt;/em&gt;: Evolution must occur by a net gain in new information. However, this is completely disregarded. We will simply assume that all beneficial mutations produce evolutionary change (including so called 'neutral mutations' which become beneficial later on).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Assumption 2&lt;/em&gt;: The rate of beneficial mutations is widely thought to be 1 for every million mutations. Indeed, scientists have observed millions more harmful or 'neutral' mutations than beneficial mutations. But we will assume that the frequency of occurrence is 1 beneficial mutation per 1,000 mutations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Assumption 3&lt;/em&gt;: It will be assumed that 5,000 mutations are needed to make a species 'evolve' into another species (where the two species cannot interbreed). Although the number needed for new single-celled species to arise is probably less, other higher animals require millions more beneficial mutations than accounted for here (40 million mutational differences exist between chimpanzees and humans[1], though different genus).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Assumption 4&lt;/em&gt;: We will assume that the total amount of species that have lived in the past is 10 million. In fact, this is the upper end of the estimate for species living today. If 99% of all species have become extinct as many Darwinists claim, then our assumption is extremely generous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Assumption 5&lt;/em&gt;: It will be assumed that every single beneficial mutation is fixed in the population after occurrence. This is very unrealistic (in favour of evolution, of course). Beneficial mutations can be lost from a population in a variety of ways; sexual reproduction and death being just a few causes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Calculating the chance that 50 million species have evolved from a common ancestor:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chance of 1 beneficial occurring: 1 in 1,000.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chance of 2 beneficials occurring: 1 in 1,000&lt;sup&gt;2&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chance of 5,000 beneficials occurring (needed to make one species evolve into another): 1 in 10&lt;sup&gt;15,000&lt;/sup&gt; (i.e. 1 in 1,000&lt;sup&gt;5,000&lt;/sup&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chance that 10 million species evolved: 1 in 10&lt;sup&gt;15,000&lt;sup&gt;10 million&lt;/sup&gt;&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore: 1 in 10&lt;sup&gt;150 billion&lt;/sup&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4157" LastEditorUserId="1306" LastEditDate="2013-08-04T16:49:47.680" LastActivityDate="2020-11-02T10:29:21.997" Title="How does the modern theory of evolution solve these apparent problems?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;information&gt;" AnswerCount="3" CommentCount="7" FavoriteCount="4" ClosedDate="2013-08-02T17:40:52.813" ContentLicense="CC BY-SA 3.0" />
  <row Id="9588" PostTypeId="5" CreationDate="2013-08-02T13:57:08.770" Score="0" Body="&lt;p&gt;This could include biological aspects of human societies, eusocial non-human groups such as bee, ant, or mole rat colonies, and presocial groups such as bird flocks, wolf packs, and many other species.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="4101" LastEditDate="2013-10-31T18:23:00.540" LastActivityDate="2013-10-31T18:23:00.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9589" PostTypeId="4" CreationDate="2013-08-02T13:57:08.770" Score="0" Body="Communal living, cooperation in care of young, and/or division of labor within animal species." OwnerUserId="3952" LastEditorUserId="4101" LastEditDate="2013-10-31T18:23:00.540" LastActivityDate="2013-10-31T18:23:00.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9590" PostTypeId="2" ParentId="9587" CreationDate="2013-08-02T14:06:51.873" Score="2" Body="&lt;p&gt;1: Not a paradox.  Mutations are generally protected against, especially in more complex organisms.  Protection mechanisms are not perfect, hence mutations still arise.  Plus, diversity can arise through other mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2: &quot;&lt;em&gt;...these mutations are so small they cannot be gotten rid of by natural selection, and that the vast majority are harmful...&lt;/em&gt;&quot; is a very dumb and self-contradictory statement.  If there is an effect it can be selected for or against.  Also, 100 mutations compared to 3 billion bases...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3: This is nonsensical.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4: Very confused assumptions and statistics.  You previously pointed out that many mutations happen in an individual.  Individuals &lt;strong&gt;do not&lt;/strong&gt; evolve, &lt;strong&gt;populations&lt;/strong&gt; do.  You don't need a single individual to mutate a lot, you need changes in genotype to accumulate, and millions of years is a very, &lt;strong&gt;very&lt;/strong&gt; long time.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-02T14:06:51.873" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9591" PostTypeId="5" CreationDate="2013-08-02T14:14:07.087" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-08-02T14:14:07.087" LastActivityDate="2013-08-02T14:14:07.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9592" PostTypeId="4" CreationDate="2013-08-02T14:14:07.087" Score="0" Body="Behaviours that transfer information between organisms" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-08-02T14:30:41.507" LastActivityDate="2013-08-02T14:30:41.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9593" PostTypeId="5" CreationDate="2013-08-02T14:23:15.847" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-08-02T14:23:15.847" LastActivityDate="2013-08-02T14:23:15.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9594" PostTypeId="4" CreationDate="2013-08-02T14:23:15.847" Score="0" Body="Educated guesses about the structure and function of things that do not currently exist. Many 'what if' and 'why not' questions fit this category. Questions should be posed so that they can be answered, not just discussed." OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-08-05T01:19:27.393" LastActivityDate="2013-08-05T01:19:27.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9595" PostTypeId="2" ParentId="9587" CreationDate="2013-08-02T15:03:45.877" Score="6" Body="&lt;p&gt;Thought I'd try this one too...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) The DNA repair mechanisms in an organism can be fairly minimal ( bacteria with smaller genomes such as &lt;em&gt;&lt;a href=&quot;http://www.sciencemag.org/site/feature/data/genomes/270-5235-397.pdf&quot;&gt;M genetalium&lt;/a&gt;&lt;/em&gt; do not seem to have DNA repair enzymes at all) or there can be many redundant backup genes for DNA repair (I'm thinking of &lt;em&gt;&lt;a href=&quot;http://science1.nasa.gov/science-news/science-at-nasa/1999/ast14dec99_1/&quot;&gt;D radiodurans&lt;/a&gt;&lt;/em&gt;, a bacterium found growing in the Chernobyl reactor after the disaster).  In each of these cases the DNA repair genes do not &lt;em&gt;stop&lt;/em&gt; mutations, they only reduce the number of mutations that occur.  Its well known that all sorts of living things can die of radiation poisoning and new mutations that have occurred recently are observed in all living things.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The argument has been given some &lt;a href=&quot;http://en.wikipedia.org/wiki/Devolution_%28biology%29&quot;&gt;detail in Wikipedia&lt;/a&gt;.  I would just say here that if some mutations has little selective power, but when there are enough of them to show a real disadvantage, then they will be eliminated from the gene pool.  They don't just all of a sudden get together and say 'here we are - you are dead!'  Selection is pretty good at finding pretty small disadvantages and kicking out the responsible variants. I guess the answer is the system is more robust than is assumed in this statement. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's not to say that low profile mutations can't combine and kill a living thing - they do.  Every generation of people genetic diseases kill thousands of people.  There are also lots of others who do not experience such diseases.  No family will be exempt from such defects over time, but nearly all families will continue as well.  The proportion being predicted here is not realistic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are species that go extinct too.  So all this does happen, but not in the proportions or degree being speculated. Really mountains are being made of molehills here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) There may be some cases where 5000 mutations (or even fewer) might prevent interbreeding between subpopulations to create species of a sort.  But in most cases it takes a lot more mutations than that to create a new species.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://ncse.com/creationism/analysis/evolving-bacteria&quot;&gt;Bacterial species are entirely different from animals and plants&lt;/a&gt;.  They don't need to breed to make offspring in the sense eukaryotes do.  Often they can't.  Bacterial species usually reproduce by single celled fission - they cells just split.  occasionally they transfer DNA, but they can do so between species by more than one means.  In the link its noted that bacterial speciation has been observed in the lab.  Just among the 30 or so E coli strains that are sequenced the number of genes can vary by 50%.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So though there are very few species of bacteria named, its also possible to say that there are many trillions of bacterial species, because they work in such a different way than we are used to seeing among animals and plants. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) While I can't really verify the numbers here, the idea that we could estimate all the possible species seems difficult.  There are definitely more species possible then there are atoms in the universe.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many more powerful arguments that there is one common ancestor to all living thing on earth.  Each living thing shares exactly the same mechanisms for preserving information - DNA, copying the DNA into RNA and then translating this into protein.  The idea that this would evolve in the same way twice seems completely unlikely.  Moreover there are genes in bacteria that have the same shape and work in the same way as in human beings and every other animal.  In fact the phylogenetic 'tree of life' shows that the more similar two living things are, the closer they resemble each other in terms of their sequence.  This is the primary argument for the last universal ancestor (LUA).  Most folks would have to have a counterargument that against this evidence.  The generation of a ribosome in the laboratory from primordial chemicals might be such an argument, since we think it took nearly a trillion years for it to happen the first time, I would be genuinely astonished to see it happen again.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-08-02T15:03:45.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9596" PostTypeId="2" ParentId="9587" CreationDate="2013-08-02T16:01:40.337" Score="29" Body="&lt;p&gt;OK, I'll have a go although you really shouldn't combine so many questions into one.&lt;/p&gt;&#xA;&lt;h2&gt;1 The mutation protection &amp;quot;paradox&amp;quot;&lt;/h2&gt;&#xA;&lt;p&gt;As already mentioned while many mutations are caught and corrected, not all of them are. You have to consider that a body (the human one, for example) contains &lt;a href=&quot;http://scienceblogs.com/gregladen/2011/11/28/how-many-cells-are-there-in-th/&quot; rel=&quot;nofollow noreferrer&quot;&gt;several trillion cells&lt;/a&gt;, &lt;em&gt;each&lt;/em&gt; of which contains 3 billion nucleotides each of which can be mutated. So, if the human body has, say, 50 trillion cells (a relatively conservative estimate), that means that a mutation &lt;em&gt;could&lt;/em&gt; occur at any of&lt;/p&gt;&#xA;&lt;p&gt;                              &lt;span class=&quot;math-container&quot;&gt;$3e10^9 * 5e10^{13} = 15e10^{22}$&lt;/span&gt; = 150000000000000000000000&lt;/p&gt;&#xA;&lt;p&gt;different sites. So even though the cell is pretty good at catching and correcting errors, some are bound to get through from pure statistical chance. In any case, you &lt;em&gt;know&lt;/em&gt; that not all errors are corrected, diseases such as cancer are often the direct result of such mutations and errors.&lt;/p&gt;&#xA;&lt;p&gt;I should also point out that in sexually reproducing species (such as humans) mutations are passed on to offspring only if they occur in &lt;a href=&quot;http://en.wikipedia.org/wiki/Gametogenesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;one of the cells&lt;/a&gt; that become gametes (sperm or eggs) so this does not accurately represent the number of available sites that can give rise to mutations that can directly affect evolution for sexual species. Other species however, do not reproduce sexually. For example, cutting a worm like &lt;em&gt;C. elegans&lt;/em&gt; in half will result in two worms so a mutation in any of its cells could be passed on to its offspring.&lt;/p&gt;&#xA;&lt;p&gt;Anyway, point mutations are not the only way that diversity is generated. Even in the absence of mutations, processes such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosomal_crossover&quot; rel=&quot;nofollow noreferrer&quot;&gt;chromosomal cross-over&lt;/a&gt; during gamete cell division (this is what makes you into a mixture of your Mom and Dad) would still produce differences that selection can act upon.&lt;/p&gt;&#xA;&lt;h2&gt;2 Genetic entropy&lt;/h2&gt;&#xA;&lt;p&gt;This one is a bit harder to answer, largely because it is complete poppycock. I'll try though. Let's see, we do &lt;em&gt;not&lt;/em&gt; have &amp;quot;more mutations than our parents&amp;quot;, what an absurd idea! The silent assumption here is that there was a &amp;quot;perfect&amp;quot; genome and each mutation is carrying us further from it. Therefore, since my parents were closer to this platonic ideal of the perfect DNA, each mutation that occurs in my cells takes their genomes a further step from that perfection.&lt;/p&gt;&#xA;&lt;p&gt;This is very simply wrong. There was never a perfect genome, each cell in each individual of each species in the world is constantly undergoing mutations and has always done so. The genome is &lt;strong&gt;dynamic&lt;/strong&gt;, not static and it has never been static, it can't be. DNA is a chemical substance and undergoes chemical reactions (such as mutations) all the time. Like all other chemicals it exists in a thermodynamic equilibrium, but not a static one. The only way that I have &amp;quot;more mutations&amp;quot; than my parents is if you accept &lt;em&gt;as a premise&lt;/em&gt; that humanity comes from the perfect genomes of Adam and Eve. Since this is what Mr. Sanford is, presumably, attempting to demonstrate, using it as a premise is, at best, a circular argument.&lt;/p&gt;&#xA;&lt;p&gt;Unless you assume the existence of a platonic ideal of a genome you cannot say whether I have more or fewer mutations than my parents because how can you compare them? In order to say that I have more mutations than my parents, you would need to quantify the number of mutations that each of us has and that cannot be done. How do you count mutations? You would need a reference genome of the ancestral human and we don't have that.&lt;/p&gt;&#xA;&lt;p&gt;The rest of the argument is even more nonsensical. Mutations can either be completely neutral and therefore &amp;quot;unselectable&amp;quot; or they can have an effect. &lt;strong&gt;By definition&lt;/strong&gt;, if a mutation has an effect, it can be selected for or against. That's how selection works. So, stating that these tiny mutations (which do exist) cannot be selected for/against &lt;em&gt;and yet&lt;/em&gt; are harmful is a direct contradiction. You can only have one or the other. If they are harmful, there will be a selective pressure to change/correct/lose these mutations.&lt;/p&gt;&#xA;&lt;p&gt;In any case, if these things &amp;quot;are left to build up in all people until the entire human race becomes extinct&amp;quot; all that means is that these things build up in individuals of a species and the species changes. Ummm, well, yes, we have a name for that, it's called evolution.&lt;/p&gt;&#xA;&lt;p&gt;Just a final point, tRNAs have their own specific genes, a random mutation in an intergenic region will have no effect on them, why should it? This just shows the fundamental ignorance of the author in question.&lt;/p&gt;&#xA;&lt;p&gt;Oh, and the whole &amp;quot;Junk DNA&amp;quot; is a very complex question. Yes, we now know that a lot of what was termed &amp;quot;Junk DNA&amp;quot; has a function (this was no surprise by the way, &amp;quot;Junk&amp;quot; was never intended to be taken literally). All this means is that mutations in non-coding DNA can also be harmful. OK, fine, then they will be selected against because that is how evolution works.&lt;/p&gt;&#xA;&lt;h2&gt;3 &amp;quot;meta-informaton paradox&amp;quot; (whatever that is)&lt;/h2&gt;&#xA;&lt;p&gt;This idea is often bandied by creationists but is a basic misunderstanding. Mutations are random(ish), evolution &lt;strong&gt;is not&lt;/strong&gt; remotely random. Advantageous mutations that make an individual more likely to reproduce will tend to be selected for and spread across a population while deleterious mutations will tend to be selected against and be removed from the gene pool. This is not a random process at all.&lt;/p&gt;&#xA;&lt;p&gt;As for the &amp;quot;meta-information&amp;quot;, nothing is &amp;quot;independent&amp;quot;. The cell is a complex system with extremely complicated interactions and a lot of cross-talk between the different processes. The DNA is not separate from the cell, it is an integral part of it. The Aristotelian idea of reductionist logic where you study complex systems by cutting them into little bits and understanding those bits is all very well as an intellectual tool but that is all it is, a tool. In reality, complex systems should be studied in their entirety, you cannot disassociate DNA from DNA regulation.&lt;/p&gt;&#xA;&lt;h2&gt;4 The pseudo math hypothesis&lt;/h2&gt;&#xA;&lt;p&gt;Let's have a look at these assumptions.&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Assumption 1: &amp;quot;Evolution must occur by a net gain in new information. &amp;quot;&#xA;Of course not. Evolution can create a net loss in complexity (information) just as often (indeed, probably more so) as a net gain. The classic example of this are viruses. They have evolved into lean, mean, minimalist killing machines. They have &lt;em&gt;nothing&lt;/em&gt; that is not absolutely essential. Hardly a net gain in information.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Assumption 2: I don't know where these numbers are coming from, whenever you read a phrase that starts with &amp;quot;scientists have observed&amp;quot;, run away. What scientists? How have they observed this? How do they define beneficial? Anyway, let's say these numbers are right (I really really doubt it, but let's say they are for the sake of argument).&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Assumption 3: Huh? Let's just throw some random numbers and see if they stick. There is no magical number of changes that results in &lt;a href=&quot;https://en.wikipedia.org/wiki/Speciation&quot; rel=&quot;nofollow noreferrer&quot;&gt;speciation&lt;/a&gt;. In mutations as in real estate, it's &amp;quot;location, location, location&amp;quot;. The question is not how &lt;em&gt;many&lt;/em&gt; mutations but where they have occurred and what effect they have had.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Assumption 4: Wow, this one is just completely wrong. To pick just one problem here, if 10 million species is the upper limit of species living today, and 99% of all species have become extinct, how does it follow that 10 million can also be a good estimate of all the species that have come before? If the 10 million of today are only 1% of all the species that have ever lived (99% are extinct right?) then it follows that the number of species that have existed is around one billion.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Assumption 5: It is most certainly not true that every beneficial mutation is fixed. Many are, others aren't. Also, bear in mind that the same mutation can be both beneficial and harmful in different contexts. For example, a mutation that makes me more resistant to cold would be very useful during an ice age but less so (and could be harmful) during a period of high temperatures. To take a classic example, there is a known mutation in some humans that makes them susceptible to &lt;a href=&quot;http://en.wikipedia.org/wiki/Sickle-cell_disease&quot; rel=&quot;nofollow noreferrer&quot;&gt;sickle-cell anaemia&lt;/a&gt;. However, the &lt;em&gt;same&lt;/em&gt; mutation also protects from malaria. So, is this one harmful or beneficial? That depends on whether you are living somewhere where malaria is prevalent or not.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;OK, so now the numbers. These wonderful probabilities all assume that evolution happens through &amp;quot;beneficial&amp;quot; mutations. First of all, that is not the only way that genomes change. I mentioned chromosomal crossing over earlier and you also have things like &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_drift&quot; rel=&quot;nofollow noreferrer&quot;&gt;genetic drift&lt;/a&gt; (you also have all sorts of other weird things such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Horizontal_gene_transfer&quot; rel=&quot;nofollow noreferrer&quot;&gt;horizontal transfer&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;p&gt;In any case, it does not take X beneficial mutations to make a new species. As I said, there is no magic number and evolution is not restricted to beneficial mutations. Just mutations.&lt;/p&gt;&#xA;&lt;p&gt;However, the most serious problem in this reasoning is that you are not calculating probabilities, you are calculating frequencies. What the argument you are presenting says is that it will take &lt;span class=&quot;math-container&quot;&gt;$10^{150billion}$&lt;/span&gt; events for 10 million species to evolve from a common ancestor. It says absolutely nothing about the probability of such events because you are not taking into account the size of the event pool.&lt;/p&gt;&#xA;&lt;p&gt;Let me explain. If you toss a coin, you have a 50-50 chance of getting either heads or tails. Therefore, getting 5 heads in a row is not very likely &lt;strong&gt;if you throw five times&lt;/strong&gt;. If, however, you throw a few billion coins a few trillion times, you are very very likely to at some point get 5 heads in a row. In order to calculate the probability of something you need to take into account the number of tests performed.&lt;/p&gt;&#xA;&lt;p&gt;If we keep the arbitrary numbers you have quoted, we have 10 million species, let's say each of them has a genome of 1 million base pairs and each has just 10 cells whose genome is passed on to their offspring (non-sexually reproducing species are actually the vast majority but most of them are unicellular so let's just take 10 as an average). Let us also assume that the creationists are right, the world is about ten thousand years old and let's say that species live for an average of two years (absolutely wrong of course but let's just pick small numbers). Finally, let's say that each species has only 1 million living individuals (again wildly conservative, just think of the number of ants in the world). This means that we are talking about&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;10 million species * 10 cells each * 1 million individuals * 1 million bases per cell = 100000000000000000000&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;If the rate of mutations is a tiny (much much smaller than the real value) 1 mutation every 24 hours, this means that there are &lt;span class=&quot;math-container&quot;&gt;$10^{20} * 365$&lt;/span&gt; potential mutations a year. And, therefore, there have been &lt;span class=&quot;math-container&quot;&gt;$10^{20} * 3650000 = 365*10^{23}$&lt;/span&gt; opportunities for mutation in the last 10000 years, that's 365 followed by 23 zeroes, that's a hell of a lot of chances. So, yes, if one in a thousand of them were beneficial that still makes it really quite likely that such mutations have occurred and have caused speciation events. This becomes even more likely if we take a realistic estimate of the time elapsed (10000 years is extreme for all but the most bullheaded of creationists).&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2020-11-02T10:29:21.997" LastActivityDate="2020-11-02T10:29:21.997" CommentCount="11" ContentLicense="CC BY-SA 4.0" />
  <row Id="9597" PostTypeId="1" CreationDate="2013-08-02T16:36:53.470" Score="3" ViewCount="92" Body="&lt;p&gt;I was wondering what is the range of SNP density across species and model organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I.e., what would be a reasonable estimate for the SNP density (i.e., x SNPs for each 1 Kb) in:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;humans&lt;/li&gt;&#xA;&lt;li&gt;humans with the highest variation (i.e., Africans)&lt;/li&gt;&#xA;&lt;li&gt;flies&lt;/li&gt;&#xA;&lt;li&gt;mouse&lt;/li&gt;&#xA;&lt;li&gt;lab mice with highest variation (i.e., isogenic lab mouse 1 with isogenic lab mouse 2 with the highest variation)&lt;/li&gt;&#xA;&lt;li&gt;model organism with the highest snp density (could be lab or naturally occurring)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1661" LastEditorUserId="107" LastEditDate="2013-08-02T22:41:48.440" LastActivityDate="2014-08-02T06:55:32.660" Title="Genetic variation in humans and model organisms (measured by SNPs)" Tags="&lt;snp&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9598" PostTypeId="2" ParentId="2699" CreationDate="2013-08-02T16:48:13.347" Score="0" Body="&lt;p&gt;Who says we are not streamlined?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One could easily imagine body structures that would cause much greater drag in air and humans do not have them.&lt;/p&gt;&#xA;" OwnerUserId="137" LastActivityDate="2013-08-02T16:48:13.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9599" PostTypeId="1" CreationDate="2013-08-02T20:30:52.207" Score="6" ViewCount="896" Body="&lt;p&gt;Pretty self descriptive, without being able to view the source of the noise how can we tell the difference between a sound in front of us and a sound behind us if pitch, volume and distance are all the same. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also assume that it is not biased to one side more than the other, e.g its not to your left or right but directly in front or behind. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested in knowing if it is a part of the ear that makes this distinction, or a function of the brain. &lt;/p&gt;&#xA;" OwnerDisplayName="user3393" LastActivityDate="2016-10-06T16:21:53.543" Title="How can we tell which direction sound is coming from?" Tags="&lt;hearing&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9600" PostTypeId="2" ParentId="9599" CreationDate="2013-08-02T21:14:29.443" Score="3" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Head-related_transfer_function&quot; rel=&quot;nofollow&quot;&gt;head-related transfer function&lt;/a&gt;. Sound coming from front, and from back differ because of the human body's asymmetry in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Vertical_sound_localization#The_Cone_of_Confusion&quot; rel=&quot;nofollow&quot;&gt;vertical direction where the biaural cues such as inter-aural timing and intensity differences are identical&lt;/a&gt;. The shape of the ear, and body is necessary for this perception, but eventually, the signal must be analyzed by the brain for localization.&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2013-08-02T21:14:29.443" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9601" PostTypeId="1" AcceptedAnswerId="9603" CreationDate="2013-08-02T22:08:02.840" Score="11" ViewCount="2488" Body="&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quite a few plant species can be used for medicinal purposes &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_plants_used_in_herbalism&quot; rel=&quot;noreferrer&quot;&gt;wiki&lt;/a&gt;. As an example, &lt;em&gt;Filipendula ulmaria&lt;/em&gt; is rich in acetylsalicylic acid (aspirin).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An allele that produces a substance which is beneficial for a predator should not get fixed in the population! &lt;em&gt;Why are there so many drug-like plants?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Thoughts&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are some (intuitive, unclear or far-fetched, non-exhaustive and non-exclusive) hypotheses I can think of:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Because plants want their seeds to get ingested in order to propagate&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is it because there are so many substances that affect our homeostasy that many plants are toxic and many are healthy just by chance. Containing healthy substances are not adaptations but by-product of evolution.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The substances that are beneficial for us actually evolved to repulse predators. These substances are toxic at high dosage and therefore are efficient against predators that are small or eat a lot of plants (herbivorous). These substances at low dosage might actually have a benefical effect. For example a substance that make blood thicker is very toxic except if you eat just a bit of it while bleeding.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;We (primate or whatever taxon you want to consider) evolved in order to get advantage of the surrounding envirronment. Sbstances that were neutral became beneficial. The advantage of being sensitive to various products cause that, by chosing our food source, we can heal. Therefore, by evolving sentivity to various substances, our behaviour can act as a reinforcement to immunity (and other anti-illness system). If this is true, we might expect that the frequency of presence of a plant species affect the probability that out homeostasy get affected when eating it.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Lineage selection. Lineages that produce substances that are active in predators body in a way or another are undergoing many various selection forces because of these substances. Therefore they get a higher speciation rate than other lineages.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Keeping some non-herbivorous species in large population size (by helping them) is the best way to keep herbivorous species in small population (because of territory competition, predators relationships, etc... ) &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2016-02-23T01:13:35.267" LastActivityDate="2016-02-23T01:13:35.267" Title="Why are there so many medicinal plants?" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;pharmacology&gt;&lt;metabolism&gt;&lt;ethnobiology&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9602" PostTypeId="2" ParentId="9601" CreationDate="2013-08-02T22:41:10.490" Score="8" Body="&lt;p&gt;Firstly, most plants or other natural medicinals existed way before we knew about them; it's not that plants mimic drugs, its that drugs mimic plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question succinctly, compounds that we can use for our own medical benefit often do other things, we just adapt them for our own purposes.  Penicillin is probably the best example.  It didn't evolve to allow humans to fight bacteria, it arose in fungi and helped fungi attack bacteria; we just appropriated it.  Similar with plant compounds like taxol (technically fungi again).  Another good example can be found in my &lt;a href=&quot;https://biology.stackexchange.com/questions/9517/why-is-venom-more-common-in-fish-and-snakes-than-other-vertebrates/9522#9522&quot;&gt;recent answer about snake venom&lt;/a&gt;.  While a lot of those compounds are toxic to humans, they are very similar or even identical to compounds that in different doses can be beneficial.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Substances like capsaicin (aka spiciness) and caffeine are actually irritants that plants use to prevent predation, but we, in certain uses and doses, go wild for them.  Same for the substances in mustard, ginger, or pepper.  Imagine all the plant or animal chemicals we &lt;em&gt;don't&lt;/em&gt; use!&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2013-08-02T22:41:10.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9603" PostTypeId="2" ParentId="9601" CreationDate="2013-08-02T23:34:13.250" Score="19" Body="&lt;p&gt;Perhaps the question may also be phrased, &quot;Why is it common for plants to produce chemicals that possess pharmacological or toxicological effects in man and animals?&quot;, and to that question it is often reasoned that plants, being sessile and otherwise defenceless food sources for predators, produce compounds that affect the physiology of animals in such a way as to make it not beneficial for a predator to consume them, which is close to your 3rd hypothesis. Remember that pharmacological benefit is largely anthropocentric, and relative at that. For instance, a plant compound that lowers blood pressure could be used as treatment of hypertension, but if the plant were to be consumed in its native state in appreciable quantity, it could put the eater into shock, cardiac arrest, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most pharmacologically active compound from plants comprise a class of compounds known as &lt;em&gt;secondary metabolites&lt;/em&gt;: metabolic intermediates that are not appreciably involved with functions of growth, respiration, etc. (often interpreted as evidence for a defence mechanism). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Try this wikipedia article and see what you think: &lt;a href=&quot;http://en.wikipedia.org/wiki/Plant_defense_against_herbivory&quot;&gt;http://en.wikipedia.org/wiki/Plant_defense_against_herbivory&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The major classes of secondary metabolites in plants are: terpenes, which are polyisoprenoids, phenolic compounds, including the polyphenolic compounds, which are a popular study in natural products research, and alkaloids (along with other nitrogenous compounds).&lt;/p&gt;&#xA;" OwnerUserId="4140" LastActivityDate="2013-08-02T23:34:13.250" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9604" PostTypeId="1" CreationDate="2013-08-03T02:29:08.640" Score="1" ViewCount="102" Body="&lt;p&gt;I asked on the cooking site, but was directed here.  This is my original question &lt;a href=&quot;https://cooking.stackexchange.com/questions/35726/botulinum-toxin-in-home-canned-green-beans&quot;&gt;https://cooking.stackexchange.com/questions/35726/botulinum-toxin-in-home-canned-green-beans&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reading is quite long, however I merely want to know the &lt;strong&gt;minimum&lt;/strong&gt; temperature and &lt;strong&gt;minimum&lt;/strong&gt; time at which that temperature must be maintained in order to destroy botulinum toxin.  I want to review a study where the determination was made.  Can anyone assist?&lt;/p&gt;&#xA;" OwnerUserId="3869" LastEditorUserId="-1" LastEditDate="2017-04-13T12:33:29.980" LastActivityDate="2013-08-03T13:43:29.250" Title="Botulinum Toxin" Tags="&lt;cell-biology&gt;&lt;food&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9605" PostTypeId="1" CreationDate="2013-08-03T02:56:09.567" Score="0" ViewCount="329" Body="&lt;p&gt;I am looking for an alloy with low melting temperature (&amp;lt; 350°C) which is not toxic when in direct constant contact with skin, food and overall in domestic environment. My application is a solder that can be used for soldering a ring.&lt;/p&gt;&#xA;" OwnerUserId="4160" LastActivityDate="2013-08-03T03:18:36.497" Title="Non toxic low melting point alloy" Tags="&lt;toxicology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9606" PostTypeId="2" ParentId="9605" CreationDate="2013-08-03T03:18:36.497" Score="1" Body="&lt;p&gt;I'm not a metallurgist, which you should probably ask... but there is this that I found:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.rotometals.com/Low-Melting-Fusible-Alloys-s/21.htm&quot; rel=&quot;nofollow&quot;&gt;Low Melting Fusible Alloys&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both Cadmium and Lead are toxic, but Bismuth, Indium, and Tin are not. An alloy of those might be what you're looking for. Indium raises the price-point considerably, as it's a few magnitudes more expensive than Bismuth and Tin. &lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-08-03T03:18:36.497" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9607" PostTypeId="2" ParentId="8880" CreationDate="2013-08-03T03:21:47.953" Score="7" Body="&lt;p&gt;First, allow me to provide the link to an old paper that deals with development in &lt;em&gt;Ananas comosus&lt;/em&gt;, it should be freely available and answer this question in more detail: &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.1936.tb06884.x/pdf&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.1936.tb06884.x/pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, to briefly explain the observation that a mature plant will grow from the region where the leaves of the pineapple attach to the fruit, it should be noted that the pineapple fruit develops at the top of the central stem of the plant in a developmental process known as influorescence (please see a picture of a pineapple plant). Since the top portion of the fruit is in fact the end of the primary stem, this region contains the apical meristem, a collection of stem cells that are apparently is sufficient to give rise to a mature organism. Pineapple development has apparently been a topic of constant research for nearly a century (due to its economic importance), so there are quite a number of papers that can provide much more detail, but many of these are not freely available.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In nature the primary means of pineapple propagation is the formations of lateral shoots, the growth of which consequently are accelerated by influoresence of the main shoot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the actual way the plant grows is not quite as simple to answer, as plant development is often as complicated as animal development, but in general it is a function of cell division and elongation. In the root apical meristem, there is a region known as the quiescent centre which contains the actual root stem cells. Directly behind the quiescent centre is a region known as the merismatic zone, which features extensive cell division, and directly behind that is the elongation region where the cells grow, effectively pushing the root tip through the soil. In the region behind the elongation region, the maturation zone where the cells have reached full length, cells begin to form more rigid cell walls and differentiate into the different tissues of the root.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The shoot apical meristem is dome-shaped, the top of the dome is known as the central zone and is analogous to the quiescent centre of the root apical meristem, the sides of the dome are the peripheral zone, a region of rapidly dividing cells that give rise to the leaves, and the central region of the dome is the rib zone that gives rise to the stem structures. Elongation, differentiation, and maturation also occur below the meristem region, but involve the additional complexities of leaf organogenesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There should be considerable additional information on plant development online.&lt;/p&gt;&#xA;" OwnerUserId="4140" LastEditorUserId="4140" LastEditDate="2013-08-03T03:53:19.020" LastActivityDate="2013-08-03T03:53:19.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9608" PostTypeId="2" ParentId="9361" CreationDate="2013-08-03T03:35:40.683" Score="4" Body="&lt;p&gt;&lt;strong&gt;Answering your question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well, considering there is a plethora of facilities that deal with the cloning of plants and animals, as well as altering specific DNA in order to create a better plant or animal. Tests have been done with rats to try and create stronger and smarter rats, and tests have been done on countless other animals to try to develop immunity to dementia and Alzheimers. In the agricultural industries of the world, new types of corn, tomatoes, rice, and other types of crops are engineered on a daily basis, and new versions of these plants are made very commonly. The problem, however, is that a vast quantity of these plants are rejected from being planted. Some plants that are engineered either taste too bad, or they are less efficient than the plant at which they were modifying. As far as inventing a new species, you have to be more specific as to what you are asking. If science creates a new animal from another animal, it is likely of the same family and genus, like breeding a dog from another dog. Creating another type of mammal or reptile or bacteria that isn't part of a specific genus would be a breakthrough, as I am sure that all types of cloning and scientific pairing have been done to the same general Genus and Species... I am assuming, however, that it will be possible to engineer lifeforms at the molecular level by the next 50 to 100 years, as science and technology is getting more and more advanced. So, by the next few centuries, it would only seem logical to assume that new species would be created. However, the practice of creating new species, or even operating a laboratory/facility that deals with the concept, is illegal in a large number of countries, and has several guidelines in others. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I am only 13, so if any of this information is to be used anywhere else, I would advise not to cite me as a credible source. All this information is from my knowledge, and my knowledge is from school studies and personal readings. This is all my information, though. If any wording sounds similar to another source, keep in mind that one human brain functions similarly to another on several accounts and coincidences are often found.  I can assure you that if the documented information above is verified by plagiarism experts as my own wording, as I have taken the liberty to scan my own work. I hope I answered your question, and I am sorry for the long disclaimer ranting of this paragraph.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="4161" LastActivityDate="2013-08-03T03:35:40.683" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9609" PostTypeId="1" CreationDate="2013-08-03T07:00:31.480" Score="0" ViewCount="335" Body="&lt;p&gt;Let's say that the threshold potential of a neuron is +40 mV to make a muscle twitch. Now suppose we have two signals of +20 mV. So, this signal will cause the twitch in muscle because it has reached the threshold potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose that we have many signal of +20 mV. Will this cause a lot of twitch, the same twitch or no twitch at all in the muscle? In other words, how will the twitch be greater?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please be a little simple.&lt;/p&gt;&#xA;" OwnerUserId="1765" LastEditorUserId="3952" LastEditDate="2013-08-03T08:36:39.450" LastActivityDate="2013-09-02T14:22:17.550" Title="All or none phenomenon" Tags="&lt;physiology&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9610" PostTypeId="1" CreationDate="2013-08-03T11:31:52.710" Score="4" ViewCount="114" Body="&lt;p&gt;What is the trigger for DNA to produce proteins or RNA? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found enough material to study the inner workings of the cell and DNA; but, I can't find an explanation of the mechanics the cell uses to react to its inner state or external events and in turn initiate transcription.&lt;/p&gt;&#xA;" OwnerUserId="4163" LastEditorUserId="1590" LastEditDate="2013-08-04T06:51:00.977" LastActivityDate="2013-08-05T07:33:59.707" Title="What triggers DNA to produce proteins?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;transcription&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9611" PostTypeId="2" ParentId="9604" CreationDate="2013-08-03T11:38:51.703" Score="2" Body="&lt;p&gt;The short answer is: unless you burn the sample completely to ashes, you cannot be sure you destroyed all BT particles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Denaturation is a naturally occuring process and it works pretty much like radioactive decay. It happens over time, so if you had a solution of BT without any bacteria or spores and left it at room temperature, after some (very long) time the toxin would be destroyed. By adding heat (or acid) you accelerate the denaturation, but it still is a statistical phenomenon. If at a certain temperature half of toxin particles are destroyed within a second, it means that within a minute one in $2^{60}$ will be left. But 1 in $2^{60}$ is not zero. If you keep the temperature for two minutes, one toxin particle in $2^{120}$ will be left. You can never be 100% sure all toxin was destroyed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This also means, that there is no one set &quot;minimum time and minimum temperature&quot;. The higher the temperature, the lower the time needed. You can keep food at room temperature for a very long time and the toxin will be destroyed (though I doubt that the food itself will survive that kind of time).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, one molecule of toxin will not kill you. Think about BT injections as anti-wrinkle therapy. A small amount of toxin in injected, it paralyses small facial muscles and the face looks smoother, younger. The effect wears off, so you have to repeat the injection every now and then. In order to make food safe to eat, you don't have to destroy all BT molecules. From a booklet &lt;em&gt;Food Safety Hazards and Controls for the Home Food Preparer&lt;/em&gt; (2006 edition, available at &lt;a href=&quot;http://www.hi-tm.com&quot; rel=&quot;nofollow&quot;&gt;http://www.hi-tm.com&lt;/a&gt;): a healthy adult can eat up to 1000 spores with no ill effects, &lt;em&gt;Clostridium botulinum&lt;/em&gt; bacteria and spores are considered destroyed after 2.4 minutes at $250^\circ \mathrm{F}$ ($121^\circ \mathrm{C})$ - this in fact reduces the number of spores $10^{12}$ times and is called &lt;em&gt;commercial food sterilization&lt;/em&gt;, the toxin is considered destroyed after boiling for 10 minutes but the temperature of $165^\circ \mathrm{F}$ ($74^\circ \mathrm{C})$ will not destroy it. This booklet also advises to boil for 10 minutes any homemade canned food if you are not perfectly sure the original procedure was appropriate.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastActivityDate="2013-08-03T11:38:51.703" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9612" PostTypeId="2" ParentId="9609" CreationDate="2013-08-03T13:40:12.643" Score="1" Body="&lt;p&gt;I think you are asking about &lt;a href=&quot;http://en.wikipedia.org/wiki/Cooperativity&quot; rel=&quot;nofollow noreferrer&quot;&gt;cooperativity&lt;/a&gt;.  In many biological systems the action of many individuals are coupled together such that when an individual is activated, the others are more likely to act as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The classic example of cooperativity is hemoglobin a protein which has four sites to bind oxygen (one in each of four protein subunits).  When there is enough oxygen present for a single binding site to bind oxygen, the other three will have an increased affinity for oxygen.  This makes the binding curve relatively steep.  Take a look at the graph. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SUvy0.png&quot; alt=&quot;saturation of hemoglobin by oxygen&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When one oxygen is bound, three others also become bound. The more individuals in a cooperative system, the sharper the curve becomes until a very small change in a few individuals creates a very large effect very quickly.  &quot;all or nothing&quot; as you say. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Muscle contraction also is cooperative.  In this case there are many individual muscle fibers, both the myosin thick filaments, and the actin thin filaments.  Each fiber consists of chains of interwoven individual proteins.  When a myosin individual protein acts against a thin filament other myosins in that filament and those on other thick filaments that are bound to the same thin filament will react to the change in tension and also be more likely to activate and pull.  This causes the entire muscle to quickly start to contract together.  Most researches feel that all the various other factors contributing to muscle contraction, calcium release and uptake, other proteins that are associated with the thick and thin filaments etc, are cooperative as well.  A search for 'muscle contraction cooperativity' will give &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16465469&quot; rel=&quot;nofollow noreferrer&quot;&gt;many&lt;/a&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2269565/&quot; rel=&quot;nofollow noreferrer&quot;&gt;references&lt;/a&gt; like &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11964067&quot; rel=&quot;nofollow noreferrer&quot;&gt;these&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-08-03T13:40:12.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9614" PostTypeId="1" CreationDate="2013-08-03T21:22:22.207" Score="3" ViewCount="8333" Body="&lt;p&gt;I found this &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5Xdc1.png&quot; alt=&quot;picture&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;very disturbing: bombastic tabloid-style writing in capital and the content is doubtful. If it was correct or close &lt;em&gt;&quot;does it really take something like 26 seconds for a body lotion to enter into bloodstream?&quot;&lt;/em&gt;, you select a lotion with very high level of fat -- now your heart will pump  blood with a very high-level of fat, possible source for heart failure. If you have a dry skin and you put 40%-fat lotion to your skin, it makes it more flexible. I am very-very skeptical whether any fat gets into your bloodstream. I am new to things such as blood lipids (blood fats) and mechanisms how the body lotions really penetrate into the skin. How? And which factors determine the time and does any get actually into bloodstream and after which kind of processes by the body? Is this just a hoax?&lt;/p&gt;&#xA;" OwnerUserId="1705" LastEditorUserId="3615" LastEditDate="2013-08-04T18:22:44.673" LastActivityDate="2017-08-21T18:02:50.123" Title="Do body lotions enter into bloodstream of people? And how do they do it?" Tags="&lt;blood-circulation&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9615" PostTypeId="1" CreationDate="2013-08-03T21:48:15.907" Score="1" ViewCount="183" Body="&lt;p&gt;If you took a newborn animal and completely isolated it from its species, would it be capable of assuming a fight or flight distance preset by its species, due to their being no basis for what could harm the animal?&lt;/p&gt;&#xA;" OwnerUserId="4166" LastEditorUserId="107" LastEditDate="2013-08-04T20:16:09.803" LastActivityDate="2013-10-04T17:17:43.803" Title="Is &quot;Fight or Flight&quot; distance genetic" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9616" PostTypeId="2" ParentId="8361" CreationDate="2013-08-03T21:58:16.180" Score="0" Body="&lt;p&gt;When you're awake; the sensations around you as well as your mental will, keep your mind active. How the air smells and what needs to be done all contribute to your day. In order to sleep your brain must weaken these receptors significantly, though not enough that if we heard something too loud or unfamiliar (such as a predator), we overlap those boundaries that keep us resting and wake. Now of course i am talking about the middle of the night. As morning arrives the amount of stimuli needed to overcome the wall that is sleep is diminished, allowing something such as the crowing of a rooster to wake us up.&lt;/p&gt;&#xA;" OwnerUserId="4166" LastActivityDate="2013-08-03T21:58:16.180" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9617" PostTypeId="2" ParentId="9614" CreationDate="2013-08-04T09:50:30.740" Score="4" Body="&lt;p&gt;Lotions, like any other drug, can effectively enter the blood system. However, the fraction of the applied lotion that actually enters is really small, and it only achieves a significant concentration in the zone near the application. The skin, if healthy, offers a very high resistance to the passage of substances. Moreover, the bloodstream actually dilutes even more the little fraction it achieves to enter, further reducing its effects. If the skin is damaged the penetration is greater, though you'll never be able to get drunk by dropping booze in an injury.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="69" LastEditDate="2013-08-04T19:53:39.490" LastActivityDate="2013-08-04T19:53:39.490" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9619" PostTypeId="2" ParentId="8807" CreationDate="2013-08-04T13:18:43.980" Score="1" Body="&lt;p&gt;Other laxatives can exacerbate the effects of lactulose, leading to diarrhea, and could eventually lead to dehydration and general GI issues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neomycin and antacids in general raise the pH of the gut, making it more basic, and reducing the peristaltic movements. Lactulose, meanwhile, is broken down to primarily lactic acid (if I recall) in the gut, and creates a more acidic environment. The acidic environment increases peristaltic movement in the bowel, and in turn the patient eliminates waste.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are on concomitant antacids or other drugs that raise the pH of the lower gut, you are reducing the effects of lactulose, and in a worse case scenario, making the constipation worse.&lt;/p&gt;&#xA;" OwnerUserId="3370" LastActivityDate="2013-08-04T13:18:43.980" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9620" PostTypeId="2" ParentId="9615" CreationDate="2013-08-04T13:49:27.903" Score="1" Body="&lt;p&gt;It probably is somewhat genetic.  A good example is pigeons.  When you approach them, they turn their back to you so that if you get close enough they can escape / fly away.  I'd be surprised if this is only a learned behavior, but I also note that pigeons who have been fed let you approach to a closer distance than other birds, so in this example a distance is not completely hard wired.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such behaviors are more likely a combination of learned and genetic, especially as the animal becomes more complex (has a larger brain).  This is a major concern of '&lt;a href=&quot;http://en.wikipedia.org/wiki/Ethology&quot; rel=&quot;nofollow&quot;&gt;ethology&lt;/a&gt;'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think few inherited behaviors are &lt;a href=&quot;https://en.wikipedia.org/wiki/Ethology#Fixed_action_patterns_and_animal_communication&quot; rel=&quot;nofollow&quot;&gt;completely inflexible&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-10-04T17:17:43.803" LastActivityDate="2013-10-04T17:17:43.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9621" PostTypeId="1" AcceptedAnswerId="9622" CreationDate="2013-08-04T14:02:01.053" Score="2" ViewCount="22875" Body="&lt;p&gt;I am basically a &lt;a href=&quot;http://en.wikipedia.org/wiki/Vegetarian&quot; rel=&quot;nofollow&quot;&gt;vegetarian&lt;/a&gt; and I find it very difficult to get an actual biological answer for this question on search engine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are couple of links which discuss these argument but can not be acclaimed as a proof as being Egg either a veg or non-veg food item. Below are couple of links which I found depicted this in authors perception:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://veg.tribe.net/thread/6bc5671e-70d6-4aa9-a1af-f46b627aa809&quot; rel=&quot;nofollow&quot;&gt;Egg Non-Veg (a proof)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://log.amitshah.net/2006/02/eggs-vegetarian-or-non-vegetarian/&quot; rel=&quot;nofollow&quot;&gt;Egg is veg&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Vegetarian&quot; rel=&quot;nofollow&quot;&gt;Types of vegetarian&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Vegetarian_mark&quot; rel=&quot;nofollow&quot;&gt;If it is veg why products are marked with red dots&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Is there any biological proof to consider &lt;strong&gt;White Eggs&lt;/strong&gt; either as vegetarian or non-vegetarian?&lt;/p&gt;&#xA;" OwnerUserId="4170" LastEditorUserId="9943" LastEditDate="2015-01-01T13:32:11.490" LastActivityDate="2015-01-01T13:32:11.490" Title="Can white eggs be considered as non-vegetarian?" Tags="&lt;food&gt;&lt;diet&gt;&lt;vegetation&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2015-01-02T03:14:00.383" ContentLicense="CC BY-SA 3.0" />
  <row Id="9622" PostTypeId="2" ParentId="9621" CreationDate="2013-08-04T15:37:18.510" Score="14" Body="&lt;p&gt;Of course eggs are not vegetarian. Eggs are, well, the &lt;em&gt;eggs&lt;/em&gt; of chickens (usually). Chickens are animals so their eggs are animal matter as well. Whether or not the egg has been fertilized is completely irrelevant, eggs are chicken just as much as &lt;a href=&quot;https://en.wikipedia.org/wiki/Drumstick_%28poultry%29#Cuts_of_poultry&quot;&gt;drumsticks&lt;/a&gt; are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The color of the egg has nothing at all to do with it. All eggs are, by definition, animal cells. Basically, the chicken's egg is the equivalent to the human &lt;a href=&quot;http://en.wikipedia.org/wiki/Egg_cell&quot;&gt;ovum&lt;/a&gt;. In both humans and chickens, the female will regularly produce eggs and discard them. In the case of a human woman this is the monthly period. When an egg is not fertilized, it is discarded along with some cells of the wall of the uterus. Similarly, in chickens, the female produces and lays eggs. If an egg has been fertilized, it can grow into a new chicken. If it has not been fertilized, it cannot become a new chicken but is most certainly still an animal cell.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes, eggs are most certainly animal, not plant or any other kind of matter. Whether or not you should eat them is up to your own moral guidelines to decide. While they are animal tissue, no animal has been killed to obtain them and no harm comes to the chicken if we harvest them. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-08-04T15:37:18.510" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="9623" PostTypeId="1" CreationDate="2013-08-04T16:08:57.453" Score="5" ViewCount="35754" Body="&lt;p&gt;I've been reading a lot about the oxidative dissimilation etc, and often I see different sources use NADH and NADH&lt;sub&gt;2&lt;/sub&gt; in the same reactions. One source uses NADH and another uses NADH&lt;sub&gt;2&lt;/sub&gt; in the exact same way. Is there a difference or is it just a different name for the same substance?&lt;/p&gt;&#xA;" OwnerUserId="4172" LastEditorUserId="948" LastEditDate="2013-08-04T16:18:12.897" LastActivityDate="2014-06-10T10:54:42.980" Title="Is there a difference between NADH and NADH2?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9625" PostTypeId="2" ParentId="9610" CreationDate="2013-08-05T07:33:59.707" Score="1" Body="&lt;p&gt;This question is not easily answered as there are a multitude of factors involved in the production of proteins.  DNA - the molecule - does not &quot;determine&quot; when proteins will be produced.  The environment (truly environmental, extracellular, intracellular, etc.) of the organism governs this.  If you have not found enough material to satisfy your inquiries I recommend Jim Watson et. al. Molecular Biology of the Gene.  A classic.&lt;/p&gt;&#xA;" OwnerUserId="4175" LastActivityDate="2013-08-05T07:33:59.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9626" PostTypeId="1" CreationDate="2013-08-05T07:40:00.920" Score="5" ViewCount="100" Body="&lt;p&gt;What method would you use to genotype SNPs in low quality samples? I ideally want to genotype hundreds of SNPs in hundreds of scat samples (very low amount of target DNA, potentially degraded and highly contaminated by other DNA).&lt;/p&gt;&#xA;" OwnerUserId="4176" LastEditorUserId="3624" LastEditDate="2013-08-13T10:01:33.377" LastActivityDate="2014-02-10T11:20:44.780" Title="What method would you use to genotype SNPs in low quality samples?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9627" PostTypeId="2" ParentId="8996" CreationDate="2013-08-05T07:43:51.233" Score="-1" Body="&lt;p&gt;Yes, maintenance of the genome.  But not DNA specifically, but DNA and all of its associated proteins.&lt;/p&gt;&#xA;" OwnerUserId="4175" LastActivityDate="2013-08-05T07:43:51.233" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9629" PostTypeId="2" ParentId="8996" CreationDate="2013-08-05T08:57:42.927" Score="1" Body="&lt;p&gt;DNA has been shown to be important for biofilm formation in certain bacteria.  This is extracellular DNA that comes from cell lysis.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-05T08:57:42.927" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9630" PostTypeId="2" ParentId="9623" CreationDate="2013-08-05T09:28:57.723" Score="4" Body="&lt;p&gt;They are often used interchangeably to indicate the reduced form of $\ce{NAD+}$.  The overall reaction when oxidizing some molecule $\ce{RH2}$ is: $\ce{RH2 + NAD+ -&amp;gt; NADH + H+ + R}$.  The proper reduced $\ce{NAD+}$ is $\ce{NADH}$ (it accepts two electrons and one proton), but sometimes $\ce{NADH2}$ is used to account for that second hydrogen that gets removed from the substrate being oxidized.  The notation $\ce{NADH2}$ doesn't really take into account the fact that the second hydrogen is charged, and not bound to the $\ce{NAD}$ in the same way that the first hydrogen is, so it is confusing.  The notation: &quot;$\ce{NADH + H+}$&quot; is more correct and is also sometimes used.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastEditorUserId="3473" LastEditDate="2014-06-10T10:54:42.980" LastActivityDate="2014-06-10T10:54:42.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9631" PostTypeId="1" AcceptedAnswerId="14775" CreationDate="2013-08-05T10:02:16.963" Score="8" ViewCount="410" Body="&lt;p&gt;I am working on an idea to provide nearly unlimited amounts of water in desert regions. To make this commercially viable. I would use the water to irrigate desert sand and grow crops. Given my extremely limited understanding of biology, I cannot find an answer to the following question:&lt;/p&gt;&#xA;&lt;p&gt;Are there any food crops (preferably high valuable/low maintenance ones), that can grow in a desert, given that I can just provide the seed, water and fertilizer and stop sandstorms.&lt;/p&gt;&#xA;&lt;p&gt;My motivation for investigating this is the following map showing regions that are either already deserts or at risk of becoming deserts:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/yiwVX.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://en.wikipedia.org/wiki/Desertification&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Desertification&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="205" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-02-01T23:21:55.640" Title="Any food crops that could grow in a desert provided that they get fertilizer and water" Tags="&lt;botany&gt;&lt;microbiology&gt;&lt;soil&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9632" PostTypeId="2" ParentId="8996" CreationDate="2013-08-05T10:03:34.207" Score="3" Body="&lt;p&gt;DNA has the following functions other than genetic material :&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;It can function as a molecule that attaches to TLR ( Toll like Receptor ) on or in cells and so  can contribute to innate immune response.&lt;/li&gt;&#xA;&lt;li&gt;It can act as carbon source. ( We have nucleases enzymes in our intestines.)&lt;/li&gt;&#xA;&lt;li&gt;It can be structural component of biofilms.&lt;/li&gt;&#xA;&lt;li&gt;It can also influence pH in cells as it is an acid.&lt;/li&gt;&#xA;&lt;li&gt;It is a structural component of neutrophil extracellular traps to wrap up microbes.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Please feel free to correct any errors I have made.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2013-08-05T17:21:18.437" LastActivityDate="2013-08-05T17:21:18.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9633" PostTypeId="2" ParentId="9352" CreationDate="2013-08-05T14:43:55.630" Score="0" Body="&lt;p&gt;This is indeed a very good question, that I have spent a long time thinking about myself.  My take on this is that there is indeed a very close relationship between inbreeding and speciation, but that inbreeding actually PRECEDES speciation ! The key to this rather counter-intuitive point of view is that inbreeding actually has several advantages, including that of resulting in cleaner genomes in those offspring that survive inbreeding depression. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In populations that have high degrees of inbreeding, because of, for example, small sizes of populations, or high tendencies to self fertilisation, the recessive mutations that cause inbreeding depression will be progressively eliminated, and there will consequently be very little inbreeding depression. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In such a context, there will thus be no barrier to exploiting other advantages of inbreeding such as reducing the cost of sex, or keeping together advantageous gene combinations. Small groups of individuals would thus be better off breeding among one another than with the ancestral stock, leading to speciation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested, or just intrigued, by this kind of concept, I invite you to read the rather long essay I wrote on the subject (The existence of species rests on a metastable equilibrium between inbreeding and outbreeding. An essay on the close relationship between speciation, inbreeding and recessive mutations, Etienne Joly, &lt;a href=&quot;http://www.biologydirect.com/content/6/1/62&quot; rel=&quot;nofollow&quot;&gt;http://www.biologydirect.com/content/6/1/62&lt;/a&gt; ).&#xA;And please do not hesitate to get in touch with me directly  by email ( atnjoly(at)mac.com ) if you have comments or any further questions after reading this essay.&lt;/p&gt;&#xA;" OwnerUserId="4178" LastEditorUserId="4178" LastEditDate="2014-04-02T13:35:05.170" LastActivityDate="2014-04-02T13:35:05.170" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9634" PostTypeId="1" AcceptedAnswerId="9636" CreationDate="2013-08-05T15:33:38.417" Score="1" ViewCount="41" Body="&lt;p&gt;We know that mycorrhizal association helps the plant to absorb nutrients.&#xA;Why can't this association be exploited in agriculture ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can't we add spores of the specific fungi to specific plant and enjoy the benefit of this association as we would not have to add many fertilizers ?( We could add organic manure whose main drawback is the time it takes to release nutrients. The fungi could probably solve the problem.)&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-08-05T18:02:11.567" Title="Utilising Mycorrhizal Association" Tags="&lt;agriculture&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9636" PostTypeId="2" ParentId="9634" CreationDate="2013-08-05T18:02:11.567" Score="3" Body="&lt;p&gt;Mycorrhizal fungi are often used in small-scale agriculture for just that reason.  If you search mycorrhizae on amazon they sell it by the tub.  I think its especially used in organic gardening for just what you said, the slightly less-processed organic fertilizers are harder to take up by plants without their mycorrhizae partners.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure about how widespread the practice of applying mycorrhizae is in large-scale non-organic farming.  Judging by how big of a problem fertilizer runoff is, my guess is that a lot of companies have decided that their bottom line is best served by just swamping everything with artificial fertilizers.  I'm not sure how mycorrhizae is produced either, it might really be prohibitively expensive to scale production of it up that much.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-05T18:02:11.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9637" PostTypeId="1" AcceptedAnswerId="9643" CreationDate="2013-08-05T19:21:43.960" Score="3" ViewCount="43012" Body="&lt;p&gt;Sinus congestion often seems to be accompanied by excess pressure on the outer ears (as anyone who has shared a transcontinental flight with an infant can attest to) or fluid buildup in the canals.  An increase the capillary pressure within the ear canals would explain the pressure, but what is the physiological connection between the sinus pressure and pressure in the ears?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most obvious answer I can think of is that any direct drainage from the sinuses would cause a backup of fluid into the Eustachian tubes.  This would only explain pressure coming from the other side of the eardrum, but is such pressure simply relieved by blood pressure transfer to the capillaries in the ear canal, or is there a non-trivial mechanism by, e.g., a vagal circuit which governs the relationship between the sinuses and the outer ear? &lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2018-01-09T19:23:52.680" Title="How are the paranasal sinuses linked with the capillaries in the ear canals?" Tags="&lt;human-anatomy&gt;&lt;human-ear&gt;&lt;blood-pressure&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9638" PostTypeId="1" AcceptedAnswerId="16820" CreationDate="2013-08-05T19:32:33.963" Score="8" ViewCount="8909" Body="&lt;p&gt;I found this bug in my apartment in Chicago.  We had bed bugs in our house the previous year (but we thought we got rid of them).  This bug was very small - maybe 2 millimeters in length.  These photos are all of the very same bug (just different lighting).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/U72Md.png&quot; alt=&quot;bug photos&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4180" LastEditorUserId="3952" LastEditDate="2013-08-06T01:49:55.647" LastActivityDate="2014-04-24T06:59:51.530" Title="Species Identification - small insect: is this a bed bug?" Tags="&lt;entomology&gt;&lt;species-identification&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2021-01-05T05:11:49.553" ContentLicense="CC BY-SA 3.0" />
  <row Id="9639" PostTypeId="1" AcceptedAnswerId="9642" CreationDate="2013-08-05T19:58:28.273" Score="0" ViewCount="2289" Body="&lt;p&gt;I have read many papers that refer to cell type, cell state and cell function, but I haven't found an explicit definition for each of these terms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example &lt;a href=&quot;http://vir.sgmjournals.org/content/75/9/2367.full.pdf&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; (Brown et al. 1994. &lt;em&gt;J General Virology&lt;/em&gt; 75: 2367-2377) refers to cell type and cell state without providing an explicit definition of both terms.  I have a vague idea of what these terms mean but a more explicit definition would help me greatly in understanding them.&lt;/p&gt;&#xA;" OwnerUserId="1661" LastEditorUserId="107" LastEditDate="2013-08-05T20:05:33.263" LastActivityDate="2013-08-06T02:15:16.573" Title="Cell state and cell function" Tags="&lt;cell-biology&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9642" PostTypeId="2" ParentId="9639" CreationDate="2013-08-05T23:06:10.793" Score="2" Body="&lt;p&gt;Mainly cell type refers to the differentiation degree to form a cell population whose characteristics are identifiable by using simple microscopy, stains or immunological methods. Examples of cell types would be T8 lymphocytes, peripheral astrocytes or hepatocytes. Cell types can be pathological too, like tumor cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cell state makes references to the current physiological condition of a given cell. A given cell type can be found in different proliferation states, metabolic conditions (i.e: An adipocyte or a hepatocyte will have different metabolic profiles depending on the insulin and glucagon balance), electrophysiological state (The human oocyte rapidly changes its membrane potential once a spermatozoid has entered) or even degree of differentiation (The typical example are B lymphocytes, which can be in a &quot;naïve&quot; state if they haven't found an antigen, or into a mature state. Once they have matured, thay can be subdivided into cells that actively produce antibodies and cells that divide actively).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A cell function usually refers to a process that occurs inside a cell, or to the physiological function that cell type has in the whole organism. Cell functions could be metabolism, signaling, cell division, etc.; while also could be the likes of detoxification (hepatocytes), hormone production (Langerhans cells) or contraction (myocytes).&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="948" LastEditDate="2013-08-06T02:15:16.573" LastActivityDate="2013-08-06T02:15:16.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9643" PostTypeId="2" ParentId="9637" CreationDate="2013-08-05T23:17:21.137" Score="10" Body="&lt;p&gt;There is no direct link between the capillaries in the sinuses and the ear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Eustachian tubes drain the middle ear (between the eardrum and the inner ear) into the nasopharynx, the part of the throat that is just behind the nose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VlH7m.jpg&quot; alt=&quot;Eustachian tubes and middle ear via American Flyers&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The para-nasal sinuses drain into the nasal passages themselves at different points. The sinuses and middle ear constantly produce some fluid, which is either reabsorbed or drained.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Y6yyr.jpg&quot; alt=&quot;Paranasal Sinuses via Harvard Women&amp;#39;s Health Watch&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Often what happens is that in the case of a common cold or other upper respiratory tract infection, the nasopharynx and nasal mucosa are both infected. The inflammation causes swelling and blocks off the Eustachian tubes and the drainage pathways of the sinuses and the trapped fluid itself causes sinus &amp;amp; ear pain and can get infected causing sinusitis and otitis media. Alternatively a viral infection can also go up into the middle ear and sinuses causing direct infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The process that occurs when you go on a plane is slightly different. The Eustachian tubes and sinus openings collapse due to pressure and thus the natural fluid that is produced accumulates as well as there being an inability to neutralise the internal and external pressure (thus why making your ears 'pop' works- you force the Eustachian tubes open via positive pressure)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SouAk.gif&quot; alt=&quot;Blocked Eustachian tube via Merck Manual&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding blood supply of the paranasal sinuses and the ear:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ear is supplied by the posterior auricular and superficial temporal arteries of the external carotid artery.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IJi09.png&quot; alt=&quot;Branches of the external carotid artery via Medical Mnemonics&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paranasal sinuses are supplied by various branches of the internal and external carotid artery including the maxillary artery, anterior and posterior ethmoidal arteries, ophthalmic artery, supraorbital and supratrochlear arteries&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VZzd5.jpg&quot; alt=&quot;Branches of the internal carotid artery via Loyola University&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4182" LastEditorUserId="4182" LastEditDate="2013-08-06T05:23:26.203" LastActivityDate="2013-08-06T05:23:26.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9644" PostTypeId="2" ParentId="9261" CreationDate="2013-08-05T23:22:31.623" Score="1" Body="&lt;p&gt;Actually there are monolayers in some extremophilic archeon, wich have both layers of the regular membranes attached by covalent bonds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the main reason is that membranes are formed by virtue of hydrophobic interactions. Phospholipids are amphipathic mollecules wich have a polar &quot;head&quot; (given by the negative charge of the phosphate group) and an hydrophobic &quot;tail&quot; (usually two alliphatic chains). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mollecule tries to avoid the state of minimal entropy, wich in this case would be to &quot;swim&quot; freely in the water. In this hypothetical state, water mollecules would need to orientate themselves in order to minimize the contact with the hydrophobic tail (wich are very big mollecular gropus who doesn't atract the polar water mollecules) and to maximize the contact with the polar head. If this mollecule finds more mollecules of their kind they will stick together by their hydrophobic tails, because that will reduce the urge to organize water mollecules, and by so, raising the entropy of the system. There are some posible conformation wich allow to do this, and one or other will produce depending of the composition of the lipid mix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, membranes serve mainly as selective barriers wich separate the internal cell, whose conditions are regulated, and the outside. Membranes can have embeded enzymatical systems, such as photosystems, respiratory chains or some key metabolic paths. Also, they usually contain sensitive proteins who respond to the external condictions and regulate the behaviour of the cell. Other functions can be found, but those are the most important.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-08-05T23:22:31.623" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9645" PostTypeId="2" ParentId="8745" CreationDate="2013-08-05T23:35:06.330" Score="2" Body="&lt;p&gt;The easiest way to understand this, in my opinion, is to think in social insects. In the ants, for example, there are polymorphisms, since the workers don't have the same phenotype as the queen or the soldiers. Also, one could argue that the whole colony is a massive metaorganism or superorganism, formed by the summation of all the individual ants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As in an ant colony, in the case of Physalia, each one of the zooids have a fully formed body (cnidarians have a distinct body plan, consisting of a sac-like digestive system with a mouth crowned by tentacles, two embriologycal layers, etc.) and thus each zooid should be considered to be different individuals. In Physalia, the zooids are physically attached, but that's no different than siamese twins, who aren't usually considered to be only one organism.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="3952" LastEditDate="2013-08-06T00:35:21.530" LastActivityDate="2013-08-06T00:35:21.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9646" PostTypeId="1" AcceptedAnswerId="9648" CreationDate="2013-08-06T00:23:52.703" Score="4" ViewCount="108" Body="&lt;p&gt;As &lt;a href=&quot;http://www.eva.mpg.de/neandertal/index.html&quot; rel=&quot;nofollow&quot;&gt;Neanderthal DNA has been sequenced&lt;/a&gt;, is it possible to create a living Neanderthal?&lt;/p&gt;&#xA;" OwnerUserId="4183" LastActivityDate="2013-08-06T02:44:50.503" Title="Is it possible to clone a Neanderthal?" Tags="&lt;dna-sequencing&gt;&lt;cloning&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9647" PostTypeId="1" AcceptedAnswerId="9649" CreationDate="2013-08-06T01:09:26.990" Score="2" ViewCount="23401" Body="&lt;p&gt;There are two types of diabetes mellitus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a. Type 1 diabetes mellitus&#xA;b. Type 2 diabetes melliuts&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is either of them a sex linked disease? Can either one be inherited? My book says, &quot;this disease is transmitted as a recessive genetic characteristic.&quot; What does this mean?&lt;/p&gt;&#xA;" OwnerUserId="1765" LastEditorUserId="16299" LastEditDate="2015-12-06T04:42:42.340" LastActivityDate="2017-01-30T17:20:07.673" Title="Is diabetes mellitus a sex-linked disease?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9648" PostTypeId="2" ParentId="9646" CreationDate="2013-08-06T02:44:50.503" Score="3" Body="&lt;p&gt;Not any time soon.  By far the greatest challenge is getting the DNA sequence from the computer into a form that could be implanted into an embryo.  Craig Venter's team was able to build a bacterial genome &lt;a href=&quot;http://www.sciencemag.org/content/329/5987/52.abstract&quot; rel=&quot;nofollow&quot;&gt;from scratch&lt;/a&gt;, but that was incredibly painstaking work, requiring the assembly of many small fragments of DNA into a single circular chromosome.  With current technology that process becomes prohibitively difficult for a human-like genome.  You would have to build each chromosome from scratch, these chromosomes are linear, and you'd need to associate with them the various histones and other proteins help tightly fold them together.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another huge problem is epigenetics.  The next generation sequencing methods used for the neanderthal genome just give you DNA sequences, not what epigenetic modifications are present on that DNA.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Genomic_imprinting&quot; rel=&quot;nofollow&quot;&gt;Genomic imprinting&lt;/a&gt; in mammals is very important, and presents problems even in normal cloning efforts where genomes are taken wholesale from live animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not to mention that 1% of the current genome is contaminated with human DNA (not meant as a criticism, its amazing what they have been able to do with a toe bone if this work stands up to peer review).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And none of this takes into account the ethical problems associated with this.  Would you clone it in a human?  Chimp?  Either way its got serious ethical questions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dont take my word for it though, here is the leader of the project &lt;a href=&quot;http://readingeagle.com/article.aspx?id=125240&quot; rel=&quot;nofollow&quot;&gt;commenting&lt;/a&gt; on this question a few years ago:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Paabo said because the Neanderthal DNA was scattered in imperfect&#xA;  fossils, the notion of cloning a Neanderthal was far-fetched.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&quot;Starting from the DNA extracted from a fossil, it is and will remain&#xA;  impossible,&quot; he said. &quot;There is not really an improvement on current&#xA;  technologies that would make that possible.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-06T02:44:50.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9649" PostTypeId="2" ParentId="9647" CreationDate="2013-08-06T03:04:59.263" Score="8" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is either of them a sex linked disease? Can either one be inherited? My book says, &quot;this disease is transmitted as a recessive genetic characteristic.&quot; What does this mean?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Neither are sex-linked. Type 1 can be directly inherited (in a non-Mendelian fashion), but Type 2 genetic factors mostly increase risks. &quot;Recessive genetic traits&quot; are traits that only express themselves when ONLY the recessive alleles are present in the organism (a dominant allele, if present, will 'overpower' recessive one).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Longer info:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Diabetes_mellitus_type_1#Cause&quot; rel=&quot;noreferrer&quot;&gt;Diabetes mellitus Type 1 (Juvenile Diabetes)&lt;/a&gt; is inherited, but it is autosomal with complex dominant/recessive rules:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Type 1 diabetes is a polygenic disease, meaning many different genes contribute to its onset. Depending on locus or combination of loci, it can be dominant, recessive, or somewhere in between.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That results in some interesting, albeit complex, expressions:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The risk of a child developing type 1 diabetes is about 10% if the father has it, about 10% if a sibling has it, about 4% if the mother has type 1 diabetes and was aged 25 or younger when the child was born, and about 1% if the mother was over 25 years old when the child was born.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Diabetes_mellitus_type_2#Genetics&quot; rel=&quot;noreferrer&quot;&gt;Diabetes mellitus Type 2&lt;/a&gt; does have genetic components, but the vast majority merely increase the &lt;em&gt;risk of developing&lt;/em&gt; Type 2 Diabetes. Environmental factors play a large role in Type 2.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Excess body fat is associated with 30% of cases in those of Chinese and Japanese descent, 60-80% of cases in those of European and African descent, and 100% of Pima Indians and Pacific Islanders.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="3952" LastEditDate="2013-08-06T06:21:28.710" LastActivityDate="2013-08-06T06:21:28.710" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="9650" PostTypeId="1" AcceptedAnswerId="9651" CreationDate="2013-08-06T04:42:35.243" Score="3" ViewCount="652" Body="&lt;p&gt;Found in Russia in the kitchen. It is about 3 mm long.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4NIcn.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BFqsz.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3280" LastActivityDate="2013-08-06T06:14:28.170" Title="What kind of insect is this?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9651" PostTypeId="2" ParentId="9650" CreationDate="2013-08-06T05:55:30.683" Score="7" Body="&lt;p&gt;That is a flour beetle, the two most common and likely types are the confused flour beetle and red flour beetle but to identify look at the antennae. I'd suggest it is &lt;a href=&quot;http://ento.psu.edu/extension/factsheets/flour-beetle&quot;&gt;the confused flour beetle&lt;/a&gt; because the antenna go from thin to fat quite gradually, though the pictures may not be good enough for that to be certain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other commonly used names are tribolium (the genus name) or flour weevil. They are also used in labs as a model organism, groups in my last two labs have used them. &lt;a href=&quot;http://www.orkin.com/other/beetles/flour-beetles/&quot;&gt;They are a pest&lt;/a&gt; and you should probably get rid of them.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Both types of beetles are often found not only in infested grains,&#xA;  but in crevices in pantries and cabinet, as well. Damage to food is&#xA;  caused somewhat by the beetles' feeding, but also by their dead&#xA;  bodies, fecal pellets, and foul-smelling secretions. In addition to&#xA;  creating a foul odor, the beetles' presence encourages the growth of&#xA;  mold.&quot; - &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Confused_flour_beetle&quot;&gt;Wiki&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-08-06T06:14:28.170" LastActivityDate="2013-08-06T06:14:28.170" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9652" PostTypeId="2" ParentId="9578" CreationDate="2013-08-06T11:34:57.270" Score="3" Body="&lt;p&gt;Here is a quite nice &lt;a href=&quot;http://chemistry.about.com/library/weekly/aa082602a.htm&quot; rel=&quot;nofollow&quot;&gt;Chemistry of Autumn Leaf Color&lt;/a&gt;. And &lt;a href=&quot;http://www.na.fs.fed.us/fhp/pubs/leaves/leaves.shtm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; is a less chemical, but more detailed explanation regarding the triggering of colour change, which is quite similar to the one from the University of Illinois that @Oreotrephes already gave.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I understand it, during sunny days a lot of chlorophyll is broken down, but also built up. When after the summer the days get cold and dark, chlorophyll is built up slower (or not any more at some point) and you start to see the colour from the carotenoids and anthocyanins. A harsh change from sunny to cold and dark is supposedly bringing up the brightest colours. At some point, also the carotenoids break down and leaves get brown. The faster the change to cold and dark the larger is the frame between having all chlorophyll broken down and having the other colouring molecules broken down (-&gt; bright colours).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But that's the amateurs explanation.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-08-06T11:34:57.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9653" PostTypeId="1" CreationDate="2013-08-06T11:52:11.977" Score="9" ViewCount="265" Body="&lt;p&gt;Most textbooks seems to restrict pathogens to the domains bacteria and eukarya. Are there any pathogenic archaeans?&lt;/p&gt;&#xA;" OwnerUserId="81" LastEditorUserId="24354" LastEditDate="2020-07-22T04:02:32.947" LastActivityDate="2020-07-22T04:02:32.947" Title="Are there any pathogenic archaeans?" Tags="&lt;microbiology&gt;&lt;pathology&gt;&lt;archaea&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9654" PostTypeId="1" CreationDate="2013-08-06T11:57:27.077" Score="9" ViewCount="832" Body="&lt;p&gt;I remember hearing various sleep related advice as a child, like &quot;sleep on your right side&quot;, or &quot; have your head pointed in X direction&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any biological reason why sleeping on one side versus another, or with a head pointed in some direction is beneficial for humans?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2013-08-07T00:31:45.470" Title="Is there a preferred sleeping position for humans?" Tags="&lt;human-biology&gt;&lt;sleep&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9655" PostTypeId="2" ParentId="9653" CreationDate="2013-08-06T13:22:43.517" Score="4" Body="&lt;p&gt;To date, there isn't a single species that may be considered pathogenic to animals or plants. There are archeon who live in association with animals (in the case of human, they have been found in the gut microbiota aswell as certain skin surfaces) that are mainly methanogens. This could lead to think that archaons could produce &quot;pathologic farting&quot;, but that condition has never been described. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of ascidians and other marine invertebrates, some archeon have been found living in symbiosis, with the microbe aiding the animal by means of nitrogen fixation. One could think that, since they're able to live inside the organisms, they could behave as opportunistic pathogens, but none has been described.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, it actually exists at least one known species who could be classified as parasitic, the nanoarchaeota &lt;em&gt;Nanoarchaeum equitans&lt;/em&gt;, which has been described as a symbiont of some hyperthermophilic archaeon. Despite that description as symbiont, &lt;em&gt;Nanoarchaeum&lt;/em&gt; cannot live by its own, while its companion does. Moreover, its genome contains the typical traits associated to parasitism, with great reduction in genome size and loss of many key pathways and cell functions, including methabolic pathways an even some key components of its transcriptional and translational machinery. Since there is no known function of the Nanoarchaeum itself, it should be considered as a parasite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the lack of evidence may be biased, since few people has used metagenomic approach to look for archeon in clinical samples, and some rare cases may be found in the future.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="137" LastEditDate="2013-08-06T16:25:29.043" LastActivityDate="2013-08-06T16:25:29.043" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9656" PostTypeId="1" CreationDate="2013-08-06T18:54:22.543" Score="3" ViewCount="346" Body="&lt;p&gt;Has it been demonstrated that the memory of human brain is just connections between neurons, not &quot;long&quot; molecules such as RNA or proteins?&lt;/p&gt;&#xA;" OwnerUserId="4186" LastEditorUserId="1306" LastEditDate="2013-08-07T14:00:15.787" LastActivityDate="2013-08-07T14:00:15.787" Title="Molecules and human memory" Tags="&lt;biochemistry&gt;&lt;neuroscience&gt;&lt;brain&gt;&lt;memory&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9658" PostTypeId="2" ParentId="9654" CreationDate="2013-08-06T20:49:19.137" Score="4" Body="&lt;p&gt;The enWikipedia &lt;a href=&quot;https://en.wikipedia.org/wiki/Sleeping_positions&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; summarizes the best/only real research on positions that I am aware of.  I read a book in high school (that is to say it was old and I have no idea what the title was) that claimed that the semi-fetal position was the best, as it supposedly maximized protection without compromising breathing too much.  I can't say I've seen anything that would indicate your head's direction actually matters, except as it depends on the position of the rest of your body.  Do you mean facing North or the door?  That's some Feng Shui stuff or something similar, which is meaningless.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of which side to sleep on, there is actually an answer!  Well, maybe.  Sleeping on your left side aggravates heartburn more than sleeping on the right side&lt;sup&gt;&lt;a href=&quot;http://www.nytimes.com/2010/10/26/health/26really.html&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;&lt;/sup&gt;, but sleeping on your left may be somewhat associated with heart problems.&lt;sup&gt;&lt;a href=&quot;http://www.nytimes.com/2011/02/22/science/22qna.html&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;&lt;/sup&gt;  From what I can read from the studies, the heartburn one sounds more causative, but then again dying is worse than a little heartburn...  In the end, though, about the only thing that matters is that sleeping on yours side can lower the amount of snoring (annoying) and sleep apnea (unhealthy).&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-06T20:49:19.137" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9659" PostTypeId="2" ParentId="9653" CreationDate="2013-08-06T22:06:10.763" Score="1" Body="&lt;p&gt;Actually, there exist at least one reference to a negative effect of &lt;em&gt;Nanoarchaeum&lt;/em&gt; towards its host. Jahn et al (2008) describes that single Ignicoccus cells wich had more than two Nanoarchaeum cells attached were unable to grow, while those with two or less could form a colony. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's true that there isn't strong evidence to considere &lt;em&gt;Nanoarchaeum&lt;/em&gt; as a parasite in the traditional sense, provided this is the only reference I have found to a negative (or positive) effect of this archeon. It's also true that even traditional symbiots such as micorhizic fungi can be harmful in certain conditions, and because of that, this lonely example wouldn't be representative. However, untill this reference there were the same evidence to consider this archaeon as a symbiot or as a parasite, and for unkown reasons the first hypothesis was assumed by default. This results sugest that &lt;em&gt;Nanoarcheum&lt;/em&gt; is potentially harmful and, since there still isn't any evidence that demostrate that Nanoarchaeum has any benefit, I strongly believe the consideration of a putative parasite should be encouraged and used as the default hypothesis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some authors prefer to use the term &quot;intimal association&quot;, and they define it as &quot;a highly specialized system combining characteristics of symbiosis, commensalisms, and parasitism&quot; wich tries to be something neutral beween the two hypothesis. However I find that expression unnecesary, confuse and with an strong lack of meaning; mainly because that kind of relationship can be described with classical ecologycal terms.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="4168" LastEditDate="2013-08-06T22:12:11.980" LastActivityDate="2013-08-06T22:12:11.980" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9660" PostTypeId="2" ParentId="9654" CreationDate="2013-08-07T00:31:45.470" Score="4" Body="&lt;p&gt;&lt;em&gt;Disclaimer: Not in any way my area of expertise. Maybe someone else can expand&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;In relation to pregnancy, there exist one australian study (&lt;a href=&quot;http://www.bmj.com/content/342/bmj.d3403&quot; rel=&quot;nofollow&quot; title=&quot;Stacey et al. 2011. Association between maternal sleep practices and risk of late stillbirth: a case-control study. BMJ 342:d3403&quot;&gt;Stacey et al. 2011&lt;/a&gt;) that reports an increased risk of still-birth for women that sleep on their back at the later stages of pregnancy. The purported mechanism is pressure from the uterus on the inferior vena cava and aorta, restricting blood flow. Lowest risk was found for women that sleep on their left side (less pressure on the liver). Another recent study from Ghana (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0020729213000945&quot; rel=&quot;nofollow&quot; title=&quot;Owusu et al. 2013. Association of maternal sleep practices with pre-eclampsia, low birth weight, and stillbirth among Ghanaian women. International Journal of Gynecology &amp;amp; Obstetrics 121(3):  261–265&quot;&gt;Owusu et al. 2013&lt;/a&gt;) has found similar results, with associations between sleep position (supine position) and birth weight or risk of still birth. However, the studies are relatively small and the results must be further corroborated.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2013-08-07T00:31:45.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9661" PostTypeId="2" ParentId="9656" CreationDate="2013-08-07T03:52:18.920" Score="9" Body="&lt;p&gt;The idea that memories could be stored as RNA or proteins is an old one.  It got a lot of attention decades ago when James McConnell did a number of experiments where he conditioned planarian flatworms to respond to certain stimuli, ground them up, fed them to worms that hadn't gone through the conditioning.  He claimed to have observed that the worms fed conditioned worms learned to respond to the stimuli faster.  This supported the idea that memories were just RNA or proteins, and thus survived the grinding up process.  His results were not readily reproducible, and so the idea fell out of favor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been a number of studies at this point that have been able to look at the firing of individual neurons and shown that there are unique patterns that respond to different stimuli, for example: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10966627&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/10966627&lt;/a&gt;  So I think it is pretty well established that there are certain connections between neurons that are critical, sometimes even individual neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That doesn't necessarily rule out that there are unique RNA or proteins in those specific neurons, and they are whats actually storing the memory.  I'm not a neuroscientist, but I think the biggest argument against such a storage system is simply the speed with which you can recognize something.  When you see a face you know you nearly instantly recognize the person, and have a flood of memories about that person.  If the memories were somehow stored in RNA or protein structures, I think it would take much longer to somehow &quot;read-out&quot; that data from the molecular structure.  The only thing that really works that fast are the action potentials in neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An interesting comparison might be made to the system in our bodies that DOES have molecular-based memory, the immune system.  When you get sick with a cold you've never been sick with, your immune system doesn't immediately recognize the antigens that come from that virus.  Through the process of somatic hypermutation, your body produces B- and T-cells that have protein receptors that recognize the viruses and the cells infected by the viruses and go and kill them.  A small subset of the T and B cells that have the molecular recognition of that cold become 'memory' cells.  These memory cells that go into a quiescent phase, waiting around until the next time that cold infects you.  But that time they 'remember' it immediately, and you dont get nearly as sick, if at all, because the genes for those recognition proteins are stored in the memory cells.  The activation of immunological memory cells takes a long time as compared to remembering a face, or some other normal memory function, so such a molecular system couldn't be responsible.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastEditorUserId="4177" LastEditDate="2013-08-07T03:57:59.103" LastActivityDate="2013-08-07T03:57:59.103" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9662" PostTypeId="1" AcceptedAnswerId="17896" CreationDate="2013-08-07T08:39:19.083" Score="2" ViewCount="225" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Color_blindness#Red.E2.80.93green_color_blindness&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Color_blindness#Red.E2.80.93green_color_blindness&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Protanopia (1% of males): Lacking the long-wavelength sensitive retinal cones, &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Deuteranopia (1% of males): Lacking the medium-wavelength cones, &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Do they lack &lt;em&gt;all&lt;/em&gt; those cones, or are they just (severely) short? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/9662/do-colorblinds-have-less-cones-or-no-cones-of-a-certain-type&quot;&gt;&lt;/a&gt;&#xA;&lt;a href=&quot;https://biology.stackexchange.com/questions/9663/colorblinds-can-match-any-colors-with-some-mixture-of-just-two-primary-colors&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3141" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-06-05T06:19:12.593" Title="Do people with colorblindness have less cones or no cones of a certain type?" Tags="&lt;neuroscience&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9664" PostTypeId="1" AcceptedAnswerId="9666" CreationDate="2013-08-07T08:51:23.703" Score="4" ViewCount="657" Body="&lt;p&gt;The 3 types of cone cells in normal humans allow them to view 3 types of colors and any color made from mixing and matching those 3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, 2 types of cone cells should only allow to view just 2 types of colors and any colors made from those two. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But that is clearly not the case. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Color_blindness#Red.E2.80.93green_color_blindness&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Color_blindness#Red.E2.80.93green_color_blindness&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Protanopes, deuteranopes, and tritanopes are dichromats; that is, they can match any color they see with some mixture of just two primary colors (whereas normally humans are trichromats and require three primary colors). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also, from personal experience, I'm colorblind and can see and differentiate all 3 red, green, and blue. It's just the hues between red-green and green-blue I can't distinguish much... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How exactly do dichromats see all three colors when they lack one type of cone cell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/9662/do-colorblinds-have-less-cones-or-no-cones-of-a-certain-type?lq=1&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3141" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2018-05-02T06:40:20.003" Title="If people with colorblindness lack one type of cone cells, shouldn't they be unable to recognize one particular color?" Tags="&lt;neuroscience&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9665" PostTypeId="1" AcceptedAnswerId="50823" CreationDate="2013-08-07T09:00:05.827" Score="4" ViewCount="197" Body="&lt;p&gt;These things recently appeared in my tap water Copenhagen Denmark, this summer 2013. They are very small, and have a feather like structure. I've called the water supply, and they thought that it was some tracer put in there by humans to trace if the warm water supply leaks into the tap water. But I could not show them the pictures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/abDMQ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZKmBz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hakjO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are they? Are they dangerous?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For size comparison: the green stuff is located on the top right of a piece of A4 paper.&lt;/p&gt;&#xA;" OwnerUserId="4188" LastEditorUserId="1306" LastEditDate="2013-08-07T13:59:15.610" LastActivityDate="2016-08-18T08:20:45.190" Title="Green feather-like formations in tap water - what is it? (with pictures)" Tags="&lt;zoology&gt;&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9666" PostTypeId="2" ParentId="9664" CreationDate="2013-08-07T13:37:06.503" Score="6" Body="&lt;p&gt;Cones do not literally interpret colors.  The three cones work together to encode a signal that is abstractly interpreted by your brain in higher processing centers.  Here is what neuroscientists currently think the decoding scheme looks like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Cone_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/1/1e/Cones_SMJ2_E.svg&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leads to what's called &lt;a href=&quot;https://en.wikipedia.org/wiki/Opponent_process&quot; rel=&quot;nofollow noreferrer&quot;&gt;opponent process&lt;/a&gt;, an antagonist mechanism whereby the perception of green/red are a matter of the contrast between the two.  In a deuteranopes, the mechanism of antagonism is missing, so the colors can not be differentiated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What this implies is that (to some extent) a single color has no meaning.  Colors are only meaningful in the context of other colors.&lt;/p&gt;&#xA;" OwnerUserId="1853" LastEditorUserId="3141" LastEditDate="2018-05-02T06:40:20.003" LastActivityDate="2018-05-02T06:40:20.003" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="9667" PostTypeId="1" CreationDate="2013-08-07T15:05:43.110" Score="3" ViewCount="813" Body="&lt;p&gt;Do neuroscientists already know what areas of the brain are involved in mental calculations? Has any fruitful research been done on that or not yet? Do you think that if we understand what areas of our brain are responsible for doing arithmetical tasks we may one day have the ability to improve someone's calculation skills by non-invasive methods?&lt;/p&gt;&#xA;" OwnerUserId="4191" LastActivityDate="2013-08-25T04:30:39.013" Title="What areas of the brain are involved in doing arithmetic operations?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9668" PostTypeId="1" AcceptedAnswerId="9673" CreationDate="2013-08-07T16:16:17.737" Score="18" ViewCount="29126" Body="&lt;p&gt;Is it possible that a human or any other creature can die from pain?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I googled and found different answers. Some articles say Yes while others say No.&lt;/p&gt;&#xA;" OwnerUserId="4192" LastEditorUserId="107" LastEditDate="2013-08-07T18:49:19.753" LastActivityDate="2016-05-04T15:16:21.390" Title="Can one die from pain?" Tags="&lt;human-biology&gt;&lt;death&gt;&lt;pain&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9669" PostTypeId="1" AcceptedAnswerId="9672" CreationDate="2013-08-07T17:06:48.693" Score="5" ViewCount="422" Body="&lt;p&gt;The point of my question is not to talk about events that are uncontrolled by living organisms. My question is about controlled randomness, or I'd like to say adaptive random process. Process that are random because it was selected in order to be random.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first thing that pop in my mind when thinking of &quot;adaptive random process&quot; in biology is Fair Meiosis. &lt;strong&gt;Do you have other examples of &quot;adaptive random process&quot;?&lt;/strong&gt; An individual might display a random behaviour in order to avoid that others to predict its future behaviour. Is there any evidence for such things? Do you know any other evidence on what I called &quot;adaptive random process&quot;?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-08-07T18:33:28.227" LastActivityDate="2016-04-25T18:08:30.537" Title="Randomness in living systems" Tags="&lt;evolution&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;meiosis&gt;&lt;theoretical-biology&gt;" AnswerCount="2" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9670" PostTypeId="1" AcceptedAnswerId="9675" CreationDate="2013-08-07T17:24:52.370" Score="4" ViewCount="665" Body="&lt;p&gt;How and why did Fair Meiosis evolve?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can hardly think that it provided a fitness advantage to the individual carrying the mutation. Why would it? Or did it evolve through lineage selection? Or was it some kind of pre-existing characteristic of meiosis that have no energy cost and therefore never disappear?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I call fair meiosis the process of meiosis in which each chromosome has an equal chance of transmission.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm trying to make my questions clearer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any selection pressure in favour of alleles causing a fair meiosis? If yes, why? It doesn't seem to me to provide any advantage to the individual carrying this allele.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-08-07T20:25:10.973" LastActivityDate="2013-08-08T11:16:17.480" Title="Why did Fair Meiosis evolve?" Tags="&lt;evolution&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;meiosis&gt;&lt;theoretical-biology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9671" PostTypeId="1" AcceptedAnswerId="10726" CreationDate="2013-08-07T17:28:04.193" Score="3" ViewCount="11068" Body="&lt;p&gt;I have heard that there is a difference between viral and human genetic material. What is that difference?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I take my cells and take DNA out of them and insert only a small part of it having a sequence, say, AGTTC, and viral DNA with the same sequence, can my body distinguish between the two? If so, how?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-05T14:26:30.253" LastActivityDate="2013-10-05T14:33:52.343" Title="Difference between viral and human genetic material" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;immunology&gt;&lt;virology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9672" PostTypeId="2" ParentId="9669" CreationDate="2013-08-07T18:40:05.020" Score="2" Body="&lt;p&gt;In an evolution mutations are often random and lead to differences in phenotype that can be adaptive under certain pressures.  A lot of times mutation is a random process, but here are three cases I can think of off of the top of my head where I would say the organism is 'trying' to do it:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HIV is a retrovirus, which means in its viral form its genome is single stranded RNA, which is then converted into double stranded DNA within the host.  That conversion is carried out by a virally encoded reverse transcriptase.  This enzyme has a much higher error rate when making the RNA into DNA because it cannot proofread like our DNA polymerases.  This means that HIV mutates incredibly fast.  Many of these mutants are not very fit, but since there is so much selective pressure against staying the same due to attack from the immune system, some mutants will be much more fit if they can avoid that attack.  Its a numbers game, and by making lots of random mutants HIV is very good at it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A related, but different case is found in the diversity generating retroelements of certain bacteriophages.  These are double stranded DNA viruses that infect bacteria.  The bacteria these viruses infect could mutate to escape the viruses by losing a certain receptor that the virus binds to.  It was observed however that the the virus would mutate incredibly quickly to bind to a different receptor, a lot faster than would be expected for a DNA virus.  Also, it was found that these viruses contained reverse transcriptases, which is bizarre, since there is no reverse transcription step in a dsDNA viral life-cycle (so we thought).  To make a long story short, this virus will transcribe the DNA that codes for its binding proteins into RNA, then use its reverse transcriptase to turn that RNA BACK into DNA, but uses a sophisticated targeting strategy so that it only mutates the region that is used for binding to the bacteria.  It will only mutate adenine residues, leaving the C's, T's and G's alone.  This is a much more clever system than HIV, because this virus uses site-specific mutations on its binding feet, and doesn't mutate its core proteins, the mutation of which would probably just lead to viruses that couldnt replicate.  Here a reference for the interested: &lt;a href=&quot;http://www.nature.com/nature/journal/v431/n7007/abs/nature02833.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nature/journal/v431/n7007/abs/nature02833.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just so you dont think this is reserved to viruses, we do this as well with our immune system.  In order to recognize antigens in attacking pathogens, our immune cells have two methods for making diverse, random, receptors.  First is V(D)J recombination, where the multiple diverse copies of the V, D and J regions of antibodies and receptors are combined at random to make one set.  Wiki says theres 3x10^11 possible combinations &lt;a href=&quot;http://en.wikipedia.org/wiki/V%28D%29J_recombination&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.  After that, theres also &lt;a href=&quot;http://en.wikipedia.org/wiki/Somatic_hypermutation&quot; rel=&quot;nofollow&quot;&gt;somatic hypermutation&lt;/a&gt; during the proliferation of B cells.  In this process, the random mutation rate is hugely increased in the region of the B cell receptor gene, specifically for making slightly different versions of the already 'OK' receptor to make it a great receptor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;General theme: raising your mutation rate, either across the board(HIV) or specifically (DGRE and SHM) is a good way to intentionally add randomness for a beneficial purpose (to the extent that you can attribute 'intent' to a viral particle).&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-07T18:40:05.020" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9673" PostTypeId="2" ParentId="9668" CreationDate="2013-08-07T19:14:11.973" Score="6" Body="&lt;p&gt;I very much doubt it. You may however die from whatever's &lt;em&gt;causing&lt;/em&gt; the pain. The reason you feel pain is so you stop doing whatever is causing the pain. Hence someone knows not to touch a hot fire because it is painful. But the pain itself is not actually the danger - it's the fire burning away skin. So pain is actually a good thing, a survival mechanism. So for something that is meant to prevent death it's hard to imagine it doing the opposite. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps if you were in SO much pain you may be unable to breath and paralysed - but even then I still think you'd go unconscious before that would happen, and you'd start breathing again, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only other thing I can imagine is having a cardiac event, and the heart stopping. Again, this would be because of stress. Other than that - you may commit suicide on account of insufferable pain, however it's a different situation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However pain never comes on its own for no reason, just like smoke needs a fire. In this case it's the fire - not the smoke, that will kill you!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;People who've ever been in a desperate or life threatening situation like a car accident, have often walked on a broken leg for example - feeling no pain. In this case the body was giving them a chance to escape what might have been a lion, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, no - I don't think you can. However I cannot give a 100% correct answer. It would take just one example to prove that however!&lt;/p&gt;&#xA;" OwnerUserId="4194" LastActivityDate="2013-08-07T19:14:11.973" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9674" PostTypeId="2" ParentId="9670" CreationDate="2013-08-07T19:57:55.637" Score="3" Body="&lt;p&gt;I think that &lt;em&gt;Fair meiosis&lt;/em&gt; (I assume that you are referring to that chromosomes have an equal chance of transmission) can be seen as a byproduct of recombination at meiosis, which makes every chromosome a mosaic of maternal and paternal chromosomes. Therefore, selection does not act on chromosomes as a single unit, and &quot;unfair&quot; meiosis becomes meaningless. The &quot;value&quot; of &quot;fair meiosis&quot; most likely lies in the adaptive value of recombination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Addition: To expand on the value of recombination, it has been suggested that the specific value of recombination is to break up linkages and thereby prevent meiotic drive (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1806752&quot; rel=&quot;nofollow&quot; title=&quot;Haig &amp;amp; Grafen. 1991. Genetic scrambling as a defence against meiotic drive. J Theor Biol 153(4):531-58.&quot;&gt;Haig &amp;amp; Grafen 1991&lt;/a&gt;, also see &lt;a href=&quot;http://www.oxfordscholarship.com/view/10.1093/acprof%3aoso/9780199267972.001.0001/acprof-9780199267972&quot; rel=&quot;nofollow&quot; title=&quot;Okasha. 2006. Evolution and the Levels of Selection. Oxford University Press&quot;&gt;Okasha 2006&lt;/a&gt;). &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1806752&quot; rel=&quot;nofollow&quot; title=&quot;Haig &amp;amp; Grafen. 1991. Genetic scrambling as a defence against meiotic drive. J Theor Biol 153(4):531-58.&quot;&gt;Haig &amp;amp; Grafen 1991&lt;/a&gt; also specifically discuss selection for recombination. For an interesting analogy between economy and fair meiosis (veil-of-ignorance vs fair meiosis) see &lt;a href=&quot;http://dx.doi.org/10.1017/S0266267112000119&quot; rel=&quot;nofollow&quot; title=&quot;Okasha. 2012. SOCIAL JUSTICE, GENOMIC JUSTICE AND THE VEIL OF IGNORANCE: HARSANYI MEETS MENDEL. Economics and Philosophy 28(1): 43-71.&quot;&gt;Okasha. 2012&lt;/a&gt;. Okasha notes that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In both, randomization is used to deprive self-interested agents (genes and individuals) of information about their identity, forcing them to adopt an impartial perspective.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In summary he also writes that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A gene that distorts segregation in its favour can spread despite reducing its host’s&#xA;  fitness. This harms genes at unlinked loci, who are thus under selection to&#xA;  restore fair meiosis if they can. One effect of fair meiosis is to equalize the&#xA;  interests of all the genes, thus ensuring they work for the common good.&#xA;  One way of achieving this is to destroy linkage, given that segregation&#xA;  distortion typically involves linked genes working in concert.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Okasha's paper also has a nice and accessible description of the biological process, and of the selective forces that are operating to counterbalance meiotic drive/segregation disorders.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-08-08T11:16:17.480" LastActivityDate="2013-08-08T11:16:17.480" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9675" PostTypeId="2" ParentId="9670" CreationDate="2013-08-07T22:59:21.410" Score="1" Body="&lt;p&gt;There's a more meta-level discussion on meiosis, which is that there is an advantage for genes which can get themselves selected in meiosis more often would prosper.  This is a prediction of the biologist Robert Trivers, working with Bill Hamilton in the late '60s, known also as the 'selfish gene'.  In fact the reason the selfish gene theory was so successful was that selfish genes - individual genes which propagated to offspring more often than 50% of the time. The Dawkins book 'The Selfish Gene' discusses this whole idea and its ramifications in great detail. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So at different times in evolutionary history, its hard to imagine that meiosis was completely 'fair' (50/50% change of any segment of DNA being chosen). In fact its pretty clear from genetic analysis now that some longer segments of DNA tend to be transmitted in one piece, though overall its still felt that the propagation if 50% likely for any given segment.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Over the long run, its been shown, mostly through game theory, that honesty is the best and most profitable policy.  The most famous of these experiments was the &lt;a href=&quot;http://en.wikipedia.org/wiki/Prisoner%27s_dilemma&quot; rel=&quot;nofollow&quot;&gt;Prisoner's dilemma&lt;/a&gt; competition where all comers have been invited to submit computer programs which can either betray or cooperate.  Overall cooperative programs with some safegaurds which punished cheaters win overall.  Over time its been shown that systems tend to defend themselves from cheaters and that cooperation and 'fairness' do much better than mobs of cheaters running amok. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cheaters and unfairness still continue to happen though - systems which are fair tend to invite in a small number of cheaters.  Say what you will about the income tax as a system!  there is variance over time as to how 'fair' a system can be. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dawkins has even said he sometimes thinks he should have titled the 'selfish gene' something else instead: '&lt;a href=&quot;http://en.wikipedia.org/wiki/Nice_Guys_Finish_First&quot; rel=&quot;nofollow&quot;&gt;Nice Guys Finish First&lt;/a&gt;'.  I doubt that the book would quite have done as well though... we all should be fair, but it doesn't seem to invite book sales.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-08-07T22:59:21.410" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9676" PostTypeId="2" ParentId="9032" CreationDate="2013-08-08T00:21:25.097" Score="1" Body="&lt;p&gt;When cells are not producing proteins they are performing their specialized functions.  Consider red blood cells carrying oxygen.  Or gut epithelial cells aiding in your digestion.  The list goes on...liver cells have a different role than the keratin cells in your hair.  There is a lot of transport that goes on as well in an certain cells that is carried out by motor proteins such as myosins, kinesins, and dyneins.  Cells are producing ATP to power these motors and many other integral functions. Also, consider cell replication and the machinery needed for that to occur. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may visit Wikipedia for more information on motor proteins.&#xA;&lt;a href=&quot;https://en.wikipedia.org/wiki/Motor_protein&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Motor_protein&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4175" LastActivityDate="2013-08-08T00:21:25.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9677" PostTypeId="1" AcceptedAnswerId="9678" CreationDate="2013-08-08T00:38:51.083" Score="6" ViewCount="1147" Body="&lt;p&gt;In certain species only the dominant male gets to mate (or given strong preference), and yet the sex ratio remains 1:1. (I'm thinking in particular of gorillas). How does this happen? It doesn't seem like Fisher's argument should apply in this case.&lt;/p&gt;&#xA;" OwnerUserId="4195" LastEditorUserId="3624" LastEditDate="2013-08-08T13:15:04.617" LastActivityDate="2013-08-08T13:15:04.617" Title="How can sex ratios remain Fisherian (1:1) in species where only the dominant male gets to mate" Tags="&lt;evolution&gt;&lt;selection&gt;&lt;sex-ratio&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9678" PostTypeId="2" ParentId="9677" CreationDate="2013-08-08T01:16:54.737" Score="13" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fisher%27s_principle&quot;&gt;Fisher's principle&lt;/a&gt; applies to such cases as much as it does to species where only pairs mate.  Consider a species where a successful male has exclusive mating with a harem of 20 females, and for each such male, 19 other males are not able to mate.  A female has 100% chance of mating, and a male has a 5% (1 in 20) chance of mating. Assume a female has two offspring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this scenario, an equal sex ratio would mean having a &lt;em&gt;female&lt;/em&gt; offspring would lead to an expected number of grand-offspring of 2 (100% chance of 2 offspring from that female).  Having a &lt;em&gt;male&lt;/em&gt; offspring would also lead to an expected number of 2 grand-offspring (95% times 0 offspring plus 5% times 20 harem females each having 2 offspring).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would happen if the ratio of births was off from 1 to 1, say 5 females were born for each male? Then expected number of grand offspring would be for a female is still 2, but for a male it is 25% (chance of taking a harem of 20 females against the 3 other males born alongside those 20 females) x 40 (20 harem matings x 2 offspring) = 10. Hence with a lopsided sex ratio in this situation, having a male is much more valuable genetically than having a female.  If a mutant arose which produced more male offspring in this imbalanced situation, it would have success until the population sex ratio became close to 1:1.&lt;/p&gt;&#xA;" OwnerUserId="231" LastEditorUserId="231" LastEditDate="2013-08-08T01:27:11.110" LastActivityDate="2013-08-08T01:27:11.110" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9679" PostTypeId="5" CreationDate="2013-08-08T02:40:00.980" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-08-08T02:40:00.980" LastActivityDate="2013-08-08T02:40:00.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9680" PostTypeId="4" CreationDate="2013-08-08T02:40:00.980" Score="0" Body="The people-biota-environment interface: organisms used by humans, and the ways humans conceive of those organisms. This can include wild, managed or domesticated organisms used for food, medicine, and other purposes, as well as &quot;folk&quot; understandings of taxonomy, botany, zoology, conservation, and the environment." OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-08-09T08:05:52.783" LastActivityDate="2013-08-09T08:05:52.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9681" PostTypeId="1" AcceptedAnswerId="9697" CreationDate="2013-08-08T06:52:05.310" Score="2" ViewCount="112" Body="&lt;p&gt;The oligodendrocytes makes the myelin sheath in CNS and schwann cells make it in PNS. What decides where the oligodendrocyte or Schwann cell will attach and start forming myelin sheath? Is it genetically determined? Is it random? Is there any disease associated with improper positioning of node of Ranvier?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2013-08-08T13:16:40.343" LastActivityDate="2013-08-10T00:33:35.390" Title="What decides the position of the node of Ranvier?" Tags="&lt;neuroscience&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9682" PostTypeId="1" AcceptedAnswerId="9705" CreationDate="2013-08-08T06:57:56.563" Score="2" ViewCount="129" Body="&lt;p&gt;It is being said that organs can be obtained for transplant from the pigs. What is special about pigs that we are using them? Why can't we use monkeys or chimpanzees with whom we share a more recent common ancestor?&lt;/p&gt;&#xA;" OwnerUserId="4058" LastEditorUserId="107" LastEditDate="2013-08-08T13:17:18.093" LastActivityDate="2013-08-09T20:09:48.193" Title="Use of pigs for obtaining transplant organs" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9683" PostTypeId="2" ParentId="9677" CreationDate="2013-08-08T10:05:31.080" Score="3" Body="&lt;p&gt;mgkrebbs has already covered the maths that leads to the preservation of ratio, so I'll not recap.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might have noticed that the argument only remains true if you don't know whether the particular male you produce is likely to be the dominant male or not. If you could &quot;know&quot; in advance that your particular son was more likely to be dominant it would make sense to skew their sex ratio towards male and &lt;em&gt;vice versa&lt;/em&gt;. It may interest you to know that this actually happens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Males born to high ranking females are more likely to succeed than males born to low ranking females. This makes intuitive sense as they'll get better access to food and the same genetic traits that help a female become dominant may help the male become dominant too. What's fascinating is that this actually leads to top ranking females having a male-skewed sex ratio among their offspring, and low ranking females having a female-skewed sex ratio.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0003347286801154&quot; rel=&quot;nofollow&quot;&gt;Great expectations: dominance, breeding success and offspring sex ratios in red deer&lt;/a&gt; for the original paper. I do not know what the mechanism behind the sex selection is.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-08-08T10:05:31.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9684" PostTypeId="1" AcceptedAnswerId="9728" CreationDate="2013-08-08T13:13:16.907" Score="5" ViewCount="302" Body="&lt;p&gt;The official &lt;a href=&quot;http://www.genenames.org/data/hgnc_data.php?hgnc_id=30224&quot;&gt;HUGO gene nomenclature&lt;/a&gt; page says that GPR172A (Gamma-hydroxybutyrate receptor) and SLC52A2 (riboflavin transporter, member 2) are the same. The sequence reported by &lt;a href=&quot;http://www.fasebj.org/content/21/3/885&quot;&gt;Andriamampandry&lt;/a&gt; seems to be the same, but I find no other evidence. Can anyone enlighten me? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I'm wondering if I should add the &lt;a href=&quot;http://en.wikipedia.org/wiki/Template%3aPBB/79581&quot;&gt;SLC52A2 information&lt;/a&gt; to the &lt;a href=&quot;http://en.wikipedia.org/wiki/GHB_receptor&quot;&gt;GHB receptor Wikipedia page&lt;/a&gt;.)&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2019-04-24T16:42:29.153" Title="Are SLC52A2 and GPR172A really the same?" Tags="&lt;proteins&gt;&lt;nomenclature&gt;&lt;receptor&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9685" PostTypeId="1" CreationDate="2013-08-08T13:57:04.293" Score="2" ViewCount="170" Body="&lt;p&gt;I have one sequence that composed of sequences of three genes. I should determine the direction of each gene, but two of these genes are disrupted, and I can't determine the initial codon. Does anyone knows how I can determine the direction of genes?&lt;/p&gt;&#xA;" OwnerUserId="4197" LastEditorUserId="107" LastEditDate="2013-08-08T14:15:13.277" LastActivityDate="2013-08-08T14:44:52.830" Title="Determination of gene direction" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;sequence-analysis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9686" PostTypeId="2" ParentId="9685" CreationDate="2013-08-08T14:44:52.830" Score="1" Body="&lt;p&gt;I'd first try translating it and looking to see if there are big regions that jump out at you that do not have stop codons in them.  I normally use &lt;a href=&quot;http://web.expasy.org/translate/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; tool for quick and dirty translations, it gives you all 6 reading frames.  Also, you could just try &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&amp;amp;BLAST_PROGRAMS=blastx&amp;amp;PAGE_TYPE=BlastSearch&amp;amp;SHOW_DEFAULTS=on&amp;amp;LINK_LOC=blasthome&quot; rel=&quot;nofollow&quot;&gt;BLASTX&lt;/a&gt;ing your sequence if it is short enough.  BLASTX translates your DNA in all 6 reading frames and will search the protein database for matching proteins.  Most anything will have a hit in there, and if you get a hit it will show you the DNA sequence and reading frame that got translated.  If your sequence is too big, break it down into smaller chunks until BLASTX works.  One of your chunks will have your gene in it, and it will get a protein hit.  You'll also need to break it up if you have two genes in one chunk, but you only get results for one of them because its longer and gives better hits.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-08T14:44:52.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9689" PostTypeId="1" AcceptedAnswerId="9761" CreationDate="2013-08-08T16:43:29.527" Score="3" ViewCount="12341" Body="&lt;p&gt;What is a  genomic imprint? How does genomic imprinting take place?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I say that &quot;this&quot; allele is maternally imprinted does it mean that the allele of the gene is passed only by the mother? If a pedigree is given, how can we identify whether the trait is paternally imprinted or maternally imprinted?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please try to explain all this in as simple words as possible.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1590" LastEditDate="2013-08-14T08:07:18.467" LastActivityDate="2013-08-14T08:36:55.073" Title="What is genomic imprinting?" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;epigenetics&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9690" PostTypeId="2" ParentId="8072" CreationDate="2013-08-08T18:08:55.340" Score="1" Body="&lt;p&gt;I agree entirely with Matt, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK27142/&quot; rel=&quot;nofollow&quot;&gt;Abbas and Janeway&lt;/a&gt;'s books are the standard for even graduate-level introductory Immunology. Both are easy to read and well organized. Definitely start here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, depending on what you have access to and the depth of reading you want to do, there was an &lt;em&gt;Annual Review of Immunology&lt;/em&gt; issue some years ago (maybe 2003?) that discussed a number of B Cell topics (signaling, fate decisions, etc). I also see that there is a newer article: &#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19827951&quot; rel=&quot;nofollow&quot;&gt;&quot;B Cell Signaling and Fate Decision&quot;&lt;/a&gt;&#xA;&lt;em&gt;Annual Review of Immunology&lt;/em&gt; 28: 21-55 (Volume publication date April 2009)&#xA;Tomohiro Kurosaki, Hisaaki Shinohara, and Yoshihiro Baba&#xA;that might be pretty general if you have access through a university.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good luck. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, I think the disagreement about BCR crosslinking is for survival/development (i.e., are '&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16557260&quot; rel=&quot;nofollow&quot;&gt;tonic' signals&lt;/a&gt; sufficient to allow cells through development?) As for activation, B cells are triggered either by antigen-specific BCR crosslinking or more general &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23241902&quot; rel=&quot;nofollow&quot;&gt;TLR activation&lt;/a&gt; (e.g., LPS). &lt;/p&gt;&#xA;" OwnerUserId="4139" LastEditorUserId="107" LastEditDate="2013-08-10T18:54:56.153" LastActivityDate="2013-08-10T18:54:56.153" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9691" PostTypeId="2" ParentId="9339" CreationDate="2013-08-08T18:25:13.080" Score="0" Body="&lt;p&gt;Good answer Android. &#xA;Recognition of self vs non-self is the central theme of immunology. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wanted to clarify and kind of oversimplify a part of Android's response though...&#xA;B Cells and T Cells get their antigen receptors made by DNA rearrangement as immature cells. This is a random process and leads to receptors capable of binding (theoretically) anything. As these cells are developing in controlled environments, anything they see is 'self'. If they react to these 'self' antigens, the cells are eliminated. Later in life, antigen receptor activation turns from a self-eliminating event into an activating event. If all goes well, this mature population has already been screened for anti-self cells, so anything that activates them is assumed to be foreign and therefore a threat. &lt;/p&gt;&#xA;" OwnerUserId="4139" LastActivityDate="2013-08-08T18:25:13.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9693" PostTypeId="2" ParentId="8719" CreationDate="2013-08-08T18:39:04.760" Score="2" Body="&lt;p&gt;You are right to say that Plasma Cells are terminally differentiated, so they don't become the memory cells, or calm back down or anything. But all Plasma Cells are not the same, there are Short-Lived Plasma Cells (SLPCs) that are less specific, but arise rapidly after stimulation, and there are Long-Lived Plasma Cells (LLPCs) that come about later and have more specific antigen binding.&#xA;SLPCs are rapidly activated, but also rapidly lost. These are the cells that Android was talking about when s/he said that apoptotic programs are initiated as soon as cells become activated and are eventually eliminated by these mechanisms.&#xA;LLPCs are the cells that stay in your body for a much longer time (theoretically for life, but probably not practically unless you get hit by a bus in a couple of years). When you get a vaccination, these are the cells that produce antibody that can be detected in the blood for a number of years (what testing your antibody titer looks for). These cells are in pretty limited supply, so we know less about them. My guess is that they are not actively eliminated, but may become eliminated over time by other mechanisms (purposely undefined here).&lt;/p&gt;&#xA;" OwnerUserId="4139" LastActivityDate="2013-08-08T18:39:04.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9695" PostTypeId="2" ParentId="9689" CreationDate="2013-08-08T22:42:39.750" Score="0" Body="&lt;p&gt;It is incorrect to say that a trait is imprinted, although the phrase is often used.  I will simplify this by talking about just two chromosomes.  A mammal will have one chromosome from mother and one that is nearly identical inherited from the father.  The genes on each chromosome typically have an equal likelihood of being expressed.  An imprinted allele creates silencing on one chromosome and gene expression from solely the other parent. There are many more complexities and Wikipedia is a great source as well as Geneimprint &lt;a href=&quot;http://www.geneimprint.com/site/what-is-imprinting&quot; rel=&quot;nofollow&quot;&gt;http://www.geneimprint.com/site/what-is-imprinting&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See the link regarding Parental Imprinting, the definition is concise.&#xA;&lt;a href=&quot;http://groups.molbiosci.northwestern.edu/holmgren/Glossary/Definitions/Def-M/molecular_imprinting.html&quot; rel=&quot;nofollow&quot;&gt;http://groups.molbiosci.northwestern.edu/holmgren/Glossary/Definitions/Def-M/molecular_imprinting.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4175" LastEditorUserId="4175" LastEditDate="2013-08-09T16:58:14.247" LastActivityDate="2013-08-09T16:58:14.247" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9696" PostTypeId="2" ParentId="9339" CreationDate="2013-08-08T23:37:49.053" Score="1" Body="&lt;p&gt;I often have to reiterate this question in my head to clarify to myself how it works, though I tend to take an approach that asks more: What is different between a part of the body and something foreign which triggers an immune response?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the part that concerns B and T cells:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The adaptive immune system (B and T cells) is based on random genetic reshuffling, producing an 'immune cell army' in which every 'soldier' (every cell) recognises a unique target. This 'army' is so vast in diversity that it covers virtually every molecule that occurs in the world - including those of the own body.&lt;/li&gt;&#xA;&lt;li&gt;This method requires the elimination of those randomly created cells which recognise the body's own substances. The mechanism of elimination is extremely beautiful and makes great use of the way genetics work: Because every cell contains ALL genetic information for your body (except that in almost all cell types the vast majority of it isn't being used most of the time), it is possible to have a few cells which will simply randomly produce bits that belong to a completely different part of the body. This way, everything that belongs into the body will be present where these specialised cells live - which is the bone marrow and the thymus. Thanks to them, it is possible to test every single B and T cell against everything that occurs in the body - and kill them if it turns out they recognise something.&lt;/li&gt;&#xA;&lt;li&gt;This is how you end up with an army that only reacts to things which are not part of the body.&lt;/li&gt;&#xA;&lt;li&gt;In other words, an individual cell doesn't distinguish foreign from body, it simply doesn't react to anything aside from its specific target - which should be foreign if the earlier selection mechanism worked.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Aside from this, the main method by which B and T cells determine whether to activate or not is &lt;strong&gt;context&lt;/strong&gt;, which means two things:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;B and T cells require co-stimulation to activate - T cells from the so-called antigen-presenting cells (APCs), and B cells from T cells.&lt;/li&gt;&#xA;&lt;li&gt;In order to be activated, adaptive immune cells (T cells in particular) depend on the levels of certain inflammatory messengers (known as cytokines) in their environment. In other words, the presence of inflammation is a signal to immune cells that in this location where they currently are, abnormal processes are happening and there may be a need for them to take action. As the reasonable response, they will activate or enter a state ready for activation.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Both APCs and inflammation are mainly provided by parts of the innate immune system, adding another safety barrier with more recognition mechanisms to tell self from non-self.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-08-08T23:37:49.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9697" PostTypeId="2" ParentId="9681" CreationDate="2013-08-09T00:16:16.353" Score="3" Body="&lt;p&gt;A combination of differentiation site, chemical guidance during migration, and signaling cues form a variety of sources. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The final step in the generation of an oligodendrocyte is the&#xA;  development of a mature myelinating phenotype, and this is largely&#xA;  regulated by axonal signals. It seems likely that both soluble and&#xA;  cell mediated signals from adjacent axons are integrated into the&#xA;  developmental profile of oligodendrocyte precursors resulting in cell&#xA;  differentiation, up-regulation of myelin gene expression and formation&#xA;  of the myelin organelle. Candidates for axonally derived soluble&#xA;  factors include FGFs (Bansal et al., 1996 and Qian et al., 1997) and&#xA;  thyroid hormone (Barres et al., 1994a and Barres et al., 1994b), while&#xA;  axonal cell surface molecules such as L1, MAG, NCAM and N-cadherin may&#xA;  regulate formation of the myelin sheath (Payne and Lemmon, 1993 and&#xA;  Trapp, 1990).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12385864&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/12385864&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know of any diseases that just mess with positioning but there are diseases that kill oligodendrocytes (like multiple sclerosis).&lt;/p&gt;&#xA;" OwnerUserId="1853" LastEditorUserId="1853" LastEditDate="2013-08-10T00:33:35.390" LastActivityDate="2013-08-10T00:33:35.390" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9698" PostTypeId="2" ParentId="378" CreationDate="2013-08-09T00:43:47.513" Score="3" Body="&lt;p&gt;Pigliucci gives a good review of some aspects of this topic in &lt;a href=&quot;http://evolution.binghamton.edu/evos/wp-content/uploads/2009/08/Pigliucci-evolvability.pdf&quot; rel=&quot;nofollow&quot;&gt;&quot;Is evolvability evolvable?&quot; (2008)&lt;/a&gt;. He sees what you're asking about, which he calls &quot;evolvability&quot;, as one of the key topics for the future of the study of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's very conceptually dense evo-devo-theory, so I'll probably do a poor job trying to explain it, but he tries to set up a framework that deals not just with things like life-history (per kmm's answer) and mutation/recombination rate (low fidelity in HIV per GWW's answer, and, I suppose, the evolution of sex itself), but also with constraints that evolve at various levels to &quot;positively channel&quot; mutation (that is, the understanding that while mutations are effectively random, the phenotypes that emerge, and are acted upon by natural selection, are not random, but are channelled by the developmental system of the organism).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He also includes the role of development in opening up &quot;phenotypic space&quot; into which a lineage may evolve. For instance, single-celled organisms have a limit on size and complexity, the evolution of multicellularity opens up this huge zone of evolvability. In a sense, this is also the &quot;evolution of evolution&quot;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nrg2278&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Pigliucci M&lt;/strong&gt;. 2008. Is evolvability evolvable? Nat Rev Genet 9: 75–82.&lt;/a&gt; Behind paywall, but &lt;a href=&quot;http://evolution.binghamton.edu/evos/wp-content/uploads/2009/08/Pigliucci-evolvability.pdf&quot; rel=&quot;nofollow&quot;&gt;free pdf here&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-08-09T00:43:47.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9699" PostTypeId="1" CreationDate="2013-08-09T05:51:43.663" Score="4" ViewCount="10848" Body="&lt;p&gt;After eating your lunch or dinner, if you take a brisk walk, most of the time your stomach aches. Why does that happen? What happens with respect to the body metabolism?&lt;/p&gt;&#xA;" OwnerUserId="3918" LastEditorUserId="3952" LastEditDate="2013-08-09T06:16:52.353" LastActivityDate="2015-01-10T03:43:54.887" Title="Why does the stomach ache if you take a brisk walk after lunch or dinner" Tags="&lt;human-biology&gt;&lt;food&gt;&lt;digestive-system&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9700" PostTypeId="2" ParentId="8922" CreationDate="2013-08-09T07:56:30.643" Score="12" Body="&lt;p&gt;Limiting the conversation to mammals, and taking relative brain size as a proxy for intelligence (which, of course is not necessarily &quot;true&quot;, but at least is quantifiable), the answer is &lt;strong&gt;yes: body-size relative  brain size correlates with   body-size relative longevity in mammals&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;using a global database of 493 species, we provide evidence showing that mammals with enlarged brains (relative to their body size) live longer and have a longer reproductive lifespan (&lt;a href=&quot;http://dx.doi.org/10.1111/j.1420-9101.2010.01976.x&quot;&gt;González-Lagos et al.&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They present data by species in the paper, which is available free online, but so as to have something on SE, I've mocked up a chart based on the averages they give for each mammal order: &lt;img src=&quot;https://i.stack.imgur.com/dPYT1.jpg&quot; alt=&quot;by Oreotrephes, after González-Lagos et al. 2010 Fig 1&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1111/j.1420-9101.2010.01976.x&quot;&gt; &lt;strong&gt;González-Lagos C, Sol D, Reader SM&lt;/strong&gt;. 2010. Large-brained mammals live longer. Journal of Evolutionary Biology 23: 1064–1074.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-08-10T01:49:57.413" LastActivityDate="2013-08-10T01:49:57.413" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9701" PostTypeId="1" AcceptedAnswerId="9702" CreationDate="2013-08-09T12:09:59.237" Score="4" ViewCount="1357" Body="&lt;p&gt;Are there insects that change their behavior upon detecting the nearby presence of other dead insects? If there are, can you provide an example?&lt;/p&gt;&#xA;" OwnerUserId="2947" LastEditorUserId="107" LastEditDate="2013-08-09T14:15:39.257" LastActivityDate="2013-08-09T14:25:23.680" Title="Do insects respond to the detection of dead insects?" Tags="&lt;entomology&gt;&lt;ethology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9702" PostTypeId="2" ParentId="9701" CreationDate="2013-08-09T13:47:38.410" Score="9" Body="&lt;p&gt;Yes, it is a common behaviour and is called &lt;em&gt;necromone signaling&lt;/em&gt; (&lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs11692-009-9069-4&quot;&gt;Yao et al 2009&lt;/a&gt;, see references in paper for many examples), and is probably used to avoid predators, parasites and disease. The chemicals used are often similar (unsaturated fatty acids), and seem to have an old evolutionary history (~400 million years). Many groups of species can also detect infected, not yet dead, conspecifics. Removal of dead individual is also common in e.g. ants (&lt;em&gt;necrophoric behavior&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper referred to earlier (beside reviewing earlier evidence) also provides experiments of detection/avoidence in isopods and Tent&#xA;caterpillars (&lt;em&gt;Malacosoma americanum&lt;/em&gt;), where they show avoidance based on crushed conspecifics, unsaturated fatty acids and (for isopods) intact corpses. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Naturally, the same type of compounds are used by e.g. species of carrion beetles (&lt;a href=&quot;http://en.wikipedia.org/wiki/Silphidae#Forensic_research&quot;&gt;Silphidae&lt;/a&gt;) to find their animal hosts, but then for the purpose of reproduction.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-08-09T14:25:23.680" LastActivityDate="2013-08-09T14:25:23.680" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9703" PostTypeId="1" CreationDate="2013-08-09T17:27:16.157" Score="0" ViewCount="35" Body="&lt;p&gt;Have there been any experimentally-verified systems of microRNAs targeting a gene set (e.g., in cancer, perhaps)?&lt;/p&gt;&#xA;" OwnerUserId="4201" LastEditorUserId="107" LastEditDate="2013-08-09T20:09:55.813" LastActivityDate="2013-08-09T22:54:56.183" Title="Known MicroRNA - Gene Systems?" Tags="&lt;gene-expression&gt;&lt;microrna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9705" PostTypeId="2" ParentId="9682" CreationDate="2013-08-09T20:09:48.193" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Xenotransplantation#Potential_future_animal_organ_donors&quot; rel=&quot;nofollow&quot;&gt;Monkeys and many other primates are too small to provide organs that will provide the needs of a human host&lt;/a&gt;. The fact that primates are so close to humans physiologically is not always a win as transplanted organs will bring diseases into the host that can be quite dangerous. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides, because even &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000815.htm&quot; rel=&quot;nofollow&quot;&gt;human human transplants induce immune rejection of organs&lt;/a&gt;. Its typical that immune suppressants will be a lifetime treatment for the patient.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, the cost of a pig organ is negligible and their organs are about the right size, and I would bet that activists don't protest pig transplants nearly as much as primate donors. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-08-09T20:09:48.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9706" PostTypeId="2" ParentId="9684" CreationDate="2013-08-09T21:24:17.673" Score="1" Body="&lt;p&gt;Its fairly common for a gene to have multiple names. I cant say for certain, but Jax and GeneCards also lists them as being synonymous so I would say its safe to say they are the same&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.informatics.jax.org/marker/MGI:1289288&quot; rel=&quot;nofollow&quot;&gt;http://www.informatics.jax.org/marker/MGI:1289288&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.genecards.org/cgi-bin/carddisp.pl?gene=SLC52A2&quot; rel=&quot;nofollow&quot;&gt;http://www.genecards.org/cgi-bin/carddisp.pl?gene=SLC52A2&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit in reply to comment:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In higher level Eukaryotes the vast majority of genes have more than one isoform as a result of alternative splicing, and this can drastically change the protein sequence and function of that protein. So even if it comes from the gene, two different isoforms can have completely unrelated functions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to ensembl, this gene has 14 isoforms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://useast.ensembl.org/Homo_sapiens/Gene/Splice?g=ENSG00000185803;r=8:145577795-145584932&quot; rel=&quot;nofollow&quot;&gt;http://useast.ensembl.org/Homo_sapiens/Gene/Splice?g=ENSG00000185803;r=8:145577795-145584932&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course there could also be some type of post translational modification that could also change the function, but Id say mostly likely if the same gene produces two different functioning proteins its because of alternative splicing.&lt;/p&gt;&#xA;" OwnerUserId="4199" LastEditorUserId="4199" LastEditDate="2013-08-11T19:24:51.090" LastActivityDate="2013-08-11T19:24:51.090" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9707" PostTypeId="2" ParentId="9703" CreationDate="2013-08-09T22:54:56.183" Score="1" Body="&lt;p&gt;Yes. Below is a link to a review of ncRNA (non-coding RNAs) and their role in disease. There are many examples in this review in all sorts of diseases, one of which is miR-200, which is thought to play a role in some cancers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also some tables in the paper that list the miRNA and the disease they are linked to. They also have a reference for each one, so you could read more about that particular miRNA and its function, including the gene it regulates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nrg/journal/v12/n12/full/nrg3074.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nrg/journal/v12/n12/full/nrg3074.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Im not sure if that article is open to the public or not. If you cant access it you could always check out the wikipedia entry for miR-200&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mir-200&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Mir-200&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-08-09T22:54:56.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9709" PostTypeId="2" ParentId="9699" CreationDate="2013-08-10T03:46:56.760" Score="4" Body="&lt;p&gt;The reasons for Exercise-related Transient Abdominal Pain are unknown. The current theories are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Irritation of the parietal peritoneum, a structure lining the abdominal wall as it rubs against the visceral peritoneum, which lies against it and over the top of the abdominal organs&lt;/li&gt;&#xA;&lt;li&gt;Strain on the ligaments that suspend the abdominal organs (however somewhat unlikely as it occurs during swimming&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jPwAL.jpg&quot; alt=&quot;abdominal contents&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It used to be thought that blood was diverted away from the diaphragm during exercise causing pain however that has been found to be incorrect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this link: &lt;a href=&quot;http://www.ausport.gov.au/ais/nutrition/factsheets/hydration/cramps_and_stitch&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ausport.gov.au/ais/nutrition/factsheets/hydration/cramps_and_stitch&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4182" LastActivityDate="2013-08-10T03:46:56.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9710" PostTypeId="1" AcceptedAnswerId="17961" CreationDate="2013-08-10T09:46:36.893" Score="2" ViewCount="92" Body="&lt;p&gt;Why does the composition of fat in animals vary?  Is there an evolutionary advantage to producing fat that is less or more saturated?&lt;/p&gt;&#xA;" OwnerUserId="411" LastEditorUserId="411" LastEditDate="2013-08-10T10:24:32.053" LastActivityDate="2014-06-07T12:06:47.920" Title="Why is duck fat less saturated than cow fat?" Tags="&lt;evolution&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9712" PostTypeId="1" AcceptedAnswerId="9748" CreationDate="2013-08-10T13:40:17.320" Score="3" ViewCount="289" Body="&lt;p&gt;When the sinuses flare up, it can get very painful.  Thus, my question - what biological mechanisms cause the congestion and especially the pain associated with sinusitis?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-08-14T07:20:43.350" Title="What causes sinus pain and congestion?" Tags="&lt;human-biology&gt;&lt;pain&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9713" PostTypeId="1" AcceptedAnswerId="9718" CreationDate="2013-08-10T17:41:40.047" Score="2" ViewCount="735" Body="&lt;p&gt;What's the difference between &lt;strong&gt;Cytoplasmic&lt;/strong&gt; pool and &lt;strong&gt;Granular&lt;/strong&gt; storage pool when speaking about neurotransmitters and synaptic cleft. I encountered this here:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Amphetamine’s mechanism of action&#xA;  thus depends on the cytoplasmic, newly synthesized, rapidly metabolized pool of dopamine.&#xA;  Methylphenidate’s mechanism of action depends&#xA;  on the granular storage pool (Brust, 2004)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Reference&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brust, J. C. M. (2004). Neurological aspects of substance abuse. Philadelphia, PA, Elsevier.&lt;/p&gt;&#xA;" OwnerUserId="4206" LastActivityDate="2019-06-25T01:09:47.190" Title="What's the difference between Cytoplasmic pool and Granular storage pool?" Tags="&lt;biochemistry&gt;&lt;neurotransmitter&gt;&lt;synapses&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9715" PostTypeId="1" AcceptedAnswerId="9719" CreationDate="2013-08-10T22:04:54.897" Score="12" ViewCount="7666" Body="&lt;p&gt;Humans have very strict tradition of hygiene, such as washing hands before eating, using utensils, and in general keeping as much distance between food and dirt as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the same time, most animals would eat off the floor or eat food with foreign particles stuck to it ( after being dropped on the floor). Many animals, like cats groom themselves, practically licking off (and swallowing?) dirt off their coats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do animals suffer adverse effects, such as indigestion or disease from consuming food that is dirty by human standards?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is it something about the human digestive system that cannot handle the same kinds of dirt that animals can?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="16866" LastEditDate="2017-04-03T18:03:02.980" LastActivityDate="2017-04-03T18:03:02.980" Title="Do animals get sick from eating dirty food or eating off the floor?" Tags="&lt;human-biology&gt;&lt;zoology&gt;&lt;pathology&gt;&lt;food&gt;&lt;digestive-system&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9716" PostTypeId="1" CreationDate="2013-08-10T22:19:56.497" Score="7" ViewCount="10550" Body="&lt;p&gt;It's a fact that some people sleep with their eyes open, but why does that happen? Is it normal behavior, not a symptom of any sort of disorder? Are there any (dis)advantages to sleeping with eyes open?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2016-06-17T14:34:02.027" Title="Why do people sleep with their eyes open?" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9718" PostTypeId="2" ParentId="9713" CreationDate="2013-08-10T23:36:33.540" Score="1" Body="&lt;p&gt;Neurotransmitters like dopamine are synthesized in the cytoplasm and then imported into synaptic vesicles.  When the neurotransmitters are released it is by a fusion of the synaptic vesicle with the neuron's cell membrane, emptying the contents into the synaptic cleft.  Re-uptake of the neurotransmitter back into the pre-synaptic neuron's cytoplasm is done by active transporters, in Dopamine's case by DAT.  The cytoplasmic pool refers to the dopamine in the cytoplasm, while the granular pool refers to the dopamine stored in the synaptic vesicles.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-10T23:36:33.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9719" PostTypeId="2" ParentId="9715" CreationDate="2013-08-11T01:45:20.687" Score="16" Body="&lt;p&gt;I'm sure it varies wildly based on the animal and what they're eating.  In general, if in the course of an animal's natural feeding process it picks up a little dirt, it has evolved to cope with that.  Animal's behaviors and guts have evolved to fit their food source and lifestyle.  For a behavioral example, seals will eat rough rocks to help breakdown bones (and barf them up when they get too smooth).  Guts have evolved symbiotic relationships with microbes that are specifically adapted to the food source, termites have microbes to help them break down wood, whereas we don't have the microbe population to pull that off.  Interesting side note: it was &lt;a href=&quot;http://www.nature.com/news/2010/100407/full/news.2010.169.html&quot;&gt;found&lt;/a&gt; that one of the gut microbes in some Japanese people has gotten a horizontally transferred gene from a bacteria that lives on seaweed, probably helping them break down seaweed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There could be a problem when the body is challenged with dirt that contains uncommon substances that the body isn't adapted to.  I'm sure if a cat rolled around in soil contaminated with a lot of arsenic it probably wouldn't be doing very well after licking off all the dirt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This does bring up an interesting current medical hypothesis called the &lt;a href=&quot;https://en.wikipedia.org/wiki/Hygiene_hypothesis&quot;&gt;Hygiene Hypothesis&lt;/a&gt;.  Basically, these things you are talking about, utensils, antibacterial soap, etc. are all very very recent developments in human evolution.  As a result, proponents of this hypothesis think that our bodies are adapted to challenges by microbes and parasites, and depriving our bodies of that exposure when we are young totally screws up the development of our immune systems.  This would explain why we see a huge increase in allergies and autoimmune diseases in the developed world, our immune systems are totally miscalibrated, and freak out over harmless things like pollen (allergies), or worse, attack self-antigens (anti-insulin antibodies in type I diabetes).  Human children are animals, and baby animals should play in the dirt!&lt;/p&gt;&#xA;" OwnerUserId="4177" LastEditorUserId="4177" LastEditDate="2013-08-11T01:57:55.737" LastActivityDate="2013-08-11T01:57:55.737" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9720" PostTypeId="1" CreationDate="2013-08-11T02:00:12.280" Score="2" ViewCount="171" Body="&lt;p&gt;During photosynthesis, there is a point at which the light intensity is such that the rate of photosynthesis exactly matches the rate of respiration called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Compensation_point&quot; rel=&quot;nofollow&quot;&gt;compensation point&lt;/a&gt;. What this means is that the plant can essentially utilize the $\ce{CO_2}$ produced during respiration for photosynthesis and the $\ce{O_2}$ produced during photosynthesis for respiration. But, does this mean, that a plant which has been given an initial supply of $\ce{CO_2}$ and $\ce{O_2}$ and then subsequently put into another gas (still in compensation point light intensity), say nitrogen, can survive indefinitely? (or as long as it's life span). &lt;/p&gt;&#xA;" OwnerUserId="4013" LastActivityDate="2013-08-11T02:15:28.777" Title="Can plants survive indefinitely without external supply of gases at compensation point?" Tags="&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9721" PostTypeId="2" ParentId="9720" CreationDate="2013-08-11T02:15:28.777" Score="2" Body="&lt;p&gt;If the plant is growing the system will fall out of equilibrium due to more carbon going into biomass than oxygen.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-11T02:15:28.777" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9722" PostTypeId="1" CreationDate="2013-08-11T04:21:40.323" Score="7" ViewCount="968" Body="&lt;p&gt;I was trying to do some stimulation for SSVEPs by strobing a solid black square and a solid white square. Weird thing was, I ended up seeing weird grid like patterns that looked like this, always of the inverted color.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;  _        _&#xA; / \      / \&#xA; | |      | |&#xA; \ / _--_ \ / _--_&#xA;  O |    | O |    |&#xA; / \ ---- / \ ----&#xA; | |      | |&#xA; \_/ _--_ \_/ _--_&#xA;  O |    | O |    |&#xA;     ----     ----&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;And that sort of pattern repeats itself around the strobing area (where the convex areas are always of opposite color than the current color on the screen).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm inclined to think about light and dark adaptation, but it still seems weird that it'd be shaped like that in particular. So... What's going on?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Additional info that I should've realized was necessary &gt;_&amp;lt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Strobe area: ~14x10.5 cm&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Strobe frequency: 2 frames/half-cycle @ Laptop Vsync (~60 Hz) ~ 15 Hz &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Viewing distance: ~55-60 cm and shorter.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Screen is backlit. Not sure about brightness metrics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pattern isn't offset to one corner like I've drawn, it's more evenly spaced. Horizontal bars are more accentuated than vertical ones (and the dark-on-light phenomenon is more visible for me than the light-on-dark). Moving in closer increases the visibility of the effect (I guess that was to be expected), and changes the number of times the pattern repeats across the screen (but it's hard to count them). The larger the area in my visual field the more times the pattern repeats. I'd say that at about 60 cm it's just one box, but with my nose a handful of cm away from the screen (it's hard to measure by myself &gt;_&amp;lt;), there are maybe three in the horizontal direction... Or at least tens of them (increasingly large as it gets toward the center in both dimensions), depending on how focused in on the screen I am.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's really really hard to count them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't had the chance to check with other people yet, but I'll try some time (this is just something I saw while working on a personal project).&lt;/p&gt;&#xA;" OwnerUserId="4208" LastEditorUserId="3624" LastEditDate="2013-10-21T15:21:32.077" LastActivityDate="2020-05-16T18:12:53.583" Title="Reason for seeing grid-like patterns when strobing a solid black-white image?" Tags="&lt;vision&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9724" PostTypeId="1" CreationDate="2013-08-11T14:27:07.120" Score="2" ViewCount="74" Body="&lt;p&gt;Why is it that sometimes, when we wake up, we are able to remember what we were just dreaming, but sometimes we don't remember any of it?&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="3952" LastEditDate="2013-08-12T00:44:11.987" LastActivityDate="2014-05-28T09:31:09.070" Title="Why are dreams sometimes remembered and sometimes forgotten?" Tags="&lt;memory&gt;&lt;dreaming&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9725" PostTypeId="1" CreationDate="2013-08-11T14:48:54.347" Score="5" ViewCount="65" Body="&lt;p&gt;I have heard that honeybees send out scouts, then based on the scout reports more bees go then come back and report and so they are supposed to be efficient decision makers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you give as complete as possible of a description of how honeybee decision making works with regard to:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;finding new food/water sources for the hive&lt;/li&gt;&#xA;&lt;li&gt;deciding where to place a new colony&lt;/li&gt;&#xA;&lt;li&gt;how they determine if a big enough predator is around to merit a swarm&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you could point to published material that would also be appreciated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some links:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs00265-011-1298-8?LI=true#page-1&quot;&gt;http://link.springer.com/article/10.1007%2Fs00265-011-1298-8?LI=true#page-1&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://cis.uws.ac.uk/research/journal/V9/V9N3/bees.pdf&quot;&gt;http://cis.uws.ac.uk/research/journal/V9/V9N3/bees.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.igi-global.com/article/honey-bee-swarm-cognition/44981&quot;&gt;http://www.igi-global.com/article/honey-bee-swarm-cognition/44981&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4209" LastEditorUserId="4209" LastEditDate="2013-08-11T15:01:25.950" LastActivityDate="2013-08-11T15:01:25.950" Title="Honeybee decision process: new food, new home, new threat" Tags="&lt;entomology&gt;&lt;sociality&gt;&lt;communication&gt;&lt;learning&gt;" AnswerCount="0" CommentCount="5" ClosedDate="2014-12-22T01:53:48.247" ContentLicense="CC BY-SA 3.0" />
  <row Id="9726" PostTypeId="1" AcceptedAnswerId="9841" CreationDate="2013-08-11T21:11:14.757" Score="5" ViewCount="921" Body="&lt;p&gt;I digested two plasmids, one with EcoRI and AgeI and the other with EcoRI and XmaI. Digests looked as expected, so I purified the respective fragments and set up the T4 DNA ligation (AgeI and XmaI sites are compatible).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After E.coli transformation, culture and miniprep from 12 of the resulting cultures, I digested the isolate from the minipreps with BclI to confirm I had the correct product (because there was one BclI site in the insert and another one in 1.4kb away in the backbone). The results of this digest clearly show that there are two different ligation products: four lanes share one banding pattern and the other eight share a pattern which is different from it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I checked both plasmids for other restriction sites of the enzymes used which I overlooked before, but found none. Because EcoRI and XmaI/AgeI sites are radically different (AATT vs. CCGG), I would exclude the possibility of the insert being ligated in reverse orientation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any common causes of unexpected ligation variants besides unnoticed restriction sites and reverse ligation?&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-08-11T21:51:25.223" LastActivityDate="2013-08-18T16:06:40.880" Title="What are common causes of unexpected ligation products?" Tags="&lt;synthetic-biology&gt;&lt;plasmids&gt;&lt;restriction-enzymes&gt;&lt;ligation&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9727" PostTypeId="1" CreationDate="2013-08-12T01:19:44.907" Score="4" ViewCount="63" Body="&lt;p&gt;I was enjoying Richard Smith's excellent answer to &lt;a href=&quot;https://biology.stackexchange.com/questions/1008/are-there-any-motile-plants?rq=1&quot;&gt;this question&lt;/a&gt;, and wondered:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you consider the pollen/seed distribution range to be plant locomotion, is there a database that compares these distances across plant taxa, or perhaps a paper that treats these distances as a trait (in a phylogenetic context, for example)? One might assume that in the transition from wind-pollination to animal pollination (or from wind seed dispersal to animal seed dispersal) there is a sacrifice of decreased distance for increased &quot;accuracy&quot;, but maybe this isn't the case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems like this information should be around somewhere – it has relevance to evolution, speciation, climate change adaptation, etc.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2017-04-10T17:16:40.730" Title="Is there a database of pollen-seed distances across plant species?" Tags="&lt;botany&gt;&lt;reproduction&gt;&lt;literature&gt;&lt;database&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9728" PostTypeId="2" ParentId="9684" CreationDate="2013-08-12T02:16:49.353" Score="5" Body="&lt;p&gt;This isn't a case of gene splicing causing different protein variants.  In the studies that identified these two functions (GHB sensitivity and riboflavin transport), they were using DNA derived from mRNA (cDNA), which means what was being expressed in their experiments did not have introns, so there was no chance for alternative splicing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This gene has a weird history, here is the summary:&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0014579302027758&quot; rel=&quot;nofollow noreferrer&quot;&gt;Takeda et al. 2002&lt;/a&gt;: Identification of G protein-coupled receptor genes from the human genome sequence&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Takeda and co. download a copy of the human genome and translate it looking for GPCRs.  They look at all the ORF that DIDNT have introns: &quot;We collected intronless open reading frames (ORFs), which were long enough to cover GPCRs from the human genome&quot;. They also only look at things with 6-8 transmembrane helices as determined by the prediction program SOSUI.  One of the GPCRs they found was named hGCRP41 (hypothetical protein similar to GPCR) accession number: &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/nuccore/AB083623&quot; rel=&quot;nofollow noreferrer&quot;&gt;AB083623&lt;/a&gt;.  They report it probably has 8 transmembrane helices, and 418aa.  &lt;strong&gt;This protein probably doesn't exist because they read straight through two introns in their analysis.  The protein also terminates in the middle of a frame-shifted exon.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;&lt;a href=&quot;http://www.pnas.org/content/100/11/6759.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ericsson et al. 2003&lt;/a&gt;: Identification of receptors for pig endogenous retrovirus&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Next, Ericsson et al come along looking for receptors for the pig endogenous retrovirus and find this gene.  They used cDNA to make a bunch of transduced cell lines that had difference human cDNAs expressed.  They found two related proteins that could serve as receptors to the pig endogenous retrovirus.  They named the first one &lt;strong&gt;HuPAR-1&lt;/strong&gt;, which is 445aa long and has 11 transmembrane helices.  This is the length of one of the proper splice variants of this gene.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;&lt;a href=&quot;http://www.fasebj.org/content/21/3/885.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Andriamampandry et al. 2007&lt;/a&gt;: Cloning and functional characterization of a gammahydroxybutyrate receptor identiﬁed in the human brain&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Andriamampandry is looking for gammahydroxtbutyrate (GHB) receptors by using cDNA and seeing which cDNA-transduced cells become sensitive to GHB.  They find two nice proteins that are sensitive to GHB, &lt;strong&gt;GHBh1&lt;/strong&gt; and C12K32.  &lt;strong&gt;GHBh1&lt;/strong&gt; is identical to &lt;strong&gt;HuPAR-1&lt;/strong&gt;, it has 445aa and 11 transmembrane helices.  C12K32 is a frameshifted version of GHBh1 that is slightly longer, but has the same number of helices. They had previously found a &lt;a href=&quot;https://www.fasebj.org/doi/abs/10.1096/fj.02-0846fje&quot; rel=&quot;nofollow noreferrer&quot;&gt;512aa ortholog in rats&lt;/a&gt;, in 2013.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;&lt;a href=&quot;http://jn.nutrition.org/content/140/7/1220.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yao et al. 2010&lt;/a&gt;: Identification and Comparative Functional Characterization of a New Human Riboflavin Transporter hRFT3 Expressed in the Brain.&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Finally, we have Yao et al, who searched for homologs to their Riboflavin transporters.  They found one in a cDNA library, and it was 445aa long.  But they noticed upon BLASTing it that people had been calling it a GPCR.  They point out that this is weird since it has 11 transmembrane helices, and go on to show that it is a Riboflavin transporter, concluding: &quot;The molecular function of GPR172A has yet to be determined. We designated it &lt;strong&gt;hRFT3&lt;/strong&gt; (GenBank accession no. &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/nuccore/AB522904&quot; rel=&quot;nofollow noreferrer&quot;&gt;AB522904&lt;/a&gt;) based on its functional characterization as shown below.&quot;  This paper is in pretty poor form, because somehow they don't address the Andriamampandry paper which presented data supporting its function as a GPCR.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;So this protein, in this specific spliced formation, has been shown to be a virus receptor, a GHB G protein-coupled receptor, and a riboflavin transporter.  It is very weird that it is a GPCR with 11 transmembrane domains... they very rarely have more or less than 7.  I'd wait for more studies to confirm both of these findings before I'd accept that this protein is an XXL GPCR moonlighting as a riboflavin transporter.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastEditorUserId="51272" LastEditDate="2019-04-24T16:42:29.153" LastActivityDate="2019-04-24T16:42:29.153" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="9730" PostTypeId="1" AcceptedAnswerId="9735" CreationDate="2013-08-12T05:21:08.423" Score="13" ViewCount="35770" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_height&quot;&gt;wikipedia article on human height&lt;/a&gt; reports mean height for many different countries by sex but it does not report standard deviations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the standard deviation of adult human heights within sexes?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously the size of the standard deviation would vary across countries and by other factors.  That said, I think good data on a few representative countries would be sufficient to get a reasonable sense of what it typically is and the extent to which the standard deviation varies.&lt;/p&gt;&#xA;" OwnerUserId="451" LastEditorUserId="451" LastEditDate="2016-06-15T02:40:54.243" LastActivityDate="2016-06-15T02:40:54.243" Title="What is the standard deviation of adult human heights for males and females?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9732" PostTypeId="2" ParentId="9726" CreationDate="2013-08-12T06:09:38.863" Score="3" Body="&lt;p&gt;Could be insert polymerization.  If you have your stretch of DNA like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; (5')-AATTagctagcatcgtgatcgacg-(3')&#xA;          ||||||||||||||||||||&#xA;     (3')-tcgatcgtagcactagcagcGGCC-(5')&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;And you take that, flip it around, it will ligate onto itself, like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; (5')-AATTagctagcatcgtgatcgacg-(3')(5')-CCGGcgacgatcacgatgctagct-(3')&#xA;          ||||||||||||||||||||              ||||||||||||||||||||&#xA;     (3')-tcgatcgtagcactagcagcGGCC-(5')(3')-gctgctagtgctacgatcgaTTAA-(5')&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This is easy enough to check for.  Just calculate the size fragments you'd expect from a vector with two inserts (there'd be an extra BcII cutsite now, and the extra fragment would probably be the size of the insert).  If this is just out of curiosity, and one of your things is the correct size, I'd ignore the ones that didn't work and go ahead with your ones that did.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you do have a problem with it, or you are getting all your clones polymerizing, you can treat your insert with an &lt;a href=&quot;http://en.wikipedia.org/wiki/Alkaline_phosphatase#Use_in_research&quot; rel=&quot;nofollow&quot;&gt;alkaline phosphatase&lt;/a&gt;.  This will eat off the (5') phosphate that the ligase needs to stick the on to the (3') hydroxyl.  The result is that an insert cant bind to another insert, but once it finds a vector it will be able to ligate:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; insert to insert:    AATTagctagcatcgtgatcgacg-(3') :( CCGGcgacgatcacgatgctagct-(3')&#xA;                         ||||||||||||||||||||              |||||||||||||||||||| &#xA;                    (3')-tcgatcgtagcactagcagcGGCC  :( (3')-gctgctagtgctacgatcgaTTAA&#xA;&#xA; insert to vector:    ....ctagct-(3')     AATTagctagcatcgtgatcgacg-(3')(5')-CCGGcgacg....&#xA;                      ||||||||||              ||||||||||||||||||||              |||||||||&#xA;                      ....gatcgaTTAA-(5')(3')-tcgatcgtagcactagcagcGGCC     (3')-gctgc....&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;There will be nicks on the top left, and bottom right, but the bug you put it into should clean those up for you.  You can get alkaline phosphatase for fairly cheap from lots of places, NEB is always a safe bet.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-12T06:09:38.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9733" PostTypeId="2" ParentId="9715" CreationDate="2013-08-12T07:41:07.883" Score="3" Body="&lt;p&gt;Animals certainly occasionally get sick from eating contaminated food, just as humans used to before our standards of sanitation improved.  There are various adaptations/considerations for this. Apologies for not being able to find scholarly references. Here are some anecdotes, some of which are speculation/urban legend:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Predators eat fresh meat, which is less likely to be spoiled&lt;/li&gt;&#xA;&lt;li&gt;Vultures lack feathers on their heads and bathe frequently to minimize exposure&lt;/li&gt;&#xA;&lt;li&gt;Dogs supposedly eat grass to induce vomiting when they've eating something bad (fairly disputed)&lt;/li&gt;&#xA;&lt;li&gt;Rats and other scavengers have excellent senses of smell, and can likely detect common contamination or over-spoilage&lt;/li&gt;&#xA;&lt;li&gt;Some scavengers may have more aggressive digestive systems to reduce infections&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Only 100 years ago, humans weren't so well off ourselves. While food hygiene is only part of it, our increased sanitation has reduced mortality from infectious diseases substantially.  &lt;a href=&quot;http://www.cdc.gov/mmwr/preview/mmwrhtml/mm4829a1.htm&quot; rel=&quot;nofollow&quot;&gt;From the CDC:&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In 1900, the three leading causes of death were pneumonia,&#xA;  tuberculosis (TB), and diarrhea and enteritis, which (together with&#xA;  diphtheria) caused one third of all deaths (Figure 2). Of these&#xA;  deaths, 40% were among children aged less than 5 years (1). In 1997,&#xA;  heart disease and cancers accounted for 54.7% of all deaths, with 4.5%&#xA;  attributable to pneumonia, influenza, and human immunodeficiency virus&#xA;  (HIV) infection (2).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It would be interesting to find a break down of the improvement from agriculture/cooking, water/sewage, medicine, etc. &lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-08-12T07:41:07.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9734" PostTypeId="2" ParentId="5125" CreationDate="2013-08-12T07:55:55.937" Score="1" Body="&lt;p&gt;Mind all of you, even the cerebellum sleeps. The waves that are generated in the neocortex predict the same waves in the cerebellum. There probably is no active vision, but the activation patterns of the dreaming visual cortex may give the sleep walking person an idea of the world around him/her. This might, however imply that a great deal of luck is involved in getting somewhere in one piece (given that the patient even moves outside...). During normal REM sleep we speak of complete muscle atonia, the eyes not included. However, this does not work that well in all patients, meaning that they start living their dream. Mind you as well that keeping balance is partially programmed in the muscular innervation (connection patterns in the spinal cord that registers and partially controls muscle tone of agonists and antagonists), and in part by the cerebellum indeed. The cerebellum, however can be devided in a cortex and in cerebellar nuclei. The cortex is not involved in keeping balance as such, much of this is programmed by the cerebellar and pontine nuclei. &lt;/p&gt;&#xA;" OwnerUserId="4213" LastActivityDate="2013-08-12T07:55:55.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9735" PostTypeId="2" ParentId="9730" CreationDate="2013-08-12T07:57:18.363" Score="15" Body="&lt;p&gt;It's probably around 7 cm for men and 6 cm for women.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.econ.upf.edu/docs/papers/downloads/1002.pdf&quot;&gt;The Evolution of Adult Height in Europe&lt;/a&gt;, which is a source for some of the statistics reported on that Wikipedia page, gives averages, standard deviations, and sample sizes for both sexes across 10 european countries (and across a number of different age cohorts).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taking their numbers for men and women born between 1966 and 1978, the average male standard deviation of height across all ten countries is 7 cm (range 6.7-7.3) and female 6.1 (range 5.6-6.4).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a more global context, &lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0018962&quot;&gt;Subramanian et al.&lt;/a&gt; give heights with standard deviations for a much wider selection of countries, mostly &quot;developing countries&quot;. Unfortunately for your question, they only report numbers for women. However, these  look pretty similar to the Europe numbers: the across-country average SD for women is 6.3. (with all these countries, the &lt;em&gt;range&lt;/em&gt; is greater at 5.4-8.1, but 32 out of the 54 countries have SDs within the Europe range for women, i.e. 5.6-6.4)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: for this estimate I just ran averages across years/countries, I didn't weight the averages by sample size.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0018962&quot;&gt; &lt;strong&gt;Subramanian SVS, Özaltin EE, Finlay JEJ&lt;/strong&gt;. 2010. Height of nations: a socioeconomic analysis of cohort differences and patterns among women in 54 low- to middle-income countries. PLoS ONE 6: e18962–e18962.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-09-02T00:00:25.353" LastActivityDate="2013-09-02T00:00:25.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9737" PostTypeId="1" CreationDate="2013-08-12T12:46:51.820" Score="5" ViewCount="1237" Body="&lt;p&gt;I remember hearing a saying that goes like &amp;quot;men think of sex every 7 minutes (or seconds?)&amp;quot;. I take this saying to mean that men have sex related thoughts more often than women.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;I'm interested if these thoughts are related to hormone expression within the male body.&lt;/strong&gt; particularly, I'm interested in the very few seconds before a sexual thought emerges - one moment a man is thinking about daily stuff, next moment his thinking has sexual content. &lt;strong&gt;What is responsible for this shift in thinking?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;I've read that &lt;a href=&quot;http://en.wikipedia.org/wiki/Oxytocin#Actions_within_the_brain&quot; rel=&quot;noreferrer&quot;&gt;oxytocin is responsible for men feeling romantic attachment to a partner&lt;/a&gt;, but is there a hormone that initiates sexual thoughts or fantasy? For example, would a burst of testosterone increase the likelihood of a man thinking of sex?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-06-26T14:02:24.890" Title="Do hormones make men think of sex?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9738" PostTypeId="2" ParentId="9737" CreationDate="2013-08-12T13:39:48.957" Score="3" Body="&lt;p&gt;Interestingly it does seem as if this is at least in part the case.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Testosterone levels are tied to sexual impulses, but also &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0924977X97000953&quot; rel=&quot;nofollow&quot;&gt;risky behavior&lt;/a&gt; and &lt;a href=&quot;http://www.tandfonline.com/doi/abs/10.1300/J076v21n03_02#.Ugjj3WRga5c&quot; rel=&quot;nofollow&quot;&gt;aggression&lt;/a&gt;.  Its responsible for &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0378512299000729&quot; rel=&quot;nofollow&quot;&gt;sexual drive in women as well&lt;/a&gt;.  Low testosterone can cause depression and loss of the ability to make decisions.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You'll note that the work cited is done on criminals, patients and rats.  Remember that is not medically or scientifically ethical to change the androgen levels of a functioning human being.  Testosterone supplements might increase the &lt;a href=&quot;http://www.medscape.com/viewarticle/540617_2&quot; rel=&quot;nofollow&quot;&gt;chances of prostate cancer&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While its not scientific, there's a fascinating set of interviews about how testosterone affects human thinking at &lt;a href=&quot;http://www.thisamericanlife.org/radio-archives/episode/220/transcript&quot; rel=&quot;nofollow&quot;&gt;this transcript of American life, Act 2&lt;/a&gt; :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After testosterone, there was no narrative. There was no language&#xA;  whatsoever. It was just, I would see a woman who was attractive or not&#xA;  attractive. She might have an attractive quality, nice ankles or&#xA;  something, and the rest of her would be fairly unappealing to me.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;But &lt;strong&gt;that was enough to basically just flood my mind with aggressive,&#xA;  pornographic images, just one after another&lt;/strong&gt;. It was like being in a&#xA;  pornographic movie house in my mind. And I couldn't turn it off. I&#xA;  could not turn it off. Everything I looked at, everything I touched,&#xA;  turned to sex.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-06-26T14:02:24.890" LastActivityDate="2014-06-26T14:02:24.890" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9739" PostTypeId="1" AcceptedAnswerId="9740" CreationDate="2013-08-12T15:21:29.580" Score="11" ViewCount="1269" Body="&lt;p&gt;Reading this &lt;a href=&quot;https://biology.stackexchange.com/questions/5007/how-is-evolution-possible-in-contemporary-humans&quot;&gt;question&lt;/a&gt; of the stack exchange got me thinking. I believe human evolution is an ongoing process and will not stop. Are there any predictions/theories about the phenotypes and genotypes of humans in the future? and how they may differ in a few thousand years compared to present day?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I remember watching a youtube video and in the video the user predicts that there will be two branches of human species; a short dwarf like species and a much taller species. I'm still skeptical about this claim. Is there any evidence to back it up?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One could argue that modern medicine is preventing natural selection. How will this effect human evolution?&lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-10-21T06:23:07.040" Title="Are there any scientifically based predictions or theories of future human evolution?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9740" PostTypeId="2" ParentId="9739" CreationDate="2013-08-12T16:44:28.010" Score="8" Body="&lt;p&gt;Its pretty much impossible to predict what will happen in the evolution of species.  Evolution is a parallel search with millions (or in the case of humans 8+ billion) of threads.  Our adaptive capacities have never been fully understood and will always surprise us I think.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course that doesn't stop people from trying!  The &lt;a href=&quot;http://news.bbc.co.uk/2/hi/6057734.stm&quot; rel=&quot;nofollow&quot;&gt;prediction you mention&lt;/a&gt; is based on one man's ideas of dominant selection pressures on humanity now... for a men's TV show.  In Dr Curry's scenario, technology users, and economic disparity, producing Eloi and Morlock like dimorphism as in the HGWells book &quot;Time Machine&quot;. This seems like hogwash to me.  All socioeconomic classes try to find high quality partners and height and attractiveness will be hard to stamp out in a large segment of humanity.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Economic elites breed slowly and even if they will try to skim the evolutionary cream of humanity off the top, there will be plenty of beautiful, tall and smart people who will lack economic opportunity in my opinion.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been more serious, IMHO, questions about whether medical technology, which lets the sick recover and may even compensate for genetically problematic traits.  There are no inoffensive examples I can think of so I'll take male pattern hair loss - apologies.  If medicine allows all men (and women) to grow a thick shock of hair regardless of our genes then the baldness traits might spread through the species.  Sure it could happen, but then most bald and balding people end up having children now anyway.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact since civilization has started feeding the hungry, making the hunting of wild beasts less important, causing the shrinkage of the male physique (&lt;a href=&quot;http://phys.org/news175332184.html&quot; rel=&quot;nofollow&quot;&gt;we used to be much more muscular&lt;/a&gt;), inventing medicine and schools where smarts can be selected for, and giving us all more choice when it comes to mates, &lt;a href=&quot;http://www.pnas.org/content/104/52/20753.long&quot; rel=&quot;nofollow&quot;&gt;evolution has accelerated for human beings&lt;/a&gt;. The authors specifically cite social factors as being more important in our evolution now.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-08-13T12:33:26.960" LastActivityDate="2013-08-13T12:33:26.960" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9742" PostTypeId="1" AcceptedAnswerId="9746" CreationDate="2013-08-12T22:37:29.150" Score="5" ViewCount="565" Body="&lt;p&gt;Can anyone identify the plant below? It's in a backyard in Pennsylvania, and the photo was taken today.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8WHLK.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2013-12-12T21:28:00.027" Title="Plant identification?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9743" PostTypeId="1" CreationDate="2013-08-13T02:54:52.107" Score="3" ViewCount="127" Body="&lt;p&gt;It is difficult to assume that the massive number of co-ordinated developmental sequences in a developing embryo is controlled by molecular signalling alone. Is anyone aware of a molecular or developmental clock within the genome which control the on off states of the genes concerned with developmental sequences? If it has not been reported is it likely to exist? (This is not about the molecular clock in evolution.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming there is a molecular clock, is it possible that the clock is switched on at the time of fertilization, and the zygote transfers the elapsed time to the progressive generations of the cells?&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="107" LastEditDate="2013-08-13T03:24:37.740" LastActivityDate="2020-05-21T19:29:29.530" Title="Is there a realtime molecular clock within the genome to co-ordinate the developmental sequences in an embryo?" Tags="&lt;development&gt;&lt;embryology&gt;&lt;cytogenetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9744" PostTypeId="1" CreationDate="2013-08-13T08:11:02.237" Score="4" ViewCount="4204" Body="&lt;p&gt;Of these three words, perhaps &lt;strong&gt;Neurotransmitter&lt;/strong&gt; is the most obvious. I took a look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Neuromodulation&quot; rel=&quot;nofollow&quot;&gt;Wikipedia page for Neuromodulation&lt;/a&gt; and found that this is pretty similar to Neurotransmitter too. I guess Neuromediator is somewhat more broad. Could someone clarify these nomenclature for me?&lt;/p&gt;&#xA;" OwnerUserId="4206" LastEditorUserId="69" LastEditDate="2013-08-13T10:23:02.350" LastActivityDate="2013-08-13T23:46:49.370" Title="Neuromediator, Neuromodulator, Neurotransmitter?" Tags="&lt;neuroscience&gt;&lt;terminology&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9745" PostTypeId="1" AcceptedAnswerId="9747" CreationDate="2013-08-13T10:35:39.983" Score="8" ViewCount="9106" Body="&lt;p&gt;We have lots of lily flowers inside our garden. Their flowers are open in day and closed in night. How do lilies sense day and night and open and close their flowers?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="107" LastEditDate="2013-08-14T00:42:50.517" LastActivityDate="2016-01-09T16:13:30.120" Title="How do lilies sense day and night and open and close their flowers?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9746" PostTypeId="2" ParentId="9742" CreationDate="2013-08-13T10:37:14.220" Score="2" Body="&lt;p&gt;Those flowers don't come from the same plant as that big leaf in the front do they?  Cant help you with the leaves, but the flower looks like a &lt;a href=&quot;http://en.wikipedia.org/wiki/Daylily&quot; rel=&quot;nofollow noreferrer&quot;&gt;daylily&lt;/a&gt;. source: I know nothing about plants, but happen to have a mom who got a degree in horticulture :)&#xA;&lt;img src=&quot;https://i.stack.imgur.com/NcyZk.jpg&quot; alt=&quot;Sweet daylily picture from wikipedia&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-13T10:37:14.220" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9747" PostTypeId="2" ParentId="9745" CreationDate="2013-08-13T11:11:55.380" Score="5" Body="&lt;p&gt;The three main cues for flower opening/closing used by plants are temperature, light and humidity (&lt;a href=&quot;http://jxb.oxfordjournals.org/content/54/389/1801.full&quot;&gt;van Doorn &amp;amp; van Meteren 2003&lt;/a&gt;, freely available pdf), with the first two being most common. Plants with daily opening and closing of flowers can be divided into nocturnal (open at night) and diurnal (open at day). There exists several different mechanisms for how flowers open and close, and these include e.g. reversible expansion and contraction of cells by changes in water balance and differential growth of cells due to temperature (in either the petals themselves or cells at the base of flowers). See the previously referred paper for examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The evolutionary advantages and molecular mechanisms (along with the circadian clock of plants) behind opening and closing of flowers are open research fields. Several evolutionary hypothesis exists for explaining different flowering strategies, and these often deal with efficient pollination (close when good pollinators are absent), protection against frost, conservation of resources (e.g. water) or predator/pathogen defence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not know what the specific mechanism in lilies is, and it can possibly/probably differ between different species. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-08-13T11:37:04.720" LastActivityDate="2013-08-13T11:37:04.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9748" PostTypeId="2" ParentId="9712" CreationDate="2013-08-13T11:13:10.260" Score="3" Body="&lt;p&gt;Inflamed sinuses are often &lt;a href=&quot;http://en.wikipedia.org/wiki/Nasal_congestion#Causes&quot; rel=&quot;nofollow&quot;&gt;associated with some kind of illness or irritant&lt;/a&gt; such as flu, the common cold, or hay-fever. &lt;a href=&quot;http://www.webmd.com/allergies/sinus-pain-pressure-11/colds&quot; rel=&quot;nofollow&quot;&gt;As an example the cold causes&lt;/a&gt; sinus pain and inflammation because the virus is attacking/located in the nasal passages which &lt;strong&gt;causes swelling in the mucus membrane&lt;/strong&gt; (the mucus membrane lines the sinus cavities). The swelling, along with increased mucus production, combines to create &lt;strong&gt;clogging and the pressure associated causes pain&lt;/strong&gt;. Humidity will help loosen the mucus and anti-inflammatory medication should help reduce pain by reducing the mucus build up and swelling - thus relieving pressure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The increase in mucus production is &lt;a href=&quot;http://news.discovery.com/human/health/mucus-cold-flu-season-120105.htm&quot; rel=&quot;nofollow&quot;&gt;because of the role it plays in our bodies&lt;/a&gt;&lt;/strong&gt; - it is produced to trap foreign bodies and help keep our system clean. The more mucus we produce the more our bodies are trying to clean up. This can cause an excess which is difficult to clear such that our sinuses become blocked and dried mucus becomes an irritant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sinusitis&quot; rel=&quot;nofollow&quot;&gt;Sinusitis&lt;/a&gt; &lt;em&gt;is&lt;/em&gt; the painful condition of swelling in the mucus membrane&lt;/strong&gt;. &lt;em&gt;Sinus&lt;/em&gt; comes from the latin for bent or curved surface, and &lt;em&gt;-itis&lt;/em&gt; is from greek meaning swelling or inflammation linked to disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary: Painful sinuses, aka sinusitis, are painful because of infection in the mucus membrane producing swelling and excessive mucus build-up.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-08-14T07:20:43.350" LastActivityDate="2013-08-14T07:20:43.350" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9749" PostTypeId="1" CreationDate="2013-08-13T15:27:17.950" Score="2" ViewCount="3511" Body="&lt;p&gt;Myostatin inhibitors, which are being developed to treat muscle wasting diseases like muscular dystrophy, are likely to be abused by athletes. What are the potential long-term side-effects of taking a myostatin inhibitor? Will it have different side-effects for patients compared to healthy athletes (especially young athletes that are still developing)?  Could there be adverse drug interactions with other common performance enhancing drugs like EPO, hGH, and anabolic steroids?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources I've explored (StackExchange is only allowing me to insert two hyperlinks):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;New Muscle Drugs Could Be The Next Big Thing In Sports Doping&lt;/em&gt; - NPR story by Jon Hamilton &lt;/li&gt;&#xA;&lt;li&gt;Wikipedia entry on myostatin&lt;/li&gt;&#xA;&lt;li&gt;Wyeth found one of its drugs to be safe in a clinical trial, but it stopped development because the drug was ineffective at increasing muscle mass.&lt;/li&gt;&#xA;&lt;li&gt;An internet search mainly brings up dieting and body building forums, which I do not trust.&lt;/li&gt;&#xA;&lt;li&gt;According to a review by &lt;a href=&quot;http://ajpheart.physiology.org/content/300/6/H1973&quot; rel=&quot;nofollow&quot;&gt;Breitbart et al. 2011&lt;/a&gt;, myostatin inhibition does not have negative effects on cardiac tissue.&lt;/li&gt;&#xA;&lt;li&gt;According to a review by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192366/&quot; rel=&quot;nofollow&quot;&gt;Allen et al. 2012&lt;/a&gt;, the increase in muscle mass caused by myostatin inhibition leads to be metabolic health (e.g. lower glucose levels and higher insulin sensitivity).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4221" LastActivityDate="2018-09-11T11:18:37.010" Title="What are potential side effects of myostatin inhibitors?" Tags="&lt;physiology&gt;&lt;pharmacology&gt;&lt;muscles&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9750" PostTypeId="1" AcceptedAnswerId="44364" CreationDate="2013-08-13T15:47:14.707" Score="5" ViewCount="380" Body="&lt;p&gt;I know there is some mechanism in humans by which we start to ignore a certain stimuli if it persists for a long time (e.g., we don't feel our shoes all the time !).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can the same thing happen in &lt;em&gt;Mimosa pudica&lt;/em&gt;? Can it again get it's original arrangement of leaves if it is stimulated without interruption?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it should do this, otherwise it will not be able to grow if it is surrounded by bushes from all the sides as it will be stimulated constantly and so will be unable to photosynthesize properly.  &lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3340" LastEditDate="2016-03-17T05:51:01.853" LastActivityDate="2016-03-17T08:08:17.597" Title="What happens if we continuously stimulate a mimosa plant?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9751" PostTypeId="2" ParentId="9424" CreationDate="2013-08-13T16:11:20.237" Score="1" Body="&lt;p&gt;Each &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/SNP/get_html.cgi?whichHtml=how_to_submit#REFSNP&quot; rel=&quot;nofollow&quot;&gt;rsid&lt;/a&gt; identifies a unique SNP in the genome. Thus there should not be any entry in the files that have the same rsid but different chromosomes and/or positions. If you do find this, it is likely that you have data from different versions of the assembled genomes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To find genetic variants associated, i.e. correlated, with your trait, you need to focus on the genotype at each of the SNPs. For example, SNP rs3094315 is an A/G polymorphism, i.e. an individual can either have the genotype AA, AG, or GG. To find if it is associated with tongue rolling, you would count the number of AA, AG, and GG individuals (alternatively you could sum the number of A and G alleles) in the group that can roll their tongue and compare those numbers to the group that cannot. You would then repeat this for each SNP that you want to test. For most SNPs, there will be no difference in proportion. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, this is not a modest undertaking as this a cornerstone of human and statistical genetics. There are many issues that could strongly bias your results (e.g. population stratification, genotyping error, linkage disequilibrium, multiple testing). To learn more, you can read about the Cochrane-Armitage Trend Test and the &lt;a href=&quot;http://pngu.mgh.harvard.edu/~purcell/plink/&quot; rel=&quot;nofollow&quot;&gt;PLINK&lt;/a&gt; software. If you are really serious I recommend &lt;em&gt;Applied Statistical Genetics with R&lt;/em&gt; by Andrea S. Foulkes.&lt;/p&gt;&#xA;" OwnerUserId="4221" LastActivityDate="2013-08-13T16:11:20.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9752" PostTypeId="2" ParentId="9102" CreationDate="2013-08-13T19:28:13.793" Score="1" Body="&lt;p&gt;For a really brief introduction, I recommend the 37 page paper&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.e-booksdirectory.com/details.php?ebook=8525&quot; rel=&quot;nofollow&quot;&gt;Bioinformatics - An Introduction for Computer Scientists&lt;/a&gt; by Jacques Cohen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is a well written text, assuming some knowledge about algorithms, computing and maths, but not about biology. It helped me a lot getting comfortable with the field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Afterwards, I'd stick to Durbin's &quot;Biological Sequnce Analysis&quot; (as already mentioned by Bitwise) as a book that provides you with the theoretical foundations of the models used in bioinformatics. It focuses on Sequence processing, which is what you want as far as I understood your question. It is also quite accessible from a computer scientist's or mathematician's point of view.&lt;/p&gt;&#xA;" OwnerUserId="4222" LastActivityDate="2013-08-13T19:28:13.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9753" PostTypeId="1" AcceptedAnswerId="9755" CreationDate="2013-08-13T23:18:57.520" Score="2" ViewCount="355" Body="&lt;p&gt;I work in the PV industry and was asked a question recently during a presentation. Could Bioluminescence provide enough light to power a PV array during off peak hours? I understand the PV portion and the light spectrums needed to power the photovoltaics, but I have no clue how the science of Bioluminescence works or what type of light is emitted. I have the suspicion that this may be theoretically possible, but would require too much raw material? Any insight would be appreciated. &lt;/p&gt;&#xA;" OwnerUserId="4224" LastEditorUserId="107" LastEditDate="2013-08-14T00:40:59.340" LastActivityDate="2013-08-14T01:32:40.387" Title="Bioluminescence and photovoltaics" Tags="&lt;bioluminescence&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9754" PostTypeId="2" ParentId="9744" CreationDate="2013-08-13T23:46:49.370" Score="5" Body="&lt;p&gt;&lt;strong&gt;Neurotransmitters&lt;/strong&gt; were classically the most specific in terms of demands on experimental demonstration (thus, the so-called &quot;classical neurotransmitter&quot;) but the chief role of neurotransmitter is direct neuron-to-neuron communication via the synaptic cleft in which the post-synaptic neuron has channels that readily engage the neurotransmitter.  Classical neurotransmitters also require inactivation and are stored in vesicles in the presynaptic terminal (while under the modern definition, these last two requirements aren't as strict, allowing peptides and gasses like NO to be considered a neurotransmitter).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Neuromodulators&lt;/strong&gt;, are more of an extra-synaptic application... a bath in the extracellular medium that modulates the excitability of a population of cells.  In this regard,neurotransmitters can be considered neuromodulators when their action is on channels outside of the synaptic cleft.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have never heard the term neuromediator before, but looking at the results on Google suggest that it is the result of translation from Easterm European languages (Polish and Romanian) and seems to be synonymous with neurotransmitter.&lt;/p&gt;&#xA;" OwnerUserId="1853" LastActivityDate="2013-08-13T23:46:49.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9755" PostTypeId="2" ParentId="9753" CreationDate="2013-08-14T01:32:40.387" Score="2" Body="&lt;p&gt;Here is a report addressing this, I haven't read it in detail, but I've skimmed it and it looks like they've done a pretty good job, and address a number of key points, talk about the emission spectra of certain organisms, etc.&#xA;&lt;a href=&quot;http://www.thecrownestate.co.uk/media/279839/bioluminescence_-_a_source_of_marine_energy.pdf&quot; rel=&quot;nofollow&quot;&gt;Bioluminescence – a source of marine energy?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the conclusion: &quot;The low light output of bioluminescent species relative to solar light may render the conversion of bioluminescent light into electrical energy uneconomic as a stand-alone option.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I agree with them that it would be possible to extract energy that way.  I also agree that its not even close to economical.  You lose energy at so many steps, you have chemical energy in whatever the cells eat to grow, then some small fraction of that chemical energy will be turned into light energy, most of that light will shoot out in the wrong direction and just get absorbed by other stuff in the culture.  If you want to use bugs, a better option would probably be a microbial fuel cell, where microbes sit on an electrode, oxidize some chemical, and take that electron and dump it straight onto the electrode.  This is still a pretty inefficient process as far as energy production technologies are concerned, but at least it skips the waste associated with conversion of the chemical energy into light energy and then back into electricity.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-14T01:32:40.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9756" PostTypeId="2" ParentId="9739" CreationDate="2013-08-14T01:54:27.200" Score="1" Body="&lt;p&gt;It is an interesting question, and I definitely agree with shigeta's question about medical technologies enabling the transmission of certain negative traits that would probably otherwise be less frequent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remember, evolution is really just a numbers game of whose genes get passed on the most.  In general this was very strongly correlated with the fitness of that individual at being the best at getting food, attracting mates, and not getting dead.  At this point we've got a fast food joint on every corner, and most people in the developed world live to be able to reproduce as many times as they see fit regardless of any reasonable form of fitness.  Most people find a partner if they want one, and the incredibly fit do not procreate en masse like male leaders of packs of animals since polygamy is not an acceptable practice in many societies (notable human exceptions are cases like Genghis Khan who is thought to have fathered a ridiculous number of children [albeit this is not a great example of selection for a very nice trait]).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just think about traits that people have who reproduce less, and traits people have who reproduce more, and we're evolving towards the latter.  There is an absolutely hilarious (and depressing) intro to a movie based on taking these sorts of arguments to one extreme.. but I'm not sure this is the right venue to post it :)&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-14T01:54:27.200" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9757" PostTypeId="2" ParentId="7350" CreationDate="2013-08-14T03:45:10.037" Score="6" Body="&lt;p&gt;A few observations to add to Paul's:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Urinating on yourself in winter could be a fatal thermoregulatory mistake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Urinating on your substrate could hinder locomotion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having a continual slick of high osmolarity fluid on your skin would be damaging to the epithelium and work at odds to the action of the kidneys.&lt;/p&gt;&#xA;" OwnerUserId="4226" LastActivityDate="2013-08-14T03:45:10.037" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9758" PostTypeId="1" AcceptedAnswerId="9770" CreationDate="2013-08-14T06:13:09.287" Score="8" ViewCount="428" Body="&lt;p&gt;I was looking at diabetes the other day, and I noticed something strange. Lower amounts of lipase are a symptom of diabetes, as is overweightness. However, since lipase is the enzyme that breaks down fats, shouldn't a lack of it mean that less of it enters your blood stream and is simply excreted instead? In that case, how come diabetic people are often overweight?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question has been bugging me for ages, does anyone know why?&lt;/p&gt;&#xA;" OwnerUserId="4227" LastActivityDate="2013-08-21T16:36:15.817" Title="Why are diabetic people often overweight?" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;&lt;enzymes&gt;&lt;blood-circulation&gt;&lt;lipids&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9759" PostTypeId="1" AcceptedAnswerId="9760" CreationDate="2013-08-14T06:43:45.167" Score="1" ViewCount="518" Body="&lt;p&gt;Restriction enzymes cut the DNA of bacteriophages. Have bacteriophages evolved any mechanism to protect themselves from it ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-08-14T12:41:37.430" Title="Can viruses protect themselves against restriction enzymes?" Tags="&lt;bacteriology&gt;&lt;restriction-enzymes&gt;&lt;virus&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9760" PostTypeId="2" ParentId="9759" CreationDate="2013-08-14T07:58:36.347" Score="3" Body="&lt;p&gt;I guess you are talking about &lt;a href=&quot;http://en.wikipedia.org/wiki/Restriction_modification_system&quot; rel=&quot;nofollow&quot;&gt;the restriction modification system&lt;/a&gt;, not restriction enzymes in general (which are used a lot in the lab, for example). &#xA;If so, this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC281580/pdf/microrev00018-0065.pdf&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; might help answer your question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have not read through it totally, but at least some viruses trigger the downregulation of restriction enzymes to make them cleaving their DNA less likely. Restriction enyzmes are also quite selective for the site they cut at, so single nucleotide changes at this site, might, if the phage is lucky, not change the function of the encoded gene, but keep the restriction enzyme from binding (and thus cleaving) at that site. Mutating helps a lot. And it is fast in those little critters.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastEditorUserId="1858" LastEditDate="2013-08-14T12:41:37.430" LastActivityDate="2013-08-14T12:41:37.430" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9761" PostTypeId="2" ParentId="9689" CreationDate="2013-08-14T08:06:26.947" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;**** &quot;What is a genomic imprint? How does genomic imprinting take place?&quot;**&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Genomic imprinting is an &lt;a href=&quot;http://en.wikipedia.org/wiki/Epigenetics&quot; rel=&quot;nofollow noreferrer&quot;&gt;epigenetic&lt;/a&gt; mechanism  of inheritance which allows genes to be expressed differently depending on which parent they come from. This means it is modification of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Genome&quot; rel=&quot;nofollow noreferrer&quot;&gt;genome&lt;/a&gt;, or changes what the genome produces, without changing the &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA&quot; rel=&quot;nofollow noreferrer&quot;&gt;nucleotide (DNA)&lt;/a&gt; sequence. The result of imprinting in &lt;a href=&quot;http://en.wikipedia.org/wiki/Ploidy&quot; rel=&quot;nofollow noreferrer&quot;&gt;diploid&lt;/a&gt; organisms is that one of the two &lt;a href=&quot;http://en.wikipedia.org/wiki/Allele&quot; rel=&quot;nofollow noreferrer&quot;&gt;alleles&lt;/a&gt; is &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene_silencing&quot; rel=&quot;nofollow noreferrer&quot;&gt;silenced&lt;/a&gt;.  &lt;a href=&quot;http://people.ucalgary.ca/~browder/imprinting.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;This page provides a good overview of imprinting.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two major mechanisms are proposed called DNA methylation and histone modification though &lt;a href=&quot;http://www.geneimprint.com/site/what-is-imprinting&quot; rel=&quot;nofollow noreferrer&quot;&gt;others may yet be discovered&lt;/a&gt;. &lt;a href=&quot;http://www.cell.com/trends/genetics/abstract/S0168-9525%2897%2901180-3&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA methylation silences a gene&lt;/a&gt; by adding methyl groups to nucleotides (it modifies the nucleotide but not the sequence) which affects how they are expressed, whilst the exact mechanism is unknown (at least I can't find one on scholar) it does appear to be a key factor in &lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001849&quot; rel=&quot;nofollow noreferrer&quot;&gt;some cancer growths&lt;/a&gt;. Genes can also be silenced by &lt;a href=&quot;http://en.wikipedia.org/wiki/Histone#Structure&quot; rel=&quot;nofollow noreferrer&quot;&gt;histone modification&lt;/a&gt;, binding a gene to histones reduces its activity, ie it produces less product.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genomic imprinting was &lt;a href=&quot;http://www.sciencemag.org/content/145/3628/130.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;first described in Mealy Bugs&lt;/a&gt; (or at least this is one of the first described) which silence half of their genome in males. Whilst females are fully diploid, the male is also diploid but one half of the genome is silenced, making them effectively haploid. This is done by turning one half of the genome &lt;a href=&quot;http://en.wikipedia.org/wiki/Heterochromatin&quot; rel=&quot;nofollow noreferrer&quot;&gt;heterochromatic&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;****&quot;If I say that &quot;this&quot; allele is maternally imprinted does it mean that&#xA;  the allele of the gene is passed only by the mother? If a pedigree is&#xA;  given, how can we identify whether the trait is paternally imprinted&#xA;  or maternally imprinted?&quot;**&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Specific control of a gene, rather than entire chromosomes described above, is only known in plants and some mammals. In this case, when a gene is imprinted, the gene is silenced. An example is &lt;em&gt;Igf2&lt;/em&gt; in mice described in the below diagram which is &lt;a href=&quot;http://groups.molbiosci.northwestern.edu/holmgren/Glossary/Definitions/Def-M/molecular_imprinting.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;maternal imprinting (ie the mothers allele is silenced)&lt;/a&gt;. When the mother has a mutant allele and the father a normal allele and normal offspring is produced. When the male passes on the &lt;em&gt;Igf2&lt;/em&gt; mutant the offspring is mutant because the mother's normal copy was imprinted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zpHB1.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Igf2 gene can be seen in the above diagram. This is the one of the&#xA;  first evidences of genomic imprinting discovered. In the first part of&#xA;  the diagram a mutant gene trying to make the mouse offspring dwarf is&#xA;  passed from the mother. It can be seen that the mouse is not dwarf&#xA;  because the allele for size in this mouse is an imprinted. The&#xA;  maternal allele is not expressed, so the dwarf trait is not expressed&#xA;  in the offspring, only the normal size trait from the father is. In&#xA;  the second part of the diagram the father passes on the mutant gene&#xA;  and therefore all the offspring will be dwarf because the size trait&#xA;  is completely dependent on the paternal allele, which in this case is&#xA;  dwarf. - &lt;a href=&quot;http://sharonap-cellrepro-p3.wikispaces.com/Creating+Variation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Creating Variation&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://sharonap-cellrepro-p3.wikispaces.com/Creating+Variation&quot; rel=&quot;nofollow noreferrer&quot;&gt;The page&lt;/a&gt; this diagram and quote comes from also has a good section on genomic imprinting.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-08-14T08:36:55.073" LastActivityDate="2013-08-14T08:36:55.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9762" PostTypeId="2" ParentId="2891" CreationDate="2013-08-14T09:28:09.350" Score="1" Body="&lt;p&gt;I don't know how harmful the exposure to a camera flash could be to organisms that live in complete darkness. However, since the animals that live in this conditions are usually blind, and the time of exposure is quite short, it's reasonable to assume that the damage produced should be minimal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of caves, permanent artificial illumination is very destructive to the environment, but the effect is due mainly to temperature changes and the introduction of organisms coming from more illuminated parts of the cave (cave organisms are usually slow and react poorly to light, so they are an easy prey if they're under light). In fact, for tourist activity, the use of lanterns or miner helmets is highly recommended.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of abyssal ecosystems, ecological invasions are less likely, since there still exist a vertical barrier based in temperature, oxygen and carbon dioxide concentration and pressure. However, in this ecosystems there exist many animals which are very sensitive to light, due to the prominence of bioluminescence. Some of this animals could be damaged by the kind of light you describe. However, it's very unlikely that the main functioning of this ecosystems could be affected because of its extensive size. Moreover, the low population densities it has implies that even very long submersions would encounter only a few samples (with the exception of volcanic vents and some other geological curiosities which, in fact, are even more isolated from the rest of the biosphere by physical and chemical barriers), so the global effect should be negligible.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="1858" LastEditDate="2013-08-14T13:08:43.637" LastActivityDate="2013-08-14T13:08:43.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9763" PostTypeId="2" ParentId="9758" CreationDate="2013-08-14T09:32:17.710" Score="2" Body="&lt;p&gt;Source : Tortora and Derrickson Principles of anatomy and physiology&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read in the section on diabetes that &quot; The breakdown of stored triglycerides causes weight loss&quot;.&#xA; I assume that diabetic people are often overweight not simply because they have diabetes but because they also have many other disorders associated with it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please feel free to correct me !&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-08-21T16:36:15.817" LastActivityDate="2013-08-21T16:36:15.817" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9764" PostTypeId="2" ParentId="9739" CreationDate="2013-08-14T10:38:10.920" Score="4" Body="&lt;p&gt;Predicting future evolution is always extremely difficult (or impossible), and this is especially true for long-lived organisms such as humans. Therefore, your question is basically impossible to answer objectively. However, the question made me wonder about what research there is on the topic, and if there are any hypotheses or attempts to measure current selective pressures. A quick litterature search yielded a couple of interesting papers that you might be interested to look more closely at (along with hidden &quot;gems&quot; like &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0035626&quot; rel=&quot;nofollow&quot;&gt;&quot;Do Women Prefer More Complex Music around Ovulation?&quot;&lt;/a&gt;). They all touch on aspects of ongoing evolution or selection in humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0168952506002174&quot; rel=&quot;nofollow&quot; title=&quot;Reed &amp;amp; Aquadro. 2006. Trends in Genetics 22(9): 479–484&quot;&gt;&lt;strong&gt;Reed &amp;amp; Aquaro. 2006. Mutation, selection and the future of human evolution&lt;/strong&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Finally, it is frequently speculated that both positive and negative selection acting in modern humans is slowing down or coming to a halt because of our increasing insulation from the demands of the environment by the use of technology. The lessons being learned from studies in humans and other species, in fact, suggest that we will continue to be under certain forms of strong selection well into the distant future.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In summary, the maintenance of our genomes against deleterious mutations could have been a major selective component in shaping levels of human genetic variation. In addition to the probable role of rank-order selection (Box 1), the purging of deleterious alleles in gametogenesis might be a particularly efficient way to achieve this. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Furthermore, although selection against mildly deleterious alleles might be relaxed in modern humans, selection for the fixation of new alleles could be intensifying (and these could be detected with genome-wide data and statistical approaches; cf. Ref. [45]). This suggests a shift from the maintenance of our genomes against new mutations towards accelerated genetic change for a subset of new mutations (and possibly an associated shift from genetic drift to genetic draft dynamics [55]) as a theme for the future of human evolution.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bjps.oxfordjournals.org/content/63/1/145&quot; rel=&quot;nofollow&quot; title=&quot;Powell. 2012. The Future of Human Evolution. British journal for the philosophy of science 63(1): 145 -175&quot;&gt;&lt;strong&gt;Powell. 2012. The Future of Human Evolution&lt;/strong&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Abstract&lt;/strong&gt;&lt;br&gt;&#xA;  There is a tendency in both scientific and humanistic disciplines to think of biological evolution in humans as significantly impeded if not completely overwhelmed by the robust cultural and technological capabilities of the species. The aim of this article is to make sense of and evaluate this claim. In Section 2, I flesh out the argument that humans are ‘insulated’ from ordinary evolutionary mechanisms in terms of our contemporary biological understandings of phenotypic plasticity, niche construction, and cultural transmission. In Section 3, I consider two obvious objections to the above argument based on the growing literatures related to gene-culture coevolution and recent positive selection on the human genome, as well as a pair of less common objections relating to the connection between plasticity, population size and evolvability. In Section 4, I argue that both the ‘human evolutionary stasis argument’ and its various detractor theories are premised on a fundamental conceptual flaw: they take evolutionary stasis for granted, since they fail to conceive of stabilizing selection as a type of evolution and drift as a universal tendency that dominates in the absence of selection. Without the continued operation of natural selection, the very properties that are purported to reduce the evolutionary response to selection in humans would themselves drift into non-functionality. I conclude that properly conceived, biological evolution is a permanent and ineradicable fixture of any species, including Homo sapiens.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276617/&quot; rel=&quot;nofollow&quot; title=&quot;Keightley. 2012. Rates and Fitness Consequences of New Mutations in Humans. Genetics 190(2): 295–304.&quot;&gt;&lt;strong&gt;Keightley. 2012. Rates and Fitness Consequences of New Mutations in Humans&lt;/strong&gt;&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The human mutation rate per nucleotide site per generation (mu) can be estimated from data on mutation rates at loci causing Mendelian genetic disease, by comparing putatively neutrally evolving nucleotide sequences between humans and chimpanzees and by comparing the genome sequences of relatives.&lt;br&gt;&#xA;  ...&lt;br&gt;&#xA;  A genome-wide deleterious mutation rate of 2.2 seems higher than humans could tolerate if natural selection is &quot;hard,&quot; but could be tolerated if selection acts on relative fitness differences between individuals or if there is synergistic epistasis. I argue that in the foreseeable future, an accumulation of new deleterious mutations is unlikely to lead to a detectable decline in fitness of human populations. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jstor.org/stable/10.1086/591690&quot; rel=&quot;nofollow&quot; title=&quot;Nettle &amp;amp; Pollet. 2008. Natural Selection on Male Wealth in Humans. American Naturalist 172(5).&quot;&gt;&lt;strong&gt;Nettle &amp;amp; Pollet. 2008. Natural Selection on Male Wealth in Humans&lt;/strong&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Abstract:&lt;/strong&gt;&lt;br&gt;&#xA;  Although genomic studies suggest that natural selection in humans is ongoing, the strength of selection acting on particular characteristics in human populations has rarely been measured. Positive selection on male wealth appears to be a recurrent feature of human agrarian and pastoralist societies, and there is some evidence of it in industrial populations, too. Here we investigate the strength of selection on male wealth, first in contemporary Britain using data from the National Child Development Study and then across seven other varied human societies. The British data show positive selection on male income driven by increased childlessness among low‐income men but a negative association between personal income and reproductive success for women. Across cultures, selection gradients for male wealth are weakest in industrial countries and strongest in subsistence societies with extensive polygyny. Even the weakest selection gradients observed for male wealth in humans are as strong as or stronger than selection gradients reported from field studies of other species. Thus, selection on male wealth in contemporary humans appears to be ubiquitous and substantial in strength.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-10-13T09:28:54.913" LastActivityDate="2014-10-13T09:28:54.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9765" PostTypeId="1" AcceptedAnswerId="9767" CreationDate="2013-08-14T10:57:37.217" Score="4" ViewCount="2270" Body="&lt;p&gt;There are many poisonous fungi in nature. For example &lt;em&gt;Amanita Phalloides&lt;/em&gt;. &#xA;&lt;strong&gt;What reasons could a fungus need poison for?&lt;/strong&gt; Some species, like venomous snakes, use poison to kill other species as prey. But what about fungi? I can't think of any purpose for poison in fungi. If poison has no real function in fungi shouldn't evolution get rid of it? &lt;/p&gt;&#xA;" OwnerUserId="4229" LastEditorUserId="1590" LastEditDate="2013-08-14T11:16:18.250" LastActivityDate="2015-01-09T23:32:43.823" Title="Why are some fungi poisonous?" Tags="&lt;evolution&gt;&lt;mycology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9766" PostTypeId="1" CreationDate="2013-08-14T11:31:05.840" Score="2" ViewCount="16258" Body="&lt;p&gt;Everytime some tries to take a photo of me with a flash I manage to close my eyes (blink).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's not intentional and it's quite annoying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why am I doing it?&lt;/p&gt;&#xA;" OwnerDisplayName="user4230" LastActivityDate="2013-08-14T19:20:58.253" Title="Why do I always close my eyes when someone takes a photo of me using a flash?" Tags="&lt;eyes&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9767" PostTypeId="2" ParentId="9765" CreationDate="2013-08-14T11:34:45.720" Score="7" Body="&lt;p&gt;The same reason some plants are poisonous: to stop animals from eating them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The visible part of the fungus is called, rather misleadingly, the fruiting body. It exists to produce and spread spores and thus produce the next fungal generation. Getting eaten, rather obviously, inhibits its ability to do this. Being poisonous discourages animals from eating the fruiting body and thus permits it to complete its life cycle.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-08-14T11:34:45.720" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9768" PostTypeId="2" ParentId="9766" CreationDate="2013-08-14T12:13:33.190" Score="5" Body="&lt;p&gt;What you are describing is called a &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Corneal_reflex&quot; rel=&quot;nofollow&quot;&gt;corneal reflex&lt;/a&gt;&quot; and it is a measure to protect the eye from too bright light or foreign bodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is a involuntary movement (i.e. not intentional, as you say), mediated by the cranial nerves, specifically the ophtalmic branch of the trigeminal and the temporal and zygomatic branches of the facial nerve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have to admit that I had a very hard time finding an exact complete explanation of the phenomenon, which makes me think (but I may be wrong) that it has not been widely researched. Although it is not difficult to imagine how the trigeminal nerve could be stimulated by a foreign body touching the cornea, it seems that several theories exist on how light can stimulate it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The great part of the information that I could find at this regard are about a similar reflex, called the  the &lt;a href=&quot;http://en.wikipedia.org/wiki/Photic_sneeze_reflex&quot; rel=&quot;nofollow&quot;&gt;photic sneeze reflex&lt;/a&gt; or or ACHOO (Autosomal Cholinergic Helio-Ophtalmologic Outburst) syndrome. This occurs in ~1/4 of the population, and consists of sneezing when looking at the Sun.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case, several theories have been proposed, that essentially boil down to the fact that some other nerve (e.g. the optic nerve) stimulates the trigeminal after having being itself stimulated by bright light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From: &quot;General anaesthesia and the photosternutatory reflex&quot; - Yarrow - &lt;em&gt;Anaesthesia&lt;/em&gt;. &lt;strong&gt;2003&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The physiology underlying the photosternutatory reflex remains unclear and several mechanisms have been proposed. The theory of optic-trigeminal summation holds that the optic and trigeminal nerves are intimately linked in the midbrain. Bright light stimulates the optic nerve, causing photophobia and pain via the ophthalmic branch of the trigeminal nerve. Conversely, nasal irritation can lead to blinking and lacrimation. It is suggested that intense stimulation of the optic nerve could cause sneezing if the maxillary branch of the trigeminal nerve was stimulated as well as the ophthalmic branch. The theory of parasympathetic generalisation invokes co-activation by one stimulus of neighbouring parasympathetic branches. Light falling on the retina stimulates pupillary constriction (via the third cranial nerve) and lacrimation&#xA;  (via the seventh). A stimulus of sufficient intensity could generate&#xA;  enough parasympathetic activity to cause nasal congestion and secretions, and&#xA;  stimulate sneezing by an effect on the maxillary branch of the trigeminal nerve.&#xA;  The theory of parasympathetic hypersensitivity suggests that individuals&#xA;  with photic sneezing may have a more active or sensitive parasympathetic system,&#xA;  leading to hypersensitive nasal mucosa.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Although what you describe does not involve sneezing I think we can assume the same, or a similar afferent pathway is activated also in that case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recent works also found an activation of visual regions of the cortex in response to this stimulus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the conclusions of:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0009208&quot; rel=&quot;nofollow&quot;&gt;When the Sun Prickles Your Nose: An EEG Study Identifying Neural Bases of Photic Sneezing&lt;/a&gt; - Langer et al. - &lt;em&gt;PLoS One&lt;/em&gt;, &lt;strong&gt;2010&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We propose that the photic sneeze phenomenon might be the consequence of higher sensitivity to visual stimuli in the visual cortex and of co-activation of somatosensory areas. The ‘photic sneeze reflex’ is therefore not a classical reflex that occurs only at a brainstem or spinal cord level but, in stark contrast to many theories, involves also specific cortical areas.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2013-08-14T19:20:58.253" LastActivityDate="2013-08-14T19:20:58.253" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9769" PostTypeId="1" CreationDate="2013-08-14T12:21:45.673" Score="2" ViewCount="52" Body="&lt;p&gt;I'm at the moment analyzing cytokine array data. The available material on the statistical analysis of these data is more than unsatisfactory. Since a lot of effort is being made in the analysis of gene microarray and MALDI-TOF proteome data, I seek to apply these methods on my cytokine arrays.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is a good introductory text on microarray analysis, especially quality control and error estimation?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="852" LastActivityDate="2013-08-15T15:08:30.663" Title="Material on the analysis of (micro)array data" Tags="&lt;proteins&gt;&lt;statistics&gt;&lt;biostatistics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9770" PostTypeId="2" ParentId="9758" CreationDate="2013-08-14T12:53:37.180" Score="8" Body="&lt;p&gt;How are diabetes and obesity connected in light of low lipase activity?&lt;br&gt;&#xA;Short answer: There's more than one type of diabetes.  (And to complicate things, there's also more than one type of lipase.  It's unclear from the question which type were mentioned in what you read.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Diabetes mellitus&lt;/em&gt; is usually divided into Type 1 (insulin-deficient) and Type 2 (insulin-resistant).  Obesity is a risk factor for Type 2 diabetes, but not all diabetics are overweight. In fact, people with Type 1 are often lean.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Decreased lipase activity is not a major symptom of diabetes.  However, these two articles suggest that plasma lipase activity may be lower in cases of Type 1 diabetes but not Type 2.&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC498152/&quot;&gt;Junglee, D. et al., Low pancreatic lipase in insulin-dependent diabetics, 1983.&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC498704/&quot;&gt;Dendona, P. et al., Exocrine pancreatic function in diabetes mellitus, 1984.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4228" LastEditorUserId="107" LastEditDate="2013-08-14T13:59:47.243" LastActivityDate="2013-08-14T13:59:47.243" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9771" PostTypeId="2" ParentId="2955" CreationDate="2013-08-14T12:56:35.210" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;It may be different for other people, but for me, anything above 32°C&#xA;  (90°F) is very uncomfortable, and my body is inclined to seek cooler&#xA;  temperatures&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think you've rather nailed the key point here. I'm going to deduce from your question that you live in a temperate country? Every year, foreign students from India come over to my university in Leicester, UK. Even when the temperature is, to us, unpleasantly hot they will be shivering in their coats and complaining it's too cold. Similarly, were I to go over to India I'd be suffering in the heat while they're thinking it's a lovely comfortable temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I believe, the answer is nothing to do with the ability of the body to maintain certain temperatures - you'd need to go considerably above 32°C or below 21°C to reach temperatures the body &lt;em&gt;can't&lt;/em&gt; cope with - but rather a question of &lt;a href=&quot;http://en.wikipedia.org/wiki/Acclimatization&quot; rel=&quot;nofollow&quot;&gt;acclimatisation&lt;/a&gt;. You find 21°C comfortable and 32°C comfortable because that is the temperature that you've become used to. You can probably even recognise this from your own experience: I'm sure you've experienced days in spring feeling delightfully warm when days of the same actual temperature in autumn feel unpleasantly cold.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-08-14T12:56:35.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9773" PostTypeId="2" ParentId="9769" CreationDate="2013-08-14T15:31:11.220" Score="3" Body="&lt;p&gt;A good place to start would be &lt;a href=&quot;http://link.springer.com/book/10.1007/978-1-60327-337-4/page/1&quot; rel=&quot;nofollow&quot;&gt;Statistical Methods for Microarray Data Analysis&lt;/a&gt;. I'd also suggest papers from the labs of &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/?term=%28%28speed+t%5bAuthor%5d%29+AND+review%5bPublication+Type%5d%29+AND+microarray&quot; rel=&quot;nofollow&quot;&gt;Terry Speed&lt;/a&gt;, &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed?term=%28%28churchill%20ga%5bAuthor%5d%29%20AND%20review%5bPublication%20Type%5d%29%20AND%20microarray&quot; rel=&quot;nofollow&quot;&gt;Gary Churchill&lt;/a&gt;, &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/?term=%28%28quackenbush+j%5bAuthor%5d%29+AND+review%5bPublication+Type%5d%29+AND+microarray&quot; rel=&quot;nofollow&quot;&gt;John Quackenbush&lt;/a&gt;, and &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/?term=%28Smyth+GK%5bAuthor%5d%29+AND+microarray&quot; rel=&quot;nofollow&quot;&gt;Gordon Smyth&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I found some papers that specifically reflect on your exact issue: how to apply the methods developed for DNA microarrays to analyze protein arrays.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://cancerres.aacrjournals.org/content/65/8/2985.long&quot; rel=&quot;nofollow&quot;&gt;Eckel-Passow &lt;em&gt;et al.&lt;/em&gt; Experimental design and analysis of antibody microarrays: applying methods from cDNA arrays. &lt;em&gt;Cancer Res.&lt;/em&gt; 2005 Apr 15;65(8):2985-9.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0076687906110150#&quot; rel=&quot;nofollow&quot;&gt;Royce &lt;em&gt;et al.&lt;/em&gt; Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies. &lt;em&gt;Methods Enzymol.&lt;/em&gt; 2006;411:282-311.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4221" LastEditorUserId="4221" LastEditDate="2013-08-15T15:08:30.663" LastActivityDate="2013-08-15T15:08:30.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9774" PostTypeId="1" AcceptedAnswerId="13589" CreationDate="2013-08-14T15:44:02.033" Score="2" ViewCount="2275" Body="&lt;p&gt;&lt;strong&gt;Actual question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have reason to believe (details see below) that in a ligation I carried out, an EcoRI sticky end (EcoRI: G'AATT_C) and an XmaI sticky end (XmaI: C'CCGG_G) were somehow ligated together, a process during which at least the EcoRI site was lost: the plasmid had a BamHI site very near the XmaI site, and a BamHI/EcoRI digest produced only one band compared to three bands in the undigested control (three conformations of circular plasmid).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How could ends as incompatible as EcoRI and XmaI be ligated?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Detailed Background or: Why I believe incompatible sites were ligated&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is chronologically further to: &lt;a href=&quot;https://biology.stackexchange.com/questions/9726/what-are-common-causes-of-unexpected-ligation-products&quot;&gt;What are common causes of unexpected ligation products?&lt;/a&gt;. Briefly: I digested two plasmids, one with EcoRI and XmaI (p1), the other with EcoRI and AgeI (p2) [XmaI and AgeI produce compatible sticky ends], then carried out a ligation between a 1.4kb insert isolated from p2 (structure EcoRI-1.4kb-AgeI) into the 3.4kb backbone isolated from p1 (structure XmaI-20bp-BamHI-3.4kb-EcoRI). After transformation, I tested the ligation product by digest with EcoRI and BamHI, which should produce again 3.4kb + 1.4kb. The gel was poor quality but allowed the conclusion that there were different ligation products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Repeating the EcoRI/BamHI digest and gel more carefully showed there were only two variants: Variant A (8 colonies) produced the two expected bands 3.4kb and 1.4kb. Variant B (4 colonies) only produced a clear 3.4kb band, nothing else visible in the lane: in other words, it only carried either an EcoRI or a BamHI site and was in total smaller than variant A (confirmed by undigested controls). Thus, I conclude that B was simply the same 3.4kb backbone, re-ligated without the 1.4kb insert. Since the BamHI site was untouched in the backbone during the preparatory EcoRI/XmaI digestion, I assume that the EcoRI site was not recovered during the ligation of variant B.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(The ligation was carried out overnight at 16 deg C, using Promega T4 DNA ligase and buffer and a molar ratio of 3:1 insert:vector at a total volume of 20uL. The E.coli for transformation were Invitrogen OneShot Stbl3 and have been routinely and successfully used in the lab for a long time. The analytical digestion used Promega EcoRI and BamHI in Buffer Multi-Core, which Promega claims offers 75-100% efficiency for both enzymes. Incubation was 1.5h at 37°C.)&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2019-01-16T09:33:19.483" Title="What can cause incompatible sticky ends to be ligated?" Tags="&lt;synthetic-biology&gt;&lt;restriction-enzymes&gt;" AnswerCount="3" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9775" PostTypeId="1" CreationDate="2013-08-14T16:19:28.743" Score="3" ViewCount="4966" Body="&lt;p&gt;When we ingest food, the epiglottis covers the trachea and the uvula covers the nasal passage. But what happens when we breathe? Why does the air go into our trachea and not the oesophagus? &lt;/p&gt;&#xA;" OwnerUserId="4235" LastActivityDate="2016-04-28T18:55:13.790" Title="Why does air from the nasal cavity not go into the oesophagus?" Tags="&lt;human-biology&gt;&lt;breathing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9776" PostTypeId="2" ParentId="9775" CreationDate="2013-08-14T17:48:39.590" Score="4" Body="&lt;p&gt;Swallowing food requires muscle strength to force the food down the oesophagus, which is a soft tube that collapses when empty, simply because the body is very crowded (space-efficient) and empty spaces collapse unless forced open. Only when you swallow, the oesophageal muscles force space to be made for food coming through.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In contrast, the trachea and bronchi are covered in almost-circular or C-shaped cartilage which holds them open and stable for air to flow through. You can see it here: &lt;a href=&quot;http://en.wikipedia.org/wiki/Bronchi&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Bronchi&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Concluding, air does not enter the oesophagus because it is always closed. Additionally, when the chest expands for breathing, the lungs expand and create suction down the trachea and not into the stomach (simply because this is where they connect).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exception of course is if air is trapped in the swallowing motion with (or without) food. In this case it &lt;em&gt;will&lt;/em&gt; enter the oesophagus and cause you to burp.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-08-14T17:48:39.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9778" PostTypeId="1" AcceptedAnswerId="9789" CreationDate="2013-08-14T19:48:33.327" Score="8" ViewCount="353" Body="&lt;p&gt;According to Wikipedia, we know that color-vision photopigments appeared in the common ancestors of tetrapods and fish at least 360 MY ago.  Would life have been less colorful before the evolution of color vision?  &lt;/p&gt;&#xA;" OwnerUserId="4237" LastEditorUserId="3971" LastEditDate="2013-08-29T14:21:54.407" LastActivityDate="2013-08-29T14:21:54.407" Title="Was life less colorful before color vision evolved?" Tags="&lt;evolution&gt;&lt;vision&gt;&lt;pigmentation&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9780" PostTypeId="2" ParentId="6900" CreationDate="2013-08-14T22:53:55.290" Score="4" Body="&lt;p&gt;Sexual arousal, in and of itself, is pleasurable in a way that hunger is not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to why this is, perhaps visual stimulation and anticipation improves the sexual function of animals more than it improves eating.  One possible explanation is &lt;a href=&quot;http://dx.doi.org/10.1016/S1090-5138%2802%2900103-4&quot; rel=&quot;nofollow&quot;&gt;sperm competition&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Either arousal state can be induced by visual stimuli.  However, the respective hormones work differently.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Ghrelin&quot; rel=&quot;nofollow&quot;&gt;Ghrelin&lt;/a&gt; doesn't affect hunger and feeding&lt;a href=&quot;http://dx.doi.org/10.1038/35051587&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt; the way that &lt;a href=&quot;http://dx.doi.org/10.1016/j.physbeh.2004.08.018&quot; rel=&quot;nofollow&quot;&gt;dopamine&lt;/a&gt; affects arousal and mating&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11805404&quot; rel=&quot;nofollow&quot;&gt;(2)&lt;/a&gt;.  Also, starvation has been found to decrease dopamine concentration&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/316524&quot; rel=&quot;nofollow&quot;&gt;(3)&lt;/a&gt; in those same areas that sexual stimulation increases it&lt;a href=&quot;http://dx.doi.org/10.1016/0149-7634%2894%2900020-2&quot; rel=&quot;nofollow&quot;&gt;(4)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4228" LastActivityDate="2013-08-14T22:53:55.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9782" PostTypeId="1" AcceptedAnswerId="9784" CreationDate="2013-08-15T03:20:29.287" Score="2" ViewCount="1250" Body="&lt;p&gt;The lac operon has 3 genes: lacZ , lacY and lacA. I have seen that the m-RNA transcript of these genes has stop codons in between. So, how can the RNA be made continuously? Won't the RNA Pol detach if there is a stop codon in between?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2013-08-15T03:34:39.777" LastActivityDate="2013-08-15T05:00:35.800" Title="How can a continuous RNA be transcribed in the lac operon?" Tags="&lt;rna&gt;&lt;gene-expression&gt;&lt;mrna&gt;&lt;operons&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9783" PostTypeId="1" AcceptedAnswerId="9785" CreationDate="2013-08-15T03:57:50.667" Score="2" ViewCount="300" Body="&lt;p&gt;How are bidirectional promoters expressed ? (Won't RNA Pol have to go in 3'-5' direction?)&#xA;Why are they more commonly found in eukaryotes than prokaryotes?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-08-15T08:06:41.573" Title="Expression of bidirectional promoters" Tags="&lt;gene-expression&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9784" PostTypeId="2" ParentId="9782" CreationDate="2013-08-15T05:00:35.800" Score="3" Body="&lt;p&gt;RNA Pol doesn't worry about stop codons.  Transcription termination can occur through the formation of a hairpin in the new RNA sequence, or through the action of Rho proteins.  A lot of the time prokaryotes have polycistronic mRNAs, that is, mRNAs with multiple protein coding regions.  The stop codons are detected during translation, so you will often have all three lac proteins being translated at once off of the same mRNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a nice section on &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21601/&quot; rel=&quot;nofollow&quot;&gt;transcription termination&lt;/a&gt;, or look up Rho-independent or Rho-dependent transcription termination for more info.  &lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-15T05:00:35.800" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9785" PostTypeId="2" ParentId="9783" CreationDate="2013-08-15T05:14:17.590" Score="4" Body="&lt;p&gt;Genes controlled by bidirectionl promoters are in head-to-head configurations, meaning that their 5' ends are facing one-another.  Remember that DNA is double stranded, so this means one gene is on the 'top' strand and one gene is on the 'bottom' strand.  Check out the diagram below, genes are in capitals, bidirectional promoter in parenthesis.  Both genes are transcribed 5'-&gt;3'&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;                                         --&amp;gt; Gene 1&#xA; 5'-atgcagtcatga(ctgactaagt...tcagtcatga)CTGACTGACTAGTCAT-3'&#xA;    |||||||||||| ||||||||||||||||||||||| ||||||||||||||||&#xA; 3'-TACGTCAGTACT(gactgattca...agtcagtact)gactgactgatcagta-5'&#xA;      Gene 2 &amp;lt;--&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;As for why they are more commonly found in eukaryotes, those questions are definitely hard to answer.  It has been shown that genes on bidirectional promoters are expressed together more often than two genes that are next to each other on different promoters.  That means this might be a eukaryotic strategy similar to prokaryote's usage of polycistronic mRNA, an easy way to have similar expression patterns of genes that should often be expressed in similar amounts.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastEditorUserId="4177" LastEditDate="2013-08-15T08:06:41.573" LastActivityDate="2013-08-15T08:06:41.573" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9786" PostTypeId="2" ParentId="1145" CreationDate="2013-08-15T09:55:45.970" Score="-1" Body="&lt;p&gt;The Wikipedia protostome vs. deuterostome figure depicts a &quot;prototype&quot; deuterostome, such as an echinoderm or an amphibian.&#xA;In amniotes (reptiles and their descendants - birds and mammals), the giant amniotic egg full of yolk led to profound changes in early embryogenesis, including the disappearance of the true blastopore. (Its analogue as organizer of gastrulation is the Hensen's node, but it is dorsal and does not form the anus.) Placental mammals have secondarily lost the amniotic egg, but a substantial part of their gastrulation movements still reflect its former presence.&#xA;Although in us the blastopore does not form the anus and does not even exist, we are still classified as deuterostomes because of our clear kinship with amphibians.&lt;/p&gt;&#xA;" OwnerUserId="4241" LastActivityDate="2013-08-15T09:55:45.970" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9787" PostTypeId="1" AcceptedAnswerId="9794" CreationDate="2013-08-15T11:01:39.807" Score="4" ViewCount="15836" Body="&lt;p&gt;A virus can either participate in a lysogenic cycle or a lytic cycle. What decides that?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2018-03-08T14:21:56.003" Title="What decides whether a lysogenic cycle or a lytic cycle will take place?" Tags="&lt;virus&gt;" AnswerCount="2" CommentCount="1" ClosedDate="2018-03-12T19:23:55.213" ContentLicense="CC BY-SA 3.0" />
  <row Id="9788" PostTypeId="1" CreationDate="2013-08-15T11:07:40.867" Score="7" ViewCount="79" Body="&lt;p&gt;I'm looking for a database or a systematic way to search for organisms which meet certain criteria. My criteria descending importance are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;growth substrate&lt;/li&gt;&#xA;&lt;li&gt;chemolithoautotrophy (on which substrate)&lt;/li&gt;&#xA;&lt;li&gt;overflow metabolite&lt;/li&gt;&#xA;&lt;li&gt;methanogen&lt;/li&gt;&#xA;&lt;li&gt;Nitrogen-fixation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Is there a database / some other means to find this information other than manual digging?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried NCBI taxonomy, LINNAEUS, uBio, KEGG, organism-tagger and others, but these don't appear to be capable of this kind of query. They all seem to require the organism name to begin with. But maybe I'm missing something?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks for any hints.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ingvar&lt;/p&gt;&#xA;" OwnerUserId="1312" LastEditorUserId="3340" LastEditDate="2014-11-15T10:23:09.537" LastActivityDate="2014-12-15T10:28:39.797" Title="How to search for organisms by criteria such as growth substrate and overflow metabolites?" Tags="&lt;species-identification&gt;&lt;database&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9789" PostTypeId="2" ParentId="9778" CreationDate="2013-08-15T11:14:57.970" Score="4" Body="&lt;p&gt;It is likely that the world have been less colourful before colour vision evolved, though that is my opinion, I will now back it up a little.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Certainly some of the colour we see in nature serves a function outside of the use of visual stimuli.&lt;/strong&gt; For example plants have green leaves because of the way that functions with photosynthesis - it absorbs enough energy whilst not so much that the leaves burn. For more on the green leaves in plants &lt;a href=&quot;https://biology.stackexchange.com/questions/450/why-do-plants-have-green-leaves-and-not-red&quot;&gt;see this classic Biology SE question with it's very good answers&lt;/a&gt;. Other examples could include functions such as &lt;a href=&quot;http://www.raptorresearchfoundation.org/education/feather-facts&quot; rel=&quot;nofollow noreferrer&quot;&gt;thermal regulation or light contrast&lt;/a&gt; for camouflage (if anyone has other valid examples then please comment and I'll add them in).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there is likely to have been an increase in the prevalence of colour in nature since the evolution of colour vision. &lt;strong&gt;Colour is used as a visual stimulus in numerous ways.&lt;/strong&gt; My first example is flower colouration. &lt;a href=&quot;http://www.jstor.org/stable/2444019&quot; rel=&quot;nofollow noreferrer&quot;&gt;Flowers use coloured petals as a stimulant to attract pollinators&lt;/a&gt;. Another example is the use of colour in mate attraction. &lt;a href=&quot;http://www.smh.com.au/technology/sci-tech/animal-attraction-peacocks-and-sexual-selection-20130814-2rvp4.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Peacocks tails&lt;/a&gt;, the &lt;a href=&quot;http://www.rspb.org.uk/wildlife/birdguide/name/b/blackbird/index.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;orange bills of blackbirds&lt;/a&gt;, and the &lt;a href=&quot;http://www.biomedcentral.com/1471-2148/9/53/&quot; rel=&quot;nofollow noreferrer&quot;&gt;brightly coloured cichlid fish.&lt;/a&gt; All of these examples take advantage of colour vision, without it they simply wouldn't be as discernible from less colourful variants and given the cost of producing them it is unlikely they would evolve as often as they do. A third example is camouflage, the most striking example I can think of is &lt;a href=&quot;http://en.wikipedia.org/wiki/Cuttlefish#Camouflage&quot; rel=&quot;nofollow noreferrer&quot;&gt;cuttlefish&lt;/a&gt; which match themselves very well to their background.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although I haven't provided direct evidence that the world was less colourful I have provided a potential theory. Hopefully the examples I've presented have convinced you that my theory of the world being less colourful, even possibly only marginally less so, is not developed without thought. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will point out &lt;strong&gt;it is entirely possible the world was equally or even more colourful before&lt;/strong&gt; - no colour vision would allow colours to &lt;em&gt;drift&lt;/em&gt; around more, selection on colour in the context of camouflage would reduce the variety of colour we see as selection would favour colours matching the surroundings (if camouflage was necessary to survival in a grass environment we would expect most things to look quite green). To this end, I don't think we can currently answer your question firmly but we can put out theories as to how it would have been.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2013-08-15T11:20:42.480" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9790" PostTypeId="2" ParentId="3177" CreationDate="2013-08-15T12:30:11.813" Score="10" Body="&lt;p&gt;Because the intermediate stages are not evolutionarily favoured. That's why.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sound and light perception are useful without any generative capability. An organism with a tiny amount of perception for either of these things has an advantage over those without; and an organism with a tiny amount more has an advantage over those with a tiny bit less. This advantage forms the basis for selection and thus improved sensory capabilities (balanced, of course, by the cost of those capabilities).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Being able to perceive radio on the other hand provides no useful information about the world at low level perception so even if an organism was to randomly mutate so as to detect radiowaves* there would be no selection for this ability, and thus no mechanism to drive the evolution of advanced radio reception. Without the ability to perceive radiowaves there is no possibility of evolving the ability to generate radio signals in a controlled manner.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*-In fact, since radiowaves generally interact very little with organic materials unlike heat, light and sound even this first step of random mutation is much less likely than for sense that have evolved.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-08-15T12:30:11.813" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="9791" PostTypeId="1" AcceptedAnswerId="9796" CreationDate="2013-08-15T16:18:56.657" Score="7" ViewCount="8256" Body="&lt;p&gt;Before the discovery of &lt;em&gt;Australopithecus afarensis&lt;/em&gt; in the 1970s, most anthropologists believed that an increase in brain capacity had preceded bipedal locomotion. However, this &lt;a href=&quot;http://en.wikipedia.org/wiki/File%3aLucy_Skeleton.jpg&quot; rel=&quot;nofollow&quot;&gt;reconstruction of the Lucy skeleton&lt;/a&gt; shows that the &lt;em&gt;A. afarensis&lt;/em&gt; was bipedal even with a brain size of around 400 cc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the &lt;a href=&quot;http://en.wikipedia.org/wiki/File%3aLucy_blackbg.jpg&quot; rel=&quot;nofollow&quot;&gt;actual Lucy skeleton&lt;/a&gt; does not include feet, and only has two partial leg bones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do anthropologists determine, based on the bones preserved, that &lt;em&gt;A. afarensis&lt;/em&gt; was bipedal?&lt;/p&gt;&#xA;" OwnerUserId="104" LastEditorUserId="4101" LastEditDate="2013-10-14T18:38:35.110" LastActivityDate="2018-06-27T22:34:01.563" Title="What is the evidence that australopithecines were bipedal?" Tags="&lt;evolution&gt;&lt;movement&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9792" PostTypeId="2" ParentId="7465" CreationDate="2013-08-15T16:24:17.663" Score="2" Body="&lt;p&gt;Eric Davidson should be your first port of call for GRN related work!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He published a great paper not so long ago demonstrating exactly what you're talking about. By including spatio-temporal dynamics of gene expression (e.g. differential equations modelling the time scale of gene expression) they constructed a boolean logic based predictive model for gene expression in early sea urchin development. Their results were not only accurate, but actually made predictions about genes that they hadn't experimentally tested...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check it out:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.caltech.edu/content/modeling-genes-development&quot; rel=&quot;nofollow&quot;&gt;http://www.caltech.edu/content/modeling-genes-development&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/early/2012/08/22/1207852109.abstract&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/early/2012/08/22/1207852109.abstract&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4242" LastActivityDate="2013-08-15T16:24:17.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9794" PostTypeId="2" ParentId="9787" CreationDate="2013-08-15T16:38:35.057" Score="4" Body="&lt;p&gt;It depends on a few factors, such as how many phages infected the cell, whether or not the cell is in good growth conditions, and so on. If the cell is in stress or has low amounts of nutrients, the lysogenic pathway is typically activated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The underlying mechanism has to do with a protein cascade involving either the cro or cI protein that is encoded by the virus. The cI protein is a repressor, and it will prevent the lytic genes from being transcribed. By default the virus will transcribe the lytic genes, so they must be repressed for lysogeny to occur. Similarly, cro is also a transcriptional repressor. The two proteins work in opposition to each other. cro binds to an operator, oR3, that is involved in repressing cI, which may prevent cI from being expressed and thus preventing it from repressing lytic genes (however the importance of this is debatable because if you replace oR3, the cell can apparently still lyse).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are numerous other proteins, such as N and Q, that are involved. The N protein has to be transcribed by the polymerase ‘anti-terminating’, or reading through a termination signal. This will happen more frequently when the protein RNase III is present at high concentrations. The N protein is a lytic regulator. Thus, when there are high amounts of RNase III there will be more N expressed which leads to the lytic cycle. RNase III is not a viral protein. It is a host protein and the host expresses more of it when nutrients are abundant. This is how the virus is able to ‘sense’ if nutrients are high enough to enter the lytic cycle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The whole system is way more complicated but this is it in a nutshell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.genet.39.073003.113656&quot; rel=&quot;nofollow&quot;&gt;http://www.annualreviews.org/doi/full/10.1146/annurev.genet.39.073003.113656&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-08-15T16:38:35.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9796" PostTypeId="2" ParentId="9791" CreationDate="2013-08-15T23:42:59.363" Score="11" Body="&lt;p&gt;Mainly because of the characteristics of the pelvic joint with the femur and the foramen magnum (the hole the spinal cord uses to connect with the encephalon). Also, there are more specimens other than Lucy, and there also exist fossil footprints (for instance the Laetoli footprints). All this evidence points to a bipedal walking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/f4Bgg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.talkorigins.org/faqs/homs/pelvis.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.talkorigins.org/faqs/homs/pelvis.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, the &lt;em&gt;Asutralopithecus&lt;/em&gt; pelvis resembles human pelvis more than chimpanzee's (wich is adapted to a primarily quadrupedal movement).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LZjqC.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;https://web.archive.org/web/20160817080843/http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Primates.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://web.archive.org/web/20160817080843/http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Primates.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this image you can see the position of the foramen magnum in a typical pure quadrupedal mammalian, such as a dog. The foramen inserts in the posterior part of the cranium. In the human, the foramen inserts in the base of the skull, due to de erected position. In chimpanzees, which have quadrupedal march, but can also display some bipedal movements, the foramen is slightly displaced towards the basis of the cranium, in an intermediate position between both.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xeh4i.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.fcnym.unlp.edu.ar/museo/educativa/serypertenecer/principal/australopitecinos.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.fcnym.unlp.edu.ar/museo/educativa/serypertenecer/principal/australopitecinos.html&lt;/a&gt; (Spanish)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this image it shows the foramen in chimpanzees, &lt;em&gt;Australopithecus&lt;/em&gt; and modern humans, and you can see that the position in the second is at the base of the skull, just like in &lt;em&gt;Homo&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is assumed that the bipedal locomotion is an adaptation to the savanna environment, where trees were rare. Bipedalism also allows a better visual field and it has more energetic efficiency.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="9686" LastEditDate="2018-06-27T22:34:01.563" LastActivityDate="2018-06-27T22:34:01.563" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="9797" PostTypeId="1" AcceptedAnswerId="9803" CreationDate="2013-08-16T04:52:24.757" Score="3" ViewCount="444" Body="&lt;p&gt;I see this very curious patterns on the sun-facing side of a &lt;strong&gt;jasmine&lt;/strong&gt; (probably) leaf - visible with a makeshift microscope (about 50x)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are them? Pores? Are there other plants with similar textures?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The microscope is made out of a webcam, as described &lt;a href=&quot;http://www.bbc.co.uk/science/0/22600308&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/T7Axb.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1869" LastEditorUserId="1869" LastEditDate="2013-08-16T08:09:52.413" LastActivityDate="2013-08-16T09:04:43.240" Title="What are these stars in my microscopic image?" Tags="&lt;botany&gt;&lt;microscopy&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9798" PostTypeId="1" CreationDate="2013-08-16T07:11:07.170" Score="4" ViewCount="276" Body="&lt;p&gt;I know how plasmids can replicate independently of the main genome and know that they confer various properties to the bacteria and are useful in conjugation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is - what is the advantage of plasmid replicating on their own? (Would there be any disadvantage if they were controlled by the main genome instead?)&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="460" LastEditDate="2013-08-16T17:37:19.333" LastActivityDate="2014-04-08T17:13:14.060" Title="Why do plasmids replicate on their own?" Tags="&lt;bacteriology&gt;&lt;plasmids&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9800" PostTypeId="1" AcceptedAnswerId="9804" CreationDate="2013-08-16T07:56:31.337" Score="10" ViewCount="246" Body="&lt;p&gt;Pouring salt in the wounds is so painful. I am sure you all experienced this. whats happend there?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="115" LastEditDate="2013-08-16T08:47:19.383" LastActivityDate="2013-08-16T09:09:43.593" Title="Why pouring salt in the wounds is painful?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9801" PostTypeId="1" AcceptedAnswerId="9813" CreationDate="2013-08-16T08:29:17.177" Score="5" ViewCount="59" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Health_threat_from_cosmic_rays&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;, and &lt;a href=&quot;https://space.stackexchange.com/questions/604/is-it-possible-to-get-pregnant-through-natural-means-in-space&quot;&gt;Space.SE&lt;/a&gt; seem to indicate humans become infertile in space due to the increased exposure to cosmic rays. Knowing as we do that Antarctica is holey, and subject to increased radiation (atleast UV if not broad-spectrum), I find myself wondering whether any studies on fertility were ever conducted on that continent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So ... Are there any studies on the fertility levels of humans/mammals as a function of their stay at Antarctica?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:58:55.703" LastActivityDate="2013-08-17T02:27:36.547" Title="Are there any studies on the fertility levels of humans/mammals as a function of their stay at Antarctica?" Tags="&lt;reproduction&gt;&lt;radiation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9802" PostTypeId="2" ParentId="9798" CreationDate="2013-08-16T08:40:23.133" Score="3" Body="&lt;p&gt;In plasmids with high number of copies, the plasmid needs a certain density to be able to supply its function. If a given cell contains a few dozens of plasmid mollecules, and this is its optimal density, the easiest way to achieve this is to downregulate the replication by its own presence or the presence of one of its components. This also allows a random segregation during cell division, due basically by simple diffusion. It's also easier for the plasmid to achieve its optimal density once it has enter in a new cell by conjugation or transformation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plasmids are also subject to selection, so it is reasonable to assume that the more independent and more contagious a plasmid is, the bigger its presence in the population. In fact, it is a reasonable hypothesis to assume that many viruses are parasitic plasmids (many viruses in fact have a similar genomic structure and share many traits with them).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in plasmids with low number of copies the replication events can be dependent of the genome replication as you describe (despite the fact that many plasmids of this kind still regulate its own replication by itself). In this case, though, the line between plasmid and chromosome is less clear. In some organisms some big plasmids seems to form part of the genomic organization in the whole strain, and they usually contain important genes. This plasmids behave just like regular chromosomes, and they segregate by the same mechanisms the rest of the genome use. For those plasmids the terms minichromosome and megaplasmid are used, and the choice usually depends of the kind of genes it contains.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-08-16T08:40:23.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9803" PostTypeId="2" ParentId="9797" CreationDate="2013-08-16T09:04:43.240" Score="2" Body="&lt;p&gt;Despite low resolution, I'd say those are trichomes. &lt;em&gt;Jasminum&lt;/em&gt; is genera that produce essential oils, so it have glandular hairs and other trichomes wich help to rettain the oil layer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZBxyX.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://cms.herbalgram.org/herbalgram/issue53/article2207.html?ts=1376643526&amp;amp;signature=b4349f7f3ca6f6a47823f4754237eaac&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://cms.herbalgram.org/herbalgram/issue53/article2207.html?ts=1376643526&amp;amp;signature=b4349f7f3ca6f6a47823f4754237eaac&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image displayed above shows glandular and non-glandular trichomes in lavander shown by scanning electron microscopy. I'm afraid I couldn't find anything about &lt;em&gt;Jasminum&lt;/em&gt; in particular, but I think it must be the same kind of structure.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-08-16T09:04:43.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9804" PostTypeId="2" ParentId="9800" CreationDate="2013-08-16T09:09:43.593" Score="6" Body="&lt;p&gt;De salt particles are alien bodies and can damage the tissue by mechanical means (This would also happen if you pour sand into an open wound). Also, the exposed tissue is vulnerable to dehydration, wich happens faster if the osmotic pressure is higher. Finally, nerve tissue is particulary sensible to changes in the ion composition of its sorroundings, so the added sodium may affect the action potential of the nociceptors. &lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-08-16T09:09:43.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9805" PostTypeId="1" CreationDate="2013-08-16T09:28:49.817" Score="2" ViewCount="3118" Body="&lt;p&gt;What is the best color for a PPG signal?&#xA;Red, green, blue or infra-red?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm asking because commercial oximeter sensors usually use a pair of red and infra-red LEDs. But recently, I've seen a lot of sensors using green LEDs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="4246" LastEditorDisplayName="user3795" LastEditDate="2013-08-16T12:45:50.260" LastActivityDate="2013-08-16T18:03:12.573" Title="What is the best color for a PPG signal (photoplethysmography)?" Tags="&lt;human-biology&gt;&lt;hematology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9806" PostTypeId="2" ParentId="9805" CreationDate="2013-08-16T14:46:13.863" Score="1" Body="&lt;p&gt;The reason red and infra-red are used is the difference in absorbance at those two frequencies between oxygenated and unoxygenated hemoglobin. Using the difference in these two frequencies allows the concentration of oxyhemoglobin to be calculated. (The red LED is at the frequency where oxyhemoglobin and hemoglobin have identical absorbance).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I know, there's no reason why a green LED wouldn't work. You would only be able to measure the PPG signal and not the oximetry data (unless you used two different LEDs and did some math). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0305049197002307&quot; rel=&quot;nofollow&quot;&gt;Absorption curves&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2013-08-16T14:46:13.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9807" PostTypeId="1" CreationDate="2013-08-16T15:48:47.907" Score="1" ViewCount="56" Body="&lt;p&gt;I am designing synthetic ribozymes, and need to see the secondary structure that arises from its flanking arms binding to a target mRNA. I've used Mfold as well as IDT's OligoAnalyzer (Hairpin), but these only allow from prediction of secondary structure of the ribozyme folding on itself (which is thermodynamically less stable that 20-40 perfectly complementary nucleotides along the arms).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any software that will allow for simultaneous prediction of secondary structure of &lt;em&gt;two&lt;/em&gt; RNA molecules?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2013-08-16T15:55:11.433" LastActivityDate="2013-08-16T15:55:11.433" Title="Visualizing secondary RNA structure binding to target" Tags="&lt;bioinformatics&gt;&lt;rna&gt;&lt;structural-biology&gt;&lt;structure-prediction&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9808" PostTypeId="2" ParentId="9805" CreationDate="2013-08-16T18:03:12.573" Score="1" Body="&lt;p&gt;Found the difference in colors :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Longer wavelenght penetrate deeper. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;because main artifacts are caused by changes in the blood volume at the measurement site. During movement, the changes in venous blood volume are larger than those in arterial one. While the penetration depth of light is dependent on its wavelength, and green&#xA;light do not penetrate as deeply as infrared light. Therefore, the green PPG would include less information from various non-pulsatile sources than the infrared PPG.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I also looked up multi-spectral ppg and from what I read they all give you an exploitable PPG signal, it really depends from what you want to do.&#xA;For oximeter you need red and ifr light source. but if ou just want a pulse meter shorter wavelenght are better.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://embc.embs.org/files/2013/3170_FI.pdf&quot; rel=&quot;nofollow&quot;&gt;http://embc.embs.org/files/2013/3170_FI.pdf&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.biofotonika.lu.lv/fileadmin/user_upload/lu_portal/projekti/biofotonika/Publikacijas/A3/Asare_8073_76_Praga.PDF&quot; rel=&quot;nofollow&quot;&gt;http://www.biofotonika.lu.lv/fileadmin/user_upload/lu_portal/projekti/biofotonika/Publikacijas/A3/Asare_8073_76_Praga.PDF&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4246" LastActivityDate="2013-08-16T18:03:12.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9810" PostTypeId="1" CreationDate="2013-08-16T21:26:14.467" Score="6" ViewCount="607" Body="&lt;p&gt;Recently there has been this video going around of a snake that had been decapitated.  Its body swung around to the decapitated head and the head attacked the body on &quot;reflex&quot;.  Now we know that most reflex arcs bypass the brain.  So if it is the case that this strike attack is reflex then how is that suppressed when the snake is alive? Why aren't snakes always reflexively attacking themselves? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.theguardian.com/world/video/2013/aug/15/decapitated-copperhead-snake-bites-itself-video&quot; rel=&quot;nofollow&quot;&gt;Here is the video.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this some other phenomenon than reflexive attack?&lt;/p&gt;&#xA;" OwnerUserId="4252" LastEditorUserId="948" LastEditDate="2013-08-17T02:46:13.217" LastActivityDate="2013-08-19T20:11:33.360" Title="If a dead snake reflexively attacks itself, why does it not always attack itself?" Tags="&lt;neuroscience&gt;&lt;zoology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9812" PostTypeId="2" ParentId="9810" CreationDate="2013-08-17T01:52:06.663" Score="2" Body="&lt;p&gt;It seems that National Geographic were just as curious, in their interview in &lt;a href=&quot;http://newswatch.nationalgeographic.com/2013/08/16/how-did-a-decapitated-snake-bite-itself/&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; with &lt;a href=&quot;http://nationalzoo.si.edu/AboutUs/Staff/BiosAndProfiles/MurphyJames.cfm&quot; rel=&quot;nofollow&quot;&gt;James Murphy&lt;/a&gt;, he states the answer to your final question - that even though the snake is dead, it can still reflexively 'attack' the nearest object - in this case, the remains of its own body - as it is not attached, it is a 'foreign object' and the reflexes result in an 'attack'.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-08-17T01:52:06.663" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9813" PostTypeId="2" ParentId="9801" CreationDate="2013-08-17T02:27:36.547" Score="1" Body="&lt;p&gt;I haven't been able to find a study on fertility, but it would be important to note the difference between radiation considered.  The dangerous radiation discussed in both of your links are cosmic rays as you noted.  Our main defense against this sort of radiation is the earth's magnetic field.  The hole you are talking about is in the ozone layer, which is much more important in UV protection than cosmic ray protection.  The amount of incident cosmic rays is slightly more at latitudinal extremes due to the deflection away from the equator by the magnetic field, but this is only 1.5 to 2 times greater, see &lt;a href=&quot;http://www.issibern.ch/PDF-Files/Spatium_11.pdf&quot; rel=&quot;nofollow&quot;&gt;fig. 8&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unless we figure out how to punch a hole in the magnetic field as well, the main threat in the arctic is skin cancer from UV, not infertility from cosmic rays.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-17T02:27:36.547" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9814" PostTypeId="1" AcceptedAnswerId="9817" CreationDate="2013-08-17T05:58:54.433" Score="1" ViewCount="132" Body="&lt;p&gt;How do plasmids protect themselves from restriction enzymes released by bacteria (i.e., against bacteriophages)?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2013-08-17T20:25:57.920" LastActivityDate="2013-08-17T20:25:57.920" Title="How do plasmids protect themselves against restriction enzymes?" Tags="&lt;bacteriology&gt;&lt;plasmids&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9815" PostTypeId="1" AcceptedAnswerId="9816" CreationDate="2013-08-17T06:16:53.877" Score="5" ViewCount="2838" Body="&lt;p&gt;Bacteriophages have sequences which often do not have specific sites for restriction enzymes of bacteria to cut at and so can attack the bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wouldn't it be better if bacteria had something &quot;universal&quot; like an enzyme that simply cuts the nucleotide sequence &quot;randomly&quot;? Is there any particular advantage of cutting at only a few restriction sites?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2013-08-17T14:07:11.350" LastActivityDate="2013-11-12T00:53:38.187" Title="What is the advantage of restriction enzymes cutting only at specific sites?" Tags="&lt;bacteriology&gt;&lt;restriction-enzymes&gt;&lt;virus&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9816" PostTypeId="2" ParentId="9815" CreationDate="2013-08-17T07:25:44.847" Score="5" Body="&lt;p&gt;Such universal restriction enzymes would be very dangerous to leave lying around even if contained within a vacuole. Remember that bacteria are prokaryotes and have no nuclear membrane to protect their DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The analogy would be having a burglar alarm capable of burning down the house in order to protect it against thieves.&lt;/p&gt;&#xA;" OwnerUserId="4228" LastActivityDate="2013-08-17T07:25:44.847" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="9817" PostTypeId="2" ParentId="9814" CreationDate="2013-08-17T08:17:08.620" Score="2" Body="&lt;p&gt;The strains that we use in the lab have defective restriction machinery.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of DH5α it is mostly because of the &lt;code&gt;endA1&lt;/code&gt; and &lt;code&gt;hsdR17&lt;/code&gt; mutation. The former mutation eliminates an endonuclease that can degrade plasmids and the latter one eliminates the restriction system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check &lt;a href=&quot;http://ecoliwiki.net/colipedia/index.php/DH5_alpha&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="948" LastEditDate="2013-08-17T20:25:04.630" LastActivityDate="2013-08-17T20:25:04.630" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9818" PostTypeId="2" ParentId="9815" CreationDate="2013-08-17T08:52:51.220" Score="4" Body="&lt;p&gt;Notice that viral DNA is not the only foreign DNA that a bacterial can meet during its bacterial adventures. Plasmids, conjugated DNA and DNA inserted by transformation exist, and it may confer ecological advantages. Because of that, even if the enzymes would recognize only non genomic DNA and destroy it effectively, it's still more useful to have some criteria and allow to stay some alien DNA, while destroying some other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Restriction sites are pretty small, so the chances of getting one target in a viral genome is quite big. Bacterial DNA is protected by methylation, which is recognized by this enzymes and prevents them to break the DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Restriction enzymes are not the only means bacteria have in order to defend from foreign DNA. Bacteria usually carry exonucleases that recognize single stranded DNA and linear DNA, which is common in viral genomes, but not in non-infected bacterial cells. This enzyme lacks the specificity that restriction systems possess, and can work combined (for instance, a restriction cleavage may form linear DNA, which will be detected by exonucleases as potentially harmful DNA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to this, bacteria and archaeons have a special antiviral defense, named CRISPR-CAS system, that acts like an immune system. CRISPR-CAS inserts in a special region of the bacterial genome viral DNA fragments from previous infection. When a new virus infects the cell, those viral fragments are expressed as a special kind of RNA (CRISPR-RNA) which, if the virus has already infected this cell, will attach to viral DNA and will serve as a marker. Then, the RNA-marked DNA is recognized by special nucleases. This defense system allows to obtain acquired resistance that (unlike vertebrate immune system) is also inheritable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Concluding, not all foreign DNA is harmful, since plasmids and other could provide some advantage to the cell. Restriction-modification systems aren't the only defense system that the bacteria has against foreign DNA, but all of them must be able to differentiate between desirable and harmful DNA. The combination of many different defense systems allow to patch the limitations of them individually, and so different species will invest differently in one or other, depending of the ecological pressures they have to face.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="4168" LastEditDate="2013-08-17T22:04:43.857" LastActivityDate="2013-08-17T22:04:43.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9819" PostTypeId="1" CreationDate="2013-08-17T09:38:39.817" Score="4" ViewCount="91" Body="&lt;p&gt;Are there any statistics available on how much energy organisms use for each biological functions (i.e. something similar to the line of &quot;Bacteria spend X% of energy on information processing, Y% for tissue maintenance and Z% for locomotion. Mammals spend...&quot;). I'm particularly interested on how much energy is spent on information processing.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I vaguely remember seeing such stats somewhere, but for the love of god I can't remember where...&lt;/p&gt;&#xA;" OwnerUserId="4256" LastActivityDate="2015-01-23T06:55:35.813" Title="Statistics on energy consumption breakdown per biological functions across organisms?" Tags="&lt;evolution&gt;&lt;biochemistry&gt;&lt;bioinformatics&gt;&lt;systems-biology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9820" PostTypeId="2" ParentId="9815" CreationDate="2013-08-17T12:45:34.707" Score="2" Body="&lt;p&gt;Restriction enzymes are only &lt;em&gt;half&lt;/em&gt; of the system. The other half is the methylation system. The majority of restriction enzymes &lt;em&gt;won't&lt;/em&gt; cut at their target site if it is methylated in the correct way. The system works to identify foreign DNA because the foreign DNA is not methylated in the correct way so it will be cut but the bacteria's own DNA is methylated so it will not be cut. Think of it as a lock and key mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A generic DNAase wouldn't be able to function in this fashion.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-08-17T12:45:34.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9822" PostTypeId="1" AcceptedAnswerId="9826" CreationDate="2013-08-17T16:58:50.150" Score="1" ViewCount="93" Body="&lt;p&gt;Suppose you hybridize two plants - One has a red flower and a long stalk, the other has a pink flower and a short stalk. This resulted in these 4 type of plants, with ratio 1:1:1:1 &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Long stalk red flower&lt;/li&gt;&#xA;&lt;li&gt;Long stalk pink flower&lt;/li&gt;&#xA;&lt;li&gt;Medium stalk red flower&lt;/li&gt;&#xA;&lt;li&gt;Medium stalk pink flower&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;What possible genotype could the parents have that would result this way?&lt;/p&gt;&#xA;" OwnerUserId="4259" LastEditorUserId="3615" LastEditDate="2013-08-20T10:11:51.667" LastActivityDate="2013-08-20T10:11:51.667" Title="Genetics - Is this hybridization possible?" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9823" PostTypeId="1" CreationDate="2013-08-17T17:00:39.763" Score="1" ViewCount="7657" Body="&lt;p&gt;I was wondering whether it makes a difference when during the menstrual cycle a female is donating blood in terms of:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Blood quality (iron or hormones levels)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Her health/safety&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I am aware that females can donate blood during menstruation as the blood they lose does not directly come from circulatory system and the amount is not that big after all. As for the hormones - their levels do change considerably during the cycle and can affect a whole range of things. Can they also affect the blood quality or are such fluctuations rather negligible?&lt;/p&gt;&#xA;" OwnerUserId="4258" LastActivityDate="2016-08-25T23:00:25.190" Title="Are there more/less favourable phases of menstrual cycle to donate blood?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9824" PostTypeId="1" CreationDate="2013-08-17T17:44:11.827" Score="4" ViewCount="8870" Body="&lt;p&gt;I am confused about the term DNA-binding domain. Does it mean that there are some parts of the DNA that tend to coil up? Does it happen because some proteins tend to stick around that area? Also it is my understanding that with some proteins DNA (say for bacteria like &lt;em&gt;E. coli&lt;/em&gt;) tends to coil up. Do we know what is the approximately the size of these coils? What is a ‘motif’ in this context.&lt;/p&gt;&#xA;" OwnerUserId="4260" LastEditorUserId="22057" LastEditDate="2017-01-29T19:14:42.437" LastActivityDate="2017-01-29T19:14:42.437" Title="What is a DNA-binding domain?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;dna&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9825" PostTypeId="2" ParentId="9823" CreationDate="2013-08-17T18:09:40.763" Score="3" Body="&lt;p&gt;1)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hormones involved with Menstruation (FSH, LH, Estrogen, Progesterone, etc.) will vary depending in concentration depending on the time-frame:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cTtvG.png&quot; alt=&quot;Wikipedia chart - Menstruation&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are correct in saying that not much blood is actually lost in the menstrual fluid: &lt;a href=&quot;http://en.wikipedia.org/wiki/Menstruation#Overview&quot; rel=&quot;nofollow noreferrer&quot;&gt;Less than 80mL (80cc)&lt;/a&gt;, although the blood's origin is ultimately the circulatory system. Does it affect the quality of the blood? No. Usually not enough iron is lost during menstruation to make a difference between being able to donate blood and not donate. However, women who bleed heavier than the average &lt;em&gt;can&lt;/em&gt; experience &lt;em&gt;anemia&lt;/em&gt; (iron deficiency) - although &lt;em&gt;anemia&lt;/em&gt; attributed to menstruation is often &lt;a href=&quot;http://www.nature.com/ajg/journal/v94/n1/full/ajg199914a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;misdiagnosed gastrointestinal issues (up to 86% error rate)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One thing to consider is that &lt;a href=&quot;http://www.blood.co.uk/giving-blood/faqs/&quot; rel=&quot;nofollow noreferrer&quot;&gt;common pain medications can affect blood content&lt;/a&gt;, and thus a woman taking aspirin cannot donate &lt;strong&gt;platelets&lt;/strong&gt; for 5 days after she stops, and a woman taking NSAIDs (like Ibuprofen) cannot donate for 2 days after she stops.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2)  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...the combination of blood loss from periods and donation will make iron deficiency anaemia more likely, particularly if the periods are heavy or prolonged. This effect can be minimised by taking supplemental iron. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In general, as long as the woman feels well or the pain is controlled, she is perfectly capable of donating as long as her iron levels reach the minimums. The blood makeup is not significantly different, although hormone and iron levels will minimally fluctuate. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;As always, this response is based upon information during some light research. I am not a doctor, and the information presented in this response may be modified later to increase accuracy or remove errors upon the discovery of new information.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-08-17T18:09:40.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9826" PostTypeId="2" ParentId="9822" CreationDate="2013-08-17T18:36:17.240" Score="4" Body="&lt;p&gt;&lt;strong&gt;Flower Color&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;em&gt;Heterozygous&lt;/em&gt; (Rp) x &lt;em&gt;Homozygous recessive&lt;/em&gt; (pp) cross can produce the distribution:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;         p      p&#xA;&#xA;   R    Rp     Rp  = Red, Red&#xA;&#xA;   p    pp     pp  = pink, pink&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Stalk Length&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To &lt;em&gt;me&lt;/em&gt;, there appears to be another allele involved or a lack of allele, and definitely Co-Dominance. The only way I could think of a way to get the ratio of stalk lengths in the question after a few minutes thought is if one of the plants are missing a gene before the cross (akin to &lt;a href=&quot;http://en.wikipedia.org/wiki/Turner_syndrome&quot; rel=&quot;nofollow&quot;&gt;Turner Syndrome&lt;/a&gt;) - the example that follows puts the missing gene on the Short-stalked parents:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;SS = Short&lt;br&gt;&#xA;TT = Tall&lt;br&gt;&#xA;ST = Medium&lt;br&gt;&#xA;SX = Short&lt;br&gt;&#xA;TX = Tall&lt;br&gt;&#xA;X = Missing Gene / Nothing&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;         S      X&#xA;&#xA;   T    ST      TX = Medium, Tall&#xA;&#xA;   T    ST      TX = Medium, Tall&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So ultimately the cross would look like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;        Sp     Xp&#xA;&#xA;   TR   STRp   TXRp = (#3), (#1)&#xA;&#xA;   Tp   STpp   TXpp = (#4), (#2)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2013-08-17T18:48:30.180" LastActivityDate="2013-08-17T18:48:30.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9827" PostTypeId="1" AcceptedAnswerId="9846" CreationDate="2013-08-17T19:24:36.703" Score="1" ViewCount="466" Body="&lt;p&gt;A 62­ year-­old male was admitted to the hospital complaining of shortness of breath. His chest X­-ray showed a rightsided cavitary lesions. His medical history indicated he had smoked one pack of cigarettes per day for past 40 years and has had cavitary tuberculosis in about 20 years ago. Recently he is receiving cytostatic therapy for his acute myeloblastic leukaemia. A biopsy specimen of the lung was obtained. Biopsy from lesion shows tubular eukaryotic septated hyphae with diameter of 5­10 μm that are infiltrating the lung tissue. Culture on Saboraud’ media shows conidia with spores in radiating columns. &lt;strong&gt;Which is the most like cause of the findings?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The disease is systemic - affecting lungs. &#xA;Organism has septated hyphae with conidia. &#xA;&lt;strong&gt;Is there any other possibilities for the disease?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="107" LastEditDate="2013-08-17T20:33:30.367" LastActivityDate="2013-08-27T05:23:28.013" Title="Is this case Histoplasma capsulatum?" Tags="&lt;microbiology&gt;&lt;homework&gt;&lt;mycology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9828" PostTypeId="2" ParentId="9824" CreationDate="2013-08-17T20:16:11.137" Score="6" Body="&lt;p&gt;Welcome to Biology.SE!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Protein_domain&quot; rel=&quot;nofollow noreferrer&quot;&gt;domain&lt;/a&gt;&quot; in biochemistry and molecular biology is usually used to refer to a part of a protein that has a conserved structure and function, is similar between related proteins, and can generally exist or function on its own if it was separated from the rest of the protein. A &lt;a href=&quot;http://en.wikipedia.org/wiki/Dna_binding_domain&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA-binding domain&lt;/a&gt; is a protein structure that has a high affinity for DNA, and so binds to it when the two molecules are in the same vicinity. An example is a type of protein called a &lt;a href=&quot;http://en.wikipedia.org/wiki/Transcription_factor&quot; rel=&quot;nofollow noreferrer&quot;&gt;transcription factor&lt;/a&gt;, which binds to DNA in the nucleus of the cell (in &lt;a href=&quot;http://en.wikipedia.org/wiki/Eukaryotes&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eukaryotes&lt;/a&gt;, bacteria and Archaea don't have nuclei - the DNA just floats free) and causes changes in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Transcription_(genetics)&quot; rel=&quot;nofollow noreferrer&quot;&gt;transcription&lt;/a&gt; of genes. The following image from &lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Transcription_Factors.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;WikiMedia&lt;/a&gt; shows how transcription factors work in general.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JUfh3.png&quot; alt=&quot;transcription factors&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;DNA coiling&quot; is a very generic term that describes many different things. The basic structure of DNA itself is a coil, with two sugar chains (the &lt;em&gt;deoxyribose&lt;/em&gt; in DeoxyriboNucleic Acid or DNA) coiling around each other, and attached by nucleic acid bases. In the eukaryotic cell, individual strands of DNA are associated with structural proteins to create &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromatin&quot; rel=&quot;nofollow noreferrer&quot;&gt;chromatin&lt;/a&gt;, which is what makes up chromosomes in the nucleus of each cell. In the first stage, naked DNA is wrapped or coiled around structural proteins called &lt;a href=&quot;http://en.wikipedia.org/wiki/Histone&quot; rel=&quot;nofollow noreferrer&quot;&gt;histones&lt;/a&gt; into a structure called a nucleosome. These then stack into a &quot;solenoid&quot; or fiber structure, which makes up so-called &quot;relaxed&quot; chromatin - regions of the genome where active transcription is taking place. If a part of a chromosome has been marked as inactive, or during certain steps in the cell cycle when one cell splits into two (&lt;a href=&quot;http://en.wikipedia.org/wiki/Mitosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;mitosis&lt;/a&gt;), the fibers further coil into condensed chromatin, forming the typical structure many people associate with chromosomes. This image, from &lt;a href=&quot;http://en.wikipedia.org/wiki/File:DNA_to_Chromatin_Formation.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;, visualizes each step in the process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IiYor.jpg&quot; alt=&quot;chromatin structure&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The word &quot;motif&quot; can sometimes mean the same thing as domain - for example, someone might refer to a &quot;DNA-binding motif&quot; in a protein. However, a motif is typically smaller than a domain, can occur in DNA, RNA, and proteins, and has to do with the specific sequence. A &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Structural_motif&quot; rel=&quot;nofollow noreferrer&quot;&gt;structural motif&lt;/a&gt;&quot; in a protein is something like a &lt;a href=&quot;http://en.wikipedia.org/wiki/Basic-helix-loop-helix&quot; rel=&quot;nofollow noreferrer&quot;&gt;helix-loop-helix&lt;/a&gt; or a &lt;a href=&quot;http://en.wikipedia.org/wiki/Beta_hairpin&quot; rel=&quot;nofollow noreferrer&quot;&gt;beta-hairpin turn&lt;/a&gt; that can appear in multiple different kinds of protein domains, and doesn't necessarily have the same exact function in those different domains, but typically has a fairly conserved sequence that is very similar. As an example, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Zinc_finger&quot; rel=&quot;nofollow noreferrer&quot;&gt;zinc finger&lt;/a&gt; motif is found in protein domains that bind DNA, RNA, and other proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of this terminology can be very confusing at first, but if you stick with it it'll get easier over time. Biochemistry and molecular biology are fascinating fields, so keep up your studies!&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-08-17T20:16:11.137" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="9829" PostTypeId="2" ParentId="1470" CreationDate="2013-08-17T21:58:37.847" Score="4" Body="&lt;p&gt;Insects do not posses closed circulatory system, but a space where organs float in a fluid called hemolymph. They don't have blood vessels (but some arthropodes have pumps that act a like heart). The hemolymph allows nutrients and excretion products to diffuse, but usually doesn't serve as a means to transmit oxygen to the tissues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In insects, the oxygen is pumped through a series of little tubes named tracheae. Trachae connect the tissue directly to the air, allowing gas diffusion efficiently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antennae and wings have very little metabolic needs, mainly because (in the first case) they're formed by some neurons. Movement is achieved by muscles located in the base of the antenna (where it doesn't have circulation issues). The nerve tissue has the neuron bodies located in the basis too, so the nutrients and oxygen can diffuse through the axon.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="4168" LastEditDate="2013-08-20T10:00:50.243" LastActivityDate="2013-08-20T10:00:50.243" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9830" PostTypeId="1" AcceptedAnswerId="10137" CreationDate="2013-08-17T23:31:24.470" Score="9" ViewCount="1542" Body="&lt;p&gt;I live in Michigan.  I just saw a bee that I think I've seen before, but only this time was I so struck by its uniqueness and - for lack of a better word - &lt;em&gt;scariness&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll describe it.  It was maybe an inch and a half long.  Maybe bigger, maybe smaller (I'll admit that I was hurrying to get away from it).  It looked like a queen bee, but longer and slightly thinner.  However it had wings that were very profoundly orangish-red.  Like burnt orange maybe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't been able to find any matching pictures online.  It is theoretically possible that it was covered in pollen, and I am incorrect about what I think I saw, but assuming it wasn't (as I do believe this isn't the first time I've seen this guy or one of his friends), does anyone have any clues as to what this could be?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt;  PHOTOS&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After considerable patience. I was able to capture some photos of this guy.  One of these photos is post-processed a little to emphasize the color.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A couple things about these photos.  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;They were extremely difficult to take because the bee never stops moving.  I don't know if this behavior is useful for identification, but he is always in the same place (in front of one house), and he flys back and forth between a small crack in the sidewalk (a nest?), and between 5 and 10 feet away.  He moves like a dragonfly (that's the best way I can think to describe it), and he doesn't stop - he'll seem like he is going to land, and then flies off.  This morning was an exception.&lt;/li&gt;&#xA;&lt;li&gt;These photos do not fully capture the depth and vividness of the redness of his wings, nor do they adequately convey just how large he is.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/FwGB8.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uBWDd.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4261" LastEditorUserId="4261" LastEditDate="2013-08-30T13:24:48.387" LastActivityDate="2013-08-30T13:58:40.463" Title="Bee (?) identification" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9831" PostTypeId="2" ParentId="9586" CreationDate="2013-08-18T01:19:58.310" Score="1" Body="&lt;p&gt;You may need to study each disease individually or do a literature review.  The Online Mendelian Inheritance in Man website may be a good starting point &lt;a href=&quot;http://www.omim.org/&quot; rel=&quot;nofollow&quot;&gt;http://www.omim.org/&lt;/a&gt;&#xA;The Centers for Disease Control and Prevention lists several diseases with a variety of different statistics here:  &lt;a href=&quot;http://www.cdc.gov/DiseasesConditions/&quot; rel=&quot;nofollow&quot;&gt;http://www.cdc.gov/DiseasesConditions/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4175" LastActivityDate="2013-08-18T01:19:58.310" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9832" PostTypeId="1" CreationDate="2013-08-18T03:14:00.140" Score="4" ViewCount="864" Body="&lt;p&gt;I know cock's lower eye lids moves to meet the upper one when it closes its eye.  What other animals does this?  BTW, &quot;cock-eyed&quot; can mean upside down, I think.&lt;/p&gt;&#xA;" OwnerUserId="352" LastActivityDate="2014-08-06T14:36:33.497" Title="What animal's lower eye lid moves to upper one when closing eyes?" Tags="&lt;zoology&gt;&lt;eyes&gt;&lt;movement&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9833" PostTypeId="1" AcceptedAnswerId="9845" CreationDate="2013-08-18T03:47:47.647" Score="5" ViewCount="4762" Body="&lt;p&gt;I saw a documentary where they inserted the gene of a mouse that basically is the starting &quot;build an eye&quot; command into a fruit fly, and a fruit fly eye grew. My question is, if eyes of different types of animal had different evolutionary beginnings (I don't know much about arthropod eye evolution, but for a different example, as I understand it, cephalopod eyes evolved from skin cells while vertebrate eyes evolved from brain cells), then &lt;strong&gt;how is it that the same gene controls the growth of two such evolutionary different eyes&lt;/strong&gt;?&lt;/p&gt;&#xA;" OwnerUserId="3920" LastActivityDate="2017-05-25T13:21:48.623" Title="How can fruit flies and mice share the same gene that says to build an eye if they evolved separately?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;eyes&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9834" PostTypeId="1" CreationDate="2013-08-18T06:45:36.497" Score="0" ViewCount="4931" Body="&lt;p&gt;The question is relatively easy (the answer however..). We all know this feeling &quot;being watched&quot; and more often than not this is a real thing. If someone is staring at us from the side or from the back we sort-of &quot;feel&quot; it and we evenf eel the direction where it's coming from.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't seem to find a plausible answer for this though:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;We actually see the people staring from the corner of our eyes - false, I tested this thoroughly and it also happens when your eyes are closed or someone's behind you.&lt;/li&gt;&#xA;&lt;li&gt;Eyes don't send out energy (or &quot;beams&quot;) as far as I know. They &quot;receive&quot; light but don't send any out, except for reflection.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, what causes this strange phenomenon?&lt;/p&gt;&#xA;" OwnerUserId="3198" LastActivityDate="2013-08-19T04:56:49.293" Title="How come that we &quot;feel&quot; it when someone's watching us" Tags="&lt;human-biology&gt;&lt;brain&gt;&lt;sensation&gt;" AnswerCount="3" CommentCount="7" ClosedDate="2013-08-19T11:00:38.993" ContentLicense="CC BY-SA 3.0" />
  <row Id="9835" PostTypeId="1" AcceptedAnswerId="25784" CreationDate="2013-08-18T08:58:30.930" Score="3" ViewCount="654" Body="&lt;p&gt;We have a hypothesis that a drug may block the voltage-gated calcium channels (VGCC) in annelid worms. We are wondering whether there are any correlations between VGCCs and neuron conduction velocities.  If there are fluctuations in calcium ion contents, would there be any changes in conduction velocities? Or if the channel is blocked, would it block the entire action potential along the worm's giant axon?&lt;/p&gt;&#xA;" OwnerUserId="3207" LastEditorUserId="9943" LastEditDate="2014-12-10T23:02:56.350" LastActivityDate="2014-12-11T06:28:34.760" Title="Do voltage-gated calcium channels affect neuronal conduction speeds?" Tags="&lt;neuroscience&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9836" PostTypeId="2" ParentId="9834" CreationDate="2013-08-18T10:21:45.373" Score="2" Body="&lt;p&gt;I would guess hearing plays a part, as a powerful human sense  that works in 360 degrees.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just as a hypothesis, I'd imagine that small sounds help you sense people behind you, and that this, plus chance, plus the very human capacity to see meaning in random events, gives the impression that there's a way to sense that someone not just behind you but actively looking at you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In our every-day experience (that is, not in an artificial experimental setting), there are a lot of ways to bias our observations / data collection. For instance,  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;a half-conscious glance behind you is quickly forgotten (data discarded) if you realize it was just somebody strolling past, but remembered (data retained) if you see someone staring fixedly at you. This will spuriously increase your positive results (that is, the impression that &quot;every time I look behind me, my sense that someone is looking is confirmed&quot;)&lt;/li&gt;&#xA;&lt;li&gt;on the other hand, if someone is staring at you from behind, but you don't notice, you also do not retain that negative data, because, by definition, &lt;em&gt;you didn't notice&lt;/em&gt;. So there is a strong effect that is spuriously decreasing your negative results.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, as Brandon Invergo mentioned, we'd like to see a testing protocol along the lines of a blindfold and earphones playing white noise on the &quot;senser&quot;, and the &quot;watcher&quot; behind the senser staring or looking away at random intervals, and a large number of trials. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not to diminish the fact that some people have much better situational/interpersonal awareness than others (say, a ninja vs. me), but I really imagine that this is more an effect of cognition (putting together small cues from hearing/peripheral vision/smell etc.) than of any difference in sensation.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-08-18T10:21:45.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9837" PostTypeId="2" ParentId="7900" CreationDate="2013-08-18T11:33:09.417" Score="2" Body="&lt;p&gt;I think the jury is out on this one, there are examples of evidence both for and against reachability of local equilibrium and even these examples can be interpreted in many ways. I present three pieces of evidence and some interpretations. In general, my feeling after reading about this is that the assumption of equilibrium is ingrained in mathematical models for convenience and &lt;a href=&quot;http://egtheory.wordpress.com/2013/08/16/fitness-landscapes/&quot; rel=&quot;nofollow noreferrer&quot;&gt;historic reasons&lt;/a&gt; not because there is solid evidence for it. (I expand more on this in &lt;a href=&quot;http://egtheory.wordpress.com/2013/08/18/empirical-epistasis/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this blog post&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;h3&gt;Evidence against: vestigial features and macroevolutionary change&lt;/h3&gt;&#xA;&lt;p&gt;From a genome-wide perspective, it seems that equilibrium is at odds with the intuition of naturalists. Consider for example vestigial features of your own body like your appendix, goose bumps, tonsils, wisdom teeth, third eyelid, or the second joint in the middle of your foot made immobile by a tightened ligament (see video below). Wouldn't it be more efficient (and thus produce marginally higher fitness) if you didn't spend the energy to construct these features? Of course, this naturalist argument is not convincing since we don’t know if there are any small mutations that could remove these vestigial features from our development, I could just be describing a different local optimum that lays on the other side of a fitness valley from my current vertex.&lt;/p&gt;&#xA;&lt;p&gt;The other tempting naturalist example of macroevolutionary changes like speciation is also not convincing for static fitness landscapes. The usual retort is that on these timescales the environment is not constant and depends on the organisms through mechanisms like niche-construction or frequency-dependence. This defense of local equilibria is actually a central part of the punctuated equilibrium theory of evolution; the environment changes (either through an external effect like meteor or internal effect like migration or niche-construction) and the wild-type becomes not locally optimal, but adaptation quickly carries the species to a new nearby local optimum where it remains for a long period of time until the next environmental change. Naturalistic observations are insufficient to settle this question, so we need to turn to experiments.&lt;/p&gt;&#xA;&lt;h3&gt;Evidence for: affinity maturation&lt;/h3&gt;&#xA;&lt;p&gt;The length of evolutionary process leading to &lt;a href=&quot;http://egtheory.wordpress.com/2013/06/23/micro-macro-evolution/#affinity&quot; rel=&quot;nofollow noreferrer&quot;&gt;affinity maturation&lt;/a&gt; is very short, typically a local equilibrium is found after only 6-8 nucleotide changes in CDR (Crews et al., 1981; Tonegawa, 1983; Clark et al., 1985), so you need only a few point mutations to quickly develop a drastically better tuned antibody -- an adaptive process that happens on the order of days. There are two reservations to keep in mind:&lt;/p&gt;&#xA;&lt;p&gt;First, the adapted B-cells were not experimentally isolated and all of their point-mutations were not checked to guarantee that a fitness peak was reached. In both theoretical and experimental treatments of evolution, it is known that fitness increases tend to show a pattern of geometrically diminishing returns (Lenski &amp;amp; Travisano 1994; Orr, 1998; Cooper &amp;amp; Lenski, 2000) which means that after a few generations the fitness change will be so small that the fixation time in the large population of B-cells will be longer than the presence of the pathogen causing the immune response. We might not be seeing more steps because the next steps might have a fitness increase too small to fixate before the environment (and thus, fitness landscape) changes again.&lt;/p&gt;&#xA;&lt;p&gt;Second, as can be seen from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Activation-Induced_(Cytidine)_Deaminase&quot; rel=&quot;nofollow noreferrer&quot;&gt;AID protein&lt;/a&gt; (and other mechanisms) increasing the rate of mutation by a factor of &lt;span class=&quot;math-container&quot;&gt;$10^6$&lt;/span&gt; along the gene encoding antibody proteins, this is a fitness landscape that has been shaped by previous evolution of the human immune system to find fit mutants as quickly as possible. This biases the phenomenon towards landscapes where local maxima would be easier to find than usual, and thus makes it not a good candidate for considering evolution under more typical conditions.&lt;/p&gt;&#xA;&lt;h3&gt;Evidence against: long-term evolution experiment&lt;/h3&gt;&#xA;&lt;p&gt;A more typical setting might be the evolution of &lt;i&gt;E. coli&lt;/i&gt; in a static fitness landscape. Here, biologists have run &lt;a href=&quot;http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment&quot; rel=&quot;nofollow noreferrer&quot;&gt;long-term experiments&lt;/a&gt; tracking a population for &lt;a href=&quot;http://myxo.css.msu.edu/ecoli/celebrate50K.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;over 50,000 generations&lt;/a&gt; (Lenski &amp;amp; Travisano 1994; Cooper &amp;amp; Lenski, 2000; Blount et al. 2012) and continue to still find adaptations and marginal increases in fitness. This suggests that a local optimum is not quickly found, even though the environment is static. However, it is difficult to estimate the number of adaptive mutations that fixed in this population, and Lenski (2003) estimated that as few as 100 adaptive point-mutations fixated in the first 20,000 generations. It is also hard to argue that the population doesn't traverse small fitness valleys between measurements, which could be used to suggest that the colony is hopping from one easy-to-find local equilibrium to the next.&lt;/p&gt;&#xA;&lt;h3&gt;References&lt;/h3&gt;&#xA;&lt;p&gt;Blount, Z. D., J. E. Barrick, C. J. Davidson, and R. E. Lenski. (2012). Genomic analysis of a key innovation in an experimental Escherichia coli population. &lt;i&gt;Nature&lt;/i&gt; 489: 513-518.&lt;/p&gt;&#xA;&lt;p&gt;Clark, S.H., Huppi, K., Ruezinsky, D., Staudt, L., Gerhard, W., &amp;amp; Weigert, M. (1985). Inter- and intraclonal diversity in the antibody response to influenza hemagglutin. &lt;i&gt;J. Exp. Med.&lt;/i&gt; 161: 687.&lt;/p&gt;&#xA;&lt;p&gt;Cooper, V.S., &amp;amp; Lenski, R.E. (2000). The population genetics of ecological specialization in evolving &lt;i&gt;Escherichia coli&lt;/i&gt; populations. &lt;i&gt;Nature&lt;/i&gt; 407: 736-739.&lt;/p&gt;&#xA;&lt;p&gt;Crews, S., Griffin, J., Huang, H., Calame, K., &amp;amp; Hood, L. (1981). A single V gene segment encodes the immune response to phosphorylcholine: somatic mutation is correlated with the class of the antibody. &lt;i&gt;Cell&lt;/i&gt; 25: 59.&lt;/p&gt;&#xA;&lt;p&gt;Kauffman, S.A., &amp;amp; Weinberger E.D. (1989). The NK model of rugged fitness landscapes and its application to maturation of the immune response. &lt;i&gt;Journal of Theoretical Biology&lt;/i&gt;, 141(2): 211-245.&lt;/p&gt;&#xA;&lt;p&gt;Lenski, Richard E. (2003). &amp;quot;Phenotypic and Genomic Evolution during a 20,000-Generation Experiment with the Bacterium Escherichia coli&amp;quot;. In Janick, Jules. &lt;i&gt;Plant Breeding Reviews&lt;/i&gt; (New York: Wiley) 24(2): 225–65.&lt;/p&gt;&#xA;&lt;p&gt;Orr, H.A. (1998). The population genetics of adaptation: the distribution of factors fixed during adaptive evolution. &lt;i&gt;Evolution&lt;/i&gt; 52: 935-949.&lt;/p&gt;&#xA;&lt;p&gt;Tonegawa, S. (1983). Somatic generation of antibody diversity. &lt;i&gt;Nature&lt;/i&gt; 302: 575.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-08-19T10:02:47.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9838" PostTypeId="2" ParentId="9833" CreationDate="2013-08-18T11:45:40.503" Score="9" Body="&lt;p&gt;The documentary was probably talking about Halder's paper in Science (&lt;a href=&quot;http://courses.washington.edu/devbio/Halder1995.pdf&quot; rel=&quot;noreferrer&quot;&gt;Science, Halder et al., v.267&lt;/a&gt;). If you'll read the abstract (especially the bottom part) You'll notice that the gene is a control gene that is responsible for starting a chain of interactions at the end of which the real fly-specific 'eye-building' process begins. Basically this is like using the same kind of electrical switch to turn on the light in your room (mouse) or an air conditioner (fly).&lt;/p&gt;&#xA;" OwnerUserId="953" LastEditorUserId="953" LastEditDate="2013-08-18T14:25:07.010" LastActivityDate="2013-08-18T14:25:07.010" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9841" PostTypeId="2" ParentId="9726" CreationDate="2013-08-18T16:06:40.880" Score="0" Body="&lt;p&gt;A second investigation has suggested that the ligation product in question was indeed the vector, without ligated insert!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The vector also contained a BamHI site close to the XmaI site, so in a subsequent digest with EcoRI and BamHI, I was expecting to see the same band sizes that I ligated together in the first place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All colonies contained plasmids that produced the long (vector) band, and the same eight as before produced the shorter (insert) band as well. However, those four which were aberrant in the previous experiment were this time lacking the shorter band.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means the eight colonies with two bands contained the desired ligation product, while the other four contained a plasmid which was restricted at a single site (undigested it would have produced three bands like the control).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the BamHI site was in the vector and untouched throughout the whole process, I conclude that those four were missing the EcoRI site, which should have been regenerated during the ligation, and hence indeed the EcoRI site and the XmaI site must have been ligated without insert somehow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long story short&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that either &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;An exonuclease digested the sticky ends of the vector away, or&lt;/li&gt;&#xA;&lt;li&gt;The sticky ends simply degraded by chance&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;resulting in a blunt-ended re-ligation of the vector without insert and consequently loss of the EcoRI site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe these to be quite important things to consider in cloning - in subsequent experiments I have had several colonies growing on negative control plates (i.e. colonies transformed with a control ligation that contained no insert), all of which were probably due to loss of sticky ends and blunt ligations, resulting in functional plasmids that conferred ampicillin resistance despite containing an undesired plasmid.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-08-18T16:06:40.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9842" PostTypeId="2" ParentId="9834" CreationDate="2013-08-18T19:53:19.103" Score="10" Body="&lt;p&gt;To quote the University of Sidney site:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;People often think that other people are staring at them even when&#xA;  they aren't research led by the University of Sydney has found.&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;When in doubt, the human brain is more likely to tell its owner that&#xA;  they're under the gaze of another person, researchers from the&#xA;  University of Sydney and The Vision Centre reveal in a recent article&#xA;  in Current Biology.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also, from the scientific paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We presented participants with synthetic faces viewed under high and&#xA;  low levels of uncertainty and manipulated the faces by adding noise to&#xA;  the eyes. Then, we asked the participants to judge relative gaze&#xA;  directions. We found that all participants systematically perceived&#xA;  the noisy gaze as being directed more toward them. This suggests that&#xA;  the adult nervous system internally represents a prior for gaze and&#xA;  highlights the importance of experience in developing our&#xA;  interpretation of another’s gaze.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So you, and I, overestimate how often people is staring at us.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For details, see: &lt;a href=&quot;http://sydney.edu.au/news/84.html?newsstoryid=11335&quot;&gt;http://sydney.edu.au/news/84.html?newsstoryid=11335&lt;/a&gt; and &lt;a href=&quot;https://www.cell.com/current-biology/retrieve/pii/S0960982213003321&quot;&gt;https://www.cell.com/current-biology/retrieve/pii/S0960982213003321&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3570" LastActivityDate="2013-08-18T19:53:19.103" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9844" PostTypeId="2" ParentId="9834" CreationDate="2013-08-19T04:56:49.293" Score="1" Body="&lt;p&gt;I think the phenomenon should be studied separately in two conditions it happens (though in one of them it only happens &lt;strong&gt;subjectively&lt;/strong&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;When it happens outside of the peripheral vision, e.g. when your eyes closed, or  someone's behind you&lt;/li&gt;&#xA;&lt;li&gt;When it happens within the peripheral vision (approximately 180), i.e. corners &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For the first part, I agree with Sherin quoted the scientific paper &quot;People often think that other people are staring at them even when they aren't&quot;.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But for the second part, we often experience that when we stare at people from the corners, they turn their heads and say &quot;What ?&quot;. Perhaps recognition of this corner staring has something to do with &lt;strong&gt;extra foveal perception&lt;/strong&gt; and of course the emotional part of it would be &lt;strong&gt;the emotional salience of being stared at&lt;/strong&gt;. And because this extra foveal perception is less accurate than the perception in eyes' focus, it may result in false perception of &quot;being watched&quot; too. It's worth to mention that, because &quot;eyes&quot;, &quot;faces&quot;, and &quot;staring&quot; really have a high emotional valence for us,maybe we became very adept in recognition of them in our peripheral vision through many years of accumulative experience (I'm a fan of information processing approach to cognitive development). For more information about extra foveal perception, you may take a look at the seminal research carried out by Henderson (2003), &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1364661303002481&quot; rel=&quot;nofollow&quot;&gt;&quot;Human gaze control during real-world scene perception&quot;&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4206" LastActivityDate="2013-08-19T04:56:49.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9845" PostTypeId="2" ParentId="9833" CreationDate="2013-08-19T06:52:33.700" Score="11" Body="&lt;p&gt;Both fruit flies (&lt;em&gt;Drosophila&lt;/em&gt;) and mice (&lt;em&gt;Mus&lt;/em&gt;) are classified  under &lt;em&gt;Bilateria&lt;/em&gt;.&lt;br&gt;&#xA;The presence of such a &lt;a href=&quot;https://en.wikipedia.org/wiki/Conserved_sequence&quot;&gt;highly conserved sequence&lt;/a&gt; in both species suggests that they share a &lt;a href=&quot;https://en.wikipedia.org/wiki/Urbilaterian&quot;&gt;urbilaterian ancestor&lt;/a&gt; who also used a similar gene to turn on eye formation (not create the whole eye, just start the process).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even though the structure of insect and mammalian eyes diverged evolutionarily after the common ancestor, the switch that starts eye development worked so well there was little need to change it.  I suppose one could say that it remains backwards compatible.&lt;/p&gt;&#xA;" OwnerUserId="4228" LastEditorUserId="4228" LastEditDate="2013-08-19T09:44:38.510" LastActivityDate="2013-08-19T09:44:38.510" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9846" PostTypeId="2" ParentId="9827" CreationDate="2013-08-19T07:15:43.013" Score="2" Body="&lt;p&gt;Is there any other possibilities for the disease?&lt;br&gt;&#xA;Yes.  At 37°C, &lt;a href=&quot;http://www.mycology.adelaide.edu.au/Mycoses/Dimorphic_systemic/Histoplasmosis/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Histoplasma capsulatum&lt;/em&gt;&lt;/a&gt; usually doesn't form hyphae.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/um3Dq.jpg&quot; alt=&quot;from Wikimedia Commons: histology section showing H. capsulatum with methenamine silver stain&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Were the hyphae branching, like this?&lt;img src=&quot;https://i.stack.imgur.com/oLpWg.jpg&quot; alt=&quot;Histopathologic image of pulmonary invasive mycosis&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If &quot;conidia with spores in radiating columns&quot; means the pictures below, &lt;img src=&quot;https://i.stack.imgur.com/6mXvq.jpg&quot; alt=&quot;CDC micrograph of _A. fumigatus_ with conidia&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/0JCoo.jpg&quot; alt=&quot;photomicrograph from www.aspergillus.org.uk&quot;&gt;&lt;br&gt;&#xA;We have enough to say that this is &lt;strong&gt;not&lt;/strong&gt; a case of &lt;em&gt;Histoplasma capsulatum&lt;/em&gt; and there is &lt;strong&gt;definitely&lt;/strong&gt; another possibility for this disease.&lt;br&gt;&#xA;Conidia with radiating chains of spores is pathognomonic for &lt;a href=&quot;http://www.mycology.adelaide.edu.au/Mycoses/Opportunistic/Aspergillosis/&quot; rel=&quot;nofollow noreferrer&quot;&gt;aspergillosis&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4228" LastEditorUserId="4228" LastEditDate="2013-08-27T05:23:28.013" LastActivityDate="2013-08-27T05:23:28.013" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9847" PostTypeId="1" CreationDate="2013-08-19T11:07:32.377" Score="3" ViewCount="107" Body="&lt;p&gt;Some biological features scale with the animal mass (see &lt;a href=&quot;https://biology.stackexchange.com/questions/8357/what-are-some-examples-of-scaling-laws-in-biology&quot;&gt;previous Q&amp;amp;A&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming the same concentration of nociceptors on the skin surface, I'm wondering how painful a 1 cm wound will be perceived in mouse, human or elephant. Despite the same firing number of nociceptors, will the mouse feel more pain as a bigger percentage of the body has been injured? Is it known whether pain sensing follows &lt;a href=&quot;http://en.wikipedia.org/wiki/Allometry&quot; rel=&quot;nofollow noreferrer&quot;&gt;allometric rules&lt;/a&gt;?&lt;/p&gt;&#xA;" OwnerUserId="444" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-08-19T11:07:32.377" Title="Does pain scale with mammal mass?" Tags="&lt;neuroscience&gt;&lt;skin&gt;&lt;pain&gt;&lt;allometry&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9848" PostTypeId="1" AcceptedAnswerId="9852" CreationDate="2013-08-19T11:22:26.400" Score="1" ViewCount="92" Body="&lt;p&gt;The famous Hershey and Chase Experiment uses phages to inject genes into cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the beginning, Professor Yamanaka injected 24 types of genes into cells to figure out which genes turn a cell into ES cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Did he also use phages?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2013-08-19T14:45:04.043" Title="Method to inject genes into cells" Tags="&lt;cell-biology&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9850" PostTypeId="1" AcceptedAnswerId="19632" CreationDate="2013-08-19T13:41:51.413" Score="16" ViewCount="1944" Body="&lt;p&gt;Walking past the park today, I heard a cicada so loud I thought at first it must be some sort of large power tool. How is it that that very small animals like cicadas (crickets, etc.) can make such loud sounds? It seems intuitive that larger animals should be able to make louder sounds, but perhaps:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) I just fundamentally misunderstand the physics involved&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) A theoretical larger animal &lt;em&gt;should&lt;/em&gt; be able to make louder sounds, but cicadas are just extremely efficient, making up for their small size&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c) ?&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2015-06-26T17:28:33.773" Title="How do small animals make loud sounds?" Tags="&lt;entomology&gt;&lt;biophysics&gt;&lt;hearing&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9851" PostTypeId="2" ParentId="7922" CreationDate="2013-08-19T14:31:14.347" Score="7" Body="&lt;p&gt;&lt;a href=&quot;http://egtheory.wordpress.com/2013/08/18/empirical-epistasis/&quot; rel=&quot;noreferrer&quot;&gt;Very little&lt;/a&gt; is known about the structure of fitness landscapes.&lt;/p&gt;&#xA;&lt;p&gt;H.A. Orr (2005; also Whitlock et al., 1995; Kryazhimskiy et al., 2009) explains that &lt;strong&gt;most experimental results do not actually attempt to measure the fitness landscape&lt;/strong&gt;, but instead report just the average fitness versus time and average number of acquired adaptations versus time. This can't be used to discern epistatic interactions, or any combinatorial structure of the landscape. In general, the &lt;strong&gt;theory of adaptive walks has developed without reference to real data&lt;/strong&gt; and even the most refined theories can only correspond in vague qualitative ways (see Kryazhimskiy et al., 2009 for the best example I know).&lt;/p&gt;&#xA;&lt;p&gt;Szendro et al. (2013) surveyed the few recent experiments that conducted a methodical examination of all mutations in a subset of loci of model organisms, but &lt;strong&gt;most studies (6 out of 12) were able to empirically realize only small fitness landscapes of just 4 to 5 loci (so 16 to 32 vertexes)&lt;/strong&gt;, with the largest full fitness landscape having length 6 with all 64 vertexes examined (Hall et al., 2010), and the largest number of vertexes in a single study being 418 out of the possible 512 in a length 9 landscape (O’Maille et al., 2008). These are extremely small landscapes, and thus don't have much power in distinguishing proposed theoretical models.&lt;/p&gt;&#xA;&lt;p&gt;After extensive searching, I have not been able to find examples of theorists doing worst case analysis of fitness landscapes. The &lt;strong&gt;closest to worst-case analysis is Orr-Gillespie theory&lt;/strong&gt; (Gillespie, 1991; Orr, 2002; 2006; Kryazhimskiy et al., 2009) that assumes that the wild-type is still very fit after an environmental change, and so beneficial mutations are extremely rate. This allows the authors to introduce &lt;a href=&quot;http://en.wikipedia.org/wiki/Extreme_value_theory&quot; rel=&quot;noreferrer&quot;&gt;extreme value theory&lt;/a&gt; and consider just the asymptotic properties of distribution tails thus allowing a more general treatment with fewer parameters; in some cases leading to a full classification of adaptive trajectories (Kryazhimskiy et al., 2009). This approach is easier to relate to experiment, but unfortunately &lt;strong&gt;completely ignores the combinatorial structure (beyond first-order) of the fitness landscape&lt;/strong&gt; and always just samples the next potential mutant from the tail of a distribution without taking into account how it is progressing in the landscape. Although Orr (2006) introduced the basics of fitness landscape structure, the structure was much simpler than the NK model; he used Perelson &amp;amp; Macken's (1995) block model with each block as completely unstructured beyond first-order.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h3&gt;References&lt;/h3&gt;&#xA;&lt;p&gt;Gillespie, J.H. (1991). &lt;em&gt;The causes of molecular evolution&lt;/em&gt;. Oxford University Press.&lt;/p&gt;&#xA;&lt;p&gt;Hall, D. W., Agan, M., &amp;amp; Pope, S. C. (2010). Fitness epistasis among 6 biosynthetic loci in the budding yeast Saccharomyces cerevisiae. &lt;em&gt;Journal of Heredity&lt;/em&gt;, 101: S75-S84.&lt;/p&gt;&#xA;&lt;p&gt;Kryazhimskiy, S., Tkacik, G., &amp;amp; Plotkin, J.B. (2009). The dynamics of adaptation on correlated fitness landscapes. &lt;em&gt;Proc. Natl. Acad. Sci. USA&lt;/em&gt; 106(44): 18638-18643.&lt;/p&gt;&#xA;&lt;p&gt;O’Maille, P. E., Malone, A., Dellas, N., Hess, B. A., Smentek, L., Sheehan, I., Greenhagen, B.T., Chappell, J., Manning, G., &amp;amp; Noel, J.P. (2008). Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases. &lt;em&gt;Nature Chemical Biology&lt;/em&gt;, 4(10): 617-623.&lt;/p&gt;&#xA;&lt;p&gt;Orr, H.A. (2002). The population genetics of adaptation: the adaptation of DNA sequences. &lt;em&gt;Evilution&lt;/em&gt; 56: 1317-1330.&lt;/p&gt;&#xA;&lt;p&gt;Orr, H.A. (2005). The genetic theory of adaptation: a brief history. &lt;em&gt;Nature Reviews Genetics&lt;/em&gt; 6(2): 119-127.&lt;/p&gt;&#xA;&lt;p&gt;Orr, H.A. (2006). The population genetics of adaptation on correlated fitness landscapes: the block model. &lt;em&gt;Evolution&lt;/em&gt; 60(6): 1113-1124.&lt;/p&gt;&#xA;&lt;p&gt;Perelson, A.S., &amp;amp; Macken, C.A. (1995). Protein evolution of partially correlated landscapes. &lt;em&gt;Proc. Natl. Acad. Sci. USA&lt;/em&gt; 92:9657-9661.&lt;/p&gt;&#xA;&lt;p&gt;Szendro, I. G., Schenk, M. F., Franke, J., Krug, J., &amp;amp; de Visser, J. A. G. (2013). Quantitative analyses of empirical fitness landscapes. &lt;em&gt;Journal of Statistical Mechanics: Theory and Experiment&lt;/em&gt; 2013(01): P01005.&lt;/p&gt;&#xA;&lt;p&gt;Whitlock, M.C., Phillips, P.C., Moore, F.B.-G., &amp;amp; Tonsor, S.J. (1995). Multiple fitness peaks and epistasis. &lt;em&gt;Annu. Rev. Ecol. Syst.&lt;/em&gt; 26: 601-629.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-08-19T14:31:14.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9852" PostTypeId="2" ParentId="9848" CreationDate="2013-08-19T14:45:04.043" Score="2" Body="&lt;p&gt;Remember, phages infect bacteria. It &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867406009767&quot; rel=&quot;nofollow&quot;&gt;looks&lt;/a&gt; like he used something called &lt;a href=&quot;http://www.cellbiolabs.com/sites/default/files/RTV-050-pmxs-gfp-retroviral-vector.pdf&quot; rel=&quot;nofollow&quot;&gt;pMXs-based retroviral vectors&lt;/a&gt; instead, which is based on the Moloney murine leukemia virus (MMLV).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have never heard of that virus before, but I do know of others used in vivo to deliver genes, including Lentivirus, Adenovirus, and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18854481&quot; rel=&quot;nofollow&quot;&gt;Adeno-associated virus&lt;/a&gt;. All have their strengths and weaknesses. Adenovirus is large so you can fit a big gene inside it, but it tends to illicit a high immune response. AAV, on the other hand, is very small but has a much more mild immune response. It can fit a gene about 4kb long inside or half that if you use a fast expressing form called self-complementary AAV. What is nice about AAV is one of the subtypes (technically callled serotype) can cross the blood brain barrier, so it has already been used in clinical trials to try and treat neurological diseases, including &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20970382&quot; rel=&quot;nofollow&quot;&gt;Parkinson’s&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-08-19T14:45:04.043" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9853" PostTypeId="1" AcceptedAnswerId="9854" CreationDate="2013-08-19T15:33:00.400" Score="1" ViewCount="44" Body="&lt;p&gt;I have a hard time finding out a small detail about the ventricle system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the CSF flows into the 4th ventricle, there's a small foramen in the lateral aspect, as well as an open space bounded by the medulla and cerebellum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do both these lead the same place? Is the space under the arachnoid matter only accessed through the small foramen, whereas the space between the medulla and cerebellum leads into the spinal column?&lt;/p&gt;&#xA;" OwnerUserId="3032" LastActivityDate="2013-08-20T08:57:32.340" Title="Confusion regarding the ventricle system in the brain" Tags="&lt;brain&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9854" PostTypeId="2" ParentId="9853" CreationDate="2013-08-19T16:13:45.127" Score="2" Body="&lt;p&gt;I've found the answer. The entire brain and spinal cord is bounded by the arachnoid mater, thus both channels would lead into the subarachnoid space, which also circulates the fluid into the spinal cord region. The CSF exits through the arachnoid granulations, which are like valves, found on the dorsal midline, into the superior sagital sinus, where it returns to the blood stream.&lt;/p&gt;&#xA;" OwnerUserId="3032" LastEditorUserId="3032" LastEditDate="2013-08-20T08:57:32.340" LastActivityDate="2013-08-20T08:57:32.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9855" PostTypeId="2" ParentId="1343" CreationDate="2013-08-19T16:54:32.223" Score="4" Body="&lt;p&gt;The incisal and occlusal edges of teeth are more translucent since there is only enamel in this area and the dentin core is deeper inside. The dentin is more opaque and reflect the light back and it looks lighter whereas the enamel is translucent and allow more light to pass through and less light is reflected back so it looks darker. Many human teeth the incisal edge is translucent or darker for the same reason.&lt;/p&gt;&#xA;" OwnerUserId="4216" LastActivityDate="2013-08-19T16:54:32.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9860" PostTypeId="2" ParentId="9758" CreationDate="2013-08-19T19:00:00.300" Score="-2" Body="&lt;p&gt;People with type 1 Diabetes have a heritable defect in their genes. People with type 2 Diabetes eat too much. The prevalence of type 2 diabetes has increased by a factor of 2 since the 1970's. This means more patients for the endocrinologists and more insulin sales for the pharmaceutical companies.   &lt;/p&gt;&#xA;" OwnerUserId="4274" LastActivityDate="2013-08-19T19:00:00.300" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9861" PostTypeId="1" CreationDate="2013-08-19T19:45:11.643" Score="4" ViewCount="91" Body="&lt;p&gt;I'm interested in the sleep patterns of wild animals, that still use sun for controlling their biological clock. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Animals entrain their biological clock to the day/night cycle using light as the entrainment signal. The biological clock follows the day/night cycle: dim light initiates melatonin secretion, while bright morning light stops melatonin production. &lt;a href=&quot;http://en.wikipedia.org/wiki/Melatonin&quot; rel=&quot;nofollow noreferrer&quot;&gt;Melatonin&lt;/a&gt; is involved in sleep regulation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here, I have plotted the day duration over the course of the year for Northeast US, around Washington DC. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is &lt;strong&gt;given the day duration plot below, would the total sleep duration for wild animals vary over the course of the year?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, would animals sleep longer in the winter time and shorter in the summer time?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tYOWr.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2017-03-20T10:48:57.920" Title="Does sleep duration vary for animals based on time of the year?" Tags="&lt;zoology&gt;&lt;sleep&gt;&lt;circadian-rhythms&gt;&lt;melatonin&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9862" PostTypeId="2" ParentId="9810" CreationDate="2013-08-19T20:11:33.360" Score="2" Body="&lt;p&gt;+1 to Damien, just a few more thoughts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you notice it took several whacks of the head to get the bite reflex to trigger. I know that many animals have reflexes that will suppress other reflexes so that fluid motions can be achieved (righting reflexes are examples).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know if anyone has studied the species enough to know this definitely, but I bet that snakes behaviorally/reflexively doge their own tail so that they don't keep hitting themselves in the head.  After the head is severed, higher level restrictions are lost, fight paths are probably lose inhibition, and the reflex to bite anything hitting you in the mouth takes over.  That said it probably had to hit the mouth just right to get this to trigger.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking for some definitive information on bite reflexes in snakes, and will edit if I find anything relative.  I have experience from studying amphibian reflexes years ago, and I have feeling this general trend will hold true for snakes (but I'm looking for someone who has actually studied it). &lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2013-08-19T20:11:33.360" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9863" PostTypeId="1" CreationDate="2013-08-19T20:42:46.003" Score="3" ViewCount="7147" Body="&lt;p&gt;What is the genetic basis of the A/B/B+/O/etc. blood type system? Are there definitive loci that correspond to each or can multiple different genotypes produce the same antigen profile? Also, is the blood type of a child necessarily one of the blood types of the parents, or can an A/B female cross to A/B male produce a child with blood type O?&lt;/p&gt;&#xA;" OwnerUserId="1693" LastActivityDate="2013-09-02T06:39:07.717" Title="What is the genetic basis of blood type (ABO) system?" Tags="&lt;genetics&gt;&lt;physiology&gt;&lt;immunology&gt;&lt;hematology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9865" PostTypeId="1" AcceptedAnswerId="9866" CreationDate="2013-08-20T00:20:54.777" Score="2" ViewCount="344" Body="&lt;p&gt;If all of the characteristics of life are required for something to be defined as living, how can we account people or other life that can not reproduce?&lt;/p&gt;&#xA;" OwnerUserId="4276" LastEditorUserId="3553" LastEditDate="2016-06-08T15:57:21.053" LastActivityDate="2016-06-08T15:57:21.053" Title="Is reproduction intrinsically part of life?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;life&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2016-06-09T09:38:21.870" ContentLicense="CC BY-SA 3.0" />
  <row Id="9866" PostTypeId="2" ParentId="9865" CreationDate="2013-08-20T03:16:17.317" Score="3" Body="&lt;p&gt;Every species has the ability to reproduce.  Of course, individuals within a species can be born with a mutation that keeps them from reproducing, or lose the ability to reproduce at some point in life.  However, to say that once these individuals fail to meet that criteria they are no longer forms of life would be a fairly absurd semantics argument.  It might be useful to note in an evolutionary sense that those individuals can no longer pass on their genes, which is could select against whatever it was the resulted in that individual being sterile.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could probably reword the characteristics of life to stress species instead of individuals, but then theres a problem with microbes which have very poorly, or non-existent species.  But in general, this is not something a biologist is going to lose sleep over.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-20T03:16:17.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9867" PostTypeId="1" AcceptedAnswerId="17931" CreationDate="2013-08-20T06:29:29.600" Score="1" ViewCount="117" Body="&lt;p&gt;Pardon all of my questions below.  I'm basically looking to find online resources regarding my inquiry.  If you can answer any of them off the bat, that would be awesome!!  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that humans and mammals give off certain frequencies from our nervous systems.  For example, dogs are able to sense when their master is coming home, even when their distance is close to a mile away.  Also, cats are able to sense when a human is about to die.  They can feel the frequency the person is giving off, and react differently.  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Where can I learn more about this frequency that humans give off?  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Has anyone ever done research on this subject?  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is this electromagnetic frequency or something else?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are there devices that can measure this frequency that the human nervous system gives off?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are there devices that can generate this frequency that the human nervous system gives off?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1594" LastActivityDate="2014-06-06T05:00:44.067" Title="Can someone provide resources on human electromagnetic frequencies?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9868" PostTypeId="1" AcceptedAnswerId="9945" CreationDate="2013-08-20T08:02:14.923" Score="2" ViewCount="453" Body="&lt;p&gt;Is there any general rule to say this must be RNA virus infection and the other one DNA virus infection?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example of a case: 5 children develop a bright red rash on the face and turns violet after a few days and then disappears. Then maculopapular rash appears on the trunk, buttocks and extremities. It soon fades from the trunk but persists on the thights and forearms. Two children have also had a slight fever and a sore throat, but all were not terribly sick. What is the genetic material of the most likely causative agent?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Right answer is: Single-stranded DNA, since most probably causative agent is erythema infectiosum caused by parvovirus B19. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not want to remember all microbes by heart.&#xA;&lt;strong&gt;How can you deduce that this must be a DNA infection and probably single-stranded?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2013-08-22T20:37:24.083" LastActivityDate="2013-08-23T13:40:20.457" Title="How to deduce if RNA virus infection or DNA virus infection" Tags="&lt;dna&gt;&lt;microbiology&gt;&lt;rna&gt;&lt;virology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9870" PostTypeId="1" CreationDate="2013-08-20T09:04:03.840" Score="4" ViewCount="2220" Body="&lt;p&gt;&lt;strong&gt;At first I want to clarify that I do know that there are naturally poisonous plants and plants that can hold radioactive stuff or toxic material from the environment.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I mean by &quot;diseases&quot; (I guess there is a special term for that in English) is Bovine Spongiform Encephalopathy and similar serious issues caused by eating animals, by that you cannot develop when consuming plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I know there are no diseases causes by eating fruit and vegetables (of course, except parasites if you don't wash it properly and an infected cow or bunny pooped on it ;D)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it because the parasites and diseases infecting plants are so specialised for their &quot;body-type and genetics&quot; that they cannot operate inside an animal body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could somebody explain that to me in more depth why by eating plants you cannot get a disease (except allergic reaction/intolerance or toxicities as mentioned earlier)?&lt;/p&gt;&#xA;" OwnerUserId="3118" LastEditorUserId="3952" LastEditDate="2013-08-21T09:53:11.807" LastActivityDate="2015-06-30T20:11:25.210" Title="Why doesn't human consumption of plants cause infectious diseases the way consumption of animals can?" Tags="&lt;botany&gt;&lt;medicinal-chemistry&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="9871" PostTypeId="2" ParentId="9863" CreationDate="2013-08-20T09:26:28.437" Score="2" Body="&lt;p&gt;I can answer only half your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not necessary that the child has to have the blood group of parents.&#xA;The inheritance is like this :&#xA;1.There are 3 alleles Ia , Ib and Io.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2.Ia and Ib are codominant i.e. they will both be expressed if present together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3.Ia and Ib are dominant over Io. So, blood group O can only be expressed if the genotype is IoIo. IaIa or IaIo is blood group A and IbIb or IbIo is blood group B.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5.IaIb is blood group AB&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in the case of both the parents being AB blood group,the child can not have O group.S/he can have any other blood group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The inheritance of negative and positive blood group follows simple mendelian inheritance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please feel free to correct me!&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-08-20T09:26:28.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9872" PostTypeId="2" ParentId="9870" CreationDate="2013-08-20T09:59:12.533" Score="8" Body="&lt;p&gt;If you mean if there are viruses, pathogenic bacteria or fungi that may cause diseases both in plants and in animals, the response would be that this is very unlikely (But even so, some fungi and bacteria could do it if some circumstances are given). This is due to some key factors:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, the philogenetic distance between plants and animals is huge. Diseases transmitted by the consumption of animals are called zoonosis, and obviously it is more likely to catch a zoonosis by eating pork than eating shrimps or clams. While it's true that certain parasites have different hosts and use them to transmit themselves (for instance, many platyhelmintha uses mollusks or insects to spread themselves towards mammalian or avian hosts) parasites than have only one kind of host usually are adapted to live inside them, and they usually are unable to infect different organisms. Very few parasites can infect a human and a starfish, and even fewer can infect at the same time a human and a tomato plant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, and related to the first, plant physiology differs completely from animal physiology. Plants usually defend themselves by their natural barriers (cuticles, cell walls), hypersensitive response (programmed cell death in order to limit the spread of a pathogen), isolation and/or outgrowing of the pathogen and accumulation of chemicals. Animals main mechanism is immune system. There are very different strategies and very few organisms can effectively avoid all of them at the same time. In the case of viruses, they would even have to face the fact that animals and plants have huge genetic differences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Third even if they could, the pathogen will face competition against other pathogens that would be more specialized. Bacteria and fungi can be really hostile towards their microfoes, using a wide array of strategies. This hypothetical pathogen would be very unspecific, so they would have a hard time against more focused microbes. It should be noted, however, that unspecialized organisms usually have a great advantage if the environment have some perturbation, and they also are more resilient toward stress. Many plant pathogens are generalistic organisms that attacks when the plant is harmed or stressed. The same applies to many opportunistic infections in animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite all of this, there are some diseases that should be mentioned. Some fungi of the &lt;em&gt;Clavyceps&lt;/em&gt; genera are plan pathogens, but they produce toxins than can affect the nervous system of animals, causing an intoxication called ergotism (the most famous of this chemicals is the lisergic acid, also known as LSD). Other fungi can produce toxins while they grow in plant tissue. Moreover, there are many fungi that can grow both in plant tissue and as animal parasites (mainly arthropods and nematodes), but in this case the plant pathogenesis usually occurs only when high fungal concentration is achieved or the plant is already damaged. While it's not a real infection, plant pathogens can cause allergic reactions. Finally, phytopathogenic fungi and some bacteria can cause infections in wounds or mucoses in individuals with a compromised immune system, but in this case the source seems to be the spores in the air.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="16514" LastEditDate="2015-06-30T20:11:25.210" LastActivityDate="2015-06-30T20:11:25.210" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9873" PostTypeId="1" AcceptedAnswerId="9874" CreationDate="2013-08-20T13:09:04.630" Score="2" ViewCount="3937" Body="&lt;p&gt;What's the difference between 'Orbit' and 'Globe' in eye's anatomy. Do they refer to the same ? I encountered this in this text:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... ciliary ganglion, which is approximately 3 mm in size, and located&#xA;  2-3 mm posterior to the globe and lateral to the optic nerve,...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4206" LastActivityDate="2013-08-20T13:15:13.653" Title="Difference between 'Orbit' and 'Globe' in eye anatomy?" Tags="&lt;eyes&gt;&lt;nomenclature&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9874" PostTypeId="2" ParentId="9873" CreationDate="2013-08-20T13:15:13.653" Score="3" Body="&lt;p&gt;I've found a rough answer myself:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The globe of the eye, or bulbus oculi, is the eyeball &lt;strong&gt;apart from its&#xA;  appendages&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Globe_%28human_eye%29&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Globe_%28human_eye%29&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... the orbit is the &lt;strong&gt;cavity or socket of the skull&lt;/strong&gt; in which the eye and&#xA;  &lt;strong&gt;its appendages&lt;/strong&gt; are situated. &quot;Orbit&quot; can refer to the bony socket, or it can also be used to imply the contents.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Orbit_%28anatomy%29&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Orbit_%28anatomy%29&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4206" LastActivityDate="2013-08-20T13:15:13.653" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9875" PostTypeId="1" CreationDate="2013-08-20T15:32:08.373" Score="4" ViewCount="133" Body="&lt;p&gt;Why do I not have any cells left in my positive panning plate after transferring from the negative panning plate during immunopanning? I am trying to purify retinal ganglion cells from postnatal rats and use a Thy1.1 antibody harvested from a hybridoma cell line supernatant in the positive panning plate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following transfer of the cell suspension from the negative to the positive panning plate there are no cells in the pre-trypsinization supernatant, nothing stuck to the panning plate, and no cells in the post-trypsinization supernatant so I have no idea where they could have gone. Checking the negative panning plates however shows that there are many cells stuck to those plates, so could my RGCs have been lost at some point during the transfer and when?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks v much in advance for your help.&lt;/p&gt;&#xA;" OwnerUserId="4280" LastEditorUserId="3971" LastEditDate="2013-08-21T15:36:46.473" LastActivityDate="2013-12-19T17:27:54.487" Title="Missing cells from immunopanning" Tags="&lt;neuroscience&gt;&lt;cell-biology&gt;&lt;cell-sorting&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9876" PostTypeId="1" CreationDate="2013-08-20T16:21:15.537" Score="11" ViewCount="17331" Body="&lt;p&gt;When you have cavities in your teeth taking any sweetend drinks or food causes sensitivity or pain. What could be the reason?&lt;/p&gt;&#xA;" OwnerUserId="4216" LastActivityDate="2015-05-23T03:33:26.143" Title="Why does it hurt when you take sweets, if you have cavities in your teeth?" Tags="&lt;human-biology&gt;&lt;teeth&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9877" PostTypeId="2" ParentId="1573" CreationDate="2013-08-20T18:03:56.163" Score="5" Body="&lt;p&gt;The stuffiness is due to edema or swelling of the mucous membrane covering the nasal cavity. The swelling is caused by vasodialatation or dialatation of the capillaries and leaky vessels which accumulate fluid within the mucous membrane.&#xA;The runny nose is mainly due to hyperactivity of the mucous cells of the lining which causes vastly more secretion than normal, triggered by the inflammatory reaction to the infection.&lt;/p&gt;&#xA;" OwnerUserId="4216" LastActivityDate="2013-08-20T18:03:56.163" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9878" PostTypeId="2" ParentId="9015" CreationDate="2013-08-20T18:48:48.557" Score="7" Body="&lt;p&gt;This is a skull of a child of around 5 plus years; based on the eruption status and is an example of  classic development and eruption pattern of of the teeth at that age. everyone goes through it. It probably looks scary to persons unfamiliar with normal anatomy and because the outer cortical plate has been removed to show the developing tooth germs. This is out of a anatomy museum meant for medical or dental students.&#xA;At no point of time during the eruption is a cavity left behind. As the tooth erupts the base of the crypt (cavity) gets filled up.&lt;/p&gt;&#xA;" OwnerUserId="4216" LastActivityDate="2013-08-20T18:48:48.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9879" PostTypeId="2" ParentId="8923" CreationDate="2013-08-20T19:16:32.850" Score="5" Body="&lt;p&gt;The answer is a simple no. Cavities in the teeth caused by dental decay cannot heal. Enamel which is affected by dental decay cannot heal as they are fully formed at the time of eruption and then on only deteriorates. The deeper part of the tooth which has dentin cannot heal the cavity formation, however it can produce a protective barrier between the advancing cavity front and the pulp inside. The cementum the third mineralised tissue of the tooth cannot heal a decay cavity. Its main function is to attach the tooth to the bony socket through the periodontal fibres.&lt;/p&gt;&#xA;" OwnerUserId="4216" LastActivityDate="2013-08-20T19:16:32.850" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9880" PostTypeId="1" CreationDate="2013-08-20T19:17:27.337" Score="2" ViewCount="6915" Body="&lt;p&gt;Is it possible to get infected with the amoeba, &lt;em&gt;Naegleria fowleri&lt;/em&gt;, through your ears, or is the nose the only way it can enter to cause infection? How commonly is it found in your stool as well?&lt;/p&gt;&#xA;" OwnerUserId="4281" LastEditorUserId="107" LastEditDate="2013-08-31T17:46:27.473" LastActivityDate="2014-09-11T02:34:26.847" Title="Can Naegleria fowleri enter through your ear?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9881" PostTypeId="2" ParentId="8302" CreationDate="2013-08-20T19:39:09.177" Score="4" Body="&lt;p&gt;Human teeth and animal teeth are not fragile. It is meant to last a life time, barring physical injury. If anything makes it fragile it is ourselves. The main two causes of tooth loss is dental decay and gum disease. Both are cause by the soft tenacious bacteria filled biofilm called 'Plaque&quot;. If there is no plaque then there is no dental caries(cavities) and no periodontal disease(gum disease).&#xA;Wild animals don't have both and eskimos did not have these diseases till they were exposed to modern civilization. Raw fibrous food have a terrific cleaning effect and effectively removes plaque. And even if there is plaque, since there is no refined carbohydrates there is no decay.&#xA;If you want to prevent dental decay remove plaque completely, by brushing ,flossing and sealing all the pits and fissures where plaque can lodge. Follow this and one can eat all the sugary things without worrying about their teeth if not anything else.&lt;/p&gt;&#xA;" OwnerUserId="4216" LastActivityDate="2013-08-20T19:39:09.177" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9882" PostTypeId="2" ParentId="9876" CreationDate="2013-08-20T19:41:45.517" Score="4" Body="&lt;p&gt;This is a bit of a basic answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the website article &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/001055.htm&quot; rel=&quot;nofollow&quot;&gt;&quot;Dental cavities&quot;&lt;/a&gt; (Medline Plus), the bacteria normally in your mouth converts many foods, particularly starch and sugar into acid that forms a part of plaque.  These in turn cause dental caries or decay, according to &lt;a href=&quot;http://en.wikipedia.org/wiki/Dental_caries&quot; rel=&quot;nofollow&quot;&gt;this Wikipedia article&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dental caries, also known as tooth decay or a cavity, is an infection, bacterial in origin, that causes demineralization and destruction of the hard tissues (enamel, dentin and cementum), usually by production of acid by bacterial fermentation of the food debris accumulated on the tooth surface&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A possible reason you would feel pain from a cavity in contact with sweet foods and drinks, or anything really, is due to the cavity being large enough that nerves are exposed.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-08-20T19:41:45.517" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9884" PostTypeId="2" ParentId="9870" CreationDate="2013-08-20T20:26:00.867" Score="1" Body="&lt;p&gt;I think a main problem here is limiting logic.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By eliminating both toxic/poisonous plants, plants that have evolved to discourage you from eating them, and improperly &quot;washed&quot; plants, things which contain non-plant mater that can make you sick, you are not left with the possibility of diseases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;BSE is caused by prions, which are mater of serious debate and research in academics at the moment.  The leading cause of transmission is likely ingestion (1, 2), but it is quite possible that it arises as a mutation sporadically in certain mammals (3).&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Coming back to your question, let's suppose two scenarios:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;First let's suppose that a prion, or really any other pathogen, were to fall onto a piece a fruit from another mammal.  If you, or a cow, were to eat it in this unclean state you have the chance to develop disease.  But we would not eat the plant in this unclean state because we are to have it properly washed.  The same is true for pathogenic microorganisms that are naturally occurring on plants.  I think you addressed this well in the question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But let us propose another situation where a plant evolves a new protein, or a new form of a protein as is the case in the prion.  For simplicity let's call this protein &quot;X.&quot;  X may or may not be toxic to the plant, and cause disease in the plant.  If it does, it would likely have selective pressure against the population it was in (even if it was infectious to plants like a prion).  But we may not, at least in the beginning be able to tell if the plant has the protein in it, so we go ahead and eat it (and for the sake of argument, we won't cook it, which is bad news for all kinds of pathogens).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If that protein causes sickness in an animal (like humans) we would say that it is toxic, and we would exclude it per your preamble.  If it is stable enough, it would remain toxic in our bodies, and should anyone be unfortunate enough to eat us or roll around in are carcass, there would be a small but theoretical chance they could get sick as well.  Again it would likely be excluded from this question as a toxin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think these get at what you are asking, but I think there is a spirit of what you are asking which goes further:&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Why aren't contagious agents produced by plants?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Miguel addresses the problem quite nicely.  First, the genetic distance between humans and plants is so vast that a prion-like protein developing is highly unlikely.  Second, plants themselves are unlikely to make good pathogens.  Finally, natural selection has favored the production of toxins and irritants when plants have sought chemical means to deter animals (as opposed to a physical deterrent like a thorn).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prions work because of shared/similar proteins existing within species.  A similarly shared protein that we would had with plants would probably be so basic that it was shared by the vast majority of eukaryotes, and if it existed, would likely be capable of destroying a good deal of life, including the plant itself.  Thankfully most of the very basic proteins we make a well regulated, and have mechanisms in place to “throw away” miss folded questions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we move past the genetic distance, and ignore the conditions that would be needed to select for plant being pathogens, let’s look at other obstacles plants would face.  Plants aren’t very good at locomotion, so it would need to get on us by direct contact, carried to us from the elements, or by some other animal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good case example would be C. immitis, a fungus.  It needs the spores to be kicked up and inhaled by an individual who is in some way compromised (normally).  Once this happens, it can begin the next hard step which is to grow.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The immune system of a healthy individual would definitely recognize any fungal or plant matter as foreign object and try to get rid of it.  Also note that a pathogenic plant would be limited in size by our behavior.  I think even a sloth would not allow a flower or tree to grow out of its back or arm.  Anything big enough would cause itching and/or illicit a behavioral effort to physically remove it.  Many microbial infections do cause itching, which if you are larger than a microbe, is a good way to have your whole body scratched off your host.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But let’s assume that our pathogen has made it on a human, found a place where it can grow, found enough food to live there (presumably us), has matched our immune system, is small enough that we haven’t been able to physically remove it (think algae), and/or made it to an internal part of body like our lungs where we have a harder time getting rid of it.  After doing all that, it has to grow to the point where it can get back out of bodies, and then back into another human and start over.  A prion-like pathogen would also have to replicate to significant enough numbers to be transmitted host to host.  Transmission is a very difficult process, and as Miguel points out, normally requires a good deal of species dependent specialization and adaption&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;In summary:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I have hard time imaging how a plant, even a small one like alga, could undergo enough selective pressure to become an infectious agent.  It would be further complicated by that fact that you were eating it in your question, which means it would have to contend with the GI track.  The genetic distance makes a prion like pathogen highly improbable if not outright impossible.  Toxins, however, are in great abundance in the plant world, and seem to be a good way to get animals to leave you alone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I think about plant toxins, I always like to think of the Sumac family.  Cashews evolved to be delicious and were cultivated for it, poison ivy evolved to be painful and is destroyed for it, and when we think of the family, we always think of the pain first. [Sorry I know that’s entirely off topic, feel free to delete via edit.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) Johnson CJ, Pedersen JA, Chappell RJ, McKenzie D, Aiken JM (2007) Oral Transmissibility of Prion Disease Is Enhanced by Binding to Soil Particles. PLoS Pathog 3(7): e93. doi:10.1371/journal.ppat.0030093 &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) Bartelt-Hunt SL, Bartz JC (2013) Behavior of Prions in the Environment: Implications for Prion Biology. PLoS Pathog 9(2): e1003113. doi:10.1371/journal.ppat.1003113 &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3) Liberski PP. (2012) Historical overview of prion diseases: a view from afar. Folia Neuropathol. 50(1):1-12.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2013-08-20T21:50:38.927" LastActivityDate="2013-08-20T21:50:38.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9885" PostTypeId="2" ParentId="9880" CreationDate="2013-08-20T23:14:41.290" Score="4" Body="&lt;p&gt;Ears? &lt;a href=&quot;http://en.wikipedia.org/wiki/Primary_amoebic_meningoencephalitis&quot; rel=&quot;nofollow noreferrer&quot;&gt;No.&lt;/a&gt; The tympanic membrane (eardrum) is a watertight barrier between the outer ear and middle ear. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Exposure to the organism is extremely common due to its wide distribution in nature, but thus far lacks the ability to infect the body through any method other than direct contact with the olfactory nerve, which is exposed only at the extreme vertical terminus of the paranasal sinuses; the contaminated water must be deeply insufflated into the sinus cavities for transmission to occur.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qzBG6.gif&quot; alt=&quot;Anatomic chart&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short: Don't huff warm lake water too deeply through your nose, and you'll probably never get it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You shouldn't find it in your stool. &lt;em&gt;Other&lt;/em&gt; amoebic infections can be found in your stool, as they can attack the lining of your intestines, but Naegleria, specifically, will reside in your sinuses and brain until you die or receive treatment.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-08-20T23:14:41.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9886" PostTypeId="1" CreationDate="2013-08-21T01:08:18.180" Score="1" ViewCount="505" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;I would appreciate suggestions for my year-long AP Biology project. Such a project would consists of a standard experiment, to be done over the period of a year, so it would have &amp;gt;to be fairly substantial.&lt;/p&gt;&#xA;&lt;p&gt;I'm interested in anything cell/DNA/molebio related with a mathematical connection. I &amp;gt;would prefer something other than mere statistical analysis, maybe something like &amp;gt;differential equations.&lt;/p&gt;&#xA;&lt;p&gt;I have access to standard undergraduate lab equipment; assume that I'm able to procure all necessary materials and that I'm capable of performing the experiment. Thank you for the help.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;As per the suggestion of shigeta below, I leafed through the links, and found gene circuits interesting. So, what exactly is a gene circuit, how are they modeled, and what are they used for?&lt;/p&gt;&#xA;" OwnerUserId="4283" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-08-21T19:32:52.633" Title="Suggestions for an experiment?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;dna&gt;&lt;mathematical-models&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2013-08-21T17:13:37.757" ContentLicense="CC BY-SA 3.0" />
  <row Id="9888" PostTypeId="5" CreationDate="2013-08-21T03:52:58.370" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-08-21T03:52:58.370" LastActivityDate="2013-08-21T03:52:58.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9889" PostTypeId="4" CreationDate="2013-08-21T03:52:58.370" Score="0" Body="Current and past changes in climate as they relate to biological systems. This may include biological drivers of or impacts from changes in temperature, precipitation, atmospheric CO2, sea level, etc." OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-08-21T07:47:27.520" LastActivityDate="2013-08-21T07:47:27.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9891" PostTypeId="2" ParentId="9875" CreationDate="2013-08-21T13:49:18.037" Score="1" Body="&lt;p&gt;Immunopanning in my experience takes an awful lot of optimization, but is worth it when it works.  I would plan, if you have the resources, to sac rats just for assay optimization before you even begin to try to get real data out (assuming your planning for a steady stream of primary cells).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, there are some real easy checks you can try do first.  Try to get a rough cell count on what you put on your negative plate (depending on your prep steps, that can actually be a bit tricky), and then count the cells again as you transfer the cell suspension to the positive plates.  If you don’t have any cells left, or you have very little cells left, then you might be losing all your population on your negative plate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you do have cells in suspension, I would start to question your positive plate.  Are you making them yourself or are you buying them coated? Which rat strain are you using?  Perhaps you need to titer your antibody concentration on the plate.  There are really a whole lot of steps in immunopanning that can be optimized.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2013-08-21T13:49:18.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9892" PostTypeId="2" ParentId="5099" CreationDate="2013-08-21T14:56:00.467" Score="2" Body="&lt;p&gt;I don't think that any use has been discovered yet for pheomelanin. I can't find sources about the claim that it increases UV absorption so I guess we can't say that yet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would simply guess that it's not harmful enough to warrant elimination via natural selection (in places where people are less exposed to UV, that is), and may, in certain societies, have increased sexual fitness. However even this is hard to tell, because historically red hair has been considered both an identitarian, desirable feature (as for Gauls during Roman times who would even bleach their hair with limewater to obtain reddish-blond hair) and abhorrent and cause for discrimination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vestiges and by-products of useful mutations may accumulate endlessly if their impact on overall fitness is marginal. In this case the useful effect would be the inhibition of eumelanin the skin, which is desirable in low lit/cold climates. This may in turn cause greater pheomelanin production and allows the normally concealed pheomelanic phenotype to show.&lt;/p&gt;&#xA;" OwnerUserId="4288" LastActivityDate="2013-08-21T14:56:00.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9893" PostTypeId="1" CreationDate="2013-08-21T14:59:06.403" Score="4" ViewCount="292" Body="&lt;p&gt;This may be anecdotal...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Indian sub-continent is in the rainy part of summer. It follows the mosquito population goes up. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when I sliced my palm, I expected the mosquitoes to collect there in force. Yet whilst they continued to go about their business on the forearms, face and elsewhere - the blood flowing out of my palm held no attraction for them. This even after I deliberately stood still for nearly a minute! Perhaps the clotting process/platelets/etc were a repellent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do mosquitoes not collect blood after platelets activate?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2014-04-27T03:32:31.153" Title="Why do mosquitoes not collect blood after platelets activate?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9894" PostTypeId="1" AcceptedAnswerId="9906" CreationDate="2013-08-21T15:02:28.830" Score="5" ViewCount="2983" Body="&lt;p&gt;I found that, when I smell watermelon aroma outdoors, someone nearby has mowed  the grass. Is there an underlying basis?&lt;/p&gt;&#xA;" OwnerUserId="4123" LastEditorUserId="4123" LastEditDate="2013-08-21T20:16:07.930" LastActivityDate="2017-05-27T15:18:48.803" Title="Why does freshly cut grass smell like a watermelon?" Tags="&lt;botany&gt;&lt;olfaction&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9895" PostTypeId="2" ParentId="9886" CreationDate="2013-08-21T16:41:55.980" Score="3" Body="&lt;p&gt;This is a bit hard - most possible answers you still aren't going to like, but I'll give you three suggestions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It sounds like you want to take something with a mathematical model and try to modulate it with molecular biology.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems unlikely that I can really give you a specific project, but there are four sources  I will recommend you look at.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think I'd suggest the further limiting assumptions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;you want to work with E coli - its the easiest and most readily available organism to work with.&lt;/li&gt;&#xA;&lt;li&gt;you want to work with a system that is self contained within a single plasmid - so it relies only upon 2 genes to act, 3 at the outside or you will have issues getting it all to work.   &lt;/li&gt;&#xA;&lt;li&gt;you want a mathematical system that already has a well fit model that  you will peturb.  building a new model might be a bit of a big first off project.  (but who am I to tell you what to do - these are just suggestions).  &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The First suggestion I have is &lt;a href=&quot;http://biodynamics.ucsd.edu/&quot; rel=&quot;nofollow&quot;&gt;Jeff Hasty at UCSD&lt;/a&gt;.  He has focused a lot on oscillating gene circuits.  He has simple systems that might be reproducible with a small lab, most recent work that combines a GFP oscillator with LUX is pretty cool. Both oscillators and LUX are independently good systems to work with. .  I've been a science fair judge and I can tell you, just reproducing one of his systems would be an impressive lot of work&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another body of work to look at is &lt;a href=&quot;http://scholar.google.com/citations?hl=en&amp;amp;user=u7WiGLQAAAAJ&amp;amp;sortby=pubdate&amp;amp;view_op=list_works&quot; rel=&quot;nofollow&quot;&gt;Adam Arkin&lt;/a&gt;. He has looked at lots of circuitry component candidates.  Articles such as &quot;The hunt for the biological transistor&quot; might get you thinking.  This is a broader body of work, and so it might take a while to get an idea from it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Third, if this is boring to you and you want to look more broadly, you can look through the &lt;a href=&quot;http://igem.org/Main_Page&quot; rel=&quot;nofollow&quot;&gt;iGEM competitions&lt;/a&gt;.  These are projects with oscillators and bio synthesis systems which sometimes have mathematical models associated with them.  The big advantage here is that you might be able to start or join an iGEM team and then some or all the plasmids will be made already - mol bio gets very expensive if someone doesn't gift you some materials. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-08-21T16:41:55.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9896" PostTypeId="1" AcceptedAnswerId="9964" CreationDate="2013-08-21T17:13:25.007" Score="1" ViewCount="558" Body="&lt;p&gt;In the late fall, bats hibernate in clusters with many bats pressed together and holding on to one another. Which of the following supposed advantages of huddling behavior is, in reality, not true?&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Any heat generated by any bat is shared by other bats.&lt;/li&gt;&#xA;&lt;li&gt;Less surface area is exposed to the environment.&lt;/li&gt;&#xA;&lt;li&gt;Huddling behavior decreases the amount of food needed for bats to stay warm.&lt;/li&gt;&#xA;&lt;li&gt;In this configuration, less heat is needed for each bat and, therefore, each bat requires less food.&lt;/li&gt;&#xA;&lt;li&gt;Huddling behavior helps bats stay warm while they feed.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2013-08-21T20:05:21.720" LastActivityDate="2013-08-24T13:48:04.290" Title="Why do bats huddle during late fall?" Tags="&lt;physiology&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="9899" PostTypeId="2" ParentId="5267" CreationDate="2013-08-21T19:34:33.800" Score="2" Body="&lt;p&gt;If you want to align sequencing results over the reference sequence and check the sequences for presence of spontaneous mutations, the easiest way would be to use &lt;a href=&quot;http://sequlator.com&quot; rel=&quot;nofollow&quot;&gt;Sequlator&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sequlator is a convenient because it has a pairwise alignment, reverse complement, editing and navigation functions but lacks irrelevant functions. With Sequlator one can manipulate any way existing alignments, or manually assemble sequencing reads into an alignment with the reference sequence. After elimination of poorly sequenced fragments, discrepancies with the reference sequence are revealed in the consensus of the resulting alignment. And it is free and Java-based meaning that it works on Windows, Linux and Mac computers&lt;/p&gt;&#xA;" OwnerUserId="4291" LastEditorUserId="107" LastEditDate="2013-08-30T12:25:21.853" LastActivityDate="2013-08-30T12:25:21.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9901" PostTypeId="1" AcceptedAnswerId="9907" CreationDate="2013-08-21T20:06:34.507" Score="2" ViewCount="736" Body="&lt;p&gt;We were studying butterflies in class and I asked my 7th grade teacher, but she deemed the concept &quot;too complicated.&quot; I'm really curious now, not only about butterflies but insects in general...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="4293" LastEditorUserId="4293" LastEditDate="2013-08-22T17:05:45.080" LastActivityDate="2013-08-22T17:05:45.080" Title="What happens during metamorphosis?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9902" PostTypeId="1" AcceptedAnswerId="9922" CreationDate="2013-08-21T20:26:21.547" Score="3" ViewCount="954" Body="&lt;p&gt;I'm working on a mini project for a milk dispenser machine, using a peltier device to cool the milk down, I have to choose between a copper or aluminum cooling block (see pictures bellow). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I'm worried about health issues in the long run, (oxidation and stuff), I have no idea what to choose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would you guys recommend me ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mxKBX.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HuRJL.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4292" LastActivityDate="2013-08-22T18:16:57.240" Title="copper vs aluminum, what's the safest for health?" Tags="&lt;toxicology&gt;&lt;milk&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9906" PostTypeId="2" ParentId="9894" CreationDate="2013-08-21T21:21:51.247" Score="10" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qO1zl.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cis-3-Hexenal&quot; rel=&quot;noreferrer&quot;&gt;cis-3-hexenal&lt;/a&gt; is probably the main reason.  It is one of the main chemicals in fresh-cut grass smell (lots of references besides wiki if you google it).  &lt;a href=&quot;https://www.ideals.illinois.edu/bitstream/handle/2142/16898/2_Genthner_Elizabeth.pdf&quot; rel=&quot;noreferrer&quot;&gt;This&lt;/a&gt; fairly comprehensive paper on watermelon odorants also says that they find a lot of cis-3-hexenal in fresh cut watermelon.  See tables 3.1, 3.2 and 3.3.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-08-21T21:21:51.247" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9907" PostTypeId="2" ParentId="9901" CreationDate="2013-08-21T22:06:07.343" Score="3" Body="&lt;p&gt;It depends of what order and even what family of insects we are talking about. Insects may have complete or incomplete metamorphosis, being the complete more complicated. Even inside the first group (wich in fact contains most of the insects since coleoptera, diptera, lepidoptera and himenoptera have complete metamorphosis) there are important differences. However, I'll try to explain some basics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, metamorphosis is a molting-related process. It's regulated by the same hormones and they share many characteristics. In insects with uncomplete metamorphosis, this is very visible, since the &quot;metamorphosis&quot; is the last molt, wich usually involves growth, sexual maturity and the development of functional wings. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The choice between a regular larval molt is determined primarily by the levels of juvenil hormone, wich decays during the last larval instar (pupae and adult are instars, too). The molting is triggered by a peak of ecdysone, an steroid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once the insect has entered into the state of pupae, the organs start to suffer diverse changes. The formation of adult organs &lt;em&gt;de novo&lt;/em&gt; arise from some special structures called imaginal discs, wich are clusters of stem cells that are more or less isolated in the larvae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XQXkP.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Position of the imaginal discs in Drosophila. &lt;a href=&quot;http://www.devbio.biology.gatech.edu/?page_id=367&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that diptera larvae lack legs, mandibles and even head, while coleptera larvae usually have true legs, a set of mandibles and many other adult features.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Mp2n3.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A typical larva of a coleoptera of the genus &lt;em&gt;Lucanus&lt;/em&gt;. Note the mandibles and the legs. &lt;a href=&quot;http://bugguide.net/node/view/15821&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some other organs remain more or less the same, such as the hearts or many parts of the nervous system. On the other side, some larval organs needs to dissapear and suffer programmed cell death. The gut, many parts of the nervous system, between others, suffer modifications that may be more or less drastic. In many cases this happen by simple growth and differenciation of the tissue or degeneration by apoptosis, but in some others the whole organs suffers apoptosis and regenerates itself with adult characteristics.  For example, the innervation of the abdominal parapods (false legs) in caterpillars suffer a progressive degeneration, while the opposite happens in toracic nerves, wich will have to control legs and wings. This whole process is pretty similar to embrionic development and it shares many traits with it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, metamorphosis in other animals, such as crustaceans, vertabrates (fishes and amphibians), echinodermae, annelidae, cnidaria and many others will probably vary widely. I know for sure that amphibians metamorphosis is regulated by tiroid hormones, but I'm not even sure that many of the other examples have even been studied at a phisiological level. &lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-08-21T22:06:07.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9908" PostTypeId="1" AcceptedAnswerId="9909" CreationDate="2013-08-21T23:14:44.820" Score="5" ViewCount="439" Body="&lt;p&gt;Building off of this question: &lt;a href=&quot;https://biology.stackexchange.com/questions/9894/why-does-freshly-cut-grass-smell-like-a-watermelon&quot;&gt;Why does freshly cut grass smell like a watermelon?&lt;/a&gt;, is it usually the case that things that we perceive as having similar smells are, in fact, the same or a similar chemical hitting our noses (as in the case of cis-3-hexanal in watermelon/cut grass), or is it often a cognitive thing (we're bad at parsing smells, so when confronted with a new smell, we fish around in our experience to find something that seems familiar, even if there's not much chemical similarity)?&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2018-12-11T02:02:00.953" Title="Are similar smells usually based on similar chemicals?" Tags="&lt;biochemistry&gt;&lt;sensation&gt;&lt;perception&gt;&lt;olfaction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9909" PostTypeId="2" ParentId="9908" CreationDate="2013-08-22T01:13:59.263" Score="5" Body="&lt;p&gt;With regards to the similar chemicals having similar smells, it does seem that there are trends with smell association and functional group.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Aroma_compound#Aroma_compounds_classified_by_structure&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; wiki article has a good list of compounds and their smells, and some classes definitely give similar types of smells, amines are rotting/fecal smells (hence the names putrescine and cadaverine), while esters are often fruity.  As you can see its not perfect, but there are definitely patterns.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some weird dose-dependent effects like in the case of indole which is labeled as flowery/fecal, which are two pretty distinct smells.  Apparently its fecal at high doses, and smells like jasmine at low doses.  My guess is that this has to do with different binding affinities of the different olfactory receptors (ORs) that are expressed in the olfactory receptor neurons (ORNs).  Many odorants will bind to multiple ORs, which means they will stimulate a characteristic sub-population of ORNs.  The binding to the different ORs will of course have different affinities.  This probably means that at low concentrations of indoles, you stimulate a certain population of ORNs that your brain recognizes as nice flowers, but as you increase the concentration you get the activation of ORNs with ORs that have a weaker binding to indole, changing the population of activated ORNs to one that your brain recognizes as feces.  Its definitely a strange pairing though..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not familiar enough with the literature to know if the similar smelling things have similar ORN activation patterns, but my guess would be that they do.  If you have a population of different ORs that your odorant is binding to, a slightly different odorant will probably bind to a similar subset of ORs, just off by a few if its missing or has gained a functional group that is in the binding pocket of some of the ORs.  This probably means that if you are presented with a chemical that you have never smelled before, it will probably activate a similar ORN population as other similar chemicals, and your brain will probably say it smells like one of those similar chemicals.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastEditorUserId="4177" LastEditDate="2013-08-22T08:55:15.670" LastActivityDate="2013-08-22T08:55:15.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9910" PostTypeId="2" ParentId="9876" CreationDate="2013-08-22T02:03:48.510" Score="10" Body="&lt;p&gt;The outer shell of a tooth is enamel, which is hard and dense so that not much can penetrate it.  Under that is &lt;a href=&quot;http://en.wikipedia.org/wiki/Dentin&quot;&gt;dentin (or dentine)&lt;/a&gt;, which is bony but has microscopic channels running through it to the center of the tooth where the pulp and nerve reside.  If the enamel is breached, as with a cavity, crack, or wear, the dentin is exposed to the environment of the mouth.  When sugar comes against the dentin, it draws fluid out of the microscopic channels (because sugar attracts water strongly).  The fluid flow causes pressure changes around the nerve of the tooth, which reports the change to the brain where it registers as pain.  Dentin is &lt;a href=&quot;http://en.wikipedia.org/wiki/Dentine_hypersensitivity&quot;&gt;highly sensitive&lt;/a&gt; not just to sugar, but also to hot, cold, pressure, and other stimuli.  (This sugar response is a short term one; the influence of sugar on bacteria is a longer-term effect in which the acid generated by the bacteria eats away the enamel layer.)  &lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2013-08-22T02:03:48.510" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9911" PostTypeId="1" CreationDate="2013-08-22T04:50:07.840" Score="9" ViewCount="1745" Body="&lt;p&gt;The answer to &lt;a href=&quot;https://space.stackexchange.com/questions/1/how-far-could-we-send-someone-before-they-get-a-lethal-dose-of-radiation&quot;&gt;this question&lt;/a&gt; on the Space.SE indicates women are more susceptible to radiation in space than men.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CzmmU.jpg&quot; alt=&quot;Radiation susceptibility in men and women&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is this the case? Is it merely that women have less muscle mass (which being more dense than fat) and therefore may receive a greater dose when exposed?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:58:55.703" LastActivityDate="2015-09-11T18:40:43.760" Title="Why are women more susceptible to radiation?" Tags="&lt;radiation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9912" PostTypeId="1" CreationDate="2013-08-22T04:59:51.827" Score="0" ViewCount="589" Body="&lt;p&gt;I love worm composting (I use red wiggler worms), but wondering how similar or different the &lt;em&gt;Caenorhabditis elegans&lt;/em&gt; and &lt;em&gt;Eisenia fetida&lt;/em&gt; are?&lt;/p&gt;&#xA;" OwnerUserId="4297" LastEditorUserId="4136" LastEditDate="2013-08-22T10:49:08.967" LastActivityDate="2013-08-22T10:49:08.967" Title="What is the difference between these worms: Caenorhabditis elegans and Eisenia fetida?" Tags="&lt;invertebrates&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9913" PostTypeId="1" AcceptedAnswerId="9915" CreationDate="2013-08-22T06:40:55.800" Score="10" ViewCount="20227" Body="&lt;p&gt;Type II Restriction enzymes usually cut only at palindromic sequences. Is there any specific reason for that? Is there any advantage for bacteria if they cleave phage DNA at this type of sequence?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="22057" LastEditDate="2019-03-04T17:54:20.887" LastActivityDate="2019-03-05T15:14:24.790" Title="Why do Type II Restriction Endonucleases cleave at palindromic sequences?" Tags="&lt;biochemistry&gt;&lt;bacteriology&gt;&lt;restriction-enzymes&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="9914" PostTypeId="2" ParentId="9912" CreationDate="2013-08-22T07:09:49.793" Score="1" Body="&lt;p&gt;&lt;em&gt;Caenorhabditis elegans&lt;/em&gt; is a nematode. &lt;em&gt;Eisenia fetida&lt;/em&gt; is an annelid. They both are lophotrochozoans (more specifically, trochozoans). &lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Time of Divergence&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://dx.doi.org/10.2307/2640769&quot; rel=&quot;nofollow&quot;&gt;Michael Lynch&lt;/a&gt;, there are about 41 amino-acid substitutions per site between Annelida and Nematoda. According to Lynch's data, I estimated that this difference is roughly equal 100 million years. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, assuming the rate of molecular evolution was constant, their common ancestors lived about 100 million years ago.&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Difference on Anatomy&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;Nematodes have &lt;a href=&quot;//en.wikipedia.org/wiki/Body_cavity#Pseudocoelom&quot;&gt;pseudocoelom&lt;/a&gt; while annelids have &lt;a href=&quot;//en.wikipedia.org/wiki/Coelom&quot;&gt;eucoelom&lt;/a&gt;. Therefore nematodes do not have a vascular blood system. However, annelids do have one. Nematodes also lack a layer of circular muscle, which annelids have. This layer of muscle allows annelids to move by shorten and elongate their bodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;C. elegans&lt;/em&gt; in particular does not have a female gender. There are only male worms and hermaphrodite worms. Only the male can fertilize other worms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;E. fetida&lt;/em&gt; is hermaphroditic and two of them can fertilize each other.&lt;/p&gt;&#xA;" OwnerUserId="4136" LastActivityDate="2013-08-22T07:09:49.793" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9915" PostTypeId="2" ParentId="9913" CreationDate="2013-08-22T07:36:50.250" Score="4" Body="&lt;p&gt;First, not all restriction enzymes cut at palindromic sequences.&#xA;A lot of them do though, simply because it is more effective. Recognising a palindromic sequence enables them to cut both strands of DNA at the &quot;same&quot; site, because the strand will have the same sequence only in different directions at that site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://en.wikipedia.org/wiki/Palindromic_sequence#Restriction_Enzyme_Sites&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt; for example.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-08-22T07:36:50.250" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9916" PostTypeId="1" AcceptedAnswerId="9935" CreationDate="2013-08-22T10:34:27.770" Score="2" ViewCount="1142" Body="&lt;p&gt;I think the main reason is the natural selection that is causing methicillin-resistance.&#xA;However, I am not completely sure what this means practically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here, the original question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MRSA was isolated in the throat secretion of patient hospitalized with bronchitis. Which of the following&#xA;statements best characterizes this microorganism?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;a. its MIC is increased to methicillin, but not to penicillin&lt;/li&gt;&#xA;&lt;li&gt;b. methicillin-resistance is associated with production of β-lactamases&lt;/li&gt;&#xA;&lt;li&gt;c. Methicillin-resistance is caused by changes in configuration (mutation) of PBP&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the right answer?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2013-08-25T17:38:51.770" LastActivityDate="2013-09-01T01:42:27.730" Title="Factor causing Methicilin-resistance in MRSA?" Tags="&lt;microbiology&gt;&lt;homework&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9917" PostTypeId="1" AcceptedAnswerId="9932" CreationDate="2013-08-22T10:55:57.207" Score="2" ViewCount="138" Body="&lt;p&gt;I got this question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Diphteria toxin is produced only by those strains of C. diphtheria that have which of the following characteristics?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Encapsulated&lt;/li&gt;&#xA;&lt;li&gt;glucose fermenters&lt;/li&gt;&#xA;&lt;li&gt;lysogenic for b-prophage&lt;/li&gt;&#xA;&lt;li&gt;only mitis-strains&lt;/li&gt;&#xA;&lt;li&gt;sucrose fermenters&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I think the right answer is &lt;strong&gt;lysogenic for b-prophage&lt;/strong&gt;, since Freeman found out that toxic gene is encoded by lysogenic phage infecting all toxigenic strains in 1951.&#xA;However, I am not sure what &quot;b-&quot; means in &quot;b-prophage&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which part is &quot;b-&quot; in Prophage?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="3971" LastEditDate="2013-08-26T22:11:48.083" LastActivityDate="2013-08-26T22:11:48.083" Title="Which strains of C. diphteria are causing Diphteria toxin?" Tags="&lt;microbiology&gt;&lt;homework&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9918" PostTypeId="1" AcceptedAnswerId="9933" CreationDate="2013-08-22T11:07:33.917" Score="1" ViewCount="63" Body="&lt;p&gt;I am not sure which word is the best here for &lt;em&gt;colonisation of alveoli by acid fast-mycobacteria&lt;/em&gt;. I found this question, and I am getting confused by the term &lt;em&gt;obstruction of alveoli&lt;/em&gt; because I tend to relate it to COPD which is not a case here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which of the following is the predominant pathogenic mechanism of tuberculosis?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;a) cell-mediated hypersensitivity&lt;/li&gt;&#xA;&lt;li&gt;b) obstruction of alveoli by large number of acid-fast mycobacteria&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I think the right answer is &quot;obstruction of alveoli by large number of acid-fast mycobacteria&quot;, but I am not sure if you can say that acid-fast mycobacteria obstruct alveoli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are acid-fast mycobacteria &quot;obstructing&quot; alveoli or just colonizing?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2013-08-25T17:42:59.883" LastActivityDate="2013-08-25T17:42:59.883" Title="Can acid-fast M. tubercolosis obstruct alveoli?" Tags="&lt;microbiology&gt;&lt;homework&gt;&lt;tuberculosis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9920" PostTypeId="1" AcceptedAnswerId="27808" CreationDate="2013-08-22T15:24:59.477" Score="9" ViewCount="215" Body="&lt;p&gt;&lt;strong&gt;Is there any mathematical model to predict the behaviour and long-term consequence of counter-acting selection at different time scale?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, let's consider the bi-allelic gene &lt;strong&gt;A&lt;/strong&gt;, with alleles &lt;strong&gt;A&lt;sub&gt;1&lt;/sub&gt;&lt;/strong&gt; and &lt;strong&gt;A&lt;sub&gt;2&lt;/sub&gt;&lt;/strong&gt;. During a long period of &lt;strong&gt;n&lt;sub&gt;1&lt;/sub&gt;&lt;/strong&gt; generations &lt;strong&gt;A&lt;sub&gt;1&lt;/sub&gt;&lt;/strong&gt; is slightly beneficial (differential of selection: &lt;strong&gt;s&lt;sub&gt;1&lt;/sub&gt;&lt;/strong&gt;). After this period, follows a short period of &lt;strong&gt;n&lt;sub&gt;2&lt;/sub&gt;&lt;/strong&gt; generations when &lt;strong&gt;A&lt;sub&gt;2&lt;/sub&gt;&lt;/strong&gt; is highly beneficial (differential of selection: &lt;strong&gt;s&lt;sub&gt;2&lt;/sub&gt;&lt;/strong&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What mathematical model describes the frequency fluctuations of alleles and which allele will get fixed at the long term given the initial frequency ( &lt;strong&gt;&lt;em&gt;f&lt;sub&gt;0&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; ), assuming infinite population size and random mating. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3340" LastEditDate="2014-12-06T10:52:46.920" LastActivityDate="2015-01-22T03:44:08.897" Title="Model for fluctuating selection" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;natural-selection&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9921" PostTypeId="1" AcceptedAnswerId="9923" CreationDate="2013-08-22T15:29:07.203" Score="0" ViewCount="278" Body="&lt;p&gt;What  information is greatly lacking which does not allow us to propose a  solid theory for origin of life ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1306" LastEditDate="2013-08-22T17:09:01.257" LastActivityDate="2017-10-13T09:50:17.507" Title="Why can't we propose a solid theory regarding origin of life?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="5" ClosedDate="2017-10-23T04:40:42.707" ContentLicense="CC BY-SA 3.0" />
  <row Id="9922" PostTypeId="2" ParentId="9902" CreationDate="2013-08-22T15:42:11.807" Score="3" Body="&lt;p&gt;Assuming the answer can't be &lt;strong&gt;C) Stainless Steel&lt;/strong&gt; I would go with Aluminum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The USDA &lt;a href=&quot;http://www.ams.usda.gov/AMSv1.0/getfile?dDocName=STELDEV3004791&quot; rel=&quot;nofollow&quot;&gt;specifically mandates (1)&lt;/a&gt; stainless steel 300:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Milk contact surfaces shall be made of stainless steel of the 300&#xA;  series, equally corrosion-resistant non-toxic metals or heat-resistant&#xA;  glass.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is the copper tinned?  From what I can tell after reading some &lt;a href=&quot;http://nvlpubs.nist.gov/nistpubs/nbstechnologic/nbstechnologicpaperT90.pdf&quot; rel=&quot;nofollow&quot;&gt;old sources (2)&lt;/a&gt; un-tinned copper will be corroded by milk.  You have the advantage of &lt;a href=&quot;http://www.nap.edu/openbook.php?record_id=9782&amp;amp;page=137&quot; rel=&quot;nofollow&quot;&gt;a cool temperature lowering contamination risk (3)&lt;/a&gt;, but many states following the FDA specifically &lt;a href=&quot;http://www.cga.ct.gov/2001/pub/Chap430.htm&quot; rel=&quot;nofollow&quot;&gt;removed the allowance of tinned copper (Sec. 22-201)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the effects of life long dosing of Al are becoming more and more &lt;a href=&quot;http://iospress.metapress.com/content/k10718165465535u/?genre=article&amp;amp;issn=1387-2877&amp;amp;volume=35&amp;amp;issue=1&amp;amp;spage=7&quot; rel=&quot;nofollow&quot;&gt;clearly tied to Alzheimer's (4)&lt;/a&gt;, the effects build up over time.  Copper has a tendency to be more &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/4043443&quot; rel=&quot;nofollow&quot;&gt;acute (5)&lt;/a&gt; and &lt;a href=&quot;http://books.google.com/books?id=6eWpW1ypIdUC&amp;amp;vq=copper&amp;amp;dq=The%20dietary%20significance%20of%20adventitious%20iron,%20zinc,%20copper%20and%20lead%20in%20domestically%20prepared%20food.&amp;amp;source=gbs_navlinks_s&quot; rel=&quot;nofollow&quot;&gt;pronounced (6,&lt;/a&gt; &lt;a href=&quot;http://informahealthcare.com/doi/abs/10.1080/00313029600169264&quot; rel=&quot;nofollow&quot;&gt;7),&lt;/a&gt; and further it can tasted in low amounts  and discolor the food (8).  It can be said that water flows through Cu pipes, but soda is put in Al cans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The research for this has been quite enjoyable, and led to things I didn't even think of.  &lt;a href=&quot;http://www.clark.wa.gov/recycle/A-Z/Materials/cleanersandpolishers.html&quot; rel=&quot;nofollow&quot;&gt;A alternative cleaning&lt;/a&gt; site has even recommended using milk to clean Cu pans.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Again so my final recommendation is to follow USDA guidelines and use stainless steel, but my second choice would be Aluminum.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Citations:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) USDA. 2011, July. Milk for Manufacturing Purposes and its Production and Processing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) US DOC. 1917, April. STRUCTURE OF THE COATING ON TINNED SHEET COPPER IN RELATION TO A SPECIFIC CASE OF CORROSION. Technologic Papers OF THE Bureau of Standards. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3) COMMITTEE ON COPPER IN DRINKING WATER, NATIONAL RESEARCH COUNCIL. &lt;em&gt;Copper in Drinking Water.&lt;/em&gt; NATIONAL ACADEMY PRESS. 2000.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(4) Walton, J.R. Aluminum Involvement in the Progression of Alzheimer's Disease. Journal of Alzheimer’s Disease 35 (2013) 7–43. DOI 10.3233/JAD-121909&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(5) Reilly C. The dietary significance of adventitious iron, zinc, copper and lead in domestically prepared food. Food Addit Contam. 1985 Jul-Sep;2(3):209-15.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(6) Conor Reilly. Metal Contamination of Food:&#xA;Its Significance for Food Quality and Human Health. Pg 50. John Wiley &amp;amp; Sons, Apr 15, 2008&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(8) ibid pg. 16&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(7) Lee A. Price, et al. Chronic copper toxicosis presenting as liver failure in an Australian child. Pathology. 1996, Vol. 28, No. 4 , Pages 316-320 (doi:10.1080/00313029600169264)&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2013-08-22T18:16:57.240" LastActivityDate="2013-08-22T18:16:57.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9923" PostTypeId="2" ParentId="9921" CreationDate="2013-08-22T16:01:56.300" Score="9" Body="&lt;p&gt;First of all, we &lt;a href=&quot;http://en.wikipedia.org/wiki/Abiogenesis&quot;&gt;do have&lt;/a&gt; some solid theories to explain the origin of life. That said, the main thing missing in order to be able to accept one of these theories with a decent amount of certainty is the ability to run a planetary scale experiment for a few billion years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The theories are fine, the problem is that we cannot really test them. In order to test a theory that describes the origin of life, we will have to recreate the original conditions (think of a test tube the size of the Earth) and then pump energy into the system and watch what happens over the next few billions of years. This is not really feasible, for obvious reasons. I really doubt you will be able to get funding for an experiment that will run that long.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-08-22T23:21:13.197" LastActivityDate="2013-08-22T23:21:13.197" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9924" PostTypeId="1" AcceptedAnswerId="13601" CreationDate="2013-08-22T16:08:02.683" Score="5" ViewCount="1278" Body="&lt;p&gt;How to distinguish those flowers of the forest outskirts: hawkweeds (Hieracium), hawksbeard (Crepis) and hawkbits (Leontodon)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not asking about concrete species it should be extremely hard since they have hundreds forms, but what are observable differences between genus?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read wikis articles but still not sure that I could distinct those flowers in the field right way.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Leontodon&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Leontodon&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hieracium&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Hieracium&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Crepis&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Crepis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4300" LastActivityDate="2014-10-02T18:41:49.117" Title="How to distinguish those flowers in outskirts: hawkweeds (Hieracium), hawksbeard (Crepis) and hawkbits (Leontodon)?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9925" PostTypeId="2" ParentId="9774" CreationDate="2013-08-22T16:22:29.630" Score="0" Body="&lt;p&gt;My best guess to explain this phenomenon has been spontaneous degradation of the sticky ends, followed by blunt-ended ligation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, single-stranded exonuclease activity either from a contaminating enzyme or from EcoRI/XmaI/AgeI could be imaginable. For example, using buffer Multi-Core is discouraged for EcoRI due to potential STAR activity - maybe it developed exonuclease activity and some plasmids ended up blunt-ended before the ligation.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-08-22T16:22:29.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9926" PostTypeId="1" AcceptedAnswerId="9930" CreationDate="2013-08-22T16:26:40.973" Score="6" ViewCount="610" Body="&lt;p&gt;People with Huntington's disease have &lt;em&gt;HTT&lt;/em&gt; genes with more than 37 copies of CAG repeat. The risk of extra copies being generated is higher during sperm formation than during ovum formation. Why is it so?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interesting fact: People with HD allele inherited from father develop symptoms earlier than if that allele is inherited from mother.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2013-08-22T19:59:34.230" LastActivityDate="2015-11-20T19:10:05.660" Title="Inheritance of Huntington's disease" Tags="&lt;genetics&gt;&lt;pathology&gt;&lt;genomics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9927" PostTypeId="1" AcceptedAnswerId="9928" CreationDate="2013-08-22T18:16:38.330" Score="3" ViewCount="106" Body="&lt;p&gt;Mitochondria are considered endosymbionts originated from a prokaryote. So, do they have a DNA repair mechanism ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-21T19:51:45.270" LastActivityDate="2013-10-21T19:51:45.270" Title="Do mitochondrial DNA have repair enzymes?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;dna&gt;&lt;mitochondria&gt;&lt;dna-damage&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9928" PostTypeId="2" ParentId="9927" CreationDate="2013-08-22T18:16:38.330" Score="1" Body="&lt;p&gt;Yes, mtDNA can be repaired by enzymes coded by nuclear genes.&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22992591&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/22992591&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-08-22T18:16:38.330" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9929" PostTypeId="1" CreationDate="2013-08-22T18:30:03.990" Score="3" ViewCount="3224" Body="&lt;p&gt;I'm using cuffdiff 2.1.1 to look for differential gene expression between two conditions. Each condition has 2 biological replicates. The results I get look promising from a log fold change perspective - lots of genes that I would expect to be affected have the highest fold change values. However, from a q-value perspective very few of the results look promising, having q values &gt; 0.05.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, given 2 replicates, how is the q value calculated? Surely if there was high variance between replicates but the difference between experimental conditions was also large then the q-values would be correspondingly high? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case, can I, or should I, really trust the q-values?&lt;/p&gt;&#xA;" OwnerUserId="4242" LastEditorUserId="4242" LastEditDate="2014-02-09T21:21:19.993" LastActivityDate="2014-02-09T21:21:19.993" Title="RNA-seq analysis - q-values in cuffdiff" Tags="&lt;bioinformatics&gt;&lt;statistics&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9930" PostTypeId="2" ParentId="9926" CreationDate="2013-08-22T18:35:10.457" Score="5" Body="&lt;p&gt;Excellent question. The answer is that, in general, there is a higher rate of mutation in spermatogenesis compared to oogenesis. This is because there are more cell divisions during spermatogenesis, which allows for opportunities for mutation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, repeat diseases like Huntington’s sometimes have a phenomenon known as anticipation. This is when the disease gets phenotypically (and genetically) more severe with each successive generation. The exact molecular basis of this is not completely understood, but it is just well known that DNA polymerase tends to make more mistakes in large repeat regions, causing an expansion of the repeat. Anticipation is not linked to gender, I just wanted to point out that these repeats are prone to mutations that will expand the repeat and cause disease&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see anticipation in this graph. This example is for Fragile X. The higher the repeat number in the parent, the greater the chance the child develops the disease. The parent doesnt have the disease, but what happens is the repeat mutates and gets expanded to the point where the disease will develop.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nmcSV.gif&quot; alt=&quot;Anticipation&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, put these two facts together and you have your answer. A male's sperm tends to have a higher overall mutation rate, and the region responsible for Huntingtons is already prone to disease causing mutations as it is. The result ends up being the disease gets ‘inherited’ more often from the father &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/gim/journal/v14/n8/full/gim201234a.html&quot; rel=&quot;noreferrer&quot;&gt;Picture from here&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-08-22T18:35:10.457" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9932" PostTypeId="2" ParentId="9917" CreationDate="2013-08-22T20:11:56.253" Score="2" Body="&lt;p&gt;Real simple: Beta!  Often called &quot;&lt;a href=&quot;http://textbookofbacteriology.net/phage_2.html&quot; rel=&quot;nofollow&quot;&gt;phage beta&lt;/a&gt;&quot; b-prophage is a more modern way to write it.  I knew that one off the top of my head, but I like to refer the general public interested in bacteriology to &lt;a href=&quot;http://textbookofbacteriology.net/index.html&quot; rel=&quot;nofollow&quot;&gt;Tadar's online text.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's nicely done, and I wish that it had been around when I was studying bacteriology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specific to your question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hence, Corynebacterium diphtheriae can only produce the toxin&#xA;  responsible for the disease if it carries a temperate virus called&#xA;  phage beta. Only lysogenized streptococci  produce the erythrogenic&#xA;  toxin (pyrogenic exotoxin) which causes the skin rash of scarlet&#xA;  fever; and some  botulinum toxins are synthesized only by lysogenized&#xA;  strains of C. botulinum.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2013-08-22T20:11:56.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9933" PostTypeId="2" ParentId="9918" CreationDate="2013-08-22T20:15:23.713" Score="2" Body="&lt;p&gt;Mycobacteria are on the order of 2µm in length and 0.2µm in diameter.  Alveoli are on the order of 200µm in diameter.  Obstruction is possible, but &lt;em&gt;M. tuberculosis&lt;/em&gt; grows rather slowly.  Too slowly, in fact, to avoid being engulfed by alveolar macrophages.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, obstruction does not sufficiently explain the predominant symptoms of tuberculosis:  &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemoptysis&quot; rel=&quot;nofollow&quot;&gt;bloody sputum&lt;/a&gt; and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Tubercle_%28anatomy%29&quot; rel=&quot;nofollow&quot;&gt;tubercles&lt;/a&gt; themselves.&lt;/p&gt;&#xA;" OwnerUserId="4228" LastActivityDate="2013-08-22T20:15:23.713" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9934" PostTypeId="1" CreationDate="2013-08-22T20:36:41.973" Score="3" ViewCount="113" Body="&lt;p&gt;I am interested in the multifactorial process about infectious diseases of the lower respiratory system and their progression to a skin infection. &#xA;Possible agens are zwitterions, viruses, fungi, amoebas, bacteria and/or parasites. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Zwitterions&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Small protein segments, much unknown but their importance is much greater than known. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Viruses&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Parvovirus B19 &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Example of a case: 5 children develop a bright red rash on the face and turns violet after a few days and then disappears. Then maculopapular rash appears on the trunk, buttocks and extremities. It soon fades from the trunk but persists on the thights and forearms. Two children have also had a slight fever and a sore throat, but all were not terribly sick. What is the genetic material of the most likely causative agent?&lt;/li&gt;&#xA;&lt;li&gt;It is a skin infection. Not so severe. Little upper respiratory infection but not necessary caused by the agent. Infects many so spread probably by respiratory droplets. **But how a respiratory infection can lead to a skin infection?*&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Bacteria&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;....&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Amoebas&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;...&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Fungi&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;....&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Parasites&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;...&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2016-09-19T14:40:16.060" LastActivityDate="2016-09-19T14:40:16.060" Title="How can an infection of lower respiratory tract lead to a skin infection?" Tags="&lt;microbiology&gt;&lt;skin&gt;&lt;infectious-diseases&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ClosedDate="2016-09-21T07:29:51.010" ContentLicense="CC BY-SA 3.0" />
  <row Id="9935" PostTypeId="2" ParentId="9916" CreationDate="2013-08-22T21:12:20.243" Score="3" Body="&lt;p&gt;I think you can normally think about similar pressures leading to extended-spectrum beta-lactamase (ESBLs) and  methicillin/oxacillin-resistant Staphylococcus aureus (MRSA).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Going to the core of your question: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.bios.2013.05.031&quot; rel=&quot;nofollow&quot;&gt;&quot;Currently, the reported mechanism of methicillin resistance in S. aureus is the production of a distinctive penicillin binding protein 2a (PBP2a), which exhibits low affinity toward β-lactams&quot;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But to really read on it you need to back to &lt;a href=&quot;http://dx.doi.org/10.1007/BF02184683&quot; rel=&quot;nofollow&quot;&gt;Liu et al.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again &lt;a href=&quot;http://textbookofbacteriology.net/staph.html&quot; rel=&quot;nofollow&quot;&gt;Todar's is a great source&lt;/a&gt; for a good broad reading on staph including MRSA.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Response to Edit [inclusion of full question]:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;TSDR: The answer is C.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's break down the three options given in the question and learn about MRSA along the way.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a. its MIC is increased to methicillin, but not to penicillin&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;First, for people who may not know, MIC is short for &lt;a href=&quot;https://en.wikipedia.org/wiki/Minimum_inhibitory_concentration&quot; rel=&quot;nofollow&quot;&gt;minimum inhibitory concentration&lt;/a&gt;.  Simply, the MIC is a basic measurement of how much of any given agent is need to stop the growth of a bacterial colony.  Often we think of current medical antibiotics when thinking of MIC, but even simpler things like table salt and sugar have a MIC for a given species.  Thus this sentence is making the assertion that the bacteria found in the patent have an increased resistance to methicillin but not to penicillin.  This leads us to ask the obvious question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can Staphylococcus aureus (staph going forward) be methicillin resistant but not penicillin resistant?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a bit of a trick question, but let's break it down to the needed components: What is Methicillin, what is/are penicillin(s), and how are staph resistant to them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First that it should be noted that &lt;a href=&quot;https://en.wikipedia.org/wiki/Penicillin&quot; rel=&quot;nofollow&quot;&gt;penicillins&lt;/a&gt; can actually refer to a whole class of antibiotics which all use &lt;a href=&quot;https://en.wikipedia.org/wiki/Beta-lactam&quot; rel=&quot;nofollow&quot;&gt;β-Lactam&lt;/a&gt; and the specific set of antibiotics:  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;benzylpenicillin (penicillin G), procaine benzylpenicillin (procaine&#xA;  penicillin), benzathine benzylpenicillin (benzathine penicillin), and&#xA;  phenoxymethylpenicillin (penicillin V). (&lt;a href=&quot;https://en.wikipedia.org/wiki/Penicillin&quot; rel=&quot;nofollow&quot;&gt;from wiki&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It should be noted that more correct way to address the whole class of antibiotics would be &lt;a href=&quot;https://en.wikipedia.org/wiki/Beta-lactam_antibiotic&quot; rel=&quot;nofollow&quot;&gt;β-Lactam antibiotics&lt;/a&gt;, not penicillins, and that if you wanted to talk about more specifically penicillin derived compounds you would be discussing &lt;a href=&quot;https://en.wikipedia.org/wiki/Penam&quot; rel=&quot;nofollow&quot;&gt;penams&lt;/a&gt;.  For even further clarification, penicillin as drug most likely refers to &lt;a href=&quot;https://en.wikipedia.org/wiki/Benzylpenicillin&quot; rel=&quot;nofollow&quot;&gt;benzylpenicillin&lt;/a&gt;, and for the rest of this answer I will use penicillin to refer to benzylpenicillin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus we should think of penicillin as an early antibodic that work by preventing the dividing/genesis of cell walls and certain organelles via binding to &lt;a href=&quot;https://en.wikipedia.org/wiki/Penicillin-binding_protein&quot; rel=&quot;nofollow&quot;&gt;penicillin binding proteins&lt;/a&gt; (PBPs).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Meticillin&quot; rel=&quot;nofollow&quot;&gt;Methicillin&lt;/a&gt; is also a β-Lactam antibiotic, and it's &lt;a href=&quot;https://en.wikipedia.org/wiki/Mechanism_of_action&quot; rel=&quot;nofollow&quot;&gt;MOA&lt;/a&gt; is similar to penicillin.  It was developed/discovered after penicillin and was seen a answer to Gram-positive bacteria that were breaking down penicillin via β-lactamase.  Methicillian still works by binding to PBPs, but it escapes the bacteria's counter to penicillin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leads us to address how penicillin resistance and methicillin resistance commonly occur in staph.  First, many staph strains and other bacteria use β-lactamases to breakdown antibiotics so they no longer can bind to PBP's (1).  But methicillin is particularly suited by its side chains to not be degraded by β-lactamases.  In their &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC181513/pdf/aac00005-0048.pdf&quot; rel=&quot;nofollow&quot;&gt;ground breaking work&lt;/a&gt; on the subject, Hartman and Tomasz identified that methicillin resistance was not in the acquisition of a β-lactamase, but in a mutation in PBP's that prevented methicillin binding (2).  There they tested 4 strains of staph, two were methicillin resistant (MR), and two were methicillian susceptible (MS).  You will note that all but 1 didn't have β-lactamase activity, and where &lt;em&gt;more susceptible to penicillin&lt;/em&gt; than methicillin (ibid).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;BUT&lt;/em&gt; this does not mean that MR strains are not also penicillin resistant, instead it shows that the resistance can be independent of each other.  Therefore &quot;A&quot; is wrong because it tries to draw a correlation that is not there.  In reality many MR strains are also β-lactamase positive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This also address the problem with &quot;B.&quot;  While it is possible that a β-lactamase could bind to methicilin and lead to degradation of the antibiotic, &lt;strong&gt;the main mechanism of methicillin resistance is the mutation of PBPs (ibid, 3), in particular BPB2a (4, 5).&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We are then left with the task of figuring out why &quot;C&quot; is the correct choice.  Indeed &quot;C&quot; is the given reason for the failure of &quot;A&quot; and &quot;B,&quot; but we can still go deeper into how and perhaps why BPB2a mutated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For that I think it is best that we turn back to &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC358041/&quot; rel=&quot;nofollow&quot;&gt;Chambers' review&lt;/a&gt; of the subject.  Forgive my over quoting, but it's done so well there and the text is now open.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Methicillin resistance is associated with production of a novel PBP&#xA;  that is not present in susceptible staphylococci. Resistant strains of&#xA;  S. aureus produce an additional 78- kilodalton PBP (Fig. 1), termed&#xA;  PBP2a or PBP2' (assumed to be identical for the purposes of this&#xA;  review), that has a low binding affinity for beta-lactam antibiotics.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;PBP2a is highly conserved. Limited proteolysis of PBP2a from unrelated&#xA;  strains of S. aureus (123) and coagulasenegative staphylococci (31),&#xA;  whether homogeneous or heterogeneous, generates remarkably similar&#xA;  peptide fragments.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Presumably PBP2a can substitute for essential PBPs when these have&#xA;  been saturated by drug and can perform the functions necessary for&#xA;  cell wall assembly (22, 122).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In some strains, PBP2a is inducible by beta-lactam antibiotics and its&#xA;  production differs according to growth conditions (34, 122, 125, 159).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, they didn't quite have the staphylococcal cassette chromosome &lt;em&gt;mec&lt;/em&gt; (&lt;a href=&quot;https://en.wikipedia.org/wiki/SCCmec&quot; rel=&quot;nofollow&quot;&gt;SCCmec&lt;/a&gt;) figured out at that point.  The genetics is quite complex. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;How does MRSA genetically accomplish resistance?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;As we already established, the resistance comes from the production of an alternate PBP, PBP2a.  SCCmec is interesting for several reasons.  First of all, it's much larger than a plasmid, and contains information for several genes.  That's why it's called cassette &lt;em&gt;chromosome.&lt;/em&gt;  Further it normally incorporates into the same part of the genome in staph, in an area know as OrfX (6).  This means that even during horizontal transfer, that the cassette has to direct it's integration into the genome, which is exceedingly uncommon, or at least there are not many other know examples (7, 8).  This cassette can be spread horizontally between staph, and even with other species (ibid, 9).  Even if the integration site (integration site sequence, ISS) is slightly different, this specificity is carried out by cassette chromosome recombinases (ccr), wich are also on SCCmec (8).  This is carried out by ccr-medated recombination of the target chromosome, and further details on the process are considered outside the scope of this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The actual gene that encodes PBP2a is called &lt;em&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/MecA_%28gene%29&quot; rel=&quot;nofollow&quot;&gt;mecA&lt;/a&gt;&lt;/em&gt;.  But as we mentioned above, PBO2a production can be induced and regulated.  It is likely less favorable to produce it in the absence of antibodies, and after serial passage of bacteria in antibiotic free broth, you find that PBP2a expression can drop drastically.  Therefore regulatory and other useful proteins encoded by SCCmec.  When placed in a β-Lactamase environment, MecR1 causes a single transduction cascade to start transcription of &lt;em&gt;mecA&lt;/em&gt; (10).  Conversely, MecI provides a negative feedback loop to MecR1, and in the absence of β-Lactamase, will lead to the down regulation of &lt;em&gt;mecA&lt;/em&gt; (ibid, 11).  The actual action of MecR1 is to cleave MecI, thereby remove the suppression of &lt;em&gt;mecA&lt;/em&gt; by MecI.  I actually learned something new when reading the wiki on MRSA, but didn't do further research on the subject:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;mecA&lt;/em&gt; is further controlled by two co-repressors, BlaI and BlaR1. &lt;em&gt;blaI&lt;/em&gt;&#xA;  and &lt;em&gt;blaR1&lt;/em&gt; are homologous to &lt;em&gt;mecI&lt;/em&gt; and &lt;em&gt;mecR1&lt;/em&gt;, respectively, and normally&#xA;  function as regulators of &lt;em&gt;blaZ&lt;/em&gt;, which is responsible for penicillin&#xA;  resistance. The DNA sequences bound by MecI and BlaI are&#xA;  identical; therefore, BlaI can also bind the mecA operator to&#xA;  repress transcription of mecA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This represents the general pattern of resistance of MRSA, but there is a rich diversity in the particulars of how each strain manages expression.  Two of the main identifiers are how the &lt;em&gt;mecA&lt;/em&gt; gene complex and &lt;em&gt;ccr&lt;/em&gt; gene complex are configured (carriage).  The other two identifiers are the ISS and whether or not the ISS is repeated in the target chromosome (and how many times it's repeated) (8).  If we just consider the mecA and ccr carriage, then we get a great summary from IWG-SCC (ref 8):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The mec gene complex is composed of mecA, its regulatory genes, and&#xA;  associated insertion sequences. The class A mec gene complex (class A&#xA;  mec) is the prototype complex, which contains mecA, the complete mecR1&#xA;  and mecI regulatory genes upstream of mecA, and the hypervariable&#xA;  region (HVR) and insertion sequence IS431 downstream of mecA. The&#xA;  class B mec gene complex is composed of mecA, a truncated mecR1&#xA;  resulting from the insertion of IS1272 upstream of mecA, and HVR and&#xA;  IS431 downstream of mecA. The class C mec gene complex contains mecA&#xA;  and truncated mecR1 by the insertion of IS431 upstream of mecA and HVR&#xA;  and IS431 downstream of mecA. There are two distinct class C mec gene&#xA;  complexes; in the class C1 mec gene complex, the IS431 upstream of&#xA;  mecA has the same orientation as the IS431 downstream of mecA (next to&#xA;  HVR), while in the class C2 mec gene complex, the orientation of IS431&#xA;  upstream of mecA is reversed. C1 and C2 are regarded as different mec&#xA;  gene complexes since they have likely evolved independently. The class&#xA;  D mec gene complex is composed of mecA and ΔmecR1 but does not carry&#xA;  an insertion sequence downstream of ΔmecR1 (as determined by PCR&#xA;  analysis).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;ccr gene complex.The ccr gene complex is composed of the ccr gene(s)&#xA;  and surrounding open reading frames (ORFs), several of which have&#xA;  unknown functions. Currently, three phylogenetically distinct ccr&#xA;  genes, ccrA, ccrB, and ccrC, have been identified in S. aureus with&#xA;  DNA sequence similarities below 50% (Fig. 2 and 3). The ccrA and ccrB&#xA;  genes that have been identified to date have been classified into four&#xA;  allotypes. In general, ccr genes with nucleotide identities more than&#xA;  85% are assigned to the same allotype, whereas ccr genes that belong&#xA;  to different allotypes show nucleotide identities between 60% and 82%.&#xA;  All ccrC variants identified to date have shown ≥87% similarity; thus,&#xA;  there is only one ccrC allotype. We suggest describing their&#xA;  differences as alleles by using previously used numbers, e.g., ccrC1&#xA;  allele 2 or ccrC1 allele 8.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;All of this is nicely summarized in &lt;a href=&quot;http://aac.asm.org/content/53/12/4961/T1.expansion.html&quot; rel=&quot;nofollow&quot;&gt;their table&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;\begin{array} {|r|r|r|}&#xA;\hline&#xA;SCCmec ~type  &amp;amp;ccr ~gene ~complex  &amp;amp;mec ~gene  ~complex \\&#xA;\hline&#xA;I &amp;amp;1 ~(A1B1) &amp;amp;B \\&#xA;\hline&#xA;II &amp;amp;2 ~(A2B2)&amp;amp;A \\&#xA;\hline&#xA;III &amp;amp;2 ~(A3B3)&amp;amp;A \\&#xA;\hline&#xA;IV &amp;amp;2 ~(A2B2)&amp;amp;B \\&#xA;\hline&#xA;V &amp;amp;5 ~(C)&amp;amp;C2 \\&#xA;\hline&#xA;VI &amp;amp;4 ~(A4B4)&amp;amp;B \\&#xA;\hline&#xA;VII &amp;amp;5 ~(C)&amp;amp;C1 \\&#xA;\hline&#xA;VIII &amp;amp;4 ~(A4B4)&amp;amp;A \\&#xA;\hline&#xA;\end{array}&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;To sum up, methicillin-resistance is caused by the encoding of a novel PBP, PBP2a, along with other factors, which is both genetically stable and transferable via the use of SCCmec.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) Pathak A et al. High prevalence of extended-spectrum β-lactamase-producing pathogens: results of a surveillance study in two hospitals in Ujjain, India. Infect Drug Resist. 2012;5:65-73. doi: 10.2147/IDR.S30043. Epub 2012 Apr 5. [Note that many of the great sentinel studies on drug resistant bacteria occur in the massive hospitals in India].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) B Hartman and A Tomasz. Altered penicillin-binding proteins in methicillin-resistant strains of Staphylococcus aureus. Antimicrob Agents Chemother. 1981 May; 19(5): 726–735. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3) Liu, H. et al. Detection of borderline oxacillin-resistant Staphylococcus aureus and differentiation from methicillin-resistant strains. Eur J Clin Microbiol Infect Dis. 1990 Oct;9(10):717-24.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(4) Tawil N. et al. The differential detection of methicillin-resistant, methicillin-susceptible and borderline oxacillin-resistant Staphylococcus aureus by surface plasmon resonance.  Biosens Bioelectron. 2013 Nov 15;49:334-40. doi: 10.1016/j.bios.2013.05.031. Epub 2013 Jun 4.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(5) Chambers HF. Methicillin-resistant staphylococci. Clin Microbiol Rev. 1988 Apr;1(2):173-86.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(6) Huletsky A et al.  New real-time PCR assay for rapid detection of methicillin-resistant Staphylococcus aureus directly from specimens containing a mixture of staphylococci. J Clin Microbiol. 2004;42(5):1875-84. DOI: 10.1128/JCM.42.5.1875-1884.2004&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(7) Schoenfelder SM et al. Success through diversity - how Staphylococcus epidermidis establishes as a nosocomial pathogen. Int J Med Microbiol. 2010 Aug;300(6):380-6. doi: 10.1016/j.ijmm.2010.04.011. Epub 2010 May 6.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(8) IWG-SCC. Classification of staphylococcal cassette chromosome mec (SCCmec): guidelines for reporting novel SCCmec elements.  Antimicrob Agents Chemother. 2009 Dec;53(12):4961-7. doi: 10.1128/AAC.00579-09. Epub 2009 Aug 31.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(9) Stürenburg E. Rapid detection of methicillin-resistant Staphylococcus aureus directly from clinical samples: methods, effectiveness and cost considerations.  Ger Med Sci. 2009 Jul 6;7:Doc06. doi: 10.3205/000065.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(10) Jensen SO and Lyon BR. &quot;Genetics of antimicrobial resistance in Staphylococcus aureus&quot;. Future Microbiol 4 (5): 565–82. doi:10.2217/fmb.09.30. PMID 19492967&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(11) Oliveira DC, de Lencastre H.  Methicillin-resistance in Staphylococcus aureus is not affected by the overexpression in trans of the mecA gene repressor: a surprising observation. PLoS One. 2011;6(8):e23287. doi: 10.1371/journal.pone.0023287. Epub 2011 Aug 2.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2013-09-01T01:42:27.730" LastActivityDate="2013-09-01T01:42:27.730" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9936" PostTypeId="2" ParentId="9934" CreationDate="2013-08-22T22:24:42.763" Score="3" Body="&lt;p&gt;One might argue that since replication takes place in erythroblasts &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8211117&quot; rel=&quot;nofollow&quot;&gt;(Brown, Anderson, &amp;amp; Young, 1993)&lt;/a&gt;, that it's not actually a respiratory infection either.  Fluids are simply more hospitable to the virus and more transmissible.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the rash, perhaps it is because the P antigen receptor that &lt;a href=&quot;http://en.wikipedia.org/wiki/Erythrovirus&quot; rel=&quot;nofollow&quot;&gt;erythrovirus&lt;/a&gt; uses to infect erythroblasts is also expressed on endothelial cells, like those in skin (and alveolar) capillaries .&lt;/p&gt;&#xA;" OwnerUserId="4228" LastActivityDate="2013-08-22T22:24:42.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9937" PostTypeId="1" CreationDate="2013-08-23T01:05:17.647" Score="2" ViewCount="120" Body="&lt;p&gt;After researching the definition of Assay, I am left with the idea that an assay refers to scientific screening. It could be of chemicals, microbes, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that during drug-discovery assays scientists screen for chemical compounds that may make up an effective drug.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But could someone explain, or provide me with some links that further discuss the process of assays, or how they work or take place during drug discovery?&#xA;Frankly, I'm also still a bit confused about the definition of &quot;Assay&quot; itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="4303" LastActivityDate="2013-08-24T13:33:09.297" Title="Assays during drug discovery" Tags="&lt;molecular-biology&gt;&lt;pharmacology&gt;&lt;assay-development&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9939" PostTypeId="1" CreationDate="2013-08-23T04:24:10.990" Score="3" ViewCount="96" Body="&lt;p&gt;With changes in our solar system, such as planets moving away from the sun and the reduction in solar radiation, which other planets in our solar system could have been, in the past, in a suitable zone for life to originate?&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="3952" LastEditDate="2013-08-23T06:25:27.237" LastActivityDate="2013-08-23T12:19:01.940" Title="In our solar system which other planet could have been in the &quot;habitable zone&quot; in the past?" Tags="&lt;astrobiology&gt;&lt;life&gt;&lt;speculative&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9941" PostTypeId="1" AcceptedAnswerId="10576" CreationDate="2013-08-23T06:29:26.410" Score="4" ViewCount="659" Body="&lt;p&gt;I want to know what makes the balance of the Prolactin abnormal. Is that related to the presence of a nodule near the pituitary?  &lt;/p&gt;&#xA;" OwnerUserId="4306" LastActivityDate="2013-09-25T08:45:05.473" Title="Abnormal Prolactin Level" Tags="&lt;endocrinology&gt;" AnswerCount="3" CommentCount="1" ClosedDate="2013-10-03T21:07:57.543" ContentLicense="CC BY-SA 3.0" />
  <row Id="9942" PostTypeId="2" ParentId="9937" CreationDate="2013-08-23T10:53:03.580" Score="4" Body="&lt;p&gt;An assay may be thought of as &lt;strong&gt;a trial or test&lt;/strong&gt; that is designed to quantitatively determine the amount of a substance in a sample.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus a biochemist might use a protein assay to quantitatively determine the amount of protein in a sample, or a pharmacologist might assay a sample to quantitatively determine the amount of drug present, or an enzymologist might carry out an enzyme assay to determine the amount of enzyme activity in a sample.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's take the case of the enzymologist. I take a liver sample, homogenize it, centrifuge and take the supernatant (soluble) fraction. I want to quantitatively determine the amount of a given enzyme activity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do this by performing a test by (say) adding a sample of the supernatant to a cocktail that 'does something' only if the enzyme of interest is present.  The 'do something' could be a color change, where the cocktail  contains  everything needed for the enzyme to work (all substrates, cofactors etc) and where the enzyme transforms one of the substrates to a coloured product.  I now have an enzyme assay which tells me if the enzyme is present (the trial), which may be made quantitative with reference to the amount of color produced in a given time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I remember things, Sherlock Homes was pretty good at the assays, using them to make trials of his geological samples, but I cannot find the quote.&lt;/p&gt;&#xA;" OwnerUserId="1136" LastActivityDate="2013-08-23T10:53:03.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9943" PostTypeId="2" ParentId="9939" CreationDate="2013-08-23T12:19:01.940" Score="2" Body="&lt;p&gt;This answer is also speculative, but according to the planetary habitable zone models proposed by &lt;a href=&quot;http://www.pik-potsdam.de/~bloh/pdffile/1193.pdf&quot; rel=&quot;nofollow&quot;&gt;&quot;Habitable zone for Earth-like planets in the solar system&quot;&lt;/a&gt; (Franck et al. 2000), a key finding was that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;an Earth-like planet at Martian distance&#xA;  would have been habitable up to about 500 Ma ago while the position of Venus was always outside the habitable zone.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, Mars could have been habitable, but as it is much smaller than Earth, it has a smaller gravitational field presumably a major factor in how it lost much of its atmosphere.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-08-23T12:19:01.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9944" PostTypeId="1" AcceptedAnswerId="10224" CreationDate="2013-08-23T13:39:02.920" Score="0" ViewCount="1830" Body="&lt;p&gt;In a hypothetical scenario, if you cut open a person's skull to show the live brain, and then you slowly start to crush it..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At what point would the person loose consciousness? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would the person be feeling all this time?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would it cause pain?&lt;/p&gt;&#xA;" OwnerUserId="3141" LastActivityDate="2019-02-12T17:32:43.417" Title="What would happen if you slowly crushed a live brain?" Tags="&lt;brain&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9945" PostTypeId="2" ParentId="9868" CreationDate="2013-08-23T13:40:20.457" Score="1" Body="&lt;p&gt;If you mean simply by looking at symptoms, then there is no way, especially if in the context of a medical visit.  You're better off learning the usual suspects and figuring out the patients risk and likelihood for a given infection.  A good example is Hepatitis.  Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) have similar (enough) outward symptoms, but the former is a DNA virus and the latter an RNA virus.  In fact, looking at enWikipedia's &lt;a href=&quot;https://en.wikipedia.org/wiki/Hepatitis#Acute_2&quot; rel=&quot;nofollow&quot;&gt;list of acute causes&lt;/a&gt;, it's all over the place!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you can actually assay for it in the lab, then of course.  &lt;a href=&quot;http://www.virology.ws/2012/07/19/a-dna-virus-with-the-capsid-of-an-rna-virus/&quot; rel=&quot;nofollow&quot;&gt;Although...&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-23T13:40:20.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9946" PostTypeId="2" ParentId="9944" CreationDate="2013-08-23T14:25:02.013" Score="4" Body="&lt;p&gt;It seems there's way too many variables here.  Crushing can occur in a number of ways, leading to different primary damage in different regions first and different people have a different level of system failure thresholds.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Technically, there are no pain sensors on the brain, so you wouldn't feel any pain in the classical sense.  However, it's hard to determine how you would affect the pain interpretation circuits (again, &quot;crushing&quot; can occur a number of different ways); you could inadvertently cause pain signals.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Losing consciousness would also depend on when what region of brian is crushed.  And how it's crushed.  Most of our higher processing regions associated with consciousness are on the very outer surface of our brain.  In one scenario, if it just gets compressed, and damage tend to accumulate in the center of the brain first, it would be a different outcome than if it was some kind of shear crushing force that damaged outer brian first.&lt;/p&gt;&#xA;" OwnerUserId="1853" LastActivityDate="2013-08-23T14:25:02.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9947" PostTypeId="1" AcceptedAnswerId="9948" CreationDate="2013-08-23T21:21:25.770" Score="4" ViewCount="2352" Body="&lt;p&gt;Both the genes for blond hair and ginger hair are recessive, so they need both parents to give the same gene for it to take affect. What happens when a person has 1 copy of a recessive gene and another copy of a different recessive gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They don't have enough of the recessive genes to have either blond or ginger hair, but they don't have a dominant gene to &quot;take charge&quot;?&lt;/p&gt;&#xA;" OwnerUserId="680" LastEditorUserId="4101" LastEditDate="2013-09-05T00:40:12.693" LastActivityDate="2013-09-05T00:40:12.693" Title="What hair color will result in someone inheriting both blond and ginger genes?" Tags="&lt;human-genetics&gt;&lt;genetics&gt;&lt;pigmentation&gt;&lt;hair&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9948" PostTypeId="2" ParentId="9947" CreationDate="2013-08-23T21:45:35.013" Score="8" Body="&lt;p&gt;Hair color is not so simple as that.  Most traits, especially those as complex as color, are controlled by many alleles at many loci.  That's why there are different kinds of brown, blond, and red hair in the population.  There is no &quot;hair color gene.&quot;  A &lt;a href=&quot;http://www.nature.com/ng/journal/v39/n12/full/ng.2007.13.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;fascinating paper&lt;/a&gt; came out a few years ago, identifying &lt;strong&gt;&lt;em&gt;dozens&lt;/em&gt;&lt;/strong&gt; of SNPs playing a role in hair and eye color.  It's a deep, deep rabbit hole that we have only begun to plunge into.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: To summarize, it's &lt;strong&gt;very&lt;/strong&gt; complex.  This paper performed genome-wide association scans looking at two comparisons each for eyes (Blue and green, blue and brown), hair (red or not, blond or brown), and skin (freckles, sun-sensitivity).  The researchers looked in a group of Icelandic and Dutch individuals, which means they only looked at a small portion of human variability (i.e., very few African or Asian genomes, for example).  Still, just from those simple comparisons, their scans:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;revealed 104 associations that reached genome-wide significance, accounted for by 60 distinct SNPs, of which 32 showed genome-wide association with only one pigmentation trait, 12 with two traits and 16 with three traits.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That is to say, they found 60 DNA bases that explained their data.  Roughly half of those only affected one thing (eye, or hair, or skin, but only one), a fifth of those single base changes contributed to two different traits, and a full 25% of those SNPs were related with three traits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's still pretty hefty.  Basically, they found 60 things that can affect hair, eye, or skin color, and some of those can affect some or all of those at the same time.  And they only looked at people from two countries.  Here's a figure where they summarize the seven strongest SNPs; you can see how tricky it can be to explain colors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fPEpc.jpg&quot; alt=&quot;Figure 1&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-08-28T22:50:44.230" LastActivityDate="2013-08-28T22:50:44.230" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="9949" PostTypeId="1" AcceptedAnswerId="9957" CreationDate="2013-08-24T03:21:41.950" Score="1" ViewCount="1930" Body="&lt;p&gt;I read that wherever there is polytomy there is an unresolved pattern of divergence. I don't understand why this is so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When divergence takes place, is it necessary that there will be division into only 2 paths? Can't there be more than 2 paths with all the paths being equally related to each other (that is, no 2 paths being related more to each other than to a third path)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, does a fully-resolved phylogenetic tree have to be dichotomous?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3952" LastEditDate="2013-08-24T08:00:30.817" LastActivityDate="2013-08-24T10:54:07.023" Title="Does a fully-resolved phylogenetic tree have to be dichotomous?" Tags="&lt;evolution&gt;&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9951" PostTypeId="1" CreationDate="2013-08-23T20:56:30.630" Score="1" ViewCount="1418" Body="&lt;h2&gt;Briefing&lt;/h2&gt;&#xA;&lt;p&gt;Some days ago I noted that 3 cookies left on my desk since 3 months ago are still &amp;quot;fresh&amp;quot;, and by that I mean... not spongy like some cookies that get soft after some time outside.&lt;br /&gt;&#xA;However this particular brand of cookies do get spongy, I'm not sure why don't these do!&lt;/p&gt;&#xA;&lt;p&gt;I also noted that there is a cockroaches/flies infestation in a home nearby, so these are getting in my house, but none of those insects dare to eat the cookies.&lt;/p&gt;&#xA;&lt;p&gt;So, I decided to make an experiment inspired in the well known experiment of &lt;a href=&quot;http://www.celestialhealing.net/vegetarian/MD_Burgers.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Watermelon vs McDonalds Burger&lt;/a&gt; where a watermelon decomposes extremely quick, and the burger does not. This article even mentions one that hasn't decomposed after two decades!&lt;br /&gt;&#xA;I understand that watermelon decomposes so fast mainly because of the sugar/water that it contains, but that is another story, let me tell you what I want to do.&lt;/p&gt;&#xA;&lt;h2&gt;Problem&lt;/h2&gt;&#xA;&lt;p&gt;In this experiment the only notable variables taken into account were: Visual appearance (picture), and time.&lt;/p&gt;&#xA;&lt;p&gt;For my cookies I want to do a similar experiment, but I want to know which variables should I consider, so far I only have these in mind, but I want to know what else can be considered for food products:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Date of packaging&lt;/li&gt;&#xA;&lt;li&gt;&amp;quot;Best before&amp;quot; date label&lt;/li&gt;&#xA;&lt;li&gt;Visual appearance (daily pics)&lt;/li&gt;&#xA;&lt;li&gt;Time gone by before going spongy&lt;/li&gt;&#xA;&lt;li&gt;Humidity of room (3 daily measures across the day)&lt;/li&gt;&#xA;&lt;li&gt;Temperature of room (3 daily measures across the day)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;And the samples will be:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Being in a closed room (eg. my room)&lt;/li&gt;&#xA;&lt;li&gt;Being in an open room (eg. dinning room)&lt;/li&gt;&#xA;&lt;li&gt;Exposing to insects directly (eg. roaches, ants, flies)&lt;/li&gt;&#xA;&lt;li&gt;Adding a drop of &lt;em&gt;&amp;quot;morning saliva&amp;quot;&lt;/em&gt; (mainly for the bacteria)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;h3&gt;Question is&lt;/h3&gt;&#xA;&lt;p&gt;In general, what do I need for food experiments? I think these are OK, but maybe I'm overdoing it on some, and maybe I need to consider some other parameters.&lt;br /&gt;&#xA;My experiment's objective is to see if it decomposes, why does it take X time to do so, or why doesn't it decompose at all, if it is safe to eat, or if it shenanigans like McBurgers.&lt;/p&gt;&#xA;" OwnerUserId="4319" OwnerDisplayName="Goodwine" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-08-24T23:36:15.790" Title="What should be evaluated in food decomposition experiment?" Tags="&lt;food&gt;&lt;experimental-design&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9952" PostTypeId="1" AcceptedAnswerId="9959" CreationDate="2013-08-24T03:38:21.163" Score="1" ViewCount="1596" Body="&lt;p&gt;Bacteria use restriction enzymes to cut DNA of bacteriophages. Virus mutates really fast. Won't a point mutation in restriction site render the restriction enzymes of the bacteria useless ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how effective are restriction enzymes in protecting bacteria ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1306" LastEditDate="2013-08-24T15:06:51.110" LastActivityDate="2013-08-24T15:09:42.390" Title="How effective are restriction enzymes in protecting bacteria?" Tags="&lt;bacteriology&gt;&lt;restriction-enzymes&gt;&lt;virus&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9953" PostTypeId="1" CreationDate="2013-08-24T03:46:00.163" Score="3" ViewCount="44" Body="&lt;p&gt;I'm investigating HIV-RT 3KLF and 1LWF trying to find a perfect pose of thymine. Which residues on HIV-RT is Thymine supposed to contact on 3KLF and 1LWF? Where exactly is the nucleotide binding domain on 3KLF and 1LWF?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please provide a journal article as proof. &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2013-08-24T05:14:38.967" LastActivityDate="2013-08-24T09:21:07.760" Title="HIV-RT nucleotide contact residues" Tags="&lt;hiv&gt;&lt;reverse-transcription&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9954" PostTypeId="1" CreationDate="2013-08-24T03:48:43.240" Score="2" ViewCount="244" Body="&lt;p&gt;Scientists have developed statistical tools that distinguish &quot;distant&quot; homologies from coincidental molecular homoplasy in extremely divergent sequences.&#xA;What are these tools?How are they used ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have very less knowledge about statistics.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-08-24T16:21:53.567" LastActivityDate="2013-08-25T09:03:22.157" Title="What are the statistical tools for distinguishing molecular analogy from homology?" Tags="&lt;statistics&gt;&lt;phylogenetics&gt;&lt;homology&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="9955" PostTypeId="1" AcceptedAnswerId="9965" CreationDate="2013-08-24T08:26:38.207" Score="6" ViewCount="4413" Body="&lt;p&gt;Is it true that wasps don't sting if struck by hand while flying? I know of one person who claims to have done this at least 20 times and has never been stung. And out of curiosity (not that I'd want to kill them), what about bees?&lt;/p&gt;&#xA;" OwnerUserId="4310" LastActivityDate="2018-08-02T08:43:14.613" Title="Is it true that bees and wasps don't sting if struck by hand while they are in flight?" Tags="&lt;entomology&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9956" PostTypeId="2" ParentId="8937" CreationDate="2013-08-24T08:43:38.433" Score="3" Body="&lt;p&gt;As far as I know, the main challenges the plants have to face in cold environment are metabolism reduction and membrane fluidity. If the temperature is even lower, they may face freezing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Increasing the metabolism is quite hard, because plants usually are unable to increase their temperature by its own. Plant may produce more pigments in order to absorb more sunlight; grow trichomes and other structures that may generate an air layer which acts as an insulator or simply reduce its metabolism by, for instance, hibernation. The amount of stomata is also related to temperature, and a plant growing in low temperature needs less stomata.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In bacteria sometimes there exist isoforms of many enzymes that are expressed during different conditions, and since plants usually have large genomes with tons of duplications, it's reasonable that some plants may express different genes for the same processes in high and in low temperature. One group of genes that are certainly expressed in cold exposition are membrane desaturases, which introduce unsaturation in the lipids, increasing the fluidity of the membranes. Some plants also protect themselves of freezing by accumulation of some substances, such as glycerol or proline, avoiding the formation of ice inside the cells.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="3615" LastEditDate="2013-08-24T14:49:47.013" LastActivityDate="2013-08-24T14:49:47.013" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9957" PostTypeId="2" ParentId="9949" CreationDate="2013-08-24T09:07:30.023" Score="3" Body="&lt;p&gt;In theory, yes, every tree has to be dichotomous. You can understand a trichotomy in a tree as the summatory of two dichotomies that had happened so close in time that you cannot know wich was first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given a certain population, assume that some individuals colonize a new environment, got reproductively isolated and form a new specie. This is the typical speciation process. In this case, the two species, share a common ancestor. If you go back in time, all the individuals of the new specie will descend of only one individual. The same goes for the original specie. If you go back further, this individuals will share an ancestor, too. This is the conceptual meaning of the dichotomy, but normally it is impossible to determinate wich was exactly the common ancestor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now imagine that the original population formed not one, but two new species. And that this process happened about the same time as the one described before. It is conceptually possible that a set of three brothers were the origin of three different species (wich will be a true trichotomy), but not only it's very unlikely, but it's virtually impossible to prove. Since two close dichotomies are far more probable than a trichotomy, it's assumed that every tree has to be dichotomous, and that a trichotomy is in fact due to lack of resolution.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="4168" LastEditDate="2013-08-24T10:54:07.023" LastActivityDate="2013-08-24T10:54:07.023" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9958" PostTypeId="2" ParentId="9953" CreationDate="2013-08-24T09:21:07.760" Score="2" Body="&lt;p&gt;Thymine must make contact in two places on HIV-RT before being added to nucleotide strand. First contact is made with the fingers region then contact is made at the N-Site. &#xA;&lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0008867&quot; rel=&quot;nofollow noreferrer&quot;&gt;Allosteric Regulation of HIV-1 Reverse Transcriptase by ATP for Nucleotide Selection&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/02aFt.png&quot; alt=&quot;Finger and N-Site&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2013-08-24T09:21:07.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9959" PostTypeId="2" ParentId="9952" CreationDate="2013-08-24T11:22:36.510" Score="3" Body="&lt;p&gt;Note that a given bacterium will probably have more than one restriction enzyme, so the viral genome probably won't ever run out of targets. Even if it did, restriction enzymes could suffer mutations that may change the specificity. When you talk about microorganisms, it's more accurate to think in populations rather than individuals, since the colony would be able to grow again if they have at least one cell. Viruses need a certain density to spread, so even if the bacteria cannot defend against, it may be able to survive simply because the virus run out of hosts before some cells can be infected. This is even easier if the bacteria have some kind of resistance form.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, restriction-modification systems aren't the only defense line against viruses. Many bacteria have a system called CRISPR-CAS that acts like an immune system, inserting RNA fragments into the bacterial chromosome and using them as &quot;antibodies&quot; by hybridization. In this context, you can assume that restriction-modification systems, alongside other nucleases they usually carry, act as an innate immune system, while the CRISPR-CAS would be an analog to acquired immunity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/copis.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diagram of the CRISPR-CAS system. &lt;a href=&quot;http://www.nature.com/nature/journal/v468/n7320/fig_tab/468045a_F1.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, not every environment has the same viral density. Some habitats may be protected against viruses by some means, like the gut microbiota (the carbon intake goes through the stomach acid and tons of hydrolases, which is very destructive for viruses); while some others may have an incredible amount due to lack of biodiversity and high cell densities (this is the case of most extreme environments). &lt;em&gt;E. coli&lt;/em&gt;, as a gut bacteria, would probably have enough with only restriction-modification enzymes (In fact, while it have a CRISPR system, it seems to be repressed), while many others will need more defenses.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="1306" LastEditDate="2013-08-24T15:09:42.390" LastActivityDate="2013-08-24T15:09:42.390" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9960" PostTypeId="2" ParentId="9951" CreationDate="2013-08-24T11:36:06.297" Score="1" Body="&lt;p&gt;You could weigh the cookies in a time course to see how quickly the cookies are degraded. Also, you could take some samples and make cultures in Petri dishes to see if there are differences in the microbiota associated with each one. In this line, maybe you'd want to sterilize the samples by some means, just to ensure they have the same microbial conditions. You could also measure the porosity of the samples by pacing them in water and measure how much water it can absorb, or something like that. I assume you do not have an HPLC engine, but you could also make extracts and see how the spectra varies over time. &lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="107" LastEditDate="2013-08-24T23:36:15.790" LastActivityDate="2013-08-24T23:36:15.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9961" PostTypeId="2" ParentId="9937" CreationDate="2013-08-24T11:49:13.910" Score="4" Body="&lt;p&gt;I'm a pharmacy student and I can try to explain how they do to find new drugs. &#xA;In fact, there are many diferent ways to do so, it depends of what kind of new drug you are searching for. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes you're working on a disease which the pathological molecular mechanism of action are well-known and where many drugs are already effective. In this case, the 'assay' may just be about improving a well-known molecule by adding or changing a small part of the molecule (replace a ketone by an alcohol for exemple). Always in this case, you know on what molecular receptor you have to act, its 3D structure, its composition, its location in the human body and maybe the most important (but you don't know this every time and in this case, you could begin by this point) how and what part of your drug acts on any part of the receptor. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then you have molecular libraries where you can search your new drug. They are alimented by different ways: someone who found a new chemical reaction that can add a chemical function where you could not before and generate several new compounds by applying his new method. All this compounds can be given to a national library where access is possible. You can also find intermediate compounds of reaction. This happens in public research because private laboratories keep their discoveries secret. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes you're working on a disease where the usual drug doesn't match really with the receptor, in this case, you have 3D tools that can modelize molecule and receptor in order to quantify how they match. This is achieved on many many molecule from this library and these methods generate few drugs that match the best. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then you work on these drugs to improve them and make them compatible whith digestive barriers if you want an oral drug, or with the galenic form you need. This point is about improving the matching with the receptor by changing few parts of the molecule. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact when you know on which molecule you want to act, it all start with IT tools that mesure interactions between this molecule you want to act on and other random molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you don't know molecular mechanisms of your disease, you have to find it before, otherwise you're gonna work double-blind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a few part of the reality, I hope that answered the last part of your question. &lt;/p&gt;&#xA;" OwnerUserId="4313" LastEditorUserId="806" LastEditDate="2013-08-24T13:33:09.297" LastActivityDate="2013-08-24T13:33:09.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9962" PostTypeId="2" ParentId="9750" CreationDate="2013-08-24T12:19:22.230" Score="2" Body="&lt;p&gt;&lt;em&gt;Mimosa&lt;/em&gt; leaves have mechanoreceptor cells which sense the mechanical stress through proteins called mechanoreceptors (they are similar to the ones responsible for sense of touch in animals). When stimulated the mechanoreceptors cause ion channels to open leading to depolarization. This generates an action potential (AP; like neurons) which in turn activates the motor cell (&lt;a href=&quot;http://dx.doi.org/10.1007/s00442-013-2873-7&quot; rel=&quot;nofollow&quot;&gt;Visnovitz et al., 2007&lt;/a&gt;). Motor cells cause leaf movements by change in their interior turgor pressure (similar to opening and closing of stomata). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Repolarization (like in neuronal AP) takes time and &lt;em&gt;Mimosa&lt;/em&gt; would not respond to stimuli that are too frequent. The time required for the turgor pressure to relax would be an additional factor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am no plant biologist but if I compare this situation with that in neurons, I can speculate that long term non-responsiveness similar to LTD may happen because of down-regulation of mechanoreceptors. It has actually been shown that &lt;em&gt;Mimosa&lt;/em&gt; does actually become insensitive to a persistent stimulus such as a continual water drop and moreover exhibits a long-term &quot;memory&quot; of this non-responsiveness (&lt;a href=&quot;http://dx.doi.org/10.1007/s00442-013-2873-7&quot; rel=&quot;nofollow&quot;&gt;Gagliano et al., 2014&lt;/a&gt;). However, the exact molecular mechanism has not been elucidated. Again, there would be thresholds (on amplitude and frequency) for the signal to elicit these kind of changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;&lt;sub&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Visnovitz T, Világi I, Varró P, Kristóf Z. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2634336/&quot; rel=&quot;nofollow&quot;&gt;Mechanoreceptor Cells on the Tertiary Pulvini of Mimosa pudica L.&lt;/a&gt; &lt;em&gt;Plant Signaling &amp;amp; Behavior&lt;/em&gt;. 2007;2(6):462-466. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Gagliano, Monica, et al. &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2634336/&quot; rel=&quot;nofollow&quot;&gt;Experience teaches plants to learn faster and forget slower in environments where it matters.&lt;/a&gt;&quot; &lt;em&gt;Oecologia&lt;/em&gt; 175.1 (2014): 63-72.&lt;/sub&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-03-17T06:28:38.260" LastActivityDate="2016-03-17T06:28:38.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9963" PostTypeId="2" ParentId="8449" CreationDate="2013-08-24T12:59:14.587" Score="1" Body="&lt;p&gt;Well.. This is a tough question (Something that has bugged me for years and still doing so). I don't fully agree that replicative potential came first. This is just my opinion based on some reasoning and I dont really have any reference. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you compare a nucleotide and a protein, the likelihood of formation of protein is much higher because:-&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Amino acids are simpler molecules and simplest of them did appear in the famous Urey-Miller experiment. Nucleotides on the other hand are much more complex&lt;/li&gt;&#xA;&lt;li&gt;Peptide/amide bond formation is a well known phenomenon even in non-biological chemistries whereas Phosporic esters cant be called common compounds.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In my opinion function evolved first and then its codification. Initially the cell division must have been just like a huge drop dividing into two. I would like to differ from mgkrebbs on this. Lipids are simple molecules and they can spontaneously form compartments such as miscelles based on simple principles of thermodynamics. If miscelles get huge they can divide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I still cannot understand whether it is chemical &lt;em&gt;reproduction&lt;/em&gt; that came fist or sustained multispecies chemical reactions. I tend to believe the second with relatively more confidence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The popular RNA world hypothesis is justified by certain observations and fits nicely in the Darwinian scheme of biology that we are so used to believe in all the time. But it doesn't answer the previously mentioned thermodynamic perspective. Also I fail to understand why an ancient RNA would code a protein. What advantage would it have to code a protein in the first place. So to conclude I don't have a doubt that proteins came first. The initial soup and the basic functionalities were provided by them. Then nucleotides evolved parallely and they became catalysts of protein synthesis. So the reactants came before the catalysts and the better catalyst got &lt;em&gt;selected&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I again iterate that this is just my opinion which you may consider pondering over along with the answers that others have provided. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-08-25T08:30:50.600" LastActivityDate="2013-08-25T08:30:50.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9964" PostTypeId="2" ParentId="9896" CreationDate="2013-08-24T13:48:04.290" Score="2" Body="&lt;p&gt;This is basically a trick question and a bit of a cheap shot. All of the reasons cited boil down to &quot;bats huddle to conserve heat&quot;, they are basically the same, single, reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order for bats to feed, they need to move, fly out of their cave or wherever they happen to sleep and go forth and look for food. Therefore, they will not be able to huddle while feeding because they will be flying around trying to find fruit or donkeys or whatever each species feeds on. Unless they can figure out a way to huddle while flying, they will not be able to huddle while feeding and so number 5 is wrong.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-08-24T13:48:04.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9965" PostTypeId="2" ParentId="9955" CreationDate="2013-08-24T14:17:11.087" Score="1" Body="&lt;p&gt;I think what your friend advised is incorrect, or they are very lucky.  According to &lt;a href=&quot;http://www.ipm.ucdavis.edu/PMG/PESTNOTES/pn7449.html&quot; rel=&quot;nofollow&quot;&gt;&quot;Bee and Wasp Stings&quot;&lt;/a&gt; from the University of California Davis, they specifically state:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Unless someone accidentally collides quite hard with or swats at a bee or wasp, it is not likely to sting.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also, if you swat at some species, they are likely to become agitated, making the situation potentially far worse.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="4101" LastEditDate="2013-08-24T15:26:57.353" LastActivityDate="2013-08-24T15:26:57.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9966" PostTypeId="2" ParentId="8272" CreationDate="2013-08-24T14:32:47.280" Score="7" Body="&lt;p&gt;One other important event that can kill the person is that the atmospheric pressure on Mars surface is less than one percent that of earth at ground level. Suddden exposure to extremely low atmospheric pressure will immediately release dissloved gases within blood and and other body fluids as bubbles and the individual is likely to get a very severe form of Decompression sickness as in divers coming up too fast. The person is likely to lose conciousness and die within a couple of meters after leaving the shelter.&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="4216" LastEditDate="2013-08-24T18:39:02.930" LastActivityDate="2013-08-24T18:39:02.930" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="9967" PostTypeId="2" ParentId="9955" CreationDate="2013-08-24T15:03:44.237" Score="6" Body="&lt;p&gt;I can confirm that I have often enough slapped a wasp or bee in flight without being stung. The reason is probably pure chance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is kind of like asking if a human can bite when slapped. If I come up to you and slap you, fast and hard, you will probably not be able to bite my hand because of surprise and the blinding speed with which I hit you. If, however, you happen to be talking to me and have your mouth open at the time, you might be able to pull off a quick bite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a similar vein, if I happen to swap a wasp (no anagram intended) and hit it on the sting, I will probably be stung. If I hit it on the side and move fast enough, I doubt it will have the time to reorient itself and sting me before my hand is gone.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2015-07-13T11:52:37.990" LastActivityDate="2015-07-13T11:52:37.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9968" PostTypeId="2" ParentId="9954" CreationDate="2013-08-24T15:41:39.470" Score="2" Body="&lt;p&gt;There are lots of statistical algorithms that allow you to evaluate the similarity between two given sequences. For instance, blast allows you a rapid comparison between your sequence and other sequences in a database; while Clustal, with a similar functioning, allows you to compare a set of given sequences between them. They are very simple algorithms, but very fast and useful, and basically they score an alignment by counting how many positions between the two entries are the same. Other algorithms function in a similar fashion, but they use hidden Markov models to compare your sequence with a consensual sequence in order to identify motifs and domains. I'm sure there are even more advanced programs, but I don't know them and don't think it's the point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Homology usually refers to things that share the same origin, while analogy refers to things that do the same function but their origin isn't shared. While the algorithms I've described you only search for similarity or identity, you must notice a few things:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) Homology of function doesn't necessarily correlate with high similarity. Two proteins can have the same global structure and their sequences be completely different. The three-dimensional structure is the same, and probably there'll be key amino acids that will remain very similar. This is very obvious in many proteases, which share only the three catalytic amino acids (catalytic triad) between them, and vary enormously even between strains of the same species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) Protein domains vary in size from a few dozen to a few hundred amino acids. The odds that exactly the same sequence evolves in two separate moments are very low. Especially in highly conserved domains, which usually carry out key functions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c) Proteins usually have a modular structure with more than one domain. New proteins often evolve by switching and combining domains by translocation. So, even if the same domain has evolved in two separate times, the association between these two &quot;twin&quot; domains with other domains will probably reveal its unusual origin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's why usually the term molecular analogy is not used, and if so, it would refer for example to structurally different domains that catalyze the same reaction or that share the same structure. Note that even if the analogy as you describe isn't impossible by itself, the software won't be able to differentiate them unless the sequence appears associated with others. Furthermore, the origin of many of the current protein families is so far in the past that it's quite impossible to reconstruct it, even more so with the high diversity in prokaryotes.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="1306" LastEditDate="2013-08-24T15:53:20.830" LastActivityDate="2013-08-24T15:53:20.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9970" PostTypeId="1" AcceptedAnswerId="9977" CreationDate="2013-08-24T18:48:16.433" Score="5" ViewCount="8024" Body="&lt;p&gt;If a person positions him/herself upside down and swallows food, will it reach the stomach against gravity? If so how?&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="16866" LastEditDate="2017-04-03T17:54:09.107" LastActivityDate="2020-01-23T04:05:46.157" Title="Can food swallowed when a person is upside down reach the stomach?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;food&gt;&lt;human-physiology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9973" PostTypeId="1" CreationDate="2013-08-24T19:22:52.773" Score="2" ViewCount="53" Body="&lt;p&gt;This sparks HCV immediately in my mind.&#xA;However, there may be other possibilities too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What can you deduce from elevated transaminases if you only know that the healthy adult patient received blood transfusion in Africa?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2013-08-24T19:22:52.773" Title="Elevated transaminases after blood transfusion?" Tags="&lt;microbiology&gt;&lt;homework&gt;&lt;transfusion&gt;&lt;hepatitis&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9976" PostTypeId="1" AcceptedAnswerId="9978" CreationDate="2013-08-24T20:10:08.893" Score="15" ViewCount="276" Body="&lt;p&gt;It is fairly common knowledge that the lens in its normal state absorbs ultraviolet (UV) radiation.  An interesting notion has come up from time to time in my reading that suggests there are a small number of conditions that result in humans being able to 'see' ultraviolet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What conditions may cause this?  Also, those affected, would they 'see' it has a different shade of violet?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="4101" LastEditDate="2013-10-16T18:01:14.990" LastActivityDate="2013-10-16T18:01:14.990" Title="Are there specific conditions that allow humans to see ultraviolet wavelengths" Tags="&lt;eyes&gt;&lt;vision&gt;&lt;light&gt;&lt;uv&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9977" PostTypeId="2" ParentId="9970" CreationDate="2013-08-24T20:21:45.740" Score="8" Body="&lt;p&gt;The eminent @JanDvorak has basically provided the full answer, but yes, it is possible.  You can easily try this yourself, just lean off a bed and swallow something (small) and see what happens.  &lt;a href=&quot;https://en.wikipedia.org/wiki/Peristalsis&quot; rel=&quot;noreferrer&quot;&gt;Peristalsis&lt;/a&gt; in the esophagus is responsible for moving food down into the stomach.  The big proof of this is that astronauts can &lt;a href=&quot;https://en.wikipedia.org/wiki/Space_food&quot; rel=&quot;noreferrer&quot;&gt;eat when in space&lt;/a&gt;, when weightless.  Their food is moved into the stomach just fine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's easier to do it upright (&lt;code&gt;peristalsis + gravity&lt;/code&gt;) as opposed to upside down (&lt;code&gt;peristalsis - gravity&lt;/code&gt;) but definitely quite possible.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-24T20:21:45.740" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9978" PostTypeId="2" ParentId="9976" CreationDate="2013-08-24T20:28:54.550" Score="14" Body="&lt;p&gt;You will be interested in &lt;a href=&quot;https://en.wikipedia.org/wiki/Aphakia&quot;&gt;Aphakia&lt;/a&gt;, which is the lack of an eye lens usually through surgery but sometimes from birth.  These individuals supposedly see UV as a whitish-blue or whitish-violet:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This appears to be because the three types of colour receptor (red, green and blue) have similar sensitivity to ultraviolet, so it comes out as a mixture of all three - basically white, but slightly blue because the blue sensors are somewhat better at picking up UV.&lt;a href=&quot;http://www.theguardian.com/science/2002/may/30/medicalscience.research&quot;&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-24T20:28:54.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9979" PostTypeId="1" CreationDate="2013-08-24T22:11:09.050" Score="8" ViewCount="160" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.livescience.com/28036-neanderthals-facts-about-our-extinct-human-relatives.html&quot; rel=&quot;nofollow&quot;&gt;&quot;Neanderthals: Facts About Our Extinct Human Relatives&quot;&lt;/a&gt; (Szalay, 2013), Neanderthals dominated Europe during the last Ice Age, but may have died out before the arrival of Homo Sapiens (according to research detailed in &lt;a href=&quot;http://www.pnas.org/content/110/8/2781&quot; rel=&quot;nofollow&quot;&gt;&quot;Radiocarbon dating casts doubt on the late chronology of the Middle to Upper Palaeolithic transition in southern Iberia&quot;&lt;/a&gt; (Wood et al. 2012).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a number of theories floating around in the literature - everything from inability to adapt to climate change  to dietary deficiencies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does the latest research suggest as the cause of the Neanderthal extinction?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;(refereed papers would be appreciated)&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="4150" LastEditDate="2013-09-10T01:31:30.953" LastActivityDate="2013-09-10T01:31:30.953" Title="What does the evidence suggest about how Neanderthals became extinct?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;extinction&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9980" PostTypeId="2" ParentId="1581" CreationDate="2013-08-25T02:39:16.700" Score="18" Body="&lt;p&gt;While fish tend to move from side to side (lateral undulation) for which a vertical tail makes sense, the land ancestors of marine mammals had their limbs under them and so their spines were already adapted to up and down movement (dorsoventral undulation). When these animals moved to marine environments, they continued up and down movement in their swimming, for which a horizontal tail makes sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(&lt;a href=&quot;http://en.wikipedia.org/wiki/Fish_fin#Evolution_of_fins&quot;&gt;The wikipedia article on fins&lt;/a&gt; gives some more detail, and links to &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evograms_03&quot;&gt;this webpage on Berkeley.edu&lt;/a&gt;. A paper by &lt;a href=&quot;http://www.evolbiol.ru/large_files/whales.pdf&quot;&gt;Thewissen et al.&lt;/a&gt; suggests that for cetaceans, dorsoventral undulation as a swimming strategy came first, and the horizontal tail evolved later.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;More detail:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a third example beyond fishes and marine mammals, the icthyosaurs and other aquatic reptiles developed vertical tails, even though like marine mammals they evolved from four-footed land animals. This may be because the legs/spines/gaits of land &lt;em&gt;reptiles&lt;/em&gt; differ from those of land &lt;em&gt;mammals&lt;/em&gt;, so that the earliest icthyosaurs swam with lateral undulation, &lt;a href=&quot;http://www.ucmp.berkeley.edu/people/motani/ichthyo/vert.html&quot;&gt;as reflected in their spinal modifications&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://laelaps.wordpress.com/2007/08/24/everyone-back-in-the-pool-from-artiodactyl-to-cetacean/&quot;&gt;This blog post&lt;/a&gt; by Brian Switek gives a really superb run-down on the issue, with figures and citations. I'll quote this part which deals with the dorsoventral undulation theory:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...mammals and their relatives were carrying their legs underneath their bodies and not out to the sides since the late Permian, and so the motion of their spine adapted to move in an up-and-down motion rather than side-to-side like many living reptiles and amphibians. Thus Pakicetus[the pre-cetacean land mammal] would not have evolved a tail for side-to-side motion like icthyosaurs or sharks because they would have had to entirely change the way their spinal column was set up first.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Switek goes on to to talk about exceptions in some marine mammals:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At this point some of you might raise the point that living pinnipeds like seals and sea lions move in a side-to-side motion underwater. That may be true on a superficial level, but pinnipeds primarily use their modified limbs (hindlimbs in seals and forelimbs in sea lions) to move through the water; they aren’t relying on propulsion from a large fluke or caudal fin providing most of the propulsion with the front fins/limbs providing lift and allowing for change in direction. &lt;em&gt;This diversity of strategies in living marine mammals suggests differing situations encountered by differing ancestors with their own suites of characteristics, but in the case of whales it seems that their ancestors were best fitted to move by undulating their spinal column and using their limbs to provide some extra propulsion/direction.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-11-05T21:42:59.257" LastActivityDate="2014-11-05T21:42:59.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9981" PostTypeId="2" ParentId="5063" CreationDate="2013-08-25T02:53:49.193" Score="3" Body="&lt;p&gt;This is a part answer to your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;three-factor anatomical model of human idea generation and creative drive&lt;/strong&gt; presented in &lt;a href=&quot;http://industrial.design.iastate.edu/232/files/2013/01/nihms68453.pdf&quot; rel=&quot;nofollow&quot;&gt;&quot;frontotemporal and dopaminergic control of idea generation and creative drive&quot;&lt;/a&gt; (Flaherty, 2005) focus on interactions in and between the temporal lobes, frontal lobes, and the limbic system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Increase in the quantity of idea generation, at times at the expense of quality is associated with changes in the &lt;strong&gt;temporal lobe&lt;/strong&gt;.  Conversely, &lt;strong&gt;frontal lobe&lt;/strong&gt; deficits may decrease the quantity of ideas generated, largely due to judgements of an idea's worth.  The authors assert that interaction between the two mainly affects verbal and some non-verbal creativity&#xA;.&#xA;Further,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mesolimbic dopamine influences novelty seeking and creative drive. Dopamine agonists and&#xA;  antagonists have opposite effects on goal-directed behavior and hallucinations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors emphasise that creative drive is not the same as skill, and that the 3-factor model is an alternative to the left and right brain hemisphere skills based model.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-08-25T02:53:49.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9982" PostTypeId="2" ParentId="9667" CreationDate="2013-08-25T04:30:39.013" Score="2" Body="&lt;p&gt;This is a part answer to your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.pnas.org/content/103/28/10775.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;&quot;Arithmetic processing in the brain shaped by cultures&quot;&lt;/a&gt; (Tang, 2006), the parts of the brain that are activated while doing arithmetic is to an extent, governed by culture, in the article, the authors assert:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Using&#xA;  functional MRI, we demonstrated a differential cortical representation&#xA;  of numbers between native Chinese and English speakers.&#xA;  Contrasting to native English speakers, who largely employ a&#xA;  language process that relies on the left perisylvian cortices for&#xA;  mental calculation such as a simple addition task, native Chinese&#xA;  speakers, instead, engage a visuo-premotor association network&#xA;  for the same task. Whereas in both groups the inferior parietal&#xA;  cortex was activated by a task for numerical quantity comparison.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(The article also includes fMRI imagery examples).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also seems that recognition of simple arithmetic starts at an early age, according to &lt;a href=&quot;http://icds.uoregon.edu/wp-content/uploads/2011/08/Berger-PNAS-final.pdf&quot; rel=&quot;nofollow&quot;&gt;&quot;Infant brains detect arithmetic errors&quot;&lt;/a&gt; (Berger et al. 2006).&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-08-25T04:30:39.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9983" PostTypeId="2" ParentId="7651" CreationDate="2013-08-25T08:19:06.247" Score="1" Body="&lt;p&gt;If by 'fishery' you mean &quot;amount of fish &lt;em&gt;caught&lt;/em&gt;&quot;, the answer is a qualified no. Sweden's catch has been stable or perhaps slightly increasing since a low in 2005, but the catch is still much lower than a decade ago (&lt;a href=&quot;http://www.scb.se/Pages/Product____9734.aspx?Produktkod=JO1101&amp;amp;displaypublications=true&quot; rel=&quot;nofollow noreferrer&quot;&gt;Statistics Sweden&lt;/a&gt;). This is presumably due in large part to the quotas set on Total Allowable Catch for various sea regions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If by 'fishery' you mean &quot;amount of fish in the sea&quot;, the answer is a qualified yes. Most Swedish cod catch (&gt;90%) comes from the Baltic, where stocks have been recovering since 2006 after steep declines in the eighties (ICES &lt;a href=&quot;http://www.ices.dk/sites/pub/Publication%20Reports/Advice/2013/2013/cod-2532_201304112231.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;full report&lt;/a&gt; and &lt;a href=&quot;http://www.ices.dk/sites/pub/Publication%20Reports/Advice/2013/Popular/cod-2532_popular.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;executive summary&lt;/a&gt; for Eastern Baltic). Presumably, this recovery is also due in large part to the quotas set on Total Allowable Catch, i.e. to the reduction in cod mortality due to fishing. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/E8s4V.jpg&quot; alt=&quot;figure by me, data from Statistics Sweden[1] and ICES[2&quot;&gt;&#xA;&lt;em&gt;Sweden's cod catch for all regions, and the ICES estimated Spawning Stock Biomass of cod in the Eastern Baltic. Both are in thousands of metric tons, but note that the scales differ by a factor of ten)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;No idea how this is affecting import/export, although Statistics Sweden might have that data. One biology related possibility is that Eastern Baltic stocks (presumably accessed more by Sweden) are doing better than North Sea stocks (presumably accessed more by Norway), but that's just a guess, you'd have to check the data.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-08-25T08:19:06.247" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9984" PostTypeId="2" ParentId="9954" CreationDate="2013-08-25T09:03:22.157" Score="1" Body="&lt;p&gt;As Miguel puts it, homology means similarity of origin and therefore of some structural properties. Whereas analogy means similarity of function (like insect wings and bird wings provide the same function of flying).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A homoplastic trait may still be homologous because same set of genes may be involved, whose DNA/protein sequence may be homologous. &#xA;Just thought of an example that was illustrated in PhD comics some days back- about dogs and hyenas- they both have snouts and look similar but hyenas are more related to cats. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is an example of convergent evolution but the genes giving rise to snout- the structural proteins the homeotic genes, growth signaling molecules or whatever is responsible for this trait is present in both animals. This trait has a good deal of structural homology. Now, the rigor with which we say that two traits are similar is another factor. It depends on how many variables you use to define a trait. For e.g. a snout shape can be defined using- snout dimensions, angles, bone morphology, texture etc. The more variables you add the more rigorous it becomes. Sometimes the extra variables don't give any extra info and you may choose to remove these variables (this is precisely what is done in a statistical method called Principal Component Analysis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If phylogentic study is based on these common convergent characters (snout) then we'll end up predicting that dogs and hyenas are related which is erroneous. Therefore multiple gene families are to be considered while doing phylogenetic analysis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we go back to butterfly-bird example; both have wings that are used for flying but they are structurally very different- therefore the genes responsible might also be different. &#xA;Since the structure itself is different you wont be able to compare the two traits using structural variables. You need variables that define function. For e.g. Thrust generated, fluttering speed, angle of attack etc. (of course they need to be normalized with respect to body size).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you have the set of variables (random variables in statistical terms) you can apply statistical tests to compare them.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-08-25T09:03:22.157" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="9986" PostTypeId="1" AcceptedAnswerId="9987" CreationDate="2013-08-25T14:18:44.627" Score="4" ViewCount="3375" Body="&lt;p&gt;I'd like to know what kind of power human body needs to maintain life, in still state (average daily power consumption of an average man is also of interest). In terms of watts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've only managed to find one figure - 1700 kcal per day without physical activity. That converts to 80 watts, which seems (intuitively) a bit low, so I wonder if it's the right figure or not.&lt;/p&gt;&#xA;" OwnerUserId="3228" LastActivityDate="2020-01-13T19:11:11.713" Title="Human body power consumption in still state" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9987" PostTypeId="2" ParentId="9986" CreationDate="2013-08-25T14:56:19.637" Score="6" Body="&lt;p&gt;You're basically correct.  I don't know if you've found the Wikipedia article on &lt;a href=&quot;https://en.wikipedia.org/wiki/Basal_metabolic_rate&quot; rel=&quot;noreferrer&quot;&gt;Basal Metabolic Rate&lt;/a&gt; but it's got everything you need, including a bunch of formulas you can use to figure out an average value for a given body type.  There are also many online calculators, such as &lt;a href=&quot;http://www-users.med.cornell.edu/~spon/picu/calc/beecalc.htm&quot; rel=&quot;noreferrer&quot;&gt;this one&lt;/a&gt;.  You can easily figure out averages, which I think is what you want, but between two individuals the number can change quite a bit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does 80 watts sound so low?  This is more of a physics.se answer, but &lt;strong&gt;Watts&lt;/strong&gt; are a unit of &lt;strong&gt;power&lt;/strong&gt; which mean they measure energy use over time; &lt;strong&gt;W=J/s&lt;/strong&gt;, or Joules per second.  Every second.  Have you ever touched a 75 watt lightbulb?  They're hot as hell.  If your human does &lt;strong&gt;&lt;em&gt;nothing&lt;/em&gt;&lt;/strong&gt; all day, s/he will be like an inefficient incandescent lightbulb on for a full 24 hours.  Maybe that seems low but electricity is relatively cheap these days.  To use another classic physics experiment, 1700kcal=7000kJ=a lot of ice turned into steam.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No wonder my father always made me turn the light off in the bathroom...&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-25T14:56:19.637" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9988" PostTypeId="1" CreationDate="2013-08-25T15:43:42.333" Score="1" ViewCount="484" Body="&lt;ol&gt;&#xA;&lt;li&gt;Is animal fat harmful to our body or is it harmful if the amount eaten exceeds a certain amount?&lt;/li&gt;&#xA;&lt;li&gt;I have heard fat is more concentrated than protein. If I am correct then we can get more energy from fat. Then why is fat not desirable?&lt;/li&gt;&#xA;&lt;li&gt;Our ancestors used all the parts from their hunt, even the fat. How did it work for them?&lt;/li&gt;&#xA;&lt;li&gt;Would eating fat be beneficial for an athlete? (May be for different purposes: power, endurance or building muscle)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1870" LastEditorUserId="1306" LastEditDate="2013-08-26T02:29:16.903" LastActivityDate="2013-08-26T02:29:16.903" Title="Does animal fat and meat contributes differently to our body?" Tags="&lt;biochemistry&gt;&lt;food&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9989" PostTypeId="1" AcceptedAnswerId="9997" CreationDate="2013-08-25T16:04:20.670" Score="1" ViewCount="192" Body="&lt;p&gt;A 5-year-old boy returns from summer camp with several minor cuts and abrasions on legs. He has fever&#xA;and extensive cellulitis, subcutaneous tissue and muscles are involved. Necrotic tissues were surgically&#xA;reomoved and broad spectrum antibiotics were used. Which of the following microorganisms usually&#xA;causes necrotizing fasciitis?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;a. bacillus cereus&lt;/li&gt;&#xA;&lt;li&gt;b. clostridium tetani&lt;/li&gt;&#xA;&lt;li&gt;c. A-group streptococci&lt;/li&gt;&#xA;&lt;li&gt;d. Micrococcus sp.&lt;/li&gt;&#xA;&lt;li&gt;e. Staphylococcus aureus&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It is so severe that I started think that Staphylococcus aureus is possible.&#xA;My previous answer was A-group streptococci, but I disagree with it now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is causing the case?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2013-08-25T18:01:43.580" Title="Is this necrotizing skin infection caused by Staphylococcus aureus?" Tags="&lt;microbiology&gt;&lt;homework&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9990" PostTypeId="1" AcceptedAnswerId="10000" CreationDate="2013-08-25T16:44:04.383" Score="12" ViewCount="14202" Body="&lt;p&gt;Is there any reason why AUG is the initiation codon?&#xA;Can’t translation start with different codons?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="22057" LastEditDate="2019-04-02T16:24:37.390" LastActivityDate="2019-04-08T13:10:08.687" Title="Why is AUG the initiation codon?" Tags="&lt;evolution&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;translation&gt;&lt;mrna&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="9991" PostTypeId="1" AcceptedAnswerId="10016" CreationDate="2013-08-25T16:49:07.140" Score="5" ViewCount="164" Body="&lt;p&gt;The eukaryote and prokaryote mechanism for translation is slightly different. Is there any advantage of the eukaryote translation mechanism ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit : I specifically want to know why eukaryotic ribosome first attaches to tRNA and then to mRNA but prokaryotic ribosome can do this in either order. Is there any advantage of the former ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="948" LastEditDate="2013-10-14T17:59:23.587" LastActivityDate="2013-10-14T17:59:23.587" Title="What is the advantage of the way eukaryotes initiate translation?" Tags="&lt;proteins&gt;&lt;translation&gt;&lt;mrna&gt;&lt;ribosome&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9992" PostTypeId="1" AcceptedAnswerId="10250" CreationDate="2013-08-25T16:59:37.983" Score="2" ViewCount="267" Body="&lt;p&gt;The anticodon of an incoming tRNA base pairs with the complementary mRNA codon in the A site.Hydrolysis of GTP increases the efficiency and accuracy of this step.&#xA;How does GTP do so ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-09-04T07:16:35.260" Title="How does GTP help in the step of codon recognition?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;rna&gt;&lt;ribosome&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9993" PostTypeId="1" AcceptedAnswerId="10001" CreationDate="2013-08-25T17:03:21.847" Score="25" ViewCount="6606" Body="&lt;p&gt;We all know CO₂ as a waste product of metabolism . Does CO₂ have any helpful role , apart from having a role in pH of blood ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3340" LastEditDate="2014-11-11T07:26:21.693" LastActivityDate="2015-03-26T22:06:02.063" Title="Is there any use of CO₂ in human body?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;metabolism&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="9994" PostTypeId="2" ParentId="9989" CreationDate="2013-08-25T17:14:36.147" Score="1" Body="&lt;p&gt;No. It is caused by A-group streptococci. Source Murray and empirical evidence.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2013-08-25T17:14:36.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9995" PostTypeId="2" ParentId="9916" CreationDate="2013-08-25T17:37:55.517" Score="0" Body="&lt;p&gt;Acquisition of a new PBP (eg methicillin resistance in staphylococcus aureus), source Murray.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I think the answer is C: change in configuration (mutation) of PBP, which can interpreted as acquisition of a new PBP.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2013-08-28T08:02:41.910" LastActivityDate="2013-08-28T08:02:41.910" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9996" PostTypeId="2" ParentId="9990" CreationDate="2013-08-25T17:50:25.027" Score="3" Body="&lt;p&gt;First of all, it is the &lt;em&gt;coding sequence&lt;/em&gt;, the open reading frame (ORF), and not the gene that starts with an AUG. Also, there are actually quite a few ORFs that start with different initiation codons, they are just the exceptions rather than the norm. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the need, you can think of START and STOP codons as punctuation. The AUG is read like the first (capital) letter of a sentence (if you will allow me to stretch the definition of punctuation a little). Read up on the process of &lt;a href=&quot;http://en.wikipedia.org/wiki/Translation_%28biology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;translation&lt;/a&gt;, the ribosome  will attach to the mRNA molecule which includes &lt;a href=&quot;http://en.wikipedia.org/wiki/Untranslated_region&quot; rel=&quot;nofollow noreferrer&quot;&gt;UTRs&lt;/a&gt;, it uses the AUG codon as an indication that it should now start translating. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;UTRs are the untranslated regions and often contain regulatory sequences that can control translation. However, these should not be in the final protein product so the cellular machinery needs a way of knowing where the UTR ends and the coding sequence begins. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2019-03-23T23:55:32.487" LastActivityDate="2019-03-23T23:55:32.487" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="9997" PostTypeId="2" ParentId="9989" CreationDate="2013-08-25T18:01:43.580" Score="1" Body="&lt;p&gt;Staphylococcal infection is more likely to cause abscesses and Streptococcal infection is more likely to cause cellulitis. It is not clear how a 5 year old did not get medical attantion till he got to this serious state. Why was culture not done? Surgical removal of necrotic tissue due to cut and bruises? doesn't tally with cellulitis. Incision and drainage is a standard proceedure for absecesses, is that what was done? Is this a hypothetical question?&lt;/p&gt;&#xA;" OwnerUserId="4216" LastActivityDate="2013-08-25T18:01:43.580" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="9998" PostTypeId="1" AcceptedAnswerId="9999" CreationDate="2013-08-25T18:31:41.647" Score="0" ViewCount="67" Body="&lt;p&gt;Male patient who is working in the hospital and may be infected with contaminated blood had hepatitis&#xA;with genome IA 5 years ago. His hepatitis A at that time was confirmed with the rise of anti.HAV IgM and&#xA;later with anti-­HAV IgG type antibodies. His wife is known to have antibodies against C hepatitits. The&#xA;patient had icteric illness in about three weeks ago. Which are the best indicators in&#xA;diagnosing his hepatitis?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Right answer is: Detection of HBsAg and anti-HCV antibodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this is because&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;to check if he has hepatitis B by HBsAg&lt;/li&gt;&#xA;&lt;li&gt;to check if he has HepC by the antibody&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Serum antigen of HB tells us about the levels of IgM and IgG. &#xA;If vaccinated, then IgG should be positive, I think?&#xA;&lt;strong&gt;What does HBsAg tell you?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why do we need to detect anti-HCV?&#xA;If they are found, what does it mean?&lt;/strong&gt; &#xA;I think that then it means if found that he does not have hepatitis C then.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2013-08-25T20:22:12.353" Title="How to Diagnose this hepatitis A, B and C case?" Tags="&lt;microbiology&gt;&lt;homework&gt;&lt;hepatitis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="9999" PostTypeId="2" ParentId="9998" CreationDate="2013-08-25T20:22:12.353" Score="3" Body="&lt;p&gt;The last sentence of the question doesn't make it clear what's being asked. But it seems to be asking: &lt;code&gt;What version of Hepatitis did he get from the contaminated blood?&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To that end...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Serum antigen of HB tells us about the levels of IgM and IgG. If vaccinated, then IgG should be positive, I think? What does HBsAg tell you?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;HBsAg gives you the knowledge of whether or not there's an acute infection of Hep-B. &lt;a href=&quot;http://en.wikipedia.org/wiki/Hepatitis#Diagnosis&quot; rel=&quot;nofollow&quot;&gt;Hep-B IgM antibodies indicate an &lt;em&gt;acute&lt;/em&gt; infection&lt;/a&gt;, whilst IgG antibodies would show up due to his previous exposure/immunization. If the patient has Hep-B IgM, the icteric illness was probably a re-infection of Hep-B.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why do we need to detect anti-HCV? If they are found, what does it mean? I think that then it means if found that he does not have hepatitis C then.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That would my assumption as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You run the HBsAg and can get two outcomes: IgM(+)/IgG(+) or IgM(-)/IgG(+). The former indicates the icteric illness was probably a reinfection of Hep-B.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You run the anti-HCV and get two outcomes: (+) or (-). The former indicates a present infection, the latter indicates no Hep-C.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What might throw you off is the wife's anti-HepC antibodies. If she was formerly infected and infected the patient (or vice versa) then you'd &lt;em&gt;expect&lt;/em&gt; to find a (+) anti-HCV result.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I might come back to this after thinking on it a bit more, but that's the best I have for now.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-08-25T20:22:12.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10000" PostTypeId="2" ParentId="9990" CreationDate="2013-08-25T21:03:36.110" Score="12" Body="&lt;p&gt;A good question (if a little mixed up on transcription vs. translation!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AUG is not always the start codon, but whatever the codon is it will always code for Methionine (or fMet, but still a variation on Met), even if the codon codes for a different amino acid otherwise. A  separate transfer RNA (tRNAi, the initiator tRNA) is used for the arrangement of this first step, guided by eIF2 [in eukarya].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this respect it's less a question of &quot;why AUG&quot; than &quot;why this specific initiator tRNA&quot;, the answer being that it's got certain sequence elements and modifications that distinguish it from the elongating tRNAs which bind elongation factors and hence are targeted to the ribosomal A and B sites instead of the ribosomal P site (with function being dependent on form, basically it's shaped to set up transcription rather than to elongate an existing nascent chain polypeptide).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Identity elements appear to finely tune the structure of the initiator tRNA, and growing evidence suggests that the body of the tRNA is involved in transmitting the signal that the start codon has been found to the rest of the pre-initiation complex.&quot; — &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795131/pdf/nihms-161803.pdf&quot;&gt;Kolitz and Lorsch, 2010&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The other start codons are just from natural chemical variation (or evolution, whichever way you want to look at it) giving rise to different codon-recognising protein shapes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The machinery for starting translation works, and as such is &quot;conserved&quot; - evolution has kept it, and that's why it is always the same codon (more or less). Archaea have a very similar shaped tRNAi acceptor stem, and is an equally good ligand, which shows how ancient the system is and gives an idea of how fundamentally difficult it must be for an organism to change a system like this through mutation (3.5 billion years of evolution can't be wrong! etc. haha).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not to just gloss over the part where I said that non-AUG codons get used too (in yeast and mammalian cells), the following is from a study in which it was found changing 1 (and only 1) of the AUG bases still permitted translation initiation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Naturally occurring misrecognition indicates that discriminating two base-paired near-cognate codons from the perfect three-base-paired AUG&#xA;  codon is subject to mistakes. Mutations in translation&#xA;  initiation factors, such as eIF1 and eIF2b, further increase the levels of these mistakes.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Two base-pairing interactions between non-AUG codons and the anticodon of&#xA;  the Met-tRNAi are sufﬁcient to trigger translation initiation, suggesting that wild-type eIF1 plays a role in&#xA;  monitoring proper base-pairing interactions when scanning for the AUG start site. It would be predicted that&#xA;  the Met-tRNAi, not a cognate tRNA matching an individual non-AUG codon, is used in translation initiation at these non-AUG start codons.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The translation initiation complex will bind only the Met-tRNAi as&#xA;  opposed to other tRNAs because Met-tRNAi has unique&#xA;  sequence and structural features that allow it to be&#xA;  loaded onto eIF2 of the ternary complex and enable it&#xA;  to ﬁt into the P site of the ribosome&quot; — &lt;a href=&quot;http://www.genetics.org/content/186/4/1187.full.pdf&quot;&gt;Maduzia &lt;em&gt;et al&lt;/em&gt;, 2010&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Basically the consensus is that it's not really possible to say why the methionine codon, &quot;it's just a structural thing&quot;, which is a bit of a circular argument really.&lt;/p&gt;&#xA;" OwnerUserId="4202" LastActivityDate="2013-08-25T21:03:36.110" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10001" PostTypeId="2" ParentId="9993" CreationDate="2013-08-25T21:22:19.120" Score="28" Body="&lt;p&gt;Before I restrict the answer to human metabolism, I recon it is important to mention that &#xA;CO&lt;sub&gt;2&lt;/sub&gt; is the source of the carbon atoms of glucose in photosynthesis (in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Light-independent_reactions&quot;&gt;Calvin cycle&lt;/a&gt;). [In photosynthesis CO&lt;sub&gt;2&lt;/sub&gt; is 'fixed']. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even with the above restriction, I am certain I  cannnot do justice to every helpful aspect of CO&lt;sub&gt;2&lt;/sub&gt; in mammalian metabolism, and I'll restrict myself to just one area that came to mind on reading your question: the requirement for carbon dioxide (in the form of bicarbonate) for fatty acid biosynthesis (FAS) and, in a bit more general sense, mammalian/bacterial biotin-dependent carboxylation reactions. Depeding on other contributions, I might be able to extend this a bit later. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jbc.org/content/281/5/e5&quot;&gt;Salih Wakil&lt;/a&gt; showed that CO&lt;sub&gt;2&lt;/sub&gt; is an absolute requiement for fatty acid biosynthesis, but &lt;strong&gt;carbon atoms from CO&lt;sub&gt;2&lt;/sub&gt; do not appear in the fatty acid product&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We now know that FAS begins with the carboxylation of acetyl-CoA to malonyl-CoA, catalyzed by the enzyme &lt;a href=&quot;http://en.wikipedia.org/wiki/Acetyl-CoA_carboxylase&quot;&gt;acetyl-CoA carboxylase&lt;/a&gt;. Acetyl-CoA, ATP and &lt;strong&gt;bicarbonate&lt;/strong&gt; are the substrates for this enzyme, and malonyl-CoA is a key product. One of the many interesting properties of this enzyme is that it contains &lt;a href=&quot;http://en.wikipedia.org/wiki/Biotin&quot;&gt;biotin&lt;/a&gt;, which (in this case) may be considered a carrier of 'active' CO&lt;sub&gt;2&lt;/sub&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This explains the requriement for carbon dioxide but why no carbon from CO&lt;sub&gt;2&lt;/sub&gt; in the final product? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is now known that in subsequent FAS reactions, a derivative of malonyl-CoA condenses with a derivative of acetyl-CoA (I am simplifying here) to give a four-carbon compound with loss of CO&lt;sub&gt;2&lt;/sub&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, carbon dioxide (in the form of bicarbonate) is an obligate requiement for mammalian fatty acid biosynthesis, but no CO&lt;sub&gt;2&lt;/sub&gt;-derived carbon is incorporated into fatty acids.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carbon dioxide is also required for oxaloacetate formation from pyruvate. This reaction may be though of a method of 'filling up' a key &lt;a href=&quot;http://en.wikipedia.org/wiki/Citric_acid_cycle&quot;&gt;Krebs Cycle&lt;/a&gt; intermediate (a  so-called &lt;a href=&quot;http://en.wikipedia.org/wiki/Anaplerotic_reactions&quot;&gt;anapleurotic&lt;/a&gt; reaction).  The enzyme here is &lt;a href=&quot;http://en.wikipedia.org/wiki/Pyruvate_carboxylase&quot;&gt;pyruvate carboxylase&lt;/a&gt; and the substrates for the reaction are pyruvate, &lt;strong&gt;bicarbonate&lt;/strong&gt; and ATP, with oxaloacetate being a key product.  This enzyme also contains biotin and (like acetyl CoA carboxylase), CO&lt;sub&gt;2&lt;/sub&gt; becomes covalently bound to biotin during the reaction cycle.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pyruvate-CoA carboxylase was discovered by &lt;a href=&quot;http://www.jbc.org/content/280/18/e15.full?sid=2034e625-3271-4210-a544-03b531e655af&quot;&gt;Harland.G Wood&lt;/a&gt; and C. Werkman in bacteria (See &lt;a href=&quot;http://www.jbc.org/content/238/8/2603.full.pdf&quot;&gt;here&lt;/a&gt; for a good reference on the early work on pyruvate carboxylase). Its discovery was very controversial because at the time it was thought that animal/bacterial cells could not 'fix' CO&lt;sub&gt;2&lt;/sub&gt;; that is it was though that CO&lt;sub&gt;2&lt;/sub&gt; is only 'fixed' in photosynthesis.  This discovery disproved that piece of dogmatism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A third enzyme that requires CO&lt;sub&gt;2&lt;/sub&gt;  as substrate (in the form of bicarbonate) is &lt;a href=&quot;http://en.wikipedia.org/wiki/Propionyl-CoA_carboxylase&quot;&gt;propionyl-CoA carboxylase&lt;/a&gt;.  This enzyme occurs in mitochondria and functions in odd-chain fatty acid metabolism.  It also &lt;strong&gt;contains biotin&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have concentrated on some biochemical aspects of your question.  The three enzymes mentioned, acety-CoA carboxylase, pyruvate carboxylase and propionyl-CoA carboxylase all require CO&lt;sub&gt;2&lt;/sub&gt; in the form of bicarbonate as substrate, &lt;strong&gt;all contain biotin&lt;/strong&gt;, and (as far as I am aware) all play very central roles in mammalian metabolism.  (They also all require ATP as substrate).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of the many interesting aspects of &lt;a href=&quot;http://en.wikipedia.org/wiki/Biotin&quot;&gt;biotin&lt;/a&gt;, I'll mention just one.  Egg white contains a protein, &lt;a href=&quot;http://en.wikipedia.org/wiki/Avidin&quot;&gt;avidin&lt;/a&gt;, which binds biotin very, very tightly.  In fact the biotin-avidin interaction is one of the strongest non-covalent interactions known.  As far as I am aware, no-one knows the function of avidin in egg white.  Some bacteria contain a similar  (but evolutionarily unrelated) protein called &lt;a href=&quot;http://en.wikipedia.org/wiki/Streptavidin&quot;&gt;streptavidin&lt;/a&gt;. No one knows the function of steptavidin either (again, as far as I am aware). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biochemj.org/bj/030/0048/0300048.pdf&quot;&gt;The original Wood &amp;amp; Werkman paper:&lt;/a&gt; was published in the the &lt;em&gt;Biochemical Journal&lt;/em&gt; in 1936&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The utilisation of CO&lt;sub&gt;2&lt;/sub&gt; in the dissimilation of glycerol by the propionic acid bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Harland Goff Wood and Chester Hamlin Werkman.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biochemical Journal, &lt;a href=&quot;http://www.biochemj.org/bj/030/1/default.htm?S=0&quot;&gt;Volume 30&lt;/a&gt;, January 1936, pp 48-53&lt;/p&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="1136" LastEditDate="2013-08-25T23:48:13.737" LastActivityDate="2013-08-25T23:48:13.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10002" PostTypeId="1" AcceptedAnswerId="42520" CreationDate="2013-08-26T00:07:17.570" Score="13" ViewCount="944" Body="&lt;p&gt;I found a seemingly diseased tree when I was out playing tennis yesterday... What is growing on this tree leaf? Is this a disease? If so, is it contagious? I have zero knowledge in botany, but I'm curious about what is happening to these trees. :) &#xA;&lt;img src=&quot;https://i.stack.imgur.com/LuHeQ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4155" LastEditorUserId="16866" LastEditDate="2019-02-17T17:39:56.247" LastActivityDate="2020-03-27T19:04:05.640" Title="What is Growing on These Tree Leaves? (Image)" Tags="&lt;species-identification&gt;&lt;botany&gt;&lt;ecology&gt;&lt;mycology&gt;&lt;trees&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10003" PostTypeId="2" ParentId="8701" CreationDate="2013-08-26T00:50:16.627" Score="0" Body="&lt;p&gt;It's worth noting that there are sustainable and biodiverse agricultural systems that have been called &quot;slash and burn&quot; by outsiders. In many parts of the world, these managed successionary stages of &quot;swidden-fallow&quot; or &quot;shifting cultivation&quot; have created dynamic and resilient anthropogenic landscapes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://classes.yale.edu/02-03/anth500a/projects/project_sites/00_neidel/hanunoo&amp;amp;ifugao.htm&quot; rel=&quot;nofollow&quot;&gt;Hal Conklin's studies on Hanunóo agriculture&lt;/a&gt; are the classics in this field. For a good, general introduction try &lt;a href=&quot;http://www.cfc.umt.edu/rattan/pdfs/Swidden%20agriculture.pdf&quot; rel=&quot;nofollow&quot;&gt;this powerpoint&lt;/a&gt;, which also notes that sustainable swiddening is closer in ecological impact to natural tree-fall disturbance, which usually has been taken to &lt;em&gt;promote&lt;/em&gt; forest biodiversity (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Intermediate_Disturbance_Hypothesis&quot; rel=&quot;nofollow&quot;&gt;Intermediate Disturbance Hypothesis&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not to say that there aren't forests undergoing slash and burn that are being permanently transformed, and in a direction of lower biodiversity and lower human utility (i.e. &quot;bad&quot;/&quot;destruction&quot;), or to say that all traditional agricultural systems are necessarily sustainable; only that under many of the biological and philosophical criteria that fileunderwater raises, &lt;strong&gt;there do exist sustainable and biologically rich human-biological systems that have been called 'slash-and-burn'&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-08-26T00:50:16.627" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10004" PostTypeId="2" ParentId="10002" CreationDate="2013-08-26T00:54:13.047" Score="2" Body="&lt;p&gt;Briefly, these look like &lt;a href=&quot;http://en.wikipedia.org/wiki/Gall&quot; rel=&quot;nofollow noreferrer&quot;&gt;insect galls&lt;/a&gt;; which are reactions of plant tissue caused by parasitic insects (often wasps) laying eggs inside the leaf. I'm sure someone can answer in more detail, though!&lt;/p&gt;&#xA;&lt;p&gt;Cf. &lt;a href=&quot;https://biology.stackexchange.com/questions/761/how-do-galls-form?lq=1&quot;&gt;How do plant galls form?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-08-27T04:39:46.597" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10005" PostTypeId="2" ParentId="9988" CreationDate="2013-08-26T02:02:36.633" Score="1" Body="&lt;p&gt;Have you read the Wikipedia article on &lt;a href=&quot;https://en.wikipedia.org/wiki/Fat&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fat&lt;/a&gt;?  It has literally &lt;strong&gt;all&lt;/strong&gt; of the answers you are seeking.  However...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1: Every single thing is bad for you if you get too much of it.  Animal fat, sugar, water, you can over-do it on anything.  Fat can be bad for you but it is definitely required.  In particular, &quot;&lt;em&gt;Vitamins A, D, E, and K are fat-soluble, meaning they can only be digested, absorbed, and transported in conjunction with fats. Fats are also sources of essential fatty acids, an important dietary requirement.&lt;/em&gt;&quot;  Fat does a host of other things, as mentioned in the article.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2: Fat is indeed a concentrated store of energy, but there's more to life than just energy.  &lt;a href=&quot;https://en.wikipedia.org/wiki/Protein_%28nutrient%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;Protein&lt;/a&gt;, like other nutrients, are required for life.  Protein happens to be &lt;em&gt;particularly&lt;/em&gt; important, providing the structure for all our cells, is required for muscle growth, and provides amino acids, which are needed to make other proteins in your body.  Proteins are used as hormones, cellular messengers, immune receptors, so on and so forth.  You couldn't live without protein.  Energy, while concentrated in fat, could come from elsewhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3: It worked just the same for them as for us.  I will add, however, that our ancestors did not necessarily use every part from every animal, and these days, we actually use every part of many animals, just not always for food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4: Sure?  Energy is good, but protein is probably better.  &quot;&lt;em&gt;Athlete&lt;/em&gt;&quot; is a vague term, as strength-training and endurance activities are very different from each other.  Protein is probably better for strength, carbohydrates are probably better for endurance.  But you can ask over at &lt;a href=&quot;https://fitness.stackexchange.com/&quot;&gt;https://fitness.stackexchange.com/&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:51.727" LastActivityDate="2013-08-26T02:02:36.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10006" PostTypeId="1" CreationDate="2013-08-26T06:10:06.377" Score="0" ViewCount="48" Body="&lt;p&gt;Can we remove impacted teeth by key hole surgery, rather than an open technique, like lithotripsy?&lt;/p&gt;&#xA;" OwnerUserId="4323" LastEditorUserId="107" LastEditDate="2013-08-27T01:11:13.630" LastActivityDate="2013-12-25T03:33:04.877" Title="Can we remove impacted teeth by key hole surgery?" Tags="&lt;anatomy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10008" PostTypeId="1" AcceptedAnswerId="15673" CreationDate="2013-08-26T08:18:17.713" Score="9" ViewCount="14570" Body="&lt;p&gt;Why are e.g. ducklings, goslings, turkey and chicken chicks (partly) yellow?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the chemistry background to this? What compounds from the egg cause this to happen?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the evolutionary background to this? How could it help the bird to survive?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While domestication has led to selection of all-white adult birds and thus more common all-yellow babies, why does an all-&lt;em&gt;yellow&lt;/em&gt; baby become an all-&lt;em&gt;white&lt;/em&gt; adult, in terms of biochemistry?&lt;/p&gt;&#xA;" OwnerUserId="4123" LastEditorUserId="316" LastEditDate="2018-12-17T18:17:44.053" LastActivityDate="2020-04-18T10:57:35.543" Title="Why are certain baby (water)fowl yellow?" Tags="&lt;evolution&gt;&lt;development&gt;&lt;ornithology&gt;&lt;pigmentation&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="10009" PostTypeId="1" AcceptedAnswerId="10014" CreationDate="2013-08-26T08:27:18.180" Score="12" ViewCount="1872" Body="&lt;p&gt;The genetic code is redundant, there are 20 amino acids for 64 possible nucleotide combinations (triplet codons). Therefore some amino acid are coded by several different codons. While leucine is coded by 6 codons, tryptophan is coded only by one codon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[I am aware that the set of codons that code for one given amino acid tend to look alike each other more than random. Usually it is only the last base that does not affect the amino-acid that is encoded.] &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I therefore do not think that the genetic code can be entirely be explained by “it happened to occur that way the first time” (at the origin of life or in the last universal common ancestor) “and it never changed”. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, my questions are: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Why are some amino acids coded by a several codons while others are coded only by one or two?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Specifically, why is methionine coded by only one codon — AUG — which has also to serve as a start signal?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In general, how (by what mechanisms, selective pressures) has the genetic code evolved to give this pattern of redundancies?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="22057" LastEditDate="2018-12-04T13:55:40.240" LastActivityDate="2018-12-04T21:49:48.653" Title="How did the genetic code evolve?" Tags="&lt;evolution&gt;&lt;molecular-genetics&gt;&lt;molecular-evolution&gt;&lt;translation&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="10012" PostTypeId="1" CreationDate="2013-08-26T12:01:29.917" Score="0" ViewCount="101" Body="&lt;p&gt;I was curious about a fact given in my biology textbook as to why the Japanese have  3 pairs o floating ribs unlike the rest who have just two?&lt;/p&gt;&#xA;" OwnerUserId="4326" LastActivityDate="2013-08-26T13:16:41.353" Title="Axial skeletal system" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10013" PostTypeId="2" ParentId="10012" CreationDate="2013-08-26T13:16:41.353" Score="2" Body="&lt;p&gt;Because your textbook is probably worded poorly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears that the Japanese (and several other ethnic groups) apparently have a &lt;a href=&quot;http://en.wikipedia.org/wiki/False_ribs#Tenth_rib&quot; rel=&quot;nofollow&quot;&gt;higher proclivity for the 10th rib to be a true floating rib&lt;/a&gt;, but &lt;strong&gt;every&lt;/strong&gt; ethnic group has the chance of having a floating 10th rib.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With that said, the one McGraw-Hill book cited in the Wiki article is the &lt;strong&gt;&lt;em&gt;only&lt;/em&gt;&lt;/strong&gt; source I've seen for this higher morphology rate. I, personally, wouldn't trust just one source, and (if true) the rate may not be much higher.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-08-26T13:16:41.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10014" PostTypeId="2" ParentId="10009" CreationDate="2013-08-26T14:10:10.810" Score="10" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/653/why-20-amino-acids-instead-of-64&quot;&gt;This question&lt;/a&gt; is closely related, and the &lt;a href=&quot;http://www.americanscientist.org/issues/pub/the-invention-of-the-genetic-code&quot; rel=&quot;nofollow noreferrer&quot;&gt;fascinating link&lt;/a&gt; posted by @JohnSmith is a good read.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, with a four-base system, and a codon size of 1, you get four possible amino acids.  Silly system.  A codon size of 2 gives 16.  Not too shabby, but not a lot of room for growth, and not enough for those 20 amino acids.  Codons of size 3 gives 64 - plenty of room to work with and it covers all your forseeable amino acids, and then some, without being too wasteful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The redundancy, known as &lt;strong&gt;degeneracy&lt;/strong&gt;, is pretty straightforward.  There's room to expand, and any redundancy/degeneracy will only reduce the likelihood of errors.  That's a huge benefit.  For some amino acids, the first two bases are enough.  That third position can be quite tolerant to mutation, which is very beneficial to organisms.  It appears to be even more fine-tuned, to the degree that redundancy often not only reduces the likelihood of mutation but also reduces the damage caused when a base does mutate.  Swapping a hydrophobic AA for another hydrophobic one is less likely to cause aberrant protein function, and anything with a &lt;strong&gt;U&lt;/strong&gt; in the middle is probably hydrophobic.  Convenient!  I'll also note that, while it's not perfect or even a significant correlation, the more popular amino acids tend to get more redundancy; tryptophan is traditionally the least common AA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, there are a few &lt;a href=&quot;https://en.wikipedia.org/wiki/Non-proteinogenic_amino_acids&quot; rel=&quot;nofollow noreferrer&quot;&gt;non-proteinogenic amino acids&lt;/a&gt;, so, as the linked question/answer above points out, maybe in the future there will be more amino acids.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-08-26T14:10:10.810" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10015" PostTypeId="1" CreationDate="2013-08-26T14:24:12.357" Score="4" ViewCount="5785" Body="&lt;p&gt;Is there a subtle difference between these two concepts or are they basically the same thing? When I mean differentiated, I don't mean terminally differentiated. &lt;/p&gt;&#xA;" OwnerUserId="90" LastEditorUserId="4101" LastEditDate="2013-08-28T21:06:11.120" LastActivityDate="2014-12-11T08:16:03.753" Title="What is the difference between &quot;lineage restriction&quot; and &quot;differentiated&quot; in terms of stem cell biology" Tags="&lt;stem-cells&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10016" PostTypeId="2" ParentId="9991" CreationDate="2013-08-26T16:21:22.243" Score="3" Body="&lt;p&gt;As far as I understand it (and I'll preface this by saying that initiation is &lt;strong&gt;not&lt;/strong&gt; my strongest point), but prokaryotes utilize the beautiful &lt;strong&gt;AGGAGG&lt;/strong&gt; Shine-Dalgarno sequence.  Usually around 8bp upstream of the start codon, it is this sequence that the prokaryotic ribosome seeks out to initiate translation.  It does this through a complementary region in the 3' sequence of the ribosomal RNA.  Upon complementary binding, the ribosome and mRNA are correctly bound.  Convenient!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In eukaryotes, however, there is no consensus SD sequence, so a different mechanism must be used; the complex of 40S and Methionine tRNA serves this purpose.  The two together scan the mRNA, looking for an &lt;strong&gt;AUG&lt;/strong&gt; start codon which the tRNA is complementary to.  This eventually brings the full ribosome (40S + 60S) together to start translation.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-26T16:21:22.243" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10017" PostTypeId="2" ParentId="5668" CreationDate="2013-08-26T18:05:35.060" Score="1" Body="&lt;p&gt;To quote the PI from the BBC article:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;But, Dr Dabiri explained, the jellyfish were unlikely to be the &amp;quot;primary ocean mixers&amp;quot;.  &amp;quot;Crustaceans - like copepods and krill - are likely the primary biogenic mixers, because there are so many of them,&amp;quot; he explained.&lt;/p&gt;&#xA;&lt;p&gt;&amp;quot;But much of the open ocean is like desert,&amp;quot; he added, &amp;quot;and the density of these animals is unlikely to be sufficient (to cause mixing).&amp;quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;My guess therefore is no, jellyfish would not be sufficient to dramatically change the current structure of ocean layers.  Animals in general, as the paper and its references suggest, &lt;strong&gt;do&lt;/strong&gt; contribute significantly, on-par with tides and wind.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-08-26T18:05:35.060" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10018" PostTypeId="1" AcceptedAnswerId="10262" CreationDate="2013-08-26T19:15:07.447" Score="2" ViewCount="152" Body="&lt;p&gt;I am creating a transcription template for expression in PURExpress and was confused about the annealing temperature to use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have two primers with the T7 promoter and an RBS on the forward primer and a termination sequence on the reverse primer.  The melting temperature of these primers are 84.4 and 83.8 degrees C.  The melting temperature of the regions that are complementary to the gene of interest I want to amplify by PCR are both about 65 degrees C.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What annealing temperature should I use a h?  Since at the beginning of the PCR reaction I will have mostly template that will have the complementary sequences of the primers binding to the GOI and not the 5' and 3' extensions.&lt;/p&gt;&#xA;" OwnerUserId="3247" LastActivityDate="2013-09-04T16:00:03.033" Title="Creating expression template from PCR: What annealing temperature to use?" Tags="&lt;pcr&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10019" PostTypeId="2" ParentId="7586" CreationDate="2013-08-26T19:39:49.030" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902570/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902570/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to the other answer(s), E. coli has been shown to have filamentous spikes even under controlled conditions. This is not the same situation as it sounds like you have a non synchronized culture in which this happens, but it could be related.&lt;/p&gt;&#xA;" OwnerUserId="4263" LastActivityDate="2013-08-26T19:39:49.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10020" PostTypeId="1" AcceptedAnswerId="10055" CreationDate="2013-08-26T22:11:47.167" Score="2" ViewCount="716" Body="&lt;p&gt;For yeast and other organisms, DNA can be readily taken up into the cell naturally or through membrane disruption. What does applying a voltage to cells do exactly that allows more recombination to occur?&lt;/p&gt;&#xA;" OwnerUserId="4263" LastActivityDate="2013-10-26T18:45:33.320" Title="How does electroporation mediated recombination work?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;transformation&gt;&lt;recombination&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10021" PostTypeId="2" ParentId="3858" CreationDate="2013-08-26T22:11:50.653" Score="0" Body="&lt;p&gt;Sparking occurs from having too many salts or possible not enough solution. After fine tuning my electroporation for very high amounts of DNA (16+ ug), what I've found to help are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Make sure you are using the proper amount of liquid solution to transform. Too little will end up sparking&lt;/li&gt;&#xA;&lt;li&gt;Clean up your DNA. I wash with twice the recommend amount of buffer PE, but I don't great evidence of how much the 2nd PE wash helps&lt;/li&gt;&#xA;&lt;li&gt;Elute your DNA clean up with water&lt;/li&gt;&#xA;&lt;li&gt;Drop dialyze your DNA. This is probably the most important step to prevent arcing&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4263" LastActivityDate="2013-08-26T22:11:50.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10022" PostTypeId="1" AcceptedAnswerId="10025" CreationDate="2013-08-27T00:02:31.720" Score="4" ViewCount="588" Body="&lt;p&gt;I'm naturally thinking this is a bee, but I cannot find it anywhere in any insect identifiers. I caught this picture on top of my doorway, it's about 1 1/2 inches in length, and its torso seems to be coated in a layer of hair, and the rest of its body is narrow. The thick layer of hair may or may not be accurate, I didn't want to get too close to it, but that's how it appeared at least.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bwviH.jpg&quot; alt=&quot;Unidentified Insect&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/qc8ng.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/8Belf.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS - Found in Kentucky, and I'm not sure why one pic shows wings and the other one doesn't...&lt;/p&gt;&#xA;" OwnerUserId="4328" LastEditorUserId="4328" LastEditDate="2013-08-27T01:44:18.777" LastActivityDate="2020-03-05T03:46:41.700" Title="What type of insect is this?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10023" PostTypeId="2" ParentId="8499" CreationDate="2013-08-27T00:06:43.600" Score="2" Body="&lt;p&gt;Everybody said it already, but there is none.  The original HWE equation ($(p+q)^2=1$) works because you've got two variables and two equations ($p+q=1$) to work with (in reality, these are just one equation and one variable, since $q=1-p$ so $p+(1-p))^2=1$).  Now you have three variables and still only the one equation ($p+q+r=1$) which is, mathematically, impossible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You need go out and measure some frequencies.  In particular, you need to measure two of them - I'd choose two of the homozygous types for convenience's sake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This basically summarizes everything nicely for ya: &lt;a href=&quot;http://www.bio.miami.edu/dana/dox/trinomial.html&quot; rel=&quot;nofollow&quot;&gt;http://www.bio.miami.edu/dana/dox/trinomial.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-27T00:06:43.600" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10025" PostTypeId="2" ParentId="10022" CreationDate="2013-08-27T00:56:18.527" Score="11" Body="&lt;p&gt;From the general body plan, it looks like it's probably a &lt;a href=&quot;http://en.wikipedia.org/wiki/Asilidae&quot;&gt;robber fly&lt;/a&gt;. Here's a &lt;a href=&quot;http://www.uky.edu/Ag/CritterFiles/casefile/insects/flies/robber/robber.htm&quot;&gt;page of specifically Kentucky robber flies&lt;/a&gt; – it's possible yours could be a Bearded Robber Fly.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-08-27T00:56:18.527" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10026" PostTypeId="1" AcceptedAnswerId="10028" CreationDate="2013-08-27T01:17:32.410" Score="1" ViewCount="1958" Body="&lt;p&gt;I had recently read an article that the possibility of having natural blue rose is extremely rare because of the absence of delphinidin in most roses. Are all blue roses just a product of cross-breeding?&lt;/p&gt;&#xA;" OwnerUserId="4330" LastEditorUserId="948" LastEditDate="2013-08-29T13:15:14.747" LastActivityDate="2014-01-16T04:24:07.550" Title="Is there any natural blue rose?" Tags="&lt;botany&gt;&lt;plant-anatomy&gt;&lt;ethnobiology&gt;&lt;pigmentation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10027" PostTypeId="2" ParentId="10006" CreationDate="2013-08-27T02:19:23.367" Score="1" Body="&lt;p&gt;The impacted tooth is partially or fully enclosed in the bone. Even if accessed by a drill hole to reach the tooth. The tooth is too hard to be cut up into smaller sections with any of the conventional equipments available through an endoscope.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tooth is a composite of three highly organized, mineralised tissues. The bulk of the tooth is formed by dentin and has around 30% organic content almost similar to that of bone. A large part of the organic content is collagen a tough fibre. Where as kidney stones etc are aggregates of minerals etc and are much more susceptible for pulverisation by shock waves from a lithotripter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides an impacted tooth is either partially of fully inclosed in bone. So that too rules out the use of a lithotripter.&lt;/p&gt;&#xA;" OwnerUserId="4216" LastActivityDate="2013-08-27T02:19:23.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10028" PostTypeId="2" ParentId="10026" CreationDate="2013-08-27T02:46:15.600" Score="3" Body="&lt;p&gt;There are no roses (that is, flowers of genus &lt;em&gt;Rosa&lt;/em&gt; species) that naturally express a &quot;true&quot; blue color. Through cross-breeding, &lt;a href=&quot;http://www.everyrose.com/everyrose/roses/browse.lasso&quot; rel=&quot;nofollow&quot;&gt;there are lilac-mauve rose horticultural varieties&lt;/a&gt; (&quot;Blue Nile&quot;,&quot;Blue Moon&quot;,&quot;Lady X&quot;, etc.), and through genetic engineering (actually inserting delphinidin-producing genes) &lt;a href=&quot;http://www.wired.com/wiredscience/2011/09/blue-roses-for-sale/&quot; rel=&quot;nofollow&quot;&gt;there are mauve-lavender varieties&lt;/a&gt; (&quot;Applause&quot;). The insertion of delphinidin-producing genes did not yield blue colour roses as hoped is due to the acidity of the rose petals, which itself changed the delphinidin blue to mauve-lavender instead. The next breakthrough will be to switch off the acidity of the rose petals to create a true blue rose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;More info&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia article &lt;a href=&quot;http://en.wikipedia.org/wiki/Blue_rose&quot; rel=&quot;nofollow&quot;&gt;Blue Rose&lt;/a&gt; gives good coverage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bulbnrose.x10.mx/Heredity/King/RosePigments/RosePigments.html&quot; rel=&quot;nofollow&quot;&gt;Here's a nice scientific bibliography of rose pigments with some good information on blues&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2014-01-16T04:24:07.550" LastActivityDate="2014-01-16T04:24:07.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10029" PostTypeId="1" AcceptedAnswerId="10030" CreationDate="2013-08-27T02:53:24.323" Score="5" ViewCount="303" Body="&lt;p&gt;The mitochondria in the sperm are digested upon entry into the egg, making mDNA inheritance exclusively female. What is the advantage of this? Wouldn't some male mDNA be beneficial because of the advantages of (at least a little) sexual reproduction?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&#xA;&quot;Postfertilization autophagy of sperm organelles prevents paternal mitochondrial DNA transmission&quot; (behind paywall, &lt;a href=&quot;http://www.sciencedaily.com/releases/2011/11/111103143515.htm&quot; rel=&quot;nofollow&quot;&gt;here's a ScienceDaily article discussing the results&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both answers seem valid but it is hard to quantify the relative costs.&lt;/p&gt;&#xA;" OwnerUserId="4321" LastEditorUserId="4321" LastEditDate="2016-09-29T17:04:45.823" LastActivityDate="2016-09-29T17:04:45.823" Title="Why is there sperm mitochondrial suicide?" Tags="&lt;reproduction&gt;&lt;mitochondria&gt;&lt;autophagy&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10030" PostTypeId="2" ParentId="10029" CreationDate="2013-08-27T03:16:41.963" Score="7" Body="&lt;p&gt;Maternal inheritance of mitochondrial DNA is very well conserved, although some species, such as &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/11280005&quot;&gt;some mussels&lt;/a&gt;, show &lt;a href=&quot;https://en.wikipedia.org/wiki/Paternal_mtDNA_transmission&quot;&gt;paternal inheritance&lt;/a&gt;.  As for why or what the advantage is, some of it is due to basic logistics: sperm cells have ~100-1000 mitochondria, egg cells have 10&lt;sup&gt;5&lt;/sup&gt;-10&lt;sup&gt;6&lt;/sup&gt;, so male contributions are largely washed out.  Plus, most mitochondria in sperm are toward the tail, which does not always or necessarily get inside the egg.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a more selection-based mechanism of the actual destruction, think about what sperm do.  They are small packets of energy that do nothing but race until they die.  That's it.  Energy production, which occurs in the mitochondria, produces reactive oxygen that can damage genomes.  The mt-genome in the egg is far less likely to be damaged.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, I might look to chromosome uniformity.  Heteroplasmy &lt;em&gt;does&lt;/em&gt; occur now and again, and it's not usually a good thing.  Mitochondria are very important, so it makes sense to have an all-or-nothing approach, lest any deleterious genomes persist.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-27T03:16:41.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10031" PostTypeId="2" ParentId="2477" CreationDate="2013-08-27T04:29:14.347" Score="2" Body="&lt;p&gt;I don't know of video course, but here are two book recommendations:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1892784351&quot; rel=&quot;nofollow noreferrer&quot;&gt;Botany in a Day&lt;/a&gt; by Elpel is superb in terms of being an approachable, systematic look at plant identification and basic botanical knowledge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, as I mentioned in &lt;a href=&quot;https://biology.stackexchange.com/questions/8190/resource-plant-anatomy-lifecycle-vocabulary/9216#9216&quot;&gt;this answer&lt;/a&gt;, the &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0064603024&quot; rel=&quot;nofollow noreferrer&quot;&gt;Botany Coloring Book&lt;/a&gt; is a great resource for basic self-education on botany / plant anatomy.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-08-27T04:29:14.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10032" PostTypeId="1" AcceptedAnswerId="10033" CreationDate="2013-08-27T04:35:09.293" Score="2" ViewCount="64" Body="&lt;p&gt;People may tend to spend time in a hot water spring. Is it possible to get hyperthermia (like a sun stroke) due to this?&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="4101" LastEditDate="2013-08-27T19:39:05.600" LastActivityDate="2013-08-27T19:39:05.600" Title="Is it possible to suffer from hyperthermia by spending too much of time in the hot springs?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10033" PostTypeId="2" ParentId="10032" CreationDate="2013-08-27T05:22:41.850" Score="2" Body="&lt;p&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/20457444&quot; rel=&quot;nofollow&quot;&gt;You betcha!&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We report a case of acute hepatic failure combined with disseminated&#xA;  intravascular coagulopathy, acute renal failure, and neurological&#xA;  deficit caused by heat stroke after bathing in a hot spring.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Generically, the term you're looking for is non-exertional heat stroke.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2013-08-27T05:22:41.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10034" PostTypeId="1" CreationDate="2013-08-27T06:24:08.057" Score="4" ViewCount="131" Body="&lt;p&gt;Are there differences in the components of saliva among species? Also, do the functions of saliva differ between species?&lt;/p&gt;&#xA;" OwnerUserId="4323" LastEditorUserId="4101" LastEditDate="2013-08-27T19:33:44.813" LastActivityDate="2014-07-28T16:56:39.210" Title="Is there differences in components of saliva among species" Tags="&lt;anatomy&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10035" PostTypeId="1" CreationDate="2013-08-27T06:31:57.033" Score="0" ViewCount="124" Body="&lt;p&gt;What determines the strength of a tree. A morphologically strong looking tree found broken down at trunk. can we determine the strength/ life of a plant&lt;/p&gt;&#xA;" OwnerUserId="4323" LastActivityDate="2013-08-28T03:12:24.850" Title="What determines the strength of a tree" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2017-03-29T16:27:49.757" ContentLicense="CC BY-SA 3.0" />
  <row Id="10036" PostTypeId="1" CreationDate="2013-08-27T06:37:42.220" Score="0" ViewCount="8790" Body="&lt;p&gt;What determines the size and shape of a cell? They differ at different tissues / organs/ species&lt;/p&gt;&#xA;" OwnerUserId="4323" LastEditorUserId="9943" LastEditDate="2015-03-22T13:53:24.640" LastActivityDate="2015-03-22T13:53:24.640" Title="What determines the size and shape of a cell?" Tags="&lt;anatomy&gt;&lt;cell&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ClosedDate="2015-03-22T19:26:59.880" ContentLicense="CC BY-SA 3.0" />
  <row Id="10037" PostTypeId="1" AcceptedAnswerId="10071" CreationDate="2013-08-27T07:20:17.047" Score="2" ViewCount="98" Body="&lt;p&gt;Is anyone aware of any attempts to count or approximate the number of trees there are in Sweden or Scandinavia? I have a small popular science side project for which this would be useful&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="3624" LastEditDate="2013-08-28T11:33:32.557" LastActivityDate="2013-08-28T13:54:56.103" Title="Tree census data for Sweden/Scandinavia?" Tags="&lt;botany&gt;&lt;statistics&gt;&lt;demography&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10038" PostTypeId="2" ParentId="10036" CreationDate="2013-08-27T07:59:45.130" Score="3" Body="&lt;p&gt;This is quite a hard to answer question.&#xA;There are different cell cycle molecules that, if mutated or knocked out, have shown to cause the cell to have a different shape or &quot;overgrow&quot; in size or not grow at all...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might find some insight &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15589139?dopt=AbstractPlus&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are lots of factors that influence cell size and shape, thus it is a very complex system to study. For example, cell shape is influenced by the cytoskeleton but also other factors. &lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-08-27T07:59:45.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10039" PostTypeId="2" ParentId="10037" CreationDate="2013-08-27T10:14:28.557" Score="0" Body="&lt;p&gt;Did a bit of a search, but could not find any Scandinavian specific statistics; however, I did find &lt;a href=&quot;http://epp.eurostat.ec.europa.eu/statistics_explained/index.php/Forestry_statistics&quot; rel=&quot;nofollow&quot;&gt;European Commission Forestry Statistics&lt;/a&gt; page, within this site there are some stats by country.  Further, the website &lt;a href=&quot;http://noltfox.metla.fi/nordic.htm&quot; rel=&quot;nofollow&quot;&gt; &#xA;About Forestry in Northern European countries &lt;/a&gt; also has a few links to country based data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-08-27T10:14:28.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10040" PostTypeId="1" CreationDate="2013-08-27T10:55:03.420" Score="2" ViewCount="46" Body="&lt;p&gt;In organism that have a preformed germ-line like Drosophila where germ cells are pre-allocated in the oocyte, are there technically no adult pluripotent stem cells since germ line cells can't be developed from somatic stem cells?&lt;/p&gt;&#xA;" OwnerUserId="90" LastActivityDate="2013-08-27T18:37:49.063" Title="potency in preformed germ-line" Tags="&lt;stem-cells&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10041" PostTypeId="1" AcceptedAnswerId="10047" CreationDate="2013-08-27T11:04:14.590" Score="0" ViewCount="903" Body="&lt;p&gt;Related to the question &lt;a href=&quot;https://biology.stackexchange.com/questions/8979/what-causes-the-colors-we-see-in-eyes&quot;&gt;What causes the colors we see in eyes?&lt;/a&gt;, I am wondering why human eyes are restricted in colour. Most common eye colours are blue, green and brown. Why not yellow, orange, purple, red and so on?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am guessing this is related to the function of the iris and that other colours do not have the same effect on light absorbing or something like that.&lt;/p&gt;&#xA;" OwnerUserId="3198" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-10-21T15:54:51.490" Title="Why are human eye colours limited?" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;pigmentation&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10042" PostTypeId="1" AcceptedAnswerId="10043" CreationDate="2013-08-27T11:46:38.220" Score="5" ViewCount="1333" Body="&lt;p&gt;The human genome project released it's first complete genome nearly ten years ago. Since then many species have also been sequenced. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am trying to find a list of completed (and possibly ongoing/initiated) projects sequencing other species along with some very basic summary data such as number of genes (divided amongst the sex chromosomes and autosomes), length of DNA, number of chromosomes etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is for a presentation I am giving at a conference and would make a nice addition to my talk.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2017-01-20T15:14:57.810" Title="What species have had their genomes sequenced/are being sequenced?" Tags="&lt;genetics&gt;&lt;dna-sequencing&gt;&lt;genomes&gt;&lt;human-genome&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10043" PostTypeId="2" ParentId="10042" CreationDate="2013-08-27T11:57:36.700" Score="3" Body="&lt;p&gt;The &lt;a href=&quot;http://www.genomesonline.org/&quot; rel=&quot;nofollow&quot;&gt;GOLD database (Genomes Online DB)&lt;/a&gt; contains data on the sequencing status, and also some stats (number of chromosomes, genome size) -- but this extra data is not available for all species.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2013-08-27T11:57:36.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10044" PostTypeId="2" ParentId="10042" CreationDate="2013-08-27T12:10:24.043" Score="1" Body="&lt;p&gt;The &lt;a href=&quot;https://genome10k.soe.ucsc.edu/&quot; rel=&quot;nofollow&quot;&gt;Genome 10K project&lt;/a&gt;, in their words &quot;aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus.&quot;. &lt;a href=&quot;https://genome10k.soe.ucsc.edu/species&quot; rel=&quot;nofollow&quot;&gt;Here is their species list&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-08-27T12:10:24.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10045" PostTypeId="2" ParentId="10042" CreationDate="2013-08-27T14:38:26.637" Score="3" Body="&lt;p&gt;There are several lists on Wikipedia, for example for &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_sequenced_plant_genomes&quot; rel=&quot;nofollow&quot;&gt;plants&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_sequenced_bacterial_genomes&quot; rel=&quot;nofollow&quot;&gt;bacteria&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_sequenced_eukaryotic_genomes&quot; rel=&quot;nofollow&quot;&gt;eucaryotes&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-08-27T14:38:26.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10046" PostTypeId="1" AcceptedAnswerId="10052" CreationDate="2013-08-27T16:31:05.323" Score="4" ViewCount="3848" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Chargaff%27s_rules&quot; rel=&quot;nofollow&quot;&gt;Chargaff's rules&lt;/a&gt; say that the number of Adenine of the number of Thymine in a genome are equal (nA=nT) and similarly nC=nG. This makes obvious sense knowing that C binds to G and A to T.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what about the ratio $\frac{nA+nT}{nC+nG}$?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there variation along species of this ratio that is higher than expected by random processes? If yes, what causes this variation?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2017-07-17T22:20:42.697" Title="Is there variation of AT/CG ratio along species?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;dna&gt;&lt;molecular-genetics&gt;&lt;natural-selection&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10047" PostTypeId="2" ParentId="10041" CreationDate="2013-08-27T16:32:48.493" Score="5" Body="&lt;p&gt;There is only one main &amp;quot;coloring&amp;quot; agent, or pigment, in the eyes.  That pigment is &lt;a href=&quot;https://en.wikipedia.org/wiki/Melanin&quot; rel=&quot;noreferrer&quot;&gt;melanin&lt;/a&gt;.  To a much lesser extent, at least in health individuals, you can have lipofuscin produced which gives a golden-amber color to the eyes.  It should be noted that lipofuscin is most likely produced because of oxidation damage/stress in your eye, and not something to be hoping for (&lt;a href=&quot;https://www.sciencedirect.com/science/article/pii/S0039625700001405?np=y&quot; rel=&quot;noreferrer&quot;&gt;Beatty et al&lt;/a&gt; has a good review of the subject (1)).&lt;/p&gt;&#xA;&lt;p&gt;Indeed, lipofuscin in the eyes can be seen as a symptom to physicians, so for the rest of the answer I will only consider melanin, eumelanin and pheomelanin in particular, as the normative pigment in the iris.&lt;/p&gt;&#xA;&lt;p&gt;To make additional colors, we would need to develop an additional pigment, and or modify eumelanin so that it produces different scattering properties.  So why do we have melanocytes in the eye producing melanin in the first place?&lt;/p&gt;&#xA;&lt;p&gt;As much as we might consider it as a factor now, sexual selection was probably not the main pressure for having pigment in the eyes.  Instead UV protection almost assuredly is (2, 3).  Thus for another pigment to be selected for, it would probably need to do a better job protecting us vs. UV (also, further selection in humans is hampered by all kinds of things like behavior, medicine, and life span).&lt;/p&gt;&#xA;&lt;p&gt;Eumelanin does a good job protecting us from UV (2, 3) and in fact does a better job than phenomelanin (4).  It seems incredibly unlikely that we would develop the necessary evolutionary pressure to have our pigment epithelium to produce a totally foreign pigment.&lt;/p&gt;&#xA;&lt;p&gt;And that is what prevents us from naturally having a whole rainbow of colors in our iris.  One could conceivably engineer a better pigment, and have the genetic information needed to produce it delivered in gene therapy (I hate to think of people purposefully infecting their pigment epithelia).  I, for one, wouldn’t sign up for that.&lt;/p&gt;&#xA;&lt;p&gt;(1) Beatty S. et al. The role of oxidative stress in the pathogenesis of age-related macular degeneration. Surv Ophthalmol. 2000 Sep-Oct;45(2):115-34.&lt;/p&gt;&#xA;&lt;p&gt;(2) Hu DN. et al. Role of ocular melanin in ophthalmic physiology and pathology. Photochem Photobiol. 2008 May-Jun;84(3):639-44. doi: 10.1111/j.1751-1097.2008.00316.x. Epub 2008 Mar 8.&lt;/p&gt;&#xA;&lt;p&gt;(3) Simon JD, Peles DN. The red and the black.  Acc Chem Res. 2010 Nov 16;43(11):1452-60. doi: 10.1021/ar100079y. Epub 2010 Aug 24.&lt;/p&gt;&#xA;&lt;p&gt;(4) Hu DN et al. Uveal melanocytes, ocular pigment epithelium, and Müller cells in culture: in vitro toxicology. Int J Toxicol. 2002 Nov-Dec;21(6):465-72.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-21T15:54:51.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10048" PostTypeId="2" ParentId="10040" CreationDate="2013-08-27T16:33:57.317" Score="3" Body="&lt;p&gt;In almost all metazoa, the pro-germline cells get segregated from other stem cells at an early stage of development and they thrive and differentiate in their neighborhood. This is important in order to preserve the germline. This &lt;a href=&quot;https://biology.stackexchange.com/questions/8016/how-are-new-people-created-from-the-dna-of-an-aged-person-i-e-why-are-we-young/8017#8017&quot;&gt;post&lt;/a&gt; provides some basic explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, even drosophila have adult multipotent stem cells and help in the formation of midgut as reported by &lt;a href=&quot;http://www.nature.com/nature/journal/v439/n7075/abs/nature04333.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; study.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-08-27T18:37:49.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10049" PostTypeId="2" ParentId="10046" CreationDate="2013-08-27T16:47:46.140" Score="3" Body="&lt;p&gt;Yes that ratio varies and is generally referred to as &lt;strong&gt;GC-content&lt;/strong&gt; which is expressed as percentage. Earlier, people used GC-content as one of the identifiers for a group of organisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though there have been quite a few studies on the evolution and variation of GC-content, there is still no clear explanation for why certain organisms have a certain level of GC-content- it exerts no great bias on the protein composition though it is argued that it controls protein expression. Chemical mutability is higher for &lt;code&gt;C-&amp;gt;U&lt;/code&gt; and &lt;code&gt;A-&amp;gt;G&lt;/code&gt; because of deamination but this might not be the sole criterion. You may refer to this nice &lt;a href=&quot;http://www.genetics.org/content/159/2/907.short&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt; for details.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="1306" LastEditDate="2013-08-27T17:05:45.233" LastActivityDate="2013-08-27T17:05:45.233" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10050" PostTypeId="1" AcceptedAnswerId="10053" CreationDate="2013-08-27T17:12:20.907" Score="7" ViewCount="2991" Body="&lt;p&gt;Traditionally, the individual was considered to be the smallest unit on which Natural Selection (NS) acts. Today, we usually consider the gene as being the unit of NS. Of course, we should also consider all sequences that affect the fitness even though they are not genes (even though the do not code for polypeptide). And theoretically, any sequence of DNA does have an effect on fitness because it influences the time and energy for DNA replication (although it might be negligible). The decision of considering the gene as the smallest unit of NS seems rather arbitrary to me. We might as well consider a group of genes or a given exon of even a smaller sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are my questions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;What factors influence the minimal size of a sequence to be considered as a unit on which NS acts? Mutation rate, generation time, selection differential for this sequence, recombination rate, ...?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Could we consider a nucleotide as a unit of NS? Why?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How does the &lt;a href=&quot;http://en.wikipedia.org/wiki/Quasispecies_model&quot;&gt;quasispecies model&lt;/a&gt; fit into the question of what is the smallest unit of NS? (for those interested, you will also find a very good explanation of this model in Martin Nowak's book called &lt;em&gt;Evolutionnary Dynamic: exploring the equations of life&lt;/em&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is it worth talking about that? Is this question biologically relevant? Or is it rather a question based on a choice of definition such as &quot;Is a virus alive?&quot;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;As I asked several questions, let me know if I should split my post into several. Otherwise, please do not hesitate to answer only very partially to this post!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Terdon's answer makes sense to me. I should be a bit more accurate in the reas of my question.  I read &lt;em&gt;The extended Phenotype&lt;/em&gt; from &lt;em&gt;Richard Dawkins&lt;/em&gt; quite a long time ago and if I'm not mistaken, Dawkins says the following things&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A unit on which selection acts has to be:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;active&lt;/li&gt;&#xA;&lt;li&gt;germ-line&lt;/li&gt;&#xA;&lt;li&gt;replicator&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;A replicator has the 3 following properties:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;fecundity&lt;/li&gt;&#xA;&lt;li&gt;longevity&lt;/li&gt;&#xA;&lt;li&gt;fidelity while being copied&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Therefore for fidelity to be respected a unit of selection has to be a sequence which is not too long, so that it is not too often modified by recombination or mutation. He argues in this sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He also argues that nucleotides are not possible unit of selection. Indeed, it is hard to imagine a nucleotide being an active replicator. The word active means that it influences its not probability to be replicated. I don't think a nucleotide can do such a thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately I don't have the book with me right now and I can't check what I have said, give you a citation nor a more accurate a reference. If anyone has some citations from this book, it will be welcome for the discussion!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-08-27T21:08:56.813" LastActivityDate="2013-08-28T13:12:08.093" Title="Smallest unit on which selection can act" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;theoretical-biology&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10051" PostTypeId="1" AcceptedAnswerId="10054" CreationDate="2013-08-27T17:25:23.480" Score="4" ViewCount="1039" Body="&lt;p&gt;I'm currently reading William Cheselden's book &lt;em&gt;Osteographia or The Anatomy of the Bones&lt;/em&gt;, which was published in 1733 (for the pretty pictures, naturally; not up to date anatomy). When he addresses the topic of bone marrow, he says,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Every cylindrical bone has a large middle cavity, which contains an oily marrow, and a great number of lesser cells towards their extremities, which contain a bloody marrow. [...] The bloody marrow is also found in all spongy cells of the bones. [...] The use of the first kind of marrow I imagine is to soften, and render less brittle, the harder fibres of bones near which it is seated; and that the other marrow is of the same use to the less compact fibres, which the more oily marrow might have made to soft; and that for this reason, there is less of the oily marrow, and more of the bloody in young bones than in old ones.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Which strikes me as completely incorrect -- though correct me if I'm wrong. So, when was the purpose of marrow in hematopoiesis discovered, and by whom?&lt;/p&gt;&#xA;" OwnerUserId="4333" LastActivityDate="2013-08-27T17:58:03.567" Title="When was the purpose of bone marrow discovered?" Tags="&lt;human-biology&gt;&lt;hematology&gt;&lt;history&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10052" PostTypeId="2" ParentId="10046" CreationDate="2013-08-27T17:41:12.070" Score="6" Body="&lt;p&gt;That ratio is essentially, as WYSIWYG pointed out, called &lt;strong&gt;GC-content&lt;/strong&gt;.  In actuality, GC-content is reported as $(G+C)/(A+C+G+T)$, converted to percent; i.e., what percent of the genome is G or C.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is vast variation in GC-content, both amongst species and within a given species' own genome.  For example, in humans the first intron and exon are generally more GC-rich than following introns/exons.&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16922687&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt;&lt;/sup&gt;  Genes themselves are often found in higher GC areas,&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1345710/&quot; rel=&quot;noreferrer&quot;&gt;2&lt;/a&gt;,&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/10377985&quot; rel=&quot;noreferrer&quot;&gt;11&lt;/a&gt;&lt;/sup&gt; in particular CpG islands are found near a large number of (mammalian) promoters.&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1292996/&quot; rel=&quot;noreferrer&quot;&gt;3&lt;/a&gt;&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Across species, there can be a big difference.  Yeast and &lt;em&gt;Arabidopsis&lt;/em&gt; are both around 35%&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/15&quot; rel=&quot;noreferrer&quot;&gt;4&lt;/a&gt;,&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/4&quot; rel=&quot;noreferrer&quot;&gt;5&lt;/a&gt;&lt;/sup&gt; whereas &lt;em&gt;Plasmodium falciparum&lt;/em&gt; is around 24%;&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/33&quot; rel=&quot;noreferrer&quot;&gt;6&lt;/a&gt;&lt;/sup&gt; &lt;em&gt;Carsonella&lt;/em&gt; are even lower, at around 16.5%.&lt;sup&gt;&lt;a href=&quot;http://www.sciencemag.org/content/314/5797/267&quot; rel=&quot;noreferrer&quot;&gt;14&lt;/a&gt;&lt;/sup&gt;  On the other hand, the plankton &lt;em&gt;Emiliania huxleyi&lt;/em&gt; is around 65%&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/2&quot; rel=&quot;noreferrer&quot;&gt;7&lt;/a&gt;&lt;/sup&gt;.  We can use these differences to study genomic history.  Bacteria often have genes from all over the place thanks to horizontal gene transfer, and GC-content can be used to differentiate between their own genes and those from horizontal gene transfer;&lt;sup&gt;&lt;a href=&quot;http://genomebiology.com/2003/4/9/R57&quot; rel=&quot;noreferrer&quot;&gt;8&lt;/a&gt;&lt;/sup&gt; a good example is the CRISPR-Cas system,&lt;sup&gt;&lt;a href=&quot;http://www.microbemagazine.org/index.php?option=com_content&amp;amp;view=article&amp;amp;id=335%3athe-crispr-system-protects-microbes-against-phages-plasmids&amp;amp;catid=143&amp;amp;Itemid=262&quot; rel=&quot;noreferrer&quot;&gt;9&lt;/a&gt;&lt;/sup&gt; even in a virus!&lt;sup&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v494/n7438/full/nature11927.html&quot; rel=&quot;noreferrer&quot;&gt;10&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a list of a few things genomic GC-content is correlated with:&lt;sup&gt;&lt;a href=&quot;http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001107&quot; rel=&quot;noreferrer&quot;&gt;15&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;genome size&lt;/li&gt;&#xA;&lt;li&gt;whether the bacterium is free-living or not&lt;/li&gt;&#xA;&lt;li&gt;the environment&lt;/li&gt;&#xA;&lt;li&gt;aerobiosis&lt;/li&gt;&#xA;&lt;li&gt;nitrogen utilization&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In the lab, high GC-content often means a harder region to work with, as the presence of three instead of two bonds (between A and T) requires more energy to break;&lt;sup&gt;&lt;a href=&quot;http://www.nfstc.org/pdi/Subject04/pdi_s04_m01_02_f.htm&quot; rel=&quot;noreferrer&quot;&gt;12&lt;/a&gt;&lt;/sup&gt; anything involving primers can be made more annoying, including (especially, to some) sequencing.  There is a theory that high GC-content would be an adaptation to high temperatures, to avoid DNA damage, but that is controversial.&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088632/&quot; rel=&quot;noreferrer&quot;&gt;13&lt;/a&gt;,&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16499870&quot; rel=&quot;noreferrer&quot;&gt;16&lt;/a&gt;,&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9169555&quot; rel=&quot;noreferrer&quot;&gt;17&lt;/a&gt;,&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16815305&quot; rel=&quot;noreferrer&quot;&gt;18&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-08-27T18:13:06.197" LastActivityDate="2013-08-27T18:13:06.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10053" PostTypeId="2" ParentId="10050" CreationDate="2013-08-27T17:54:14.013" Score="7" Body="&lt;p&gt;The smallest unit that can be selected is, of course, the single nucleotide. The most striking examples of this are Single Nucleotide Polymorphisms (SNPs), many of which confer selective (dis)advantages. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To take a simple example, imagine a SNP that introduces a frameshift mutation, rendering a gene incapable of producing its protein. If that protein is something relatively important like p53, the SNP in question will be lethal and will be selected against. So, to take your questions one by one:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;What factors influence the minimal size of a sequence to be considered as a unit on which NS acts? Mutation rate, generation time, selection differential for this sequence, recombination rate, ...?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;any sequence unit whose alteration can affect fitness is a candidate for NS.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Could we consider a nucleotide as a unit of NS? Why?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Yes, if it can affect fitness (which it can, see above) it can be selected for or against.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How does the quasispecies model fit into the question of what is the smallest unit of NS? &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;As far as I can tell, it is irrelevant. NS can act on &lt;em&gt;any&lt;/em&gt; self-replicating entity as long as the process of replication can produce variation that can affect fitness. If I understand correctly, the quasispecies model simply posits a group of entities with a very very high mutational rate. However, the rate of mutation does not affect the smallest unit that NS can act on, as I said above, &lt;em&gt;anything&lt;/em&gt; that can affect fitness will be subject to NS.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is it worth talking about that? Is this question biologically relevant? Or is it rather a question based on a choice of definition such as &quot;Is a virus alive?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, it is worth talking about it if you have the misconception that the smallest unit is a gene :). No, but seriously, it is an interesting concept and a very useful tool. The selfish gene hypothesis for example, helped us see the world of evolution in terms of sequences rather than species or individuals. NS did not change, our conception of it did. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;These are all useful conceptual tools that allow us as scientists to understand complex questions. However, NS is not a directed or conscious process so &lt;em&gt;it&lt;/em&gt; does not care or know what it acts on. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;PS. Please do not confuse protein-coding sequences with genes. As I said in my comment, there are many genes that do not produce proteins (tRNA genes for example) and that was even before the waters were muddied in the past few years. The current definition of gene is something like:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;any nucleotide sequence with a job to do&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Read the ENCODE papers for a more technical definition or take this one from &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A gene is a molecular unit of heredity of a living organism. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;UPDATE: First of all, you have to remember that Dawkins wrote &lt;em&gt;The Extended Phenotype&lt;/em&gt; more than 30 years ago, in a time when the only complete genomes available were those of a few viruses. The first bacterial genome was sequenced in the mid nineties and the first human genome draft human in 2000. It was a time when selection was seen as acting at the level of the individual, and the importance of genes was underestimated. Dawkins books were instrumental in bringing genes into the spotlight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if he &lt;em&gt;did&lt;/em&gt; argue that a nucleotide cannot be selected (I have not read this particular book) he was simply wrong. A nucleotide can indeed affect its chances of being replicated. Think about it, if you have a &lt;code&gt;G&lt;/code&gt; at a given position in the genome, and that &lt;code&gt;G&lt;/code&gt; is mutated to an &lt;code&gt;A&lt;/code&gt;, then the chances of the original &lt;code&gt;G&lt;/code&gt; being replicated are obviously very low. Therefore, the nucleotide 'affected' its chances of replication. Alternatively, a mutation of a single nucleotide in the promoter of a gene can also cause the entire gene not to be transcribed and, as I mentioned before, frameshift mutations can wreak havoc as well. All of these are down to single nucleotides. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, our vision of what a gene is has changed &lt;em&gt;enormously&lt;/em&gt; since Dawkins wrote his book, we understand the genome much better now, and we have realized that it is far more complex than originally believed. 30-year old literature about genes, even if written by such luminaries as Rihard Dawkins, should be taken with a pinch of salt today. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-08-28T13:12:08.093" LastActivityDate="2013-08-28T13:12:08.093" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10054" PostTypeId="2" ParentId="10051" CreationDate="2013-08-27T17:58:03.567" Score="2" Body="&lt;p&gt;Answer: In the late 1800s, by a few different guys building on each other.&lt;/p&gt;&#xA;&lt;p&gt;I personally had no idea, but a little searching around found this little gem, which seems up our alley: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3069519/&quot; rel=&quot;nofollow noreferrer&quot;&gt;The origins of bone marrow as the seedbed of our blood: from antiquity to the time of Osler&lt;/a&gt;.  It's only ten pages so definitely worth a read, but a few passages of note:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Neumann and Bizzozero... are credited with making the initial observations leading to the recognition of the marrow as the seat of blood formation... In his report published in October 1868, Neumann described the presence of nucleated red blood cells in the bone marrow sap of humans and rabbits by squeezing bone. He was the first to conclude that during postembryonic life, erythropoiesis was taking place in the marrow.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;However, Neumann concluded erroneously that the proliferation of marrow cells occurred inside the blood vessels of the marrow; the concept of marrow sinusoids was not coined until Minot's description in 1901.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It later says that, in the mid-1880s Osler stated&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;that there can be no doubt that nucleated red cells originate in the bone marrow...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It's actually a pretty interesting read, all in all, and like all of the best discoveries in science, it seems like a few people built on each others' work over the years, with a bunch sort of figuring it out around the same time.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-08-27T17:58:03.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10055" PostTypeId="2" ParentId="10020" CreationDate="2013-08-27T18:18:06.980" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Electroporation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Electroporation&lt;/a&gt; is a fairly common way to introduce exogenous nucleic acids into cells. Its name essentially describes the process - an electric voltage potential is applied across a biological membrane, eventually leading to the production of conducting hydrophilic pores. The image below is from the Wikipedia page linked above, showing non-conducting (upper) hydrophobic and conducting (lower) hydrophilic pores. Depending on the voltage, membrane composition, and other factors, these pores can eventually &quot;heal&quot; and close back up, or join together and lead to the rupture of the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/c/cc/Pore_schematic.svg/500px-Pore_schematic.svg.png&quot; alt=&quot;electroporation&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Electroporation is used in the lab as a method of &lt;a href=&quot;http://en.wikipedia.org/wiki/Transfection&quot; rel=&quot;nofollow noreferrer&quot;&gt;transfecting&lt;/a&gt; or transporting nucleic acids (usually DNA) into cells, to make them express genes they otherwise wouldn't, or to otherwise alter the genetic machinery. The transfected DNA can either remain in its own structure (such as a &lt;a href=&quot;http://en.wikipedia.org/wiki/Plasmid&quot; rel=&quot;nofollow noreferrer&quot;&gt;plasmid&lt;/a&gt;), or be incorporated (recombined) into the host genome, similar to what happens during a &lt;a href=&quot;http://en.wikipedia.org/wiki/Retrovirus&quot; rel=&quot;nofollow noreferrer&quot;&gt;retrovirus&lt;/a&gt; infection. Whether or not this happens is dependent on the structure and sequence of the construct being introduced, not the method of introduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in reference to your question, electroporation doesn't do anything that &lt;em&gt;directly&lt;/em&gt; allows more recombination to occur - all it is is a method of transportation. However, electroporation may allow for certain constructs to be introduced into the host more efficiently, or for a larger quantity of them to be introduced, leading to a greater &lt;a href=&quot;http://en.wikipedia.org/wiki/Transformation_efficiency&quot; rel=&quot;nofollow noreferrer&quot;&gt;transformation efficiency&lt;/a&gt;. Some cells, especially primary cells like neurons, for example, may only be transfected with any sort of efficiency with electroporation. However, electroporation can also have its down sides, as it can be rather stressful to the cells, and if the voltages and timing aren't properly adjusted can lead to high levels of cell death.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.863" LastActivityDate="2013-08-27T18:18:06.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10056" PostTypeId="1" AcceptedAnswerId="10072" CreationDate="2013-08-27T19:46:35.097" Score="4" ViewCount="5074" Body="&lt;p&gt;Related to my earlier question, &lt;a href=&quot;https://biology.stackexchange.com/questions/8857/how-does-the-human-liver-regrow&quot;&gt;&quot;How does the human liver regrow?&quot;&lt;/a&gt;, am curious as to why the liver is the only major organ that has this capability?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is it that other major organs, such as the heart and lungs etc are not able to regrow in the same fashion?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="-1" LastEditorDisplayName="user3795" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2018-05-18T07:50:56.853" Title="Why is the liver the only internal organ of the human body to regrow?" Tags="&lt;human-biology&gt;&lt;organs&gt;&lt;liver&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10057" PostTypeId="2" ParentId="10046" CreationDate="2013-08-27T20:09:02.507" Score="1" Body="&lt;p&gt;GC-content varies greatly among prokaryots, and it is used as a taxonomic characteristic. It is specially elevated in extremophyles, such as halophiles and thermophyles, and it's thought to be an adaptation to high temperature and other chemical and physical stresses. GC bonds are stronger than AT, so it's supossed to acts as a protection agains denaturalizing agents.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-08-27T20:09:02.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10059" PostTypeId="2" ParentId="10035" CreationDate="2013-08-28T03:12:24.850" Score="1" Body="&lt;p&gt;I was letting my fingers surfed in the internet about this question and found this interesting article : &lt;a href=&quot;http://www.caves.org/section/vertical/nh/55/TreeAnchors.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.caves.org/section/vertical/nh/55/TreeAnchors.pdf&lt;/a&gt; &#xA;Your  question is too broad so I guess the link gives a general answer.&#xA;hope this helps&lt;/p&gt;&#xA;" OwnerUserId="4330" LastActivityDate="2013-08-28T03:12:24.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10060" PostTypeId="1" AcceptedAnswerId="10061" CreationDate="2013-08-28T03:37:25.457" Score="2" ViewCount="259" Body="&lt;p&gt;From: &lt;a href=&quot;http://www.nal.usda.gov/wicworks/Topics/FG/Chapter4_InfantFormulaFeeding.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.nal.usda.gov/wicworks/Topics/FG/Chapter4_InfantFormulaFeeding.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Discard any infant formula remaining after a feeding. The mixture of infant formula with saliva provides an ideal breeding ground for disease-causing micro-organisms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why is this so? Doesn't Saliva contain anti-bacterial properties?&lt;/p&gt;&#xA;" OwnerUserId="1809" LastEditorUserId="115" LastEditDate="2013-09-06T16:47:10.603" LastActivityDate="2013-09-06T16:47:10.603" Title="Why does the mixture of infant formula with saliva provide an ideal breeding ground for disease-causing micro-organisms?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10061" PostTypeId="2" ParentId="10060" CreationDate="2013-08-28T04:31:09.600" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Doesn't Saliva contain anti-bacterial properties?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, in particular some IgA antibodies and lysozyme, but there are also plenty, and I mean &lt;strong&gt;plenty&lt;/strong&gt; of bacteria in your mouth at any given point; we do, after all, still have to brush our teeth!  In fact, animal (including human) bites should be treated lest they lead to sepsis.  Those bacteria would &lt;em&gt;love&lt;/em&gt; all the magnificent nutrients in infant formula.  Contact with an infant's mouth will introduce bacteria to the formula, as will exposure to air, contact with your hand, and anything else it experiences.  As an example, in the past few years, there have been some cases (from China, I believe, someone correct me if I'm wrong) of formula contaminated with bacteria, which were more than happy to stick around.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-28T04:31:09.600" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10062" PostTypeId="1" CreationDate="2013-08-28T04:39:08.737" Score="2" ViewCount="1349" Body="&lt;p&gt;I have been trying to understand how the tRNA transporting the correct amino acid required by the ribosome reaches the ribosome. The only way I can imagine this happening is that all types of tRNA+amino acid reach the ribosome, bombard the ribosome, and the ribosome will 'accept' only the one that matches what it is waiting for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can not imagine any other mechanism in the cell's cytoplasm that will somehow filter or push the correct tRNA+amino acid and move it towards the ribosome that needs it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do we explain this mystery?&lt;/p&gt;&#xA;" OwnerUserId="4339" LastEditorUserId="4339" LastEditDate="2013-08-29T01:13:07.573" LastActivityDate="2013-08-29T01:13:07.573" Title="How are the correct tRNAs transported to the ribosome?" Tags="&lt;biochemistry&gt;&lt;translation&gt;&lt;ribosome&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10064" PostTypeId="2" ParentId="10062" CreationDate="2013-08-28T05:15:10.297" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;The only way I can imagine this happening is that all types of tRNA+amino acid reach the ribosome, bombarding the ribosome, and the ribosome will 'accept' only the one that matches what it is waiting for.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yup, basically.  &lt;a href=&quot;https://upload.wikimedia.org/wikipedia/commons/9/94/Protein_translation.gif&quot; rel=&quot;nofollow&quot;&gt;This is an extremely cool figure&lt;/a&gt; showing the process. There are various elongation factors that aid the process, such as EF-Tu, which essentially waits until there is a good codon-anticodon match before hydrolyzing GTP and allowing the tRNA/amino acid to enter the ribosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This process can be particularly salient when you look at a concept such as codon-usage bias.  Certain tRNAs are more common in the cell, so if a given mRNA uses codons to match those tRNA instead of matching other degenerate but less common anti-codons, translation will occur faster.  This is more obvious in organisms such as &lt;em&gt;E. coli&lt;/em&gt; where growth is paramount.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-28T05:15:10.297" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10066" PostTypeId="2" ParentId="2020" CreationDate="2013-08-28T05:55:06.110" Score="-1" Body="&lt;p&gt;Cocaine hits the brain with dopamine creating the desired high, which, the users seek. When used repeatedly, the brain begins to confuse it's own production with the user's introduction. Slowly, the brain begins to depend on the user's introduction and slows its own production to the point where it no longer produces it. This lack of production causes the part of the brain responsible for dopamine to shrink. It shrinks because it is tissue that is not being used and therefore doesn't get the proper blood flow to it and begins lose its health. Blood stimulation is lost, cell health is lost and size is thereby lost. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The brains of heavy cocaine users display little to no age-related brain shrinkage as compared to non-users because their brain has already shrunk to its limit. The shrink is due to lack of fresh blood stimulation. It is like a sponge that no longer is getting water and shrivels. After 2 days the sponge stops shrinking, it doesn't eventually shrink to a dust particle. It shrinks to its water-free size, the same way the cocaine user's brain shrinks to a blood-stimulation-free size. Age can't further shrink what's already maxed out in shrinkage. &lt;/p&gt;&#xA;" OwnerUserId="4340" LastActivityDate="2013-08-28T05:55:06.110" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10067" PostTypeId="1" CreationDate="2013-08-28T06:23:20.127" Score="5" ViewCount="653" Body="&lt;p&gt;If blood loss necessitates immediate cell division to replace lost cells, does the increase in cell division correlate to shortening of telomeres? Does it further cause the Hayflick Limit to be reached sooner? Does blood loss accelerate apoptosis?&lt;/p&gt;&#xA;" OwnerUserId="4340" LastEditorUserId="4101" LastEditDate="2013-09-02T23:55:31.950" LastActivityDate="2016-12-10T16:59:47.323" Title="Does Blood Loss Shorten Telomeres?" Tags="&lt;hematology&gt;&lt;telomere&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10068" PostTypeId="2" ParentId="10067" CreationDate="2013-08-28T07:11:40.773" Score="6" Body="&lt;p&gt;Nope, nope, and nope.  A cursory glance over any page on &lt;a href=&quot;https://en.wikipedia.org/wiki/Haematopoiesis&quot;&gt;hematopoesis&lt;/a&gt; will reveal that blood cells are replenished from HSC, hematopoetic stem cells, which are self-renewing stem cells.  Telomerase is activated in stem cells.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-28T07:11:40.773" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10069" PostTypeId="1" AcceptedAnswerId="10070" CreationDate="2013-08-28T07:40:57.000" Score="2" ViewCount="1138" Body="&lt;p&gt;When I am &quot;hungry&quot;, I need something to eat physically. But what about &quot;appetite&quot;? I think it is a psychological phenomenon. Is that correct?&lt;/p&gt;&#xA;" OwnerUserId="4306" LastActivityDate="2013-08-28T08:43:22.353" Title="The difference between &quot;Hunger&quot; and &quot;Appetite&quot;" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10070" PostTypeId="2" ParentId="10069" CreationDate="2013-08-28T07:57:42.740" Score="1" Body="&lt;p&gt;According to the website &lt;a href=&quot;http://bodyandhealth.canada.com/channel_section_details.asp?text_id=5819&amp;amp;channel_id=1055&amp;amp;relation_id=17814&quot; rel=&quot;nofollow&quot;&gt;&quot;Appetite vs. hunger&quot;&lt;/a&gt;, the difference is very similar to what you were saying:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hunger is the need to eat.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hunger is instinctive, it is the body's way of letting you know it needs sustenance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Appetite is the desire to eat.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is a coordination between the brain and the stomach, this is learned behaviour.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some further information can be found in the article preview &lt;a href=&quot;http://www.jstor.org/discover/10.2307/986759?uid=2129&amp;amp;uid=2&amp;amp;uid=70&amp;amp;uid=4&amp;amp;sid=21102587970823&quot; rel=&quot;nofollow&quot;&gt;&quot;The Biological Nature of Appetite&quot;&lt;/a&gt; (Stellar, 1992)&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorDisplayName="user3795" LastEditDate="2013-08-28T08:43:22.353" LastActivityDate="2013-08-28T08:43:22.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10071" PostTypeId="2" ParentId="10037" CreationDate="2013-08-28T10:26:35.523" Score="1" Body="&lt;p&gt;I would definatley look at data from &lt;a href=&quot;http://www.slu.se/riksskogstaxeringen&quot; rel=&quot;nofollow&quot;&gt;Swedish National Forest Inventory (Riksskogstaxeringen)&lt;/a&gt;. They have time series data of multiple variables (DBH, size classes, species, dead wood etc) from plots all over the country. Extrapolations based on these data should produce reasonable estimates of total tree count, and probably the most accurate one that can be obtained at the moment. As an example, &lt;a href=&quot;http://www.lansstyrelsen.se/jamtland/SiteCollectionDocuments/Sv/publikationer/2012/Uppfoljning-av-biologisk-mangfald-med-data-fran-Riksskogstaxeringen.pdf&quot; rel=&quot;nofollow&quot;&gt;this report&lt;/a&gt; (in swedish) includes graphs on trees/km$^2$ for different species and areas (page 17 ff), but this is only based on areas that can support productive forestry.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-08-28T13:54:56.103" LastActivityDate="2013-08-28T13:54:56.103" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10072" PostTypeId="2" ParentId="10056" CreationDate="2013-08-28T11:01:12.003" Score="6" Body="&lt;p&gt;Maybe it is due to two factors:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The liver is one of the few solid non-tubular organs. If a tubular organ is damaged, all the layers that composes it must regenerate. This layers usually have different cell types, which is always nasty for regeneration since some of them may be formed by specialized tissue (for instance, myocytes are very difficult to regenerate. If the organ has a muscle layer, such as the esophagus, regeneration will be more difficult). Furthermore, damage in a tubular organ usually involves perforation, which will disrupt its function even if the injure isn't big.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Hepatocytes are pretty undifferentiated cells. They are basically enzymatic sacks with some vacuoles and mitochondrion, but they remain as your typical animal cell. They have a regular nucleus, they don't have any cytoskeletal adaptation and their vacuoles don't compose the most part of their cytoplasm (in a healthy liver). Cells with so little morphological specialization usually regenerate with no problem. Plus, the liver itself is constantly exposed to chemical damage due to toxins, drugs and other chemical compounds that may be present in the diet. This situation is special and don't apply for any other organs, with the exception of the kidneys (which, in fact is a very complicated tubular organ).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="28778" LastEditDate="2018-05-18T06:37:19.873" LastActivityDate="2018-05-18T06:37:19.873" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="10073" PostTypeId="1" CreationDate="2013-08-28T11:18:50.827" Score="3" ViewCount="45" Body="&lt;p&gt;The estimated number of species on Earth, as reported in this &lt;a href=&quot;http://www.nature.com/news/2011/110823/full/news.2011.498.html&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; is around 8.7 million. I am fascinated by how nature produces such a wide variety of species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As per my understanding, many species have gone extinct, that is, were not able to adapt to changing conditions on Earth. Perhaps the number of species before few thousands of years were larger than today. Can we estimate the approximate number of species at a given point in the past, using available data?&lt;/p&gt;&#xA;" OwnerUserId="655" LastEditorUserId="3952" LastEditDate="2013-08-28T11:30:21.120" LastActivityDate="2013-08-29T13:10:19.740" Title="Estimation of number of species at an earlier time" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10075" PostTypeId="1" CreationDate="2013-08-28T14:09:38.780" Score="0" ViewCount="229" Body="&lt;p&gt;This is a difficult question because there are many types of community-acquired pneumonia (CAP): typical acute, atypical acute and chronic.&#xA;Most common microorganisms are also different among different groups: children, adults, elderly, immunocompromised and people at risk of different diseases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some options:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Streptococcus pneumoniae&lt;/li&gt;&#xA;&lt;li&gt;Hemophilus influenzae&lt;/li&gt;&#xA;&lt;li&gt;Escherichia coli&lt;/li&gt;&#xA;&lt;li&gt;Klebsiella pneumoniae&lt;/li&gt;&#xA;&lt;li&gt;Pseudomonas aeruginosa&lt;/li&gt;&#xA;&lt;li&gt;bronchiectasis&lt;/li&gt;&#xA;&lt;li&gt;Chlamydia pneumoniae&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Not any virus, since they are present in only about 20% of diseases.&#xA;Streptococcus pneumonia is probably a good choice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the most common reason for community acquired pneumonia?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2013-08-29T08:08:10.740" LastActivityDate="2013-08-29T12:15:19.810" Title="What is it the most common reason for community acquired pneumonia?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10077" PostTypeId="2" ParentId="10075" CreationDate="2013-08-28T16:56:03.020" Score="2" Body="&lt;p&gt;You are right in that there are several ways to split down CAP, and plenty of different pathogens to look at.  But then we are looking for the &lt;strong&gt;most&lt;/strong&gt; common.  Pnumonia is most common in children and adults over the age of 75 (or 65 depending on who's counting).  Luckily there are plenty of good reviews for both populations.&lt;/p&gt;&#xA;&lt;p&gt;From the pediatric side we have &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/23481110&quot; rel=&quot;nofollow noreferrer&quot;&gt;Iroh Tam PY&lt;/a&gt;(1):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Pneumonia occurs more often in early childhood than at any other age,&#xA;with the exception of adults older than 75 years, and kills more&#xA;children than any other disease worldwide&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;As far as pathogens:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Streptococcus pneumoniae and Haemophilus influenzae type b (Hib) have&#xA;been characterized as 2 bacteria predominately responsible for cases&#xA;of fatal pneumonia in children.  However, widespread introduction&#xA;of Hib and pneumococcal conjugate vaccines has led to significant&#xA;declines, especially of Hib, although Streptococcus pneumoniae is&#xA;still the predominant bacteria isolated from bacterial CAP in&#xA;children.  There is increasing recognition of the prevalence of mixed&#xA;bacterial and viral infections, which have been documented in 23% to&#xA;33% of cases of pneumonia.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Then we move to the geriatric side of things with &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/22688530&quot; rel=&quot;nofollow noreferrer&quot;&gt;Falcone et al&lt;/a&gt; (2):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Common pathogens include H. influenzae, enteric gram-negative bacilli,&#xA;the atypical organisms, S. aureus, Pseudomonas aeruginosa, and M.&#xA;catarrhalis, although the relative prevalence of each tends to vary&#xA;among studies. Among elderly individuals with aspiration pneumonia,&#xA;gram-negative bacilli are the predominate organisms (49 %), followed&#xA;by anaerobic bacteria (16 %) and S. aureus (12 %).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Though I should note, having done them myself, getting accurate cultures is difficult, and viral levels a very likely to be under reported because of handling and skill.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;For example, in different prospective studies in which the&#xA;microbiologic etiology of CAP was systematically sought in the&#xA;elderly, a definite or presumptive pathogen was often reported in &amp;lt;60&#xA;% of the patients. (2)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;And again in children:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;There are 2 main challenges in the diagnosis of CAP: the first is the&#xA;definition of CAP, particularly in young children, in whom bacterial&#xA;and viral infections can occur with similar frequencies, and in whom&#xA;overdiagnosis of mild symptoms and signs may lead to unnecessary&#xA;antibiotic use; the second is the identification of a causative pathogen, which is frequently impractical and inadequate in children, and&#xA;in whom the failure to isolate an organism can result in unnecessary&#xA;antibiotic use. (1)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Taking into account more global sources, I'm actually thinking Hib infection has dropped more due to vaccination than I gave it credit for, putting my bet on S. pneumoniae, and showing my regional experience may not be representative (3, 4, 5, 6).&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;(1) Iroh Tam PY. Approach to common bacterial infections: community-acquired pneumonia. Pediatr Clin North Am. 2013 Apr;60(2):437-53. doi: 10.1016/j.pcl.2012.12.009. Epub 2013 Jan 12&lt;/p&gt;&#xA;&lt;p&gt;(2) Falcone M. et al. Pneumonia in frail older patients: an up to date. Intern Emerg Med. 2012 Oct;7(5):415-24. Epub 2012 Jun 12.&lt;/p&gt;&#xA;&lt;p&gt;(3) Brown JS. Community-acquired pneumonia. Clin Med. 2012 Dec;12(6):538-43.&lt;/p&gt;&#xA;&lt;p&gt;(4) Kurutepe S, Ecemiş T, Ozgen A, Biçmen C, Celik P, Aktoğu Özkan S, Sürücüoğlu S. [Investigation of bacterial etiology with conventional and multiplex PCR methods in adult patients with community-acquired pneumonia]. Mikrobiyol Bul. 2012 Oct;46(4):523-31.&lt;/p&gt;&#xA;&lt;p&gt;(5) Tao LL, Hu BJ, He LX, Wei L, Xie HM, Wang BQ, Li HY, Chen XH, Zhou CM, Deng WW. Etiology and antimicrobial resistance of community-acquired pneumonia in adult patients in China. Chin Med J (Engl). 2012 Sep;125(17):2967-72.&lt;/p&gt;&#xA;&lt;p&gt;(6) Capelastegui A, España PP, Bilbao A, Gamazo J, Medel F, Salgado J, Gorostiaga I, Lopez de Goicoechea MJ, Gorordo I, Esteban C, Altube L, Quintana JM; Poblational Study of Pneumonia (PSoP) Group. Etiology of community-acquired pneumonia in a population-based study: link between etiology and patients characteristics, process-of-care, clinical evolution and outcomes.  BMC Infect Dis. 2012 Jun 12;12:134. doi: 10.1186/1471-2334-12-134.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-08-29T12:15:19.810" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10080" PostTypeId="2" ParentId="8540" CreationDate="2013-08-28T17:10:59.857" Score="2" Body="&lt;p&gt;The specific characteristics sought after will vary &lt;strong&gt;widely&lt;/strong&gt;, but that being said, there are a few key features many groups look for.  I've talked to and heard a number of individuals at a number of different companies, and there are a lot of different techniques and pathways looked for.  In general, however, &lt;strong&gt;the single, most important factor is value&lt;/strong&gt;.  If the drug won't make money, it's almost never considered &quot;promising.&quot;  Maybe that's a sad fact of the way the world works, but it's a fact.  The average drug costs around &lt;strong&gt;$1 billion (USD)&lt;/strong&gt; to bring to market so the successful ones damn well better recoup that (Orphan drugs and companies actively pursuing them often have an easier time of this, as the FDA is understandably less restrictive and fast-tracks their progress).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's not actually so simple.  It's a large, crowded market out there, and there is a lot of intellectual property floating around.  A wise businesswoman told me that her company focuses on the middle-ground.  A target that is &lt;em&gt;too&lt;/em&gt; promising is probably already owned by Genentech, so they aim for the ones that are below the attention of the giants but still quite profitable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After that, it's mainly what you might expect.  &lt;strong&gt;High avidity&lt;/strong&gt;, &lt;strong&gt;long half-life&lt;/strong&gt; coupled with &lt;strong&gt;low toxicity&lt;/strong&gt; (more on this later), small size (if possible), and a &lt;strong&gt;realistic time frame&lt;/strong&gt;.  A month can mean millions of dollars, so working for a decade is not necessarily a possibility.  Often, companies will use &lt;strong&gt;high-throughput screens&lt;/strong&gt; of thousands, even millions of small molecules to look for an effect.  The screening process is usually extremely rigorous, and many potential candidates are eliminated as not good enough.  Sometimes they do some fancy stuff such as &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18446295&quot; rel=&quot;nofollow&quot;&gt;3D modeling&lt;/a&gt; but it is definitely a field where brute force can still be successful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Often those screens are used against primary cells to test for toxicity.  In fact, throughout the entire process, toxicity is a huge factor.  A full &lt;strong&gt;20%-40%&lt;/strong&gt; of drug attrition is due to safety and liability issues.  It's a constant balance: &lt;em&gt;nothing&lt;/em&gt; can risk the health of healthy, control volunteers, but sometimes more risk is acceptable.  The first HIV/AIDS drugs were incredibly toxic, but that was okay because it was still better than the alternative.  These days, the toxicity requirements for HIV/AIDS treatments such as HAART are stricter.  Short-term antibiotics are allowed more risk since you only take them for five/seven days, whereas long-term medication for chronic illnesses are held to much higher standards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, loss of eyesight might be preferable to death, but it's unacceptable if treating the flu.  The mantra I've been told is three things:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Don’t treat one thing but cause another&lt;/li&gt;&#xA;&lt;li&gt;Don't cause cancer&lt;/li&gt;&#xA;&lt;li&gt;Don’t cause birth defects or alter the ability to have children&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Toxicologists are conservative, willing to throw the baby out with the bathwater.  In short, &lt;strong&gt;Fail Early&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-28T17:10:59.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10082" PostTypeId="1" CreationDate="2013-08-28T17:25:37.987" Score="2" ViewCount="244" Body="&lt;p&gt;Can the colour of skin change with age? Can a dark skinned person become fair or vice versa?  Can Melanocyte production vary?&lt;/p&gt;&#xA;" OwnerUserId="4323" LastEditorUserId="3971" LastEditDate="2013-08-29T14:21:48.857" LastActivityDate="2013-08-29T14:21:48.857" Title="Can the colour of skin change with age" Tags="&lt;human-biology&gt;&lt;skin&gt;&lt;pigmentation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10083" PostTypeId="2" ParentId="10060" CreationDate="2013-08-28T18:00:02.573" Score="0" Body="&lt;p&gt;Whether infant formula or food for adult consumption - should be discarded if there is salivary contamination since there is universal presence of microorganisms in saliva. These act as culture media and the microorgnisms rapidly degrade the food, not to mention the selective overgrowth of pathogenic microorganisms.&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="4216" LastEditDate="2013-09-06T15:59:11.747" LastActivityDate="2013-09-06T15:59:11.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10084" PostTypeId="2" ParentId="9911" CreationDate="2013-08-28T18:10:01.677" Score="6" Body="&lt;p&gt;It's actually because of the greater risk &quot;&lt;em&gt;from breast, ovarian, and uterine cancers&lt;/em&gt;&quot; (&lt;a href=&quot;http://www.space.com/22252-women-astronauts-radiation-risk.html&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt;).  There's a more scientific write-up &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21574861&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, and while I don't have access the abstract implies that a more rigorous update of the exposure criteria upheld sex differences.  From a more terrestrial perspective, The Nuclear Information and Resource Service (&lt;a href=&quot;http://www.nirs.org&quot; rel=&quot;nofollow&quot;&gt;nirs.org&lt;/a&gt;) has &lt;a href=&quot;http://www.nirs.org/radiation/radhealth/radiationwomen.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; rather incensed piece on the issue.  They cite a &lt;a href=&quot;http://www.nap.edu/catalog.php?record_id=11340&quot; rel=&quot;nofollow&quot;&gt;2006 NAS report&lt;/a&gt; which&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;finds that harm to women (cancer) is 50% higher than the comparable harm to men from radiation doses that fall within the legal limit to the public over a lifetime.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Basically, it looks like females are more likely to get cancer from radiation, and once they do, those cancers are more likely to cause more harm.  &lt;a href=&quot;http://online.liebertpub.com/doi/full/10.1089/jwh.2014.4914&quot; rel=&quot;nofollow&quot;&gt;According to the executive summary of NASA's 2014 in-depth report&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[A] 45-year-old man has a 344-day limit versus a 187-day limit for a 45-year-old woman, due to radiation exposures on the space station that would be typical at the time of solar maximum.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The effect of body size, however, could be the opposite.  &lt;a href=&quot;http://healthland.time.com/2011/07/21/the-hazards-of-height-tall-people-may-be-more-prone-to-cancers/&quot; rel=&quot;nofollow&quot;&gt;Taller women get more cancer&lt;/a&gt;, with &lt;a href=&quot;http://www.thelancet.com/journals/lanonc/article/PIIS1470-2045%2811%2970154-1/fulltext&quot; rel=&quot;nofollow&quot;&gt;that study&lt;/a&gt; showing a 16% increase in incidence for every 10cm (4in) height increase.  That increase, however, is among certain types, such as melanomas, and not the above-mentioned &quot;&lt;em&gt;breast, ovarian, and uterine cancers&lt;/em&gt;.&quot;  Males, being taller, could therefore get more cancer overall; it turns out &lt;a href=&quot;http://healthland.time.com/2011/07/13/almost-every-type-of-cancer-kills-more-men-than-women-study-shows/&quot; rel=&quot;nofollow&quot;&gt;males usually die more from most cancers&lt;/a&gt;, just not (obviously) &quot;&lt;em&gt;breast, ovarian, and uterine cancers&lt;/em&gt;.&quot;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="3340" LastEditDate="2015-09-11T18:40:43.760" LastActivityDate="2015-09-11T18:40:43.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10085" PostTypeId="2" ParentId="10082" CreationDate="2013-08-28T19:44:32.897" Score="2" Body="&lt;p&gt;Vitiligo is a loss of skin pigmentation that causes patches of lighter skin as the immune system attacks melanocytes. It can eventually progress to cover the entire body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ongenae, K., Van Geel, N. and Naeyaert, J.-M. (2003), Evidence for an Autoimmune Pathogenesis of Vitiligo. Pigment Cell Research, 16: 90–100. doi: 10.1034/j.1600-0749.2003.00023.x&lt;/p&gt;&#xA;" OwnerUserId="4342" LastEditorUserId="4342" LastEditDate="2013-08-28T21:17:03.200" LastActivityDate="2013-08-28T21:17:03.200" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10086" PostTypeId="2" ParentId="10073" CreationDate="2013-08-28T19:51:03.750" Score="1" Body="&lt;p&gt;according to the National Science Foundation press release&lt;a href=&quot;http://www.nsf.gov/news/news_summ.jsp?cntn_id=111785&amp;amp;org=NSF&amp;amp;from=news&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;Species Have Come and Gone at Different Rates than Previously Believed&quot;&lt;/a&gt; indeed show what &lt;a href=&quot;https://biology.stackexchange.com/questions/10073/estimation-of-number-of-species-at-an-earlier-time#comment13227_10073&quot;&gt;Atl LED suggests&lt;/a&gt;, that the progression is not linear, with the study showing that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The previously thought exponential increase in diversity is not there.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Further, there is the &lt;a href=&quot;http://paleodb.org/cgi-bin/bridge.pl&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;Palaeobiology Database&lt;/a&gt;, that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;seeks to provide researchers and the public with information about the entire fossil record. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The site also has links to further papers of the topic.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-08-29T13:10:19.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10088" PostTypeId="2" ParentId="10082" CreationDate="2013-08-28T19:54:45.390" Score="2" Body="&lt;p&gt;There are all sorts of things that can stimulate &lt;a href=&quot;https://en.wikipedia.org/wiki/Melanocyte&quot; rel=&quot;nofollow&quot;&gt;melanocytes&lt;/a&gt;, most notably UV rays (ie from the Sun).  So yes, melanogenesis can very over age and exposure to the Sun.  Young infants often are lacking build ups of melanin in their skin, eyes, and hair, which is why these things darken with age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other more pathogenic ways to change melanogenesis, including malnutrition, but UV exposure this health common way.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2013-08-28T19:54:45.390" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10090" PostTypeId="1" AcceptedAnswerId="10091" CreationDate="2013-08-28T20:47:47.300" Score="3" ViewCount="569" Body="&lt;p&gt;As the question states, what are the limits of retroviral genetic delivery systems? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are they limited to adding additional gene sequences to a cell, or can they actually overwrite specified segments of DNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or, more aptly described, can they remove one segment of DNA, and insert a new segment (whether the same or different length) in the spot where the old segment used to be?&lt;/p&gt;&#xA;" OwnerUserId="4344" LastEditorUserId="4101" LastEditDate="2013-08-28T21:04:13.677" LastActivityDate="2013-08-29T13:13:07.783" Title="Can retroviral delivery systems &quot;overwrite&quot; genes?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;virology&gt;&lt;retrovirus&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10091" PostTypeId="2" ParentId="10090" CreationDate="2013-08-28T21:03:20.800" Score="4" Body="&lt;p&gt;Retroviruses, such as HIV, have a genome that is composed of RNA.  Once inside the host cell, that RNA is reverse-transcribed into DNA; it is that DNA which is &lt;strong&gt;inserted&lt;/strong&gt; into the host genome.  All retroviral genomes are integrated through &lt;em&gt;insertion&lt;/em&gt;; there is never any &lt;em&gt;replacement&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some retroviruses do, however, disrupt normal gene function.  Mouse mammary tumor virus (MMTV) or Human T-lymphotropic viurs (HTLV) will often insert inside or near host genes termed &quot;oncogenes,&quot; that, when disrupted, can lead to cancer formation.&lt;sup&gt;&lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJM199911183412121&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;,&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1814689&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;&lt;/sup&gt;  Viruses could cause up to 15% of cancers in humans.&lt;sup&gt;&lt;a href=&quot;http://carcin.oxfordjournals.org/content/21/3/405.full&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;&lt;/sup&gt;  So, no actual genetic replacement, but there can definitely be genetic disruption and a deleterious functional change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This ability, to insert new genes, has recently been touted as a new way to cure many diseases.  &lt;a href=&quot;http://www.latimes.com/news/science/la-sci-gene-therapy-20130712,0,737038.story&quot; rel=&quot;nofollow&quot;&gt;Here's&lt;/a&gt; the most recent case, where the researchers used a retroviral backbone to insert a functional gene into some children; i.e., genetic engineering (Side note: Every time you see an article saying how scientists used HIV to cure a disease or something, this is what they mean.  It's akin to calling dental X-rays &quot;giant death lasers that fight cavities.&quot;).  With luck we will get better and better at it, but right now it's only successful in limited cases for very specific diseases; massive genetic engineering of humans is still far off (unless you count bone marrow transplants).&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-08-28T21:26:58.380" LastActivityDate="2013-08-28T21:26:58.380" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10092" PostTypeId="2" ParentId="3599" CreationDate="2013-08-28T21:03:36.040" Score="1" Body="&lt;p&gt;It isn't really a specific light intensity that an organism will interpret as the start of a photoperiod. Maynard Johnson reported in 1939 that intensity of light used had an effect on the rate at which mice would shift their circadian rhythms. So, brighter light has a stronger effect, but there isn't a cutoff point that I'm aware of. Johnson was using illumination as low as 2.5 foot candles, which is pretty dim. Aschoff and Pittendrigh did some more work on light intensity in the 50s and 60s, but I don't think anyone ever found anything resembling a cutoff point, only the degree to which intensity had an effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Computer monitors are pretty bright. Luminance rating is typically 250-350 cd/m2, which, for comparison with Maynard's experiment, is eqivalent to 23-32 foot-candles. &lt;a href=&quot;http://computer.howstuffworks.com/monitor6.htm&quot; rel=&quot;nofollow&quot;&gt;http://computer.howstuffworks.com/monitor6.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Johnson, Maynard S. &quot;Effect of continuous light on periodic spontaneous activity of white‐footed mice (Peromyscus).&quot; Journal of Experimental Zoology 82.2 (1939): 315-328.&lt;/p&gt;&#xA;" OwnerUserId="4342" LastActivityDate="2013-08-28T21:03:36.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10094" PostTypeId="1" CreationDate="2013-08-29T04:08:04.783" Score="2" ViewCount="92" Body="&lt;p&gt;Can we identify an individual from their palm lines. Is there any uniqueness for palm lines among family members ?&lt;/p&gt;&#xA;" OwnerUserId="4323" LastEditorUserId="1590" LastEditDate="2013-08-29T06:35:07.307" LastActivityDate="2013-08-30T05:40:20.127" Title="Can we identify an individual from their palm lines" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10095" PostTypeId="1" CreationDate="2013-08-29T04:08:54.407" Score="3" ViewCount="310" Body="&lt;p&gt;I think it can do two things:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The cell may be duplicating the genome during S phase.&lt;/li&gt;&#xA;&lt;li&gt;The cell may be transcribing the DNA into mRNA. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Question: Can the two activities occur at the same time or one at a time? In other words, are cells efficient multi-taskers?&lt;/p&gt;&#xA;" OwnerUserId="4346" LastActivityDate="2013-08-30T10:56:23.900" Title="When DNA is at its uncondensed form, what can it do?" Tags="&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10096" PostTypeId="1" CreationDate="2013-08-29T04:16:06.093" Score="4" ViewCount="196" Body="&lt;p&gt;Calcium hydroxide induces dentine formation in permanent teeth, while it causes resorption of tooth in deciduous teeth. How is this dual role explained?&lt;/p&gt;&#xA;" OwnerUserId="4323" LastEditorUserId="4323" LastEditDate="2013-08-29T12:10:06.970" LastActivityDate="2014-06-26T18:01:06.007" Title="What is an explanation of the dual role of calcium hydroxide in teeth?" Tags="&lt;human-biology&gt;&lt;teeth&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10097" PostTypeId="2" ParentId="2362" CreationDate="2013-08-29T06:00:51.453" Score="2" Body="&lt;p&gt;The mechanism of oral wound healing is similar to that elsewhere in the body. Depending on the type/ extend of wound, it may be primary or secondary.The clot and the encrustations are the part of the healing process.&lt;/p&gt;&#xA;" OwnerUserId="4323" LastActivityDate="2013-08-29T06:00:51.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10100" PostTypeId="1" CreationDate="2013-08-29T07:51:46.200" Score="2" ViewCount="1798" Body="&lt;p&gt;Why do rodents' teeth continue to grow? Enamel formation and/or root formation continue throughout rodents' lives. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the mechanism that causes this? &lt;/p&gt;&#xA;" OwnerUserId="4323" LastEditorDisplayName="user3795" LastEditDate="2013-08-29T10:36:02.993" LastActivityDate="2013-09-28T11:33:33.763" Title="Why do rodents' teeth continue to grow?" Tags="&lt;anatomy&gt;&lt;teeth&gt;&lt;rodents&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10101" PostTypeId="2" ParentId="10094" CreationDate="2013-08-29T07:52:52.843" Score="1" Body="&lt;p&gt;It was tricky searching for this through the morass of palmistry sites.  But, in the field of biometrics, I found the article &lt;a href=&quot;http://www.biometrics.gov/documents/palmprintrec.pdf&quot; rel=&quot;nofollow&quot;&gt;&quot;Palm Print Recognition&quot;&lt;/a&gt;, which states that (bolding mine):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because fingerprints &lt;strong&gt;and palms&lt;/strong&gt; have both &lt;strong&gt;uniqueness&lt;/strong&gt; and permanence..&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;it has been used for identification the same as fingerprints. The only reason it is not as widespread as fingerprints is largely due to logistics such as computer processing.&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-08-29T07:52:52.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10102" PostTypeId="1" CreationDate="2013-08-29T07:55:41.043" Score="8" ViewCount="179" Body="&lt;p&gt;Do you have any classic references for mathematical approaches in bioinformatics that are applicable to linguistics (or vice versa)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;br&gt; &#xA;I am mainly interested in approaches to reconstruct the history of languages, the rate of language mutation, phylogenies of languages, etc.&lt;/p&gt;&#xA;" OwnerUserId="4347" LastEditorUserId="3624" LastEditDate="2013-08-29T10:47:43.670" LastActivityDate="2013-08-30T00:54:15.967" Title="Examples of references for mathematical approaches in bioinformatics that are applicable to linguistics?" Tags="&lt;bioinformatics&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;literature&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10105" PostTypeId="2" ParentId="2362" CreationDate="2013-08-29T08:21:09.010" Score="13" Body="&lt;p&gt;To build on the answers from @Armatus and @S-Sunil&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The healing mechanism involves the inflammatory process, which is the same in almost the entire body. In particular in both skin and mucosa (both referred to as &quot;epithelial&quot; tissues), when there is a break, platelets and clotting factors clot off any bleeding vessels, white blood cells (neutrophils and macrophages in particular) collect and destroy any bacteria, dead cells and muck, and then the process of regeneration occurs (with ongoing inflammation), where stem cells in the surrounding tissue regrow cells, new blood vessels may be formed and scar tissue is laid down to give extra strength. Eventually after these stages of healing, there is &quot;remodelling&quot; where the structure basically gets better.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Kr34a.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to why oral wounds heal quickly and don't get infected that much? There are a bunch of reasons. One is that the head and neck has an excellent blood supply- just think of scalp wounds where you bleed like crazy but then they heal very well. Another is that mucous membranes have immune functions that stop invading microbes. Generally speaking we divide this into &quot;innate&quot; immunity which is a general response, and &quot;adaptive&quot; immunity which is tailored towards specific bugs. The mucosa has both. There are neutrophils and macrophages (innate) which live in that area, there are lymphoid patches (like lymph nodes, and adaptive), there are immunoglobulins specific to mucosa (IgA) which is adaptive in nature, and the epithelial lining cells themselves will signal to the rest of the immune system if there is damage or an infection. Plus, saliva itself has chemicals and enzymes which break down oral bugs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vU03f.jpg&quot; alt=&quot;Oral immunity&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the oral bacteria themselves are not particularly invasive. Just think, every time you brush your teeth, you cause multiple abrasions in your mouth. In fact, measurable amounts of bacteria from the mouth end up in your bloodstream every time  you brush your teeth! And yet, we don't end up with bloodstream infections as a result. This is partially because the rest of our immune system (and the structure of our heart and vessels) is intact, and partially because oral bacteria are not very invasive or pathogenic. They kind of have a sweet deal living in your mouth minding their own business and not killing their host, and even causing infection in an oral wound would make their continued survival less likely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition I should probably point out that skin has a great deal of bacteria on it as well, and yet we rarely get infections from them (unless colonised by an invasive species), for the same reasons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3FSJa.png&quot; alt=&quot;colonisation, invasion, infection&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4182" LastActivityDate="2013-08-29T08:21:09.010" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10106" PostTypeId="2" ParentId="10100" CreationDate="2013-08-29T09:42:09.953" Score="2" Body="&lt;p&gt;The article &lt;a href=&quot;http://www.lafebervet.com/small-mammal-medicine/medical-topics/dental-anatomy/&quot; rel=&quot;nofollow&quot;&gt;&quot;Dental Anatomy of Rabbits and Rodents&quot;&lt;/a&gt; (Crossley et al. 2010) provides a basic review of rodent teeth, as there are over 1700 species.  But, in general, the teeth are constant replaced due to abrasion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What the mechanism is for continual dental growth in rodents are, in part, discussed in the article &lt;a href=&quot;http://www.stembook.org/node/551&quot; rel=&quot;nofollow&quot;&gt;&quot;Tooth organogenesis and regeneration&quot;&lt;/a&gt; (Thesleff and Tummers), where they state&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;During the cap and bell stages the lateral sides of the epithelial bud start enveloping the underlying dental mesenchyme, and from this point onwards the leading edge of the epithelium is called the cervical loop. The basal epithelial cell layer of the loop bordering the dental papilla is known as the inner enamel epithelium and the part facing the dental follicle is known as the outer enamel epithelium. The core of the loop is populated by loosely arranged stellate reticulum cells and a thin layer of stratum intermedium cells facing the inner enamel epithelium This cervical loop structure is maintained in continuously growing teeth and constitutes the epithelial part of the adult stem cell niche (Harada et al., 1999; Tummers and Thesleff, 2003: Tummers and Thesleff, 2008)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerDisplayName="user3795" LastActivityDate="2013-08-29T09:42:09.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10107" PostTypeId="2" ParentId="10102" CreationDate="2013-08-29T09:44:11.200" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Branching_process&quot; rel=&quot;nofollow&quot;&gt;Branching processes&lt;/a&gt; (from probability theory) were originally developed to study the extinction of family names (&lt;a href=&quot;http://en.wikipedia.org/wiki/Galton%E2%80%93Watson_process&quot; rel=&quot;nofollow&quot;&gt;Galton-Watson process&lt;/a&gt;), but are also used to study biological extinction and general evolutionary processes. One example that applies ideas from branching processes and phylogenetic methods to reconstruct ancient languanges can be found in &lt;a href=&quot;http://www.pnas.org/content/100/15/9079.long&quot; rel=&quot;nofollow&quot; title=&quot;Forster &amp;amp; Toth. 2003. Toward a phylogenetic chronology of ancient Gaulish, Celtic, and Indo-European. Proceedings of the National Academy of Sciences 100(15): 9079-9084.&quot;&gt;Forster &amp;amp; Toth (2003)&lt;/a&gt;. The basic concepts of branching processes can be found in most textbooks on probability theory, but a classic reference is &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0486495086&quot; rel=&quot;nofollow&quot; title=&quot;T.H. Harris. 1963. The Theory of Branching Processes. Springer-Verlag. Berlin.&quot;&gt;Harris 1963&lt;/a&gt; (&lt;a href=&quot;http://www.rand.org/content/dam/rand/pubs/reports/2009/R381.pdf&quot; rel=&quot;nofollow&quot;&gt;pdf&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is maybe not exactly what you are after but should be related to your question.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-08-29T14:54:54.950" LastActivityDate="2013-08-29T14:54:54.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10108" PostTypeId="2" ParentId="10095" CreationDate="2013-08-29T10:23:13.483" Score="2" Body="&lt;p&gt;At least in bacteria they can. In optimal conditions, &lt;em&gt;E. coli&lt;/em&gt; divides itself about once every 20-30 minutes. Wich is more important, the replication time of its genome is about 40-50 minutes. That means that, in exponential phase, &lt;em&gt;E. coli&lt;/em&gt; has at least two active replication bubbles. Since the density of ribosomes must be more or less constant, aswell that the new cells needs to synthetise peptidoglycan and other cell components, that means that replication and transcription occurs simultanously. If not, ribosomes, enzimes, tRNAs and mRNAs would be diluded in every replication event.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In eukarya I see no reason of why that shouldn't be possible. The formation of chromatin is not a random event and some specific proteins are required during short periods of time during some steps of mitosis, so it's logic to assume that some specific parts are not compacted or that transcriptional activity can occur even in chromatin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The specific region that is duplicating itself in a given time will probably be unable to transcribe, because the polymerase complex is pretty big and they need to open the double helix, and that. But this is somehow like children playing in the train tracks. Once the train aproaches, the children stay apart, and they continue again when the train has gone.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="4168" LastEditDate="2013-08-30T10:56:23.900" LastActivityDate="2013-08-30T10:56:23.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10109" PostTypeId="1" CreationDate="2013-08-29T11:39:55.970" Score="15" ViewCount="2269" Body="&lt;p&gt;I'm thinking of the human genome specifically, but more general answers are welcome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As RNA polymerase moves along the DNA helix it follows a single strand.  The two DNA strands are unwound locally by a helicase enzyme. However, after some distance, I imagine that either the polymerase must move around the axis of the DNA OR the DNA must somehow be rotated along it's length to relieve the twisting by the polymerase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't quite understand how the DNA is free to rotate, being part of a very long molecule. However the other option is also causing me a problem: the growing (nascent) mRNA can be tens of thousands of bases long while still attached to the RNA polymerase and the DNA template.  If the RNA polymerase follows the helix of the DNA, does it also drag the full transcript around with it?  &lt;/p&gt;&#xA;" OwnerUserId="1128" LastEditorUserId="9943" LastEditDate="2020-04-03T23:36:27.837" LastActivityDate="2020-04-03T23:36:27.837" Title="Does RNA polymerase move around DNA or does DNA rotate beneath the polymerase?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;rna&gt;&lt;transcription&gt;" AnswerCount="4" CommentCount="4" FavoriteCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="10113" PostTypeId="2" ParentId="10109" CreationDate="2013-08-29T12:13:34.070" Score="4" Body="&lt;p&gt;Both the DNA and the RNA polymerase complexes moves along the DNA molecule like it was a track. While the new mRNA is big, it would never be as big as the whole genome, so the reference point is the DNA molecule. Plus, the functioning of the movement of this enzymes is quite similar to other proteins that move &quot;climbing&quot; long polymers, such as actin polymers or microtubules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the theoretical models that describes the movement of this kind of proteins is the model of rectified thermal diffusion, based on Richard Feynman's idea of the Brownian ratchet. A Brownian ratchet is a device that allows the conversion of Brownian random movements into a directional force.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Brownian_ratchet&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Brownian_ratchet&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The polymerases consume ATP, which enable them to suffer cyclic conformational changes (one change per ATP consumed), which allows the complex to attach to the molecule and detach. Once the complex has detached, by simple diffusion it moves in a random direction. Then, it attaches again. If the movement has occurred in the right sense, it will stay where it ended, while if it has gone in the wrong sense it will return to its previous position. As only a few movements are allowed, the complex will only move in that sense, even if the motor force is random.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know exactly what conformational changes occurs in the RNA polymerase, but this general process seems to apply to almost any motile protein, including those enzymes that travel across polymers. Since the motor force is simple diffusion, and since the mRNA molecule doesn't need to &quot;travel&quot; with the polymerase (it just floats joined to it, but doesn't &quot;pull&quot;), I think there isn't any trouble with this.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="1306" LastEditDate="2013-08-29T12:58:33.920" LastActivityDate="2013-08-29T12:58:33.920" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10114" PostTypeId="2" ParentId="10090" CreationDate="2013-08-29T13:13:07.783" Score="2" Body="&lt;p&gt;Just to give a simpler example of what Amory has explained. Viruses &lt;em&gt;can&lt;/em&gt; overwrite existing information, just not the way you would think if coming from the world of computers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As already mentioned, viruses have the ability to insert their genetic information into the host's genome. They do this by essentially cutting the host DNA open and inserting themselves between the cuts. This insertion can disrupt a gene, thereby, in a sense, overwriting it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To take a simple metaphor, consider the following sentence (a &quot;gene&quot;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hello, my name is Bob.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If I were to insert a new sequence of characters into that sentence, it's meaning would be lost:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hellalkehfgawpif galsdhfblasud hyflaishbflaegfvlhD BFHDFLHFEiDBFKHDBfo, my name is Bob&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;While the original sentence is still there so it has not been &lt;em&gt;overwritten&lt;/em&gt; in the strictest sense of the term, the information it contains has now been lost to the cell so the result is the same. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-08-29T13:13:07.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10115" PostTypeId="5" CreationDate="2013-08-29T13:55:29.287" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-08-29T13:55:29.287" LastActivityDate="2013-08-29T13:55:29.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10116" PostTypeId="4" CreationDate="2013-08-29T13:55:29.287" Score="0" Body="Pigmentation refers to the coloration in plants or animals due to the presence of pigment in the tissue." OwnerUserId="3971" LastEditorUserId="1306" LastEditDate="2013-08-29T16:14:38.600" LastActivityDate="2013-08-29T16:14:38.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10117" PostTypeId="5" CreationDate="2013-08-29T14:25:40.183" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-08-29T14:25:40.183" LastActivityDate="2013-08-29T14:25:40.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10118" PostTypeId="4" CreationDate="2013-08-29T14:25:40.183" Score="0" Body="Retroviruses are single-stranded RNA viruses that reverse-transcribe their genome into DNA that is then integrated into the host genome." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-08-29T15:52:30.110" LastActivityDate="2013-08-29T15:52:30.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10119" PostTypeId="2" ParentId="10109" CreationDate="2013-08-29T14:49:13.790" Score="2" Body="&lt;p&gt;The partial &lt;a href=&quot;https://biology.stackexchange.com/a/10113/1128&quot;&gt;answer by Miguel&lt;/a&gt; helped a lot but I needed to go and read about the extra part that I was missing: &lt;a href=&quot;http://en.wikipedia.org/wiki/Topoisomerases&quot; rel=&quot;nofollow noreferrer&quot;&gt;Topoisomerases&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The DNA is unwound beneath the RNA polymerase, which causes supercoiling in front and behind.  For long transcripts to proceed, the current theory is that the DNA template has to be cut, unwound and re-ligated and that this is performed by &lt;a href=&quot;http://en.wikipedia.org/wiki/Topoisomerases&quot; rel=&quot;nofollow noreferrer&quot;&gt;Topoisomerases&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This raises the questions as to how often the DNA gets cut and re-ligated during active transcription and does this produce a noticeable effect (i.e. mutation)?&lt;/p&gt;&#xA;" OwnerUserId="1128" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-08-29T14:49:13.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10120" PostTypeId="1" AcceptedAnswerId="10121" CreationDate="2013-08-29T15:26:46.113" Score="5" ViewCount="822" Body="&lt;p&gt;On the high-wavelength side of things, we see almost-infrared as reddish, with a slight tinge of magenta. On the low side, we see violet fading into the same magenta color. Why is that? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see it clearly on any hue chart. There's an unbroken flow from one to the other, even though the wavelengths are literally as far apart as they can be while still remaining visible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that color vision is limited due to several biological factors(cone receptivity, absorption, etc), but why do the colors on both side fade into each other? Is it just our brain making things &quot;neat&quot; and continuous?&lt;/p&gt;&#xA;" OwnerUserId="4349" LastActivityDate="2019-06-20T06:49:47.573" Title="Why do our eyes &quot;wrap&quot; hue from UV to IR?" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;vision&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10121" PostTypeId="2" ParentId="10120" CreationDate="2013-08-29T16:23:09.560" Score="4" Body="&lt;p&gt;Basically.  You are most likely looking at the electromagnetic spectrum, which is linear and conveniently makes sense... except for magenta.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Colors as we perceive them are additive and made up of Red, Green, and Blue; this is opposed to subtractive color we learned about while finger-painting in kindergarten (Red, Yellow, Blue).  The three types of cones in our eyes each are sensitive to one of these colors, and it is from the combinations of Red, Green, and Blue that we see all the colors we see.  Yellow, for example, is when the red and green cones are both stimulated.  Purple/violet is from red and blue stimulated together.  This is the single special case, as you point out, because red and blue are at opposite sides of the spectrum from each other.  Our brain has two options:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Use the color smack-dab in the middle aka Green&lt;/li&gt;&#xA;&lt;li&gt;Make a new one as if they wrapped around&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Green is far away and already taken, so our brain intelligently invents Magenta.  This produces, instead of a linear EM spectra, a circular color wheel that looks very intuitive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jZXua.jpg&quot; alt=&quot;Hue circle&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-29T16:23:09.560" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10123" PostTypeId="2" ParentId="5587" CreationDate="2013-08-29T17:51:54.157" Score="5" Body="&lt;p&gt;This very recent (and freely available) review pretty much sums the problem up in the introduction:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/clpt.2012.202&quot;&gt;http://dx.doi.org/10.1038/clpt.2012.202&lt;/a&gt; (Barton et al., 2013: Prospects for Treatment of Latent HIV)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And here's an update more specifically on the problems with actually curing an individual of HIV infection, if you have access: &lt;a href=&quot;http://dx.doi.org/10.1016/S0140-6736(13)60104-X&quot;&gt;http://dx.doi.org/10.1016/S0140-6736(13)60104-X&lt;/a&gt; (Katlama et al., 2013: Barriers to a cure for HIV: new ways to target and eradicate HIV-1 reservoirs)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially, current antiretroviral therapy (ART) is able to nearly fully suppress active HIV, practically restoring the individual to a healthy status, including the prevention of transmission from them. However, the therapy needs full adherence (missing a dose can already cause viral loads to rise) and is lifelong. The reason for this is because HIV integrates into the genome of host CD4+ T cells, of which there are latent populations in places difficult to reach with therapeutics such as peripheral lymph nodes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently, some rare individuals actually achieve a &quot;functional cure&quot;, i.e. the body is able to suppress viral replication for a given period of time (5 years) without ART. But these patients &quot;are characterised by a favourable HLA profile and potent HIV-specific CD8 T-cell responses that are associated with a low viral DNA reservoir&quot; (Katlama et al). They also mention another group of five patients who did not seem to have a favourable genetic profile and were still able to control HIV following cessation of ART for several years (&lt;a href=&quot;http://dx.doi.org/10.1097/QAD.0b013e32833b61ba&quot;&gt;http://dx.doi.org/10.1097/QAD.0b013e32833b61ba&lt;/a&gt; Hocqueloux, 2010: Long-term immunovirologic control following antiretroviral therapy interruption in patients treated at the time of primary HIV-1 infection). So it seems there are plenty reports of people who are able to remain free of detectable viral loads and maintain CD4+ T cell counts for a long time after treatment, but it doesn't seem like any of them stay permanently virus-free.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2013-08-29T17:51:54.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10124" PostTypeId="1" AcceptedAnswerId="10127" CreationDate="2013-08-29T21:06:45.753" Score="2" ViewCount="115" Body="&lt;p&gt;What sort of telomere elongation methods are there currently? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would this stop aging? (edit: &lt;a href=&quot;https://biology.stackexchange.com/questions/186/is-telomere-length-a-reliable-measure-of-health-lifespan?rq=1&quot;&gt;No, probably&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I couldn't turn up anything good on google. I was thinking that maybe you could sequence the telomeres, trim them all at a certain point, and then engineer a polymerase molecule to extend from that same point. Is this how it's done? &lt;/p&gt;&#xA;" OwnerUserId="3012" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-08-29T22:46:51.657" Title="Telomere elongation methods?" Tags="&lt;senescence&gt;&lt;telomere&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10125" PostTypeId="1" AcceptedAnswerId="10126" CreationDate="2013-08-29T21:09:08.793" Score="14" ViewCount="3238" Body="&lt;p&gt;Does transferring blood between two people also transfer all the white blood cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why can't AIDS victims with low t-cell count just get blood transfusions till they have more t-cells? Why can't someone who's over a cold give blood to someone with a cold to cure them? I know this is silly, but I really want to know why this won't work.  &lt;/p&gt;&#xA;" OwnerUserId="3012" LastActivityDate="2017-01-24T05:46:51.353" Title="Does a blood transfusion cure disease?" Tags="&lt;hematology&gt;&lt;transfusion&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10126" PostTypeId="2" ParentId="10125" CreationDate="2013-08-29T21:45:23.920" Score="13" Body="&lt;p&gt;Not really no.  Most blood transfusions we think about are red blood cells or platelets, which don't have the immune function you're asking for.  &lt;strong&gt;That's a good thing.&lt;/strong&gt;  Usually, if there are white blood cells in the transfused blood, the host's immune system will recognize them as foreign and destroy them.  Remember, your cells all look like foreign invaders to my cells; blood transfusions of red blood cells are carefully matched to limit negative reactions.  There is also a process called transfusion-associated graft versus host disease in which the donor white blood cells will attack the host cells; this mainly occurs in immune-compromised individuals, but GvHD is definitely something to avoid.  Blood transfusions are usually filtered and irradiated to remove, among other things, white blood cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, people are beginning to use white blood cells as treatment.  A new therapy being studied heavily for all sorts of diseases, from cancer to HIV, is to take the hosts &lt;strong&gt;own&lt;/strong&gt; white blood cells and grow them up in the lab to select for the strongest and most effective cells.  The researchers then wipe out the individual's immune system and give them a dose of their own, super-powered white blood cells, hoping that works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes it kind of does.  They've also been trying a new system, similar to what you propose, using bone marrow.  They had a huge success with an HIV-positive individual now referred to as &quot;the Berlin patient.&quot;  They gave him a marrow transfusion which would produce HIV-immune white blood cells and replaced his immune system.  He was and is effectively cured of HIV/AIDS.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-08-29T21:45:23.920" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10127" PostTypeId="2" ParentId="10124" CreationDate="2013-08-29T22:46:51.657" Score="2" Body="&lt;p&gt;It would be simpler to simply activate telomerase genes or insert them using some vector virus. However, telomerase is a key component in the process of tumoral transformation. Basically, if you don't let cells die they will stack mutations until they become tumoral.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-08-29T22:46:51.657" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10128" PostTypeId="2" ParentId="10102" CreationDate="2013-08-30T00:30:12.503" Score="6" Body="&lt;p&gt;There are a number of more recent papers dealing with phylogenetic methods in reconstructing language history as well, including work by Colin Renfrew and Quentin Atkinson.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are two recent high-profile papers. Unfortunately, both are still behind paywalls, but even reading the list of papers they cite / that cite them would be a great way to answer your question.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.1204678110&quot;&gt; &lt;strong&gt;Bouchard-Côté A, Hall D, Griffiths TL, Klein D&lt;/strong&gt;. 2013. Automated reconstruction of ancient languages using probabilistic models of sound change. Proceedings of the National Academy of Sciences 110: 4224–4229.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1126/science.1166858&quot;&gt; &lt;strong&gt;Gray RD, Drummond AJ, Greenhill SJ&lt;/strong&gt;. 2009. Language phylogenies reveal expansion pulses and pauses in Pacific settlement. Science 323: 479–483.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Maybe not quite as high-profile, but available online, one of my classmates did his (superb) undergraduate thesis as a Biology/Linguistics double major in exactly this topic. I think it could be a very useful place to start, although there have certainly been developments in the field in the last six years:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.swarthmore.edu/SocSci/Linguistics/Papers/2006/saunders_arpy.pdf&quot;&gt; &lt;strong&gt;Saunders, A.&lt;/strong&gt; 2006. Linguistic Phylogenetics of the Austronesian Family: a performance review of methods adapted from biology.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;See also the wikipedia page &lt;a href=&quot;http://en.wikipedia.org/wiki/Quantitative_comparative_linguistics&quot;&gt;Quantitative Comparative Linguistics&lt;/a&gt;, this Stanford &lt;a href=&quot;http://www.stanford.edu/~tylers/notes/qp/Linguistic_phylogenetics_4-23-09.pdf&quot;&gt;how-to&lt;/a&gt;, and this interesting article &lt;a href=&quot;http://geocurrents.info/cultural-geography/linguistic-geography/linguistic-phylogenies-are-not-the-same-as-biological-phylogenies#ixzz2dPRUbM6y&quot;&gt;Linguistic Phylogenies Are Not the Same as Biological Phylogenies&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-08-30T00:54:15.967" LastActivityDate="2013-08-30T00:54:15.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10131" PostTypeId="2" ParentId="10094" CreationDate="2013-08-30T05:40:20.127" Score="-2" Body="&lt;p&gt;Studies show correlations between palm primary lines and lip lines and palatal rugae patterns.Familial uniqueness should be there.&lt;/p&gt;&#xA;" OwnerUserId="4351" LastActivityDate="2013-08-30T05:40:20.127" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10132" PostTypeId="1" AcceptedAnswerId="10134" CreationDate="2013-08-30T06:15:35.853" Score="0" ViewCount="72" Body="&lt;p&gt;Sorry for such a question,if it is too naive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any definition of complexity about gene and protein according their function?If so,what is the relation between them?&lt;/p&gt;&#xA;" OwnerUserId="4347" LastEditorUserId="4347" LastEditDate="2013-08-30T07:23:44.197" LastActivityDate="2013-08-30T10:37:08.303" Title="Is there any definition of complexity about gene and protein according their function?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;bioinformatics&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10133" PostTypeId="2" ParentId="10109" CreationDate="2013-08-30T06:43:51.823" Score="1" Body="&lt;p&gt;There is an alternative view that polymerases are sort of DNA motors that move DNA while they themselves remain static. I cannot find that reference now but I read this ~5 years back in a Nature Reviews article. The notion of transcription and replication &lt;em&gt;factories&lt;/em&gt; also fits this model. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Highly transcribed regions do have a higher propensity to acquire mutations [&lt;a href=&quot;http://www.sciencemag.org/content/268/5217/1616.short&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although I am not sure about it but sequence composition of genes might also have a role. The pitch of the helix along with other physical parameters are dependent on sequence composition. It has been shown that geneic regions have different composition compared to non-transcribed regions (geneic regions have higher GC content [&lt;a href=&quot;http://www.genetics.org/content/159/2/907.short&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-08-30T06:43:51.823" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10134" PostTypeId="2" ParentId="10132" CreationDate="2013-08-30T08:43:06.493" Score="3" Body="&lt;p&gt;Proteins and genes usually are classified in superfamilies and families acording with its inner structure (mainly its domain organization). Domains are parts of the protein with its own 3D structure that usually have their own function and acts more or less in an independent manner. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this doesn't talk very much about their complexity. Myoglobin and hemoglobin, for instance, are very related proteins and thus are classified in the same family. However, hemoglobin forms tetramers, while myoglobin is a single molecule. It's not unheard that very close-related proteins may differ in their association with other proteins, polymeration pattern, addition of new domains, etc. Very similar poteins may have very different functions, i.e. catalyzing similar reaction in opposite directions or in very different pathways, or acting in different parts of the cell or the organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In biology, it is desirable for any classification to be based in evolutionary criteria, since not only it is a more neutral and unbiased way to classify biological things, but also provide information about the origin and structure of those. You could classify proteins by their structure, number of motifs, number of domains, number of different domains, size, function (in fact, there is a very useful and widely used classification for enzymes), etc; and you could classify the genes according to its number of exons, structure of its promoter/enhancer, policystronic or not, etc. However, this classification will usually prove itself to be inferior to an evolutionary classification.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="4168" LastEditDate="2013-08-30T10:37:08.303" LastActivityDate="2013-08-30T10:37:08.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10135" PostTypeId="1" AcceptedAnswerId="10136" CreationDate="2013-08-30T10:01:39.407" Score="6" ViewCount="1241" Body="&lt;p&gt;Recently, I was reading the question &lt;a href=&quot;https://biology.stackexchange.com/questions/5769/photosynthesis-light-intensity&quot;&gt;&quot;Photosynthesis - light intensity&lt;/a&gt;, particularly the answer, that states that different species require different intensity of light.  My question is what is the lowest threshold of light intensity for photosynthesis of any species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, how have that species adapted to take full advantage of the low intensity?&lt;/p&gt;&#xA;" OwnerDisplayName="user3795" LastEditorUserId="-1" LastEditorDisplayName="user3795" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2013-08-30T11:34:32.697" Title="What is the lowest intensity threshold of light for photosynthesis in any species?" Tags="&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10136" PostTypeId="2" ParentId="10135" CreationDate="2013-08-30T10:59:54.423" Score="6" Body="&lt;p&gt;&lt;strong&gt;Disclaimer&lt;/strong&gt;: photosynthesis is not my field of expertise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume you are asking about the amount of light needed for photosynthesis to take place, not the light intensity needed to sustain the plant? Since photosynthesis is an interaction between chlorophyll and single photons I would assume that photosynthetic reactions could take place with just single photons of suitable wavelength (i.e. at the limit of defining light intensity), but to measure this might be extremely hard in practice. The article &lt;a href=&quot;http://www.astrobio.net/exclusive/451/photosynthesis-in-the-abyss&quot;&gt;Photosynthesis in the Abyss&lt;/a&gt; indicates that this might be the case, saying that in deep sea environments &quot;&lt;em&gt;A single molecule of bacteriochlorophyll receives a single photon only about once every 8 hours&lt;/em&gt;&quot; (see also &lt;a href=&quot;http://physicsworld.com/cws/article/news/2013/jan/11/proteins-boost-quantum-coherence-in-bacteria&quot;&gt;this&lt;/a&gt; popular science article). The conditions for deep sea photosynthesis is described in &lt;a href=&quot;http://www.pnas.org/content/102/26/9306.abstract&quot;&gt;Beatty et al. (2005)&lt;/a&gt;, which report photosynthesis by green sulfur bacteria at hydrothermal vents, where the only source of light is geothermal radiation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, as stated earlier, photosynthesis is not my subject field so I do not know how credible this information is.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-08-30T11:34:32.697" LastActivityDate="2013-08-30T11:34:32.697" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10137" PostTypeId="2" ParentId="9830" CreationDate="2013-08-30T13:53:26.127" Score="12" Body="&lt;p&gt;Nice pictures! From the back pattern, size, and antennae shape, I'd say this is very likely a Cicada Killer wasp (&lt;em&gt;Sphecius speciosus&lt;/em&gt;), cf., for instance, &lt;a href=&quot;http://aggie-horticulture.tamu.edu/galveston/beneficials_images/1c_archives/beneficial-03A-GCMGA1552_cicada_killer.JPG&quot;&gt;this picture&lt;/a&gt; taken at a similar angle to yours.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many good resources online about Cicada Killers, including &lt;a href=&quot;http://msue.anr.msu.edu/news/cicada_killer_wasps_are_no_cause_for_concern&quot;&gt;this page&lt;/a&gt; from the MSU Extension Office, and the Wikipedia entry &lt;a href=&quot;http://en.wikipedia.org/wiki/Sphecius_speciosus&quot;&gt;&lt;em&gt;Sphecius speciosus&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be interesting to see if you could find the distinctive burrow (&lt;a href=&quot;http://www.cyberbee.net/column/stinging/cicadakiller.shtml&quot;&gt;photo&lt;/a&gt; / &lt;a href=&quot;http://www.youtube.com/watch?v=tomdi65QPxs&quot;&gt;video&lt;/a&gt;) of your resident wasp!&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2013-08-30T13:58:40.463" LastActivityDate="2013-08-30T13:58:40.463" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="10139" PostTypeId="2" ParentId="8154" CreationDate="2013-08-30T15:31:25.090" Score="3" Body="&lt;p&gt;For circadian rhythm, the gold standard is melatonin secretion (blood or saliva). Also, core body temperature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;see: Circadian temperature and melatonin rhythms, sleep, and neurobehavioral function in humans living on a 20-h day&lt;/p&gt;&#xA;&#xA;&lt;p&gt;James K. Wyatt , Angela Ritz-De Cecco , Charles A. Czeisler , Derk-Jan Dijk&#xA;American Journal of Physiology - Regulatory, Integrative and Comparative PhysiologyPublished 1 October 1999Vol. 277no. R1152-R1163&lt;/p&gt;&#xA;" OwnerUserId="4355" LastActivityDate="2013-08-30T15:31:25.090" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10140" PostTypeId="1" AcceptedAnswerId="15143" CreationDate="2013-08-30T16:24:59.320" Score="15" ViewCount="845" Body="&lt;p&gt;Growing up in the U.S., I was warned at various times of the dire consequences of a variety of introduced pests (usually insects).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Japanese_beetle&quot; rel=&quot;noreferrer&quot;&gt;Japanese beetles&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Gypsy_moth&quot; rel=&quot;noreferrer&quot;&gt;gypsy moths&lt;/a&gt;, and most recently the &lt;a href=&quot;http://en.wikipedia.org/wiki/Brown_marmorated_stink_bug&quot; rel=&quot;noreferrer&quot;&gt;brown marmorated stink bug&lt;/a&gt; are all introduced pests that, at various times, were described as serious threats to our ecology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These threats aren't confined to arthropods, either.  The &lt;a href=&quot;http://en.wikipedia.org/wiki/Achatina_fulica&quot; rel=&quot;noreferrer&quot;&gt;giant African land snail&lt;/a&gt; is causing a stir in Florida (indeed, Florida seems to suffer from an &lt;a href=&quot;http://www.myfwc.com/nonnatives&quot; rel=&quot;noreferrer&quot;&gt;excessive variety of introduced species&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Lack of native predators&quot; is frequently cited as the primary reason many invasive species are considered such a risk to the ecology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that these introduced species can place tremendous pressure on native species that fill similar ecological niches, and may even push these species out of the region due to competition for food and habitat.  However, do the overall ecologies that these species are introduced to adjust over long periods of time?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The numbers of Japanese beetles and gypsy moths don't seem anywhere as high as when I was a child.  Has the ecosystem adjusted, or has the overpopulation self-corrected as the species ran low on food through over-consumption?  Or are the populations still just as problematic now as they were 30 years ago, and I just am not seeing the bigger picture?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the &lt;em&gt;long-term&lt;/em&gt; impact that we've seen from invasive, introduced species?  Is there a significant difference on the long-term impact between introduced flora, arthropods, or mammals?&lt;/p&gt;&#xA;" OwnerUserId="225" LastEditorUserId="5006" LastEditDate="2013-12-01T20:24:48.950" LastActivityDate="2017-04-12T22:24:16.083" Title="Do invasive species cause long-term damage to ecosystems they invade?" Tags="&lt;ecology&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10141" PostTypeId="1" CreationDate="2013-08-30T16:40:44.993" Score="3" ViewCount="219" Body="&lt;p&gt;People are beginning to seriously research space travel applications of &lt;a href=&quot;http://en.wikipedia.org/wiki/Therapeutic_hypothermia&quot; rel=&quot;nofollow&quot;&gt;therapeutic hypothermia&lt;/a&gt;, specifically for reducing metabolism and stress on &lt;a href=&quot;http://www.space.com/22520-incredible-technology-mars-astronauts-suspended-animation.html&quot; rel=&quot;nofollow&quot;&gt;humans traveling to Mars&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that as you decrease the temperature, the metabolism decreases. My question is regarding the relationship between ageing and metabolism. Do we have any data that answers the question if lowered metabolism also lowers the rate of ageing? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm wondering if these hypothetical astronauts going to Mars are actually losing 6 months of their lifespan in an unconscious state, or is their ageing rate being lowered as well? And by how much?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the sake of simplicity, let's ignore the effects of radiation on ageing during the travel.&lt;/p&gt;&#xA;" OwnerUserId="1086" LastEditorUserId="3952" LastEditDate="2013-08-31T10:15:11.197" LastActivityDate="2013-08-31T10:15:11.197" Title="Hibernation, Metabolism and Aging" Tags="&lt;metabolism&gt;&lt;senescence&gt;&lt;life-history&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10142" PostTypeId="1" CreationDate="2013-08-30T16:55:14.950" Score="2" ViewCount="597" Body="&lt;p&gt;What tests could be run to test the purity and type of HCG?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We are looking to purchase HCG from China but the purity and quality varies between labs, we are able to receive samples of the raw peptide and can use a contracted lab to perform tests but due to my academic background I have no clue which tests to request to determine the purity and type of the raw powder. The following is what we should be receiving from the labs in China.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Product Description &#xA;CAS Number: 9002-61-3 &#xA;pI = 2.951&#xA;Extinction Coefficient: EmM = 3.88 (278nm)2&#xA;Synonym: Choriogonin, hCG &#xA;The molecular weight is approximately 37.9 kDa (with &#xA;approximately 31% carbohydrate by weight). The &#xA;theoretical molecular weight is 37.9 kDa based on the &#xA;native form, which contains 2 subunits. The α subunit &#xA;has a molecular weight of 14.9 kDa of which &#xA;approximately 10.2 kDa is for the polypeptide and &#xA;approximately 4.7 kDa for the carbohydrate. The &#xA;β subunit has a molecular weight of 23 kDa of which &#xA;approximately 16.0 kDa is for the polypeptide and &#xA;approximately 7.0 kDa is for the carbohydrate.3,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer Mad Scientists Question, the peptide is &quot;supposed&quot; to be CGA (1081) for use on humans. This is why it is so important for us to find a test that can define the qualities of the raw peptide.&lt;/p&gt;&#xA;" OwnerUserId="4357" LastEditorUserId="4360" LastEditDate="2013-09-01T18:11:38.727" LastActivityDate="2021-02-05T11:00:45.067" Title="What tests can be performed to test the purity and quality of the raw peptide HCG (Human Chorionic Gonadotropin)" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;molecular-genetics&gt;&lt;lab-techniques&gt;&lt;medicinal-chemistry&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10143" PostTypeId="1" AcceptedAnswerId="10147" CreationDate="2013-08-30T17:24:21.653" Score="8" ViewCount="9455" Body="&lt;p&gt;I believe a &quot;mechanistic study&quot; means a study where a medicinal product is being used but the purpose of the study is to investigate the patient or disease, not the medicinal product.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this differ from any other type of study?  What is the purpose of this study?  Why would we not be interested in the medicinal product?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please provide a very simple example that a non-scientist could understand.&lt;/p&gt;&#xA;" OwnerUserId="4358" LastEditorUserId="43480" LastEditDate="2019-02-25T22:16:27.993" LastActivityDate="2019-02-25T22:16:27.993" Title="What is a &quot;mechanistic study&quot;?" Tags="&lt;terminology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10144" PostTypeId="1" AcceptedAnswerId="10145" CreationDate="2013-08-30T18:09:17.237" Score="3" ViewCount="66" Body="&lt;p&gt;I am looking for a database that would provide classification of various types of RNA - information about its structure, function, etc.&lt;/p&gt;&#xA;" OwnerUserId="3751" LastActivityDate="2013-08-30T18:59:01.097" Title="Is there any database with RNA classification?" Tags="&lt;rna&gt;&lt;database&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10145" PostTypeId="2" ParentId="10144" CreationDate="2013-08-30T18:59:01.097" Score="3" Body="&lt;p&gt;Rfam is a database about RNA families, similar to Pfam (wich is for proteins). I think it's what you're looking for.&#xA;&lt;a href=&quot;http://rfam.sanger.ac.uk/search&quot; rel=&quot;nofollow&quot;&gt;http://rfam.sanger.ac.uk/search&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could also enjoy miRbase, a database for micro RNAs: &lt;a href=&quot;http://www.mirbase.org/&quot; rel=&quot;nofollow&quot;&gt;http://www.mirbase.org/&lt;/a&gt;&#xA;There are tRNA databases, too, like this one: &lt;a href=&quot;http://trnadb.bioinf.uni-leipzig.de/&quot; rel=&quot;nofollow&quot;&gt;http://trnadb.bioinf.uni-leipzig.de/&lt;/a&gt;&#xA;And this tool for predict RNA secondary structure (However, this kind of tools aren't as good as they proteinic counterpart): &lt;a href=&quot;http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form&quot; rel=&quot;nofollow&quot;&gt;http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-08-30T18:59:01.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10146" PostTypeId="1" CreationDate="2013-08-30T19:25:17.160" Score="-2" ViewCount="425" Body="&lt;p&gt;Understanding biological systems, molecular biologists need to “reverse  engineer” them. Is this evidence that the systems were engineered to begin with? &lt;/p&gt;&#xA;" OwnerUserId="4360" LastActivityDate="2013-08-31T14:54:41.650" Title="Are biological systems engineered? They are often reverse engineered at a molecular level!!" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;biochemistry&gt;&lt;genetics&gt;&lt;molecular-biology&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="0" ClosedDate="2015-03-11T04:17:08.023" ContentLicense="CC BY-SA 3.0" />
  <row Id="10147" PostTypeId="2" ParentId="10143" CreationDate="2013-08-30T19:31:59.877" Score="7" Body="&lt;p&gt;A mechanistic study aims to uncover a mechanism. It can be a mechanism of the disease (exactly how does the disease do damage to the body), or a mechanism of a drug (exactly how does the drug prevent or repair the damage) that is being investigated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Understanding mechanism, be it mechanism of disease or mechanism of the drug, is very important toward targeted improvements of treatments, as opposed to trying lots and lots of compounds, hoping that someday we'll find one that's better.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Non-mechanistic studies involving drugs aim to show that the drug provides a clinically relevant health benefit over competing treatments, or to determine the safe dosage of a drug. At that point, the mechanism of action of a drug is known to a reasonably large extent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, there are many different things that need to be known for drugs to reach the market. Mechanism is one of them.&lt;/p&gt;&#xA;" OwnerUserId="34" LastActivityDate="2013-08-30T19:31:59.877" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10148" PostTypeId="2" ParentId="10146" CreationDate="2013-08-30T19:34:52.657" Score="3" Body="&lt;p&gt;No. We can reverse-engineer diamonds, or oil, or waves, or the sound of leaves in the wind. Neither of these were engineered. Thus, whether or not we can reverse-engineer something does not tell anything about the origin of the thing.&lt;/p&gt;&#xA;" OwnerUserId="34" LastActivityDate="2013-08-30T19:34:52.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10149" PostTypeId="2" ParentId="10146" CreationDate="2013-08-30T19:35:08.643" Score="0" Body="&lt;p&gt;In regular engineering one begins with a plan to construct a machine that serves a &#xA;given function and then builds the machine according to plan. In reverse &#xA;engineering, by contrast, one starts with a finished machine and tries to determine &#xA;what its purpose is and how it was constructed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scott Minnich, a University of &#xA;Idaho molecular biologist and prominent proponent of intelligent design, will &#xA;often remark in his public lectures that the only way for biologists to understand &#xA;the workings of the cell is to approach its various systems as a reverse engineer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus the molecular biologist may take a functioning system in the cell, perturb it, &#xA;see how the cell behaves differently to infer the system’s function. Alternatively, &#xA;the molecular biologist may interfere at various points in the system’s self assembly to determine how the system is constructed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In all such cases, the molecular biologist acts as an engineer making intelligent interventions and not as a gambler throwing dice. If we need the science of engineering to understand biological systems, then it wouldn't be a stupid bet that the systems are themselves designed.&lt;/p&gt;&#xA;" OwnerUserId="4357" LastActivityDate="2013-08-30T19:35:08.643" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10150" PostTypeId="2" ParentId="10146" CreationDate="2013-08-30T20:09:25.063" Score="7" Body="&lt;p&gt;No.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I looked up a definition of 'reverse engineering'. Wikipedia states: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Reverse engineering is the process of discovering the technological principles of a device, object, or system through analysis of its structure, function, and operation. It often involves taking apart something (a mechanical device, electronic component, computer program, or biological, chemical, or organic matter) and analyzing its workings in detail to be used in maintenance, or to try to make a new device or program that does the same thing without using or simply duplicating (without understanding) the original.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;How else are you suppose to study something? Anything?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I dont want to answer a question with a question so I will continue. If you are working with a complex system, you will need to study the individual pieces. Although it is helpful to sometimes to look at the system of a whole, doing that introduces many variables that makes it impossible to tell what is really going on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some will say you need to do this because biological systems are so complex and that this is 'evidence' for a creator. That is silly. I can agree that biological systems are complex, but that is not evidence for a creator. Complexity is not a good thing. I think sometimes people have a naive view of a cell that it is organized and everything works perfectly and there is precision in everything (or even a lot of things). But thats not true. It is messy. Cells are chaotic. They are a freshman's dorm room. I study splicing, a very complex process.  And I just read a paper where they looked at highly conserved transcripts with no known alternative isoforms. And what did they find? &lt;a href=&quot;http://www.pnas.org/content/early/2009/01/29/0813128106&quot;&gt;They found that in small amounts every exon was being spliced incorrectly.&lt;/a&gt; Sure, most of the time it was spliced correctly. They even called it high fidelity. But the gene they looked at had 5 exons. Consider that the largest gene in humans has over 300 exons, and if all of those are being spliced incorrectly, it adds up. If an exon is misspliced 1/1000 times, and you have 300 exons, that means 1/3 of your transcripts are not what you want. It adds up to a lot of wasted effort by the cell, and it certainly would be better if there was no splicing (or at least less) for large genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thats just one example but you could literally pick any component of the cell and find inefficiency. Sure, 1/1000th is good accuracy fot splicing, but lets have some context. Since we are talking about designers, does anyone here use a watch (designed by mere mortals) that stops working one minute out of every thousand? A computer that shuts down randomly one minute of every thousand? Me either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is 'reverse engineering' evidence of a designer? No, its evidence that cells are a mess and we need to separate the noise from whatever it is we want to study.  &lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-08-30T20:09:25.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10156" PostTypeId="2" ParentId="5267" CreationDate="2013-08-31T00:44:05.747" Score="1" Body="&lt;p&gt;In &lt;a href=&quot;http://mafft.cbrc.jp/alignment/software/&quot; rel=&quot;nofollow&quot;&gt;Mafft&lt;/a&gt;, the command to align new sequences to an existing reference alignment is:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;mafft --add new_sequences.fta existing_alignment.fta &amp;gt; output.fta&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://mafft.cbrc.jp/alignment/software/addsequences.html&quot; rel=&quot;nofollow&quot;&gt;this part&lt;/a&gt; of the documentation for more details.&#xA;It is a nice program to use for alignment, in any case...&lt;/p&gt;&#xA;" OwnerUserId="4335" LastActivityDate="2013-08-31T00:44:05.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10157" PostTypeId="2" ParentId="8778" CreationDate="2013-08-31T02:47:04.673" Score="3" Body="&lt;p&gt;I suffer from calcium oxalate stones.  My doctor pointed me to this study:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9096270&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/9096270&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;tl;dr;  For calcium oxalate, drinking Mineral Water high in Calcium and Magnesium may reduce the risk of forming stones.&lt;/p&gt;&#xA;" OwnerUserId="4367" LastActivityDate="2013-08-31T02:47:04.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10158" PostTypeId="1" AcceptedAnswerId="10159" CreationDate="2013-08-31T03:37:22.653" Score="0" ViewCount="1159" Body="&lt;p&gt;I know that after or before someone's ears pops because of pressure changes, he/she can hear the sound such as laughter. But can these two things (&quot;her ears popped with pressure&quot; and &quot;she can hear the laughter&quot;) happen at the same time?&lt;/p&gt;&#xA;" OwnerUserId="4285" LastEditorUserId="107" LastEditDate="2013-08-31T17:33:09.890" LastActivityDate="2013-08-31T17:33:09.890" Title="While someone's ears pops with pressure, can he/she hear other sound at the same time?" Tags="&lt;hearing&gt;&lt;human-ear&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10159" PostTypeId="2" ParentId="10158" CreationDate="2013-08-31T09:19:48.573" Score="5" Body="&lt;p&gt;Yes, of course they can. What happens when your ears feel 'full' like on an aeroplane is that the air pressure in the middle ear is different from the air pressure outside. When you 'pop' your ears, you push open the Eustachian tubes that connect the middle ear to the throat and make the pressure equal. No matter what the air pressure, the air still conducts sounds. The difference is that your ear drum moves a bit less if the middle ear pressure and outside pressure is different, thus why sound is muffled before you pop your ears.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VlH7m.jpg&quot; alt=&quot;Eustachian tubes&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4182" LastActivityDate="2013-08-31T09:19:48.573" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="10160" PostTypeId="2" ParentId="10141" CreationDate="2013-08-31T09:48:21.887" Score="3" Body="&lt;p&gt;Therapeutic hypothermia certainly is an extremely useful short-term treatment for hypoxic and ischaemic injury to tissues (caused by loss of blood flow and/or oxygen) and is part of the protocol for treating people in intensive care who have had out of hospital cardiac or respiratory arrest as well as being used during heart surgery in cardiopulmonary bypass. In addition there is currently research into treating people who have just had heart attacks and strokes, both conditions where there is acute loss of blood flow due to a clot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there is little evidence as regards use of chronic (long term) hypothermia to prevent aging. While severe hypothermia does suppress cellular respiration and slow down metabolism and bodily function, it also often causes other abnormalities such as:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Disturbances in cardiac conduction that can lead to cardiac arrest&lt;/li&gt;&#xA;&lt;li&gt;Markedly reduced blood flow to skin and limbs which can lead to tissue death in fingers, toes, etc.&lt;/li&gt;&#xA;&lt;li&gt;Clotting dysfunction (haemorrhage if there is any injury)&lt;/li&gt;&#xA;&lt;li&gt;Pulmonary oedema - fluid in the lungs causing inability to oxygenate and/or ventilate the blood&lt;/li&gt;&#xA;&lt;li&gt;Increase in infections&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There is, however, quite a lot more evidence in regards to slowing down cell ageing from oxidative stress using diet energy restriction and this has been replicated in rodents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, there really isn't any good evidence at this stage in regards to long term hypothermia, but currently, given the high risks of cardiac dysfunction and death, without invasive monitoring and intervention (such as in an ICU) it is not feasible.&lt;/p&gt;&#xA;" OwnerUserId="4182" LastActivityDate="2013-08-31T09:48:21.887" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10162" PostTypeId="1" CreationDate="2013-08-31T11:25:49.187" Score="12" ViewCount="4492" Body="&lt;p&gt;I would like to download a plant database containing photos and species details. Do you know if there are any openly available online?&lt;/p&gt;&#xA;" OwnerUserId="4370" LastEditorUserId="25568" LastEditDate="2016-08-29T20:30:50.623" LastActivityDate="2018-06-27T17:27:25.867" Title="Are there any open plant databases (database/library/collection), containing species information and pictures?" Tags="&lt;bioinformatics&gt;&lt;botany&gt;&lt;species-identification&gt;&lt;taxonomy&gt;&lt;database&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10163" PostTypeId="2" ParentId="10162" CreationDate="2013-08-31T11:49:50.140" Score="1" Body="&lt;p&gt;The United States Department of Agriculture have a plant database (&lt;a href=&quot;http://plants.usda.gov&quot; rel=&quot;nofollow&quot;&gt;http://plants.usda.gov&lt;/a&gt;) where you can download search results and checklists. Look at their &lt;a href=&quot;http://plants.usda.gov/download.html&quot; rel=&quot;nofollow&quot;&gt;download&lt;/a&gt; page. However, I think that you can only download text (no pics), and it mostly (only?) contain plants found in the US. I have not used the download functionality myself, so I do not know anything about flexibility or interface. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-08-31T16:18:46.373" LastActivityDate="2013-08-31T16:18:46.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10164" PostTypeId="2" ParentId="10162" CreationDate="2013-08-31T12:53:51.743" Score="5" Body="&lt;p&gt;Large online &lt;a href=&quot;http://en.wikipedia.org/wiki/Flora_%28publication%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;floras&lt;/a&gt; have the advantage of not only having details and often photographs and illustrations, but also being (more or less) definitive, that is, botanists will refer to them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See my answer &lt;a href=&quot;https://biology.stackexchange.com/questions/9201/a-source-for-leaf-architecture-of-different-plant-species-genus/9208#9208&quot;&gt;here&lt;/a&gt; for links to examples, and also for some of the problems with using floras (e.g. not easily downloadable). &lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-08-31T13:23:17.007" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10165" PostTypeId="1" CreationDate="2013-08-31T13:26:14.210" Score="3" ViewCount="41" Body="&lt;p&gt;Imides or dicarbonyl amides are an interesting class of compounds that includes the pharmaceuticals thalidomide, aniracetam and a few other drugs. These compounds, however, are cyclic and I'm wondering whether there's an enzyme found in the human body that specifically catalyses the degradation of non-cyclic imides. I'm thinking that fatty acid amide hydrolase (FAAH) may catalyse the hydrolysis of non-cyclic imides at least as a minor metabolic pathway. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-08-31T13:26:14.210" Title="Are there any enzymes synthesised by humans that specifically catalyse the hydrolysis of non-cyclic Imides?" Tags="&lt;metabolism&gt;&lt;enzymes&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10166" PostTypeId="2" ParentId="10146" CreationDate="2013-08-31T14:54:41.650" Score="3" Body="&lt;p&gt;No. If I wanted to study the sun, I might build a space ship to take me there. Does that mean the sun was put in place by a space ship? I can study your knee using X-rays, does that mean you knee was made by X-rays? The fact that you can use method X to analyze object Y in no way implies that object Y was created using method X. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To take another example, think of balancing rocks like &lt;a href=&quot;http://www.amusingplanet.com/2012/04/10-famous-balancing-rocks-around-world.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;these&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GZEh4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I were to &quot;study&quot; them I could make the &quot;intelligent&quot; decision (I am using intelligent in the freest possible sense of the word) to poke the thing to see if it is really balancing or otherwise attached. If I were to do so, I would be acting, to use &lt;a href=&quot;https://biology.stackexchange.com/a/10149/1306&quot;&gt;@Jason's&lt;/a&gt; terminology, &quot;as an engineer making intelligent interventions and not as a gambler throwing dice&quot;. I would choose the place to poke carefully, near the top perhaps, so that it would return a maximum of useful information (fall), I would not just push them randomly. Does that imply that the rock was placed by an intelligent designer?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To go back to your basic question. First of all, we do not &quot;need&quot; to reverse engineer systems in order to understand them, in fact, with very few exceptions, we can't reverse engineer biological systems (which is also taken as &quot;evidence&quot; for intelligent design by the way, in a wonderful example of screwed if you do, screwed if you don't). Most analyses of biological systems consist of &lt;em&gt;observing&lt;/em&gt; them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, even if we were to reverse engineer that does not in any way imply that the systems were engineered in the first place. That is like saying that if I see you walking down the road today, that implies that yesterday you walked backwards up the same road. If we were to successfully reverse engineer a biological system, that could imply that &lt;em&gt;we&lt;/em&gt; are intelligent, but it would imply nothing of the existence of a creator of these systems, let alone the intelligence of such a being.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-08-31T14:54:41.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10168" PostTypeId="1" CreationDate="2013-08-31T15:52:51.960" Score="5" ViewCount="112" Body="&lt;p&gt;Silver amalgam fillings predominantly contain silver a known bactericidal agent and mercury which a known toxin and has bactericidal property. So how is it that the plaque bacteria survive near the filling margins and produce fresh caries?&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="9943" LastEditDate="2014-12-11T02:42:13.337" LastActivityDate="2019-02-23T03:02:30.433" Title="How can fresh cavities form at the margins of sliver amalgam fillings on teeth?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;teeth&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10169" PostTypeId="1" AcceptedAnswerId="10175" CreationDate="2013-08-31T16:55:21.413" Score="3" ViewCount="1425" Body="&lt;p&gt;Can a methylated strand of DNA be replicated without removing methylation? Does it make any difference if the strand is methylated or not (during replication)?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-08-31T22:20:02.627" LastActivityDate="2013-08-31T22:24:50.900" Title="Can replication occur if DNA is methylated?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;epigenetics&gt;&lt;replication&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10170" PostTypeId="1" CreationDate="2013-08-31T17:00:29.470" Score="2" ViewCount="307" Body="&lt;p&gt;I am pretty unfamiliar to pharmacology. I'm doing a research on drug abuse, particularly opioids' mechanism of action. I encountered several times evidences that come from studies using &lt;strong&gt;antagonists&lt;/strong&gt; especially &lt;strong&gt;naloxone&lt;/strong&gt; that are to prove something is &lt;strong&gt;'a specific opioid effect'&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Opioid-induced miosis in the human ... This action is a specific&#xA;  opioid effect as demonstrated by its antagonism by naloxone.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I wanted to know the rationale behind these kind of conclusions. Also an elaboration on the role antagonists play in drug research will be appreciated. &lt;/p&gt;&#xA;" OwnerUserId="4206" LastActivityDate="2013-08-31T17:19:40.883" Title="What Role Antagonists Play in the Study of Drugs?" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;&lt;receptor&gt;&lt;opioid&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10172" PostTypeId="2" ParentId="10170" CreationDate="2013-08-31T17:18:26.093" Score="4" Body="&lt;p&gt;An &lt;a href=&quot;http://en.wikipedia.org/wiki/Receptor_antagonist&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;antagonist&lt;/em&gt;&lt;/a&gt; is a substance that blocks a particular pathway (a receptor). You can therefore test whether a particular drug acts through the opioid system by using an opioid antagonist. If your substance still works despite the presence of the antagonist (which should block the opoiod receptors), you can conclude that it is not working thorough the opioid system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conversely, if your drug is blocked by an opioid antagonist, that is good evidence that your drug works through the opioid system.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-08-31T17:18:26.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10173" PostTypeId="2" ParentId="10170" CreationDate="2013-08-31T17:19:40.883" Score="3" Body="&lt;p&gt;What many drugs and compounds do is bind to cell receptors. These receptors then change shape and various things may happen in the cell as a result (including relaying a message to other cells).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something that binds to a receptor and causes activity is called an agonist. Something that binds to a receptor and causes a partial response is called a partial agonist. Something that binds to a receptor but does not cause activity is called an antagonist as it takes up those receptor sites meaning that nothing else can bind to them and cause and effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An opioid effect is one of many effects caused by opioids. Naloxone is an opioid antagonist. It binds to the same receptors as opiates but without causing an effect. If a normal person has naloxone it won't actually cause an effect. If someone who has taken an opiate takes naloxone however, the naloxone will compete for receptor spots, knocking off the opiate and reversing the opiate effect. Also, if someone takes naloxone and then immediately has an opiate, that opiate will not work particularly well as some of those receptors are already taken up with naloxone. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps.&lt;/p&gt;&#xA;" OwnerUserId="4182" LastActivityDate="2013-08-31T17:19:40.883" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10174" PostTypeId="1" CreationDate="2013-08-31T19:28:23.177" Score="4" ViewCount="2605" Body="&lt;p&gt;I'm trying to figure out whether it is better for the plant to reproduce by planting its whole fruits with seeds inside them, or picking the seeds out and planting them without the fruit. In my case it's chili pepper, but I'm also interested in other plants that reproduce through fruits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I heard that the whole fruit concept is about providing the seeds with some energy in form of their shell (the fruit) to give them a head start in terms of initial growth into a seedling. Is that true? Do all seeds benefit from growing from inside its fruit, or is it not very significant?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastEditorUserId="19468" LastEditDate="2019-01-27T18:32:02.760" LastActivityDate="2019-08-19T12:35:18.293" Title="Plant a whole fruit or only seeds?" Tags="&lt;botany&gt;&lt;seeds&gt;&lt;germination&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10175" PostTypeId="2" ParentId="10169" CreationDate="2013-08-31T22:05:38.717" Score="5" Body="&lt;p&gt;Absolutely.  It's a pretty cool process, actually.  Most (&lt;a href=&quot;http://www.sciencemag.org/content/341/6146/1237905&quot; rel=&quot;noreferrer&quot;&gt;well...&lt;/a&gt;) DNA methylation occurs in the context of what are called &lt;strong&gt;CpG&lt;/strong&gt;; that is, a &lt;strong&gt;C&lt;/strong&gt; (Cytosine) followed by a &lt;strong&gt;G&lt;/strong&gt; (Guanine).  Because C and G are the Watson-Crick pair for each other, the sequence on the opposite strand will &lt;strong&gt;also&lt;/strong&gt; be CG.  Usually, both Cs are methylated, which turns out to be rather critical for maintenance of methylation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA replication occurs through a semi-conservative mechanism, which means each old, original strand is copied and paired with a new strand.  The new strand has no methylation on it, however; it is at this point that the enzyme DNA methyltransferase (DNMT1, specifically) comes into play.  DNMT1 finds the CpGs methylated on one strand (&quot;hemimethylated&quot;) and methylates the other strand, providing complete inheritance.  &lt;a href=&quot;http://www.fbmc.fcen.uba.ar/materias/genmol/bibliografia-1/review%20DNA%20methylation%20in%20mammals.pdf&quot; rel=&quot;noreferrer&quot;&gt;Here&lt;/a&gt; is a nice summary, and &lt;a href=&quot;http://www.igh.cnrs.fr/equip/mechali/publications/RevieworiginsNRCMB2010.pdf&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; is a review that (briefly) summarizes the evidence that CpGs may play a role in irigins of replication (the jury's still out).&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-08-31T22:24:50.900" LastActivityDate="2013-08-31T22:24:50.900" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10176" PostTypeId="1" AcceptedAnswerId="10181" CreationDate="2013-08-31T22:33:16.310" Score="3" ViewCount="1317" Body="&lt;p&gt;I wonder if it matters if an average person eats the same amount of food distributed between a few (2-3) meals during the day, or constantly having small snacks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested in several aspects of such food consumption:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;How does it affect appetite?&lt;/li&gt;&#xA;&lt;li&gt;How does it affect fat accumulation?&lt;/li&gt;&#xA;&lt;li&gt;Are there any notable side effects caused by either way of eating?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2017-05-11T13:19:26.580" Title="Eating rarely but a lot, or often but little" Tags="&lt;human-biology&gt;&lt;food&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10177" PostTypeId="2" ParentId="10174" CreationDate="2013-09-01T01:01:17.690" Score="6" Body="&lt;p&gt;&lt;strong&gt;I'd argue that this relates to species-specific strategies of seed dispersal, so the answer depends on which species you're asking about.&lt;/strong&gt; Here's an answer for chili peppers, which I think illustrates how complex and idiosyncratic these strategies can be.&lt;/p&gt;&#xA;&lt;p&gt;As I mentioned in &lt;a href=&quot;https://biology.stackexchange.com/questions/8425/is-schoons-hard-shell-muskmelon-a-hybrid/9534#9534&quot;&gt;this answer&lt;/a&gt;, the seedsavers' manual &lt;a href=&quot;http://books.google.com/books?id=N08guuBXT5gC&amp;amp;lpg=PP1&amp;amp;dq=%22seed%20to%20seed%22&amp;amp;hl=zh-CN&amp;amp;pg=PA153#v=snippet&amp;amp;q=capsicum&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Seed to Seed&lt;/a&gt; has great info on most plants, including the genus &lt;em&gt;Capsicum&lt;/em&gt; (chili peppers). They say to clean the seeds from the peppers, and then dry them thoroughly but not in direct sun.&lt;/p&gt;&#xA;&lt;p&gt;The &lt;a href=&quot;http://tewksburylab.org/what-we-do/projects/the-chili-project/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tewksbury lab&lt;/a&gt; has done someone amazing work on &lt;em&gt;Capsicum&lt;/em&gt; evolution and seed dispersal from a biological standpoint. As published in &lt;a href=&quot;http://dx.doi.org/10.1038/35086653&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tewksbury and Nabhan 2001&lt;/a&gt; (behind paywall, but described well in &lt;a href=&quot;https://sitn.hms.harvard.edu/sitnflash_wp/2012/11/issue131b/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this Science in the News article&lt;/a&gt;) &lt;em&gt;Capsicum&lt;/em&gt; fruits have evolved specifically to be eaten by birds, who do not have the receptors that make the fruits taste spicy to us and other mammals.&lt;/p&gt;&#xA;&lt;p&gt;Essentially then, what you're trying to do when you hand-germinate seeds is to mimic the process of the fruit being eaten and passing through a bird gut. &lt;a href=&quot;http://dx.doi.org/10.1038/35086653&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tewksbury and Nabhan&lt;/a&gt; found that seeds from fruits eaten by birds actually germinated at a slightly higher rate than their control group of hand-processed seeds. In contrast, seeds eaten by mammals (who in normal settings totally avoid these spicy chilis) were destroyed and did not germinate.&lt;/p&gt;&#xA;&lt;p&gt;Seed dispersal mediated by birds and other animals is one way that &lt;a href=&quot;https://biology.stackexchange.com/questions/1008/are-there-any-motile-plants?rq=1&quot;&gt;plants can be motile&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/35086653&quot; rel=&quot;nofollow noreferrer&quot;&gt; &lt;strong&gt;Tewksbury JJJ, Nabhan GPG&lt;/strong&gt;. 2001. Seed dispersal. Directed deterrence by capsaicin in chilies. Nature 412: 403–404.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://books.google.com/books?id=N08guuBXT5gC&amp;amp;lpg=PP1&amp;amp;dq=%22seed%20to%20seed%22&amp;amp;pg=PA103#v=onepage&amp;amp;q=%22cucumis%22&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Whealy K&lt;/strong&gt;. 2012. Seed to Seed. Chelsea Green Publishing (p. 152)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-09-01T01:07:44.217" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10179" PostTypeId="1" AcceptedAnswerId="10685" CreationDate="2013-09-01T06:32:22.413" Score="13" ViewCount="3935" Body="&lt;p&gt;I have seen species of birds, insects and fishes with splendid colours. But when it comes to mammals (including us humans), they almost always appear in shades of brown, grey, orange, or in black and white. I don't recall seeing any pink, green and purple. Why is that so?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bBZdV.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1283" LastEditorUserId="3952" LastEditDate="2013-09-01T09:06:32.413" LastActivityDate="2014-11-03T14:52:15.820" Title="Why is mammal coloration so dull?" Tags="&lt;mammals&gt;&lt;pigmentation&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10180" PostTypeId="1" CreationDate="2013-09-01T07:12:39.043" Score="1" ViewCount="1638" Body="&lt;p&gt;It seems to me that my forearm is naturally in a more pronated position than the anatomic (supinated) position and that it actually takes work to make it hold the supinated position. Anyone an expert in human anatomy/physiology here or know of any sources that could point towards a more scientific answer?&lt;/p&gt;&#xA;" OwnerUserId="4375" LastActivityDate="2018-12-31T03:40:31.393" Title="Is the resting state of the forearm in the pronated or supinated position?" Tags="&lt;physiology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10181" PostTypeId="2" ParentId="10176" CreationDate="2013-09-01T07:42:00.337" Score="2" Body="&lt;p&gt;1)Eating little with many breaks is healthy..&#xA;Eating rarely but many times increases your fat...&#xA;The logic is simple.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before the Logic..let me shoot a fact. &#xA;&lt;strong&gt;In mammals: conversion from glucose to fatty acids has a direct pathway(I am speaking biochemistry), but there is no direct path for conversion of fats to glucose..(whereas in plants both paths are direct..)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So If you eat more food at one time, the glucose which body needs is used and the remaining glucose is converted to fat.&#xA;when the body again needs glucose, it needs to take a long pathway to convert fat into glucose(* only if you workout), by that time your Hypothalamus gets a signal and you feel hungry. So you again eat to satisfy your hypothalamus and the process continues, with more accumulation of fat in your body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But in the little meals, there is no accumulation of fat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2)In either case, the Appetite is affected in the normal and same way. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3)There are no side effects for either pathway, but you have other side effects from the fat accumulated. :P&lt;/p&gt;&#xA;" OwnerUserId="4376" LastEditorUserId="4376" LastEditDate="2017-05-11T13:19:26.580" LastActivityDate="2017-05-11T13:19:26.580" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10182" PostTypeId="2" ParentId="10179" CreationDate="2013-09-01T09:04:16.353" Score="-3" Body="&lt;p&gt;The Answer is simple..EVOLUTION..&#xA;The colour of an living organisms depends on 2 things 1) attracting other sex. 2) escape from the predators.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In birds and insects: They doesn't much depend on other sex for living(except for the process of reproduction)and there is no need t exhibit  physical work for attracting other sex... For example if you take a peacock the male needs to be colourful to attract female. but there is no physical work....Let The Other example be some Insect,then if it is colourful.. a predator may not eat for its bright colour..&#xA;this made insects and birds evolute into colourful..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But in mammals. the attracting and escape both depend on physical work... a lion being handsome cannot attract lioness..  :P It need to be physically healthy to escape from predators and give an enough competition to other lions in his territory...&#xA;this made evolution for mammals much depend on their capability of body.. rather than physical attractiveness.. for example in a forest a tigress will obviously pair with a Tiger which has more territory than a more attractive handsome tiger without territory(this is not a case with insects)..&lt;/p&gt;&#xA;" OwnerUserId="4376" LastEditorUserId="4376" LastEditDate="2013-09-01T12:10:33.873" LastActivityDate="2013-09-01T12:10:33.873" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10183" PostTypeId="1" AcceptedAnswerId="42576" CreationDate="2013-09-01T10:03:46.303" Score="5" ViewCount="1190" Body="&lt;p&gt;My textbook says that in &lt;em&gt;all cases of ecological succession&lt;/em&gt; (xerarch, hydrarch, etc.), the ultimate &lt;strong&gt;climax community&lt;/strong&gt;, assuming constancy of environment, is a &lt;strong&gt;mesic community&lt;/strong&gt;. Xeric or hydric pioneers are ultimately succeeded by mesic climax communities. Why is this so? In an environment under consideration, if for example water stress prevails (characteristic of xeric environments) shouldn't the final community be xeric and hence better adapted to the environment? Is my book wrong, or is there something I am missing in the understanding of the development of climax communities? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, I did find it written somewhere that mesic communities do depend on the climate of the place. But then doesn't the fact it is mesic contradict a few climatic conditions wherein ecological succession might occur?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:-&lt;br&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ecological_succession&quot; rel=&quot;nofollow&quot;&gt;Ecological Succession&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Climax_community&quot; rel=&quot;nofollow&quot;&gt;Climax Community&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="16866" LastEditDate="2019-02-17T17:38:26.860" LastActivityDate="2019-02-17T17:38:26.860" Title="Mesophytic Climax community in succession?" Tags="&lt;botany&gt;&lt;ecology&gt;&lt;trees&gt;&lt;environment&gt;&lt;ecosystem&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10184" PostTypeId="1" CreationDate="2013-09-01T10:34:26.063" Score="4" ViewCount="4413" Body="&lt;p&gt;Well I'm well aware that it is proven that DNA contains  genetic material via transformation and Hershey-Chase Experiment of T2 bacteriophage. Still I was wondering what is the reason only DNA contains it and not protein or RNA.&#xA;What I've learned is that DNA is the most stable of all these molecules and it has the ability to replicate itself.&#xA;Other than this I can't find any solid answere.&#xA;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="4377" LastEditorUserId="4101" LastEditDate="2013-09-01T14:19:00.580" LastActivityDate="2019-01-11T15:27:10.187" Title="Why Only DNA can Contain Hereditary Material?" Tags="&lt;dna&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10185" PostTypeId="2" ParentId="2235" CreationDate="2013-09-01T10:53:21.380" Score="-3" Body="&lt;p&gt;You can store your DNA for 1 week at -4C and for one month at -20C but with storing DNA over these period of time there is a deduction of 10-15% of yield from your DNA sample.&lt;/p&gt;&#xA;" OwnerUserId="4377" LastActivityDate="2013-09-01T10:53:21.380" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10186" PostTypeId="1" CreationDate="2013-09-01T13:25:03.223" Score="2" ViewCount="879" Body="&lt;p&gt;How do you calculate or experimentally determine the entropy of enzymes or protein?  In particular, I am interested in Boltzmann and conformational entropy, and Gibbs free energy.  Any references are welcome.&lt;/p&gt;&#xA;" OwnerUserId="4347" LastEditorUserId="10401" LastEditDate="2015-10-18T01:55:27.497" LastActivityDate="2015-10-18T01:55:27.497" Title="How to calculate or know by experiment the entropy of enzymes or protein?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;enzymes&gt;&lt;enzyme-kinetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10187" PostTypeId="1" AcceptedAnswerId="10192" CreationDate="2013-09-01T15:24:27.403" Score="0" ViewCount="98" Body="&lt;p&gt;A fish lives at the depth of 1000-2000m and another at the depth of 200-700m. Which of them would have a more developed gill system ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-09-01T15:31:56.247" LastActivityDate="2013-09-02T15:26:58.300" Title="Which fish will have more developed gills?" Tags="&lt;physiology&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10188" PostTypeId="1" AcceptedAnswerId="10625" CreationDate="2013-09-01T15:50:11.730" Score="7" ViewCount="3498" Body="&lt;p&gt;Lets say that the cell wants to make a particular protein. Transcription of the appropriate gene is done and the mRNA is made. mRNA attaches to the ribosome and the translation is initiated in a &quot;normal&quot; way. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What exactly would happen if an amino acid required in the protein is absent ? I know that the protein would not be manufactured properly but I want to exactly know what would happen to the ribosome and the mRNA. Are they destroyed? Are they simply separated? Who regulates this?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1306" LastEditDate="2013-09-01T19:19:05.640" LastActivityDate="2013-09-29T10:23:10.233" Title="What exactly happens if during translation, an amino acid is not present?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;ribosome&gt;&lt;mrna&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10189" PostTypeId="1" CreationDate="2013-09-01T16:43:50.230" Score="2" ViewCount="216" Body="&lt;p&gt;By this I mean to ask whether say &lt;strong&gt;ethyl butanoate&lt;/strong&gt; is hydrolysed in humans into &lt;em&gt;ethanol&lt;/em&gt; and &lt;em&gt;butyric (butanoic) acid&lt;/em&gt;. This is of interest to me as a pharmacology researcher because butyric acid, for instance, serves as a potent &lt;strong&gt;histone deacetylase&lt;/strong&gt; (HDAC) inhibitor and hence increases gene expression but it has very poor oral bioavailability and I am curious as to whether there's any theoretical basis for suspecting that using butyric acid esters as prodrugs would be a more efficient way of delivering butyric acid. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the molecular structure of ethyl butanoate:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1xvAA.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-09-01T16:43:50.230" Title="Are simple esters like those used as flavouring agents metabolised into their constituent carboxylic acids and alcohols in the human body?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10190" PostTypeId="2" ParentId="10186" CreationDate="2013-09-01T16:49:05.280" Score="2" Body="&lt;p&gt;In practice, like Energy calculations, Entropy is a relative numbers and difficult to get.  Computational chem and bio have been working on this problem with mixed success.  The summary of what I'm going to say here is that when you try to calculate the differences in entropy (or energy for that matter), &lt;a href=&quot;http://modem.ucsd.edu/html/publications/MMPBSA_review.pdf&quot; rel=&quot;nofollow&quot;&gt;the Gibbs Free Energy differences in most biological processes such as enzyme/substrate binding, protein/protein or protein/DNA interactions or protein folding etc is so small compared to the errors in these calculations that the computations are hard to believe&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Entropy is ultimately a term one would use in calculating the &lt;a href=&quot;http://en.wikipedia.org/wiki/Gibbs_free_energy&quot; rel=&quot;nofollow&quot;&gt;Gibb's free energy&lt;/a&gt; which will tell whether a given chemical or molecular process will occur.  So it's a valuable number to have.  Gibbs Free Energy (G) equals Enthalpy (heat) minus the temperature (T) times the change in entropy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;G&lt;/em&gt; = H - T$\Delta$S&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://entropysite.oxy.edu/wiki_entropy.html&quot; rel=&quot;nofollow&quot;&gt;Entropic term&lt;/a&gt;, $\Delta$S is described in chemical systems often as a change in the combinatorial change of the system and the change in the heat capacity of the system. The first of these could broadly described as a 'mixing' term.  When more than one solvents or a solvent and a solute diffuse into each other mix completely, the number of possible states is maximized.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heat capacity of the system is a more often the focus of entropy calculations for proteins and biological molecules.  This is because the conformations of the biological molecules, especially how free they are to move around are thought to contribute to the entropic part of &lt;em&gt;G&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So attempts have been made to estimate from NMR and crystallography as well as molecular dynamics how much domains and side chains are free to move.  Unfortunately this is only an insufficient proxy for biological entropy.  A substantial if not dominant contribution to the &lt;em&gt;T$\Delta$S&lt;/em&gt; term comes from &lt;em&gt;solvent&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is this so?  Water molecules form structures around proteins which are not static, but do involve many water molecules residing there on the average to see them in crystal structures and NMR experiments.  While the individual waters are exchanging rapidly, they are not in the same entropic state in water solution as they are when they form a hydration shell around an aromatic or charged side chain.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Attempts have been made to parametrize the solvent entropy by looking at the buried nonpolar surface in a folded protein, looking at the mobility of sidechains before and after folding/binding, but these metrics appear to be configuration dependent to the point that they can't calculate the protein entropy via these efforts, at least heretofore. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conventionally, molecular dynamics tries to calculate this by surrounding the proteins or other molecules with water molecules and some approximation of the overall entropy is calculated on the entire system.  It turns out that small differences between the water molecular models and the simplifications in ball and stick/Hooke potential water models we make are also problematic approximations when there are hundreds or thousands of water molecules in the simulation. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-09-01T22:38:37.410" LastActivityDate="2013-09-01T22:38:37.410" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10191" PostTypeId="1" CreationDate="2013-09-01T16:51:46.757" Score="3" ViewCount="277" Body="&lt;p&gt;As far as I know, there was no report of &quot;life&quot; popping up in a lab or in nature so far.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Everything that we know is only some copy with similarity to previous life-forms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We certainly can mix some amino acids and stuff, and even some of the chemicals can retain some structure for a certain time and even form some proto-RNA-like structure (not sure how they called it in one document I have seen), but it's very very far from a living organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it mean that life cannot be &quot;sparked&quot; in today's Earth like conditions or, was it not even sparked here to begin with? I have read, as many others have done, this article: &lt;a href=&quot;http://www.bbc.co.uk/news/science-environment-23872765&quot; rel=&quot;nofollow noreferrer&quot;&gt;New research&lt;/a&gt; supports an idea that the Red Planet was a better place to kick-start biology billions of years ago than the early Earth was. They argue that you need molybdenum to create life-like structures and that it's not common in the right form on Earth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do you as biologists think about the statement that life cannot evolve on Earth because the conditions in the beginning of the Earth were not good for life to develop.&lt;/p&gt;&#xA;" OwnerUserId="3118" LastEditorUserId="43323" LastEditDate="2018-07-19T14:10:52.867" LastActivityDate="2018-07-19T14:10:52.867" Title="Is the missing &quot;life-ingredient&quot; in today's Earth's existence the reason why we cannot recreate life?" Tags="&lt;life-history&gt;&lt;life&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="10192" PostTypeId="2" ParentId="10187" CreationDate="2013-09-01T16:55:40.693" Score="3" Body="&lt;p&gt;200m is still pretty deep...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I'd give my money for the surfacers. Oxygen concentration decreases with the depth, and so abyssal fishes have very low metabolism, mainly focused on anaerobic muscles. This is also true for fishes that live in the bottom (benthic), which probably also applies for those living in a few hundred meters. If not, they will probably be active swimmers and then they will probably need bigger gills in order to maintain aerobic movement. Even if we're talking about abyssal and non-abyssal benthic species, I think the abyssal ones would probably be even more anaerobic.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="3615" LastEditDate="2013-09-02T15:26:58.300" LastActivityDate="2013-09-02T15:26:58.300" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10193" PostTypeId="2" ParentId="10191" CreationDate="2013-09-01T17:14:07.210" Score="6" Body="&lt;h1&gt;Three important concepts about abiogenesis&lt;/h1&gt;&#xA;&lt;p&gt;Let's start with three important concepts&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Definition of life&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;You'll need to give a good definition of life, because biologists actually don't have one (it is a matter of philosophy to define life, not biology).&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Time it took for life to emerge&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Life as we know it emerged only after a huge period of time (hundreds of millions of years), which we obviously cannot reproduce in a lab.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Current competition&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Even if some kind of protolife would appear at some point, it would still have to face the competition with its veteran partners. Hypothetical protocells would be eaten by some microbe with no doubt.&lt;/p&gt;&#xA;&lt;h1&gt;Panspermia&lt;/h1&gt;&#xA;&lt;p&gt;The idea of panspermia (the hypothesis that the life may have appeard in outer space or in another planets, and then &amp;quot;contaminate&amp;quot; the Earth) has been on the scene in many forms for quite a long time. Regularly we hear of some study which proposes that life, or at least some key biomolecule, may have formed in asteroids, comets, in Mars or somewhere else. They're quite interesting, mainly because they suggest more than one way that life may have appeared.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Molybdenum&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;While molybdenum is rare in the Earth, it still exists and so the study doesn't deny the posibility that life may have formed in the Earth. Nowadays, molybdenum is used by many organisms as part of the core of some key enzymes, such as nitrogenase (the enzyme complex that catalyzes the conversion of molecular nitrogen into nitrate). Molybdenum has very interesting catalytic qualities and may have been a key factor for the origin of life.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Phosphorus on Mars&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;However, those studies say that Mars has higher concentration of phosphorus, which is one of the main components of life, and that was pretty rare in the early Earth. The hypothesis is interesting but, without experimental data, it is only that. The authors suggest that nowadays those phenomena may happen in Mars, so the hypothesis may be confirmed in a few years as the exploration of the Red Planet continues.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2017-07-20T00:22:47.870" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10194" PostTypeId="1" CreationDate="2013-09-01T17:56:00.560" Score="2" ViewCount="108" Body="&lt;p&gt;Which part or parts of the the genome are the sequences located. Are they spread across the chromosomes? If so how are they accessed sequentially with precision during embrygenesis?&lt;/p&gt;&#xA;" OwnerUserId="4216" LastActivityDate="2013-09-02T04:04:17.523" Title="Which part of the genome are the developmental sequences of embryogenesis located?" Tags="&lt;molecular-genetics&gt;&lt;development&gt;&lt;embryology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10195" PostTypeId="1" AcceptedAnswerId="15370" CreationDate="2013-09-01T18:07:14.587" Score="10" ViewCount="415" Body="&lt;p&gt;There two main mathematical models to describe the process of genetic drift are Moran model and Wright-Fisher model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions concern the assumptions of these models, the existence of other models of genetic drift, explanation of the advantage/disadvantage of these models and the empirical results supporting one or another model.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;What are the assumptions of each of these models?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;stable population size?&lt;/li&gt;&#xA;&lt;li&gt;iteroparous/semelparous&lt;/li&gt;&#xA;&lt;li&gt;what about the probability density function of the fitness?&lt;/li&gt;&#xA;&lt;li&gt;…?&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What advantage/disadvantage do these models have? Or I should say, to which population do these various model applies?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What kind of biological population has been empirically shown to fit better one model rather than another one? What are the key experiments to test the validity of these models?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Please do not hesitate to post even if you answer only partially to the questions! Thank you!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-02-24T18:44:29.077" LastActivityDate="2014-02-26T21:18:19.997" Title="Genetic Drift: Models, assumptions and empirical observations" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10196" PostTypeId="2" ParentId="10188" CreationDate="2013-09-01T19:02:31.393" Score="3" Body="&lt;p&gt;&lt;strong&gt;Point to know : aminoacyl-tRNA binds to mRNA its not just t-RNA..&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if there is no Amino-acid there is no aminoacyl-tRNA of that aminoacid.. so if there is no aminoacyl-tRNA, the anticodon of tRNA doesn't form a bond with mRNA, so the protein production halts (until the Amino acid produced).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the protein is not formed within a certain long time, the premature protein folds itself and breaks. Then a molecule (example: ubiquitin for certain type of bacteria) attaches to this premature protein and marks it for degradation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But there are still chances of protein production with slight mutations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutation: tRNA with the same anticodon and different aminoacid can easily bind to the A site of the ribosome in the absence of the correct aminoacyl-tRNA, so the protein production doesn't stop in this case but the protein has a mutation with different aminoacid.&lt;/p&gt;&#xA;" OwnerUserId="4376" LastEditorUserId="4376" LastEditDate="2013-09-01T19:26:26.440" LastActivityDate="2013-09-01T19:26:26.440" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10197" PostTypeId="2" ParentId="10194" CreationDate="2013-09-01T19:10:52.963" Score="5" Body="&lt;p&gt;This is a very general question. The &quot;developmental sequences&quot; are just genes like any other. Like all genes they are semi-randomly distributed through the genome. While there are gene-rich and gene-poor areas in the genome, with some exceptions --notably the &lt;a href=&quot;http://en.wikipedia.org/wiki/Homeobox&quot; rel=&quot;nofollow&quot;&gt;homeobox genes&lt;/a&gt;--, genes are not grouped by function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to how they are accessed sequentially, that is a huge question but it is not specific to embryogenesis. Genes will always need to be turned on/off at specific times and in response to specific stimuli. This is particularly obvious during development but is not exclusive to it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The basic way this happens is through feedback and control loops. Gene A activates the transcription of gene B which activates gene C which then deactivates A. If you manage to turn on A, the rest will follow. One of the ways this can happen in developing embryos is through maternal mRNA. These are mRNA molecules that are present in the fertilized egg and which &lt;a href=&quot;http://people.ucalgary.ca/~browder/maternal_control.html&quot; rel=&quot;nofollow&quot;&gt;begin to be translated&lt;/a&gt;. This gives us a starting point to activate gene A, which then turns on B etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This answer is a huge simplification but a full answer could take up a couple (or 40) of PhD projects.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-09-02T04:04:17.523" LastActivityDate="2013-09-02T04:04:17.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10198" PostTypeId="2" ParentId="10180" CreationDate="2013-09-01T22:31:06.337" Score="3" Body="&lt;p&gt;The main reason why the anatomic position is supinated is because the radius and ulna are crossed when the arm is pronated and parallel when the arm is supinated. It doesn't have anything to do with the resting state of the arm, it's just the easiest way to arrange the bones neatly for description and analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WBOm7.jpg&quot; alt=&quot;Arm pronated and supinated&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4342" LastEditorUserId="15950" LastEditDate="2018-12-31T03:40:31.393" LastActivityDate="2018-12-31T03:40:31.393" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="10199" PostTypeId="2" ParentId="9863" CreationDate="2013-09-02T00:31:42.060" Score="1" Body="&lt;p&gt;There is only one locus involved in ABO blood type, the ABO gene on chromosome 9. It has three alleles: A, B, and O.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We have two copies of every gene, one from each parent. Because the O allele is recessive to A and B, there are blood types with multiple genotypes. AO and AA will both produce blood type A, and BO and BB will both produce blood type B. Only OO will produce blood type O, and AB will get you blood type AB. The specific cross you mentioned (AB x AB) will never produce a child with blood type O, because neither of the parents had any O alleles for the child to inherit. However, any other blood type is possible with this particular cross.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The + or - you sometimes see is a separate system called the rhesus blood type system. The genetics involved in that are actually a bit complicated, but they don't involve the ABO gene at all. &lt;/p&gt;&#xA;" OwnerUserId="4342" LastEditorUserId="115" LastEditDate="2013-09-02T06:39:07.717" LastActivityDate="2013-09-02T06:39:07.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10200" PostTypeId="2" ParentId="10194" CreationDate="2013-09-02T01:02:20.547" Score="2" Body="&lt;p&gt;Terdon is right on the money when it comes to how is the coordination done, and I know of at least one student working on this for her thesis. However, to answer your other question directly, there was a great &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923361/&quot; rel=&quot;nofollow&quot;&gt;review in 2010&lt;/a&gt;, which was taught in my genetics class that year.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important to note that we still don't know all the genes that are involved with meaningful certainty.  Further, it would be exceedingly difficult to fund and conduct Hong et al's work in the US.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you read the article you will notice that several genes that are involved are genes that are active through out life at various levels.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923361/figure/F4/&quot; rel=&quot;nofollow&quot;&gt;Figure 4&lt;/a&gt; gives a good example of how spread out the information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notice that the three categories of genes they used were even quite different: Stem Cell Specific Genes, Muscle, fat and connective tissue genes, Significantly Enriched GO term&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when you think about how diverse the genes are, it would be even odder for them to be clustered together.  Again, they are probably not truly random, but they don't seem to have a pattern.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To quote their take home:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, by comparing with published data, we identified three groups of maternal genes with distinct regulation profiles during wk 4–9 of development, which provided a molecular basis for the anatomically distinct developmental events that occur between early embryogenesis and subsequent organogenesis and histogenesis.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;More important, our genome-wide and detailed developmental profiling&#xA;  of the patterns of gene expression has revealed that genes involved in&#xA;  the same biological processes are often regulated coordinately. This&#xA;  finding has led us to hypothesize that patterns of gene expression, if&#xA;  known in sufficient detail as in the present study, might be used to&#xA;  predict a role for the gene in a developmental process.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hong Yi, Lu Xue, and Ming-Xiong Guo, et al. FASEB J. 2010 September; 24(9): 3341–3350.&#xA;doi:  10.1096/fj.10-158782 PMCID: PMC2923361&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2013-09-02T01:08:56.167" LastActivityDate="2013-09-02T01:08:56.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10203" PostTypeId="1" CreationDate="2013-09-02T05:06:08.880" Score="7" ViewCount="382" Body="&lt;p&gt;So I find these flies every year in my mulch, and I've never seen them anywhere else. The mulch becomes full of their larvae, which I feed to my toad and lizards. There are so many that you can hear them moving. The adults are black, look like a wasp or hornet, and have a curious green patch on the underside of their abdomen, which is a clear patch showing some kind of liquid. The larvae are brown and have a little hair on them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dpKx7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pbmOq.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's about one inch I think maybe a little less. I hope the quality is good enough, because I used my iPod for the picture and you can't do macro with it. Also, I live in Hillsboro Oregon. I am near a small forest and in the suburbs.&lt;/p&gt;&#xA;" OwnerUserId="4379" LastEditorUserId="4150" LastEditDate="2013-09-08T07:18:22.137" LastActivityDate="2013-09-27T11:22:13.970" Title="Identification of this fly?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10204" PostTypeId="2" ParentId="1951" CreationDate="2013-09-02T06:02:15.813" Score="0" Body="&lt;p&gt;A Mole may be a Hamartoma or a benign tumor. A congenital mole is usually a hamartoma, while acquired mole a benign tumor. In a few people mole very slowly grow in size.  &lt;/p&gt;&#xA;" OwnerUserId="4323" LastActivityDate="2013-09-02T06:02:15.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10209" PostTypeId="1" CreationDate="2013-09-02T12:36:13.900" Score="1" ViewCount="60" Body="&lt;p&gt;I answered to this question: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In most forms of the disease, the bacillus M. tuberculosis spreads slowly and widely&#xA;  in the lungs, causing the formation of hard nodules (tubercles) in the&#xA;  respiratory tissues and form cavities in the lungs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and got zero points.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the correct answer to the question?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="3624" LastEditDate="2013-09-03T10:48:10.993" LastActivityDate="2013-09-03T10:48:10.993" Title="What are the characteristic structures of bacillus M. tuberculosis and what they cause?" Tags="&lt;microbiology&gt;&lt;homework&gt;&lt;tuberculosis&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10210" PostTypeId="1" AcceptedAnswerId="10254" CreationDate="2013-09-02T15:40:25.897" Score="8" ViewCount="74092" Body="&lt;p&gt;Most plants do not have centrioles, so what organelle enables them to multiply?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="47557" LastEditDate="2019-08-14T20:44:09.277" LastActivityDate="2019-08-14T20:44:22.613" Title="How do plant cell divide without centrioles?" Tags="&lt;cell-biology&gt;&lt;plant-physiology&gt;&lt;cell-division&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="10211" PostTypeId="1" AcceptedAnswerId="10216" CreationDate="2013-09-02T15:44:10.800" Score="4" ViewCount="1028" Body="&lt;p&gt;The centrioles are aligned at 90 degree with each other. What is the function of this?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-09-02T15:54:31.797" LastActivityDate="2013-09-02T20:37:27.460" Title="Why are centrioles aligned at 90 degree with each other?" Tags="&lt;cell-biology&gt;&lt;homework&gt;&lt;cell-division&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10212" PostTypeId="1" AcceptedAnswerId="15977" CreationDate="2013-09-02T15:46:17.530" Score="1" ViewCount="726" Body="&lt;p&gt;Fibroblasts are some of the most commonly used cells in cell biology. What are the properties of those cells which makes them commonly used ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-21T09:02:00.093" Title="Why are fibroblast used so commonly in cell biology?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10213" PostTypeId="1" AcceptedAnswerId="10249" CreationDate="2013-09-02T16:05:23.687" Score="0" ViewCount="67" Body="&lt;p&gt;At least in the case of Cystic Fibrosis it happens that a mutant protein (which could actually function!) is held in the ER because the ER detects it as misfolded. Does this happen in every type of mutant protein?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, should I conclude that such genetic disorders are caused because of the total absence of a protein rather than because of a misfolded protein? If not, why would the ER or anything else in the cell allow some mutated proteins to do any job (Like in the case of Sickle cell anaemia, where an amino acid substitution happens)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do scientists conclude that a misfolded protein could have done a good enough job (Like in the case of cystic fibrosis)?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-09-02T21:03:44.263" LastActivityDate="2013-09-04T06:59:22.307" Title="Function of ER in reviewing mutated proteins" Tags="&lt;genetics&gt;&lt;cell-biology&gt;&lt;proteins&gt;&lt;protein-folding&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10216" PostTypeId="2" ParentId="10211" CreationDate="2013-09-02T20:37:27.460" Score="3" Body="&lt;p&gt;As far as I know, the &lt;em&gt;function&lt;/em&gt; is not truly known, although there are some seriously interesting guesses.  Part of the problem seems, from scanning the literature, to be that it's not &lt;em&gt;easy&lt;/em&gt; or obvious to disrupt centriole orientation.  &lt;a href=&quot;http://www.plosbiology.org/article/info%3adoi/10.1371/journal.pbio.0050149&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; in PLoS Biology presents some really interesting results, in particular two piece of evidence:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Centriole orientation, to some degree, is dictated by the &quot;mother&quot; centriole during centriole division and is thus passed on from cell to (daughter) cell.&lt;/li&gt;&#xA;&lt;li&gt;Defects in centriole orientation can result in organelle localization defects in the cell (e.g. nuclear orientation), and at least some of these defects are genetic.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So it seems that orientation is, in some part, a product simply of centriole division, but that there are some gene products that do help determine orientation and localization.  &lt;a href=&quot;http://www.biolbull.org/content/120/3/285.abstract&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; puts forth the hypothesis that centriole orientation determines the axis of cell division which can affect embryo orientation, whereas &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18425533&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; suggests that external environmental factors could translate into altered centriole, and therefore cellular, orientation.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-02T20:37:27.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10217" PostTypeId="1" CreationDate="2013-09-02T21:43:36.637" Score="3" ViewCount="327" Body="&lt;p&gt;I've been referred to here from &lt;a href=&quot;https://philosophy.stackexchange.com/questions/8052/why-are-things-conscious&quot;&gt;https://philosophy.stackexchange.com/questions/8052/why-are-things-conscious&lt;/a&gt;. Could you guys help out? Here's the question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the reason for animals or more general entities being conscious? How did this evolve? What is the advantage?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm aware of ideas that consciousness is merely a illusion, however I find them less than convincing. The counter-argument would follow the line &quot;if consciousness is an illusion, who has the illusion and more importantly why?&quot;. Additionally I believe that consciousness is a bare empirical fact. Even more, it is the basis for empirical thought. That &quot;consciousness is an illusion&quot; is not a good idea has been discussed by e.g. Searle (a video can be found here &lt;a href=&quot;http://www.youtube.com/watch?v=yCii726A4Jc&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.youtube.com/watch?v=yCii726A4Jc&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what are good explanatory models for consciousness?&lt;/p&gt;&#xA;" OwnerUserId="4386" LastEditorUserId="-1" LastEditDate="2017-04-13T12:42:22.377" LastActivityDate="2013-10-20T09:49:01.247" Title="Why are things conscious?" Tags="&lt;neuroscience&gt;" AnswerCount="3" CommentCount="12" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10218" PostTypeId="1" CreationDate="2013-09-02T21:43:38.800" Score="6" ViewCount="1256" Body="&lt;p&gt;I'm studing for my bachelor's degree in Natural Science and I have to chose the path for my future life. I have to chose the right kind of graduate studies. Since I love computer science, maths and marine biology more in details I love the tropical ecology especially that of the coral reefs and atols in the pacific ocean, the whales (e.g. the humpback whales and their migrations), the computer simulations and mathematical models. Thus, I want to ask you if is there a branch of marine biology that allow me to study and specialize myself in tropical ecology and in math &amp;amp; computer science too, because in my current course we don't have any exams of computer science and only one of maths, and I'm feeling sad for this. The right path coul be the computational biology? Exist in biology, some field called &quot;Computational Marine Biology&quot; or &quot;Computational Marine Tropical Ecology&quot;? One last thing, what about Ecoinformatics?&lt;/p&gt;&#xA;" OwnerUserId="4385" LastEditorUserId="4385" LastEditDate="2013-09-20T11:01:14.917" LastActivityDate="2013-11-23T18:22:23.377" Title="Could be an union/synergy between Math, Computer Science and Marine Biology?" Tags="&lt;bioinformatics&gt;&lt;ecology&gt;&lt;mathematical-models&gt;&lt;marine-biology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10219" PostTypeId="2" ParentId="9979" CreationDate="2013-09-02T22:27:49.483" Score="2" Body="&lt;p&gt;This is one of those active areas of research where there isn't a lot of consensus among researchers. There isn't even consensus as to whether it was an extinction in the strictest sense, because we now have evidence from genomic research that Neanderthals interbred with modern humans. Research is still being done on a lot of different hypotheses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/scitable/knowledge/library/what-happened-to-the-neanderthals-68245020&quot; rel=&quot;nofollow&quot;&gt;This article by K. Harvati&lt;/a&gt; is a decent short summary of the current state of the field, and includes references to recent articles.&lt;/p&gt;&#xA;" OwnerUserId="4342" LastActivityDate="2013-09-02T22:27:49.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10220" PostTypeId="2" ParentId="2020" CreationDate="2013-09-02T23:44:03.593" Score="2" Body="&lt;p&gt;The mechanism of action of cocaine is dependent on pre-existing dopamine production and secretion. Normally, secreted dopamine is cleared from the synapse via the dopamine transporter (DAT) located on presynaptic dopaminergic terminals. Cocaine inhibits&#xA;this reuptake of dopamine, increasing it's duration of action on post-synaptic dopamine receptors. Thus, cocaine's effect depends on neuronal dopamine production. Without intrinsic dopamine, cocaine would have no effect. This is actual not exactly true though because cocaine also inhibits serotonin and norepinepherine reuptake transporters as well but the same argument applies to those neurotransmitters as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The overall effect of cocaine on the nervous system is extremely complex as it prolongs the action of dopamine, serotonin and norepinephrine wherever those reuptake transporters are present. There is a particularly high density of DAT in the basal ganglia and nucleus accumbens. What these areas of the brain normally do is under intense study and debate. The accumbens may play a role in goal directed behavior and incentive salience, which is the attribution of value to various actions or objects in the environment. This is what naturally guides us to perform one action over another. The simplistic view is that cocaine &quot;highjacks&quot; this system such that cocaine itself acquires greater incentive salience than natural reinforcers such as food, sex, money etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Getting back to the original question regarding why cocaine causes brain atrophy. This appears to be a finding quoted from a paper by the original inquirer. It is not obvious to me what the mechanism of this atrophy would be. I suggest you look at the discussion section of the paper from which that abstract was quoted to see what the authors suggest. However, to my knowledge, such atrophy has not been widely discussed in the cocaine literature but I could be wrong. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For further information see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065181/&quot; rel=&quot;nofollow&quot; title=&quot;Sulzer. 2011. How Addictive Drugs Disrupt Presynaptic Dopamine Neurotransmission. Neuron 69(4): 628–649.&quot;&gt;&lt;em&gt;Sulzer. 2011. How Addictive Drugs Disrupt Presynaptic Dopamine Neurotransmission&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4387" LastEditorUserId="3624" LastEditDate="2013-09-04T10:33:55.790" LastActivityDate="2013-09-04T10:33:55.790" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10221" PostTypeId="2" ParentId="9244" CreationDate="2013-09-02T23:55:34.950" Score="2" Body="&lt;p&gt;Stick a probe in your neuron-of-interest. Now stimulate the organisms in some way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All the stimuli that make your neuron fire are the neuron's receptive field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example 1:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You probe a neuron in the primary sensory cortex of a human subject. Next, you stimulate the patient with light touch to their skin. Let's say you find that the neuron only fires when you stimulate the right thumb. Thus, light touch to the right thumb is that neuron's receptive field. The neuron doesn't fire to light touch to any other part of the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example 2:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You probe a neuron in the primary auditory ganglion. Next you stimulate the patient with different sound frequencies. The neuron only fires at only a narrow band of sound frequencies. The receptive field of that neuron is that specific band of sound frequencies.&lt;/p&gt;&#xA;" OwnerUserId="4387" LastActivityDate="2013-09-02T23:55:34.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10223" PostTypeId="2" ParentId="3737" CreationDate="2013-09-03T00:05:56.570" Score="16" Body="&lt;p&gt;You are correct in that the neurons themselves do not sense pain. However, the brain contains layers of coverings, blood vessels, the scalp and some muscles. All of these other structures have pain receptors. The coverings of the brain are called meninges and consist of the dura, arachnoid and pia. The dura in particular has a lot of pain receptors and may be responsible for many headaches. As a neurosurgeon I have seen this first hand during awake brain surgery when we open the dura. The patient usually doesn't report any pain when you drill a hole in their skull. However, they start to report dull pain or headache when you stimulate or touch the dura.&lt;/p&gt;&#xA;" OwnerUserId="4387" LastEditorUserId="4387" LastEditDate="2013-09-04T03:52:55.130" LastActivityDate="2013-09-04T03:52:55.130" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10224" PostTypeId="2" ParentId="9944" CreationDate="2013-09-03T00:16:38.843" Score="3" Body="&lt;p&gt;It depends on what part of the brain you are &quot;crushing.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When we do brain surgery we often do exactly what you describe. That is, we open the skull and often remove part of the brain. However, in our case usually the part we are removing is diseased or malfunctioning to begin with. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are areas of the brain that are known as eloquent and those that are considered &quot;not eloquent.&quot; This is an overly simplistic but educationally instructive way to classify things. Eloquent brain regions are those regions that when disturbed will cause an obvious and devastating neurological injury. Examples are primary motor/sensory cortex, broca's area, wernicke's area etc. Noneloquent areas are those that can be damaged or resected and the sequelae are less obvious. For example, you can remove quite a bit of frontal lobe before you notice a problem. However, an appropriate and sensitive behavioral test/instrument may still pick up the deficit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Damage to the brainstem and thalamus is more devastating and even small injury to this area can cause major deficits and changes in the level of consciousness. Injury to different levels of the brainstem produces different level of consciousness. Again, it really depends on the precise location and extent of injury and there is no single answer to your question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the brain itself has no pain receptors the patient would not really feel much pain even if you caused major deficits. However, again it depends on the location. You could theoretically irritate thalamic sensory regions and cause chronic pain syndromes but your lesion would have to be pretty precise.&lt;/p&gt;&#xA;" OwnerUserId="4387" LastEditorUserId="4387" LastEditDate="2013-09-04T03:51:49.673" LastActivityDate="2013-09-04T03:51:49.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10225" PostTypeId="2" ParentId="5381" CreationDate="2013-09-03T00:24:02.777" Score="1" Body="&lt;p&gt;Good question. The answer really depends. There is a normal range of plasma sodium concentration that ranges from about 135 to 145 mM. You body has multiple endocrinologic and neurological mechanisms to closely regulate this concentration. So even if you went out and ate a ton of salty snacks, your body would still keep your plasma sodium concentration within this range. A salt concentration much lower or greater than this can start to cause problems depending on how fast it happens and how far from the normal value. Brain surgery patient are often given lots of extra salt to keep their brains &quot;salty&quot; as this protects from cerebral edema and counteracts salt wasting that often occurs with brain injury. However, the opposite or very high sodium concentrations are also not good. As you said, a diet high in salt can lead to high blood pressure and chronic high blood pressure can cause damage the small blood vessels in the brain and cause small strokes over time or very high blood pressure can cause larger bleeds. Usually we see this in patients with very high uncontrolled blood pressures in the 170-200s systolic range. I'm kind of pulling those numbers out of my memory and you would have to check the literature to verify.&lt;/p&gt;&#xA;" OwnerUserId="4387" LastEditorUserId="4387" LastEditDate="2013-09-03T00:30:31.070" LastActivityDate="2013-09-03T00:30:31.070" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10226" PostTypeId="2" ParentId="8565" CreationDate="2013-09-03T00:44:58.890" Score="0" Body="&lt;p&gt;Amphetamine isn't a DAT inhibitor. It actually causes exocytosis of dopamine vesicles. That is why cocaine is activity dependent as it's mechanism depends on presynaptic activity whereas amphetamine is activity independent.&lt;/p&gt;&#xA;" OwnerUserId="4387" LastActivityDate="2013-09-03T00:44:58.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10227" PostTypeId="1" CreationDate="2013-09-03T02:05:32.160" Score="0" ViewCount="44" Body="&lt;p&gt;First - I do not know if this is the best site to pose this question.  However, stack exchange does not appear to have an ecology sub-site. That said, this appears to be the most appropriate place post this question.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider this chart:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7RTMv.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The chart was retrieved from here &lt;a href=&quot;https://www2.ucar.edu/climate/faq/how-much-has-global-temperature-risen-last-100-years&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am curious as to whether anyone has any thoughts regarding this trend - note, however, that this is one chart among several that I came across on reputable site. All seem to depict this observed &quot;capping&quot; effect between roughly 2000 and 2010+. Unfortunately, I don't have much to offer right now since I am still looking into it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any input is appreciated. &lt;/p&gt;&#xA;" OwnerUserId="4388" LastActivityDate="2013-09-03T03:36:19.413" Title="What are some possible causes that might explain why the global temperature has remained relatively constant in the last decade?" Tags="&lt;climate-change&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2013-09-03T05:26:04.233" ContentLicense="CC BY-SA 3.0" />
  <row Id="10228" PostTypeId="2" ParentId="10227" CreationDate="2013-09-03T03:36:19.413" Score="1" Body="&lt;p&gt;Not my field but I have a couple of thoughts:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;According to your link, the blue line represents the change in the trend and the red bars are the temperatures. These have not remained &lt;em&gt;that&lt;/em&gt; stable, it is the bar that gives that illusion:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zPXzf.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A much more important point are the grey bars extending above and below each year's value. This is the range of uncertainty, the actual values could be anywhere within the range of those bars. Notice how the uncertainty decreases the closer you get to the current date. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I think a lot of the stability you observe is probably due to the line hiding the detail and the far lower precision of the older measurements.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-09-03T03:36:19.413" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10229" PostTypeId="1" CreationDate="2013-09-03T03:38:40.277" Score="0" ViewCount="1056" Body="&lt;p&gt;Richard Dawkins says evolution doesn't have any goal. But I think evolution has one. At the end evolution creates intelligent being. If we find another earth like planet evolution sould have the same pattern. Evolution is not a chaotic event. Am I wrong?&lt;/p&gt;&#xA;" OwnerUserId="1870" LastActivityDate="2013-09-03T05:28:12.570" Title="I think evolution has goal" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ClosedDate="2013-09-03T09:20:09.180" ContentLicense="CC BY-SA 3.0" />
  <row Id="10230" PostTypeId="2" ParentId="10229" CreationDate="2013-09-03T05:12:21.560" Score="6" Body="&lt;p&gt;Yes you are wrong I am afraid. Evolution is the process of change through time of species by inherited changes. Heritable differences mainly come about from random mutation in the genome. These genetic differences between individuals lead to fitness differences between individuals, ie one individual is better able to produce offspring, thus spreading more of its genes in to the following generation, than another individual. For example, environmental change causes selection for a dark body morph in moths, stabding genetic variation and new mutations affecting body colour is then more favored by selection, and those with the dark body genes survive and reproduce better.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no end or goal to evolution. It is often mistakenly said that humans have stopped evolving. This is wrong and to suggest we have is to suggest that evolution is directed and has an ultimate goal. As long as genetic fitness variation exists there will always be some level of evolution because there is a difference between individuals in selection coefficient. Selection is also very unstable, it can change drastically an rapidly, evolution could only then stop if selection was constant and favored one &quot;ultimate genotype&quot; over all others in which case all genetic variation would cease to exist. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we found another planet which had the exact same conditions and time as earth we may find the same species, but it is not likely. It requires the same mutations and selection processes occurring. Analogous to this is the observation of &quot;many solutions to one problem&quot; where different species use different adaptations to deal with a common problem. For example, geting oxygen is difficult for water deelling species. Sea mammals like whales gather oxygen by going to the surface and breathing and then holding their breath. Fish have evolved gills, a different solution to the same problem, to harvest oxygen from the water. These solutions evolve from random changes with selection acting only on the results (those that could filter oxygen from the water or hold their breath the best survived and reproduce best).&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-09-03T05:28:12.570" LastActivityDate="2013-09-03T05:28:12.570" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="10231" PostTypeId="2" ParentId="10217" CreationDate="2013-09-03T07:50:42.410" Score="1" Body="&lt;p&gt;While it's still a very philosophical question, and neuroscience is not my speciality, I think that selfconscious comes from the integration of several informational sources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our brain has maps, that's a fact. We have maps to locate sensorial signals (in fact, all our senses are neural maps representations), to locate our muscles and we even have secondary maps that allow to compare the movements we desire to make and the movements we are actually making. The integration of all of this maps leads to a pretty accurate idea of ourself, and that's critical for selfconciousness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, our brains uses our senses to create images of our immediate sorroundings. They also need to locate other important places (for instance, even if you're at home you would proably have a mental idea of how far your workplace is). Moreover, we have a psicological idea of time wich places ourselfes in a present after a bunch of events that have already happened andd before a set of possible events that we have modelized or predicted with the information from the past. All of this creates an idea of our place in the world.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By combining this two ideas we have a global mental model of our own state, our own desires, our own characteristics, etc... placed in an mental image of the world based in our previous experience. Of course memories and thoughts would have its place, too, but they are more complicated to explain briefly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Transversely, I don't think that computers would develop selfconciousness by its own even if someday they have more computational power than the brain. First, a computer doesn't need an idea of itself as a phisical being, unless it is programmed to do so (a robot would probably have it, thought). Second, the inner logical architecture of computers and brains is quite different, being maybe the lack of biologycal instincts the most relevant difference. Of course all of this should be programmable. My point is that is quite unlikely that it appears by itself and that a selfconcious computer is a pretty unpractical device.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-09-03T07:50:42.410" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10232" PostTypeId="2" ParentId="10210" CreationDate="2013-09-03T10:14:42.137" Score="2" Body="&lt;p&gt;Plant cells without centrioles build special vesicles from their Golgi apparatus which are important for cell division.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://preuniversity.grkraj.org/html/2_CELL_DIVISION.htm&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; website has a nice comparison of different modes of cell division. Look for &quot;Cytokinesis by Phragmoplasts&quot; to get to the relevant part. Phragmoplasts are not exactly a replacement for centrioles, but the whole process is a little different.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-09-03T10:14:42.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10234" PostTypeId="1" CreationDate="2013-09-03T11:54:54.123" Score="2" ViewCount="3890" Body="&lt;p&gt;What is the meaning of calcium conductance in ion channels. I encountered this in the following text:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It was established that the µ and δ opioid receptors &lt;strong&gt;open potassium&#xA;  channels, which results in reduction of calcium conductance&lt;/strong&gt; (Simon, 2005).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also why should opening a potassium channel reduce calcium conductance. How are they related ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Simon, E. J. (2005). Opiates: Neurobiology. In J. H. Lowinson, P. Ruiz, R. B. Millman &amp;amp; J. G. Langrod (Eds.), Substance abuse : a comprehensive textbook (4th ed., pp. xxiv, 1421 p.). Philadelphia: Lippincott Williams &amp;amp; Wilkins.&lt;/p&gt;&#xA;" OwnerUserId="4206" LastEditorUserId="3632" LastEditDate="2013-09-14T13:42:18.397" LastActivityDate="2013-09-14T13:42:18.397" Title="What is 'calcium conductance'?" Tags="&lt;neuroscience&gt;&lt;cell-biology&gt;&lt;cell-membrane&gt;&lt;opioid&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10235" PostTypeId="1" AcceptedAnswerId="24607" CreationDate="2013-09-03T12:04:45.303" Score="4" ViewCount="150" Body="&lt;p&gt;How is movement of proteins and lipids between different domains of cell membrane prevented?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is the noncytosolic layer not able to do lateral movements between domains but cytosolic layer is able to do so?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-12-06T11:26:05.263" Title="Domains in cell membrane" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10236" PostTypeId="2" ParentId="9183" CreationDate="2013-09-03T12:09:26.500" Score="2" Body="&lt;p&gt;Not exactly matching your question, but I think that the idea (from stochastic demography) that life histories should be buffered against environmental variability in influential vital rates (&lt;a href=&quot;http://www.pnas.org/content/95/1/213.abstract&quot; rel=&quot;nofollow&quot; title=&quot;Pfister. 1998. Patterns of variance in stage-structured populations: Evolutionary predictions and ecological implications. PNAS 95(1)&quot;&gt;Pfister, 1998&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15122504&quot; rel=&quot;nofollow&quot; title=&quot;Morris &amp;amp; Doak. 2004. Buffering of life histories against environmental stochasticity: accounting for a spurious correlation between the variabilities of vital rates and their contributions to fitness. American Naturalist 163(4): 579-590&quot;&gt;Morris &amp;amp; Doak, 2004&lt;/a&gt;) can be related to this issue, even if it is mainly (originally) dealing with stationary environmental fluctuations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, fluctuations in vital rates cause the stochastic population growth rate to decrease. This can be described by Tuljapurkar's approximation (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0040580982900107&quot; rel=&quot;nofollow&quot; title=&quot;Tuljapurkar. 1982. Population dynamics in variable environments. III. Evolutionary dynamics of r-selection. Theoretical Population Biology 21: 141–165&quot;&gt;Tuljapurkar, 1982&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$log \lambda_s = log \lambda_d - \frac {1}{2\lambda_d^2} \sum_{i,j} V(a_{ij})S^2_{ij}-\phi$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $\lambda_s$ is the stochastic growth rate, $\lambda_d$ is the deterministic growth rate based on average conditions, $V(a_{ij})$ is variance in vital rates (here matrix entires) and $S^2_{ij}$ is sensitivity in vital rates. $\phi$ represents covariances between rates, which can be important, but can sometimes be ignored for simplicity. This equation shows that the effect of variability in vital rates on stochastic growth rate (which can be interpreted as a measure of fitness) is a product of sensitivity to change and the amount of variability. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of the negative consequences on stochastic population growth, selection is expected to minimize variance in population growth rate. &lt;a href=&quot;http://www.pnas.org/content/95/1/213.abstract&quot; rel=&quot;nofollow&quot; title=&quot;Pfister. 1998. Patterns of variance in stage-structured populations: Evolutionary predictions and ecological implications. PNAS 95(1)&quot;&gt;Pfister (1998)&lt;/a&gt; predicted (based on an evolutionary argument and the equation above) that a species should have smaller temporal variances in the life history traits it is most sensitive to. Therefore, across species, there should be a negative correlation between the sensitivity and the temporal variance of vital rates. This also means that the evolution of life histories and the tolerance of species to variability in environmental conditions are shaped by their life-history patterns. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A consequence of this is that in a long-lived species (as an example), you should find larger variabilty in juvenile survival than in adult survival, since population growth rate is more sensitive to variability in the latter. The lower variability in adult survival can then be seen as an expression of &quot;hardiness&quot; to variability in environmental conditions, and this theory can therefore be used to understand likely evolutionary trajectories of different species, also under a climate change scenario. The ways to minimize the negative effects of variability in population growth in this theory is to either be hardy in important traits (change in environmental conditions doesn't translate much into variability in vital rate) or to decrease the sensitivity in vital rates that vary a lot (which amounts to modifying the life-history pattern of the species). Your question mainly deals with longevity, and this is influenced by both maturation age and adult survival. Therefore, this theory can be useful to think about which species should develop a &quot;hardy&quot; strategy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this answer completely ignores tipping-points in environmental tolerances, nonlinear responses and the genetic variation that selection can act on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Related articles you might want to check out are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20462133&quot; rel=&quot;nofollow&quot; title=&quot;Van de Pool et al. 2010. Effects of climate change and variability on population dynamics in a long-lived shorebird. Ecology 91(4):1192–204&quot;&gt;Van de Pool et al (2010)&lt;/a&gt;, &lt;a href=&quot;http://www.esajournals.org/doi/abs/10.1890/07-0774.1&quot; rel=&quot;nofollow&quot; title=&quot;Morris et al. 2009. Longevity can buffer plant and animal populations against changing climatic variability. Ecology 89(1)&quot;&gt;Morris et al. (2008)&lt;/a&gt; and &lt;a href=&quot;http://www.jstor.org/stable/10.1086/430642&quot; rel=&quot;nofollow&quot; title=&quot;Doak et al. 2005. Correctly Estimating How Environmental Stochasticity Influences Fitness and Population Growth. American naturalist 166(1)&quot;&gt;Doak et al 2005&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="5239" LastEditDate="2013-12-28T01:34:06.723" LastActivityDate="2013-12-28T01:34:06.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10237" PostTypeId="1" AcceptedAnswerId="11387" CreationDate="2013-09-03T12:10:45.817" Score="2" ViewCount="1648" Body="&lt;p&gt;In eukaryotes the nuclear envelope is continuous with the ER, so what helps it out of that?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-09-16T15:43:00.240" LastActivityDate="2013-11-08T18:01:03.287" Title="How is the mRNA transported out of the endoplasmic reticulum?" Tags="&lt;cell-biology&gt;&lt;mrna&gt;" AnswerCount="3" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="10238" PostTypeId="2" ParentId="10234" CreationDate="2013-09-03T14:07:05.283" Score="4" Body="&lt;p&gt;Conductance is the inverse of resistance, and measures how much of a given substance flows throught a channel. In this context, it means how many calcium ions enter the cell in a period of time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are at least two ways potassium channels may prevent the calcium to enter in the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Potassium intake by ion channels decrease the membrane potential, restoring it to its rest state. Since many calcium channels are voltage-dependent, a reduction of the membrane potential would close them, effectively decreasing the calcium conductance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Potassium channels may be coupled to different signaling pathways (i.e. G proteins), wich may affect indirectly other calcium channels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of opioid receptors it seems to be the first mechanism. With potassium channels open, the neuron is less likely to be activated, because it needs higher stimulation to reach the action potential. Calcium channels open in neurons mainly during action potential events (althought they may exist other calcium channels that open in other conditions, i. e in response to hormones or neuromodulators).&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-09-03T14:07:05.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10240" PostTypeId="2" ParentId="10237" CreationDate="2013-09-03T19:58:01.977" Score="0" Body="&lt;p&gt;Translation can occur either in the cytoplasm or in the ER. At one point it was believed that all mRNA begin being translated in the cytoplasm. However, if the protein the mRNA codes for happened to be a secretory protein or a membrane protein, it would have a certain sequence near the start of it (N-terminal sequence). This sequence binds to something called the Signal Recognition Particle (SRP). And once the SRP binds to the mRNA/ribosome/partially-synthesized peptide, it would help it locate to the ER.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to summarize: Many proteins that need to be synthesized at the ER have a certain sequence that binds to SRP. The mRNA begins being translated in the cytoplasm, but once SRP binds it is moved to the ER.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course people now are starting to think this is wrong or at least not the whole story. You can read about the SRP and why some people think its wrong in the intro of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3718476/&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-09-03T19:58:01.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10242" PostTypeId="2" ParentId="10237" CreationDate="2013-09-03T20:52:56.837" Score="1" Body="&lt;p&gt;The proteins mediating the transport of mRNA out of the nucleus (nucleoplasm/karyoplasm) are called &quot;karyopherins&quot; and belong to the nuclear pore complex family.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prior the creation of the final form of mRNA, various proteins are attached to the so called pre-mRNA and a mRNA-protein-complex is built (co-transcriptional). Some of these proteins carry factors for splicing and processing, later RNA-binding proteins are added. (RNA binding proteins such as $Npl3p$, $Gbp2p$ and $Hrb1p$ (serine/arginine-rich proteins) accompany mRNA out of the nucleus. )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After mRNA processing mRNA export is initiated by dephosphorylation of $Npl3p$, leading to binding of $Mex67$ (Saccharomyces c.), forming a complex that interacts with the nuclear pore complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is the way mRNA is able to leave the nucleus.&lt;/p&gt;&#xA;" OwnerUserId="4394" LastEditorUserId="4394" LastEditDate="2013-09-03T21:52:23.083" LastActivityDate="2013-09-03T21:52:23.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10243" PostTypeId="1" CreationDate="2013-09-03T22:11:56.707" Score="1" ViewCount="85" Body="&lt;p&gt;Why do we choose a grammar from a lot of grammars that can describe structure of proteins? Usually, there are a lot of (maybe infinite) grammars that can describe one language. Why do we choose a specific one? Especially the language of proteins of gene just has finite sentences or words.&lt;/p&gt;&#xA;" OwnerUserId="4347" LastEditorUserId="107" LastEditDate="2013-09-04T00:09:48.693" LastActivityDate="2013-09-04T12:28:24.193" Title="Why to choose a grammar from a lot of grammars that can describe structure of proteins?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2014-07-31T11:46:07.087" ContentLicense="CC BY-SA 3.0" />
  <row Id="10244" PostTypeId="1" AcceptedAnswerId="10257" CreationDate="2013-09-04T03:43:54.733" Score="1" ViewCount="2439" Body="&lt;p&gt;How many loci in the human genome are heterozygous? How about other species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;br&gt;&#xA;I was wondering, considering for example the whole world population, how many of the human genes actually have two or more different alleles, or, vice versa, which genes everybody shares because there are no different versions of them. Since this seems not to be clear, I don't consider a mutation in a single individual an allele, maybe take 1% occurrence amongst all individuals as a start? I'm no biologist though...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By loci I mean whatever you think makes sense. Again, I don't mean single bases, preferably something like the classic idea of a gene. But I'm happy for whatever you can tell me.&lt;/p&gt;&#xA;" OwnerUserId="4396" LastEditorUserId="4101" LastEditDate="2013-09-04T17:55:21.063" LastActivityDate="2020-03-22T06:53:17.927" Title="Amount of Heterozygosity" Tags="&lt;genomics&gt;&lt;genomes&gt;&lt;human-genome&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10245" PostTypeId="1" AcceptedAnswerId="10248" CreationDate="2013-09-04T06:02:11.530" Score="4" ViewCount="1436" Body="&lt;p&gt;&lt;em&gt;Clostridium tetani&lt;/em&gt; (&lt;em&gt;C. tetani&lt;/em&gt;) is a bacterium commonly found in soil and is excreted in the faeces of many animals (both mammals and birds) and serves, by means of the exotoxin, &lt;em&gt;tetanospasmin&lt;/em&gt;, causes the life-threatening condition &lt;strong&gt;tetanus&lt;/strong&gt;. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-09-04T08:07:59.590" Title="How long can C. Tetani survive in soil?" Tags="&lt;bacteriology&gt;&lt;bacterial-toxins&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10246" PostTypeId="2" ParentId="10243" CreationDate="2013-09-04T06:17:37.927" Score="2" Body="&lt;p&gt;I did not understand your question completely but this is what I guess you want to know:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Why genetic code evolved to be what it is ?&lt;/li&gt;&#xA;&lt;li&gt;How the sequence of the protein coded by a mRNA give rise to a particular structure ?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Answer to first question cant be definitive. The textbook explanation for why a 3-letter code exists is because a 2-letter code cannot describe all the 22 amino acids, with all its permutations. But then comes another question: why only 22 amino acids. I can't even speculate the answer to this question; the simple amino acids are fine but for an example why lysine and not a similar amino acid with a shorter side chain - no idea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, given 22 amino acids, a 3-letter code and 4 nucleotides, the multiple codons for an amino acid are similar in sequence (usually the first two bases are conserved in accordance with the &lt;a href=&quot;http://en.wikipedia.org/wiki/Wobble_base_pair&quot; rel=&quot;nofollow&quot;&gt;wobble hypothesis&lt;/a&gt;. The last base usually doesnt base pair strongly with the tRNA and is of minimal importance).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The answer to second question is somewhat straightforward. The sequence can give rise to infinitely many structures but in a given environment (consisting of the solvent, other solutes etc), the sequence adopts a particular structure in accordance with the free energy minimization principle. There is a possibility that given an environment a protein can have two different optimal structures and can switch between these two structures.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="1306" LastEditDate="2013-09-04T12:28:24.193" LastActivityDate="2013-09-04T12:28:24.193" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10247" PostTypeId="2" ParentId="10245" CreationDate="2013-09-04T06:35:47.933" Score="4" Body="&lt;p&gt;Clostridia form endospores and can survive for years as a dormant spore. You can check this &lt;a href=&quot;http://aem.asm.org/content/77/7/2352.full&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; about viability of clostridial endospores but it doesn't really talk about how long it can survive. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-09-04T06:35:47.933" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10248" PostTypeId="2" ParentId="10245" CreationDate="2013-09-04T06:52:46.897" Score="5" Body="&lt;p&gt;Soon after asking this question I found a reliable source, &lt;em&gt;&lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000615.htm&quot;&gt;the National Institutes of Health&lt;/a&gt;&lt;/em&gt;. It can survive for over 40 years.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-09-04T08:07:59.590" LastActivityDate="2013-09-04T08:07:59.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10249" PostTypeId="2" ParentId="10213" CreationDate="2013-09-04T06:59:22.307" Score="1" Body="&lt;p&gt;Membrane proteins have to go to the ER from where they are transported to the Golgi apparatus. Usually these proteins are translocated into the ER while translation is still going on. There are chaperones (such as calbindin) in ER which help in translocation and also catalyze initial steps of folding. ER is also involved in unfolded protein response. Unless the protein is properly folded it is not transported to Golgi. However, this process is regulated at many steps and I wont add a detailed explanation of the mechanism, in this answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To conclude ER is involved in this case because the protein considered is a membrane protein.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-09-04T06:59:22.307" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10250" PostTypeId="2" ParentId="9992" CreationDate="2013-09-04T07:16:35.260" Score="1" Body="&lt;p&gt;GTP based structural changes (even motor actions) are very common in biological systems. For e.g. G-proteins, Rab-GTPase (vesicular transport), Ran-GTPase (Nuclear export/import).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So all these GTP-bound proteins make use of an intrinsic or assisted GTPase activity to convert GTP to GDP. This conversion causes change in the structure of the associated protein. Going back to the GTP bound form requires proteins called GEF (Guanine nucleotide Exchange Factors).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in the case of translation elongation, the elongation factor is a GTPase which changes confirmation upon GTP hydrolysis. This confirmational change twists the tRNA so that the bound amino acid moves closer to the peptidyl-transferase center (if P-site is in the left then the amino acid is bound to the rightward &lt;code&gt;CCA&lt;/code&gt; tail of tRNA. The twist causes the amino acid to move leftwards- towards the P-site). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can refer books like Genes by Lewin for details. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-09-04T07:16:35.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10252" PostTypeId="1" AcceptedAnswerId="10260" CreationDate="2013-09-04T09:07:47.053" Score="0" ViewCount="12726" Body="&lt;p&gt;Which is the strongest muscle of human body ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Confusion b/w &lt;strong&gt;Masseter muscle&lt;/strong&gt; (Muscle of Jaw) and &lt;strong&gt;Tongue&lt;/strong&gt; and &lt;strong&gt;Muscle of Heart&lt;/strong&gt; and &lt;strong&gt;Muscle of Uterus&lt;/strong&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3557" LastEditorUserId="1306" LastEditDate="2013-09-04T13:47:29.003" LastActivityDate="2019-04-04T16:37:17.047" Title="Strongest muscle of Human Body" Tags="&lt;muscles&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10253" PostTypeId="2" ParentId="10244" CreationDate="2013-09-04T09:59:51.433" Score="0" Body="&lt;p&gt;The number of possible genotypes from only a few loci is great, and can be calculated using the formula &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;k(k+1)/2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where k is the number of alleles at a particular locus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The parameter k also represents the expected number of homozygous genotypes, and &lt;strong&gt;k[(k-1)/2]&lt;/strong&gt; represents the expected number of &lt;strong&gt;heterozygous genotypes&lt;/strong&gt;. The observed heterozygosity can be compared to the expected heterozygosity, and the deviations between these values can indicate important population dynamics. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/D6dIJ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3557" LastActivityDate="2013-09-04T09:59:51.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10254" PostTypeId="2" ParentId="10210" CreationDate="2013-09-04T11:56:38.540" Score="9" Body="&lt;p&gt;There are many different ways to make a spindle in plant cells: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mitotic spindles may be organized at centriolar centrosomes (only in final divisions of spermatogenesis), polar organizers (POs), plastid MTOCs, or nuclear envelope MTOCs (NE-MTOCs).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Of these, only the latter has been observed in angiosperms (flowering plants). For more info (and the source of the quote), see &lt;a href=&quot;http://dx.doi.org/10.1111/j.1672-9072.2007.00538.x&quot; rel=&quot;nofollow noreferrer&quot;&gt;Brown &amp;amp; Lemmon, &quot;The Pleiomorphic Plant MTOC: An Evolutionary Perspective&quot;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="112" LastEditorUserId="47557" LastEditDate="2019-08-14T20:44:22.613" LastActivityDate="2019-08-14T20:44:22.613" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="10256" PostTypeId="1" AcceptedAnswerId="10258" CreationDate="2013-09-04T13:11:19.823" Score="2" ViewCount="102" Body="&lt;p&gt;Acetyl-CoA has a number of biochemical roles in the body and I'm curious as to whether anybody knows where I can find at least a semi-comprehensive list (i.e. comprising all the &lt;strong&gt;major&lt;/strong&gt; roles in the human body it serves) of the biochemical reactions in which acetyl-CoA partakes in the human body. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2014-04-09T12:43:53.557" Title="Where can I find an at least Semi-Comprehensive list of what biochemical reactions Acetyl-CoA participates in?" Tags="&lt;biochemistry&gt;&lt;coa&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10257" PostTypeId="2" ParentId="10244" CreationDate="2013-09-04T13:23:41.400" Score="3" Body="&lt;p&gt;If you want an actual number, well, it depends (of course).  First off, what is your definition of loci?  That term is broad, and can be construed to mean everything from large, megabase-length genes to every individual base.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, it turns out there are some serious runs of homozygosity (ROH, meaning long regions of the genome that are homozygous) in human populations.  This of course will vary widely from population to population, and amongst outbred individuals.  &lt;a href=&quot;http://dx.doi.org/10.1016/j.ajhg.2012.06.014&quot; rel=&quot;nofollow noreferrer&quot;&gt;This paper&lt;/a&gt; has some AMAZING figures that are worth checking out but are a little more involved.  Here is a table from &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013996&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper&lt;/a&gt; which is likewise quite excellent; also, check out &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013996#pone-0013996-g003&quot; rel=&quot;nofollow noreferrer&quot;&gt;figure 3&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Sh7so.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your new/edited question is actually very difficult to answer.  For an extreme example, look at the &lt;a href=&quot;https://en.wikipedia.org/wiki/Human_leukocyte_antigen&quot; rel=&quot;nofollow noreferrer&quot;&gt;Human leukocyte antigen&lt;/a&gt;; some have hundreds or thousands of alleles, but if you were homozygous for each it would be bad (disease susceptibility) but you'd be fine otherwise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, it depends on what you consider an allele or locus.  Most studies look at single base changes (SNPs) because they are 1. easy and 2. useful.  It turns out that there are &lt;strong&gt;a lot&lt;/strong&gt; of these single changes.  The Human HapMap project is hard at work on this and &lt;a href=&quot;http://www.nature.com/nature/journal/v449/n7164/full/nature06258.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;recently published&lt;/a&gt; a data set with 3.1 million of these SNPs, among 270 individuals from different populations, roughly one every kilobase.  In a similar vein, the &lt;a href=&quot;http://www.1000genomes.org/home&quot; rel=&quot;nofollow noreferrer&quot;&gt;1000 genomes&lt;/a&gt; project &lt;a href=&quot;http://www.nature.com/nature/journal/v491/n7422/full/nature11632.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;recently published&lt;/a&gt; an enormous catalog of variation from almost 1,110 individuals in 14 populations.  Both projects focused on major variants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best answer I can give you from these studies is that, within a given population, any two DNA strands are around 80% identical, of which around 0.5% is by direct relation (&lt;a href=&quot;http://www.nature.com/nature/journal/v449/n7164/fig_tab/nature06258_T5.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;table 5&lt;/a&gt;.  Those numbers vary &lt;em&gt;hugely&lt;/em&gt; between populations, with Yoruba Nigerians being the most diverse, followed by Utah Whites and then Han Chinese and Tokyo Japanese.  This is just an average across the entire genome, as purported functional differences are comparably rare, with over &lt;a href=&quot;http://www.nature.com/nature/journal/v491/n7422/full/nature11632.html#f4&quot; rel=&quot;nofollow noreferrer&quot;&gt;85% of protein-altering changes&lt;/a&gt; being very rare (&amp;lt;0.5% frequency).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, almost every single site we know of has more than one version &lt;em&gt;somewhere&lt;/em&gt;.  Most traits are &lt;strong&gt;very&lt;/strong&gt; complex and are affected by many genes, so even similar appearances can come from very different genetics.  Individuals tend to be highly heterozygous, even if populations on a whole have limited heterozygosity.  A single pair of siblings mating can produce massive defects, showing just how necessary our heterozygosity is.  We each have dozens of large, lethal mutations (deletions, mostly) that don't usually matter thanks to heterozygosity.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-09-04T17:56:17.507" LastActivityDate="2013-09-04T17:56:17.507" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="10258" PostTypeId="2" ParentId="10256" CreationDate="2013-09-04T13:32:48.873" Score="1" Body="&lt;p&gt;I may be missing some fantastic resource, but my first thought is to send you to &lt;a href=&quot;http://www.genome.jp&quot; rel=&quot;nofollow noreferrer&quot;&gt;KEGG&lt;/a&gt;.  Is that crazy?  Maybe, but a simple search for Acetyl-CoA in humans can give you tons of useful information, including GO terms, enzymes, genes, and, yes, &lt;a href=&quot;http://www.kegg.jp/kegg-bin/search_pathway_text?map=hsa&amp;amp;keyword=acetyl-coa&amp;amp;mode=1&amp;amp;viewImage=true&quot; rel=&quot;nofollow noreferrer&quot;&gt;biochemical reactions&lt;/a&gt;; just use the KEGG Pathways tool and specify humans (hsa).  You can click on each individual pathway for more information, such as the &lt;a href=&quot;http://www.kegg.jp/dbget-bin/www_bget?pathway+hsa04725&quot; rel=&quot;nofollow noreferrer&quot;&gt;cholinergic synapse&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Qy0c8.png&quot; alt=&quot;Cholinergic synapse pathway&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2014-04-09T12:43:53.557" LastActivityDate="2014-04-09T12:43:53.557" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10260" PostTypeId="2" ParentId="10252" CreationDate="2013-09-04T15:33:51.500" Score="4" Body="&lt;p&gt;You'll be interested in &lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Muscle#The_.22strongest.22_human_muscle&quot; rel=&quot;nofollow noreferrer&quot;&gt;THIS&lt;/a&gt;&lt;/strong&gt; Wikipedia article. It really depends on how you define &amp;quot;strongest&amp;quot; (Newtons, Wattage, Newtons per Kilogram, etc.). Here are a few relevant excerpts from the article:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In ordinary parlance, muscular &amp;quot;strength&amp;quot; usually refers to &lt;strong&gt;the ability to exert a force on an external object&lt;/strong&gt;—for example, lifting a weight. By this definition, the &lt;strong&gt;masseter&lt;/strong&gt; or jaw muscle is the strongest. The 1992 Guinness Book of Records records the achievement of a bite strength of 4,337 N (975 lbf) for 2 seconds. What distinguishes the masseter is not anything special about the muscle itself, but its advantage in working against a much shorter lever arm than other muscles.&lt;/p&gt;&#xA;&lt;p&gt;If &amp;quot;strength&amp;quot; refers to &lt;strong&gt;the force exerted by the muscle itself&lt;/strong&gt;, e.g., on the place where it inserts into a bone, then the strongest muscles are those with the largest cross-sectional area. This is because the tension exerted by an individual skeletal muscle fiber does not vary much. Each fiber can exert a force on the order of 0.3 micronewton. By this definition, the strongest muscle of the body is usually said to be the &lt;strong&gt;quadriceps femoris&lt;/strong&gt; or the &lt;strong&gt;gluteus maximus&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;p&gt;The &lt;strong&gt;heart&lt;/strong&gt; has a claim to being &lt;strong&gt;the muscle that performs the largest quantity of physical work in the course of a lifetime&lt;/strong&gt;. Estimates of the power output of the human heart range from 1 to 5 watts.[14] This is much less than the maximum power output of other muscles; for example, the quadriceps can produce over 100 watts, but only for a few minutes. The heart does its work continuously over an entire lifetime without pause, and thus does &amp;quot;outwork&amp;quot; other muscles. An output of one watt continuously for eighty years yields a total work output of two and a half gigajoules.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-09-04T15:33:51.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10262" PostTypeId="2" ParentId="10018" CreationDate="2013-09-04T16:00:03.033" Score="0" Body="&lt;p&gt;It seems the answer, which may be context specific, is to use an annealing temperature about 5 degrees below the entire oligo melting temperature.  I did not get any bands at lower temperatures.&lt;/p&gt;&#xA;" OwnerUserId="3247" LastActivityDate="2013-09-04T16:00:03.033" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10264" PostTypeId="1" AcceptedAnswerId="17133" CreationDate="2013-09-04T17:47:57.503" Score="4" ViewCount="2079" Body="&lt;p&gt;I harvested some lentivirus from 293T cells and want to titre the result. I infected 293T cells on a well plate with 400,000 cells per well which I infected with virus stock, and 1 in 10, 100 and 1000 dilutions (as well as a few uninfected wells). After 72h incubation I trypsinised the cells and used FACS to titre first, but 293T do not express the promoter under which GFP is located in some samples and hence these do not appear on FACS. As an alternative, I extracted the genomic DNA from all samples using a QIAGEN DNeasy kit (also the samples which I was able to titre by FACS already) and then performed qPCR on them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I used the ABI PRISM 7000 SDS: &lt;a href=&quot;http://www.cgenetool.com/products/abi_prism_7000.shtml&quot; rel=&quot;nofollow&quot;&gt;http://www.cgenetool.com/products/abi_prism_7000.shtml&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Included on the PCR plate were:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Number standards: 1000, 10k, 100k, 1m copies&lt;/li&gt;&#xA;&lt;li&gt;Samples in triplicate&lt;/li&gt;&#xA;&lt;li&gt;No-template controls as well as untransduced controls&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Each of those was doubled, once with primers and probe for WPRE (an element specific for the lentivirus) and once with primers and probe for beta-actin (a housekeeping gene present in all cells).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The results returned by the machine include for each well the cycle at which the threshold fluorescence was crossed - along with the automatically calculated quantity of copies (which the software calculates from the standards I assume).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since I named the triplicate samples identically, it also automatically calculated the mean quantitiy among each triplicate (practical, eh?). I checked if there were any outliers which should have been excluded from the means but everything was fine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So now for example I have a result of 700k for the quantity of WPRE in sample A. The quantity of beta-actin in sample A was 6.82 x 10&lt;sup&gt;6&lt;/sup&gt;. The transfection was 400,000 cells per well, sample A was transfected with 10uL of viral stock diluted 1:100.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How do I calculate the virus titre per mL from this?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been given the formula: WPRE Qty / (b-act Qty*0.5) * cells in well (400k) * dilution factor (100), but am struggling to figure out a) why b-act Qty is divided by 2, b) whether the result would be virus titre per uL or per 10uL (transfection volume) and c) how beta-actin can have almost 10&lt;sup&gt;7&lt;/sup&gt; copy numbers consistently across all samples when there were only supposed to be about 10&lt;sup&gt;5&lt;/sup&gt; cells...&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-09-05T13:10:38.830" LastActivityDate="2014-05-04T14:10:59.300" Title="How to calculate virus titre from qPCR" Tags="&lt;molecular-genetics&gt;&lt;pcr&gt;&lt;lentivirus&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10265" PostTypeId="1" CreationDate="2013-09-04T17:55:44.073" Score="17" ViewCount="25466" Body="&lt;p&gt;As we know, cellulose is the most abundant polysaccharide in nature. Why don't we have an enzyme to digest cellulose?&lt;/p&gt;&#xA;" OwnerUserId="4403" LastEditorUserId="24354" LastEditDate="2020-04-10T22:34:07.497" LastActivityDate="2020-04-11T20:32:59.610" Title="Why do we have no enzyme to digest cellulose?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;zoology&gt;&lt;enzymes&gt;&lt;carbohydrates&gt;" AnswerCount="4" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10266" PostTypeId="1" AcceptedAnswerId="10299" CreationDate="2013-09-04T19:28:17.180" Score="4" ViewCount="1626" Body="&lt;p&gt;What are some secretory pathways that can be used to secrete a recombinant bacterial enzyme from E. coli?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a recombinant protein (29kDa) that I will express in E. coli BL21 cells.  For now I have been sonicating E. coli to extract the enzyme, but in the future I would like E. coli to secrete the enzyme.&lt;/p&gt;&#xA;" OwnerUserId="3247" LastActivityDate="2015-07-29T07:36:42.787" Title="How to secrete a recombinant protein from E. coli?" Tags="&lt;molecular-biology&gt;&lt;synthetic-biology&gt;&lt;recombinant&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10267" PostTypeId="2" ParentId="5278" CreationDate="2013-09-04T19:43:19.767" Score="1" Body="&lt;p&gt;Urine on the ground smells when there is no rain. Water evaporates, but solutes in it do not. Rain washes solutes deeper into the ground.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the urine of a healthy person it is urea and bilirubin that smell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other causes of smelly urine:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Certain foods, like asparagus, onions, garlic and coffee can add to urine odor. &lt;/li&gt;&#xA;&lt;li&gt;Dehydration (more concentrated solutes)&lt;/li&gt;&#xA;&lt;li&gt;Untreated diabetics secrete glucose and ketones in urine&lt;/li&gt;&#xA;&lt;li&gt;Urinary tract infection&lt;/li&gt;&#xA;&lt;li&gt;Liver disease&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Here's one source:&#xA;&lt;a href=&quot;http://www.healthline.com/health/urine-odor#Diet&quot; rel=&quot;nofollow&quot;&gt;http://www.healthline.com/health/urine-odor#Diet&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4025" LastActivityDate="2013-09-04T19:43:19.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10268" PostTypeId="1" AcceptedAnswerId="10272" CreationDate="2013-09-04T19:46:58.860" Score="2" ViewCount="98" Body="&lt;p&gt;A plaice fish bought for human feed has been cleaned and cooked. &#xA;Some parts of the raw body have been left out of the fridge at about 22°C for about 15 hours. &#xA;During the following night a luminescence phenomenon has been observed on the meat of the fish. &lt;img src=&quot;https://i.stack.imgur.com/1TOal.jpg&quot; alt=&quot;light_picture&quot;&gt;&lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second shot has been taken in a dark environment with a professional camera using a high sensitivity and long-time exposure. &#xA;&lt;img src=&quot;https://i.stack.imgur.com/EgKE8.jpg&quot; alt=&quot;dark_image&quot;&gt;&#xA;What could it be?&lt;/p&gt;&#xA;" OwnerUserId="4405" LastEditorUserId="4101" LastEditDate="2013-09-13T20:16:05.563" LastActivityDate="2013-12-19T22:45:34.537" Title="observed luminescence in a piece of plaice" Tags="&lt;microbiology&gt;&lt;ichthyology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10269" PostTypeId="2" ParentId="5332" CreationDate="2013-09-04T20:08:59.043" Score="1" Body="&lt;p&gt;Dehydration results in decreased blood volume (hypovolemia) and in slight decrease of blood pressure. The body recognises dehydration by these ways:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Baroreceptors in the aorta detect the drop of blood pressure - this results in activation of the sympathetic nerves and the release of adrenaline from the adrenal medulla - this leads to constriction of the arteries ad increased heart rate.&lt;/li&gt;&#xA;&lt;li&gt;Volume receptors in the heart atria detect hypovolemia - this result in the secretion of the antidiuretic hormone from the pituitary gland - this results in water retention in the kidneys. &lt;/li&gt;&#xA;&lt;li&gt;Osmoreceptors in the hypothalamus detect increased blood osmolality - this triggers the release of the hormone ADH.&lt;/li&gt;&#xA;&lt;li&gt;Juxtaglomerular apparatus in the kidneys detect decreased perfusion, what results in the renin-angiotensin-aldosterone release cascade, which results in water retention in the kidneys.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;All these mechanisms are activated in the compensated &lt;a href=&quot;http://www.ehealthstar.com/hypovolemia/hypovolemic-shock&quot; rel=&quot;nofollow&quot;&gt;hypovolemic shock&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4025" LastActivityDate="2013-09-04T20:08:59.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10270" PostTypeId="2" ParentId="10256" CreationDate="2013-09-04T20:37:02.437" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://metacyc.org/&quot; rel=&quot;nofollow&quot;&gt;Metacyc&lt;/a&gt; is an excelent methabolic pathways database that includes all kind of organisms. Of course you can search for methabolic compound.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-09-04T20:37:02.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10271" PostTypeId="2" ParentId="10265" CreationDate="2013-09-04T21:44:16.220" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Why don't we have any enzyme to digest cellulose?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why should we?  We don't use it as a source of energy so why bother?  Even animals that do &quot;digest&quot; cellulose, like ruminants, only do so because of symbiotic bacteria; it would be a poor system indeed in which every organism utilized the same resource.  We occupy enough of the food chain as it is.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-04T21:44:16.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10272" PostTypeId="2" ParentId="10268" CreationDate="2013-09-04T21:51:28.707" Score="3" Body="&lt;p&gt;It's probably bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://seafood.oregonstate.edu/.pdf%20Links/Glowing-Seafood.pdf&quot; rel=&quot;nofollow&quot;&gt;Here's a pdf&lt;/a&gt; describing the phenomenon, along with an in-depth history of the reported occurrence, which should tell you everything you might want to know.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These seafood products exhibited luminescence due to the presence of certain bacteria that are capable of emitting light.  Luminescence by bacteria is due to a chemical reaction catalyzed by luciferase, a protein similar to that found in fireflies... Most of these species require salt except for the two nonmarine luminescent bacteria.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is some link to potential pathogenicity, so I'd recommend &lt;strong&gt;not&lt;/strong&gt; eating it.  That document also requests that you contact the researcher, so why not?  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4780581&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a potentially-relevant paper but 1. is very old, 2. is in Russian, and 3. I have no access to it.  And &lt;a href=&quot;http://www.sciencemadness.org/talk/viewthread.php?tid=1485&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; supposedly tells you how to isolate them.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="3952" LastEditDate="2013-12-19T22:45:34.537" LastActivityDate="2013-12-19T22:45:34.537" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10274" PostTypeId="2" ParentId="10265" CreationDate="2013-09-04T22:58:47.600" Score="12" Body="&lt;p&gt;While it's true that cellulose is full of calories, it's very difficult to get the calories out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Symbiotic bacteria take ages to digest cellulose, and as a result animals that digest cellulose with specialized symbiotic bacteria have a huge gut to house them in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's likely that the reason humans can't digest cellulose is because mammals generally can't. And mammals generally can't because it's way too much work, and we don't need to.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2013-09-04T22:58:47.600" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10276" PostTypeId="1" CreationDate="2013-09-05T03:38:06.457" Score="4" ViewCount="166" Body="&lt;p&gt;I had a problem that I was wondering if it could be solved by one of the techniques/algorithms used in bioinformatics to give the extent of similarity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a Problem Statement: we have a sensor (its like a magnetic compass and has a dial with twelve equal zones- 30 degrees each) that every second outputs where its pointing. The typical random output of the sensor may look like (for example):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;30 30 30 30 30 30 120 120 120 120 120 120 60 60 60 60 60 60 330 330 330 330 30 30 30 30 210 210 210 210 210 60 60 60 60 60 60 60 60 60 60 60 60 60 ……… etc. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;We wanted to see if we can calculate a measure of similarity of two 4-minute sequence samples taken at different times during the day. (It would be great if we could state something like - the sequences are similar and there is a 1 in million (say) chance that we may be wrong.)&lt;/p&gt;&#xA;" OwnerUserId="4407" LastEditorUserId="4101" LastEditDate="2013-10-06T20:45:23.977" LastActivityDate="2013-10-06T20:45:23.977" Title="How to calculate extent of Sequence similarity" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;" AnswerCount="4" CommentCount="2" ClosedDate="2014-07-31T13:05:40.800" ContentLicense="CC BY-SA 3.0" />
  <row Id="10277" PostTypeId="1" AcceptedAnswerId="10280" CreationDate="2013-09-05T06:00:46.597" Score="5" ViewCount="2877" Body="&lt;p&gt;If we consider the pathway of breakdown of glucose which includes glycolysis, the citric acid cycle and the electron transport chain, all these processes takes place in some  prokaryotes and eukaryotes. In prokaryotes all these processes take place in cytoplasm while in eukaryotes the last two processes take place in mitochondria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So is there any advantage of performing the last two processes in the mitochondria? Does it yield more energy? If there is no advantage, what is the point of having a mitochondria (at least for this process)?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="22057" LastEditDate="2019-06-14T13:33:14.160" LastActivityDate="2019-06-14T13:33:14.160" Title="Is there any advantage of having mitochondria for aerobic respiration?" Tags="&lt;evolution&gt;&lt;biochemistry&gt;&lt;mitochondria&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="10278" PostTypeId="1" AcceptedAnswerId="10293" CreationDate="2013-09-05T09:40:23.623" Score="2" ViewCount="119" Body="&lt;p&gt;What are the criteria that the researchers use to choose whether a protein is an SR protein or and SR-like protein?&lt;/p&gt;&#xA;" OwnerUserId="3751" LastEditorUserId="3340" LastEditDate="2013-09-05T12:20:50.753" LastActivityDate="2013-09-05T18:40:59.447" Title="How do you differentiate between SR protein and SR-like protein?" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10279" PostTypeId="1" AcceptedAnswerId="10281" CreationDate="2013-09-05T10:56:16.097" Score="1" ViewCount="63" Body="&lt;p&gt;I have tried going to the &lt;a href=&quot;http://www.rcsb.org/pdb/home/home.do&quot; rel=&quot;nofollow&quot;&gt;RCSB website&lt;/a&gt; and quite frankly it was useless since when I looked up receptors like say the metabotropic glutamate receptor 2 (mGluR2) I got no helpful results. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="112" LastEditDate="2013-09-05T11:37:44.930" LastActivityDate="2013-09-05T11:37:44.930" Title="Where can I find pdb files for macromolecules like receptors?" Tags="&lt;bioinformatics&gt;&lt;structural-biology&gt;&lt;pdb&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10280" PostTypeId="2" ParentId="10277" CreationDate="2013-09-05T11:25:25.400" Score="4" Body="&lt;p&gt;From the evolutionary point of view, the eukaryotes acquired these metabolisms (except glycolysis) from their prokaryotic endosymbionts. Not all prokaryotes have the ETC. The free living ancestor of mitohondria is supposed to be the alpha-proteobacterium. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, glycolysis is a common pathway in lot of lifeforms perhaps because of abundance of glucose. TCA cycle is coupled with ETC at certain steps which makes it essentially a part of aerobic metabolism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The reason for having a dedicated organelle for respiration&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ATP synthesis is a membrane process. Imagine a large prokaryotic cell- as big as an animal cell. Such a cell cannot take care of its energetic demands which primarily consists of protein synthesis with the given area of membrane i.e it needs much more ATP-synthases than it can have to cope up with the energy demands of maintaining such a huge cell (this index is approximated based on surface to volume ratio). Therefore it is wise to harbor multiple efficient organelles i.e. mitochondria which themselves have just a small essential genome and proteome to maintain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a better understanding, please read &lt;a href=&quot;https://doi.org/10.1038/nature09486&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; article. I just loved it. &#xA;There is also a book by the same author about mitochondria called &lt;strong&gt;Power, Sex, Suicide&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2019-06-14T12:11:10.310" LastActivityDate="2019-06-14T12:11:10.310" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="10281" PostTypeId="2" ParentId="10279" CreationDate="2013-09-05T11:37:27.397" Score="1" Body="&lt;p&gt;As pointed out in the comments, if you look for PDB files and you don't find them in the PDB, there is no solved structure. However, you can look in databases that contain models of proteins. Especially for the receptors the coverage has been increasing in recent years and so you may be lucky. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good starting place to look for protein information is &lt;a href=&quot;http://www.uniprot.org/uniprot/Q14416#section_x-ref&quot; rel=&quot;nofollow&quot;&gt;UniProt&lt;/a&gt;, where you find links to the &lt;a href=&quot;http://www.proteinmodelportal.org/query/uniprot/Q14416&quot; rel=&quot;nofollow&quot;&gt;Protein Model Portal&lt;/a&gt; and &lt;a href=&quot;http://swissmodel.expasy.org/repository/smr.php?sptr_ac=Q14416&amp;amp;csm=801976D034AA8100&quot; rel=&quot;nofollow&quot;&gt;SwissModel&lt;/a&gt;. They contain models based on the &lt;a href=&quot;http://www.pdb.org/pdb/explore/explore.do?structureId=3sm9&quot; rel=&quot;nofollow&quot;&gt;PDB structure for Metabotropic glutamate receptor 3&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2013-09-05T11:37:27.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10282" PostTypeId="2" ParentId="10276" CreationDate="2013-09-05T11:44:32.507" Score="1" Body="&lt;p&gt;Well. You perhaps need not use the bioinformatic algorithms of string matching. These algorithms were primarily developed because of the extensive search space. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your problem you just need to compare two recording experiments and you should use mathematical metrics for it. You have a 60x4 i.e 240 dimensional random variable. Moreover this variable is not discrete, it is continuous. For similarity measurements you have to use statistical tests or otherwise define a cutoff either on each element of the vector or the total magnitude defined by any norm. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-09-05T11:44:32.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10283" PostTypeId="2" ParentId="10264" CreationDate="2013-09-05T12:14:19.520" Score="1" Body="&lt;p&gt;I have 2 doubts here. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;You obtain your viruses from the media whereas Actb measurements can be performed only in the cell lysates. &lt;/li&gt;&#xA;&lt;li&gt;Actb is just a reference to normalize for the cell count: higher the cell count higher will be the viral titre because of higher number of infected cells. But that is immaterial if your aim is lentiviral transduction where you are only interested in obtaining titre values and not measuring the efficiency of its formation. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;You can simply do qPCR with the media sample and the standards and regress the measured Ct values of the samples to obtain titres.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-09-05T12:14:19.520" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10284" PostTypeId="1" AcceptedAnswerId="10438" CreationDate="2013-09-05T12:28:52.533" Score="4" ViewCount="3518" Body="&lt;p&gt;Brain cells are cells require one of the highest amount of energy of any cell of body. So why do they use a shuttle which will transfer electrons from NADH produced in glycolysis to FAD(and there by reduce the no of ATP that can be made ) ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2020-05-14T17:24:45.177" Title="Why do brain cells use shuttles that pass electrons from NADH to FAD?" Tags="&lt;mitochondria&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10285" PostTypeId="1" AcceptedAnswerId="10288" CreationDate="2013-09-05T12:32:34.423" Score="2" ViewCount="4925" Body="&lt;p&gt;In many  animals GTP is produced in citric acid cycle. While in  plants,bacteria and some animals ATP is produced. Why is this so ? What is the advantage ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-09-05T13:07:12.623" Title="Why in some cells is GTP made in citric acid cycle and in some ATP?" Tags="&lt;mitochondria&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10286" PostTypeId="5" CreationDate="2013-09-05T12:37:06.967" Score="0" Body="&lt;p&gt;A genus of &lt;a href=&quot;http://biology.stackexchange.com/tags/retrovirus/info&quot;&gt;retroviruses&lt;/a&gt; characterized by a slow incubation period. Famous lentiviruses include HIV (Human Immunodeficieny Virus), SIV, and FIV. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disabled lentiviruses, viruses with the genome engineered to make them non-replicative and therefore incapable of productive infection, are used to deliver DNA efficiently into hard-to-transfect animal cells. Moreover, lentivirus-mediated transductions cause integration of the desired DNA element in the genome of host cells, thereby making stably transgenic cell lines. It is, however, difficult to control the site of integration and copy number.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="4101" LastEditDate="2013-10-14T22:18:21.550" LastActivityDate="2013-10-14T22:18:21.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10287" PostTypeId="4" CreationDate="2013-09-05T12:37:06.967" Score="0" Body="A genus of retroviruses with a lengthy incubation time, in particular HIV. Commonly used as DNA transduction agents in animal cells. " OwnerUserId="3340" LastEditorUserId="4101" LastEditDate="2013-10-14T22:18:29.270" LastActivityDate="2013-10-14T22:18:29.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10288" PostTypeId="2" ParentId="10285" CreationDate="2013-09-05T13:07:12.623" Score="4" Body="&lt;p&gt;This step is catalyzed by succinyl-CoA synthase which has two different isoforms- one which produces GTP while the other produced ATP.&#xA;It seems from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15234968&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; study that predominantly anabolic tissues prefer the GTP-producing form whereas the predominantly catabolic tissues use the ATP-producing from. &#xA;In the same paper they discuss that GTP is important for protein synthesis and it is also involved in production of phospho-enolpyruvate by PEP-carboxykinase in mitochondria; therefore playing an important role in anabolic processes.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-09-05T13:07:12.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10289" PostTypeId="2" ParentId="10276" CreationDate="2013-09-05T16:22:25.563" Score="1" Body="&lt;p&gt;I tend to agree that bioinformatics has no special general help for matching sequences of numbers.  Most of the specialized algorithms in bioinformatics are string oriented.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If distance metrics, Fourier or wavelet decomposition don't work, you might want to look for motifs in your sequence, then you might try a motif dictionary similar to an alignment algorithm.  They are like NGram algorithms, but then they extend out. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Build dictionary of all sequences of numbers from your reference sequence: say of 5 or 7 length.  &lt;/li&gt;&#xA;&lt;li&gt;Identify identical or better yet linear combinations of those dictionary entries and then expand the comparison by one index in either direction to get the maximal length of comparable identity/similarity.&lt;/li&gt;&#xA;&lt;li&gt;List all your 'hits' by a score - a length and distance based metric.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;is this the sort of thing you were looking for?&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-09-05T16:22:25.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10290" PostTypeId="1" CreationDate="2013-09-05T16:51:43.500" Score="6" ViewCount="507" Body="&lt;p&gt;I just saw a video about the biology between sunburn, UVA and UVB and the different things we know about sunburn in humans. ( &lt;a href=&quot;http://www.youtube.com/watch?v=ZSJITdsTze0&quot; rel=&quot;noreferrer&quot;&gt;http://www.youtube.com/watch?v=ZSJITdsTze0&lt;/a&gt; )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder what keeps plants from getting sunburned? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By sunburned I meant that ultraviolet light injures the plant so that it requires some sort of healing process for the plant to be as healthy/strong/resistant to disease as a plant that isn't harmed.&lt;/p&gt;&#xA;" OwnerUserId="4409" LastEditorUserId="4409" LastEditDate="2014-02-11T17:55:40.953" LastActivityDate="2014-02-11T17:55:40.953" Title="Why don't plants get sunburned?" Tags="&lt;botany&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10291" PostTypeId="1" AcceptedAnswerId="10370" CreationDate="2013-09-05T17:14:59.347" Score="3" ViewCount="2228" Body="&lt;p&gt;I know that metabolism as a whole can never be at equilibrium (otherwise the cell is dead !) but I wonder whether a few reactions in the cell could be at chemical equilibrium at a  given point of time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible theoretically ? Is there any real example ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-09-05T17:24:52.023" LastActivityDate="2013-09-14T17:17:26.017" Title="Can any one reaction in a cell be at equilibrium?" Tags="&lt;biochemistry&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="10292" PostTypeId="1" CreationDate="2013-09-05T18:23:36.493" Score="7" ViewCount="412" Body="&lt;p&gt;Question is rather self-explanatory, but segmented into two parts. I'm attempting to make use of a repression system that employs cleaving RNA at specific areas with ribozymes with the intent of degrading (or just inactivating) them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This scenario seems more likely in eukaryotes, as they have capped 5' UTRs and a polyA tail at 3' UTRs that lend to RNA stability. &lt;strong&gt;How quickly and how much will an uncapped RNA degrade? What about the lack of a polyA tail?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since prokaryotes lack these structures, I am restricted to the use of UTR regions in my particular instance. &lt;strong&gt;Is there any similar mechanism, whether in general or for specific proteins, that will allow me to exploit a UTR region for RNA inactivation in prokaryotes?&lt;/strong&gt; Please keep in mind adding synthetic sequences to these UTR regions is certainly a possibility.&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2014-12-05T12:33:38.713" Title="How significant is RNA degradation with removal of cap/polyA's in eukaryotes, or UTR's in prokaryotes?" Tags="&lt;rna&gt;&lt;synthetic-biology&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10293" PostTypeId="2" ParentId="10278" CreationDate="2013-09-05T18:40:59.447" Score="0" Body="&lt;p&gt;Im not 100% certain. If something is called an x-like protein, it usually means it is homologous and has some sequence and / or structural similarity to x. However, there may not be enough biochemical evidence to say definitively that it is in family x. &lt;a href=&quot;http://www.cell.com/molecular-cell/abstract/S1097-2765%2808%2900804-6&quot; rel=&quot;nofollow&quot;&gt;I came across this paper&lt;/a&gt; where they are speaking about an SR-like protein. They said:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;While budding yeast lack alternative splicing, they do have three SR-like proteins: Npl3, Gbp2, and Hrb1. However, these have been best characterized for their roles in mRNA export, leaving their potential roles in splicing largely unexplored.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So in this case the protein has a serine/arginine binding domain and an RNA binding domain (just like SR proteins) but most of the biochemistry points to them being involved RNA export, not splicing (splicing, of course is what SR proteins are known for). So, they get the name SR-like. It will vary though. There is not a unified protein naming system&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-09-05T18:40:59.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10294" PostTypeId="1" AcceptedAnswerId="10298" CreationDate="2013-09-05T20:21:59.013" Score="2" ViewCount="4104" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ukppe.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have two questions pertaining to this pedigree &#xA;I believe it to be an  autosomal recessive trait.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;The probability that individuals IV-1 and IV-2 would give rise to an affected individual would be:&lt;/strong&gt;&#xA;A. 1/4 b. 1/2 c. 1/8 d. 1/12 e. 1/24&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Suppose individual IV-2 was unaffected. The probability of his marriage giving rise to an affected child would be:&lt;/strong&gt;&#xA;A. 1/4 b. 1/2 c. 1/8 d. 1/12 e. 1/24&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I worked on this problem for the last hour or so and figured up question 1 to be 1/2 and question two to be 1/4. I don't feel this is correct. I feel like I am missing something. If you don't mind showing the calculations for how you came about an answer that would be greatly appreciated.&lt;/p&gt;&#xA;" OwnerUserId="4410" LastEditorUserId="69" LastEditDate="2013-09-05T21:47:33.100" LastActivityDate="2014-05-15T22:17:16.493" Title="Genetics: pedigree following a rare trait autosomal recessive" Tags="&lt;genetics&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10296" PostTypeId="2" ParentId="10290" CreationDate="2013-09-05T21:30:15.727" Score="3" Body="&lt;p&gt;The following study shows evidence that UVB does damage plant DNA.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Rousseaux et al. Ozone depletion and UVB radiation: Impact on plant DNA damage in southern South America. Proc Natl Acad Sci U S A. 1999 December 21; 96(26): 15310–15315.&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC24816/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC24816/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2014-01-05T21:33:59.373" LastActivityDate="2014-01-05T21:33:59.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10297" PostTypeId="1" CreationDate="2013-09-05T22:04:02.440" Score="0" ViewCount="274" Body="&lt;p&gt;I know that the RISC (RNA-induced silencing complex) is one of the primary complexes involved in gene regulation through RNAi.  What I want to know is, what role exactly does Dicer play in this complex?&lt;/p&gt;&#xA;" OwnerUserId="4413" LastActivityDate="2013-09-06T05:25:45.823" Title="How does the enzyme Dicer function in the RISC complex?" Tags="&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10298" PostTypeId="2" ParentId="10294" CreationDate="2013-09-05T22:31:56.843" Score="2" Body="&lt;h1&gt;Question 1&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;Okay, so I'll go through my own process for you here step by step, moving down the tree.  Here's an annotated version of your diagram with my own thoughts (it's been a while since I've done this but should hopefully be accurate):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wvSU5.jpg&quot; alt=&quot;Annotated pedigree chart&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Generation 2:&lt;/strong&gt;  As you realised, the trait is autosomal recessive so the female (II:2) has the genotype &lt;em&gt;aa&lt;/em&gt;.  The male is considered wild type unless informed otherwise, giving him a genotype of &lt;em&gt;AA&lt;/em&gt;.  I think you had worked all this out, but they are shown in red on the diagram.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Generation 3:&lt;/strong&gt; Using the two genotypes of the parents from II (red), we know that all the progeny in generation III are carriers - i.e. &lt;em&gt;Aa&lt;/em&gt; genotypes.  This is indicated for III:6 in orangey-brown.  I think you also worked this out successfully.  However in your original chart, III:7 is noted as &lt;em&gt;Aa&lt;/em&gt;.  III:7 is from outside of the affected family and would therefore again be considered to have be wild type and therefore instead have the genotype &lt;em&gt;AA&lt;/em&gt; - shown in purple.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Generation 4:&lt;/strong&gt; In order to work out the potential genotypes of IV:1 we have to do a cross between the two parents III:6 and III:7 - which works out as follows:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;        |          Male          |&#xA;        |     A            a     |&#xA;        |------------------------|&#xA;F       |                        |&#xA;e     A |    AA            Aa    |&#xA;m       |                        |&#xA;a       |                        |&#xA;l     A |    AA            Aa    |&#xA;e       |                        |&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;As you can see, there is a 50% chance of IV:1 being healthy &lt;em&gt;AA&lt;/em&gt; and a 50% chance of being a carrier &lt;em&gt;Aa&lt;/em&gt; - shown in green.  As IV:2 is affected, we know his genotype is &lt;em&gt;aa&lt;/em&gt; (pink).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Generation V:&lt;/strong&gt;  Now for answer to your first question.  If IV:1 had the &lt;em&gt;AA&lt;/em&gt; genotype then the child could &lt;strong&gt;never&lt;/strong&gt; be affected, reducing the odds to 50% immediately. Of this remaining 50%: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;        |          Male          |&#xA;        |     a            a     |&#xA;        |------------------------|&#xA;F       |                        |&#xA;e     A |    Aa            Aa    |&#xA;m       |                        |&#xA;a       |                        |&#xA;l     a |    aa            aa    |&#xA;e       |                        |&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;50% of the offspring would be affected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Therefore the probability of V:I being affected is $\frac{1}{2} \times \frac{1}{2} = \frac{1}{4}$&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h1&gt;Question 2&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;The second question seems very odd to me.  If IV:2 was unaffected in the literal sense of the word they would be wild-type &lt;em&gt;AA&lt;/em&gt;.  This would make the probability of them having an affected child as 0.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As this isn't one of your options, I assume they mean that IV:2 is a carrier (&lt;em&gt;Aa&lt;/em&gt;).  We are this time therefore crossing either &lt;em&gt;AA&lt;/em&gt; or &lt;em&gt;Aa&lt;/em&gt; (IV:1) with &lt;em&gt;Aa&lt;/em&gt; (IV:2).  Again, if IV:1 is heterozygous dominant (&lt;em&gt;AA&lt;/em&gt;) none of her children will be affected.  This means the odds are again reduced by a half.  In the case that she is heterozygous &lt;em&gt;Aa&lt;/em&gt; then the cross becomes:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;        |          Male          |&#xA;        |     A            a     |&#xA;        |------------------------|&#xA;F       |                        |&#xA;e     A |    AA            Aa    |&#xA;m       |                        |&#xA;a       |                        |&#xA;l     a |    Aa            aa    |&#xA;e       |                        |&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Giving 25% healthy, 50% carrier and 25% affected.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;As you're looking for affected children: $\frac{1}{2} \times \frac{1}{4} = \frac{1}{8}$&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2013-09-05T22:31:56.843" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10299" PostTypeId="2" ParentId="10266" CreationDate="2013-09-05T22:32:52.637" Score="2" Body="&lt;p&gt;According to the &lt;a href=&quot;http://2012.igem.org/Team%3aKyoto/Secretion/Project&quot; rel=&quot;nofollow&quot;&gt;2012 iGEM Kyoto team&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Twin Arginate Translocation pathway(TAT) is [an endogenous] secretion system in E.coli. This system can carry proteins that have torA signal amino acid sequences at N terminal. TatA, TatB, TatC and TatD compose Tat complex on inner membrane. Tat complex recognizes torA signal peptide and then it transports protein (with torA) from cytoplasm to periplasm. In addition, protein that has passed through TAT pathway cut off the torA signal. Proteins which are secreted by this system have no tag that obstruct the activation of the protein.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The team created a cassette with the TAT genes to increase the expression of the pathway and also included the Kil gene, which perforates the outer membrane, possibly aiding the external diffusion of the secreted protein. They noted, rather tongue-in-cheek, that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Needless to say, function of outer membrane as membrane is essential for E.coli to survive. In other words, overexpression of Kil causes cell death. In this reason, we must find suitable amount of expression.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note&lt;/strong&gt;: according to &lt;a href=&quot;http://2012.igem.org/Team%3aKyoto/Notebook#SecretionNotebook&quot; rel=&quot;nofollow&quot;&gt;their lab notebook&lt;/a&gt;, the team never observed extracellular GFP via confocal microscope (search that page for 'confocal'). So. Beware :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their project page also includes some references to the following literature:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Tracy Palmer and Ben C. Berks &quot;The twin-arginine translocation (Tat) protein export pathway&quot;&lt;/li&gt;&#xA;&lt;li&gt;J. H. Choi. S. Y. Lee &quot;Secretory and extracellular production of recombinant proteins using Escherichia coli&quot;&lt;/li&gt;&#xA;&lt;li&gt;G. Miksch · E. Fiedler · P. Dobrowolski · K. Friehs &quot;The kil gene of the ColE1 plasmid of Escherichia coli controlled by a growth-phase-dependent promoter mediates the secretion of a heterologous periplasmic protein during the stationary phase&quot;&lt;/li&gt;&#xA;&lt;li&gt;Brad A. Seibel* and Patrick J. Walsh &quot;Trimethylamine oxide accumulation in marine animals: relationship to acylglycerol storage&quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="51" LastActivityDate="2013-09-05T22:32:52.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10300" PostTypeId="2" ParentId="10297" CreationDate="2013-09-06T05:25:45.823" Score="1" Body="&lt;p&gt;Dicer is an endo-ribonuclease belonging to the RNAse-III class. Dicer is not a part of the RISC. It however helps in the formation of RISC by cleaving dsRNA or the stem of hairpin RNA on two ends which liberates a small dsRNA product. Then one of the strands is loaded into the RISC.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several reviews on this topic and there is a video as well which you can find on youtube.  &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-09-06T05:25:45.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10301" PostTypeId="1" CreationDate="2013-09-06T05:26:42.837" Score="0" ViewCount="88" Body="&lt;p&gt;Could an instance of forced cellular growth cause some cells to have their self-destruct mechanisms to malfunction or 'turn off'thus preventing apoptosis?&lt;/p&gt;&#xA;" OwnerUserId="4414" LastActivityDate="2014-01-04T08:28:34.663" Title="Is forced cell growth related to apoptosis?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10302" PostTypeId="2" ParentId="10301" CreationDate="2013-09-06T05:42:54.450" Score="1" Body="&lt;p&gt;It is trivial to assume that forced growth will overcome apoptosis which is what you see in the immortalized cell lines and in cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the interesting thing is that there are instances in which forced growth causes apoptosis. The classic example is of the brain in which expression of SV40 t-antigen to make cells proliferative actually caused loss of tissue [&lt;a href=&quot;http://www.jneurosci.org/content/24/42/9232.full&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;,&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/089662739290247B&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Knockdown of Aif (apoptosis inducing factor) also causes neurodegeneration and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22869892&quot; rel=&quot;nofollow&quot;&gt;thymic hypoplasia&lt;/a&gt; by causing increase in oxidative damage.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-09-06T05:59:38.500" LastActivityDate="2013-09-06T05:59:38.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10303" PostTypeId="2" ParentId="10291" CreationDate="2013-09-06T05:52:43.143" Score="2" Body="&lt;p&gt;I am assuming that you know the difference between steady state and equilibria. Your definition of equilibrium is correct; fwd rate = bkwd rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a steady state the levels of a component remain constant over time but that may be because of many reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As terdon indicates many protein-protein binding events are in equilibrium (binding and unbinding reactions; which gives rise to terms like association/dissociation constants). Many metabolic reactions are also in equilibrium. Enzymes don't change the equilibria. They just accelerate both the rates and help attain equilibria faster.&#xA;So, if a metabolic pathway has slow rate limiting steps then the faster steps go to  equilibrium.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-09-06T05:52:43.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10305" PostTypeId="1" CreationDate="2013-09-06T11:58:14.457" Score="3" ViewCount="218" Body="&lt;p&gt;I &lt;a href=&quot;https://biology.stackexchange.com/questions/10256/where-can-i-find-an-at-least-semi-comprehensive-list-of-what-biochemical-reactio&quot;&gt;asked a question&lt;/a&gt; on bio stackexchange a few days from which I was hoping to be able to arrive at an answer for this question myself but I have had no such luck so now I am going to just ask outright: other than &lt;strong&gt;acetyl-L-carnitine&lt;/strong&gt; are there any orally-bioavailable compounds (in particular orally-bioavailable to &lt;strong&gt;humans&lt;/strong&gt;)  that exists that can serve as an &lt;strong&gt;acetyl group donor&lt;/strong&gt; for &lt;strong&gt;CoA&lt;/strong&gt;? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My main motivation for asking this question is that I know that acetyl-L-carnitine indirectly promotes the acetylation of histones by serving as an acetyl donor for CoA by serving as a substrate for &lt;strong&gt;carnitine O-acetyltransferase&lt;/strong&gt; and then this resulting acetyl-CoA then donates an acetyl group to histones by means of the enzyme &lt;strong&gt;histone acetyltransferase&lt;/strong&gt;. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-07-04T17:22:27.547" Title="Other than Acetylcarnitine what other orally-bioavailable Acetyl donors exist to assist in the conversion of CoA to acetyl-CoA?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;coa&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10306" PostTypeId="2" ParentId="10276" CreationDate="2013-09-06T15:03:29.660" Score="0" Body="&lt;p&gt;You can try &lt;a href=&quot;http://en.wikipedia.org/wiki/Dynamic_time_warping&quot; rel=&quot;nofollow&quot;&gt;dynamic time warping&lt;/a&gt;, or &lt;a href=&quot;http://en.wikipedia.org/wiki/String_kernel&quot; rel=&quot;nofollow&quot;&gt;string kernel&lt;/a&gt; as a measure of similarity. However, &lt;em&gt;similarity&lt;/em&gt; is highly context-dependent, and you may have to invent your own notion of similarity. First you need to ask yourself what do you consider similar. This is a hard problem, and borrowing arbitrary solutions from different fields may not be the best idea.&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2013-09-06T15:03:29.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10307" PostTypeId="1" CreationDate="2013-09-06T15:28:53.723" Score="1" ViewCount="323" Body="&lt;p&gt;I think I know why -- &lt;strong&gt;bioavailability&lt;/strong&gt; problems but since I have no firm evidence to support this theory I thought I would ask the biology stackexchange community for their input. I'd like some firm &lt;strong&gt;bioavailability&lt;/strong&gt; data of &lt;strong&gt;sodium butyrate&lt;/strong&gt; in mammals, preferably humans. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="4101" LastEditDate="2013-10-29T14:34:07.837" LastActivityDate="2013-10-29T14:34:07.837" Title="Why can't sodium butyrate be delivered orally in humans and other mammals?" Tags="&lt;pharmacology&gt;&lt;pharmacodynamics&gt;&lt;pharmacokinetics&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10308" PostTypeId="5" CreationDate="2013-09-06T15:30:46.590" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-09-06T15:30:46.590" LastActivityDate="2013-09-06T15:30:46.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10309" PostTypeId="4" CreationDate="2013-09-06T15:30:46.590" Score="0" Body="This tag refers to how the body interacts with drugs such as how the body absorbs, distributes, metabolises and excretes (these four aspects of pharmacokinetics are often abbreviated ADME) said drugs. " OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-09-06T17:48:59.270" LastActivityDate="2013-09-06T17:48:59.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10310" PostTypeId="5" CreationDate="2013-09-06T15:32:02.800" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-09-06T15:32:02.800" LastActivityDate="2013-09-06T15:32:02.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10311" PostTypeId="4" CreationDate="2013-09-06T15:32:02.800" Score="0" Body="This is how drugs interact with the body, typically by interacting with macromolecular targets such as receptors and enzymes. " OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-09-06T17:49:07.287" LastActivityDate="2013-09-06T17:49:07.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10312" PostTypeId="2" ParentId="10276" CreationDate="2013-09-06T17:24:04.257" Score="1" Body="&lt;p&gt;The first thing that comes on my mind is to use &lt;a href=&quot;https://en.wikipedia.org/wiki/Cross-correlation&quot; rel=&quot;nofollow noreferrer&quot;&gt;cross-correlation&lt;/a&gt; (CCF).&#xA;Essentially you compare one trace with variously shifted version of the other to see if there is a correlation between them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example (I am using R but you should be able to adapt this to your software of choice, I have added comments), say A and B are very similar, but shifted of a certain amount in the x axis (10 units in the example) and C is extremely different&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;# Set the random seed to get a reproducible example&#xA;set.seed(12345)&#xA;# Number of points per trace&#xA;n &amp;lt;- 1000&#xA;# All of the possible sensor values&#xA;values &amp;lt;- seq(0, 330, 30)&#xA;# Sample with replacement to get 100 random values&#xA;A &amp;lt;- sample(values, n, replace=TRUE)&#xA;# Let B = A shifted by 10 positions and then change one value every 5&#xA;B &amp;lt;- c(A[-1:-10], A[1:10])&#xA;B[seq(0, n, 5)] &amp;lt;- sample(values, n/5, replace=TRUE)&#xA;# C is a completely different trace&#xA;C &amp;lt;- sample(values, n, replace=TRUE)&#xA;# Plot the traces (I'm offsetting B and C just for visual clarity)&#xA;plot(A, t=&quot;l&quot;, col=&quot;red&quot;, lwd=2, ylim=c(0, 1200))&#xA;points(B + 360, t=&quot;l&quot;, col=&quot;green&quot;, lwd=2)&#xA;points(C + 720, t=&quot;l&quot;, col=&quot;blue&quot;, lwd=2)&#xA;&#xA;# Now calculate the CCF&#xA;c.AB &amp;lt;- ccf(A,B, 100)&#xA;c.BC &amp;lt;- ccf(B,C, 100)&#xA;c.AC &amp;lt;- ccf(A,C, 100)&#xA;&#xA;# Superimpose the CCF plots&#xA;plot(c.AB$lag, c.AB$acf, t=&quot;o&quot;, col=&quot;green&quot;, ylim=c(-0.5,1), ylab=&quot;CCF&quot;, xlab=&quot;Lag&quot;)&#xA;points(c.BC$lag, c.BC$acf, t=&quot;o&quot;, col=&quot;red&quot;)&#xA;points(c.AC$lag, c.AC$acf, t=&quot;o&quot;, col=&quot;blue&quot;)&#xA;abline(v=10, col=&quot;grey&quot;, lty=3)&#xA;legend(&quot;topleft&quot;, c(&quot;A-B&quot;, &quot;B-C&quot;, &quot;A-C&quot;), col=c(&quot;green&quot;, &quot;red&quot;, &quot;blue&quot;), lty=1, lwd=2, pch=20)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The CCF graphs look like this:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/OcoCY.jpg&quot; alt=&quot;CCF plot&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This graphs means that there is a strong positive correlation (max correlation = 1, here you have 0.8) between A and B and that they are shifted of 10 units. You can see this because the peak is at lag=10, corresponding to the gray dashed line, so the maximum correlation is when you shift trace B by 10 units.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B and C and A and C are instead uncorrelated.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2013-09-06T17:24:04.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10313" PostTypeId="1" AcceptedAnswerId="10315" CreationDate="2013-09-06T17:45:36.557" Score="10" ViewCount="19257" Body="&lt;p&gt;FADH&lt;sub&gt;2&lt;/sub&gt; is produced in the conversion of Succinate to Fumarate in the tricarboxylic acid cycle. Why is this so? Why not NADH?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="22057" LastEditDate="2018-05-08T14:55:53.743" LastActivityDate="2018-05-09T08:19:53.707" Title="Why is FAD, rather than NAD+, reduced in the succinate dehydrogenase reaction of the Tricarboxylic Acid Cycle?" Tags="&lt;biochemistry&gt;&lt;mitochondria&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="10315" PostTypeId="2" ParentId="10313" CreationDate="2013-09-07T03:06:29.200" Score="7" Body="&lt;p&gt;In general, $\ce{NADH}$ and $\ce{FADH2}$ are coenzymes. The structure of the main part of an enzyme determines which coenzyme or which prosthetic group will work with the concerned enzyme. Unlike most other TCA cycle enzymes, Succinic Dehydrogenase involves the participation of $\ce{FAD}$ rather than $\ce{NAD}$ and that is a consequence of its specific structure.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another possible reason might have to do with the energy gap available. The conversion of succinate to fumarate liberates less free energy as compared to other oxidation reactions. Ususally, the steps which are coupled with NADH reduction have a free energy change of about $\Delta G=-100$ to $-150~ \pu{kcal/mol}$ but the conversion catalysed by succinic dehydrogenase has a free energy change of $ -80~ \pu{kcal/mol}$ (rough figures) and hence releases less energy. It therefore might not be feasible to couple with $\ce{NADH}$ reduction but it would be favourable (thermodynamically) to couple with an easy-to-reduce (since the reduction potential is higher and hence reduction is more favourable) and hence less energetic molecule $\ce{FADH2}$.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from structural and thermodynamic requirement, one last possible reason might be that succinic dehydrogenase is a part of the mitochondrial membrane and involved in the Electron Transport Chain. Here, flavin molecules are excellent electron transporters (in comparison to nicotinamide based reductants) and therefore it might be more profitable to use a flavin based reductant to later facilitate easy electron transport and proton transfer.&lt;br&gt;&#xA;Again all these are probable reasons and I dont know for sure.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="28778" LastEditDate="2018-05-09T08:19:53.707" LastActivityDate="2018-05-09T08:19:53.707" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="10316" PostTypeId="1" CreationDate="2013-09-07T03:37:22.467" Score="2" ViewCount="435" Body="&lt;p&gt;&lt;strong&gt;Taurine&lt;/strong&gt; and &lt;strong&gt;arginine&lt;/strong&gt; play a key role in the feline diet but I am unaware as to where exactly they fit in. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-09-07T05:20:07.593" LastActivityDate="2013-09-11T13:36:01.940" Title="Why are Taurine and Arginine essential components of the feline diet?" Tags="&lt;amino-acids&gt;&lt;diet&gt;&lt;feline&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10318" PostTypeId="1" AcceptedAnswerId="10321" CreationDate="2013-09-07T11:08:36.750" Score="2" ViewCount="361" Body="&lt;p&gt;Strictly speaking, what is the definition of cDNA?  This confuses me, since usually it is said to refer to DNA that is complementary to mRNA.  Is this correct?  Is it restricted to mature mRNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also find directionality very confusing.  As I understand it, mRNA has a sequence equivalent (less introns, after splicing) to the so-called 'coding strand' of DNA.  Does this mean that cDNA made from mRNA, at least before treated with a DNA polymerase, is also complementary to the original genomic DNA?  Is this the better definition (I have seen this used as well, though the first definition seems far more common).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, as I understand it each chromosome has a forward and reverse strand, defined by convention, but that the 'coding' strand of a given gene is random.  This seems counter-intuitive... is it just because both strands are equivalent?  Does it introduce complications in terms of the cell 'knowing' which strand is the coding strand for a gene?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most upvoted reply to this question (&lt;a href=&quot;http://www.biostars.org/p/3423/&quot; rel=&quot;nofollow&quot;&gt;http://www.biostars.org/p/3423/&lt;/a&gt;) confused me even further.  I feel the same way as 'Onefishtwofish' does, in the replies.  Can anyone clarify?&lt;/p&gt;&#xA;" OwnerUserId="4418" LastActivityDate="2013-09-07T14:51:33.137" Title="Complementarity of cDNA" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;transcription&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10319" PostTypeId="1" AcceptedAnswerId="10356" CreationDate="2013-09-07T12:19:56.313" Score="1" ViewCount="129" Body="&lt;p&gt;I'm looking for an example of bacteria that could receive ultrasound (at any ultrasound frequency) signal and possibly perform some (re)action afterwards.&lt;/p&gt;&#xA;" OwnerUserId="3751" LastEditorUserId="3751" LastEditDate="2013-09-07T16:31:11.907" LastActivityDate="2013-09-09T18:51:34.250" Title="Are there any bacteria that can receive ultrasound signals?" Tags="&lt;bacteriology&gt;&lt;ultrasound&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10321" PostTypeId="2" ParentId="10318" CreationDate="2013-09-07T14:51:33.137" Score="2" Body="&lt;p&gt;It's a good question and has confused me as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A standard definition of cDNA is that it is a double stranded (ds) product of mature mRNA. I suppose it is possible to get a nascent RNA strand copied into cDNA, but I've never heard of that being done.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because cDNA is dsDNA, the original strand is made from your mRNA as the complementary strand, but then you dispose of the RNA and make the second strand to get a stable, reproducable molecule. The total dsDNA molecule is what we refer to as cDNA (not a single strand of this material).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;consider this simplified DNA molecule:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ATG-INTRON-CTCTAG&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TAC-INTRON-GAGATC&lt;/p&gt;&#xA;&#xA;&lt;p&gt;this could be transcribed into the following mRNA (corresponding to Met-INTRON-Leu-Stop):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AUG-INTRON-CUCUAG&lt;/p&gt;&#xA;&#xA;&lt;p&gt;before nuclear export the intron is removed, making mature mRNA:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AUGCUCUAG&lt;/p&gt;&#xA;&#xA;&lt;p&gt;you make cDNA from this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ATGCTCTAG&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TACGAGATC&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, you have both a coding and a complementary strand in your cDNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for directionality on the chromosome, genes can be in either direction (meaning that they can use either strand as the coding strand), but remember that the forces that contribute to transcription are just locally determined (assembly of transcription factors, etc) and pay no heed to what direction they're going or strand they are on relative to any other gene. The strands are labeled as positive and negative, but that's just a reference for orientation. A good place to browse the human (or other species) genome is the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=9606&quot; rel=&quot;nofollow&quot;&gt;NIH's map viewer&lt;/a&gt;. Click on a chromosome to see the genes mapped to it. Note the column labeled 'O' is for orientation.&lt;/p&gt;&#xA;" OwnerUserId="4139" LastActivityDate="2013-09-07T14:51:33.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10322" PostTypeId="1" AcceptedAnswerId="10342" CreationDate="2013-09-07T15:46:46.830" Score="1" ViewCount="456" Body="&lt;p&gt;Mitosis in eukaryotes happen in this order: DNA replicates and then the cell divides. Why doesn't it happen in reverse order (i.e., cell divides and then replicates the DNA)?&#xA;I am talking about diploid cells.&#xA;Why has evolution favoured the first way? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-09-08T14:45:08.353" LastActivityDate="2018-05-01T21:08:09.053" Title="Why can't cell division happen the other way around?" Tags="&lt;evolution&gt;&lt;cell-biology&gt;&lt;mitosis&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10323" PostTypeId="1" AcceptedAnswerId="11279" CreationDate="2013-09-07T15:50:40.893" Score="1" ViewCount="179" Body="&lt;p&gt;Whenever there are minor/major injury to blood vessels, the platelets, fibrin, thrombin, etc. are recruited. They then seal the wound and block bleeding.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What tells them that their job is done?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2013-11-04T02:41:08.487" LastActivityDate="2014-01-03T03:47:34.930" Title="What stops the coagulation process?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10324" PostTypeId="2" ParentId="10316" CreationDate="2013-09-07T16:00:02.327" Score="2" Body="&lt;p&gt;From the &lt;a href=&quot;http://en.wikipedia.org/wiki/Taurine#In_animal_nutrition&quot; rel=&quot;nofollow&quot;&gt;Taurine Wikipedia article:&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The absence of taurine causes a cat's retina to slowly degenerate, causing eye problems and (eventually) irreversible blindness – a condition known as central retinal degeneration (CRD), as well as hair loss and tooth decay. Decreased plasma taurine concentration has been demonstrated to be associated with feline dilated cardiomyopathy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Arginine&lt;/strong&gt; is an &lt;em&gt;Essential&lt;/em&gt; Amino Acid for cats (and many other mammals - including Humans while we're infants). That is, they cannot synthesize it on their own and must obtain it entirely from their diet. &lt;a href=&quot;http://feline-nutrition.org/answers/answers-what-is-arginine-and-is-it-essential&quot; rel=&quot;nofollow&quot;&gt;A 10lb. (5kg) cat will require about .86g of Arginine&lt;/a&gt; - which is abundant in all meats and can be met with a few ounces of food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could not find anything particularly &lt;em&gt;special&lt;/em&gt; about Arginine as opposed to other EAA's for cats.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2013-09-11T13:36:01.940" LastActivityDate="2013-09-11T13:36:01.940" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10325" PostTypeId="1" AcceptedAnswerId="10332" CreationDate="2013-09-07T16:11:24.797" Score="1" ViewCount="2658" Body="&lt;p&gt;I found that some books include cytokinesis within mitosis, but some other books I have referred to include only the dividing of the nucleus as mitosis and do not include cytokinesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone help me out? Please include a source in your answer.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-31T16:39:36.783" LastActivityDate="2016-04-24T21:55:37.640" Title="Does mitosis include cytokinesis?" Tags="&lt;terminology&gt;&lt;mitosis&gt;&lt;cytokinesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10326" PostTypeId="1" CreationDate="2013-09-07T16:14:44.927" Score="4" ViewCount="322" Body="&lt;p&gt;I am really confused as to when kinetochores are attached to centromeres. Are they attached soon after replication or after condensation ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2015-04-11T21:21:51.400" Title="When do kinetochores attach?" Tags="&lt;mitosis&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10327" PostTypeId="2" ParentId="10322" CreationDate="2013-09-07T19:39:30.313" Score="1" Body="&lt;p&gt;The biggest problem is this: if you have only one copy of the DNA how is it going to divide it between the two cells so that both have a complete copy?&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2013-09-07T19:39:30.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10328" PostTypeId="1" CreationDate="2013-09-07T20:49:04.577" Score="2" ViewCount="179" Body="&lt;p&gt;Crocodiles and some dinosaurs have a second set of ribs between the sternum and pelvis called &lt;a href=&quot;https://en.wikipedia.org/wiki/Gastralium&quot; rel=&quot;nofollow&quot;&gt;gastralia&lt;/a&gt;. Where are the gastralia attached to the rest of the skeleton? &lt;/p&gt;&#xA;" OwnerUserId="4420" LastEditorUserId="460" LastEditDate="2013-09-08T02:40:24.010" LastActivityDate="2013-09-08T02:40:24.010" Title="Where are the gastralia (stomach ribs) attached?" Tags="&lt;zoology&gt;&lt;anatomy&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10329" PostTypeId="1" AcceptedAnswerId="20223" CreationDate="2013-09-07T22:50:41.277" Score="2" ViewCount="851" Body="&lt;p&gt;Imagine we want to read impulses within single neurons in the brain. Can we do that now for a single region within the brain? If not, what is the smallest region that can be monitored for an activity in real time? Is there a more advanced method than electroencephalography for scaning brain activity in real time?&lt;/p&gt;&#xA;" OwnerUserId="4421" LastEditorUserId="460" LastEditDate="2013-09-08T02:40:19.840" LastActivityDate="2014-08-04T20:30:40.440" Title="How precise is EEG?" Tags="&lt;human-biology&gt;&lt;brain&gt;&lt;electrophysiology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10331" PostTypeId="1" AcceptedAnswerId="10354" CreationDate="2013-09-08T00:24:18.303" Score="1" ViewCount="75" Body="&lt;p&gt;Toxoplasmosis modifies the rat's brain to make them love (and be eaten by) cats. It also infects ~30% of humans, and modifies traits in several bad ways (i.e. schizophrenia and increased reaction time). However, humans are thought to be a &quot;dead end&quot; for the parasite. Thus, there is a significant selection pressure for humans to develop resistance but no (or almost no) pressure for toxoplasmosis to counter human resistance. If so, why are so many people infected?&lt;/p&gt;&#xA;" OwnerUserId="4321" LastActivityDate="2013-09-09T16:02:34.030" Title="Human defenses to toxoplasmosis" Tags="&lt;brain&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10332" PostTypeId="2" ParentId="10325" CreationDate="2013-09-08T05:18:20.740" Score="2" Body="&lt;p&gt;Cytokinesis is separate from mitosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What edition are you looking at?  To quote from the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26831/&quot; rel=&quot;nofollow&quot;&gt;Fourth Edition&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The cell cycle culminates in the division of the cytoplasm by cytokinesis. In a typical cell, cytokinesis accompanies every mitosis, although some cells, such as Drosophila embryos (discussed later) and vertebrate osteoclasts (discussed in Chapter 22), undergo mitosis without cytokinesis and become multinucleate. Cytokinesis begins in anaphase and ends in telophase, reaching completion as the next interphase begins.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The mouse-over definition of cytokinesis there is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Division of the cytoplasm of a plant or animal cell into two, as distinct from the division of its nucleus (which is mitosis)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-08T05:18:20.740" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10333" PostTypeId="1" AcceptedAnswerId="10341" CreationDate="2013-09-08T07:40:10.000" Score="3" ViewCount="259" Body="&lt;p&gt;When mammals consume food and digest it or drink fluids that are then filtered by their kidneys, are the waste products generated simply depleted versions of what they consumed? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there other byproducts of metabolism and filtration contained in that waste that are generated by the body and are not directly a part of the food or liquid that was consumed that are excreted?&lt;/p&gt;&#xA;" OwnerUserId="4423" LastEditorUserId="16651" LastEditDate="2015-12-11T04:53:36.000" LastActivityDate="2015-12-11T04:53:36.000" Title="Are the byproducts of mammalian digestion simply depleted versions of the food or liquid consumed?" Tags="&lt;physiology&gt;&lt;mammals&gt;&lt;digestion&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10334" PostTypeId="1" AcceptedAnswerId="10338" CreationDate="2013-09-08T07:24:02.027" Score="2" ViewCount="131" Body="&lt;p&gt;I'd like to get some clarification on specifically how the matter from the fat reserves of the Adipocyte physically leaves the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, if you were to somehow follow every atom in the fat reserves of the cells of a dieting person, then, via what hole would these atoms ultimately exit the body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the answer to this question merely &quot;exhaling through the mouth&quot;? Or do they come out in feces too?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note 1&lt;/strong&gt;: This question is not to be confused with the question: &quot;How does mass leave your body in general?&quot; For there are several ways to accomplish this. (e.g. shedding skin cells, cutting off your arm, cutting your hair, sweating, dehydration, liposuction, bleeding, spitting, blowing your nose, etc...)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note 2&lt;/strong&gt;: Please see this other similar StackExchange post here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://physics.stackexchange.com/questions/2605/how-does-mass-leave-the-body-when-you-lose-weight&quot;&gt;https://physics.stackexchange.com/questions/2605/how-does-mass-leave-the-body-when-you-lose-weight&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4423" OwnerDisplayName="tondog" LastEditorUserId="-1" LastEditDate="2017-04-13T12:40:13.457" LastActivityDate="2013-09-20T02:32:36.353" Title="How does the matter that makes up the fat of your fat cells ultimately leave your body--following weight loss?" Tags="&lt;respiration&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10336" PostTypeId="1" CreationDate="2013-09-08T08:43:26.327" Score="1" ViewCount="506" Body="&lt;p&gt;I have a sequence ATG GGG CCC TTT AAA TAA and want to use it as antisense RNA in my vector. How should I clone it? I am confused with the direction of my clone. I looking for the direction and sequence of the clones. &lt;/p&gt;&#xA;" OwnerUserId="4424" LastEditorUserId="107" LastEditDate="2013-09-08T14:34:21.453" LastActivityDate="2013-09-10T12:17:39.373" Title="how to clone a gene fragment in two direction as sense and antisense in vector" Tags="&lt;molecular-biology&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10337" PostTypeId="1" AcceptedAnswerId="10339" CreationDate="2013-09-08T11:55:28.407" Score="7" ViewCount="2255" Body="&lt;p&gt;What is the evolutionary reason behind sharing the same path for food and air?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, we have a nose and lungs, yet they are linked by the pharynx, which is shared with the mouth and oesophagus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wouldn't it make more evolutionary sense for the nose + lungs to have their own &quot;path&quot;, while the mouth and stomach have a separate system? This would prevent &quot;choking&quot;, allow for breathing while eating/drinking, etc.&lt;/p&gt;&#xA;" OwnerUserId="4425" LastEditorUserId="107" LastEditDate="2013-09-08T14:19:11.387" LastActivityDate="2013-09-09T15:24:19.697" Title="evolutionary reason behind sharing the same path for food and air?" Tags="&lt;evolution&gt;&lt;embryology&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10338" PostTypeId="2" ParentId="10334" CreationDate="2013-09-08T12:23:10.763" Score="5" Body="&lt;p&gt;Yes, they are mostly exhaled. The carbon, hydrogen and oxygen that the fats are made of recombine to become $CO_2$ and $H_2 O$ and are exhaled. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's the same overall chemical reaction as if the fats / carbohydrates were burnt, except it's by a different pathway, and the energy produced goes (mostly) towards driving other chemical reactions rather than becoming light and heat.&lt;/p&gt;&#xA;" OwnerUserId="4427" LastActivityDate="2013-09-08T12:23:10.763" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10339" PostTypeId="2" ParentId="10337" CreationDate="2013-09-08T14:18:09.600" Score="9" Body="&lt;p&gt;While it might make more logical sense to have separate passageways for air and food/water, this did not happen in evolutionary history due to the peculiarities of lung development. Vertebrate lungs develop as an outpouching of the gut tube, which itself has a very long evolutionary history (probably homologous among all &lt;a href=&quot;http://www.ucmp.berkeley.edu/phyla/deuterostomia.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;deuterostomes&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the image below, the trachea has budded off the esophagus. Further lung development will involve the differentiation of main, secondary, and tertiary bronchi as well as the alveoli, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DEwMh.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additional images and description at &lt;a href=&quot;http://www.uoguelph.ca/zoology/devobio/210labs/lung1.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.uoguelph.ca/zoology/devobio/210labs/lung1.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Air-filled organs like lungs and swim bladders actually have a broad distribution going way down into fishes. Human (and other mammalian) lungs are likely homologous with ancestral air-filled organs of fishes. We can't be certain, but there is no reason to think that mammalian lungs are a de novo evolutionary innovation. So our airway and food-ways are tied together developmentally and are constrained by evolutionary history.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for breathing and eating (swallowing) at the same time, most mammals can do this, and baby humans can as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like most anatomical systems that seem as though they could have evolved better, this system works most of the time and has worked well enough for hundreds of millions of years.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-09-08T14:18:09.600" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10341" PostTypeId="2" ParentId="10333" CreationDate="2013-09-08T16:59:11.820" Score="9" Body="&lt;p&gt;The answer really depends on what aspect of the urine and feces one is considering.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the atomic level, no, urine and feces are composed entirely of atoms taken from our environment. As one would expect, as there is no &quot;Humanium&quot; on the periodic table. In fact, all the atoms in urine and feces were originally created by stars.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the molecular level, yes. The body produces molecules that we do not ingest, or that we ingest in minute quantities, such as urea and bile.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the cellular level, yes. The body produces, for instance, red blood cells even if the person eats a vegan diet with no blood intake. The proteins that make up the cells are created by breaking down ingested proteins into their constituent amino acids, which are then used to construct new proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also at the cellular level are the huge amount of bacterial cells that we support. Estimates of the number of bacterial cells in our body range from ten to 100 times the number of our own cells. The bacterial component in feces is massive - up to 1/3 of feces by weight are bacteria. Urine, being produced from the blood by the kidneys, is relatively sterile.&lt;/p&gt;&#xA;" OwnerUserId="4428" LastActivityDate="2013-09-08T16:59:11.820" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10342" PostTypeId="2" ParentId="10322" CreationDate="2013-09-08T18:45:26.807" Score="3" Body="&lt;p&gt;If you are thinking of a process like meiosis but followed by DNA duplication, the problem is that this would create daughter cells that do not have the same genome as the parent cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The diploid genome of a sexually reproducing species' cell has different alleles of the same locus. If the cell replicates itself by passing one chromatid to each daughter cell which then duplicate that to make a diploid genome, the resulting cells will not have the same DNA as the original one since each of the daughter cells will have inherited only one of the available alleles. They will then make an exact copy of the DNA they have inherited and become diploid but with a new genome, one that did not exist in their parent. This is not good since the cells of an organism need to have the same genome in order to function in the same way. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-09-08T18:45:26.807" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10343" PostTypeId="2" ParentId="10329" CreationDate="2013-09-08T23:08:02.630" Score="2" Body="&lt;p&gt;The smallest area that the EEG can measure is related to the electrode density. Even with research setups with 100s of electrodes, the smallest measurable region is on the order of a square centimeter or so on the skull surface. Brain regions deeper in the brain produce a 'blurred' signal that shows up on several electrodes at once.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;fMRI, on the other hand, can measure smaller areas in three dimensions, but not as often.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2013-09-08T23:08:02.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10345" PostTypeId="1" AcceptedAnswerId="10347" CreationDate="2013-09-09T02:31:33.533" Score="3" ViewCount="148" Body="&lt;p&gt;Is it true that people will pass out when subject to pain too much to bear, or there's no such threshold? What's the reason for passing out under acute pain, even if no physical injuries occur (e.g, loss of blood, etc.)?  &lt;/p&gt;&#xA;" OwnerUserId="4431" LastActivityDate="2013-09-09T11:53:09.387" Title="What's the mechanism for pain-induced swoon?" Tags="&lt;human-biology&gt;&lt;pain&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10346" PostTypeId="1" AcceptedAnswerId="10348" CreationDate="2013-09-09T03:32:11.720" Score="3" ViewCount="908" Body="&lt;p&gt;Do they act directly on the muscle and actually relax muscle tissue and ease spasms, or do they just prevent your brain from receiving signals that inform you of tight muscles?   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the latter case, it seems like your brain would sort of become &quot;immune&quot; to the pain even though the muscle is still in a spasm.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm obviously not a biologist, just curious about this.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do muscle relaxants work?   &lt;/p&gt;&#xA;" OwnerUserId="4150" LastActivityDate="2013-09-09T12:07:29.643" Title="How do muscle relaxants work?" Tags="&lt;human-anatomy&gt;&lt;neurotransmitter&gt;&lt;muscles&gt;&lt;pain&gt;&lt;tissue&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10347" PostTypeId="2" ParentId="10345" CreationDate="2013-09-09T08:48:21.767" Score="0" Body="&lt;p&gt;Swooning, fainting otherwise termed Syncope or Primary shock (Triggered by pain or any unpleasant stimuli through the vaso vagal effect), is due to generalised vasodilation. The capillaries loose their tone and dilate resulting in an increase in volume capacity of the vascular system. This results in draining of blood to the dependent areas due to gravity thus hindering blood supply to the brain which shuts down and results in collapse (fainting) of the individual. This is a safety mechanism. Once the patient is in the lying down position the blood supply to the brain returns and the patient recovers. An individual who has fainted should not be propped up as this may result in seizures or worse.&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="4101" LastEditDate="2013-09-09T11:53:09.387" LastActivityDate="2013-09-09T11:53:09.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10348" PostTypeId="2" ParentId="10346" CreationDate="2013-09-09T12:07:29.643" Score="3" Body="&lt;p&gt;Check out the &lt;a href=&quot;https://en.wikipedia.org/wiki/Muscle_relaxant&quot; rel=&quot;nofollow&quot;&gt;muscle relaxant&lt;/a&gt; article on Wikipedia, it's pretty straight forward.  In short, there are two main types: Neuromuscular blockers, than act at the junction between the neuron and the muscle; and spasmolytics/antispasmodics, which (mainly) act on the central nervous system to reduce excitation or increase inhibition.  Most of the ones I've heard of, such as diazepam, are in the latter category.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-09T12:07:29.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10349" PostTypeId="1" AcceptedAnswerId="10784" CreationDate="2013-09-09T12:20:48.733" Score="3" ViewCount="2251" Body="&lt;p&gt;Were any 6 armed &quot;tetrapod&quot; fossils ever found? I've seen some lobe finned fish with two sets of shoulders in an evolutionary bio book... I'm curious because I'd like 4 limbed and 2 winged dragons to have existed :)&lt;/p&gt;&#xA;" OwnerUserId="4433" LastActivityDate="2020-05-21T08:32:06.390" Title="Are there any 6 limbed reptile fossils?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10351" PostTypeId="1" AcceptedAnswerId="10393" CreationDate="2013-09-09T14:06:14.587" Score="4" ViewCount="1066" Body="&lt;p&gt;Consciousness is an electrical and chemical interaction in the brain, caused by neurons firing and chemical interactions. How does a mechanical &quot;force&quot; cause this to stop working?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;i.e. How does a mechanical action (such as a punch to the head) cause this electrical/chemical system to stop working (leading to unconsciousness)?&lt;/p&gt;&#xA;" OwnerUserId="4425" LastEditorUserId="4150" LastEditDate="2013-09-10T17:13:19.120" LastActivityDate="2013-10-24T21:28:09.797" Title="Mechanical cause of loss of consciousness" Tags="&lt;neuroscience&gt;&lt;human-anatomy&gt;&lt;neurotransmitter&gt;&lt;neuroanatomy&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10352" PostTypeId="2" ParentId="10336" CreationDate="2013-09-09T15:11:16.447" Score="2" Body="&lt;p&gt;Tour sequence's complementary is TAC CCC GGG AAA TTT ATT. Together they form a DNA strand. Now replicate this and then, after transcription of both the DNA you get the RNA sequence you wanted. Use it as sense or antisense.&lt;/p&gt;&#xA;" OwnerUserId="4435" LastEditorUserId="107" LastEditDate="2013-09-10T12:17:39.373" LastActivityDate="2013-09-10T12:17:39.373" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10354" PostTypeId="2" ParentId="10331" CreationDate="2013-09-09T16:02:34.030" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Thus, there is a significant selection pressure for humans to develop resistance but no (or almost no) pressure for toxoplasmosis to counter human resistance.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, I think in this case &quot;Significant&quot; isn't qualified. Significant selective pressure can come in many forms, but as you mention about 30% of humans are infected with &lt;em&gt;Toxopolasma&lt;/em&gt;, and the vast majority remain capable and functional. Remember that &lt;strong&gt;selective pressure&lt;/strong&gt; applies to the ability to take advantage of resources and reproduce. People with toxoplasmosis are almost always capable of surviving and reproducing, so I doubt the pressure is all that much.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also significant incentive for &lt;em&gt;Toxoplasma&lt;/em&gt; to develop the ability to adapt to humans, as it would open up a whole new resource for them to take advantage of. How fast the parasite is capable of adapting, or even if it's possible to eventually include humans in their life cycle, is something that would take some studying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our immune systems, in turn, try to kill the parasite regardless of whether we're being taken advantage of or not. You might be interested in reading up on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Red_Queen_hypothesis&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Red Queen Hypothesis&lt;/strong&gt;&lt;/a&gt; - a theory that delineates how the immune system is at constant war with its environment and potential new threats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your last question...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... why are so many people infected?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That's easy. :-) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cats have become a popular pet, and most of the time the parasite doesn't significantly affect us. If either of those changes, you'll see a change in infection rates.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-09-09T16:02:34.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10355" PostTypeId="1" CreationDate="2013-09-09T17:10:05.323" Score="1" ViewCount="79" Body="&lt;p&gt;In arabidopsis, 2 cell types arise in the root epidermis : root hair cells and hairless epidermal cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The immature epidermal cells that are in contact with 2 underlying cells of root cortex differentiate into root hair cells whereas the immature epidermal cells having contact with only one cortical cell do not develop root hair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the advantage of this ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-09-09T17:10:05.323" Title="Root hair formation in Arabidopsis" Tags="&lt;botany&gt;&lt;gene-expression&gt;&lt;plant-anatomy&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10356" PostTypeId="2" ParentId="10319" CreationDate="2013-09-09T17:37:17.980" Score="1" Body="&lt;p&gt;I'm going to post a quick answer here, really a thought piece.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually to detect a sound wave you need a sounding board about the wavelength of the sound. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria are on the order of a few microns in length. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ultrasound&quot; rel=&quot;nofollow&quot;&gt;Ultrasound frequencies range from 2 to 200 MHz&lt;/a&gt; (and up I assume).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mcsquared.com/wavelength.htm&quot; rel=&quot;nofollow&quot;&gt;To have a wavelength on the order of 3 microns, a 100 MHz wave would be needed&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So only on the very high end of the range.  If bacteria make sound though, they probably are on this frequency range.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder if this has been looked at?  Not sure it has.  While in biology you never say never - if a bacterium really needs to pick up a wave it might have a clever adaptation to do so, but in the 100MHz + frequency range seems more likely. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-09-09T18:51:34.250" LastActivityDate="2013-09-09T18:51:34.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10358" PostTypeId="1" CreationDate="2013-09-09T21:43:39.740" Score="1" ViewCount="94" Body="&lt;p&gt;The question might seem weird. Does sympathetic nervous system acts 'bilaterally' meaning if you shout to a person's left ear a loud noise (e.g. by headphones), will it activate sympathetic system just on the left or on the both sides. For example it will only dilate left pupil or dilate both ?&lt;/p&gt;&#xA;" OwnerUserId="4206" LastActivityDate="2013-09-09T21:50:36.377" Title="Does sympathetic nervous system acts bilaterally for pupil dilation or other two sided organs?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10359" PostTypeId="2" ParentId="10358" CreationDate="2013-09-09T21:50:36.377" Score="4" Body="&lt;p&gt;Yes, they do. At least in the case of pupils. In fact, the absense of simultaneous regulation of the diameter of the pupil is used as a medical test for the evaluation of brain damage.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-09-09T21:50:36.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10361" PostTypeId="1" CreationDate="2013-09-10T06:29:11.873" Score="2" ViewCount="72" Body="&lt;p&gt;If a patient has a complete removal of his/her stomach (i.e. a &lt;a href=&quot;https://en.wikipedia.org/wiki/Gastrectomy&quot; rel=&quot;nofollow&quot;&gt;total gastrectomy&lt;/a&gt;), then does that cause a person to be more prone to infections from eating unsanitary food?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm asking this question because the stomach plays a role in sterilizing food and, hence, without a stomach it would follow that one might be more prone to getting intestinal infections.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="16299" LastEditDate="2015-12-31T17:30:35.203" LastActivityDate="2015-12-31T17:30:35.203" Title="Does having a total gastrectomy (removal of the stomach) cause individuals to be more prone to infections?" Tags="&lt;infection&gt;&lt;stomach&gt;&lt;surgery&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10362" PostTypeId="1" AcceptedAnswerId="10363" CreationDate="2013-09-10T08:09:53.257" Score="3" ViewCount="107" Body="&lt;p&gt;I'm working on a project where I need to find certain cellulolytic bacteria. I was looking at this list : &lt;a href=&quot;http://webcache.googleusercontent.com/search?q=cache:CrtQ9T6K7m8J:www.wzw.tum.de/mbiotec/cellmo.htm+&amp;amp;cd=1&amp;amp;hl=nl&amp;amp;ct=clnk&amp;amp;gl=be&quot; rel=&quot;nofollow&quot;&gt;http://webcache.googleusercontent.com/search?q=cache:CrtQ9T6K7m8J:www.wzw.tum.de/mbiotec/cellmo.htm+&amp;amp;cd=1&amp;amp;hl=nl&amp;amp;ct=clnk&amp;amp;gl=be&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How could I selectively separate one of the bacteria types that I had in mind from that list?&#xA;So how would I have to extract the bacteria from the compost? &lt;/p&gt;&#xA;" OwnerDisplayName="user4436" LastActivityDate="2013-09-10T08:41:37.060" Title="Extract bacteria from compost?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10363" PostTypeId="2" ParentId="10362" CreationDate="2013-09-10T08:41:37.060" Score="3" Body="&lt;p&gt;A first (and obvious) approach is the use of cellulose agar in order to isolate all the celluloltic bacteria in the sample. Be careful, however, since the nutrient requirements of some of those microbes may be higher and then they won't grow with only cellulose (they may need some other compounds, like a nitrogen source). Be careful with fungi, too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have the proper equipment, it would be ideal to extract DNA and analyze the environmental rRNA 18s sequences. With this, you should be able to know if your bacteria is present in your sample. If so, proceed with the previous steps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you had a set of suspected colonies, you must proceed with more specific culture media (wich would depend of the exact bacteria you're looking for. For example, if you're looking for &lt;em&gt;Clostridium&lt;/em&gt;, you should try to grow your sample in an anaerobic jar and test the ability to reduce sulphur). With this approach, you may reach a point where you can't differenciate similar species. At this point, mollecular characterization is the best option, with the use of rRNA 18s again. Note that the mollecular approach, while relative expensive, can be performed in every step, so you can combine cultures and DNA analyses at will.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, if you're looking for an specific bacteria, it would be useful to know wich one is, so the community can give you more accurate responses.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-09-10T08:41:37.060" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10364" PostTypeId="1" CreationDate="2013-09-10T12:15:23.653" Score="2" ViewCount="61" Body="&lt;p&gt;What role do hippo signalling have on squamous cells in oral health &amp;amp; diseases&lt;/p&gt;&#xA;" OwnerUserId="4323" LastActivityDate="2014-03-24T04:58:05.443" Title="What is the role of hippo signalling in oral squamous cells" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10365" PostTypeId="1" AcceptedAnswerId="10371" CreationDate="2013-09-10T15:34:36.227" Score="2" ViewCount="226" Body="&lt;p&gt;Cytosine residues in DNA that can be methylated (i.e. CpG sites) are likely to be in the same methylation state if they are geographically (proximally) close together. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can only find one paper that states this empirically (1), that 90% of CpG sites within 50bp of one another are in the same methylation state - see below graph.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6r46G.png&quot; alt=&quot;Relationship between methylation status and geographical proximity&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However this study is quite dated now (in the fields of epigenetics at least), and is very general. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know whether CpG's in different regions of the genome are more/less likely to be correlated than in other regions (say, exons vs. promoter regions). It would also be interesting to know whether the correlations change with age, and whether this is related to any disease processes? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for the input. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Eckhardt, et al, 2006. Nature Genetics. doi: &lt;a href=&quot;http://dx.doi.org/10.1038/ng1909&quot; rel=&quot;nofollow noreferrer&quot;&gt;2010.1038/ng1909&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastActivityDate="2013-09-10T16:55:33.937" Title="How correlated are proximally related CpG sites in human DNA?" Tags="&lt;human-biology&gt;&lt;dna&gt;&lt;human-genome&gt;&lt;dna-methylation&gt;&lt;cpg&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10366" PostTypeId="5" CreationDate="2013-09-10T15:39:05.617" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-09-10T15:39:05.617" LastActivityDate="2013-09-10T15:39:05.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10367" PostTypeId="4" CreationDate="2013-09-10T15:39:05.617" Score="0" Body="A methyl group can be added to a cytosine residue, usually one that neighbors a guanine (known as a CpG - cytosine-phosphate-guanine - site). This can affect chromatin and histone structures, as well as directly influencing binding of various factors, thereby altering the transcription of genes." OwnerUserId="740" LastEditorUserId="1306" LastEditDate="2013-10-14T22:08:28.933" LastActivityDate="2013-10-14T22:08:28.933" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10368" PostTypeId="5" CreationDate="2013-09-10T15:41:59.317" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-09-10T15:41:59.317" LastActivityDate="2013-09-10T15:41:59.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10369" PostTypeId="4" CreationDate="2013-09-10T15:41:59.317" Score="0" Body="CpG refers to any cytosine nucleotide in DNA that neighbors a guanine. CpG site comes from &quot;cytosine-phosphate-guanine site&quot;. These sites have the potential for a methyl (or other derivative) to be attached. Dense regions of CpG's are known as CpG islands." OwnerUserId="740" LastEditorUserId="740" LastEditDate="2013-09-10T16:30:04.083" LastActivityDate="2013-09-10T16:30:04.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10370" PostTypeId="2" ParentId="10291" CreationDate="2013-09-10T16:28:29.360" Score="5" Body="&lt;p&gt;I think there are a few principles that we need to consider before answering your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(a) When a reaction is at equilibrium, the rate of any elementary reaction is exactly balanced by that of the reverse process.  This is an important one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above principle follows from transition-state theory, which holds that the activated state for the reaction in one direction is that same for that in the reverse direction.  It also follows from the principle of microscopic reversibility at equilibrium or, more correctly, the principle of detailed balance at equilibrium, which states that “in a system at equilibrium each collision has its exact counterpart in the reverse direction, and that &lt;strong&gt;the rate of every chemical process is exactly balanced by that of the reverse process&lt;/strong&gt;” (my emphasis) [Laidler, 1987, p 130]. It is important to realise that these two points of view are equivalent.  To again quote Laidler (p130), if one is working within the framework of TST “the principle of microscopic reversibility presents nothing new”. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To put it bluntly: a system where any elementary reaction, either explicitly or implicitly, is not exactly balanced by the reverse process is not at equilibrium. By this criteria, the actin example alluded to above &lt;em&gt;cannot&lt;/em&gt;, even loosely, be considered at equilibrium. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This principle has many important consequences, even when a system is not at equilibrium.  One is that the the &lt;strong&gt;product of the ratios&lt;/strong&gt; of rate constants around a cycle (closed loop) equal the equilibrium constant for the cycle (see Cornish-Bowden, 2004, p 104). [see Addendum for an example of where this consequence was not adhered to].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(b) When a species is in a steady-state, the rate of formation equals the rate of breakdown. The steady-state concentration may differ markedly from the equilibrium concentration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(c) As &lt;a href=&quot;https://biology.stackexchange.com/users/3340/wysiwyg&quot;&gt;@WYSIWYG&lt;/a&gt; has &lt;a href=&quot;https://biology.stackexchange.com/a/10303/1136&quot;&gt;pointed out&lt;/a&gt;, an enzyme (catalyst) does not change the equilibrium constant for the uncatalyzed reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(d) When we are dealing with equilibria, we are usually interested in Gibbs free energy changes.  For example (Silbey &amp;amp; Alberty, 2001, p 277).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;#916;G&lt;sup&gt;o&lt;/sup&gt;' = -RT ln K’ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(In the above equation K’ is the apparent equilibrium constant, that is the equilibrium constant at specified pH, and &amp;#916;G&lt;sup&gt;o&lt;/sup&gt;' is the standard transformed Gibbs free energy of a biochemical reaction.  More on this distinction, if you are interested, in the Silbey and Alberty reference quoted above). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The important point is that there is a relatively simple relationship between Gibbs free energy and the equilibrium constant. The Gibbs free energy, of course, gives a measure of the spontaneity of a reaction and also its capacity to do work.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the transformed Gibbs free energy is of a reaction (&amp;#916;G') is zero, the reaction (at specified pH) is at equilibrium and cannot perform useful work, and reactions with negative &amp;#916;G' may be considered ‘spontaneous’.  It is also important to realize that equilibrium is a dynamic state: chemical bonds are continuously being broken and energy is continuously being redistributed (with no loss of energy). [I am dealing here with the transformed free energy, &amp;#916;G', that is the free energy change at specified pH, rather than &amp;#916;G (the pH independent value), as this is the most useful when considering a biochemical reaction.  However, similar conclusions apply to &amp;#916;G]. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Having got those out of the way, I can now attempt to answer your question (slightly rephrased). Can a reaction in a metabolic pathway be at equilibrium?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be extremely pedantic, if there is a flux through the pathway (net conversion of first substrate to end product) then the answer is &lt;em&gt;no&lt;/em&gt; (Newsholme &amp;amp; Start, 1973, p 11). That is, if there is a flux through the pathway, &amp;#916;G' cannot be exactly zero for any individual reaction.   However, &lt;strong&gt;reactions in a metabolic pathway may be very close to equilibrium&lt;/strong&gt; (Newsholme &amp;amp; Start, 1973, chapter 1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let’s (once again) rephrase your question.  Are there any examples of reactions in metabolic pathways that are close to equilibrium, and how can we determine this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To again quote Newsholme &amp;amp; Start (1973, p11)  “In a series of reactions that constitute a metabolic pathway, a few may be displaced far from equilibrium, whereas the majority of reactions may be close to equilibrium”. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how can this be determined? One way would be to measure the ratio of products to substrates (or the ratio of product to substrate pairs) in the cell, and compare this with the equilibrium constant.  Note that it is only the ratio of substrate/product pairs we are interested in, not the absolute concentrations. We might be interested in the NAD&lt;sup&gt;+&lt;/sup&gt;/NADH ratio in the cell, for example.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is, we measure the &lt;strong&gt;mass action ratio&lt;/strong&gt; and compare this with the equilibrium constant.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such measurements are fraught with difficulties, but let’s agree that they can be made. We could rapidly freeze the tissue sample to -190&amp;deg;C (using liquid nitrogen), for example, and then measure the ratio of metabolites.  Finally, it should be pointed out that comparison of mass-action ratio with the equilibrium constant is not the only way of deducing that a reaction is near equilibrium, and agreement between alternative methods is highly desirable before any firm conclusions are drawn. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let’s consider glycolysis as an example.  It is generally agreed that the reactions catalyzed by &lt;a href=&quot;http://www.genome.jp/dbget-bin/www_bget?ec:5.3.1.9&quot; rel=&quot;nofollow noreferrer&quot;&gt;phosphoglucoisomerase&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphoglycerate_mutase&quot; rel=&quot;nofollow noreferrer&quot;&gt;phosphoglycerate mutase&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphoglycerate_mutase&quot; rel=&quot;nofollow noreferrer&quot;&gt;enolase&lt;/a&gt; are all close to equilibrium: the mass action ratios and the equilibrium constants are about the same (see Newsholme &amp;amp; Start, 1973, p 98).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also generally agreed that the reactions catalyzed by &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphofructokinase&quot; rel=&quot;nofollow noreferrer&quot;&gt;phosphofructokinase&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Pyruvate_kinase&quot; rel=&quot;nofollow noreferrer&quot;&gt;pyruvate kinase&lt;/a&gt; are far from equilibrium (see Newsholme &amp;amp; Start, 1973, p 98).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the rationale? In general, it is control reactions catalyzed by regulatory enzymes that are displaced from equilibrium. (A key property of a regulatory enzyme is that the activity is controlled by factors other than substrate concentration). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The enzyme &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphofructokinase&quot; rel=&quot;nofollow noreferrer&quot;&gt;phosphofructokinase&lt;/a&gt; is a good example.  This enzyme plays a key role in the regulation of glycolysis. Measurement of the mass-action ratio for this enzyme gives a value of 0.029, where the equilibrium constant for the reaction is about 1000 (see Newsholme &amp;amp; Start, 1973, p31). It is clear that physiologically this enzyme catalyzes a reaction that is far from equilibrium. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion, many reactions in metabolic pathways may be close to equilibrium, but regulatory enzymes almost always catalyze reactions that are displaced from equilibrium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, if anyone wishes to provide more recent references or to otherwise improve the answer, feel free to edit. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Addendum&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a well-known controversy in the enzyme kinetics field where the requirement that product of the ratios of rate constants around a closed loop equal the equilibrium constant for the cycle was not adhered to, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1134645/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Selwyn (1993)&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1130917/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Topham &amp;amp; Brocklehurst (1992)&lt;/a&gt;.  These authors were critizing the work of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1131997/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Varon &lt;em&gt;et al&lt;/em&gt; (1992)&lt;/a&gt;, who made a bit of a hash of things. If you are interested in this area, you may wish to read up on this controversy, which is very informative. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1134645/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Selwyn’s paper&lt;/a&gt; is a great start). [All the above papers are freely available in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/&quot; rel=&quot;nofollow noreferrer&quot;&gt;PubMed Central&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cornish-Bowden, A. (2004) Fundamentals of Enzyme Kinetics. 3rd Edn. Portland Press.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Laidler, K. J. (1987) Chemical Kinetics 3rd Edn. Harper &amp;amp; Row.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Newsholme, E.A. &amp;amp; Start, C (1973) Regulation in Metabolism. John Wiley &amp;amp; Sons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Silbey, R. J. &amp;amp; Alberty, R.A (2001) Physical Chemistry. 3rd Edn. John Wiley. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biochemist.org/bio/03303/0057/033030057.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eric Arthur Newsholme&lt;/a&gt; (1935–2011) Obituary &lt;/p&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-09-12T13:11:48.897" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10371" PostTypeId="2" ParentId="10365" CreationDate="2013-09-10T16:55:33.937" Score="2" Body="&lt;p&gt;I've got to dash off so I won't be able to give a fully in-depth answer today, but this basically boils down to the concept of CpG islands.  Something like 70-80% of CpGs are methylated in humans, so if they were randomly scattered around the genome there is already a pretty high chance nearby CpGs are in the same state.  However, because of CpG islands, CpGs of similar state are indeed grouped together, depending on promoter activity (to simplify things a bit).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, if you look for articles that &lt;em&gt;cite&lt;/em&gt; your article, a plethora of useful references show up.  In particular, &lt;a href=&quot;http://www.nature.com/nrg/journal/v9/n6/full/nrg2341.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this bad boy&lt;/a&gt; has a handy figure 1 which displays the overall landscape.  Maybe that's too broad of a view, but in general, like methylation patterns cluster together; otherwise, there'd be no such thing as a methylation pattern!  &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006291X09007049&quot; rel=&quot;nofollow noreferrer&quot;&gt;This paper&lt;/a&gt; has a neat figure which sums it all up nicely:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/okUSL.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, it's usually high-methylation or low-methylation; rarely is there anything in between.  There's a lot more in there so I'd recommend going through some of them; I'll try to get back to this later.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-10T16:55:33.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10372" PostTypeId="1" AcceptedAnswerId="16424" CreationDate="2013-09-10T18:07:16.943" Score="2" ViewCount="1618" Body="&lt;p&gt;An inbred strain of plants has a mean height of 24cm. A second strain of the same species also has a mean height of 24cm. When these plants are crossed the F1 are also 24cm in height.However, when the F1 are crossed the F2 plants show a wide range of heights, the greatest number are similar to P1 and F1 but apprx. 4 out of 1000 are only 12cm tall and 4 of 1000 are 40cm tall. What fraction of the F2 plants will be apprx. 28cm in height ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a)3/4&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b)9/16&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c)56/256&lt;/p&gt;&#xA;&#xA;&lt;p&gt;d)none&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer given is c).&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-09-12T12:28:53.970" LastActivityDate="2014-04-08T17:09:15.360" Title="Genetics problem-Height of a plant" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10373" PostTypeId="1" AcceptedAnswerId="10374" CreationDate="2013-09-10T20:21:08.343" Score="8" ViewCount="12423" Body="&lt;p&gt;Let's say I have a picture of an insect wing and a ruler on the same image. Is there any computer program that I can use to calibrate with the ruler and then get a measurement on the wing length? Would the software be able to export these data to a spreadsheet?&lt;/p&gt;&#xA;" OwnerUserId="1906" LastActivityDate="2015-04-20T20:36:51.400" Title="Free software for measuring parts of an image?" Tags="&lt;software&gt;&lt;measurement&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ClosedDate="2015-04-20T22:11:00.167" ContentLicense="CC BY-SA 3.0" />
  <row Id="10374" PostTypeId="2" ParentId="10373" CreationDate="2013-09-10T20:27:04.657" Score="11" Body="&lt;p&gt;&lt;a href=&quot;http://rsbweb.nih.gov/ij/&quot;&gt;ImageJ&lt;/a&gt; is all you need. Particularly see the documentation sections on &lt;a href=&quot;http://rsbweb.nih.gov/ij/docs/guide/146-30.html#sub%3aSet-Scale...&quot;&gt;setting the image scale&lt;/a&gt; and &lt;a href=&quot;http://rsbweb.nih.gov/ij/docs/guide/146-30.html#toc-Subsection-30.1&quot;&gt;measuring&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-09-10T20:27:04.657" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10375" PostTypeId="1" CreationDate="2013-09-10T21:27:07.873" Score="5" ViewCount="1254" Body="&lt;p&gt;I have read in some papers about the layers L1-L5 of the brain (e.g. in &lt;a href=&quot;https://www.google.com/search?q=a%20cellular%20mechanism%20for%20cortical%20associations&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; paper). I could not find a definition of these layers. I have found information about the layers V1-V5 in the visual cortex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where exactly are L1-L5? And do these definitions vary across mammals?&lt;/p&gt;&#xA;" OwnerUserId="17" LastActivityDate="2017-02-17T15:59:33.150" Title="L1 - L5 layers of the brain" Tags="&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10376" PostTypeId="1" AcceptedAnswerId="10386" CreationDate="2013-09-10T22:14:19.210" Score="20" ViewCount="7263" Body="&lt;p&gt;I'm a maths major and I have an interest in learning biology. I know very, very little; I know how babies are made and that's about it. Could anyone recommend a stimulating text to read for its own sake and also to use to learn biology?&lt;/p&gt;&#xA;" OwnerUserId="4440" LastEditorUserId="22057" LastEditDate="2017-12-21T11:09:42.620" LastActivityDate="2017-12-21T11:09:42.620" Title="Introductory biology text for an outsider" Tags="&lt;book-recommendation&gt;" AnswerCount="5" CommentCount="3" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="10377" PostTypeId="2" ParentId="10375" CreationDate="2013-09-10T23:01:06.807" Score="9" Body="&lt;p&gt;V1-V5 are different (sub) regions of the visual cortex itself.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UvkCw.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;sup&gt;via &lt;a href=&quot;http://www.tecsyn.com&quot; rel=&quot;noreferrer&quot;&gt;http://www.tecsyn.com&lt;/a&gt; &lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The layers L1-L5 (some regions have a layer 6) refer to the different cellular strata in the depth dimension of the cortical mass.  This stratification occurs to some extent or another in various areas.  Different sections of the cortex, e.g., the primary motor cortex have a predominant level 5 (for the pyramidal tract).  Something like the visual cortex has more cells in layers 4 and 6.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RLvax.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt; From &lt;a href=&quot;http://www.unige.ch/cyberdocuments/theses2003/RivaraC-B/images/fig.2.jpg&quot; rel=&quot;noreferrer&quot;&gt;http://www.unige.ch/cyberdocuments/theses2003/RivaraC-B/images/fig.2.jpg&lt;/a&gt; &lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Layers 2 and 3 tend to carry interconnections between different areas of the cortex, and the topmost layer is generally less dense.&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2013-09-10T23:22:36.600" LastActivityDate="2013-09-10T23:22:36.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10378" PostTypeId="2" ParentId="10376" CreationDate="2013-09-11T01:39:15.713" Score="7" Body="&lt;p&gt;There are tons of books and it is quite hard to find one that gives such a broad overview. &lt;a href=&quot;https://www.amazon.ca/Campbell-Biology-9th-Jane-Reece/dp/0321558235/ref=sr_1_2?ie=UTF8&amp;amp;qid=1513808241&amp;amp;sr=8-2&amp;amp;keywords=campbell+biology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Campbell Biology&lt;/a&gt; is a book that basically covered the first year of my Bachelor degree in biology. I am not sure it would be very stimulating though! If there is a specific branch of biology that interests you, let us know we'll be able to give you a better advice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a math Major you might enjoy some fields of biology that are highly mathematized. For example, system biology or theoretical evolutionary biology. For the latter, you might like to read &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/0674023382&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evolutionary Dynamics: Exploring the Equations of Life&lt;/a&gt; book from Martin Nowak. But I am afraid it might not be a nice idea to directly jump into some specific subject before having a good overview of the life sciences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise you might appreciate some books of popular (but good level) science such as &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/0192880519&quot; rel=&quot;nofollow noreferrer&quot;&gt;the Extended Phenotype&lt;/a&gt; from Richard Dawkins. This book is very stimulating and I think it starts with some basic definitions of biological concepts such those of &quot;alleles&quot; or &quot;phenotype&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I gave you two examples of books from the field of theoretical evolutionary biology. For more recommendations in this field, please have a look at &lt;a href=&quot;https://biology.stackexchange.com/questions/16470/books-on-population-or-evolutionary-genetics&quot;&gt;Books on population or evolutionary genetics?&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps a bit!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2017-12-20T22:17:44.157" LastActivityDate="2017-12-20T22:17:44.157" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10379" PostTypeId="1" AcceptedAnswerId="10383" CreationDate="2013-09-11T02:20:35.057" Score="3" ViewCount="2815" Body="&lt;p&gt;When I use my own data to build Bayesian phylogenetic trees using the software Mrbayes, after many generations, it never reaches stopping status (namely, the average standard deviation of split frequencies below 0.01). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What should I do to get to this point?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The dtype is protein, 37 taxa were included, the model I used was as follows: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;prset aamodel=fixed(wag);&#xA;lset rates=Invgamma; &#xA;mcmc ngen=100000 samplefreq=100&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="4442" LastEditorUserId="57" LastEditDate="2013-09-11T11:08:12.140" LastActivityDate="2013-09-11T18:00:42.197" Title="Molecular Evolution: Mrbayes never stops?" Tags="&lt;evolution&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10380" PostTypeId="1" AcceptedAnswerId="11359" CreationDate="2013-09-11T05:16:59.413" Score="6" ViewCount="642" Body="&lt;p&gt;I ask this question because earlier today I heard from a lecturer at my university that a sheep's brain cannot utilise ketone bodies as an energy source and hence with insufficient glucose supply for their brains they die. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="3340" LastEditDate="2015-06-04T11:49:05.553" LastActivityDate="2015-06-04T11:49:05.553" Title="Are the brains of any herbivorous animals capable of utilising ketone bodies as an energy source?" Tags="&lt;bioenergetics&gt;&lt;diet&gt;&lt;lipids&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10381" PostTypeId="1" CreationDate="2013-09-11T13:31:59.517" Score="2" ViewCount="126" Body="&lt;p&gt;At least one of the journal articles that reported on such clinical trials allured to the &lt;strong&gt;nicotinamide-tryptophan pathway&lt;/strong&gt; that I assume must be related to the metabolism of tryptophan into serotonin since at least one of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/155389%E2%80%8E&quot; rel=&quot;nofollow&quot;&gt;these journal articles&lt;/a&gt; placed some emphasis on the &lt;strong&gt;serotonin hypothesis of depression&lt;/strong&gt;. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastActivityDate="2013-09-11T13:31:59.517" Title="Why is a nicotinamide-tryptophan combination used to treat affective episodes in a few older clinical trials?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10382" PostTypeId="1" CreationDate="2013-09-11T16:29:03.717" Score="3" ViewCount="864" Body="&lt;p&gt;If I need to preform a genome-wide high throughput screen using pooled shRNA library infection followed by deconvolution by deep sequencing, how would I determine the optimal infection rate at which the majority of cells only be infected with single copy of shRNA? Thanks!&lt;/p&gt;&#xA;" OwnerUserId="4446" LastActivityDate="2013-09-11T16:29:03.717" Title="Virus titre and copy number of integration" Tags="&lt;lentivirus&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10383" PostTypeId="2" ParentId="10379" CreationDate="2013-09-11T18:00:42.197" Score="2" Body="&lt;p&gt;There are a few things you can try to get better convergence. I'd try the following in increasing order of difficulty/effort/processing time.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Be satisfied with a higher standard deviation of split frequencies. The MrBayes manual says &quot;A rough guide is that an average standard deviation below 0.01 is very good indication of convergence, while values between 0.01 and 0.05 may be adequate depending on the purpose of your analysis.&quot; Especially if you are interested only in the best supported parts of the tree, this is a viable option. 0.01 is only a guideline.&lt;/li&gt;&#xA;&lt;li&gt;Run the model for more generations. Maybe it is on the way to converging, but it hasn't gotten there yet. 100000 is not really that many. Try 200000 or 500000 and see if the model space is still being explored. You can examine the &lt;code&gt;.p&lt;/code&gt; files using &lt;a href=&quot;http://tree.bio.ed.ac.uk/software/tracer/&quot; rel=&quot;nofollow&quot;&gt;Tracer&lt;/a&gt;. You may already be doing this, and this is why you know it is not converging. If you look at the plots of the log-likelihoods, they will become relatively stable when the run has reached the optimal location.&lt;/li&gt;&#xA;&lt;li&gt;Try running with a different amino acid model or without the inverse gamma rate prior. If you can get a simpler model to converge, then &lt;/li&gt;&#xA;&lt;li&gt;Increase the number of chains to 4 or 8. If you have the ability to run in parallel, this will greatly speed up your analyses.&lt;/li&gt;&#xA;&lt;li&gt;Try iteratively changing the heating parameter by setting &lt;code&gt;Temp&lt;/code&gt; to a lower value, which will increase the likelihood of a swap. By default, &lt;code&gt;Temp = 0.1&lt;/code&gt;. You can watch the progress of the analysis in the command line and see which are the heated chains and which is the cold chain.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-09-11T18:00:42.197" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10384" PostTypeId="2" ParentId="10364" CreationDate="2013-09-11T22:19:56.570" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1534580710004296&quot; rel=&quot;nofollow&quot;&gt;Mutations in the Hippo signalling pathway cause unusual organ growth in flies&lt;/a&gt;.  After a good deal of intensive research, its been shown that Hippo genes are responsible for suppressing organ growth in development, increasing cell death and slowing proliferation.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given this role, its not surprising that Hippo genes are also important in cancer.  I'm not an expert in cancer, but a quick search turned up an association of cancer with the Yki (YAP in mammals) transcription activator, an oncogene from the Hippo Pathway.  &lt;a href=&quot;http://cancerres.aacrjournals.org/content/68/8/2789.long&quot; rel=&quot;nofollow&quot;&gt;YAP suppression has been linked to cancerous growth&lt;/a&gt;.  &lt;a href=&quot;http://cancerres.aacrjournals.org/content/65/17/7561.full&quot; rel=&quot;nofollow&quot;&gt;And its also been shown that YAP is amplified in oral squamous cell carcinoma cells&lt;/a&gt;.  This last is circumstantial but consistent with what we know about YAP. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-09-11T22:19:56.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10386" PostTypeId="2" ParentId="10376" CreationDate="2013-09-12T05:21:10.707" Score="15" Body="&lt;p&gt;I found the Campbell Biology textbook to be quite comprehensive and approachable. I think many introductory biology courses use it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0321558235&quot;&gt;http://www.amazon.com/Campbell-Biology-Edition-Jane-Reece/dp/0321558235&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4427" LastActivityDate="2013-09-12T05:21:10.707" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10387" PostTypeId="1" CreationDate="2013-09-12T06:56:44.570" Score="10" ViewCount="16332" Body="&lt;p&gt;Fetal hearts use glucose as their primary metabolic substrate.  Adult hearts use free fatty acids, which are less efficient (require more $O_2$ to synthesize the same amount of ATP); however, during cardiac failure, the heart can switch to glucose utilization.  Why doesn't it just use glucose all the time?&lt;/p&gt;&#xA;" OwnerUserId="4449" LastEditorUserId="4449" LastEditDate="2013-09-12T21:30:53.220" LastActivityDate="2017-08-23T21:46:25.617" Title="Why does the heart use lipids (and not glucose)?" Tags="&lt;biochemistry&gt;&lt;cardiology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10388" PostTypeId="2" ParentId="10351" CreationDate="2013-09-12T09:40:14.907" Score="0" Body="&lt;p&gt;A hit can break blood vessels, produce inflammation and exert pressure in the brain tissue. Pressure in fact can alter the composition and distribution of the cerebrospinal fluid. Since the nervous cells are very sensible to oxygen deficit and the composition of their surroundings, phisical damage can lead to loss of brain function. Moreover, while it's true that cerebral activity is due to chemical reactions, it's also true that this activity must be focused in very specific points (synapses), wich may be damaged by an strong hit.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-09-12T09:40:14.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10389" PostTypeId="2" ParentId="10387" CreationDate="2013-09-12T09:51:18.590" Score="11" Body="&lt;p&gt;Lipids require more oxygen to burn, but also they are cheaper to store (since they have great calorific power than carbohydrates and they're hydrophobic, thus not requiring water for their storage). The body can store so much lipids that it becomes an almost everlasting energy source (A normal adult have enough energy stored as fat to allow basal metabolism for weeks to months), which cannot apply to glucose. If fat is not present, glucose would have vanished from the body long time ago. Glucose levels must be maintained at a certain level, because it's the main energy source for the brain (which cannot use lipids ). The brain can use ketone bodies (product of fat oxidation) as a last resort.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For all the previous reasons, the heart (and many other organs, like the liver) uses fat while possible. If possible just means when not starving to death and with sufficient oxygen supply. This second condition doesn't apply to heart failure. In this case, oxygen supply fails and the tissue switch to glucose just because they can use it without oxygen (glycolysis and lactic fermentation).&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="-1" LastEditDate="2017-02-15T20:26:50.887" LastActivityDate="2017-02-15T20:26:50.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10390" PostTypeId="1" AcceptedAnswerId="10391" CreationDate="2013-09-12T13:12:26.940" Score="1" ViewCount="136" Body="&lt;p&gt;I read somewhere that recently some people are trying to use harmless bacteria that live symbiotically in humans to express some portions of antigens of the harmful ones. Some people have raised concern that continuous exposure to the same antigen may lead to adaptibility of immune system to that epitope and render it useless when the germ actually comes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can't we use the same procedure for exposing some parts of MHC of the donor to the recipient before transplantation, so that, by the time the real transplant is done it may become adapted ? How much time would it take for this to occur ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can already see one drawback : In emergency transplants, this can not be used due to time factor. Can you see any other drawbacks ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-09-12T17:00:12.340" Title="Adaptability in immune system" Tags="&lt;immunology&gt;&lt;transplantation&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="10391" PostTypeId="2" ParentId="10390" CreationDate="2013-09-12T13:47:30.763" Score="3" Body="&lt;p&gt;No. MHC works differently from any other antigen. MHC is involved in the maturation of T lymphocytes in the thymus. Forming lymphocytes need to recognise the MHC with a certain affinity (lymphocytes with too much affinity for the MHC are destroyed). In all this process there is no intervention of foreign antigens, so the system you propose won't work because the lymphocytes would search the MHC of the graft and they would attach them with abnormal affinity. This would trigger autoimmune response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you propose is the main functioning of allergy vaccines. You expose the immune system to low dose of antigen during long time, and that would make the body to not react aggressively to the substance. However, this phenomenon is based in B lymphocytes, which recognaise soluble antigens and little cells (humoral immune system) instead of whole cells (cellular immunity).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the domains of science fiction, however, it would be technically possible to transfect thymal cells in order to express the MHC of the donor, since it would express both. Actually, this should be theoretically easy (The thymal cells seems to express almost any protein in the body, in order to prevent autoimmunity), but it face the problem of thymal degeneration.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastEditorUserId="3615" LastEditDate="2013-09-12T17:00:12.340" LastActivityDate="2013-09-12T17:00:12.340" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="10393" PostTypeId="2" ParentId="10351" CreationDate="2013-09-12T16:00:58.337" Score="5" Body="&lt;p&gt;Mechanical force can compress neurons and cause action potentials as you probably experienced in the form of hitting the funny bone. Strong enough acceleration of the brain tissue may be causing massive excitation of neurons as indicated by &lt;a href=&quot;http://dx.doi.org/10.1016/S0301-0082%2802%2900018-7&quot;&gt;animal EEG study&lt;/a&gt;. It suggests that the loss of consciousness is due to generalized epileptic seizure. However, it is not fully agreed upon: quoting wikipedia entry on &lt;a href=&quot;http://en.wikipedia.org/wiki/Concussion&quot;&gt;Concussion&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is not known whether the brain in concussion is structurally&#xA;  damaged or whether there is mainly a loss of function with only&#xA;  physiological changes.[14][needs update] Cellular damage has&#xA;  reportedly been found in concussed brains, but it may have been due to&#xA;  artifacts from the studies.[15] It is now thought that structural and&#xA;  neuropsychiatric factors may both be responsible for the effects of&#xA;  concussion.[16]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And following quote is from &lt;a href=&quot;http://dx.doi.org/10.1056/NEJMcp064645&quot;&gt;this&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The brief loss of consciousness that characterizes concussion appears&#xA;  to be the result of rotational forces exerted at the junction of the&#xA;  upper midbrain and thalamus that cause transient disruption of the&#xA;  functioning of the reticular neurons that maintain alertness.&#xA;  (Allan H. Ropper, M.D., and Kenneth C. Gorson, M.D.; N Engl J Med 2007; 356:166-172 January 11, 2007)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="460" LastActivityDate="2013-09-12T16:00:58.337" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10396" PostTypeId="2" ParentId="10351" CreationDate="2013-09-12T16:34:58.167" Score="1" Body="&lt;p&gt;Loss of consciousness, or &lt;strong&gt;syncope&lt;/strong&gt;, can be caused by a number of factors, almost all of which relate to lack of proper blood flow: high G-forces, low blood pressure, low blood sugar, cardiac arrhythmia, and vasovagal responses, such as when I give blood.  These all make sense and are moderately well understood.  The mechanism of loss of consciousness due to &lt;em&gt;mechanical&lt;/em&gt; trauma, however, is less well understood, in part because it can be tricky to study.  It almost definitely has to do with lowered blood flow as well, and in particular direct trauma to the brain stem, which regulates consciousness.&lt;/p&gt;&#xA;&lt;p&gt;Basically, you need to rattle the brain inside its cage, slamming it against the skull.  The easiest way to get knocked out from a punch is usually to the chin; the rotational force is much harder for the brain to cushion against, and is a very &lt;em&gt;sharp&lt;/em&gt; force.  The displacement of the brain from such a force can compress blood vessels, cutting off blood flow to the brain.  There's also some evidence that the higher brain and the brain stem can twist around each other, which certainly worsens things.  There's even a theory that consciousness is rooted in the &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0079612305500025&quot; rel=&quot;nofollow noreferrer&quot;&gt;neurological structure&lt;/a&gt;, which might support the idea that unconsciousness is caused by parts of the &lt;a href=&quot;http://www.bbc.co.uk/news/science-environment-13751783&quot; rel=&quot;nofollow noreferrer&quot;&gt;brain inhibiting each other&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;strong&gt;ETA&lt;/strong&gt; This isn't exactly a reliable source, but the guy writing &lt;a href=&quot;http://regressing.deadspin.com/what-happens-when-a-boxer-is-beaten-to-death-and-how-w-1450957999&quot; rel=&quot;nofollow noreferrer&quot;&gt;this piece&lt;/a&gt; for Deadspin &lt;em&gt;is&lt;/em&gt; board-certified in internal medicine, and had this (uncited) to say:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Researchers have examined the brain waves of recently concussed animals and determined that their brains resemble that of an animal suffering an epileptic seizure. This comes as a bit of a surprise, because the brain waves (measured by an electroencephalogram) show hyperactivity, which implies that when a fighter is glassy-eyed and unable to answer the referee's questions appropriately, his neurons might actually be overactive, not underactive.&lt;/p&gt;&#xA;&lt;p&gt;But a hyperactive brain is not the only problem. When the head is hit at high speed, shearing movements within the skull can cause micro-hemorrhages of the blood vessels within the brain tissue. If the shearing force is large enough, or if the head is it hard enough, a large bleed can occur. This becomes a medical emergency because the skull is fixed, enclosed space. As blood accumulates, usually in the form of a subdural hematoma, it can squish the brain and potentially compromise critical neural functions like breathing; death becomes imminent.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-24T21:28:09.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10397" PostTypeId="1" CreationDate="2013-09-12T16:35:59.263" Score="12" ViewCount="314" Body="&lt;p&gt;Whether it is mechanical (trauma), chemical (anaesthesia) or electrical - which part of the brain is shut down to cause loss of consciousness?&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="460" LastEditDate="2013-09-12T17:17:22.363" LastActivityDate="2014-10-29T02:45:40.247" Title="Which part of the brain needs to be shut down to lose conciousness?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;neurology&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10399" PostTypeId="2" ParentId="7019" CreationDate="2013-09-12T18:06:19.260" Score="1" Body="&lt;p&gt;The mouth or the oral cavity is lined by oral mucous membrane. The oral mucous membrane has two parts the epithelium and its supporting connective tissue known as lamina propriya. The charecter of the epithelium and lamina propriya varies to a great extent from the gingiva and hard palate to the floor of the mouth based on functional requirements. However basically the mucous membrane lining the oral cavity is not designed for absorbing nutrients, which was the primary question.&#xA;As for the oral glucose gel - read the American Red Cross, Scientific Advisory Council recommendation that the buccal absorption of glucose is limited and not recommended. &lt;a href=&quot;http://www.instructorscorner.org/media/resources/SAC/Advisory%20Glucose%20for%20Diabetes%20Final%20for%20Posting%20%201_7_12.pdf&quot; rel=&quot;nofollow&quot;&gt;ARC SAC Advisory&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4216" LastActivityDate="2013-09-12T18:06:19.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10400" PostTypeId="2" ParentId="10397" CreationDate="2013-09-12T21:41:57.353" Score="0" Body="&lt;p&gt;Two structures are required for consciousness: the brain stem reticular activating system (RAS) and one cerebral hemisphere, as stated &lt;a href=&quot;http://en.wikipedia.org/wiki/Coma&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.  e.g. a lesion in the RAS or bicerebral injury will induce loss of consciousness.&lt;/p&gt;&#xA;" OwnerUserId="4449" LastEditorUserId="6511" LastEditDate="2014-10-28T20:00:29.800" LastActivityDate="2014-10-28T20:00:29.800" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10401" PostTypeId="2" ParentId="10397" CreationDate="2013-09-12T23:17:58.857" Score="8" Body="&lt;p&gt;There is no widely-accepted neurological structure that mediates 'consciousness.' Even if some structures have been shown to be necessary for consciousness, they have not been shown to be sufficient. This is true with anesthetic mechanisms as well -- their ability to paralyze and block pain signals is fairly well-understood, but the mechanism of loss-of-consciousness is still unknown.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still, 'consciousness' has to be there, somewhere between being awake and being dead, states which anesthetics can readily bridge (&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743249/&quot;&gt;review&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nevertheless, at some level of anesthesia between behavioral unresponsiveness and the induction of a flat EEG [indicating the cessation of the brain’s electrical activity, one of the criteria for brain death (22)], consciousness must vanish. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Later in the same review:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The evidence from anesthesia and sleep states (Fig. 2–3) converges to suggest that loss of consciousness is associated with a breakdown of cortical connectivity and thus of integration, or with a collapse of the repertoire of cortical activity patterns and thus of information (Fig. 2). Why should this be the case? A recent theory suggests a principled reason: information and integration may be the very essence of consciousness (52). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is consistent with my own take. Consciousness itself is the subjective experience of 'brain,' so it can't be lost, just poorly integrated.&lt;/p&gt;&#xA;" OwnerUserId="3336" LastActivityDate="2013-09-12T23:17:58.857" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10402" PostTypeId="1" AcceptedAnswerId="11041" CreationDate="2013-09-13T03:22:39.143" Score="8" ViewCount="11303" Body="&lt;p&gt;&lt;strong&gt;Why is it beneficial for trees to grow that tall?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This sounds like a kid's question &lt;code&gt;Mom, Dad... why are trees so tall?&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Costs and Benefits&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some obvious costs:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Need much Carbon and other nutrients&lt;/li&gt;&#xA;&lt;li&gt;maintenance cost&lt;/li&gt;&#xA;&lt;li&gt;energy cost (for growing, to bring water (and nutrients) up to the higher leaves, etc...)&lt;/li&gt;&#xA;&lt;li&gt;Sensitivity to wind&lt;/li&gt;&#xA;&lt;li&gt;etc...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Potential benefits I can think of:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Competition for sunlight&lt;/li&gt;&#xA;&lt;li&gt;Better dispersal&lt;/li&gt;&#xA;&lt;li&gt;protection against predation&lt;/li&gt;&#xA;&lt;li&gt;Some birds (maybe especially those that are potentially good seed dispersers) prefer to land on high trees (avoiding the cost of regaining altitude). Being high attract these birds which eat the fruits and disperse the seeds. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Are there other potential benefits?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Specific to palm trees&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am currently in Bali, Indonesia looking at palm trees that seem to have a very low competition for sun light (the forest is not dense, the light is intense), there are no tall predators (but being tall might be a protection against climbing predators as well and there are indeed monkeys and other potential climbing predators) and looking at coconuts, papaya and banana I can hardly think that being tall helps to disperse further away (seeds dispersal by &lt;a href=&quot;http://en.wikipedia.org/wiki/Seed_dispersal_syndrome&quot; rel=&quot;nofollow&quot;&gt;barochory&lt;/a&gt;). So, &lt;strong&gt;why (evolutionary reasons) are palm trees so high?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2016-05-19T20:28:44.353" LastActivityDate="2016-05-19T20:28:44.353" Title="Why is it beneficial for trees to grow that tall?" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;natural-selection&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10403" PostTypeId="1" AcceptedAnswerId="20389" CreationDate="2013-09-13T05:06:50.723" Score="7" ViewCount="4662" Body="&lt;p&gt;what is the best way to eliminate clumping suspension cells used for transfection. Anti clumping agents interfere transfection and hence can't be used. Though maintaining the cell density low helps, but doesn't help in the long run.&lt;/p&gt;&#xA;" OwnerUserId="4457" LastActivityDate="2014-08-10T22:48:24.453" Title="How to reduce/eliminate cell clumping in suspension CHO cells, without using an anti clumping agent?" Tags="&lt;lab-techniques&gt;&lt;cell-culture&gt;&lt;transformation&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10404" PostTypeId="1" AcceptedAnswerId="10406" CreationDate="2013-09-13T05:11:17.837" Score="5" ViewCount="17237" Body="&lt;p&gt;Mature mammalian erythrocytes have all the characteristics of a eukaryotic cell except that they don't have a nucleus, they don't have any cell organelles. Does this mean that erythrocytes are classified as prokaryotic? &lt;/p&gt;&#xA;" OwnerUserId="4013" LastEditorUserId="22057" LastEditDate="2016-06-28T18:52:36.943" LastActivityDate="2020-08-26T13:23:56.040" Title="Are mature erythrocytes prokaryotic?" Tags="&lt;cell-biology&gt;&lt;taxonomy&gt;&lt;red-blood-cell&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10405" PostTypeId="2" ParentId="10402" CreationDate="2013-09-13T05:26:27.173" Score="3" Body="&lt;p&gt;The height of tree species varies, of course, as each tree fills a given niche, much like animals do; you might as well ask why blue whales grow so big.  The answer, of course, is that they seek out and successfully get the nutrients they require.  It is advantageous for some trees to be huge and get the most sunlight possible and so some trees do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the specific case of palm trees, however, they aren't true trees but rather a grass, which means they are a monocot and (I'm a little shaky on plant physiology but...) that the outside isn't living but the inside is.  Monocots grow straight up, in one main shoot, and palm tree follow the same pattern.  Tons of sunlight, nothing to come mow or it down, and nowhere to go but up means they'll be big.  True trees, on the other hand, have what is called &lt;em&gt;heartwood&lt;/em&gt; in the center, which is technically dead tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another thing to think about is that trees aren't moving, so they only way they can improve their condition is by growth.  An animal, on the other hand, can migrate to follow food; growth, particularly for mammals, also has a huge heat cost.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-13T05:26:27.173" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="10406" PostTypeId="2" ParentId="10404" CreationDate="2013-09-13T05:54:44.250" Score="15" Body="&lt;p&gt;No.  Nobody considers red blood cells to be prokaryotic, perhaps most importantly because they are &lt;em&gt;part&lt;/em&gt; of a eukaryotic organism.  Red blood cells begin life with the full complement of organelles, including a nucleus and mitochondria, but our RBCs shed their organelles during maturation.  In actuality, though, only mammalian RBCs lack nuclei; other animals' RBCs still hold on to their traditional eukaryotic characteristics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an analogy, apoptotic or necrotic cells don't have intact organelles, but they are still considered eukaryotic.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-13T05:54:44.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10407" PostTypeId="1" CreationDate="2013-09-13T07:39:42.317" Score="2" ViewCount="259" Body="&lt;p&gt;I am a newbie in biology and I am simply trying to discover the field of genomics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider the question - &lt;strong&gt;Are genetic tests accurate?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't believe they are as the genes may not provide the complete information or maybe there are other genes responsible for a particular trait but they may not be known at the point when the test is conducted. This may not be the right answer though — I simply wish to understand from people here as to what they can say about the accuracy of these tests. If they are not accurate, can you explain why that is the case?&lt;/p&gt;&#xA;" OwnerUserId="4458" LastEditorUserId="1306" LastEditDate="2013-09-13T14:07:24.187" LastActivityDate="2013-10-13T19:39:51.280" Title="Accuracy of a particular genetics test" Tags="&lt;genomics&gt;&lt;genetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10408" PostTypeId="1" CreationDate="2013-09-13T08:36:40.657" Score="1" ViewCount="21" Body="&lt;p&gt;I noticed that HRH (histamine receptor) has an inter-cellular and cytoplasmic binding site of anti-histamines which are equal in binding energy. Does anyone know what is the function of the well formed cytoplasmic ligand binding site?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2013-09-13T12:15:40.027" LastActivityDate="2013-09-13T12:15:40.027" Title="histamine inter-cellular and cytoplasmic binding site" Tags="&lt;proteins&gt;&lt;protein-evolution&gt;&lt;cell-signaling&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10409" PostTypeId="1" AcceptedAnswerId="10449" CreationDate="2013-09-13T08:38:52.390" Score="2" ViewCount="100" Body="&lt;p&gt;I know this might seem contradictory since by definition a vitamin is an essential part of the diet but I have read that &lt;strong&gt;nicotinamide&lt;/strong&gt;, a form of vitamin B3, can be synthesised from &lt;strong&gt;L-tryptophan&lt;/strong&gt;. Is it possible for a person to synthesise all their vitamin B3 requirements from one's dietary intake of L-tryptophan?&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="4101" LastEditDate="2013-09-13T17:33:31.703" LastActivityDate="2013-10-15T16:39:56.180" Title="How essential is vitamin B3 to the diet?" Tags="&lt;vitamins&gt;&lt;diet&gt;&lt;biosynthesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10411" PostTypeId="1" AcceptedAnswerId="10428" CreationDate="2013-09-13T12:39:00.487" Score="1" ViewCount="598" Body="&lt;p&gt;Are plasmid genes always expressed? If so, then isn't a bacterium wasting it's resources in expressing genes (like antibiotic resistance) which are not required in &quot;normal&quot; conditions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, then what triggers bacteria to express genes of recombinant plasmids? Can a bacterium survive in &quot;normal&quot; conditions if it is deprived of all the plasmids?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="10276" LastEditDate="2015-01-16T11:52:41.753" LastActivityDate="2015-01-16T11:52:41.753" Title="Expression of plasmid genes" Tags="&lt;genetics&gt;&lt;bacteriology&gt;&lt;gene-expression&gt;&lt;plasmids&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10412" PostTypeId="1" AcceptedAnswerId="10417" CreationDate="2013-09-13T12:41:49.717" Score="4" ViewCount="85" Body="&lt;p&gt;I have read that neurons have proportionately less MHC molecules than other cells of the body. What is the advantage of this?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-13T15:49:49.617" LastActivityDate="2013-10-13T15:49:49.617" Title="Number of MHCs in neurons" Tags="&lt;neuroscience&gt;&lt;immunology&gt;&lt;mhc&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10413" PostTypeId="1" CreationDate="2013-09-13T13:51:10.197" Score="2" ViewCount="359" Body="&lt;p&gt;Are the processes and canaliculi formed and contacts established after the osteocytes are embeded in the matrix or are they formed during the embedding process itself. Is there any evidence to suggest either?&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="4216" LastEditDate="2013-09-17T17:36:45.650" LastActivityDate="2014-07-27T18:49:09.763" Title="How do processes of one osteocyte establish contact with processes of the adjacent cells within the mineralized matrix?" Tags="&lt;development&gt;&lt;histology&gt;&lt;bone-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10414" PostTypeId="1" AcceptedAnswerId="10416" CreationDate="2013-09-13T16:13:18.373" Score="2" ViewCount="1526" Body="&lt;p&gt;A common saying is that women are generally more attracted towards men who are already in a relationship, and this phenomena does seem to have its own place in popular culture that is not matched by a corresponding male preference for women who are already in a relationship. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From an intuitive viewpoint I think it would make sense from the woman's viewpoint in an system of information economics where the fact that a male is engaged in a successful relationship with another female, or several other females, might provide extra and positive information about the evolutionary value of the male.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But how about the possibility for a male to use the same trick?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any empirical evidence for this behaviour at all either in humans or in other species, or is this just a cultural artefact in some human societies? If there is empirical support, is there a consensus on the plausible evolutionary pathways involved here?&lt;/p&gt;&#xA;" OwnerUserId="4461" LastEditorUserId="9124" LastEditDate="2015-02-08T05:29:17.433" LastActivityDate="2015-02-08T05:29:17.433" Title="Female preference for males who are already in a relationship" Tags="&lt;evolution&gt;&lt;psychology&gt;&lt;sociobiology&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2013-09-13T20:56:18.170" ContentLicense="CC BY-SA 3.0" />
  <row Id="10415" PostTypeId="2" ParentId="10407" CreationDate="2013-09-13T16:13:41.227" Score="2" Body="&lt;p&gt;Like the comment said this question is very broad but Im going to try and clear some things up for you. A &quot;genetic test&quot; is just simply a test that tells you whether or not you have a certain genotype. Yes, it is often times used to tell if a person has a disease or not, but that doesnt always have to be the case. I may just want to know, for example, if a mouse I have carriers a certain transgene. The reason why genetic tests are good at determining if someone has a disease is because many diseases are simple, or at least have a well-defined genotype. Sure, you can make a genetic test for a complex disease like obesity if you want, but no one does this because as you pointed out in your question there are sometimes more than one gene involved, so a genetic test for that would not be very good.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But for genetic tests of diseases of a known genotype, they are very accurate. Of course you have some false positives and false negatives. Look up the terms selectivity and sensitivity. If you have a sensitive test you will catch a lot of people with the disease but also many false positives. If you have a selective test you will not have many false positives but you may miss people who actually have the disease. Its a trade-off. Testing someone twice will clear things up usually.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And then there are cases where you have a disease with a known genotype but still have an inaccurate genetic test on rare occasions. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19716110&quot; rel=&quot;nofollow&quot;&gt;Heres a paper about a disease known as Spinal Muscular Atrophy&lt;/a&gt;. There is a genetic test that works 95% of the time but sometimes it does not match up with the phenotype. In the paper they find a mutation that explains why the genetic test does not match the phenotype. Two things are interesting about the paper. One, the genetic test is not wrong, its just that the phenotype is not what you'd expect. And two, not all people who have a discordant genetic test have this mutation. So whats going on in these patients and why their test doesnt match their phenotype is anyone's guess.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first point is especially important so I will repeat it. The genetic test was not wrong, the phenotype just did not match it as expected. Genotype and phenotype are not always correlated, and mistakes can happen when you assume they are.&lt;/p&gt;&#xA;" OwnerUserId="4199" LastEditorUserId="4199" LastEditDate="2013-09-13T18:50:33.283" LastActivityDate="2013-09-13T18:50:33.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10416" PostTypeId="2" ParentId="10414" CreationDate="2013-09-13T17:37:30.660" Score="4" Body="&lt;p&gt;This is a widely researched topic in the overlap between social sciences and evolutionary biology.  Evolution has become very influential in understanding human interaction and preferences. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This chapter from &quot;The Adapted Mind : Evolutionary Psychology and the Generation of Culture&quot; will give you an idea of how all this plays out in the big picture - its a fairly comprehensive review of many factors considered in human mate choice.  The study may be psychological, but the logic is derived from biology these days.  (stackexchange won't let me link to google books - you can search for the title and look at chapter 6).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolutionary tendencies will favor more successful offspring.  But for people it includes not only the genetic qualities of the mate (appearance, height, disease resistance, health) but also social qualities (how reliable or willing a mate is to support offspring).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First off you can see that there are many many factors which women take into consideration in their preferences.  Its commonly said they are more complex than men, but that's another question.  You have to take a range of factors holistically including the social environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't find this particular issue addressed in the literature, but I think that it might be attractive to women in some social settings.  If there is a lot competition for 'quality' mates or resources for instance - if you have very few secure males or pessimistic females might create pressure which would cause females to prefer males which were successful. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its pretty easy to feel good about hypotheses like this.  I couldn't find a specific study, but perhaps someone else will.  There's a lot of such papers out there.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I should say that men are as easily led to do things by 'mate choice' psychology that aren't totally healthy or socially acceptable.  That's biology. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-09-13T17:37:30.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10417" PostTypeId="2" ParentId="10412" CreationDate="2013-09-13T18:19:57.870" Score="2" Body="&lt;p&gt;Antigen presentation by MHC will induce a cytotoxic response by the immune system, which is usually a good thing in the body since most cells can just divide and replicate again.  Neurons, however, are particularly ineffective at regenerating from such an attack, and are not easy to come by; they are also rather important!  Better not to risk it, eh?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, neuronal expression of MHC is actually a pretty complex case, and &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001354&quot; rel=&quot;nofollow&quot;&gt;this open-access article&lt;/a&gt; is a good start down the rabbit hole (see also &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0165572801004805&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, &lt;a href=&quot;http://download.cell.com/neuron/pdf/PIIS0896627309007557.pdf?intermediate=true&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, and &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1044743112002035#&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; if you have access).&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-13T18:19:57.870" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="10418" PostTypeId="2" ParentId="10407" CreationDate="2013-09-13T18:47:33.650" Score="1" Body="&lt;p&gt;@von-mises summed it up nicely enough, but you'll want to read the Wikipedia articles on &lt;a href=&quot;http://en.wikipedia.org/wiki/Heredity&quot; rel=&quot;nofollow noreferrer&quot;&gt;heredity&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Heritability&quot; rel=&quot;nofollow noreferrer&quot;&gt;hereitability&lt;/a&gt;, in particular the latter.  Our genes can tell us so much about ourselves, but it's not always that simple.  As you mention, there are lots of other factors that could and usually do come into play.  Often times there isn't just one gene, but rather many genes playing a role (these are called polygenic traits).  For example, see my &lt;a href=&quot;https://biology.stackexchange.com/a/9948/4101&quot;&gt;answer to a question on hair color&lt;/a&gt;; there are dozens of simple changes that can affect the color of hair and eyes.  These complex traits are really hard to tease out!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, not everything is 100% from genes; the environment can also play a &lt;em&gt;huge&lt;/em&gt; role.  Often we talk about how heritable a gene or a trait is by giving a percent, meaning how much of is due to genes you inherit from your parents.  The &lt;a href=&quot;http://en.wikipedia.org/wiki/Heritability_of_IQ&quot; rel=&quot;nofollow noreferrer&quot;&gt;heritability of IQ&lt;/a&gt; is an interesting read for an introduction to the concept.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what is the use of the genetic tests?  Well, for starters, ancestry is really interesting and useful for people.  Not just paternity or maternity (which is obviously accurate and widespread) but knowing where you are from.  &lt;a href=&quot;http://refer.23andme.com/a/clk/1CBc1K&quot; rel=&quot;nofollow noreferrer&quot;&gt;23andMe&lt;/a&gt; is a great service (I'm 2.9% Neanderthal!) for finding out where you came from genetically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are, additionally, a number of traits that we've studied, or that do have strong genetic factors.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Sickle-cell_disease&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sickle-cell disease&lt;/a&gt; is a classic example of something just from your genotype, whereas other things are less determinate; for example, the heritability of baldness is around 81%, and I know from my genome that I have a slightly lower chance of becoming bald.  There are other, more serious health risks that people would want to be tested for (BRCA for breast cancer, LRRK2 for Parkinson's, APOE for Alzheimer's) as well as inherited traits that are very genetically determined (like sickle-cell or Tay-Sachs).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, the genetic tests are very good at determining what the genotype is, which can be very useful for certain traits but completely useless for others.  The more we learn about what our genes do the more we learn how complicated the whole system is.  We are more than just our genes.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-09-13T18:47:33.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10421" PostTypeId="1" CreationDate="2013-09-13T22:13:03.643" Score="4" ViewCount="257" Body="&lt;p&gt;This is my first post here, so excuse me for its simplicity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Viruses can infiltrate a cell, overtake it and multiply. It has projecting fibers whose ends are shaped as kind of a &quot;key&quot; to a mobile sentry on the cells membrane so it can be permitted access into the cell. When it enters the endosome of a cell, a protein pump blows an acidic gas onto the virus to break it down, thinking it's a special nutrient. But the virus expects this of course, and when the protecting fibers break off (and so too the body of the virus) proteins are released that rips apart the skin of the endosome so the virus can escape.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are just two of many things the virus does to compromise a cell. Its entire existence is for the sole purpose for infecting a cell, and it seems to know how to do that perfectly. How did the virus evolve to know how to do things like this?&lt;/p&gt;&#xA;" OwnerUserId="4130" LastEditorUserId="1306" LastEditDate="2013-09-13T22:21:35.030" LastActivityDate="2013-09-14T06:26:30.857" Title="How did viruses learn to utilize the workings of a cell?" Tags="&lt;evolution&gt;&lt;cell-biology&gt;&lt;virus&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10422" PostTypeId="1" CreationDate="2013-09-13T22:27:09.597" Score="-1" ViewCount="762" Body="&lt;p&gt;Why does evolution (namely the evolution of primates into humans) take place both uniformly and universally on the earth? Why aren't there any creatures who have not taken the same evolutionary steps as their same species elsewhere on earth? For example, why aren't there any humans on other parts of the world who look the same as our evolutionary descendants?&lt;/p&gt;&#xA;" OwnerUserId="4130" LastActivityDate="2014-05-04T06:32:51.540" Title="Does evolution take place universally?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="4" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10423" PostTypeId="2" ParentId="10422" CreationDate="2013-09-14T02:15:01.807" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Why does evolution (namely the evolution of primates into humans) take place both uniformly and universally on the earth? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;: it doesn't. All human beings descended from the same group of &lt;em&gt;Homo sapiens&lt;/em&gt;. There has been some genetic deviation since, but not enough to call it a &quot;species&quot;. Evolution happens, but at very long time scales and not at any sort of defined pace. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/On_the_Origin_of_Species#Summary_of_Darwin.27s_theory&quot; rel=&quot;noreferrer&quot;&gt;Read this first. &lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long answer&lt;/strong&gt;: As the link above shows, evolution is dependent on several key factors. Heritable variation and change to selective pressures. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why aren't there any creatures who have not taken the same evolutionary steps as their same species elsewhere on earth?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Think of humans! Different races, especially ones that have not intermixed, are significantly different. indigenous Africans, indigenous Europeans, and indigenous Japanese, for example. All of these races has genetically diverged into distinct populations with different traits, but the isolation between them hasn't been that long. That's why all humans can still reproduce. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why aren't there any humans on other parts of the world who look the same as our evolutionary descendants?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Over a very long period of time, &lt;em&gt;Homo sapiens&lt;/em&gt; had evolved to become a more advanced, competitively dominant species. although Neanderthals and Homo sapiens did intermix for a while, &lt;a href=&quot;http://en.wikipedia.org/wiki/Homo_neanderthalensis#Extinction_hypotheses&quot; rel=&quot;noreferrer&quot;&gt;we're not completely sure how they went extinct&lt;/a&gt;. One of the reasons stated is that it's hard for a worse species to exist when a better species comes along. &lt;/p&gt;&#xA;" OwnerUserId="4464" LastActivityDate="2013-09-14T02:15:01.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10424" PostTypeId="2" ParentId="10421" CreationDate="2013-09-14T02:18:21.740" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Viral_evolution&quot; rel=&quot;nofollow&quot;&gt;Scientists are unsure,&lt;/a&gt; but it seems that viruses have been around a very long time, and have been specific to every domain of life and possibly even may have infected the last common ancestor. It isn't impossible to imagine a co-evolving arms race that makes both viruses and cells as complex as they are today. &lt;/p&gt;&#xA;" OwnerUserId="4464" LastActivityDate="2013-09-14T02:18:21.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10425" PostTypeId="2" ParentId="10422" CreationDate="2013-09-14T05:54:34.580" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;My question was why does evolution take place at the same rate with the same results to every member of the species all around the world?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It doesn't.  Evolution acts on &lt;em&gt;populations&lt;/em&gt;, not individuals.  I will never evolve, you will never evolve, but humans are evolving, and sure, certain pockets evolve at different rates.  &lt;a href=&quot;http://ncse.com/files/pub/evolution/excerpt--evolution--fb.pdf&quot;&gt;Here's&lt;/a&gt; a long but straight-forward write up that deals with perhaps the best example, beak size in Darwin's finches.  A select population of birds on an island may be evolving rapidly and differently than that same species elsewhere, perhaps eventually resulting in a divergent species.  There is no need for natural selection to operate equally everywhere; in fact, the pressures must be different otherwise we would never see the diverse set of species we do observe.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-14T05:54:34.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10426" PostTypeId="2" ParentId="10421" CreationDate="2013-09-14T06:26:30.857" Score="3" Body="&lt;p&gt;It's a numbers game.  Viruses can produce thousands, millions, even billions of copies every day, and only one of them needs to be slightly better to get ahead.  Rhinoviruses make roughly &lt;a href=&quot;http://www.jsmf.org/grants/2007010/&quot; rel=&quot;nofollow&quot;&gt;one error&lt;/a&gt; every time the genome is replicated; over many, many replications a single change can arise giving an advantageous effect.  As another example, it's been said that HIV mutates every single spot on its genome every single day.  Evolution is simply a waiting game.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.the-scientist.com/?articles.view/articleNo/34189/title/Catching-the-Cold/&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; is a pretty cool write up detailing the process.  It says exactly what I said: large numbers, high mutation rate.  Besides, the virus only has to take advantage of cellular processes, not make new ones every time.  That's much more efficient.  It also details some specific changes that explain some differences between similar viruses.  It's amazing, but a single base change can mean a single protein is different which can mean a different receptor is used for binding, which can make all the difference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And there's this cool quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[T]here may well be more viruses in a single common cold infection than there have been primates in the entire history of life on Earth.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-14T06:26:30.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10428" PostTypeId="2" ParentId="10411" CreationDate="2013-09-14T09:05:07.790" Score="2" Body="&lt;p&gt;It would depend of the plasmid, the genes it contains and the promotors those genes have. Basically, regulation of extrachromosomal genes follow the same patterns of the rest. Bacteria, Archaea and some other organisms that can have plasmids will express the genes if the promotors of those genes are constitutive, or if they trigger by conditions that are present in a given moment. The degree of expression would be a function of the characteristics of the promoter and the number of copies of the plasmid. Finally, the number of copies of the plasmid would depend of its size and the characteristics of its replication origin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Organisms can loss the plasmids if doing so don't suposse a negative effect (this is a big problem in industrial microbiology, since the recombinant strains may be unstable and reduce its productivity). In laboratory, a plasmid containing resistance genes towards an specific antibiotic would remain stable as long as this antibiotic is present in the media. The characteristics of its replication origin also play a big role determining the stabilty of plasmids. You can even select for the loss of plasmids, take the example of URA3 in &lt;em&gt;Saccaromyces&lt;/em&gt; (not a bacteria, but the mechanisms are the same), wich can be used as a negative selection factor if the media contains 5-fluoroorotic acid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there's no particular advantage in expressing plasmidic genes all the time. When that happens, actually there exist an evolutionary pressure against the presence of the plasmid, and thus it trends to dissapear. Bacteria can survive without plasmids (with the exception of some that carry megaplasmids that acts more than little chromosomes. In some of this cases, the plasmid may contain genes for important methabolic pathways and other key elements of the cell, thought if the genes they carry are very importants, like polymerases or ribosomal RNAs, the term minichromosome is prefered). However, plasmids may contain genes that confer an important advantage to the population (like in presence of an antibiotic), and if so the plasmid spread. If at some point the ecological pressure cease, the plasmid would turn unstable again. Note that it's not impossible to have horizontal genes transfer between plasmid and chromosomes, and plasmids (alongside viruses and foreign transformed DNA) are important sources of new genetic material.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-09-14T09:05:07.790" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10429" PostTypeId="1" AcceptedAnswerId="10432" CreationDate="2013-09-14T10:34:06.903" Score="2" ViewCount="1588" Body="&lt;p&gt;I'm trying to be vegan, and purely natural foods lack sufficient calcium for the Recommended Daily Intake. Links 2 to 4 (but not 1) assert a correlation between calcium supplements and disease. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[1. &lt;a href=&quot;http://www.webmd.com/osteoporosis/features/calcium-supplements-pills?page=2&quot; rel=&quot;nofollow noreferrer&quot;&gt;WebMD&lt;/a&gt; :] &quot;Keep in mind that there's really not that much difference between getting calcium in a supplement and calcium in food.&quot;&lt;br&gt;&#xA;  &quot;Calcium-fortified foods -- such as cereals, some juices, and soy milk -- are excellent sources of the mineral, experts tell WebMD.&quot;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;[2. &lt;a href=&quot;http://www.health.harvard.edu/blog/high-calcium-intake-from-supplements-linked-to-heart-disease-in-men-201302065861&quot; rel=&quot;nofollow noreferrer&quot;&gt;health.harvard.edu&lt;/a&gt; :] An 8-ounce portion of off-the-shelf orange juice contains about 300 mg of calcium. The calcium in fortified soy milk also compares favorably to whole milk.&#xA;  Breakfast cereals (which are also fortified) contain substantial amounts of calcium, especially when combined with low-fat milk.&#xA;  A portion of oatmeal on its own contains just 100 mg of calcium. “But if you cut up some dried figs and add it to a bowl of oatmeal with milk, you easily get about half of what you need without having any supplements,” Dr. Hauser says.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;[3. &lt;a href=&quot;http://well.blogs.nytimes.com/2013/04/08/thinking-twice-about-calcium-supplements-2/?_r=0&quot; rel=&quot;nofollow noreferrer&quot;&gt;NY Times Blog&lt;/a&gt; :] All the researchers agree that, given the widespread use of supplemental calcium, better studies are needed to clarify possible risks and benefits, and to whom they may apply.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Until such information is available, consumers seeking to preserve their bones would be wise to rely primarily on dietary sources of the mineral and to pursue regular weight-bearing or strength-building exercises, or both. Walking, running, weight lifting and working out on resistance machines is unquestionably effective and safe for most adults, if done properly.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;[4. &lt;a href=&quot;http://www.nytimes.com/2011/01/25/health/25brody.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;NY Times&lt;/a&gt; :]  The institute’s expert committee, which included bone specialists, concluded that most people don’t need supplements of these critical nutrients and warned of serious health risks from the high doses some now take — including &lt;a href=&quot;http://health.nytimes.com/health/guides/disease/kidney-stones/overview.html?inline=nyt-classifier&quot; rel=&quot;nofollow noreferrer&quot;&gt;kidney stones&lt;/a&gt; and heart disease linked to calcium supplements, and the very falls and fractures that vitamin D is meant to protect against.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;5.&lt;/strong&gt; How and why would the calcium carbonate from calcium supplements be asserted as worse than that in the fortified foods?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;6.&lt;/strong&gt; Isn't solid calcium carbonate (e.g. in supplements) chemically the same as aqueous calcium carbonate (e.g. in fortified drinks)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;7.&lt;/strong&gt; Are calcium supplements really worse than fortified foods with calcium?&lt;/p&gt;&#xA;" OwnerUserId="4466" LastEditorUserId="4466" LastEditDate="2017-08-15T07:00:06.343" LastActivityDate="2017-08-15T07:00:06.343" Title="Calcium for Humans: Supplements vs Fortified Sources" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;" AnswerCount="2" CommentCount="0" ClosedDate="2017-08-16T06:34:55.177" ContentLicense="CC BY-SA 3.0" />
  <row Id="10430" PostTypeId="1" AcceptedAnswerId="10433" CreationDate="2013-09-14T13:54:38.433" Score="6" ViewCount="1474" Body="&lt;p&gt;As I understand it, radiation poisoning (acute radiation syndrome) is fatal because the radiation kills cells. However, why do victims experience hair loss at such an early stage in the process?&lt;/p&gt;&#xA;" OwnerUserId="4427" LastActivityDate="2013-09-14T14:50:24.853" Title="Why does radiation sickness cause hair to fall out?" Tags="&lt;radiation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10432" PostTypeId="2" ParentId="10429" CreationDate="2013-09-14T14:39:23.203" Score="4" Body="&lt;p&gt;This is close to a personal medical question, so I'll try and be vague and avoid advice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's nothing inherently &lt;em&gt;bad&lt;/em&gt; about calcium supplements, and those links and thousands of others that are easy to find tend to all say that same thing.  Basically, for typical people on a typical diet, enough calcium is supplied through food that supplements are unnecessary.  The problem arises when people take &lt;a href=&quot;http://www.mayoclinic.com/health/drug-information/DR602363/DSECTION=side-effects&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;too many&lt;/strong&gt;&lt;/a&gt; supplements, such that their intake is significantly higher than the daily recommended intake.  These people can experience a number of symptoms, including &lt;a href=&quot;http://www.3fatchicks.com/avoid-a-calcium-overdose-how-much-is-too-much/&quot; rel=&quot;nofollow&quot;&gt;kidney&lt;/a&gt; and &lt;a href=&quot;http://well.blogs.nytimes.com/2013/02/18/dangers-of-too-much-calcium/&quot; rel=&quot;nofollow&quot;&gt;heart&lt;/a&gt; failure.  Fortified food and supplements are, as best as I can tell, no different, except that food is simpler route for intake with built-in limit-setting.  That is, you can easily pop five calcium pills (&lt;strong&gt;BAD IDEA&lt;/strong&gt;) but nobody is ever going to drink five containers of fortified soy &quot;milk&quot; on a whim.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My go-to example is that of astronauts.  Astronauts who are in space for extended periods of time must take calcium supplements, in addition to a strict exercise regimen to help stem the tide of bone loss.  Bone loss still occurs, however, because they can only take so much calcium before it starts to cause serious heart problems.  There's nothing inherently wrong with calcium supplements but for most people they are completely unnecessary.  You should talk to your primary care physician and perhaps a dietician.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2015-05-31T01:17:01.353" LastActivityDate="2015-05-31T01:17:01.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10433" PostTypeId="2" ParentId="10430" CreationDate="2013-09-14T14:50:24.853" Score="6" Body="&lt;p&gt;Radiation poisoning causes mutations in DNA that affect normal cell function, often causing them to die.  Cells normally have a number of repair mechanisms but if the damage is too great they won't be able to do so.  In particular, cells that are dividing quickly will not have time to repair their DNA before division and so die far quicker than other cells.  Chemotherapy is built on this concept.  By selectively introducing drugs or radiation that target fast-dividing cells, the cancer cells, which are very dividing rapidly and unchecked, are killed off before most normal cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are some cells in the body that are very rapidly dividing.  &lt;a href=&quot;http://www.breastcancer.org/tips/hair_skin_nails/hair_loss&quot;&gt;Hair cells&lt;/a&gt; are one such type, hence hair will often fall out during chemotherapy or radiation sickness.  Another big cell type are those in the &lt;a href=&quot;http://curiosity.discovery.com/question/radiation-make-hair-fall-out&quot;&gt;gut&lt;/a&gt;, which are constantly dividing.  That's why you often see people in movies who have been exposed to radiation vomiting.  The radiation targets those cells first, hence those are the first symptoms.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-14T14:50:24.853" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10434" PostTypeId="1" AcceptedAnswerId="10435" CreationDate="2013-09-14T17:21:12.500" Score="5" ViewCount="156" Body="&lt;p&gt;What evolutionary process lead to so much variation in MHC? What is the advantage of having such variation?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-13T15:49:40.913" LastActivityDate="2013-10-13T15:49:40.913" Title="Variation in MHC in humans" Tags="&lt;evolution&gt;&lt;immunology&gt;&lt;mhc&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10435" PostTypeId="2" ParentId="10434" CreationDate="2013-09-14T22:39:24.177" Score="5" Body="&lt;p&gt;Here are two free articles that go into the subject very nicely, I think:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://web.udl.es/usuaris/e4650869/docencia/GenClin/content/recursos_classe_%28pdf%29/revisionsPDF/MHCcomplex.pdf&quot; rel=&quot;nofollow&quot;&gt;Major Histocompatibility Complex (MHC)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/277/1684/979.long&quot; rel=&quot;nofollow&quot;&gt;How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The MHC loci are the &lt;em&gt;single most important&lt;/em&gt; determinant of our immune system's response to foreign invaders and are absolutely necessary for discrimination between self and non-self.  Because of the massive diversity amongst those pathogens, no one single MHC allele will allow the best response.  For example, the delta-32 deletion that bears resistance to HIV also increases susceptibility to West Nile; if you're more likely to suffer from the latter, that is a fitness reduction that could be selected against.  Thus, more alleles will survive in the population as all can be advantageous.  This is called &lt;a href=&quot;https://en.wikipedia.org/wiki/Balancing_selection&quot; rel=&quot;nofollow&quot;&gt;balancing selection&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, the microbial invaders mutate and evolve much, &lt;em&gt;much&lt;/em&gt; faster than our genome does, so you want to have the greatest breadth of MHC present in the population and in an individual in order to maximize resistance to whatever may arise.  At a population level, it is also advantageous because it means that the entire populace won't succumb to a certain infection.  If everyone has similar alleles one virus could wipe everyone out; we observe something similar happen with our crops, for example, when grown in massive monocultures.  There is also a fair amount of evidence, mainly in humans and mice I believe, supporting a role for MHC in mate selection.  Individuals seem to find potential mates with different MHC alleles more attractive, presumably to maximize the fitness of their offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MHC is an absolutely fascinating subject (I'm researching it at the moment!).&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-09-15T17:16:21.217" LastActivityDate="2013-09-15T17:16:21.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10436" PostTypeId="1" AcceptedAnswerId="10439" CreationDate="2013-09-15T00:16:22.433" Score="11" ViewCount="10598" Body="&lt;p&gt;Was there actually any useful knowledge gained from the Nazi experiments on human test subjects? Wikipedia cites freezing and phosphine gas reactions, but I would like to know other potential results from the Nazis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At a first glance, it looks like the problem is that, in addition to the obvious ethical issues, there was also a lack if scientific rigor. Is this true or can some results actually be of some use?&lt;/p&gt;&#xA;" OwnerUserId="4471" LastEditorUserId="4101" LastEditDate="2013-09-15T06:08:13.903" LastActivityDate="2018-12-16T05:54:09.423" Title="What did we learn with Nazi human experimentation?" Tags="&lt;human-biology&gt;&lt;history&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10437" PostTypeId="2" ParentId="7121" CreationDate="2013-09-15T01:43:45.937" Score="1" Body="&lt;p&gt;I think a lot of your questions try to split the hair; &lt;em&gt;is this happening at the chemical or the histological level&lt;/em&gt; and I do get what you're asking, but you should know that the distinction is often not worth making. Pretty much whenever a neuron's involved, the interesting biology is multi-scale.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Is the membrane continuous along these tubules, or does the tubule just end somewhere inside the muscle fiber?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The membranes are continuous.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;When the muscle is twitching...&lt;/strong&gt; is this neurological of nature, or is it related to a molecular cause in the muscle itself?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Most things you'd call a muscle twitch are at the whole-muscle-group scale, involving the coordinated contraction of many individual motor units, so it's basically neurological.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;When the muscle is cramping...&lt;/strong&gt; I'm almost certain this arises in the muscle. What causes it? A malfunction with regard to the calcium ions?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A &lt;em&gt;muscle cramp&lt;/em&gt; is a colloquialism for a couple of things that are quite different from each other. Overall, as with the previous question, if someone's experiencing a muscle cramp that means it's a fairly macroscopic phenomenon and it likely involves a whole group of muscle filaments, so it's neurological. Most spasms and cramps are neurologically mediated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The connections with electrolyte balances (cramps from low sodium, potassium, magnesium, or calcium) also hint at the neurological basis because neurons act on each other (and on muscles) by forming or dissipating ion gradients. You may know that low dietary calcium can lead to muscle cramps; if this was relevant to the calcium release within the myocyte (from the sarcoplasmic reticulum) then the calcium-starved muscles wouldn't be expected to chronically contract (which requires calcium) but to chronically relax. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, there's a lot of room for feedback mechanisms. So, let's say a person experiences a muscle tear; the tear is small enough that it doesn't compromise the function of the entire muscle group. In this case it's adaptive for the local damage to 'signal' to the rest of the muscle group to initiate spasm so as to stabilize the damaged structures as they're repaired. In this scenario the local damage would 'inform' a neurological (and/or endocrine) response that actually effects the spasm.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Lastly, and on a slightly different subject, &lt;strong&gt;what are the microlesions in the muscles that occur during strength training, and what is the overcompensation that happens?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Last time I was updated on this (not my bag), there were some large questions remaining. The tricks used by growing muscle to establish large, regular arrays of contractile machinery, that is organized over many spatial orders of magnitude, are poorly understood. There are structures that monitor the overall organization and that detect any large deformations. Regarding overcompensation, let's play through a generic scenario. A muscle cell is loaded too much and becomes physically damaged. It has to stop taking orders (stop responding to contraction/relaxation signals) and to initiate repairs. The overcompensation results because muscle cell's not really capable of knowing how large it was before the damage, so the safe amount of repairs to do is &lt;em&gt;extra.&lt;/em&gt; Probably there are epigenetic processes that let a muscle cell 'count' the number of times its been greatly damaged and to scale-up the response appropriately.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you just consider two likely sources of damage -- mechanical strain and lactic acidosis -- you can see that there are widely different mechanisms that would be required to detect the damage and to initiate repairs. &lt;/p&gt;&#xA;" OwnerUserId="3336" LastActivityDate="2013-09-15T01:43:45.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10438" PostTypeId="2" ParentId="10284" CreationDate="2013-09-15T05:51:40.623" Score="3" Body="&lt;p&gt;In the absence of unanimous consensus and sources regarding the actual distribution of these shuttles,(wikipedia favours G3P shuttle abundance) let me try to explain the cause if the glycerol-phosphate shuttle is assumed to be prominent in brain cells. Several possible reasons might lead to this:- &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) The existing metabolic pathways are all intertwined to form a complex metabolic net. This means that invariably, the intermediates of any pathway are the products or intermediates of several other pathways. Therefore, the G3P shuttles require Glycerol-phosphate and Glycerol-phosphate dehydrogenase (I and II) which might be naturally abundant in brain owing to its use in strict lipid metabolic control in nervous tissue. This means that tapping the already high G3P for use as a shuttle compared to synthesising and operating a distinct metabolic shuttle is more profitable. Furthermore, operating Malate aspartate shuttle migh require intermediates whose high concentrations (required to maintain the shuttle) might negatively interfere with existing metabolic pathways like protein synthesis and regulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) This shuttle has much faster operation time than Malate-Aspartate shuttle and hence is very useful in shuttling reducing equivalents fast in muscles and brain. Compared to the malate aspartate shuttle, it is shorter and hence faster and less prone to cessation due to unavailable intermediates or enzymatic disruption. Due to several enzymes working in Malate-aspartate shuttle, it has a narrower pH and temperature optima than the G3P shuttle which is shorter and depends on lesser intermediates, and hence is less prone to disruption.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3)The last and the most far-fetched (but relevant)reason is that the loss of one ATP may not cause much of a problem because of already high respiratory rate, high Oxygen delivery to brain and ability of the body to quickly transfer available energy sources to brain at the cost of other parts, at times of energy stress. This means that replacing the shuttle with a more energetically conserving one may not have a strong driving force for evolution to operate on, and therefore the presence of G3P may be because of something like phylogenetic inertia, that is, the prevalence of an ancestral character just because it is neutral and does not influence the fitness in a considerable manner. Therefore, the ancestral G3P shuttle would just not have been replaced here but this is very unlikely as G3P shuttle is prominent in 2 very high energy-demanding organs, muscles and brain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Except the last outrageously far-fetched reason, all other reasons should be enough to explain its prominent presence (if it is true) in brain tissues.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2013-09-15T05:51:40.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10439" PostTypeId="2" ParentId="10436" CreationDate="2013-09-15T06:07:45.333" Score="11" Body="&lt;p&gt;Basically nothing.  The Nazis did unfathomably terrible things of little value, and they did it poorly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jlaw.com/Articles/NaziMedEx.html&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt;&lt;sup&gt;*&lt;/sup&gt; is a fascinating, albeit long, read.  It goes through some of the ethics of the data, but first lists some more of the &quot;experiments&quot; the Nazis performed.  To add to your list: high-altitude, sea water potability, tuberculosis, poisoning, artificial insemination, and numerous woundings.  They also did terrible things to twins.  Aside from being torturous and cruel, the &quot;experiments&quot; rarely if ever used anesthetics and were usually designed to kill the prisoner.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article goes on to list a few case studies where some of the Nazi works came up and &lt;em&gt;could&lt;/em&gt; have been considered, but were repeatedly shot down.  It then details a number of reasons why the &quot;experiments&quot; were worthless.  In particular,&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;[I]t is doubtful that physiological responses of the tortured and maimed victims represented the responses of the people for whom the experiments were meant to benefit.&quot;&lt;/li&gt;&#xA;&lt;li&gt;Nazi &quot;researchers&quot; were racists who were looking to validate their own beliefs.  No good science comes from that.&lt;/li&gt;&#xA;&lt;li&gt;The results weren't ever actually published.&lt;/li&gt;&#xA;&lt;li&gt;The &quot;data&quot; are inconsistent.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The article moves into ethical arguments and hypotheticals, but ends up saying theoretically some of it could be considered, or that &quot;&lt;em&gt;Absolute censorship of the Nazi data does not seem proper, especially when the secrets of saving lives may lie solely in its contents.&lt;/em&gt;&quot;  It's a complicated scenario where that would arise.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Editing a few years later to add this &lt;a href=&quot;http://www.nybooks.com/articles/archives/2015/nov/19/medical-research-dangers-human-subjects/&quot; rel=&quot;nofollow&quot;&gt;discussion from the NY Review of Books&lt;/a&gt;.  It's a little removed in tone, and is over-generous as regards the intent of the Nazi torturers, but makes the interesting point that one good thing to come out of the experience was the first codified guidelines for human experimentation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As part of the judgment, the court issued the celebrated Nuremberg Code in 1947—the first, shortest, and in many ways most uncompromising of the major ethical codes and regulations for the conduct of medical research on humans. Although the code had no legal authority in any country, it had great influence on ideas about human experimentation, and subsequent international codes and legislation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In particular, the concept of &quot;informed consent&quot; is directly traceable to the Nuremberg Code:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first provision of the Nuremberg Code is unqualified: “The voluntary consent of the human subject is absolutely essential.” No exceptions are permitted... Furthermore, the code is clear that consent must be given by subjects who are fully informed.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;*&lt;sub&gt;&lt;sub&gt;I should note that the article is from a Jewish law website, so some may discount that as not a perfectly neutral source.  Which is silly.&lt;/sub&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2015-11-06T17:18:13.273" LastActivityDate="2015-11-06T17:18:13.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10440" PostTypeId="2" ParentId="10218" CreationDate="2013-09-15T06:34:15.217" Score="3" Body="&lt;p&gt;This advice is America-centric; graduate programs in other countries may be different, especially in regards to assigned course work, etc. But this should more-or-less be solid. Also, I'm assuming you're interested in a PhD.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know if what you're looking for is a proper field, but that doesn't matter.  Ideally, grad school is where you do research on your own terms, and what lab you join is the single most important consideration. What you want is a competent program that:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;gives you the flexibility to create your own subfield&lt;/li&gt;&#xA;&lt;li&gt;has supportive and knowledgeable faculty that you can work under&lt;/li&gt;&#xA;&lt;li&gt;has excellent computer science AND marine biology programs (or analogs)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;First, find faculty who are doing research you are interested in, and look at the programs available at their schools. Since they're the most important consideration, everything else will fall into place after that. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next, email 5 of those professors with an introduction of what you're interested in, particularly about their research.  Ask them what programs are most appropriate at their university, and how flexible you can be in taking appropriate coursework. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At some point, you'll probably want to decide if you want to be more of a marine biologist or a computer scientist. Your diploma at the end of the decade is only going to say one of those things.  That shouldn't make a huge difference as to your job outlook, but is worth thinking about.  Practically, the question is whether you want to get your hands dirty, go out on a boat, and collect your own data.  Alternatively, if you join a CS program, you are more likely to be analyzing large datasets collected by other scientists. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At &lt;em&gt;most&lt;/em&gt; universities, you'll likely only have the option to join a biology program. But there are certainly excellent CS programs with biology oriented faculty.  Even then, the CS faculty is more likely to be doing genomics and such.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For practical recommendations, the University of Washington in Seattle would probably have something appropriate to your interests. While I was there, my lab was adjacent to an Oceanography lab that had a video wall for visualizing ocean currents and such. Not precisely marine biology, but UW has a very collaborative faculty and I'm sure the two departments work together.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;UW also has a strong computational biology program that you can go into either through CS or through one of the many biology programs. You should also check out the Institute for Systems Biology at UW. I saw a presentation there specifically about DNA exchange between marine microorganisms.  I'm not saying UW is your best option, I just know that school because I did my PhD there. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A final word of advice. Once you're in a program, it's very likely your interests will change as you learn about other research going on. And also, it's quite possible you won't get into the lab you want simply because of money or logistics. With both of these in mind, be flexible about where you're willing to go. What you do during your PhD isn't really that important anyway.  If you're going to be research scientist, it's what you do during your Postdoc that will establish your career. Just take the opportunity to learn everything you can and see what's out there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps.  Good luck!&lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-09-15T06:34:15.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10441" PostTypeId="1" CreationDate="2013-09-15T14:16:31.867" Score="1" ViewCount="89" Body="&lt;p&gt;It is common that we soak raisins in water, and they acquire water by endosmosis. That means that the cells are permeable to water, right? Then why don't they lose water when kept in air? Or kept in sugar without any water? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Also, take the example of peeled potatoes. Put them in a hypertonic solution, and they lose water, but when kept there, in air, they don't. How come?&lt;/p&gt;&#xA;" OwnerUserId="4013" LastEditorUserId="4013" LastEditDate="2013-09-15T15:35:04.210" LastActivityDate="2013-09-15T15:47:01.863" Title="Why don't raisins lose water when in air?" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10442" PostTypeId="1" AcceptedAnswerId="10453" CreationDate="2013-09-15T14:50:46.333" Score="6" ViewCount="782" Body="&lt;p&gt;Why is there wide variation in genome size amongst groups of protists, insects, amphibians and plants, but less variation within groups of mammals and reptiles?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-09-18T14:29:13.463" LastActivityDate="2013-10-09T03:05:10.623" Title="Variations in Genome Sizes" Tags="&lt;evolution&gt;&lt;genomics&gt;&lt;genomes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10443" PostTypeId="1" CreationDate="2013-09-15T14:52:32.533" Score="0" ViewCount="73" Body="&lt;p&gt;When an animal eats something, it obtains matter and energy right? But, what are the 3 possible fates of the matter and 3 possible fates energy. I don't understand what they are even asking. What would be the 3 possible fates of each. &lt;/p&gt;&#xA;" OwnerUserId="4473" LastEditorUserId="3340" LastEditDate="2015-06-04T11:48:43.650" LastActivityDate="2015-06-04T11:48:43.650" Title="3 fates of this matter" Tags="&lt;homework&gt;&lt;food&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10444" PostTypeId="1" AcceptedAnswerId="10460" CreationDate="2013-09-15T14:56:46.623" Score="1" ViewCount="1790" Body="&lt;p&gt;Humans have approximately 21000 genes but they probably make more proteins than that. This has been explained by many mechanisms like alternative RNA splicing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is - If what we call as &quot;introns&quot; and &quot;exons&quot; vary so much, then how is the  number of introns present in a genome determined ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="948" LastEditDate="2013-09-15T17:26:09.790" LastActivityDate="2013-09-16T16:31:09.007" Title="Number of introns in a genome" Tags="&lt;rna&gt;&lt;genomics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10445" PostTypeId="2" ParentId="10443" CreationDate="2013-09-15T15:07:31.357" Score="3" Body="&lt;p&gt;I think the poster wants only a simple answer, so I am going to answer in simple terms. The fates can be -&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1 Used in cellular respiration as fuel and some amount can be converted to useful energy which can be used to build other substances and some energy can be lost as heat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2.The animal can become prey for other animal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3.The animal throws away some matter as feces.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-09-15T15:07:31.357" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10446" PostTypeId="1" AcceptedAnswerId="10450" CreationDate="2013-09-15T15:15:27.070" Score="5" ViewCount="10594" Body="&lt;p&gt;Can hormones such as testosterone, aldosterone and estrogen cross the blood brain barrier?&#xA;I looked on Wikipedia and there no mention of it in the testosterone article. Through Googling around I also didn't find a list of which hormones can cross the barrier.&lt;/p&gt;&#xA;" OwnerUserId="152" LastEditorUserId="231" LastEditDate="2015-08-03T19:30:57.577" LastActivityDate="2015-08-03T19:44:11.763" Title="Which hormones can cross the blood brain barrier?" Tags="&lt;brain&gt;&lt;endocrinology&gt;&lt;blood-brain-barrier&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10447" PostTypeId="2" ParentId="10441" CreationDate="2013-09-15T15:26:25.657" Score="0" Body="&lt;p&gt;They already have!  Raisins are dried-out grapes, and according to a brief search are less than 20% water by weight but over 50% sugar by weight.  They've lost plenty of water already.  Your average grape is probably hypertonic to most solutions and thus will not &lt;em&gt;readily&lt;/em&gt; lose more water.  Additionally, for water to be lost to air, it must be vaporized via evaporation, which is slow, inefficient from something as dry as raisins, and miniscule in effect.  Sun-dried raisins already went through that process.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-09-15T15:47:01.863" LastActivityDate="2013-09-15T15:47:01.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10448" PostTypeId="2" ParentId="10441" CreationDate="2013-09-15T15:32:00.600" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;That means that the cells are permeable to water, right?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Correct.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Then why don't they lose water when kept in air?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They do, but it occurs very, &lt;strong&gt;&lt;em&gt;very&lt;/em&gt;&lt;/strong&gt; slowly. It might take a few months (or years in some areas), but if you leave raisins exposed to air they will eventually become harder until the water reaches equilibrium with the surrounding air.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This slow process is why there are &lt;a href=&quot;http://www.thekitchn.com/tip-how-to-plump-up-your-raisi-83724&quot; rel=&quot;nofollow&quot;&gt;tips on how to reconstitute raisins that are too hard&lt;/a&gt; to make them more moist and plump after getting a bad batch or finding old ones in your kitchen.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-09-15T15:32:00.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10449" PostTypeId="2" ParentId="10409" CreationDate="2013-09-15T15:44:11.193" Score="1" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15895512&quot; rel=&quot;nofollow&quot;&gt;one study&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It was calculated that if the excretory percentage of niacin metabolites in the urine were 60%, of the tryptophan ingested, the conversion factor would be a value of 67, meaning that is 67 mg of tryptophan is equal to 1 mg of niacin.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, the study has a pretty low power with only 10 participants and an indirect measure of niacin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it &lt;em&gt;possible&lt;/em&gt; that a person could get all of their niacin from tryptophan? Probably - you just need to eat enough tryptophan, which is also &lt;a href=&quot;http://en.wikipedia.org/wiki/Essential_amino_acid&quot; rel=&quot;nofollow&quot;&gt;an Essential Amino Acid&lt;/a&gt;. The body may preferentially keep Tryptophan (which it does not store) until Niacin runs out (which also cannot be stored). &lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-09-15T15:44:11.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10450" PostTypeId="2" ParentId="10446" CreationDate="2013-09-15T16:09:10.317" Score="5" Body="&lt;p&gt;Yes, both steroid and peptidic hormones can enter the brain, the obvious proof being that the brain responds to changing blood concentration of hormones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The situation is different for steroid hormones (such as estrogen, testosterone, cortisol etc) which are small and lipophilic, and peptidic hormones (such as insulin, ghrelin, prolactin etc) which are big and hydrophilic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The blood-brain barrier (BBB) is selectively permeable to steroid hormones: some of them (such as the gonadal steroids) can readily pass the BBB, while others (such as corticosteroids) pass only in small concentrations. This may however be modulated by hormone carrier proteins in the plasma.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See: &lt;a href=&quot;http://www.jci.org/articles/view/109433/scanned-page/145&quot; rel=&quot;nofollow&quot;&gt;Transport of Steroid Hormones through the Rat Blood-Brain Barrier&lt;/a&gt; - Pardridge et al., &lt;strong&gt;JCI&lt;/strong&gt;, &lt;em&gt;1979&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;When speaking of peptidic hormones, the classic hypothesis is that hormones pass through the areas where the BBB is &quot;leaky&quot;, i.e. where capillaries are fenestrated. &#xA;These include &lt;a href=&quot;https://en.wikipedia.org/wiki/Circumventricular_organs&quot; rel=&quot;nofollow&quot;&gt;circumventricular organs&lt;/a&gt; such as the median eminence (where the terminals of many neuroendocrine neurons are located), or the organum vasculosum of the lamina terminalis (OVLT), important for reproduction and osmoregulation. The &lt;a href=&quot;https://en.wikipedia.org/wiki/Choroid_plexus&quot; rel=&quot;nofollow&quot;&gt;chorioid plexus&lt;/a&gt; is also often mentioned as a site for hormone entrance and/or sensing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, how exactly hormones enter the brain is still very unclear.&#xA;Our lab published a paper on this topic recently: &#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23297228&quot; rel=&quot;nofollow&quot;&gt;Rapid sensing of circulating ghrelin by hypothalamic appetite-modifying neurons&lt;/a&gt; - Schaeffer et al., &lt;strong&gt;PNAS&lt;/strong&gt;, &lt;em&gt;2013&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="6307" LastEditDate="2015-08-03T19:44:11.763" LastActivityDate="2015-08-03T19:44:11.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10451" PostTypeId="2" ParentId="10446" CreationDate="2013-09-15T16:15:18.453" Score="2" Body="&lt;p&gt;Yeah indeed they can.  The obvious proof is puberty and development, but a more involved look into how that is achieved can be found in &lt;a href=&quot;http://endo.endojournals.org/content/153/9/4111.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; free article from last year.  In particular,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nearly every mechanism by which a substance can cross or interact with the BBB is used by one hormone or the other. In general, steroid hormones cross the BBB by transmembrane diffusion whereas thyroid hormones, peptide hormones, and regulatory proteins cross by saturable systems.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In particular, I like figure 1:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hhBSf.png&quot; alt=&quot;Figure 1&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-15T16:15:18.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10452" PostTypeId="1" CreationDate="2013-09-15T16:55:08.403" Score="3" ViewCount="897" Body="&lt;p&gt;I've been reading the British National Formulary 65 (BNF-65) and it mentioned that in some, especially at higher dosages, sedating (&lt;em&gt;first-generation&lt;/em&gt;) antihistamines, can produce paradoxical excitatory (or &lt;em&gt;stimulating&lt;/em&gt;) effects and so I felt like asking the age-old question, &quot;Why?&quot; because as I hope is obvious by my questions I am fascinated by drug action and I felt there was no better place to ask this question than here on biology stackexchange.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2013-09-15T17:29:24.923" LastActivityDate="2013-09-15T17:29:24.923" Title="What's the Mechanism of Paradoxical Excitatory Effects with Sedating Antihistamines?" Tags="&lt;pharmacology&gt;&lt;histamine&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ClosedDate="2014-12-09T10:09:42.147" ContentLicense="CC BY-SA 3.0" />
  <row Id="10453" PostTypeId="2" ParentId="10442" CreationDate="2013-09-15T17:12:10.390" Score="9" Body="&lt;p&gt;You're asking about the &lt;a href=&quot;https://en.wikipedia.org/wiki/C-value_paradox&quot; rel=&quot;noreferrer&quot;&gt;C-value enigma&lt;/a&gt;, in particular this kind of diagram:&lt;sup&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/User:Abizar&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CDIuX.png&quot; alt=&quot;genome size variations&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The quick answer is that there is no &quot;why&quot; in evolution; things happen and if they're beneficial they tend to stick around more than the deleterious things.  The longer, (slightly) more satisfying answer is &lt;strong&gt;non-coding DNA&lt;/strong&gt;.  Thanks to non-coding DNA the size of a genome doesn't even correlate to the number of &lt;em&gt;genes&lt;/em&gt;.  The human genome, for example, has over 20,000 genes but is less than two percent protein-coding; the flower &lt;em&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Utricularia_gibba#Genetic_efficiency&quot; rel=&quot;noreferrer&quot;&gt;Utricularia gibba&lt;/a&gt;&lt;/em&gt;, however, has over 28,000 genes with about two orders of magnitude smaller of a genome, due to the fact that its genome is 97% protein-coding.  In short, there is no real meaning to be found in genome size variation due to non-coding portions, which while they are sometimes important regulators can often be just transposons (40% of our genome).  I will also point out that all of those groups you mention have species with significant &lt;a href=&quot;https://en.wikipedia.org/wiki/Polyploid&quot; rel=&quot;noreferrer&quot;&gt;polyploidy&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The are a number of other interesting ideas.  In the process of researching this, I stumbled upon the &lt;strong&gt;&lt;a href=&quot;http://www.genomesize.com/index.php&quot; rel=&quot;noreferrer&quot;&gt;Animal Genome Size Database&lt;/a&gt;&lt;/strong&gt;, which is an absolute gem of a treasure trove.  It's an unbelievable mine where I've spent a good half-hour just reading.  In particular, the &lt;a href=&quot;http://www.genomesize.com/statistics.php&quot; rel=&quot;noreferrer&quot;&gt;statistics pages&lt;/a&gt; list interesting correlations for certain groups.  Mammalian genome size, for example, correlates:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Positively with red blood cell size, despite lack of nuclei&lt;/li&gt;&#xA;&lt;li&gt;Negatively with metabolic rate&lt;/li&gt;&#xA;&lt;li&gt;Not at all with developmental rate or longevity&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For amphibians, however, there is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Positive correlation with red blood cell and nucleus sizes in both frogs and salamanders&lt;/li&gt;&#xA;&lt;li&gt;Negative correlation with developmental rate in many groups&lt;/li&gt;&#xA;&lt;li&gt;Negative correlation with brain complexity in both frogs and salamanders&lt;/li&gt;&#xA;&lt;li&gt;No strong relationship with metabolic rate in either frogs or salamanders&lt;/li&gt;&#xA;&lt;li&gt;Some association with intensity and frequency of metamorphosis&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you have time, I &lt;strong&gt;highly&lt;/strong&gt; recommend reading through T. Ryan Gregory's PhD thesis entitled &lt;a href=&quot;http://www.genomesize.com/rgregory/thesis/&quot; rel=&quot;noreferrer&quot;&gt;The C-Value Enigma&lt;/a&gt;.  It's around 350 pages, but each chapter is in separate pdfs and is the most in-depth treatment I've seen, despite being about a decade old.  It's been moderately life-changing for me to read, some of the interpretations he presents challenged my thinking on the subject of genome evolution entirely.  Should genomes be treated as individuals, and what would that mean?  I digress.  Chapters 3, 4, 6, and 7 are what you'll want, in particular the last twenty or so pages of chapter 7.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dr. Gregory now has a faculty position and his &lt;a href=&quot;http://www.gregorylab.org/research/&quot; rel=&quot;noreferrer&quot;&gt;lab's research page&lt;/a&gt; is a little easier to read.  I love this image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4pi2a.jpg&quot; alt=&quot;TEs&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As genome size increases in eukaryotes, the percentage of the genome composed of genes (white circles) becomes smaller. Conversely, the percentage of the genome made up of transposable elements (black circles) increases with genome size.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It seems like the best way to look at genome size and find some meaning is within a specific group.  There are correlations, for example, that are present in frogs and salamanders, but not in either group alone.  Some of the groups are very unbalanced; in insects, only &lt;em&gt;Orthoptera&lt;/em&gt; tend to have very large genomes.  Interestingly, a number of those groups also undergo some form of metamorphosis, but the correlations aren't what you might have expected:  insects that develop quickly and metamorphose have smaller genomes, but &quot;&lt;em&gt;[i]n a more general sense, small genome size seems linked to rapid diversification... Conversely, insects without metamorphosis may possess very large genomes...&lt;/em&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-09T03:05:10.623" LastActivityDate="2013-10-09T03:05:10.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10454" PostTypeId="1" CreationDate="2013-09-15T17:45:08.017" Score="2" ViewCount="214" Body="&lt;p&gt;Acidic and Basic soils experience phosphate sequestration through binding with either calcium, aluminum, or iron. How do plant that thrive in acidic and basic soils obtain the necessary phosphate? Blueberries are an example that I particularly enjoy.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5vryn.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Thanks to the University of Hawaii for posting this picture.&lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-09-21T07:38:05.610" Title="How Do Acid and Base Loving Plants Get Enough PO4?" Tags="&lt;soil&gt;&lt;ph&gt;&lt;phosphate&gt;&lt;biochemistry&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10455" PostTypeId="1" CreationDate="2013-09-15T18:17:52.413" Score="5" ViewCount="270" Body="&lt;p&gt;Are there any linear, rotary or oscillatory molecular motors in the cells which can have fixed frequeny and which can be used as a reference for elapsed time timer? This question is with relevence to my earlier question 'Is there a realtime molecular clock within the genome to co-ordinate the developmental sequences in an embryo?'&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="4101" LastEditDate="2013-10-14T22:00:24.623" LastActivityDate="2013-10-16T12:34:36.380" Title="There are linear and rotary molecular motors in the cells. Do any of them have a fixed or stable frequency or speed?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;embryology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10456" PostTypeId="1" AcceptedAnswerId="34133" CreationDate="2013-09-15T19:01:47.243" Score="3" ViewCount="232" Body="&lt;p&gt;I recall reading that much of the energy a cat produces from its food comes from proteins which I assume would produce energy via being catabolised into amino acids which in turn, if glucogenic, would undergo gluconeogenesis and then, by means of being metabolised into glucose, enter glycolysis and the resulting pyruvate would be converted to acetyl-CoA and enter the TCA cycle to produce energy. I'm wondering whether this recollection is accurate and whether cats could, like humans, use ketone bodies for their sole fuel source if need be. &lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="3340" LastEditDate="2015-06-04T11:48:10.613" LastActivityDate="2015-06-04T11:48:10.613" Title="Can cats use ketone bodies as only source of energy?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10457" PostTypeId="1" CreationDate="2013-09-15T20:37:01.750" Score="5" ViewCount="102" Body="&lt;p&gt;I have traditionally thought of and heard about life-history traits (e.g., size at first reproduction, number of offspring, size of offspring, survival, etc., etc.) as drawing from a finite pool of resources that an organism has, and therefore exhibiting tradeoffs. So, for instance, an organism that invests in a lot of offspring would experience a decreased probability of survival.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has recently come to my attention that this is not always the case, and I'm not sure why. I have been directed to the work of David Houle, who wrote extensively on the topic of life-history traits, but some of his work is inaccessible to me intellectually. I was hoping that somebody had a more digestible explanation or was maybe more familiar with Houle's work.&lt;/p&gt;&#xA;" OwnerUserId="1906" LastEditorUserId="1906" LastEditDate="2013-09-16T03:15:39.133" LastActivityDate="2014-07-20T16:41:13.173" Title="Why might you NOT observe a tradeoff between two life-history traits?" Tags="&lt;life-history&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10459" PostTypeId="2" ParentId="10443" CreationDate="2013-09-16T06:22:16.860" Score="1" Body="&lt;p&gt;Maybe this video might help you:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=q52qtdrvah8&quot; rel=&quot;nofollow&quot;&gt;Matter and Energy in Organisms&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-09-16T06:22:16.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10460" PostTypeId="2" ParentId="10444" CreationDate="2013-09-16T15:30:36.233" Score="2" Body="&lt;p&gt;Yes, the individual number of exons/introns will vary in a transcript, but what you can do is just count all possible exons of a gene&#xA;For example, lets say you have an alternative exon in these two isoforms. The XX's are exons&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;XX---XX---XX---XX&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;XX--------XX---XX&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We would say this gene has 4 exons and 3 introns, even though one isoform only has 3 exons. Its the transcript that varies in number of exons, the gene remains constant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heres a slightly more complex example. Mutually exclusive exons&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;XX---XX--------XX&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;XX--------XX---XX&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We would still say it has four exons. Pretend that every exon of every isoform is included and thats how you get the number of exons in gene. So for the above example, just pretend both mutually exclusive exons are included&lt;/p&gt;&#xA;&#xA;&lt;p&gt;XX---XX---XX---XX&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15217358&quot; rel=&quot;nofollow&quot;&gt;According to this old paper&lt;/a&gt; there are 8.8 exons per gene (7.8 introns). Their gene number count is high because its older, but they estimate that there are 207,344 introns in the human genome. &lt;/p&gt;&#xA;" OwnerUserId="4199" LastEditorUserId="3615" LastEditDate="2013-09-16T16:31:09.007" LastActivityDate="2013-09-16T16:31:09.007" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10461" PostTypeId="2" ParentId="10436" CreationDate="2013-09-16T15:43:18.767" Score="6" Body="&lt;p&gt;This is an interesting question and one that really has two parts: the factual and the ethical. I remember discussing this topic in my 'ethics training' classes in graduate school (where I admit that I may have acted as an ass simply to demonstrate that our ethics training was unfailable).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The factual: &quot;Are there any valuable findings published by the Nazis?&quot; Actually, yes. There is a classic anatomical atlas by &lt;a href=&quot;http://en.wikipedia.org/wiki/Eduard_Pernkopf&quot; rel=&quot;noreferrer&quot;&gt;Eduard Pernkopf&lt;/a&gt;, '&lt;a href=&quot;http://www.amazon.com/s/ref=nb_sb_noss?url=search-alias=aps&amp;amp;field-keywords=Pernkopf%20Anatomy&quot; rel=&quot;noreferrer&quot;&gt;Pernkopf Anatomy&lt;/a&gt;,' that was quite probably put together using the bodies of &lt;a href=&quot;http://www.nytimes.com/1996/11/26/science/doctors-question-use-of-nazi-s-medical-atlas.html?pagewanted=all&amp;amp;src=pm&quot; rel=&quot;noreferrer&quot;&gt;political prisoners as subjects&lt;/a&gt;. However, it may be that this is the only text that has real value, but it's enough to get us to the second question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ethical: &quot;Should we persist in using information assembled under unethical conditions? Doesn't this provide an incentive to these practices - or at least not condemn them sufficiently?&quot; Here my assly behavior was meant to send a message of, 'all morals/ethics are relative. And why should we not benefit from all sources possible? I would deny funding for unethical methods, but I would still read the paper. (obviously this part of my answer is just opinion and really shouldn't be printed here, but I think the question demands that it be considered) &lt;/p&gt;&#xA;" OwnerUserId="4139" LastActivityDate="2013-09-16T15:43:18.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10462" PostTypeId="1" AcceptedAnswerId="10463" CreationDate="2013-09-16T16:45:38.440" Score="5" ViewCount="91" Body="&lt;p&gt;I &lt;a href=&quot;http://web.udl.es/usuaris/e4650869/docencia/GenClin/content/recursos_classe_%28pdf%29/revisionsPDF/MHCcomplex.pdf&quot; rel=&quot;nofollow&quot;&gt;read that&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Doherty and Zinkernagel found that MHC- heterozygotes present more&#xA;  antigens to the immune system than homozygotes; yet, the infected&#xA;  heterozygous mice in their experiment all died, apparently from&#xA;  overresponsiveness.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Can MHC-heterozygotes be more susceptible to autoimmune disorders and allergies because there is a tendency of over responsiveness ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-13T15:49:30.930" LastActivityDate="2013-10-13T15:49:30.930" Title="A possible cause of autoimmunity" Tags="&lt;immunology&gt;&lt;autoimmune&gt;&lt;mhc&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10463" PostTypeId="2" ParentId="10462" CreationDate="2013-09-16T17:26:47.473" Score="5" Body="&lt;p&gt;It looks moderately muddled, but perhaps.  This paper&lt;sup&gt;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/276/1658/925.full&quot;&gt;1&lt;/a&gt;&lt;/sup&gt; is a good place to start; it's free and the intro lists a number of more recent studies.  That study found a connection to lifetime reproductive success in sticklebacks (a fish) with intermediate MHC diversity.  This 2007 study in mice&lt;sup&gt;&lt;a href=&quot;http://www.genetics.org/content/176/4/2501.full&quot;&gt;2&lt;/a&gt;&lt;/sup&gt; is a particularly nice one, dealing with a inbred line outbred to wild mice, finding again, no advantage to heterozygotes.  There are others, but most deal with the concept descriptively (self-delighting in their continued refutation of a commonly-held belief) or predictively (such as this from PNAS in 1992&lt;sup&gt;&lt;a href=&quot;http://www.pnas.org/content/89/22/10896.full.pdf&quot;&gt;3&lt;/a&gt;&lt;/sup&gt; or a 2009 review&lt;sup&gt;&lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/364/1513/117.full&quot;&gt;4&lt;/a&gt;&lt;/sup&gt;) but specific and proven reasons are sparse.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The general feeling is that it may remain unclear what sort of genetic interactions are involved in MHC (additive effects, overdominance, etc.) but it is probably also complicated due to the nature of immunology.  For example, a paper from 2003&lt;sup&gt;&lt;a href=&quot;http://iai.asm.org/content/71/4/2079.full&quot;&gt;5&lt;/a&gt;&lt;/sup&gt; points out that in an immunological response, only a few peptides dominate the response; there may be no real advantage to having extra ones if they are unused, and having those others around might dilute the useful response (That paper also takes an interesting view of serial infections, and shows that heterozygotes are indeed &lt;em&gt;advantaged&lt;/em&gt; during coinfection).  The above PNAS publication&lt;sup&gt;&lt;a href=&quot;http://www.pnas.org/content/89/22/10896.full.pdf&quot;&gt;3&lt;/a&gt;&lt;/sup&gt; gives the idea, which the stickleback paper&lt;sup&gt;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/276/1658/925.full&quot;&gt;1&lt;/a&gt;&lt;/sup&gt; recapitulated, that if more alleles are present, more T-cells will be self-reactive and will therefore be purged, resulting in an overall decreased T-cell availability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other hypotheses are present in the review&lt;sup&gt;&lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/364/1513/117.full&quot;&gt;4&lt;/a&gt;&lt;/sup&gt; I mentioned, such as perhaps positive selection efficiency is not MHC-diversity dependent whereas negative selection is, or indeed increased autoimmune reactions as you guessed.  My guess would be some combination of the above, with selection for heterozygotes being favored in the real world for multiple and repeated infections but certain specifics resulting in a homozygote preference, of which autoimmunity is likely playing a role.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-09-16T17:32:12.437" LastActivityDate="2013-09-16T17:32:12.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10465" PostTypeId="1" AcceptedAnswerId="10481" CreationDate="2013-09-16T21:15:13.843" Score="0" ViewCount="87" Body="&lt;p&gt;I've searched the internet for several minutes and I've looked at DAT but I'm having trouble finding the DAT binding location. Where (and to which aa) does dopamine and cocaine bind to hDAT1?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2013-09-18T09:00:48.387" Title="DAT1 dopamine and cocaine binding" Tags="&lt;protein-binding&gt;&lt;dopamine&gt;&lt;cocaine&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10466" PostTypeId="1" AcceptedAnswerId="10467" CreationDate="2013-09-16T21:47:55.290" Score="2" ViewCount="32355" Body="&lt;p&gt;A patient has a saline solution IV drip into the vein. They have somehow moved around and the needle has fallen out of the vein, but remained in the body. Nobody has noticed and for a few hours water has accumulated like a balloon in the arm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens? Is it dangerous? If untreated, would the body absorb the water, or would it remain as a balloon / pocket? If a pocket of water forms, what is the treatment?&lt;/p&gt;&#xA;" OwnerUserId="4477" LastActivityDate="2019-05-27T09:54:00.797" Title="What happens if an IV drip with a saline solution slips out of the vein, but keeps dripping into the body?" Tags="&lt;hematology&gt;&lt;hydration&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10467" PostTypeId="2" ParentId="10466" CreationDate="2013-09-17T00:09:14.760" Score="0" Body="&lt;p&gt;&lt;strong&gt;CALL YOUR VET ASAP.&lt;/strong&gt; The following information is &lt;strong&gt;&lt;em&gt;NOT&lt;/em&gt;&lt;/strong&gt; from a medical or veterinary professional. It is based off of human physiology and doesn't necessarily apply to other mammals. I cannot guarantee the accuracy or effectiveness of any information that follows.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;They have somehow moved around and the needle has fallen out of the vein, but remained in the body. Nobody has noticed and for a few hours water has accumulated like a balloon in the arm.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is called &quot;infiltration&quot;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YhDGQ.jpg&quot; alt=&quot;Diagram of Infiltration and Extravasation&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/S47rB.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is it dangerous?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It can be, depending on what was in the IV.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If untreated, would the body absorb the water, or would it remain as a balloon / pocket? If a pocket of water forms, what is the treatment?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Taken from &lt;a href=&quot;http://w3.rn.com/news/clinical_insights_details.aspx?Id=34318&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;If the infiltration is severe, you may consider the application of a compress in addition to elevating the affected limb. Check your institution’s policy regarding which type of compress (warm or cold) should be applied. Generally speaking, if the infiltration solution was isotonic, a warm compress is used to alleviate discomfort and help absorb the infiltration by increasing circulation to the affected area. However, sloughing can occur from the application of a warm compress to an area infiltrated with certain medications such as potassium chloride. In certain situations, a cold compress is recommended.&quot;&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-09-17T00:09:14.760" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10468" PostTypeId="1" CreationDate="2013-09-17T06:26:05.307" Score="6" ViewCount="281" Body="&lt;p&gt;If selection pressure results in conservation of DNA sequences, what is the most plausible explanation for the existence of &lt;a href=&quot;http://en.wikipedia.org/wiki/Ultra-conserved_element&quot; rel=&quot;nofollow&quot;&gt;ultra-conserved elements&lt;/a&gt; (refs &lt;a href=&quot;http://www.sciencemag.org/content/304/5675/1321&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.pnas.org/content/109/19/E1183&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) given that there hasn't been any significant validation of the functional significance of these elements other than a lot of bioinformatic analyses across different genome datasets? If these are of such high significance, does this mean that there is still some significant gap in our understanding of fundamental biology or is there another explanation? The second reference in particular show that there are UCEs shared between plants and animals, but are not syntenic (which is not necessarily a surprise) so it might suggest that at least a class of UCEs are associated with structural rather than functional elements. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears that there are at least several different 'classes' of ultra-conserved elements, based on the number of matching/identical bps, their spatial distribution across the genome and the species in which they exist. Even though there is probably no single explanation that would account for all the possible functions they can have, it is surprising that they are difficult to test functionally. This is again probably due to a lack of understanding about their properties and therefore no real method to validate their function. I think this is where we need to think outside the box to come up with the answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What would be the most obvious (and possibly not so obvious) function for UCEs?&lt;/strong&gt;   &lt;/p&gt;&#xA;" OwnerUserId="4026" LastEditorUserId="4026" LastEditDate="2013-09-17T23:16:27.327" LastActivityDate="2014-05-14T13:52:47.337" Title="What is the potential function of ultra-conserved elements in the genome?" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10469" PostTypeId="2" ParentId="10455" CreationDate="2013-09-17T07:06:13.570" Score="4" Body="&lt;p&gt;There are molecular motors but the frequency is a function of energy input (ATP); similar to the angular velocity dependence on amount of current in electrical motors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concept of molecular motor may not be suitable for a clock like device. There are clocks based on genetic circuits, which produce stable oscillations. Examples include the circadian clock, cell division, menstrual cycle etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Developmental events involve checkpoints and the timing is regulated by several factors such as number of cells, concentration of some protein etc. However, I haven't come across a master clock that integrates and synchronizes all these signals for precise developmental timing. That makes it an interesting area of research.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-09-17T07:06:13.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10470" PostTypeId="1" CreationDate="2013-09-17T08:48:09.360" Score="3" ViewCount="230" Body="&lt;p&gt;I am trying to validate the variants I found using whole genome sequencing . The standard practice, I have seen in the two publications below were to check for the number of heterozygous SNPs called by the SNP array.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) &lt;a href=&quot;http://www.nature.com/nbt/journal/v30/n1/full/nbt.2065.html?WT.ec_id=NBT-201201&quot; rel=&quot;nofollow&quot;&gt;Performance comparison of whole-genome sequencing platforms&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To further assess the accuracy of the variant calling, ... Of the 260,112 heterozygous calls detected with the Omni array, 99.5% were present in the entire SNV data set, 99.34% were concordant calls and only 0.16% were platform-specific SNVs. This demonstrates that both platforms are sensitive to known SNVs and that few known single-nucleotide polymorphisms (SNPs) are detected by only one platform.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;2) &lt;a href=&quot;http://www.nature.com/nbt/journal/v30/n1/full/nbt.2053.html&quot; rel=&quot;nofollow&quot;&gt;Optimised filtering reduces the error rate in detecting genomic variants by short-read sequencing&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To confirm that shared SNVs are indeed true variants, we used Illumina single-nucleotide polymorphism (SNP) arrays and selected all SNPs heterozygous on the SNP array.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My question is - why are only &lt;strong&gt;heterozygous&lt;/strong&gt; SNPs chosen for validation when using Illumina Omni arrays?&lt;/p&gt;&#xA;" OwnerUserId="4480" LastActivityDate="2013-10-19T16:43:16.617" Title="Why only heterogeneous SNVs for validation using genotyping arrays?" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;genomics&gt;&lt;snp&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10471" PostTypeId="2" ParentId="10468" CreationDate="2013-09-17T12:57:19.090" Score="6" Body="&lt;p&gt;Probably &lt;a href=&quot;http://www.plosbiology.org/article/info%3adoi/10.1371/journal.pbio.0030007&quot;&gt;development&lt;/a&gt;, in particular &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616699&quot;&gt;transcriptional regulation&lt;/a&gt;.  To quote each link in turn,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development, including many transcription factors. These highly conserved non-coding sequences are likely to form part of the genomic circuitry that uniquely defines vertebrate development.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[Highly conserved non-coding sequences] are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17086198&quot;&gt;Additionally&lt;/a&gt;,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Here we report that 45% of these sequences functioned reproducibly as tissue-specific enhancers of gene expression at embryonic day 11.5. While directing expression in a broad range of anatomical structures in the embryo, the majority of the 75 enhancers directed expression to various regions of the developing nervous system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These regions tend to be highly clustered in around 200 areas, and most of them are non-coding.  ncRNA is often regulatory, and those UCE clusters are associated closely with developmental genes.  That being said, not all of them are clustered near known genic regions, which might be a good indicator that there are heretofore unknown genes in those areas; UCEs might be &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891336/&quot;&gt;useful for discovery&lt;/a&gt;.  And &lt;a href=&quot;http://www.pnas.org/content/108/2/786.full&quot;&gt;here's a paper&lt;/a&gt; trying to give a role to one in cancer.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-09-17T13:11:44.747" LastActivityDate="2013-09-17T13:11:44.747" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10472" PostTypeId="1" AcceptedAnswerId="10473" CreationDate="2013-09-17T13:29:16.850" Score="1" ViewCount="4512" Body="&lt;p&gt;I apologize if this hypothesis sounds strange by I was wondering if any research had been done on a phenomenon which I've seen and have corroborated with many other - the idea that over time spouses tend to start looking similar to each other. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My hypothesis is that this is really a one-way street with the wife tending to look more like the husband. The reason being that after coitus her body is flooded with his genetic material which may lead to some mixing of DNA outside of the egg. Furthermore once the woman is pregnant she enter into a symbiotic relationship with an organism whose DNA is approximately 50% foreign. Her body must then adapt to the presence of that new genetic material. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize this may sound strange and Lamarkian but I was curious if the phenomenon itself had been investigated.&lt;/p&gt;&#xA;" OwnerUserId="4481" LastActivityDate="2017-08-07T22:53:27.243" Title="Do spouses begin to share genes over time?" Tags="&lt;genetics&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10473" PostTypeId="2" ParentId="10472" CreationDate="2013-09-17T13:43:18.133" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.it.2012.03.002&quot;&gt;Microchimerism (Mc)&lt;/a&gt; is an interesting concept, and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;refers to the harboring of a small number of cells (or DNA) that originated in a different individual. Naturally acquired Mc derives primarily from maternal cells in her progeny, or cells of fetal origin in women.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In women, it has &lt;strong&gt;nothing&lt;/strong&gt; to do with transfer during/after sex but rather is due to the presence of the developing fetus.  There is definite long-term persistence of microchimerism, although not much is yet known about its effects.  &lt;a href=&quot;http://www.ijdb.ehu.es/web/paper.php?doi=10.1387/ijdb.082767hg&quot;&gt;Here is a nice and free review from 2010&lt;/a&gt; dealing with the subject.  Most if not all of the effects have to do with immune function, in particular autoimmunity.  It is &lt;em&gt;definitely&lt;/em&gt; not a mechanism by which couples begin to look similar.  That is social, in particular a result of living in the same environment with similar activities and tastes.  Male contribution to cellular content in the embryo is almost nil, as sperm die and the transcript count in the successful sperm is puny compared to the egg.  Most RNA content in the embryo is maternal until it switches to embryo.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-09-17T13:48:18.620" LastActivityDate="2013-09-17T13:48:18.620" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10474" PostTypeId="1" AcceptedAnswerId="17292" CreationDate="2013-09-17T13:46:21.220" Score="7" ViewCount="5409" Body="&lt;p&gt;I am curious about how much more a child can be alike to one parent than the other. If a child were to inherit all the alleles that are shared between both parents from one parent, but inherit all alleles from the other parent which the first parent doesn't possess, wouldn't this make the child genetically more uniquely similar to the second parent? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question would be aided by understanding of how many alleles on average a person already shares with another person. Taking into account regional areas probably yield more similar people, I would imagine the average couple would share more than two randomly chosen people on the planet.&lt;/p&gt;&#xA;" OwnerUserId="4482" LastEditorUserId="4482" LastEditDate="2013-09-19T17:40:29.317" LastActivityDate="2016-03-18T13:52:51.447" Title="On average how many genes / alleles do people share?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10475" PostTypeId="1" AcceptedAnswerId="10490" CreationDate="2013-09-17T16:43:26.300" Score="3" ViewCount="780" Body="&lt;p&gt;Logistic regression is a common analysis tool used for GWAS when your response variable of interested is qualitative. It comes as one of the standard tools in most GWAS packages (e.g. PLINK).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most logistic regression models for GWAS would be setup as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\log{\frac{P(Y=1)}{1-P(Y=1)}} = \beta_0 + \beta_1*X$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where $X$ is number of copies of the minor allele for a particular SNP of interest and $Y$ is disease stuatus. However, suppose that my case-control data is matched (In my case matched by age, BMI, reported ethnicity, and distance to procurement site). I don't think standard logistic regression (as I have outlined above) is valid. What does everybody do? I don't see options for this in packages like PLINK.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also posted this question on (&lt;a href=&quot;http://www.biostars.org/p/81394/&quot; rel=&quot;nofollow&quot;&gt;http://www.biostars.org/p/81394/&lt;/a&gt;) before I realized they were no longer part of stackexchange. &lt;/p&gt;&#xA;" OwnerUserId="4483" LastActivityDate="2013-09-19T09:03:48.590" Title="GWAS: matched-pairs and logistic regression" Tags="&lt;gwas&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10476" PostTypeId="1" CreationDate="2013-09-17T17:14:53.153" Score="4" ViewCount="2220" Body="&lt;p&gt;&lt;strong&gt;The question&lt;/strong&gt; is fairly simple - does formaldehyde or methanol fixation in preparation for immunocytochemistry/immunofluorescent staining affect the pH of the lysosomes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Some background:&lt;/strong&gt; I'm trying to look at the intracellular trafficking of a fluorescently-labeled lysosomal enzyme. Cells are grown &lt;em&gt;in vitro&lt;/em&gt; and treated with the labeled protein, which is taken up into the cells via &lt;a href=&quot;https://en.wikipedia.org/wiki/Receptor-mediated_endocytosis&quot; rel=&quot;nofollow&quot;&gt;receptor-mediated endocytosis&lt;/a&gt;. The protein-receptor complex targets the late endosome-lysosome pathway, where eventually the acidic pH of the lysosome causes the two to dissociate and the receptor to recycle, while the enzyme stays and does its thing. I've labeled the enzyme with two different dyes - Alexa Fluor 488, which is supposedly &lt;a href=&quot;http://www.lifetechnologies.com/us/en/home/references/molecular-probes-the-handbook/fluorophores-and-their-amine-reactive-derivatives/alexa-fluor-dyes-spanning-the-visible-and-infrared-spectrum.html?icid=fr-alexa-3#head1&quot; rel=&quot;nofollow&quot;&gt;pH-insensitive between 4 and 10&lt;/a&gt;, and &lt;a href=&quot;https://www.lifetechnologies.com/us/en/home/references/newsletters-and-journals/bioprobes-journal-of-cell-biology-applications/bioprobes-issues-2012/bioprobes-68-november-2012/phrodo-ph-indicators.html&quot; rel=&quot;nofollow&quot;&gt;pHrodo Red&lt;/a&gt;, which has greatly-increased fluorescence as the pH drops. Alexa488 is the brightest of the Alexa dyes, and is widely used in all sorts of applications. pHrodo is not as bright (as far as I can tell, it's been difficult to find comparisons), but its pH-dependence helps lower the effect of non-specific extracellular binding, and it seems to work in my system so far.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So what's the problem?&lt;/strong&gt; I'm developing an assay that will measure the ability of certain substances to block the uptake of this enzyme into the cell. Since I'll be measuring a lack of signal, the higher I can get the uninhibited signal to be, the better. Like I said, pHrodo works OK, but it could be better. The problem is that my Alexa-labeled protein has an extremely low signal to noise ratio, when I would have expected the exact opposite. I'm wondering if, in my system, the Alexa dye really &lt;strong&gt;is&lt;/strong&gt; somewhat pH-sensitive, and is not fluorescing as well when in the acidic lysosome. I'm encountering a few other issues as well, and while before I was performing live-cell imaging, I'm starting to toy with the idea of fixing the cells first, as that will positively impact some other things I want to try.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Hence my question:&lt;/strong&gt; Will fixing the cells with 4% formaldehyde in PBS (standard ICC/IF protocol) affect the pH of the lysosomes? Would methanol fixation do the same thing? Any other suggestions for increasing signal?&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-10-23T13:44:36.840" Title="How does formaldehyde/PBS or methanol fixation of cells affect lysosomal pH?" Tags="&lt;cell-biology&gt;&lt;lab-techniques&gt;&lt;cell-culture&gt;&lt;protocol&gt;&lt;fluorescent-microscopy&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10477" PostTypeId="1" AcceptedAnswerId="10478" CreationDate="2013-09-17T17:33:16.773" Score="2" ViewCount="3489" Body="&lt;p&gt;The preferred question would have been what is the total number of cells in a full term human foetus and how many cell divisions are required to reach that number. However estimates of total cell numbers in foetus could not be found. From the abstract of the &lt;a href=&quot;http://informahealthcare.com/doi/abs/10.3109/03014460.2013.807878&quot; rel=&quot;nofollow&quot;&gt;July 5, 2013&lt;/a&gt; article published in Annals of Human Biology, the adult human body consists of approximately $3.72 \times 10^{13}$ cells (37.2 Trillion). The question is: what would be the approximate number of cell divisions required to reach that number (Ignoring the fact that different tissues may reach full differentiation at different times)?&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="107" LastEditDate="2013-09-18T01:20:41.983" LastActivityDate="2013-09-18T01:20:41.983" Title="How many consecutive cell divisions are required to form the adult human body from the single cell zygote?" Tags="&lt;human-biology&gt;&lt;development&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10478" PostTypeId="2" ParentId="10477" CreationDate="2013-09-17T18:46:29.197" Score="2" Body="&lt;p&gt;Sounds like just a math problem if you allow that cells dying and different rates of division are not to be accounted for:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$2^N = 40 \times 10^{12}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$log_2(40 \times 10^{12}) = N$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$N = 45.185$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so 45 or so divisions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;is that what you are looking for? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="107" LastEditDate="2013-09-18T01:19:41.010" LastActivityDate="2013-09-18T01:19:41.010" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="10479" PostTypeId="1" CreationDate="2013-09-17T23:14:33.830" Score="5" ViewCount="542" Body="&lt;p&gt;Viruses at this period of time do not fit the current definition of life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Much of the reasoning behind this is that we currently believe that all life must be made up of cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, many biologist/scientists say that viruses are not living because all they are is just chemicals carrying out their predefined chemistry. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has anyone every considered the fact that cells, the supposed building blocks of life, themselves simply only carry out predefined chemical actions? All actions cells carry out are chemically driven, not consciously or spiritually driven. Cells do not make choices, they follow chemical directions present in their DNA and RNA. Viruses act very similarly, following the action transcribed in their DNA or RNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can we really even draw a defined line of what life is?&lt;/p&gt;&#xA;" OwnerDisplayName="undefined" LastEditorUserId="4101" LastEditDate="2013-09-25T00:06:31.790" LastActivityDate="2015-06-19T22:16:41.377" Title="Changing the definition of life?" Tags="&lt;virus&gt;&lt;life&gt;" AnswerCount="2" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10480" PostTypeId="1" CreationDate="2013-09-18T01:24:41.280" Score="4" ViewCount="678" Body="&lt;p&gt;I want to buy some sheeps in order to eat my garden's grass.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much grass does a sheep eat each day ??&lt;/p&gt;&#xA;" OwnerUserId="4489" LastActivityDate="2013-09-18T01:24:41.280" Title="how much grass does a sheep eat in square meters per day?" Tags="&lt;zoology&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2013-09-20T15:14:52.273" ContentLicense="CC BY-SA 3.0" />
  <row Id="10481" PostTypeId="2" ParentId="10465" CreationDate="2013-09-18T09:00:48.387" Score="2" Body="&lt;p&gt;The following paper answers your question in detail:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18568020&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/18568020&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It seems like the following aa are responsible for the binding, but please refer to the paper for more details:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Val152,Tyr156,Asn157,Ser422,(Asp79)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4491" LastActivityDate="2013-09-18T09:00:48.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10482" PostTypeId="2" ParentId="10479" CreationDate="2013-09-18T14:03:39.093" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;...many biologist/scientists say that viruses are not living because everything they do is just chemicals carrying out their predefined chemistry.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't think that's correct. Many definitions of life exclude viruses because they lack the apparatus to perform the life functions themselves, especially reproduction. They don't seem to qualify as parasites because, when they've infected a cell, they no longer occupy a bounding structure (other then the cell itself.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When viruses are acting like a living thing, they look like misbehaving cell. Here's a similar puzzle; what organism is cancer? Viruses are basically rogue genes, just like cancer cells are basically rogue cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Organisms carrying out their predefined chemistry,&quot; is basically saying that living systems are deterministic. The interesting question is, &lt;em&gt;are very complex systems that emerge from stochastically-driven events themselves deterministic?&lt;/em&gt; Are organisms like a clockwork?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably you should check out Schrödinger's &lt;em&gt;What is Life?&lt;/em&gt; to get started.&lt;/p&gt;&#xA;" OwnerUserId="3336" LastActivityDate="2013-09-18T14:03:39.093" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="10483" PostTypeId="2" ParentId="10479" CreationDate="2013-09-18T14:17:54.580" Score="16" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;How can really even draw a defined line of what life is?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's easy, really: just make one.  In the answer I &lt;a href=&quot;https://biology.stackexchange.com/a/9455/4101&quot;&gt;linked to&lt;/a&gt; I go into the reasons why viruses aren't alive (spoiler alert: no ribosomes) and what our current definition is, but the bigger question is &lt;strong&gt;why does it matter?&lt;/strong&gt;  We can draw the line wherever we want to, but it's still an arbitrary construct placed onto the universe by humans so we can sleep at night.  It's similar to intelligence.  We draw arbitrary lines around primates and dolphins and elephants and pigs and what have you, because they're the smartest and most thinking, but that's only for our own (legal) convenience.  Intelligence and awareness is a spectrum, there needn't be a point beyond which you &quot;count.&quot;  There's no reason life can't be the same way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit 1.5 years later to add a &lt;a href=&quot;http://aeon.co/video/science/what-is-life-is-death-real-why-its-so-hard-to-tell/&quot; rel=&quot;nofollow noreferrer&quot;&gt;short, somewhat fanciful video&lt;/a&gt; I just watched, it goes into some of the complexity and difficulty with defining life; viruses show up about half way through.  It waxes philosophical toward the end, but that's sort of my point.  Arbitrary delineations are just that.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-06-19T22:16:41.377" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10486" PostTypeId="2" ParentId="10470" CreationDate="2013-09-18T18:01:27.020" Score="0" Body="&lt;p&gt;i think the chance of a sequencing platform calling something A/A when the microarray calls it B/B is virtually nil. Just doesn't happen.&lt;/p&gt;&#xA;" OwnerUserId="1241" LastActivityDate="2013-09-18T18:01:27.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10487" PostTypeId="1" CreationDate="2013-09-18T19:21:58.493" Score="3" ViewCount="4904" Body="&lt;p&gt;I'm talking about moments when you watch a film and you bristle, or when you listen to music, etc.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What kind of neurotransmitter flow changes?&lt;/p&gt;&#xA;" OwnerUserId="4497" LastEditorUserId="1231" LastEditDate="2013-09-19T03:46:30.603" LastActivityDate="2019-08-14T02:59:54.663" Title="What happens in your brain when you receive information which causes you to bristle?" Tags="&lt;neuroscience&gt;&lt;neurotransmitter&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10489" PostTypeId="2" ParentId="10476" CreationDate="2013-09-18T21:33:32.950" Score="1" Body="&lt;p&gt;In my opinion, cell fixation shouldn't change the pH. However unbuffered formalin will oxidize and lower the pH, but using PBS should buffer around pH 7.&#xA;Maybe Glutaraldehyde fixation would also be an option, if the others are not working...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this website by leica very useful, maybe it will also help you:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.leicabiosystems.com/pathologyleaders/fixation-and-fixatives-2-factors-influencing-chemical-fixation-formaldehyde-and-glutaraldehyde/&quot; rel=&quot;nofollow&quot;&gt;http://www.leicabiosystems.com/pathologyleaders/fixation-and-fixatives-2-factors-influencing-chemical-fixation-formaldehyde-and-glutaraldehyde/&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4491" LastActivityDate="2013-09-18T21:33:32.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10490" PostTypeId="2" ParentId="10475" CreationDate="2013-09-19T09:03:48.590" Score="2" Body="&lt;p&gt;My first thought was to suggest a mixed effects model, so I will describe that first. But having had a Google there are models known as &quot;Conditional logistic regression&quot; models in which you can include any data structure as a covariate, which may be more appropriate, but I cannot vouch for them as I haven't used them. I would suggest reading the documentation.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Mixed effects models&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;I only know how to do this in R (stats language - &lt;a href=&quot;http://www.r-project.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;www.r-project.org&lt;/a&gt;), but if you're using PLINK (so presumably also UNIX) R is pretty straightforward.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a couple of packages available for mixed effects models, my personal preference is function &lt;code&gt;lme&lt;/code&gt; in package &lt;code&gt;nlme&lt;/code&gt; (&lt;a href=&quot;http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/lme.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;CRAN link&lt;/a&gt;). This type of model allows you to specify 2 types of independent variable (e.g. age, BMI, ethnicity... in your case);&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Fixed effects - such as age, sex (something that is a phenotype of the samples),&lt;/li&gt;&#xA;&lt;li&gt;Random effects - such as batch or other &quot;technical&quot; consideration,&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This means you can format a model as you would before, but include an additional &quot;random effects&quot; term for your &quot;matched&quot; variable;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;model = lme( fixed= outcome ~ exposure + covariate1, random= 1|matched )&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Conditional logistic regression models&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;In the &lt;code&gt;survival&lt;/code&gt; package for R there is a function called &lt;code&gt;clogit&lt;/code&gt; (&lt;a href=&quot;http://stat.ethz.ch/R-manual/R-devel/library/survival/html/clogit.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;CRAN link&lt;/a&gt;) which seems to do exactly what you want. Although I have never used it myself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I can gather this allows you to run a logistic regression with an additional covariate &lt;code&gt;strata(matched)&lt;/code&gt;, so your model may look like&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;model = clogit( outcome ~ exposure + covariate1 + strata(matched) )&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Disclaimer!&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;This may not be exactly what you are after, as I'm not familiar with your data, so I would suggest heading over to &lt;a href=&quot;https://stats.stackexchange.com/&quot;&gt;https://stats.stackexchange.com/&lt;/a&gt; as well, and searching for questions about regression analysis and paired observations - if none answer your question then ask a fresh one.&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2017-04-13T12:44:17.897" LastActivityDate="2013-09-19T09:03:48.590" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10491" PostTypeId="2" ParentId="9941" CreationDate="2013-09-19T10:59:18.743" Score="0" Body="&lt;p&gt;I am not sure whether I understand your question right, but prolactin levels can be abnormal under several conditions like cancer, drug abuse, stress, breast surgery etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its secretion is mainly controlled (inhibited) by Dopamine. Other hypothalamic factors like VIP, TRH, PRH etc. are enhancers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please specify your question for a detailed answer.&lt;/p&gt;&#xA;" OwnerUserId="4491" LastEditorUserId="4491" LastEditDate="2013-09-19T20:31:44.170" LastActivityDate="2013-09-19T20:31:44.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10492" PostTypeId="1" CreationDate="2013-09-19T11:20:43.810" Score="14" ViewCount="69279" Body="&lt;p&gt;Which cells in a human have the longest lifespan? Which cell has the shortest lifespan?&lt;/p&gt;&#xA;" OwnerUserId="4323" LastEditorUserId="4150" LastEditDate="2013-09-19T17:37:25.917" LastActivityDate="2016-10-27T12:06:19.437" Title="Which human cells have the longest and shortest lifespan?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10493" PostTypeId="1" AcceptedAnswerId="10496" CreationDate="2013-09-19T15:42:50.170" Score="6" ViewCount="10190" Body="&lt;p&gt;Wikipedia says :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The kidneys secrete a variety of hormones, including erythropoietin,&#xA;  and the enzyme renin.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Can a substance be both an enzyme and a hormone ? Why is renin both an enzyme and a hormone ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2018-04-25T20:20:38.010" Title="Renin - enzyme or hormone?" Tags="&lt;endocrinology&gt;&lt;enzymes&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10494" PostTypeId="2" ParentId="10470" CreationDate="2013-09-19T15:47:45.037" Score="1" Body="&lt;p&gt;The purpose of validating is to find genuine SNPs and not those caused by sequencing or amplification errors. It is extremely unlikely you will have a false homozygous SNP as a result of error. Just think about it. The same error, at the same base, occuring 80%+ of the time? Its not going to happen unless you have low coverage, and these SNPs should be thrown out anyway. You may have some cases where a genuine heterozygous SNP is called as a homozygous SNP. But that isnt much of a problem. It is still a genuine SNP. It would only be a problem if you were only interested in homozygous SNPs, in which case you will just need to validate everything biochemically, which you will need to do anyways.&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-09-19T15:47:45.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10495" PostTypeId="2" ParentId="10492" CreationDate="2013-09-19T15:54:35.247" Score="5" Body="&lt;p&gt;Some mature neurons can last a lifetime.  Gastrointestinal cells such as those in the colon might be shortest-lived, and skin may give them a run for their money.  However, depending on how you define lifespan, egg and sperm cells could beat those numbers.  Also, some immune cells only last a few days under certain scenarios, such as the aptly-named short-lived plasma cells.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-19T15:54:35.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10496" PostTypeId="2" ParentId="10493" CreationDate="2013-09-19T15:56:37.960" Score="8" Body="&lt;p&gt;Yes, something can be both a hormone and an enzyme. There are a group of hormones known as peptide hormones. These are proteins (such as enzymes) that act as hormones indirectly (and maybe directly too?). A hormone is a chemical secreted by a cell that has some effect on another cell elsewhere in the body. In this case, the chemical just happens to be an enzyme. &lt;a href=&quot;http://en.wikipedia.org/wiki/Peptide_hormone&quot;&gt;You can read about them on Wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Renin is secreted by the kidney, but its involved in arterial vasoconstriction (outside of kidney cells), so it is a hormone. And its also a peptide/enzyme, so it is considered both a hormone and an enzyme&lt;/p&gt;&#xA;" OwnerUserId="4199" LastEditorUserId="4199" LastEditDate="2013-09-19T18:06:12.220" LastActivityDate="2013-09-19T18:06:12.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10497" PostTypeId="1" AcceptedAnswerId="10501" CreationDate="2013-09-19T16:23:58.437" Score="1" ViewCount="446" Body="&lt;p&gt;I have searched the net and I have not been able to come up with an clear answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt; Here is the para quoted from Nature &lt;a href=&quot;http://www.nature.com/news/medical-research-cell-division-1.13273&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/news/medical-research-cell-division-1.13273&lt;/a&gt;&#xA;&lt;strong&gt;&quot;So began WI-38, a strain of cells that has arguably helped to save more lives than any other created by researchers. Many of the experimental cell lines available at that time, such as the famous HeLa line, had been grown from cancers or were otherwise genetically abnormal. *&lt;em&gt;WI-38 cells became the first 'normal' human cells available&lt;/strong&gt; in virtually unlimited quantities to scientists and to industry and, as a result, have become the most extensively described and studied normal human cells available to this day&quot;.&lt;/em&gt;*&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="4216" LastEditDate="2013-09-19T18:06:11.500" LastActivityDate="2013-09-19T21:32:34.423" Title="How is it that the WI-38 cell line isolated by Hayflick in 1962 is still very much around and not affected by the 'Hayflick Limit'?" Tags="&lt;cell-biology&gt;&lt;senescence&gt;&lt;cell-culture&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10500" PostTypeId="1" CreationDate="2013-09-19T20:31:22.740" Score="2" ViewCount="99" Body="&lt;p&gt;What other educational topics are linked to the Nitrogen Cycle? I am a Science teacher, and I need to organise my lessons. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="4505" LastActivityDate="2014-10-31T12:23:53.080" Title="What Biology topics are linked to the Nitrogen Cycle?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ClosedDate="2013-09-22T12:51:49.413" ContentLicense="CC BY-SA 3.0" />
  <row Id="10501" PostTypeId="2" ParentId="10497" CreationDate="2013-09-19T21:10:34.313" Score="5" Body="&lt;p&gt;The answer is that the majority of the cells were frozen from very early in their Hayflick lifetimes e.g. after 9 population doublings. They have been thawed out judiciously and only as needed thus preserving a lot of frozen stocks.  When an ampule of cells frozen at, for instance 9 population doubling, is thawed, the cells pick up where they left off and still have 41 doubling a to go.  So the magic of exponential growth combined with the fact that they keep dividing after being thawed has made for a decades- long supply . Does this answer the question to your satisfaction?&lt;/p&gt;&#xA;" OwnerUserId="4506" LastActivityDate="2013-09-19T21:10:34.313" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10502" PostTypeId="2" ParentId="10497" CreationDate="2013-09-19T21:32:34.423" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/WI-38#History&quot; rel=&quot;nofollow&quot;&gt;WI-38 are the cell lines which led to the proposal of the Hayflick limit&lt;/a&gt; and are the classic example of cells which will only divide ~40 times.  they are not exempt - they are the example that proved the rule. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lots of cell lines are commonly available, but have to recultivated regularly from animal/tissue source.  If they can be frozen, then the extraction of new cells doesn't happen so often without exceeding the limit of divisions.  This allows the cell lines to be used widely for experiments despite the limitations on their division in culture. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other cell lines like HeLa and other tumor cells or Stem Cells can, under the proper conditions, divide without limit and are easier to culture in large volumes, but are often inappropriate for a given research project.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-09-19T21:32:34.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10503" PostTypeId="2" ParentId="10500" CreationDate="2013-09-19T22:10:10.763" Score="0" Body="&lt;p&gt;The nitrogen cycle is a highly biological process. Nitrogen gas is ~75% of the earth's atmosphere and N&lt;sub&gt;2&lt;/sub&gt; is the most chemically stable form of Nitrogen for conditions in the Earth's crust.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nitrogen is one of the four most essential and universal elements to terrestrial life (Carbon Hydrogen and Oxygen being the others).  &lt;a href=&quot;http://en.wikipedia.org/wiki/Nitrogen_cycle&quot; rel=&quot;nofollow&quot;&gt;Nitrogen fixation&lt;/a&gt;, the name given to the various processes which make chemically reactive forms of Nitrogen available to living things. Ammonia (NH&lt;sub&gt;3&lt;/sub&gt; / NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;) and Nitrites / Nitrates (NO&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt;, NO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt;) are chemically unstable compared to N&lt;sub&gt;2&lt;/sub&gt; and the conventional biosynthetic processes in the cell can use any of these forms to make proteins, nucleic acids and other biologically active molecules necessary for life.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ammonia and similar compounds like Urea come from the biological byproducts of  living cells - waste.  These are readily recycled in the soil by plants and microorganisms and I imagine some animals and insects.  Nitrogen is a limiting resource for living things and most biomes are pretty efficient at recycling reduced nitrogen from primary (NH&lt;sub&gt;3&lt;/sub&gt;) secondary (NHR&lt;sub&gt;2&lt;/sub&gt;), tertiary (NR&lt;sub&gt;3&lt;/sub&gt;) and quaternary amines (NR&lt;sub&gt;4&lt;/sub&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the biosphere has a great demand for bio-useful nitrogen and in most places on earth in deep water and soil microorganisms can break down N&lt;sub&gt;2&lt;/sub&gt; directly into nitrates/nitrites. This happens deep underwater or underground because the enzymes which perform this activity are delicate and ruined by O&lt;sub&gt;2&lt;/sub&gt;.  This process is entirely performed by anaerobic microorganisms. In recent decades, the ecological importance of subterranean microbial communities has become better appreciated for the complex structure and ecological roles it plays. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An interesting side note to this is that up to the early 20th century, the growth of life and human civilization was really limited by the intense labor required to grow food.  While hydrogen oxygen and carbon are essentially free - obtained from water, atmospheric oxygen and CO&lt;sub&gt;2&lt;/sub&gt; by plants, Nitrogen was the limiting factor in many cases to growing more crops or animals for food.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Haber_process&quot; rel=&quot;nofollow&quot;&gt;The Haber process&lt;/a&gt;, which converts nitrogen and hydrogen gas under high temperature and pressure into ammonia over a catalyst was such an important discovery - it allowed the industrial preparation of effective fertilizers and &lt;a href=&quot;http://hnrs353.wordpress.com/science-section/the-haber-process-and-the-green-revolution/&quot; rel=&quot;nofollow&quot;&gt;was instrumental in creation of the green revolution&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3340" LastEditDate="2014-10-31T12:23:53.080" LastActivityDate="2014-10-31T12:23:53.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10504" PostTypeId="1" CreationDate="2013-09-17T02:01:11.467" Score="1" ViewCount="1166" Body="&lt;p&gt;It is said that L-amino acids such as histidine, methionine, aspartic acid, glutamic acid, asparagine and glutamine can revert plant stomata closure, increase quality of fruits and assist maturity. It is also said that the best way to apply is through foliar feeding.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to start experimenting with different amino acid foliar feeds but would first like to know if there is a recommended maximum/minimum/recomended Parts per million(PPM) , for foliar feeding of these compounds.&lt;/p&gt;&#xA;" OwnerUserId="4508" OwnerDisplayName="damien" LastEditorUserId="1320" LastEditDate="2013-11-20T18:34:30.027" LastActivityDate="2014-07-18T22:23:11.920" Title="What is the recommended PPM when foliar feeding L-amino acids" Tags="&lt;plant-physiology&gt;&lt;amino-acids&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10505" PostTypeId="2" ParentId="10504" CreationDate="2013-09-17T13:21:20.370" Score="1" Body="&lt;p&gt;I know that some of the amino acids you listed are commonly found in fish fertilizer. I haven't read any studies on the use of these amino acids individually and not sure where you would purchase them separately. If you're just experimenting in your own garden I would just use fish fertilizer according to the label directions. If you look for fish fertilizer studies you'll probably find more info.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I've never heard of these opening up the stomata of the plants. The only references I've read indicate that foliar sprays are best applied in the early morning or late day when the stomata is already open. This is how the nutrients get absorbed from the leaves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know that I would want to intentionally manipulate stomata closure. The plant knows when it needs to breath.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where did you read the above info? I'd be interested in seeing it.&lt;/p&gt;&#xA;" OwnerUserId="6581" OwnerDisplayName="OrganicLawnDIY" LastActivityDate="2013-09-17T13:21:20.370" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10506" PostTypeId="2" ParentId="10217" CreationDate="2013-09-20T03:22:11.367" Score="-1" Body="&lt;p&gt;Neuroscience is my specialty.  What we call consciousness is thought to be an evolutionary elaboration of a property of cells called &quot;irritability&quot;, which is the cell's ability to respond to signals from its environment.  There are many manifestations of this: chemicals binding to protein receptors, light interacting with proteins (as in photosynthesis), mechanical forces causing cell movement, bacterial chemo-taxis, and the list goes on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The analogy is like this.  What we call eating and elimination are analogous to cell metabolism.  As a whole organism we must eat to replenish the body, and eliminate the waste produced. A single cell must also absorb nutrients to maintain itself and eliminate the waste products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, it is like a fractal.  The same functions displayed by individual cells also manifest at the level of the whole organism. So, as the GI tract is the organ analogous to cell metabolism, the nervous system is the organ analogous to cell irritability.  One could imagine that what we experience as our personal consciousness is in fact like taking an integral over the irritability of all the cells in our nervous system.  Many people focus on the neurons, but all the cells in the brain contribute to the brain's function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, this form of explanation is not really an explanation as much as it is a description of our biology.  The obvious question arises: why are cells irritable? Because, irritability is basically the individual consciousness of an individual cell.  Well, one then realizes that the response properties of cells to stimuli come from the action of the molecules and forces that make up the cell. The immediate forces are non-covalent interactions, mainly poorly understood even in terms of physics, such as forms of adhesion (consider Velcro or glue). These are emergent properties that stem from the assemblage of molecules of which cells are composed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But let us grant that physicists eventually come to understand such &quot;derived&quot; forces in terms of the elementary four forces of the universe: electromagnetism, gravity, strong and weak nuclear.  Then, it is clear that there is a potential contained in these forces to combine in ways that cause complex molecular assemblies that self-organize and display irritability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, the issue of consciousness presumably links back to somehow being an inherent emergent property of the forces of nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, this is all relatively uncontroversial, but building such a chain of explanation is not really an explanation as much as just being a description of how things are organized in the world.  And I think it is clear to any thinking person that a description of something is not the same as an explanation of something.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if you follow this far, then you can appreciate why the Greeks thought that Atlas, who held up the world, stood on the back of a tortoise, and this tortoise was on top of another tortoise who was on top of another tortoise, all the way to infinity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We have simply replaced Atlas and the tortoises with language of modern science.  It is still an infinite regress.  The short answer to &quot;why are things conscious&quot; is that it seems to be a property of the universe to display consciousness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, there is one great man who thought about this problem and constructed what I consider the best explanation.  This was Gottfried Leibniz, the man who invented calculus.  Leibniz invented the idea of a &quot;monad&quot;, and he considered monads as the basic units, the atoms, in the sense of being the indivisible units of reality.  The monad, as an atom, is pure consciousness.  So, Leibniz came to the conclusion that the reason there is consciousness is because consciousness is the fundamental building block of reality.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Monads are what everything is made of: us, cells, atoms, quarks, electrons, etc.  These are all different forms of monads.  According to Leibniz, they are all different forms of consciousness, and they combine in fractal patterns to make forms of consciousness within forms of consciousness within forms of consciousness.  And this pattern goes in both directions from the infinitely small to the infinitely large.  According to this idea, just because something does not seem to be conscious in the same form we are conscious does not mean it is not conscious. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is how Leibniz solved what is called the &quot;mind body problem&quot;, which is really the heading under which your question falls.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If one wishes merely for intellectual understanding of the nature of our consciousness, it is my opinion that Leibniz' ideas are the best available.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you wish to go beyond mere intellectual understand to a deeper level of awareness of these issues, then I suggest you look up and study the works of a writer named Patanjali.&lt;/p&gt;&#xA;" OwnerUserId="4510" LastEditorUserId="4510" LastEditDate="2013-09-20T03:33:53.490" LastActivityDate="2013-09-20T03:33:53.490" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10507" PostTypeId="2" ParentId="8282" CreationDate="2013-09-20T03:49:30.893" Score="12" Body="&lt;p&gt;While Luke's answer is perfectly correct, the answer can be given in a more intuitive manner.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, the main point is that it is increased positive voltage (inside the axon) that opens the sodium ion channels to propagate the action potential. The question is: how fast can this voltage get to the sodium channels?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In an unmyelinated axon, the movement of voltage across the membrane is due to ion flux (i.e the flow of ions through the channels, the current), and this movement is limited by the time it takes for the sodium ions to diffuse into the axon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, in a myelinated axon, the first bolus of sodium enters at the axon hillock.  Because the capacitance is low, this means that the voltage can propagate down the axon, not by ion diffusion, but as an electrical field.  The electrical field carries the voltage force much much faster than ion diffusion. Therefore, when the ions first enter, the voltage force moves, basically at the speed of light to the next node, where the voltage force opens the sodium ion channels there.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, by allowing the voltage to be carried by the electrical field, the effect is that the distance between the nodes is effectively eliminated.  Myelinated axons conduct faster because they are &gt;&gt;effectively&amp;lt;&amp;lt; much shorter than unmyelinated axons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, the optimized distance between nodes mentioned by Luke is exactly that distance in a given type of neuron's axon where the voltage force decays to the bare minimum needed to activate the sodium ion channels at the next node.&lt;/p&gt;&#xA;" OwnerUserId="4510" LastActivityDate="2013-09-20T03:49:30.893" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10508" PostTypeId="2" ParentId="7553" CreationDate="2013-09-20T04:07:17.557" Score="2" Body="&lt;p&gt;The short answer is: neurons do NOT always die quickly when deprived of nutrients.  The longer answer is the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am a professional researcher in brain ischemia (ischemia = no blood flow), which is the topic of the question. Armatus' answer was correct insofar as neurons have very limited energy reserves and therefore loose ATP very quickly. Gianpaolo R gave the correct time course for ATP loss.  However, Gianpaolo R's explanation of cell death applies only if the ischemia lasts for about 20-30 minutes.  In this case, the cells swell and lyse by a process called necrosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if the duration without blood flow (which is the duration with no oxygen and nutrients) is less than 20 - 30 minutes, then the cells do not die by necrosis.  It is less well-known to lay people, but well-known to neurologists that the neurons will die days or weeks after the ischemia in a process called &quot;delayed neuronal death&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is also less known to lay people is that if the duration of ischemia is less than about 7 minutes (this depends on the species, e.g. human, rat mouse, etc), no neurons die, and in fact, they are protected for a short while from a similar insult.  This is a phenomenon known as &quot;ischemic preconditioning&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The explanation of necrosis is uncontroversial.  However, no one knows what causes delayed neuronal death or preconditioning responses.  The excitotoxicity mentioned by Armatus is a popular theory in the field, that has been largely discredited for a variety of reasons I will not go into here.  It is also popular to believe the delayed neuronal death is due to a process called apoptosis, but this also has fallen out of favor in recent years.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, right now, there are many competing ideas as to why the neurons die in a delayed fashion, and the simple fact is, no one knows for sure why they die in this way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you may imagine, being a worker in this field, I have a theory that I think is the most feasible of all.  But it is a mathematical theory that applies to any injured cell, not just neurons deprived of blood flow.  The theory is very simple conceptually.  It says that when a cell is injured it gets damaged (call it D), but also activates genetic responses to protect itself (call this S).  If the genetic protective responses are greater than the damage, that is, if S &gt; D, then the cell recovers and lives.  If the damage is greater than the stress responses (D &gt; S), the cell dies.  The rate at which the cell recovers or dies is inversely proportional to |D - S| after D and S have run their course interacting with each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This last statement precisely answers your questions. Neurons will die quickly when |D-S| is a large number.  They will die slowly when |D-S| is a small number.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, this is just a qualitative description. The theory actually consists of mathematical equations that predict many things. You will note it is a true theory and does not rely on the biological specifics of the system under study. I am currently measuring the theory in my lab.  I am confident it will be a very useful theory not only for explaining brain ischemia, but many other forms of cell injury.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The original article detailing this theory can be obtained &lt;a href=&quot;http://www.med.wayne.edu/degracialab/PDFs/2012B1%20DeGracia%20et%20al%20jcbfm201210a.pdf&quot; rel=&quot;nofollow&quot;&gt;at this link.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4510" LastEditorUserId="4510" LastEditDate="2013-09-20T04:21:30.753" LastActivityDate="2013-09-20T04:21:30.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10509" PostTypeId="1" CreationDate="2013-09-20T04:34:45.260" Score="2" ViewCount="59" Body="&lt;p&gt;What's behind the amazing colour combinations in pests &amp;amp; insects ? Do this colour combination signals any character/ poison of the pest/insect ? &lt;/p&gt;&#xA;" OwnerUserId="4323" LastEditorUserId="1306" LastEditDate="2013-09-20T05:15:27.447" LastActivityDate="2013-09-20T05:15:27.447" Title="What's behind the amazing colour combinations in pests &amp; insects?" Tags="&lt;zoology&gt;&lt;pigmentation&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10510" PostTypeId="2" ParentId="10493" CreationDate="2013-09-20T04:54:59.993" Score="1" Body="&lt;p&gt;Hormone is just a different class of protein and is not usually an enzyme. Peptide hormones have no catalytic potential and serve only as signaling ligands. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There can be secreted enzymes which is common in the digestive tract but these are not called hormones. Hormone is purely a signaling molecule. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-09-21T17:16:34.973" LastActivityDate="2013-09-21T17:16:34.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10512" PostTypeId="1" AcceptedAnswerId="10514" CreationDate="2013-09-20T13:47:38.247" Score="5" ViewCount="12363" Body="&lt;p&gt;Apparently in cardiomyocytes, there is an inward rectifying potassium channel that operates during phase 4 of the cardiomyocyte action potential.  I have heard that despite this potassium channel being referred to as an &lt;em&gt;inward rectifying channel&lt;/em&gt;, that &lt;em&gt;in vitro&lt;/em&gt; the channel in fact still transports potassium from the inside to the outside of the cell.  It appears that &lt;a href=&quot;https://en.wikipedia.org/wiki/Inward-rectifier_potassium_ion_channel&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt; seems to suggest otherwise (?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone please explain what the inward rectifier potassium channel does and its role in phase 4 of the myocyte action potential?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="20758" LastEditDate="2017-06-07T12:22:24.770" LastActivityDate="2017-06-07T12:22:24.770" Title="How do inward rectifier potassium channels work in the heart?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;cell-membrane&gt;&lt;electrophysiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10513" PostTypeId="2" ParentId="5589" CreationDate="2013-09-20T14:23:46.407" Score="5" Body="&lt;p&gt;Telomeres do not &quot;cause&quot; ageing as such - although you are right that they limit the number of times a somatic cell can divide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each time a cell divides the chromosomes are replicated in an imperfect way, and as such a small amount of DNA is lost from the end of the chromosome during each round of cell division. Telomeres are just extensions to the chromosomes, so that the DNA that is lost is not important. When a cell runs out of telomeres it ceases to divide. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However it is a big generalization to say that telomere length is therefore correlated with lifespan. For instance a recent study has shown that mice have telomeres 5-10x the length of humans, but live 30x shorter (1).&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Inter-species differences in lifespan&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Whilst I am no expert on these 2 plants, it is quite an obvious thing to say that organisms age at different rates. Mice, for instance, live 3 years in a protective environment, whereas humans can live 30x that. The difference is down to the life strategies acquired by natural selection: it is more advantageous for a mouse to develop very fast to reproductive maturity and have as many offspring as possible, because there is a very high mortality rate for mice. Conversely for humans, in takes more than a decade for us to reach reproductive maturity! Our &quot;rate&quot; of development/ageing is lower, which is completely related to our reproductive strategies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I imagine that a very similar story is true for plants - for some it will be advantageous for them to &quot;live fast, die young&quot;, whereas for others the best strategy might be to take a long time creating less, but more robust, offspring.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;At the molecular level&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;I have answered a related question previously (&lt;a href=&quot;https://biology.stackexchange.com/questions/2055/do-trees-age-on-a-microscopic-level/&quot;&gt;Do trees age on a microscopic level?&lt;/a&gt;) which might be of interest to you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, the phenotype of ageing is associated with irreparable damage at the molecular level - be it to DNA, organelles, protein aggregations... you name it! Organisms that have a higher metabolic rate, such as mice, accumulate this damage faster. This gives them the benefit of being able to reproduce much earlier, at the cost of reduced overall lifespan.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants age slightly differently, but at the genetic level much the same repair pathways are conserved throughout the kingdoms of life, with some alterations of course - for instance plants seem almost completely immune to cancer (2)! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I argue in the linked to question above, plants have a potentially indefinite replicative potential, as every cell has the capability of regenerating its telomeres, because plants do not have a conserved germ line as animals do - any cutting from a plant has the potential to create an entirely new plant. This varies from plant to plant of course, and plants are still susceptible to damage, they just have modified/adapted repair pathways to cope with their specific lifestyle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You ask whether it is the telomeres or the &quot;rate&quot; that differs between the plants - the answer is almost certainly a combination of both, amongst the other myriad of factors that influence lifespan!&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Refs&lt;/h3&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Colado, et al, 2013. &lt;strong&gt;Telomere dynamics in mice and humans&lt;/strong&gt;. &lt;em&gt;Seminars in hematology&lt;/em&gt; [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23956466&quot; rel=&quot;nofollow noreferrer&quot;&gt;PubMed&lt;/a&gt;]&lt;/li&gt;&#xA;&lt;li&gt;Doonan &amp;amp; Sablowski, 2010. &lt;strong&gt;Walls around tumours - why plants do not develop cancer&lt;/strong&gt;. &lt;em&gt;Nature reviews cancer&lt;/em&gt; [&lt;a href=&quot;http://dx.doi.org/10.1038/nrc2942&quot; rel=&quot;nofollow noreferrer&quot;&gt;DOI&lt;/a&gt;]&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2013-09-20T14:51:18.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10514" PostTypeId="2" ParentId="10512" CreationDate="2013-09-21T00:42:50.063" Score="2" Body="&lt;p&gt;According to Boron's medical physiology textbook:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Although inward rectifying potassium channels pass current better in&#xA;  the inward than the outward direction, the membrane potential (Vm) is&#xA;  typically never more negative than Ek (equilibrium potential of potassium across the membrane). Thus,net inward K+ current does&#xA;  not occur physiologically. As a result, the activation of GIRK&#xA;  channels (G protein coupled inwardly rectifying potassium channel)&#xA;  hyperpolarizes cardiac cells by increasing K+ conductance or outward&#xA;  K+ current.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="107" LastEditDate="2013-09-22T14:34:43.853" LastActivityDate="2013-09-22T14:34:43.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10518" PostTypeId="2" ParentId="10454" CreationDate="2013-09-21T07:38:05.610" Score="1" Body="&lt;p&gt;Fixation of phosphorous occurs when the chemical equations tip in favour of less soluble compounds. Plants are able to absorb Orthophosphate ions, such as H&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; and HPO&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;2-&lt;/sup&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;Orthophosphate is most available to plants at pH values near neutrality. It is believed that in relatively acidic soils, orthophosphate ions are precipitated or sorbed by species of Al(III) and Fe(III). In alkaline soils, orthophosphate may react with calcium carbonate to form relatively insoluble hydroxyapatite:&#xA;&lt;br&gt;&lt;br&gt;&#xA;3HPO&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;2-&lt;/sup&gt; + 5CaCo&lt;sub&gt;3&lt;/sub&gt;(s) + 2H&lt;sub&gt;2&lt;/sub&gt;O -&gt; Ca&lt;sub&gt;5&lt;/sub&gt;(PO&lt;sub&gt;4&lt;/sub&gt;)&lt;sub&gt;3&lt;/sub&gt;(OH)(s) +5HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; + OH&lt;sup&gt;-&lt;/sup&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;Environmental Chemistry, Seventh Edition&lt;/em&gt; -Stanley E. Manahan&lt;/p&gt;&#xA;&lt;p&gt;This does tend to make it more difficult for plants to obtain their phosphorous when it is stuck to something that they cannot absorb, but it is not hopeless. These equations are equilibria, so they can be made to go both directions by adding or removing reagents from each side.&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The plants will pull from the left side of the equations by removing the orthophosphate ions. More will be released to maintain the equilibrium.&lt;/li&gt;&#xA;&lt;li&gt;In acidic or basic environments, rainwater will serve as a base or acid to push the equations from the right.&lt;/li&gt;&#xA;&lt;li&gt;Decaying organic matter releases orthophosphates that the plant can absorb.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;In this way, plants living in acidic or basic environments would still obtain enough phosphorous.&lt;/p&gt;&#xA;" OwnerUserId="1522" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-09-21T07:38:05.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10519" PostTypeId="1" AcceptedAnswerId="19625" CreationDate="2013-09-21T09:58:39.867" Score="7" ViewCount="82002" Body="&lt;p&gt;If the extracellular potassium concentration surrounding a myocyte increases, then the potassium gradient accross the cell membrane decreases, and therefore the resting membrane potential will become more positive.  Similarly, if extracellular potassium decreases, the resting membrane potential will be more negative.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With this in mind, how does the heart rate change when extracellular potassium concentration increases/decreases?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="6422" LastEditDate="2014-07-12T20:27:00.333" LastActivityDate="2016-04-09T09:23:07.897" Title="What is the effect of extra-cellular potassium concentration on heart rate and conduction velocity?" Tags="&lt;cardiology&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10520" PostTypeId="1" CreationDate="2013-09-21T13:24:52.153" Score="4" ViewCount="1191" Body="&lt;p&gt;As far as i know when you accept cocaine in your blood some cocaine molecules reach some synapses in your brain and fill some Reuptake tunnels preventing the cell to simply &quot;do not know that fired neurotransmitters have achieved their task&quot; and doing so the cell fires neurotransmitters again becuase &quot;it&quot; simple do not know that &quot;it&quot; have achieved its task.&#xA;In this case cocaine molecules fill Reuptake tunnels in Dopamin Serotonin and Norepinephrine&#xA;orientated neurons.But since the firing occurs when an electrical signal occur how the neurotransmitters are fired again when such electrical signal does not exist?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If im mistaken in my physiology knowledge explained above please correct me!&lt;/p&gt;&#xA;" OwnerUserId="4497" LastEditorUserId="9943" LastEditDate="2015-03-31T01:07:03.960" LastActivityDate="2015-03-31T01:07:03.960" Title="What happens in the synapse when cocaine administration occurs in the human brain" Tags="&lt;neuroscience&gt;&lt;neurotransmitter&gt;&lt;neurophysiology&gt;&lt;synapses&gt;&lt;cocaine&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10521" PostTypeId="2" ParentId="9941" CreationDate="2013-09-21T16:00:56.633" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://www.webmd.com/a-to-z-guides/prolactin-15129&quot; rel=&quot;nofollow&quot;&gt;Prolactin is a hormone which is produced by the pituitary gland&lt;/a&gt;.  Prolactin is named because it was found to be elevated in women who are lactating, its also produced by men and in elevated levels during sleep. Because of this, like many blood factors and hormones it probably has more than a single purpose. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When there is an abnormal growth from the pituitary gland, since the tissue produces prolactin, &lt;a href=&quot;http://www.mayoclinic.com/health/pituitary-tumors/DS00533/DSECTION=symptoms&quot; rel=&quot;nofollow&quot;&gt;abnormal pituitary tissue can also produce extraordinary amounts of prolactin&lt;/a&gt;. I don't think this means that its a cancer, but its a sign that there is an unusual pituitary condition. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2376090/&quot; rel=&quot;nofollow&quot;&gt;It can even be the result of taking some drugs&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of these tests are from experience - we find that this happens a lot, but the causes are usually not understood well. Cancers in particular are quite unpredictable and can have many different properties from one case to another.  &lt;a href=&quot;http://bmb.oxfordjournals.org/content/75-76/1/81.full&quot; rel=&quot;nofollow&quot;&gt;Pituitary tumors are the most common central nervous system tumors, so common they are found in autopsies 3-27% of the time, often never having been found previously&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-09-21T16:00:56.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10522" PostTypeId="1" AcceptedAnswerId="10537" CreationDate="2013-09-21T16:47:05.580" Score="3" ViewCount="147" Body="&lt;p&gt;In reptiles, the sound is conducted from the tympanic membrane to the inner ear by a single bone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the disease otosclerosis the stapes of humans become fused to the other middle ear bones( or to the oval window ). This disease leads to the loss of hearing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is - From what seems like superficial resemblance between otosclerosis and having one bone in reptiles, what is the difference between the two that leads to loss of hearing in one case but not in another ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3624" LastEditDate="2014-03-27T14:08:01.783" LastActivityDate="2014-03-28T08:39:42.740" Title="Difference in reptile inner ear and otosclerosis" Tags="&lt;physiology&gt;&lt;hearing&gt;&lt;herpetology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10523" PostTypeId="1" AcceptedAnswerId="10536" CreationDate="2013-09-21T19:40:37.663" Score="2" ViewCount="3210" Body="&lt;p&gt;It ought to be some combination of C, O, and H, I presume. But really why should I care if eggshell gets in my eggs while I'm cooking? &lt;/p&gt;&#xA;" OwnerUserId="1913" LastEditorUserId="107" LastEditDate="2013-09-21T20:07:42.147" LastActivityDate="2015-06-16T13:32:51.927" Title="What is the chemical composition of an egg shell?" Tags="&lt;ornithology&gt;&lt;organic-chemistry&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="10524" PostTypeId="1" CreationDate="2013-09-21T19:49:11.500" Score="1" ViewCount="2194" Body="&lt;p&gt;I want to understand why the face becomes dry after shaving and if shaving affects hormones? I've heard that after shaving, hair grows back faster, why? Shaving damages hair follicles and they become inflamed. One could get an infection JUST by shaving because tissue is ripped from the hair follicles. So maybe the increase in hair growth can be attributed to the natural blood rush that brings nutrients to the damaged follicles when they are inflamed after shaving....&lt;/p&gt;&#xA;" OwnerUserId="1913" LastEditorUserId="1306" LastEditDate="2013-09-22T17:04:29.813" LastActivityDate="2013-09-26T21:43:28.517" Title="Why does shaving dehydrate the skin? Is there an hormonal effect involved?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="10527" PostTypeId="1" AcceptedAnswerId="10529" CreationDate="2013-09-20T17:31:10.700" Score="3" ViewCount="153" Body="&lt;p&gt;It's in the news that some experiment was able to capture some alien specimens during a meteor shower:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ibtimes.com/aliens-are-here-scientists-say-they-have-proof-alien-life-there-should-be-plenty-skepticism-1408322&quot; rel=&quot;nofollow&quot;&gt;http://www.ibtimes.com/aliens-are-here-scientists-say-they-have-proof-alien-life-there-should-be-plenty-skepticism-1408322&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite all the skepticism that has already been said about this finding, what would be a proof that such specimem came from outer space? Is there any established protocol to assure that some form of life didn't come from Earth?&lt;/p&gt;&#xA;" OwnerUserId="657" OwnerDisplayName="woliveirajr" LastEditorUserId="4101" LastEditDate="2013-09-22T00:26:26.727" LastActivityDate="2013-09-22T00:26:26.727" Title="What would classify those findings of the University of Sheffield experiment as aliens?" Tags="&lt;astrobiology&gt;&lt;life&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10529" PostTypeId="2" ParentId="10527" CreationDate="2013-09-22T00:26:10.147" Score="3" Body="&lt;p&gt;I wouldn't say that there is an established protocol - claims of alien life are not commonly testable or even legitimate - but if something were discovered and deemed &quot;alive,&quot; a fairly good sign it was alien would be if its genetic makeup were based on something other than DNA or RNA.  That would be a dead giveaway the organism had side-stepped every known organism on Earth and while that doesn't prove alien-ness, it would certainly hint strongly of a non-Terran genesis.  There are arguments for and &lt;a href=&quot;https://en.wikipedia.org/wiki/Carbon_chauvinism&quot; rel=&quot;nofollow&quot;&gt;against&lt;/a&gt; carbon/&lt;a href=&quot;https://en.wikipedia.org/wiki/CHNOPS&quot; rel=&quot;nofollow&quot;&gt;CHNOPS&lt;/a&gt;-based life but that is nowhere near as definitive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, there's another really good technique.  I don't like to resort to &lt;em&gt;ad hominem&lt;/em&gt; attacks, but ideally the discovery should be by someone who has not &lt;a href=&quot;http://www.slate.com/blogs/bad_astronomy/2013/01/15/life_in_a_meteorite_claims_by_n_c_wickramasinghe_of_diatoms_in_a_meteorite.html&quot; rel=&quot;nofollow&quot;&gt;already made verifiable false claims on the same topic&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-22T00:26:10.147" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10530" PostTypeId="1" AcceptedAnswerId="10535" CreationDate="2013-09-22T01:21:20.340" Score="5" ViewCount="157" Body="&lt;p&gt;In 2012, the leading cause of death was Ischemic Heart Disease.  In 1st world countries, what is the life expectancy for people who do not die of Ischemic Heart Disease?  I'm interested in the USA, but I'm happy for you to provide information on other 1st world countries if USA data is unavailable.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My motivation for asking the question is a curiosity of how much our life expectancy would increase if IHD was abolished.&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2013-09-22T15:51:40.183" Title="What would life expectancy be in the western world in the absence of Ischemic heart disease?" Tags="&lt;cardiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10531" PostTypeId="1" CreationDate="2013-09-22T01:26:00.537" Score="3" ViewCount="105400" Body="&lt;p&gt;My blood pressure readings differ a lot when I read them while seated and while I lay down on a bed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tie the strap in both cases to my left bicep and rest for a minute before noting the readings down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, one reading I took was:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Seated: 130-85&#xA;Laying on bed: 115-75&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These were noted down one after the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure if there should be this much difference in the readings and is this something to be worried about.&lt;/p&gt;&#xA;" OwnerUserId="4519" LastEditorUserId="4519" LastEditDate="2013-09-22T02:40:38.923" LastActivityDate="2013-09-22T08:24:22.613" Title="Blood pressure difference while seated and laid down" Tags="&lt;blood-pressure&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ClosedDate="2013-09-22T12:51:13.160" ContentLicense="CC BY-SA 3.0" />
  <row Id="10532" PostTypeId="2" ParentId="10531" CreationDate="2013-09-22T08:24:22.613" Score="1" Body="&lt;p&gt;I can't offer specific advice as to your personal readings, but it is normal to expect a difference in blood pressure between sitting &amp;amp; supine (lying down) positions.&lt;/p&gt;&#xA;&lt;p&gt;I have taken this quote from &lt;a href=&quot;http://healthcaresciencesocw.wayne.edu/vs/6_7.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;the Department of Health Care Sciences at Wayne State University website&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;h3&gt;Effects of body position on blood pressure&lt;/h3&gt;&#xA;&lt;p&gt;Blood pressure is commonly measured in the seated or supine position; however, the two positions give different measurement values. With that in mind, any time a value is recorded, body position should also be recorded. It is widely accepted that diastolic pressures while sitting are higher than when a patient is supine by as much as 5 mmHg. When the arm is at the level of the heart, systolic pressure can be 8 mmHg higher, such as when a patient is in the supine position rather than sitting. A patient supporting their own arm (isometric exercise) may increase the pressure readings. If the patient’s back is not supported (i.e., when a patient is seated on an exam table instead of a chair) the diastolic pressure may be increased by 6 mmHg. Crossing the legs also may raise systolic pressure by 2-8 mmHg. Arm position plays a dramatic role in value errors as well. If the arm is below the level of the heart, values will be too high; if the arm is above the level of the heart, values will be underestimated. For every inch the arm is above or below the level of the heart, a 2 mmHg difference will be found (Pickering et al. Circ 2005;111:697-716).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So if you are comparing your own blood pressure day-to-day, make sure you keep a consistent position.&lt;/p&gt;&#xA;&lt;p&gt;Additionally, if you are reading guidelines for healthy/risk blood pressures, make sure you take this into account.&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-09-22T08:24:22.613" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10533" PostTypeId="1" CreationDate="2013-09-22T15:19:36.177" Score="2" ViewCount="113" Body="&lt;p&gt;I'm a physicist asking questions on an aspect of cellular metabolism, so excuse my biological ignorance! Hypoxia is a frequent complication of certain tumour types, and has quite an implication for treatment prognosis - at certain low oxygen levels, metabolic functions become massively reduced or even halted and eventually necrosis sets in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is what kind of partial pressures will cell division typically be halted at? From &lt;a href=&quot;http://jnci.oxfordjournals.org/content/93/4/266.full&quot; rel=&quot;nofollow&quot;&gt;this review paper&lt;/a&gt;, it indicates that below 8-10 mmHg, adequate metabolistic functions cannot be maintained. In this case, the critical parameter being measured is ATP production. However, I've seen quotes for Chinese Hamster Ovary cells of 0.5-1mmHg. In radiotherapy, &quot;hypoxia&quot; as a condition is defined as &amp;lt; 2.5 mmHg but this doesn't tell me much w.r.t cell division or lack thereof. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know a ball park figure for the cessation of cell division, in a typical cell line, and where I might find information on this? Thanks!&lt;/p&gt;&#xA;" OwnerUserId="4520" LastEditorUserId="948" LastEditDate="2013-09-22T17:10:39.580" LastActivityDate="2013-09-22T17:10:39.580" Title="Critical pO2 threshold for cell division?" Tags="&lt;cell-biology&gt;&lt;cellular-respiration&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10535" PostTypeId="2" ParentId="10530" CreationDate="2013-09-22T15:51:40.183" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2013141&quot; rel=&quot;nofollow&quot;&gt;This paper from 1991&lt;/a&gt; is intervention-based, so it reports the effects of behavior modification on lifespan in people who turned 35 in 1990.  The authors report the gains for each individual behavior and then say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Eliminating coronary heart disease mortality is estimated to extend the average life expectancy of a 35-year-old man by 3.1 years and a 35-year-old woman by 3.3 years&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Which they feel is a modest increase but I rather disagree.  &lt;a href=&quot;http://ije.oxfordjournals.org/content/30/6/1260.full.pdf&quot; rel=&quot;nofollow&quot;&gt;This report&lt;/a&gt; estimates the that reduction in death due to heart disease of over 50% between 1950 and 1995 gained around 3.5 years, although most of that is probably due to better medical treatments.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15157279&quot; rel=&quot;nofollow&quot;&gt;This 2004 study&lt;/a&gt; used 1998 data from the UK and estimated that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The average gain in life expectancy from the elimination of cardiovascular disease risk as a cause of death was 4.0 years for all the 35 year-old men in the sample (n = 24), and 1.8 years for all the 35 year-old women in the sample (n = 32).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Although I would note the low sample size.  I didn't expect to find much, so I was surprised to find these... and with similar results!  One big issue is that a lot of the more recent research has focused on smoking, weight/BMI, and blood pressure reduction, rather than all IHD/CHD/CAD; I found tons of those.  As a side note, simply reducing TV watching to less than two hours a day can lead to a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22777603&quot; rel=&quot;nofollow&quot;&gt;gain of almost 1.5 years&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-22T15:51:40.183" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10536" PostTypeId="2" ParentId="10523" CreationDate="2013-09-22T17:17:23.803" Score="7" Body="&lt;p&gt;It's the same stuff that makes up most sea shells, calcium carbonate, $CaCO_3$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incidentally, this explains why egg shells dissolve in vinegar (acetic acid which, since it is an acid, provides the Hydrogen ions in the reaction below): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$CaCO_3+ 2H^+ -&amp;gt; Ca^{2+} + H_2O +CO_2$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This simple reaction (which is what would happen in your stomach as well) produces water, calcium ions and carbon dioxide, none of which are particularly harmful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The specific reaction with acetic acid is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$CaCO_3 + 2CH_3COOH → Ca(CH_3COO)_2 + H_2O + CO_2$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;which also produces calcium acetate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, there is nothing particularly toxic about $CaCO_3$, it's basically chalk. I wouldn't recommend eating a &lt;em&gt;lot&lt;/em&gt; of it but you shouldn't freak out if some falls into your omelet either. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, don't forget that an egg has exited a chicken's anus (well, &lt;em&gt;cloaca&lt;/em&gt;) so their shells are likely to have come into contact with feces and they &lt;em&gt;are&lt;/em&gt; porous so they are not necessarily the cleanest thing around. This is just not because of any chemical toxicity.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-09-22T19:37:18.167" LastActivityDate="2013-09-22T19:37:18.167" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="10537" PostTypeId="2" ParentId="10522" CreationDate="2013-09-22T18:07:46.437" Score="4" Body="&lt;p&gt;Good question. To understand it perfectly, you'll need a good reference to a text on detailed explanation of sound conduction by the ear ossicles in reptiles and humans. I couldn't find anything better than these &lt;a href=&quot;http://en.wikibooks.org/wiki/Engineering_Acoustics/Conductive_Mechanisms_of_Hearing&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.drtbalu.co.in/bonecond_phy.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But these are partly inadequate in addressing your questions and are a bit involved in the physics used.&lt;br&gt;&#xA;But, if we leave the physical details aside below is the possible reason as to why a single bone in case of reptile conducts just fine but in humans fails to conduct.&lt;br&gt;&#xA; The reptile ear has evolved such that &lt;strong&gt;it uses a single bone for conduction&lt;/strong&gt;, while the human ear is &lt;strong&gt;functioning with three transmitting ossicles&lt;/strong&gt; (the only example i could think of). This is similar to the working of a watch. You can create a time-keeping device by using a combination of three gears (old play watches) or a combination of a large number of gears (my &lt;em&gt;Timex Retrogade&lt;/em&gt;). Both have the same function, but if we fuse several gears in the second case to equal the number in the first (hypothetically only), it will obviously stop working. In our analogy, the ear has evolved such that the sound is optimally transmitted due to several effects like, resonance, impedance, transformation and simple amplification along the ossicles, and all these functions depend very specifically on the shape and orientation of the various conducting elements of the system. And therefore, even a slight disfigurement might severely impair the conduction of sound. Therefore, had the human ear system evolved to work with one ossicle, it would have evaded osteosclerosis by being able to conduct with one ossicle also.   &lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3624" LastEditDate="2014-03-28T08:39:42.740" LastActivityDate="2014-03-28T08:39:42.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10538" PostTypeId="2" ParentId="8554" CreationDate="2013-09-22T20:06:33.547" Score="5" Body="&lt;p&gt;Older papers initially presumed that it was part of a &lt;a href=&quot;http://physrev.physiology.org/content/56/4/829.long&quot;&gt;mechanism called &quot;catch&quot;&lt;/a&gt; in invertebrates like molluscs which is a &quot;sustained contraction.&quot;  However, paramyosin was also found in &lt;a href=&quot;https://www.sciencedirect.com/science/article/pii/0305049176903102&quot;&gt;insects&lt;/a&gt;.  There is a &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/18616971&quot;&gt;very detailed review on invertebrate muscle from 2008&lt;/a&gt; that you should read through (or, you know, search through) points out that recent evidence has shown that paramyosin is &lt;strong&gt;not&lt;/strong&gt; involved in catch; that review also has this to say on the subject (emphasis added):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Furthermore, paramyosin’s presence in almost &lt;strong&gt;every invertebrate muscle&lt;/strong&gt; (including those with relatively small thick filaments) suggests that paramyosin should &lt;strong&gt;not be considered a ‘special’ molecule whose presence needs explanation&lt;/strong&gt;. Paramyosin is instead an everyday constituent of invertebrate muscles, similar, for instance, to the giant sarcomere associated proteins (see Hooper and Thuma, 2005). Indeed, a more salient question might be &lt;strong&gt;why vertebrates do not have paramyosin&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-22T20:06:33.547" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10539" PostTypeId="1" AcceptedAnswerId="10540" CreationDate="2013-09-22T20:13:08.357" Score="4" ViewCount="1080" Body="&lt;p&gt;I came across &lt;a href=&quot;https://www.facebook.com/photo.php?v=10151746969578159&amp;amp;set=vb.217038473158&amp;amp;type=2&amp;amp;theater&quot; rel=&quot;nofollow noreferrer&quot;&gt;this video on Facebook&lt;/a&gt; where a plant closes its leaves when touched. Unfortunately the video does not mention the name of this plant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What's the name of this plant, and where can I see it?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HEyMh.png&quot; alt=&quot;crazy plant&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user3130" LastEditorUserId="22057" LastEditDate="2016-10-21T18:24:45.417" LastActivityDate="2017-05-17T09:39:36.350" Title="What is this plant which closes its leaves when touched?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10540" PostTypeId="2" ParentId="10539" CreationDate="2013-09-22T20:35:41.020" Score="8" Body="&lt;p&gt;It is a &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mimosa_pudica&quot;&gt;Mimosa pudica&lt;/a&gt;&lt;/em&gt;, a wonderful plant. According to wikipedia you can find it in the following places:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mimosa pudica is native to South America and Central America. It has been introduced to many other regions and is regarded as an invasive species in Tanzania, South Asia and South East Asia and many Pacific Islands. It is regarded as invasive in parts of Australia and is a declared weed in the Northern Territory, and Western Australia although not naturalized there. Control is recommended in Queensland. It has also been introduced to Nigeria, Seychelles, Mauritius and East Asia but is not regarded as invasive in those places. In the United States of America, it grows in Florida, Hawaii, Virginia, Maryland, Puerto Rico, Texas, and the Virgin Islands.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you think that's impressive, look at this video of &lt;a href=&quot;http://en.wikipedia.org/wiki/Venus_flytrap&quot;&gt;&lt;em&gt;Dionaea muscipula&lt;/em&gt;&lt;/a&gt; the venus fly trap:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=O7eQKSf0LmY&quot;&gt;https://www.youtube.com/watch?v=O7eQKSf0LmY&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="231" LastEditDate="2013-09-22T21:26:51.640" LastActivityDate="2013-09-22T21:26:51.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10542" PostTypeId="1" CreationDate="2013-09-23T01:03:54.277" Score="4" ViewCount="1372" Body="&lt;p&gt;Is melatonin properly produced in daytime sleep in full darkness? Or does it require only nighttime sleep?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, what other biological implications are there, if any, to daytime sleeping? Melatonin production is the only biological implication I could find so far.&lt;/p&gt;&#xA;" OwnerUserId="4525" LastActivityDate="2013-12-19T19:27:55.593" Title="Melatonin production - requires nighttime, or just full darkness?" Tags="&lt;sleep&gt;&lt;melatonin&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10544" PostTypeId="1" AcceptedAnswerId="10545" CreationDate="2013-09-23T16:53:46.667" Score="5" ViewCount="1206" Body="&lt;p&gt;&lt;a href=&quot;http://www.scientificamerican.com/article.cfm?id=identical-twins-genes-are-not-identical&quot; rel=&quot;nofollow&quot;&gt;http://www.scientificamerican.com/article.cfm?id=identical-twins-genes-are-not-identical&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to this article some identical twins show differences with respect to their copy number variants. How is this possible? If mitosis of an egg can lead to this difference, why can't mitosis of any cell in our body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we assume that identical twins are exactly identical, then if we make a clone of a twin will all three be exactly identical?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-09-23T21:16:38.197" LastActivityDate="2017-05-24T15:45:04.437" Title="Are identical twins exactly the same?" Tags="&lt;genetics&gt;&lt;reproduction&gt;&lt;mitosis&gt;&lt;twins&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10545" PostTypeId="2" ParentId="10544" CreationDate="2013-09-23T17:08:06.263" Score="6" Body="&lt;p&gt;Errors in division occur all the time and can show up in any dividing cell; this is, of course, important for cancer biology.  If one of my cells replicates oddly right now it likely won't matter since it's only one out of trillions, but if that happened at a very early age in development it could be present in many if not all of my cells.  Identical twins indeed come from the same egg-sperm fusion event but they develop separately from a very early state.  It's trivial to imagine a minor replication error in DNA at an early cell stage that results in different genotypes between so-called identical twins.  Besides, we've known for years that identical twins can have major epigenetic differences, so this isn't particularly ground-breaking.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If we assume that identical twins are exactly identical, then if we make a clone of a twin, will all three be exactly identical?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Depends on your definition of &quot;clone&quot; but how identical is identical?  If you mean exact, then probably not; at the very least they will have different numbers of cells, for example, not to even mention CNV or epigenetics.  If you want some SciFi cloning thing then, well, join the club.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-23T17:08:06.263" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10546" PostTypeId="2" ParentId="10544" CreationDate="2013-09-23T19:29:52.497" Score="2" Body="&lt;p&gt;Identical twins do start out identical, but their DNA will quickly diverge. Not in a dramatic way, but in point mutations, at random locations, in different cells.  Think of how there is a certain error rate associated with DNA replication - so even from that very first cell, when it divides to form a second cell, there is a chance there may be mutations in the DNA copy.  It is highly unlikely that both twins will make the same mistake in copying the DNA in exactly the same location.  Now repeat that idea millions and millions of times, as they develop, forming all the cells they need to form their bodies, and throughout their lives.  Mutations are random, and they accumulate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I made a video about this topic - &lt;a href=&quot;http://youtu.be/gkwN4eXU7yA&quot; rel=&quot;nofollow&quot;&gt;Are Identical Twins Really Identical?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4527" LastActivityDate="2013-09-23T19:29:52.497" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10548" PostTypeId="1" CreationDate="2013-09-23T22:39:47.887" Score="0" ViewCount="170" Body="&lt;p&gt;First, my background - I'm a newcomer to biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is a gene circuit, and how might I simulate one in a laboratory? Thank you. &lt;/p&gt;&#xA;" OwnerUserId="4283" LastActivityDate="2013-12-02T20:31:14.937" Title="Gene Circuits; experiments" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10549" PostTypeId="1" CreationDate="2013-09-23T23:29:59.017" Score="3" ViewCount="710" Body="&lt;p&gt;There are four alleles of Adh which are Adh-1, Adh-2, Adh-3 and Adh-4.  Their respective frequencies are 0.11, 0.84, 0.01 and 0.04.  What are the Hardy-Weinberg frequencies of the possible 10 genotypes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My Attempt:  First I thought that there were more than 10 genotypes (4*3*2*1) = 24.  I've never done HWE with 4 genotypes so im not sure how to use $p+q=1$ or $p^2+2pq+q^2=1$.&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="4199" LastEditDate="2013-09-25T15:52:10.543" LastActivityDate="2013-09-25T22:29:23.793" Title="Possible Genotypes of 4 Alleles of Adh" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10550" PostTypeId="1" CreationDate="2013-09-24T00:02:19.010" Score="2" ViewCount="5025" Body="&lt;h1&gt;1&lt;/h1&gt;&#xA;&lt;p&gt;There is a population not at HWE where red eye = &lt;span class=&quot;math-container&quot;&gt;$a^+$&lt;/span&gt; (dominant) and white eyes = &lt;span class=&quot;math-container&quot;&gt;$a^-$&lt;/span&gt;.&lt;/p&gt;&#xA;&lt;p&gt;If:&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$a^+/a^+ = 0.6$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$a^-/a^+ = 0.1$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$a^-/a^- = 0.3$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;what are the frequencies of the &lt;span class=&quot;math-container&quot;&gt;$a^+$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$a^-$&lt;/span&gt; alleles?&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;My attempt&lt;/strong&gt;: So if it's not at HWE then I should divide the heterozygotes equally to get &lt;span class=&quot;math-container&quot;&gt;$a^+ = 0.65$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$a^- = 0.35$&lt;/span&gt;.&lt;/p&gt;&#xA;&lt;h1&gt;2&lt;/h1&gt;&#xA;&lt;p&gt;We are now at HWE.  What are the frequencies in the next generation?&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;My attempt&lt;/strong&gt;: so if &lt;span class=&quot;math-container&quot;&gt;$a^+ (p) = 0.65$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$a^- (q) = 0.35$&lt;/span&gt; then &lt;span class=&quot;math-container&quot;&gt;$p^2 = 0.42$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$q^2 = 0.12$&lt;/span&gt;.  Then using &lt;span class=&quot;math-container&quot;&gt;$p^2 + 2pq + q^2 = 1$&lt;/span&gt;, I can figure out that the heterozygotes make up &lt;span class=&quot;math-container&quot;&gt;$0.46$&lt;/span&gt;.  So the frequency of the &lt;span class=&quot;math-container&quot;&gt;$a^+$&lt;/span&gt; allele is &lt;span class=&quot;math-container&quot;&gt;$0.42 + 0.46 = 0.88$&lt;/span&gt;, and then &lt;span class=&quot;math-container&quot;&gt;$a^-$&lt;/span&gt; should be &lt;span class=&quot;math-container&quot;&gt;$0.12$&lt;/span&gt; (because they should add to 1)&lt;/p&gt;&#xA;&lt;h1&gt;3&lt;/h1&gt;&#xA;&lt;p&gt;What is the frequency 5 generations later in HWE?&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;My attempt&lt;/strong&gt;:  Wouldn't it be the same answer as #2. I'm not sure how more generations in HWE would change the allele frequencies.&lt;/p&gt;&#xA;" OwnerUserId="558" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-07T23:25:18.427" Title="Hardy Weinberg Equilibrium after 5 Generations" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;hardy-weinberg&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10551" PostTypeId="1" AcceptedAnswerId="10555" CreationDate="2013-09-24T01:41:38.330" Score="5" ViewCount="1996" Body="&lt;p&gt;In graphs of survivorship curves, I'm seeing that the Type II curves are straight lines, and the supplementary text says that the mortality rate is constant (i.e. the slope of the line is constant). However, it's also clearly stated that the y-axis is a logarithmic scale, which means that the original Type II curve is exponential:&#xA;$$\ln y=-rx+b$$&#xA;$$y=Ae^{-rx}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This implies that the real mortality rate is not constant, but changes as $$y'=-Ar(e^{-rx})$$&#xA;How are we defining the word &lt;em&gt;rate&lt;/em&gt;, anyway?&lt;/p&gt;&#xA;" OwnerUserId="4478" LastEditorUserId="3624" LastEditDate="2013-09-24T11:41:30.953" LastActivityDate="2016-11-24T21:27:21.883" Title="Survivorship Curves: Type II curve mortality rate is not constant?" Tags="&lt;ecology&gt;&lt;mathematical-models&gt;&lt;demography&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10553" PostTypeId="1" AcceptedAnswerId="24611" CreationDate="2013-09-24T06:57:33.700" Score="5" ViewCount="93" Body="&lt;p&gt;I want to do some statistical analysis and I have a preference for real data so I was wondering if there's somewhere I can get such data for free without a heap of bother in phoning those involved in the studies in question.&lt;/p&gt;&#xA;" OwnerUserId="1813" LastEditorUserId="1813" LastEditDate="2016-12-21T23:03:19.720" LastActivityDate="2016-12-21T23:03:19.720" Title="Are there any online resources one can use to access raw clinical trial data without having to contact those involved in the study?" Tags="&lt;statistics&gt;&lt;clinical-trial&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10555" PostTypeId="2" ParentId="10551" CreationDate="2013-09-24T10:40:11.583" Score="5" Body="&lt;p&gt;$r$ is the individual mortality rate per time step. Survivorship curves (plotted on a log scale) show the proportion of individuals surviving with time, and with a Type II curve a constant proportion is dying at each time step (constant mortality with age, $r$). When the model is expressed as $y$ you are looking at the number of individuals surviving to a time step, which is an negative exponential for Type II, since a smaller and smaller proportion of the population remains at each time step. Therefore $y'$ is the change (slope) in the number of individuals surviving over time. This can be seen as a rate, but it is not the mortality rate of individuals, and it is not accurate to describe it as the &quot;..&lt;em&gt;real mortality rate..&lt;/em&gt;&quot;.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an introduction to survivorship curves you can also look at &lt;a href=&quot;http://www.nature.com/scitable/knowledge/library/survivorship-curves-16349555&quot;&gt;&quot;Survivorship Curves&quot; from Nature Education&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-09-24T10:48:39.680" LastActivityDate="2013-09-24T10:48:39.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10557" PostTypeId="1" AcceptedAnswerId="10567" CreationDate="2013-09-24T13:30:03.140" Score="1" ViewCount="683" Body="&lt;p&gt;If we have humans A, B and C who are different:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A is thin (skinny) without significant muscle or fat mass.&lt;/li&gt;&#xA;&lt;li&gt;B is muscular&lt;/li&gt;&#xA;&lt;li&gt;C is fat&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Which one of them has the best body for survival in accidents like car crash, aircraft crash, fall from the ladder, fall down the stairs, being hit by a car, slip in the bathroom, etc?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the effects of muscle and fat mass on survivability?&lt;/p&gt;&#xA;" OwnerUserId="4531" LastActivityDate="2013-09-24T22:31:22.310" Title="What are the effects of muscle and fat mass on survivability?" Tags="&lt;human-biology&gt;&lt;muscles&gt;&lt;death&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10558" PostTypeId="2" ParentId="10550" CreationDate="2013-09-24T13:54:50.793" Score="3" Body="&lt;p&gt;You are almost correct, but with a few modifications/comments.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The calculations in &lt;strong&gt;Q1&lt;/strong&gt; are independent of HWE, and are just calculating the current allele frequencies in the population based on genotype frequencies (i.e. would be the same irrespectively of if the population is in HWE or not).&lt;/li&gt;&#xA;&lt;li&gt;In &lt;strong&gt;Q2&lt;/strong&gt; it is unclear if the questions is asking for genotype frequencies or allele frequencies. Your answer of genotype frequencies of $p^2=0.42$ ($a^+a^+$), $q^2 =0.12$ ($a^-a^-$) and $2pq =0.46$ ($a^+a^-$) is correct if you assume the allele frequencies from &lt;strong&gt;Q1&lt;/strong&gt; and HWE. However, your allele frequencies are incorrect and should be $p = 0.42 + 0.46/2 = 0.65$ and $q = 0.12 + 0.46/2 = 0.35$, i.e. the same as in &lt;strong&gt;Q1&lt;/strong&gt;. Remember that the allele frequencies shouldn't change under HWE.&lt;/li&gt;&#xA;&lt;li&gt;Yes frequencies should not change in &lt;strong&gt;Q3&lt;/strong&gt;. This is the textbook definition of HWE, i.e. that allele and genotype frequencies remain constant between generations in the absence of evolutionary forces (i.e. under the HWE).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-09-24T14:36:41.270" LastActivityDate="2013-09-24T14:36:41.270" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10561" PostTypeId="2" ParentId="9337" CreationDate="2013-09-24T19:54:29.823" Score="0" Body="&lt;p&gt;Check out &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2542979/&quot; rel=&quot;nofollow&quot;&gt;Sleep Architecture in Unrestrained Rhesus Monkeys (Macaca mulatta) Synchronized to 24-Hour Light-Dark Cycles&lt;/a&gt;.  From the abstract: &quot;With minor exceptions, most notably a delay in peak delta activity, sleep-wake architecture, regulation, and consolidation in rhesus monkeys strongly resembles that of humans.&quot;&lt;/p&gt;&#xA;" OwnerUserId="4535" LastActivityDate="2013-09-24T19:54:29.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10562" PostTypeId="1" AcceptedAnswerId="10563" CreationDate="2013-09-24T20:08:37.703" Score="3" ViewCount="485" Body="&lt;p&gt;I am thinking about an invasive species that was introduced into North America just a few (&amp;lt;20) generations ago. Using microsatellite genotypes (105 loci), I have identified almost no significant linkage across the genome. I'm tempted to speculate that this has something to do with rapid population expansion that has caused LD to decay that quickly, but I'm not sure whether this is a reasonable train of thought. Can anybody think of why this might or might not be the case?&lt;/p&gt;&#xA;" OwnerUserId="1906" LastActivityDate="2013-09-24T20:33:24.460" Title="Does a large effective population size result in faster decay of linkage disequilibrium (LD)?" Tags="&lt;genetics&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10563" PostTypeId="2" ParentId="10562" CreationDate="2013-09-24T20:33:24.460" Score="4" Body="&lt;p&gt;It is certainly possible as yes, rapid population growth will reduce LD.  From &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8056320&quot; rel=&quot;nofollow&quot;&gt;Slatkin, 1994&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In a rapidly growing population, however, there will be little chance of finding significant nonrandom associations even between completely linked loci if the growth has been sufficiently rapid.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Or &lt;a href=&quot;http://www.nature.com/nrg/journal/v3/n4/full/nrg777.html&quot; rel=&quot;nofollow&quot;&gt;Nature Reviews, 2002&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Przeworski... showed that population growth tends to decrease the extent of LD, especially for longer periods of growth. By contrast, population subdivision tends to increase the extent of LD, especially when a sample contains individuals from several strongly differentiated subpopulations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;See also &lt;a href=&quot;http://www.nature.com/nrg/journal/v3/n4/box/nrg777_BX1.html&quot; rel=&quot;nofollow&quot;&gt;box 1&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Rapid population growth decreases LD by reducing genetic drift.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-24T20:33:24.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10564" PostTypeId="2" ParentId="10548" CreationDate="2013-09-24T20:50:36.687" Score="3" Body="&lt;p&gt;I'm just going to give a broad idea of what a biological circuit is.  There's definitely more than one way to define them, but hopefully this will give you some idea.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Broadly, biological circuits are reminiscent of electrical circuits in that energy or information flows through the cell.  In biological pathways (a more typical terminology), genes in the cell (usually proteins) will use a signal (usually in the form of a chemical compound or a modification of a protein, but sometimes a simple ion or even electrical current (rarely)).  The signal then can be transmuted into a different chemical compound or it can even alter a protein so that it functions differently.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are a couple of classic examples.  The first is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Citric_acid_cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;Citric acid cycle&lt;/a&gt; (also called the Krebs cycle), discovered in the 1930s.  Here you can see that Citrate is chemically transformed into acetate and carbon dioxide and chemical energy in the form of NADH (reduced nicotinic acid dinucleotide).  Each step of the cycle has a different compound which is handled by a different protein enzyme.  While all the proteins and compounds may coexist in the same part of the cell, there is nonetheless an orderly circuit of chemical energy mediated by the genes of the cell and controlled by the cell as it adjusts the amount of enzymes available for each step of the cycle.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0cj7k.png&quot; alt=&quot;citric acid cycle&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example of an entirely different sort of gene pathway works differently but has the same set of concepts.  Mitogen Activated Kinases (MAPKs) are proteins which have generally two states an activated state and an inactivated one.  As you can see below, an outside signal like high salt osmolarity or a signalling molecule is sensed by a receptor on the cell surface.  By some method a MAP Kinase is activated, perhaps by the addition of a phosphate to the surface of the protein or by dimerizing the MAPK.  Once activated, the MAPK will then phoshphorylate another kinase, which may activate yet another.  Finally a protein in the nucleus will be activated and cause transcription of some target genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/h6h9T.png&quot; alt=&quot;MAP KINSE SIGNALLING PATHWAY &quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the latter case, a very small change to the protein costs little energy and information is being transmitted, but by biochemical signals where proteins are modified and affect other proteins.  That's a more subtle circuit than in the former case where relatively many individual molecules might be processed by enzymes together.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This hopefully gives you some idea of what a biological circuit looks like.  There are many other examples and subtle variations but that's a quick tour. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Experiments involving these pathways are too numerous to mention - individual proteins may be modified, their concentration within the cell can be altered by say mutations in the chromosome, pathway intermediate compounds like Succinate might be added to see how the citric acid cycle responds, isotopic labeled compounds can be added to see where they go in the cell.  There's nearly 100 years of experiments here.  that's a lot. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully this will just give you some idea of where to start.  Nearly any biochemistry textbook covers these topics in better detail, but then they are often over 1000 pages long!  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-09-24T20:50:36.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10565" PostTypeId="1" CreationDate="2013-09-24T21:15:24.443" Score="1" ViewCount="775" Body="&lt;p&gt;I need help with one of the questions on my biochemistry assignment&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Choose the correct statement on proteins:&#xA;a) proteins are folded by alpha-helix&#xA;b) proteins can preserve their function even if they only partially change their shapes&#xA;c) proteins are composed of amino acids&#xA;d) all of the above&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance! :)&lt;/p&gt;&#xA;" OwnerUserId="4537" LastEditorUserId="4101" LastEditDate="2013-09-24T21:16:07.183" LastActivityDate="2013-09-24T21:30:05.127" Title="Which is the correct statement on proteins?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;homework&gt;&lt;amino-acids&gt;&lt;protein-folding&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10566" PostTypeId="2" ParentId="10565" CreationDate="2013-09-24T21:30:05.127" Score="1" Body="&lt;p&gt;Do you have a textbook?  That will definitely have the answer early on in the chapter.  Also, have you tried reading the &lt;a href=&quot;http://en.wikipedia.org/wiki/Protein&quot; rel=&quot;nofollow&quot;&gt;protein Wikipedia article&lt;/a&gt;, in particular the &lt;a href=&quot;http://en.wikipedia.org/wiki/Protein#Structure&quot; rel=&quot;nofollow&quot;&gt;structure&lt;/a&gt; subsection.  You will find the information you want there.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-24T21:30:05.127" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10567" PostTypeId="2" ParentId="10557" CreationDate="2013-09-24T22:31:22.310" Score="3" Body="&lt;p&gt;For car crashes, it's a mixed bag:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.insure.com/car-insurance/fat-guys-survive-car-crashes-better.html&quot; rel=&quot;nofollow&quot;&gt;Better&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.annarbor.com/news/overweight-men-have-higher-chance-of-surviving-a-car-crash-university-of-michigan-study-finds/&quot; rel=&quot;nofollow&quot;&gt;Better&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.huffingtonpost.com/2013/01/23/car-crashes-deadlier-obese-survive_n_2528402.html&quot; rel=&quot;nofollow&quot;&gt;Worse&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.dailymail.co.uk/health/article-1340781/Obese-likely-die-car-accidents-say-doctors-fat-crash-test-dummies.html&quot; rel=&quot;nofollow&quot;&gt;Worse&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Basically, it looks like, if wearing a seat belt, slightly overweight is more likely to survive a car crash, but if no seat belts are worn they are at a disadvantage; the very obese are always more likely to die, however.  Also, some of this was found only for males, not females.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-24T22:31:22.310" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10568" PostTypeId="2" ParentId="10364" CreationDate="2013-09-25T02:10:31.983" Score="-1" Body="&lt;p&gt;Hippo Signal may affect the turnover rate of oral mucosa&lt;/p&gt;&#xA;" OwnerUserId="4351" LastActivityDate="2013-09-25T02:10:31.983" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10570" PostTypeId="1" CreationDate="2013-09-25T02:53:02.523" Score="6" ViewCount="12461" Body="&lt;p&gt;I am doing an experiment in which I am growing &lt;em&gt;S. mutans&lt;/em&gt; in agar dishes, and I am not sure how I would measure the growth of the &lt;em&gt;S. mutans&lt;/em&gt;. I am also not sure if I would do this by measuring cell mass or by cell count. Any ideas?&lt;/p&gt;&#xA;" OwnerUserId="4524" LastEditorUserId="4101" LastEditDate="2013-09-25T03:32:44.983" LastActivityDate="2018-04-05T10:15:53.627" Title="How do I measure bacterial growth in agar dishes (either by cell mass or by cell count)?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10572" PostTypeId="1" AcceptedAnswerId="10577" CreationDate="2013-09-25T04:10:24.817" Score="7" ViewCount="116698" Body="&lt;p&gt;I fell over on my bicycle trying to avoid running over a rattlesnake, and ended up badly skinning my knee. It immediately began to bleed, but soon clotted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has been &lt;strong&gt;2 days&lt;/strong&gt; now and it has formed a thin scab and is healing well as far as I can tell. I was chilly from the air conditioning, and I noticed the wounded knee was much warmer than the healthy knee. It was very warm, while the other was rather cold to the touch.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read &lt;a href=&quot;https://biology.stackexchange.com/a/8741/1827&quot;&gt;here&lt;/a&gt; about skin healing, and thought, maybe it is because the blood rushed there to clot the wound. But, the wound is already clotted and sealed and the worst is over. So my question is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why is my wound and the area around it so much warmer &lt;em&gt;days&lt;/em&gt; after the injury?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1827" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-07-05T16:19:03.027" Title="Why Do Healing Wounds Feel Warmer To The Touch?" Tags="&lt;skin&gt;&lt;healing&gt;&lt;injury&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10573" PostTypeId="2" ParentId="3278" CreationDate="2013-09-25T04:20:09.680" Score="34" Body="&lt;p&gt;It is a result from the insecticide you are using.  From &lt;a href=&quot;http://www4.ncsu.edu/~coby/schal/2011Schal_Mallis_Fact_or_Fiction.pdf&quot;&gt;this excerpt from the 10th Edition of the Mallis Handbook on Pest Control&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Neurotoxic insecticides cause tremors and muscle spasms, flipping the cockroach on its back. A healthy cockroach can easily right itself, but without muscle coordination, the cockroach dies on its back. Cockroaches exposed to slow-acting insecticides that target respiration (energy production) also can die “face-down,” as they run out of energy without experiencing muscle spasms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here's also a &lt;a href=&quot;http://www.bio.umass.edu/biology/kunkel/cockroach_faq.html#Q6&quot;&gt;website from UMass&lt;/a&gt; describing it in more detail:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Most of these insecticides are organophosphate nerve poisons.  The nerve poison often inhibits cholinesterase, an enzyme that breaks down acetyl choline (ACh), a neurotransmitter.  With extra ACh in the nervous system, the cockroach has muscular spasms which often result in the cockroach flipping on its back.  Without muscular coordination the cockroach cannot right itself and eventually dies in its upside down-position.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And an entomology professor even &lt;a href=&quot;http://www.maxim.com/funny/ask-maxim-blood-cockroaches-and-poison&quot;&gt;answered this for Maxim&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Most insecticides are poisons that target a bug’s nervous system. When you spray a roach, those neurotoxins cause tremors and muscle spasms, which flip&#xA;  it onto its back, and without muscle coordination, that’s the position it dies in&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-25T04:20:09.680" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10574" PostTypeId="2" ParentId="10572" CreationDate="2013-09-25T06:00:07.667" Score="4" Body="&lt;p&gt;The increase in temperature is due to dilatation of the capillaries in an area of inflammation, here brought about by trauma and is one of the five cardinal signs of inflammation'. This is a natural process which helps to bring in more blood supply for repair and removal of damaged tissue components.&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="4216" LastEditDate="2013-09-25T07:01:32.533" LastActivityDate="2013-09-25T07:01:32.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10575" PostTypeId="2" ParentId="8279" CreationDate="2013-09-25T07:42:37.950" Score="3" Body="&lt;p&gt;You can remember this easily as the rule of threes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can survive:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;3 minutes without air. (death by asphyxiation)&lt;/li&gt;&#xA;&lt;li&gt;3 hours without shelter (death by hypothermia, heatstroke).&lt;/li&gt;&#xA;&lt;li&gt;3 days without water. (death by dehydration)&lt;/li&gt;&#xA;&lt;li&gt;3 weeks without food. (death by starvation)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Going beyond those guidelines will generally do you permanent damage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further reading: &lt;a href=&quot;http://www.wildernesscollege.com/basic-survival-skills.html&quot; rel=&quot;nofollow&quot;&gt;http://www.wildernesscollege.com/basic-survival-skills.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4539" LastEditorUserId="4539" LastEditDate="2013-09-25T13:04:40.200" LastActivityDate="2013-09-25T13:04:40.200" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10576" PostTypeId="2" ParentId="9941" CreationDate="2013-09-25T08:45:05.473" Score="2" Body="&lt;p&gt;The main abnormality in prolactin levels is hyperprolactinemia, meaning blood levels of prolactin above the normal range, not during pregnancy or lactation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The major cause of these abnormal prolactin levels are tumors consisting of pituitary lactotroph cells--called prolactinomas--which secrete prolactin. This is generally corrected with synthetic dopamine analogues, as dopamine negatively regulates secretion of prolactin in lactotroph cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a 2010 review with further detail:&#xA;&lt;a href=&quot;http://joe.endocrinology-journals.org/content/206/1/1.full.pdf&quot; rel=&quot;nofollow&quot;&gt;http://joe.endocrinology-journals.org/content/206/1/1.full.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4539" LastActivityDate="2013-09-25T08:45:05.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10577" PostTypeId="2" ParentId="10572" CreationDate="2013-09-25T09:22:26.230" Score="9" Body="&lt;p&gt;This is a normal part of the inflammatory process. Inflammation is your body's localised defensive response to tissue injury of any kind, and it is characterised by four cardinal signs- redness, swelling, heat and pain (severe inflammation involves a fifth, loss of function). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your body is performing three main processes here:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Mobilisation of the body's defences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Involves release of vasoactive chemicals, which cause the blood vessels to dilate and increase blood flow to the area. This causes the pain and heat, The blood vessels also produce cell-adhesion molecules which make immune cells (leukocytes) stick to the walls of the your blood vessels.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Containment and destruction of pathogens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The immune system then goes to work clearing up any bacteria which have got into the wound. The leukocytes release chemicals called cytokines to attract more immune cells, to contain and destroy bacteria.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Tissue cleanup and repair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dead cells, cell fluid and other debris (pus) is then absorbed by the lymphatic system. Platelets and endothelial cells then secrete growth factors which stimulate cells called fibroblasts to multiply and produce collagen. The heat also increases metabolic rate and increases the rate of tissue repair.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="4539" LastActivityDate="2013-09-25T09:22:26.230" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10578" PostTypeId="2" ParentId="10570" CreationDate="2013-09-25T13:28:28.457" Score="4" Body="&lt;p&gt;The most simple way is seeding the plates with a suspension of bacteria ensuring that you spread the solution properly. Then you can count the number of colonies, wich would be equal to the number of single cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to mesure the growth speed, usually it's simpler to just measure the diameter of the colonies, always ensuring you inoculate the plates with the same amount of inoculum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, it's even easier to estimate the growth if your culture is un liquid media and you measure the optic density with an spectophotometer.&lt;/p&gt;&#xA;" OwnerUserId="4168" LastActivityDate="2013-09-25T13:28:28.457" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10579" PostTypeId="1" AcceptedAnswerId="10581" CreationDate="2013-09-25T16:30:15.770" Score="2" ViewCount="351" Body="&lt;p&gt;E. G. Gray is Neuro scientist who found and described first the two major morphologically defined synapse types (Gray Type I (asymmetric) and II (symmetric)) in his work &#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1244535/&quot; rel=&quot;nofollow&quot;&gt;E G Gray (Oct. 1959). “Axo-somatic and axo-dendritic synapses of the cerebral cortex: an electron microscope study”. In: Journal of Anatomy 93.4, pp. 420–433&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However I am unable to find his full name nor further information about his life.&lt;/p&gt;&#xA;" OwnerUserId="3042" LastEditorUserId="3042" LastEditDate="2014-03-18T14:32:51.760" LastActivityDate="2014-03-18T14:32:51.760" Title="What is the full name of E. G. Gray?" Tags="&lt;neuroscience&gt;&lt;history&gt;&lt;synapses&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10580" PostTypeId="2" ParentId="10549" CreationDate="2013-09-25T16:47:39.563" Score="2" Body="&lt;p&gt;Those Hardy-Weinberg equations are the general case, used for only two alleles.  This question is basically &lt;a href=&quot;https://biology.stackexchange.com/q/8499/4101&quot;&gt;answered here, for three alleles&lt;/a&gt;; you've got a situation of four alleles.  That means you need to have:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$(p+q+r+s)^2=1$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where $p$, $q$, $r$, and $s$ are the frequencies of your respective alleles.  This expands out to the rather unwieldy:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$p^2+2pq+2pr+2ps+q^2+2qr+2qs+r^2+2rs+s^2=1$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now it becomes a plug 'n chug assignment; simply assign the frequencies and calculate.&lt;/p&gt;&#xA;&#xA;&lt;blockquote class=&quot;spoiler&quot;&gt;&#xA;  &lt;p&gt; Assuming $p$ is Adh-1, $q$ is Adh-2, etc., $p^2=0.0121$, $2pq=0.1848$, and so on.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-09-25T22:29:23.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10581" PostTypeId="2" ParentId="10579" CreationDate="2013-09-25T16:52:46.483" Score="1" Body="&lt;p&gt;Edward George Gray went by the first name of George, which isn't evident from his initials (he was born Edward George), but I happened to stumble upon the Wikipedia article below.  From there, I found his obituary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.independent.co.uk/arts-entertainment/obituary-george-gray-1115676.html&quot; rel=&quot;nofollow&quot;&gt;his obituary&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;GEORGE GRAY was a pioneer in the study of brain ultrastructure. He was Professor of Cytology in the anatomy department at University College London from 1967 to 1977 and then headed the Laboratory of Biological Ultrastructure at the National Institute for Medical Research. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From the Wikipedia article for &lt;a href=&quot;http://en.wikipedia.org/wiki/Synaptosome&quot; rel=&quot;nofollow&quot;&gt;synaptosome&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In a collaborative study with the electron microscopist George Gray from University College London, Victor P. Whittaker eventually showed that the acetylcholine-rich particles derived from guinea-pig cerebral cortex were synaptic vesicle-rich pinched-off nerve terminals.  Whittaker coined the term synaptosome to describe these fractionation-derived particles and shortly thereafter synaptic vesicles could be isolated from lysed synaptosomes&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="57" LastEditorUserId="3952" LastEditDate="2013-09-25T22:39:23.480" LastActivityDate="2013-09-25T22:39:23.480" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10582" PostTypeId="1" CreationDate="2013-09-25T17:20:54.407" Score="2" ViewCount="80" Body="&lt;p&gt;On Cooking.se, somebody asked &lt;a href=&quot;https://cooking.stackexchange.com/questions/36958/why-does-the-fat-on-my-chicken-broth-sometimes-solidify-sometimes-not&quot;&gt;a question&lt;/a&gt; about the fat in chicken stock sometimes being liquid and sometimes solid once the stock has cooled. The only answer until now suggests that the difference is due to the percentage of saturated fat in the chicken lard, which will vary depending on the chicken's food. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not entirely happy with this explanation. I am aware that the proportion of saturated to unsaturated fat in an organism's cell walls will vary with diet, and could imagine that the fat stored within its adipose tissue will be different too. The person who provided the answer also posted references which confirm that part. But I doubt that the effect will be strong enough that, if an animal on low-saturated-fat diet is processed to lard, the resulting lard will be a viscous liquid, as opposed to the usual soft solid. If my memory doesn't fail me, my grandma used to keep her animals on a mostly starch-based diet, and still was able to process them for (solid) lard. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can somebody confirm or disprove this theory? &lt;/p&gt;&#xA;" OwnerUserId="1578" LastEditorUserId="-1" LastEditDate="2017-04-13T12:33:29.980" LastActivityDate="2013-09-28T22:25:52.790" Title="Can a chicken's lard become liquid depending on its diet?" Tags="&lt;zoology&gt;&lt;diet&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10583" PostTypeId="1" CreationDate="2013-09-25T18:14:48.420" Score="3" ViewCount="5508" Body="&lt;p&gt;I understand that animals are naturally scared of humans because we basically slaughtered every living thing we found in our way for millennia. How long does it take for them to genetically 'forget' we are a threat?&lt;/p&gt;&#xA;" OwnerUserId="3989" LastEditorUserId="3989" LastEditDate="2013-09-25T21:00:38.830" LastActivityDate="2014-12-17T09:50:22.427" Title="Why are urban birds still scared of humans?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10584" PostTypeId="1" CreationDate="2013-09-25T18:28:17.180" Score="3" ViewCount="461" Body="&lt;p&gt;I am a dilettante when it comes to dead zones. I realize that they vary from fleeting algal blooms to continuous dead zones. For the continuous dead zones it would seem to me that adding a &quot;bubbler&quot; like for fish tanks might help restore the depleted oxygen content, which would increase microbial activity and thereby increase the quantity of nitrogen removed from the water (hopefully) before it reaches the open ocean where the fleeting algal blooms occur. Has this been investigated or could it at least be assessed from a scientific perspective? &lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="4101" LastEditDate="2013-09-25T18:31:48.153" LastActivityDate="2013-10-01T03:21:35.397" Title="Would Bubling Oxygen Through &quot;Dead Zones&quot; Like A Fish-Tank Make Much Difference?" Tags="&lt;aquaculture&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10587" PostTypeId="2" ParentId="10583" CreationDate="2013-09-26T11:07:07.713" Score="9" Body="&lt;p&gt;Perhaps counter-intuitively, fear of humans is often a learned behaviour. There are accounts, such as one made by Charles Darwin following his visit to the Galapagos islands;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In Charles Island, which had then been colonized about six years, I saw a boy sitting by a well with a switch in his hand, with which he killed the doves and finches as they came to drink. He had already procured a little heap of them for his dinner, and he said that he had constantly been in the habit of waiting by this well for the same purpose. It would appear that the birds of this archipelago, not having as yet learnt that man is a more dangerous animal than the tortoise or the Amblyrhynchus, disregard him, in the same manner as in England shy birds, such as magpies, disregard the cows and horses grazing in our fields.&lt;/p&gt;&#xA;&lt;p&gt;From &amp;quot;The Voyage of the Beagle&amp;quot; - &lt;a href=&quot;http://www.ling.upenn.edu/courses/hum100/Beagle17.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.ling.upenn.edu/courses/hum100/Beagle17.html&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Birds born and bred in proximity to humans will have learned that we are actually to be avoided.&lt;/p&gt;&#xA;&lt;p&gt;Ducks and swans, for instance, (and this is quite anecdotal) live in very close proximity to a lot of humans in cities, and feel confident walking picking up food. However if you try to get close to one they are very quick to get out of the way. The only exceptions to this are learned behaviours, such as when someone stands and feeds them.&lt;/p&gt;&#xA;&lt;p&gt;In the wild animals may be cautious of humans if we are much bigger than them, but if they have no experience at all of human contact they  may just ignore them. This quite often happens with film crews in Antarctica, as in the below image from the BBC's Frozen Planet series.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZEdzp.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-09-26T11:07:07.713" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10588" PostTypeId="2" ParentId="7721" CreationDate="2013-09-26T14:27:48.423" Score="3" Body="&lt;p&gt;Well nerve crossing or misinterpretation of nerve signal by the brain does not happen all the time. In case it happens frequently then I guess it would be Multiple Sclerosis or might be &lt;a href=&quot;http://www.ehwidaho.com/fsp.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fibromyalgia syndrome&lt;/a&gt;. In multiple sclerosis, the Myelin sheath surrounding neuron when gets damaged causes certain problem with nerve signal transmission to the brain. But that is not the main cause. The main cause can be found in &lt;a href=&quot;http://www.peripheralneuropathytreatments.com/neuropathy.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Neuropathy&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;When nerve cells are damaged, perhaps by a temporary restriction in their access to oxygen, they too atrophy or shrink a little, thus the synaptic junctions widens.  Just like with a spark plug in your car or lawn mower, if this gap gets too wide, the spark cannot make the jump. A normal sized nerve signal cannot jump this enlarged gap either, &lt;strong&gt;so the signal either does not get through or it gets misdirected to another part of the body and is misinterpreted as pain&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4R2hh.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;So I can say that the nerve cells in the place where you feel real pain fails to transmit the signal to brain via its neighboring nerve cell instead that signal passes through some other node randomly (or it might take the same path every time you touch the pain area) and signal the brain which gets misinterpreted and make you feel that you have pain in the misinterpreted region.&lt;/p&gt;&#xA;" OwnerUserId="4547" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-09-26T14:27:48.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10589" PostTypeId="2" ParentId="10551" CreationDate="2013-09-26T14:50:56.333" Score="0" Body="&lt;p&gt;This is a statistical property of the curve - in time to event analysis (which is what a survivorship curve is), a constant hazard (the instantaneous probability of an event occurring in time t given it has not occurred already) will yield an exponentially distributed survival function. When graphed on a log axis, this function looks like a straight line.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2013-09-26T14:50:56.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10590" PostTypeId="1" AcceptedAnswerId="10591" CreationDate="2013-09-26T19:16:23.887" Score="3" ViewCount="328" Body="&lt;p&gt;On a hiking trip to the Alps I found trees whose leaves showed those spots you see on the picture. I am curious about what the cause is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://imgur.com/N4NzQ6E&amp;amp;cN6iLHR#0&quot; rel=&quot;nofollow noreferrer&quot;&gt;Higher resolution pictures of front and back side.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FeJLt.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4550" LastEditorUserId="1306" LastEditDate="2013-09-27T01:13:58.340" LastActivityDate="2013-09-27T01:13:58.340" Title="What is the cause of the spots on this leaf?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10591" PostTypeId="2" ParentId="10590" CreationDate="2013-09-26T19:42:32.073" Score="4" Body="&lt;p&gt;This is a &lt;a href=&quot;http://msue.anr.msu.edu/news/why_do_my_maple_leaves_have_spots&quot; rel=&quot;nofollow&quot;&gt;&quot;Tar Spot&quot;&lt;/a&gt; disease usually found in Europe and North America. It mostly affects the Maple tree leaves. Tar spot is caused by &lt;a href=&quot;http://en.wikipedia.org/wiki/Rhytisma_acerinum&quot; rel=&quot;nofollow&quot;&gt;'Rhytisma acerinum'&lt;/a&gt; a plant pathogen fungus. This pathogen does not seem harm to tree but disturbs the leaves as it finds a suitable condition in summer with bit of wetness. It enters the leaves through stoma and then creates yellow lesions of various sizes over the leaf area which later gradually turns into brown-black tar colored spot. It reduces the photosynthesis process of leaves and thus creating more wide dark spots on the leaves. After sometime the leaves will fall.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Entire detail is available in the Wikipedia link with the detail of the pathogen. (Add some more info if you find this detail not enough)&lt;/p&gt;&#xA;" OwnerUserId="4547" LastActivityDate="2013-09-26T19:42:32.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10592" PostTypeId="1" AcceptedAnswerId="10606" CreationDate="2013-09-26T21:30:27.497" Score="2" ViewCount="120" Body="&lt;p&gt;I'm assuming bacteria, but will take any suggestions.  Organism must survive primarily on the acetate (plus trace elements), but I can give/take electrons, if necessary.  Not interested in strict anaerobes.  I've tried &lt;em&gt;Shewanella oneidensis&lt;/em&gt;, but have not succeeded in getting it to eat any acetate (just lactate).  Feel free to give journal refs.  Self-promotion won't be frowned upon if it's helpful.  :-)  Opportunity for joint pub, if successful.  &lt;/p&gt;&#xA;" OwnerUserId="4551" LastEditorUserId="1306" LastEditDate="2013-09-26T21:55:54.267" LastActivityDate="2013-09-27T14:19:15.310" Title="Aerobe or facultative anaerobe organism that metabolizes acetate?" Tags="&lt;microbiology&gt;&lt;metabolism&gt;&lt;bacteriology&gt;&lt;yeast&gt;&lt;archaea&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10593" PostTypeId="2" ParentId="10584" CreationDate="2013-09-26T21:37:30.293" Score="2" Body="&lt;p&gt;Actually, if you could get the oxygen in there, you would probably turn the dead zone into a &quot;feast zone,&quot; because all that algae would be food.  But I think it would be prohibitively expensive.  Fish tanks aren't deep, so it doesn't take much pressure to force air bubbles into the bottom.  And they're not large in volume, so you don't need huge amounts of air bubbling.  Oceans, or even rivers or harbors, would be another matter.&lt;br&gt;&#xA;Also, some of the algal blooms are poisonous &quot;red tides.&quot;&lt;/p&gt;&#xA;" OwnerUserId="4551" LastActivityDate="2013-09-26T21:37:30.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10594" PostTypeId="2" ParentId="10524" CreationDate="2013-09-26T21:43:28.517" Score="2" Body="&lt;p&gt;First of all 'Testosterone' hormone controls the growth of hair on our body and also oil secretion. Depending up on the nature of a person's body, this hormone controls the growth of the hair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why shaving facial hair leaves the skin dry ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First let me explain the reason behind the oiliness of the skin. Sebum is produced by the sebaceous glands and is a complex made up of cholesterol, free fatty acids, glycerides, squalene, and wax esters. Sebum and sweat, along with the epidermal lipids discussed earlier, make up the oil on the surface of the skin. Some people will have more oily skin and some have less which depends on the nature of body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While shaving the sharp razor cuts the hair and also damages the skin and hair follicles. The level of damage to skin also depends whether you are shaving downwards or upwards. Because upward shaving usually causes more damage to skin and hair follicle. Complete detail of damage to hair follicle can be found in this article: &lt;a href=&quot;http://blog.modernmechanix.com/exploring-the-science-of-shaving/&quot; rel=&quot;nofollow&quot;&gt;Science of shaving&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Shaving also removes skin lipids and water content creates pores which exposes the skin. If the surrounding atmosphere is dry then skin loses water. Or if the surrounding is moist or humid then water content will be balanced. That is the reason why we use artificial face moisturizer for immediate remedy to avoid infection and balance the wetness of face. So it takes a while for the skin to get back to normal state if nothing is done after shaving which sometime leads to acne or rashes due to infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another reason for dry face is use of hot water which removes skin oil instantaneously. So lukewarm water or cold water will further reduce the dryness of the skin. (Use of shaving cream with high alkaline content will obviously result in dry skin. This holds for soaps also.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Complete details can be found in the first link provided and &lt;a href=&quot;http://www.livestrong.com/article/301811-my-skin-is-dry-after-shaving/&quot; rel=&quot;nofollow&quot;&gt;Drying skin after shave&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4547" LastActivityDate="2013-09-26T21:43:28.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10596" PostTypeId="2" ParentId="10542" CreationDate="2013-09-26T21:49:50.863" Score="0" Body="&lt;p&gt;It certainly does not &lt;em&gt;require&lt;/em&gt; full darkness.  I've often slept quite restfully with the reading lamp left on all night, and children who are afraid of the dark do this habitually.  However, full darkness may PROMOTE melatonin release.&lt;/p&gt;&#xA;" OwnerUserId="4551" LastActivityDate="2013-09-26T21:49:50.863" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10599" PostTypeId="1" AcceptedAnswerId="10641" CreationDate="2013-09-27T07:35:01.900" Score="2" ViewCount="661" Body="&lt;p&gt;I've just read about krokodil and saw some quite hideous pictures about what it does to the human body. I guess just desomorphine alone wouldn't have this effect. &lt;br/&gt;&#xA;Which ingredient(s) causes the damage to the tissue? &lt;/p&gt;&#xA;" OwnerUserId="673" LastActivityDate="2013-09-30T16:38:57.990" Title="Which is the tissue damaging agent in krokodil (street desomorphine)" Tags="&lt;physiology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10600" PostTypeId="1" CreationDate="2013-09-27T07:45:11.783" Score="4" ViewCount="65" Body="&lt;p&gt;I want to find the &lt;strong&gt;RNAseq&lt;/strong&gt; data available on domestic animals in different environments. If &lt;strong&gt;microarray&lt;/strong&gt; data is available, it would be more useful. If you know I would appreciate to inform me.&lt;/p&gt;&#xA;" OwnerUserId="4553" LastEditorUserId="107" LastEditDate="2013-09-27T12:09:27.357" LastActivityDate="2013-09-27T14:35:30.447" Title="RNA-seq Data on domestic animal with different environment" Tags="&lt;bioinformatics&gt;&lt;rna&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10601" PostTypeId="2" ParentId="10542" CreationDate="2013-09-27T09:21:06.277" Score="1" Body="&lt;p&gt;The immediate thought came to my mind was relation between Melatonin and Serotonin. Because both hormones have sleep related function. I read that both are light sensitive. Melatonin is produced by pineal gland in brain whereas Serotonin is at gut and CNS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Melatonin&quot; rel=&quot;nofollow&quot;&gt;Light dependence(Wikipedia)&lt;/a&gt; of Melatonin is explained here where they say blue light produces more Melatonin and wavelength of light &amp;lt;530nm will have effect on Melatonin production. If the light intensity is more then Melatonin will not be produced. So what they say is if there is darkness(artificial) or dim light environment then this hormone will be produced and induces sleep. Almost everywhere they explain Melatonin whose production is sensitive to light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(But even in the afternoon when there is bright light some of us feel sleepy which is mainly due to Serotonin released after heavy meal which is produced from tryptophan. This will again effect the sleep. It is obvious that without food we can not sleep at night. So Serotonin and Melatonin are interrelated as explained here &lt;a href=&quot;http://www.thesleepguru.co.uk/insomniatryptophan-melatonin-and-serotonin&quot; rel=&quot;nofollow&quot;&gt;Link1&lt;/a&gt; and &lt;a href=&quot;http://www.livestrong.com/article/336314-serotonin-vs-melatonin/&quot; rel=&quot;nofollow&quot;&gt;Link2&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="4547" LastActivityDate="2013-09-27T09:21:06.277" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10602" PostTypeId="1" CreationDate="2013-09-27T10:27:32.583" Score="1" ViewCount="268" Body="&lt;p&gt;If any given molecule is polar, and is capable of hydrogen bonding, I can be sure that it's hydrophilic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, are those two the only conditions that make a molecule hydrophilic?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2013-09-27T21:08:23.057" Title="Hydrophilicity and polarity" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2013-10-03T21:08:12.577" ContentLicense="CC BY-SA 3.0" />
  <row Id="10603" PostTypeId="2" ParentId="10203" CreationDate="2013-09-27T11:22:13.970" Score="7" Body="&lt;p&gt;Black soldier fly &lt;em&gt;Hermetia illucens&lt;/em&gt;&lt;img src=&quot;https://i.stack.imgur.com/012Ha.jpg&quot; alt=&quot;Black soldier fly.&quot;&gt;. &lt;a href=&quot;http://en.wikipedia.org/wiki/Hermetia_illucens&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Hermetia_illucens&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a good key to the Dipteran families &lt;a href=&quot;ftp://delta-intkey.com/britin/dip/www/key.htm&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;. Although it is for British families, it is very thorough.&lt;/p&gt;&#xA;" OwnerUserId="445" LastActivityDate="2013-09-27T11:22:13.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10605" PostTypeId="1" AcceptedAnswerId="20307" CreationDate="2013-09-27T13:11:09.550" Score="2" ViewCount="126" Body="&lt;p&gt;If a frog is gradually exposed to increasing concentration of salts can they acclimatise or will they die of exosmosis ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-08-07T14:36:22.437" Title="Osmoregulatory Acclimatization in amphibians" Tags="&lt;homework&gt;&lt;osmoregulation&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10606" PostTypeId="2" ParentId="10592" CreationDate="2013-09-27T14:19:15.310" Score="1" Body="&lt;p&gt;You could try &lt;em&gt;Paracoccus denitrificans.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a study where acetate is used as the growth-limiting substrate: &lt;a href=&quot;http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.320.1692&amp;amp;rep=rep1&amp;amp;type=pdf&quot; rel=&quot;nofollow&quot;&gt;http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.320.1692&amp;amp;rep=rep1&amp;amp;type=pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the details of its version of acetate kinase: &lt;a href=&quot;http://www.uniprot.org/uniprot/A1B9S8&quot; rel=&quot;nofollow&quot;&gt;http://www.uniprot.org/uniprot/A1B9S8&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd be happy to collaborate with you further on this.&lt;/p&gt;&#xA;" OwnerUserId="4539" LastActivityDate="2013-09-27T14:19:15.310" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10607" PostTypeId="2" ParentId="8997" CreationDate="2013-09-27T14:29:50.597" Score="1" Body="&lt;p&gt;Human tooth decay is mostly from eating foods high in sugar.  So animals don't generally get cavities.  (Except for humans' pets.)  But animals can have other tooth problems.  For example, elephants grind down their molars from eating so much plant material.  Fortunately for them, they have a supply of new molars that come in regularly.  Unfortunately for them, that supply is limited.  When an elephant runs out of molars, it dies of starvation.  Another example is plaque on dogs' teeth, which can lead to gum disease just like in humans.&lt;/p&gt;&#xA;" OwnerUserId="4551" LastActivityDate="2013-09-27T14:29:50.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10608" PostTypeId="2" ParentId="10600" CreationDate="2013-09-27T14:35:30.447" Score="3" Body="&lt;p&gt;There is something called &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/&quot; rel=&quot;nofollow&quot;&gt;GEO&lt;/a&gt;, which is maintained by the NIH and is a massive collection of data obtained from RNA seq, microarray, etc. experiments. One thing you can do is search for a paper that has done what you are looking for. The paper may have a GEO accession number, and you can use that number at the GEO website to find the data you want. You may also search GEO directly but Im not too familiar with it. It may just be easier to find a paper with a GEO accession number.&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-09-27T14:35:30.447" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10609" PostTypeId="2" ParentId="7251" CreationDate="2013-09-27T14:41:01.203" Score="1" Body="&lt;p&gt;I've done experiments with yeast, and they can easily ferment glucose at the rate of 4g/L/d.  Probably faster, if one were to optimize it.  So your numbers don't seem crazy.&lt;/p&gt;&#xA;" OwnerUserId="4551" LastActivityDate="2013-09-27T14:41:01.203" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10610" PostTypeId="1" AcceptedAnswerId="43274" CreationDate="2013-09-27T15:03:57.573" Score="3" ViewCount="206" Body="&lt;p&gt;There are several promising techniques for connectomics based on iterative sectioning and imaging of tissue with scanning electron microscopes (e.g. FIB-SEM and ATUM)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By looking at such micrographs, one can identify synapses:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp; &amp;nbsp; &lt;img src=&quot;https://i.stack.imgur.com/6DctQ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there &lt;strong&gt;any&lt;/strong&gt; way to measure &lt;strong&gt;synaptic strength&lt;/strong&gt; using these types of techniques?&lt;/p&gt;&#xA;" OwnerUserId="4498" LastEditorUserId="1306" LastEditDate="2013-09-27T16:12:57.690" LastActivityDate="2016-02-12T13:39:25.177" Title="Deducing synaptic strength from electron micrographs?" Tags="&lt;brain&gt;&lt;microscopy&gt;&lt;synapses&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10611" PostTypeId="2" ParentId="1588" CreationDate="2013-09-27T15:35:22.643" Score="0" Body="&lt;p&gt;Studies have been done in which saturated fats and cis-unsaturated fats in the diet were replaced with trans-fatty acids. In all cases there were increases in LDL cholesterol, blood triglycerides and Lp(a) lipoprotien, and decreases in HDL cholesterol and particle size of LDl cholesterol. All of these changes result in an increase in the risk of cardiovascular disease. Beyond that the incidence of CHD in prospective studies looking at trans fatty acid consumption has been greater than what would be predicted from the changes in blood lipid profiles. Over the past decades it has become clear that trans fatty acids increase the risk of CHD more than do saturated fats. In addition, they have been shown to increase systemic inflammation and decrease endothelial cell function. The FDA suggests that consumption of trans fats should be kept at 2 gms/ day or lower.  &lt;/p&gt;&#xA;" OwnerUserId="4556" LastActivityDate="2013-09-27T15:35:22.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10612" PostTypeId="1" AcceptedAnswerId="10613" CreationDate="2013-09-27T16:13:58.837" Score="8" ViewCount="115" Body="&lt;p&gt;I'm looking for a website that shows the population sizes of a species (doesn't matter which) as a function of time at a geographic coordinate. Is there a government website or other free database with such information?&lt;/p&gt;&#xA;" OwnerUserId="4557" LastActivityDate="2013-09-27T18:12:12.833" Title="Is there a website that shows population sizes?" Tags="&lt;ecology&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10613" PostTypeId="2" ParentId="10612" CreationDate="2013-09-27T18:12:12.833" Score="9" Body="&lt;p&gt;You can access the Imperial College global population dynamics database.  They will have time series data at specific locations.  &lt;a href=&quot;http://www3.imperial.ac.uk/cpb/databases/gpdd&quot;&gt;http://www3.imperial.ac.uk/cpb/databases/gpdd&lt;/a&gt;&#xA;There is a sister database as well that might be useful. &lt;a href=&quot;http://lits.bio.ic.ac.uk:8080/litsproject/&quot;&gt;http://lits.bio.ic.ac.uk:8080/litsproject/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These contain several hundred time series, and you can see a paper that used them here:  &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2011.01702.x/abstract&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2011.01702.x/abstract&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1097" LastActivityDate="2013-09-27T18:12:12.833" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10614" PostTypeId="2" ParentId="10602" CreationDate="2013-09-27T18:42:13.137" Score="2" Body="&lt;p&gt;I think the answer is no. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The definition of polarity is basically that a molecule has a dipole, and as water has a very large dipole, if a molecule will mix with water readily, its usually pretty polar. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Water also can share its hydrogens in hydrogen bonding, which is an actual shared covalent bond where a hydrogen atom is shared between two acceptors.  The hydrogen bond is fairly weak (~ 0.5 kcal/mol) but water does a lot of hydrogen bonding.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So hydrogen bonding and polarity are often a shared characteristic of an molecule, but are not the same thing.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ions are quite hydrophilic but do not need to be hydrogen bond donors or acceptors.   Chloride  (Cl - ) is not a hydrogen bonding atom - its so acidic that it exists nearly entirely in the Cl- form in water solution. But its definitely electro negative and really soluable in water. Are Ions polar though?  Chloride is symmetrical and so its not really polar.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still is there a polar molecule which is neither a hydrogen bond donor or acceptor?  Acetone and the cyanide ion (CN-) are a polar molecules which have no hydrogen bond donor, but can accept them.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think &lt;a href=&quot;http://en.wikipedia.org/wiki/Sulfate#Structure_and_bonding&quot; rel=&quot;nofollow&quot;&gt;sulfate is an example of a polar molecule&lt;/a&gt; which does not form hydrogen bonds. &#xA;Sulfate (SO4 -- )  has four S-O bonds arranged in a tetrahedron but each of them is highly polar - with 90% of the negative charge on the oxygen.  But like the Chloride ion its so acidic that it much prefers its free ionic state.  It would have very little hydrogen bonding character even when its in water.  Sulfate can form hydrogen bonds, but I think they will only be stable when there are several of them at once.  &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0022283688903415&quot; rel=&quot;nofollow&quot;&gt;Sulfate binding protein has seven hydrogen bonds when it binds sulfate&lt;/a&gt;, using the &lt;a href=&quot;http://en.wikipedia.org/wiki/Chelation#Chelate_effect&quot; rel=&quot;nofollow&quot;&gt;chelation effect&lt;/a&gt; to make the binding strong enough to be stable. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-09-27T21:08:23.057" LastActivityDate="2013-09-27T21:08:23.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10615" PostTypeId="1" AcceptedAnswerId="10617" CreationDate="2013-09-28T02:46:30.540" Score="5" ViewCount="2918" Body="&lt;p&gt;In my biology book's section on disaccharide metabolism and glycolysis, it states that sugars other than glucose must be acted upon to enter glycolysis. Let's take sucrose as an example. Sucrose is hydrolyzed in the small intestine by sucrase. The resulting fructose and glucose are absorbed and transported to the liver via the portal vein. My question concerns the fate of fructose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To undergo glycolysis, the book states that fructose is converted into either fructose-6-phosphate (F6P) or fructose-1-phosphate (F1P). Let's say it is converted to F1P. Aldolase splits this into dihydroxyacetone phosphate and D-glyceraldehyde. Triose kinase then converts D-glyceraldehyde to glyceraldehyde-3-phosphate, a glycolytic intermediate. Where is this occurring in the body? Are we still in the liver? I can't imagine that all the fructose we consume is undergoing glycolysis in the liver. To leave the liver as a sugar, it would have had to been converted to glucose, right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In classes I've taken, I've been told that sugars that enter the liver are pretty much all converted to glucose. Once they are converted to glucose, they can be distributed to the rest of the body, stored as glycogen, etc. If we are going straight from fructose to F1P to a glycolytic intermediate, we couldn't have left the liver. How is such a transformation even useful? Anyone care to shed some light on this?&lt;/p&gt;&#xA;" OwnerUserId="4561" LastEditorUserId="16299" LastEditDate="2015-12-31T17:29:17.020" LastActivityDate="2015-12-31T17:29:17.020" Title="How are non-glucose sugars metabolized in the body?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;metabolism&gt;&lt;glucose&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10617" PostTypeId="2" ParentId="10615" CreationDate="2013-09-28T04:32:51.587" Score="2" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;Where is this occurring in the body?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fructolysis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Almost totally in the liver.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;To leave the liver as a sugar, it would have had to been converted to glucose, right?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Correct, but it's not a direct conversion.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Fructose is metabolized almost completely in the liver in humans, and is directed toward &lt;strong&gt;replenishment of liver glycogen and triglyceride synthesis&lt;/strong&gt;...&lt;/em&gt;&#xA;&lt;em&gt;&lt;strong&gt;...Increased concentrations of DHAP and glyceraldehyde-3-phosphate in the liver drive the gluconeogenic pathway toward glucose-6-phosphate, glucose-1-phosphate and glycogen formation.&lt;/strong&gt; It appears that fructose is a better substrate for glycogen synthesis than glucose and that glycogen replenishment takes precedence over triglyceride formation. Once liver glycogen is replenished, the intermediates of fructose metabolism are primarily directed toward triglyceride synthesis.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;So, Fructose is almost entirely made into &lt;em&gt;something else&lt;/em&gt; first, and then that &lt;em&gt;something&lt;/em&gt; (Glycogen or the Glycerol from triglycerides) gets broken down into Glucose or an intermediate.&lt;/p&gt;&#xA;&lt;p&gt;Fructose stays in the liver because Fructokinase has a pretty low Km (0.5 mM) compared to Glucokinase (12mM) for Fructose, so almost all of the Fructose that enters the liver is phosphorylated into F1P - which cannot leave.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-09-28T04:32:51.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10618" PostTypeId="1" AcceptedAnswerId="10620" CreationDate="2013-09-28T10:25:05.970" Score="5" ViewCount="12260" Body="&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Intron&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For example, introns are extremely common within the nuclear genome of higher vertebrates (e.g. humans and mice), where protein-coding genes almost always contain multiple introns, while introns are rare within the nuclear genes of some eukaryotic microorganisms,[8] for example baker's/brewer's yeast (Saccharomyces cerevisiae). In contrast, the mitochondrial genomes of vertebrates are entirely devoid of introns, while those of eukaryotic microorganisms may contain many introns. &lt;strong&gt;Introns are well known in bacterial and archaeal genes, but occur more rarely than in most eukaryotic genomes.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In my biochemistry course we learned that bacteria have no introns and eukaryots nearly always have them. What's correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do viruses have introns as the Wikipedia article claims?&lt;/p&gt;&#xA;" OwnerUserId="152" LastEditorUserId="152" LastEditDate="2013-09-28T12:46:57.437" LastActivityDate="2018-11-09T21:34:36.977" Title="Which organisms have introns?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10619" PostTypeId="1" CreationDate="2013-09-28T10:42:23.423" Score="1" ViewCount="524" Body="&lt;p&gt;Now I just learn that estrus is a trait in all mammals except Humans. So does it occur significantly in Humans? Of course I'm aware of the cliched &quot;horny&quot;, &quot;aroused&quot; etc., but is it a biological function in Humans too? and if so, when and what is it called?&lt;/p&gt;&#xA;" OwnerUserId="4566" OwnerDisplayName="Dhanushanth R" LastEditorUserId="3632" LastEditDate="2013-09-28T16:42:45.807" LastActivityDate="2013-10-29T15:45:42.893" Title="Is there a human form of estrus?" Tags="&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10620" PostTypeId="2" ParentId="10618" CreationDate="2013-09-28T19:34:43.633" Score="6" Body="&lt;p&gt;As a general rule, a blanket statement in Biology should always be considered false.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It so happens that bacteria do have 'introns' (or at least the intron genomic sequence has been determined) in the sense of the cis-acting autocatalytic Group I and II introns. These are sequences of RNA that adopt such a conformation to catalyze their own excision from an mRNA transcript, and thus may be considered ribozymes, enzyme made of ribonucleic acid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although not generally considered 'introns' segments of RNA are removed during the course of tRNA in both prokaryotes and eukaryotes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now introns that are removed by the action of the spliceosome are strictly found in eukaryotes, as bacteria lack the spliceosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There seem to be a considerable number of papers regarding the question of intron (particularly spliceosomal) phylogeny that should be relatively easy to find if you are so interested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One example paper in which viral introns (Group I) are reported:&#xA;&lt;a href=&quot;http://nar.oxfordjournals.org/content/22/13/2532.abstract&quot; rel=&quot;noreferrer&quot;&gt;http://nar.oxfordjournals.org/content/22/13/2532.abstract&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4140" LastActivityDate="2013-09-28T19:34:43.633" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10621" PostTypeId="2" ParentId="10582" CreationDate="2013-09-28T22:25:52.790" Score="2" Body="&lt;p&gt;Without going into the biochemical details of fatty acid digestion, mobilization, and synthesis, the brief answer is that the animal regulates its own fatty acid composition to within a specified range regardless of its food. Lipid metabolism does not differ from the metabolism of other compounds, in that it is a highly regulated, enzyme-mediated process, which ultimately is genetically determined.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It must be stressed that a heterotroph assimilates its food, not as complete macromolecules, but as their base components. For example, the starch-fed chickens you described would digest the starch down completely to glucose, which would then be converted in the liver to fatty acids. These fatty acids would be, of course, those that the chicken had the enzymes to synthesize, which are consequently mostly saturated fatty acids of a certain length that happen to solidify when cooled.&lt;/p&gt;&#xA;" OwnerUserId="4140" LastActivityDate="2013-09-28T22:25:52.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10622" PostTypeId="1" AcceptedAnswerId="10624" CreationDate="2013-09-28T23:18:32.033" Score="1" ViewCount="581" Body="&lt;p&gt;If I understand right, after repolarization, much of the potassium is outside the membrane and much of the sodium / calcium is inside. How does it get back to the original concentrations (i.e. potassium inside and sodium/calcium outside)?&lt;/p&gt;&#xA;" OwnerUserId="4557" LastActivityDate="2013-09-29T09:29:34.597" Title="What happens to potassium after an action potential?" Tags="&lt;action-potential&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10624" PostTypeId="2" ParentId="10622" CreationDate="2013-09-29T09:29:34.597" Score="4" Body="&lt;p&gt;During the repolarization, relatively few ions need to cross the membrane for the membrane voltage to change and therefore the change in ions concentration outside and inside the cell is neglible. After repolarization, the concentrations are restored by the continuous action of Na⁺/K⁺-ATPase. The same happens for calcium, but I don't know exactly what kind of pump is used.&lt;/p&gt;&#xA;" OwnerUserId="3523" LastActivityDate="2013-09-29T09:29:34.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10625" PostTypeId="2" ParentId="10188" CreationDate="2013-09-29T10:23:10.233" Score="2" Body="&lt;p&gt;&lt;strong&gt;It is not true that the anticodon of an uncharged tRNA can't bind to the mRNA.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria have a mechanism called &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Stringent_response&quot; rel=&quot;nofollow&quot;&gt;stringent response&lt;/a&gt;&lt;/em&gt;. This response is complicated, here is a shorter and simplified explanation. Further informations can be found at the wikipedia pages linked in the text.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If during translation a certain amino acid is absent, an uncharged tRNA binds in the ribosome, causing the synthesis of the alarmone &lt;a href=&quot;http://en.wikipedia.org/wiki/%28p%29ppGpp&quot; rel=&quot;nofollow&quot;&gt;(p)ppGpp&lt;/a&gt; by activation of the RelA enzyme (in E. coli), associated with the 50S subunity of the ribosome. The translation blocks and (p)ppGpp interacts with β subunit of RNApol causing:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;the reduction of its affinity for the σ70 transcription factor and therefore reducing the transcription of rRNA genes;&lt;/li&gt;&#xA;&lt;li&gt;the increase of its affinity for σS and σN, transcription factors needed, rispectively, for the adaptation at the stationary phase and the lack of N. Also biosynthesis of amino acids is enhanced.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Once the situation is restored, the enzyme SpoT (coli) hydrolizes (p)ppGpp.&lt;/p&gt;&#xA;" OwnerUserId="3523" LastActivityDate="2013-09-29T10:23:10.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10626" PostTypeId="1" CreationDate="2013-09-29T10:50:08.457" Score="8" ViewCount="1001" Body="&lt;p&gt;I'm studying &amp;quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=PMC3396368&quot; rel=&quot;nofollow noreferrer&quot;&gt;Deep sequencing the circadian and diurnal transcriptome of Drosophila brain&lt;/a&gt;&amp;quot; Hughes &lt;em&gt;et al.,&lt;/em&gt; 2012. I've got some problems with the materials and methods.&lt;/p&gt;&#xA;&lt;p&gt;Before RNAseq, the authors amplify RNA. They use two kits: Poly(A) based and non-poly(A) based. For the samples Poly(A) based amplified they do a sequencing to generate 100 bp paired-end and for the samples Non poly(A) based they do a sequencing to generate 75 bp single-ends.&lt;/p&gt;&#xA;&lt;p&gt;I read in the strategy:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Total RNA was amplified, and ribosomal RNA was depleted, using a non-poly(A)-based amplification kit, which significantly diminishes the 3' bias in downstream libraries used for RNA-seq (see Methods).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;I don't understand why they use both kits. Actually, they say that they want to asses the bias introduced by an alternative amplification methods BUT the following sequencing is not the same in both cases so there is more than one parameter which change between the two protocols so I don't understand how they can compare.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;For the poly(A) based I understand that the rRNA are not polyadenylated so they remove rRNA from the amplified sample. However, don't they remove non-coding RNA too (long or short)?&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;For the non poly(A) based, I don't understand how they remove the rRNA but I understand that since they don't select the RNA according to their poly(A) tails they keep the rest of the RNAs which are not kept in the poly(A) based amplification.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When I look to the RUM statistics, I see that there are fewer total aligned reads in non-poly(A) based: 70-80% (non polyA) and 80-90% (polyA). So it seems like we lose some information with non-poly(A) based.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;To sum up, why the authors use Poly(A) and non-poly(A)? Why do they show all the rest of the results from the non-poly(A) amplification since they have less aligned read? How do they compare since the following sequencing is not the same? How the rRNA are removed in both techniques and especially in non-poly(A)?&lt;/p&gt;&#xA;&lt;p&gt;I didn't find the protocols kit with exactly the same name but here are the links to the protocols which are closer (I think).&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mscience.com.au/upload/pages/nugen/nugen_ov_rna_seq-brochure.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.mscience.com.au/upload/pages/nugen/nugen_ov_rna_seq-brochure.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://excilone.com/client/document/ug-arcturusE%E2%80%9E%C2%A2-riboamp%C3%82-hs-plus-amplification-kit-user-guide_38.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://excilone.com/client/document/ug-arcturusE%E2%80%9E%C2%A2-riboamp%C3%82-hs-plus-amplification-kit-user-guide_38.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4564" LastEditorUserId="948" LastEditDate="2020-10-16T23:39:06.817" LastActivityDate="2020-10-16T23:39:06.817" Title="RNA seq and using of Poly(A) or non-Poly(A) based amplification of RNA" Tags="&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="10627" PostTypeId="2" ParentId="10619" CreationDate="2013-09-29T14:52:32.380" Score="1" Body="&lt;p&gt;By 'human estrus', I take it to mean that the female shows some increased desire when they are fertile.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the height of fertility, which coincides with estrus, female behavior changes a stronger interest in sexual activity is exhibited.  In many primates in general, the female may give of a strong scent or even physically show color or swelling that indicates even to observers of other species that they are fertile, also engendering sexual behavior in the males.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://pin.primate.wisc.edu/factsheets/entry/gelada_baboon/behav&quot; rel=&quot;nofollow&quot;&gt;For instance, baboons are well known for reddening of the female's rump and they also emit a strong scent&lt;/a&gt;.  Non - primates also show estrus - most of us know how dogs and cats can change their behavior.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human signs of Estrus is of great interest to primatologists, evolutionary biologists and psychologists as it influences the biology and the social nature of people.  It has been proposed that humans do not exhibit estrus and this is still an influential idea. Certainly its difficult to look at a woman and tell whether she is ovulating and most women themselves cannot tell when that is happening.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still, examination of behavior and appearance have shown that womens appearance does change over their monthly fertility cycle.  Women's &lt;a href=&quot;http://www.livescience.com/25457-fertile-women-attractiveness.html&quot; rel=&quot;nofollow&quot;&gt;faces may become thinner at higher fertility&lt;/a&gt; and this and other cues &lt;a href=&quot;http://en.wikipedia.org/wiki/Estrous_cycle#Humans&quot; rel=&quot;nofollow&quot;&gt;make them more desirable on the average&lt;/a&gt;.  &lt;a href=&quot;http://news.discovery.com/human/life/women-ovulation-hormones-behavior.htm&quot; rel=&quot;nofollow&quot;&gt;While their sexual desire is not clearly higher, female perception of men's faces changes too&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While this is quite different than the typical definition of estrus, the biochemical cycle of fertility does affect human social behavior and preferences, perceptions.  The evolutionary reasons for these changes are probably adapted to the highly social nature of human existence and the fact that offspring are such a large investment. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-09-29T14:52:32.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10628" PostTypeId="2" ParentId="10520" CreationDate="2013-09-29T22:37:15.617" Score="5" Body="&lt;p&gt;You are correct that cocaine &quot;fills the tunnel&quot; (the pharmacology terminology is that it &quot;blocks the transporter&quot;).  But it is not an autoreceptor, so the reuptake transporter does not send a stop signal, it just removed neurotransmitter from the cleft.  But once you've blocked it with cocaine, neurotransmitter is not being removed from the cleft so it has a much longer and stronger signaling effect on the post-synaptic neuron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But cocaine can also block sodium channels, which assist in action potential propagation and that has more of a local anesthetic effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The effect you are thinking of would pertain to auto-receptors, not reuptake transporters.  Autoreceptors tend to be more like the post-synaptic targets of the neurotransmitter.&lt;/p&gt;&#xA;" OwnerUserId="1853" LastActivityDate="2013-09-29T22:37:15.617" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10632" PostTypeId="1" CreationDate="2013-09-30T04:17:31.953" Score="11" ViewCount="32364" Body="&lt;p&gt;Non-allelic or non-alletic&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I stumbled across the term in my Human Genetics textbook. It didn't explain it there, and a quick google search only showed scientific papers that refer to 'recombinations with non-allelic genes' without explaining what they are. &lt;/p&gt;&#xA;" OwnerUserId="4568" LastActivityDate="2020-04-01T00:14:40.080" Title="What's a non-allelic gene?" Tags="&lt;genetics&gt;&lt;recombination&gt;" AnswerCount="7" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10633" PostTypeId="1" AcceptedAnswerId="10652" CreationDate="2013-09-30T05:35:31.990" Score="15" ViewCount="1097" Body="&lt;p&gt;Are the photoreceptors in our eyes not fast enough to register the fast moving bullet, or is the brain not powerful enough to make sense of something happening that fast?&lt;/p&gt;&#xA;" OwnerUserId="3141" LastEditorUserId="9943" LastEditDate="2015-08-29T14:06:28.050" LastActivityDate="2016-09-03T06:24:48.923" Title="Is it a limitation of the eyes, or the brain, that we can't see a moving bullet?" Tags="&lt;brain&gt;&lt;vision&gt;&lt;perception&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10634" PostTypeId="2" ParentId="7836" CreationDate="2013-09-30T07:34:15.913" Score="1" Body="&lt;p&gt;There is a paper for transfection of mammalian cells here which has a bit of &lt;a href=&quot;http://dx.doi.org/10.1186/1472-6750-13-52&quot; rel=&quot;nofollow&quot;&gt;comparison of stop codon and protein yield&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise &lt;a href=&quot;http://dx.doi.org/10.1093/nar/gkl074&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; suggests having a 'rare' codon after the stop to prevent readthrough. But yes, I'm not sure why one wouldn't simply put two stops after each other.&lt;/p&gt;&#xA;" OwnerUserId="4570" LastEditorUserId="57" LastEditDate="2013-09-30T23:09:11.573" LastActivityDate="2013-09-30T23:09:11.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10635" PostTypeId="1" CreationDate="2013-09-30T10:39:21.990" Score="5" ViewCount="79" Body="&lt;p&gt;Most modern rodenticides are claimed to cause death no earlier than several days after ingestion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's quite strange - once a chemical was ingested it will be absorbed in the digestive system and enter the blood stream and rapidly spread around the body (something like within ten hours - that's what most human medications claim in &lt;em&gt;pharmacokinetics&lt;/em&gt; sections of their manuals). I'm pretty sure a rodent is very similar to a human in terms of digestive system functioning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then how do rodenticides not kill the rodent earlier than in several days after ingestion?&lt;/p&gt;&#xA;" OwnerUserId="466" LastActivityDate="2013-10-01T09:00:24.127" Title="How do rodenticides with delayed effect work?" Tags="&lt;biochemistry&gt;&lt;mammals&gt;&lt;toxicology&gt;&lt;rodents&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10637" PostTypeId="1" AcceptedAnswerId="10638" CreationDate="2013-09-30T12:02:22.910" Score="3" ViewCount="754" Body="&lt;p&gt;I'm working on a project that concerns movement and the human body. Before I begin to experiment, I need an answer to a question I'm sure has an answer, but doesn't Google well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I need to know is firstly whether I can assume that if people have the same height, they will also have the same leg length?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, if two different people have an identical height, will they take the same amount of time to cover the same distance when running at the same speed, regardless of their unique technique for running?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An Example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Say I'm with a friend, we're both 6 feet tall exactly, we both get on to treadmills side-by-side and set it to a speed of 7.5km/hour. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Will we be moving exactly the same body parts at the same time - will our feet land on the treadmill at the same time?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a possibility that people of the same height do not have the same leg length? If so, how likely is it on average?&lt;/p&gt;&#xA;" OwnerUserId="4572" LastEditorUserId="1306" LastEditDate="2013-09-30T16:09:16.183" LastActivityDate="2017-02-15T09:48:55.650" Title="Do people of the same height walk at the same speed?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10638" PostTypeId="2" ParentId="10637" CreationDate="2013-09-30T12:38:25.577" Score="3" Body="&lt;p&gt;People of the same height can easily have different leg lengths. Think western women models - currently they are typically women with relatively long legs while ordinary people can easily have shorter legs for the same total height. There's even &lt;a href=&quot;http://en.wikipedia.org/wiki/Body_proportions#Leg-to-body_ratio&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;leg-to-body ration&lt;/em&gt; section in &lt;em&gt;Body proportions&lt;/em&gt; Wikipedia article&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is why pedometers always require &lt;em&gt;calibration&lt;/em&gt; - the procedure in which you have to walk a known distance and count steps and then know how much steps you need per mile. There're no tables that would assist by assuming certain steps-per-mile ration for known height.&lt;/p&gt;&#xA;" OwnerUserId="466" LastEditorUserId="4101" LastEditDate="2013-09-30T13:30:21.037" LastActivityDate="2013-09-30T13:30:21.037" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10639" PostTypeId="2" ParentId="9338" CreationDate="2013-09-30T15:40:08.323" Score="3" Body="&lt;p&gt;To answer your title question: Yes, that is a valid principle of curing HIV. In fact that's pretty much the basic idea behind treating any infection.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;1) HIV strains use a combination of two receptors to enter a cell: CD4 and either CXCR4 or CCR5. It can infect and hide out in any cell which expresses both of these receptors; namely CD4+ T cells and some macrophages.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2) Yes. Except that there are populations of dormant CD4+ T cells in some hard-to-reach tissues such as lymph nodes.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;3 &amp;amp; 4) There are currently five strategies against HIV, and each strain may be vulnerable against one of them but not another - or may develop resistance during treatment. This is why HAART (highly active anti-retroviral therapy) always comprises drugs of three different strategies. An article recommended to me on this is &lt;a href=&quot;http://perspectivesinmedicine.org/content/2/2/a007385.full&quot; rel=&quot;nofollow&quot;&gt;Shattock and Rosenberg, 2012: Microbicides: Topical Prevention against HIV&lt;/a&gt;. Or in particular, this graphic from the article is a great summary: &lt;a href=&quot;http://perspectivesinmedicine.org/content/2/2/a007385/F1.expansion.html&quot; rel=&quot;nofollow&quot;&gt;http://perspectivesinmedicine.org/content/2/2/a007385/F1.expansion.html&lt;/a&gt;. Briefly: Drugs either inhibit viral entry into a cell by blocking the receptors mentioned above; or they target the viral reverse transcriptase (two strategies for this one), integrase or protease. *)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;5) No - although partial activity by the drugs against human enzymes is the cause of side effects.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;6) Yes, and we are doing so already (or rather, take them orally - no need for bothersome injections). The only problem is that the above-mentioned dormant cell populations are already infected and have integrated HIV, but it is not being active and hence not noticed by the immune system and not affected by our drugs. As long as HAART is maintained, viral loads in the blood are reduced to near-zero and the patient is for all intents and purposes healthy (including not transmitting HIV) - any latent virus that activates will immediately be wiped out. However, when HAART is interrupted even briefly, the virus can relapse.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Reaching those dormant populations is the focus of current research. If a person starts HAART very shortly after initial infection, before the virus can reach those populations, it is possible to cure them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of third world, the problem is not the drugs but getting them to the people who need them (money, transport, distribution, legal systems, civil wars etc.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*) These are not simply 'chemical X from virus' and 'destroy chemical X'. Our drugs do not destroy the viral particles themselves but prevent them from replicating in a live system. If you mix HIV particles and the drugs in a test tube, leave it for 20min, filter the particles out and inject them into somebody, you will still infect them. There has probably been research into antibodies to target viral particles but I don't know any detail of this.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2013-10-01T17:14:59.383" LastActivityDate="2013-10-01T17:14:59.383" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10640" PostTypeId="2" ParentId="10626" CreationDate="2013-09-30T16:33:38.790" Score="4" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Yes, it was odd that they said that. The second protocol with the polyA based method had another purpose though, which was &quot;examine the reproducibility of period-regulated genes in an independent genetic background&quot;. I would suspect this was its main purpose, and not so much to look at fragment bias, &lt;a href=&quot;http://genomebiology.com/content/12/3/R22&quot; rel=&quot;nofollow&quot;&gt;which has already been done in other papers&lt;/a&gt;. They didnt even publish this data in the main paper, they put it in the supplement. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Yes, this would remove any transcript without a polyA tail. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;One way of purifying is by using oligos that are antisense specifically to rRNA. The oligos will be attached to some solid phase, on a column or a bead or something, and the rRNA will stick to it and everything that doesnt is what will remain in your sample&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It is not safe to say that you lose information with polyA based kits. The polyA based technique had reads that were single end and only 75bp long. This is compared to the other protocol which was 100bp paired. Reads that are 75bp will align much more easily than 200 bp (100 x 2 since its paired). However, there will not be as much certainty in the alignments, as there is a greater chance it will align to multiple locations in the genome, or align to the wrong location. So yes they have more reads aligned but I would be hesitant to make any conclusions from this. And if you look at total numbers of reads, the non-polyA method aligned more. Again, I dont think the main purpose was to show that one method is better than another.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Basically the method you choose depends on your experiment and your samples. Random hexamers will give you non-coding RNA which is important in some experiments, and that is its main advantage. It will also give more uniform coverage across the gene (no 3' bias). Poly(A) selection will give you only mRNA, however you will miss any transcripts that are degraded or partially degraded. If you have a high quality sample or a large amount of starting material this is less of a concern. As mentioned before you end up missing parts of the 5' end on some transcripts with this method. If you have a low abundance transcript that you are trying to find, polyA selection is probably best, as it is more likely to be captured and you will capture the whole thing, rather than just getting bits and pieces of it with random hexamers. They both have advantages and disadvantages. Hopefully this helps you or someone make a decision. &lt;/p&gt;&#xA;" OwnerUserId="4199" LastEditorUserId="4199" LastEditDate="2013-11-12T21:13:20.527" LastActivityDate="2013-11-12T21:13:20.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10641" PostTypeId="2" ParentId="10599" CreationDate="2013-09-30T16:38:57.990" Score="0" Body="&lt;p&gt;&lt;strong&gt;Note: Don't click on the links, or even search for information, if you don't have a strong stomach&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I've read, it's not necessarily 100% known, most likely because it's not easy to study (small, reclusive users who die quickly of a complex concoction) but the &lt;a href=&quot;http://www.independent.co.uk/news/world/europe/has-krokodil--the-horrific-street-drug-that-rots-the-flesh-of-addicts--made-the-switch-from-russia-to-the-us-8844314.html&quot; rel=&quot;nofollow&quot;&gt;line everyone has quoted is&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;They extract [the drug] and even though they believe that most of the oil and gasoline is gone, there is still remnants of it. You can imagine just injecting a little bit of it into your veins can cause a lot of damage… it eats you from the inside out&quot;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That's from Dr. Frank LoVecchio in Phoenix, Arizona, who saw two cases within a week.  It's not hugely scientific, but it's not wrong.  Krokodil is never pure and highly toxic chemicals are thus injected into the veins.  If you want specifics, then &lt;a href=&quot;http://animalnewyork.com/2011/flesh-rotting-cheap-heroin-alternative-is-hot-in-russia/&quot; rel=&quot;nofollow&quot;&gt;gasoline&lt;/a&gt;, &lt;a href=&quot;http://www.narconon.org/drug-information/krokodil.html&quot; rel=&quot;nofollow&quot;&gt;hydrochloric acid, phosphorous scraped off matchboxes&lt;/a&gt;, &lt;a href=&quot;http://content.time.com/time/world/article/0,8599,2078355,00.html#ixzz1Puyb832o&quot; rel=&quot;nofollow&quot;&gt;paint thinner, iodine&lt;/a&gt;, and &lt;a href=&quot;http://www.nzherald.co.nz/drug-abuse/news/article.cfm?c_id=181&amp;amp;objectid=10734328&quot; rel=&quot;nofollow&quot;&gt;cleaning oils&lt;/a&gt;.  Injecting any one of those should be enough to kill a repeated user.  Those substances rupture blood vessels, and the subsequent leakage creates gangrenous wounds like you see in the pictures.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-09-30T16:38:57.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10642" PostTypeId="2" ParentId="10584" CreationDate="2013-09-30T16:55:40.860" Score="1" Body="&lt;p&gt;Going from our comment train I thought I'd put this into an answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is similar to the proposal to &lt;a href=&quot;http://science.howstuffworks.com/environmental/green-science/iron-sulfate-slow-global-warming.htm&quot; rel=&quot;nofollow&quot;&gt;dump iron into the sea as that's also supposed to be a limiting reagent for growth&lt;/a&gt;.  There the goal was to sequester carbon from carbon dioxide as dead plankton which would sink into the depths of the ocean.  I'm assuming they did their home work and the cost of producing iron metal, which uses a lot of oxygen is actually worth it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its interesting to observe here that oxygen depletion was not a concern here.  Assuming they have done enough work to show that iron is the only reagent needed to induce the algal blooms, that's a different angle on the problem than you propose. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case the critiques are many because of the scale proposed &lt;a href=&quot;http://deepseanews.com/2012/10/here-we-go-again-with-dumping-iron-into-the-ocean/&quot; rel=&quot;nofollow&quot;&gt;are likely to create other unanticipated side effects&lt;/a&gt;, not the least of which is the massive release of the powerful greenhouse gas nitrous oxide.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The iron dumping experiment was mostly rejected because it was too simplistic.  So, this proposal would require a model - there's no simple back of the envelope calculation that would give a thumbs up/down on this proposal.  The question is - what's the next limiting factor after oxygen/nitrogen?  I'd be surprised if that was not dependent upon location climate and local water chemistry.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lot of red tides are caused by fertilizer and sewage dumps so you may be on to something here. If the goal is to remove nitrogen from the water, not only would it work, but would the cost be reasonable for what you're hoping to get?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unless someone has already built the model I'd guess it would be up to you.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-09-30T16:55:40.860" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10643" PostTypeId="1" CreationDate="2013-09-30T17:33:53.420" Score="1" ViewCount="239" Body="&lt;p&gt;After meiosis each spermatid get either the X chromosome or the Y chromosome. I know that the 4 spermatids formed from 1 spermatogonia are connected by cytoplasm and so the proteins made by X or Y chromosome can be shared by all the 4 cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know what proteins made by X or Y chromosome are exclusive to the X or Y chromosome and are needed to convert spermatids to sperms.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-11-11T12:08:29.803" Title="Need of X or Y chromosome protein after meiosis" Tags="&lt;genetics&gt;&lt;proteins&gt;&lt;reproduction&gt;&lt;meiosis&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10644" PostTypeId="1" CreationDate="2013-09-30T17:36:34.803" Score="4" ViewCount="89" Body="&lt;p&gt;The first polar body formed after meiosis-I is completed in oocyte, may or may not divide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is the statement that &quot;it may or may not divide&quot;? Is it random ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="5762" LastEditDate="2014-07-17T11:09:54.183" LastActivityDate="2014-07-17T11:09:54.183" Title="Division of Polar Body" Tags="&lt;reproduction&gt;&lt;meiosis&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10645" PostTypeId="1" AcceptedAnswerId="10658" CreationDate="2013-09-30T17:41:19.877" Score="4" ViewCount="344" Body="&lt;p&gt;Is it necessary that rate of evolution of longer lived trees will be lesser than that of annuals ? I understand that new individuals will come up faster in annuals  and it may adapt to varying conditions faster but does it necessarily imply that long lived trees will evolve slower ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-02-11T10:52:52.250" Title="Rate of Evolution of population of long lived individuals" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10649" PostTypeId="1" CreationDate="2013-09-30T18:35:01.300" Score="1" ViewCount="4125" Body="&lt;p&gt;I know that sieve tubes do not have ribosomes, nuclei and cytoskeletal elements.&#xA;What other organelles does it not have? Does it have a cytoplasm?&lt;/p&gt;&#xA;" OwnerUserId="4058" LastEditorUserId="4101" LastEditDate="2013-09-30T18:46:42.810" LastActivityDate="2017-11-06T00:56:48.583" Title="Organelles present in sieve tubes" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10651" PostTypeId="1" CreationDate="2013-09-30T18:55:29.737" Score="3" ViewCount="120" Body="&lt;p&gt;If  an arteriole leading to a capillary bed is dilated will the pressure in the vein coming out from the bed decrease ? Will the velocity of blood in the vein change ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-10-01T13:27:34.910" Title="Effect of arteriole dilation on vein" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10652" PostTypeId="2" ParentId="10633" CreationDate="2013-09-30T20:36:20.700" Score="13" Body="&lt;p&gt;It's less a problem of speed and more of raw photon count. Assuming a brightly lit day, the bullet will move so fast that it doesn't reflect enough photons to register against the background. High speed images of bullets usually involve a very bright flash (and other controlled settings) for the camera to pick it up. (Also, a very short flash helps the bullet to appear stationary in the image.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, seeing where your bullets are going is pretty useful. Therefore tracer bullets were created, which are essentially a pyrotechnic flare that you substitute in every 5th bullet, typically in machine gun ammunition. Proof that if you make a bullet bright enough, you can register it just fine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Tracer_ammunition&quot;&gt;http://en.wikipedia.org/wiki/Tracer_ammunition&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-09-30T20:36:20.700" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10653" PostTypeId="2" ParentId="10649" CreationDate="2013-09-30T20:49:07.540" Score="2" Body="&lt;p&gt;The sieve tubes of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Phloem&quot; rel=&quot;nofollow&quot;&gt;phloem&lt;/a&gt; in &lt;a href=&quot;http://en.wikipedia.org/wiki/Angiosperm&quot; rel=&quot;nofollow&quot;&gt;angiosperms&lt;/a&gt; consist of &lt;a href=&quot;http://en.wikipedia.org/wiki/Sieve_tube_element&quot; rel=&quot;nofollow&quot;&gt;sieve tube elements or members&lt;/a&gt;. These are cells which lose their nucleus, ribosomes, and vacuoles at maturity.  They of course have cytoplasm, and it is connected by channels to companion cells (which do have these organelles).  The sieve tube elements retain mitochondria and plastids. See the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sieve_tube_element&quot; rel=&quot;nofollow&quot;&gt;Wikipedia page&lt;/a&gt; and &lt;a href=&quot;http://facweb.furman.edu/~lthompson/bgy34/plantanatomy/plant_cells.htm&quot; rel=&quot;nofollow&quot;&gt;this page&lt;/a&gt; for more details.&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2013-09-30T20:49:07.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10654" PostTypeId="1" CreationDate="2013-10-01T01:27:05.693" Score="2" ViewCount="52" Body="&lt;p&gt;Is there a classification of methods for inferring genetic interactions? I mean some work published, utilizes genetical genomics data.  Is this possible with expression data alone? And how about perturbation screens? I guess they all need information about mutants/genetic variations?&lt;/p&gt;&#xA;" OwnerUserId="4578" LastEditorUserId="3632" LastEditDate="2013-10-01T02:34:54.873" LastActivityDate="2014-04-02T21:26:07.403" Title="What are the methods for infering genetic interactions?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10655" PostTypeId="2" ParentId="10584" CreationDate="2013-10-01T02:25:01.553" Score="1" Body="&lt;p&gt;Bubbles have actually been tried as described on Wikipedia. Usually the issue is layer stratification where the top layer has oxygen but the bottom layer where the decomposition of algae takes place lacks oxygen. Therefore mixers have been employed to bring the de-oxygenated water to the surface where it naturally re-oxygenates. It is interesting to note that one proposed and highly experimental idea is to use mixers to bring cold water from below to reduce the surface temperature to prevent or weaken hurricanes.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;During heavy rain, London's sewage storm pipes overflow into the River Thames, sending dissolved oxygen levels plummeting and threatening the species it supports.[14] Two dedicated McTay Marine vessels, oxygenation barges Thames Bubbler and Thames Vitality are used to replenish oxygen levels, as part of an ongoing battle to clean up the river, which now supports 115 species of fish and hundreds more invertebrates, plants and birds.[14]&lt;/p&gt;&#xA;&lt;p&gt;The dissolved oxygen concentration within Cardiff Bay are maintained at or above 5 mg/L. Compressed air is pumped, from five sites around the Bay, through a series of steel reinforced rubber pipelines, laid on the beds of the Bay and Rivers Taff and Ely. These are connected to approximately 800 diffusers. At times this is insufficient and the Harbour Authority is using a mobile oxygenation barge built by McTay Marine with liquid oxygen stored in a tank. Liquid oxygen is passed through an electrically heated vapouriser and the gas is injected into a stream of water which is pumped from, and returned to, the bay. The barge is capable of dissolving up to 5 tonnes of oxygen in 24 hours.[15]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Water_aeration&quot; rel=&quot;nofollow noreferrer&quot;&gt;Water Aeration&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-01T03:21:35.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10656" PostTypeId="1" CreationDate="2013-10-01T05:11:23.980" Score="1" ViewCount="438" Body="&lt;p&gt;I was telling the theory of evolution to my friends. But they asked me for the proof. They said, we are not seeing any such transition species at present. Neither we have such evidence for evolution. What should I do? I saw many proofs like archaeoptaryx, but now it has been proved that it is fully functional bird and others are also not supporting the theory of evolution given by Darwin! &lt;/p&gt;&#xA;" OwnerUserId="4541" LastActivityDate="2013-10-13T01:26:45.667" Title="Is evolution true as Darwin said?" Tags="&lt;evolution&gt;" AnswerCount="5" CommentCount="8" FavoriteCount="1" ClosedDate="2013-10-15T04:56:40.230" ContentLicense="CC BY-SA 3.0" />
  <row Id="10657" PostTypeId="2" ParentId="10656" CreationDate="2013-10-01T05:26:20.720" Score="4" Body="&lt;p&gt;The best proof of evolution is not in the fossil record, but perhaps in the living things you see around us right now. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance the rise of antibiotic resistant bacteria is the direct result of selection. The environment for the bacteria changed - we introduced antibiotics.  The vast majority of the bacteria die, but eventually the survivors are resistant- just in the space of a few years.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adaptation and even speciation is occurring around us and can be observed directly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A case that all of has seen, and was one of the most important to Darwin's argument in the Origin of Species is how we breed domestic animals.  By selecting animals with characteristics they find desirable, all sorts of animals are created by the use of selection - breeding the animals you want and then not breeding animals with characteristics that are not desirable.  Cats, dogs, horses, sheep - using selection any animal you want can be modified &lt;a href=&quot;http://www.sonoma-marinfair.org/ugly-dog-gallery&quot; rel=&quot;nofollow&quot;&gt;nearly to the point you can't recognize it&lt;/a&gt;.  This is a multibillion dollar industry when you think of all the livestock and pet breeders in the world. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most famous scientific experiment along this lines is &lt;a href=&quot;http://www.americanscientist.org/issues/pub/early-canid-domestication-the-farm-fox-experiment/1&quot; rel=&quot;nofollow&quot;&gt;Dmitry Belyaev's domesticated fox experiment&lt;/a&gt; where over 40 years the foxes who were the friendliest to humans and bred them together.  As a control experiment the most hostile foxes were also bred together.  The result is an animal which is as friendly as a golden retriever, even though no fox had ever before been taken as a pet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are dozens of other stories.  Selection for breeding plants is another such success story.  Though it takes more work and time, Selection is as reliable as electronics as a technology. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Making someone believe something that they don't want to is much harder though.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-10-01T14:43:10.603" LastActivityDate="2013-10-01T14:43:10.603" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10658" PostTypeId="2" ParentId="10645" CreationDate="2013-10-01T05:41:49.383" Score="4" Body="&lt;p&gt;That is true to a certain extent in normal environments, where there is not an excess prevalence of mutagenic elements. The &quot;&lt;a href=&quot;http://www.biomedcentral.com/1471-2148/8/344&quot; rel=&quot;nofollow&quot;&gt;Generation Time Hypothesis&lt;/a&gt;&quot; explains why a &lt;strong&gt;smaller generation time&lt;/strong&gt; and hence a &lt;em&gt;higher reproductive rate&lt;/em&gt; ( as in annuals) corresponds to a &lt;strong&gt;higher rate of mutation&lt;/strong&gt; (substitutions in DNA) and therefore have a faster evolutionary rate as compared to slow reproducing and longer generation time individuals(for example, long-lived trees). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since &quot;fitness&quot;-increasing adaptations produced by somatic variations are very less, the formation of new offsprings giving rise to individuals carrying a DNA which has been subjected to processes (Repeated divisions, replications and translations, amphimixis, and different environment) making it more vulnerable to mutation, becomes mandatory, to propel evolution. This process is much faster in annuals than in long lived trees like &lt;a href=&quot;http://www.fs.fed.us/psw/publications/documents/psw_gtr095/psw_gtr095_harvey&quot; rel=&quot;nofollow&quot;&gt;Sequoia&lt;/a&gt;. Moreover &lt;em&gt;Sexual selection&lt;/em&gt; (especially in animals) operates at a much slower rate in longer-generation time individuals. Next, smaller individuals, having higher metabolic rates usually have shorter generation time (more pronounced in case of animals). Higher metabolic activity is linked to greater mutation rate (&lt;a href=&quot;http://www.nature.com/scitable/knowledge/library/does-life-history-affect-molecular-evolutionary-rates-101925082&quot; rel=&quot;nofollow&quot;&gt;Due to metabolic intermediates acting as mutagens&lt;/a&gt;) and hence faster evolutionary rate. Higher metabolic rate also is linked to higher temperature (faster mutation) and these individuals have a geographic distribution favouring the tropics.(&lt;a href=&quot;http://en.wikipedia.org/wiki/Effective_evolutionary_time&quot; rel=&quot;nofollow&quot;&gt;Again increases evolutionary rate&lt;/a&gt;)  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All these, imply faster evolution for short lived individuals(which usually have higher reproductive rate) as compared to long lived trees. But under &quot;normal&quot; environmental conditions (not drastic and fast changes), the evolutionary rate of large individuals is fast enough to preserve their existence (as the Sequoia prevalence indicates). However, in fast changing environment, larger and long-lived individuals are more likely to be wiped out (probably, this applied to Dinosaurs!).&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2014-02-11T10:52:52.250" LastActivityDate="2014-02-11T10:52:52.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10659" PostTypeId="2" ParentId="10656" CreationDate="2013-10-01T07:54:16.627" Score="9" Body="&lt;p&gt;I saw an excellent public science talk a few weeks ago. The speaker presented 5 questions which, if you answer yes to, you can only come to the conclusion that evolution exists. Firstly though we should define evolution: Evolution is the change in the inherited characteristics of biological populations over successive generations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was one of the best arguments I've seen put forward so I'll try to recreate it here. Put this to them and see what they say - and just in case they say no to any, I've put answers in for you ;) There is no hard evidence for the first four points because they are so damn obvious that if people say no, even after a logic based argument, then all they will ever say is no, they shouldn't need a scientific paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;1) Do individuals reproduce?&lt;/em&gt;&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer to this is undeniably yes, you were the result of reproduction. Reproduction exists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;2) Is there variation among individuals?&lt;/em&gt;&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, again this is undeniable. Do we all look and act the same? No. Are some people taller than others? Yes. Some more physically fit than others? Yes. Is everyone's hair or eye color the same? No. See, undeniable. Variation exists. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;3) Do some individuals die before they get to reproduce?&lt;/em&gt;&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously yes. Children unfortunately die (of natural causes) which means they do no get to reproduce. Just go look in a cemetery or open the obituaries page of you newspaper and you'll likely find some one who died before they could have reproduced. Some people also never reproduce, because of life choices or fertility problems. Variance in reproductive success exists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;4) Do offspring resemble parents?&lt;/em&gt;&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer to this is also yes, when two humans reproduce they (normally) produce something that resembles a human. And when that human reaches maturity they will likely look a more like their parents than a random stranger. Personally I was looking at old family photos recently and I honestly though I had found a picture of me marrying my mother, that's how similar my dad and I look. Heritability of variance exists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;5) Does heritable variation lead to differences in reproductive success?&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you've answered yes to all of the above then you really should be answering yes to this one too. As a hypothetical illustrative scenario, imagine two male deer. One has big antlers and one has small antlers. The size of antlers is largely genetically determined. The male with big antlers is seen as more attractive by a female. She chooses to mate with him. She gives birth to his offspring (n=2, 1 male 1 female) who inherit his genes for large antlers. This repeats with several females in the population (n=10). The smaller male has fewer mating events (n=2) and therefore sires fewer males in the next generation. The next generation contains more males with large antlers (n=10) than small antlers (n=2). This is evolution, the change in the inherited characteristics of biological populations over successive generations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example is humans. We know &lt;a href=&quot;http://www.plannedparenthood.org/health-topics/mens-sexual-health/male-infertility-22754.htm&quot; rel=&quot;noreferrer&quot;&gt;some men have low sperm counts leading to low probability of successful mating&lt;/a&gt;. Further, we know that &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20103481&quot; rel=&quot;noreferrer&quot;&gt;male infertility can be genetically&lt;/a&gt; caused for example by Y-linked genetic defects. Therefore we can expect that males with low sperm counts, caused by Y-linked defects, will have fewer offspring than a healthy male (given equal opportunity to mate) and because all males inherit their fathers Y chromosome they too will have low sperm counts. They will be represented at a lower level in the population's next generation. Again, this is evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Speciation:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It then doesn't take much to jump from this to speciation. It involves the introduction of isolating mechanisms. These can be things like geography (allopatric speciation), or sympatric mechanisms like morphology, behavior, or any trait which prevents one group of individuals mating with another. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll illustrate first, and take the more difficult type - sympatric speciation. Again imagine our deer population. This time there is variance in sperm morphology, and female reproductive tracts. Males can produce two different types of sperm, one (male type S) is a slow moving but more resistant to the hostile female reproductive tract (because it is resistant to all types of antibody the females can produce), the other is faster (male type F) but less resistant (because it is resistant to only some of antibody the females can produce). Female reproductive tracts vary in the number of different antibodies they produce, one produces &quot;all&quot; that can be produced (female type R) and the other only a subset of the full array (female type W).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What will happen is that type S males will be more successful when mating with type R females because their sperm survive (whereas type F males have no sperm fertilizing the egg). However, type F males will be more successful in sperm competition than type S when mating to type W females. Repeated over many generations, these incompatibilities will cause distinct mating groups which do not overlap, i.e. species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In reality it is much simpler to demonstrate this with allopatric speciation. Here two groups of one species become isolated by a geographical feature, like a river. Over time these populations evolve differently (because genetic mutation is random and selection might differ on opposite sides of the river). When they get the opportunity to mate after X generations, they can't because they have evolved genetic incompatibilities (offspring fail to survive, eggs can't bee fertilized).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the absolute classic examples is an experiment using fruit flies by Diane Dodd.   In her experiment she reared a population in two groups, one on starch based food, and one on maltose based food. After many generations (35 I think) the two groups showed mating preference, which is a reproductive isolating barrier, within their groups (mating pairs were more often formed from within treatments). &lt;a href=&quot;http://www.jstor.org/stable/2409365&quot; rel=&quot;noreferrer&quot;&gt;Here is the paper&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7mhwG.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Picture from &lt;a href=&quot;http://evolution.berkeley.edu/&quot; rel=&quot;noreferrer&quot;&gt;http://evolution.berkeley.edu/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="231" LastEditDate="2013-10-01T22:14:38.963" LastActivityDate="2013-10-01T22:14:38.963" CommentCount="15" ContentLicense="CC BY-SA 3.0" />
  <row Id="10660" PostTypeId="2" ParentId="10656" CreationDate="2013-10-01T08:08:50.543" Score="4" Body="&lt;p&gt;Despite evolution is generally macroscopically appreciable after a long time, there are some examples observable right now.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;A classic example is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Peppered_moth_evolution&quot; rel=&quot;nofollow&quot;&gt;evolution of the &lt;strong&gt;peppered moth&lt;/strong&gt;&lt;/a&gt; (Biston betularia) in the last two hundred years. Originally the predominant color was white, which camouflaged them against light-coloured trees such as &lt;em&gt;Betula&lt;/em&gt; plants, while dark-colored moths were rare. During the Industrial Revolution in England the pollution blackened many trees, causing most of the light-coloured moths to die off from predators. The black-coloured ones (called &lt;em&gt;carbonaria&lt;/em&gt;) flourished because of their ability to hide on the darkened trees. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The best example about whole species evolving is the &lt;strong&gt;ring species&lt;/strong&gt;. Here is a good definition from wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In biology, a ring species is a connected series of neighbouring populations, each of which can interbreed with closely sited related populations, but for which there exist at least two &quot;end&quot; populations in the series, which are too distantly related to interbreed, though there is a potential gene flow between each &quot;linked&quot; species. Such non-breeding, though genetically connected, &quot;end&quot; populations may co-exist in the same region thus closing a &quot;ring&quot;.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Ring species provide important evidence of evolution in that they illustrate what happens over time as populations genetically diverge, and are special because they represent in living populations what normally happens over time between long deceased ancestor populations and living populations, in which the intermediates have become extinct. Richard Dawkins observes that ring species &quot;are only showing us in the spatial dimension something that must always happen in the time dimension.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can continue the reading at the related &lt;a href=&quot;http://en.wikipedia.org/wiki/Ring_species&quot; rel=&quot;nofollow&quot;&gt;wikipedia article&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3523" LastEditorUserId="3523" LastEditDate="2013-10-01T08:29:58.237" LastActivityDate="2013-10-01T08:29:58.237" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="10661" PostTypeId="2" ParentId="10635" CreationDate="2013-10-01T09:00:24.127" Score="3" Body="&lt;p&gt;These poisons prevent recirculation of vitamin K and thus formation of prothrombin which is essential for coagulation of blood and are required for maintaining the integrity of capillaries. The depletion of vitamin K is slow and in a couple of days internal hemorrhage occurs extensively and the animal dies of shock. Early recognition of poisoning in humans and other animals can easily be treated with administration of vitamin K. &#xA;&lt;a href=&quot;http://en.m.wikipedia.org/wiki/Rodenticide&quot; rel=&quot;nofollow&quot;&gt;http://en.m.wikipedia.org/wiki/Rodenticide&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4216" LastActivityDate="2013-10-01T09:00:24.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10662" PostTypeId="1" AcceptedAnswerId="10668" CreationDate="2013-10-01T11:10:41.107" Score="4" ViewCount="714" Body="&lt;p&gt;What determines if a metal is suitable for transplantation such as in the hip? What I am most interested in however is why might some metals be toxic to animals once in the body?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="107" LastEditDate="2013-10-01T12:55:32.530" LastActivityDate="2013-10-03T19:03:17.133" Title="What makes a metal safe to use for an artificial joint?" Tags="&lt;biochemistry&gt;&lt;medicinal-chemistry&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10664" PostTypeId="1" AcceptedAnswerId="10666" CreationDate="2013-10-01T13:21:39.957" Score="4" ViewCount="15500" Body="&lt;p&gt;Simple terminology question:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Is there a hard boundary between &lt;em&gt;in vitro&lt;/em&gt; and &lt;em&gt;ex vivo&lt;/em&gt;?&lt;/li&gt;&#xA;&lt;li&gt;Is there a hard boundary between &lt;em&gt;in vivo&lt;/em&gt; and &lt;em&gt;ex vivo&lt;/em&gt;?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Suppose a sensory neuron is electrically recorded in the following settings:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Surgically accessing through the animal's skin, and patch-clamped,&lt;/li&gt;&#xA;&lt;li&gt;Tissue surrounding the neuron is almost separated, but still dangling from the larger part of the animal, and patch-clamped,&lt;/li&gt;&#xA;&lt;li&gt;Same as above, but the slight dangling connection is cut,&lt;/li&gt;&#xA;&lt;li&gt;The sensory neuron is isolated and put in an artificially oxygenated medium&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The sensory neuron is assumed to have purely feedforward signal, and is perfectly healthy in all conditions. Which conditions, if any, are &lt;em&gt;in vivo&lt;/em&gt;, &lt;em&gt;in vitro&lt;/em&gt;, or &lt;em&gt;ex vivo&lt;/em&gt;? (Feel free to propose better hypothetical experiments. I know this example is not the best.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I the only one confused about these terminologies?&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2019-03-21T14:57:08.893" Title="What is an 'ex vivo' experiment?" Tags="&lt;terminology&gt;&lt;experimental&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10665" PostTypeId="2" ParentId="10651" CreationDate="2013-10-01T13:27:34.910" Score="3" Body="&lt;p&gt;All else being &lt;strong&gt;constant&lt;/strong&gt;, velocity of the Venous blood will be reduced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Flow-Rate Equation: Q=AV&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Q = Flow Rate&lt;/li&gt;&#xA;&lt;li&gt;A = Area (of the &quot;pipe&quot;)&lt;/li&gt;&#xA;&lt;li&gt;V = Velocity of the Fluid&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If we assume that the body will try to maintain a constant &lt;em&gt;Q&lt;/em&gt;, then an increase in the &lt;em&gt;A&lt;/em&gt; of the Arteriole means a &lt;strong&gt;reduced&lt;/strong&gt; &lt;em&gt;V&lt;/em&gt; to compensate and a corresponding drop in Venous fluid velocity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we start to assume that things are not constant, then the story becomes more complicated. Since Venous pressure is largely maintained by musculature and other actions, &lt;em&gt;not&lt;/em&gt; heart contractions (though the system is essentially closed-loop), an increase in Arteriole flow-rate doesn't &lt;em&gt;always&lt;/em&gt; correspond to an increase in Venous flow-rate. When there is an imbalance - either due to mechanical interference or something else - conditions like &lt;a href=&quot;http://medical-dictionary.thefreedictionary.com/subcutaneous+edema&quot; rel=&quot;nofollow&quot;&gt;subcutaneous edemas&lt;/a&gt; can occur where the interstitial (between-tissues) fluid builds up enough to cause discomfort or damage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Normal Disclaimer: I am not a medical professional. The above us based upon an Undergraduate level of knowledge.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-10-01T13:27:34.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10666" PostTypeId="2" ParentId="10664" CreationDate="2013-10-01T13:35:55.527" Score="6" Body="&lt;p&gt;&lt;em&gt;Ex vivo&lt;/em&gt; simply means &quot;outside the normal, living organism&quot;, whereas &lt;em&gt;in vitro&lt;/em&gt; means &quot;within glass&quot;, usually in a cultured system.  They are not exactly same as there is no need for the work to be done in a culture system, although both are &lt;strong&gt;not&lt;/strong&gt; &lt;em&gt;in vivo&lt;/em&gt;.  Harvested tissue could be examined &lt;em&gt;ex vivo&lt;/em&gt; without being in a test tube, or surgical systems could be tested &lt;em&gt;ex vivo&lt;/em&gt; on artificial organ models.  &lt;em&gt;In vivo&lt;/em&gt; requires the natural, living organism, although it depends on just how much you are perturbing the natural.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your scenarios,&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;em&gt;in vivo&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;ex vivo&lt;/em&gt;, as it is not within the normal organism, although I could understand someone taking issue with that; definitely not &lt;em&gt;in vivo&lt;/em&gt;, which is usually for normal conditions only, even including temperature.&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;ex vivo&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;If you mean the artificially oxygenated environment of a tissue culture system, then &lt;em&gt;in vitro&lt;/em&gt;; if you mean the artificially oxygenated environment of a lab bench with an open $O_2$ valve, then &lt;em&gt;ex vivo&lt;/em&gt; would suffice.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-01T14:00:04.693" LastActivityDate="2013-10-01T14:00:04.693" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10667" PostTypeId="2" ParentId="10664" CreationDate="2013-10-01T13:44:58.157" Score="3" Body="&lt;p&gt;(Not only) &lt;a href=&quot;http://en.wikipedia.org/wiki/In_vivo&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; states that &lt;em&gt;in vitro&lt;/em&gt; and &lt;em&gt;in vivo&lt;/em&gt; have a very hard boundary between them. I something is studied in the context of an organism, without being extracted, it is &lt;em&gt;in vivo&lt;/em&gt;, as soon as it is extracted it is &lt;em&gt;in vitro&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Strictly speaking, I would count only the first of your neuron examples as &lt;em&gt;in vivo&lt;/em&gt;, because it is still expected to be working like it does inside the organism. As soon as you start having it dangling out, the original &quot;environment&quot; is destroyed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The relation between &lt;em&gt;ex vivo&lt;/em&gt; and &lt;em&gt;in vitro&lt;/em&gt; is less defined. &#xA;I would count example 2 as &lt;em&gt;ex vivo&lt;/em&gt;, but not &lt;em&gt;in vitro&lt;/em&gt;, as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Ex_vivo&quot; rel=&quot;nofollow&quot;&gt;Wikipedia article for ex vivo&lt;/a&gt;  describes. Same goes for example 3. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example 4 is of course &lt;em&gt;in vitro&lt;/em&gt;. Debatable is, if &lt;em&gt;in vitro&lt;/em&gt; excludes &lt;em&gt;ex vivo&lt;/em&gt;. It is still taken out of an organism, not grown artificially, so I would still consider it &lt;em&gt;ex vivo&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-10-01T13:44:58.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10668" PostTypeId="2" ParentId="10662" CreationDate="2013-10-01T14:21:17.943" Score="4" Body="&lt;p&gt;There are a number of reasons why a given metal may be toxic to an animal:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Radioactive metals are the easy ones.&lt;/li&gt;&#xA;&lt;li&gt;Some metals can affect the normal biosynthetic pathways within the body.  Lead is a good example of this, as it can take the place of calcium; I believe beryllium does the same for magnesium.&lt;/li&gt;&#xA;&lt;li&gt;Some metals themselves are very reactive.  Hexavalent chromium ($Cr(VI)$) is highly reactive, and will cause damage through severe oxidative reactions, whereas $Cr(III)$ is largely okay.&lt;/li&gt;&#xA;&lt;li&gt;A lot of metals are okay, even required, at some level, but become toxic at too high a concentration.  Iron, for example.&lt;/li&gt;&#xA;&lt;li&gt;People can simply have allergies to metals.  Nickel in silver jewelry is a good example, although in my experience it can be overcome.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The basic gist is that some metals are required for life, some aren't but aren't too terrible, and some are completely toxic to it.  Different organisms can vary a bit in which metals are useful or not.  A good implant will of course not be toxic at all, and will be strong and long-lasting.  Titanium is often used, given its strength and general nonreactiveness, but so is cobalt, despite being toxic to some degree.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Ref: &lt;a href=&quot;http://jbjs.org/article.aspx?articleid=24918&quot; rel=&quot;nofollow&quot;&gt;Metal Sensitivity in Patients with Orthopaedic Implants.  Hallab, et al. J Bone Joint Surg Am, 2001 Mar 01;83(3):428-428&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-01T14:21:17.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10669" PostTypeId="2" ParentId="10656" CreationDate="2013-10-01T15:55:00.953" Score="2" Body="&lt;p&gt;Of course you dont see a transition species at present! A transitions species is what existed between two other species. When it &quot;becomes&quot; the new species, the transition species no longer exists. Transition species only exist in the past. Its also important to remember that species are a spectrum. When we divide things up into discreet species it makes it seem all neat and tidy but really it is not because of the large amount of variation that exists within a species. When the variation becomes so great that certain members of the species may not be able to interbreed, we break it into two species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also do not see why you need to visually see evolution to believe it exists. The strongest evidence can be found in DNA or protein sequences. Look at any conserved protein and see the similarities. I will give you a link that shows the difference between the mouse and human version of a protein called p53. p53 is studied a lot because it is thought to have a role in cancer. Im not even sure if p53 is considered a &quot;highly conserved&quot; gene, but look at how similar it is!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ebi.ac.uk/Tools/services/web/toolresult.ebi?jobId=clustalw2-I20131001-161406-0148-38128470-oy&quot; rel=&quot;nofollow&quot;&gt;ps53 protein alignment&lt;/a&gt;*&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How many generations difference do you think there is between a mouse and human? [remeber humans did not evolve from mice, they just had a common ancestor, so what I mean is how many generations have elapsed since the last common ancestor]? &lt;a href=&quot;http://www.jimmunol.org/content/172/5/2731.full&quot; rel=&quot;nofollow&quot;&gt;It is estimated that mice / humans disverged some 70 million years ago.&lt;/a&gt; Lets say a generation (age difference between parent and child) is ~30 years in humans (it is much much much much less in mice but lets forget about that) that means there were some ~2 million generations, and thats being conservative. &lt;a href=&quot;http://massgenomics.org/2012/08/de-novo-mutations-and-human-disease.html&quot; rel=&quot;nofollow&quot;&gt;This website &lt;/a&gt;claims there are 74 de novo[new] mutations in humans each generation. Technically this is not all mutations but again we are being conservative. So that is about a 150 million mutation difference between humans and the ancestor that became both humans and mice&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question to you is this: Look again at the similarities between human and mouse p53. You see how there are some differences? Dont you think it is entirely possible that the differences can be accounted for after having 150,000,000 chance mutations?**&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now imagine this happening to every gene, not just p53. That is evolution&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Not sure how long this link will be valid but you can see the sequences at these links and do the alignment yourself &lt;a href=&quot;http://www.ebi.ac.uk/Tools/msa/clustalw2/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/protein/200203?report=fasta&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/protein/200203?report=fasta&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/protein/23491729?report=fasta&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/protein/23491729?report=fasta&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;**Actually double that to account for mouse evolving from the common ancestor but like I said, wanted to be conservative&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-10-01T15:55:00.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10670" PostTypeId="2" ParentId="9247" CreationDate="2013-10-01T16:37:33.270" Score="1" Body="&lt;p&gt;You're talking about the difference between &quot;taste&quot; and &quot;flavor.&quot; In common speech we use these words synonymously, but they actually mean different things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taste refers to the five sensations your tongue can detect -- sweet, sour, salty, bitter and umami. There's growing evidence for a sixth taste, &quot;fat.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Flavor refers to the combination of several factors:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) taste, as just described,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) the aromas of esters, flavinoids, ketones, and other compounds in your food, detected by the nose. This happens a) before you take a bite, and b) as you chew and swallow, releasing different compounds and higher concentrations into your nose through your retronasal passage,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) physical sensations such as texture, heat and cold, visual appearance and even sound (for example, the crunch of celery or potato chips)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) chemesthetic effects, like the astringency of tannins or the &quot;artificial&quot; heat of chili peppers. (The compound responsible for chili heat actually down-regulates physical heat receptors so they're more sensitive. Menthol up-regulates them to create a cooling sensation.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5) Emotional and social factors, like the memory of your grandmother's homebaked bread, or many people's aversion to raw fish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of this put together is why blackberries and strawberries are both sweet and tart, yet blackberries taste like blackberries and strawberries taste like strawberries.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-- The collected works of Karen Page &amp;amp; Andrew Dornenburg&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-- &quot;Tastebuds And Molecules,&quot; Francois Chartier&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-- LOTS of personal empirical evidence (I'm a chef) &lt;/p&gt;&#xA;" OwnerUserId="4582" LastActivityDate="2013-10-01T16:37:33.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10671" PostTypeId="2" ParentId="10662" CreationDate="2013-10-01T17:34:06.090" Score="1" Body="&lt;p&gt;I think  @Amory answer is a good one but I would like to add a new point for the last part of your question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our normal body cells can recruit the immune system when there is infection but the transplants can not. Some findings suggest that bacteria can form a biofilm over that part and  so can become difficult to treat with antibiotics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source : I read this in a book called Good Germs, Bad Germs by Jessica Snyder Sachs&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-10-01T19:13:46.363" LastActivityDate="2013-10-01T19:13:46.363" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="10673" PostTypeId="1" CreationDate="2013-10-01T19:07:12.443" Score="0" ViewCount="804" Body="&lt;p&gt;I tried googling this but couldn't get much information on this. Most of the articles were about induction of flowering.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am more interested in knowing what factors influence the conversion of juvenile phase to adult phase in plants and not the induction of flowering.&#xA;Can a plant survive if it is artificially kept in a juvenile phase ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2020-03-01T16:02:10.403" Title="Change of phase from juvenile to adult in plants" Tags="&lt;botany&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10674" PostTypeId="1" AcceptedAnswerId="10682" CreationDate="2013-10-01T19:18:49.960" Score="3" ViewCount="612" Body="&lt;p&gt;In muscle cells most of the ATP's phosphate is with creatinine phosphate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why is the displacement of the phosphate group done ? Is it because creatinine phosphate would give it's phosphate more easily ? Is it done so that the negative feedback by ATP on mitochondria is not there and more and more ATP can be generated ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-10-02T20:07:20.753" Title="Need of Creatinine Phosphate" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10675" PostTypeId="1" AcceptedAnswerId="10677" CreationDate="2013-10-01T22:12:57.860" Score="1" ViewCount="273" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Terminologia_Anatomica&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; the Terminologia Anatomica (international anatomy standard) the lymphatic trunks are part of the cardiovascular system instead of the lymphoid system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why did they make that choice?&lt;/p&gt;&#xA;" OwnerUserId="152" LastEditorUserId="152" LastEditDate="2013-10-01T22:38:47.807" LastActivityDate="2013-10-02T03:34:52.170" Title="Why are Lymphatic trunks part of the Cardiovascular system?" Tags="&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10676" PostTypeId="1" AcceptedAnswerId="10716" CreationDate="2013-10-02T03:21:07.363" Score="3" ViewCount="203" Body="&lt;p&gt;It has been noted that elephants trained for war, as was done occasionally in earlier times, have still shown a tendency to panic in battle much more often when compared to a war horse trained for the same purpose.  However, is this due to an innate quality of elephant behavior, or a result of poorer training methods due to humans simply having less experience training elephants than horses?  &lt;strong&gt;Are elephants naturally more fearful creatures than horses or other beasts of war&lt;/strong&gt;?&lt;/p&gt;&#xA;" OwnerUserId="3713" LastActivityDate="2013-10-04T17:47:15.647" Title="Fear in elephants" Tags="&lt;zoology&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10677" PostTypeId="2" ParentId="10675" CreationDate="2013-10-02T03:34:52.170" Score="3" Body="&lt;p&gt;The definition of &quot;&lt;em&gt;vascular&lt;/em&gt;&quot; is as follows:-  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;of, relating to, affecting, or consisting of a vessel or vessels, esp.&#xA;  those that carry blood:  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;By this defninition, the cardio-&lt;em&gt;vascular&lt;/em&gt; system doesn't need to include only the blood vessels and the heart. It includes all conducting and distributing vessel elements including those which carry the lymph-Lymphatic vessels. The cardiovascular system stands for the &quot;circulatory system&quot;+ the heart tissues and since lymph is an essential part  of the circulation (of nutrients, hormones, wastes etc), the cardiovascular system must include the lymphatic system.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lymphoid system is a completely different entity which includes spleen, the lymphoid tissue (MALT), the lymph nodes and the lymph vessels. Hence the lymphatic vessels belong to both, the cardiovascular system and the lymphatic system, but the MALT and Spleen (arguable and disputed) are only a part of the lymphatic system and not of the cardiovascular system.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;MALT&lt;/em&gt;= &lt;em&gt;Mucosal Associated Lymphoid TIssue&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2013-10-02T03:34:52.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10678" PostTypeId="2" ParentId="8384" CreationDate="2013-10-02T16:23:47.427" Score="1" Body="&lt;p&gt;Normally, when you need two unique adapters, say A &amp;amp; B, on either end of unknown insert sequences, cohesive-end ligation is difficult because the insert sequences are &quot;unknown&quot;. So you have to do blunt-end adapter ligation, in a reaction containing Unknown Inserts + adapter A + adapter B. This can result in 3 possible versions of insert-ligated product: A-insert-A, B-insert-B and &lt;strong&gt;A-insert-B&lt;/strong&gt;, among which only &lt;strong&gt;A-insert-B&lt;/strong&gt; is the only desired product. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Ligation of A-tailed inserts with Y-adapters gives you 100% &lt;strong&gt;A-insert-B&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Lets now assign a directionality to the insert - say from base 1 to base 400. Following Y-adapter ligation, you will have 2 kinds of insert-ligated products per insert: &lt;strong&gt;A-Insert (1--&gt;400)-B&lt;/strong&gt; and &lt;strong&gt;A-Insert(400--&gt;1)-B&lt;/strong&gt;, both of which are very useful. Each will create a separate clonal cluster and you will get sequence information starting at both base 1 and base 400 of the insert, since in single-read sequencing, the instrument always sequences from Adapter A. However, to know that both these sequences belong to the same insert, one will need to do paired-end sequencing.&lt;/p&gt;&#xA;" OwnerUserId="4590" LastActivityDate="2013-10-02T16:23:47.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10679" PostTypeId="1" AcceptedAnswerId="10778" CreationDate="2013-10-02T18:04:06.310" Score="0" ViewCount="86" Body="&lt;p&gt;The mountain blue bird build nests to attract females and exhibit aggression towards other males during breeding season. Which of the following is likely to give the birds maximal evolutionary fitness?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) stronger aggressive behaviour only during egg laying &lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) stronger aggressive behaviour during nest building rather than during hatching of eggs&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c) stronger aggression when egg is first laid than during nest building&lt;/p&gt;&#xA;&#xA;&lt;p&gt;d) greater aggression during hatching eggs than during nest building&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2013-10-02T18:12:53.220" LastActivityDate="2013-10-08T10:49:59.160" Title="Male behaviour during breeding season" Tags="&lt;homework&gt;&lt;reproduction&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10680" PostTypeId="2" ParentId="8997" CreationDate="2013-10-02T19:19:52.463" Score="4" Body="&lt;p&gt;If this is in comparison to humans, the animals are more or less free from the two common dental diseases by which teeth are lost in humans. These are dental caries (dental decay)  and periodontal disease (gum disease). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Common to both the diseases is the biofilm which forms on the teeth known as dental plaque.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the plaque is colonised by acidogenic (acid producing) micro organisms cavities are produced in the presence of refined carbohydrates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The gum disease is produced by bacterial toxins from the plaque causing inflammation of the surrounding gum resulting in loss of supporting structures of the tooth including bone resulting in loosening and loss of teeth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In animals in the wild, plaque accumulation is effectively controlled by the coarse unprocessed diet which has a very good scrubbing effect. Besides wild animals are not exposed to refined carbohydrates like sugars. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence wild animals do not have these two diseases. However domesticated animals on human diet are prone to similar diseases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In wild animals severe attrition (wear) and fracture of teeth are more common. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wild animals will not survive long without adequate number of functional teeth. &lt;/p&gt;&#xA;" OwnerUserId="4216" LastActivityDate="2013-10-02T19:19:52.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10681" PostTypeId="2" ParentId="8940" CreationDate="2013-10-02T20:07:01.053" Score="2" Body="&lt;p&gt;Normally, cells do not proliferate without a &quot;command&quot;. The &quot;zones of genetic activity&quot; you mentioned are defined by gradients of morphogenic molecules (and cell interactions). In the adult organism the original &quot;map&quot; of concentrations of these molecules is already realized and the pattern they defined before is no longer present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another closely linked idea is that most cells in mature tissues are not able to proliferate, because they have already undergone the process of differentiation. In contrast, stem cells maintain their ability to reproduce. [There are still some ways to de-differentiate some types of cells, i.e. to obtain induced stem cells in vitro.] Thus, embrya are composed of embryonic stem cells, while adult organisms have several restricted pools of stem cells (for example, in haematopoetic organs, where new blood cells are produced.)&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2013-10-02T20:07:01.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10682" PostTypeId="2" ParentId="10674" CreationDate="2013-10-02T20:07:20.753" Score="2" Body="&lt;p&gt;Creatine phosphate is used as a buffer in high energy using cells, such as muscles. In a cell you have a pool of ATP, which is needed for things like muscle contraction, and then you have your pool of creatine phosphate, which can not directly be used as energy for muscle contraction. The cell only stores so much energy as ATP. And during high energy activities it can be depleted quite fast. The problem is that it takes a lot of time to make ATP through oxidative phosphorylation. And while glycolysis is faster, you dont get nearly as much ATP. Creatine phosphate solves this problem by acting as a reserve of ATP, so when ATP is depleted, the creatine phosphate can transfer a phosphate to ADP, and thus restoring ATP without needing to wait for glycolysis or the electron transport chain to complete. &lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-10-02T20:07:20.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10683" PostTypeId="1" AcceptedAnswerId="10686" CreationDate="2013-10-02T20:14:39.980" Score="7" ViewCount="347" Body="&lt;p&gt;Imagine that I built a concrete-walled pool the size of a football field and filled it with fresh water - obtained from another lake but free of bacteria, plantlife, eggs, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would it ever, over time, become a life-filled &quot;lake&quot; - with fish, amphibians, algae, plants and other water-dwellers?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If yes, how?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would the chain of events look like?  I'm assume plant-life would get there first but how would it develop an established eco-system?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please re-tag as appropriate as I am new to this SE site.&lt;/p&gt;&#xA;" OwnerUserId="1192" LastActivityDate="2013-11-19T23:49:56.430" Title="If I built a concrete pool, would it ever contain fish?" Tags="&lt;ecology&gt;" AnswerCount="3" CommentCount="9" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10684" PostTypeId="1" CreationDate="2013-10-02T21:23:38.243" Score="2" ViewCount="442" Body="&lt;p&gt;I am a mathematics grad student researching knot theory, and I've recently discovered that there is a connection between knot theory and DNA structure (if I understand correctly, when DNA strands repackage, they do it in a way similar to what is known as Skein relations in knot theory, therefore tools from knot theory can be applied to DNA research).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem is that I have almost no background in biology, therefore it is difficult for me to understand how exactly DNA repackages and what happens on the molecular level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could anyone suggest some basic (and preferably not too long) text which gives an introduction to the structure of DNA? I have some basic background in organic chemistry, and I am not really looking to understand the topic thoroughly, just to visualize what's going on so I could see the analogy to the mathematical theory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance!&lt;/p&gt;&#xA;" OwnerUserId="4592" LastActivityDate="2013-10-03T03:50:26.970" Title="Basic text/notes on DNA structure (for non-biologists)" Tags="&lt;dna&gt;&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10685" PostTypeId="2" ParentId="10179" CreationDate="2013-10-02T22:03:46.347" Score="10" Body="&lt;p&gt;I don't think, there is a precise answer about the evolutionary mechanisms, but &quot;mechanically&quot;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;mammals have principally just two types of pigments: eumelanin and pheomelanin, both of which have their color variants, but within a known range. Bird pigments, besides melanins, include carotenoids and porphyrins. Arthropods generally have carotenoids, melanins and ommochromes [and other pigments?]. E.g. carotenoids and ommochromes alone can create rather &quot;exotic&quot; coloration from a mammal point of view (green, pink, violet).&lt;/li&gt;&#xA;&lt;li&gt;both birds and insects actively utilize iridescence. With fur it seems to be technically much more difficult to achieve than with feather or scales.&lt;/li&gt;&#xA;&lt;li&gt;many (most?) mammals do not differentiate colors. Birds have much better vision abilities in this respect. From a selectionist point of view this cuts out a considerable part of selection acting upon coloration, which could otherwise produce broader spectrum of phenotypes.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2013-10-02T22:03:46.347" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10686" PostTypeId="2" ParentId="10683" CreationDate="2013-10-02T22:27:20.980" Score="5" Body="&lt;p&gt;if the pool were just sitting out in open air, on earth and all that good stuff, it certainly would, given enough time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This thought experiment is in the same vein that inspired Darwin when he reflected on his experiences on his visit to the Galapagos islands.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think about it - the many islands which are formed by upheaval were lifeless when they first emerged from the ocean.  Over time, the winds or storms eventually populated them all - just about every island has animal life on it.  Not all animal types are found there that are best for the climate; its a matter of accident that some birds or lizards are found on the galapagos islands.  These accidental landings don't happen very often and sometimes a single animal will generate many species which will fill the role that other animals would normally fill on the mainland continents at the same latitude.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is what happened on the islands- in different islands, Darwin found finches of sizes and shapes would be eating insects from bark or ant hills that might be done by an animal &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eventually, if you wait long enough a frog, then maybe a couple of fish will find their way into the pool from a nearby waterway (yeah that could take a long time I know).  If it takes too long then a new species will show up.  If you build walls around the pool it might not happen.  These accidents of animals showing up by accident can take millions of years. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This experience of Darwins' has inspired an entire field of biology - &lt;a href=&quot;http://en.wikipedia.org/wiki/Island_biogeography&quot;&gt;Island biogeography&lt;/a&gt;.  Each island is an experiment and ecological niches can be observed by taking a series of islands and seeing how different animals take up the various ecological roles on each.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Island_biogeography#Research_experiments&quot;&gt;A famous experiment EO Wilson and colleagues did was to fumigate some mangrove islands and watching them repopulate&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-10-02T22:27:20.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10687" PostTypeId="2" ParentId="10684" CreationDate="2013-10-02T22:34:41.100" Score="3" Body="&lt;p&gt;this is a special topic, I'm assuming you have looked over the &lt;a href=&quot;http://www.blc.arizona.edu/molecular_graphics/dna_structure/dna_tutorial.html&quot; rel=&quot;nofollow&quot;&gt;basic Watson and Crick stuff&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe closer to your interests DNA does tangle and needs constant maintenance of the amount of winding to keep it properly ordered.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would look at topoisomerases and DNA origami to start with. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Topoisomerase&quot; rel=&quot;nofollow&quot;&gt;Topoisomerases&lt;/a&gt; are a class of enzymes that help &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16710299&quot; rel=&quot;nofollow&quot;&gt;DNA pack up and wind up into the compact forms of the chromosome when its wound into solenoids in chromatin&lt;/a&gt; and unwind into the looser forms when it is loose.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_origami&quot; rel=&quot;nofollow&quot;&gt;DNA origami&lt;/a&gt; is a field of study which uses DNA as a self assembling template for &lt;a href=&quot;http://www.nature.com/news/fast-dna-origami-opens-way-for-nanoscale-machines-1.12038&quot; rel=&quot;nofollow&quot;&gt;making three dimensional structures&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe this helps?  let me know if we can narrow the specifics of your interests. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-10-02T22:34:41.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10688" PostTypeId="1" AcceptedAnswerId="10704" CreationDate="2013-10-03T00:15:30.537" Score="9" ViewCount="1160" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Animal_echolocation&quot; rel=&quot;noreferrer&quot;&gt;Echolocation&lt;/a&gt; is the ability to obtain spatial information of the surroundings from echos generated by the animal. There are bats and other vertebrates that naturally use it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering if this is limited to vertebrates, or if there are examples among the invertebrate, especially insects.&lt;/p&gt;&#xA;" OwnerUserId="460" LastEditorUserId="3624" LastEditDate="2013-10-03T19:52:49.093" LastActivityDate="2013-10-07T18:59:38.377" Title="Are there echolocating insects?" Tags="&lt;entomology&gt;&lt;invertebrates&gt;&lt;ultrasound&gt;&lt;echolocation&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10689" PostTypeId="2" ParentId="10684" CreationDate="2013-10-03T03:50:26.970" Score="3" Body="&lt;p&gt;We could help you more if you explained &lt;em&gt;how&lt;/em&gt; DNA is similar to Skein relations or, conversely, explain what Skein relations are so we can understand how they're similar to DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As always, the best and most accessible resource will be a university text book. I would recommend &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21054/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Alberts&lt;/a&gt;, as I recall, it explains this topic quite well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're after something a bit more visual, I found some nice ones (click on an image to be taken to its source):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.gistsupport.org/learning-center/cells-cancer-and-more/how-dna-is-packaged-in-a-cell.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/GBUIt.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.shmoop.com/images/biology/biobook_dna_graphik_11.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/DJwVp.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://biologicalexceptions.blogspot.fr/2012/04/on-geometry-and-genomes.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/A4hYb.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.boddunan.com/articles/miscellaneous/51-general-reference/2396-cell-structure-and-expression-energy-conversion-and-cytoskeleton.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/KCkVE.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-10-03T03:50:26.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10690" PostTypeId="1" CreationDate="2013-10-03T04:16:19.663" Score="5" ViewCount="216" Body="&lt;p&gt;This salamander was found in a small forest pond somewhat near the Oregon coast. In the area are many rough skinned newts and a small number of another type of salamander that I still can't find the species of. I'm guessing it is either the salamander species or a rough skinned newt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5kiWI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/4RjYy.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4422" LastEditorUserId="4422" LastEditDate="2013-12-27T20:19:02.347" LastActivityDate="2014-07-02T05:58:52.900" Title="Identification of this Salamander" Tags="&lt;zoology&gt;&lt;species-identification&gt;&lt;herpetology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10691" PostTypeId="2" ParentId="10683" CreationDate="2013-10-03T06:26:31.443" Score="4" Body="&lt;p&gt;I recently dug a pond in a forest, and the first things to happen was not actually plant life. First I found small aquatic animals that lived in the mud, then I found salamander axolotyls and water striders, and crawdads. Salamanders (especially newts), water striders, and crawdads all migrate between ponds to breed and when old ones dry up, as well as various other aquatic animals. The aquatic mud dwellers might have been washed there by rain, or they might have migrated there like the others. In the case of a lake, all of these will happen, although slower because of a lack of sediment with concrete walls. The fish would depend on whether or not there is a waterway connecting the lake to an area where fish already live. These events would happen in the first year except for fish, and pretty soon algae will be growing right after the animals moved, or during, and plants will start to grow as well, their seeds or whatever they use to spread will make their way to the lake. I have found though that lakes, especially man made ones, often contain very little large plant life. As for the time it takes, one year will start it off with basic predator prey relationships, and will slowly grow from there over the course of years.&lt;/p&gt;&#xA;" OwnerUserId="4422" LastActivityDate="2013-10-03T06:26:31.443" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10692" PostTypeId="1" AcceptedAnswerId="10701" CreationDate="2013-10-03T09:29:36.093" Score="1" ViewCount="2540" Body="&lt;p&gt;I am reading a paper which discusses Maize Genome Structure. Descriptions of the  structure is given in the papers introduction.&#xA;I know about heterochromatin &quot;heterochromatin stains intensely, indicating tighter packing. Heterochromatin is usually localized to the periphery of the nucleus&quot;&#xA;but, could someone explain what is knob heterochromatin? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks for help.&lt;/p&gt;&#xA;" OwnerUserId="3230" LastActivityDate="2013-10-03T22:32:52.363" Title="what is knob heterochromatin?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;chromosome&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10693" PostTypeId="2" ParentId="10692" CreationDate="2013-10-03T09:39:02.917" Score="0" Body="&lt;p&gt;I found it in &lt;a href=&quot;http://www.nature.com/nrg/journal/v9/n6/glossary/nrg2341.html&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Heterochromatic knob&#xA;  A chromosomal region that can &#xA;  be identified microscopically as &#xA;  being darkly stained compared &#xA;  with surrounding chromatin. &#xA;  DNA sequence analysis has &#xA;  shown that knobs often contain &#xA;  highly repeated DNA &#xA;  sequences. They were &#xA;  described initially in the &#xA;  1930’s by McClintock during &#xA;  her studies of maize &#xA;  chromosome structure&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3230" LastEditorUserId="1306" LastEditDate="2013-10-03T20:59:06.737" LastActivityDate="2013-10-03T20:59:06.737" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10694" PostTypeId="1" AcceptedAnswerId="21529" CreationDate="2013-10-03T10:11:41.053" Score="5" ViewCount="15503" Body="&lt;p&gt;I just learned that in video cameras, every frame of the video has its own shutter speed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mediacollege.com/video/camera/shutter/shutter-vs-fps.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/UZPfP.png&quot; alt=&quot;shutter speed vs framerate&quot;&gt;&#xA;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And I know how frame-rate in human eye works out, well, not completely, hence the question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Frame_rate&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Frame_rate&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The human eye and its brain interface, the human visual system, can process 10 to 12 separate images per second, perceiving them individually.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;How much (or what is the equivalent of) shutter-speed in those individual images?&lt;/p&gt;&#xA;" OwnerUserId="3141" LastEditorUserId="3141" LastEditDate="2013-10-03T22:21:46.490" LastActivityDate="2019-01-19T20:33:47.240" Title="What is the equivalent of shutter-speed in Human eye?" Tags="&lt;vision&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10695" PostTypeId="2" ParentId="7248" CreationDate="2013-10-03T10:19:52.880" Score="1" Body="&lt;p&gt;It's hypothesized that planar cell polarity is many cases functionally associated with asymmetry of (primary) cilia (&lt;a href=&quot;http://www.nature.com/ng/journal/v40/n1/full/ng0108-10.html&quot; rel=&quot;nofollow&quot;&gt;Axelrod (2008)&lt;/a&gt;). So, the phenomenon of primary cilium migration could be not that infrequent. One example is the development of ependymal cells in brain ventricules: They are multiciliated and the cilia are motile, but ciliogenesis starts from a single cilium, which is not motile and which migrates from the apex to the rostral end of the cell:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jneurosci.org/content/30/7/2600.full&quot; rel=&quot;nofollow&quot;&gt;Mirzadeh et al (2010)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.stanford.edu/group/axelrodlab/papers/Bayly_NRG11.pdf&quot; rel=&quot;nofollow&quot;&gt;Bayly &amp;amp; Axelrod (2011)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Seemingly less clear (for me, at least) cases are non-motile single cilia on the lens fiber cells and may be, embryal node cilia (which are motile in the mature state):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0955067410001183&quot; rel=&quot;nofollow&quot;&gt;Wallingford (2010)&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0012160609013906&quot; rel=&quot;nofollow&quot;&gt;Sugiyama et al (2010)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2013-10-03T10:19:52.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10696" PostTypeId="1" CreationDate="2013-10-03T12:00:43.080" Score="3" ViewCount="2392" Body="&lt;p&gt;The retrovirus (oncovirus) contains RNA. It also has a molecule called reverse transcriptase. This molecule transcribes RNA into cDNA. This cDNA is the DNA copy of viral RNA genome&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RNA has Uracil instead of thymine and DNA has thymine instead of uracil. So, how can RNA be converted into DNA? Where does Uracil go and where does thymine come from?&lt;/p&gt;&#xA;" OwnerUserId="1765" LastEditorUserId="3615" LastEditDate="2013-10-05T20:37:22.137" LastActivityDate="2013-10-05T20:37:22.137" Title="How is RNA of retrovirus converted into cDNA?" Tags="&lt;virus&gt;&lt;retrovirus&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10699" PostTypeId="2" ParentId="10696" CreationDate="2013-10-03T15:08:06.563" Score="2" Body="&lt;p&gt;I think it might be of use to show you the difference between uracil and thymine&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/W1O92.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are very similar structures. The part that is involved in base pairing is actually the Nitrogen and the  oxygen furthest from the sugar. See below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ocp0q.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So having an extra methyl group on the other side of the molecule does not interrupt basepairing. And remember, with DNA/RNA synthesis you have a template, and the new strand is based on the template. So, when the RT enzyme Medhat mentions encounters an adenine in the template RNA, it will pair it with a thymidine. And when it encounters a uracil, it is able to pair it with an adenine. The enzyme is structured specifically to only allow in thymine and not uracil, which is how it makes the distinction.&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-10-03T15:08:06.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10700" PostTypeId="2" ParentId="10696" CreationDate="2013-10-03T15:25:32.787" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;RNA has Uracil instead of thymine and DNA has thymine instead of uracil. So, how can RNA be converted into DNA?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think you may want to ask a more basic question.  DNA and RNA are extremely similar, with only an oxygen being the difference.  This has vast consequences for organisms, and life as we know it uses DNA and RNA for very separate purposes.  DNA stores the genome providing the instructions for life, and RNA in a nutshell is how that message gets converted into protein for a useful action.  RNA is generally less stable than DNA, so this arrangement works out well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA is regularly and constantly transcribed to RNA, so Thymine is regularly used in favor of Uracil.  &lt;a href=&quot;https://biology.stackexchange.com/q/171/4101&quot;&gt;There is a &lt;em&gt;fantastic&lt;/em&gt; answer here on Biology.SE already dealing with &lt;strong&gt;why&lt;/strong&gt; so I suggest reading that&lt;/a&gt;.  The &lt;strong&gt;how&lt;/strong&gt; is pretty straightforward, there are different molecules used!  DNA polymerases incorporate Thymine whereas RNA polymerases incorporate Uracil.  The reverse transcriptase that is encoded by the retrovirus does just this: it transcribes RNA to DNA, using Thymine instead of Uracil.  Both Uracil and Thymine are present in the cell and are thus available for use.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-10-03T19:54:17.883" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10701" PostTypeId="2" ParentId="10692" CreationDate="2013-10-03T15:31:39.693" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://mnl.maizegdb.org/mnl/61/133eubanks.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here's a good summary of knobs&lt;/a&gt;, which says that they are &amp;quot;&lt;em&gt;typically telomeric&lt;/em&gt;,&amp;quot; &amp;quot;&lt;em&gt;tandemly repeated DNA sequences [that] appear as distinct, heteropycnotic regions located at certain sites on specific chromosomes and look much like beads on a string&lt;/em&gt;&amp;quot; and are involved in:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;increased recombination&lt;/p&gt;&#xA;&lt;p&gt;neocentromere activity&lt;/p&gt;&#xA;&lt;p&gt;preferential segregation&lt;/p&gt;&#xA;&lt;p&gt;chromosome breakage and chromatin loss&lt;/p&gt;&#xA;&lt;p&gt;sex differences in recombination&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The introduction to &lt;a href=&quot;http://www.pnas.org/content/78/7/4490.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper&lt;/a&gt; gives some of the same information.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-03T22:32:52.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10702" PostTypeId="2" ParentId="10688" CreationDate="2013-10-03T15:48:36.627" Score="1" Body="&lt;p&gt;As far as I can tell, the answer is no.  It's hard to prove a negative so the best I can do is that none of the articles in the literature I've been able to comb through have any mention of invertebrates at all.  What I can give you is that &lt;a href=&quot;http://www.sciencemag.org/content/325/5938/325&quot; rel=&quot;nofollow&quot;&gt;some moths use clicks to jam bat echolocation&lt;/a&gt; and &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S096098220500686X&quot; rel=&quot;nofollow&quot;&gt;some fish are sensitive to echolocation&lt;/a&gt;, &quot;&lt;em&gt;raising the possibility that fish may exhibit negative phonotactic behaviour in the way that moths do.&lt;/em&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-03T15:48:36.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10704" PostTypeId="2" ParentId="10688" CreationDate="2013-10-03T17:39:49.997" Score="8" Body="&lt;p&gt;Some moth actually do use clicks for their own echolocation: &quot;Noctuid moths (Noctuidae) are the only group of invertebrates for whom echolocation was&#xA;demonstrated&quot;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.lapshin.iitp.ru/lapsh98e.pdf&quot;&gt;Lapshin &amp;amp; Vorontsov 1998&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.lapshin.iitp.ru/lapsh93e.pdf&quot;&gt;Lapshin et al 1994&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2013-10-03T17:39:49.997" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10706" PostTypeId="2" ParentId="10662" CreationDate="2013-10-03T19:03:17.133" Score="3" Body="&lt;p&gt;If the question is why a transplant implant like an artificial hip may be made from a metal, then toxicity issues of the metals are not the main question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it would be better to focus on &lt;a href=&quot;http://emedicine.medscape.com/article/1230696-overview&quot; rel=&quot;nofollow&quot;&gt;metal sensitivity&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Metal sensitivity is not a specific immune response as with transplanted organs, but a non specific response to a foreign substance in contact with the body. While  &lt;a href=&quot;http://en.wikipedia.org/wiki/Surgical_stainless_steel&quot; rel=&quot;nofollow&quot;&gt;Surgical stainless steel&lt;/a&gt; and similar hardened alloys which contain iron, nickel, chromium and molybdenum are popular for metal components of implants, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18042333&quot; rel=&quot;nofollow&quot;&gt;even plastic coated pieces can cause scarring and irritation&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This reaction is highly variable from one individual to the next and can have no effect or cause further surgery or rejection of the implant.  &lt;a href=&quot;http://www.medicinenet.com/script/main/art.asp?articlekey=155237&quot; rel=&quot;nofollow&quot;&gt;the cause is poorly understood and so diagnosis is still in an exploratory state&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since oxidation and rust seem to cause more irritation, it seems that corrosion resistance is an important part of implant metal choices.   Hardness, durability and Cost is also an issue since I'm sure gold and platinum would also be great choices from a cost perspective. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-10-03T19:03:17.133" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10707" PostTypeId="1" AcceptedAnswerId="10709" CreationDate="2013-10-03T19:20:25.390" Score="2" ViewCount="4265" Body="&lt;p&gt;I'm a first year student and I'm not sure if I understand correctly the role played by the antibiotic 'kanamycin' in the growing of culture E. coli (Rosetta).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anybody explain me why we use 'kanamycin' antibiotic and kanamycin resistance gene during that process?&lt;/p&gt;&#xA;" OwnerUserId="4593" LastActivityDate="2013-10-06T08:45:36.890" Title="The antibiotic 'kanamycin' in the growing of culture E. coli" Tags="&lt;ecoli&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10708" PostTypeId="2" ParentId="10688" CreationDate="2013-10-03T19:51:46.197" Score="3" Body="&lt;p&gt;As others have indicated, I also haven't seen direct evidence of echolocation in insects. However, there is much evidence that the auditory system of e.g. moths can hear ultrasound generated by bats (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3032.2003.00355.x/full&quot; rel=&quot;nofollow&quot; title=&quot;Waters. 2003. Bats and moths: what is there left to learn? Physiological Entomology 28(4): 237–250.&quot;&gt;Waters, 2003&lt;/a&gt;). According to &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3032.2003.00355.x/full&quot; rel=&quot;nofollow&quot; title=&quot;Waters. 2003. Bats and moths: what is there left to learn? Physiological Entomology 28(4): 237–250.&quot;&gt;Waters (2003)&lt;/a&gt; moths mainly use this to avoid predation. The review also contain many useful references and examples of moth ultrasound detection, and specifics on the physiological adaptations. Since moths apparantly can detect ultrasounds (and generate them), this also opens the possibility that some species could use it for echolocation. But from what I have seen, no direct evidence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, many insects use high-frequency sounds, but we often do not know exactly for what purpose. If you are interested, this webpage on &lt;a href=&quot;http://www.slu.se/sv/fakulteter/nl-fakulteten/om-fakulteten/institutioner/institutionen-for-ekologi/research/ovrigt/fjarilsljud/&quot; rel=&quot;nofollow&quot;&gt;sounds in butterflies (in Swedish)&lt;/a&gt; have a couple of examples that you can listen to (recorded by a professor emeritus as my old department). Look at the subpages for each species for embedded .wav where the ultasounds are played in slowmotion. Again, the exact use of these sounds are mostly unknown, but they are believed to be used to attrach mates or scare predators, but might potentially (if we are speculating) be used for echolocation in some species.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-10-07T18:59:38.377" LastActivityDate="2013-10-07T18:59:38.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10709" PostTypeId="2" ParentId="10707" CreationDate="2013-10-04T02:30:32.047" Score="1" Body="&lt;p&gt;Absolutely, &lt;strong&gt;Positive Selection&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are looking for the bacteria which &lt;em&gt;have&lt;/em&gt; the gene (probably a plasmid) you (or someone else for you) put into the bacteria.  That gene lets them live in the presence of kanamycin, and any bacteria that don't have it, or that try to get rid of it, will die.  Thus you can select for the bacteria you want by killing everything else off (hopefully your sample is not contaminated with other bacteria also resistant to kanamycin).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I totally thought there would be a good wiki article on positive selection but there isn't.  The reason it's positive selection is that you are selecting for bacteria that have something; instead of negative selection where you would be killing them for having something.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find plenty more if you search &quot;positive selection&quot; or more generally &quot;artificial selection.&quot;&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="948" LastEditDate="2013-10-04T03:03:31.100" LastActivityDate="2013-10-04T03:03:31.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10710" PostTypeId="1" CreationDate="2013-10-03T23:00:33.363" Score="21" ViewCount="47740" Body="&lt;p&gt;As far as I know, DNA is the construction protocol of all organisms on Earth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it change when influenced by time and environment (physical laws)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As parents with schizophrenia are more likely to have children with schizophrenia and an individual with no genetic predisposition for schizophrenia can suffer from such a condition because of drug abuse or environmental influence, does this prove that human DNA is changing during our lifespan?  &lt;/p&gt;&#xA;" OwnerUserId="4497" OwnerDisplayName="Flux" LastEditorUserId="57" LastEditDate="2013-10-04T08:12:02.363" LastActivityDate="2014-09-12T01:40:18.987" Title="Does our DNA change during our lives?" Tags="&lt;genetics&gt;&lt;dna&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10711" PostTypeId="2" ParentId="10710" CreationDate="2013-10-04T02:55:45.487" Score="18" Body="&lt;p&gt;To quickly answer your question, yes DNA changes over the life time of many organisms including humans.  You have a whole host of mechanisms in your body that try to prevent your DNA from changing, but they are not perfect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good example of this is DNA degradation due to aging.  When discussing aging in biology, we use the technical term &lt;a href=&quot;https://en.wikipedia.org/wiki/Senescence&quot;&gt;senescence&lt;/a&gt;.  Of interest here is the shortening of &lt;a href=&quot;https://en.wikipedia.org/wiki/Telomere&quot;&gt;telomeres&lt;/a&gt; due to mistakes made in your cells as they continue to divide (copying the DNA to each new daughter cell).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a grown adult, there's not some master well of DNA somewhere such that if you change it there it will immediately change the DNA throughout your body.  Most of the cells in your body have DNA in them (red blood cells are just one example of cells that don't have DNA in the traditional sense). Most of these cells can and will divide over time (&lt;a href=&quot;https://en.wikipedia.org/wiki/Mitosis&quot;&gt;mitosis&lt;/a&gt;) to produce new cells with copies of that DNA.  However, there are also plenty of cells that don't divide often or at all in healthy adults.  If one is concerned about schizophrenia, it would be important to note that many neurons in the &lt;a href=&quot;https://en.wikipedia.org/wiki/Central_nervous_system&quot;&gt;CNS&lt;/a&gt; are in this group of static cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering environmental effects, there are plenty of things that can change your DNA. Radiation, gamma and x-rays in particular, do a great job of disrupting, degrading, and occasionally mutating DNA.  The class of chemicals and physical agents that can change DNA are called &lt;a href=&quot;https://en.wikipedia.org/wiki/Mutagen&quot;&gt;mutagens&lt;/a&gt;.  This shares a root with the verb mutate, which is when something is acting on genetic material to cause it change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will note that I said genetic material, and not DNA.  Without getting too far into the debate of what is &quot;alive,&quot; DNA is most certainly not the only &quot;construction protocol&quot; for earthly organisms.  RNA is one common alternative, but there are weirder ones that are hard to describe like prions.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorDisplayName="user4518" LastEditDate="2013-10-04T08:03:28.723" LastActivityDate="2013-10-04T08:03:28.723" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="10712" PostTypeId="2" ParentId="10643" CreationDate="2013-10-04T07:14:40.070" Score="1" Body="&lt;p&gt;X chromosome has many important genes required for general housekeeping. So we need not really talk about X-chromosome genes. &lt;a href=&quot;http://ghr.nlm.nih.gov/chromosome/X/show/Genes&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a list of genes present on the X-chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;@Armatus, if all those genes were on autosomes then presence of Y wont be mandatory for male development. There are autosomal genes that are involved in sexual development for e.g. Anti-Mullerian Hormone gene is present on chromosome 19. However, there must be a master regulator that is male specific and since sex determination is chromosomal in mammals, the Y-chromosome must encode that master regulator. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sry, encoded in Y-chromosome, is one such protein that is absolutely essential for male sexual development. Having said that, it could be very well possible that the basic genes required in the process of spermatogenesis are autosomally encoded. &lt;strong&gt;In fact it is so&lt;/strong&gt;. I just took the list of genes that were associated with sepermatogenesis in KEGG and checked their chromosomal locations. They are all autosomal.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Gene --- position&#xA;SPATA1  ---  1p22.3&#xA;SPATA25  ---  20q13.12&#xA;SPATA32  ---  17q21.31&#xA;SPATA9  ---  5q15&#xA;SPATA19  ---  11q25&#xA;SOHLH1  ---  9q34.3&#xA;SPATC1L  ---  21q22.3&#xA;SPATA18  ---  4q12&#xA;SPATA2  ---  20q13.13&#xA;SPATA21  ---  1p36.13&#xA;SPATA2L  ---  16q24.3&#xA;GMCL1  ---  2p13.3&#xA;SPATA7  ---  14q31.3&#xA;SPATA5  ---  4q28.1&#xA;SPATA6L  ---  9p24.2&#xA;SPATA4  ---  4q34.2&#xA;SPATA24  ---  5q31.2&#xA;SPATS2L  ---  2q33.1&#xA;SPATA16  ---  3q26.31&#xA;SPATA6  ---  1p33&#xA;SPATA12  ---  3p14.3&#xA;SPATS1  ---  6p21.1&#xA;SPATC1  ---  8q24.3&#xA;SPATA22  ---  17p13.3&#xA;SOHLH2  ---  13q13.3&#xA;SPATA13  ---  13q12.12&#xA;SPATS2  ---  12q13.12&#xA;SPATA20  ---  17q21.33&#xA;ASUN  ---  12p11.23&#xA;SPATA8  ---  15q26.2&#xA;SPATA17  ---  1q41&#xA;SPATA3  ---  2q37.1&#xA;SPATA5L1  ---  15q21.1&#xA;GMCL1P1  ---  5q35.3&#xA;SPATA41  ---  15q26.3&#xA;SPATA42  ---  1p13.3&#xA;SPATA33  ---  16q24.3&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-11-11T12:08:29.803" LastActivityDate="2014-11-11T12:08:29.803" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="10715" PostTypeId="2" ParentId="10710" CreationDate="2013-10-04T15:04:14.927" Score="6" Body="&lt;p&gt;A DNA change will only be passed on if it occurs in a germ line cell (the cells that become eggs or sperm). If you have a mutation in, say, a liver cell, that will not be passed on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I dont think thats what you are talking about. From reading your question and comment closely I think the answer is &quot;no&quot;. A person who becomes schizophrenic because of drug use does not become any more prone to having schizophrenic kids than a person who doesnt do drugs. Drugs can upset the chemical balance in your brain and that can mimic certain genetic diseases, but what happens in your brain because of drug use can absolutely under no conditions be passed on to your child.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your piano comment things are slightly more complicated. Being good at playing piano is a result of a complex interaction of many factors, some of which may be genetic. A long line of pianists generation after generation may be a result of genes that, say, sharpen a persons auditory perception so they can hear and interpret notes better. However, I am sure that the parents encouraged piano playing and practice for their children, which is just as important.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But most importantly, playing the piano a lot will not in any way cause changes to your DNA that will make your children better at playing the piano. Your genes dont care how well you play the piano. Mutation is random, and that is the only way DNA can change.&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-10-04T15:04:14.927" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="10716" PostTypeId="2" ParentId="10676" CreationDate="2013-10-04T17:37:32.110" Score="2" Body="&lt;p&gt;I doubt if a comparison between these two animals in war situation is in order. These two animals serve different roles.&lt;/p&gt;&#xA;&lt;p&gt;Here is a reference to an article in Wikipedia on &lt;a href=&quot;http://en.wikipedia.org/wiki/War_elephant&quot; rel=&quot;nofollow noreferrer&quot;&gt;War Elephants&lt;/a&gt;. Elephants have been used in war for thousands of years pretty effectively till the enemies discover their weakness and use it to their advantage. Making the elephant panic is one of the ways to counter them. Here is a list of methods from the above article:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Elephants had a tendency to panic themselves: after sustaining painful wounds or when their driver was killed they would run amok&lt;/p&gt;&#xA;&lt;p&gt;One famous historical method for disrupting elephant units was the war pig......&lt;/p&gt;&#xA;&lt;p&gt;At the Megara siege during the Diadochi wars, for example, the Megarians reportedly poured oil on a herd of pigs, set them alight, and drove them towards the enemy's massed war elephants. The elephants bolted in terror from the flaming squealing pigs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It is for sure that many horses also panic in war situations. However a panicked elephant can cause more havoc than a horse. It appears that to prevent a panicked elephant from running amuck back into the ranks&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The driver, called a mahout, was responsible for controlling the animal. In many armies, the mahout also carried a chisel-blade and a hammer to cut through the spinal cord and kill the animal if the elephant went berserk.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;In recent times elephants in temple festivals in india do occasionaly panic and run amuck when the high explosive fire works are set of. However most of the elephants seem to tolerate it.&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-04T17:47:15.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10717" PostTypeId="1" CreationDate="2013-10-04T21:47:05.790" Score="1" ViewCount="3057" Body="&lt;p&gt;I haven't read it but I'm asking for a quick answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I know, Terence McKenna's theory of evolution in humans main concept is that a hominid has tried in their diet psilocybin mushrooms, and the experience they integrated changed their mind in a way that led to &quot;us.&quot;&lt;/p&gt;&#xA;" OwnerUserId="4497" LastEditorUserId="1320" LastEditDate="2013-10-07T18:32:56.887" LastActivityDate="2021-01-28T04:35:15.813" Title="Does Darwin's Theory of Evolution refute Terence McKenna theory &quot;Stoned Ape&quot; theory of human evolution?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;physiology&gt;&lt;brain&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10718" PostTypeId="2" ParentId="10717" CreationDate="2013-10-04T22:02:51.707" Score="10" Body="&lt;p&gt;Briefly the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Terence_McKenna#.22Stoned_Ape.22_theory_of_human_evolution&quot; rel=&quot;nofollow&quot;&gt;Stoned Ape theory&lt;/a&gt;&quot; posits that psychoactive Psilocybin mushrooms in the diet of pre-Homo sapiens primates catalyzed the change Homo sapiens.  It suggests that the mushrooms conveyed selective benefits to consumers of the mushrooms, dissolving the 'egos' of our ancestors and allowing them to form communities.  It may also be sexual stimulant, goes the theory and so may have conveyed an advantage there. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this theory is not terribly popular now, but it is difficult to refute or to prove.  The only real proof would be to take a hominid or any other species and give them the fungus and see if they become intelligent.   Just because this has not happened does not disprove the theory.  the only other way to prove this really would be to have a time scope and look back and see what happened.  Its a similar question as to how life emerged on Earth.  We have some interesting evidence but conclusive proof is going to be hard to get. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found a &lt;a href=&quot;http://www.lycaeum.org/~sputnik/McKenna/Evolution/&quot; rel=&quot;nofollow&quot;&gt;large collection of supporting evidence&lt;/a&gt;.  Even the definition of human intelligence and whether it is so unique is &lt;a href=&quot;http://blogs.discovermagazine.com/crux/2011/12/07/bursting-the-bubble-of-human-intelligence/#.Uk86-dLktyI&quot; rel=&quot;nofollow&quot;&gt;subject to debate&lt;/a&gt;.  Certainly there are other primates who appear to be as or more social than we.  I think &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_human_intelligence#Models&quot; rel=&quot;nofollow&quot;&gt;other theories&lt;/a&gt; seem as or more likely.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Darwin's theory of evolution doesn't refute many theories of how something happens in evolutionary history.  The Panspermia hypothesis is taken quite seriously at this point - could it be that life originated elsewhere then was introduced here by meteorites.  The origin of Species doesn't have a lot to say about that.  I think the same is true for the emergence of human intelligence, which at this point we believe is unique on Earth.  Hard to make an irrefutable theory based upon a single example. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-11-22T18:34:48.250" LastActivityDate="2013-11-22T18:34:48.250" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10719" PostTypeId="2" ParentId="10717" CreationDate="2013-10-04T22:27:32.143" Score="8" Body="&lt;p&gt;Refute?  No.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Shigeta summarized the work pretty well, and though I have my own opinions on McKenna's theory the fact is that Darwin and McKenna are &lt;em&gt;not&lt;/em&gt; opposed.  The &quot;Stoned Ape theory&quot; is a specific idea for how human intelligence might have appeared from earlier hominids.  Darwin (and &lt;a href=&quot;http://en.wikipedia.org/wiki/Alfred_Russel_Wallace&quot; rel=&quot;noreferrer&quot;&gt;Wallace&lt;/a&gt;) proposed a broad theory that has borne out for the process of evolution by natural selection.  Evolution applies to populations large and small, whether human, primate, or bacterial.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution, however, is not particularly predictive and would say nothing about what might happen should some primates eat some entheogens.  McKenna's idea could fit into reality, although as Shigeta said it is difficult to prove, but there is technically no Darwinian reason why it couldn't have happened.  Darwin did write about human evolution in &lt;em&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/The_Descent_of_Man,_and_Selection_in_Relation_to_Sex&quot; rel=&quot;noreferrer&quot;&gt;The Descent of Man&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="1306" LastEditDate="2013-10-05T23:30:49.333" LastActivityDate="2013-10-05T23:30:49.333" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10720" PostTypeId="1" CreationDate="2013-10-05T02:00:03.757" Score="13" ViewCount="42581" Body="&lt;p&gt;Here's the (real) story: A young man has stunning blue eyes. On his mother's side are lots of instances of blue eyes, but on his father's side is no history of blue eyes. &lt;strong&gt;Both parents have brown eyes.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When he was born, with these bright blue eyes, it was considered a &quot;miracle&quot;. As an adult, he still has these potent blue eyes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is this possible?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I obviously understand the popular science behind dominant and recessive genes. The mother could be Bb, but if the father was BB, it doesn't seem possible that he could have blue eyes... but I've read more on eye colour recently, and it appears to be a lot more complicated than I initially thought.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, this article goes into some detail explaining &lt;a href=&quot;http://genetics.thetech.org/how-blue-eyed-parents-can-have-brown-eyed-children&quot; rel=&quot;nofollow noreferrer&quot;&gt;How Blue Eyed Parents Can Have Brown Eyed Children&lt;/a&gt;, but I've not seen anything that talks about it being the other way around: Could a BB parent have a bb child?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, how? And what is the rough probability of such a thing?&lt;/p&gt;&#xA;" OwnerUserId="3550" LastEditorUserId="3550" LastEditDate="2016-11-30T18:10:05.563" LastActivityDate="2016-12-04T05:18:15.537" Title="Is it possible for two brown-eyed parents to have blue-eyed child?" Tags="&lt;genetics&gt;&lt;eyes&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10721" PostTypeId="2" ParentId="10720" CreationDate="2013-10-05T03:09:53.870" Score="19" Body="&lt;p&gt;&lt;strong&gt;Possible, yes but probable, no.&lt;/strong&gt; (I assume that the history of the parental family as you mention is important)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let us first consider &lt;strong&gt;HERC2&lt;/strong&gt; (&lt;strong&gt;H&lt;/strong&gt;=brown, &lt;strong&gt;h&lt;/strong&gt;=blue) and &lt;strong&gt;OCA2&lt;/strong&gt; (&lt;strong&gt;O&lt;/strong&gt;=brown, &lt;strong&gt;o&lt;/strong&gt;=blue) as per the names mentioned in the reference you cite, to be completely unlinked, such that they are &lt;em&gt;independently&lt;/em&gt; assorted. Since the father's lineage has no history of the recessive phenotype(blue), and the genes segregate independently (our assumption), we can conclude that the father is homozygous for the dominant allele in both the genes(&lt;strong&gt;HHOO&lt;/strong&gt;). In this scenario, it is &lt;em&gt;very unlikely&lt;/em&gt; to get blue eyed children, but is still possible in the following two ways:-  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The father's lineage does have a recessive gene (which probably entered his family gene pool due to &lt;em&gt;non-consanguineous&lt;/em&gt; mates carrying a heterozygous phenotype in either of the gene pair &lt;strong&gt;HERC2&lt;/strong&gt; or &lt;strong&gt;OCA2&lt;/strong&gt;), and has evaded expression by &lt;em&gt;pure chance&lt;/em&gt; or because the recessive gene carrier entered into the family very close to the father,i.e. probably just one or two generations above the father(so that not enough generations have passed to allow the homozygous recessive trait to develop). In each of these cases, one or both the gene loci in the father might be heterozygous(&lt;strong&gt;HhOO&lt;/strong&gt; or &lt;strong&gt;HHOo&lt;/strong&gt; or &lt;strong&gt;HhOo&lt;/strong&gt;) and coupled with the mother's heterozygous genotype(a good guess considering the history of many recessive phenotypes), might produce a blue-eyed child due to homozygosity in any one of the gene.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There is a &lt;em&gt;mutation&lt;/em&gt; in the germinal cells of the father which creates a non-functional mutant allele and thus can give a blue-eyed child with a heterozygous mother.&lt;br&gt;&#xA;But in either case, considering independent assortment, the chances are very bleak.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;But if we also take into account the linkage of the two genes, then the probability rises significantly. Now there is a good chance that the father's lineage might contain a heterozygous (or homozygous recessive) allele pair on a single chromosome, which due to their tight linkage, might pass on without any recombinations and therefore might evade phenotypic expression more efficiently(although, since a dominant allele in both the genes is required for the dominant phenotype, the extra evasion efficiency due to linkage is less). As given at the end of your reference, suppose there is one chromosome in the parental ancestry that carries both the recessive genes. If they are linked, the chances of brown eyed parents to have blue eyed children &lt;em&gt;decreases&lt;/em&gt; (and the chance of being heterozygous also decreases) thus making it more likely that the father's lineage could have a recessive allele in spite of there being no significant expression in his family history. Therefore, more tightly they are linked, greater is the probability that the father is heterozygous. Linkage does not significantly lessen the possibility for the father to have a blue-eyed child since the mother does contain a recessive linked- phenotypic pair in all probability. (Actually, the probability is also based on &lt;em&gt;which combinations are linked&lt;/em&gt;, but the possibility of there being a heterozygous allele remains positive with most combinations).This again gives some chance for brown eyed parents with the history you mention, to have a blue eyed child.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, there is a chance but the probabilities depend a lot on the linkage, the linked combinations, and the actual genotypes of the parents but there is always a possibility.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;ADDITION&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just to add a bit of information, the kind of &lt;strong&gt;recessive epistasis&lt;/strong&gt; we described here, where the homozygous recessive (at the hypostatic,&lt;strong&gt;HERC2&lt;/strong&gt;, loci) phenotype resembles the phenotype for the recessive condition at the modifier pair (&lt;strong&gt;OAC1&lt;/strong&gt;), is only a part of the story. Actually, certain polygenic influences further complicate the situation by introducing a variety of phenotypes. &lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2016-12-04T05:18:15.537" LastActivityDate="2016-12-04T05:18:15.537" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10722" PostTypeId="1" AcceptedAnswerId="10723" CreationDate="2013-10-05T04:00:42.970" Score="-1" ViewCount="132" Body="&lt;p&gt;I've been wondering for some time, but say that my mother's egg chose another sperm cell, and a baby was eventually produced. Would I still be born, but end up with different characteristics/features? &lt;/p&gt;&#xA;" OwnerUserId="4601" LastActivityDate="2013-10-05T07:11:26.697" Title="Would I still exist if" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="6" ClosedDate="2013-10-05T07:27:37.193" ContentLicense="CC BY-SA 3.0" />
  <row Id="10723" PostTypeId="2" ParentId="10722" CreationDate="2013-10-05T07:11:26.697" Score="3" Body="&lt;p&gt;For every sperm that fertilises an egg there are millions/billions/&quot;a sh**load&quot; that don't make it. Within that pool of unused sperm there is considerable genetic variation. If we assume that DNA is the only factor which makes &quot;you you&quot; then the chance of picking one of those  sperm and it having the exact same DNA is small. Of course environment also has a large effect so even two identical sperm and egg combinations would produce two people with different physical and mental attributes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this does not answer your question then this is not really a biological question though and should really be on the philosophy SE. &lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2013-10-05T07:11:26.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10725" PostTypeId="2" ParentId="7779" CreationDate="2013-10-05T10:15:43.087" Score="1" Body="&lt;ol&gt;&#xA;&lt;li&gt;The ability of the forelimbs in bats (as well as in other tetrapods) to grow depends on the proliferation activity and ossification of cartilage in growing zones of the bones. Adult bats do not grow (as is the rule for mammals) and wing parameters (wing span and area) show growth curves with more or less pronounced plateau, which asymptotically leans to &quot;adult&quot; values. (This reflects progressive ossification of the cartilage.) As one could intuitively expect, variability in wing relative parameters decreases with age, meaning that juveniles before their first flights show more diversity in wing shapes than flying juveniles and those, in turn, approach gradually the narrow variability of these parameters of the adults.&lt;/li&gt;&#xA;&lt;li&gt;Juvenile bats start performing their first short flights even before weaning. The main requirement for the flight ability per se is a certain threshold value of wing loading. Sustained flights start roughly half-way to maturity and correlate with the emergence of the above mentioned plateau on the growth curves. The flight abilities improve together with aerodynamic characteristics of the wing: duration of flight increases, beat frequency decreases, but beat power increases etc.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Some references:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jstor.org/discover/10.2307/1378165&quot; rel=&quot;nofollow&quot;&gt;Jones (1967)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/BF00569202&quot; rel=&quot;nofollow&quot;&gt;Buchler (1980)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-7998.1995.tb04494.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Hughes et al (1995)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ias.ac.in/jarch/jbiosci/22/193-202.pdf&quot; rel=&quot;nofollow&quot;&gt;Isaac, Marimuthu (1997)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2013-10-05T13:20:14.587" LastActivityDate="2013-10-05T13:20:14.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10726" PostTypeId="2" ParentId="9671" CreationDate="2013-10-05T11:54:21.513" Score="4" Body="&lt;p&gt;To sum up: If we are not talking about chromosome organization, nucleotide sequences and overall genome architecture (which are incomparably different in eukaryotes and [even their] viruses) the differences in the genetic material are as follows:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;viruses are much more diverse in their choice of genetic material, which is in the cornerstone of viral higher systematics. It can be DNA or RNA, single- or double-stranded, circular or linear. Animals, in turn, possess only double stranded DNA as their genetic material: linear dsDNA for the nuclear genome and [usually] circular dsDNA for the their mitochondrial genomes.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;DNA termini pose a special problem for the maintenance of the molecule and show very unusual organization in terms of DNA sequence and structure. Repetitive terminal sequences of eukaryotic chromosomes have 3'-overhangs, which form a special quadruplex form of DNA. Termini of viruses are naturally much more diverse and are (nearly?) never of the same structure as in Eukaryotes. [Circularization/decicrularization is one of the mechanisms recruited by viruses]. (&lt;a href=&quot;http://www.frontiersin.org/Cancer_Molecular_Targets_and_Therapeutics/10.3389/fonc.2012.00201/abstract&quot; rel=&quot;nofollow&quot;&gt;Deng et al 2012&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;DNA methylation is normally present in varying degrees in animals and in vertebrates most of the cytosines in CpG dinucleotides are methylated. Viruses differ considerably from one another in this respect, but it seems that smaller viral genomes are generally under-methylated and larger genomes do not show under-methylation, although it depends on the stage. This conclusion is based partly on indirect evidence that CpG motifs are considerably much less frequent in smaller viruses. Integrated &quot;genetic parasites&quot; like retroviruses are normally rich in CpG and are highly methylated. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2396429/pdf/gkn121.pdf&quot; rel=&quot;nofollow&quot;&gt;Hoelzer et al 2008&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;although I couldn't find relevant literature, I'd hypothesize that the highly packed genetic material in viral particles may potentially exist in more compact forms of the DNA helix (in dsDNA viruses). Most of the dsDNA in cells is present in a so-called B-form, but there are more compact A-form and less compact left-turned Z-form (there are other forms, most of which are biologically not relevant). (&lt;a href=&quot;https://en.wikipedia.org/wiki/Nucleic_acid_double_helix&quot; rel=&quot;nofollow&quot;&gt;cf. Wikipedia for an introduction&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2013-10-05T14:33:52.343" LastActivityDate="2013-10-05T14:33:52.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10730" PostTypeId="1" AcceptedAnswerId="68343" CreationDate="2013-10-05T22:14:49.323" Score="6" ViewCount="412" Body="&lt;p&gt;I found this spider on my balcony in Sunnyvale, CA. It sat in a irregular net. The body was approx. 6mm long. Which species does it belong to?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xyQH4.jpg&quot; alt=&quot;Spider in its web under a table on my balcony&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/qqoYf.jpg&quot; alt=&quot;The same spider on a newspaper.&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4607" LastActivityDate="2017-11-27T21:29:03.620" Title="Identify this spider" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10731" PostTypeId="1" CreationDate="2013-10-05T23:21:40.327" Score="0" ViewCount="169" Body="&lt;p&gt;I have heard of some rumors going around about a living organism based on non-carbon. Is Has research been done with real form of life based on non-carbon? Or carbon-based life is only type of life what humans know of?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Carbon_chauvinism&quot; rel=&quot;nofollow&quot;&gt;Carbon chauvinism&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="4608" LastEditorUserId="10401" LastEditDate="2015-01-01T01:54:04.483" LastActivityDate="2015-01-01T01:54:04.483" Title="Is there already discovered non-carbon form of life?" Tags="&lt;life-history&gt;&lt;life&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10732" PostTypeId="2" ParentId="10731" CreationDate="2013-10-06T06:54:02.723" Score="2" Body="&lt;p&gt;In a word, no.  There are some good chemical reasons to expect all life to be carbon-based.&#xA;Of course, it is no longer a silly fantasy to imagine an artificial intelligence that might qualify as life.  (Still FAAAARRRR in the future, though, if ever.)&lt;/p&gt;&#xA;" OwnerUserId="4551" LastActivityDate="2013-10-06T06:54:02.723" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10733" PostTypeId="2" ParentId="10710" CreationDate="2013-10-06T07:12:57.907" Score="5" Body="&lt;p&gt;It's become quite clear that your &lt;em&gt;active&lt;/em&gt; genome changes all the time, due to various effects.  There is also gathering evidence that epigenetic changes can occur in somatic cells and be inherited by the offspring.  But these seem to be stress-related.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, for schizophrenia: If the family had a gene that triggered schizophrenia, which was normally inactive, then stress/drugs could cause an epigenetic change which would make the &quot;schizophrenia gene&quot; active.  And this epigenetic change could conceivably (see what I did there?) be passed along to offspring.&lt;/p&gt;&#xA;" OwnerUserId="4551" LastActivityDate="2013-10-06T07:12:57.907" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10734" PostTypeId="2" ParentId="10694" CreationDate="2013-10-06T07:30:02.057" Score="1" Body="&lt;p&gt;Not all of your rods/cones fire at any given moment.  Exception is when a bright flash of light is viewed.  Recovery time from the resulting flash blindness is pretty slow -- seconds.  But there's some photobleaching there, so maybe that's not fair.&lt;/p&gt;&#xA;" OwnerUserId="4551" LastActivityDate="2013-10-06T07:30:02.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10735" PostTypeId="2" ParentId="10707" CreationDate="2013-10-06T08:45:36.890" Score="2" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.emdmillipore.com/is-bin/INTERSHOP.enfinity/WFS/Merck-US-Site/en_CA/-/USD/ViewPDF-Print.pdf;sid=IusRzR8X54wRzU1GAnZ9mrfXpWgDPXWwGsUPm6y6AJ-vrpGZDgtyZxkpNbCccDRuopgB0RzO39M4ypbegG-kJrBdAx8IidPHEXGp7KcOcrrlQ6r8jaGYBL2T?RenderPageType=ProductDetail&amp;amp;CatalogCategoryID=pUWb.s1Ow04AAAEjRhl9.zLX&amp;amp;ProductUUID=ck2b.s1OTAMAAAEiHT1RV1.Y&amp;amp;PortalCatalogUUID=ywGb.s1LAyMAAAEWzdUfVhTl&quot; rel=&quot;nofollow&quot;&gt;this data sheet&lt;/a&gt;, the genotype of the strain Rosetta&lt;sup&gt;TM&lt;/sup&gt;(DE3)pLysS is F&lt;sup&gt;-&lt;/sup&gt; ompT hsdS (r&lt;sup&gt;-&lt;/sup&gt; m&lt;sup&gt;-&lt;/sup&gt;) gal dcm (DE3) pLysSRARE (Cam&lt;sup&gt;R&lt;/sup&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This strain carries certain tRNA genes on the same plasmid as the LysS gene, and these tRNAs boost expression from genes containing rare (in E. coli) codons. The plasmid encodes chloramphenicol resistance (Cam&lt;sup&gt;R&lt;/sup&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have a protocol that suggests growing your strain under kanamycin selection then presumably you have an additional plasmid present which carries your gene of interest. Then, as the accepted answer says, you are selecting positively for the correct strain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know how stable the pLysSRARE plasmid is, but I would have expected that you should also maintain selection for chloramphenicol resistance.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-10-06T08:45:36.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10736" PostTypeId="2" ParentId="10694" CreationDate="2013-10-06T09:17:41.393" Score="2" Body="&lt;p&gt;There is nothing comparable to a shutter of the camera in the eye. The eyelid is like a lens hood. When the eyelid is open the image is continuously projected on to the retina unlike in a movie camera. However if the question is on frames per second (number of static images) required to produce a sense of seamless motion &lt;a href=&quot;http://www.100fps.com/how_many_frames_can_humans_see.htm&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; might be of some help. In video camera instead of a shutter speed it is the number of times the image on the sensor is sampled(recorded) per second electronically. The eye is more similar to a video camera. The retina has rods and cones which has variable 'refresher' rates which makes it more complicated to calculate exact figures.&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="4216" LastEditDate="2013-10-06T11:35:02.970" LastActivityDate="2013-10-06T11:35:02.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10737" PostTypeId="1" CreationDate="2013-10-06T10:51:53.427" Score="10" ViewCount="6144" Body="&lt;p&gt;Organisms excrete nitrogenous wastes in the form of urea, uric acid or ammonia. But isn’t that a bit of a waste? There is a shortage of biologically available nitrogen in the ecosystem, and plants convert nitrogen in ammonia and nitrates into amino acids. Why do organisms then deaminate these amino acids and then excrete them? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to me that it would make much more sense to store the nitrogen for further use. I understand that ammonia is toxic, but surely it could be stored in some specialized structure. &lt;/p&gt;&#xA;" OwnerUserId="4013" LastEditorUserId="22057" LastEditDate="2020-04-05T21:20:16.013" LastActivityDate="2020-05-04T22:20:50.527" Title="Why do organisms excrete nitrogenous wastes?" Tags="&lt;human-biology&gt;&lt;energy-metabolism&gt;&lt;nitrogen-cycle&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="10738" PostTypeId="1" AcceptedAnswerId="10782" CreationDate="2013-10-06T15:29:43.330" Score="8" ViewCount="896" Body="&lt;p&gt;Found this mushroom today. It's a kind of puffball mushroom and I think pestle puffball but I hope someone can confirm that/point me to other likely species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was in Central Eastern Sweden (Uppsala) in a pine and birch forest. Autumn has been quite dry so the season may be a bit delayed. They were in bunches of 2-5 mushrooms, they are about 1-4cm across the ball and the stem is quite fat plus about 1-3cm long. They are white through the middle.&lt;img src=&quot;https://i.stack.imgur.com/BMGbz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2013-10-08T23:35:20.263" Title="Puffball mushroom species ID?" Tags="&lt;species-identification&gt;&lt;mycology&gt;&lt;mushroom&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10739" PostTypeId="1" CreationDate="2013-10-06T17:02:34.947" Score="11" ViewCount="4194" Body="&lt;p&gt;What is the fungus pictured below? The photo was taken October 6, 2013 near San Antonio, TX.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have Googled it and my results suggest Laetiporus root rot (&lt;em&gt;Laetiporus sulfureus&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://extension.psu.edu/pests/plant-diseases/all-fact-sheets/oak-diseases&quot; rel=&quot;noreferrer&quot;&gt;this website&lt;/a&gt; the presence of this fungus indicates the tree should be removed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any chance that this is something else? I would hate to remove such a beautiful oak tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1XJQ1.jpg&quot; alt=&quot;Unknown Fungus on Oak Tree&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4612" LastEditorUserId="3624" LastEditDate="2013-10-07T09:18:55.427" LastActivityDate="2018-09-19T04:09:02.623" Title="Yellow/Orange Fungus on Oak Tree" Tags="&lt;species-identification&gt;&lt;mycology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10741" PostTypeId="1" CreationDate="2013-10-06T17:24:27.147" Score="6" ViewCount="94" Body="&lt;p&gt;Considering the complexity of embryogenesis, a temporal referance would be helpful to coordinate the developmental sequences during embryogenesis and fetal development which is to be completed within the gestation period. Can telomere shortening if consistant be used as a reference by every cell to do what it is destined to do at particular time frame? This is without considering the influence of telomerase etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is also without prejudice to the role of DNA directed molecular signalling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To repeat the question is telomere shortening consistant over consecutive cell divisions from zygote to a differentiated cell? If so can it function as temporal control of embryogenesis?&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="4216" LastEditDate="2013-10-06T18:10:51.843" LastActivityDate="2014-07-23T16:32:35.993" Title="Is telomere shortening consistant over consecutive cell divisions from zygote to a differentiated cell?" Tags="&lt;dna&gt;&lt;embryology&gt;&lt;telomere&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10742" PostTypeId="1" AcceptedAnswerId="10756" CreationDate="2013-10-06T18:56:59.927" Score="6" ViewCount="8367" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Kin_selection#Hamilton.27s_rule&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hamilton's rule&lt;/a&gt; states that if $rB&amp;gt;C$ then a gene giving altruistic behaviour will increase in frequency in the population. What would happen if $rB=C$? Will an individual perform the altruistic act?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="5095" LastEditDate="2017-02-04T10:16:38.367" LastActivityDate="2017-02-04T10:16:38.367" Title="What if $rB=C$ in Hamilton's rule?" Tags="&lt;evolution&gt;&lt;ethology&gt;&lt;sociobiology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10743" PostTypeId="2" ParentId="10737" CreationDate="2013-10-06T21:05:45.673" Score="6" Body="&lt;p&gt;Some amino acids are essential, that is, they cannot be synthesized.  For all the others, however, you need building blocks.  Nitrogen, and specifically ammonia, is required for non-essential amino acid synthesis, the transfer of which is accomplished through a process called transamination.  Amino acids are also broken down for energy as a metabolic process, producing glutamate (in addition to energy-containing molecules such as pyruvate).  The body has thus produced some amino acids and metabolized others for energy,  but glutamate must be deaminated to remove the nitrogen, which by this point is now in excess.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To evolve a specialized storage unit for highly toxic substances could be useful, I suppose, but it would be unlikely and would pose a huge risk compared to just getting rid of 'em.  I'd rather urinate a few times a day than save a lot of toxic material for later and run the risk of something malfunctioning and killing me; besides, eventually that storage unit would get full.  You could ask the same question for any substance we might eventually want.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-06T21:05:45.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10744" PostTypeId="1" AcceptedAnswerId="10745" CreationDate="2013-10-06T21:26:09.943" Score="1" ViewCount="301" Body="&lt;p&gt;This question is a follow-up to &#xA;&lt;a href=&quot;https://biology.stackexchange.com/questions/5170/the-probability-of-indirect-human-fertilization&quot;&gt;this&lt;/a&gt; one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been wondering how small that probability is. As we all know, &quot;safe&quot; sex, that is (correctly) using a condom and all that, isn't perfectly safe. So, in order to put this question into perspective, I'd like to know which one (safe sex or indirect insemination) has the greater chance to lead to impregnation. In other words, can you explain the probability of this scenario in terms a layman like me can understand?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance!&lt;/p&gt;&#xA;" OwnerUserId="4615" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-10-06T21:50:51.500" Title="The probability of indirect human fertilization (follow-up)" Tags="&lt;human-biology&gt;&lt;reproduction&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10745" PostTypeId="2" ParentId="10744" CreationDate="2013-10-06T21:50:51.500" Score="0" Body="&lt;p&gt;Safer sex techniques are more risky.  Perfect condom use is associated with around a &lt;a href=&quot;http://www.contraceptivetechnology.com/CTFailureTable.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;2% pregnancy rate&lt;/a&gt; within a year.  According to that, even sterilization has a 0.1% (male) or 0.5% (female) rate.  Combining techniques is, of course, safer.  &quot;Indirect,&quot; as you proposed in the other question, will border on an infinitesimally small chance, as answered &lt;a href=&quot;https://biology.stackexchange.com/q/5170/4101&quot;&gt;there&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2013-10-06T21:50:51.500" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10746" PostTypeId="1" CreationDate="2013-10-06T21:52:31.413" Score="9" ViewCount="11717" Body="&lt;p&gt;It seems like most mammals, e.g. dogs, have long snouts. My pet dog's snout would seem to me like an evolutionary disadvantage, since her canine teeth are way out at the end of her jaw, which acts as a force-reducing lever. I suppose the lever does increase the jaws' range of motion and possibly allow the jaw to snap shut more quickly. For an herbivore such as a horse, I don't see any advantage to the long snout. It doesn't need to snap its jaws shut rapidly, and it doesn't need to wrap its mouth around anything very large.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a mechanical reason for the long snout, or is the evolutionary advantage due to some other factor such making the nose have enough surface area to give a sensitive sense of smell?&lt;/p&gt;&#xA;" OwnerUserId="4617" LastEditorUserId="4617" LastEditDate="2013-10-06T23:30:51.203" LastActivityDate="2014-08-30T18:27:21.143" Title="Why do most mammals have long snouts?" Tags="&lt;evolution&gt;&lt;anatomy&gt;&lt;mammals&gt;&lt;muscles&gt;" AnswerCount="5" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10748" PostTypeId="1" CreationDate="2013-10-07T01:59:37.123" Score="3" ViewCount="1543" Body="&lt;p&gt;I'm sorry if this seems like a silly question, but I was brushing up on some cell cycle dynamics and realized that everyone was talking about the differences between metaphase I and II, and since metaphase II was so different from metaphase I (random orientation, tetrad, etc...) the distinguishing of the two didn't seem difficult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I also always hear that metaphase II is similar to mitotic metaphase. In fact, I can't really figure out what the observable difference would be, though I'm certain this must be possible?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How exactly is metaphase II of meiosis different from metaphase of mitosis? I'm sorry if this seems like a silly question, but I haven't been able to figure it out.&lt;/p&gt;&#xA;" OwnerUserId="4618" LastActivityDate="2013-10-07T01:59:37.123" Title="Distinguishing between mitotic metaphase and metaphase II of meiosis" Tags="&lt;meiosis&gt;&lt;mitosis&gt;&lt;cell-division&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10749" PostTypeId="1" CreationDate="2013-10-07T02:10:09.510" Score="4" ViewCount="388" Body="&lt;p&gt;I have noticed that my garter snake only eats after it has smelled it's prey to make sure it is a slug, and it doesn't matter whether it's moving or not. If I were to coat, say, a caterpillar with slug slime, would my snake try eating it?&lt;/p&gt;&#xA;" OwnerUserId="4422" LastEditorUserId="3624" LastEditDate="2013-10-22T11:51:06.307" LastActivityDate="2014-07-07T14:51:26.183" Title="Will a garter snake eat unusual prey if made to smell like something normal?" Tags="&lt;zoology&gt;&lt;food&gt;&lt;ethology&gt;&lt;olfaction&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10751" PostTypeId="2" ParentId="10742" CreationDate="2013-10-07T02:15:43.380" Score="4" Body="&lt;p&gt;As far as I understand it, Hamilton's &quot;rule&quot; isn't really meant to apply individually, it's meant as a way of thinking about kin selection and altruism that can be reduced to individual cases.  The reality is that B and C can rarely, if ever, be easily measured or determined.  If the two sides were equal then who knows?  You'd have to observe it.  Presumably it would split 50-50.  Or maybe laziness takes over.  Or maybe some species are inherently altruistic.  That being said, exact equality is a near-impossible occurrence in the wild, and B and C are movable targets, so you'd have to measure it, which is, as stated, very, very difficult.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-07T02:15:43.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10752" PostTypeId="2" ParentId="10746" CreationDate="2013-10-07T03:09:16.993" Score="3" Body="&lt;p&gt;Obviously there is an evolutionary advantage for those animals which has a long snout/muzzle. That is why they are still around.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For carnivores the canine is the most important tooth and it is positioned strategically at the front corners of the jaw. Canines are meant to pierce and is essential for holding on to the prey and preventing from escaping. They are also essential for tearing flesh.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lower jaw or the mandible is a class 3 lever. The lesser mechanical advantage is compensated by the extremely powerful muscles. Since the muscles are closer to the joint or fulcrum the movement produced by the muscles are amplified at the outer end of the jaw allowing for wider opening of the mouth. Since the canines are sharp and long there is enough force to pierce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Herbivores like cattle and sheep have no canines (horses do have canines). The longer snout/muzzle may help in grazing as it would help in reaching the ground along with longer necks. The longer snout/muzzle means more space for the premolars and molars which can be more in number or larger fro grinding the food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Crocodiles which are not mammals also have long snouts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short the longer snout/muzzle in different animals developed due to evolutionary advantage based mainly on diet.&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="4216" LastEditDate="2013-10-07T05:11:41.197" LastActivityDate="2013-10-07T05:11:41.197" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10753" PostTypeId="2" ParentId="10746" CreationDate="2013-10-07T03:41:29.270" Score="2" Body="&lt;p&gt;You say &quot;snout&quot; but you might more specifically mean &quot;muzzle&quot; if you're focusing on the teeth aspect.  Ram Manohar M hypothesizes some good reasons that make sense but for some other examples of snouts, here's a &lt;a href=&quot;http://animals.pawnation.com/mammals-long-noses-7903.html&quot; rel=&quot;nofollow&quot;&gt;fun link&lt;/a&gt; that describes a few uses:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Tapir: &quot;&lt;em&gt;nose and upper lip form a trunk he uses to grip, handy for grabbing and cleaning branches and plucking fruit.&lt;/em&gt;&quot;&lt;/li&gt;&#xA;&lt;li&gt;Aardvark: &quot;&lt;em&gt;finds all his food through his sense of smell, so his long nose leads the way in his quest for dinner.&lt;/em&gt;&quot;&lt;/li&gt;&#xA;&lt;li&gt;Proboscis monkey: &quot;&lt;em&gt;The large nose amplifies the male monkey's mating calls, gaining the female's attention and potentially intimidating the competition.&lt;/em&gt;&quot;&lt;/li&gt;&#xA;&lt;li&gt;And of course the Elephant.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-07T03:41:29.270" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10754" PostTypeId="2" ParentId="10022" CreationDate="2013-10-07T04:01:31.933" Score="2" Body="&lt;p&gt;Yes, I would say that is a bearded robber fly. Robber flies are similar to dragonflies in that they catch prey by catching it in midair. They will attack mostly bees, wasps, and hornets, and I have seen many catching bumblebees in the wild. I have even seen some sit near a yellow jacket nest and catch a hornet when it comes out. They suck out the juices of their prey with a proboscis using methods similar to spiders. They will also bite when handled, as I have found out through experience.&lt;/p&gt;&#xA;" OwnerUserId="4422" LastActivityDate="2013-10-07T04:01:31.933" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10755" PostTypeId="2" ParentId="9382" CreationDate="2013-10-07T04:11:01.293" Score="1" Body="&lt;p&gt;It may also be a squash bug, they look pretty similar. They even have enlarged front legs too.&lt;/p&gt;&#xA;" OwnerUserId="4422" LastActivityDate="2013-10-07T04:11:01.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10756" PostTypeId="2" ParentId="10742" CreationDate="2013-10-07T04:16:23.227" Score="7" Body="&lt;p&gt;I agree with @Amory in the sense that Hamilton's rule is not a rule that applies to each specific individual and explain their behavior (or other traits). The Hamilton's rule describe the direction (and not the dynamic) of how a social traits evolve. A social trait is any trait which does not only affect the fitness of its carrier but also affect the fitness of other individuals in the population. Theoretically, all (or almost) traits are actually somehow social traits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$RB&amp;gt;C$ is a simplistic way of looking at Hamilton's rule which might bring you to some confusion. This formula makes more sense to me by replacing $B$ by $\frac{dw(x,y,z)}{dx}$ and $C$ by $\frac{dw(x,y,z)}{dy}$. $w(x,y,z)$ is the fitness function of a focal individual expressing trait $x$ and interacting with an individual drawn from a subpopulation expressing trait $y$ (expected value of the probability distribution of trait expression of individuals in the subpopulation) in a population expressing trait $z$ (expected value again). In the particular case where there is no population structure $y$ equals $z$. $\frac{dw(...)}{dx}$ describes the partial derivative of the fitness function according to the variable $x$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore the Hamilton's rule can be rewritten as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$R\cdot\frac{dw(x,y,z)}{dx}&amp;gt;\frac{dw(x,y,z)}{dy}$$ where $R$ is the coefficient of relatedness which can itself be expressed as a correlation between the variables $x$ and $y$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Altruistic behavior evolves if (but not &quot;if and only if&quot;) this rule is respected. Hope this reformulation of Hamilton's rule helps a bit understanding it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the special case where $R\cdot\frac{dw(x,y,z)}{dx}=\frac{dw(x,y,z)}{dy}$ then, the trait of interest is not selected (neither counter selected). Therefore the trait will evolve under genetic drift alone. While the allele frequencies are modified by drift, the Hamilton's rule might (or might not) differ from the equality and then the trait would not be neutral anymore.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2017-02-04T05:41:44.293" LastActivityDate="2017-02-04T05:41:44.293" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10759" PostTypeId="2" ParentId="9176" CreationDate="2013-10-07T07:01:02.150" Score="0" Body="&lt;p&gt;It looks very much like a squash bug, which look close too assassin bugs but don't eat insects, probably explaining what it was doing in your mulch. I have the same thing.&lt;/p&gt;&#xA;" OwnerUserId="4422" LastActivityDate="2013-10-07T07:01:02.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10760" PostTypeId="2" ParentId="8407" CreationDate="2013-10-07T07:19:50.593" Score="0" Body="&lt;p&gt;It is a common house centipede. Apparently they're everywhere but I've never seen one before.&lt;/p&gt;&#xA;" OwnerUserId="4422" LastActivityDate="2013-10-07T07:19:50.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10762" PostTypeId="1" AcceptedAnswerId="10775" CreationDate="2013-10-07T10:47:00.100" Score="9" ViewCount="2465" Body="&lt;p&gt;I have spent months as a student working on trying to form a tricky protein crystal. But I have never actually had explained to me why the structure will be useful. Once elucidated, what can we potentially learn from the structure in terms of biological significance? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there examples of drugs, or treatments that have only been made possible because of a known crystal structure?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally speaking, why do people spend all the money on synchrotrons, laboratories, robots and so on, for a crystal structure? &lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2018-07-06T12:41:20.167" LastActivityDate="2018-07-06T12:41:20.167" Title="What are the benefits of elucidating the crystal structure of a protein?" Tags="&lt;literature&gt;&lt;structural-biology&gt;&lt;xray-crystallography&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="10763" PostTypeId="2" ParentId="10290" CreationDate="2013-10-07T11:59:59.920" Score="1" Body="&lt;p&gt;Plants have more leaf surface area which is exposed to Sun and plants do need sunlight for Photosynthesis to produce food and oxygen. But how plants avoid getting sunburned ? (Sunburn for plants might mean like leaf getting dry or premature falling off etc). To explain this first we need to know the leaf structure and its mechanism to absorb light and heat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Leaf structure:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZEgrs.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;(Image courtesy &lt;a href=&quot;http://books.google.co.in/books?id=yC97pHFDYHAC&amp;amp;pg=PA164&amp;amp;lpg=PA164&amp;amp;dq=minute%20pores%20on%20surface%20of%20plant%20leaf&amp;amp;source=bl&amp;amp;ots=nvukK7wKSW&amp;amp;sig=t1YumlWVDnVcj0c6cmefBXZ4PMI&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=5npSUoGXBsKn0AWN7YHwCQ&amp;amp;ved=0CGAQ6AEwCA#v=onepage&amp;amp;q=minute%20pores%20on%20surface%20of%20plant%20leaf&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Complete Biology&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The major functionality of &lt;a href=&quot;http://en.wikipedia.org/wiki/Plant_cuticle&quot; rel=&quot;nofollow noreferrer&quot;&gt;Waxy Cuticle&lt;/a&gt; on upper surface is(&lt;a href=&quot;http://waynesword.palomar.edu/termlf2.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Leaf Terminology)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Insulation - Acts as an insulator preventing more heat absorption by the leaf surface. The lower surface of the leaf has 'Stomata' with 'Guard cell' which keeps the leaf temperature moderate by preventing maximum water evaporation. The plants have well adapted to various environment conditions by having various compositions in its waxy cuticle. This has prevented plants from losing water and getting leaf dry.&lt;/li&gt;&#xA;&lt;li&gt;Light reflection - Surface of plant leaves also has hairy structures which will reflect the light and thus reducing the leaf surface from maximum light fall.&lt;/li&gt;&#xA;&lt;li&gt;As we know the diffusion and osmosis process in plants to balance the water content in the cell across its body, we can say that depending on environment and temperature plants have mechanism to deliver water to leaves.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;To summarize plants have developeb mechanism to prevent heating up of leaf surface which will dry it out. Hence they have evolved and adapted themselves to various environment to avoid getting sunburned. Similar question was answered here &lt;a href=&quot;http://wiki.answers.com/Q/Why_do_most_plants_not_burn_in_the_sun&quot; rel=&quot;nofollow noreferrer&quot;&gt;Why do plants do not burn&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other side if there is any change in the environmental condition due to global warming or Ozone hole effect then dangerous rays from the Sun could damage the leaves.&lt;/p&gt;&#xA;" OwnerUserId="4547" LastActivityDate="2013-10-07T11:59:59.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10764" PostTypeId="1" AcceptedAnswerId="10765" CreationDate="2013-10-07T13:11:23.800" Score="3" ViewCount="1234" Body="&lt;p&gt;I'm designing a protein that I'd like to use in FRET reporting.  General idea on the shape is:&#xA;FRETprotein1--Linker--CleavageSite--Linker--FRETprotein2.  I would like to know what AA are best for the linker, or does it matter?  I have heard &lt;code&gt;SSG&lt;/code&gt; is a good choice, but when I started a lit review I become unconvinced.  If it doesn't matter, I may try and put more convenient restriction sites there.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a good way to theoretically determine optimal length?  I realize that may change depending on which FRET protein pair is chosen.  The cleavage sites are between 15-18 AA long.  Unfortunately, I don't think I can give any more detail than that on the cleavage sites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Response to answer:&#xA;So far there have been no FRET systems or tests published with the cleavage sites I want to study.  In fact, I haven't even heard of anyone else trying.  If I'm forced into a positive FRET probe, which I'm worried that I am, does anyone have any FRET pairings that don't interfere with Texas-Red on the spectrum?  My first choices were Venus and Cerulean, but if I have to make a positive probe then I don't think they are a good choice.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2013-10-28T16:07:09.227" LastActivityDate="2013-10-28T16:07:09.227" Title="Is there an optimal composition and length for protein linkers in FRET?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;synthetic-biology&gt;&lt;protein-folding&gt;&lt;fret&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10765" PostTypeId="2" ParentId="10764" CreationDate="2013-10-07T14:01:00.310" Score="3" Body="&lt;p&gt;I am also about to undertake some FRET studies (this week in fact). FRET linkers are a thing of tinkering, unfortunately. Förster resonance energy transfer, or FRET, is a phenomena that decays with $ 1/{r^6} $, the radius between the donor and acceptor. When constructing FRET reporters, there are a few things to keep in mind:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Length of linker&lt;/strong&gt;. The length of the linker (including any cleavage sites), follows an concave optimization curve. A linker too long (&gt; 18 amino acids) or too short (&amp;lt; 5 amino acids) and the FRET signal rapidly diminishes. When considering a FRET reporter in which no cleavage site is introduced, I've seen reporter an optimal linker length of 7-8 amino acids. When including a cleavage site, I've seen optimal liker lengths reporter of 18 amino acids. TO my knowledge, there is no theoretical way to predict the FRET efficiency based on linker sequence, and from scientists I've talked to, they conduct a trial-and-error approach using purified protein products to screen for an optimal length if it appears necessary to do so.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Type of FRET reporter&lt;/strong&gt;. Cleavable FRET reporters fall into two classes. Positive reporters, in which signal appears after cleavage, must use longer linkers to separate fluorophores enough to reduce the FRET phenomenon. Negative reporter, in which FRET signal is lost after cleavage, must necessarily employ both short cleavage sites and linkers, to maximize the FRET phenomenon prior to cleavage. Since you mention the cleavage site itself is 15-18 AA, I would certainly expect very little FRET when uncleaved, assuming that the linker and cleavage site are unstructured, as the distance between the two fluorophores is quite large for the FRET phenomenon. Alternatively, intramolecular FRET reporters are usually designed as positive FRET controls, using short linkers to maximize the FRET phenomenon. When tagging two proteins seperately for FRET, short linkers are also chosen, relying on some external interaction to bring them together, however, this requires a lot of optimization of linker length for both fluorophores for maximum efficiency.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Choice of linker amino acids&lt;/strong&gt;. This part here is somewhat subjective. The choice I often see in the literature are the tiny and small amino acids (especially Ser, Ala and Gly). The choice of these is mostly because they will likely have the least interaction among the linker structure and adjoining proteins and will be the most flexible. The linker should be chosen to avoid use of putative sites for modification (e.g., phosphorylation, glycosylation), rigid geometry (Pro, or bulky aromatics) and excessive charged amino acids.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I should note that I have found no comprehensive review of these three parameters for FRET construct design, and I have gleaned them from the literature. In my opinion, linker length is more critical to optimize than its amino acid sequence, provided that the linker does not lend itself to stable/rigid geometry and modification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would also suggest seeing if FRET constructs have been made using your cleavage site of interest already, and perhaps use the same linking sequences. From this, you could construct a slightly shorter and longer construct to see if one is more optimal over the other.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-10-07T14:01:00.310" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10766" PostTypeId="2" ParentId="7673" CreationDate="2013-10-07T14:26:00.900" Score="6" Body="&lt;p&gt;Adenosine causes humans to become sleepy. But how ? &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;During day time we consume food which is broken down into glucose. This glucose is broken down by &quot;&lt;a href=&quot;http://people.eku.edu/ritchisong/301notes1.htm&quot;&gt;Glycolysis&lt;/a&gt;&quot; in cell's cytoplasm during which ATP is produced. This produced ATP is is then used by body as an energy supplier. ATP breaks down into ADP and then AMP with the release of energy which our body consumes for doing work. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1h8zf.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Fig 1- Structure of &lt;a href=&quot;http://www.creationresearch.org/crsq/articles/36/36_1/atp.html&quot;&gt;Adenosine to ATP&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adenosine is produced continuously and starts to accumulate around and in Adenosine receptors such as A1, A2a, A2b and A3 (as shown in fig below).Adenosine inhibit signal propagation and energy production in at least A1. (Not all the receptors induce sleep when they receive Adenosine.) &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Adenosine_A1_receptor&quot;&gt;A1 receptor&lt;/a&gt;&quot; receives adenosine and induces sleep. A1 receptors are implicated in sleep promotion by inhibiting wake-promoting cholinergic neurons in the basal forebrain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DSA6r.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Continuous inhibition of A1 receptor by Adenosine slowly induces sleep by relaxing the brain and muscles but without substantially weakening their abilities!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is Adenosine metabolized ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During sleep the accumulated Adenosine is metabolized by Adenosine deaminase enzyme which catalyzes the irreversible deamination of 2'-deoxyadenosine and adenosine to deoxyinosine and inosine. With the reduction in the Adenosine content the body is excited from sleep slowly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in short summarize:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The accumulation of adenosine during waking periods is thus associated&#xA;  with the depletion of the ATP reserves stored as glycogen in the&#xA;  brain. The increased adenosine levels trigger non-REM sleep, during&#xA;  which the brain is less active, thus placing it in a recovery phase&#xA;  that is absolutely essential—among other things, to let it rebuild its&#xA;  stores of glycogen. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Because adenosine is continuously metabolized by the enzyme adenosine&#xA;  desaminase, the decline in adenosine production during sleep quickly&#xA;  causes a general decline in adenosine concentrations in the brain,&#xA;  eventually producing conditions more favourable to awakening.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(Refer this page: &lt;a href=&quot;http://thebrain.mcgill.ca/flash/a/a_11/a_11_m/a_11_m_cyc/a_11_m_cyc.html&quot;&gt;MOLECULES THAT BUILD UP AND MAKE YOU SLEEP&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="4547" LastEditorUserId="5754" LastEditDate="2014-05-14T06:52:08.527" LastActivityDate="2014-05-14T06:52:08.527" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10767" PostTypeId="2" ParentId="10762" CreationDate="2013-10-07T14:28:00.630" Score="5" Body="&lt;p&gt;I always wondered this myself, but the structure of a protein  can end up being quite important for a number of reasons.  Most relate to the fact that protein function often depends on specific domains, and while a protein may have multiple functional domains it is important for all domains to be properly aligned and constructed in three-dimensional space.  Misfolded proteins often have negative phenotypes, so being able to visualize the improperly folded areas can be enlightening.  Perhaps more commonly, these techniques can be used to validate an artificially produced protein before approving it for therapy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, while we can know the sequence of amino acids in a protein very easily we don't necessarily know which ones are useful.  A region oriented toward the outside of a protein may partake in a biological function.  If a specific protein domain is imbedded inside the center of the protein, it is not very available for function, either by the protein or for other targets such as antibodies.  For example, one of the big projects in HIV research now is to get very good and very fine structure of viral proteins on the envelope of the virus; knowing which regions are readily accessible would make for potential good drug/cell/antibody targets.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, the structure itself can give some insight as to function.  Proteins may not have homology by amino acid sequence, but similarly-structured proteins can have similar functions.  People smarter than me can recognize those features and can learn quite a bit about a protein just from its shape.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Here's a fun little anecdote I conveniently just came upon.  It's a quote from &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0307277453&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Your Inner Fish&lt;/em&gt;&lt;/a&gt; by Neil Shubin (© 2008) about two researchers, Linda Buck and Richard Axel, who in 1991 discovered a family of genes that allow us to smell.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Experiments showed that odor receptors have a characteristic structure with a number of molecular loops that help them convey information across a cell.  This was a big clue, because Buck and Axel could then search the genome of a mouse for every gene that makes this structure.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-09T03:47:28.627" LastActivityDate="2013-10-09T03:47:28.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10769" PostTypeId="2" ParentId="10762" CreationDate="2013-10-07T15:24:46.430" Score="4" Body="&lt;p&gt;Expanding on something Amory said:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are very beneficial in drug discovery. This is because it is absolutely essential that you have a structure to do any sort of molecular dynamic simulation. In the early phases of drug discovery it is cheap and easy to do these types of experiments on a computer, rather than setting up an assay for different potential therapeutics. You just take the crystal stucture of the protein, and a structure of your compound, and a program will simulate how they will interact with each other. From this you can see if the compound is able to enter the active site of the protein, the orientation it would be in, etc. Using a supercomputer you can do this with hundreds of compounds in a matter of hours. Molecular dynamics has other useful purposes, drug discovery is just one example. &lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-10-07T15:24:46.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10770" PostTypeId="2" ParentId="10742" CreationDate="2013-10-07T15:30:45.163" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Hamilton's rule states that if rB&gt;C then a gene giving altruistic&#xA;  behaviour will increase in frequency in the population.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;To start here are some examples of how Hamilton's Rule works...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a population of four individuals a pair of adults mate. A first unrelated male (r=0) is genetically coded to help raise their offspring by an allele (selfless) at the &quot;sociality&quot; gene. A second male, also with r=0, has a different allele (selfish) at the same locus which makes him not help with offspring care. The pair raises 4 offspring if they go it alone, and 10 if another male helps. By helping, a male sacrifices his ability to mate so produces no offspring. Going it on his own he would produce 4 offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By helping, when r=0, a male passes on no copies of his genes to the next generation (fitness = 0, no offspring in the next generation have genes that are identical by descent [ibd] to his), by being selfish he passes on 4ibd copies of half of his genes (fitness = 2 = 4*0.5). Thus the male carrying the selfish allele should do better and genes promoting social behavior should not evolve in the population because 0*(10)&amp;lt;2 (by helping he sacrifices the fitness score of 2, this is the cost).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now with related males, say the father's brothers. This time the males will on average be related to the offspring of the pair with a relatedness coefficient of r=0.25. With the same results of helping and selfish behavior, genes for social behavior should evolve because 0.25*10&gt;2, the selfless male has more IBD genes in the population than the selfish male. The next generation would have many individuals in it with the selfless allele.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Hamilton's rule is used to estimate whether &quot;selfless&quot; type alleles will spread through a population,&lt;/strong&gt; to do so there must be some sort of relatedness within a group otherwise r=0 so rB will never be greater than C. In populations where relatives stay together there is more chance that altruistic behavior will affect a relative, when relatives can't/don't disperse away from each other much then genes promoting altruism should evolve. In more fluid societies they should not be as common.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Hamilton's rule is not definitive though.&lt;/strong&gt; The closer that rB and C are to each other, the weaker selection will be at driving out alleles which reduce fitness, that is because the gain of having the correct allele is so marginal. For example, if r=0.5, B=100, and C=49, then selfless alleles are 2% fitter than selfish alleles. In comparison, if we keep r=0.5 and B=100, but change C to 40, then the rB&gt;C still holds and selfless alleles have more strongly favorable selection (they are 25% fitter) so will spread more rapidly. If C=0 the behavior is likely to evolve because r=0 is unlikely in a population (even if you only include polymorphic loci).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;What would happen if rB=C? Will an individual perform the altruistic&#xA;  act?&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Whether animals can use Hamilton's rule to decide behaviors plastically is different application of the equation in Hamilton's rule.&lt;/strong&gt; It is a similar concept, but evolution does not happen with the individual; the genetic makeup of an individual will not change as a result of selection. However, ignoring the definition of how Hamilton's rule is used you could use the same equation to estimate likely behavioral outcomes when an individual is given a choice. Here is an example where an individual is given the option to give or keep food and can judge relatedness, it is a very simplified model. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example: A locus has two alleles G and g. Individuals can then be GG, Gg, and gg and each genotype has an easily discernible unique trait. Thus when a GG individual meets a GG individual it knows it is perfectly related, r=1. For Gg r=0.5, and gg r=0. When the individuals meet our focal individual (GG) has the option to either provide something for the other one or not provide (let's say give it some food). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For our GG individual the cost of providing the food to the other is the energy it took to find the food, say 50 calories. The benefit to the recipient is the energy within the food, lets say 120 calories. Thus we can say, GG should give the food to the other individual if the other is GG (because 1*120 &gt; 50) or Gg (0.5*120 &gt; 50) but not when it is gg (0*120 &amp;lt; 50). If we reduce the value of the food to 80 calories it becomes that GG should not help Gg (0.5*80 &amp;lt; 120).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;There are a few limitations to consider...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, how well can an individual quantify relatedness? Just using Wrights Coefficient of Relatedness we would come out with roughly accurate measures on average. But there is variability due to mutations and the second law of Mendelian inheritance; independent assortment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, how well can an individual judge benefit of its actions? The effect on the recipient is likely to be complex, it could have serious knock-on effects such as increased fitness later in life, longer lifespan, the action might reduce predation risk for the recipient that day etc..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thirdly and similarly, how well can the provider judge the cost it incurs? If it is giving away food, it does not know if and when it will actually find it's next food item, foraging might cause it to be predated upon, and it might lose out on a mating opportunity if a receptive mate comes by while it is foraging etc..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;When rB truly equals C (unlikely due to the complex nature of r, B and C) or is approximately equal,&lt;/strong&gt; then the individual will be less likely to make the correct choice. When it is obvious that the cost is large and benefit is small it is more likely to make the correct decision. This is analogous to the ability of selection to drive out the incorrect allele as outlined above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;This is a rewrite of a previous answer made after some thinking and I think it provides a much better answer than the previous incarnation which I have deleted&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2013-10-07T15:30:45.163" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10771" PostTypeId="1" AcceptedAnswerId="10777" CreationDate="2013-10-07T16:26:07.103" Score="5" ViewCount="218" Body="&lt;p&gt;I designed a synthetic construct on paper and got it synthesized from a company. The objective was to make a vector which can be used to study both transcriptional and post-transcriptional regulation by different cis-elements (2-3 different cis-elements can be studied simultaneously).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The construct is like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;SmaI-RES1-CMV-RES1’-GFP-MCS1-SV40PA-Linker-RES2-CMV-RES2’-RFP-MCS2-SV40PA-Linker-RES3-CMV-RES3’- YFP-MCS3-SV40PA-ΔLinker-SmaI&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;where:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;RES1 = KpnI [GGTACC] &#xA;RES1’= SalI [GTCGAC] &#xA;MCS1 = EcoRI+BamHI [GAATTCTGGATCC] &#xA;RES2 = ClaI [ATCGAT] &#xA;RES2’= NheI [GCTAGC] &#xA;MCS2 = SpeI+HindIII [ACTAGTAAGCTT] &#xA;RES3 = XbaI [TCTAGA] &#xA;RES3’= PvuI [CGATCG] &#xA;MCS3 = NotI+SacI[GCGGCCGCGAGCTC]&#xA;Kozak consensus sequence = GCCACCATGG&#xA;Linker (100bp) = AATTCTGGATCCTGCAGCTTATAATGGTTACAAATAAAGCAATAGCATCACAAATTTCACAAATAAAGCATTTTTTTCGAATTTCGATTCCACCGCCGCCTTCTATGAAAGGTTGGGCTTCGGAATCGTTTTCCGGGACGCCGGCTGGATGATCCTCCAGCGCGGGGATCTCATGC&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;GFP, RFP and YFP are fast turnover variants with MODC pest sequence. I took the sequences for these proteins from Evrogen website. I took the Sv40 polyA signal sequence from one of their vectors in order to avoid any event of incompatibility. Kozak sequence was also taken from those vectors only. The total size it ~4.8kb. For CMV promoter I took the standard sequence used in most vectors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With this vector I could clone any post-transcriptional regulatory sequence between stop codon and SV40PA, and could change promoters as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With the CMV promoter and no 3'UTRs I see a very faint expression of GFP, but could not see any RFP expression. I used pMaxGFP and dsRed as a control for filter sensitivity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I transfected the plasmid in Hela and Neuro2a and at various concentrations (1-5μg) using lipofectamine. The controls express well (transfected 1μg each) but I see very faint GFP expression and dont see any RFP expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I checked the sequencing QC report given by the company and there were no indels or other mismatches. I am clueless about why the construct fails to express. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the linker a problem; is 100bp not sufficient ? &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-10-07T22:13:31.477" Title="Synthetic construct with multiple ORFs not expressing" Tags="&lt;molecular-biology&gt;&lt;synthetic-biology&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10772" PostTypeId="1" CreationDate="2013-10-07T17:17:16.763" Score="1" ViewCount="389" Body="&lt;p&gt;The current issue of the magazine Lonely Planet India(Oct 2013) presents a photo of Camargue Horses which are white coated and mentions that they are born with dark hair. A search shows that the &lt;a href=&quot;http://library.thinkquest.org/5053/Europe/CamargueHorse.html&quot; rel=&quot;nofollow&quot;&gt;foal are either black, grey or brown coated&lt;/a&gt; and gradually turn white around the Third/fourth year.&#xA;What could be the possible advantage of that kind of difference between the young and the adult?&lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="3971" LastEditDate="2013-10-07T20:52:25.137" LastActivityDate="2013-10-07T21:01:21.383" Title="Why would the Camargue horses have a white coat while the foal have a dark coat?" Tags="&lt;zoology&gt;&lt;pigmentation&gt;&lt;hair&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10773" PostTypeId="2" ParentId="10772" CreationDate="2013-10-07T18:00:31.400" Score="2" Body="&lt;p&gt;Our own hair will also turn gray (indeed, yours seems to be on its way, if you don't mind me saying so) but there need not be an advantage to that; if it doesn't affect our ability to have successful children it probably doesn't matter much to evolution or selection.  When it comes to animals that interact with humans, though, many traits are selected for, even those without an advantage, in fact often we select for disadvantageous traits (if they were advantageous, we might not need to select for them in the first place).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As &lt;a href=&quot;http://www.nature.com/ng/journal/v40/n8/full/ng.185.html&quot; rel=&quot;nofollow&quot;&gt;this 2008 paper from Nature Genetics&lt;/a&gt; goes into, the &quot;graying with age [phenotype] is an autosomal dominant trait&quot; overwhelmingly caused by &quot;a 4.6-kb duplication in intron 6 of STX17 (syntaxin-17) that constitutes a cis-acting regulatory mutation&quot;.  To answer your question, though:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Gray horse provides a notable example of how humans have cherry-picked mutations with favorable phenotypic effects in domestic animals... The prestige of riding a white horse has thus led to selection of the Gray-causing mutation by humans; this mutation is by far the most common cause of white color in horse.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This phenotype is actually often detrimental, as white/gray horses can have &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/early/2010/01/28/rspb.2009.2202.full&quot; rel=&quot;nofollow&quot;&gt;eye problems and higher rates of skin cancer&lt;/a&gt;; Camargue's are &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1034/j.1600-0749.2000.130109.x/pdf&quot; rel=&quot;nofollow&quot;&gt;particularly susceptible to melanomas&lt;/a&gt;, present in around 70% of horses by age 15.  There does seem to be some benefit, though, as the second paper I linked suggests these horses are subject to fewer fly attacks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;: I seem to have been unclear and you seem to have misunderstood my answer.  Let me break it down:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/store/10.1046/j.1365-2052.2002.00885.x/asset/j.1365-2052.2002.00885.x.pdf?v=1&amp;amp;t=hmi5d6rq&amp;amp;s=86b1359f9f35b4615b68954b13a91dffd2c72323&quot; rel=&quot;nofollow&quot;&gt;Camargue horses are gray&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/ng/journal/v40/n8/full/ng.185.html&quot; rel=&quot;nofollow&quot;&gt;Gray color&lt;/a&gt; is a &lt;a href=&quot;http://onlinelibrary.wiley.com/store/10.1046/j.1365-2052.2002.00895.x/asset/j.1365-2052.2002.00895.x.pdf?v=1&amp;amp;t=hmi5czos&amp;amp;s=24508048294618b49ce32e11c76432a81a7a126f&quot; rel=&quot;nofollow&quot;&gt;simple&lt;/a&gt; mendelian &lt;a href=&quot;http://onlinelibrary.wiley.com/store/10.1111/j.1365-2052.2005.01334.x/asset/j.1365-2052.2005.01334.x.pdf?v=1&amp;amp;t=hmi5g69n&amp;amp;s=7714528dbcbcf42ffacba24ae5554306408e33b9&quot; rel=&quot;nofollow&quot;&gt;autosomal dominant&lt;/a&gt; phenotype caused by a loss of pigment in adulthood.&lt;/li&gt;&#xA;&lt;li&gt;Gray color &lt;a href=&quot;http://onlinelibrary.wiley.com/store/10.1034/j.1600-0749.2000.130109.x/asset/j.1600-0749.2000.130109.x.pdf?v=1&amp;amp;t=hmi5yphk&amp;amp;s=e25dd2867bc0d28a5b355cd3c6a7a6a45839a6a6&quot; rel=&quot;nofollow&quot;&gt;is generally bad&lt;/a&gt; but &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/early/2010/01/28/rspb.2009.2202.full&quot; rel=&quot;nofollow&quot;&gt;sometimes good&lt;/a&gt;; either way, it's probably not a &lt;em&gt;huge&lt;/em&gt; detriment.&lt;/li&gt;&#xA;&lt;li&gt;Camargue horses &lt;a href=&quot;http://download.springer.com/static/pdf/599/art%253A10.1007%252Fs00335-002-2174-7.pdf?auth66=1381350202_5fecef18ab65aa99095f503d1ac1b814&amp;amp;ext=.pdf&quot; rel=&quot;nofollow&quot;&gt;are homozygous for gray color&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Humans have in the past selected for gray color in &lt;em&gt;horses in general&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;That is an example of why something negative or pointless might persist, as would a dominant inheritance pattern that is fixed in a population: negative traits that are only weakly deleterious have a non-negligible chance of fixation.  Asking what the advantage is is somewhat of a moot question because every single Camargue horse has the trait; asking what caused a seemingly-negative phenotype to become fixed is a good question, but likely an unanswerable one as it occurred long ago.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note, how long a breed has been in an area does not simply imply breed purity.  Here's a quote from the &lt;a href=&quot;http://imh.org/index.php/exhibits/online/horse-breeds-of-the-world/item/2135-camargue&quot; rel=&quot;nofollow&quot;&gt;International Museum of the Horse&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Through the centuries many armies have passed by the Camargue, including the Greeks, Romans and Arabs. The horses brought with these armies influenced the Camargue over time. It has even been suggested that the Camargue has had some influence on the early breeds in Spain as armies took them back home.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-07T21:01:21.383" LastActivityDate="2013-10-07T21:01:21.383" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10774" PostTypeId="1" CreationDate="2013-10-07T18:15:41.817" Score="2" ViewCount="89" Body="&lt;p&gt;There was some experiment in which a S phase cell was fused with other cell and the other cell also began to replicate DNA. Would the same happen if fused with nerve cell ? Why or why not?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-12-05T08:57:22.737" Title="Fusion of neuron with a S phase cell" Tags="&lt;cell-biology&gt;&lt;mitosis&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10775" PostTypeId="2" ParentId="10762" CreationDate="2013-10-07T18:25:42.407" Score="10" Body="&lt;p&gt;&lt;a href=&quot;http://rcsb.org/pdb/home/home.do&quot; rel=&quot;nofollow noreferrer&quot;&gt;Protein structures&lt;/a&gt;, which can be obtained from protein crystals or from concentrated solutions of pure protein via NMR, are arguably the primary source of knowledge that we have about how genes perform their function on the molecular level.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've added a link to RCSB.org above - they write up a story on an important protein structure monthly(?) - its a great way to pick up some fascinating stories. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The precise atomic positions from a protein structure are indispensible for several reasons.  Since biological processes are all fundamentally chemical ones.  The specific positions of the atoms reveal how proteins, nucleotides, lipids, drugs and other biological molecules specifically interact.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Protein structures broke the ground in biological inheritance (Watson / Crick / Franklin's DNA structure) &lt;/li&gt;&#xA;&lt;li&gt;Protein structures of lysozyme and proteases were the first to show exactly how proteins bind their substrates and enzymatically catalyze chemical reactions.  &lt;/li&gt;&#xA;&lt;li&gt;Protein structure of hemoglobin in both oxy- and deoxy- forms (i.e. with and without oxygen bound). showed that proteins change their spatial arrangement to modulate their function.  &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This list goes on to more recent breakthroughs in how signals and molecules interact with the cell through the membrane.  There is literally no topic in cellular biology which has not substantially benefitted from having a protein structure revealed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The advantages of working with protein crystals are that they can be larger proteins and certain kinds of difference experiments an be more easily performed when a protein crystal is obtained.  For instance if you have a crystal of a 100 kDa (~900 amino acid) protein, you can often find the binding pocket of the enzyme without a tremendous amount of work. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The disadvantage of working with protein crystals, as you probably know well is that getting crystals is often a quixotic effort soaking up months or years, often with little or no results.  Pretty demoralizing until you hit the target.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're astounded to think that proteins, which are often hundreds or thousands of times larger than a salt or mineral you usually find in crystals...you are dead on.  The crystals are often very tiny - a decent sized crystal measures about a millimeter on one side, but often are only a fraction of that size.  That's why protein crystals often are taken to synchrotrons, linear accellerators or other free electron X-ray sources which are millions (?) of times more intense than a dental x-ray. I would guess that most protein crystal structures are obtained using special beamlines created especially for biological crystallography. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That sort of tells you the funding priority science is willing to put into x-ray protein crystal structures.  Simply the idea that protein crystals might be easier to grow in microgravity (along with the low weight of the experiment) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11536985&quot; rel=&quot;nofollow noreferrer&quot;&gt;justified over a decade of protein crystal growth experiments on the shuttle and ISS&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interesting note: The Guardian (which is based in the UK where crystallography, protein or otherwise started out) has posted a short video outlining h&lt;a href=&quot;http://www.theguardian.com/science/video/2013/oct/09/100-years-x-ray-crystallography-video-animation&quot; rel=&quot;nofollow noreferrer&quot;&gt;ighlights of crystallography's contributions over the past 100 years&lt;/a&gt;.  If you watch assiduously you will see protein crystallography cropping up with a litany of nobel prizes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;New thoughts: &#xA;There are signs that crystal structures are coming to an end.  Using an electron micrograph to simply take a picture of many thousands of individual proteins laying about can be digitally averaged to create low resolution structures they &lt;a href=&quot;https://www.sciencedirect.com/science/article/pii/S0304416517302374&quot; rel=&quot;nofollow noreferrer&quot;&gt;are gradually becoming higher resolution&lt;/a&gt; and are a lot less work than preparing and making a protein crystal - and it works well on larger proteins and protein complexes! &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2018-07-02T21:32:31.403" LastActivityDate="2018-07-02T21:32:31.403" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="10777" PostTypeId="2" ParentId="10771" CreationDate="2013-10-07T21:23:54.130" Score="5" Body="&lt;p&gt;I'm afraid there's not much of answer but back to the bench with you! (That's why it's called re-search).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several factors that could be playing a role here.  You could have transcriptional or translational read through.   You should check your sequence and the cells you are going into to make sure you aren't getting Amber (UAG) suppression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before you do anything, you should check your DNA of all your groups.  Run it uncut on a gel and make sure the majority of the DNA is super coil.  The next easiest thing to check is translation problems.  Get an GFP antibody, possibly a few that recognize different epitopes, and see if your GFP is coming out the right size.  It may not be processed correctly or folded correctly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can run into problems by optimizing the sequence.  First, &lt;a href=&quot;http://www.nature.com/nsmb/journal/v20/n2/abs/nsmb.2466.html&quot; rel=&quot;nofollow&quot;&gt;synonymous mutations can cause folding variants&lt;/a&gt; (1).  Second, you might be causing a hair pen or other disadvantageous secondary or tertiary structure.  If you can't detect any problems in your Western, you might consider doing a Northern to trouble shoot the transcription.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you rule everything else out, and you are just getting poor expression, then the only way I know to boost over CMV is to use T7.  The problem with T7 is always going to be what use for a source.  If you can use BSR/T7 cells and you can get your hands on them, they work great.  Otherwise you're looking at a T7 plasmid or MVA-T7 as common sources.  The plasmids never lead to a great deal of expression in anyone's hands I've ever known.  MVA-T7 works, but to say that it confounds things would be the under statement of the year.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2013-10-07T22:13:31.477" LastActivityDate="2013-10-07T22:13:31.477" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10778" PostTypeId="2" ParentId="10679" CreationDate="2013-10-08T10:49:59.160" Score="3" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;a) stronger aggressive behaviour only during egg laying&lt;/p&gt;&#xA;&lt;p&gt;c) stronger aggression when egg is first laid than during nest building&lt;/p&gt;&#xA;&lt;p&gt;d) greater aggression during hatching eggs than during nest building&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;These all occur after the stage which determines fitness. Egg laying (a and c) and Egg hatching (d) occur after the male has won the right to mate.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;b) stronger aggressive behaviour during nest building rather than&#xA;during hatching of eggs&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Assuming the behavior increases mating success and fitness, the answer is B because this is the only strategy that attracts more females and gets rid of rival males before it is too late (i.e. before the female mates). This is also assuming that the female can/will only mate once.&lt;/p&gt;&#xA;&lt;p&gt;In chronological order the answers run &amp;quot;B,C/A,D&amp;quot; (C &amp;amp; A are really one and the same in my eyes). Mating occurs between B and C.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-08T10:49:59.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10779" PostTypeId="1" AcceptedAnswerId="10780" CreationDate="2013-10-08T11:08:27.327" Score="2" ViewCount="32250" Body="&lt;p&gt;Cushing's syndrome results from increased levels of cortisol in the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cortisol as I understand it however, promotes the breakdown of glycogen and amino-acids in the process of gluconeogenesis, to increase blood sugar - opposing the action of insulin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why then does Cushing's syndrome lead to weight gain rather than weight loss?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2015-10-09T07:03:49.270" Title="Why is weight gain a symptom of Cushing's Syndrome?" Tags="&lt;pathology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10780" PostTypeId="2" ParentId="10779" CreationDate="2013-10-08T11:54:16.597" Score="2" Body="&lt;p&gt;Cortisol is released when body goes through stress situations like while working out in gym, physiological activities outdoor etc. As you have already mentioned about what Cortisol does, it accumulates in the body after the stress situation and then with the intake of food and other nutrients it replaces the consumed carbohydrate and fat in the body i.e. a kind refueling. So this is how Cortisol maintains the body weight normally if our body gets enough exercise or has proper metabolism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whereas in Cushing' syndrome which comes usually by taking glucocorticoid drugs, or diseases that result in excess cortisol, adrenocorticotropic hormone (ACTH), or CRH levels. In this case Cortisol content will be more than the normal level which in turn requires more carbohydrate. So cortisol metabolizes the food and reefuels the body even when there is no requirement within the body. So because of excessive cortisol content body simply gets excessive fat accumulated in various parts which mainly results in obesity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One more explanation from &lt;a href=&quot;http://www.examiner.com/article/stress-and-obesity-101-what-are-the-effects-of-stress-induced-cortisol-on-obesity&quot; rel=&quot;nofollow&quot;&gt;High level of Cortisol effects&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Chronically high levels of cortisol plays a big role in the development of obesity.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cortisol helps the body handle stress; so, when stress goes up,&#xA;  cortisol also goes up. Cortisol stimulates fat and carbohydrate&#xA;  metabolism during stressful situations. This leads to increased blood&#xA;  sugar levels required for fast energy. In turn, this stimulates&#xA;  insulin release which can lead to an increase in appetite.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;blockquote&gt;&#xA;  &lt;p&gt;Adrenaline increases alertness and metabolism by helping fat cells release&#xA;  energy. When the immediate stress is over, the adrenaline levels&#xA;  return to normal. But, cortisol lingers to help bring the body back&#xA;  into balance after stress. One of the ways it gets things back to&#xA;  balance is by increasing appetite to replace the carbohydrate and fat&#xA;  used for the flight or fight response.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The problem is that in today's society, stress-causing situations do&#xA;  not really require the body to use up a lot of energy. So, cortisol&#xA;  ends up causing the body to refuel after stress even when it doesn't&#xA;  really need to refuel. This excess fuel or glucose is converted into&#xA;  fat resulting in increased storage of fat.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4547" LastActivityDate="2013-10-08T11:54:16.597" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10781" PostTypeId="1" CreationDate="2013-10-08T12:32:09.290" Score="2" ViewCount="69" Body="&lt;p&gt;Woodpeckers found on the South American mainland are able to peck insects from the bark of trees. Would the woodpecker finch have been able to survive if woodpeckers had found their way to the Galapagos Islands where this finch is found? &lt;/p&gt;&#xA;" OwnerUserId="4629" LastEditorUserId="107" LastEditDate="2013-10-08T13:03:36.300" LastActivityDate="2013-10-08T13:03:36.300" Title="Natural selection and the Galapagos Islands" Tags="&lt;evolution&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2013-10-09T13:18:42.607" ContentLicense="CC BY-SA 3.0" />
  <row Id="10782" PostTypeId="2" ParentId="10738" CreationDate="2013-10-08T20:10:21.890" Score="3" Body="&lt;p&gt;Given what you've said in the comments, and how much more common they are, I'm going with my first gut reaction of Lycoperdon perlatum.  The big give away for me was that you said there was a good taste.  L. Perlatum has a rich nutty flavor (my wife grows them), but Handkea excipuliformis (pestle puffballs) don't have much taste if any.  They are seriously notably bland.  H. excipuliformis can take on the flavor of what ever you cook them with, so if you cooked in a nut oil or with nuts, then you would have given the flavor that way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not that I support taste as a primary means of id...  In this case most of the puffballs are edible so you were in a low risk situation.  I just don't want to start a wave of fungus ID's that include taste info!&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3632" LastEditDate="2013-10-08T23:35:20.263" LastActivityDate="2013-10-08T23:35:20.263" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10784" PostTypeId="2" ParentId="10349" CreationDate="2013-10-08T21:44:27.833" Score="3" Body="&lt;p&gt;I think, you misidentified the unpaired anal fin of coelacanth as an extra pair of limbs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I personally haven't ever heard of six-legged vertebrates, although the phenomenon of supernumerary legs is well known as an anomaly. Such anomalies can be easily induced in different vertebrates (including mice: &lt;a href=&quot;http://www.pnas.org/content/91/12/5436.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Rutledge et al&lt;/a&gt;), if you treat their embrya with retinoid acid (which normally defines embryonic polarity) or fibroblast growth factor. In nature, different factors can lead to development of extra legs, and the most well-known and wide-spread cases are limb abnormalities in amphibians, induced by trematodes and pollution (including retinoid acid mimics?) (&lt;a href=&quot;http://tiee.ecoed.net/vol/v2/issues/frontier_sets/amphibians/pdf/Frontiers-Blaustein-Johnson.pdf&quot; rel=&quot;nofollow&quot;&gt;Blaustein &amp;amp; Johnson&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, I would not be surprised by a discovery of a fossil amphibian with extra limbs. But such a find then should be interpreted as an abnormality, if not proved otherwise. It's true that the fore and the hind limbs are serial homologues, but their number seems to have been fixed very early (in contrast to the number of the fingers).&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2013-10-08T21:44:27.833" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10785" PostTypeId="2" ParentId="5273" CreationDate="2013-10-09T02:09:28.587" Score="1" Body="&lt;p&gt;Sorry for digging out this old question. But I think that given you have an unrooted tree, the common ancestor maybe not the correct answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you need to do is this:&#xA;Suppose you have an unrooted tree with n tips (species), and thus 2n-3 branches. You should cut the tree in half in all these possible branches. By doing this, you will have 4n-6 subtrees. The smallest subtree containing all your selected species will be your answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is different from common ancestor because for an unrooted tree, it could be put in a way that those species not picked by you are clustered first, all your selected species becomes the outgroup. But if you &quot;re-root&quot; the tree properly, you could still make your selected species cluster together as a small, exclusive clade.&lt;/p&gt;&#xA;" OwnerUserId="4635" LastEditorUserId="69" LastEditDate="2013-10-09T13:18:14.713" LastActivityDate="2013-10-09T13:18:14.713" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10787" PostTypeId="2" ParentId="8361" CreationDate="2013-10-09T07:44:09.280" Score="1" Body="&lt;p&gt;At night several changes occur in the body due to absence of sunlight and other surrounding changes. The biological clock inside the body performs certain function in a healthy body whenever changes are sensed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many receptors in our body located on cell membrane. They are made up of proteins and their function is to receive information from neurotransmitters. This information will be sent to specific part of the brain. If we take sensory information then it is &lt;a href=&quot;http://en.wikipedia.org/wiki/Parietal_lobe&quot; rel=&quot;nofollow&quot;&gt;Parietal lobe&lt;/a&gt;. This lobe receives the sensory information from all over the body and responds to it when body is active. During sleep, the senses that go through the thalamus, are shut down by gating either in the Nucleus Reticularis Thalami (NRT) or in the Thalamus itself. GABAergic inhibition of the thalamus, most likely deriving from the NRT is probably a part of the reason that sensory stimuli doesn't penetrate during sleep.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is also influenced by release of hormones in the body whose level when rises in the blood causes certain changes in the concentration at some regions such as receptors which gets blocked temporarily and stops signaling the brain. There is a study on how muscle relaxes when we sleep can be found here &lt;a href=&quot;http://media.utoronto.ca/media-releases/health-medicine/study-identifies-how-muscles-are-paralyzed-during-sleep/&quot; rel=&quot;nofollow&quot;&gt;Muscle sleep&lt;/a&gt;. So it is all the neurotransmitters job at the receptors which stops signals going into brain but internal to the brain it will be active controlling other routine works which it has to do when we are asleep.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main thing to note here is the 5 different stages of sleep such as non-REM and REM sleep. During those stages several changes take place in the body. The below website gives an excellent insight into different changes happening inside the body when body takes rest at night.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please refer to &quot;&lt;a href=&quot;http://www.dailymail.co.uk/health/article-90598/What-happens-body-youre-asleep.html&quot; rel=&quot;nofollow&quot;&gt;What happens to your body while you are asleep&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;" OwnerUserId="4547" LastActivityDate="2013-10-09T07:44:09.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10788" PostTypeId="2" ParentId="3545" CreationDate="2013-10-09T09:44:11.120" Score="0" Body="&lt;p&gt;This is a question that keeps coming up now and then when PhDs or post-docs discuss transfection. A probable answer for which I do not have supporting literature is this: If you have the transfection complex in the medium while the cells are dividing, it is possible that they can enter the nucleus following mitosis when the nuclear membrane is still forming, thus giving it access to the transciption mechanism in the nucleus.&lt;/p&gt;&#xA;" OwnerUserId="4637" LastActivityDate="2013-10-09T09:44:11.120" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10789" PostTypeId="1" AcceptedAnswerId="10790" CreationDate="2013-10-09T10:01:38.947" Score="8" ViewCount="9466" Body="&lt;p&gt;Carbohydrates are often defined as compounds with only C, H, and O and the H and &lt;strong&gt;&lt;em&gt;usually&lt;/em&gt;&lt;/strong&gt; the O atoms are in a 2:1 ratio.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exceptions like deoxyribose exist, but why is it recognized as a carbohydrate?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What distinguishes a carbohydrate from other compounds?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2016-09-26T20:35:46.407" Title="The real definition of carbohydrates" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10790" PostTypeId="2" ParentId="10789" CreationDate="2013-10-09T10:22:09.113" Score="16" Body="&lt;p&gt;The definition of carbohydrates as &lt;em&gt;compounds containing $C$, $H$ and $O$ usually with the empirical formula ${C_m(H_2O)_n}$,&lt;/em&gt; is outdated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More rigorous and a accurate definition would be &lt;strong&gt;Polyhydroxy Aldehydes and Ketones composed of Carbon, Hydrogen and Oxygen.&lt;/strong&gt; Moreover, the nomenclature including &lt;em&gt;Mono-, Di-, Oligo-&lt;/em&gt; and &lt;em&gt;Poly-&lt;/em&gt; &quot;Saccharide&quot; is preferred over the now obsolete and too-general term &quot;carbohydrate&quot;, since the etymological origin of the word &quot;carbohydrate&quot; is from the greek words &lt;em&gt;Carbo-&lt;/em&gt; for carbon and &lt;em&gt;hydor-&lt;/em&gt; for water which indicates that the carbohydrates are &quot;hydrates&quot; of carbon and have the empirical formula ${C_m(H_2O)_n}$, which is not always true. Instead &quot;saccharide&quot; is derived from the greek word for &quot;sugar&quot; and hence is much more accurate as it does not limit the definition to any empirical formula.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from the polyhydroxy aldehyde or ketone characteristic of carbohydrate, they have a marked structural and functional variation from other biomolecules. This includes the absence of $S$ (as in proteins), $P$ and $N$ (as in proteins and nucleic acids), presence of Glycosidic bond (as compared to peptide bond in proteins, phosphodiester bond in nucleic acid, and ester linkages in fats or glycerides) and much greater structural uniformity as compared to other biomolecules.However, these characteristics are not absolute as is evident from the fact that several monosaccharide derivatives do contain $S$ or $N$ atoms. Actually, the entire group of amino-sugars (Hexosamines etc.) are usually classified under carbohydrates since they are primarily monosaccharide derivatives obtained through enzymatic amination. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These characteristics distinguish this class of compounds without having to assign a empirical formula to it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ADDENDUM&lt;br&gt;&#xA;Adding the clause &lt;em&gt;compounds which can, on simple hydrolysis yield polyhydroxy aldehyde or ketones&lt;/em&gt; in the definition helps involve certain non-reducing sugars like Sucrose.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2014-03-07T05:32:23.360" LastActivityDate="2014-03-07T05:32:23.360" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10791" PostTypeId="1" AcceptedAnswerId="10800" CreationDate="2013-10-09T10:55:53.490" Score="1" ViewCount="352" Body="&lt;p&gt;Is it possible to determine if a certain specific mutation had a spontaneous origin (for example from a mistake of the DNA polymerase) as opposed to an induced origin (for example, from some genotoxic agent)?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="3624" LastEditDate="2013-10-10T08:53:28.437" LastActivityDate="2013-10-22T18:13:33.363" Title="Can you detect if a mutation is spontaneous or induced?" Tags="&lt;molecular-genetics&gt;&lt;toxicology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10796" PostTypeId="1" CreationDate="2013-10-09T14:29:07.043" Score="0" ViewCount="3765" Body="&lt;p&gt;Richard Dawkins mentions in his book &lt;em&gt;The Greatest Show on Earth&lt;/em&gt; that dogs are exactly similar to both humans and chimps. Supposing that a cell contains the genetic similarity between 2 species, he says &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The human/dog cell should have an identical resemblance score to the chimpanzee/dog cell because humans and chimpanzees have exactly the same degree of relation to dogs. It should be identical, too, to the monkey/dog cell and the lemur/dog cell. This is because humans, chimpanzees, monkeys and lemurs are all connected to the dog via their common ancestor, an early primate (which probably looked a bit like a lemur)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;He later says that this will be found within &quot;&lt;strong&gt;statistical margins of error&lt;/strong&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the common ancestor of both chimps and humans was more similar to chimps than to humans, it stands to reason that chimps will be more genetically similar to the common ancestor than humans. Therefore (not a direct therefore), dogs and humans can't be exactly similar as dogs and chimpanzees are, even theoretically. Humans and apes are even more dissimilar. Therefore ape/dog cell will not be exactly same value as the human/dog cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please explain where I am wrong.&lt;/p&gt;&#xA;" OwnerUserId="4641" LastEditorUserId="4641" LastEditDate="2013-10-09T19:29:48.877" LastActivityDate="2019-10-19T07:45:31.437" Title="Genetically speaking, are dogs exactly similar to humans and chimps both?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;human-genetics&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10797" PostTypeId="1" AcceptedAnswerId="10798" CreationDate="2013-10-09T16:09:27.000" Score="4" ViewCount="1145" Body="&lt;p&gt;I am starting to use microarrays and maybe this is a dumb question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using Illumina microarrays, linear gene expression can be negative? Or maybe some artefacts have been introduced?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And, in this case, how to correct them? With scaling (adding the absolute value of the minimum negative value) or flooring (converting negative values to zeros)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="3466" LastActivityDate="2018-10-12T21:08:08.510" Title="Negative value on linear gene expression in microarrays" Tags="&lt;gene-expression&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10798" PostTypeId="2" ParentId="10797" CreationDate="2013-10-09T16:53:20.450" Score="6" Body="&lt;p&gt;I'm not personally familiar with Illumina arrays, but I can give some notes here.  This link is a &lt;a href=&quot;http://res.illumina.com/documents/products/technotes/technote_gene_expression_data_quality_control.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper which describes the array quality controls specifically&lt;/a&gt;. This presentation describes the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18467348&quot; rel=&quot;nofollow noreferrer&quot;&gt;calculation of the intensities in bioconductor&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer is yes: you will find negative numbers sometimes.  They should be rare.  The Intensities numbers from a scanner which essentially takes an image of the bead fluorescence on the glass slide and tries to subtract a background signal.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The background is the typical level of signal you see on a bead with no sample DNA bound to it.  You will get some pixels lighting up a bit even there.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In expression microarrays, this is not a perfect system as each bead has a different nucleotide sequence on it.  Each bead has a specific DNA sequence has non-specific binding which is pretty much unique on the slide.  That is to say, the oligomer on the bead might bind strongly to DNA from your sample which is not its reverse complement to varying degrees.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think what happened is that there will be a handful of cases you can find a bead which has less fluorescence than the background controls on the slide.  It's possible that the probe has a design flaw but I would generally assume that the negative number means that there is no detectable target cDNA in the sample for that oligo.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I probably wouldn't convert the number to a zero, but you could probably justify it to yourself in some cases.  Most difference experiments are the logarithm of the ratio so zero is not a great number in those cases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;@Luke 's comments are well said.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that negative values can still represent signal because of the variance of sequence-dependent effects for the purposes of scaling, and difference experiments.  But I'd tend to think of them as zero signal in any case.  There are probably genes which express at or below detection threshold all the time, which is not zero information, so the number has some value. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2018-10-12T21:08:08.510" LastActivityDate="2018-10-12T21:08:08.510" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="10799" PostTypeId="2" ParentId="10796" CreationDate="2013-10-09T17:10:40.897" Score="8" Body="&lt;p&gt;Dawkins is overgeneralizing.  Genetic distance is a fairly new field, and a heated topic, since your answer depends upon which genes you are comparing.  If you picked ONLY strongly-conserved genes for your genetic distance comparison, then you'd find that humans, bonobos, dogs, mice, mosquitos, shrimp, and bakers' yeast are all equally distant (and that the distance is small).  But if you pick ONLY very weakly-conserved genes for your genetic distance comparison, you can get crazy results -- humans are more closely related to yeast than to horses, for example.  (Creationists have had a heyday making fun of some early genetic distance studies that, in retrospect, had poorly-chosen genes.)  So biologists doing genetic distance comparisons try to pick genes that are common to many species, and that have some drift to them, but not so much that the answers are obviously goofy.  Another problem that has arisen is that sometimes an entire gene in several species appears to have been obtained from a very dissimilar species, in a different phylum or kingdom even.  (Current theory is that this is the work of viruses.)  The &quot;tree of life&quot; paradigm might need to be changed to the &quot;web of life.&quot;  Needless to say, there's still a lot of argument about which (and how many) genes to pick for genetic distance studies.&lt;/p&gt;&#xA;" OwnerUserId="4551" LastActivityDate="2013-10-09T17:10:40.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10800" PostTypeId="2" ParentId="10791" CreationDate="2013-10-09T17:26:46.143" Score="3" Body="&lt;p&gt;Here's a quick answer; hopefully someone will give a more complete one.  But meanwhile you've got something.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some genotoxic agents have predictable results.  For example, they cause Gs to substitute for Cs, or they cause mutations at specific spots on the genome.  So if you had a bunch of mutations in a single cell (or collection of related cells) that matched the &lt;em&gt;modus operandus&lt;/em&gt; of a known genotoxic agent, then it would be reasonable to conclude that the mutations were induced.  But not all genotoxic agents are like that.  And if you only have 1 or 2 mutations, that's not enough to prove they were induced.  Also, of course, it depends on your sample size and your controls.&lt;/p&gt;&#xA;" OwnerUserId="4551" LastActivityDate="2013-10-09T17:26:46.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10802" PostTypeId="1" CreationDate="2013-10-09T21:26:44.903" Score="2" ViewCount="120" Body="&lt;p&gt;I was reading &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenoptosis&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; and felt like the argument is being made that organisms die for the good of species. Isn't this nonsense?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This especially bugged me:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;'Age-induced, soft, or slow phenoptosis'&quot; is the slow deterioration and death of an organism due to accumulated stresses over long periods of time. In short, it has been proposed that aging, heart disease, cancer, and other age related ailments are means of phenoptosis. &lt;strong&gt;&quot;'Death caused by aging clears the population of ancestors and frees space for progeny carrying new useful traits.'&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Per the selfish nature of genes, it might be okay if it was only your offspring you are dying for, but even that only when you know you can't reproduce further. And the above argument says that old age death is exactly that.&lt;/p&gt;&#xA;" OwnerUserId="4643" LastEditorUserId="4101" LastEditDate="2013-10-09T21:52:52.917" LastActivityDate="2013-10-10T16:19:42.737" Title="Phenoptosis, behavior evolved for good of species?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10803" PostTypeId="1" AcceptedAnswerId="10815" CreationDate="2013-10-09T21:50:00.703" Score="0" ViewCount="5261" Body="&lt;p&gt;What kind of objects can be qualified as artifacts? How do we distinguish such objects?&lt;/p&gt;&#xA;" OwnerUserId="3751" LastActivityDate="2014-02-06T14:33:51.343" Title="What are artifacts in microbiology?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10804" PostTypeId="1" CreationDate="2013-10-09T22:52:35.767" Score="1" ViewCount="409" Body="&lt;p&gt;Predict how the composition of the cell membrane of a lizard might change from winter to summer. Justify predictions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone please help me figure this out. Does it have to do with fluidity?&lt;/p&gt;&#xA;" OwnerUserId="4645" LastEditorUserId="3971" LastEditDate="2013-10-10T01:14:33.660" LastActivityDate="2013-10-10T05:18:50.887" Title="Lizards are sometimes called cold-blooded because they depend on their surrounding temperatures to keep them warm." Tags="&lt;biochemistry&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10805" PostTypeId="1" AcceptedAnswerId="10807" CreationDate="2013-10-09T23:48:13.690" Score="1" ViewCount="66" Body="&lt;p&gt;What are the mechanics (set of biochemical reactions) allowing a given genotoxic agent&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;to modify the mutation rate at a given spot?&lt;/li&gt;&#xA;&lt;li&gt;to induce only a given type of mutation (from Gs to Cs for example)?&lt;/li&gt;&#xA;&lt;li&gt;some other consequence of the kind that you think is worth talking about!&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am not necessarily seeking for a very detailed explanation of the biochemical pathway but rather some kind of understanding of how such things are possible (not evolutionary speaking but in terms of physiology and cytology).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question comes in reaction to &lt;a href=&quot;https://biology.stackexchange.com/questions/10791/spontaneous-or-induced-mutation-detection&quot;&gt;this post&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-10-10T00:42:02.197" Title="Genotoxic agent and their metabolic pathway" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;metabolism&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10806" PostTypeId="1" AcceptedAnswerId="10812" CreationDate="2013-10-10T00:11:38.717" Score="7" ViewCount="18003" Body="&lt;p&gt;Why do different bacteria have different shapes? Is it only related to their function?&lt;/p&gt;&#xA;" OwnerUserId="3751" LastEditorUserId="4101" LastEditDate="2013-10-10T00:43:02.483" LastActivityDate="2014-09-17T09:53:16.107" Title="Why do different bacteria have different shapes?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10807" PostTypeId="2" ParentId="10805" CreationDate="2013-10-10T00:41:02.707" Score="1" Body="&lt;p&gt;In terms of DNA mutations, it's usually just pure chemistry.  The &lt;a href=&quot;https://en.wikipedia.org/wiki/Mutagen#DNA_reactive_chemicals&quot; rel=&quot;nofollow noreferrer&quot;&gt;mutagens&lt;/a&gt; article gives a brief rundown of some of the usual suspects, but to pick a few of the ones I'm familiar with:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;UV light can cause &lt;a href=&quot;https://en.wikipedia.org/wiki/Pyrimidine_dimers&quot; rel=&quot;nofollow noreferrer&quot;&gt;pyrimidine dimers&lt;/a&gt;, which clearly is a dimerization of Cytosines or Thymines, which can cause replication issues.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Deamination&quot; rel=&quot;nofollow noreferrer&quot;&gt;Deaminases&lt;/a&gt;, which remove amine groups, is probably the coolest example.  Deamination can occur naturally, &lt;a href=&quot;https://biology.stackexchange.com/q/171/4101&quot;&gt;turning Cytosine into Uracil&lt;/a&gt;, but is often done deliberately as part of &lt;a href=&quot;https://en.wikipedia.org/wiki/Bisulfite_sequencing&quot; rel=&quot;nofollow noreferrer&quot;&gt;bisulfite sequencing&lt;/a&gt; to determine methylation status.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Alkylation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Alkylation&lt;/a&gt; can occur, in particular of &lt;a href=&quot;http://www.atdbio.com/content/15/Mutagenesis-and-DNA-repair#Methylation-of-guanine&quot; rel=&quot;nofollow noreferrer&quot;&gt;Guanine&lt;/a&gt;, which can lead to a preference in binding for Thymine; subsequent replication will result in an Guanine to Adenine conversion.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Similarly, there are many &lt;a href=&quot;https://en.wikipedia.org/wiki/Base_analog&quot; rel=&quot;nofollow noreferrer&quot;&gt;base analogs&lt;/a&gt; that will fill in for a given nitrogenous base.  These analogs often prefer to bind to an &quot;incorrect&quot; base as above (and in the figure below with &lt;a href=&quot;https://en.wikipedia.org/wiki/5-bromouracil&quot; rel=&quot;nofollow noreferrer&quot;&gt;5-bromouracil&lt;/a&gt;) which will lead to specific errors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/B9y35.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a more intentional basis, biotechnological tools such as &lt;a href=&quot;https://en.wikipedia.org/wiki/Zinc_finger_nucleases&quot; rel=&quot;nofollow noreferrer&quot;&gt;zinc finger nucleases&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Transcription_activator-like_effector_nuclease&quot; rel=&quot;nofollow noreferrer&quot;&gt;TALENs&lt;/a&gt;, and the (oh-so-sexy) &lt;a href=&quot;https://en.wikipedia.org/wiki/CRISPR&quot; rel=&quot;nofollow noreferrer&quot;&gt;CRISPR system&lt;/a&gt; can be used to specifically alter genome sequences of choice.  ZFNs are in particular being used as a gene therapy tool for just that reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise, viruses (and transposons) that insert into the genome can cause specific mutations or errors if they do so non-randomly.  Figuring that out, though, can be tricky; most oncoviruses cause mutations through specific genes that allow uncontrolled growth and tumorigenesis, not in a site-directed manner.  There is, however, a growing hypothesis that certain retroviruses which tend not to cause cancer, in particular HIV, may be inserting into sites with certain characterizations, such as chromatin level.  That is far from known, though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're looking for random causes, that's easy.  Anything that disrupts DNA repair mechanisms such as p53 or Rb will do that.  For chemicals, &lt;a href=&quot;https://en.wikipedia.org/wiki/Intercalation_%28chemistry%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;intercalators&lt;/a&gt; such as ethidium bromide and thalidomide insert in between DNA bases and prevent proper DNA repair.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2013-10-10T00:41:02.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10808" PostTypeId="1" CreationDate="2013-10-10T01:06:18.663" Score="4" ViewCount="1789" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;A doctor needed to administer 5% albumin to a patient. Albumin is normally administered dissolved in 0.9% saline solution. Since the physician did not have any 5% albumin solution, he diluted 25% albumin with water and administered this to the patient. Describe what you think happened to the blood cells of the patient as a result?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So this is what I think:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the doctor dilutes the 25% albumin, that will make the solution have a lower concentration of solute, creating a &lt;em&gt;hypotonic&lt;/em&gt; solution. Therefore the water will move into the cells, causing them to swell, lyse or burst.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this correct?&lt;/p&gt;&#xA;" OwnerUserId="4645" LastEditorUserId="4101" LastEditDate="2013-10-10T03:13:34.047" LastActivityDate="2014-05-08T12:14:56.530" Title="Hypotonic or Hypertonic solution and why?" Tags="&lt;homework&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10809" PostTypeId="1" AcceptedAnswerId="13456" CreationDate="2013-10-10T03:45:29.663" Score="29" ViewCount="1283" Body="&lt;p&gt;The occurrence of Heart cancer (similar, but not the same as Rhabdomyosarcoma) is extremely rare, about 1 per year according to &lt;a href=&quot;http://www.mayoclinic.com/health/heart-cancer/AN01288&quot;&gt;MayoClinic&lt;/a&gt;. The reason for this rarity is explained to be the post-mitotic nature of cardiac muscles. Since they stop dividing early in the life cycle of humans and grow only by increasing in volume, they are very less prone to oncogenic activation events caused due to mutation as a result of an error in DNA replication (since they do not replicate their DNA as they do not divide).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although I am not an expert in tumours and cancers, I think that malignant tumours in nervous tissue, i.e. brain tumours are fairly common, at least more common than heart cancer by several orders of magnitude. But neurons constituting these tissues are also permanently in interphase and hence do not divide. &#xA; Moreover, secondary malignancies in Brain and nervous tissue is also much more common than secondaries in heart (rare) though metastatic secondary tumours, I believe, do not require oncogenic transformations in the host tissue. A metastatic fragment of a primary malignancy transported by blood is enough to cause secondary tumours.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How then these tumours (primary and metastatic-secondary) are more common in nervous tissue than heart, though both are post mitotic, i.e. permanently in interphase?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.localhealth.com/article/heart-cancer&quot;&gt;Here&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14728061&quot;&gt;here&lt;/a&gt; are a few links which give some basics of cardiac malignancies, though they don't address the question quite directly. &lt;a href=&quot;http://www.cancerfightingstrategies.com/oxygen-and-cancer.html#sthash.ymFogW69.dpbs&quot;&gt;The study here&lt;/a&gt; provides possible explanation of lack of cancer due to high oxygen content.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2014-01-05T02:44:37.093" LastActivityDate="2014-01-05T02:44:37.093" Title="Extremely rare occurence of Heart cancer?" Tags="&lt;human-biology&gt;&lt;cancer&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10810" PostTypeId="2" ParentId="10804" CreationDate="2013-10-10T05:11:15.520" Score="2" Body="&lt;p&gt;Just going to follow up on your thought here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fluidity of the cell membrane does vary with composition.  Off the top of my head there are four main components of the animal cell membrane:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) proteins.  membrane proteins are responsible for the import and export of nutrients, waste, information etc from the cell, so lets assume that this needs to be fairly constant part of the composition while the seasons change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) cholesterol and similar compounds.  These are flat an inflexible compounds which will tend to lower the fluidity of the membrane. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) unsaturated fatty acids and lipids.  These are long carbon chained compounds with some double bonds in them.  Because the double bonds cause the chains to be less mobile, but they don't pack well as they are not as flexible, so tend to make the membrane a bit more fluid.  Think about how butter (mostly saturated fats) is solid at room temperature while olive oil (monounsaturated oil) is liquid. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) saturated fatty acids and lipids.  These are completely mobile carbon chains.  Without any double bonds, these tend to be the &lt;a href=&quot;http://chemwiki.ucdavis.edu/Biological_Chemistry/Lipids/Fatty_Acids#Melting_Points_of_Saturated_vs._Unsaturated_Fatty_Acids&quot; rel=&quot;nofollow&quot;&gt;more flexible and can create a more tightly packed membrane, resulting in a stiffer membraine&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can imagine for the cell to maintain the same flexibility at the lower winter temperatures (4) and (2) would tend to decrease and (3) might tend to decrease.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this make sense? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-10-10T05:18:50.887" LastActivityDate="2013-10-10T05:18:50.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10811" PostTypeId="2" ParentId="10808" CreationDate="2013-10-10T07:24:39.547" Score="1" Body="&lt;p&gt;Albumin wont form a true solution and wont affect the osmolarity greatly (colloid forming molecules like proteins can affect osmotic pressure to an extent. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Oncotic_pressure&quot; rel=&quot;nofollow&quot;&gt;oncotic pressure&lt;/a&gt;).. and since there is no solute the solution would be hypotonic.. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what effect it will have on the blood cells depends on how much solution was injected. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-10-10T07:24:39.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10812" PostTypeId="2" ParentId="10806" CreationDate="2013-10-10T11:36:05.497" Score="14" Body="&lt;p&gt;Reasons for Bacteria with different shapes as given in &lt;a href=&quot;http://en.wikipedia.org/wiki/Bacteria&quot;&gt;Wikipedia/Bacteria&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;The wide variety of shapes is determined by the bacterial cell wall and cytoskeleton, and is important because it can influence the&#xA;  ability of bacteria to acquire nutrients, attach to surfaces, swim&#xA;  through liquids and escape predators.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is an article based on research by Kevin D. Young &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2169503/&quot;&gt;Bacterial morphology: Why have different shapes?&lt;/a&gt; which highlights 3 main points which defines the shape of Bacteria:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Nutrient uptake&lt;/strong&gt;: Cell shape, in and of itself, affects nutrient acquisition and argues that other nutritional situations may create conditions that favor one bacterial shape over another.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Motility&lt;/strong&gt;: Motility imposes a heavy selective pressure on cell shape. Fast cells are better off as rods with a certain length-to-width ratio, chemotactic cells must adopt shape ratios in line with their environments, and cells that forage near surfaces or navigate viscous environments may do best if they are slightly curved or spiral.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Predation&lt;/strong&gt;: In their struggle against being eaten, bacteria have adopted morphological defenses that may have produced the wealth of shapes we now observe.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;These factors play a role in shaping bacteria. Further he explains what in general gives the shape to bacteria:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bacterial morphology is affected by a combination of selective pressures - access to nutrients, cell division, attachment/dispersal, predation and motility (among others). Among these different factors, our understanding of the relationship between motility and cell shape is most complete; for example, highly motile bacteria are usually rods with a specific (optimal) shape and size, and movement through viscous fluids seems to a favor spiral shape. But since multiple selective forces are always in play, there is at the moment no way to predict cell shape based on the environment or vice versa.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.infection-research.de/fileadmin/user_upload/Perspectives2009/August2009/Perspective-BacterialShapes--12_08_2009.pdf&quot;&gt;Shape Matters: Why bacteria care how they look&lt;/a&gt; - This article highlights Kevin's work explaining why shapes matter for bacteria and they take it seriously for survival.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So adaptations to various environments could be possible but depending upon the environment we can not predict the shape of bacteria because some other factor might have played major role in giving shape to it. But the above mentioned 3 main factors gives some explanation.&lt;/p&gt;&#xA;" OwnerUserId="4547" LastActivityDate="2013-10-10T11:36:05.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10813" PostTypeId="2" ParentId="10802" CreationDate="2013-10-10T16:19:42.737" Score="1" Body="&lt;p&gt;I don't really have an opinion on whether or not this is the main or even &lt;em&gt;a&lt;/em&gt; reason for the evolution of senescence and death, but it is certainly not &lt;em&gt;nonsense&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Death can indeed be good for a species. Diversity is always good and the death of the elders allows phenotypes that have been selected for more recently to take hold in the gene pool. If the young need to compete with the old, this will make it harder for them to grow and reproduce. In situations with a limited food supply, having to support old individuals who can no longer forage/hunt for themselves will be a strain on the species/society/pod or whatever it is we are looking at.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, genotypes that encourage the death of elders who are past the age of reproduction could be selected for. This does not contravene the selfish gene hypothesis at all, these individuals have already reproduced, the selfish gene no longer 'cares' about them. The main idea of the selfish gene hypothesis is that the genes themselves 'want' to be passed on, not that the genes 'want' to save themselves. Once their host has reproduced, they loose interest so to speak. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The selfish gene theory is just a conceptual tool, it should not be taken literally. It does not suggest that genes are actually selfish or in charge of their own evolution in any way. It is just a useful approach to take when studying evolution and was instrumental in our understanding that the gene (the nucleotide actually) and not the individual is the &lt;a href=&quot;https://biology.stackexchange.com/q/10050/1306&quot;&gt;smallest unit of selection&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, in the strictest sense, the statement in your question is absolutely compatible with the selfish gene hypothesis. If you can no longer pass your genes along, you are useless and just a drain on the species, why should you keep living?&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-10-10T16:19:42.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10815" PostTypeId="2" ParentId="10803" CreationDate="2013-10-10T16:26:58.937" Score="1" Body="&lt;p&gt;An artifact in biology usually refers to experimental error or other spurious results. In the context of microbiology, you will get artifacts if, for example,  you sneeze on the plate you are growing a colony on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term is generally used for any result that is not actually true but stems from bad analysis or experimental procedures. Take, for example, this &lt;a href=&quot;http://www.biology-online.org/dictionary/Artifact&quot; rel=&quot;nofollow&quot;&gt;definition&lt;/a&gt; from biology-online.com:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Something artificial, a distortion that does not reflect normal anatomy or pathology, not usually found in the body. For example: in radiology, the appearance on an x-ray of a surgical metal clip that obscures the clear view of an anatomical structure. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-10-10T16:26:58.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10816" PostTypeId="1" AcceptedAnswerId="10817" CreationDate="2013-10-10T17:34:04.143" Score="-5" ViewCount="599" Body="&lt;p&gt;I thought about this statement a while ago:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Natural selection sucks, it says those who love too much (or too many) will die the easiest and fastest. Sad but true.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Only family (biologically of course) should be loved. This isn't rather an ethics question but whether those who love too many or too much die easiest. true?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;NEW QUESTION&lt;/strong&gt;&lt;/em&gt;: What about if you love your subject, mathematics, to death? You'll give up meditating, personality, gym, friends, goldfish, everything just to find out new theorems. What is the take on this? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Surely you'll take a bird's eye view right after the accomplishment (or perhaps failure sometimes) and see what you've accumulated in losses (or in earnings). But Is it in the right path of the true purpose?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given the person is highly into itself, such that it operates on an ideology instead of what the current trends are (in this case, stay healthy^^), it would be great to love. Nothing else would matter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biologically, it wouldn't make sense. &lt;strong&gt;If I loved something like mathematics, how in the world could I produce babies?&lt;/strong&gt; Geniuses like Erdos never had children but, my god take a look at his work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;^^I'm not sure if my claim is correct, which is the matter of this question: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Should we stay healthy or go beyond our health (as the Curie's did) to discover science?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4652" LastEditorUserId="4652" LastEditDate="2013-10-13T00:03:35.683" LastActivityDate="2013-10-13T17:31:36.160" Title="Is love biologically useful?" Tags="&lt;human-biology&gt;&lt;behaviour&gt;&lt;natural-selection&gt;" AnswerCount="2" CommentCount="8" ClosedDate="2015-03-10T03:48:48.040" ContentLicense="CC BY-SA 3.0" />
  <row Id="10817" PostTypeId="2" ParentId="10816" CreationDate="2013-10-10T18:06:59.197" Score="9" Body="&lt;p&gt;The idea that we only love our family according to biology is not true, but its also not clear what people mean by the word 'love'.  There are many ways to interpret that word!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this doesn't totally suck any romantic ideas out of you, but metaphysical concepts of love and romantic ideas of love are not always relevant when you talk about biology.  A case for the universal human family and world peace can be made. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In evolutionary biology love usually has a different meaning than most people mean, but maybe one similar to what you refer to here; Love is often considered to be the bond with one's offspring to help ensure that they succeed and reproduce.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This idea is most often expressed in terms of &quot;kin selection&quot;.  A theory that an individual is helpful to your reproductive success if they carry genes similar to you.  In particular ant colonies may be entirely built around the solidarity of the family unit: all the workers are birthed from the queen and they themselves do not reproduce, but they do work together because, to put it plainly, helping the hive is helping themselves reproduce. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biologist Sarah Hrdy has written an excellent book that looks at the biological origins and variety of ways that &lt;a href=&quot;http://en.wikipedia.org/wiki/Sarah_Blaffer_Hrdy#Mother_Nature&quot;&gt;motherhood creates social and emotional relationships, which is not entirely a human idea of motherhood&lt;/a&gt;, but biological and mind expanding for the evolutionary take.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the idea that only close relatives should be loved is not quite right. Even intuitively we see adults adopting children distinctly unlike them in appearance, people devoting their lives to the general good, etc etc. Biology cannot pretend that this sort of behavior doesn't exist - it can only try to explain it within the framework of what we understand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its well understood that cooperation and social cohesion are also the result of evolutionary forces.  The primary reference for this is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Prisoner%27s_dilemma#The_iterated_prisoners.27_dilemma&quot;&gt;iterated Prisoner's Dilemma&lt;/a&gt; experiment; in systems where individuals are interacting over and over again, helping others creates a system of cooperation where reciprocity where everyone benefits because the payoffs are stability, security, safety etc.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again this might not sound like 'love', but in human social, cooperative situations it can be professed as love. Love of country, profession, causes etc if you will. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a big debate about whether &lt;em&gt;altruism&lt;/em&gt; exists: many biologists believe that an extended from of kin selection is in play - that we're all one sort of human family.  This is essentially an argument that all our energies are self interested on some level - we're just trying to further the interests of the human race because it will help our own offspring do well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it might go further than that - we also care for non human and even ugly very distant forms of life if you look at some people's lives.  One can argue that the realization that caring about the ecosystem is self-interest and not altruistic.  The distance at which this extends kin selection is pretty far, but anyway the argument goes on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Additional Points: Lots of human interests like science, are a sort of love? They don't seem to help reproduction.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a pretty deep point, really.  I'd say it can help to understand question to start with uncles and grandmothers.  Lots of animals do not reproduce, and this is considered okay by kin selection.  Take a look at wolf packs.  The alpha male is the only animal to mate, the other males seem to be hanging out.  First of all the wolves may be closely related, so the avuncular role of taking care of cousins and nephew/nieces is one kin selection argument.  But even if they weren't, there is the fact that pack structure is not biologically altruistic; the other males and females who do not mate may still do so in the future.  In the meantime, the pack cooperation creates a more secure condition where offspring can have a better chance of success.  Lots of creative, cultural, scientific work is similar as far as I can see.  We can adopt non-reproductive pursuits and still feel that we are doing something worthwhile.  I guess the same can be said for adoption, social causes, religion and just about anything else people do which is not having children. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can this be a selective advantage - included by evolution into the human instinct?  I'd cite the &lt;a href=&quot;http://en.wikipedia.org/wiki/Grandmother_hypothesis#The_grandmother_effect&quot;&gt;grandmother effect&lt;/a&gt; here.  There is some evidence to support the idea that women live longer after menopause because it creates more successful grandchildren.  While this is not a direct effect, any mutation that extends the caregiving instinct would be sustained in the gene pool.  Its possible that if such a caregiving instinct of uncles and grandmothers were to extend to other people, even beyond the family, that it would be sustained in the gene pool.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed being smart and or rich usually doesn't increase the &lt;em&gt;number&lt;/em&gt; of children humans have.  In fact the opposite is the case for both &lt;a href=&quot;http://en.wikipedia.org/wiki/Total_fertility_rate#Developed_or_developing_countries&quot;&gt;statistical&lt;/a&gt; and &lt;a href=&quot;http://www.theguardian.com/commentisfree/2013/aug/07/smart-women-not-having-kids&quot;&gt;anecdotal&lt;/a&gt; evidence.  Few would say that this is a bad thing.  Human being are getting a better deal when they spend energy on better quality offspring, not quantity.  You can look at the &lt;a href=&quot;http://en.wikipedia.org/wiki/R/K_selection_theory&quot;&gt;r/K selection theory&lt;/a&gt; for a better understanding of this argument, but some animals have chosen cheap offspring and many of them - think cockroach or guppy.  These animals would rather eat their offspring than try to feed it.  Humans, more than nearly any other animal i believe, spend their lives caring for helpless offspring until they are ready for life.  Modern life has only extended this from a few years to nearly 20 years.  But it certainly works - the only animal that can compete with human beings is other human beings. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that makes sense.  There's some speculating here, but its hard to dispute that people devote their time and energy to all sorts of things besides mating.  In the end biology has to accommodate such behavior.  Biological theories we call laws don't change the behavior of living things;  its always the other way around. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-10-13T17:31:36.160" LastActivityDate="2013-10-13T17:31:36.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10818" PostTypeId="2" ParentId="7074" CreationDate="2013-10-10T23:29:38.347" Score="11" Body="&lt;p&gt;This is a common phenomena which most of us come across. Seeing flashes of light, stars and other shapes in the eyes occur when the body goes through stressful activities. For example while you are climbing the blood flow will be more to other prominent parts like hands and lower waist so brain and eyes will get less supply of blood as well as nutrients. Hence those flashes or stars are visible to us. This phenomena is called &amp;quot;Phosphene&amp;quot; and a phosphene is a phenomenon characterized by the experience of seeing light without light actually entering the eye.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphene&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia/Phosphene&lt;/a&gt; gives an explanation for occurrence of Phosphenes:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Phosphene is &amp;quot;seeing stars&amp;quot;, from a sneeze, laughter, a heavy and deep cough, blowing of the nose, a blow on the head or low blood pressure (such as on standing up too quickly or prior to fainting). It is possible these involve some mechanical stimulation of the retina, but they may also involve mechanical and metabolic (such as from low oxygenation or lack of glucose) stimulation of neurons of the visual cortex or of other parts of the visual system.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/yD2EH.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So seeing flashes of light can be due to:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Blood shifting.&lt;/li&gt;&#xA;&lt;li&gt;Low blood sugar(causes weakness).&lt;/li&gt;&#xA;&lt;li&gt;Head trauma.&lt;/li&gt;&#xA;&lt;li&gt;Headache.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;So to summarize this thing, we should have enough nutrients, water supply to the body whenever we come across stressful activities. Phosphenes are temporary stuff which do not harm eyes.&lt;/p&gt;&#xA;" OwnerUserId="4547" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-10T23:29:38.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10819" PostTypeId="1" AcceptedAnswerId="10825" CreationDate="2013-10-11T01:48:33.430" Score="2" ViewCount="164" Body="&lt;p&gt;If the reason &lt;em&gt;Why Men Don't Listen and Women Can't Read Maps&lt;/em&gt; is genetic, then one of the genes in the Y chromosome is to blame and in theory could be identified.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Correct or incorrect?&lt;/p&gt;&#xA;" OwnerUserId="4654" LastEditorUserId="1306" LastEditDate="2013-10-11T05:06:40.593" LastActivityDate="2013-12-13T22:13:53.367" Title="Would it be correct to state that any biological difference between the sexes has to be found in the Y chromosome?" Tags="&lt;dna&gt;&lt;human-genetics&gt;" AnswerCount="2" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="10820" PostTypeId="2" ParentId="10487" CreationDate="2013-10-11T10:44:11.317" Score="2" Body="&lt;p&gt;One thing is that we can't control the Goosebumps. It is an involuntary function caused by the Sympathetic Nervous System which is the major part of the Automatic Nervous System. The major function of the SNS is fight to flight response along with maintaining homeostasis in which case it internally will be alert maintaining body status from the background. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before sending any response to target tissue when there is input to SNS it has to secrete neurotransmitters but before this to the sympatho-adrenal response of the body, as the preganglionic sympathetic fibers that end in the adrenal medulla (but also all other sympathetic fibers) secrete acetylcholine, which activates the great secretion of adrenaline (epinephrine) and to a lesser extent noradrenaline (norepinephrine) from it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So whenever SNS senses (message flow is bidirectional) any stress it responds it in following action mentioned:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At the synapses within the ganglia, preganglionic neurons release acetylcholine, a neurotransmitter that activates nicotinic acetylcholine receptors on postganglionic neurons. In response to this stimulus postganglionic neurons - with two important exceptions - release norepinephrine, which activates adrenergic receptors on the peripheral target tissues. The activation of target tissue receptors causes the effects associated with the sympathetic system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Once the receptors receive the information then the response flows to the target tissue via neurons with the help of the neurotransmitters. To explain goosebumps technically:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Properly known as piloerection, horripliation or pilomotor reflex, the bumps we get are stimulated by fear and cold and they are essentially just a temporary change in the skin. These stimulants cause a nerve discharge from the sympathetic nervous system (which is an involuntary portion of nerves we have) and the nerve discharges create muscle contractions called arrrectores pilorum that raise the hair follicles in our skin. It is the elevation of the hair that causes the Goosebumps.  The name Goosebumps actually comes from the fact that plucked goose feathers resemble the human hair follicles.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DMAu2.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Goosebumps also occur when we listen to surprise songs, sad songs or some other kind of thrilling music. Researchers have tried to explain it and they call it &quot;Frisson&quot;.&#xA;Check out this small video which talks about it. It is nice:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=-EA2eWZuYDs&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.youtube.com/watch?v=-EA2eWZuYDs&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also refer to this website: &lt;a href=&quot;http://www.personal.psu.edu/afr3/blogs/SIOW/2011/10/what-are-goosebumps.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Goosebumps&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4547" LastActivityDate="2013-10-11T10:44:11.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10821" PostTypeId="1" CreationDate="2013-10-11T11:14:49.063" Score="4" ViewCount="389" Body="&lt;p&gt;There are 'acidic' and 'basic' amino acids like aspartate and histidine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When protein is synthesized with those amino acids, what ensures that the to-be-assembled amino acids will not bond to the amine groups or acidic groups in the functional groups of the amino acids in the polypeptide?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2013-10-11T15:36:58.640" Title="Why don't amino acids get linked in the functional groups of acidic and basic amino acids?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;amino-acids&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10822" PostTypeId="1" CreationDate="2013-10-11T12:28:44.973" Score="5" ViewCount="940" Body="&lt;p&gt;Does the body lose or gain energy when drinking or eating hot things compared to more neutral temperature things?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the one hand, &#xA;The body could somehow convert the heat energy into human usable energy,&#xA;And on the other hand, &#xA;The body heats up and needs to be cooled down, and this way it loses energy.&lt;/p&gt;&#xA;" OwnerUserId="4656" LastEditorUserId="3340" LastEditDate="2015-06-04T11:47:52.993" LastActivityDate="2015-06-04T11:47:52.993" Title="Does the body lose energy or gain energy relatively when drinking or eating hot things?" Tags="&lt;food&gt;&lt;bioenergetics&gt;&lt;temperature&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10823" PostTypeId="2" ParentId="10821" CreationDate="2013-10-11T12:30:38.790" Score="5" Body="&lt;p&gt;When the amino acid comes to the ribosome it is in the form of an aminoacyl tRNA in which the carboxyl group of the amino acid is esterified with the 3' OH group of the ribose moiety at the 3' end of the tRNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is already a growing peptide bound in the P site of the ribosome with a free -COOH group which will react with the -NH&lt;sub&gt;2&lt;/sub&gt; group of the incoming amino acid in the A site to form the next peptide bond. This reaction takes place in the context of what is essentially an enzymic active site. The reactants will be held in the correct positions for catalysis to take place (in this case the catalysis is carried out by the ribozyme activity of the small ribosomal RNA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the answer is that the selectivity of this reaction is just another example of the way in which enzymes are able to carry out highly-specific reactions. So, for example, the enzyme hexokinase, which phosphorylates glucose at the 6 position has, potentially, four other -OH groups that, chemically speaking, could be phosphorylated.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-10-11T12:30:38.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10824" PostTypeId="2" ParentId="10822" CreationDate="2013-10-11T13:24:24.657" Score="4" Body="&lt;p&gt;Gains heat; humans are not particularly well-adapted to make use of heat as an energy source.  In a simple matter, if something you eat is hot when it goes in then the average temperature of the body has increased.  More relevantly (and to get this more on-topic for biology), &lt;a href=&quot;http://www.fitday.com/fitness-articles/nutrition/healthy-eating/how-is-body-temperature-affected-by-eating.html&quot; rel=&quot;nofollow&quot;&gt;eating &lt;em&gt;anything&lt;/em&gt;&lt;/a&gt; will generally increase your body temperature, as in order to digest the food your rate of metabolism will rise.  Metabolism produces a lot of heat, and that's what you feel after eating, especially a big meal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something like cold water, however, that doesn't require a whole lot of metabolism, will cool you down.  In fact, even &lt;a href=&quot;http://blogs.smithsonianmag.com/science/2012/07/a-hot-drink-on-a-hot-day-can-cool-you-down/&quot; rel=&quot;nofollow&quot;&gt;drinking hot water might cool you down&lt;/a&gt;.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22574769&quot; rel=&quot;nofollow&quot;&gt;The paper&lt;/a&gt; cited there claims that drinking a hot drink on a hot day will disproportionally increase your sweat response such that you actually cool down.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-11T13:24:24.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10825" PostTypeId="2" ParentId="10819" CreationDate="2013-10-11T13:57:47.047" Score="11" Body="&lt;p&gt;&quot;&lt;em&gt;Blame&lt;/em&gt;&quot; is a strong word.  The human Y chromosome has &lt;a href=&quot;http://uswest.ensembl.org/Homo_sapiens/Location/Chromosome?chr=Y;r=Y:1-59373566&quot;&gt;only a few dozen protein-coding genes&lt;/a&gt;.  One of the most important, for males anyway, is &lt;a href=&quot;https://en.wikipedia.org/wiki/SRY&quot;&gt;SRY&lt;/a&gt;, the sex-determining region.  This is a transcription factor that is responsible for modulating the expression of other genes; those genes need not be on the Y chromosome.  SOX9 for example is itself a transcription factor, is upregulated by SRY, and is found on chromosome 11.  &lt;em&gt;Most&lt;/em&gt; of the genes associated with maleness are found elsewhere.  Moreover, once the testes form, they can be potent secretors of hormones that cause a number of physical changes.  So is SRY to blame, or SOX9, or the testes?  It depends on how direct you want your genes to be.  If you're blaming SRY you're not wrong, but at that point you might as well blame fate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oh, and there are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19828794&quot;&gt;epigenetic differences between the sexes&lt;/a&gt;.  You could also make some arguments about the &lt;a href=&quot;https://en.wikipedia.org/wiki/XIST_%28gene%29&quot;&gt;Xist gene&lt;/a&gt; responsible for X-inactivation in females.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-11T14:03:42.707" LastActivityDate="2013-10-11T14:03:42.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10826" PostTypeId="2" ParentId="10816" CreationDate="2013-10-11T14:30:38.317" Score="2" Body="&lt;p&gt;Shigeta brings up the question of altruism which Richard Dawkins famously explains in the context of evolution in The Selfish Gene. This is probably the easiest way to translate feelings of love into biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EO Wilson has also addressed the idea of kinship and  altruism, providing arguments on both sides of the issue at this point. He was an early champion of kinship as a basis for altruism, but has more recently suggested that it requires too much mathematics for the individual to decipher without any real data (I mean you would need a lot of data and some time to figure out whether to save your cousin or your niece and have to make assumptions about your own risk). I think Dawkins ideas make a lot of sense even if they do assume some unconscious math, after all, we can catch baseballs - something that requires a lot of math to solve on paper, but we do it in an instant in our head.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It may be helpful to consider the tribal nature of humans throughout much of our evolution. Who needs math when the real question is merely,'Is this person a member of my tribe or not?'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we need to consider romantic love, consider couching it in similar language. 'Can I form a strong bond with this person so that we can successfully raise children?' &lt;/p&gt;&#xA;" OwnerUserId="4139" LastActivityDate="2013-10-11T14:30:38.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10827" PostTypeId="2" ParentId="10821" CreationDate="2013-10-11T15:36:58.640" Score="1" Body="&lt;p&gt;I think it does happen that peptide linkages can happen to side chains.  For the reasons that @AlanBoyd lays out, this won't happen in conventional peptide synthesis and is in principle the answer to the question here.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To add a note though: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Nonribosomal_peptide&quot; rel=&quot;nofollow noreferrer&quot;&gt;Non ribosomal peptide synthases&lt;/a&gt; can produce peptides with many subsequent unorthodox modifications.   If you look at the structure of &lt;a href=&quot;http://en.wikipedia.org/wiki/Bacitracin&quot; rel=&quot;nofollow noreferrer&quot;&gt;bacitracin&lt;/a&gt;, I believe the large ring is closed by condensation between a lysine amine and the carboxylate of the amino acid on the other end of the ring.   There should be plenty of other examples. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8MD0Z.png&quot; alt=&quot;bacitracin&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So called secondary metabolism pathways create many diverse compounds - nearly anything seems to be possible. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-10-11T15:36:58.640" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10828" PostTypeId="2" ParentId="9481" CreationDate="2013-10-11T16:52:02.657" Score="2" Body="&lt;p&gt;UV rays cause damage is by thinning the walls of surface blood vessels, leading to bruising, bleeding, and the appearance of blood vessels through the skin. Longwave UV radiation (UV-A) accounts for up to 95% of the UV radiation that reaches the earth's surface. Although UV-A is less intense than UV-B, it is more prevalent and can penetrate deeper into the skin layers, affecting the connective tissue and blood vessels, which results in premature aging - &lt;a href=&quot;http://en.wikipedia.org/wiki/Photoaging&quot; rel=&quot;nofollow noreferrer&quot;&gt;Photoaging&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the same time UVB – is even more dangerous than UVA radiation and also causes skin damage and skin cancer. It affects the surface skin layer. The skin responds by releasing chemicals that dilate blood vessels. This causes fluid leakage and inflammation – better known as sunburn.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not quite sure what chemicals are generated by UV radiations beneath the skin surface. I guess it might be excess &lt;strong&gt;free radicals&lt;/strong&gt; which accumulate and cause damage to blood vessels since they are delicate. There is one theory which talks about damages to skin due to &lt;a href=&quot;http://en.wikipedia.org/wiki/Free-radical_theory_of_aging#cite_note-ReferenceC-10&quot; rel=&quot;nofollow noreferrer&quot;&gt;Free Radical theory of aging&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To give an example how UV radiation affects the blood vessel here:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In actinic purpura, UV radiation damages the structural collagen that supports the walls of the skin's tiny blood vessels. Particularly in older people, this collagen damage makes blood vessels more fragile and more likely to rupture following a slight impact.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Below figure to give an idea of how strong UV radiations are:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/3ZpYN.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4547" LastActivityDate="2013-10-11T16:52:02.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10829" PostTypeId="1" AcceptedAnswerId="10833" CreationDate="2013-10-12T07:56:49.233" Score="9" ViewCount="89788" Body="&lt;p&gt;Everytime I see a ladybug I ask myself this question.&#xA;Why does every ladybug have a different amount of points on its back? Is it because of its age? Or because of its genes? Is it inheritable?&lt;/p&gt;&#xA;" OwnerUserId="4660" LastEditorUserId="3776" LastEditDate="2013-10-12T14:29:47.153" LastActivityDate="2019-04-23T14:43:12.323" Title="Why do ladybugs have a different number of points on their backs" Tags="&lt;genetics&gt;&lt;entomology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10830" PostTypeId="1" AcceptedAnswerId="10835" CreationDate="2013-10-12T14:17:48.173" Score="1" ViewCount="757" Body="&lt;p&gt;I can deactivate $\alpha$-amylase in ways such as extreme temperature controls, pH controls of the solution it stays in, or adding salt to the solution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, are there any other unique or elaborate ways to deactivate the enzyme? (maybe the lock-and-key hypothesis also works for enzymes &lt;strong&gt;&lt;em&gt;AND&lt;/em&gt;&lt;/strong&gt; enzymes?)&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2013-10-12T18:12:01.400" Title="Creative ways to deactivate alpha-amylase taken from fungi" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10832" PostTypeId="2" ParentId="10829" CreationDate="2013-10-12T14:44:00.017" Score="2" Body="&lt;p&gt;It is because of genes, and is completely inheritable!   First I want point out that there spots, or points, do not change over time.  Rather the spot number and location is fixed when Coccinellidae are pupa (tween aged insects).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will notice I said Coccinellidae instead of ladybug.  That is because &quot;ladybugs&quot; are actually several different species of insect.  Thus we refer to the whole family of ladybugs, Coccinellidae.  The spot number, shape, and color is different for different species, which gives you the variation in the number of points. &lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2013-10-12T14:44:00.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10833" PostTypeId="2" ParentId="10829" CreationDate="2013-10-12T15:05:38.467" Score="11" Body="&lt;p&gt;The spots on the back of Ladybugs over the surface is defense mechanism to avoid predators. The spots come in different shapes and different numbers. Some say that those dots tell us their age. Since some ladybugs have 24 spots which means its age would be 24 years and that is not at all possible. So this is a popular misconception running around us.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the real truth about the number of spots on the ladybugs' back is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The number of spots on a ladybug does have significance. The spots and other markings do help you identify the species of ladybug. Some species have no spots at all. The record-holder for most spots is the 24-spot ladybug ( Subcoccinella 24-punctata), which has 24 spots, of course. Ladybugs aren't always red with black spots, either. The twice-stabbed ladybug ( Chilocorus stigma) is black with two red spots.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So now we know that the number of spots on the back of Ladybugs will help us to identify what species it belongs to. To give an insight into different species of them you can refer to this &lt;a href=&quot;http://www.nhm.org/site/activities-programs/citizen-science/lost-ladybug-project/identifying-ladybugs&quot; rel=&quot;noreferrer&quot;&gt;Identifying Ladybugs&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Zdrv4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above image shows &lt;strong&gt;different species of Ladybugs&lt;/strong&gt; where you can see the varying number of spots in each bugs' back. More information can be found here &lt;a href=&quot;http://www.ladybuglady.com/stripes.htm&quot; rel=&quot;noreferrer&quot;&gt;Stripes on Ladybugs&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4547" LastActivityDate="2013-10-12T15:05:38.467" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10835" PostTypeId="2" ParentId="10830" CreationDate="2013-10-12T18:12:01.400" Score="2" Body="&lt;p&gt;Amylase inhibitors have attracted much attention because of their potential in treating type 2 diabetes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can inactivate most enzymes by using a specific inhibitor. One class of inhibitors consists of molecules that resemble the substrate molecules but are not acted upon in the same way. These will bind to the active site and will prevent the substrate from binding. An inhibitor of many amylases is &lt;a href=&quot;http://en.wikipedia.org/wiki/Acarbose&quot; rel=&quot;nofollow&quot;&gt;acarbose&lt;/a&gt;. This is a competitive inhibitor which means that inhibition is overcome by high concentrations of substrate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if that isn't enough to get you started &lt;a href=&quot;http://digitool.library.mcgill.ca/webclient/StreamGate?folder_id=0&amp;amp;dvs=1381600893612~578&quot; rel=&quot;nofollow&quot;&gt;here is an entire thesis on the topic of amylase inhibitors&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to permanently block activity the ideal compound would be one which binds to and covalently modifies the active site, destroying enzyme activity. This would be an irreversible inhibitor. I haven't been able to find a reference to such a compound however.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-10-12T18:12:01.400" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10836" PostTypeId="1" AcceptedAnswerId="30815" CreationDate="2013-10-12T19:46:27.180" Score="7" ViewCount="758" Body="&lt;p&gt;Cytoplasmic determinants are spread unevenly in the egg, and so when embryo starts forming (cells start dividing), the determinants are also unequally divided between cell. This unequal distribution later plays a major role in differentiation and gene regulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Protostomes undergo determinate cleavage. Their cells' fates are determined very early in development, whereas deuterostomes undergo indeterminate cleavage. So, if you take away a cell at early stage of development, it can be replaced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now if we compare the division of cytoplasmic determinants in protostomes and deuterostomes, what I said in the first paragraph seems true (to some extent) for only protostomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Do deuterostome oocytes have even distribution of cytoplasmic determinants initially and  divide unequally only after certain number of divisions?&lt;/li&gt;&#xA;&lt;li&gt;Are there any studies showing correlation between the stage at which determination happens in deuterostome and beginning of unequal division of determinants?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3340" LastEditDate="2015-03-25T09:42:39.030" LastActivityDate="2015-03-26T22:04:25.860" Title="Cytoplasmic determinants - protostomes and deuterostomes" Tags="&lt;reproduction&gt;&lt;gene-expression&gt;&lt;development&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10838" PostTypeId="2" ParentId="10796" CreationDate="2013-10-13T01:12:04.453" Score="0" Body="&lt;p&gt;Yes and no.  Yes their DNA, like every living thing’s DNA, is made of the same building blocks of A’s, T’s, G’s, and C’s.  But their DNA isn’t exactly alike.   All those A’s, T’s, G’s, and C’s are put together in different orders for dogs and people. You have to understand that 4% with chimps is a difference of actually 35 million single nucleotide differences and ∼90 Mb of insertions and deletions. With a dog only 25% matches up perfectly with a human. I think what he was saying was that all living matter has a common ancestor. From fruit fly to human being according to macro evolution we all came from the same ancestor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://genetics.thetech.org/ask-a-geneticist/dog-vs-human-dna&quot; rel=&quot;nofollow&quot;&gt;http://genetics.thetech.org/ask-a-geneticist/dog-vs-human-dna&lt;/a&gt;&#xA;&lt;a href=&quot;http://genome.cshlp.org/content/15/12/1746.long&quot; rel=&quot;nofollow&quot;&gt;http://genome.cshlp.org/content/15/12/1746.long&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4663" LastActivityDate="2013-10-13T01:12:04.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10839" PostTypeId="2" ParentId="10656" CreationDate="2013-10-13T01:26:45.667" Score="-4" Body="&lt;p&gt;There are six different types of evolution and they all happen on different levels.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Cosmic evolution- the origin of time, space and matter. Big Bang &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Chemical evolution- the origin of higher elements from hydrogen. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Stellar and planetary evolution- Origin of stars and planets. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Organic evolution- Origin of life from inanimate matter. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Macro-evolution- Origin of major kinds. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Micro-evolution- Variations within kinds. Only this one has been observed. For instance poodles and great danes are descendant from the same thing. A wolf. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Are you asking about macro evolution or micro evolution? Or one of the other 4?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Speciation does not show macro evolution in any way, shape, or form. And the ring species you refer to moths changing colors, that is micro evolution. A moth changing into another moth would even be micro evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Man thought up species and defined them. If it looks like a duck and quacks like a duck, it didn't evolve into a different animal because it changed the color of it's feathers.&lt;/p&gt;&#xA;" OwnerUserId="4663" LastActivityDate="2013-10-13T01:26:45.667" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10840" PostTypeId="1" CreationDate="2013-10-13T02:00:21.443" Score="2" ViewCount="151" Body="&lt;p&gt;My school is very fortunate to have a DNA sequencer, and I want to find an opportunity to learn how to use it. I'm currently taking AP Biology this year, and I hope to do an independent study in biology next year, concerning DNA. I'm sure there's plenty I can do with the sequencer, but do you have any cool project ideas?&lt;/p&gt;&#xA;" OwnerUserId="4664" LastActivityDate="2013-10-13T02:00:21.443" Title="What to do with a DNA sequencer?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;&lt;dna-sequencing&gt;" AnswerCount="0" CommentCount="8" ClosedDate="2013-10-13T10:31:52.400" ContentLicense="CC BY-SA 3.0" />
  <row Id="10841" PostTypeId="1" AcceptedAnswerId="13762" CreationDate="2013-10-13T12:13:18.470" Score="4" ViewCount="1517" Body="&lt;p&gt;This article about &lt;a href=&quot;http://news.ufl.edu/2013/10/08/alzheimers-test/&quot; rel=&quot;nofollow&quot;&gt;testing for Alzheimer's&lt;/a&gt;, via changes in the ability to smell, said:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;She thought of peanut butter because, she said, it is a “pure odorant”&#xA;  that is only detected by the olfactory nerve and is easy to access.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm not clear on what that means. Assuming a person had their mouth closed, then wouldn't &lt;em&gt;any&lt;/em&gt; odor be detected only by the olfactory nerve? Wouldn't a lemon, say, work exactly the same?&lt;/p&gt;&#xA;" OwnerUserId="704" LastEditorUserId="16866" LastEditDate="2020-04-16T04:59:05.360" LastActivityDate="2020-04-16T04:59:05.360" Title="What is a &quot;pure odorant&quot;?" Tags="&lt;terminology&gt;&lt;olfaction&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10842" PostTypeId="1" AcceptedAnswerId="14616" CreationDate="2013-10-13T12:40:03.337" Score="5" ViewCount="63" Body="&lt;p&gt;I know that turtle brains, particularly those of individual species that hibernate and burrow are particularly resilient to hypoxia and any tissue damage secondary to a hypoxic event.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the known molecular mechanisms behind this resiliency?  Does it have to do with the ability of their blood to store/release oxygen over extended periods, or is it molecular factors in the neural tissue that protect it from insult?  &lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2014-01-25T07:59:50.570" Title="What are the molecular mechanisms that make the turtle brain more resistant to hypoxia?" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10843" PostTypeId="1" AcceptedAnswerId="10876" CreationDate="2013-10-13T14:18:56.767" Score="11" ViewCount="21548" Body="&lt;p&gt;I'm designing a set of primers and reading about the principles of primer design one of which is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;GC Clamp: The presence of G or C bases within the last five bases from&#xA;  the 3' end of primers (GC clamp) helps promote specific binding at the&#xA;  3' end due to the stronger bonding of G and C bases. More than 3 G's&#xA;  or C's should be avoided in the last 5 bases at the 3' end of the&#xA;  primer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is how essential is it to have a GC clamp?&lt;/p&gt;&#xA;" OwnerUserId="1763" LastActivityDate="2019-01-23T17:32:14.333" Title="When designing primers how important is the GC clamp?" Tags="&lt;pcr&gt;&lt;primer&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10844" PostTypeId="2" ParentId="10841" CreationDate="2013-10-13T14:57:42.597" Score="3" Body="&lt;p&gt;I could not find a concrete definition after searching several sources, but after reading a few papers I think the term &lt;strong&gt;Pure Odorant&lt;/strong&gt; refers to its Olfactory Bulb profile. Peanut Butter will stimulate specific Olfactory nerves, and &lt;em&gt;only&lt;/em&gt; that set of nerves, whereas &lt;em&gt;impure&lt;/em&gt; Odorants may stimulate part of the profile and also other parts of the Bulb depending upon the impurity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, Peanut Butter has a unique smell that you can't replicate, and thus cannot mistake in either flavor or scent when compared to similar compounds. You may  not even be able to tell it was Peanut Butter at all if not for the scent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A Lemon would not work the same way, as the major Odorant in a Lemon is &lt;a href=&quot;http://en.wikipedia.org/wiki/Limonene&quot; rel=&quot;nofollow&quot;&gt;Limonene&lt;/a&gt; - which is present in all citrus fruits. You would activate the same neuronal pathways for Lemons that you would with Oranges, Limes, and Grapefruits. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's my best assessment.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-10-13T14:57:42.597" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10845" PostTypeId="1" AcceptedAnswerId="10852" CreationDate="2013-10-13T15:16:51.650" Score="4" ViewCount="204" Body="&lt;p&gt;I have often heard that right and left ovaries alternate in releasing ovum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it always true? What controls this rhythm? Is it simply because the other ovary is unresponsive to LH or FSH? If so, why?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-13T15:53:47.640" LastActivityDate="2013-10-13T16:20:04.720" Title="Alternating Ovulation" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;reproduction&gt;&lt;ovulation&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10846" PostTypeId="1" AcceptedAnswerId="10847" CreationDate="2013-10-13T15:19:29.527" Score="8" ViewCount="16436" Body="&lt;p&gt;Do red blood cells have no MHC? (I have often heard that they do not.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so why are they not destroyed by immune cells?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="28778" LastEditDate="2017-05-11T21:41:15.567" LastActivityDate="2017-07-06T14:55:37.723" Title="Presence of MHC on red blood cells" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;hematology&gt;&lt;red-blood-cell&gt;&lt;mhc&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10847" PostTypeId="2" ParentId="10846" CreationDate="2013-10-13T15:45:06.590" Score="10" Body="&lt;p&gt;They &lt;a href=&quot;http://pathmicro.med.sc.edu/bowers/mhc.htm&quot;&gt;do not&lt;/a&gt;, at least not normally or noticeably.  MHC I occurs on all nucleated cells, and red blood cells do not have nuclei.  If they did indeed have MHC on them, blood transfusions would be as successful and as tricky as organ donation.  There are &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/9781118493595.ch32/pdf&quot;&gt;reports&lt;/a&gt; of MHC detection on red blood cells, but the amount is orders of magnitude smaller than elsewhere, only present for certain MHC alleles, and often transient.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-14T00:53:29.720" LastActivityDate="2013-10-14T00:53:29.720" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="10848" PostTypeId="5" CreationDate="2013-10-13T15:47:28.743" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-10-13T15:47:28.743" LastActivityDate="2013-10-13T15:47:28.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10849" PostTypeId="4" CreationDate="2013-10-13T15:47:28.743" Score="0" Body="The major histocompatibility complex is an extremely diverse genome region in vertebrates that is responsible for antigen presentation.  There are two main classes, MHC I and MHC II." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-13T16:03:03.893" LastActivityDate="2013-10-13T16:03:03.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10850" PostTypeId="5" CreationDate="2013-10-13T15:56:52.670" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-10-13T15:56:52.670" LastActivityDate="2013-10-13T15:56:52.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10851" PostTypeId="4" CreationDate="2013-10-13T15:56:52.670" Score="0" Body="Occurring halfway through the menstrual cycle, ovulation is the release of an egg." OwnerUserId="4101" LastEditorUserId="3632" LastEditDate="2013-10-13T17:14:08.607" LastActivityDate="2013-10-13T17:14:08.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10852" PostTypeId="2" ParentId="10845" CreationDate="2013-10-13T16:20:04.720" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://humrep.oxfordjournals.org/content/15/4/752.full&quot; rel=&quot;nofollow&quot;&gt;Nope, not true&lt;/a&gt;.  It's a pretty common myth; that paper cites a  reference from 1932 in primates claiming to show that the ovaries alternate.  A few papers before this, in particular &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1988887?dopt=Abstract&quot; rel=&quot;nofollow&quot;&gt;this one from 1991&lt;/a&gt; showed that ovulation was &lt;em&gt;not&lt;/em&gt; alternating, but this was the first to do so in actually fertile woman.  In particular,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Alternate ovulation occurred in 61 of the 119 succeeding ovulations (51.3%, not significant) which means that there was no consistent tendency to alternation. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Alternation only occurred half the time.  Neither did they find a difference between side preference; right-side ovulation occurred in just over 50% of the cases, not significantly different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;FSH, follicle-stimulating hormone, and LH, luteinizing hormone, stimulate each ovary equally, but one ovary will get slightly ahead.  Ovulation (and indeed pregnancy at times) is a positive-feedback loop, meaning the response will be exponential; if one ovary is even just slightly ahead it will rapidly dominate the other.  The less-developed one quickly senses the other is ahead of the game and ceases to respond.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-13T16:20:04.720" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10853" PostTypeId="1" AcceptedAnswerId="10855" CreationDate="2013-10-13T20:05:40.060" Score="6" ViewCount="415" Body="&lt;p&gt;Are there estimates of the minimum number of genes required to sustain life? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In what I mean by life here, I don't include viruses.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-14T18:39:18.333" LastActivityDate="2013-10-14T18:39:18.333" Title="Number of genes required to sustain life" Tags="&lt;cell-biology&gt;&lt;genetics&gt;&lt;life&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10854" PostTypeId="1" AcceptedAnswerId="10856" CreationDate="2013-10-13T23:50:23.353" Score="13" ViewCount="74591" Body="&lt;p&gt;I wanted to understand what is the difference between systolic and diastolic readings of blood pressure. I understand 120-80 to about 100-60 is considered normal but does the difference in the two values in the reading hold any significance?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read some text &lt;a href=&quot;http://en.wikipedia.org/wiki/Systolic_blood_pressure&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Diastolic_blood_pressure&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4519" LastActivityDate="2016-07-03T21:07:09.527" Title="Blood Pressure: Significance of difference between systolic and diastolic" Tags="&lt;blood-pressure&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10855" PostTypeId="2" ParentId="10853" CreationDate="2013-10-14T02:09:17.503" Score="9" Body="&lt;p&gt;Depends on what kind of life you want!  &lt;a href=&quot;http://www.essentialgene.org/&quot;&gt;The Database of Essential Genes&lt;/a&gt; lists genes essential for life for a number of species, although I would be wary of some of the numbers; bacterial results are probably more reliable but it lists 118 for humans and 2114 for mice.  There are a bunch of different numbers for different &lt;em&gt;E. coli&lt;/em&gt; strains, with larger numbers being published earlier, go figure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It of course varies by species.  In mid-August of this year, scientists reported the smallest genome yet: 112kb with only 137 protein-coding genes (predicted).  Crazy!  That doesn't mean it's the smallest number of genes though, just what we've found.  Some &lt;a href=&quot;http://www.nature.com/msb/journal/v2/n1/full/msb4100090.html&quot;&gt;folks in 2006 predicted&lt;/a&gt; the smallest would be 113kb and 151 genes - pretty close close to the above, all in all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For something a little more familiar and studied, though, Craig Venter has made synthetic biology his goal.  Part of trying to create life is knowing what the bare minimum is.  Working with &lt;em&gt;Mycoplasma genitalium&lt;/em&gt;, he and his crew &lt;a href=&quot;http://www.theguardian.com/science/2007/jun/08/genetics.research&quot;&gt;knocked out each gene&lt;/a&gt; and found that 381 were indeed essential.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="1306" LastEditDate="2013-10-14T02:13:42.920" LastActivityDate="2013-10-14T02:13:42.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10856" PostTypeId="2" ParentId="10854" CreationDate="2013-10-14T02:17:12.480" Score="16" Body="&lt;p&gt;The difference between systolic (the upper number) and diastolic (the lower number) pressures is known as the &lt;a href=&quot;https://en.wikipedia.org/wiki/Pulse_pressure&quot;&gt;pulse pressure&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Systemic pulse pressure = P&lt;sub&gt;systolic&lt;/sub&gt; - P&lt;sub&gt;diastolic&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For a typical blood pressure reading of 120/80 mmHg the pulse pressure is therefore 40 mmHg.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is proportional to &lt;a href=&quot;https://en.wikipedia.org/wiki/Stroke_volume&quot;&gt;stroke volume&lt;/a&gt;, the amount of blood pumped from the heart in one beat, and inversely proportional to the compliance or flexibility of the blood vessels, mainly the &lt;a href=&quot;https://en.wikipedia.org/wiki/Aorta&quot;&gt;aorta&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A low (also called narrow) pulse pressure means that not much blood is being expelled from the heart, and can be caused by a number of factors, including severe blood loss due to trauma, &lt;a href=&quot;https://en.wikipedia.org/wiki/Congestive_Heart_Failure&quot;&gt;congestive heart failure&lt;/a&gt;, shock, a narrowing of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Aortic_valve&quot;&gt;valve&lt;/a&gt; leading from the heart to the aorta (&lt;a href=&quot;https://en.wikipedia.org/wiki/Aortic_valve_stenosis&quot;&gt;stenosis&lt;/a&gt;), and fluid accumulating around the heart (&lt;a href=&quot;https://en.wikipedia.org/wiki/Cardiac_tamponade&quot;&gt;tamponade&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;High (or wide) pulse pressures occur during exercise, as stroke volume increases and the &lt;a href=&quot;https://en.wikipedia.org/wiki/Total_peripheral_resistance&quot;&gt;overall resistance&lt;/a&gt; to blood flow decreases. It can also occur for many reasons, such as &lt;a href=&quot;https://en.wikipedia.org/wiki/arteriosclerosis&quot;&gt;hardening of the arteries&lt;/a&gt; (which can have numerous causes), various deficiencies in the aorta (mainly) or other arteries, including &lt;a href=&quot;https://en.wikipedia.org/wiki/Aortic_regurgitation&quot;&gt;leaks&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Arteriovenous_fistula&quot;&gt;fistulas&lt;/a&gt;, and a usually-congenital condition known as &lt;a href=&quot;https://en.wikipedia.org/wiki/Arteriovenous_malformation&quot;&gt;AVM&lt;/a&gt;, pain/anxiety, fever, anemia, pregnancy, and more. Certain medications for high blood pressure can widen pulse pressure, while others narrow it. A chronic increase in pulse pressure is a risk factor for heart disease, and can lead to the type of arrhythmia called &lt;a href=&quot;https://en.wikipedia.org/wiki/Atrial_fibrillation&quot;&gt;atrial fibrillation&lt;/a&gt; or A-Fib. &lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2013-11-30T16:02:33.543" LastActivityDate="2013-11-30T16:02:33.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10861" PostTypeId="1" CreationDate="2013-10-14T15:33:00.847" Score="8" ViewCount="1559" Body="&lt;p&gt;I admit I'm not very learned on the subject of evolution, I just started researching it for myself about a week ago. One of the things that I don't understand is why humans and almost every other animal/bug/fish etc. on earth has a symmetrical body. What advantage does this have for the survival of the fittest? It must be quite important, since it re-occurs so frequently and early in the evolutionary family tree.     &lt;/p&gt;&#xA;" OwnerUserId="4671" LastEditorUserId="1306" LastEditDate="2013-10-14T15:59:08.033" LastActivityDate="2013-10-19T21:10:24.310" Title="Why are humans and almost every species on earth symmetrical?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10862" PostTypeId="1" AcceptedAnswerId="10864" CreationDate="2013-10-14T19:20:12.340" Score="2" ViewCount="276" Body="&lt;p&gt;Can IgG antibodies be produced in the secondary immune response without the help of T cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the affinity of antibody for antigens higher during secondary immune response?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-14T20:24:18.400" LastActivityDate="2013-10-14T20:24:18.400" Title="Antibody production in secondary immune response" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;immunology&gt;&lt;antibody&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10863" PostTypeId="1" CreationDate="2013-10-14T19:56:42.080" Score="5" ViewCount="143" Body="&lt;p&gt;In shade-loving plants, the &lt;a href=&quot;https://en.wikipedia.org/wiki/Compensation_point&quot;&gt;light compensation point&lt;/a&gt; is reached at low irradiance because:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A. Leaves have more chlorophyll per reaction center&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B. These plants have greatly reduced respiration rates&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C. Shade-loving plants synthesize anthocyanins&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am mainly confused between A and C. I am sure that A is factually correct but I don't know whether it is correct in this context.&lt;/p&gt;&#xA;" OwnerUserId="4058" LastEditorUserId="107" LastEditDate="2013-10-14T20:40:08.183" LastActivityDate="2014-10-09T15:17:32.647" Title="Shade-loving Plants" Tags="&lt;botany&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10864" PostTypeId="2" ParentId="10862" CreationDate="2013-10-14T20:23:37.707" Score="1" Body="&lt;p&gt;1)  The secondary response &lt;a href=&quot;http://www.pnas.org/content/107/27/12192.full&quot; rel=&quot;nofollow&quot;&gt;requires CD4&lt;sup&gt;+&lt;/sup&gt; T cells&lt;/a&gt; to activate &lt;a href=&quot;http://www.annualreviews.org/doi/pdf/10.1146/annurev.iy.09.040191.001205&quot; rel=&quot;nofollow&quot;&gt;memory B cells&lt;/a&gt;.  That first paper actually gives some evidence that some of the rapidity could arise because T cells and memory B cells are in very close proximity to each other in germinal centers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Yes.  The affinity of antibodies increases during the &lt;em&gt;initial&lt;/em&gt; infection, both through &lt;a href=&quot;https://en.wikipedia.org/wiki/Isotype_switching&quot; rel=&quot;nofollow&quot;&gt;isotype switching&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Affinity_maturation&quot; rel=&quot;nofollow&quot;&gt;affinity maturation&lt;/a&gt;, producing far superior antibodies.  Upon reactivation, memory B cells can undergo further somatic hupermutation.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-14T20:23:37.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10865" PostTypeId="5" CreationDate="2013-10-14T21:52:03.450" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-10-14T21:52:03.450" LastActivityDate="2013-10-14T21:52:03.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10866" PostTypeId="4" CreationDate="2013-10-14T21:52:03.450" Score="0" Body="An addictive narcotic stimulant derived from the coca plant.  Cocaine functions by inhibiting the reuptake of neurotransmitters such as dopamine and serotonin." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-14T22:17:54.813" LastActivityDate="2013-10-14T22:17:54.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10867" PostTypeId="5" CreationDate="2013-10-14T21:53:36.037" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-10-14T21:53:36.037" LastActivityDate="2013-10-14T21:53:36.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10868" PostTypeId="4" CreationDate="2013-10-14T21:53:36.037" Score="0" Body="Children born from the same pregnancy.  Twins can result from either a single zygote (monozygotic, or identical twins) or from two, separately-fertilized egg cells (dizygotic, or fraternal twins)." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-14T22:18:00.203" LastActivityDate="2013-10-14T22:18:00.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10869" PostTypeId="5" CreationDate="2013-10-14T21:55:18.013" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-10-14T21:55:18.013" LastActivityDate="2013-10-14T21:55:18.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10870" PostTypeId="4" CreationDate="2013-10-14T21:55:18.013" Score="0" Body="The regulation of osmotic pressure within an organism through active maintenance of solute concentration." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-14T22:18:33.487" LastActivityDate="2013-10-14T22:18:33.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10871" PostTypeId="5" CreationDate="2013-10-14T21:59:39.010" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-10-14T21:59:39.010" LastActivityDate="2013-10-14T21:59:39.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10872" PostTypeId="4" CreationDate="2013-10-14T21:59:39.010" Score="0" Body="The use and interpretation of sound waves to aid in navigation.  Used mainly by bats and toothed whales." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-14T22:18:07.157" LastActivityDate="2013-10-14T22:18:07.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10873" PostTypeId="1" CreationDate="2013-10-14T23:04:30.663" Score="-1" ViewCount="1538" Body="&lt;p&gt;What are the geological uses of fossils and how could it be utilised?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.icr.org/article/508/&quot; rel=&quot;nofollow&quot;&gt;The Institute for Creation Science&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fossils are typically found in sedimentary rock, almost all of which were originally deposited as sediments by moving water. Subsequent processes hardened them into sedimentary rock, as overlying pressure squeezed the water out and the grains were cemented together. Often plants and animals were trapped, being buried in the sediments. As the sediments hardened into sedimentary rock, the dead things hardened into fossils.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4629" LastEditorUserId="4101" LastEditDate="2013-10-15T00:58:37.563" LastActivityDate="2013-10-15T00:58:37.563" Title="What are uses of fossils?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2013-10-15T02:26:56.047" ContentLicense="CC BY-SA 3.0" />
  <row Id="10874" PostTypeId="2" ParentId="10873" CreationDate="2013-10-15T00:25:58.410" Score="2" Body="&lt;p&gt;Since you're talking about Geo, then the short answer to that would be:&lt;/p&gt;&#xA;&lt;p&gt;To check how long such specie (animals or plants) existed on the planet (earth obviously)!&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;For example:&lt;/strong&gt; You came to know about Dinosaurs using the Fossils and you made up their whole skeleton and then using your imagination you created the body.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Usage:&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Keeping the above example in mind, fossils are used to know the period of extinction of the living being or the existance or both.&lt;/p&gt;&#xA;&lt;p&gt;Fossils are sometimes used as Fossil fuel too, but that's in liquid form when they are decomposed anaerobically by the bacteria and all that info, please check the reference for this.&lt;/p&gt;&#xA;&lt;p&gt;And what is the last paragraph about? Some information eh? I was not able to understand its usage and utility to the question! Sorry :)&lt;/p&gt;&#xA;&lt;h3&gt;Reference&lt;/h3&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Fossil_fuel&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Fossil_fuel&lt;/a&gt; (Fossil Fuel)&lt;/p&gt;&#xA;" OwnerUserId="4674" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-15T00:25:58.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10876" PostTypeId="2" ParentId="10843" CreationDate="2013-10-15T03:41:21.297" Score="10" Body="&lt;p&gt;It's hard to provide an objective answer. If you have a decent length and good complexity, even a single terminal 3' &lt;code&gt;G&lt;/code&gt; or &lt;code&gt;C&lt;/code&gt; would do. Of course, one has to take into account the primer's overall &lt;code&gt;GC:AT&lt;/code&gt; ratio and things like annealing temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's &lt;a href=&quot;http://www.bio.net/mm/methods/2000-August/084438.html&quot;&gt;a link to diverse opinions&lt;/a&gt; on the topic and it has this nugget (which I subscribe to when possible):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;FWIW, my preferred offerings to the PCR gods are primers with a single&#xA;  G or C 3', FWIW. Seems to keep 'em happy most phases of the moon.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerDisplayName="user4675" LastActivityDate="2013-10-15T03:41:21.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10877" PostTypeId="2" ParentId="10863" CreationDate="2013-10-15T04:48:44.127" Score="1" Body="&lt;p&gt;I think the answer is &lt;strong&gt;&lt;em&gt;A&lt;/em&gt;&lt;/strong&gt;. As for &lt;strong&gt;&lt;em&gt;C&lt;/em&gt;&lt;/strong&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Anthocyanin&quot; rel=&quot;nofollow&quot;&gt;Anthocyanins&lt;/a&gt; are located in the vacuole and their light absorption does not affect the process of photosynthesis which occurs in the chloroplast. Anthocyanins do participate in prevention of High-Light Stress (or &lt;a href=&quot;http://en.wikipedia.org/wiki/Photoinhibition&quot; rel=&quot;nofollow&quot;&gt;Photoinhibition&lt;/a&gt;) but they have no role to play in gathering light energy for photosynthesis. Therefore, to improve the quantum efficiency (quanta of light per &lt;strong&gt;CO₂&lt;/strong&gt; molecule fixed or &lt;strong&gt;O₂&lt;/strong&gt; evolved, or any other quantifiable photochemical event) of the light reaction, anthocyanins play no role.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, if there are more chlorophyll molecules per reaction centre, i.e. there is a greater number of chlorophylls in the LHC (&lt;a href=&quot;http://en.wikipedia.org/wiki/Light-harvesting_complex&quot; rel=&quot;nofollow&quot;&gt;Light Harvesting Complex&lt;/a&gt;), or the Antennae system, then the quantum efficiency can be improved, the absorption band widened and thus the light compensation point is reached earlier. The extra molecules of chlorophyll  absorb energy at their specific wavelengths of light and transmit this energy to the main reaction centre by FRET(&lt;a href=&quot;http://en.wikipedia.org/wiki/F%C3%B6rster_resonance_energy_transfer&quot; rel=&quot;nofollow&quot;&gt;Fluorescence resonance energy transfer&lt;/a&gt;). Therefore, greater the number of chlorophylls per reaction centre, greater is the light energy absorbed and transmitted to the reaction centre and hence, better is the quantum efficiency.&lt;br&gt;&#xA;More technically, having more chlorophylls open up more pathways for photochemical energy &lt;a href=&quot;http://en.wikipedia.org/wiki/Quenching_%28fluorescence%29&quot; rel=&quot;nofollow&quot;&gt;quenching&lt;/a&gt;, and thus improves the efficiency by minimizing fluorescent losses.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3340" LastEditDate="2014-10-09T15:17:32.647" LastActivityDate="2014-10-09T15:17:32.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10879" PostTypeId="2" ParentId="9993" CreationDate="2013-10-15T07:36:45.363" Score="13" Body="&lt;p&gt;Some additional points about role of bicarbonate (which is directly formed from carbon dioxide as described by TomD):&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Helps is neutralizing the acidic chyme when it enters intestine.&lt;/li&gt;&#xA;&lt;li&gt;Formation of shells in invertebrates and eggshells in birds and reptiles. Shells are formed by deposition of calcite (calcium carbonate) which primarily happens by increased bicarbonate and calcium secretion.&lt;/li&gt;&#xA;&lt;li&gt;Bicarbonate is also important for chloride transport (Anion exchange). In RBCs it happens through &lt;a href=&quot;http://en.wikipedia.org/wiki/Band_3&quot;&gt;Band3&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-10-15T07:36:45.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10880" PostTypeId="1" CreationDate="2013-10-15T08:34:03.333" Score="1" ViewCount="159" Body="&lt;p&gt;I have not spoken to my mother in 15 years but recently connected with her and her side of the family. I was primarily raised in a different sub-culture after the age of 4. As it turns out I &quot;accidentally&quot; have a lot in common with my maternal relatives. We like and dislike many of the same things. Is there some dominate trait in our nature which affects our psychology to cause us to agree on everything from TV, food and lifestyle?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2013-10-16T06:05:44.037" Title="Why do I have a lot in common with my mother?" Tags="&lt;genetics&gt;&lt;epigenetics&gt;" AnswerCount="1" CommentCount="8" ClosedDate="2013-10-28T16:31:00.383" ContentLicense="CC BY-SA 3.0" />
  <row Id="10882" PostTypeId="1" CreationDate="2013-10-15T14:44:40.343" Score="0" ViewCount="251" Body="&lt;p&gt;Suppose we have a population of about 1000 with an environment that does not change a lot (e.g. the atmosphere is more or less the same) and we leave this population to evolve. From what I understand some genes will be lost because they won't be suited enough to continue in the next generation. Also the generations can only reproduce within their generation (e.g. a male can only have reproduce with people from his generation). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: won't some genes, combined with others have a better chance to make the individual &quot;better&quot; but they for example make it less fit right now. Or will the mutation of the genes actually &lt;strong&gt;promise&lt;/strong&gt; that eventually we will hit that minimum of the function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to point out that I'm a computer scientist and my biology is awful. I'm looking at this from evolutionary algorithms point of view in particular genetic algorithms.&lt;/p&gt;&#xA;" OwnerUserId="4679" LastEditorUserId="3632" LastEditDate="2013-10-18T14:15:25.147" LastActivityDate="2013-11-17T15:10:32.223" Title="Won't natural selection miss the overall minimum of a function?" Tags="&lt;evolution&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="2" CommentCount="10" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10883" PostTypeId="1" CreationDate="2013-10-15T14:48:34.370" Score="5" ViewCount="109" Body="&lt;p&gt;I need free online data about heart murmurs to study these:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;heart murmur frequency , S2 heart sound frequency and its split,&#xA;  murmur timing, and duration, murmur intensity, S3 sound presence and&#xA;  intensity, S1 presence and intensity, presence of ejection sounds and&#xA;  arrhythmias&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I will cite your source then if I can use your data freely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would really have the same data as used in this paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Heart energy signature spectrogram for cardiovascular diagnosis&#xA;  Vladimir Kudriavtsev, Vladimir Polyshchuk and Douglas L Roy&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No pediatric ECG data here&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.beecardia.com/physiobank/database/ptbdb?locale=en&amp;amp;page=2&quot; rel=&quot;nofollow&quot;&gt;beecardio&lt;/a&gt; (aggregation of many ECG databases) &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Does anyone have simple data for my task?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I remember that some CD of some book has some standardised nicely organised sounds that you can use freely.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2015-05-18T22:22:32.387" LastActivityDate="2015-05-18T22:22:32.387" Title="Calling for Free Online Data for Paediatric ECG?" Tags="&lt;cardiology&gt;&lt;database&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10884" PostTypeId="1" AcceptedAnswerId="10912" CreationDate="2013-10-15T15:45:31.010" Score="0" ViewCount="236" Body="&lt;p&gt;What are the effects of addition of these chemicals to actively respiring cells ?&#xA;Which of them would lead to INHIBITION of aerobic respiration ? Would cytochromes be actually taken up by cells ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a.addition of CO&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b.addition of CO2&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c.addition of cytochromes and flavoprotein&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-10-16T18:27:13.393" LastActivityDate="2014-10-09T15:47:36.460" Title="cellular respiration" Tags="&lt;physiology&gt;&lt;homework&gt;&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10885" PostTypeId="1" AcceptedAnswerId="10890" CreationDate="2013-10-15T16:05:03.513" Score="2" ViewCount="229" Body="&lt;p&gt;What dissociates first - the last tRNA, mRNA and release factors or the subunits of ribosomes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried searching this from Lehninger but couldn't get a clean answer.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-16T03:22:06.533" LastActivityDate="2013-10-16T03:22:06.533" Title="Termination of translation" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;translation&gt;&lt;ribosome&gt;&lt;mrna&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10886" PostTypeId="2" ParentId="10843" CreationDate="2013-10-15T17:03:07.630" Score="3" Body="&lt;p&gt;I will offer my own (empirical) account of primer design. A GC-clamp aids in specificity of the priming and therefore contributes to the overall efficiency of the PCR reaction. In the past, I have (out of necessity) designed primers that had both too much GC-clamping on the 3' end, and used primers without any GC-clamping. These PCR reactions were performed successfully, with differing levels of primer-dimer formation and overall efficiency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my experience, GC-clamping is nice, but not strictly required for good PCR. My general rule-of-thumb is to terminate my primers with 2 G/C wherever possible. If something is going to fail, it is not usually the PCR.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-10-15T17:03:07.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10887" PostTypeId="1" AcceptedAnswerId="10889" CreationDate="2013-10-15T18:18:19.093" Score="2" ViewCount="2494" Body="&lt;p&gt;What is the difference of pressure a human eyeball cornea (cornea, lens and other elements separating vitreous body from air) can handle? Or asking differently: what the outside pressure should be to &quot;blow up&quot; a healthy man's eyeball?&lt;/p&gt;&#xA;" OwnerUserId="4680" LastActivityDate="2013-10-15T21:39:59.193" Title="What is the strength of human cornea?" Tags="&lt;eyes&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10888" PostTypeId="2" ParentId="10885" CreationDate="2013-10-15T20:46:57.920" Score="1" Body="&lt;p&gt;just off the top of my head... since the ribosome is made of 2 large complexes which assemble and clamp onto the mRNA, &lt;a href=&quot;http://en.wikipedia.org/wiki/File%3aProtein_translation.gif&quot; rel=&quot;nofollow&quot;&gt;I'd say it was the tRNA first, then the ribosome and mRNA would detach simultaneously&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-10-15T20:46:57.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10889" PostTypeId="2" ParentId="10887" CreationDate="2013-10-15T21:39:59.193" Score="2" Body="&lt;p&gt;Normal pressure in the eye&lt;sup&gt;&lt;a href=&quot;http://www.webmd.com/eye-health/tonometry?page=3&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;,&lt;a href=&quot;http://www.emedicinehealth.com/glaucoma_overview/article_em.htm&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;&lt;/sup&gt; is between 10 and 21 mmHg (somewhere around 1.3-2.8 kPa or 0.01-0.03 atm) with pathology occurring at around 30 mmHg.&lt;sup&gt;&lt;a href=&quot;http://www.uniklinikum-saarland.de/de/einrichtungen/kliniken_institute/experimentelle_ophthalmologie/forschung/iop_sensing/&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;&lt;/sup&gt;  Clearly the cornea can handle that, but how much more?  There's a lot more evidence as far as I could see for how well surgeries hold up, with 150-300+ mmHg (20-40 kPa, 0.2-0.4 atm).&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21761419&quot; rel=&quot;nofollow&quot;&gt;4&lt;/a&gt;&lt;/sup&gt;  One source&lt;sup&gt;&lt;a href=&quot;http://ac.els-cdn.com/S0079670097000361/1-s2.0-S0079670097000361-main.pdf?_tid=b96e9016-35d5-11e3-b5c3-00000aab0f27&amp;amp;acdnat=1381867961_2f422e3bf7a9ef106026e1beaa009ad5&quot; rel=&quot;nofollow&quot;&gt;5&lt;/a&gt;&lt;/sup&gt; from 1998 cites work supposedly showing that the &lt;a href=&quot;https://en.wikipedia.org/wiki/Corneal_stroma&quot; rel=&quot;nofollow&quot;&gt;stroma&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;gives the cornea 100 times more strength than is necessary to withstand the maximum intraocular pressure under physiological conditions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So maybe around 200 kPa, for just the stroma?  Interestingly, a &lt;a href=&quot;http://www.natureworldnews.com/articles/2403/20130612/cornea-layer-discovery-make-eye-surgeries-safer-researchers.htm&quot; rel=&quot;nofollow&quot;&gt;new eye layer was discovered&lt;/a&gt; earlier this year; this Dua's Layer is incredibly thin - 15 microns - but can withstand pressures of around 100-200 kPa (750-1500 mmHg, 1-2 atm).&lt;sup&gt;&lt;a href=&quot;http://medtube.net/tribune/new-anatomical-structure-in-the-cornea-of-%E2%80%8B%E2%80%8Bthe-human-eye/&quot; rel=&quot;nofollow&quot;&gt;6&lt;/a&gt;,&lt;a href=&quot;http://www.biosciencetechnology.com/articles/2013/08/commotion-over-new-cornea-layer#.Ul2hPSSoU2U&quot; rel=&quot;nofollow&quot;&gt;7&lt;/a&gt;&lt;/sup&gt;  The large range there is due to some conflicting numbers in those links; the 200 kPa is the more widely reported one, but again, that's just for one layer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, of course, there is this: a beautiful 2009 &lt;a href=&quot;http://scholar.lib.vt.edu/theses/available/etd-04242009-094655/unrestricted/Bisplinghoff_Thesis-R3.pdf&quot; rel=&quot;nofollow&quot;&gt;thesis by Jill Aliza Bisplinghoff from Virginia Tech&lt;/a&gt; which thoroughly examines the issue.  As an answer to your question, it includes the following such gems:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The high rate pressurization of 20 human eyes resulted in a mean rupture pressure of &lt;strong&gt;0.97 ± 0.29 MPa (7275.60 ± 2175.18 mm Hg)&lt;/strong&gt;... A student T-test revealed that the difference in the rupture pressure between the equatorial mean of 0.93 ± 0.30 MPa (6975.57 ± 2250.19 mm Hg) and the meridional mean of 1.13 ± 0.21 MPa (8475.70 ± 1575.13 mm Hg) was not significant (p=0.16)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A pneumatic cannon was used to impact eyes with a variety of projectiles at multiple velocities... The projectiles selected for the test series included a 6.35 mm diameter metal ball, a 9.25 mm diameter aluminum rod, and an 11.16 mm diameter aluminum rod... A range of internal eye pressures were produced that varied from &lt;strong&gt;1256 mmHg (24.3 psi) to 22843 mmHg (442 psi)&lt;/strong&gt;... [and] resulted in zero globe rupture. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-15T21:39:59.193" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10890" PostTypeId="2" ParentId="10885" CreationDate="2013-10-15T22:04:22.600" Score="3" Body="&lt;p&gt;Shigeta's got a point: the ribosome is latched onto the mRNA so those two are intrinsically linked.  You're really asking whether the ribosome comes off first or whether the tRNA does, but it's actually the new polypeptide, which makes sense:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The stop codon is recognized by a protein, the polypeptide chain release factor (RF), which triggers the hydrolytic release of the nascent polypeptide chain from the P-site-bound peptidyl-tRNA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://ac.els-cdn.com/S0968000400016698/1-s2.0-S0968000400016698-main.pdf?_tid=333a78d0-35e3-11e3-a8f0-00000aab0f01&amp;amp;acdnat=1381873748_0f2d5644cec3df13987a3c4ec209e13d&quot; rel=&quot;nofollow noreferrer&quot;&gt;This minireview&lt;/a&gt; puts forth a model (see below) where, in &lt;em&gt;E. coli&lt;/em&gt; at least, the 50S ribosome subunit is then dissociated from the mRNA/30S subunit/tRNA complex, following which the final tRNA is removed.  &lt;a href=&quot;http://www.nature.com/emboj/journal/v22/n2/full/7594928a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;An in-depth review&lt;/a&gt; from a few years later gives more context.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Iv1VY.png&quot; alt=&quot;Figure 3&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-15T22:04:22.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10891" PostTypeId="1" AcceptedAnswerId="10893" CreationDate="2013-10-15T22:47:47.433" Score="8" ViewCount="14144" Body="&lt;p&gt;What is the strict difference between mutation and DNA damage?  As far as I understand it, a mutation is an alteration in the genetic sequence, having &quot;tricked&quot; the repairing machinery and thus getting replicated in the future.  DNA damage, on the other hand, is any alteration of the DNA molecule including breaks, chemical alterations of the molecule, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, are mutations considered a type of DNA damage?  I would thank the strict definition of both concepts.&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="4101" LastEditDate="2013-10-16T00:47:59.883" LastActivityDate="2018-03-23T12:38:54.093" Title="Difference between mutation and DNA damage" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;mutations&gt;&lt;dna-damage&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10892" PostTypeId="2" ParentId="10880" CreationDate="2013-10-15T23:30:16.593" Score="1" Body="&lt;p&gt;In this answer I mainly repeat the comments!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several reasons why you might share some traits with your mother.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;genetic (see below)&lt;/li&gt;&#xA;&lt;li&gt;epigenetic&lt;/li&gt;&#xA;&lt;li&gt;environmental influence while being in the womb&lt;/li&gt;&#xA;&lt;li&gt;environmental influence up to the time you were 4 years old&lt;/li&gt;&#xA;&lt;li&gt;the two environment were not so different (maybe because your adoptive parents wanted to follow the will of your mother or just because by chance your adoptive parents have similar behaviour that your mother)&lt;/li&gt;&#xA;&lt;li&gt;multiple testing issue (see below)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;These reasons can be classified into three categories:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;environmental variance&lt;/li&gt;&#xA;&lt;li&gt;genetic variance&lt;/li&gt;&#xA;&lt;li&gt;poor observation (statistic mistake)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The phenotypic variance in a population is influenced by the environmental variance + the genetic variance + the variance due to the interactions between the environmental and genetic variances. The heritability can be calculated as the part of the phenotypic variance which are genetically determined. Such calculations make sense only for populations not for a given parent-offpsring pair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;genetic&lt;/strong&gt;: It does not make sense to ask whether the variance of a trait is dominant or recessive. It makes sense to say that &quot;liking pink&quot; is dominant over &quot;liking blue&quot;. Therefore, you should tell us what is the variant of a given trait that you share with your mother. In such case we might tell you if this variant is dominant or not over the other variants. But of course, this works only for traits that are at least slightly genetically determined. liking a color will certainly not have a strong genetic variance for example. And even if a trait is 100% genetically determined, complex genetic architecture might make it hard to answer. For example a given variant might be dominant in a given genetic background but recessive in another. Finally, I should say that it costs to perform the necessary study (Genome Wide Association Studies) to know exactly the part of the variance of a given trait that is genetically determined. And of course, such studies depend on the population we look at.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Multiple testing issue&lt;/strong&gt;: Without realizing, you actually looked at many different traits. You might have looked at your favorite color, your favorite beer, the way you wash your teeth, the sport you practice, the color of room, whether you are calm or impulsive, etc... You might not have paid attention only to things that match but you would have found as many similarities (not the same ones though) with any other human on earth.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-10-16T06:05:44.037" LastActivityDate="2013-10-16T06:05:44.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10893" PostTypeId="2" ParentId="10891" CreationDate="2013-10-16T00:52:22.093" Score="5" Body="&lt;p&gt;Have you read the &lt;a href=&quot;https://en.wikipedia.org/wiki/DNA_repair#DNA_damage_and_mutation&quot; rel=&quot;nofollow&quot;&gt;DNA repair article on Wikipedia&lt;/a&gt;?  The DNA damage and mutation section answers exactly what you're asking:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;DNA damages and mutation are fundamentally different. &lt;strong&gt;Damages are physical abnormalities&lt;/strong&gt; in the DNA... [and] can be recognized by enzymes, and, thus, they &lt;strong&gt;can be correctly repaired&lt;/strong&gt; if redundant information, such as the undamaged sequence in the complementary DNA strand or in a homologous chromosome, is available for copying.... In contrast to DNA damage, a &lt;strong&gt;mutation is a change in the base sequence of the DNA&lt;/strong&gt;. A mutation &lt;strong&gt;cannot be recognized by enzymes once the base change is present in both DNA strands, and, thus, a mutation cannot be repaired&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here's the entry from the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/mesh/68004249&quot; rel=&quot;nofollow&quot;&gt;NCBI MeSH Glossary&lt;/a&gt; saying the same thing:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION... They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And for &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/mesh/68009154&quot; rel=&quot;nofollow&quot;&gt;mutation&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-28T12:23:13.063" LastActivityDate="2013-10-28T12:23:13.063" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10894" PostTypeId="1" AcceptedAnswerId="10937" CreationDate="2013-10-16T08:51:25.337" Score="5" ViewCount="2342" Body="&lt;p&gt;I have been doing a lot of reading on quantitative genetics and the &lt;a href=&quot;http://www.bio.tamu.edu/users/ajones/gmatrixonline/whatisg.html&quot; rel=&quot;nofollow&quot;&gt;G- (and B-) matrix&lt;/a&gt; lately. I get the principle behind performing the analysis now but I am still not sure how to do it. I'd like to be able to try it out with some dummy/old data in R to see how it is done.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's pretend I have measured 5 traits of Drosophila (Wing length, lifespan, eye pigmentation, bristle number, and fitness). Could I construct a G-matrix for the population from this data and also get a B-matrix to measure the selection on the traits?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Aims of the post:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) What information (trait measurements, fitness scores etc.) is needed to construct G- and B- matrices?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) I would like to find print or online material that would guide me in actually implementing this method. It seems like there is an awful lot of papers saying that G-matrices are great, but no one actually says how to do them in real life...&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="3624" LastEditDate="2014-03-18T10:44:39.113" LastActivityDate="2014-03-18T10:44:39.113" Title="What is needed for a G-matrix?" Tags="&lt;evolution&gt;&lt;literature&gt;&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10895" PostTypeId="5" CreationDate="2013-10-16T08:58:33.120" Score="0" Body="&lt;p&gt;Many of the phenotypic traits we can observe are affected by more than one gene. Traits affected by many genes are called quantitative, metric, or polygenic traits.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-10-16T09:30:17.750" LastActivityDate="2013-10-16T09:30:17.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10896" PostTypeId="4" CreationDate="2013-10-16T08:58:33.120" Score="0" Body="Quantitative genetics is the study of inheritance at the phenotypic level. " OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-10-16T09:30:10.127" LastActivityDate="2013-10-16T09:30:10.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10897" PostTypeId="2" ParentId="9521" CreationDate="2013-10-16T10:55:41.623" Score="1" Body="&lt;p&gt;It's true that the expression of a promoter is context-dependent, i.e. depends on the overall status of the cell, but some work has been made to boil down such context-dependency into some measurable parameter. For example, for constitutive promoters such a parameter seems to be the growth rate. You could characterize promoters by that:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gerosa, L. et al. Dissecting specific and global transcriptional regulation of bacterial gene expression. Mol. Syst. Biol. 9, 658 (2013)&lt;/p&gt;&#xA;" OwnerUserId="4683" LastActivityDate="2013-10-16T10:55:41.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10898" PostTypeId="2" ParentId="10455" CreationDate="2013-10-16T12:34:36.380" Score="2" Body="&lt;p&gt;These molecular motors' response maybe dynamic and nonlinear. But it entirely dependent on the external influence and also the characteristics of the motor itself including number of active motors involved in operation. As it is microscopic, it will not possible to analyse by assumptions and say they have some random frequency. They do have certain frequency of operation (I do not know whether they are controlled by biological clock or some master clock but they are controlled by nucleus of the cell) and &lt;a href=&quot;http://alevine.chem.ucla.edu/187/motors/motors-1.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;Modeling molecular motors&quot;&lt;/a&gt; explains how motors act on the filament inside the cell. It mainly talks about the influence of external force on the operation of motor and also speed(v) of the motor. The following excerpt from that paper talks about the external force on motor.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The action  of  the  motor is induced by generalized forces, which for&#xA;  the motor/filament system may be identified  as the mechanical force&#xA;  fext  applied  to the  motor, and  the chemical potential difference&#xA;  Dm, which measures the free-energy change per consumed ‘‘fuel’’&#xA;  molecule. The force fext describes external forces, for example of&#xA;  optical tweezers,  microneedles, or the viscous load of an object that&#xA;  is carried. fext could also include viscous friction forces between&#xA;  the motor and the surrounding solvent if the latter  is considered as&#xA;  ‘‘external.’’ The chemical  potential  difference Dm is for the&#xA;  process of the hydrolysis of Adenosinetriphosphate (ATP) to&#xA;  Adenosinediphosphate(ADP) and phosphate (P).&#xA;  &lt;img src=&quot;https://i.stack.imgur.com/De9iO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The frequency of molecular motor according to &lt;a href=&quot;http://arxiv.org/pdf/1302.3196.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;&lt;strong&gt;Biophysics of Molecular Motor&lt;/strong&gt;&quot;&lt;/a&gt; has been classified into two categories:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Density controlled: In the density-controlled model, it is assumed that the depolymerization rate is proportional to the motor density at the terminal site of the microtubule. Here the frequency of motor is dependent on density of the motor.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Flux controlled: Filament depolymerization is determined by the flux of motors&#xA;to the end. Here the frequency is dependent on the flux of the motor.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In both the above cases the length of the filament on which motor is acting is also important. These models have been analysed and plotted on a graph to give a clear picture of it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8LR6n.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper explains the catastrophe frequency, the frequency at which the filament shrinks. Shrinking of of a filament is due to motor. So the paper concludes saying the catastrophe frequency is 0.5 per min for a 8um length of filament.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JxNmt.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Catastrophe = the transition from growing to shrinking of dynamic microtubules).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To summarize, these motors do have speed and frequency of operation but they are not fixed. They vary in a non linear fashion due dynamic environment. But the motor tries to be as much stable and resistant as possible.&lt;/p&gt;&#xA;" OwnerUserId="4547" LastActivityDate="2013-10-16T12:34:36.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10899" PostTypeId="1" AcceptedAnswerId="10900" CreationDate="2013-10-16T14:45:09.170" Score="-2" ViewCount="361" Body="&lt;p&gt;There are different types of blood cells in the human body i.e. red blood cells, neutrophils, basophils, eosinophils, monocytes, T-cells, B-cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the cellular components of these cells? What are the organelles that are found in these cells? I can't find this information anywhere.&lt;/p&gt;&#xA;" OwnerUserId="1765" LastEditorUserId="1320" LastEditDate="2013-10-16T15:54:25.553" LastActivityDate="2015-05-21T10:22:57.517" Title="Cellular components of blood cells" Tags="&lt;hematology&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2015-10-10T06:17:28.140" ContentLicense="CC BY-SA 3.0" />
  <row Id="10900" PostTypeId="2" ParentId="10899" CreationDate="2013-10-16T15:02:58.377" Score="4" Body="&lt;p&gt;It's pretty straightforward.  White blood cells have all the usual organelles while mature red blood cells are missing most of them.  WBC can have &lt;em&gt;specialized&lt;/em&gt; lysosomes depending on their function, as well as granules if they are granulocytes. &lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="6194" LastEditDate="2015-05-21T10:22:57.517" LastActivityDate="2015-05-21T10:22:57.517" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10901" PostTypeId="1" AcceptedAnswerId="10902" CreationDate="2013-10-16T16:03:01.803" Score="5" ViewCount="116" Body="&lt;p&gt;If the sole known function of a gene is to activate a transcription factor, would that gene also be considered a transcription factor, or is there a word for such genes that are further upstream on the transcription activation cascade?&lt;/p&gt;&#xA;" OwnerUserId="1906" LastActivityDate="2013-10-22T01:48:19.397" Title="Can genes that activate transcription factors also called be called transcription factors?" Tags="&lt;genetics&gt;&lt;transcription&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10902" PostTypeId="2" ParentId="10901" CreationDate="2013-10-16T16:30:51.743" Score="6" Body="&lt;p&gt;Yes.  For an example, see &lt;a href=&quot;http://www.bu.edu/nf-kb/gene-resources/target-genes/&quot;&gt;this list of targets of NF-kB&lt;/a&gt; (a transcription factor).  Many other transcription factors are included there.  As for a TF that does &lt;em&gt;nothing&lt;/em&gt; except activate another, &lt;em&gt;single&lt;/em&gt; TF?  I don't know that those exist - TFs tend to modulate multiple genes.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-16T16:30:51.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10903" PostTypeId="2" ParentId="10901" CreationDate="2013-10-16T16:40:36.667" Score="5" Body="&lt;p&gt;From the &lt;a href=&quot;http://en.wikipedia.org/wiki/Transcription_factor&quot;&gt;wikipedia&lt;/a&gt; article on TFs:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In molecular biology and genetics, a transcription factor (sometimes called a sequence-specific DNA-binding factor) is a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to messenger RNA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The nature of the gene affected is irrelevant, a protein is a transcription factor if it binds to a gene's promoter and regulates that gene's transcription. Whether the regulated gene also codes for a TF does not enter into it. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-10-16T16:40:36.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10904" PostTypeId="1" AcceptedAnswerId="10914" CreationDate="2013-10-16T17:27:19.653" Score="2" ViewCount="223" Body="&lt;p&gt;Does anyone know of an .NET (C#,VB.NET, maybe F#) DNA parser?  If not I will probably make one, it doesn't seem like it would be hard.  My general idea was to generate something that would report the codon biases and go back and adjust the bias for engineering.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize the later part is a bit specific, but if anyone knew about an open .NET program that annualized/parsed the codon bias, I'd be interested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2013-10-16T22:40:49.170" Title=".Net DNA/Codon Parser" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="10905" PostTypeId="1" AcceptedAnswerId="10997" CreationDate="2013-10-16T17:45:32.277" Score="1" ViewCount="194" Body="&lt;p&gt;From my experience humans can detect UV - not by seeing it but by pain in their eyes. Many people (me too) feel pain when looking at UV lamps. When looking at sun through clouds I still can feel pain very often even if the after -all-image is not very bright (because of the clouds) but when I look at a light bulb or when I look at sun through sun-watching lenses (which cut all UV) I don't feel that pain despite of them being much brighter than the cloudy sun. I also have read about it once or two.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, can this be true (I mean humans can detect UV with their eyes) or that's just a coincidence? And if it's true, how it happens?&lt;/p&gt;&#xA;" OwnerUserId="4680" LastActivityDate="2013-10-21T21:46:46.683" Title="Detecting UV by humans" Tags="&lt;eyes&gt;&lt;uv&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="10906" PostTypeId="1" AcceptedAnswerId="10913" CreationDate="2013-10-16T18:59:20.457" Score="4" ViewCount="6093" Body="&lt;p&gt;Can  parasite, microbes be passed from mother to fetus through the placenta ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know some like HIV can be.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-10-16T22:35:37.123" Title="Transmission of disease from mother to fetus" Tags="&lt;pathology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10908" PostTypeId="2" ParentId="10906" CreationDate="2013-10-16T19:57:25.867" Score="2" Body="&lt;p&gt;Parasite are organisms, and they can pass through mother to her child while its in hers womb. Toxoplasma gondii is an example, it passed from mother to child as it moves through her body, and since child is present inside her, of course it will get into the child.&lt;/p&gt;&#xA;&lt;p&gt;You can diagnose for the parasites, or can even get them treated well just like getting your self treated, but measurements should be taken while treating as the their might be a danger of miscarriage.&lt;/p&gt;&#xA;&lt;p&gt;So the answer is &lt;strong&gt;Yes&lt;/strong&gt;, parasites can pass through the body of mother to her baby. Since the baby is inside her being a part of her body.&lt;/p&gt;&#xA;&lt;p&gt;There is an infection called &lt;strong&gt;toxoplasmosis&lt;/strong&gt; which doesnot passed from person to person, yet it can pass while in pregnancy.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Chagas&lt;/strong&gt; disease is a disease that can get transferred from Mother to her child, during pregnancy. Which is called by a Parasite called &lt;strong&gt;Trypanosoma cruzi&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;h3&gt;Reference:&lt;/h3&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://voices.yahoo.com/can-parasite-passed-unborn-children-via-their-4839156.html?cat=70&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://voices.yahoo.com/can-parasite-passed-unborn-children-via-their-4839156.html?cat=70&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://kidshealth.org/parent/infections/parasitic/toxoplasmosis.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://kidshealth.org/parent/infections/parasitic/toxoplasmosis.html&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.livescience.com/21432-chagas-disease-mother-child-pregnancy.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.livescience.com/21432-chagas-disease-mother-child-pregnancy.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4674" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-16T19:57:25.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10909" PostTypeId="2" ParentId="10861" CreationDate="2013-10-16T19:59:01.150" Score="5" Body="&lt;p&gt;[If we are talking about animals, there is a number of types of body symmetry: asymmetry, radial, bilateral, spiral, rotational, glide and metameric symmetries. Bilateral and radial are the two basic types, which served as main classificatory character for animal mega-systematics in the past.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's assumed that body symmetry is associated with general environmental gradients.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Animals with (elements of) radial symmetry have one dorso-ventral axis which echos only one environmental gradient: substrate/water column, depth etc. Besides this polarity, resources/signals/danger may come from any direction. Imagine a Hydra polyp with its foot attached to a waterweed and its tentacles surrounding the mouth on the opposite end and expecting the victim to come from any side.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Body of bilateral animals possesses the same dorso-ventral axis and yet another polarity, orthogonal to it: the anterior-posterior axis. This axis is conjugated with the gradient created by locomotion: the anterior margin of the body is likely to encounter something new first. This principle lies in the basis of cephalization: most bilaterial animals have more or less shaped &quot;head&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolutionary changes in body symmetry are thus thought to be associated with changes in life-style, e.g.:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;there is a hypothesis that cnidarians were originally bilateral (and many of them still show some degree bilaterality), but lost it after becoming sedentary.&lt;/li&gt;&#xA;&lt;li&gt;non-walkers echinoderms originated from fully bilateral animals and later acquired their famed pentameric radial symmetry (were they originally fully sedentary like modern stalked sea lilies?). This symmetry, however was again distorted towards secondary bilaterality (not matching the original plane of symmetry) in endobenthic forms: sand dollars and some holothurians.&lt;/li&gt;&#xA;&lt;li&gt;worms like nematodes or priapulids are dwellers of viscous media, similar in all directions: dorso-ventral gradient of environment in this case is absent or weak. Though the original bilateral symmetry is very clear in their body plans, signs of radial symmetry prevail in some organ systems, including the general vermiform appearance. Thus, nematodes combine triradial (head sensilla, pharynx), biradial (musculature) and bilateral (nervous system, genitalia, tail) symmetries.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2013-10-19T21:10:24.310" LastActivityDate="2013-10-19T21:10:24.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10910" PostTypeId="1" CreationDate="2013-10-16T20:45:59.603" Score="3" ViewCount="335" Body="&lt;p&gt;It's always the same explanation that currents are able to &quot;hop&quot; along Ranvier nodes instead of passing continuously along the axon making saltatory conduction more efficient than continuous conduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if we take this down to the molecular level, I cannot understand how they are different. Conduction in unmyelinated nerve fibers are first triggered by an effective stimulus, changing the cell membrane potential and thus opening the voltage gated sodium channels, causing an explosive influx of sodium ions. The action potential is conducted along the fiber through stimulating sodium channels in nearby regions, causing rapid flow of sodium ions into the cell in membrane immediately near the segment of stimulation and this process repeats as the action potential passes unidirectionally along the axon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conduction in myelinated nerve fibers are usually described as hopping along the axon, but on the molecular basis, sodium channels are congregated at the site of Ranvier nodes, large numbers of sodium ions that made its way into the cell swim down the axon in the cytoplasma of the nerve fiber reaching the next ranvier node, changing the membrane potential in that specific site therefore triggering another influx of sodium ions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to put the question simply, the mechanism of continuous conduction is triggering voltage gated sodium channels continuously along the way, whereas the mechanism of saltatory conduction is triggering-swimming-triggering-swimming...how does this difference essentially make saltatory conduction faster?&lt;/p&gt;&#xA;" OwnerUserId="4685" LastActivityDate="2013-10-16T20:45:59.603" Title="How is saltatory conduction faster than conduction of unmyelinated fibers?" Tags="&lt;neuroscience&gt;&lt;cell-biology&gt;&lt;biophysics&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2013-10-17T05:45:49.523" ContentLicense="CC BY-SA 3.0" />
  <row Id="10912" PostTypeId="2" ParentId="10884" CreationDate="2013-10-16T21:40:53.047" Score="2" Body="&lt;p&gt;Carbon Monoxide &quot;CO&quot; would definitely inhibit aerobic respiration. This is in fact the mechanism of the toxicity of compounds such as carbon monoxide and cyanide, namely, carbon monoxide binds (coordinates) with an affinity several orders of magnitude greater than oxygen to the heme group of mitochrondrial cytochrome oxidase, thus inhibiting the enzyme. When the respiratory electron chain is no longer drawn by the reduction of molecular oxygen, the hydrogen ion gradient across the mitochrondrial inner membrane is depleted, and ATP production halts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carbon dioxide would not effect the electron transport chain directly, but is rather involved in the reactions of the citric acid cycle, although, in all likelihood, the cell would die of acidosis before CO₂ concentrations became great enough to reverse the citric acid cycle. Cytochromes and flavoproteins are complex molecules that if the cell were to endocytize them, it would simply digest them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not know your degree of experience in biochemistry, but if you wish, search on the internet for protein structural images of cytochrome oxidase or hemoglobin bound to oxygen and carbon monoxide. Oxygen binds the iron of the heme group at an angle, while carbon monoxide binds directly perpendicular to the heme ring. This difference in geometry is partially responsible for the differential affinity of the two species for heme.&lt;/p&gt;&#xA;" OwnerUserId="4140" LastEditorUserId="3340" LastEditDate="2014-10-09T15:47:36.460" LastActivityDate="2014-10-09T15:47:36.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10913" PostTypeId="2" ParentId="10906" CreationDate="2013-10-16T22:35:37.123" Score="5" Body="&lt;p&gt;Pregnant mothers can indeed pass on various microbes to their fetuses but it is not always directly through the placenta, as the placenta can be protective.  Although the blood of the mother and fetus do not mix directly, the two can interact.  Maternal proteins can flow across to the fetus, as maternal antibodies are actually the source of a newborn's immune system for a few months, and maternal immune cells have even been found in fetuses, which of course means other cells or viruses can get across.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HIV is a good example for your question, actually.  HIV can infect newborns through the placenta, but the &lt;a href=&quot;http://www.health.am/aids/more/how_is_hiv_transmitted_from_mother_to_child/&quot;&gt;majority&lt;/a&gt; of infections &lt;a href=&quot;http://www.retrovirology.com/content/9/1/101#B1&quot;&gt;occur during birth&lt;/a&gt;, not &lt;em&gt;in utero&lt;/em&gt;.  Birth is a pretty bloody process, and the rupturing of the amniotic sac &lt;a href=&quot;http://www.acog.org/~/media/For%20Patients/faq113.pdf&quot;&gt;exposes the infant&lt;/a&gt; to anything in the mother's blood, which is when most infections occur.  For HIV specifically, physicians can all but prevent mother-to-infant transmission by administering anti-HIV drugs just before birth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cdc.gov/std/pregnancy/stdfact-pregnancy.htm&quot;&gt;Here is a list from the CDC&lt;/a&gt; of some STDs which details how infections may be passed on to newborns; most clarify that it mainly happens during the birthing process.  That being said, plenty of diseases will cause transplacental infections.  &lt;a href=&quot;http://emedicine.medscape.com/article/235213-overview&quot;&gt;Usually they are viruses&lt;/a&gt;, as viruses are simply smaller, but there are definitely bacterial and parasitic examples, such as &lt;a href=&quot;http://jid.oxfordjournals.org/content/194/10/1367.full&quot;&gt;&lt;em&gt;Borrelia duttonii&lt;/em&gt;&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16482813&quot;&gt;&lt;em&gt;Trypanosoma cruzi&lt;/em&gt;&lt;/a&gt;, and &lt;em&gt;Toxoplasma gondii&lt;/em&gt;.  &lt;a href=&quot;http://www.radcliffehealth.com/sites/radcliffehealth.com/files/books/samplechapter/1483/Hall_final_lowres_chap8-53031280rdz.pdf&quot;&gt;Here's a list of bacterial&lt;/a&gt; ones and &lt;a href=&quot;http://www.perinatology.com/exposures/infectionlist.htm&quot;&gt;here's a list of viral&lt;/a&gt; ones.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-16T22:35:37.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10914" PostTypeId="2" ParentId="10904" CreationDate="2013-10-16T22:40:49.170" Score="1" Body="&lt;p&gt;I don't know much (read: anything) about the &lt;a href=&quot;https://en.wikipedia.org/wiki/.NET_Framework&quot; rel=&quot;nofollow&quot;&gt;.NET framework&lt;/a&gt; but a little search turned up &lt;a href=&quot;https://research.microsoft.com/en-us/projects/bio/mbf.aspx&quot; rel=&quot;nofollow&quot;&gt;Microsoft's .NET Bio&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;.NET Bio (formerly Microsoft Biology Foundation [MBF]) is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Free (as in beer) and open source!  And from &lt;a href=&quot;http://julmar.com/blog/mark/?p=143&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; it looks pretty cool.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-16T22:40:49.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10915" PostTypeId="5" CreationDate="2013-10-16T22:46:14.507" Score="0" Body="&lt;p&gt;See also &lt;a href=&quot;/questions/tagged/radiation&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;radiation&amp;#39;&quot; rel=&quot;tag&quot;&gt;radiation&lt;/a&gt; for general questions pertaining to damaging light.&lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="4101" LastEditDate="2013-10-31T19:24:45.790" LastActivityDate="2013-10-31T19:24:45.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10916" PostTypeId="4" CreationDate="2013-10-16T22:46:14.507" Score="0" Body="Non-visible light with a higher energy and shorter wavelength than violet light, UV is notable for its ability to cause DNA damage." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-16T23:54:26.503" LastActivityDate="2013-10-16T23:54:26.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10917" PostTypeId="1" AcceptedAnswerId="10930" CreationDate="2013-10-16T22:57:51.057" Score="4" ViewCount="949" Body="&lt;p&gt;I'm used to working with bacteria - some of the more common laboratory strains sometimes come with an order from some vendors.  What's the most convenient source to order &lt;a href=&quot;http://wiki.yeastgenome.org/index.php/Commonly_used_strains&quot; rel=&quot;nofollow&quot;&gt;common straings of Saccharomyces&lt;/a&gt; for lab work? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1320" LastEditDate="2013-10-20T17:53:14.327" LastActivityDate="2015-09-11T13:05:28.990" Title="Sources for common laboratory Saccharomyces strains?" Tags="&lt;yeast&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10918" PostTypeId="2" ParentId="10917" CreationDate="2013-10-17T03:21:28.297" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.atcc.org/&quot; rel=&quot;nofollow&quot;&gt;ATCC&lt;/a&gt; is the place I would go to, just like purchasing cell lines or bacterial lines. The reference ATCC catalog numbers are also listed with each of the common strains you have linked. Depending on the purpose, you could just go to your local grocery store for baker's yeast.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-10-17T03:21:28.297" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10921" PostTypeId="1" CreationDate="2013-10-17T11:28:26.427" Score="2" ViewCount="138" Body="&lt;p&gt;In our lab we would like to study the chemotaxis of PBMCs towards conditioned medium obtained following treatment of cancer cells with different compounds.&#xA;My questions are regarding the method of purification of PBMCs from whole blood:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;I have read a number of protocols saying that during the isolation process the buffers used should not contain calcium or magnesium ions, as these can cause the activation of the PBMCs. Is that so? From my knowledge Ca+2 is a second messenger only in TCR signaling. I am not sure reegarding the other cells present, and how magnesium is relevant at all.&lt;/li&gt;&#xA;&lt;li&gt;Even if I use PBS (without any calcium or magnesium ions) to isolate the PBMCs from blood, in the end I resuspend the isolated PBMCs in medium which does contain these ions. Is there any rationale to use calcium and magnesium-free buffers for the isolation when  the final medium contains these ions anyway?&lt;/li&gt;&#xA;&lt;li&gt;When I begin the assay, should the PBMCs be activated or not? In other words, do chemokines also activate the PBMCs or are chemotaxis and activation two totally independent processes? How should activation/no activation affect my results?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance.&lt;/p&gt;&#xA;" OwnerUserId="3026" LastActivityDate="2013-10-17T11:28:26.427" Title="A number of questions regarding chemotaxis assay using PBMCs" Tags="&lt;immunology&gt;&lt;cancer&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10922" PostTypeId="2" ParentId="7871" CreationDate="2013-10-17T12:56:38.747" Score="5" Body="&lt;p&gt;In GWA studies you tend to analyze your &quot;lead&quot; SNPs in regions where genotypes are correlated (known as linkage disequilibrium).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you find an association between another SNP with the outcome, and this SNP is correlated with the original variant, you can perform a &lt;em&gt;conditional&lt;/em&gt; analysis where you adjust for the original SNP in the model. This is to test if the association between the 2nd SNP is independent of the first, or whether it is just because they are correlated (in LD).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So performing a conditional analysis is just seeing if the association observed is an independent signal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At least, this is how I have interpreted it perviously!&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;E.g. SNP-A is found to be associated with increased risk of type-2 diabetes (T2D).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;SNP-B is later found to be associated with risk of T2D as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;SNP-A and SNP-B are correlated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To see if the association between SNP-B and T2D is independent of the first association, you would adjust for SNP-B in the model (a &lt;em&gt;conditional&lt;/em&gt; analysis).&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;First model: lm( T2D  ~  SNP-A + confounders)&#xA;Second model: lm( T2D  ~  SNP-A + confounders + SNP-B)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;If the association between SNP-A (and/or SNP-B) and T2D is still significant then they have some independent effect on risk of T2D. If the association disappears then they are only both associated because they are correlated in the individuals.&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2013-10-17T13:01:42.880" LastActivityDate="2013-10-17T13:01:42.880" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10923" PostTypeId="1" AcceptedAnswerId="10928" CreationDate="2013-10-17T15:22:43.367" Score="3" ViewCount="1198" Body="&lt;p&gt;I'm currently working on some ribozyme binding, and I'm looking for a tool that will essentially analyze the regions of the degree of complementarity in two sequences in order to extrapolate efficiency of binding. After thinking about it, I'm essentially looking for &quot;the opposite&quot; of BLAST, in that BLAST looks for regions of &lt;em&gt;similarity&lt;/em&gt; in sequences in the &lt;em&gt;same&lt;/em&gt; orientation, while I'm looking for  regions of &lt;em&gt;complementarity&lt;/em&gt; in sequence in the &lt;em&gt;opposite&lt;/em&gt; orientation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Does such a tool exist?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT 1&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To clarify, I'm looking for a tool that can detect the most optimal regions of complementarity in two sequences when both are aligned as such:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;5' TCGAAUAACTCGTCUGAUGAGUCGCUGAAAUGCGACGAAACCGTTAACGGA 3'&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;3'   GTTTTACGCAAAGCAGCGTAAAGTCGCTGAGTAGTCACTTTAATGAC   5'&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="307" LastEditorUserId="4101" LastEditDate="2013-10-17T16:13:03.543" LastActivityDate="2016-02-29T14:46:12.663" Title="Bioinformatics tool for &quot;pairwise alignment&quot; of complementary sequences?" Tags="&lt;bioinformatics&gt;&lt;rna&gt;&lt;blast&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10924" PostTypeId="1" AcceptedAnswerId="10950" CreationDate="2013-10-17T16:08:39.983" Score="1" ViewCount="123" Body="&lt;p&gt;What is the order in which this DNA samples would would reassociate ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;e.coli DNA&lt;/p&gt;&#xA;&#xA;&lt;p&gt;plasmid DNA&lt;/p&gt;&#xA;&#xA;&lt;p&gt;viral DNA&lt;/p&gt;&#xA;&#xA;&lt;p&gt;satellite DNA&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA-RNA hybrid&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a homework question and I have not been given any information about the condition in which they are reassociated.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-10-18T20:04:32.130" Title="Reassociation of DNA" Tags="&lt;dna&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10925" PostTypeId="5" CreationDate="2013-10-17T16:16:08.340" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2013-10-17T16:16:08.340" LastActivityDate="2013-10-17T16:16:08.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10926" PostTypeId="4" CreationDate="2013-10-17T16:16:08.340" Score="0" Body="The Basic Local Alignment Search Tool is a widely-used tool for finding and evaluating DNA or protein sequences.  Users can utilize either their own sequences or the genomes of hundreds of organisms.  It can be found at http://blast.ncbi.nlm.nih.gov/Blast.cgi" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-17T22:36:31.390" LastActivityDate="2013-10-17T22:36:31.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10928" PostTypeId="2" ParentId="10923" CreationDate="2013-10-17T17:10:50.443" Score="4" Body="&lt;p&gt;I'm not sure this is what you need since the sequences you posted are not actually complementary as far as I can tell. However, &lt;a href=&quot;https://www.ebi.ac.uk/~guy/exonerate/&quot; rel=&quot;nofollow&quot;&gt;&lt;code&gt;exonerate&lt;/code&gt;&lt;/a&gt; is one of the most powerful tools out there and can do this as well. Using these sequences as examples:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&gt;query&#xA;  TAGCTTATTGATGGGAGGAGAGTCCGTGCACATGACAGACCTTGGCTGTCCCAGACTGCAGGAAGCCCAGG&lt;br&gt;&#xA;  &gt;target&#xA;  CCTGGGCTTCCTGCAGTCTGGGACAGCCAAGTCTGTTATGTGCACGTACTCTCCTCCCCTCAATAAGCTA&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And this command (should be run on a *nix system):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;exonerate -m coding2coding -q qq.fa -t test.fa -s 0&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I get this output:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;C4 Alignment:&#xA;------------&#xA;         Query: query [revcomp]&#xA;        Target: target&#xA;         Model: genome2genome&#xA;     Raw score: 312&#xA;   Query range: 71 -&amp;gt; 0&#xA;  Target range: 0 -&amp;gt; 70&#xA;&#xA; 71 :                                                          CCA       :  6&#xA;      CCTGGGCTTCCTGCAGTCTGGGACAGCCAAGGTCTGTCATGTGCACGGACTCTCCTCProTCAATA&#xA;      |||||||||||||||||||||||||||||| |||||| ||||||||| |||||||||||+||||||&#xA;      CCTGGGCTTCCTGCAGTCTGGGACAGCCAA-GTCTGTTATGTGCACGTACTCTCCTCProTCAATA&#xA;  1 :                                                          CCC       : 65&#xA;&#xA;  5 : AGCTA :  1&#xA;      |||||&#xA; 66 : AGCTA : 70&#xA;&#xA;vulgar: query 71 0 - target 0 70 + 312 M 30 30 G 1 0 M 26 26 C 3 3 M 11 11&#xA;&#xA;C4 Alignment:&#xA;------------&#xA;         Query: query&#xA;        Target: target [revcomp]&#xA;         Model: genome2genome&#xA;     Raw score: 309&#xA;   Query range: 0 -&amp;gt; 71&#xA;  Target range: 70 -&amp;gt; 0&#xA;&#xA;  1 :                      GTC                                           : 66&#xA;      TAGCTTATTGATGGGAGGAGAValCGTGCACATGACAGACCTTGGCTGTCCCAGACTGCAGGAAGC&#xA;      ||||||||||| |||||||||||+||||||||| ||||| ||||||||||||||||||||||||||&#xA;      TAGCTTATTGAGGGGAGGAGAValCGTGCACATAACAGA-CTTGGCTGTCCCAGACTGCAGGAAGC&#xA; 70 :                      GTA                                           :  6&#xA;&#xA; 67 : CCAGG : 71&#xA;      |||||&#xA;  5 : CCAGG :  1&#xA;&#xA;vulgar: query 0 71 + target 70 0 - 309 M 21 21 C 3 3 M 15 15 G 1 0 M 31 31&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Basically it gives you two alignments, one reading the target 3-&gt;5 and the query 5-&gt;3 and one the other way around. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, you could do a translated blast search, tBLASTx which will translate both target and query sequence and so, should find complementary regions.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-10-21T15:31:07.317" LastActivityDate="2013-10-21T15:31:07.317" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="10929" PostTypeId="2" ParentId="10882" CreationDate="2013-10-17T17:15:52.267" Score="2" Body="&lt;p&gt;What I think the question is &quot;Why wouldn't an organism be more efficient from selection than the environment demands?&quot;  Please let me know if I'm hitting the mark here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A scenario suggested by the question is this: If there is selection pressure on say an animal to resist a disease, and then it evolves two resistance systems to the disease.  This could be an immune response and a taste for a certain plant containing compounds with remedial properties.  If either system is adequate to resist the disease, hasn't selection gone above and beyond what is needed? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, the answer is either not recently, or all the time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, for 'not really' you have to consider the &lt;a href=&quot;http://en.wikipedia.org/wiki/Red_Queen%27s_Hypothesis&quot; rel=&quot;nofollow&quot;&gt;importance of competition.  Reading about the Red Queen's Hypothesis is helpful here.&lt;/a&gt;. First there is a natural random mutation rate, which can cause one of the system to become less effective.  Or if the disease is also changing to increase its efficiency, then either one or both of the defense mechanisms in this case would fail from time to time.  Then having two systems would not be too much. There is a clear benefit to having redundant systems of resistance here. For both these broad categories of reasons, you have much redundancy and interdependence among the genes which create traits in living things (phenotypes).  Because of the background mutation rate, traits which are not needed disappear relatively quickly; because of competition, those which convey an advantage, even if a small one, have a strong likelihood to stay in the gene pool.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;now: &quot;all the time&quot; There are cases where traits are exhibited that are not efficient though. Evolution works over generations, typically selection influences traits on the order of 10s of generations and the population can show traits which are not helpful if the environment or the competition has changed drastically.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of this is the current obesity epidemic in the developing world. The sudden availability of cheap food has caused those people who have access to become obese.  This is because they have a heavily reinforced trait to save up fat because humans experience famines regularly.  Its going to take a long time before efficient energy storage in human beings is lost.  In the meantime, people are not living to reproducing age at the same level of fitness they might have.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to add a note on genetic algorithms.  The difference between genetic algorithms to achieve the same efficiencies as biological systems are worth thinking about:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;As far as failing to find a global minimum, natural selection usually has many more samples.  A typical selection experiment with flies or worms often have thousands or tens of thousands of individuals screened.  GA models of reasonable complexity have usually a few score at most - am I right?  A bacterial or yeast experiment can have 10^9 individuals. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The genetic system of the chromosome itself is tremendously complex.  We can't even model itself and so the product of millions of generations of selection already will has a heretofore unmodelable response to selection. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The typical selection environment is equally undefinable, so a survey of living things in a complex environment has unpredictable effects.  While most of us think as laboratory experiments as being less complex, its not completely true.  I was at a talk recently that mentioned how E coli K12 seems to have diverged in various laboratory environments despite the fact that its mostly been in frozen stocks since being isolated in the mid 20th century.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-10-18T14:28:14.243" LastActivityDate="2013-10-18T14:28:14.243" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10930" PostTypeId="2" ParentId="10917" CreationDate="2013-10-17T18:19:04.043" Score="2" Body="&lt;p&gt;The &lt;em&gt;Saccharomyces Genome Database&lt;/em&gt; has a list of sources &lt;a href=&quot;http://wiki.yeastgenome.org/index.php/Strains&quot; rel=&quot;nofollow&quot;&gt;here.&lt;/a&gt; One of them is the &lt;em&gt;Japanese Yeast Genetic Stock Center&lt;/em&gt;: I checked their site out and found that they charge &amp;yen;390 per strain which is around USD4. There is also a USD5 fee on all orders. I searched for a couple of standard strains, and these were in the catalogue, so it looks like a good possibility. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Incidentally I have used USD here rather than $ because there seems to be a bug when typing that symbol  twice in a post - try it and you'll see what I mean.)&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-10-17T18:19:04.043" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10931" PostTypeId="2" ParentId="10882" CreationDate="2013-10-17T20:30:12.640" Score="1" Body="&lt;p&gt;Im going to take a stab at this. I think he is saying that sometimes there will be mutations that will occur in a population that are beneficial, but only in certain environments. But he is asking, wont these mutations be eliminated often, since they may not be in an environment where their advantage is obvious?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, there is something incorrect in your original post. You said &quot;From what I understand some genes will be lost because they won't be suited enough to continue in the next generation&quot;. It is kind of unusual for a whole gene to be lost. Especially from a whole population! I think what you mean is 'allele'. And yes some alleles will be lost. But fitness is a gradient. Just because a mutation does not have an obvious advantage does not mean it will be lost. Most mutations are not really noticeable. In a recent post here, I think I quoted a website that says there are 70 or so de novo mutations every generation in humans. This means that both you and I have 70 new mutations that our parents did not. But we are both functioning just fine (I hope!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And some of these mutations may be beneficial in certain environments, but dont do anything in others. Lets say that one of my de novo mutations was to make me sweat less. Not really noticeable, right? And it really wont give me fitness advantage or disadvantage, so natural selection wont really act on it. It's frequency should remain at about a constant level in the population . But now lets say something happens to the world climate and there is a drought that lasts for centuries over N. America. My mutation would now give me a fitness advantage since my body would lose less water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to answer what I think your question was, natural selection will not always act on every mutation. It has to clearly give a fitness disadvantage to select against it, or an advantage to select for it. So if it gives no immediate advantage, it may not spread through the gene pool very quickly, if at all, but it will still be there. So when it is in an environment where it is advantageous, it will still be around, and then it will begin to spread through the population.&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-10-17T20:30:12.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10932" PostTypeId="1" AcceptedAnswerId="10933" CreationDate="2013-10-17T21:36:40.583" Score="0" ViewCount="757" Body="&lt;p&gt;I was reading an article, when I read a sentence saying, &lt;strong&gt;His mother ... nearly died less than three years later during Mathers' 73-hour birth.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does mean by 73-hour birth?&lt;/p&gt;&#xA;" OwnerUserId="4674" LastActivityDate="2013-10-17T22:20:38.970" Title="What is meant by 73 hour birth" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2013-10-18T11:02:20.140" ContentLicense="CC BY-SA 3.0" />
  <row Id="10933" PostTypeId="2" ParentId="10932" CreationDate="2013-10-17T22:20:38.970" Score="1" Body="&lt;p&gt;I could find that topic related to &lt;a href=&quot;http://en.wikipedia.org/wiki/Eminem&quot; rel=&quot;nofollow&quot;&gt;Eminem's&lt;/a&gt; mother, Debbie Mathers-Briggs, who almost died delivering her first son(Eminem) at the end of a 73-hour labor or 73-hour birth. That &quot;73 hour birth&quot; means she was in labor(to undergo the efforts of childbirth) for &quot;73 hours&quot;.&lt;/p&gt;&#xA;" OwnerUserId="4547" LastActivityDate="2013-10-17T22:20:38.970" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10934" PostTypeId="1" CreationDate="2013-10-17T22:50:28.147" Score="2" ViewCount="760" Body="&lt;p&gt;In &lt;a href=&quot;http://www.bbc.co.uk/news/health-24567412&quot; rel=&quot;nofollow&quot;&gt;this BBC news article&lt;/a&gt; a study shows that during sleep brain cells shrink to open up the gaps between neurons and allow fluid to wash the brain clean.  But do the cells shrink and undergo the whole procedure during REM sleep and lucid dreaming?&lt;/p&gt;&#xA;" OwnerUserId="4497" LastEditorUserId="4101" LastEditDate="2013-10-18T01:16:17.453" LastActivityDate="2014-03-19T14:50:05.247" Title="Do brain cells shrink during REM sleep or a lucid dream?" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;brain&gt;&lt;sleep&gt;&lt;dreaming&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10935" PostTypeId="2" ParentId="10934" CreationDate="2013-10-18T00:11:51.993" Score="2" Body="&lt;p&gt;For those who have access, &lt;a href=&quot;http://www.sciencemag.org/content/342/6156/373.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;here's the full text&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having read the paper, I can't give you a good answer.  This study was performed in mice, not humans, and &quot;sleep&quot; was achieved in a few ways.  Mice normally sleep most of the day, so it was easy to get mice sleeping normally.  They also induced &quot;sleep&quot; through anesthesia (incidentally, they saw these same results in anesthetized mice, which I think is &lt;em&gt;quite&lt;/em&gt; interesting).  The state of &quot;sleep&quot; was confirmed mainly through the measurement of &lt;a href=&quot;https://en.wikipedia.org/wiki/Neural_oscillation&quot; rel=&quot;nofollow noreferrer&quot;&gt;brain waves&lt;/a&gt;, in particular the &lt;a href=&quot;https://en.wikipedia.org/wiki/Delta_wave&quot; rel=&quot;nofollow noreferrer&quot;&gt;delta wave&lt;/a&gt;.  Delta waves correlate to deep sleep, and that's what they measured.  Panels D and G from figure 1 (below) basically confirm just that - the mice were asleep - and that's all we know so far.  More exciting research to be done!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CNvOJ.jpg&quot; alt=&quot;Figure 1&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-18T00:11:51.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10936" PostTypeId="1" CreationDate="2013-10-18T02:52:02.460" Score="2" ViewCount="244" Body="&lt;p&gt;Question is rather self-explanatory. I'm looking for a non-cleavable RNA sequence to act as an RNA linker. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I mention 3- or 4-nucleotides only, but making such a sequence with 2 nucleotides is rather easy as seen below, but I've encountered some difficulties in transcription.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;GAGGAAGGGAAAGGGGAAAAGGGGGAAAAA...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This also works for just about any random sequence of G's and A's.&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="307" LastEditDate="2013-10-18T14:28:28.873" LastActivityDate="2014-01-19T02:15:50.513" Title="Are there known 3- or 4-nucleotide RNA linkers with no RE sites?" Tags="&lt;rna&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10937" PostTypeId="2" ParentId="10894" CreationDate="2013-10-18T07:46:22.717" Score="1" Body="&lt;p&gt;To construct the G-matrix you need additive genetic variances and covariances for all traits, so you normally need results from breeding experiments (e.g. phenotypic midparent-offspring data), that you can do parent-offspring regressions on. Don't know any good online sources but see &lt;a href=&quot;http://books.google.no/books?id=hFjNvMWBk14C&amp;amp;pg=PA535&amp;amp;lpg=PA535#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot; title=&quot;Balding et al. 2007. Handbook of Statistical Genetics, Volume 1. Wiley&quot;&gt;Balding et al. 2007&lt;/a&gt; p. 534ff for some info. I've seen methods that claim that the G-matrix can be estimated directly from phenotypic data from unrelated individuals (e.g. &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs12041-011-0021-x&quot; rel=&quot;nofollow&quot; title=&quot;Zintzaras. 2011. Estimating genetic correlations based on phenotypic data: a simulation-based method.&amp;quot; Journal of Genetics 90(1): 51-58&quot;&gt;Zintzaras 2011&lt;/a&gt;) or from genomic info e.g. SNPs (&lt;a href=&quot;http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002637&quot; rel=&quot;nofollow&quot; title=&quot;Vattikuti et al. 2013. Heritability and Genetic Correlations Explained by Common SNPs for Metabolic Syndrome Traits. PLOS Genetics&quot;&gt;Vattikuti et al. 2013&lt;/a&gt;), but are not familiar with these and do not know how reliable they are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A clear background on using mixed models to estimate the G-matrix, including examples/tutorials, can be found in &lt;a href=&quot;http://www.wildanimalmodels.org/tiki-download_wiki_attachment.php?attId=22&quot; rel=&quot;nofollow&quot; title=&quot;Wilson et al. 2009. An ecologist’s guide to theanimal model. Journal of Animal Ecology 79: 13–2.&quot;&gt;Wilson et al (2009)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or did you have something else/something more specific in mind?&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-10-21T09:01:20.600" LastActivityDate="2013-10-21T09:01:20.600" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="10938" PostTypeId="1" CreationDate="2013-10-18T10:10:49.620" Score="4" ViewCount="1094" Body="&lt;p&gt;The oxygen anion in the phosphate group is likely to be bonded with a hydrogen cation and thus forming a hydroxyl.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the phosphate group is condensed with glycerol to make a phospholipid, is the hydroxyl from the glycerol molecule taken or the hydroxyl from the phosphate group taken?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe it's related to the difference of electronegativity of oxygen and phosphorus which causes unequal sharing of electrons between atoms, thus making a hydroxyl from one side easier to get taken off than the hydroxyl from the other side is.&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2015-05-29T05:45:11.767" Title="Which hydroxyl from either the phosphate or the glycerol is taken during synthesis of a phospholipid head?" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10939" PostTypeId="2" ParentId="1515" CreationDate="2013-10-18T11:56:13.820" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://www.frozenevolution.com/origin-rh-blood-group-polymorphism&quot; rel=&quot;nofollow&quot;&gt;http://www.frozenevolution.com/origin-rh-blood-group-polymorphism&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The high proportion of Rh-negative persons in the European population&#xA;  could be connected with the fact that, until recently, big cats (the&#xA;  definitive host of Toxoplasma gondii) were practically not present&#xA;  here and thus toxoplasmosis was rare (and Rh-negative persons were at&#xA;  an advantage compared to the rest of the population). The low&#xA;  percentage of Rh-negative persons in Africa (less than 1%) could be&#xA;  related to the high prevalence of toxoplasmosis there, which often&#xA;  approaches 100%.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4695" LastEditorUserId="107" LastEditDate="2013-10-18T12:58:25.483" LastActivityDate="2013-10-18T12:58:25.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10940" PostTypeId="2" ParentId="1515" CreationDate="2013-10-18T12:21:40.367" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://www.sott.net/article/228188-Toxoplasma-gondii-Cat-parasite-may-affect-cultural-traits-in-human-populations&quot; rel=&quot;nofollow&quot;&gt;http://www.sott.net/article/228188-Toxoplasma-gondii-Cat-parasite-may-affect-cultural-traits-in-human-populations&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Lafferty suggested that because climate affects the persistence of&#xA;  infectious states of Toxoplasma in the environment, it helps drive the&#xA;  geographic variation in the parasite's prevalence by increasing&#xA;  exposure risk. The parasite's eggs can live longer in humid,&#xA;  low-altitude regions, especially at mid latitudes that have infrequent&#xA;  freezing and thawing. Cultural practices of food preparation such as&#xA;  rare or undercooked meats, or poor hygiene, can increase exposure to&#xA;  infection, as can having cats as pets. Lafferty added, &quot;Toxoplasmosis&#xA;  is one of many factors that may influence personality and culture,&#xA;  which may also include the effects of other infectious diseases,&#xA;  genetics, environment and history. Efforts to control this infectious&#xA;  pathogen could bring about cultural changes.&quot;   / this is why I feel&#xA;  rh- is a newer blood grouping due to the last ice age conditions.&#xA;  these were the conditions in nw Europe back then and the rh- trait has&#xA;  persisted in that area. it just all makes sense . you may also search&#xA;  out &quot; congenital toxoplasmosis infection &quot; and I believe you will find&#xA;  when a pregnant woman gets toxo infection the baby comes out with the&#xA;  same symptom ology as erythroblastosis fetalis, rhesus disease.this is&#xA;  why all pregnant women are cautioned to avoid cat feces and stay away&#xA;  from cat boxes where they defecate.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;OPINION ? i'll have you know i'm 61 y old retired medical worker who has studied biology and etc my whole life . this opinion is not just anyone's .  btw i'm o- myself  /&lt;/p&gt;&#xA;" OwnerUserId="4695" LastEditorUserId="107" LastEditDate="2013-10-18T12:59:16.753" LastActivityDate="2013-10-18T12:59:16.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10942" PostTypeId="2" ParentId="1515" CreationDate="2013-10-18T12:52:38.227" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18766148&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/18766148&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;RESULTS:&lt;/p&gt;&#xA;&lt;p&gt;RhD-positive subjects have been confirmed to be less sensitive to the influence of latent toxoplasmosis on reaction times than Rh-negative subjects. While a protective role of RhD positivity has been demonstrated previously in four populations of men, the present study has shown a similar effect in 226 female students. Our results have also shown that the concentration of testosterone in saliva strongly influences (reduces) reaction times (especially in men) and therefore, this factor should be controlled in future reaction times studies.&lt;/p&gt;&#xA;&lt;p&gt;CONCLUSIONS:&lt;/p&gt;&#xA;&lt;p&gt;The observed effects of RhD phenotype could provide not only a clue to the long-standing evolutionary enigma of the origin of RhD polymorphism in humans (the effect of balancing selection), differences in the RhD+ allele frequencies in geographically distinct populations (resulting from geographic variation in the prevalence of Toxoplasma gondii), but might also be the missing piece in the puzzle of the physiological function of the RhD molecule.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4695" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-18T13:16:02.947" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10944" PostTypeId="2" ParentId="10938" CreationDate="2013-10-18T16:43:00.513" Score="0" Body="&lt;p&gt;My recollection is that the formation of a phospholipid normally involves acylation of glycerol 3-phosphate. Glycerol 3-phosphate is a glycolytic intermediate, and so there is no actual phosphorylation of a glycerol; the phosphate on the glycerol will have come from the phosphorylation of glucose or of fructose 6-phosphate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a kinase reaction the oxygen of the -OH in the acceptor acts as a nucleophile at the P of the phosphate, so in terms of your question the O atom comes from the acceptor, not the donor. Presumably if there was a glycerol kinase (I expect there is) it would have the same mechanism so the O would come from the glycerol.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-10-18T16:43:00.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10945" PostTypeId="1" AcceptedAnswerId="13824" CreationDate="2013-10-18T17:30:32.883" Score="5" ViewCount="22846" Body="&lt;p&gt;As seen under a &lt;a href=&quot;http://en.wikipedia.org/wiki/Polarized_light_microscopy&quot; rel=&quot;nofollow noreferrer&quot;&gt;polarization microscope&lt;/a&gt;,&lt;img src=&quot;https://i.stack.imgur.com/0pejh.gif&quot; alt=&quot;enter image description here&quot;&gt; the &lt;strong&gt;A-Band&lt;/strong&gt; in skeletal muscle fibres is so named because it is &lt;em&gt;anisotropic&lt;/em&gt; in its refractive index which is a characteristic of orderly crystalline structure. On the other hand, the &lt;strong&gt;I-Band&lt;/strong&gt; is so named because of its &lt;em&gt;isotropic&lt;/em&gt; nature, as far as its refractive index is considered, which is characteristic of Amorphous substances or substances which lack long-range order. Both are &lt;em&gt;filamentous&lt;/em&gt; (as opposed to globular) in the sarcomere (Actin is present as F-Actin).   &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But then why this difference in the characteristics of refractive index,&#xA;  which is indicative of order (i.e crystalline or amorphous?) in their&#xA;  molecular structure?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Moreover, is the &lt;strong&gt;H-Band&lt;/strong&gt; anisotropic?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, then the anisotropy of the remaining part of &lt;strong&gt;A-Band&lt;/strong&gt; must be a consequence of the relative arrangement of Actin and Myosin which are independently isotropic, and hence cannot give a possible isotropic arrangement.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If yes, then that indicates that the myosin filaments are anisotropic in themselves and actin filaments are isotropic. But, in the region of their overlapping (&lt;strong&gt;A-Band minus H-Band&lt;/strong&gt;), the overlap is between an anisotropic (myosin) and an isotropic (actin) component which shouldn't be anisotropic because the randomness of actin filaments (i.e. its isotropicity) should make the entire configuration isotropic?   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am sorry if I am wrong in my understanding of isotropic and anisotropic characteristics, or if my question sounds too &quot;physics-related&quot;, but this has been bothering me for quite some while now.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://physics.stackexchange.com/questions/82124/anisotropic-refractive-index-with-isotropic-components&quot;&gt;Here&lt;/a&gt; is a directly related question I asked on physics.se. It partly solves the problem of possible arrangement of isotropic elements to generate anisotropy.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="-1" LastEditDate="2017-04-13T12:40:13.457" LastActivityDate="2014-01-07T21:03:53.530" Title="Isotropy of sarcomere bands in skeletal muscle cells" Tags="&lt;structural-biology&gt;&lt;biophysics&gt;&lt;microscopy&gt;&lt;histology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10946" PostTypeId="1" AcceptedAnswerId="10947" CreationDate="2013-10-18T19:08:28.283" Score="1" ViewCount="40" Body="&lt;p&gt;Most of the time, our genes have common interests with our &quot;self&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We reproduce well if and only if our genes reproduce well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In some cases, like in bees, the haploid bees can survive better if they help their queen reproduce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In humans and other species, are there samples that give individuals &quot;incentive&quot; to help non family member to reproduce for the sake of their genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;No filial altruism&lt;/li&gt;&#xA;&lt;li&gt;No reciprocal altruism&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So I need a sample between individual based evolution and gene base evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, many genocide are done against the best and brightest. I wonder what sort of genes encode &quot;kill the best and brightest&quot; and how does that kind of gene survive well in the gene pool?&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="3632" LastEditDate="2013-10-18T19:18:57.307" LastActivityDate="2013-10-18T20:00:53.593" Title="What are examples of genes succesfully reproducing in ways that is in conflict with helping the individual creating offspring" Tags="&lt;evolutionary-game-theory&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10947" PostTypeId="2" ParentId="10946" CreationDate="2013-10-18T19:29:16.487" Score="3" Body="&lt;p&gt;The prototypical example of this is &lt;em&gt;t&lt;/em&gt;, whose existence was predicted by &lt;a href=&quot;http://en.wikipedia.org/wiki/Robert_Trivers&quot; rel=&quot;nofollow&quot;&gt;Robert Trivers&lt;/a&gt; and featured prominently in &lt;a href=&quot;http://en.wikipedia.org/wiki/Selfish_gene&quot; rel=&quot;nofollow&quot;&gt;the Selfish Gene&lt;/a&gt;.  The current dominant point of view in evolutionary biology is that genes act in their own interest and even the 'self' is just a manifestation of the gene's reproductive properties.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;t&lt;/em&gt; is a locus in some male mice. &lt;a href=&quot;http://books.google.com/books/about/Genes_in_Conflict.html?id=-_IhmQEACAAJ&quot; rel=&quot;nofollow&quot;&gt;The &lt;em&gt;t&lt;/em&gt; gene characterizes very well the selfishness of a selfish gene&lt;/a&gt;.  While most paternal genes are found in 50% of offspring, &lt;em&gt;t&lt;/em&gt; is found in over 3/4 of offspring.  Somehow it manages to reproduce at the &lt;em&gt;expense of the other loci in the male mouse&lt;/em&gt;.  &lt;em&gt;t&lt;/em&gt; itself is not known to convey any advantages to its host organism.  the males tend to be smaller and sometimes even reproductively disadvantaged.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does that go some way to answering this question?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Animal behavior such as cheating or adopting are often interpretable as reproductive advantages.  Killing the best and brightest definitely are to the advantage of those who are doing the killing.  This SNL Skit has always said it best to me. &quot;&lt;a href=&quot;http://snltranscripts.jt.org/79/79shominids.phtml&quot; rel=&quot;nofollow&quot;&gt;... and now I am smart!&lt;/a&gt;&quot;.  Such kill offs so rarely include killing one's own offspring.  I'm not sure they can be called in conflict with reproductive advantage.  EO Wilson's essay &quot;On Human Nature&quot; does a reasonable case for saying that wars and famines are in fact produced by evolutionary advantage, however cruel and ugly they may be. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-10-18T19:29:16.487" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10948" PostTypeId="2" ParentId="10923" CreationDate="2013-10-18T19:54:02.150" Score="2" Body="&lt;p&gt;You could try using a tool to estimate the binding affinities of the two sequences, i.e. OligoCalc&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.basic.northwestern.edu/biotools/OligoCalc.html&quot; rel=&quot;nofollow&quot;&gt;http://www.basic.northwestern.edu/biotools/OligoCalc.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4696" LastActivityDate="2013-10-18T19:54:02.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10949" PostTypeId="2" ParentId="10946" CreationDate="2013-10-18T20:00:53.593" Score="1" Body="&lt;p&gt;Complex behaviours like altruism rarely boil down to a single gene, so it's hard to find a concrete example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is one lead:&#xA;&lt;a href=&quot;http://scan.oxfordjournals.org/content/early/2010/10/28/scan.nsq083.full&quot; rel=&quot;nofollow&quot;&gt;http://scan.oxfordjournals.org/content/early/2010/10/28/scan.nsq083.full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you think about it, being altruistic is detrimental to your personal fitness, but inproves the fitness of the population (within certain parameters).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've only ever heard of clear examples of this in simple game-theoretic simulations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There may be some good examples here:&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Kin_selection&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Kin_selection&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HTH&lt;/p&gt;&#xA;" OwnerUserId="4696" LastActivityDate="2013-10-18T20:00:53.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10950" PostTypeId="2" ParentId="10924" CreationDate="2013-10-18T20:04:32.130" Score="2" Body="&lt;p&gt;The rate is determined by the size and complexity of the sequence. Short, non-repetitive sequences should re-associate (at a given r.t.p.) faster than longer, repetitive DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm guessing that that is what this question is getting at.&lt;/p&gt;&#xA;" OwnerUserId="4696" LastActivityDate="2013-10-18T20:04:32.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10952" PostTypeId="2" ParentId="714" CreationDate="2013-10-19T01:57:30.267" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;People with blood type O are more resistant to malaria and syphilis&#xA;  than those with the A and/or B proteins.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From the &lt;a href=&quot;http://books.google.com/books?id=YRcAVvmE6eMC&amp;amp;pg=PA40&amp;amp;lpg=PA40&amp;amp;dq=type%20o%20blood%20are%20more%20resistant%20to%20syphilis&amp;amp;source=bl&amp;amp;ots=o7PjHip_kh&amp;amp;sig=m3q9yz-tSu4TlxL37sAaYthKIEM&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=-eVhUufrOo-K9ASZ3IEY&amp;amp;ved=0CC4Q6AEwAA#v=onepage&amp;amp;q=type%20o%20blood%20are%20more%20resistant%20to%20syphilis&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Encyclopedia of Evolution, Stanley A. Rice&lt;/strong&gt;, page 40&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4695" LastEditorUserId="16310" LastEditDate="2015-06-23T10:51:19.837" LastActivityDate="2015-06-23T10:51:19.837" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10954" PostTypeId="2" ParentId="7400" CreationDate="2013-10-19T12:54:04.970" Score="1" Body="&lt;p&gt;Think of it this way: Life always goes uphill, from less developed to more adapted, better at surviving and reproducing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Early life would be a basic mechanism, trivial in nature, that under the right conditions would kind of replicate itself (kind of, since the replica would be less similar to the original, than when comparing current parent-child similarity). This would basically be a cell. And a cell would remain a cell unless combining with other cells and specializing in functionality would have a certain benefit. Check out &lt;a href=&quot;http://www.youtube.com/watch?v=U6QYDdgP9eg&quot; rel=&quot;nofollow&quot;&gt;this educational video on abiogenesis&lt;/a&gt; by cdk007, based on Jack Szostak's work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, you know that evolution isn't the process of change of all individuals of a species in a single direction, towards another species. It's a process of forking. So, basic cells of species A could evolve into single cells of species B, but that would only mean the extinction of A if the new environment with the new organisms becomes hostile, if resources are scarce, if species A is less adapted than everyone else, so everyone else occupies A's niche.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, when multicellular organisms evolve, there are A LOT of monocellular organisms already present and occupying important niches. All available sources of energy are being used. If something isn't used - it's a new niche for any accidental mutation that enables the organism to use that niche and prosper as a new species. So anyway you look at it, multicellular organisms won't start existing without single cell organisms surrounding them. So all multicellular organisms will have an environment that includes these &quot;bacteria&quot;, so they will adapt to this environment. It's easier to learn to live with something rather than learning to fight with them and then occupy their niche, because the killing and changing to occupy the niche requires much more changes in the organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Life on earth is balanced, such as each species occupies its important place in the circulation of substances. This happened not just by chance, but it's the only probable outcome from the process of evolution by natural selection. Having a world that's totally rid of any trace of primitive life forms is next to impossible. On earth we still have species of archaea that are similar to species present on earth billions of years ago. Read &lt;a href=&quot;http://en.wikipedia.org/wiki/Nanoarchaeum_equitans&quot; rel=&quot;nofollow&quot;&gt;this article on Wikipedia&lt;/a&gt; about &lt;code&gt;Nanoarchaeum equitans&lt;/code&gt; to get a grasp on the diversity of life.&lt;/p&gt;&#xA;" OwnerUserId="4701" LastActivityDate="2013-10-19T12:54:04.970" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10955" PostTypeId="1" AcceptedAnswerId="10978" CreationDate="2013-10-19T14:21:42.153" Score="3" ViewCount="617" Body="&lt;p&gt;Please can you give me a very brief explanation about all functions in the ventral stream architecture summarized in this figure: &lt;img src=&quot;https://i.stack.imgur.com/ZlFnp.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This figure is from Serre et al.'s &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17925239&quot; rel=&quot;nofollow noreferrer&quot;&gt;A quantitative theory of immediate visual recognition&lt;/a&gt;. Prog Brain Res. 2007.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read multiple articles about this model, but I still don't understand the basic aim, especially behind the two operations (Gaussian-like and max-like operations).. So please can someone explain to me in details the ventral stream pathway (from V1-V2-V4-IT-PFC) including the two operations in this model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example : I don't understand how the cells in S1 are constructed...&lt;/p&gt;&#xA;" OwnerUserId="4702" LastEditorUserId="460" LastEditDate="2013-10-20T19:41:25.423" LastActivityDate="2013-10-20T20:14:37.153" Title="Ventral stream pathway and architecture proposed by Poggio's group" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;vision&gt;&lt;computational-model&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10957" PostTypeId="1" CreationDate="2013-10-19T15:53:30.873" Score="4" ViewCount="86" Body="&lt;p&gt;I just read about the &lt;a href=&quot;http://www.sciencedaily.com/releases/2013/10/131017173906.htm&quot; rel=&quot;nofollow&quot;&gt;discovery of the 1.8-million-year-old human skull in Georgia&lt;/a&gt;, and how it suggests that early humans were all one species instead of distinct ones. Would an archaeologist unearthing dog bones a million years from now know that a Great Dane and a Chihuahua are the same species?&lt;/p&gt;&#xA;" OwnerUserId="4705" LastEditorUserId="4101" LastEditDate="2013-10-31T21:15:20.000" LastActivityDate="2013-11-30T21:53:28.983" Title="How much can you learn about species variation from a skeleton?" Tags="&lt;evolution&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10958" PostTypeId="1" CreationDate="2013-10-19T18:33:41.480" Score="7" ViewCount="616" Body="&lt;p&gt;I´m using water container placed on a radiator to humidify room air. Someone might argue that it is a perfect nest for bacteria. I have to put copper coins into the water to kill the bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to do an experiment, have two similair containers filled with water one with copper coins, the other without them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to compare how many bacteria are living in those containers, how can I do that? (in home conditions)&lt;/p&gt;&#xA;" OwnerUserId="4707" LastEditorUserId="1320" LastEditDate="2013-10-19T21:42:26.177" LastActivityDate="2014-08-19T03:55:22.950" Title="How to measure bacterial content" Tags="&lt;bacteriology&gt;&lt;experimental-design&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10959" PostTypeId="1" AcceptedAnswerId="10960" CreationDate="2013-10-19T18:47:32.440" Score="5" ViewCount="157" Body="&lt;p&gt;In 1950, Bragg, Kendrew and Perutz published &quot;&lt;a href=&quot;http://rspa.royalsocietypublishing.org/content/203/1074/321.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;Polypeptide chain configurations in crystalline proteins&lt;/a&gt;&quot; (&lt;em&gt;open access&lt;/em&gt;) and were famously 'proved wrong' by Pauling, Corey and Branson the following year, in the paper that documented the alpha and gamma helices, &quot;&lt;a href=&quot;http://www.pnas.org/cgi/reprint/37/4/205&quot; rel=&quot;noreferrer&quot;&gt;Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain&lt;/a&gt;&quot; (&lt;em&gt;also OA&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm reading about this (as reviewed &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC208735/pdf/10011207.pdf&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; for example) where the idea is that Bragg &lt;em&gt;et al&lt;/em&gt; were disproved - in the words of the Pauling paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;None of these authors propose either our 3.7-residue [α] helix or our 5.1- residue [γ] helix. On the other hand, we would eliminate by our basic postulates all of the structures proposed by them. The reason for the difference in results obtained by other investigators and by us through essentially similar arguments is that both Bragg and his collaborators . . . discussed in detail only helical structures with an integral number of residues per turn, and moreover assume only a rough approximation to the requirements about interatomic distances bond angles, and planarity of the conjugated amide group, as given by our investigations of simpler substances. We contend that these stereochemical features must be very closely retained in stable configurations of polypeptide chains in proteins, and that there is no special stability associated with an integral number of residues per turn in the helical molecule.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There was one however, the &lt;a href=&quot;http://en.wikipedia.org/wiki/3_10_helix&quot; rel=&quot;noreferrer&quot;&gt;3&lt;sub&gt;10&lt;/sub&gt; helix&lt;/a&gt; which was correctly identified by Perutz's group in 1950. I don't have any access to library facilities at present and online resources aren't quite the same as a solid textbook. I'm wondering if any of the other forms described were in fact correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To list, these were:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2&lt;sub&gt;7&lt;/sub&gt;a&lt;/li&gt;&#xA;&lt;li&gt;2&lt;sub&gt;7&lt;/sub&gt;b&lt;/li&gt;&#xA;&lt;li&gt;2&lt;sub&gt;8&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;2&lt;sub&gt;13&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;2&lt;sub&gt;14&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;3&lt;sub&gt;8&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;( 3&lt;sub&gt;10&lt;/sub&gt; )&lt;/li&gt;&#xA;&lt;li&gt;4&lt;sub&gt;11&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;4&lt;sub&gt;13&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;2&lt;sub&gt;13&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I'll continue looking in the meantime but it's hard to search when there are subscripts in names, and I would think more experienced protein scientists could give me a quicker answer (or just direct me to where I should be reading)&lt;/p&gt;&#xA;" OwnerUserId="4202" LastActivityDate="2013-10-21T17:35:51.493" Title="Which of Perutz et al's protein structures other than 3₁₀ helix were correct?" Tags="&lt;proteins&gt;&lt;structural-biology&gt;&lt;protein-folding&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10960" PostTypeId="2" ParentId="10959" CreationDate="2013-10-19T19:37:40.833" Score="4" Body="&lt;p&gt;I think you've got the list of good predictions from the Bragg, Perutz, and Kendrick paper.  And the 3&lt;sub&gt;10&lt;/sub&gt; helix was not really right either - it did turn out to show up occasionally in protein structures though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the time all of these secondary structure elements were well evidenced from noncrystalline diffraction data and small molecule crystal structures. Examples being collagen from hair and spider silk fiber diffraction patterns. Fiber diffraction of hair, whose ordered structure consists mainly of alpha helices somewhat aligned to the fiber axis (along the length of the hair) or the mainly beta sheets which constitute silk.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because it was known that these substances contain mainly protein, building models which would show how regular peptide polymers would produce these patterns.  This happened in chemistry and physics departments worldwide.  The paper you cite is representative to the field.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12966187&quot; rel=&quot;nofollow&quot;&gt;Pauling caused a splash in the spring of 1951 by publishing descriptions of the alpha helix and the beta sheet&lt;/a&gt; (both parallel and antiparallel).  The main advantage that Pauling had was that he had studied the structure of simple di-amino acid structures (notably glycyl-glycine) and understood that the peptide bond had some double bond like properties which prevented it from rotating freely.  As the discoverer of &lt;a href=&quot;http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1954/&quot; rel=&quot;nofollow&quot;&gt;valence bond theory&lt;/a&gt;, which united quantum mechanics and chemistry and established the basis for at least most organic/biological chemical structures Pauling must have been practically alone in this insight at the time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This next set the stage for the dramatic race to discover the structure of DNA. If you read &lt;a href=&quot;http://www.brown.edu/Courses/BI0020_Miller/dh/guide.html&quot; rel=&quot;nofollow&quot;&gt;Watsons' memoir&lt;/a&gt;, he describes how the MRC in Cambridge was still feeling the heat,  competing with CalTech and Pauling.  He and the young lab there was holding their own against the MRC Cambridge with its multiple nobel laureates; a lab which had established the relationship of x-ray diffraction and chemical structure (the notes on chapter 7 are interesting - follow the link).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking back on it, Pauling's main advantage was that he understood the peptide bond better than the rest of the world. By the time DNA was being resolved, the conformations of organic molecules were understood by many and the playing field should have been more level.  I'm not sure I buy the arguments that Pauling would have got the structure without seeing the diffraction patterns and even then maybe not. I might not give such strong credence to the idea that Pauling would have gotten the DNA structure so quickly if he had been able to travel.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course Perutz and Kendrew verified the peptide alpha helix themselves when they solved the first crystal structures of hemoglobin and myoglobin, having the final say.  The structures contain a small amount of 3&lt;sub&gt;10&lt;/sub&gt; helix but are otherwise full of alpha helices.  I'm not sure that the secondary structure was entirely confirmed until the 1958 when myoglobin was resolved.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-10-21T17:35:51.493" LastActivityDate="2013-10-21T17:35:51.493" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10962" PostTypeId="2" ParentId="10958" CreationDate="2013-10-19T21:50:18.423" Score="0" Body="&lt;p&gt;I have no idea, how your containers look like [and I doubt that's the best way to humidify air] and I don't think there is any chance to get rid of bacteria by putting some copper coins inside, but any-case:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The easiest way to measure concentration of bacteria utilized in laboratory practice is with the aid of a spectrophotometer. There are lots of protocols on-line, but basically you need a spectrophotometer able to measure absorption at 600 nm, special cuvettes and pipettes. One major drawback is that this way you get &lt;strong&gt;relative&lt;/strong&gt; amounts of bacteria, and to get an idea, of how much cells in one unit of volume you actually have, you need calibration. [Calibration curves are unfortunately not transferable from photometer to photometer or from one bacterial culture to another one]. Calibration is generally performed by measuring absorption of media with different &lt;em&gt;a priori known&lt;/em&gt; concentrations of bacteria. To get such control media, one needs a more laborious trick: measure individual cells from a known volume under a microscope (pour, say 1 mkl of the medium on a glass and &quot;just&quot; count &lt;strong&gt;all&lt;/strong&gt; cells).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, you likely need a centrifuge, capable of rotating at 5000 g, because bacterial content in your water is not going to be high enough and you have to collect the cells and re-suspend them later in much smaller volume.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2013-10-19T21:50:18.423" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10963" PostTypeId="2" ParentId="10958" CreationDate="2013-10-19T22:11:21.003" Score="5" Body="&lt;p&gt;There is evidence that copper pots have antibacterial effects when used for storing drinking water (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22524115&quot; rel=&quot;noreferrer&quot;&gt;Sudha, et al. 2012&lt;/a&gt;), so the copper coins will probably have a similar effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The easiest way to test this at home would probably be to buy a test kit from an online vendor - these are relatively inexpensive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some Googling produced this website [&lt;a href=&quot;http://appslabs.com.au/index.php?main_page=index&amp;amp;cPath=410_44&quot; rel=&quot;noreferrer&quot;&gt;appslabs.com.au&lt;/a&gt;], which has some tests for common types of bacteria. There are undoubtedly others too, if these don't sound suitable&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2013-10-19T22:11:21.003" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10967" PostTypeId="2" ParentId="10217" CreationDate="2013-10-20T09:49:01.247" Score="3" Body="&lt;p&gt;&lt;strong&gt;Disclaimer&lt;/strong&gt;: there is a very large amount of literature on the subject and I am in no way expert enough to properly review it here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, here's a few papers that review the issue and may serve as a basis to look up other references&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23754370&quot; rel=&quot;nofollow&quot;&gt;Evolution of consciousness: phylogeny, ontogeny, and emergence from general anesthesia&lt;/a&gt; - Mashour and Alkire, &lt;strong&gt;PNAS&lt;/strong&gt; &lt;em&gt;2013&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We propose that the stepwise emergence from general anesthesia can serve as a reproducible model to study the evolution of consciousness across various species and use current data from anesthesiology to shed light on the phylogeny of consciousness. Ultimately, we conclude that the neurobiological structure of the vertebrate central nervous system is evolutionarily ancient and highly conserved across species and that &lt;strong&gt;the basic neurophysiologic mechanisms supporting consciousness in humans are found at the earliest points of vertebrate brain evolution&lt;/strong&gt;.&lt;br&gt;&#xA;  [...]&#xA;  The distinction between phenomenal and access consciousness was noted, but phenomenal consciousness itself reflects the dissociable neurobiologica processes of &lt;strong&gt;awareness&lt;/strong&gt; and &lt;strong&gt;arousal&lt;/strong&gt;. Awareness refers to the content of consciousness (red apple vs. blue sky), whereas arousal refers to brain activation and level-of-consciousness (alert vs. drowsy vs. asleep vs. anesthetized). A number of current theories about consciousness propose that the cortex is the primary site containing the neural correlates of awareness, whereas midline subcortical brain structures provide ascending arousal influences to the cortex&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is also reviewed in this paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15766888&quot; rel=&quot;nofollow&quot;&gt;Subjective experience is probably not limited to humans: the evidence from neurobiology and behavior.&lt;/a&gt; - Baars, &lt;strong&gt;Conscious Cogn.&lt;/strong&gt;, &lt;strong&gt;2005&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Thus consciousness is not a metaphysical absolute, but a scientific construct like any other. In humans, the standard behavioral index of conscious cognition is accurate or verifiable report. It has been used scientifically since the beginning of psychophysics in the 1820s. Accurate report is highly reliable, but of course it is subject to limitations like any other empirical measure (Baars, 1988).&lt;br&gt;&#xA;  [...]&lt;br&gt;&#xA;  In humans the thalamus and cortex are crucial for supporting the contents of consciousness (Edelman &amp;amp; Tononi, 2000). Thalamus is often considered to be an extension of cortex, an added sandwich of interacting layers that controls most traffic to and from cortex. &lt;strong&gt;Local damage to cortical sensory regions, like the fusiform gyrus for face perception, results in a loss of conscious knowledge about faces but not about other visual features like color, location, or size. If the intralaminar nuclei of the thalamus are lesioned bilaterally, the conscious state is lost.&lt;/strong&gt; By comparison, large lesions to cerebellum, basal ganglia, and spinal cord do not impair either conscious contents or state. Cerebellar damage can cause paralysis but not loss of consciousness. Lesion evidence on these points is supported by stimulation experiments using electrodes, transcranial magnetic stimulation (TMS), and microdialysis. It is also reflected in functional brain imaging. The evidence is therefore very strong that &lt;strong&gt;the T-C system supports consciousness&lt;/strong&gt;. That is why many neuroscientists consider the T-C system to be the “seat” of conscious experience, and have done so for at least a century.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Again, citing from the first paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The recent experiments with general anesthesia in humans suggest that phylogenetically ancient structures in the brainstem and diencephalon—with only limited neocortical involvement—are sufficient to support primitive consciousness. Where, then, does consciousness arise on the evolutionary timeline? One might be tempted to conclude that consciousness commenced as our mammalian ancestors evolved just beyond reptiles and their predominantly subcortical brains. However, paleontological findings suggest that the synapsid line that gave rise to mammals and the sauropsid line that gave rise to reptiles and birds both diverged from the primitive anapsid line at a single point ~315 million years ago. Furthermore, there is significant evidence that avian species are capable of higher cognition and even consciousness itself. For example, birds demonstrate evidence of explicit episodic recall (i.e., conscious memory of an event) and theory of mind (i.e., attribution of subjective mental events to another being). Thus, it would be misguided to try to identify a single point at which consciousness emerged because evidence suggests that consciousness evolved along two independent lineages.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="115" LastActivityDate="2013-10-20T09:49:01.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10968" PostTypeId="1" CreationDate="2013-10-20T11:54:58.047" Score="1" ViewCount="559" Body="&lt;p&gt;How do organelles such as ribosomes, ER, Golgi and vesicles produce CFTR protein and mucus?&lt;/p&gt;&#xA;" OwnerUserId="4711" LastActivityDate="2013-10-22T03:24:21.460" Title="Question about production of CFTR protein" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10969" PostTypeId="2" ParentId="2109" CreationDate="2013-10-20T11:55:34.533" Score="2" Body="&lt;p&gt;Selfish behaviour is not necessarily preferred. It depends on the game (game theory). For example, in absence of relatedness and reciprocity, we would expect:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;All the population defect in the Prisoner's dilemna&lt;/li&gt;&#xA;&lt;li&gt;Some defect and some cooperate in the snow-drift game&lt;/li&gt;&#xA;&lt;li&gt;Either all inds defect or all inds cooperate (depending on initial condition because it is an unstable equilibrium) in the stag hunt game.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;When there is relatedness (genetic correlation) between individuals, Hamilton's theory of inclusive fitness says that: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$R\cdot\frac{dw(x,y,z)}{dx}&amp;gt;\frac{dw(x,y,z)}{dy}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where the letter &lt;code&gt;d&lt;/code&gt; means partial derivative, the function &lt;code&gt;w()&lt;/code&gt; is the fitness function and the parameters of the fitness function represent the trait of the focla individual (x), the mean trait in the subpopulation (y) and the mean trait in the populaiton (z). &lt;a href=&quot;https://biology.stackexchange.com/posts/10756/edit&quot;&gt;For more information&lt;/a&gt; This fitness function depends one the ratio of the fecundity function of cooperating over defecting. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These fecundity functions in the prisoner's dilemna equals the baseline fecundity (usually we write down 1) plus the payoff when the other cooperate times the probability that the interacting individual cooperate plus the payoff when the interacting individual defect times the probability that it defects. It gives:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$f(cooperate) = 1 + (B-C)x + C(1-x)$$ if the individuals get the payoff &lt;code&gt;B-C&lt;/code&gt; when the interacting individual also cooperates and &lt;code&gt;C&lt;/code&gt;when the interactzing individual defects. &lt;code&gt;x&lt;/code&gt;is the probability that the other individual cooperates. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually, the first equation above is written under the form:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$RB&amp;gt;C$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead of R, you might as well consider another correlation, a correlation of behaviour due to reciprocity. The equation becomes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$kB&amp;gt;C$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might as well consider both, reciporcity and relatedness which give:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$BR-C+k\cdot(B-RC)$$&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2013-10-20T11:55:34.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10970" PostTypeId="1" AcceptedAnswerId="10985" CreationDate="2013-10-20T12:06:47.867" Score="7" ViewCount="1007" Body="&lt;p&gt;Do we have any empirical evidence in favor of species (or lineage) selection? Do we know some cases that can only be explained (or seem to be only explained) by lineage selection? What are today the best study cases in favor of lineage selection?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, how could we find any evidence for lineage selection?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: I call lineage selection a differential in speciation and/or extinction rate that drive the proportion of lineage (species for example) displaying a given trait (emergent traits or not) to increase or decrease over time.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2013-10-23T14:34:27.833" Title="Empirical evidence for species selection" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;extinction&gt;&lt;speciation&gt;&lt;selection&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10971" PostTypeId="1" AcceptedAnswerId="10973" CreationDate="2013-10-20T13:39:10.167" Score="3" ViewCount="4832" Body="&lt;p&gt;&lt;a href=&quot;http://www.genome.gov/glossary/index.cfm?id=504&quot; rel=&quot;nofollow&quot;&gt;Lyonization&lt;/a&gt; or &lt;a href=&quot;http://www.nature.com/nature/journal/v190/n4773/abs/190372a0.html&quot; rel=&quot;nofollow&quot;&gt;X-chromosome inactivation&lt;/a&gt; is the conversion of all but one, X-chromosomes in Females into non-coding heterochromatin (i.e. deactivated) leading to the formation of one or more &lt;a href=&quot;http://en.wikipedia.org/wiki/Barr_body&quot; rel=&quot;nofollow&quot;&gt;Barr bodies.&lt;/a&gt; The selection of the X-chromosome to be inactivated is different in different animals. In female Marsupials, the inactivation is always of the Paternal X-chromosome while in placental mammals, the selection is &lt;a href=&quot;http://www.sciencemag.org/content/303/5658/644&quot; rel=&quot;nofollow&quot;&gt;random&lt;/a&gt;. (Although the extent of lyonization is not completely random and varies &lt;a href=&quot;http://www.clinchem.org/content/44/1/61.long#xref-ref-1-1&quot; rel=&quot;nofollow&quot;&gt;directionally with age&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If the X-chromosome to be inactivated is randomly selected in&#xA;  placental mammals (including humans), then why don't the females&#xA;  heterozygous for a X-linked recessive disorder do not show the&#xA;  phenotype of the disease though the functional gene is equally likely&#xA;  (as compared to the defective) to be the one to be lyonized?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are &lt;a href=&quot;http://en.wikipedia.org/wiki/X-inactivation&quot; rel=&quot;nofollow&quot;&gt;some evidences&lt;/a&gt; of genes escaping inactivation and managing to exhibit themselves but I don't think they can account for all the recessive x-linked disorders.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2014-07-13T20:51:40.023" Title="Lyonization and X-linked disorders?" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;cytogenetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10973" PostTypeId="2" ParentId="10971" CreationDate="2013-10-20T17:22:28.223" Score="3" Body="&lt;p&gt;The simple answer is that which X chromosome is inactivated varies in different cell lineages, so typically a female will have cells exhibiting either wild-type or mutant phenotypes. It was &lt;a href=&quot;http://en.wikipedia.org/wiki/Mary_F._Lyon&quot; rel=&quot;nofollow&quot;&gt;Mary Lyon&lt;/a&gt;'s observation of mosaicism in heterozygous mouse coat colour that gave the phenomenon its name. So in the case of a recessive disease there will be a phenotype, but in many cases the 50% of cells expressing the normal gene will provide sufficient functional cells to get by. From the Wikipedia article about Mary Lyon:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Her research has allowed us to understand the genetic control mechanisms of chromosome X, which explains the absence of symptoms in numerous healthy women that are carriers of diseases associated with this chromosome.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit - response to comments:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plug, I &lt;em&gt;et al&lt;/em&gt;. (2006) Bleeding in carriers of hemophilia. Blood 108: 52-56&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A wide range of factor VIII and IX levels is observed in heterozygous carriers of hemophilia as well as in noncarriers. In female carriers, extreme lyonization may lead to low clotting factor levels. We studied the effect of heterozygous hemophilia carriership on the occurrence of bleeding symptoms. A postal survey was performed among most of the women who were tested for carriership of hemophilia in the Netherlands before 2001. The questionnaire included items on personal characteristics, characteristics of hemophilia in the affected family members, and carrier testing and history of bleeding problems such as bleeding after tooth extraction, bleeding after tonsillectomy, and other operations. Information on clotting factor levels was obtained from the hospital charts. Logistic regression was used to assess the relation of carrier status and clotting factor levels with the occurrence of hemorrhagic events. In 2004, 766 questionnaires were sent, and 546 women responded (80%). Of these, 274 were carriers of hemophilia A or B. The median clotting factor level of carriers was 0.60 IU/mL (range, 0.05-2.19 IU/mL) compared with 1.02 IU/mL (range, 0.45-3.28 IU/mL) in noncarriers. Clotting factor levels from 0.60 to 0.05 IU/mL were increasingly associated with prolonged bleeding from small wounds and prolonged bleeding after tooth extraction, tonsillectomy, and operations. Carriers of hemophilia bleed more than other women, especially after medical interventions. Our findings suggest that not only clotting factor levels at the extreme of the distribution, resembling mild hemophilia, but also mildly reduced clotting factor levels between 0.41 and 0.60 IU/mL are associated with bleeding.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Bimler, D &amp;amp; Kirkland, J (2009) Colour-space distortion in women who are heterozygous for colour deficiency. Vision Research 49: 536-543&lt;/p&gt;&#xA;&#xA;&lt;p&gt;from the Introduction:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;About 15% of women are heterozygous for some form of colour vision deficiency (CVD). That is, they possess a genetic abnormality on one of their two X chromosomes, affecting the photopigments (opsins) which subserve colour vision. The retina of a heterozygous woman is a mosaic in which some cone cells express the aberrant gene while others express the normal copy, depending on which X chromosome is active (inactivation of one X chromosome occurs randomly in retinal stem-cells at some stage of fetal development). The normal cells are sufficient to provide full trichromatic vision.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-10-21T16:10:39.687" LastActivityDate="2013-10-21T16:10:39.687" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="10974" PostTypeId="2" ParentId="10968" CreationDate="2013-10-20T17:41:49.927" Score="2" Body="&lt;p&gt;CFTR (&lt;a href=&quot;http://en.wikipedia.org/wiki/Cystic_fibrosis_transmembrane_conductance_regulator&quot; rel=&quot;nofollow&quot;&gt;cystic fibrosis transmembrane conductance regulator&lt;/a&gt;) is an integral glycoprotein of the plasma membrane, and mucous is rich in secreted glycoproteins. All proteins are made on ribosomes: CFTR will be cotranslationally inserted into the ER membrane while secretory glycoproteins are cotranslationally sent across the same membrane into the lumen of the ER. In the ER the initial glycans are added to specific amino acid residues. The folding of all proteins is carefully monitored by chaperones in the ER to avoid misfolded proteins reaching the cell surface. Various folding factors also come into play, including peptidyl proline isomerase and protein disulphide isomerase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Proteins destined for the cell surface leave the ER in COPII-coated vesicles (CFTR will be in the vesicle membrane, secretory glycoproteins in the vesicle lumen) and are targetted to the Golgi where the glycosylation process is completed. Another round of vesicle transport gets the proteins to the cell surface - when these vesicles fuse with the inner surface of the plasma membrane the vesicle content is secreted into the surroundings, while the vesicle membrane proteins enter the plasma membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The classic example of a CFTR defect, resulting in cystic fibrosis, is due to the &amp;Delta;F508 mutation - the loss of a single amino acid results in misfolding, and the defective protein is held in the ER resulting in loss of CFTR function at the cell surface. Overcoming this retention is one of the targets for CFTR therapy, because if the &amp;Delta;F508 protein does manage to pass through the secretory pathway to the cell surface it provides sufficient channel function to abolish cystic fibrosis symptoms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't cited any references here because this is all standard biochemistry/molecular cell biology textbook stuff, so should be easy to confirm.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-10-20T17:41:49.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10975" PostTypeId="2" ParentId="10958" CreationDate="2013-10-20T17:52:31.933" Score="3" Body="&lt;p&gt;I think you might be better advised to try plating out samples of the water and counting bacterial colonies. There has been some good advice on doing basic microbiology at home &lt;a href=&quot;https://biology.stackexchange.com/questions/9283/how-to-obtain-bacteria-samples-at-home/9284#9284&quot;&gt;elsewhere on this site&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2013-10-20T17:52:31.933" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10977" PostTypeId="2" ParentId="5670" CreationDate="2013-10-20T19:26:20.753" Score="2" Body="&lt;p&gt;Yes! As a matter of fact Animal Cells do have vacuoles.  Even though they are much smaller than the Large Central Vacuole of Plant Cells they still do exist in Animal Cells.  Unlike the Large Central Vacuole of the Plant Cells they do not take up 90% of the cells and there are multiple vacuoles, but small ones might I add.  Also in a Plant Cell there is only one vacuole the Large Central Vacuole.&lt;/p&gt;&#xA;" OwnerUserId="4713" LastActivityDate="2013-10-20T19:26:20.753" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10978" PostTypeId="2" ParentId="10955" CreationDate="2013-10-20T20:05:33.160" Score="2" Body="&lt;p&gt;This is a typical architecture of computation proposed as a model for &lt;a href=&quot;http://en.wikipedia.org/wiki/Two-streams_hypothesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;ventral stream of visual processing in primates&lt;/a&gt;. It has a long history (e.g., &lt;a href=&quot;http://dx.doi.org/10.1016/j.neunet.2012.09.016&quot; rel=&quot;nofollow noreferrer&quot;&gt;Neocognitoron by Fukushima was 1980&lt;/a&gt;) and still widely accepted in machine learning (e.g., &lt;a href=&quot;http://en.wikipedia.org/wiki/Deep_learning&quot; rel=&quot;nofollow noreferrer&quot;&gt;deep learning&lt;/a&gt;) and neuroscience.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.imgur.com/NCwoxM9.png?1&quot; alt=&quot;Neocognitron&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is motivated by the organization of V1 simple cells and complex cells. &lt;a href=&quot;http://en.wikipedia.org/wiki/Simple_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;Simple cells in V1&lt;/a&gt; can be approximately thought of as edge detectors at a specific retinal location. This is why on the figure you cite, they are represented as a circle with a bar (a cartoon receptive field). The simple cells can only detect things very locally, meaning if the edge appears at a different location in your field of view, it will not respond.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematically, you can think of a spatial filter that detects an edge (e.g., oriented Gabor patch) multiplied to your retinal image, and summed. For example the filter below will detect match a 45 degree bar aligned on the hot-colored area, but will have less activity if the bar is shifted out of the specific position.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/7/75/Gabor_filter.png&quot; alt=&quot;oriented Gabor patch&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Complex_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;complex cells in V1&lt;/a&gt;, on the other hand is still an edge detector, but has some location invariance. In other words, when the edge is slightly displaced, the response of complex cells does not seem to change. It is believed that this is because complex cells pull from multiple simple cells with the same orientation. This is what you see in your figure where a single complex cell pulls information from the same orientation simple cells but at different locations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematically, a soft-max operation or a max operation over the simple cell outputs can lead to a good complex cell model. But, it is not limited to such operations. In fact, &lt;a href=&quot;http://memming.wordpress.com/2011/12/08/bayesian-spike-triggered-covariance-analysis/&quot; rel=&quot;nofollow noreferrer&quot;&gt;quadratic&lt;/a&gt; or other nonlinear models are also widely used in computational neuroscience.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The full hierarchy for ventral stream is then simply obtained by extending repeatedly using the simple-cell-complex-cell analogy. For each stack simple cell layer extracts some local feature (by computing on the previous layer's complex cell's output), and complex cell layer makes it invariant over space. From edges in V1, one can get corners on the next layer, then complex contours, and all the way up to objects. At least that's how the story goes.&lt;/p&gt;&#xA;" OwnerUserId="460" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.880" LastActivityDate="2013-10-20T20:14:37.153" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="10979" PostTypeId="2" ParentId="546" CreationDate="2013-10-20T21:07:44.487" Score="2" Body="&lt;p&gt;Yes, we can survive temperatures above 100 F (38 C) but surviving such temperatures requires continuous fluid intake.  Since sweat evaporates quickly in an arid (dry) environment we tend to be unaware of how much water we're losing.  This leads to heat exhaustion, then heat stroke, then death.  Survival time depends on how well hydrated you are and whether or not you can replace the lost fluid.&lt;/p&gt;&#xA;" OwnerUserId="4714" LastEditorUserId="3624" LastEditDate="2013-10-22T09:41:45.070" LastActivityDate="2013-10-22T09:41:45.070" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10980" PostTypeId="2" ParentId="10958" CreationDate="2013-10-20T22:37:14.030" Score="4" Body="&lt;p&gt;I would first like to address a couple of your underlying assumptions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Most &quot;copper&quot; looking coins (in North America anyway) are actually a bronze alloy, reflecting a change from ~95% Cu to ~95% steel. As a result, I don't think that there would be much antimicrobial effect from the coins. Now, if you did really have copper in the water (like copper piping), then the best antimicrobial effects are likely to come from regular stirring/agitation to make sure the bacteria contact the copper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Having some tap water sitting in a warm area is not really a &quot;perfect&quot; breeding ground for bacteria. A perfect breeding ground would contain nutrients (at the very least, sugar). Whatever bacteria you would find is likely the bacteria that circulates in your home air, or other contaminants (like sneezing).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your question, how to measure the bacterial load in each bowl, I think the simplest method to do at home would be as @Alan Boyd suggests. Take a small sample of water from each dish, and plate them out on some kind of growth plate (such as a LB agar). After 16-18 hours of growth on the plate, you would just count the number of colonies on each plate, and get a simple measurement of bacterial load from each bowl.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The drawback to this method is that it does not tell you what kind of bacteria are growing, or whether they are likely to cause illness (pathogenic).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For reference, &lt;a href=&quot;http://www.sciencebuddies.org/science-fair-projects/project_ideas/MicroBio_Agar.shtml&quot; rel=&quot;nofollow&quot;&gt;here is a detailed overview&lt;/a&gt; of the most common types of agar plates used for microbiology purposes. This is also a protocol for &lt;a href=&quot;http://www.ehow.com/how_6132952_homemade-agar-plates.html&quot; rel=&quot;nofollow&quot;&gt;how to make your own plates at home&lt;/a&gt;, using readily available gelatin as a gelling agent, rather than using agar (which can be found in some ethnic supermarkets, but is less available).&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2013-10-22T01:36:45.967" LastActivityDate="2013-10-22T01:36:45.967" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="10981" PostTypeId="2" ParentId="10936" CreationDate="2013-10-20T22:46:05.643" Score="1" Body="&lt;p&gt;I don't know the answer, but you could simply brute force the answer by generating all possible combinations of 3- or 4-nt length sequences, and comparing against the &lt;a href=&quot;http://rebase.neb.com/rebase/rebase.html&quot; rel=&quot;nofollow&quot;&gt;restriction enzyme database (REbase)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would not take long to do. There are $ 3^4 $ and $ 4^4 $ combinations, respectively. Depending on your purpose, it might be possible when not considering engineered restriction enzymes (which are not likely to have recognition sequences found in nature).&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-10-20T22:46:05.643" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10982" PostTypeId="1" CreationDate="2013-10-20T22:55:51.900" Score="2" ViewCount="83" Body="&lt;p&gt;As far as I know, plant cell shapes are a difficult thing to pin down. However plant cells have cell walls and so can be very rigid. However the only plant cells I've seen have been either block shaped or tube shaped. Are there more exotic examples of cell shapes, particularly in plants? For instance have plants ever used honeycomb patterns or other forms of tesselation?&lt;/p&gt;&#xA;" OwnerUserId="4440" LastActivityDate="2014-04-01T20:48:34.897" Title="Exotic Cell Shapes" Tags="&lt;cell-biology&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10983" PostTypeId="2" ParentId="10938" CreationDate="2013-10-21T05:55:16.483" Score="1" Body="&lt;p&gt;In all phosphorylation reactions, the &lt;strong&gt;oxygen&lt;/strong&gt; of the hydroxyl group in the &lt;strong&gt;substrate&lt;/strong&gt; attacks &lt;code&gt;P&lt;/code&gt; of phosphate. This is because of high partial positive charge on &lt;code&gt;P&lt;/code&gt; which is bonded to four highly electronegative oxygen atoms. When the bond forms between the substrate oxygen atom and phosphorus of terminal phosphate, electrons are transferred to the &lt;code&gt;O&lt;/code&gt; that bridges the ester bond between 2nd and 3rd phosphate. Therefore the &lt;code&gt;O&lt;/code&gt; of the substrate is retained and that of the terminal phosphate (of ATP) becomes the part of the 2nd phosphate (now terminal phosphate of ADP).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TaDCB.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://chemwiki.ucdavis.edu/Organic_Chemistry/Organic_Chemistry_With_a_Biological_Emphasis/Chapter_10%3A_Phosphoryl_transfer_reactions/Section_10.2%3A_Phosphorylation_reactions_-_kinase_enzymes&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-05-29T05:45:11.767" LastActivityDate="2015-05-29T05:45:11.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10985" PostTypeId="2" ParentId="10970" CreationDate="2013-10-21T09:36:37.880" Score="5" Body="&lt;p&gt;A commonly used empirical example of &lt;em&gt;species selection&lt;/em&gt; (a.k.a clade selection, lineage selection) is &lt;a href=&quot;http://en.wikipedia.org/wiki/Marine_larval_ecology&quot; rel=&quot;nofollow&quot;&gt;pelagic larvae&lt;/a&gt; in sessile ocean species. See &lt;a href=&quot;http://rsbl.royalsocietypublishing.org/content/9/3/20130068.short&quot; rel=&quot;nofollow&quot; title=&quot;Maliska et al. 2013. Developmental mode influences diversification in ascidians. Biologi Letters 9(3)&quot;&gt;Maliska et al (2013)&lt;/a&gt; for a recent paper discussing this in Tunicata and &lt;a href=&quot;http://www.jstor.org/stable/10.1086/507994&quot; rel=&quot;nofollow&quot; title=&quot;Jablonski &amp;amp; Hunt. 2006. Larval Ecology, Geographic Range, and Species Survivorship in Cretaceous Mollusks: Organismic versus Species-Level Explanations. American Naturalist 168(4)&quot;&gt;Jablonski &amp;amp; Hunt (2006)&lt;/a&gt; for larval modes in gastropods. The idea is to some extent really intuitive - pelagic larvae means higher dispersal rates, so the species will be exposted to and can colonize new environments. This can lead to speciation through adaptive radiation. Larger ranges also means lower extinction rates (e.g. through less population synchrony). If the trait is fixed within a lineage, this lineage as a whole will, as compared to an sister lineage lacking the trait, contain more species (i.e. species selection). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, you can also argue that pelagic larvae will lead to higher gene flow between populations, which could inhibit speciation. Therefore, the effect of pelagic larvae, and how these mechanisms are weighted in practice, is really an empirical question (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC17878/&quot; rel=&quot;nofollow&quot; title=&quot;Duda &amp;amp; Palumbi. 1999. Developmental shifts and species selection in gastropods. PNAS 96(18)&quot;&gt;Duda &amp;amp; Palumbi, 1999&lt;/a&gt; and &lt;a href=&quot;http://www.jstor.org/stable/10.1086/507994&quot; rel=&quot;nofollow&quot; title=&quot;Jablonski &amp;amp; Hunt. 2006. Larval Ecology, Geographic Range, and Species Survivorship in Cretaceous Mollusks: Organismic versus Species-Level Explanations. American Naturalist 168(4)&quot;&gt;Jablonski &amp;amp; Hunt, 2006&lt;/a&gt; for discussions on this issue).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.ecolsys.39.110707.173510&quot; rel=&quot;nofollow&quot; title=&quot;Jablonski. 2008. Species selection: Theory and data. Annual review Ecology, Evolution, and Systematics 39: 501-524.&quot;&gt;Jablonski (2008)&lt;/a&gt; provides a nice general review of species selection (concept, mechanisms, theoretical models and data), and &lt;a href=&quot;http://www.oxfordscholarship.com/view/10.1093/acprof%3aoso/9780199267972.001.0001/acprof-9780199267972&quot; rel=&quot;nofollow&quot; title=&quot;Okasha. 2006. Evolution and the Levels of Selection. Oxford University Press&quot;&gt;Okasha (2006)&lt;/a&gt; (chap. 7) is good for a theoretical/philosophical treatment of levels of selection. Also remember that traits are selected for at the individual level, but can (especially if fixed) still act on a lineage level. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-10-23T14:34:27.833" LastActivityDate="2013-10-23T14:34:27.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10986" PostTypeId="1" CreationDate="2013-10-21T10:11:26.050" Score="6" ViewCount="455" Body="&lt;p&gt;I'm interested in a statistical tool to get bacterial codon usage at genomic level. Ideally, the tool should be flexible to analyse hundreds of bacterial genomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've looked in MeSH terms database but I'm a bit lost &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=%28%22Genetic%20Code%22%5BMesh%5D%29%20AND%20%22Software%22%5BMesh%5D&quot; rel=&quot;nofollow noreferrer&quot;&gt;when I search for &quot;Genetic Code&quot; and Software&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking for an output like this one:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WRyGm.gif&quot; alt=&quot;enter link description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="4101" LastEditDate="2013-10-24T13:29:53.140" LastActivityDate="2014-05-04T15:18:49.780" Title="Whole genome amino acid composition tool?" Tags="&lt;bacteriology&gt;&lt;amino-acids&gt;&lt;genomes&gt;&lt;codon-usage&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="10987" PostTypeId="1" CreationDate="2013-10-21T12:28:25.127" Score="2" ViewCount="4726" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Some websites state that the enzyme zymase (which I understand to be a complex of several enzymes) is responsible for catalyzing glycolysis in order to produce pyruvate. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;On the other hand, some other websites state that zymase is responsible for catalyzing the conversion of pyruvate to acetaldehyde, and acetaldehyde to ethanol and carbon dioxide.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Which one of the above is correct? And, what are the names of the enzymes that are collectively called zymase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thank you for your time and consideration. Good day! &lt;/p&gt;&#xA;" OwnerUserId="4719" LastEditorUserId="3632" LastEditDate="2013-10-21T12:52:47.590" LastActivityDate="2017-05-03T14:17:19.243" Title="Is Zymase, A Complex of Enzymes? Which ones?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10988" PostTypeId="1" AcceptedAnswerId="10990" CreationDate="2013-10-21T13:01:03.230" Score="2" ViewCount="530" Body="&lt;p&gt;If I am not mistaken, during exposure to electricity sources it is the magnitude of the current and not the voltage that kills the human body.  If so, what is the order of magnitude of current that human body can sustain, and for what duration?  How do defibrillators exploit this?&lt;/p&gt;&#xA;" OwnerUserId="4720" LastEditorUserId="4101" LastEditDate="2013-10-21T16:01:59.403" LastActivityDate="2013-10-24T09:20:33.567" Title="Breakdown current for human body" Tags="&lt;cardiology&gt;&lt;electrophysiology&gt;&lt;death&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10989" PostTypeId="2" ParentId="10987" CreationDate="2013-10-21T13:05:59.647" Score="3" Body="&lt;p&gt;This is all correct it seems, but maybe the term is more of historical interest rather than current science.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Zymase is a term which is no longer in use in the scientific literature.  It seems to have disappeared in the 1950s.   The latest reference I can see is 1970s.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason seems to be that &lt;a href=&quot;http://en.wikipedia.org/wiki/Zymase&quot; rel=&quot;nofollow&quot;&gt;Zymase was purifiable from yeast with 19th century techniques&lt;/a&gt;.  The term was coined in 1897.  This is probably because in brewers yeast the Zymase components are either in a protein complex or contained within a compartment in the cell that could be separated from the rest of the organism.  &lt;a href=&quot;http://www.degruyter.com/view/j/bchm2.1935.237.issue-1-3/bchm2.1935.237.1-3.1/bchm2.1935.237.1-3.1.xml&quot; rel=&quot;nofollow&quot;&gt;Here's an early reference - german isn't so great&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Zymase activity was shown to vary from one strain of yeast to another, which makes the discovery seem more a manifestation of the physiology of that one strain of yeast.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Later work showed that Zymase activity was organizable into a more universal set of genes which are conserved in all living things and called the '&lt;a href=&quot;http://en.wikipedia.org/wiki/Citric_acid_cycle&quot; rel=&quot;nofollow&quot;&gt;citric acid cycle&lt;/a&gt;' or &lt;a href=&quot;http://www.nobelprize.org/nobel_prizes/medicine/laureates/1953/krebs-lecture.pdf&quot; rel=&quot;nofollow&quot;&gt;the Krebs Cycle.&lt;/a&gt; Krebs performed his work without reference to Zymase, where biochemicals were added to a culture and their transformation tracked. So, Zymase seems more like a historical footnote...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedias' entry sounds as if the extraction was not very pure - its called a 'press juice' so I think it would be difficult to describe exactly which specific enzymes were in Zymase.  I'd naively assume that nearly all the citric acid cycle enzymes would be involved in Zymase activity, where observed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many of the enzymes in the citric acid cycle form large complexes with themselves and other of the enzymes, which might be responsible for the original discovery of Zymase. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-10-21T17:34:25.110" LastActivityDate="2013-10-21T17:34:25.110" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10990" PostTypeId="2" ParentId="10988" CreationDate="2013-10-21T15:11:58.157" Score="2" Body="&lt;p&gt;According to Wikipedia &lt;a href=&quot;http://en.wikipedia.org/wiki/Electric_shock&quot; rel=&quot;nofollow noreferrer&quot;&gt;Electric shock&lt;/a&gt;, the Magnitude of electric shock to a body is mainly due to current as well as voltage. Various factor of the environment will also play a major role in damaging the body while under contact. The following quote explains it:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The minimum current a human can feel depends on the current type (AC or DC) and frequency. A person can feel at least 1 mA (rms) of AC at 60 Hz, while at least 5 mA for DC. At around 10 milliamperes, AC current passing through the arm of a 68 kg (150 lb) human can cause powerful muscle contractions; the victim is unable to voluntarily control muscles and cannot release an electrified object. This is known as the &quot;let go threshold&quot; and is a criterion for shock hazard in electrical regulations. The current may, if it is high enough, cause tissue damage or fibrillation which leads to cardiac arrest; more than 30 mA of AC (rms, 60 Hz) or 300 – 500 mA of DC can cause fibrillation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To give a clear picture of how various current threshold will affect human body see the image below. (Complete data is available here &lt;a href=&quot;http://www.me.utexas.edu/~longoria/me340/leks/notes/18_ElectricalSafety_IrwinKernsCh21.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;Electrical Safety&quot;&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/om48j.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even High Voltage also can be fatal to human body which is enough to cause damage.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;High voltage electrical energy greatly reduces the body's resistance by quickly breaking down human skin. Once the skin is punctured, the lowered resistance results in massive current flow. Ohm's law is used to demonstrate the action.&#xA;  At 1,000 volts, Current = Volts/Ohms = 1,000/500 = 2 Amps, which can cause cardiac arrest and serious damage to internal organs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now what is the length of time that body is under electrical contact. This length of time exposure is also critical.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When muscular contraction caused by stimulation does not allow the victim to free himself from the circuit, even relatively low voltages can be extremely dangerous, because the degree of injury increases with the length of time the body is in the circuit. LOW VOLTAGE DOES NOT IMPLY LOW HAZARD!&#xA;  100mA for 3 seconds = 900mA for .03 seconds&#xA;  in causing fibrillation&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(Complete detail is available &lt;a href=&quot;https://www.osha.gov/SLTC/etools/construction/electrical_incidents/eleccurrent.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;How Electrical Current Affects the Human Body&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="4547" LastActivityDate="2013-10-21T15:11:58.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10991" PostTypeId="1" CreationDate="2013-10-21T16:46:50.887" Score="3" ViewCount="81" Body="&lt;p&gt;According to my previous question in &lt;a href=&quot;https://biology.stackexchange.com/questions/10955/ventral-stream-pathway-and-architecture-proposed-by-poggios-group/10978#10978&quot;&gt;ventral Stream pathway and architecture&lt;/a&gt;, I want now to get a brief example about how the S1 layer is constructed. In other words, how all the simple units are tuned with the gaussian-Like tuning (for example). I am only interested to get such a cartoon example in step by step how this operation can be achieved in given of inputs (which inputs? and what we mean about these inputs?) in order to obtain the tuned simple units.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We all know that each simple unit is obtained after a tuning operation around their inputs (Subunits) in order to select an optimal output which corresponds to the preferred orientation for such a simple unit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, I know that the S1 layer units perform a convolution on regions of the raw input image using gabor filters at different orientations and sizes. The entire population of S1 units represents a convolution map of Gabor filters of different sizes and orientations with the entire raw image (really I didn't understand this point) &lt;a href=&quot;http://www.dtic.mil/dtic/tr/fulltext/u2/a454973.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;you can read the subsection 2.2 in this article&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image below contains the image to be recognized by the brain and some simple units obtained after the tuning operation. So what I want is to obtain a brief example which can include the details (step by step) of how the operation of tuning can be achieved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/o6rHh.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://biology.stackexchange.com/questions/10955/ventral-stream-pathway-and-architecture-proposed-by-poggios-group/10978#10978&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;i didn't understand well the concept. That's why i need a real example with a specific image which can contains all the steps described in my attached image (step by step) because i still don't understand what we mean about inputs x, etc.&#xA;So please if anyone can give me a real example with a specific image which can respond briefly to this attached image&lt;/p&gt;&#xA;" OwnerUserId="4702" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-11-19T00:32:39.590" Title="The Operation of tuning in the S1 layer of ventral model" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;vision&gt;&lt;computational-model&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="10992" PostTypeId="1" AcceptedAnswerId="10994" CreationDate="2013-10-21T16:48:28.473" Score="4" ViewCount="606" Body="&lt;p&gt;I know that papain is a proteolytic enzyme present in papaya. It is often used to tenderise meat.  What is the function of papain in papaya?  Is papain sweet? Does it function as an antibiotic?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-21T17:16:34.767" LastActivityDate="2013-10-21T17:16:34.767" Title="Function of papain in papaya" Tags="&lt;botany&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10994" PostTypeId="2" ParentId="10992" CreationDate="2013-10-21T17:15:55.420" Score="3" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Papain&quot; rel=&quot;nofollow&quot;&gt;Papain&lt;/a&gt; is a &lt;a href=&quot;https://en.wikipedia.org/wiki/Cysteine_protease#Biological_importance&quot; rel=&quot;nofollow&quot;&gt;cysteine protease&lt;/a&gt;, for which Wikipedia should be sufficient:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cysteine proteases play multi-faceted roles, virtually in every aspect of physiology and development in plants such as in growth and development, in senescence and apoptosis (programmed cell death), in accumulation and mobilization of storage proteins such as in seeds. In addition, they are involved in signalling pathways and in the response to biotic and abiotic stresses. In humans they are responsible for apoptosis, MHC class II immune responses, prohormone processing, and extracellular matrix remodeling important to bone development.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-21T17:15:55.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10995" PostTypeId="2" ParentId="546" CreationDate="2013-10-21T18:21:18.573" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Some 200 years ago Dr.Charles Blagden, then secretary of Royal Society&#xA;  of London, went into  a room that had been heated to a temperature of&#xA;  126 degree Celsius ( 260 Fahrenheit) , taking with him a few friends ,&#xA;  a small dog in a basket and a steak.The entire group remained there&#xA;  for 45 minutes. Dr.Blegden and his friends emerged unaffected.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This shows the power of homeothermy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source : Helena Curtis ( 5th edition) Chp. 38&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-10-21T18:21:18.573" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10997" PostTypeId="2" ParentId="10905" CreationDate="2013-10-21T21:46:46.683" Score="4" Body="&lt;p&gt;First to address some of the comments:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Concentrated UV damage does hurt your skin, it's called sunburn.  Lighter amounts of UV damage can cause cancer over time.  UV damage can be &quot;felt&quot;, as can photonic pressure in extreme cases.  The issue at hand is &quot;what is detection.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Back to your eyes:&#xA;As addressed in &lt;a href=&quot;https://biology.stackexchange.com/questions/9976/are-there-specific-conditions-that-allow-humans-to-see-ultraviolet-wavelengths&quot;&gt;this answer&lt;/a&gt;, the human retina is able to detect UV light if it is not blocked by the lens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe your question, restated slightly, is &quot;can we call the pain experienced by UV damage to our eyes human detection of UV light.&quot;  Generically I think the answer is no, because we lack the specificity to determine that it is UV light. Many forms of &lt;a href=&quot;https://en.wikipedia.org/wiki/Ionizing_radiation&quot; rel=&quot;nofollow noreferrer&quot;&gt;ionizing radiation&lt;/a&gt; can lead to pain, and we would be unable to distinguish between them.  We cannot tell the gradation from UV to gamma, despite the damage they might cause.  Contrast this to the visible light spectrum, where we are quite good at determining the wave length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further, you could have similar damage caused by &lt;a href=&quot;http://dx.doi.org/10.1097/ICU.0b013e3283654e09&quot; rel=&quot;nofollow noreferrer&quot;&gt;infection&lt;/a&gt;, where again you couldn't distinguish between the pain and fuzzy sensation caused by the very beginning of infection vs slight &lt;a href=&quot;http://dx.doi.org/10.1016/j.survophthal.2011.03.001&quot; rel=&quot;nofollow noreferrer&quot;&gt;UV damage&lt;/a&gt; (&lt;a href=&quot;http://dx.doi.org/10.1017/S000711451100523X&quot; rel=&quot;nofollow noreferrer&quot;&gt;though blueberry might help&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does UV light damage your eyes? Absolutely in large enough doses.  Can it be called detection?  Probably not.  We can deduce UV damage from lots of things, including changes in the color of the pigmentation of your eyes (gold flakes = bad).  When we get to the level of deduction, however, we might as well be using machines to detect UV light and save our eyes (and skin) the trouble.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2013-10-21T21:46:46.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="10998" PostTypeId="1" CreationDate="2013-10-21T22:28:55.033" Score="1" ViewCount="417" Body="&lt;p&gt;I'm trying to find the effect of pH on living things like E. coli and such. At first I thought of using a buffer solution which maintains its level of pH, but it's possible that the inactive ions of each buffer have their own effect on living things that I can't account for. On the other hand, I could use hydrochloric acid and sodium hydroxide at different concentrations by diluting it. This will be a little bit more effort (I'll be diluting the acid and base myself), but much cheaper than the buffers, and I'll know that the only other ions present beside H+ and OH- are just Na+ and Cl-, the ingredients of table salt. According to &lt;a href=&quot;http://aem.asm.org/content/58/8/2513.full.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper, the effect of pH on the population also depended on the acid (HCl vs lactic acid).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like a second opinion on this:&#xA;&lt;strong&gt;If I'm investigating the effect of pH on growth of living things, do I use specially made buffers or just properly diluted HCl and NaOH?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4478" LastActivityDate="2013-10-22T02:07:11.487" Title="Effect of pH on life? Use buffer or HCl? How about lactic acid?" Tags="&lt;ecoli&gt;&lt;ph&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="10999" PostTypeId="1" CreationDate="2013-10-21T22:45:48.917" Score="2" ViewCount="1084" Body="&lt;p&gt;A population of 600 birds faced a problem of biological magnification resulting in a large number of deaths reducing their population to 350. But 230 births also took place and 21 birds immigrated into the population while 13 birds migrated out. How many deaths took place in the population? What is the growth rate of this small population?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I guess we need to use the &#xA;PGR = (BIRTHS + IMMIGRATION) - (DEATH + EMIGRATION) / INITIAL POPULATION x 100%&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So.. I keep getting -2% as my answer, but apparently the correct answer is -41.7% &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="4645" LastEditorUserId="3624" LastEditDate="2013-10-22T08:51:46.737" LastActivityDate="2013-10-22T08:51:46.737" Title="Population Growth Rate Question?" Tags="&lt;homework&gt;&lt;population-dynamics&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11000" PostTypeId="2" ParentId="5599" CreationDate="2013-10-22T01:42:47.050" Score="-3" Body="&lt;p&gt;Movement is life. If the human body where to undergo this kind of temperature that would be below the normal temperature for the human body, we would in fact either have to move more and or do more as in eat, exercise, communicate etc. If your body did not have this mental capacity basic survival skill you would be in the process of slowing the function of your body down leading to death. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also the person who had swam in freezing water had a better tolerance to the cold than normal, but this does not mean that if a person had the capacity to tolerate cold temperatures that this kind of treatment of the body whould be good for you.&#xA;Over a short period of time your body can undergo extream circumstamces so it was a basic survival skill that had kicked in from the metal material of that persons being telling their physicsal as in nervous system that if they were going to survive they would have to move in order to regulate their body temperature.&lt;/p&gt;&#xA;" OwnerUserId="4725" LastEditorUserId="6" LastEditDate="2013-10-22T10:01:46.833" LastActivityDate="2013-10-22T10:01:46.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11001" PostTypeId="2" ParentId="10901" CreationDate="2013-10-22T01:48:19.397" Score="-1" Body="&lt;p&gt;You need to re-write your question, it is ambiguous and your use of terms is incorrect... Assumption: by &quot;activation&quot; you mean &quot;activation of transcription resulting in the expression of the transcription factor&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Transcription factors are proteins&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Genes are comprised of DNA elements&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A transcription factor can be involved in initiating the EXPRESSION of a transcription factor, whereafter that second distinct transcription factor initiates the EXPRESSION of another gene that encodes another transcription factor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Answer: No, genes do not &quot;activate&quot; transcription factors*&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Unless you are proposing the philosophical question of whether the DNA binding domain itself, which endows the transcription factor with a state of being active duty (i.e. fulfilling its purpose as a transcription factor), and thus that purpose is fulfilled only when the DNA binds the the TF, then a DNA binding domain can indeed &quot;activate&quot; the TF... but I'm pretty sure this isn't what you're asking.&lt;/p&gt;&#xA;" OwnerUserId="4726" LastActivityDate="2013-10-22T01:48:19.397" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11003" PostTypeId="2" ParentId="10998" CreationDate="2013-10-22T02:07:11.487" Score="1" Body="&lt;p&gt;That is a variable that you have the pleasure defining yourself. Just know that using a buffer will introduce other atoms that could affect the &quot;living things&quot;. Conversely, if you don't use a buffer, it is likely that the pH of your &quot;living things&quot; will be easily altered by the metabolism of your living things (IMHO, this is worse).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know the details of your project, but recommend:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-use a buffer like.. Tris, phosphate...&#xA;-use 10 mM Tris-Cl without any extra electrolyte (aside of the HCl or NaOH that you use to modulate the pH of your buffer to different pH's that you want to test)&#xA;-e.g. Tris-Cl pH 7, 8, 9.. or Phosphate pH 2,3,4,5,6,7,8,9..&lt;/p&gt;&#xA;" OwnerUserId="4726" LastActivityDate="2013-10-22T02:07:11.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11006" PostTypeId="2" ParentId="10968" CreationDate="2013-10-22T03:24:21.460" Score="0" Body="&lt;p&gt;There are a couple nice videos here: &lt;a href=&quot;https://synbiota.com/projects/325/&quot; rel=&quot;nofollow&quot;&gt;https://synbiota.com/projects/325/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also check out some DNA sequences and some protein structures (PDB files) if you want to learn more.&lt;/p&gt;&#xA;" OwnerUserId="4726" LastActivityDate="2013-10-22T03:24:21.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11007" PostTypeId="1" AcceptedAnswerId="11027" CreationDate="2013-10-22T08:33:29.143" Score="1" ViewCount="882" Body="&lt;p&gt;Majority of crustacean larvae have expanded carapace drawn out into processes as an adaptation for :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a. Protection from enemies&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b. Planktonic habit&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer given is b but I think it should be (a) as carapace functions as an exoskeleton. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please help!&lt;/p&gt;&#xA;" OwnerUserId="4058" LastActivityDate="2016-03-06T19:01:51.923" Title="Function of carapace" Tags="&lt;zoology&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11008" PostTypeId="2" ParentId="10999" CreationDate="2013-10-22T08:49:26.993" Score="5" Body="&lt;p&gt;As you have phrased it, the question can be understood in two ways. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The population size at t+1 is 350, after births, deaths and migration have taken place.&lt;/li&gt;&#xA;&lt;li&gt;The population size is 350 after deaths, but you also have to take births and migration into account to calculate population size at t+1&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;For &lt;strong&gt;alternative 1&lt;/strong&gt; the growth rate is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$pgr = \frac{(230+21)-(488+13)}{600} = -0.417$, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;with $\Delta N=-250 \Rightarrow -250 = 230+21-deaths-13$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For &lt;strong&gt;alternative 2&lt;/strong&gt; the growth rate is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$pgr = \frac{(230+21)-(250+13)}{600} = -0.02$&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2013-10-22T08:49:26.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11009" PostTypeId="1" AcceptedAnswerId="11010" CreationDate="2013-10-22T09:56:18.903" Score="11" ViewCount="20685" Body="&lt;p&gt;Going back to my high school days we were taught about dominant and recessive genes. We were taught how to calculate the geneotype and pheneotype of potential offspring using a small table (forgotten the actual table name). But it never occurred to me then what determines if a gene is dominant or recessive and how this is carried out biologically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take my example below, there is a 50% change that an offspring will carry both the tall (T) and short (t) genes. What determines that the tall gene T has a dominant effect over the short gene t. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I know that there is going to be differences between the different genes (i.e. eye colour), but is there a general description any one and provide which states how a gene becomes dominant and how the dominant effect is carried out biologically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/X3IFx.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="4108" LastEditDate="2016-12-04T22:06:20.053" LastActivityDate="2017-09-13T08:27:14.143" Title="What determines if an allele is dominant or recessive?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="11010" PostTypeId="2" ParentId="11009" CreationDate="2013-10-22T11:40:09.050" Score="8" Body="&lt;p&gt;Dominance is seldom complete. Owing to effects like co-dominance, incomplete dominance, collaborative (additive) effects of polygenes, our classical concept of dominance doesn't work. Having said that, there are certain ways in which a gene, if showing complete dominance can be analysed from the molecular level.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In an individual heterozygous for a certain trait, the following possibilities exist:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Both the alleles, though different, code for a protein (which might be an enzyme or a regulatory protein) which is functional and is indistinguishable atleast in terms of its functions. In this case, no matter if the person is heterozygous or homozygous for either allele, the concerned protein will be in sufficient amounts and will always be functional. These alleles can be treated as the same allele while performing Mendelian analysis though their products might differ slightly, leading to formation of two (or more) functionally similar &lt;strong&gt;&lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Alloenzyme&quot; rel=&quot;nofollow noreferrer&quot;&gt;Alloenzymes&lt;/a&gt;&lt;/em&gt;&lt;/strong&gt; (as opposed to Isozymes which are similar enzymes produced by genes at different loci).  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Haplosufficiency&lt;/em&gt;&lt;/strong&gt;. In this case, one of the two alleles codes for a functional protein and the other either codes for a non-functional protein (or does not code at all). But, even in heterozygous condition where only one allele producing functional protein is present, the amount of protein produced is sufficient to show the phenotype and hence, even in heterozygous individuals, enough protein is coded for by the single functional allele exhibiting the normal phenotype. If the two non-functional alleles are present as a homozygous pair, no functional protein is synthesised and hence the phenotype is not shown (i.e a different phenotype is shown). Here, the functional allele is Haplosufficient (able to produce enough protein in heterozygous condition) and is called the dominant since it expresses its phenotype both in heterozygous and homozygous conditions. this is pretty common.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Complete Haploinsufficiency&lt;/em&gt;&lt;/strong&gt;. Here again one allele codes for a functional protein while the other does not. But this time, if the functional allele is present in heterozygous condition, then the amount of the protein produced is not at all sufficient and hence the phenotype is not exhibited. Here the non-functional allele is said to be dominant because heterozygous phenotype resembles the phenotype of homozygous non-functional allele (where no protein is synthesized) since the functional allele is completely haploinsufficient (unable to produce enough protein in heterozygous condition). This method is pretty rare.(e.g rare autosomal dominant dyskeratosis congenita) &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;If there is &lt;strong&gt;partial haplosufficiency /partial haploinsufficiency&lt;/strong&gt;, the phenomenon of incomplete dominance can be explained. (heterozygous individual produces protein not sufficient for a full-blown phenotype but just a partial expression of the phenotype)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Here, &quot;functional&quot; refers to being actually &quot;functional&quot; as in case of flower colour (anthocyanin synthesis) or just performing certain kind of a conversion leading to a particular effect on thephenotype.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="6194" LastEditDate="2017-09-13T08:27:14.143" LastActivityDate="2017-09-13T08:27:14.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11011" PostTypeId="1" CreationDate="2013-10-22T14:25:25.190" Score="8" ViewCount="2101" Body="&lt;p&gt;When examining an incubated plate, it is rather clear that holding the plate in one hand and the lid in another is best for aseptic technique, or simply resting the lid on the plate as shown below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ft2TK.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I can't seem to find an answer for &lt;em&gt;what to do&lt;/em&gt; with your Petri dish lid when doing manipulations like plating. It's pretty obvious that the above practice is, well, practically impossible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, I always went under the assumption that when placing the Petri dish lid on the workspace, the orientation of the lid did not particularly affect risk of contamination, assuming that you're technique is indeed aseptic (ethanoled workbench, Bunsen burner, etc). However, discussing with collegues has resulted in mixed answers. Some say it doesn't matter, some say the lid should be facing up, some say down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;When doing manipulations like plating, is there a common practice for exactly how to place your Petri dish lid?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="1306" LastEditDate="2013-10-22T20:54:13.283" LastActivityDate="2014-06-23T12:33:56.257" Title="Does the Petri dish lid orientation on workbench affect aseptic technique?" Tags="&lt;lab-techniques&gt;" AnswerCount="3" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11012" PostTypeId="2" ParentId="11011" CreationDate="2013-10-22T14:53:38.640" Score="5" Body="&lt;p&gt;DISCLAIMER: I am a computational biologist and haven't touched a Petri dish since I was an undergraduate biology student.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would expect that the best thing to do would be to place the lid face down. &#xA;When placed so on the bench, it is only the tip of the lid that comes into contact with your (presumably sterile-ish) bench. If you place it face up, the interior of the lid will come into contact with the air of the lab. Despite the presence of the bunsen, I would expect that to gather more contamination. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the lid is larger than the dish itself, the lip of the lid never touches the dish. Therefore, if the lip of the lid touches the bench and becomes contaminated that is not a big problem since that contamination should be blocked from spreading to the actual culture. If, on the other hand, the lid were placed face up, the interior of the lid (which hangs just above your culture when closed) will have come into contact with possibly contaminated air and could then cause contaminants to drop onto your culture. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-10-22T14:53:38.640" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11013" PostTypeId="1" AcceptedAnswerId="11050" CreationDate="2013-10-22T15:10:07.200" Score="0" ViewCount="136" Body="&lt;p&gt;Growth hormone and insulin like growth factors are diabetogenic, so I assume that people with high growth hormone (say due to pituitary tumor) may be at high risk for diabetes.  Has any correlation been established between these two? I know that diabetes is a multifactorial disorder and so only a correlation may be established.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-23T15:22:16.557" LastActivityDate="2018-02-22T09:07:50.503" Title="Growth Hormone and diabetes" Tags="&lt;endocrinology&gt;&lt;pathology&gt;&lt;experimental&gt;&lt;diabetes-mellitus&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11014" PostTypeId="1" AcceptedAnswerId="11019" CreationDate="2013-10-22T15:18:24.287" Score="1" ViewCount="37" Body="&lt;p&gt;I read in Tortora and Derrickson that giving diuretics to diabetes insipidus patients may in fact alleviate the symptoms of the disease.  How is this possible?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-22T15:59:30.697" LastActivityDate="2013-10-22T16:07:50.853" Title="Giving diuretics to insipidus patient" Tags="&lt;endocrinology&gt;&lt;pathology&gt;&lt;homeostasis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11015" PostTypeId="1" AcceptedAnswerId="11018" CreationDate="2013-10-22T15:22:39.163" Score="3" ViewCount="315" Body="&lt;p&gt;I read in &lt;a href=&quot;http://bcs.wiley.com/he-bcs/Books%20?action=index&amp;amp;bcsId=6205&amp;amp;itemId=0470565101&quot; rel=&quot;nofollow&quot;&gt;Tortora and Derrickson&lt;/a&gt; that goitre is associated with &lt;a href=&quot;http://en.wikipedia.org/wiki/Euthyroid&quot; rel=&quot;nofollow&quot;&gt;euthyrodism&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is that possible?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-22T15:57:28.047" LastActivityDate="2013-10-22T20:04:34.727" Title="Euthyrodism and goitre" Tags="&lt;endocrinology&gt;&lt;homeostasis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11016" PostTypeId="2" ParentId="11011" CreationDate="2013-10-22T15:33:07.960" Score="0" Body="&lt;p&gt;In my experience, I have always used some kind of selection marker (typically antibiotics). In this case, it doesn't matter at all because any miniscule amount of foreign contamination would not be expected to carry an antiobitic resistance gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, when following sterile bench technique by wiping the benchtop with ethanol and working near a flame, then it also does not matter. The ethanol will take care of surface contaminants, and the flame keeps the air around it from being contaminated.  Also, when working with selection markers, the flame is usually unnecessary if the rest of your technique is aseptic.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-10-22T15:33:07.960" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11018" PostTypeId="2" ParentId="11015" CreationDate="2013-10-22T15:56:33.417" Score="4" Body="&lt;p&gt;In this context, euthyroidism refers to the amount of hormone present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.thyroid.org/what-is-a-goiter/&quot; rel=&quot;nofollow&quot;&gt;What is a goiter&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The term “goiter” simply refers to the abnormal enlargement of the thyroid gland. It is important to know that the presence of a goiter does not necessarily mean that the thyroid gland is malfunctioning. A goiter can occur in a gland that is producing too much hormone (hyperthyroidism), too little hormone (hypothyroidism), or the correct amount of hormone (euthyroidism). A goiter indicates there is a condition present which is causing the thyroid to grow abnormally.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;See also &lt;a href=&quot;http://www.aerzteblatt.de/int/archive/article/127610&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.jfponline.com/fileadmin/php/qhi/qhi_redirect.php?article_id=5072&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for more of the same info.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;ETA:&lt;/strong&gt; According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2804541/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Chronic lymphocytic thyroiditis (CLT), also known as Hashimoto thyroiditis, is an autoimmune, inflammatory process that causes up to 55% to 65% of all euthyroid goitres...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Although, as the link I already gave above state, regular ol' iodine deficiency can still cause euthyroid goiter.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-22T20:04:34.727" LastActivityDate="2013-10-22T20:04:34.727" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11019" PostTypeId="2" ParentId="11014" CreationDate="2013-10-22T16:02:01.120" Score="2" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Diabetes_insipidus&quot; rel=&quot;nofollow&quot;&gt;Wikipedia has your answer&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It seems paradoxical to treat an extreme diuresis with a diuretic, but the thiazide diuretics will decrease distal convoluted tubule reabsorption of sodium and water, thereby causing diuresis. This decreases plasma volume, thus lowering GFR [glomerular filtration rate] and enhancing the absorption of sodium and water in the proximal nephron. Less fluid reaches the distal nephron, so overall fluid conservation is obtained.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The source for that is an &lt;a href=&quot;http://jasn.asnjournals.org/content/15/11/2948.long&quot; rel=&quot;nofollow&quot;&gt;editorial from 2004&lt;/a&gt; that has some good other sources, including what appears to be the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1849045/&quot; rel=&quot;nofollow&quot;&gt;1959 original paper&lt;/a&gt; finding this seemingly-paradoxical result.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Thiazide diuretics inhibit the NaCl co-transporter (NCC/TSC) in the renal distal convoluted tubule (DCT). The DCT is water impermeable and considered to be part of the diluting segment. Therefore, the water-preserving effect of thiazides is unlikely related to a direct effect on the DCT. In fact, the most widely accepted hypothesis suggests that the antidiuretic action of thiazides is secondary to increased renal sodium excretion. The renal sodium loss causes extracellular volume contraction leading to lowered GFR and increased proximal tubular sodium and water reabsorption. Hence, less water and solutes are delivered to the distal tubule and collecting duct and are lost as urine.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-22T16:07:50.853" LastActivityDate="2013-10-22T16:07:50.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11021" PostTypeId="2" ParentId="11011" CreationDate="2013-10-22T17:39:53.437" Score="4" Body="&lt;p&gt;Working with petri plates both microbially and in tissue culture, there is one rule of thumb to follow. Contamination falls. Your main enemy is time, how long the medium is exposed (bar actually touching the surfaces). Ethanol DOES NOT sterilize the working surface. Think of it as a convenient scrubbant which evaporates quickly. The flame DOES NOT work to sterilize the air (except in the heated column above it, where you can't work). The flame creates an updraft near your workspace (see the rule of thumb), reducing falling contamination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Placing the lid on a &quot;clean&quot; working surface is a common and reasonable practice. If you are coordinated, holding the lid in the non-dominant hand can also be done. If you are using a 'hockey stick' spreader (dip in alcohol, then flame, then spread a dispensed drop after cooling), there may be a better way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Get a good petri plate turntable (might have to lubricate it with dry graphite).&#xA;Dry your petri plates for a while until no free moisture is visible in the dish.&#xA;Obtain some small volume glass pipettes (say 1 ml), with smooth tips, and sterilize them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you are ready to plate your suspension, place your petri dish on the turntable, remove the lid and give a good spin.  Dispense 0.2-1 ml of your suspension onto the medium directly, working the tip on the medium surface from the center to the edge, keeping a wet edge (surface tension). If you press too hard or hold the pipette too vertical, it digs in. Quick to learn this though. Replace the lid, and rest the plate a little while on the bench. A perfect spread (slight spiral) every time. Okay, a little practice helps. No flame, no alcohol, more free time for beer. Moisture content in the media is the only issue, but drying the plates inverted in a standard microbial incubator is easy enough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've used this method for years, with no major contamination issues.&lt;/p&gt;&#xA;" OwnerUserId="4732" LastEditorUserId="1306" LastEditDate="2013-10-22T23:32:35.297" LastActivityDate="2013-10-22T23:32:35.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11022" PostTypeId="2" ParentId="10720" CreationDate="2013-10-22T18:06:21.543" Score="8" Body="&lt;p&gt;It's also worth mentioning that the example suggested is incorrect. Human eye color is multigenic (i.e. MORE than 2 genes, probably more like 7) with more than one possible allele per gene. Epistasis can certainly occur, and combinations can happen which give rise to very uncommon colors, such as yellow. A simple one or two gene model will suggest brown eyes can't have blue eyed kids, and that is incorrect. This also ignores the frequent occurrence of mosaicism at the tissue level, which can yield kids with two different eye colors, or irises with two colors within them, which neither parent might have shown.&lt;/p&gt;&#xA;" OwnerUserId="4732" LastActivityDate="2013-10-22T18:06:21.543" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11023" PostTypeId="2" ParentId="10791" CreationDate="2013-10-22T18:13:33.363" Score="0" Body="&lt;p&gt;The above answer is mostly right. In the lab one can show that induced mutations are caused by exposure, compared to unexposed controls (e.g. in bacteria). The induced mutations will have a frequency, position, and type which can be typified. As a group, theyc ompris a &quot;spectrum&quot; of mutations. In a real case problem, such as humans exposed to diesel exhaust, the number of mutations and their trype are usually going to be too few to have a&quot;spectrum&quot;. Naturally occurring (a serious misnomer in its own right) could also occur in those same positions and types. The usual language is that the observed mutations are consistent with an exposure, but does not prove the exposure caused them.&lt;/p&gt;&#xA;" OwnerUserId="4732" LastActivityDate="2013-10-22T18:13:33.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11024" PostTypeId="2" ParentId="10683" CreationDate="2013-10-22T18:31:23.050" Score="2" Body="&lt;p&gt;The answer is yes, absolutelyvne enough time. You can do this experiment yourself. Get a clean glass jar, hell even sterilize if if you like (your oven overnight at 250 F will do it).   Fill it about 3/4 with clean (or even sterilized) water, and leave it outside in a mixed sunny shady spot for a few weeks, in moderate weather. It's small volume will get cooked by constant direct sun, which will impede the results.&#xA;After a few weeks (might be faster), look closely into the water (through the sides of the jar) with a magnifying glass, or better still, sample the water and look under a microscope. You won't see, but they are there, multiple bacterial species.&#xA;You will see single celled algae, small pond creatures (hydra, rotary-topped species (multiple)), paramecia, and multi-celled algal forms in strings. These are all fallen in from airborne dust and windblown particles.  You likely won't get fish, but if you are lucky, you might get a few brine shrimp.  And yes, particles of blown or bird-carried dirt etc can easily carry shrimp, amphibian, or plausibly, viable fish eggs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what do they feed on?  There's no food in the water you put in !!  CO2, nitrogen, Oxygen, etc are readily available from the air. A few cells of bacteria or algal forms seed the clean water, and begin fixing CO2, nitrogen etc, and now you have a food source. Wind-carried (or bird-carried) small organisms can now survive in a web of bacteria-plant-animal interactions.&#xA;By the way, you can also run a control jar, where you sterilize the jar, fill it with boiling hot water, and quickly cover it tightly with foil. Place it beside your open jar, and it will grow...nothing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note, &quot;toxic&quot; algae are often not toxic to small organisms and other algae. Their toxins (neurotoxins usually) affect mostly only higher organisms, such as fish and humans. Algal blooms kill fish and birds, they seldom sterilize the pond.&lt;/p&gt;&#xA;" OwnerUserId="4732" LastActivityDate="2013-10-22T18:31:23.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11025" PostTypeId="1" CreationDate="2013-10-22T20:32:21.313" Score="3" ViewCount="2938" Body="&lt;p&gt;OK, I have rheumatoid arthritis and I've been injecting Humira 2 times a month for the last 8 months.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I know rheumatoid arthritis is simply an immune system disorder which makes the immune system produce more proteins called Tumor Necrosis Factor alpha which regulate body disorders.&#xA;When I inject Humira I actually import a protein called Adalimumab which is a TNFα inhibitor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far so good but my question is &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does my body throw this protein away after some time? How is this protein removed from my body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about the way Adalimumab inhibits TNF, does it bind to TNF?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also the details of how rheumatoid arthritis appears are not well known but the main reason is because of the patients DNA isn't it?&lt;/p&gt;&#xA;" OwnerUserId="4497" LastEditorUserId="1306" LastEditDate="2013-10-23T01:31:47.940" LastActivityDate="2017-04-06T15:02:02.070" Title="How does Humira work when injected into patients with rheumatoid arthritis?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;human-genetics&gt;&lt;autoimmune&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11026" PostTypeId="1" CreationDate="2013-10-22T20:55:10.273" Score="6" ViewCount="40887" Body="&lt;p&gt;When extracellular $K^+$ concentration increase by a certain amount, excitability of cells is higher because the resting potential shifts toward a higher equilibrium potential of $K^+$, therefore causing depolarization. However, when there concentration of extracellular $Ca^{2+}$ increases, excitability of cells decreases. If $Ca^{2+}$ and $K^+$ are both positively charged ions, what is the cause behind their opposite physiological effects? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not a biology student, so detailed answers would be kindly appreciated. Thank you!&lt;/p&gt;&#xA;" OwnerUserId="4685" LastEditorUserId="5144" LastEditDate="2014-06-02T10:55:58.063" LastActivityDate="2016-04-05T08:34:57.887" Title="How does extracellular potassium ion concentration and calcium ion concentration affect the excitability of a cell?" Tags="&lt;physiology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11027" PostTypeId="2" ParentId="11007" CreationDate="2013-10-22T21:04:38.830" Score="2" Body="&lt;p&gt;&lt;strong&gt;Preface&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Any question about adaptation on macro-level has very little meaning and no precise answer.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There are two types of larvae in invertebrates: primary (&quot;original&quot;) and secondary (evolved from post-larval stages). Not digging into the details, nauplius (together with metanauplius) is the only type of primary larvae in Crustacea and it never has a carapace.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&quot;Majority&quot; is by far too strong term, even if we are talking about all larval types. If we just take the largest crustacean orders with species numbers &gt; 1000, together comprising 92% of crustacean species (species numbers are from &lt;a href=&quot;http://www.mapress.com/zootaxa/2011/f/zt03148p191.pdf&quot; rel=&quot;nofollow&quot;&gt;Ahyong et al, 2011&lt;/a&gt;, they seem to be largely correct):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Decapoda - 14.7 k species - rarely have nauplius, marine forms do have planktonic carapaced larvae (principally - zoea)&lt;/li&gt;&#xA;&lt;li&gt;Isopoda - 10.7 k - no carapace&lt;/li&gt;&#xA;&lt;li&gt;Amphipoda - 9.9 k - no carapace&lt;/li&gt;&#xA;&lt;li&gt;Podocopida - 6.2 k - no carapace&lt;/li&gt;&#xA;&lt;li&gt;Harpacticoida - 6.0 k - no carapace&lt;/li&gt;&#xA;&lt;li&gt;Cyclopoida - 4.2 k - no carapace&lt;/li&gt;&#xA;&lt;li&gt;Calanoida - 3.1 k - no carapace&lt;/li&gt;&#xA;&lt;li&gt;Siphonostomatoida - 2.5 k - no carapace&lt;/li&gt;&#xA;&lt;li&gt;Cumacea - 1.5 k - have carapace, but development is direct&lt;/li&gt;&#xA;&lt;li&gt;Mysida - 1.2 k - have carapace, but development is direct&lt;/li&gt;&#xA;&lt;li&gt;Tanaidacea - 1.1 k - have carapace, but development is direct&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So, &quot;majority&quot; could be applied to Decapoda only.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fabula&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we substitute &quot;adaptation&quot; with &quot;main biological function&quot; (as you have done) or more correctly &quot;main physiological role&quot;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would prefer the (a), because carapace does function as a protective structure in those decapod larvae which don't rely on behavioral anti-predatory defenses: &lt;a href=&quot;http://link.springer.com/article/10.1007/BF00385256&quot; rel=&quot;nofollow&quot;&gt;see Morgan&lt;/a&gt;: &quot;Fishes quickly learned to avoid spined prey, which ... may also increase the rate of evolution of the character&quot;. Non-carapaced larvae rely principally on behavior only.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only contribution of carapace to planktonic life-style in zoea is participation of its spines [when they are pronounced] in parachuting (&lt;a href=&quot;http://www.nrcresearchpress.com/doi/pdf/10.1139/z84-176&quot; rel=&quot;nofollow&quot;&gt;Chia et al&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[The above should be largely true also for the cypris larva of the cirripeadians, which are enclosed in a non-spined bivalve carapace.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the morphological point of view, [at least in adult forms of decapods] carapace creates a chamber for gills, so a morphologist would argue that &lt;em&gt;this&lt;/em&gt; is the &quot;main function&quot; of carapace.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2016-03-06T19:01:51.923" LastActivityDate="2016-03-06T19:01:51.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11028" PostTypeId="1" CreationDate="2013-10-22T21:53:33.063" Score="3" ViewCount="219" Body="&lt;p&gt;I'm doing research for a series I'm writing. in it the main character is pregnant however goes off to fight a criminal organization who have been killing her friends and i want her appearance to show that she may not be pregnant however she fights and defends as if she is mindful of heavy impacts could cause a miscarriage&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering how far into a pregnancy is it before visible signs of it is apparent and risk of physical trauma causing miscarriage increases, if there is also a point during the pregnancy where the fetus could mutate via outside interference then that would be good to know too however I can go without that information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NOTE: I want to know this information so that even though the world in this series I'm writing is totally fictional, one can begin to question how fictional it really is when some parts are based off actual science and logic of real life.&lt;/p&gt;&#xA;" OwnerUserId="4378" LastEditorUserId="4101" LastEditDate="2013-10-24T22:33:42.010" LastActivityDate="2013-11-24T04:27:18.117" Title="How far into a pregnancy is it before visible signs of it is apparent and risk of physical trauma increases" Tags="&lt;human-biology&gt;&lt;reproduction&gt;&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11029" PostTypeId="2" ParentId="11025" CreationDate="2013-10-22T22:13:11.443" Score="5" Body="&lt;p&gt;Adalimumab is an antibody that binds to tumor necrosis factor alpha. Antibodies have high-affinity binding sites for their antigen, and for a small antigen such as TNF-alpha, would bind to it and prevent it from binding to its target receptors. Antibodies, like all proteins, degrade after a certain period of time and are removed from circulation, and since the body does not produce more of this antibody, it must be re-administered every few weeks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanism of this pharmacological is in a sense somewhat ironic in that in nature the chief role of antibodies is binding and neutralization of foreign and potentially dangerous antigens, however, this antibody binds and neutralizes a feature of the immune system itself. This element of the immune system is a cytokine, TNF-alpha, whose function is to promote inflammation, which draws white blood cells to the site of the inflammation and activates them. TNF-alpha also induces fever, and suppresses tumor formation and viral replication by activating programmed cell death pathways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aggressive immune responses always cause collateral damage to surrounding tissues, however, in autoimmune diseases such as rheumatoid arthritis the damage is compounded by the fact that the target of the immune response is an element of the body itself. A central function of the immune system is to induce tolerance to self; sometimes tolerance fails and while there are genetic components involved, the process is yet to be well-understood.&lt;/p&gt;&#xA;" OwnerUserId="4140" LastActivityDate="2013-10-22T22:13:11.443" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="11032" PostTypeId="2" ParentId="9417" CreationDate="2013-10-23T01:58:42.060" Score="1" Body="&lt;p&gt;If you want to express them in an operon, make sure you have an RBS at the 5' end of each coding sequence. If you place one 10bp downstream without it having an RBS, it will be transcribed, but not translated... If you want more help, paste the DNA code of each as a comment. &lt;/p&gt;&#xA;" OwnerUserId="4735" LastActivityDate="2013-10-23T01:58:42.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11034" PostTypeId="2" ParentId="10476" CreationDate="2013-10-23T02:14:54.440" Score="1" Body="&lt;p&gt;Yes, they will both affect pH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to the above comment, both, but methanol especially dehydrates samples - removal of water will most definitely affect the pH in organelles. This will be time dependent. Both duration of fixation, and time after fixation before you assess the cells will affect the pH of the organelles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because you fix the cells in a non-aqueous environment (I presume you're using standard fixation), you don't use buffer during fixation. We might be able to answer better if you post the general protocol you follow. &lt;/p&gt;&#xA;" OwnerUserId="4735" LastActivityDate="2013-10-23T02:14:54.440" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11036" PostTypeId="2" ParentId="9521" CreationDate="2013-10-23T02:24:05.140" Score="0" Body="&lt;p&gt;Years of discussion about this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Polymerases Per Second.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A standard unit to measure the inputs and outputs of a BioBrick Device.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PoPS have yet to be directly measured in vivo.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://openwetware.org/wiki/PoPS&quot; rel=&quot;nofollow&quot;&gt;http://openwetware.org/wiki/PoPS&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*understanding this would be a great feat and it would get us one step closer to measuring complex systems. &lt;/p&gt;&#xA;" OwnerUserId="4735" LastActivityDate="2013-10-23T02:24:05.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11037" PostTypeId="2" ParentId="7835" CreationDate="2013-10-23T03:05:28.060" Score="1" Body="&lt;p&gt;I used pEYFP-N1 (stock vector) where the spacing between the CMV promoter and the EYFP start codon is ~88 nt, and the expression is high.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also cloned a protein 5' of the EYFP, only 4 nt after the CMV promoter. The expression of this fusion was also high. Because I was only using the chimeric protein in experiments, I did not try to assess differences in EYFP expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look here: &lt;a href=&quot;https://synbiota.com/projects/19/sequences&quot; rel=&quot;nofollow&quot;&gt;https://synbiota.com/projects/19/sequences&lt;/a&gt; you'll see the basic pEYFP-N1 vector and the separation between the CMV promoter and the EYFP coding sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On wiki: &quot;The TATA element and BRE typically are located close to the transcriptional start site (typically within 30 to 40 base pairs).&quot;&lt;/p&gt;&#xA;" OwnerUserId="4735" LastActivityDate="2013-10-23T03:05:28.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11038" PostTypeId="1" AcceptedAnswerId="11046" CreationDate="2013-10-23T05:36:18.803" Score="1" ViewCount="413" Body="&lt;p&gt;One guide I have been using to tell me if I really am gaining a lot of weight is a ring around my 2nd last finger on my right hand, if I can slip it on and off without any resistance then I'm fine, however I've been basing this from the notion that if I gain weight it's proportionally distributed around my body, as such, if I get fatter so do my fingers&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I am wondering, is fat distributed proportionally around the body (ie. if your waist gets bigger then your fingers will get bigger along with it)?&lt;/p&gt;&#xA;" OwnerUserId="4378" LastEditorUserId="6" LastEditDate="2013-10-23T10:14:43.073" LastActivityDate="2013-10-23T13:08:24.150" Title="Is fat distributed proportionally around the body?" Tags="&lt;nutrition&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11039" PostTypeId="1" CreationDate="2013-10-23T05:43:43.350" Score="23" ViewCount="28183" Body="&lt;p&gt;The Japanese Wikipedia states that the average human body temperature is 36.0 °C (&lt;a href=&quot;https://ja.wikipedia.org/wiki/%E3%83%92%E3%83%88&quot;&gt;here&lt;/a&gt;,&quot;ヒト&quot;).&lt;br&gt;&#xA;The statement references the data from the Japanese government.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually all of my Japanese friends think the same.&lt;br&gt;&#xA;A body temperature of 37.5 °C is considered a serious illness in Japan, justifying absence from work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most other countries' sources cite 37.0 °C as an average.&lt;br&gt;&#xA;Is there a biological explanation for this apparent discrepancy?&lt;/p&gt;&#xA;" OwnerUserId="3535" LastEditorUserId="-1" LastEditDate="2014-08-03T14:54:51.363" LastActivityDate="2017-04-10T19:13:17.597" Title="In Japan, the official average body temperature is 36.0 °C. Why so different from that of Europe?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;temperature&gt;" AnswerCount="4" CommentCount="7" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="11040" PostTypeId="2" ParentId="11009" CreationDate="2013-10-23T07:01:43.743" Score="4" Body="&lt;p&gt;Fisher and Wright provided two different models in order to explain why newly arisen mutations tend to be recessive. I am not sure though if this answer your question!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fisher's model&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;...there is a tendency always at work in nature which modifies the&#xA;  response of the organism to each mutant gene in such a way that the&#xA;  wild type tends to become dominant.&quot;&#xA;  Given that most mutations are deleterious, there is selection to make fixed mutations dominant over almost any mutations that could appear.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Wright's model&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;...mutations are most frequently in the direction of inactivation and&#xA;  that for physiological reasons inactivation should generally behave as&#xA;  recessive.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are 2 physiological reasons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Deleterious mutations are mutations that usually cause a protein to not work properly. Given that the kinetics of reaction is usually not linear but is a function which derivative is decreasing over the number of enzyme, if we divide by 2 the number of functionning protein, we divide by less than two the reaction rate. Therefore, a deleterious mutation is usually recessive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The reagents of a given reaction are often the products of another one. If this other reaction is slow compare to the reaction that followed, diminishing the rate the following reaction will not have a big impact on the rate of the overall metabolic pathway. Therefore, most deleterious mutations are recessive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More information &lt;a href=&quot;http://www.zoology.ubc.ca/~otto/Talks/Dominance/Dominance.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that there is a correlation between the impact a mutation has on fitness and its recessivity (the worst is a mutation, the higher is its recessivity).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-04-27T23:14:51.757" LastActivityDate="2015-04-27T23:14:51.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11041" PostTypeId="2" ParentId="10402" CreationDate="2013-10-23T09:40:17.280" Score="4" Body="&lt;p&gt;Beside the reasons you've given I would add environmental disturbance (e.g. flooding) as a evolutionary factor that could explain selection for taller individuals. Many palms also inhabit and thrive in disturbed habitats (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1744-7429.1998.tb00069.x/pdf&quot; rel=&quot;nofollow&quot; title=&quot;Frangi &amp;amp; Lugo. 1998. A Flood Plain Palm Forest in the Luquillo Mountains of Puerto Rico Five Years After Hurricane Hugo. Biotropica 30(3).&quot;&gt;Frangi &amp;amp; Lugo, 1998&lt;/a&gt;; &lt;a href=&quot;http://www.scielo.br/scielo.php?pid=s1676-06032005000100004&amp;amp;script=sci_arttext&quot; rel=&quot;nofollow&quot; title=&quot;Salm. 2005. The importance of forest disturbance for the recruitment of the large arborescent palm Attalea maripa in a seasonally-dry Amazonian forest. Biota Neotropica 5(1).&quot;&gt;Salm, 2005&lt;/a&gt;), which indicates that this could potentially (i.e. speculative) be an important factor for this taxon. Palms also have the combination of tall height and a relatively low &quot;wind profile&quot; (relative to many other groups of trees), which indicates that they are adapted to exposed/disturbed habitats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This, along with the reasons you've already given, seems to cover the most obvious evolutionary reasons for selection on tree height. However, these will naturally trade-off against negative effects on e.g. fecundity from investing and maintaining biomass.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-10-23T09:46:48.910" LastActivityDate="2013-10-23T09:46:48.910" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11043" PostTypeId="1" CreationDate="2013-10-23T11:57:32.937" Score="3" ViewCount="45" Body="&lt;p&gt;Some cancer tumors suppress themselves from spreading. When such tumors are removed by surgery, the metastasis process is accelerated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isn't it possible to put such tumors into external device like hemodialysis device and slow metastasis process this way?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any experiments or clinical usages of own body tissues in such a devices? Not for cancer, but probably for some other reasons, in humans and animals? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some sort of grafting for animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such a tissue can interact with main body by blood and cause some effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3VmaJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1584" LastActivityDate="2013-10-23T17:11:54.803" Title="External tissues, connected to the body?" Tags="&lt;hematology&gt;&lt;tissue&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11044" PostTypeId="1" CreationDate="2013-10-23T12:04:33.923" Score="18" ViewCount="13821" Body="&lt;p&gt;The atmosphere pressure is 10 meters of water (approx). This means that it is impossible to lift water higher than 10 meters with vacuum or сapillary action (on Earth, under normal conditions).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are trees higher than 10 meters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do they lift water to their tops?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words: how cohesion-tension theory can be true if it apparently contradicts the laws of physics? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE 2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Atmospheric pressure helps to rise the water, not resists rising. What is resisting is water weight. When water column is 10 meters high, then atmospheric pressure can't help anymore. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any adhesion/cohesion mechanism can't help here too, because it acts only in thin molecular layer. To transfer action force further the pressure is required, which is insufficient at 10 meters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE 3&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we had capillary small enough to rise water to 10 meters and then we will build smaller capillary which we expect will rise water higher, we will fail. Water column will break and does not climb higher than 10 meters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eGEXX.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Menisci acts like small piston and can't help rising water higher than 10 meters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE 4&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Common pressure distribution in capillary is follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uscvI.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$P_0$ is atmospheric pressure. As you see, right under menisci, the pressure is lowered by $2 \sigma / R$ where $R$ is the radius of menisci and $\sigma$ is surface tension. The entire term is called &quot;Laplace pressure&quot;. As you see, it can't supersede atmospheric pressure, because water continuity will be broken in the case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I.e. no any menisci can rise water higher than 10 meters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The existence of higher trees PROVES that there are some other significant mechanisms, not adhesion/cohesion, not capillary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE 5&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Current version, as I understood it, is based on a declaration, that a water, if put into thin capillary, can behave like a solid body. Particularly, it can resist tension up to minus 15 atmospheres. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a &lt;strong&gt;tensile strength of concrete&lt;/strong&gt;, so I don't believe that without additional proofs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it is just not hard to make thin tube, put water into it and check, how high it can climb.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Was it done ever?&lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="1584" LastEditDate="2013-10-24T06:28:33.383" LastActivityDate="2014-09-22T12:29:42.500" Title="How do trees lift water higher than 10 meters?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;biophysics&gt;" AnswerCount="4" CommentCount="21" FavoriteCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="11045" PostTypeId="1" AcceptedAnswerId="11047" CreationDate="2013-10-23T12:27:28.923" Score="4" ViewCount="1943" Body="&lt;p&gt;What were the criteria devised for the numbering convention employed in human chromosomes? When was it fixed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Correct me if I am wrong; it appears that chromosome pairs 1 to 22 were originally ordered in terms of perceived structural size, which ended up fitting neatly with the quantity of base pairs (but not with the quantity of genes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sex chromosomes in turn were arbitrarily assigned as &quot;pair 23&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this sound?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="4738" LastEditorUserId="1320" LastEditDate="2013-10-23T14:07:53.000" LastActivityDate="2013-10-23T14:07:53.000" Title="Criteria for the numbering of human chromosomes" Tags="&lt;molecular-genetics&gt;&lt;human-genome&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11046" PostTypeId="2" ParentId="11038" CreationDate="2013-10-23T13:08:24.150" Score="2" Body="&lt;p&gt;@fileunderwater's suggestion to use a scale is probably the best answer you could get, but looking at this broadly, the answer is no.  The oft-referenced &lt;a href=&quot;http://www.webmd.com/a-to-z-guides/body-fat-distribution&quot; rel=&quot;nofollow&quot;&gt;apple and pear shapes&lt;/a&gt; are indeed &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7628000&quot; rel=&quot;nofollow&quot;&gt;very real&lt;/a&gt; and have &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2585758/&quot; rel=&quot;nofollow&quot;&gt;medical consequences&lt;/a&gt;.  One of the issues is that there are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2908522/&quot; rel=&quot;nofollow&quot;&gt;sex differences&lt;/a&gt; in fat distribution.  There is no evidence I can find that finger fat is a good correlate of overall body fat, although admittedly yours could be.  It is also likely a function of how much overweight you were when you began the &quot;experiment&quot; i.e. the relationship probably isn't linear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, in men the &lt;a href=&quot;http://www.nature.com/ijo/journal/v30/n4/full/0803154a.html&quot; rel=&quot;nofollow&quot;&gt;ratio of the &lt;em&gt;length&lt;/em&gt; of the second and fourth digits&lt;/a&gt; are otherwise meaningful.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-23T13:08:24.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11047" PostTypeId="2" ParentId="11045" CreationDate="2013-10-23T13:29:26.183" Score="5" Body="&lt;p&gt;Why do you think it was &quot;fixed?&quot;  Here's a &lt;a href=&quot;http://www.nature.com/nrg/journal/v3/n10/full/nrg905.html&quot; rel=&quot;noreferrer&quot;&gt;nice review&lt;/a&gt; of the history of human cytogenetics, which included not only the original image from 1956 but points out &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1748444/&quot; rel=&quot;noreferrer&quot;&gt;a report&lt;/a&gt; which comments on the standardization of chromosome number.  The autosomes were indeed numbered by length, and the sex chromosomes are traditionally put at the end as they are &quot;numbered&quot; 23 but clearly function quite differently.  Gene content was decades away from being known at the time, and honestly isn't even known now.  It's also just as arbitrary; simple size is easy enough and makes for rather nice pictures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/l0c4S.gif&quot; alt=&quot;FISH!&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-23T13:29:26.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11049" PostTypeId="1" AcceptedAnswerId="11052" CreationDate="2013-10-22T22:14:23.133" Score="7" ViewCount="1901" Body="&lt;p&gt;I am looking for a &lt;code&gt;family tree&lt;/code&gt; for plants, particularly veg / herbs / fruit. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something similar to: &lt;img src=&quot;https://i.stack.imgur.com/ViXeH.gif&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it could be slightly less technical than all the Latin names too :). The aim is to easily find out what plants are related such as Cabbage, Broccoli, sprouts, Cauliflower (all Brassicaceae). Currently having to look them all up on Wikipedia which is quite painful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example, but a plant version. &lt;img src=&quot;https://mapsandmemories.edublogs.org/files/2012/01/classification-animals-qybz56.gif&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4734" OwnerDisplayName="dogmatic69" LastEditorUserId="15950" LastEditDate="2019-01-01T19:17:31.690" LastActivityDate="2020-11-14T12:29:44.643" Title="Family tree for edible plants?" Tags="&lt;botany&gt;&lt;taxonomy&gt;&lt;phylogenetics&gt;&lt;ethnobiology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="11050" PostTypeId="2" ParentId="11013" CreationDate="2013-10-23T15:21:19.410" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3053958&quot; rel=&quot;nofollow&quot;&gt;Yes&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;That GH has an effect on glycaemic control is most evident from the abnormal glucose tolerance seen in acromegalics...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;acromegaly&lt;/code&gt; is defined as &lt;code&gt;abnormal growth of the hands, feet, and face, caused by overproduction of growth hormone by the pituitary gland.&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such an effect has been &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8300053&quot; rel=&quot;nofollow&quot;&gt;known for decades&lt;/a&gt;, which makes sense given how interrelated the axes are.  Although I think the best evidence is the fact that the &lt;a href=&quot;http://www.genotropin.com/&quot; rel=&quot;nofollow&quot;&gt;side effects of growth hormone therapy&lt;/a&gt; says that &lt;code&gt;Some patients have developed diabetes mellitus...&lt;/code&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-23T15:21:19.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11051" PostTypeId="1" AcceptedAnswerId="11053" CreationDate="2013-10-23T15:27:26.197" Score="3" ViewCount="272" Body="&lt;p&gt;I'm a total novice when it comes to biology, and I'm really just looking for an answer to a question that has been posed to me by people who deny evolution fervently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution dictates that we've gone from simple, single cell organisms to complex, multicellular organisms. If we consider the hand, for example, the hand is made up of various cells. Those cells are created according to DNA, which acts like a cell-level instruction manual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where are the &quot;instructions&quot; for &lt;em&gt;where those cells go&lt;/em&gt;? I.e Where are the instructions that state that various cells have to line up in a thin, long, appendage structure to form a finger, or hand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This isn't a particularly difficult question, I imagine. If it's been asked before, apologies. I don't know any of the technical terminology; this is just something that I would like to learn about.&lt;/p&gt;&#xA;" OwnerUserId="3186" LastActivityDate="2013-10-24T03:58:43.790" Title="Evolutionary Cell Structuring" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="11052" PostTypeId="2" ParentId="11049" CreationDate="2013-10-23T15:38:09.780" Score="17" Body="&lt;p&gt;Basically just search &quot;thing you want&quot; and &quot;phylogeny&quot; and you'll find a million results on Google.  For you, I might recommend the &lt;a href=&quot;http://botanistinthekitchen.wordpress.com/&quot; rel=&quot;noreferrer&quot;&gt;Botanist in the Kitchen blog&lt;/a&gt;, which has a &lt;a href=&quot;http://botanistinthekitchen.wordpress.com/the-plant-food-tree-of-life/phylogenetic-tree-view/&quot; rel=&quot;noreferrer&quot;&gt;whole page on the subject&lt;/a&gt; and has assembled this phylogeny, including many, many others.  It's pretty impressive!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kPRbh.jpg&quot; alt=&quot;Plant food phylogeny&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-23T15:38:09.780" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="11053" PostTypeId="2" ParentId="11051" CreationDate="2013-10-23T16:29:26.163" Score="8" Body="&lt;p&gt;The main governing principle is very simple and one of the most elegant mechanisms in biology. It is based on concentration gradients. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Briefly, certain cells secrete signaling molecules (called &lt;a href=&quot;http://en.wikipedia.org/wiki/Morphogen&quot; rel=&quot;noreferrer&quot;&gt;morphogens&lt;/a&gt;) that are detected by other cells. These molecules then activate the transcription of genes in the target cells. Since the molecules in question are produced by a subset of cells, their concentration varies according to the distance between the receiving cell and the producing cells. Different concentrations of the signalling molecules have different effects and this allows the formation of really quite complex patterns.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can be illustrated very well using Wolpert's classic &lt;a href=&quot;http://embryo.asu.edu/pages/french-flag-model&quot; rel=&quot;noreferrer&quot;&gt;French Flag Model&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/I1UuL.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, different concentration thresholds of the morphogen result in different patterns of gene expression. This simple system can give extremely complex results (such as yourself, for example). It gets more complex when there are multiple morphogens acting in tandem. Say morphogen1 is produced by cells on the left and morphogen2 by cells on the right, cells in the middle will have varying concentrations of both morphogens and will react accordingly:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xIAmF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just about every pattern formation during development boils down to differential concentrations of diffusing morphogen molecules, it really is a wonderful example of how simple systems can give rise to extremely complex results. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;On an unrelated note, this has absolutely nothing to do with evolution. At least no more so than any other biological process. If your friends do not accept evolution, I don't see how they can use this as an argument. Even if a god created humanity in his or her image as these people tend to believe, babies are still born and they still develop in the womb. As far as I know, even the most fundamentalist Christians do not believe in a mechanic god that puts babies together in the womb from some kind of IKEA kit. Even if humans sprung fully formed from the hands of this god, individual infants are still formed out of multiple cells. There is therefore a need for a mechanism that can coordinate this process, whether this mechanism evolved or was designed is irrelevant, it is still there and extremely easily observable (images taken from &lt;a href=&quot;http://dev.biologists.org/content/133/3/385/F1.large.jpg&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/a4SQ2.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image above shows the locations and concentrations of various morphogens in a fruit fly embryo. You can see the concentration gradients clearly.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-10-23T16:45:05.417" LastActivityDate="2013-10-23T16:45:05.417" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11055" PostTypeId="2" ParentId="11043" CreationDate="2013-10-23T17:11:54.803" Score="3" Body="&lt;p&gt;I've actually wondered this myself from time to time, without ever bothering to look it up.  Well, &lt;a href=&quot;http://online.wsj.com/news/articles/SB10001424052748703555804576102081795100672&quot; rel=&quot;nofollow noreferrer&quot;&gt;it's actually happening&lt;/a&gt;.  That WSJ article says the following, which just blows my mind:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Researchers at the Rogosin Institute are taking tumor cells from mice, encapsulating them in beads made from a seaweed-derived sugar called agarose, and implanting them in the abdomen of cancer patients. There, cells in the beads secrete proteins researchers believe could signal a patient's cancer to stop growing, shrink or even die.&lt;/p&gt;&#xA;&lt;p&gt;So far, at least 30 patients have been treated with the cancer beads in an initial human study, and a phase two or intermediate-stage trial has been launched—with the approval of the U.S. Food and Drug Administration—to test the technique in patients with advanced colon, pancreatic and prostate cancers.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;You can find the info on the &lt;a href=&quot;http://clinicaltrials.gov/ct2/show/study/NCT01053013&quot; rel=&quot;nofollow noreferrer&quot;&gt;Phase II trial here&lt;/a&gt;; they are currently at the &amp;quot;recruiting participants&amp;quot; point.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;[The treatment] consists of small beads that contain mouse cancer cells from a mouse kidney cancer cell line. The cells in the beads produce substances that have been shown to slow or stop the growth of tumors in experimental animals, veterinary patients, and 23 humans with different types of cancers in a Phase 1 safety trial.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-23T17:11:54.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11057" PostTypeId="2" ParentId="11044" CreationDate="2013-10-23T18:53:38.270" Score="4" Body="&lt;p&gt;Here's &lt;a href=&quot;https://www.youtube.com/watch?v=BickMFHAZR0&quot; rel=&quot;nofollow&quot;&gt;Veritasium on youtube&lt;/a&gt; has one explanation which is same as @AlanBoyd's comment.&lt;/p&gt;&#xA;&#xA;&lt;blockquote class=&quot;spoiler&quot;&gt;&#xA;  &lt;p&gt; Meta-stable liquid can have negative pressure.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2013-10-23T19:02:30.260" LastActivityDate="2013-10-23T19:02:30.260" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="11058" PostTypeId="1" AcceptedAnswerId="11088" CreationDate="2013-10-23T18:56:49.620" Score="17" ViewCount="89498" Body="&lt;p&gt;This is a medicine-related question that I've been wondering about. I've been watching medical lectures on YouTube regarding the human body and was wondering about how surgeons treat a severed artery or vein (think Juggular or Carotid)? Specifically I was curious about what kind of tools they use and what the technique is for performing this operation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And before anyone asks, no, I don't need to treat someone with this kind of injury :).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,&#xA;mj&lt;/p&gt;&#xA;" OwnerUserId="4488" LastActivityDate="2015-07-08T20:41:04.877" Title="how to close a severed artery/vein?" Tags="&lt;medicine&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="11059" PostTypeId="1" AcceptedAnswerId="11062" CreationDate="2013-10-23T19:04:05.033" Score="5" ViewCount="2964" Body="&lt;p&gt;I am novice to biochemistry and biology in general. I am reading Lehninger Principles of Biochemistry, and I found the following sentence at the beginning of the chapter on glycolysis:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A bacterium such as Escherichia coli can obtain from glucose the carbon&#xA;  skeletons for every amino acid, nucleotide, coenzyme, fatty acid, or&#xA;  other metabolic intermediate it needs for growth.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Does this mean that &lt;em&gt;E.coli&lt;/em&gt; can survive in a medium containing H₂O and glucose alone? &lt;em&gt;E.coli&lt;/em&gt; can synthesize any other nutrient it needs?&lt;/p&gt;&#xA;" OwnerUserId="561" LastEditorUserId="3340" LastEditDate="2014-10-10T10:27:50.850" LastActivityDate="2014-10-10T10:30:04.080" Title="Can Escherichia coli survive on glucose and water alone?" Tags="&lt;ecoli&gt;&lt;glucose&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11060" PostTypeId="2" ParentId="11059" CreationDate="2013-10-23T19:39:01.540" Score="4" Body="&lt;p&gt;Yes, but no. In other words, this quote is not probably not true in the ways you'd think.  Bacteria &lt;em&gt;can&lt;/em&gt; survive on practically nothing for long periods of time, but whether you call that life is subjective. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nitrogen is necessary for all the co-enzymes and proteins to sustain life. In order to get energy, if E coli. needs to metabolize nitrogen to waste at all, all the bacteria would eventually all die out.  The same feat for human beings would be to add a little sugar into sewage and surviving on it.  Nobody would die right away, but its hard to call that living maybe. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unless a medium is exchanged, E coli in a laboratory culture will start a massive die off.  &lt;a href=&quot;http://www.its.caltech.edu/~skopf/ESE_Bi168/files/nrmicro1340.pdf&quot; rel=&quot;nofollow&quot;&gt;When the E coli culture becomes terminal in this way, a portion of the bacteria go into stationary phases where the bacteria can survive for very long times - for months or possibly years&lt;/a&gt;.  So some of the bacteria would survive, but they would be dormant. You might not call this survival, but tens of thousands of bacteria are still alive and can generate colonies if transferred to fresh media. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Laboratory cultures and media are of course artificial conditions which don't reflect the environment which bacteria are adapted.  In their life cycle, they typically have other sorts of behavior and experience low nutrient conditions often enough.  Bacteria are also different in that a 99.99% die off can be considered a typical event in some cases.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-10-24T14:44:12.510" LastActivityDate="2013-10-24T14:44:12.510" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11061" PostTypeId="2" ParentId="10109" CreationDate="2013-10-23T21:16:06.350" Score="1" Body="&lt;p&gt;I would have to agree that the &quot;transcription factories&quot; (several RNA Polymerases and some other proteins combined) attract DNA and transcription factors, and then start transcription while they remain static.  One such factory can actually transcribe many genes at once. &#xA;Most books and online sources still describe the Polymerase as moving along the DNA and carrying out transcription, but this has been proven wrong.&#xA;source:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8799830&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/8799830&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;can't find the article on Nature either, but I heard about it too.&lt;/p&gt;&#xA;" OwnerUserId="4742" LastActivityDate="2013-10-23T21:16:06.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11062" PostTypeId="2" ParentId="11059" CreationDate="2013-10-23T21:17:39.250" Score="8" Body="&lt;p&gt;The minimum requirement for &lt;em&gt;E. coli&lt;/em&gt; and other bacteria to grow and survive is called &lt;strong&gt;minimal medium&lt;/strong&gt;.  It's even defined at &lt;a href=&quot;http://www.merriam-webster.com/medical/minimal%20medium&quot; rel=&quot;nofollow&quot;&gt;Merriam-Webster&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a medium that contains only inorganic salts, a simple carbon source (as carbon dioxide or glucose), and water&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Water and glucose are pretty easy, but the source of salts may often change; regardless, you &lt;strong&gt;really&lt;/strong&gt; need some potassium, phosphate, and nitrogen for amino acid synthesis.  &lt;a href=&quot;http://textbookofbacteriology.net/nutgro_3.html&quot; rel=&quot;nofollow&quot;&gt;This page&lt;/a&gt; has a bunch of information on bacterial growth, including some &quot;recipes&quot; for a few bacterial strains.  For &lt;em&gt;E. coli&lt;/em&gt;, the classic media is &lt;a href=&quot;http://openwetware.org/wiki/M9_medium&quot; rel=&quot;nofollow&quot;&gt;M9&lt;/a&gt;, which over at &lt;a href=&quot;http://www.sigmaaldrich.com/catalog/product/sigma/m6030?lang=en&amp;amp;region=US&quot; rel=&quot;nofollow&quot;&gt;Sigma&lt;/a&gt; is made of:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;33.9g Na₂HPO₄.7H₂O&lt;/li&gt;&#xA;  &lt;li&gt;15g KH₂PO₄&lt;/li&gt;&#xA;  &lt;li&gt;5g NH₄Cl&lt;/li&gt;&#xA;  &lt;li&gt;2.5g NaCl&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;  &#xA;  &lt;p&gt;per litre of solution. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Media.html&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; are &lt;a href=&quot;http://www.madsci.org/~lynn/micro/techniques/pour_plates/MINagar.html&quot; rel=&quot;nofollow&quot;&gt;some&lt;/a&gt; other &lt;a href=&quot;http://proteinexpression.wordpress.com/2012/02/29/minimal-medium-for-protein-expression-in-e-coli/&quot; rel=&quot;nofollow&quot;&gt;recipes&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="3340" LastEditDate="2014-10-10T10:30:04.080" LastActivityDate="2014-10-10T10:30:04.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11063" PostTypeId="2" ParentId="11028" CreationDate="2013-10-23T21:36:22.383" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.webmd.com/baby/features/pregnancy-stages-baby-body&quot; rel=&quot;nofollow&quot;&gt;Around the second trimester&lt;/a&gt;.  That's an article from WedMD, which says quite a few things.  To summarize, by the end of the first trimester:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;You may be noticing some of the first physical signs of pregnancy: breasts that are sore or tingle at the slightest touch, skin that's drier or oilier than usual, and &quot;morning sickness&quot; -- which may or may not restrict itself to the morning hours. As many as 70% to 80% of pregnant women have it, but not feeling morning sickness doesn't mean there's anything wrong with the baby.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the second trimester:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Most pregnant women begin to &quot;show&quot; during the second trimester. You likely gained less than 5 pounds during your first trimester, but now the number on the scale is edging relentlessly upward. As your second trimester proceeds, you'll gain an average of 1 to 2 pounds per week.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The exact time and rate of &quot;showing&quot; can vary, including whether or not &lt;a href=&quot;http://www.justmommies.com/articles/when-will-i-show.shtml&quot; rel=&quot;nofollow&quot;&gt;this is your first pregnancy&lt;/a&gt;.  By the third trimester, the infant is rapidly becoming more and more capable of surviving on its own.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-23T21:44:30.167" LastActivityDate="2013-10-23T21:44:30.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11064" PostTypeId="5" CreationDate="2013-10-24T00:15:48.437" Score="0" Body="" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-24T00:15:48.437" LastActivityDate="2013-10-24T00:15:48.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11065" PostTypeId="4" CreationDate="2013-10-24T00:15:48.437" Score="0" Body="A structural aberrancy in DNA, as opposed to a sequence change (mutation).  Often caused by reactive species." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-24T00:15:48.437" LastActivityDate="2013-10-24T00:15:48.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11068" PostTypeId="2" ParentId="11044" CreationDate="2013-10-24T08:28:25.360" Score="12" Body="&lt;p&gt;&lt;em&gt;Disclaimer: This is not my field of research.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;First, this is not a complete answer to our question. A nice explanation of the current hypothesis of water transport in trees (Dixon-Joly cohesion-tension theory, &lt;a href=&quot;http://www.jstor.org/stable/91804&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Dixon &amp;amp; Joly. 1894. On the Ascent of Sap. Philosophical Transactions of the Royal Society of London B 186.&quot;&gt;originally proposed 1894&lt;/a&gt;) can be found at &lt;a href=&quot;http://www.science4all.org/le-nguyen-hoang/the-amazing-physics-of-water-in-trees/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;The Amazing Physics of Water in Trees&lt;/em&gt;&lt;/a&gt; but also in &lt;a href=&quot;http://jxb.oxfordjournals.org/content/48/10/1753&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Tyree. 1997. The Cohesion-Tension theory of sap ascent: current controversies. Journal of Experimental Botany 48(10).&quot;&gt;Tyree (1997)&lt;/a&gt;. The key points are that the &lt;a href=&quot;https://en.wikipedia.org/wiki/Stoma&quot; rel=&quot;nofollow noreferrer&quot;&gt;stoma&lt;/a&gt; (leaf surface pores) are so small that the menisci can withstand huge water columns, that water has strong cohesive forces, and that water is transported using the negative pressure that is created by transpiration. The webpage linked above contains a beautiful visualization of how multitudes of stomata and menisci create strong negative pressures:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ppmkU.png&quot; alt=&quot;Water transport in trees, from www.science4all.org/le-nguyen-hoang/the-amazing-physics-of-water-in-trees&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, much of the current discussion in the comments (an indication that the question might be a poor fit for Bio-SE?) revolves around the plausibility of the cohesion-tension theory, and specifically on whether water can sustain strong negative pressures. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1631070506002283&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Caupin &amp;amp; Herbert. 2006. Cavitation in water: a review. Comptes Rendus Physique 7(9-10).&quot;&gt;Caupin &amp;amp; Herbert (2006)&lt;/a&gt; review &lt;a href=&quot;https://en.wikipedia.org/wiki/Metastability&quot; rel=&quot;nofollow noreferrer&quot;&gt;metastability&lt;/a&gt; and cavitation in water (in a physics journal), and contains experimental results on negative pressures in water. The paper references a large number of experiments under various experimental setups (I cannot fairly judge these). In their conclusion they state that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Among the countless cavitation experiments, only the ones with special care about water purity can reach large negative pressures; with a variety of techniques, they all obtain Pcav around −25 MPa at room temperature (see Fig. 3 (b)), which falls far away from the theoretical value (from −120 to −140 MPa). There is a notable exception: experiments with mineral inclusions achieve −140 MPa. The large gap between these data requires special attention.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So basically, the theoretical estimates lie at -130MPa and empirical results at -25MPa (-250 atmospheres), and water can clearly achieve large negative pressures. This would also mean that the current estimates are much larger than what is needed for the cohesion-tension theory to work (atmospheric pressure= 0.1MPa, negative pressure in water column at 50m ~ -0.5MPa).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They also have a section specifically discussing trees:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;7.1. Water in nature&lt;br&gt;&#xA;  The law of hydrostatics teaches us that the pressure drop in a water column of 10.2 m is 0.1 MPa. This points out that negative pressures can be reached in the ascending sap of tall trees. In fact additional effects (viscous flow, drought) make the pressure in the sap negative even at smaller heights. The cohesion-tension theory, first proposed by Dixon and Jolly [56], explains that the sap column is held at the top by the meniscus in the pore of the leaves: by Laplace’s law, the meniscus curvature allows a pressure jump between the outside air pressure and the negative pressure in the sap. The trees thus contain large amounts of metastable liquids. Cavitation may sometimes occur, disrupting the liquid column and stopping the flow (xylem emboly). The complex hydraulic architecture of trees limits the damage, and strategies exist to refill the embolied xylem channels. Much work has been devoted to this topic, and is reviewed in Refs. [110,111].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is also evidence that the risk of xylem embolism increases with tree height, and this creates a trade-off between water transport efficiency and structural adaptations to deal with embolism (&lt;a href=&quot;http://www.pnas.org/content/105/33/12069&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Domec et al. 2008. Maximum height in a conifer is associated with conflicting requirements for xylem design. PNAS 105(33).&quot;&gt;Domec et al. 2008&lt;/a&gt;). This is for instance facilitated by the pit aperture diameter of tracheids, with apertures decreasing with height along a tree, causing increased resistance to embolism but at the same time lower water conductance. This will clearly limit the height of trees, and the paper indicates that the tallest Douglas firs are at the edge of what they can achieve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another recently published paper that should be relevant is '&lt;em&gt;Methods for measuring plant vulnerability to cavitation: a critical review&lt;/em&gt;' by &lt;a href=&quot;http://jxb.oxfordjournals.org/content/early/2013/07/24/jxb.ert193.full&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Cochard et al. 2013. Methods for measuring plant vulnerability to cavitation: a critical review. Journal of Experimental Botany&quot;&gt;Cochard et al. (2013)&lt;/a&gt;, but I haven't had time to look closely at this. See abstract below:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Abstract:&lt;/strong&gt;&lt;br&gt;&#xA;  Xylem cavitation resistance has profound implications for plant physiology and ecology. This process is characterized by a ‘vulnerability curve’ (VC) showing the variation of the percentage of cavitation as a function of xylem pressure potential. The shape of this VC varies from ‘sigmoidal’ to ‘exponential’. This review provides a panorama of the techniques that have been used to generate such a curve. The techniques differ by (i) the way cavitation is induced (e.g. bench dehydration, centrifugation, or air injection), and (ii) the way cavitation is measured (e.g. percentage loss of conductivity (PLC) or acoustic emission), and a nomenclature is proposed based on these two methods. A survey of the literature of more than 1200 VCs was used to draw statistics on the usage of these methods and on their reliability and validity. Four methods accounted for more than 96% of all curves produced so far: bench dehydration–PLC, centrifugation–PLC, pressure sleeve-PLC, and Cavitron. How the shape of VCs varies across techniques and species xylem anatomy was also analysed. Strikingly, it was found that the vast majority of curves obtained with the reference bench dehydration-PLC method are ‘sigmoidal’. ‘Exponential’ curves were more typical of the three other methods and were remarkably frequent for species having large xylem conduits (ring-porous), leading to a substantial overestimation of the vulnerability of cavitation for this functional group. We suspect that ‘exponential’ curves may reflect an open-vessel artefact and call for more precautions with the usage of the pressure sleeve and centrifugation techniques. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-09-22T12:29:42.500" LastActivityDate="2014-09-22T12:29:42.500" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11069" PostTypeId="2" ParentId="10988" CreationDate="2013-10-24T09:20:33.567" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.allaboutcircuits.com/vol_1/chpt_3/4.html&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; deals with the issue in detail.&lt;/p&gt;&#xA;" OwnerUserId="4720" LastActivityDate="2013-10-24T09:20:33.567" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11070" PostTypeId="1" CreationDate="2013-10-24T10:34:30.473" Score="0" ViewCount="8744" Body="&lt;p&gt;We say cell wall is dead but nobody says cell membrane is dead.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is cell membrane living or dead ? If it is not dead then why is it not included in protoplasm : &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Protoplasm is the living contents of a cell that is surrounded by a&#xA;  plasma membrane.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(Source : Wikipedia)&lt;/p&gt;&#xA;" OwnerUserId="4745" LastActivityDate="2013-10-24T16:53:35.187" Title="Is cell membrane living" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="6" ClosedDate="2016-06-11T18:22:24.623" ContentLicense="CC BY-SA 3.0" />
  <row Id="11071" PostTypeId="2" ParentId="10923" CreationDate="2013-10-24T11:08:37.160" Score="2" Body="&lt;p&gt;Just run blast with only the &lt;code&gt;Plus-Minus&lt;/code&gt; alignments. See &lt;a href=&quot;http://www.biostars.org/p/51697/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; post in biostar; it is similar to what you are interested in. This is for the standalone version. I am not sure about how to do it in the online blast. &#xA;If you have just two sequences then you can use UNAfold for checking complementarity. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-10-25T11:34:40.283" LastActivityDate="2013-10-25T11:34:40.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11072" PostTypeId="1" AcceptedAnswerId="11073" CreationDate="2013-10-24T13:13:59.610" Score="4" ViewCount="124" Body="&lt;p&gt;I have &lt;em&gt;Drosophila melanogaster&lt;/em&gt; which I am doing an eye pigmentation assay on in the future. To do this I will dissolve the heads, 10 of them removed from frozen whole flies, in acidified ethanol for at least 48 hours (in the dark at 25 degrees) and then measure the colour of the liquid using a nanodrop. Specifically, this measures how well the liquid reflects red light, quantifying how much red pigment is in there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know what causes the red colour in the eye and if leaving it dissolving for extended periods of time will (or is likely to) result in changes of what I measure? (ie is the material causing the redness in the eye susceptible to deterioration, which would change the colour of the liquid it is dissolving in over time) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have any methods type papers tested this by comparing those dissolved for longer periods to those over shorter periods?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-10-24T20:11:18.500" LastActivityDate="2013-10-24T20:11:18.500" Title="What makes drosophila eyes red? and is it stable?" Tags="&lt;lab-techniques&gt;&lt;pigmentation&gt;&lt;drosophila&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11073" PostTypeId="2" ParentId="11072" CreationDate="2013-10-24T13:59:46.913" Score="3" Body="&lt;p&gt;There's been a fair amount of work on this subject but a lot of it is old - see for example &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1209276/&quot; rel=&quot;nofollow&quot;&gt;this 1945 paper&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1209403/&quot; rel=&quot;nofollow&quot;&gt;this 1948 paper&lt;/a&gt;.  That latter one in particular goes into some good stuff: color in the wildtype is due to red and brown pigments, which the authors separated by using acidic ethanol (after grinding up the flies).  Here's a &lt;a href=&quot;http://www.jstor.org/stable/2423042&quot; rel=&quot;nofollow&quot;&gt;1961 paper from JSTOR&lt;/a&gt; that goes into a bit more detail on some of the red pigments (drosopterin, and isodrosopterin, and neodrosopterin) and looks like a good reference for some other, more basic work on Dmel eye pigmentation.  More to the point, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23436441&quot; rel=&quot;nofollow&quot;&gt;here's a 2013 minireview&lt;/a&gt; on the chemical synthesis of drosopterins, which is useful mainly for referencing a lot of other work, in particular &lt;a href=&quot;https://www.sciencedirect.com/science/article/pii/S0065280608601125&quot; rel=&quot;nofollow&quot;&gt;this overly detailed&lt;/a&gt; chapter from 1970.  That last one has tons of info about some of these pigment-causing proteins in insects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only particular reference to stability I could find was from that chapter, on page 144:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The simple pterines (group 2) are chemically stable under normal physiological conditions, while the substituted (groups I and 3) and conjugated pterines are unstable. Light catalysed oxydation of the polyhydroxy side chain at C-6 is a normal phenomenon. The hydrogenated pterines are extremely unstable, especially at pH 7. Tetrahydrobiopterin, for instance, is oxidized within seconds in the light, but more slowly in the dark. [sic]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-24T13:59:46.913" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11074" PostTypeId="1" AcceptedAnswerId="11079" CreationDate="2013-10-24T15:05:27.770" Score="1" ViewCount="277" Body="&lt;p&gt;I'm a newbie in biology and medicine. I understand that Henrietta Lacks provided the cells that formed the HeLa cell line with which much research has been done. Henrietta Lacks died of cancer. If we assume that she did not have cancer, every cell in her body could divide for an infinite period of time, and she never sustained any trauma ever, would Henrietta Lacks have been immortal?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,&#xA;mj&lt;/p&gt;&#xA;" OwnerUserId="4488" LastActivityDate="2013-10-24T16:56:04.903" Title="Henrietta Lacks Cell Line - Immortality" Tags="&lt;cell-division&gt;&lt;medicine&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11075" PostTypeId="1" AcceptedAnswerId="11077" CreationDate="2013-10-24T15:46:15.683" Score="13" ViewCount="22721" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XnSdE.jpg&quot; alt=&quot;The image I don&amp;#39;t understand&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't understand what this graph is supposed to explain, especially what the signs +/+ or -/- mean. I just know it characterises some rats.&lt;/p&gt;&#xA;" OwnerUserId="4746" LastEditorUserId="4101" LastEditDate="2013-10-24T20:48:04.953" LastActivityDate="2019-11-17T05:28:02.973" Title="What do the signs +/+ +/- mean in this image?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11076" PostTypeId="2" ParentId="11074" CreationDate="2013-10-24T16:04:32.697" Score="2" Body="&lt;p&gt;I believe your question is unclear, but if am I am understanding the question as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If H.L., or anyone, did not develop cancer, was never introduced to any physical insult, would they be immortal?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The answer is no, they would not.  When we talk about aging in biology, we use the technical term &lt;a href=&quot;https://en.wikipedia.org/wiki/Senescence&quot; rel=&quot;nofollow&quot;&gt;senescence&lt;/a&gt;.  Without a cancerous influence normal aging would occur, and cell division would be halted by a &lt;a href=&quot;http://dx.doi.org/10.1177/1535370213493069&quot; rel=&quot;nofollow&quot;&gt;number of factors&lt;/a&gt;.  One of the best researched causes of aging is &lt;a href=&quot;https://en.wikipedia.org/wiki/Telomere&quot; rel=&quot;nofollow&quot;&gt;telomere&lt;/a&gt; &lt;a href=&quot;http://dx.doi.org/10.1111/febs.12326&quot; rel=&quot;nofollow&quot;&gt;shortening&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason that HeLa cells can be passed indefinitely is that they are &lt;a href=&quot;https://en.wikipedia.org/wiki/Biological_immortality&quot; rel=&quot;nofollow&quot;&gt;immortalized&lt;/a&gt;.  You can only get a few &lt;a href=&quot;https://en.wikipedia.org/wiki/Cell_culture#Passaging_cells&quot; rel=&quot;nofollow&quot;&gt;passages&lt;/a&gt; (allowing the cells to grow out from one plate to the next) out of primary cells directly from a human.  This varies some based on the cell type, but is a good rule of thumb.  The basic rule as to how often this can be done is described as the &lt;a href=&quot;https://en.wikipedia.org/wiki/Hayflick_limit&quot; rel=&quot;nofollow&quot;&gt;Hayflick limit&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So no, free of cancer and all insults may mean you lead a long life, but you will most certainly not be immortal.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2013-10-24T16:04:32.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11077" PostTypeId="2" ParentId="11075" CreationDate="2013-10-24T16:17:52.657" Score="24" Body="&lt;p&gt;Diploid organisms, such as we are, generally have two copies of each gene (excepting the sex chromosomes in males).  In order to display the genotype for each, geneticists use shorthand.  When referring to a gene, + means the &lt;a href=&quot;https://en.wikipedia.org/wiki/Wild_type&quot;&gt;wildtype&lt;/a&gt;, which is the &quot;normal&quot; version, and - means that the gene is missing, often a knockout.  So a typical individual's genome for a particular gene will be +/+, a hemizygote (one copy deleted) is +/-, and a complete knockout is -/-.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image is talking about &lt;a href=&quot;https://en.wikipedia.org/wiki/Peroxisome&quot;&gt;peroxisomes&lt;/a&gt;, claiming that they are required for life, specifically the gene &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/5830&quot;&gt;Pex5&lt;/a&gt;.  You can look at the graph at see that compared to the wildtype (open circles), the -/- individuals (open squares) don't make it to a normal birth weight; their lifespan is less than three days.  The +/- hemizygotes (filled circles) match the +/+ wildtype, indicating that this locus displays &lt;a href=&quot;https://en.wikipedia.org/wiki/Haploinsufficiency&quot;&gt;haplosufficiency&lt;/a&gt;, which means that only one functioning copy is needed for a typical phenotype.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-24T16:40:52.167" LastActivityDate="2013-10-24T16:40:52.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11078" PostTypeId="1" AcceptedAnswerId="24274" CreationDate="2013-10-24T16:40:02.913" Score="4" ViewCount="193" Body="&lt;p&gt;I need to make RNA:DNA duplexes. I can make 100 to 200 ug of mRNA through &lt;em&gt;in vitro&lt;/em&gt; transcription, and I know how to use reverse transcription to make a cDNA library, but I have questions with this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mRNA I make with IVT is all poly A RNA, and the reverse transcription kit I have says to use 5ug of total RNA or 500ng of poly A RNA. I need to make at least 10ug of RNA:DNA, which is 20 times the suggested limit for poly A RNA, so a direct scale up probably isn't practical. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't find a literature precedent for making such large amounts of DNA through reverse transcription, everything I have found that uses RNA:DNA duplexes used short strands that were chemically synthesized and combined, my mRNA is 1800 bases long, so I can't just order an oligo, I have to make it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT : I can't comment on my own question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The duplexes will be about 1800 bases long, it's for firefly luciferase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trying to make the DNA for the duplex from the original DNA template presents other issues. While it would be easy to cut it out from the plasmid, it would be double stranded, and I would have to mix with the RNA and heat it up to dissociate everything and hope that the RNA bound before the DNA strands reassociated. I also think it would complicate my controls, because it would be harder to say that any expression I see after delivering these duplexes came from the RNA and not the DNA. Of course synthesizing the DNA from the RNA could also introduce that problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some crude calculations suggests that the dNTPs are the limiting reagent for a transcript this size, and that even with 5ug of mRNA I should have enough oligo dT primer for the reaction. I right now I am running reactions from 0.5 to 5ug of mRNA, 1uL of primer, and 4uL of dNTPs, to make sure I have enough. Hopefully the gel will turn out ok.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I got the results. So far it looks like 3.0ug of mRNA works the best. It has the darkest band, and looks like the right length. Less mRNA gives fainter bands that appear too short, and more mRNA gives slightly fainter bands that appear slightly too short. Also, I ran the reaction for 2 hours instead of 1.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2013-10-28T15:25:35.267" LastActivityDate="2014-11-24T06:34:51.430" Title="Large scale reverse transcription?" Tags="&lt;molecular-biology&gt;&lt;mrna&gt;&lt;reverse-transcription&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11079" PostTypeId="2" ParentId="11074" CreationDate="2013-10-24T16:42:47.410" Score="8" Body="&lt;p&gt;No, there was nothing special about Henrietta Lacks, apart from the fact that her cells have been used for so many years (without her knowledge or consent, by the way). She was not immortal, her tumor cells were. The HeLa cell line comes from her &lt;a href=&quot;http://en.wikipedia.org/wiki/Cervical_cancer&quot;&gt;cervical cancer&lt;/a&gt; cells. The rest of the cells of her body were not immortal any more than yours or mine are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such immortality is a classic characteristic of cancer, in fact it is a hallmark of tumor cells. Normal cells die when they are told to, &lt;a href=&quot;https://en.wikipedia.org/wiki/Apoptosis&quot;&gt;apoptosis&lt;/a&gt; (programmed cell death) is a normal part of a functioning, healthy organism. Tumors are collections of cells that replicate uncontrollably and do not do what they're told, including dying like good little soldiers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is why we often use tumoral cells for cultures, since they have been immortalized, it is relatively easy to keep them alive in the lab. This means, essentially, that they produce an enzyme called &lt;a href=&quot;https://en.wikipedia.org/wiki/Telomerase&quot;&gt;telomerase&lt;/a&gt; which lengthens &lt;a href=&quot;https://en.wikipedia.org/wiki/Telomere&quot;&gt;telomeres&lt;/a&gt;. In normal cells, the telomeres get shorter with each round of &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitosis&quot;&gt;mitosis&lt;/a&gt; and when they get shorter than a certain threshold, they are targeted for apoptosis. Cancer cells are protected from this by the telomerase and can therefore undergo many more rounds of reproduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the cells are not special because of the person they came from, they are special because they are cancer cells.  &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-10-24T16:56:04.903" LastActivityDate="2013-10-24T16:56:04.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11080" PostTypeId="2" ParentId="11070" CreationDate="2013-10-24T16:53:35.187" Score="1" Body="&lt;p&gt;It is neither living nor dead. It is simply not alive the way that any other collection of chemicals is not alive. Is salt alive or dead?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A cell's membrane consists of a collection of chemicals (mainly &lt;a href=&quot;https://en.wikipedia.org/wiki/Lipids&quot; rel=&quot;nofollow noreferrer&quot;&gt;lipids&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Proteins&quot; rel=&quot;nofollow noreferrer&quot;&gt;proteins&lt;/a&gt;). Individual chemicals can never be considered living or dead, any more than rocks or water can be living or dead. While the actual definition of life is &lt;a href=&quot;https://biology.stackexchange.com/q/7053/1306&quot;&gt;tricky&lt;/a&gt;, everyone agrees that in order to be alive you need to (at the very least)&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Somehow interact with your environment&lt;/li&gt;&#xA;&lt;li&gt;Be able to make more copies of yourself&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Therefore, the cells themselves are alive but the individual parts of the cells are not since they cannot make copies of themselves (this gets &lt;a href=&quot;https://biology.stackexchange.com/q/8360/1306&quot;&gt;complicated&lt;/a&gt; when considering some organelles but never mind that here). Similarly, you are alive but your teeth are not. While you can make more of you (you can have children) your teeth cannot make more teeth.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2013-10-24T16:53:35.187" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="11082" PostTypeId="2" ParentId="2232" CreationDate="2013-10-24T18:52:31.190" Score="5" Body="&lt;p&gt;The easiest and most simplistic way to look at it is to assume that the amount of genetic material halves each generation.  On average, humans are about 0.1% to 0.15% different from each other, so in order to get that you'd need around $1/2^{10}=0.0976\%$ and $1/2^9=0.1953\%$. The exponent numbers $2^9$ and $2^{10}$ are 512 and 1024, respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Armatus' Dawkins bit is almost word-for-word what &lt;a href=&quot;http://books.google.com/books?id=6dmMsgRaOIEC&amp;amp;pg=PA145&amp;amp;lpg=PA145&amp;amp;dq=dawkins+1/128+baseline&amp;amp;source=bl&amp;amp;ots=wG-Y3BYWvv&amp;amp;sig=JFjQbyxBgloCHobXeGtXn6epuuI&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=LmZpUraSOOqbiAKptoCQDQ&amp;amp;ved=0CDYQ6AEwAQ#v=onepage&amp;amp;q=dawkins%201%2F128%20baseline&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;he actually said&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;By the time we get to third cousins, &quot;we are getting down near the baseline probability that a particular gene possessed by A will be shared by any random individual taken from the population&quot;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Dawkins was ball-parking that a bit, although he was really talking only about a specific gene.  The inbreeding coefficient is &lt;a href=&quot;http://www.nature.com/nrg/journal/v7/n10/glossary/nrg1960.html#df8&quot; rel=&quot;nofollow&quot;&gt;properly defined&lt;/a&gt; as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The probability that an individual carries two identical-by-descent alleles at a locus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Which takes care of some of the fudging.  With that in mind, though, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6857549&quot; rel=&quot;nofollow&quot;&gt;within eight generations&lt;/a&gt; the odds are less than even you even share &lt;em&gt;any&lt;/em&gt; genetic material with an ancestor/offspring. That's actually a mathematical analysis (with plenty of assumptions!) from the mid-80s but it's an interesting read: you can look up values for certain relations going back a bit.  The answer will vary depending on the background &quot;average&quot; you care about.  Europeans, for example, are &lt;a href=&quot;http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001556&quot; rel=&quot;nofollow&quot;&gt;particularly closely related&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed, &quot;&lt;a href=&quot;http://www.nature.com/ng/journal/v36/n11s/full/ng1435.html&quot; rel=&quot;nofollow&quot;&gt;&lt;code&gt;[g]enetic variation is geographically structured, as expected from the partial isolation of human populations during much of their history.&lt;/code&gt;&lt;/a&gt;&quot;  If you want a perhaps easier-to-read explanation of some of the math, I would suggest this &lt;a href=&quot;http://www.nature.com/nrg/journal/v7/n10/full/nrg1960.html&quot; rel=&quot;nofollow&quot;&gt;2006 review&lt;/a&gt;, in particular box 2.  From that, a silly back-of-the-envelope calculation from 0.1% related gives a path of around 10 individuals, which is a little more distant than your third cousin.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="3624" LastEditDate="2013-10-25T11:05:20.573" LastActivityDate="2013-10-25T11:05:20.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11083" PostTypeId="2" ParentId="11044" CreationDate="2013-10-24T19:09:05.357" Score="5" Body="&lt;p&gt;Another disclaimer: this is not my field and I am not competent to judge the content of the paper that I am bringing to your attention.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I said above that I wouldn't make another contribution, but I found something else worth sharing in this context and which complements the answer from @fileunderwater&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://pubs.acs.org/doi/pdf/10.1021/la3036242&quot; rel=&quot;noreferrer&quot;&gt;Wang Z et al. (2012) Capillary Rise in a Microchannel of Arbitrary Shape and Wettability: Hysteresis Loop. Langmuir 28: 16917-16926&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This paper includes modelling, free energy calculations and experimentation on this problem. The maths is far beyond me, but they do come to a very interesting conclusion, namely that although a tree cannot start from a position of no liquid in the xylem and then fill up to the top it can start very small and grow beyond the height that can be maintained by simple capillary action and up to 100 m as long as the water column is never broken.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper is behind a paywall, but I reproduce below what is essentially the discussion section. Although this gives a flavour of the work, I must emphasise that it presents a very turgid theoretical treatment of the problem and is well worth a look.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;V. IMPLICATION FOR WATER TRANSPORT TO THE TOPS OF TALL TREES&#xA;  Most plant physiologists accept the “cohesion-tension theory” as the explanation for the ascent of sap.26 In this qualitative theory, the move of water depends upon three important physical-chemical properties of water, which actually corre- spond to capillary rise (cohesion), cavitation (tension), and the hydrated wall (low contact angle), respectively. In this section, we focus only on the implication of the general force balance and loop hysteresis in the capillary rise of a tall tree. The height to which water in a tree rises is dependent on the size of the transport conduits. If one cuts down a tree and looks inside, the capillary dimensions of the relatively large conduits (the xylem tube) are on the order of 100 μm.27 As a result, the capillary rise is about 0.1 m. If capillary pressure alone were to explain the water rise to the treetop of a 100 m tall tree, such as the coastal redwoods of California, a capillary radius of about 100 nm is required. It was suggested that the relevant capillary dimension is the air−water interfaces in the cell walls of the uppermost leaves. The matrix of cellulose microfibrils is highly wettable, and the spacing among them yields effective pore diameters of about 10 nm. It has been pointed out that it is not necessary for the capillary to have a small bore throughout its length. Only the bore at the meniscus (i.e., in the uppermost leaf) is relevant.27 This consequence has been proved in our general expression of force balance, eq 4. Note that a microchannel containing corners or cusps on its cross section is not considered in the derivation of eq 4. Liquid filaments extend to infinity in the corners or cusps.28 Nonetheless, the elevation of the liquid column is still inversely proportional to the characteristic dimension of the cross section of the tube. For the solutions satisfying the force balance, nevertheless, there exists the issue of physical stability.&#xA;  A small bore at the uppermost leaf connected to a larger xylem conduit reveals the presence of a convergent micro- channel. As a consequence, multiple stable heights are possible, as described in the aforementioned analyses. However, the final state depends on the initial condition. The liquid will rise to a stable height corresponding to the larger xylem conduit if the microchannel is initially empty. In other words, the liquid will not rise of its own accord to the stable height near the top of the convergent channel because it will not be able to traverse the larger conduit of the channel. This situation is, nonetheless, stable if the liquid is sucked up to the top and then the suction is removed. How does a tall tree acquire such large negative (suction) pressures from above? As demonstrated in our experiments, the gradual rise of an initially immersed cone is able to maintain the stability of the meniscus on the top of the truncated cone as long as the force balance is satisfied. Note that the contact angle in the vicinity of the small pore mouth can be tuned up to fulfill the force balance when the microchannel is not high enough. The slow growth of the tree can be regarded as a gradual rise of the convergent channel. As long as water transport to the pores on the uppermost leaves is not interrupted throughout the entire course of the tree’s growth to 100 m, this stable height can be achieved without resorting to suction.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-10-24T19:09:05.357" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11084" PostTypeId="1" CreationDate="2013-10-25T00:03:23.973" Score="9" ViewCount="4285" Body="&lt;p&gt;I am a mathematics student looking for a hobby and this has come up as a potential hobby. Thus I am interested in buying a high-magnification microscope that is within the limits of my budget. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My first question is, is high-magnification always better? That is, what are some examples, if any, where high-magnification isn't preferred?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, I am thinking of getting either the &quot;OMAX 40X-2000X Digital Lab LED Binocular Compound Microscope with Built-in 1.3MP USB Camera and Double Layer Mechanical Stage&quot;. I have no idea what most of that jargon means, except that it is digital and it can magnify up to 2000x. &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/B006MX03Q0&quot;&gt;http://www.amazon.com/40X-2000X-Binocular-Compound-Microscope-Mechanical/dp/B006MX03Q0/ref=pd_sbs_indust_4&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any reason I shouldn't get this microscope?&lt;/p&gt;&#xA;" OwnerUserId="4652" LastEditorUserId="3952" LastEditDate="2013-10-25T00:49:33.477" LastActivityDate="2018-07-11T18:20:03.113" Title="Microscope recommendation for an amateur?" Tags="&lt;microscopy&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11085" PostTypeId="2" ParentId="9223" CreationDate="2013-10-25T00:34:19.527" Score="1" Body="&lt;p&gt;According to &lt;em&gt;&lt;a href=&quot;http://books.google.com/books/about/A_source_book_of_biological_names_and_te.html?id=LDXwAAAAMAAJ&quot; rel=&quot;nofollow noreferrer&quot;&gt;A Source-Book of Biological Names and Terms&lt;/a&gt;&lt;/em&gt; by Jaeger, the appropriate terms are the simple, obvious ones:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&quot;Geographical&quot;&lt;/strong&gt; for place-derived names and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&quot;Personal&quot;&lt;/strong&gt; for person-derived names.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YCNcw.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-10-25T00:34:19.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11086" PostTypeId="2" ParentId="8279" CreationDate="2013-10-25T01:54:21.533" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.abc.net.au/science/articles/2012/07/24/3549931.htm&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;1 year and 17 days only on water and electrolytes.&lt;/strong&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually, he went water only for about 75 days &lt;em&gt;(read that elsewhere, can't remember)&lt;/em&gt; and then they supplemented his water only diet with &lt;a href=&quot;http://www.medicinenet.com/electrolytes/article.htm&quot; rel=&quot;nofollow&quot;&gt;electrolytes&lt;/a&gt;. &lt;em&gt;He's done it under medical supervision and gained 7 KG in 5 years after the fast. So the weight does stay off (obviously, if you go and stay into a healthier diet).&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="4750" LastActivityDate="2013-10-25T01:54:21.533" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11088" PostTypeId="2" ParentId="11058" CreationDate="2013-10-25T03:12:20.883" Score="33" Body="&lt;p&gt;I'm going to take a shot at putting a whole lot of information into a small answer, so let me know what parts need more explanation.  To any others experienced with closure, I am certainly skipping plenty of steps and ideas in attempt to convey the general.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;******A general warning that graphic surgical images are used below.******&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;The Setup:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;You asked about &quot;severed&quot; jugular and carotid injuries, so we will focus on neck injuries, with a focus on insults to the R/L &lt;a href=&quot;https://en.wikipedia.org/wiki/Common_carotid_artery&quot; rel=&quot;noreferrer&quot;&gt;common carotid arteries (CCA)&lt;/a&gt; and the R/L &lt;a href=&quot;https://en.wikipedia.org/wiki/Internal_jugular_vein&quot; rel=&quot;noreferrer&quot;&gt;internal jugular vein (IJV)&lt;/a&gt;.  To get everyone on the same page visually, we are talking about the large blood vessels in this image:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/B5Tzn.png&quot; alt=&quot;dissection of human neck&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the sake of simplicity, we will deal with injuries that are focused directly on these vessels.  In reality, there are so many different and important tissues tightly packed in the neck that there are often many complications and multiple vessels that need to be dealt with near simultaneously.  Further, we will suppose that our patient (pt) is unlucky to have a &quot;severed&quot; vessel in his neck, but lucky enough to have immediate access to &lt;a href=&quot;https://en.wikipedia.org/wiki/Advanced_Trauma_Life_Support&quot; rel=&quot;noreferrer&quot;&gt;ATLS&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just like you should have learned in your basic neighborhood CPR/aid class, you address the ABC's (MD's add DE): &lt;a href=&quot;https://en.wikipedia.org/wiki/ABC_%28medicine%29&quot; rel=&quot;noreferrer&quot;&gt;&lt;strong&gt;A&lt;/strong&gt; irway, &lt;strong&gt;B&lt;/strong&gt; reathing, &lt;strong&gt;C&lt;/strong&gt; irculation&lt;/a&gt; (&lt;a href=&quot;http://dx.doi.org/10.2147/IJGM.S28478&quot; rel=&quot;noreferrer&quot;&gt;&lt;strong&gt;D&lt;/strong&gt; isability, &lt;strong&gt;E&lt;/strong&gt; xposure&lt;/a&gt;).  In reality when presented with a pt bleeding from the neck, you will almost always begin by applying pressure at the wound site, while you address the airway.  When I say &quot;applying pressure&quot; I literally mean a nurse or medic putting their fingers up against where it is bleeding and trying to stop it like a hose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We will assume that a clear airway is established, the pt is breathing normally enough, and under &lt;a href=&quot;https://en.wikipedia.org/wiki/General_anaesthesia&quot; rel=&quot;noreferrer&quot;&gt;general anaesthesia&lt;/a&gt;.  We will also give us the advantage of having the head, and to a little lesser extent body, packed down with ice.  This will give us precious time, and help &lt;a href=&quot;http://dx.doi.org/10.3978/j.issn.2225-319X.2013.03.03&quot; rel=&quot;noreferrer&quot;&gt;prevent brain damage&lt;/a&gt;.  All else is presumed to be well with the pt, and all we need to do is fix the bleed in his neck.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Identifying the problem:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Now that we have our idealized pt ready to fix, the first thing you have to do is to identify where the bleed is.  Assuming you have serious bleeding, like one would come from a &quot;severed&quot; CCA or IJV that normally means cutting open the wound quickly and in a controlled manner.  Again, the neck is full of tissue you don't want to damage, so a &lt;a href=&quot;https://en.wikipedia.org/wiki/Anatomical_terms_of_location#Anterior_and_posterior&quot; rel=&quot;noreferrer&quot;&gt;anterior&lt;/a&gt; &lt;a href=&quot;https://en.wikipedia.org/wiki/Sternocleidomastoid_muscle&quot; rel=&quot;noreferrer&quot;&gt;sternocleidomastoid&lt;/a&gt; incision is &lt;a href=&quot;http://www.acssurgery.com/acssurgery/institutional/getChapterByIDHTML.action?chapId=part07_ch04&amp;amp;type=tab&quot; rel=&quot;noreferrer&quot;&gt;normally called for&lt;/a&gt; when you are looking for where the CCA or IJV is damaged.  As opposed to coming from the top the way we would dissect a cadaver (as in the drawing above), the sternocleidomastoid incision will give us a side view into the neck like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sY24T.jpg&quot; alt=&quot;anterior sternocleidomastoid incision&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The point at this stage is to &lt;a href=&quot;http://www.trauma.org/archive/vascular/PVTmanage.html&quot; rel=&quot;noreferrer&quot;&gt;gain control of the bleed&lt;/a&gt;.  You don't want to just go digging in where the vessel is bleeding, because you are likely to cause more damage than help (and in this case, loose the pt).  Instead you are going to clamp above and below where the vessel is bleeding.  This will let you suck out the blood and see what's going on.  If you happen to have a large wound in a large vein, there's a chance that a clamp won't give you sufficient control of the bleeding.  In that case you have to also use a catheter to stop the bleeding (&lt;a href=&quot;http://www.acssurgery.com/acssurgery/institutional/getChapterByIDHTML.action?chapId=part07_ch04&amp;amp;type=tab&quot; rel=&quot;noreferrer&quot;&gt;in obtaining distil control to be specific&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In our case, this means dissecting the &lt;a href=&quot;https://en.wikipedia.org/wiki/Carotid_sheath&quot; rel=&quot;noreferrer&quot;&gt;carotid sheath&lt;/a&gt;.  This needs to be done very carefully so that you don't damage the &lt;a href=&quot;https://en.wikipedia.org/wiki/Vagus_nerve&quot; rel=&quot;noreferrer&quot;&gt;vagus nerve&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may have noticed I kept putting &quot;severed&quot; in quotes.  That's because it matters how the vessels are damaged.  Were they crushed or ground apart? Cut jagged or cleanly? Transverse or longitudinal?  All of these change the exact procedures into how you go forward.  Clearly a vessel that has a small tear is easier to repair than one that has been totally separated with jagged shredding from a crush injury.  Veins and arteries won't retract from the insult in the same way either, so how you find them can be a bit different.  Here is a flow chart that shows the basic decisions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lIOuJ.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Put it back together Doc: [warning of graphic images]&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;You may notice that there are basically two end points for either veins or arteries: repair it or ligate it.  There are many different technical/specific ways either can be done, but those are beyond the scope of this answer.  If the sight of open wounds bothers you, note I am going to start using actual surgical photos below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When it's possible it's better to repair the vessel.  That means that you can close the artery where it is.  If there is just a small hole, you can suture the hole closed.  With the CCA or IJV it's more likely that you are going to need a patch.  This means that you take another piece of vein or a synthetic replacement, and suture it into the hole.  I always like to tell people surgery is a lot more tailoring than most people realize (not that this is as easy as sewing fabric).  Below is an example of where a patch would be used in the CCA:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First the tear in the artery:&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/P5h0r.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And after the patch has been added:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tLzE2.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suturing and patching can only be used to close the vessels when tension isn't needed to repair the wound.  If the laceration or severing of the vessels are such that it has come mostly (not completely) apart, but you can still get the ends together with NO tension,  end-to-end anastomosis repair can be utilized.  This means that you take the two ends, with branches if there are any at the wound, and suture them back together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again here is an example of the opening in the artery (popliteal):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1wWGA.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And here it is again after end-to-end anastomosis repair:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4fqsY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now let's say that you really did get the vessel cut in half.  That's a bit of bad news for you, you're going to have to ligate the vessel.  That means sewing up the end of it to close it down.  You start above the injury in arteries and below in veins, and then you tie at least three loops--many prefer five loops--down on the vein, and make a clean cut leaving at least two loops on the part staying in the body.  Then you do the same thing on the other side of the injury.  I think this is best displayed by a video, unfortunately most of the good ones I know of are not available to the public.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=4cEnVlwKkZY&quot; rel=&quot;noreferrer&quot;&gt;This video&lt;/a&gt; certainly not the best technique I've ever seen but it get's the idea across.  I will search for a better video as I have time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now if it is possible, a surgeon will try to make a graft deal with the ligation.  The first choice is a &lt;a href=&quot;http://www.springerreference.com/docs/html/chapterdbid/338141.html&quot; rel=&quot;noreferrer&quot;&gt;interposition graft&lt;/a&gt;.  This means taking a larger vein graft and connecting the two ends of the severed vessel.  You do this after making clean ends with the ligations from above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here we have the femoral artery prepped for an interposition graft:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/KQbSJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And here is interposition graft in place:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dOM3n.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In certain cases, this is not possible.  As strange as it sounds, the ligation may just be left in place, depending on where it is.  &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Is that all?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;No, not by a long shot, but that is the basics.  There are many different techniques that can be used, with new and better ones being invented often.  For example instead of suturing, chemical cauterizing of the ligation can be used and is quicker.  That also allows the surgery to be done through a scope.  But the basics remain the same:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Stop the bleeding, gain basic access, get full control of the bleeding, obtain full exposure/access, sew up the problem,&lt;/strong&gt; put everything back, close up, give fluids, and send them to ICU.  Even after getting everything right in surgery, the recovery can be quite difficult.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Sources and Further Reading&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Note: I will try to come back with primary sources, I started from knowing what to do and searched for sources.  Here are two great sources which contain more complete information:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Trauma.org  This is a great site for use by actual medical professionals when addressing trauma.  They don't really cover the basics, but they do give wonderful care write ups.  Here is the relevant reference for this answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Karim B, &lt;strong&gt;'Peripheral Vascular Trauma'&lt;/strong&gt; trauma.org 7:3, March 2002. &lt;a href=&quot;http://www.trauma.org/archive/vascular/PVTmanage.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.trauma.org/archive/vascular/PVTmanage.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Acssurgery.com  Even more than Trauma.Org, this site is designed for use by clinicians.  Relevant reference:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wisner DH, Galante JM, &lt;strong&gt;INJURIES TO THE NECK&lt;/strong&gt; acssurgery.com 7:4, 2010. &lt;a href=&quot;http://www.acssurgery.com/acssurgery/institutional/getChapterByIDHTML.action?chapId=part07_ch04&amp;amp;type=tab&quot; rel=&quot;noreferrer&quot;&gt;http://www.acssurgery.com/acssurgery/institutional/getChapterByIDHTML.action?chapId=part07_ch04&amp;amp;type=tab&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="15051" LastEditDate="2015-07-08T20:41:04.877" LastActivityDate="2015-07-08T20:41:04.877" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="11089" PostTypeId="1" AcceptedAnswerId="11095" CreationDate="2013-10-25T04:27:15.313" Score="1" ViewCount="2684" Body="&lt;p&gt;My questions: When does fetus begins to acquire antibodies from mother? Does it continue throughout the pregnancy?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From Wikipedia: &lt;a href=&quot;http://en.wikipedia.org/wiki/Passive_immunity&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Passive_immunity&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This occurs around the third month of gestation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From Helena Curtis Biology :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;During the last month of pregnancy , the baby usually begins to acquire antibodies from its mother,....&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I believe that both these sources are reliable but they contradict when the transfer of antibodies starts.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-25T13:18:46.220" LastActivityDate="2013-10-25T14:08:31.327" Title="Transfer of antibodies from mother to fetus" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;antibody&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11090" PostTypeId="1" CreationDate="2013-10-25T07:33:41.813" Score="4" ViewCount="1928" Body="&lt;p&gt;In his book &quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/The_Selfish_Gene&quot; rel=&quot;nofollow&quot;&gt;The Selfish Gene&lt;/a&gt;&quot;, Richard Dawkins says that retaliator emerges as an evolutionary stable strategy. But I think dove is also a kind of retaliator and so if dove increases,  the hawks and others can exploit them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is retaliator an ESS? If not, which strategy is ESS?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Definitions:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;hawk : They always fight hard and retreat only when injured.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;doves : They merely threaten in a dignified way and never hurt anyone.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If a hawk fights a dove, dove runs away. If dove meets dove they go on posturing until one of them is tired and retreats. If a hawk meets hawk they fight until someone gets seriously injured or dies.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;retaliators : A retaliator plays dove at the beginning of every fight. If opponent attacks, he attacks , if opponent behave like a dove he behaves like a dove. When 2 retaliators meet they behave like doves.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;bully : A bully behave like a hawk until someone hits back. Then, he runs away.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;prober retaliator : He is like a retaliator but he tries a brief escalation of the contest. He is hawk like if opponent doesn't strike back. If opponent strikes back he behave like a dove. If he is attacked he retaliates.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The pay offs: 50 for winning, 0 for losing, -100 for being seriously injured. and -10 for wasting time in a long contest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;https://en.wikipedia.org/wiki/The_Selfish_Gene&quot; rel=&quot;nofollow&quot;&gt;The Selfish Gene&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3624" LastEditDate="2013-10-25T09:58:17.663" LastActivityDate="2015-04-15T13:25:43.807" Title="What are the ESSs among hawks, doves, retaliators, bully and prober retaliators?" Tags="&lt;evolution&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="1" ClosedDate="2015-04-16T11:25:19.627" ContentLicense="CC BY-SA 3.0" />
  <row Id="11091" PostTypeId="1" AcceptedAnswerId="11096" CreationDate="2013-10-25T08:19:35.073" Score="4" ViewCount="6760" Body="&lt;p&gt;Why isn't the IgA secreted in breast milk digested due to proteases of the digestive system in the baby?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Immunoglobulin_A&quot; rel=&quot;nofollow&quot;&gt;Wikipedia says&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The secretory component of sIgA protects the immunoglobulin from being&#xA;  degraded by proteolytic enzymes, thus sIgA can survive in the harsh&#xA;  gastrointestinal tract environment and provide protection against&#xA;  microbes that multiply in body secretions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But what exactly does the secretory component do?  What is the secretory component?  Is IgA absorbed in the circulation of fetus? I remember reading it somewhere that it is not absorbed, at least in humans. Please answer these questions focusing more on humans. Though, information about other animals will be appreciated as well.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-25T13:17:20.683" LastActivityDate="2013-10-25T14:09:33.707" Title="Transfer of antibodies in breast milk of humans" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;antibody&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11092" PostTypeId="1" CreationDate="2013-10-25T09:45:25.010" Score="6" ViewCount="435" Body="&lt;p&gt;There seem to be no nocioceptors (pain and temperature sensitive nerve endings) in subcutaneous fat. there are nocioceptors and other receptors in veins running through fat, but these can be avoided. Does this mean that subcutaneous fat can be cut, or otherwise traumatised, such as with diathermy (burning) without causing pain?&lt;/p&gt;&#xA;" OwnerUserId="4753" LastActivityDate="2020-08-13T06:07:05.647" Title="Nocioception (pain perception) in subcutaneous tissue" Tags="&lt;neuroscience&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11093" PostTypeId="2" ParentId="11084" CreationDate="2013-10-25T13:33:07.200" Score="9" Body="&lt;p&gt;Higher magnification is definitely NOT always better. Indeed, the microscope you are considering is designed for maximum magnification of 1,000x. The 2,000x is achieved by adding 20x eyepieces BUT it creates what is known as 'false magnification'. 2,000x is beyond the resolving power of a light microscope so what happens is that the image is magnified 2,000x but without a corresponding improvement in resolution. In fact, you will notice a degradation in image quality....it's like magnifying a pdf on your computer....it gets bigger but you still can't read it! And in any event, you will never use 2,000x let alone 1,000x! Read this article &lt;a href=&quot;http://www.microscope.com/education-center/articles/false-magnification/&quot;&gt;http://www.microscope.com/education-center/articles/false-magnification/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, I advise against buying an integrated digital microscope. Far better to buy a standard trinocular microscope and add a microscope camera. The reason is that the camera will be obsolete within about one year while the microscope should last a lifetime. If anything goes wrong with he camera, you will have to buy an entirely new microscope. Moreover, with separate scope/camera, you can switch cameras on the same microscope or use the camera on a different microscope. For more info read this article &lt;a href=&quot;http://www.microscope.com/education-center/articles/digital-microscope-options/&quot;&gt;http://www.microscope.com/education-center/articles/digital-microscope-options/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look for a lifetime warranty. A mechanical stage is standard and helps move the slides on the stage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In full disclosure, I own www.microscope.com so give me a call if you would like any further assistance. You will not find false magnification or false advertising on our website!&lt;/p&gt;&#xA;" OwnerUserId="4756" LastActivityDate="2013-10-25T13:33:07.200" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11094" PostTypeId="2" ParentId="11084" CreationDate="2013-10-25T13:38:33.150" Score="4" Body="&lt;p&gt;To answer your other question, you need a low power (also known as dissecting or stereo) microscope in order to see close-up views of specimens visible to the naked eye. For example, you can see a bee, but you need a stereo microscope to see the wonders of its eye. Similarly, you can see a rock or a diamond but you need a microscope to see the crystalline structure. Typical magnification ranges are 7x-45x or 50x with most work undertaken in the 20-30x range.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For viewing cells on slides, you need a high power (also known as biological or compound) microscope. Typically, these range from 40x-1,000x.&lt;/p&gt;&#xA;" OwnerUserId="4756" LastActivityDate="2013-10-25T13:38:33.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11095" PostTypeId="2" ParentId="11089" CreationDate="2013-10-25T14:08:31.327" Score="2" Body="&lt;p&gt;Both are technically correct.  Here's a review that goes into some detail about the process: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251916&quot; rel=&quot;nofollow&quot;&gt;IgG Placental Transfer in Healthy and Pathological Pregnancies&lt;/a&gt;.  It's worth a read if you're interested in the subject.  In particular, it cites a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8955500&quot; rel=&quot;nofollow&quot;&gt;study of immunoglobulin transport&lt;/a&gt; which:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;demonstrated a continuous rise in IgG levels in the fetal circulation between 17 and 41 weeks of gestation. Fetal IgG concentrations were only 5%–10% of the maternal levels at weeks 17–22 but reached 50% of the maternal concentrations at weeks 28–32. The majority of IgG is acquired by the fetus during the last 4 weeks of pregnancy, and fetal IgG concentrations usually exceed maternal ones by 20%–30% at full term.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So it begins a wee bit before week 17, so definitely within the &lt;strong&gt;second&lt;/strong&gt; trimester, but it is only by the &lt;strong&gt;third&lt;/strong&gt; that concentrations begin to be truly meaningful.  However, most of the antibody acquired, going above the maternal level, is done in the last &lt;strong&gt;month&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-25T14:08:31.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11096" PostTypeId="2" ParentId="11091" CreationDate="2013-10-25T14:09:33.707" Score="6" Body="&lt;p&gt;It is!  Here is an &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3257684/&quot; rel=&quot;nofollow noreferrer&quot;&gt;amazing review from 2011&lt;/a&gt; that &lt;em&gt;literally&lt;/em&gt; has all the answers.  I'm not kidding, &lt;strong&gt;all&lt;/strong&gt; of them.  I would marry this review if I could.&lt;sup&gt;1&lt;/sup&gt;  It also includes information on other animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main takeaway is that IgA from milk is &lt;strong&gt;not&lt;/strong&gt; readily absorbed by the infant body.  Secreted IgA is mainly to provide a protective coating for the mucosa while the infant is developing its own nascent immune system.  IgG passed along from the placenta (your &lt;a href=&quot;https://biology.stackexchange.com/q/11089/4101&quot;&gt;other question&lt;/a&gt;) provides the main source of absorbed antibodies.  As it says in the review:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Milk sIgA is not taken up by the infant’s intestinal mucosa. In fact, gut closure in humans occurs before birth and little immunoglobulin is absorbed intact in the intestine after birth. However, the presence of sIgA in the intestinal lumen is part of the protective function of the epithelial barrier in the intestine... Secretory IgA is considered to be the primary immunoglobulin responsible for immune protection of mucosal surfaces such as the intestine.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In terms of enzymatic activity, the digestive system will in indeed chomp up the antibodies; that's part of the reason breast feeding should continue as needed.  That's okay, because there's plenty to go around:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Much of the immunoglobulin consumed in an immune milk can be expected to be partially or completely digested, however some portion of the immunoglobulin will remain intact or at least partially intact and capable of binding to an antigen.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It turns out that immunoglobulins are moderately resistant to digestion, at least more so than other milk proteins.  There's a section in there detailing some experiments where Ab was given to individuals:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In adult humans consuming a bovine whey protein concentrate, approximately 59% of IgG and IgM was detected by radial immunodiffusion from effluents from the jejunum, while 19% was detected in the ileum. These estimates of digestion of immunoglobulin compare with estimates of digestion of milk proteins in adult humans which are approximately 42% complete at the end of the jejunum and 93% complete by the end of the ileum, again underscoring the relative resistance of immunoglobulins to digestion in the gastrointestinal tract.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Digestive enzymes vary as to which antibody they prefer to digest, but at least some of them will technically digest the antibody, but still leave functional Fab fragments, which are still immunologically active and useful to the infant immune system.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;1: Did I mention I love this review?  I love it.&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2013-10-25T14:09:33.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11097" PostTypeId="1" CreationDate="2013-10-25T14:11:42.657" Score="4" ViewCount="630" Body="&lt;p&gt;I am going to build a simple bioreactor for microalgae growth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I already have fluid filters pore size: 0.2um, diameter: 25mm&#xA;&lt;a href=&quot;https://nl.vwr.com/app/catalog/Product?article_number=514-4039&quot; rel=&quot;nofollow&quot;&gt;https://nl.vwr.com/app/catalog/Product?article_number=514-4039&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder if I can use them for air filtration to avoid the bacteria when pumping in the air.&#xA;Or do I necessarily need air filters?&lt;/p&gt;&#xA;" OwnerUserId="4757" LastEditorUserId="3624" LastEditDate="2013-10-25T14:31:07.640" LastActivityDate="2013-12-28T03:38:03.287" Title="Need for proper air filter for bioreactor?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11099" PostTypeId="1" AcceptedAnswerId="11104" CreationDate="2013-10-25T15:50:53.833" Score="2" ViewCount="457" Body="&lt;p&gt;Here is a quotation from &lt;a href=&quot;http://en.wikipedia.org/wiki/Kin_selection&quot; rel=&quot;nofollow&quot;&gt;this wikipedia page&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The relatedness parameter (r) in Hamilton's rule was introduced in&#xA;  1922 by Sewall Wright as a coefficient of relationship that gives the&#xA;  probability that at a random locus, the alleles there will be&#xA;  identical by descent.[14] Subsequent authors, including Hamilton,&#xA;  sometimes reformulate this with a regression, which, unlike&#xA;  probabilities, can be negative.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here is my question:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;What are all the different definitions of relatedness in biology?&lt;/strong&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;how do we calculate them?&lt;/li&gt;&#xA;&lt;li&gt;what do they mean?&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-10-25T16:40:58.827" LastActivityDate="2013-10-25T17:55:33.113" Title="The concepts of relatedness - Hamilton's rule and kin selection" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;evolutionary-game-theory&gt;&lt;sociality&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11100" PostTypeId="1" AcceptedAnswerId="11103" CreationDate="2013-10-25T16:36:33.210" Score="5" ViewCount="152" Body="&lt;p&gt;&quot;&lt;em&gt;Evolvability is the capacity of a system for adaptive evolution.&lt;/em&gt;&quot; (&lt;a href=&quot;http://en.wikipedia.org/wiki/Evolvability&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;) There are several other definitions though:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Who was the first person to use the word &quot;evolvability&quot;?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Who was the first to introduce the concept of evolvability? in which article?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4101" LastEditDate="2013-10-25T17:31:54.293" LastActivityDate="2013-10-25T17:31:54.293" Title="Who was the first to talk about evolvability?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;history&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11102" PostTypeId="1" AcceptedAnswerId="11124" CreationDate="2013-10-25T17:10:15.310" Score="7" ViewCount="264" Body="&lt;p&gt;Does knowing the sex of each of a couple’s first N children have any marginal value in predicting the sex of child N+1? By “marginal” I mean predictive power beyond other known effects, e.g., the race of the parents, the mother’s weight, season of birth (list from &lt;a href=&quot;http://www.stat.columbia.edu/~gelman/presentations/ziff.pdf&quot; rel=&quot;nofollow&quot;&gt;this presentation&lt;/a&gt; by Andrew Gelman).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that many claims that some variable can predict a child have been accused of resting on shaky statistics (see the presentation linked to above). But the sex of preceding children seems like it could be a strong predictor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE: answering fileunderwater's question&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Can you expand on why (by what mechanisms) you think that it could be a strong predictor? Male sex-chromosome bias in sperm?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, sex-chromosome bias was my first thought. I almost focused my question specifically on that but the fact that I saw maternal weight listed as a predictor in the Gelman presentation made me think there might be other relevant factors that I wouldn't think of. So I broadened the scope of the question.&lt;/p&gt;&#xA;" OwnerUserId="4697" LastEditorUserId="4697" LastEditDate="2013-10-26T19:03:36.460" LastActivityDate="2015-11-18T03:46:14.920" Title="Does knowing the sex of each of a couple’s first N children have any marginal value in predicting the sex of child N+1?" Tags="&lt;human-biology&gt;&lt;sex-ratio&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="11103" PostTypeId="2" ParentId="11100" CreationDate="2013-10-25T17:30:29.567" Score="1" Body="&lt;p&gt;My literature searches have turned up dead ends, so this is less of a full answer and more of some groundwork, but Google ngrams &lt;a href=&quot;https://books.google.com/ngrams/graph?content=evolvability&amp;amp;year_start=1800&amp;amp;year_end=2000&amp;amp;corpus=15&amp;amp;smoothing=0&amp;amp;share=&amp;amp;direct_url=t1%3B%2Cevolvability%3B%2Cc0&quot; rel=&quot;nofollow&quot;&gt;suggests&lt;/a&gt; somewhere around 1931 for the first usage, with meaningful usages beginning in earnest int he early 70s.  Their book previews from that era are sadly lacking; I can't find the usage of the ones from the &lt;a href=&quot;http://books.google.com/books?id=1FV_MwAACAAJ&amp;amp;dq=%22evolvability%22&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=fqZqUueHAajEigKN44GYCw&amp;amp;ved=0CFkQ6AEwCTi-AQ&quot; rel=&quot;nofollow&quot;&gt;40s&lt;/a&gt; and &lt;a href=&quot;http://books.google.com/books?id=4EgAAAAAMAAJ&amp;amp;q=%22evolvability%22&amp;amp;dq=%22evolvability%22&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=fqZqUueHAajEigKN44GYCw&amp;amp;ved=0CFQQ6AEwCDi-AQ&quot; rel=&quot;nofollow&quot;&gt;50s&lt;/a&gt; they &lt;em&gt;do&lt;/em&gt; list sadly, but there are definitely some misnomers that show up in programming.  There's a &lt;a href=&quot;http://books.google.com/books?id=dKAoAAAAMAAJ&amp;amp;q=%22evolvability%22&amp;amp;dq=%22evolvability%22&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=fqZqUueHAajEigKN44GYCw&amp;amp;ved=0CEMQ6AEwBDi-AQ&quot; rel=&quot;nofollow&quot;&gt;1973&lt;/a&gt; work and one from &lt;a href=&quot;http://books.google.com/books?id=nGCsaJo0yzYC&amp;amp;pg=PA109&amp;amp;dq=%22evolvability%22&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=fqZqUueHAajEigKN44GYCw&amp;amp;ved=0CDQQ6AEwATi-AQ#v=onepage&amp;amp;q=%22evolvability%22&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;1977&lt;/a&gt; that at least appear to be the correct usage, with the one from 1973 using it as a &quot;new&quot; concept.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-25T17:30:29.567" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11104" PostTypeId="2" ParentId="11099" CreationDate="2013-10-25T17:55:33.113" Score="1" Body="&lt;p&gt;Is that really trying to imply that there are significantly different definitions?  It seems to me the intent was just to put it in terms of an equation with more useful numbers.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14239792&quot; rel=&quot;nofollow&quot;&gt;This terrifying paper&lt;/a&gt; from 1964 gives some of the follow-up works, in particular works from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1209694/&quot; rel=&quot;nofollow&quot;&gt;Cockerham in 1954&lt;/a&gt; and a number of papers by Kempthorne, in particular &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1209710/&quot; rel=&quot;nofollow&quot;&gt;this from 1955&lt;/a&gt; and &lt;a href=&quot;http://books.google.com/books?id=tTErAAAAYAAJ&amp;amp;pg=PA21&amp;amp;lpg=PA21&amp;amp;dq=kempthorne+the+role+of+systems+of+mating+in+the+determination+of+means+variances+and+covariances+in+genetic+populations&amp;amp;source=bl&amp;amp;ots=gQ9P0HjyyJ&amp;amp;sig=lnETEq_ESbb-oh6HFNGt0rhmZHI&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=-K5qUu_JDMzLigKczYHYAQ&amp;amp;ved=0CCwQ6AEwAA#v=onepage&amp;amp;q=kempthorne%20the%20role%20of%20systems%20of%20mating%20in%20the%20determination%20of%20means%20variances%20and%20covariances%20in%20genetic%20populations&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;this from 1963&lt;/a&gt;.  There is also &lt;a href=&quot;https://en.wikipedia.org/wiki/Malecot%27s_method_of_coancestry&quot; rel=&quot;nofollow&quot;&gt;Malecot's method of coancestry&lt;/a&gt; from 1948. (&lt;a href=&quot;http://www.worldcat.org/title/mathematiques-de-lheredite/oclc/489892082&quot; rel=&quot;nofollow&quot;&gt;WorldCat.org link&lt;/a&gt;)  The idea was mainly to look relatedness outside of the specific limitations present in Wright's work.  Some of the math in those are more accessible than others...&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-25T17:55:33.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11105" PostTypeId="5" CreationDate="2013-10-25T19:30:42.347" Score="0" Body="" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-25T19:30:42.347" LastActivityDate="2013-10-25T19:30:42.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11106" PostTypeId="4" CreationDate="2013-10-25T19:30:42.347" Score="0" Body="Magnetic Resonance Imaging is a radiological tool used to create images of an organism of higher quality than x-rays." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-25T19:30:42.347" LastActivityDate="2013-10-25T19:30:42.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11107" PostTypeId="1" AcceptedAnswerId="11113" CreationDate="2013-10-25T21:54:08.367" Score="5" ViewCount="387" Body="&lt;p&gt;Microarray has various uses, and to analyse the data a main function classification is used. There are many methods used to classify the data but what are the best and most frequently used methods? Are there any well-known, web-based tools for microarray analysis?  Where can I find datasets of gene expression profiles, where I can find and &lt;em&gt;understand&lt;/em&gt; the matrix of the dataset?&lt;/p&gt;&#xA;" OwnerUserId="4759" LastEditorUserId="4759" LastEditDate="2013-10-25T23:07:34.213" LastActivityDate="2013-10-27T19:05:46.387" Title="Microarray data and analysis tools" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;microarray&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11108" PostTypeId="1" CreationDate="2013-10-26T02:15:27.180" Score="1" ViewCount="85" Body="&lt;p&gt;I am going to make some mice ill with arthritis. The medicine which I am testing as control is known to cause extreme fatigue. I think I've improved it. I'd like to humanly measure their stamina in the presence of something like morphine. How would I ethically do this?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2013-10-26T14:26:32.983" Title="Protocol for measuring stamina of arthritic mice" Tags="&lt;protocol&gt;&lt;mice&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11109" PostTypeId="2" ParentId="11108" CreationDate="2013-10-26T02:45:27.037" Score="3" Body="&lt;p&gt;I believe the standard is an graded-speed treadmill test.  An example pub:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jap.physiology.org/content/92/6/2245.abstract&quot; rel=&quot;nofollow&quot;&gt;Genetic variability in forced and voluntary endurance exercise performance in seven inbred mouse strains&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is a particular ethical concern, you should always have your institutional review panel review it.  If you call up your department of animal resources (or what ever it is called in your institution) they will almost always give lists of preferred LOPs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another option would be to score time sleeping if you have them under behavioral surveillance.  The problem with this is the large amount of man hours needed, even watching tapes at high speed.  Instead I recommend you check this paper out:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.jneumeth.2009.06.010&quot; rel=&quot;nofollow&quot;&gt;Evaluation of two automated metrics for analyzing partner preference tests&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then to get accurate scoring, I would put a strongly colored bedding pad in a corner so the computer could pick it up.  Be sure to put the bedding in at least a week before so the mice get used to it and actually sleep on it.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2013-10-26T14:26:32.983" LastActivityDate="2013-10-26T14:26:32.983" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11112" PostTypeId="2" ParentId="11108" CreationDate="2013-10-26T13:19:54.953" Score="2" Body="&lt;p&gt;If the mice will be incapable of walking on a treadmill, which suggests that they will be very ill, you could just measure their homecage activity. There is some normal, baseline level of activity in a cage. You could compare controls to placebos to experimentals. If the drug you are testing increases homecage activity, then it would appear to be effective. Xie et al. &lt;a href=&quot;http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-61779-576-3_13&quot; rel=&quot;nofollow noreferrer&quot;&gt;describe a fairly comprehensive system&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CPnfC.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://mouse-activity.com/Home-Cage-Activity-Monitor&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here is one example&lt;/a&gt;. Basically it is a very sensitive, 4-post scale that is designed to determine in xy space when the mouse is in the cage.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-10-26T13:19:54.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11113" PostTypeId="2" ParentId="11107" CreationDate="2013-10-26T14:06:51.413" Score="4" Body="&lt;p&gt;This is a fairly broad question and a book or two will give a more complete answer.  I'm assuming you are interested in expression microarrays.  Genotyping microarrays are also very popular these days and are quite different though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Where can I understand the matrix of the dataset ?&lt;/strong&gt;&#xA;This is a little unclear as a question, but I'll start with a numerical description.  Microarray data is reducible to a one dimensional array of intensities.  As a vector of numbers, each representing the amount of a given species of RNA in a sample, it has many interpretations.  Most of what is said here applies to RNASeq data too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These numbers are sequence dependent - that is, they should not be interpreted as an absolute count of a specific mRNA in the sample, so comparing two entries in the vector (e.g. &quot;gene A has 10% more RNA than gene B&quot;) will probably not be useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For this reason, microarray experiments are typically done as difference experiments, where two or more conditions are compared, producing a matrix of numbers, where N rows represent N experiments, and the M columns each represent a probe set / gene.  The transpose of this matrix is also common. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;**Methods to classify microarray results. ** &#xA;Taking the matrix of data, there are many ways of interpreting data in matrix form and most of them have been tried credibly with microarray data. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most common are to take a set of probe sets whose biological action are related (e.g. all in a metabolic pathway and display them as a heat map where the columns have been &lt;a href=&quot;http://en.wikipedia.org/wiki/Hierarchical_clustering&quot; rel=&quot;nofollow noreferrer&quot;&gt;clustered by a distance based algorithm&lt;/a&gt; to produce a tree, where neighbors have the greatest numerical similarity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CTVS1.png&quot; alt=&quot;heat map&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For purely numerical methods, &lt;a href=&quot;http://en.wikipedia.org/wiki/Principle_component_analysis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Principal Component Analysis&lt;/a&gt; is often used (despite the fact that &lt;a href=&quot;http://machine-master.blogspot.com/2012/08/pca-or-polluting-your-clever-analysis.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this is not a great method&lt;/a&gt;), but Self Organizing Maps, neural nets and just about any machine learning algorithm have been used.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most common method by far though, is Analysis of Variants (&lt;a href=&quot;http://en.wikipedia.org/wiki/Anova&quot; rel=&quot;nofollow noreferrer&quot;&gt;ANOVA&lt;/a&gt;), where the probe sets/ genes have been scored by their greatest to smallest variance.  The most common case of this is a two condition difference experiment where the largest differences are taken as results.  This is not a great experiment, but the data is not super cheap to produce. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;**Microarray data repositories **&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gene Expression Omnibus&lt;/a&gt; (GEO) is a highly regarded repository for microarray data, with over a million sets of data. They also have some tools, see below. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EMBL &lt;a href=&quot;http://www.ebi.ac.uk/arrayexpress/&quot; rel=&quot;nofollow noreferrer&quot;&gt;ArrayExpress&lt;/a&gt; claims to have slightly more data than GEO (1.2 M assays). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many many specialized microarray websites, mostly focusing on a particular organism (E coli for instance) or problem (like cancer).  Google is pretty helpful for this sort of thing once you have the right keywords. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;**Web based tools for microarray analysis **&#xA;There are several tools you will use for microarray analysis and there are lots of websites for different aspects of this data.  I'm going to cite a couple, but the most commonly used tools are command line tools like R/bioconductor or the software that comes from the array manufacturer.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/geo2r/&quot; rel=&quot;nofollow noreferrer&quot;&gt;GEO2R&lt;/a&gt; is a great tool to browse expression data experiments.  It does a simple version of ANOVA and will really help you find some cool biology quickly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://sasquatch.ucsd.edu/vampire/&quot; rel=&quot;nofollow noreferrer&quot;&gt;VAMPIRE&lt;/a&gt; is a web analysis suite for microarray analysis.  Scaling the data into numbers from images to intensities to data analysis to compare several arrays.  Its probably one of the most comprehensive analysis sites out there. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-10-27T19:05:46.387" LastActivityDate="2013-10-27T19:05:46.387" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11114" PostTypeId="5" CreationDate="2013-10-26T14:44:52.253" Score="0" Body="" OwnerUserId="4101" LastEditorUserId="3624" LastEditDate="2017-03-09T01:21:52.500" LastActivityDate="2017-03-09T01:21:52.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11115" PostTypeId="4" CreationDate="2013-10-26T14:44:52.253" Score="0" Body="Questions dealing with biological processes in relation to temperature, for instance temperature effects on metabolism, enzyme function or development time. Temperature can be measured on many different scales, e.g. in degrees Fahrenheit or Celsius, or Kelvin." OwnerUserId="4101" LastEditorUserId="3624" LastEditDate="2017-03-08T22:26:26.613" LastActivityDate="2017-03-08T22:26:26.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11117" PostTypeId="1" CreationDate="2013-10-27T12:45:32.343" Score="6" ViewCount="131" Body="&lt;p&gt;I've read &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9728893&quot; rel=&quot;noreferrer&quot;&gt;on this publication&lt;/a&gt; that every drug that induces CYP3A can reduce the effectiveness of clarithromycin. Clarithromycin inhibits CYP3A.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But it does not say anything about the opposite situation: does a low concentration of CYP3A increase the effect of clarithromycin?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dmd.aspetjournals.org/content/34/2/305.long&quot; rel=&quot;noreferrer&quot;&gt;This research&lt;/a&gt; shows how DHA can inhibit CYP3A.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the final question is: does a high concentration of DHA increase the effect of clarithromycin?&lt;/p&gt;&#xA;" OwnerUserId="4763" LastEditorUserId="43480" LastEditDate="2018-07-25T22:48:01.417" LastActivityDate="2019-08-20T02:00:55.410" Title="Does DHA increase the effects of clarithromycin?" Tags="&lt;microbiology&gt;&lt;pharmacology&gt;&lt;medicinal-chemistry&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11119" PostTypeId="1" CreationDate="2013-10-27T15:41:55.643" Score="8" ViewCount="779" Body="&lt;p&gt;Referring to &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_genetic_hybrids&quot; rel=&quot;nofollow&quot;&gt;interspecific hybrids&lt;/a&gt;, I have the following two questions:- &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quoting from wikipedia:-&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The offspring of an interspecific cross are very often sterile; thus,&#xA;  hybrid sterility prevents the movement of genes from one species to&#xA;  the other, keeping both species distinct. Sterility is often&#xA;  attributed to the different number of chromosomes the two species&#xA;  have, for example donkeys have 62 chromosomes, while horses have 64&#xA;  chromosomes, and mules and hinnies have 63 chromosomes. Mules,&#xA;  hinnies, and other normally sterile interspecific hybrids cannot&#xA;  produce viable gametes, because differences in chromosome structure&#xA;  prevent appropriate pairing and segregation during meiosis, meiosis is&#xA;  disrupted, and viable sperm and eggs are not formed. However,&#xA;  fertility in female mules has been reported with a donkey as the&#xA;  father.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;1) The sterility of hybrids prevents interspecific gene exchange and is necessary in case the hybrid has odd number of total chromosomes (the hybridized species has odd and even pairs of chromosomes individually), where equal meiotic division would not be possible, and is also necessary to avoid sex determination problems that may arise from such hybridizations genetically. &lt;strong&gt;What is the molecular (genetic) reason behind the sterility?&lt;/strong&gt; In other words, why is the expression of primary sexual organs and its further proliferation to effect reproduction not possible, although the genes required for it are already present in the hybrids? Is this due to epigenetic mechanisms or is the reason inherent in the hybrid nature of the genome?   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) This might probably sound a bit naive, but &lt;strong&gt;why are these hybrids viable?&lt;/strong&gt; They have 2 non-homologous haploid pairs of chromosomes which have a huge variety(compared to two homologous pairs) of different non-allelic genes. Why are all the essential functions not hindered by the presence of such &lt;em&gt;considerably&lt;/em&gt; unrelated set of chromosomes?   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably related to the question is the fact that certain &lt;a href=&quot;http://www.thefreedictionary.com/allopolyploidy&quot; rel=&quot;nofollow&quot;&gt;allopolyploids&lt;/a&gt; are viable and become an entirely new species, but others are not. Is it because here are 2 sets of each combining species' chromosomes (and hence allowing proper meiotic pairing) or is there some other reason pertaining to the nature of the combined sets of chromosome?&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2015-05-28T13:02:21.600" LastActivityDate="2020-04-11T23:01:55.323" Title="Genetic expression in interspecific hybrids" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;sex&gt;&lt;hybridization&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11121" PostTypeId="1" AcceptedAnswerId="11123" CreationDate="2013-10-27T21:33:46.067" Score="4" ViewCount="1516" Body="&lt;p&gt;After reading a Youtube comment, I started reading on Luc Montagnier's &lt;a href=&quot;http://en.wikipedia.org/wiki/Luc_Montagnier#Research_on_electromagnetic_signals_from_DNA&quot; rel=&quot;nofollow&quot;&gt;research on electromagnetic signals from DNA&lt;/a&gt;. I haven't been able to find a source that would clearly explain what it's about. I would like to know, if possible, &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;what the claims are exactly; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;what experiments were carried out; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;whether the results have been replicated independently;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;whether the results contradict anything considered firmly established scientific knowledge (it seems Montagnier says they do) and, if so, how;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;what the criticism is.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I know it's a lot to ask, but if you could make your answers accessible, it would be great. Please don't refrain from using technical language where it's necessary, but do try to give a general picture for those (including me) who might not understand it.&lt;/p&gt;&#xA;" OwnerUserId="1278" LastEditorUserId="1306" LastEditDate="2013-10-28T16:53:23.143" LastActivityDate="2014-04-10T16:27:25.697" Title="What is Luc Montagnier's research on electromagnetic signals from DNA about?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="10" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11123" PostTypeId="2" ParentId="11121" CreationDate="2013-10-28T10:58:31.593" Score="1" Body="&lt;p&gt;I think that &lt;a href=&quot;https://biology.stackexchange.com/users/1278/ymar&quot;&gt;ymar&lt;/a&gt; poses an excellent set of questions that should be discussed on these forums.  It brings back memories (sic) of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Water_memory&quot; rel=&quot;nofollow noreferrer&quot;&gt;memory of water controversy&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;I'll quote from &lt;a href=&quot;https://twitter.com/AndyCoghlan1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Andy Coghlan&lt;/a&gt;'s excellent &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;ved=0CC0QFjAA&amp;amp;url=http%3A%2F%2Fclip2net.com%2Fclip%2Fm9285%2F1312440671-scorn_over_claim_of_teleported_dna-285kb.pdf%3Fnocache%3D1&amp;amp;ei=3DpuUqj9JIew7AbX-oEg&amp;amp;usg=AFQjCNGOB7ipQN-hQi8f-ln6oirZewzANw&amp;amp;sig2=HWeJn-pPubbXVOFLsVmBhw&amp;amp;bvm=bv.55123115,d.ZGU&quot; rel=&quot;nofollow noreferrer&quot;&gt;article&lt;/a&gt; published in &lt;a href=&quot;http://www.newscientist.com/article/mg20927952.900-scorn-over-claim-of-teleported-dna.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;New Scientist in 2011&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Draw your own conclusions.  (The emphases are mine).&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;... So what have&#xA;Montagnier and his team actually found? Full details of the&#xA;experiments are not yet available, but the basic set-up is as follows.&lt;/p&gt;&#xA;&lt;p&gt;Two adjacent but physically separate test tubes were placed within a&#xA;copper coil and subjected to a very weak extremely low frequency&#xA;electromagnetic field of 7 hertz. The apparatus was isolated from&#xA;Earth's natural magnetic field to stop it interfering with the&#xA;experiment. One tube contained a fragment of DNA around 100 bases&#xA;long; the second tube contained pure water.&lt;/p&gt;&#xA;&lt;p&gt;After 16 to 18 hours, both&#xA;samples were independently subjected to the polymerase chain reaction&#xA;(PCR), a method routinely used to amplify traces of DNA by using&#xA;enzymes to make many copies of the original material.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;The gene&#xA;fragment was apparently recovered from both tubes, even though one&#xA;should have contained just water&lt;/strong&gt; (see diagram).&lt;/p&gt;&#xA;&lt;p&gt;DNA was only recovered&#xA;if the original solution of DNA - whose concentration has not been&#xA;revealed - had been subjected to several dilution cycles before being&#xA;placed in the magnetic field. In each cycle it was diluted 10-fold,&#xA;and &amp;quot;ghost&amp;quot; DNA was only recovered after between seven and 12&#xA;dilutions of the original. It was not found at the ultra-high&#xA;dilutions used in homeopathy.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Physicists in Montagnier's team suggest&#xA;that DNA emits low-frequency electromagnetic waves which imprint the&#xA;structure of the molecule onto the water&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;p&gt;This structure, they claim,&#xA;is preserved and amplified through quantum coherence effects, and&#xA;because it mimics the shape of the original DNA, the enzymes in the&#xA;PCR process mistake it for DNA itself, and somehow use it as a&#xA;template to make DNA matching that which &amp;quot;sent&amp;quot; the signal&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I always knew there was something suspect about genetics!  Stick to biochemistry, that's what I say :-)&lt;/p&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-31T23:25:30.730" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11124" PostTypeId="2" ParentId="11102" CreationDate="2013-10-28T12:15:36.280" Score="6" Body="&lt;p&gt;For those who are interested in sex ratio bias itself, the &lt;a href=&quot;https://en.wikipedia.org/wiki/Human_sex_ratio&quot; rel=&quot;nofollow noreferrer&quot;&gt;enWikipedia article&lt;/a&gt; is pretty good.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for predictive power, a Bayesian might tell you that by knowing a couple can and did have a male/female should improve, if only slightly, your belief that their next would be the same.  It's by no means predictive and probably largely indiscernible from random chance, but hey it's something!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More to the point, at the very least you might as well just guess their next child will be a &lt;strong&gt;son&lt;/strong&gt;.  As the link above will tell you, the human sex ratio at birth has varied but in general males are more likely to be born - somewhere &lt;a href=&quot;http://data.un.org/Data.aspx?q=sex+ratio+birth&amp;amp;d=PopDiv&amp;amp;f=variableID%3a52%3btimeID%3a113&amp;amp;c=2,4,6,7&amp;amp;s=_crEngNameOrderBy:asc,_timeEngNameOrderBy:desc,_varEngNameOrderBy:asc&amp;amp;v=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;around 1.03 to 1.08&lt;/a&gt; males per female.  Here's &lt;a href=&quot;http://www.cdc.gov/nchs/data/nvsr/nvsr53/nvsr53_20.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;another in-depth study&lt;/a&gt;, from 2005, dealing with the last few decades in the US.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That study has Figure 3 (below) and Table 3, which show the raw birth ratio over successive births, and the data are pretty clear: &lt;strong&gt;successive births reduce bias&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XxZKG.png&quot; alt=&quot;Sex ratio by birth order&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Those numbers are way more clear than I thought they would - just watch those means move!  I wish there were more information on the variances - clearly there's more down by the 8th child - but that's pretty solid.  Here's another study from &lt;a href=&quot;http://aje.oxfordjournals.org/content/150/9/957.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Denmark in 1999&lt;/a&gt; doing some of the same stuff (Denmark was &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10601107&quot; rel=&quot;nofollow noreferrer&quot;&gt;popular&lt;/a&gt; for this work).  They include the absolutely &lt;em&gt;fascinating&lt;/em&gt; Table 2 (below), which breaks down the odds of giving birth to a male given whatever came before.  Which, in the end, is as predictive as you can get, right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JRp8f.png&quot; alt=&quot;Sex ratio change by birth order&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, it's sort of what you'd expect: the more females you have, the more likely you are to have another female; the more males, the more likely the next is a male.  They used about 1.4 million kids but there are some interesting oddities in that table at the extremes.  The best chance for a male?  Your fifth kid, following FMFM.  Best for a female?  Your fifth, after MMMF.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some definite issues that can twist the data, particularly when families have another kid to try to get a child of a specific sex.  If you can tease out some of those environmental factors, you'd be better at guessing; still, I wouldn't bet the house on it.  Memorize that table but, when in doubt:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Guess male&lt;/li&gt;&#xA;&lt;li&gt;Lotta females first?  Maybe guess another one.&lt;/li&gt;&#xA;&lt;li&gt;A bunch of males?  Guess another male.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-28T12:15:36.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11125" PostTypeId="1" CreationDate="2013-10-28T14:44:25.720" Score="9" ViewCount="1114" Body="&lt;p&gt;After birth neurons generally do not divide. But is there any specific type of rare cancer or tumour where neurons divide? And if there is such a cancer, then how is it possible for a neuron to regain the division power? &lt;/p&gt;&#xA;" OwnerUserId="4772" LastEditorUserId="3624" LastEditDate="2013-10-28T15:27:10.750" LastActivityDate="2019-06-18T08:14:42.797" Title="Are there any types of cancer that cause neurons to divide?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;cancer&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="11126" PostTypeId="2" ParentId="2452" CreationDate="2013-10-28T15:40:01.050" Score="0" Body="&lt;p&gt;With longer sequences, the dNTPs become limiting. Try to add more dNTPs while keeping the amount of primer the same. Don't be afraid to run several reactions at different amounts of reagent to find the optimal amount. Also, increase your reaction time. The reverse transcriptase and DNA polymerase need more time to cover a longer transcript.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2013-10-28T16:20:12.760" LastActivityDate="2013-10-28T16:20:12.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11127" PostTypeId="1" CreationDate="2013-10-28T16:06:43.197" Score="2" ViewCount="70" Body="&lt;p&gt;I'm working on building some FRET reporters.  In addition to a cleavage site (of varying composition from 15-18AA), a 1 AA linker, I'm using Venus and Cerulean.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Initially I was &lt;a href=&quot;https://biology.stackexchange.com/questions/10764/is-there-an-optimal-composition-and-length-for-protein-linkers-in-fret&quot;&gt;worried that 18AA would be too long&lt;/a&gt;, but it does in fact give a fair signal.  For reference, I believe the Förster radius (Ro) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1366774/&quot; rel=&quot;nofollow noreferrer&quot;&gt;is 54Å&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am now working on further optimization.  Does the removal of the intial methionine cause any problems for Venus if it is the second protein in the FRET pair?  The basic layout is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cerulean - Link - Cleavage - Link - Venus&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And I'm wondering if cutting the Met from Venus might bring me 1 AA closer and therefore a slightly better signal.  I have seen it published both ways, and I was wondering if anyone had tried both or just knew theoretically that it wouldn't matter.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-10-30T13:41:04.393" Title="Removal of the Initial Methionine in Venus for FRET" Tags="&lt;proteins&gt;&lt;lab-techniques&gt;&lt;fluorescent-microscopy&gt;&lt;fret&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11128" PostTypeId="2" ParentId="973" CreationDate="2013-10-28T16:38:23.430" Score="1" Body="&lt;p&gt;I keep my RNA in 1mM sodium citrate pH 6.4. Citrate is a chelator, and helps trap the divalent metals many RNAses need to work. The lower pH also helps inhibit RNAse activity. EDTA could work as a chelator, but it only chelates well at pH's where RNAse activity is worse. Citrate gives both chelation and low pH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course I also keep my RNA at -80.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2013-10-28T16:38:23.430" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11130" PostTypeId="1" AcceptedAnswerId="20162" CreationDate="2013-10-28T17:33:26.513" Score="7" ViewCount="575" Body="&lt;p&gt;This source &lt;a href=&quot;http://answers.yahoo.com/question/index?qid=20061009043743AA0em2H&quot;&gt;here&lt;/a&gt;  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...research has shown that it is STILL the males that compete for&#xA;  females.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;says that male sea horses compete for mates but this source &lt;a href=&quot;http://www.sciencedaily.com/releases/2008/05/080501125451.htm&quot;&gt;here&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Females exhibit a competitive behavior that's normally a male-type&#xA;  attribute, and males end up being choosy, which is normally a more&#xA;  female-type attribute.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;.says that female sea horses compete for mates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone provide me a trustable source regarding this ? I would also like to know if there are any recent papers exploring why males get pregnant in sea horses.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-10-28T19:29:27.610" LastActivityDate="2014-08-02T17:28:41.773" Title="Competition for mates in sea horses" Tags="&lt;physiology&gt;&lt;ecology&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11131" PostTypeId="1" CreationDate="2013-10-28T17:56:45.363" Score="7" ViewCount="1621" Body="&lt;p&gt;I am currently researching image manipulation in the life sciences and stumbled upon a Western Blot looking very similar to the image below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For creating the image I have cut out the blot using the Fuzzy Select Tool of GIMP and then greatly adjusted the local contrast of the blot as well as the background. By using the Fuzzy Select Tool some pixels of the original background are also captured. That is why the blot shown has a brighter background around the edges. I normally would not expect to see bright edges around a blot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While I know how Western Blots look when they are captured with a digital camera, I do not know about techniques like Chemiluminescent Blotting (I am an undergraduate student in Computer Science). Maybe there is a blotting technique that results in an image like the one i created.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is it possible to get a Western Blot result like this without inappropriate modification of the image?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Y8x7z.png&quot; alt=&quot;imitated part Western Blot&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4775" LastEditorUserId="4775" LastEditDate="2013-10-28T18:37:12.313" LastActivityDate="2013-10-29T19:53:14.523" Title="Can this image be the result of a Western Blot?" Tags="&lt;imaging&gt;&lt;western-blot&gt;" AnswerCount="2" CommentCount="10" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11132" PostTypeId="1" AcceptedAnswerId="13530" CreationDate="2013-10-28T18:28:34.253" Score="4" ViewCount="131" Body="&lt;p&gt;I know how estimates of species richness in a small area are made. But how do you estimate the total number of species on a global scale? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One example of such a method can be found in &lt;a href=&quot;http://www.plosbiology.org/article/info%3adoi/10.1371/journal.pbio.1001127&quot; rel=&quot;nofollow&quot; title=&quot;Mora et al. 2011. How Many Species Are There on Earth and in the Ocean? PLOS Biology 9(8): e1001127. doi:10.1371/journal.pbio.1001127,&quot;&gt;Mora et al. 2011&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3624" LastEditDate="2013-10-28T19:44:38.307" LastActivityDate="2013-11-17T01:32:21.193" Title="How do you estimate global species richness?" Tags="&lt;ecology&gt;&lt;biodiversity&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11133" PostTypeId="1" AcceptedAnswerId="11143" CreationDate="2013-10-28T18:34:29.417" Score="6" ViewCount="549" Body="&lt;p&gt;Here is the Wright-Fisher model of genetic drift:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{(2N)!}{k!(2N-k)!}p^kq^{2N-k} \Leftrightarrow \binom{2N}{k}p^kq^{2N-k}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $\binom{2N}{k}$ is the binomial coefficient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This formula gives the probability of obtaining $k$ copies of an allele at generation $t+1$ given that there are $p$ copies of this allele at generation $t$. $N$ is the population size and $2N$ is the number of copies of each gene (this model applies to diploid population only).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;From this formula, how can we calculate the probability of extinction of an allele in say 120 generations starting at a given frequency, let's say 0.2?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can we calculate the probability of extinction rather than fixation of an allele present at frequency $p$ if we wait an infinite amount of time?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-10T11:47:46.620" LastActivityDate="2014-08-13T14:42:31.413" Title="Probability of Extinction under Genetic Drift" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="11134" PostTypeId="1" CreationDate="2013-10-28T18:35:42.793" Score="4" ViewCount="1033" Body="&lt;p&gt;If a fungus releases its digestive enzymes outside its body, how does it protect itself from digestion? How do fungi growing nearby protect themselves?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried searching this on google but couldn't get an answer.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1306" LastEditDate="2013-10-28T19:00:58.353" LastActivityDate="2014-05-06T17:37:35.760" Title="How does a fungus protect itself from digestion by other fungi?" Tags="&lt;mycology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11135" PostTypeId="1" AcceptedAnswerId="11149" CreationDate="2013-10-28T18:46:08.517" Score="3" ViewCount="377" Body="&lt;p&gt;Normally, insects' muscles are attached to their exoskeleton but what happens to this attachment when they are moulting?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry if this is an extremely silly question but I have wondered about it for a long time and have tried searching it.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="4101" LastEditDate="2013-10-29T17:01:36.247" LastActivityDate="2013-10-29T17:01:36.247" Title="Attachment of muscles during molting in insects" Tags="&lt;physiology&gt;&lt;entomology&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11136" PostTypeId="1" CreationDate="2013-10-28T19:06:33.497" Score="3" ViewCount="54" Body="&lt;p&gt;Are adenosine or its catabolites increased in inflamed airways? How can I assess this? I am trying to use inhibitors for adenosine deaminase, xanthine oxidase, and purine nucleoside phosphorylase, but I don't have a protocol.&lt;/p&gt;&#xA;" OwnerUserId="4740" LastEditorUserId="4101" LastEditDate="2013-10-28T19:29:18.723" LastActivityDate="2013-10-28T19:29:18.723" Title="Adenosine metabolism" Tags="&lt;molecular-biology&gt;&lt;immunology&gt;&lt;enzymes&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11137" PostTypeId="2" ParentId="11131" CreationDate="2013-10-28T19:24:58.277" Score="1" Body="&lt;p&gt;Here's an example of a chemiluminescent blot:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4dgqp.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For those who care, the first column on the left is the weight standard, the next two are pooled pellets, and the rest are increasing fractions of purified HIV using a mouse monoclonal anti-p24 (capsid) antibody.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This blot is pretty clean (although for my work it was pretty disappointing...) but here's one that looks less-than-ideal, and perhaps more like your example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XIlfR.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are lysates and pelleted supernatant from Jurkat uninfected (left) and HIVIIIB-infected (right) cultures, detected with a mouse monoclonal anti-tsg101 antibody.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I agree with shigeta's comment that your image might not be exactly what I would expect, but that doesn't necessarily mean it was done maliciously; as you can see, there can be a fair amount of variation in how blots turn out depending on the equipment used, the type of membrane, the protein itself, and so on.  I try to be pretty conservative with image filters but there's &lt;strong&gt;a lot&lt;/strong&gt; you can do with those guys that can be shady but falls short of Photoshop.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-28T19:24:58.277" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11138" PostTypeId="1" AcceptedAnswerId="11147" CreationDate="2013-10-28T20:16:54.863" Score="3" ViewCount="9400" Body="&lt;p&gt;As I understand it, the &lt;em&gt;dry weight&lt;/em&gt; of something is its weight minus the weight of its water content. Is this the definition? What about &lt;em&gt;dry cell weight&lt;/em&gt;?&lt;/p&gt;&#xA;" OwnerUserId="561" LastEditorUserId="1306" LastEditDate="2013-10-29T00:31:04.203" LastActivityDate="2013-12-03T11:43:56.837" Title="What is the definition of &quot;dry weight&quot; and &quot;dry cell weight&quot;?" Tags="&lt;nomenclature&gt;&lt;definitions&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="11139" PostTypeId="2" ParentId="8247" CreationDate="2013-10-28T20:53:14.270" Score="-1" Body="&lt;p&gt;I think they are asking how to clean surfaces like benchtops.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bleach might work. But a better solution would be to get a box of aluminum foil. The processes for making the foil are very harsh, so it's doubtful any protein would survive the process, not to mention that there are no proteins involved in aluminum manufacture to contaminate the process. Just be sure to always use gloves when handling the foil or you'll contaminate it.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2013-10-28T20:53:14.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11141" PostTypeId="2" ParentId="11097" CreationDate="2013-10-29T02:50:11.347" Score="1" Body="&lt;p&gt;Well then you need to get a filter specific for air filtering.  I recommend Polytetrafluorethylene PTFE membrane filter.  Now the only issues are size and &quot;how sterile.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a lot of vendors out there that supply these.  If your institution has an agreement with VWR, they certainly have them.  If not, I have used &lt;a href=&quot;http://www.sartorius.com/en/products/bioprocess/air-gas-filters/&quot; rel=&quot;nofollow&quot;&gt;Sartorius&lt;/a&gt; in the past, but I don't have any particular brand loyalty to them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me know if you need any more help.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2013-10-29T02:50:11.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11143" PostTypeId="2" ParentId="11133" CreationDate="2013-10-29T06:59:27.793" Score="2" Body="&lt;p&gt;&lt;strong&gt;update&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The answer is &lt;a href=&quot;https://math.stackexchange.com/questions/585578/biology-wright-fisher-model-of-genetic-drift&quot;&gt;here&lt;/a&gt;!&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Original comment/answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.genetics.org/content/61/3/763.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kimura and Ohta (1969)&lt;/a&gt; showed that assuming an initial frequency of $p$, the mean time to fixation $\bar t_1(p)$ is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\bar t_1(p)=-4N\left(\frac{1-p}{p}\right)ln(1-p)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;similarly they showed that the mean time to loss $\bar t_0(p)$ is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\bar t_0(p)=-4N\left(\frac{p}{1-p}\right)ln(p)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Combining the two, they found that the mean persistence time of an allele $\bar t(p)$ is given by $\bar t(p) = (1-p)\bar t_0(p) + p\bar t_1(p)$ which equals&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\bar t(p)=-4N\cdot \left((1-p)\cdot ln(1-p)+p\cdot ln(p)\right)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This does not answer any of the two questions!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This answer gives...&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;the average persistence time&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;but not...&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;the probability of fixation rather than extinction if we wait an infinite amount of time&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;neither...&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;the probability that the allele get extinct over a period of say 120 generations&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can someone improve this answer?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:19:22.807" LastActivityDate="2013-12-10T19:22:14.520" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="11144" PostTypeId="1" AcceptedAnswerId="11165" CreationDate="2013-10-29T07:58:15.157" Score="0" ViewCount="127" Body="&lt;p&gt;It's known the human eye takes 24 images per second. But does this refresh?&#xA;For example after sleeping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or will it always be the same interval?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I talk about when the eye takes the images. So it are 24 images in the second, but this second is not defined. It can start at 09:00:00.00 or 09:00:00.50. Will this change after taking a sleep?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope it is clear what I'm talking about.&lt;/p&gt;&#xA;" OwnerUserId="4779" LastActivityDate="2013-10-30T07:10:31.607" Title="Does the eye image interval refresh?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2013-10-31T01:04:27.290" ContentLicense="CC BY-SA 3.0" />
  <row Id="11145" PostTypeId="1" CreationDate="2013-10-29T09:46:45.567" Score="2" ViewCount="133" Body="&lt;p&gt;I am writing a paper about DNA sequence prediction. DNA sequence prediction is done across various areas of biology, including, for example, RSS sequence prediction (in immunology) and prediction of promoter regions in vertebrate DNA sequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was just wondering how one would describe such specific areas as &quot;RSS sequence prediction&quot; and &quot;promoter region prediction&quot;. To be concrete, I wanted to write something like:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This paper describes a method of DNA sequence prediction using&#xA;  standard Bayesian modelling techniques. While there is much existing&#xA;  work on DNA sequence prediction, most of this work is in the context&#xA;  of biological research. Typically the techniques used are very&#xA;  specific to the biological subdomain under consideration. Also, these&#xA;  techniques often use use additional biological information about the&#xA;  biological sequences under consideration, besides the sequence data&#xA;  itself.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is the term &lt;code&gt;subspeciality&lt;/code&gt; the correct term to use here? Would &lt;code&gt;biological area&lt;/code&gt; or &lt;code&gt;biological domain/subdomain&lt;/code&gt; be better, or some other term?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incidentally, if anyone knows other areas where DNA sequence prediction is used, please mention it/them. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="284" LastEditorUserId="284" LastEditDate="2013-10-29T10:13:46.263" LastActivityDate="2013-10-29T10:13:46.263" Title="Terminology question about the correct term for areas of biological research" Tags="&lt;terminology&gt;&lt;structure-prediction&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="11146" PostTypeId="2" ParentId="11145" CreationDate="2013-10-29T10:06:27.253" Score="1" Body="&lt;p&gt;I think your suggestions are fine - there are a few ways you could write this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I might use some variant of;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The techniques used may be specific to the research question, and particular considerations may also be required depending on the accepted norms within the academic field&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="740" LastActivityDate="2013-10-29T10:06:27.253" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11147" PostTypeId="2" ParentId="11138" CreationDate="2013-10-29T14:25:29.603" Score="4" Body="&lt;p&gt;According to my Henderson's Dictionary of Biological Terms, &lt;em&gt;dry weight&lt;/em&gt; is&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The weight or mass of organic matter or soil after removal of water by heating to constant weight.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So yes, your definition is correct and it is also applicable to cells. The dry weight of cells is the weight left when their water content has been removed by heating.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-10-29T14:25:29.603" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11149" PostTypeId="2" ParentId="11135" CreationDate="2013-10-29T16:47:34.130" Score="2" Body="&lt;p&gt;You can find a concise answer &lt;a href=&quot;http://books.google.co.uk/books?id=NXJEi8fo7CkC&amp;amp;pg=PA242&amp;amp;lpg=PA242&amp;amp;dq=muscle+attachment+ecdysis&amp;amp;source=bl&amp;amp;ots=p4ogAYGaZL&amp;amp;sig=Ak0nE5SKw7gQJ44b_0Vhiro_ZxY&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=d-RvUuqVOIiy0QWazIDACQ&amp;amp;redir_esc=y#v=onepage&amp;amp;q=muscle%20attachment%20ecdysis&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; in a section from The Insects: Structure and Function  by R. F. Chapman, eds. Stephen J. Simpson, Angela E. Douglas. 5th Edition. Cambridge University Press.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In essence the source says that the muscle attachment to the cuticle is maintained during the moulting process, while the new cuticle is formed under the old cuticle. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As a result the insect is able to continue its activities after apolysis during the development of the new cuticle. The connections to the old cuticle are broken at about the time of ecdysis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Connections to the new cuticle are formed at the same time as the old ones are broken.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-10-29T16:47:34.130" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11152" PostTypeId="1" CreationDate="2013-10-29T18:59:47.987" Score="4" ViewCount="273" Body="&lt;p&gt;I ran an enrichment analysis with custom annotations using TopGO and surprisingly I obtained new GO terms inside the significant GO terms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is that  possible? The only reason I can imagine this is possible is because TopGO adds new GO terms based on the input GO terms, since GO ontology is structured hierarchically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please let me know if you need more details about the experiment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Code:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://drive.google.com/file/d/0B8-ZAuZe8jldbjNuTHhNeXRVX00/edit?usp=sharing&quot; rel=&quot;nofollow&quot;&gt;https://drive.google.com/file/d/0B8-ZAuZe8jldbjNuTHhNeXRVX00/edit?usp=sharing&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TopGO output:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://drive.google.com/file/d/0B8-ZAuZe8jldZnlYUzlxZ3psMWc/edit?usp=sharing&quot; rel=&quot;nofollow&quot;&gt;https://drive.google.com/file/d/0B8-ZAuZe8jldZnlYUzlxZ3psMWc/edit?usp=sharing&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks, Bernardo&lt;/p&gt;&#xA;" OwnerUserId="4717" LastActivityDate="2015-06-28T21:34:48.233" Title="New GO terms after TopGO enrichment?" Tags="&lt;rna-sequencing&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ClosedDate="2015-06-29T22:58:02.257" ContentLicense="CC BY-SA 3.0" />
  <row Id="11153" PostTypeId="2" ParentId="11131" CreationDate="2013-10-29T19:53:14.523" Score="4" Body="&lt;p&gt;I do not think that a publication quality blot should have such an artifact, but I was able to find something similar by purposely over blotting (not the same as over exposing) a gel.  If you use too much primary, secondary, or developing reagent, you can get your HRP signal to &quot;burn in&quot; a membrane where you get a distinct &quot;negative band.&quot;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By negative band I mean a region that is more clear/white than background. This happens mostly when you have way too much secondary antibody.  Normally when this happens, the CENTER of the band burns in first so you would see a white center with dark edges.  And that's only when you are imaging the membrane as it is burning in.  Often the whole band is white.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After going through the westerns of grad-student who is working with me, I found this image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8iB4e.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It came with the clear notation that it was burned in and disregarded (said student was learning how to do Westerns at the time).  It's a GAPDH blot for those that care.  When this does happen, it's obvious because you can then see the band with your naked eye on the membrane.  Again this would be a reason to not publish the blot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image could have non-maliciously been edit via compression, screens, filters, etc as mentioned by others in the comments.  This is the only way I can think of to experimentally have a similar image.  Ether way I don't think the image should be reported as is.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2013-10-29T19:53:14.523" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11156" PostTypeId="1" AcceptedAnswerId="11251" CreationDate="2013-10-30T00:32:10.070" Score="1" ViewCount="1440" Body="&lt;p&gt;I always wondered what ophthalmologists see inside someone's eye and what they're looking for. The whole thing is a mystery to me. Are there any photos of what the eye of a patient looks like from the doctor's point of view?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2013-11-02T16:57:05.663" Title="What does ophthalmologist see in your eye?" Tags="&lt;human-anatomy&gt;&lt;eyes&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11157" PostTypeId="1" CreationDate="2013-10-30T00:33:11.960" Score="17" ViewCount="5530" Body="&lt;p&gt;Why do humans find baby animals like cats, dogs, ... so cute?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As these are potential competitors (when grown up!) or even natural enemies (like e.g. tigers, leopards, ..), the protection instinct (reasonable for the babies of your species) should therefore not apply.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't imagine any reason why evolution let mankind adore foreign species that much.&#xA;Maybe only humans liking the enemy's kids survived, because they weren't killed by the baby's parents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the evolutionary reason?&lt;/p&gt;&#xA;" OwnerUserId="4785" LastEditorUserId="4785" LastEditDate="2015-07-06T15:36:04.837" LastActivityDate="2018-03-01T21:27:53.520" Title="Why do humans find baby animals cute?" Tags="&lt;evolution&gt;&lt;instinct&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="11158" PostTypeId="1" CreationDate="2013-10-30T00:55:42.033" Score="6" ViewCount="17428" Body="&lt;p&gt;I'm trying to figure out how to modify my working conditions so that I can program longer without harming my eyes. Because doing so experimentally hasn't given conclusive results so far, I decided to ask for studies in this area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does looking at a bright screen in a well lit room strain eyes more than looking at dark screen in a dark room for prolonged periods of time? Or is there a middle ground somewhere in-between that is most harmless? Or is it a combination of contrasting screen/background?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not asking for medical advice here. I already went to several doctors and they gave me different, sometimes contradicting answers, so I'm just looking for research.&lt;/p&gt;&#xA;" OwnerUserId="1373" LastEditorUserId="4101" LastEditDate="2013-10-30T13:42:13.420" LastActivityDate="2016-12-17T19:26:48.647" Title="Does bright environment strain eyes more than dim?" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;light&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11159" PostTypeId="1" CreationDate="2013-10-30T06:45:38.210" Score="6" ViewCount="94" Body="&lt;p&gt;I heard the hypothesis, that the (main) reason of aging is the increasing number of mutations in body tissues. The higher the number of mutations is, the older tissue is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this true? And how well supported is the idea?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have somebody measured the numbers of mutations in different tissues at different ages, and if so, where I can get these numbers?&lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="3624" LastEditDate="2013-10-30T18:57:04.837" LastActivityDate="2014-05-01T10:42:41.853" Title="How well supported is the hypothesis that aging is mainly caused by the number of mutations in tissues?" Tags="&lt;genetics&gt;&lt;senescence&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11160" PostTypeId="1" CreationDate="2013-10-30T06:51:20.220" Score="3" ViewCount="74" Body="&lt;p&gt;It is said on Wikipedia, that the precursor of &lt;a href=&quot;http://en.wikipedia.org/wiki/Blastocyst&quot; rel=&quot;nofollow&quot;&gt;blastocyst&lt;/a&gt; is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Morula&quot; rel=&quot;nofollow&quot;&gt;morula&lt;/a&gt;, and that the precursor of morula is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Zygote&quot; rel=&quot;nofollow&quot;&gt;zygote&lt;/a&gt;. This gives us the part of genealogy tree of cell types. Unfortunately, no full genealogy can be found in Wikipedia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where can I find a more complete picture, preferably a full tree of cell types including information about each type?&lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="4101" LastEditDate="2013-10-31T14:21:07.200" LastActivityDate="2013-10-31T14:21:07.200" Title="Where can I find a full genealogy of human cell types?" Tags="&lt;cell-biology&gt;&lt;development&gt;&lt;differentiation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11161" PostTypeId="2" ParentId="11158" CreationDate="2013-10-30T06:56:42.963" Score="1" Body="&lt;p&gt;I think the principle is &quot;everything in moderation&quot;. Environment should be not very bright and not very dimmed. Also, the contrast should be moderate too, i.e. having bright screen in dark room is not good. Also, he type of work should not be very constant, i.e. you should sometimes change looking at the screen to looking in the window and similar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remember, that the light is required for stimulating the brain activity.&lt;/p&gt;&#xA;" OwnerUserId="1584" LastActivityDate="2013-10-30T06:56:42.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11162" PostTypeId="2" ParentId="11157" CreationDate="2013-10-30T07:00:13.343" Score="-1" Body="&lt;p&gt;The only humans survived were those, who liked baby animals. Because that humans domesticated wolfs, horses and so on, which gave them the superiority above other humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume, that everything what exist, should be approved by evolution somehow. Hence, IF humans actually likes baby animals, THEN it should be approved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I remembered, that humans were domesticating animals and this technology was helping them (us) to survive. Also I remembered, that domestication is usually started with adoption of animal babies. Adoption was occurring by chance, on the basis of non-motivated congenital (genetic) love to baby animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, my explanation is: some of human species were liking animal babies and this caused domestication. Then domestication caused evolution advantages, and these species won the competition with other human species. We are descendants of former species and conserve our sympathies to baby animals. Those who were not liking them -- died millions years ago. &lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="1584" LastEditDate="2014-03-10T13:25:47.090" LastActivityDate="2014-03-10T13:25:47.090" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="11163" PostTypeId="2" ParentId="11156" CreationDate="2013-10-30T07:02:43.930" Score="0" Body="&lt;p&gt;They look at retina. Google for it. The look of retina can evident of some diseases. This is the subject of medical education.&lt;/p&gt;&#xA;" OwnerUserId="1584" LastActivityDate="2013-10-30T07:02:43.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11164" PostTypeId="2" ParentId="11157" CreationDate="2013-10-30T07:08:59.363" Score="11" Body="&lt;p&gt;In German we call it &quot;Kindchenschema&quot; which is unfortunately translated only to the more unspecific &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cuteness&quot;&gt;Cuteness&lt;/a&gt;&quot;, but sometimes also to &quot;baby schema&quot;. This seems to be applying to most (care taking) mammals, also over species borders. The specific looks release hormones in the adult triggering care taking behaviour. This is to ensure the babies safety. That it not only works with the own parents helps ensuring the baby is cared for even if the parents cannot do it themselves.&#xA;Interestingly, the head and eye shape seems to trigger this hormone release. And it is the same for many animals. Like always, evolution uses the same winning scheme over and over again. This is why you can get a dog to care for abandoned kittens, and why you will find those puppies ever so cute.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-10-30T07:08:59.363" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="11165" PostTypeId="2" ParentId="11144" CreationDate="2013-10-30T07:10:31.607" Score="1" Body="&lt;p&gt;Human eyes do not take 24 images per second. Refresh done in parallel, each pixel separately, and the rate depends on the rate of color changing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the work of eye is closer to MPEG encoding than to uncompressed AVI.&lt;/p&gt;&#xA;" OwnerUserId="1584" LastActivityDate="2013-10-30T07:10:31.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11166" PostTypeId="1" AcceptedAnswerId="76132" CreationDate="2013-10-30T10:19:22.083" Score="4" ViewCount="373" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To improve sleep by reducing blue-light melatonin disruption, I wear night-glasses that filter short wavelengths (e.g. something like &lt;a href=&quot;https://www.google.com.au/search?q=blue%20light%20blocking%20glasses&amp;amp;site=imghp&amp;amp;tbm=isch&amp;amp;tbo=u&amp;amp;source=univ&quot; rel=&quot;nofollow noreferrer&quot;&gt;these&lt;/a&gt;). With these glasses on, both the top and bottom bars of this test image will appear visually identical:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.imgur.com/H8I3fFz.png&quot; alt=&quot;RGB wavelength image. Bottom bar with zero blue value&quot;&gt;&#xA;&lt;sub&gt;(Source: Personally derived from this public domain &lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Linear_visible_spectrum.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;image&lt;/a&gt; and released to public domain)&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the colour spectrum you &quot;see&quot; while filtering the blue light will not appear to be either of these bars; instead some partially de-saturated hybrid of the two. I think this is probably due to a pervasive blue wavelength of the LCD back-light regardless of defined colour contrast.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there is something else odd going on. If I wear these glasses for several hours and then remove them for some reason - all the blue colours I should see will be muted, partially de-saturated or even interpreted as a shade of green for at least several minutes afterwards (I haven't stop-watched the effect). Freaky.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is this selective shift of colour perception occurring for a while after removing wavelength filtered glasses?&lt;/p&gt;&#xA;" OwnerUserId="4788" LastActivityDate="2018-08-09T22:50:28.240" Title="What causes a selective shift of colour perception after removing wavelength filtered glasses?" Tags="&lt;perception&gt;&lt;light&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11167" PostTypeId="2" ParentId="11160" CreationDate="2013-10-30T13:08:12.663" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_distinct_cell_types_in_the_adult_human_body&quot; rel=&quot;nofollow&quot;&gt;Wikipedia has a page listing cell types&lt;/a&gt; which classifies their origin as endodermal or ectodermal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't been able to find a source for a complete lineage of all cell types, and I have gained the impression that there is no complete picture, except in some specific cases such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Haematopoiesis&quot; rel=&quot;nofollow&quot;&gt;the haemopoietic lineage&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.tedxtelaviv.com/2010/07/18/ehud-shapiro-uncovering-the-human-cell-lineage-tree/&quot; rel=&quot;nofollow&quot;&gt;Here is a TEDX talk by a researcher in the field&lt;/a&gt;, and &lt;a href=&quot;http://cordis.europa.eu/fp7/ict/fet-proactive/docs/flagship-ws-june10-18-ehud-shapiro_en.pdf&quot; rel=&quot;nofollow&quot;&gt;here is a slideshow&lt;/a&gt; by the same person which lays out the problem and its importance.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-10-30T13:08:12.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11168" PostTypeId="2" ParentId="11158" CreationDate="2013-10-30T13:41:39.323" Score="1" Body="&lt;p&gt;Here's a link from the Oklahoma State University's Environmental Health and Safety suggestions on &lt;a href=&quot;http://ehs.okstate.edu/modules/ergo/Eye.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;office ergonomics&lt;/a&gt;.  It's got the following:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;If the light in the work area is too bright or too dim, the human eye has to work extra hard to compensate for these harsh environmental factors. People may not even be aware that their eyes are under duress, but over time they may develop symptoms of eyestrain.&lt;/p&gt;&#xA;&lt;p&gt;Solution: Use indirect, ambient lighting and an adjustable light source at the desk, where extra illumination is required.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Most sources seem to discuss the effect of too much brightness, although there's a good chance that's a function of the fact that we often &lt;em&gt;need&lt;/em&gt; interior lighting.  Where there are suggestions, it's usually to achieve some level of parity, such as from &lt;a href=&quot;http://www.allaboutvision.com/cvs/irritated.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Adjust the brightness of the display so it's approximately the same as the brightness of your surrounding workstation. As a test, look at the white background of this Web page. If it looks like a light source, it's too bright. If it seems dull and gray, it may be too dark.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;As a side note, I would recommend &lt;a href=&quot;http://justgetflux.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;f.lux&lt;/a&gt;.  It's a piece of software that, outside of daylight hours, adjusts your screen's color.  I can barely look at another computer after dark anymore.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-30T13:41:39.323" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11169" PostTypeId="1" CreationDate="2013-10-30T14:29:08.180" Score="2" ViewCount="393" Body="&lt;p&gt;I am trying to build a small horizontal electrophoresis chamber from scratch. I want to use it for comet assay and I will be using only 1 slide, so it's going to be about 3cm wide, 10cm long and 4cm high, just enough to fit the slide and a small amount of buffer. As far as I know such thing is not commercially available, so before I make it I want to make sure that it's going to work. The main issue is the cost of the electrode (has to be platinum wire). I don't want to spent that much money just to realize that it doesn't work. &#xA;My question is: is a 3cm electrode in a 60-70cm&lt;sup&gt;3&lt;/sup&gt; enough? Basically, are there any physical restrictions on the size and the position of the electrodes and the shape of the chamber?&#xA;Since I am a biologist and my knowledge in physics are quite limited, I would greatly appreciate any information about this.&lt;/p&gt;&#xA;" OwnerUserId="4789" LastEditorUserId="4101" LastEditDate="2013-10-30T14:49:33.667" LastActivityDate="2013-11-29T15:53:26.703" Title="Should the length of the electrodes in the electrophoresis chamber be proportional to chamber's size?" Tags="&lt;dna&gt;&lt;molecular-genetics&gt;&lt;lab-techniques&gt;&lt;gel-electrophoresis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11170" PostTypeId="2" ParentId="11169" CreationDate="2013-10-30T15:35:16.190" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://teach.genetics.utah.edu/content/build_gel_box.pdf&quot; rel=&quot;nofollow&quot;&gt;These instructions for building an electrophoresis chamber&lt;/a&gt; don't comment on the minimum length of wire, but on the other hand they suggest using something called Monel Seizing Wire (Ni/Cu alloy - £8.95 for 10 m in the UK) or 20-gauge copper wire, so if you follow their advice you probably don't need to worry about cost. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I imagine that alloy electrodes won't last as long, but they would be cheap to replace - in fact you would be looking for opportunities to use up all of your excess wire!&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-10-30T15:35:16.190" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11171" PostTypeId="1" AcceptedAnswerId="11196" CreationDate="2013-10-30T16:29:21.020" Score="3" ViewCount="2123" Body="&lt;p&gt;I heard a point, that all (human) body atoms are recycled withing short period like few years. Recycled means &quot;old&quot; atoms are replaced by &quot;new&quot; ones during metabolism, leaving only structure unchanged.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But this looks contradicting with knowledge about DNA. DNA molecule looks unchanged and the fate of all it's atoms looks known. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes I know there are some spontaneous damages which are repaired, but most of DNA atoms remain in place. Even during cell division, 50% of atoms goes to one of the descendant cells. I.e. they don't go outisde body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if the point is wrong concerning DNA atoms, then may it is wrong at all?&lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="69" LastEditDate="2014-03-17T12:19:45.980" LastActivityDate="2014-03-17T12:19:45.980" Title="Are all body atoms really recycled several times during a life?" Tags="&lt;dna&gt;&lt;metabolism&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11172" PostTypeId="1" CreationDate="2013-10-30T16:36:01.930" Score="3" ViewCount="24" Body="&lt;p&gt;Is it possible somehow to attach antibody to silicon or to other electronic component chemical, and have electronic detector of correspondent antigen?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does such devices exist?&lt;/p&gt;&#xA;" OwnerUserId="1584" LastActivityDate="2013-10-30T16:36:01.930" Title="Are there any antigen electronic sensors?" Tags="&lt;immunology&gt;&lt;antibody&gt;&lt;antigen&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ClosedDate="2014-12-11T11:07:45.150" ContentLicense="CC BY-SA 3.0" />
  <row Id="11173" PostTypeId="1" CreationDate="2013-10-30T16:46:34.900" Score="-3" ViewCount="977" Body="&lt;p&gt;Bible says that antediluvian people lived for 800-900 of years. Nowadays apologists say that it is possible and that we just can't know the truth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that one of the basic science principles is the suggestion of similarity of laws of nature. I.e. if we see ancient human fossils, similar to modern human remnants, then we should expect they are of similar age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But does science have some other age proofs besides this? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;May be, for example, from migration data or from some other sources?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isn't it possible in principle, that some virus epidemic in ancient times cause humans to live shorter, due to virus DNA embedded into all of the human DNAs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We don't know abut the all reasons of aging and also we don't know about all means of horizontal gene transfer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What if, a lifespan is a feature, which can be transferred horizontally by a virus or somehow else? &lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="4101" LastEditDate="2013-10-31T14:25:06.240" LastActivityDate="2013-10-31T14:25:06.240" Title="How is it proved, that antediluvian people didn't live for hundreds of years?" Tags="&lt;lifespan&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2013-11-01T21:32:00.773" ContentLicense="CC BY-SA 3.0" />
  <row Id="11174" PostTypeId="2" ParentId="11125" CreationDate="2013-10-30T16:55:29.833" Score="6" Body="&lt;p&gt;I think that most mature cells do not divide in all tissues. If an organism needs to repair tissues, it uses tissue cell precursors -- stem cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case of neurons, these are &lt;a href=&quot;http://en.wikipedia.org/wiki/Neuroblast&quot; rel=&quot;nofollow noreferrer&quot;&gt;neuroblasts&lt;/a&gt;. Neuroblasts can divide and can repair brains under some circumstances (I don't know under which). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a cancer grown from neuroblasts, called &lt;a href=&quot;http://en.wikipedia.org/wiki/Neuroblastoma&quot; rel=&quot;nofollow noreferrer&quot;&gt;neuroblastoma&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it is very improbable to have tumor from neurons, because division genes are turned off in mature cells. Can't state it is not occurring in practice.&lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="50613" LastEditDate="2019-06-18T08:14:42.797" LastActivityDate="2019-06-18T08:14:42.797" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="11175" PostTypeId="2" ParentId="11039" CreationDate="2013-10-30T17:02:10.353" Score="4" Body="&lt;p&gt;The discrepancy can be partly explained by where the temperature was measured from since the human body temperature ranges from 36.5 and 37.5 °C. For example it is 36.8 ± 0.4 °C when measured under the tongue (&lt;a href=&quot;http://en.wikipedia.org/wiki/Human_body_temperature&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Human_body_temperature&lt;/a&gt;). Additionally The body temperature of a healthy person varies during the day by about 0.5 °C (0.9 °F) with lower temperatures in the morning and higher temperatures in the late afternoon and evening, as the body's needs and activities change.&lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="6511" LastEditDate="2014-08-03T11:42:18.743" LastActivityDate="2014-08-03T11:42:18.743" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="11176" PostTypeId="2" ParentId="11173" CreationDate="2013-10-30T18:09:10.453" Score="7" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;I know that one of the basic science principles is the suggestion of similarity of laws of nature. I.e. if we see ancient human fossils, similar to modern human remnants, then we should expect they are of similar age.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Well, similar physiology. Modern humans, throughout recorded history, rarely broke the 100-years-old mark. Our evolutionary cousins &lt;a href=&quot;http://pin.primate.wisc.edu/factsheets/entry/chimpanzee&quot; rel=&quot;noreferrer&quot;&gt;rarely break half of that&lt;/a&gt; and in the wild &lt;a href=&quot;http://www.enchantedlearning.com/subjects/apes/gorilla/&quot; rel=&quot;noreferrer&quot;&gt;reach old age at our &amp;quot;Middle Age&amp;quot; equivalent.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;So, knowing that &lt;em&gt;as we are&lt;/em&gt; is exceptionally long-lived for members of our clade, it would be absolutely incredible and far beyond expectations for an evolutionary ancestor to live &lt;strong&gt;8x-9x&lt;/strong&gt; longer than some of the longest-lived members of our tree (and would be one of the longest living complex organisms &lt;em&gt;ever&lt;/em&gt;).&lt;/p&gt;&#xA;&lt;p&gt;Impossible? No. We can only interpret data from the past; we do not have any records from the time period. In that way, you're entirely correct if you're looking for additional proof.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;But does science have some other age proofs besides this?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This depends on what you consider 'other' proof. Most of the estimations of age of found fossils relies on comparative morphology: We assume that because our joints and teeth wear-out at a certain rate, we can compare the rate of decay of teeth and joints of fossils and get an estimate. If it's true that our extinct cousins experienced similar wear 'n tear as we do (and we &lt;em&gt;don't&lt;/em&gt; have any reason to think otherwise; the bones may be slightly different, but they are made up of the same material), then we can use the comparative morphology as a reasonable estimate.&lt;/p&gt;&#xA;&lt;p&gt;If we assume that their bones and teeth wore out much, &lt;em&gt;much&lt;/em&gt; slower (it would have to be about 10x slower while also being made of similar material) then our age estimates would have to be adjusted.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;May be, for example, from migration data or from some other sources?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Migration data would be incredibly difficult to produce. You would have to follow one family as they migrated, and fossils are rare enough as-is. Data like that would be practically impossible to gather.&lt;/p&gt;&#xA;&lt;p&gt;Perhaps some Population Geneticist has run some genomic data and is capable of making a similar claim through the molecular clock hypothesis, but I am as-yet unaware of anything like this.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Isn't it possible in principle, that some virus epidemic in ancient times cause humans to live shorter, due to virus DNA embedded into all of the human DNAs?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;In principle? Yes. But there &lt;strong&gt;isn't&lt;/strong&gt; any evidence for that. Keep in mind that in order for the viral DNA to be integrated into &lt;em&gt;all&lt;/em&gt; of humanity then it would have had to infect us when our numbers were very, &lt;em&gt;very&lt;/em&gt; small. Evidence does show a bottlenecking event in humans &lt;a href=&quot;http://en.wikipedia.org/wiki/Population_bottleneck#Humans&quot; rel=&quot;noreferrer&quot;&gt;about 70,000 years ago&lt;/a&gt; - but this was thought to have been caused by a supervolcano eruption which dramatically changed the environment and &lt;em&gt;not&lt;/em&gt; a virus. Both genomic and geological evidence come together to support that hypothesis.&lt;/p&gt;&#xA;&lt;p&gt;So, while you are &lt;em&gt;correct&lt;/em&gt; that - in &lt;em&gt;theory&lt;/em&gt; a population of humans could have been infected by a virus which mutated their DNA and caused a dramatic reduction in lifespan at the same time as a bottlenecking event - we have no &lt;em&gt;other&lt;/em&gt; evidence supporting that, either genomic, geological, or evolutionary.&lt;/p&gt;&#xA;&lt;p&gt;Given the &lt;em&gt;lack&lt;/em&gt; of evidence, we should remember our &lt;strong&gt;Occam's Razor&lt;/strong&gt; - In the absence of evidence, the simplest explanation is usually the correct one.&lt;/p&gt;&#xA;&lt;p&gt;So it's either an &lt;em&gt;exceptionally&lt;/em&gt; long-lived species of an already-long-living family contracted a virus at the same time a bottlenecking event occurred and didn't leave behind any evidence, &lt;em&gt;or&lt;/em&gt; our ancestors lived about as long as our evolutionary cousins do now and it's &lt;em&gt;us&lt;/em&gt; who are exceptionally long-lived because of evolutionarily advantageous things like &lt;a href=&quot;http://en.wikipedia.org/wiki/Grandmother_hypothesis&quot; rel=&quot;noreferrer&quot;&gt;The Grandmother Hypothesis&lt;/a&gt; and advancements in technology - which is supported by genomic evidence, fossil evidence, geological evidence, and recorded history.&lt;/p&gt;&#xA;&lt;p&gt;We cannot ever &lt;em&gt;truly&lt;/em&gt; know what happened several hundred thousand years ago. We weren't there and nobody was writing anything down. However, Science is evidence-based, implying that scientific opinion follows the argument with the most supporting evidence behind it.&lt;/p&gt;&#xA;&lt;p&gt;If the evidence changes and begins to favor another argument, then so will the scientific community (ideally speaking).&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-10-30T18:09:10.453" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11178" PostTypeId="1" AcceptedAnswerId="15167" CreationDate="2013-10-30T19:56:05.970" Score="1" ViewCount="191" Body="&lt;p&gt;I've done O- and N- linked enzymatic deglycosylation of purified and lyophilized proteins. Following some modifications to the &lt;a href=&quot;http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Bulletin/edeglybul.pdf&quot; rel=&quot;nofollow&quot;&gt;manufacture's protocol&lt;/a&gt;, I had great results. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I now want a student to deglycosylate some total cell lysates (TCL) of infected cells.  Can he just Vacufuge/vac-spin Triton-X  TCL's and then proceed with the deglycosylation?  The first step is often resuspend in water.  I'm wondering if ether the salts would need be removed by dialysis, or if it doesn't matter, if he can start just from the lysate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The antibodies we have for western detection are excellent, so that is unlikely to be a limiting factor.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2014-02-20T04:04:38.993" Title="Enzymatic Protein Deglycosylation of TCL" Tags="&lt;proteins&gt;&lt;lab-techniques&gt;&lt;western-blot&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11179" PostTypeId="2" ParentId="11171" CreationDate="2013-10-30T20:00:19.250" Score="4" Body="&lt;p&gt;I think you're right. DNA contradicts the notion of &quot;total mass turnover.&quot; So the point is not generally correct. Of course, &lt;em&gt;how&lt;/em&gt; incorrect the statement is reflected by the mass ratio of DNA to non-DNA components -- most all of those other components do turn over multiple times in a lifespan (including things that seem frozen-out like bone calcium).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Turns out the order of magnitude estimate for the mass of DNA in a human is (&lt;a href=&quot;http://ask.metafilter.com/67006/What-is-the-mass-of-my-DNA&quot; rel=&quot;nofollow&quot;&gt;http://ask.metafilter.com/67006/What-is-the-mass-of-my-DNA&lt;/a&gt;) something like a pound. So the statement is on the order of 1% error for a typical adult human.&lt;/p&gt;&#xA;" OwnerUserId="3336" LastActivityDate="2013-10-30T20:00:19.250" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="11180" PostTypeId="1" AcceptedAnswerId="11181" CreationDate="2013-10-30T20:29:07.393" Score="1" ViewCount="4758" Body="&lt;p&gt;See it used here: &lt;a href=&quot;http://en.wikipedia.org/wiki/Fed-batch&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Fed-batch&lt;/a&gt;. In the table giving the different strategies to control growth in a fed-batch culture, one finds, for example: &quot;&lt;em&gt;on-line&lt;/em&gt; measurement of glucose&quot;. What does it mean? Is there an &lt;em&gt;off-line&lt;/em&gt; meassurement? What does it mean?&lt;/p&gt;&#xA;" OwnerUserId="561" LastActivityDate="2013-10-30T20:44:59.310" Title="What is an on-line measurement? What is an off-line measurement?" Tags="&lt;terminology&gt;&lt;definitions&gt;&lt;measurement&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11181" PostTypeId="2" ParentId="11180" CreationDate="2013-10-30T20:38:46.993" Score="2" Body="&lt;p&gt;On-line means that's it's &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23663747&quot; rel=&quot;nofollow&quot;&gt;generally continuous&lt;/a&gt;, or constantly taking the measure, through a &lt;a href=&quot;http://doi.org/10.1016/j.talanta.2004.08.051&quot; rel=&quot;nofollow&quot;&gt;tube connecting the batch.&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Offline is used for things that are taken out of the reactor, or removed from the process.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus it's &quot;on&quot; or &quot;off&quot; the system depending on whether it's contained within the normal piping/fludics of the system: &quot;On&quot; is in the system, &quot;Off&quot; is out of the system.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2013-10-30T20:44:59.310" LastActivityDate="2013-10-30T20:44:59.310" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11182" PostTypeId="1" CreationDate="2013-10-30T22:34:14.120" Score="1" ViewCount="8987" Body="&lt;p&gt;I know the first law is energy can only be converted from one form to the other, therefore in the breakdown of glucose 40% potential energy is converted to ATP and 60% is converted to thermal and unusable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the second law adhere to the breakdown of glucose? Isn't it just the same as the first?&lt;/p&gt;&#xA;" OwnerUserId="4645" LastActivityDate="2014-02-03T15:18:29.480" Title="How do the first and second law of thermodynamics adhere to breakdown of glucose?" Tags="&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11184" PostTypeId="5" CreationDate="2013-10-31T01:45:29.283" Score="0" Body="" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T01:45:29.283" LastActivityDate="2013-10-31T01:45:29.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11185" PostTypeId="4" CreationDate="2013-10-31T01:45:29.283" Score="0" Body="A system, usually in the context of bacteria, that is used to coordinate activity and behavior with other, nearby organisms." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T01:45:29.283" LastActivityDate="2013-10-31T01:45:29.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11186" PostTypeId="1" CreationDate="2013-10-31T02:21:27.567" Score="1" ViewCount="189" Body="&lt;p&gt;that contracts rapidly, in 10 seconds or less, by .5mm or more, when bombarded by electrons as from a cathode ray tube? or expands? could either be living tissue or dead organic matter.  thanks! &lt;/p&gt;&#xA;" OwnerUserId="4793" LastEditorUserId="3632" LastEditDate="2013-10-31T13:51:10.127" LastActivityDate="2013-10-31T13:51:10.127" Title="Does a piezoelectric organic substance exist?" Tags="&lt;muscles&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11187" PostTypeId="2" ParentId="11186" CreationDate="2013-10-31T02:50:42.593" Score="1" Body="&lt;p&gt;I think your question is a bit specific, but piezoelectric organic substances do exist. There was a paper in nature that researchers at Berkeley published.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please see the following journal article:&#xA;&lt;a href=&quot;http://www.nature.com/nnano/journal/v7/n6/full/nnano.2012.69.html#affil-auth&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nnano/journal/v7/n6/full/nnano.2012.69.html#affil-auth&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also see the following public article:&#xA;&lt;a href=&quot;http://www.extremetech.com/extreme/129389-berkeley-scientists-turn-harmless-virus-into-piezoelectric-generator&quot; rel=&quot;nofollow&quot;&gt;http://www.extremetech.com/extreme/129389-berkeley-scientists-turn-harmless-virus-into-piezoelectric-generator&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4794" LastActivityDate="2013-10-31T02:50:42.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11188" PostTypeId="2" ParentId="5128" CreationDate="2013-10-31T02:59:56.573" Score="2" Body="&lt;p&gt;The reasons your field of view is not circular are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Even when looking directly forward your nose, brows, and cheeks obstruct your view.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;You have two eyes which are aligned horizontally.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The field of view is measured by a method called perimetry, and looks approximately as depicted in &lt;a href=&quot;http://vision.arc.nasa.gov/personnel/al/papers/64vision/17_files/image026.jpg&quot; rel=&quot;nofollow&quot;&gt;this graphic&lt;/a&gt;. The guide &lt;a href=&quot;http://vision.arc.nasa.gov/personnel/al/papers/64vision/17.htm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; provides further comments on the graphic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see in the image I linked to, the field of view (were it to be approximated with a rectangle) spans 180° horizontally and 130° vertically. Yielding a width-to-height ratio of 0.72. &lt;strong&gt;Which is better approximated by the traditional 4:3 screen size and NOT by modern 16:9 displays&lt;/strong&gt;. Having said that, 16:9 may not necessarily be a worse format, as &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0025556475901078&quot; rel=&quot;nofollow&quot;&gt;researchers found&lt;/a&gt; that horizontal saccades are faster than vertical ones.&lt;/p&gt;&#xA;" OwnerUserId="4795" LastEditorUserId="4795" LastEditDate="2013-11-08T09:36:16.633" LastActivityDate="2013-11-08T09:36:16.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11189" PostTypeId="1" AcceptedAnswerId="11194" CreationDate="2013-10-31T03:04:41.907" Score="1" ViewCount="1223" Body="&lt;p&gt;I'm trying to obtain a better understanding of the Guthrie Test, which checks whether people have a disease called PKU. &#xA;The Guthrie test uses bacteria to check for Phenylalanine (the amino acid) in blood samples. If both Phe and B-2-thienylalanine are available on the medium, the bacteria will grow. However, if only B-2-thienylalanine is available the bacteria will not grow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In all of the articles I can find, I have seen no explanation, just a link to a paper that I can't find on the internet.:&#xA;&quot; A standard culture of Bacillus subtilis was incubated on agar in the presence of an antagonist of phenylalanine (B-2-thienylalanine), which prevents the bacteria from growing.3 &quot; &lt;a href=&quot;http://labmed.ascpjournals.org/content/40/12/748.full#ref-3&quot; rel=&quot;nofollow&quot;&gt;Link&lt;/a&gt;&#xA;The reference they mention here is:&#xA;&quot;The inhibition assay: Its use in screening urinary specimens for metabolic differences associated with mental retardation&quot; by R. Guthrie from 1960.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do we know what mechanism this protein is inhibiting?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help would be greatly appreciated.&lt;/p&gt;&#xA;" OwnerUserId="4794" LastActivityDate="2013-10-31T08:16:10.543" Title="Why does beta-2-Thienylalanine inhibit bacterial growth?" Tags="&lt;metabolism&gt;&lt;bacteriology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11190" PostTypeId="1" CreationDate="2013-10-31T07:14:14.830" Score="1" ViewCount="127" Body="&lt;p&gt;Where exactly do dimethyltryptamine and sigma 1-type opioid receptor interact? I read in this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155724/#!po=31.8182&quot; rel=&quot;nofollow&quot;&gt;When the Endogenous Hallucinogenic Trace Amine N,N-Dimethyltryptamine Meets the Sigma-1 Receptor&lt;/a&gt; but it does not say where exactly they interact only that they do.&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="3336" LastEditDate="2013-10-31T15:25:34.500" LastActivityDate="2013-10-31T15:25:34.500" Title="Dimethyltryptamine and Sigma 1-type opioid receptor interaction" Tags="&lt;proteins&gt;&lt;pharmacology&gt;&lt;hallucinogens&gt;&lt;pharmacodynamics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11191" PostTypeId="2" ParentId="11190" CreationDate="2013-10-31T07:30:36.957" Score="1" Body="&lt;p&gt;From your article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sig-1Rs localize at the interface between the endoplasmic reticulum (ER) and mitochondrion, which is known as the mitochondria-associated ER membrane (MAM).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Consequently, they are found in a variety of areas within the central nervous system as well as in other types of cells throughout the body (notably cardiac cells).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An important biological activity of sigma receptor activation is the inhibition of ion channels, which operates through protein-protein interactions without mediation by G proteins and protein kinases. In addition to modulating various types of voltage-activated K+ channels, the sigma-1 receptor associates with the Kv1.4 K+ channel in posterior pituitary nerve terminals, as well as in Xenopus oocytes. Sigma receptor ligands also modulate N-, L-, P/Q-, and R-type Ca2+ channels in rat sympathetic and parasympathetic neurons. Sigmareceptor ligands modulate cardiac voltage-gated Na+ channels (hNav1.5) in human embryonic kidney 293 (HEK293) cells, COS-7 cells, and neonatal mouse cardiac myocytes. To evaluate the capacity of DMT to induce physiological responses by binding to sigma receptors, we examined the action of DMT on voltage-activated Na+ current.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fontanilla D, Johannessen M, Hajipour AR, Cozzi NV, Jackson MB, Ruoho AE. The hallucinogen N,N-dimethyltryptamine (DMT) is an endogenous sigma-1 receptor regulator. Science. 2009;323:934–937.  &lt;a href=&quot;http://dx.doi.org/10.1126/science.116612&quot; rel=&quot;nofollow&quot;&gt;[DOI]&lt;/a&gt;&lt;br&gt;&#xA;  (reference 24 in the article that you cite)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2013-10-31T12:20:14.420" LastActivityDate="2013-10-31T12:20:14.420" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11192" PostTypeId="2" ParentId="11186" CreationDate="2013-10-31T07:36:38.077" Score="1" Body="&lt;p&gt;I don't know if it would contract by the amount that you are after, but bone (which has both organic and inorganic components) is piezoelectric.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an overview, see &lt;a href=&quot;http://silver.neep.wisc.edu/~lakes/BoneElectr.html&quot; rel=&quot;nofollow&quot;&gt;http://silver.neep.wisc.edu/~lakes/BoneElectr.html&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;They suggest that two different mechanisms are responsible for these effects: classical piezoelectricity due to the molecular asymmetry of collagen in dry bone, and fluid flow effects, possibly streaming potentials in wet bone.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="57" LastActivityDate="2013-10-31T07:36:38.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11193" PostTypeId="2" ParentId="11152" CreationDate="2013-10-31T08:13:59.110" Score="1" Body="&lt;p&gt;These new GO terms seem to be the parents of the already GO terms present in my original dataset.&lt;/p&gt;&#xA;" OwnerUserId="4717" LastActivityDate="2013-10-31T08:13:59.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11194" PostTypeId="2" ParentId="11189" CreationDate="2013-10-31T08:16:10.543" Score="3" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Beta-2-Thienylalanine&quot; rel=&quot;nofollow&quot;&gt;&amp;beta;-2-thienylalanine&lt;/a&gt; is an analogue of phenylalanine. It is incorporated into proteins in place of phenylalanine, and the resulting proteins are inactive because of the substitution. Consequently growth medium supplemented with &amp;beta;-2-thienylalanine will not support bacterial growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Addition of phenylalanine to a medium containing &amp;beta;-2-thienylalanine will result in a competition between the two compounds - if there is an excess of phenylalanine then this will out-compete the analogue and incorporation of the analogue will be minimised, allowing growth. Blood from a patient with PKU contains phenylalanine, so the addition of this to the growth medium will relieve inhibition of growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.patents.com/us-6030819.html&quot; rel=&quot;nofollow&quot;&gt;Here is a link to a patent application&lt;/a&gt; in which a screen for &lt;em&gt;E. coli&lt;/em&gt; strains overproducing phenylalanine was based upon the same principle.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-10-31T08:16:10.543" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11196" PostTypeId="2" ParentId="11171" CreationDate="2013-10-31T10:45:00.057" Score="7" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Rudolph_Schoenheimer&quot; rel=&quot;noreferrer&quot;&gt;Rudolf Shoenheimer&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/David_Rittenberg&quot; rel=&quot;noreferrer&quot;&gt;David Rittenberg&lt;/a&gt; were key figures in introducing the isotopic tracer technique to biology.&lt;/p&gt;&#xA;&lt;p&gt;This technique, which may be dated to the discovery of deuterium by &lt;a href=&quot;http://en.wikipedia.org/wiki/Harold_Urey&quot; rel=&quot;noreferrer&quot;&gt;Urey&lt;/a&gt; in 1933, produced a revolution in biological thought.&lt;/p&gt;&#xA;&lt;p&gt;Much of the early work was done at the Department of Biological Chemistry at Columbia University under the chairmanship of &lt;a href=&quot;http://en.wikipedia.org/wiki/Hans_Thacher_Clarke&quot; rel=&quot;noreferrer&quot;&gt;H. T. Clark&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Up to this time it was thought that the components of tissues were relatively stable, and that ingested food was metabolized immediately to provide a source of energy.&lt;/p&gt;&#xA;&lt;p&gt;The first experiments showed that when deuterated fatty acids were fed to mice, most of the label was initially deposited in adipose tissue.&lt;/p&gt;&#xA;&lt;p&gt;It was concluded that adipose tissue acts a 'fuel depot' that is in a state of metabolic flux and is the direct source of fatty acids burned as a fuel (see &lt;a href=&quot;http://www.jbc.org/content/276/46/42619&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; for refs). Fats present in food are not primarily used an an immediate energy source.&lt;/p&gt;&#xA;&lt;p&gt;When a stable isotope of nitrogen became available (N&lt;sup&gt;15&lt;/sup&gt;), it was found that proteins were also 'in a state of dynamic flux' and were being continuously regenerated and broken down.&lt;/p&gt;&#xA;&lt;p&gt;The first experiments were done with N&lt;sup&gt;15&lt;/sup&gt;-labeled tyrosine and it it worth quoting from the paper (&lt;a href=&quot;http://www.jbc.org/content/127/1/333.full.pdf+html?sid=9c28a31f-2f01-42a3-81f6-121c14272032&quot; rel=&quot;noreferrer&quot;&gt;Studies in Protein Metabolism. VII The metabolism of tyrosine&lt;/a&gt; by D Rittenberg Rudolf Schoenheimer &amp;amp;  S. Ratner)&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The results indicate that in our rat the nitrogen of at least one&#xA;amino acid, tyrosine, was only partly excreted in the urine, while&#xA;almost half of it was retained in the body proteins.&lt;/p&gt;&#xA;&lt;p&gt;Of this deposited nitrogen only a fraction was found attached to the original&#xA;carbon chain, namely to tyrosine, while the bulk was distributed over other&#xA;nitrogenous groups of the proteins&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Shortly after giving a series of lectures at Harvard University in 1941, &lt;a href=&quot;http://en.wikipedia.org/wiki/Rudolph_Schoenheimer&quot; rel=&quot;noreferrer&quot;&gt;Shoenheimer&lt;/a&gt; took his own life.  The lectures were published posthumously as a classic book called The &lt;a href=&quot;http://www.geocities.jp/minakami30jp/ds/eds.html&quot; rel=&quot;noreferrer&quot;&gt;Dynamic State of Body Constituents&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Further information about the early  work on isotopes, their role in changing completely the way we think about metabolism, and the role of Columbia University in shepherding in this great era, may be found in the following open-access article by &lt;a href=&quot;http://www.fasebj.org/content/26/5/1771&quot; rel=&quot;noreferrer&quot;&gt;Eugene. P. Kennedy&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jbc.org/content/276/46/42619&quot; rel=&quot;noreferrer&quot;&gt;Hitler’s Gift and the Era of Biosynthesis&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Another good reference on the work of Schoenheimer may be found &lt;a href=&quot;http://jn.nutrition.org/content/121/11/1701.long&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;So are all proteins broken down and regenerated?  I know of any one exception and that is the lens crystallins where there is virtually no turnover&#xA;throughout the life of an individual.&lt;/p&gt;&#xA;&lt;p&gt;The crystallins in our lens are synthesized at birth and remain with us virtually unchanged for life.&lt;/p&gt;&#xA;&lt;p&gt;There is a &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001529&quot; rel=&quot;noreferrer&quot;&gt;very nice open-access paper&lt;/a&gt; on this published in PLOS One:&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Radiocarbon Dating of the Human Eye Lens Crystallines Reveal Proteins without Carbon Turnover throughout Life&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;(Lynnerup &lt;em&gt;et al.&lt;/em&gt; 2007)&lt;/p&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-11-01T18:31:32.410" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11197" PostTypeId="5" CreationDate="2013-10-31T16:41:04.913" Score="0" Body="&lt;p&gt;Although cytokinesis usually takes place alongside the final stages of mitosis, the two are separate processes; questions about &lt;a href=&quot;/questions/tagged/mitosis&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;mitosis&amp;#39;&quot; rel=&quot;tag&quot;&gt;mitosis&lt;/a&gt; should use that tag.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T16:41:04.913" LastActivityDate="2013-10-31T16:41:04.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11198" PostTypeId="4" CreationDate="2013-10-31T16:41:04.913" Score="0" Body="The process of cytoplasmic division that leads to two daughter cells that usually occurs after mitosis." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T16:41:04.913" LastActivityDate="2013-10-31T16:41:04.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11199" PostTypeId="1" CreationDate="2013-10-31T16:52:37.963" Score="2" ViewCount="61" Body="&lt;p&gt;I am interested in knowing which freshwater fish are affected by magnetic fields.  I've heard that Lake Sturgeon are, but would like more references. This is for a project that will have buried 3 phase power cables.&lt;/p&gt;&#xA;" OwnerUserId="4796" LastEditorUserId="4101" LastEditDate="2013-10-31T16:59:49.613" LastActivityDate="2016-05-03T20:55:14.347" Title="What Freshwater Fish Are Affected By Magnetic Fields" Tags="&lt;ichthyology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11200" PostTypeId="1" CreationDate="2013-10-31T17:26:56.157" Score="3" ViewCount="73" Body="&lt;p&gt;I am trying to generate some candidate traits to measure in a fitness assay of wildtype outbred (lab population) flies. The key trait I will measure is lifespan. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for some additional traits which can be &lt;strong&gt;measured from the same flies&lt;/strong&gt; as those in the lifespan assay &lt;strong&gt;without harming or killing the fly in the process&lt;/strong&gt;. For example, I could measure wings using a technique devised by the Houle Lab called &lt;a href=&quot;http://www.youtube.com/watch?v=Nq-OIGKzdLk&quot; rel=&quot;nofollow&quot;&gt;WingMachine&lt;/a&gt;. I think I could also do some other measures with the same equipment, leg length etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The traits should also be present in both sexes (can be monomorphic or dimorphic) and quick to measure; I'm aiming for 200-250 measures/collections/images a day. Traits that can be measured properly in a fly which has died of old age would also work. Traits can be morphological, behavioral etc..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What other traits can be done like this?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-11-04T10:00:41.603" LastActivityDate="2014-06-09T18:58:34.427" Title="Non-fatal / low-harm measurement of Drosophila traits" Tags="&lt;lab-techniques&gt;&lt;drosophila&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11201" PostTypeId="2" ParentId="11199" CreationDate="2013-10-31T17:27:09.973" Score="1" Body="&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00657119&quot; rel=&quot;nofollow&quot;&gt;Sockeye salmon&lt;/a&gt; species &lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00612020&quot; rel=&quot;nofollow&quot;&gt;definitely&lt;/a&gt; do, although admittedly the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614721/&quot; rel=&quot;nofollow&quot;&gt;interesting salmon&lt;/a&gt; are those that spend significant time in the ocean.&lt;/li&gt;&#xA;&lt;li&gt;Here's some evidence that &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3515494/&quot; rel=&quot;nofollow&quot;&gt;carp can&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pnas.org/content/early/2012/06/29/1205653109&quot; rel=&quot;nofollow&quot;&gt;Raindbow trout&lt;/a&gt; are also &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19669766&quot; rel=&quot;nofollow&quot;&gt;capable&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/srep/2012/121011/srep00727/full/srep00727.html&quot; rel=&quot;nofollow&quot;&gt;Zebrafish&lt;/a&gt; are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15753024&quot; rel=&quot;nofollow&quot;&gt;also able&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15277551&quot; rel=&quot;nofollow&quot;&gt;Japanese eels&lt;/a&gt; too, of which some are freshwater. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-10-31T17:27:09.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11202" PostTypeId="5" CreationDate="2013-10-31T17:57:48.527" Score="0" Body="" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T17:57:48.527" LastActivityDate="2013-10-31T17:57:48.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11203" PostTypeId="4" CreationDate="2013-10-31T17:57:48.527" Score="0" Body="A process defining organisms that grow and adapt to stimuli while maintaining a state of organization and energy production and being capable of reproduction." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T17:57:48.527" LastActivityDate="2013-10-31T17:57:48.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11204" PostTypeId="5" CreationDate="2013-10-31T18:10:04.267" Score="0" Body="&lt;p&gt;The process in which a protein folds into a three-dimensional shape to achieve proper functioning.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="28834" LastEditDate="2017-03-29T16:00:36.580" LastActivityDate="2017-03-29T16:00:36.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11205" PostTypeId="4" CreationDate="2013-10-31T18:10:04.267" Score="0" Body="The process in which a protein folds into a three-dimensional shape to achieve proper functioning." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T18:10:04.267" LastActivityDate="2013-10-31T18:10:04.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11206" PostTypeId="5" CreationDate="2013-10-31T19:12:33.303" Score="0" Body="" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T19:12:33.303" LastActivityDate="2013-10-31T19:12:33.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11207" PostTypeId="4" CreationDate="2013-10-31T19:12:33.303" Score="0" Body="A chip-based assay that allows parallel detection of thousands of samples, such as DNA, at once." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T19:12:33.303" LastActivityDate="2013-10-31T19:12:33.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11208" PostTypeId="5" CreationDate="2013-10-31T19:20:14.237" Score="0" Body="" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T19:20:14.237" LastActivityDate="2013-10-31T19:20:14.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11209" PostTypeId="4" CreationDate="2013-10-31T19:20:14.237" Score="0" Body="Hard projections in the mouths of vertebrates used mainly to mechanically digest food.  Teeth can also be used for the purposes of defense or obtaining meals, especially in the case of hunting." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T19:20:14.237" LastActivityDate="2013-10-31T19:20:14.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11210" PostTypeId="5" CreationDate="2013-10-31T19:21:03.553" Score="0" Body="&lt;p&gt;For the visible spectrum, use &lt;a href=&quot;/questions/tagged/light&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;light&amp;#39;&quot; rel=&quot;tag&quot;&gt;light&lt;/a&gt;; for ultraviolet light, use &lt;a href=&quot;/questions/tagged/uv&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;uv&amp;#39;&quot; rel=&quot;tag&quot;&gt;uv&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T19:21:03.553" LastActivityDate="2013-10-31T19:21:03.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11211" PostTypeId="4" CreationDate="2013-10-31T19:21:03.553" Score="0" Body="Ionizing electromagnetic waves, usually harmful to most biological beings." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T19:21:03.553" LastActivityDate="2013-10-31T19:21:03.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11212" PostTypeId="5" CreationDate="2013-10-31T19:23:44.503" Score="0" Body="" OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2013-10-31T19:23:44.503" LastActivityDate="2013-10-31T19:23:44.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11213" PostTypeId="4" CreationDate="2013-10-31T19:23:44.503" Score="0" Body="Electromagnetic radiation, specifically the range of wavelengths visible to humans (&quot;visible light&quot;)." OwnerUserId="4101" LastEditorUserId="16866" LastEditDate="2020-01-02T19:22:58.883" LastActivityDate="2020-01-02T19:22:58.883" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="11214" PostTypeId="2" ParentId="10957" CreationDate="2013-10-31T20:33:54.070" Score="1" Body="&lt;p&gt;It seems as if this article is purely speculative. They didn't mention any DNA testing, but instead discussed physical features.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two &quot;types&quot; of archaeologists: clumpers and splitters. Clumpers (like the author of this article) believe that there is wide variety among members of the same species, and so it is often wrong to categorize every new hominid fossil as being a different species. Splitters like to &quot;split&quot; their findings into new species, even though there is no evidence that speciation had ever occurred; they just decide that since the remains look different, they must have speciated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the future, I hope that archaeologists will have more sophisticated means of sequencing the DNA of ancient remains, allowing them to construct an accurate phylogeny&lt;/p&gt;&#xA;" OwnerUserId="4797" LastActivityDate="2013-10-31T20:33:54.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11215" PostTypeId="2" ParentId="9206" CreationDate="2013-10-31T23:55:01.147" Score="4" Body="&lt;p&gt;Group selection, in the extreme, yields eusociality due to the shared fate of the replicators in the group.  In a multicellular sexual organism, this &quot;shared fate&quot; of the &quot;group&quot; is the shared prospect that all replicators (alleles) have for making it into the next generation via the meotic lottery that produces the gamete.  Since they share this prospective fate they have an evolutionary incentive to cooperate in the construction of specialized cells that are, in effect, &quot;sterile caste&quot; members of the total &quot;hive&quot;.  Similarly, if it is possible to subject all members of a group of individuals to a shared fate through multiple generations -- they will tend to evolve highly cooperative social structures.  However, one of the confusing aspects of the eusocial insect colonies is whether they evolved to be that way through shared fate of individual organisms, or some variant on the meotic lottery's shared fate of alleles.  The answer appears to be, primarily, that it is a peculiar form of meotic lottery in which the genes of the parents have extended phenotypes in the children that, in essence, parasitically castrate the vast majority of the children to help rear more offspring for the parents -- in particular the queen.  In this respect, one can view the evolution of eusociality in the social insects as a perverse form of individual selection where the genes of, say, the queen, cooperate in constructing not just the queen's body but, also, the entire hive.  The sterile castes are simply extended phenotypes of the queen (and the  drone with which she mates).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &quot;The Social Conquest of Earth&quot; by E. O. Wilson for an in-depth treatment of eusociality and its evolution as set forth by Nowak et al in their recent paper &quot;The Evolution of Eusociality&quot;.  See also &quot;The Extended Phenotype&quot; by Richard Dawkins -- in particular the chapter &quot;Host Phenotypes of Parasite Genes&quot;.&lt;/p&gt;&#xA;" OwnerUserId="4798" LastActivityDate="2013-10-31T23:55:01.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11216" PostTypeId="1" AcceptedAnswerId="11220" CreationDate="2013-11-01T03:32:51.573" Score="4" ViewCount="242" Body="&lt;p&gt;I am working on mathematically modeling HIV and Tuberculosis Co-infection dynamics, and am working with 12 differential equations describing the behavior of all of the compartments and parameters. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, I just have one question: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which is harder, in general: For a susceptible person to contract HIV, or a HIV+ person to contract AIDS?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please pardon my ignorance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerDisplayName="user4800" LastActivityDate="2013-11-01T13:28:09.293" Title="Which is harder to contract - HIV or AIDS?" Tags="&lt;hiv&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11217" PostTypeId="1" CreationDate="2013-11-01T09:29:25.130" Score="4" ViewCount="235" Body="&lt;p&gt;I think I once saw a video of a caterpillar that could get infected by a parasite, and could die of that, unless a specific kind of spider would eat the parasite, and so once the caterpillar is infected it goes looking for that spider. I can't find that video anymore though, nor any reference on this, so I'm beginning to doubt myself. Does this behaviour really exist?&lt;/p&gt;&#xA;" OwnerUserId="4802" LastEditorUserId="3624" LastEditDate="2013-11-01T11:37:44.397" LastActivityDate="2013-11-14T20:14:14.507" Title="Is it true that there is a spider that eats parasites from caterpillars" Tags="&lt;entomology&gt;&lt;ethology&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11218" PostTypeId="1" CreationDate="2013-11-01T10:34:26.597" Score="3" ViewCount="8186" Body="&lt;p&gt;I know that mucosa inside the nose absorbs cocaine molecules when snorting cocaine, but what difference is there compared to swallowing?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also more cocaine administration equals more cocaine molecules in the brain equals more inhibition of repute equals more serotonin–norepinephrine–dopamine in the synaptic clefts equals more work for receptors equals more intense effect, right?  What about the duration of a particular molecule which inhibits reuptake? How long this particular molecule stands there?&lt;/p&gt;&#xA;" OwnerUserId="4497" LastEditorUserId="4101" LastEditDate="2013-11-01T13:58:10.583" LastActivityDate="2013-12-31T15:47:27.047" Title="What is the physiological difference between snorting/swallowing cocaine" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;neurotransmitter&gt;&lt;cocaine&gt;&lt;pharmacokinetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11219" PostTypeId="1" AcceptedAnswerId="11222" CreationDate="2013-11-01T12:35:14.170" Score="2" ViewCount="484" Body="&lt;p&gt;There are lots of questions about how and why there is genetic variation between organisms of the same species, but I haven't been able to find a numerical value for the expected amount of genetic variation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say we have two different samples of MRSA252. We sequence these samples and get the full genomes of ~3 million base pairs each. What percentage of these bases would we expect to be different (assuming there is no sequencing error)? I figure it will be about 1%, but I haven't been able to find a source.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure the answer will depend on the specific species, but I'm looking for a ballpark figure for bacteria. An academic source would be much appreciated.&lt;/p&gt;&#xA;" OwnerUserId="4803" LastEditorUserId="4803" LastEditDate="2013-11-01T13:21:47.907" LastActivityDate="2013-11-01T17:22:25.757" Title="How much natural genetic variation is there between bacteria of the same species?" Tags="&lt;dna&gt;&lt;bacteriology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11220" PostTypeId="2" ParentId="11216" CreationDate="2013-11-01T13:28:09.293" Score="2" Body="&lt;p&gt;Your question depends hugely on the factors at play.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The rate of transmission depends on the route of infection.  Wikipedia has a &lt;a href=&quot;https://en.wikipedia.org/wiki/HIV/AIDS#Transmission&quot; rel=&quot;nofollow&quot;&gt;good breakdown&lt;/a&gt; showing the wide variability.  Are they getting a blood transfusion?  90%.  Mother-to-infant?  25%.  Male-to-female vaginal sex?  No higher than 0.3%.  Not to mention that the incidence varies massively between countries, as does the most common route of infection.&lt;/li&gt;&#xA;&lt;li&gt;The rate of progression to AIDS also depends on a large number of factors including age, viral load, various genotypes, access to medical treatment, and, of course, &lt;a href=&quot;https://en.wikipedia.org/wiki/Long-term_nonprogressor&quot; rel=&quot;nofollow&quot;&gt;long-term nonprogressor (LTNP) status&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The incidence of LTNPs is around &lt;a href=&quot;http://www.niaid.nih.gov/volunteer/hivlongterm/Pages/default.aspx&quot; rel=&quot;nofollow&quot;&gt;1 in 500&lt;/a&gt;, or 0.2%, which overlaps with but is at the low end of transmission rates for some routes of infection.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-11-01T13:28:09.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11221" PostTypeId="2" ParentId="11218" CreationDate="2013-11-01T13:56:32.203" Score="1" Body="&lt;p&gt;You can easily google for this question and find plenty of disreputable sources, but this is another case where &lt;a href=&quot;https://en.wikipedia.org/wiki/Cocaine#Routes_of_administration&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; does an okay job.  There are some misleading and erroneous sentences, but this one basically sums it up:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Compared to ingestion, the faster absorption of insufflated cocaine results in quicker attainment of maximum drug effects.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Mainly, take a look at &lt;a href=&quot;https://www.sciencedirect.com/science/article/pii/0378874181900635&quot; rel=&quot;nofollow&quot;&gt;this 1981 article&lt;/a&gt;.  The researchers gave participants cocaine, measured drug activity, and did then did a great review of the literature.  They found that, like plenty of other drugs, &lt;strong&gt;ingesting cocaine results in a slower but longer-lasting effect&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your stomach is not an efficient route of absorption for things besides water, alcohol, and aspirin; besides, it's highly acidic.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-11-01T13:56:32.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11222" PostTypeId="2" ParentId="11219" CreationDate="2013-11-01T14:33:45.610" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I'm sure the answer will depend on the specific species, but I'm looking for a ballpark figure for bacteria.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes indeed it will.  Bacteria are a huge domain of life; you might as well ask for variability between all plants or between all animals.  Bacteria can live in very different environments, and the whole things is made more complex by widespread horizontal transfer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still, for bacteria, you can't do much better than &lt;em&gt;E. coli&lt;/em&gt;, and boy are they a mess.  Here's a &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs00248-010-9717-3&quot; rel=&quot;nofollow&quot;&gt;paper from 2010 that blew my mind&lt;/a&gt;.  The authors sequenced 61 &lt;em&gt;E. coli&lt;/em&gt; genomes and found:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...that any given E. coli genome sequenced will have only roughly 20% of its genes part of the E. coli core, and the remaining 80% are not found in all other E. coli genomes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;20% variability &lt;em&gt;within a species&lt;/em&gt;.  20%, one species.  &lt;em&gt;E.coli&lt;/em&gt; is an extreme example, but still, species is a stupid concept.  Here's a &lt;a href=&quot;http://www.biomedcentral.com/1471-2164/7/167&quot; rel=&quot;nofollow&quot;&gt;2006 paper&lt;/a&gt; finding that plenty of unique &lt;em&gt;Campylobacter&lt;/em&gt; proteins simply aren't in plenty of &lt;em&gt;Campylobacter&lt;/em&gt; species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a more broad scale, here's an &lt;a href=&quot;http://hal.inria.fr/docs/00/62/25/73/PDF/gb-2010-11-4-r45.pdf&quot; rel=&quot;nofollow&quot;&gt;excellent (and free) paper&lt;/a&gt; you should look at.  It examines islands of &quot;microdiversity&quot; among various species, finding that some species are easily 50%-75% different.  A simple way to estimate this is too look at gene number for bacterial species, which should make it clear that some of these bugs vary by up to an order of magnitude.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short: A lot.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-11-01T14:33:45.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11223" PostTypeId="1" AcceptedAnswerId="11226" CreationDate="2013-11-01T16:00:35.453" Score="4" ViewCount="397" Body="&lt;p&gt;I have read that IQ is highly heritable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How could this be tested?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For honest testing, it seems to me that only children who were abandoned should have been tested, to exclude education effect. Was it really done?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intelligence is one of the traits, that can be inherited both by genes and by education. You can't educate your children to have blue eyes, but you can educate them to count or to read.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to study heritability of intelligence, educational inheritance should be excluded.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that usual way to study heritability is to compare variability for monozygotic and dizigotic twins. Being sufficient for other traits, this method is highly insufficient for intelligence (which is obvious). Having identical perception system, monozygotic twins will respond identically to an education, so they will be more closely educated, even if IQ is completely independent of genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to study IQ heritability, subjects should be studied under different education conditions. I.e. they should be abandoned by parents and/or adopted separately. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: was this done or not?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, then the question is, how education effects were eliminated? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also I would like to know, if my reasoning about why just studying twins is insufficient is wrong.&lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="1584" LastEditDate="2013-11-03T19:00:29.257" LastActivityDate="2013-11-04T00:30:01.337" Title="How was the heritability of IQ tested?" Tags="&lt;genetics&gt;&lt;intelligence&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11225" PostTypeId="2" ParentId="11219" CreationDate="2013-11-01T17:22:25.757" Score="1" Body="&lt;p&gt;There is a database of Multi Locus Sequence Typing (MLST) data for &lt;em&gt;E. coli&lt;/em&gt; at &lt;a href=&quot;http://mlst.ucc.ie/mlst/&quot; rel=&quot;nofollow&quot;&gt;http://mlst.ucc.ie/mlst/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These data are limited to sequences at seven genes: adk, fumC, gyrB, icd, mdh, purA and recA. Furthermore for each of these genes only part of the sequence (in the range 452-536 bp) is characterised.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each strain tabulated is represented by a genotype consisting of the alleles present at each of these loci. There are many different alleles found for each locus ranging from 240 variants at recA to 431 variants at fumC.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I ran a pairwise comparison (87398 comparisons -nowhere near the maximum possible, but I didn't have time to let my script run all pairwise combinations) and found that the average total divergence at these loci was 1.3%&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although this is a very different perspective from the one described by @Amory, I think it is nicely complementary, and it reveals that even at genes shared by all strains of &lt;em&gt;E.coli&lt;/em&gt; there is a degree of sequence divergence that is quite close to your guess of 1%.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-11-01T17:22:25.757" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11226" PostTypeId="2" ParentId="11223" CreationDate="2013-11-01T18:27:06.157" Score="6" Body="&lt;p&gt;I don't really know what you mean by &quot;abandoned children&quot;.  Adopted children?  Children in the wild?  Have you read the &lt;a href=&quot;https://en.wikipedia.org/wiki/Heritability_of_IQ&quot;&gt;Wikipedia article&lt;/a&gt; on the subject?  If you want to know how it was studied, just take a look at the references, it's pretty straightforward.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heritability simply means how much &lt;em&gt;variation&lt;/em&gt; in a trait is due to &lt;em&gt;genetics&lt;/em&gt;, which is usually easiest to test in monozygotic twins.  Here's a &lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF01067188&quot;&gt;good example&lt;/a&gt; where they did just that - they compared identical (monozygotic) and fraternal (dizygotic) twins raised apart or separately, finding:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;General cognitive ability yielded a heritability estimate of about .80 in two assessments 3 years apart as part of the Swedish Adoption/Twin Study of Aging. This is one of the highest heritabilities reported for a behavioral trait. Across the two ages, average heritabilities are about .60 for verbal tests, .50 for spatial and speed-of-processing tests, and .40 for memory tests. For general cognitive ability, the phenotypic stability across the 3 years is .92 and stable genetic factors account for nearly 90% this stability.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencemag.org/content/250/4978/223&quot;&gt;Here's another example doing basically the same thing&lt;/a&gt;.  The rest of the enWiki article gives a good breakdown of all the various factors involved in making this such a complex issue, as well as what was studied.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-11-01T18:27:06.157" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11227" PostTypeId="1" CreationDate="2013-11-01T19:21:42.050" Score="2" ViewCount="56" Body="&lt;p&gt;I read that viruses are called intermediate between living and non-living particles. Well, if so, then where did they originate from?  From living or non-living? If they originated from either living or non-living then how could they have both the characteristics of living and non-living?&lt;/p&gt;&#xA;" OwnerUserId="4806" LastEditorUserId="4101" LastEditDate="2013-11-01T20:20:21.607" LastActivityDate="2013-11-01T20:20:21.607" Title="What is the origin of viruses? How could they get both living and non-living characteristics?" Tags="&lt;evolution&gt;&lt;virology&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2013-11-02T14:21:20.907" ContentLicense="CC BY-SA 3.0" />
  <row Id="11229" PostTypeId="1" CreationDate="2013-11-01T21:46:51.483" Score="1" ViewCount="20" Body="&lt;p&gt;I would like to use MultiPipMaker for testing a genome alignment between two sequences, each sequence is in .fasta format, but the problem is that when I submit the couples of file that I need, the web browser sends an email that the blastz has timed out. Does anybody know why is the that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The address of the program is: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://pipmaker.bx.psu.edu/cgi-bin/multipipmaker&quot; rel=&quot;nofollow&quot;&gt;http://pipmaker.bx.psu.edu/cgi-bin/multipipmaker&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks&lt;/p&gt;&#xA;" OwnerUserId="4808" LastActivityDate="2013-11-01T21:46:51.483" Title="issues with MultiPipMaker" Tags="&lt;genomes&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11230" PostTypeId="1" CreationDate="2013-11-01T21:47:55.130" Score="7" ViewCount="9990" Body="&lt;p&gt;In &lt;em&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12701.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evolutionary ecology: Novelty makes the heart grow fonder&lt;/a&gt;&lt;/em&gt;, they say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Thus, it seems that the diverse coloration in this species is promoted by both natural and sexual selection.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I had always thought of sexual selection as a subset of natural selection. What's the right way to think about the relationship between the two?&lt;/p&gt;&#xA;" OwnerDisplayName="user4518" LastEditorUserId="6307" LastEditorDisplayName="user4518" LastEditDate="2017-06-10T04:59:47.203" LastActivityDate="2017-06-10T04:59:47.203" Title="What is the relationship between sexual and natural selection?" Tags="&lt;natural-selection&gt;&lt;sexual-selection&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11231" PostTypeId="2" ParentId="11230" CreationDate="2013-11-01T22:01:20.457" Score="4" Body="&lt;p&gt;You're not wrong, per se, but in practice they refer to two different concepts.  I honestly think the &lt;a href=&quot;https://en.wikipedia.org/wiki/Sexual_selection&quot; rel=&quot;nofollow&quot;&gt;Wikipedia article&lt;/a&gt; does a good job, in particular this sentence:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In summary, while natural selection results from the struggle to survive, sexual selection emerges from the struggle to reproduce.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It also cites Darwin:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The sexual struggle is of two kinds; in the one it is between individuals of the same sex, generally the males, in order to drive away or kill their rivals, the females remaining passive; whilst in the other, the struggle is likewise between the individuals of the same sex, in order to excite or charm those of the opposite sex, generally the females, which no longer remain passive, but select the more agreeable partners.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The whole argument is moot when dealing with individuals that aren't reproducing sexually, of course.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-11-01T22:01:20.457" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11232" PostTypeId="2" ParentId="7515" CreationDate="2013-11-01T22:04:45.557" Score="1" Body="&lt;p&gt;Helicos stopped shipping reagents around 2010-2011, as they couldn't compete with Illumina. For now it seems that reverse transcription -&gt; Illumina-sequenced cDNA is so much cheaper than any other option, that's the method that is dominant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oxford Nanopore has discussed direct RNA profiling, but unfortunately their first product still hasn't shipped (for DNA or otherwise), and they haven't even released data, it may be a little while longer.&lt;/p&gt;&#xA;" OwnerUserId="991" LastActivityDate="2013-11-01T22:04:45.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11235" PostTypeId="1" AcceptedAnswerId="11239" CreationDate="2013-11-02T07:03:28.597" Score="1" ViewCount="98" Body="&lt;p&gt;I asked this question &lt;a href=&quot;https://biology.stackexchange.com/questions/11190/dimethyltryptamine-and-sigma-1-type-opioid-receptor-interaction/11191?noredirect=1#11191&quot;&gt;Dimethyltryptamine and Sigma 1-type opioid receptor interaction&lt;/a&gt; but it seems that I didn't express myself well. I was looking for the place on Sigma 1 type opioid receptor where dimethyltryptamine binds rather than the location of Sigma 1 type opioid receptor.&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-11-02T09:20:06.837" Title="Dimethyltryptamine binding site on Sigma 1 type opioid receptor?" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11236" PostTypeId="2" ParentId="11230" CreationDate="2013-11-02T07:15:35.777" Score="3" Body="&lt;p&gt;To Darwin's point of view, sexual and natural selection are two different mechanisms. Then, we tended to consider that sexual selection is part of natural selection. The part of natural selection that is not attributed to sexual selection is sometimes called ecological selection. Today, our understanding of these mechanisms brought us to consider the meaning of these words slightly differently. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Natural selection is not anymore the result of a struggle for survival. It is any process yielding to a change in allele frequency through a long-enough term difference in fitness. Fitness is a index of how much an individual, a gene or whatever, leave copies of itself after a long and short enough amount of time (one might not agree with this definition I guess). Take two strains of bacteria in two petri dish, consider they are one population and let the bacteria grow. One strain will grow faster and the allele frequency will vary over time. It is the result of natural selection although there were no competition, no struggle at all given that they were not in contact.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sexual selection is a type of natural selection that involves sexual competition. There are two types of sexual competition, the so-called inter- and intra-sexual competition. Inter-sexual competition means that one sex chose the other one, while for intra-sexual there is no choice from the other sex. For example, if you see two animals fighting, they either fight to have the physical acces to the other sex (intra-) or they fight and then, let the female decide which one is the best to mate with (inter-). These two concept of intra- and inter-sexual competition might somehow overlap in some specific case. I would argue that the concept of sexual competition and therefore of sexual selection have never been accurately defined. Therefore, I would not complain if one prefers to give up the concept of sexual selection to use only the concept of natural selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many articles state that sexual and natural selection act on a trait with the same or opposite directions. Given the above argumentations, you could as well say that there are two different forces of natural selection. if the trait is at state 'A', then the individual is very attractive to the other sex but is likely to not be able to escape a predator. This is the case of most of the trait we think of when talking about trait evolving through sexual selection. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Handicap_principle&quot; rel=&quot;nofollow&quot;&gt;Zahavi's handicap principle&lt;/a&gt; for more information.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-09T08:08:01.223" LastActivityDate="2013-11-09T08:08:01.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11237" PostTypeId="1" CreationDate="2013-11-02T07:51:12.743" Score="13" ViewCount="909" Body="&lt;p&gt;Fitness is certainly the most important concept in the theory of evolution. &lt;strong&gt;My question does not have to do with practical measures of fitness but with the theoretical definition of it&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am a bit lost with the concept of fitness. Below I give some possible definitions of fitness and I am hoping to get critics for these definitions. The broad question is &lt;strong&gt;What is the definition of fitness?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the following, to make things easier I will consider only one bi-allelic locus. For simplicity, I will assume a panmictic population of infinite size evenly distributed into age classes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Let the variable $M$ be the mean time of a generation in the species of interest. Measure the allele frequency $p(t)$ and measure the frequency $p(t+M)$. By comparing the two you get the ratio of fitness of the two different genotypes. Obviously it does not work if we have sexual reproduction or diploid selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Genotype the individuals and wait until they die by counting the number of offspring they had and take the mean per genotype ($W_{AA}$, $W_{Aa}$, $W_{aa}$). This method would not work if they have different lifespan. One individual might make two babies in 8 years and the other would make two babies in 2 years but they would have he same fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Do the same that at 2) but don't wait until they die, wait 1 month, Or 2 years?, or $M$?, or $2\cdot M$?, or...? What is the right decision? The more you wait, the closest you will be to the long term effect of natural selection. The less you wait, the more probable you will suffer of genetic drift.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) Fitness is just a measure of natural selection that is not perfectly accurate because it is measured at short-term. In some circumstances, our measure on this short term is representative (Wright-Fisher equation) enough of what will happen on the long term.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2017-05-11T19:26:51.250" LastActivityDate="2017-05-11T19:26:51.250" Title="What does fitness really mean?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;" AnswerCount="2" CommentCount="11" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="11238" PostTypeId="1" AcceptedAnswerId="11247" CreationDate="2013-11-02T08:12:37.247" Score="1" ViewCount="160" Body="&lt;p&gt;In the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Radial_basis_function_network&quot; rel=&quot;nofollow&quot;&gt;radial basis function network&lt;/a&gt;, I didn't understand what was meant by &quot;center vector for neuron i&quot;, in other words &quot;center of the RBF units called also prototype&quot;.&lt;/p&gt;&#xA;" OwnerUserId="4702" LastEditorUserId="4101" LastEditDate="2013-11-02T15:11:44.637" LastActivityDate="2013-11-02T15:11:44.637" Title="Radial Basis Function Network (RBF Network)" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;vision&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11239" PostTypeId="2" ParentId="11235" CreationDate="2013-11-02T09:20:06.837" Score="1" Body="&lt;p&gt;There is no definitive answer to this question since the 3D structure of the receptor has not been determined. In this paper;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Laurini et al. (2012) Another Brick in the Wall. Validation of the σ1 Receptor 3D Model by Computer-Assisted Design, Synthesis, and Activity of New σ1 Ligands. Molecular Pharmaceutics 9:3107-3126&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;the authors report the analysis of their molecular model of the receptor. They design 33 new ligands for the putative binding site with binding affinities across five orders of magnitude and then go on to show that the experimentally-determined affinities are in very good agreement with their &lt;em&gt;in silico&lt;/em&gt; studies. The paper provides lots of information about the proposed binding site. The paper also describes the use of &lt;em&gt;in silico&lt;/em&gt; alanine scanning mutagenesis to assess the relative importance of residues proposed to form the binding site: these are D126,I128,T151,V152,E172,Y173 and L182. Of these D126 and Y173 seem to be critical.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I must stress that this work does not directly investgate the binding of dimethyltryptamine, and the ligands that are used are not based on an indole ring structure. The molecular model used by the authors was first published in an earlier paper.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Laurini et al. (2011) Homology Model and Docking-Based Virtual Screening for Ligands of the sigma(1) Receptor ACS Medicinal Chemistry Letters 2:834-839&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I tried to find out if that paper looks at dimethyltryptamine but unfortunately there seems to be a broken link at the source. Here is the abstract of that paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This study presents for the first time the 3D model of the sigma(1) receptor protein as obtained from homology modeling techniques, shows the applicability of this structure to docking-based virtual screening, defines a computational strategy to optimize the results based on a combination of 3D pharmacophore-based docking and MM/PBSA free energy of binding scoring, and provides evidence that these in silico models and recipes are powerful tools on which virtual screening of new sigma(1) ligands can be based. In particular, the validation of the applicability of docking-based virtual screening to homology models is of utmost importance, since no crystal structure is available to date for the sigma(1) receptor, and this missing information still constitutes a major hurdle for a rational ligand design for this important protein target.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-11-02T09:20:06.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11240" PostTypeId="1" AcceptedAnswerId="11243" CreationDate="2013-11-02T12:19:43.953" Score="20" ViewCount="1051" Body="&lt;p&gt;There are many &lt;a href=&quot;http://en.wikipedia.org/wiki/Species#Definitions_of_species&quot; rel=&quot;noreferrer&quot;&gt;definitions of &amp;quot;species&amp;quot;&lt;/a&gt; which usually take the form&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Two individuals are of the same species if ...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;An implied (rarely made explicit) property of any sensible species definition is that the relation &lt;strong&gt;&amp;quot;is the same species as&amp;quot;&lt;/strong&gt; should be an &lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Equivalence_relation&quot; rel=&quot;noreferrer&quot;&gt;equivalence relation&lt;/a&gt;&lt;/strong&gt; (the reason why this is sensible is that only such a relation partitions the set of all individuals into &lt;em&gt;equivalence classes&lt;/em&gt;, that is, separate species). In particular, it should be &lt;strong&gt;transitive&lt;/strong&gt;, that is&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;If A and B are of the same species, and B and C are of the same&#xA;species, then it follows that A and C are also of the same species.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;br&gt;&#xA;&lt;h3&gt;It appears to me that all species definitions in use violate that property.&lt;/h3&gt;&#xA;&lt;br&gt;&#xA;&lt;h1&gt;Example&lt;/h1&gt;&#xA;&lt;p&gt;Are the &lt;strong&gt;Chihuahua&lt;/strong&gt; &lt;img src=&quot;https://i.stack.imgur.com/rRIrN.jpg&quot; alt=&quot;enter image description here&quot; /&gt; and the &lt;strong&gt;Great Dane&lt;/strong&gt; &lt;img src=&quot;https://i.stack.imgur.com/3R0zY.jpg&quot; alt=&quot;enter image description here&quot; /&gt; of the same species?&lt;/p&gt;&#xA;&lt;p&gt;Not according to the &amp;quot;biological&amp;quot; species definition, which states:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Two individuals are of the same species if and only if they can &lt;strong&gt;produce fertile offspring.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Since that is (presumably) not true of Chihuahua and Great Dane, according to that definition, the two dog breeds are not of the same species.&lt;/p&gt;&#xA;&lt;h2&gt;However...&lt;/h2&gt;&#xA;&lt;p&gt;Let us say that the Chihuahua can produce fertile offspring with the &lt;strong&gt;Dachshund&lt;/strong&gt;...&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lHzsW.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;... and the Dachshund with the &lt;strong&gt;Golden Retriever&lt;/strong&gt;...&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TpUqC.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;... and that at last with the &lt;strong&gt;Great Dane&lt;/strong&gt; as desired.&lt;/p&gt;&#xA;&lt;p&gt;Then, if we assume transitivity, Chihuahua and Great Dane &lt;em&gt;are&lt;/em&gt; of the same species &lt;strong&gt;- contradiction!&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;br&gt;&#xA;&lt;h1&gt;Another Example&lt;/h1&gt;&#xA;&lt;p&gt;Are the &lt;strong&gt;Chimpanzee&lt;/strong&gt; &lt;img src=&quot;https://i.stack.imgur.com/KnHwQ.jpg&quot; alt=&quot;enter image description here&quot; /&gt; and the &lt;strong&gt;White Oak&lt;/strong&gt; &lt;img src=&quot;https://i.stack.imgur.com/RDoOH.jpg&quot; alt=&quot;enter image description here&quot; /&gt; of the same species?&lt;/p&gt;&#xA;&lt;p&gt;Intuitively, they are of course not, the very idea seems ridiculous. Sure enough, with the definition (a variation of the &amp;quot;genetic&amp;quot; species definition)&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Two individuals are of the same species if and only if &lt;strong&gt;their genome differs in less than 0.5% of base pairs.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;the two are indeed &lt;em&gt;not&lt;/em&gt; of the same species.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;However, we can again construct a &amp;quot;chain&amp;quot; of intermediate individuals, each of which is similar enough to its predecessor to satisfy the definition, eventually connecting Ape and Tree and violating transitivity again.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;br&gt;&#xA;&lt;h1&gt;My question to biologists: How is this problem resolved in practice? Are there any species definitions that preserve transitivity?&lt;/h1&gt;&#xA;" OwnerDisplayName="user4810" LastEditorUserId="-1" LastEditorDisplayName="user4810" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-04-22T19:50:47.023" Title="Transitivity of Species Definitions" Tags="&lt;zoology&gt;&lt;definitions&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11241" PostTypeId="2" ParentId="11240" CreationDate="2013-11-02T13:02:41.700" Score="2" Body="&lt;p&gt;Further to my comment above &lt;a href=&quot;http://ponderingsfrompluto.wordpress.com/2011/03/16/new-dogbreed-chi-dane-dane-or-great-mexican/&quot; rel=&quot;nofollow&quot;&gt;here is a link&lt;/a&gt; describing the impregnation of a female Great Dane by a male Chihuahua, followed by the birth of viable puppies. Apparently the converse was not possible because the Chihuahua mother could not carry the puppies to term since they were too large. My opinion is that this latter problem still does not make them separate species. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-11-02T13:02:41.700" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11242" PostTypeId="1" CreationDate="2013-11-02T13:48:08.773" Score="5" ViewCount="14682" Body="&lt;p&gt;I expect vesicle formation and fusion to require energy input; however, I'm not sure about &lt;strong&gt;&lt;em&gt;which of endocytosis and exocytosis require energy and how they use the energy input&lt;/em&gt;&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do they belong to active or passive transport?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastEditorUserId="16866" LastEditDate="2018-12-20T14:23:22.370" LastActivityDate="2018-12-20T14:23:22.370" Title="Does endo- and (or) exocytosis require energy? Do they belong to active / passive transport?" Tags="&lt;cell-biology&gt;&lt;energy&gt;&lt;membrane-transport&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11243" PostTypeId="2" ParentId="11240" CreationDate="2013-11-02T14:32:01.380" Score="11" Body="&lt;p&gt;I am pretty sure you cannot jump from an oak tree to an ape with whatever common definition of species you're using. But this is some kind of practical implication of your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concept of species was already being used by Aristotle and was kept up to now although the grouping of living things into species might not be a clever thing to do. I don't think there is any non-arbitrary, logical way of making groups out of living organisms. &lt;a href=&quot;http://www.unil.ch/gse/page95929_fr.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; is a podcast (It is in French, sorry!) that is interesting for those wanting to learn about how the concept of species evolved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The case you describe is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Ring_species&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ring species&lt;/a&gt;. There has been lots of discussion in philosophy about the concept of species. The concept of species is unclear and if accurately defined, then in practice we don't really follow this definition to improve efficiency in how we name lineages. The term lineage has a much more rigorous meaning and is often of greater usefulness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Ensatina eschscholtzii&lt;/em&gt; (a salamander; see &lt;a href=&quot;https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-11-245&quot; rel=&quot;nofollow noreferrer&quot;&gt;DeVitt et al. 2011&lt;/a&gt; and other articles from the same group) is a classic example of ring species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should definitely have a look at the post &lt;a href=&quot;https://biology.stackexchange.com/questions/39664/how-could-humans-have-interbred-with-neanderthals-if-were-a-different-species&quot;&gt;How could humans have interbred with Neanderthals if we're a different species?&lt;/a&gt; which discuss the concept of species. Some other sources of info include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Species_problem&quot; rel=&quot;nofollow noreferrer&quot;&gt;Species problem wikipedia&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://lifesci.rutgers.edu/~heylab/sconcept/introduction.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reduction of species&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The evolutionist view of the species concept: &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionarily_Significant_Unit&quot; rel=&quot;nofollow noreferrer&quot;&gt;ESU&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://plato.stanford.edu/entries/species/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Stanford dictionary&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-04-22T19:50:47.023" LastActivityDate="2019-04-22T19:50:47.023" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="11244" PostTypeId="1" AcceptedAnswerId="11307" CreationDate="2013-11-02T15:01:09.720" Score="6" ViewCount="353" Body="&lt;p&gt;I'm reading a study (full text &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695983/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;) that examine the dynamic of nuclear translocation of a transcription factor in budding yeast, in response of calcium stress. They found that it occurs in bursts, which distribution of durations is plotted on this normalized histogram:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CKN4k.png&quot; alt=&quot;burst duration distribution&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the text they say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Normalized histograms, $h(t)$, of total burst duration at two calcium concentrations are both well-fit by $h(t)=te^{-t/\tau}$, with $\tau$ = 70 sec (black line).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And also&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This distribution was consistent with two rate-limiting stochastic steps, each with a timescale of ~70 sec.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Can someone explain me the second sentence cited?&lt;/p&gt;&#xA;" OwnerUserId="3523" LastActivityDate="2013-11-05T12:40:53.100" Title="What does it mean for a distribution to be &quot;consistent with a two rate-limiting stochastic steps&quot;?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11245" PostTypeId="2" ParentId="11242" CreationDate="2013-11-02T15:03:49.233" Score="4" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Exocytosis&quot; rel=&quot;nofollow&quot;&gt;Wikipedia is your friend&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Exocytosis... is the durable, &lt;strong&gt;energy-consuming process&lt;/strong&gt; by which a cell directs the contents of secretory vesicles out of the cell membrane and into the extracellular space.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Endocytosis&quot; rel=&quot;nofollow&quot;&gt;and&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Endocytosis is an &lt;strong&gt;energy-using process&lt;/strong&gt; by which cells absorb molecules (such as proteins) by engulfing them.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Emphasis mine.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3021750&quot; rel=&quot;nofollow&quot;&gt;Here's a nifty paper&lt;/a&gt; which gave some evidence a few decades ago for some basic intracellular thresholds for budding and fusion, and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2126013&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; shows that endocytosis definitely requires ATP, using a novel assay.  Check the sources, too, some of them are excellent.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-11-02T15:03:49.233" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11246" PostTypeId="1" CreationDate="2013-11-02T15:05:00.707" Score="4" ViewCount="421" Body="&lt;p&gt;If cancer is fundamentally a genetic disease, how might an environmental factor such as smoking cause cancer?&lt;/p&gt;&#xA;" OwnerUserId="4806" LastEditorUserId="4101" LastEditDate="2013-11-02T15:16:41.053" LastActivityDate="2013-11-03T14:58:56.330" Title="How does smoking, an environmental factor, cause cancer, fundamentally a genetic disease?" Tags="&lt;genetics&gt;&lt;cancer&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11247" PostTypeId="2" ParentId="11238" CreationDate="2013-11-02T15:08:26.000" Score="2" Body="&lt;p&gt;In RBF networks each neuron in the hidden layer applies a computation that is related to its &quot;center vector&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First consider the set of input neurons as a vector $\mathbf{x}$, and that each hidden layer neuron receives the complete input vector as its own input. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, each hidden layer neuron $i$ is parametrised through a vector (center vector) $\mathbf{c_i}$ of equal dimension than $\mathbf{x}$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The computation of each hidden layer neuron $i$ consists of:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Evaluate the distance (according to a metric, which may or may not be Euclidean) between the input $\mathbf{x}$ and the center vector $\mathbf{c_i}$. When the input is equal to the center vector, the output for that neuron will be maximal (see 2).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Evaluate a Gaussian function that decays with increasing distance between the vectors. That's the output of each hidden layer neuron. In the following equation, $\beta$ is a parameter that specifies the decay rate of the Gaussian (converse to the standard deviation in a regular Gaussian distribution).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;\begin{equation}&#xA;\rho_i(\mathbf{x})=\exp{[-\beta\Vert\mathbf{x}-\mathbf{c_i}\Vert^2]}&#xA;\end{equation}&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now combine linearly the output of all hidden layer neurons to obtain the total neural network output. For that, you need an additional set of parameters or weights $a_i$ (one $a_i$ for each hidden layer neuron, but the $a_i$ values are scalars while each $\mathbf{c_i}$ is a vector). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The final equation, that yields the total network output (a scalar value), is: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;\begin{equation}&#xA;\varphi(\mathbf{x}) = \sum_{i=1}^N a_i \rho(||\mathbf{x}-\mathbf{c}_i||)&#xA;\end{equation}&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And that's it.&lt;/p&gt;&#xA;" OwnerUserId="3570" LastActivityDate="2013-11-02T15:08:26.000" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11248" PostTypeId="2" ParentId="11246" CreationDate="2013-11-02T15:15:59.940" Score="4" Body="&lt;p&gt;Because cigarette smoke contains many &lt;a href=&quot;https://en.wikipedia.org/wiki/Carcinogen&quot; rel=&quot;nofollow&quot;&gt;carcinogens&lt;/a&gt;.  Carcinogens can cause cancer by directly affecting the genome.  Wikipedia has a &lt;a href=&quot;https://en.wikipedia.org/wiki/List_of_cigarette_smoke_carcinogens&quot; rel=&quot;nofollow&quot;&gt;list&lt;/a&gt; of those present in cigarette smoke, which includes classics such as lead, benzene, and formaldehyde, not to mention radioactive polonium.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="1320" LastEditDate="2013-11-02T17:50:36.683" LastActivityDate="2013-11-02T17:50:36.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11249" PostTypeId="2" ParentId="11242" CreationDate="2013-11-02T16:08:27.457" Score="3" Body="&lt;p&gt;Just to extend the answer from @Amory slightly, I think that the terms active and passive transport are best kept for describing transmembrane movement of molecules. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of exocytosis the only transmembrane event is when a secreted protein is first inserted (usually cotranslationally) across the endoplasmic reticulum membrane. I'm not aware of any evidence that this uses more energy than that already expended during polpeptide elongation by the ribosome. At that point the secreted protein is topologically extracytoplasmic, and everything else is achieved by rounds of vesicle formation and fusion of vesicles with target membranes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same is true in reverse for endocytosis. Any molecule that is internalised in an endocytic vesicle is still extracytoplasmic unless some process specifically moves it across the membrane of the vesicle, or a downstream organelle such as the endosome. At that point whether the transport process was active or passive would depend upon the properties of the carrier system.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-11-02T16:08:27.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11250" PostTypeId="1" AcceptedAnswerId="17174" CreationDate="2013-11-02T16:15:11.123" Score="6" ViewCount="1281" Body="&lt;p&gt;Martin Nowak in his book &quot;Evolutionary Dynamics&quot; talks about a given correlation between genome size and mutation rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What correlation does exactly exist between these two concepts?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Is it a linear correlation?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What is the coefficient of correlation?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Does this correlation exist in many different taxa?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;One will need to make whether we talk about mutation rate per base per generation or for the whole genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some references to accompany claims are welcome!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-02-21T15:27:46.857" LastActivityDate="2014-05-06T04:41:19.203" Title="Correlation between genome size and mutation rate?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11251" PostTypeId="2" ParentId="11156" CreationDate="2013-11-02T16:57:05.663" Score="3" Body="&lt;p&gt;The name of the instrument is &lt;a href=&quot;http://en.wikipedia.org/wiki/Ophthalmoscope&quot; rel=&quot;nofollow&quot;&gt;ophthalmoscope&lt;/a&gt;. It is used to determine the health status of your retina. Retina is the one of the few places in the body where you can observe the blood vessels directly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The link also includes a picture of what your eye looks like from doctor's point of view. &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-11-02T16:57:05.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11252" PostTypeId="2" ParentId="11237" CreationDate="2013-11-02T16:57:48.267" Score="4" Body="&lt;p&gt;The concept of fitness is very general. An adequate definition of fitness is hard to specify in the same way that a definition of &quot;species&quot; is hard to give. To be useful, scientific or technical definition of such broad concepets will often need to be so narrow that more than one is needed. A uselessly broad definition of fitness might be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Fitness is modeled as a utility function, where higher fitness is indicated by a higher score&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here every important detail about whatever's fitness is being tested, how that fitness is measured, and the environment in which that fitness is determined are simply wadded up together and transformed into a different question that is no easier to answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hypothetical problems you raise with various definitions are not (in essence) problems with the definitions, but problems with the definitions not being applicable to the domain in which such problems matter. You have to define your criteria for success, and then these constraints can be translated into a &quot;fitness&quot; function that allows the desired predictions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some issues that might matter are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Are predictions about populations, or individuals.&lt;/li&gt;&#xA;&lt;li&gt;Are predictions about dynamic fitness (snapshot at some time) or long-run steady state fitness.&lt;/li&gt;&#xA;&lt;li&gt;Are predictions about quantitative values (like heights) or discrete values (like sex).&lt;/li&gt;&#xA;&lt;li&gt;How do you want to present error in your predictions - p value, sensitivity/specificity, confidence interval, etc.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I'm sure this is not the kind of answer you were looking for, but I think part of your question revolves around a confusion that there is &quot;one&quot; technical definition for fitness. Part of the process of learning is comparing different presentations of the same concept, and realizing where they are different. A full walk over all the different ways one could evaluate and apply fitness would be a book, not a short answer. Perhaps some other people can provide good links to more detailed information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just found a &lt;a href=&quot;http://scienceblogs.com/evolvingthoughts/2007/01/22/fitness/&quot; rel=&quot;nofollow&quot;&gt;blog posting&lt;/a&gt;, by Dr. John S. Wilkins, which says some of the same things. His perspective comes with a good pedigree; his PhD work was on trying to define &quot;species&quot; and he has authored a couple of books on the subject.&lt;/p&gt;&#xA;" OwnerUserId="1688" LastEditorUserId="1688" LastEditDate="2013-11-04T22:18:27.597" LastActivityDate="2013-11-04T22:18:27.597" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11254" PostTypeId="1" AcceptedAnswerId="11260" CreationDate="2013-11-02T17:29:24.607" Score="3" ViewCount="2143" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Dinosaur&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Dinosaur&lt;/a&gt;, Dinosaurs were the dominant terrestrial vertebrates for 135 million years.&#xA;They had a lot of time to evolve. My question is: why were dinosaurs not smarter than us, and why was their society not complex like ours is? &lt;/p&gt;&#xA;" OwnerUserId="4811" LastEditorUserId="16866" LastEditDate="2017-06-02T18:28:03.763" LastActivityDate="2017-06-02T18:28:03.763" Title="Why were dinosaurs not as smart as humans are?" Tags="&lt;evolution&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11255" PostTypeId="1" AcceptedAnswerId="11257" CreationDate="2013-11-02T18:59:22.943" Score="1" ViewCount="235" Body="&lt;p&gt;Do you know some examples of virus or a viroid (or a prion) that originated from a known living organism? How does the virus/viroid/prion lives? Does it paratize the organism from which the virus originated?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks to the first answers I have examples of newly originated prions. Does someone know such an example about viruses?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-04T08:00:07.477" LastActivityDate="2013-11-04T08:00:07.477" Title="Examples of virus originated from a living system" Tags="&lt;evolution&gt;&lt;virus&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11257" PostTypeId="2" ParentId="11255" CreationDate="2013-11-02T22:54:13.123" Score="1" Body="&lt;p&gt;Prion diseases are still very poorly understood, but one of the dominant theories is that they are misfolded proteins that cause disease by catalyzing the misfolding of more proteins of the same type.  If that is the case, then they arise from the organism that they affect simply by protein misfolding.  In the case of &lt;a href=&quot;http://en.wikipedia.org/wiki/Bovine_spongiform_encephalopathy&quot; rel=&quot;nofollow&quot;&gt;bovine spongiform encephalopathy&lt;/a&gt; (mad cow disease) being transmitted to humans and resulting in new variant Creutzfeldt-Jakob disease, it seems like it might be transmissible between species, but it probably needs to infect a closely related species so that the protein has a homolog it can act upon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can't say I know of any examples where people have shown the &lt;em&gt;de novo&lt;/em&gt; creation of a virus from a living organism.  There are definitely virus protein homologs in the genomes of organisms, but directionality is hard to argue since its common for viruses to pick up host genes, or leave behind viruses genes.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastEditorUserId="1320" LastEditDate="2013-11-03T10:05:21.227" LastActivityDate="2013-11-03T10:05:21.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11258" PostTypeId="2" ParentId="11246" CreationDate="2013-11-02T23:57:20.527" Score="1" Body="&lt;p&gt;There are carcinogens in smoke but they've not been shown to be the cause of cancer in smokers.  Note that some smokers never develop cancer or heart disease; some have lived more than 100 years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just because something is classified as a carcinogen doesn't mean it causes cancer in everyone and doesn't mean a given exposure to a particular carcinogen has any effect at all.  All smoking does is increase one's risk of developing cancer.  That it increases risk is not a fact but the association between smoking and cancer is significant, statistically.  (This means it meets certain mathematical criteria and is, therefore, not mere opinion).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chromosomal replication is not perfect and a healthy cell can replicate only a limited number of times.  Cancer is characterized (in part) by a loss of this control.    When DNA mutates in a way that results in the loss of this control an otherwise-healthy cell (now a mutation) results.  Smoking increases cell turnover and the increased turnover increases the likelihood this type of mutation will occur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can think of skin cancers in the same way.  This is the reason an exposure resulting in a color change (sunburn, tanning including that from a tanning booth) increases the risk of skin cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Over a typical lifetime we develop a handful of cancerous tumors.  They're killed by our immune system.  Symptoms of malignant cancer develop when the immune system hasn't been effective.&lt;/p&gt;&#xA;" OwnerUserId="4714" LastEditorUserId="1320" LastEditDate="2013-11-03T14:58:56.330" LastActivityDate="2013-11-03T14:58:56.330" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11260" PostTypeId="2" ParentId="11254" CreationDate="2013-11-03T08:39:23.203" Score="8" Body="&lt;p&gt;&lt;strong&gt;We are all equally evolved&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All life that exist on earth today had the exact same amount of time to evolve (3.5 billion years). Therefore, one cannot say that one species is more evolved than another one. It just makes no sense (at least if &quot;more evolved&quot; means &quot;have evolved for more time&quot;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Being a dominant species/clade for some time (whatever dominant may mean to you) doesn't make this species/clade more evolved than any other one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Your question need not be specific to intelligence&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can think of any other &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenotype&quot; rel=&quot;nofollow noreferrer&quot;&gt;phenotypic&lt;/a&gt; trait (wings, toxins in the skin, good eyes, good smell, strong leaves, etc...) and ask this same question. You seem to assume that being smart should be some kind of goal or necessary direction toward which species should evolve. Following your reasoning I would rather ask why the hagfishes, the oyster, the lampreys or the turtles are so dumb although they exist for so long (once again remember that this notion that some lineages have existed longer than others is flawed).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might also want to have a look at: &lt;a href=&quot;https://biology.stackexchange.com/questions/57356/why-evolution-should-not-be-equated-with-progress&quot;&gt;Why evolution should not be equated with progress?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Being clever is not a goal of evolution&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of these trait have associated cost to the benefice they might bring. For example having a big brain asks for much energy (20% of ATP in humans) and it also has a cost due to its weight. The sperm whale for example has a brain that weights 7.8 kg. Obviously it is not a big cost for such a big animal to carry heavy organs while it would be impossible for a migratory bird to carry such a brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;taking different evolutionary path&lt;/strong&gt; This part is not complete!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the question of why Homo sapiens are smart while Tyranosaurus rex are not or why wings evolved in bat and not in mice is rather interesting and hard to answer. I can think of 2 main causes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) The newly arising trait (which is usually not the trait you can observe today. Big brain did not appear suddenly, first there were individuals they had slightly bigger brains than the other individuals in the population) is not beneficial over the wildtype trait. There are so many parameters that will affect if a trait is beneficial or not. You can think of the predators, the humidity in the environnement, the social structure, the population size, the type of reproduction, the genetic background etc...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, think of a species that is fixed, has no social contact, has nothing it can really predict in the environnement. What would an individual from this species do with a brain? Think of a bird that needs to make food stock for the winter. This bird needs to remember where it hide something. It has been found by the way that some birds have an awesome spatial memory, way better than humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The trait never happen to occur (or never in a strong enough individual, or never in a population big enough to not suffer from to much drift while the trait is at low frequency) just because the necessary mutation never happen. Mutation is just a random process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example. It seems rather hard for a tree to have the necessary mutations to have develop a brain! But we don't need to go to such a extreme example. If you split a population of clone mice in two, the two subpopulation will evolve differently (even in absence of genetic drift (infinite population size)) just because  some mutations occur on one side while some others occur on the other side. Or maybe the same mutation might occur but once in an individual that has low fitness and once in a very fit individual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Evolution of human cognition abilities&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what are the factors that drive humans to evolve big brains? This question is not solved yet. We have many models to explain this but I don't we have much solutions to test these models. The 2 most common models explain big brains&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;for social purposes (understanding relationship between other individuals, being able to coordinate the movement for a hunt, etc...) &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;due to sexual selection. Being intelligent would be a proxy for having good genes.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For more information concerning the evolution of human cognition, &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_human_intelligence&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; wikipedia article might be a good start.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why do you think mutation is a random process?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Our genetic data are encoded into a succession of 4 types of &lt;a href=&quot;http://en.wikipedia.org/wiki/Dna&quot; rel=&quot;nofollow noreferrer&quot;&gt;nucleotide bases&lt;/a&gt; (A,T,C and G). A mutation results from a modification of this sequence such as a replacement of a T by a C. These mutations are due to mistakes usually while duplicating the DNA. Most of these mistakes do not affect the fitness (survival + reproduction ability) of the individual, very often these mutation are deleterious and rarely these mutations are beneficial. Some mutations are more probable than others but nevertheless some individuals have a higher mutation rate than others. In order to make things slightly more complicated, some sequences have a higher mutation rate than others. For example, the sequence &lt;code&gt;AAAAAAAAAAAA&lt;/code&gt; is more likely to mutate than the sequence &lt;code&gt;ATGTGCATCTA&lt;/code&gt;. But even if some mutations are more likely to occur it is still a random process (we couldn't talk about likelihood otherwise!). Two clones living in the exact same environment that both have a baby at the exact same time wil not create babies with the exact same genome given the randomness of mutations. One baby might have a very bad mutation that will make him die, while the other baby might synthesize (=construct) a new enzyme that increases its digestive capacity.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2017-06-02T15:14:48.760" LastActivityDate="2017-06-02T15:14:48.760" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="11261" PostTypeId="1" CreationDate="2013-11-03T10:36:52.730" Score="2" ViewCount="89" Body="&lt;p&gt;I'm working on a short presentation of treatments of macular degeneration for a biomedical&#xA;optics seminar on macular degeneration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since I don't have any relevant medical or biological background (B.Eng. Electrical Engineering, now M.Sc. Biomedical Engineering w. a major in Biophysics) I need some help with&#xA;understanding the function of VEGF inhibitors, and how they work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It doesn't need to go into all details as it is one of three treatments that I'm supposed to present, but enough to explain how it works, in about roughly 5 minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could anyone help me please? &lt;/p&gt;&#xA;" OwnerUserId="345" LastEditorUserId="389" LastEditDate="2014-03-03T21:10:23.700" LastActivityDate="2014-05-02T22:03:40.517" Title="Function of an VEGF inhibitor in the treatment of macular degeneration" Tags="&lt;pharmacology&gt;&lt;eyes&gt;&lt;pharmacodynamics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11262" PostTypeId="2" ParentId="11261" CreationDate="2013-11-03T12:51:25.157" Score="1" Body="&lt;p&gt;The Wikipedia page for &lt;a href=&quot;http://en.wikipedia.org/wiki/VEGF&quot; rel=&quot;nofollow noreferrer&quot;&gt;vascular endothelial growth factor&lt;/a&gt; (VEGF) looks pretty useful - it explains that VEGF stimulates the growth of blood vessels. If this gets out of balance, for example in diabetic retinopathy and wet form age-related macular degeneration, one treatment is to attempt to reduce levels of VEGF in the circulation, using monoclonal antibodies directed against VEGF, or to antagonise the action of VEGF using drugs that target the VEGF receptors.&lt;/p&gt;&#xA;&lt;p&gt;Two milestones in anti-VEGF therapy are described in these papers:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Ng et al. (2006) Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nature Reviews Drug Discovery 5: 123-132 &lt;em&gt;(This paper describes the first approved aptamer drug: an RNA directed against VEGF.)&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;Ferrara et al. (2006) Development of ranibizumab, an anti-vascular endothelial growth factor antigen binding fragment, as therapy for neovascular age-related macular degeneration. Retina 26:859-870 &lt;em&gt;(This paper describes a therapy based upon an antibody fragment directed at all isoforms of VEGF-A.)&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;A very recent review of anti-VEGF therapies is:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Freund et al. (2013) An update on the pharmacotherapy of neovascular age-related macular degeneration. Expert Opinion on Pharmacotherapy 14:1017-1028&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-11-03T12:51:25.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11263" PostTypeId="1" AcceptedAnswerId="11280" CreationDate="2013-11-03T17:20:50.373" Score="37" ViewCount="86320" Body="&lt;p&gt;There are a bunch of &lt;a href=&quot;https://en.wikipedia.org/wiki/List_of_sequence_alignment_software&quot; rel=&quot;noreferrer&quot;&gt;different alignment tools out there&lt;/a&gt;, and I don't want to get bogged down in the maths behind them as this not only between software but varies from software version to version.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two main divides in the programs; some use local alignments and others use global alignments. My question is threefold:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What are the fundamental differences between the two?&lt;/li&gt;&#xA;&lt;li&gt;What are the advantages and disadvantages of each?&lt;/li&gt;&#xA;&lt;li&gt;When should one use either a global or local sequence alignment?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2017-06-13T05:54:29.587" LastActivityDate="2018-09-27T17:43:12.600" Title="What is the difference between local and global sequence alignments?" Tags="&lt;bioinformatics&gt;&lt;sequence-analysis&gt;&lt;sequence-alignment&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="11265" PostTypeId="1" AcceptedAnswerId="52379" CreationDate="2013-11-03T17:51:17.147" Score="5" ViewCount="158" Body="&lt;p&gt;What happens when someone takes an anti-venom for an animal they weren't bit by, either for incorrect identification of the animal they were bit by or if they weren't bit at all?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for the immune system reaction, and possibly why it reacts as it does.&lt;/p&gt;&#xA;" OwnerUserId="3458" LastEditorUserId="57" LastEditDate="2013-11-03T18:56:09.647" LastActivityDate="2016-10-13T09:27:11.920" Title="Is an antivenom venomous?" Tags="&lt;biochemistry&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11266" PostTypeId="1" CreationDate="2013-11-02T16:39:28.597" Score="3" ViewCount="348" Body="&lt;p&gt;If I put a piece of wood in a humid environment (basically humid air), it will start to rot. Does the humidity influence the rotting speed, and if so, what is the relation between the rotting speed and humidity?&lt;/p&gt;&#xA;" OwnerDisplayName="user2611" LastEditorUserId="3340" LastEditDate="2013-11-04T19:07:15.150" LastActivityDate="2014-07-03T00:00:17.933" Title="Humidity for wood rotting" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11267" PostTypeId="2" ParentId="11266" CreationDate="2013-11-02T19:14:51.943" Score="0" Body="&lt;p&gt;I'm afraid this is not a topic of chemistry, the main degradation process in wood decay is a matter of biological attack, of course life needs water so if the ambient is very humid the wood decompose very well if the ambient is dry the wood can be conserved easier.&#xA;However wood is not a substance but a complex material, you have to investigate the degradation process for all the components. Chemically holocellulose is the most degradable part of wood, his microcrystalline structure improve the resistance but cycle of imbibitions can blow up the structure leading to a larger surface more suitable for degradation. The hydrolysis of cellulose however doesn't occur at normal temperature only &lt;strong&gt;peeling off&lt;/strong&gt; can occur under 100 °C.&#xA;Lignin is more and more durable if a little bunch of micro and macro organism wouldn't decompose it we would be sub-merged by a large quantity of lignin.&lt;/p&gt;&#xA;" OwnerUserId="4826" OwnerDisplayName="G M" LastActivityDate="2013-11-03T19:51:03.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11268" PostTypeId="1" CreationDate="2013-11-02T16:44:38.023" Score="1" ViewCount="156" Body="&lt;p&gt;Given a piece of wood, how does putting it in the sun or not influence the rate of decay due to rot (assuming that it's in an otherwise humid environment)?&lt;/p&gt;&#xA;" OwnerDisplayName="Rik" LastEditorUserId="3340" LastEditDate="2013-11-04T19:08:10.623" LastActivityDate="2014-01-03T21:47:52.723" Title="How does ultraviolet light influence the decay process of wood?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11269" PostTypeId="1" CreationDate="2013-11-03T20:34:52.870" Score="3" ViewCount="177" Body="&lt;p&gt;&lt;a href=&quot;http://www.filedropper.com/investigationofusingyeasttomakedoughrise&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; are the notes I made for an experiment I was doing (I didn't put it here as it is too long)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(please ignore the numbers at the end of the pdf file)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The graph looks like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2ksN8.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you see on the graph, the numbers are the same as the ones below &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1. The effect running out of glucose has on the yeast growth&lt;/strong&gt;&#xA;Our yeast increased in number by dividing rapidly. They use glucose to respire and release energy. They need energy to grow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. Why the yeast starts to grow again&lt;/strong&gt;&#xA;The yeast  starts to decrease in volume when they ran out of glucose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;3. Describing patterns in graphs&lt;/strong&gt;&#xA;The yeast breaks down the starch to glucose&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem is, &lt;strong&gt;why did the yeast rise at the end&lt;/strong&gt;, I forgot?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance&lt;/p&gt;&#xA;" OwnerUserId="4819" LastEditorUserId="1590" LastEditDate="2013-11-05T09:49:10.843" LastActivityDate="2015-12-08T17:50:53.593" Title="Why did the yeast rise?" Tags="&lt;homework&gt;&lt;population-dynamics&gt;&lt;yeast&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11270" PostTypeId="1" AcceptedAnswerId="11273" CreationDate="2013-11-03T20:51:56.923" Score="4" ViewCount="4865" Body="&lt;p&gt;The plasmid vector I am referring to is pCR 2.1 - TOPO. I added the vector to the E coli and plated them up onto LB+amp+X-gal plate, then incubated. After incubation the plates had two types of bacterial culture on them, one white and one blue. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that the blue cultures have accepted the plasmid as they are able to grow on ampicillin, so have the ampicillin resistance gene, and are able to convert the X-gal substrate to blue via the lac Z gene. What i'm confused about is the white colonies. If the colonies are able to grow on ampicillin, surely they have accepted the gene because they have the resistance, and surely they should to be able to convert the X-gal?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why are these not expressing the lac Z gene? Is it that the lac Z gene and ampicillin resistance aren't on the same plasmid, or is it that the lac z gene didn't make it into the plasmid?&lt;/p&gt;&#xA;" OwnerUserId="3382" LastActivityDate="2015-10-15T03:39:55.673" Title="How does blue white screening work in selecting E coli that have taken up a plasmid vector?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;ecoli&gt;&lt;plasmids&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11271" PostTypeId="2" ParentId="11263" CreationDate="2013-11-03T22:27:21.660" Score="9" Body="&lt;p&gt;Global alignment is when you take the entirety of both sequences into consideration when finding alignments, whereas in local you may only take a small portion into account. This sounds confusing so here an example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say you have a large reference, maybe 2000 bp. And you have a sequence, which is about 100 bp. Let's say that the reference contains the sequence almost exactly. If you did a local alignment, you would have a very good match. But if you did a global alignment, it may not match. Instead, it may look for matches throughout the entire reference, so you'd end up with an alignment with many large gaps. It does not matter that it matches near perfectly at one particular region on the reference, because it's looking for matches globally (i.e. throughout the reference). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have a really good match it may not matter what type of alignment you use. But when you have mismatches and such it starts to get important. This is because of the scoring algorithms used. In the example above let's say that there is a 100bp region in the reference that matches your 100bp sequence with 85% accuracy. In local alignment it's very likely it will align there. Now let's say that the first 30 bp of your sequence matches a region in the beginning of the reference 95%, and the next 30bp matches a region in the middle of the reference 85%, and the final 40bp matches a region at the end of the reference about 90%. In global alignment the best match is the gapped alignment, whereas in local alignment the ungapped alignment would be best. I think in general gap penalties are less in global alignments, but I'm not really an expert on the scoring algorithms.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you want to use depends on what you are doing. If you think your sequence is a subsequence of the reference, do a local alignment. But if you think your entire sequence should match your entire reference, you would do a global alignment.  &lt;/p&gt;&#xA;" OwnerUserId="4199" LastEditorDisplayName="user13145" LastEditDate="2016-10-22T06:02:36.967" LastActivityDate="2016-10-22T06:02:36.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11272" PostTypeId="2" ParentId="7515" CreationDate="2013-11-03T22:33:22.100" Score="0" Body="&lt;p&gt;There was a paper that just came out about in situ RNA seq, but at the moment the limit of the sequence obtained is an underwhelming 4 bp. Still, its a cool technique and if it is advanced it could be useful in single cell RNA-seq, without the need of amplification or library prep&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23852452&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/23852452&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2013-11-03T22:33:22.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11273" PostTypeId="2" ParentId="11270" CreationDate="2013-11-03T22:42:49.903" Score="3" Body="&lt;p&gt;The traditional blue/white screening is set up so that blue colonies are considered negative for the insert, and white colonies are positive for recombinant DNA. The gene responsible is the lacZ gene, or beta-galactosidase. This enzyme converts a synthetic substrate, X-gal, into an insoluble blue compound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pCR2.1 TOPO plasmid is a blue/white selection plasmid in which white colonies are considered positive for the insert. The way this works is by inserting the DNA sequence to clone inside the coding region for lacZ. By having any inserted DNA interrupting the sequences of lacZ, so that the enzyme has lost its function (because it is no longer being translated correctly in the bacteria). On the other hand, no insert present means that lacZ is ligated back together, and the entire enzyme is correctly made, and therefore can metabolize the X-gal substrate to form an insoluble blue dye.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="-1" LastEditDate="2015-10-15T03:39:55.673" LastActivityDate="2015-10-15T03:39:55.673" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="11274" PostTypeId="2" ParentId="3695" CreationDate="2013-11-03T22:54:13.950" Score="6" Body="&lt;p&gt;I think during the early &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_nervous_systems&quot;&gt;evolution of nervous systems&lt;/a&gt; it was very important to have long axon cells. For example a worm has 3 giant axons which are almost the same length than the worm itself. So there was selection pressure on the length of the axon. The neuron requires a lot of energy to send signals to other neurons. Neurons use energy on nanowatt scale, average human cells use energy on picowatt scale... By long axons it requires less energy to send the message through a single axon than send it through multiple axons. That's the same why we use limited amount of undersea internet cables - currently about 200. If there is more data than a single cable can handle, only then lay we a parallel cable. So a possible answer is evolution of worm nervous systems combined with energy consumption optimization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another answer can be that neurons would be never capable to build multiple action potentials parallel. Maybe they cannot consume enough energy to hold charges separated by multiple axons. I don't intend to look for the details of that. It is technically possible to have &lt;a href=&quot;http://uanews.org/story/how-neurons-get-wired&quot;&gt;neurons with multiple axons&lt;/a&gt;, so you can grow things like that, but it is not clear if their axons can work parallel or not, and if they don't work parallel does they interfere the communication of each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About single axon neural networks there are existing &lt;a href=&quot;http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.161.3556&amp;amp;rep=rep1&amp;amp;type=pdf&quot;&gt;mathematical models&lt;/a&gt;. Until there is no mathematical model how a neural network with multiple axons would work, or there is no evidence of it is not possible to build such a thing, you cannot say for sure that it is because of the mathematics of neural networks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I have this 3 theories. I think you can find more about this topic by googling a lot, and making new experiments. For me it was enough. :-)&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2013-11-04T01:04:04.137" LastActivityDate="2013-11-04T01:04:04.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11275" PostTypeId="2" ParentId="11223" CreationDate="2013-11-04T00:30:01.337" Score="3" Body="&lt;p&gt;A classic study of IQ heritability is Skodak &amp;amp; Skeels (1949). They studied heritability of IQ in children who were adopted at a very young age, with IQ data of the children, of their biological mothers, and of their adoptive mothers. It is important to keep in mind that heritability is a measure of the proportion of &lt;em&gt;variance&lt;/em&gt; that is attributable to genetic inheritance &lt;em&gt;in the population&lt;/em&gt;; it is formally the ratio between genetic variance in a population to the phenotypic variance in a population. The above mentioned study found a high heritability between biological mothers and their children (0.88), but no heritability between adoptive mothers and their children. Yet the mean IQ of children were similar to adoptive mothers, and much higher than their biological mothers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not a contradiction. High heritability does not mean that environmental factors are not important. Indeed, environmental factors (such as upbringing, education, socioeconomic status) may have a large effect on mean values, hence why the children had IQs similar to their adoptive mothers. However, heritability explains &lt;em&gt;variance&lt;/em&gt; not mean; in the above study, there is a high correlation between where children fell on the normal distribution of IQ scores among the children and where their biological mothers fell on the distribution of biological mothers, but no correlation with where their adoptive mothers fell on the distribution of adoptive mothers.&lt;/p&gt;&#xA;" OwnerUserId="4829" LastActivityDate="2013-11-04T00:30:01.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11276" PostTypeId="1" AcceptedAnswerId="11293" CreationDate="2013-11-04T00:48:22.927" Score="3" ViewCount="563" Body="&lt;p&gt;I'm not sure if this question belongs more in physics or biology (or maybe even computer science)... but biology seemed to fit more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What changes in the state of our brains when we learn things?  Because I looked on the internet and I learned about artificial neural networks, and every resource I've found teaches of neural networks that have weights that are trained/evolved and then are static at runtime; you simply train the weights and then once you use them in simulations, they never change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Purely feedforward neural networks that rely on this can't react to new situations differently if they've experienced it before.  They react exactly the same each time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suppose that theoretically, a recurrent neural network that was big enough could really learn, but in practice, these have been used as purely memory slots for an existing method defined by the weights, not as storage of new methods of doing things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is, physically, chemically, biologically, what changes in the neurons and the connections between them when we learn things?  I don't think we really understand how it comes together on a grand scale yet, but I'm pretty sure we've figured out that much.  I want to learn how to model a simplified version of it mathematically/programmatically.&lt;/p&gt;&#xA;" OwnerUserId="4830" LastEditorUserId="4830" LastEditDate="2013-11-04T00:58:06.987" LastActivityDate="2017-08-01T14:36:21.270" Title="What in neurons and their connections changes during the process of learning?" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11277" PostTypeId="2" ParentId="11026" CreationDate="2013-11-04T01:37:09.400" Score="4" Body="&lt;p&gt;If extracellular $Ca^{2+}$ concentration increased, it makes the extracellular membrane more positive then it used to be, then it would take the membrane potential to lower level then the excitability of the cells will be decreased&lt;/p&gt;&#xA;&#xA;&lt;p&gt;if extracellular $K^+$ increased more than the concentration inside the cell than it will make the $K^+$ on extracellular space move inside the call down the concentration gradient, it would take the potential membrane to higher state make it easier to reach the threshold (easier to be excitable) &lt;/p&gt;&#xA;" OwnerUserId="3851" LastEditorUserId="5144" LastEditDate="2014-06-02T10:57:12.003" LastActivityDate="2014-06-02T10:57:12.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11279" PostTypeId="2" ParentId="10323" CreationDate="2013-11-04T02:26:17.297" Score="1" Body="&lt;p&gt;Exposed collagen at the site of vessel damage simultaneously initiates plates aggregation and the clotting cascade. So, when the wound is sealed and no more collagen is exposed, which is the main factor to activate the cascade, the blood clothing cascade stops.&lt;/p&gt;&#xA;" OwnerUserId="3851" LastActivityDate="2013-11-04T02:26:17.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11280" PostTypeId="2" ParentId="11263" CreationDate="2013-11-04T04:38:20.697" Score="33" Body="&lt;p&gt;The very basic difference between a local and a global alignments is that in a local alignment, you try to match your query with a substring (a portion) of your subject (reference). Whereas in a global alignment you perform an end to end alignment with the subject (and therefore as von mises said, you may end up with a lot of gaps in global alignment if the sizes of query and subject are dissimilar). You may have gaps in local alignment also.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Local Alignment&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;5' ACTACTAGATTACTTACGGATCAGGTACTTTAGAGGCTTGCAACCA 3' &#xA;             |||| |||||| |||||||||||||||&#xA;          5' TACTCACGGATGAGGTACTTTAGAGGC 3'&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Global Alignment&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;5' ACTACTAGATTACTTACGGATCAGGTACTTTAGAGGCTTGCAACCA 3'&#xA;   |||||||||||    |||||||  |||||||||||||| |||||||&#xA;5' ACTACTAGATT----ACGGATC--GTACTTTAGAGGCTAGCAACCA 3'&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I shall give the example of the well known dynamic programming algorithms.&#xA;In the &lt;a href=&quot;https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm&quot; rel=&quot;noreferrer&quot;&gt;Needleman-Wunsch&lt;/a&gt; (Global) algorithm, the score tracking is done from the (m,n) co-ordinate corresponding to the bottom right corner of the scoring matrix (i.e. the end of the aligned sequences) whereas in the &lt;a href=&quot;https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm&quot; rel=&quot;noreferrer&quot;&gt;Smith-Waterman&lt;/a&gt; (local), it is done from the element with highest score in the matrix (i.e. the end of the highest scoring pair). You can check these algorithms for details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can adopt any scoring schemes and there is no fixed rule for it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Global alignments are usually done for comparing homologous genes whereas local alignment can be used to find homologous domains in otherwise non-homologous genes. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-09-16T05:01:58.837" LastActivityDate="2016-09-16T05:01:58.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11281" PostTypeId="1" CreationDate="2013-11-04T05:00:00.867" Score="2" ViewCount="228" Body="&lt;p&gt;I am planing to screen my cell cultures for mycoplasma contamination using the Hoechst 33258 DNA staining method. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This method is suitable for adherent cultures. Is this method suitable for suspension cultures? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If yes, what is the procedure to attach my suspension culture on coverslip and prevent washout of cells during staining.   &lt;/p&gt;&#xA;" OwnerUserId="4832" LastEditorUserId="5144" LastEditDate="2016-05-27T13:41:57.113" LastActivityDate="2016-05-27T13:41:57.113" Title="Attaching suspension cells to coverslip during mycoplasma contamination detection" Tags="&lt;cell-biology&gt;&lt;mycoplasma&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11282" PostTypeId="1" CreationDate="2013-11-04T05:32:53.477" Score="1" ViewCount="434" Body="&lt;p&gt;Polypeptides made by ribosomes which attach to rER will go into the rER to form the tertiary structure. Those polypeptides made by free ribosomes usually stay in cytoplasm. So are there any enzymes in cytoplasm to help them to form tertiary structure?&lt;/p&gt;&#xA;" OwnerUserId="4651" LastActivityDate="2013-11-05T01:32:23.987" Title="Are there any enzymes in cytoplasm to help the newly-synthesized polypeptide to form tertiary structure?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11284" PostTypeId="2" ParentId="11255" CreationDate="2013-11-04T07:57:35.053" Score="0" Body="&lt;p&gt;Prion diseases arise spontaneously fairly often.  There are only ~170 total cases of human infection by mad cow disease, but there are ~50 cases/year of Creutzfeldt-Jakob disease, which is a spontaneous strain of prion diseases in humans. There is a strong case that Alzheimer's and Parkinson's diseases (among others) are similar in nature, in which case it's a much more frequent occurrence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, they are the consequence of a misfolding and aggregation of a naturally occurring protein produced in our brains.  In this sense, they are nothing like the complexity required to produce a de novo virus. The closest viral analogy would be retroviruses, which could insert their genome into your DNA, die off, and then possibly spontaneously revive at a later date.&lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-11-04T07:57:35.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11285" PostTypeId="2" ParentId="11171" CreationDate="2013-11-04T08:20:23.757" Score="1" Body="&lt;p&gt;Y'all are neglecting the fact that cells die and are continually replaced, which would include replicating the DNA with new atoms.  The most interesting study I've seen on this is summarized in this &lt;a href=&quot;http://www.nytimes.com/2005/08/02/science/02cell.html?pagewanted=all&quot; rel=&quot;nofollow&quot;&gt;New York Times article&lt;/a&gt;. Above ground nuclear testing up until 1963 released a great deal of Carbon-14 into the atmosphere.  This ultimately became incorporated into the DNA of anyone living at the time, and was used as a marker for how quickly specific tissues turned over in the body.&lt;/p&gt;&#xA;" OwnerUserId="3460" LastActivityDate="2013-11-04T08:20:23.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11286" PostTypeId="1" AcceptedAnswerId="14044" CreationDate="2013-11-04T08:22:37.020" Score="33" ViewCount="56439" Body="&lt;p&gt;Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastEditorUserId="3553" LastEditDate="2016-08-22T04:38:22.430" LastActivityDate="2019-12-17T10:52:44.013" Title="Why is ATP the preferred choice for energy carriers?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;molecular-evolution&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="16" ContentLicense="CC BY-SA 3.0" />
  <row Id="11289" PostTypeId="2" ParentId="11281" CreationDate="2013-11-04T09:30:02.697" Score="1" Body="&lt;p&gt;If you are working with suspension cells, it's always easier to use Flow cytometry but if you want to use microscopy then I would suggest using chamber slides. You just have to put your cell suspension inside the chamber and then stick the cells to the microscope slide. After that you can do whatever treatment you want just by putting in the chamber the proper solution and wash afterwards. The more the steps the more cells you'll lose mostly because of pipetting so try to pipette always at the same corner and be gentle. To stick the cells to the slide your best option is to centrifuge the slide. Unfortunately in my lab that wasn't an option so I just fixed the cells with methanol while there were suspended in PBS and it worked very well. Most of the cells were attached to the slide and the staining was perfect.&#xA;Hope I helped. Good luck!  &lt;/p&gt;&#xA;" OwnerUserId="4789" LastActivityDate="2013-11-04T09:30:02.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11290" PostTypeId="1" AcceptedAnswerId="12403" CreationDate="2013-11-04T10:09:17.783" Score="2" ViewCount="7965" Body="&lt;p&gt;It's almost half a century since the lac operon was discovered but isn't it weird that the precise role of transacetylase isn't clearly understood ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Beta-galactoside_transacetylase&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; a wikipedia article with a link to a journal article which proposes a function of this enzyme. This article was written in 2002 but in most of the text books I have referred to ( written well after 2002 ), no function is mentioned.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MY QUESTION : What are the difficulties that are not allowing us to understand the precise role of this enzyme ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1320" LastEditDate="2013-11-04T18:55:47.693" LastActivityDate="2016-06-16T14:14:24.350" Title="Why is the function of lacA (encoding thiogalactoside transacetylase) not clearly understood?" Tags="&lt;biochemistry&gt;&lt;gene-expression&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11291" PostTypeId="1" AcceptedAnswerId="11300" CreationDate="2013-11-04T10:15:58.530" Score="1" ViewCount="725" Body="&lt;p&gt;I read in Campbell that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;....splicing and poly A tail addition may also occur while transcription is still under way.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;How can the poly(A) tail be added while transcription is still going on?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1320" LastEditDate="2013-11-04T18:52:58.180" LastActivityDate="2013-11-05T06:20:09.513" Title="Is the poly(A) tail added while transcription is still underway?" Tags="&lt;genetics&gt;&lt;mrna&gt;" AnswerCount="2" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="11293" PostTypeId="2" ParentId="11276" CreationDate="2013-11-04T11:19:47.163" Score="3" Body="&lt;p&gt;What changes in the process of learning:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The connections (the way one neuron is connected to another). New synapses can form or dissolve in the process of learning. The glial cells such as astrocytes and microglia can facilitate this process.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Strength of connections: Existing connections can be made weaker or stronger in the process of triggering the same circuit. This happens by up/down regulation of the ion channels at the synaptic junctions.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This process is not fully understood and is an active area of research. You can find some mathematical models too for learning processes such as Long Term Potentiation etc.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-11-04T11:19:47.163" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11295" PostTypeId="1" CreationDate="2013-11-04T12:50:58.237" Score="0" ViewCount="6513" Body="&lt;p&gt;Epithelial tissues are found on all the surfaces of the body; including external surfaces and surfaces of organs etc. &#xA;Are there any surfaces which do not have epithelial? I have read in my book that almost all the surfaces has epithelial tissues but there are some exceptions. What are the exceptions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, almost all the epithelial tissues are avascular. But there are some exceptions which are vascular? Which epithelial tissues are vascuar?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*I'm talking about a human body.&lt;/p&gt;&#xA;" OwnerUserId="1765" LastActivityDate="2015-11-19T05:19:49.563" Title="Which surfaces contain no epithelial tissues and which epithelial tissues are vascular?" Tags="&lt;tissue&gt;" AnswerCount="1" CommentCount="10" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11296" PostTypeId="2" ParentId="11266" CreationDate="2013-11-04T16:36:59.087" Score="1" Body="&lt;p&gt;Rotting is a biochemical reaction: basically catabolism (breaking down of complex compounds to simpler compounds). Cellulose or lignin or any other structural polysaccharide will not undergo spontaneous hydrolysis. This reaction is catalyzed by enzymes produced by the microorganisms like fungi and bacteria (the term for these decomposers is &lt;strong&gt;saprophyte&lt;/strong&gt;). Saprophytes prefer to grow in humid and warm environments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the primary role of humidity is to promote the growth of decomposers. Simultaneously it provides the water required for the hydrolysis. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-11-04T16:36:59.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11297" PostTypeId="2" ParentId="11268" CreationDate="2013-11-04T16:42:40.850" Score="1" Body="&lt;p&gt;Ultraviolet light is microbicidal. See &lt;a href=&quot;https://biology.stackexchange.com/questions/8788/what-is-the-relationship-between-uv-wavelength-and-penetration-depth-into-human/8789#8789&quot;&gt;this&lt;/a&gt; post.&#xA;As I answered in this &lt;a href=&quot;https://biology.stackexchange.com/questions/11266/humidity-for-wood-rotting&quot;&gt;previous&lt;/a&gt; post, micro-organisms are essential for rotting. Since UV kills these microbes it will reduce the rate of rotting. The heat from sun will also dry the wood and further decelerate rotting.  &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-11-04T19:10:02.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11298" PostTypeId="1" AcceptedAnswerId="11350" CreationDate="2013-11-04T16:54:42.923" Score="4" ViewCount="210" Body="&lt;p&gt;Rickettsiales are widely regarded as the ancestor of eukaryotic mitochondria through endosymbiosis.&#xA;Cyanobacteria are widely regarded as the ancestor of eukaryotic chloroplasts through endosymbiosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These two organelles bear striking similarities in terms of structure and mechanics. There seems to be plenty of information regarding speculation on the endosymbiosis that led from these free-living organims to the organelles. However I can't seem to find much on speculated relationships between these organisms in terms of common structures.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My Quesions : Are the electron transport systems and chemiosmosis simply ubiquitous phenomena in prokaryotes, or are these similarities evidence of highly conserved common ancestry? Or is there another answer?&#xA;Is there any information regarding the phylogenetics of Rickettsiales and Cyanobacteria. Do these two organisms belong to a single small clade or were these biochemistries (ETCs, ATP Synthases, etc) ubiquitous at some point and have simply been preserved in these two organisms today?&lt;/p&gt;&#xA;" OwnerUserId="1710" LastEditorUserId="-1" LastEditDate="2013-11-06T04:15:15.877" LastActivityDate="2013-11-06T07:20:03.263" Title="Common Ancestry of ETCs and ATP Synthase complexes" Tags="&lt;biochemistry&gt;&lt;mitochondria&gt;&lt;phylogenetics&gt;&lt;chloroplasts&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11299" PostTypeId="2" ParentId="11244" CreationDate="2013-11-04T18:37:49.790" Score="1" Body="&lt;p&gt;Well.. First assume the chemical reactions to be a &lt;a href=&quot;http://en.wikipedia.org/wiki/Poisson_process&quot; rel=&quot;nofollow&quot;&gt;Poisson's process&lt;/a&gt; (which is a right stochastic approximation for processes such as chemical reactions and radioactive decay etc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the event of a burst follows a Poisson's distribution, the time interval between two reaction events follows an exponential distribution. (See wikipedia page on Poisson's distribution for details)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the both two mentioned steps have approximately equal time scale of ~70 sec we can expect that the mean delay between two reaction events to be equal to 70 sec. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exponential distribution with a mean &lt;code&gt;τ&lt;/code&gt; is:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;p(t)=e^(-t/τ)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-11-04T18:43:37.413" LastActivityDate="2013-11-04T18:43:37.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11300" PostTypeId="2" ParentId="11291" CreationDate="2013-11-04T18:52:02.303" Score="2" Body="&lt;p&gt;It's slightly more complicated than the comments above indicate.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Glover-Cutter, K et al. (2007) RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nature Structural &amp;amp; Molecular Biology 15: 71-78&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors present evidence that RNA polII pauses 0.5 - 1.5 kb downstream of the poly(A) site where processing factors are recruited (cleavage stimulation factor, or CstF, and cleavage polyadenylation specificity factor, CPSF). So the polymerase is still engaged with the template and the premRNA when processing is initiated, although it may not be actively elongating the transcript. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Localisation of the active polII-3' end processing complex well downstream of the poly(A) consensus sequence agrees well with the cleavage of &lt;em&gt;Chironomus&lt;/em&gt; BR1 transcripts after 600 bases of downstream sequence has been transcribed. This model is also supported by the fact that efficient poly(A) site cleavage requires an intact RNA tether linking the poly(A) site with the downstream polymerase.&quot; (&lt;em&gt;references are cited in the original&lt;/em&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is a semantic question as to whether you call this cotranscriptional processing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[Incidentally this is yet another example which contradicts the commonly-stated idea that evolution acts to optimise everything to conserve ATP - here we have the transcription process discarding the energy from approximately 1000 phosphodiester bonds &lt;em&gt;per transcript&lt;/em&gt;.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE&#xA;@WYSIWYG The polymerase goes past the site where the poly(A) will eventually be added, and makes another 1000 bases of RNA before pausing to recruit factors that are needed for the subsequent cleavage at the pol(A) site which now lies &quot;behind it&quot;. After that the poly (A) tail is added at the newly created 3' end. So the initiation of poly(A) addition (in the sense that the cleavage is an obligatory first step in the process) is accomplished while the polymerase is still engaged. I agree that the actual addition of the poly(A) cannot in any way be considered to be cotranscriptional. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was trying to make the point out that it isn't simply a case of the polymerase encountering the cleavage site and dropping off to allow a second unlinked process to take place.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-11-04T19:51:53.597" LastActivityDate="2013-11-04T19:51:53.597" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11302" PostTypeId="2" ParentId="7847" CreationDate="2013-11-04T20:01:22.420" Score="4" Body="&lt;p&gt;Muscle contraction occurs when the brain tells the body to move. The brain then starts an action potential down the motor neurons, until it reaches the terminal bouton. At the terminal bouton, it releases the neurotransmitter, acetylcholine, which travels through the myoneural junction and into the myoneural cleft. ACH binds to the receptor, which causes an action potential in both directions along the cell membrane. &#xA;    The action potential repels the potassium, which travels down the cell membrane until it falls into a transverse tubule. K+ continues to fall into a transverse tubule and accumulates, which increases voltage (-70 to -50 mV). The voltage change causes the calcium gates to open and to diffuse the calcium. &#xA;    Calcium then binds to troponin, which in turn binds to tropomyosin and pulls it, exposing the g-actin binding site that allows myosin and actin to bind. The myosin head changes shape (called power or working stroke) and pulls the actin towards the M line, and the muscle contracts. Similar to a tug of war, the myosin heads (your hands) pull on the actin (the rope) to contract a muscle. Like team members in a tug of war, the myosin heads alternate between pulling and holding on to the actin; the only way that myosin will release actin is to add ATP, which forces the two apart and thus relaxes the muscle (as mentioned above).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, a lack of potassium, sodium, or calcium would prevent the muscle from contracting but won't relieve a muscle cramp. The common advice of eating a banana actually does help relieve cramps but not because of the potassium. Bananas also have sugar and fat, which are converted into ATP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Muscle cramps are primarily caused by a lack of ATP in the body. ATP forces the myosin to release the actin; thus, the muscle relaxes and the cramp is relieved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another cause could be the lack of magnesium, which helps the ATPase sodium/potassium pump, which, in turn, returns the voltage to resting potential and relaxes the muscle.&lt;/p&gt;&#xA;" OwnerUserId="4836" LastEditorUserId="-1" LastEditDate="2017-11-11T15:50:47.527" LastActivityDate="2017-11-11T15:50:47.527" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11303" PostTypeId="1" CreationDate="2013-11-04T20:44:07.863" Score="2" ViewCount="4272" Body="&lt;p&gt;I was wondering the other day outside, thinking about varieties of species and their aggression levels, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I had a theory that since these highly aggressive, powerful, and viciously advantageous animals in fights with humans, such as lions, tigers, rhinos, elephants, etc. are so strong and aggressive in the wild compared to us humans and smaller animals, do they have more testosterone?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like, in animals, does testosterone correlate with size, possibly explaining why a lion is heaps more slender, muscular, fit, agile, aggressive, and vicious than a typical human?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, does the bigger size and aggression in wild animals correlate to their higher testosterone, such as larger size equal to larger testosterone in comparison to other smalelr or less aggressive animals, or is it different?&lt;/p&gt;&#xA;" OwnerUserId="4837" LastActivityDate="2013-11-04T22:31:49.400" Title="Do bigger animals have more testosterone?" Tags="&lt;zoology&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11304" PostTypeId="2" ParentId="11244" CreationDate="2013-11-04T21:49:39.640" Score="2" Body="&lt;p&gt;The rate limiting step of a reaction is the slowest component of the reaction. So if there are two steps in a reaction, each of these steps will have a rate, and the slowest of those two rates will determine the overall rate of the whole reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a simple example, consider the equation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$A + B + C\rightarrow AB+C\rightarrow ABC$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the rate of $A+B \rightarrow AB$ is fast, but the rate of $AB+C \rightarrow ABC$ is slow, then the overall reaction will still be slow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The figure in your question is showing the distribution of the burst &lt;strong&gt;durations&lt;/strong&gt;, and highlighting the fact that the calcium level has no effect on the burst duration. The second quote is a bit confusing, this is my interpretation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The functional form which they fitted to the distribution indicates that the expected burst duration is about 70 seconds. I'm not completely sure which stochastic steps they are referring to, maybe translation and subsequent localisation (I think transcription would happen on a different timescale and so could be ignored in this case).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, this paper is a really excellent example of an organism harnessing stochasticity to its advantage in order to synchronise its response to a stimulus (calcium in this case). I just think that it is so cool that the mean response to the signal level can be different to the response to the mean signal level - so counter-intuitive to me. And so much fun!!&lt;/p&gt;&#xA;" OwnerUserId="445" LastActivityDate="2013-11-04T21:49:39.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11305" PostTypeId="2" ParentId="11303" CreationDate="2013-11-04T22:06:18.317" Score="2" Body="&lt;p&gt;It is not that easy. Off the top of my hat I can try to pinpoint a few fallacies in your theory:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Scaling of the body happens in three dimensions and thus to a power law. As such allometric equations have to be applied when dealing with the total amount of substance in the body. Different species have different correlation factors of body mass to total substance amounts.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Angiogenesis (the formation of blood vessels) is affected by Allometry (the relationship of body size to the 'biology')&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Diffusion factors are similar in closely related species. This means in order for messenger molecules with a short acting range/half-life (e.g. nitric oxide), the total amount in the animal may indeed be likely higher and the messenger in question may be produced on-site (e.g. endothelium). Testosterone as the name indicates, is however produced in the testes and released in the blood stream.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The sensitivity and regulation of the receptors themselves (which react to a substance) can be different in different species. It may also be weakly responsive to begin with at the genetic and ultimately the folded protein level. A good example of that is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanocortin_1_receptor&quot; rel=&quot;nofollow&quot;&gt;melanocortin receptor MC1R&lt;/a&gt; in a gross section of the white human population. Even if you were to produce the same level of melanotonin, the melanocytes wouldn't respond to the same degree as in Humans with darker skin.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Messenger molecules can be re-purposed and take over or be given additional roles and functions over evolutionary-time. Again, Melatonin may serve here as an example.&lt;br&gt;&#xA;After all a given messenger is already evolutionary tested, especially in regard to cross-talk, Haptens, and other adverse molecular interactions in the animal species and comes with the full set of molecular machinery adapted to it, - a &quot;luxury&quot; a new messenger doesn't have. As such pressure usually exists to re-use given messengers.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Like, in animals, does testosterone correlate with size, possibly&#xA;  explaining why a lion is heaps more slender, muscular, fit, agile,&#xA;  aggressive, and vicious than a typical human?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I doubt you will find typical humans or typical human populations from a biological perspective. Your view may be skewed by economic factors.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Basically, does the bigger size and aggression in wild animals&#xA;  correlate to their higher testosterone, such as larger size equal to&#xA;  larger testosterone in comparison to other smalelr or less aggressive&#xA;  animals, or is it different?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To a large degree the behavior is determined by the niche the animal is in. As to which concerted molecular messengers make the &quot;evolutionary cut&quot;, by best influencing an animals behavior in its given &quot;time-domain&quot; is another question. As the question is complex much is still researched.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take this counter-example: A mouse and an elephant have very different masses resulting in different inertial forces. Fleeing from an enemy will take different strategies in regard to the central nervous system as well as the body, and demand different levels of messenger molecules at different places, at different times for both animals. Yet the substances in question will likely be similar.&lt;/p&gt;&#xA;" OwnerUserId="1450" LastEditorUserId="1450" LastEditDate="2013-11-04T22:31:49.400" LastActivityDate="2013-11-04T22:31:49.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11306" PostTypeId="2" ParentId="11237" CreationDate="2013-11-04T22:53:54.427" Score="2" Body="&lt;p&gt;As I see it, your question is also encompassing an inquiry for a theory of fitness.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In recent years the &lt;a href=&quot;http://en.wikipedia.org/wiki/Inclusive_fitness&quot; rel=&quot;nofollow&quot;&gt;inclusive fitness theory&lt;/a&gt; has seen its share of interest, which can be applied to social entities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Freely citing from wikipedia here:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An organism is judged by the number of offspring it has, how they support them, and how their offspring could support others&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As for the mathematics and informatics &lt;a href=&quot;http://dx.doi.org/10.1016/j.tpb.2012.11.007&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;JY Wakanoa et al. &quot;A mathematical description of the inclusive fitness&#xA;  theory&quot;, Theoretical Population Biology, Vol84. March 2013. pg 46–55&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;explains:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Recent developments in the inclusive fitness theory have revealed that&#xA;  the direction of evolution can be analytically predicted in a wider&#xA;  class of models than previously thought, such as those models dealing&#xA;  with network structure. ...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It takes a Markov chain approach.&lt;/p&gt;&#xA;" OwnerUserId="1450" LastActivityDate="2013-11-04T22:53:54.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11307" PostTypeId="2" ParentId="11244" CreationDate="2013-11-05T01:18:29.823" Score="2" Body="&lt;p&gt;WYSIWYG is almost there, but you need one more piece of information to make this explicit. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The distribution cited in the paper is $h(t)\propto te^{-t/\tau}$ (we're going to ignore normalizing constants today). We can recognize this as a particular case of the &lt;em&gt;Gamma distribution&lt;/em&gt;, with PDF:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$f_{\mathrm{Gamma}}(t\,\big|\,k,\theta)\propto t^{k-1}e^{-t/\theta}.$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, $h(t)$ looks like the PDF of a $\mathrm{Gamma}(2,\tau)$ random variable,&#xA;$$h(t)\propto f_{\mathrm{Gamma}}(t\,\big|\,2,\tau)\propto te^{-t/\tau}.$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the authors of the paper are claiming that the burst duration $\tau_{\mathrm{burst}}$ is a random variable with a $\mathrm{Gamma}(2,70\,\mathrm{ sec})$ distribution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do we get from that to &quot;This distribution was consistent with two rate-limiting stochastic steps?&quot;&#xA;If we recall from our stats class (or look up properties of the Gamma distribution on Wikipedia), a Gamma distribution with integer values of $k$ is &lt;em&gt;the distribution of the waiting time for $k$ events to occur in a Poisson process.&lt;/em&gt; The setup of a Poisson process is that you are tracking the occurrence of unlikely/infrequent events in time, so the fact that the distribution $h(t)$ of burst times looks like a $\mathrm{Gamma}(2,\tau)$ suggests that the burst duration $\tau_{\mathrm{burst}}$ is determined by the occurrence of 2 stochastic events (with the same &quot;frequency&quot; $1/\tau$). In other words, this distribution is consistent with the following scenario: a nuclear localization occurs, and then will stop after two particular events, where the timing of the events is governed by a Poisson process (which, as WYSIWYG pointed out, is a reasonable model for the occurrence of chemical reactions with reasonably slow kinetics, i.e. you can count individual reactions in time). If this is true, the distribution of $\tau_{\mathrm{burst}}$ will look like $te^{-t/\tau}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors generalize that statement somewhat by saying that technically there could be more events/reactions required to terminate a localization burst, but all but 2 of those reactions happen extremely rapidly, i.e. there are 2 rate-limiting steps in the decision process (both of which happen to have the same value for $\tau$).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Edit: I realized that one more mathematical point might make this more clear: The statement about the Gamma distribution and Poisson processes above is equivalent to the statement that the sum of $k$ &lt;a href=&quot;http://en.wikipedia.org/wiki/Iid&quot; rel=&quot;nofollow&quot;&gt;iid&lt;/a&gt; random variables with distribution $\mathrm{Exponential}(\tau)$ is a random variable with a $\mathrm{Gamma}(k,\tau)$ distribution. Thus $h(t)$ is literally (up to normalization) the distribution of a sum of 2 independent exponential random variables. If you read up on the connection between the exponential distribution and waiting times that might make the claim in the paper seem more transparent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;https://en.wikipedia.org/wiki/Gamma_distribution#Special_cases&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Gamma_distribution#Special_cases&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Exponential_distribution&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Exponential_distribution&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4840" LastEditorUserId="4840" LastEditDate="2013-11-05T12:40:53.100" LastActivityDate="2013-11-05T12:40:53.100" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11308" PostTypeId="2" ParentId="11282" CreationDate="2013-11-05T01:32:23.987" Score="1" Body="&lt;p&gt;There are several types of proteins that do this, all of which fall under the category of &lt;a href=&quot;https://en.wikipedia.org/wiki/Chaperone_%28protein%29&quot; rel=&quot;nofollow&quot;&gt;molecular chaperones&lt;/a&gt;. In particular, &lt;a href=&quot;https://en.wikipedia.org/wiki/Chaperonin&quot; rel=&quot;nofollow&quot;&gt;chaperonins&lt;/a&gt; such as GroEL/GroES complex in &lt;em&gt;E. coli&lt;/em&gt;, sequester newly-formed polypeptides to allow them to fold their tertiary structure and avoid aggregation. Another widely studied class of these proteins are heat shock proteins (Hsps): these are involved generally in acclimating cells to stresses (such as heat), and some of these Hsps have been specifically implicated as chaperones. I'm a new user, so I can't post a 3rd link, but just google Heat shock proteins and you'll find plenty of information.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2013-11-05T01:32:23.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11311" PostTypeId="1" AcceptedAnswerId="11314" CreationDate="2013-11-05T05:58:21.847" Score="4" ViewCount="153" Body="&lt;p&gt;I am going to be working with genetics data in my organization's data warehouse next year and helping our biotechnology department.  I work in academic research, but I have very little genomics background.  I was able to find the book called &quot;Bioinformatics for Geneticists&quot; (Edited by Michael R. Barnes &amp;amp; Ian C. Gray) at a used book store for a couple dollars.  It looks like it was published in 2003.  Do you think this book is too outdated, or would I still get a good introduction to the subject?  If you think it's too outdated, what book(s) do you recommend?&lt;/p&gt;&#xA;" OwnerUserId="1594" LastActivityDate="2013-11-05T07:15:06.617" Title="Is the book &quot;Bioinformatics for Geneticists&quot; outdated?" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;book-recommendation&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11312" PostTypeId="2" ParentId="11291" CreationDate="2013-11-05T06:20:09.513" Score="2" Body="&lt;p&gt;As others have stated, splicing does happen cotranscriptionally but you cannot be actively transcribing the RNA while it is being transcribed. However, it is generally accepted that a transcript can be polyadenylated while the RNA polymerase is still transcribing - this is called the torpedo model. The distinction is that the transcript has been cleaved between the polymerase and the polyA, but they were still part fo the same transcriptional event.  See the figure here...&#xA;&lt;a href=&quot;http://www.nature.com/nsmb/journal/v11/n12/fig_tab/nsmb1204-1156_F1.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nsmb/journal/v11/n12/fig_tab/nsmb1204-1156_F1.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3619" LastActivityDate="2013-11-05T06:20:09.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11313" PostTypeId="1" AcceptedAnswerId="11324" CreationDate="2013-11-05T06:58:20.667" Score="5" ViewCount="18952" Body="&lt;p&gt;It is common practice to use ice packs on injuries that cause bruising and swelling. It seems to be  an effective method to assist in reducing swelling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does ice reduce welling?&lt;/p&gt;&#xA;" OwnerDisplayName="user22339" LastEditorDisplayName="user22339" LastActivityDate="2013-11-05T15:57:55.977" Title="Why does ice reduce swelling?" Tags="&lt;medicinal-chemistry&gt;&lt;injury&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11314" PostTypeId="2" ParentId="11311" CreationDate="2013-11-05T07:15:06.617" Score="2" Body="&lt;p&gt;I haven't read through all of it, but from the second edition, which I found available online &lt;a href=&quot;http://ibi.cqupt.edu.cn/download/bioinformatics/Bioinformatics+for+Geneticists+2ed.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, it seems to me that it might be a good introduction, but (as expected from the publishing date) it is really missing out on all the next generation sequencing stuff. Which is important, not only because it is my favourite field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure what you want to get from it? You say you have little genomics background, but then you got a book that expects you to know the genetics, but explains the bioinformatics.&#xA;There's a basic description of the background of sequencing at the &lt;a href=&quot;http://www.genome.gov/25019999&quot; rel=&quot;nofollow&quot;&gt;NIH website&lt;/a&gt;, maybe that helps.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-11-05T07:15:06.617" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="11315" PostTypeId="2" ParentId="954" CreationDate="2013-11-05T07:15:45.750" Score="4" Body="&lt;p&gt;Meiosis, as you know, have two stages, Meiosis I and II. The oocyte is arrested &lt;strong&gt;during&lt;/strong&gt; metaphase II of MEOISIS II. This arrest is facilitated by a complex called &quot;Cytostatic Factor&quot; (CSF). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After fertilization, the sperm induces a rise in intracellular calcium ion which activates and enzyme, Calmodulin Kinase II. This complex, through a series of phosphorylation and ubiquitination, degrades the CSF comples and in turn, activates APC (Anaphase Promoting Complex). APC will then degrades cyclins, securins and this will promotes the completion of Meiois II. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sperm must ignite some process in female that puts female meiosis II going on before sperm can fuse with egg.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think the statement is a bit incorrect. The sperm will ignite (I prefer induce) the above changes &lt;strong&gt;and&lt;/strong&gt; fuse at the same time. Because, what starts all the process above is part of the sperm's cytoplasm that need to be assimilated into the oocyte's cytoplasm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this clears it all up. Or if you are interested, I can provide the long list of signalling pathways that leads to zygotic development.&lt;/p&gt;&#xA;" OwnerUserId="4845" LastEditorUserId="3624" LastEditDate="2013-11-05T13:24:55.230" LastActivityDate="2013-11-05T13:24:55.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11316" PostTypeId="1" CreationDate="2013-11-05T09:42:01.993" Score="2" ViewCount="177" Body="&lt;p&gt;I'm reading an article (full text &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695983/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;) that analyze the dynamics of localization of a GFP-tagged transcription factor (Crz1) over the time at the single-cell level, by taking movies in a fluorescent microscope.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Methods section they say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fluorescence cell images were segmented using a Hough transformation algorithm in Matlab, provided by Sharad Ramanathan. Localization score was determined by the difference between the mean intensity of the 5 brightest pixels in the cell and mean intensity of the rest of the pixels in the cell.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The segmentation process here seems to be the identification of cells over the background. They then calculate a &lt;em&gt;localization score&lt;/em&gt;, for each frame of the video, for every cell. Now there's the part that I can't understand:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bursts were identified by thresholding traces at &gt;1 standard deviations above background noise, estimated from the lowest 20% of values.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I searched some definitions of &quot;background noise&quot;, but I can't figure out what does it mean in this particular context. Moreover, &quot;lowest 20% of values&quot; of what?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it plausible that they define it for the lowest 20% of values of localization scores over the time, at the cell each time considered?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe can be useful a screenshot of a single cell in a photogram of the video:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sraiz.png&quot; alt=&quot;cell pixels&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3523" LastEditorUserId="3523" LastEditDate="2013-11-06T07:56:52.793" LastActivityDate="2014-05-05T12:34:52.943" Title="Image analysis of GFP-tagged protein localization bursts" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;microscopy&gt;&lt;experimental&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11317" PostTypeId="1" CreationDate="2013-11-05T11:11:51.260" Score="3" ViewCount="755" Body="&lt;p&gt;The short version of my question is this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It's some time in the future. I go into my back garden and focus my telescope on the Moon. The surface is virtually covered with giant greenhouses, growing food to support the cities that have sprung up there. The question is: &lt;em&gt;what plants are they growing in those greenhouses&lt;/em&gt;?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Factors such as temperature, water, soil quality etc. can be controlled easily enough if you already have the ability to build sealed greenhouses in a vacuum. There are also a number of experiments on growing food in closed systems where air and water are recycled (the Biosphere 2 project being the best known). The low gravity can't be controlled, but there have been a number of experiments on plant growth in microgravity conducted on the international space station, so growing plants in Lunar gravity should be possible. There have also been some interesting results from growing plants in an Earth-based approximation to Lunar soil.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, another important issue is the length of the Lunar day, which is 28 Earth days long, meaning that the Sun shines continuously for two Earth weeks, followed by two weeks of total darkness. I'm interested in what's known about how plants could adapt to this, but I haven't been able to find any research papers on the subject. Of course it would be possible to simulate an Earth day using artificial lighting, but the energy costs of doing this on a large scale would be rather high, so for economic reasons future Lunar farmers would likely want to keep it to a minimum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my first question is, has any research been done on the effect of extreme changes in day length on plant growth?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, is there any type of food plant that would be particularly likely to cope with such an environment (perhaps with some suitable genetic modifications)? For example, would normal crop plants such as cereals be able to build up enough sugar reserves in two weeks to survive the next two weeks in total darkness? If not, is there another type of plant that's more likely to be able to adapt to this? Or as an alternative strategy, is there any crop that grows fast enough that its shoots could be harvested after only two weeks of continuous sunlight? (Some individuals would have to be grown to maturity under artificial light in order to produce seeds, of course.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, I'd be grateful for pointers towards research on any other issues that I might have missed that are relevant to the problem of large-scale Lunar agriculture.&lt;/p&gt;&#xA;" OwnerUserId="3347" LastEditorUserId="3347" LastEditDate="2013-11-06T07:45:42.930" LastActivityDate="2017-08-20T01:17:06.403" Title="Growing crops on the Moon" Tags="&lt;plant-physiology&gt;&lt;speculative&gt;" AnswerCount="1" CommentCount="23" ContentLicense="CC BY-SA 3.0" />
  <row Id="11318" PostTypeId="2" ParentId="967" CreationDate="2013-11-05T11:26:46.553" Score="4" Body="&lt;p&gt;Members of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cucurbitaceae&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cucurbitaceae&lt;/a&gt; family (squash, pumpkin, cucumber, melon etc.) are unique* in that they possess two distinct phloems, see figure below. The fascicular phloem (FP) is the main transport conduit, and more closely resembles the phloems of other plant families. Its role is to transport photosynthates and other nutrients (Turgeon &amp;amp; Oparka, 2010).The extra fascicular phloem (EFP), is more minor and has an atypical composition for a phloem. Although we have been aware of this dual phloem system for centuries (Crafts, 1932; Fischer, 1883, 1884, 1886), it is often ignored!!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The minor strands of EFP have been found to be the source of the extreme bleeding observed in cucurbits (Zhang &lt;em&gt;et al&lt;/em&gt;., 2010). However this excessive bleeding has meant that cucurbits are a very popular model plant for phloem composition studies, since copious amounts of phloem contents are easily accessible. This is problematic since we now know that the exudate originates from the atypical EFP strands, making it a poor model (maybe is isn't even a phloem at all)!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason that the EFP does not block upon wounding is that it lacks blocking and sealing mechanisms (such as P proteins and pectins), which usually exist in order to protect the phloem from damage or disease, and to prevent the loss of vital metabolites. The fact that these are not present in EFP, along with the fact that EFP is rich in defensive proteins (Walz &lt;em&gt;et al&lt;/em&gt;., 2004), may suggest a defensive role for this secondary phloem. Its anatomical placement around the vital vascular transport conduits supports this idea.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;&lt;img src=&quot;https://i.stack.imgur.com/NF0qV.jpg&quot; alt=&quot;The dual phloem system found in cucurbits&quot;&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;*No others are known, but could definitely exist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Bibliography&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Crafts, A. S. “Phloem Anatomy, Exudation, and Transport of Organic Nutrients in Cucurbits.” Plant Physiology 7, no. 2 (1932): 183–225.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Fischer, A. “Das Siebröhrensystem von Cucurbita.” Berichte Deutsche Botanische Gesell 1 (1883): 276–279.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Fischer, A. “Neue Beiträge Zur Kenntniss Der Siebröhren.” Berichte Über Die Verhandlungen Der Königlich-Sächsischen Gesellschaft Der Wissenschaften Zu Leipzig, Mathematisch-Physische Klasse 38 (1886): 291–336.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Fischer, A. Untersuchungen Über Das Siebröhren System Der Cucurbitaceen. Berlin, 1884.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Turgeon, R. and Oparka, K. “The Secret Phloem of Pumpkins.” Proceedings of the National Academy of Sciences 107, no. 30 (2010): 13201 –13202.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Walz, C. and Giavalisco, P. and Schad, M. and Juenger, M. and Klose, J. and Kehr, J. “Proteomics of Curcurbit Phloem Exudate Reveals a Network of Defence Proteins.” Phytochemistry 65, no. 12 (2004): 1795–1804.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Zhang, B. and Tolstikov, V. and Turnbull, C. and Hicks, L. M. and Fiehn, O. “Divergent Metabolome and Proteome Suggest Functional Independence of Dual Phloem Transport Systems in Cucurbits.” Proceedings of the National Academy of Sciences 107, no. 30 (2010): 13532.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="445" LastActivityDate="2013-11-05T11:26:46.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11319" PostTypeId="2" ParentId="11317" CreationDate="2013-11-05T11:39:14.473" Score="1" Body="&lt;p&gt;&lt;strong&gt;Plants are adapted to the conditions we have here on earth&lt;/strong&gt;, therefore, for them to grow on the moon we would have to recreate the conditions found on earth (or at least find conditions that we can create and they can grow in). To do this we would need to replicate climate (temperature, air pressure, humidty etc.), provide (sun)light at the necessary intervals and intensity, provide water, air, and nutrients of the right composition, intervals and intensity. That is a simplified version... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In reality there is great variation in how plants require these things&lt;/strong&gt;. Some cope with long dark periods better than others, some cope with drought better than others, some cope with chemical variation in the soil better than others so answering this question is hard. But generally growing plants on the moon will require the ability to recreate (to some degree depending on the sensitivity of the plant) the conditions a plant has evolved under on earth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Thus to answer your questions:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Length of day can have strong effects on growth patterns, two weeks of darkness is likely to be a major upset for plants! Just transplanting plants of the same species from different latitudes can affect the growth patterns because of changes in length of day. Try putting some plants in darkness for two weeks and see what happens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants all vary in their ability to meet the requirements of space growth. There will only be a short list of plants that could with &quot;small&quot; modifications to the moon's environment, the more we adapt (adding artificial light, watering, adding nutrients etc) the longer that list would become - the limitation is in our ability to adapt the moon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See above for reasons why plants might struggle. Oh and we would need to consider the effects of reduced gravity too...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nasa.gov/audience/foreducators/spacelife/topics/plants/index.html#.UnjYE_mkpJk&quot; rel=&quot;nofollow&quot;&gt;Here's a little something from nasa&lt;/a&gt; about how plants are used in space vehicles. And &lt;a href=&quot;http://www.nasa.gov/audience/foreducators/topnav/materials/listbytype/How_Plants_Grow_in_Space.html&quot; rel=&quot;nofollow&quot;&gt;another on light and gravity&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-11-05T11:58:15.343" LastActivityDate="2013-11-05T11:58:15.343" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="11320" PostTypeId="2" ParentId="11182" CreationDate="2013-11-05T12:56:54.227" Score="1" Body="&lt;p&gt;The Second Law of Thermodynamics is intimately linked to the thermodynamics of the breakdown of glucose. By &quot;the thermodynamics of the breakdown of glucose,&quot; I mean: is the breakdown of glucose &lt;em&gt;spontaneous&lt;/em&gt;, is it thermodynamically favorable?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may have seen the criteria for the thermodynamic favorability of a reaction in terms of Gibbs Free Energy:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\Delta G = \Delta H - T\Delta S\leq0$$&#xA;That is, for a reaction to be favorable, the change in Gibbs free energy from the initial state (glucose) to the final state (carbon dioxide, water, and energy) must be negative. This equation is valid for systems at constant temperature and pressure, which is assumed to be satisfied in biological systems. According to &lt;a href=&quot;https://en.wikipedia.org/wiki/Cellular_respiration#Aerobic_respiration&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;, $\Delta G$ for the breakdown of glucose is negative, $\Delta G = -2880$ kJ/mol.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there is a nice &lt;a href=&quot;https://en.wikipedia.org/wiki/Gibbs_free_energy#Free_energy_of_reactions&quot; rel=&quot;nofollow&quot;&gt;derivation&lt;/a&gt; on Wikipedia that the above equation is nothing more than a statement of the second law of thermodynamics, applied to the case of constant temperature and pressure. So in sum, the second law of thermodynamics is the reason that glucose can be broken down in such a way that useful energy is released in the form of ATP, i.e. that the reaction is spontaneous or thermodynamically favorable. Saying that the Gibbs Free Energy of the breakdown products is lower than that of glucose itself is the same as saying that the breakdown of glucose does not decrease the total entropy of the reaction and its environment.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2013-11-05T12:56:54.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11321" PostTypeId="1" CreationDate="2013-11-05T14:05:21.703" Score="3" ViewCount="845" Body="&lt;p&gt;If primers weren't present in &lt;a href=&quot;http://en.wikipedia.org/wiki/Polymerase_chain_reaction&quot; rel=&quot;nofollow&quot;&gt;PCR&lt;/a&gt; at what temperature would DNA re-anneal? I am wondering how primers manage to bind on DNA strands before DNA manages to anneal back together.&lt;/p&gt;&#xA;" OwnerUserId="4846" LastEditorUserId="3776" LastEditDate="2013-11-05T15:48:05.853" LastActivityDate="2013-11-06T00:45:55.173" Title="At what temperature does DNA re-anneal?" Tags="&lt;molecular-biology&gt;&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11323" PostTypeId="1" AcceptedAnswerId="13410" CreationDate="2013-11-05T15:36:00.000" Score="11" ViewCount="9032" Body="&lt;p&gt;The length of &lt;a href=&quot;http://en.wikipedia.org/wiki/Okazaki_fragments&quot;&gt;Okazaki fragments&lt;/a&gt; in the &lt;a href=&quot;http://www.nature.com/scitable/content/dna-replication-of-the-leading-and-lagging-14668888&quot;&gt;lagging strand&lt;/a&gt; is about 100-200 nucleotides in eukaryotes and about 1000-2000 nucleotides in prokaryotes. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What (molecular mechanism, enzyme type ) determines the length of&#xA;  these Okazaki fragments?&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Moreover, which, longer or shorter, fragments would be more&#xA;  advantageous (energetically and considering accuracy)?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Longer fragments means less use of &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_ligase&quot;&gt;DNA ligase&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_polymerase_I&quot;&gt;DNA polymerase-I&lt;/a&gt; (prokaryotes) and other enzymes required to convert the okazaki fragments with dispersed RNA primers into a normal strand, and hence lesser scope of mistakes during replication in the lagging strand. Shorter Okazaki fragments improve telomere longevity, by reducing the capped-off portion after every division. Which of these views is correct?&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3615" LastEditDate="2014-01-27T15:28:05.643" LastActivityDate="2018-08-30T14:30:21.417" Title="Difference in length of Okazaki fragments" Tags="&lt;evolution&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;replication&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11324" PostTypeId="2" ParentId="11313" CreationDate="2013-11-05T15:57:55.977" Score="8" Body="&lt;p&gt;Swelling is one of the signs of inflammation. Inflammation involves release of histamine by mast cells present in the tissues. Histamine causes vasodilation and leads to leakage of fluid from the blood, along with which neutrophils and other WBCs also enter the area. They phagocytose microbes that might have entered with the injury.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Applying ice would cause vasoconstriction* (i.e. narrowing of blood vessels.) which would reduce the leakage of tissue fluid and hence swelling. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;*If you wonder why ice(or any cool thing) causes vasoconstriction think why you turn pale in winter ? Vasoconstriction reduces blood flow to the particular area and hence the exchange of heat is reduced which conserves body heat in cold environments.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-11-05T15:57:55.977" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11325" PostTypeId="1" AcceptedAnswerId="17925" CreationDate="2013-11-05T16:05:54.583" Score="3" ViewCount="259" Body="&lt;p&gt;Raynaud's phenomenon can be a serious health issue, as the blood flow to the extremities, mainly the fingers is compromised, causing fingers to blanche, and then turn blue. Severe Raynaud's can cause gangrene in illnesses like progressive/ diffuse scleroderma.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not asking about connective tissue disease per se, but what occurs during an actual Raynaud event (for a better way of putting it), not what precipitates the condition to occur within a particular person and not another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;what are the underlying biological processes that cause the blood flow to be compromised like this?&lt;/p&gt;&#xA;" OwnerDisplayName="user22339" LastEditorDisplayName="user22339" LastActivityDate="2014-07-27T16:40:54.610" Title="What happens during a Raynauds episode?" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;blood-circulation&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11326" PostTypeId="1" AcceptedAnswerId="11327" CreationDate="2013-11-05T16:06:49.920" Score="1" ViewCount="259" Body="&lt;p&gt;Source 1:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/rYNf0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source  1 shows a map of a particular area. In this map you will find the  mountain ranges 1 and 2, the species P, Q and R. Two possible pedigrees of  the ancestral history of the species P, Q and R are drawn .&#xA;Which mountain range was formed first (historically) and which  pedigree is correct?&lt;/p&gt;&#xA;" OwnerUserId="4847" LastEditorUserId="3615" LastEditDate="2013-11-05T16:12:15.663" LastActivityDate="2013-11-05T16:21:51.783" Title="Which mountain range was formed first (historically) and which the pedigree is correct?" Tags="&lt;evolution&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11327" PostTypeId="2" ParentId="11326" CreationDate="2013-11-05T16:15:24.343" Score="2" Body="&lt;p&gt;If mountain range &lt;code&gt;1&lt;/code&gt; was formed first, pedigree &lt;code&gt;1&lt;/code&gt; is correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If mountain range &lt;code&gt;2&lt;/code&gt; was formed first, none of the two pedigree seem correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If mountain range &lt;code&gt;1&lt;/code&gt; was formed first you would first have the split of the initial population into population &lt;code&gt;P&lt;/code&gt; and the population &lt;code&gt;Q+R&lt;/code&gt;. Then, the formation of mountain range &lt;code&gt;2&lt;/code&gt; split the population &lt;code&gt;Q+R&lt;/code&gt; into &lt;code&gt;Q&lt;/code&gt; and &lt;code&gt;R&lt;/code&gt;. Therefore, &lt;code&gt;Q&lt;/code&gt; and &lt;code&gt;R&lt;/code&gt; are more closely related than they both are to &lt;code&gt;P&lt;/code&gt;. Therefore Pedigree &lt;code&gt;1&lt;/code&gt; is correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can apply the same kind of reasoning by guessing that mountain range &lt;code&gt;2&lt;/code&gt; was formed first and you will realize that you would expect a pedigree different than Pedigree &lt;code&gt;1&lt;/code&gt; and Pedigree &lt;code&gt;2&lt;/code&gt;. If mountain range &lt;code&gt;2&lt;/code&gt; appeared first then, the correct Pedigree would display the population/species/lineages &lt;code&gt;P&lt;/code&gt; and &lt;code&gt;Q&lt;/code&gt; more closely related to each other than they both are to &lt;code&gt;R&lt;/code&gt;. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-05T16:21:51.783" LastActivityDate="2013-11-05T16:21:51.783" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11328" PostTypeId="1" CreationDate="2013-11-05T16:44:10.067" Score="1" ViewCount="701" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;1: Is it true that the genetic variation of kale plants is smaller&#xA;  than wild cabbage?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think so, because of human selection of the kale plants.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;2: Are broccoli and cauliflower more sensitive to changing&#xA;  environmental conditions than wild cabbage?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think so, because domesticated crops have a lower genetic diversity than wild varieties. Genetic diversity is useful for adaptation&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;3: Is it a good recommendation to grow new Sprout plants from the&#xA;  seed of wild cabbage plants?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't think this is the best idea, because genetically engineered Sprout plants could be much better.&lt;/p&gt;&#xA;" OwnerUserId="4847" LastEditorUserId="6" LastEditDate="2013-11-06T07:05:28.843" LastActivityDate="2013-11-06T07:05:28.843" Title="Genetic variation and sensitivity of wild cabbage" Tags="&lt;evolution&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11329" PostTypeId="2" ParentId="11328" CreationDate="2013-11-05T17:14:23.307" Score="1" Body="&lt;p&gt;I am going to assume that Kale is a plant derived from wild cabbage and has been selected upon for certain attributes by humans for 1000's of generations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1 &lt;strong&gt;There are two principle reasons why genetic (allelic) diversity might be lower in the kale subgroup than in the wild cabbage.&lt;/strong&gt; Firstly, strong selection imposed by humans may have diminished allelic diversity. Strong selection can drive alleles to fixation. Secondly, if the kale has come from a small sub-population of the wild cabbage it may have been through a genetic bottleneck, this is likely to reduce allelic diversity because, unless all alleles from the original population are captured in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Founder_effect&quot; rel=&quot;nofollow&quot;&gt;founder populations&lt;/a&gt;, some alleles will be lost by &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_drift&quot; rel=&quot;nofollow&quot;&gt;genetic drift&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2 &lt;strong&gt;Generally allelic diversity is a &quot;good&quot; thing in an unstable environment.&lt;/strong&gt; It allows different trait combinations and variation in traits to occur. If the environment changes drastically then it could impose severe selective forces on the population, those with high allelic diversity are likely to come up with a combination of alleles that survives. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.g. Humans only allow the cabbages over 18cm in diameter to reproduce in to the next generation. 5 loci affect cabbage size, each having a &quot;large cabbage&quot; (C) allele and a &quot;small cabbage&quot; (c) allele. Having 5 c alleles gives a cabbage size of 15cm. Each C allele adds 1cm. If a population has fixed the c allele at 3 loci (i.e. there is low genetic diversity) then none of the cabbages will be &gt;18cm. If a population has both the C and c allele at all loci then some of the population will be over 18cm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3 &lt;strong&gt;The final question is difficult to answer,&lt;/strong&gt; it depends on what you define as &quot;a good recommendation,&quot;  that is very subjective. If the aim is to maximize allelic diversity then yes, if it is to maximize cabbage size it is probably no (because the &quot;genetically engineered&quot; plants have been selected upon for large cabbages - they might have the C alleles fixed in the populations!)&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-11-05T19:27:30.877" LastActivityDate="2013-11-05T19:27:30.877" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11330" PostTypeId="1" CreationDate="2013-11-05T18:09:03.320" Score="3" ViewCount="311" Body="&lt;p&gt;Instead of using a textbook, is there an alternative curriculum, that simply lists a set of pubmed research articles for each topic covered in a typical undergrad molecular biology course?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am currently learning molecular biology by reading a textbook.  Different chapters focus on different topics such as Cells and Genomes, Cell Chemistry, Proteins, DNA, Gene Expression, etc...  However, I'd prefer to learn these topics directly from research papers on pubmed.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;For example, I would imagine the DNA &quot;chapter&quot; of such a curriculum would include the Watson Crick paper on DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As another example, searching for &quot;Protein&quot; in pubmed reveals a ton of research papers, but which subset of them cover the topics taught in an intro molecular biology course?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Note: The pubmed articles don't have to be free or open access, I'm ok with getting the papers through my university library.  Also if an alternative curriculum such as this doesn't exist, maybe there is a supplemental one?  Or maybe you can recommend a set of papers that you'd include in such a curriculum?&lt;/p&gt;&#xA;" OwnerUserId="4849" LastActivityDate="2013-11-06T23:47:40.280" Title="How to learn molecular biology through pubmed research articles?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;proteins&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11332" PostTypeId="2" ParentId="11330" CreationDate="2013-11-05T19:26:10.347" Score="3" Body="&lt;p&gt;Tom Silhavy would use a similar method in the first year graduate Molecular Biology course.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;His text was basically a set of papers bound into a book &quot;&lt;a href=&quot;http://books.google.com/books/about/The_Power_of_bacterial_genetics.html?id=uG3wAAAAMAAJ&quot; rel=&quot;nofollow&quot;&gt;The power of bacterial genetics: a literature based course&lt;/a&gt;&quot;.  I'm not sure its in print anymore, but a used copy can be had.  If you find a copy you can just fetch the papers if you like. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can't do much better than finding excellent papers to read.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Briefly, the class covered the development of selection for mutations and mapping them onto genes - use of bacteriophage and replicate plating.  The papers started in the 40s and went on from there to the heyday of molecular biology.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was an awesome course to take... an awesome baptism of fire.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As they say... Whatever doesn't kill you, will select you for a distinguishing phenotype. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-11-06T20:06:30.493" LastActivityDate="2013-11-06T20:06:30.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11333" PostTypeId="1" CreationDate="2013-11-05T20:03:34.853" Score="2" ViewCount="1186" Body="&lt;p&gt;What are the mistakes in here?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image below shows a part of the energy flow diagram in an ecosystem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CFHnA.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1. Part P of the biomass of the primary producers does not get consumed. Give a concrete example of how this energy can get to the decomposers.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this energy can get to the decomposers, because the biomass simply dies. E.g. dead animals, dead trees, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. The amount of energy that is represented by R may end up with the decomposers in different ways. Name three ways.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can come up with natural cell dead (dissimilation after assimilation). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;3. The energy that is released through dissimilation, is not only released in the form of heat. What can this energy 'Q' be used for by the organism?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this energy (e.g. dissimilation of glucose) could be used for movements by the organism.&lt;/p&gt;&#xA;" OwnerUserId="4847" LastEditorUserId="4847" LastEditDate="2013-11-05T21:44:03.807" LastActivityDate="2014-12-05T09:22:10.953" Title="Energy flow in an ecosystem" Tags="&lt;homework&gt;&lt;ecology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11334" PostTypeId="2" ParentId="11316" CreationDate="2013-11-05T20:09:07.337" Score="0" Body="&lt;p&gt;I don't know a whole lot about signal processing but I am a little familiar with artificial intelligence. Perhaps this wiki would be helpful &lt;a href=&quot;http://en.wikipedia.org/wiki/Image_segmentation&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Image_segmentation&lt;/a&gt;. I am familiar with k-means clustering discussed there and as a trivial segmentation method it would indeed identify the cell versus the background of the photo. The Hough transformation would be more sophisticated and probably more useful for this application but if you want to get a sense of the process the naive k-means algorithm may be helpful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I interpret the &quot;lowest 20% of values&quot; to refer to the localization score values, the lowest being those who are darkest in your image. That is, the background the cell is imaged on. The background noise refers to the fact that a signal processing algorithm without any preprocessing may try to identify patterns from the background of the image rather than the cell subject matter, which is the part the researchers are after. This is why they perform the segmenting. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, imagine a k-nearest neighbors algorithm &lt;a href=&quot;http://en.wikipedia.org/wiki/K-nearest_neighbors_algorithm&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/K-nearest_neighbors_algorithm&lt;/a&gt; for computing a &quot;localization score&quot; for image brightness. Your paper is interested in the intensity of GFP for a cell. In the image, pixels on the border of the cell with its background will have artificially low score values because of the background: the adjacent pixels that are in the background and not part of the cell are dark, but that doesn't mean anything related to the biology of the problem. This is the noise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lowest 20% of values, then, should refer to a single image, not to a series over time.&lt;/p&gt;&#xA;" OwnerUserId="4851" LastEditorUserId="4851" LastEditDate="2013-11-05T20:19:35.920" LastActivityDate="2013-11-05T20:19:35.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11335" PostTypeId="1" CreationDate="2013-11-05T20:16:37.150" Score="8" ViewCount="422" Body="&lt;p&gt;I'm trying to identify this mushroom my sister found at her campus' lawn. It is brown, looks somewhat like a turtle or a brain and is growing inside of a dead tree trunk. Geographically the campus is in Haifa, Israel in case that helps. Any ideas?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Images:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jSsUm.jpg&quot; alt=&quot;turtle mushroom from the side&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/AMlCY.jpg&quot; alt=&quot;to get a sense of scale&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/xTvSQ.jpg&quot; alt=&quot;looks like a brain?&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4852" LastEditorUserId="4101" LastEditDate="2013-11-05T22:44:03.733" LastActivityDate="2019-02-05T15:38:59.147" Title="Strange looking mushroom found in a dead tree" Tags="&lt;species-identification&gt;&lt;mycology&gt;&lt;mushroom&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11336" PostTypeId="2" ParentId="11330" CreationDate="2013-11-05T20:40:26.410" Score="3" Body="&lt;p&gt;If you are interested in quantitative/systems biology, the reading list for a course like this at Princeton has been &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950154/&quot; rel=&quot;nofollow noreferrer&quot;&gt;published&lt;/a&gt; (with some context for each paper). I know this course reading list has also been taught at Stanford. They definitely look like good papers, and some of them are fairly recent.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;Edit: I remembered another book of classic literature I've heard is good: &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0879696028&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Landmarks of Cell Biology&lt;/a&gt;. If you look at the Table of Contents, you can get quite a few of the articles straight from PubMedCentral, and with a reasonable university license you can download the rest. It's been an inspiration to at least one rising star &lt;a href=&quot;https://sysbio.med.harvard.edu/biologists/sophie-dumont-phd-0&quot; rel=&quot;nofollow noreferrer&quot;&gt;professor&lt;/a&gt; at UCSF (link to a fun bio-sketch).&lt;/p&gt;&#xA;" OwnerUserId="4840" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-11-06T23:47:40.280" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11338" PostTypeId="1" CreationDate="2013-11-05T20:52:05.003" Score="2" ViewCount="36" Body="&lt;p&gt;Let's say I am growing cells under two conditions, and let's say I measure U1 snRNA levels in both using digital PCR.  If the U1 snRNA level is reduced in one sample, how safe is it to say that U1 snRNP is also reduced in that sample?&lt;/p&gt;&#xA;" OwnerUserId="4199" LastEditorUserId="3128" LastEditDate="2014-05-26T08:12:04.070" LastActivityDate="2014-05-26T08:12:04.070" Title="How closely correlated is the level of an snRNA with the level of its corresponding snRNP?" Tags="&lt;rna&gt;&lt;pcr&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11339" PostTypeId="1" CreationDate="2013-11-05T21:27:38.757" Score="3" ViewCount="79" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Millions of years ago fossil fuels originated from plants. A nitrogen&#xA;  atom from fossil fuel is now inside in a protein molecule in your&#xA;  body. What is the shortest path that the nitrogen atom could have&#xA;  taken starting with plants that lived millions of years ago, until the&#xA;  protein molecule in your body. Use those points:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;&lt;p&gt;consumers&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;producers&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;reducers&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;fossil fuels&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;$NO_x$&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I guess the route could be producers -&gt; reducers -&gt; fossil fuels -&gt; consumers -&gt; $NO_x$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But this could be wrong, because NO does not have to be produced by consumers.&lt;/p&gt;&#xA;" OwnerUserId="4847" LastActivityDate="2013-11-05T21:27:38.757" Title="Shortest route for a Nitrogen atom from fossil fuel to a protein in your body?" Tags="&lt;molecular-biology&gt;&lt;microbiology&gt;&lt;homework&gt;&lt;ecology&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-12-11T09:14:10.760" ContentLicense="CC BY-SA 3.0" />
  <row Id="11340" PostTypeId="1" CreationDate="2013-11-05T21:38:01.467" Score="1" ViewCount="54" Body="&lt;p&gt;Like, I am trying to learn more chemistry, but also computer programming from the higher-level programming methodologies, frameworks, languages, APIs, XML, web development, and I'm also hoping to improve especially with computer hardware/electrical engineering, and I am trying to improve my pixel art/graphic design/animation skills all at the same time, that is no set schedule for any, and just learning whatever I get my hands on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to learn this way for a human, or will this eventually become too much, and I'll have to sort them/order what I learn separately?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have not been seeing very much success, but I do keep learning. The problem? Well, I can't get a good grasp on any subject because I am interchangeably attempting to learn all of the aforementioned subjects sporadically, interchangeably, and without any fine schedule. Is this a wrong way for a human to learn, or is the human brain capable of constantly &amp;amp; linearly learning anything in any order very well?&lt;/p&gt;&#xA;" OwnerUserId="4853" LastActivityDate="2013-11-05T21:38:01.467" Title="Is there a limit to how much concise information a human can learn adequately?" Tags="&lt;brain&gt;&lt;information&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2014-07-22T17:55:33.500" ContentLicense="CC BY-SA 3.0" />
  <row Id="11342" PostTypeId="2" ParentId="9075" CreationDate="2013-11-05T22:10:16.150" Score="0" Body="&lt;p&gt;Maybe it serves to show others that we may be consuming something poisonous. We cry when we are sad to alert others of our distress. There may be better ways to show something is poisonous, but a child doesn't have any real way to alert who ever is feeding it that it may be poisonous. If I was feeding my baby something, and they had that reaction, I would not give that to them again. &lt;/p&gt;&#xA;" OwnerUserId="4855" LastActivityDate="2013-11-05T22:10:16.150" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11343" PostTypeId="1" CreationDate="2013-11-05T22:13:02.657" Score="3" ViewCount="1442" Body="&lt;p&gt;How do you determine if a plant is autotrophic or heterotrophic, and are there any traits in particular that can be used to classify species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As two examples, how should &lt;a href=&quot;https://en.wikipedia.org/wiki/Melampyrum_pratense&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Melampyrum pratense&lt;/em&gt;&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Broomrape&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Orobanche&lt;/em&gt;&lt;/a&gt; be classified?&lt;/p&gt;&#xA;" OwnerUserId="4854" LastEditorUserId="3624" LastEditDate="2013-11-08T09:35:28.933" LastActivityDate="2013-11-08T09:35:28.933" Title="How to determine if a plant is autotrophic or heterotrophic?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11345" PostTypeId="2" ParentId="11321" CreationDate="2013-11-06T00:45:55.173" Score="1" Body="&lt;p&gt;To answer your second question, one of the main reasons primers anneal before your target re-anneals to itself is not because it binds stronger, but because you add primers in large molar excess to their targets.  The primers will find your template faster than your template will find another matching template, and once the primer is annealed the template cant bind onto another template even if that reaction is more energetically favorable.  This molar excess is a requirement for the exponential amplification in PCR, and when you start to lose the excess primer concentration you lose exponential increase due to your targets re-annealing (and you get the production of unwanted PCR artifacts like chimeras).  As for the temperature, it depends on your template, but I guess it has to be somewhere between the primer annealing temp and the temp of your melting step.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-11-06T00:45:55.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11349" PostTypeId="2" ParentId="11316" CreationDate="2013-11-06T07:01:27.887" Score="1" Body="&lt;p&gt;Yep, the Hough Transform is a way to pick out shapes you're interested in, in this case they probably have it set to find circles, and they use that to segment the image.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that you have interpreted their methods correctly.  For each cell they make a trace of localization score vs. time, localization score defined in arbitrary units as the difference between the mean of the five brightest pixels and the mean of the remaining pixels in the cell.  I think the lowest 20% refers to the frames in the video that have the lowest 20% of localization scores.  They take the lowest 20% of localization scores, calculate a standard deviation, and then for any frame that has a localization score that is more than 1 standard deviation above the mean of those 20%, you say that frame exhibits a burst of localization.  If I'm understanding this correctly, this process would be repeated on every individual cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My interpretation is that the 20% doesn't have anything to do with the signal intensity from the background pixels, and it comes from analyzing the series over time, not a single image.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-11-06T07:01:27.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11350" PostTypeId="2" ParentId="11298" CreationDate="2013-11-06T07:20:03.263" Score="2" Body="&lt;p&gt;Rickettsia and Cyanobacteria are not part of a small clade that share these features.  ATP synthases are present across all domains of life, and they are all homologous, i.e. derived from a common ancestor.  The means its fairly likely that the last universal common ancestor had some form of ATP synthase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ETCs and ATP synthases are part of the chemiosmotic theory put forward by Mitchell.  Whats beautiful about this mechanism is that you just need a single ATP synthase to make your energy, and it can be used regardless of your metabolism, be it a Cyano or a Rickettsia.  All you need to do is somehow couple your metabolism to a proton motive force across your membrane, and then you just let the protons fall back down their electrochemical gradient, powering the formation of ATP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Organisms from all corners of the tree of life use this strategy, so this is not some special common feature linking the organisms that ultimately became eukaryotic organelles.  Its worth noting that there are alternatives to ETCs and proton motive force-based ATPases, you can make ATP by substrate-level phosphorylation like in fermentation metabolisms.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-11-06T07:20:03.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11351" PostTypeId="1" AcceptedAnswerId="19456" CreationDate="2013-11-06T09:35:22.113" Score="6" ViewCount="422" Body="&lt;p&gt;I am planning a fitness assay of &lt;em&gt;Drosophila melanogaster&lt;/em&gt;. I'd like to get a good measure of lifetime reproductive success (lrs) but I don't want to count all the offspring produced over a lifetime by 100's of focal flies. The solution I am toying with is to count offspring production over the first few days or weeks. But before I commit to this I need to know if there is existing research material on the following: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Does early reproductive output correlate well with lrs?&lt;/strong&gt; (this could be a low correlation if a fly trades early-life offspring production for late-life offspring production)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How much of a fly's reproductive output does one need to count before they have a good estimator of lrs?&lt;/strong&gt; (does counting the offspring produced in the first day of life correlate well to overall lrs or do I need to count more - 5 days, 10 days, 50 days...)&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="3952" LastEditDate="2015-04-20T20:03:48.417" LastActivityDate="2016-04-10T09:50:50.847" Title="Measuring fitness / lifetime reproductive success (LRS) in Drosophila" Tags="&lt;lab-techniques&gt;&lt;literature&gt;&lt;drosophila&gt;&lt;fitness&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11352" PostTypeId="2" ParentId="11343" CreationDate="2013-11-06T10:02:47.890" Score="2" Body="&lt;p&gt;This in part depends on how you define &lt;strong&gt;heterotrophic&lt;/strong&gt;. The most common definition is the inability to synthesise energy-containing molecules, most commonly by fixing carbon through photosynthesis (but dont forget &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemoautotroph&quot; rel=&quot;nofollow&quot;&gt;chemotrophs&lt;/a&gt;). However, I've sometimes seen definitions that also include dependency on external sources for nutrition (e.g. nitrogen) but also to supplement carbon sources. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using the first, main definition a lack of chlorophyll is a sufficient trait to define heterotrophic plants, which clearly places &lt;em&gt;Orobanche&lt;/em&gt; (lacks chlorophyll) in the heterotroph category. If you use the second definition you will include more species, but it also becomes much more tricky to draw the line between autotrophs and heterotrophs. I know that &lt;em&gt;Melampyrum pratense&lt;/em&gt; is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Parasitic_plant&quot; rel=&quot;nofollow&quot;&gt;hemiparasite&lt;/a&gt;, but don't know exactly to what extent, and therefore cannot say if it is accurate to label it as heterotrophic (using the second looser definition - it has fully functional photosynthesis). Checking whether a hemiparasitic plant can establish, survive and reproduce without its host should be a useful way to establish if it is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Obligate_parasite&quot; rel=&quot;nofollow&quot;&gt;obligate&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/Facultative_parasite&quot; rel=&quot;nofollow&quot;&gt;facultative&lt;/a&gt; hemiparasite (I suspect that &lt;em&gt;Melampyrum pratense&lt;/em&gt; will be found in the latter category). &lt;strong&gt;Myco-heterotrophy&lt;/strong&gt; can also be obligate and facultative, and can involve transfer of both carbon sources and nutrients, see &lt;a href=&quot;http://aob.oxfordjournals.org/content/104/7/1255.full&quot; rel=&quot;nofollow&quot; title=&quot;Merckx et al. 2009. Myco-heterotrophy: when fungi host plants. Annals of Botany 104(7).&quot;&gt;Merckx et al (2009)&lt;/a&gt; for a review. Insect-eating plants such as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Venus_flytrap&quot; rel=&quot;nofollow&quot;&gt;Venus flytrap&lt;/a&gt; are however sometimes called &lt;strong&gt;partial heterotrophs&lt;/strong&gt;, based on the fact that they get part/most of their nitrogen from insect trapping, while still obtaining their energy from photosynthesis. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-11-06T12:09:15.370" LastActivityDate="2013-11-06T12:09:15.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11353" PostTypeId="1" CreationDate="2013-11-06T10:57:06.853" Score="5" ViewCount="81" Body="&lt;p&gt;I am doing research in Lipid metabolism in different yeast species and I would like to look into ecology of them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to classify them to a Generalist/specialist based on different Parameters (growth on carbon sources, pH, temperature,...).&#xA;I wonder if you have any experiences with that classification and if any of you know which indexes are used for that in microbial ecology?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you very much for your answer!&#xA;Martin&lt;/p&gt;&#xA;" OwnerUserId="4860" LastActivityDate="2014-01-08T19:31:46.157" Title="Generalism - specialism index in microbial ecology" Tags="&lt;ecology&gt;&lt;yeast&gt;&lt;growth-media&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11354" PostTypeId="2" ParentId="10305" CreationDate="2013-11-06T12:40:48.497" Score="1" Body="&lt;p&gt;This is only a guess, maybe acetic acid, ie vinegar?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Acids are effectively hydrogen salts, but the acetyl ion might be alkaline like the hydroxyl ion, making acetic acid less acidic than most? As in water, pH neutral, is a combination of hydrogen and hydroxyl, H and OH, ions?&lt;/p&gt;&#xA;" OwnerUserId="4862" LastActivityDate="2013-11-06T12:40:48.497" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="11355" PostTypeId="2" ParentId="11330" CreationDate="2013-11-06T14:46:22.053" Score="1" Body="&lt;p&gt;There are in fact various books where each chapter is written like a published review. These are not text books, but they are very technical. Off the top of my head I can think of this one for example:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hatfield DL, Berry MJ, Gladyshev VN. Editors. (2011) Selenium: Its molecular biology and role in human health, 3rd Edition. Springer. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Like all such books, it consists of various chapters, each of which is a short review of the relevant topic by leading authors in the field. The problem with this is that a certain level of knowledge is assumed. Using your example, you won't be able to understand the original DNA paper if you don't understand the results of X-Ray crystalography experiments. Published articles assume that the reader is already an expert and they won't explain basic concepts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A better way would be to read your textbook and then, once you have read and understood a chapter, look into that chapter's references and read through those. Most serious textbooks include published articles at the end of each chapter, if yours does not, get a new textbook.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, another choice would be to read a review article. Those of the &lt;a href=&quot;http://www.cell.com/cellpress/trends&quot; rel=&quot;nofollow&quot;&gt;Trends&lt;/a&gt; and &lt;a href=&quot;http://www.current-opinion.com/default.aspx&quot; rel=&quot;nofollow&quot;&gt;Current Opinion&lt;/a&gt; series are particularly good. They tend to be very well written and, most importantly, highlight the seminal papers in their references. Just pick one that is about a subject you are interested in and then look at the references. The important papers in the field will be marked with &lt;code&gt;•&lt;/code&gt; and seminal works with &lt;code&gt;••&lt;/code&gt;. So, read the review and then read the &lt;code&gt;••&lt;/code&gt; papers.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-11-06T14:46:22.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11356" PostTypeId="2" ParentId="10986" CreationDate="2013-11-06T17:15:20.193" Score="3" Body="&lt;p&gt;I have written a &lt;a href=&quot;https://dl.dropboxusercontent.com/u/14062712/ensembl_get_codon_count.pl&quot; rel=&quot;nofollow&quot;&gt;script&lt;/a&gt; that will get you started. It downloads all protein coding transcripts of the species of interest from Ensembl and prints the codon use for each codon on each transcript. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will need to install the &lt;code&gt;Bio::EnsEMBL::Registry&lt;/code&gt; Perl module, see &lt;a href=&quot;http://www.ensembl.org/info/docs/api/api_installation.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for instructions. The script also uses the &lt;a href=&quot;http://search.cpan.org/~grommel/Math-Round-0.06/Round.pm&quot; rel=&quot;nofollow&quot;&gt;&lt;code&gt;Math::Round&lt;/code&gt;&lt;/a&gt; module, everything else should be installed by default with your Perl distribution. Finally, the script expects to be run from a Unix/Linux operating system.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Example run&lt;/h3&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; ensembl_get_codon_count.pl human &amp;gt; human.csv&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;h3&gt;Example output&lt;/h3&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Gene Name   Gene ID      Transcript ID  Ala_GCC Ala_GCC_% Ala_GCA Ala_GCA_% Ala_GCG Ala_GCG_% Ala_GCT Ala_GCT_%&#xA;CRLF2   ENSG00000205755 ENST00000400841    6       40        6      40         0       0         3       20&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;In the example above, the transcript ENST00000400841 of the human CRLF2 gene, contains a total of 15 Alanine residues, 6 of which are coded for by the GCC codon (40%), 6 by the GCA codon (40%) and 3 by the GCT codon (20%). The GCG codon is not used (0%). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a cut version of the output, the actual output lines are much longer since they include all codons and there will be one line per protein coding transcript.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This script should at least get you started since it will provide you with the raw data needed to perform your statistical analyses. If you use it in published work, I would appreciate it if you could let me know (my email is included in the script) and perhaps mention me in the acknowledgements :). &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-11-06T17:15:20.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11357" PostTypeId="1" CreationDate="2013-11-06T17:28:25.000" Score="2" ViewCount="545" Body="&lt;p&gt;This was a test question, and I'm not too sure about the answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which statement about phenotypic plasticity is false?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a. Because the plasticity of a phenotypic trait may be costly to maintain, it will not be favoured in stable environments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b. A trait that is an adaptation will not vary with environmental conditions within one generation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c. Phenotypic plasticity can itself be an adaptation to varying environmental conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;d. Variation in phenotype among populations of a given species across different environments is only caused by phenotypic plasticity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you could explain the answer to me, that would be great.&lt;/p&gt;&#xA;" OwnerUserId="4863" LastEditorUserId="1306" LastEditDate="2013-11-06T18:12:27.483" LastActivityDate="2013-11-07T17:52:05.930" Title="Which statement about phenotypic plasticity is false?" Tags="&lt;evolution&gt;&lt;homework&gt;&lt;ecology&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="11358" PostTypeId="2" ParentId="11357" CreationDate="2013-11-06T19:12:37.853" Score="2" Body="&lt;p&gt;I think the answer should be (d) as variation in phenotype among populations of species living in different environments are not caused only by phenotypic plasticity, they may also be caused by genetic differences which arose due to different selective pressures.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-11-06T19:12:37.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11359" PostTypeId="2" ParentId="10380" CreationDate="2013-11-06T21:40:24.073" Score="2" Body="&lt;p&gt;My answer is limited to sheep.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;The metabolites referred to as ketone bodies (which I will refer to as ketones from now on) are acetoacetate and β-hydroxybutyrate. In humans these are produced in the liver when the amount of acetoacetyl CoA being produced exceeds the capacity of the TCA cycle. These acetyl groups are instead used to produce acetoacetate, and this can be reduced to β-hydroxybutyrate.&lt;/p&gt;&#xA;&lt;p&gt;The production of significant amounts of ketones occurs during fasting (diabetic ketosis will not be considered here). Once glycogen has run out, the bodies requirement for glucose has to be met by gluconeogenesis (mainly in the liver) - glucose is synthesised from various carbon skeletons including glycerol and the products of amino acid catabolism (coming from muscle protein turnover). This means that in the liver the function of the TCA cycle shifts almost entirely to supplying oxaloacetate for gluconeogenesis, via the activity of phosphoenolpyruvate carboxykinase. Thus there is no oxaloacetate available for citrate synthase, so acetyl CoA cannot enter the TCA cycle. However, because fasting also results in fat mobilisation the level of acetyl CoA in liver cells goes up (acetyl CoA is the end product of fatty acid breakdown).&lt;/p&gt;&#xA;&lt;p&gt;So what is going on here? During fasting the fuel economy of the body has to switch from being heavily glucose-based to one which uses carbon from fat and from protein. The ketones are the manifestation of this, and many tissues become heavy users of ketones during fasting as blood levels rise to 5 mM within a few days. This means that the glucose being produced by the liver can be directed towards tissues which are more dependent upon glucose. The classic example of such a tissue is the brain, but in humans even the brain begins to use ketones heavily during fasting.&lt;/p&gt;&#xA;&lt;p&gt;In ruminants the situation is entirely different. Ruminants rely upon the bacteria in the rumen to metabolise carbohydrate in their diet and this results in large amounts of alimentary ketones entering the blood directly. For their glucose supply ruminants rely entirely upon gluconeogenesis, and the substrate for this is propionate, another end product of bacterial metabolism in the rumen: a lactating dairy cow will synthesise over 3 kg of glucose per day.&lt;/p&gt;&#xA;&lt;p&gt;So, when I read this question my reaction was that the statement must be incorrect - surely it would make sense for sheep to use ketones in all tissues. However my intuition was wrong - according to&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Pell JM.&amp;amp; Bergmane N(1983) Cerebral metabolism of amino acids and glucose in fed and fasted sheep. Am. J. Physiol. 244: E282-E289&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;cited in&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Heitmann RN &lt;em&gt;et al.&lt;/em&gt; (1987) Hepatic ketogenesis and peripheral ketone body utilization in the ruminant. J. Nutrition 117: 1174-1180&lt;/p&gt;&#xA;&lt;p&gt;&amp;quot;Although there is some oxidation of ketone bodies by the brain tissues of humans and rats during prolonged fasting, Pell and Bergman ,using an elegant in vivo preparation, have shown no significant uptake or oxidation of ketone bodies by sheep brain.&amp;quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I don't have access to the Pell &amp;amp; Bergmane paper so I cannot explain what they actually did. What is clear from the review by Heitmann &lt;em&gt;et al&lt;/em&gt;. however is that fasting ruminants respond in the same way that we do, switching to hepatic ketogenesis, and presumably they also maintain gluconeogenesis, using not propionate, but amino acid carbon skeletons. The context of the statement quoted above suggests that even in the fasted state the sheep brain doesn't use ketones.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-11-07T06:47:35.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11360" PostTypeId="2" ParentId="11357" CreationDate="2013-11-06T21:50:47.257" Score="4" Body="&lt;p&gt;I'll try to answer but I'll encounter some difficulties: first because I don't know what you mean by &quot;plasticity&quot;. Does it mean non-reversible developmental plasticity or reversible flexibity. Then, because, I don't really like the word adaptation! Anyway'll try...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;a&lt;/code&gt;: Plasticity  is some kind of mechanism allowing organisms to adapt to various environment. If the environment is stable and under the assumption the plasticity is associated with a intrinsic (physiological for example) cost, then a population would tend to evolve so that they always display the most optimal phenotype. I would argue that this is under the assumption that we gave enough time for the right mutations happen and under the assumptions that such mutation might exist!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;b&lt;/code&gt; I don't really understand this statement. Does it mean that between two generations (which mean in one generation time) an adaptation cannot vary.…in what terms? in frequency? Through time any trait vary because of selection, environment, genetic drift and mutations. And to what environment is the trait under consideration adapted for? Can we accept that the environment is changing from one generation to the other in this question? What does this question has to do with plasticity? I guess that when one says that a trait is an adaptation it means (among other things) that the population has no more variance for this trait. Therefore, only mutations would bring variations if there were no environmental change making the trait not adaptive anymore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;c&lt;/code&gt;: Well, yes. Plasticity is an adaptation to fluctuating environment. It allows to display a rather optimal phenotype in multiple different environments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Answer &lt;code&gt;d&lt;/code&gt; is wrong for sure. There is variation within a population due to genetic variance and non-adaptive environmental variance (and their interactions). Variance due to plasticity is just some kind of subset of the variance du to the genetic-environnment interaction&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps a bit!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-07T17:52:05.930" LastActivityDate="2013-11-07T17:52:05.930" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11361" PostTypeId="1" AcceptedAnswerId="11363" CreationDate="2013-11-07T01:40:18.737" Score="5" ViewCount="3152" Body="&lt;p&gt;I thought that the definition of species is &quot;can interbreed&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;https://en.wikipedia.org/wiki/Wildcat&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The wildcat (Felis silvestris) is a small cat found throughout most of&#xA;  Africa, Europe, and southwest and central Asia into India, China, and&#xA;  Mongolia. Because of its wide range, it is classed by the IUCN as&#xA;  Least Concern. However, crossbreeding with housecats is extensive and&#xA;  has occurred throughout almost the entirety of the species' range.[2]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So why does it have a different name than the house cat?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;https://en.wikipedia.org/wiki/Species&quot; rel=&quot;nofollow&quot;&gt;Species&lt;/a&gt; at Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, the difficulty of defining species is known as the species problem.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;While I understand that sometimes problems arise, what makes biologist mark the wild cat as a distinct species from the house cat? If they are genetically different, how different?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Donkeys can breed with horses. The result is sterile. Tigers can breed with lions with lots of complication. Wildcat seems to interbreed with housecat without problem whatsoever. Or does it? That's actually the essence of the question.&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="3624" LastEditDate="2014-10-02T22:29:45.943" LastActivityDate="2014-10-02T22:29:45.943" Title="Are wild cats the same species as house cats?" Tags="&lt;evolution&gt;&lt;taxonomy&gt;&lt;phylogenetics&gt;&lt;hybridization&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11363" PostTypeId="2" ParentId="11361" CreationDate="2013-11-07T09:13:59.880" Score="6" Body="&lt;p&gt;There are many definitions of species - look at the &lt;a href=&quot;https://en.wikipedia.org/wiki/Species&quot;&gt;wikipedia page&lt;/a&gt; for an overview (this is a large and tricky subject). Some hybridization is not uncommon between &quot;proper&quot; species (often in narrow contact zones), also with fully or partially fertile hybrids. Definitions of species in these cases often comes down to genetic similarity/dissimilarity of populations. Even though hybridization is taking place it usually does so at very low rates, so the gene pools stay relatively distinct. The &lt;em&gt;biological species concept&lt;/em&gt; (which is what you are referring to) is also problematic when it comes to e.g. &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/devitt_01&quot;&gt;ring species&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for wild cats and domestic cats, my feeling is that modern evidence (e.g. molecular studies and phylogenies) places domesticated cats firmly as a subspecies of wild cats (Driscoll &lt;em&gt;et al&lt;/em&gt;. &lt;a href=&quot;http://www.sciencemag.org/content/317/5837/519.abstract?ijkey=5518ddd37586e97b77c5285ab20a5dfe24c8c1e0&amp;amp;keytype2=tf_ipsecsha&quot;&gt;2007&lt;/a&gt;, &lt;a href=&quot;http://www.pnas.org/content/106/Supplement_1/9971&quot;&gt;2009&lt;/a&gt;), with the domesticated cat as &lt;em&gt;Felis silvestris catus&lt;/em&gt;. In the study by &lt;a href=&quot;http://www.pnas.org/content/106/Supplement_1/9971&quot;&gt;Driscoll &lt;em&gt;et al&lt;/em&gt;. (2009)&lt;/a&gt;, domesticated cats fall in the same mtDNA clade as &lt;em&gt;F. silvestris lybica&lt;/em&gt;. However, domesticated cats were traditionally described as a separate species (by Linnaeus), and this has stuck and some still label them as separate species (as does &lt;a href=&quot;http://www.vertebrates.si.edu/msw/mswcfapp/msw/index.cfm&quot;&gt;Mammal Species of the World&lt;/a&gt;). I can imagine that some who argue for species status now might use a mixture of ecological, phenetic, and biological species definitions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From Driscoll &lt;em&gt;et al&lt;/em&gt;. (2009):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In contrast, the world's domestic cats carried genotypes that differentiated them from all local wildcats except those from the Near East. Domestic cats show no reduction in genetic diversity compared with the wild subspecies (37), thus giving no indication for a founding genetic bottleneck. Multiple genetic analyses produced concordant results, in each case tracing the maternal origins of cat domestication to at least 5 wildcat lines (A through E, Fig. 2B) originating in the Near East. The domestic cat is referred to as a sixth subspecies, F. silvestris catus, although it is clear that domestic cats derive very recently from F. silvestris lybica (37). &#xA;  &lt;br&gt;&lt;br&gt;&#xA;   ... the vast majority of sampled domestic cats fall into the same mtDNA clade, which also includes F. silvestris lybica...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is also evidence that hybridization can help adaptation by facilitating gene transfer (even though hybrid fertility/viability might be low), so you might want to check out e.g. results from the &lt;a href=&quot;http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11041.html&quot;&gt;Heliconius Genome Consortium (2012)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="1320" LastEditDate="2013-11-07T12:47:01.297" LastActivityDate="2013-11-07T12:47:01.297" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="11365" PostTypeId="2" ParentId="8995" CreationDate="2013-11-07T15:28:25.943" Score="5" Body="&lt;p&gt;Have you ever tried to read a complicated book after several hours of hard work that required a high concentration? Imagine that you have forced a particular area of your brain. After a hard work, the areas of the brain that we used to finish a work seem don't respond to any stimulation and make us feeling tired and as we can't understand what we are doing anymore. This happens because we have forced that particular area of the brain and it needs to reinforce the connections it made and to do this, it has to sleep, such as we do during the conscious (you know you are going to sleep) sleeping. Eventually we can say that some particular areas of our brain must sleep if forced to a hard work and they do it when you feel like you can't get something which you know you can. A recent study has demonstrated this by understanding physiological functions of sleeping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nature article of Vyazovsky V. et al. Vol. 472, pages 443-447, April 2011 (I am not copying the link anyway, have to search it by yourself). Or to Science of Bushey D. et al. Vol. 332, pages 1576-1581, June 2011. And on Nature Review Neuroscience of Diekelmann S. And Born J. Vol 11 number 2, pages 114-126, February 2010.&lt;/p&gt;&#xA;" OwnerUserId="4818" LastEditorUserId="6" LastEditDate="2013-11-07T21:39:11.953" LastActivityDate="2013-11-07T21:39:11.953" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11367" PostTypeId="1" CreationDate="2013-11-07T15:35:44.437" Score="2" ViewCount="504" Body="&lt;p&gt;I am looking to start doing some work tracking the size and growth of individual bacterial cells in the microscope. In order to analyze the images I need software that can segment the cells, accurately determine their shape, and track cell lineages on a 'movie' of images collected from one experiment. Given the constraints of my microscope setup, the easiest thing for me to do is to use a strain of bacteria constitutively expressing GFP and segment the cells based on fluorescent intensity. This is functionally equivalent to segmented phase-contrast images of wild-type cells, i.e. I'm not that interested in changes in fluorescence or using fluorescence as a gene expression reporter, though my needs may head in that direction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't want to reinvent the wheel (and I think that it's better if the community consolidates around a few programs that everyone uses so that experiments can be more comparable), so I'm looking for a previously published package that is robust and easy to use. Flexibility at measuring fluorescent tracking is nice, but at this stage is not crucial. The two packages that I have seen are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22179594&quot; rel=&quot;nofollow&quot;&gt;Schnitzcells&lt;/a&gt; from the Elowitz lab at CalTech and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21414037&quot; rel=&quot;nofollow&quot;&gt;Microbetracker&lt;/a&gt; from the Emonet and Jacobs-Wagner groups at Yale. Unfortunately they were released at the same time and don't provide a good comparison of the pros/cons of each tool.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, my question is &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What are your recommendations for an image analysis suite (from the two packages above or another package you have used)?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Let me know if I can make my criteria more clear or anything else. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2014-04-18T05:20:49.003" Title="Image Processing Suite for bacterial microscopy: Schnitzcells or MicrobeTracker?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;microbiology&gt;&lt;bacteriology&gt;&lt;microscopy&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11368" PostTypeId="1" CreationDate="2013-11-07T16:21:32.167" Score="6" ViewCount="725" Body="&lt;p&gt;My daughter (10th grade) is doing a science fair project on the toxicity of triclosan for the algae Selenastrum capricornutum. She is wondering the best way to measure the effect, given the limited resources at the school. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Should she use the school’s UV/Vis spectrophotometer or just do low-tech cell counting?  &lt;/li&gt;&#xA;&lt;li&gt;If she uses the UV/Vis, does she have to do a calibration curve where she manually counts the cells for some number of data points?  &lt;/li&gt;&#xA;&lt;li&gt;Or can she just compare %absorbance to the controls and before/after numbers?  &lt;/li&gt;&#xA;&lt;li&gt;Or is it already know for this particular algae at a particular wavelength that a certain %absorbance equals a certain number of cells?  &lt;/li&gt;&#xA;&lt;li&gt;If she uses the UV/Vis, does that indicate the total number of cells, dead or alive, or does it only measure live cells? &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The trial is over 96 hours.    Thanks!&lt;/p&gt;&#xA;" OwnerUserId="4866" LastEditorUserId="4866" LastEditDate="2013-11-07T17:04:17.287" LastActivityDate="2013-11-08T10:01:36.047" Title="Measuring algae growth or death" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11371" PostTypeId="1" CreationDate="2013-11-08T03:07:35.810" Score="3" ViewCount="159" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Retrotransposon&quot; rel=&quot;nofollow&quot;&gt;retrotransposons&lt;/a&gt; and certain &lt;a href=&quot;http://en.wikipedia.org/wiki/Transposable_element&quot; rel=&quot;nofollow&quot;&gt;DNA-transposons&lt;/a&gt;, are &quot;jumping&quot; sequences which may be incorporated elsewhere in the genomic DNA of an organism, through varying mechanisms. This insertion is almost random in case of retrotransposons and most DNA-transposons, but some transposing enzymes show specificity in selection of insertion sites. In either case, the &quot;copy-paste&quot; mechanism of transposition is essentially a random process(considering the frequency and place of transposition) and therefore, the extent of transposition should vary among all individuals, and all cells of a single individual. My question is,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is the extent of transposition random and varied among the different&#xA;  somatic cells of an individual or is there a regulatory mechanism which ensures that&#xA;  there is not much difference in the net content of DNA (caused by unequal transposition) by equalizing&#xA;  the extent of transposition in different individuals or different&#xA;  cells of the same individual? If not, does this unequal c-value in different cell cause any troubles?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2013-12-05T16:43:03.963" LastActivityDate="2014-01-05T09:46:29.413" Title="Transposons and the net amount of DNA" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11373" PostTypeId="1" AcceptedAnswerId="11375" CreationDate="2013-11-08T04:54:22.120" Score="8" ViewCount="1191" Body="&lt;p&gt;I'm investigating how hierarchical groups of a larger organization with a common goal tend to come to conflict with one another over time.  As you decompose a large group (for example a corporation), peer groups may compete in an effort to accomplish short-term goals in an effort to further the corporation as a whole.  For example, two groups of software developers might fight for time on the corporations computer system to finish their immediate deadlines.  Though this typically can be resolved through mediation and compromise, there is a human element where one group might inflate the real need to use such a resource.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was then wondering if the same situation could ever arise in an ant colony.  Are ants truly purely social and never come to conflict within a colony?  Or can they end up fighting internally if food or space is ever scarce?&lt;/p&gt;&#xA;" OwnerUserId="4869" LastActivityDate="2016-06-06T22:44:05.723" Title="Do ants within a colony ever fight or come to conflict?" Tags="&lt;entomology&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11375" PostTypeId="2" ParentId="11373" CreationDate="2013-11-08T06:42:10.367" Score="4" Body="&lt;p&gt;There has been several major transitions (John Maynard Smith and Eors Szathmary) and systematically there is opportunity for conflict to arise…. and it does! There is conflict along genes within a chromosome (example the Psr gene of Nasonia vitripennis, see R. Trivers and A. Burt &lt;em&gt;Genes in conflict&lt;/em&gt;), along chromosome within an individual and along individual within a colony. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ants has been much studies (see E.O. Wilson, L. Keller, M. Chapuisat) and it has been found that there are tons of different reproduction system in those species. There are conflict between queens, between workers and between queen and workers to reproduce. In some species, a colony have several queens, in others, there are several queens fighting early in life for the right of being the unique queen. In some species, workers can fight to take over the queen and take her function. In some species, workers reproduce sometimes even if there is a queen. There is conflict over who will survive depending on how much related one is to the other one. For example, there is conflict over sex-ratio, the queen is as much related to her sons than to her daughters but the workers are more related to their sisters than to their brothers (because of haplo-diploidy, see Robert Trivers).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are various factors limiting the conflicts: high relatedness (Hamilton, Trivers), Cost of a fight, absence of information, power asymmetries. Ants evolved various strategy. There is a &quot;police&quot; who kill worker's spawn. We might as well consider lineage selection that select for cooperative colonies (note that L. Lehmann and L. Keller argue that group selection and kin selection are the same concept!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I basically repeated some stuff I read (or learned in class) but I am personally not sure that all that makes sense! I don't know if really the frequency of conflicts is not simply related to the mutation-selection balance. Criticisms are welcome!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In reaction to your comment:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conflicts always have to do with reproduction or survival in evolutionary biology. One might make three categories of conflict:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1)Those involving the right of reproducing&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2)those involving the probability of dying (I prefer not to be a forager because forager have a very high mortality)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Those that concern the survival of kin individuals. The &quot;purpose&quot; (if I might use this agency way of speaking) of any one to to increase its inclusive fitness (Hamilton, but don't read Hamilton, there is lots of easy source of information on kin selection). Therefore, one will rather help its brother to survive rather than his cousin as it is more closely related to its brother. Similarly, beccause of the haplo-diploidy nature of sex determination system in hymenoptera, workers are more closely related to other workers than to the males while the queen is as much closely related to her daughters and sons. Therefore, we would expect a conflict over the sex ratio, queen trying to have a sex-ratio of 1:1 while the workers are trying to have a sex-ratio of 75:25 (if there is only one father).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want more specific information about sex-ratio in ants, kin selection, group selection please ask it in another post. Note that there is already some discussions one these subjects on Biology.SE. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-08T15:16:43.963" LastActivityDate="2013-11-08T15:16:43.963" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11376" PostTypeId="2" ParentId="5645" CreationDate="2013-11-08T07:12:05.387" Score="1" Body="&lt;p&gt;The lateral and axial resolution depends on the numerical aperture of your objective (lateral = lambda/2NA; axial = 2lambda/NA^2). You can improvee the axial resolution with FLI by using a confocal approach or with 2-photon microscopy (2PM). In 2PM you need absorption of two infrared photons to get emission. The probability of 2 infrared absorption depends quadratically on the excitation intensity. Therefore, fluorescence is restricted where the illumination beam is focused which give a better sectioning. An advantage of 2PM is the higher penetration depth and reduce phototoxicity. Indeed you can use 2 infrared photons to excite fluorophore which required visible excitation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Temporal resolution depends on the area you want to measure and the integration time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Resolution is limited by the diffraction. In the best case with the 3 imaging techniques you mentioned you can get ~200-300 nm in lateral resolution and 500 - 800 nm in axial resolution&#xA;Higher resolution can be achieved by using super resolution techniques. They are separated in two groups. The first one exploid the photo-physical properties of the fluorophore to excite and de-excite it. This allows to resolve sub-diffraction areas. This is the case STED (Stimulated emission depletion) microscopy or SSIM (saturated structured illimination microscopy). The second group use the fluctuation of the fluorophore emission to localize it better. It includes techniques such as STORM (STochastic Optical Reconstruction Microscopy, PALM (Photo-Activated Localization Microscopy) and SOFI (super-resolution optical ﬂuctuation imaging).&lt;/p&gt;&#xA;" OwnerUserId="126" LastActivityDate="2013-11-08T07:12:05.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11377" PostTypeId="1" AcceptedAnswerId="11386" CreationDate="2013-11-08T09:59:42.503" Score="6" ViewCount="33530" Body="&lt;p&gt;What is the difference between Coding Sequences (CDS) and cDNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are Coding sequences the sequences that is transcribed to mRNA and cDNA in contrast DNA obtained by reverse polymerization of matured mRNA?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastActivityDate="2019-10-04T12:18:01.153" Title="Difference between CDS and cDNA" Tags="&lt;dna&gt;&lt;molecular-genetics&gt;&lt;genomics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11378" PostTypeId="2" ParentId="11368" CreationDate="2013-11-08T10:01:36.047" Score="3" Body="&lt;p&gt;I don't think it's wise to use a spectrophotometer for this experiment, as it is a total count, i.e. it can't distinguish between dead and alive cells very well, and so she might not see a clear difference between her treated and untreated algae. If she has access to a haemocytometer and a good microscope, then she can count the living cells directly, and calculate the cells/ml using a simple formula.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This paper has a nice overview of how to count algae using a haemocytometer, and if her species of algae can swim, then she would need to use the iodine solution mentioned in here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://weis.science.oregonstate.edu/files/weis/Protocols/Symbiodinium/Cell%20Counts.pdf&quot; rel=&quot;nofollow&quot;&gt;http://weis.science.oregonstate.edu/files/weis/Protocols/Symbiodinium/Cell%20Counts.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="4872" LastActivityDate="2013-11-08T10:01:36.047" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11379" PostTypeId="1" CreationDate="2013-11-08T11:54:36.573" Score="1" ViewCount="336" Body="&lt;p&gt;I want to use the method of Single Cell Gel Electrophoresis (comet assay). I have many samples, but I don't have the appropriate microscope. So I have to preserve my slides until the time comes for staining and microscopic analysis. I've read many different protocols, and I can't decide which is the best. Also, after the staining and the analysis, I might need to reuse the same slide. Is that possible? and if yes, what should I do?&lt;/p&gt;&#xA;" OwnerUserId="4789" LastEditorUserId="107" LastEditDate="2013-11-08T13:25:27.727" LastActivityDate="2013-11-08T13:25:27.727" Title="Which is the best way to fix and preserve comet assay slides before staining with Ethidium Bromide?" Tags="&lt;lab-techniques&gt;&lt;dna-damage&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11380" PostTypeId="2" ParentId="11377" CreationDate="2013-11-08T12:05:23.947" Score="2" Body="&lt;p&gt;The definition of coding sequence is, to my mind, a little confusing. It is actually the sequence of DNA in the gene which has the &lt;strong&gt;same&lt;/strong&gt; sequence as the corresponding mRNA (except it has T instead of U). Now, you will often see definitions that say that the coding sequence is the DNA that is &lt;em&gt;transcribed&lt;/em&gt;, but this isn't really correct because during transcription the RNA polymerase actually copies (transcribes) the other strand of the DNA (i.e. the one that is complementary to the coding sequence). And I would go one step further and say that the coding sequence excludes introns. You could also refer to the &lt;em&gt;coding strand&lt;/em&gt; of the DNA, to encompass the entire transcriptional unit including introns as a way of referring to the strand which carries the coding sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are correct in your definition of cDNA (except its reverse transcription not reverse polymerisation). The the full-length cDNA sequence for a protein-coding gene will encompass the CDS but, as @terdon points out in his comment, will also include untranslated regions at the 5' and 3' ends.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-11-08T21:15:59.720" LastActivityDate="2013-11-08T21:15:59.720" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11381" PostTypeId="1" CreationDate="2013-11-08T13:32:20.383" Score="16" ViewCount="327" Body="&lt;p&gt;What is the best practice when preprocessing microarray data using a detection filter (on scanner p-value)?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose I have a microarray dataset that I have to normalize with Loess and correct with ComBat. When should I apply a detection filter, relative to the other steps in the process?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my experimental design, I have two pipelines to test:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Normalize per sample between 0 - 1&lt;/li&gt;&#xA;&lt;li&gt;ComBat&lt;/li&gt;&#xA;&lt;li&gt;Loess normalization between samples&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Loess normalization between samples&lt;/li&gt;&#xA;&lt;li&gt;ComBat&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Is there any best practice for the timing of applying a detection filter?&lt;/p&gt;&#xA;" OwnerUserId="3466" LastEditorUserId="27323" LastEditDate="2017-01-21T11:47:46.920" LastActivityDate="2021-05-17T06:06:45.820" Title="At which step should I apply a detection filter when preprocessing microarray data? (Before/After normalization, batch effects removal)" Tags="&lt;bioinformatics&gt;&lt;experimental-design&gt;&lt;microarray&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11383" PostTypeId="1" AcceptedAnswerId="11388" CreationDate="2013-11-08T14:14:26.457" Score="4" ViewCount="4463" Body="&lt;p&gt;What is the Pianka's Index?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;How does it work?&lt;/li&gt;&#xA;&lt;li&gt;How can one calculate this index?&lt;/li&gt;&#xA;&lt;li&gt;How often is it used?&lt;/li&gt;&#xA;&lt;li&gt;In what context do people usually use it?&lt;/li&gt;&#xA;&lt;li&gt;Can one infer any statistical significance with this index?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2017-10-24T18:55:12.403" LastActivityDate="2017-10-24T18:55:12.403" Title="Index of ecological niche overlap" Tags="&lt;ecology&gt;&lt;statistics&gt;&lt;theoretical-biology&gt;&lt;ecosystem&gt;&lt;community-ecology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11384" PostTypeId="1" AcceptedAnswerId="13528" CreationDate="2013-11-08T14:32:15.907" Score="7" ViewCount="391" Body="&lt;p&gt;I would like to have an example of application and a brief description/definition (two or three lines) of the following fields. I would like to understand the exact differences between them. Other related informations are also extremely appreciated e.g. if these are fields in growth, the name of the best researcher in that field, best institution etc.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Computational Ecology;&lt;/li&gt;&#xA;&lt;li&gt;Mathematical Ecology;&lt;/li&gt;&#xA;&lt;li&gt;Numerical Ecology;&lt;/li&gt;&#xA;&lt;li&gt;Statistical Ecology;&lt;/li&gt;&#xA;&lt;li&gt;Ecoinformatics.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4385" LastEditorUserId="4385" LastEditDate="2013-11-08T14:44:14.910" LastActivityDate="2013-11-18T04:15:00.660" Title="Definitions and examples of some math-releated ecology branches" Tags="&lt;bioinformatics&gt;&lt;ecology&gt;&lt;mathematical-models&gt;&lt;computational-model&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11385" PostTypeId="1" AcceptedAnswerId="15204" CreationDate="2013-11-08T17:21:19.427" Score="3" ViewCount="221" Body="&lt;p&gt;I am making mRNA by in vitro transcription for transfection purposes. There is a lot of literature about how protein expression is increased and innate immune activation is decreased by substituting uridine for pseudouridine and cytidine for 5-methylcytidine. I decided to try this, but my yield was lower and the mRNA was shorter than when using natural nucleotides. The papers all say they made the mRNA by simply using the new nucleotides in their in vitro transcription kits, but they never mention any further changes to the protocol. Now I would assume that since pseudouridine and 5-methylcytidine are a little different from the normal substrates for RNA polymerase that they might not be incorporated as quickly and the resulting reaction rate would slow down. It might be possible that the Polyadenylate polymerase that adds the polyA tail doesn't recognize the modified mRNA as well. Both a slower reaction rate and less efficient tailing could make a lower yield of shorter mRNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone here have any experience with IVT using modified nucleotides and can suggest something to improve yields?&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="1320" LastEditDate="2013-11-08T21:17:30.977" LastActivityDate="2014-02-21T00:04:25.420" Title="mRNA with Pseudouridine and 5-methylcytidine?" Tags="&lt;transcription&gt;&lt;mrna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11386" PostTypeId="2" ParentId="11377" CreationDate="2013-11-08T17:55:42.170" Score="13" Body="&lt;p&gt;The difference boils down to &lt;a href=&quot;http://en.wikipedia.org/wiki/Untranslated_region&quot; rel=&quot;noreferrer&quot;&gt;UnTranslated Regions&lt;/a&gt;. A CDS or coding sequence is the part of a transcript that is actually translated into protein. Therefore a CDS will (almost) always start with an AUG codon and stop at one of the three STOP codons (UAA,UGA,UAG).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The transcript however (note that I am referring to mature transcripts that have already been spliced so introns have been removed) will also contain the UTRs which are not actually translated into protein. A cDNA sequence is derived from the transcript by reverse transcription and will, therefore, also contain the 5' and 3' UTRs. For example, see this schematic diagram of an unspliced transcript:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MtXrs.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The CDS of the gene depicted in image above will only contain the ATG, the STOP and the two green regions (exons). The cDNA will contain all that and, in addition, the two UTRs. Of course, both the cDNA and the CDS will not contain the introns. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-11-08T17:55:42.170" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11387" PostTypeId="2" ParentId="10237" CreationDate="2013-11-08T18:01:03.287" Score="1" Body="&lt;p&gt;I'd make a comment if I could, but I don't think mRNA ever enters the ER. When a ribosome is building a protein destined for export or for being inserted into the membrane, it travels to the ER membrane and binds to a protein in that membrane called Sec61, which guides the new peptide sequence through the membrane. However the portion of the ribosome that reads the mRNA is always in the cytoplasm. So the mRNA never enters the ER, it just gets close the cytoplasmic side of the ER membrane.&lt;img src=&quot;https://i.stack.imgur.com/4SdWJ.png&quot; alt=&quot;Image of the protein translocation process&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have an image from a German website.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2013-11-08T18:01:03.287" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11388" PostTypeId="2" ParentId="11383" CreationDate="2013-11-08T20:47:15.923" Score="2" Body="&lt;p&gt;Pianka's index of niche overlap is defined in his papers from &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.es.04.110173.000413&quot; rel=&quot;nofollow&quot; title=&quot;Pianka. 1973. The Structure of Lizard Communities. Annual Review of Ecology and Systematics 4: 53-74.&quot;&gt;1973&lt;/a&gt; and &lt;a href=&quot;http://www.pnas.org/content/71/5/2141.full.pdf&quot; rel=&quot;nofollow&quot; title=&quot;Pianka. 1974. Niche Overlap and Diffuse Competition. PNAS 71(5): 2141-2145.&quot;&gt;1974&lt;/a&gt;, as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$O_{kl}=\dfrac{\sum_i^n{p_{il} p_{ik}}}{\sqrt{\sum_i^n{p_{il}^2} \sum_i^n{p_{ik}^2}}}$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $O_{kl}$ is the resource overlap between species $k$ and $l$, and since the index is symmetric $O_{kj} = O_{lk}$. $p_{ib}$ represents the proportion of resource $i$ that is used by species $b$. The index is a modification of one presented in &lt;a href=&quot;http://www.jstor.org/discover/10.2307/2459090?uid=3738744&amp;amp;uid=2&amp;amp;uid=4&amp;amp;sid=21102888267967&quot; rel=&quot;nofollow&quot; title=&quot;MacArthur &amp;amp; Levins. 1967. The Limiting Similarity, Convergence, and Divergence of Coexisting Species. American Naturalist 101: 377-385.&quot;&gt;MacArthur &amp;amp; Levins (1967)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As apparent from the formula, the only thing you need to calculate the index are estimates of resource use from the resources that both species depend on. The tricky part can be to determine how you calculate proportianal use of all resources. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't used the index myself, and cannot really say anything about how common it is. I have seen references to it though. &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.es.04.110173.000413&quot; rel=&quot;nofollow&quot; title=&quot;Pianka. 1973. The Structure of Lizard Communities. Annual Review of Ecology and Systematics 4: 53-74.&quot;&gt;Pianka (1973)&lt;/a&gt; use it to study overlap between lizard species, and how the distribution of niche overlaps differ between habitat types. I haven't seen any statistical tests on it, but you should be able to use resampling or bootstrap to determine the uncertainty in the index.  &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-11-09T07:35:33.887" LastActivityDate="2013-11-09T07:35:33.887" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="11389" PostTypeId="1" CreationDate="2013-11-08T21:01:12.737" Score="1" ViewCount="228" Body="&lt;p&gt;This is a pretty big task, and I have several work-arounds, but I am looking for an efficient way to go from PAS stained slides of lung tissue to defined ROI's over the whole slide (presumably via BLOB detection).  I am hoping to get every airway epithelium annotated as an ROI so I can get colorimetric/masking data from the ROI. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's the simply stated goal, but there are several issues along the way.  The imager we are using produces files in the &lt;a href=&quot;http://openslide.org/formats/mirax/&quot; rel=&quot;nofollow&quot;&gt;MRXS format&lt;/a&gt;.  &lt;a href=&quot;http://download.openslide.org/docs/JPatholInform_2013_4_1_27_119005.pdf&quot; rel=&quot;nofollow&quot;&gt;Satyanarayanan group's work&lt;/a&gt; at &lt;a href=&quot;http://openslide.org/&quot; rel=&quot;nofollow&quot;&gt;OpenSlide&lt;/a&gt; has been great in the initial hurtles of exporting the files into very large tiled TIFF files (~2-5GB each, under JPEG compression, generating a few hundred a week).  This has it's own bugs, but the mailing list has been solid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given a very large series of very large tiled TIFF files, what is the best way to train a BLOB (or other) detection method to find an ROI?  Using small images, I've gotten acceptable mapping with WIKA, but every time I try on larger images I run into errors and corruptions (when I don't run into memory limits).  Is ImageJ the best choice for this?  If so which plugins would you recommend trying?  I've used what comes FIJI and I've been exploring over others.  LOCI will load ~80% of the image correctly then run into tiling problems.  Given that you can't choose the ROI strictly on color, but human's can quickly ID it, I think a computer will be able to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have two systems I'm trying this on:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;64-bit Ubuntu, 32GB RAM, FX-9590 processor &#xA;64-bit Windows 7, 16GB RAM, 2x E5430 processor&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The Win7 machine is the one required for the imager, and I'm trying to do the analysis on the more powerful Ubuntu box.  &lt;a href=&quot;http://www.diagnosticpathology.org/content/8/1/92&quot; rel=&quot;nofollow&quot;&gt;Deroulers et al&lt;/a&gt; produced an interesting work on the subject, however, my group hasn't been able to implement the system as of yet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would prefer an open solution, but a proven solution with propitiatory software would also be acceptable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought the over-arching question would fit here, but if people think I should break it up and put smaller questions on SO, I will.  I'm just not sure we're tackling this the best way from slide to graph.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2013-11-08T22:17:23.513" LastActivityDate="2013-11-08T22:17:23.513" Title="Workflow for batch analysis of ROI in histology samples" Tags="&lt;bioinformatics&gt;&lt;software&gt;&lt;imaging&gt;&lt;histology&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="11390" PostTypeId="1" CreationDate="2013-11-08T22:39:56.350" Score="2" ViewCount="803" Body="&lt;p&gt;After scanning the microarray chip we get RAW data with different formats depending on the type of microarray used. However, these RAW data files can be normalized and processed to generate gene expression data matrix. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been trying to figure out what exactly is the result of the processed data and what is the format of that data. As I've seen so far, there's no specific format for processed data. Of course most of them agree that columns represent experiments and rows represent genes, but the additional information at the top, they're usually different but I'm not sure based on what. Can anyone suggest me with the most common used formats? Is there any additional information to that processed data file in case I wanted to apply classification on it?&lt;/p&gt;&#xA;" OwnerUserId="4759" LastActivityDate="2014-05-19T03:24:47.500" Title="Microarray gene expression matrix format" Tags="&lt;microarray&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="11392" PostTypeId="1" AcceptedAnswerId="11403" CreationDate="2013-11-09T06:50:59.383" Score="3" ViewCount="857" Body="&lt;p&gt;What is the physiological mechanism behind systemic hypertension resulting from obstructive sleep apnea?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2013-11-09T17:00:06.923" Title="Why does hypertension occur in obstructive sleep apnea?" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11394" PostTypeId="1" AcceptedAnswerId="13405" CreationDate="2013-11-09T07:48:38.213" Score="1" ViewCount="462" Body="&lt;p&gt;In &lt;a href=&quot;http://link.springer.com/article/10.1007/s10641-010-9606-0#page-1&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article the athors used the Standardized Selection Ratio (SSR) in order to infer what is the preferred host (anemone) of anemonefish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a quotation coming from their methods:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;  The “preferred host” of anemonefish was assessed calculating the “Standardized&#xA;Selection Ratio (SSR)” (values between 0 and 1) (Manly et al. 1993). Manly’s standardized&#xA;selection ratio represents the probability that an individual will use a particular habitat&#xA;type, taking into account the different resource availability. For each anemonefish species (i) inhabiting an anemone species (j), SSR was calculated as:&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;$$SSR = \frac{wi}{\sum{}{wj}} $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $wi = \frac{oi}{pj}$&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;    `Oi` is the relative frequency of the anemonefish species i and `pj` the relative frequency&#xA;of the anemone species j. Higher values of SSR indicate a strong preference for the&#xA;selected resource. The Log- Likelihood statistic (χ2L) (Manly et al. 1993) was used to&#xA;check the significance of the observed distribution under a null hypothesis of a random&#xA;host choice.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1402006772&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is the book they cite (Manly et al. 1993).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you help me understanding basically what they did and how they calculated their &lt;code&gt;SSR&lt;/code&gt; and p.values. If $wi = \frac{oi}{pj}$ what does &lt;code&gt;wj&lt;/code&gt; equals to?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-12T06:56:52.577" LastActivityDate="2013-11-12T06:56:52.577" Title="Standardized Selection Ratio (SSR)" Tags="&lt;ecology&gt;&lt;statistics&gt;&lt;biostatistics&gt;&lt;ecosystem&gt;&lt;community-ecology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11397" PostTypeId="1" AcceptedAnswerId="12404" CreationDate="2013-11-09T09:15:48.270" Score="2" ViewCount="963" Body="&lt;p&gt;How many Botulinum toxin molecules or grams are contained in one medical unit of Botox?&lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="1320" LastEditDate="2013-11-10T14:26:43.857" LastActivityDate="2013-11-10T14:26:43.857" Title="What is one Botulinum toxin medical unit?" Tags="&lt;bacterial-toxins&gt;&lt;dose&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="11400" PostTypeId="1" AcceptedAnswerId="44309" CreationDate="2013-11-09T14:02:58.320" Score="3" ViewCount="1217" Body="&lt;p&gt;The standard answer found in intro course to evolutionary biology to the question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;what is evolution?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is a change in allele frequency over time!&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I believe a complete definition should encompass the following concepts:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;mutations &lt;/li&gt;&#xA;&lt;li&gt;copy number variation (&lt;a href=&quot;http://en.wikipedia.org/wiki/Copy-number_variation&quot; rel=&quot;nofollow noreferrer&quot;&gt;CNV&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;codon usage&lt;/li&gt;&#xA;&lt;li&gt;chromosome numbers&lt;/li&gt;&#xA;&lt;li&gt;phenotypic change (whether heritable or not)&lt;/li&gt;&#xA;&lt;li&gt;Complex phenotypic trait such as plasticity and developmental noise&lt;/li&gt;&#xA;&lt;li&gt;maybe some other things...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My questions are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Would it be worth it to talk about phenotype in a definition of evolution?&lt;/li&gt;&#xA;&lt;li&gt;What are the alternative definitions that have been proposed?&lt;/li&gt;&#xA;&lt;li&gt;What is your definition?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Note: I would rather talk about genetic evolution, but if you think it is worth making one definition for genetic and cultural (and some other stuff maybe) evolution, you're free to suggest it!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2018-04-13T16:14:59.007" LastActivityDate="2018-04-13T16:14:59.007" Title="How to define &quot;evolution&quot;?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="11402" PostTypeId="1" CreationDate="2013-11-09T16:45:06.337" Score="1" ViewCount="44776" Body="&lt;p&gt;I'm 17 and I'm about 160 cm and my weight is 47 kg . I just want to know if I will still grow taller ?&lt;/p&gt;&#xA;" OwnerUserId="4881" LastEditorUserId="3615" LastEditDate="2013-11-09T17:28:13.297" LastActivityDate="2015-02-15T04:53:29.993" Title="Will I grow taller? How can i tell?" Tags="&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ClosedDate="2013-11-15T00:04:11.987" ContentLicense="CC BY-SA 3.0" />
  <row Id="11403" PostTypeId="2" ParentId="11392" CreationDate="2013-11-09T16:50:45.597" Score="3" Body="&lt;p&gt;From &lt;a href=&quot;http://www.nature.com/hr/journal/v32/n7/full/hr200973a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Obstructive sleep apnea syndrome and hypertension: mechanism of the linkage and 24-h blood pressure control&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;OSAS directly induces negative intrathoracic pressure and decreases pulmonary stretch receptor stimulation, chemoreceptor stimulation, hypoxemia, hypercapnia and microarousal. These changes potentiate various risk factors, including the sympathetic nervous system, renin-angiotensin-aldosterone system and inflammation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wmOy4.jpg&quot; width=&quot;500&quot; /&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Summary:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Low oxygen levels at night increase oxidative stress to the body inducing inflammatory reactions and damage to the interior of blood vessels&lt;/li&gt;&#xA;&lt;li&gt;Nitrogen monoxide production is decreased, decreasing flow-mediated dilation of blood vessels&lt;/li&gt;&#xA;&lt;li&gt;Frequent night-time awakenings bring elevated sympathetic nervous system activity&lt;/li&gt;&#xA;&lt;li&gt;During episodes of hypoxia, blood pressure and heart rate increase&lt;/li&gt;&#xA;&lt;li&gt;&quot;Increased sympathetic nervous activity may also cause coronary spasm and induce vasospastic angina pectoris.&quot;&lt;/li&gt;&#xA;&lt;li&gt;&quot;[P]eriodic negative intrathoracic pressure (−80 mm Hg, at most), together with a midnight surge of BP, exerts mechanical stress on the ventricular and atrial walls, resulting in the development of left ventricular hypertrophy and left atrial remodeling and, consequently, an elevated risk of heart failure and atrial fibrillation&quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerDisplayName="user4518" LastEditorDisplayName="user4518" LastEditDate="2013-11-09T17:00:06.923" LastActivityDate="2013-11-09T17:00:06.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="12403" PostTypeId="2" ParentId="11290" CreationDate="2013-11-09T17:01:04.337" Score="4" Body="&lt;p&gt;Note: This is NOT my field. However, given @biogirl's question, it appears that there aren't many people in this field in the first place. From what I can gather, here are the reasons why I think it has been difficult to study.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I. &lt;em&gt;The lac operon has strong polarity.&lt;/em&gt; By this I mean that when the lac operon is induced, &lt;em&gt;lacZ&lt;/em&gt; (the first gene in the operon) is translated much more than &lt;em&gt;lacA&lt;/em&gt; (the last gene in the operon). &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4863045&quot; rel=&quot;nofollow&quot;&gt;Measurements&lt;/a&gt; have recorded the molar ratio of $\beta$-galactosidase : thiogalactoside transacetylase (the protein products of &lt;em&gt;lacZ&lt;/em&gt; and &lt;em&gt;lacA&lt;/em&gt;) upon induction of the operon at 3:1 to 5:1; i.e. when the lac operon is induced 3 to 5 molecules of $\beta$-gal are produced for every one of the transacetylase. If you factor in the relative length of each of these proteins ($\beta$-gal is 1024 a.a.s, transacetylase is 203), &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15123418&quot; rel=&quot;nofollow&quot;&gt;it works out&lt;/a&gt; that &lt;em&gt;lacZ&lt;/em&gt; is being translated at least 10 times faster than &lt;em&gt;lacA&lt;/em&gt; when the lac operon is induced. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15123418&quot; rel=&quot;nofollow&quot;&gt;Sidney Altman's lab&lt;/a&gt; has attributed this to the fact that there is a cleavage site between &lt;em&gt;lacY&lt;/em&gt; and lacA where RNAses can cleave the nascent mRNA transcript, removing &lt;em&gt;lacA&lt;/em&gt; from the operon and reducing the production rate of transacetylase. So it appears the cell needs quite a bit less &lt;em&gt;lacA&lt;/em&gt; than &lt;em&gt;lacZ&lt;/em&gt;---if indeed they need it at all, see point 2---which makes it harder to study.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4863045&quot; rel=&quot;nofollow&quot;&gt;Brown JL, Brown DM, Zabin I. (1967). J Biol Chem. 242(18):4254-8.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15123418&quot; rel=&quot;nofollow&quot;&gt;Li Y, Altman S. (2004). J Mol Biol. 339(1):31-9.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;II. lacA &lt;em&gt;seems to provide only a small fitness advantage under somewhat contrived conditions.&lt;/em&gt; In &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/789355&quot; rel=&quot;nofollow&quot;&gt;A paper&lt;/a&gt; from the 70s researchers presented competition experiments between $lacA^{+}$ and $lacA^{-}$ strains in media with $\beta$-galactosides as the only carbon source. For 50 generations there was no competitive advantage of one strain over the other (ratio of $lacA^{+}$ : $lacA^{-}$ stayed at 1). When after 50 generations the researchers added a lot of IPTG, a non-hydrolyzable $\beta$-galactoside, $lacA^{+}$ outcompeted $lacA^{-}$; the &lt;a href=&quot;https://en.wikipedia.org/wiki/Fitness_%28biology%29#Absolute_fitness&quot; rel=&quot;nofollow&quot;&gt;absolute fitness&lt;/a&gt; of wild-type:mutant could be calculated to be $\approx 1.05$. This means that the wild-type produced 105 cells for every 100 produced by the mutant. I am not a population geneticist, so I don't know if that is a large value or not. For comparison, I used to work in cyanobacterial circadian rhythms, and the absolute fitness advantage for having a circadian clock with the same period as the light-dark cycle in the environment works out to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9671734&quot; rel=&quot;nofollow&quot;&gt;$&amp;gt;1.11$&lt;/a&gt;, which is twice as advantageous as the one reported for $lacA^{+}$ over $lacA^-$. In any case, the experimental situation in which $lacA^+$ has a competitive advantage seems rather contrived: growing with $\beta$-galactosides as the sole carbon source with a significant amount of non-hydrolyzable analoges around gumming up the $\beta$-galactoside metabolic machinery.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/789355&quot; rel=&quot;nofollow&quot;&gt;Andrews KJ, Lin EC. (1976). J Bacteriol. 128(1):510-3.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My read from these observations is that the physiological role of &lt;em&gt;lacA&lt;/em&gt; is challenging for a biologist to untangle due to the small size of its effect on bacterial physiology. Fitness advantages of 5% may certainly be useful on evolutionary timescales, but they suggest that the benefit afforded by the enzyme will be very hard to discriminate from noise or other confounding factors in the system. The fact that &lt;em&gt;lacA&lt;/em&gt; production is much lower than &lt;em&gt;lacZ&lt;/em&gt; in times of lac operon induction also would make it hard to measure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A postdoc I used to work with advised me, &quot;don't go looking for 2-fold changes in biology,&quot; by which he meant don't spend too much time on questions where the size of the effect you are looking at is minor and very difficult to distinguish from noise, bias, measurement error, or other confounding variables. Obviously there are limitations to this advice; a lot can be learned from the the combination of several seemingly minor effects that have big cumulative consequences for an organism. But as a rule of thumb, it's so hard to get strong results when your effect size is so small that going after small effects is justifiable only if you have a good reason to believe there is some profound, fundamental biology behind them. My view is that the consensus of the scientific community up to this point has been that untangling the role of &lt;em&gt;lacA&lt;/em&gt; in the lac operon and more broadly in bacterial physiology would involve too much work for too little payoff.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2013-11-09T17:01:04.337" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="12404" PostTypeId="2" ParentId="11397" CreationDate="2013-11-09T17:19:51.963" Score="4" Body="&lt;p&gt;1 unit is approximately 10 pg&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.rxlist.com/myobloc-drug.htm&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One unit of MYOBLOC (botulinum toxin type b) corresponds to the calculated median lethal intraperitoneal dose (LD50) in mice. The method for performing the assay is specific to Solstice Neurosciences' manufacture of MYOBLOC (botulinum toxin type b) . Due to differences in specific details such as the vehicle, dilution scheme and laboratory protocols for various mouse LD50 assays, units of biological activity of MYOBLOC (botulinum toxin type b) cannot be compared to or converted into units of any other botulinum toxin or any toxin assessed with any other specific assay method. Therefore, differences in species sensitivities to different botulinum neurotoxin serotypes preclude extrapolation of animal dose-activity relationships to human dose estimates. The specific activity of MYOBLOC (botulinum toxin type b) ranges between 70 to 130 Units/ng.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;UPDATE&lt;/p&gt;&#xA;&#xA;&lt;p&gt;10 pg of &lt;a href=&quot;http://en.wikipedia.org/wiki/Botulinum_toxin&quot; rel=&quot;nofollow&quot;&gt;toxin&lt;/a&gt; (150 kDa) is 4 x 10&lt;sup&gt;9&lt;/sup&gt; molecules&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-11-09T18:13:40.277" LastActivityDate="2013-11-09T18:13:40.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="12405" PostTypeId="2" ParentId="11402" CreationDate="2013-11-09T17:31:53.447" Score="6" Body="&lt;p&gt;I guess there are two main solutions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) From the science of &lt;a href=&quot;http://en.wikipedia.org/wiki/Anthropometry&quot; rel=&quot;nofollow&quot;&gt;antropometry&lt;/a&gt; you might find some clues of the probability that you have of growing taller. For example, if your body (hairs and stuff) already look like an adult body, then you would probably not grow much more. See @MCM's answer who gives a solution that will be way more useful to you than my answer!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Knowing the size of your parents you can infer your expected size. Below are some comments on this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any phenotypic trait has shows some part of variance. This variance is explained by genetic variance, environmental variance and the variance due to the interaction of genetic and environment. In equation it gives:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$V_P=V_G+V_E+V_{GxE}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dividing the genetic variance by the phenotypic variance gives the heritability&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$H=\frac{V_G}{V_P}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Estimations of heritability (in the narrow sense, see &lt;a href=&quot;http://en.wikipedia.org/wiki/Heritability&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; for more info) can also be realized with selection experiments or parent-offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heritability of height in humans is around 0.6 (Welcome to anyone who can give an accurate value and a good reference) which is quite high. It means that more than half of the variance in height among humans has to be accounted to genetic variance. If your parents are tall, don't lose hope, you have quite a good probability to grow tall.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-02-15T04:53:29.993" LastActivityDate="2015-02-15T04:53:29.993" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13403" PostTypeId="2" ParentId="11400" CreationDate="2013-11-09T18:22:43.070" Score="2" Body="&lt;p&gt;Theoretical biology spans multiple disciplines and the unaccompanied term &lt;em&gt;evolution&lt;/em&gt; is defined differently in each:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As such chemical evolution is different from time evolution in physics and many other systems in theoretical biology that &quot;evolve&quot;. These do play a role in theoretical biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, what &lt;code&gt;standard answer&lt;/code&gt; to &lt;code&gt;evolution&lt;/code&gt; in the field of theoretical biology are you referring to?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I recall learning that an allele as a special[:species:] gene variant, is defined as such as being present in at least one percent of the population. That definition has broadened &lt;a href=&quot;http://ghr.nlm.nih.gov/glossary=allele&quot; rel=&quot;nofollow&quot;&gt;meanwhile&lt;/a&gt;. A definition that has broadened.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Point in case, I don't believe there to be an evolutionary master-framework to (yet) exist, along the lines of desires for a &lt;em&gt;Theory of Everything&lt;/em&gt; in physics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, as soon as you cross the boundaries of biological evolution, like let's say in the most primitive of living, biological entities, you are bound to cross over to &lt;em&gt;cultural evolution&lt;/em&gt; as well. ( I am no expert on the subject, there are probably other intermittent steps as well). Synergistic effects in the process of evolution may even be considered in &lt;em&gt;Quorum Sensing's&lt;/em&gt; most favorite model: &lt;em&gt;Vibrio fischeri&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A simple search on the subject instantly yielded me:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Evolution of alkaline phosphatase in marine species of Vibrio&quot;. J Bacteriol....&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In other words: molecular evolution, as being part of the many evolutiony research focuses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea and gross effects of Darwinian evolution are often rather straightforward at first glance. All the little details, that have to be accounted for -with scientific rigor-, as science itself is evolving, are probably where the team-work starts, as do the discussion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the only fixture you can count on is &lt;em&gt;team&lt;/em&gt; in &lt;em&gt;science&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The introduction to the evolutionary topic at hand, that you would use in an abstract or introduction would depend on the scientific sub-discipline, and would likely already be readily available through peer-publication. &lt;/p&gt;&#xA;" OwnerUserId="1450" LastActivityDate="2013-11-09T18:22:43.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13404" PostTypeId="2" ParentId="11402" CreationDate="2013-11-09T18:35:54.890" Score="7" Body="&lt;p&gt;Simpler answer (although I like Remi.b's):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to know for sure go to a doctor and have them look at your Epiphyseal Plates in your long bones (Femur, Tibula, Fibula). If they've fused, you won't grow anymore. If they're still distinct then you'll continue to grow until they fuse. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For males that can happen as late as early-20's. However, depending on genetics, you might not gain that much height. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a graph you might be interested in:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uZSxd.png&quot; alt=&quot;United States growth rates until age 20&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You're at the tail-end of probably your last growth spurt. You have probably 2-3 years' worth of growing left, but don't expect miracles. You've got maybe another 1-2cm.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-11-09T18:35:54.890" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13405" PostTypeId="2" ParentId="11394" CreationDate="2013-11-09T18:57:39.007" Score="1" Body="&lt;p&gt;I can see why you might be confused! The authors chose bad notation, since the way they wrote it $w_i$ clearly depends not just on the choice of anenomefish species $i$ but also on the choice of anenome species $j$. And it is not clear how exactly they are performing their sum in the definition of SSR: sum over all possible anenome-anenomefish species pairs or only over all anenomefish species? The former makes sense but is extremely unclear, and the latter doesn't make sense because there's no way to interpret that as a probability that an anenomefish will choose a particular anenome because the sum of the SSR for all the different anenome species would not necessarily be 1, so the probability of an anenomefish species choosing &lt;em&gt;some&lt;/em&gt; species of anenome would not be 1! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;NOTE: The reference to Manly 1993 was incorrect (you cited a 1995 paper); they actually cite a book: Manly B, McDonald L, Thomas D (1993) Resource selection by animals. &lt;em&gt;Statistical design and analysis for field studies&lt;/em&gt;. Chapman and Hall, London. This would probably be the best place to look to get an exact answer to your question. I think that would be the best place to look first.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2013-11-09T18:57:39.007" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13408" PostTypeId="1" AcceptedAnswerId="13409" CreationDate="2013-11-10T03:15:02.523" Score="5" ViewCount="1096" Body="&lt;p&gt;Recently doing a little reading on interspecies hybrids I noticed that it seems interspecies hybrids are most often much larger than either parent.  Notably, Ligers, Dzo and Savannah Cats, but it seems like all or at least most.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a reason for this genetic expression in hybrids?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I am incorrectly inferring this to be the case let me know that instead.&lt;/p&gt;&#xA;" OwnerUserId="4884" LastEditorUserId="1320" LastEditDate="2013-11-10T10:42:34.467" LastActivityDate="2013-11-10T10:42:34.467" Title="Why are interspecies hybrids so often larger than either parent species" Tags="&lt;hybridization&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13409" PostTypeId="2" ParentId="13408" CreationDate="2013-11-10T03:59:39.690" Score="4" Body="&lt;p&gt;While they do not necessarily constitute the majority, it is true that there is a large number of interspecies hybrids whose members are larger in size than the parent species, and there exist explanations that account for this phenomenon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you are describing is an example of &lt;a href=&quot;http://www.macroevolution.net/heterosis.html#.Un8A9ZSxOpk&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;positive heterosis&lt;/em&gt;&lt;/a&gt;, or hybrid vigor.  While the rationale for plants is more complex, it commonly arises between related species in mammals as a sort of &lt;em&gt;heterozygote advantage&lt;/em&gt; in which the contrast in genetic contribution during conception spawns some phenotypic benefit.  The exact implementation of this varies from species to species, but &lt;a href=&quot;http://blogs.discovermagazine.com/gnxp/2009/09/why-ligers-are-huge/#.Un8AIpSxOpk&quot; rel=&quot;nofollow&quot;&gt;this link here&lt;/a&gt; is a nice, concise explanation for why ligers might be so large.&lt;/p&gt;&#xA;" OwnerUserId="4882" LastActivityDate="2013-11-10T03:59:39.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13410" PostTypeId="2" ParentId="11323" CreationDate="2013-11-10T04:44:34.530" Score="5" Body="&lt;p&gt;I have found one more possible reason from &lt;a href=&quot;https://www.goodreads.com/book/show/13400.Molecular_Biology_of_the_Cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bruce Alberts' &lt;em&gt;The Molecular Biology of the Cell&lt;/em&gt;&lt;/a&gt;: (Ch. 5 page 254)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nucleosomes are spaced at intervals of about 200 nucleotides pairs along the DNA strand , which may explain why new Okazaki fragments are synthesized on the lagging strand at intervals of 100-200 nucleotides in eukaryotes, instead of 1000-2000 nucleotides as in bacteria. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As already discussed by me and @SatwikPasani in the comments, increasing telomere longevity in eukaryotes by reducing the length of okazaki fragments, and consequently reducing the part of telomere cut-off after every division might be another reason for having shorter fragments in eukaryotes as compared to prokaryotes which do not contain telomeres.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt; : Having thought over it again, the relation between Okazaki fragment length and telomeres do not seem logical as only &lt;strong&gt;RNA primer&lt;/strong&gt; length is important when considering telomere length.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1101/cshperspect.a010173&quot; rel=&quot;nofollow noreferrer&quot;&gt;Balakrishnan and Bambara (2013)&lt;/a&gt; explain the regulation of (and differences between) prokaryotic and eukaryotic Okazaki fragments in detail.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3340" LastEditDate="2018-08-30T14:30:21.417" LastActivityDate="2018-08-30T14:30:21.417" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="13411" PostTypeId="2" ParentId="2281" CreationDate="2013-11-10T05:53:55.280" Score="3" Body="&lt;p&gt;Yes there are several published sources (with photos) of whales born with protruding vestigial legs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://digitallibrary.amnh.org/dspace/bitstream/handle/2246/4849/N0009.pdf;jsessionid=55D6453968F5461B1B6BFF8D53C81F16?sequence=1&quot; rel=&quot;nofollow&quot;&gt;http://digitallibrary.amnh.org/dspace/bitstream/handle/2246/4849/N0009.pdf;jsessionid=55D6453968F5461B1B6BFF8D53C81F16?sequence=1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Modern Right Whales have rudimentary legs--completely inside their bodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;approaching the inquiry with the most skeptical determination, one cannot help being convinced, as the dissection goes on, that these rudiments [in the Right Whale] really are femur and tibia. The synovial capsule representing the knee-joint was too evident to be overlooked. An acetabular cartilage, synovial cavity, and head of femur, together represent the hip-joint. Attached to this femur is an apparatus of constant and strong ligaments, permitting and restraining movements in certain directions; and muscles are present, some passing to the femur from distant parts, some proceeding immediately from the pelvic bone to the femur, by which movements of the thigh-bone are performed; and these ligaments and muscles present abundant instances of exact and interesting adaptation. &quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://etb-whales.blogspot.com/2012/03/hind-limb-rudiments-on-modern-whales_1221.html&quot; rel=&quot;nofollow&quot;&gt;http://etb-whales.blogspot.com/2012/03/hind-limb-rudiments-on-modern-whales_1221.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4886" LastActivityDate="2013-11-10T05:53:55.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13412" PostTypeId="1" AcceptedAnswerId="13424" CreationDate="2013-11-10T12:12:54.687" Score="1" ViewCount="148" Body="&lt;p&gt;Does a human body decompose in a completely sterile environment ? If yes, what decomposes it ? And how fast ? What happens in vacuum ? Can it remain exactly the same ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="4889" LastEditorUserId="3340" LastEditDate="2013-11-11T12:07:32.277" LastActivityDate="2013-11-11T12:07:32.277" Title="Body's decomposition" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13414" PostTypeId="1" AcceptedAnswerId="13443" CreationDate="2013-11-10T17:01:13.123" Score="17" ViewCount="1017" Body="&lt;p&gt;I found this photo in a &lt;a href=&quot;https://www.facebook.com/photo.php?fbid=628341997202095&amp;amp;set=a.370464582989839.74242.113791238657176&amp;amp;type=1&amp;amp;theater&quot; rel=&quot;noreferrer&quot;&gt;local news page&lt;/a&gt;. The page claims that this fish is a new species that was found by a Malaysian fisherman. Is this true or is it a known fish and already has a name?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LvGHD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user3130" LastEditorUserId="16866" LastEditorDisplayName="user3130" LastEditDate="2019-04-17T01:41:05.480" LastActivityDate="2019-04-17T01:41:05.480" Title="A weird-looking fish with a shield" Tags="&lt;species-identification&gt;&lt;zoology&gt;&lt;ichthyology&gt;&lt;marine-biology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13415" PostTypeId="1" CreationDate="2013-11-10T19:46:14.917" Score="7" ViewCount="3194" Body="&lt;p&gt;I've read about DNA sequence motifs, but still don't understand what makes some sequence a DNA sequence motif. Is this a well-defined concept? For, example, &#xA;&lt;a href=&quot;http://www.nature.com/nbt/journal/v24/n4/full/nbt0406-423.html&quot; rel=&quot;noreferrer&quot;&gt;What are DNA sequence motifs?&lt;/a&gt; says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sequence motifs are short, recurring patterns in DNA that are presumed&#xA;  to have a biological function. Often they indicate sequence-specific&#xA;  binding sites for proteins such as nucleases and transcription factors&#xA;  (TF). Others are involved in important processes at the RNA level,&#xA;  including ribosome binding, mRNA processing (splicing, editing,&#xA;  polyadenylation) and transcription termination.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For example, I've been working with Recombination Signal Sequences (RSS), which are important in immunology. However, from what I can tell, RSS are not themselves motifs, but they do contain motifs. E.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308075/&quot; rel=&quot;noreferrer&quot;&gt;Conservation of sequence in recombination signal sequence spacers&lt;/a&gt;&#xA;says&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Previously, the RSS has been described as possessing both a conserved heptamer and a conserved nonamer motif.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, apparently, the heptamer and nonamer component of the RSS are themselves motifs, but the RSS itself is not. Can anyone explain why? Thanks.&lt;/p&gt;&#xA;" OwnerUserId="284" LastActivityDate="2014-07-31T09:38:26.663" Title="What makes a DNA sequence motif a DNA sequence motif?" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13416" PostTypeId="1" CreationDate="2013-11-10T19:52:47.093" Score="4" ViewCount="2076" Body="&lt;p&gt;The amplification on vector transgenic microorganisms and the subsequent purification does not seem that complicated. Also, what are the processes that biotechnological industries follow, in detail, on their production? &lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="107" LastEditDate="2013-11-11T02:46:15.357" LastActivityDate="2020-05-07T06:07:47.113" Title="Why are antibodies so expensive?" Tags="&lt;antibody&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13418" PostTypeId="1" CreationDate="2013-11-10T22:34:27.240" Score="1" ViewCount="505" Body="&lt;p&gt;Why is the 4.4 kb band barely visible? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, what is the mass (ng) of DNA in band X if lane S contains 250 ng of digested lambda phage DNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JLXfe.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4892" LastEditorUserId="1320" LastEditDate="2013-11-11T14:35:59.017" LastActivityDate="2013-11-11T14:35:59.017" Title="Why is the 4.4 kb band barely visible in this HindIII digest of lambda DNA?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13420" PostTypeId="1" CreationDate="2013-11-11T00:37:00.747" Score="1" ViewCount="173" Body="&lt;p&gt;In this paper (On the &lt;a href=&quot;http://goo.gl/CIG95j&quot; rel=&quot;nofollow&quot;&gt;expression of a structural gene&lt;/a&gt;) I am confused about what is being plotted in Figure 6. The x-axis contains the fraction of radioactive day and y-axis contains the enzyme formation (I assume this is just the concentration of enzyme like Figure 5?). Different point shapes are different times after mating. If so, why are there multiple points of each time? Why are there multiple measurements for say 48 mins past mating? Is the correct interpretation that for each condition, they are showing the fraction of radiolabeled material for each number of day post thaw, like figure 5? It is unclear. &lt;/p&gt;&#xA;" OwnerUserId="1693" LastEditorUserId="1693" LastEditDate="2013-11-11T01:52:04.177" LastActivityDate="2013-11-11T23:02:20.007" Title="explanation of conjugation experiment in bacteria" Tags="&lt;genetics&gt;&lt;microbiology&gt;&lt;rna&gt;&lt;gene-expression&gt;&lt;ecoli&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13421" PostTypeId="1" AcceptedAnswerId="13431" CreationDate="2013-11-11T07:23:27.757" Score="4" ViewCount="2392" Body="&lt;p&gt;What is the physiological mechanism behind the diuretic effect of caffeine?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2014-08-22T06:33:21.970" Title="Why does caffeine consumption cause one to urinate more?" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13422" PostTypeId="2" ParentId="13415" CreationDate="2013-11-11T07:56:45.143" Score="4" Body="&lt;p&gt;Motif means a pattern. For any array of objects to be called a pattern, it has to have at least more than one instance. &#xA;To define more precisely, a motif should have significantly (statistical) higher occurrence in a given array compared to what you would obtain in a randomized array of same components (expecting at random). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[&lt;em&gt;Here i use the term array to mean an arranged set such as a genome (array of nucleotides with their position in the sequence) or a protein structure (array of amino acids with their vector positions). A randomized array with same components is generated by shuffling the elements and their values; for e.g. assign the same collection of nucleotides to random positions&lt;/em&gt;] &lt;/p&gt;&#xA;&#xA;&lt;p&gt;RSS nonamers/heptamers are called a motif because they are a pattern of sequence which &lt;code&gt;a)&lt;/code&gt; has more than one occurrence &lt;code&gt;b)&lt;/code&gt; the occurrence is significantly higher than a random expectation. Generally in sequence motifs randomization is not usually done because the genome size is too huge. In such conditions if your sequence has &gt;= 2 occurrences throughout the genome it may be considered a motif. Lets assume a 10bp sequence. Its random probability = 1/4¹⁰. Therefore in 1048576 bp (1Gb) there is a likelihood of finding one instance of that sequence on random. So I assumed that if that sequence has &gt;=2 instances it can be called a motif. However, I am not sure about this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RSS is not a motif because the entire RSS is not conserved; the conserved 'motifs' are interrupted by sequences. This is analogous to lets say a promoter which is a functional region of the DNA. Promoter can have binding sites for different transcription factors and these &lt;em&gt;operator sites (TFBS)&lt;/em&gt; can constitute a motif (if they are conserved) but not the entire promoter.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-07-31T09:38:26.663" LastActivityDate="2014-07-31T09:38:26.663" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13424" PostTypeId="2" ParentId="13412" CreationDate="2013-11-11T12:07:13.963" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Does a human body decompose in a completely sterile environment ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No it wont. Unstable molecules like ATP will quickly degrade spontaneously. The stable ones like many proteins and lipids wont degrade spontaneously. Enzymes are essential to degrade them and are to be supplied extraneously.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What happens in vacuum ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Body will dry up :P&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-11-11T12:07:13.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13425" PostTypeId="1" AcceptedAnswerId="13434" CreationDate="2013-11-11T12:49:24.637" Score="3" ViewCount="3621" Body="&lt;p&gt;It is widely know that each cell cycle during DNA replication some fraction of the telomeres is lost, and this phenomenon is called the end replication problem. Well this is due to the fact that the DNA polymerase only adds nucleotides in 5´--&gt; 3´ direction, thus the synthesis of one of the two DNA strands will need some RNA primers for its polymerization (and DNA polymerase will replicate DNA in a &quot;jumping&quot; pattern). Then, in the very end of the synthesis of this strand (called lagging strand) one last fraction will not be copied from the template as even if the last primer is set in the very end of the chromosome, once this RNA is degraded a void space is going o remain invisible for DNA polymerase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well this is all well known, but my question is whether during each DNA replication it is ONLY the telomere of the chromatid whose origin was in the lagging strand  which will be shortened? (Thus chromosome shortening is happening in a truly asymmetrical and stochastic pattern)&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="3615" LastEditDate="2014-01-27T15:26:14.647" LastActivityDate="2014-01-27T15:26:14.647" Title="Telomere shortening during replication" Tags="&lt;dna&gt;&lt;molecular-genetics&gt;&lt;telomere&gt;&lt;replication&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13427" PostTypeId="1" CreationDate="2013-11-11T13:16:52.207" Score="2" ViewCount="29" Body="&lt;p&gt;what are the &quot;next day&quot; actions that one has to take, when accidentally ingests contaminated drink/food from Aspergillus or Penicillium or Candida fungus?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it feasible to take N-acetyl-L-cysteine supplements? What other measures minimize the damage from the mycotoxins?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What kind of supplements and/or treatments reduce the superoxides produced as effect of the mycotoxins?&lt;/p&gt;&#xA;" OwnerUserId="4897" LastActivityDate="2013-11-11T13:16:52.207" Title="Gliotoxin ingestion and actions needed" Tags="&lt;toxicology&gt;&lt;mycology&gt;" AnswerCount="0" CommentCount="0" ClosedDate="2013-11-14T13:39:56.970" ContentLicense="CC BY-SA 3.0" />
  <row Id="13428" PostTypeId="2" ParentId="13418" CreationDate="2013-11-11T14:35:21.497" Score="2" Body="&lt;p&gt;First of all, the 4.4 kb HindIII band is derived from the right end of &amp;lambda; DNA, so during storage it anneals to the 23.1 kb left arm fragment via &amp;lambda;'s 12 bp cohesive ends. You can solve this problem by preheating the markers to 65&amp;deg;C for a few minutes then cooling rapidly (i.e. on ice). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a stained gel the intensity of a band is proportional to the amount of DNA in that band. This is why the heavier bands are more intense. The fragment X in lane 2 is similar in intensity to the 0.5 kb &amp;lambda; fragment so DNA content of the two bands is similar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The amount of DNA in the 0.5 kb band is 250 ng *(0.5/48.5) where 48.5 is the size of wild-type &amp;lambda; DNA. I'll leave it for you to complete the calculation.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-11-11T14:35:21.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13429" PostTypeId="1" CreationDate="2013-11-11T14:39:36.667" Score="1" ViewCount="20" Body="&lt;p&gt;I listened a talk where the speaker said that this can probably be possible by Weak Quantum Cognition Theory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see that there is no evidence at the moment, only theory.&#xA;I see no pathways by which this could happen directly such that the &lt;strong&gt;quantum entanglement&lt;/strong&gt; and &lt;strong&gt;quantum superposition&lt;/strong&gt; could happen.&#xA;They should happen in a series, but I see no system holding the signal going on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this is a only a hypothesis, without any supportive  evidence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably, some type of synaptic cleft can be controlled, but still I see no evidence or no pathway or pathways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not understand which pathway/pathways this could happen.&#xA;What is the target mechanism? Presynaptic membrane or postsynaptic neuron?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which are possible pathways that could control the secretion of synaptic cleft?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2013-11-11T15:04:07.280" LastActivityDate="2013-11-11T15:04:07.280" Title="Which pathways/mechanisms could control some Synaptic clefts in series by Somatic Nervous System?" Tags="&lt;synapses&gt;&lt;cognition&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13430" PostTypeId="1" AcceptedAnswerId="13435" CreationDate="2013-11-11T17:16:23.660" Score="1" ViewCount="211" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;A protein synthesis assay was carried out in vitro. A&#xA;  polyribonucleotide containing U and C in proportion 1:5 (positions of&#xA;  U and C are random) was used as a template. Which amino acids and in&#xA;  what proportions will be incorporated into the synthesized polypeptide&#xA;  molecules?&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;А. 1Phe : 5Pro : 3Leu.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;B. 1Leu : 1Pro : 1Ser : 1Phe.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;C. 1Phe : 5Ser : 5Pro : 5Leu.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;D. 1Phe : 25Pro : 5Ser : 5Leu.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;E. 5Leu : 5Pro.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;First thing I am not sure is whether only U and C is there. I have tried solving this sum taking both the conditions into consideration . I also tried solving it from options but could not succeed.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="6" LastEditDate="2013-11-11T19:28:28.753" LastActivityDate="2018-02-26T02:27:13.243" Title="Proportion of amino acids from a random polymer of U and C" Tags="&lt;molecular-biology&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13431" PostTypeId="2" ParentId="13421" CreationDate="2013-11-11T17:32:45.167" Score="6" Body="&lt;p&gt;Caffeine inhibits the secretion of the antidiuretic hormone (ADH), so it increases diuresis, but this effect is small and transient.&#xA;&lt;a href=&quot;http://en.citizendium.org/wiki/Vasopressin&quot; rel=&quot;nofollow&quot;&gt;http://en.citizendium.org/wiki/Vasopressin&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Caffeine in amounts up to 400 mg/day (~4 cups of coffee) does not results in net dehydration, since the amount of water lost due to slightly increased diuresis is much smaller than the amount of water in coffee.&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19774754&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/19774754&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In some people, caffeine may irritate the bladder and thus trigger more frequent urination, but this is not increased diuresis and the total volume of the urine is not increased.&lt;/p&gt;&#xA;" OwnerUserId="4025" LastEditorUserId="4025" LastEditDate="2014-08-22T06:33:21.970" LastActivityDate="2014-08-22T06:33:21.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13432" PostTypeId="1" AcceptedAnswerId="13465" CreationDate="2013-11-11T17:38:45.797" Score="5" ViewCount="5981" Body="&lt;p&gt;I'm teaching a class how to do PCR &amp;amp; gel electrophoresis soon and would like it if you could check through my basic step by step instructions - it's a while since I've done one. Is there anything there that is wrong, missing, or should be excluded in the following?&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;A)    Collect all ingredients from the refrigerator and keep cool (on ice). Leave the TAQ in the freezer until required.&lt;/p&gt;&#xA;&lt;p&gt;B)    Make master mix by adding all ingredients (ddH20, MgCl2, PCR Buffer, F Primer, R Primer, dNTP) (excl. TAQ)&lt;/p&gt;&#xA;&lt;p&gt;.......&lt;/p&gt;&#xA;&lt;p&gt;W)    Take the gel to the UV camera and take a picture. Large DNA molecules move through the gel slowest so will be nearest to the wells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;(The students will use primers they designed to sex 6 DNA samples from 3 species of birds, males should produce 1 band &amp;amp; females 2 bands in the gel)&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;strong&gt;for the full version see the answer below&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-11-13T22:32:21.890" Title="Basic step by step methods for PCR &amp; Gel electrophoresis class" Tags="&lt;lab-techniques&gt;&lt;pcr&gt;&lt;gel-electrophoresis&gt;&lt;protocol&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13433" PostTypeId="1" AcceptedAnswerId="13452" CreationDate="2013-11-11T18:42:11.743" Score="2" ViewCount="2167" Body="&lt;p&gt;Why does sodium-potassium pump consume about 2/3 energy of a cell ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A.maintains appropriate membrane potential&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B.helps in co-transport&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it should be A. &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-11-12T15:16:57.443" Title="Homework : Sodium Potassium pump" Tags="&lt;cell-biology&gt;&lt;homework&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13434" PostTypeId="2" ParentId="13425" CreationDate="2013-11-11T18:46:42.823" Score="3" Body="&lt;p&gt;In replication, both the chromosomal halves (which are simultaneously threaded through the replication complex) have a lagging and a leading strand. A part of the segment will be replicated as leading and a part as lagging.&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/vdD7H.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3776" LastEditDate="2013-11-16T15:15:59.180" LastActivityDate="2013-11-16T15:15:59.180" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13435" PostTypeId="2" ParentId="13430" CreationDate="2013-11-11T18:53:46.303" Score="3" Body="&lt;p&gt;The first thing to mention is that this is the type of experiment that &lt;a href=&quot;http://en.wikipedia.org/wiki/Marshall_Warren_Nirenberg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Marshall Nirenberg&lt;/a&gt; performed in order to break the genetic code, and for which he got the Nobel prize in 1968. We stand on the shoulders of giants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the ratio is U:C, 1:5, then it is easy to calculate the probability of encountering each of the 8 possible codons composed by just U and C. So for example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the probability of UUU is (1/6)&lt;sup&gt;3&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the probability of UUC is (1/6)&lt;sup&gt;2&lt;/sup&gt;*(5/6)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a Table that gives all of the values and demonstrates that the answer is (D).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QmNka.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-11-11T18:53:46.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13436" PostTypeId="1" CreationDate="2013-11-11T19:09:15.523" Score="1" ViewCount="1041" Body="&lt;p&gt;Is it because CO&lt;sub&gt;2&lt;/sub&gt; is more soluble in water or has it got to do with the alkaline pH of plasma ?I here mean only aqueous CO&lt;sub&gt;2&lt;/sub&gt; transport from body cells to lungs.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3340" LastEditDate="2014-10-09T13:34:15.193" LastActivityDate="2014-10-09T13:34:15.193" Title="Why can CO₂ be transported dissolved in plasma?" Tags="&lt;physiology&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="13437" PostTypeId="2" ParentId="13420" CreationDate="2013-11-11T23:02:20.007" Score="2" Body="&lt;p&gt;There are three variables being shown here: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The amount of time samples were stored in the freezer to allow $^{32}$P decay (x-axis),&lt;/li&gt;&#xA;&lt;li&gt;The length of time samples were allowed to grow in a nonradioactive environment before being frozen (points with different symbols), and&lt;/li&gt;&#xA;&lt;li&gt;The rate of $\beta$-galactosidase production when cells were thawed and grown in the presence of the transcriptional inducer IPTG (y-axis).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Let's break those down a bit more:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The x-axis measures &quot;fraction of $^{32}$P decay.&quot; In terms of the experimental protocol, this translates to &quot;length of time left in the freezer.&quot; For the $^{32}$P-decay experiments, samples are stored in the freezer for various lengths of time, where metabolic processes, like DNA replication or enzyme production, are shut down or drastically slowed. Although metabolism has been shut down, $^{32}$P can still beta-decay into $^{31}$S (according to &lt;a href=&quot;https://en.wikipedia.org/wiki/Phosphorus-32&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;), which promotes the breakdown of any DNA containing (formerly) radioactive isotopes. The implication is that the longer you leave samples in the freezer, the more $^{32}$P will decay and the more formerly radioactive DNA will be degraded. So you can read the trend in the x-axis either as &quot;increasing fraction of $^{32}$P decay&quot;, &quot;increasing amount of time left in freezer,&quot; or &quot;decreasing fraction of intact $z^+$ DNA.&quot; The different points corresponding to, say, &quot;48 minutes past mating&quot; correspond to samples that were frozen down 48 minutes past mating but kept in the freezer for different lengths of time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The y-axis measures &quot;percent survival of enzyme-forming capacity.&quot; I think that it's safe to interpret this as the rate of $\beta$-galactosidase production relative to the rate with no $^{32}$P-decay. In other words, if you plot $\beta$-galactosidase production over time (as in Figure 5) for different conditions, you'll measure a slope, the rate of enzyme production. If you normalize all these rates from different conditions by the rate when there was no radioactivity (and thus no degradation of $z^+$ DNA in the freezer), you'll get the values plotted on the y-axis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The final interpretation of this plot is that the $\beta$-galactosidase production rate is sensitive to the loss of the introduced $z^+$ DNA when the loss occurs soon after mating, but if cells are allowed to grow enough to divide once or twice before DNA degradation, then the loss of the original conjugated $z^+$ DNA does not affect the $\beta$-galactosidase production rate. This data is consistent with the idea that the DNA form of a gene is constantly required for sustained $\beta$-galactosidase production, and after several rounds of division the $z^+$ DNA has been replicated and is no longer radioactive and prone to degradation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's a lot of data in this plot (ah, the elegance of 1960s molecular biology!) so it can take a while to digest. Hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2013-11-11T23:02:20.007" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13438" PostTypeId="2" ParentId="9815" CreationDate="2013-11-11T23:36:19.627" Score="1" Body="&lt;p&gt;There are generic DNA cutting enzymes! E.g. &lt;a href=&quot;http://mic.sgmjournals.org/content/147/2/315.full.pdf&quot; rel=&quot;nofollow&quot;&gt;DNase A &lt;/a&gt; (journal), &lt;a href=&quot;http://en.wikipedia.org/wiki/Deoxyribonuclease_I&quot; rel=&quot;nofollow&quot;&gt;DNase I &lt;/a&gt; (wikipedia), and &lt;a href=&quot;http://subtiwiki.uni-goettingen.de/wiki/index.php/NucA&quot; rel=&quot;nofollow&quot;&gt;NucA&lt;/a&gt; (Bacillus subtilis annotation). The outer layers of human skin &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0017581&quot; rel=&quot;nofollow&quot;&gt;contain active dnase&lt;/a&gt;, with just such a protective role as one apparent reason. This is one of the (many) sources of contamination that can mess up dna experiments.&lt;/p&gt;&#xA;" OwnerUserId="1688" LastEditorUserId="1688" LastEditDate="2013-11-12T00:53:38.187" LastActivityDate="2013-11-12T00:53:38.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13440" PostTypeId="1" CreationDate="2013-11-12T02:43:30.707" Score="5" ViewCount="6126" Body="&lt;p&gt;Quoting wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Jackson's skin had been a medium-brown color for the entire duration&#xA;  of his youth, but starting in the mid-1980s, it gradually grew paler.&#xA;  The change gained widespread media coverage, including rumors that he&#xA;  might be bleaching his skin. According to J. Randy Taraborrelli's&#xA;  biography, in 1986, Jackson was diagnosed with vitiligo and lupus; the&#xA;  vitiligo partially lightened his skin, and the lupus was in remission;&#xA;  both illnesses made him sensitive to sunlight. The treatments he used&#xA;  for his condition further lightened his skin tone, and, with the&#xA;  application of pancake makeup to even out blotches, he could appear&#xA;  very pale. Jackson was also diagnosed with vitiligo in his&#xA;  autopsy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;1) Is this plausible?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Is it likely to be an actual disease, or would there be so many mitigating factors that it is unlikely a person would suffer to the extent he did?&lt;/p&gt;&#xA;" OwnerUserId="4903" LastEditorUserId="3776" LastEditDate="2013-11-12T07:13:44.447" LastActivityDate="2016-02-02T02:20:10.480" Title="Is the Michael Jackson skin pigmentation disease realistic?" Tags="&lt;human-biology&gt;&lt;pigmentation&gt;&lt;skin&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13441" PostTypeId="1" AcceptedAnswerId="13449" CreationDate="2013-11-12T04:04:24.553" Score="2" ViewCount="671" Body="&lt;p&gt;The testes (at least in human males) are vascular organs, the vascularization extending even o the interstitial spaces of the seminiferous tubules. The function of the scrotal sac, is to isolate the testes from the abdominal cavity, and provide a lower temperature ($1-2^\circ \text C$ lower than normal body temperature of $37^\circ \text C$). &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But since the blood is the main temperature-buffer maintaining the&#xA;  normal body temperature and the scrotal (testicular) tissues are&#xA;  considerably vascularized, why doesn't the blood flow raise the&#xA;  scrotal temperature to normal body temperature?  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If the reason is the location of scrotum external to the abdomen, then all limbs and limb-extremities are located in the similar way (and in those cases, heat dissipation would be faster than in case of scrotum due to less surrounding insulation by thighs and clothes), and hence the temperature of all parts except the interior of the head and abdomen must be at considerably lower temperature? Is this the case?&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2013-11-12T14:22:29.833" Title="Scrotal temperature and vascularization" Tags="&lt;human-biology&gt;&lt;reproduction&gt;&lt;human-anatomy&gt;&lt;temperature&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13443" PostTypeId="2" ParentId="13414" CreationDate="2013-11-12T08:40:36.423" Score="11" Body="&lt;p&gt;The front part of the fish looks like part of the cranium of a fish. I'd bet that the tusks have been &quot;made&quot; by removing some bones in the middle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well, after having looked at the links given by Remi.b, it seems that it's not even necessary to remove bones. This is probably a Peristediidae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find some images on &lt;a href=&quot;http://www.fishbase.org/identification/specieslist.php?famcode=581&amp;amp;areacode=&quot; rel=&quot;noreferrer&quot;&gt;fishbase&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1486" LastActivityDate="2013-11-12T08:40:36.423" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13444" PostTypeId="1" CreationDate="2013-11-12T10:23:16.420" Score="4" ViewCount="633" Body="&lt;p&gt;I was wondering what biological limitations make the dimension of the insects small compared to the dimension of the mammals. I know in other eras insect were bigger!&lt;/p&gt;&#xA;" OwnerUserId="4826" LastActivityDate="2013-11-13T21:23:02.083" Title="Why insects are so small compared to mammals?" Tags="&lt;evolution&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13445" PostTypeId="2" ParentId="13444" CreationDate="2013-11-12T10:58:20.463" Score="10" Body="&lt;p&gt;The standard answer to this question is - it's down to the delivery of oxygen to respiring tissues. Insects depend upon a process that is essentially diffusion-driven (via spiracles and the tracheal system) whereas vertebrates have a circulatory system that allows oxygen absorbed in the lungs to be carried via the blood to peripheral tissues. And of course the blood contains specialised carrier cells (red cells) which in turn are packed with haemoglobin which acts as a molecular carrier for oxygen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The giant dragonflies of the Carboniferous (&lt;em&gt;Meganeura&lt;/em&gt;) existed at a time when oxygen levels in the atmosphere were much higher than now (32.5% &lt;em&gt;vs&lt;/em&gt; 20.9%), so the diffusion-driven gas exchange system could support a larger body size.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-11-13T21:23:02.083" LastActivityDate="2013-11-13T21:23:02.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13446" PostTypeId="1" AcceptedAnswerId="13447" CreationDate="2013-11-12T11:41:20.140" Score="2" ViewCount="169" Body="&lt;p&gt;I'm wondering if a plant can be programmed (by modifying its genes) to grow into any shape that it's programming instructs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that a plants genes are its instructions of how to convert the nutrients in the soil into the plant we see. So, instead of producing an apple tree or a giant sequoia, couldn't a plant be programmed to shape itself into a house, desk, or even at a stretch of the imagination, a &lt;a href=&quot;http://en.wikipedia.org/wiki/Bioship&quot; rel=&quot;nofollow&quot; title=&quot;bioship&quot;&gt;bioship&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking for any links, or explanations of why this could/couldn't be done by anyone with more experience than I that could guide my research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am hoping that a plant behaves just like any other system. That it has inputs (nutrients, sunlight etc.) a function that describes it (its genes) and an output, the plant that grows. With this in mind, I suppose it would only be a matter of modifying the genes to produce the desired output (with the constraint being the available input).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you,&#xA;Paul&lt;/p&gt;&#xA;" OwnerUserId="4905" LastEditorUserId="4905" LastEditDate="2013-11-12T16:53:27.557" LastActivityDate="2013-11-12T16:53:27.557" Title="Can a plant be programmed to produce any arbitrary object?" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;synthetic-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13447" PostTypeId="2" ParentId="13446" CreationDate="2013-11-12T12:07:57.257" Score="1" Body="&lt;p&gt;It could not fit in a comment...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Any material have some physical limitations and living tissue are not exceptions. A plant cannot resist to very high pressure without changing shape for example. Outside of these problems of material sciences I think the major considerations are technical…&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) It is possible to influence the shape of a plant by changing its DNA code, changing its physical and chemical environment (micro or macro environment) or by injecting some substance. Today we might be able to influence the number of branching of certain plants species for example. But we are terribly far from having enough knowledge in biology (in genotype-phenotype map, in biochemical pathway) in order to transform a dandelion into a shopping mall! Even we had already described all chemical pathway linking genes to phenotypic traits, it is immensely more complex to think of which kind of DNA sequence might transform a plant into something that is so different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know if anyone has ever created a totally synthetic (and not copied from already existing sequences) DNA sequence and could predict the impact it would have on the organism phenotype. Some people were able to create a totally artificial self replicating RNA though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: Some people play with the properties of the DNA molecule in order to create various tissues. This might interest you as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One can highly improve this answer by giving some results of studies on synthetic life.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-12T12:14:12.067" LastActivityDate="2013-11-12T12:14:12.067" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13448" PostTypeId="1" AcceptedAnswerId="13457" CreationDate="2013-11-12T13:31:57.933" Score="2" ViewCount="69" Body="&lt;p&gt;Is there an easy way to list authors of biology articles by&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;University&lt;/li&gt;&#xA;&lt;li&gt;country&lt;/li&gt;&#xA;&lt;li&gt;number of published articles&lt;/li&gt;&#xA;&lt;li&gt;sum of citations of all articles he/she wrote&lt;/li&gt;&#xA;&lt;li&gt;fields of study (population genetics)&lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For example, I want to know who are the 10 most popular/cited authors in population genetics in UK's universities. How can I achieve such search?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, do WebOfKnowledge provide such tools?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please, let me know if this question should be asked on another SE website.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-12T14:10:45.940" LastActivityDate="2013-11-13T16:02:43.117" Title="List authors (scientists) by various attribute" Tags="&lt;review&gt;&lt;peer-review-journal&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13449" PostTypeId="2" ParentId="13441" CreationDate="2013-11-12T13:58:13.570" Score="3" Body="&lt;p&gt;The fingers and toes (for example) ARE at lower temperatures than the interior of the torso.  It's why it's so easy to get frostbite on the extremities. As for temperature regulation of the testes, you have to also consider that humans evolved without clothes...i.e. The testes just &quot;hang out&quot; and get lots of airflow, as opposed to modern times, when they are typically under (usually) more than one layer of clothing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, for reference, I took some quick IR temp readings on myself:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Room temp: 19.9C&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fingertip: 27.0C&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Palm: 31.8C&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Axilla: 34.6C&lt;/p&gt;&#xA;" OwnerUserId="4908" LastEditorUserId="4908" LastEditDate="2013-11-12T14:22:29.833" LastActivityDate="2013-11-12T14:22:29.833" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="13450" PostTypeId="2" ParentId="13436" CreationDate="2013-11-12T14:19:00.353" Score="3" Body="&lt;p&gt;The bulk of CO&lt;sub&gt;2&lt;/sub&gt; is transported as bicarbonate/carbonic acid.  The conversion between CO&lt;sub&gt;2&lt;/sub&gt; and carbonic acid is catalyzed by carbonic anhydrase in red blood cells, otherwise the conversion would be very slow. The bicarbonate is then shuttled out of the RBCs and into the blood plasma. The CO&lt;sub&gt;2&lt;/sub&gt; (gas) in blood plasma accounts for &amp;lt;10% of CO&lt;sub&gt;2&lt;/sub&gt; transport, and the solubility isn't that much different from that in water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: Guyton and Hall Textbook on Medical Physiology&lt;/p&gt;&#xA;" OwnerUserId="4908" LastEditorUserId="1320" LastEditDate="2013-11-12T14:50:46.190" LastActivityDate="2013-11-12T14:50:46.190" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="13451" PostTypeId="2" ParentId="13440" CreationDate="2013-11-12T15:03:19.887" Score="11" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;1) Is this plausible?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is absolutely plausible. His particular condition was called &lt;a href=&quot;http://en.wikipedia.org/wiki/Vitiligo&quot; rel=&quot;nofollow noreferrer&quot;&gt;Vitiligo&lt;/a&gt;&#xA; (as stated in your quote) and isn't that uncommon, albeit not usually as severe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Skin pigmentation expression changes over time, sometimes dramatically.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;2) Is it likely to be an actual disease, or would there be so many mitigating factors that it is unlikely a person would suffer to the extent he did?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Vitiligo is a &lt;em&gt;very&lt;/em&gt; well-documented disease, and like every disease, there's a broad range of affectation. Treatments options are very limited, and so makeup or other methods are often used to disguise the affected skin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's some more pictures of people with Vitiligo at varying stages:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/W9WBF.jpg&quot; alt=&quot;Girl with severe vitiligo&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2DKsn.jpg&quot; alt=&quot;Man with severe vitiligo&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JeGYO.jpg&quot; alt=&quot;Woman with vitiligo&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/x5Zjz.jpg&quot; alt=&quot;Woman with vitiligo&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-11-12T15:03:19.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13452" PostTypeId="2" ParentId="13433" CreationDate="2013-11-12T15:09:40.280" Score="3" Body="&lt;p&gt;I can't yet comment, so here's a (sort of) answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've only ever heard the &quot;2/3 of cellular expenditure&quot; rule applied to neurons, and frankly, it wouldn't make much sense in any cell other than a neuron.  The Guyton and Hall Textbook of Medical Physiology says, &quot;For some cells, such as electrically active nerve cells, 60 to 70 percent of the cells' energy requirement may be devoted to pumping Na+ out of the cell and K+ into the cell.&quot;  A cardiac muscle cell, for example, would probably use more of its energy for contraction than pumping ions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a neuron, the bulk of energy expenditures are for electrical signalling done via allowing sodium and potassium ions to temporarily run DOWN their respective gradients.  As such, the &quot;purpose&quot; of a neuron is to pump ions across a membrane and then let them run back when needed.  Since a neuron doesn't really DO much else, it makes sense that the bulk of the energy produced will go towards pumping ions.  A practical example is the use of barbiturate comas to reduce metabolic activity in the brain.  Flat-lining the EEG drops metabolic requirements by ~50% (Source: Medscape).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please keep in mind that this answer is specific to neurons...other cells perform other functions, and those other functions will take up significant fractions of energy produced.  Further, other cells probably aren't devoting large fractions of their energy towards signalling, and so the fraction of energy devoted to pumping ions will be markedly less.  They'll still be pumping ions to maintain a gradient to perform tasks like membrane transport and osmotic control, but those tasks are ancillary to the &quot;purpose&quot; of those cells.  I can't find any solid numbers for Na/K ATPase energy expenditures in non-neuronal tissue at the moment, but if I do, I'll update appropriately.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE:&#xA;With regards to the question itself, which I apparently forgot to answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can a cell function without an appropriate membrane potential? Can co-transport run without a membrane potential?&lt;/p&gt;&#xA;" OwnerUserId="4908" LastEditorUserId="4908" LastEditDate="2013-11-12T15:15:04.400" LastActivityDate="2013-11-12T15:15:04.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13453" PostTypeId="2" ParentId="13433" CreationDate="2013-11-12T15:16:57.443" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Why does sodium-potassium pump consume about 2/3 energy of a cell ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's A, assuming we're talking about a cell-type that heavily utilizes the potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On to some of the comments...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If the cell isn't a neuron then there will be no processes directly collapsing the resting potential. - Alan Boyd&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Incorrect, Pacemaker cells collapse the membrane potential frequently and don't have any resting membrane potential, only hyperpolarization-repolarization cycles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neurons are merely the most prominent users and best examples as they're entire existence is dedicated to the membrane potential.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the absence of the pump, the channels would allow a steady ion flux completely neutralizing the membrane potential from the active GHK potential to the donnan-equilibrium state This would mean (a) is the answer. But I am not sure on this. - Satwik Pasani&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Correct to some extent. The leaky ion channels (which are usually K+ channels) would allow the equilibrium to be reached for a handful of ions. This &lt;em&gt;still&lt;/em&gt; prevents utilization of the potential, however, and is an easy way to kill something.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-11-12T15:16:57.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13454" PostTypeId="1" AcceptedAnswerId="13505" CreationDate="2013-11-12T15:37:44.053" Score="14" ViewCount="30685" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Semen#Composition_of_human_semen&quot;&gt;seminal fluid&lt;/a&gt; contains fructose as the main energy source for the sperm and not glucose. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why is fructose and not glucose the primary energy source for these&#xA;  sperm, since glucose is the preferred energy source for most other&#xA;  tissues?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="1306" LastEditDate="2013-11-12T19:02:46.883" LastActivityDate="2018-03-10T12:49:28.063" Title="Why is fructose not glucose the main energy source of sperm?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;reproduction&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13455" PostTypeId="1" AcceptedAnswerId="13458" CreationDate="2013-11-12T18:09:53.810" Score="2" ViewCount="417" Body="&lt;p&gt;I know that salt is used as preservative as it dehydrates microbes. Is there any other advantage like - altering pH or inactivating microbial enzymes ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-08-04T02:49:18.783" Title="Use of salt as preservative" Tags="&lt;microbiology&gt;&lt;homework&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13456" PostTypeId="2" ParentId="10809" CreationDate="2013-11-12T19:36:37.497" Score="10" Body="&lt;p&gt;This is a specific version of the great cancer question: &quot;Why are some cancers more common than others?&quot; The answer is either &quot;Some have more common causes&quot;, and (or) &quot;Some are cured spontaneously more often&quot;. So now all you are asking is &quot;What causes cancer?&quot; and &quot;How do we cure it?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that, I don't expect a general definitive answer will be forthcoming. A specific answer might be possible, but I doubt there will be any existing experiments that address this. With the obvious caveat that only experimental or statistical results can really answer your question, here are a couple of off-the-cuff hypothesis for consideration:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1 - Differences in stem cell populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently, differentiation can actually be targeted as part of a treatment in some neuroblastoma cases - see the section on &quot;Differentiation therapy&quot; in &lt;a href=&quot;http://www.mskcc.org/pediatrics/childhood/neuroblastoma/treatment&quot;&gt;this page from Sloan-Kettering&lt;/a&gt;. Cardiac stem cells &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16050255&quot;&gt;seem to exist&lt;/a&gt;, but a difference in relative population and turnover rates between brain and heart might be related to the relative frequencies of these types of cancers. @WYSYWIG referred to neural progenitors in his comment above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2 - A filtering effect due to a more extreme selection pressure in the uniformly stressful environment of the a beating heart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although there is a relation between elevated levels of oxidative stress and cancer causing mutations, it could be that this only matters in a punctuated stress environment, where cells have down time to recover. A sustained stress environment might actually helps prevent cancer. The path from normal to cancer cell &lt;a href=&quot;http://www.nature.com/milestones/milecancer/full/milecancer14.html&quot;&gt;requires multiple mutations&lt;/a&gt;, and I would not expect most pre-cancerous cells to be more fit than correctly wired ones. The extra stress of the cardiac environment might produce an elevated mutation rate, but also produce an even higher rate of apoptosis in early &quot;sick&quot; cells before they accumulate enough mistakes to become become cancerous, resulting in a net decrease in the rate of cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both of these ideas fit with heart cancer being less common and with metastasis from elsewhere being more common in heart than primary cancer, but unfortunately, a higher rate of clearing of sick cells would necessitate a higher rate of replacement from stem cells, so these two hypotheses partially cancel each other. Again, hypotheses without experiments are not really answers.&lt;/p&gt;&#xA;" OwnerUserId="1688" LastActivityDate="2013-11-12T19:36:37.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13457" PostTypeId="2" ParentId="13448" CreationDate="2013-11-12T19:47:26.457" Score="4" Body="&lt;p&gt;I don't think that you can do this systematically in Web of Science but you can do it in an exploratory way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Initial search: &lt;em&gt;Topic&lt;/em&gt; - &quot;population genetics&quot; + &lt;em&gt;Address&lt;/em&gt; - UK&lt;/p&gt;&#xA;&#xA;&lt;p&gt;sort by &lt;em&gt;Times cited&lt;/em&gt; is probably more useful than the default (&lt;em&gt;newest to oldest&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;open &lt;em&gt;Authors&lt;/em&gt; in sidebar - this is a list of the top 100 names&#xA;can refine to the top 10, or whatever&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example consider Brian Charlesworth:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Open an item with his name in the author list (he has some single author items)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Click on the link of his name to see his papers&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Click on &lt;em&gt;Create citation report&lt;/em&gt; to see charts of published items per year and citations per year&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;It may be that you know all this.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-11-12T19:47:26.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13458" PostTypeId="2" ParentId="13455" CreationDate="2013-11-12T20:18:30.653" Score="3" Body="&lt;p&gt;High salt environments are strongly hypertonic and disrupt the osmotic gradients of cells.  Excess salt gets forced in (disrupting function) and cell water gets drawn out.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In simpler terms, it dehydrates them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This link has more info regarding what is required to live in high salt environments (and by corollary, why organisms without such features die):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Halophile&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Halophile&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4908" LastActivityDate="2013-11-12T20:18:30.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13459" PostTypeId="1" CreationDate="2013-11-12T21:01:46.297" Score="3" ViewCount="3577" Body="&lt;p&gt;What is the difference between radiation doses of a medical scanner and airport security scanner (X-Ray full body scan)? Is it the same kind of radiation? Does it pose any danger for people who fly often?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastEditorUserId="1373" LastEditDate="2013-11-13T10:03:16.913" LastActivityDate="2013-11-13T14:45:21.227" Title="Difference between Medical and Airport scanner radiation" Tags="&lt;radiation&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13462" PostTypeId="2" ParentId="5670" CreationDate="2013-11-13T05:36:03.983" Score="1" Body="&lt;p&gt;Yes, animal cells do have vacuoles. They just have a larger number of them and some sites call them with different names. In a plant cell there is just one vacuole. Pictures of cells in textbooks,online,etc should show you that they have vacuoles, despite contrary beliefs elsewhere. &lt;/p&gt;&#xA;" OwnerUserId="4913" LastEditorUserId="3776" LastEditDate="2013-11-30T04:36:06.630" LastActivityDate="2013-11-30T04:36:06.630" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13464" PostTypeId="2" ParentId="13459" CreationDate="2013-11-13T12:27:04.820" Score="1" Body="&lt;p&gt;As per the American Association of Physicists in Medicine the radiation exposure from full body airport scanners is equivalent to what an individual receives every 1.8 minutes on the ground from natural background radiation or equivalent to every 12 seconds during an airplane flight. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.aapm.org/pubs/reports/RPT_217.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.aapm.org/pubs/reports/RPT_217.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Back scatter full body scanners at airports use X-rays. &lt;/p&gt;&#xA;" OwnerUserId="4216" LastEditorUserId="4216" LastEditDate="2013-11-13T13:27:07.463" LastActivityDate="2013-11-13T13:27:07.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13465" PostTypeId="2" ParentId="13432" CreationDate="2013-11-13T13:04:31.537" Score="4" Body="&lt;p&gt;I've run a test following this protocol to the letter...&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;PCR step by step:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Collect all ingredients (excluding TAQ) from the refrigerator and keep cool (on ice). Leave the TAQ in the freezer until required.&lt;/li&gt;&#xA;&lt;li&gt;Make master mix by adding all ingredients (excluding TAQ) using fresh pipette tips for each ingredient and using the volume specified&#xA;in the PCR reaction mix recipe.&lt;/li&gt;&#xA;&lt;li&gt;Vortex &amp;amp; lightly spin down on a centrifuge.&lt;/li&gt;&#xA;&lt;li&gt;Add the required amount of TAQ to master mix (insert in to the liquid) and mix using the pipette to draw some liquid up and down.&lt;/li&gt;&#xA;&lt;li&gt;Add master mixes to labeled PCR tubes in the required volumes as specified by the protocol.&lt;/li&gt;&#xA;&lt;li&gt;Add DNA to PCR tubes (using fresh pipette tips for each DNA sample) again using the volume specified in the protocol. Label your tubes&#xA;carefully (and on both the lid and tube).&lt;/li&gt;&#xA;&lt;li&gt;Lightly spin down the PCR tubes on a centrifuge.&lt;/li&gt;&#xA;&lt;li&gt;Run PCR in the thermocycler according to your protocol.&lt;/li&gt;&#xA;&lt;li&gt;Collect samples from thermocycler and place in fridge until needed.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;Gel Electrophoresis step by step:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Make 1xTAE (enough to make the agarose gel and to place in the electrophoresis apparatus).&lt;/li&gt;&#xA;&lt;li&gt;Make an agarose gel (about 5 mm thick) by melting agarose and 1xTAE in the microwave; allow the liquid to cool a little before adding it&#xA;to the mold.&lt;/li&gt;&#xA;&lt;li&gt;Once the gel is cool, place it in the electrophoresis apparatus, cover it with 1xTAE (just covering the gel) and then remove the comb.&lt;/li&gt;&#xA;&lt;li&gt;Collect the PCR products from the fridge/thermocycler.&lt;/li&gt;&#xA;&lt;li&gt;Make spots of loading dye on parafilm. The loading dye is premixed with GelRed so your samples show under UV light.&lt;/li&gt;&#xA;&lt;li&gt;Add one sample to a spot, mix it by drawing the liquid in and out of the pipette tip, and then carefully add to a well in the agarose&#xA;gel. Take care not to puncture the gel or spill any of the liquid out&#xA;of its well. Discard the pipette tip.&lt;/li&gt;&#xA;&lt;li&gt;Repeat the previous step for each sample and for a negative control (master mix and milli-q water instead of DNA). Use a fresh tip for&#xA;every sample.&lt;/li&gt;&#xA;&lt;li&gt;Load PCR Ladder, also mixed with loading dye, in to a well.&lt;/li&gt;&#xA;&lt;li&gt;Connect the electrophoresis apparatus to a power supply, with negative electrode (black) nearest to the wells containing the&#xA;samples.&lt;/li&gt;&#xA;&lt;li&gt;Set the power to run 80-120 volts.&lt;/li&gt;&#xA;&lt;li&gt;Wait until about a finger-width gap appears between the blue and purple bands (approximately 20-30 minutes).&lt;/li&gt;&#xA;&lt;li&gt;Disconnect the power and collect the gel carefully from the liquid.&lt;/li&gt;&#xA;&lt;li&gt;Take the gel to the UV camera and take a picture. Large DNA molecules move through the gel slowest so will be nearest to the&#xA;wells.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;And got a perfect result...&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5qiU0.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The order is Control, female, male, female, male, female, male, ladder. Males have one band, females have two. The final pair didn't show too well on the picture but were clear enough on the screen in the camera room. Thanks for the tips everyone! Sorry the picture is low quality.&lt;/p&gt;&#xA;&lt;p&gt;Feel free to recreate these guidelines but remember to credit the Biology Stackexchange Community!&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-11-13T13:04:31.537" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13466" PostTypeId="2" ParentId="13459" CreationDate="2013-11-13T14:45:21.227" Score="5" Body="&lt;p&gt;The type of radiation is quite different in a medical X-ray vs. an airport scanner.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Medical X-rays are high frequency (beyond ultraviolet) radiation, typically on a wavelength of a few angstroms.  While I would emphasize that @Ram is right to point out that there &lt;a href=&quot;http://hps.org/physicians/documents/Doses_from_Medical_X-Ray_Procedures.pdf&quot; rel=&quot;noreferrer&quot;&gt;is not very much radiation&lt;/a&gt; in a medical X-ray since electronic detectors have been in place over film, the radiation itself is capable of penetrating the entire body and causes ionization.  The body can tolerate a certain amount of this, but that's why we use X-rays - they go through just about anything but bone/minerals and metals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Airport security scanners emit &lt;a href=&quot;http://en.wikipedia.org/wiki/Terahertz_radiation&quot; rel=&quot;noreferrer&quot;&gt;terahertz radiation&lt;/a&gt;, which has a wavelength between microwave and infrared.  This is a very low level of energy per photon.  Terahertz radiation will not penetrate more than a centimeter of light material, which is more suitable to find hidden metal objects (which reflect terawaves).  Relative to X-rays it causes practically no radiation damage.  The intensity of the radiation is also pretty low since these scans are also detected by digital cameras, which are quite sensitive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Compare the machinery.  X-ray technicians, who might have to take dozens of X-ray exposures a day, usually go behind a protective screen to take a medical x-ray.  The airport body scanners are open to the air and the terahertz radiation spills out into the crowd and the workers stand by it every day.  It has practically no expectation of being hazardous.  This device is pretty good as frequent fliers can have as many scans per year as are needed and health concerns are not significant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its always possible we might find some issues with Terahertz radiation in the future, but its hard to imagine it - its safer than standing 2 feet away from a working, closed oven. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-11-13T14:45:21.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13469" PostTypeId="1" CreationDate="2013-11-13T18:32:18.090" Score="0" ViewCount="47" Body="&lt;p&gt;In an amphibian blood entering the right atrium shows higher levels of oxygenation than that in left atrium when : &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A.It is hyperactivated&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B.it is hibernating&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C.it is submerged&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D.it is in the terrestrial habitat&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it should be C.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1306" LastEditDate="2013-11-13T19:47:04.430" LastActivityDate="2014-12-09T13:46:58.387" Title="Amphibian blood circulation" Tags="&lt;physiology&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13470" PostTypeId="1" AcceptedAnswerId="13493" CreationDate="2013-11-13T19:23:26.087" Score="4" ViewCount="270" Body="&lt;p&gt;If a brain is exposed to an intermittent light source, are specific areas going to fire? If yes, which of them? Is there a experimental data about this effect? &lt;/p&gt;&#xA;" OwnerUserId="4818" LastEditorUserId="9943" LastEditDate="2016-02-19T12:34:42.717" LastActivityDate="2016-02-20T10:34:39.633" Title="What will happen if we expose the brain to intermittent light?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13471" PostTypeId="1" AcceptedAnswerId="13477" CreationDate="2013-11-13T19:44:15.183" Score="0" ViewCount="220" Body="&lt;p&gt;Are there multiple copies of circular DNA and &lt;strong&gt;membrane bound&lt;/strong&gt; ribosomes IN CHLOROPLAST ? &#xA;Are polysomes found in them ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-11-14T05:56:04.967" Title="Ribosomes and DNA in chloroplast" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13472" PostTypeId="1" AcceptedAnswerId="13473" CreationDate="2013-11-13T19:58:02.947" Score="1" ViewCount="343" Body="&lt;p&gt;If isozymes are seperated using electrophoresis, which of the following will be the principle of separation ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A.charge density&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B.molecular weight&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C.polarity of molecule &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it should be B.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-11-14T07:35:14.720" Title="Electrophoretic mobility of isozymes" Tags="&lt;molecular-biology&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13473" PostTypeId="2" ParentId="13472" CreationDate="2013-11-13T21:00:28.683" Score="3" Body="&lt;p&gt;(B) is incorrect. I think the answer is (C) but to my mind those other two options are badly worded.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is an explanation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The classic example of isozymes is the case of &lt;a href=&quot;http://en.wikipedia.org/wiki/Lactate_dehydrogenase&quot; rel=&quot;nofollow&quot;&gt;lactate dehydrogenase&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you will see if you visit the Wikipedia page the enzyme is a tetramer, and there are two subunit types, the &lt;em&gt;muscle&lt;/em&gt; or M type and the &lt;em&gt;heart&lt;/em&gt; or H type. Consequently there are 5 isozymes, ranging from M&lt;sub&gt;4&lt;/sub&gt; to H&lt;sub&gt;4&lt;/sub&gt; with all possible combinations in between. Different tissues express these two subunit types to different degrees and so are characterised by a different pattern of isozymes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The M type is encoded by the LDHA gene and the H type by the LDHB gene. I obtained the sequences of the two proteins and analysed them:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;LDHA: 332 amino acids; 36.7 kD; pI=8.45&lt;/p&gt;&#xA;&#xA;&lt;p&gt;LDHB: 334 amino acids; 36.6 kD; pI=5.93&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see from this that the ability to separate these isozymes depends upon charge and not molecular weight. That big difference in pI (isoelectric point) means that at neutral pH the LDHA protein will carry a net positive charge while the LDHB protein will be negatively charged. Consequently each tetramer will have a unique overall charge. &lt;a href=&quot;http://www.molvis.org/molvis/v11/a85/acosta-fig3.html&quot; rel=&quot;nofollow&quot;&gt;You can find some details and an image of an electrophoresis result here.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, protein electrophoresis is much more sensitive to charge differences than it is to molecular mass except in the special case of SDS-PAGE when the large amount of negatively-charged detergent that binds to the proteins masks their intrinsic charge differences. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another classic example of this is the ability to &lt;a href=&quot;https://www.mun.ca/biology/scarr/Hemoglobin_Electrophoresis.html&quot; rel=&quot;nofollow&quot;&gt;separate haemoglobin S in sickle cell patients from haemoglobin A in normal blood&lt;/a&gt;. In this case the only difference between the two molecules is a single Glu&gt;Val substitution in two of the monomers in each tetramer. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-11-14T07:35:14.720" LastActivityDate="2013-11-14T07:35:14.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13475" PostTypeId="1" CreationDate="2013-11-14T01:49:24.177" Score="1" ViewCount="127" Body="&lt;p&gt;I want to know how and how often does cootranscription takes place? Can transcription regulators influence splicing during cotranscription?&lt;/p&gt;&#xA;" OwnerUserId="601" LastActivityDate="2013-11-14T11:56:13.723" Title="How cotranscription events affect splicing?" Tags="&lt;transcription&gt;&lt;splicing&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13476" PostTypeId="1" AcceptedAnswerId="13478" CreationDate="2013-11-14T02:36:43.477" Score="4" ViewCount="2217" Body="&lt;p&gt;everyone. I've just been introduced to the procedure of Western blotting from my reading, though I'm not entirely sure about some points. I'd appreciate it if someone could help me with this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What exactly is the function of the blocking buffer?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does one need a secondary antibody?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When discussing nitrocellulose membranes, say of a 0.45 5m pore size, what does 5m refer to?&lt;/p&gt;&#xA;" OwnerUserId="4283" LastEditorUserId="948" LastEditDate="2013-11-20T15:25:48.810" LastActivityDate="2013-11-20T15:25:48.810" Title="Western blotting questions?" Tags="&lt;proteins&gt;&lt;gel-electrophoresis&gt;&lt;western-blot&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13477" PostTypeId="2" ParentId="13471" CreationDate="2013-11-14T05:56:04.967" Score="3" Body="&lt;p&gt;The chloroplast, having multiple circular copies of its chromosome and its own tRNA and ribosome genes more resembles the bacterial systems it is descended from.  See @A.Kennard comment &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Polysomes being found in bacteria frequently are single mRNA to which are attached multiple ribosomes.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC335575/pdf/pnas00676-0293.pdf&quot; rel=&quot;nofollow&quot;&gt;This paper shows that chloroplast polysomes were observed in the mid 1960s by centrifugal sedimentation&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-11-14T05:56:04.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13478" PostTypeId="2" ParentId="13476" CreationDate="2013-11-14T07:32:41.447" Score="7" Body="&lt;p&gt;&lt;strong&gt;Blocking buffer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once the proteins in the gel have been transferred to the nitrocellulose membrane it is necessary to coat the rest of the surface of the membrane with an unrelated protein. This is necessary because all proteins will bind non-specifically to the nitrocellulose. Once the membrane has been blocked the only way that antibiody proteins (the probe) will bind to the membrane is via the transferred proteins that they recognise. The usual source of a blocking protein is defatted milk powder, i.e. casein, although some people use (or used to use) bovine serum albumin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Secondary antibody&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a typical blotting experiment you expose first with a &lt;em&gt;primary antibody&lt;/em&gt; directed against the protein of interest, for example this might be an IgG raised in a rabbit. Then in a second step you add a &lt;em&gt;secondary antibody&lt;/em&gt; which will bind to the first one - in this case this might be goat ant-rabbit IgG (i.e. anti-rabbit IgG raised in a goat). Why is this done? The secondary antibody is in the form of an antibody-enzyme conjugate, typically with horseradish peoxidase, and the final development of the blot detects the presence of the conjugated enzyme.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why use a secondary antibody? Two reasons: - firstly, there will sometimes be a degree of amplification if more than one secondary antibody molecule binds each primary antibody molecule; but more important is that it means that it is not necessary to produce an enzyme conjugated form of every primary antibody, which is time-consuming and quite tricky. So in your work you may be studying several different proteins using Westerns, but you will be able to use the same secondary antibody to detect all of them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Pore size&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That should be 0.45 - 0.5 &amp;micro;m. Pore sizes are measured in micrometres.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-11-18T21:28:56.270" LastActivityDate="2013-11-18T21:28:56.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13479" PostTypeId="1" AcceptedAnswerId="13481" CreationDate="2013-11-14T08:04:45.857" Score="2" ViewCount="1205" Body="&lt;p&gt;What are the energetics of protein digestion during which the enzyme pepsin is &quot;activated&quot; (whatever that means) by HCl?  I've looked and been unable to find anything like a chemical equation that includes an energy term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, pepsin, being an enzyme, is not used up in that sought-for equation.  Is HCl used up?  If so, what are the products?  How and in what form is the chlorine removed, assuming the HCl is consumed in the equation?&lt;/p&gt;&#xA;" OwnerUserId="4798" LastActivityDate="2013-11-14T16:19:40.980" Title="Energetics and Products of Pepsin/HCl Protein Digestion" Tags="&lt;digestive-system&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13481" PostTypeId="2" ParentId="13479" CreationDate="2013-11-14T09:35:20.270" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Pepsin#Precursor&quot; rel=&quot;nofollow noreferrer&quot;&gt;This is well-explained on the Wikipedia page for pepsin.&lt;/a&gt; You are misinterpreting the use of the word &lt;em&gt;activated&lt;/em&gt;. The protein is secreted by chief cells in the gastric glands in the form of pepsinogen, an inactive pro- form which has an extra ~40 amino acids at its N-terminus (the propeptide). The propeptide binds at the catalytic site of the enzyme and keeps it inactive. At low pH (this is where the HCl comes in - HCl secreted by parietal cells of the gastric glands acidifies the stomach) the protein is able to cleave off its own propeptide, making it fully active.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tx3xF.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-11-14T16:19:40.980" LastActivityDate="2013-11-14T16:19:40.980" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13484" PostTypeId="2" ParentId="13475" CreationDate="2013-11-14T11:56:13.723" Score="1" Body="&lt;p&gt;Co-transcriptional splicing (CTS) is very widespread. Different studies (which are done on different cell types) report different frequencies of CTS. Most of them report a frequency of ~0.8 in different cells except for mouse liver which was reported to have a frequency of 0.45&#xA;This is the &lt;a href=&quot;http://f1000.com/prime/reports/pubmed/23638305&quot; rel=&quot;nofollow noreferrer&quot;&gt;article&lt;/a&gt; that summarizes these different studies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Can transcription regulators influence splicing during cotranscription?&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes.. including factors such as nucleosome positions.. this &lt;a href=&quot;https://biology.stackexchange.com/questions/8743/transcription-factor-binding-site-located-in-intron/8751#8751&quot;&gt;post&lt;/a&gt; may be helpful.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-11-14T11:56:13.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13485" PostTypeId="2" ParentId="9427" CreationDate="2013-11-14T12:19:02.390" Score="2" Body="&lt;p&gt;Just to fully document the IUPAC advice on this, here is the relevant section from the &lt;em&gt;Nomenclature for  Incompletely Specified Bases in Nucleic Acid Sequences&lt;/em&gt; as reproduced &lt;a href=&quot;http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html#400&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; in the link provided by @Hamish McWilliam.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;5.2. Modified nucleotides&lt;/p&gt;&#xA;&lt;p&gt;In a number of organisms DNA and RNA are modified at certain positions. For instance, the DNA of Escherichia coli is usually methylated on N-6 of the adenine residue in the sequence 5'-GATC-3' [23]. The present nomenclature does not allocate any specific symbol to these modified nucleotides for the following reasons. (1) The presence or absence of a given modification depends upon the location of the DNA. Sequences modified in one organism may not be modified in another. (2) Modification is usually statistical, in that only a proportion of possible sites for modification may actually be utilised in vivo. Modification of a nucleotide or base in a given polynucleotide is not a function of the sequence per se. Although it is recognised that stable RNA species (tRNA and rRNA) often carry a constant pattern of post-translational modification. the present nomenclature is not intended to overlap with or supplant existing systems. It would probably be impossible to devise a simple and logical system that avoided all conflict with previous usage. One should therefore recognise that such conflict is possible and take steps to prevent it from generating confusion, for example in relation to the symbols B, D and S, which have been recommended for 5-bromouridine, 5,6-dihydrouridine and thiouridine respectively [1], or W, which is sometimes used for wyosine.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-11-14T12:19:02.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13486" PostTypeId="1" AcceptedAnswerId="13491" CreationDate="2013-11-14T17:14:58.437" Score="22" ViewCount="105027" Body="&lt;p&gt;I am always so confused whether to do a chi square test or a t test in the sums given by my biostats teacher. Does anyone have a simple rule to decide this?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2019-10-28T16:09:27.780" Title="Deciding between chi square and t test" Tags="&lt;homework&gt;&lt;biostatistics&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="13488" PostTypeId="1" AcceptedAnswerId="16429" CreationDate="2013-11-14T17:45:18.730" Score="4" ViewCount="801" Body="&lt;p&gt;Will it make a difference in running speed if we run samples of same no of bases but different AT - GC content ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-08T19:38:46.977" Title="Is AT or GC content important in electrophoresis?" Tags="&lt;molecular-biology&gt;&lt;homework&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13489" PostTypeId="1" AcceptedAnswerId="13492" CreationDate="2013-11-14T17:54:12.700" Score="2" ViewCount="318" Body="&lt;p&gt;Which of the following methods would yield the most purified protein fraction?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A. Salt precipitation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B. Charge separation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C. Affinity purification&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first one is the most commonly used, is it the best ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1320" LastEditDate="2013-11-14T19:33:00.077" LastActivityDate="2016-12-20T23:30:50.670" Title="Protein purification methods" Tags="&lt;molecular-biology&gt;&lt;homework&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13490" PostTypeId="2" ParentId="13489" CreationDate="2013-11-14T18:08:41.777" Score="3" Body="&lt;p&gt;In my protein purification experience, affinity purification is the most selective purification strategy. This makes sense because affinity tends to be very specific, and only one protein should in theory be preferentially separated by the column. Think how specific the antibody-antigen interaction is compared to the differences in, say, charge between proteins (which could be very slight). When I was purifying proteins I would pretty much always start with affinity purification. If more purity was desired after the affinity purification step, I could perform salt precipitation or charge separation on the affinity-purified sample, which had already been cleared of major contaminants/nuisance proteins by affinity purification.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2013-11-14T18:08:41.777" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13491" PostTypeId="2" ParentId="13486" CreationDate="2013-11-14T18:32:00.613" Score="24" Body="&lt;p&gt;This is a very subtle question and I encourage you to read the Wikipedia articles on these different subjects (t-test, chi-squared test, p-value, etc) because the authors worked hard to combat common misconceptions about these commonly used statistical tests. Here is a rather oversimplified rule-of-thumb for these different tests:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;t-test: Used when you are looking at the &lt;em&gt;means&lt;/em&gt; of different populations. For example, you might want to determine whether the difference in the mean gene expression level between treated and untreated cells is different, or if the gene expression level of cells in a certain environment differs from what you would expect in a null hypothesis. &lt;strong&gt;Assumptions:&lt;/strong&gt; You are assuming that the populations you are looking at are normally distributed. The variance of the populations is not known (that would be a Z-test), but it is assumed that the variance of each population is the same. Finally, for the t-test to work, the samples of the data from the two populations are assumed to be independent.&lt;/li&gt;&#xA;&lt;li&gt;$\chi^2$ test: Several possibilities for this. The most common in biology is the Pearson $\chi^2$ test, which is used when you are looking at &lt;em&gt;categorical data&lt;/em&gt;, like the number of pea plants with white or purple flowers and round or wrinkled seeds, and trying to see whether the number of individuals in each category is consistent with some null hypothesis (such as the number in each category you'd expect if the genes for flower color and seed shape are not linked). &lt;strong&gt;Assumptions:&lt;/strong&gt; The data points were randomly and independently gathered from the population, and you have a reasonably large number of samples.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I'd hate to have made a huge mistake, so please edit my answer and/or contribute your own if you think I am completely misrepresenting these topics!&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2013-11-14T18:32:00.613" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13492" PostTypeId="2" ParentId="13489" CreationDate="2013-11-14T19:28:39.507" Score="3" Body="&lt;p&gt;The choice of strategy for protein purification of course varies by application.  As @A.Kennart points out, affinity chromatography is the most popular right now.  It can be expensive.  If you have an expression system for a recombinant protein its more common than not to add a poly-Histdine tag on the N or C terminus or some other protein fusion.  So there are cases where you won't be able to use it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance if the protein you are looking for is not coming from a recombinant source / is not sequenced, it can get expensive and time consuming - getting an antibody made requires that you have a somewhat pure prep of the protein in the first place. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most common reason we still use all these methods are because different levels of purity and different raw materials show up in different contexts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case where the protein has never been isolated before or you have a sample (like a cell sample rich in a particular protein) then salt and sizing columns are very useful.  Salt precipitation is useful when you have a lot of sample and you need to make some rough cuts.  Even if the gene is well characterized, it may depend on expression in its native organ. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've prepped protein using ammonium sulfate precipitation from homogenized whole tissue for instance.  That's great - the result got rid of well over 90% of the material, but the outcome has hundreds of bands on the gel.  In this case an affinity column was used next; immobilized conconavalin A would bind to the glycosides on the target product.  If I had put the whole tissue homogenate I would have destroyed the affinity column by stuffing it full of meaty gunk.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Charge affinity columns with salt gradients are often still needed after affinity chromatography. Some folks don't need pure protein, but affinity chromatography (esp his tags) will still have many bands left on a protein gel and those contaminants always leave your experiment in question. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-11-14T19:28:39.507" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13493" PostTypeId="2" ParentId="13470" CreationDate="2013-11-14T19:33:48.750" Score="5" Body="&lt;p&gt;It is thought that there are no active optical receptors in the brain normally, its possible some effect might show up in the future, it would be minor at best. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Shining light into the brain is standard procedure in &lt;a href=&quot;http://en.wikipedia.org/wiki/Optogenetics&quot; rel=&quot;nofollow noreferrer&quot;&gt;optogenetics&lt;/a&gt; experiments. A subpopulation of neurons is transformed to express an optical receptor to modulate genetic or signalling properties of the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the reason I say it would be small effect on a native brain is that these experiments do give good results and are run with controls which do not have the optical receptors added, which typically show no change in brain activity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RgTlS.jpg&quot; alt=&quot;optogenetic modulation of activity in a rat prefrontal cortex&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Channelrhodopsin-2 (ChR2) induces temporally precise blue light-driven activity in rat prelimbic prefrontal cortical neurons. a) In vitro schematic (left) showing blue light delivery and whole-cell patch-clamp recording of light-evoked activity from a fluorescent CaMKllα::ChR2-EYFP expressing pyramidal neuron (right) in an acute brain slice. b) In vivo schematic (left) showing blue light (473 nm) delivery and single-unit recording. (bottom left) Coronal brain slice showing expression of CaMKllα::ChR2-EYFP in the prelimbic region. Light blue arrow shows tip of the optical fiber; black arrow shows tip of the recording electrode (left). White bar, 100 µm. (bottom right) In vivo light recording of prefrontal cortical neuron in a transduced CaMKllα::ChR2-EYFP rat showing light-evoked spiking to 20 Hz delivery of blue light pulses (right). Inset, representative light-evoked single-unit response.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Image taken from the linked Wikipedia page and originally from &lt;a href=&quot;http://www.neuro-cloud.net/nature-precedings/baratta&quot; rel=&quot;nofollow noreferrer&quot;&gt;Baratta et al.&lt;/a&gt;.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1306" LastEditDate="2013-11-14T23:31:09.873" LastActivityDate="2013-11-14T23:31:09.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13494" PostTypeId="2" ParentId="11217" CreationDate="2013-11-14T20:14:14.507" Score="3" Body="&lt;p&gt;Oddly enough it is a bit difficult to find good field studies where the diet of spiders was studied.  I have a feeling it's a hard thing to get funding for.  Luckily some do exist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Peucetia_viridans&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Peucetia viridans&lt;/em&gt;&lt;/a&gt; has been shown to eat from the &lt;a href=&quot;https://en.wikipedia.org/wiki/Chrysididae&quot; rel=&quot;nofollow&quot;&gt;Chrysididae family&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Lepidoptera&quot; rel=&quot;nofollow&quot;&gt;Lepidoptera order&lt;/a&gt;, but I didn't find an &lt;a href=&quot;http://www.americanarachnology.org/joa_free/joa_v7_n2/joa_v7_p149.pdf&quot; rel=&quot;nofollow&quot;&gt;explicit statement&lt;/a&gt; that it ate the larvae out of the caterpillar.  Likewise &lt;a href=&quot;https://en.wikipedia.org/wiki/Lynx_spider&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Oxyopes globifer&lt;/em&gt;&lt;/a&gt; was &lt;a href=&quot;http://www.jstor.org/stable/4129800&quot; rel=&quot;nofollow&quot;&gt;found to have eaten&lt;/a&gt; from the &lt;a href=&quot;https://en.wikipedia.org/wiki/Braconidae&quot; rel=&quot;nofollow&quot;&gt;Braconidae family&lt;/a&gt; and Lepidotera.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At this point you might be wondering why I'm looking for spiders that have been shown to eat both &lt;a href=&quot;https://en.wikipedia.org/wiki/Parasitoid&quot; rel=&quot;nofollow&quot;&gt;parasitoids&lt;/a&gt; (Chrysididae and Braconidae) and caterpillars (Lepidotera).  It my assumption that in the scenario you describe a spider that would normal eat ether the caterpillar or the larvae would be just as happy to eat them both if it was lucky enough to find them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could find &lt;a href=&quot;http://www.jstor.org/stable/4216863&quot; rel=&quot;nofollow&quot;&gt;one example&lt;/a&gt; where it seems wolf spiders under the right conditions might seek out larvae, and I found a &lt;a href=&quot;http://flic.kr/p/85yeys&quot; rel=&quot;nofollow&quot;&gt;fun photo&lt;/a&gt; of a wolf spider eating larvae (though not the kind in the study).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I never saw the video you were talking about, and I too could not find it.  It is not unreasonable to assume that an opportunistic spider wouldn't just take the opportunity to feed on both, or that it might find the larvae more tasty and just eat them.  I've not found a spider seeking caterpillar as of yet.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2013-11-14T20:14:14.507" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13497" PostTypeId="2" ParentId="13486" CreationDate="2013-11-15T06:42:49.737" Score="5" Body="&lt;p&gt;&lt;strong&gt;Additional Info&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;T-test&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As A.Kennard said t-test is applied when the random variable is normally distributed. How to know what is normally distributed is a relevant question. Regular measures which suffer some random error of measurement are normally distributed. The mean values estimated from different samples (the experiment that generates that sample may have &lt;strong&gt;any&lt;/strong&gt; distribution) follow normal distribution. For e.g mean time interval of a radioactive decay- the interval itself is exponentially distributed but the mean of the mean decay interval will be normally distributed. You can reason that it is again an error of measurement that leads to variation in the mean value calculated in different samples. This is called the &lt;em&gt;central limit theorem&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A normal distribution has two parameters- mean and variance i.e. you need to know these values beforehand to construct a normal distribution. A uniform distribution has no parameters- that doesn't mean that uniformly distributed samples have no mean or variance (in this case mean and variance are sample properties not distribution parameters).&#xA;A t-test or z-test is done to see if a sample is a representative of a given normal distribution. That again means that the calculated mean and variance are equivalent to the corresponding distribution parameters. In case of z-test you know the population variance (distribution parameter). You may ask how can anyone possibly know the population variance beforehand. An example is a case in which you already know the error rate of your measuring device (may be provided by the manufacturer or interpreted from its design).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;$\chi^2$ test&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several variants of the $\chi^2$ test. But what is common between them is that they refer to &lt;strong&gt;$\chi^2$ distribution&lt;/strong&gt;. Variances, which are always positive cannot be a normally distributed. These follow $\chi^2$ distribution. The F-test for variances uses the ratio of the $\chi^2$ statistic of the two random variables denoting variances. Even in the Pearson $\chi^2$ test, the test statistic is a sum of squares which makes it always positive. &#xA;In fact this $\chi^2$ distribution is also used in t-test. As . Kennard said, one of the assumptions of t-test is that the population variance is unknown but assumed to be equal. Since population variance is unknown it has to be estimated from the sample. Like the case with all estimates you dont have a fixed value but a range of acceptable values falling in some confidence intervals. T-distribution is basically an average of several normal distributions with variance values falling in the allowed confidence interval of a $\chi^2$ distribution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not necessary that categorical data are to be tested by $\chi^2$ test. Coin toss experiment gives rise to a categorical but it can be tested against a binomial distribution. So $\chi^2$ test can be used for categorical data but it is not the only test. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;&lt;code&gt;Bottomline&lt;/code&gt;&lt;/em&gt;&lt;/strong&gt;: a statistic tested by a $\chi^2$ test has $\chi^2$ &lt;strong&gt;distribution&lt;/strong&gt; as its sampling distribution. That statistic should be a square/sum of squares- something that can never possibly have a negative value. Perhaps that is why it is called $\chi$ &lt;strong&gt;&lt;em&gt;squared&lt;/em&gt;&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-11-16T15:52:41.020" LastActivityDate="2013-11-16T15:52:41.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13498" PostTypeId="2" ParentId="9913" CreationDate="2013-11-15T06:46:30.813" Score="2" Body="&lt;p&gt;These REs, that recognize palindromes, are mostly homodimers and hence the same sequences (for each monomer)for recognition, only they are reversed. This explains the palindromes.&lt;/p&gt;&#xA;" OwnerUserId="4921" LastEditorUserId="3776" LastEditDate="2013-11-15T16:32:46.433" LastActivityDate="2013-11-15T16:32:46.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13499" PostTypeId="1" AcceptedAnswerId="13515" CreationDate="2013-11-15T09:37:25.677" Score="3" ViewCount="182" Body="&lt;p&gt;I wanted to use the &lt;code&gt;compana()&lt;/code&gt; function from the &lt;code&gt;adehabitat&lt;/code&gt; package in R. I don't really understand the meaning of the data in the example they provide (from aebisher et al., 1993).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two main arguments of the &lt;code&gt;compana&lt;/code&gt; function are:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;compana(used, avail, other.arguments…)&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;&lt;p&gt;used&lt;br&gt;&#xA;  a matrix or a data frame describing the percentage of use of habitats (in columns) by animals (in rows).&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;avail&lt;br&gt;&#xA;  a matrix or a data frame describing the percentage of availability of habitats (in columns) by animals (in rows).&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What does...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;[..] a data frame describing the percentage of availability of habitats by animals&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;mean ?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By 'Availability of a habitat', I guess it means the proportions of these habitats that were not used. Isn't it? But then, how can this be categorized into different species? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess I am missing something easy in the functioning of this statistical tool!&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;One can run that in R to get more info:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;install.packages(&quot;adehabitat&quot;)&#xA;require(adehabitat)&#xA;?compana&#xA;# The following code comes from the example provided in the help page&#xA;data(pheasant)&#xA;pheasant$mcp&#xA;pheasant$studyarea&#xA;compana(pheasant$mcp, pheasant$studyarea,&#xA;                   test = &quot;parametric&quot;)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="16866" LastEditDate="2016-01-14T22:00:55.353" LastActivityDate="2016-01-14T22:00:55.353" Title="Niche overlap Index" Tags="&lt;zoology&gt;&lt;ecology&gt;&lt;biostatistics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13501" PostTypeId="1" AcceptedAnswerId="13508" CreationDate="2013-11-15T12:52:10.193" Score="3" ViewCount="571" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;In a small tribal population, the frequencies of two alleles A and a&#xA;  at a particular locus were 0.3 and 0.7, respectively. However, not all&#xA;  the individuals with genotype aa could live up to the reproductive age&#xA;  and the relative fitness of this genotype was found to be 0.5. The&#xA;  remaining genotypes had a relative fitness of 1. What is the expected&#xA;  percentage of heterozygotes among newborns in the next generation?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My answer is : 37 % but the answer given 43.52 %&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did the following : First I assumed the population to be of 100 individuals and then I counted the no of individuals with respective genotypes. Then I assumed that each person leaves 1 offspring except the aa ones which leave 0.5 offsprings and then I calculated the new genotype frequency from this.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-11-18T11:27:16.143" Title="Hardy Weinberg Equilibrium problem" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;hardy-weinberg&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13502" PostTypeId="1" CreationDate="2013-11-15T13:23:43.233" Score="-4" ViewCount="918" Body="&lt;p&gt;Planets like Mercury and Venus do not have moons, and they do not appear to harbor (higher) life (forms). How significant is it for the emergence of life on a planet that it has a moon? How does it affect the planet's ecosystem, especially seasons and periods?&lt;/p&gt;&#xA;" OwnerUserId="4923" LastEditorUserId="6139" LastEditDate="2017-03-20T13:51:53.077" LastActivityDate="2017-03-20T13:51:53.077" Title="What significance does the moon have for the development of life on earth, and for earth's ecology?" Tags="&lt;ecosystem&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2013-11-15T16:32:27.777" ContentLicense="CC BY-SA 3.0" />
  <row Id="13503" PostTypeId="2" ParentId="13502" CreationDate="2013-11-15T14:22:29.650" Score="4" Body="&lt;p&gt;This question is indeed off topic here but the reason these planets don't have moons is pure chance. Different moons have different origins, some could be meteorites or other drifting bodies that were captured by the planet's gravity, others could be pieces of the planet itself that were spun off before it solidified or from an impact event. Others could be mass ejected from the sun which was captured by the planet and so on and so forth. Whether any of these events occurred in a planet's history is down to chance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for ecosystems, since the only planet we know of that has one is the Earth, we have no idea how other ecosystems would be affected by the presence or absence of a moon. The absence of tides would be the most obvious effect but you could also get tidal effects if you have an erratic orbit around the sun or if you have other large bodies close enough to affect you.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-11-16T03:51:43.677" LastActivityDate="2013-11-16T03:51:43.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13504" PostTypeId="1" AcceptedAnswerId="100731" CreationDate="2013-11-15T15:01:39.117" Score="3" ViewCount="4315" Body="&lt;p&gt;This image was included in something I was browsing through.&#xA;It reminds me of my lion head rabbit, but the head shape doesn't match.&lt;/p&gt;&#xA;&lt;p&gt;Is this some kind of Siberian wild rabbit?&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DP670.jpg&quot; alt=&quot;Its sooooo fluuuuuufy!!!&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="4925" LastEditorUserId="16866" LastEditDate="2021-05-15T06:07:31.600" LastActivityDate="2021-05-15T19:28:30.760" Title="What species is this rabbit-like animal?" Tags="&lt;species-identification&gt;&lt;zoology&gt;&lt;mammals&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="13505" PostTypeId="2" ParentId="13454" CreationDate="2013-11-15T15:20:02.007" Score="8" Body="&lt;p&gt;I have been searching this for a while and I got something of an answer, which I am posting below.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are primarily two advantages of using the &lt;a href=&quot;http://en.wikipedia.org/wiki/Polyol_pathway&quot;&gt;polyol pathway&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Aldose_reductase&quot;&gt;aldose reductase&lt;/a&gt; to produce fructose from glucose via sorbitol:-  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Quoting the book &lt;a href=&quot;https://www.inkling.com/read/principles-of-medical-biochemistry-meisenberg-simmons-3rd/chapter-22/fructose-is-the-principal-sugar&quot;&gt;here&lt;/a&gt;, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Seminal fluid contains up to 11 mmol/L (200 mg/dl) of free fructose.&#xA;  It is the major energy source for the sperm cells in their&#xA;  all-important race for the ovum. The advantage of fructose over&#xA;  glucose may be that many bacteria, which compete with the sperm cells&#xA;  for the available nutrient, prefer glucose to other energy sources.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thus, to avoid other competitive bacteria and cells from utilising the energy source of sperm, fructose is used as the energy source since the bacteria prefer glucose.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2)Another reason is that the metabolism of sorbitol into fructose is energetically efficient way (no ATP required) as compared to glycolytic conversion of glucose into fructose(G$\rightarrow$G6P$\rightarrow$F6P$\rightarrow$F). Tapping the polyol pathway is energetically preferred to metabolizing fructose produced during glycolysis.This is only to show the possible evolution of the polyol pathway once the advantage of using fructose as the energy source was established. It does not explain why the fructose was advantageuos but just that if it was advantageous, the semen-producers would develop the currently existing machinery to produce fructose as the exclusive source of energy.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, sperms (seminal secretion) contains fructose as the primary energy source and not glucose.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2013-11-16T02:27:27.660" LastActivityDate="2013-11-16T02:27:27.660" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13506" PostTypeId="1" CreationDate="2013-11-15T15:43:14.043" Score="15" ViewCount="5118" Body="&lt;p&gt;I've heard that with the  distribution of our genome women have less variation on the bell curve than men. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any basis for this? It was my understanding that women have more genetic variation than men due to having two X chromosomes and there being more variation on gene expression within the X chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've also seen a theory that with traits linked to genes on the X-chromosome in women being averaged across the genetic variants found on each of a woman's two X-chromosomes, this would reduce the likelihood of extreme traits (men have just one X-chromosome, precluding this averaging process).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any biological possibility for men to have more genetic variation than women, and if so what would be a potential reason for it?&lt;/p&gt;&#xA;" OwnerUserId="586" LastEditorUserId="22057" LastEditDate="2016-03-23T01:47:04.257" LastActivityDate="2017-11-02T19:36:32.593" Title="Do men have a higher genetic variance than women?" Tags="&lt;genetics&gt;&lt;population-genetics&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13507" PostTypeId="1" CreationDate="2013-11-15T15:51:47.307" Score="6" ViewCount="7570" Body="&lt;p&gt;I've heard that Asians (I'm not entirely sure which subgroup was being referred to) tend to be more genetically homogenous than other races, with people of African lineage being on the other end of the spectrum being the least homogenous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any truth in the claim that Asians or a specific subcategory such as South East Asians have less genetic variance than other races?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen papers like &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12012367&quot; rel=&quot;nofollow noreferrer&quot;&gt;Extreme mtDNA homogeneity in continental Asian populations&lt;/a&gt; for example, but I don't understand enough to know if that answers my question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If Asians have less genetic variance, would that lead to less variance in phenotypes?&lt;/p&gt;&#xA;" OwnerUserId="586" LastEditorUserId="586" LastEditDate="2013-11-20T00:59:51.087" LastActivityDate="2017-03-27T03:52:40.593" Title="Are Asians more genetically homogenous than other races?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13508" PostTypeId="2" ParentId="13501" CreationDate="2013-11-15T15:58:07.300" Score="5" Body="&lt;p&gt;Your reasoning is incorrect, because once you have the number of individuals surviving after the 50% mortality you can't just give them all one identical offspring, you have to mate them with one another.&lt;/p&gt;&#xA;&lt;p&gt;However, I can't get the answer given, instead I get 47.9%&lt;/p&gt;&#xA;&lt;p&gt;Here is my reasoning:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;f(&lt;strong&gt;A&lt;/strong&gt;)=0.3&lt;/p&gt;&#xA;&lt;p&gt;f(&lt;strong&gt;a&lt;/strong&gt;)=0.7&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;calculate genotype frequencies:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;AA&lt;/strong&gt; = 0.3&lt;sup&gt;2&lt;/sup&gt; = 0.09&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;aa&lt;/strong&gt; = 0.7&lt;sup&gt;2&lt;/sup&gt; = 0.49&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Aa&lt;/strong&gt; = 2 * 0.3 * 0.7 = 0.42&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;(these add to 1 as expected)&lt;/p&gt;&#xA;&lt;p&gt;use 1000 individuals for nice round numbers&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;number &lt;strong&gt;AA&lt;/strong&gt; = 90&lt;/p&gt;&#xA;&lt;p&gt;number &lt;strong&gt;aa&lt;/strong&gt; = 490&lt;/p&gt;&#xA;&lt;p&gt;number &lt;strong&gt;Aa&lt;/strong&gt; = 420&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Now apply 50% mortality in &lt;strong&gt;aa&lt;/strong&gt; individuals:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;number &lt;strong&gt;AA&lt;/strong&gt; =&amp;gt; 90&lt;/p&gt;&#xA;&lt;p&gt;number &lt;strong&gt;aa&lt;/strong&gt; =&amp;gt; 245&lt;/p&gt;&#xA;&lt;p&gt;number &lt;strong&gt;Aa&lt;/strong&gt; =&amp;gt; 420&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;now calculate new allele frequencies in mating population:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;f(&lt;strong&gt;A&lt;/strong&gt;) = (90 + 90 + 420)/1510 = 600/1510&lt;/p&gt;&#xA;&lt;p&gt;f(&lt;strong&gt;a&lt;/strong&gt;) = (245 + 245 + 420)/1510 = 910/1510&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;calculate proportion of heterozygote offspring&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;= 2 * f(&lt;strong&gt;A&lt;/strong&gt;) * f(&lt;strong&gt;a&lt;/strong&gt;)&lt;/p&gt;&#xA;&lt;p&gt;= (1200 * 910)/(1510 * 1510)&lt;/p&gt;&#xA;&lt;p&gt;= 0.479&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I hope someone can see where I'm going wrong.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-11-15T15:58:07.300" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13509" PostTypeId="1" AcceptedAnswerId="13513" CreationDate="2013-11-15T16:54:55.217" Score="1" ViewCount="1247" Body="&lt;p&gt;Leena is a molecular biology student. She purifies two fragments of DNA, 800 and 300 base pairs long. These were obtained from a plasmid after digesting it with HindIII. Each of these fragments has a single EcoRI recognition site.&#xA;Leena wants to join these two fragments to get a 1.1kb gene as shown in Figure 7.1. She suspects that this gene has a unique protein-coding sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;She, therefore, mixes the two fragments in the presence of excess DNA ligase in an appropriate buffer and incubates the mixture. She removes an aliquot (a small part of the reaction mixture) after 30 minutes and loads it on an agarose gel to check the results. She is surprised to find many bands along with the expected 1.1kb band  in the gel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PhCka.png&quot; alt=&quot;fig 7.1&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;FIG 7.1&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/31V8t.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Leena is interested in the 1.1kb fragment shown in Figure 7.1. Hence, she elutes the 1.1kb fragment from the gel shown in Figure 7.2 and subjects part of this sample to HindIII digestion. She obtains the expected pattern with two bands, 800 and 300 base pairs long. To confirm its restriction map, she subjects the remaining sample to complete EcoRI digestion. Which pattern of bands would she obtain?&#xA;&lt;img src=&quot;https://i.stack.imgur.com/bBonJ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer given is this and I understand why this is the answer and other options given in the question(not posted here) are definitely not the answer but I do not understand why there are no 0.4kb fragments, 1.1kb fragments here.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-11-15T19:26:13.590" Title="Gel electrophoresis question" Tags="&lt;molecular-biology&gt;&lt;homework&gt;&lt;gel-electrophoresis&gt;&lt;restriction-enzymes&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13510" PostTypeId="1" CreationDate="2013-11-15T16:57:15.323" Score="1" ViewCount="69" Body="&lt;p&gt;If cytoplasmic determinants are distributed before fertilisation then how can an amphibian's embryo, whose dorsal side is determined after fertilisation develop ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-11-15T16:57:15.323" Title="Cytoplasmic determinants in amphibians" Tags="&lt;embryology&gt;&lt;evo-devo&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13511" PostTypeId="2" ParentId="13507" CreationDate="2013-11-15T16:59:53.753" Score="4" Body="&lt;p&gt;Don't worry, caucasians all look the same to Asians too. This is because of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cross-race_effect&quot; rel=&quot;nofollow&quot;&gt;cross-race effect&lt;/a&gt;: we are able to effectively distinguish people we are more familiar with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But as for the most genetically diverse race, &lt;a href=&quot;http://en.wikipedia.org/wiki/Race_and_genetics&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; might be of interest: &quot;Sub-Saharan Africans have greater genetic diversity than other populations.&quot; The research paper the quotation is based on is found &lt;a href=&quot;http://deepblue.lib.umich.edu/bitstream/handle/2027.42/62133/21011_ftp.pdf?sequence=1&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be honest, I don't see the point of this question. The answer depends on what classifies under a race: Do Asians include Indians? What qualifies as Caucasian? etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only thing that can be gained by exploring race-specific genetic distinctions is if you want to promote some racial supremist attitude like that guy with the toothbrush mustache.&lt;/p&gt;&#xA;" OwnerUserId="4922" LastEditorUserId="4922" LastEditDate="2013-11-15T17:18:07.013" LastActivityDate="2013-11-15T17:18:07.013" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13512" PostTypeId="2" ParentId="13509" CreationDate="2013-11-15T17:24:46.287" Score="1" Body="&lt;p&gt;You are being too smart for this question ;) If you assume that the enzyme is perfect, you've optimized the amount of template, and you leave the reaction for a really long time then there will be &lt;em&gt;complete digestion.&lt;/em&gt; If you assume complete digestion, then there won't be any 1.1kb fragments. Furthermore, if you work out all the possible orientations of the 800bp and 300bp that were ligated together (each piece can be in the orientation shown and the opposite orientation) and you force an &lt;em&gt;EcoRI&lt;/em&gt; cut at every available &lt;em&gt;EcoRI&lt;/em&gt; site, then you won't have any 0.4 kb fragments from imcomplete digestion, either. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In reality, I've never been able to optimize my reaction conditions to get complete digestion of my template, and I always have some residual template around, so it's good your thinking that way for &quot;real-world&quot; preparation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you do not assume incomplete digestion, in addition to the 1.1kb and 0.4kb bands missing from this gel, I calculate that there should be a 1kb band as well.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Edit: I goofed up the last paragraph. It should read: &quot;If you do not assume &lt;em&gt;complete&lt;/em&gt; digestion, in addition to the 1.1kb and 0.4kb bands missing from the complete digestion gel, I calculate that there should be a 1kb band as well.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastEditorUserId="4840" LastEditDate="2013-11-15T19:26:13.590" LastActivityDate="2013-11-15T19:26:13.590" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13513" PostTypeId="2" ParentId="13509" CreationDate="2013-11-15T17:41:48.937" Score="1" Body="&lt;p&gt;@A. Kennard beat me to it. Here is my answer, assuming complete digestion. The two HindIII fragments can ligate to give four different products as shown below. I have marked one end of each HindIII fragment to help in seeing polarity, and I have left the ligated junction as a gap to help see what is going on. I don't understand the point about the 1 kb band.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jRTU0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-11-15T17:41:48.937" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13515" PostTypeId="2" ParentId="13499" CreationDate="2013-11-15T18:38:09.430" Score="0" Body="&lt;p&gt;Not 100% sure, but this would be my guess:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;used&quot; would be the percent of time spent in a certain habitat, while &quot;avail&quot; is the amount of that habitat that specific animal encounters in its life.  This example explains what I mean:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Say you have some sort of ground squirrel that lives in rocky outcrop(R).  Next to the hole is a field (F), and across the field are some trees(T) with squirrel food in them.  The squirrel spends all of its time in these three habitats, but it doesn't like the field much because its exposed and can be attacked by predators, so when it goes out for food it runs quickly across the field, gets food, and runs back.  Say it spends 60% of its time at home, 10% of its time running through the field, and 30% of its time in the trees eating.  Those give you your &quot;used&quot; numbers.  But, the relative proportion of the habitats that the squirrel ever occupies (relative size), are very different.  By area, the field is 75%, the trees are 15%, and the rocks are 10%.  In this example, your &quot;used&quot; matrix would look like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;used&#xA;            R    F    T&#xA;Squirrel  0.6  0.1  0.3&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and your &quot;avail&quot; matrix would look like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;avail&#xA;            R    F    T&#xA;Squirrel  0.1  0.75  0.15&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;With this information you can do a statistics to test whether the squirrel randomly picks habitats, or prefers certain ones.  If it randomly picked habitats, you'd expect it's &quot;used&quot; percentages to look like its &quot;avail&quot; percentages, i.e. it spends ~75% of its time in the field because it just wanders around aimlessly between rocks, field and trees.  But since you observe a pretty sizable increase in time spent in low-availability habitats, you are likely to see a statistically significant preference for certain habitats (rocks for sure, and maybe trees).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, if you have multiple species, this program probably tests to see how similar two species' patterns of habitat preference and avoidance are, and uses that to define niche overlap.  The &quot;avail&quot; could be the same if they both travel through the same rocks, field and trees, but if another species has a larger foraging area, its F and T percentages in the &quot;avail&quot; matrix will go up relative to the R.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, not totally certain about this interpretation, but it seems to make sense to me from the R documentation.&lt;/p&gt;&#xA;" OwnerUserId="4177" LastActivityDate="2013-11-15T18:38:09.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13516" PostTypeId="2" ParentId="13501" CreationDate="2013-11-15T19:51:12.240" Score="6" Body="&lt;p&gt;This is basically the same solution as @AlanBoyd's answer, but since he asked me to, I will post my solution as well (also a reason to try out $\mathcal{MathJax}$ a bit more).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$f(A)=p=0.3, \\f(a)=q=0.7$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;and the standard formulas:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$f(AA)=p^2\\&#xA;f(Aa)=2pq\\&#xA;f(aa)=q^2$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;gives these genotypes in the parental generation (G1), before and after selection (using the fitness vector $w$):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;\begin{array}{c|cccc}&#xA;\text{genotype} &amp;amp; \text{freq G1} &amp;amp; w &amp;amp; \text{freq breed.pop} &amp;amp; \text{freq breed. rescaled}\\&#xA;\hline&#xA;AA &amp;amp; 0.09 &amp;amp; 1 &amp;amp; f(AA)\cdot w_{AA}=0.09 &amp;amp; 0.119\\&#xA;Aa &amp;amp; 0.42 &amp;amp; 1 &amp;amp; f(Aa)\cdot w_{Aa}=0.42 &amp;amp; 0.556 \\&#xA;aa &amp;amp; 0.49 &amp;amp; 0.5 &amp;amp; f(aa)\cdot w_{aa}=0.245 &amp;amp; 0.325\\&#xA;\text{sum} &amp;amp; 1 &amp;amp; &amp;amp; 0.755 &amp;amp; 1&#xA;\end{array}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genotype frequencies in the breeding population (rescaled so that they sum to one) are then used to calculate allele frequencies as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$f(A)=f(AA)+\frac{f(Aa)}{2} = 0.397\\&#xA;f(a)=f(aa)+\frac{f(Aa)}{2} = 0.603$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are then used to calculate the genotype frequencies in the next generation (G2), using the same HW-equations as in the beginning:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\begin{align}&#xA;f(AA)&amp;amp;=0.397^2=0.158 \\&#xA;f(Aa)&amp;amp;=2\cdot0.397\cdot0.603=0.479 \\&#xA;f(aa)&amp;amp;=0.603^2=0.363 \\&#xA;\end{align}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not understand where the given answer $f(Aa)=0.435$ is coming from.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-11-18T11:27:16.143" LastActivityDate="2013-11-18T11:27:16.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13518" PostTypeId="1" AcceptedAnswerId="13522" CreationDate="2013-11-16T11:26:20.530" Score="7" ViewCount="1325" Body="&lt;p&gt;I am hoping to measure growth rates of a bacterial culture in several growth conditions. I am concerned that these growth conditions may cause cell death, which would lead to a decreased correspondence between optical density and number of live cells, so I want to independently measure the number of live cells. I understand that plating serial dilutions of a culture and counting the number of colonies to calculate the Colony Forming Units (CFU) per mL is the gold standard for measuring the number of viable cells. However, I have seven different conditions I want to test in parallel, and making 3+ plates for each condition (to do serial dilutions) and taking measurements at several points in the growth curve leads to a &lt;em&gt;lot&lt;/em&gt; of plates. In general this method seems more labor intensive than what I need. I am mostly doing this as a sanity check, so it seems like a lot of work just for a sanity check. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: are there any alternative methods to CFU plating for measuring cell viability, given that I am doing a lot of experiments in parallel? I don't have access to a FACS machine, so cell sorting won't work. I have read &lt;a href=&quot;https://biology.stackexchange.com/questions/11368/measuring-algae-growth-or-death&quot;&gt;this question&lt;/a&gt; on measuring live cells in algae. I'm not sure that a hemocytometer is the right alternative for my particular high-throughput application (though you could convince me otherwise). The best answer to this question would compare from experience the precision, accuracy, sensitivity, and ease of use of this alternative method with CFU plating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="4840" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2017-05-05T00:47:37.993" Title="Alternatives to CFU plating for measuring number of viable cells?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;lab-techniques&gt;&lt;measurement&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13519" PostTypeId="1" CreationDate="2013-11-16T11:30:57.157" Score="1" ViewCount="79" Body="&lt;p&gt;In a &lt;a href=&quot;https://biology.stackexchange.com/questions/13518/alternatives-to-cfu-plating-for-measuring-number-of-viable-cells&quot;&gt;separate question&lt;/a&gt; I've described my general experimental setup where I need to measure the number of live cells in a growing bacterial culture in a fairly rapid and high-throughput manner. In that question I'm asking if there are any alternatives to the gold standard of CFU plating for making this measurement. As I wrote that question, it occurred to me that if I could just make CFU plating easier to do with lots of samples (esp. using fewer plates), then this method could work just as well. So my question here is if there is a way to make CFU serial dilution plating easier when I have to measure the number of live cells in 7+ different growth conditions every hour of growth?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="4840" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-11-16T11:30:57.157" Title="Improving throughput of CFU plating?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;lab-techniques&gt;&lt;measurement&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13520" PostTypeId="1" AcceptedAnswerId="13521" CreationDate="2013-11-16T17:23:32.280" Score="5" ViewCount="1054" Body="&lt;p&gt;The DNA molecules contain phosphate groups involved in $3'\rightarrow 5'$phosphodiester linkages. These groups, in the bonded state with deoxyribose, contain 1 negative charges ($\ce{3'-PO4^{-}-5'}$). This means that the two strands are very highly negatively charged. What than stabilizes the double helix, preventing the natural electrostatic repulsion between the two strands?   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[I am assuming that the phosphate groups are dissociated under physiological pH, correct me if I am wrong.]&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2013-11-16T19:02:20.100" LastActivityDate="2013-11-17T11:14:07.543" Title="Stability of helical strands of DNA?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;structural-biology&gt;&lt;nucleic-acids&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13521" PostTypeId="2" ParentId="13520" CreationDate="2013-11-16T18:36:44.740" Score="7" Body="&lt;p&gt;There is indeed a repulsive force between the phosphates in the DNA backbone. (The pK of the phosphate is very low so it will be ionised at all physiologically-relevant pH.) This is why DNA behaves like a stiff rod over short distances. However cations in solution will help to shield some of this repulsion. This is why DNA melting temperature decreases as the ionic strength of the buffer is reduced (by increasing the repulsive force relative to the favourable energy term coming from the base-pairing).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When DNA is condensed these repulsive forces are masked by cations like &lt;a href=&quot;http://en.wikipedia.org/wiki/Spermine&quot; rel=&quot;nofollow&quot;&gt;spermine&lt;/a&gt;, and of course by histones.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="3776" LastEditDate="2013-11-17T11:14:07.543" LastActivityDate="2013-11-17T11:14:07.543" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13522" PostTypeId="2" ParentId="13518" CreationDate="2013-11-16T20:04:54.273" Score="6" Body="&lt;p&gt;I've only used it for mammalian work, but the &lt;a href=&quot;http://www.roche-applied-science.com/webapp/wcs/stores/servlet/ProductDisplay?catalogId=10001&amp;amp;partNumber=3.8.9.5.1.3#tab-0&quot;&gt;Cedex HiRes Analyzer&lt;/a&gt; from Roche is pretty sweet. From their &lt;a href=&quot;http://www.roche-applied-science.com/webapp/wcs/stores/servlet/ProductDisplay?catalogId=10001&amp;amp;partNumber=3.8.9.5.1.3#tab-3&quot;&gt;docs&lt;/a&gt; you can analyze particles from 1-90 μm in size (the cells I work with are about 20 μm), and there are a ton of configuration options depending on your needs. As long as your cells can be stained with Trypan Blue (it's been a long time since I've done bacterial work, pardon my ignorance) to look at viability, then this machine should work quite well. When set to &lt;em&gt;Maximum&lt;/em&gt; (i.e., the analysis takes as long as possible), I get results in less than 4 minutes per sample - and this includes about a minute for the sample to settle in the flow cell. If you lower the sensitivity, you can get results faster.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically the way it works is you take 300 μl of your liquid culture (diluted if you think the concentration is too high), and add it to a sample cup. Put all your cups in the tray, fill out the sample info and analysis options in the MultiRun screen, and hit Start. The machine includes all the reagents onboard, so it mixes the Trypan Blue with your samples, then injects the proper amount into a flow cell. The sample is allowed to settle, then a high-resolution image is taken of the entire length of the flow cell. Then, depending on your sensitivity settings, a certain number of frames are taken from the full-length image and analyzed. An average count is then generated based on all the images, and your final numbers are spit out. You can then print or save a report of the cell counts and viability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The software comes with some analysis tools as well, so if you keep multiple cultures going over time with different growth conditions, you can aggregate the data for each one and generate graphs of cell counts, viability, cell size, etc. - there are at least 10 or 20 parameters to choose from. All the image analysis options are configurable, so if you look at the results and think the machine is picking too many dead cells, or not enough, you can change the parameters to your liking, and save the options as a custom analysis type.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One option I like that would beat the pants off CFU-based counting (besides the drastically-reduced time) is the fact that the machine can detect aggregation of the cells. One issue with CFUs is that it's hard sometimes to know that a certain colony really arose from just one parent cell - if you let the colonies grow long enough you may be able to tell based on size, but it's a tough call. Since the Cedex is looking at the cells themselves, it doesn't matter if they're aggregated or not, as they'll all get counted (assuming the aggregation particle doesn't contain a huge amount of cells, like 50+, that can't be resolved by the software due to occlusion of the image).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know how much these guys cost, so depending on your budget you may not be in the market for one, but if you're going to be doing a lot of counting then one of these is invaluable. I'm sure other companies make similar instruments, but I haven't used them, so I don't know how they compare to the HiRes. I do know that the person at my company that was responsible for buying the HiRes is very good about researching possible alternatives, so this one is probably as close to the top of the line as we could find, for the needs that we have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good luck with your counting!&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-11-16T20:04:54.273" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13523" PostTypeId="1" AcceptedAnswerId="13534" CreationDate="2013-11-16T20:38:44.973" Score="5" ViewCount="2263" Body="&lt;p&gt;I know that &lt;em&gt;in vivo&lt;/em&gt; there are a lot fewer transmembranous proteins in general, and that they are produced at a lower rate than their free counterparts. This is mainly because transmembrane proteins are only required in a 2D space on the membrane rather than a 3D cytoplasmic or extracellular space. This (again, very broadly speaking) means that the probability they will interact with their target is higher.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also know that this is one of the reasons that producing crystals for X-ray crystallography is notoriously difficult for transmembrane proteins. What are the other reasons that make transmembrane proteins typically tough crystallisation candidates?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What specific part of the crystallisation process yields such poor success rates of transmembrane protein structure elucidation?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="1320" LastEditDate="2013-11-17T16:42:25.300" LastActivityDate="2017-07-21T23:00:11.120" Title="Why are transmembrane proteins difficult to crystallise?" Tags="&lt;cell-biology&gt;&lt;proteins&gt;&lt;xray-crystallography&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13524" PostTypeId="1" AcceptedAnswerId="24739" CreationDate="2013-11-16T23:31:33.787" Score="7" ViewCount="153" Body="&lt;p&gt;&lt;strong&gt;Who (and in which article) was the first to reformulate Hamilton's rule using the letters $B$ and $C$?&lt;/strong&gt;. See below comments on this reformulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hamilton, in his &lt;a href=&quot;http://www.uvm.edu/~pdodds/files/papers/others/1964/hamilton1964a.pdf&quot;&gt;1964's article&lt;/a&gt; gave a mathematical formulation to explain the direction of social traits. Below is its formulation. Note: Hamilton used quite a complicated formulation, I hope I am not misunderstanding its meaning. Please let me know if it is the case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$R\cdot\frac{dw(x,y,z)}{dx}&amp;gt;\frac{dw(x,y,z)}{dy}$$ where $R$ is the coefficient of relatedness which can itself be expressed as a correlation between the variables $x$ and $y$. $w(x,y,z)$ is the fitness function of a focal individual expressing trait $x$ and interacting with an individual draw from a subpopulation expressing trait $y$ (expected value of the probability distribution of trait expression of individuals in the subpopulation) in a population expressing trait $z$ (expected value again).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most often this formula is expressed in the following form:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$RB&amp;gt;C$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$B$ and $C$ are called cost and benefit of the social trait. I believe that $B$ and $C$ are often not understood as a consequence of a change of the social trait but rather as a cost and benefit of carrying the social trait (compare to not carrying it).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="5144" LastEditDate="2014-12-09T20:10:59.027" LastActivityDate="2014-12-09T20:10:59.027" Title="Reformulation of Hamilton's rule" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13525" PostTypeId="1" AcceptedAnswerId="13535" CreationDate="2013-11-16T23:57:25.293" Score="2" ViewCount="496" Body="&lt;p&gt;I am trying to figure out how to identify which protein in a complex mixture is producing a certain effect.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an assay for the effect, so anything (a fraction of the mixture) can be tested on microplate.   The part of the mixture producing the effect is pretty definitely a protein (or has a protein component).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, the mixture is serum... which contains &gt;10,000 proteins and peptides, some in tiny amounts and some in huge amounts.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is not enough information to go the other way, ie guess what is producing the effect and test that by itself (or remove it from serum and test the depleted serum as a confirmation).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also no possibility to use affinity (use a receptor as bait, etc) because many components of serum stick to the cells in the assay (or, practically to any cells).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I need a way to narrow this down from &quot;serum&quot; to one specific protein (or a handful), but how?&lt;/p&gt;&#xA;" OwnerUserId="4934" LastActivityDate="2013-11-17T22:30:51.070" Title="How to identify active protein in a complex mixture?" Tags="&lt;proteins&gt;&lt;protein-binding&gt;&lt;purification&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13526" PostTypeId="1" AcceptedAnswerId="15501" CreationDate="2013-11-16T23:58:34.170" Score="4" ViewCount="307" Body="&lt;p&gt;&lt;strong&gt;Which elements of the following list are  assumptions of the Hamilton's rule?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Population structure (non-panmictic population)&lt;/li&gt;&#xA;&lt;li&gt;Additivity&#xA;&lt;ul&gt;&#xA;&lt;li&gt;= Fitness of the heterozygote equals the mean of the fitnesses of both homozygotes&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;No epistasis or pleiotropy&lt;/li&gt;&#xA;&lt;li&gt;Stable population size&lt;/li&gt;&#xA;&lt;li&gt;Inifinite population size&lt;/li&gt;&#xA;&lt;li&gt;Sexual reproduction&lt;/li&gt;&#xA;&lt;li&gt;Selection on diploids or selection on haploids&lt;/li&gt;&#xA;&lt;li&gt;Recombination (cross-over)&lt;/li&gt;&#xA;&lt;li&gt;Mendelian segregation&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Semelparity_and_iteroparity&quot; rel=&quot;nofollow&quot;&gt;Iteroparous&lt;/a&gt; population&lt;/li&gt;&#xA;&lt;li&gt;smooth fitness landscape&lt;/li&gt;&#xA;&lt;li&gt;mutation rate is high enough&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are there assumptions of Hamilton's rule that are not listed above?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-03-05T10:03:18.773" LastActivityDate="2014-03-05T16:39:31.113" Title="Assumptions of Hamilton's rule" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;&lt;evolutionary-game-theory&gt;&lt;sociality&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13528" PostTypeId="2" ParentId="11384" CreationDate="2013-11-17T01:22:25.127" Score="5" Body="&lt;p&gt;Although work in those areas is definitely all related, there are some kind of general differences in how those labels tend to be used, and I'll take a stab at defining them:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematical ecology - this is typically the creation of theoretical models composed purely from math (i.e. not stochastic computer models). Examples include a lot of classics from ecological theory, such as &lt;a href=&quot;http://mathworld.wolfram.com/Lotka-VolterraEquations.html&quot;&gt;Lotka-Volterra models&lt;/a&gt; of predation and competition, but there are also people who still do this kind of research, such as &lt;a href=&quot;http://eebweb.arizona.edu/Faculty/chesson/storage_effect.htm&quot;&gt;Peter Chesson in his research on the storage effect&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Numerical ecology - this is not a term that I've heard used very frequently, but I think it tends to cluster pretty closely with mathematical ecology, perhaps with more of an emphasis on also including and analyzing empirical data. I hear it used more to refer to techniques than actual ongoing areas of research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Statistical ecology - I think this term gets used more loosely because obviously statistics are important to most ecology research. It can either refer to research that makes heavy use of advanced statistics because the questions that its getting at are hard to untangle from other effects, or research that uses a statistical model to make its point (note that statistical models are generally different from the mathematical models mentioned above in that their goal is generally to determine how likely something is to happen rather than to untangle some fundamental principle of ecology). A lot of studies on neutral vs. niche-based community assembly would probably fall into the category of statistical ecology. &lt;a href=&quot;http://www.southampton.ac.uk/biosci/news/2009/10/20_niche_versus_neutral_theory.page&quot;&gt;Here is one of many examples&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ecoinformatics - maybe this is just because I study ecoinformatics, but I tend to think that this is the most distinct of the fields that you mentioned, although it certainly still has a great deal of overlap with the others, especially since it's a pretty diverse subfield. In general, ecoinformatics focuses on making use of large datasets in ecology. This involves both research on developing methods for doing this (for example, I study ways to efficiently collect information from ecological wireless sensor networks. Another good example is the &lt;a href=&quot;http://kellylab.berkeley.edu/keck-engine/&quot;&gt;development of GIS tools&lt;/a&gt;) and research that uses these methods (e.g. a study that uses GIS to synthesize sensor data and observations of a given organism to determine what that organism's range will be as climate change progresses, or that otherwise seeks to &lt;a href=&quot;http://csilimnology.org/&quot;&gt;pull ecological concepts out of the data&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Computational ecology - I left this until last, because I think it's the vaguest of the labels you listed. It definitely includes ecoinformatics, but it probably also includes a lot of statistical ecology (and perhaps numerical and mathematical ecology too). I think that the main reason that it's a useful label is that it can catch areas of research that don't really fit in to the other labels. For instance, I once saw a study on &lt;a href=&quot;http://se-server.ethz.ch/staff/af/fi159/d/dr013.pdf&quot;&gt;quantifying niche space using support vector machines&lt;/a&gt;. It was really interesting, and maybe it could be classified as ecoinformatics or statistical ecology, but it didn't really quite fit into either of those. So I guess I tend to see computational ecology as a catch-all term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are just the impressions that I have gotten - if others chime in too we can probably build a better consensus definition of these labels.&lt;/p&gt;&#xA;" OwnerUserId="3824" LastActivityDate="2013-11-17T01:22:25.127" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13530" PostTypeId="2" ParentId="11132" CreationDate="2013-11-17T01:32:21.193" Score="3" Body="&lt;p&gt;You might be interested in the below works as well as the references that they cite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;May, R. M. (1988). How many species are there on Earth? Science, 241(4872), 1441–1449.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Millennium Ecosystem Assessment. (2005). Ecosystems and Human Well-Being: Synthesis (p. 137). Washington, D.C.: Island Press.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's worth noting that many estimates of species richness at large scales are based on the use of the species-area relationship to upscale richness measurements from small scales to large scales.&lt;/p&gt;&#xA;" OwnerUserId="4936" LastActivityDate="2013-11-17T01:32:21.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13532" PostTypeId="2" ParentId="13504" CreationDate="2013-11-17T04:06:10.677" Score="5" Body="&lt;p&gt;Thanks to @Satwik's tip about google image search, I was able to figure out that the animal in question is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Viscacha&quot; rel=&quot;noreferrer&quot;&gt;Viscacha&lt;/a&gt;. Though the source answer is thanks to &lt;a href=&quot;http://www.reddit.com/r/pics/comments/m10e0/wise_bunny_meditates/&quot; rel=&quot;noreferrer&quot;&gt;reddit&lt;/a&gt;, so take that as you will. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Viscachas or vizcachas are rodents of two genera (Lagidium and Lagostomus) in the family Chinchillidae. They are closely related to chinchillas, and look similar to rabbits, apart from their longer tails&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4925" LastActivityDate="2013-11-17T04:06:10.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13534" PostTypeId="2" ParentId="13523" CreationDate="2013-11-17T07:29:23.013" Score="9" Body="&lt;p&gt;There are several factors that make obtaining crystal structures from membrane proteins more difficult.  In brief, nearly every stage of obtaining the structure via crystallography is more difficult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First: &lt;em&gt;protein expression&lt;/em&gt;.  Large amounts of pure, well-folded protein are required and this is much more difficult to achieve than it is with a soluble protein. Since membrane proteins are bound within a membrane, the mechanisms to translate the peptide into the membrane and to fold the protein in the membrane are different.  They may involved folding factors which are only available in a particular compartment of the cell (making bacteria impossible as a system of expression).  In high amounts in the cell, their hydrophobicity might tend to result in clumps of unfolded protein instead of gobs of membrane-associated protein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next: &lt;em&gt;Purifying the protein&lt;/em&gt; is more difficult.  The expressing cells are usually broken open in the presence of detergent to get the proteins to float around as individual proteins in detergent micelles.   The wrong detergents might break up the membrane protein and it may lose its fold - the concentration of detergent must be carefully managed and kept at optimal levels or the micelles might break up and the protein will be ruined.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Crystallizing the protein&lt;/em&gt; is quite a bit more difficult too.  Membrane proteins in detergent micelles which may or may not be charged themselves look like oily blobs with hopefully a domain or two of folded proteins sticking out of them.  Compared to a soluble protein with a nice ordered surface in every direction instead of a detergent micelle which might undergo a phase change at high concentration or by the addition of a salt or change in pH, membrane proteins take a task that might take thousands of trials and adds new dimensions to worry about.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The proteins are 2D-like, but the crystals still have to be 3D for crystallography to work usually.  Protein crystals are small, but those derived from membrane proteins - which tend to organize into planes like the membranes they inhabit - are often thin, which can make them too delicate and small to get a good set of data even from synchrotron beams.  As a result, the crystals are commonly too small or thin to use at first, requiring extensive optimization after the first crystal are found. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a few cases &lt;a href=&quot;https://en.wikipedia.org/wiki/Electron_crystallography#Protein_structures_determined_by_electron_crystallography&quot; rel=&quot;nofollow noreferrer&quot;&gt;some membrane proteins have been solved with 2D crystals using electron microscopy&lt;/a&gt; on crystalline arrays of porins and rhodopsins in membranes. That was a ton of work but they were the first membrane protein structures by years and years. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not to make all this sound impossible - once you have crystals, they can usually be improved; &lt;a href=&quot;http://sbkb.org/update/research/tips-for-crystallizing-membrane-proteins&quot; rel=&quot;nofollow noreferrer&quot;&gt;there are good starting points to crystallization and purification with detergents&lt;/a&gt;.  It's just that a process which can already take quite a bit of time (years) and can sometimes end in frustration takes even longer and is less certain with a membrane protein. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2017-07-21T23:00:11.120" LastActivityDate="2017-07-21T23:00:11.120" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13535" PostTypeId="2" ParentId="13525" CreationDate="2013-11-17T09:49:35.713" Score="5" Body="&lt;p&gt;This is a classical protein purification problem - you have to find ways to fractionate your mixture so that each fraction can be assayed for the activity you are interested in. When you find the active fraction you then subject that to a different type of fractionation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Salting out&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The solubility of proteins is affected by the ionic strength of the buffer. If the ionic strength is raised above a critical value (which is a characteristic of an individual protein) the protein  will precpitate, usually without being denatured. By doing a series of such precipitations at increasing ionic strengths a protein mixture can be fractionated according to this property. The salt used is ammonium sulphate, because of its very high solubility. You can find more details at this Wikipedia page (&lt;a href=&quot;http://en.wikipedia.org/wiki/Ammonium_sulfate_precipitation&quot; rel=&quot;nofollow&quot;&gt;ammonium sulphate precipitation&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Ion exchange chromatography&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Proteins have different intrinsic charges, and the net charge on a protein will vary with pH. This property is exploited in&lt;a href=&quot;http://en.wikipedia.org/wiki/Ion_exchange_chromatography&quot; rel=&quot;nofollow&quot;&gt; ion-exchange chromatography&lt;/a&gt;. In this technique the protein mixture interacts with a solid matrix carrying fixed charges. Under the correct conditions your protein plus others will bind to the matrix, while lots of other proteins won't. That's already a purification step, but you can then treat the matrix with buffers of increasing ionic strength. Weakly-bound proteins will be eluted from the matrix first, and as the ionic strength of the elution buffer increases proteins will elute in order of strength of interaction. By performing this procedure with the matrix in the form of a chromatography column and collecting eluate fractions you can achieve another step in the purification of your protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Size exclusion chromatography (gel filtration)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This technique is used to fractionate a mixture of molecules according to size. In this case the solid matrix that is used is charaterised by pores of a specific size. Proteins that are too large to enter the pores will pass through quickly;  small proteins will spend a lot of time moving in and out of the pores and so will pass through slowly; and proteins of intermediate size will spend some time in the pores. Essentially the average time spent passing through the matrix will depend upon size. &lt;a href=&quot;http://en.wikipedia.org/wiki/Ammonium_sulfate_precipitation&quot; rel=&quot;nofollow&quot;&gt;Read more here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are just three of the possible fractionation procedures - others, including  hydrophobic interaction chromatography are described &lt;a href=&quot;http://en.wikipedia.org/wiki/Ion_exchange_chromatography&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;). The key point to grasp is that using any one of these techniques will give you your protein in a fraction which also contains other proteins, but if you apply them sequentially you will progressively remove contaminants because each approach is based on a different physical property of proteins, and your target will have a unique combination of these properties. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At each step you will be assaying fractions to locate the protein of interest, and also running fractions on  SDS-PAGE to get a feeling for the number of proteins left. If you have an assay that lends itself to measuring some kind of unit of activity (as you would with an enzyme), then by also measuring the protein content of the active fraction you can express the purity as a &lt;em&gt;specific activity&lt;/em&gt; (units of activity per mg protein). At each step in your purification this specific activity should increase because you recover most of the activity, but discard a lot of the proteins that were present in the previous material. The increase in specific activity can be used to assign &#xA;a &lt;em&gt;purification factor&lt;/em&gt; to each step. A useful purification step will give a reasonable yield in combination with sigificant purification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, what order to do these steps in? I've listed them in a logical order - salt precipitation is a low-tech method that can give a quick first step and which has the advantage that it concentrates the target protein (since the precipitate is redissolved in fresh buffer). Size-exclusion chromatography doesn't deal well with large amounts of protein so is best left until later. However, protein purification is a craft, and an expert will use the available techniques according to the exact nature of the project.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the tone of your original question I had inferred that you were a beginner, but from your comments, apparently not, since you are thinking in terms of mass spec as an endpoint.  A starting concentration of pg/mL is quite a challenge, and clearly you are never going to have enough material to see your molecule on standard gels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are a couple of thoughts on aspects of your problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that  in trying to purify minor components of serum a good starting point is to deplete the serum of its major proteins. &lt;a href=&quot;http://www.rndsystems.com/Products/IDR012&quot; rel=&quot;nofollow&quot;&gt;This is a link to an imunodepletion product&lt;/a&gt;, and &lt;a href=&quot;http://www.bio-rad.com/LifeScience/pdf/Bulletin_2823.pdf&quot; rel=&quot;nofollow&quot;&gt;here is a related product&lt;/a&gt; from Biorad (no connection with either company and no recommendation implied).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also found these papers which may be of interest. (Incidentally I think you'll find that each of the techniques I described is still used, perhaps just with modern instrumentation.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22341353&quot; rel=&quot;nofollow&quot;&gt;Li,J &lt;em&gt;et al.&lt;/em&gt; (2012) Purification, identification and profiling of serum amyloid A proteins  from sera of advanced-stage cancer patients. JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES 889: 3-9 &lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21184852&quot; rel=&quot;nofollow&quot;&gt;Fertin, M &lt;em&gt;et al.&lt;/em&gt; (2011) Strategy for purification and mass spectrometry identification of SELDI peaks corresponding to low-abundance plasma and serum proteins. JOURNAL OF PROTEOMICS 74: 420-430&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, a quick look at the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood_plasma&quot; rel=&quot;nofollow&quot;&gt;plasma&lt;/a&gt; reveals that brain natriuretic peptide seems to be present at the levels that you are considering  perhaps you should look for papers describing its purification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other than that I think you have to hope that a proteomics expert will come by and give you an expert answer.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-11-17T22:30:51.070" LastActivityDate="2013-11-17T22:30:51.070" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13536" PostTypeId="1" AcceptedAnswerId="13538" CreationDate="2013-11-17T13:57:13.153" Score="2" ViewCount="724" Body="&lt;p&gt;RT is capable of synthesizing a complementary dna strand ( as in HIV life cycle.) Then why is&#xA;DNA pol used when cDNA (synthesizing the second strand of it ) has to be synthesized from mRNA ( For eg.to construct a cDNA library) ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1320" LastEditDate="2013-11-17T15:31:13.990" LastActivityDate="2013-11-17T15:31:13.990" Title="Why use DNA polymerase in making cDNA?" Tags="&lt;dna&gt;&lt;rna&gt;&lt;biotechnology&gt;&lt;retrovirus&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13537" PostTypeId="1" CreationDate="2013-11-17T14:33:06.177" Score="3" ViewCount="7213" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SdWKx.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note : Consider the y axis as 1,2,3,4(not 2,3,4) and x axis as time. Roman numerals should be considered from I-X ( some are not correct here )&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which stages show mitosis?&lt;/strong&gt;&lt;br&gt;&#xA;My answer : III-V&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which stages show meiosis?&lt;/strong&gt;&lt;br&gt;&#xA;My answer : VII-X&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I right ?&lt;/p&gt;&#xA;" OwnerUserId="4058" LastEditorUserId="3624" LastEditDate="2013-11-18T09:31:30.757" LastActivityDate="2018-12-19T06:07:40.890" Title="Interpreting graph of mitosis and meiosis" Tags="&lt;homework&gt;&lt;meiosis&gt;&lt;mitosis&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13538" PostTypeId="2" ParentId="13536" CreationDate="2013-11-17T14:54:22.980" Score="2" Body="&lt;p&gt;Reverse transcriptase, as the name suggests, uses an RNA template to create a DNA transcript (i.e., complement). Once the DNA complement has been made, DNA polymerase is used because it uses a DNA template to produce a DNA complementary strand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your specific example, HIV contains a positive-stranded, RNA genome. The HIV RT can use either RNA or DNA templates to produce DNA complements, and this is how the single-stranded RNA genome is transcribed into double-stranded DNA, before integration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To my knowledge, the RT enzymes sold commercially (for applications like RT-PCR) are typically a mix of an RT enzyme and a DNA polymerase, isolated from other retroviruses, such as murine leukemia virus. An important consideration for lab application is the production of cDNA that truly represents the RNA template of interest. Since RT enzymes typically lack a 3'-&gt;5' exonuclease activity, they are unable to &quot;proof-read&quot; the complement strand as it is being produced. In contrast, there are very efficient proof-reading DNA polymerase, and this is why a DNA polymerase (with high proof-reading ability) is used after first-strand synthesis by RT.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-11-17T14:54:22.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13539" PostTypeId="1" CreationDate="2013-11-17T16:32:56.510" Score="3" ViewCount="187" Body="&lt;p&gt;I don't know if this might have been highlighted in recent research, but a textbook I have states that &quot;the exact way in which promoter sequence affects [transcription] initiation is unclear&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm wondering if anyone can suggest sources for more information, or perhaps has seen recent research papers highlighting the properties that cause such variation between strong promoters and the weakest?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've tried researching but the older research is descriptive rather than mechanistic and the search terms involved are quite ubiquitous so it's hard to actually find more on this specific point.&lt;/p&gt;&#xA;" OwnerUserId="4202" LastActivityDate="2013-12-05T15:07:10.793" Title="How does promoter sequence affect initiation?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13540" PostTypeId="2" ParentId="13506" CreationDate="2013-11-17T19:24:48.617" Score="5" Body="&lt;p&gt;This question is very interesting and I &lt;strong&gt;would love to have a reference to an article that provides such evidence&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Decomposing your question:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Is it true that there is more genetic variance among males than among females (in humans I guess)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If the answer to (1) is yes then: Why is it so?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I am trying to address these two points below&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1. Is it true that there is more genetic variance among males than among females ?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are different ways of understanding your question 1. Do you want to talk about…&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Allele richness&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Heterozygosity&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Polymorphism&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Part of the genetic variance in phenotypic variance (heritability). I don't think it is what you meant though!&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Therefore, the question is slightly unclear and I don't know of any paper who address any of these questions anyway. So... I don't know!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. Assuming (1) is true, then Why is it so?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many possible explanations for such observation (assuming this pattern has been observed). Below I give some hypothesis I can think of. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;There might have a higher selection (survival differential) among females than males. In a consequence, genetic variance among young females is higher than among older females. In total, genetic variance among females would be lower to that of males.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There might have a very high variance on the Y-chromosom but not on the X-chromosom. This might for example be a consequence of the arrest of recombination that occur on the Y-chromosom. As a consequence of this arrest of recombination, selection hardly purge deleterious mutations (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Muller%27s_ratchet&quot; rel=&quot;nofollow&quot;&gt;Muller's Ratchet&lt;/a&gt;). See Shigeta's answer for a more detailed overview of this point. See shigeta's answer for more information.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Males might migrate more. If one look at the sex-specific genetic variance in a population (and not on the world-wide metapopulation), this variance might be greater for the sex that migrate more because different genetic background might be brought from other neighbor populations.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Higher selection within mitochondria in females very early in life (in the egg for example) resulting in a decreased mitochondrial genetic variance in females. This is maybe a bit far-fetched.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There might have other hypotheses for species for which sex of an individual is not determined by sex-chromosomes. (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Sex-determination_system&quot; rel=&quot;nofollow&quot;&gt;Sex Determination System&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Depending on what you mean in your question, I guess we might find many other hypotheses when thinking of migration, different fitness landscape (different optimum), different selection intensity.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;We might as well think of genetic variance of gender-specific gametes (especially for &lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_life_cycle&quot; rel=&quot;nofollow&quot;&gt;haplon-diplontic&lt;/a&gt; species for example)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;This evidence (assuming it has been observed) was a &lt;a href=&quot;http://en.wikipedia.org/wiki/Type_I_and_type_II_errors&quot; rel=&quot;nofollow&quot;&gt;False Positive&lt;/a&gt;!&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Note:&#xA;@terdon provided a very good explanation (which was deleted) of why males might cause most of the genetic diversity but as @terdon and I discussed (in the comments that were also deleted) this is not an explanation for greater diversity among males. The reason is that the variation is created via mutation in the testis and the ovary. The fact that most mutations happen in males does not influence the sex-specific diversity because males sire as many male offsprings than female offsprings (so do females!).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-10-18T22:59:09.500" LastActivityDate="2015-10-18T22:59:09.500" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13542" PostTypeId="1" AcceptedAnswerId="13544" CreationDate="2013-11-18T03:01:59.247" Score="2" ViewCount="5536" Body="&lt;p&gt;So 5'-AUG-3' is the start codon on an mRNA transcript &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does that mean that the tRNA anticodon is 5'-CAU-3'? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://waynesword.palomar.edu/codons.htm&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt;, I see that the tRNA anticodon for methionine is UAC, and the chart doesn't specify which end is 5' and which end is 3', but I'm guessing it's 3'-UAC-5'. I thought nucleotides are supposed to be written 5' to 3', and that's a norm, but apparently it isn't the case here? Am I missing something?&lt;/p&gt;&#xA;" OwnerUserId="4941" LastEditorUserId="3776" LastEditDate="2013-11-18T03:28:16.100" LastActivityDate="2014-03-08T01:43:48.950" Title="Orientations of codon and anticodon" Tags="&lt;molecular-biology&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13543" PostTypeId="1" CreationDate="2013-11-18T03:12:14.387" Score="1" ViewCount="67" Body="&lt;p&gt;If I do a transduction with a P1 lysate prepared from a strain that is &lt;em&gt;pro&lt;/em&gt;*C*::Tn10 and the recipient is wild type, will all my recombinants  be ProC- and Tet resistant since the Tn10 is in the &lt;em&gt;proC&lt;/em&gt; gene?&lt;/p&gt;&#xA;" OwnerUserId="4942" LastEditorUserId="4942" LastEditDate="2013-11-18T03:18:57.777" LastActivityDate="2013-11-18T03:18:57.777" Title="Transduction with P1 lysate prepared from strain that is proC::Tn10" Tags="&lt;molecular-genetics&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13544" PostTypeId="2" ParentId="13542" CreationDate="2013-11-18T03:34:36.590" Score="2" Body="&lt;p&gt;The tRNA anticodons are both complementary and anti-parallel. That means for $5'-\text{AUG}-3'$, the tRNA anticodon would be $3'-\text{UAC}-5'$.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ls8mB.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image has the mRNA oriented with the $5'$ end on the right end. It shows both, complementarity and anti-parallel configuration. The reference you cite might have cited the anticodons $3'\rightarrow 5'$ and mRNA codons $5'\rightarrow 3'$. In general, we usually cite the codes from $5'\rightarrow 3'$ but it doesn't matter until it is explicitly specified or unambiguous. &lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2014-03-08T01:43:48.950" LastActivityDate="2014-03-08T01:43:48.950" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13546" PostTypeId="1" CreationDate="2013-11-18T04:34:12.427" Score="1" ViewCount="672" Body="&lt;p&gt;Gene R is genetically linked to gene T with a recombination frequency of 0.3. Gene T and gene X assort independently from each other. Your colleague tells you that gene T and gene X reside on the same chromosome. How is this possible? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I know that R and T are on the same chromosome. T and X assort independently, so they should be on different chromosome. And then due to recombination, X gene crosses over so that it's also on the same chromosome as T and R? Can someone please help me?&lt;/p&gt;&#xA;" OwnerUserId="4941" LastEditorUserId="3615" LastEditDate="2013-11-18T13:30:49.680" LastActivityDate="2013-11-18T13:41:42.853" Title="Recombination frequency, linked genes, and independent assortment" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13547" PostTypeId="1" AcceptedAnswerId="13557" CreationDate="2013-11-18T06:30:12.193" Score="2" ViewCount="1388" Body="&lt;p&gt;I'm mostly curious about &lt;strong&gt;glycerol&lt;/strong&gt;, which I use as a sweetener. I've been told that it can cause intoxication, because it is an alcohol. Is this true?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, are there any good sugar alcohols which can be used safely without intoxication (or nasty side effects)?&lt;/p&gt;&#xA;" OwnerUserId="4943" LastEditorUserId="1320" LastEditDate="2013-11-18T21:20:39.200" LastActivityDate="2013-11-18T21:20:39.200" Title="Can sugar alcohols, and glycerol in particular, cause intoxication?" Tags="&lt;alcohol&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13549" PostTypeId="2" ParentId="13546" CreationDate="2013-11-18T13:41:42.853" Score="1" Body="&lt;p&gt;The comments pretty much answer the main concern here. But just to sum up:-  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;....T and X assort independently, so they should be on different&#xA;  chromosome....&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not necessarily. They can be on the same chromosome at such a distance that there is usually atleast one chiasma formation between them, and will undergo independent assortment, i.e.  &lt;em&gt;segregation of one gene among the gametes will be independent of the other&lt;/em&gt;. They will pretty much act and segregate like mendelian factors. Specifically, if the recombination frequency is 0.5 (50cM or map units' distance on the chromosome), they will assort independently.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;....And then due to recombination, X gene crosses over so that it's also&#xA;  on the same chromosome as T and R....&quot;  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This part is a little bit unclear. I assume (correct me if I am wrong) is that you are assuming &lt;code&gt;X,T,R&lt;/code&gt; to be alleles, which can be present on only one chromatid and hence recombination might change their distribution and positions relative to one another. But as the question states, they are genes (or specifically gene loci) which are present on both chromatids and their relative position is fixed. The recombination frequencies refer to the recombination of different alleles at this locus.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2013-11-18T13:41:42.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13550" PostTypeId="1" AcceptedAnswerId="13559" CreationDate="2013-11-18T13:44:10.893" Score="0" ViewCount="130" Body="&lt;p&gt;In whole animal cloning ( eg. Dolly ) the nucleus is taken from a somatic cell. So isn't shortening of telomeres a problem ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-11-19T12:00:35.357" Title="Telomeres in cloning experiments" Tags="&lt;genetics&gt;&lt;cloning&gt;&lt;telomere&gt;&lt;biotechnology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13551" PostTypeId="1" AcceptedAnswerId="13552" CreationDate="2013-11-18T14:02:21.807" Score="0" ViewCount="51" Body="&lt;p&gt;I understand how a plasmid library is made and how each clone is put on the nitrocellulose membrane and nucleic acid hybridization is done. What I don't understand is how each clone is &quot;identified&quot; and separately put on the membrane?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1320" LastEditDate="2013-11-18T14:34:59.253" LastActivityDate="2013-11-18T14:34:59.253" Title="What happens between making a DNA library and screening by nucleic acid hybridization?" Tags="&lt;cloning&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13552" PostTypeId="2" ParentId="13551" CreationDate="2013-11-18T14:33:54.750" Score="1" Body="&lt;p&gt;The library is 'created' during a ligation reaction: plasmid vector + insert (e.g. cDNA). That DNA is used to transform &lt;em&gt;E. coli&lt;/em&gt;, and, after plating out the transformation mixture, single bacterial colonies are obtained. Each colony contains, to a first approximation, a single plasmid species (i.e with a single insert). So each colony represents a clone, in the terms that you use. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know if anyone really does things like this any more, but originally each plate would be transferred to nitrocellulose, for probing, and to a fresh plate for archiving. This way, any colony identified as positive after nucleic acid hybridisation could be picked from the archive plate for further characterisation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This screening can be done on large format Petri dishes to reduce the number of plates needed. I know of one lab which in the 1980s used to screen &amp;lambda; libraries after plating out for plaques on cafeteria trays. That was the heroic era of molecular biology.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-11-18T14:33:54.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13553" PostTypeId="2" ParentId="13506" CreationDate="2013-11-18T14:48:57.870" Score="4" Body="&lt;p&gt;This is an interesting question and we should probably have a statistical geneticist around, so further answers may show up better than this one.  So I'm also assuming the question is: Is the rate of variation on the X,Y and autosomal chromosomes different?  Also assuming XY male heterogamy as humans have - different sex chromosomes will give different results between male/female. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main distinction being - if males absorb more mutations on X as well as Y, then it would be nigh on impossible to see this phenomenon statistically since those chromosomes get passed on to females immediately. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its important to remember that some of the X and Y regions do recombine even in men in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Pseudoautosomal_region&quot; rel=&quot;nofollow&quot;&gt;pseudoautosomal regions&lt;/a&gt;. The Y also maintains itself with a &lt;a href=&quot;http://www.nature.com/nature/journal/v423/n6942/full/nature01723.html&quot; rel=&quot;nofollow&quot;&gt;self-recombination event in meiosis&lt;/a&gt;.  So the message here applies to the SDR (sex determining regions) of the X and Y chromosomes - other regions are quite possibly not different than the other chromosomes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway I've found this modeling paper &lt;a href=&quot;http://www.genetics.org/content/184/4/1141.full.pdf&quot; rel=&quot;nofollow&quot;&gt;&quot;Patterns of Neutral Genetic Variation on Recombining Sex Chromosomes&quot;&lt;/a&gt; which estimates and compares the relative coalescence time for variations on the autosomal, X and Y regions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case the models in the paper says 'yes they are different and Y non-autosomal regions accumulate variants faster'.   The coalescence time is the amount of time for a variation to spread into the general population on one of these 3 types of regions.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In cases where there is neutral selectional pressure &quot;Close to the SDR, expected coalescence times are shorter on Y chromosomes and longer on X chromosomes than for&#xA;autosomal sites.&quot;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Which is to say speeds for incorporating variations are Y &gt; X &gt; autosomal&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the paper goes on to say that when there are more than one competing versions of the Y chromosome in a population (which seems likely to be the case), then the spread of variations on the Y goes to a normal autosomal rate.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So its likely that this effect is small overall.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has been documented that &lt;a href=&quot;http://news.nationalgeographic.com/news/2003/02/0214_030214_genghis.html&quot; rel=&quot;nofollow&quot;&gt;some Y chromosomes are very competitive&lt;/a&gt; though. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-11-18T14:48:57.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13554" PostTypeId="1" CreationDate="2013-11-18T16:30:08.837" Score="5" ViewCount="674" Body="&lt;p&gt;Since they seem to be quite connected, I'm curious if anyone knows of research comparing the Hayflick limit (and presumably by extension telomere length) between different taxa. I've heard the Hayflick limit numbers 40-50 thrown out repeatedly for humans (probably relating to the WI-38 tissue line), but how universal is this really? I Know there are particularly long lived species, but has research been done to correlate this with telomeric length, or do they simply have slower cell division?&#xA;I suppose it is worth mentioning that a Hayflick limit of 40 rounds of division is massively different from 50, since each round of division conceivably could double the number of cells...&lt;/p&gt;&#xA;" OwnerUserId="1710" LastActivityDate="2013-12-06T01:54:16.403" Title="How much does the Hayflick limit/telomere length vary across taxa and within humans?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;dna&gt;&lt;senescence&gt;&lt;telomere&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13555" PostTypeId="1" AcceptedAnswerId="13593" CreationDate="2013-11-18T17:41:07.563" Score="3" ViewCount="1304" Body="&lt;p&gt;Inspired by a question asked to me by a classmate, I have the following question about &lt;a href=&quot;http://en.wikipedia.org/wiki/Light-independent_reactions&quot; rel=&quot;nofollow&quot;&gt;Light-independent&lt;/a&gt; (dark phase) reactions in photosynthesis:-&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Let us suppose an algae sample was exposed to light for a considerable&#xA;  time so that &lt;em&gt;maximum&lt;/em&gt;( if there is a limit) NADPH concentration was&#xA;  achieved. Now if the sample is placed in dark and radioactive&#xA;  &lt;strong&gt;¹⁴CO₂&lt;/strong&gt; bubbled, will the cell be radiolabelled after some time of&#xA;  bubbling continuously?   &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I guess the answer depends on the active life of ATP and NADPH , the products of light reaction. If they are considerably stable, such that they are in sufficient concentration for executing &lt;a href=&quot;http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/dark.htm&quot; rel=&quot;nofollow&quot;&gt;Calvin cycle&lt;/a&gt; although their production (apart from respiratory ATP production) has ceased due to absence of light. If they are, then the ATP and NADPH produced during the initial exposure period will carry out carbon fixation with radioactive carbon and hence radio labelled sugars will be recoverable from the sample. If not, they will quickly degenerate (by hydrolysis, utilization or likewise) and they will be unable to carry out fixation after &lt;em&gt;some fixed time&lt;/em&gt; after stopping the light.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What, under normal conditions, should be &lt;em&gt;the time&lt;/em&gt; after which the light-reaction products are no longer capable of fixing &lt;strong&gt;CO₂&lt;/strong&gt; by Calvin cycle? And, ultimately, will the presence of radioactivity in sugars for the scenario above depend on the species of plant?   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[I am ignoring all radioactivity due to dissolution of &lt;strong&gt;¹⁴CO₂&lt;/strong&gt; in cytoplasm]&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3340" LastEditDate="2014-10-09T15:45:52.273" LastActivityDate="2014-10-09T15:45:52.273" Title="Independence of Light independent reaction in photosynthesis?" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13556" PostTypeId="1" AcceptedAnswerId="13558" CreationDate="2013-11-18T18:39:06.790" Score="2" ViewCount="409" Body="&lt;p&gt;It's possible that this question is better suited for stack overflow, but I think the ecologists on this site might be better equipped to answer it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm trying to study two geographically-isolated populations of the same species. Inspecting the distributions, I see that both are bimodal (there's some seasonality to their occurrence), but the peaks in one population are much higher and much narrower (i.e., the variance of the local peaks is smaller).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What sort of statistical test would be appropriate to determine whether these differences are significant?&lt;/p&gt;&#xA;" OwnerUserId="1906" LastEditorUserId="3624" LastEditDate="2013-11-18T20:29:22.543" LastActivityDate="2013-11-21T08:54:19.927" Title="How do I compare the variance of a distribution of species in one area versus another?" Tags="&lt;ecology&gt;&lt;statistics&gt;&lt;species&gt;&lt;species-distribution&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13557" PostTypeId="2" ParentId="13547" CreationDate="2013-11-18T18:42:04.187" Score="3" Body="&lt;p&gt;Well, I was intrigued by this, and my intuitive response was that it would never be toxic at reasonable doses, but I was wrong.&lt;/p&gt;&#xA;&lt;p&gt;A quick Google search led me to this paper:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19514878&quot; rel=&quot;nofollow noreferrer&quot;&gt;Andresen, &lt;em&gt;H. et al.&lt;/em&gt; (2009) Severe glycerol intoxication after Menière's disease diagnostic--case report and overview of kinetic data. Clin. Toxicol. 47: 312 - 6&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Apparently in the Klockhoff test for Menière's disease the patient is given an oral glycerol dose of 1.2 - 1.5 g/kg (50% in water) then observed over a period of 4-5 h. The other details of the test don't concern us here. In this case report a patient suffering neurological symptoms was found to have previously undergone a Klockhoff test at another hospital, and it was estimated that he must have received a dose of 3.88 –3.95 g/kg.&lt;/p&gt;&#xA;&lt;p&gt;Here are two sections from the paper's introduction (references removed).&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Glycerol is well known as a nontoxic substance (LD50 &amp;gt; 25 g/kg in the rat). Possible side effects of the Klockhoff test include headache and nausea. During treatment of brain edema, additional adverse effects such as diarrhea and vomiting were reported, symptoms comparable to those reported for intensive osmolar diuretics. The GESTIS database ranks glycerol in general as a substance with very low toxicity. However, severe symptoms after oral ingestion of glycerol have been reported to occur. Doses exceeding 0.7 g/kg BW have been regarded as potentially toxic for adults. After doses of up to 1.4 g/kg BW, only mild symptoms such as headache, nausea, and diuresis appear. Reportedly, these symptoms are also associated with glycerol treatment of brain edema. In individual cases, an oral dose of 100 g of glycerol has been reported to cause drowsiness, cyanosis, renal pain, and bloody diarrhea.&lt;/p&gt;&#xA;&lt;p&gt;Martindale Reference Desk reports headache, thirst, nausea, and hyperglycemia as adverse effects. Glycerol may also produce cardiac arrhythmia and hyperosmolar nonketonic coma. These effects are mainly based on its dehydrating properties. Hemolysis has been reported to exclusively occur after intravenous infusion. In fact, most of the major toxic effects of glycerol, such as hemolysis, hemoglobinuria, and renal failure, seem to strictly correlate with serum concentration of glycerol and the route of administration.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It appears then that any toxic effects of glycerol are not due to its alcohol nature &lt;em&gt;per se&lt;/em&gt; but rather because it can become elevated in the blood leading to osmotic effects. The authors estimated that 10 h after administraion of the glycerol the concentration in the patient's serum was approximately 39 mM, compared to a physiological basal level in the range 0.05–0.3 mmol/L. The patient's serum level fell to the basal level over a period of 30 hours.&lt;/p&gt;&#xA;&lt;p&gt;Just to put this in some perspective, in the UK the legal alcohol limit for drivers is 80 mg/100 mL which corresponds to 17.4 mmol/L.&lt;/p&gt;&#xA;&lt;p&gt;I think that recommending sugar alcohols would fall under the heading of medical advice (not that I have any such recommendations).&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-11-18T20:52:36.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13558" PostTypeId="2" ParentId="13556" CreationDate="2013-11-18T19:55:42.863" Score="3" Body="&lt;p&gt;These are just some preliminary ideas...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think you should look at the seasonal distributions separately, since the bimodal distribution is the outcome of two fairly separate processes. The two distributions might also be controlled by different mechanisms, so that e.g. winter distributions might be more sensitive to yearly climate. If you want to look at population differences and reasons for these I think it is therefore more useful to study seasonal distributions separately. An exploratory analysis could be to compare distribution percentiles (north/south and east/west coordinates) to look at range edges, or to use a fixed number of edge observations to establish borders. The weighted centre-point of population distributions can be used to look for differences in overall position. If you have grid occurences, percentage overlap between species/populations could maybe also be useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you haven't already, you look also look at &lt;a href=&quot;http://www.cs.princeton.edu/~schapire/maxent/&quot; rel=&quot;nofollow&quot;&gt;Maxent&lt;/a&gt;, which is a widely used software for modelling species distributions and habitats. Look at &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1472-4642.2010.00725.x/abstract&quot; rel=&quot;nofollow&quot; title=&quot;Elith et al. 2011. A statistical explanation of MaxEnt for ecologists. Diversity and distributions 17(1): 43–57.&quot;&gt;Elith et al. (2011)&lt;/a&gt; for an overview. If you want to look at changes over time (even if this doesn't seem to be your main point) you should also check out dynamic occupancy models that use occurrence records to model species distribution while taking detectability into account, e.g. &lt;a href=&quot;http://www.esajournals.org/doi/abs/10.1890/08-0141.1&quot; rel=&quot;nofollow&quot; title=&quot;MacKenzie et al. 2009. Modeling species occurrence dynamics with multiple states and imperfect detection. Ecology 90&quot;&gt;MacKenzie et al. (2009)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for a simple test for differences in variance (basically a test of homoscedasticity), there is &lt;a href=&quot;http://en.wikipedia.org/wiki/Levene%27s_test&quot; rel=&quot;nofollow&quot;&gt;Levine's test&lt;/a&gt;, which is used to compare variances of distributions between groups. &lt;a href=&quot;http://en.wikipedia.org/wiki/Bartlett%27s_test&quot; rel=&quot;nofollow&quot;&gt;Bartlett's test&lt;/a&gt; is an alternative, but Levene's test is supposed to be more robust to non-normality. In R the Levene's and Bartlett's tests are found in &lt;code&gt;library(car)&lt;/code&gt;. However, these are only suitable for unimodal distributions so, again, you should look at seasons independently. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2013-11-21T08:54:19.927" LastActivityDate="2013-11-21T08:54:19.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13559" PostTypeId="2" ParentId="13550" CreationDate="2013-11-18T20:41:31.757" Score="1" Body="&lt;p&gt;Yes, it is. Dolly died of cancer in early years. Length of the telomeres depends on the donor tissue: &quot;In Dolly's study, the animal produced from fetal tissue appeared to have telomere lengths non-distinguishable from normal controls, while the other two, including Dolly, which originated from adult cells, were found to have shorter telomeres.&quot; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC305328/&quot; rel=&quot;nofollow&quot;&gt;Xu &amp;amp; Yang, 2003&lt;/a&gt;) This statement doesn't mean that embryonic cells are the only cells able to maintain telomere length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This also doesn't mean, that offspring of animals cloned from nuclei with shorter telomeres, inherits this shortedness: &lt;a href=&quot;https://www.jstage.jst.go.jp/article/jrd/57/5/57_11-017A/_article&quot; rel=&quot;nofollow&quot;&gt;Miyashita et al, 2011&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Xu &amp;amp; Yang, 2003 review is pretty old, you can find &lt;a href=&quot;http://scholar.google.de/scholar?q=telomeres%20cloned%20animals&amp;amp;as_ylo=2007&quot; rel=&quot;nofollow&quot;&gt;newer articles on the topic&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2013-11-18T20:41:31.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13562" PostTypeId="1" AcceptedAnswerId="13564" CreationDate="2013-11-19T04:57:58.117" Score="1" ViewCount="165" Body="&lt;p&gt;As far as the genetic content of each cell is concerned I have read to my satisfaction that all cells of a person's body except the red blood cells (with no nucleus and so no genetic message) and the gametes ( with just half the genetic copy or 23 of the 46 chromosomes) have the same DNA copy and so all the 60,000-80,000 estimated genes. The only difference is that which genes are active and which are dormant. For example the gene for insulin would be present in all cells but would be active and functional only in the cells of pancreas assigned the function of insulin production.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is:-&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What is the factor or process or molecule or information that&#xA;  tells a cell or helps it to activate the genes necessary for its own&#xA;  growth and more importantly its designated function?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4947" LastEditorUserId="1320" LastEditDate="2013-11-19T09:18:00.893" LastActivityDate="2013-11-19T09:18:00.893" Title="DNA and gene activation" Tags="&lt;molecular-genetics&gt;&lt;genomics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13564" PostTypeId="2" ParentId="13562" CreationDate="2013-11-19T05:28:01.373" Score="2" Body="&lt;p&gt;Your question refers to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10061/&quot; rel=&quot;nofollow&quot;&gt;differential gene expression&lt;/a&gt; and methods of &lt;a href=&quot;http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Promoter.html&quot; rel=&quot;nofollow&quot;&gt;Eukaryotic gene regulation&lt;/a&gt;. This is a &lt;em&gt;very&lt;/em&gt; broad question for there are a lot of methods to control gene expression. They can function as transcription control, mRNA processing control, translational control, post-translational control and so on in eukaryotes. In prokaryotes, the methods include &lt;a href=&quot;http://en.wikipedia.org/wiki/Operon&quot; rel=&quot;nofollow&quot;&gt;the operon model&lt;/a&gt; etc, which is much simpler than eukaryotes and multicellualr organisms but still quite complicated when studied in its entirety. &lt;a href=&quot;http://www.csun.edu/~cmalone/pdf360/Ch20-1%20euk%20gene%20reg.pdf&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; and &lt;a href=&quot;http://carroll.molbio.wisc.edu/466_class_files/lecture_notes/466n_Lectures_22-23_white.pdf&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; are few places where you can study differential gene expression. As an introductory text,  chapter 19 of &lt;a href=&quot;http://bcs.whfreeman.com/thelifewire/default.asp?s=&amp;amp;n=&amp;amp;i=&amp;amp;v=&amp;amp;o=&amp;amp;ns=0&amp;amp;t=&amp;amp;uid=0&amp;amp;rau=0&quot; rel=&quot;nofollow&quot;&gt;Life:The science of Biology by Purves, Sadava, Orions and Heller&lt;/a&gt;(the link is to a supplementary-material site and not to the book itself), Otherwise, to elucidate all mechanisms here would become too long and in any case uncomprehensive. &lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="1320" LastEditDate="2013-11-19T06:08:02.390" LastActivityDate="2013-11-19T06:08:02.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13565" PostTypeId="1" AcceptedAnswerId="13571" CreationDate="2013-11-19T08:25:17.750" Score="1" ViewCount="218" Body="&lt;p&gt;I'm looking for an application where you can find pathways by selecting a chemical occurring in it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, for example,&#xA;selecting 6-phosphogluconolactone brings up the pentose phosphate pathway or any other where it occurs as an intermediate or product.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Same could be possible for endocrine or any other signalling. The target organism is human.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there anything like this in existence?&lt;/p&gt;&#xA;" OwnerUserId="673" LastEditorUserId="1320" LastEditDate="2013-11-19T19:26:54.910" LastActivityDate="2013-11-19T19:26:54.910" Title="(Web)app to search metabolic/signalling pathways" Tags="&lt;biochemistry&gt;&lt;bioinformatics&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13566" PostTypeId="1" CreationDate="2013-11-19T08:59:47.843" Score="-1" ViewCount="465" Body="&lt;p&gt;Imagine an animal that is incapable of digesting a particular kind of food. Now suppose the mutations for digesting that food were to suddenly appear within the population. There still has to be a corresponding change in the animal's behavior, correct? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I mean, I don't go around thinking, &quot;Gee, how could I get the best out of my genes to get ahead of my competition?&quot; There seems to be a need for changing behaviour to get the benefit of the new mutations, which for me allows room for divine providence (e.g. A God) to guide evolution at the level of animal behavior at least.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I missing something? Does evolution by selection not require device providence etc?&lt;/p&gt;&#xA;" OwnerUserId="625" LastEditorUserId="1590" LastEditDate="2016-08-19T20:44:55.510" LastActivityDate="2016-08-19T20:44:55.510" Title="Does evolution by selection require that individuals consciously change behaviour in an effort to suit their genes?" Tags="&lt;evolution&gt;&lt;philosophy-of-science&gt;" AnswerCount="3" CommentCount="13" FavoriteCount="1" ClosedDate="2016-08-18T12:42:49.637" ContentLicense="CC BY-SA 3.0" />
  <row Id="13567" PostTypeId="2" ParentId="13566" CreationDate="2013-11-19T09:14:45.967" Score="11" Body="&lt;p&gt;The theory of evolution via selection does not require any kind of divine intervention. It proposes that &lt;a href=&quot;http://en.wikipedia.org/wiki/Mutation&quot; rel=&quot;nofollow&quot;&gt;mutations&lt;/a&gt; randomly occur within the DNA, this causes changes in the phenotype (e.g. allowing digestion of a common food source), these changes can be good or bad (beneficial or deleterious). As a result, those with &quot;good&quot; mutations achieve more reproductions (the fitness of those mutant allele carriers is higher) and those mutations spread through the population. You can not direct the evolution of your DNA because &lt;strong&gt;mutation is random&lt;/strong&gt;, even if we artificially induce mutations, &lt;strong&gt;we can not direct what the mutation does to the phenotype&lt;/strong&gt; (though we can sometimes induce specific mutations known to have certain phenotypic effects). Selection favours some phenotypes over others but can only work with the mutations it is presented with - it can not direct the evolution of animals with wheels if mutations that allow wheels to form do not occur. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this sequence you can see the evolution of a phenotype is best explained in a most parsimonious way without the inclusion of divine intervention. It is the principles of &lt;a href=&quot;http://en.wikipedia.org/wiki/Occam%27s_razor&quot; rel=&quot;nofollow&quot;&gt;Occam's Razor&lt;/a&gt;. &lt;strong&gt;Calling divine intervention in to this theory would add further, and unwarranted, complication to the model&lt;/strong&gt; and we would then have to find strong evidence for the existence of a divine being, something which is still yet to happen in the eyes of most evolutionary biologists. Strong evidence has been found which suits the theory without divine intervention (including unnecessary and untestable components to a theory goes against the basic principles of science).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Selection itself, though largely involved in evolution, is not necessary for traits to evolve. The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16120807&quot; rel=&quot;nofollow&quot;&gt;neutral theory&lt;/a&gt; proposed by &lt;a href=&quot;http://en.wikipedia.org/wiki/Motoo_Kimura&quot; rel=&quot;nofollow&quot;&gt;Motoo Kimura&lt;/a&gt; and developed in the last few decades suggests that traits can evolve with out selection, via genetic drift. This means traits develop in populations purely due to random sampling of neutral (or near neutral) random alleles. The relative importance of Selectionist vs Neutralist theories remains hotly debated within evolutionary biology.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Explaining your imaginary scenario with a current theory of evolution: A new digestive enzyme&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The scene:&lt;/strong&gt; There is a population of 100 deer. 50 males and 50 females. There is a potential for variance in mating success and that mating success is defined solely by the strength of the male. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Selection affects a trait:&lt;/strong&gt; Males that digest their food better grow bigger and stronger. Thus selection favours males that get the most out of their food. If the ability to digest is completely genetically determined by a single locus (for simplification lets say it is) and there is only one allelic variant (one version of the gene) in our first generation then mating success will be equal among the males. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A mutant arises:&lt;/strong&gt; In the next generation a single male carries a mutation in that locus. It is a mutated version of the gene which makes a key digestive enzyme work more efficiently. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Selection acts:&lt;/strong&gt; This male is 10% larger and stronger than other males, and therefore sires more offspring in the next generation than any other male. These next generation offspring (technically half if it was a single mutation in a diploid organism - the other half have the ancestral haplotype) have the mutant allele. Then those males with the mutant allele also get more of the matings and so on and so on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The allele is then spreading through the population.&lt;/strong&gt; It will continue until all members of the population have the same allele (fixation) or will start over if a new allele arises which is even better. That's all evolution is, no divine beings necessary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What if the allele was neutral?&lt;/strong&gt; If the gene for a digestive enzyme existed but was not necessary in an organisms diet it would not know it could go out and use that food source. It may not even be able to. For example, a single fruitfly carries a mutation which has no cost and allows it to digest lactose. It is unlikely to be able to utilize that allele, because dairy products are not part of it's diet and not available in the wild. The allele would only drift in the population, eventually being lost (most likely as it starts at low frequency) or becoming fixed in the population. You can see a &lt;a href=&quot;http://griffinevo.wordpress.com/2013/10/18/fisher-wright-genetic-drift-simulation-for-use-in-r/&quot; rel=&quot;nofollow&quot;&gt;genetic drift simulation I wrote in R here&lt;/a&gt;. You can set f=1 and then play around with population size, number of generations, and replicates to get a feel for this process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note it is worth considering the effects of pleiotropy (if an allele has a good effect on one trait but a negative effect on another - including traits in different environments) and linkage (if the good allele is close to some deleterious mutations in the DNA it will struggle to spread until it is separated by recombination).&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-11-20T23:08:19.730" LastActivityDate="2013-11-20T23:08:19.730" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="13568" PostTypeId="1" CreationDate="2013-11-19T09:32:55.907" Score="11" ViewCount="20630" Body="&lt;p&gt;Most of us have one dominant hand. We find it nigh on impossible to do very delicate or dextrous activities with our other-hand. This seems like an apparent weakness, and a rather odd one when you first think about it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cursory internet searches revealed unexpected findings. One website said it has mostly negative effects on the brain. However I don't trust the source at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd be interested to know about the &quot;story&quot; about the good and bad of ambidextrous physiology. Particularly, I am interested in the neuroscience of ambidextrous people. &lt;/p&gt;&#xA;" OwnerUserId="4949" LastEditorUserId="3553" LastEditDate="2015-11-23T03:49:42.600" LastActivityDate="2015-12-10T08:40:24.883" Title="What are the advantages and disadvantages of being ambidextrous?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;brain&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13569" PostTypeId="1" CreationDate="2013-11-19T11:46:33.350" Score="1" ViewCount="2918" Body="&lt;p&gt;What matter if I increase the temperature to 95&amp;deg;C. So double-strand DNA denatured into two ssDNA, and then I decrease the temperature to room temperature. Are they able to reassociate after denaturation?&lt;/p&gt;&#xA;" OwnerUserId="3894" LastEditorUserId="1320" LastEditDate="2013-11-19T11:58:15.980" LastActivityDate="2013-11-19T21:23:35.217" Title="Can two denatured DNA strands reassociate?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13570" PostTypeId="2" ParentId="13550" CreationDate="2013-11-19T12:00:35.357" Score="1" Body="&lt;p&gt;After cloning, the recipient cell is converted into embryonic stem cell. When it is a stem cell, it can produce enzyme telomerase itself which a naturally occurring enzyme that maintains telomeres and prevents them from shortening during cell division in cells. So i think there are no problem on shortening of telomeres.&lt;/p&gt;&#xA;" OwnerUserId="3894" LastActivityDate="2013-11-19T12:00:35.357" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13571" PostTypeId="2" ParentId="13565" CreationDate="2013-11-19T13:30:49.103" Score="1" Body="&lt;p&gt;KEGG  &lt;a href=&quot;http://www.genome.jp/kegg/kegg2.html&quot; rel=&quot;nofollow&quot;&gt;http://www.genome.jp/kegg/kegg2.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GLAMM &lt;a href=&quot;http://glamm.lbl.gov/&quot; rel=&quot;nofollow&quot;&gt;http://glamm.lbl.gov/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I had to truncate to gluconolactone to make the search work in both cases.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-11-19T15:33:18.580" LastActivityDate="2013-11-19T15:33:18.580" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13572" PostTypeId="2" ParentId="5676" CreationDate="2013-11-19T19:12:44.387" Score="13" Body="&lt;p&gt;How humans evolved to have head / beard hair that continues to grow longer than other animals is a topic that many anthropologists &amp;amp; biologists are still not sure about &amp;amp; there is no general consensus as to &quot;why&quot; yet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The three main views that I am aware of however are : &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1) Evolution of the &quot;Aquatic Ape.&quot;&lt;/strong&gt; (Ingram, 2000: Morgan 1997; 1982) &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Infants, in order to hold onto their mothers in the water, would latch onto her hair. Limiting separation from the mother &amp;amp; increasing chances of survivability&lt;/li&gt;&#xA;&lt;li&gt;Longer hair meant that infants / small children would need to swim less in order to get to their mother&lt;/li&gt;&#xA;&lt;li&gt;Believed to be supported even further when you consider that aquatic mammals are almost always hairless, indicating that at one point, humans were highly &quot;aquatic&quot; mammals.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2) No real benefit, but used as a tool for &quot;mate selection.&quot;&lt;/strong&gt; (Darwin, 1871; Cooper 1971)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The view held by many of the Darwin school of thought (I do not mean that as a derogatory), is that at first, &quot;hairiness&quot; was sexually attractive, but eventually &quot;hairlessness&quot; became more sexually attractive in most places (i.e. the face to see facial expressions &amp;amp; socialize better; Wong &amp;amp; Simmons 2001)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A sign of &quot;virility&quot; &amp;amp; &quot;health&quot; as can be seen in the mate-selection behavior of lions. Which is true even today as human diagnostic material for health (Klevay, 1972).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;3) Practical evolutionary benefits for the human species specifically&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;A lot of body heat escapes from the head, probably the most important part of your body. Hair is a good insulator that can keep in heat. This increases survivability in colder climates. (Wong &amp;amp; Simmons 2001; Bubenick 2003). (A disputed but considered credible reason, especially when you compare hair length and types across different regions throughout history)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Protection against damaging UV rays (while still permitting adequate Vit.D3 to come through) &amp;amp; some protection from free-radicals or other harmful particles. Because we became bi-pedal, the head was the main area exposed to the sun (as well as some of our back). Extending hair's usefulness to even hot environments, while other body hair became less important with the development of sweat glands (Wheeler 1985).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Heightened &quot;Situational Awareness&quot; through &quot;Touch sense.&quot; A concept that may seem silly at first but has some evidence to support the theory. Though the hair is not &quot;alive,&quot; it is connected to the follicles &amp;amp; your nerves. In a nutshell, it may help to increase &quot;sensory awareness&quot; &amp;amp; &quot;data gathering&quot; of your environment, which would favor longer hair. This would be an asset in survivability (Kardong 2002; keratin.com 2010; Sabah 1974; washington.edu)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Though not a collegiate Journal article, if reasonably credible, this small article is an interesting case for supporting hair &amp;amp; &quot;Touch sense&quot; in &quot;recent history&quot; &amp;amp; in combat-survival : &lt;a href=&quot;http://www.sott.net/article/234783-The-Truth-About-Hair-and-Why-Indians-Would-Keep-Their-Hair-Long&quot;&gt;http://www.sott.net/article/234783-The-Truth-About-Hair-and-Why-Indians-Would-Keep-Their-Hair-Long&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I personally lean 90% &quot;Evolutionary benefits&quot; &amp;amp; 10% &quot;Mate selection&quot; as to reasons why humans' hair continues to grow longer than other animals. Beard &amp;amp; head.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this info was a little helpful. &#xA;There are copious amounts of other respectable articles on each point, but I only referenced a few.&lt;/p&gt;&#xA;" OwnerUserId="4953" LastEditorUserId="4953" LastEditDate="2013-11-19T19:40:54.370" LastActivityDate="2013-11-19T19:40:54.370" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13573" PostTypeId="1" CreationDate="2013-11-19T20:13:14.657" Score="3" ViewCount="822" Body="&lt;p&gt;How common is complete &lt;a href=&quot;http://en.wikipedia.org/wiki/Heterochromia_iridum&quot; rel=&quot;nofollow&quot;&gt;heterochromia&lt;/a&gt;? &lt;em&gt;(One iris is a different color from the other)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any statistics available for this? If no, why not?&lt;/p&gt;&#xA;" OwnerUserId="4954" LastEditorUserId="3624" LastEditDate="2014-11-24T10:13:40.527" LastActivityDate="2014-12-02T13:22:27.817" Title="How common is complete heterochromia?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13574" PostTypeId="1" CreationDate="2013-11-19T20:48:10.257" Score="4" ViewCount="961" Body="&lt;p&gt;In Adaptive dynamic :  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;what is the difference between &lt;strong&gt;Ecological Differentiation&lt;/strong&gt; and &lt;strong&gt;Ecological Divergence&lt;/strong&gt; ?&lt;/p&gt;&#xA;" OwnerUserId="4955" LastActivityDate="2013-12-24T14:31:52.963" Title="DIfference between diversification and differentiation" Tags="&lt;evolution&gt;&lt;differentiation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13575" PostTypeId="2" ParentId="13569" CreationDate="2013-11-19T20:48:47.393" Score="1" Body="&lt;p&gt;Yes, heating the DNA above 94°C for some length of time will melt, or denature, dsDNA into two ssDNA strands. Upon cooling, the complementary strands will come back to anneal. The degree and completeness of annealing, or association, is dependent on a number of factors including the rate of cooling and structural properties of the DNA itself (%GC content, secondary structure). I would not expect that the majority of ssDNA strands will completely anneal to a single, complementary dsDNA strand. What is more likely is that the DNA mix will look more like spaghetti with one strand partly annealed to two other strands. When performing PCR, the primers are designed to be specific, and added in excess, so that you bias the odds of annealing to favour a primer:ssDNA association. If this weren't the case, we could not possibly have efficient PCR amplification.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="948" LastEditDate="2013-11-19T21:23:35.217" LastActivityDate="2013-11-19T21:23:35.217" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13576" PostTypeId="1" CreationDate="2013-11-19T21:21:00.380" Score="4" ViewCount="200" Body="&lt;p&gt;An interesting question that was asked during a lecture about human reproduction: what is the biological mechanism behind some pregnant women getting monthly spotting that they mistake for a regular period? I've found articles and research papers about bleeding during zygote implantation, ectopic pregnancies and problems with the placement of the placenta, but nothing regarding menses-like bleeding during otherwise unproblematic pregnancies.&lt;/p&gt;&#xA;" OwnerUserId="4587" LastActivityDate="2014-07-29T12:12:19.403" Title="Why do some women have menstruation-like spotting throughout their pregnancy?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13577" PostTypeId="2" ParentId="13566" CreationDate="2013-11-19T21:23:48.907" Score="6" Body="&lt;p&gt;@rg255 already did a good job answering the main thrust of your question, I will address this part: &quot;There seems to be a huge amount of room for divine providence to guide evolution at the level of animal behavior, at least. Why then do scientists with a philosophical materialist outlook gloss over this?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course there is &quot;room&quot;, there is room in the theory of evolution to posit that small, green, tasty but mean little pixies come and push the new food down the creature's gullets, thus teaching them to use new food sources. There is room to posit that invisible, intelligent lichen from Alpha Centauri are actually using brain waves to guide the evolutionary choices of species in a global scale. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While there is clearly room to posit these theories, there is absolutely no evidence for them. The scientific community is not &quot;glossing over&quot; anything, it is just ignoring various (infinite in fact) theories for which we have absolutely no evidence in favor of those for which we have. This is a classic fallacy that was very nicely put to sleep by &lt;a href=&quot;http://en.wikipedia.org/wiki/Russell%27s_teapot&quot; rel=&quot;nofollow&quot;&gt;Russell's teapot&lt;/a&gt; argument:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many orthodox people speak as though it were the business of sceptics to disprove received dogmas rather than of dogmatists to&#xA;  prove them. This is, of course, a mistake. If I were to suggest that&#xA;  between the Earth and Mars there is a china teapot revolving about the&#xA;  sun in an elliptical orbit, nobody would be able to disprove my&#xA;  assertion provided I were careful to add that the teapot is too small&#xA;  to be revealed even by our most powerful telescopes. But if I were to&#xA;  go on to say that, since my assertion cannot be disproved, it is&#xA;  intolerable presumption on the part of human reason to doubt it, I&#xA;  should rightly be thought to be talking nonsense. If, however, the&#xA;  existence of such a teapot were affirmed in ancient books, taught as&#xA;  the sacred truth every Sunday, and instilled into the minds of&#xA;  children at school, hesitation to believe in its existence would&#xA;  become a mark of eccentricity and entitle the doubter to the&#xA;  attentions of the psychiatrist in an enlightened age or of the&#xA;  Inquisitor in an earlier time.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you feel that the world you observe is best explained by assuming the existence of an omniscient god who guides the evolutionary process, then that is your right. However, the fact that you believe this to be true does not make it so any more than my believing it to be false disproves it. We are not glossing anything over when we don't take that belief seriously, no more than when we don't take Russell's teapot seriously. The Christian faith, like many others, is built on the assumption that a god exists, it will never attempt to prove or disprove that assumption because such proof would be sacrilege, the entire edifice is built on &lt;em&gt;faith&lt;/em&gt; not evidence. If we do not share that belief, why should we attempt to fit our observations into the ideological scaffold provided by someone else's belief system? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you feel that one theory explains what you observe better than another, the onus is on you to prove it so. That is in fact the beauty of science, it is what sets it apart from most other areas of human endeavor: we change our minds when presented with compelling evidence to do so. Indeed, the history of science is littered with discarded theories. If you can come up with any decent evidence to support a theory, then that theory will (eventually) be taken seriously. Until you do, asking others to consider it based solely on the fact that you believe it to be true is hubris to say the least.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1590" LastEditDate="2016-08-17T08:50:09.003" LastActivityDate="2016-08-17T08:50:09.003" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="13579" PostTypeId="1" CreationDate="2013-11-19T22:39:18.167" Score="1" ViewCount="1101" Body="&lt;p&gt;So I'm asking this in reference to the injection of insulin, which is commonly done subcutaneously (in the hypodermis, a fatty part of skin). Now I know proteins usually get into the blood when digested through the stomach/intestines - but I was wondering how they manage to get into the blood when injected into muscles/fat? I know there are capillaries pretty much everywhere, but from what I've researched proteins are too large to get through capillary walls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That begs the question then, how do proteins manage to get into the blood stream when injected? I can't really envisage large capillaries, because surely they'd have huge holes in them or whatever to allow large proteins like insulin in. Any help on this one? Cheers&lt;/p&gt;&#xA;" OwnerUserId="4957" LastActivityDate="2013-12-20T21:28:13.197" Title="How do proteins get into the blood stream?" Tags="&lt;proteins&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13580" PostTypeId="1" CreationDate="2013-11-19T22:53:22.877" Score="11" ViewCount="387" Body="&lt;p&gt;After watching this &lt;a href=&quot;https://www.youtube.com/watch?v=pwNMvUXTgDY&quot;&gt;SciShow video&lt;/a&gt; on sleep, I wonder about &lt;a href=&quot;http://en.wikipedia.org/wiki/Lucid_dream&quot;&gt;lucid dreaming&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically: &lt;em&gt;Does lucid dreaming and associated directed agency within Lucid Dreaming decrease the regenerative effect of sleep?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is, if I gained the skill of lucid dreaming - would I be negatively tampering with the brain's autonomous healing processes for the period that I had conscious control or even simply objective awareness during sleep?&lt;/p&gt;&#xA;" OwnerUserId="4788" LastEditorUserId="1306" LastEditDate="2013-11-19T23:54:23.253" LastActivityDate="2015-07-25T12:51:00.640" Title="Does Lucid Dreaming decrease the regenerative effect of sleep?" Tags="&lt;brain&gt;&lt;sleep&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13581" PostTypeId="2" ParentId="13539" CreationDate="2013-11-19T23:04:53.297" Score="2" Body="&lt;p&gt;I agree that it is hard to search for papers but from graduate level classes this is some of the additional insight I have gained. Sequence context of promoters is important. Specific DNA sequences (motifs) can act as binding sites for specific transcription factors and combinations of these transcription factors help recruit RNA pol II to the promoter. These combinations of proteins are spatially and temporally regulated and will help decide if gene that is next to promoter will be activated. A luciferase reporter assay is often used to determine the strength of a promoter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example is as follows: A strong promoter might have certain histone marks that would recruit proteins to remodel the chromatin to be more accessible exposing binding sites of transcription factors that help recruit RNA Pol II. A weaker promoter might have less transcription factor binding sites or less chromatin accessibility and thus it is harder for RNA Pol II to be recruited. There are also some kinetics aspects you must keep in mind.&lt;/p&gt;&#xA;" OwnerUserId="766" LastActivityDate="2013-11-19T23:04:53.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13582" PostTypeId="2" ParentId="13416" CreationDate="2013-11-19T23:16:59.950" Score="2" Body="&lt;p&gt;There are some pretty good articles on Wikipedia about antibody production &lt;a href=&quot;http://en.wikipedia.org/wiki/Monoclonal_antibodies#Production&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Polyclonal_antibody#Production&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. My crude understanding is that, you will have to grow and animal and bleed or sacrifice it to extract antibodies. This process along with purification costs a bit of time + money. Additionally, antibodies for humans must be grown under more stringent conditions to avoid contaminants and reacting to human immune system.&lt;/p&gt;&#xA;" OwnerUserId="766" LastActivityDate="2013-11-19T23:16:59.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13583" PostTypeId="2" ParentId="11390" CreationDate="2013-11-19T23:22:35.730" Score="2" Body="&lt;p&gt;The RAW signal values from each microarray are transformed and processed to give you normalized signal values for each microarray. The transformation and processing steps are standard but different for each manufacture. Each manufacture uses a different method/technology to obtain signal values. Thus, signal values are not directly comparable between different microarray technologies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Experiments using different technologies might get similar RANK of results but the normalized signal values will be different. You can have a look at &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/&quot; rel=&quot;nofollow&quot;&gt;GEO&lt;/a&gt; for a list of datasets and commonly used technologies. I have no clue what you mean by applying classification (are you looking to cluster the results from different microarray technologies run on the same experiment? I'm pretty sure a comparison of microarray technologies has been done before/already)&lt;/p&gt;&#xA;" OwnerUserId="766" LastActivityDate="2013-11-19T23:22:35.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13584" PostTypeId="1" CreationDate="2013-11-20T01:50:53.710" Score="4" ViewCount="743" Body="&lt;p&gt;Some motivational speakers may say that regrets are only useful to learn something from.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the other advantages?&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="3615" LastEditDate="2013-11-20T09:06:22.160" LastActivityDate="2013-11-20T13:17:15.607" Title="What is the evolutionary advantage of regret?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13585" PostTypeId="1" AcceptedAnswerId="13592" CreationDate="2013-11-20T02:14:00.497" Score="4" ViewCount="138" Body="&lt;p&gt;Photographed in Rocky Point, Mexico. Any ideas about this plant? Thank you!  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://imgur.com/x591gWV&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.imgur.com/x591gWV.jpg&quot; title=&quot;Hosted by imgur.com&quot; /&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4150" LastActivityDate="2013-11-20T20:40:13.913" Title="Identification of this plant?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13586" PostTypeId="2" ParentId="13584" CreationDate="2013-11-20T11:12:28.960" Score="6" Body="&lt;p&gt;Very interesting question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First I'd like to highlight that this question relates to a very hypothetical field of evolutionary biology which is &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionary_psychology&quot; rel=&quot;noreferrer&quot;&gt;evolutionary psychology&lt;/a&gt;. This wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionary_approaches_to_depression&quot; rel=&quot;noreferrer&quot;&gt;evolutionary approaches to depression&lt;/a&gt; might be of interest as well. One sentence says: &quot;Feelings of regret associated with depression also cause individuals to reflect and analyze past events in order to determine why they happened and how they could have been prevented&quot;. It basically says the same thing than you said in your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What other advantages might &quot;regrets&quot; have? Before trying to answer it, I'd like to ask : is it necessary that it has advantages? A behavior or a feeling might as well be a by-product of selection for big brains. It might therefore not be selected for but it exists only because there is not much selection against this by-product trait.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our brain are often considered to have evolved for social purposes. I would hypothesize that if someone express &quot;regrets&quot;, he might benefit from other's care and pity. And the best way to express &quot;regrets&quot; is to feel the &quot;regrets&quot;. Robert Trivers would maybe say that in order to fool someone else (make someone else think we regret) the best thing to do is to fool ourself (make ourself feel &quot;regrets&quot;). See &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/B008PGKA56&quot; rel=&quot;noreferrer&quot;&gt;his book, the folly of fools&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-20T13:17:15.607" LastActivityDate="2013-11-20T13:17:15.607" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13587" PostTypeId="2" ParentId="13507" CreationDate="2013-11-20T12:52:28.380" Score="6" Body="&lt;p&gt;I will side-step the question of 'race', as you seem to be using it (like most people) in the sense that has no scientific basis, but the answer to your question goes something like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The amount of genetic variation in a given population is mostly the function of the geographical distance from Africa. Roughly, populations in Africa are most genetically variable as they are the oldest (they have been there for the longest time in human evolutionary history and therefore there was a long time for mutations to accumulate in their genomes). Because all the other populations in the world have originated from these original African populations, they have a subset of that original variation - they are less variable. The further you get from Africa the less variation remains (a very simplistic scenario: a group of Africans left and settled down in the Middle East; then a group of Middle Easterners went further up to Europe and further east to India; then the Indians moved further north and east etc. etc.; in each stage, only a subset of the previous variation would be travelling along).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A famous image depicting this phenomenon is in Ramachandran, S. et al. (2005). Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proceedings of the National Academy of Sciences of the United States of America, 102(44), 15942–15947. doi:10.1073/pnas.0507611102 figure 1B&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zUo3j.png&quot; alt=&quot;[Source](http://www.pnas.org/content/102/44/15942)&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the Y axis you have a measure of genetic relatedness (more relatedness = less variation) and on the X axis you have rough geographic distance that takes into account major geographic barriers (like seas etc.). Green is Eurasia and blue is Australia and Oceania. Red is variation within the groups (so, Europeans only, Australians only etc.) The variation  between the populations explained by this geographic distance is close to 80% - which is huge. If I get this right, it means that most of the genetic differences between people in different populations are a simple consequence of living outside Africa. And the variation within each population is tiny (12%) compared to the between population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a simplified view, because we now know that there were other species of humans that lived when our ancestors left Africa, and that thay had sex together as our ancestors spread around the globe, so a small portion of the others' DNA is still present in us today. Also this picture may be slightly different depending on what region of the genome you're looking at. But the major picture stands.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Going back to your question - &quot;Asians&quot; (populations with ancestry in east Asia) are on average more genetically homogenous than &quot;Australians&quot;, &quot;Americans&quot;, and &quot;Africans&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: A paper I like that should explain all this much better: Barbujani, G., &amp;amp; Colonna, V. (2010). Human genome diversity: frequently asked questions. Trends in genetics : TIG, 26(7), 285–295. doi:10.1016/j.tig.2010.04.002 &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0168952510000788&quot; rel=&quot;nofollow noreferrer&quot;&gt;link&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="752" LastEditorUserId="-1" LastEditDate="2017-03-27T03:52:40.593" LastActivityDate="2017-03-27T03:52:40.593" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="13588" PostTypeId="2" ParentId="10717" CreationDate="2013-11-20T18:03:44.653" Score="2" Body="&lt;p&gt;The stoned ape &quot;theory&quot; (&quot;we owe our very existence as a species to psychedelics&quot;) isn't theory, despite it's pretense. There is no support for it in evidence, or in theory. Nor can there be because in its own terms it defies both. It's founder seems to have thought himself a genius, and solicited a cult-like following determined to spread his message, as their own. He had no college-level science education - see facts and citations below (*).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bear in mind the &quot;theorist's&quot; target audience when he wrote Food of the Gods. Not scientists nor anyone scientifically literate. In his own words: &quot;[The target audience is] the 18-25 year old group that is drug-friendly but has no rationale except that it's a good time&quot; (Gracie, Zarkov &amp;amp; McKenna interview). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for his understanding of evolution, the scope of his grasp, here's what he thought science says - if you believe what he says. No harm to have smelling salts in easy reach if you're minimally educated in biology, i.e. high school level:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Conventional evolutionary theory tells us that small adaptive changes eventually become genetically scripted into the species&quot; (OMNI interview)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously that's 180 degrees backward from true or accurate, a recitation of what Lamarck thought - over 200 years ago, and before anyone ever heard of Darwin, or natural selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's nothing theoretical in the &quot;stoned apes&quot; storyline, despite its claim. It's not a theory, its malarkey of the same type as Creationism - but from the opposite fringe: new age psychedelia, not old time religion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(rolls eyeballs) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;*TM was at quite a disadvantage for science ed. For any major in college, even liberal arts - there's normally a 'general studies' science requirement. Its a minimal basic in higher ed, across the board. But TM's college program (Tussman Experimental) is one that specifically, uniquely excluded science. And short-lived as it was, the college was roundly criticized in its day on that very point. Its founder made excuses, e.g. this quote (from Tussman's book EXPERIMENT AT BERKELEY): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;It is recognized that the program does nothing in the way of integrating science with the social sciences and humanities. We leave this two-culture problem for wiser men to solve. In this respect, however, our students are either better OR WORSE OFF than others&quot; (caps added for emphasis). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously lame? Colleagues in education didn't buy it. For example, this remark from Sidney Rosen (Univ of Illinois): &quot;By his admission that he cannot find a way of integrating scientific ideas into a basic two-year program, Mr. Tussman is guilty of contradicting the educational goals he defends ... It is difficult for me to see how the curriculum can flourish without science as an integral part.&quot; - Journal of Research in Science Teaching 7: 271 (1970)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prescient? The college didn't flourish, it floundered. It was already crashing when Rosen wrote that. In fact, the 'experiment' seems to have perhaps been a case of politics in education, masquerading as 'educational reform.' TM himself offers an interesting remark along just such lines: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;... it was an experimental program... this thing called the Tussman Experimental College. I arrived at Berkeley the year after the Free Speech Movement ... in an effort to keep the place from blowing sky high they had told this left-wing professor that he could have an experimental section of the university&quot; (www.tripzine.com/listing.php?id=terence1)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the kind of info those who think they're all into McKenna, all about his rap and 'ideas' - have no clue.  Zero, none.  Knowing anything whatsoever, that's able to be factually established, double-checked and verified as true and accurate, valid - ain't its ticket.&lt;/p&gt;&#xA;" OwnerUserId="4962" LastEditorUserId="69" LastEditDate="2013-11-25T21:44:45.980" LastActivityDate="2013-11-25T21:44:45.980" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13589" PostTypeId="2" ParentId="9774" CreationDate="2013-11-20T18:31:57.700" Score="1" Body="&lt;p&gt;The answer from @Armatus got me looking at star activities again. EcoRI is prone to exhibit star activity in non-optimal buffers. In the case of this enzyme this tends to be a relaxation of site specificity, so HAATTC and GAATTD would be possible cut sites. The cleavage at such sites produces the standard sticky end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what if there is a star site near to the XmaI site such that a digest at the true EcoRI site and also at the star site removes the XmaI site and so allows recircularisation. If the configuration was, for example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;....GAATTC.................[XmnI].GAATTD...GGATCC....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the ligated product would have neither EcoRI nor XmnI sites.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-11-20T18:31:57.700" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13590" PostTypeId="2" ParentId="13579" CreationDate="2013-11-20T18:44:01.377" Score="1" Body="&lt;p&gt;Found the answer - the lymph capillaries. I've not researched them too in depth but from what I've read thus far, their job is to essentially pick up fluids not picked up by the blood capillaries. They have walls that allow proteins to enter but make it very hard for fluid to flow out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wiki states that an average of 20 litres of blood gets processed each day by the blood, with roughly 17 litres through the blood capillaries/system (1), with the remaining 3 litres through the lymphatic system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are also prevalent around skin. 70% of lymph capillaries are found near the skin (2). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) &lt;a href=&quot;http://en.wikipedia.org/wiki/Lymphatic_system&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Lymphatic_system&lt;/a&gt;&#xA;2) &lt;a href=&quot;http://www.lymphnotes.com/article.php/id/151/&quot; rel=&quot;nofollow&quot;&gt;http://www.lymphnotes.com/article.php/id/151/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4957" LastEditorUserId="4957" LastEditDate="2013-11-20T20:45:50.100" LastActivityDate="2013-11-20T20:45:50.100" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13591" PostTypeId="1" CreationDate="2013-11-20T20:02:55.027" Score="1" ViewCount="2401" Body="&lt;p&gt;Gibson assembly uses T5 exonuclease to chew back the 5' end of dsDNA to generate overhangs. However, T5 exonuclease, in contrast to lambda exonuclease, is reported to have ssDNA endonuclease activity (&lt;a href=&quot;https://www.neb.com/products/m0363-t5-exonuclease#tabselect0&quot; rel=&quot;nofollow&quot;&gt;https://www.neb.com/products/m0363-t5-exonuclease#tabselect0&lt;/a&gt;). Why doesn't his cause problems during gibson assembly? Is it just because these don't yield viable assemblies? Or is it because this activity is inhibited somehow, such as the T5 concentration is too low?&lt;/p&gt;&#xA;" OwnerUserId="3619" LastActivityDate="2014-06-17T10:04:22.113" Title="Why doesn't T5 exonuclease have endonuclease activity in Gibson assembly?" Tags="&lt;cloning&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13592" PostTypeId="2" ParentId="13585" CreationDate="2013-11-20T20:40:13.913" Score="3" Body="&lt;p&gt;[Not really a precise answer (and I'm not a botanist after all).]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's likely a lycopodiophyte. Looks like a Huperzia species, but it's impossible to tell exactly from the provided photo [if the species is not familiar, of course]. Of great help would be general appearance of the plant and form of sporangia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can try this key: &lt;a href=&quot;http://www.efloras.org/florataxon.aspx?flora_id=1&amp;amp;taxon_id=10527&quot; rel=&quot;nofollow&quot;&gt;Lycopodiaceae of North America&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2013-11-20T20:40:13.913" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13593" PostTypeId="2" ParentId="13555" CreationDate="2013-11-20T21:24:22.227" Score="2" Body="&lt;p&gt;It turns out that the so-called light independent reactions are not light-independent at all: there are several regulatory mechanisms in place to prevent the turning of the Calvin Cycle when there is no light energy available to produce ATP/NADPH. The hypothetical situation you described in your question demonstrates the necessity of such regulation. The cell cannot allow levels of ATP and NADPH to drop too low because those two factors are required for everything. So if you let the Calvin Cycle run when there is no means of fueling it (ultimately) from light energy, then the Calvin Cycle will run until ATP/NADPH is too low to sustain it further, at which point the cell dies. So several key enzymes in the Calvin cycle are activated indirectly by light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the most well-studied regulatory mechanisms is the ferrodoxin/thioredoxin regulatory system. The enzyme &lt;a href=&quot;https://en.wikipedia.org/wiki/Ferredoxin-thioredoxin_reductase&quot; rel=&quot;nofollow&quot;&gt;Ferredoxin-Thioredoxin reductase&lt;/a&gt; takes electrons from ferredoxin (which is reduced by light energy via the photosystems) and transfers it to thioredoxin, a disulfide-based redox protein. Then thioredoxin reduces several key enzymes in the Calvin Cycle, which activates them (through conformational changes induced by disulfide bonds). The upshot is that when light is around to facilitate reduction, the metabolic enzymes of the Calvin cycle can work, but in the dark the cell oxidizes and these enzymes are turned off, switching off the Calvin cycle and arresting CO$_2$ fixation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An orthogonal direction of light regulation of the &quot;light-independent&quot; reactions is &lt;a href=&quot;http://5e.plantphys.net/article.php?id=81&quot; rel=&quot;nofollow&quot;&gt;RuBisCO Activase&lt;/a&gt;, which is required to modify the RuBisCO active site to be active. This requires ATP hydrolysis, which amplifies the sensitivity of the Calvin Cycle to ATP availability. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The takeaway is the light-independent reactions may not directly require light as an input, but they are regulated by light availability. I tried to look up how much time in the dark would be required to shift the redox balance such that the Calvin Cycle enzymes would be inactivated, but I couldn't find that data. People in the literature, however, seem to believe it would be quick &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1360138599013916&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is some description of this at &lt;a href=&quot;https://en.wikipedia.org/wiki/Light-independent_reaction#Light-dependent_regulation&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;. If you want to look further, &lt;a href=&quot;http://pmb.berkeley.edu/profile/bbuchanan&quot; rel=&quot;nofollow&quot;&gt;Bob Buchanan&lt;/a&gt; at Berkeley made a lot of seminal advances in this area; a review of his you might want to check out is &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.pp.31.060180.002013&quot; rel=&quot;nofollow&quot;&gt;(2)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1360138599013916&quot; rel=&quot;nofollow&quot;&gt;(1): Ruelland E, Miginiac-Maslow M. (1999). &lt;em&gt;Trends in Plant Science&lt;/em&gt;. 4(4): 136-141&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.pp.31.060180.002013&quot; rel=&quot;nofollow&quot;&gt;(2): Buchanan BB. (1980). &lt;em&gt;Annual Review of Plant Physiology&lt;/em&gt;. 31:341-374.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2013-11-20T21:24:22.227" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13594" PostTypeId="2" ParentId="13591" CreationDate="2013-11-20T21:46:12.400" Score="1" Body="&lt;p&gt;I've never actually done a Gibson assembly, but looking over the protocols at the New England Biolabs website, I think the answer must be that the ssDNA exposed by the T5 exonuclease is quickly protected from the ssDNA-endonuclease activity because it (the exposed DNA) anneals with the complementary sequence on the other component of the assembly reaction. Following that, any gaps are repaired and sealed by DNA polymerase and DNA ligase. All of these enzymes are of, course, present at the same time in the one-step assembly reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, under the conditions of the assembly reaction, the low-level ssDNA endonuclease activity of the T5 exonuclease is simply outcompeted by the other reactions taking place.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2013-11-20T22:50:00.723" LastActivityDate="2013-11-20T22:50:00.723" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13595" PostTypeId="1" AcceptedAnswerId="21525" CreationDate="2013-11-20T21:47:09.770" Score="22" ViewCount="7096" Body="&lt;p&gt;I read a story this week on Richard Lenski who has been 'evolving' &lt;em&gt;E. coli&lt;/em&gt; for more than 50,000 generations now.  One comment I read was from someone who doesn't accept Evolution who pointed out that we haven't seen a single celled organism 'evolve' into a multi-celled organism.  Another person responded and said that a bacteria is not going to evolve into something that isn't a bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if Evolution created single celled organisms and then multi-celled organisms how might that change have happened?  And is it possible to recreate that set of driving forces to make a bacteria something other than a bacteria?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To that end, what advantage does being multi-cellular have over being unicellular (if that's even a word)?&lt;/p&gt;&#xA;" OwnerUserId="4965" LastEditorUserId="1320" LastEditDate="2013-11-20T21:50:44.237" LastActivityDate="2019-03-28T01:48:50.927" Title="Why would a single celled organism evolve to be multi-celled?" Tags="&lt;evolution&gt;&lt;cell-biology&gt;" AnswerCount="7" CommentCount="6" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13596" PostTypeId="2" ParentId="9572" CreationDate="2013-11-21T03:43:22.333" Score="1" Body="&lt;p&gt;Difference between kosher and non-kosher animals&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rabbi Zamir Cohen, in his book The Coming Revolution - Science Discovers the Truths of the Bible, quotes modern day scientists that have made an incredible discovery of a major difference in the way the blood flows in the species that are kosher and those that are not. In non-kosher mammals, the vertebral arteries flow directly to the brain through the rete mirabile. However, in cloven-hoofed, cud-chewing mammals and permitted foul, the vertebral arteries drain into the carotid artery and do not have any direct flow to the brain. There will therefore be an immediate drop in blood pressure at the time of shechita that causes the animal to lose consciousness, thus feeling no pain.&lt;/p&gt;&#xA;" OwnerUserId="4967" LastActivityDate="2013-11-21T03:43:22.333" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13597" PostTypeId="2" ParentId="13595" CreationDate="2013-11-21T04:10:32.100" Score="8" Body="&lt;p&gt;For one thing, larger organisms are much more energy efficient.  This is what is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Kleiber%27s_law&quot; rel=&quot;nofollow&quot;&gt;Kleiber's Law&lt;/a&gt; where the caloric requirement scales as the 3/4 power to the body mass. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another thing is that when all the cells cooperate to form a multicellular organism, each given individual is more likely to reproduce and less likely to die due to environmental variation because cooperation creates stability.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Multicellular_organism#Hypotheses_for_origin&quot; rel=&quot;nofollow&quot;&gt;There are several theories about &lt;em&gt;how&lt;/em&gt; this came about&lt;/a&gt;,but those are the elements of &lt;em&gt;why&lt;/em&gt;.  Collaboration and efficiency improve the chances of survival, which is to say that selection will favor multicellular organisms however they came to be. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-09-23T17:42:23.117" LastActivityDate="2014-09-23T17:42:23.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13600" PostTypeId="1" AcceptedAnswerId="13630" CreationDate="2013-11-21T12:11:02.923" Score="3" ViewCount="628" Body="&lt;p&gt;I found it hard to get numbers on global primary production, but apparently it's somewhere around 50-60 $Gt / year$ for carbon content in the terrestrial production, and a similar figure for the oceans. Global oil and coal extraction together are around 10 $Gt/year$, only a part of which is pure carbon (iirc, around 80%). Since carbon in the air actually increases, does that mean that most or all of the carbon fixed in Net Primary Productivity go back into the atmosphere through consumption and destruction of the biomass?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was assuming that the biosphere in total was fixing more carbon that it emitted, and that the surplus was what turned into oil and coal. But with these figures it looks a lot more like a full circle that nets to zero input / output. Which is true, or is that unknown? &lt;/p&gt;&#xA;" OwnerUserId="1864" LastEditorUserId="1864" LastEditDate="2013-11-23T16:44:05.050" LastActivityDate="2013-11-23T18:46:24.610" Title="Where does all the carbon go?" Tags="&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13601" PostTypeId="2" ParentId="9924" CreationDate="2013-11-21T16:03:47.570" Score="3" Body="&lt;p&gt;It's quite hard to answer this question and the best would be to follow a flora, which I'll not just copy informations from to past here.&#xA;So following are general observations subject to numerous exceptions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Hieracium&lt;/em&gt;&lt;/strong&gt; generally have lanceolate to oval leaves, not or little toothed, most hairy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Crepis&lt;/em&gt;&lt;/strong&gt; and &lt;strong&gt;&lt;em&gt;Leontodon&lt;/em&gt;&lt;/strong&gt; have generally Taraxacum-like leaves, that means, dentate to lobed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some &lt;strong&gt;&lt;em&gt;Crepis&lt;/em&gt;&lt;/strong&gt; have leafy stems (but some don't), while &lt;strong&gt;&lt;em&gt;Leontodon&lt;/em&gt;&lt;/strong&gt; always have their leaves concentrated to the base, forming a rosette.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[edit on 2014, october 2]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Be aware that there is another genus of the Asteraceae family which may be mistaken with the Crepis/Leontodon/Hieracium group, although it's easier to distinguish. It's the Hypochaeris genus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Hypochaeris&lt;/em&gt;&lt;/strong&gt; have few but not so homogenous species as there are within the other genera. &#xA;&lt;strong&gt;&lt;em&gt;Hypochaeris radicata&lt;/em&gt;&lt;/strong&gt; (which may be the most common species in France and wester Europe) have all its leaves basal, forming a rosette and sticking to the ground (never erected). These leaves are always lobed (neither entire, nor toothed), with erected hard hairs covering there upper faces.&#xA;&lt;strong&gt;&lt;em&gt;Hypochaeris maculata&lt;/em&gt;&lt;/strong&gt; may be mistaken with some Hieracium : it have hairy smooth entire leaves wich are (all or mostly?) basal forming a rosette.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[Addition on August, the 5, 2014]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also &lt;strong&gt;&lt;em&gt;Leontodon&lt;/em&gt;&lt;/strong&gt; and &lt;strong&gt;&lt;em&gt;Hypochaeris&lt;/em&gt;&lt;/strong&gt; have hollow stem just below the capitulum(1). When you press the stem just below the capitulum, you fell it flattens under your finger, and if you use the nail to make an incision in the stem, you will see it is hollow like a pipe.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;NB : Taraxacum also have hollow stems but they are fully hollow (from the base up to the capitulum), while Leontodon just have the upper part of the stem which is hollow.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Leontodon&lt;/em&gt;&lt;/strong&gt; are almost always monocephal, that means, the stems are not branched : they have only one capitulum per stem, while &lt;strong&gt;&lt;em&gt;Crepis&lt;/em&gt;&lt;/strong&gt; and &lt;strong&gt;&lt;em&gt;Hieracium&lt;/em&gt;&lt;/strong&gt; and &lt;strong&gt;&lt;em&gt;Hypochaeris&lt;/em&gt;&lt;/strong&gt; mostly (if not always) have branched stems carrying several capitula.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) the capitulum is the type of &lt;a href=&quot;http://en.wikipedia.org/wiki/Inflorescence&quot; rel=&quot;nofollow&quot;&gt;inflorescence&lt;/a&gt; in the Asteraceae family. It's also called &quot;head&quot; (and actually, &quot;capitulum&quot; is the latin word for head).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may like to have a look at &lt;a href=&quot;http://bota-phytoso-flo.blogspot.fr/2013/11/pissenlits.html&quot; rel=&quot;nofollow&quot;&gt;this page [in french]&lt;/a&gt; presenting some common yellow and ligulate weeds from the Asteraceae family to get some illustrations of what I explained here.&lt;/p&gt;&#xA;" OwnerUserId="4820" LastEditorUserId="4820" LastEditDate="2014-10-02T18:41:49.117" LastActivityDate="2014-10-02T18:41:49.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13606" PostTypeId="1" CreationDate="2013-11-22T00:00:52.660" Score="1" ViewCount="234" Body="&lt;p&gt;Since the my first encounter with doraemon manga, I've been wondering many things, one of them is the small light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming we had an instrument, such as small light, which enabled people to grow and shrink as they wanted to, what would be the smallest and the most compact functional form of a person?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, I can rule out that we couldn't be as small as an atom because we couldn't be function as human being if we were compressed into 1 atom. So did 1 molecule. and so did 1 cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, you need more than 1 cell to construct organs, i.e. I couldn't imagine an eye which consists only several atoms or molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, there should be a limit to the the size of human organs in order to fully retain their functions and thence, there should also be a limit to the minimum size of human organs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the limits of size of each of human organs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the limits of size of human then?&lt;/p&gt;&#xA;" OwnerUserId="4980" LastActivityDate="2015-05-31T21:01:53.273" Title="Hypothetically, what is the smallest functional form of human?" Tags="&lt;molecular-biology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13607" PostTypeId="1" AcceptedAnswerId="13611" CreationDate="2013-11-22T00:26:02.543" Score="2" ViewCount="121" Body="&lt;p&gt;Reading one of Sir Arthur Clarke's scifi stories, I came across a statement something to the effect of, existence of a single species automatically implies the existence of many other species. So considering multi-cellular organisms, something more complex than a virus/bacteria, if we know for a fact that there is one species (plant/animal whatever) then without directly observing any other species or any obvious evidence, can we deduce that there must be other species? Assume we are in a completely new environment like a brand new planet discovered with life on it. Does the existence of a  species imply existence of many other species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="4053" LastEditorUserId="1320" LastEditDate="2013-11-22T07:56:42.380" LastActivityDate="2013-11-23T09:12:51.073" Title="Does the existence of one species imply the existence of many other?" Tags="&lt;evolution&gt;&lt;life&gt;&lt;speculative&gt;&lt;speciation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13608" PostTypeId="1" CreationDate="2013-11-22T00:45:37.150" Score="1" ViewCount="11945" Body="&lt;p&gt;I thought that these were just different format of the same data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But it seems there isn't a way to convert SNP (single nucleotide polymorphism) data to STR (short tandem repeat) data. Am I right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I understand SNPs is basically a &quot;diff&quot; between some base human dna (parts that never change) and given dna. While STRs are strands of dna that differs between individuls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if there are enough SNPs (i.e. all of them), it would be trivial to deduce STRs, right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, currently 23andMe tests the whole mitochondrial genome. Does it mean that one can easily deduce STRs?&lt;/p&gt;&#xA;" OwnerUserId="4981" LastEditorUserId="4981" LastEditDate="2013-11-22T11:03:11.947" LastActivityDate="2013-11-22T11:03:11.947" Title="What is the difference between SNP and STR?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;dna-sequencing&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13609" PostTypeId="2" ParentId="13608" CreationDate="2013-11-22T07:13:55.310" Score="4" Body="&lt;p&gt;The solution is in the name!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;SNP&lt;/strong&gt;: single nucleotide polymorphism&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The name tells us that it is a change that affect one single nucleotide and that there can be multiple of these (&lt;em&gt;polymorphism&lt;/em&gt; could be rewritten as &lt;em&gt;multiple forms&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the &lt;a href=&quot;http://en.wikipedia.org/wiki/Single-nucleotide_polymorphism&quot; rel=&quot;nofollow&quot;&gt;SNP Wikipedia page&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[A SNP] is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes in a human.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, for instance, if you take 8 individuals and sequence their gene XYZ, you may find, at a certain &lt;em&gt;locus&lt;/em&gt; (=position) on the gene:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Individual 1: AAGGTG &lt;strong&gt;C&lt;/strong&gt; AGCAGTC&lt;br&gt;&#xA;Individual 2: AAGGTG &lt;strong&gt;T&lt;/strong&gt; AGCAGTC&lt;br&gt;&#xA;Individual 3: AAGGTG &lt;strong&gt;T&lt;/strong&gt; AGCAGTC&lt;br&gt;&#xA;Individual 4: AAGGTG &lt;strong&gt;T&lt;/strong&gt; AGCAGTC&lt;br&gt;&#xA;Individual 5: AAGGTG &lt;strong&gt;C&lt;/strong&gt; AGCAGTC&lt;br&gt;&#xA;Individual 6: AAGGTG &lt;strong&gt;C&lt;/strong&gt; AGCAGTC&lt;br&gt;&#xA;Individual 7: AAGGTG &lt;strong&gt;T&lt;/strong&gt; AGCAGTC&lt;br&gt;&#xA;Individual 8: AAGGTG &lt;strong&gt;T&lt;/strong&gt; AGCAGTC  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The position highlighted in bold is a SNP. In this case we only have either C or T (and this produces 2 different alleles for gene XYZ).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://learn.genetics.utah.edu/content/health/pharma/snips/&quot; rel=&quot;nofollow&quot;&gt;page from University of Utah&lt;/a&gt; has a very clear animation on SNPs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;STR&lt;/strong&gt;: &lt;a href=&quot;http://en.wikipedia.org/wiki/Microsatellite&quot; rel=&quot;nofollow&quot;&gt;short tandem repeat&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are short repeated sequences. They're &lt;em&gt;in tandem&lt;/em&gt;, that is, one after the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;STR consist of a few (2-6) nucleotides that are repeated several (5-100) times.&lt;br&gt;&#xA;For instance &lt;a href=&quot;http://www.biology.arizona.edu/human_bio/activities/blackett2/str_description.html&quot; rel=&quot;nofollow&quot;&gt;this page from the University of Arizona&lt;/a&gt; gives the example of D7S280, one STR with sequence (GATA)&lt;sub&gt;n&lt;/sub&gt; (that is, GATA repeated n times)&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;  1 aatttttgta ttttttttag agacggggtt tcaccatgtt ggtcaggctg actatggagt&#xA; 61 tattttaagg ttaatatata taaagggtat gatagaacac ttgtcatagt ttagaacgaa&#xA;121 ctaacgatag atagatagat agatagatag atagatagat agatagatag atagacagat&#xA;181 tgatagtttt tttttatctc actaaatagt ctatagtaaa catttaatta ccaatatttg&#xA;241 gtgcaattct gtcaatgagg ataaatgtgg aatcgttata attcttaaga atatatattc&#xA;301 cctctgagtt tttgatacct cagattttaa ggcc&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;In this case, variations between individuals reside in the number of times the sequence is repeated.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2013-11-22T07:13:55.310" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13610" PostTypeId="1" CreationDate="2013-11-22T07:54:17.513" Score="0" ViewCount="12711" Body="&lt;p&gt;I read the wikipedia entry and I am sort of confused.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In dog, the nose is toward the front. That's anterior. So I conclude that human nose is anterior.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In dog, the head is on the back. So that's dorsal. So I concluded that humans' top head is dorsal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet that's not how things seem to work on anatomy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We call humans' top head anterior. We also call human nose direction as ventral.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How could that be?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The whole system of anterior, dorsal, ventral, posterior is there so we can see humans like we see dogs (at least anatomically).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet it changes again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So which one is right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me put it this way&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dog's chin is ventral from the eye&#xA;In humans, is humans' chin ventral from the eye too? or posterior?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about the nose? Dog's nose is it's anterior most organ.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In humans, is the nose anterior too?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I mean, if we're going to have different terms for humans and dogs, might as well use words like up, down, front, back right?&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="1320" LastEditDate="2013-11-24T15:05:55.697" LastActivityDate="2013-11-24T15:05:55.697" Title="For the human head, which direction is anterior, and which direction is ventral?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13611" PostTypeId="2" ParentId="13607" CreationDate="2013-11-22T08:35:03.247" Score="2" Body="&lt;p&gt;I am not sure I'm providing the kind of answer you would expect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question is very conceptual. For such question it is important to very well define the concepts you're using. For example, the concept of species is not well defined (and will certainly never be well defined as it does not represent a natural category to my point of view). Also, the separation you do between complex and non-complex species might not be obvious. For example, you create two categories which are bacteria/virus and multicellular. But you kind of forget the many of the eukaryotes which belong to non of these two categories. Or some bacteria that might almost be considered as multicellular.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it would help answering your question if we had the arguments of Sir Arthur Clark for saying such things. Below are two arguments I could use to defend your statement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Speciation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you consider than one population rarely (or virtually never) go under sufficiently major changes before undergoing speciation, then you would never have only one species which is very different from the others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ecology:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One might consider that one species cannot by itself be responsible of a whole cycle of elements. Therefore, if the species we observe can theoretically live forever (equilibrium), then, it implies that other species must exist to recycle their wastes. But this hypothesis has nothing to do with the separation of species per complexity that you do.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Update:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following your comment: So what you had in mind seem roughly the same than my &quot;Ecology&quot; argument. The difference is that I emphasized on the fact that one species alone cannot live for ever because they degrade their resources through time. I did not want to say that one individual of one species cannot live without the presence of another individual of another species. This individual would need the presence of the other species not for himself but rather but its great-great-grand-children when one resource would have been totally consumed by the ancestors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For your curiosity, here is base of the tree of life. What is eukarotic but not plants, animals or fungi are called &lt;a href=&quot;http://fr.wikipedia.org/wiki/Protistes&quot; rel=&quot;nofollow&quot;&gt;protista&lt;/a&gt; and are all (or almost all?!) unicellular. You'll notice that viruses/viroid and prions does not belong to this tree. It would be a bit long to explain why they are no represented and it would have nothing to do with your question :D&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-23T09:12:51.073" LastActivityDate="2013-11-23T09:12:51.073" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13613" PostTypeId="2" ParentId="13606" CreationDate="2013-11-22T09:08:36.513" Score="4" Body="&lt;p&gt;This question is for Doctor Frankenstein!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer would depend on what you would accept to consider being a human.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Does it still need to be able to make simple calculation in order to be a human?&#xA;Yes, because otherwise we would have lost some functions. But then you may ask…&lt;/li&gt;&#xA;&lt;li&gt;Does it need to have big enough hands in order to fulfill the social function of hand shaking.&lt;/li&gt;&#xA;&lt;li&gt;Does it has to be attractive to the other sex?&lt;/li&gt;&#xA;&lt;li&gt;Does it need a heart or is it fine if oxygen diffusion through tissue only is enough for this creature to live?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I guess that if you change the number of cells you will necessarily change the functionality. I am not saying that small guys are not as functional as big guys. For example, big guys are better runner, while small guys are better climber. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Are we allowed to shrink the cells to have minimal sized cells?&lt;/li&gt;&#xA;&lt;li&gt;Are we allowed to shorten the DNA in order to shrink the cells?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Notes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;There are approximatively 200 different cell types in a human&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;My reference is not a peer-reviewed article (&lt;a href=&quot;http://sciencenetlinks.com/student-teacher-sheets/cells-your-body/&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref&lt;/a&gt;). Wikipedia lists cell types and it doesn't seem to go over 200. However, it is important to realize that it probably very much depend on how you define cell types.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Terminologica Anatomica lists over 7,500 names parts of the human body&lt;/li&gt;&#xA;&lt;li&gt;There are 13 or 14 (depending on the gender) gland types&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23829164&quot; rel=&quot;nofollow noreferrer&quot;&gt;This article&lt;/a&gt; provides an estimation of the number of cells in the human body &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Artificial_cell#The_minimal_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; (wikipedia) is a discussion on the concept of the minimal cell&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/10853/number-of-genes-required-to-sustain-life/10855#10855&quot;&gt;Here&lt;/a&gt; and &lt;a href=&quot;https://biology.stackexchange.com/questions/651/what-is-the-smallest-number-of-amino-acids-required-for-life&quot;&gt;here&lt;/a&gt; (biology.SE) are discussions on the minimum number of genes/amino acid to sustain life&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/1382/which-organism-has-the-smallest-genome-length&quot;&gt;Here&lt;/a&gt; (biology.SE) is a discussion on which species has been found to have the smallest genome&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-05-31T21:01:53.273" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13614" PostTypeId="1" CreationDate="2013-11-22T10:54:27.287" Score="5" ViewCount="93" Body="&lt;p&gt;Living in Australia there were less ticks for example during the use of DDT, now there are more ticks prevalent here. I am wondering if any insect species have declined permanently as the result of the DDT use, and if some have repopulated disproportionately (compared to populations prior to the use of DDT- if there is such data) since it's cessation of use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How has the use and subsequent ban of &lt;a href=&quot;http://en.wikipedia.org/wiki/DDT&quot; rel=&quot;noreferrer&quot;&gt;DDT (dichlorodiphenyltrichloroethane)&lt;/a&gt; affected insect populations?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any studies on this?&lt;/p&gt;&#xA;" OwnerDisplayName="user22339" LastEditorDisplayName="user22339" LastEditDate="2013-11-22T11:27:51.293" LastActivityDate="2018-05-30T14:44:39.897" Title="How has the use and subsequent ban of DDT affected insect populations?" Tags="&lt;entomology&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13615" PostTypeId="1" CreationDate="2013-11-22T14:08:20.490" Score="5" ViewCount="93" Body="&lt;p&gt;From what I've understood from what I've read (which might be wrong), enamel rods extend away from the dentin in our teeth. As young people grow, the rods are thickened.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the technical limitations and/or problems/challenges of trying to extend/grow the rods/crystals while the teeth are in the mouth?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One issue I guess could be that the enamel is porous, and so chemicals could affect the other parts of the teeth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But one example of trying to improve the quality of tooth enamel is Novamin, which some manufacturers have claimed creates a glass on the tooth. But I don't understand what that means.&lt;/p&gt;&#xA;" OwnerUserId="4983" LastActivityDate="2014-05-08T17:05:51.153" Title="What limits our ability to grow enamel rods?" Tags="&lt;teeth&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13616" PostTypeId="1" CreationDate="2013-11-22T14:21:51.160" Score="5" ViewCount="116" Body="&lt;p&gt;I filmed the creatures below this August in the Mediterranean (specifically, the port of &lt;a href=&quot;http://en.wikipedia.org/wiki/Fornells,_Minorca&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fornells&lt;/a&gt; in Minorca of the Balleares). The images were taken from a boat moored just outside the harbor and floating above a field of &lt;a href=&quot;http://en.wikipedia.org/wiki/Posidonia_oceanica&quot; rel=&quot;nofollow noreferrer&quot;&gt;posidonia&lt;/a&gt; in case that is relevant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There were &lt;em&gt;many&lt;/em&gt; of them and they were whizzing about at high speed:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9F96b.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/T5XQY.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is to give you an idea of the scale. The jellyfish on the right was about the size of half a tennis ball.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZPvlZ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They were a very strange sight since there were so many of them and moving so fast. You can see a video of them in motion here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=GJCzjXALRJ0&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.youtube.com/watch?v=GJCzjXALRJ0&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image quality is not very good but you can see how fast the things were moving. So, any idea what these are? I am assuming they are larvae of something or other but what? &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2016-03-20T13:48:00.620" LastActivityDate="2016-03-20T13:48:00.620" Title="What are these flitting sea worms?" Tags="&lt;species-identification&gt;&lt;marine-biology&gt;" AnswerCount="0" CommentCount="0" ClosedDate="2014-07-27T01:13:16.317" ContentLicense="CC BY-SA 3.0" />
  <row Id="13618" PostTypeId="1" CreationDate="2013-11-22T17:19:56.860" Score="6" ViewCount="126" Body="&lt;p&gt;I am working on an (expensive) synthetic construct, which happens to have many &quot;repetitive&quot; sequences within it that are integral to its function. Primarily, the two sequences that are worrying me are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A long polyA (about 15 nucleotides).&lt;/li&gt;&#xA;&lt;li&gt;A consecutive sequence of two nucleotides: GGGUUUGGUUGU, etc.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I've heard from many some of the transcription horrors they've been through because of similar sequences with similar nucleotides. However, some advise that transcribing it shouldn't be a problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How predictably can RNA polymerase transcribe these sorts of sequences in &lt;em&gt;E.coli&lt;/em&gt;&lt;/strong&gt;?&lt;/p&gt;&#xA;" OwnerUserId="307" LastEditorUserId="15330" LastEditDate="2015-04-14T12:42:42.230" LastActivityDate="2015-04-14T14:20:10.420" Title="How predictably will RNA polymerase not transcribe repetitive sequences?" Tags="&lt;rna&gt;&lt;synthetic-biology&gt;&lt;transcription&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13621" PostTypeId="1" CreationDate="2013-11-23T04:28:09.670" Score="1" ViewCount="223" Body="&lt;p&gt;Does anyone know of a protein/molecule that can be attached to one end of the DNAs temporarily ? eg. i would like to only to allow one strand of DNA be ligated to another DNA molecule to either it's 3' or 5' but not both. thanks&lt;/p&gt;&#xA;" OwnerUserId="233" LastActivityDate="2013-11-23T04:28:09.670" Title="3' or 5' DNA capping protein" Tags="&lt;dna&gt;&lt;ligation&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13622" PostTypeId="1" CreationDate="2013-11-23T05:27:45.043" Score="4" ViewCount="74" Body="&lt;p&gt;Check out this photo of my pepper plant this cloudy morning: (click for full res)&#xA;&lt;a href=&quot;https://i.stack.imgur.com/DW8pN.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/DW8pNm.jpg&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually (and this can be seen on 2 and a half of the 4 fruits in this pic) the fruits are &quot;disconnected&quot; from the plant's juice flow when they're ripe. Then the fruit starts to dry. Yet the middle one in the pic is dry while its &quot;cord&quot; is still green (literally). Why does it not become dry like his fellows do?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's also another interesting situation going on with the lower right fruit's &quot;cord&quot;, which is half-dry. I wonder why it has been like this for a little over a month now without change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lighting conditions are pretty poor for this plant, so I use a 40 watt incandescent lamp for it and 4 other plants 24/7.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;Please, excuse my poor vocabulary :)&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2013-11-23T05:27:45.043" Title="Why is this dry pepper fruit still &quot;powered&quot;?" Tags="&lt;botany&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="13623" PostTypeId="2" ParentId="10218" CreationDate="2013-11-23T05:52:50.347" Score="2" Body="&lt;p&gt;Alexander's advice is excellent in the general case, but since I faced a very similar problem when I applied to grad schools last year, I wanted to offer my perspective on this specific union of fields. Many people (including me) believe that this intersection is about to be a really important field - ecologists are starting to recognize the need for scientists with these skills, but there is not yet a lot of infrastructure in place to train such scientists. This presents a challenge to people like you and me right now. On the other hand, it means that if we can find a way to acquire these skills, we should be pretty well set up to help establish this field (bonus: we should be pretty well set up to get jobs).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am personally of the opinion that if your interests are truly interdisciplinary, it's a really good idea to go somewhere that has a framework in place to support interdisciplinary work. Otherwise, you can end up in a situation where your adviser doesn't feel equipped to offer guidance on large portions of your projects, which can strain your working relationship and stymie your progress. Despite the lip service paid to the importance of interdisciplinary research, however, programs that are set up to provide interdisciplinary mentoring can be hard to find. The best course of action depends very specifically on how you want to combine these fields.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to stay rooted in biology and use computer science and math as tools without doing research that furthers them as fields, you're in luck. There are a lot of labs with PIs who do this kind of research and many more who are interested in finding people who can, as terdon said, &quot;do their modeling.&quot; I would be careful of the latter scenario while you're still in the learning phase of your career, however. As a student, your goal should be to learn how to best do the research that you want to. If you are the lone modeler/math person in a group, you may be in high demand but your rate of learning will probably be a lot slower than if you had an adviser who was actually doing what you are interested in. If these are your interests, your options are pretty varied but take a look at UC Berkley, and UC Davis. Also UW, as Alexander suggested. There are indeed good collaborations between biology and computer science there. I found it helpful to search for people who were studying macroecology, but that might be a label that is used more for terrestrial systems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if you want to do research that actually furthers computer science in addition to biology, things get more complicated (I don't know if there are people who do both math research and biology research so I can't speak to that). Don't constrain your thinking by believing that you have to get a degree in one or the other; dual degree programs exist (and that may sound intimidating, but they aren't necessarily more work, just different work), although they are so few and far between that you might decide that it makes the most sense to just choose one field. If this is what you want to do, take a look at UC Santa Barbara - they do a ton of marine bio research and are home to the National Center for Ecological Analysis and Synthesis. Also, again, UW. I'd recommend my program too, but it's neither marine nor tropical.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, if you want to get a feel for how open a lab is to you doing interdisciplinary research, I found that it was best to just ask explicitly. If a place offered joint appointments (i.e. the ability for me to be co-advised by professors in two departments), dual degrees, or even just had research groups that involved people from multiple departments, I took that as a great sign.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, don't start out with low expectations for finding a match for your interests. That said, it will ultimately be valuable to be flexible, as both finding a perfect match and getting accepted to it definitely requires a lot of luck. The considerations that I've brought up here won't make or break your grad school experience or your eventual career. They're just things to keep in mind if you have the option. I also apologize that it's probably a bit late in the application season for this to be useful to you, but I had such a horrible time grappling with these same issues that I just wanted to put what I learned out there in case it can help anyone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;: I forgot to address ecoinformatics! Ecoinformatics can fall into either the &quot;computer science as a tool&quot; category or the &quot;furthering both computer science and biology&quot; category, although it falls into the latter category much more frequently than modeling does. It still all comes down to what exactly you want to do. Look at research in computer science journals. If doing that sort of thing appeals to you as much as biology research, then you should be thinking about trying to pursue both fields. I found doing some pure computer science research helpful for figuring this out, but you probably don't have time for that.&lt;/p&gt;&#xA;" OwnerUserId="3824" LastEditorUserId="3824" LastEditDate="2013-11-23T18:22:23.377" LastActivityDate="2013-11-23T18:22:23.377" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13624" PostTypeId="2" ParentId="6827" CreationDate="2013-11-23T05:57:45.273" Score="2" Body="&lt;p&gt;I don't think you can ever ask or answer for that matter WHY questions in biology. The only answer there is: because it works. Asking why questions implies that there was a reason, and reason cannot exist alone by itself. Reason is held by someone or something. And reason is something that doesn't exist, it is something we created and use for our own purposes and we cannot attribute it to anything else having one. Now, if you asked &quot;how?&quot;, that's an answer biology was created for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There could have been many outcomes to everything in biology but this is the one that appeared and works. This doesn't mean that it is some sort of theoretical or practically optimum, but the law of this universe is survive long enough to improve if needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that this is an opinion, but it's as close to the answer that you can get. If someone gives an answer to the WHY question, you could never prove it, or you could find evidence for all the possible reasons. And we can't also tap into the reasons of the universe because our intellect and modes of expression are way lower than the universe has.&lt;/p&gt;&#xA;" OwnerUserId="233" LastActivityDate="2013-11-23T05:57:45.273" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13625" PostTypeId="1" AcceptedAnswerId="13629" CreationDate="2013-11-23T02:35:25.833" Score="2" ViewCount="713" Body="&lt;p&gt;Do people often blow out the air from their lungs when living in cold climatic conditions to keep their lungs warm?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I ask this question because it could connect to how people in different areas construct linguistic sounds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, the Germanic families of Language (German, English,...) use a lot of air from the lungs to construct the sound? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is that because the Europeans living in cold climate often blow out a lot of air from the lung to keep warm and as a result gradually they construct air-driven linguistic sounds?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For people living in warm climates (ex: Sino-Tibetan language like Chinese, Thai), we mostly use the tongue to construct sounds, and we use very little air from our lungs to make sound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I posted this question to some forums &amp;amp; some people said it’s baloney. However, there's one thing for sure, the environment shapes how local people construct sound. People construct the sound like that because it is constrained by something. One thing can not stand alone, it must be the karma or outcome of something else.&lt;/p&gt;&#xA;" OwnerUserId="4989" OwnerDisplayName="Kiti" LastEditorUserId="16866" LastEditDate="2016-02-04T04:53:19.507" LastActivityDate="2016-02-04T04:53:19.507" Title="Do people often blow out the air from their lungs a lot when living in the cold condition to keep their lungs warm?" Tags="&lt;human-biology&gt;&lt;temperature&gt;&lt;lungs&gt;&lt;language&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13626" PostTypeId="1" CreationDate="2013-11-23T08:24:58.087" Score="1" ViewCount="37" Body="&lt;p&gt;I want to use some yeast mutants to conduct gene functional analysis, and the gene was isolated from plants. Can anybody give me some information regarding the websites or agencies from which I can purchase the yeast mutants? &lt;/p&gt;&#xA;" OwnerUserId="4677" LastActivityDate="2013-11-23T08:24:58.087" Title="Where can I get yeast mutants?" Tags="&lt;molecular-biology&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2014-11-24T15:16:58.310" ContentLicense="CC BY-SA 3.0" />
  <row Id="13627" PostTypeId="1" AcceptedAnswerId="13659" CreationDate="2013-11-23T09:40:56.747" Score="1" ViewCount="26" Body="&lt;p&gt;In Mendel's crosses was it desirable for the plants to be able to cross-pollinate and self pollinate easily ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-11-25T17:19:13.783" Title="Is ability to easily pollinate desirable?" Tags="&lt;homework&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13628" PostTypeId="1" AcceptedAnswerId="13677" CreationDate="2013-11-23T09:53:59.480" Score="1" ViewCount="40" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Arrange this in sequence :&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;i. Heat loss exceeds heat production.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;ii.As body temperature falls, heat loss decreases.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;iii.Body temperature equals environmental temperature.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;iv.Metabolic activities fall to the basal level.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am confused between i,iii,ii,iv and iv,i,ii,iii.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-11-26T16:08:05.957" Title="Order of events in hibernation" Tags="&lt;physiology&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13629" PostTypeId="2" ParentId="13625" CreationDate="2013-11-23T10:03:16.760" Score="1" Body="&lt;p&gt;Heat loss hypothesis:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would rather think that blowing while speaking means that one has to inspire often and therefore he would lose much heat by convection. According this hypothesis, I would rather expect to see southern people blowing lots while speaking. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Metabolism hypothesis:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We might say that at low temperature the metabolism increases and therefore the consumption of oxygen should increase. As shown &lt;a href=&quot;http://www.scielo.cl/scielo.php?pid=S0716-078X2000000100012&amp;amp;script=sci_arttext&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for example. This would make blowing much air more profitable for people living in cold environments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Articulation hypothesis:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One might as well hypothesize that the cold would tend to make articulation more complex and using much air would help to be well understood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: It would be interesting to look at many local scales if it is indeed true that the colder the more air people use. At global scale, I am afraid that the observations are quite dependent and statistically speaking, there is not much evidence that cold environment correlates with blowing much air while speaking&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-23T10:10:16.847" LastActivityDate="2013-11-23T10:10:16.847" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13630" PostTypeId="2" ParentId="13600" CreationDate="2013-11-23T10:15:14.233" Score="3" Body="&lt;p&gt;Good question! The way that the carbon budget stays balanced was a bit of a mystery until recently. The amount of carbon in the atmosphere (and the rate at which it was increasing) was lower than models suggested that it should be, given rates of photosynthesis, respiration, and other carbon releasing processes. Somewhere, there was a &quot;missing carbon sink&quot; that wasn't being accounted for. After many years of debating whether the sink was terrestrial or aquatic, it turned out to be a little of both (which is the conclusion to just about every debate in ecology), although somewhat skewed towards the terrestrial (I think). &lt;a href=&quot;http://www.nature.com/climate/2007/0708/full/climate.2007.35.html&quot; rel=&quot;nofollow&quot;&gt;Forests&lt;/a&gt; were sequestering more carbon than had been thought, and so were oceans to some extent (although ocean sequestration relied on a chemical reaction that is in danger of reversing if the water warms up too much). For a thorough account, see this &lt;a href=&quot;http://environment.nationalgeographic.com/environment/global-warming/missing-carbon/&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But it sounded like you weren't wondering what the missing sink was so much as how there continues to be enough carbon in the air for plants to photosynthesize (if I'm interpreting your question correctly). Carbon gets back into the air for the most part because of cellular respiration, which all organisms, including plants, do. Net primary productivity takes plant cellular respiration into account, but there are still tons of living things on earth eating plants (and thus taking in their carbon) and then breathing it back out after they break down the carbon-containing molecules for energy. There is also natural combustion and volcanoes and such putting carbon back into the air.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt; (to address the new part of your question): Oil and coal were produced when large quantities of carbon were buried deep under ground (and thus subjected to lots of pressure) for thousands of years. This is suspected to have happened during the aptly name Carboniferous era, which featured giant plants and, scientists hypothesize, no decomposers to break them down. Since we have much decomposers now, and much smaller plants, oil and carbon are not currently being produced. This is why we call them non-renewable resources. By extracting them from the ground and burning them, we are taken carbon that had effectively been removed from the pool of actively cycling carbon and adding it back in. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The carbon cycle doesn't really have input or output (except the occasional carbon exchange with outer space), because it is defined as already including standing sinks like oil and coal. When we take carbon out of a sink, like oil or coal, it needs to go somewhere else. Terrestrial and aquatic sinks can store some of the additional carbon that we're adding to the not-underground part of the cycle. However, they can't store all of it, so some is staying in the atmosphere instead.&lt;/p&gt;&#xA;" OwnerUserId="3824" LastEditorUserId="3824" LastEditDate="2013-11-23T18:46:24.610" LastActivityDate="2013-11-23T18:46:24.610" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13631" PostTypeId="1" CreationDate="2013-11-23T14:31:00.123" Score="3" ViewCount="29303" Body="&lt;p&gt;&lt;a href=&quot;https://www.breastfeeding.asn.au/bf-info/breastfeeding-and-work/expressing-and-storing-breastmilk&quot; rel=&quot;nofollow&quot;&gt;https://www.breastfeeding.asn.au/bf-info/breastfeeding-and-work/expressing-and-storing-breastmilk&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Previously frozen— thawed in refrigerator but not warmed&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;4 hours or less (ie the next feeding) &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Store in refrigerator&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;24 hours   &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Do not refreeze&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;But in freezer the temperature is still below normal, still is there a probability of bacteria growth?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wish to understand the reasons behind the warning. Answers with references will be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="1809" LastEditorUserId="6289" LastEditDate="2014-05-23T17:12:34.437" LastActivityDate="2019-07-31T09:34:38.147" Title="Why aren't we allowed to refreeze previously thawed breastmilk in refrigerator?" Tags="&lt;human-biology&gt;&lt;food&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13632" PostTypeId="2" ParentId="13631" CreationDate="2013-11-23T14:44:27.883" Score="3" Body="&lt;p&gt;This is just a guess, but I don't think this is a food safety issues, its more a case of 'this food is gross now' issue.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I was a teenager I worked in a frozen food processing plant.  The freezers were giant boxes where freon was condensed on gigantic coils into a liquid and then the liquid freon would rain down on to the food passing under on a conveyer belt.  The vegetables were frozen instantly and it was quite tasty - frozen just a few minutes after being cleaned. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As industrial freezing is very quick and such flash freezing, the quality of the food is preserved in a pretty fresh state. [its horrible for the ozone in the atmosphere but this was in the 80s and I hope they changed the process].  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Milk is a mixture of water based nutrients and globs of fat, which give the milk is homogeneous white color and its smooth texture.  Freezing milk in a typical refrigerator would take hours and ice crystals would form and separate out the two phases - the fatty portions would separate.  Try it with a glass of milk and see.   This is the same reason that you don't re-freeze ice cream, which has even heavier creme proportions (even fattier).  The texture is completely gone. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-11-23T14:44:27.883" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="13633" PostTypeId="2" ParentId="5325" CreationDate="2013-11-23T20:44:52.193" Score="2" Body="&lt;p&gt;Cellulose is one of the most common sources of fiber in the nutritional sense. Because oranges are plants, their cells have cell walls, made out of cellulose, so some of the fiber in an orange is surrounding each individual cell. Both vascular cells and pith cells tend to have particularly thick cell walls, so they are probably higher in fiber (&lt;a href=&quot;http://www.foodgenetics.com/2010/07/06/is-orange-pith-good-for-you/&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; also suggests that the pith is particularly high in fiber - vascular tissue is probably not mentioned because it is less prominent).&lt;/p&gt;&#xA;" OwnerUserId="3824" LastActivityDate="2013-11-23T20:44:52.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13634" PostTypeId="2" ParentId="117" CreationDate="2013-11-24T03:42:17.380" Score="0" Body="&lt;p&gt;What about PCR using labeled nucleotides? Might have to run several reactions to get miligram quantities you need, but 35 nucleotides seems really really small for growth in bacteria, and purification would be extremely difficult. But 35 bases might even be too small for PCR, hardly bigger than your primers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you do need to grow in e coli, it might make sense to create a plasmid with multiple repeats of the 35 base sequence separated by the same restriction site. You can grow e coli in c13 n15 media, but it's expensive and you have &quot;train&quot; the cells over several generations because the heavier isotopes create differences in chemical kinetics that make the labeled nutrients hard for enzymes to use, but I've seen people do this for making proteins for NMR.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I bet you need this labeled DNA for NMR, don't you?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have you considered phosphate NMR? No need to label it, P-31 is already NMR active.&#xA;If it must be C13 N15, I highly recommend having it synthesized, it will be expensive, but that 35 base length and the requirement for single strandedness are ideal for chemical synthesis.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2013-11-24T03:42:17.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13635" PostTypeId="2" ParentId="1483" CreationDate="2013-11-24T03:51:20.163" Score="0" Body="&lt;p&gt;I'd make a comment if I could, but our lab has worked with a lot of poly lysine peptides for binding DNA. In our experience, lysine works better than arginine, and both work a lot better than histidine. Histidine has a lower pka, so it tends to be less positively charged at physiological pH. As far as proteins binding to specific DNA sequence, the double helix has two grooves, major and minor. The &quot;sides&quot; of the base pairs are accessible through the grooves, and proteins probably recognize patterns in those grooves. An A-T pair presents a different shape than a G-C pair, and DNA binding portions of proteins can discriminate these bumps and bind to the helix.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2013-11-24T03:51:20.163" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13636" PostTypeId="2" ParentId="13631" CreationDate="2013-11-24T04:18:24.537" Score="1" Body="&lt;p&gt;I don't know why I can't comment, but this seems simple enough that you could do an experiment and freeze it and see what happens. One possibility that comes to mind is that fat globules formed during freezing will clog the nipple on the bottle and make it harder for the baby to drink. Breast milk isn't homogenized, so the fats are more likely to separate than normal cow milk from the store. It also isn't pasteurized, so it will spoil faster than store bought milk too, but if you keep it cold and don't let the experiment run for more than a couple days it should be ok. To be safe, don't feed the experimental sample to the baby.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2013-11-24T04:18:24.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13637" PostTypeId="2" ParentId="11028" CreationDate="2013-11-24T04:27:18.117" Score="1" Body="&lt;p&gt;As far as &quot;mutations&quot; go, I think the term you're looking for is teratogenesis. Birth defects are most likely to form early in the pregnancy, but different toxins can have different windows. As an embryo develops, different tissues are growing and differentiating. If it is exposed to the right toxin at that time, that tissue may be damaged and not develop properly. If the tissue gets past that stage, exposure to the same toxin might have no affect at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia may be a decent starting point: &lt;a href=&quot;http://en.wikipedia.org/wiki/Teratogen&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Teratogen&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Studying birth defects is hard because it's tissue specific, toxin specific, and time specific. For some reason pregnant women just don't like to volunteer for studies on potentially dangerous chemicals.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2013-11-24T04:27:18.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13638" PostTypeId="1" CreationDate="2013-11-24T08:15:50.947" Score="2" ViewCount="288" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tAMlh.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pheromone Traps are used for fruit fly control. But I have no idea which ingredients or chemicals are used for preparing Pheromone trap&lt;/p&gt;&#xA;" OwnerUserId="4990" LastActivityDate="2013-11-24T08:15:50.947" Title="What are the ingredients of Pheromone Trap using for controlling Fruit flies of cucumber?" Tags="&lt;biochemistry&gt;&lt;microbiology&gt;&lt;entomology&gt;&lt;pathology&gt;&lt;agriculture&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13639" PostTypeId="2" ParentId="13610" CreationDate="2013-11-24T12:24:18.730" Score="4" Body="&lt;p&gt;Humans are are upright in their &lt;strong&gt;anatomical position&lt;/strong&gt; - fig. 1 - from which all directions and terminology stems.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wxVnc.jpg&quot; alt=&quot;Anatomical Position&quot;&gt;&#xA;&lt;sup&gt;Figure 1: Anatomical Position&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of this, &lt;strong&gt;anterior is &lt;em&gt;normally&lt;/em&gt; the same direction as ventral&lt;/strong&gt; and &lt;strong&gt;posterior &lt;em&gt;normally&lt;/em&gt; the same as dorsal&lt;/strong&gt; - fig. 2.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/d8Vw8.png&quot; alt=&quot;Normal anterior/ventral and posterior/dorsal&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;Figure 2: Normal directions in humans&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cranial anatomy is a special case, however, as the entire axis of the body bends round during embryonic development as seen in fig. 3.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RjN0n.png&quot; alt=&quot;Bending of the developmental axis&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;Figure 3: Bending of the developmental axis&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leads to the cranium being a little odd, where dorsal is equivalent to superior and ventral to anterior &lt;strong&gt;in this area of the body only&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IiVQA.png&quot; alt=&quot;Resultant differences in brain directions&quot;&gt;&#xA;&lt;sup&gt;Figure 4: Resultant difference in neuroanatomy conventions&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, for convenience, &lt;strong&gt;anterior and posterior retain their original directions even in this area&lt;/strong&gt;.  Therefore you could eliminate a large amount of your difficulties by just using these terms instead for most of the body.  &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;To answer your specific questions:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So I conclude that human nose is anterior&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So I concluded that humans' top head is dorsal. Yet ...We call humans' top head anterior&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The top of the head is &lt;em&gt;technically&lt;/em&gt; dorsal, however in practice would never really be referred to as such, instead being &lt;strong&gt;superior&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In humans, is humans' chin ventral from the eye too? or posterior?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The human chin is both inferior to the eye (looking straight at the face in the coronal plane) and &lt;strong&gt;anterior&lt;/strong&gt; to the eye (but only marginally).  It's more obvious if we look at the tip of the nose instead, which again is both inferior and anterior to the eye.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In humans, is the nose anterior too?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, the nose is anterior.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2013-11-24T12:24:18.730" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13640" PostTypeId="2" ParentId="13574" CreationDate="2013-11-24T13:40:33.747" Score="1" Body="&lt;p&gt;As already said in a comment: I would guess that ecological divergence emphasizes on the process of speciation by niche differentiation while ecological differentiation emphasizes on the process of niche differentiation due to overlapping niche of non-necessarily closely related species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But looking to some articles, it seems that they use both term without making any difference. As found on &lt;a href=&quot;http://link.springer.com/article/10.1007/s002270000441#page-1&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, I would rather advice to no consider too much difference in meaning between ecological divergence and differentiation. But take time to define accurately the words you're using, especially if you talk about cases that fall on the border of two concepts!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-24T13:54:50.817" LastActivityDate="2013-11-24T13:54:50.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13641" PostTypeId="1" AcceptedAnswerId="13644" CreationDate="2013-11-24T13:50:01.663" Score="3" ViewCount="9203" Body="&lt;p&gt;What does &quot;Niche Complementarity&quot; mean?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;On &lt;a href=&quot;http://www.encyclo.co.uk/define/Niche%20complementarity&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; website they define &quot;Niche Complementarity&quot; as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The tendency for coexisting species which occupy a similar position along one niche dimension&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't quite understand this definition. The tendency to do what?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Notes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;I know what is an ecological niche and therefore what is a niche dimension. There is no need to define this.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I am particularly interested in the use of this concept in speciation and adaptive radiation.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="6307" LastEditDate="2017-07-15T02:38:36.050" LastActivityDate="2017-07-15T02:38:36.050" Title="Definition of &quot;Niche Complementarity&quot;" Tags="&lt;ecology&gt;&lt;terminology&gt;&lt;speciation&gt;&lt;community-ecology&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13642" PostTypeId="2" ParentId="13625" CreationDate="2013-11-24T15:31:24.927" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;In a cold climate, do people often blow out the air from their lungs a lot when living in the cold condition to keep their lungs warm?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No, and it wouldn't make any sense: breathing more means inhaling more cold air that needs to be warmed up, so the result is a heat loss. The more so, as cold air (&amp;lt; 0°C) has a low water vapor pressure, while the lung likes to have the air at body temperature and well moistened. Which means that you also loose the vaporization heat of the water. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The function of moistening and heating the cold and dry air as well as recollecting some of the heat and water when breathing out is done by the nose. So the sensible (and done) thing in cold weather is to avoid breathing by mouth and instead keep your mouth shut and breathe by nose.&lt;br&gt;&#xA;Nevertheless, neither German nor English, nor any of the Scandinavian Germanic languages is spoken through the nose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My experience is that cold air (personal minimum: -40 °C) in the mouth is very unpleasant, and makes me cough as it is still cold when it arrives in the throat, but of course breathing out by mouth is less of a problem. But breathing out by mouth and in by nose means that the nose cannot recollect the heat and moisture from the outgoing air.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, the amount of breathing is linked rather to oxygen demand and $CO_2$ to be gotten rid of), and even the fastest speaking people I know do not get close to hyperventilation by speaking, not even speaking German or English. &#xA;Which means that speaking Germanic languages needs less breath to produce the sounds than what you need to breathe for physilogical reasons even at not much above base rate metabolism (sitting while talking) anyways. Which would imply that the breathing difference between Germanic and Sino-Tibetan languages would not cause an important driving force in language evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A side point is that I don't agree with your concept of cold climate. Both Germany and England are counted as &lt;a href=&quot;http://en.wikipedia.org/wiki/Temperate&quot; rel=&quot;nofollow&quot;&gt;temperate climate&lt;/a&gt;. Actually, &lt;a href=&quot;http://www.weatheronline.co.uk/weather/maps/city?LANG=en&amp;amp;CEL=C&amp;amp;SI=mph&amp;amp;MAPS=over&amp;amp;CONT=euro&amp;amp;LAND=DL&amp;amp;REGION=0001&amp;amp;WMO=10637&amp;amp;UP=0&amp;amp;R=0&amp;amp;LEVEL=160&amp;amp;NOREGION=1&quot; rel=&quot;nofollow&quot;&gt;Frankfurt&lt;/a&gt; has higher minimum temperature all year round than &lt;a href=&quot;http://www.weatheronline.co.uk/weather/maps/city?LANG=en&amp;amp;CEL=C&amp;amp;SI=mph&amp;amp;MAPS=over&amp;amp;CONT=asie&amp;amp;LAND=CI&amp;amp;REGION=0026&amp;amp;WMO=55591&amp;amp;UP=0&amp;amp;R=0&amp;amp;LEVEL=160&amp;amp;NOREGION=1&quot; rel=&quot;nofollow&quot;&gt;Lhasa&lt;/a&gt; (as you mentioned &lt;em&gt;Tibetan&lt;/em&gt; in your language family). &#xA;Also note that the Indo-Germanic language family covers a range of climates from tropic to polar just as the Sino-Tibetan covers some cold regions as well), so maybe language families that are spoken &lt;em&gt;only&lt;/em&gt; in polar regions vs. such that are spoken &lt;em&gt;only&lt;/em&gt; in tropic regions would be better to look at (see e.g. the &lt;a href=&quot;http://en.wikipedia.org/wiki/File%3aPrimary_Human_Language_Families_Map.png&quot; rel=&quot;nofollow&quot;&gt;Wikipedia language family map&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are probably some confounding influences that need to be taken into account. In cold weather, you do not sit or stand around chatting with people as much. And in the polar climates, historically farming has hardly been possible. So you have populations where hunting has been very important for survival, and regions with very low population density. Both mean that on average, you'll be silent instead of talking. As for having a chat with someone, you'd ask them in - or the length of the chat is limited by temperature.&lt;br&gt;&#xA;Which means that if cold is a driving force for the type of pronouciation that evolves, it would be a rather weak link. And in any case, speaking less will overcompensate all these breathing differences.&lt;/p&gt;&#xA;" OwnerUserId="848" LastEditorUserId="848" LastEditDate="2013-11-24T16:33:37.303" LastActivityDate="2013-11-24T16:33:37.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13643" PostTypeId="1" AcceptedAnswerId="13653" CreationDate="2013-11-24T15:41:59.467" Score="3" ViewCount="390" Body="&lt;p&gt;The methods section inside a paper I'm reading make mention of &lt;strong&gt;replicate lines&lt;/strong&gt;.&lt;br&gt;&#xA;Example: &quot;We founded 10 replicate lines from a single clone&quot;. This is in the context of experimental evolution and artificial selection of &lt;em&gt;Chlamydomonas&lt;/em&gt; in a laboratory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you please explain to me what a replicate line is? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a reference to the paper:&lt;br&gt;&#xA;Collins, S., Sültemeyer, D., &amp;amp; Bell, G. (2006). Rewinding the tape: selection of algae adapted to high $CO_2$ at current and Pleistocene levels of $CO_2$. &lt;em&gt;Evolution&lt;/em&gt; 60, 7, 1392-401. DOI: &lt;a href=&quot;http://dx.doi.org/10.1111/j.0014-3820.2006.tb01218.x&quot; rel=&quot;nofollow&quot;&gt;10.1111/j.0014-3820.2006.tb01218.x&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4992" LastEditorUserId="948" LastEditDate="2013-11-25T16:08:31.490" LastActivityDate="2013-11-25T16:08:31.490" Title="What's a replicate line?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13644" PostTypeId="2" ParentId="13641" CreationDate="2013-11-24T16:07:53.670" Score="1" Body="&lt;p&gt;As it has been said by @A.kennard in the comments, the definition the OP found is not complete. The full definition on the link he gave (&lt;a href=&quot;http://www.encyclo.co.uk/meaning-of-Niche%20complementarity&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;) is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Niche Complementarity:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The tendency for coexisting species which occupy a similar position along one niche dimension to differ along another.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The concept that two competing species will tend to evolve different evological niche is called character displacement. The definition from &lt;a href=&quot;https://en.wikipedia.org/wiki/Character_displacement&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt; is&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Character displacement is the phenomenon where differences among similar species whose distributions overlap geographically are accentuated in regions where the species co-occur, but are minimized or lost where the species’ distributions do not overlap.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2017-07-14T20:28:37.973" LastActivityDate="2017-07-14T20:28:37.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13645" PostTypeId="1" CreationDate="2013-11-24T16:14:48.757" Score="4" ViewCount="6964" Body="&lt;p&gt;I was reading this Wikipedia article about the &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_history_of_Italy&quot; rel=&quot;nofollow&quot;&gt;genetic history of Italy&lt;/a&gt;, and I found it interesting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are however a few things that puzzle me, because they seem to contradict each other. For example it states that because of the Alps forming a natural barrier Italy is, along with Finland, a genetic island in Europe. Does this mean Italians and Finns are genetically separated from all other Europeans, and to what extent? Later in the same article it says that &quot;In Italy as elsewhere in Europe the most common haplogroup is haplogroup H&quot;, which would seem to contradict the genetic island theory. After all, Italy has been colonized by countless populations throughout its history, which might suggest the Alps didn't really stop the gene flow from neighboring countries (not to mention that other European countries are equally separated by mountains, like Spain).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have no background in genetics whatsoever, so excuse my ignorance, I'm just trying to understand an article that seems very confusing and throws lots of different information together. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;: Thanks for the quick reply! I've found &lt;a href=&quot;http://www.nytimes.com/2008/08/13/science/13visual.html?_r=0&quot; rel=&quot;nofollow&quot;&gt;another link&lt;/a&gt; (which seems to be more reliable than Wikipedia's unverified claim), though it still sounds like a weird theory to me. &lt;/p&gt;&#xA;" OwnerUserId="4993" LastEditorUserId="5006" LastEditDate="2013-11-26T09:28:53.993" LastActivityDate="2015-09-17T08:33:51.710" Title="Are Italians genetically separated from other Europeans?" Tags="&lt;genetics&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13646" PostTypeId="2" ParentId="13645" CreationDate="2013-11-24T17:13:30.260" Score="7" Body="&lt;p&gt;I'm afraid that the &quot;genetic island&quot; idea is almost certainly wrong because&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The wikipedia page offers no evidence for this claim:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Following scientific research carried out by Dutch geneticists, Italy has proven to be one of the last two remaining genetic islands across Europe (along with Finland), this due to the presence of the Alpine mountain chain that, over the centuries, has prevented large migration flows aimed at colonizing the Italian lands.&lt;strong&gt;[citation needed]&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Remember that any random &lt;del&gt;idiot&lt;/del&gt; person can edit a wikipedia page. If there is no supporting reference for a claim you find in wikipedia, you should treat it as suspect.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;As you point out, the Alps only block entry on the north of Italy. Italy, however, is a pretty large peninsula, completely open to the sea along its entire length. For example, here is a map of Greek and Phoenician colonies circa 530bc (&lt;a href=&quot;http://en.wikipedia.org/wiki/Colonies_in_antiquity#Greek_colonies&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/t86oOm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, significant parts of the coast of what today is Italy were colonized by Greeks and Phoenicians. There were many subsequent waves of migration and/or invasion by various tribes such as&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The &lt;a href=&quot;http://www.ancient.eu.com/Migration_Age/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lombards&lt;/a&gt; (&lt;a href=&quot;http://en.wikipedia.org/wiki/Lombards#Invasion_and_conquest_of_the_Italian_peninsula&quot; rel=&quot;nofollow noreferrer&quot;&gt;image source&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/erup9m.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The Visigoths who &lt;a href=&quot;http://en.wikipedia.org/wiki/Sack_of_Rome_%28410%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;sacked Rome in AD410&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;The Ostrogoths whose &lt;a href=&quot;http://en.wikipedia.org/wiki/Ostrogothic_Kingdom&quot; rel=&quot;nofollow noreferrer&quot;&gt;kingdom&lt;/a&gt; in its prime contained most of modern Italy&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LABbHm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/History_of_the_Jews_in_Italy&quot; rel=&quot;nofollow noreferrer&quot;&gt;many Jewish communities&lt;/a&gt; in Italy that go as far back as the Roman era.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;An article by &lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0050794&quot; rel=&quot;nofollow noreferrer&quot;&gt;Brisighelli &lt;em&gt;et al.&lt;/em&gt;&lt;/a&gt; (which is actually quoted at the very top of the Wikipedia page you linked to) mentions that (emphasis mine):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A total of 583 individuals were sampled from across the Italian Peninsula, &lt;strong&gt;from ten distant&lt;/strong&gt; (if homogeneous by language) &lt;strong&gt;ethnic communities&lt;/strong&gt; — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;[...]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Italy shows patterns of molecular variation mirroring other European countries&lt;/strong&gt;, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were &lt;strong&gt;most likely modulated during Neolithic times&lt;/strong&gt;.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;[...]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Before the Roman conquest, ancient Italy was characterized only by the presence of &lt;strong&gt;Indo-European populations&lt;/strong&gt; living in the Italian Peninsula since the second millennium BC, corresponding to the period between the Iron Age and Romanization. During all this period there were also increasing contacts with the &lt;strong&gt;Phoenician and Greek colonists&lt;/strong&gt;: the former being largely present on the coasts of Sardinia and western Sicily and the latter in Southern Italy.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;[...]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;At the beginning of the first millennium BC &lt;strong&gt;the following native tribes could be distinguished on the Italian territory&lt;/strong&gt;: the &lt;strong&gt;Ligures&lt;/strong&gt;, on the coast that bears their name, in the northern Apennine valleys, part of the pre-alpine valleys and the western Po Valley; the Sicani, in the interior of Sicily; and the &lt;strong&gt;Itali&lt;/strong&gt;, in present-day Calabria (from whom comes the name ‘Italy’, which was to be extended to all the territory of the peninsula). Besides the already mentioned &lt;strong&gt;Terramare&lt;/strong&gt; tribe, on the southern edge of the Po Valley, and the &lt;strong&gt;Villanovans&lt;/strong&gt;, probably from Eastern Europe who settled throughout Central Italy, there were also the &lt;strong&gt;Umbrians&lt;/strong&gt; to the east of the upper basin of the Tiber. The &lt;strong&gt;Veneti&lt;/strong&gt;, who occupied the territory that still bears their name, originally came from &lt;strong&gt;Illyria&lt;/strong&gt; as did the &lt;strong&gt;Messapii&lt;/strong&gt; (now modern Salento or South Apulia) and Iapyges, who settled in present-day Puglia (Apulia) &lt;a href=&quot;https://i.stack.imgur.com/erup9m.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;5&lt;/a&gt;. Many other populations of Central-Southern Italy were created by the mixing of local and foreign elements dating back to the previous millennium; it is the case of the &lt;strong&gt;Sabines&lt;/strong&gt; and &lt;strong&gt;Latini&lt;/strong&gt; who settled in Lazio together with &lt;strong&gt;Falisci&lt;/strong&gt;, &lt;strong&gt;Aequi, Volsci, Hernici and Ausones&lt;/strong&gt;. The interior of Abruzzo was dominated by the &lt;strong&gt;Vestini, Paeligni and Marsi&lt;/strong&gt;, while the central Adriatic coast was populated by &lt;strong&gt;Picentes, Marrucini and Frentani&lt;/strong&gt;. The Apennine area of Molise and Basilicata was peopled by the &lt;strong&gt;Samnites and Lucanians&lt;/strong&gt;. In Calabria and Sicily there were also the &lt;strong&gt;Bruttii and Siculi&lt;/strong&gt;.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;[...]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Molecular indices indicated that &lt;strong&gt;most of the Italian samples show diversity values that are comparable to other European populations&lt;/strong&gt;. However, some differences were shown to exist, especially in isolated Ladin populations. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;h2&gt;References&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Brisighelli F, Álvarez-Iglesias V, Fondevila M, Blanco-Verea A, Carracedo Á, et al. (2012) &lt;em&gt;Uniparental Markers of Contemporary Italian Population Reveals Details on Its Pre-Roman Heritage.&lt;/em&gt; PLoS ONE &lt;strong&gt;7&lt;/strong&gt;(12): e50794. &lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0050794&quot; rel=&quot;nofollow noreferrer&quot;&gt;doi:10.1371/journal.pone.0050794&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-11-24T17:13:30.260" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13648" PostTypeId="1" AcceptedAnswerId="13658" CreationDate="2013-11-24T21:35:37.303" Score="3" ViewCount="66" Body="&lt;p&gt;My understanding of r- and k-selectors does not go deeper than the &lt;a href=&quot;https://en.wikipedia.org/wiki/R/K_selection_theory&quot; rel=&quot;nofollow&quot;&gt;wikipedia article&lt;/a&gt;. I understand k-selectors to be creatures that put tendentially more effort and energy into rearing their offspring, but produce tendentially less offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With cannibalism I don't mean eating their own on rare occasions, like after a plane crash in the Andes, but exibiting cannibalism outside of extreme situations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My gut feeling tells me that expanding much energy into raising an offspring and then eating her does not make much sense, but the world is big, there's lots of different species of animals and most of them are weird once look closely enough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good answer explains why one species is a rather to be seen as a k-selector, and in what contexts the cannibalism happens. Since we are talking about a sliding scale of behaviours, the question might as well be read as: What cannibal is the strongest k-selector?&lt;/p&gt;&#xA;" OwnerUserId="3037" LastEditorUserId="3824" LastEditDate="2013-12-03T10:38:29.290" LastActivityDate="2013-12-03T10:38:29.290" Title="Are there cannibalistic k-selectors?" Tags="&lt;evolution&gt;&lt;life-history&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="13651" PostTypeId="1" CreationDate="2013-11-25T01:42:08.360" Score="2" ViewCount="820" Body="&lt;p&gt;If we go down the evolutionary tree of humans, (&lt;em&gt;Homo sapiens&lt;/em&gt;, &lt;em&gt;Homo erectus&lt;/em&gt;, ...), what will be the first non-primate ancestors?&lt;/p&gt;&#xA;" OwnerUserId="4419" LastEditorUserId="5006" LastEditDate="2013-11-26T10:13:09.663" LastActivityDate="2013-11-26T10:13:09.663" Title="What is the most recent non-primate ancestors of humans?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13652" PostTypeId="2" ParentId="13651" CreationDate="2013-11-25T02:12:25.883" Score="5" Body="&lt;p&gt;According to the &lt;a href=&quot;http://tolweb.org/Eutheria/15997&quot; rel=&quot;noreferrer&quot;&gt;Tree of Life&lt;/a&gt;, tree shrews (&lt;a href=&quot;http://tolweb.org/Scandentia/15964&quot; rel=&quot;noreferrer&quot;&gt;Scandentia&lt;/a&gt;) are the sister group to Primates. So Scandentia are the most closely related extant mammals that are not Primates. Here's an image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HadJ9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-11-25T02:12:25.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13653" PostTypeId="2" ParentId="13643" CreationDate="2013-11-25T03:02:06.870" Score="1" Body="&lt;p&gt;In the context of experimental evolution, replicate lines are simply separate experimental (or control) lines the are established from the founder population at the beginning of the experiment. In this paper, the authors must have established 10 separate experimental lines that then evolved in different carbon dioxide levels. For example, 10 separate aliquots of algae are drawn from the same source population and then separately subjected to the agent of selection. These replicate lines should remain separate and not be mixed or crossed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Replicate lines are useful in experimental evolution for a few reasons. Because you are studying a population that is experiencing a selection pressure, you expect that genetic changes are in response to that pressure. However, changes can also occur due to drift. Replicate lines (and a consistent response to selection among them) is important to ensure that changes are a response to selection rather than to some other force (drift, mutation). Some drift is bound to happen when the lines are founded, because you are selecting a subset of the population, which is actually a good thing. Each line gets a random subset of genes which then evolve together. This potentially allows discovery of different genetic pathways to the same adaptive response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The background and lots of examples are in Garland and Rose, &lt;em&gt;&lt;a href=&quot;http://www.ucpress.edu/book.php?isbn=9780520261808&quot; rel=&quot;nofollow&quot;&gt;Experimental Evolution&lt;/a&gt;&lt;/em&gt; (UC Press, 2009). &lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2013-11-25T03:02:06.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13655" PostTypeId="1" AcceptedAnswerId="14149" CreationDate="2013-11-25T06:05:55.613" Score="1" ViewCount="51" Body="&lt;p&gt;While reading an article on mitochondrial inheritance I came across &lt;a href=&quot;http://dx.doi.org/10.1093/humupd/dmq002&quot; rel=&quot;nofollow&quot;&gt;this link&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The results state that mitochondrial DNA replication is regulated in different cells of an embryo at different levels. How is this regulated?&lt;/p&gt;&#xA;" OwnerUserId="4947" LastEditorUserId="4947" LastEditDate="2013-11-25T14:37:44.923" LastActivityDate="2013-12-25T20:13:08.243" Title="Regulation of the replication of mtDNA at embryonic level" Tags="&lt;molecular-genetics&gt;&lt;genomics&gt;&lt;embryology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13656" PostTypeId="2" ParentId="13655" CreationDate="2013-11-25T08:01:53.447" Score="0" Body="&lt;p&gt;Mitochondria divide by binary fission. The regulation of this division differs between eukaryotes. In many single-celled eukaryotes, their growth and division is linked to the cell cycle.&lt;/p&gt;&#xA;" OwnerUserId="4996" LastActivityDate="2013-11-25T08:01:53.447" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13657" PostTypeId="1" CreationDate="2013-11-25T11:20:28.900" Score="3" ViewCount="1725" Body="&lt;p&gt;I have a problem with a bacterial transformation of a yeast gene that I can not solve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I isolated yeast DNA and did a PCR to get my product. I am using pCGCUm vector with a GFP construct. I digest both my plasmid and my product with SmaI and ClaI for 4h each. After that I purify the product from a gel and perform a ligation with high efficiency T4 ligase for 30 minutes at 22°C. Then I transform my electrocompetent cells with electroporation (2000V, 5ms), recover it in 0.5ml LB for 2h and plate it on LB-A plates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First time I only did:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;insert1&lt;/li&gt;&#xA;&lt;li&gt;insert2&lt;/li&gt;&#xA;&lt;li&gt;Empty vector&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and it did not work (empty plates for insert and confluent growth (after 18h) of some weird colonies on EV).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did the same ligation again and this time I included controls&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is what I did:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;insert1&lt;/li&gt;&#xA;&lt;li&gt;insert2&lt;/li&gt;&#xA;&lt;li&gt;Empty vector&lt;/li&gt;&#xA;&lt;li&gt;negative control (EK cells + electroporation)&lt;/li&gt;&#xA;&lt;li&gt;positive control (EK cells + undigested vector)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now I got:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;insert1 (no colonies)&lt;/li&gt;&#xA;&lt;li&gt;insert2 (big colonies a lot of them)&lt;/li&gt;&#xA;&lt;li&gt;Empty vector (big colonies a lot of them)&lt;/li&gt;&#xA;&lt;li&gt;negative control (EK cells + electroporation) (no colonies)&lt;/li&gt;&#xA;&lt;li&gt;positive control (EK cells + undigested vector) (big colonies a lot&#xA;of them)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The negative control suggests that my competent cells are ok, at least they are not resistant to AMP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What confuses me is that even with positive control I get some weird big colonies - if I got nice transformants here I would assume that either digestion of ligation was not successful, but now I doubt that).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another thing that is weird is that now I got that colonies also on my insert2 plate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The scan image of big colonies looks like that:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/P8TSx.png&quot; alt=&quot;Empty vector plate&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a question if anyone has had that kind of colonies? I was thinking of maybe having contaminated cuvettes for electroporation but I had them in 100% EtOH for 3 days and then dried in fume hood for 3 hours before electroporation.&lt;/p&gt;&#xA;" OwnerUserId="4860" LastEditorUserId="948" LastEditDate="2013-11-25T15:59:57.797" LastActivityDate="2013-12-29T09:39:02.777" Title="Problem with bacterial transformation with electroporation" Tags="&lt;lab-techniques&gt;&lt;ecoli&gt;&lt;protocol&gt;&lt;transformation&gt;&lt;competent-cells&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13658" PostTypeId="2" ParentId="13648" CreationDate="2013-11-25T16:21:37.737" Score="1" Body="&lt;p&gt;My answer is messy and incomplete! I very welcome editing!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As soon as an individual is killed, on might as well eat the dead, but the act of killing might not be for the purpose of eating. We might even say that eating a dead might not only be for the purpose of getting energy and matter but only to clean the living place. And killing might appear in many circumstances. The best way to consider such issue is certainly by using the quite fundamental model of kin selection theory. It fits as much to species that gain energy by eating the dead or not. The difference imply just a minor change in the payoff matrix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The decision of one (the actor) to kill (and eat) another individual (the recipient) depends on:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the relatedness of the actor to the recipient (note a relatedness is not necessarily symmetric)&lt;/li&gt;&#xA;&lt;li&gt;The competition this recipient causes on the actor&lt;/li&gt;&#xA;&lt;li&gt;The cost (energy cost, risk of being injured or killed) of killing&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Many species (ants, wolves) might kill or injured individuals of the same species, when for example there is competition for reaching a status in the hierarchy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that the definition of k-selected species is not very accurate. First because there are limit cases. But also because r and k can relate to the function that describes the population growth of a species or might describe the amount of energy the parents spend into one offspring which is not necessarily the same thing. If we think of the parental care, we can think of the lions. When a male win the right to access to the females of another male, he will kill the babies that might be potential competitors to his progeny (because they take energy from the females or because females are not fertile before having lost their babies).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Killing its own offsprings is certainly not less common in k-selected species. You might think it is such a big cost to kill one of its own offspring when one has few offspring but what is important is to think in percentage. Killing 50% of the progeny has the same cost of an r-selected species than for a k-selected species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If one has a probability of 10% to be able to raise its offspring to adult age. But this probability raised to more than 20% if it accepts to kill an offspring to save energy for the next offspring, then it wins by doing so. THen we might ask: &quot;so would one make an offspring if it intends to kill it?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well it does not necessarily intend to kill it. It might need to decide late in the season whether or not it has better to kill its own offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, maybe offspring might be used as a reserve of energy and matter for its siblings or for its parents.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2013-11-25T16:21:37.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13659" PostTypeId="2" ParentId="13627" CreationDate="2013-11-25T17:19:13.783" Score="2" Body="&lt;p&gt;Yes, the fact that pea plants were easy to pollinate was desirable and helpful in understanding the effects of Mendelian factors (genes) but for the proper study of the factors expressed CROSS POLLINATION of homozygous plants having different phenotype and genotype ( e.g. cross between RR and rr) was preffered rather than self pollination.&lt;/p&gt;&#xA;" OwnerUserId="4947" LastActivityDate="2013-11-25T17:19:13.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13660" PostTypeId="1" AcceptedAnswerId="13661" CreationDate="2013-11-25T17:21:10.270" Score="8" ViewCount="4038" Body="&lt;p&gt;I was thinking about how alcohol is used to sterilize, and I was wondering if it would be possible to use alcohol as an antibiotic? if it kills bacteria, couldn't (conceivably) alcohol in the bloodstream kill any bacteria there, and the alcohol would be cleaned out by the liver later? Or would the concentration of alcohol necessary be too high and cause poisoning?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry if this has an extremely obvious answer, but all of the results I found in Google were about drinking alcohol while on antibiotics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could, in theory, alcohol (delivered in any way) be used as an antibiotic? If so, how? If not, why?&lt;/p&gt;&#xA;" OwnerUserId="4999" LastActivityDate="2013-11-25T18:23:25.357" Title="Could alcohol be used as an antibiotic?" Tags="&lt;human-biology&gt;&lt;antibiotics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13661" PostTypeId="2" ParentId="13660" CreationDate="2013-11-25T18:23:25.357" Score="12" Body="&lt;p&gt;No.  &lt;a href=&quot;http://www.cdc.gov/handwashing/&quot;&gt;The CDC&lt;/a&gt; recommends using a hand sanitizer at at least 60% ethanol.  &lt;a href=&quot;http://www.omniscienceblog.com/rubbing-alcohol&quot;&gt;Most preparations used in the lab&lt;/a&gt; are 70% ethanol.  Humans start to risk death somewhere around the &lt;a href=&quot;http://www.brad21.org/bac_charts.html&quot;&gt;0.3% alcohol level (BAC)&lt;/a&gt;, especially around 0.5%.  People have gone higher, but even 1% BAC would be completely useless against bacteria.  You'd be dead long before the bacteria died.  Besides, if you've got bacteria in your blood, you've got &lt;a href=&quot;https://en.wikipedia.org/wiki/Bacteremia&quot;&gt;bigger problems&lt;/a&gt; than a simple infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a pinch, though, it &lt;em&gt;can&lt;/em&gt; be used as a topical antiseptic, as per &lt;a href=&quot;http://www.straightdope.com/columns/read/2978/can-liquor-be-used-as-an-emergency-antiseptic&quot;&gt;this fun article&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2013-11-25T18:23:25.357" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13662" PostTypeId="1" AcceptedAnswerId="14072" CreationDate="2013-11-25T23:13:06.780" Score="4" ViewCount="139" Body="&lt;p&gt;During the &lt;a href=&quot;http://pubs.niaaa.nih.gov/publications/arh294/245-255.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;alcohol metabolic pathway&lt;/a&gt;, harmful by-products are made like acetaldehyde, hydroxyethyl, superox­ide anions, and hydroxyl radicals. How do these toxic compounds harm our tissues? Many of these intermediates are the compounds that are &lt;a href=&quot;https://biology.stackexchange.com/questions/5087/what-is-the-molecular-basis-of-hangovers/5095#5095&quot;&gt;responsible for hangovers&lt;/a&gt;, but are they also the molecular cause of liver damage?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2013-12-19T17:48:43.620" Title="What makes alcohol harmful to mammals?" Tags="&lt;biochemistry&gt;&lt;metabolomics&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13663" PostTypeId="2" ParentId="762" CreationDate="2013-11-26T03:43:59.707" Score="2" Body="&lt;p&gt;Interesting and thought provoking. Though I am curious why you wouldn't think plants and animals are conscious. Maybe they aren't self aware like you are, but if a lioness preserves herself to tend her cubs, is she not aware of the fact that things can exist or no longer exist? That life can be lost? No matter at what level you may perceive, this realization in her will trigger an emotion ( chemical reaction) which in turn will give her the fortitude to continue to survive, or as we sometimes see in nature, to not. How are we different? I hate this cut off that I see. &quot; if it doesn't do it on the level that we do it then it don't do it at all&quot;. That's silly, if you believe in an evolutionary development of genetic material how can you not believe that emotions and awareness have levels of development too? Sounds a bit like the &quot;chosen one&quot; complex. Once you take that road, you're a hop skip and a jump from the creationist and 6000 year old earth.&lt;/p&gt;&#xA;" OwnerUserId="5003" LastEditorUserId="3776" LastEditDate="2013-11-26T05:54:22.763" LastActivityDate="2013-11-26T05:54:22.763" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13664" PostTypeId="1" AcceptedAnswerId="13668" CreationDate="2013-11-26T05:01:36.713" Score="6" ViewCount="167" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Two species that reduce one another's fitness on microevolutionary&#xA;  (short-term) timescales can increase each other's macroevolutionary&#xA;  (long-term) fitness&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Opinions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;Intuitive Examples:&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Body Size&lt;/strong&gt; - Predator-prey relationships or interference relationships&#xA;(fighting, e.g. for territory) are often documented to put seletion&#xA;pressures to grow in body size, often a positive feedback loop. In&#xA;the short term the presence of the natural enemy in this case often&#xA;leads to decreased population fitness (probability of being&#xA;eaten/probability of fatal conflict over territory). But in the long&#xA;term such large body sizes acts as an advantage over potential future&#xA;enemies of the same kind. This is particularly relevant to marine&#xA;ecosystems - where the size of fish often determine where in the food&#xA;chain that fish is.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Speed/agility&lt;/strong&gt; - Predators and prey that rely on speed/agility to&lt;br&gt;&#xA;capture (predator) or escape (prey) undergo an evolutionary arms race&#xA;leading to positive feedback of speed/agility boosting morphologies. &#xA;In the short-term the natural enemy of the prey acts as a burden to&lt;br&gt;&#xA;population fitness (probability of being eaten) but in deep time the &#xA;prey has acquired morphological advantages over potential future&lt;br&gt;&#xA;natural enemies such as competitors for resources.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Venomousness&lt;/strong&gt; -&lt;a href=&quot;http://www.youtube.com/watch?v=myh94hpFmJY&quot; rel=&quot;nofollow&quot;&gt;Why do venomous animals live in warm climates?&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2013-12-03T20:28:57.763" LastActivityDate="2013-12-03T20:28:57.763" Title="Natural enemies boost deep evolutionary fitness?" Tags="&lt;evolution&gt;&lt;ecology&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;&lt;adaptation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13665" PostTypeId="1" AcceptedAnswerId="13679" CreationDate="2013-11-26T05:13:37.803" Score="4" ViewCount="492" Body="&lt;p&gt;Me and some friends are interested in opinions for the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Conjecture&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The maximum number of species must be limited by the maximum&#xA;  combinatorial/permutational space that can be occupied by DNA. Thus if&#xA;  there is a maximum physical genome size this is what will determine&#xA;  the maximum number of species that can possibly exist.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Explanation&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.G. say maximum number of DNA base pairs able to fit in a genome was $3$, each base pair can be one of either ${A,G,T,C}$. Then there are $4^3 = 64$ possible combinations of genomes. Extrapolate to genome sizes of $x$ base pairs, then there are $4^x$ combinations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Questions&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would it be possible to claim that the underlying &quot;blueprint&quot; that codes for living diversity sets the &lt;em&gt;absolute maximum&lt;/em&gt; for the total &quot;diversity space&quot;? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;**Does it make sense to define the total number of species life can achieve with the simple function:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$S &amp;lt; 4^x$, where X is the maximum genome size measured in DNA base pairs?**&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Notable Comments&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;@Shigeta: for $S&amp;lt;4^x$ the combinations involved quickly dwarf the&#xA;  number of atoms in the universe at ~10^80.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;@rg255: Even at this simplification of: $S&amp;lt;20^{x/3}$ there are&#xA;  $1.024e+13$ possible combinations with just 10 codons, many many more&#xA;  than there is likely species in the world.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="1590" LastEditDate="2016-08-17T08:46:16.800" LastActivityDate="2016-08-17T08:46:16.800" Title="Biodiversity is restricted by genome combinatorics?" Tags="&lt;evolution&gt;&lt;dna&gt;&lt;theoretical-biology&gt;&lt;genomes&gt;&lt;species&gt;" AnswerCount="4" CommentCount="27" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13667" PostTypeId="2" ParentId="13665" CreationDate="2013-11-26T05:59:24.460" Score="6" Body="&lt;p&gt;That's an interesting conjecture about the total amount of genetic variation that is possible. I would modify a few things. First, since the size of genomes varies greatly among organisms (from &lt;a href=&quot;http://www.genomesize.com/prokaryotes/&quot; rel=&quot;nofollow&quot;&gt;0.5 Mb to 15 Mb&lt;/a&gt; just for prokaryotes), there should be a fifth character in your set, representing the absence of a nucleotide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also issues of whether various combinations are equivalent. For instance, bacterial genomes are often circular, so if we could convert one genome into another simply by rotating it, we would consider those genomes identical. For example, if the genomes each had 99 As and 1 T, it would not be meaningful to say that they are different just because of the location of the T. I think this would require use of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Multinomial_theorem&quot; rel=&quot;nofollow&quot;&gt;multinomial coefficient&lt;/a&gt; to count the number of identical variants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding your main thesis, your use of the term &quot;species&quot; has no relation to how that term is used among biologists. Biological species include genetic variation, so each of them would include many of your species. Also, one criteria for identifying species is the clustering of these sequences (and the absence of other, intermediate sequences). This implies both that many possible DNA sequences simply cannot produce a viable organism and competition among similar genotypes is an important aspect of species identity.&lt;/p&gt;&#xA;" OwnerUserId="5006" LastEditorUserId="5006" LastEditDate="2013-11-28T05:31:55.463" LastActivityDate="2013-11-28T05:31:55.463" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13668" PostTypeId="2" ParentId="13664" CreationDate="2013-11-26T07:55:45.697" Score="3" Body="&lt;p&gt;The question is interesting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am afraid about the use of the word &quot;fitness&quot; in you question. The fitness is usually defined as the number of offsprings an individual can sire in its lifetime. Most often we talk about relative fitness which is the relative number of offspring in an individual can sire in its lifetime compare to the individual in the population that sire the greatest number of offsprings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How would you compare fitness of individuals between different species? Just by counting the number of offspring they left behind? Or did you mean that most fit species are actually those species that can outcompete others? If yes, then I would say that saying&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Two species that reduce one another's fitness on microevolutionary (short-term) timescales can increase each other's macroevolutionary (long-term) fitness&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;can be restated &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Two species that reduce one another's fitness on microevolutionary (short-term) timescales can increase each other's macroevolutionary (long-term) species competition ability&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and it is actually just a special case of&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One species that evolve under many strong selection pressure ends up being a very competing species.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The explanation is the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One species that undergoes one selective pressure, will see its genetic variance decreases. The weak individuals will disappear letting places to the strong individuals. Then newly arisen variance (mutation) will come up only in the strong individuals (as the other ones disapeared). This is what J.Gould meant by saying &quot;Natural selection creates the fit&quot;. As a consequence a species that undergo many successive selection pressure will end up with purified and very strong genotypes while, in a species that were free to evolve without selection they would have evolved many different genomes with some good mutations nested in very poor genetic background.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could as well use the concept of lineage selection and states that lineage that succeeds to outcompete others will thrive while species that suffer from competition with other species will get extinct. As a result, if you compare all species that were in competition with another species in the past with all species that were not in competition, you will find out that those that were in competition are more resistant to competition. But I guess this is not exactly what you meant when saying: &quot;Two species that reduce one another's fitness on microevolutionary (short-term) timescales can increase each other's macroevolutionary (long-term) fitness&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally you might think of the ability of species to evolve better. This ability is called &quot;evolvability&quot; (see &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0691134049&quot; rel=&quot;nofollow&quot;&gt;this book&lt;/a&gt; for example). You might say that species that undergo many selection pressures were selected to resist to newly arisen selection pressure. As a result, species that are under competition might end up with a greater evolvability than those that were not under selection. Resulting that species that were under competition will tend to increase to always increase their fitness in the long term.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-11-26T10:15:10.640" LastActivityDate="2013-11-26T10:15:10.640" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="13669" PostTypeId="1" AcceptedAnswerId="13670" CreationDate="2013-11-26T08:32:51.900" Score="4" ViewCount="433" Body="&lt;p&gt;I am an Indian with a small thin stature with some deposition of fat around my belly.I was wondering if genes play a role in fat deposition in the body for Indian, Chinese, European or African people. Fat deposition may differ among all these people around the belly, thighs etc.&#xA;These people also differ in their stamina and speed naturally.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For example here in India in the game of cricket there has been no &#xA;  fast bowler out of 1.2 billion people who can do fast bowling&#xA;  because it requires a lot of strength and stamina.Also on field&#xA;  athleticism is also very bad compared to Australian or South African&#xA;  players.I assume that may be its because of some cultural or genetic&#xA;  problem.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5008" LastEditorUserId="5006" LastEditDate="2013-11-26T10:41:14.330" LastActivityDate="2019-01-20T09:48:16.697" Title="Do genes play a role in the athleticism and shape of a person?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13670" PostTypeId="2" ParentId="13669" CreationDate="2013-11-26T09:02:27.523" Score="8" Body="&lt;p&gt;All these characteristics you observe (speed, ability to play cricket, belly size, height, etc…) are what what we call in biology a list of phenotypic traits. Basically, the phenotype is a characteristic of an organism that we can eventually measure or describe (physiological, behavioural, morphological, and life history are four common classes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a given population the phenotypic variance (the variance in height for example) can be expressed as the sum of the genetic variance (=the genetic variance underlying the phenotypic trait of interest), the environmental variance (=the environmental variance underlying the phenotypic trait of interest) and the variance due to the interactions between genes and environment (the variance due to the interaction that is underlying the phenotypic trait of interest).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematically expressed it gives:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$V_{phenotype} = V_{genetic}+V_{environment} + V_{gen X env}$$&lt;/span&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, for each trait there is a given part of the variance that is explained by the environment and a given part that is explained by the genes. We might go a bit further and defined the concept of heritability (in the narrow sense, see &lt;a href=&quot;http://en.wikipedia.org/wiki/Heritability&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia article&lt;/a&gt; for more info). The heritability (in the narrow sense) is the ratio of the phenotypic variance to the additive genetic variance. Mathematically expressed it gives:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$h^2 = \frac{V_{additive}}{V_{phenotype}}$$&lt;/span&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each trait has it's given heritability. The heritability can be defined only for a trait in a population (which defines &lt;span class=&quot;math-container&quot;&gt;$V_{genetic}$&lt;/span&gt;) and its environment (which defines &lt;span class=&quot;math-container&quot;&gt;$V_{environment}$&lt;/span&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, the heritability of height in human is around 0.8 (&lt;a href=&quot;https://www.scientificamerican.com/article/how-much-of-human-height/&quot; rel=&quot;nofollow noreferrer&quot;&gt;non-peer reviewed source&lt;/a&gt;). Which means that 80% of the variance in height in the world-wide population is explained by the genetic variance. See &lt;a href=&quot;https://biology.stackexchange.com/questions/42273/why-is-a-heritability-coefficient-not-an-index-of-how-genetic-something-is&quot;&gt;this post&lt;/a&gt; for more info about the concept of heritability&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your question, you also used (before your question was re-edited!) the word fitness (also it is not really present in your question). The fitness is a very important concept in biology, it is the ability of an individual to survive and sire offsprings. Our phenotypic traits influence our ability to sire offsprings and therefore our genes influence our fitness. If the whole phenotypic variance is explained by the environmental variance only, then, even the the trait is under selection, there will be no change in allele frequency due to selection. Note: an allele is a gene variant. If eye color is a gene, brown eyes and blue eyes are alleles (to make it easy). This change in allele frequency is called a response &lt;span class=&quot;math-container&quot;&gt;$R$&lt;/span&gt; to selection &lt;span class=&quot;math-container&quot;&gt;$S$&lt;/span&gt;. This link between selection, the response and the narrow sense heritability &lt;span class=&quot;math-container&quot;&gt;$h^2$&lt;/span&gt; is given by:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$R=S\cdot h^2 $$&lt;/span&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to answer your question. &lt;code&gt;Yes&lt;/code&gt;, part of the variance in height, belly size, cricket playing ability, etc… is genetically coded. As the fitness depends on phenotypic traits, &lt;code&gt;Yes&lt;/code&gt;, the fitness is genetically coded (otherwise there would have no response to selection). Therefore we're not all equal to playing crickets!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2019-01-20T01:02:41.460" LastActivityDate="2019-01-20T01:02:41.460" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="13671" PostTypeId="1" CreationDate="2013-11-26T10:58:58.530" Score="1" ViewCount="2149" Body="&lt;p&gt;I am doing an experiment to amplify the 16S rRNA gene from bacteria present in gut contents of fish. After extracting DNA, I perform one-step PCR with universal bacterial primers (27F, 1492R) and I see a strong band of expected length (approx 1500bp). My DNA extraction readings range from 50ng/ul in some samples, to 150ng/ul in others, as measured with Nanodrop.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this band represent all of the 16S genes present in the sample? Thus, does this band represent 16S genes from all of the bacterial species present in the sample?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do I need to perform a microbiome profiling PCR to differentiate and identify all of these species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="5012" LastActivityDate="2013-11-26T10:58:58.530" Title="Bacterial 16S rRNA PCR amplification with universal primers" Tags="&lt;molecular-biology&gt;&lt;microbiology&gt;&lt;pcr&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13673" PostTypeId="1" CreationDate="2013-11-26T15:33:27.657" Score="0" ViewCount="1447" Body="&lt;p&gt;I'm looking for very old (centuries) treaty or recent (20 &amp;amp; 21th century) research that state what some of the laws of Nature are, particularly concerning wild animals' behaviour. Such as; every animal does this, no animal does that, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Laws that could be then used to simulate or reproduce natural behaviours or check against unnatural ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Added&lt;/em&gt;: I'm looking for more simple laws, such as &quot;no (wild) animal eats cooked food&quot;. Assuming it's true then humans broke that law of Nature. It's the relation to Nature that interests me. I used the word behaviour in the large sense, as in, what are the laws that animals seem to follow (dos  and don'ts) in the world. I suppose that by looking at what the human is the only one to do we can find lots of those laws.&lt;/p&gt;&#xA;" OwnerUserId="5014" LastEditorUserId="5014" LastEditDate="2013-11-26T17:04:15.337" LastActivityDate="2013-11-26T17:37:39.987" Title="What are the universal laws of Nature concerning animals' behaviour?" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2013-11-26T16:29:57.797" ContentLicense="CC BY-SA 3.0" />
  <row Id="13675" PostTypeId="1" AcceptedAnswerId="13686" CreationDate="2013-11-26T15:54:48.543" Score="2" ViewCount="123" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Oligoribonucleotide X was treated with phosphatase (for removal of 3'&#xA;  and 5' - terminal phosphates), then with RNAase T1, which cleaves all&#xA;  phosphodiester bonds located in a 3' position of guanosine in a&#xA;  5'-specific manner. &lt;img src=&quot;https://i.stack.imgur.com/Pm033.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;As a result, oligonucleotides L, M and N were generated in equal&#xA;  amounts. Each of them was further treated with phosphatase and&#xA;  subjected to alkaline hydrolysis. Results are listed in the table&#xA;  below.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3t09a.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Then experiment was modified: oligoribonucleotide X after treatment&#xA;  with phosphatase was hydrolyzed with RNAaseP, which cleaves all&#xA;  phosphodiester bonds in a 3'-position of pyrimidines in a 5' -&#xA;  specific manner.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TpCNW.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This hydrolysis yielded five products in approximately equimolar&#xA;  concentrations: uridine monophosphate, cytidine monophosphate and&#xA;  oligonucleotides P, Q and R. After resolution of the mixture and&#xA;  alkaline hydrolysis of these oligonucleotides data listed in the table&#xA;  below were obtained.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/17P03.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My thinking : G can not be at the 5' end otherwise we would get a single Guanosine also in the first experiment. G can also not be at the second last from 3' end as we have not got any singles. We have got A and C in a duplet and so they must have been at the 3' end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also have trouble understanding the significance of &quot;mole/mole of oligoribonucleotide&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am trying to fit  in other results but am unable to do so. &#xA;A GOOD HINT WILL BE APPRECIATED MORE THAN A DIRECT ANSWER.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks  &lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-11-26T16:01:42.907" LastActivityDate="2013-12-14T09:12:03.490" Title="Determining sequence of oligoribonucleotide" Tags="&lt;molecular-biology&gt;&lt;homework&gt;&lt;rna&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="13676" PostTypeId="2" ParentId="13673" CreationDate="2013-11-26T16:02:44.330" Score="2" Body="&lt;p&gt;This seems to be rather impossible to answer! Very fundamental laws of nature are rather found in physics, mathematics or philosophy than in biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The theory of evolution is generally considered as a field that brings light to the whole science of biology. T. Dobzhanski famously said: &quot;Nothing in Biology Makes Sense Except in the Light of Evolution&quot; So I guess you might be interested to &quot;laws&quot; coming from that field. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm afraid you will some more knowledge in animal behavior than what you can acquire from this simple question before starting simulating. You can easily spend 5 years studying animal behavior and still having much things to learn from that field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would guess you might be interested in the concept of selfishness and altruism. I don't know your level of knowledge in biology. The following might seem a bit complicated (although it is a very brief and inaccurate summary of the real science that study these fields), if so, I would invite you learn about basic stuff in biology and evolutionary biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Selfishness and altruism&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to have natural selection, you need:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;variation&lt;/li&gt;&#xA;&lt;li&gt;heritability (of the trait that present some variation)&lt;/li&gt;&#xA;&lt;li&gt;different reproductive success (or success of copying itself) according to the trait which is heritable.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Following, this idea, an allele that behave altruistically (providing benefit (in terms of ability to copy itself) to someone else to its cost (always in the same terms)) will disappear  to the benefit of the selfish allele and therefore altruistic behavior should never be found in nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, we find altruistic behavior (and that was one of the greatest flaw Darwin could think about his theory):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Because of relatedness (Hamilton's law)&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;An animal would always behave in order to increase its inclusive fitness (=direct fitness + indirect fitness)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Because of genetically correlated behavior&lt;/li&gt;&#xA;&lt;li&gt;Because of upper level selection&lt;/li&gt;&#xA;&lt;li&gt;Because behaving in a way will directly or indirectly influence the way others will behave with you&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now, that's a very big field. I can't develop everything in this answer! If you liked the discussion of selfishness and altruism, you might be interested to read &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Selfish_Gene&quot; rel=&quot;nofollow noreferrer&quot;&gt;the selfish gene&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Extended_Phenotype&quot; rel=&quot;nofollow noreferrer&quot;&gt;the extended phenotype&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to go a bit deeper into mathematical formulation you might be interested in evolutionary &lt;a href=&quot;http://en.wikipedia.org/wiki/Game_theory&quot; rel=&quot;nofollow noreferrer&quot;&gt;game theory&lt;/a&gt; and &lt;a href=&quot;http://www.britannica.com/EBchecked/topic/1552117/Hamiltons-rule&quot; rel=&quot;nofollow noreferrer&quot;&gt;hamilton's rule&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/10742/what-if-rb-c-in-hamiltons-rule/10756#10756&quot;&gt;Here&lt;/a&gt; is a quick formulation of Hamilton's rule on this website&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt; (in reaction to your comment)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, you're not looking for a scientific law/theory/evidence/etc... you're looking for a simple observation in the nature that fit all animals. Here are some examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;There is no wheeled animals (see &lt;a href=&quot;https://biology.stackexchange.com/questions/7932/why-are-there-no-wheeled-animals&quot;&gt;this&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;li&gt;There is no animal that migrate every year from Earth to Mars&lt;/li&gt;&#xA;&lt;li&gt;All animals need a source of organic carbon&lt;/li&gt;&#xA;&lt;li&gt;All animals possess some flagellates cells (I think)&lt;/li&gt;&#xA;&lt;li&gt;All animals reproduce (not necessarily sexually)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you want to talk only about behavior, then you might have some trouble to generalize things to all animals because, there are many non-motile animals, many animals that have no brain, many animals that does not even have organs, … As a side note: It is possible that if you accept that a sponge (which is at the base of the Animalia kingdom see &lt;a href=&quot;http://tolweb.org/tree/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this website&lt;/a&gt; if you want to learn about what is classified to be an animal) produce some kind of behavior, you will have to accept that an oak tree also have behavior&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;.&#xA;Ah you meant animal in opposition to human?! Humans are included in my above list. If you look for differences then between human and all other animals, than you won't many other things than the brain and the behavior indeed. I hope nobody lost a whole life of work listing what human can do and what animals can't!&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Human have a complete and articulate language (I don't fully remember what adjective we use to differentiate human to animal language)&lt;/li&gt;&#xA;&lt;li&gt;Human are conscious that the are conscious that they are! It is quite hard to show that animals are not!&lt;/li&gt;&#xA;&lt;li&gt;Humans are the only animals that drive a car!&lt;/li&gt;&#xA;&lt;li&gt;etc…&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You're using the word law in a weird way. You might to have a look to&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Scientific_law&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Scientific_law&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Scientific_law&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Scientific_law&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2013-11-26T17:37:39.987" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="13677" PostTypeId="2" ParentId="13628" CreationDate="2013-11-26T16:08:05.957" Score="2" Body="&lt;p&gt;I think the order &lt;code&gt;i,ii,iii&lt;/code&gt; should be correct, since the fall in temperature occurs after the heat loss exceeds production and will continue only till the temperature equals the ambient temperature. &lt;code&gt;iv&lt;/code&gt; is the reason for &lt;code&gt;i&lt;/code&gt;. Hence &lt;code&gt;iv,i,ii,iii&lt;/code&gt; sounds pretty convincing to me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With &lt;code&gt;i,iii,ii,iv&lt;/code&gt; , the main problem is that there can not be any appreciable fall in temperature &lt;code&gt;ii&lt;/code&gt; after the temperature equals the environmental temperature &lt;code&gt;iii&lt;/code&gt;. And &lt;code&gt;iv&lt;/code&gt; seems more probably to be the reason for &lt;code&gt;i&lt;/code&gt; rather than the reverse&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2013-11-26T16:08:05.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13678" PostTypeId="1" CreationDate="2013-11-26T17:08:44.587" Score="4" ViewCount="100" Body="&lt;p&gt;Flatus frequency is affected by diet, so I was wondering if flatus production solely depends on the food eaten, meaning that some people never ever release flatus because they don't eat any flatus-producing food. I guess if they say they don't, they're probably in denial...&lt;/p&gt;&#xA;" OwnerUserId="5017" LastActivityDate="2014-07-06T14:41:04.890" Title="Do all humans experience flatus regardless of their diet?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13679" PostTypeId="2" ParentId="13665" CreationDate="2013-11-26T20:22:09.250" Score="8" Body="&lt;p&gt;Yes, we can say the number of species is limited as you conjecture.  However, quick estimation shows that the limitation has no apparent usefulness:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A reasonable estimate of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Genome#Genome_size&quot;&gt;largest known genome&lt;/a&gt; is 150 GB (150,000,000,000 or 1.5e11 nucleobases).  The limit would be 4 raised to that power.  That limit is so high that it is too large for most calculators to calculate.  For instance. Wolframalpha.com fails to calculate 4 raised to 1e11, its maximum being about 4 raised to 1e9.  The result of 4 to the 1.0e9 power is about 1.0e602059991 or 10 raised to the 602059991'th power.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That rough result, 1.0e602059991, is so enormous that it is exponentially greater than the number of atoms in the universe &lt;a href=&quot;http://www.universetoday.com/36302/&quot;&gt;(which is less than 1.0e100)&lt;/a&gt;.  Hence, assuming the definition of species requires an organism to use at least one atom for its body, there is no consequence to saying the number of species must be less than this number.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The number of possible combinations of nucleotides is so outrageously large that it does not constrain the number of unique individual organisms or species.&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2013-11-26T20:22:09.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13680" PostTypeId="1" AcceptedAnswerId="13683" CreationDate="2013-11-26T20:47:53.420" Score="11" ViewCount="1040" Body="&lt;p&gt;In every non-life example I can envision, a copy of a copy is always a degraded or less pure version of the original unless some outside influence acts to correct the copy back toward the ideal represented by the original. Photocopies get blurrier with each generation. Casts from a mold are distorted from the original from which the mold was made. In fact, each cast degrades the mold itself. When data is copied on computers or across networks, parity checks verify that no mistakes were made, but even then, every long once in a while, combinations of errors can cause a false positive in a parity check. So given enough time, the copies would degrade.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In eukaryotes, new individual organisms always begin as a zygote, so in all kingdoms, reproduction boils down to the genesis of a single cell. This involves correctly building the DNA as well as all of the other complex architecture of the cell. Why doesn't this cell degrade like every other example I can think of? In fact, cells are capable of such perfect reproduction that the system generally supports the introduction of additional randomness in order to promote the possibility of productive change. I can think of some probable contributing factors that make this work, but I must be missing something. I can't imagine that this model would actually work the way it does - so well in fact that the design actually improves over time. What am I missing or underestimating?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Contributing Factors (I guess):&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Perfect Building Blocks:&lt;/em&gt; Cellular development follows a pattern at every level, and ultimately operates all the way down to the molecular level. At that level, nearly all building blocks are identical. Life is built of stable atoms, not something like plutonium, and in the rare event that an atom does change, the result is simply a different kind of atom, which still tends toward a stable form in the long term. Because the structures of life are ultimately made of stable components that are plentiful everywhere in the environment, the essential structures being copied are precise and can be copied precisely. Photocopies and casts are not precise to the molecular level, so copying them is more approximate by nature. Digital data propagation, however, is a very similar process. Bits are also theoretically perfect building blocks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Fitness Correction:&lt;/em&gt; When mistakes do degrade the reproduction process, rather than maintaining or randomly improving upon it, there is a correction mechanism that removes the defects from the process. Those defects do not survive to reproduce. This evolutionary process acts to keep the reproductive pattern focused back upon a theoretical ideal which is independent of a specific physical form to be copied. &lt;code&gt;This seems like the most essential element of the explanation, because it is ultimately only through progression that digression can be avoided, but it is also the part that seems the most dubious. Astronomical quantities of defects would have to be produced before developing just one advantageous feature. I would expect living creatures to be 99% defective with only 1% surviving to breed. I would expect 99.9% of zygotes to expire without being born or sprouting from seed. I would expect all sexual organs (ovaries, testes, stamen, etc.), if not the majority of the whole body, to be mostly dead cells, with just a few successes surviving to fertilization. I would expect 99.9% of the genome to be experimental, almost completely unusable liability to the species. Essentially, I would expect premature death to far outweigh successful life everywhere and at all times. And even so, I would still expect evolution to be even slower than it has been.&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Mutation Management Mechanisms:&lt;/em&gt; I understand that there are mechanisms in reproduction that decrease the likelihood of mutation in more established and stable parts of the genome compared with sections that are more open for discussion - epigenetic structures, HOX genes, etc. Portions of all genomes have been established and functional for hundreds of millions of years, so I gather that there are mechanisms for protecting them (I suspect probably far more than we have yet discovered).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note:&lt;/strong&gt; The numbers I present are fuzzy and are based not on calculations but on general impressions I get of the magnitude of the numbers involved and the relative rareness of useful mutations. Is there any place where this kind of calculation has been performed with more realistic approximations of probabilities?&lt;/p&gt;&#xA;" OwnerUserId="5018" LastEditorUserId="1306" LastEditDate="2013-11-27T01:56:27.850" LastActivityDate="2015-03-17T13:21:06.227" Title="Why, specifically, does each generation, on average, improve upon the design of the species rather than degrade it?" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;replication&gt;&lt;molecular-evolution&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13681" PostTypeId="2" ParentId="13665" CreationDate="2013-11-27T00:05:27.993" Score="3" Body="&lt;p&gt;I'm going to define a species according to the biological species concept, probably the most widely &quot;accepted&quot; species concept where a species is a group of individuals that reproduce, or have the potential to do so. Using a simplified example I will show you that gene*environment interactions affecting phenotype can allow separate species to occur despite being genetically identical. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine a very short section of DNA which affects seminal fluid proteins in a fruit fly. It is  just 10 bases long. The first three triplets of bases code for a protein constructed of three amino acids which affects the females behavior upon receipt of the male ejaculate. The final base regulates the expression of the first codon and is sensitive to developmental environmental factors (let us say nutrient richness). When the development of the male fly is in a nutrient rich background the section of DNA produces all three codons in equal amount to construct a protein and that protein stimulates the female to release eggs for fertilization. If we take a genetically identical male reared in a nutrient poor environment then the regulatory base increases the production of the first codon's amino acid. This makes a different protein structure which no longer stimulates the female in to releasing eggs, therefore the males from nutrient poor backgrounds can not reproduce with the females from a nutrient rich background, and these two genetically identical populations are different species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus I would say, &lt;strong&gt;no, the theoretical maximum number of species is not capped by the length of the DNA.&lt;/strong&gt; However, given that just the potential number of bases (current highest estimates recorded are 150,000,000,000) far far far exceeds the number of species in the world, we can say that the number of base combinations is not the limiting factor on the biodiversity we see. That is down to evolution (selective and neutral processes). &lt;strong&gt;Phenotypes determine the ability of two individuals to reproduce, phenotypes are the result of more than just genetics:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$phenotype = genotype + environment + genotype*environment$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further, as &lt;strong&gt;@mgkrebbs has already stated&lt;/strong&gt;, the number of possible species (given by $4^x$ when $x$ is 150,000,000,000)  is, not only far more than the number of species that do exist, but also far more than the number of atoms in the universe. Assuming each species requires at least one atom then the number of atoms available will halt increasing numbers of species before the number of possible base combinations does.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-11-27T13:24:41.010" LastActivityDate="2013-11-27T13:24:41.010" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="13683" PostTypeId="2" ParentId="13680" CreationDate="2013-11-27T01:48:16.720" Score="29" Body="&lt;p&gt;You have clearly given this a lot of thought. Unfortunately, as @adam.r said, you are laboring under certain misapprehensions. The quick answer is that each generation does not &quot;improve&quot; on the last. That is a common misconception. In a bit more detail:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;First of all, your copying metaphor is a bad one. There was no &quot;perfect original&quot;, I expand on this theme at length in my answer &lt;a href=&quot;https://biology.stackexchange.com/a/9596/1306&quot;&gt;here&lt;/a&gt; but, briefly, all species are constantly changing. They are not moving away from a platonic ideal of the perfect species (or towards it for that matter), they are simply changing in response to the world around them. What's 'good' today is not necessarily 'good' tomorrow.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Your copy machine metaphor does hold for changes from one generation to the next though. Copying DNA is &lt;em&gt;fraught&lt;/em&gt; with errors. There is a huge cellular machinery in place whose only job is to catch and correct those errors. Nevertheless, many get through and result in diversity that can then be selected for or against through the process of natural selection. So, the copies &lt;em&gt;do&lt;/em&gt; actually degrade. That, in fact, is the very basis of how evolution works.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Another important point is that most changes are neutral. They have absolutely no effect one way or the other. There are many reasons for this but the main ones are&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The vast majority of DNA does not actually code for protein. What it &lt;em&gt;does&lt;/em&gt; do is an area of active research but minor changes in sequences that don't code for protein are extremely unlikely to cause a change in phenotype. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Almost all of the information necessary to produce a viable organism is in the &lt;strong&gt;genes&lt;/strong&gt;, and genes represent a very small (~5% in human for example) percentage of the genome. Changes that affect the fitness of an individual are almost invariably found in the coding sequences of genes. This means that of the ~30 billion possible sites for mutation in any given cell, 95% of them (even less actually since only &lt;a href=&quot;http://en.wikipedia.org/wiki/Exon&quot; rel=&quot;nofollow noreferrer&quot;&gt;exons&lt;/a&gt; count and they're ~2%) will not cause a phenotypic effect. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The genetic code is redundant. Basically, DNA is &quot;read&quot; in &quot;words&quot; of three &quot;letters&quot;, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Codon&quot; rel=&quot;nofollow noreferrer&quot;&gt;codons&lt;/a&gt;. Since there are 4 bases in the genome (A,C,T and G) this means there are 64 possible codons. Each codon specifies a particular &lt;a href=&quot;http://en.wikipedia.org/wiki/Amino_acid&quot; rel=&quot;nofollow noreferrer&quot;&gt;amino acid&lt;/a&gt; (the building blocks of proteins) and a given sequence of codons will result in a specific sequence of amino acids. However, there are only 22 amino acids, many of which are specified by the same codon:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yHBxX.gif&quot; alt=&quot;the genetic code&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see in the image above, in most cases, changing the third letter of the codon does not affect the amino acid that will be specified. This means that even for those mutations (changes) that occur in the coding region of genes, the chances are relatively high that they won't actually result in any phenotypic change. If you change the genetic code but the changed codon still codes for the same amino acid there will be no change in phenotype.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;As for your contributing factors:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Perfect Building Blocks&lt;/em&gt;: Nope, sorry this one is wrong. First of all there is no such thing as a minor change that involves changing an atom. Any change that happens at the atomic level is &lt;em&gt;huge&lt;/em&gt; by definition. That kind of thing happens a the hearts of stars and in nuclear reactors. The chemical reactions in our body involve changing &lt;em&gt;molecules&lt;/em&gt; not atoms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no such thing as a minor change really, if you replace one atom in a molecule by another, you are significantly changing the properties of that molecule (this is less true for large, complex macromolecules where some changes can indeed be minor). If you were to change, for example, a single atom in normal table salt ($NaCl$) from sodium to hydrogen, you would get $HCl$, &lt;a href=&quot;http://en.wikipedia.org/wiki/Hydrochloric_acid&quot; rel=&quot;nofollow noreferrer&quot;&gt;hydrochloric acid&lt;/a&gt; and not something you want to put in your soup.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are no perfect building blocks, in biology &lt;em&gt;nothing&lt;/em&gt; is perfect, that only happens in math. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, the organism does &lt;em&gt;not&lt;/em&gt; follow the same pattern from the organismal to the cellular to the molecular (never mind atomic) level. In fact, there are very different organizational principles at play at the different levels and the way that cells are organized (see &lt;a href=&quot;https://biology.stackexchange.com/a/11053/1306&quot;&gt;here&lt;/a&gt; for example) has nothing to do with the way that a cell's contents are organized. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stability is overrated. In fact, our bodies contain loads of unstable (reactive) chemicals, oxygen being chief among them. By definition, chemical reactions involve changing molecules (not atoms, but we don't deal with that level, biological effects tend to be at the molecular, not atomic level). All reactions that go on in the factory that is your body involve the changing of one molecule into another. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Fitness Correction:&lt;/em&gt; Actually, at the cellular level, the corrections try to faithfully reproduce the template they are copying from. When a cell copies itself, it will also copy its DNA. It does so by using its own DNA as a template. There is no &quot;theoretical ideal&quot;, the cell has no information about the genome of its parent, only its own. As I mentioned above, there are various corrective mechanisms whose job it is to spot errors and correct them. They have no way of knowing whether a given change will be beneficial or harmful to the individual, as far as these processes are concerned, any change is bad and should be corrected. The only thing they do is try to make a daughter cell's genome identical to the parent cell's.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a change makes it past the cellular level, &lt;em&gt;then&lt;/em&gt; it can be selected for or against based on whether it makes the individual carrying it more or less likely to reproduce. This, however, is not a directed process. It just happens. If a mutation makes a male blue whale stronger, it is more likely to be the one that catches up with the racing female and so more likely to reproduce. There is no direction other than the selective process itself. There is no one around comparing new individuals to an ideal and selecting accordingly. If you're better at reproducing than your peers, your genes will be selected. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually, many many gametes are discarded. Many cells die. You just don't know about it because they die before you can see them. So deleterious (very bad) changes &lt;em&gt;do&lt;/em&gt; occur. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;I would expect 99.9% of the genome to be experimental, almost completely unusable liability to the species.&quot; In a way this is true. Despite &lt;a href=&quot;https://genome.ucsc.edu/encode/&quot; rel=&quot;nofollow noreferrer&quot;&gt;recent findings&lt;/a&gt;, 98% of the human genome does not directly affect the phenotype. It is only the 2% that represents the protein coding parts of genes that has a direct effect on fitness. In fact, in the human genome specifically, there is a short sequence that does not code for any protein and does not (directly, though there are various theories about this) affect our phenotype, that has been making copies of itself and propagating in our genome for generations. Today, this sequence (Alu) represents ~10% of the human genome, that's twice as much as all our genes together!&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Mutation Management Mechanisms:&lt;/em&gt; The basic protection mechanism you mention in your question is quite simply death. Mutations that render housekeeping genes (like the HOX cluster) inactive kill the organism that carries them. That does not mean they don't occur, it simply means that when they occur, we don't see them because the individual carrying the mutation is dead (see point 3). &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-03-17T13:21:06.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13684" PostTypeId="1" CreationDate="2013-11-27T08:54:51.440" Score="6" ViewCount="1010" Body="&lt;p&gt;Is it possible to express both the MHC class-1 and MHC class-2 both in one cell?&lt;/p&gt;&#xA;" OwnerUserId="5021" LastActivityDate="2013-12-31T00:20:17.377" Title="Question about the expression of MHC" Tags="&lt;immunology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13686" PostTypeId="2" ParentId="13675" CreationDate="2013-11-27T10:15:44.797" Score="1" Body="&lt;p&gt;Here are a few hints which might help you:-  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) You get free &lt;code&gt;UMP&lt;/code&gt; and &lt;code&gt;CMP&lt;/code&gt; (in contrast to &lt;code&gt;UMP + C&lt;/code&gt; or &lt;code&gt;CMP + U&lt;/code&gt;) in the second experiment before alkaline hydrolysis.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) There are two &lt;code&gt;CMP&lt;/code&gt; in &quot;N&quot; oligoribonucleotide, and a free cytidine (and not &lt;code&gt;CMP&lt;/code&gt;) in &quot;M&quot; and &quot;Q&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3)Use the fact that all oligoribonucleotides were treated with phosphatase before being subjected to alkaline hydrolysis.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Referring to your comment, I dont know why do you think consecutive cytidine is not possible).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are a few hints that helped me solve this. If you want further clarification or the answer, tell me in the comments.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Answer for reverse derivation:- $5'-UACGCCGAC-3'$&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2013-12-14T09:12:03.490" LastActivityDate="2013-12-14T09:12:03.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13687" PostTypeId="1" CreationDate="2013-11-27T15:44:37.320" Score="2" ViewCount="1343" Body="&lt;p&gt;It's very well known that the Y chromosome is what determines maleness, but more specifically this seems to happen thanks to the SRY gene located on it. Some individuals have an XX karyotype, but because of unequal crossing-over between X and Y chromosomes during meiosis in the father, one of the X chromosomes ends up containing the SRY gene, and the individual develops into a male (De La Chapelle Syndrome). &#xA;So I was wondering, is the SRY gene all that's really needed for an individual to be, unquestionably, a male? It's kinda odd how XX males have male genitalia but are classified as intersex solely because their karyotype is a typical feminine one (which should be irrelevant given how they also possess the SRY gene).&lt;/p&gt;&#xA;" OwnerUserId="5026" LastActivityDate="2015-10-06T00:11:56.493" Title="Is the SRY gene the sole responsible of biological male sex?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13689" PostTypeId="2" ParentId="13687" CreationDate="2013-11-27T18:10:56.860" Score="2" Body="&lt;p&gt;To my knowledge, the &lt;strong&gt;SRY gene is the only gene that cause variance in sex determination&lt;/strong&gt; in humans. Of course, many genes are then involved in &lt;strong&gt;sex determination cascade&lt;/strong&gt; but none these genes have variance in humans. Because environmental variance has no impact on gene determination in humans (to my knowledge and despite a few highly criticized articles) and therefore, &lt;strong&gt;nothing else than the SRY gene explains the sex determination&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genes that are involved in the cascade of sex determination are not necessarily on the sexual chromosomes. On the Y chromosome, there are some genes that are male beneficial (beneficial for the male function) but these genes are not involved in the sex determining system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In all species, the sex is determined by the environment and/or the genes. The best way to look at it is by &lt;a href=&quot;http://en.wikipedia.org/wiki/Norms_of_reaction&quot; rel=&quot;nofollow noreferrer&quot;&gt;reaction norms&lt;/a&gt;. On the below picture, think of the x-axis as being the temperature. Then, if you ask the question &quot;Does the temperature influence the probability to develop into one sex or another?&quot; One should answer. &quot;It depends on the range of temperature you're looking at!&quot; If you look at only very high temperature (far right) or very low temperature (far left), only the genotype explains the sex determination. If you look at mid-range of temperature, then both the genotype and the environment determines the sex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1Aqjz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;N. Perrin and L. Beukeboom are writing what is probably going to be a very good book that will obviously interest you. I think the book is going to be publish in 2014 only. &lt;a href=&quot;http://www.amazon.fr/The-Evolution-Sex-Determination-Beukeboom/dp/0199657149/ref=sr_1_1?ie=UTF8&amp;amp;qid=1385574752&amp;amp;sr=8-1&amp;amp;keywords=Perrin%20sex&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here is the amazon link&lt;/a&gt; to pre-command it.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-10-06T00:11:56.493" LastActivityDate="2015-10-06T00:11:56.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13690" PostTypeId="1" AcceptedAnswerId="30015" CreationDate="2013-11-27T20:41:45.673" Score="5" ViewCount="4559" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Calico_cat&quot; rel=&quot;nofollow noreferrer&quot;&gt;Calico cats&lt;/a&gt; are cats that have 3 fur colors and are always female or males two X chromosomes.&lt;/p&gt;&#xA;&lt;p&gt;I've seen many cats that will have 2 fur colors (one of them is usually white) and another, third, color which is a darker shade of one of the other colors. As exampled in the pictures below (taken from the internet). Are those considered Calico cats?&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/V01Sk.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/V01Sk.jpg&quot; alt=&quot;pic of cat 1&quot; /&gt;&lt;/a&gt;&lt;br /&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://i3.mirror.co.uk/incoming/article1381837.ece/ALTERNATES/s615/%C2%A3%C2%A3%C2%A3%20Larry%20the%20Downing%20street%20cat%20fights%20with%20the%20George%20Osborne%20cat%20Freya-1381837&quot; rel=&quot;nofollow noreferrer&quot;&gt;mirror.co.uk&lt;/a&gt;)&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://pressdispensary.co.uk/q991467/images/cat-image-for-press.jpg&quot; alt=&quot;pic of cat 2&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="680" LastEditorUserId="15950" LastEditDate="2020-12-20T12:16:15.210" LastActivityDate="2020-12-20T12:16:15.210" Title="Are these cats calico?" Tags="&lt;genetics&gt;&lt;zoology&gt;&lt;feline&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="13691" PostTypeId="1" AcceptedAnswerId="13694" CreationDate="2013-11-27T22:36:41.477" Score="10" ViewCount="47112" Body="&lt;p&gt;What happens if one looks directly at infrared LEDs? Sometimes I see this kind of LED at night as red dots and I'm also courious about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering what would happen if one looks directly to these LEDs, because we see them everywhere like in remote controls, CCTV cameras, sensors, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the difference between infrared and visible light to our eyes?&#xA;(I mean why is it impossible to look directly to visible light while we can look to infrared?)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;LED: Light-emitting diode&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/emyzJ.jpg&quot; alt=&quot;Infrared LEDs&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5029" LastEditorUserId="5029" LastEditDate="2017-11-06T15:30:01.173" LastActivityDate="2017-11-06T15:30:01.173" Title="Is it safe to look at infrared LEDs?" Tags="&lt;eyes&gt;&lt;vision&gt;&lt;light&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13692" PostTypeId="1" CreationDate="2013-11-27T23:02:07.360" Score="1" ViewCount="748" Body="&lt;p&gt;I need some clarification on the concept of &lt;em&gt;gram dry cell weight&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The unit acronym &lt;strong&gt;gDCW&lt;/strong&gt; stands for &lt;em&gt;gram dry cell weight&lt;/em&gt;. My interpretation is that 1 gDCW is equivalent to 1 gram of dry cells, but I am not sure. Is this accurate?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, the &lt;a href=&quot;https://biology.stackexchange.com/q/11138/561&quot;&gt;dry cell weight&lt;/a&gt; of mouse cells is roughly 300 pico grams. Therefore, in this case, one gram of dry mouse cells contains $10^{12}/300$ mouse cells (1 picogram $=10^{-12}$ grams). And if one says that there are 0.6 mmol of alanine per gDCW of mouse cells, this means that the total alanine content of $10^{12}/300$ mouse cells is 0.6 mmol. Is this accurate?&lt;/p&gt;&#xA;" OwnerUserId="561" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2013-11-27T23:09:57.410" Title="On the definition of gDCW (gram dry cell weight)" Tags="&lt;nomenclature&gt;&lt;definitions&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13693" PostTypeId="1" CreationDate="2013-11-27T23:25:56.930" Score="7" ViewCount="475" Body="&lt;p&gt;A controversial concept in Biology &lt;a href=&quot;http://ib.berkeley.edu/courses/ib160/past_papers/beroukhim.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;Group Selection&quot;&lt;/a&gt;, has caused confusion and conflict amongst scientists since the since the mid 1990s. The more general realm of study is termed the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Unit_of_selection#Species_selection_and_selection_at_higher_taxonomic_levels&quot; rel=&quot;nofollow noreferrer&quot;&gt;unit of selection&lt;/a&gt;&quot; discussion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Definition&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A simple working definition for &quot;group selection&quot; &lt;em&gt;(edit/discuss this!)&lt;/em&gt; is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Selection for traits that would be beneficial to a population of units at the&#xA;  expense of an individual unit possessing the trait&quot; (&lt;a href=&quot;http://www.everythingbio.com/?s=group%20selection&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;&quot;What examples of group-selection are there?&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To add more structure, perhaps answers would consider the following details: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Organism/Species in question&lt;/li&gt;&#xA;&lt;li&gt;Unit that experiences cost in fitness&lt;/li&gt;&#xA;&lt;li&gt;Group that experiences benefit in fitness&lt;/li&gt;&#xA;&lt;li&gt;Group-selected trait&lt;/li&gt;&#xA;&lt;li&gt;Explanation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Forward Example&lt;/strong&gt; &lt;em&gt;(trait whose presence benefits the group)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;&lt;em&gt;Organism:&lt;/em&gt;&lt;/strong&gt; Homo sapiens, Humans&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;&lt;em&gt;Unit:&lt;/em&gt;&lt;/strong&gt; Cells and their genes&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;&lt;em&gt;Group:&lt;/em&gt;&lt;/strong&gt; Collection of all cells in one individual Human body&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;&lt;em&gt;Group-selected trait:&lt;/em&gt;&lt;/strong&gt; anti-cancer traits, e.g. apoptosis (programmed cell death) via p53 (&quot;guardian angel&quot; gene that &quot;kills&quot; cancerous cells)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;&lt;em&gt;Explanation:&lt;/em&gt;&lt;/strong&gt; Apoptosis is costly to the perspective of a cell, since it kills the cell and its genes. This enables the individual as a whole to live for long enough to mate and yeild offspring. Fitness of cells relative to other cells in the body is reduced, but fitness of the genome as a whole of that individual is increased relative to other individuals of that population -as a result of cancer-directed apoptosis.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reverse Example&lt;/strong&gt; &lt;em&gt;(trait whose absence benefits the group)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;&lt;em&gt;Organism:&lt;/em&gt;&lt;/strong&gt; Cervus elaphus, Red Deer&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;&lt;em&gt;Unit:&lt;/em&gt;&lt;/strong&gt; Individual red deer and their genomes&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;&lt;em&gt;Group:&lt;/em&gt;&lt;/strong&gt; Isolated population of red deer and the population gene pool&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;&lt;em&gt;Group-selected trait:&lt;/em&gt;&lt;/strong&gt; Lethal potential of antlers (e.g. sharp single antler instead of two blunt antlers).&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;&lt;em&gt;Explanation:&lt;/em&gt;&lt;/strong&gt; Consider a one-antlered stag, whose single antler is imbued with a jagged edge and is the product of a point mutation in his genome. During a &lt;a href=&quot;http://en.wikipedia.org/wiki/Rut_%28mammalian_reproduction%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;rut&lt;/a&gt; he is able to win against other males as his antler inflicts potentially fatal injuries. This allows him to mate many females and have many offspring - however this leaves the population at risk of becoming extinct since the mating season would either have too few males to form a rut, or due to deleterious inbreeding defects in the next generation.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Links&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Wiki: &lt;a href=&quot;http://en.wikipedia.org/wiki/Group_selection&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Group_selection&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;History: &lt;a href=&quot;http://ib.berkeley.edu/courses/ib160/past_papers/beroukhim.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://ib.berkeley.edu/courses/ib160/past_papers/beroukhim.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Published Review: &lt;a href=&quot;http://arxiv.org/abs/1204.6491&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://arxiv.org/abs/1204.6491&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Of course do not feel restrained in your answers by the above suggestions - the point is to discuss the topic and learn!&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2017-03-16T19:26:47.557" LastActivityDate="2017-03-16T19:26:47.557" Title="Empirical evidence for Group Selection?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;&lt;adaptation&gt;&lt;altruism&gt;" AnswerCount="2" CommentCount="12" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13694" PostTypeId="2" ParentId="13691" CreationDate="2013-11-28T00:08:05.400" Score="12" Body="&lt;p&gt;Infrared wavelengths are EM waves of longer wavelengths than visible light. Also, visible waves are more energetic than IR waves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of this, Visible light has the ability to excite organic receptor molecules in our eyes called Rods and Cones. These molecules stimulate cell responses and in turn excite cell responses in our nerves called an Action Response. Still unclear to most scientists is how the brain composes these action responses into an image, though a great deal of research is being done to date.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason why &quot;nothing happens&quot; when we aim infrared lights into our eyes (which I still wouldn't suggest) is that the photoreceptor molecules that we use to see don't have the necessary bonding configuration to accept the energy from these impinging EM waves.&#xA;&lt;br&gt; However, don't go thinking that nothing happens. Infrared radiation is a type of radiation that is usually a measurable heat source. IR is one of the broader parts of the EM spectrum. My point is to say, that when you &quot;radiate&quot; some thing with an IR source:&#xA;&lt;br&gt;1) You don't know if it is also radiating other EM waves unless you know the specs. &#xA;&lt;br&gt;2) You're still exciting molecules with that energy even if it isn't causing a seen effect. I highly doubt anything will happen unless you have a very high powered IR source. You shouldn't really ever focus high power lasers of any source onto your body, because higher intensities could inflict damage.&#xA;&lt;br&gt;&lt;br&gt;&#xA;To Learn more about IR radiation:&#xA;&lt;br&gt;&lt;a href=&quot;http://coolcosmos.ipac.caltech.edu/cosmic_classroom/ask_astronomer/faq/radiation.shtml&quot; rel=&quot;noreferrer&quot;&gt;http://coolcosmos.ipac.caltech.edu/cosmic_classroom/ask_astronomer/faq/radiation.shtml&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;IR (InfraRed) &lt;br/&gt;&#xA;EM (ElectroMagnetic)&lt;/p&gt;&#xA;" OwnerUserId="4794" LastEditorUserId="-1" LastEditDate="2017-01-04T04:06:15.833" LastActivityDate="2017-01-04T04:06:15.833" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="13695" PostTypeId="1" AcceptedAnswerId="13697" CreationDate="2013-11-28T03:07:09.930" Score="3" ViewCount="382" Body="&lt;p&gt;I am not a biologist but I just wonder if all species are interdependent. I mean if the tiger becomes extinct does it affect the ecosystem? If the mosquito or mouse become extinct does it affect the environment and us?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am asking because this question was raised by one of my friends when I was in favor of protecting tigers, lions but I had no answer to &quot;&lt;strong&gt;tiger extinction will not affect humans&lt;/strong&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, is it true that the extinction of any species will affect all other species?&lt;/p&gt;&#xA;" OwnerUserId="5008" LastEditorUserId="3952" LastEditDate="2013-12-02T03:32:15.443" LastActivityDate="2013-12-03T01:15:53.963" Title="Interdependency between organsims on our planet and its relation to ecosystem?" Tags="&lt;ecology&gt;&lt;extinction&gt;&lt;environment&gt;&lt;ecosystem&gt;&lt;conservation-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13696" PostTypeId="2" ParentId="10632" CreationDate="2013-11-28T03:46:53.977" Score="4" Body="&lt;p&gt;It is my understanding that a non-allelic gene is one that affects another's traits, but is not as a typical dominant / recessive manner. If I am correct, this is the same thing as  &lt;strong&gt;&lt;em&gt;epistasis&lt;/em&gt;&lt;/strong&gt; - meaning that one gene modifies how another is expressed.&#xA;There exists epistatic genes for horse coat color. One gene is the coat color itself (horses may have either brown or red color alleles at this loci), the second gene is for a protein that allows the coat color gene to be expressed. &#xA;For example, a horse has two brown alleles at the coat color locus. It also has a wild type gene in the second (modifier) position. This modifier allows the color brown to be expressed and the horse is brown.&#xA;B/B, wt/wt --&gt; Brown&#xA;If the horse has the two brown alleles, but has a mutant allele at the modifier position, then coat color is not expressed and the horse is white.&#xA;B/B, mt/mt --&gt; white&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the modifier alleles are separate genes from the coat color alleles, the two are non-allelic - yet they both affect the same trait in some way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="4139" LastActivityDate="2013-11-28T03:46:53.977" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13697" PostTypeId="2" ParentId="13695" CreationDate="2013-11-28T08:29:09.610" Score="4" Body="&lt;p&gt;The problem is not really that we don't understand some stuff (lthough this is certainly true) but that an ecosystem, or the biosphere is a highly complex network of interactions. This network is continuously displaying some &lt;a href=&quot;http://en.wikipedia.org/wiki/Chaos_theory&quot; rel=&quot;nofollow&quot;&gt;chaotic&lt;/a&gt; (determinist but not foreseeable) behavior. In such a system it becomes very hard or practically impossible to predict what the impact of a change (even a minor one) might be. To illustrate, one could say that killing half of the world's lions might cause the population of rabbits in Norway (!) to increase but killing two thirds might cause the same population of rabbits to decrease. Note: Stuart Kauffman wrote some articles where he argues that life is a system which is always balancing between chaotic dynamic and non-chaotic dynamic. Today, many conservation biologists use the tools of &lt;a href=&quot;http://en.wikipedia.org/wiki/Graph_theory&quot; rel=&quot;nofollow&quot;&gt;graph theory&lt;/a&gt; (network analysis) in order to get a better understanding of how things are influenced by a minor change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But defending an endangered species like the pandas or elephants is certainly much more a matter of ethics than of human security faced with environmental shifts. I would guess (a reference on how the world's money is spent on conservation action would be interesting) that an important part of the money  spent on programs for the defense of endangered species are for ethical reasons, just because these species are big, clever, sing well or display nice colors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many false reasons in ecology (in the political sense of the word) where people act for their ethics rather than to defend humans from environmental change. (I don't mean that ethics is stupid, or that only defending the environment for the benefit of the human species should be considered). You may already have heard &quot;the amazonian forest is the lung of our planet&quot; suggesting that this forest produces lots of $O_2$. This is completely wrong! Cutting down this forest would not change much in terms of either $O_2$ or $CO_2$ levels (except if the wood is burned!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to summarize I would say:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;We spend quite a lot of money defending species for ethical reasons rather than to protect humans from environmental shifts.&lt;/li&gt;&#xA;&lt;li&gt;Changing a little thing might affect the world-wide biosphere in a way that is practically impossible to predict.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="1306" LastEditDate="2013-11-28T16:49:02.980" LastActivityDate="2013-11-28T16:49:02.980" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13699" PostTypeId="1" CreationDate="2013-11-28T13:40:46.070" Score="3" ViewCount="885" Body="&lt;p&gt;What kinds of detergent-free bacterial lysis buffers exist? The proteins we're extracting will be later analyzed by LC-MS/MS, and we're looking for a lysis buffer that won't interfere with this downstream analysis.&lt;/p&gt;&#xA;" OwnerUserId="5031" LastEditorUserId="1590" LastEditDate="2016-03-23T09:22:40.820" LastActivityDate="2016-05-20T10:15:01.080" Title="Bacterial cell lysis buffer used in proteomics procedures" Tags="&lt;proteins&gt;&lt;lab-techniques&gt;&lt;protocol&gt;&lt;proteomics&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13700" PostTypeId="1" AcceptedAnswerId="13736" CreationDate="2013-11-28T18:13:34.150" Score="1" ViewCount="577" Body="&lt;p&gt;I'd like to be able to measure the activity of $\beta$-galactosidase in living cells with simple optical (maybe fluorescence) microscopy. Ideally I'd like to do a minimum of genetic engineering, and use this assay with strains I already have (that have a WT lactose system), i.e. a fluorescent lactose-mimic would be ideal. Additionally, it would be nice if the lifetime of the fluorescent byproduct of $\beta$-gal activity was short, so I could detect a decrease in $\beta$-gal activity as well as an increase. Does such a fluorescent analog exist? I'm hoping to look at the switch from lactose to glucose utilization under the microscope, so I want lactose-using cells to light up and glucose-using cells to be dark, or vice versa. It does not have to be fully quantitative--a qualitative sense is fine. &lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2013-11-30T18:53:35.127" Title="Assay for Beta-galactosidase activity in single cell microscopy" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;metabolism&gt;&lt;microscopy&gt;&lt;fluorescent-microscopy&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13701" PostTypeId="2" ParentId="5649" CreationDate="2013-11-28T19:36:39.627" Score="0" Body="&lt;p&gt;There are neurons all over the body, not just in the brain.  The area with the most neurons, beside the brain, is the heart.  It's been theorized that some memory could reside in these cells.  I'm a big believer that if you keep an open mind people will throw garbage in it, but this particular phenomena seems worthy of further study. &lt;/p&gt;&#xA;" OwnerUserId="5033" LastEditorUserId="3776" LastEditDate="2013-11-29T01:12:01.263" LastActivityDate="2013-11-29T01:12:01.263" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13702" PostTypeId="2" ParentId="13700" CreationDate="2013-11-28T22:41:04.470" Score="1" Body="&lt;p&gt;I found &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19689207&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Zhang GJ &lt;em&gt;et al&lt;/em&gt;. (2009) &lt;em&gt;In vivo&lt;/em&gt; optical imaging of LacZ expression using lacZ transgenic mice. Assay Drug Dev Technol.7:391-9. doi: 10.1089/adt.2009.0195.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Abstract&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;beta-Galactosidase (beta-gal) (encoded by the lacZ gene) has been widely used as a transgene reporter enzyme. The ability to image lacZ expression in living transgenic animals would further extend the use of this reporter. It has been reported that 7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one)-beta-d-galactopyranoside (DDAOG), a conjugate of beta-galactose and 7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one), is not only a chromogenic lacZ substrate but that the cleavage product has far-red fluorescence properties detectable by in vivo imaging. In an attempt to noninvasively image lacZ expression in vivo, we applied fluorescence imaging to a G protein-coupled receptor (GPR56), knockout (KO) mouse model, in which the lacZ gene is introduced in the GPR56 locus. Compared to wild-type (WT) mice, GPR56KO/LacZ mice showed three- to fourfold higher fluorescence intensity in the head area 5 min after tail-vein injection of DDAOG. beta-Gal staining in sections of whole brain showed strong lacZ expression in homozygotes, but not in WT mice, consistent with lacZ activity detected by in vivo imaging. The kidneys were also visualized with fluorescence imaging both in vivo and ex vivo, consistent with beta-gal staining findings. Our results demonstrate that fluorescence imaging can be used for in vivo real-time detection of lacZ activity by fluorescence imaging in lacZ transgenic mice. Thus, this technology can potentially be used to noninvasively image changes of certain endogenous molecules and/or molecular pathways in transgenic animals.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2917367/&quot; rel=&quot;nofollow noreferrer&quot;&gt;The work in the paper is cited in a more recent paper&lt;/a&gt; which reports beta-gal-based chemiluminescent imaging in mice.&lt;/p&gt;&#xA;&lt;p&gt;It's unclear if any of this would be successful at a single bacterial cell level.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-11-29T07:45:07.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13703" PostTypeId="1" AcceptedAnswerId="13724" CreationDate="2013-11-28T23:03:00.347" Score="7" ViewCount="1247" Body="&lt;p&gt;I am looking for references to papers containing the time intervals spent in different phases of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_cycle&quot; rel=&quot;nofollow&quot;&gt;cell cycle&lt;/a&gt; (ej., G0, G1, S, G2, M for eukaryotes) for different cells. In particular, I am interested in E. coli and CHO (Chinese Hamster Ovary cells), but any reference to studies of this kind for any typical cell will be useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll accept an answer containing a representative sample of references to the literature on this subject. Preferably recent papers (since 2010).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you can provide the times spent in each phase but don't have references at hand, that will also be useful.&lt;/p&gt;&#xA;" OwnerUserId="561" LastEditorUserId="561" LastEditDate="2013-11-29T16:21:53.720" LastActivityDate="2019-04-17T12:08:54.647" Title="Time spent in phases of cell cycle" Tags="&lt;cell-biology&gt;&lt;mitosis&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13704" PostTypeId="2" ParentId="13687" CreationDate="2013-11-29T05:17:18.833" Score="1" Body="&lt;p&gt;Check out this recent &lt;a href=&quot;http://www.sciencemag.org/content/early/2013/11/20/science.1242544&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; in Science (AOP). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They say that two genes- &lt;em&gt;Sry&lt;/em&gt; and &lt;em&gt;Eif2s3y&lt;/em&gt; are sufficient to provide the entire functionality of the Y chromosome. Alhough, there is reduced number of spermatids in these mice (Genotype :&lt;em&gt;XO-Sry-Eif2s3y&lt;/em&gt;), the viable ones are able to give rise to healthy offsprings. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-11-29T05:17:18.833" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13705" PostTypeId="2" ParentId="13657" CreationDate="2013-11-29T08:56:27.123" Score="1" Body="&lt;p&gt;I did try another transformation:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;again with our electrocompetent cells&lt;/li&gt;&#xA;&lt;li&gt;Cells form other lab&lt;/li&gt;&#xA;&lt;li&gt;chemically competent cells I made&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The good thing is that on chemically competent cells there is no weir colonies, however efficiency of transformation was very low, but still, I think it is ok - will confirm it in next day if I really got the right insert.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand my electroporation still did not clear out. I got colonies on both our cells and cells from other lab, however in much lower amount there. I will try to change the cuvettes and try to use different electroporator as this seems to be the only thing that could make problems - although I am still not convinced about that :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your help and I will report the progress so if somebody else will have that problem again he could maybe benefit from my findings.&lt;/p&gt;&#xA;" OwnerUserId="4860" LastActivityDate="2013-11-29T08:56:27.123" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13706" PostTypeId="1" CreationDate="2013-11-29T09:56:42.000" Score="1" ViewCount="77" Body="&lt;p&gt;I am reading an article about single-cell sequencing:&#xA;&lt;a href=&quot;http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2720.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2720.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And came across the concept of &quot;hyperbranched amplicons&quot;. I googled for it but don't get much luck. The best I could find is it mentioned in another single-cell sequencing method here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Multiple_displacement_amplification&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Multiple_displacement_amplification&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone give me a definition for it?&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2013-11-29T09:56:42.000" Title="what are hyperbranched amplicons in DNA sequencing?" Tags="&lt;dna&gt;&lt;dna-sequencing&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13707" PostTypeId="1" AcceptedAnswerId="13709" CreationDate="2013-11-29T09:59:17.870" Score="2" ViewCount="2147" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mesosome&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; wikipedia page says that mesosomes are artifacts produced by chemical fixing techniques. Most of my textbooks still show a mesosome and describes it as having functions like - respiration, helping in DNA replication, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has the idea that it is an artifact been widely accepted by the scientific community ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-11-29T11:08:50.677" Title="Mesosome - does it exist?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13708" PostTypeId="1" AcceptedAnswerId="13718" CreationDate="2013-11-29T10:32:31.283" Score="4" ViewCount="339" Body="&lt;p&gt;I have already posted this on chat but haven't got any response. A recent &lt;a href=&quot;https://biology.stackexchange.com/questions/13693/empirical-evidence-of-group-selection&quot;&gt;question&lt;/a&gt; on group selection stimulated me to ask this here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;QUESTIONS: Why should bacteria conjugate? If we consider that a bacterium is another bacterium's rival (in terms of obtaining resources) why should a bacterium &quot;share&quot; it's antibiotic resistance gene, for example, with another bacterium? I can think of 2 reasons. One is group selection, and the other is &quot;Gene Selection&quot;. Group selection has been highly criticized in recent years, and individual selection has dominated thinking, but here my support goes for gene selection rather than individual selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gene selection seems to me the easier explanation over individual selection. Even if we consider the fact that a colony is made from divisions of single cells and the cells are extremely similar and also that conjugation is more probable between cells of a colony, we should also consider that conjugation can happen between very different bacterial species.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-12-28T01:33:21.953" Title="Does conjugation support gene selection?" Tags="&lt;evolution&gt;&lt;bacteriology&gt;&lt;genetics&gt;&lt;horizontal-gene-transfer&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="13709" PostTypeId="2" ParentId="13707" CreationDate="2013-11-29T11:08:50.677" Score="3" Body="&lt;p&gt;I've always wondered about mesosomes. They were controversial 35 years ago when I was working in a related field. I decided to check the current status of the term.&lt;/p&gt;&#xA;&lt;p&gt;I checked for research activity in this area using a Web of Science search &amp;quot;mesosome&amp;quot; in Title: this gave just 54 hits. I list the most recent here (unless otherwise indicated, these are single hits per year).&lt;/p&gt;&#xA;&lt;p&gt;2010; 2008; 2004 (human cell mesosome??); 1994; 1988 (geology); 1983; 1982 (2); 1980&lt;/p&gt;&#xA;&lt;p&gt;So it doesn't seem to be a very active area of research. The 2008 and 2010 papers are from the same group. The earlier paper is:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Li, X et al. (2008) Mesosome formation is accompanied by hydrogen peroxide accumulation in bacteria during the rifampicin effect. MOLECULAR AND CELLULAR BIOCHEMISTRY 311: 241-247   DOI: 10.1007/s11010-007-9690-4&lt;/p&gt;&#xA;&lt;p&gt;Abstract: Ultrastructural alteration and hydrogen peroxide localization were examined in Xanthomonas campestris pv. phaseoli during rifampicin effect using transmission electron microscopy. Bacterial cells were treated with rifampicin and then were examined by electron microscopy to observe the changes of ultrastructure or hydrogen peroxide accumulation in living cells that took place before lysis. Intriguingly, rifampicin treatment led to presence of an additional location of hydrogen peroxide accumulation within the cells. There was an association between the frequency and size of the additional location of hydrogen peroxide accumulation and the concentration of rifampicin. Furthermore, an additional ultrastructure, mesosomes, was also present in cells during rifampicin effect. The frequency and size of mesosome increased with the increasing concentration of rifampicin. Result of multiple linear regression showed that the size of mesosome plays as a key factor in the quantity of excess hydrogen peroxide accumulation in cells during rifampicin effect. Linear correlation was confirmed between quantity of excess hydrogen peroxide accumulation and the size of mesosome in cells during rifampicin effect. This finding intensely indicated that mesosomes are just the additional location of hydrogen peroxide accumulation in cells under cellular injury caused by rifampicin treatment. The mesosome formation is always accompanied by excess hydrogen peroxide accumulation in X. campestris pv. phaseoli during rifampicin effect.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This paper has been cited 7 times. One of those citations is from:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Saier, MH. &amp;amp; Bogdanov, V. (2013)  Membranous Organelles in Bacteria. JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY 23: 5-12   DOI: 10.1159/000346496   &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.karger.com/Article/FullText/346496&quot; rel=&quot;nofollow noreferrer&quot;&gt;Free full text here&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;The language used in this review seems to support the existence of mesosomes as some sort of intermediate in the formation of intracellular membranes in prokaryotes. This review is a polemic in favour of the idea that prokaryotes do indeed contain intracellular membrane-bounded compartments. It has no abstract, but the first paragraph gives a flavour of its stance:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The traditional view of life on Earth divides the living world into two major groups, prokaryotes and eukaryotes. These two groups were originally suggested to differ in very basic respects. While eukaryotes had complex cell structures including a cytoskeleton and intracellular membrane-bounded organelles, prokaryotes were believed to lack them. In fact, numerous textbooks and current sources still note this distinction and hold it to be true. For example, in Campbell’s Biology [Campbell, 1993, p. 515] it is stated without equivocation: ‘Prokaryotic cells lack membrane-enclosed organelles.’ In ‘Functional Anatomy of Prokaryotic and Eukaryotic Cells’ [Tortora et al., 2009, chapt. 4] it is similarly claimed that ‘Prokaryotes lack membrane-enclosed organelles, specialized structures that carry on various activities’. In the current Wikipedia, under ‘Prokaryote’ the following statement can be found: ‘The prokaryotes are a group of organisms whose cells lack a cell nucleus (karyon) or any other membrane-bounded organelles’. In the same online compendium under ‘Organelle’, one can read: ‘whilst prokaryotes do not possess organelles per se, some do contain protein-based microcompartments’. Proteinceous microcompartments will be the subject of a forthcoming Journal of Molecular Microbiology and Biotechnology written symposium, but this one will show that these generalizations, suggesting a lack of subcellular compartmentalization in prokaryotes, are blatantly in error [Murat et al., 2010a].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-11-29T11:08:50.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13710" PostTypeId="2" ParentId="9487" CreationDate="2013-11-29T14:44:00.373" Score="4" Body="&lt;p&gt;This is a perfectly reasonable question based on a self-adminstered (human) trial. Morever, the proposer bases their observations not on one subject but several reports. The impromptu survey of friends etc. is also acceptable. By the way, self-reported intakes/output records are an accepted method in nutrition research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My 2-year-old child exhibited the symptoms described above, after consuming two Oreo biscuits in the afternoon. That evenings soiled nappy (diaper) revealed a dark but otherwise well-textured stool. When my concerned partner brought this to my attention, it immediately reminded me of the use of carmine red and related food dyes for the measurement of gastrointestinal transit times. The principle here is that the dyes are not absorbed in the gut, so the time from consumption to excretion gives a measure of bowel function. Short transit time means no constipation and is considered a sign of great bowel function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on the observations reported for Oreos, my educated guess would be that Oreo products contain miniscule amounts of non-absorbed colorants - something that is generally regarded as safe. Self-reported symptoms are generally considered valid by health professionals. I am still intrigued by the Oreo colouring puzzle, as this colourant must be natural.  &lt;/p&gt;&#xA;" OwnerUserId="5037" LastEditorUserId="-1" LastEditDate="2014-03-25T18:42:47.730" LastActivityDate="2014-03-25T18:42:47.730" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13711" PostTypeId="1" AcceptedAnswerId="16597" CreationDate="2013-11-29T15:08:08.437" Score="5" ViewCount="1809" Body="&lt;p&gt;Hypoglycemia (Low blood sugar) is said to be among the potential causes of human-faintings. I was wondering by which mechanism this happens. Google search results are abundant; there are lists of various causes and solutions, but I couldn't find a direct answer to my question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it a controlled reduction of heart function to save energy? Is it an uncontrolled shock reaction (malfunction)? I'm looking for an answer along those lines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="5038" LastEditorUserId="5038" LastEditDate="2014-07-22T01:14:23.357" LastActivityDate="2014-07-22T01:14:23.357" Title="By what mechanism can hypoglycemia induce fainting?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13712" PostTypeId="1" CreationDate="2013-11-29T16:08:05.007" Score="5" ViewCount="2342" Body="&lt;p&gt;This insect is about 0.5 mm in length, so it is very small. It doesn't have legs I don't believe, I am not too good at this but I don't know if it's a worm or more like a cocoon for something.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do find this alarming because I found this one underneath my bed sheet on the mattress. Now I do recall seeing something similar on the crack of the shaky tile floor, so I can't tell if it's just an apartment pest or it actually lives in mattresses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Location: Toronto, Canada&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pp79M.jpg&quot; alt=&quot;One side&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vYXD1.jpg&quot; alt=&quot;Back side&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5039" LastEditorUserId="16866" LastEditDate="2019-12-01T03:17:50.610" LastActivityDate="2019-12-01T03:17:50.610" Title="Can anyone identify this caterpillar / cocoon?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="13713" PostTypeId="1" CreationDate="2013-11-29T17:11:21.530" Score="2" ViewCount="44" Body="&lt;p&gt;I've been looking at some journals lately that look at carbon emission from lakes where some lakes act as sources and other act as sinks. The paper that I have been looking at is &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www3.nd.edu/~underc/east/publications/documents/Cole_94Science.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www3.nd.edu/~underc/east/publications/documents/Cole_94Science.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where they show that lakes are sources of CO&lt;sub&gt;2&lt;/sub&gt; to the atmosphere. What are the equations that are used to determine the saturation of CO&lt;sub&gt;2&lt;/sub&gt; in surface waters? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The recent IPCC report also mentions that lakes act as sources of CO&lt;sub&gt;2&lt;/sub&gt; but does not give any indication of the equations used to come up with these values. Presumably, to determine the concentration of carbon in the surface water you need to use other measured variables such as temperature. Can anyone suggest a method for estimating this concentration ?&lt;/p&gt;&#xA;" OwnerUserId="3178" LastEditorUserId="1590" LastEditDate="2013-12-01T08:30:36.560" LastActivityDate="2013-12-02T18:19:20.450" Title="Calculation of saturation of carbon in surface waters" Tags="&lt;climate-change&gt;&lt;limnology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13714" PostTypeId="1" CreationDate="2013-11-29T17:42:35.183" Score="3" ViewCount="96" Body="&lt;p&gt;I've written a computer program which beeps, then beeps after 10 sec, then beeps after 11 sec, then beeps after 12 sec, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried the following &quot;experiment&quot; on myself: do only one breath between the beeps, so slowing breath until I can't do it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After finishing this &quot;training&quot; and starting to breath normally again, I felt enormous &quot;freshness&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this experiment safe for health? How does it influence health?&lt;/p&gt;&#xA;" OwnerUserId="4186" LastActivityDate="2014-02-06T19:39:20.340" Title="Gradual slowing breath, its effect on health" Tags="&lt;human-biology&gt;&lt;breathing&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13715" PostTypeId="1" AcceptedAnswerId="14464" CreationDate="2013-11-29T18:07:05.093" Score="8" ViewCount="190" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;When swine flu hit the population it spiked in certain areas and&#xA;  tapered off in neighboring regions, it hits hardest where people have least protection and this pattern is more pronounced (&lt;a href=&quot;http://www.youtube.com/watch?v=CmM5mqMzl08&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;)&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Apparently incidences of &lt;strong&gt;murder&lt;/strong&gt; spreads in a similar pattern to infectious diseases such as swine flu according to a 26-year study of the city of Newark, New Jersey (&lt;a href=&quot;http://www.nj.com/news/index.ssf/2012/12/newark_homicide_trend_is_treat.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;summary&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be interesting to hear your opinions, but some interesting questions I would like to ask are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;To what extent could murder and the epidemiology infectious disease&#xA;patterns resemble each other?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What factors could you suggest may lead to their apparent&#xA;similarities?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Given that murder could be modeled as an infectious disease could we&#xA;apply epidemiological interventions to murder?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2017-04-11T21:26:05.143" LastActivityDate="2017-04-11T21:26:05.143" Title="Could murder be modeled as an infectious disease?" Tags="&lt;pathology&gt;&lt;behaviour&gt;&lt;epidemiology&gt;&lt;collective-behaviour&gt;&lt;network&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13716" PostTypeId="1" CreationDate="2013-11-29T18:23:31.540" Score="3" ViewCount="1273" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Is there a maximum threshold of pain a Human can experience, beyond which point there is no noticeable difference?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I ask this question in part to better understand the definition of pain and its different facets, e.g. Is there a quantitative measure of pain? Are there various types of pain, or are they all part of the same fundamental experience?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would also be interesting to know since I could perhaps be allowed to claim: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;well at least I know I cannot feel more pain than X&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thank you for your opinions.&lt;/p&gt;&#xA;" OwnerUserId="5005" LastActivityDate="2013-12-04T13:22:47.107" Title="Is there a maximum pain threshold?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;physiology&gt;&lt;pain&gt;&lt;injury&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13718" PostTypeId="2" ParentId="13708" CreationDate="2013-11-29T19:08:09.367" Score="2" Body="&lt;p&gt;Interesting Question (glad the &lt;a href=&quot;https://biology.stackexchange.com/questions/13693/empirical-evidence-of-group-selection&quot;&gt;&quot;group selection&quot;&lt;/a&gt; post got you thinking!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Me and two friends thought about your question during our Biology BSc at ICL (in fact we also thought about an even more puzzling phenomenon called &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Transformation_%28genetics%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;bacterial transformation&quot;&lt;/a&gt;&lt;/em&gt; which is like conjugation, but they incorporate genes from &lt;em&gt;dead&lt;/em&gt; bacteria!!) our first year course convener recognized our answers as &quot;most likely candidates&quot; so here they are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1. Stress-induced Experimentation Hypothesis&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The likelihood of conjugation/transformation occurring may change for a bacterial population as a whole depending on how stressed it is (or perhaps how unfamiliar the environment is?). Stress signals could cause the population to be more &quot;risky&quot; and take up the DNA from surrounding living/dead bacteria and incorporate it with its own genome: &quot;the hell, we're out of options.. lets transform into something that resembles the indigenous species of this strange ecosystem!&quot;. Indeed Bacteria have memory (see: &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemotaxis&quot; rel=&quot;nofollow noreferrer&quot;&gt;chemotaxis&lt;/a&gt;) this means that perhaps they can be able to tell whether they have been receiving more stress &lt;em&gt;now&lt;/em&gt; as opposed to &lt;em&gt;before&lt;/em&gt;, meaning they can &quot;trial and error&quot; with various genes that have been imported within their plasmids! — &quot;Let's try this gene, oh wait... I'm dying, hmm let's kill off this plasmid and take some more genes!&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In reply to this my course convener said: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;ah yes, a switch from asexual to sexual reproduction occurs in&#xA;  many organisms under stress. The genes that cause the&#xA;  sex/transformation to occur may gain a net benefit from recombination&#xA;  with genes taken from other organisms/the environment.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. Diversity Plagarism Hypothesis&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we look at the entire population of conjugating bacteria as a single competitive unit itself (e.g. like a tissue is a coordinated group of specialized cells) that can compete with other populations of bacteria who cannot conjugate the conjugating population will &quot;win&quot;. This is because a conjugating population will always have much higher phenotypical diversity as it can mix traits between the individuals. This means a conjugating population is much more efficient at undergoing natural selection for beneficial traits or trait combinations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think of natural selection (coupled with mutation) as an &lt;strong&gt;inventor&lt;/strong&gt;... something that helps you invent much &quot;fitter bacteria&quot; is the ability to pull things apart from this bacterium and that bacterium and glue them together, this is essentially what conjugation/transformation does!! it allows you to pull bits from this bacterium and stick it to bits from that bacterium to get a &quot;super-bacterium&quot;. It's like open source technology (free to share) as opposed to patented technology!! Conjugation is immediately a good thing because it means you can &quot;steal&quot; cool technology from living/dead bacteria and incorporate it into your population's gene pool!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this was helpful!&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-12-28T01:33:21.953" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="13719" PostTypeId="2" ParentId="13700" CreationDate="2013-11-29T20:37:48.590" Score="0" Body="&lt;p&gt;I posted this as an answer because it was too long for a comment. In general, your experimental approach is feasible, however, the devil is in the details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, your biggest challenge will be to gain access to suitable optics. Imaging individual eukaryotic cells is relatively easy with any diffraction-limited optical microscope, because their scale is usually 10-20 $\mu$m. Bacteria are a much smaller cell size, and they (mostly) cannot be imaged using diffraction-limited techniques on a single cell level. To image a single cell requires super-resolution optics/techniques.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, it sounds like you're doing diauxic shift curves. It may not be necessary to image at a single cell level, and you may be able to get away with making good measurements of cells in aggregate using any camera-equipped microscope, or even an optical plate reader since you mentioned $\beta$-gal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;@Alan Boyd pointed out a chemiluminescent substrate for $\beta$-gal which could work well if you have access to an optical imager that can give you readouts of photon counts/second. This would give you readings of average enzymatic activity (which you can correlate to expression level).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, you describe having cells be bright/dark depending on the utilized substrate and that would be harder to achieve. There are many ways I envision to do this, but they all take some amount of genetic manipulation. Perhaps the easiest thing to do might be to make an expression plasmid that places LacZ under control of an IPTG-inducible promoter. These plasmids are very common and would give you an easy entry to image lactose usage.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-11-29T20:37:48.590" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13720" PostTypeId="1" AcceptedAnswerId="13880" CreationDate="2013-11-30T02:51:58.687" Score="1" ViewCount="813" Body="&lt;p&gt;I have a deviated  nasal septum and I always suffer from  common cold I was just wondering how a deviated nasal septum can be the cause for chronic common cold&lt;/p&gt;&#xA;" OwnerUserId="5008" LastActivityDate="2013-12-08T19:02:47.230" Title="How is deviated nasal septum related to cold" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13724" PostTypeId="2" ParentId="13703" CreationDate="2013-11-30T10:53:43.667" Score="9" Body="&lt;p&gt;This is the data for a few cell types:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&#xA;Cell type   Total      G1      S      G2      M      Ref&#xA;----------------------------------------------------------&#xA;Neuro2a        9       2       5      1.5    0.5     [1]&#xA;Hela         16.2     7.7     7.2     0.8    0.5     [2]&#xA;A549          18       7      7.5     2.5     1      [3]&#xA;MCF7         21.3      9      9.3      2      1      [4]&#xA;CHO           15       6      6.8     1.2    0.65    [5]&#xA;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The timescale is in hours. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://doi.org/10.1073/pnas.77.3.1526&quot; rel=&quot;nofollow noreferrer&quot;&gt;De Laat et al. 1980&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/2693468&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kumei et al. 1989&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/2752214&quot; rel=&quot;nofollow noreferrer&quot;&gt;Orfanoudakis et al. 1989&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/6871842&quot; rel=&quot;nofollow noreferrer&quot;&gt;Taylor et al. 1983&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC369707/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Harada and Morris 1981&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2019-04-17T12:08:54.647" LastActivityDate="2019-04-17T12:08:54.647" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="13726" PostTypeId="1" AcceptedAnswerId="13789" CreationDate="2013-11-30T14:44:11.370" Score="1" ViewCount="870" Body="&lt;p&gt;What are the differences between HPRD and BIOGRID protein-protein interactions databases?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What are their purposes? Why do we need two different databases?&lt;/li&gt;&#xA;&lt;li&gt;How is data collected into each one?&lt;/li&gt;&#xA;&lt;li&gt;How different are they in the interactions they contain?&lt;/li&gt;&#xA;&lt;li&gt;Is one considered more reliable than the other?&lt;/li&gt;&#xA;&lt;li&gt;Which one is more commonly used when benchmarking models?&lt;/li&gt;&#xA;&lt;li&gt;Are there any other commonly used PPI databases?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1190" LastEditorUserId="5005" LastEditDate="2013-12-17T02:22:10.767" LastActivityDate="2013-12-17T02:22:10.767" Title="What are the differences between HPRD and BIOGRID databases?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;software&gt;&lt;database&gt;&lt;protein-interaction&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13729" PostTypeId="1" CreationDate="2013-11-30T15:40:56.813" Score="7" ViewCount="752" Body="&lt;p&gt;I am looking for recommendations to good textbooks introducing modern immunology. Review articles, preferably modern (post 2000) would also be useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please, include a brief comment with each book recommendation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;About book listing questions on SE:&lt;/strong&gt; I understand that SE sites in general have adopted in the last year a policy against book listing questions. Instead, book lists should be moved to tag wikis. However, since BiologySE is still beta and young and the &lt;a href=&quot;https://biology.stackexchange.com/tags/immunology/info&quot;&gt;tag-wiki for immunology&lt;/a&gt; is mostly empty, I believe we would benefit from a question listing good introductory books to modern immunology, at least temporarily. Eventually, when Biology.SE matures, this question should be closed or locked, and the book recommendations herein moved to the tag-wiki for immunology. Moreover, for most other SE sites I have seen, the tag-wikis usually gather information that first appeared in questions like this, even if the question is eventually closed or locked. That's why I think this question will be useful to the community, at least temporarily.&lt;/p&gt;&#xA;" OwnerUserId="561" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2018-05-26T11:26:53.377" Title="Modern immunology textbooks" Tags="&lt;immunology&gt;&lt;literature&gt;&lt;book-recommendation&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13730" PostTypeId="2" ParentId="13729" CreationDate="2013-11-30T16:25:29.120" Score="2" Body="&lt;p&gt;&lt;strong&gt;Cellular and Molecular Immunology&lt;/strong&gt;&lt;br&gt;&#xA; Abul K. Abbas MBBS (Author), Andrew H. H. Lichtman MD PhD (Author), Shiv Pillai MD (Author) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This was my Fall 2011 Basic Immunology text for a hybrid med-school/undergrad class at my University.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I have not read others&lt;/em&gt;, but every time the topic of Immune responses comes up in other Undergrad courses, I have been well or exceedingly informed because of it.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-11-30T16:25:29.120" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13731" PostTypeId="2" ParentId="13729" CreationDate="2013-11-30T16:59:54.153" Score="2" Body="&lt;p&gt;The MCM's book is good one.&#xA;I recommend the book &lt;em&gt;BRS Microbiology and Immunology&lt;/em&gt;, because then you can see the thing in the real context and have good exercises too.&#xA;&lt;em&gt;First Aid for the USMLES Step 1&lt;/em&gt; then explains you how to read for immunology and gives you rather good summary about the topic and some mnemonics.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2013-11-30T16:59:54.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13732" PostTypeId="1" CreationDate="2013-11-30T17:07:59.230" Score="0" ViewCount="26" Body="&lt;p&gt;We have identified vaccine candidates via an ex-vivo RNA-seq approach. Next step would be to perform conservation of these candidates (about 20) between multiple bacterial strains (about 200). I would like to know your suggestions to perform this step.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From my bioinformatic experience, it could be possible to start with a first rough screening using blastp or blastx against a multiple strain database, and more accurate approaches would be then performed to validate this results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please let me know your suggestions and possible references you might consider helpful to answer this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your help. Best regards, Bernardo&lt;/p&gt;&#xA;" OwnerUserId="4717" LastActivityDate="2013-12-01T18:54:03.057" Title="How to get conservation of vaccine candidates between hundreds of bacterial strains?" Tags="&lt;bioinformatics&gt;&lt;microbiology&gt;&lt;bacteriology&gt;&lt;phylogenetics&gt;&lt;blast&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13734" PostTypeId="2" ParentId="13684" CreationDate="2013-11-30T17:46:07.660" Score="0" Body="&lt;p&gt;You should find a mechanism to make this possible - mechanism that controls the ignition of the expression of MHC-I and MHC-II at the same time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, parallelism is required by the cell.&#xA;Some think such parallelism exists in one process in childbirth, for instance.&#xA;I personally think that such processes are in series, than exact parallelism, because such machinery would require large amount of memory, which our cells do not have, and fine tuning machinery, which is would require too much energy to keep to maintain the control system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In reality, the processes seem to be happening at the same time, because there is so many of them.&#xA;However, I think this is a paralysis, since different processes are occurring.&#xA;But to show that two processes happen in exactly the same time would require the fine tuning machinery which should be found first, and also the energy aspect would require too much energy to control it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Third argument against such parallelism is in probability theory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I take an example about the logic behind how to falsify your statement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Statement:&lt;/strong&gt; If something is a B-cell, then it can express MHC-I and MHC-II at exactly the same time.&#xA;&lt;strong&gt;Contraposition of this:&lt;/strong&gt; This something cannot express MHC-I or MHC-II at exactly the same time, then it is not a B-cell. This is wrong because this something is still B-cell, although it cannot express MHC-I or MHC-II in all situations.&lt;br&gt;&#xA;Another perspective, the probability that these two events happen at the same time in time space with one independent system is zero.&#xA;The probability that these two events happen at the same time in time space with two independent systems is zero still. You need to have three systems to make this possible: fine tuning machine and the machines that expresses this. However, I have not seen such machinery to exist.&#xA;Generally, one point in probability space is always zero.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2013-11-30T17:46:07.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13735" PostTypeId="1" CreationDate="2013-11-30T18:01:25.047" Score="1" ViewCount="796" Body="&lt;p&gt;I would like to BLASTP a list of protein sequences in fasta format against multiple protein databases. Since I'm only interested in the first hit of each database, it is possible that BLAST result would need to be parsed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you know if this strategy is a good one, or you suggest me others?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your help. Best regards, Bernardo&lt;/p&gt;&#xA;" OwnerUserId="4717" LastActivityDate="2014-05-01T07:36:53.813" Title="Blast a sequence against multiple databases" Tags="&lt;bioinformatics&gt;&lt;bacteriology&gt;&lt;blast&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13736" PostTypeId="2" ParentId="13700" CreationDate="2013-11-30T18:53:35.127" Score="0" Body="&lt;p&gt;Here is a &lt;a href=&quot;http://www.lifetechnologies.com/us/en/home/references/molecular-probes-the-handbook/enzyme-substrates/detecting-glycosidases.html&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt; to on the Invitrogen/Life Technologies webpage detailing various probes to detect the activity of glycosidases, including $\beta$-galactosidase. These include DDAOG as mentioned by @Alan Boyd, as well as Fluorescein Digalactoside, Resorufin Galactoside, and  Methylumbelliferyl Galactoside, among others. NB, this is an Invitrogen/Life Technologies website, so all the reagents they mention are ones sold by the company; there may be others not mentioned here. Of these, DDAOG is very stable, which would allow for measuring the initiation of $\beta$-gal activity, but might not work to measure decreases in $\beta$-gal activity (without bleaching the dye). Resorufin Galactoside is sensitive and stable at physiological pH, allowing measurement over a long period of time. Fluorescein Digalactoside is the most sensitive assay, but since it requires the removal of 2 galactose moieties for full fluorescence it's activation time may be slow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For my particular usage (limited access to near-red frequencies), I think that Resorufin Galactoside or Fluorescein Digalactoside might be the best choices. However, given the cost of these probes, I might be better off just finding some lab with a strain with gfp under the lac promoter in the chromosome and asking them for a sample!&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2013-11-30T18:53:35.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13739" PostTypeId="2" ParentId="13735" CreationDate="2013-12-01T15:41:04.223" Score="0" Body="&lt;p&gt;If it's a species with already sequenced genome and you use a genome mapping approach, you probably get gene id's &quot;automatically&quot; during transcriptome assembly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it's a de novo approach, and all you get is a list of sequences, &lt;a href=&quot;http://www.genome.jp/tools/kaas/&quot; rel=&quot;nofollow&quot;&gt;KAAS&lt;/a&gt; would help you to identify orthologous genes already known in other bacterial genomes (there you'll find even predefined subsets of genomes to blast against, 'for Prokaryotes' being one of them).&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2013-12-01T15:41:04.223" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13740" PostTypeId="1" CreationDate="2013-12-01T18:50:51.690" Score="1" ViewCount="77" Body="&lt;p&gt;What's the reason why researchers usually use cell lines from &quot;blast cells&quot; (so, immature, like lymphoblastoid cells) for measuring gene expression data? Is that they are growing up, which would make their expression data higher and more significant?&lt;/p&gt;&#xA;" OwnerUserId="5054" LastActivityDate="2013-12-02T04:50:56.617" Title="The reason why researchers usually use cell lines from &quot;blast cells&quot;?" Tags="&lt;gene-expression&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13741" PostTypeId="2" ParentId="13732" CreationDate="2013-12-01T18:54:03.057" Score="2" Body="&lt;p&gt;This website will allow you to blast all sequenced microbial genomes:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recovering the full gene sequence might be a bit of a hassle, since BLAST will only allow you to recover the region that matched your query. You may need to set up your own pipeline for this. You may also be able to identify a &quot;protein family&quot; or &quot;cluster of orthologous genes&quot; using the BLAST results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you have the full sequence, you can perform a multiple sequence alignment with CLUSTAL, Muscle, or another program. This will help you to identify the conserved regions.&lt;/p&gt;&#xA;" OwnerUserId="5006" LastActivityDate="2013-12-01T18:54:03.057" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13742" PostTypeId="2" ParentId="2529" CreationDate="2013-12-01T19:56:45.090" Score="2" Body="&lt;p&gt;No. Museums are the traditional repository for fossils, and the process of &quot;digitizing&quot; their collections is slow and labor intensive. Often, the museums only aim to digitize what me might call the &quot;meta-data&quot; associated with the fossil, as was done here:&#xA;&lt;a href=&quot;http://ucmpdb.berkeley.edu/cgi/ucmp_query2?admin=&amp;amp;query_src=ucmp_index&amp;amp;table=ucmp2&amp;amp;spec_id=V8111&amp;amp;one=T&quot; rel=&quot;nofollow&quot;&gt;http://ucmpdb.berkeley.edu/cgi/ucmp_query2?admin=&amp;amp;query_src=ucmp_index&amp;amp;table=ucmp2&amp;amp;spec_id=V8111&amp;amp;one=T&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A truly comprehensive database is not feasible in the near future. A single photograph likely would not be sufficient to characterize the fossil -- the interesting components of fossils are often microscopic. For example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/99/14/9117.full.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/99/14/9117.full.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even taking a single photograph can be very labor intensive, and fossils can be fragile. Proper photo-documentation would probably require multiple images. More generally, a comprehensive database would probably need to include non-photographic data relating to the fossil -- such as chemical composition of non-visual imaging techniques (X-ray, IR, UV, etc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the foreseeable future, &quot;comprehensive&quot; collections will be housed in museums without full digital representation. The only way to know how comprehensive these collections are is to ask the museum curator, who will be aware of the scope and limitations of the collection.&lt;/p&gt;&#xA;" OwnerUserId="5006" LastActivityDate="2013-12-01T19:56:45.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13743" PostTypeId="1" AcceptedAnswerId="13748" CreationDate="2013-12-01T19:58:36.303" Score="4" ViewCount="574" Body="&lt;p&gt;Why do we need deep sequencing? Why cannot the sequencing technologies read all the nucleotides correctly at the first read? Sorry since this question is too trivial, I don't have a biological background at all, and I have just started doing research in CompBio. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="5054" LastEditorUserId="5005" LastEditDate="2013-12-05T12:39:05.950" LastActivityDate="2014-02-20T17:03:11.117" Title="Why do we need deep sequencing?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;genomes&gt;&lt;polymerase&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13745" PostTypeId="1" AcceptedAnswerId="13747" CreationDate="2013-12-01T21:06:23.697" Score="6" ViewCount="775" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering just the &quot;Kingdom Animalia&quot; branch of organisms. It is clear that bigger does not necessarily mean better - there is large variation in body size...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the 94 µm long Tantulocarid arthropod (&lt;em&gt;Stygotantulus stocki&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Aa2Iu.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To the 25.5 m long Blue Whale (&lt;em&gt;Balaenoptera musculus&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4MeT4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;What trade-offs exist between having a particular body size (very large, very small) to other traits and factors? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Alternatively, what evolutionary/ecological advantages/disadvantages are there to having a large or small body size?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2014-12-14T16:10:44.363" LastActivityDate="2014-12-14T17:19:05.193" Title="Body size, what are the evolutionary trade-offs?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;physiology&gt;&lt;ecology&gt;&lt;ecophysiology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13746" PostTypeId="1" AcceptedAnswerId="13759" CreationDate="2013-12-01T21:38:14.963" Score="15" ViewCount="990" Body="&lt;p&gt;It is tragic, but apparently Killer whales and Dolphins can commit suicide too (e.g. &lt;a href=&quot;http://orcaed.wordpress.com/tag/suicide-in-killer-whales/&quot;&gt;here&lt;/a&gt;)... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This suggests they can become depressed. I wondered whether they were &quot;clinically&quot; depressed like many people are, and what other mental illnesses have been observed in animals in general. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Which mental disorders have been observed in animals? Which animals?&lt;/li&gt;&#xA;&lt;li&gt;What is the prevalence of these mental disorders in those animals?&lt;/li&gt;&#xA;&lt;li&gt;Are the causes and treatments of these disorders similar to Humans?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Strange thought&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Organisms that have not evolved the ability to make &quot;conscious choices&quot; cannot decide to end their life.&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2013-12-01T21:44:10.797" LastActivityDate="2019-04-03T13:10:17.807" Title="Do animals suffer from &quot;Human&quot; mental disorders?" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;behaviour&gt;&lt;psychology&gt;&lt;death&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13747" PostTypeId="2" ParentId="13745" CreationDate="2013-12-01T21:50:04.483" Score="9" Body="&lt;p&gt;I don't think one can fully answer to such a broad question. It depends on the population, the environment (presence of predators for example), the genetic background (having a big stomach is good but only if the intestin is big too), the population's social relations, .. Many traits are correlated and one might want to say that a given trait is beneficial but it is not because this trait is correlated (because of genetic, physical or social constraints).&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Trade-offs&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Here is a list of possible advantages/disadvantages.&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;visibility to predators&lt;/li&gt;&#xA;&lt;li&gt;ability to hunt bigger preys or to manipulate smaller preys&lt;/li&gt;&#xA;&lt;li&gt;running faster&lt;/li&gt;&#xA;&lt;li&gt;be more impressive&lt;/li&gt;&#xA;&lt;li&gt;fighting ability&lt;/li&gt;&#xA;&lt;li&gt;energy consumption for maintaining a body&lt;/li&gt;&#xA;&lt;li&gt;Quantity/quality of food to be found&lt;/li&gt;&#xA;&lt;li&gt;homothermy (heat loss)&lt;/li&gt;&#xA;&lt;li&gt;sustaining its own weight&lt;/li&gt;&#xA;&lt;li&gt;Rooms for the organs&lt;/li&gt;&#xA;&lt;li&gt;Attractiveness to the other sex&lt;/li&gt;&#xA;&lt;li&gt;being more able to move freely (in viscous environment (water))&lt;/li&gt;&#xA;&lt;li&gt;mechansisms for bringing nutrients and air to the tissues&lt;/li&gt;&#xA;&lt;li&gt;density of the body (water)&lt;/li&gt;&#xA;&lt;li&gt;excretion of wastes&lt;/li&gt;&#xA;&lt;li&gt;moving in small habitats&lt;/li&gt;&#xA;&lt;li&gt;Hiding in small areas&lt;/li&gt;&#xA;&lt;li&gt;bearing big and complex structures&lt;/li&gt;&#xA;&lt;li&gt;Parental care&lt;/li&gt;&#xA;&lt;li&gt;flying better&lt;/li&gt;&#xA;&lt;li&gt;acceleration in each movement&lt;/li&gt;&#xA;&lt;li&gt;etc...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;&lt;strong&gt;Allometric relations&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;You might be interested in &lt;a href=&quot;http://en.wikipedia.org/wiki/Life_history_theory&quot; rel=&quot;noreferrer&quot;&gt;life-history traits&lt;/a&gt;, and in &lt;a href=&quot;http://en.wikipedia.org/wiki/Allometry&quot; rel=&quot;noreferrer&quot;&gt;allometric relations&lt;/a&gt;. You might be interested by &lt;a href=&quot;http://www.jstor.org/discover/10.2307/2461259?uid=3737760&amp;amp;uid=2129&amp;amp;uid=2&amp;amp;uid=70&amp;amp;uid=4&amp;amp;sid=21103030048387&quot; rel=&quot;noreferrer&quot;&gt;this article&lt;/a&gt; as well. The reason for allometric relations can be found &lt;a href=&quot;http://en.wikipedia.org/wiki/Square-cube_law&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;If an animal were isometrically scaled up by a considerable amount, its relative muscular strength would be severely reduced, since the cross section of its muscles would increase by the square of the scaling factor while its mass would increase by the cube of the scaling factor. As a result of this, cardiovascular and respiratory functions would be severely burdened.&lt;/p&gt;&#xA;&lt;p&gt;In the case of flying animals, the wing loading would be increased if they were isometrically scaled up, and they would therefore have to fly faster to gain the same amount of lift. Air resistance per unit mass is also higher for smaller animals, which is why a small animal like an ant cannot be seriously injured from impact with the ground after being dropped from any height.&lt;/p&gt;&#xA;&lt;p&gt;As was elucidated by J. B. S. Haldane, large animals do not look like small animals: an elephant cannot be mistaken for a mouse scaled up in size. This is due to allometric scaling: the bones of an elephant are necessarily proportionately much larger than the bones of a mouse, because they must carry proportionately higher weight. To quote from Haldane's seminal essay On Being the Right Size, &amp;quot;...consider a man 60 feet high...Giant Pope and Giant Pagan in the illustrated Pilgrim's Progress.... These monsters...weighed 1000 times as much as Christian. Every square inch of a giant bone had to support 10 times the weight borne by a square inch of human bone. As the human thigh-bone breaks under about 10 times the human weight, Pope and Pagan would have broken their thighs every time they took a step.&amp;quot; Consequently, most animals show allometric scaling with increased size, both among species and within a species.&lt;/p&gt;&#xA;&lt;p&gt;The giant monsters seen in horror movies (e.g., Godzilla or King Kong) are also unrealistic, as their sheer size would force them to collapse. However, the buoyancy of water negates to some extent the effects of gravity. Therefore, sea creatures can grow to very large sizes without the same musculoskeletal structures that would be required of similarly sized land creatures, and it is no coincidence that the largest animals to ever exist on earth are aquatic animals.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/21961/why-do-small-organisms-make-faster-movements-than-big-organisms&quot;&gt;This post&lt;/a&gt; talks about the reasons for the allometric relations between animal size and speed of movements.&lt;/p&gt;&#xA;&lt;p&gt;Concerning the relation between heat loss and size, you might be willing to have a look to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Kleiber%27s_law&quot; rel=&quot;noreferrer&quot;&gt;Kleiber's law&lt;/a&gt;. This law has been extensively debated and is today thought (or known) to be wrong.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;em&gt;Just a philosophical note&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;You might also be interested in the philosophical discussion of adaptation, optimality, cost and benefit like &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0521598362&quot; rel=&quot;noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;this book&lt;/a&gt; (which I haven't read!) for example.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-14T17:19:05.193" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13748" PostTypeId="2" ParentId="13743" CreationDate="2013-12-01T22:03:43.160" Score="9" Body="&lt;p&gt;&lt;strong&gt;Short Answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a nutshell, DNA sequencing technology has a limit to how long a stretch of DNA it can read in &lt;em&gt;one go&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long Answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what most commonly occurs is the length of DNA you wish to sequence needs to be (almost randomly) chopped up into given lengths (depending on the technology) and each length or read is sequenced in parallel. But now you don't know which lengths to stick together! i.e. the ordering of these chopped up lengths. So you sequence it many times over (deeper) and this way you can align contiguous ends of these lengths together like a jigsaw puzzle. The more times you sequence the more accurately the 'contigs' will be aligned.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;DNA Assembly Diagram&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/93qef.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Comment if you want more details, but the technical term you want to google is &lt;a href=&quot;https://www.google.co.uk/search?q=sequencing%20assembly&amp;amp;oq=sequencing%20assembly&amp;amp;aqs=chrome..69i57j0l5.2193j0j4&amp;amp;sourceid=chrome&amp;amp;espv=210&amp;amp;es_sm=93&amp;amp;ie=UTF-8&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;sequencing assembly&quot;&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the &lt;a href=&quot;http://en.wikipedia.org/wiki/Dna_assembly&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;:)&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2014-02-20T17:03:11.117" LastActivityDate="2014-02-20T17:03:11.117" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="13752" PostTypeId="2" ParentId="13740" CreationDate="2013-12-02T04:50:56.617" Score="3" Body="&lt;p&gt;Some of the reasons why immature blast cells are studied:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;They have self renewal ability &lt;/li&gt;&#xA;&lt;li&gt;Can be differentiated to different types of cells&lt;/li&gt;&#xA;&lt;li&gt;Serve as model for studying development: this is quite pertinent to the gene expression studies. Because it is important to know what changes take place during differentiation and simply looking at the differentiated state won't explain that process. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-12-02T04:50:56.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13753" PostTypeId="2" ParentId="13735" CreationDate="2013-12-02T05:02:08.760" Score="1" Body="&lt;p&gt;To scan multiple databases:-&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Download all the databases that you intend to match against (all databases will have a download option)&lt;/li&gt;&#xA;&lt;li&gt;Download standalone BLAST executables from NCBI&lt;/li&gt;&#xA;&lt;li&gt;Pool all the sequences from the different databases and make a BLAST database using the program &lt;code&gt;makeblastdb&lt;/code&gt; (it is better to check for redundant sequences and remove them for improved performance)&lt;/li&gt;&#xA;&lt;li&gt;Run &lt;code&gt;blastp&lt;/code&gt; with desired parameters against this database &lt;/li&gt;&#xA;&lt;li&gt;The &lt;em&gt;first hit&lt;/em&gt; wont mean much. Use cutoffs on &lt;code&gt;E-value&lt;/code&gt; or &lt;code&gt;Bit-Scores&lt;/code&gt; or &lt;code&gt;precentage identity&lt;/code&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Now, if you vaccine targets a protein it is good to study the protein sequence conservation. BLAST isn't a really good option for studying conservation by comparing different orthologs. Use tools for multiple sequence alignment like &lt;code&gt;ClustalW&lt;/code&gt; or &lt;code&gt;T-COFFEE&lt;/code&gt;. In my opinion it is also better to use &lt;code&gt;BLOSUM&lt;/code&gt; for scoring the alignments compared to &lt;code&gt;PAM&lt;/code&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It might also be important to look at the protein structures. You can try &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;VAST&lt;/strong&gt;&lt;/a&gt; if possible.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2013-12-02T05:09:48.737" LastActivityDate="2013-12-02T05:09:48.737" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13754" PostTypeId="2" ParentId="6839" CreationDate="2013-12-02T11:04:38.593" Score="1" Body="&lt;p&gt;Check &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10818/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; link out, It's a little simplistic but hopefully, will give the info you want so you can search elsewhere. &lt;/p&gt;&#xA;" OwnerUserId="5061" LastEditorUserId="-1" LastEditDate="2015-09-07T04:38:45.217" LastActivityDate="2015-09-07T04:38:45.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13756" PostTypeId="1" AcceptedAnswerId="13849" CreationDate="2013-12-02T13:20:31.970" Score="3" ViewCount="130" Body="&lt;p&gt;The major nutritional mechanisms include chemoautotrophy, heterotrophy (including parasitism and saprotrophy) and photoautotrophy. All of these modes of nutrition developed first in prokaryotic ancestors, and gradually, through the course of evolution, these prokaryotes formed complex eukaryotic, multicellular organisms. Some of these complex descendants (the majority of Kingdom Plantae) possessed the photoautotrophic mode and some (the majority of Kingdom Animalia, some of Kingdom Protista &amp;amp; Kingdom Fungi) possessed the heterotrophic mode.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, since all the three modes developed quite early in evolutionary history, why didn't any chemoautotrophic multicellular, eukaryotic organism develop? (Or, if they did, why did they not form a wide-diverse group as the organisms with other two modes of nutrition did.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(One possible reason could be lesser availability of chemoautotrophic substrates, but I have no proof, nor any argument to support this.)&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3952" LastEditDate="2013-12-02T18:57:07.260" LastActivityDate="2013-12-06T18:47:00.243" Title="Chemoautotrophy in large organisms?" Tags="&lt;evolution&gt;&lt;nutrition&gt;&lt;speculative&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13757" PostTypeId="2" ParentId="13712" CreationDate="2013-12-02T17:35:36.013" Score="1" Body="&lt;p&gt;It's carpet beetle larvae.&#xA;It's a serious pest, right behind the bedbug. The larvae were found on an old mattress.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found about 4 more afterwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NqlFY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5039" LastActivityDate="2013-12-02T17:35:36.013" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13758" PostTypeId="2" ParentId="13713" CreationDate="2013-12-02T18:19:20.450" Score="1" Body="&lt;p&gt;Take a look at Paragraph 2. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll outline it in more or less plain english (I hope). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;for 37 lakes they used this method: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) they took a sample of water from 0.1 to 0.25 m below the surface.  Using a thermos bottle.  This would minimize change of the gas composition of the water with a change of temperature.  The bottle was not sealed, but left out for a while in the air there at the lake (it was &quot;equilibrated with ambient air&quot;).  If you were looking for issues you might or might not like this.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) a sample of air 1m above the lake was taken.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) they got a gas chromatograph to measure the CO2 in the air above the water sample, as well as in the air from above the lake.  They might have taken the readings right there at the sampling point, or not its not clear. They may have also sealed bottles up and taken them to the lab.  It sort of sounds like a point of sample measurement. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the air above the water samples had more CO2 than the air above the lake, they called the water supersaturated as the water was emitting CO2.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This method does its best to simplify the question of whether fresh water bodies are saturated with CO2 and emitting it or if they might be absorbing it.  By not outgassing the CO2 in the water and trying to get an absolute content of CO2, they are able to get around the various organisms and minerals in the water and pH which would vary the amount of CO2 the lakes can hold.  they are just focusing on whether the water is giving off CO2.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-12-02T18:19:20.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13759" PostTypeId="2" ParentId="13746" CreationDate="2013-12-02T18:33:02.210" Score="7" Body="&lt;p&gt;You will be hard-pressed to find any scientific data on this question. Psychology in humans is already a difficult study, at times failing to demonstrate results with real scientific rigor. When studying animal psychology, you face another substantial barrier - language. Although some primates have been taught to communicate with sign language, the best of them are still far from the level of proficiency of a human. We can measure brain activity and observe behavior, which can lead us to strong suspicions about what is going on in an animal's mind, but very little can actually be proven.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mostly, all we can do is speculate about such questions. You will find some veterinarians out there who treat pets for mental conditions, but you will find at least as many people calling them quacks as those who believe in the validity of their work. And certainly, they can't prove to you that a treatment has helped an animal. It's subjective.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we see an animal do something which in a human might reliably be interpreted as a sign of depression, it's possible that this interpretation is appropriate for the animal as well. It's also possible that there is some totally foreign unrelated explanation. The problem we find when trying to scientifically discuss matters which cannot be proven scientifically is that scientists must be careful to state what they know and nothing more. So they might say &quot;We cannot prove that the porpoise is depressed&quot;, or &quot;Science cannot prove the existence of a God.&quot; This is often misinterpreted as evidence against the finding - that the porpoise is not depressed; that there is no God. This is a fallacy. Rather, we should recognize that we have different ways of exploring questions like these.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't prove it to you, but I know that my Beagle had a rich emotional life. I know this because I spent huge amounts of time with him. He was a close friend of mine. I would just as soon question whether my wife has real emotions as my dog. I can't prove that my wife's emotions are real either, but I don't have to. It would be silly to assume that everything she shares with me is some sort of evolutionary programming, and not real emotion. Now, when I extend this to cetaceans, I must admit that I don't have any friends in those circles. So I can only guess.&lt;/p&gt;&#xA;" OwnerUserId="5018" LastEditorUserId="5018" LastEditDate="2013-12-02T19:49:17.403" LastActivityDate="2013-12-02T19:49:17.403" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="13760" PostTypeId="2" ParentId="13746" CreationDate="2013-12-02T18:50:32.387" Score="0" Body="&lt;p&gt;Good question: We know that prion diseases affect the psychology of animals (Scrapie, Mad Cow). But without a doubt genetic regulation of endocrine and neurotransmitter pathways is subject to the same folly as in &lt;em&gt;Homo sapiens&lt;/em&gt;. Sorry I can't support that with links to publications...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;update: There are many animal models: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/746371&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/746371&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5066" LastActivityDate="2013-12-02T18:50:32.387" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13761" PostTypeId="2" ParentId="10548" CreationDate="2013-12-02T20:31:14.937" Score="0" Body="&lt;p&gt;A genetic circuit can be likened to electrical circuits, except rather than switches, resistors, wires, &lt;em&gt;etc.&lt;/em&gt;, you use promoters, ribosomal binding sites, coding sequences, repressors, &lt;em&gt;etc.&lt;/em&gt; - This will get you well acquainted with the new jargon around bioengineering: &lt;a href=&quot;http://parts.igem.org/Main_Page&quot; rel=&quot;nofollow&quot;&gt;http://parts.igem.org/Main_Page&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="5066" LastActivityDate="2013-12-02T20:31:14.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13762" PostTypeId="2" ParentId="10841" CreationDate="2013-12-02T20:45:39.840" Score="2" Body="&lt;p&gt;To answer this question, you need some background info first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are three &quot;systems&quot; used for the sense of smell. The first is the olfactory system. This system allows us to recognize what a smell is. You can tell the difference between gardenias and grass because of your olfactory system. The second system is the trigeminal system. This system tells you whether an odor is irritating or pleasing. It gets its name from the trigeminal nerve--the nerve that gives feeling to your entire face. Your sense of smell is all tangled up with the trigeminal nerve, meaning that some odors are painful to smell and some are not. When you smell ammonia and it stings your nose, that is the trigeminal system at work. The third is the vomeronasal system. It's thought to be use for detecting pheromones. However, it isn't important to this explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So. What is meant by a &quot;pure&quot; odorant? It means that it &lt;em&gt;only&lt;/em&gt; smells. It doesn't create a reaction in the trigeminal system. It only activates the olfactory system. Those who have lost their sense of smell are still able to distinguish many smells because of the reaction by the trigeminal system. One study I've read tested 47 different smells for people who have lost function in their olfactory system. Out of those 47, 45 of them were identified by the people with no sense of smell. The two that were not identified (decanoic acid and vanillin) didn't stimulate the trigeminal system and are thus considered to be &quot;pure&quot; odorants. In other words, pure odorants are odors that only smell and don't feel like anything. There are very few &quot;pure&quot; odorants, and peanut butter is one of them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, when someone says Alzheimer's changes the ability to smell, they have to make sure they're &lt;em&gt;only&lt;/em&gt; testing smell and not touch too. That's why they need to use a &quot;pure&quot; odorant. Otherwise, the Alzheimer's patient might still be able to identify the scent and the test would be useless. &lt;/p&gt;&#xA;" OwnerUserId="5068" LastActivityDate="2013-12-02T20:45:39.840" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13763" PostTypeId="2" ParentId="13680" CreationDate="2013-12-02T21:19:30.113" Score="9" Body="&lt;p&gt;I’ll add a slightly different perspective, although terdon’s answer already contains the relevant facts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thing that makes DNA endure in the face of imperfect copying is that, like computer storage, it’s &lt;em&gt;digital&lt;/em&gt;. The &lt;a href=&quot;https://en.wikipedia.org/wiki/Digital_data&quot;&gt;relevant property of digital data&lt;/a&gt; here is that individual pieces of information aren’t given on a scale, they’re drawn from a strongly limited number of possible alternative values. That property allows error correction to take place: if possible values were continuous, error correction fundamentally wouldn’t work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This gives the appearance of error-less copying. In reality it’s anything but, same as with computer storage and data transfer. Nevertheless, as you’ve noted, errors &lt;em&gt;will&lt;/em&gt; accumulate, even with an error correction mechanism in place. And even though most of these errors have no influence on the outcome (due to downstream effects like the degeneracy of the genetic code), &lt;a href=&quot;https://en.wikipedia.org/wiki/Mutation#By_impact_on_protein_sequence&quot;&gt;many more are detrimental than are positive&lt;/a&gt;. In direct contradiction of this we can see that species (but &lt;em&gt;not&lt;/em&gt; individuals!) &lt;em&gt;improve&lt;/em&gt; their adaptation in each generation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why? &lt;em&gt;Because &lt;a href=&quot;https://en.wikipedia.org/wiki/Natural_selection#Evolution_by_means_of_natural_selection&quot;&gt;evolution&lt;/a&gt;&lt;/em&gt;. More specifically, because &lt;a href=&quot;https://en.wikipedia.org/wiki/Purifying_selection&quot;&gt;natural selection acts in a purifying manner&lt;/a&gt; to rid the gene pool of defects. This is a fundamental part of Darwin’s and Wallace’s argument. Less adapted individuals have an (ever so slightly) reduced chance at reproducing, and therefore prevent detrimental changes in the gene pool from accumulating.&lt;/p&gt;&#xA;" OwnerUserId="166" LastActivityDate="2013-12-02T21:19:30.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13764" PostTypeId="2" ParentId="13618" CreationDate="2013-12-02T22:43:03.640" Score="4" Body="&lt;p&gt;I don't think repetitive sequences are intrinsically problematic to an &lt;em&gt;E coli&lt;/em&gt;. Bacteria also deal with things like &lt;a href=&quot;http://www.nature.com/embor/journal/v4/n2/full/embor733.html&quot; rel=&quot;nofollow&quot;&gt;polyadenylation&lt;/a&gt;. Basically, you have nothing to lose from trying -- &lt;em&gt;E coli&lt;/em&gt; is one of the more robust expression platforms, and it's difficult to predict whether the sequence will fold into some tertiary structure (which can easily impede translation.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I think the predictability should be set at the baseline for &lt;em&gt;E coli&lt;/em&gt; RNA polymerase error rate, which is about $10^{-5}$.&lt;/p&gt;&#xA;" OwnerUserId="3336" LastEditorUserId="3336" LastEditDate="2013-12-06T18:12:06.587" LastActivityDate="2013-12-06T18:12:06.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13765" PostTypeId="2" ParentId="13695" CreationDate="2013-12-03T01:15:53.963" Score="3" Body="&lt;p&gt;Remi.b's answer is spot on - predicting the effects of losing a given species is nigh on impossible. However, I do think that there are some general trends that can give us some intuition, and make the campaign to protect certain species more than just an ethical issue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biodiversity (i.e. having a wide range of different organisms (and genetically diverse organisms)) has a number of potential benefits (for references see the work of &lt;a href=&quot;http://www.cbs.umn.edu/explore/departments/eeb/faculty-research/directory/g-david-tilman&quot; rel=&quot;nofollow&quot;&gt;David Tilman&lt;/a&gt;, among others):&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Improved resilience to catastrophic events.&lt;/li&gt;&#xA;&lt;li&gt;Improved temporal stability of populations within an ecosystem (which kind of dovetails with (1))&lt;/li&gt;&#xA;&lt;li&gt;Improved ecosystem productivity (this has mostly been studied in terms of the amount of biomass grown by plants in an ecosystem, but may generalize to other kinds of ecosystem functioning)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Ecosystem services are effects that various ecosystems have on the world that makes it more hospitable to humans. While some may be, as Remi.b suggested, overhyped, some are very real, such as bioremediation (the removal of compounds toxic to humans from the air and water), the continued presence of pollinators and nutrient-rich soil in which to grow crops, and carbon sequestration. Given that the continuation of these ecosystem services is necessary for our long-term survival as a species, it is in our interest to ensure that ecosystems remain intact to provide them. Increasing resilience and temporal stability of ecosystems reduces the chance that we will lose ecosystems and the services they provide. Increasing the productivity of an ecosystem in many cases increases the extent to which it can perform that service (this is most obvious in the case of carbon sequestration). (NOTE: I'm phrasing this all in terms of human survival because I think that's the most clear cut argument. I think there are other arguments, but they're murkier)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, this raises the question of how much of an impact the loss of a single species (such as a tiger) is likely to have on the benefits associated with biodiversity. There are a few hypotheses here, but in any specific case the impacts will be fairly dependent on the role of the extinct species in the ecosystem. The loss of some species (keystone species) will have a disproportionate impact on the rest of the environment. While it is hard to predict which species will turn out to be keystone species until it is too late, apex predators (like tigers) are more likely than average to be keystone species, or to have an important but not disproportionate role in the ecosystem. This makes sense, because such predators are fairly often the only species at their trophic level in an ecosystem, and having more trophic levels dramatically increases the biodiversity possible in an ecosystem. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if there isn't reason to think that a certain species is relatively important to an environment, there can sometimes be benefit in trying to save it via what's called &quot;the umbrella effect.&quot; This boils down to the idea that saving one species generally involves saving the rest of the ecosystem that it lives in. So sometimes, from a funding perspective, it makes the most sense to choose the most charismatic species from a given ecosystem and attempt to get public investment in saving that species. An attempt to save this species can then result in preserving a great deal of biodiversity in the rest of the ecosystem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, ultimately, no, we cannot know how important a given organism is to an ecosystem or to human well-being. But we can make some fairly well-informed guesses. &lt;/p&gt;&#xA;" OwnerUserId="3824" LastActivityDate="2013-12-03T01:15:53.963" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13766" PostTypeId="1" CreationDate="2013-12-03T05:03:50.780" Score="2" ViewCount="4685" Body="&lt;p&gt;Could someone clearly define what a gene variant is with an example. I am totally confusing myself with SNPs, alleles, variants and how the major and minor allele are defined. An example with gene names would be really helpful.&lt;/p&gt;&#xA;" OwnerUserId="5071" LastEditorUserId="22057" LastEditDate="2016-05-30T22:23:21.420" LastActivityDate="2016-05-30T22:23:21.420" Title="Definition and example of Gene Variant" Tags="&lt;genetics&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13767" PostTypeId="2" ParentId="13766" CreationDate="2013-12-03T06:39:06.967" Score="5" Body="&lt;p&gt;A fairly easy-to-understand example is that of the &lt;a href=&quot;https://en.wikipedia.org/wiki/ABO_blood_group_system&quot; rel=&quot;nofollow&quot;&gt;ABO blood group system&lt;/a&gt;. In this case, there is a single &lt;em&gt;gene&lt;/em&gt; involved - &lt;em&gt;ABO&lt;/em&gt;, which codes for an enzyme that modifies sugar groups on the surface of red blood cells. This &lt;em&gt;ABO&lt;/em&gt; gene has three &lt;em&gt;variants&lt;/em&gt; or &lt;em&gt;alleles&lt;/em&gt; &amp;mdash; &lt;em&gt;i&lt;/em&gt;, &lt;em&gt;I&lt;sup&gt;A&lt;/sup&gt;&lt;/em&gt;, and &lt;em&gt;I&lt;sup&gt;B&lt;/sup&gt;&lt;/em&gt;. &lt;em&gt;i&lt;/em&gt; (coding for Type O blood) is recessive, which means that its &lt;a href=&quot;https://en.wikipedia.org/wiki/Phenotype&quot; rel=&quot;nofollow&quot;&gt;phenotype&lt;/a&gt; can only be observed if there are two copies of it &amp;ndash; &lt;em&gt;ii&lt;/em&gt; &amp;ndash; one from the mother and one from the father. &lt;em&gt;I&lt;sup&gt;A&lt;/sup&gt;&lt;/em&gt; and &lt;em&gt;I&lt;sup&gt;B&lt;/sup&gt;&lt;/em&gt; are &lt;a href=&quot;https://en.wikipedia.org/wiki/Dominance_relationship#Co-dominance&quot; rel=&quot;nofollow&quot;&gt;co-dominant&lt;/a&gt;, meaning that both can be expressed at the same time, and their phenotypes can be observed even if there is only one copy of that allele &amp;mdash; for example, &lt;em&gt;I&lt;sup&gt;A&lt;/sup&gt;i&lt;/em&gt; would give Type A blood (as would &lt;em&gt;I&lt;sup&gt;A&lt;/sup&gt;I&lt;sup&gt;A&lt;/sup&gt;&lt;/em&gt;), &lt;em&gt;I&lt;sup&gt;A&lt;/sup&gt;I&lt;sup&gt;B&lt;/sup&gt;&lt;/em&gt; would give Type AB, and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Major and minor alleles (at least in my mind) simply refer to the frequency with which an allele is found in a given population: a &lt;em&gt;minor&lt;/em&gt; allele is one that is expressed less-often than a &lt;em&gt;major&lt;/em&gt; one. The term &lt;em&gt;minor allele frequency&lt;/em&gt; is sometimes used as a numerical representation of expression &amp;mdash; a certain allele is only expressed in 3% of the population, for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These terms are all from classical genetics &amp;mdash; talking about genes and variants without really knowing (or needing to know) what exactly the gene was made up of. Of course, we now know that genes are composed of sequences of DNA nucleotide &lt;em&gt;base pairs&lt;/em&gt; (A, T, C, and G), which are then translated by 3bp-&lt;em&gt;codons&lt;/em&gt; into proteins, where each codon corresponds to one of 20 &lt;em&gt;amino acids&lt;/em&gt;, plus &lt;em&gt;START&lt;/em&gt; and &lt;em&gt;STOP&lt;/em&gt; sequences. It is in this context of DNA sequence analysis that terms like &lt;a href=&quot;https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism&quot; rel=&quot;nofollow&quot;&gt;SNP&lt;/a&gt; or Single Nucleotide Polymorphism are used. If you were to compare two alleles, say &lt;em&gt;I&lt;sup&gt;A&lt;/sup&gt;&lt;/em&gt; and &lt;em&gt;I&lt;sup&gt;B&lt;/sup&gt;&lt;/em&gt;, any single-nucleotide difference between the two could be termed a SNP. Frequently, SNPs are often notated based on the changes the difference would bring to the translated protein sequence &amp;mdash; for example, a AAG codon codes for the amino acid lysine, while GAG encodes glutamatic acid. In other cases, a SNP would make no difference to the protein sequence &amp;mdash; for example, TTA, TTG, CTC, CTA, CTG, and CTT all encode leucine. You can find the DNA codon table &lt;a href=&quot;https://en.wikipedia.org/wiki/DNA_codon_table&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should keep in mind that SNPs are not the only source of variation in genetic sequences &amp;mdash; deletions, translocations, repetitions, inversions, frame shifts, and other mechanisms can all alter the DNA sequence at a particular &lt;em&gt;locus&lt;/em&gt; or site. Taken together, all of these differences are often referred to as &lt;em&gt;mutations&lt;/em&gt;, which simply means &quot;changes.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this was helpful, please let us know if you still have questions.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="1306" LastEditDate="2013-12-03T17:30:02.077" LastActivityDate="2013-12-03T17:30:02.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13769" PostTypeId="1" AcceptedAnswerId="13781" CreationDate="2013-12-03T08:53:07.253" Score="18" ViewCount="4045" Body="&lt;p&gt;The word flu derives from the Italian phrase &quot;influenza de freddo&quot; meaning &quot;influence of the cold&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed it is that time of the year when my colleagues seem to have the flu/cold more often than not. I remember during university, winter lectures would be riddled with people coughing and sneezing - the so called &quot;freshers flu&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Is there statistical evidence for this claim?&lt;/li&gt;&#xA;&lt;li&gt;If so, what are the causes/factors involved? &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/445/why-do-we-get-runny-noses-in-the-cold&quot;&gt;Another post&lt;/a&gt; asks why our noses get runnier during cold whether, is this related?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-03-21T19:21:20.417" Title="Do we actually get more sick (flu/cold) during winter?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;pathology&gt;&lt;medicine&gt;&lt;infection&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13770" PostTypeId="5" CreationDate="2013-12-03T09:52:13.260" Score="0" Body="&lt;p&gt;A science drawing on a broad range of disciplines including chemistry, physics, biology, and geology. It revolves around the study of lakes, rivers, ponds, streams and wetlands, and is not limited to freshwater. Posts on Biology SE should focus on the biological aspects of this discipline such as ecology.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-12-03T14:20:04.233" LastActivityDate="2013-12-03T14:20:04.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13771" PostTypeId="4" CreationDate="2013-12-03T09:52:13.260" Score="0" Body="The science of inland waters, posts on Biology SE should focus on the biological aspects of this discipline." OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-12-03T14:19:54.063" LastActivityDate="2013-12-03T14:19:54.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13772" PostTypeId="2" ParentId="13690" CreationDate="2013-12-03T11:09:38.353" Score="3" Body="&lt;p&gt;Tortoiseshell cats (which is the normal name for Calico style cats in Europe) arise due to a gene on the X chromosome. Some patches are ginger, and some tabby due to the deactivation of one X chromosome in each cell at an early stage of development. This produces a tortoiseshell-like pattern.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you see in these tabby cats with the white colouring is due to temperature dependence, this gives the patterning on the feet/nose etc. Tortoiseshell cats looks quite different, where the different coloured patches of fur are random.&lt;/p&gt;&#xA;" OwnerUserId="1300" LastActivityDate="2013-12-03T11:09:38.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13775" PostTypeId="1" AcceptedAnswerId="13780" CreationDate="2013-12-03T12:43:46.330" Score="1" ViewCount="121" Body="&lt;p&gt;The typical procedure to obtain cDNA from genomic extracted DNA is the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RNA is extracted from desired tissue, RNA/DNA hybrid is obtained by virtue of reverse transcriptase RNA dependent DNA polymerase, H RNAse creates gaps in RNA of DNA/RNA hybrid and with the aid of a typical DNA polymerase dsDNA is transcribed, right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, the newly synthesized cDNA is linear (like a &quot;small chromosome&quot;)? &#xA;How is it protected from the nucleolytic activity?&#xA;Is the procedure really like I described or does the reverse transcriptase already give a dsDNA from single stranded mRNA?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="3624" LastEditDate="2013-12-03T16:15:49.410" LastActivityDate="2013-12-11T00:03:44.800" Title="Clarification of the procedures to amplify cDNA needed" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13776" PostTypeId="1" CreationDate="2013-12-03T13:16:47.590" Score="9" ViewCount="235" Body="&lt;p&gt;Is it possible to make birds confused by repeating recorded chirping or singing? Or do they always perceive them as usual, even if the situation is clearly not as described by those sounds?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;mating song when there's no mate&lt;/li&gt;&#xA;&lt;li&gt;danger/alarm cries when nothing's going on&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Specifically, I'm interested in public placed with a lot of traffic using looping speakers to scare off birds that like to dump upon almost unsuspecting citizens. Like underground entrances and city malls. Does the effectiveness decrease over time because of that?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2016-05-17T18:08:37.410" Title="Can you &quot;spam&quot; bird sounds so that birds no longer interpret them right?" Tags="&lt;ornithology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13777" PostTypeId="1" CreationDate="2013-12-03T13:59:51.637" Score="7" ViewCount="3146" Body="&lt;p&gt;Are the two cells that are derived from one cell, ‘twin sisters’ or a ‘mother and a daughter’?  In other words, can a cell really be divided to live an &quot;immortal&quot; life or is cell reproduction the reality of cell life that accounts cell age difference between two successive generations, cell aging-associated senescence in cell reproduction, and cell line survival after the death of old cells.&lt;/p&gt;&#xA;" OwnerUserId="5078" LastActivityDate="2013-12-04T22:11:38.727" Title="Cell life: division for immortality or reproduction with aging" Tags="&lt;cell-biology&gt;&lt;reproduction&gt;&lt;senescence&gt;&lt;cell-division&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13780" PostTypeId="2" ParentId="13775" CreationDate="2013-12-03T19:35:05.297" Score="2" Body="&lt;p&gt;Here is the rough procedure that I've used to prepare cDNA before&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Extract RNA from desired tissue (select for mRNA using the polyA tail of mRNA)&lt;/li&gt;&#xA;&lt;li&gt;Conduct reverse transcription. This requires a primer complementary to the polyA tail to get the reverse transcriptase started (&lt;strong&gt;Edit&lt;/strong&gt;:You could also use random primers to prime reverse transcription. This eliminates the redundant polyT sequence from the cDNA. This is the method used in the Illumina TruSeq high throughput sequencing library prep kit). Now you have a collection hybrid RNA/DNA double strands&lt;/li&gt;&#xA;&lt;li&gt;Digest the RNA strand specifically. This can be accomplished with RNAse H as you mention, or by introducing basic conditions, which degrade RNA much more rapidly than DNA due to the 2'OH of RNA. &lt;em&gt;Now you have linear ssDNA complementary to the inital mRNA templates.&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;From this point your applications may differ. If you are doing microarrays, all you need is ssDNA, since you want to hybridize the cDNA to the array. If your downstream use of the cDNA requires dsDNA, then you need to synthesize a complementary strand to the cDNA (and potentially amplify the product). This can be accomplished through PCR random primers, or some more complicated PCR that will incorporate extra sequences on either side of your cDNA (e.g. bar-codes and adapters in RNA-Seq). &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How is [the cDNA] protected from the nucleolytic activity?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you are digesting the product of reverse transcription with RNAse H, that enzyme digests RNA specifically, so your DNA is unharmed. If you are going with an alkaline conditions treatment, then the RNA will be degraded in those conditions much more quickly than the DNA due to the presence of the 2' OH group in RNA which can act as a nucleophile for a self-cleavage reaction.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastEditorUserId="4840" LastEditDate="2013-12-11T00:03:44.800" LastActivityDate="2013-12-11T00:03:44.800" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13781" PostTypeId="2" ParentId="13769" CreationDate="2013-12-03T20:10:42.513" Score="12" Body="&lt;p&gt;The combination of these two reports from the CDC give information about the comparative prevalence of flu infection in the &lt;a href=&quot;http://www.cdc.gov/mmwr/preview/mmwrhtml/mm6223a5.htm?s_cid=mm6223a5_e&quot; rel=&quot;nofollow noreferrer&quot;&gt;winter&lt;/a&gt; (September '12- May '13) and &lt;a href=&quot;http://www.cdc.gov/mmwr/preview/mmwrhtml/mm6242a3.htm?s_cid=mm6242a3_e&quot; rel=&quot;nofollow noreferrer&quot;&gt;summer&lt;/a&gt; (May '13 - September '13). I'm going to assume that 2012-2013 was a fairly representative year as far as the level of detail of &quot;do we get sick more in the winter&quot; goes. Particularly striking are the graphs linked to in both documents of the number of flu-infected respiratory specimens per week: &lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Winter (infected specimens out of 311,000 tested):&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Nj7DA.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Summer (infected specimens out of 52,000 tested):&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5UqJv.gif&quot; alt=&quot;Summer influenza cases&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Together these two figures cover data Sept '12 - Sept '13. Note the difference in scale on the vertical axis. Forgive me if I don't run any statistical tests, but I think you can spot the trend.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sum of all the Winter cases represents 23% of the 311,333 specimens tested from Sept '12 to May '13, and the sum of all the bars in the Summer figure represents 3.9% of the 52,150 respiratory specimens tested from May '13-Sept '13.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Still left to answer&lt;/strong&gt;: &lt;em&gt;Why is this the case?&lt;/em&gt; In my preliminary research it seems like we still don't fully know the answer to this one; I'll leave someone else to speculate.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;: Some tentative answers to &lt;em&gt;why is there a seasonal flu outbreak&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This review &lt;a href=&quot;http://jvi.asm.org/content/81/11/5429.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;(1)&lt;/a&gt; does a nice job of laying out some of the current ideas about the cause of the seasonal flu. One interesting note is that seasonal flu is a phenomenon of temperate climates: in tropical regions flu outbreaks occur on a much less regular periodic schedule. Some possible causes mentioned by the authors (paraphrased from the article):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;It takes time for virus to mutate enough to be infectious again to people who were already infected with it.&lt;/li&gt;&#xA;&lt;li&gt;The efficacy of the immune system may vary seasonally, say, due to changes in daylight hours/vitamin D and melatonin levels (which have been shown to affect immune system function in hamsters)&lt;/li&gt;&#xA;&lt;li&gt;Flu is transmitted better in more crowded conditions + in winter people are more crowded together. This is a popular explanation, but the authors claim that it has not been satisfactorily tested. It &lt;em&gt;has&lt;/em&gt; been argued convincingly that the 1918 flu epidemic was exacerbated by the crowded condition of army barracks in WWI (see citation in paper).&lt;/li&gt;&#xA;&lt;li&gt;Indoor heating encourages air recirculation, which allows virus to persist in the air around you longer.&lt;/li&gt;&#xA;&lt;li&gt;Viruses survive/persist better in cold, dry conditions. This may allow them to spread in the atmosphere longer during the winter, and be more easily transmitted from person to person via &quot;bioaerosols&quot; (sneezes).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Ultimately, as I said before, we don't really know yet. Reading that list you can imagine several ways in which a few of those factors are not at all causal and are rather just strongly correlated with the &quot;true&quot; cause of flu seasonality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jvi.asm.org/content/81/11/5429.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;(1): Lofgren et al. Influenza Seasonality: Underlying Causes and Modeling Theories. (2007). &lt;em&gt;J. Virol.&lt;/em&gt; 81(11): 5429-5436. doi:10.1128/JVI.01680-06&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4840" LastEditorUserId="4840" LastEditDate="2013-12-03T20:36:02.943" LastActivityDate="2013-12-03T20:36:02.943" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="13783" PostTypeId="1" CreationDate="2013-12-03T20:41:59.420" Score="4" ViewCount="72" Body="&lt;p&gt;I was rooting through the literature, but there is too much work on the topic of detecting loops in RNA and the RNA helices that go with them.  Can anyone point to a good review on this topic or even better describe some better performing algorithms? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-12-10T22:25:04.183" Title="Finding RNA Loops" Tags="&lt;bioinformatics&gt;&lt;rna&gt;&lt;structure-prediction&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13784" PostTypeId="1" AcceptedAnswerId="13793" CreationDate="2013-12-03T21:50:49.187" Score="2" ViewCount="652" Body="&lt;p&gt;I wonder what a bird would sing if it didn't have its parents around (or any other birds for that matter) to learn its chirping sounds from.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested in how a bird would sing...&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;in complete isolation from creatures communicating through sound;&lt;/li&gt;&#xA;&lt;li&gt;in isolation from its own species, but with other birds;&lt;/li&gt;&#xA;&lt;li&gt;in isolation from all birds (other animals and creatures are there for it)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;For example,&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Would a bird even feel the need to speak up if there wasn't any other vocalizing creature around?&lt;/li&gt;&#xA;&lt;li&gt;Would a bird learn other species' signals? Would it only learn from one species, the one which it would think of a fitting mate?&lt;/li&gt;&#xA;&lt;li&gt;Would a bird try to mimic a non-flying creature's signals?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;These are similar questions, but if you think they should be separated, let me know in the comments.&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2013-12-04T07:17:29.550" Title="How do birds learn their tunes in isolation from their own species?" Tags="&lt;ornithology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13785" PostTypeId="1" CreationDate="2013-12-03T22:06:32.900" Score="6" ViewCount="17246" Body="&lt;p&gt;I had my students conduct a fermentation experiment manipulating sugar amounts (number of sugar packets in solution) and measuring CO₂ production via capture in a balloon and measuring circumference (very common HS lab experiment). I also had them conduct a trial with two packets of Equal sweetener. To everyone's surprise two packets of the &quot;zero calorie&quot; sweetener produced as much CO₂ as four packets of sugar. Can anyone shed light on why this would have occurred? Equal contains maltodextrin and dextrose in addition to the aspartame. I'm assuming that yeast are able to metabolize one or more of these substances, but I haven't been able to find a more detailed explanation.&lt;/p&gt;&#xA;" OwnerUserId="1710" LastEditorUserId="3340" LastEditDate="2014-10-09T15:18:33.343" LastActivityDate="2019-10-31T15:10:04.250" Title="Why do yeast ferment Equal sweetener" Tags="&lt;microbiology&gt;&lt;yeast&gt;&lt;fermentation&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13786" PostTypeId="2" ParentId="13785" CreationDate="2013-12-03T22:22:37.193" Score="2" Body="&lt;p&gt;I don't have a definitive answer to this, but a little over a decade ago I was in an undergraduate lab that had a similar thing happen - a small amount of metabolism of a &quot;control&quot; group of bacteria fed artificial, sugar/calorie free sweeteners instead of sugar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our running theories at the time were:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Contamination. Always a problem in laboratory experiments, and &lt;em&gt;especially&lt;/em&gt; undergraduate lab experiments.&lt;/li&gt;&#xA;&lt;li&gt;Trace contaminants. &quot;Zero calorie&quot; isn't actually &lt;em&gt;0&lt;/em&gt;, it's just &lt;em&gt;small&lt;/em&gt;, and hardy microorganisms may be able to do just fine with small amounts of nutrients. If there's another factor limiting their growth, that may result in the identical CO₂ results.&lt;/li&gt;&#xA;&lt;li&gt;Some intermediate compound or the like that &lt;em&gt;is&lt;/em&gt; useful for metabolism. As you said, possibly the ability to use maltodextrin or dextrose.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="67" LastEditorUserId="3340" LastEditDate="2014-10-09T15:18:00.820" LastActivityDate="2014-10-09T15:18:00.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13787" PostTypeId="2" ParentId="13785" CreationDate="2013-12-03T22:30:28.203" Score="2" Body="&lt;p&gt;Equal is marketed as a &quot;zero calorie&quot; sweetener, with respect to human digestion. The sweetening agents are aspartame (Asp-Phe; a dipeptide) and acesulfame K. The maltodextrin and dextrose are probably bulking agents to give the product a free-flowing, poweder consistence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;fermentables&quot; in question are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Dextrose. This is another name of glucose, and is the most easily metabolized sugar in the Equal packet.&lt;/li&gt;&#xA;&lt;li&gt;Maltodextrin is an oligomer of D-glucose linked by $\alpha$(1,4) linkages. If this were the disaccharide of glucose-glucose, or maltose, then yeast could readily ferment this. However, yeast cannot hydrolyze maltodextrin and therefore cannot metabolize it.&lt;/li&gt;&#xA;&lt;li&gt;Aspartame is a dipeptide which can easily be fermented.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Therefore, yeast will happily metabolize dextrose and aspartame, but not the other two agents.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2013-12-04T00:11:03.787" LastActivityDate="2013-12-04T00:11:03.787" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13788" PostTypeId="2" ParentId="13785" CreationDate="2013-12-03T22:41:18.227" Score="6" Body="&lt;p&gt;Your sugar substrate was sucrose. Yeast cells metabolise this by secreting an enzyme, invertase, which splits the disaccharide into glucose and fructose both of which can be fermented by yeast to produce CO&lt;sub&gt;2&lt;/sub&gt;.&lt;/p&gt;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.equal.com/equal-original/faqs#classic09&quot; rel=&quot;nofollow noreferrer&quot;&gt;this site&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Equal Original (blue packaging)  is a zero calorie sweetener that contains aspartame and acesulfame potassium as its sweetening ingredients along with a bulking agent.&lt;/p&gt;&#xA;&lt;p&gt;Equal Original PACKETS: dextrose with maltodextrin, aspartame, acesulfame potassium&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This agrees with what you say - that the sweetener that you used contained dextrose - and leaves me very confused. Dextrose is another name for glucose so how can this contain zero calories?&lt;/p&gt;&#xA;&lt;p&gt;The answer lies in &lt;a href=&quot;http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=101.60&quot; rel=&quot;nofollow noreferrer&quot;&gt;the legal definition of zero calories&lt;/a&gt;  = less than 5 calories per serving (presumably per package in this case.) So let's assume that by adding two packs you were adding 8 calories equivalent of glucose.&lt;/p&gt;&#xA;&lt;p&gt;Calorie content of carbohydrate = 4 calories per gram&lt;/p&gt;&#xA;&lt;p&gt;Two packs could contain 8 calories = 2 g glucose.&lt;/p&gt;&#xA;&lt;p&gt;The molecular weight of glucose = 180&lt;/p&gt;&#xA;&lt;p&gt;therefore 2 g = 2/180 moles&lt;/p&gt;&#xA;&lt;p&gt;if completely fermented to CO&lt;sub&gt;2&lt;/sub&gt; each mole -&amp;gt; 6 moles CO&lt;sub&gt;2&lt;/sub&gt;&#xA;12/180 moles CO&lt;sub&gt;2&lt;/sub&gt; = 0.75 litres of CO&lt;sub&gt;2&lt;/sub&gt;.&lt;/p&gt;&#xA;&lt;p&gt;I conclude that there is enough glucose in two packets of Equal to generate a reasonable amount of CO&lt;sub&gt;2&lt;/sub&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Yeast cannot ferment maltodextrins. It is possible that aspartame (aspartyl-phenylalanine-methyl ester) could be metabolised, but I think the dextrose/glucose solution is the best explanation.&lt;/p&gt;&#xA;&lt;p&gt;EDIT:&#xA;I meant to say, just to illustrate that this is a significant amount of glucose, standard rich yeast medium is 2 g glucose /100 ml (2 % w/v).&lt;/p&gt;&#xA;&lt;p&gt;EDIT #2 My back-of-an-envelope calculation has a fundamental error in it, but luckily I am the first to spot it. If glucose is being used fermentatively, then only one third of the carbon will end up in CO&lt;sub&gt;2&lt;/sub&gt;, with the remainder going to ethanol. This means 0.25 litres instead of 0.75 litres. Yeast is so oriented towards fermentation that even in the presence of oxygen the fermentative pathway will dominate.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-12-06T19:47:11.197" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13789" PostTypeId="2" ParentId="13726" CreationDate="2013-12-04T01:30:21.917" Score="2" Body="&lt;p&gt;&lt;strong&gt;Short Answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a nutshell, there are two major differences:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Species range:&lt;/strong&gt; BioGRID integrates multiple species' protein-protein interaction (PPI) data, whereas HPRD focuses mainly on &lt;em&gt;Human&lt;/em&gt; data.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Functionality:&lt;/strong&gt; HPRD has some GUI tools that can interact directly with it's database (e.g. BLAST - for searching proteins and their binding partners via sequence alignment) whereas BioGRID is mostly just a database.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AWiXr.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long Answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;strong&gt;bold&lt;/strong&gt; are the unique features of each database.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.hprd.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;&lt;em&gt;About HPRD:&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Human Protein Reference Database represents a&#xA;  centralized platform to visually depict and integrate information&#xA;  pertaining to &lt;strong&gt;domain architecture, post-translational modifications,&#xA;  interaction networks&lt;/strong&gt; and &lt;strong&gt;disease association&lt;/strong&gt; for each protein in the&#xA;  &lt;strong&gt;human&lt;/strong&gt; proteome. All the information in HPRD has been &lt;strong&gt;manually&#xA;  extracted&lt;/strong&gt; from the &lt;strong&gt;literature&lt;/strong&gt; by expert biologists who read, interpret&#xA;  and analyze the published data. HPRD has been created using an object&#xA;  oriented database in Zope, an open source web application server, that&#xA;  provides versatility in query functions and allows &lt;strong&gt;data to be&#xA;  displayed dynamically.&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;&lt;em&gt;FAQ HPRD:&lt;/em&gt;&lt;/strong&gt; &lt;em&gt;Why did you decide to develop yet another database instead of integrating other existing databases?&quot;&lt;/em&gt;&#xA;  We believe that biological databases are still in their early stages&#xA;  and no protein database can be considered as an established standard.&#xA;  We feel that a variety of databases trying to solve problems in&#xA;  diverse ways provide the biologists the possibility of choosing their&#xA;  favorite. Our approach is radically different from existing databases&#xA;  and we want to offer biologists the possibility of choosing instead of&#xA;  imposing one database by default. Besides, most of the databases are&#xA;  automated and &lt;strong&gt;ours is manually curated to avoid errors&lt;/strong&gt;. We are also&#xA;  trying to &lt;strong&gt;provide information that few other databases provide&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://wiki.thebiogrid.org/doku.php/aboutus&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;&lt;em&gt;About Biogrid:&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Biological General Repository for Interaction Datasets (BioGRID)&#xA;  is a public database that archives and disseminates &lt;strong&gt;genetic&lt;/strong&gt; and&#xA;  protein interaction data from &lt;strong&gt;model organisms&lt;/strong&gt; and humans&#xA;  (thebiogrid.org). BioGRID currently holds over &lt;strong&gt;720,000 interactions&lt;/strong&gt;&#xA;  curated from both &lt;strong&gt;high-throughput datasets&lt;/strong&gt; and &lt;strong&gt;individual focused&#xA;  studies&lt;/strong&gt;, as derived from over &lt;strong&gt;41,000 publications&lt;/strong&gt; in the primary&#xA;  literature. Complete coverage of the &lt;strong&gt;entire literature is maintained&#xA;  for budding yeast (S. cerevisiae)&lt;/strong&gt;, &lt;strong&gt;fission yeast (S. pombe)&lt;/strong&gt; and thale&#xA;  &lt;strong&gt;cress (A. thaliana)&lt;/strong&gt;, and efforts to expand curation across multiple&#xA;  metazoan species are underway. Current &lt;strong&gt;curation drives are focused on&#xA;  particular areas of biology&lt;/strong&gt; to enable insights into &lt;strong&gt;conserved networks&lt;/strong&gt;&#xA;  &lt;strong&gt;and pathways&lt;/strong&gt; that are relevant to &lt;strong&gt;human health&lt;/strong&gt;. The BioGRID 3.2 web&#xA;  interface contains new search and display features that enable rapid&#xA;  queries across multiple data types and sources. BioGRID provides&#xA;  interaction data to several model organism databases, resources such&#xA;  as Entrez-Gene, SGD, TAIR, FlyBase and other interaction&#xA;  meta-databases. The entire BioGRID 3.2 data collection may be&#xA;  downloaded in multiple file formats, including IMEx compatible PSI MI&#xA;  XML. &lt;strong&gt;For developers, BioGRID interactions are also available via a&#xA;  REST based Web Service and Cytoscape plugin.&lt;/strong&gt; All BioGRID documentation&#xA;  is available online in the BioGRID Wiki.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2013-12-04T01:47:46.447" LastActivityDate="2013-12-04T01:47:46.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13790" PostTypeId="1" CreationDate="2013-12-04T02:05:59.877" Score="2" ViewCount="42644" Body="&lt;p&gt;What is the ancestral relationship between &lt;strong&gt;cats&lt;/strong&gt;, &lt;strong&gt;dogs&lt;/strong&gt; and &lt;strong&gt;bears&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I presume they are more closely related to one another than other &lt;a href=&quot;http://en.wikipedia.org/wiki/Paraphyly&quot; rel=&quot;nofollow&quot;&gt;paraphyletic&lt;/a&gt; clades of mammal.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Which came first?&lt;/li&gt;&#xA;&lt;li&gt;What did their common ancestors look like?&lt;/li&gt;&#xA;&lt;li&gt;What are their geographical origins?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2013-12-05T10:34:10.640" LastActivityDate="2015-12-06T12:43:48.200" Title="Cats, Dogs and Bears - how are they related?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;mammals&gt;&lt;phylogenetics&gt;&lt;speciation&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13791" PostTypeId="1" AcceptedAnswerId="13829" CreationDate="2013-12-04T02:22:46.927" Score="7" ViewCount="18905" Body="&lt;p&gt;Only mammals have mammaries and mammary glands.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What evolutionary factors determines the number of mammaries (nipples/teats/breasts) a species has? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it always an even number? &lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2013-12-07T10:44:36.677" LastActivityDate="2017-10-31T17:32:29.113" Title="The number of nipples (breasts) a species has?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;physiology&gt;&lt;mammals&gt;&lt;organs&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13792" PostTypeId="1" AcceptedAnswerId="13794" CreationDate="2013-12-04T03:25:53.000" Score="3" ViewCount="969" Body="&lt;p&gt;Is the ability to roll your tongue or not truly inherited or genetic? What I have gathered from school has been contradicting with evidence I found elsewhere. &lt;/p&gt;&#xA;" OwnerUserId="4929" LastActivityDate="2013-12-04T08:08:23.413" Title="Is tongue rolling genetic?" Tags="&lt;genetics&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13793" PostTypeId="2" ParentId="13784" CreationDate="2013-12-04T07:17:29.550" Score="4" Body="&lt;p&gt;Birds have to learn their song patterns. &#xA;They are able to chirp, but the songs with &quot;meaning&quot; are learned from their parents or whatever they learned to be their &quot;parent&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.summer10.isc.uqam.ca/Page/docs/readings/WHITE_Stephanie/Brainard%20and%20Doupe%20review.pdf&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a paper that related bird song learning to human learning (of speech, for example). &#xA;Birds brought up by parents from another species learned to sing their songs. &#xA;There are many birds that learn to imitate other animals or sounds, so in isolation from all birds they will probably do this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't recall where, but I read a paper once, where little finches brought up by humans developed a song resembling the &quot;Hello there, now there's food&quot;, their caretaker always greeted them with. (Not the speech, but the overall sound pattern.) They might not understand the signals, but they try to communicate nevertheless. Some birds use sound from other species to mock others, scare them off or lure them into thinking they might be more powerful than they are. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Birds brought up in total isolation do sing, but not the typical songs you know from their species. Deaf birds who can't hear themselves, though, do not (always) sing.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-12-04T07:17:29.550" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13794" PostTypeId="2" ParentId="13792" CreationDate="2013-12-04T08:08:23.413" Score="5" Body="&lt;p&gt;I could only find fairly old literature on the subject, so take this with caution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some papers seem to indicate some sort of genetic component to tongue rolling, although the precise molecular basis are not really described (but, again, these are 30-40 years old papers...)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7187238&quot; rel=&quot;noreferrer&quot;&gt;Inheritance of ear wax types, ear lobe attachment and tongue rolling ability.&lt;/a&gt; - Cruz-Gonzalez and Lisker - &lt;em&gt;Acta Anthropogenet.&lt;/em&gt;, &lt;strong&gt;1982&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The mode of inheritance of ear wax type, ear lobe attachment and tongue rolling ability were studied in 77 families with a total of 293 children. The results clearly showed that the dry ear wax type and the attached ear lobe type represent the homozygous state for two pairs of autosomal recessive genes. The evidence for the same being true regarding the lack of ability to roll the tongue was less conclusive in our material, but this could be due to difficulties in communication between the examined individuals and the examiners.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2629620&quot; rel=&quot;noreferrer&quot;&gt;Tongue-rolling phenotypes and geographical variation in the United Kingdom&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The distribution of tongue-rolling phenotypes in a sample (n = 477) of undergraduate students of the University College of Swansea (U.K.) was studied. The birthplaces of these students were also recorded. England was divided into six areas, and Wales was left as an area on its own. The data suggest that those students who come from north-east are more non-rollers, which may be due to mixture with Scandinavians.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3211668&quot; rel=&quot;noreferrer&quot;&gt;Left-handedness and tongue-rolling ability.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;948 undergraduates at The Ohio State University were administered the 10-item Edinburgh Handedness Inventory and asked to indicate the extent to which they could turn up the sides of their tongues. Significantly fewer left-handers than right-handers (62.8% and 74.8%, respectively) reported being able to turn up either or both sides. Sex differences in tongue-rolling ability were also noted. Among the 403 men included in the final sample, 77.4% could roll their tongues, whereas only 69.7% of the 491 women could do so.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This paper, however says (luckily Google finds a &lt;a href=&quot;https://genepi.qimr.edu.au/contents/p/staff/CV003.pdf&quot; rel=&quot;noreferrer&quot;&gt;PDF here&lt;/a&gt;... seriously it should be illegal to have papers from the 70s behind paywalls... but I digress):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://udel.edu/~mcdonald/mythtongueroll.html&quot; rel=&quot;noreferrer&quot;&gt;No evidence for a genetic basis of tongue rolling or hand clasping&lt;/a&gt; - Martin, &lt;em&gt;J Hered.&lt;/em&gt;, &lt;strong&gt;1975&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;OCCASIONALLY one still finds in elementary genetics courses and elsewhere, the ability to roll the tongue and the manner of clasping the hands cited as examples of simply inherited human polymorphisms. This is despite extensive evidence to the contrary that has accumulated over several decades. Sturtevant T found that about 65 percent of persons studied were able to tum 1.JP the edges of the tongue and although some people were able to learn the ability, family data indicated that it was inherited as a simple dominant allele. However, Matlock reported 7 out of 33 monozygotic (MZ) twin pairs discordant for the ability, and Sturtevant concluded that there is sufficient nongenetic inftuence to make the character practically useless as a genetic marker. He confessed to being &quot;still embarrassed to see it listed in some current works as an established Mendelian case.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The paper is also cited in the &lt;a href=&quot;http://udel.edu/~mcdonald/mythtongueroll.html&quot; rel=&quot;noreferrer&quot;&gt;&quot;Myths of Human Genetics&quot;&lt;/a&gt; page of the University of Delaware.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, all in all, it seems that there is evidence against a Mendelian transmission of this character, although these studies are quite old and some further analysis is warranted to exclude non Mendelian (read epigenetic) transmission of tongue rolling.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2013-12-04T08:08:23.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13795" PostTypeId="1" CreationDate="2013-12-04T10:16:15.217" Score="3" ViewCount="653" Body="&lt;p&gt;For example monkeys/apes only eat part of a fruit and then throw the rest. Cats (big and small species) only eat some parts of their prey and then they abandon it.&lt;br&gt;&#xA;Humans on the contrary leave as few leftover as possible.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do we know about the parts that animals eat ? and how do we know it ?&lt;/p&gt;&#xA;" OwnerUserId="5014" LastEditorUserId="5014" LastEditDate="2013-12-04T11:15:02.607" LastActivityDate="2014-08-12T09:20:17.087" Title="Why do animals only eat some parts of their food?" Tags="&lt;food&gt;&lt;ethology&gt;&lt;natural-selection&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13797" PostTypeId="1" AcceptedAnswerId="20245" CreationDate="2013-12-04T11:52:41.493" Score="19" ViewCount="348" Body="&lt;p&gt;The human eye is, very subtly, sensitive to the polarization of light. This is  an effect known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Haidinger%27s_brush&quot;&gt;Haidinger's brush (see Wikipedia article of this name)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What, if anything, is known or at least intelligently speculated about the evolutionary &quot;grounding&quot; for this effect? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way to put this question: &lt;a href=&quot;http://en.wikipedia.org/wiki/Cephalopod_eye&quot;&gt;Some cephalopods&lt;/a&gt; and the &lt;a href=&quot;http://icb.oxfordjournals.org/content/43/4/549.full&quot;&gt;mantis shrimp&lt;/a&gt; have sight that is sensitive to polarization of light and this sense is clearly begotten by evolutionary forces as it helps these animals detect prey and predators. So, is our subtle ability to perceive polarized light a leftover from a genetic forebear that benefitted from this ability? Or is it simply an artifact of the physics of the eye? The physics of Haidinger's brush is quite different from the topology of retinal cells that confers this ability in cephalopods and others I have read about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A second question and related is: what is our nearest common genetic forebear that is known to exploit polarization sensitivity of its sight?&lt;/p&gt;&#xA;" OwnerUserId="5084" LastEditorUserId="1306" LastEditDate="2013-12-04T14:44:46.513" LastActivityDate="2014-08-05T13:46:39.493" Title="Haidinger's brush: Is this a by-product of the eye's physics, or are there any evolutionary grounds for it?" Tags="&lt;evolution&gt;&lt;vision&gt;&lt;perception&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13798" PostTypeId="1" CreationDate="2013-12-04T12:57:38.130" Score="3" ViewCount="29" Body="&lt;p&gt;As we know, when we do qRT-PCR, the two most commonly used methods are absolute quantification and relative quantification, both the methods are involved in dealing with normalization of house-keeping genes or internal control genes (like GAPDH, Actin). In the microarray experiments, the similar normalization should also be adopted (I did not have any experimence with this kind of experiment). But I do know that someone obtained GEO file from NCBI, and simply did t-test analysis to find differenced expressed genes without any operation with the internal control genes. So I wander whether this is the right way, if not, what should we do with internal control genes to normalize data?&lt;/p&gt;&#xA;" OwnerUserId="4677" LastActivityDate="2013-12-04T12:57:38.130" Title="Are there any differences between qRT-PCR and GEO (microarray data from NCBI) regarding dealing with internal control genes?" Tags="&lt;microarray&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13799" PostTypeId="2" ParentId="13777" CreationDate="2013-12-04T13:16:30.283" Score="0" Body="&lt;p&gt;In term of eukaryotic cells, most of them are mortal and will indeed age (the famous telomere sequence for example). However due to mutation some cells do achieve immortality such as HeLa cell line widely used in bio research. &lt;/p&gt;&#xA;" OwnerUserId="5087" LastActivityDate="2013-12-04T13:16:30.283" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13800" PostTypeId="2" ParentId="13716" CreationDate="2013-12-04T13:22:47.107" Score="3" Body="&lt;p&gt;When the pain receptors are fully loaded then it's not possible to excite these receptor greater. However the perception of pain has a large psychological component and is not well understood. Your brain could modulate your perception of pain naturally or due to illness. &lt;/p&gt;&#xA;" OwnerUserId="5087" LastActivityDate="2013-12-04T13:22:47.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13801" PostTypeId="1" CreationDate="2013-12-04T13:26:23.763" Score="1" ViewCount="368" Body="&lt;p&gt;I recently purchased some Maltose Binding Protein and as the name suggests this protein binds to maltose. The problem I have is the protein arrive with maltose bound. I know this through native mass spectrometry analysis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a way of removing the maltose bound to my protein sample while also keeping the protein in its native state?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples of two states from the PDB can be seen here: &lt;a href=&quot;http://www.rcsb.org/pdb/explore/explore.do?structureId=1a7l&quot; rel=&quot;nofollow&quot;&gt;Bound&lt;/a&gt; and &lt;a href=&quot;http://www.rcsb.org/pdb/explore/explore.do?structureId=1omp&quot; rel=&quot;nofollow&quot;&gt;unbound&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="158" LastActivityDate="2013-12-04T13:47:15.313" Title="Removing Sugars Bound to a Protein" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13802" PostTypeId="2" ParentId="13801" CreationDate="2013-12-04T13:47:15.313" Score="1" Body="&lt;p&gt;It's not clear from the question what the biological source of the maltose binding protein (MBP) is. As you may know &lt;em&gt;E. coli&lt;/em&gt; MBP is used as a fusion partner in an expression-purification system marketed by New England Biolabs (this becomes relevant below).&lt;/p&gt;&#xA;&lt;p&gt;My initial thought upon reading your question was to suggest &lt;a href=&quot;http://en.wikipedia.org/wiki/Dialysis_(biochemistry)&quot; rel=&quot;nofollow noreferrer&quot;&gt;dialysis&lt;/a&gt;. However I found some hints online that this might be problematical and eventually &lt;a href=&quot;https://www.neb.com/tools-and-resources/%7E/media/0E935EB84D7E49789325E4E57212D954.ashx&quot; rel=&quot;nofollow noreferrer&quot;&gt;found this on a FAQ at the New England Biolabs site&lt;/a&gt;. Looks like this may be your answer.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;: In order to rebind MBP to the column, the maltose must be removed. Can this be done by dialysis?&lt;/p&gt;&#xA;&lt;p&gt;Dialysis does not work very well to remove maltose from maltose-binding protein. This is a general phenomenon of binding protein/ligand interactions; after the free ligand is gone, ligand that is released from the binding site usually finds another binding site before it encounters the dialysis membrane (28). We have determined empirically that binding the fusion to a chromatography resin and then washing away the maltose is much more effective. We prefer standard chromatography (e.g. DEAE) as the separation step, since it can separate the Factor Xa and MBP from the protein of interest. In case MBP co-elutes with the protein of interest, we include a large volume washing step to remove the maltose before starting the salt gradient. This way, the mixture can be run over an amylose column afterward if necessary.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So, in summary they are suggesting that you bind the protein to an ion exchange column; wash with lots of buffer; then elute the cleaned-up protein (using salt or a change of pH  - you will have to know something about your protein's behaviour on the column to do this).&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-12-04T13:47:15.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13803" PostTypeId="1" AcceptedAnswerId="13804" CreationDate="2013-12-04T16:24:49.560" Score="3" ViewCount="205" Body="&lt;p&gt;How large a garden do you need if you are to survive on them producing enough oxygen in a closed chamber?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And which are the most effective plants?&lt;/p&gt;&#xA;" OwnerUserId="743" LastEditorUserId="743" LastEditDate="2013-12-04T16:46:13.623" LastActivityDate="2013-12-04T17:05:21.073" Title="How many plants are needed to survive in an airtight chamber?" Tags="&lt;botany&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13804" PostTypeId="2" ParentId="13803" CreationDate="2013-12-04T17:05:21.073" Score="5" Body="&lt;p&gt;According to &lt;a href=&quot;http://news.google.com/newspapers?nid=1310&amp;amp;dat=19950809&amp;amp;id=5kZWAAAAIBAJ&amp;amp;sjid=GOsDAAAAIBAJ&amp;amp;pg=5465,1880502&quot; rel=&quot;noreferrer&quot;&gt;this news article&lt;/a&gt;, in a NASA experiment one man survived for 15 days in a sealed chamber containing 30,000 small wheat plants. If you read the article you will find that this did not produce a completely balanced system - some excess oxygen had to be removed, and some extra CO&lt;sub&gt;2&lt;/sub&gt; had to be pumped in. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-12-04T17:05:21.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13806" PostTypeId="1" CreationDate="2013-12-04T18:05:09.350" Score="1" ViewCount="59" Body="&lt;p&gt;I've seen in MIQE guidelines that calibration curves a needed when performing RT-qPCR. I'll use genomic DNA to perform these calibration curves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is that I don't know the range of concentrations to test. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genes I will check for differential expression have logFC between 2-8 (base 2 log). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;50 ng/μL is the sample concentration I will have when performing the Comparative CT Experiment, but 98% is ribosomal RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please let me know you suggestions and possible reference books/papers to revise.&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="4717" LastEditDate="2015-04-17T19:40:25.830" LastActivityDate="2015-04-17T19:40:25.830" Title="RT-qPCR of selected differential expressed genes: which dilutions in calibration curve?" Tags="&lt;pcr&gt;&lt;rna-sequencing&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13807" PostTypeId="1" CreationDate="2013-12-04T18:51:09.430" Score="3" ViewCount="68" Body="&lt;p&gt;It seems like the orange juice thats been sitting in the fridge for awhile always tastes sweeter than the juice just brought from the grocery store. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can juice ripen in the container ? By that I mean, the concentration of fructose and other sugars increases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I remember learning in Bio class that fruit releases a chemical that causes nearby fruit to also ripen faster. I'm not sure of the source of this chemical but my question leads me to believe that it is in the juice itself. &lt;/p&gt;&#xA;" OwnerUserId="5090" LastEditorUserId="5090" LastEditDate="2014-12-11T22:34:23.740" LastActivityDate="2014-12-11T22:34:23.740" Title="Can juice have a higher sugar content after packaging?" Tags="&lt;food&gt;" AnswerCount="0" CommentCount="0" ClosedDate="2014-08-12T05:36:12.277" ContentLicense="CC BY-SA 3.0" />
  <row Id="13808" PostTypeId="1" AcceptedAnswerId="13940" CreationDate="2013-12-04T21:21:50.183" Score="8" ViewCount="2171" Body="&lt;p&gt;I was recently reading about colinearity in the HOX genes that give an organism its high-level body plan (where the order of the HOX genes on the chromosome follow the head-to-tail order of body segments, such that the head gene comes before the thorax gene, comes before the abdomen gene, etc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm really just a layman  interested in this stuff (only completed A &amp;amp; P I), but I was under the impression that the location of genes on a chromosome has no bearing on the expression of those genes or phenotype of the organism -- in other words, that genes can be anywhere on any chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do we understand how the order of the HOX genes ends up being expressed as the order of the body segments? Do we know why the positioning of these genes matters when the order of other genes don't?&lt;/p&gt;&#xA;" OwnerUserId="866" LastEditorUserId="16866" LastEditDate="2019-04-22T19:45:08.573" LastActivityDate="2019-12-26T20:55:23.637" Title="How does the colinearity of the HOX genes determine the body plan of an organism?" Tags="&lt;gene-expression&gt;&lt;genetics&gt;&lt;development&gt;" AnswerCount="3" CommentCount="10" FavoriteCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="13809" PostTypeId="2" ParentId="13777" CreationDate="2013-12-04T22:11:38.727" Score="9" Body="&lt;p&gt;First of all, in eukaryotes (as far as I'm aware), older cells can be distinguished from younger cells due to &lt;a href=&quot;https://en.wikipedia.org/wiki/Telomere&quot;&gt;telomere&lt;/a&gt; shortening, so there is an ageing process. HeLa cells mentioned by @Gary Chou have a more active &lt;a href=&quot;https://en.wikipedia.org/wiki/Telomerase&quot;&gt;telomerase&lt;/a&gt; which mitigates telomere shortening, allowing cells to continue to divide indefinitely. I think it's a very interesting question whether this immortality eliminates any sense of &quot;older&quot; and &quot;younger&quot; cells from in HeLa cell culture. I suspect not, but I am not sure on the specifics. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general this question will depend on how an organism divides (we're going to talk single-celled organisms from now on). For example, the yeast &lt;a href=&quot;https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae#In_the_study_of_aging&quot;&gt;&lt;em&gt;Saccharomyces cerevisiae&lt;/em&gt;&lt;/a&gt; is a budding yeast, which means that it divides by budding a smaller cell off of the larger cell. This clearly allows for an interpretation of &quot;mother cells&quot; and smaller &quot;daughter cells.&quot; Indeed, as lots of research on ageing in &lt;em&gt;S. cerevisiae&lt;/em&gt; has shown, beyond being larger, the mother cell undergoes &lt;strong&gt;replicative ageing&lt;/strong&gt;: over time the mother cell is less capable of growth and division--she gets old!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps the most interesting case of all (and maybe the one you had in mind) is when the organism divides symmetrically, like the bacteria, which undergo &lt;a href=&quot;https://en.wikipedia.org/wiki/Binary_fission#Binary_fission_of_prokaryotes&quot;&gt;binary fission&lt;/a&gt;. For decades, as far as scientists could tell, the two cells that were the product of one bacterium dividing looked identical, and all measurements seemed to indicate that the cells were &quot;sisters,&quot; i.e. exactly the same, both newborn. So if in the right conditions bacteria could continue to divide indefinitely, it seemed that bacteria were immortal, since each division reset the ageing clock for each bacterium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, a seminal study in 2005 &lt;a href=&quot;http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0030045&quot;&gt;(1)&lt;/a&gt; changed this view. The researchers took time-lapse microscope movies of a colony of &lt;em&gt;Escherichia coli&lt;/em&gt; from a single cell. &lt;em&gt;E. coli&lt;/em&gt; is rod-shaped, so when it divides it has to synthesize two new ends or &lt;em&gt;poles&lt;/em&gt;, one for each cell, so just after division each cell has a &quot;new pole&quot; that was made in the process of that division and an &quot;old pole&quot; which had originated before. In this study Stewart &lt;em&gt;et al.&lt;/em&gt; kept track of the old poles in the growing colony, and they defined the age of a cell as the age of its old pole. They found that older cells (i.e. cells with older poles) displayed replicative ageing, just like yeast! They grew more slowly and were less capable of dividing. This was examined rigorously by Wang &lt;em&gt;et al.&lt;/em&gt; &lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822%2810%2900524-5&quot;&gt;(2)&lt;/a&gt; in a &quot;mother machine&quot; in which bacteria were able to grow in constant nutrient conditions (by flowing fresh media across them) in dead-end channels. The cell at the dead-end of the channel always inherited the old pole, and so was a &quot;mother&quot; to all future cells. They found that, while a cell line was able to grow for very long periods of time completely stably, after hundreds of generations there was an increased likelihood for the cells to display signs of stress. They attributed to the accumulation of toxic factors in the mother cell over time. So even in cells dividing by binary fission, there appears to be some difference between the two cells arising from the division, depending on how old the pole that they inherit is. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These effects in bacteria are small, and require watching many generations to reveal. Even in light of these results many researchers will still call the &quot;mother&quot; cell the cell about to divide and the &quot;daughter cells&quot; the cells that result from division, implying that there is no difference between &quot;daughters.&quot; Stewart &lt;em&gt;et al.&lt;/em&gt; claim that on the basis of their work this conception of bacterial division must be revised, and that instead of division producing two identical daughters, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the old pole cell should be considered an aging parent repeatedly producing rejuvenated offspring. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Furthermore, they add a nice philosophical touch to their findings:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These results suggest that no life strategy is immune to the effects of aging, and therefore immortality may be either too costly or mechanistically impossible in natural organisms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0030045&quot;&gt;(1): Stewart EJ et al. (2005) Aging and Death in an Organism That Reproduces by Morphologically Symmetric Division. &lt;em&gt;PLoS Biol.&lt;/em&gt; 3(2): e45&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822%2810%2900524-5&quot;&gt;(2): Wang P et al. (2010) Robust Growth of &lt;em&gt;Escherichia coli&lt;/em&gt;. &lt;em&gt;Curr. Biol.&lt;/em&gt; 20(12): 1099-1103.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2013-12-04T22:11:38.727" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13810" PostTypeId="1" AcceptedAnswerId="13815" CreationDate="2013-12-04T23:00:46.197" Score="0" ViewCount="270" Body="&lt;p&gt;I am sure many of us know the feeling of that tingling chill down our spines when listening to certain music. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I experienced this most when my younger brother played an emotional piano piece for a talent show (brought me to tears). &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What causes that? &lt;/li&gt;&#xA;&lt;li&gt;Is music the only stimulus to elicit that spine-tingling? &lt;/li&gt;&#xA;&lt;li&gt;And in terms of evolution, why?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2013-12-17T02:18:28.743" LastActivityDate="2014-02-20T13:20:38.360" Title="Chills down the spine with certain music?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;behaviour&gt;&lt;sensation&gt;&lt;hearing&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13812" PostTypeId="1" CreationDate="2013-12-05T00:53:53.560" Score="4" ViewCount="1496" Body="&lt;p&gt;I have read about Rhesus D Hemolytic Disease of the Newborn, sometimes called &quot;Rh disease&quot;. It's rare, but it can happen when an Rh+ baby is conceived by an Rh- mother.  This raises many questions. I have heard this problem only happens with humans; if so, why doesn't it affect other mammals like Rhesus monkeys?  Where along the evolutionary time-line did Rh disease come about in the first place?&lt;/p&gt;&#xA;" OwnerUserId="5092" LastEditorUserId="12995" LastEditDate="2015-01-14T00:28:25.423" LastActivityDate="2015-01-14T00:28:25.423" Title="Why isn't Rh disease present in other mammals?" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;human-genetics&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13815" PostTypeId="2" ParentId="13810" CreationDate="2013-12-05T07:17:43.280" Score="3" Body="&lt;p&gt;It is called a frisson, and actually, there has been a study about it, available &lt;a href=&quot;http://www.cogsci.msu.edu/DSS/2008-2009/Huron/HuronFrisson.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&#xA;The frisson is kind of the same you get from cold weather, fear, or... well, other things not suitable to discuss if not knowing how old people reading this might be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually, they found that this works best if you include familiarity. In their case, asking study participants to bring their favourite emotional music, in you case hearing it played by your brother.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How this evolutionary came by is unclear. But as it resembles the shivers you would call &quot;a tingling sense of danger&quot; it might stem from a reaction to uncertainty or at least unclear danger. In this case, it is meant to enable you to concentrate on whatever is coming, and maybe (but that's one of my own theories) this is how it came to connect to pleasant emotions as well: You want to be able to concentrate, delve into the emotion. This could explain, why it works best with familiar pieces: you already know that you want to listen closely.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-12-05T07:17:43.280" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13816" PostTypeId="2" ParentId="13790" CreationDate="2013-12-05T09:44:51.693" Score="6" Body="&lt;p&gt;Cats, dogs and bears all belong to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Carnivora&quot;&gt;Carnivora&lt;/a&gt; clade of mammals, but they are not the only ones belonging to this clade.&#xA;For instance, cats are more closely related to mongoose and hyenas than to dogs or bears, who in turn are more closely related to raccoons, weasels, and walruses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their common ancestors likely displayed various adaptations to a carnivorous diet, as the name of the clade suggests, and which are still present in many extant Carnivora (the panda being a well-known exception).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Together with many other groups of mammals, Carnivora are part of a clade named &lt;a href=&quot;http://en.wikipedia.org/wiki/Laurasiatheria&quot;&gt;Laurasiatheria&lt;/a&gt; thus named because they may have originated in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Laurasia&quot;&gt;Laurasia&lt;/a&gt; supercontinent, which comprises nowadays north America and Eurasia.&lt;/p&gt;&#xA;" OwnerUserId="1486" LastActivityDate="2013-12-05T09:44:51.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13817" PostTypeId="1" CreationDate="2013-12-05T13:03:49.923" Score="2" ViewCount="163" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is quite mind boggling to imagine what it would be like to be missing sight, sound, touch, smell, taste etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Which organism holds the record for most extreme sensory limits for: sight, smell and sound? (one for each)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This would help give an idea of the &quot;biological limits&quot; of sense.&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2013-12-06T10:45:50.920" LastActivityDate="2013-12-06T10:45:50.920" Title="Organisms with the most extreme sensory capabilities? (sight, smell, sound)" Tags="&lt;neuroscience&gt;&lt;zoology&gt;&lt;neuroanatomy&gt;&lt;sensation&gt;&lt;perception&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2013-12-06T16:28:40.557" ContentLicense="CC BY-SA 3.0" />
  <row Id="13818" PostTypeId="2" ParentId="13539" CreationDate="2013-12-05T15:07:10.793" Score="2" Body="&lt;p&gt;Echoing what was already mentioned: the DNA sequence directly affects the ability to bind sigma factors (&lt;a href=&quot;http://en.wikipedia.org/wiki/Sigma_factor&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Sigma_factor&lt;/a&gt;). Sequence --&gt; bonding --&gt; how often sigmas bind and for how long they bind --&gt; initiation of transcription&lt;/p&gt;&#xA;" OwnerUserId="5098" LastActivityDate="2013-12-05T15:07:10.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13819" PostTypeId="1" AcceptedAnswerId="13948" CreationDate="2013-12-05T15:37:14.393" Score="6" ViewCount="289" Body="&lt;p&gt;Today a colleague of mine asked the following question:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&amp;quot; Assuming I need to build from 0, a chromosome of a fish, with short reads&#xA;but no other reference whatsoever &lt;strong&gt;[de novo assembly]&lt;/strong&gt;:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;how much work is that?&lt;/li&gt;&#xA;&lt;li&gt;Is there a generic software (like SAMtools) that will align the reads in a&#xA;scaffold one can use?&lt;/li&gt;&#xA;&lt;li&gt;Basically, given a reasonably clear pipeline in terms of software, is it still blood sweat and tears or is it just a matter of getting it on a cluster?&amp;quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Very grateful for any suggestions, sources of information, software etc.&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-12-12T19:34:34.323" Title="How easy is it to carry out de novo sequence assembly?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;software&gt;&lt;sequence-assembly&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13821" PostTypeId="2" ParentId="13743" CreationDate="2013-12-05T16:19:51.007" Score="1" Body="&lt;p&gt;Another important point is that we almost always sequence a population of cells, not just a single cell. Cancer cell populations, for example, can have multiple sub-populations of cells with different genetics (subclones). Deep read sequencing allows us to see this heterogeneity, and also measure the abundance of each sub-clone. Even with a single cell, we can see the abundance of different alleles... Usually 50-50 in normal cells, but can get pretty crazy in cancer.&lt;/p&gt;&#xA;" OwnerUserId="3597" LastActivityDate="2013-12-05T16:19:51.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13822" PostTypeId="1" CreationDate="2013-12-05T17:06:13.167" Score="2" ViewCount="328" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Why does low Na&lt;sup&gt;+&lt;/sup&gt; levels cause hypotension (low blood pressure).&#xA;  Alternatively, why does excessive intake of Na&lt;sup&gt;+&lt;/sup&gt; cause&#xA;  hypertension or high blood pressure?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From what I understand, there are two different mechanisms at play. &lt;a href=&quot;http://en.wikipedia.org/wiki/Renin#Secretion&quot; rel=&quot;nofollow noreferrer&quot;&gt;Renin&lt;/a&gt; secretion from kidneys occur during low salt levels in blood and hence, under low sodium concentration, high amount of Renin secretion from kidneys should actually raise the blood pressure, via the Renin-Angiotensin loop, constricting the arteries. Under high sodium concentrations, low renin secretion should be accompanied by low pressure. &lt;a href=&quot;https://biology.stackexchange.com/questions/5088/how-does-sodium-in-ones-diet-affect-blood-pressure&quot;&gt;If the osmotic entry of water into blood raising the blood volume&lt;/a&gt; and thus pressure, plays a role here, will not, on increase of blood volume, decreased &lt;a href=&quot;http://en.wikipedia.org/wiki/Vasopressin&quot; rel=&quot;nofollow noreferrer&quot;&gt;Vasopressin&lt;/a&gt; increase urinary output and thus control the blood volume, not allowing it to cause any body changes? Why isn't the first effect (renin) significant here as compared to the second (osmotic entry).&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-12-03T16:53:00.507" Title="Sodium levels and blood pressure" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;endocrinology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13823" PostTypeId="1" CreationDate="2013-12-05T17:11:34.453" Score="2" ViewCount="9766" Body="&lt;p&gt;A common fact is that Ammonia, Urea and Uric acid are the most common excreted metabolites and their removal needs varying amount of water, highest for ammonia (hence suited only for aquatic animals) and lowest for uric acid (suited for desert animals). Why is this so? Is it because of different solubility of these compounds in water or their toxicity? If it is the latter, how would excess water reduce the toxicity of a compound? This is a bit over-simplistic question, but I want to understand the tradeoffs involved in selecting the mode of excretion, ammonotelic, ureotelic, uricotelic.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2017-12-14T09:01:46.150" Title="Excretion of various wastes and water requirement" Tags="&lt;biochemistry&gt;&lt;zoology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13824" PostTypeId="2" ParentId="10945" CreationDate="2013-12-05T21:02:06.810" Score="1" Body="&lt;p&gt;This is sort of technical answer, but I hope its helpful I hope. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All these bands in the sarcomere are anisotropic.  Isotropy would imply that the structure/properties of something is equally ordered or coherent in all 3 directions.  The sarcomere has definite structure along its longer axis so the H band is anisotropic.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the H band is a small structure compared to the actin and myosin components of the sarcomere, much of the signal that one measures via diffraction or polarization experiments is from those two fibers and less information would be discernible from the anchoring portion (H band) of the myosin filament.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of the A and H bands, which are identified by electron microscopy, the structure along the sarcomere axis is not very strong - they are thin sections of the sarcomere and tend to function structurally to connect the actin and myosin axes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of this the information that you might get from A and H band segment studies will be that 'these bands are not very ordered along the axis of the sarcomere'.  That's not a lot of information, and we know this from other experiments.  But it is information nonetheless because they have some spatial organization. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-01-07T21:03:53.530" LastActivityDate="2014-01-07T21:03:53.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13825" PostTypeId="1" CreationDate="2013-12-05T23:24:09.940" Score="0" ViewCount="2749" Body="&lt;p&gt;In fruit flies, red eyes are dominant over white eyes. Show a cross between two white-eye fruit flies.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do I know if the white-eye fruit flies are homozygous or heterozygous?&lt;/p&gt;&#xA;" OwnerUserId="5106" LastEditorUserId="1590" LastEditDate="2013-12-06T08:10:19.153" LastActivityDate="2018-07-27T10:59:31.360" Title="Punnett Square Help" Tags="&lt;homework&gt;&lt;gene-expression&gt;" AnswerCount="5" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13827" PostTypeId="2" ParentId="13825" CreationDate="2013-12-06T00:29:08.357" Score="1" Body="&lt;p&gt;Because red is &lt;strong&gt;dominant&lt;/strong&gt; over white, in order for the flies to express the &lt;strong&gt;recessive&lt;/strong&gt; white eye trait they &lt;em&gt;must&lt;/em&gt; be homozygous for the recessive white allele - I.e (no pun intended) &lt;code&gt;rr&lt;/code&gt;. &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2013-12-06T00:29:08.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13828" PostTypeId="2" ParentId="13554" CreationDate="2013-12-06T01:54:16.403" Score="2" Body="&lt;p&gt;Many studies, including those of Hayflick himself, have found a strong correlation between a species' Hayflick limit and its maximum lifespan. For example, Galapagos tortoises, which can live over a century, have a Hayflick limit of 90-125, and mice, which live only a few years, have a Hayflick limit of 14-28.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the mechanism connecting the maximum number of cell divisions and maximum lifespan is not entirely clear. Cell division is associated much more with growth and development than with the maintenance of mature tissues. Cells that have stopped dividing can be perfectly functional for decades. Cells that &lt;strong&gt;don't&lt;/strong&gt; stop dividing are called &quot;cancer&quot;. So, while the correlation is strong, the reason for the correlation remains something of a mystery.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rose, Michael R. 2005. The Long Tomorrow: How Advances in Evolutionary Biology Can Help us Postpone Aging. Oxford University Press, New York. pp 20-23&lt;/p&gt;&#xA;" OwnerUserId="4342" LastActivityDate="2013-12-06T01:54:16.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13829" PostTypeId="2" ParentId="13791" CreationDate="2013-12-06T02:33:41.403" Score="9" Body="&lt;p&gt;The number of mammary glands a species has is related to litter size. The relationship generally follows the &quot;one-half rule,&quot; which states that the average litter size is equal to half the number of mammaries. The number of mammaries also tends to put an upper limit on litter size. It's not necessarily a hard limit, but survival tends to drop noticeably when number of offspring being nursed exceeds number of mammaries.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The number of mammaries is almost always even, but a notable exception is the Virginia possum, which has thirteen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gilbert, A.N. 1986. Mammary number and litter size in Rodentia: The &quot;one-half rule&quot;. Proc. Natl. Acad. Sci. USA. Vol. 83, pp. 4828-4830.&lt;/p&gt;&#xA;" OwnerUserId="4342" LastActivityDate="2013-12-06T02:33:41.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13830" PostTypeId="2" ParentId="13825" CreationDate="2013-12-06T03:34:35.557" Score="2" Body="&lt;p&gt;In order for any recessive trait to be expressed, it must be homozygous for that recessive trait. If an individual was heterozygous, the recessive allele would be masked by the dominant allele, giving it the dominant phenotype. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, since white eyes are recessive, fruit flies with white eyes will always be homozygous (aa) for that recessive trait. A fruit fly that is heterozygous (Aa) for this trait would have red eyes.&lt;/p&gt;&#xA;" OwnerUserId="4929" LastActivityDate="2013-12-06T03:34:35.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13831" PostTypeId="1" CreationDate="2013-12-06T04:10:04.477" Score="2" ViewCount="298" Body="&lt;p&gt;Can someone please help me with the following questions. I've written my specific questions right after the text question.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Human immunodeficiency virus (HIV) is a retrovirus. Its genome is a single (+) stranded RNA that is packaged with the reverse transcriptase enzyme within a protein capsid. This is further packaged into an envelope that is derived from the plasma membrane of the host cell in which the virus had replicated. The surface of the envelope is covered with the envelope glycoprotein, called gp120 &amp;amp; gp41. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) HIV specifically infects the T-helper (TH) cells of the human immune system. If the HIV enters the host cell by means of host receptor recognizing a viral protein, what would be the most likely ligand and its corresponding receptor during HIV infection? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) Some individuals are resistant to HIV infection even after repeated exposure. Assuming that these individuals express a normal level of the functional receptor that you have recognized above, how can you explain their resistance to HIV? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;c) In recent years, therapies have been developed to fight AIDS using nucleotide analogs. The drug used to combat AIDS is Azidothymine (AZT). The structure of AZT is very similar to thymidine except that in AZT, the 3’-OH group on the deoxyribose sugar is replaced by an azido (N3) group. Which process of the life cycle of HIV do you think is inhibited by AZT? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;d) Combination therapy is the new treatment strategy for treating HIV patients. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;i. Why is combination therapy more successful in preventing the emergence of the disease resistant clones? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ii. If the combination therapy involves a drug that prevents… &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) HIV binding to the target cell, what protein does this target? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Integration of HIV genome into host cell genome, what protein does this target? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) The cleaving of viral polypeptide into individual proteins, what protein does this target? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;e) If the AIDS patient were given combination therapy, would the patient still be able to transmit the HIV virus to his/ her partner (Yes/ No)? Explain your choice. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;**&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) No idea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) Maybe their T-helper cells have some sort of mutation that makes it impossible for HIV to bind to them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c) I'm thinking &quot;formation of HIV RNA&quot; because in the absence of 3' -OH bonds, phosphodiester bonds cannot form.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;d) &#xA;    i. It kind of makes sense because a virus being resistant to multiple drugs would be very unlikely but maybe there's some definite reason why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ii. No clue. Is this talking about proteins of the virus or of the host? Also, enzymes are also proteins, right?&lt;/p&gt;&#xA;" OwnerUserId="5109" LastEditorUserId="107" LastEditDate="2014-03-08T21:02:04.173" LastActivityDate="2014-07-27T04:32:55.653" Title="How HIV Affects and Its Treatment using Combination Therapy" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;homework&gt;&lt;microbiology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13832" PostTypeId="1" AcceptedAnswerId="13833" CreationDate="2013-12-06T05:37:36.337" Score="1" ViewCount="3147" Body="&lt;p&gt;Both names are widely used, with what appears to me as a slight prevalence of “epinephrine” in scientific literature and an overwhelming prevalence of “adrenaline” in popular media.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any well-documented and/or well-motivated guidelines for the usage of these terms?&lt;/p&gt;&#xA;" OwnerUserId="4795" LastActivityDate="2015-06-28T20:47:24.423" Title="Epinephrine vs. Adrenaline" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;&lt;nomenclature&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13833" PostTypeId="2" ParentId="13832" CreationDate="2013-12-06T05:47:30.297" Score="5" Body="&lt;p&gt;Apparently I asked too soon. Summarizing my recent findings, I conclude that &lt;strong&gt;adrenaline&lt;/strong&gt; is the better term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be more explicit, here is why:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The US National Library of Medicine &lt;a href=&quot;http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html&quot; rel=&quot;nofollow&quot;&gt;recommends “epinephrine”&lt;/a&gt;, this is however mainly due to historical reasons (adrenaline used to be a trademark name in the USA).&lt;/li&gt;&#xA;&lt;li&gt;This &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1127537/&quot; rel=&quot;nofollow&quot;&gt;quite comprehensive paper on the issue&lt;/a&gt; presents a series of arguments for the use of “adrenaline”. These include: Better compatibility with other languages (where epinephrine is not at all in use); Better integration with other biological terms (adrenergic receptors, adrenal gland, adrenectomy, etc.); Better historical accuracy (epinephrine used to be the name for a neurochemically inactive crude extract from the adrenal glands).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I find the arguments of the referenced publication convincing, though I would recomend you read them in full. &lt;/p&gt;&#xA;" OwnerUserId="4795" LastEditorUserId="4795" LastEditDate="2015-06-28T20:47:24.423" LastActivityDate="2015-06-28T20:47:24.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13834" PostTypeId="1" AcceptedAnswerId="13840" CreationDate="2013-12-06T06:37:05.940" Score="5" ViewCount="1205" Body="&lt;p&gt;The title pretty much says it all. It is widely taught that a gene in a eukaryotic system could produce more than one protein due to post-transcriptional modification, but I do not believe I have come across any specific examples of this. Are any such systems known? Or is this more theoretical? &lt;/p&gt;&#xA;" OwnerUserId="3514" LastEditorUserId="5005" LastEditDate="2013-12-07T14:39:04.140" LastActivityDate="2014-02-21T23:28:33.043" Title="What are some examples of genes that code for multiple proteins?" Tags="&lt;proteins&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;splicing&gt;&lt;protein-expression&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13835" PostTypeId="2" ParentId="13834" CreationDate="2013-12-06T07:12:38.057" Score="6" Body="&lt;p&gt;There are a large number of ways a protein variant can be produced by post translational modification.  The question may seem obvious, but its really quite broad. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can start this out.  I doubt I know all the ways a single transcript can produce variant proteins.   A detailed description might be more like a review article than an answer here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, there are very rare cases of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9699460&quot;&gt;eukaryotic polycistronic mRNA&lt;/a&gt;: mRNA which code for more than one protein.  In this case, after translation, the mRNA are processed to make multiple monocistronic RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there are proteins with molecules added by covalent bonding to the protein.  Glycoproteins are notoriously variable. Many other small molecules can be bonded to a protein to make a variant of this sort: ubiquitinization, N-acetylation, SUMO domains, lysine methylation are just a few of the more common covalent modifications of proteins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are RNA editing which removes some of the coding RNA to make alternative splice RNA.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The list goes on and on. So does any of this come close to what you wanted to know? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-12-06T07:12:38.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13836" PostTypeId="2" ParentId="13825" CreationDate="2013-12-06T08:15:30.893" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;In fruit flies, red eyes are dominant over white eyes. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Red is dominant (&lt;code&gt;A&lt;/code&gt;) which means we can deduce that white is recessive (&lt;code&gt;a&lt;/code&gt;). Therefore &lt;code&gt;AA&lt;/code&gt; individuals are red eye, and so to are &lt;code&gt;Aa&lt;/code&gt; because the dominant red allele overrides the white recessive allele. Then the only way a fly can be white eyed is with &lt;code&gt;aa&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Show a cross between two white-eye fruit flies.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Both white eyed flies are &lt;code&gt;aa&lt;/code&gt; so all four possible outcomes are &lt;code&gt;aa&lt;/code&gt; in a single locus punnet square.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2013-12-06T08:15:30.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13837" PostTypeId="2" ParentId="13823" CreationDate="2013-12-06T09:06:57.333" Score="2" Body="&lt;p&gt;Ammonia is more water soluble and also more toxic than either urea or uric acid but it is energetically less expensive. So, in regions where deficiency of water is not a problem, ammonia is an excretory product. Where water is scarce urea or uric acid is the excretory product but it is energetically more expensive to manufacture them. So, you can see an obvious trade off between energy expenditure and water conservation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can refer to any introductory biology book like campbell for further reading.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE : &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ammonia    : Most toxic , Easily Soluble , Less Energy Requirement&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Urea       :Moderately toxic , Moderately soluble , More energy requirement(As needed to be processed from ammonia&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Uric Acid:Least toxic , Least soluble , Highest energy requirement ( As needed to be processed from ammonia )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is obvious now what tradeoffs are involved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only tradeoff not deducible from above is that of the eggs/youngs. In birds, eggs are not permeable for water so the best option is to excrete waste in form of uric acid so that high concentration of waste does not build up. Uric acid is excreted in form of solid palette which can stay in the egg without any harm. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can also think of tadpoles which live exclusively in water and so they excrete ammonia but the frogs live both in land and water and so while on land they excrete urea as dessication is the main problem there.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-12-07T08:38:57.537" LastActivityDate="2013-12-07T08:38:57.537" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="13838" PostTypeId="1" AcceptedAnswerId="13845" CreationDate="2013-12-06T11:17:16.077" Score="3" ViewCount="281" Body="&lt;p&gt;Can overly bright artificial light harm plants? Is it possible to achieve a level of brightness so high that it does more harm than good to plants? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If sunlight can be filtered of infrared light spectrum, so the plants don't burn from high temperature, but if it's possible, then that too.&lt;/p&gt;&#xA;" OwnerUserId="1373" LastEditorUserId="184" LastEditDate="2013-12-06T17:07:33.243" LastActivityDate="2013-12-06T17:17:43.383" Title="Is there a limit to acceptable brightness for plants?" Tags="&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13839" PostTypeId="2" ParentId="13825" CreationDate="2013-12-06T11:56:17.097" Score="3" Body="&lt;p&gt;Just to add an extended perspective to all of the answers submitted so far. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The classic white-eye phenotype in &lt;em&gt;Drosophila&lt;/em&gt; is associated with a gene, &lt;em&gt;white&lt;/em&gt; (or &lt;em&gt;w&lt;/em&gt;) that is carried on the X chromosome (females XX, males XY) i.e. it is a sex-linked phenotype. Male white-eyed flies are therefore technically not homozygous, they are hemizygous since they only have one X chromosome and thus one copy of the gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other white-eyed phenotypes due to segregation of two genes (brown and scarlet) - this is the standard two-factor cross example in many genetics courses. In this case (no sex linkage is involved) a white-eyed fly is homozygous for the recessive allele at both loci.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-12-06T11:56:17.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13840" PostTypeId="2" ParentId="13834" CreationDate="2013-12-06T13:13:14.407" Score="5" Body="&lt;p&gt;The answer is not simple - @shigeta mentioned a few mechanisms leading to single gene-to-multi protein relationships - and the answer is certainly not short (there are thousands of these genes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But anyway &quot;alternative splicing&quot; seems to be the primary mechanism according to &lt;a href=&quot;http://www.nature.com/nature/journal/v456/n7221/edsumm/e081127-07.html&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;this article&lt;/strong&gt;&lt;/a&gt;, so rather than listing all alternatively splicing genes, here are the databases (+links):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Alternative splicing gene database (click on blue for link):&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://www.genebee.msu.su/edas/index.html&quot; rel=&quot;nofollow&quot;&gt;EDAS&lt;/a&gt;:&lt;/strong&gt; EST derived alternative splicing database&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://genome.imim.es/cgi-bin/u12db/u12db.cgi&quot; rel=&quot;nofollow&quot;&gt;U12DB&lt;/a&gt;:&lt;/strong&gt; A database of U12 spliceosomal introns&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://www.fast-db.com/fastdb2/frame.html&quot; rel=&quot;nofollow&quot;&gt;FASTdb&lt;/a&gt;:&lt;/strong&gt; Friendly Alternative Splicing and Transcript database&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://bip.umiacs.umd.edu:8080&quot; rel=&quot;nofollow&quot;&gt;BIPASS&lt;/a&gt;:&lt;/strong&gt; Bioinformatics Pipeline for Alternative Splicing&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://www.bioinformatics.ucla.edu/ASAP2&quot; rel=&quot;nofollow&quot;&gt;ASAP II&lt;/a&gt;:&lt;/strong&gt; Alternative Splicing Database&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://www.ebi.ac.uk/astd/main.html&quot; rel=&quot;nofollow&quot;&gt;ASTD&lt;/a&gt;:&lt;/strong&gt; Alternative Splicing and Transcript Diversity database&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://jbirc.jbic.or.jp/h-dbas&quot; rel=&quot;nofollow&quot;&gt;H-DBAS&lt;/a&gt;:&lt;/strong&gt; Human database of alternative splicing&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://hollywood.mit.edu&quot; rel=&quot;nofollow&quot;&gt;Hollywood&lt;/a&gt;:&lt;/strong&gt; Alternatively spliced mRNA database&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://genome.ewha.ac.kr/ECgene&quot; rel=&quot;nofollow&quot;&gt;Ecgene&lt;/a&gt;:&lt;/strong&gt; Genome annotation for alternative splicing&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://discover.nci.nih.gov/spliceminer&quot; rel=&quot;nofollow&quot;&gt;SpliceMiner&lt;/a&gt;:&lt;/strong&gt; Collection of splice variants for human genes&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2014-02-21T23:28:33.043" LastActivityDate="2014-02-21T23:28:33.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13841" PostTypeId="1" AcceptedAnswerId="13844" CreationDate="2013-12-06T14:30:32.963" Score="6" ViewCount="373" Body="&lt;p&gt;When the telomerase enzyme is not active the telomere shortens every time the cell duplicates leading to a reproductive limit (&lt;a href=&quot;http://en.wikipedia.org/wiki/Hayflick_limit&quot; rel=&quot;nofollow&quot;&gt;Hayflicks limit&lt;/a&gt;).&#xA;On one hand this is a believed reason for aging. On the other hand this makes a mutated cell more difficult to acquire cancer, since in order to become cancerous, it would need to mutate such that the telomere enzyme becomes active.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The telomere enzyme is not active in most human cells.&#xA;Therefore activating the telomerase enzyme in somatic (body) cells could theoretically decrease aging but would also increase the risk of cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I right to assume that in order to avoid aging of humans one would first need to &quot;solve cancer&quot;?&lt;/p&gt;&#xA;" OwnerUserId="5049" LastEditorUserId="5005" LastEditDate="2014-03-18T09:54:04.350" LastActivityDate="2019-05-12T18:35:22.790" Title="Is solving cancer required in order to avoid aging?" Tags="&lt;human-biology&gt;&lt;dna&gt;&lt;cancer&gt;&lt;senescence&gt;&lt;telomere&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13842" PostTypeId="2" ParentId="13834" CreationDate="2013-12-06T14:42:31.700" Score="4" Body="&lt;p&gt;Just for balance, &lt;a href=&quot;http://www.pnas.org/content/95/16/9226&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; is an example of a single protein being constructed from two primary gene products (two separate genes involved) via protein splicing.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-12-06T14:42:31.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13844" PostTypeId="2" ParentId="13841" CreationDate="2013-12-06T16:57:17.580" Score="9" Body="&lt;p&gt;Interesting question. My answer is no, but it requires a rather science-fiction style answer - at least it's beyond current technology, but here goes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My Assumptions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I make the simplifying assumption that ageing is only related to telomere length. Thus by &quot;avoid ageing&quot; I assume you mean &quot;avoid telomere shortening&quot;. Also to clarify things for others, I'll clear up the role of telomeres in aging and cancer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1722017&quot; rel=&quot;nofollow&quot;&gt;Telomeres in cancer&lt;/a&gt;&lt;/em&gt;&lt;/strong&gt; - it has been hypothesised that telomeres act as &quot;mitotic clocks&quot; - keeping track of how many times a cell can divide before it stops. This &quot;time limit&quot; is supposed to put a halt to cancerous cells before becoming malignant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;&lt;a href=&quot;http://learn.genetics.utah.edu/content/begin/traits/telomeres/&quot; rel=&quot;nofollow&quot;&gt;Telomeres in aging&lt;/a&gt;&lt;/em&gt;&lt;/strong&gt; - Since telomeres set a limit to the number of times a cell can divide this essentially sets a time limit for the organism as a whole - those cells that divide faster (e.g. hair and skin cells) go out first (grey hair and wrinkles) etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All we need to do is come up with a way to somehow &quot;maintain&quot; average telomere length at some &quot;safe&quot; length, i.e. we keep them at a length that is long enough to prevent us from aging but short enough so that a cancerous cell will not be able to proliferate to dangerous numbers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, every now and then we provide &quot;telomere length booster jabs&quot; (this is some abstract fictional idea of course). This is like adding more time to our lives when we are about to run out: &quot;Oh look, I only have three months left!&quot;, &quot;Don't you worry, with our new telomere booster jab you will have an extra 3 months!&quot;... &lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2014-03-21T19:25:26.557" LastActivityDate="2014-03-21T19:25:26.557" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13845" PostTypeId="2" ParentId="13838" CreationDate="2013-12-06T17:17:43.383" Score="4" Body="&lt;p&gt;The wikipedia page on &lt;a href=&quot;https://en.wikipedia.org/wiki/Photosynthetic_efficiency&quot; rel=&quot;nofollow&quot;&gt;photosynthetic efficiency&lt;/a&gt; has some useful insight here:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Photosynthesis increases linearly with light intensity at low intensity, but at higher intensity this is no longer the case. Above about 10,000 lux or ~100 watts/square meter the rate no longer increases. Thus, most plants can only utilize ~10% of full mid-day sunlight intensity. &lt;a href=&quot;https://en.wikipedia.org/wiki/Photosynthetic_efficiency#cite_note-HallAndRao-5&quot; rel=&quot;nofollow&quot;&gt;(5)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If photosynthesis is inefficient, excess light energy must be dissipated to avoid damaging the photosynthetic apparatus. Energy can be dissipated as heat (non-photochemical quenching), or emitted as chlorophyll fluorescence.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, briefly, yes. Too much light can harm plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer the second question: yes, there exist filters for a large variety of wavelengths of light. You could certainly filter out infrared light, just as most sunglasses filter out some UV light wavelengths. However, just filtering out infrared light would not filter out all photons that could cause damage; likewise, all wavelengths of light have the capacity to heat up what they hit, not just infrared wavelengths.&lt;/p&gt;&#xA;" OwnerUserId="184" LastActivityDate="2013-12-06T17:17:43.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13846" PostTypeId="1" CreationDate="2013-12-06T17:41:57.123" Score="3" ViewCount="719" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from being able to sense color, &lt;a href=&quot;http://en.wikipedia.org/wiki/Cone_cell&quot; rel=&quot;nofollow&quot;&gt;cone cells&lt;/a&gt; are able to perceive finer detail and more rapid changes in images, because their response times to stimuli are faster than those of rods. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Fovea_centralis&quot; rel=&quot;nofollow&quot;&gt;fovea centralis&lt;/a&gt; is where cone cells are most concentrated and is responsible for sharp central vision (foveal vision), which is necessary in humans for reading, driving, and any activity where visual detail is of primary importance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is hard to imagine what it would be like to be missing the fovea centralis, and even harder to imagine what it would be like to have one the size of the entire retina! In any case it seems that having a bigger fovea centralis would be beneficial for survival, so why do we have so much peripheral vision?&lt;/p&gt;&#xA;" OwnerUserId="5005" LastActivityDate="2014-03-08T20:00:28.673" Title="Why don't we have more cone cells (bigger fovea)?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;eyes&gt;&lt;vision&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13847" PostTypeId="2" ParentId="13699" CreationDate="2013-12-06T17:49:21.027" Score="0" Body="&lt;p&gt;There are a few techniques available for this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some recommend a urea-based technique, others recommend a chloroform. Do you have more information about your specific needs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.omicsonline.com/ArchiveJPB/2010/July/03/JPB-03-212.php&quot; rel=&quot;nofollow&quot;&gt;A Chloroform-Assisted Protein Isolation Method Followed by Capillary NanoLC-MS Identify Estrogen-Regulated Proteins from MCF7 Cells&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="184" LastActivityDate="2013-12-06T17:49:21.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13848" PostTypeId="1" CreationDate="2013-12-06T18:46:13.227" Score="0" ViewCount="486" Body="&lt;p&gt;While I'm eating my orange, I felt as if I was eating avocado. It might be genetic manipulations perhaps but it made me think if they have a common evolutionary ancestor. Is there?&lt;/p&gt;&#xA;" OwnerUserId="5112" LastActivityDate="2013-12-07T19:07:12.200" Title="Does avocado and orange have a common ancestor?" Tags="&lt;evolution&gt;&lt;food&gt;&lt;fruit&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13849" PostTypeId="2" ParentId="13756" CreationDate="2013-12-06T18:47:00.243" Score="1" Body="&lt;p&gt;I've been thinking about this question for a few days and along the lines of @ThomasIngalls comment, the simple answer is that cooperation between organisms has such a huge advantage in selection that any chance a eukaryote would become a chemautotroph would simply not adapt fast enough to compete with those that are already holding these niches. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The chemautotrophs I'm aware of are usually archaeabacteria.  They are optimized to grow slowly and have a large number of genes that can break down the unusual chemical compounds to grow in an inorganic often anoxic environment.  These bacteria have genes evolved from the chemautotrophic earliest days of life on earth.  They live deep within the earth, under ground, in volcanic vents.  There are &lt;a href=&quot;http://en.wikipedia.org/wiki/Giant_tube_worm#Energy_and_nutrient_source&quot; rel=&quot;nofollow&quot;&gt;animals that live in some of these environments&lt;/a&gt;, but its simply too easy for these to use the bacteria that are already growing here readily rather then re-evolve the genes to do it by themselves. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eukaryotes are already symbiotes - they used bacteria to create ATP and photosynthetically fix carbon to the extent that they absorbed them as mitochondria and chloroplasts respectively.  If eukaryotes were under a tremendous amount of selective pressure, some of them might absorb symbiotic chemautotrophs, but without such pressure, it doesn't happen when you are competing against plants with roots and animals that eat for their energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Forming systems of organisms is much more stable than having individual species that can do it all.  This question is actually similar to other questions that ask why we don't have metal armor, run as fast as cheetahs, etc.  Evolution doesn't actually create super animals that are completely self contained.  The ones that reproduce the best are the ones that can actually spread out the risk of survival and contribute to an ecosystem.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It kind of makes me think of human beings - the only superorganism on the planet in this regard.  We don't really need to compete against any organism - we are in fact killing most of them out there without really thinking about it.  That might now turn out to be good for us long term. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-12-06T18:47:00.243" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13850" PostTypeId="2" ParentId="13848" CreationDate="2013-12-06T18:59:39.880" Score="6" Body="&lt;p&gt;Here is a website that presents very accuerately the tree of life: tolweb.org/tree &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, they have a common ancestor just like any other living things! How closely related are they?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both species are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Eukaryotes (cells with a nucleus)&lt;/li&gt;&#xA;&lt;li&gt;Archaeplastidae (plants)&lt;/li&gt;&#xA;&lt;li&gt;Angiosperms (flowering plants)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Then, they split their way! Here is the tolweb.org page that correspond to this speciation: &lt;a href=&quot;http://tolweb.org/Angiosperms/20646&quot; rel=&quot;nofollow&quot;&gt;http://tolweb.org/Angiosperms/20646&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The avocado is in the Laurales family: &lt;a href=&quot;http://tolweb.org/Laurales/20672&quot; rel=&quot;nofollow&quot;&gt;http://tolweb.org/Laurales/20672&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The orange is in the Rutacea (sapindales, rosids, eudicots) family: &lt;a href=&quot;http://tolweb.org/Sapindales/21051&quot; rel=&quot;nofollow&quot;&gt;http://tolweb.org/Sapindales/21051&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can use the left arrow on the tree of these pages to come back through times and see the different speciation event that seperate both species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the orange is a eudicots, the avocado is part of the magnolids. The oldest fossil records of an angiosperm lived about 132MYA (see Crane et al., 2004). So the two species diverge for quite a long time! In order to give a comparison, they are as distant than humans and rabbits (it is a rough personal estimation, I don't have any reference for that!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: The orange is called Citrus sinensis in latin. The species originated in China. The avocado is called Persea americana and it originated in central american (as their names indicate).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know what make you feel that they are closely related. Maybe someone might say some words about their chemical compounds (and their flavour) but at first glance these two fruits taste very differently to me. Or maybe they have some remarkably similar phenotypic traits due to convergence evolution... I don't quite know about that! &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-12-07T19:07:12.200" LastActivityDate="2013-12-07T19:07:12.200" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13852" PostTypeId="1" AcceptedAnswerId="13855" CreationDate="2013-12-06T20:55:06.217" Score="1" ViewCount="41" Body="&lt;p&gt;I am interested to know how environment-cancer relationship knowledge has developed.&#xA;I know that all began when Muller first proved that mutation could be induced via ionizing radiation, X rays in the case, and hypothesized for the first time the role that this could have on carcinogenesis. Do you know further data and the main or most significant events that leaded from that point until the current state of the art? (like when smoking and cancer were proved related)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(all factors enhancing risk would be included in the query, as human behavioral aspects (such as diet), work environment...)&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="3657" LastEditDate="2013-12-06T23:31:48.733" LastActivityDate="2013-12-07T02:32:11.680" Title="Cancer history on environment-cancer relationship" Tags="&lt;cancer&gt;&lt;history&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13853" PostTypeId="1" AcceptedAnswerId="13860" CreationDate="2013-12-06T22:40:11.930" Score="9" ViewCount="1601" Body="&lt;p&gt;The question of complexity is classic in the very first lectures of evolutionary biology where the teacher usually tries to tell the students that complexity does not necessarily increase and that humans are not more complex than other organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why does complexity tend to increase through evolutionary time?&lt;/li&gt;&#xA;&lt;li&gt;What are the different hypotheses to explain this pattern?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;When writing &quot;Mass extinction&quot; on google image, we find many graphs displaying the number of families (or other taxa) through evolutionary times with the five mass extinctions. What would it look like to draw such graph replacing the family richness in the y-axis by :&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mean complexity among all living things?&lt;/li&gt;&#xA;&lt;li&gt;Complexity of the most complex taxon?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I suppose that anyone who wishes to answer to this post will necessarily need to define the words &quot;complexity&quot;. He or she might define it in terms of number of genes, number of metabolic pathways, length of DNA sequence, number of cell types, some kind of index taken from information theory. When asking my questions I had in mind a definition close to &quot;number of genes&quot; or &quot;number of metabolic pathways&quot;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="2999" LastEditDate="2017-03-06T21:02:36.357" LastActivityDate="2018-01-25T18:27:18.780" Title="Why and how does complexity usually tend to increase through time?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;theoretical-biology&gt;&lt;molecular-evolution&gt;&lt;information-theory&gt;" AnswerCount="4" CommentCount="17" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="13854" PostTypeId="2" ParentId="13699" CreationDate="2013-12-07T02:13:50.963" Score="2" Body="&lt;p&gt;I'm a HUGE fan of &lt;a href=&quot;http://www.biochem.mpg.de/226356/FASP&quot; rel=&quot;nofollow&quot;&gt;FASP&lt;/a&gt; (filter-aided sample preparation) which is an in-solution preparation/digestion. It is very fast, allows you to not worry about a protein precipitation step, and gets rid of all MS incompatible substances with the wash steps (so doesn't matter what lysis buffer you use). It requires very few, inexpensive materials (a pack of 100 centrifuge filter units is less than 250 USD from VWR) and has great recovery. &lt;a href=&quot;http://www.nature.com/nmeth/journal/v6/n5/abs/nmeth.1322.html&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; is the link to the Nature Methods paper that the linked protocol is based on (the linked protocol is an updated, faster version of the Nature Methods one).&lt;/p&gt;&#xA;" OwnerUserId="5115" LastActivityDate="2013-12-07T02:13:50.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13855" PostTypeId="2" ParentId="13852" CreationDate="2013-12-07T02:32:11.680" Score="1" Body="&lt;p&gt;Actually, &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Chimney_sweeps%27_carcinoma&quot; rel=&quot;nofollow&quot;&gt;soot wart&lt;/a&gt;&quot; was identified by Percival Pott in 1775. It is the first reported occupational cancer (it is a squamous cell carcinoma of the skin of the scrotum). It was shown in 1922 that an active ingredient of coal soot was a carcinogen. I'm not sure of an expansive, technical text on environmental cancers, but you may want to check out &#xA;&quot;The Emperor of All Maladies: A Biography of Cancer&quot; which covers the origins of man's understanding of cancer starting with the ancient Greeks, progressing to mention Percival Pott, and then moving on to modern day science and medicine. This book won the Pulitzer in nonfiction a few years ago and is well worth your time.&lt;/p&gt;&#xA;" OwnerUserId="5115" LastActivityDate="2013-12-07T02:32:11.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13856" PostTypeId="2" ParentId="8139" CreationDate="2013-12-07T02:48:04.823" Score="-1" Body="&lt;p&gt;Pharmacology cross reference: Recombinant type I interferons are injected as therapeutics. Viral infections would seem like logical indications, but interferons are both expensive and have considerable adverse effects, e. g., flu-like symptoms on injection, anemia and depression. Their application is therefore limited to life-threatening viral diseases, e. g. hepatitis C.&lt;/p&gt;&#xA;" OwnerUserId="5117" LastActivityDate="2013-12-07T02:48:04.823" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13857" PostTypeId="2" ParentId="13699" CreationDate="2013-12-07T05:52:10.070" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://www.embl.de/pepcore/pepcore_services/protein_purification/extraction_clarification/cell_lysates_ecoli/french_press/&quot; rel=&quot;nofollow&quot;&gt;why not use a french press&lt;/a&gt;?   put a few thousand PSI on the sample and the cells just pop open.  The lysis buffer contains no detergents:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Lysis buffer:&#xA;50 mM Tris-HCl pH 7.5&#xA;50-200 mM NaCl*&#xA;1 mM MgCl2&#xA;5 mM DTT&#xA;1 mM PMSF&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;the salt concentration is variable and you could probably do without the DTT too if thats a problem ...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-12-07T05:52:10.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13858" PostTypeId="1" AcceptedAnswerId="13861" CreationDate="2013-12-07T09:59:00.000" Score="1" ViewCount="2388" Body="&lt;p&gt;Orbital frontal cortex is where decisions are made.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does the word orbital there mean?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I looked around in wikipedia and never find it.&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="5005" LastEditDate="2013-12-07T14:39:12.610" LastActivityDate="2013-12-09T10:59:27.007" Title="What does orbital mean in orbital frontal cortex?" Tags="&lt;brain&gt;&lt;human-anatomy&gt;&lt;nomenclature&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13859" PostTypeId="2" ParentId="13858" CreationDate="2013-12-07T12:12:30.590" Score="0" Body="&lt;p&gt;Quick search on &lt;a href=&quot;http://www.etymonline.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;etymonline&lt;/a&gt; for &lt;a href=&quot;http://www.etymonline.com/index.php?allowed_in_frame=0&amp;amp;search=orbital&amp;amp;searchmode=none&quot; rel=&quot;nofollow noreferrer&quot;&gt;Orbital&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;orbital (adj.):&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;1540s with reference to &lt;strong&gt;eye sockets&lt;/strong&gt;;&lt;/p&gt;&#xA;&lt;p&gt;1839 with reference to heavenly bodies;&lt;/p&gt;&#xA;&lt;p&gt;from orbit&lt;/p&gt;&#xA;&lt;p&gt;(n.) + -al (1).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So my best guess is that it's related to eyes.&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-12-09T08:47:09.697" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13860" PostTypeId="2" ParentId="13853" CreationDate="2013-12-07T12:35:30.763" Score="4" Body="&lt;p&gt;This is actually a very interesting yet difficult question to give a single precise answer to. I will try and summarize for you a &quot;meta answer&quot;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Complexity Science&lt;/em&gt;&lt;/strong&gt; Some consider complexity not to be a Biological topic as such, since it is a property that accumulates in non-biological systems e.g. economics, technology, music, language - in fact anything that &quot;evolves&quot; through time. This new field of science is called &quot;Complexity Science&quot; or &quot;Complex Systems&quot; and is primarily a field of mathematics or information theory: &lt;a href=&quot;http://en.wikipedia.org/wiki/Complex_systems&quot; rel=&quot;nofollow noreferrer&quot;&gt;Complex systems&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Complexity in Biology&lt;/em&gt;&lt;/strong&gt; What I can say is that these kinds of questions have started an almost new field in Biology, called &quot;diversity evolution&quot;, here is a very interesting paper: &lt;a href=&quot;http://arxiv.org/abs/nlin.AO/0210026&quot; rel=&quot;nofollow noreferrer&quot;&gt;Diversity Evolution&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Defining Complexity&lt;/em&gt;&lt;/strong&gt; You were right to mention Complexity first needs to be defined, and as an early field of science this is where much focus has been recently. There are quite a few definitions but it is perhaps too controversial to list any particulars... &lt;a href=&quot;http://www.spatialcomplexity.info/files/2011/10/Spatial-Complexity-Lecture-1.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;HERE&lt;/a&gt; is a whole UCL lecture dedicated to defining Complexity! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Topics of Complexity Science&lt;/em&gt;&lt;/strong&gt; I have written enough, so perhaps this lovely diagram of the topics of Complexity Science will be of some help:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OcXdO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2017-03-06T16:57:21.460" LastActivityDate="2017-03-06T16:57:21.460" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13861" PostTypeId="2" ParentId="13858" CreationDate="2013-12-07T14:43:24.213" Score="5" Body="&lt;p&gt;&lt;strong&gt;Orbitofrontal cortex&lt;/strong&gt;: the area of the cerebral cortex located at the base of the frontal lobes above the &lt;em&gt;orbits&lt;/em&gt; (or eye sockets), involved especially in social and emotional behaviour.&lt;/p&gt;&#xA;" OwnerUserId="5032" LastEditorUserId="107" LastEditDate="2013-12-07T22:59:28.573" LastActivityDate="2013-12-07T22:59:28.573" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13862" PostTypeId="2" ParentId="832" CreationDate="2013-12-07T15:10:01.620" Score="0" Body="&lt;p&gt;It is a phrase in common parlance without scientific meaning, fitting in the same category as &lt;em&gt;devolved&lt;/em&gt; or &lt;em&gt;devolution&lt;/em&gt;. It is as @terdon said:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There is no such thing as more or less evolved.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In a scientific context you should always find the evolutionary measure in question and the methods for quantifying that measure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a biological context the phrase would fail to find meaning, when evolution is a function of fitness. In such context fitness is inevitably tied to environmental parameters. The more complex these parameters, the more niches may be available for potential species, with temperature being one of the strongest factors (See: &lt;a href=&quot;http://en.wikipedia.org/wiki/Effective_evolutionary_time&quot; rel=&quot;nofollow noreferrer&quot;&gt;Effective evolutionary time Hypothesis&lt;/a&gt; ). Take this assertion with the necessary caution, as it is far outside my expertise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mostly I have come across the phrase &lt;em&gt;more evolved&lt;/em&gt; in reference to large, tangible species, and also in science fiction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tell your student, to always be aware that in the end the unicellular species make life for us on this planet viable - we coevolved. But they also eventually consume/recycle us in one way or another, and surely will outlast us. It takes extreme effort and finesse for a large, energetic multicellular host to obtain, maintain and retain its niche on this planet. In all of the field of molecular biology there is nothing quite like Immunology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;For a mind experiment, let the student imagine soil with different pH, of the same plant species which equal seeding-times.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The outcome may be something as shown below. The phrase &quot;more evolved&quot; clearly fails to describe such a scenario of one generation of plant species, and hence is not suitable in an objective description of evolution.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Sidenote: Al3+-ions are toxic to plants, stuning root growth and phosphate intake. With increased pH, more aluminum dissolves.&lt;/em&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/bZHr4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1450" LastEditorUserId="3624" LastEditDate="2014-01-16T19:53:24.543" LastActivityDate="2014-01-16T19:53:24.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13863" PostTypeId="1" AcceptedAnswerId="30916" CreationDate="2013-12-07T15:48:21.380" Score="5" ViewCount="788" Body="&lt;p&gt;I was reading &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitotic_crossover&quot;&gt;this&lt;/a&gt; article in wikipedia and came across this :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It has been suggested that recombination takes place during G1, when&#xA;  the DNA is in its 2-strand phase, and replicated during DNA synthesis. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If For example - allele A is present on 1 and a is present on 1' and recombination happens such that a is present on 1 and A on 1' and then both get duplicated during S phase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how are the daughter cells going to be different from one another and from the mother cell in terms of phenotype? (obviously the alleles around these alleles are going to change) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can this result in twin spotting in drosophila or any other trait occurring due to coming together of homozygous alleles by mitotic crossovers ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2015-04-03T04:37:56.393" Title="Mitotic crossover happens in G1?" Tags="&lt;dna&gt;&lt;mitosis&gt;&lt;recombination&gt;&lt;allele&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13864" PostTypeId="1" AcceptedAnswerId="13868" CreationDate="2013-12-07T16:45:51.960" Score="12" ViewCount="1058" Body="&lt;p&gt;Down's syndrome occurs when either the egg or the sperm cell contain on extra chromosome 21. To my understanding, women are born with all the egg cells in place already, so there's no further cell divisions, and thus no further chance of having one cell with an extra chromosome.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the chance of having a baby with Down's syndrome &lt;a href=&quot;https://en.wikipedia.org/wiki/Down_syndrome#Epidemiology&quot;&gt;increase with age&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At maternal age 20 to 24, the probability is one in 1562; at age 35 to 39 the probability is one in 214, and above age 45 the probability is one in 19&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why is this so, when the egg cells are complete at birth?&lt;/p&gt;&#xA;" OwnerUserId="3037" LastEditorUserId="57" LastEditDate="2013-12-07T17:52:23.763" LastActivityDate="2014-05-01T19:34:32.323" Title="Why does the chance of having a baby with Down's syndrome increase with the age of the mother?" Tags="&lt;reproduction&gt;&lt;meiosis&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13865" PostTypeId="2" ParentId="5295" CreationDate="2013-12-07T17:21:01.603" Score="2" Body="&lt;p&gt;I'm new so I can't make this a comment, and I don't think the other commenter addressed your questions so here it goes: I don't think there will be much difference, if any, between 0.2 and 0.3 OD. Once you get higher and the cells start transitioning into a stationary phase is a different story. Did you mean to ask about 0.03 OD as well (you wrote 03.)? I'm not an expert in E. Coli, but they would probably be less likely to produce proteins that are contact inhibited. Sub-optimal temperatures may have a minor effect on growth, but I don't believe this will initiate much change or induce production of large amounts of cold shock proteins.&lt;/p&gt;&#xA;" OwnerUserId="5115" LastActivityDate="2013-12-07T17:21:01.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13866" PostTypeId="2" ParentId="13791" CreationDate="2013-12-07T17:48:17.340" Score="4" Body="&lt;p&gt;As an addition to the excellent post by Erin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a name-giving key feature,mammals have mammary glands.&lt;br&gt;&#xA;&quot;&lt;em&gt;Animals that are bilaterally symmetric have mirror symmetry in the sagittal plane&lt;/em&gt;&quot;, which includes Chordates such as mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some have seen this iconic picture, showing the bilateral symmetry in chordates:&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/vOa9p.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is easy to see why &lt;strong&gt;most commonly even number of mammary glands are found in mammals&lt;/strong&gt;, given that they form in pairs, distal from the notochord.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolutionary, an uneven number of mammaries may be explained through a subjectively-mild mutation which may be retained as a &lt;a href=&quot;http://en.wikipedia.org/wiki/Vestigiality&quot; rel=&quot;nofollow noreferrer&quot;&gt;vestigial-like feature&lt;/a&gt;, somewhat-functional or not. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a molecular level, unilateral mammary glands likely involve key developmental pathways such as hedgehog and likely has underlying polygeneic root causes, - for the termination of gland formation on one side.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this intersting paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Kohei Amakasu, Katsushi Suzuki, Hiroetsu Suzuki* &quot;The Unilateral&#xA;  Urogenital Anomalies (UUA) Rat&quot;, Comp Med. 2009 June; 59(3): 249–256.&lt;/strong&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;We established an inbred rat strain with unilateral urogenital&#xA;  anomalies from an incidentally identified male rat with unilateral&#xA;  renal agenesis and an undescended left testis. These rats were&#xA;  characterized by unilateral renal agenesis in both sexes, undescended&#xA;  testes with agenesis and hypoplasia of the accessory sex organs in&#xA;  male rats, and complete and partial agenesis of the uterine horn in&#xA;  female rats. All of these urogenital anomalies were unilateral and&#xA;  restricted to the left side; we named this phenotype unilateral&#xA;  urogenital anomalies (UUA). Breeding tests showed that these&#xA;  abnormalities were inherited as polygenic traits&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is noteworthy that the mammary glands in the male human population didn't decrease fitness to such a degree where evolutionary pressure would have lead to cease gland formation altogether, by adding extra information to the sex-chromosome(s). As such human males retain mammary glands, albeit typically never reaching a functional state.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The factors weighting against such additional genes are, that the default formation in most mammals is the female body plan, which conserves functional mammary glands to potentially feed their offspring, chipping away at the chance of genes involved in the cessation of mammary gland formation.&lt;br&gt;&#xA;Secondly, selection pressure for information retained on the sex-chromosomes is higher, as opposed to autosomal (non-sex) genes. (See this nice concise post by &lt;em&gt;Danielle Venton&lt;/em&gt;,  &lt;a href=&quot;http://gbe.oxfordjournals.org/content/3/1338.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Degenerating Y Chromosome&lt;/a&gt;,Genome Biol Evol (2011)  3  1338-1339. )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Concluding, naturally, &lt;strong&gt;it would be easy for an asymmetric sponge to have an uneven number of protrusions or orifices, less so for humans&lt;/strong&gt;, unless the orifice is located along an axis of symmetry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hedgehog&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Hedgehog&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Ad biological symmetry:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vkLj8.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1450" LastActivityDate="2013-12-07T17:48:17.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13867" PostTypeId="1" AcceptedAnswerId="16997" CreationDate="2013-12-07T18:20:43.733" Score="1" ViewCount="193" Body="&lt;p&gt;I know that species have been classified on basis of reproduction , DNA similarity , niche, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Has there been a classification based on locus of genes ?&lt;/strong&gt; What are the drawbacks/shortcomings of classifying this way ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isn't it simple to classify on this basis as - a species can have variation at a locus but the position of that locus with respect to a chromosome is fixed in every individual of that species. This fact can eliminate the subjective criteria of DNA similarity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I think this isn't valid for bacteria as there is so much recombination going on. &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-05-15T01:46:09.547" Title="Definition of species - location of gene" Tags="&lt;genetics&gt;&lt;phylogenetics&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13868" PostTypeId="2" ParentId="13864" CreationDate="2013-12-07T18:30:57.087" Score="10" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;The frequency rises with maternal age due to a peculiarity of meoisis&#xA;  in female mammals.  Meiosis is originated in the fetal ovary,&#xA;  arresting at metaphase I with the homologous  chromosomes aligned for&#xA;  segregation. Cells remain in this state until the time of ovulation,&#xA;  often  decades later in humans. The longer cells remain in the&#xA;  arrested state, the greater the chance  that there will be a&#xA;  nondisjunction event when meiosis resumes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source : &lt;a href=&quot;http://www.madsci.org/posts/archives/2005-07/1121714807.Ge.r.html&quot;&gt;http://www.madsci.org/posts/archives/2005-07/1121714807.Ge.r.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think you have the misconception that egg cells have completed meiosis by the time female is born. This is not true ( as indicated above in the answer). At birth, they are in metaphase I , after puberty, each month some of them divide further but only one survives and get arrested at metaphase II . Only after fertilization is the meiosis complete.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-12-07T18:30:57.087" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="13869" PostTypeId="1" CreationDate="2013-12-07T23:56:56.947" Score="1" ViewCount="635" Body="&lt;p&gt;I found that many friends of mine are quite easy in sexual relationship. Ex, I knew a lot of girls went to the night club &amp;amp; met a stranger &amp;amp; brought home to sleep  with him even she had never known his name. The next morning, the guy left her &amp;amp; she starts to do the same way to get another guy maybe in 3 days or so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So that triggered my thought. I wonder &quot;Are early human beings (about 100 - 200 K years ago) far more promiscuous than we are now?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My hypothesis is &quot;Yes&quot;, that is &quot;Early human beings are far more promiscuous than we are now&quot;. So how i came up this? Cos Human came from Chimpanzee right?, so if we want to know early human, then we could study Chimpanzee. The early human &amp;amp; Chimpanzee could have some similarities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a research saying that &quot;Chimpanzees are far more promiscuous than humans&quot; &lt;a href=&quot;http://www.nature.com/news/specials/chimpgenome/interactive/chimp_interactive_graphic_pf.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/news/specials/chimpgenome/interactive/chimp_interactive_graphic_pf.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, that proved my hypothesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, when human evolved, they started to realized that promiscuousness wss not healthy &amp;amp; not good for society so they started to develop some regional/society (ex,  monogamous relationship) codes to prevent that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you approve my hypothesis?&lt;/p&gt;&#xA;" OwnerUserId="4989" LastEditorUserId="5144" LastEditDate="2014-02-27T20:25:07.413" LastActivityDate="2014-04-28T22:58:40.347" Title="Were early human beings (about 100 - 200 K years ago) far more promiscuous than we are now?" Tags="&lt;sex&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13870" PostTypeId="1" CreationDate="2013-12-08T00:24:07.503" Score="5" ViewCount="90" Body="&lt;p&gt;I ask this question in relation to the origin of life. I realise it would probably be better suited to a geology stack exchange, but it does not yet exist. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Miller-Urey experiment gives a lab based demonstration of how organic compounds may have been produced. It recreates that conditions that are thought to have existed in the early atmosphere (Hadean period).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ubb9S.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What this experiment relies on however is an assumption that the atmosphere lacked oxygen (reducing). The Miller-Urey experiment does not produce proteins if it is conducted in a oxidizing environment. I've seen that there is some debate over the oxidation state of the atmosphere, and the main evidence for a reducing atmosphere is that life wouldn't have been able to begin without it. Is there evidence supporting an oxidized early atmosphere, and if so, how did life come about?&lt;/p&gt;&#xA;" OwnerUserId="3382" LastActivityDate="2013-12-08T15:27:36.237" Title="Is there any evidence telling us what the oxidation state of early earth's atmosphere was?" Tags="&lt;evolution&gt;&lt;life&gt;&lt;protein-evolution&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13871" PostTypeId="2" ParentId="9001" CreationDate="2013-12-08T09:35:59.063" Score="1" Body="&lt;p&gt;Copper hydroxide does not dissolve very well in water, which means you will have trouble soaking them into your gels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, even if you managed to add enough copper hydroxide beforehand (in the wells), it is unlikely that the copper(II) ions, if any existes, will travel along with the protein due to its size. (Copper hydroxide itself does not have any charge.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the paper Stella mentioned, the copper salts are used after electrophoresis to produce a negative image, which is exactly what you cannot do with copper hydroxide.&lt;/p&gt;&#xA;" OwnerUserId="4136" LastEditorUserId="4136" LastEditDate="2013-12-08T09:44:33.453" LastActivityDate="2013-12-08T09:44:33.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13872" PostTypeId="2" ParentId="13870" CreationDate="2013-12-08T13:15:15.250" Score="3" Body="&lt;p&gt;There are wikipedia pages on &lt;a href=&quot;http://en.wikipedia.org/wiki/Geological_history_of_oxygen&quot; rel=&quot;nofollow&quot;&gt;Geological history of oxygenation&lt;/a&gt; and on &lt;a href=&quot;http://en.wikipedia.org/wiki/Great_Oxygenation_Event&quot; rel=&quot;nofollow&quot;&gt;Great Oxygenation Event&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know much about geology and someone else might be able to give an exhaustive list of evidence (and method of measuring) concerning the oxygen concentration on earth but that would be a very long answer I guess! Rather than a full answer, I give you a list of wikipedia pages below that will interest you and should help answering your own question.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Banded_iron_formation&quot; rel=&quot;nofollow&quot;&gt;Banded Iron Formation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_dietary_antioxidants#History&quot; rel=&quot;nofollow&quot;&gt;Evolution_of_dietary antioxidants&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Huronian_glaciation&quot; rel=&quot;nofollow&quot;&gt;Huronian Glaciation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ice_core&quot; rel=&quot;nofollow&quot;&gt;Ice core&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-12-08T15:27:36.237" LastActivityDate="2013-12-08T15:27:36.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13873" PostTypeId="2" ParentId="13846" CreationDate="2013-12-08T16:22:46.870" Score="3" Body="&lt;p&gt;We use central vision for a lot more things today than in the past. Peripheral vision is most important in navigation, so those who lose their central field retain the ability to navigate around objects. It is important that this is fast and sensitive in the dark as well as light. It isn't important for it to be in colour; this would mean it would be less sensitive in the dark and colour isn't important in navigation and also it would take longer. Navigation is of vital importance as it can be the difference between survival or death in the flight or fight response. Similarly it is important in the fight part, being able to see a foe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's our foveas were bigger, well we would lose the above. What would we gain? The ability to see more at full resolution and colour. It's impossible for us to concentrate on more than we can see in our central field already. in fact we dart our gaze around to focus on many things because we can't focus on multiple things at once. By this I mean thinking about what we see not processing it. Of course we would also require a much larger brain to be able to process it all, processing the central field takes a lot of brain matter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in conclusion, it's not helpful. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-12-08T16:22:46.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13874" PostTypeId="2" ParentId="13832" CreationDate="2013-12-08T16:26:06.983" Score="4" Body="&lt;p&gt;Epinephrine and norepinephrine is used in the US mainly. This is where the term epi-pen comes from. Everywhere else we tend to use Adrenaline and noradrenaline. Epinephrine is typically only used in literature arising from the US or US English speaking countries. In most countries they use adrenaline and also include Epinephrine so our American cousins don't miss our publications. Adrenaline is the better term as it is more widely understood by scientists, health professionals and the public. However at the end of the day they're the same thing. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-12-08T16:26:06.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13875" PostTypeId="2" ParentId="13831" CreationDate="2013-12-08T16:42:19.173" Score="2" Body="&lt;p&gt;a) HIV uses a certain receptor that's expressed widely on T helper cells. As this is homework I suggest looking at the wikipedia article to look this up for yourself. It is under tropism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) You mentioned mutation. That's very true but this question is excluding people with that mutation called the delta 32 mutation. Thus HIV can infect these people, but what happens to any virus in the context of infection? How does the human body deal with viral infections. Is there any variation that would account for why some people can be resistant to HIV and others not be? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;c) Yes! Well done :) You're thinking along the right lines. Look up the drug on wikipedia and look up it's mechanism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;d) i) Yeah exactly that. But more than that. There's optimal HIV which in the absence of drugs does the best job at infecting. If we give a drug then HIV has to mutate away from optimal HIV to stay alive, but it's weaker. Give multiple drugs and it can't mutate away from all of them because if it did it would be so far from optimal it would be a rubbish virus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ii) 1) It could affect the HIV binding receptor protein or the protein with which it binds on the host cell. So both! Logic would dictate we would use self receptor blockade because at least they're more conserved but I'm sure both are probably used. Enzymes and receptors are both proteins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2 + 3) Look up the lifecycle of HIV&lt;/p&gt;&#xA;&#xA;&lt;p&gt;e) Theoretically possible. He might not take the drugs. If he takes the drugs unlikely because the virus basically becomes undetectable. Look this up, it should be on wikipedia again. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-12-08T16:42:19.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13876" PostTypeId="2" ParentId="13714" CreationDate="2013-12-08T16:51:06.300" Score="1" Body="&lt;p&gt;You can try as much to slow down your breathing but the body will speed it up if it requires. What you've probably done is relaxed and just basically meditated. It's not the breathing but the relaxing yourself to slow your breathing and the focus which has refreshed you. I say conduct some experiments, like listen to calming music and relax and don't monitor your breathing and see if you feel the same. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;//updating answer&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Slowing your breathing builds up the carbon dioxide in your body. This is bad for the body so it forces you to breathe. In fact our breathing is seriously tightly controlled so that our body tightly controls the carbon dioxide (or more correctly the pH) in our blood. There are some groups of patients in which permanent slow breathing exists. In these people their carbon dioxide climbs and the kidneys have to compensate. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1757" LastEditDate="2014-02-06T19:39:20.340" LastActivityDate="2014-02-06T19:39:20.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13877" PostTypeId="2" ParentId="9001" CreationDate="2013-12-08T17:16:42.217" Score="1" Body="&lt;ol&gt;&#xA;&lt;li&gt;Protein electrophoresis is often done in an alkaline pH (8.6), which is not exactly nice if you want to use $Cu(OH)_2$. &lt;/li&gt;&#xA;&lt;li&gt;If you need quantitation, you can use Coumassie blue or Amido black. If you want sensitivity you can use silver. These existing stuff are quite OK. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5122" LastEditorUserId="107" LastEditDate="2013-12-08T23:58:17.313" LastActivityDate="2013-12-08T23:58:17.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13879" PostTypeId="1" AcceptedAnswerId="13881" CreationDate="2013-12-08T18:49:01.613" Score="2" ViewCount="136" Body="&lt;p&gt;What is the molecular basis of the stability of the bacterium Thermus aquaticus and the enzyme Taq Pol it produces ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried googling this but did not get a good answer.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-12-08T19:39:33.177" Title="Why is Thermus aquaticus and Taq Pol stable?" Tags="&lt;biochemistry&gt;&lt;bacteriology&gt;&lt;adaptation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13880" PostTypeId="2" ParentId="13720" CreationDate="2013-12-08T19:02:47.230" Score="3" Body="&lt;p&gt;Nasal septum deviation is a condition where the cartilage which divides the nasal cavity into two nasal passages isn't centrally aligned, making one of the nostrils smaller and thus obstructed. Now, in our nose we have something called &lt;a href=&quot;http://en.wikipedia.org/wiki/Mucociliary_clearance&quot; rel=&quot;nofollow&quot;&gt;mucociliary clearance&lt;/a&gt; and that is the mechanism getting rid of unwanted particles and pathogens that get into contact with the mucous membranes in the nose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Studies show that in individuals with a deviated septum the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19816701&quot; rel=&quot;nofollow&quot;&gt;nasal mucociliary clearance time is slower than in individuals whose nasal passages are symmetrical&lt;/a&gt;. From this information one can conclude that the particles and pathogens that you inhale are getting to spend more time inside your nasal passages, thus giving the pathogens a better chance at striving and giving you sinusitis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By looking at the information above you could think that the connection between nasal septum deviation and chronic sinusitis is clear. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11859650&quot; rel=&quot;nofollow&quot;&gt;This literary review&lt;/a&gt; however states that the correlation between a deviated nasal septum and having chronic sinusitis is still unclear.&lt;/p&gt;&#xA;" OwnerUserId="4587" LastActivityDate="2013-12-08T19:02:47.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13881" PostTypeId="2" ParentId="13879" CreationDate="2013-12-08T19:39:33.177" Score="2" Body="&lt;p&gt;Here is an article from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242557/&quot; rel=&quot;nofollow&quot;&gt;Razvi and Scholtz&lt;/a&gt; that help you understand the thermostability found in thermophilic proteins. They compared protein stability of thermophilic proteins and their homologous versions in mesophilic bacteria (i.e., bacteria that grow in more normal temperature ranges), and compiled these proteins into a database. Their method was to make estimates of protein stability curves for each of these proteins through a model of free energy based on the known physical parameters of these proteins. From the article: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] the most common way to attain a higher [melting temperature] in proteins from thermophiles is to raise the stability curve to higher values of ΔG (higher intrinsic stability) at all temperatures.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is achieved through mutation of just the linear sequence of the protein. Fundamentally, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;...each of the methods of stabilization are results of features like an increased number of hydrogen bonds, salt bridges, improved core packing, shorter and/or tighter surface loops, enhanced secondary structure propensities, or oligomerization.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also, everything I have seen about the genus thermus places them as Gram negative bacteria.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242557/&quot; rel=&quot;nofollow&quot;&gt;Razvi and Scholtz. Lessons in stability from thermophilic proteins. Protein Science, 15(7) 2006.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2013-12-08T19:39:33.177" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13883" PostTypeId="1" CreationDate="2013-12-09T02:33:34.373" Score="4" ViewCount="4513" Body="&lt;p&gt;My professor was talking about double mutant analysis with null mutants, and how double mutant analysis won't work with hypomorphs.  I really don't understand the concept of double mutant analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He was talking about pathways - if A and B are in the same pathway, then you would mutate A and he said something about the phenotype being identical.  If A and B are in different pathways, you could mutate both of them and there would be a &quot;stronger&quot; phenotype.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;He also said it would only work with null mutants, not with hypomorphs, because with hypomorphs some of the pathway would still be active, not completely shut off.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I really don't understand any of this - what a double mutant is, the whole pathway thing, why the phenotype is &quot;identical&quot; or &quot;stronger&quot;, or why you use hypomorphs.  I would really appreciate a rundown on the idea of double mutant analysis because my professor's explanation was so unclear.  Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="5124" LastActivityDate="2014-11-05T23:34:56.560" Title="Double mutant analysis with null mutants" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13884" PostTypeId="1" CreationDate="2013-12-09T04:54:25.243" Score="6" ViewCount="117" Body="&lt;p&gt;I'm stopped at a stoplight and, with nothing to do, my thoughts wander to the timed don't-walk sign that governs any pedestrians who might wish to cross the street I'm driving along. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can see two such signs, one on my side of the cross street, and one across the way. They are synchronized: each counts down the seconds at exactly the same time as the other, as far as I can tell, lighting up as &quot;5&quot;, then a second later as &quot;4&quot;, etc. Nothing's wrong with my ocular nerve or brain, as far as I know. Can you fill in the blanks please? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can be &amp;hellip;% sure that the lights are synchronized within &amp;hellip; seconds of one another. (Not something trivial like &quot;100&quot; and &quot;1&quot;, of course.)&lt;/p&gt;&#xA;" OwnerUserId="988" LastEditorUserId="9943" LastEditDate="2015-04-24T12:00:12.043" LastActivityDate="2018-08-19T18:44:37.320" Title="How well do we notice asynchronicity?" Tags="&lt;brain&gt;&lt;vision&gt;&lt;psychophysics&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13886" PostTypeId="1" AcceptedAnswerId="13891" CreationDate="2013-12-09T07:08:48.220" Score="7" ViewCount="15281" Body="&lt;p&gt;Searching the internet, I have found lots of conflicting information from various fitness sites concerning when the human body burns fats, proteins and carbohydrates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My basic understanding was that the body will first utilize glucose and glycogen stores, followed by fats and finally proteins once the fat and glycogen stores become depleted.  Also I believe there is some overlap in this process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However many fitness websites claim that during high intensity physical activity, the body will prefer to burn protein over fat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scientifically speaking, when does the body ordinarily burn the following food groups (proteins, fats and carbohydrates) and how does exercise influence this process?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are able to provide graphs or data to back up your answer this will be extra helpful because I am bored of all the speculation I see on other sites.&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2013-12-09T12:42:26.847" Title="Under what conditions does the body burn fats, proteins and carbohydrates?" Tags="&lt;fitness&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13887" PostTypeId="2" ParentId="13858" CreationDate="2013-12-09T10:59:27.007" Score="2" Body="&lt;p&gt;The boney component of the anatomical orbit&lt;strong&gt;strong text&lt;/strong&gt; (in lay terms the eye socket) is the &lt;strong&gt;area&lt;/strong&gt; bordered by the zygomatic, frontal, maxilla, sphenoid, palatine, lacrimal and ethmoid bones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Fa1sV.png&quot; alt=&quot;Bones of the human orbit&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The use of the word &lt;strong&gt;orbit&lt;/strong&gt; (red) in &lt;strong&gt;&lt;em&gt;orbito&lt;/em&gt;&amp;#65279;frontal cortex&lt;/strong&gt; refers to the positioning of this part of the frontal cortex (green) being &lt;em&gt;directly behind the orbit&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Z7EYb.png&quot; alt=&quot;Orbitofrontal cortex location&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2013-12-09T10:59:27.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13888" PostTypeId="1" AcceptedAnswerId="17480" CreationDate="2013-12-09T11:31:00.317" Score="4" ViewCount="179" Body="&lt;p&gt;I am investigating the public data of &lt;a href=&quot;http://www.physionet.org/physiobank/database/mitdb/201.hea&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its specification&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;201 2 360 650000&#xA;201.dat 212 200 11 1024 972 -519 0 MLII&#xA;201.dat 212 200 11 1024 982 30947 0 V1&#xA;# 68 M 1960 2851 x1&#xA;# Digoxin, Hydrochlorthiazide, Inderal, KCl&#xA;# The PVCs are uniform and late-cycle.  Junctional escape beats occur following&#xA;# episodes of ventricular trigeminy.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The data is taken from the interval $[200000, 205000]$ in the following picture with the sample rate 500 Hz. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7G2te.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There seems to be more than Premature Ventricular Contractions (PVC), extrasystoles, so possible ventricular tachycardia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same patient has six minutes later this&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/I2TbR.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think you can see clearer here those PVCs, when the ventricle is starting to contract too early.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both are very pathological situations.&#xA;&lt;strong&gt;How can you differentiate between the two?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are there PVCs in both pictures?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2013-12-09T11:36:07.497" LastActivityDate="2014-05-17T12:17:35.540" Title="Is this ventricular tachycardia?" Tags="&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13889" PostTypeId="2" ParentId="13883" CreationDate="2013-12-09T12:06:11.740" Score="5" Body="&lt;ul&gt;&#xA;&lt;li&gt;What is a double mutant ?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://www.google.co.in/url?sa=i&amp;amp;source=images&amp;amp;cd=&amp;amp;cad=rja&amp;amp;docid=oyWeZKs27m55GM&amp;amp;tbnid=Cgm37N6LCmpoBM%3a&amp;amp;ved=0CAgQjRw&amp;amp;url=http%3A%2F%2Fcommons.wikimedia.org%2Fwiki%2FFile%3ARedeux_Double_Mutant_Asp70His31.png&amp;amp;ei=56ulUpDCEc6FrAeBzoHQDg&amp;amp;psig=AFQjCNExbc-VVeS7RxkLzPhWLiPjGk5nHg&amp;amp;ust=1386675559374129&quot;&gt;this&lt;/a&gt; image.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this mutant 1 has one mutation, mutant 2 has another mutation while the double mutant has &quot;double&quot;  or 2 mutations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Key : A,B means double mutation , A means mutation in A and B means mutation in B.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Types of double mutations&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a)Additive phenotype:  A, B = A + B   Implies that A and&#xA;  B function independently and on different processes.&lt;br&gt;&#xA;   Eg.  A =&#xA;  short roots, B = no root hairs A, B = short roots with no root&#xA;  hairs. &#xA;  Conclusion: A and B function independently on different&#xA;  aspects of root development (A is required for normal root growth&#xA;  and B is required for root hair development.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;b) Epistatic phenotype: A, B = either A or B&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;i) If A = B = A, B   then epistasis implies that both genes function in the same pathway and that each gene is essential to the process.   Eg. A = short roots, B = short&#xA;  roots A, B = short roots.  Both A and B are  required for&#xA;  normal growth of roots.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;ii)         If A is opposite in phenotype to B, and A, B = A, then epistasis implies that  A and B are in the&#xA;  same pathway and B is a negative regulator of A.   Eg. A = long&#xA;  roots, B = short roots A, B = long roots.  A is required to&#xA;  suppress root growth and B is a negative regulator of A. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;c)&#xA;  Synergistic phenotype: A, B &gt;&gt;&gt; A or B.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Implies that A and B contribute independently to the same process.   Eg. A = long roots (wt = 2 cm, A = 4 cm)    B =&#xA;  long roots (B = 4 cm)  A, B = very long roots (20 cm).  A and&#xA;  B negatively control root growth independently of one another and&#xA;  are performing partially redundant functions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;When your professor was saying that if A and B are in same pathway and you mutate A and phenotype comes as if both A and B have been mutated, then he was probably referring to the epistatic phenotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When he was talking about having a stronger effect by mutating them both, he was talking about Synergistic phenotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source : &lt;a href=&quot;http://www3.botany.ubc.ca/biol433/lecture%20outlines/Double%20mutant%20rules.htm&quot;&gt;Double mutant analysis&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-12-09T12:06:11.740" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13890" PostTypeId="1" CreationDate="2013-12-09T12:31:41.473" Score="1" ViewCount="27" Body="&lt;p&gt;I decided to mix beer with vodka hoping it would make me more drunk due to the alcohol content but then remembered the rest ISNT alcoholic and i cant figure out if mixing beer with vodka or other spirits would increase the alcohol content or not i would really like an answer to this as well as any health risks if there are any, thanks.&lt;/p&gt;&#xA;" OwnerUserId="5127" LastActivityDate="2013-12-09T12:31:41.473" Title="mixing beer with spirits, increase alcohol content?" Tags="&lt;alcohol&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2013-12-09T12:45:11.783" ContentLicense="CC BY-SA 3.0" />
  <row Id="13891" PostTypeId="2" ParentId="13886" CreationDate="2013-12-09T12:42:26.847" Score="10" Body="&lt;h1&gt;Introduction&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;The system that regulates body energy store consumption is hugely complicated, but is mainly a cooperation between hormones released by the pancreas (insulin - lowers blood sugar and glucagon - raises blood sugar) and the liver (as the bodies main glycogen store and factory for various energy related tasks).&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Fed State&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;In the &lt;strong&gt;fed state&lt;/strong&gt; (high blood glucose e.g. after a meal), the body produces a large amount of insulin.  When the ratio of insulin:glucagon is high (≈0.5):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Dietary glucose is absorbed by the &lt;strong&gt;liver&lt;/strong&gt; when glucose concentrations are over 8mM.  This glucose is then either &#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;used in respiration by the liver&lt;/li&gt;&#xA;&lt;li&gt;converted to glycogen to be &lt;em&gt;stored&lt;/em&gt; in the liver&lt;/li&gt;&#xA;&lt;li&gt;converted into fatty acids which are then transported out to the periphery in very-low-density lipoproteins (VLDLs)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Adipose tissue&lt;/strong&gt; (fat tissue) takes up glucose in the blood.  This glucose is then:&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;used in respiration by the adipose tissue&lt;/li&gt;&#xA;&lt;li&gt;converted into fatty acids then tri-acyl-glycerols (TAGs) - fat.  VLDLs from the liver can also be absorbed by adipose cells to be used for this.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Skeletal Muscle&lt;/strong&gt; again directly absorbs glucose from the blood&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;During contraction glucose is used directly in respiration to fuel the activity &lt;/li&gt;&#xA;&lt;li&gt;In preparation for future contraction it is converted into glycogen and &lt;em&gt;stored&lt;/em&gt; in the cell&lt;/li&gt;&#xA;&lt;li&gt;Amino acids are incorporated into cellular proteins &lt;em&gt;though if they are superfluous then they can be used in respiration&lt;/em&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;The brain&lt;/strong&gt; directly absorbs glucose and uses it in respiration&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h1&gt;Early Fasting State&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;Where the insulin:glucagon ratio has dropped to around 0.15&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;In the &lt;strong&gt;liver&lt;/strong&gt; &#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Glycogenolysis&lt;/em&gt; is activated to release glucose from stored glycogen to compensate for falling plasma glucose levels (signalled by elevated glucagon)&lt;/li&gt;&#xA;&lt;li&gt;Triglycerides in the liver are preferentially broken down for hepatic respiration - fatty acids are transported &lt;em&gt;in&lt;/em&gt; from the blood to meet the livers own energy demands&lt;/li&gt;&#xA;&lt;li&gt;The liver begins the process of &lt;em&gt;gluconeogenesis&lt;/em&gt; - making glucose from non-carbohydrate precursors&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Adipose tissue&lt;/strong&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Rapidly starts lipolysis - stored fats are broken down into free fatty acids and glycerol.&lt;/li&gt;&#xA;&lt;li&gt;Some of the free fatty acids are used for the adipose tissues own respiratory demands&lt;/li&gt;&#xA;&lt;li&gt;The majority is released to the periphery to be utilised by other tissues&lt;/li&gt;&#xA;&lt;li&gt;The glycerol released can't be used by most tissues, but is taken up by the liver where it can be used to make glucose by gluconeogenesis &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Skeletal Muscle&lt;/strong&gt; &#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Uptake of glucose from the periphery is &lt;em&gt;reduced&lt;/em&gt; to preserve glucose for cells that can't easily use other fuels - e.g. the brain or red blood cells&lt;/li&gt;&#xA;&lt;li&gt;Free fatty acids become the main fuel for skeletal muscles to conserve the glucose for elsewhere&lt;/li&gt;&#xA;&lt;li&gt;Unlike in the liver, glycogenolysis is &lt;em&gt;not&lt;/em&gt; activated as there are no glucagon receptors in muscle tissue.  This means glucose is only produced from glycogen when muscles are actively contracting, as before.&lt;/li&gt;&#xA;&lt;li&gt;At this point proteins can start to be broken down,  their skeletons used as an immediate source of energy and amino acids released to be taken up by the liver and used in gluconeogenesis &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;The brain&lt;/strong&gt; directly absorbs glucose and uses it in respiration.  Fatty acids can not be used as these do not cross the blood brain barrier&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h1&gt;Late Fasting State&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;If there has still been no glucose intake, the insluin:glucagon ratio falls even further, to around 0.05.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Liver&lt;/strong&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;No further glucose has entered the liver and within 24h all hepatic glycogen stores have been depleted&lt;/li&gt;&#xA;&lt;li&gt;Gluconeogenesis becomes the principle source of all plasma glucose - the liver creates new glucose from:&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Amino acids - muscle &amp;amp; liver protein breakdown&lt;/li&gt;&#xA;&lt;li&gt;Glycerol - from adipose tissue&lt;/li&gt;&#xA;&lt;li&gt;Lactate - from red blood cells and muscles&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;High amounts of fatty acids are converted into Acetyl CoA to be used in respiration by the liver, but too much Acetyl-CoA is produced.  The remainder is converted into ketone bodies that are useless to the liver, so jettisoned to be used by other tissues (esp. the brain)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Adipose tissue&lt;/strong&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;As the fast continues into a few days, adipose tissue adapts to producing large amounts of free fatty acids.  &lt;em&gt;This becomes sufficient for most body tissues&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;These fatty acids are used preferentially by all tissues that can use them, conserving glucose for the brain&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Skeletal Muscle&lt;/strong&gt; &#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Fuelled almost entirely by fatty acids and ketone bodies from the liver and adipose tissue&lt;/li&gt;&#xA;&lt;li&gt;Protein breakdown continues to release carbon skeletons and amino acids for gluconeogenesis - but this is &lt;em&gt;inhibited&lt;/em&gt; in the presence of high levels of ketone bodies to prevent unnecessary muscle wastage (still allowing the human to hunt)&lt;/li&gt;&#xA;&lt;li&gt;Amino acids are incorporated into cellular proteins &lt;em&gt;though if they are superfluous then they can be used in respiration&lt;/em&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;The brain&lt;/strong&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Once ketone levels reach a critical level, they can cross the blood brain barrier to be used as a supplementary energy source&lt;/li&gt;&#xA;&lt;li&gt;However, it is not sufficient alone, so a net source of glucose is needed from somewhere in the body&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h1&gt;Progressing to starvation&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;This process can continue for a number of weeks, with the body eventually exhausting fatty acids in adipose tissue and being unable to produce ketone bodies in the liver, losing the inhibition of proteolysis causing a last ditch response of muscle breakdown for energy.  Death is usually from heart failure resulting from cardiac muscle breakdown.&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Summary&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;This chart might be useful in summary, it shows where the glucose levels in the blood are coming from at various stages, the gluconeogenesis line indicating protein and fatty acid breakdown:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/I47Zy.png&quot; alt=&quot;Glucose sources in fed fasting starved states&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Exercise&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;Exercise has to be &lt;strong&gt;very&lt;/strong&gt; intense to have any effect on this system in normal situations.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Resting Muscle&lt;/strong&gt; metabolises stored fatty acids for its own energy.  Glycogen stores are replenished from glucose ready for more vigorous contraction.  &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Brisk Walking&lt;/strong&gt; fatty acid metabolism again provides almost all the energy&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Sprinting&lt;/strong&gt; Glycogen stores are used, respiration is almost entirely anaerobic as blood vessels are constricted by the muscle activity and ventilation has not had time to increase.  Lactic acid is produced, which can be used by the liver for gluconeogenesis&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Middle distance running&lt;/strong&gt;: aerobic metabolism takes over as the body adjusts to the higher oxygen demand.  Lactate is still the major end product&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;One example of where this may be more noticeable is during a marathon.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;0 Mins&lt;/strong&gt; - Muscle is resting at the start line, as above.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;10 mins&lt;/strong&gt; - Muscle and liver glycogen released to power muscle contraction &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;2 Hours&lt;/strong&gt; - A marathon requires roughly 700g of glycogen to complete, however the liver can only store around 500g.  This is largely depleted after roughly 20 miles.  Blood glucose levels fall rapidly and the body switches to fatty acid metabolism.  This only provides around 60% of the power output and pace falls off (&lt;em&gt;known as hitting the wall&lt;/em&gt;).  At this point, virtually every reserve power source is being used simultaneously to keep the body going.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Finish&lt;/strong&gt; - Muscle and liver glycogen are entirely depleted. If glucose levels haven't been maintained by other means, hypoglycaemia results causing confusion, hallucinations and even coma and death. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MvxbS.png&quot; alt=&quot;Energy sources in a marathon&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2013-12-09T12:42:26.847" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="13892" PostTypeId="1" CreationDate="2013-12-09T14:28:15.753" Score="4" ViewCount="378" Body="&lt;p&gt;We've begun to try out the SCA Matlab toolbox (latest version) downloaded from Dr. Rama Ranganathan's website, and, following the included tutorials, would like to apply it to our protein family. The SCA calculation involves determining independent components (IC) of positional covariation by applying the &quot;Infomax&quot; algorithm to a few top eigenmodes (that have been obtained from the positional correlation matrix). Here, we observed that the output (IC vector weights) seems to depend on the no. of top eigenmodes chosen as input (i.e. on choice of the parameter kmax). If this is indeed the case, then is there some &quot;working rule&quot; to optimally choose kmax (say, based on the number of significant eigenmodes turning up)? Since this isn't made very clear in the tutorials (at least to me), I thought of trying my luck here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would really appreciate some guidance/pointers from SCA users. Thanks a lot! &lt;/p&gt;&#xA;" OwnerUserId="5128" LastActivityDate="2013-12-09T14:28:15.753" Title="Statistical Coupling Analysis (SCA) to identify coevolved residues: use of ICA" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;structural-biology&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2014-11-15T04:05:59.963" ContentLicense="CC BY-SA 3.0" />
  <row Id="13893" PostTypeId="1" AcceptedAnswerId="13894" CreationDate="2013-12-09T14:35:58.883" Score="0" ViewCount="2330" Body="&lt;p&gt;I have noticed that while sitting in the Sukhasan posture(picture below) for a long time, my feet suddenly become all stiff and i am unable to move it. What I deduce from the experience is that it is static, though I fail to understand how it accumulated at my feet.Does anyone have an explanation for this?&#xA;&lt;img src=&quot;https://i.stack.imgur.com/UnEK6.png&quot; alt=&quot;Sukhasan Posture&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3660" LastActivityDate="2013-12-09T16:09:02.507" Title="Static in limbs" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13894" PostTypeId="2" ParentId="13893" CreationDate="2013-12-09T16:09:02.507" Score="2" Body="&lt;p&gt;I have no idea how &amp;quot;static&amp;quot; comes into this, do you mean static electricity? Why would that be related?&lt;/p&gt;&#xA;&lt;p&gt;Anyway, what you are probably experiencing is simple numbness caused by your posture applying pressure to a nerve:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Zeh21.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;In the image above, the right leg is likely to be pressing the the left which can cause &lt;a href=&quot;http://en.wikipedia.org/wiki/Paresthesia&quot; rel=&quot;nofollow noreferrer&quot;&gt;paresthesia&lt;/a&gt;, more commonly known as &amp;quot;pins and needles&amp;quot;. As explained in the NIH's &lt;a href=&quot;http://www.ninds.nih.gov/disorders/paresthesia/paresthesia.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;paresthesia information page:&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Most people have experienced temporary paresthesia -- a feeling of &amp;quot;pins and needles&amp;quot; -- at some time in their lives &lt;strong&gt;when they have sat with legs crossed for too long&lt;/strong&gt;, or fallen asleep with an arm crooked under their head. It happens when sustained pressure is placed on a nerve. The feeling quickly goes away once the pressure is relieved.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-12-09T16:09:02.507" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13896" PostTypeId="1" CreationDate="2013-12-09T23:49:08.807" Score="7" ViewCount="134" Body="&lt;p&gt;&lt;a href=&quot;http://www.nrdc.org/wildlife/animals/bees.asp&quot;&gt;Colony Collapse Disorder&lt;/a&gt; is a well studied phenomenon relating to the decline of bee populations - has this disorder, or its equivalent, been observed in other colony-based species?&lt;/p&gt;&#xA;" OwnerDisplayName="user5130" LastEditorUserId="3624" LastEditDate="2013-12-18T15:30:29.167" LastActivityDate="2014-03-18T19:27:47.067" Title="Has Colony Collapse Disorder (or its equivalent) been noted in other species?" Tags="&lt;entomology&gt;&lt;ecology&gt;&lt;conservation-biology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13897" PostTypeId="1" AcceptedAnswerId="13915" CreationDate="2013-12-10T00:55:54.717" Score="7" ViewCount="308" Body="&lt;p&gt;&lt;a href=&quot;http://cir.ca/news/fda-halts-23andmes-dna-testing&quot; rel=&quot;nofollow noreferrer&quot;&gt;The recent news&lt;/a&gt; about the FDA stopping the google backed 23andMe service selling any more kits got me thinking. I understand the company may have been selling it as a medical tool prematurely, but what is it about SNP analysis that makes it so poor as at predicting disposition? Even other SNP companies have similar problems with accuracy and can't agree on disease disposition &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21502420&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Tonellato &lt;em&gt;et al.&lt;/em&gt;, 2011)&lt;/a&gt;. Why might they differ from 23andMe's predictions?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2018-02-16T14:09:55.653" LastActivityDate="2018-07-10T19:41:04.460" Title="What about 23andMe's SNP test gives it such bad efficacy as a diagnostic tool?" Tags="&lt;genomics&gt;&lt;human-genome&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13900" PostTypeId="1" AcceptedAnswerId="13901" CreationDate="2013-12-10T11:04:02.597" Score="2" ViewCount="44" Body="&lt;p&gt;In Pfu turbo DNA Polymerase AD information sheet (and possibly in many other) different amplification targets are divided in Genomic DNA targets, Vector DNA targets and cDNAs. &#xA;What is the difference between the first two?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="948" LastEditDate="2013-12-10T15:45:58.213" LastActivityDate="2013-12-10T15:45:58.213" Title="Difference vector target and genomic target" Tags="&lt;pcr&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13901" PostTypeId="2" ParentId="13900" CreationDate="2013-12-10T12:06:15.390" Score="3" Body="&lt;p&gt;Genomic DNA is a DNA that has whole set of genetic data of an organism. You usually extract it with a whole DNA extraction kit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vector DNA is a vector (usually a plasmid, it can also be artificial chromosome,...the type of vector depends on the species and strategy you are using) that has you desired string of DNA in it (for example a gene you want to insert in to a organism) and you are using it to get your recombinant DNA to the organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope it helps!&lt;/p&gt;&#xA;" OwnerUserId="4860" LastActivityDate="2013-12-10T12:06:15.390" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13904" PostTypeId="1" CreationDate="2013-12-10T16:22:14.477" Score="0" ViewCount="161" Body="&lt;pre&gt;&lt;code&gt;                      GrandParents                  -- 1&#xA;                            |&#xA;                            |&#xA;                -------------------------&#xA;                |S                      |D          -- 2&#xA;            ---------                ----------&#xA;            |S(A)   |D               |S(A)    |S(A) -- 3&#xA;            |S      |D                              -- 4&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;S = Son&#xA;D = Daughter&#xA;(A) = Affected with a degenerative disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is how to identify the type of inheritance of the disease - whether&#xA;X-based, Autosomal dominant or recessive. Which sex of fourth generation are likely to have the disease? Does it depend on the disease?&lt;/p&gt;&#xA;" OwnerUserId="5137" LastEditorUserId="3615" LastEditDate="2013-12-10T16:54:27.313" LastActivityDate="2013-12-14T12:46:32.327" Title="Identifying the inheritance pattern" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13905" PostTypeId="1" AcceptedAnswerId="13922" CreationDate="2013-12-10T16:37:55.193" Score="4" ViewCount="1181" Body="&lt;p&gt;What is the most genetically simple organism (except viruses) on this planet?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By simple I mean the least number of genes.&lt;/p&gt;&#xA;" OwnerUserId="3118" LastEditorUserId="561" LastEditDate="2013-12-10T16:54:03.580" LastActivityDate="2013-12-12T17:48:41.067" Title="What is the most genetically simple organism except viruses?" Tags="&lt;dna&gt;&lt;genetics&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="13906" PostTypeId="2" ParentId="13904" CreationDate="2013-12-10T17:16:07.440" Score="1" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As said @Biogirl, &quot;This pedigree can not lead to one absolute answer&quot;. We miss information in order to answer this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Should we make the assumption that the allele causing the disease (A) necessarily come from the lineage you draw or can it come from the partners of the second generation (offspring of GrandParents)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, depending on your answer to this question...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If yes (= if the allele causing (A) comes from the GrandParents):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;This genealogy is impossible if the type of inheritance is as simple as you suggested (either recessive or dominant, no epigenetics, no epistasis, no effect of the environment, no protein-mediated disease via the vomb,... even if it can be autosomal, sexual or mitochondrial genes) &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If no (= if the allele causing (A) do not come from the GrandParents only)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Everything is possible (from the space of possibilities that you suggested)&#xA;&lt;ul&gt;&#xA;&lt;li&gt;some possibilities would be more probable than others (depending especially on the allele frequencies)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-12-14T12:46:32.327" LastActivityDate="2013-12-14T12:46:32.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13907" PostTypeId="2" ParentId="13783" CreationDate="2013-12-10T22:25:04.183" Score="2" Body="&lt;p&gt;I frankly don't trust Mfold or RNAfold for finding structure. There are just too many false positives and without experimental verification, it's not reliable. For finding hypothetical local structure, it's great. However to find evolutionary conserved structure MSA methods like what has been used with Rfam are a more suitable way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since you asked for Reviews, any of Sean Eddy's Rfam updates are good. I also suggest checking out &lt;a href=&quot;https://www.mendeley.com/groups/545791/rna-structure/&quot; rel=&quot;nofollow&quot;&gt;https://www.mendeley.com/groups/545791/rna-structure/&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But for now, I think &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16500677&quot; rel=&quot;nofollow&quot;&gt;Revolutions in RNA Secondary Structure Prediction&lt;/a&gt; by David Mathews who developed the Turner rules and Mfold is a good start.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2013-12-10T22:25:04.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13908" PostTypeId="1" AcceptedAnswerId="13912" CreationDate="2013-12-11T03:29:05.600" Score="1" ViewCount="2125" Body="&lt;p&gt;I'm doing my High School biology final on Progeria, and am wondering what type of mutation causes this disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that the LMNA gene codes for the &quot;prelamin A&quot; protein, and that protein contains a farnesyl group that is then not able to be removed (in the case of Progeria). The abnormal form (with the farnesyl still attached) of prelamin A is then called progerin, and attaches to the nuclear rim resulting in an abnormally formed cell nucleus, making mitosis impossible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this a structural mutation? What sort of mutation is this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="5139" LastActivityDate="2013-12-11T08:18:54.473" Title="What type of mutation causes Progeria?" Tags="&lt;proteins&gt;&lt;genetics&gt;&lt;transcription&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13909" PostTypeId="1" AcceptedAnswerId="14031" CreationDate="2013-12-11T06:11:44.140" Score="2" ViewCount="188" Body="&lt;p&gt;I know microalgae have not less protein and starch, grow quickly, require less. So, is it possible to use them for producing food (replace rice and wheat) and live on it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Currently, I only saw people eat it as an extra-nutrition.&lt;/p&gt;&#xA;" OwnerUserId="5141" LastEditorUserId="24354" LastEditDate="2020-04-14T23:15:02.483" LastActivityDate="2020-04-14T23:15:02.483" Title="Is it possible to use microalgae to produce food and live on it?" Tags="&lt;food&gt;&lt;nutrition&gt;&lt;algae&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="13910" PostTypeId="1" CreationDate="2013-12-11T06:17:42.983" Score="-3" ViewCount="938" Body="&lt;p&gt;I am currently writing a mathematical biology paper, however it is very hard for me to follow the existing literature due to specialized terms. I have tried googling but most explanations are very technical and filled with more biology jargon. I have absolutely zero biology experience, so if anyone could please give a very very basic, non technical/rigorous, and intuitive explanation of the following terms, that would be great.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Nucleotide&lt;/li&gt;&#xA;&lt;li&gt;Protein&lt;/li&gt;&#xA;&lt;li&gt;DNA &lt;/li&gt;&#xA;&lt;li&gt;Adenine, Thyine, Cytosine, Guanine&lt;/li&gt;&#xA;&lt;li&gt;RNA&lt;/li&gt;&#xA;&lt;li&gt;Single Nucleotide Polymorphisms (SNP)&lt;/li&gt;&#xA;&lt;li&gt;Base: e.g. &quot;1% of the human genome (about 30 million base pairs) will&#xA;be treated.&quot;&lt;/li&gt;&#xA;&lt;li&gt;Eukaryotic&lt;/li&gt;&#xA;&lt;li&gt;Genome&lt;/li&gt;&#xA;&lt;li&gt;Genome sequence&lt;/li&gt;&#xA;&lt;li&gt;Whole-genome&lt;/li&gt;&#xA;&lt;li&gt;Partial-genome&lt;/li&gt;&#xA;&lt;li&gt;GC content&lt;/li&gt;&#xA;&lt;li&gt;conservation: e.g. &quot;degree of evolutionary conservation&quot;&lt;/li&gt;&#xA;&lt;li&gt;conserved region: e.g. &quot;functional elements are more likely to be&#xA;found in DNA regions that are the best conserved across species&quot;&lt;/li&gt;&#xA;&lt;li&gt;conserved sequence&lt;/li&gt;&#xA;&lt;li&gt;chromosome&lt;/li&gt;&#xA;&lt;li&gt;binary sequence&lt;/li&gt;&#xA;&lt;li&gt;non-coding DNA/RNA&lt;/li&gt;&#xA;&lt;li&gt;non-protein-coding genes/sequence/portion/elements&lt;/li&gt;&#xA;&lt;li&gt;protein-coding genes/sequence/portion/elements&lt;/li&gt;&#xA;&lt;li&gt;gene sequencing&lt;/li&gt;&#xA;&lt;li&gt;gene promoters&lt;/li&gt;&#xA;&lt;li&gt;purifying selection&lt;/li&gt;&#xA;&lt;li&gt;positive selection&lt;/li&gt;&#xA;&lt;li&gt;functional element: e.g. “…classes of functional non-coding elements&#xA;remain to be discovered”&lt;/li&gt;&#xA;&lt;li&gt;non-functional element: e.g. &quot;identify all non-functional elements in&#xA;the human genome.&quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5142" LastActivityDate="2013-12-12T17:10:08.213" Title="Basic definitions for biology terminology" Tags="&lt;terminology&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2013-12-11T08:02:15.493" ContentLicense="CC BY-SA 3.0" />
  <row Id="13911" PostTypeId="2" ParentId="13910" CreationDate="2013-12-11T07:18:01.967" Score="3" Body="&lt;p&gt;There are too many questions that ask for too many explanations, I don't think anybody wants to answer to all that. It is not really possible to give a &quot;very basic without technical term&quot; definitions to most of these words. If you want to write an article in mathematical biology, I am afraid you will have to take some time to learn a bit about biology. Go through some books that will guide in the basic understanding of biology. I know we all would like things to be easy when starting a new field but unfortunately there is no easy answer to your questions. &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0321558235&quot; rel=&quot;nofollow&quot;&gt;This book&lt;/a&gt; for example might help you. It is a classic in first year Bachelor in biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have some specific questions, you are very welcome to ask them. But this post asks for a whole book!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a small quickly written text that will maybe help you a bit. Note: it might be oversimplified sometimes!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA is a big molecule made of (among other things) nucleotides. There are 4 nucleotides (adénine, cytosine, tyrosine (or Uracile on RNA) and guanine often just called ACTG and they can be categorized in two types of molecule depending on their number of cycles) which sequence form the genetic information. DNA, in eukaryotes (which are cells that contains DNA in a nucleus (which is the case of all non-virus, non-bacteria and non-archaebacteria)) is grouped into chromosomes (which are usually represented by a &quot;X&quot; as they more or less appears at the metaphase (a phase during the life cycle of a cell)).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA is transcribed into mRNA (a kind of RNA) which is then translated into protein (by rRNA and tRNA). While RNA and DNA are made of nucleotides, the protein is made of amino acids. Three nucleotides (one codon) codes for 1 amino acid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the genome there are sequences that code for proteins, sequences that code for RNA, sequences that allows other proteins to bind into in order to influence gene expression, promotors, enhancers… You will have to accept taking some time learning a bit about that stuff I guess.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sequencing is the (artificial) process of reading a DNA sequence. This can be achieved on a whole genome or on small chosen sequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the nucleotides G binds only with C and A binds only with T (two nucleotides together form a base pair)(there are two strands of DNA linked by the nucelotides), the amount of G equals the amount of C and same for A and T. The GC content gives the proportion of G and C of the total number of nucleotides of a sequence (or a whole genome). Oh by the way, a genome is the totality of the DNA of a given individual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Positive/purifying selection are cases of natural selection. Natural selection is a process by which the frequencies of alleles (variant of a gene) does not vary randomly. They vary according to the reproductive success (= fitness) they confer to the individuals that bear the allele. Positive selection on an allele means that this allele is selected for. Purifying selection refers to the wildtype allele (most frequent allele) is selected for and all mutations (DNA modifications) that appear are deleterious and therefore counterselected,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A SNP is a genetic variation between individuals in a population (or along populations or species) that involves only one nucleotide.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="1320" LastEditDate="2013-12-12T17:10:08.213" LastActivityDate="2013-12-12T17:10:08.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13912" PostTypeId="2" ParentId="13908" CreationDate="2013-12-11T08:18:54.473" Score="4" Body="&lt;p&gt;Hutchinson–Gilford progeria syndrome is almost always due to to a &lt;em&gt;de novo&lt;/em&gt; mutation (i.e. not an inherited mutation) in the lamin A gene (&lt;em&gt;LMNA&lt;/em&gt;). The mutation responsible is a C-to-T substitution at position 1824. Remarkably this doesn't change the encoded amino acid but rather creates a new splice donor site in the RNA transcript. When this splice site is used it results in the deletion of information corresponding to about 50 amino acids internal to the protein and near to the C terminus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During biogenesis of normal lamin A a C-terminal -CAAX motif is recognised as a signal for isoprenylation, in this case farnesylation. The added lipid group acts as a C-terminal membrane anchor. However this anchor is subsequently removed when the protein is proteolytically cleaved near the C-terminus, removing 15 amino acids including the C-terminal cysteine (by this point the three C-terminal residues have been trimmed away). The cleavage site for this final modification is missing in HGPS lamin A so the farnesyl group cannot be removed. The accumulation of unprocessed lamin A causes the observed defects in the nuclear membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eriksson et al. (2003) Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome. Nature 423: 293-298 &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Capell et al. (2005) Inhibiting farnesylation of progerin prevents the characteristic nuclear blebbing of Hutchinson-Gilford progeria syndrome. Proc. Natl. Acad. Sci. USA 102: 12879-12884 &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-12-11T08:18:54.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13914" PostTypeId="2" ParentId="5099" CreationDate="2013-12-11T10:20:02.567" Score="4" Body="&lt;p&gt;I don't think that the role of pheomelanin is known yet. To produce larger amounts of it, you need mainly two conditions: A weak (or absent) MC1R signalling and the availibility of the amino acid cysteine. If MC1R signalling is strong, the preferred way goes into the direction of eumelanin. Its known for quite a while that pheomelanin produces reactive oxygen species which either directly cause DNA damage or do it indirectly by using up the cells storage of antioxidants. You can find more details in this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23650156&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt; as well as links to a number of original papers.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-11T10:20:02.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13915" PostTypeId="2" ParentId="13897" CreationDate="2013-12-11T12:28:55.333" Score="4" Body="&lt;p&gt;The long and short of it is that genetic variation is actually not very predictive in comparison to &quot;environmental&quot; effects such as lifestyle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Only a quarter of the variation in lifespan between twins is attributable to inherited factors (including genetics and epigenetics) [1] - the rest is environmental, from lifestyle to air quality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most genetic variants (such as those measured on the chip used by 23andMe) have a very small impact on outcomes such as &quot;Risk of disease X, Y or Z&quot;. Many risk loci have been identified, but without a full understand of what this risk means, the results of the 23andMe analysis can be misleading.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some few rare genetic variants have a larger impact on diseases (such as early onset diabetes), but this comes under the &quot;monogenic&quot; category of genetic variation, rather than the common variants typically observed in large populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, genetic risk scores are, at the moment, only indicative of an individuals risk, and to get the real picture a lot more information is required - for instance smoking is a better predictor of early mortality than any &quot;common&quot; (&gt;=5% frequency in a population) genetic variants, likewise a high fat diet is more indicative of cardiovascular disease.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Skytthe A, Pedersen NL, Kaprio J, et al. Longevity studies in&#xA;GenomEUtwin. Twin Res. 2003;6(5):448–454. [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14624729&quot; rel=&quot;nofollow&quot;&gt;PubMed link&lt;/a&gt;]&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastActivityDate="2013-12-11T12:28:55.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13917" PostTypeId="2" ParentId="13904" CreationDate="2013-12-11T14:09:18.003" Score="1" Body="&lt;p&gt;We are missing some information, but (by what I recall from my little inheritance genetics knowledge) it looks X-based. I will make up some of the missing information.&#xA;Lets say, an &quot;affected X&quot; is H (I wanted to use x, but it will be harder to see), HY will be diseased, XH will be carrier, but not diseased. XX/XH means unclear if carrying.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Grandparents:               XY-------------XH&#xA;                                    |&#xA;                           -------------------&#xA;                           |                  |&#xA;Parents&amp;amp;Partners      XH---XY                 XH---XY&#xA;                         |                        |&#xA;                     ---------               ----------&#xA;                     |        |              |         |&#xA;F1                  HY       XX/XH          HY         HY&#xA;                     |        |&#xA;F2                  YX       XX/XH&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The F2 son is not carrying (because he is healthy). The F2 daughter could be carrying if her mother was, but even then does not have to. Unless her dad was also carrying it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please correct me, if I am totally off.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2013-12-11T14:09:18.003" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13918" PostTypeId="1" AcceptedAnswerId="13921" CreationDate="2013-12-11T14:36:54.740" Score="2" ViewCount="140" Body="&lt;p&gt;Miraculously, transplanted stem cells find their way to the bone marrow missing the stem cells. How do they achieve this?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastEditorUserId="1320" LastEditDate="2013-12-12T17:45:36.897" LastActivityDate="2013-12-12T17:45:36.897" Title="How do transplanted stem cells find their way to bone marrow?" Tags="&lt;stem-cells&gt;&lt;transplantation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13921" PostTypeId="2" ParentId="13918" CreationDate="2013-12-11T19:26:13.933" Score="3" Body="&lt;p&gt;The transplantation is an equivalent of a process that naturally occurs in human body, homing of the hematopoietic stem cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Immature hematopoietic stem cells have the ability to pass the bone marrow barrier, and therefore is able to migrate between bones and other organs within an individual. (e.g. thymus, which is how it can produce T cells.) Williams et al. believe that the process, homing, is a complex interaction and is similar to the migration of leukocytes to inflammatory sites. &lt;a href=&quot;http://dx.doi.org/10.1016/S0076-6879%2807%2900427-2&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Peripheral stem cell transplantation makes use of this ability. The donor first will be administered with certain drugs to proliferate stem cells in bone marrow and hereby raising the concretion of hematopoietic stem cells in blood. Those stem cells in blood then will be collected and transfused into the recipient. Eventually those cells will find their way home.&lt;/p&gt;&#xA;" OwnerUserId="4136" LastEditorUserId="1320" LastEditDate="2013-12-12T17:44:50.457" LastActivityDate="2013-12-12T17:44:50.457" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13922" PostTypeId="2" ParentId="13905" CreationDate="2013-12-11T21:08:41.083" Score="7" Body="&lt;p&gt;&lt;em&gt;Mycoplasma genitalium&lt;/em&gt; was one of the first full bacterium genomes sequenced and since its a symbiotic organism that lives on the moist and warm genital skin surface it doesn't need as many genes as many bacteria.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/474?project_id=57707&quot; rel=&quot;noreferrer&quot;&gt;It has a 582 kbp genome sequence&lt;/a&gt; with only &lt;a href=&quot;http://en.wikipedia.org/wiki/Mycoplasma_genitalium&quot; rel=&quot;noreferrer&quot;&gt;521 genes&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But that is so &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7569993&quot; rel=&quot;noreferrer&quot;&gt;1995&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The 159 kbp genome of &lt;em&gt;Candidatus carsonella&lt;/em&gt; was &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17038615&quot; rel=&quot;noreferrer&quot;&gt;published in 2006&lt;/a&gt;. It is thought to only contain 182 genes.  Its an endosymbiont of some sap eating insects.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the current record holder, published this year, is &lt;em&gt;Nasuia deltocephalinicola&lt;/em&gt;, discovered survey of insect endosymbionts, has only &lt;a href=&quot;http://gbe.oxfordjournals.org/content/5/9/1675.full&quot; rel=&quot;noreferrer&quot;&gt;112 kbp in its genome&lt;/a&gt;. &lt;a href=&quot;http://www.giantvirus.org/top.html&quot; rel=&quot;noreferrer&quot;&gt;Smaller than some viruses&lt;/a&gt;.  It's thought to contain 137 protein coding genes with 29 tRNA genes, so its not a lot smaller than Carsonella in terms of gene count. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's no reason to expect that this is the minimal viable genome by any means.  I'm sure this response will need revision in a year or two. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;M. genitalium&lt;/em&gt; has become the model system for minimal genome work.  Many of these other bacteria might be difficult to culture, molecular biology lab techniques might have to be developed, so hopping onto newly discovered bacteria isn't always the best idea from a standpoint of producing science.  It does suggest that M gentalium doesn't need all of its genes!  A possible cause for these extra genes might be a more complex immune response in human beings where its found.  It might also be because of the symbiotic requirements of insects is simpler.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1320" LastEditDate="2013-12-12T17:48:41.067" LastActivityDate="2013-12-12T17:48:41.067" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13923" PostTypeId="2" ParentId="13819" CreationDate="2013-12-12T00:11:41.083" Score="4" Body="&lt;p&gt;You can try looking around biostars.org, which is like stackexchange, but for bioinformatics.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Velvet is one example of a de novo assembler.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But 30 bp is really short, and animals have big genomes (not as tough as lots of plants and fungi, but still tough)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you would get is a bazillion short contigs.  It would not be pretty.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastEditorUserId="5148" LastEditDate="2013-12-12T19:34:34.323" LastActivityDate="2013-12-12T19:34:34.323" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13924" PostTypeId="1" AcceptedAnswerId="13951" CreationDate="2013-12-12T00:15:26.983" Score="9" ViewCount="421" Body="&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that with genetic engineering we can customize organisms as bio-weapons. Which species have the most worrying potential to be weaponized for mass destruction?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_warfare&quot; rel=&quot;noreferrer&quot;&gt;&lt;strong&gt;&lt;em&gt;Biological warfare&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt; — is the use of biological toxins or infectious agents such as bacteria, viruses, and&#xA;  fungi with intent to kill or incapacitate humans, animals or plants as&#xA;  an act of war.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Examples:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;E.G. bio-weapon species:&lt;/strong&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/Anthrax#History&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Anthrax fungus&lt;/em&gt;&lt;/a&gt; -  was first tested as a biological warfare agent by Unit 731 of&#xA;  the Japanese Kwantung Army in Manchuria during the 1930s; some of this&#xA;  testing involved intentional infection of prisoners of war, thousands&#xA;  of whom died. Anthrax, designated at the time as Agent N, was also&#xA;  investigated by the Allies in the 1940s.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;E.G. bio-weapon vector:&lt;/strong&gt; &lt;a href=&quot;http://www.telegraph.co.uk/news/worldnews/europe/italy/1510482/Nazis-tried-to-halt-Allies-in-Italy-with-malaria-epidemic-attack.html&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Anopheles labranchiae (malarial mosquito)&lt;/em&gt;&lt;/a&gt; - According to Prof Frank Snowden, a history professor at Yale&#xA;  University whose book The Conquest of Malaria in Italy draws on&#xA;  American archives and the diaries of Italian soldiers, the scheme was&#xA;  orchestrated in the autumn of 1943 by Erich Martini, a medical&#xA;  entomologist, Nazi Party member and friend of the SS commander&#xA;  Heinrich Himmler.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2014-03-18T13:49:17.263" LastActivityDate="2014-03-26T12:31:52.360" Title="Organisms as potential Bio-Weapons?" Tags="&lt;pathology&gt;&lt;mycology&gt;&lt;infection&gt;" AnswerCount="4" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13925" PostTypeId="2" ParentId="13743" CreationDate="2013-12-12T00:23:37.170" Score="3" Body="&lt;p&gt;Deep sequencing is naturally error prone.  Sequencing will never be perfect, because no enzyme will ever perform 100.00000% perfectly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Illumina sequencing, you put your starting molecule down on the flowcell, then the polymerase makes a cluster of copies around it.  But at each step of building each copy, there's a chance the polymerase will make a mistake.  Then at sequencing, a single complementary labeled dideoxynucleotide is added to the complementary chain.  But there is always a chance the enzyme will make a mistake.  Then after the base is read, the label needs to be cleaved.  Another step where the enzyme might make a mistake.  Then the base is converted to deoxy, another possible error.  Even if each step is very unlikely to fail, after a lot of steps, there will be enough problems that the cluster won't show the correct color uniformly.  The software tries to compensate, but the result is that you &lt;strong&gt;will&lt;/strong&gt; have reads with inaccuracies.  That's why you have to have depth.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2013-12-12T00:23:37.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13926" PostTypeId="1" AcceptedAnswerId="13927" CreationDate="2013-12-12T01:01:58.403" Score="15" ViewCount="9923" Body="&lt;p&gt;The Genome of a cell or organism is the same as that of the entire organism. However, the proteome of an organism is much greater than that of each cell (unless the organism is unicellular). &#xA;How do you account for the presence of more variation among of proteins than there are in genes?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The simple answer would be &quot;there are more proteins than genes&quot;, but I'm more interested in why. Is it sufficient to say that during gene expression a single gene codes for multiple proteins (Alternative Splicing) and ribosomes translating mRNA to polypeptide chains (Posttranslational modification)? Could someone expand more on this? &lt;/p&gt;&#xA;" OwnerUserId="5085" LastEditorUserId="1590" LastEditDate="2016-03-26T09:46:03.457" LastActivityDate="2019-03-28T03:49:30.233" Title="Why is there more variation in proteins than genes?" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13927" PostTypeId="2" ParentId="13926" CreationDate="2013-12-12T01:14:39.250" Score="16" Body="&lt;p&gt;There are several concepts to understand:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Alternative splicing&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;From one gene, several proteins can be constructed depending on which introns are spliced.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Tissue-specific genetic expression&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Genes are differentially expressed (and differentially spliced) depending on the tissue.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Post-transcriptional modifications&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Those are modifications that are made directly on the proteins (in opposition with alternative splicing which are modifications made on the RNA)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Structure of the proteins&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Proteins may fold (to what we call primary, secondary, tertiary and quaternary structures) differently in different environment.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Therefore there is variance in proteome between cells although there is no variance in genome between cells (except mutations and red blood cells). Moreover, one gene sequence can give rise to many different proteins due to the processes of alternative splicing and PMT. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="16866" LastEditDate="2019-03-28T03:49:30.233" LastActivityDate="2019-03-28T03:49:30.233" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="13928" PostTypeId="1" CreationDate="2013-12-12T01:16:18.477" Score="4" ViewCount="116" Body="&lt;p&gt;If this is the wrong place to post this question, then I will delete it and post it were it belongs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have heard many conflicting things about circumcision.  I have heard that it reduces the rate of STDs, including AIDS, and cancer in the man and his wife.  On the other hand, I have also heard that circumcising babies can cause psychological harm and increases the rate of urinary tract infections.  Are there any reliable studies on this issue and what do the conclude?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for any and all answers.&lt;/p&gt;&#xA;" OwnerUserId="5149" LastActivityDate="2013-12-12T06:39:31.970" Title="What evidence is there on the medical effects of circumcision?" Tags="&lt;medicine&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13929" PostTypeId="2" ParentId="13928" CreationDate="2013-12-12T06:39:31.970" Score="3" Body="&lt;p&gt;This question has already been answered over at the &lt;a href=&quot;http://skeptics.stackexchange.com&quot;&gt;Skeptics site&lt;/a&gt; in great detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;https://skeptics.stackexchange.com/questions/4398/does-circumcision-reduce-hiv-risk&quot;&gt;Does circumcision reduce HIV risk?&lt;/a&gt; and &lt;a href=&quot;https://skeptics.stackexchange.com/questions/1367/does-circumcision-lead-to-a-net-increase-in-quality-of-life&quot;&gt;Does circumcision lead to a net increase in quality of life?&lt;/a&gt;. The answers are well-sourced and there are answers addressing both sides of the issue.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2013-12-12T06:39:31.970" CommentCount="2" CommunityOwnedDate="2013-12-12T06:39:31.970" ContentLicense="CC BY-SA 3.0" />
  <row Id="13930" PostTypeId="2" ParentId="13808" CreationDate="2013-12-12T06:48:16.200" Score="3" Body="&lt;p&gt;Quoting from some parts of &lt;a href=&quot;http://en.wikipedia.org/wiki/Sean_B._Carroll&quot; rel=&quot;nofollow&quot;&gt;Sean Carroll&lt;/a&gt;'s book - &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0393327795&quot; rel=&quot;nofollow&quot;&gt;Endless forms most beautiful&lt;/a&gt;, I have tried to provide you with an answer but, remember that this can never suffice for the reading of this great book.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, we do understand how the hox genes' expression is regulated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From page 126-127&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;......The establishment of these Hox zones and their subsequent action&#xA;  in sculpting the different forms of repeated parts is the fundamental&#xA;  genetic logic upon which the modular forms of large,biletarian animals&#xA;  is built.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The genetic logic relies on genetic switches at two levels. One set of&#xA;  switches belongs to the Hox genes themselves. these switches activate&#xA;  each Hox gene in different zones that will become different modules of&#xA;  the animal. Another set of switches contain signature sequences that&#xA;  are recognized by Hox proteins and that control how other genes are&#xA;  expressed in different modules.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In both arthropods and vertebrates, the Hox genes are developed in&#xA;  zones along the main body axis. The distinct zones of each Hox gene's&#xA;  expression domain are governed by genetic switches, and seperate&#xA;  switches control Hox gene patterns in different tissues such as the&#xA;  ...... Because of the logic of the genetic switches, the cells that&#xA;  belong to one module express different Hox proteins or combinations of&#xA;  Hox proteins than those in adjacent modules....&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Let us take an example of Ubx gene which leads to formation of wings in the 2nd and 3rd thoracic segments of  drosophila. This gene is turned off in the first thoracic segment  but in the second and third segments, it is turned on. This regulation can be achieved because of the genetic switches which in turn can be switched on or off by activators and repressors. These activators and repressors are unevenly distributed in the embryo and so regulation of switches in different parts of the embryo is possible.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3776" LastEditDate="2014-01-13T10:32:39.193" LastActivityDate="2014-01-13T10:32:39.193" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13931" PostTypeId="1" AcceptedAnswerId="13932" CreationDate="2013-12-12T06:55:03.580" Score="7" ViewCount="298" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5TwGp.jpg&quot; alt=&quot;A bird with vertically elongated body, perched upright, moderately long beak&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ZjQ3x.jpg&quot; alt=&quot;The bird now extended its neck taking a gopher like stance&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/bSXuV.jpg&quot; alt=&quot;The same bird having white ventral surface and soiled brown back, back to its resting position&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These photographs have been taken in Warora, India. Could someone please help identify this bird?&lt;/p&gt;&#xA;" OwnerUserId="5150" LastEditorUserId="22057" LastEditDate="2017-05-09T19:33:25.963" LastActivityDate="2017-05-09T19:33:25.963" Title="Bird identification: Warora, India" Tags="&lt;species-identification&gt;&lt;taxonomy&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13932" PostTypeId="2" ParentId="13931" CreationDate="2013-12-12T07:15:06.873" Score="10" Body="&lt;p&gt;This is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Indian_Pond_Heron&quot; rel=&quot;nofollow noreferrer&quot;&gt;pond heron or paddy bird&lt;/a&gt;. The de-facto source for identifying Indian birds is &lt;a href=&quot;http://www.flipkart.com/birds-indian-subcontinent-2nd/p/itmczyt8ck3x2ape&quot; rel=&quot;nofollow noreferrer&quot;&gt;Birds of the Indian Subcontinent&lt;/a&gt; by Richard Grimmett, Carol Inskipp and Tim Inskipp. The book is remarkably complete and contains the vast majority of species found in the Indian Subcontinent. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/6qHQOl.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/6qHQOl.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3631" LastEditorUserId="16866" LastEditDate="2017-05-09T19:17:01.573" LastActivityDate="2017-05-09T19:17:01.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13933" PostTypeId="1" AcceptedAnswerId="13934" CreationDate="2013-12-12T07:34:24.483" Score="4" ViewCount="218" Body="&lt;p&gt;What is the duration (Life&quot;) of pfu turbo DNA polymerase AD. I am trying o Amplification a 3.3kb fragment and the PCR schedule is 6 hours long. The manufacturers notes just specify that its activity remains 94-99% in 1 hour at 95, nothing more.&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="3632" LastEditDate="2013-12-12T14:09:42.743" LastActivityDate="2018-10-05T15:59:21.097" Title="pfu Turbo DNA polymerase AD" Tags="&lt;pcr&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13934" PostTypeId="2" ParentId="13933" CreationDate="2013-12-12T08:51:43.217" Score="7" Body="&lt;p&gt;I don't know the exact half-life of this special Pfu polymerase, but generally Pfu polymerases are pretty stable. This &lt;a href=&quot;http://www.biocompare.com/Application-Notes/41999-Pfu-DNA-Polymerase-As-A-Hot-Start-Alternative/&quot;&gt;source&lt;/a&gt; gives a half life of 18-25 hours at 95°C, meaning you keep the enzyme at 95°C for the whole time a you still have 50% activity after that time. Since you don't do that, I wouldn't worry too much about the activity. To be safe, you can add an extra long (probably 10-15 minutes) single amplification step before cooling down.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-12T08:51:43.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13935" PostTypeId="2" ParentId="13926" CreationDate="2013-12-12T09:34:36.370" Score="6" Body="&lt;p&gt;To comment on the &quot;why&quot; question: I would say that its a relatively simple way to get a high number of proteins with more or less slight differentiations. This can include exons which are only present in special environments or cell types and so on. It saves a lot of energy for keeping all the information about every single transcript (the BNC2 gene for example can produce up to 90.000 different mRNA transcripts coding for up to 2000 different proteins of unknown function, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16942855&quot;&gt;here&lt;/a&gt;) and makes the genome a lot less complex, despite the fact that we now need an also complex regulation.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-12T09:34:36.370" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13936" PostTypeId="2" ParentId="13819" CreationDate="2013-12-12T10:16:07.337" Score="2" Body="&lt;p&gt;I really like the genious software suite. It can multithread and really use the performance of your computer. Even complicated things like De Novo assembly are very very intuitive. &lt;/p&gt;&#xA;" OwnerUserId="3887" LastActivityDate="2013-12-12T10:16:07.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13937" PostTypeId="2" ParentId="13924" CreationDate="2013-12-12T10:22:14.460" Score="4" Body="&lt;p&gt;No doubt influenza. The horizontal shift makes it very virulent and only a few mutations allow it to transfer from birds to mammals (as little as two). See &lt;a href=&quot;http://www.newscientist.com/article/dn23368-china-bird-flu-may-be-two-mutations-from-a-pandemic.html#.UqmN7GRDvqE&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. There was a big push not to publish these as it would be so easy to make recombinantly. However, thanks to quick &lt;a href=&quot;http://www.jci.org/articles/view/69377&quot; rel=&quot;nofollow&quot;&gt;work&lt;/a&gt;, we have determined that our seasonal flu vaccine protects against this variant. &lt;/p&gt;&#xA;" OwnerUserId="3887" LastActivityDate="2013-12-12T10:22:14.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13938" PostTypeId="2" ParentId="13924" CreationDate="2013-12-12T10:35:18.787" Score="4" Body="&lt;p&gt;I would put all zoonotic viruses into this. They passed a species barrier, are new to our immune system and there are no vaccines against them. The flu is one example, corona viruses are another (SARS or even newer MERS). With SARS we had a lot of luck that this didn't end in a bigger epidemic.&#xA;A good book about these viruses is the book &quot;Outbreak&quot; (hence the title) by David Quammen.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2013-12-12T17:43:42.217" LastActivityDate="2013-12-12T17:43:42.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13939" PostTypeId="1" CreationDate="2013-12-12T10:54:03.743" Score="1" ViewCount="293" Body="&lt;p&gt;I have no background in science as I am a computer programmer, but I am trying to get information on phase response curves, human sleep and exposure to bright light as I am trying to get to grips with a possible diagnosis of delayed sleep phase disorder.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6KT9C.gif&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The point marked &lt;em&gt;phase delay&lt;/em&gt; is typically where someone would go to sleep and they would typically wake a couple hours after the peak marked &lt;em&gt;phase advance&lt;/em&gt;. What is the physiological process that cause the move from &lt;em&gt;delay&lt;/em&gt; to &lt;em&gt;advance&lt;/em&gt; via the point marked &lt;em&gt;singularity&lt;/em&gt;? In other words, why does light cause a delay initially but then cause an advance?&lt;/p&gt;&#xA;" OwnerUserId="5146" LastActivityDate="2013-12-12T10:54:03.743" Title="What is the cause of singularity in phase response curve of human sleep and bright light?" Tags="&lt;sleep&gt;&lt;circadian-rhythms&gt;&lt;chronobiology&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13940" PostTypeId="2" ParentId="13808" CreationDate="2013-12-12T16:43:15.693" Score="3" Body="&lt;p&gt;You might be interested in &lt;a href=&quot;http://books.google.ch/books?hl=fr&amp;amp;lr=&amp;amp;id=fMTjQCVrsloC&amp;amp;oi=fnd&amp;amp;pg=PA113&amp;amp;dq=Chromatin+architectures+and+Hox+gene+collinearity.&amp;amp;ots=wvuDC8hVc7&amp;amp;sig=rzSkeNbLXzNoYXKRbh2n-8YUoU8&amp;amp;redir_esc=y#v=onepage&amp;amp;q=Chromatin%20architectures%20and%20Hox%20gene%20collinearity.&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;this book&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When writing Hox Gene collinearity (or colinearity as it is often misspelled as explain in wiki!) on Google scholar or WebOfKnowledge you will get many results on the subject. It is still today an ongoing debate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below are some sentences I pick up from these articles. It is certainly hard to understand as I hardly understood what I wrote! The best for you is to go through &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22252486&quot; rel=&quot;nofollow&quot;&gt;this review&lt;/a&gt;. It is not easy (at least for me but it is not at all my field) but I think it is the best source of information you can find on the subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3382278/&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23587240&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; might also help you to understand the debate on the subject.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;There are several types of collinearity:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Spatial collinearity&lt;/code&gt; is the sequential 3' to 5' expression of Hox Genes along a body axis. &lt;code&gt;Spatial collinearity&lt;/code&gt; can be associated with time dependence where the most 3' is expressed first. This is defined as &lt;code&gt;temporal collinearity&lt;/code&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two main models to explain the mechanisms hidden behind this ordering.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;1) Collinearity is based on transcriptional regulation and specifically that is limited by the progressive 3' to 5' opening of Hox cluster chromatin and/or mediated by global control regions&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2) Collinearity depends on interactions between the Hox genes themselves. These interactions include 'posterior prevalence', a negative interaction among Hox proteins that clearly relates to functional collinearity in Drosophila.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Evolution:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is suggested that collinearity evolved by repeated tandem duplication of an ancestral ur-Hox Gene&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="866" LastEditDate="2013-12-12T17:09:37.147" LastActivityDate="2013-12-12T17:09:37.147" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13941" PostTypeId="1" AcceptedAnswerId="13984" CreationDate="2013-12-12T17:26:00.043" Score="4" ViewCount="965" Body="&lt;p&gt;I understand that one can translate a nucleotide sequence and run PSI-BLAST on the protein (proteins if you take the 6 reading frames), but I'm looking for distant homology for bacterial small RNAs (typically 50-200 nucleotides long and noncoding).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is no such resource, what are the main obstacles to this implementation?&lt;/p&gt;&#xA;" OwnerUserId="991" LastEditorUserId="5005" LastEditDate="2013-12-12T19:23:24.187" LastActivityDate="2014-12-13T10:46:12.047" Title="Is there a PSI-BLAST for nucleotide sequences?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;sequence-analysis&gt;&lt;blast&gt;&lt;homology&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13942" PostTypeId="1" AcceptedAnswerId="13947" CreationDate="2013-12-12T18:32:25.337" Score="4" ViewCount="100" Body="&lt;p&gt;Transplanted organs from the donor are attacked by antibodies from the recepient. So can't we construct &lt;strong&gt;anti-antibodies and destroy specifically those antibodies which are causing the rejections ?&lt;/strong&gt; (Instead of giving immuno suppressants) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well, I can think of some problems :&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;You would have to administer this for life time which is really expensive.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;So, what if anti - antiantibodies were made by the body ? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Any other problems you can think of ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="5144" LastEditDate="2014-03-17T11:16:15.483" LastActivityDate="2017-11-21T22:26:20.653" Title="Anti-antibodies for preventing transplant rejection" Tags="&lt;immunology&gt;&lt;antibody&gt;&lt;transplantation&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13943" PostTypeId="2" ParentId="13941" CreationDate="2013-12-12T18:33:45.990" Score="2" Body="&lt;p&gt;Assuming you are using PSI-BLAST to recruit coding homologous nucleotide sequences to your query nucleotide sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a work-around using PSI-BLAST itself: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Translate your nucleotide sequence into amino acid sequence &lt;/li&gt;&#xA;&lt;li&gt;Run psi-blast to recruit matching homologous protein sequences&lt;/li&gt;&#xA;&lt;li&gt;Store the names or database IDs (e.g. genbank accession numbers) of the best matching proteins&lt;/li&gt;&#xA;&lt;li&gt;Acquire nucleotide sequences of your matches by searching the IDs against a nucleotide database&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Extra details:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;This type of alignment is called a &quot;codon alignment&quot; (as opposed to DNA alignment or protein alignment)&lt;/li&gt;&#xA;&lt;li&gt;This assumes your DNA protein codes for a protein whose functionality is constrained by evolution&lt;/li&gt;&#xA;&lt;li&gt;You must remove all introns from your sequence prior to aligning&lt;/li&gt;&#xA;&lt;li&gt;Your first codon must be a start codon (ATG)&lt;/li&gt;&#xA;&lt;li&gt;Your last codon must be a stop codon.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2013-12-12T18:53:40.303" LastActivityDate="2013-12-12T18:53:40.303" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="13944" PostTypeId="1" AcceptedAnswerId="13958" CreationDate="2013-12-12T18:35:32.540" Score="2" ViewCount="2516" Body="&lt;p&gt;Why is histidine an essential amino acid for children but not for adults ? What changes in the body occur which lead to the formation of histidine in adults but not in children ? What causes these changes ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE : Source : Campbell Biology&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2013-12-12T19:41:54.037" LastActivityDate="2015-08-03T08:52:02.703" Title="Histidine - why essential for children?" Tags="&lt;nutrition&gt;&lt;amino-acids&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13945" PostTypeId="1" AcceptedAnswerId="13950" CreationDate="2013-12-12T18:48:41.693" Score="3" ViewCount="133" Body="&lt;p&gt;Has there any mutations been recorded which cause harmful effects due to change in the part of pre-mRNA responsible for proper m-RNA splicing ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-12-12T20:06:50.690" Title="Mutation in pre-mRNA sequence" Tags="&lt;rna&gt;&lt;mutations&gt;&lt;mrna&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="13946" PostTypeId="2" ParentId="13942" CreationDate="2013-12-12T18:55:39.067" Score="4" Body="&lt;p&gt;Within an organism, antibodies which bind to other antibodies in the body would be eliminated during &lt;a href=&quot;http://en.wikipedia.org/wiki/Clonal_selection&quot; rel=&quot;nofollow&quot;&gt;clonal selection&lt;/a&gt;.  They are not made by the body after that period, which is in the first few months of life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such antibodies would have to be introduced from the outside.  Many have been designed or engineered for biotech and as therapeutics. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-12-12T20:08:13.290" LastActivityDate="2013-12-12T20:08:13.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13947" PostTypeId="2" ParentId="13942" CreationDate="2013-12-12T19:13:43.650" Score="4" Body="&lt;p&gt;The root of the problem in this case are not the antibodies but the antibody producing cells (APC). They are capable of producing vast amounts of antibody, so I doubt that this approach would be successful. The problem with targeting these APCs is, that you have to know exactly which are the ones which cause the problem, if you want to target them specifically.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-12T19:13:43.650" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13948" PostTypeId="2" ParentId="13819" CreationDate="2013-12-12T19:17:32.790" Score="3" Body="&lt;p&gt;If you only want to use only sequencing techniques, you have a problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To get a feeling of what kind of results to expect, consider &lt;a href=&quot;http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2835.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper published recently in Nature Genetics. They tried to assemble a whale genome de novo. They had 7 (!) paired-end libraries with different insert lengths ranging from 170bp to 20kb. Read lengths were mostly 100bp and in some cases 49bp. Average genome coverage was 91x.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assembling this extensive data, they end up with over 100,000 contigs when the assembly is done.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you really can't get a high-quality complex (i.e. large) genome assembled from only short-read sequencing data using the standard techniques.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, recent approaches such as libraries with much longer reads lengths (&lt;a href=&quot;http://elife.elifesciences.org/content/2/e00569&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) or the use of Hi-C data (&lt;a href=&quot;http://www.nature.com/nbt/journal/v31/n12/full/nbt.2768.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/nbt/journal/v31/n12/full/nbt.2727.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) do offer a way of getting high-quality complex genome assemblies using only sequencing data. &lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2013-12-12T19:17:32.790" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13949" PostTypeId="2" ParentId="13941" CreationDate="2013-12-12T19:46:20.423" Score="3" Body="&lt;p&gt;If you have a non-coding gene sequence (e.g. regulatory sequence) this answer should hold your solution:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background theory&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Firstly you must realize that PSI-BLAST is built for detecting &quot;romote homologues&quot;,  (i.e. those that have a very &quot;distant evolutionary relationship&quot; to your query) - from a &lt;strong&gt;&lt;em&gt;database&lt;/em&gt;&lt;/strong&gt; of sequences. It is therefore known to be a &quot;sensitive&quot; analysis which can recruit distantly related matches but has a small chance of recruiting some false matches - &quot;rogue homologues&quot;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Secondly PSI-BLAST is known as a &quot;profile method&quot; that is it uses multiple sequences that are cumulatively recruited with each &quot;psi-blast iteration&quot;, to build an empirical profile of amino acid residues along the positions of your query. This is in the same family of analyses as &quot;Hidden markov models&quot; (HMMs) in that HMMs use multiple sequences to build an empirical profile that is able to recruit distant homologous, except the &quot;profile&quot; includes probabilistic pathways to all the recruited sequences.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My Answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suggest you use a software package called &lt;strong&gt;&lt;em&gt;HMMER&lt;/em&gt;&lt;/strong&gt;. Indeed this method shares critical theoretical similarity to PSI-BLAST as well as functionality in your case (searching for remote nucleotide sequence matches in a database vs. a nucleotide query), it also does not assume your sequence is protein-coding - here is the &lt;a href=&quot;http://en.wikipedia.org/wiki/HMMER&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt; description:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;HMMER is a free and commonly used software package for sequence&#xA;  analysis written by Sean Eddy.&lt;a href=&quot;http://en.wikipedia.org/wiki/HMMER&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt; Its general usage is to identify&#xA;  homologous protein or nucleotide sequences. It does this by comparing&#xA;  a profile-HMM to either a single sequence or a database of sequences.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other possible answers&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are afraid of using HMMER, then here is a list of all alignment software tools represented in a table that allows you to focus on only those that use nucleotide sequence as input:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_sequence_alignment_software&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/List_of_sequence_alignment_software&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2013-12-12T19:51:46.847" LastActivityDate="2013-12-12T19:51:46.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13950" PostTypeId="2" ParentId="13945" CreationDate="2013-12-12T20:06:50.690" Score="6" Body="&lt;p&gt;Yes, you can find mutations in the genomic DNA which affect splice acceptor sites. &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_splicing&quot;&gt;Wikipedia&lt;/a&gt; lists the following outcome:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mutation of a splice site resulting in loss of function of that site.&#xA;Results in exposure of a premature stop codon, loss of an exon, or&#xA;inclusion of an intron. &lt;/li&gt;&#xA;&lt;li&gt;Mutation of a splice site reducing specificity. May result in&#xA;variation in the splice location, causing insertion or deletion of&#xA;amino acids, or most likely, a disruption of the reading frame.&lt;/li&gt;&#xA;&lt;li&gt;Displacement of a splice site, leading to inclusion or exclusion of&#xA;more RNA than expected, resulting in longer or shorter exons.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The article lists two interesting papers: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lim KH, Ferraris L, Filloux ME, Raphael BJ, Fairbrother WG (2011). &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21685335&quot;&gt;Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes&lt;/a&gt;&quot;. Proc. Natl. Acad. Sci. U.S.A. 108 (27) 11093–11098.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ward AJ, Cooper TA (2010). &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19918805&quot;&gt;The pathobiology of splicing&lt;/a&gt;&quot;. J. Pathol. 220 (2) 152–163.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both papers are open access.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-12T20:06:50.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13951" PostTypeId="2" ParentId="13924" CreationDate="2013-12-12T20:25:14.157" Score="10" Body="&lt;p&gt;There is both a set &quot;list&quot; of agents, but more importantly, a set of properties that an organism needs to be in order to be truly worrisome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, the list:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.bt.cdc.gov/agent/agentlist-category.asp&quot;&gt;CDC&lt;/a&gt; classifies agents into one of three categories, Class A, B, or C.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Class A: These are organisms that are hard to control, highly transmissible, and lethal:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Anthrax (Bacillus anthracis)&#xA;Botulism (Clostridium botulinum toxin)&#xA;Plague (Yersinia pestis)&#xA;Smallpox (variola major)&#xA;Tularemia (Francisella tularensis)&#xA;Viral hemorrhagic fevers (filoviruses [e.g., Ebola, Marburg] and arenaviruses [e.g., Lassa, Machupo])&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Class B: These are organisms that are fairly easy to disseminate, make people sick but don't necessarily have high mortality rates, and may be difficult to detect.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Brucellosis (Brucella species)&#xA;Epsilon toxin of Clostridium perfringens&#xA;Food safety threats (e.g., Salmonella species, Escherichia coli O157:H7, Shigella)&#xA;Glanders (Burkholderia mallei)&#xA;Melioidosis (Burkholderia pseudomallei)&#xA;Psittacosis (Chlamydia psittaci)&#xA;Q fever (Coxiella burnetii)&#xA;Ricin toxin from Ricinus communis (castor beans)&#xA;Staphylococcal enterotoxin B&#xA;Typhus fever (Rickettsia prowazekii)&#xA;Viral encephalitis (alphaviruses [e.g., Venezuelan equine encephalitis, eastern equine encephalitis, western equine encephalitis])&#xA;Water safety threats (e.g., Vibrio cholerae, Cryptosporidium parvum)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;And finally, Class C, which are emerging threats that may be dangerous if engineered largely due to their novelty and their potential lethality/transmissability. The CDC uses examples like Nipah virus and hantavirus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So that's the list of what the CDC thinks is a big deal. You'll note influenza isn't even on there. I'd argue that any given novel influenza strain belongs in Class C, and likely not Class A because, while potentially both transmissible and virulent, a known vaccine exists and simply needs to be formulated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of properties for an organism, I'd suggest the following, in no particular order (it likely depends on what said organism is meant to do):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Highly virulent: The disease needs to be able to cause human disease, with high rates of both morbidity and mortality.&lt;/li&gt;&#xA;&lt;li&gt;Highly transmissible: Unless the goal is to cause a &quot;one off&quot; incident, the disease needs to be able to establish a productive chain of human-to-human infections. Humans can't be a dead-end host. Ideally, this needs to be direct human to human transmission, rather than a vector born disease like West Nile.&lt;/li&gt;&#xA;&lt;li&gt;Stable and amenable to engineering. It needs to be something that's easy to culture and grow in large numbers. This one often gets overlooked somewhat, but despite the fact that its now somewhat commonplace, bioengineering isn't exactly easy.&lt;/li&gt;&#xA;&lt;li&gt;Not amenable to treatment. The organism needs to not be easily treatable - broad spectrum antibiotics, existing vaccine stock, etc. mean that the normal public health infrastructure can address, or at least mitigate, an attack. For an attack to be truly effective, it needs to swamp existing infrastructure, and one way to do that is to necessitate intensive, unusual care in hospitals and out of the ordinary action on the part of public health officials.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="67" LastActivityDate="2013-12-12T20:25:14.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13952" PostTypeId="1" AcceptedAnswerId="13953" CreationDate="2013-12-12T20:51:27.640" Score="3" ViewCount="248" Body="&lt;p&gt;I am part of a project elucidating some structures that are required for bacterial transformation. We have the opportunity to screen inhibitors of the system to stop it from functioning. I am not a microbiologist and have never worked with transformation, and this research process would be time and resource intensive. I am weighing up the pros and cons, however am struggling with how the inhibitors could be practically applied. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How useful would stopping transformation be?&lt;/strong&gt; My thoughts so far boil down to:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could it enhance controls by allowing two separate strains to grow on the same plate without any genetic conference?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could it be applied to stop contamination of genetic information from otherwise insignificant contaminants?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any other problems that transformation is causing in laboratory experiments?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastActivityDate="2013-12-12T21:13:07.667" Title="When might an inhibitor of bacterial transformation be useful?" Tags="&lt;microbiology&gt;&lt;pharmacology&gt;&lt;bacteriology&gt;&lt;transformation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13953" PostTypeId="2" ParentId="13952" CreationDate="2013-12-12T21:13:07.667" Score="3" Body="&lt;p&gt;In the research lab? I thought about it for a while and found no usage. But it could be interesting for clinical applications to prevent bacteria spreading their resistance genes (which are usually organized on extra chromosomal plasmids) and thus preventing multi-resistant bacteria.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-12T21:13:07.667" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13954" PostTypeId="2" ParentId="9742" CreationDate="2013-12-12T21:28:00.027" Score="1" Body="&lt;p&gt;The flower is a &lt;em&gt;Hemerocallis fulva&lt;/em&gt; (Hemerocallidaceae).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The leaf seems to be a Cucurbitaceae, as said above, the same family as the zucchini&lt;/p&gt;&#xA;" OwnerUserId="5121" LastActivityDate="2013-12-12T21:28:00.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13955" PostTypeId="2" ParentId="13944" CreationDate="2013-12-13T07:36:15.507" Score="1" Body="&lt;p&gt;There are many articles in health literature debating on the question. Everytime the experimental setup seem to me quite basic and I am affraid that one cannot infer many things from these experimental designs. I guess the ethics is limiting much of the medical experimentation (which is good!). Usually it is just the report of observations of what happen to the global health of a patient when one amino acid is missing in their food. Therefore, these articles does not explain much about the metabolism reasons of these needs (which was your question) but only try to define what are the needs. Moreover statistics seem sometimes a bit fuzzy (or absent) to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway &lt;a href=&quot;http://ajcn.nutrition.org/content/46/4/593.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; is a review of these results and there is a whole paragraph on the question of histidine. The best is that you read it yourself. To make it short: Histidine doesn't seem to be more important to the children than other amino acid. Moreover there is big storage of histidine in our body suggesting that one that is histidine deprived for a while might use these stored histidines.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-12-13T11:00:39.993" LastActivityDate="2013-12-13T11:00:39.993" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13956" PostTypeId="1" AcceptedAnswerId="13983" CreationDate="2013-12-13T10:00:31.087" Score="2" ViewCount="454" Body="&lt;p&gt;For example,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;say species A is common ancestor of B, and C. Species B is a common ancestor of D and E.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We would expect that there will be more genetic similarity between D and E than D and C. And those genetic similarity must exist in B.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other word, we won't expect genetic similarity that don't &quot;cross&quot; the common ancestor or the evolutionary tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exception is probably genetically engineered bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, am I correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some people say that we have similarity with pigs and chimps even though our common ancestors may be to far off. That won't happen right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To summarize&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I expect that evolutionary tree will form a well, tree. Genetic similarity would infect &quot;nearby&quot; trees and can't jump between trees without connectors, such as common ancestors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is that what we observe for ALL species?&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="554" LastEditDate="2013-12-13T10:06:26.773" LastActivityDate="2015-12-26T18:32:00.997" Title="Is there any genetic similarity that defy evolution theory?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13957" PostTypeId="2" ParentId="13956" CreationDate="2013-12-13T10:36:32.287" Score="7" Body="&lt;p&gt;Your question seems rather confused to me, I don't quite understand it. Below I try to explain some stuff, I am not quite sure it would help you finding the answer to your question. Let me know if it helps you and how I can improve this answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While natural selection selects for a given &lt;a href=&quot;http://en.wikipedia.org/wiki/Allele&quot; rel=&quot;noreferrer&quot;&gt;allele&lt;/a&gt; (gene variant), mutations create new variation. And because of this process of mutation there is genetic pattern in species D that would cannot be found in species B (assuming that we have the DNA of species D). But what is similar between B and D were probably also present in their common ancestor B. The exceptions are molecular convergent evolution and &lt;a href=&quot;http://en.wikipedia.org/wiki/Horizontal_gene_transfer&quot; rel=&quot;noreferrer&quot;&gt;horizontal gene transfer&lt;/a&gt; (natural of artificial).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of common ancestry …&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Humans have similarities with pigs&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Example: endothermic amniotes&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Humans have similarities with a bug&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Example: bilaterial symmetry&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Humans have similarities with jellyfish&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Example: Heterotrophy&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Humans have similarities with an oak tree&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Example: We have mitochondrias&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Humans have similarites with any living things on earth!&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Example: Genetic information is hold into a DNA/RNA molecule.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/o0q9p.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you might observe that D is genetically speaking more similar to C than to E… This can be due to:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Horizontal gene transfer (artifical or natural)&lt;/li&gt;&#xA;&lt;li&gt;The mutation rate (or ability to fix mutations) in one lineage might be greater than in another lineage.&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;For example, if lineage E underwent many mutations, they might be genetically speaking have accumulated many difference compare to D, way more than the number of difference that D has with C.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;The phylogeny might be wrong&lt;/li&gt;&#xA;&lt;li&gt;There might have had some convergent evolution.&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Think about fishes which opsins in the eyes need to be adapted to the amount of light which depends on the turbidity of the water. After the three lineages splitted, the change of envirronment might have occured the sequence &lt;code&gt;AATGATCCT&lt;/code&gt; suddenly became beneficial. Only two lineages had the chance to produce the right mutation. Or maybe lineage E live at low depth and therefore it doesn't need this mutation because there is enough light at low depth anyway.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Therefore, one should not expect a common ancestor to be the arithmetic mean (supposing it means something) of the current species. And one should not expect that two closely related species on the tree of life should &lt;em&gt;necessarily&lt;/em&gt; be more genetically similar to each other than any of the two to a third species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the phylogeny is constructed mostly based on genetic data. Which makes that two closely related species (on our tree which is not necessary the absolute tree of life) are (almost) necessarily more genetically similar (it is kind of a definition then).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-12-15T08:47:58.663" LastActivityDate="2013-12-15T08:47:58.663" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="13958" PostTypeId="2" ParentId="13944" CreationDate="2013-12-13T10:47:53.197" Score="1" Body="&lt;p&gt;If an amino acid is essential it means that we cannot synthesise it &lt;em&gt;de novo&lt;/em&gt; from central metabolites, or from another amino acid. Since histidine isn't related structurally to any other amino acid we can assume that in this case we would require a pathway for &lt;em&gt;de novo&lt;/em&gt; biosynthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biosynthetic pathway enzymes for histidine in yeast (&lt;em&gt;Saccharomyces cerevisiae&lt;/em&gt;) are encoded by the genes &lt;em&gt;HIS1&lt;/em&gt; - &lt;em&gt;HIS7&lt;/em&gt;. In a BLAST search using yeast His4p against &lt;em&gt;Arabidopsis&lt;/em&gt; (plants can make histidine)  there is a significant match to a histidinol dehydrogenase (the penultimate step in the pathway). In a similar search against humans there is no significant hit. Expanding the search to all mammals there is only one significant match, which is to the Tibetan antelope, &lt;em&gt;Pantholops hodgsonii&lt;/em&gt;. This puzzled me, but when I searched with the antelope sequence as probe I got lots of perfect matches to bacterial histidinol dehydrogenases, so presumably the antelope sequence is a contaminant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also searched for human matches to His1p (encodes ATP phosphoribosyltransferase - the first step in the pathway) and His3p (encodes imidazoleglycerol-phosphate dehydratase - the sixth step in the pathway) and found no significant matches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I conclude that humans have no capacity for histidine biosynthesis and thus histidine must be essential in the diet.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-12-13T10:47:53.197" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13959" PostTypeId="1" AcceptedAnswerId="13961" CreationDate="2013-12-13T13:32:51.720" Score="2" ViewCount="1311" Body="&lt;p&gt;Chimps are our closer relative.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any genetic similarity between humans and chimps must exist on the common ancestor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pig branch out sooner. So, any genetic similarity between humans and pigs must be on common ancestor between humans and pigs. That must be on common ancestor between humans and chimps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But chimps may evolve differently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hmmm... I am confused.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually is there any?&lt;/p&gt;&#xA;" OwnerUserId="554" LastActivityDate="2016-10-29T11:02:23.427" Title="Are there genetic similarity between humans and pigs that don't exist in chimps?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13960" PostTypeId="1" CreationDate="2013-12-13T14:05:57.803" Score="4" ViewCount="3341" Body="&lt;p&gt;The Tiger and Yellow Fever Mosquito visually look very similar. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recognizing the difference is important for tracking and controlling the spread of Yellow Fever, Dengue fever and other diseases. Especially important, now that the range of the two have overlapped in the United States.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have some questions about the commonalities of these mosquitoes.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Evolutionarily, How can the similarities be explained?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do they both have the black body with white stripes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the best way to tell them apart?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;A. aegypti&lt;/em&gt;, the Yellow Fever Mosquito&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NtVpX.jpg&quot; alt=&quot;aegypti, the Yellow Fever Mosquito &quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;A. albopictus&lt;/em&gt;, the Tiger Mosquito&#xA;&lt;img src=&quot;https://i.stack.imgur.com/StMdH.jpg&quot; alt=&quot;albopictus, the Tiger Mosquito&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="948" LastEditDate="2013-12-13T15:14:54.353" LastActivityDate="2013-12-13T21:41:48.710" Title="What are the visual, behavioral similarities and differences between Yellow Fever Mosquito (Aedes aegypti) and the Tiger Mosquito (Aedes albopictus)?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;entomology&gt;&lt;ecology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13961" PostTypeId="2" ParentId="13959" CreationDate="2013-12-13T14:07:29.220" Score="7" Body="&lt;p&gt;Yes there are! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it would make more intuitive sense to you if you would have switched the words chimps and humans in your question: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Are there genetic similarity between chimps and pigs that don't exist in humans?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Then, you would directly answer, of course, there are genes concerning bipedalism, brain (FoxP2 for example), digestive track (adult production of lactase for example) and so, and so… which are different in humans but might not have much reasons to be so different between pigs and chimps. Those mutations occured on the human lineage after the split between human and chimps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Are there genetic similarity between humans and pigs that don't exist in chimps?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes. Most of these difference are due to mutations that occurred in the chimps lineage after the split of the original lineage into human lineage and chimps lineage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following are improbable but would also allow to explain such similarities:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Genetic_admixture&quot; rel=&quot;nofollow&quot;&gt;Genetic admixture&lt;/a&gt; or &lt;a href=&quot;https://en.wikipedia.org/wiki/Introgression&quot; rel=&quot;nofollow&quot;&gt;introgression&lt;/a&gt; between human and pig after humans and chimps lineages splitted.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Convergent evolution.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Maybe pigs and human got the same beneficial mutation that never appeared in the chimps lineages.&lt;/li&gt;&#xA;&lt;li&gt;Maybe pigs and human, due to the fact that today live in cold climates evolved the sequence &lt;code&gt;ATTCGCTGA&lt;/code&gt; which cause them to produce a more efficient shivering!&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="22956" LastEditDate="2016-10-29T11:02:23.427" LastActivityDate="2016-10-29T11:02:23.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13962" PostTypeId="1" AcceptedAnswerId="13963" CreationDate="2013-12-13T17:33:06.547" Score="5" ViewCount="18930" Body="&lt;p&gt;I live in the suburbs of Washington DC where it recently snowed. I was admiring all of the tracks left behind by wildlife of all kinds when I came across these prints, that I was unable to recognize from charts of common animals prints online.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6kOnM.jpg&quot; alt=&quot;animal print 1&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eMm3I.jpg&quot; alt=&quot;animal print 3&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rN7JV.jpg&quot; alt=&quot;animal print 4&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is unique about them, is that each print, has 3 points, and there is only one straight line of prints, about 2-3 feet apart, where as I would imagine a deer, or other 4 legged animal would leave staggered footprints. We have a lot of deer in these parts but these dont seem to match deer print patterns I've seen online.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each print is about 5 inches by 4 inches at their widest/longest points (they are longer then they are wider).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note, the snow has melted somewhat since they were initially made.&lt;/p&gt;&#xA;" OwnerUserId="5157" LastActivityDate="2016-12-06T13:24:43.763" Title="Identification - What kind of animal leaves these tracks?" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13963" PostTypeId="2" ParentId="13962" CreationDate="2013-12-13T18:11:07.977" Score="5" Body="&lt;p&gt;The only candidate I could imagine is &lt;a href=&quot;https://www.google.com/search?q=hare%20footprints&quot; rel=&quot;nofollow&quot;&gt;hare&lt;/a&gt;.&#xA;Sometimes it leaves a single track from its fore-limbs (from a theoretical point of view, I'd say it happens when the snow is relatively deep.)&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2013-12-14T22:44:02.470" LastActivityDate="2013-12-14T22:44:02.470" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13964" PostTypeId="1" AcceptedAnswerId="13965" CreationDate="2013-12-13T18:19:16.350" Score="3" ViewCount="145" Body="&lt;p&gt;Is it possible to spray stem cells on fully grown skeleton to get fully grown humans?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Currently, just read about recent advances, and wondered if something like this is possible.&lt;/p&gt;&#xA;" OwnerUserId="5159" LastEditorUserId="6" LastEditDate="2013-12-15T12:03:43.647" LastActivityDate="2013-12-15T12:03:43.647" Title="Can humans be printed?" Tags="&lt;human-biology&gt;&lt;stem-cells&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13965" PostTypeId="2" ParentId="13964" CreationDate="2013-12-13T18:50:14.433" Score="3" Body="&lt;p&gt;No.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Very early in the development of an organism, it is just a clump of cells.  Then those cells communicate, and determine where they are in the clump, which determines their eventual fate in the full organism.  In mammals, for instance, cells split into three different layers, and the skin and nerve cells develop from cells in the outermost layer...etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can't just dump a bunch of stem cells somewhere and expect them to know where they are and what they should be developing into.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2013-12-13T18:50:14.433" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13966" PostTypeId="2" ParentId="13959" CreationDate="2013-12-13T19:17:08.213" Score="2" Body="&lt;p&gt;This question doesn't make a lot of sense.  Humans, chimps and pigs are all eukaryotes, share a lot of sequence similarity due to common ancestry.  We are all vertebrates, we are all placental mammals.  So there is a lot of similar sequence between us, more than we have with lizards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So humans, chimps and pigs all have a common ancestor. Is it possible that there are some sequences where the human versions have drifted farther from the common ancestor than either chimps and pigs have?  Sure, it's possible but probably not very common.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's link to ensembl's page on one random gene, the transferrin receptor.  You can see the % identity between the orthologues of a number of species.  Chimps and humans are 99% identical.  Pigs are 76%.  All the primates whose transferrin sequences are known are in the 90's percentage wise, the other mammals are not nearly so close a match.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?db=core;g=ENSG00000072274;r=3:195754054-195782085;t=ENST00000360110&quot; rel=&quot;nofollow&quot;&gt;http://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?db=core;g=ENSG00000072274;r=3:195754054-195782085;t=ENST00000360110&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's another gene, where the gene has changed much less over time, but pigs are still not as similar to human as chimp&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?db=core;g=ENSG00000138379;r=2:190920423-190927455;t=ENST00000260950&quot; rel=&quot;nofollow&quot;&gt;http://www.ensembl.org/Homo_sapiens/Gene/Compara_Ortholog?db=core;g=ENSG00000138379;r=2:190920423-190927455;t=ENST00000260950&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2013-12-13T19:17:08.213" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13967" PostTypeId="2" ParentId="13960" CreationDate="2013-12-13T21:41:48.710" Score="3" Body="&lt;p&gt;For the best way to tell them apart, see this guide: &lt;a href=&quot;http://www.cdc.gov/dengue/resources/30Jan2012/comparisondenguevectors.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.cdc.gov/dengue/resources/30Jan2012/comparisondenguevectors.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, it seems that the silver pattern on the torso is different (lyre-shaped for Yellow Fever Mosquito, more linear for Asian Tiger Mosquito).  Location is probably also an important determinant.&lt;/p&gt;&#xA;" OwnerUserId="3673" LastActivityDate="2013-12-13T21:41:48.710" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13968" PostTypeId="2" ParentId="10819" CreationDate="2013-12-13T22:13:53.367" Score="4" Body="&lt;p&gt;Imagine a culture where girls are chastised for taking risks, and heavily punished when they take risks and fail, but where boys are encouraged to take risks, and praised highly when things work out their way.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wouldn't you expect that when put in a situation where such individuals are supposed to make a high stakes action based on risk assessment, that those girls would show much higher stress levels than the boys would?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Big biological difference, having nothing at all to do with the Y chromosome,or genetics at all.  Just the environment.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2013-12-13T22:13:53.367" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13969" PostTypeId="2" ParentId="13964" CreationDate="2013-12-13T23:00:35.777" Score="2" Body="&lt;p&gt;A skeleton is itself very complicated.  It's not just apatite in the shape of a skeleton.  The bones have structure, and many have bone marrow.  Tiny cells navigate through the bone matrix, keeping it sound.  Those cells, and the ones in the marrow, need a blood supply to keep them alive.  Plus, what swbarnes2 said.&lt;/p&gt;&#xA;" OwnerUserId="4551" LastActivityDate="2013-12-13T23:00:35.777" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13971" PostTypeId="1" AcceptedAnswerId="13975" CreationDate="2013-12-14T03:51:26.440" Score="3" ViewCount="2241" Body="&lt;p&gt;I know cyanide inhibits complex IV in the electron transport chain, but I don't understand why this makes it so toxic. If cyanide is bound to the complex, can't the electrons just bypass it   and reduce oxygen directly? That way fewer protons would be pumped out of the matrix, but most still would, and aerobic respiration would just be less efficient, rather than stopping entirely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially what I'm asking is what causes the electrons to get &quot;stuck&quot;?&lt;/p&gt;&#xA;" OwnerUserId="5160" LastEditorUserId="6" LastEditDate="2013-12-15T12:03:05.113" LastActivityDate="2018-04-10T01:33:00.737" Title="Why is cyanide poisonous?" Tags="&lt;biochemistry&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13975" PostTypeId="2" ParentId="13971" CreationDate="2013-12-14T19:57:39.090" Score="2" Body="&lt;p&gt;Cyanide binds cytochrome oxidase so as to prevent the binding of oxygen. Electron transport is reduced to zero, and none of the oxygen breathed in can be used. Cytochrome oxidase is one of a superfamily of proteins which act as the terminal enzymes of respiratory chains, so if the cyanide is binding to the cytochrome then it inhibits the process and making it dangerous. Another example I would give rotenone which binds competitively.  &lt;/p&gt;&#xA;" OwnerUserId="5164" LastEditorUserId="23604" LastEditDate="2018-04-10T01:33:00.737" LastActivityDate="2018-04-10T01:33:00.737" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13976" PostTypeId="1" CreationDate="2013-12-14T19:58:58.003" Score="6" ViewCount="4734" Body="&lt;p&gt;People often say, including those with extensive knowledge in biology, that a certain species of animal will evolve in one way or another:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;From changing environments.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Mutations.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Possibly even genetic engineering from human animals.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;My question lies in the fact that, aside from the latter option, why haven't any differences in animals'(except humans) markup, morphology, intelligence, DNA, behavior, or any habits changed over thousands or (possibly millions) of years?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A cockroach has had the same behavior it has today &lt;a href=&quot;http://en.wikipedia.org/wiki/Cretaceous&quot; rel=&quot;nofollow noreferrer&quot;&gt;more than 10 million years ago&lt;/a&gt;, and there have been no advancements in the species in the slightest bit. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It makes you question evolution, because why don't other animals (like cockroaches) have any changes over 10+ million years, yet humans, like me and you somewhat, have, in a relative period of time similar to the linked geological period above, evolved from spear tossing hominids into someone brilliant enough to even ponder this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If modern humans are the result of mutations in genes, why has no one species over the course of hundreds of millions of years been fit enough, or advanced mentally as we have, or even in any slightest bit?&lt;/p&gt;&#xA;" OwnerDisplayName="user5165" LastEditorUserId="22057" LastEditDate="2019-03-28T15:10:22.400" LastActivityDate="2019-03-28T15:53:20.217" Title="Why do most animals never seem to evolve over millenia?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;human-genetics&gt;&lt;ethology&gt;&lt;behaviour&gt;" AnswerCount="5" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="13978" PostTypeId="2" ParentId="13964" CreationDate="2013-12-14T20:13:54.803" Score="0" Body="&lt;p&gt;See spryaing stem cells is not that easy as it sounds.The main difficulty working with stem cell is keeping their stem cell characteristics intact till the development actually begins.Stem cell can be amny types such as pluripotent,totipotent,multipotent etc.As you asked bone,bone is also a result of stemcell.So point is first you have to generate bone and bone generation is a massive and intricate process.You need many growth factors for this process and these growth factors are developmental time specific it means it is expressed at only a certain point of time.So I think it's difficult &lt;/p&gt;&#xA;" OwnerUserId="5164" LastActivityDate="2013-12-14T20:13:54.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13980" PostTypeId="2" ParentId="13976" CreationDate="2013-12-14T20:38:34.060" Score="2" Body="&lt;p&gt;This is a tricky question. &#xA;First, evolution tend to be slow, although there have been recent examples of very fast evolution as well. So for most evolutionary processes, we are not present long enough to see them either happening or see the outcome. Therefore its also hard to say that no evolution is happening - see your cockroach example. How do you know that these animals are the same as 10 Mio years ago? And even if it is like this, it can also mean that these animals fit their niche so good, that there is not much pressure for further adaption. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can change pretty fast as examples from mites (here a report in the &lt;a href=&quot;http://www.bbc.co.uk/news/science-environment-22039872&quot; rel=&quot;nofollow noreferrer&quot;&gt;BBC&lt;/a&gt;, this is the &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/ele.12107/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;original publication&lt;/a&gt;). Another example of fast evolution (of bigger animals) are the Cichlids in the Lake Victoria, which developed new after the last time the lake dried up completely something like 12.000 years ago. After that, an estimated 300 endemic species developed (see &lt;a href=&quot;http://www.sciencemag.org/content/273/5278/1091.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;) which was then reduced by pollution and other environmental problem. The remaining species are evolving again to occupy the free niches (see &lt;a href=&quot;http://www.nature.com/news/2010/100707/full/466174a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of the human, we are pretty lucky, that no other intelligent animal has come up so far. They would have fought for the same biological niche and living space with one species eventually dying out. This has, for example, happened to all the other homo species (habilis, erectus, neanderthalensis). As a species, we are quite young (around 200.000 years), so there is something going on. And there is genetic diversion between humans, but still not as much, that we cannot cross each other anymore. And with 7 billion of us now present, it's not that easy for mutations to come through at our reproduction rate.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="3340" LastEditDate="2019-03-28T14:22:46.613" LastActivityDate="2019-03-28T14:22:46.613" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="13981" PostTypeId="2" ParentId="13976" CreationDate="2013-12-14T22:28:36.983" Score="16" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;How come most animals never seem to evolve over millennia?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The word &quot;seem&quot; in your question should not be disregarded. You seem to assume that cockroaches (or most animals as you say) did not change much the last tens or hundreds of thousands of years. But what do you know about that (no offence here)? Have you actually reviewed many kinds of research that estimate the rate of evolution of different randomly chosen lineages in the past 500,000 years? I think you assume that other species evolved slower than humans rather than know it. And you will certainly put much more importance to the evolution of the gene FoxP2 (involved in language) than to a gene allowing cockroaches to have a better sense of smell. This is a biased view of what is a rate of evolution. It would be much wiser to consider a rate of evolution as something like the number of newly arising mutations that succeeded to get fixed in the population. See Haldane's rate of evolution and the Darwin unit. Please don't make the mistake to think that being smart (or complex) is some kind of the goal of evolution and those that are not smart (or complex) are &quot;less evolved&quot; or that they evolved more slowly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You also seem to want to point on the evolution of DNA and evolution of habits. I guess you might be appreciative of the evolution of human knowledge and culture. But this is obviously something that does not have to do with genetic evolution but is rather a matter of cognitive capacity. You cannot compare the change of culture and traditions of insects and humans as insects have mostly no traditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, this is obviously true that different lineages evolve at different rates. Many things influence this rates such as the population size, the mutation rate, the generation time, the selection pressure (which itself might depend on social structure or the rate of environmental change for example). In these terms, I would rather believe of Homo sapiens as a lineage that should have a rather slow evolutionary rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Homo sapiens is quite a recent species. And speciation is often linked with phenotypic divergence, with niche competition and niche complementarity and therefore with a high rate of evolution. In these terms, I would believe that humans are a lineage with high evolutionary rate.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-28T15:53:20.217" LastActivityDate="2019-03-28T15:53:20.217" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="13982" PostTypeId="1" CreationDate="2013-12-14T23:53:40.093" Score="4" ViewCount="90" Body="&lt;p&gt;They typically need to be given ~150mg, once a day, and it'll last for two weeks. The drug is very water insoluble, becomes almost like a paste, not suitable for tube feeding. And yes, this is for for real lifesaving medical research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best we can come up with right now is putting them to sleep, mixing the powder into Nutella, and putting it under their tongue. The idea being they'll wake up and swallow the mixture. &lt;/p&gt;&#xA;" OwnerUserId="5168" LastEditorUserId="3615" LastEditDate="2013-12-15T14:44:31.493" LastActivityDate="2015-02-09T00:22:04.617" Title="What is the best way to orally administer a water insoluble powdered drug to macaque monkeys?" Tags="&lt;pharmacology&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="13983" PostTypeId="2" ParentId="13956" CreationDate="2013-12-15T10:09:27.777" Score="4" Body="&lt;p&gt;&lt;em&gt;You have an excellent answer from Remi.b already but I just wanted to add/emphasise this (because there is always more than one way of explaining something and IMO the site benefits from having many answers to the questions)...&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The tree we construct does not necessarily accurately reflect what happened in evolution.&lt;/strong&gt; If B &amp;amp; C evolved from A, and D &amp;amp; E came from B, we would create this tree if we measured using the correct indicator. But the methods we have are not perfect. The first evolutionary trees were based on morphological descriptions etc. and clearly some of the classifications were going to be wrong. These days we use molecular methods, which are probably more accurate but could also be wrong some times. For example if we based our phylogeny on one SNP variant we could have some idea about the phylogeny between a few species, but if we based it on millions of SNPs we would have a much better idea - as technology &amp;amp; models improve that is becoming more realistic. The key point here being there is a difference between the trees we can draw from evidence, and the real evolutionary tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If, for example, D evolved from B but was more genetically similar to  C it could be due to convergent evolution (if the same mutations are selected for in C and D but neutrally or negatively in B). This is because, if there is a shared standing genetic variation at the point of speciation or the same mutations occur after speciation, and then C &amp;amp; D are imposed under similar selection and B is not, the allele favored in that environment will spread in C &amp;amp; D but not B (it may drift in B). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine this with humans, where populations split off around the globe. Two populations spread from Africa (A) in to Southern Europe (SE) and Western Asia (WA). Population WA then derived two more populations - Central Asian (CA) and Eastern European (EE). If the Eastern European population developed a habit for drinking cow milk, and that information passed to the Southern Europeans, then selection would favor the ability to digest lactose in those two populations. If we then used the lactase persistence SNP (which had standing genetic variation at the time of divergence) to derive a phylogeny the populations SE and EE would appear related because the allele for lactase persistence is common, but in A WA &amp;amp; CA it would be rare (neutrally evolved). In this case the phylogeny we construct would be different to the true phylogenetic tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically if there is genetic variation at the point of divergence, or convergent selection, or any gene flow occurs after divergence it makes assessing the phylogeny more difficult and prone to error. &lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2013-12-15T10:09:27.777" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13984" PostTypeId="2" ParentId="13941" CreationDate="2013-12-15T10:47:12.173" Score="2" Body="&lt;p&gt;First check if your RNA sequences are described by existing covariance models (CMs) available in &lt;a href=&quot;http://rfam.sanger.ac.uk/&quot; rel=&quot;nofollow&quot;&gt;Rfam&lt;/a&gt;. You can do this using the &lt;a href=&quot;http://infernal.janelia.org/&quot; rel=&quot;nofollow&quot;&gt;Infernal package&lt;/a&gt; to search the Rfam database of CMs. For those RNA sequences which match an Rfam CM, you can then use that CM to search the sequence databases for additional matches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For those that do not match an Rfam CM, you will want to build your own models. In order to do this you need to identify homologues for each sequence which you can use to produce an alignment from which a model can be built. In order to do this you will want to use a method which is RNA aware and uses a rigorous search method. For example from the &lt;a href=&quot;http://fasta.bioch.virginia.edu/&quot; rel=&quot;nofollow&quot;&gt;FASTA suite&lt;/a&gt;, which has an RNA mode which adjusts the scoring accordingly:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm&quot; rel=&quot;nofollow&quot;&gt;Smith and Waterman&lt;/a&gt; for local/local alignment (e.g. SSEARCH)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm&quot; rel=&quot;nofollow&quot;&gt;Needleman–Wunsch&lt;/a&gt; for global/global alignment (e.g. GGSEARCH)&lt;/li&gt;&#xA;&lt;li&gt;Hybrid alignment for global/local alignment (e.g. GLSEARCH)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Your coverage requirements and the nature of the database being searched will determine the most suitable method to use for the sequence similarity search. Combining the best search method with appropriate selection of the database to search, for example the &lt;a href=&quot;http://www.ebi.ac.uk/ena/&quot; rel=&quot;nofollow&quot;&gt;European Nucleotide Archive (ENA)&lt;/a&gt; provide a set of non-protein coding sequences (&lt;a href=&quot;ftp://ftp.ebi.ac.uk/pub/databases/ena/non-coding/&quot; rel=&quot;nofollow&quot;&gt;ftp://ftp.ebi.ac.uk/pub/databases/ena/non-coding/&lt;/a&gt;) derived from the annotations in EMBL-Bank that could be a good starting point your search. Will improve the sensitivity of your search.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given the set of homologous sequences you need to produce a multiple sequence alignment (MSA) to generate a model from. To do this you will want to use an RNA aware MSA tool, for example &lt;a href=&quot;http://www.tcoffee.org/Projects/rcoffee/&quot; rel=&quot;nofollow&quot;&gt;R-COFFEE&lt;/a&gt; or &lt;a href=&quot;http://www.clustal.org/omega/&quot; rel=&quot;nofollow&quot;&gt;Clustal Omega&lt;/a&gt; in order to produce an alignment which attempts to take into account the folding of the RNA molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given the alignment you can create a CM using Infernal or an HMM using &lt;a href=&quot;http://hmmer.janelia.org/&quot; rel=&quot;nofollow&quot;&gt;HMMER&lt;/a&gt;, and use this to search the sequence database (cmsearch or hmmsearch) to find additional homologues in the database.&lt;/p&gt;&#xA;" OwnerUserId="4117" LastEditorUserId="4117" LastEditDate="2013-12-15T13:41:49.117" LastActivityDate="2013-12-15T13:41:49.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13986" PostTypeId="1" AcceptedAnswerId="24260" CreationDate="2013-12-15T14:55:07.993" Score="10" ViewCount="24274" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/8282/why-is-saltatory-conduction-faster-than-continuous-conduction&quot;&gt;Here&lt;/a&gt; is the original question which inspired my question. As explained by the answers there, the reason saltatory conduction in myelinated neurons is faster than non-myelinated conduction is because the capacitance of the membrane is lowered by reducing the number of channels (Channel density) or equivalently, increasing the spacing between channels. I also did a preliminary study of membrane electrodynamic modelling &lt;a href=&quot;http://www.scholarpedia.org/article/Cable_theory&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.scholarpedia.org/article/Electrical_properties_of_cell_membranes&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I gathered from the linked question, the decreased capacitance overcompensates the effect of absence of channels reinforcing the sodium current, and on the whole, increases the speed of conduction by allowing the depolarizing potential to travel to the adjacent node faster than in case of an unmyelinated fibre. In view of this, I have a question:-  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Why does lower capacitance increase &quot;the effectiveness of nearby&#xA;  nodes&quot; or allow the depolarizing voltage to &quot;travel not by ion&#xA;  diffusion, but as an electric field&quot;? I am comfortable with capacitors&#xA;  and related physics, but why would lower capacitance allow propagation&#xA;  of the changing voltage as an electric field, is still unclear to me?&#xA;  (The links I have placed also help quantify the problem&#xA;  mathematically. This allows us to say that $\lambda$, or the rate of spatial&#xA;  decay of potential, increases, decreasing the effective&#xA;  length of the neuron. Why should its decrease help faster conduction?)&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;And another question is, &lt;strong&gt;how would reduced density of sodium voltage&#xA;  gated channels cause a decreased capacitance?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-07-06T06:43:06.413" Title="How is membrane capacitance related to the increased speed of saltatory conduction?" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;biophysics&gt;&lt;cell-membrane&gt;&lt;electrophysiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13988" PostTypeId="1" CreationDate="2013-12-15T23:36:47.953" Score="7" ViewCount="239" Body="&lt;p&gt;I am computer scientist working on machine learning methods applied to predicting missing Gene Ontology annotations. &#xA;In many papers, I wrote that my computational methods are very useful to suggest to the biologists  on which gene functions they should address their research, because my software need less resources (a simple laptop connected to a database) and less time (e.g. with a dataset of all the Homo sapiens Gene Ontology annotations: about 3 hours) than their biological experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now a reviewer asked me to be more precise. Truly, &lt;strong&gt;how much does an in vitro experiment to biologically validate a human Gene Ontology annotation run by biologists cost?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How much money, broadly?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How much time?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="885" LastActivityDate="2013-12-17T18:14:47.300" Title="How much does a biological experiment to validate a gene function cost?" Tags="&lt;genetics&gt;&lt;experimental-design&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13989" PostTypeId="1" AcceptedAnswerId="13990" CreationDate="2013-12-16T02:01:30.657" Score="3" ViewCount="1636" Body="&lt;p&gt;Plasmid pBr322 includes two genes that confer antibiotic resistance: a gene for ampicillin and  a gene for tetracycline. The cutting site for the restriction enzyme BamH1 is in the middle pf the tetracycline resistance gene. The cutting site for the restriction enzyme Pvu1 is in the middle of the ampicillin resistance gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you were using a cell culture plate that contained ampicillin, which restriction enzyme (BamH1 or Pvu1) would you use to cut the plasmid and excise the gene you wanted to insert?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Attempt&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would assume you need to use Pvu1 since the cutting site is in the ampicillin resistance gene, but the correct answer is BamH1. Why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help would be awesome! Thanks!&lt;/p&gt;&#xA;" OwnerUserId="4645" LastEditorUserId="3615" LastEditDate="2013-12-21T04:06:37.210" LastActivityDate="2013-12-21T04:06:37.210" Title="Which restriction enzyme would i use?" Tags="&lt;homework&gt;&lt;molecular-genetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13990" PostTypeId="2" ParentId="13989" CreationDate="2013-12-16T02:40:12.237" Score="5" Body="&lt;p&gt;Remember than Pvu1 &lt;strong&gt;cuts&lt;/strong&gt; in the middle of &lt;em&gt;Amp&lt;sup&gt;R&lt;/sup&gt;&lt;/em&gt;, and when you insert your gene you'll be disrupting its function, meaning that any transformed colonies will no longer be able to grow on Amp-containing media. This is why you want to cut with BamH1 - the disruption to the &lt;em&gt;Tet&lt;sup&gt;R&lt;/sup&gt;&lt;/em&gt; gene is irrelevant, and it leaves Amp resistance in place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The point of growing on antibiotic-containing media is to select for cells that have taken up your plasmid - cells that haven't can't grow. &lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-12-16T02:40:12.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13991" PostTypeId="2" ParentId="13976" CreationDate="2013-12-16T03:42:51.760" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;aside from the latter option, why haven't any differences in&#xA;  animals'(except humans) markup, morphology, intelligence, DNA,&#xA;  behavior, or any habits changed over thousands or (possibly millions)&#xA;  of years?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What evidence is leading you to that conclusion?  For horses, example.  (From the talkorigins article):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first equid was Hyracotherium, a small forest animal of the early Eocene. This little animal (10-20&quot; at the shoulder) looked nothing at all like a horse. It had a &quot;doggish&quot; look with an arched back, short neck, short snout, short legs, and long tail. It browsed on fruit and fairly soft foliage, and probably scampered from thicket to thicket like a modern muntjac deer, only stupider, slower, and not as agile. This famous little equid was once known by the lovely name &quot;Eohippus&quot;, meaning &quot;dawn horse&quot;. Some Hyracotherium traits to notice:Legs were flexible and rotatable with all major bones present and&#xA;  unfused. 4 toes on each front foot, 3 on hind feet. Vestiges of 1st (&amp;amp;&#xA;  2nd, behind) toes still present. Hyracotherium walked on pads; its&#xA;  feet were like a dog's padded feet, except with small &quot;hoofies&quot; on&#xA;  each toe instead of claws. Small brain with especially small frontal&#xA;  lobes. Low-crowned teeth with 3 incisors, 1 canine, 4 distinct&#xA;  premolars and 3 &quot;grinding&quot; molars in each side of each jaw (this is&#xA;  the &quot;primitive mammalian formula&quot; of teeth). The cusps of the molars&#xA;  were slightly connected in low crests. Typical teeth of an omnivorous&#xA;  browser.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So from that, you conclude that the DNA, morphology, and intelligence of horses hasn't changed at all in 50 million years?  &lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2013-12-16T03:42:51.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13992" PostTypeId="2" ParentId="13989" CreationDate="2013-12-16T05:16:16.950" Score="1" Body="&lt;p&gt;I would go with BamH1 enzyme as the cut site in pBr322 is BamHI 375 and ss you are plating  it in a ampicillin plate you need the ampicillin resistant gene to be intact for screening so by using BamHI you will not disrupt the Amp resistant gene&lt;/p&gt;&#xA;" OwnerUserId="5164" LastActivityDate="2013-12-16T05:16:16.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13993" PostTypeId="2" ParentId="10" CreationDate="2013-12-16T05:21:04.960" Score="-2" Body="&lt;p&gt;Reporter genes have become an invaluable tool in studies of gene expression.A gene consists of two functional parts: One is a DNA-sequence that gives the information about the protein that is produced (coding region). The other part is a specific DNA-sequence linked to the coding region; it regulates the transcription of the gene (promoter). The promoter is either activating or suppressing the expression of the gene.&#xA;The purpose of the reporter gene assay is to measure the regulatory potential of an unknown DNA-sequence.So it is quite helpful,it;s kind of reverse engeneering the function and then let know what exactly it does.&lt;/p&gt;&#xA;" OwnerUserId="5164" LastActivityDate="2013-12-16T05:21:04.960" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="13994" PostTypeId="1" CreationDate="2013-12-16T09:15:24.787" Score="5" ViewCount="472" Body="&lt;p&gt;People can dream, dogs can dream, cats probably too when they are sleeping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about other creatures? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can a bird dream?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do rats have dreams?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any studies about that kind of thing? What is the most simple organism that have brain structures that allow them dreaming during the sleep?&lt;/p&gt;&#xA;" OwnerUserId="3118" LastActivityDate="2013-12-30T20:51:04.777" Title="The least complex animals with ability to dream" Tags="&lt;zoology&gt;&lt;sleep&gt;&lt;dreaming&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="13995" PostTypeId="2" ParentId="13988" CreationDate="2013-12-16T10:22:39.377" Score="9" Body="&lt;p&gt;Wow that can vary from a couple of months and a few thousand dollars to a lifetime and millions of dollars.  I can give a couple of examples, but this is an extremely broad question.  Wet science is not cheap might be the message here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gene Ontology terms are meant to cover all biological roles known for genes.  Terms are added and retire regularly.  They embody thousands of person-years of work to establish the framework of what is going on in cells.  At the same time its a &lt;a href=&quot;http://www.geneontology.org/GO.doc.shtml#not&quot; rel=&quot;nofollow&quot;&gt;limited vocabulary of gene behavior&lt;/a&gt;.  It doesn't represent a complete catalog of all known gene behaviors (e.g. in such detail that it could only be the property of a specific gene) and it is also uneven in the level of its detail of its leaf terms.  Its an ontology that is manually assembled and edited and therefore subjective. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just did an overview of GO 1.2.  there are 34153 unique GO terms.  That's easily 10s of thousands of separate assays, so picking a group of important ones might be useful. There are also lots of orphan GO terms, where only one gene is currently attached to the term.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For GO annotations, a simple and typical case is a metabolic gene which has a high homology to a known gene and you are only trying to verify that biological role, and you have a functioning biological laboratory.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A breakdown might be:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;clone the gene ( \$200 to \$1000 and up): order primers, use PCR to insert the gene into a plasmid or get the gene synthesized if you have to, transform it into bacteria,  ideally sequence it to make sure you have it right. &lt;/li&gt;&#xA;&lt;li&gt;purify the protein ( \$500 maybe).  Run a check culture to see if the protein is produced, then run a full culture with induction, lyse it and then purify on an affinity chromatography column.  you may need to run a second column to get the protein pure. &lt;/li&gt;&#xA;&lt;li&gt;do a kinetics study with mass spectroscopic validation of the products (minimally about \$300).  Cost involves reagents - if you have an assay you can use a UV/Vis spectrophotometer this can be simple, if not it can be much more expensive. This part will vary with the enzyme you are looking at. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Hopefully you get all these steps right the first time.  Salaries are not included in this cost.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The more complicated the GO term, the more difficult the work will be - they are not all equal.  If the protein function can't be verified in isolation, but must be &lt;em&gt;in situ&lt;/em&gt; (i.e. in the living organism). Then you start to get into time.  What if your gene is involved in &lt;a href=&quot;http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0071985&quot; rel=&quot;nofollow&quot;&gt;protein routing&lt;/a&gt; through the &lt;a href=&quot;http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0005802&quot; rel=&quot;nofollow&quot;&gt;golgi apparatus&lt;/a&gt; and modulates the function of other proteins for instance?  That's going to require a very specialized and difficult set of experiments that should involve someone with experience in that field. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finding GO annotations which are not clear from sequence similarity - unknown functions or new genes which reflect previously unestablished GO Terms could cost even more and take a good deal longer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still, high throughput studies are being done to find and validate electronic GO annotations.  And with that scale, the cost per experiment will go down.  Take a look at &lt;a href=&quot;http://reducio.princeton.edu/cm/node/14&quot; rel=&quot;nofollow&quot;&gt;Olga Troyanskaya's research&lt;/a&gt; for an example of such an effort. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-12-17T18:14:47.300" LastActivityDate="2013-12-17T18:14:47.300" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="13996" PostTypeId="1" CreationDate="2013-12-16T12:45:24.207" Score="7" ViewCount="15510" Body="&lt;p&gt;We have hair all over the body except palms.&lt;br&gt;&#xA;What is the biological reason behind this?&lt;/p&gt;&#xA;" OwnerUserId="5180" LastEditorUserId="49230" LastEditDate="2019-03-11T17:16:36.500" LastActivityDate="2019-03-11T17:16:36.500" Title="Why don't we have hair on palms?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="13997" PostTypeId="1" AcceptedAnswerId="15924" CreationDate="2013-12-16T13:24:21.137" Score="3" ViewCount="847" Body="&lt;p&gt;T cells are formed in bone marrow and mature in Thymus. How are they transported from bone marrow to thymus ? Through the lymph vessels ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-18T19:43:01.073" Title="How are T cells transported?" Tags="&lt;immunology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13998" PostTypeId="1" AcceptedAnswerId="16427" CreationDate="2013-12-16T13:28:16.203" Score="4" ViewCount="4049" Body="&lt;p&gt;Can any foreign molecule be non- antigenic ? Can any foreign peptide be non-antigenic ? What is the difference between an antigenic and a non-antigenic peptide ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-08T19:36:29.153" Title="Antigenic and non antigenic" Tags="&lt;immunology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="13999" PostTypeId="1" AcceptedAnswerId="14340" CreationDate="2013-12-16T13:40:42.397" Score="3" ViewCount="176" Body="&lt;p&gt;I read in Bruce Alberts Molecular Biology of The Cell :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;....If,however,cells from one strain of mouse are introduced into a neonatal mouse of another strain , some of these cells survive for most of the recipient animal's life, and the recipient will now accept a graft from the original donor, even though it rejects &quot;third party&quot; grafts.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As far as I understand , in this experiment,they got these results because thymus hadn't yet learned what was &quot;own&quot; and what was &quot;foreign&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is  the reason for why &lt;a href=&quot;http://en.wikipedia.org/wiki/Microchimerism&quot; rel=&quot;nofollow&quot;&gt;maternal microchimerism&lt;/a&gt; does not invoke immune response related to the above experiment ?&lt;/strong&gt; Can we apply the same logic here ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-08T20:15:57.560" Title="Thymus and maternal microchimerism" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14000" PostTypeId="1" AcceptedAnswerId="14016" CreationDate="2013-12-16T13:54:03.923" Score="5" ViewCount="85" Body="&lt;p&gt;I read in Bruce Alberts Molecular Biology of the cell :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Normal mice,for example, cannot make an immune response against one of their own protein components of the complement system called C5.&#xA;  Mutant mice, however, lack the gene encoding C5(but are otherwise&#xA;  genetically identical to the normal mice) can make a strong immune&#xA;  response to this blood protein when immunized with it. Natural&#xA;  immunological tolerance for a particular self molecule persists only&#xA;  for as long the molecule remains present in the body. If a self&#xA;  molecule such as C5 is removed, an animal gains the ability to respond&#xA;  to it after a few weeks or months. Thus, the immune system is&#xA;  genetically capable of responding to self molecules but learns not to&#xA;  do so.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, why does an immune reaction not happen when a new protein is introduced to patients lacking it ? For example if you give clotting factor to hemophilic patient.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-12-16T17:22:57.550" Title="Immune reaction to &quot;new&quot; protein" Tags="&lt;immunology&gt;&lt;antigen&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14001" PostTypeId="1" AcceptedAnswerId="14007" CreationDate="2013-12-16T14:07:12.593" Score="4" ViewCount="53" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Toxoids produced by tetanus and diphtheria bacteria are detoxified&#xA;  with formaldehyde, yet their antigen properties remain.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source : Biological Science by Taylor&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does formaldehyde do ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-12-16T14:53:57.563" Title="Manufacturing toxoids" Tags="&lt;immunology&gt;&lt;vaccination&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14002" PostTypeId="2" ParentId="14000" CreationDate="2013-12-16T14:16:40.933" Score="2" Body="&lt;p&gt;This is a concept of the immune system called &quot;Immune tolerance&quot;. Basically it makes sure, that you cannot make antibodies against yourself (which would obviously be bad).&#xA;New antibodies are &quot;tested&quot; against the body and if there is an autoreactivity, the corresponding B-cells go into apoptosis.&#xA;If this self-protection does not work, this leads to autoimmune diseases like SLE.&#xA;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Immune_tolerance&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; article about it is quite nice for the beginning and also has a lot of references for further reading.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2013-12-16T14:34:54.620" LastActivityDate="2013-12-16T14:34:54.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14003" PostTypeId="1" AcceptedAnswerId="14008" CreationDate="2013-12-16T14:19:06.050" Score="4" ViewCount="297" Body="&lt;p&gt;I have been using old style lab book for some time now but with increasing work on computer and storing sequencing results and gel pictures on computer it would be nice to have everything on computer in a form of labbook. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does any of you uses a good ELN that would be free as I don't think university will be willing to pay for it :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your answers.&lt;/p&gt;&#xA;" OwnerUserId="4860" LastActivityDate="2017-04-21T23:08:49.707" Title="Electronic laboratory notebook (ELN)" Tags="&lt;lab-techniques&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14004" PostTypeId="2" ParentId="13998" CreationDate="2013-12-16T14:32:09.253" Score="3" Body="&lt;p&gt;Something is antigenic because it acts as an &lt;a href=&quot;http://en.wikipedia.org/wiki/Antigen&quot; rel=&quot;nofollow&quot;&gt;antigen&lt;/a&gt; - it binds to an antigen receptor in the immune system (antibody, B-cell receptor, T-cell receptor, etc.). While the concept of &quot;foreign&quot; in immunology is often (incorrectly) equated with antigen, that is not the case. For example, there are many chemicals one could think of that are foreign (non-self), but don't usually raise immune responses - nylon, for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The difference between an antigenic and non-antigenic peptide is that the antigenic peptide, &lt;em&gt;when presented in the correct circumstances&lt;/em&gt;, can raise an immune response. This means that, theoretically, the exact same peptide sequence can be both antigenic and non-antigenic depending on the environment - whether it's being presented in an immune-suppressed environment, for example. However, it's more common to classify antigenic potential based on whether it's possible for the substance to raise a response in an otherwise &quot;normal&quot; immune environment.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-12-16T14:32:09.253" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14005" PostTypeId="1" CreationDate="2013-12-16T14:37:18.260" Score="1" ViewCount="124" Body="&lt;p&gt;I read somewhere that a man dies if he is isolated from natural electromagnetic fields and waves. (I imply fields of radio frequencies and below.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it true?&lt;/p&gt;&#xA;" OwnerUserId="4186" LastEditorUserId="4186" LastEditDate="2013-12-16T14:54:36.900" LastActivityDate="2013-12-17T04:29:58.113" Title="Death because of no radio waves" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ClosedDate="2015-01-14T16:19:48.097" ContentLicense="CC BY-SA 3.0" />
  <row Id="14006" PostTypeId="2" ParentId="14003" CreationDate="2013-12-16T14:46:28.443" Score="0" Body="&lt;p&gt;I am not sure what you need.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably &lt;a href=&quot;http://www.libreoffice.org/&quot; rel=&quot;nofollow&quot;&gt;Libre Office&lt;/a&gt; (a free MS Office like program, including a rich text editor, with image support) will suffice for you.&lt;/p&gt;&#xA;" OwnerUserId="4186" LastActivityDate="2013-12-16T14:46:28.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14007" PostTypeId="2" ParentId="14001" CreationDate="2013-12-16T14:53:57.563" Score="3" Body="&lt;p&gt;The toxins of both &lt;em&gt;Clostridium tetani&lt;/em&gt; and &lt;em&gt;Corynebacterium diphtheriae&lt;/em&gt; are so toxic that you cannot use them for immunization, since the amount needed for proper antibody production would kill the individuals. For that purpose the toxins are &quot;de-toxified&quot; by reacting them with formaldehyde which takes away the toxicity but the resulting toxoids are still immunogenic.&#xA;This happens by the reaction of the formaledehyde with the free aminogroups of the sidechains of the amino acids to form azomethin groups. This changes the protein so much, that it cannot bind to glangliosides any more which renders it untoxic. The immune system can still recognize unmodified parts (for this 8-10 amino acids in one stretch are enough) and make antibodies.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-16T14:53:57.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14008" PostTypeId="2" ParentId="14003" CreationDate="2013-12-16T15:04:42.407" Score="6" Body="&lt;p&gt;I still prefer the good old[tm] Labnotebook. No dependencies on (proprietary) software or a computer. I generate quite some digital data (blots, sequencing etc.) this is stored on the servers of my university. We looked into this in our lab, but discarded the idea pretty fast. Most solutions are either expensive and/or proprietary. Then a lot of these programs are not bought, but rented for a monthly or yearly fee, so once you are in you basically will not get out there anymore. Or it takes a lot of work.&#xA;I found one free (for up to three projects), this is &lt;a href=&quot;http://www.labguru.com/&quot; rel=&quot;nofollow&quot;&gt;Labguru&lt;/a&gt;.&#xA;There is an article about this on &lt;a href=&quot;http://bitesizebio.com/articles/how-to-manage-scientific-data-electronic-lab-notebooks-compared-with-google-docs-and-wikis/&quot; rel=&quot;nofollow&quot;&gt;Bitesizebio&lt;/a&gt;, which has a few interesting comments. And there is another &lt;a href=&quot;http://www.gradhacker.org/2013/08/23/experiments-with-an-electronic-lab-notebook/&quot; rel=&quot;nofollow&quot;&gt;blog&lt;/a&gt; entry about this worth reading.&#xA;One of the problems with ELN is a legal one, since a labbook is a legal document providing evidence a what has been done and the results of it. They can be very important when it comes to patent legal battles. &lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2013-12-16T18:23:58.170" LastActivityDate="2013-12-16T18:23:58.170" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14009" PostTypeId="1" CreationDate="2013-12-16T16:31:33.537" Score="0" ViewCount="90" Body="&lt;p&gt;i am looking for likely truncation sites to prove recombination in sequences. i have 4 sequences. i believe one to be the &quot;real sequence&quot; and the other 3 to be recombinants caused by cleavage possibly due to Arg c proteinase. I know my sequences overlap due to multiple alignments i have performed using UniProt and i have chosen the enzyme due to carrying out cuts on Expasy cutter. If anyone could point me in the right direction this would be much appreciated.&#xA;many thanks in advance &lt;/p&gt;&#xA;" OwnerUserId="5182" LastEditorUserId="5182" LastEditDate="2013-12-16T18:38:05.210" LastActivityDate="2013-12-16T18:38:05.210" Title="bioinformatics /genomics" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;genomics&gt;&lt;protein-expression&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="12" FavoriteCount="0" ClosedDate="2013-12-16T18:10:55.773" ContentLicense="CC BY-SA 3.0" />
  <row Id="14010" PostTypeId="2" ParentId="13996" CreationDate="2013-12-16T16:39:37.813" Score="8" Body="&lt;p&gt;The main functional reason is we need to be able to grip things with our hands (and feet, which are also hairless), and hair would interfere with that. Physiologically, the epidermis in these parts of the body is very thick and highly keratinized, and when combined with the thick underlaying layer of dermis, this results in skin that does not support the growth and maturation of hair follicles.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-12-16T16:39:37.813" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14011" PostTypeId="2" ParentId="14009" CreationDate="2013-12-16T16:55:43.750" Score="2" Body="&lt;p&gt;The sequences you have posted seem to be (protein) amino acid sequences. The stop codon are present in DNA sequences and in mRNA sequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In DNA, the bases are A, G, C and T; stop codons are TAG, TGA and TAA.&#xA;In RNA, the bases are A, G, C and U; stop codons are UAG, UGA and UAA.&#xA;In DNA and RNA, other letters are used to specify degeneracy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you have here looks like protein sequences. So, there are no stop codons in sequences you have posted.&lt;/p&gt;&#xA;" OwnerUserId="5183" LastActivityDate="2013-12-16T16:55:43.750" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14015" PostTypeId="2" ParentId="14000" CreationDate="2013-12-16T17:13:47.050" Score="3" Body="&lt;p&gt;You are absolutely right in that there will be immune reaction against proteins that are not naturally present in the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, hemophilia is not caused by complete lack of protein. It is due to loss of function of the clotting factors due to mutations. The proteins are still present, but they do not have the ability to bind and/or activation of their catalytic function. So, there will be no immune activity against exogenous clotting factors given to hemophiliac patients.&lt;/p&gt;&#xA;" OwnerUserId="5183" LastActivityDate="2013-12-16T17:13:47.050" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14016" PostTypeId="2" ParentId="14000" CreationDate="2013-12-16T17:22:57.550" Score="3" Body="&lt;p&gt;They actually can produce antibodies against the clotting factor (as @Xylo pointed out, many patients do produce the clotting factor that's being replaced, just in insufficient quantity, which lowers a lot the risk of an immune response). The antibodies against the clotting factor are called inhibitors. See &lt;a href=&quot;http://www.hemophilia.org/NHFWeb/MainPgs/MainNHF.aspx?menuid=201&amp;amp;contentid=383&amp;amp;rptname=bleeding&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for more info.&lt;/p&gt;&#xA;" OwnerUserId="5156" LastActivityDate="2013-12-16T17:22:57.550" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14017" PostTypeId="1" AcceptedAnswerId="20014" CreationDate="2013-12-16T17:36:19.073" Score="4" ViewCount="175" Body="&lt;p&gt;If Rh- mother has Rh+ baby, the mother can become sensitized during first pregnancy and then if subsequent fetuses are also Rh+, there can be eryhtroblastosis foetalis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read that if mother is O- and baby is any +ve blood group other than O+ , then mother will not become sensitized during first pregnancy because a and b antibodies present in her blood will attack the antigen present on the fetus RBC and there will be no time for the mother to synthesize antibodies against Rh.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My Question : Can't the same logic be applied to all other blood groups? For example : A- mother and B+ baby. &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-07-28T13:00:08.213" Title="Erythroblastosis Foetalis" Tags="&lt;red-blood-cell&gt;&lt;pregnancy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14018" PostTypeId="2" ParentId="14003" CreationDate="2013-12-16T18:01:57.357" Score="0" Body="&lt;p&gt;This is not a decision you, or even your lab can make on its own.  Notebook policies are almost certainly developed by the lawyers of your university.  It would be up to them to certify any change to those policies, in coordination with IT, who would have to be on board to guarantee the integrity of the electronic data.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2013-12-16T18:01:57.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14020" PostTypeId="1" CreationDate="2013-12-16T18:46:15.423" Score="2" ViewCount="391" Body="&lt;p&gt;I would like to know were to download a table file with all reported bacteria and its corresponding PHYLUM, CLASS, ORDER and FAMILY.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, its the same table than &lt;a href=&quot;http://genomesonline.org/documents/Export/gold.xls&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt; from &lt;a href=&quot;http://genomesonline.org/cgi-bin/GOLD/index.cgi&quot; rel=&quot;nofollow&quot;&gt;GOLD genomes&lt;/a&gt; but containing the non-sequenced bacteria too:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for you help, Bernardo&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="3631" LastEditDate="2013-12-17T02:21:47.640" LastActivityDate="2013-12-17T02:21:47.640" Title="List of all reported bacteria" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14021" PostTypeId="2" ParentId="14020" CreationDate="2013-12-16T19:09:50.337" Score="6" Body="&lt;p&gt;I am not sure if such a complete list exists. There are some lists available, which look pretty complete. Have a look at &lt;a href=&quot;http://www.thelabrat.com/protocols/Bacterialspecies/&quot;&gt;Labrat&lt;/a&gt; and &lt;a href=&quot;http://www.microbexpert.com/AtoZ/Bacteria_AtoZ/Bacteria_AtoZ.html&quot;&gt;Microbexpert&lt;/a&gt;. There is also a book available, which contains an approved list of bacterial names, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK814/&quot;&gt;here&lt;/a&gt;. Otherwise you can of course search your way through &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed&quot;&gt;PubMed&lt;/a&gt; and see, what comes out.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2013-12-16T20:27:30.947" LastActivityDate="2013-12-16T20:27:30.947" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14022" PostTypeId="1" AcceptedAnswerId="14028" CreationDate="2013-12-16T19:16:03.530" Score="1" ViewCount="574" Body="&lt;p&gt;what does it mean if different protein sequences overlap upon multiple alignment, are they the same, do they have a common ancestor, are they recombinants of each other &#xA;and how does one go on to prove this&#xA;many thanks&lt;/p&gt;&#xA;" OwnerUserId="5182" LastEditorUserId="5005" LastEditDate="2013-12-17T02:22:28.580" LastActivityDate="2014-03-05T18:26:21.487" Title="what does sequences overlap indicate" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;&lt;sequence-analysis&gt;&lt;protein-evolution&gt;&lt;sequence-alignment&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14023" PostTypeId="1" AcceptedAnswerId="14025" CreationDate="2013-12-16T19:40:04.543" Score="0" ViewCount="131" Body="&lt;p&gt;First off, I'm not looking for online lectures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am trying to find creative commons licensed videos of live cells moving around without annotation or anything extra. I would prefer a few minutes of video of tumorous somatic cultures of eukaryotes in vitro and at a few different magnifications but it doesn't really matter. I don't have a microscope or I'd just get some pond water and look at multicellular organisms. The license must be creative commons or public domain, the author must be citable, and the subject organism should be known.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any ideas where to find such video? Thanks!&lt;/p&gt;&#xA;" OwnerUserId="5187" LastActivityDate="2013-12-16T23:14:57.367" Title="Looking for raw cell videos from a light microscope" Tags="&lt;cell-biology&gt;&lt;microbiology&gt;&lt;cell-culture&gt;&lt;microscopy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14025" PostTypeId="2" ParentId="14023" CreationDate="2013-12-16T23:14:57.367" Score="3" Body="&lt;p&gt;The website you want is &lt;a href=&quot;http://www.cellimagelibrary.org/&quot; rel=&quot;nofollow&quot;&gt;The Cell: An Image Library&lt;/a&gt;. They also have movies. A quick search of &lt;a href=&quot;http://www.cellimagelibrary.org/images?advanced_search=Advanced+Search&amp;amp;k=%22Homo+sapiens%22+tumor&amp;amp;image_search_parms%5bbiological_process%5d=&amp;amp;image_search_parms%5bcell_type%5d=&amp;amp;image_search_parms%5bcell_line%5d=&amp;amp;image_search_parms%5bfoundational_model_anatomy%5d=&amp;amp;image_search_parms%5bcellular_component%5d=&amp;amp;image_search_parms%5bmolecular_function%5d=&amp;amp;image_search_parms%5bncbi%5d=&amp;amp;image_search_parms%5bitem_type_bim%5d=&amp;amp;image_search_parms%5bimage_mode_bim%5d=&amp;amp;image_search_parms%5bvisualization_methods_bim%5d=&amp;amp;image_search_parms%5bsource_of_contrast_bim%5d=&amp;amp;image_search_parms%5brelation_to_intact_cell_bim%5d=&amp;amp;image_search_parms%5bprocessing_history_bim%5d=&amp;amp;image_search_parms%5bpreparation_bim%5d=&amp;amp;image_search_parms%5bparameter_imaged_bim%5d=&amp;amp;image_search_parms%5bidentity_bim%5d=&amp;amp;image_search_parms%5bhuman_dev_anatomy%5d=&amp;amp;image_search_parms%5bhuman_disease%5d=&amp;amp;image_search_parms%5bmouse_gross_anatomy%5d=&amp;amp;image_search_parms%5bmouse_pathology%5d=&amp;amp;image_search_parms%5bplant_growth%5d=&amp;amp;image_search_parms%5bteleost_anatomy%5d=&amp;amp;image_search_parms%5bxenopus_anatomy%5d=&amp;amp;image_search_parms%5bzebrafish_anatomy%5d=&quot; rel=&quot;nofollow&quot;&gt;'Homo sapiens tumor'&lt;/a&gt; revealed several Creative Commons videos of tumor cells moving around &lt;em&gt;in vitro&lt;/em&gt; with attribution and no annotation or anything else. Sometimes the site can be a bit buggy, but it's a pretty awesome resource when it works.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2013-12-16T23:14:57.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14026" PostTypeId="1" AcceptedAnswerId="14034" CreationDate="2013-12-17T00:12:18.693" Score="2" ViewCount="4891" Body="&lt;p&gt;Usually DNA sample manipulation is realized with an ice box at hand in order to avoid degradation, and also its storage is set at -20ºC. Nevertheless, DNA has been obtained from really ancient samples that were not in a cold environment and even our DNA is at 36ºC. Furthermore, when performing PCR, samples are put into a massive heat shock and at high temperatures. &#xA;Then how needed are those protocols in order to grant correct DNA quality? how much can a sample be left without need to worry? and how does this degradation happen (DNAse free environment)&lt;/p&gt;&#xA;" OwnerUserId="3657" LastActivityDate="2013-12-17T05:06:57.177" Title="DNA degradation rate" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14028" PostTypeId="2" ParentId="14022" CreationDate="2013-12-17T01:31:52.443" Score="3" Body="&lt;p&gt;Expanding on the comment by @Chris:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Short Answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overlapping sequences imply &lt;strong&gt;&lt;em&gt;evolutionarily conserved regions&lt;/em&gt;&lt;/strong&gt;, i.e. preserved by evolution through time due to theirs having some important function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long Answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming the sequences are &lt;a href=&quot;http://en.wikipedia.org/wiki/Homology_%28biology%29&quot; rel=&quot;nofollow&quot;&gt;homologous&lt;/a&gt;, overlapping regions of similarity reveal &quot;evolutionarily conserved regions&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are regions in the protein sequence that are shared by the ancestors through ancestral history due to that shared sequence bearing some important function at the phenotypic level. Evolution acts to &quot;preserve&quot; the sequence through natural selection if that function was important for fitness (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Negative_selection_%28natural_selection%29&quot; rel=&quot;nofollow&quot;&gt;Negative selection&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.g. Perhaps the shared sequence codes for an active site for an enzyme that is shared by all the ancestors you are using in the multiple sequence alignment - natural selection will then prevent changes to that sequence from occurring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look at this &lt;a href=&quot;http://www.incogen.com/bioinfo_tutorials/Bioinfo-Lecture_4-multiple-sequence-align.html&quot; rel=&quot;nofollow&quot;&gt;online lecture&lt;/a&gt; for finer detail.&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2014-03-05T18:26:21.487" LastActivityDate="2014-03-05T18:26:21.487" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14029" PostTypeId="2" ParentId="14022" CreationDate="2013-12-17T03:41:41.217" Score="0" Body="&lt;p&gt;it means those region are conserved if you compare two sequence and find similarity one example is the hox coding region which is conserved and it shows similarity&lt;/p&gt;&#xA;" OwnerUserId="5164" LastActivityDate="2013-12-17T03:41:41.217" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14030" PostTypeId="2" ParentId="13997" CreationDate="2013-12-17T03:53:49.560" Score="-3" Body="&lt;p&gt;prothymocytes are attracted to the thymus from the Bone Marrow by a chemotaxis , thymotaxin, a factor from thymic epithelial cells.&#xA;then it enters into the thymic cortex where Thy-1  and terminal deoxynucleotidyl transferase (TdT) is expressed. During TCR gene rearrangement, TdT increases TCR diversity by inserting nucleotides at the D and J junction sites. IL-2 and IL-2R are expressed leading to autocrine proliferation of T cells.&#xA;now the  pre-T cell  rearranges TCR genes (gamma/delta, alpha/beta). At this stage the pre-T cells are CD3+CD4-CD8- or &quot;double-negative&quot; cells. Double-negative cells that productively rearrange gamma and delta chain gene segments develop into CD3+CD4-CD8- gamma/delta T cells that are exported to the periphery in small numbers. Successful rearrangement of a set of TCR genes suppresses further rearrangement of TCR genes on the sister chromatid , thus each cell only expresses TCR with a single specificity.&#xA;The majority of double-negative cells will go on to rearrange alpha and beta chain gene segments. The beta chain genes are rearranged and expressed first with a pre-T alpha chain to form the pre-TCR . Once the pre-TCR recognizes some intrathymic ligand , a signal is transmitted through CD3 which:&#xA;halts further beta chain gene rearrangement (allelic exclusion)enhances alpha chain gene rearrangement causes CD4 and CD8 to be expressed&#xA;The alpha beta T cells now become CD4+CD8+ or &quot;double-positive&quot; cells. T cells which fail to productively rearrange TCR genes die by apoptosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At this point the T cells are in the deep cortex which contains epithelial cells expressing both class I and class II MHC molecules. T cells with alpha beta TCR which are capable of binding self-MHC on epithelial cells continue to proliferate and differentiate into CD4+CD8- or CD4-CD8+ T cells. Nonreactive (not self-MHC restricted) T cells die by apoptosis. Thus, T cells are positively selected for self-MHC restriction in the thymus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;T cells that survive positive selection traverse the junction between the cortex and medulla. Some of these T cells have low affinity TCR for self-MHC alone or combined with self-peptide while others have high affinity TCR. The medulla is rich in BM-derived dendritic cells and macrophages which express high levels of class I and class II MHC. T cells with high affinity TCR for self-MHC alone or combined with self-peptide interact with these dendritic cells and macrophages, and are eliminated by apoptosis. Thus, negative selection eliminates self-reactive T cells  in the thymus.&lt;/p&gt;&#xA;" OwnerUserId="5164" LastActivityDate="2013-12-17T03:53:49.560" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14031" PostTypeId="2" ParentId="13909" CreationDate="2013-12-17T04:07:55.520" Score="1" Body="&lt;p&gt;I don't see why microalgae couldn't be a main food source (putting aside the taste factor).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It contains many different lipids, carbohydrates, proteins and other essential nutrients that are digestible and would be beneficial to humans. I do know that microalgae has a very high lipid content (hence why they're often harvested for biofuels), but it can nonetheless provide nutritional value (ie. feed a starving man).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, not how this is completely different from &lt;em&gt;living solely off of microalgae&lt;/em&gt;. This likely wouldn't be possible, as us humans cannot synthesize all nutrients that we need from scratch. These nutrients are deemed &lt;a href=&quot;http://en.wikipedia.org/wiki/Essential_nutrient&quot; rel=&quot;nofollow&quot;&gt;essential nutrients&lt;/a&gt;. This problem usually arises when your diet is too restricted to certain types of food. So whether it's microalgae or any other type of consumable, you wouldn't be able to live by &lt;em&gt;only&lt;/em&gt; eating that thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another related problem is that growing microalgae is more difficult than it would seem, as is once again usually encountered in second-generation biofuel manufacturing. Temperature, light, cell density, nutrients, and much more must be precisely managed to obtain a increasingly growing population of microalgae. The pros and cons of farming microalgae for billion of hungry people would have to be contrasted with other current agricultures, like corn, soy and rice.&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2013-12-17T04:07:55.520" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14032" PostTypeId="2" ParentId="14005" CreationDate="2013-12-17T04:29:58.113" Score="3" Body="&lt;p&gt;I've never heard of such a thing, and a quick Scholar search didn't yield anything significant. In fact, artificial radio waves are used in things that usually &lt;em&gt;save&lt;/em&gt; lives, like MRIs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we were truly agnostic about this, we could say that it might or might not have an effect on human survival due to the general lack of evidence or even indication of a claim, but like &lt;a href=&quot;http://en.wikipedia.org/wiki/Russell%27s_teapot&quot; rel=&quot;nofollow&quot;&gt;the orbiting teacup&lt;/a&gt;, it's safe to assume that &lt;strong&gt;given our current extensive set of knowledge of biology, radiowaves do not affect human at all, and that as it has not been observed, the claim doesn't have a scientific basis.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2013-12-17T04:29:58.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14033" PostTypeId="2" ParentId="14003" CreationDate="2013-12-17T04:40:33.173" Score="3" Body="&lt;p&gt;Although there are some definite advantages to physical labboos, and perhaps some legal obligations, I have been loosely using &lt;a href=&quot;https://www.synbiota.com/welcome_page/welcome&quot; rel=&quot;nofollow&quot;&gt;Synbiota&lt;/a&gt; for keeping track of general procedures to be done. It has a long list of interesting features, but I particularly like the integrated DNA editing tool, as well as the ability to share projects and updates with labmates.&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2013-12-17T04:40:33.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14034" PostTypeId="2" ParentId="14026" CreationDate="2013-12-17T05:06:57.177" Score="4" Body="&lt;p&gt;DNA decomposition isn't a phenomenon that is too common. &#xA;In &lt;em&gt;nearly all&lt;/em&gt; cases, DNA is broken apart to the accidental contamination with nucleases. Long-term storage of DNA in the -20 is also suggested in order to significantly lower the rates of these nuclease enzymes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, DNA only truly fragments at very high temperatures (&gt;90-100 degrees Celsius) due to the nature of the covalent chemical bonds that form DNA. Nearly any organic molecule will degrade at very high temperatures, and some will degrade at lower temperatures due to unstable structures or heat-labile bonds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course DNA will deanneal at somewhat-high temperatures due to its double standedness , but allows for reannealing to the initial molecule once the temperature is brought down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One additional reason for potential DNA degradation is DNA shearing, which will occurs when you tear up your DNA physically due to exposure to rigorous shaking, resuspending or other &quot;violent&quot; techniques.&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2013-12-17T05:06:57.177" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14036" PostTypeId="1" CreationDate="2013-12-17T09:05:16.113" Score="2" ViewCount="195" Body="&lt;p&gt;How many different smells can a human recognize?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the space of smells is not discrete, how many dimensions it has (for example, the space of colors is three-dimensional).&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="5144" LastEditDate="2014-03-17T11:17:25.377" LastActivityDate="2014-03-17T11:17:25.377" Title="How many different smells can a human recognize?" Tags="&lt;human-biology&gt;&lt;olfaction&gt;" AnswerCount="1" CommentCount="10" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14037" PostTypeId="2" ParentId="3476" CreationDate="2013-12-17T09:08:37.037" Score="1" Body="&lt;p&gt;This is &lt;a href=&quot;http://en.wikipedia.org/wiki/Clitocybe_nebularis&quot; rel=&quot;nofollow&quot;&gt;Clitocybe Nebularis&lt;/a&gt;, an edible species.&lt;/p&gt;&#xA;" OwnerUserId="408" LastActivityDate="2013-12-17T09:08:37.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14040" PostTypeId="1" CreationDate="2013-12-17T18:16:03.260" Score="7" ViewCount="737" Body="&lt;p&gt;Is color information sent from the eye to the brain frequency-modulated, or are different colors transmitted by different axons?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that each ganglion cell is connected to multiple photoreceptors. How do ganglion cells tell the brain which photoreceptors were exactly activated and by what color?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do ganglion cells correspond to particular colors?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can one ganglion cell transmit different signals to the brain?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does the brain know which color the light has, if signals of different receptors are mixed in the ganglion?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="9943" LastEditDate="2015-03-22T12:34:25.047" LastActivityDate="2016-02-21T22:39:45.257" Title="How is color information transmitted from the eye to the brain?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;vision&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14041" PostTypeId="2" ParentId="10120" CreationDate="2013-12-17T18:34:14.983" Score="1" Body="&lt;p&gt;The question has an invalid premise. Namely, that the UV light looks like magenta/purple. It is not the case. While it it true that approaching UV end the perceived color becomes more purple (because the red protoreceptors have a second maximum there), moving further to the UV area (which is possible if the eye has the lens removed), makes the perceived color more whitish/light blue because the green receptor also has a second maximum there (somewhat further than the red one).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not know why the IR has magenta color though. It could be because of not pure source. Try using a hot piece of metal to see if it becomes more purple as it cools, I think it does not.&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="408" LastEditDate="2019-06-20T06:49:47.573" LastActivityDate="2019-06-20T06:49:47.573" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="14043" PostTypeId="1" CreationDate="2013-12-17T21:02:23.693" Score="3" ViewCount="63" Body="&lt;p&gt;Can anyone point me toward a computationally-accessible database of medical assertions? I'm looking for something where each row in the database contains a single unit of knowledge. It could either be in some sort of structured format, or be in free text.&lt;/p&gt;&#xA;" OwnerUserId="1855" LastActivityDate="2013-12-17T21:02:23.693" Title="Database of Medical Assertions" Tags="&lt;human-biology&gt;&lt;database&gt;&lt;medicine&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14044" PostTypeId="2" ParentId="11286" CreationDate="2013-12-17T22:09:39.007" Score="32" Body="&lt;p&gt;I really like this question as it is such a fundamental underpinning of all life on the planet, yet there is such sparsity of actual information on its origins and why selection rewarded ATP use over anything else. Here I am talking generally since no specific studies exist in ATP vs other candidates.&lt;/p&gt;&#xA;&lt;p&gt;A lot of the below information is taken from a relatively old article mentioned in the comments by TomD that discusses: &lt;em&gt;&amp;quot;Why nature chose phosphates.&amp;quot;&lt;/em&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2434996&quot; rel=&quot;noreferrer&quot;&gt;by Westheimer, 1987&lt;/a&gt;. The article is very influential and has been cited over a thousand times since publication. Another article that came out in the same year that this question was asked &lt;em&gt;&amp;quot;Why nature&lt;/em&gt; &lt;em&gt;&lt;strong&gt;really&lt;/strong&gt;&lt;/em&gt; &lt;em&gt;chose phosphate.&amp;quot;&lt;/em&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23318152&quot; rel=&quot;noreferrer&quot;&gt;by Kamerlin &lt;em&gt;et al.,&lt;/em&gt; 2013&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Some of the below arguments are more convincing than others, but all of them should be thought of when attempting to answer this question.&lt;/p&gt;&#xA;&lt;h2&gt;Summary.&lt;/h2&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;ATP has ancestral dominance.&lt;/strong&gt; Most other reasons derive from this.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Alternative phosphate groups or other molecules may not provide enough energy.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Alternatives may be toxic.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Other molecules, particularly phosphates, are used for inefficient high energy bursts.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Pi is a &amp;quot;good&amp;quot; leaving group.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Phosphates are fundamentally able to be regulated through electrostatic manipulation.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;ATP synthase can efficiently reattach the Pi to ADP.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Lots of Pi available to organisms because of it's ancestral dominance (&amp;quot;if it ain't broken, why fix it?&amp;quot; is at play).&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;ATP can provide more energy if needed; it's scalable to the situation. (ADP becomes AMP + Pi)&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Easily usable by a variety of proteins.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;h1&gt;Why ATP?&lt;/h1&gt;&#xA;&lt;p&gt;ATP is an efficient and relatively easily biosynthesised molecule that can fulfil multiple biochemical roles. Cells do have alternative energy carriers, some with more specialised roles, however, ATP is ubiquitous throughout our cells and inter-cellular spaces. There aren't a wealth of resources explaining why ATP is any better than other compounds, however, there is plenty of reasons why the phosphates are required.&lt;/p&gt;&#xA;&lt;h1&gt;Why not the alternatives?&lt;/h1&gt;&#xA;&lt;p&gt;Citric acids and their derivatives are a good candidate, with deductible groups and high bioavailability but they simply don't give enough energy to stabilise genetic material.&lt;/p&gt;&#xA;&lt;p&gt;Another tribasic candidate is arsenic acid. This is a fundamentally toxic compound, though, which isn't particularly great for living things.&lt;/p&gt;&#xA;&lt;p&gt;There are other phosphates too, and they are used in many organisms. In biology, they have specific functions, and not used as the general energy carrier. For example, creatine triphosphate provides a high energy phospho- anhydride bond, that is often used to quickly and anaerobically regenerate ATP, useful during high rate muscle activity for contraction.&lt;/p&gt;&#xA;&lt;p&gt;GTP is structurally very similar to ATP. GTPases are used more to initiate cellular signalling pathways. It is sometimes used as an energy source. This is a good example of an alternative energy carrier.&lt;/p&gt;&#xA;&lt;p&gt;Over the years, many proteins have specialised with a specific shape, and this chance is the primary reason behind ATP over GTP. In other words, the choice of ATP over GTP is primarily down to cellular preference of molecular shape. One of them had to emerge as being more widely used, and it was ATP that 'won'.&lt;/p&gt;&#xA;&lt;h1&gt;Efficiency and simplicity.&lt;/h1&gt;&#xA;&lt;p&gt;The reaction was once thought to be a relatively simple nucleophilic displacement. From the 2013 paper:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;...this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalysed reactions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Traditionally one will be taught that ATP is such a chemically efficient way of storing and transporting energy. This is due to the ATP-&amp;gt;ADP &amp;amp; Pi hydrolysis reaction. The phosphate groups in ATP are full of negative charges and these are repelling one another. This means that the third phosphate is &lt;strong&gt;a great leaving group&lt;/strong&gt; and breaking the phospho- anhydride bond is a favourable reaction. ...&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;...But&lt;/em&gt; the story is a lot more complicated than that. The above explanation isn't really satisfying because those same negative charge forces are repulsive of the nucleophile that is attempting to complete ATP-&amp;gt;ADP &amp;amp; Pi. A more comprehensive explanation would go along the lines of 'although a negative charge repulsion exists between the nucleophile of the protein and the phosphate, that high energy barrier can be overcome by electrostatic manipulation'. This allows an &amp;quot;on-off switch&amp;quot; for the hydrolytic reaction by tweaking the electrostatic environment. This is another great regulatory tool that the phosphates provide. This regulatory feature is important for signal and metabolic/catabolic cascades.&lt;/p&gt;&#xA;&lt;p&gt;When it comes to 'rebinding' the Pi to ADP, it is fairly easy since ADP seldom covalently binds to anything, which would require a lot of energy to recover the ADP. This also helps the bioavailability of free ADP to &lt;a href=&quot;http://www.youtube.com/watch?v=3y1dO4nNaKY&quot; rel=&quot;noreferrer&quot;&gt;ATP synthase&lt;/a&gt;, an incredibly efficient enzyme, that uses membrane proton gradient to drive the production of ATP. Talking about actual numbers is difficult here as there is only data available from Rat hepatocytes. Who is to say mammals are representative of all organisms? The estimates of energy of hydrolysis range from &lt;a href=&quot;http://sandwalk.blogspot.co.uk/2011/11/better-biochemistry-free-energy-of-atp.html&quot; rel=&quot;noreferrer&quot;&gt;ΔG˚ = -48 kJ mol-1&lt;/a&gt; to &lt;a href=&quot;https://biology.stackexchange.com/questions/576/how-on-a-physical-level-does-atp-confer-energy?rq=1&quot;&gt;-30.5 kJ mol-1&lt;/a&gt;. Note that these are considerable, but not exceptional values, so it's easy for many different proteins, that need not be very specialized, to break the bond all over the body. I couldn't even find the numbers for the synthase reaction per ATP, but a single ATP synthase can produce up to 600 ATP per minute.&lt;/p&gt;&#xA;&lt;p&gt;The final point of this efficiency is that the elements in ATP are very abundant and established in the biosphere making it readily available. This makes the phosphates a convenient biomolecule.&lt;/p&gt;&#xA;&lt;h1&gt;Multi-functionality.&lt;/h1&gt;&#xA;&lt;p&gt;ATP is ubiquitous in the body, but in some cases more energy is needed than there are ATP available. In these times of need, ATP can be used to produce more energy, breaking another phosphoanhydride bond to become AMP+2Pi. AMP however is typically a signalling molecule.&lt;/p&gt;&#xA;&lt;p&gt;With the low activation energy required to break the phosphoanhydride bond, a multitude of enzymes, far too many to list here, can make use of ATP in order to gain energy towards the activation energy for many other functions.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-12-17T10:52:44.013" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="14045" PostTypeId="1" AcceptedAnswerId="14058" CreationDate="2013-12-17T22:35:47.780" Score="6" ViewCount="227" Body="&lt;p&gt;And especially three points : &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;in which chromosomes is it located (especially for the human case) ?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;how do we know about it ?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;does the proportion and composition vary a lot from one eukaryot to another ?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="207" LastActivityDate="2013-12-21T18:35:45.263" Title="How much DNA of mitochondrial origin is incorporated in main cell's DNA?" Tags="&lt;dna&gt;&lt;mitochondria&gt;&lt;molecular-evolution&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14047" PostTypeId="1" AcceptedAnswerId="14049" CreationDate="2013-12-18T00:21:25.880" Score="4" ViewCount="715" Body="&lt;p&gt;When performing a DNA cloning, sometimes PCR amplicon is run in agarose and it is detected by ethidium bromide marking under UV light. After that, gel is sliced, DNA extracted from gel....... until eventually you have your transgenic organism. The thing is that when doing so, you use the very same DNA sample that was &quot;contaminated&quot; by ethidium bromide, so does this DNA you are using for transformation contain ethidium bromide? if so, how can it affect in numbers to mutation risk? &lt;/p&gt;&#xA;" OwnerUserId="3657" LastActivityDate="2013-12-25T16:11:32.043" Title="Ethidium bromide and mutagenesis on cloning" Tags="&lt;molecular-genetics&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14048" PostTypeId="1" AcceptedAnswerId="17312" CreationDate="2013-12-18T01:14:10.110" Score="3" ViewCount="214" Body="&lt;p&gt;Is there any explanation, gene(s) or whatever detected, that are co-related or explicitly related via mechanical bio-molecular (or at any other level) models that explain the higher or lower intelligence found in different individuals of &lt;em&gt;Homo sapiens&lt;/em&gt;?&lt;br/&gt;&#xA;If so, which and how do they work?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="6380" LastEditDate="2014-05-11T23:51:48.363" LastActivityDate="2014-05-11T23:51:48.363" Title="Is there a molecular basis to intelligence?" Tags="&lt;intelligence&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14049" PostTypeId="2" ParentId="14047" CreationDate="2013-12-18T02:24:00.967" Score="6" Body="&lt;p&gt;Purified DNA contains negligible amounts of ethidium bromide. PCR and gel clean-up kits remove it quite well. There is, though, a risk of mutation from the fact that you're visualizing the gel in UV light with ethidium bromide. The risk of mutation from UV is minimized by exposing the gel as little as possible, and by using &quot;preparative&quot; transilluminators that come with a low-light setting for cloning purposes. If you work well and quickly, the chance of mutagenesis isn't higher than the chance of a polymerase incorporating the wrong nucleotide.&lt;/p&gt;&#xA;" OwnerUserId="5156" LastEditorUserId="3632" LastEditDate="2013-12-18T03:29:16.570" LastActivityDate="2013-12-18T03:29:16.570" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14050" PostTypeId="2" ParentId="14045" CreationDate="2013-12-18T09:30:08.447" Score="5" Body="&lt;p&gt;Interesting question. I researched this a bit now and the phenomenon is termed &quot;numt&quot; for  &quot;nuclear mitochondrial DNA&quot;. This term descrives the transfer of cytoplasmic mitochondrial DNA sequences into the separate nuclear genome of a eukaryotic organism. It seems that most of these sequences are inactive. This &lt;a href=&quot;http://www.pseudogene.net/&quot;&gt;list&lt;/a&gt; at pseudogene.net has a large number of sequences in a lot of different organisms, for humans insertion between 0,2 and 14,2 kb are listed. Most of these sequences are detected in the deep sequencing projects underway these days and by comparative sequence analysis. An example is this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21151557&quot;&gt;paper&lt;/a&gt;, where they found mtDNA on chromosome 1 of homo sapiens, which was still part of the mitochondria in homo neanderthalensis.&#xA;For more information you can go to the list of papers I list below, this should be a good starting point:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11369110&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/11369110&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plosbiology.org/article/info%3adoi/10.1371/journal.pbio.0020273&quot;&gt;http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020273&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15014143&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/15014143&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18721785&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/18721785&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The papers should all be accessible, if not, let me know.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2013-12-18T10:04:14.333" LastActivityDate="2013-12-18T10:04:14.333" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14052" PostTypeId="1" AcceptedAnswerId="19624" CreationDate="2013-12-18T11:47:21.887" Score="8" ViewCount="292" Body="&lt;p&gt;I am interested in knowing the molecular mechanism behind mechanoreception/mechanotransduction (i.e. mechanism behind receptor potential generation on mechanical stimulation). I know that most mechanoreceptors (touch, stretch, pressure etc) respond to mechanical modification of plasma membrane or of some external projection embedded in plasma membrane. I want to know the molecular basis behind this mechanical transduction.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, the sensory hairs in lateral line sense organs of fishes, and equilibrium and auditory sensation in animals involve generation of receptor potential when the steriocilia( or any equivalent extracellular projection), externally embedded in gelatin, bends in specific ways, another example of mechanotransduction.&lt;br&gt;&#xA;(I don't know if all these receptors function with slight modification of the same basic framework or all of them operate with distinguishable mechanisms. If the latter is true, I just want one example of how molecular mechanism might bring about mechanoreception.)&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="9943" LastEditDate="2016-03-10T21:13:10.350" LastActivityDate="2016-03-10T21:13:10.350" Title="The mechanism of mechanoreception?" Tags="&lt;molecular-biology&gt;&lt;neuroscience&gt;&lt;physiology&gt;&lt;receptor&gt;&lt;touch&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14053" PostTypeId="2" ParentId="13896" CreationDate="2013-12-18T14:42:14.500" Score="1" Body="&lt;p&gt;In some ways tangent to what you are asking, but many cases of classical Allée effects (i.e. a positive relationship between population growth rate and population size, see &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jez.1400610202/abstract&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Allee WC, Bowen E. 1932. Studies in animal aggregations: mass protection against colloidal silver among goldfishes. Journal of Experimental Zoology 61 (2): 185–207&quot;&gt;Allée &amp;amp; Bowen, 1932&lt;/a&gt;, &lt;a href=&quot;http://www.nature.com/scitable/knowledge/library/allee-effects-19699394&quot; rel=&quot;nofollow noreferrer&quot;&gt;Drake &amp;amp; Kramer, 2011&lt;/a&gt;) should be relevant, especially after your clarification in the comments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One famous, early example of species collapse and extinction in a colony living species is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Passenger_Pigeon&quot; rel=&quot;nofollow noreferrer&quot;&gt;Passenger pigeon&lt;/a&gt;. This was an extremely common North American bird, estimated to 3-5 billion individuals, and maybe the most numerous bird species on the planet. It was heavily hunted during the 19th century (mainly by netting), which coupled to deforestation of nesting grounds led to a population crash. One of the main reasons for the rapid collapse was probably that the species was a colony nester and depended on large flocks for courtship/reproductive behaviour. This also meant that conservation measures failed when the critical situation was noticed (although hunting bans/restrictions was also weakly enforced). The few remaining wild individuals failed to breed and artificial breeding attempts also failed. The last individual died in 1914 at Cincinnati Zoological Garden (extinct in the wild from ~1900). For more information on the Passenger pigeon extinction see the &lt;a href=&quot;http://en.wikipedia.org/wiki/Passenger_Pigeon&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikpedia page&lt;/a&gt; and &lt;a href=&quot;http://www.si.edu/encyclopedia_Si/nmnh/passpig.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Encyclopedia Smithsonian&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DpcXI.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope you find this example useful, even though the collapse was initiated from hunting. There are many more examples of Allée effects in colony living species that describe similar effects, but maybe not as strikingly as the Passeger pigeon case. There is a fairly recent book &lt;em&gt;&quot;Allee Effects in Ecology and Conservation&quot;&lt;/em&gt; (&lt;a href=&quot;http://www.oxfordscholarship.com/view/10.1093/acprof:oso/9780198570301.001.0001/acprof-9780198570301&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Courchamp, Berec &amp;amp; Gascoigne. 2008. Allee Effects in Ecology and Conservation. Oxford University Press, Oxford&quot;&gt;Courchamp et al, 2008&lt;/a&gt;), which might be of interest to you. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-03-18T19:27:47.067" LastActivityDate="2014-03-18T19:27:47.067" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14054" PostTypeId="1" AcceptedAnswerId="14056" CreationDate="2013-12-18T17:59:10.923" Score="1" ViewCount="346" Body="&lt;p&gt;I know that the probability of life existing on a habitable planet is pretty slim. But, how likely is it that it hapenned millions of times in the same planet? Or was it only a few species that evolved into millions of other different species over time?&lt;/p&gt;&#xA;" OwnerUserId="5196" LastActivityDate="2013-12-18T18:49:24.623" Title="How likely is it that Earth has millions of different species?" Tags="&lt;evolution&gt;&lt;speciation&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14055" PostTypeId="2" ParentId="14054" CreationDate="2013-12-18T18:26:58.027" Score="2" Body="&lt;p&gt;The fantastic number of species that one can observe today is not a fixed value. This number changes over time. These changes are not caused by De Novo origin of life but by two processes which are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Extinction&quot; rel=&quot;nofollow noreferrer&quot;&gt;exctinction&lt;/a&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Process by which a species disappear&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Speciation&quot; rel=&quot;nofollow noreferrer&quot;&gt;speciation&lt;/a&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Process by which one species (or one lineage) becomes two.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Therefore the absolute change in number of species equals the difference between speciation and extinction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\delta_{species} = speciation.rate - extinction.rate$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a ton to say about extinction and speciation and it would take several books to tell you about this science. If you want to study the subject a bit further, I would suggest you to first grab a book of general biology or an introductory book in evolutionary biology before jumping into a book that talk about speciation and extinction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One can map how speciations events occurred frmo a unique common ancestor in order to create the diversity of life you can observe today. Such mapping are called Tree of Life. Here are the roots of the tree of life of living things on earth. You can spot Animalia, Fungi and Plants on the far right of the picture. The Common ancestor of all living things on earth is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Last_universal_ancestor&quot; rel=&quot;nofollow noreferrer&quot;&gt;LUCA&lt;/a&gt; (Last Universal Common Ancestor).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RVxCR.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a sidenote: The concept of species itself accept several definitions. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-12-18T18:49:24.623" LastActivityDate="2013-12-18T18:49:24.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14056" PostTypeId="2" ParentId="14054" CreationDate="2013-12-18T18:29:08.137" Score="4" Body="&lt;p&gt;We can be reasonably certain that ALL species that exist today share a common ancestor, a common origin. Every single species we have even encountered, for example, uses a long chain of nucleotides (DNA or RNA&lt;sup&gt;1&lt;/sup&gt;) to store its genetic information. If life had arisen through multiple independent sources, we would expect to find different solutions to the problem of passing genes to offspring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To put it another way, all forms of life we have found can be placed in one of three main classes (&lt;a href=&quot;http://en.wikipedia.org/wiki/Domain_%28biology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;superkingdoms&lt;/a&gt;): &lt;a href=&quot;http://en.wikipedia.org/wiki/Eukaryotes&quot; rel=&quot;nofollow noreferrer&quot;&gt;eukaryotes&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Prokaryotes&quot; rel=&quot;nofollow noreferrer&quot;&gt;prokaryotes&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Archaea&quot; rel=&quot;nofollow noreferrer&quot;&gt;archea&lt;/a&gt;. All other types of life come under one of those three categories (viruses are special and not really considered alive&lt;sup&gt;2&lt;/sup&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wfK5u.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, any organism we have ever seen uses the same basic systems of storing its genetic information. In fact, there are even certain genes that are conserved (similar in sequence) across &lt;em&gt;all&lt;/em&gt; domains of life (see my answer &lt;a href=&quot;https://biology.stackexchange.com/a/4979/1306&quot;&gt;here&lt;/a&gt; for some examples). That is why this version of the tree has a common root. All lines start from a single original line (commonly known as the Last Universal Common Ancestor, &lt;a href=&quot;http://en.wikipedia.org/wiki/Last_Universal_Common_Ancestor&quot; rel=&quot;nofollow noreferrer&quot;&gt;LUCA&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, all the evidence we have points to a single origin of life. There are too many shared features to assume multiple origins. Despite their enormous diversity, all organisms share certain very basic systems. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;NOTES&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;As far as I know, only certain viruses use RNA instead of DNA, all truly living creatures use DNA. Even if I'm wrong about this, the differences between RNA and DNA at this level are small enough that the common origin still holds. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;See &lt;a href=&quot;https://biology.stackexchange.com/q/9438/1306&quot;&gt;here&lt;/a&gt; for more in why viruses are not alive.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2013-12-18T18:29:08.137" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="14057" PostTypeId="1" AcceptedAnswerId="14083" CreationDate="2013-12-18T20:09:51.457" Score="2" ViewCount="299" Body="&lt;p&gt;Last night I was drying my cat with a towel after shenanigans in the rain and she sneezed! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Can cats/dogs/hamsters or other pets catch the cold? &lt;/li&gt;&#xA;&lt;li&gt;How quickly do they recover?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2013-12-19T09:33:15.257" LastActivityDate="2013-12-20T15:38:57.000" Title="Can pets catch the cold?" Tags="&lt;zoology&gt;&lt;immunology&gt;&lt;pathology&gt;&lt;infection&gt;&lt;pets&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14058" PostTypeId="2" ParentId="14045" CreationDate="2013-12-18T21:26:33.283" Score="5" Body="&lt;p&gt;We know about nuclear DNA having a mitochondrial origin mainly in two ways: (1) a sequence in the nucleus is found to closely match a sequence found in mitochondria, or (2) mitochondrial proteins are found to be encoded by the nuclear genome but not by the mitochondrial genome, and those proteins seem likely to have been necessary for sustaining life of the mitochondrial free-living ancestor. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The integration of copies of mitochondrial DNA into the nuclear genome is an ongoing process.  Pieces of DNA can float around and occasionally be spliced into a chromosome.  Most such integrated pieces are entirely nonfunctional (the functional version remaining in the mitochondria) and can pretty much be considered junk despite being replicated when the chromosome is replicated.  Useless gene-like pieces are often called nuclear mitochondrial pseudogenes or NUMTs (see, e.g., &lt;a href=&quot;http://www.pseudogene.net/&quot; rel=&quot;nofollow&quot;&gt;pseudogene.net&lt;/a&gt;).  NUMTs are of technical importance because they interfere with genome studies: the sequences of the NUMTs can easily be mistaken for true mitochondrial DNA leading to false conclusions about mitochondrial genomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A more general term is &lt;em&gt;endosymbiotic gene transfer&lt;/em&gt;, which can be used to describe nuclear DNA which was derived from DNA originally residing in mitochondria but now is no longer found there.  Some of this is nonfunctional, but much is functional, coding for proteins which after translation are sent to the mitochondria.  In fact, the &lt;a href=&quot;https://en.wikipedia.org/wiki/Human_mitochondrial_genetics#Contribution_of_mitochondrial_versus_nuclear_genome&quot; rel=&quot;nofollow&quot;&gt;overwhelming majority&lt;/a&gt; of mitochondrial proteins are coded by the nucleus, many of which probably had a mitochondrial origin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eukaryotes do vary in how much nuclear DNA is of mitochondrial origin.  A majority of functional genes are probably ancient and so tend not to vary a lot between organisms.  On the other hand, nonfunctional NUMTs are often relatively recently established and so often vary widely between organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Particular nuclear chromosomes are not associated with mitochondrial origins; the integration of free floating DNA pieces is mostly a fairly random process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more detail, you might want to see Timmis et al's review, &quot;&lt;a href=&quot;http://www.docentes.unal.edu.co/vcorredore/docs/nrg-123-04_Timmis++.pdf&quot; rel=&quot;nofollow&quot;&gt;Endosymbiotic Gene Transfer&lt;/a&gt;&quot;.  &lt;/p&gt;&#xA;" OwnerUserId="231" LastEditorUserId="231" LastEditDate="2013-12-21T18:35:45.263" LastActivityDate="2013-12-21T18:35:45.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14059" PostTypeId="1" CreationDate="2013-12-18T22:14:30.993" Score="11" ViewCount="6740" Body="&lt;p&gt;I'm looking for a downloadable list of all known (or better said, online documented) species in this straightforward format, as an example the European Frog:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kingdom: Animalia&lt;br&gt;&#xA;Division: Chordata&lt;br&gt;&#xA;Class: Amphibia&lt;br&gt;&#xA;Order: Anura&lt;br&gt;&#xA;Family: Ranidae&lt;br&gt;&#xA;Genus: Rana&lt;br&gt;&#xA;Species: Rana temporaria  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like to have this list offline in a structured text or database format that I can parse. If such a list has other useful attributes (credits, distribution, common names), it is welcome, but the above is the absolute minimum I need. I know there are more taxonomy levels in the above system (Species 2000 &amp;amp; ITIS Catalogue of Life: April 2013 ), but I only need these basic 6.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been looking at several collections and am having difficulty getting the data that I need. Either the database is incomplete, not accessible as a database, has complicated data structures, or has poorly described and slow web APIs that I cannot rely on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conceptually, it seems to me that &lt;a href=&quot;http://www.catalogueoflife.org&quot;&gt;http://www.catalogueoflife.org&lt;/a&gt; comes closest to my needs, yet their download is a tool, not a database. I do see the download has a MySQL folder containing lots of files, but I don't know how to reconstruct it into a database. It seems also that they pulled the page to describe the database download.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As simple as my question seems (I'm not a biologist, so I assumed it was simple), I have wasted several hours coming up empty. I was wondering if anybody has done the work to provide basic species info in an understandable format as requested?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for species completeness, the 1.3m of Catalogue of Life sounds really good, as I'm currently basing my system on Wikipedia, which only has 180k species. &lt;/p&gt;&#xA;" OwnerUserId="50" LastEditorUserId="3952" LastEditDate="2013-12-19T21:40:10.410" LastActivityDate="2020-11-05T18:09:33.000" Title="Is there a downloadable list of all species along with their traditional classification?" Tags="&lt;taxonomy&gt;&lt;phylogenetics&gt;" AnswerCount="5" CommentCount="4" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14060" PostTypeId="1" CreationDate="2013-12-18T23:28:24.360" Score="1" ViewCount="402" Body="&lt;p&gt;I read &quot;not for diagnostic use&quot; in every protocol i saw. why is it so? &#xA;which differences have the kits and material that are used for diagnostic purposes?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastActivityDate="2013-12-19T15:41:57.863" Title="reason for &quot;not for diagnostic use&quot; advice in protocols" Tags="&lt;protocol&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14061" PostTypeId="2" ParentId="14059" CreationDate="2013-12-18T23:30:50.203" Score="3" Body="&lt;p&gt;Have you tried NCBI?  Try this link:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/taxonomy&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/taxonomy&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2013-12-18T23:30:50.203" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14062" PostTypeId="1" AcceptedAnswerId="14066" CreationDate="2013-12-19T04:21:17.510" Score="6" ViewCount="1955" Body="&lt;p&gt;What would happen if the phospholipids in the phospholipid bi-layer were reversed, the fatty acid tails now facing outwards and the phosphate heads facing inwards? I'm assuming this will not affect the protein channels, but perhaps the loss of cholesterol in the structure of the bi-layer. Would this then mean that the fluid mosaic model no longer holds? &lt;/p&gt;&#xA;" OwnerUserId="5085" LastEditorUserId="5085" LastEditDate="2013-12-19T11:47:22.743" LastActivityDate="2019-09-16T10:36:20.580" Title="Phospholipid Bilayer structural reversal" Tags="&lt;biochemistry&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14063" PostTypeId="1" CreationDate="2013-12-19T04:39:59.160" Score="5" ViewCount="10743" Body="&lt;p&gt;The splitting of water is an endergonic (non-spontaneous) reaction, and thus would require energy (chemical work to be done) in order to happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Photosystem II, an enzyme catalyzes this splitting, but where does it get the energy from? Does it use ATP?&lt;/p&gt;&#xA;" OwnerUserId="5199" LastEditorUserId="3553" LastEditDate="2015-12-03T09:31:17.337" LastActivityDate="2015-12-04T09:45:55.140" Title="Photosynthesis: What Powers the Splitting of Water?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14064" PostTypeId="2" ParentId="14063" CreationDate="2013-12-19T06:42:45.790" Score="3" Body="&lt;p&gt;The electrones which are generated from splitting water are later used to split CO2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The general formula is: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qmHIz.png&quot; alt=&quot;General formula of photosynthesis&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Photosystem II does the first part of the reaction by splitting up water and transferring electrons to plastoquinone and also by generating H+ ions. Water gets oxidized (spends electrons) in this reaction, CO2 in the end is reduced (receives electrons). 4 photons are needed for splitting 1 water molecule and 8 photons to liberate one molecule of oxygen. For green plants the energy for this reaction comes completely from light. In the process the energy of the electrons is also used to generate ATP, not to use it.&#xA;A more detailed view can be found in the schematic diagram &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Photosynthesis#Z_scheme&quot; rel=&quot;nofollow noreferrer&quot;&gt;Z-scheme&lt;/a&gt;&quot; in the Wikipedia page on photosynthesis:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZtItq.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The figure shows the flow of the electrons and the points when they are brought to higher energy levels by light. The energy of the light is then converted in a proton gradient which is then used to generate ATP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its also possible to exchange the role of the oxygen with sulphur, the energy source is then usually heat. This is done by sulphur reducing bacteria in the deep sea in the vicinity of black smokers.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-11-08T21:47:36.263" LastActivityDate="2014-11-08T21:47:36.263" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14065" PostTypeId="1" AcceptedAnswerId="14087" CreationDate="2013-12-19T07:01:34.170" Score="6" ViewCount="931" Body="&lt;p&gt;Latent toxoplasmosis affects up to 1/3 of the human population and up to 40% of the population in Australia.  I have heard that latent toxoplasmosis has many significant undesirable effects on personality, such as decreased novelty-seeking behaviour, and decreased intelligence quotient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While these changes are statistically significant, I'm wondering if anyone knows the magnitude of these personality and cognitive changes, since a statistically significant result doesn't necessarily imply that there is a large difference in personality between those who are infected and those who aren't infected.  Also, can one succeed in an academic career path if one becomes infected with toxoplasmosis?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="24354" LastEditDate="2018-07-26T14:37:46.427" LastActivityDate="2021-03-05T20:45:20.623" Title="How much influence does toxoplasmosis have on personality and intelligence?" Tags="&lt;pathology&gt;&lt;ethology&gt;&lt;parasitology&gt;&lt;intelligence&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="14066" PostTypeId="2" ParentId="14062" CreationDate="2013-12-19T10:13:25.493" Score="7" Body="&lt;p&gt;This would have quite dramatic consequences. The layers are ordered in the way they are, because of their polarity. In the way they are ordered, the hydrophobic tails are inside and directed towards each other, the hydrophilic heads are orientated to the outside and inside. Since both sides of the membrane are surrounded by aqueous solutions, this is necessary to allow a contact between solution and cell membrane and to allow an exchange of molecules between them. If the layers would be oriented the other way, this contact and exchange wouldn't be possible. Proteins channels in the membrane wouldn't be possible as well, since the intermembrane domains are composed preferrably of amino acids with hydrophobic sidechains, while the domains on the outside of the membrane contain more hydrophilic amino acids.&#xA;A turn like this would need a completely different composition of life - meaning it couldn't be based on water like it is.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-19T10:13:25.493" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="14067" PostTypeId="1" CreationDate="2013-12-19T11:30:51.447" Score="5" ViewCount="208" Body="&lt;p&gt;Where in the body are self antigens important? In terms of central tolerance and autoimmunity, but also in terms of T cell activation?&lt;/p&gt;&#xA;" OwnerUserId="5202" LastActivityDate="2015-01-07T00:59:12.783" Title="Autoimmunity and central tolerance" Tags="&lt;immunology&gt;&lt;autoimmune&gt;&lt;antigen&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14068" PostTypeId="1" CreationDate="2013-12-19T12:18:33.253" Score="5" ViewCount="4356" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Temporal_lobe&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Temporal_lobe&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this have something to do with tempo (time?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Temporal lobe is behind (posterior) to frontal lobe, inferior to parietal lobe and is in front of occipital lobe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why it's called temporal?&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="1590" LastEditDate="2013-12-19T12:25:25.233" LastActivityDate="2018-11-30T17:18:41.893" Title="Why temporal lobe is called temporal?" Tags="&lt;brain&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14069" PostTypeId="2" ParentId="14068" CreationDate="2013-12-19T12:29:49.150" Score="13" Body="&lt;p&gt;The temporal lobe is in the temporal region of the head, near the temples of the skull, hence the name. It's name does not relate to it's biological function, it is mainly involved in processing language, visual memories, and emotions. The medulla oblongata is one region of the brain that deals with a lot of the &quot;tempo&quot; type functions (tempo as in keeping rhythm) such as controlling the heart beat and breathing rate.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Temple_%28anatomy%29&quot; rel=&quot;noreferrer&quot;&gt;Temple indicates the side of the head behind the eyes.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2013-12-20T10:09:52.840" LastActivityDate="2013-12-20T10:09:52.840" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14070" PostTypeId="2" ParentId="14060" CreationDate="2013-12-19T15:41:57.863" Score="3" Body="&lt;p&gt;the FDA has to approve diagnostics - a rigorous and expensive process.  Its a legal distinction, but also one which conveys a significant level of usefulness and reliability. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2013-12-19T15:41:57.863" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14071" PostTypeId="2" ParentId="14062" CreationDate="2013-12-19T17:41:24.483" Score="0" Body="&lt;p&gt;If the layer is opposite,then there wont be any cytoplasmic liquid(cytosol) inside the cell, as tail is Hydrophobic.If there is no cytosol,then no function of the cell.Even it becomes difficult to pass substances through the cell when layer is different.&lt;/p&gt;&#xA;" OwnerUserId="4376" LastActivityDate="2013-12-19T17:41:24.483" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14072" PostTypeId="2" ParentId="13662" CreationDate="2013-12-19T17:48:43.620" Score="1" Body="&lt;p&gt;Superoxide radicals , basically damage the lipid bilayers. affecting the efficient gradient. &#xA;for example H+ ion gradient across lipid bilayer in ETC is very important. this gradient is affected if superoxide radicals are present.&lt;/p&gt;&#xA;" OwnerUserId="4376" LastActivityDate="2013-12-19T17:48:43.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14073" PostTypeId="2" ParentId="14059" CreationDate="2013-12-19T20:38:53.873" Score="2" Body="&lt;p&gt;I suspect you will struggle to find what you are looking for.  However, you could break down your search criteria into smaller chunks to come up with some more successful (but still incomplete) results.  For example, species of what?  Do you really want ALL species (e.g.  Bacteria, Archaea, Eukaryota)?  Do you want just species that are currently alive (extant) or all species that are know to have existed at some point?  Do you want sub-species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you have decided on such things, you may be better off searching for individual country databases.  If you do decide you want ALL species, I suggest you break down each search into smaller chunks - such as 'mammalia'.  &lt;/p&gt;&#xA;" OwnerDisplayName="user5011" LastActivityDate="2013-12-19T20:38:53.873" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14076" PostTypeId="1" AcceptedAnswerId="24579" CreationDate="2013-12-19T23:35:50.193" Score="2" ViewCount="103" Body="&lt;p&gt;Assume that we have a plant, e.g. kale, which is prone to amylolysis if not harvested during a frost period.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it is harvested and put in a household freezer, such that it is frozen solid slowly enough for cell walls to burst, will the amylolysis stop, or will it still occur? Will it occur if it is kept in a fridge in the 0-4 Celsius range? If it does not occur while the vegetable is frozen, will it start after thawing? &lt;/p&gt;&#xA;" OwnerUserId="1578" LastEditorUserId="3340" LastEditDate="2014-12-05T09:28:36.940" LastActivityDate="2014-12-05T09:28:36.940" Title="Does amylolysis occur in vegetables if stored below 0⁰ Celsius?" Tags="&lt;biochemistry&gt;&lt;botany&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14077" PostTypeId="1" CreationDate="2013-12-20T05:20:33.073" Score="7" ViewCount="575" Body="&lt;p&gt;Ok so for a bit of a background, I am doing a science project looking at the action potentials of the earthworm. I anaesthatized the worms then hooked them up to a spiker box (&lt;a href=&quot;http://backyardbrains.com/products/spikerbox&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://backyardbrains.com/products/spikerbox&lt;/a&gt;) and stimulated them. &#xA;This is an average result:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ezIEN.gif&quot; alt=&quot;Average action potential (they all looked somewhat like this)&quot;&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I am confused about is why the action potential goes negative first before then going back up. From my readings online, I thought that the action potentials were meant to go up first then travel down and then continue on its course. If it helps I used a program called audacity to record the action potentials. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks very much guys. Sorry if I'm not being clear. Just ask anything if you need more information!&lt;/p&gt;&#xA;" OwnerUserId="5212" LastActivityDate="2014-09-11T01:04:38.010" Title="Confused at what is happening with these action potentials" Tags="&lt;neuroscience&gt;&lt;action-potential&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14079" PostTypeId="2" ParentId="13416" CreationDate="2013-12-20T08:04:32.053" Score="8" Body="&lt;p&gt;Making antibodies is mostly nothing you do with transgenic microorganisms. To make an antibody you first have to immunize an animal with the correct antigen. This includes have an animal facility where you can keep animals under clean conditions. If you are looking for polyclonal antibodies (meaning a whole bunch of different antibodies with different specificities) you will boost the animal before sacrificing them and isolating their blood to purify the antibodies.&#xA;If you are aiming for monoclonal antibodies then the animals will be boosted as well, then sacrificed and their spleens isolated. From the spleens you make single cell solutions from which antibody producing cells are isolated and plated one cell per well of 96 or 384 well plates and cultivate them to identify cells which produce antibodies. These cells are fused with immortal cells to produce immortal hybridoma cell lines which secrete a lot of antibodies into the cell media. These antibodies still need to be characterized to make sure the really bind the antigen of choice and not something else (in the spleen a lot a these reactions take place).&#xA;Just for estimations: Making one batch of a custom polyclonal antibody in rabbit with a given peptide sequence will cost you at least 5000\$ to 10.000\$ the last time we checked for it. Monoclonals are more expensive. So making an antibody is quite an investment on the first hand.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-20T08:04:32.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14080" PostTypeId="2" ParentId="14077" CreationDate="2013-12-20T08:21:52.107" Score="4" Body="&lt;p&gt;Nice graph. What happens when you reach the top of the potential (when you depolarize the membrane) that you need to go back to a resting potential to be able to stimulized again. The membrane gets &quot;neutralized&quot; and this reaction often over-shoots and goes below the resting potential, which is quite normal. Before reaching the normal resting potential there will be no further activation. The Wikipedia article on the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Action_potential&quot; rel=&quot;nofollow&quot;&gt;Action Potential&lt;/a&gt;&quot; contains a more complete explanation.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-20T08:21:52.107" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="14081" PostTypeId="1" CreationDate="2013-12-20T09:31:11.343" Score="16" ViewCount="22629" Body="&lt;p&gt;According to several studies quoted &lt;a href=&quot;https://skeptics.stackexchange.com/questions/5415/are-minerals-chemicals-absorbed-through-your-skin-during-bathing&quot;&gt;here&lt;/a&gt;, chemicals can be absorbed by the skin transdermally, at least under certain conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When it comes to elements in seawater like sodium, magnesium, potassium and iodine, is it possible for a human to absorb them transdermally in this instance?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it depends on various conditions, (such as length of time spent in the ocean, physiological factors (e.g. intense swimming vs. gentle bathing), temperature of the water and their respective effects on skin porousness or other factors affecting transdermal absorption), what would be they be?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if it can indeed be absorbed (e.g. from open water swimming), are the amounts significant to even measure alongside that of recommended levels for human dietary intake by advisory bodies such as FDA for those mentioned elements, or is it an extremely small amount much smaller than dietary levels of mineral intake?&lt;/p&gt;&#xA;" OwnerDisplayName="user3362" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2015-10-16T20:55:58.560" Title="Can humans transdermally absorb minerals from ocean water, and if so how much?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;ecology&gt;&lt;nutrition&gt;&lt;transdermal&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14083" PostTypeId="2" ParentId="14057" CreationDate="2013-12-20T11:02:07.950" Score="2" Body="&lt;p&gt;Yes they can. The viruses that cause a cold include rhinoviruses (up to 80%), coronaviruses and influenza (together accounting for much of the remaining 20%) and a small percentage of adenoviruses. When discussing cross species transfer, influenza is the most important to discuss as it is a fairly common cause of the &quot;common cold&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Influenza A has humans, pigs, bird and horses as its host. Different influenza strains have different hosts. Influenza can recombine if two strains infect the same host (antigenic shift) and also mutate (antigenic drift). With a combination of these influenza can and has numerous times crossed the species barrier which has caused the major flu pandemics as well as swine and avian flu. It's this reservoir that makes these viruses so hard to eradicate. When we are the only host such as in polio virus, it is a lot easier. Pigs don't adhere to national flu guidelines. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Comparing recovery times, all mammals are roughly similar although due to our slightly more evolved immune system as well as social factors of knowing what to do when we are ill we recovery very slightly earlier.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1757" LastEditDate="2013-12-20T15:38:57.000" LastActivityDate="2013-12-20T15:38:57.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14084" PostTypeId="2" ParentId="8492" CreationDate="2013-12-20T15:07:01.127" Score="2" Body="&lt;p&gt;The denaturing effect of Urea is mostly at very high concentrations.   (~Molar levels)!  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Physiologically, urea, a product of the breakdown of retired amino acids, will build up rather quickly if it weren't secreted in the urine. Looking into this, it doesn't seem as there is a clear understanding of why this causes a disease, though the buildup of a waste product definitely is a unifying concept. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Uremia - kidney failure - causes a build up of urea in the blood as the kidney eliminates urea from the blood into the bladder.  The specific effects of Urea on cell metabolism are probably numerous as the symptoms:  anorexia and lethargy, and late symptoms can include decreased mental acuity and coma. Other symptoms include fatigue, nausea, vomiting, cold, bone pain, itch, shortness of breath, and seizures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Being a metabolic waste product, it certainly would interfere with and inhibit any enzyme that produced urea - the &lt;a href=&quot;http://en.wikipedia.org/wiki/Urea_cycle&quot; rel=&quot;nofollow&quot;&gt;Urea cycle&lt;/a&gt; in particular.  Its clear that uremia is ultimately associated with cell death, oxidative stress, some cell signalling and proliferation.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm just googling around here, but I don't think there is any one single answer as to what goes wrong when the cells are exposed to too much urea. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-12-20T20:49:31.380" LastActivityDate="2013-12-20T20:49:31.380" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14085" PostTypeId="1" CreationDate="2013-12-20T15:27:31.517" Score="1" ViewCount="101" Body="&lt;p&gt;Pair-end mapping (PEM) is a technique that allows to detect structural variants in DNA by obtaining paired-end reads and the comparison of their positions in a reference genome.&#xA;Then among libraries that had insertion of 500bp, 2kb, 10kb and 40kb which one would you pick to detect the following inversions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) an inversion mediated by inverted repeats of 20 kb at its breakpoints&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) an inversion with clean breakpoints (no inverted repeats)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c) an inversion mediated by inverted repeats of 1 kb at its breakpoints&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;My guesses:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) 40kb, as if it were to be smaller than the inverted repeats length, the pair ends may align inside and nothing would be detected&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) Medium size, as if it is too small it wouldn't probably cover the area desired, and if it were bigger it would overlap too much (anyway data is needed for and answer is a blind optimization)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c) 2kb. same reasonings as a) and b). &lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="14826" LastEditDate="2015-03-29T18:02:49.373" LastActivityDate="2015-03-29T18:02:49.373" Title="Paired-end mapping exercise" Tags="&lt;homework&gt;&lt;genomics&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14087" PostTypeId="2" ParentId="14065" CreationDate="2013-12-20T15:35:02.880" Score="3" Body="&lt;p&gt;I believe its the other way around - humans may engage in riskier and more novel behavior when infected... which is the most interesting part of the story.  Its not cut and dried, but I think its quite possible that risky behavior increases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;T. gondii&lt;/em&gt; is a parasite whose typical life cycle includes both mice and cats as hosts.  The transmission involves the mice being eaten by a cat.  Mice infected with T gondii will tend to lose some interest in being sheltered in close spaces and wander out into open spaces.  &lt;a href=&quot;http://www.nature.com/news/parasite-makes-mice-lose-fear-of-cats-permanently-1.13777&quot; rel=&quot;nofollow&quot;&gt;They also lose their fear of cats&lt;/a&gt;.   That is a permanent change even if the mice are cleared of the parasite.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other animals, such as humans are secondary hosts - they can become infected by handling or close proximity to cat feces, who have a nearly 50% (45.6%) infection rate themselves. As a result toxoplasmosis is very common in humans.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Toxoplasmosis has been found to &lt;a href=&quot;http://schizophreniabulletin.oxfordjournals.org/content/33/3/757.full&quot; rel=&quot;nofollow&quot;&gt;increase novelty seeking and increases risk seeking behavior&lt;/a&gt; at least in men.  Its been shown to contribute to higher &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC117239/&quot; rel=&quot;nofollow&quot;&gt;automotive accident rates&lt;/a&gt;, schitzophrenia and &lt;a href=&quot;http://blogs.scientificamerican.com/science-sushi/2012/07/04/toxoplasmas-dark-side-the-link-between-parasite-and-suicide/&quot; rel=&quot;nofollow&quot;&gt;suicide&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Thus, the men were more likely to disregard rules and were more expedient, suspicious, jealous, and dogmatic. The personality of infected women, by contrast, showed higher warmth and higher superego strength (factors A and G on Cattell's 16PF), suggesting that they were more warm hearted, outgoing, conscientious, persistent, and moralistic. Both men and women had significantly higher apprehension (factor O) compared with the uninfected controls.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The correlation between toxoplasmosis and lower intelligence is a matter of debate, at least in this review I cite.  &lt;a href=&quot;http://lineu.icb.usp.br/~farmacia/artigos/toxo_comp_rev.pdf&quot; rel=&quot;nofollow&quot;&gt;Its still not clear whether it is a sociological correlation&lt;/a&gt; - do smart people just handle their cat poo more carefully or not at all? &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23593448&quot; rel=&quot;nofollow&quot;&gt;This more recent study&lt;/a&gt; shows that some factors might make infected humans &lt;em&gt;more&lt;/em&gt; intelligent and some researchers see toxoplasmosis as a transformative factor in humans ability to generate and use technologies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do see those links suggesting less risky behavior too.  Some say that the increase in traffic accidents is related to lower muscular coordination for instance.  There is evidence on both sides, but looking at what &lt;em&gt;T gondii&lt;/em&gt; does to mice, I would bet that some risk behavior will increase.  As such, I'd guess that researchers as such might have a slightly higher rate of toxoplasmosis, but maybe you will do a study and help figure this out!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said - anyone who tries to link a single phenomenon; host-parasite interactions; a drug; a gene; a mutation to a phenotype with a simple description is definitely oversimplifying.  The mapping from biological activity to english (or any other language) is hopefully conscious of the caveats of such talk.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-12-21T01:27:35.473" LastActivityDate="2013-12-21T01:27:35.473" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14088" PostTypeId="1" AcceptedAnswerId="14089" CreationDate="2013-12-20T16:02:56.297" Score="5" ViewCount="110" Body="&lt;p&gt;I am working on a project for health center. It involves the creation of a database of all diseases. Currently I want to classify disease on the base of their category based on international standard.&lt;br&gt;&#xA;Did anyone know where i can find one, I did a lot of research but was only able to come across this which seem not very useful to me: &lt;a href=&quot;http://www.cdc.gov/nchs/icd.htm&quot; rel=&quot;nofollow&quot;&gt;ICD&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="5215" LastEditorUserId="5144" LastEditDate="2013-12-20T21:42:00.780" LastActivityDate="2013-12-20T21:42:00.780" Title="Standard Classification of Disease" Tags="&lt;human-biology&gt;&lt;pathology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14089" PostTypeId="2" ParentId="14088" CreationDate="2013-12-20T16:09:18.243" Score="6" Body="&lt;p&gt;The two I know of off the top of my head are&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.omim.org/&quot; rel=&quot;noreferrer&quot;&gt;OMIM&lt;/a&gt; : Online Mendelian Inheritance in Man. This is very good and very well organized but only deals with inheritable diseases, no infections etc.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://disease-ontology.org/&quot; rel=&quot;noreferrer&quot;&gt;Human disease ontology&lt;/a&gt;. From their webpage:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts through collaborative efforts of researchers at Northwestern University, Center for Genetic Medicine and the University of Maryland School of Medicine, Institute for Genome Sciences.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;The DO is probably perfect for your needs.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-12-20T16:15:27.023" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14090" PostTypeId="1" AcceptedAnswerId="14091" CreationDate="2013-12-20T18:31:17.770" Score="3" ViewCount="80" Body="&lt;p&gt;I just found out today that type 1 diabetes is an autoimmune disease.  When was this discovered?  &lt;/p&gt;&#xA;" OwnerUserId="5217" LastActivityDate="2013-12-20T19:37:19.383" Title="When was it determined that Type 1 Diabetes is an autoimmune disease?" Tags="&lt;history&gt;&lt;autoimmune&gt;&lt;diabetes-mellitus&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14091" PostTypeId="2" ParentId="14090" CreationDate="2013-12-20T19:37:19.383" Score="5" Body="&lt;p&gt;This question has two answers: The difference was first described in 1936 by Harold Percival Himsworth, which described it in this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20779994&quot;&gt;article&lt;/a&gt;.&#xA;At this time it was established that there are two forms of Diabetes, one sensitive to insuline while the other is not.&#xA;The terms Diabetes type 1 and 2 where established somewhere between 1974 and 1976, for details see the review &quot;&lt;a href=&quot;http://diabetes.diabetesjournals.org/content/50/2/217.full&quot;&gt;The discovery of type 1 Diabetes&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-20T19:37:19.383" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14092" PostTypeId="2" ParentId="14088" CreationDate="2013-12-20T20:51:24.587" Score="2" Body="&lt;p&gt;I don't know if you're also interested in mental health issues, but the DSM (&lt;a href=&quot;http://www.dsm5.org/about/Pages/Default.aspx&quot; rel=&quot;nofollow&quot;&gt;Diagnostic and Statistical Manual of Mental Disorders&lt;/a&gt;) is the standard typology for that subject area. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;edit&lt;/em&gt;: I see that the Disease Ontology that @terdon lists also has mental health as a category.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-12-20T20:51:24.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14093" PostTypeId="1" CreationDate="2013-12-21T01:25:19.577" Score="1" ViewCount="1769" Body="&lt;p&gt;Only one side of the DNA ladder is copied (the sense side). The sense side starts with a 3’ end. This means the corresponding mRNA will have to assemble starting from the 5’ end. This is my initial thought, but can someone expand on it? Also, is this explained by why replication is performed in the 5' to 3' direction as suggested by this thread: &lt;a href=&quot;https://biology.stackexchange.com/questions/477/why-is-dna-replication-performed-in-the-5-to-3-direction&quot;&gt;Why is DNA replication  performed in the 5&amp;#39; to 3&amp;#39; direction?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9yepb.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5085" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2013-12-21T01:25:19.577" Title="Transcription takes place from the 5’ to the 3’ end of the m-RNA. Why?" Tags="&lt;dna&gt;&lt;rna&gt;" AnswerCount="0" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="14094" PostTypeId="1" AcceptedAnswerId="14095" CreationDate="2013-12-21T04:15:53.637" Score="1" ViewCount="678" Body="&lt;ol&gt;&#xA;&lt;li&gt;When is colchicine added to dividing cells for karyotype studies?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I know that colchicine inhibits polymerization of microtubules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2 So, why should it stop the cell cycle at metaphase when microtubules have already assembled and the next step(anaphase) requires depolymerization rather than polymerization ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-02-12T14:28:11.497" Title="Colchicine addition to cells" Tags="&lt;toxicology&gt;&lt;mitosis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14095" PostTypeId="2" ParentId="14094" CreationDate="2013-12-21T09:01:51.613" Score="3" Body="&lt;p&gt;Colchicine inhibits the formation of the microtubules by binding to tubilin and rendering it unavailable for the polymerization. Thats why the cells get arrested in the metaphase and can not go on further in the cell cycle and divide. For chromosome studies this is very useful since this is the phase where the chromatin is most condensed and can be viewed best. It inhibits the positive side producing the microtubules to prevent it from moving to the negative side, in cell division.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="-1" LastEditDate="2014-02-12T14:28:11.497" LastActivityDate="2014-02-12T14:28:11.497" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="14096" PostTypeId="1" AcceptedAnswerId="17559" CreationDate="2013-12-21T14:52:08.530" Score="1" ViewCount="319" Body="&lt;p&gt;Is this just a domain that binds proteins that have been phosphorylated? And it mediates signalling between an activated/phosphorylated protein? How is this significant with BRCA1?&lt;/p&gt;&#xA;" OwnerUserId="5219" LastActivityDate="2014-05-21T23:01:46.280" Title="What is a phospho-protein binding domain?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;cancer&gt;&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14098" PostTypeId="1" CreationDate="2013-12-21T16:09:21.283" Score="2" ViewCount="2558" Body="&lt;p&gt;Is light required for germination of every seed? If not, why don't some plants require it? Is there any difference in the quality and duration of light required ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be interesting if someone could give both  physiological and evolutionary reasons.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3952" LastEditDate="2013-12-21T17:12:01.827" LastActivityDate="2013-12-21T17:27:45.003" Title="Is light required for seed germination?" Tags="&lt;botany&gt;&lt;light&gt;&lt;germination&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="14099" PostTypeId="2" ParentId="5211" CreationDate="2013-12-21T16:18:07.193" Score="3" Body="&lt;p&gt;See &lt;a href=&quot;http://farncombe.mcmaster.ca/documents/ChronicGastroInflammationInducesAnxiety-LikeBehavior-Bercik.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper on link between inflammation and anxiety.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, quoting one of the paragraphs of this paper&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Clinical&#xA;  studies have shown increased serum inﬂammatory markers in patients with depression as well as a correlation&#xA;  between plasma cytokine levels and the severity of depression, and have described improvement in depression&#xA;  after anti-inﬂammatory treatment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Even if you do a simple google search, you will get thousands of results on this.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2013-12-21T16:18:07.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14100" PostTypeId="1" AcceptedAnswerId="14105" CreationDate="2013-12-21T16:59:53.360" Score="0" ViewCount="363" Body="&lt;p&gt;I understand that, unlike a prophage, a provirus never leaves the genome, but I don't understand how the prophage &quot;leaves&quot;.&lt;/p&gt;&#xA;" OwnerUserId="5179" LastActivityDate="2013-12-22T08:34:01.563" Title="How does a prophage leave the host cell's genome?" Tags="&lt;rna&gt;&lt;virus&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14101" PostTypeId="2" ParentId="14098" CreationDate="2013-12-21T17:27:45.003" Score="1" Body="&lt;p&gt;Here's a partial answer, based more on common-sense then in-depth knowledge:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Physiological. One reason light is not required immediately is that many seeds are in essence bundles of stored energy (as carbohydrates, I suppose). This is what makes them attractive food for birds, squirrels, humans, etc. When they're able to escape that predation, the growing plant can use that stored energy, rather than relying only on sunlight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolutionary. Seed dormancy can be a powerful tool for fitness – seeds that can remain dormant and germinate during favorable conditions could have a much higher survival rate. These conditions vary from simple: &quot;spring&quot; to more complex: &quot;after having passed through the digestive system of a certain animal&quot;; &quot;after a forest fire&quot;; &quot;when there's a gap in canopy cover / less competition for solar energy&quot;. The cues that seeds &quot;read&quot; in order to try to break dormancy and germinate during these times therefore vary among species. Within species, there are probably often a number of cues, and as @Konrad Rudolph suggests these are probably all relatively &quot;soft&quot;, or at least act in complex interaction with one another.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2013-12-21T17:27:45.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14102" PostTypeId="1" AcceptedAnswerId="14109" CreationDate="2013-12-22T02:20:38.093" Score="2" ViewCount="1481" Body="&lt;p&gt;The question was&lt;/p&gt;&#xA;&lt;p&gt;Which of the following statements is supported by these data?&lt;/p&gt;&#xA;&lt;p&gt;A. Phosphorus was the first limiting nutrient followed by nitrogen.&lt;/p&gt;&#xA;&lt;p&gt;B. Nitrogen was the first limiting nutrient followed by phosphorus.&lt;/p&gt;&#xA;&lt;p&gt;C. Phosphorus was limiting but nitrogen was not limiting.&lt;/p&gt;&#xA;&lt;p&gt;D. Nitrogen was limiting but phosphorus was not limiting.&lt;/p&gt;&#xA;&lt;p&gt;E. Neither nitrogen nor phosphorus was limiting.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/imjOr.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The answer was B: Nitrogen is the first limiting nutrient followed by phosphorus, but I do not know why. I thought it would be only phosphorus as the Nitrogen values are always greater than the control values.&lt;/p&gt;&#xA;" OwnerUserId="5222" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2013-12-22T15:05:56.687" Title="Determining limiting nutrients from a graph" Tags="&lt;biochemistry&gt;&lt;ecology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14103" PostTypeId="1" AcceptedAnswerId="14110" CreationDate="2013-12-22T03:12:51.033" Score="1" ViewCount="231" Body="&lt;p&gt;People: I have doubts about genetic heritage, but let me explain the context which has shown up this doubt for you: I was debating about sexism and the following question were put on the discussion: What kind of behavior, most of them come from men, is cultural and social, and what is a genetical heritage from our ancestry? Because I have a feeling that plenty of these behaviors that can be considered, maybe not correct, but at least justifiable. If you have some literature about this subject I would greatly appreciate it.&lt;/p&gt;&#xA;" OwnerUserId="5223" LastEditorUserId="1590" LastEditDate="2013-12-22T11:56:43.430" LastActivityDate="2013-12-24T06:25:07.087" Title="Current human behavior as a genetic heritage" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14104" PostTypeId="1" CreationDate="2013-12-22T03:30:17.000" Score="2" ViewCount="103" Body="&lt;p&gt;I have been wondering about this for this entire day today and I can't seem to find an answer. How far, exactly, does the diaphragm stretch for tidal breathing and what is its maximum stretch length?&lt;/p&gt;&#xA;" OwnerUserId="3170" LastActivityDate="2013-12-22T03:30:17.000" Title="How far does the diaphragm stretch when it contracts?" Tags="&lt;lungs&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14105" PostTypeId="2" ParentId="14100" CreationDate="2013-12-22T08:34:01.563" Score="1" Body="&lt;p&gt;This is explained reasonably well at &lt;a href=&quot;http://en.wikipedia.org/wiki/Lambda_phage#Induction&quot; rel=&quot;nofollow&quot;&gt;the Wikipedia entry for phage &amp;lambda;&lt;/a&gt;, which is the prototype lysogenic phage. Basically, integration occurs by site-specific recombination between the &lt;em&gt;attP&lt;/em&gt; region on the phage genome and the &lt;em&gt;attB&lt;/em&gt; region in the host genome. This means that in the prophage form the phage DNA is flanked by direct repeats. Excision involves the reverse process - recombination between these direct repeats. Excision is promoted by the phage-encoded Xis and Int proteins in combination with the host protein Ihf. The regulatory cascade which links cellular stress to this recombination event is detailed at the linked page.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2013-12-22T08:34:01.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14106" PostTypeId="1" AcceptedAnswerId="14146" CreationDate="2013-12-22T11:10:37.837" Score="8" ViewCount="18713" Body="&lt;p&gt;I'm not very well informed about all the things related to biology and the current achievements of science in this field so if I'm wrong in anything I say, please let me know. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many times I've come across a theory that the meaning of life itself is procreation - we simply live in order to make our species exist as long as possible. In the light of this theory, units like homosexuals or infertile people are totally useless and there's no really reason for them to exist from biological point of view. Though it's pretty obvious that in order to make us want to reproduce, something like joy of having sexual intercourse and life in general has been created. That's why units who only lack in ability to reproduce do live and most of the time they're fine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution doing adjustments in us in order to make us feel happy during our life seems to be understandable, but what about death? I've read that during death, a larger amount of DMT substance is being released in the brain - compound which is known from it's psychedelic effects, which in most cases are euphoric. It looks like we're not meant to feel 'bad' while dying, which is nice, but my question is - is it known why? What could be the evolutionary reason to create this mechanism? The unit which is about to die is not going to be useful anymore, so why bother? I'd like to somehow understand logic behind this. &lt;/p&gt;&#xA;" OwnerUserId="3063" LastActivityDate="2017-01-06T01:47:49.803" Title="Why is dimethyltryptamine (DMT) being released during death?" Tags="&lt;evolution&gt;&lt;life&gt;&lt;death&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14107" PostTypeId="1" CreationDate="2013-12-22T11:42:08.087" Score="3" ViewCount="2659" Body="&lt;p&gt;Electric shock occurs upon contact of a (human) body part with any source of electricity that causes a sufficient current through the skin, muscles, or hair.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In metals many electrons are said to be delocalised (i.e, electrons are not bound to any of the atoms). Around one electron per atom is said to be unbound to atom in mettalic lattice. So there will be motion of electrons due to thermal energy, however due to their random motion, there won't be such a significant current produced. When electric field is applied across them there will be motion of electrons in a particular direction, causing significant amount of current. In case of insulators, due to bound electrons we can't expect current through them.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When our body becomes a part of electric circuit, current is said to pass through our skin, muscles, or hair. Does it imply that there are free electrons in skin, hair, or in muscles (like those in metals)? &lt;/p&gt;&#xA;" OwnerUserId="4918" LastActivityDate="2014-04-26T07:29:36.013" Title="Are there free electrons in muscles, hair, or skin?" Tags="&lt;muscles&gt;&lt;skin&gt;&lt;hair&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14108" PostTypeId="2" ParentId="14107" CreationDate="2013-12-22T12:23:46.220" Score="3" Body="&lt;p&gt;Our body contains a lot of salt and which act as electroyte,so when we comes in contact of electric source then the electrolyte helps in the conduction of electric current through out body,&lt;/p&gt;&#xA;" OwnerUserId="5164" LastActivityDate="2013-12-22T12:23:46.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14109" PostTypeId="2" ParentId="14102" CreationDate="2013-12-22T15:05:56.687" Score="2" Body="&lt;p&gt;The control graph shows the baseline against which we can compare the other graphs. It is the graph without any changes, and hence is the graph in which one of the nutrient is limiting.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the graph for +P, there is no rise in biomass and the graph resembles the control. This shows that Phosphorous is not the first(initial) limiting nutrient, as its addition did not affect the biomass production.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The +N graph shows a significant rise in biomass, indicating that N was indeed the initial limiting nutrient. On its addition, the biomass production increased.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The +N and +P graph shows a higher biomass than +N and the control. This indicates, that while  N was established to be the first(initial) limiting reagent, addition of Phosphorous also significantly improves the biomass yield, and hence P must also have become a limiting nutrient once N was added and its limiting effect removed. That is the reason why +N+P graph is higher than just +N graph. If phosphorous would not have been limiting even on addition of N, then the +N+P graph would have resembled +N graph.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2013-12-22T15:05:56.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14110" PostTypeId="2" ParentId="14103" CreationDate="2013-12-22T15:10:08.103" Score="2" Body="&lt;p&gt;All &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenotype&quot; rel=&quot;nofollow&quot;&gt;phenotypic&lt;/a&gt; traits have some part of the variance which is explained by the environment and  some part that is explained by the genes. The heritability is then defined as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$H_N = \frac{V_{genetic}}{V_{phenotype}} = \frac{V_{genetic}}{V_{genetic}+V_{environment}+V_{interaction. gene.environment}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $V_{genetic}$ is the Variance in phenotypic traits due to genes, $V_{phenotype}$ is the total phenotypic variance, $V_{environment}$ is the variance due to environment and $V_{interaction. gene.environment}$ is the variance due to interaction between genes and environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So your question (if I understand it correctly) should rather be a list of phenotypic traits (behavior) and ask what is the heritability of each trait in the world-wide human population (or on a given subset of the human population).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think, there is no objective manner of defining a given phenotypic trait. You should chose subjectively, some behavior, define it accurately and then ask the question what is it's heritability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, it is quite hard to measure a behavior. It is much easier to estimate the heritability of height in humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several different methods in order to estimate heritability of a trait. See this &lt;a href=&quot;http://en.wikipedia.org/wiki/Heritability#Estimation_methods&quot; rel=&quot;nofollow&quot;&gt;wikipedia article&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of these experiments are not feasible on humans for ethical reasons. Some others are quite limited and are quite expensive. I don't think we have many studies that quantify the heritability of behavioral traits in humans but I might be mistaken.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As said by @AlanBoyd, there is a field called evolutionary psychology that deal with this kind of question. To my knowledge this field is mostly a purely theoretical field and therefore, it does not quite allow to measure heritability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good start into this science would be the &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionary_psychology&quot; rel=&quot;nofollow&quot;&gt;wikipedia article&lt;/a&gt; which seems quite complete.  I can give you some books but I haven't read most of them. &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1107622735&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; and &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1405191228&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; are introductory books in the field. I think &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/B00486U8N6&quot; rel=&quot;nofollow&quot;&gt;this book&lt;/a&gt; is a classic in the field. I read &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0465085970&quot; rel=&quot;nofollow&quot;&gt;this book&lt;/a&gt; and it is quite interesting. There are actually many books in this field. The best think you can do is maybe to typewrite &quot;evolutionary psychology&quot; in amazon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a sidenote: If you enter in the field of evolutionary psychology you might as well be interested by memetic evolution (evolution of culture). &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/B00814M2BW&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a classic book on the subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Be careful in these fields, I think that some ideas do not deserve to be considered as part of science while other do!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-12-24T06:25:07.087" LastActivityDate="2013-12-24T06:25:07.087" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14111" PostTypeId="1" CreationDate="2013-12-22T18:52:31.633" Score="2" ViewCount="73" Body="&lt;p&gt;This photograph was taken on the intertidal mudflats at Lindisfarne, Northumberland, UK today. It was about 40m from the shoreline at low tide. Is the green plant a species of zostera? Can anyone help with the identification?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8Fsnc.jpg&quot; alt=&quot;species &quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1216" LastEditorUserId="5144" LastEditDate="2013-12-22T20:54:16.533" LastActivityDate="2013-12-22T21:38:42.330" Title="Is this maritime plant a species of zostera?" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14112" PostTypeId="2" ParentId="14111" CreationDate="2013-12-22T21:38:42.330" Score="3" Body="&lt;p&gt;It certainly looks like a &lt;em&gt;Zostera&lt;/em&gt; species.  The ones that appear in the UK are &lt;em&gt;Zostera angustifolia&lt;/em&gt;, &lt;em&gt;Zostera noltii&lt;/em&gt;, and &lt;em&gt;Zostera marina&lt;/em&gt;.  Its hard to tell exactly which species this one is without size information and knowing the conditions of the bay.  &lt;em&gt;Z. marina&lt;/em&gt; has the broadest leaves at around 5 - 10 mm, whilst &lt;em&gt;Z. angustifolia&lt;/em&gt; has leaves just 2 - 3 mm broad.  Is 40m around the mid-water mark?  If so I would hazard a guess this is &lt;em&gt;Z. angustifolia&lt;/em&gt;.  &lt;em&gt;Z. marina&lt;/em&gt; tends to stick to areas permanently covered by the sea (sub-littoral) whilst &lt;em&gt;Z. noltii&lt;/em&gt; likes much more sheltered conditions than the middle of the bay, tending to stick to the upper shore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps!&lt;/p&gt;&#xA;" OwnerDisplayName="user5011" LastActivityDate="2013-12-22T21:38:42.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14115" PostTypeId="1" AcceptedAnswerId="14116" CreationDate="2013-12-23T07:28:52.770" Score="6" ViewCount="451" Body="&lt;p&gt;I have heard that &quot;air in the GI tract&quot; results in flatulence and burping etc, however I initially assumed that the &quot;empty&quot; GI tract was a hollow tube filled with air anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So on an empty stomach (or &quot;empty&quot; GI tract rather), does the GI tract collapse due to the pressure in the surrounding cavities, or is the GI tract normally a hollow tube filled with air, and flatulence merely a result of &quot;excess&quot; air?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2013-12-24T15:54:41.367" Title="Is the empty GI tract a hollow tube with air inside, or is it generally collapsed until food is eaten?" Tags="&lt;physiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14116" PostTypeId="2" ParentId="14115" CreationDate="2013-12-23T14:50:21.300" Score="6" Body="&lt;p&gt;Under normal circumstances the stomach and GI tract have very little &quot;gas&quot; in them - whether it be flatus, air, CO&lt;sub&gt;2&lt;/sub&gt;, or anything else - and so are essentially collapsed with the walls against each other. However, gas is continually being produced by the microorganisms that inhabit our gut, and can also come from swallowing small amounts of air, fizzy drinks, etc., so the environment is never 100% gas-free. A typical person produces on the order of 500-1500 ml (0.5-1.5 liters) of gas per day.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're interested, the Wikipedia article on &lt;a href=&quot;https://en.wikipedia.org/wiki/Flatulence&quot;&gt;flatulence&lt;/a&gt; is a good introduction.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2013-12-23T14:50:21.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14117" PostTypeId="1" CreationDate="2013-12-23T14:52:36.423" Score="4" ViewCount="2823" Body="&lt;p&gt;According to &lt;em&gt;Molecular And Cellular Biology&lt;/em&gt; (Stephen L. Wolfe),&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Membranes disperse almost instantaneously if exposed to a nonpolar environment or to &lt;strong&gt;&lt;em&gt;detergents&lt;/em&gt;&lt;/strong&gt;, which are amphipathic molecules that can form a hydrophilic coat around the hydrophobic portions of membrane lipids and proteins in water solutions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This might be a stupid question but... if detergents can 'form coats around hydrophobic portions' of membrane-suspended molecules, they must, somehow get in the hydrophobic membrane interior... right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do they get in the membrane interior? Do they form clusters like endocytic vesicles? What happens after they form hydrophilic coats around hydrophobic molecule regions?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2013-12-28T01:35:28.790" Title="How do detergents get in hydrophobic membrane interior?" Tags="&lt;cell-biology&gt;&lt;cell-membrane&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14118" PostTypeId="2" ParentId="14117" CreationDate="2013-12-23T15:19:05.793" Score="4" Body="&lt;p&gt;It depends on the concentration, but at higher concentration the detergent molecules build so called micelles, where the hydrophobic &quot;tail&quot; is orientation into the inner part and the hydrophilic &quot;head&quot; is orientated to the outside. This allows the micelle also to fuse with the membrane and then to desintegrate it.&#xA;This illustration from the Wikipedia shows the schematically:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JTNI2.png&quot; alt=&quot;Detergent micelle in water&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Surfactant&quot; rel=&quot;nofollow noreferrer&quot;&gt;surfactant article&lt;/a&gt;, which has more details.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-23T15:19:05.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14119" PostTypeId="1" CreationDate="2013-12-23T22:37:32.467" Score="2" ViewCount="157" Body="&lt;p&gt;In the year 1900 roughly 50% of the people in the United States were homozygous for the gene for blue eyes. By 1950 the number had dropped down to 30%. Just now, (2013) barely 12% of the people living in America are homozygous for the blue eye gene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given the current rates of third world immigration into the United States. When will the last blue eyed man and the last blue eyed woman conceive a child with blue eyes? Should people with blue eyes bring reverse discrimination suits?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;a href=&quot;http://www.boston.com/news/globe/living/articles/2006/10/17/dont_it_make_my_blue_eyes_brown/&quot; rel=&quot;nofollow&quot;&gt;http://www.boston.com/news/globe/living/articles/2006/10/17/dont_it_make_my_blue_eyes_brown/&lt;/a&gt; By Douglas Belkin  &lt;/p&gt;&#xA;" OwnerUserId="4274" LastEditorUserId="4274" LastEditDate="2013-12-24T14:04:36.020" LastActivityDate="2013-12-24T14:04:36.020" Title="How Much Longer For The Gene For Blue Eyes?" Tags="&lt;genetics&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="14120" PostTypeId="1" AcceptedAnswerId="14122" CreationDate="2013-12-23T23:12:05.030" Score="8" ViewCount="3841" Body="&lt;p&gt;Is it possible for cells from the same tumor to have different genetic material, and if so, to what degree is it possible (how fast do they mutate) ?&lt;/p&gt;&#xA;" OwnerUserId="5237" LastEditorUserId="57" LastEditDate="2013-12-24T07:53:35.103" LastActivityDate="2017-09-03T05:02:05.973" Title="Can cancer cells in the same person, organ, and origin have different DNA?" Tags="&lt;cancer&gt;&lt;mutations&gt;&lt;dna-damage&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14121" PostTypeId="2" ParentId="14119" CreationDate="2013-12-23T23:17:15.317" Score="7" Body="&lt;p&gt;Never.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if the country arrives at the unlikely day when there is no one alive in the United States with the blue eye phenotype, there are still plenty of people with the unexpressed recessive gene, and if two of them get together, those genes can combine to produce another blue-eyed child. If this happens twice, with one boy and one girl, and they happen to meet when they are in college and say &quot;Hey cool, you have the same inexplicably rare kind of eyes as me. I think I want to marry you.&quot; then any children they have will also be blue eyed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So even if the day came when you couldn't find a soul in the world with blue eyes, you will still never know if you've seen the end of them.&lt;/p&gt;&#xA;" OwnerUserId="5018" LastActivityDate="2013-12-23T23:17:15.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14122" PostTypeId="2" ParentId="14120" CreationDate="2013-12-23T23:30:14.180" Score="9" Body="&lt;p&gt;Cancer cells and normal cells differ on the genetic basis but they share the same genetic background, so they have not different DNA in the sense of two different people. They have to be different, since cancer cells have to accumulate mutations on a number of genes to become a cancer cell, which can survive and will not be directed into apoptosis. These are genes which control the cell cycle, certain growth factors, tumor suppressor genes, cell signalling and so on. In all these genes there need to be either activating or deactivating mutations present. Most of these mutations are point mutations (&lt;a href=&quot;http://de.wikipedia.org/wiki/SNP&quot; rel=&quot;nofollow&quot;&gt;single nucleotide polymorphisms, SNP&lt;/a&gt;), where only one base is altered to achieve a mutation. An example for such a mutation would be the mutation in the B-RAF kinase, which is involved in signaling and activating genes, where a point mutation exchanges Valine 600 to glutamic acid (V600E, for reference see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24298448&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;). These are relatively small differences between these two cells. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Cancer_Genome_Project&quot; rel=&quot;nofollow&quot;&gt;Cancer Genome Project&lt;/a&gt; aims to sequence cells from a cancer and also normal cells from the same individual and then do a comparison. Later stages tumors often tend to genetic instabilities where complete regions of the genome are duplicated, inverted or deleted, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20177397&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for a review.&#xA;A more basic overview is given by the Ebook &quot;&lt;a href=&quot;http://www.nature.com/scitable/ebooks/essentials-of-cell-biology-14749010/contents&quot; rel=&quot;nofollow&quot;&gt;Essentials of Cell Biology&lt;/a&gt;&quot; by the Nature Group, which has an &lt;a href=&quot;http://www.nature.com/scitable/ebooks/essentials-of-cell-biology-14749010/112301679#headerAndCitation&quot; rel=&quot;nofollow&quot;&gt;overview&lt;/a&gt; of cancer cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the mutation rate, this is hard to estimate. There are a few papers available here, but they focus on the mutation rate in germ cells, so these are mutations that are transmitted to the next generation. The estimates there are between 70 and 100 mutations per generation per individual, depending on the research method. You can find a nicely explained blog article &lt;a href=&quot;http://sandwalk.blogspot.de/2013/03/estimating-human-mutation-rate-direct.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, which gives a number of original references, too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mutation rate in cancer is a different thing, since this depends on which genes are mutated. The mutation rate for cancer has to be higher for the cancer cells to allow to collect the necessary transformations into a cancer cell, but these mutations seem to occur only in a few hotspot regions of the genome (Further references can be found in this article called &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24048066&quot; rel=&quot;nofollow&quot;&gt;The causes and consequences of genetic heterogeneity in cancer evolution&lt;/a&gt;&quot; and in this called &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24022702&quot; rel=&quot;nofollow&quot;&gt;Emerging patterns of somatic mutations in cancer&lt;/a&gt;&quot;). There are two article called &quot;The mutation rate and cancer&quot; which are interesting in this context. They can be found &lt;a href=&quot;http://www.pnas.org/content/93/25/14800.short&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.genetics.org/content/148/4/1483.short&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. As always, if you have problems with getting the articles, let me know, I can help there.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="14852" LastEditDate="2016-01-28T10:34:54.553" LastActivityDate="2016-01-28T10:34:54.553" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14123" PostTypeId="1" AcceptedAnswerId="14139" CreationDate="2013-12-24T01:46:06.380" Score="8" ViewCount="158" Body="&lt;p&gt;Is it customary for investigators to publish the original x-ray diffraction data used in macromolecular structural determination? If not, why not; and if so, is there an online database where these data may be downloaded?&lt;/p&gt;&#xA;" OwnerUserId="4140" LastEditorUserId="4140" LastEditDate="2013-12-24T01:51:06.773" LastActivityDate="2013-12-26T17:48:41.430" Title="Are original x-ray diffraction data available" Tags="&lt;structural-biology&gt;&lt;xray-crystallography&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14124" PostTypeId="2" ParentId="8738" CreationDate="2013-12-24T02:04:30.777" Score="2" Body="&lt;p&gt;I'm impressed to stumble upon someone who can do that with his tongue. And mainly because I can do that myself!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at the images and feeling with my tongue, this rugged area you mention is definitely too close to the nose to be the adenoids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I googled a bit (well, more like a lot) and I found this cool webpage which details that area.&#xA;&lt;a href=&quot;http://www.theodora.com/anatomy/the_pharynx.html&quot; rel=&quot;nofollow&quot;&gt;http://www.theodora.com/anatomy/the_pharynx.html&lt;/a&gt;&#xA;and I found this snippet of text:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Above the pharyngeal tonsil, in the middle line, an irregular&#xA;  flask-shaped depression of the mucous membrane sometimes extends up as&#xA;  far as the basilar process of the occipital bone; it is known as the&#xA;  pharyngeal bursa.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I've found stones in my tonsils but never in my adenoids. What I've sometimes found was dried mucus adhered to it when waking up in the morning.&#xA;I believe those stones might be rests of food (which can't really get up there).&#xA;Maybe this green mucus you found was just dried mucus? Maybe a little infection on a particular day?&#xA;I hope you get the answer, since it's passed a quite long time since you asked :)&lt;/p&gt;&#xA;" OwnerUserId="5238" LastActivityDate="2013-12-24T02:04:30.777" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14125" PostTypeId="2" ParentId="14117" CreationDate="2013-12-24T04:35:13.197" Score="3" Body="&lt;p&gt;The membrane is dispersed by detergents.  But the detergents, under the right concentrations and conditions (salt, pH, et) form micelles with smaller curvature than the lipids that compose cell membranes.  With some luck, they can form a small hydrophobic micelle bubble around the protein.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This figure is depicts detergent micelles around a membrane protein's membrane bound regions, hopefully without distorting the shape of the protein!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oPmAE.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since you asked in the comments, here is a picture of the &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0969212601002416&quot; rel=&quot;nofollow noreferrer&quot;&gt;electron density of the detergent micelle in ompF Porin crystals&lt;/a&gt; - the detergent density is blue the protein is red.  For a while in the mid 90s through maybe a few years ago there were a reasonable number of simulations including detergent molecules.  The mobility of the chains in the micelles means that no specific model structure would be accurate, but it can help understand the electromagnetic environment of the solvent in cases which are important like charge transfer in a photoreaction center or the dynamics of transport through an import/export protein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VvZSl.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-12-28T01:35:28.790" LastActivityDate="2013-12-28T01:35:28.790" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14126" PostTypeId="1" AcceptedAnswerId="14128" CreationDate="2013-12-24T07:07:20.030" Score="-2" ViewCount="153" Body="&lt;p&gt;Why is it rare for a person to have 2 (or more) infectious diseases (for example: Flu &amp;amp; Cold together at the same time)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although it's rare, it happens when the immune system is weak (e.g when patient has both AIDS and Kaposi's sarcoma).&lt;/p&gt;&#xA;" OwnerUserId="5221" LastActivityDate="2019-05-25T03:24:54.730" Title="Why it is rare for person to get infected with two Pathogens?" Tags="&lt;immunology&gt;&lt;pathology&gt;" AnswerCount="3" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="14127" PostTypeId="2" ParentId="14036" CreationDate="2013-12-24T07:52:32.583" Score="2" Body="&lt;p&gt;As nobody is suggesting an answer I'll give my guess that I already discussed in the comments and give some extra details about ongoing debates on the subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We'll start with the sense of color sight in order to make easier. One can argue that we see in 3 dimensions because we use three cells which level of activation inform the brain of the color. I guess that the whole 3D space delimited by the maximum level of activation of each three receptors can be used. Therefore, it is nothing else than the number of receptor that determine the number of dimensions in which we can sense. Now it is assuming that each receptor can send signal of different strength information of the intensity of the light or smell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to wikipedia. Mammals have about thousands of genes that code for olfactory receptors. Moreover, the question of how these receptors work is still debated&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In mammals, each olfactory receptor neuron expresses only one functional odor receptor. Odor receptor nerve cells function like a key-lock system: If the airborne molecules of a certain chemical can fit into the lock, the nerve cell will respond. There are, at present, a number of competing theories regarding the mechanism of odor coding and perception. According to the shape theory, each receptor detects a feature of the odor molecule. Weak-shape theory, known as odotope theory, suggests that different receptors detect only small pieces of molecules, and these minimal inputs are combined to form a larger olfactory perception (similar to the way visual perception is built up of smaller, information-poor sensations, combined and refined to create a detailed overall perception).[citation needed] An alternative theory, the vibration theory proposed by Luca Turin, posits that odor receptors detect the frequencies of vibrations of odor molecules in the infrared range by electron tunnelling. However, the behavioral predictions of this theory have been called into question. There is no theory yet that explains olfactory perception completely.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Note: the two competing theories for color sights: &lt;a href=&quot;http://en.wikipedia.org/wiki/Opponent_process&quot; rel=&quot;nofollow&quot;&gt;Opponent process&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Trichromatic_theory&quot; rel=&quot;nofollow&quot;&gt;Trichromacy&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this question would also be a good fit for &lt;a href=&quot;http://cogsci.stackexchange.com&quot;&gt;cognitive science beta&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-12-24T17:31:23.920" LastActivityDate="2013-12-24T17:31:23.920" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14128" PostTypeId="2" ParentId="14126" CreationDate="2013-12-24T15:45:42.017" Score="5" Body="&lt;p&gt;What makes you consider it is rare? It is not at all uncommon to be affected by two infections. Typically I agree we aren't as the number of infectious organisms that we are exposed to which cause a clinical manifestation (i.e. aren't controlled by the immune system) are low. Nevertheless, any chronic infections such as herpes viruses may often manifest when we are under stress with another infection, many bacterial pneumonias are more likely to occur when a viral infection is also present and of course the many immunosuppressed people. Arguably a lot of infections are by two or more causative agents as often if one is able to enter where it shouldn't, another may, but one is likely to be more dominant. Furthermore even our infections can get infections with bacteriophages infecting the bacteria we are infected with. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-12-24T15:45:42.017" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14129" PostTypeId="2" ParentId="14115" CreationDate="2013-12-24T15:54:41.367" Score="3" Body="&lt;p&gt;If you look below you can see two X rays. One with bowel obstruction on the right and a normal on the left. On an X ray air bubbles are black as indicated. Under normal circumstances as you can see there is very little air in the stomach and GI tract, although more frequently there will be some in the stomach due to fizzy drinks or reactions involving stomach acid producing gas in our stomach. That air later on in our GI tract tends to be a mix of carbon dioxide, methane and other waste products that bacteria in our gut have made. As Matt said, we produce quite a substantial amount of gas (500-1500 ml) per day. In an obstruction all of this can collect and further increase as microogranisms are in contact with the food for a longer duration as well as more enzymatic breakdown. And this can be seen in Figure 2. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wFxx4.jpg&quot; alt=&quot;Figure 1 is a normal bowel compared to a obstructed bowel&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2013-12-24T15:54:41.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14130" PostTypeId="1" AcceptedAnswerId="14142" CreationDate="2013-12-24T17:11:01.000" Score="4" ViewCount="890" Body="&lt;p&gt;The section of retina shows a layered arrangement of the various retinal cells. Starting from the inside (where the light strikes first) is the nerve fibre layer, ganglionic layer, amacrine cell layer, bipolar cell layer, horizontal cell layer and finally rods and cones (and that too in inverted position, i.e. the actual receptor portions are farther inwards).  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Why is this stratification inverted?&lt;/strong&gt; If the receptors would have been the innermost cells, they could have received the maximum&#xA;  quantity of unaltered light. Does this &quot;inverted&quot; arrangement, i.e.&#xA;  arrangement with the receptor cell behind a screen of several other&#xA;  layers not hinder the process of photoreception by blocking a lot of&#xA;  incident light and hence the formed image? &lt;strong&gt;What is, if any,&#xA;  advantage of this reverse arrangement?&lt;/strong&gt;  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KE7y5.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="9943" LastEditDate="2016-01-12T11:51:39.857" LastActivityDate="2016-01-12T11:51:39.857" Title="The arrangement of retinal cells?" Tags="&lt;human-biology&gt;&lt;vision&gt;&lt;eyes&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14131" PostTypeId="1" CreationDate="2013-12-24T17:51:31.710" Score="4" ViewCount="88" Body="&lt;p&gt;I wonder why gene expression data are very frequently modeled by multivariate normal distributions. What is the reason for those strong assumptions that the genes follow multivariate gaussian? Are there any reasons specific for genetics other than the reasons for general gaussian assumptions (the ease of calculation, etc.)?&lt;/p&gt;&#xA;" OwnerUserId="5054" LastEditorUserId="3340" LastEditDate="2013-12-26T09:03:26.480" LastActivityDate="2013-12-26T09:03:26.480" Title="Why genes are assumed to follow multivariate normal?" Tags="&lt;biostatistics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14132" PostTypeId="1" CreationDate="2013-12-24T18:01:32.757" Score="3" ViewCount="985" Body="&lt;p&gt;What is the window during which division into twins is possible (for instance can it still happen after implantation in the uterus)?&#xA;Is one twin the &quot;original&quot; and the other its clone?&lt;/p&gt;&#xA;" OwnerUserId="5243" LastActivityDate="2017-04-29T21:48:21.600" Title="When does identical twinning happen?" Tags="&lt;human-biology&gt;&lt;twins&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14133" PostTypeId="1" CreationDate="2013-12-24T18:11:48.823" Score="3" ViewCount="156" Body="&lt;p&gt;Can developing twins further divide and subdivide and become identical quadruplets or octuplets or...?&#xA;Can twinning be induced, either in utero or in vitro? &#xA;Might it be possible to just keep harvesting a few cells off the original clump indefinitely and making an unending stream of identical embryos for implantation in a surrogate uterus?&lt;/p&gt;&#xA;" OwnerUserId="5243" LastActivityDate="2013-12-25T16:41:46.893" Title="Is there a limit to twinning?" Tags="&lt;twins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14134" PostTypeId="1" CreationDate="2013-12-24T18:36:48.247" Score="2" ViewCount="40" Body="&lt;p&gt;If one developing twin absorbs another, when does that happen?&#xA;Is it possible for an appendage or organ to develop and be the only remaining vestige of an absorbed twin, such as a hand or a mouth, or a heart?&lt;/p&gt;&#xA;" OwnerUserId="5243" LastActivityDate="2013-12-24T18:36:48.247" Title="When do chimeras happen?" Tags="&lt;chimerism&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14136" PostTypeId="2" ParentId="1734" CreationDate="2013-12-24T21:30:16.657" Score="2" Body="&lt;p&gt;It is actually surprisingly easy and reproducible to make emulsions with defined components. We do it routinely in our lab:&#xA;&lt;a href=&quot;http://www.sciencemag.org/content/332/6026/209.full&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencemag.org/content/332/6026/209.full&lt;/a&gt; - CBT protocols&#xA;&lt;a href=&quot;http://www.sciencemag.org/content/336/6079/341.full&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencemag.org/content/336/6079/341.full&lt;/a&gt; - CST protocols&lt;/p&gt;&#xA;" OwnerUserId="5247" LastActivityDate="2013-12-24T21:30:16.657" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14137" PostTypeId="2" ParentId="14132" CreationDate="2013-12-24T22:07:16.147" Score="2" Body="&lt;p&gt;In the case of two healthy, viable identical twins, the separation generally occurs at the first division from one zygote to two cells. So they are equal partners in the split, not an original and a clone. During the first several cell divisions in the morula and blastula, there is no significant growth. So these divisions produce smaller and smaller cells. If one of these smaller cells is separated, it is very unlikely to be substantial enough to survive and implant in the uterus.&lt;/p&gt;&#xA;" OwnerUserId="5018" LastActivityDate="2013-12-24T22:07:16.147" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14139" PostTypeId="2" ParentId="14123" CreationDate="2013-12-25T03:26:54.203" Score="6" Body="&lt;p&gt;In many cases they are available.  One of the establishing principles of the Protein Data Bank (PDB) was to store not only the models (atomic positions and identities) of macromolecules and proteins, but also the originating X-ray data, more recently in structure factors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the question is 'why are they giving only the structure factors and not the original data they took' - such a task would require a lot of curation effort for very little scientific benefit.   Scaling the individual sets of data from the detector used to be a bear of a task.  The &lt;a href=&quot;http://www.rcsb.org/pdb/101/motm_disscussed_entry.do?id=1mbn&quot; rel=&quot;noreferrer&quot;&gt;original myoglobin structure&lt;/a&gt; would entail scanned films in an ancient format from the 50s.  Nobody would be able to use that now without hacking the image format, if it wasn't on paper tape or cards.  In fact in that case the structure factors are not available.  Scaling many or several data collections together was often done with custom tweaks into the 70s and then in the 90s data collection became more routine, but several generations of x-ray detectors became popular and then faded from the market.  Each had its own eccentricities and requirements for combining data sets from multiple reads.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The purpose of having structure factors available is to allow anyone to reconstruct the electron density and evaluate the interpretive act which is tracing a peptide through electron density.  Since that format is mainly independent of the detector and has been fairly consistent over the years, it delivers a significant amount of scientific bang for the buck.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want raw image data or detector-proprietary data before multiple data sets from different crystals before they were combined you will have to contact the authors, who would probably have to sift through a sea of DVDs to get to it.  In older cases it might be tapes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So as far as Structure factors, which are essentially the square root value of the combined and scaled Intensity data, they are available and a part of every submission to the pdb:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look on any X-ray Structure Page at RCSB.  For example &lt;a href=&quot;http://www.rcsb.org/pdb/explore/explore.do?structureId=4ID4&quot; rel=&quot;noreferrer&quot;&gt;this one&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a box called &quot;Experimental Details&quot; and you can download the structure factors there by clicking a link.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are looking for more than one at a time, there are bulk downloads available through their &lt;a href=&quot;http://www.rcsb.org/pdb/download/download.do&quot; rel=&quot;noreferrer&quot;&gt;download page&lt;/a&gt;.  Check the &quot;Structure Factors&quot; box.  Raw intensity data should be available if you look around for it as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Further Suggestion&lt;/strong&gt;:  I was thinking that if you look at the scaling software that comes with the X-ray detectors you might find some tutorials with unscaled raw data.  I found &lt;a href=&quot;http://www.marresearch.com/download.html#automar&quot; rel=&quot;noreferrer&quot;&gt;one example at Marresearch&lt;/a&gt; - hen egg white lysozyme.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-12-26T17:48:41.430" LastActivityDate="2013-12-26T17:48:41.430" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14140" PostTypeId="1" CreationDate="2013-12-25T05:41:04.537" Score="5" ViewCount="255" Body="&lt;p&gt;What methods can be used to determine whether they are authentic or fake?&lt;/p&gt;&#xA;" OwnerUserId="4996" LastEditorUserId="57" LastEditDate="2013-12-25T06:10:54.980" LastActivityDate="2015-01-09T13:19:24.647" Title="Identifying whether ELISA kits are authentic or fake" Tags="&lt;elisa&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14141" PostTypeId="2" ParentId="14140" CreationDate="2013-12-25T09:25:55.077" Score="5" Body="&lt;p&gt;You are getting this Elisa Kit spam from China, too? The only way I see, would be to use a known reference standard so you can titrate both the specificity and the sensitivity of the kit. Ideally you would compare it with a known and proven kit. If you have the reference available in the lab and the cheap kit is not too expensive you can give it a try. I would do it, since work time and reagents also cost money.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-25T09:25:55.077" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14142" PostTypeId="2" ParentId="14130" CreationDate="2013-12-25T09:43:22.437" Score="4" Body="&lt;p&gt;I don't have an other explanation than pointing to evolution. It was obviously not a problem to evolve the way it did. One article I found (see &quot;&lt;a href=&quot;http://www.arn.org/docs/odesign/od192/invertedretina192.htm&quot; rel=&quot;nofollow&quot;&gt;The Inverted Retina: Maladaptation or Pre-adaptation?&lt;/a&gt;&quot;) called it a sign of pre-adaptation, where forms exist before they get their final function.&#xA;Another pretty comprehensive review can be found here: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23926622&quot; rel=&quot;nofollow&quot;&gt;Evolution of Phototransduction, Vertebrate Photoreceptors and Retina.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2016-01-12T11:44:51.300" LastActivityDate="2016-01-12T11:44:51.300" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14143" PostTypeId="1" CreationDate="2013-12-25T11:41:11.757" Score="11" ViewCount="494" Body="&lt;p&gt;Last night 10 humans and 2 dogs spent Christmas together. At some point, one human dissappears for a few minutes and comes back wearing a full Santa outfit. Upon respawning, the dogs start barking aggressively until they are calmed down by non-Santa humans. They remained attentive of Santa until he left after a few more minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is this? Did the dogs not recognize the human because of his fake full beard and altered body shape (pillow under coat for fattening)? The human didn't shower or put on perfume or anything. I'm stumped by this and I'd love to learn the reason for this odd behaviour. &lt;/p&gt;&#xA;" OwnerUserId="5249" LastActivityDate="2018-04-07T16:52:56.077" Title="Dogs bark at familiar person in Santa costume. Why? Don't dogs trust smell over vision?" Tags="&lt;zoology&gt;&lt;vision&gt;&lt;ethology&gt;&lt;sensation&gt;&lt;dogs&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14144" PostTypeId="2" ParentId="14106" CreationDate="2013-12-25T13:25:30.837" Score="2" Body="&lt;p&gt;Dimethyltryptamine have been identified as normal constituents of human blood, urine,cerebrospinal fluid.Dimethyltryptamine is an  N-methylated indoleamine derivative, a serotonergic hallucinogen.It apparently acts as an agonist at some types of serotonin receptors and an antagonist at others.DMT is traditionally associated with indigenous Amazonian people, who consume a bitter decoction of at least two types of plant material, known as ayahuasca.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DMT is capable of transporting the user, within seconds, to what appears to be a fully autonomous alternate reality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is term called consensus reality the world we live in an imagination of our brain. DMT is capable of building this alternate reality with which in normal circumstances we don't feel or perceive it. DMT can cause such dramatic shifts in consciousness, such that completely novel worlds appear.Our brain use various approaches,to create a mental field which gives a unified world and these two can be classified as functional segregation and integration. As humans we are very much visual creatures and the cortex region of our brain helps us in doing that. Our brain continues to develop, changes throughout life and across the span of evolutionary time. It becomes absolutely critical in determining how the brain interprets and categorizes sensory information and thus builds the consensus world and we reach a point where our brain can create or is capable of building worlds without extrinsic influence or data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are the findings that were reported from the DMT studies&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1.Hallucination—visual, physical, auditory;&#xA;2.Entering other realities, sometimes including having contact with other sentient beings, which were described as true or real experiences rather than hallucinations;&#xA;3. Lucidity;&#xA;4. Affective distortions;&#xA;5. Ineffability;&#xA;6. Extreme intensity;&#xA;7. Spirituality, learning, or being taught about truths of the universe or self;&#xA;8. Distortion in sense of time, space, self;&#xA;9. Sense of familiarity&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is also being reported by research group.&#xA;- Merry-go-rounds, fairgrounds, clowns/jesters, circuses;&#xA;– Mischievous or playful elves/dwarves/imps;&#xA;– Insectoid and reptilian creatures, aliens;&#xA;– Futuristic hypertechnological buildings and cities;&#xA;– Complex machinery, hyper-advanced technology;&#xA;– Being observed and/or experimented upon;&#xA;– Unknown places apparently on Earth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So due all these mechanisms and effect of DMT I can say that when we are on the verge of our death our brain produces DMT in higher amounts in order to ease the pain which I assume and at the same time the alternate reality or the alien reality is something which is not yet thoroughly investigated. So I would say if an alternate world exist where humans go after death then DMT is the molecule which helps in doing it.&lt;/p&gt;&#xA;" OwnerUserId="5164" LastEditorUserId="5032" LastEditDate="2013-12-25T19:21:27.307" LastActivityDate="2013-12-25T19:21:27.307" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14145" PostTypeId="2" ParentId="14047" CreationDate="2013-12-25T16:11:32.043" Score="3" Body="&lt;p&gt;While it is possible to get mutations from the ethidium bromide, this is hardly the only source of mutations in the process.  Taq itself will introduce mutations fairly frequently, so sequence sensitive procedures typically use a higher accuracy (but slower and more expensive) polymerase, like Pfu.  As stated before, the UV can also cause mutations.  The PCR process iteself can result in primer dimers and other &quot;funky business&quot;.  Inappropriate sequences can be picked up from environmental contamination, particularly if you frequently use the same restriction enzymes in the lab, because sequences with appropriate &quot;sticky ends&quot; will be all over the place, no matter how much you clean.  If inserting into a plasmid, multiple inserts can get ligated into the final product, depending on how homologous the sticky ends of the insert are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The solution is to accurately sequence the final transgenic product before you put it in the transgenic organism.  I usually have the plasmid (I work with plasmid transfections) sequenced, as well as cleaving the plasmid insert from the plasmid and running it on a gel.  The sequencing catches any base swaps/indels and the gel makes sure there is only one copy of the insert in that particular plasmid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You would be surprised how often you get mutations and other &quot;garbage&quot; in the final product, which is why it's important to make multiple batches together.  I make mine in batches of 8, so that at least a couple will be exactly what I intended to produce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference: My own research/experience with site-directed mutagenesis and construction of plasmid vectors for transfection.&lt;/p&gt;&#xA;" OwnerUserId="4908" LastActivityDate="2013-12-25T16:11:32.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14146" PostTypeId="2" ParentId="14106" CreationDate="2013-12-25T16:35:54.497" Score="6" Body="&lt;p&gt;The issue I suspect you are struggling with is the anthropomorphization of the evolutionary process.  Evolution is an optimization process driven by random mechanisms...i.e. there is often not a &quot;reason&quot; for why certain things are the way they are.  Evolution is not a conscious &quot;designer&quot; that produces things with a specific goal in mind...it simply &quot;picks&quot; the best random alteration and enhances it.  If there is no &quot;best mutation&quot;, then there is no selection pressure to drive change overtime.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, one can ask, &quot;Why do humans have 5 fingers on each hand, instead of 6 or 4?&quot;  There is no answer, because the question itself is nonsensical.  Humans have 5 fingers simply because there is no pressure to drive a change to 6 or fingers, and so it boils down to randomness.  There is no &quot;reason&quot; humans have 2 arms, as opposed to 4.  That particular trait just randomly happened to be the one which became dominant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to return to your question of &quot;Why does the brain release DMT when dying?&quot;, the answer is that there IS no answer.  There is no selection pressure for or against that trait, it just happens.  As to the mechanism itself, I suspect that there is just a global breakdown of function in the brain, leading to a dump of ALL neurotransmitters.  When the reuptake pumps fail, the neurons just dump their contents into the extracellular space.  The result is pleasant hallucinations, giving the impression that humans are not &quot;meant&quot; to feel pain when dying.  Imposing that kind of rationale, however, is simply creating meaning out of chaos.  If you watch TV static long enough, your mind will start to see patterns which aren't there, simply because the human mind is &quot;wired&quot; to find patterns in chaos in order to better understand the environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To wrap this up, I suppose the answer to your question is that the brain is finding meaning in meaninglessness, simply because that is what the brain does.  We look for patterns to make sense out of our environment, which sometimes leads to spurious conclusions.  There is no reason that the brain hallucinates when dying, but there IS a reason that this trait appears to be a built-in mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope I was able to shed some light on the issue.  Or at the very least, not confuse you further :D&lt;/p&gt;&#xA;" OwnerUserId="4908" LastActivityDate="2013-12-25T16:35:54.497" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14147" PostTypeId="2" ParentId="14133" CreationDate="2013-12-25T16:41:46.893" Score="2" Body="&lt;p&gt;Sequentially:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes. Up to the limit of what the mother's body can tolerate.  Of course, if the cells never aggregate, that suggests some sort of fundamental problem with the embryo's developmental process, and you will probably not get a viable organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sort of and yes.  In utero, fertility drugs can cause multiple eggs to be released per cycle, which can cause fraternal twins when each egg is fertilized.  IVF can do the same thing, but you can also manually subdivide a single embryo into two (smaller) viable embryos, provided you perform the division before any cell differentiation occurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, but good luck getting an ethics review board to approve that :D&lt;/p&gt;&#xA;" OwnerUserId="4908" LastActivityDate="2013-12-25T16:41:46.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14148" PostTypeId="1" CreationDate="2013-12-25T19:34:55.053" Score="9" ViewCount="655" Body="&lt;p&gt;I'm going to be forward and say that I'm not a biologist.  I don't claim to fully understand the functionality of a neuron from an electrical/chemical perspective... I'm curiously gazing from the outside in as a computer programmer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the big new thing these days with artificial neural networks is simulating them with biological precision- that is, with spiking, actually placing the network in Euclidean space, and all sorts of other goodies (Check out the &lt;a href=&quot;https://www.humanbrainproject.eu/&quot;&gt;Human Brain Project&lt;/a&gt;; it's really cool.  Our own brains are computable, given a powerful enough computer.  Probably has a lot of fascinating and horrifying philosophical implications too.), but this isn't the only model that people have commonly used for neural networks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the past, &lt;a href=&quot;http://en.wikipedia.org/wiki/Multilayer_perceptron&quot;&gt;multilayer perceptrons&lt;/a&gt; were the big thing; I'm not going to go deep into explaining them, but essentially, each neuron simply performs a mathematical function on its inputs and then outputs it.  There's no spiking in the sense similar to our neurons.  A neuron could be blasting its output at nearly 100% indefinitely and there isn't any objective difference between that and it being at 0% or anywhere else.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I sort of went off on a tangent, &lt;strong&gt;but what I'm trying to understand is-&lt;/strong&gt; why this behavior is not observed in the system of computation that evolution has produced over the many, many years?  &lt;strong&gt;Why do we use spiking neurons instead?&lt;/strong&gt;  We have instead developed a strange system where spikes travel down chains of neurons in patterns we don't really understand yet to produce the behavior necessary for the creature to survive.  My question is, why has this been favored over something similar to multilayer perceptrons?  Is it more energy efficient to use a spiking model?  The brain does use a disproportionate amount of energy.  I wonder if it is more effective as a model for computation.&lt;/p&gt;&#xA;" OwnerUserId="4633" LastActivityDate="2014-08-16T20:33:21.223" Title="Why has evolution made neurons use spiking?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;neurotransmitter&gt;&lt;neuroanatomy&gt;" AnswerCount="4" CommentCount="4" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14149" PostTypeId="2" ParentId="13655" CreationDate="2013-12-25T20:13:08.243" Score="1" Body="&lt;p&gt;This is a topic which seems to be not very clear yet. References say that this is obviously dependent on the tissue and the &quot;gene dosage&quot; seems to play a role, and that this is probably regulated by a yet unknown factor (see &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12880201&quot; rel=&quot;nofollow&quot;&gt;Mitochondrial DNA replication: what we know.&lt;/a&gt;&quot; and &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12525854&quot; rel=&quot;nofollow&quot;&gt;Replication and transcription of mammalian mitochondrial DNA.&lt;/a&gt;&quot;).&#xA;Newer articles suggest that it depends also on the transcription of the mtDNA (see &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22207204&quot; rel=&quot;nofollow&quot;&gt;The interface of transcription and DNA replication in the mitochondria.&lt;/a&gt;&quot; and &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22465614&quot; rel=&quot;nofollow&quot;&gt;Mitochondrial transcription factor A regulates mitochondrial transcription initiation, DNA packaging, and genome copy number.&lt;/a&gt;&quot;). I will see, if there are other interesting publications, if there are problems with accessing these articles, let me know.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-25T20:13:08.243" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14150" PostTypeId="1" AcceptedAnswerId="14154" CreationDate="2013-12-25T23:16:38.643" Score="1" ViewCount="94" Body="&lt;p&gt;Relation between clownfishes and sea anemones is a classic example of mutualism. I wanted to list the species of sea anemones that are involved in this mutualism but I got lost.. Could you help me with that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How many species of sea anemones which host clownfishes are there? Could you list them?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2013-12-26T15:19:25.597" Title="Clownfishes and Sea anemones" Tags="&lt;zoology&gt;&lt;ichthyology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14152" PostTypeId="1" AcceptedAnswerId="14337" CreationDate="2013-12-26T03:11:37.687" Score="7" ViewCount="2450" Body="&lt;p&gt;I've been trying to put a phylogeny tree into a scientific paper. This tree includes ~220 species, which is too too large for one page for journal articles (Letter or A4 size). But in my paper it is crucial to show the whole tree on which the among-species distribution of a characteristic is indicated. I have looked up some journal issues but so far haven't found any similarly large phylogeny in one article. How do people usually treat this kind of situation in scientific papers? Could anybody tell me how to do it, or show me examples? Thank you so much.&lt;/p&gt;&#xA;" OwnerUserId="5253" LastEditorUserId="3624" LastEditDate="2014-01-23T11:32:36.223" LastActivityDate="2014-01-23T11:32:36.223" Title="How should I put a large phylogeny into a scientific paper?" Tags="&lt;evolution&gt;&lt;phylogenetics&gt;&lt;visualization&gt;&lt;publishing&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14153" PostTypeId="2" ParentId="14131" CreationDate="2013-12-26T09:00:12.247" Score="4" Body="&lt;p&gt;Usually if something is not expected to behave according to some scheme then the measured values for such a parameter are assumed to be normal. It is not just with gene expression but with all types of measurements like dimensions of an object, luminosity of an electric bulb, range of a bullet etc. &#xA;In any measurement, the random error is modeled using normal distribution. I don't have a very intuitive explanation for why random errors follow normal distribution but mathematically it comes from the central limit theorem. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now each gene is a variable and measurement of each gene suffers some random error; so a multivariate normal distribution is used. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When we dismiss a null hypothesis in a t-test or z-test what we are actually doing is dismissing our parsimonious notion that a sample is drawn from a given normal distribution. This means two things:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The sample belongs to some other normal distribution (different $\mu$ and $\sigma$)&lt;/li&gt;&#xA;&lt;li&gt;The sample follows some other distribution&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;But a t-test will never be able to point out the exact reason. All it tells you is that the sample is &lt;strong&gt;&lt;em&gt;not&lt;/em&gt;&lt;/strong&gt; from some given normal distribution. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-12-26T09:00:12.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14154" PostTypeId="2" ParentId="14150" CreationDate="2013-12-26T15:06:44.983" Score="2" Body="&lt;p&gt;I only found this two references, but these are only secondary sources at the moment.&#xA;Look here &quot;&lt;a href=&quot;http://animal-world.com/Aquarium-Coral-Reefs/Clown-Fish-Anemones&quot; rel=&quot;nofollow&quot;&gt;Clown Fish Anemone&lt;/a&gt;&quot; and here &quot;&lt;a href=&quot;http://animal-world.com/Aquarium-Coral-Reefs/Clown-Fish-Anemones&quot; rel=&quot;nofollow&quot;&gt;Choosing Clownfish and Anemones for Your Aquarium&lt;/a&gt;&quot;. It seems that there are only around two handful of anemones capable of supporting clownfish. &#xA;Here are some primary sources which confirm the 10 anemone species: &quot;&lt;a href=&quot;http://www.nhm.ku.edu/inverts/pdf/Fautin_anemonefishsymbiosis_1991.pdf&quot; rel=&quot;nofollow&quot;&gt;The anemonefish symbiosis: What is known and what is not&lt;/a&gt;.&quot; and &quot;&lt;a href=&quot;http://eqzotica.ucoz.ru/_ld/0/9_ANEMONES.pdf&quot; rel=&quot;nofollow&quot;&gt;Field guide to anemonefishes and their host sea anemones&lt;/a&gt;&quot;. The last two links point to PDFs which contain a lot more references.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2013-12-26T15:19:25.597" LastActivityDate="2013-12-26T15:19:25.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14156" PostTypeId="2" ParentId="14152" CreationDate="2013-12-26T15:31:05.897" Score="11" Body="&lt;p&gt;The simplest way of course is to add it to the supplementary materials. However, 220 species are not that many, you should be able to fit that into a page. You have not shown us your tree so it is kind of hard to give specific advice but I am guessing that you have a linear rather than circular tree. If you convert it to a circular tree you should be able to fit it on a single page. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are a few random examples of large circular trees I found on the internet:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rUNdh.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/N5Xoi.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/r6jZ1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you update your question to show us the actual tree I might be able to give you more specific advice. For example, you could split the tree into smaller ones, each showing a specific order or class or whatever resolution you are working on. There are various tricks you can try but they all depend on the details.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2013-12-26T15:31:05.897" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14157" PostTypeId="1" CreationDate="2013-12-26T17:01:43.363" Score="3" ViewCount="1556" Body="&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Ka/Ks_ratio&quot; rel=&quot;nofollow&quot;&gt;this wiki article&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In genetics, the &lt;strong&gt;Ka/Ks ratio&lt;/strong&gt; (or ω, dN/dS), is the ratio of the number&#xA;  of Nonsynonymous substitutions per non-synonymous site (Ka) to the&#xA;  number of synonymous substitutions per synonymous site (Ks), which can&#xA;  be used as an indicator of selective pressure acting on a&#xA;  protein-coding gene.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any modules/packages available in &lt;strong&gt;Python&lt;/strong&gt; for doing Ka/Ks analysis? I wish to carry out whole gene Ka/Ks analysis and then maybe &quot;codon level&quot; Ka/Ks analysis (i.e. within gene via sliding window). &lt;/p&gt;&#xA;" OwnerUserId="5005" LastActivityDate="2013-12-28T09:15:53.067" Title="Ka/Ks (dN/dS) analysis module for Python?" Tags="&lt;evolution&gt;&lt;bioinformatics&gt;&lt;natural-selection&gt;&lt;sequence-analysis&gt;&lt;protein-evolution&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14158" PostTypeId="2" ParentId="14157" CreationDate="2013-12-26T18:18:16.047" Score="6" Body="&lt;p&gt;Do you know about &lt;a href=&quot;http://biopython.org/wiki/Main_Page&quot; rel=&quot;nofollow&quot;&gt;BioPython&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://web.archiveorange.com/archive/v/3YdMAdgIaqmtVzgUXRSS&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt;, on another website, someone already asked this question and a pretty nice answer was provided by Brad Chapman. He gives already written functions to perform this kind of analysis (I personally haven't tried the codes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Perl there is Bio::Align::DNAStatistics. You might adapt it to Python.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://snpeff.sourceforge.net&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; might be useful as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think there are plenty of possibilities that are offered to you. You can go through some others by doing google search with the keywords &lt;code&gt;synonymous&lt;/code&gt;, &lt;code&gt;non-synonymous&lt;/code&gt; and &lt;code&gt;BioPython&lt;/code&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2013-12-28T09:15:53.067" LastActivityDate="2013-12-28T09:15:53.067" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14160" PostTypeId="1" CreationDate="2013-12-27T02:11:29.433" Score="1" ViewCount="46" Body="&lt;p&gt;I was just trying to understand how in insects, specifically mosquitoes does the process of emergency responding, stress regulation take place? Or in simpler words how are flight, fright and fight situations handled?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that insects have a ganglion system and they do, suitably, respond to external stimuli, but I would like to know if there is any chemical coordination that works specifically in emergency situations just as adrenalin and nor-adrenalin do in our case.&lt;/p&gt;&#xA;" OwnerUserId="4947" LastEditorUserId="3340" LastEditDate="2013-12-27T07:11:01.867" LastActivityDate="2013-12-27T07:11:01.867" Title="Stress regulation in mosquitoes" Tags="&lt;neuroscience&gt;&lt;entomology&gt;&lt;chemical-communication&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14161" PostTypeId="2" ParentId="14148" CreationDate="2013-12-27T02:39:22.807" Score="2" Body="&lt;p&gt;Neurons are binary, in that they either &quot;fire&quot; or &quot;don't fire&quot;.  There is no intermediate, because neuronal firing (biochemically) is an avalanche process.  Excitatory triggers raise the membrane potential and inhibitory triggers lower it.  Once the &quot;threshold voltage&quot; is reached, the neuron lights up and fires.  This is how &quot;decisions&quot; are made by neurons: inputs from many inhibitory and excitatory neurons are summed, and if the sum is above the threshold voltage, the neuron in question fires.  To use computational language, a neuron is a logic AND gate with hundreds of inputs.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Read the wikipedia article on &quot;action potentials&quot; for a more in depth discussion.&lt;/p&gt;&#xA;" OwnerUserId="4908" LastActivityDate="2013-12-27T02:39:22.807" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14162" PostTypeId="2" ParentId="14152" CreationDate="2013-12-27T09:15:51.827" Score="2" Body="&lt;p&gt;It is not always essential to show a big tree. &#xA;My opinion might be biased but it seems to me that huge figures with illegible labels are just a gimmick to make the reader feel that it is a great analysis (another case is that of networks). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all it is important to decide what is that you really want to convey from your figure. For example if your comparing some species with different clades then you can show the last common ancestor instead of showing all members of the clade. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as 220 species are concerned it will be tough to fit all of them stacked. But if you split them into two stacks it would be possible to fit with all labels legible (Paper=A4, Fontsize=6pt). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2013-12-27T09:15:51.827" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14163" PostTypeId="1" AcceptedAnswerId="26161" CreationDate="2013-12-27T09:30:48.743" Score="3" ViewCount="128" Body="&lt;p&gt;The lactobacillus, also called Döderlein's bacillus is a genus of facultative aerobic bacteria. There are several species such as Lactobacillus acidophillus and Lactobacillus reuteri.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have several questions, all linked, for the concern of speciation of bacteria species used for lactic fermentation by humans.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Are all species that are used for cheese and yoghurt fermentation part of the genus Lactobacillus?&lt;/li&gt;&#xA;&lt;li&gt;Do all species used for cheese and yoghurt fermentation form a monophyletic clade?&lt;/li&gt;&#xA;&lt;li&gt;Did the speciation of this clade occurr before or after the use of these bacteria by humans?&lt;/li&gt;&#xA;&lt;li&gt;What was the ecological niche of the ancestor(s) before humans used them for cheese and yoghurt?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="1306" LastEditDate="2013-12-27T13:57:13.383" LastActivityDate="2014-12-24T14:59:44.910" Title="Speciation and Phylogeny of Lactobacillus" Tags="&lt;bacteriology&gt;&lt;ecology&gt;&lt;phylogenetics&gt;&lt;speciation&gt;&lt;fermentation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14164" PostTypeId="1" CreationDate="2013-12-27T13:23:10.527" Score="11" ViewCount="19936" Body="&lt;p&gt;I was recently having a discussion with someone about whether lemon water actually increases the pH of your body (by which I assume they mean the blood); their claim was that once Citric acid was metabolised it results in an increase in pH due to the &quot;anionic properties of citric acid&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I looked around on the internet at it would seem that this is a common claim circulating around health forums: &lt;a href=&quot;http://www.vitalitylink.com/article-holistic-health-2055-lemon-juice-acidic-alkaline-body-water&quot; rel=&quot;noreferrer&quot;&gt;Example 1&lt;/a&gt;, &lt;a href=&quot;http://thechalkboardmag.com/why-you-should-drink-warm-water-lemon&quot; rel=&quot;noreferrer&quot;&gt;Example 2&lt;/a&gt;, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now to me this sounds like something which cannot possibly be true and appears to be a crazy health fad (they seem to spuriously appear and gain popularity now and again), and I cannot find any scientific papers or articles to support or refute their claim.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone provide a reliable scientific reference or provide a reasonable scientific explanation (preferably accessible to a layman with only A-level (college level) understanding of chemistry and biochemistry) which either supports or refute the claim that drinking lemon water (citric acid) increases the pH of the blood?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have crossposted this to &lt;a href=&quot;https://chemistry.stackexchange.com/questions/7526/is-lemon-water-an-alkalizing-agent-in-the-body&quot;&gt;Chemistry.SE&lt;/a&gt; as well, as it is a crossover between chemistry and biochemistry.&lt;/p&gt;&#xA;" OwnerUserId="1081" LastEditorUserId="-1" LastEditDate="2017-04-13T12:57:01.693" LastActivityDate="2019-04-17T16:24:03.393" Title="Is lemon water an alkalizing agent in the body?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;digestive-system&gt;&lt;homeostasis&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14165" PostTypeId="2" ParentId="14164" CreationDate="2013-12-27T13:36:46.890" Score="12" Body="&lt;p&gt;The blood pH is tightly controlled since variations are quite dangerous for us. Under normal circumstances the pH is 7.4 (with a normal range between 7.35 and 7.45). Below that we are talking about acidosis, above it about alkalosis. If the blood pH goes about 7.8 or below 6.8, death will occur. This pH is maintained by the Bicarbonate-buffering system, for details see &lt;a href=&quot;http://www.harpercollege.edu/tm-ps/chm/100/dgodambe/thedisk/bloodbuf/zback.htm&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Bicarbonate_buffering_system&quot;&gt;here&lt;/a&gt;.&#xA;Food that we take up does not directly influence the blood pH (and there is also no reason for us to do so, since this is tightly controlled and regulated), so this is a health fad. Details that debunk this myth about it can be found &lt;a href=&quot;http://drbenkim.com/ph-body-blood-foods-acid-alkaline.htm&quot;&gt;here&lt;/a&gt;, &lt;a href=&quot;http://wyntersway.com/pdf/Debunking_the_Benefits_of_Alkaline_Water.pdf&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.quackwatch.com/11Ind/young3.html&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-08-04T07:04:04.643" LastActivityDate="2015-08-04T07:04:04.643" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14166" PostTypeId="1" CreationDate="2013-12-27T14:47:48.837" Score="4" ViewCount="58" Body="&lt;p&gt;When a medicine is prepared by a biologist,then where does he first test on? And how does he know that this is the exact combination for a disease to get cured? Does he test that medicine on a human or specific sample of blood? I'm an engineering student but still I'm curious to know.&lt;/p&gt;&#xA;" OwnerUserId="5259" LastEditorUserId="3632" LastEditDate="2013-12-27T18:10:50.450" LastActivityDate="2014-01-28T14:45:15.673" Title="Where are newly discovered medicines tested" Tags="&lt;medicine&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14167" PostTypeId="2" ParentId="14166" CreationDate="2013-12-27T15:42:16.450" Score="7" Body="&lt;p&gt;This is a very broad question, so I won't attempt to answer it fully. Instead, I'd recommend starting out by reading the &lt;a href=&quot;https://en.wikipedia.org/wiki/Drug_development&quot; rel=&quot;nofollow noreferrer&quot;&gt;Drug Development&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Drug_discovery&quot; rel=&quot;nofollow noreferrer&quot;&gt;Drug Discovery&lt;/a&gt; articles on Wikipedia, and if you have more specific questions after that then feel free to ask them here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, new drugs (either small-molecule &quot;&lt;em&gt;chemicals&lt;/em&gt;&quot; or large-molecule &quot;&lt;em&gt;biologicals&lt;/em&gt;&quot;) are discovered in myriad ways, from pure accidents (see &lt;a href=&quot;https://en.wikipedia.org/wiki/Penicillin#Discovery&quot; rel=&quot;nofollow noreferrer&quot;&gt;Penicillin&lt;/a&gt;) to specifically-targeted research. Once a &lt;a href=&quot;https://en.wikipedia.org/wiki/Lead_compound&quot; rel=&quot;nofollow noreferrer&quot;&gt;lead compound&lt;/a&gt; is identified, it is put through a series of biochemical assays to determine, for example, if it inhibits certain enzymes of interest. From there, it moves into testing by cell-based &lt;a href=&quot;https://en.wikipedia.org/wiki/Assay&quot; rel=&quot;nofollow noreferrer&quot;&gt;assays&lt;/a&gt; using both normal cells and disease-specific models. All the while, investigators are looking for high specific activity (potency), low toxicity, and minimal off-target effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a compound or group of them looks promising in these &lt;a href=&quot;https://en.wikipedia.org/wiki/In_vitro&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;in vitro&lt;/em&gt;&lt;/a&gt; assays, experiments then move into animal models. The goals are similar here - high activity, low toxicity, and few (if any) side effects. The experiments get progressively more complex, with different endpoints depending on the exact aspect being studied.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is only after extensive animal testing that a compound will be tested in humans. There are different &lt;a href=&quot;https://en.wikipedia.org/wiki/Clinical_trial_phase&quot; rel=&quot;nofollow noreferrer&quot;&gt;phases&lt;/a&gt; of testing, each with different criteria, dosing patterns, number of patients, and reporting rules. The link I just gave explains each phase briefly.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Hopefully this is enough to get you started. Like I said earlier, if you have more specific questions after reading through all the references, please &lt;a href=&quot;https://biology.stackexchange.com/questions/ask&quot;&gt;let us know&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2013-12-27T15:42:16.450" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14168" PostTypeId="1" AcceptedAnswerId="14191" CreationDate="2013-12-27T17:43:05.380" Score="7" ViewCount="579" Body="&lt;p&gt;Do you have recommendations for a book that presents the different algorithm used in theoretical evolutionary biology?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't mean evolutionary or genetic algorithms (otherwise this question would not be a good fit for Biology.SE) but algorithms applied to evolutionary biology. I am not interested in statistical procedures and algorithms to reconstruct phylogenetic trees, to annotate DNA sequences or to find out synonymous changes by comparing sequences of closely related species. I am not interested in introductory book on programming.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested to computational modeling applied population genetics, kin selection, game theory, population range expansion, simulating sexual reproduction, selection for different sex determination system, evolution for robustness/evolvability, evolution of codon usage, evolution of genetic code, evolution of cognition, evolution of multicellularity, …&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't quite know if one book that encompass all these subjects exist. If not, I wold welcome suggestions of book that present the algorithmic used in some but not all of these subjects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Searching a bit in amazon, I easily found tons of book but don't quite know if they fit my expectations. Below are some examples&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.fr/The-Engine-Complexity-Evolution-Computation-ebook/dp/B00APDGG9G/ref=sr_1_1?ie=UTF8&amp;amp;qid=1388169820&amp;amp;sr=8-1&amp;amp;keywords=computation+biology+evolution&quot; rel=&quot;noreferrer&quot;&gt;Evolution as computation&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/069109666X&quot; rel=&quot;noreferrer&quot;&gt;Individual based modeling and ecology&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.fr/Models-Algorithms-Genome-Evolution-Cedric-ebook/dp/B00FA1PTHI/ref=sr_1_2?ie=UTF8&amp;amp;qid=1388169832&amp;amp;sr=8-2&amp;amp;keywords=computation+biology+evolution&quot; rel=&quot;noreferrer&quot;&gt;Models and algorithm for genome evolution&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0521538564&quot; rel=&quot;noreferrer&quot;&gt;modelling for field biologists&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0878933913&quot; rel=&quot;noreferrer&quot;&gt;Practical computing for biologist&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.fr/Evolution-As-Computation-Workshop-Princeton/dp/3642630812/ref=sr_1_4?ie=UTF8&amp;amp;qid=1388169832&amp;amp;sr=8-4&amp;amp;keywords=computation+biology+evolution&quot; rel=&quot;noreferrer&quot;&gt;Evolution as computation&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.fr/Genetic-Evolutionary-Computation-Medical-Applications/dp/0470748133/ref=sr_1_6?ie=UTF8&amp;amp;qid=1388169832&amp;amp;sr=8-6&amp;amp;keywords=computation+biology+evolution&quot; rel=&quot;noreferrer&quot;&gt;Genetic and evolutionary computation&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.fr/Genetic-Algorithms-Structures-Evolution-Programs/dp/3642082335/ref=sr_1_69?ie=UTF8&amp;amp;qid=1388166676&amp;amp;sr=8-69&amp;amp;keywords=evolution+algorithm&quot; rel=&quot;noreferrer&quot;&gt;Genetic algorithms+ data structures = evolution programs&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.fr/The-Missing-Algorithm-Cooperation-Prediction/dp/1581125992/ref=sr_1_119?ie=UTF8&amp;amp;qid=1388169248&amp;amp;sr=8-119&amp;amp;keywords=evolution+algorithm&quot; rel=&quot;noreferrer&quot;&gt;The missing algorith&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.fr/Cellular-Model-Mathematical-Bioinformatics-Computational/dp/613381960X/ref=sr_1_1?ie=UTF8&amp;amp;qid=1388169453&amp;amp;sr=8-1&amp;amp;keywords=algorithm+theoretical+biology&quot; rel=&quot;noreferrer&quot;&gt;Cellular Model: Mathematical and theoretical biology, Algorithm, Data structure, Bioinformatics, Computational biology, Artificial life, Computer simulation&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.fr/Natural-Artificial-Models-Computation-Biology/dp/3642386369/ref=sr_1_3?ie=UTF8&amp;amp;qid=1388169453&amp;amp;sr=8-3&amp;amp;keywords=algorithm+theoretical+biology&quot; rel=&quot;noreferrer&quot;&gt;Natural-Artificial-Models-Computation-Biology&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.fr/An-Introduction-Genetic-Algorithms-Paper/dp/0262631857/ref=sr_1_61?ie=UTF8&amp;amp;qid=1388166452&amp;amp;sr=8-61&amp;amp;keywords=evolution+algorithm&quot; rel=&quot;noreferrer&quot;&gt;An-Introduction-Genetic-Algorithms-Paper&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="6" LastEditDate="2013-12-28T12:18:42.790" LastActivityDate="2020-11-16T07:03:15.157" Title="Book recommendations for algorithms used in evolutionary biology" Tags="&lt;evolution&gt;&lt;theoretical-biology&gt;&lt;book-recommendation&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14169" PostTypeId="1" CreationDate="2013-12-27T20:15:46.377" Score="8" ViewCount="654" Body="&lt;p&gt;I find these in forests in Oregon, western half, though they're probably on the eastern half as well. They live under pieces of wood and bark, and have a small web across the ground. Mine will eat crickets, but I think they eat carpenter ants, termites, and maybe pillbugs/sowbugs. It seems about an inch long, red on the thorax and legs, and dark grey and slightly hairy on the abdomen. The closest to this spider I've found is sowbug killers -- they're in my backyard, but they're smaller then this spider and also are a light tan on a hairless abdomen, with lighter colored legs. The fangs also seem different shapes but I'm not sure about that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cTkVM.jpg&quot; alt=&quot;Spider 1&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Hc0iP.jpg&quot; alt=&quot;Spider 2&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/AY7VR.jpg&quot; alt=&quot;Spider 3&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/a8sfI.jpg&quot; alt=&quot;Spider 4&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4422" LastEditorUserId="16866" LastEditDate="2018-11-09T03:00:31.867" LastActivityDate="2021-01-05T22:10:30.280" Title="Identification of this spider?" Tags="&lt;species-identification&gt;&lt;zoology&gt;&lt;arachnology&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14171" PostTypeId="1" CreationDate="2013-12-28T01:43:54.037" Score="1" ViewCount="376" Body="&lt;p&gt;I'm studying Neuroscience and Fruit Flies are a pretty big deal but I don't know as much as I think I should about them.  Are there and comprehensive sources that I could read?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like a review of all the important parts of the nervous system, where they are, what they do, and how they connect.&lt;/p&gt;&#xA;" OwnerUserId="5262" LastEditorUserId="5262" LastEditDate="2013-12-31T18:49:47.443" LastActivityDate="2014-03-31T20:04:14.923" Title="Studying the fruitfly nervous system" Tags="&lt;neuroscience&gt;&lt;drosophila&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14172" PostTypeId="1" AcceptedAnswerId="14174" CreationDate="2013-12-28T02:43:59.370" Score="3" ViewCount="9433" Body="&lt;p&gt;I'd like to clear something up about antibodies that I'm not sure I've understood in the articles I've read. Looking at concepts such as &quot;affinity maturation&quot;, &quot;monovalent antigens&quot; and &quot;polyvalent antigens&quot; it seems as if there are multiple antibodies which can bind to the same antigen. (Although I think I'm right in saying that individual antibodies can only bind to one antigen?) However, when I read sentences like &quot;It has been estimated that humans generate about 10 billion different antibodies, each capable of binding a distinct epitope of an antigen&quot; on the Wikipedia page (for antibody) it does make it sound like it's one antibody per antigen? Is this the case? Or is it one antibody per epitope. Either way, to put this question in a nutshell:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it true to say that the same substance could bind with (and, therefore, be recognised by) more than one antibody, or not?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, if the answer is no, does that mean that antibodies with different binding affinities are classed as the same antibody or not?&lt;/p&gt;&#xA;" OwnerUserId="5263" LastActivityDate="2014-01-10T20:04:42.957" Title="Can more than one antibody bind the same antigen" Tags="&lt;immunology&gt;&lt;antibody&gt;&lt;antigen&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14173" PostTypeId="2" ParentId="14171" CreationDate="2013-12-28T02:45:03.507" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://flybase.org/&quot; rel=&quot;nofollow&quot;&gt;Flybase&lt;/a&gt; is a generally useful source for Drosophila anatomy/physiology including the nervous system. From there I found &lt;a href=&quot;http://www.ceolas.org/fly/&quot; rel=&quot;nofollow&quot;&gt;this link&lt;/a&gt; which has some neuroscience-specific info.&lt;/p&gt;&#xA;" OwnerUserId="3336" LastActivityDate="2013-12-28T02:45:03.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14174" PostTypeId="2" ParentId="14172" CreationDate="2013-12-28T03:19:21.600" Score="2" Body="&lt;p&gt;Let's clarify the terms. An &lt;em&gt;antigen&lt;/em&gt; is a molecule that can be associated with a particular substance (virus, pollen, dander.) When an immunoglobulin or &lt;em&gt;antibody&lt;/em&gt; recognizes an antigen it binds to a specific &lt;em&gt;epitope&lt;/em&gt;. An antibody recognizes an epitope using its &lt;em&gt;paratope&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some antigens have multiple epitopes; this means that different antibodies can simultaneously bind to them (if the epitopes are far-enough apart from each other so that binding to one doesn't preclude binding to the others.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example from my work is influenza (flu) hemagglutinin, which is a major viral coat protein. &lt;a href=&quot;http://pdbj.org/emnavi/emnavi_detail.php?id=5731&quot; rel=&quot;nofollow&quot;&gt;Here's a low-resolution structure showing a &quot;head-binding&quot; antibody fragment (actually three of them)&lt;/a&gt;, and &lt;a href=&quot;http://pdbj.org/emnavi/emnavi_detail.php?id=5794&quot; rel=&quot;nofollow&quot;&gt;here's a similar structure showing a &quot;stem-binding&quot; antibody fragment&lt;/a&gt;. Our immune repertoire (and physiology) greatly predisposes us towards producing head-binding antibodies over stem-binders. Note that each structure has three antibody fragments bound in the same state. Because the head-binder and stem-binder antibodies are well-separated in space they can both be accommodated in a single complex (as is experimentally confirmed.) In this case, up to six antibodies, using two distinct paratopes, could simultaneously bind to a single antigen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For matured (high affinity and high specificity) antibodies, each binds a specific epitope. The typical state of affairs is then explained &quot;one antibody per epitope&quot; which is overly simplistic because some epitopes can be recognized by multiple paratopes (which would be found on different antibodies.) So a given epitope can be recognized by no antibodies (a new antigen, or one that is poorly immunogenic) or by multiple ones.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is it true to say that the same substance could bind with (and, therefore, be recognised by) more than one antibody, or not?&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, that's true.&lt;/p&gt;&#xA;" OwnerUserId="3336" LastActivityDate="2013-12-28T03:19:21.600" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14175" PostTypeId="1" CreationDate="2013-12-28T08:45:32.657" Score="25" ViewCount="7949" Body="&lt;p&gt;If the &lt;strong&gt;&quot;primordial soup&quot; theory of abiogenesis&lt;/strong&gt; is to be believed, self-reproducing organisms spontaneously arose on Earth at least 3.5 billion years ago, surprisingly soon after the Earth cooled down enough to potentially harbor life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It may never have happened again, however, since all lifeforms on Earth today are similar on a molecular level (DNA), suggesting a common origin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;This appears to imply at least one of the following:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Immediately after the first spontaneous abiogenesis, environmental conditions on Earth changed dramatically,&lt;/strong&gt; making a repeat impossible.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;The first organisms that arose consumed any subsequent organisms&lt;/strong&gt; that came into being. This was suggested by Alexander Oparin, but I find it very difficult to believe since it would have to happen everywhere on Earth. Also, most single-celled organisms found today do not consume other organisms, and even where they do that does not usually lead to their complete extinction.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;The common origin theory is in fact false,&lt;/strong&gt; despite the similarities between organisms, and abiogenesis &lt;em&gt;did&lt;/em&gt; occur multiple times in the same way.&lt;/li&gt;&#xA;&lt;li&gt;Abiogenesis happened more than once, but &lt;strong&gt;only the descendants of one occurrence survived&lt;/strong&gt; till today.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Spontaneous abiogenesis never occurred on Earth after all&lt;/strong&gt; because the conditions never allowed it; instead, a proto-organism arrived on Earth from a planet where the conditions do (Panspermia).&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;The standard theory of geological history is wrong&lt;/strong&gt; (i.e. the Earth was in a &quot;fertile&quot; state for much longer before the eventual origin of life than commonly thought, due to some unknown mechanism causing radiometric dating to give wrong results).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;None of these seem likely to me, yet even less likely I find the idea that life arose spontaneously almost immediately (within a few hundred million years, possibly even faster) after the Earth's crust solidified, and never again afterwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the currently held theories on that matter? Can poeple provide references to relevant publications.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5264" LastEditorUserId="22057" LastEditDate="2017-12-10T18:13:23.517" LastActivityDate="2020-08-02T19:57:11.083" Title="Why did abiogenesis only happen once?" Tags="&lt;evolution&gt;&lt;life&gt;&lt;abiogenesis&gt;" AnswerCount="5" CommentCount="3" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="14176" PostTypeId="2" ParentId="7019" CreationDate="2013-12-28T13:01:58.710" Score="1" Body="&lt;p&gt;Actually, absorption does take place through the mouth.There is a ptyalin enzyme in the saliva which hydrolyzes carbohydrates of the food.  These contents are then absorbed in the blood through the facial vein.The facial vein opens into subclavian vein,and it opens into the superior vena cava.&lt;/p&gt;&#xA;" OwnerUserId="5265" LastEditorUserId="57" LastEditDate="2013-12-29T01:42:18.743" LastActivityDate="2013-12-29T01:42:18.743" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14178" PostTypeId="2" ParentId="14175" CreationDate="2013-12-28T17:53:24.630" Score="19" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;It may never have happened again, however, since all lifeforms on Earth today are similar on a molecular level (DNA), suggesting a common origin.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;An important distinction to make here is that all &lt;em&gt;extant&lt;/em&gt; life on Earth has a common origin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's completely possible that abiogenesis occurred many times, but whatever organisms emerged as a result became extinct early on or are not preserved in the fossil record.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Immediately after the first spontaneous abiogenesis, environmental conditions on Earth changed dramatically, making a repeat impossible.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Nope. The red bands and subsequent dating techniques suggest it took a &lt;em&gt;very&lt;/em&gt; long time for a change to occur.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first organisms that arose consumed any subsequent organisms...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Possible, but we have solid data suggesting the first functional organisms were autotrophs. That is, they made their own food from whatever they were exposed to, and the predator/prey relationship had yet to play a major role.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The common origin theory is in fact false, despite the similarities between organisms, and abiogenesis did occur multiple times in the same way.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The Common Origin Theory - as you've defined it - is almost certainly true. DNA is a constant, as is RNA, mitochondria, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That, however, doesn't mean abiogenesis couldn't have happened more than once. As I said above, the Common Origin Theory applies to &lt;em&gt;extant&lt;/em&gt; (living) species, not necessarily all organisms that have ever existed. Species go extinct all the time.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Spontaneous abiogenesis never occurred on Earth after all because the conditions never allowed it; instead, a proto-organism arrived on Earth from a planet where the conditions do (Panspermia).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That merely pushes the question of abiogensis back a bit. Why did it evolve on another world and not Earth, then? How did it survive in space? Why was it so well suited to Earth's environment if Earth-like planets are (relatively speaking) rare? &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The standard theory of geological history is wrong (i.e. the Earth was in a &quot;fertile&quot; state for much longer before the eventual origin of life than commonly thought, due to some unknown mechanism causing radiometric dating to give wrong results).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Estimations and conclusions have come from more than radiometric dating. We have fossil records, geological records spanning continents, and even ice-core records from the poles that both confirm radiometric dating &lt;em&gt;and&lt;/em&gt; establish themselves as independent evidence.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;None of these seem likely to me, yet even less likely I find the idea that life arose spontaneously almost immediately (within a few hundred million years, possibly even faster) after the Earth's crust solidified, and never again afterwards.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What are the currently held theories on that matter? Both random speculations and references to relevant publications are welcome.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This SE is not the place for random speculations. I don't have publications handy, so I may return and edit my answer when I have the impetus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most widely held theory is that all extant life, with a few possible exceptions, has evolved from a single organism that existed billions of years ago. That organism may or may not have been the only one to arise. If it was one among many variations of progenitors, we have yet to find the progenitors in the fossil or biological records. Given the extremely long time span between now and the beginnings of life, we don't expect fossil records to exist of all the organisms that existed some 3 B.Y.A. so the best we can do is speculate on what &lt;em&gt;might&lt;/em&gt; have existed to account for what we see today.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2013-12-28T17:53:24.630" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14179" PostTypeId="1" AcceptedAnswerId="14180" CreationDate="2013-12-28T23:32:42.920" Score="1" ViewCount="88" Body="&lt;p&gt;does anyone know of a fluorescent protein that upon binding of a substrate its fluorescence is activated? i've been looking on this and perhaps my keywords are not the right  ones. Thanks in advance&lt;/p&gt;&#xA;" OwnerUserId="233" LastActivityDate="2013-12-29T06:54:45.550" Title="ligand binding fluorescent protein" Tags="&lt;fluorescent-microscopy&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14180" PostTypeId="2" ParentId="14179" CreationDate="2013-12-29T00:01:56.003" Score="1" Body="&lt;p&gt;There are only 3 classes of fluorescent proteins proteins known I think.  Two of them are relevant to your needs maybe. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first are usually called 'fluorescent proteins'.  These &lt;a href=&quot;http://en.wikipedia.org/wiki/Green_fluorescent_protein&quot; rel=&quot;nofollow&quot;&gt;proteins&lt;/a&gt; are usually derived from the &lt;em&gt;A victoria&lt;/em&gt; jellyfish.  Its entirely passive in its fluorescence, but has been tuned to many levels of quantum yield and color.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There was a new sort of &lt;a href=&quot;http://www.riken.jp/en/pr/press/2013/20130614_1/&quot; rel=&quot;nofollow&quot;&gt;fluorescent protein cloned recently from japanese eels&lt;/a&gt;.  It is activated by binding to bilirubin.  Its so new that its not likely to be available, but there you go. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The third class would be the &lt;a href=&quot;http://en.wikipedia.org/wiki/Luciferase&quot; rel=&quot;nofollow&quot;&gt;luciferases&lt;/a&gt;.  They are luminescent, not fluorescent but in producing light involves binding from a cofactor called luciferase which is oxidized to produce their light.  This is not really fluorescence since the electrical stimulation that causes light production is not from incident light, but since what you are looking for might not exist I wanted to remind you of the luciferases, which bind their redox substrates to activate.  The luciferin molecule actually varies as there are several classes of luciferase.  I think Flavin and NAD are the most common substrates. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2013-12-29T06:54:45.550" LastActivityDate="2013-12-29T06:54:45.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14181" PostTypeId="2" ParentId="14175" CreationDate="2013-12-29T00:52:00.277" Score="3" Body="&lt;p&gt;Some people think that abiogenesis did occur more than once, and that the results of those occurrences are still with us. Paul Davies, for instance, is a proponent of what he calls 'the shadow biosphere' (here's a link to a popular article on his views: &lt;a href=&quot;http://www.theguardian.com/science/2013/apr/14/shadow-biosphere-alien-life-on-earth&quot; rel=&quot;nofollow&quot;&gt;http://www.theguardian.com/science/2013/apr/14/shadow-biosphere-alien-life-on-earth&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen him talk about it, and while he has pretty much zero evidence for the idea, it's an intriguing thought. His argument is basically that we're not finding the organisms in the shadow biosphere because we're just not looking in the right places or in the right way;  our discovery techniques are all biased towards our particular RNA/DNA-based life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that this doesn't really put common origin in the ground, it would just mean that there's more than one common origin for each 'type' of life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, it isn't necessary for early organisms to consume each other in order for there to have been multiple origins that subsequently went extinct. Our brand of life could simply have out-replicated the competition. &lt;/p&gt;&#xA;" OwnerUserId="92" LastActivityDate="2013-12-29T00:52:00.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14182" PostTypeId="2" ParentId="9466" CreationDate="2013-12-29T02:24:53.353" Score="8" Body="&lt;p&gt;Going on the abstract of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/m/pubmed/16707872/&quot;&gt;a study&lt;/a&gt; by J.P. Pessan, et al., fluoride intake, as well as &quot;the fact that toenails are less prone to environmental contamination,&quot; constitutes a lesser need for growth in toenails than that in fingernails. Also, fluorine being a &lt;a href=&quot;http://www.lenntech.com/periodic/elements/f.htm&quot;&gt;crucial component in maintaining the solidity of bones&lt;/a&gt;, the body may redirect more fluorine that is ingested by various means, to the hands than to the feet, due to the arguably more necessary functions of the hands (in that they are used them for agile and precise motions that tend to influence our survival), meaning less growth in toenails as evidenced in the first citation.&lt;/p&gt;&#xA;" OwnerUserId="5270" LastEditorUserId="5270" LastEditDate="2013-12-29T23:05:41.497" LastActivityDate="2013-12-29T23:05:41.497" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14183" PostTypeId="2" ParentId="14168" CreationDate="2013-12-29T06:37:18.910" Score="3" Body="&lt;p&gt;Have you looked into &quot;Fundamental of Molecular Evolution&quot; by Dan Graur &amp;amp; Li.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another suggestion in line of population genetics and different evo. theories would be -&#xA;Evolutionary Genetics: Concepts and Case studies&#xA;(Multi-author book. Editor Fox &amp;amp; Wolf)&lt;/p&gt;&#xA;" OwnerUserId="5272" LastActivityDate="2013-12-29T06:37:18.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14185" PostTypeId="1" AcceptedAnswerId="14220" CreationDate="2013-12-29T20:07:02.143" Score="2" ViewCount="1390" Body="&lt;p&gt;Animals like Sponges and Hydra and fungi like Yeast and Mushroom can reproduce both asexually and sexually. However, they only reproduce sexually if the 'circumstances' are 'bad'. Is there a specific reason for that?&lt;/p&gt;&#xA;" OwnerUserId="5221" LastActivityDate="2014-01-06T16:02:12.693" Title="Why do some animals and fungi prefer asexual reproduction?" Tags="&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14186" PostTypeId="1" AcceptedAnswerId="14198" CreationDate="2013-12-29T20:26:41.443" Score="5" ViewCount="4108" Body="&lt;ul&gt;&#xA;&lt;li&gt;My textbook says that in both groups of seedless plants (vascular plants, non-vascular plants) the gametophyte is a free-living plant, independent of the sporophyte.&#xA;I don't understand this statement and am now wondering if the sporophyte and gametophyte  are stages in a plant's lifecycle, or are they individual parts of the plant, or are the sporophyte and the gametophyte different plants altogether? Secondly, does this differ depending on the organism?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Different plants or different structures that make up the same organism?&lt;/p&gt;&#xA;" OwnerUserId="5275" LastEditorUserId="5275" LastEditDate="2013-12-29T20:42:01.003" LastActivityDate="2015-01-17T18:13:13.407" Title="Sporophyte and gametophyte" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14187" PostTypeId="1" CreationDate="2013-12-29T20:41:26.517" Score="1" ViewCount="9838" Body="&lt;p&gt;In my texbook it is written that for non- vascular seedless plants the dominant generation  is the gametophyte as the gametophyte generation is larger and longer lived.&lt;br&gt;&#xA;Is the criteria for dominant generation?-( Which generation the plant spends most of its life in?)&lt;/p&gt;&#xA;" OwnerUserId="5275" LastActivityDate="2014-01-06T16:03:21.683" Title="What does dominant generation mean" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14188" PostTypeId="1" CreationDate="2013-12-29T20:50:36.923" Score="4" ViewCount="1768" Body="&lt;p&gt;When happens when pollen grains land on the a part other than the stigma of a flower of the same species? Would the pollen be transported to the stigma or would it just sit where it landed and nothing would happen?&lt;/p&gt;&#xA;" OwnerUserId="5275" LastActivityDate="2014-01-30T11:06:03.267" Title="When happens when pollen grains land on the a part other than the stigma of a flower of the same species?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14189" PostTypeId="1" CreationDate="2013-12-29T22:21:23.130" Score="4" ViewCount="193" Body="&lt;p&gt;Is tactile perception two-dimensional or three-dimensional? Can tactile sense be mapped on 2-dimensional map of the surface of the human body or does human receive tactile signal as a 3D position (owing that internal organs can also feel pain)?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="408" LastEditDate="2013-12-30T12:44:53.607" LastActivityDate="2014-07-07T00:47:23.110" Title="Is tactile perception two-dimensional or three-dimensional?" Tags="&lt;perception&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14190" PostTypeId="1" CreationDate="2013-12-29T23:43:30.953" Score="2" ViewCount="443" Body="&lt;p&gt;When running molecular simulations, what is the consequence of not capping the n- and c-terminus?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been following gromacs tutorials and haven't come across any that deal with capping the termini, so is it important?&lt;/p&gt;&#xA;" OwnerUserId="5276" LastActivityDate="2013-12-31T05:54:36.823" Title="Molecular simulations without capping n- and c-terminus of polypeptide" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14191" PostTypeId="2" ParentId="14168" CreationDate="2013-12-29T23:49:05.800" Score="6" Body="&lt;p&gt;What you are describing usually falls under the category of computational biology or just mathematical biology. Unfortunately, the biggest part of this field is bioinformatics, or the application of statistical and/or dynamical programming techniques to sequence data. You exclude this in your question, and I would agree with you that it is a &amp;quot;boring&amp;quot; topic from a theoretical biologist's perspective, because it mostly uses computer science in a very standard way as a tool for experimental biologists.&lt;/p&gt;&#xA;&lt;p&gt;As you noticed, it is also standard to use computational models in theory papers as a way of simulating things. I think this is the sort of resources you are asking for. Unfortunately, &lt;strong&gt;specific algorithms are seldom standardized or reused in this area&lt;/strong&gt;. Typically, each paper (or sequence of related papers) uses their own models.&lt;sup&gt;[1]&lt;/sup&gt; As you read a lot of papers, you will find some common themes, but these are just standard ideas of theoretical biology expressed as simulation. I doubt that comprehensive books exist, and even if some do their utility is not clear to me due to a lack of specific algorithm (re)use.&lt;sup&gt;[2]&lt;/sup&gt; However, the most commonly used techniques are to either to solve differential equations numerically (which most would classify as mathematical modeling) or run agent-based or population-based models. General resources on these exist, and here are some discussions for the latter other SEs:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://cstheory.stackexchange.com/q/7240/1037&quot;&gt;Simulation modeling of diseases&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://cstheory.stackexchange.com/q/7286/1037&quot;&gt;Sources for Algorithmic Evolutionary Game Theory&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://cs.stackexchange.com/q/2764/55&quot;&gt;Canonical reference on agent-based computing&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Finally, &lt;strong&gt;do not confuse 'computational modeling in theoretical biology' with 'algorithmic biology'&lt;/strong&gt;. &lt;a href=&quot;http://egtheory.wordpress.com/2013/06/09/toward-an-algorithmic-theory-of-biology/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Algorithmic biology&lt;/a&gt; is a &lt;a href=&quot;https://cstheory.stackexchange.com/q/14103/1037&quot;&gt;new field&lt;/a&gt; that views ecological and evolutionary dynamics as computatioanl proccesses. Instead of using mathematical tools borrowed from physics (as is standard with the dynamic systems approaches to mathematical biology), it &lt;a href=&quot;http://egtheory.wordpress.com/2013/09/09/cstheory-of-biology/&quot; rel=&quot;nofollow noreferrer&quot;&gt;uses the tool of theoretical computer science&lt;/a&gt; (note that this is a type of math that has very little to do with programming the laptop infront of you). I know of only two books in this field:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Gregory Chaitin &amp;quot;Proving Darwin: Making biology mathematical&amp;quot;&lt;/strong&gt; - Although Chaitin had contributed significant and original thoughts to computer science in the past, &lt;a href=&quot;http://egtheory.wordpress.com/2012/06/29/proving-darwin/&quot; rel=&quot;nofollow noreferrer&quot;&gt;I would strongly advice against this book&lt;/a&gt; because it misses the point from both the biological and &lt;a href=&quot;http://egtheory.wordpress.com/2012/07/08/algorithmic-mutation/&quot; rel=&quot;nofollow noreferrer&quot;&gt;computer science&lt;/a&gt; point of view.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Leslie Valiant &amp;quot;Probably Approximately Correct: Nature's algorithms for learning and prospering in a complex World&amp;quot;&lt;/strong&gt; - in this book (based on earlier papers), Valiant recasts evolution as a type of machine learning. This is very interesting from a mathematical point of view, &lt;a href=&quot;http://egtheory.wordpress.com/2013/05/21/historicity-and-separation-of-scales/&quot; rel=&quot;nofollow noreferrer&quot;&gt;although it might not connect directly enough to biologically relevant questions&lt;/a&gt; (see also some of the discussion in &lt;a href=&quot;http://arxiv.org/abs/1308.5094&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kaznatcheev (2013)&lt;/a&gt; and &lt;a href=&quot;https://www.genetics.org/content/212/1/245.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kaznatcheev (2019)&lt;/a&gt;) and misses the computational power of frequency-dependent selection (see &lt;a href=&quot;https://www.biorxiv.org/content/10.1101/2020.05.03.075069v1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kaznatcheev (2020)&lt;/a&gt;). But I would recommend reading this book.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;h3&gt;Notes&lt;/h3&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;In general, I consider these sort of models as &lt;a href=&quot;http://egtheory.wordpress.com/2013/09/08/mathematical-models/#Heuristics&quot; rel=&quot;nofollow noreferrer&quot;&gt;heuristics&lt;/a&gt; and &lt;a href=&quot;http://egtheory.wordpress.com/2013/12/19/computational-models/&quot; rel=&quot;nofollow noreferrer&quot;&gt;I am skeptical of their usefulleness beyond rhetorical devices/examples&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;I think that literature reviews would be interesting computational modeling in specific subfields. In fact some colleagues and I have wanted to do this for the smaller area of evolutionary game theory (&lt;a href=&quot;https://cstheory.stackexchange.com/a/7296/1037&quot;&gt;This answer&lt;/a&gt; can serve as a starting point for some algorithmic considerations of EGT).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="500" LastEditorUserId="500" LastEditDate="2020-11-16T07:03:15.157" LastActivityDate="2020-11-16T07:03:15.157" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="14192" PostTypeId="2" ParentId="14175" CreationDate="2013-12-30T02:00:38.870" Score="8" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;It may never have happened again, however, since all lifeforms on&#xA;  Earth today are similar on a molecular level&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Actually, the similarity is at the chemical level where the &lt;em&gt;chirality&lt;/em&gt; of all known-life's amino acids are &quot;left-handed&quot; (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Hypothetical_types_of_biochemistry#Alternative-chirality_biomolecules&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Hypothetical_types_of_biochemistry#Alternative-chirality_biomolecules&lt;/a&gt;). Since there is no advantage to having left-handed proteins over right handed, we would expect the chemistry in a spontaneously organism to randomly chose one or the other. So, it's 99% likely that life didn't arise more then 7 times: (1/2)^7 &amp;lt; .01. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or, all the descendants of the right-handed protein life could have died-off, but this seems unlikely if there is no inherent efficiency difference.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first organisms that arose consumed any subsequent organisms that&#xA;  came into being. This was suggested by Alexander Oparin, but I find it&#xA;  very difficult to believe since it would have to happen everywhere on&#xA;  Earth&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is where your missing a big point:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;It's not necessarily eating them, or even outcompeting them once they arise, it's about cutting the legs out of the environment - eating the primordial soup of any loose complex organic matter. The places where the minimal materials for self replication machinery would have been available (since crystal-based origin of life was rejected in the 60's) would be very rare, and only on very specfic parts of the Earth...&lt;/li&gt;&#xA;&lt;li&gt;Two of the current theories for this location, were in seafloor thermal vents, or on beaches with radioactive sand. Once life arise once in one of these niches, it will gain a strong foothold in these exact locations, crowding out those places orginal &quot;ideal conditions&quot; that led to the generation of life in the first place.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Ultimately, we'll probably be better able to answer this question by looking out to other planets than by un-earthing any satisfying evidence that could be found intact from 3 billion years ago.&lt;/p&gt;&#xA;" OwnerUserId="5277" LastActivityDate="2013-12-30T02:00:38.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14193" PostTypeId="2" ParentId="9085" CreationDate="2013-12-30T03:31:56.030" Score="-1" Body="&lt;p&gt;There's really two components to ID:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A No-Go Theorem (&lt;a href=&quot;http://en.wikipedia.org/wiki/No-go_theorem&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/No-go_theorem&lt;/a&gt;) on the likelihood of spontaneously arising life, or of it reaching some threshold in evolutionary development naturally.&lt;/li&gt;&#xA;&lt;li&gt;...which leads to &quot;the design inference&quot;, which posits that the characteristic of &lt;em&gt;intelligence&lt;/em&gt; is able to overcome the problem established by the no-go: that life exist, but could not &lt;strong&gt;allegedly&lt;/strong&gt; have arisen from a random process.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now certain no-go theorems claim something is physically impossible, like transmitting information faster than the speed of light, some are about the provability in mathematics like Godel Incompleteness theorem, but the ID no-go theorem is about being statistically imprlausible- but what is implausible in a Big, Old Universe? Something like 1/Number of atoms in the universe is sufficiently low (2^82), and you can demonstrate this easily by thinking of DNA code 1/4^N where N = min num of base pairs for self-replication, where N~100,000 M genitalium. This is a very naive model, but it's a start: see George Chaitan's work for better maths: &lt;a href=&quot;http://www.youtube.com/watch?v=RlYS_GiAnK8&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=RlYS_GiAnK8&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The design inference is really Stephen Meyer's domain, and I'll refer you to him, this is much more a philosophic argument. One thing that's important to note for people who are dismissive of ID is that this is about reasoning about intelligence in the abstract, not the manifestation in physical form, not &quot;some being&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's my opinion? Could I get back to you in 300 years? We'll finally have data on thousands of other planets and whether any of them have ever harbored life, and that I think would be the falsification of ID if other life was found. But I think both a barren universe, and one with other life are both plausible given what we know now. That's why I don't get why people are so staunch on this issue: it's impossible to know the one key thing we need to know in this debate in our lifetime. But in a few generations we in fact will have this answer. We get to live in some interesting times.&lt;/p&gt;&#xA;" OwnerUserId="5277" LastActivityDate="2013-12-30T03:31:56.030" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="14196" PostTypeId="2" ParentId="14190" CreationDate="2013-12-30T12:15:42.123" Score="1" Body="&lt;p&gt;Interesting question. I have to admit, that I haven't really come across it, but for the moment it seems to me that this mechanism is used mainly to protect short alpha helices and stabilize them. &#xA;See this articles: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8347570&quot; rel=&quot;nofollow&quot;&gt;Helix stop signals in proteins and peptides: the capping box.&lt;/a&gt;&quot; and this one: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143812/&quot; rel=&quot;nofollow&quot;&gt;Helix capping.&lt;/a&gt;&quot;&#xA;A lot of research is done in combination with actin filaments, where the capping plays an important role in stabilizing the filament strands - either prohibiting the addition of new monomers and on the other hand preventing the removal of elements from the polymer strand. &#xA;This review gives an overview:&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8383512&quot; rel=&quot;nofollow&quot;&gt;F-actin capping proteins.&lt;/a&gt;&quot;&#xA;This research article might also be interesting when doing simulations:&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143170/&quot; rel=&quot;nofollow&quot;&gt;N- and C-capping preferences for all 20 amino acids in alpha-helical peptides.&lt;/a&gt;&quot; As always, if you have some problems with access to the articles, let me know.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-30T12:15:42.123" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14198" PostTypeId="2" ParentId="14186" CreationDate="2013-12-30T14:14:56.877" Score="6" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Sporophyte&quot; rel=&quot;nofollow&quot;&gt;sporophtye&lt;/a&gt; is the &lt;strong&gt;diploid stage&lt;/strong&gt; in the life cycle. In comparison, with humans, you and I would be sporophytes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Gametophyte&quot; rel=&quot;nofollow&quot;&gt;Gametophyte&lt;/a&gt; is the &lt;strong&gt;haploid stage&lt;/strong&gt; in the life cycle. In comparison, with humans, spermatozoids and ovules are gametophytes.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Independence&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note for what follows: &quot;independent&quot; can be understood in terms of &quot;ability to survive&quot;. Being independent according to its ability to survive. One might use the word &quot;independent&quot; for other concerns though! For example: &quot;Independent&quot; in the sense &quot;no nutrient exchange between the two&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, one could say that in humans, the gametophyte is not independent (in it's ability to survive) of the sporophyte. Similarly, in &lt;a href=&quot;http://en.wikipedia.org/wiki/Moss&quot; rel=&quot;nofollow&quot;&gt;moss (&lt;em&gt;bryophyta&lt;/em&gt;)&lt;/a&gt;, the gametophyte is not independent of the sporophyte because the gametophyte grows on the sporophyte using its nutrients (one could say that the gametophyte parasitize the sporophyte but that would be a bit misleading!). If the sporophyte is independent of the gametophyte (or vice-versa), it means that there is &lt;a href=&quot;http://en.wikipedia.org/wiki/Alternation_of_generations&quot; rel=&quot;nofollow&quot;&gt;alternation of generations&lt;/a&gt;. In other words, sporophyte and gametophyte live separately (like two different individuals).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Life-cycle&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find tons of examples of weird life cycles, in particular in plants, fungi and parasites but not only. And you may find many examples for which the type of sexual reproduction or the type of life-cycle are hard to defined with these relatively simple concepts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Identity&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question of identiy (how separate or genetically different should two individuals be so that we consider them to be two different individuals) is rather a question of philosophy. Such discussions about identity occur when we talk about clones (ramet and genet), about life cycle or about level of organisation/level of selection. The book &lt;a href=&quot;http://www.amazon.ca/Major-Transitions-Evolution-Revisited/dp/0262015242/ref=sr_1_3?ie=UTF8&amp;amp;qid=1420018195&amp;amp;sr=8-3&amp;amp;keywords=major+transitions+in+evolution&quot; rel=&quot;nofollow&quot;&gt;Major Transition in Evolution (Revisited)&lt;/a&gt; provides many of the philosophical discussion on the subject of identity in population genetics.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-01-17T18:13:13.407" LastActivityDate="2015-01-17T18:13:13.407" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14199" PostTypeId="2" ParentId="14188" CreationDate="2013-12-30T14:53:04.660" Score="3" Body="&lt;p&gt;Sometimes, the morphology and the topology of the flower structure is such that the pollen grains falling on certain parts are gravitationally (or hydrostatically) drawn towards the stigma.&lt;br&gt;&#xA;I remember having read that the waxy streamlined stigma of submerged hydrophytes (Vallisneria, Hydrilla)  creates mini vortices around it during steady water flow. These vortices then pull nearby pollen, (which may be sitting on nearby flower parts) towards itself. Certain hydrophyte morphologies also maximise the water flow towards stigma, which in turn gathers pollen incident elsewhere on the plant and bringing in towards the stigma.(For example, the streamlined and bladder shaped hydrophyte flowers have stigmas at their centre) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way to do this is via the common sloping surface of the petals or the perianth, which on gathering pollen, gravitationally push them to the centre of the flower where the stigma usually resides. The entire inflorescence stalk might be modified into specific shapes to do this. The common pyramidal arrangement of the inflorescence (broad at the base, tapering towards the apex) helps in gathering the pollen incident on non-stigma parts of the apex region at the bottom.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from this, pollen falling elsewhere, may again be taken up by the agents of pollination. But I believe the formation of pollen tube never occurs at any place other than stigma. Nor does any re-absorption take place.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also worth mentioning that just because pollen falls on the correct stigma does not ensure fertilization. Absence of stigma maturity/receptivity, synergid abnormality, inviable pollen etc could still hinder fertilization.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[I am not perfectly aware about studies on whether any chemical reaction occurs if pollen lands on places other than stigma. But I doubt it, since the chemical specificity required to begin the pollen tube formation is very high in most species.]&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2014-01-30T11:06:03.267" LastActivityDate="2014-01-30T11:06:03.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14200" PostTypeId="2" ParentId="14187" CreationDate="2013-12-30T15:42:42.753" Score="1" Body="&lt;p&gt;According to &quot;Wile, Dr. Jay L. Exploring Creation With Biology. Apologia Educational Ministries, Inc. 1998&quot; and reported &lt;a href=&quot;http://www.conservapedia.com/Dominant_generation&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In alternation of generations, the dominant generation is the generation that occupies the largest portion of the life cycle&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I guess that it has to be understood in terms of &quot;time&quot;. I am not quite sure though if it has to be understood in terms of &lt;a href=&quot;http://en.wikipedia.org/wiki/Generation_time&quot; rel=&quot;nofollow&quot;&gt;generation time&lt;/a&gt; of life span. Intuitively, I would say that generation time would make much more sense. Therefore, I'd say that, &lt;strong&gt;the dominant generation is the generation which have the longest mean generation time&lt;/strong&gt; (=mean time from the birth to reproduction).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As @Shigeta said in the comments: For example, in Homo sapiens, the dominant generation is the diploid phase (sporophyte, you and me) and the non-dominant generation is the haploid phase  (gametophyte, sperm/ovule).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-01-06T16:03:21.683" LastActivityDate="2014-01-06T16:03:21.683" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14201" PostTypeId="1" AcceptedAnswerId="14208" CreationDate="2013-12-30T16:59:02.093" Score="1" ViewCount="733" Body="&lt;p&gt;I have pairs of coding DNA sequences which I wish to perform pairwise &lt;strong&gt;codon alignments&lt;/strong&gt; via &lt;strong&gt;Python&lt;/strong&gt;, I have &quot;half completed&quot; the process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So far..&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I retrive pairs of orthologous DNA sequences from genbank using &lt;code&gt;Biopython&lt;/code&gt; package.&lt;/li&gt;&#xA;&lt;li&gt;I translate the orthologous pairs into peptide sequences and then align them using &lt;code&gt;EMBOSS Needle&lt;/code&gt; program.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I wish to..&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Transfer the gaps from the peptide sequences into the original DNA sequences.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would appreciate suggestions for programs/code (called from Python) that can transfer gaps from aligned peptide sequence pairs onto codons of the corresponding nucleotide sequence pairs. Or programs/code that can carry out the pairwise codon alignment from scratch.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AE2LW.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5005" LastActivityDate="2013-12-31T02:12:09.537" Title="Codon alignment via Python?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;proteins&gt;&lt;sequence-analysis&gt;&lt;sequence-alignment&gt;" AnswerCount="1" CommentCount="8" ClosedDate="2014-01-01T07:06:59.963" ContentLicense="CC BY-SA 3.0" />
  <row Id="14203" PostTypeId="1" AcceptedAnswerId="14204" CreationDate="2013-12-30T18:02:12.920" Score="0" ViewCount="103" Body="&lt;p&gt;Increasing estradiol (E2) hormone from ovarian follicles prior to ovulation has been hypothesized to play a critical role for induction of pheromones. These pheromones render females sexually receptive to males to facilitate mating. An investigator performs experiments in sheep in which females are gonadectomized, then treated with E2 or vehicle alone and allowed to breed. What can be the hypothesis &lt;/p&gt;&#xA;" OwnerUserId="5164" LastActivityDate="2013-12-30T18:13:05.713" Title="estradiol hormone role" Tags="&lt;endocrinology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14204" PostTypeId="2" ParentId="14203" CreationDate="2013-12-30T18:13:05.713" Score="2" Body="&lt;p&gt;The experiment is easy to design: Measure the concentration of the pheromones in the test sheep versus the control sheep and see what the outcome is. Further compare the reaction of the male sheep on both, control and treated sheep. Ideally you treat both animals with some kind of treatment to avoid an influence by the application method of the estradiol. Also blind the researchers to avoid their influence on the experiment.&#xA;The hypothesis would be: Has estrogen E2 an influence on the pheromones in female sheep and do these pheromones influence the male sheep.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-30T18:13:05.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14205" PostTypeId="2" ParentId="13994" CreationDate="2013-12-30T19:15:27.003" Score="4" Body="&lt;p&gt;Since mammals all share the same neural structures it is quite likely that most non human species dream, but as yet, the simplest animal I could find that has been scientifically demonstrated to dream is the rat, as proven by Massachusetts Institute of Technology (MIT).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MIT not only established that rat were capable of dreaming about the events they had experienced while awake, but that the content of the dreams could be manipulated with audio cues the rats had been trained to respond with in a specific way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Brain#Mammals&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Brain#Mammals&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://web.mit.edu/newsoffice/2012/neuroscientists-achieve-dream-engineering-0902.html&quot; rel=&quot;nofollow&quot;&gt;http://web.mit.edu/newsoffice/2012/neuroscientists-achieve-dream-engineering-0902.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5282" LastActivityDate="2013-12-30T19:15:27.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14206" PostTypeId="1" AcceptedAnswerId="14207" CreationDate="2013-12-30T19:46:25.387" Score="3" ViewCount="154" Body="&lt;p&gt;My textbook says &quot;As the seed matures it loses water and enter dormancy&quot;. I am confused as to whether this happens before the seeds are transported or after, and as to how seeds know to become dormant when required and then become active again.&lt;/p&gt;&#xA;" OwnerUserId="5275" LastActivityDate="2013-12-30T20:55:55.877" Title="Seed Dormancy and Seed Transportation" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14207" PostTypeId="2" ParentId="14206" CreationDate="2013-12-30T20:28:08.063" Score="3" Body="&lt;p&gt;I presume what the author is trying to convey is that as a seed ages, it enters a quiescent phase as a result of natural desiccation. Without more context, I'd guess that the quote you've provided here is referring to secondary dormancy, which is a response to unfavorable germination conditions. By definition, secondary dormancy occurs &lt;em&gt;after&lt;/em&gt; the seed is released from the plant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanisms of secondary dormancy are not well understood, and resumption of embryonic function could be dependent on any number of factors. Generally, dormancy continues until such time as favorable conditions are observed by the dormant seed. For &lt;em&gt;Avena sativa&lt;/em&gt;, seeds become dormant if temperatures in excess of the maximum for germination are observed. Other seeds become dormant in response to over- or dehydration, temperature variability, age, other factors, and combinations ad nauseum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the more common environmental causes of exiting dormancy include afterripening, chilling and lighting.&lt;/p&gt;&#xA;" OwnerUserId="5283" LastEditorUserId="5283" LastEditDate="2013-12-30T20:55:55.877" LastActivityDate="2013-12-30T20:55:55.877" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14208" PostTypeId="2" ParentId="14201" CreationDate="2013-12-30T20:41:33.297" Score="3" Body="&lt;p&gt;The basic process would be (in pseudocode, I don't know python well enough, I'm a Perl geek):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;$seq1=ATGCCAGGCTGA&#xA;$seq2=ATGGGACCATAA;&#xA;for ($i=0;$i&amp;lt;length($seq1);$i++){&#xA;   codons1[$i]=amino_acid&#xA;}&#xA;for ($i=0;$i&amp;lt;length($seq2);$i++){&#xA;       codons2[$i]=amino_acid&#xA;}&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;At this point you will have two arrays or hashes or tuples or dicts or whatever holding the amino acid that corresponds to each codon position of the input seqs. You go and do your translation and dS/dN thing and you can then use these lists to map back to the original nucleotides:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;for ($i=0;$i&amp;lt;length($ProteinSseq1);$i++){&#xA;  print codons1[$i]&#xA;}&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;You will need to adapt this to deal with codons correctly (i++ will only increment by one, you need to extract the triplets) and then to read the gaps but these are all programming issues that have nothing to do with the biological side of things. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2013-12-31T02:12:09.537" LastActivityDate="2013-12-31T02:12:09.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14209" PostTypeId="1" AcceptedAnswerId="14213" CreationDate="2013-12-30T20:49:08.823" Score="0" ViewCount="394" Body="&lt;p&gt;Is my understand of how seed germination comes to be and what it entails correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Seed germination: As the seed matures it loses water and enters dormancy (a state in which it’s metabolic processes slow down dramatically) after which it is dispersed.  Once the seeds have been dispersed and if they have landed in an area that meets the requirements (sufficient water, warmth, and oxygen), they may begin to grow into seedlings or they may remain dormant.  If they have not landed in a suitable area they can remain dormant for hundreds or thousands of years and wait until they are transported to a suitable area to resume growth.  Eventually once the seeds have landed in a suitable area, the seed resumes the process of growth when the seed is able to absorb, the process of resuming growth after being dormant is called germination. The water causes the seed to swell and breaks open the seed coat. The stored food in the endospore or cotyledons begins to break down, and nutrients are made available to the embryo. The food and the presence of oxygen allow cellular respiration to occur, which provides energy to the embryo for growth. The first part of the embryo to appear outside the seed is a structure called the radicle, which starts absorbing water and nutrients from its environment, eventually the radicle develops into the plant’s roots. The hypocotyl is the region of the stem nearest the seed. In many plants, it is the first part of the seedling to appear above the soil. In some dicots, as the hypocotyl grows it pulls the cotyledons and the embryonic leaves out of the soil. Photosynthesis begins as soon as the seedling’s cells that contain chloroplasts are above the ground and exposed to light. In monocots, the cotyledon usually stays in the ground when the stem emerges from the soil. &lt;/p&gt;&#xA;" OwnerUserId="5275" LastActivityDate="2013-12-30T21:10:54.617" Title="Seed Germination" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14210" PostTypeId="2" ParentId="13994" CreationDate="2013-12-30T20:51:04.777" Score="4" Body="&lt;p&gt;At least &lt;a href=&quot;http://www.uchospitals.edu/news/2000/20001027-dreamsong.html&quot; rel=&quot;nofollow&quot;&gt;one study from University of Chicago&lt;/a&gt; showed that birds dream...about singing.&lt;/p&gt;&#xA;" OwnerUserId="5283" LastActivityDate="2013-12-30T20:51:04.777" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14211" PostTypeId="1" CreationDate="2013-12-30T20:54:48.603" Score="1" ViewCount="1297" Body="&lt;p&gt;I know that asexual reproduction is also called vegetative reproduction. However I do not understand it's relation to artificial propagation. Is it a technique used for asexual reproduction (the method by which plants reproduce asexually) or is artificial propagation another name for asexual reproduction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I right when I say artificial propagation techniques provide the means for plants to reproduce asexually?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, is my understanding of asexual reproduction and artificial propagation correct:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In asexual reproduction, a parent plant produces offspring that are genetically identical to it and to each other. Asexual reproduction produces clones as the offspring and the parent are clones of one another. Asexual reproduction can be an advantage when environmental conditions are stable and an organism is well-adapted to its environment. The genetically identical off spring will also be adapted to that environment. Asexual reproduction is carried out by the different artificial propagation techniques. Artificial propagation is the cloning of a plant from a portion of its roots, stems, or leaves. In asexual reproduction in plants, also called vegetative propagation, new individuals are grown from a portion of the roots, stems, or leaves of the existing plant. Artificial propagation involves using plants’ natural ability to reproduce vegetative. This process enables farmers and gardeners to select the parent plants for specific traits.&lt;/p&gt;&#xA;" OwnerUserId="5275" LastEditorUserId="5275" LastEditDate="2013-12-31T18:03:16.943" LastActivityDate="2013-12-31T18:03:16.943" Title="Artificial Propagation and it's relation to asexual reproduction" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14212" PostTypeId="2" ParentId="14211" CreationDate="2013-12-30T20:58:08.323" Score="2" Body="&lt;p&gt;Artificial propagation is (generally) human-directed, while asexual/vegetative reproduction is a natural process. Take a look at the wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Vegetative_reproduction#Artificial_vegetative_propagation&quot; rel=&quot;nofollow&quot;&gt;vegetative reproduction&lt;/a&gt; for more information on how and why artificial propagation is sometimes preferred to vegetative reproduction.&lt;/p&gt;&#xA;" OwnerUserId="5283" LastActivityDate="2013-12-30T20:58:08.323" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14213" PostTypeId="2" ParentId="14209" CreationDate="2013-12-30T21:10:54.617" Score="1" Body="&lt;p&gt;You're not accounting for anything other than &quot;the happy path&quot; here. For instance, not all seeds care about warmth or oxygen, and not very many can last for hundreds or thousands of years, and those that do often require more than transportation to another area to germinate. Otherwise, it sounds fairly accurate.&lt;/p&gt;&#xA;" OwnerUserId="5283" LastActivityDate="2013-12-30T21:10:54.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14215" PostTypeId="2" ParentId="13684" CreationDate="2013-12-31T00:20:17.377" Score="3" Body="&lt;p&gt;Sure generally any cell that expresses MHCII will also express MHCI. Most cells in the body express MHCI as a self-identifier and to present intracellular proteins to T cells as a sort of a status update i.e. the cell will constantly be presenting peptides (pieces of endogenous proteins) on its surface bound to MHCI, if the cell becomes infected it could also present viral proteins on its surface with MHCI, which can potentially be recognized by a T cell specific for that particular epitope. B cells and antigen presenting cells such as dendritic cells and macrophages express MHCII but also need to be able to be identified as self through their basal level of MHCI presentation of self-peptides. The two MHC molecules are recognized by different cell types, MHCI by CD8 T cells and MHCII by CD4 T cells. So you could consider them to work independently from one another. The source of antigens (peptides here) and process for presenting them via MHCI and MHCII are somewhat different from one another.  &lt;/p&gt;&#xA;" OwnerUserId="5284" LastActivityDate="2013-12-31T00:20:17.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14216" PostTypeId="1" CreationDate="2013-12-31T01:13:24.950" Score="8" ViewCount="15012" Body="&lt;p&gt;Nails grow rapidly and constantly, such that without constant artificial trimming they would reach lengths difficult to manage. How did this benefit early humans, say 200kya? Were they used like claws? Did physical activity keep them at a short length? &lt;/p&gt;&#xA;" OwnerUserId="5245" LastActivityDate="2019-07-26T23:41:21.557" Title="How would constantly growing nails have aided early human?" Tags="&lt;evolution&gt;&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14217" PostTypeId="1" AcceptedAnswerId="14461" CreationDate="2013-12-31T03:42:34.127" Score="8" ViewCount="2987" Body="&lt;p&gt;In most plants bearing &lt;a href=&quot;http://en.wikipedia.org/wiki/Cleistogamy&quot; rel=&quot;nofollow&quot;&gt;cleistogamous&lt;/a&gt; flowers, &lt;a href=&quot;http://en.wikipedia.org/wiki/Chasmogamy&quot; rel=&quot;nofollow&quot;&gt;chasmogamous&lt;/a&gt; flowers are also borne by the plants. For example, &lt;a href=&quot;http://en.wikipedia.org/wiki/Viola_%28plant%29&quot; rel=&quot;nofollow&quot;&gt;Viola&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Oxalis&quot; rel=&quot;nofollow&quot;&gt;Oxalis&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Commelina&quot; rel=&quot;nofollow&quot;&gt;Commelina&lt;/a&gt; contain both these kinds of flowers.( I am unaware of a species which bears only cleistogamous flowers, which would be very unfavourable for evolutionary success)  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Cleistogamous flowers help in reproduction with minimal energy and resource expenditure. It also maximises the chance of reproduction, which is an important factor where the agents of pollination are scarce. On the other hand Chasmogamous flowers provide variablity, hybrid vigour and generate better genotypes through recombination. Both of these strategies are useful in different environment. In adverse (less pollinators, energy stress) cleistogamy would be favourable, and in other cases where no energy stress prevails, chsmogamy is advantageous.    &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;My question is, &lt;strong&gt;How can plants, if they can, regulate which strategy&#xA;  is supported? Is the ratio of cleistogamous to chasmogamous flowers&#xA;  constant irrespective of the environment, or does the prevailing&#xA;  environment have a say in deciding which of these two kinds of flowers&#xA;  will be preferred over the other? If it does, what is the regulatory&#xA;  mechanism underlying this control of flowering startegies?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;One other related question is &lt;strong&gt;whether there are any species which bear only cleistogamous flowers?&lt;/strong&gt; That would seem very unfavourable for evolution to act on.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2014-01-13T17:14:49.363" LastActivityDate="2014-01-23T15:29:22.760" Title="Regulation in plants bearing cleistogamous and chasmogamous flowers" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;reproduction&gt;&lt;plant-anatomy&gt;&lt;life-history&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14218" PostTypeId="2" ParentId="14190" CreationDate="2013-12-31T05:54:36.823" Score="0" Body="&lt;p&gt;Capping the termini neutralizes their amine or carboxylic acid moieties. If this was recapitulated in the biological context, it could be important for an accurate MD simulation to neutralize those charges. Termini are mobile enough without extra charges in the mix!&lt;/p&gt;&#xA;" OwnerUserId="3336" LastActivityDate="2013-12-31T05:54:36.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14219" PostTypeId="1" CreationDate="2013-12-31T09:27:26.657" Score="4" ViewCount="783" Body="&lt;p&gt;&lt;strong&gt;What metabolic processes does a dormant embryo in a seed carry out?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Seeds will not germinate, either because of a lack of favourable conditions, &lt;a href=&quot;http://en.wikipedia.org/wiki/Seed_hibernation&quot; rel=&quot;nofollow&quot;&gt;seed hibernation&lt;/a&gt;, or because of a genetically pre-determined physical or physiological mechanism preventing germination before a specific period or event. In addition to not germinating due to those factors, seeds can also experience &lt;a href=&quot;http://5e.plantphys.net/article.php?ch=23&amp;amp;id=8&quot; rel=&quot;nofollow&quot;&gt;dormancy&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With these germination preventing mechanisms in place, the seed will not germinate in the absence of specific triggers. But the &lt;a href=&quot;http://5e.plantphys.net/article.php?ch=23&amp;amp;id=9&quot; rel=&quot;nofollow&quot;&gt;seed viability&lt;/a&gt; period is limited in which it germinates if the trigger is available. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If any, what metabolic processes do seeds carry out in their dormant/hibernating state, on cessation of which, the seed becomes non-viable?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Does the embryo in a dessicated dormant seed respire, excrete, ingest etc, though with a reduced speed? If it does, is the depletion&#xA;  of the respiratory substrate which results in termination of seed&#xA;  viability?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3553" LastEditDate="2015-05-15T01:20:32.640" LastActivityDate="2020-05-07T03:12:22.787" Title="What metabolic processes do dormant and ungerminated seeds carry out?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;molecular-genetics&gt;&lt;germination&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14220" PostTypeId="2" ParentId="14185" CreationDate="2013-12-31T12:14:08.640" Score="1" Body="&lt;p&gt;Here is a quite intuitive and straight forward possible explanation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key is to rephrase &quot;if the conditions are bad&quot; into &quot;if the focal individual don't fit its environment&quot; or &quot;if the genome of the focal individual is not fit&quot; or &quot;if the focal individual is not fit&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If an individual has a high fitness, it has better to create clones which will be fit as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If an individual is not fit, it has better to take the risk to reproduce sexually hoping that some of the offsprings will be fit thanks random recombinations and mutations (there are usually much more mutations during meiosis than during mitosis).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Note:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sex allocation and evolution of sex is a very broad subject. Your question is linked with discussion on sex allocation. You might be interested by these books:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://books.google.fr/books/about/The_Theory_of_Sex_Allocation.html?id=KKYRi-FCmMIC&amp;amp;redir_esc=y&quot; rel=&quot;nofollow&quot;&gt;Eric Charnov&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0691089647&quot; rel=&quot;nofollow&quot;&gt;Stuart West&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0199657149&quot; rel=&quot;nofollow&quot;&gt;Perrin and Beukeboom&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;But you might simply have a first look through wikipedia &lt;a href=&quot;http://en.wikipedia.org/wiki/Sex_allocation&quot; rel=&quot;nofollow&quot;&gt;sex allocation&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Muller%27s_ratchet&quot; rel=&quot;nofollow&quot;&gt;Muller's ratchet&lt;/a&gt; or have a look to the diversity of &lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_reproduction&quot; rel=&quot;nofollow&quot;&gt;reproduction&lt;/a&gt;. You could also have a look to specialized literature, the work of S. Otto for example. Usually introductory books on evolutionary biology contain a chapter on the evolution and diversity of sexual reproduction.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-01-06T16:02:12.693" LastActivityDate="2014-01-06T16:02:12.693" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14221" PostTypeId="1" CreationDate="2013-12-31T13:21:42.120" Score="1" ViewCount="185" Body="&lt;p&gt;I have an Emotiv EPOC (EEG headset: 128 SPS, notch filter @60 Hz, felt saline contacts) I've been playing around with. Over the course of two or three hours using CCA to plot an SNR contour against frequency and time over O1, O2, P7, and P8, I noticed that a strong background signal in the alpha-wave range was existent at ~10 Hz, but then after a while of doing other things and coming back to it the strong background signal at 10 Hz disappeared but a strong background signal at a smidgen over 8 Hz was present instead.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Naturally, this leads me to ask the question: what the heck is going on? Unfortunately, that doesn't make for a good stackexchange question title, so the replacement question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can alpha wave frequencies vary within a single subject over the course of a single day? If they can, by how much, and under what conditions?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(if they can't, I have to start figuring out what the heck caused those artifacts...)&lt;/p&gt;&#xA;" OwnerUserId="4208" LastEditorUserId="14852" LastEditDate="2016-05-31T07:03:57.377" LastActivityDate="2016-05-31T07:03:57.377" Title="Alpha wave frequency variance in EEG of single subject over period of a few hours?" Tags="&lt;neuroscience&gt;&lt;neurology&gt;&lt;eeg&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14222" PostTypeId="1" AcceptedAnswerId="14227" CreationDate="2013-12-31T15:03:46.967" Score="2" ViewCount="2230" Body="&lt;p&gt;Well, I am not able to understand the exact difference between megasporocyte and archesporium. Also I'm not quite able to get, how or precisely from where do these arise?&#xA;Please help.&lt;/p&gt;&#xA;" OwnerUserId="4947" LastActivityDate="2013-12-31T17:39:24.910" Title="Terms related to megasporogenesis" Tags="&lt;botany&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14223" PostTypeId="1" AcceptedAnswerId="14229" CreationDate="2013-12-31T15:40:59.487" Score="3" ViewCount="1455" Body="&lt;p&gt;Is there a word that describes the meeting point of a plants growing stem and its root?&#xA;Is this the same term for aerial roots above soil level?&lt;/p&gt;&#xA;" OwnerUserId="5289" LastEditorUserId="3952" LastEditDate="2014-01-04T15:43:36.820" LastActivityDate="2014-01-04T15:43:36.820" Title="Scientific name for the union point of a plant stem and root" Tags="&lt;botany&gt;&lt;terminology&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14225" PostTypeId="1" AcceptedAnswerId="14226" CreationDate="2013-12-31T16:24:00.407" Score="0" ViewCount="126" Body="&lt;p&gt;How do you monitor the use of nootropics?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is a good process to measure both: side-effects and any improvements.&#xA;Where can I find resources with scientific and tested data of short and long term usage of various Nootropics? (I'm using google as well)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="5290" LastActivityDate="2019-07-01T17:16:05.630" Title="How to monitor the use of Nootropics?" Tags="&lt;brain&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14226" PostTypeId="2" ParentId="14225" CreationDate="2013-12-31T16:50:59.537" Score="3" Body="&lt;p&gt;The process of measuring the effect of nootropics would be the same as for any other drug: Do a double blinded placebo study and the follow the parameters you hope to influence. For example do &quot;brain tests&quot; if you want to test for enhanced brain function. If there is any function of your drug in the body, you will see a difference between the treatment and the control group. You could start by reading the Wikipedia article about &lt;a href=&quot;http://en.wikipedia.org/wiki/Nootropic&quot; rel=&quot;nofollow&quot;&gt;Nootropics&lt;/a&gt; which is quite exhausting and also has quite a lot of references and go on with these two papers &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18721399&quot; rel=&quot;nofollow&quot;&gt;Does taking vitamin, mineral and fatty acid supplements prevent cognitive decline? A systematic review of randomized controlled trials.&lt;/a&gt;&quot; and &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18353672&quot; rel=&quot;nofollow&quot;&gt;Cognition enhancers between treating and doping the mind.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2013-12-31T16:50:59.537" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14227" PostTypeId="2" ParentId="14222" CreationDate="2013-12-31T17:39:24.910" Score="1" Body="&lt;p&gt;In relation  to &lt;em&gt;angiospermic megasporogenesis&lt;/em&gt;, archesporium cell is the precursor of Megasporocyte.   &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.merriam-webster.com/medical/archesporium&quot; rel=&quot;nofollow&quot;&gt;Archesporium&lt;/a&gt; is defined as   the cell or group of cells from which spore mother cells develops  &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The megasporocyte is the cell(or the tissue) which &lt;strong&gt;directly&lt;/strong&gt; produces&#xA;   the megaspores.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In most angiosperm, the nucellar tissue within the ovule first differentiates into a single archesporial cell, the ancestor of the Megaspore Mother cell(MMC). In certain species, this archesporial cell may itself act as the MMC undergoing meiosis to produce the megaspores. in such cases, the archesporial cell and the megasporocyte (another name for MMC) is the same.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But in some species, the archesporial cell first undergoes a periclinic division producing two cells which further produce the parietal layer (covering of the megaspore) and a single sporogenous cell. This cell acts as the MMC, and is the megasporocyte.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus the archesporial cell may or may not be the same as the megasporocyte. It could be the ancestor of megasporocyte.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2013-12-31T17:39:24.910" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14228" PostTypeId="1" CreationDate="2013-12-31T18:16:33.837" Score="2" ViewCount="165" Body="&lt;p&gt;Why does the human  ovum prefers to be arrested at metaphase 2 of meosis before fertilization? What is the possible advantage of this process??Please help me with it.&lt;/p&gt;&#xA;" OwnerUserId="5292" LastActivityDate="2018-10-14T14:24:30.190" Title="Why does the ovum prefers to be arrested at metaphase 2 of meosis before fertilization? What is the possible advantage of this process?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;reproduction&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14229" PostTypeId="2" ParentId="14223" CreationDate="2013-12-31T18:19:28.383" Score="4" Body="&lt;p&gt;From &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/1522-239X%28200208%29113:3/4%3C224%3a%3aAID-FEDR224%3E3.0.CO;2-V/abstract&quot; rel=&quot;nofollow&quot;&gt;Basconsuelo et al 2002&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The zone of the plant axis where the arrangement of vascular systems changes from root- to stem-structure is often called “transition region”&quot; (see also the refs they cite).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea behind it is that the organization of the vascular tissues is radically different in the root in comparison to the stem, such that the switch cannot occur in one point. This transition region (in general case) crosses the air-ground interface.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2013-12-31T18:19:28.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14230" PostTypeId="1" CreationDate="2014-01-01T02:00:42.780" Score="3" ViewCount="5465" Body="&lt;p&gt;I had surgery when woke up I felt like I only had 20% energy &amp;amp; felt extremely tired. Is this a common sensation? Why do people feel so tired after surgery?&lt;/p&gt;&#xA;" OwnerUserId="4989" LastEditorUserId="1590" LastEditDate="2014-01-01T10:01:30.620" LastActivityDate="2014-09-05T02:54:00.547" Title="Why are people tired after surgery?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14231" PostTypeId="1" CreationDate="2014-01-01T09:26:43.517" Score="8" ViewCount="423" Body="&lt;p&gt;My book reads,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The fetus signals that it is mature by secreting certain hormones&#xA;  that diffuse across the placenta into mother's blood and cause the&#xA;  secretion of oxytocin from her posterior pituitary.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would like to know what exactly are these hormones and their sites of production in the foetus, as well as their mode of action.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I was wondering whether these hormones are released even during premature births? I doubt this because what I understand from the lines of my book is that it has to be a signal by the foetus that it is 'fully developed', whereas if it is not secreted it would not stimulate the secretion of oxytocin. This is creating a bit of confusion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A detailed explanation would be a great help&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you&lt;/p&gt;&#xA;" OwnerUserId="4947" LastEditorUserId="4947" LastEditDate="2014-01-06T02:39:48.887" LastActivityDate="2015-01-05T18:46:06.903" Title="Neuroendocrinal mechanism of parturition" Tags="&lt;neuroscience&gt;&lt;reproduction&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14232" PostTypeId="1" CreationDate="2014-01-01T12:20:04.007" Score="2" ViewCount="208" Body="&lt;p&gt;Tissue culture means that cells are propagated and multiplied under controlled conditions. Suppose the following situations:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a) A seed being is embedded in an &lt;em&gt;Agar&lt;/em&gt; medium and germinated under controlled conditions.&lt;br&gt;&#xA;  b) An individual cell is extracted from a parent plant and embedded in a medium, resulting in the formation of a callus (germination). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Are these both examples of tissue culture? Both situations seem to fall under my definition of tissue culture.&lt;/p&gt;&#xA;" OwnerUserId="5287" LastEditorUserId="9943" LastEditDate="2015-01-23T01:27:29.283" LastActivityDate="2015-01-23T01:27:29.283" Title="Plant tissue culture" Tags="&lt;botany&gt;&lt;cell-culture&gt;&lt;tissue&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ClosedDate="2014-12-08T02:38:28.290" ContentLicense="CC BY-SA 3.0" />
  <row Id="14234" PostTypeId="2" ParentId="14148" CreationDate="2014-01-01T17:28:11.860" Score="7" Body="&lt;p&gt;One of the many advantage of an all-or-none system is that resources can be conserved for timing events that require synchronized collaboration between many cells (like locomotion).  Binary behavior may also partially be a side effect of speed and efficient long-distance information transfer (which is one of the great advantages of neurons as cells in the first place).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It should be noted, however, that neurons aren't universally binary.  It is more accurate to say that neurons have binary properties that allow neurons to behave in a binary manner (but not all neurons do).  On top of that, many continuous (i.e. non-binary) processes underlie the neuron's excitability threshold.&lt;/p&gt;&#xA;" OwnerUserId="1853" LastActivityDate="2014-01-01T17:28:11.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14236" PostTypeId="2" ParentId="3807" CreationDate="2014-01-01T18:37:29.597" Score="2" Body="&lt;p&gt;Being a keen student of game theory and behavioural sciences one reason that comes to my mind is for the opposite wiring of brain hemispheres might be that &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;if right hemisphere controlled the right side and left hemisphere controlled the left side than cross hemisphere links and activity would be hard to achieve so the most efficient way of increasing cross hemisphere communication, links and activity with the least stress on physical resources is the opposite hemisphere wiring.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The second view that also compliments this cross arrangement might be the underlying law of increase in complexity and entropy (second law of thermodynamics), which is embedded in the universe from its births, dictates an increase in complexity hence cross wiring also achieves this underlying goal of increasing complexity because if you think about it straight wiring would have been too simple for such a complex structure as the brain.       &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5296" LastEditorUserId="9943" LastEditDate="2016-02-26T23:39:17.683" LastActivityDate="2016-02-26T23:39:17.683" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14237" PostTypeId="2" ParentId="14140" CreationDate="2014-01-02T02:11:55.080" Score="3" Body="&lt;p&gt;Just a few direct ways can figure out whether Elisa Kits are authentic or not.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Proposing to visit their factory. Generally bait company does not agree with it.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Complete range of kits. If a company has every and each ELISA Kit, it is usually fake. Unless they are very large  and professional companies, such as abcam, cellsignal, sigma, sabbiotech and so on.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;See the price. If prices are ridiculously low, but in the name of large companies such as import R&amp;amp;D raw materials packaging. This ridiculously low price can't even afford the raw materials, which company will sell at a loss?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5248" LastEditorUserId="107" LastEditDate="2015-01-09T13:19:24.647" LastActivityDate="2015-01-09T13:19:24.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14238" PostTypeId="1" AcceptedAnswerId="30914" CreationDate="2014-01-02T03:54:53.090" Score="7" ViewCount="849" Body="&lt;p&gt;In relation to mechanoreceptors (e.g. pacinian corpuscles), what stops a constant stimulus from producing action potentials? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that adaption is used to filter out stimuli that aren't changing, but what are the cellular mechanisms going on within the neurone that drive this process?  &lt;/p&gt;&#xA;" OwnerUserId="3382" LastEditorUserId="9943" LastEditDate="2015-03-30T23:09:56.010" LastActivityDate="2015-07-08T14:14:22.910" Title="What features cause mechano sensory adaptation?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14239" PostTypeId="2" ParentId="861" CreationDate="2014-01-02T10:31:26.973" Score="1" Body="&lt;p&gt;If your aim is to isolate the two haplotypes (chromosomes) maybe you should try flow cytometry. You might read this paper &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21181533&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/21181533&lt;/a&gt; by Dolezel which is leader in the field, at least for plant chromosomes. I'm pretty sure that the applicability of the method depends on the physical properties of the chromosomes you have (especially their size distribution).&lt;/p&gt;&#xA;" OwnerUserId="5297" LastActivityDate="2014-01-02T10:31:26.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14240" PostTypeId="2" ParentId="11371" CreationDate="2014-01-02T11:56:08.143" Score="1" Body="&lt;p&gt;Transposition may occur at any given time in life, and in any cell. There are several cases known where transposition interests somatic cells (give a look &lt;a href=&quot;http://www.biomedcentral.com/1741-7007/9/62/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for reference). However, the frequency of transposition events is low, and the difference in amount of DNA between different cells in an individual is low. When you reason at the level of different individuals, however, the proportion of genome affected by transposable elements may be relatively high (give a look &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17300983&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for a reference)&lt;/p&gt;&#xA;" OwnerUserId="5297" LastEditorUserId="3776" LastEditDate="2014-01-05T09:46:29.413" LastActivityDate="2014-01-05T09:46:29.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14241" PostTypeId="2" ParentId="862" CreationDate="2014-01-02T12:30:17.730" Score="0" Body="&lt;p&gt;Q1) What are the molecular and biochemical limitations to our current sequencing technologies?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A1) AFAIK: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Illumina has hard time producing long reads (although now miseq can generate reads that are 300bp and that can be paired, the so called paired end 2X300) because after a certain number of bases that are synthesized and recorded on camera (Illumina is sequencing by synthesis, basically you add bases and measure fluorescence at each cycle), i.e. after a certain number of &quot;cycles&quot; you can lose syncro, and the quality of bases decreases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PacBio can generate very long molecules, but they still have big problems with reliability of the reading of the bases (I don't know what's the problem here)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Q2) Why don't we already have long, error-free reads with high throughput?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A2) Because it's hard to do! But we are moving towards this!&lt;/p&gt;&#xA;" OwnerUserId="5297" LastActivityDate="2014-01-02T12:30:17.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14242" PostTypeId="1" AcceptedAnswerId="14243" CreationDate="2014-01-02T15:30:41.677" Score="1" ViewCount="2804" Body="&lt;ul&gt;&#xA;&lt;li&gt;Shine-Dalgarno sequence present in the prokaryotic mRNA plays a role in initiation of translation. In eukaryotes a Shine-Dalgarno like sequence is present but does not play an important role in initiation of translation.&lt;/li&gt;&#xA;&lt;li&gt;We often try to express a eukaryotic gene in a prokaryote. For example : expressing insulin gene in E.Coli.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My question : If eukaryotes do not have the shine dalgarno sequence , then how can a eukaryotic protein be expressed in a prokaryote ? (I am especially interested in knowing about this in case of cDNA expression)&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-02T22:35:40.020" Title="Shine-Dalgarno sequence and expressing proteins" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14243" PostTypeId="2" ParentId="14242" CreationDate="2014-01-02T15:56:14.793" Score="1" Body="&lt;p&gt;Eukaryotes have an analogous sequence called the Kozak sequence. cDNA is easily expressed in prokaryotes by substitution of the Kozak sequence for the Shine-Dalgarno sequence, using standard molecular biology techniques. A caveat is that not all eukaryotic protein will be properly expressed in bacteria because of they lack the ability to carry out post-translational modifications that would occur in a eukaryotic Golgi apparatus (e.g., glycosylation). Insulin is a special case because it is a small, unmodified peptides.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="948" LastEditDate="2014-01-02T22:35:40.020" LastActivityDate="2014-01-02T22:35:40.020" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14244" PostTypeId="2" ParentId="9085" CreationDate="2014-01-02T20:00:08.317" Score="0" Body="&lt;p&gt;ID addresses an obvious question which nearly everyone considers very strongly at some time. Those who don't choose to believe in God will often argue that it is a non-issue. But is it a non-issue because they are so obviously right that others have no right to voice their opinion, or because it doesn't matter? The former is a very childish view, and certainly isn't very helpful if the goal is to convince others of the &quot;correct&quot; view. And if it simply doesn't matter to Atheists, then surely we can all recognize that it matters quite a lot to others. I'm not suggesting that theists simply be allowed to rewrite the curriculum (which some have attempted), but this is a question which costs more time and energy to ignore than to address. And we have a lot to learn from each other in the process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many people, as they study evolution, very naturally begin to conclude that life could have, and therefore must have, emerged entirely by accident. This is not so different from observing that autism diagnosis has been on the rise since about the same time a certain vaccine came into widespread use, and the fact that symptoms often set in shortly after said vaccine has been given, and concluding that increased cases of autism could have been, and therefore must have been, caused by the vaccine. There is an appearance of a causal relationship, but the conclusion does not exactly follow from the evidence. In the case of the vaccine suspicions, I'm grateful that they have been solidly proved false now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the true origin of life, many of us think we know the answer. Be that as it may be, this answer is not delivered to us through the study of evolutionary biology. Anyone who tells you that science has &lt;em&gt;proved&lt;/em&gt; that we did in fact evolve without any external manipulation into what we are today, or that life emerged completely by chance, is misinterpreting the facts (or more likely, believing a rumor they heard). Anyone who tells you that science has proved the opposite, that life could not have emerged by chance, is likewise not following the logic correctly (or more likely, favors different rumors). I think that it would be a healthy exercise of critical thinking to open up this kind of discussion in a high school biology classroom, consistently reinforcing the fact that none of it on either side of the argument offers any conclusive evidence on the actual true origin of life. People who feel passionately either way on this must cringe a little at this suggestion, perhaps comparing it to the way Fox News feigns a &quot;fair and balanced&quot; presentation by presenting the plain and obvious truth on equal footing with an extremist view. But which is the extremist view on this issue? It depends on where you stand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biggest problem I foresee is that most of the instructors are so strongly biased one way or another, that they would have a hard time honestly mediating such a discussion. But, frankly, this is already the case, so I would argue that it is better to formalize this as a critical thinking exercise in the curriculum. It probably won't open anyone to new thinking on the origins of life, but hopefully, it will help them resist the next vaccine scare. And it will help them to distinguish scientific proof from speculation or belief. For many religious students, this will allow them to digest the rest of the material without feeling like it is an attack on their sacred beliefs.&lt;/p&gt;&#xA;" OwnerUserId="5018" LastEditorUserId="5018" LastEditDate="2014-03-28T15:41:10.637" LastActivityDate="2014-03-28T15:41:10.637" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14245" PostTypeId="1" CreationDate="2014-01-02T22:32:02.543" Score="4" ViewCount="142" Body="&lt;p&gt;&lt;strong&gt;Note:&lt;/strong&gt; I thought the Biology stack exchange would suit this question better than the Fitness stack exchange. Please let me know in the comments if this is not suitable here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested in tracking my resting heart rate as it decreases with aerobic training.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the moment I take it immediately after I have woken up before I get up out of bed.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the correct medical procedure(s) for taking a resting heart rate?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm aware a standardized procedure is important but what about:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Body position: Should I be sitting or lying down?&lt;/li&gt;&#xA;&lt;li&gt;Heart rate: Should I take the lowest value or an average HR?&lt;/li&gt;&#xA;&lt;li&gt;What duration should I take it for? &lt;/li&gt;&#xA;&lt;li&gt;How relaxed should I be?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In an academic situation how would one reliably take resting a heart rate?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please include answers that can be referenced to scientific or medical literature.&lt;/p&gt;&#xA;" OwnerUserId="5299" LastEditorUserId="5299" LastEditDate="2014-01-03T03:13:45.810" LastActivityDate="2014-07-06T07:36:40.473" Title="What is the correct medical procedure(s) for taking a resting heart rate?" Tags="&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14248" PostTypeId="1" CreationDate="2014-01-03T07:04:20.223" Score="2" ViewCount="67" Body="&lt;p&gt;I have recently done a phenological study using remote sensing techniques. Now I need to validate my results and my methods, that is, to determine if the phenology estimated from remote sensing is suitable to describe phenological events or not. However, I don't have empirical phenological data from the ground to do validation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any other ways to validate the phenological signal from remote sensing, that do not require empirical data from the ground? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank a lot &lt;/p&gt;&#xA;" OwnerUserId="3530" LastEditorUserId="3952" LastEditDate="2015-05-24T16:18:54.613" LastActivityDate="2015-05-24T16:18:54.613" Title="About validation process of phenological study" Tags="&lt;plant-physiology&gt;&lt;statistics&gt;&lt;life-history&gt;&lt;phenology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14249" PostTypeId="1" CreationDate="2014-01-03T07:16:29.397" Score="4" ViewCount="2554" Body="&lt;p&gt;I am aware about some basics of saltatory conduction of nerve impulses. I know that the nerve impulses (ion flow and the depolarization) are transferred from node to node in myelinated nerve fibers. In non-myelinated fibers, the ion flow and depolarization are repeated along the entire length of the axon. Thus the saltatory conduction is faster.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Why is it so that myelinated nerve fibers require less energy of activation then the non-myelinated ones?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, my book says that a rise in temperature accelerates the conduction of nerve impulses. I would like to know the reason for this.&lt;/p&gt;&#xA;" OwnerDisplayName="user3800" LastEditorUserId="9943" LastEditorDisplayName="user3800" LastEditDate="2015-09-28T11:08:22.810" LastActivityDate="2015-09-28T12:08:40.657" Title="Saltatory conduction of nerve impulses" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14250" PostTypeId="1" AcceptedAnswerId="14277" CreationDate="2014-01-03T08:30:40.650" Score="2" ViewCount="80" Body="&lt;p&gt;I read in Tortora and Derrickson that :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Enkephelins are 200 times powerful than morphine in their analgesic effects.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I wonder how exactly researchers arrive at a number (like 200 here). I also want to know what exactly is meant by &quot;powerful&quot;. &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-05T15:07:54.380" Title="How is it decided that one drug is better than others by X times?" Tags="&lt;biochemistry&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14251" PostTypeId="1" CreationDate="2014-01-03T12:12:38.053" Score="5" ViewCount="179" Body="&lt;p&gt;I've read about ecosystem services and their possible valuation - statements like &quot;honeybee pollination service in the US is worth 1.6 billion dollars&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is data available on how this would affect the cost a consumer pays for a given product? For example if the humans must do all pollination of fruits themselves, how would that affect the retail cost of these fruit?&lt;/p&gt;&#xA;" OwnerUserId="5304" LastEditorUserId="36209" LastEditDate="2017-10-25T09:53:09.160" LastActivityDate="2017-10-25T09:53:09.160" Title="How much cost would artificial pollination add to common products (fruits etc.)?" Tags="&lt;botany&gt;&lt;ecology&gt;&lt;environment&gt;&lt;ecosystem&gt;&lt;pollination&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14252" PostTypeId="1" AcceptedAnswerId="14253" CreationDate="2014-01-03T15:24:55.567" Score="1" ViewCount="332" Body="&lt;p&gt;What is the type of data you get when analyzing dna of a person? If you want to store them in a database, what type of field you will need (text,number,hex)? And what should be it's length?&lt;/p&gt;&#xA;" OwnerUserId="5306" LastEditorUserId="3632" LastEditDate="2014-01-03T17:35:28.907" LastActivityDate="2014-01-03T17:38:55.470" Title="What is the datatype of dna sample?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;genomes&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14253" PostTypeId="2" ParentId="14252" CreationDate="2014-01-03T15:50:58.840" Score="4" Body="&lt;p&gt;Assuming that you are looking at data used to describe the differences for a new individual, as opposed to a human reference genome build:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;http://en.wikipedia.org/wiki/FASTQ_format&quot; rel=&quot;nofollow&quot;&gt;fastq&lt;/a&gt; file is the typical format of data from a sequencer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would require a text field of some sort as they can be quite large, even for single reads.  If you had a specific sequencer in mind with very short read you might use a fixed length field for the data column, but its probably not worth it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After the data is processed, then the data is currently usually exchanged in the form of Variant Call Format files (a &lt;a href=&quot;http://www.1000genomes.org/node/101&quot; rel=&quot;nofollow&quot;&gt;vcf file&lt;/a&gt;) which only documents differences versus a reference genome build.  This fits nicely into an SQL table with relatively small columns.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-01-03T17:38:55.470" LastActivityDate="2014-01-03T17:38:55.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14254" PostTypeId="2" ParentId="14252" CreationDate="2014-01-03T16:01:44.877" Score="0" Body="&lt;p&gt;It will be a simple string of text. The length, however, is completely arbitrary and will depend on the source of your sequence data. Anything from 1 to several billion can be a valid sequence length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We could help more if you explained where the data is coming from.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-01-03T16:01:44.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14255" PostTypeId="1" CreationDate="2014-01-03T16:23:53.310" Score="2" ViewCount="339" Body="&lt;p&gt;First, my exposure to biology is high-school. Should the answer to the question be obvious - please take a moment to laugh, and then point me in the right direction.&#xA;A quick google search (or perhaps my search parameters were wrong) didn't give me what I seek. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Animals usually exhibit some form of &lt;a href=&quot;http://en.wikipedia.org/wiki/Reflex_arc&quot; rel=&quot;nofollow&quot;&gt;reflex&lt;/a&gt;. What I'm curious about is this - &#xA;&lt;strong&gt;Do all animals exhibit comparable reflex velocity?&lt;/strong&gt; Here I use 'reflex velocity' to mean the amount of time elapsed between stimulus, and initiation of the reflex action.&lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2014-01-08T23:22:33.820" Title="Do all animals exhibit comparable reflex velocity?" Tags="&lt;reflexes&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14257" PostTypeId="2" ParentId="14252" CreationDate="2014-01-03T17:17:26.530" Score="0" Body="&lt;p&gt;Realistically, you aren't going to store the genome as one long string of text.  Depending on how you do the sequencing, you probably won't be able to resolve repetitive regions anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is much more realistic is you will store all the differences you are confident of between the sample and a reference sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you use some kind of genotyping chip, you'd store the genotypes at each locus.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-01-03T17:17:26.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14258" PostTypeId="1" CreationDate="2014-01-03T20:45:15.507" Score="4" ViewCount="94" Body="&lt;p&gt;Are waves created by the LFP on the surfaces of neurons cell bodies? Since the cells have a resting potential, do these waves create harmonic oscillation of the membranes at particular frequencies?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there studies available that look at electrical potential waves on the cell surfaces? I think that membranes should be sensitive to the LFP since they maintain a charge.&lt;/p&gt;&#xA;" OwnerUserId="5314" LastActivityDate="2014-01-05T00:30:03.810" Title="Do local field potentials (LFP) create waves on the surfaces of nerve cells?" Tags="&lt;neuroscience&gt;&lt;biophysics&gt;&lt;neuroanatomy&gt;&lt;electrophysiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14259" PostTypeId="2" ParentId="7190" CreationDate="2014-01-04T00:05:13.073" Score="2" Body="&lt;p&gt;Rather than doing it all from scratch, if you had your own instance of BLAST, you would make a blastable database of your e.coli sequence, and do tblastn, with your putative polymerase protein sequence as the query.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This would find the best matching sequence in the genome, and will work even if there are a fair number of differences between the protein you gave it, and what your DNA sequence actually translates to.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-01-04T00:05:13.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14261" PostTypeId="2" ParentId="14251" CreationDate="2014-01-04T01:06:51.287" Score="5" Body="&lt;p&gt;The cost would increase; either because pollination services are not provided and the supply is decreased; or because the cost to producers goes up as they must pay for artificial pollination. See the extremely detailed analysis in &lt;a href=&quot;http://nature.berkeley.edu/kremenlab/Articles/Valuing%20Pollination%20Services%20to%20Agriculture.pdf&quot; rel=&quot;nofollow&quot;&gt;Winfree et al&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;edit&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I imagine what you're actually asking for is a $ figure &quot;per apple&quot;. This depends on the location, crop, market, etc., but just for a ballpark, if I'm reading the supplementary tables in &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0003128&quot; rel=&quot;nofollow&quot;&gt;Allsop et al&lt;/a&gt; correctly, the replacement value of insect pollination to apples in the Western Cape of South Africa would represent a &lt;strong&gt;6%-25% increase in production cost&lt;/strong&gt; (and, if the producers pass that along to the consumers, an equal increase in the cost to consumer).&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0003128&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Allsopp MH, de Lange WJ, Veldtman R&lt;/strong&gt;. 2008. Valuing insect pollination services with cost of replacement. PLoS ONE 3: e3128–e3128.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.ecolecon.2011.08.001&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Winfree, Gross, Kremen&lt;/strong&gt;. 2011. Valuing pollination services to agriculture. Ecol Econ 71: 9–9.&lt;/a&gt; [behind paywall, but &lt;a href=&quot;http://nature.berkeley.edu/kremenlab/Articles/Valuing%20Pollination%20Services%20to%20Agriculture.pdf&quot; rel=&quot;nofollow&quot;&gt;posted free here&lt;/a&gt;]&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-01-07T14:32:38.873" LastActivityDate="2014-01-07T14:32:38.873" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14263" PostTypeId="1" CreationDate="2014-01-04T01:49:08.287" Score="1" ViewCount="296" Body="&lt;p&gt;How much less dangerous is breathing smoke from burning wood and coal compare to smoking tobacco?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:  Sorry.  I should have made the question clearer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this were an experiment, it would be set up like this.  Subject 1 is a control, so he is exposed to smoke from burning tobacco for a year.  Subject 2 is exposed to smoke from burning maple leaves for a year.  Subject 3 is exposed to smoke from burning pine needles for a year.  The other subjects continue in this fashion, being exposed to smoke from many different sources.  The rats are examined for lung cancer through this year and for the remainder of their lives.  What would the expect results of this experiment be?&lt;/p&gt;&#xA;" OwnerUserId="5149" LastEditorUserId="5149" LastEditDate="2014-01-04T19:37:29.307" LastActivityDate="2014-01-04T19:37:29.307" Title="Effects of smoking tobacco compared to inhaling other smoke" Tags="&lt;respiration&gt;&lt;smoking&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14264" PostTypeId="1" AcceptedAnswerId="14288" CreationDate="2014-01-04T04:32:27.927" Score="3" ViewCount="359" Body="&lt;p&gt;Embryonic gene activation is a process by which the embryo begins to transcribe its newly formed genome.As the embryonic gene activation occurs during early stages the paternal genome may not have any influence at that stage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now,&#xA;My question is why does only the maternal genome play a role in embryonic gene activation?&#xA;Does paternal genome have a role in prior/post embryonic genome activation?&lt;/p&gt;&#xA;" OwnerDisplayName="user3800" LastEditorUserId="3340" LastEditDate="2014-05-01T10:23:16.063" LastActivityDate="2014-05-01T10:23:16.063" Title="Activation Of Embryonic Genome" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14265" PostTypeId="2" ParentId="14258" CreationDate="2014-01-04T15:24:48.310" Score="2" Body="&lt;p&gt;A LFP can be measured at any point in space and is just the sum of all the fields generated by nearby charges.  Conventionally, it's assumed to be some distance from a cluster of neurons, but you technically could measure the LFP near the external surface of a neuron (but that would bias your signal towards the reading of that one neuron).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;LFP's are relatively weak, but have some small influence on the neighboring cells:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biomedcentral.com/1471-2202/10/S1/P291&quot; rel=&quot;nofollow&quot;&gt;Modeling the coupling of single neuron activity to local field potentials&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1853" LastEditorUserId="1853" LastEditDate="2014-01-05T00:30:03.810" LastActivityDate="2014-01-05T00:30:03.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14266" PostTypeId="2" ParentId="14263" CreationDate="2014-01-04T15:33:24.093" Score="1" Body="&lt;p&gt;(at an epidemiological scale)&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.who.int/mediacentre/factsheets/fs339/en/&quot; rel=&quot;nofollow noreferrer&quot;&gt;WHO on tobacco&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;more than one billion smokers worldwide...&lt;/p&gt;&#xA;&lt;p&gt;Tobacco kills nearly 6 million people each year.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.who.int/mediacentre/factsheets/fs292/en/&quot; rel=&quot;nofollow noreferrer&quot;&gt;WHO on indoor air pollution&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Around 3 billion people still cook and heat their homes using solid&#xA;fuels in open fires and leaky stoves. About 2.7 billion burn biomass&#xA;(wood, animal dung, crop waste) and a further 0.4 billion use coal...&lt;/p&gt;&#xA;&lt;p&gt;Nearly 2 million people a year die prematurely from illness&#xA;attributable to indoor air pollution due to solid fuel use.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-01-04T15:33:24.093" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14267" PostTypeId="1" AcceptedAnswerId="14276" CreationDate="2014-01-04T16:17:56.223" Score="2" ViewCount="81" Body="&lt;p&gt;There is &lt;a href=&quot;http://en.wikipedia.org/wiki/Epistasis&quot; rel=&quot;nofollow&quot;&gt;epistasis&lt;/a&gt; when the effect on the phenotype of one gene is influenced by one or more other genes (called modifiers). Is there a similar concept when the effect on the phenotype of one site within a gene is influenced by one or more other sites within the same gene?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example: Think about an &lt;a href=&quot;http://en.wikipedia.org/wiki/Opsin&quot; rel=&quot;nofollow&quot;&gt;opsin&lt;/a&gt; (a light sensitive protein) that gets activited when hit by a wavelength of, say 500nm.  If the mutation &lt;code&gt;A124S&lt;/code&gt; (at position &lt;code&gt;124&lt;/code&gt; the aminoacid &lt;code&gt;A&lt;/code&gt; is replaced by the amino acid &lt;code&gt;S&lt;/code&gt;) exists, then the protein is activated when it gets hit by a wavelength of 560nm but this shift occurs only if there is a &lt;code&gt;V&lt;/code&gt; (instead of a &lt;code&gt;I&lt;/code&gt;) at position &lt;code&gt;95&lt;/code&gt;. Hope you get the idea! Are there specific words to describe such phenomena?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-01-05T09:20:35.017" LastActivityDate="2014-01-05T12:58:41.137" Title="Epistasis when interacting loci are codons within a single gene" Tags="&lt;proteins&gt;&lt;gene-expression&gt;&lt;genetics&gt;&lt;protein-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14268" PostTypeId="1" CreationDate="2014-01-04T20:02:44.883" Score="2" ViewCount="23086" Body="&lt;p&gt;Prothrombin time test is used for the monitoring of warfarin but not heparin. Why is this used for warfarin monitoring and why is it not used for heparin monitoring?&lt;/p&gt;&#xA;" OwnerUserId="1765" LastActivityDate="2020-03-21T20:32:02.647" Title="Why is prothrombin time test not used for heparin" Tags="&lt;hematology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14270" PostTypeId="2" ParentId="14268" CreationDate="2014-01-04T20:43:12.113" Score="1" Body="&lt;p&gt;Thats because the mechanism of action is different between warfarin and heparin.&#xA;Warfarin inhibits the formation of prothrombin (also known as factor II) by inhibiting the metabolization of vitamin K (for extensive details have a look at the Wikipedia article about &lt;a href=&quot;http://en.wikipedia.org/wiki/Warfarin&quot; rel=&quot;nofollow&quot;&gt;Warfarin&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heparin inhibits the blood coagulation by binding to antithrombin III which functions as a inactivator of active clotting factors as factors V, IX, X, XI and XII. It also binds calcium which is important for the blood coagulation. For more details see the Wikipedia under &lt;a href=&quot;http://en.wikipedia.org/wiki/Heparin&quot; rel=&quot;nofollow&quot;&gt;Heparin&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore Heparin interferes with the formation of Thrombin and the test does not work. A nice image of the coagulation cascade can be found &lt;a href=&quot;http://practical-haemostasis.com/Screening%20Tests/tt.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, which also shows the points where Heparin interferes. The test can be done with Batroxobin, see &lt;a href=&quot;http://en.wikipedia.org/wiki/Thrombin_time&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2016-02-18T10:02:04.533" LastActivityDate="2016-02-18T10:02:04.533" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14271" PostTypeId="1" CreationDate="2014-01-04T20:49:23.377" Score="1" ViewCount="109" Body="&lt;p&gt;What is the very first abiogenetic piece of reproducing life (small piece of RNA + ribosome that randomly occurred?) hypothesized to have used as an energy source? I'd be interested in sources to what experts in abiogenesis research have hypothesized on this subject, if any such researchers have spoken on the question.&lt;/p&gt;&#xA;" OwnerUserId="263" LastActivityDate="2014-01-04T20:49:23.377" Title="What are current abiogenesis hypotheses for first food source?" Tags="&lt;microbiology&gt;&lt;food&gt;&lt;abiogenesis&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14272" PostTypeId="2" ParentId="14187" CreationDate="2014-01-04T21:47:46.283" Score="1" Body="&lt;p&gt;The wikipedia page &lt;a href=&quot;http://en.wikipedia.org/wiki/Alternation_of_generations&quot; rel=&quot;nofollow noreferrer&quot;&gt;Alternation of Generations&lt;/a&gt; actually has a pretty sophisticated discussion of this issue, and discusses the fact that plants can and do fall at a lot of different places on a gradient of one generation being dominant over another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the root of this complexity is that this is an issue of terminology, and is connected to your concept of &quot;what is an organism&quot;, which is a complex issue in and of itself (see &lt;a href=&quot;https://biology.stackexchange.com/a/9148/3952&quot;&gt;this answer&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite this, I think that you can still usefully discuss use a number of criteria which argue for a generation being more or less dominant, including generation time, but also:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) &lt;strong&gt;size&lt;/strong&gt; (as you say in your question)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) &lt;strong&gt;morphological complexity&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) &lt;strong&gt;ability to independently undergo &quot;life&quot; processes&lt;/strong&gt; like photosynthesis and mitosis&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) &lt;strong&gt;conspicuousness/salience to humans&lt;/strong&gt; (as we're the ones making up these categories)&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-01-04T21:47:46.283" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14273" PostTypeId="1" CreationDate="2014-01-05T01:51:25.200" Score="0" ViewCount="557" Body="&lt;p&gt;Can anyone please tell me where is exactly the stomach in this image? &#xA;&lt;img src=&quot;https://i.stack.imgur.com/Ofu5t.jpg&quot; alt=&quot;Stomach_Sagittal&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a sagittal section from the University of Michigan Visible Human Browsers.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/A0qSW.png&quot; alt=&quot;image2&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Cn3OF.png&quot; alt=&quot;image3&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="5321" LastEditorUserId="5321" LastEditDate="2014-01-05T15:00:11.920" LastActivityDate="2014-10-05T02:38:02.903" Title="Stomach sagittal section" Tags="&lt;human-anatomy&gt;&lt;anatomy&gt;&lt;stomach&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14275" PostTypeId="1" CreationDate="2014-01-05T09:36:26.327" Score="7" ViewCount="360" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikivet.net/Cranial_Nerves_-_Anatomy_&amp;amp;_Physiology&quot; rel=&quot;nofollow&quot;&gt;cranial nerve innervation&lt;/a&gt; is &lt;a href=&quot;http://img.docstoccdn.com/thumb/orig/104274498.png&quot; rel=&quot;nofollow&quot;&gt;highly disproportionate&lt;/a&gt;, as far as humans are concerned.  I am not sure of the advantage of being innervated by cranial nerve versus being innervated by a normal spinal nerve branches, if any. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is any advantage to be innervated by cranial nerves, &lt;strong&gt;why is there such a largely disproportionate distribution of these cranial nerves&lt;/strong&gt;?  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Only the Vagus nerve (&lt;code&gt;X&lt;/code&gt;) innervates parts other than the head of the&#xA;  animal. While there are 3 motor nerves just for the 6 eyeball muscles&#xA;  and the ciliary muscles (&lt;code&gt;III,IV,VI&lt;/code&gt;), there is only one mixed nerve&#xA;  (&lt;code&gt;X&lt;/code&gt;) innervating heart, gastro-intestinal tract and the respiratory&#xA;  apparatus and all smooth muscles therein. While there are three nerves&#xA;  for gustatory receptors, (&lt;code&gt;VII,IX,X&lt;/code&gt;), one for retina (&lt;code&gt;II&lt;/code&gt;), cochlea&#xA;  and vestibule (&lt;code&gt;VIII&lt;/code&gt;) and the olfactory receptors (&lt;code&gt;I&lt;/code&gt;) each, the&#xA;  entire plethora of intero-receptors in thoracic and abdominal viscera,&#xA;  aortic arch, external auditory meatus, tympanic membrane etc are&#xA;  carried by a single nerve (&lt;code&gt;X&lt;/code&gt;). I am not sure if the disproportion is limited to the disproportionate area of innervation or even to the density of innervation in the target tissue.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Below are a few possible explanations that I came across while surfing the net, all without any strong arguments.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Is it because of the fineness of the senses in the head, i.e. the skin receptors in facial skin being higher than in the general body, providing a finer resolution of tactile reception? The special senses (vision, hearing, smelling and tasting) are also very fine in their resolution and might require more concentrated innervation and direct interpretation by the brain. But then the fingers and feet also have a high density of skin receptors, and the tactile sense can also be very fine (owing to several different kind of receptors) requiring dense innervation? Certain body movements (especially of hand) are very fine and detailed, requiring a very dense and co-ordinated motor neuron framework.&lt;/li&gt;&#xA;&lt;li&gt;Is it because the cranial nerves, owing to some developmental restraint or functional trade-off, can only innervate areas close to its place of origin effectively? This might explain why 11 pairs of nerves innervate only the head region and only 1 pair innervates the remaining body. I have no idea about the validity and the reason of this claim.&lt;/li&gt;&#xA;&lt;li&gt;Could it just be a random evolutionary outcome, there being absolutely no benefit of cranial innervation leading to random drift in the innervation patterns?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2014-03-11T02:42:11.393" LastActivityDate="2014-07-09T05:08:40.293" Title="Disproportion in cranial nerve innervation?" Tags="&lt;evolution&gt;&lt;neuroscience&gt;&lt;physiology&gt;&lt;neuroanatomy&gt;&lt;cranial-nerves&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14276" PostTypeId="2" ParentId="14267" CreationDate="2014-01-05T12:58:41.137" Score="1" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Epistasis#Epistasis_within_genes&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; article on epistasis has a section on epistasis &lt;em&gt;within&lt;/em&gt; genes, which it terms &lt;strong&gt;intragenic complementation&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Just as mutations in two separate genes can be non-additive if those genes interact, mutations in two codons within a gene can be non-additive. In genetics this is sometimes called intragenic complementation when one deleterious mutation can be compensated for by a second mutation within that gene. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It appears that many interesting examples of this phenomenon occur when the protein forms multimeric complexes. A multimer consisting of monomers with different mutations may function where a homogenous multimer of monomers of only one of the mutations might be inactive. See &lt;a href=&quot;http://www.pnas.org/content/94/17/9063.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Turner et al., (1997) &lt;em&gt;PNAS&lt;/em&gt; 94:9063-9068&lt;/a&gt;. The Wikipedia article mentions some examples of this under the term &lt;strong&gt;interallelic complementation&lt;/strong&gt; or &lt;strong&gt;heterozygotic epistasis&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This reminded me of the phenomenon of protein coevolution that is currently being used to try to leverage evolutionary information to solve protein structures. When the homologous sequences of a protein are known in many different species, then a reasonable assumption is that mutations in protein residues that are in close spatial proximity will correlate, e.g. if a lysine is switched to an glutamate, then other nearby residues may mutate to accommodate the change in ambient electric charge. For more information on this effect, two very interesting papers are &lt;a href=&quot;http://www.cell.com/retrieve/pii/S0092867412005090&quot; rel=&quot;nofollow&quot;&gt;Hopf TA, Colwell LJ et al., (2012) &lt;em&gt;Cell&lt;/em&gt; 149(7):1607-1621&lt;/a&gt;, where the sequences of a family of membrane proteins are used to predict their structure, and &lt;a href=&quot;http://laublab.mit.edu/wp-content/uploads/2011/03/2008laub.pdf&quot; rel=&quot;nofollow&quot;&gt;Skerker et al (2008) &lt;em&gt;Cell&lt;/em&gt; 133:1043-1054&lt;/a&gt;, where the covariation between residues in a complex of two proteins is used to re-wire the specificity of one protein for another.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2014-01-05T12:58:41.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14277" PostTypeId="2" ParentId="14250" CreationDate="2014-01-05T14:31:22.573" Score="4" Body="&lt;p&gt;In general, there is no universal way to quantify the effect of a drug; the quantification procedure depends crucially on what effect the drug is supposed to have. For example, if the drug is supposed to decrease blood thickness, then a measure of the drug's efficacy is a measurement of change in blood thickness upon application of a given concentration of drug. So I'll focus on the case of analgesics, since that's the context of your original question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While I can't say for sure how this particular quantity was measured, it appears that the effect of analgesics like morphine or enkephalins is measured by direct measurements of pain under different administered concentrations of drug. This can be done in animal or human studies. In animal studies, varying concentrations of a drug are administered, and then the response of the animal to different pain stimuli is recorded. One common example of a pain measurement is a hot plate, where the animal's foot is placed on a hot plate and the time until it tries to remove its foot is measured. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These studies can also be done in humans. In this study &lt;a href=&quot;http://journals.lww.com/anesthesiology/pages/articleviewer.aspx?year=2001&amp;amp;issue=07000&amp;amp;article=00009&amp;amp;type=abstract&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt;, the effect of a particular drug was measured by different tests, including &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;electrical shocks of increasing intensity; maximum intensity of pain subject wanted to endure was measured.&lt;/li&gt;&#xA;&lt;li&gt;pressure applied to the finger: maximum pressure subject wanted to endure was measured.&lt;/li&gt;&#xA;&lt;li&gt;heat applied to the forearm (maximum tolerable temperature measured)&lt;/li&gt;&#xA;&lt;li&gt;dominant hand immersed in ice water for up to 2 minutes. Subjects continually reported level of pain on a 0-10 scale, sum of all pain levels over course of experiment was used as measurement of total pain endured.&lt;/li&gt;&#xA;&lt;li&gt;Tourniquet applied to cut off blood supply for up to 2 minutes, pain measured in same way as above.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If these pain measurements are recorded when the patient has different levels of the drug in their system, then comparing drug effects amounts to identifying the concentration of drug at which a particular pain response is achieved. In other words&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Drug A is X times more &lt;em&gt;powerful&lt;/em&gt; than drug B if drug A causes the same effect on pain response (measured in some way like the ones measured before) as drug B at X times lower concentration.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As a side note, the initial thought I had was that this might be measured by quantifying the receptor-ligand affinity of the various drugs for the pain receptors (opioid receptors) in the nervous system. In that situation, saying that drug A was 200 times more powerful than drug B would amount to saying that A's affinity (or Kd) for a particular receptor was 200 times greater than B. Or something along those lines (see the Wikipedia article on &lt;a href=&quot;https://en.wikipedia.org/wiki/Ligand_%28biochemistry%29&quot; rel=&quot;nofollow&quot;&gt;receptor-ligand interactions&lt;/a&gt;). That would be a 'universal' way to measure drug efficacies, since a large number of drugs work by blocking certain receptors in the brain. But biology is too complicated to permit a straightforward relationship between binding affinity and perceived drug effect. At least, not yet!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References and Further Reading&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://journals.lww.com/anesthesiology/pages/articleviewer.aspx?year=2001&amp;amp;issue=07000&amp;amp;article=00009&amp;amp;type=abstract&quot; rel=&quot;nofollow&quot;&gt;(1): Luginbuhl M et al (2001). Comparison of Five Experimental Pain Tests to Measure Analgesic Effects of Alfentanil. &lt;em&gt;Anesthesiology&lt;/em&gt; 95:22-29&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1509173/?page=1&quot; rel=&quot;nofollow&quot;&gt;(2): Jackson H. (1952) The effect of analgesic drugs on the sensation of thermal pain in man. &lt;em&gt;Br. J. Pharmacol Chemother.&lt;/em&gt; 7(2): 204–214.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://pharmrev.aspetjournals.org/content/64/3/722.long&quot; rel=&quot;nofollow&quot;&gt;(3):Estrup Olesen A et al. (2012). &lt;em&gt;Pharmacological Reviews&lt;/em&gt; 64(3):722-779&lt;/a&gt; Extensive review of this subject.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2014-01-05T14:31:22.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14278" PostTypeId="1" CreationDate="2014-01-05T15:25:19.793" Score="4" ViewCount="12453" Body="&lt;p&gt;I've been reading about the complement system, as part of the human immune system. The complement system is introduced as part of the article on innate immunity on &lt;em&gt;Wikipedia&lt;/em&gt;. This classification makes obvious sense in the case of the alternative pathway, which is obviously not dependent on any specific pathogen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I'm confused about whether this is an appropriate classification for the classical pathway (and, therefore, the system writ large) since the classical pathway is activated by antigen:antibody complexes and only by certain antibody isotypes (IgG and IgM). It is, therefore, to some extent pathogen specific and it is also, clearly, activated by and dependent upon the humoral immune response (generally classed as part of adaptive immunity). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in short, is it best to classify the complement system as part of the innate immunity (and, if so, why is that?), or would it be better to restrict ourselves to the observation that it is, to a greater or lesser extent, part of both types of immunity?&lt;/p&gt;&#xA;" OwnerUserId="5263" LastEditorUserId="1306" LastEditDate="2014-01-05T16:47:38.870" LastActivityDate="2017-12-01T06:05:34.507" Title="Is the complement system a part of innate or adaptive immunity" Tags="&lt;immunology&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14279" PostTypeId="1" AcceptedAnswerId="14282" CreationDate="2014-01-05T16:39:06.080" Score="4" ViewCount="8397" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Monozygotic#Monozygotic_.28.22identical.22.29_twins&quot; rel=&quot;nofollow&quot;&gt;Twins&lt;/a&gt; could be monzygotic i.e. identical twins and dizygotic i.e. non-identical twins.Well, monozygotic twins occur when a single egg is fertilized to form a zygote which later divide into separate embryos.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, My question is &lt;strong&gt;Why does the embryo collapse splitting the progenitor cell into half?&lt;/strong&gt; &#xA;While searching for the answer I found certain theories (possibly without evidence). Following are those theories;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;An enzyme in the sperm causes them to split.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I have known only a few hyaluronidase and hydrolysing enzymes present in the sperm &lt;a href=&quot;http://en.wikipedia.org/wiki/Acrosome&quot; rel=&quot;nofollow&quot;&gt;acrosome&lt;/a&gt; which helps penetrating the ovum by lysis of Zona pellucida.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A mutation in the mother's RNA which may control embryogenesis in the first nine days.&lt;/li&gt;&#xA;&lt;li&gt;The splitting of embryo is more of a random process then genetically governed one.&lt;/li&gt;&#xA;&lt;li&gt;Genetic mutation which leads to rejection of one group of cells by the other.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerDisplayName="user3800" LastEditorUserId="1306" LastEditDate="2014-01-05T17:19:06.527" LastActivityDate="2014-01-05T17:24:21.747" Title="Causes of monozygotic twins" Tags="&lt;genetics&gt;&lt;reproduction&gt;&lt;enzymes&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14281" PostTypeId="2" ParentId="14278" CreationDate="2014-01-05T16:42:03.860" Score="5" Body="&lt;p&gt;Yes, the complement system is part of the innate immune system. It can be activated by the:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;classical pathway (activated through bound IgM and IgG molecules but&#xA;also by DNA, collagen (both are usually not available freely outside&#xA;of cells) and c-reactive protein)&lt;/li&gt;&#xA;&lt;li&gt;lectin pathway (activation by binding of mannose through the mannose&#xA;binding lectin on the cell surface)&lt;/li&gt;&#xA;&lt;li&gt;alternative pathway (activation by the constant hydrolysis of the&#xA;complement component 3 (or C3) in an antibody independent way)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My guess here would be, that the classical activation via antibodies is evolutionary younger than the other two possibilities which act more directly on bacteria and do not depend on the availability of specific (at least to some degree) antibodies. The Wikipedia article on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Complement_system&quot; rel=&quot;nofollow&quot;&gt;complement system&lt;/a&gt; is pretty extensive.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2014-01-06T15:33:19.313" LastActivityDate="2014-01-06T15:33:19.313" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14282" PostTypeId="2" ParentId="14279" CreationDate="2014-01-05T17:24:21.747" Score="4" Body="&lt;p&gt;A few possible explanations are named in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Monozygotic#Mechanism&quot; rel=&quot;nofollow&quot;&gt;Wikipedia article&lt;/a&gt; you link:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Regarding spontaneous or natural monozygotic twinning, a recent theory&#xA;  posits that monozygotic twins are formed after a blastocyst&#xA;  essentially collapses, splitting the progenitor cells (those that&#xA;  contain the body's fundamental genetic material) in half, leaving the&#xA;  same genetic material divided in two on opposite sides of the embryo.&#xA;  Eventually, two separate fetuses develop. Spontaneous division of&#xA;  the zygote into two embryos is not considered to be a hereditary&#xA;  trait, but rather a spontaneous or random event.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Monozygotic twins may also be created artificially by embryo&#xA;  splitting. It can be used as an expansion of IVF to increase the&#xA;  number of available embryos for embryo transfer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Interesting references for this are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10336022&quot; rel=&quot;nofollow&quot;&gt;The epidemiology of multiple births&lt;/a&gt;&quot;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12957099&quot; rel=&quot;nofollow&quot;&gt;Twinning.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17564530&quot; rel=&quot;nofollow&quot;&gt;On the possible cause of monozygotic twinning: lessons from the&#xA;9-banded armadillo and from assisted reproduction.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18577552&quot; rel=&quot;nofollow&quot;&gt;Monozygotic twinning associated with assisted reproductive&#xA;technologies: a review.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/news/2009/090415/full/458826a.html&quot; rel=&quot;nofollow&quot;&gt;Developmental biology: Two by two (on overview article conatining a&#xA;lot of other references)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-01-05T17:24:21.747" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14284" PostTypeId="1" AcceptedAnswerId="14285" CreationDate="2014-01-06T06:30:04.037" Score="5" ViewCount="5075" Body="&lt;p&gt;In this &lt;a href=&quot;http://www.khanacademy.org/science/biology/human-biology/neuron-nervous-system/v/electrotonic-action%20potential&quot; rel=&quot;noreferrer&quot;&gt;video&lt;/a&gt; on electro tonic potential, the tutor says that when the potassium channels open the potential drops from +40mV to -80mV, where the sodium channels have already closed at +40mV. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now in that case, &#xA;&lt;strong&gt;&lt;em&gt;wouldn't the sodium channels that usually open at -55mV open up again when the potential is on its way reaching -80mV from +40mV, thereby making changes in all the potential differences that are occurring normally(according to the video)?&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for the help.&lt;/p&gt;&#xA;" OwnerUserId="4947" LastActivityDate="2014-01-30T11:03:42.130" Title="Action potential and sodium channels" Tags="&lt;neuroscience&gt;&lt;neurology&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14285" PostTypeId="2" ParentId="14284" CreationDate="2014-01-06T08:02:43.050" Score="9" Body="&lt;p&gt;The key to understanding this is to digest the fact that there are two gates blocking a normal sodium channel. These gates are called the &lt;em&gt;activation gate&lt;/em&gt; (on the extracellular side) and the &lt;em&gt;inactivation gate&lt;/em&gt; on the intracellular side. Both of these together, or any one of these alone, if closed, can block the sodium current from entering the cell.   &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;In the &lt;strong&gt;resting state&lt;/strong&gt;, the activation gate is closed and the inactivation gate is open. There is no influx of sodium. Owing to a neurotransmitter release, there is depolarization of the plasma membrane around the channel. As soon as the potential reaches a fixed threshold value, there is a change in the conformation of the sodium channel. The voltage is sensed by a &lt;a href=&quot;http://courses.washington.edu/conj/membrane/nachan.htm&quot; rel=&quot;noreferrer&quot;&gt;biophysical voltage sensor&lt;/a&gt;, a part of the channel.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;At the &lt;strong&gt;threshold potential&lt;/strong&gt;, both the gates respond by reversing their state. But owing to the biophysical structure, the response of the activation gate is faster than the response of the inactivation gate. What happens is that the activation gate quickly opens allowing the influx of sodium ions, generating the action potential. The inactivation gate is closing but before it closes, the activation gate has been open for some time and the action potential is already fired due to considerable depolarization. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;After some time, the inactivation gate also closes completely, blocking the sodium influx. By this time, the potential is at the peak of the action potential, the potassium channels have opened, and the &lt;strong&gt;re-polarisation phase&lt;/strong&gt; begins. Here the inactivation gate is closed, thouh the activation gate is still open above the threshold potential. As the potential dips below the threshold, again the gates reverse their states but they respond with different speeds. First, the activation gate closes while the inactivation gate is still closed, and then the inactivation gate opens. In this way, during repolarisation, no sodium influx occurs since atleast one of the two gates is always closed.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I hope I answered your questions. Here are further links to understand this in greater detail. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sodium_channel&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.icb.ufmg.br/labs/lbcd/prodabi5/homepages/hugo/Hugo/drgcanais3.pdf&quot; rel=&quot;noreferrer&quot;&gt;Mechanism of sodium channel inactivation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10883/&quot; rel=&quot;noreferrer&quot;&gt;Basics of Voltage-Gated ion channels in &lt;em&gt;Neuroscience&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://nerve.bsd.uchicago.edu/FB/IEEEvoltagegated.pdf&quot; rel=&quot;noreferrer&quot;&gt;Mechanism of Voltage gated Channels in general(Detailed)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FQSzN.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;A more technical and biophysically accurate version of the diagram.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/PWqax.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2014-01-30T11:03:42.130" LastActivityDate="2014-01-30T11:03:42.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14287" PostTypeId="1" CreationDate="2014-01-06T10:34:52.753" Score="3" ViewCount="438" Body="&lt;p&gt;Is there any published data which shows the number of &lt;em&gt;Drosophila melanogaster&lt;/em&gt; fruit flies eclosing (hatching out of the pupae) against time since egg oviposition? I'm thinking there should be something like a &quot;cumulative flies eclosed&quot; plot showing the cumulative number of flies emerging per time interval after the eggs were oviposited (something like this dummy figure). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rVoXp.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I expected to find this in the Ashburner et al &lt;em&gt;Drosophila&lt;/em&gt; book but there was nothing. I am trying to see how much variance there is around the mean for an experiment design. It may be helpful to know (though I am not necessarily after specifics to this set up) we keep our flies at 25 degrees, 12:12 light dark cycle, 60% humidty on a yeast and sugar based food source. The flies are an African lab adapted population (Dahomey ca ~1970's?) and eggs in the experiment would be kept at low density so resource competition is not an issue.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-01-06T12:28:22.557" LastActivityDate="2014-01-25T07:40:06.563" Title="Drosophila melanogaster eclosion" Tags="&lt;development&gt;&lt;experimental-design&gt;&lt;drosophila&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14288" PostTypeId="2" ParentId="14264" CreationDate="2014-01-06T11:07:09.827" Score="1" Body="&lt;p&gt;The pronuclei fuse and decondensation happens and now the cell is called a zygote. There is a stage called the midblastula transition (MBT), until which only the maternal products (cytoplasmic factors such as RNAs, proteins and ribosomes) are used. After MBT the zygote starts expressing its own genes from both the paternal and maternal alleles. However, certain genomic regions are &lt;em&gt;imprinted&lt;/em&gt;  which means that one of the alleles is epigenetically silenced. It can be either paternal or maternal. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-01-06T11:07:09.827" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14289" PostTypeId="1" AcceptedAnswerId="14300" CreationDate="2014-01-06T12:45:00.713" Score="2" ViewCount="768" Body="&lt;p&gt;I have seen &lt;strong&gt;haploid&lt;/strong&gt; cancer cells (I think it was leukemia cells) in a lab. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sperms and eggs are haploid but are not destroyed by the body because they are protected by other cells surrounding them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions : &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;How are haploid and diploid cells differentiated by our immune system ?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Why are the haploid cancer cells not killed ? I know I could as well ask why any cancer cells are not killed but I want to know if there is anything specific about these cells ?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How are these cells generated ? (By meiosis ?!)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="5144" LastEditDate="2014-01-06T13:23:02.173" LastActivityDate="2018-12-24T12:33:27.927" Title="Why are haploid cancer cells not killed by immune system?" Tags="&lt;immunology&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="11" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14290" PostTypeId="1" CreationDate="2014-01-06T16:13:25.733" Score="2" ViewCount="408" Body="&lt;p&gt;After analyzing DNA sequences of an oncogene from many human cancer patients, you found that synonymous substitutions occur in a specific codon of this oncogene. Assuming that these synonymous substitutions do not exist in normal populations but do contribute to tumor development, what would be possible mechanisms that would explain how such alterations can lead to tumor phenotype?&lt;/p&gt;&#xA;" OwnerUserId="5328" LastEditorUserId="1306" LastEditDate="2014-01-06T19:02:48.977" LastActivityDate="2017-06-30T11:11:28.943" Title="How can synonymous mutations lead to cancerous or tumorous phenotypes?" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;cancer&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14293" PostTypeId="2" ParentId="2980" CreationDate="2014-01-06T17:39:47.637" Score="2" Body="&lt;p&gt;You can try Biomechanical models used in software frameworks such as &lt;a href=&quot;https://simtk.org/home/opensim&quot; rel=&quot;nofollow&quot;&gt;OpenSim&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is an example of a combined upper and lower body model in XML: &lt;a href=&quot;https://simtk.org/project/xml/downloads.xml?group_id=415#package_id684&quot; rel=&quot;nofollow&quot;&gt;ULB_Project&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5336" LastActivityDate="2014-01-06T17:39:47.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14296" PostTypeId="2" ParentId="14290" CreationDate="2014-01-06T18:11:21.447" Score="5" Body="&lt;p&gt;I think you assumed that &lt;code&gt;synonymous mutation&lt;/code&gt; means &lt;code&gt;silent mutation&lt;/code&gt;. But this is not correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Synonymous_mutation&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia (synonymous mutation)&lt;/a&gt; :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Synonymous substitutions and mutations affecting noncoding DNA are often considered silent mutations, however this is not always the case. Synonymous mutations can affect transcription, splicing, mRNA tranport, and translation, any of which could alter phenotype, rendering the synonymous mutation non-silent&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Oncogene&quot; rel=&quot;noreferrer&quot;&gt;wikipedia (Oncogene)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The proto-oncogene can become an oncogene by a relatively small modification of its original function. There are three basic methods of activation:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A mutation within a proto-oncogene, or within a regulatory region (for example the promoter region), can cause a change in the protein structure, causing&#xA;&lt;ul&gt;&#xA;&lt;li&gt;an increase in protein (enzyme) activity&lt;/li&gt;&#xA;&lt;li&gt;a loss of regulation&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;An increase in the amount of a certain protein (protein concentration), caused by&#xA;&lt;ul&gt;&#xA;&lt;li&gt;an increase of protein expression (through misregulation)&lt;/li&gt;&#xA;&lt;li&gt;an increase of protein (mRNA) stability, prolonging its existence and thus its activity in the cell&lt;/li&gt;&#xA;&lt;li&gt;gene duplication (one type of chromosome abnormality), resulting in an increased amount of protein in the cell&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;A chromosomal translocation (another type of chromosome abnormality)&#xA;&lt;ul&gt;&#xA;&lt;li&gt;There are 2 different types of chromosomal translocations that can occur:&#xA;&lt;ol&gt;&#xA;&lt;li&gt;translocation events which relocate a proto-oncogene to a new chromosomal site that leads to higher expression&lt;/li&gt;&#xA;&lt;li&gt;translocation events that lead to a fusion between a proto-oncogene and a 2nd gene (this creates a fusion protein with increased cancerous/oncogenic activity)&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the expression of a constitutively active hybrid protein. This type of mutation in a dividing stem cell in the bone marrow leads to adult leukemia&lt;/li&gt;&#xA;&lt;li&gt;Philadelphia Chromosome is an example of this type of translocation event. This chromosome was discovered in 1960 by Peter Nowell and David Hungerford, and it is a fusion of parts of DNA from chromosome 22 and chromosome 9. The broken end of chromosome 22 contains the &quot;BCR&quot; gene, which fuses with a fragment of chromosome 9 that contains the &quot;ABL1&quot; gene. When these two chromosome fragments fuse the genes also fuse creating a new gene: &quot;BCR-ABL&quot;. This fused gene encodes for a protein that displays high protein tyrosine kinase activity (this activity is due to the &quot;ABL1&quot; half of the protein). The unregulated expression of this protein activates other proteins that are involved in cell cycle and cell division which can cause a cell to grow and divide uncontrollably (the cell becomes cancerous). As a result, the Philadelphia Chromosome is associated with Chronic Myelogenous Leukemia (as mentioned before) as well as other forms of Leukemia.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You might be especially interested in the second point (&lt;code&gt;An increase in the amount of a certain protein&lt;/code&gt;)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Therefore, there is nothing impressive to find some synonymous mutations that are involved in oncogenes.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-01-06T18:11:21.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14298" PostTypeId="2" ParentId="9266" CreationDate="2014-01-06T19:11:20.640" Score="3" Body="&lt;p&gt;So after a lot of work in optimization, I thought I would post what worked best for me.  This buffer recipe was able to successfully transfer EGFR and insulin from the same lysate, and a clear band for both (large and small protein respectively). 10% SDS-PAGE gels were transferred at 1A for 10 min.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;High Current Transfer Buffer&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;48 mM Tris&lt;/li&gt;&#xA;&lt;li&gt;15 mM HEPPS&lt;/li&gt;&#xA;&lt;li&gt;1.0 mM EDTA&lt;/li&gt;&#xA;&lt;li&gt;1.3 mM NaHSO3&lt;/li&gt;&#xA;&lt;li&gt;1.3 mM N,N-dimethylformamide&lt;/li&gt;&#xA;&lt;li&gt;25 Mm gLY-GLY&lt;/li&gt;&#xA;&lt;li&gt;20% Methanol (v/v)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I do hope this can help someone else, and want to site &lt;a href=&quot;http://dx.doi.org/10.1016/j.ab.2013.07.009&quot; rel=&quot;nofollow&quot;&gt;Garic et al&lt;/a&gt; as wonderful starting point.  Their publication was made after I asked the question, as @user4148 pointed out.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2014-01-06T19:11:20.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14299" PostTypeId="1" AcceptedAnswerId="14302" CreationDate="2014-01-06T19:43:02.120" Score="9" ViewCount="17999" Body="&lt;p&gt;My book keeps giving different indicators as to whether the promoters are on the coding or template strand.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;It says the -35 region in prokaryotes must be on the coding strand. It also mentions, that the -10 and -35 regions are binding sites for RNA polymerase.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It also says that CAAT and GC, unlike -35 in prokaryotes, can also be on the template strand. Which implies that they are still most common on the coding strand. And then it shows me a figure, where a promoter sequence is shown in the template strand, with the transcription complex attached.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;All the sequences are written 5'-TATAAA-3' (for example). This also implies they are on the coding strand, since the template strand will then be 3'-&gt;5' which is the direction that transcription happens in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously I'm confused, and hope someone can clarify this. In which strand can I find the promoters? Does stuff act on the promoter sequence itself, or its complementary sequence? If the promoter can also be on the other strand, should it be reversed?&lt;/p&gt;&#xA;" OwnerUserId="3032" LastActivityDate="2014-12-18T06:25:40.603" Title="On which strand does the promoter sit?" Tags="&lt;molecular-biology&gt;&lt;transcription&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14300" PostTypeId="2" ParentId="14289" CreationDate="2014-01-06T20:05:50.787" Score="3" Body="&lt;p&gt;Now that I did some research on this, it seems to be a very rare condition of acute lymphoblastic leukemia (ALL), see this article:&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6953994&quot; rel=&quot;nofollow&quot;&gt;Chromosomes and causation of human cancer and leukemia. XLVII. severe hypodiploidy and chromosome conglomerations in ALL.&lt;/a&gt;&quot;.&#xA;This article (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3216674&quot; rel=&quot;nofollow&quot;&gt;Origin of near-haploidy in malignant hematopoietic cells.&lt;/a&gt;&quot;) hypothesizes that this might happen through gradual chromosome loss during cancer formation and that in the end one clone with a lower than normal number of chromosomes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This seems connected to a much worse outcome of the cancer than for hyperdiploidies (more chromosomes than normal). See the &quot;&lt;a href=&quot;http://atlasgeneticsoncology.org/Anomalies/nearhaploidID1145.html&quot; rel=&quot;nofollow&quot;&gt;Atlas of Genetics and Cytogenetics in Oncology and Haematology&lt;/a&gt;&quot;.&#xA;They also define why haploid (or near haploid means: Less than thirty chromosomes, down to 23 have been observed). This is not the normal haploidy found in germ cells. Se also &quot;&lt;a href=&quot;http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.24.783&amp;amp;rep=rep1&amp;amp;type=pdf&quot; rel=&quot;nofollow&quot;&gt;Isolation and Characterization of a Near-Haploid Human Cell Line&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since these chromosomal changes occur inside the nucleus I think this is mostly invisible to the immune system - so there is probably no difference how these cells escape the immune system compared to other cancer cells. I think its possible that due to the chromosomal loss some proteins which control apoptosis are lost, so the cells escape this fate as well.&#xA;Regarding the immune question, you can either start with the following articles or simply go over to Pubmed and choose some articles. In this field there is a lot of research going on.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.immunol.21.120601.141135?journalCode=immunol&quot; rel=&quot;nofollow&quot;&gt;Does the immune system see tumor as foreign or self?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/onc/journal/v27/n45/abs/onc2008271a.html&quot; rel=&quot;nofollow&quot;&gt;The tumor microenvironment and its role in promoting tumor growth&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.hindawi.com/journals/bmri/2011/918471/&quot; rel=&quot;nofollow&quot;&gt;Tumor Evasion from T Cell Surveillance&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If there are access problems, let me know.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-01-06T20:05:50.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14301" PostTypeId="2" ParentId="7726" CreationDate="2014-01-06T20:10:24.283" Score="1" Body="&lt;p&gt;One way to approach this problem would be to look at herbarium collections of the taxa that you're interested in. Usually, a flowering or fruiting specimen is easiest to identify; but no matter what character is best for your taxon, if you look at the herbarium collections and see that&#xA;-most of the collections identified to species, or &#xA;-the especially good-looking collections, or &#xA;-flowering/fruiting collections, &#xA;were made in a certain month or season, that could help you to narrow down your time window.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a bonus, in reviewing herbarium collections, you'll have given yourself a step towards being able to identify the species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some herbaria have some collections online; here, for instance, are &lt;a href=&quot;http://herbariaunited.org/specimensearch/?taxon=Puccinellia&amp;amp;taxonid=8072&amp;amp;collector=&amp;amp;colid=&amp;amp;role=prov&amp;amp;from=&amp;amp;to=&amp;amp;search=search&amp;amp;Country=gbie&amp;amp;VC=all&amp;amp;place=&amp;amp;placeid=&amp;amp;Inst=all&amp;amp;search=search#searchlist&quot; rel=&quot;nofollow&quot;&gt;records and images for online &lt;em&gt;Puccinellia&lt;/em&gt; collections&lt;/a&gt; at a number of UK herbaria.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2014-01-06T20:10:24.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14302" PostTypeId="2" ParentId="14299" CreationDate="2014-01-06T22:33:29.857" Score="9" Body="&lt;p&gt;The answer to this question depends upon the definition of the word 'promoter'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the simplest possible model of prokaryotic transcription the promoter is the site where RNA polymerase binds to the DNA before initiating RNA synthesis. In this process the &amp;sigma; factor recognises the core promoter elements directing the polymerase to bind to the DNA to form the closed complex. The next step is the switch to the open complex involving separation of the DNA strands.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Articles describing investigating the interaction of the &amp;sigma; factor with the DNA (e.g. &lt;a href=&quot;http://dx.doi.org/10.1006/jmbi.1995.0531&quot;&gt;here&lt;/a&gt;) refer to the protein making contacts with base pairs. I conclude therefore that the original question doesn't make sense - a promoter is a dsDNA entity even though we might describe it in terms of the sequence on one or other of those strands. So, for example, in a promoter the consensus -35 sequence - 5'-TTGACA -  would be present on the coding strand (upstream of the coding sequence), but the promoter property of the sequence is due to the presence of this sequence and its complement on the other strand.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-01-06T22:33:29.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14303" PostTypeId="1" CreationDate="2014-01-06T22:52:13.803" Score="1" ViewCount="209" Body="&lt;p&gt;I'm currently researching bat social calls (not echolocation calls) and have been given a series of samples (in .wav format) and wanted to know if what I can hear is actually the social calls. Below is a Graph representation of the a sample from the data I have:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WN7Nj.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This looks fine to me. From this, I can clearly tell where the social calls are. If I play at the specific peaks, then it sounds like a bat &quot;chirping.&quot; However, I've been told that social calls cannot be played back, and, therefore humans cannot hear them. I'm just trying to figure out what these noises, or, chirps might actually be. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://vocaroo.com/i/s06u3KIDO4kz&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; is a link to the .wav file: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your help :)&lt;/p&gt;&#xA;" OwnerUserId="5337" LastEditorUserId="16866" LastEditDate="2017-03-27T19:17:36.240" LastActivityDate="2017-03-27T19:50:25.863" Title="Are these bat social calls?" Tags="&lt;zoology&gt;&lt;ecology&gt;&lt;bioacoustics&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2017-03-28T16:01:31.657" ContentLicense="CC BY-SA 3.0" />
  <row Id="14305" PostTypeId="2" ParentId="14303" CreationDate="2014-01-07T00:30:03.390" Score="3" Body="&lt;p&gt;It could not fit in a comment..&lt;/p&gt;&#xA;&lt;p&gt;You recorded bats. You are interested in social calls. Socials calls can be recorded by your microphone but they cannot be read by standard media player because...&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the standard media player are limited to certain frequencies&lt;/li&gt;&#xA;&lt;li&gt;your speakers cannot produce such high sounds&lt;/li&gt;&#xA;&lt;li&gt;your ears are not able to hear many of the frequencies emitted&lt;/li&gt;&#xA;&lt;li&gt;you formatted your records in a format that cannot hold very high frequency (for reason of optimizing data compression)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;You might use some program like Adobe Audition in order to easily visualize the frequencies (vs time) of your record. (It might also help you finding all harmonics or performing Fourrier analysis)&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Bat_species_identification#Social_calls&quot; rel=&quot;nofollow noreferrer&quot;&gt;This wiki article&lt;/a&gt; says :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Social Calls&lt;/p&gt;&#xA;&lt;p&gt;This is a wide subject and there is still a lot to be discovered about bat social communication and how they use social calls in roosts and when flying. Generally a bat social call is not tonal, in other words it does not consist of a musical type note. Some bat detectors do not produce an accurate recording of a bat social call. Typically bat social calls use a lower frequency range than echolocation calls, and can thus be heard further away. Sometimes a bat will make a social call while echolocating which can cause confusion.&lt;/p&gt;&#xA;&lt;p&gt;We can see and hear how the lower frequency social calls are heard at a greater distance than the higher echolocation calls as the bat approaches and departs. Zooming in on a spectrogram, social calls are atonal and repeated rapidly about five times in each call. The social calls are interleaved between the echolocation calls. They show a ragged frequency distribution around 20 kHz. Note the FD detector divides frequencies by 10.&#xA;The echolocation calls are single &amp;quot;hockey stick&amp;quot; calls at a higher repetition rate. At this scale the hockey stick shape is not very clear, but the end frequency can be measured as 45.2 kHz. A doppler shift is recorded as the bat approaches. The frequency was measured as it passes&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2017-03-27T19:50:25.863" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="14308" PostTypeId="2" ParentId="14299" CreationDate="2014-01-07T07:46:52.713" Score="4" Body="&lt;p&gt;Promoter doesn't &lt;em&gt;sit&lt;/em&gt; anywhere.. it is just &lt;em&gt;present&lt;/em&gt; .. the &lt;strong&gt;transcription factor&lt;/strong&gt; &lt;em&gt;sits&lt;/em&gt; on it :P&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Jokes apart.. Adding a little more information to Alan Boyd's answer: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Alan Boyd points out, the terms &lt;em&gt;coding&lt;/em&gt; or &lt;em&gt;template&lt;/em&gt; refers to the region that is being transcribed. &#xA;Usually the Transcription Factors (TF) that bind to DNA have a dsDNA binding domain and therefore bind to &lt;strong&gt;both&lt;/strong&gt; the strands. However, the sequence recognition domains are specific and usually scan the DNA &lt;code&gt;5'-&amp;gt; 3'&lt;/code&gt;, subsequently &lt;em&gt;recruiting&lt;/em&gt; RNA-polymerase in the same orientation. But there are additional aspects to this: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Promoter/regulatory elements are usually upstream but are also downstream of the TSS in several cases&lt;/li&gt;&#xA;&lt;li&gt;The activity of a promoter element depends on the TF that binds to it. Some TFs can control the entire genomic locus i.e they affect several genes- both upstream and downstream.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-01-07T07:46:52.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14309" PostTypeId="1" AcceptedAnswerId="14317" CreationDate="2014-01-07T10:09:15.340" Score="4" ViewCount="711" Body="&lt;p&gt;What is the smallest oligocelluar organism?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How many cells does it have?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is motivated by this &lt;a href=&quot;https://philosophy.stackexchange.com/questions/9072/if-there-is-life-then-there-is-more-complex-life-as-well#comment22856_9095&quot; title=&quot;and it is not 100% clear that even if given relatively benign environmental conditions the development of multicelluar organisms with differentiated tissues (my definition of complex life) will occur with (near) ceartainty.&quot;&gt;comment@Philosophy.SE&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT as recommended in comments&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking for an example of an organism made of very few (the fewer, the better) sister cells (obtained by mitosis or aggregation) that are morphologically and functionally different. I would accept examples of species that exist in different &quot;conformation&quot; (unicellular and multicellular).&lt;/p&gt;&#xA;" OwnerUserId="5344" LastEditorUserId="-1" LastEditDate="2017-04-13T12:42:22.377" LastActivityDate="2014-01-11T16:00:49.547" Title="What is the smallest oligocelluar organism?" Tags="&lt;cell-biology&gt;&lt;cell-culture&gt;" AnswerCount="2" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="14311" PostTypeId="2" ParentId="5728" CreationDate="2014-01-07T12:04:32.013" Score="0" Body="&lt;p&gt;It's impossible to be sure how another individuals brain represents the world. For all we know, they way they sense depth and up and down might be completely different. The representation of colour could be completely different. Both individuals could explain it as images, but if it were possible to move another individuals representation into another individuals brain - it's likely the other individual would experience an abstract sensation that would be difficult to compare to anything else that individual has experienced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It could well be like having a compass attached to your body, sending nerve signals to your brain. You would not understand how to interpret it unless your brain has plenty of time to associate the stream of signals of direction with other signals such as your balance, vision and audio.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The brain is a very complex organ, and it probably starts out like a tiny, one celled blank sheet of paper. That blank sheet of paper is receiving continous streams of electronic signals from the various sensory organs of the body. Over time, synapses between your neurons will bond with other synapses, due to both of them receiving signals simultaneously. For example, if you are listening to music, you will hear various frequencies. Usually there will be a drum beat, which you will also sense as vibrations in the floor and your stomach. The neurons handling those two different signals will then bond together, so that at a later time - when you sense bass signals in the floor, but not in your stomach and by your ears - your brain will still recognize that drum beat in the floor as music. Some people might even feel like they hear the music.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nerves are then going from the sensor to the brain in various ways and paths, and those connections are different for everybody. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your brain will visualize stuff your way, and other people will visualize stuff their way and I believe those representations of objects and things are completely different for everybody. The representations will be compatible among different people, in such a way that physical laws are obeyed - but that is because the brain alters representations according to previous experiences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, knowing that it is impossible to be sure, I really do believe that everybody represents sensations completely different. They will be handled in similar regions of the brain due to physical similarities of the body, but within those regions in the brain there will be huge differences in representations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe that if a human, unknowingly had a compass operated into his body at birth and connected to an arbitrary nerve, then that human would experience a heightened sense of direction that it could not explain as an adult. If another human had an identical compass attached to a completely different part of his body and connected to perhaps the nerve going from one of the ears, then that human would experience the same sense of direction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disclaimer; I am a computer programmer with a keen interest in virtualized intelligence - I have no education in the area of biology. :-)&lt;/p&gt;&#xA;" OwnerUserId="5346" LastActivityDate="2014-01-07T12:04:32.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14313" PostTypeId="2" ParentId="623" CreationDate="2014-01-07T12:20:14.187" Score="0" Body="&lt;p&gt;First:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a child, it could be that the brain is not encoded with a lot of experience. Thus, processing of new information is less complex, and conclusions are made much faster. These conclusions are then encoded into the brain, making future experiences more complex. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;A child may have concluded everything it is able to conclude within the first few seconds of arriving at that bus stop.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A brain with a lot of previous experiences, is able to occupy itself with &quot;trivialities&quot;, such as watching snow flakes fall from the sky or thinking about what to have for dinner. Visualizing different tastes and smells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;A grown individual might be slower to conclude, taking more factors into account. It may also have more to ponder on.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Third:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The brain is thinking all the time. It is unconsciously cross referencing every sound, smell and other sense with previous experiences and actually quite busy. If there is a limit to the amount of energy that goes into the brain for processing stuff, a larger and larger percentage of those electrons will be busy &quot;retriggering&quot; signals. Almost like a city road map. It will take a short time for a number of cars to travel every possible route in a small city, than in a big city. Possibly, this has to happen in the brain as well, to refresh old memories.&lt;/p&gt;&#xA;" OwnerUserId="5346" LastActivityDate="2014-01-07T12:20:14.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14315" PostTypeId="1" AcceptedAnswerId="14316" CreationDate="2014-01-07T12:28:56.653" Score="4" ViewCount="108" Body="&lt;p&gt;Can you think of collective and swarm behaviors as &quot;intelligence&quot;? Would such a concept apply to a) ant colonies and b) fish swarms?&lt;/p&gt;&#xA;" OwnerUserId="5344" LastEditorUserId="3952" LastEditDate="2014-01-07T14:31:22.760" LastActivityDate="2014-01-10T13:55:25.927" Title="Do swarms show intelligence?" Tags="&lt;terminology&gt;&lt;ichthyology&gt;&lt;sociality&gt;&lt;intelligence&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14316" PostTypeId="2" ParentId="14315" CreationDate="2014-01-07T12:59:06.000" Score="5" Body="&lt;p&gt;Intelligence is something which has to have a definition, and there are many, but I would cautiously say no. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason that I say this is because swarming behavior can be largely reproduced by a &lt;a href=&quot;http://en.wikipedia.org/wiki/Swarm_behaviour#Models&quot; rel=&quot;nofollow&quot;&gt;simple set of rules&lt;/a&gt; - matching distance to your neighbors and direction and speed as well.  To me this really removes any intention or even conscious element to swarm behavior although its clear individuals do make decisions, they don't have to be more intelligent than a mouse looking for food or other kinds of animal behavior.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, others have literally built definitions of &lt;a href=&quot;http://en.wikipedia.org/wiki/Swarm_behaviour#Swarm_intelligence&quot; rel=&quot;nofollow&quot;&gt;intelligence inspired by swarming&lt;/a&gt; - a decentralized sort of mind which makes decisions based on the interactions of component individuals.  You could argue that our own brains are a similar sort of ensemble, and therefore no more different than our own intelligence if we look closely enough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So take your pick really. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-01-09T06:08:23.823" LastActivityDate="2014-01-09T06:08:23.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14317" PostTypeId="2" ParentId="14309" CreationDate="2014-01-07T13:34:29.583" Score="3" Body="&lt;p&gt;The classic example, though I am sure there are others that are smaller, is the slime mold &lt;a href=&quot;http://en.wikipedia.org/wiki/Dictyostelium_discoideum&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Dictyostelium discoideum&lt;/em&gt;&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GokQy.gif&quot; alt=&quot;Dictyostelium life cycle&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It can have &lt;a href=&quot;http://dictybase.org/tutorial/&quot; rel=&quot;nofollow noreferrer&quot;&gt;up to 100,000 cells&lt;/a&gt; and exists as both single cells and as a multicellular organism (emphasis mine):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dictyostelium amoebae &lt;strong&gt;grow as separate, independent cells&lt;/strong&gt; but interact to &lt;strong&gt;form multicellular structures when challenged&lt;/strong&gt; by adverse conditions such as starvation. &lt;strong&gt;Up to 100,000 cells signal each other by releasing the chemoattractant cAMP and aggregate together by chemotaxis&lt;/strong&gt; to form a mound that is surrounded by an extracellular matrix. This mechanism for generating a multicellular organism differs radically from the early steps of metazoan embryogenesis. However, subsequent processes depend on cell-cell communication in both Dictyostelium and metazoans. Many of the underlying molecular and cellular processes appear to have arisen in primitive precursor cells and to have remained fundamentally unchanged throughout evolution. Basic processes of development such as differential cell sorting, pattern formation, stimulus-induced gene expression, and cell-type regulation are common to Dictyostelium and metazoans.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="4579" LastEditDate="2014-01-08T18:38:59.287" LastActivityDate="2014-01-08T18:38:59.287" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="14318" PostTypeId="1" CreationDate="2014-01-07T14:36:41.173" Score="2" ViewCount="1271" Body="&lt;p&gt;Sulfonamid is an antimicrobial agent, why has it no effect on the growth of Rickettsia?&lt;/p&gt;&#xA;" OwnerUserId="5349" LastEditorUserId="5144" LastEditDate="2014-01-07T14:46:27.257" LastActivityDate="2015-10-20T15:03:12.973" Title="Why does sulfonamid not inhibit the growth of Rickettsia?" Tags="&lt;microbiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14319" PostTypeId="1" CreationDate="2014-01-07T15:40:11.647" Score="0" ViewCount="930" Body="&lt;p&gt;How does transfer of genetic material occur between Gram positive and Gram negative bacteria?&lt;/p&gt;&#xA;" OwnerUserId="5349" LastEditorUserId="1320" LastEditDate="2014-01-07T19:46:12.140" LastActivityDate="2014-01-07T19:46:12.140" Title="Gene transfer between Gram positive and Gram negative bacteria?" Tags="&lt;genetics&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14320" PostTypeId="2" ParentId="14319" CreationDate="2014-01-07T16:12:26.000" Score="1" Body="&lt;p&gt;Have a look at this two links:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.britannica.com/EBchecked/topic/48203/bacteria/272363/Exchange-of-genetic-information&quot; rel=&quot;nofollow&quot;&gt;Exchange of genetic information&lt;/a&gt;&#xA;and &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://web.mit.edu/kdrinkwa/Public/tklab/for-mfpapers/Mazodier91.pdf&quot; rel=&quot;nofollow&quot;&gt;Gene transfer between distantly related bacteria&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Especially the second should answer a lot of questions.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-01-07T16:12:26.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14321" PostTypeId="1" CreationDate="2014-01-07T17:05:10.693" Score="1" ViewCount="2457" Body="&lt;p&gt;How would you define &lt;code&gt;Regime of selection&lt;/code&gt; (or &lt;code&gt;Selection regime&lt;/code&gt;)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to a accurate definition, a developped example would be very welcome!&lt;/p&gt;&#xA;" OwnerUserId="4113" LastEditorUserId="3952" LastEditDate="2014-01-07T17:25:28.350" LastActivityDate="2016-08-03T17:28:48.313" Title="Definition of &quot;Regime of selection&quot;" Tags="&lt;evolution&gt;&lt;terminology&gt;&lt;population-biology&gt;&lt;adaptation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14322" PostTypeId="2" ParentId="14321" CreationDate="2014-01-07T17:13:07.570" Score="3" Body="&lt;p&gt;I'll kick this off with an attempt at a definition: a selection regime is&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;the set of selective pressures on a population&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;As in, &quot;alteration of selection regime resulting from harvest&quot; (Mooney &amp;amp; McGraw 2007)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or &quot;Human-induced nutrient input can change the selection regime and lead to the loss of biodiversity. For example, eutrophication caused speciation reversal in polymorphic whitefish populations through a flattening of littoral–pelagic selection gradients.&quot; (Hirsch et al 2013)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1111/eva.12087&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Hirsch PE, Eckmann R, Oppelt C, Behrmann-Godel J&lt;/strong&gt;. 2013. Phenotypic and genetic divergence within a single whitefish form - detecting the potential for future divergence. Evolutionary Applications 6: 1119–1132.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s10592-006-9148-3&quot; rel=&quot;nofollow&quot;&gt; &lt;strong&gt;Mooney E, McGraw J&lt;/strong&gt;. 2007. Alteration of selection regime resulting from harvest of American ginseng, Panax quinquefolius. Conserv Genet 8: 57–67.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-01-08T23:22:10.280" LastActivityDate="2014-01-08T23:22:10.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14323" PostTypeId="1" CreationDate="2014-01-07T18:01:00.900" Score="1" ViewCount="538" Body="&lt;p&gt;I've read that the cell nucleus was once an autonomous organism that was &quot;enslaved&quot; by the larger cell at the time of the Eukaryotic Revolution. Are there any organs in the human body that we know of that started out as autonomous organisms (of course they would be unrecognizable in their current form)?&lt;/p&gt;&#xA;" OwnerUserId="5350" LastEditorUserId="5350" LastEditDate="2014-01-07T18:07:34.223" LastActivityDate="2015-01-04T22:23:08.440" Title="Evolutionary history: did any organs start out as autonomous organisms?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14324" PostTypeId="2" ParentId="14323" CreationDate="2014-01-07T18:49:48.043" Score="7" Body="&lt;p&gt;&lt;strong&gt;Very short answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not the nucleus who was an independent organism but the &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitochondrion&quot; rel=&quot;nofollow&quot;&gt;mitochdonrion&lt;/a&gt; (&lt;a href=&quot;http://en.wikipedia.org/wiki/Organelle&quot; rel=&quot;nofollow&quot;&gt;organelle&lt;/a&gt;) (One might discuss this point and say that both are correct, it is just a philosophical issue of the identiy of the eukaryotic cell). The &lt;a href=&quot;http://en.wikipedia.org/wiki/Plastid&quot; rel=&quot;nofollow&quot;&gt;plastids&lt;/a&gt; (the &lt;a href=&quot;http://en.wikipedia.org/wiki/Chloroplasts&quot; rel=&quot;nofollow&quot;&gt;chloroplasts&lt;/a&gt; for example) were also independent organism. In consequence, in every cell, we have DNA in the nucleus and DNA in the mitochondria. The mitochondria is contained in every cell of our body and is transmitted via the ovule (and not the spermatozoid) to the offsprings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now let's think about your hypothesis that one of our organ (let's say, our liver) might have been an independent organism in the past. Therefore, this organ would contain different DNA than the rest of the cells of our body. How would you transfer the DNA of your liver to your offspring? Well, it is hardly imaginable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, it has been argued that because we now have a complex and efficient immune system, a endosymbiose would be very unlikely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But no, none of the cell in our body come from a previously different organism. But every cell of our body is some kind of chimera of two previous cells. Note: the vast majority of our DNA are present in the nucleus and not in the mitochondrion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information about endosymbiose, have to look to &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitochondrion#Origin&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Endosymbiotic_theory&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; (wiki articles)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems much more easy to have two organisms that stay together during reproduction when reproduction is mediated by &lt;a href=&quot;http://en.wikipedia.org/wiki/Cutting_%28plant%29&quot; rel=&quot;nofollow&quot;&gt;striking&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may find some funny examples (border cases) of two organisms that don't separate during reproduction in corals (&lt;a href=&quot;http://en.wikipedia.org/wiki/Symbiodinium&quot; rel=&quot;nofollow&quot;&gt;zooxanthella&lt;/a&gt;), &lt;a href=&quot;http://en.wikipedia.org/wiki/Leafcutter_ant&quot; rel=&quot;nofollow&quot;&gt;leafcutter ants&lt;/a&gt; (and their fungus), parasitoid bees (and the virus that females create in their ovary) and &lt;a href=&quot;http://en.wikipedia.org/wiki/Lichen&quot; rel=&quot;nofollow&quot;&gt;lichens&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-01-04T22:23:08.440" LastActivityDate="2015-01-04T22:23:08.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14325" PostTypeId="1" AcceptedAnswerId="14326" CreationDate="2014-01-07T19:18:59.923" Score="6" ViewCount="8162" Body="&lt;p&gt;Why are lactate level high in diabetes? For example, type II diabetes are resistant to insulin. If those patients are insulin resistant their gluconeogenesis should be working at a high rate and, because of that, lactate uptake by the liver should be removing lactate from the blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, type I diabetics don't produce insulin, so the ratio insulin/glucagon would always be very low and gluconeogenesis should be stimulated... So I don't understand why lactate levels are high in diabetes... Can someone help me?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;PS. This question came up after doing an experiment in school, with diabetic rats and normal rats. Diabetic rats had higher levels of lactate and my professor said that it was because the diabetic rats don't perform gluconeogenesis and so, lactate accumulates in the plasma. But it doesn't make sense for me.&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5354" LastEditorUserId="9943" LastEditDate="2018-12-19T08:14:58.020" LastActivityDate="2018-12-19T20:45:13.900" Title="Why would lactate be high in diabetics?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;endocrinology&gt;&lt;glucose&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="14326" PostTypeId="2" ParentId="14325" CreationDate="2014-01-07T20:08:10.100" Score="7" Body="&lt;p&gt;This condition is also known as &quot;lactic acidosis&quot; and can be pretty dangerous, since it influences the pH of the blood. &#xA;When we metabolize glucose to produce ATP and NADH it is metabolized finally to pyruvate in a process called &lt;a href=&quot;http://en.wikipedia.org/wiki/Glycolysis&quot; rel=&quot;noreferrer&quot;&gt;glyolysis&lt;/a&gt; (I am not going into detail here since this is nicely explained in the Wikipedia). Pyruvate can then be used further in the body in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Gluconeogenesis&quot; rel=&quot;noreferrer&quot;&gt;Gluconeogenesis&lt;/a&gt;, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Citric_acid_cycle&quot; rel=&quot;noreferrer&quot;&gt;Citric acid cycle&lt;/a&gt; and other pathways. &#xA;If a lot of energy is needed Pyruvate is converted by the pyruvate dehydrogenase into acetyl-CoA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem with diabetes is that the pyruvate dehydrogenase can be inhibited in diabetes. If the body then needs a lot of energy pyruvate will be converted into lactate which is released by the cells into the bloodstream.&#xA;Gluconeogenesis cannot be activated since this needs either Pyruvate, Acetyl-CoA or Oxaloacetate as starting material. The other problem with this process is that this happens in the liver and when the glucose is released into the bloodstream, it cannot be taken up by the cells due to the lack of insulin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The conversion from Pyruvate to Lactate is katalysed by the Lactate dehydrogenase and needs NADH + H+ as a co-factor. The image below is from the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Lactate_dehydrogenase&quot; rel=&quot;noreferrer&quot;&gt;Lactate dehydrogenase&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/q2UZB.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This reaction is highly exergonic which means its preferred direction is to the right side. To change this and make Pyruvate from Lactate you need an excess of NAD+ which usually only happens in the liver.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also an epidimiologic study available showing a strong correlation between elevated blood lactate levels and diabetes type II: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20797988&quot; rel=&quot;noreferrer&quot;&gt;Association of blood lactate with type 2 diabetes: the Atherosclerosis Risk in Communities Carotid MRI Study.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-01-07T20:38:18.093" LastActivityDate="2014-01-07T20:38:18.093" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="14327" PostTypeId="1" AcceptedAnswerId="14457" CreationDate="2014-01-07T21:14:57.880" Score="5" ViewCount="2565" Body="&lt;p&gt;The following graphs compare glucose decomposition in yeasts (in anaerobic vs aerobic conditions respectively)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, why doesn't the first one look like a straight line as the second one does? Don't they actually follow similar processes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2Y8m6.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5356" LastActivityDate="2014-10-09T14:38:53.997" Title="Aerobic vs anaerobic respiration comparison" Tags="&lt;cell-biology&gt;&lt;cellular-respiration&gt;&lt;fermentation&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14328" PostTypeId="2" ParentId="14323" CreationDate="2014-01-07T21:27:25.453" Score="2" Body="&lt;p&gt;Remi.b is perfectly correct if the question were restricted to humans (and yes, nucleus is not thought to be a result of symbiogenesis; actually some bacteria have similar structures).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But in the animal kingdom there several cases when certain organs &quot;start(ed) out&quot; as more or less separate organisms:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Many parasites have dwarf males and giant females (which actually feed on the host). These females when reaching maturity recruit actively swimming males, which upon attachment to female genitalia functionally become testicles and get nourishment from the female. The resulting organism can be viewed as hermaphrodite (although &quot;self-fertilization&quot; results in crossing). This phenomenon was described for example for &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jmor.1040/abstract&quot; rel=&quot;nofollow&quot;&gt;Rhizocephala&lt;/a&gt; (Crustacea).&lt;/li&gt;&#xA;&lt;li&gt;Similar cases are known for free-living organism: for example, in some species of the deep-sea &lt;a href=&quot;http://jypichthyology.info/attachments/File/Pietsch_2005a.pdf&quot; rel=&quot;nofollow&quot;&gt;anglerfishes&lt;/a&gt; males are dwarf and after attachment to females become &quot;parasitic&quot;.&lt;/li&gt;&#xA;&lt;li&gt;Siphonophorans (colonial Cnidaria) have several distinct organs (swimming bubble, locomotive organs, hunting tentacles and so on), but this differentiation is achieved via specialization of individual members of the colony - zooids. One can argue, that these organism were never separate, but for example one can still tell, which organs are medusae and which are polyps, each one of them &lt;a href=&quot;http://www.brown.edu/Faculty/Dunn_Lab/assets/Dunn_Wagner2006.pdf&quot; rel=&quot;nofollow&quot;&gt;&quot;is homologous to a free-living solitary animal&quot;&lt;/a&gt;. In other colonial hydroids one can find something reminiscent, but the degree of integrity of the whole colony never reaches that of Siphonophorans.&lt;/li&gt;&#xA;&lt;li&gt;In some species of bryozoans (which are colonial as well), several zooids (they are called &quot;heterozooids&quot; in this case) devote their lives to defend or move the colony, becoming highly specialized organs of the colonial organism.&lt;/li&gt;&#xA;&lt;li&gt;There are probably other systems fitting in the question, can't remember right now.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="1590" LastEditDate="2014-01-08T07:34:17.293" LastActivityDate="2014-01-08T07:34:17.293" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14330" PostTypeId="1" CreationDate="2014-01-08T06:03:12.650" Score="3" ViewCount="131" Body="&lt;p&gt;I began reading this paper (&lt;a href=&quot;http://www.biomedcentral.com/1471-2105/14/56&quot; rel=&quot;nofollow&quot;&gt;http://www.biomedcentral.com/1471-2105/14/56&lt;/a&gt;) and had a few questions about mass spectrometry terminology that I couldn't find answers to elsewhere.  Consider the following line:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The resulting peptide signals in the LC-MS map are referred to as features while the selection of features for fragmentation with MS/MS is called precursor ion selection.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure what an LC-MS map is, so I can't properly understand what features or precursor ion selection are: can someone define these terms for me with examples?&lt;/p&gt;&#xA;" OwnerUserId="5360" LastActivityDate="2015-05-16T13:11:55.077" Title="Mass Spectrometry Terminology" Tags="&lt;bioinformatics&gt;&lt;terminology&gt;&lt;mass-spec&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14331" PostTypeId="1" CreationDate="2014-01-08T12:55:10.020" Score="1" ViewCount="98" Body="&lt;p&gt;I would like to make my own DNA fingerprint - just for fun to have my &quot;autoportrait&quot;:).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was looking around a bit and all the commercial kits you can have are very expensive. Can you suggest me a cheaper way to do it - which DNA extraction protocol do you recommend?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have access to restriction enzymes, we have several different pcr polymerases (Herculase, pfu). Can this be used to make PCR with human DNA?&#xA;I found this list with primers for different STR loci. &lt;a href=&quot;http://www.cybertory.org/resources/CODIS/#Primers&quot; rel=&quot;nofollow&quot;&gt;http://www.cybertory.org/resources/CODIS/#Primers&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I understand it correctly I have to extract DNA, digest it with restriction enzyme and make a pcr with each of primer pair and than load it to a gel and make a picture. Am I getting it right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your answers!&lt;/p&gt;&#xA;" OwnerUserId="4860" LastActivityDate="2014-01-08T12:55:10.020" Title="DNA fingerprinting" Tags="&lt;dna&gt;&lt;human-genetics&gt;&lt;pcr&gt;&lt;restriction-enzymes&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14333" PostTypeId="1" CreationDate="2014-01-08T15:44:46.107" Score="2" ViewCount="123" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What we have are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;~20 genome sequences for a host species that come with gene annotations&lt;/li&gt;&#xA;&lt;li&gt;Several sequenced genomes for parasite/pathogens of these hosts&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the possible ways of predicting gene-to-gene interactions or gene regulatory networks between hosts and parasites?&lt;/p&gt;&#xA;" OwnerUserId="5005" LastActivityDate="2014-01-08T17:14:01.183" Title="Predicting host-pathogen gene interaction networks" Tags="&lt;genomics&gt;&lt;genomes&gt;&lt;gene-regulation&gt;&lt;network&gt;&lt;host-pathogen-interaction&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14334" PostTypeId="1" AcceptedAnswerId="14369" CreationDate="2014-01-08T15:54:46.433" Score="9" ViewCount="356" Body="&lt;p&gt;I was reading &lt;a href=&quot;https://biology.stackexchange.com/questions/7529/when-does-weak-selection-produce-qualitatively-different-results-from-strong-sel&quot;&gt;this question&lt;/a&gt; and I failed to fully understand the introductory part of it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The OP (@Artem Kaznatcheev) says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Most analytic models like to assume weak selection because it allows the authors to Taylor expand the selection function and linearize it by dropping terms that are higher order in the stength of selection. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't fully understand it. Can you help me making sense of why assuming weak selection allows one to Taylor expand the selection function. I am hoping someone would answer by presenting a mathematical model that at first does not assume weak selection and show why assuming weak selection allows the use of a Taylor series to linearize the function. I'd like to understand which terms fall down and which terms left with this assumption.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-01-31T13:47:21.227" Title="The Assumption of Weak Selection?" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;evolutionary-game-theory&gt;&lt;population-dynamics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14336" PostTypeId="1" AcceptedAnswerId="21279" CreationDate="2014-01-08T17:58:17.320" Score="7" ViewCount="524" Body="&lt;p&gt;Vitamin D acts in a way which to me is counterintuitive. It functionally supplemets Parathormone. It in the intestinal tract steps up calcium absorption by altering nuclear gene expression and also prevents calcium excretion in kidneys. All of this is understandable. But it also, like parathormone, steps up osteoclast action in bone (actually steps up both osteoclast and osteoblast, but the osteoclast action is increased more to result in net bone resorption). This means that Vitamin D increases blood calcium level by increasing bone resorption.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Then how does Vitamin D help in improving bone density, bone strength and prevent rickets or osteoporosis? All of these would require bone deposition rather than resorption.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="9268" LastEditDate="2014-09-16T06:17:19.313" LastActivityDate="2015-05-18T23:29:39.663" Title="Counterintuitive action of Vitamin D?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;endocrinology&gt;&lt;vitamins&gt;&lt;homeostasis&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14337" PostTypeId="2" ParentId="14152" CreationDate="2014-01-08T19:25:49.317" Score="2" Body="&lt;p&gt;Also, don't forget that you can deposit your full tree in &lt;a href=&quot;http://treebase.org/treebase-web/home.html;jsessionid=7568662A0CDC73BD6FCBDF11BDB5E247&quot; rel=&quot;nofollow&quot;&gt;treebase&lt;/a&gt;. So you can show the collapsed tree in the paper, and give a link to the full tree somewhere in the text.&lt;/p&gt;&#xA;" OwnerUserId="1225" LastActivityDate="2014-01-08T19:25:49.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14338" PostTypeId="2" ParentId="13641" CreationDate="2014-01-08T19:27:58.030" Score="2" Body="&lt;p&gt;There is a really good discussion of this in &lt;a href=&quot;http://www.nature.com/nature/journal/v456/n7219/full/nature07248.html&quot; rel=&quot;nofollow&quot;&gt;Chesson &amp;amp; Kuang&lt;/a&gt; &lt;em&gt;Nature&lt;/em&gt; 2008, they propose a way to measure niche complementarity accounting for competition and predation.&lt;/p&gt;&#xA;" OwnerUserId="1225" LastActivityDate="2014-01-08T19:27:58.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14339" PostTypeId="2" ParentId="11353" CreationDate="2014-01-08T19:31:46.157" Score="2" Body="&lt;p&gt;I've published a &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2011.00174.x/abstract&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; comparing different measures of specificity, if that is of any help. But if you plan to have, &lt;em&gt;e.g.&lt;/em&gt;, measures of performance on carbon sources, pH, and temperature, then you'll have three measures of specificity (i.e. one for each).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, worth to have a look at Graham Bell's &lt;a href=&quot;http://www.jstor.org/discover/10.2307/2409873?uid=3739464&amp;amp;uid=2&amp;amp;uid=3737720&amp;amp;uid=4&amp;amp;sid=21103219136401&quot; rel=&quot;nofollow&quot;&gt;inconsistency and responsiveness&lt;/a&gt;, as used by &lt;a href=&quot;http://www.nature.com/nature/journal/v452/n7184/abs/nature06554.html&quot; rel=&quot;nofollow&quot;&gt;Venail et al.&lt;/a&gt; to classify specialists and generalists.&lt;/p&gt;&#xA;" OwnerUserId="1225" LastActivityDate="2014-01-08T19:31:46.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14340" PostTypeId="2" ParentId="13999" CreationDate="2014-01-08T20:15:57.560" Score="1" Body="&lt;p&gt;You are on the right track.  This is an example of microchimerism (the maternal part is a bit off), and the key issue at hand is &lt;a href=&quot;https://en.wikipedia.org/wiki/Central_tolerance&quot; rel=&quot;nofollow noreferrer&quot;&gt;central tolerance&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;h2&gt;Background:&lt;/h2&gt;&#xA;&lt;p&gt;A good definition of microchimerism is:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Microchimerism is existence of an &lt;a href=&quot;https://en.wikipedia.org/wiki/Allotransplantation&quot; rel=&quot;nofollow noreferrer&quot;&gt;allogeneic&lt;/a&gt; DNA in a living creature. (&lt;a href=&quot;http://doi.wiley.com/10.1111/j.1365-4632.2012.05804.x&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Scientist do this on purpose for all kinds of reasons, but mostly to ether is study the immune system directly or to get a near-&lt;a href=&quot;https://en.wikipedia.org/wiki/Genetically_modified_organism#Mammals&quot; rel=&quot;nofollow noreferrer&quot;&gt;transgenic model&lt;/a&gt;.  It should be noted that this isn't perfect, and that when you try to do this, you often can lead to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=microchimerism%20autoimmune&quot; rel=&quot;nofollow noreferrer&quot;&gt;auto-immune problem&lt;/a&gt;s and often death of the mouse (30-50% survival in early work).  If you go back to one of (if not the) pioneers of immunology, &lt;a href=&quot;https://en.wikipedia.org/wiki/Peter_Medawar&quot; rel=&quot;nofollow noreferrer&quot;&gt;Peter Medawar&lt;/a&gt;, you can see when how this was done:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Mice and chickens never develop, or develop to only a limited degree,&#xA;the power to react immunologically against foreign homologous tissue&#xA;cells with which they have been inoculated in fetal life. Animals so&#xA;treated are tolerant not only of the foreign cells of the original&#xA;inoculum, but also of skin grafts freshly transplanted in adult life&#xA;from the original donor or from a donor of the same antigenic&#xA;constitution. (&lt;a href=&quot;http://www.nature.com/nature/journal/v172/n4379/pdf/172603a0.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;If you would prefer a visual layout of the experiment, &lt;a href=&quot;https://en.wikipedia.org/wiki/Thomas_Starzl&quot; rel=&quot;nofollow noreferrer&quot;&gt;Starlz&lt;/a&gt; put together one in his &lt;a href=&quot;http://dx.doi.org/10.1016/j.jamcollsurg.2005.03.023&quot; rel=&quot;nofollow noreferrer&quot;&gt;review of transplantation&lt;/a&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2987743/#R3&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pubmed&lt;/a&gt;):&#xA;&lt;img src=&quot;https://i.stack.imgur.com/J6gMo.jpg&quot; alt=&quot;Early model for microchimerism&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;After looking over the section you quoted from Alberts, I'm pretty sure he was in fact referring back to these early experiments.  But that was all the way back in the 1950's, what have we learned as the mechanism in 60 years?&lt;/p&gt;&#xA;&lt;h2&gt;Possible Mechanism:&lt;/h2&gt;&#xA;&lt;p&gt;The truth is that we don't have an absolute grasp on how this works when it doesn't cause an autoimmune problem and abort the fetus or even neonate pup.  It's import to note that it probably does cause &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894651/#__ffn_sectitle&quot; rel=&quot;nofollow noreferrer&quot;&gt;auto-immune problems&lt;/a&gt; and various other side effects (&lt;a href=&quot;https://en.wikipedia.org/wiki/Freemartin&quot; rel=&quot;nofollow noreferrer&quot;&gt;like sex differentiation&lt;/a&gt;) in mammals.&lt;/p&gt;&#xA;&lt;p&gt;But when and how it is tolerated is likely mediated by &lt;a href=&quot;https://en.wikipedia.org/wiki/Central_tolerance#Mechanisms_of_central_tolerance&quot; rel=&quot;nofollow noreferrer&quot;&gt;central tolerance&lt;/a&gt;, and the ability to get the foreign &lt;a href=&quot;https://en.wikipedia.org/wiki/Major_histocompatibility_complex&quot; rel=&quot;nofollow noreferrer&quot;&gt;MHC molecules&lt;/a&gt; tolerated by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3540904/&quot; rel=&quot;nofollow noreferrer&quot;&gt;early lymphocytes&lt;/a&gt;.  Essentially, the cells have to get incorporated into the &lt;a href=&quot;https://en.wikipedia.org/wiki/AIRE&quot; rel=&quot;nofollow noreferrer&quot;&gt;AIRE&lt;/a&gt; machinery at an &lt;a href=&quot;http://www.bloodjournal.org/cgi/doi/10.1182/blood-2010-06-286393&quot; rel=&quot;nofollow noreferrer&quot;&gt;early enough stage&lt;/a&gt; that the T-cells are selected against the foreign cells.&lt;/p&gt;&#xA;&lt;p&gt;There is enough biology here that an in-depth answer could be a dissertation, so I only want to touch on a few more points.  You should note that this was done with relatively genetically similar animals, and most modern researchers use cells modified from genetically pure mouse breeds.   We also know a lot more on how the cells &amp;quot;recognize self&amp;quot; and the &lt;a href=&quot;https://en.wikipedia.org/wiki/Human_leukocyte_antigen&quot; rel=&quot;nofollow noreferrer&quot;&gt;HLA types&lt;/a&gt; of the population.&lt;/p&gt;&#xA;&lt;p&gt;You are most likely to succeed when the MHC molecules are very similar (ie from a direct family member).  This happens when the host and foreign cells have an HLA type match.&lt;/p&gt;&#xA;&lt;h2&gt;TLDR:&lt;/h2&gt;&#xA;&lt;p&gt;The lymphocytes, mostly T-cells in this case, of fetal mammals seem to be able to look at very similar MHC molecule on a foreign cell and decide &amp;quot;eh.. close enough,&amp;quot; and build negative selection (part of &lt;a href=&quot;https://en.wikipedia.org/wiki/Thymocyte#.CE.B2-selection&quot; rel=&quot;nofollow noreferrer&quot;&gt;β-selection&lt;/a&gt;) against lymphocytes that would kill the foreign cells.  This requires that the cell be in the right place at the right time, and of course, be &amp;quot;close enough.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;Do let me know if something is not clear or needs to be expanded upon.  As someone who works in Immunology, I have difficulty determining where the detail line should be.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-01-08T20:15:57.560" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14341" PostTypeId="1" AcceptedAnswerId="14346" CreationDate="2014-01-08T20:22:16.490" Score="3" ViewCount="209" Body="&lt;p&gt;I was wondering how the body &quot;remembers&quot; viruses after having once overcome them, and while reading &lt;a href=&quot;http://science.howstuffworks.com/life/human-biology/immune-system13.htm&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; on the immune system (page 14, Vaccinations), I read:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There are many diseases that, if you catch them once, you will never catch again. Measles is a good example, as is chicken pox. What happens with these diseases is that they make it into your body and start reproducing. The immune system gears up to eliminate them. In your body you already have B cells that can recognize the virus and produce antibodies for it. However, there are only a few of these cells for each antibody. Once a particular disease is recognized by these few specific B cells, the B cells turn into plasma cells, clone themselves and start pumping out antibodies. This process takes time, but the disease runs it course and is eventually eliminated. However, while it is being eliminated, other B cells for the disease clone themselves but do not generate antibodies. This second set of B cells remains in your body for years, so if the disease reappears your body is able to eliminate it immediately before it can do anything to you.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Which made me wonder, instead of vaccinating people with weakened forms of the disease, getting their B cells to activate as described, what would be wrong with growing large colonies of B cells for a given virus and injecting them into someone who has never had the disease so that one can go straight to the last sentence of that paragraph, having many of those B cells in place before the virus is ever experienced?&lt;/p&gt;&#xA;" OwnerUserId="263" LastActivityDate="2014-01-09T20:14:48.577" Title="Are B Cells unique to an individual's immune system?" Tags="&lt;human-biology&gt;&lt;virology&gt;&lt;vaccination&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14343" PostTypeId="2" ParentId="9929" CreationDate="2014-01-08T21:26:58.040" Score="3" Body="&lt;p&gt;q-value is the corrected p-value to account for multiple testing (i.e. you are testing thousands of genes). Those with q-value &amp;lt;0.05 are significant experiment-wise. Cuffdiff uses Benjamini-Hochberg correction to compute FDR (i.e. q-value). The calculation does not depend on the number of replicates it's based on the distribution of p-values those, yes, are influenced by the number of replicates. The more replicates you have the better).&lt;/p&gt;&#xA;" OwnerUserId="5297" LastActivityDate="2014-01-08T21:26:58.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14344" PostTypeId="2" ParentId="11044" CreationDate="2014-01-08T21:31:10.860" Score="2" Body="&lt;p&gt;The following paper surveyed work on exploring water at negative pressure, from the first attempt a hundred years ago, when the largest tension reached was -3.4 MPa @ 24 degC, till the most recent measurement of water at room temperature down to -26 MPa:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://hal.archives-ouvertes.fr/docs/00/72/64/37/PDF/Caupin-JPCondensedMatter-2012.pdf&quot; rel=&quot;nofollow&quot;&gt;http://hal.archives-ouvertes.fr/docs/00/72/64/37/PDF/Caupin-JPCondensedMatter-2012.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore trees can lift water higher than 10 meters because water is pulled up by negative pressure at the top (Cohesion-tension theory CTT). The tension needed to lift water to the tallest trees is -1.2MPa, which is very plausible, since it is less than the value measured a hundred years ago.&lt;/p&gt;&#xA;" OwnerUserId="5363" LastActivityDate="2014-01-08T21:31:10.860" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14345" PostTypeId="1" AcceptedAnswerId="18986" CreationDate="2014-01-08T21:46:30.460" Score="11" ViewCount="17815" Body="&lt;p&gt;So, some people and I encountered an &lt;a href=&quot;http://advgamer.blogspot.ca/2014/01/game-39-earthrise-decapitated.html?showComment=1389180204657#c5004114215347507981&quot; rel=&quot;nofollow&quot;&gt;adventure game&lt;/a&gt; where you have a bee in a jar and need to move it from place to place before it suffocates, and someone tried to find out how long a bee would actually survive in the jar. We've found three relevant papers:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Oxygen consumption in the foraging honeybee depends on the reward rate at the food source &lt;a href=&quot;http://dx.doi.org/10.1007/s003600050045&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Oxygen consumption and body temperature of active and resting&#xA;honeybees &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16256690&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[2]&lt;/sup&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Physiological Correlates of Foraging Efforts in Honey-Bees: Oxygen&#xA;Consumption and Nectar&#xA;Load &lt;a href=&quot;http://www.jstor.org/discover/10.2307/2389615?uid=3738744&amp;amp;uid=2&amp;amp;uid=4&amp;amp;sid=21103243569047&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[3]&lt;/sup&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;which has given us what we think is a good high-end guess of 40µl of oxygen per minute consumed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, we don't know at what point the oxygen level would get too low for the bee, or if carbon dioxide poisoning  would occur. Does anyone have a source for the minimum oxygen levels a bee needs to survive, or the point at which CO₂ toxicity becomes a problem?&lt;/p&gt;&#xA;" OwnerUserId="1611" LastEditorUserId="3340" LastEditDate="2014-10-09T15:25:49.163" LastActivityDate="2014-10-09T16:21:43.377" Title="How long can a bee surive in a jar?" Tags="&lt;physiology&gt;&lt;entomology&gt;&lt;respiration&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14346" PostTypeId="2" ParentId="14341" CreationDate="2014-01-08T21:52:02.437" Score="4" Body="&lt;p&gt;Remember first that the human body nearly always, although there are exceptions, rejects any non-genetically identical graft placed into it, and therefore one cannot prepare a general colony of B-cells to confer immunity to the population at large. However, in principle, there is no impediment to removing B-cell progenitors in an individual, conditioning them to produce antibodies (which would be an artificial analogue of the natural process of 'Clonal Selection'), and re-injecting these differentiated B-cells into the patient. To my knowledge this process is currently beyond the capacity of our current cell culture techniques, as B-cell differentiation is controlled by an elaborate cell-signaling process, and even if it was feasible, it would remain impractical for several reasons. First, since the B-cell products, antibodies, can be transferred humorally, and should be tolerated by the general population, many existing treatments simply involve injecting antibodies into the patient's bloodstream. Examples of antibodies taken from volunteers' sera are the RhoGam preparations as well as IgG mixtures used to treat certain forms of immunodeficiency. There is a means of growing B-cells in culture to produce antibodies of precise specificity (i.e. monoclonal antibodies - note that clonal selection occurs in a living host for this technique, the B-cells are subsequently harvested then immortalized in culture). Adalimumab is a therapeutic monoclonal antibody.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is however, very promising work being conducted involving T-cell vaccination, which is technically similar to what you described. The advantage in using T-cells is that these leukocytes can orchestrate an immune response, mobilizing the several, diverse elements of the immune system to respond to a specific antigen. These techniques are being principally researched as cancer treatment regimens.&lt;/p&gt;&#xA;" OwnerUserId="4140" LastActivityDate="2014-01-08T21:52:02.437" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14347" PostTypeId="1" AcceptedAnswerId="14351" CreationDate="2014-01-08T22:11:53.400" Score="18" ViewCount="1998" Body="&lt;p&gt;For a long time I've just accepted, because it is just what everyone told me, that mitochondria became organelles in the cell when they were &quot;engulfed&quot; by another cell which acted like it's host. This is the endosymbiotic hypothesis. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The endosymbiotic hypothesis suggests mitochondria were originally&#xA;  prokaryotic cells, capable of implementing oxidative mechanisms that&#xA;  were not possible to eukaryotic cells; they became endosymbionts&#xA;  living inside the eukaryote.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, recently I looked at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitochondrion#Origin&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki entry&lt;/a&gt; on mitochondria and saw there that it lists two main hypothesis, endosymbiotic and autogenous. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;In the autogenous hypothesis, mitochondria were born by splitting off&#xA;  a portion of DNA from the nucleus of the eukaryotic cell at the time&#xA;  of divergence with the prokaryotes; this DNA portion would have been&#xA;  enclosed by membranes, which could not be crossed by proteins.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It also states that, given that mitochondria have some striking similarities to bacteria, the most parsimonious hypothesis for mitochondrial evolution is that of endosymbiosis. (&lt;a href=&quot;https://biology.stackexchange.com/questions/11/how-many-times-did-endosymbiosis-occur/60#60&quot;&gt;This question here&lt;/a&gt; deals with some aspects of multiple-occurence/convergent endosymbiosis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions are; &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;How strong is the evidence for either of these leading hypotheses (perhaps there is a review article)? Is there evidence that is overwhelmingly in favour of endosymbiosis? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Further, are there any other (&lt;em&gt;plausible&lt;/em&gt;) hypotheses to explain the origins of mitochondria (with or without supporting evidence)?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-12-26T08:39:25.970" Title="The Origin of Mitochondria" Tags="&lt;evolution&gt;&lt;cell-biology&gt;&lt;mitochondria&gt;&lt;eukaryotic-cells&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14348" PostTypeId="2" ParentId="14318" CreationDate="2014-01-08T22:22:23.590" Score="3" Body="&lt;p&gt;Sulfonamides competitively inhibit the enzyme dihydropteroate synthase, which is involved in the tetrahydrofolate synthesis pathway in most bacteria. Rickettsia lack this enzyme target, and thus possess a natural resistance to the antibiotic. As tetrahydrofolate is an essential compound, it is believed that Rickettsia possess an alternative enzymatic process which is not susceptible to sulfonamides, or the bacteria simply acquire the compound (or its immediate precursors) from their environment.&lt;/p&gt;&#xA;" OwnerUserId="4140" LastActivityDate="2014-01-08T22:22:23.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14349" PostTypeId="2" ParentId="14255" CreationDate="2014-01-08T23:22:33.820" Score="1" Body="&lt;p&gt;Simply stated, the reflex speeds of diverse animal species should not be the same. First, even within an individual, signal conduction speeds actually vary between nerves, on a fairly significant range of about two orders of magnitude. Conduction speeds between species, and likely even between individuals, will differ. Second, not all species possess the same reflexes, which can be, in fact, quite elaborate neural events. To qualify speeds for similar reflexes, one must use closely related species. I did find one article that found the pupillary light reflex in monkeys is essentially similar to that of humans, but this information is not sufficient to speak of the similarities between reflexes in general between the species.&lt;/p&gt;&#xA;" OwnerUserId="4140" LastActivityDate="2014-01-08T23:22:33.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14350" PostTypeId="1" AcceptedAnswerId="14352" CreationDate="2014-01-09T02:20:14.420" Score="4" ViewCount="297" Body="&lt;p&gt;The question is based on an intuition that antibiotic resistance can't come along. This mutation will probably make bacteria less tenacious. Is there any research how AR bacteria compete with normal one in an antibiotic free environment? Because if them generally lose to normal bacteria then AR bacteria is not a big threat and they can't spread to much.&lt;/p&gt;&#xA;" OwnerUserId="1169" LastActivityDate="2014-01-09T19:30:44.973" Title="Can antibiotic resistant bacteria compete with normal one in an antibiotic free environment?" Tags="&lt;bacteriology&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14351" PostTypeId="2" ParentId="14347" CreationDate="2014-01-09T05:32:14.487" Score="15" Body="&lt;p&gt;This is one of the most intriguing questions of eukaryotic evolution. As far as I know and have read, the autogenous theory is not accepted. There are quite some reviews on this topic. Also there is a wonderful book by Nick Lane on mitochondria called &lt;em&gt;Power Sex and Suicide&lt;/em&gt;. You would be interested to read it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are no sufficient evidences for the evolutionary transition from prokaryotes to eukaryotes which somewhat suggests that this was some kind of quantum jump. For example: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;There are no microfossil records for the evolutionary intermediates&lt;/li&gt;&#xA;&lt;li&gt;Almost all eukaryotic features including organelles, syngamy, nucleus etc emerged simultaneously&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So to answer how it exactly happened is quite difficult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the autogenous theory; it would have been impossible for the huge eukaryotic cell (the precursor of mitochondria) to meet its energy demands without an organelle like mitochondria i.e. a prokaryote as large as a eukayotic cell wouldn't survive. You may check &lt;a href=&quot;https://biology.stackexchange.com/questions/10277/is-there-any-advantage-of-having-a-mitochondria-for-aerobic-respiration&quot;&gt;this post&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are eukaryotic cells that lack mitochondria (eg. &lt;em&gt;Entamoeba histolytica&lt;/em&gt; ) or have one with reduced functionality. However, these are not intermediates in evolution but have lost the functionality in a retrograde manner. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is one more evidence to support the endosymbiosis theory:&#xA;There is this observation that organelles that are less numerous in a cell have retained more of their &lt;em&gt;genome&lt;/em&gt; compared to those with the organelles that are surplus numbers (eg. plastids vs mitochondria). This is called the &lt;strong&gt;Limited Transfer Window Hypothesis&lt;/strong&gt; which reasons that the organelle to nuclear gene translocation would have happened because of organellar injury and the likelihood of a cell tolerating one is higher if there are more number of organelles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17107559&quot; rel=&quot;nofollow noreferrer&quot;&gt;article&lt;/a&gt; suggests an alternative view that predatory bacteria like Bdellovibrio could have settled in a prokaryotic host. There are other cases of bacterial endosymbiont in a larger bacteria (&lt;em&gt;I need some time to mine up the reference. Read it a while back&lt;/em&gt;) but these are not the the ancestors of eukaryotes. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-01-10T12:21:27.413" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14352" PostTypeId="2" ParentId="14350" CreationDate="2014-01-09T05:40:35.867" Score="5" Body="&lt;p&gt;The antibiotic resistance adds to growth cost. In an antibiotic free medium the antibiotic-susceptible strains will outgrow the resistant ones. See &lt;a href=&quot;http://www.nature.com/nrmicro/journal/v8/n4/abs/nrmicro2319.html&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-01-09T05:40:35.867" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="14353" PostTypeId="2" ParentId="11" CreationDate="2014-01-09T06:12:42.767" Score="2" Body="&lt;p&gt;There are evidences of secondary endosymbiosis i.e. organelle within an organelle. This is quite evident in Chromaveolates. Many unicellular Chromaveolates which had been classically referred to as unicellular &lt;em&gt;Algae&lt;/em&gt;, have chloroplasts derived from other algae. This organelle in turn has a membrane bound suborganelle. For a quick reference you may see &lt;a href=&quot;http://www.nature.com/nature/journal/v492/n7427/full/nature11681.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article. &lt;em&gt;Euglena&lt;/em&gt; and diatoms are some famous examples of this phenomenon. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-01-09T06:12:42.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14355" PostTypeId="1" AcceptedAnswerId="14356" CreationDate="2014-01-09T10:22:11.900" Score="2" ViewCount="63" Body="&lt;p&gt;My question concern the abbreviation of the genus of a species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I talk about two species: &lt;em&gt;Amphiprion clarkii&lt;/em&gt; and &lt;em&gt;Amphiprion perideraion&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question 1&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's assume I haven't said a word about these species in my article yet. Should I say:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Amphiprion perideraion&lt;/em&gt; is a small fish and &lt;em&gt;Amphiprion clarkii&lt;/em&gt; is a big fish&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;or&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Amphiprion perideraion&lt;/em&gt; is a small fish and &lt;em&gt;A. clarkii&lt;/em&gt; is a big fish&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question 2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I talk about these two species in the abstract, should I use the abreviation the first time I cite them in the introduction or not?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3624" LastEditDate="2014-01-09T11:28:55.960" LastActivityDate="2014-01-09T11:28:55.960" Title="Citing species in a biology article" Tags="&lt;taxonomy&gt;&lt;publishing&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14356" PostTypeId="2" ParentId="14355" CreationDate="2014-01-09T11:20:32.647" Score="6" Body="&lt;p&gt;To avoid confusion all species names should be written in full at first, and can then be abbreviated. In this particular example it would probably not be a problem to use the second, shorter version. But what if you had four species divided into three genera with all names starting with 'A'? As for question 2, the full name usually only needs to be used in the title (if relevant) and once in the body text (which includes the abstract), so you can abbreviate after the abstract. However, this is really only a space issue, and you can use the full name at all instances (you &lt;em&gt;may&lt;/em&gt; abbreviate, but don't &lt;em&gt;have&lt;/em&gt; to), unless of course journal style prohibits this. I find it useful to write the name in full both in the abstract and once in the main text.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://www.nhm.ac.uk/hosted-sites/iczn/code/&quot;&gt;The International Code of Zoological Nomenclature&lt;/a&gt; (Appendix B: General Recommendations) for a reference. To be picky, technically, authorship and year of species names should also be included at least once in each paper (e.g. &lt;em&gt;Amphiprion clarkii&lt;/em&gt; Bennett, 1830), to clarify exactly what definition of a name you are using. However, this is often not done in practice (in fields outside taxonomy/systematics). What you often see is that people refer to a authoritative source, e.g. &quot;&lt;em&gt;... all species names used in the study follow Doe et al. (2008).&lt;/em&gt;&quot; &lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2014-01-09T11:20:32.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14357" PostTypeId="1" CreationDate="2014-01-09T13:04:01.880" Score="6" ViewCount="1313" Body="&lt;p&gt;How is primer annealing, and, consequently, PCR amplification &lt;strong&gt;affected by single nucleotide deletion or insertion inside the primer ?&lt;/strong&gt;  &lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine a primer like this:  &lt;br/&gt;GCGTCATAAAGGGGACGTG (primer)  &lt;br/&gt; and the corresponding part of template DNA has one G missing, so it looks like this:  &lt;br/&gt;GCGTCATAAAGGGACGTG (template).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The possible pairing could be  &lt;br/&gt;&#xA;GCGTCATAAAGGGGACGTG primer  &lt;br/&gt;&#xA;GCGTCATAAA_GGGACGTG template  &lt;br/&gt;&#xA;or  &lt;br/&gt;&#xA;GCGTCATAAAGGGGACGTG primer  &lt;br/&gt;&#xA;GCGTCATAAAGGG_ACGTG template  &lt;br/&gt;&#xA; or anything in between.  &lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible that amplification with such primer would be completely disrupted in normal real time PCR at 60°C annealing? Could this completely disrupt the amplification?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the mismatch was &lt;strong&gt;substitution&lt;/strong&gt;-like, I would be pretty confident, the primer would be still functional and amplification would occur. In the extreme case, it would be at least residual amplification at late Ct. There are a lot of data, how substitution mismatches affect primers and I also have a lot of personal experience with that. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, the &lt;strong&gt;deletion&lt;/strong&gt; mismatches are less studied plus googleproof. The only indication I have found is this work:  &lt;br/&gt;&#xA;Lipsky RH, Mazzanti CM, Rudolph JG, Xu K, Vyas G, Bozak D, et al. DNA melting analysis for detection of single nucleotide polymorphisms. Clin Chem. 2001;47:635-44.  &lt;br/&gt;&#xA;In that work, single nucleotide deletion had similar or lower affect on melting temperature than substitution mismatch. But it was about longer oligos.  Examples:  &lt;br/&gt;&#xA;Effect of deletion:  &lt;br/&gt;&#xA;133 bp fragment, 67 % GC, deletion SNP at position 43, delta Tm (homo-hetero duplex) = 1.2°C  &lt;br/&gt;&#xA;Effects of substitutions:  &lt;br/&gt;&#xA;152 bp fragment, 43 % GC, substitution T to C at position 68, delta Tm (homo-hetero duplex) = 0.9°C  &lt;br/&gt;&#xA;100 bp fragment, 41 % GC, substitution T to C at position 42, delta Tm (homo-hetero duplex) = 1.4°C  &lt;br/&gt;&#xA;163 bp fragment, 60 % GC, substitution C to T at position 86, delta Tm (homo-hetero duplex) = 2.2°C  &lt;br/&gt;&#xA;110 bp fragment, 59 % GC, substitution G to A at position 66, delta Tm (homo-hetero duplex) = 3.8°C  &lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions&lt;/strong&gt;:  &lt;br/&gt;&#xA;1. Can you recommend me literature about how deletion mismatches inside (not at the very end of !!!) primers affect annealing and PCR ?  &lt;br/&gt;&#xA;2. Would You guess the primer in my example would be still functional , at least partly, or would You expect no amplification at all ?  &lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT after your inputs:&lt;/strong&gt;  &lt;br/&gt;&#xA;This online application &quot; mfold.rna.albany.edu/?q=DINAMelt/Two-state-melting &quot; thinks, deletion mismatches are more destabilising than substitutions, at least for short primers. For my own example, it calculated delta Tm (homo-hetero duplex) = 12.9°C .&#xA;If I try substitution mismatches instead, delta Tm (homo-hetero duplex) is in interval 3,8°C to 5,7°C. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;New question&lt;/strong&gt;  &lt;br/&gt; If you have experience as similar as possible to my case, which is 19 nt long primer with single nucleotide deletion in the comlementary template at position cca 6 - 9 from 3' primer end, annealing temperature used at 60°C, please let me know if You achieved amplification or not.  Please, give me a respective reference, if you have it, so I will quote it in my review :-) .&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I am still interested in general info, as long as the topic is narrow enough to be about single nucleotide deletions or insertions in primers. (Not substitution mismatches).&lt;/p&gt;&#xA;" OwnerUserId="5369" LastEditorUserId="5369" LastEditDate="2014-02-02T09:04:31.617" LastActivityDate="2016-12-16T05:31:13.130" Title="Effect of single nucleotide deletion or insertion on primer annealing" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;pcr&gt;&lt;snp&gt;&lt;primer&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14358" PostTypeId="2" ParentId="14357" CreationDate="2014-01-09T13:36:05.203" Score="4" Body="&lt;p&gt;We used this kind of primers to generate out of frame mutations or to add additional bases. In my experience your PCR will work (probably a a lower efficiency) and you will get a product with an additional base. We used primers with bigger differences in PCR based site directed mutagenesis of plasmids, there up to 10 bases didn't match but the primers where also longer. For single nucleotide mismatches (either + or - one base) we used primers around this size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the literature, this publications might be useful:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://genome.cshlp.org/content/3/4/S39.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;A guide to the design and use of mismatched and degenerate&#xA;primers&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://nar.oxfordjournals.org/content/18/4/999.short&quot; rel=&quot;nofollow&quot;&gt;Effects of primer-template mismatches on the polymerase chain&#xA;reaction: Human immunodeficiency virus type 1 model studies&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://nar.oxfordjournals.org/content/25/3/654.full&quot; rel=&quot;nofollow&quot;&gt;The Effects of Internal Primer-Template Mismatches on RT-PCR: HIV-1&#xA;Model Studies&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6941.2007.00283.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Effect of primer mismatch, annealing temperature and PCR cycle number&#xA;on 16S rRNA gene-targetting bacterial community analysis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Especially the first publication contains a lot of other interestings references.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-01-09T13:36:05.203" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="14359" PostTypeId="1" CreationDate="2014-01-09T15:02:49.287" Score="1" ViewCount="18" Body="&lt;p&gt;I was looking for reviews that deal with conservation between mouse and human of proteins, noncoding RNAs, gene regulatory module (such as promoters and enhancers), gene regulatory networks post the mouse genome sequencing era &lt;/p&gt;&#xA;" OwnerUserId="5328" LastActivityDate="2014-01-09T15:02:49.287" Title="Are there any good reviews on the mouse and human conservation in coding and gene regulatory module regions?" Tags="&lt;homology&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14361" PostTypeId="1" CreationDate="2014-01-09T15:40:16.193" Score="5" ViewCount="143" Body="&lt;p&gt;At the beginning of the 20th century, Raunkiær proposed a &lt;a href=&quot;http://en.wikipedia.org/wiki/Raunki%C3%A6r_plant_life-form&quot; rel=&quot;nofollow&quot;&gt;typology of plant life-forms&lt;/a&gt; based on where they bear their buds, roughly as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;cryptophytes: belowground&lt;/p&gt;&#xA;&#xA;&lt;p&gt;hemicryptophytes: at the surface&lt;/p&gt;&#xA;&#xA;&lt;p&gt;chamaephytes: close to the surface&lt;/p&gt;&#xA;&#xA;&lt;p&gt;phanerophytes: projected above the surface&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these still held to be useful / biologically meaningful categories? Is there a different typology preferred (eg. tree/shrub/subshrub)? Or are people moving toward gradients of quantified traits instead of typologies (eg. measuring plant height, specific leaf area, etc.)?&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-01-09T17:51:04.433" LastActivityDate="2014-01-10T15:00:26.703" Title="How are Raunkiær's plant life forms viewed today?" Tags="&lt;botany&gt;&lt;terminology&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14362" PostTypeId="2" ParentId="14350" CreationDate="2014-01-09T17:34:34.073" Score="2" Body="&lt;p&gt;In short, yes. Perhaps the best way of thinking about antibiotic resistance is not to think of there being 'antibiotic resistance' genes at all, but rather ordinary alleles that are vertically transferred in the typical fashion until at a certain time a deleterious chemical agent is introduced and one specific allele just happens to mitigate the effects of that chemical. It is less a matter of competition than it is of blind chance. Now of course, in principle, the lucky genetic element that will ensure survival may come with an increased energy cost as opposed to the 'wild-type' genome expression, but considering the general mechanisms of antibiotic resistance, one or two extra gene products, maybe a slightly less active enzyme, an extra membrane transporter, the cost is typically not excessive. In culture, antibiotic-resistant bacterial strains grow essentially as fast as non-resistant strains. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now concerning the retaining of the resistance after removal of the antibiotic, if the gene is integrated into the genome with the proper regulatory apparatus, it can remain in the species essentially forever. In the case of plasmids or other mobile genetic elements, bacteria do tend to lose these through random processes between divisions, however, many of these elements do have mechanisms to preserve (plasmid addiction) and propagate themselves (horizontal gene transfer). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most important thing to remember about resistance, however, is that only an infinitesimally small proportion of the population actually needs the resistance genetic element to actually start a new resistant population upon antibiotic introduction.&lt;/p&gt;&#xA;" OwnerUserId="4140" LastActivityDate="2014-01-09T17:34:34.073" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14363" PostTypeId="2" ParentId="11295" CreationDate="2014-01-09T19:06:18.840" Score="2" Body="&lt;p&gt;I think you're talking about two different things.  I assume Rafique is referring to vascularized epithelium, but user4693 is referring to vascular epithelium.  Although the terminology is very similar, the difference is important.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;vascular epithelium&lt;/strong&gt; = endothelium of a blood or lymphatic vessel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;vascularized epithelium&lt;/strong&gt; = epithelium with a blood supply, meaning that small vessels invade the epithelium (pass between epithelial cells) rather than simply occurring in the underlying basement membrane or connective tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most epithelia are avascular (lack blood vessels).  As far as I know the only vascularized epithelium in humans is found in the inner ear (&lt;a href=&quot;http://link.springer.com/chapter/10.1007/978-3-642-70420-8_26&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;).  I've been told that the lips have vascularized epithelium (which is why they appear reddish), but I don't completely trust that source and I cannot find anything online to support it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, some pathological conditions can cause vascularization of certain epithelia, like the cornea (&lt;a href=&quot;http://bmb.oxfordjournals.org/content/100/1/209.full&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="5373" LastEditorUserId="3971" LastEditDate="2014-01-09T19:52:18.920" LastActivityDate="2014-01-09T19:52:18.920" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14365" PostTypeId="2" ParentId="14350" CreationDate="2014-01-09T19:30:44.973" Score="2" Body="&lt;p&gt;In general, antibiotic resistant strains may be a little less fit than sensitive strains in the absence of the antibiotic.  But that doesn't mean they are at all times and places instantly competed out of existence.  Once you apply the antibiotic, the resistant organisms grow from resistant organisms that were in the population to start with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ad of course once you have a large number of resistant organisms in the population, selection might encourage the increase in organisms bearing compensatory mutations, such that the growth of those organisms is closer to the growth level of sensitive organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your premise is a little weird.  Resistant organisms are out there.  XDR tuberculosis, MSRA Staph...why would you assert that those can't be problems when empirically, they obviously are?&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-01-09T19:30:44.973" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14366" PostTypeId="2" ParentId="14341" CreationDate="2014-01-09T20:14:48.577" Score="1" Body="&lt;p&gt;There is also some work with programming a patients own stem cells to become long lived plasma blasts for broadly neutralizing antibodies against HIV (and other diseases I assume). Although you are essentially asking what is harder...eliciting these broadly neutralizing antibodies with traditional vaccine approaches (difficult), or working out the complex cell signalling pathways to get from stem cell to long lived plasma blast. Even the pathway from memory b-cell to plasma blast is still not entirely understood, so we are several years away from this approach. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is so appealing though for so many reasons. Once you have a plasma cell secreting a broadly neutralizing antibody, you have it forever (or at least many many years). This circumvents the extremely expensive antibody therapeutic approach as large quantities of these proteins are indeed just expensive to make as with all protein therapeutics.  &lt;/p&gt;&#xA;" OwnerUserId="3887" LastActivityDate="2014-01-09T20:14:48.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14367" PostTypeId="2" ParentId="14059" CreationDate="2014-01-09T20:50:29.220" Score="1" Body="&lt;p&gt;Have you tried ITIS?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.itis.gov/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.itis.gov/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I once used their database. It was in MS Access format.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Now they updated their site, and you may download PostgreSQL, MySQL, SQLite, among other formats: &lt;a href=&quot;https://www.itis.gov/downloads/&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.itis.gov/downloads/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4821" LastEditorUserId="4821" LastEditDate="2017-02-11T04:47:46.737" LastActivityDate="2017-02-11T04:47:46.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14368" PostTypeId="1" CreationDate="2014-01-09T21:05:48.797" Score="4" ViewCount="4796" Body="&lt;p&gt;In the evolution of sociality among animals, different degrees are acknowledged. Some species present overlapping generations, some division of labor, and the minority present reproductive division. Those that present the three traces above are called &quot;eusocial&quot; (e.g. some wasps, some bees, all ants and termites, and an african mole).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe our own species could be eusocial? After all, homosexuality is present in virtually every culture studied by anthropologists. Some say it may bring an advantage to the group via group selection (not having kids of their own, they could study plants, medicine, weapons, and so on). What do you think? Are we an eusocial species?&lt;/p&gt;&#xA;" OwnerUserId="4821" LastActivityDate="2014-02-11T06:31:27.590" Title="Are humans an eusocial species?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;behaviour&gt;&lt;sociality&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14369" PostTypeId="2" ParentId="14334" CreationDate="2014-01-09T21:21:55.970" Score="2" Body="&lt;p&gt;This is my take in this, without experience of using the Taylor series to analyse evolutionary game theory problems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you know the Taylor series expansion of $f(x)$ at point $a$ can be written as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$f(x)= f'(a)(x-a) + \frac{f''(a)}{2!}(x-a)^2 + \frac{f^{(3)}(a)}{3!}(x-a)^3 + ... + \frac{f^{(n)}(a)}{n!}(x-a)^n + ...$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Often factors above second order are dropped as a simplification. However, to use the Taylor expansion, the function must be differentiable at point $a$, and to be differentiable it must be continuous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As @Artem Kaznatcheev writes in his question, &quot;&lt;em&gt;...with weak selection meaning the game modifies overall fitness only slightly...&lt;/em&gt;&quot; and &quot;&lt;em&gt;... it is typical to model organisms as having a base fitness that is modified slightly by the game interaction...&lt;/em&gt;&quot;. These statements imply that the overall fitness function/surface can be assumed to be relatively smooth and continuous (i.e. the payoff is negligible), which means that the Taylor series expansion can be used. If the game payoffs for a single game would determine a large proportion of the overall fitness, the fitness surface would be discontinuous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example where a Taylor series expansion is used to simplify the fitness function under weak selection is given in &lt;a href=&quot;http://www.genetics.org/content/172/1/611.full&quot; rel=&quot;nofollow&quot; title=&quot;Andre &amp;amp; Godelle. 2006. The Evolution of Mutation Rate in Finite Asexual Populations. Genetics 172(1): 611-626&quot;&gt;Andre &amp;amp; Godelle (2006)&lt;/a&gt; (see equation 20 ff).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might also find this &lt;a href=&quot;http://www.ped.fas.harvard.edu/SI.pdf&quot; rel=&quot;nofollow&quot;&gt;supplement&lt;/a&gt; to &lt;a href=&quot;http://www.nature.com/nature/journal/v466/n7310/full/nature09205.html&quot; rel=&quot;nofollow&quot; title=&quot;Nowak, Tarnita &amp;amp; Wilson. 2010. The evolution of eusociality. Nature 466.&quot;&gt;Nowak et al (2010)&lt;/a&gt; interesting (a rather controversial paper), especially page 8.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-01-17T11:09:54.697" LastActivityDate="2014-01-17T11:09:54.697" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14370" PostTypeId="1" AcceptedAnswerId="23293" CreationDate="2014-01-09T21:33:40.507" Score="7" ViewCount="770" Body="&lt;p&gt;Does anyone routinely do RNA isolation from zebrafish embryos?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have embryos from different stages but all below 24hpf. This is the protocol I follow:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Take 10-20 embryos&lt;/li&gt;&#xA;&lt;li&gt;Wash once with milliQ water&lt;/li&gt;&#xA;&lt;li&gt;Treat with 1mg/ml Proteinase-K (5min with gentle shaking) to dechorionate&lt;/li&gt;&#xA;&lt;li&gt;Wash again with milliQ water&lt;/li&gt;&#xA;&lt;li&gt;Remove water and add 250 µl Trizol&lt;/li&gt;&#xA;&lt;li&gt;Homogenize by pippeting&lt;/li&gt;&#xA;&lt;li&gt;add 750µl more of trizol&lt;/li&gt;&#xA;&lt;li&gt;Do the standard trizol extraction step (with chlorofom)&lt;/li&gt;&#xA;&lt;li&gt;Take the aqueous phase and wash again with 200µl chloroform&lt;/li&gt;&#xA;&lt;li&gt;Precipitate RNA with isopropanol&lt;/li&gt;&#xA;&lt;li&gt;Wash thrice with 70% ethanol&lt;/li&gt;&#xA;&lt;li&gt;dissolve in nuclease free water&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Despite all this I get a poor A260/A230 : ~0.4&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, this happens consistently in all samples. The RNA bands look fine on the gel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have done RNA isolation many times from cell lines and tissues and never faced this problem. Is this common with zebrafish embryos? Is there a way to fix this other than by using kits?&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-11-11T14:21:37.997" LastActivityDate="2016-12-12T05:45:37.927" Title="poor RNA quality from zebrafish embryos" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14371" PostTypeId="1" AcceptedAnswerId="14383" CreationDate="2014-01-09T21:57:32.007" Score="4" ViewCount="1066" Body="&lt;p&gt;I was wondering if you could answer some of my questions regarding sexual selection in cats (or any other animals). I would like to apologize beforehand for my incorrect term use.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;When it comes to mate choice, is mutual choice for both males and females the norm? If not, is it mostly a tomcat or a female cat who does the choosing?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Do female cats always have freedom to choose, or is it more like a rape or consensual sex? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How do cats choose their prospective partners in the wild, what are the mechanics of this process? Does a prospective partner come with the territory or are there any courtship rituals? I am interested in mate availability for female cats and sexual selection from a female cat perspective. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Thank you very much in advance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;P.S. Any other animals will do if they do not live in groups, prides or harems. I am interested in individual choices.&lt;/strong&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5376" LastEditorUserId="5376" LastEditDate="2014-01-11T23:09:05.870" LastActivityDate="2014-01-11T23:09:05.870" Title="Sexual selection in cats or other animals" Tags="&lt;zoology&gt;&lt;sexual-selection&gt;&lt;feline&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14372" PostTypeId="2" ParentId="14368" CreationDate="2014-01-09T22:08:07.440" Score="1" Body="&lt;p&gt;The question of homosexuality and its role in nepotism is interesting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to this &lt;a href=&quot;http://en.wikipedia.org/wiki/Demographics_of_sexual_orientation&quot; rel=&quot;nofollow&quot;&gt;wiki article&lt;/a&gt;, less than 10% of the population is homosexual. If you consider that homosexuality makes human eusocial because homosexual do not reproduce but help their brothers and sisters to reproduce, then you would have to consider any species where a few percentage of the population produce some kind of altruism to be eusocial. Given that all phenotypic traits theoretically have social impacts, then I would bet that you might call eusocial a lot of species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems wiser to me to limit the definition of eusocial when an important part (maybe 98% minimum) of the population do not reproduce but help others to reproduce. One might also want to consider some other restrictions for a the use of the word &quot;eusocial&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, using the argument of &quot;reproductive division&quot; I would rather not include Homo sapiens in the list of eusocial species. But it is nothing more than a question of definition. You're free to define your words the way you want and call human eusocial but make sure your interlocutor knows your definitions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, let's say we place the limit to the definition of eusociality at 1%. When more than 1% of the population does not reproduce but help their kin to reproduce, then the species is eusocial. Then, humans would seem to fit in this definition at first sight. But do homosexual in our modern society really help their kin to reproduce? In other words, do siblings of homosexual reproduce more (or have offspring that have a high fitness)? &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1691850/pdf/15539346.pdf&quot; rel=&quot;nofollow&quot;&gt;This study&lt;/a&gt; investigated the question (as pointed out by @oreotrephes in the comments) and they indeed found some pattern but the difference in reproduction between relatives of homosexual and non-relative of homosexual is is quite weak. But if homosexual don't reproduce and don't help their kin reproducing then, humans is definitely not a eusocial species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally I want to add that individuals from lots of different species have been found to perform homosexual behaviour (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Homosexual_behavior_in_animals&quot; rel=&quot;nofollow&quot;&gt;this wiki article&lt;/a&gt;). If you want to consider human as eusocial because some homosexuality, then you will have to consider sheeps, labradors and pigeons to be eusocial as well!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-02-10T01:19:02.707" LastActivityDate="2014-02-10T01:19:02.707" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="14373" PostTypeId="2" ParentId="14370" CreationDate="2014-01-09T22:12:57.977" Score="6" Body="&lt;p&gt;Usually I had no problems with RNA extractions - from various cultured cells as well as a number of different tissues from mouse. If I look at your protocol this is pretty much the same as the one we used or the one recommended &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19684565&quot;&gt;here&lt;/a&gt; for zebrafish embryo. This protocol &quot;&lt;a href=&quot;http://cshprotocols.cshlp.org/content/2010/6/pdb.prot5439.abstract&quot;&gt;Purification of RNA Using TRIzol (TRI Reagent)&lt;/a&gt;&quot; seems also interesting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What can happen is a contamination by phenol or carbohydrates, then we usually used the protocol below to clean up the sample. You can also use column based methods, but they are more expensive.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;add 1/10 vol of NH4OAc (5M), 2.5 volume 100% cold EtOH (100%) and 10µg&#xA;glycogen (for total RNA we usually didn't use any co-precipitation&#xA;agents) and mix well&lt;/li&gt;&#xA;&lt;li&gt;incubate 30 min at -80°C&lt;/li&gt;&#xA;&lt;li&gt;centrifuge 20 min at 12000g at 4°C and remove the supernatant&lt;/li&gt;&#xA;&lt;li&gt;wash with 75% ice cold EtOH&lt;/li&gt;&#xA;&lt;li&gt;centrifuge 5 min at 12000 g at 4°C and remove supernatant&lt;/li&gt;&#xA;&lt;li&gt;Re-suspend the pellet in RNAse free water (can take some time)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-01-09T22:12:57.977" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="14375" PostTypeId="2" ParentId="8183" CreationDate="2014-01-10T02:46:14.930" Score="6" Body="&lt;p&gt;&lt;strong&gt;More than 13,000.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Plants: &gt;9,000 names&lt;/strong&gt;.&#xA;In Systema Naturae 10th edition, commonly taken as the starting point of modern taxonomy, Linnaeus is reported to have published around 6,000 plant names (I haven't counted, but Müller-Wille gives 5,900 and Stearn says &quot;almost 6,000&quot;. The Wikipedia figure of 7,700 may come from a different edition of Systema Naturae).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, that's just SN10. Luckily, a wonderful source has compiled the names from all of Linnaeus's work:&#xA;The &lt;a href=&quot;http://www.nhm.ac.uk/research-curation/research/projects/linnaean-typification/index.html&quot; rel=&quot;noreferrer&quot;&gt;Linnaean Plant Name Typification Project&lt;/a&gt; of the Natural History Museum says that Linnaeus published more than 9,000 valid plant names in his life (names that are still valid under current nomenclatural conventions), and they have many of them in a &lt;a href=&quot;http://www.nhm.ac.uk/research-curation/research/projects/linnaean-typification/database/&quot; rel=&quot;noreferrer&quot;&gt;searchable database&lt;/a&gt; with references to where Linnaeus published them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Animals: &gt;4,200 names&lt;/strong&gt;.&#xA;For SN10, different authors give 4,236 or 4,378 animal names. Stearn says &quot;nearly 4,400&quot;, so perhaps he too was unsure. The total number Linnaues described in his life is probably higher, as he did write separate zoological publications like &lt;a href=&quot;http://www.biodiversitylibrary.org/item/100333#page/11/mode/1up&quot; rel=&quot;noreferrer&quot;&gt;Fauna Svevica&lt;/a&gt;, but I couldn't find a source like the project bringing together all of his animal names.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.endeavour.2006.03.001&quot; rel=&quot;noreferrer&quot;&gt; &lt;strong&gt;Müller-Wille S&lt;/strong&gt;. 2006. Linnaeus' herbarium cabinet: a piece of furniture and its function. Endeavour 30: 60–64.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.jstor.org/stable/2411603&quot; rel=&quot;noreferrer&quot;&gt;&lt;strong&gt;Stearn WT&lt;/strong&gt;. 1959. The Background of Linnaeus's Contributions to the Nomenclature and Methods of Systematic Biology.)&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-01-18T17:45:15.213" LastActivityDate="2014-01-18T17:45:15.213" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14377" PostTypeId="1" AcceptedAnswerId="14379" CreationDate="2014-01-10T05:22:37.357" Score="2" ViewCount="551" Body="&lt;p&gt;I've read about safe doses of radiation, briefly. Why is there such a thing a safe dose? Can't any radiation give you cancer? Why is it more and more dangerous to take in larger and larger doses? Just because the body can't recover as easily? Is there something fundamentally more damaging about larger doses of radiation, as opposed to smaller more frequent doses? I suppose this could go to a health forum, but I don't know of one, and I came about this question via thinking about Physics.&lt;/p&gt;&#xA;" OwnerDisplayName="anon" LastActivityDate="2014-01-10T12:45:12.247" Title="Radiation and &quot;Safe Dose&quot;" Tags="&lt;radiation&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14378" PostTypeId="2" ParentId="14377" CreationDate="2014-01-10T08:49:30.077" Score="1" Body="&lt;p&gt;First of all: Technically speaking there is no such thing as a safe dose in radiation like you can say for drugs or toxins. This is because every single event of radiation can cause damage that can cause cancer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides that, there is no need to panic about low radiation, since you define certain values which are deemed safe, because the likelihood of getting damage from this radiation is so small that it can be neglected. What we use in working with radioactive substances is the so called ALARA principle (&quot;As Low As Reasonably Achievable&quot;), so you try to keep the dose as small as possible, even if you are below the limits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taking up larger doses of radiation (or even worse taking up radioactive material) will raise your chances of receiving a harmful dose and damaging cells. A single large dose can cause a damage to your DNA, but this is also true for continued small doses. In both cases there is a certain chance of damage, which is bigger for the larger dose. But since there are more events possible for the continuous small dose, this can be as dangerous as the larger single dose.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1306" LastEditDate="2014-01-10T12:42:02.403" LastActivityDate="2014-01-10T12:42:02.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14379" PostTypeId="2" ParentId="14377" CreationDate="2014-01-10T09:16:09.203" Score="3" Body="&lt;p&gt;Great question. It is unfortunate that more people don't understand what &amp;quot;radiation&amp;quot; is and how it affects biology.&lt;/p&gt;&#xA;&lt;p&gt;Firstly, you must distinguish between ionizing radiation and non-ionizing radiation.&#xA;Wikipedia &lt;a href=&quot;https://en.wikipedia.org/wiki/Ionizing_radiation&quot; rel=&quot;nofollow noreferrer&quot;&gt;describes&lt;/a&gt; the former rather well:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Ionizing (or ionising) radiation is radiation composed of particles that individually carry enough kinetic energy to liberate an electron from an atom or molecule, ionizing it. ...&lt;/p&gt;&#xA;&lt;p&gt;When ionizing radiation is emitted by or absorbed by an atom, it can liberate an atomic particle (typically an electron, proton, or neutron, but sometimes an entire nucleus) from the atom. Such an event can alter chemical bonds and produce ions, usually in ion-pairs, that are especially chemically reactive.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;X-rays, alpha, beta, and gamma radiation are all ionizing forms of radiation. Non-ionizing radiation, as you might guess, is radiation of a sort which lacks enough energy to to strip an electron from an atom. All light is actually &amp;quot;radiation.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;The reason why ionizing radiation can be so damaging is because the molecular underpinnings of our cells depend on many very specific chemical bonds. Changing those bonds can damage or even break anything from proteins to strands of DNA itself. Our bodies naturally try to repair damage, but the &lt;em&gt;amount&lt;/em&gt; of damage is a crucial factor in how successful our bodies can be. More radiation means more damage; also greater amounts of radiation increases the chances of serious genetic damage to one or more cells. Damaging a cell's rulebook in just the right ways can disable its repair processes and even its fail-safes that keep it from becoming a hazard to the rest of the body (such as growing uncontrollably into a cancerous tumor).&lt;/p&gt;&#xA;&lt;p&gt;A more in depth explanation of radiation effects can be found at &lt;a href=&quot;http://www.epa.gov/radiation/understand/health_effects.html#q1&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.epa.gov/radiation/understand/health_effects.html#q1&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In general, the amount and duration of radiation exposure affects the severity or type of health effect. There are two broad categories of health effects: stochastic and non-stochastic.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Stochastic Health Effects&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Stochastic effects are associated with long-term, low-level (chronic) exposure to radiation. (&amp;quot;Stochastic&amp;quot; refers to the likelihood that something will happen.) Increased levels of exposure make these health effects more likely to occur, but do not influence the type or severity of the effect.&lt;/p&gt;&#xA;&lt;p&gt;Cancer is considered by most people the primary health effect from radiation exposure. Simply put, cancer is the uncontrolled growth of cells. Ordinarily, natural processes control the rate at which cells grow and replace themselves. They also control the body's processes for repairing or replacing damaged tissue. Damage occurring at the cellular or molecular level, can disrupt the control processes, permitting the uncontrolled growth of cells cancer This is why ionizing radiation's ability to break chemical bonds in atoms and molecules makes it such a potent carcinogen.&lt;/p&gt;&#xA;&lt;p&gt;Other stochastic effects also occur. Radiation can cause changes in DNA, the &amp;quot;blueprints&amp;quot; that ensure cell repair and replacement produces a perfect copy of the original cell. Changes in DNA are called mutations.&lt;/p&gt;&#xA;&lt;p&gt;Sometimes the body fails to repair these mutations or even creates mutations during repair. The mutations can be teratogenic or genetic. Teratogenic mutations are caused by exposure of the fetus in the uterus and affect only the individual who was exposed. Genetic mutations are passed on to offspring.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Non-Stochastic Health Effects&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Non-stochastic effects appear in cases of exposure to high levels of radiation, and become more severe as the exposure increases. Short-term, high-level exposure is referred to as 'acute' exposure.&lt;/p&gt;&#xA;&lt;p&gt;Many non-cancerous health effects of radiation are non-stochastic. Unlike cancer, health effects from 'acute' exposure to radiation usually appear quickly. Acute health effects include burns and radiation sickness. Radiation sickness is also called 'radiation poisoning.' It can cause premature aging or even death. If the dose is fatal, death usually occurs within two months. The symptoms of radiation sickness include: nausea, weakness, hair loss, skin burns or diminished organ function.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Another thing to understand about why the dose matters is that we are surrounded by ionizing radiation. We always have been. Our bodies have evolved needing to successfully deal with ionizing radiation. You can find a very informative and fun visualization of this fact at &lt;a href=&quot;https://xkcd.com/radiation/&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://xkcd.com/radiation/&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5366" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-01-10T12:45:12.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14380" PostTypeId="2" ParentId="14315" CreationDate="2014-01-10T13:55:25.927" Score="1" Body="&lt;p&gt;When we talk about &quot;artificial intelligence&quot; we are talking about the ability to solve problems not directly specified in the code. It doesn't need to have &quot;intention&quot; or &quot;conscience&quot;, as @shigeta suggests. So, I'd say swarms are intelligent, it's just another &quot;hardware&quot; where intelligence appears. Like shigeta said, our own mind is not different in essence from a swarm (just many times more developed).&lt;/p&gt;&#xA;" OwnerUserId="4821" LastActivityDate="2014-01-10T13:55:25.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14381" PostTypeId="2" ParentId="14327" CreationDate="2014-01-10T14:13:43.080" Score="0" Body="&lt;p&gt;I think in anaerobic conditions they are fermenting, what is different from respiration. Respiration produces much more ATP from single molecule of glucose, because the biochemical path is different, involves more steps, each one producing a little energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also note that, on the graph on the right, the X-axis goes up to 6. Which means glucose is being processed much faster on the left. Maybe that's because mitochondria are numerous and can process the sugar faster?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the curve, I can only think that fermentation is so slow that the ATP produced is being consumed by the cell in the same rate. With respiration, the ATP is produced in big amounts and thus begins to accumulate, what regulates the process to slow down. But I may be missing something important here.&lt;/p&gt;&#xA;" OwnerUserId="4821" LastEditorUserId="4821" LastEditDate="2014-01-10T14:25:07.747" LastActivityDate="2014-01-10T14:25:07.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14382" PostTypeId="2" ParentId="14327" CreationDate="2014-01-10T14:34:28.807" Score="1" Body="&lt;p&gt;Your graphs show two things: Starting at the same concentration (150mM/l) the metabolization of glucose is not linear under anaerobic conditions. The other observation is that under aerobic conditions the glucose is metabolized much slower.&#xA;This is because under anaerobic conditions on 2 molecules of ATP are generated from the metabolization of one molecule of glucose (for all the details on the biochemical pathways look into the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ethanol_fermentation&quot; rel=&quot;nofollow&quot;&gt;Ethanol Fermentation&lt;/a&gt;&quot; article in the Wikipedia) while for the complete respiration of one molecule of glucose under aerobic condition generates 32 molecules of ATP (2 from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Glycolysis&quot; rel=&quot;nofollow&quot;&gt;Glycolysis&lt;/a&gt; and 30 from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Citric_acid_cycle&quot; rel=&quot;nofollow&quot;&gt;Citric acid cycle&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to generate enough energy the yeast has to metabolize the glucose much faster when the conditions are anaerobic which explain the form of the graph, while under aerobic conditions the graph stays linear. The metabolization starts in both cases with the glycolysis, but afterwards is different. Aerobic conditions produce water and CO₂, while the anaerobic conditions produce ethanol and CO₂.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="3340" LastEditDate="2014-10-09T14:38:53.997" LastActivityDate="2014-10-09T14:38:53.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14383" PostTypeId="2" ParentId="14371" CreationDate="2014-01-10T14:38:27.220" Score="2" Body="&lt;p&gt;Wilson and Reeder (Mammal Species of the World) count 40 species of Felidae. Most of them are small cats (subfamily Felinae). Lions are in the subfamily Pantherinae, which contains only 6 species, one of them the jaguar, Panthera onca, which is solitary, like the tiger, Panthera tigris. By what I know of small cats, Puma concolor included, and the tiger and the jaguar, it seems that lion social behavior is not typical of felines. (Would add that as a comment, but can't comment with reputation &amp;lt; 50).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking for &quot;Felidae sexual selection&quot; or 'Felidae &quot;sexual selection&quot;' in google I have found some links. Look for &quot;sexual selection&quot; or &quot;Felidae&quot; in the text. Though I'm afraid most of them are not exactly what you're looking for, maybe they can open new windows of thought. Hope that helps!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.journals.elsevierhealth.com/periodicals/aaeth/article/0304-3762%2883%2990116-5/&quot; rel=&quot;nofollow&quot;&gt;http://www.journals.elsevierhealth.com/periodicals/aaeth/article/0304-3762%2883%2990116-5/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.catsg.org/cheetah/05_library/5_3_publications/E/Eaton_-_The_Evolution_of_Sociality_in_the_Felidae.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.catsg.org/cheetah/05_library/5_3_publications/E/Eaton_-_The_Evolution_of_Sociality_in_the_Felidae.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2010.01520.x/pdf&quot; rel=&quot;nofollow&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2010.01520.x/pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jstor.org/discover/10.2307/3544917?uid=26584&amp;amp;uid=3737664&amp;amp;uid=5909624&amp;amp;uid=2&amp;amp;uid=26582&amp;amp;uid=3&amp;amp;uid=67&amp;amp;uid=62&amp;amp;sid=21103320511793&quot; rel=&quot;nofollow&quot;&gt;http://www.jstor.org/discover/10.2307/3544917?uid=26584&amp;amp;uid=3737664&amp;amp;uid=5909624&amp;amp;uid=2&amp;amp;uid=26582&amp;amp;uid=3&amp;amp;uid=67&amp;amp;uid=62&amp;amp;sid=21103320511793&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Machairodontinae&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Machairodontinae&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048352?utm_source=feedburner&amp;amp;utm_medium=feed&amp;amp;utm_campaign=Feed%3A+plosone%2FPLoSONE+%28PLOS+ONE+Alerts%3A+New+Articles%29&quot; rel=&quot;nofollow&quot;&gt;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048352?utm_source=feedburner&amp;amp;utm_medium=feed&amp;amp;utm_campaign=Feed%3A+plosone%2FPLoSONE+%28PLOS+ONE+Alerts%3A+New+Articles%29&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://books.google.com.br/books?id=FhvmHW972mAC&amp;amp;pg=PA752&amp;amp;lpg=PA752&amp;amp;dq=Felidae+%22sexual+selection%22&amp;amp;source=bl&amp;amp;ots=Ns8iRUQxXW&amp;amp;sig=r5ZEgp-nH9mll5cYgB5GzNaThZs&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=FBPQUq63LPDLsQS0m4DAAw&amp;amp;ved=0CDYQ6AEwADgK#v=onepage&amp;amp;q=Felidae%20%22sexual%20selection%22&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;http://books.google.com.br/books?id=FhvmHW972mAC&amp;amp;pg=PA752&amp;amp;lpg=PA752&amp;amp;dq=Felidae+%22sexual+selection%22&amp;amp;source=bl&amp;amp;ots=Ns8iRUQxXW&amp;amp;sig=r5ZEgp-nH9mll5cYgB5GzNaThZs&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=FBPQUq63LPDLsQS0m4DAAw&amp;amp;ved=0CDYQ6AEwADgK#v=onepage&amp;amp;q=Felidae%20%22sexual%20selection%22&amp;amp;f=false&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mapoflife.org/topics/topic_203_Baculum-%28penile-bone%29-in-mammals/&quot; rel=&quot;nofollow&quot;&gt;http://www.mapoflife.org/topics/topic_203_Baculum-%28penile-bone%29-in-mammals/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0169534703003999&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0169534703003999&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4821" LastEditorUserId="4821" LastEditDate="2014-01-10T15:37:50.493" LastActivityDate="2014-01-10T15:37:50.493" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14384" PostTypeId="2" ParentId="14361" CreationDate="2014-01-10T15:00:26.703" Score="1" Body="&lt;p&gt;Oreotrephes, it all depends on the needs. Reproductive schemas don't exclude shape schemas. There has been, however, a shift to cladistics in classification, which means to give scientific names ONLY to monophyletic groups, i.e. groups that include all the descendants of a single ancestor - and only its descendants. But we still use tree/shrub distinction and epiphytes, for instance, but that's to describe the ecology of species, helping identify them, not to classify them on these grounds alone.&lt;/p&gt;&#xA;" OwnerUserId="4821" LastActivityDate="2014-01-10T15:00:26.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14385" PostTypeId="1" AcceptedAnswerId="14407" CreationDate="2014-01-10T16:40:25.000" Score="1" ViewCount="394" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xasar.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My answer ( after rounding off) is 9% -100( 0.75 X 0.25 X 0.5) but the answer given is 22 %&#xA;Am I correct ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2014-01-10T16:51:43.837" LastActivityDate="2014-01-11T02:57:22.407" Title="Blood group probability question" Tags="&lt;homework&gt;&lt;hematology&gt;&lt;red-blood-cell&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14386" PostTypeId="1" CreationDate="2014-01-10T16:48:39.237" Score="8" ViewCount="1012" Body="&lt;p&gt;Fluoride is a common active ingredient in tooth paste to prevent dental caries. It is also added or removed from the water supply in some communities for the same reason, but in children only.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding is that the fluoride in tooth paste reacts with minerals in saliva then bonds to the tooth enamel. The fluoride in water is ingested and is somehow added to the developing bones and teeth of growing children, to the benefit of making decay resistant teeth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the biochemical pathway of each process? A perfect answer will also discuss fluorosis and when that occurs and why. &lt;/p&gt;&#xA;" OwnerUserId="3970" LastEditorUserId="19099" LastEditDate="2017-05-01T14:24:45.727" LastActivityDate="2017-05-11T09:28:14.537" Title="How does fluoride prevent tooth decay?" Tags="&lt;biochemistry&gt;&lt;pathology&gt;&lt;teeth&gt;&lt;decay&gt;&lt;minerals&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14387" PostTypeId="1" AcceptedAnswerId="14393" CreationDate="2014-01-10T16:51:06.617" Score="1" ViewCount="115" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;Cells of a triple-mutant yeast strain (leu- his- trp-) were spread&#xA;either on minimal medium or on minimal medium supplemented with&#xA;various combinations of histidine, leucine, or tryptophan. The&#xA;cultures were grown at either 25C or 37C for 3 days. Colony numbers&#xA;in each plate were counted, and the data are listed in the following&#xA;table.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/exl4o.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;What kind of mutation most probably causes the his- phenotype?What&#xA;kind of mutation most probably causes the leu- phenotype?&lt;/p&gt;&#xA;&lt;p&gt;A.Point mutation&lt;/p&gt;&#xA;&lt;p&gt;B.missense mutation&lt;/p&gt;&#xA;&lt;p&gt;c.nonsense mutation&lt;/p&gt;&#xA;&lt;p&gt;d.conditional mutation&lt;/p&gt;&#xA;&lt;p&gt;e.deletion mutation&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;My questions&lt;/strong&gt; : What is the meaning of confluent in this context ? Can anyone give me a hint to solve this question ? I have no clue how to solve this.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-01-10T18:34:15.623" Title="Identifying mutations in a yeast strain" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14388" PostTypeId="1" AcceptedAnswerId="14415" CreationDate="2014-01-10T17:04:09.557" Score="1" ViewCount="583" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/e88sg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What is the map unit distance between L and S allele ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My working : If we take the normal ratio :9:3:3:1 , first one should be 9/16 = 0.5625&#xA;and then subtract 0.51 from it, we get 0.0525, similarly working we get 0.0525 difference for all 4 and so the distance is 0.0525 X 4 X 100 = 21&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is my working correct ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-11T10:32:19.493" Title="Linkage distance calculation" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;genetic-linkage&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14389" PostTypeId="1" AcceptedAnswerId="14394" CreationDate="2014-01-10T17:12:09.443" Score="1" ViewCount="628" Body="&lt;p&gt;Since adipocytes export fatty acids and glycerol and don't use them as an energy source, what is the main source of energy for adipocytes?&lt;/p&gt;&#xA;" OwnerUserId="5354" LastEditorUserId="16299" LastEditDate="2015-12-31T19:09:22.313" LastActivityDate="2015-12-31T19:09:22.313" Title="What is the energy source for adipocytes?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14390" PostTypeId="1" AcceptedAnswerId="14391" CreationDate="2014-01-10T17:23:35.323" Score="5" ViewCount="17804" Body="&lt;p&gt;I'm reading some text (purchase request) that has the following line in it.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(-)-Norepinephrine&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What does the minus sign mean in front that is in parenthesis? Is this some kind of standard way of describing charge of the molecule or something? Or is this someone's way of representing something else? Or does this mean nothing?&lt;/p&gt;&#xA;" OwnerUserId="4488" LastEditorUserId="6" LastEditDate="2014-01-10T17:54:24.423" LastActivityDate="2018-05-19T13:35:46.037" Title="What does the (-) in the molecule name mean?" Tags="&lt;organic-chemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14391" PostTypeId="2" ParentId="14390" CreationDate="2014-01-10T17:52:46.073" Score="6" Body="&lt;p&gt;The minus sign in parentheses here indicates the optical rotation, (+) means the molecule rotates linear polarized light clockwise, (-) means it rotates counterclockwise. Typically you would also write exactly which stereoisomer is meant (R or S), which is generally the more useful information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following are all valid names for the natural stereoisomer of norepinephrine:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;D-norepinephrine&lt;/li&gt;&#xA;&lt;li&gt;D-(-)-norepinephrine&lt;/li&gt;&#xA;&lt;li&gt;(R)-norepinephrine&lt;/li&gt;&#xA;&lt;li&gt;(R)-(-)-norepinephrine&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I'd recommend that you take a look at the concept of &lt;a href=&quot;http://en.wikipedia.org/wiki/Chirality_%28chemistry%29&quot; rel=&quot;noreferrer&quot;&gt;Chirality&lt;/a&gt; if you're not already familiar with it.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2014-01-10T18:10:07.310" LastActivityDate="2014-01-10T18:10:07.310" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14392" PostTypeId="1" AcceptedAnswerId="14397" CreationDate="2014-01-10T17:57:38.130" Score="1" ViewCount="1673" Body="&lt;p&gt;I have a list of mouse genes, but all our analysis happens for human genes. Is that possible to translate these mouse genes to human genes? and is there any tool that can help me on this?    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am mostly a computer science guy, I am not sure this is even possible. However, according to someone, this could happen, I don't expect a full conversion though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks. &lt;/p&gt;&#xA;" OwnerUserId="5216" LastActivityDate="2014-01-10T22:28:18.857" Title="mouse gene translated to human gene" Tags="&lt;genetics&gt;&lt;human-genome&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14393" PostTypeId="2" ParentId="14387" CreationDate="2014-01-10T18:14:38.173" Score="2" Body="&lt;p&gt;For starters, you can just google &quot;confluent&quot;.  It means that there are no colonies, but that the cells cover the whole plate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when you provide all three amino acids, the cells fill up the whole plate.  If you leave His out, but keep the plate at 25 degrees, the plate still fills up with cells, so the His- allele isn't hurting the cells at all at 25 degrees, but it's pretty nasty at 37 degrees.  That makes it conditional; the mutation only impairs His metabolism at some temperatures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is not a single cell which is surviving a lack of Leu, but there are some which are surviving the lack of Trp, and the lack of His at harmful temperatures.  Presumably, those are the small number which are lucky enough to acquire mutations which compensate for the original deleterious alleles, but NO cells were able to overcome the problem with the Leucine metabolism.  This suggests that the Leucine mutation might be a total deletion.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastEditorUserId="1320" LastEditDate="2014-01-10T18:34:15.623" LastActivityDate="2014-01-10T18:34:15.623" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14394" PostTypeId="2" ParentId="14389" CreationDate="2014-01-10T18:30:41.717" Score="1" Body="&lt;p&gt;Adipocytes use glucose as an energy source. They express the insulin-responsive glucose transporter &lt;a href=&quot;http://en.wikipedia.org/wiki/GLUT4&quot; rel=&quot;nofollow&quot;&gt;GLUT4&lt;/a&gt; just like muscle cells so that when blood glucose levels rise they are primed to take the glucose up for fatty acid biosynthesis, but they also use glucose as a fuel molecule.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-01-10T18:30:41.717" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14395" PostTypeId="1" CreationDate="2014-01-10T18:47:52.553" Score="0" ViewCount="1792" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Formation of Rh  antigen is controlled by dominant gene(R) and its&#xA;  absence by recipient gene(r).People having this antigen with genotype&#xA;  (RR or Rr) are called Rh positive and those whose blood is devoid of&#xA;  it with genotype (rr) are called Rh negative. About 85% in world are&#xA;  Europe and 97% human being in India are Rh positive.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My questions are:-&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which factors result into dominance of gene(R) and  absence of recipient gene(r)?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;With difference seen in %ratio in India and Europe, can it be concluded that environmental factors affects it.?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4326" LastEditorUserId="1320" LastEditDate="2014-02-02T16:13:46.787" LastActivityDate="2014-02-02T16:31:01.197" Title="Rh factor and dominance of gene" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;hematology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14396" PostTypeId="2" ParentId="14248" CreationDate="2014-01-10T19:14:27.323" Score="1" Body="&lt;p&gt;idea 1) It's possible that some subset of your area has higher-scale / better resolution aerial photographs available. Could you find these and use them to test your model?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;idea 2) What geographical area / timescale are you looking at? For certain areas/times, you can get a bit of data on phenology from dated herbarium specimens (ie pressed plant collections). So, for instance, you might select a few plant species that you think are good indicators of whatever phenology you're modelling, search for them on &lt;a href=&quot;http://www.gbif.org/&quot; rel=&quot;nofollow&quot;&gt;GBIF&lt;/a&gt;, consider only those specimens that match your geographical area, and look at what time of year the collections have been made. Then you could look at the first, or last, or various quantiles of phenology. It's not ideal data, but each specimen represents a very direct data point (that is, you know there was at least one individual that had flowered / leafed / whatever at that exact date and georeference), and it's available without getting your feet dirty.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;idea 3) Again depending on your geographical area and what measure of phenology you're interested in, you might even be able to use non-aerial photographs, if they're dated.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-01-10T19:20:13.617" LastActivityDate="2014-01-10T19:20:13.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14397" PostTypeId="2" ParentId="14392" CreationDate="2014-01-10T19:25:38.813" Score="2" Body="&lt;p&gt;I would recommend using &lt;a href=&quot;http://www.ensembl.org/biomart&quot; rel=&quot;nofollow&quot;&gt;Biomart&lt;/a&gt; from Ensembl. This is basically a Swiss Army Knife for converting gene names into various IDs, getting corresponding locations on the chromosomes and so on. You can upload a list of gene names and convert them into the corresponding gene IDs of other species and the convert these IDs back to gene names. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you haven't used Biomart yet, you can either start by going on their &lt;a href=&quot;http://www.ensembl.org/info/index.html&quot; rel=&quot;nofollow&quot;&gt;help page&lt;/a&gt; or by having a look on this &lt;a href=&quot;http://data.bits.vib.be/pub/trainingmaterial/tutorials/BIOMART-ID-conversion.pdf&quot; rel=&quot;nofollow&quot;&gt;tutorial&lt;/a&gt; for the conversion of IDs.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-01-10T19:25:38.813" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14398" PostTypeId="1" AcceptedAnswerId="14404" CreationDate="2014-01-10T19:27:07.683" Score="1" ViewCount="305" Body="&lt;p&gt;I read that one of the ways alcohol is carcinogenic is via accelerated mitosis due to acetaldehyde, I was wondering what pathway caused this acceleration?&lt;/p&gt;&#xA;" OwnerDisplayName="user3534" LastActivityDate="2014-01-10T22:41:30.027" Title="How does Acetaldehyde accelerate mitosis?" Tags="&lt;cancer&gt;&lt;liver&gt;&lt;alcohol&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14399" PostTypeId="1" CreationDate="2014-01-10T19:37:16.710" Score="1" ViewCount="566" Body="&lt;p&gt;The easiest carcinogenic thing for me to grasp is radiation, as it directly messes with DNA. Then it seems there are other compounds that simply mimic hormones, but these shouldn't necessarily cause cancer, right? Then there are things that can accelerate mitosis or mess with other processes, which can inadvertently mess with DNA. So my question is, in general, how many different flavors of carcinogens are there? I know there are a lot, but can someone list a good few? Maybe some examples? I'm most interested in how plastics and things like smoke cause cancer. I think a few examples would be best in aiding my understanding. Thank you! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: I also just realized this is not the Chemistry Stack Exchange, I think I am more interested in the chemistry side of this question, but it might need to be migrated.&lt;/p&gt;&#xA;" OwnerDisplayName="user3534" LastEditorUserId="3340" LastEditDate="2014-06-17T11:37:12.513" LastActivityDate="2014-06-17T21:31:35.680" Title="Carcinogens, how do they work?" Tags="&lt;cancer&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14400" PostTypeId="2" ParentId="14172" CreationDate="2014-01-10T20:04:42.957" Score="0" Body="&lt;p&gt;Yes -&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its all binding kinetics - even a monoclonal antibody will bind many different antigens. The affinity/avidity will be different depending on the interactions. The target antigen may have the lowest known K_d, but antibodies will still bind to many many other antigens. This is why when doing research using antibodies you often have to &quot;block&quot; your specimen with something like BSA or milk to try and reduce the &quot;non-specific&quot; binding. &lt;/p&gt;&#xA;" OwnerUserId="5385" LastActivityDate="2014-01-10T20:04:42.957" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14403" PostTypeId="2" ParentId="14392" CreationDate="2014-01-10T22:28:18.857" Score="0" Body="&lt;p&gt;Sounds like you are searching for homologs of mouse genes in human genome. &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi&quot; rel=&quot;nofollow&quot;&gt;BLAST&lt;/a&gt; should be able to help you finding that. You might want to find the sequences for the mouse genes on &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genbank/&quot; rel=&quot;nofollow&quot;&gt;GenBank&lt;/a&gt; and run BLAST against it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in this scenario, &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&amp;amp;PAGE_TYPE=BlastSearch&quot; rel=&quot;nofollow&quot;&gt;protein BLAST&lt;/a&gt; (BLASTp) will actually helps you more since the protein sequences are conserved better than DNA sequences are between species. In this case, you need to find the proteins coded by the mouse genes, and run BLASTp then.&lt;/p&gt;&#xA;" OwnerUserId="4136" LastActivityDate="2014-01-10T22:28:18.857" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14404" PostTypeId="2" ParentId="14398" CreationDate="2014-01-10T22:41:30.027" Score="1" Body="&lt;p&gt;First of all Alcohol and Acetaldehyde are both cytotoxic. Along in our development we learned to deal with both substances, which is shown by specific metabolism pathways to break them down (for example alcohol dehydrogenase, acetaldehyde dehydrogenase, Cytochrom P450 and so on).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alcohol and Acetaldehyde both have a negative effect on mitosis (which explains a good part of the negative effect which alcohol has on developing embryos).&#xA;Examples can be the following articles:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3526962&quot; rel=&quot;nofollow&quot;&gt;Acetaldehyde causes a prolongation of the doubling time and an&#xA;increase in the modal volume of cells in culture.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8590624&quot; rel=&quot;nofollow&quot;&gt;Alcohol inhibits cell mitosis in G2-M phase in cell cycle in a human&#xA;lymphocytes in vitro study.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9105508&quot; rel=&quot;nofollow&quot;&gt;Ethanol induces transient arrest of cell division (G2 + M block)&#xA;followed by G0/G1 block: dose effects of short- and longer-term&#xA;ethanol exposure on cell cycle and cell functions.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7389419&quot; rel=&quot;nofollow&quot;&gt;Ethanol induction of sister chromatid exchanges in human cells in&#xA;vitro.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Alcohol also has some effect on cancer - probably not by directly causing it, but at least as an additional risk factor. One article I found (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16455479&quot; rel=&quot;nofollow&quot;&gt;Alcohol and Cancer&lt;/a&gt;&quot;) mentions the following possibilities:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The mechanisms by which alcohol consumption exerts its carcinogenic&#xA;  effect have not been defined fully, although plausible events include:&#xA;  a genotoxic effect of acetaldehyde, the main metabolite of ethanol;&#xA;  increased oestrogen concentration, which is important for breast&#xA;  carcinogenesis; a role as solvent for tobacco carcinogens; production&#xA;  of reactive oxygen species and nitrogen species; and changes in folate&#xA;  metabolism.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Using &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?cmd=Link&amp;amp;dbFrom=PubMed&amp;amp;from_uid=15082451&quot; rel=&quot;nofollow&quot;&gt;Pubmed&lt;/a&gt; you can find more articles on that topic.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-01-10T22:41:30.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14407" PostTypeId="2" ParentId="14385" CreationDate="2014-01-11T02:40:53.977" Score="2" Body="&lt;p&gt;I think the quoted answer is correct.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, the probability of getting a son( and not a daughter) is $P_s=0.5$.&#xA;Next, since both the parents are heterozygous, the probability of genotype $hh$ is $P_h=0.25$. This genotype will not produce any antigen precursor, and hence there will be no antigens on RBC. As blood group O is defined by the absence of antigens, this can be classified as blood group O.For the expression of the antigen (dominant at the $H$ locus), the probability is $P_H=0.75$.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again owing to the heterozygosity of both the parents at $I$ locus, the probability of getting a blood group with genotype $I^oI^o$ is $P_I=0.25$. This is the probability, that if the antigen precursor is made, $75%$% of the times the expressed blood group will be O. Therefore the probability of blood group O due to homozygous $I$ locus and dominant $H$ locus is $P_I\times P_H=3/16$.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Net probability for blood group O=(probability due to homozygous h+probability due to homozygous I and dominant H)*probability of a son.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$P_{net}=P_s(P_h+P_HP_I)\approx 0.22$$  &lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2014-01-11T02:57:22.407" LastActivityDate="2014-01-11T02:57:22.407" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14408" PostTypeId="1" AcceptedAnswerId="14431" CreationDate="2014-01-11T03:26:00.853" Score="3" ViewCount="136" Body="&lt;p&gt;Is it the eradication of the virus (assuming rhinovirus) by white blood cells? Or does your body somehow adapt to presence of the virus?&lt;/p&gt;&#xA;" OwnerUserId="5390" LastActivityDate="2014-01-12T11:00:13.187" Title="How does your body ultimately recover from a cold?" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14409" PostTypeId="1" AcceptedAnswerId="17294" CreationDate="2014-01-11T04:44:54.900" Score="9" ViewCount="573" Body="&lt;p&gt;I was thinking that even though I know how generally the cell works, I don't really have a feeling of how volatile it is.&#xA;I want to know what is the lifetime/turnover rate of different constituents of the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the molecular level what are the lifetimes for various proteins, for ribosome, lipids, carbohydrates, DNA and RNA. What about aminoacids, nucleotides?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the organelle level what are the lifetimes of the mitochondria, golgi apparatus. Does nucleus or ER ever change if not during meiosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that the lifetime depends on the context. For example, for DNA, cells that replicate, half-life is about one replication as a whole new strand is generated. In neurons, that don't replicate for decades it's not the case. But the DNA can't just sit there. It is constantly unraveled, transcribed, damaged and repaired. So it has a different time constant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am still very interested to know any specific numbers.&lt;/p&gt;&#xA;" OwnerUserId="5391" LastEditorUserId="5391" LastEditDate="2014-06-23T17:59:27.133" LastActivityDate="2014-06-23T17:59:27.133" Title="What are the lifetimes of cellular components on organelle or molecular level?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14410" PostTypeId="1" AcceptedAnswerId="14413" CreationDate="2014-01-11T05:14:48.770" Score="1" ViewCount="364" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;The domain structure of protein Z, which is composed of 180 amino&#xA;  acids, is shown in the upper part of the figure below. Protein Z is&#xA;  palmitoylated at a cysteine residue (the third amino acid) through the&#xA;  mechanism shown in the box.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LqoU2.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Which of the following diagrams shows the correct topology of protein&#xA;  Z in the plasma membrane?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wW7tu.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the second diagram is correct because cytoplasmic side has reducing environment and so SH will not be allowed to react this way. Am I right ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-11T09:58:48.920" Title="Topology of protein" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14412" PostTypeId="2" ParentId="9155" CreationDate="2014-01-11T09:14:06.007" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Any other database better than NCBI ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A lot of people overlook some sub-databases inside NCBI and search the main nucleotide database only.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If You never tried it, you can blast the HIV sequence which You have found, against other databases. On the ncbi blast webpage, just choose the options other than &lt;em&gt;nucleotide collection (nr/nt)&lt;/em&gt;. I tend to find new sequences in &lt;em&gt;Expressed sequence tags (EST)&lt;/em&gt;, &lt;em&gt;Genomic survey sequences (GSS)&lt;/em&gt; or &lt;em&gt;Whole genome shotgun contigs (WGS)&lt;/em&gt;. Some of these databases cover unfinished sequencing project and should be a source of new data. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I am a plant person, not virus person, so maybe you will find out, that different databases are worth searching for you. Or you will find it a waste of time.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW, now some time had passed since your question. How did you solve Your HIV sequence problem ? &lt;/p&gt;&#xA;" OwnerUserId="5369" LastActivityDate="2014-01-11T09:14:06.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14413" PostTypeId="2" ParentId="14410" CreationDate="2014-01-11T09:58:48.920" Score="2" Body="&lt;p&gt;I don't think there's any oxidation or reduction going on in this reaction; certainly there is no net reduction or involvement of NADH cofactor or anything like that. Furthermore, I think that it isn't too hard (esp. since these are enzyme-catalyzed reactions) to imagine that the mechanism is simple: nucleophilic attack of the carbon of the thioester by the cysteine, forming a thioketal intermediate, resulting in ejecting the CoASH as a leaving group. No reduction or oxidation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead of oxidation or reduction, I would think about where exactly are the components of each reaction present. In order for the palmitoylation reaction to occur, you need: the protein Z N terminus, palmitoyl-CoA, and protein acyltransferase. Where are these components more likely to be present, inside or outside of the cell? Especially given that CoASH has several negatively charged phosphate groups.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2014-01-11T09:58:48.920" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14414" PostTypeId="1" AcceptedAnswerId="14419" CreationDate="2014-01-11T10:29:14.060" Score="41" ViewCount="52106" Body="&lt;p&gt;After my online research on the subject, I learnt that, biologically speaking, many scientists believe that there is no such thing as a race. &lt;em&gt;Homo sapiens&lt;/em&gt; as a species is only 200,000 years old, which has not allowed for any significant genetic diversification yet, and our DNA is 99.99% similar. I've read statements that there can be more genetic variation inside a racial group than between different racial groups, meaning that, for example, two individuals from the same &quot;race&quot; can have less in common with each other than with an individual from another &quot;race&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Race_(human_classification)&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia on Race (human classification) quote&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Scientists consider biological essentialism obsolete, and generally discourage racial explanations for collective differentiation in both physical and behavioral traits&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Q1:&lt;/strong&gt; If &lt;em&gt;Homo sapiens&lt;/em&gt; has no races (according to biologists), why are we so different morphologically? (hair/eyes/skin colour and even athletic performance seem to differ between human populations)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Q2:&lt;/strong&gt; Is it common for other species too, when genetically close populations have very different morphological traits? Are there any other mammal or animal species that exhibit biological diversity comparable to human diversity, and how do taxonomists treat these species? (excluding intentionally bred domestic species to keep the comparison fair)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;The question has been paraphrased to emphasize that it is the &lt;strong&gt;biological&lt;/strong&gt; debate that is in question, not the &lt;strong&gt;sociopolitical&lt;/strong&gt;. I.e., why is there no consensus in evidence and opinions of scientists?&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="5392" LastEditorUserId="4109" LastEditDate="2015-04-16T16:22:00.160" LastActivityDate="2019-06-05T23:58:12.463" Title="Do humans have enough biological differences to be grouped into races or subspecies?" Tags="&lt;human-genetics&gt;&lt;taxonomy&gt;" AnswerCount="6" CommentCount="5" FavoriteCount="17" ContentLicense="CC BY-SA 3.0" />
  <row Id="14415" PostTypeId="2" ParentId="14388" CreationDate="2014-01-11T10:32:19.493" Score="1" Body="&lt;p&gt;With the heterozygous genotype $LlSs$, there are two kinds of linkages possible.&lt;br&gt;&#xA;1. Cis=$LS.ls$&lt;br&gt;&#xA;2. Trans=$Ls.lS$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All the possible gametes ($LS,lS,Ls,ls$) in both cases are same, but their frequency differs based on the strength of linkage and hence, the distance on the chromosome map. In either case, the frequency of $LS$ and $ls$ will be same, and $Ls$ and $lS$ will be same. This is because, in the Cis linkage, the former pair will constitute the parental linkage and the latter will be the recombinants, but both the gametes within the pair are equally likely to be formed. The same is the case for Trans linkage where the former pair acts as the recombinants.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the given table, frequency of $llss$ is $0.01$. $llss$ can only be formed by the combination of two $ls$ gametes. Therefore the probability of an $ls$ gamete will be $\sqrt{(0.01)}=0.1$.&lt;br&gt;&#xA;The probability of getting an $ls$ gamete is $0.1$. Therefore, the probability of $LS$ is $0.1$, $lS$ is $0.4$ and $Ls$ is $0.4$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As $Ls$ and $lS$ are more probable, they are more likely to be linked, and hence the genotype will be in Trans linkage. Then the frequency of recombinants($LS,ls$) is $0.2$. The chromosomal distance is $20 \text{ cM}$ or $20\text{ map units}$.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure whether my line of arguments are true. If you do find any flaw, please let me know.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2014-01-11T10:32:19.493" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14416" PostTypeId="2" ParentId="14414" CreationDate="2014-01-11T11:11:36.527" Score="11" Body="&lt;p&gt;&lt;strong&gt;Bias&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you say &lt;code&gt;phenotype&lt;/code&gt; you mostly mean &quot;skin color&quot;, &quot;size of the nose&quot;, &quot;hair color&quot;, &quot;shape of the eyes&quot;, &quot;height&quot;, and some others. All these traits that we manage to find to explain &lt;a href=&quot;http://en.wikipedia.org/wiki/Population_stratification&quot; rel=&quot;nofollow noreferrer&quot;&gt;population structure&lt;/a&gt; among humans. But you forget all the rest of the phenotypic diversity. If you would choose 1000 randomly chosen traits (external morphology and other stuff) and make a &lt;a href=&quot;http://en.wikipedia.org/wiki/Principal_component_analysis&quot; rel=&quot;nofollow noreferrer&quot;&gt;PCA&lt;/a&gt;. Will the main axes explain much of the inter-subpopulation (or inter-racial) diversity? I am not sure about that. One cannot use one subset of the total phenotypic or genetic variance and use it in order to define several species within what was previously thought to be one. It is not because two genes are associated with the same population structure that one can define two different species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;scientific observations vs biased intuitions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[..] is it reasonable to use a genetic approach to races and claim that biological races do not exist, while it seems to be a poor indicator, when it comes to comparison of phenotypes of human populations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Similarly, one could say&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bats look like birds. We consider them as being mammals just because that is what scientific observations (genetic data or in-depth observation of the phenotypic variance) says. Should we follow scientific explanations when my personal bias intuition tells me that these observations are poor indicators?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The answer is yes if you want to increase your knowledge and no if you just want to be comforted into what you think you already know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have to confess though that I don't know much about phenotypic or morphological variations among humans. And I'd be curious if someone could give some words about that and whether or not much of the phenotypic and morphological variance is explained by what we consider being racial groups. It might be possible that very little of the total phenotypic variance is explained by racial groups but quite a lot of the face morphological variance is explained by racial groups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Concept of species&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For species that can reproduce exclusively with sex, we tend to use the concept of reproduction isolation to define a species and I really don't think that there is a pair of racial groups are sexually incompatible (however you delimit the racial groups). Eventually, there might have some slight inbreeding depression but I am not sure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might want to have a look at &lt;a href=&quot;https://biology.stackexchange.com/questions/39664/how-could-humans-have-interbred-with-neanderthals-if-were-a-different-species/39669#39669&quot;&gt;this answer&lt;/a&gt; to understand the semantic difficulties behind the concept of species&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-12-31T00:11:23.133" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="14417" PostTypeId="2" ParentId="14414" CreationDate="2014-01-11T12:05:56.950" Score="35" Body="&lt;p&gt;Well, that's just it, we &lt;em&gt;don't&lt;/em&gt; actually have much phenotypic variation. For example, compare this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0KZibm.jpg&quot; alt=&quot;Collection of human faces&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;to this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3bmJzm.jpg&quot; alt=&quot;Collection of dogs&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gReb7m.jpg&quot; alt=&quot;Collection of cat faces&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Or this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Xi6tb.jpg&quot; alt=&quot;Six human babies&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;to this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/p5fXR.png&quot; alt=&quot;Five dogs&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;This&lt;/em&gt; is phenotypic variation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9VfSo.jpg&quot; alt=&quot;Collection of pigs&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;And of course, you can't beat the birds of paradise when it comes to variation (though, strictly speaking, these are different species):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/A35gy.jpg&quot; alt=&quot;Collection off birds of paradise&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;So, as I hope is clear from the images above, phenotypic variation among humans is &lt;em&gt;tiny&lt;/em&gt; compared to other species. We just notice small differences much more because, well, it's us so little differences are much more noticeable.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="975" LastEditDate="2017-03-23T21:34:32.307" LastActivityDate="2017-03-23T21:34:32.307" CommentCount="21" ContentLicense="CC BY-SA 3.0" />
  <row Id="14418" PostTypeId="1" CreationDate="2014-01-11T12:30:59.860" Score="0" ViewCount="148" Body="&lt;p&gt;What are the physiological events that occur after there is endothelial interruption in the blood vessel?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does endothelial interruption mean here? And what could be the physiological events?&lt;/p&gt;&#xA;" OwnerUserId="1765" LastActivityDate="2014-01-11T12:30:59.860" Title="Events after Endothelial interruption" Tags="&lt;hematology&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14419" PostTypeId="2" ParentId="14414" CreationDate="2014-01-11T13:01:22.660" Score="49" Body="&lt;p&gt;Firstly, it's not true that you can't tell racial background from DNA. You most certainly can; it's quite possible to give fairly accurate phenotypic reconstruction of the features we choose as racial markers from DNA samples alone and also possible to identify real geographic ancestral populations from suitable markers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason that human races aren't useful is that they're actually only looking at a couple of phenotypic markers and (a) these phenotypes don't map well to underlying genetics and (b) don't usefully model the underlying populations. The big thing that racial typing is based on is skin colour, but skin colour is controlled by only a small number of alleles. On the basis of skin colour you'd think the big division in human diversity is (and I simplify) between white Europeans and black Africans. However, there is &lt;em&gt;vastly&lt;/em&gt; more genetic diversity within Africa than there is anywhere else. Two randomly chosen Africans will be, on average, more diverse from each other than two randomly chosen Europeans. What's more Europeans are no more genetically distinct overall from a randomly chosen African than two randomly chosen Africans are from each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This makes perfectly decent sense if you consider the deep roots of diversity within Africa (where humans originally evolved) to the more recent separation of Europeans from an African sub-population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also worth noting that the phenotypic markers of race don't actually tell you much about underlying heredity; for example there's a famous photo of twin daughters one of whom is completely fair skinned, the other of whom is completely dark skinned; yet these two are sisters. This is, of course, an extreme example but it should tell you something about the usefulness of skin colour as a real genetic marker. &lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2014-01-11T13:01:22.660" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="14420" PostTypeId="2" ParentId="14309" CreationDate="2014-01-11T16:00:49.547" Score="2" Body="&lt;p&gt;Not sure, whether it fits in your requirement (since it was not clear for me with the terdon's answer), but I'd also mention plasmodia and other cases of species with syncytial organization: they have multiple nuclei, sometimes have even macroscopic sizes, but formally there is only one cell boundary within their body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(If we broaden this definition, we may also include all kinds of protists with multiple nuclei: from &lt;a href=&quot;https://en.wikipedia.org/wiki/Diplomonad&quot; rel=&quot;nofollow&quot;&gt;diplomonads&lt;/a&gt; (which have two equal nuclei) and &lt;a href=&quot;https://en.wikipedia.org/wiki/Ciliate#Nuclei&quot; rel=&quot;nofollow&quot;&gt;ciliates&lt;/a&gt; (most of which have two functionally differentiated nuclei) to Pelomyxa or giant foraminiferans with huge numbers of nuclei.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Myxosporidia, once thought to be a group of protists and now believed to be highly aberrant metazoans - are parasites of fish (first generation) and some invertebrates (second generation), which form highly differentiated &lt;a href=&quot;http://link.springer.com/article/10.1007/BF00968848&quot; rel=&quot;nofollow&quot;&gt;plasmodial bodies&lt;/a&gt; in their hosts.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Orthonectids, a group of &quot;lower metazoans&quot;, have a biphasic life-cycle with sexual generation represented by oligocellular free-living males and females, which produce zygotes developing into &lt;a href=&quot;http://www.nature.air.ru/invertebrates/pdf_files/invert5_1%20047_051_slyusarev.pdf&quot; rel=&quot;nofollow&quot;&gt;parasitic plasmodia&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://people.oregonstate.edu/~everhars/Life_History_Strategies_FDiv_2008.pdf&quot; rel=&quot;nofollow&quot;&gt;Myxogastrid&lt;/a&gt; slime molds are famous in having plasmodial fruit bodies: they are relatives of Dictyostelium and have a similar life-cycle with mono-nuclear amoebae, which conjugate and produce the plasmodium. So, these are still formally &quot;unicellular&quot; even as fruit bodies.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Some algae have plasmodial organization with the most famous case of Caulerpa, species of which &lt;a href=&quot;https://en.wikipedia.org/wiki/Caulerpa&quot; rel=&quot;nofollow&quot;&gt;&quot;are unusual because they consist of only one cell with many nuclei, making them among the biggest single cells in the world.&quot;&lt;/a&gt;. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Cannot recall right now the name of the group (can someone help?), but there are amoebae, which are &quot;normally&quot; unicellular, but able to aggregate on rich food resources to form trophic plasmodium.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Lots of other cases.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-01-11T16:00:49.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14423" PostTypeId="2" ParentId="8272" CreationDate="2014-01-11T22:35:36.987" Score="17" Body="&lt;p&gt;Long story short, the astronaut probably wouldn't make it, and would first loose consciousness then suffocate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a lot of myth and hollywood dramatization regarding this kind of thing. Here are some:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;You will explode.&lt;/strong&gt; This is just ridiculous. The skin is air tight (relatively speaking). It is also very elastic and can pull and bend quite a great deal before tearing. Through quite a few, equally durable, tissues, it is connected to the bones, which are unaffected by negative air pressure.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Your blood will boil.&lt;/strong&gt; The circulatory system is also a closed system. It is not directly exposed to the environment. Also, the blood pressure in a healthy person is averaged around 100 mmHg and Earth's atmosphere at sea level is 700 mmHg. There is already a massive disparity, yet Earth's atmosphere doesn't go pouring into our veins at random. Likewise, the blood in a person's veins won't go pouring out into the atmosphere simply because the pressure is extremely low.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Any air in your lungs will be forcibly sucked out of you.&lt;/strong&gt; Again, this is a closed system, if you hold your breath. As long as you don't try to breathe there is nothing forcing the air from your lungs.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Your eyes will be sucked from their sockets&lt;/strong&gt;. Thank you &lt;em&gt;Total Recall&lt;/em&gt; (the original) for this myth. The eyes are very firmly in place. You might feel a pull on them, but they aren't going anywhere.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Absolutely none of these would happen in the vacuum of space and certainly not on the Martian surface.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Here's what &lt;em&gt;will&lt;/em&gt; happen:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Any liquid material on the surface of your body will vaporize. All sweat, saliva (if you open your mouth), water in the mucous, and tears on the eyes, will nearly instantly vaporize. It would be quite uncomfortable, especially the eyes, but very survivable. Long term exposure to a vacuum might damage the eyes eventually, but in this scenario there are far more pressing matters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The negative pressure may also cause your eardrums to rupture. Try to imagine the feeling your ears get on the plane at 30 thousand feet times about 100. Since you can't close your ears, plugging them with your fingers may help, but likely just postpone the inevitable pressure disparity, which will lead to at least great discomfort and possible drum rupture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you had the chance, you should take a deep breath before jumping out and avoid trying to breathe at all costs. Opening your lungs for a breath would very quickly draw whatever breath you had in them out into the atmosphere and also vaporize any fluid that was in them. Considering the rapid pace of this event, you would surely have permanent damage from this and begin suffocating and will die in a minute or two unless you get medical attention. There seems to be conflict in the procedure for this, with some sources suggesting that emptying your lungs would be better to avoid this. Considering the astronaut in your example is about to do a 200 meter dash he is going to need all the O&lt;sub&gt;2&lt;/sub&gt; he can get.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cold is also a treacherous factor. At -50C the heat from your body would dissipate so rapidly that it would likely be very debilitating, perhaps causing you to seize up and clutch your extremities to your chest. It would also be excruciatingly painful. It might cause you to fall into shock. In a total vacuum however, this does not exist. A vacuum is actually very insulating, but on Mars' what little atmosphere is there is enough for you to feel the chill.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lack of oxygen and high CO&lt;sub&gt;2&lt;/sub&gt; would be what would eventually kill you. You would eventually try to breathe and loose consciousness within a breath or two (or you might loose consciousness first then your body would try to breathe naturally). Your body would try to keep you alive as long as possible by pumping your heart faster and increasing your blood pressure, but your heart would eventually fail and you would die within seconds after that.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Evaluating your particular scenario&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There are first a few things about the scenario that seem unlikely.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The astronaut would not be naked. They remain in some of their protective gear in case of emergencies like this. He would have some protection against the cold if he had to run out without it.&lt;/li&gt;&#xA;&lt;li&gt;Certain things like extinguishers are always nearby. The idea that one was unreachable is a little silly.&lt;/li&gt;&#xA;&lt;li&gt;Space vehicles, shuttles, and buildings all are compartmentalized like a submarine. They could simply close off the affected areas.&lt;/li&gt;&#xA;&lt;li&gt;Fire only burns in the presence of oxygen (with few exceptions). After being closed off, compartments can be decompressed, halting the fire immediately. They can then begin refilling them with breathable atmosphere. This poses the same vacuum problem if the astronaut is in the affected area, but he won't be trying to run across the surface naked. People have survived rapid decompressions before without a single injury, as listed in my second source, however, others have never regained consciousness.&lt;/li&gt;&#xA;&lt;li&gt;Assuming you made it to the other building, they usually only open from the inside. So unless someone saw you coming and opened the door for you, your last minutes would be better spent desperately fighting the fire until it consumed you rather than banging on the neighbor's door.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;But let's say all of this breaks down and poor Astronaut Joe finds himself making a mad, streaker's dash across the Martian surface.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We should assume that our astronaut is both quite athletic and knowledgeable about the environment outside of his shelter, knowing that he should take a deep breath before heading out, but literally has no time to grab a shirt, goggles, breathing mask, or anything. Just him and Mars.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If he's lucky, it's not too cold and he doesn't seize up and fall into the fetal position within a few steps. Let's say it's -20C, which is pretty darn cold, but tolerable for a minute or two. I next see him flailing across the surface, trying to run in Mars' low gravity (no easy task). He begins to loose vision as a cloud of steam of what should be tears pours from his dry eyes. His eyelids then begin to stick to his eyeballs because there is no longer any lubrication. He is desperate to reach the other building, and his movements get more and more erratic, as his body is rapidly using all of the available oxygen. All the while, he is still holding his breath, knowing that if he attempts to breathe he will likely collapse within seconds and perish. But the more he struggles to make it, the more his innate urge to breathe overpowers his conscious thought to prevent it. Eventually, against his own willpower, he gasps and attempts to inhale deeply. He takes two or three dying breaths, if they can be called that, then falls to the ground unconscious. He dies shortly after when his heart stops and his brain tissues die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The whole ordeal lasts under 30 seconds and he is 100 meters at most away from his shelter. If he did get lucky and actually made it to the other building, he would likely have frostbite over much of his body, permanent damage to his eyes and ears, and possibly deadly exposure to cosmic rays.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The event would be very similar to being drug by a fishing line to the bottom of the sea and drowning.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sources:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.oneplusyou.com/q/v/space_vacuum&quot;&gt;A fun questionnaire to see how long you would last in space&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.geoffreylandis.com/vacuum.html&quot;&gt;What really happens in a vacuum&lt;/a&gt;  &lt;/p&gt;&#xA;" OwnerUserId="3970" LastActivityDate="2014-01-11T22:35:36.987" CommentCount="16" ContentLicense="CC BY-SA 3.0" />
  <row Id="14424" PostTypeId="1" AcceptedAnswerId="14432" CreationDate="2014-01-11T23:36:30.127" Score="4" ViewCount="2385" Body="&lt;p&gt;I'm having difficulty finding an explanation of how single primer amplification of DNA works in the literature available to me, can anyone explain the methodology and what it accomplishes?&lt;/p&gt;&#xA;" OwnerUserId="1763" LastActivityDate="2014-02-11T12:28:04.583" Title="How does sequence independent single primer amplification work?" Tags="&lt;pcr&gt;&lt;primer&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14425" PostTypeId="2" ParentId="10265" CreationDate="2014-01-12T02:19:51.537" Score="3" Body="&lt;p&gt;The question forgets that organisms consume materials for two reasons: To capture chemical energy (which it focuses on) and to gain molecules that the organism cannot otherwise produce. Cellulose effectively serves only one purpose in organisms that digest it: energy production. Eventually, it is broken down into H&lt;sub&gt;2&lt;/sub&gt;O and CO&lt;sub&gt;2&lt;/sub&gt;, both of which are excreted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Throughout the millennia, getting calories was not that difficult, but getting enough essential micronutrients (vitamins, minerals and amino acids) as humans moved into different environments has been where there was selective pressure. Selective pressure for other calorie sources, such as cellulose, has never really happened. Beyond this, there is &lt;a href=&quot;http://en.wikipedia.org/wiki/Nutrient_density&quot; rel=&quot;nofollow&quot;&gt;a ratio of optimal caloric intake to optimal nutrition intake&lt;/a&gt; a human should get from his diet for that human and humanity in general. A mutation or sudden symbiosis with gut bacteria  that allowed for cellulose digestion would make it even more difficult to keep that ratio, but it is non-optimal situations where selective pressure occurs. The issue here, in my opinion, is that that would be too great a selective pressure on decreasing the micronutritional requirements. The human would far too easily get calories and need to eat many times more in calories what he needed to get the necessary nutrition. So actually, there is selective pressure against cellulose digestion. Further, because of the way humans are built and the other great primates, this sudden mutation or symbiosis seems very unlikely. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, cellulose already serves a vital purpose in the gut. It is commonly called fiber, and allows the feces in the colon to remain moist enough to be passed. Some mammals have adapted colons that can pass very dry feces (the Camel's feces is so dry that you can start a fire with it), but they are typically arid climate species, where water is by far the most precious resource. So the selective pressure was on water intake, not calorie intake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there has been no selective pressures on humans to digest cellulose, nor will there ever be, so long as there is such a high need for vitamins, minerals and essential amino acids. Such selective pressure would take the form of there first being super nutrient rich foods (relative to humans), then that same food becoming calorie poor. Basically, humans would have to start replacing a meal or two per day with only vitamin supplements. Even with that, the only mammals I know of that digest cellulose are actually utilizing symbiotic gut bacteria to do so. I can't imagine the clever way humans might get that bacteria into their own guts. &lt;a href=&quot;http://en.wikipedia.org/wiki/Coprophagia&quot; rel=&quot;nofollow&quot;&gt;Actually, I can.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3970" LastEditorUserId="3970" LastEditDate="2014-01-12T15:46:19.720" LastActivityDate="2014-01-12T15:46:19.720" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14426" PostTypeId="1" AcceptedAnswerId="14427" CreationDate="2014-01-12T02:53:34.977" Score="3" ViewCount="110" Body="&lt;p&gt;I guess, we could infer that the structure of an amino acid has the same functional units as RNA is used to synthesise it. Therefore, from a logical point of view it would make sense that genes are expressed as proteins. &#xA;However, why is this the case; why are genes expressed as proteins rather than any other type of bio molecules? Also, from what are other bio molecules expressed if not for genes? &lt;/p&gt;&#xA;" OwnerUserId="5085" LastActivityDate="2014-01-12T07:22:53.283" Title="Why are genes expressed as proteins rather than other types of bio-molecules?" Tags="&lt;proteins&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14427" PostTypeId="2" ParentId="14426" CreationDate="2014-01-12T03:11:37.263" Score="1" Body="&lt;p&gt;Wow - like a biophilosophy question! The answer lies in in building up the largest diversity with minimal subunits. Efficiency if you will. In this case we are talking about amino acids. We only need 20 of them to approach unfathomable numbers of diversity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The protein acts as a messenger, as an enzyme, a carrier and it's own building unit. If you wanted that kind of range out of any other known biomolecules, you would need a gene to code for each of them, and itself a gene a completely different mechanism to build them which we can't even fathom. It's so much simpler to code for a protein, which can act as an enzyme to build other biomolecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However if you are asking about why the central dogma of molecular biology is the way it is...well then, it seems to be axiomatic. &lt;/p&gt;&#xA;" OwnerUserId="3887" LastActivityDate="2014-01-12T03:11:37.263" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14429" PostTypeId="2" ParentId="14426" CreationDate="2014-01-12T07:04:51.723" Score="1" Body="&lt;p&gt;The fact that genes are expressed as proteins and no other type of molecules is because it is one of the oldest remnants from evolutionary history and it was so successful that it has carried on throughout the eons and is now present in every known living organism. It is so old that most biologists would say that it has been present since life first began.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scientists conclude that it is one of the oldest because the genetic code is universal. That means the gene that codes for a specific protein can be inserted into a completely different organism and that organism will begin synthesizing that protein. There are very few exceptions to this rule and this is how scientists can culture bacteria to produce human enzymes such as insulin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genes do not code for any other molecules because there has been no selective pressure for it (if that can actually apply here) and proteins are quite diverse in structure and function for having so relatively few building blocks. There really are no other macromolecules quite like them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am unaware of any non-protein molecules being expressed from genes. You might say that RNA is, but you have to skew the definition of &quot;expressed&quot;. &lt;a href=&quot;http://en.wikipedia.org/wiki/Ribozyme&quot; rel=&quot;nofollow&quot;&gt;Ribozymes&lt;/a&gt; are a good example to make this case. But there is a reason the creation of RNA is called &quot;transcription&quot;, meaning the RNA is not coded from the DNA, rather it is analogous to it, while the creation of proteins is called &quot;translation&quot;, meaning that there is a code involved to get the correct result. It is also obviously clear that RNA serves for protein synthesis and is far less dynamic than proteins.&lt;/p&gt;&#xA;" OwnerUserId="3970" LastEditorUserId="3970" LastEditDate="2014-01-12T07:22:53.283" LastActivityDate="2014-01-12T07:22:53.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14430" PostTypeId="2" ParentId="14424" CreationDate="2014-01-12T10:52:21.687" Score="0" Body="&lt;p&gt;single primer amplification is used to find unknown regions of DNA if you have no idea what to use as a primer further upstream. It works on the idea that any primer given a certain temperature will misprime. That it, it will anneal to a non specific location. So it is PCR, but at this temperature, the five prime region primer will bind specifically to it's known location. On the three prime end up to 3500 bases away, the low annealing temperature will allow this specific primer to bind to something resembling its complementary sequence but not exactly. This way you will still get a successful PCR reaction. Then as the cycles continue, the 3' end binds specifically to your one primer and you can raise the temperature to make it more specific. The primer design and temperatures have to be considered very carefully.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sources&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rothlab.ucdavis.edu/protocols/semirandom.html&quot; rel=&quot;nofollow&quot;&gt;Roth Lab&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3887" LastActivityDate="2014-01-12T10:52:21.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14431" PostTypeId="2" ParentId="14408" CreationDate="2014-01-12T11:00:13.187" Score="1" Body="&lt;p&gt;Great question.&lt;/p&gt;&#xA;&lt;h3&gt;Rhino Virus&lt;/h3&gt;&#xA;&lt;p&gt;For the rhinovirus in particular, it is eradicated.&lt;/p&gt;&#xA;&lt;h3&gt;Integrase&lt;/h3&gt;&#xA;&lt;p&gt;However for some of the retroviruses and other virus that contain an enzyme called 'integrase', they actually integrate their DNA with yours. That way as your cells go about their business, they make the virus genes too. However, you have some white blood cells called CD8 T Cells that mark these 'compromised cells' for death.&lt;/p&gt;&#xA;&lt;h3&gt;Evading&lt;/h3&gt;&#xA;&lt;p&gt;Some viruses though can remain cleverly hidden and don't turn on their own genes in your genome until the immune response goes down, or you stop taking anti-retroviral drugs.  HIV is a great example of a virus you can also 'live' with but never actually eradicate. The medicines you take can kill all the circulating virus down to a non detectable level. However, when you stop taking your meds, the DNA integrated in your genome will start making the virus again, thus you will always 'live' and can never eradicate it.&lt;/p&gt;&#xA;" OwnerUserId="3887" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-01-12T11:00:13.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14432" PostTypeId="2" ParentId="14424" CreationDate="2014-01-12T11:08:44.633" Score="1" Body="&lt;p&gt;This process is called sequence-independent single primer amplification (or in short SISPA). Its used to amplify unknown sequences for amplification, for example in unknown viruses.&#xA;The primers used for this process contain random sequences which should bind to the DNA to be amplified and also known sequences, which can be used a adapters. In the first rounds of PCR only the random primers give rise to specific products, which are amplified exponentially in the later rounds of PCR since the primers fit perfectly then. This is described in detail in this publication:&quot;&lt;a href=&quot;http://www.biotechniques.com/multimedia/archive/00009/03354st06_9908a.pdf&quot; rel=&quot;nofollow&quot;&gt;Random priming PCR strategy to amplify and clone trace amounts of DNA&lt;/a&gt;&quot;&#xA;Another interesting paper describing the method is:&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1664049&quot; rel=&quot;nofollow&quot;&gt;Sequence-independent, single-primer amplification (SISPA) of complex DNA populations.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-01-12T12:03:05.630" LastActivityDate="2014-01-12T12:03:05.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14434" PostTypeId="1" AcceptedAnswerId="14448" CreationDate="2014-01-12T15:56:17.907" Score="3" ViewCount="726" Body="&lt;p&gt;Suppose we wind time back to the instance when life emerged on Earth and let evolution start over again, will human beings or any other kind of self-conscious animals evolve ultimately, inevitably? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or do these sorts of animals just evolve as a result of some randomness processes in evolution, if so, what's the probability? Is it great or small? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If randomness does exist, then to what degree will it affect our ability to depict evolution? Will we still be able to describe the general trends of evolution, for example, the trend of more and more complicated animals evolving?&lt;/p&gt;&#xA;" OwnerDisplayName="user5407" LastEditorUserId="1590" LastEditDate="2016-08-20T08:20:54.743" LastActivityDate="2016-08-20T15:48:10.730" Title="Was the evolution of humans inevitable?" Tags="&lt;evolution&gt;&lt;speculative&gt;&lt;intelligence&gt;" AnswerCount="4" CommentCount="6" ClosedDate="2016-08-25T14:00:22.967" ContentLicense="CC BY-SA 3.0" />
  <row Id="14435" PostTypeId="2" ParentId="14434" CreationDate="2014-01-12T16:27:30.733" Score="4" Body="&lt;p&gt;&lt;strong&gt;Problems of epistemology in your question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two problems of epistemology (which discussion is a matter of philosophy rather than science)&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The whole question depends on what you consider being random and what you consider being determinist. The number that come out from a dice is random unless you know exactly how the dice was thrown (and make some calculation about the cinematic of the dice).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Consciousness is in itself rather hard to define as well. Several definitions has been suggested in science and philosophy.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Anyway even with these philosophical issues behind the question, one can assume some common although improperly defined used you may have of these terms and safely answer that no, self-counsciousness is not a necessary consequence of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Evolution of cognition&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The condition under which greater cognitive abilities is beneficial are quite restrictive and even today the way that human cognition evolved is under debate. &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_human_intelligence&quot; rel=&quot;nofollow&quot;&gt;This wiki article&lt;/a&gt; will give you an introduction into this field. The immense majority of all lineage did not evolve great cognitive abilities (Have a look to different tree of life and to the diversity of life).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In humans, a fourth of the total amount of ATP (molecule that is the equivalent of a battery of living organism) is dedicated to the brain. This is a huge cost! It seems quite extraordinary that something so costly can evolve because the benefit are quite hard to grasp. For example. A bird with a heavy brain won't fly well, therefore it is counter-selected. What would a beetle do with a big brain? Well not many things. It would only be a cost with no benefit. Natural selection does not favor cognitive abilities for most of the lineages and as already said, great cognition is favored only under some restrictive conditions. Intelligence is by no-mean the end-point, the goal or the consequence of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How to answer to &quot;What is the probability&quot;?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to calculate the probability of something to happen you need some a priori knowledge.  For example, the probability of drawing the king of heart in a deck of card obviously depends on wether you consider that you know how many cards there are in the deck. You might say that you don't know how many cards are in the deck but you know that 10% of all deck in the world have 36 cards and the rest 90% of the decks have 52 cards (it would be much more complex in reality). The probability would be different. What are your a priori knowledge? What is the probability given the that X species exist at a given time, given how the environment changed over time, given that life is made of DNA, given the size of the earth, …? But then even if you give tons of information about your a priori knowledge (which include defining life and intelligence), then it seems to me terribly complicated to determine this probability with theoretical work. Doing so with empirical work is obviously impossible. We would need many earth-like planets and 4000 million years.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2016-08-20T15:48:10.730" LastActivityDate="2016-08-20T15:48:10.730" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="14439" PostTypeId="1" CreationDate="2014-01-12T21:22:57.763" Score="3" ViewCount="1444" Body="&lt;p&gt;I don't know if this is correct or not, but I have heard this from a friend and I want to get a clear explanation about this.I hope there is some one who can help me.&lt;/p&gt;&#xA;" OwnerUserId="5411" LastEditorUserId="4136" LastEditDate="2014-01-13T04:29:25.013" LastActivityDate="2014-04-15T12:05:15.260" Title="Will neurons live after the death of a human? If so, how long?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14440" PostTypeId="1" CreationDate="2014-01-12T22:12:33.440" Score="1" ViewCount="1285" Body="&lt;p&gt;I was reading my textbook and it says that breathing involves inhaling and exhaling but it doesn't say whether they happen simultaneously or sequentially. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also is my overall understanding of breathing competent?  When you breathe in air, air ends up in the lungs passing through the nasal passages (heated, moistened, cleaned) through the pharynx, through the glottis through the larynx, through the trachea and into the bronchi and then into the bronchioles. Once air gets to the lungs, Is their already carbon dioxide in the lungs waiting to be expelled or will carbon dioxide diffuse into the alveoli and into the lungs when oxygen diffuses into the blood. And after this the carbon dioxide will be expelled?&lt;/p&gt;&#xA;" OwnerUserId="5275" LastActivityDate="2014-01-24T00:33:51.700" Title="Breathing in and out" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;cellular-respiration&gt;&lt;respiration&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14441" PostTypeId="2" ParentId="10265" CreationDate="2014-01-12T23:22:27.990" Score="9" Body="&lt;p&gt;This seems one form of a common question about evolution.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being: &quot;Trait X would seem to be an advantage, so why can't organisms adapt to X?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is, why don't we have all traits that are advantageous at all?  Why not just digest cellulose, but maybe why not lignin as well?  Why shouldn't we photosynthesize our own food?  What about sonar as well as eyes?  We know that some living thing can do all these things. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer, somewhat mentioned elsewhere here, is that some advantages are not enough for the adaptation to take hold.  You have to consider that there is a cost to each such ability as well.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cellulose is energy poor and any animal which relied on cellulose would have to specialize in cellulose metabolism to the point that they might not compete against fellow animals that got their food from other sources like meat or vegetables. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks for the comment below:  addendum:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;energy poor&lt;/em&gt; in this case is a combination of how common the material is, how advantageous it is to digest (woody plants don't grow back very quickly once you eat them up).  i don't know why i wrote that there are not cellulases.  there are plenty of them and we use them a lot but they tend to be from slow growing fungi...  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;if you want to follow your question to the conclusion : &quot;celluose digestion is a huge advantage in all respects&quot; then the question is why aren't they in every bacteria that grows around plants?  because evolution is not how cellulases are created?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;in fact woody plants include other materials supporting their structure to prevent this eventuality.  lignin is a non carbohydrate semirandom fiber based on phenols that is indeed very slow to digest and difficult to get at with an enzyme... at the moment it does seem to be enough to prevent plants and paper celluose from dissolving and being eaten...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2020-04-11T20:32:59.610" LastActivityDate="2020-04-11T20:32:59.610" CommentCount="6" ContentLicense="CC BY-SA 4.0" />
  <row Id="14442" PostTypeId="1" AcceptedAnswerId="14449" CreationDate="2014-01-13T01:00:20.827" Score="1" ViewCount="106" Body="&lt;p&gt;So we know that glucose is an aldehyde that can cause cell damage to the lysine and arginine residues on proteins through the Maillard Reaction (among other damaging reactions that glucose participates in). Since everyone needs glucose to survive, though - I'm wondering - how does the body repair damage to its proteins+blood vessels that are caused by all this glucose? I'm especially interested in the blood vessels, as the damage to blood vessels is common in diabetics.&lt;/p&gt;&#xA;" OwnerUserId="103" LastActivityDate="2014-01-13T08:11:35.663" Title="How does the body repair extracellular damage caused by glucose?" Tags="&lt;senescence&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14448" PostTypeId="2" ParentId="14434" CreationDate="2014-01-13T07:46:26.837" Score="6" Body="&lt;p&gt;Evolution is largely random, because most of the processes that drive evolution are random. A few ideas you should understand to realize why it is so random.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most people are only aware of natural selection when it comes to evolution, and think that natural selection has a goal of creating new, increasingly sophisticated forms of life. None of this, of course, is true. Evolution is not only natural selection, there's also genetic drift, gene flow, and mutation, which are random. Natural selection is not technically random, but it's not the biggest player. Secondly, natural selection does not have any goals and does not move forward, create more complex life, invent adaptations, or does anything of this sort. &lt;strong&gt;Natural selection is not designed to produce perfection&lt;/strong&gt;, it just acts upon whatever variation is present in population, and favours individuals that are more successful in reproduction. Case study: 98% of our DNA doesn't code for any proteins, and presumably most of this DNA is junk. Does it sound like perfection to you, like we are the ultimate species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason I tell you all this is because, in my opinion, when asking this question of &quot;inevitability&quot;, you assume that there's some guiding hand that leads evolution towards some end-point, a climax. But there is no such guiding hand, and it takes a number of incredibly unlikely events to occur in a specific order for: Earth to be created with such conditions, life to start on Earth, collective learning to evolve in some form of live, agricultural revolution to occur so this form of life can thrive, etc. If at any stage something went different, everything would be different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Final thoughts, why are you so sure that humans won't go extinct just like 99.9% of all the species that ever existed on Earth? A typical species goes extinct in about 10 million years, and we've been around for only 200,000 years. If you accept this possibility (which is real, in my opinion), suddenly, it doesn't seem that intelligent life, and we as its representatives, is some inevitable end-point in evolution, does it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edited:&lt;/strong&gt; As to your last (new) question, &quot;if randomness in evolution exists, are we still able to describe the general trends in evolution?&quot;. Firstly, of course randomness exists in evolution! Mutations are caused by &lt;strong&gt;errors&lt;/strong&gt; in the process of DNA replication, genetic drift is caused by &lt;strong&gt;random&lt;/strong&gt; sampling by definition. Secondly, there is no universal trend to more complicated organisms being evolved, as I mentioned above. Some organisms do get more complex, but some organisms haven't changed much over very long time, some are &quot;living-fossils&quot;. Once again, evolution has no goal to create more complex life -- if, say, nautiluses or horseshoe crabs are capable of surviving and reproducing in the niches they occupy -- there's nothing else needed for their existence. Furthermore, fitness is linked to the environment, which is dynamic -- many complex species went extinct during global changes in the environment, whereas what you might call as &quot;primitive&quot; species of unicellular bacteria survived.&lt;/p&gt;&#xA;" OwnerUserId="5392" LastEditorUserId="5392" LastEditDate="2014-01-13T14:50:22.713" LastActivityDate="2014-01-13T14:50:22.713" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="14449" PostTypeId="2" ParentId="14442" CreationDate="2014-01-13T08:11:35.663" Score="1" Body="&lt;p&gt;The Wikipedia article on &quot;Advanced Glycation Endproducts&quot; (or AGE) is quite nice and in this case especially the section on &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Advanced_glycation_end-product#Clearance&quot; rel=&quot;nofollow&quot;&gt;Clearance&lt;/a&gt;&quot;, which also contains a few references.&#xA;In short the AGE which are inside of cells are taken up by the lysosome and then broken down until AGE-amino acids are left. These are secreted into the blood stream and excreted with the urine. Bigger extracellular AGE which cannot pass through the cell membrane are taken up by special receptors first and then processed, here &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8635666&quot; rel=&quot;nofollow&quot;&gt;macrophages&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9065778&quot; rel=&quot;nofollow&quot;&gt;Kupffer cells&lt;/a&gt; are included. An involvement of the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15582139&quot; rel=&quot;nofollow&quot;&gt;liver&lt;/a&gt; is also discussed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following articles are also interesting:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/s001250051591&quot; rel=&quot;nofollow&quot;&gt;Advanced glycation end-products: a review&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0167488900000872&quot; rel=&quot;nofollow&quot;&gt;The biology of the receptor for advanced glycation end products and&#xA;its ligands&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8139257&quot; rel=&quot;nofollow&quot;&gt;Pathogenic effects of advanced glycosylation: biochemical, biologic,&#xA;and clinical implications for diabetes and aging.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-01-13T08:11:35.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14450" PostTypeId="2" ParentId="14434" CreationDate="2014-01-13T08:54:41.440" Score="2" Body="&lt;p&gt;The complex forms of life we see at this moment are the result of billions of years of random mutations. To have the same outcome (or moment - &lt;em&gt;we&lt;/em&gt; are not an ultimate outcome) would require the same mutations (or mutations to the same effect) to occur in a similar enough sequence, we also would require the same (or similar) selection being applied and effects of drift (another random process in evolution). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given the extreme number of mutation events that would be involved in reaching humans (and other complex life) it becomes very clear that it is highly unlikely. Further, because mutation is random, nothing is inevitable. However, the repeated evolution of humans in not impossible (given a parallel system to evolve them within). Evolve and resequence experiments offer some support of this. In these experiments strong selection is applied over a relatively small number of generations with replicate populations and the &lt;a href=&quot;http://mbe.oxfordjournals.org/content/early/2013/11/12/molbev.mst205.full&quot; rel=&quot;nofollow&quot;&gt;number of common changes within the replicate populations can be very small&lt;/a&gt;. Even over time scales which are several orders of magnitude smaller than the 3½ billion years life has been on earth we see results which vary within a selection regime - i.e. with identical selection and standing variation the populations have little concordance in their response at the genetic level but there are certainly similarities to be found when comparing to other treatments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The amount of replication needed to evolve something similar to humans starting with the most basic building blocks of life would be unfathomable. The probability of such a sequence of mutations (and patterns in drift &amp;amp; selection) occurring again which are identical to the ones that have lead to humans is so extremely low (beyond calculable) because of the sheer number of possible routes along the evolutionary trajectory that could have occurred.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To clearly answer your question, &lt;strong&gt;no we are not an inevitable result of evolution&lt;/strong&gt;, it is (strictly speaking) possible that we could repeat our evolution but &lt;strong&gt;the probability of doing so is minuscule and too small and complex to calculate&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-01-13T15:00:20.183" LastActivityDate="2014-01-13T15:00:20.183" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="14451" PostTypeId="2" ParentId="14439" CreationDate="2014-01-13T09:13:42.967" Score="2" Body="&lt;p&gt;I think that depends somewhat on how the human dies - in particular on the conditions. If they die in a very cold environment (say at the top of some icy mountain range), they'll freeze and metabolic processes will slow down considerably, and so will cell death. But such hypothermia-based slowing down is a special case. Normally, if your heart stops or you are not getting oxygen to your brain (perhaps due to a stroke), your neurons will start dying pretty quickly. Within many minutes there will certainly be considerable permanent cell loss - certainly within hours. If oxygen is significantly depleted, ATP production will also significantly drop. If this happens, the various ATP-dependent processes will slow to a crawl (including the Na/K ATPase and other ion pumps and channels that are needed for maintaining and changing the voltage difference between the inside and outside of the cell). This in itself is bad enough as a lot of the enzymes and mechanisms that are dependent on the voltage difference will fail (and probably enough of a reason for many cells to start dying), but one of the effects of this is apparently an increase in the extracellular glutamate, which ultimately leads to (via NMDA receptors for example) an influx of calcium ions into the neurons. Too much of the calcium ions is once again toxic for a variety of the processes inside the cell and is an additional and big reason for neuronal cell death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, as far as I know, neurons don't have a good time living without sufficient oxygen and therefore after a typical human death.&lt;/p&gt;&#xA;" OwnerUserId="5367" LastActivityDate="2014-01-13T09:13:42.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14452" PostTypeId="2" ParentId="3315" CreationDate="2014-01-13T11:50:33.743" Score="0" Body="&lt;p&gt;Adding to @MCM answer, there are also chromosomal crossover that might happen between non homologous. You can have some of the genes of Y chromosome going to X chromosome or elsewhere, for instance, further expanding the possibilities for different sexualities...&lt;/p&gt;&#xA;" OwnerUserId="4821" LastActivityDate="2014-01-13T11:50:33.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14454" PostTypeId="2" ParentId="14434" CreationDate="2014-01-13T14:21:15.253" Score="0" Body="&lt;p&gt;I'll have a go at this, from a perspective devoid of any biology (which I know nothing about). You want to wind the time back to some earlier &quot;instant&quot; (when life emerges on Earth) and then run the world from that &quot;instant&quot; on a second time around. I'm taking all that quite literally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First remark. I put &quot;instant&quot; between thingies because it may be troubling from a general-relativistic perspective. Never mind that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second remark. You can't do that. You cannot wind the time back (and start over). Therefore, this is not a question of the normal scientific variety. Never mind that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the laws of physics (as they are currently thought of; and those are &lt;em&gt;freakishly&lt;/em&gt; accurate on our scales), &lt;strong&gt;if&lt;/strong&gt; there is (objective/real/fundamental) &quot;randomness&quot; in the world &lt;strong&gt;then&lt;/strong&gt; it can only be of the quantum-mechanical kind. Quantum mechanics typically deals with the very small stuff. (Ignoring Big Bangs and black holes.) Typically no-larger-than-atom stuff. Unless there is some kind of &quot;natural&quot; amplification mechanism at hand,* I don't see how quantum-mechanical randomness (if it indeed exists; there &lt;em&gt;are&lt;/em&gt; other hypotheses and interpretations of QM around) with &lt;em&gt;any&lt;/em&gt; significant probability can reroute a relatively macroscopic phenomenon such as evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if quantum-mechanical randomness exists (e.g., no hidden variables, no superdeterminism, etc.), then (in my tentative** opinion) the probability that it will reroute evolution is not zero. Just &lt;em&gt;very&lt;/em&gt; small.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess*** that &lt;strong&gt;&lt;em&gt;at least&lt;/em&gt; 99.99% of all reruns yield exactly the same biological diversity that we have today.&lt;/strong&gt; (And this will not change unless perhaps we start using quantum-mechanical amplifiers such as Geiger counters for our decisions regarding species demolition.) And &lt;em&gt;if&lt;/em&gt; evolution was to be rerouted during the second run, it would most likely be immediately after the start of the second run, when life was barely existing and thus most vulnerable to quantum-mechanical mishap.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;*I can only think of some intermediate chaotic process, but even that doesn't do it for me. (It might change the weather a bit, but evolutionary history? Nah, &lt;em&gt;very&lt;/em&gt; unlikely.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;**The tentativeness is due to personal uncertainty regarding the causes of DNA errors. However, I now believe them to be (by far) mostly chemically describable in nature (especially those that produce offspring), not only quantum-mechanically describable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;***An actual computation of a good &lt;em&gt;lower bound&lt;/em&gt; is impossible. I think I'm on the safe side.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;NB: To those who &quot;know&quot; evolution to be inherently random, I would ask: Could you distinguish between evolution based on &quot;true&quot; randomness and evolution based on &lt;a href=&quot;http://en.wikipedia.org/wiki/Pseudorandomness&quot; rel=&quot;nofollow&quot;&gt;pseudorandomness&lt;/a&gt;? I would suggest that for all biological-theoretical purposes they would be equivalent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Evolution (assumed true) doesn't come close to proving (or even suggesting) that the world/universe has inherent &quot;true&quot; randomness. Evolution doesn't require &quot;true&quot; randomness. It is perfectly fine (from a consistency-perspective) to accept evolution and be agnostic about &quot;true&quot; randomness.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;It is precisely for the purpose of this question (with its &quot;inevitable&quot;), where the distinction between random and not-random matters. The “normal” assumption of randomness is &lt;em&gt;very well suited&lt;/em&gt; to answering biological questions, but this question explicitly (and apparently inadvertently) wanders into another domain of inquiry: philosophy.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The OP's question asks about &quot;inevitable&quot;. It is precisely in that word &lt;em&gt;only&lt;/em&gt;, where the distinction between randomness and, say, pseudorandomness is crucial. If reality is pseudorandom then things are inevitable. If reality is random then things might be less inevitable. So, &lt;em&gt;for the purpose of this question&lt;/em&gt;, we need to acknowledge that we really don't know about this aspect of reality (and usually we wouldn't care, because for normal questions it doesn't matter one iota).&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user3395" LastEditorDisplayName="user3395" LastEditDate="2014-01-14T06:00:55.660" LastActivityDate="2014-01-14T06:00:55.660" CommentCount="7" CommunityOwnedDate="2014-01-14T05:55:13.130" ContentLicense="CC BY-SA 3.0" />
  <row Id="14457" PostTypeId="2" ParentId="14327" CreationDate="2014-01-13T16:49:19.740" Score="2" Body="&lt;p&gt;I think the reason as to why glucose concentration is faster in the aerobic case than the anaerobic one, is perfectly explained by Chris. To summarize:- &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The energy requirement of the organism in both the condition remains more or less&#xA;  constant. Since aerobic respiration generates more energy per glucose,(38ATP)&#xA;  it takes more time for the same concentration of the glucose to be&#xA;  depleted, than it takes in the case of anaerobic respiration where&#xA;  less energy is released.(2ATP)  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The non-linearity in case of anaerobic respiration can probably be explained thus:-&lt;br&gt;&#xA;In the aerobic case, glucose is oxidised to water and carbon dioxide, both of which do not influence the respiratory process. The first step of glycolysis, the phosphorylation of glucose has a very negative free energy change, i.e. is practically irreversible. Therefore a dip in glucose concentration will not affect the rate of energy release and therefore the rate of energy released will stay constant resulting in a linear graph. But in the anaerobic case, the final product is un-metabolised ethyl alcohol. The conversion of pyruvic acid formed as a result of glycolysis to ethyl alcohol is not so strongly irreversible(smaller free energy change), and at high product concentrations, becomes considerably reversible. This means that the ethyl alcohol produced will affect the rate of glucose metabolism, and will retard it by negative feedback (&lt;a href=&quot;http://en.wikipedia.org/wiki/Le_Chatelier%27s_principle&quot; rel=&quot;nofollow&quot;&gt;Le chatelier's principle&lt;/a&gt;). This will lower the speed of glucose utilisation at low concentrations of glucose, i.e. high concentrations of ethyl alcohol. This reduce the value of slope at lower concentrations of glucose in the graph, and hence produces the non-linearity.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2014-01-13T16:49:19.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14458" PostTypeId="1" CreationDate="2014-01-13T17:25:03.910" Score="6" ViewCount="36584" Body="&lt;p&gt;Why does lower blood calcium levels (or lower calcium levels in ECF) cause nervous hyperexcitaton? Why does it cause over stimulation of nerves and muscles and spasmic contractions of muscles?&lt;br&gt;&#xA;This is why undersecretion of parathormone causes parathyroid tetany.&lt;br&gt;&#xA;I am aware of the role of calcium in opening the synaptic vesicles for transmission of impulses and the role of calcium in muscle contraction but fail to understand how that might hep me understand the overexcitation of nerves and spasmic contraction of muscles. It actually seems that higher calcium in ECF might cause over stimulation and spasms of muscles due to sustained contraction.&lt;/p&gt;&#xA;" OwnerUserId="5414" LastEditorUserId="8804" LastEditDate="2015-01-24T07:52:07.873" LastActivityDate="2017-10-13T22:02:20.577" Title="Calcium levels and nerve hyperexcitation" Tags="&lt;physiology&gt;&lt;homework&gt;&lt;muscles&gt;&lt;neurotransmitter&gt;&lt;neurology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14459" PostTypeId="1" CreationDate="2014-01-13T17:32:22.783" Score="6" ViewCount="2042" Body="&lt;p&gt;&lt;strong&gt;Why does thyroid gland enlarge both in hypothyroidism and hyperthyroidism?&lt;/strong&gt;&lt;br&gt;&#xA;Hypothyroid goitre is due to lack of iodine in diet and hyperthyroid goitre (Exopthalmic goitre, Grave's disease) is due to oversecretion of thyroxine, or Thyroid stimulating Hormone. How does these two apparently opposite effects produce similar physical manifestation of the disorder (symptom) i.e is the enlargement of the thyroid gland? &lt;/p&gt;&#xA;" OwnerUserId="5414" LastActivityDate="2020-05-14T07:51:41.237" Title="Enlargement of thyroid gland" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14461" PostTypeId="2" ParentId="14217" CreationDate="2014-01-13T19:56:14.810" Score="1" Body="&lt;p&gt;This is a very good question, but I think the reason that it's not being answered is because it is in a sense too broad: different plant groups maintain balances of cleistogamous and chasmogamous flowers, and they modulate that balance through different mechanisms. Many of these mechanisms (genes involved, environmental cues, developmental pathways) may not be fully understood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jstor.org.ezproxy.umsl.edu/stable/27571184&quot; rel=&quot;nofollow&quot;&gt;Culley and Klooster (2007)&lt;/a&gt; categorize cleistogamy depending on the degree to which &quot;the prevailing environment has a say&quot;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;In &lt;em&gt;dimorphic cleistogamy&lt;/em&gt; CL and CH flower differ in the time or place&#xA;of production, with CL flowers produced in conditions (underground,&#xA;low light levels, early in the season) that are potentially&#xA;unfavorable for outcrossing.&lt;/li&gt;&#xA;&lt;li&gt;In &lt;em&gt;induced cleistogamy&lt;/em&gt; potentially CH flowers that experience conditions such as drought or low temperatures fail to open and self-pollinate, becoming, in effect, CL flowers.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You should check out the Culley and Klooster (available online if you make a jstor login) – they discuss &lt;em&gt;complete cleistogamy&lt;/em&gt; which addresses your last question. They report several completely CL species in their Table 1, and give references.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More generally, many different plant groups maintain balances of self-pollination and outcrossing (i.e. &quot;real sex&quot;), through an even more diverse set of mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even more generally, many plants and some animals maintain balances of sexual reproduction and clonal reproduction, through an even &lt;em&gt;more&lt;/em&gt; diverse set of mechanisms. For instance, &lt;a href=&quot;http://en.wikipedia.org/wiki/Vegetative_reproduction&quot; rel=&quot;nofollow&quot;&gt;vegetative reproduction&lt;/a&gt; (e.g., strawberry runners) is very common in many plant groups; facultative and obligate &lt;a href=&quot;http://en.wikipedia.org/wiki/Parthenogenesis&quot; rel=&quot;nofollow&quot;&gt;parthenogenesis&lt;/a&gt; in animals also occurs.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jstor.org.ezproxy.umsl.edu/stable/27571184&quot; rel=&quot;nofollow&quot;&gt;Culley, Theresa M. and Matthew R. Klooster (2007). The Cleistogamous Breeding System: A Review of Its Frequency, Evolution, and Ecology in Angiosperms. &lt;em&gt;Botanical Review.&lt;/em&gt; Vol. 73, No. 1, pp. 1-30&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-01-23T15:29:22.760" LastActivityDate="2014-01-23T15:29:22.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14462" PostTypeId="5" CreationDate="2014-01-13T21:52:10.377" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Chromatin&quot; rel=&quot;nofollow&quot;&gt;Chromatin&lt;/a&gt; is the complex of &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA&quot; rel=&quot;nofollow&quot;&gt;DNA&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Histone&quot; rel=&quot;nofollow&quot;&gt;histones&lt;/a&gt;, and other scaffolding proteins that make up a &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosome&quot; rel=&quot;nofollow&quot;&gt;chromosome&lt;/a&gt;, which in &lt;a href=&quot;http://en.wikipedia.org/wiki/Eukaryotes&quot; rel=&quot;nofollow&quot;&gt;Eukaryotes&lt;/a&gt; is located in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_nucleus&quot; rel=&quot;nofollow&quot;&gt;nucleus&lt;/a&gt; of the cell.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2014-01-13T22:39:19.513" LastActivityDate="2014-01-13T22:39:19.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14463" PostTypeId="4" CreationDate="2014-01-13T21:52:10.377" Score="0" Body="Chromatin is the complex of DNA, histones, and other scaffolding proteins that make up the chromosomes, which in eukaryotes is located in the nucleus of the cell." OwnerUserId="948" LastEditorUserId="948" LastEditDate="2014-01-13T22:39:23.437" LastActivityDate="2014-01-13T22:39:23.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14464" PostTypeId="2" ParentId="13715" CreationDate="2014-01-13T21:59:38.303" Score="12" Body="&lt;p&gt;Disclaimer: I'm an infectious disease modeler, and generally pretty skeptical of &quot;We modeled X like an outbreak!&quot; claims, because many are just an exercise in curve fitting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that, the answer is both &quot;Yes&quot; and &quot;No&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;No&quot;: Murder as an act really isn't transmissible, and if its not transmissible, it can't be modeled as an infectious disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Yes&quot;: It is probably possible to model some things in the same way we model infectious diseases, because the underlying &lt;em&gt;causes&lt;/em&gt; of murder may be somewhat 'transmissible'. Certain behaviors, cascading effects (if one family member is incarcerated it increases the likelihood that other members of that family will be incarcerated) etc. might give crime &quot;disease-like&quot; properties.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's probably largely driven by underlying social networks and the like, which are also important to infectious diseases. But then you have a problem in reasoning. For example, did murder &quot;spread&quot; along a social network, or did we merely sample a group of people with a shared underlying cause (for example, poverty, membership in gangs, etc.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's probably useful to model some of these things, but it's more useful, in my mind, to model them as their own process, rather than trying to shoehorn them into being like a disease.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2014-01-13T21:59:38.303" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14465" PostTypeId="2" ParentId="14414" CreationDate="2014-01-14T04:19:01.803" Score="16" Body="&lt;p&gt;&lt;em&gt;I decided to summarize a competing hypothesis to make our answers more balanced. I also tried to address the question about the degree of human morphological diversity compared to other animals.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;According to Woodley (2010), it is plausible that &lt;em&gt;H. sapiens&lt;/em&gt; does not belong to one species and subspecies (i.e. is polytypic). Some of the data he uses to support this hypothesis could be useful for answering our question. He claims that &lt;em&gt;H. sapiens&lt;/em&gt;, which is often considered monotypic, &lt;strong&gt;posses higher levels of morphological diversity, genetic heterozygosity and differentiation than many animal species which are considered polytypic.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Woodley cites a study by Sarich and Miele, who claimed that morphological differences between humans, on average, are equal to the differences among &lt;em&gt;species&lt;/em&gt; within other mammalian genera (excluding species bred for domestic purposes), and are typically more strongly marked than in other animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, morphological differences are known to be caused by little genetic differences too, like in the case of domestic dogs, which are still considered to be one species. Therefore, Woodley presented further evidence that looked on these inconsistencies in classification using allele frequencies and genetic diversity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He presented data from a wide range of studies, which compares genetic diversity of various mammalian species based on heterozygosity (H), which is a common indicator for genetic diversity, and describes whether both alleles are the same or not on a studied locus. According to this data (which you can find in the linked paper):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Chimpanzees exhibited H of 0.63-0.73, which is very similar to H found in humans (0.588 - 0.807), however, chimpanzees are divided into four subspecies.&lt;/li&gt;&#xA;&lt;li&gt;Some species like the grey wolf even exhibited a lower H (corresponding to lower genetic diversity) than humans (0.528 vs 0.588 - 0.807), while the grey wolf has been divided into as many as 37 subspecies.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;This data suggests that humans are more diverse both morphologically and genetically than some of the other mammalian species that have been divided into subspecies.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;br&gt;&#xA;Woodley, M. A. (2010). Is &lt;em&gt;Homo sapiens&lt;/em&gt; polytypic? Human taxonomic diversity and its implications, &lt;em&gt;Medical Hypotheses, 74&lt;/em&gt;, 195-201. doi:10.1016/j.mehy.2009.07.046 (&lt;a href=&quot;https://lesacreduprintemps19.files.wordpress.com/2011/06/woodley-2009-is-homo-sapiens-polytypic-human-taxonomic-diversity-and-its-implications.pdf&quot;&gt;full-text PDF&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="5392" LastEditorUserId="5392" LastEditDate="2014-01-15T01:53:39.190" LastActivityDate="2014-01-15T01:53:39.190" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14466" PostTypeId="1" CreationDate="2014-01-14T07:13:11.827" Score="1" ViewCount="101" Body="&lt;p&gt;I know a similar question has been asked and this is closely related to cognitive science. However, I want to know whether is there any mechanism or structure in the visual cortex which is proved to be flipping the images upside down.&lt;/p&gt;&#xA;" OwnerUserId="5213" LastActivityDate="2014-12-10T20:08:29.027" Title="Does our brain really &quot;flip&quot; images perceived by our eyes?" Tags="&lt;vision&gt;&lt;perception&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-12-10T22:42:01.950" ContentLicense="CC BY-SA 3.0" />
  <row Id="14468" PostTypeId="1" AcceptedAnswerId="14470" CreationDate="2014-01-14T09:42:09.877" Score="1" ViewCount="886" Body="&lt;p&gt;We are doing a lab on the effects of light intensity/wavelength on the rate of photosynthesis in AP bio and we were asked to visit this website here: &lt;a href=&quot;http://mhhe.com/biosci/genbio/biolink/j_explorations/ch09expl.htm&quot; rel=&quot;nofollow&quot;&gt;http://mhhe.com/biosci/genbio/biolink/j_explorations/ch09expl.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The link takes you to a shockwave applet in which you can change the wavelength/intensity and record the ATP production (%). We were supposed to try out as many different combinations of intensity/wavelength and record the respective intensity, wavelength and ATP production (%) in a chart. Now the problem I'm having is that we are to graph this data. How should I go about graphing this? One problem is that for some values in the data, the intensity might be the same with different wavelengths or the wavelength maybe the same with different intensities. Can I do two graphs? One graph? Which one would be best and how should I go about doing so? And here is the chart just in case you want to see the data:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://drive.google.com/file/d/0B4A27kix-0naMk4wNmNQejd3cGc/edit?usp=sharing&quot; rel=&quot;nofollow&quot;&gt;https://drive.google.com/file/d/0B4A27kix-0naMk4wNmNQejd3cGc/edit?usp=sharing&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5419" LastEditorUserId="3340" LastEditDate="2015-06-04T11:46:46.150" LastActivityDate="2015-06-04T11:46:46.150" Title="Question regarding Rate of Photosynthesis AP Biology Lab" Tags="&lt;ecology&gt;&lt;photosynthesis&gt;&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14470" PostTypeId="2" ParentId="14468" CreationDate="2014-01-14T10:36:33.407" Score="1" Body="&lt;p&gt;Your task is to determine how light intensity and wavelength affect ATP production. Therefore, we know for sure that your dependent variable (or response variable) should be ATP production. It is customary to depict the response variable on the vertical axis (Y-axis), so let's trying doing this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now we need to sort the other two variables. I suggest that you make one variable a control variable -- a variable that you don't change and keep constant, and the other then will be an independent variable (or explanatory variable). Then you swap them around, producing at least two plots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a nutshell:  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;You pick one value of wavelength and don't change it. Then you change the light intensity and record ATP with constant wavelength. You plot ATP (vertical axis) vs the light intensity (horizontal axis).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;You pick one value of light intensity and don't change it. Then you change the wavelength and record ATP with constant light intensity. You plot ATP (vertical axis) vs the wavelength (horizontal axis).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Make sure to generate enough data points in order to be able to fit a smooth curve.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Another option would be to make a 3-D graph, with 3 axes: Y for ATP, X for wavelength and Z for light intensity. Initially, this might seem like a better approach, however 3-D graphs are not very common in science, and maybe there is a reason for it. Your goal is to make your data &lt;strong&gt;intuitive&lt;/strong&gt;, &lt;strong&gt;easy to read&lt;/strong&gt; and &lt;strong&gt;straight to the point&lt;/strong&gt;. Science can be rather complex even without additional effort to complicate it with confusing graphs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would try it out as well, and see which one of two approaches shows you the &lt;strong&gt;trend&lt;/strong&gt; more clearly. If I had to pick one straightaway -- I would probably go with the previous option that included a control variable.&lt;/p&gt;&#xA;" OwnerUserId="5392" LastEditorUserId="5392" LastEditDate="2014-01-14T10:52:21.063" LastActivityDate="2014-01-14T10:52:21.063" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14471" PostTypeId="1" CreationDate="2014-01-14T11:59:18.483" Score="1" ViewCount="6153" Body="&lt;p&gt;I found a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21886479?dopt=Abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper estimating the number of species&lt;/a&gt; currently living on earth. Now I'm wondering If anybody tried to estimate the number of species that have lived on earth. I'm familiar with problems of &quot;species concepts&quot;. But I'm sure, there is at least a number of all known fossils.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: In contrast to the question &lt;a href=&quot;https://biology.stackexchange.com/questions/6937/how-many-organisms-have-ever-lived-on-earth&quot;&gt;How many organisms have ever lived on Earth?&lt;/a&gt;&#xA;I'm asking for species and not for individuals. The answer to my question &lt;strong&gt;can&lt;/strong&gt; be used to ansewer the queston for the number of organisms. But still, The questions is different.&lt;/p&gt;&#xA;" OwnerUserId="3941" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-01-14T15:15:25.727" Title="How many species have existed on earth?" Tags="&lt;species&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ClosedDate="2014-01-14T13:31:14.113" ContentLicense="CC BY-SA 3.0" />
  <row Id="14472" PostTypeId="1" AcceptedAnswerId="14480" CreationDate="2014-01-14T12:08:13.583" Score="9" ViewCount="1670" Body="&lt;p&gt;My question is related to one of the oldest question in ecology: &quot;What determines global patterns of species richness?&quot;. However, I want to focus on one particular part of this question, which has been bothering me for a long time.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Background information&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;One of the most widely recognized ecological patters on Earth, which is found at most scales and in most biological taxa, is the latitudinal diversity gradient (LDG) -- there are more species in the tropics than in the temperate regions, and the further away you move from the tropics, the fewer species you encounter. Furthermore, such pattern exists not only along the latitudinal gradient, but species richness also covaries with altitude in terrestrial environments and depth in marine environments, showing the same diversity gradient!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to be fair to suggest that &lt;strong&gt;energy&lt;/strong&gt; should somehow underline all these diversity gradients and create some sort of universal mechanism that would ultimately affect all species richness patterns on Earth. Unfortunately, there is no consensus on questions as grand as this one, but I'm looking for hypothesis that would specifically attempt to explain all three gradients together.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Question&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Is there a hypothesis that attempts to explain patterns of species richness along all three energy-related environmental gradients &lt;strong&gt;together&lt;/strong&gt;: latitude, altitude and depth? If there is, what it's weakness? If there's no such hypothesis, do we have reasons to believe that such a broad link across the three gradients can exist?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Please note how I'm trying to emphasize that I don't want you to list all the hypotheses that describe &lt;strong&gt;LDG only&lt;/strong&gt;, but rather the three gradients &lt;strong&gt;together&lt;/strong&gt;.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="5392" LastEditorUserId="5392" LastEditDate="2014-01-14T23:37:09.053" LastActivityDate="2014-01-15T15:35:35.170" Title="Is there a hypothesis that attempts to explain patterns of species richness along all three energy-related environmental gradients?" Tags="&lt;ecology&gt;&lt;biodiversity&gt;&lt;species-distribution&gt;" AnswerCount="3" CommentCount="12" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14473" PostTypeId="2" ParentId="14471" CreationDate="2014-01-14T12:34:39.000" Score="1" Body="&lt;p&gt;A quote from a &lt;a href=&quot;http://curiosity.discovery.com/question/how-species-actually-gone-extinct&quot; rel=&quot;nofollow&quot;&gt;Discovery movie&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Scientists have estimated that over the course of Earth's history, anywhere between 1 and 4 billion species have existed on this planet.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I know, I know... sorry. I hope someone has the original research, but in case no one does, or if you are just curious, and Discovery is fine for you, I decided to share what I know for the time being.&lt;/p&gt;&#xA;" OwnerUserId="5392" LastEditorUserId="1590" LastEditDate="2014-01-14T15:15:25.727" LastActivityDate="2014-01-14T15:15:25.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14474" PostTypeId="2" ParentId="14472" CreationDate="2014-01-14T14:12:14.163" Score="2" Body="&lt;p&gt;I've studied diversity of euglossine bees along altitudinal gradients in amazonian mountains. The references I've read showed no consensus regarding altitude. For some groups, diversity were higher at low altitudes; for other groups, it was in the middle. I've found the biggest diversity in the middle altitudes (the mountains were around Equator line). One hypothesis was about randomness: throw a lot of species inside any gradient, and most of them will overlap in the center by chance alone. Other hypothesis said about chance of recolonization. You can have extinctions anywhere, but close to Equator (low latitude) and close to sea level (low altitude) you can have species recolonizing faster, because there is more land around. After all, I don't think one simple rule will explain each and every case. And I have never thought about that below sea level. Aren't marine vulcanoes a rich environment?&lt;/p&gt;&#xA;" OwnerUserId="4821" LastActivityDate="2014-01-14T14:12:14.163" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14475" PostTypeId="2" ParentId="14472" CreationDate="2014-01-14T14:15:12.770" Score="4" Body="&lt;p&gt;Nice question!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the concern of plant diversity over altitudinal gradient it has been shown in several studies in the alps and in Andes that the greatest abundance and diversity is not found in high altitude neither in low altitude but in middle altitude. Some argue that the abundance and diversity depends on temperature and human impact that is what explain this pattern. There is a theoretical model that cut the mountains into three patches along the altitudinal gradient and assume that plants - when they reproduce - either send seeds in the same patch or in a nearby patch. Because, the patch in the middle can receive gene flow from both &quot;sides&quot; while the &quot;extremities&quot; can receive gene flow only from one &quot;side&quot;, the diversity is greater in the middle patch.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In aquatic communities, there is very few physical barrier to gene flow and therefore, speciation often occur through sympatry (I think!). Depth has an important role in isolating population (allowing allopatric speciation) because of the sensory drive evolution. Some fishes (to talk only about fishes) have &lt;a href=&quot;http://en.wikipedia.org/wiki/Opsin&quot; rel=&quot;nofollow&quot;&gt;opsins&lt;/a&gt; (proteins involved in vision) that are adapted to deep water while other fishes have opsins adapted to shallow water. This divergence, allows to push fishes to chose a preferential habitat and prevent gene flow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;High temperatures lead to high mutation rate and high mutation rate leads to high speciation rate (I think).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of past glaciation, it has been found that species in southern hemisphere are younger in average than those in northern hemisphere. Therefore, past ecology has to be taken in account when talking about present diversity. Land mass of different size might also impact species diversity differently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think a theory that explain species diversity along these three gradients might be easily found. I would tend to think these three gradients are important because they are correlated with parameters that influence species diversity in several ways. Those correlated variables are temperature, humidity, light, time of daylight, land mass, connectivity (rivers that increase gene from mountain to valley or surrounding land mass for example), human impact, …&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What did you mean &quot;energy related gradient&quot;? Are you talking about temperature? If so, can your question be reduced to &quot;How does temperature influence species diversity&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry for the missing references!&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Latitudinal_gradients_in_species_diversity&quot; rel=&quot;nofollow&quot;&gt;This wiki article&lt;/a&gt; lists pretty well (better than what I did in my above answer!) different hypothesis for explaining latitudinal gradient in species diversity. Some of these hypotheses can be used to describe effect of depth or altitude.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-01-15T11:35:37.630" LastActivityDate="2014-01-15T11:35:37.630" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14476" PostTypeId="2" ParentId="14414" CreationDate="2014-01-14T19:30:59.487" Score="10" Body="&lt;p&gt;It seems to me that many answers to this question suffer from the nasty habit of &quot;political correctness&quot;. As a zoologist, I never heard of somebody sequencing the whole DNA of any species to decide when to use or not the term &quot;race&quot;. If a group of animals comes from a side of a river, and the other comes from the other side, and they have one or a few distinctive features (color of chest pelage, tuffs of hair in the sides of head, etc), that's enough to call them both different races (or even subspecies). Of course some geographical isolation has taken place, although it hasn't been long enough to divide the two (or more) populations into full species. The same logic should be used to humans, right? Maybe some folks believe that, pretending there are no human races, then the question of racism is &quot;solved&quot;? Bad logic, to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look at &lt;a href=&quot;http://www.worldbirdnames.org&quot; rel=&quot;noreferrer&quot;&gt;http://www.worldbirdnames.org&lt;/a&gt;: they cite 10,518 extant species of birds and 20,976 subspecies. About 2 subspecies per species. How do they do that? (No DNA for most of them.) Subspecies/races are usually from different regions (like human races), their vocalizations are usually different (like human races) and their colors sometimes vary (not as much as in human races). My point is: there is NO SCIENTIFIC REASON to say there are no human races, if we're using zoological reasoning. (Unless we are not animals anymore!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For mammals, &lt;a href=&quot;http://www.catalogueoflife.org/col/browse/classification/kingdom/Animalia/phylum/Chordata/class/Mammalia/match/1&quot; rel=&quot;noreferrer&quot;&gt;http://www.catalogueoflife.org/col/browse/classification/kingdom/Animalia/phylum/Chordata/class/Mammalia/match/1&lt;/a&gt; cite: 4,843 species, 2,998 infraspecific taxa. Again, if someone show me they did complex DNA analysis for most of those infraspecific taxa, and those analysis showed that variation inside races is smaller than between races, THEN I will be forced to agree with them.&lt;/p&gt;&#xA;" OwnerUserId="4821" LastEditorUserId="4821" LastEditDate="2014-01-15T02:15:31.437" LastActivityDate="2014-01-15T02:15:31.437" CommentCount="17" ContentLicense="CC BY-SA 3.0" />
  <row Id="14480" PostTypeId="2" ParentId="14472" CreationDate="2014-01-15T12:43:35.930" Score="5" Body="&lt;p&gt;This is a big question and a very active field of research. I'm not deeply into this litterature, but you should look into the the different scaling relationships (often power laws) that have been described on metabolism vs body size, species-area relationships and species richness vs biomass. Also consider that energy-use by species in a community is considered a zero-sum game both in the neutral model (&lt;a href=&quot;http://press.princeton.edu/titles/7105.html&quot; rel=&quot;nofollow&quot; title=&quot;Hubbell. 2001. The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton&quot;&gt;Hubbell, 2001&lt;/a&gt;) and in Red Queen models of evolution. You will probably not find a definite answer to your question though, but there are some interesting intersections of ideas out there. As others have suggested you also need to consider and take into account differential historical extinction rates, and how this will influence current patterns (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2007.01020.x/abstract&quot; rel=&quot;nofollow&quot; title=&quot;Mittelbach et al. 2007. Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecology letters 10(4): 315–331&quot;&gt;Mittelbach et al. 2007&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Points of entry could be:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v405/n6783/full/405220a0.html&quot; rel=&quot;nofollow&quot; title=&quot;Gaston. 2000. Global patterns in biodiversity. Nature 405: 220-227&quot;&gt;Gaston. 2000. Global patterns in biodiversity&lt;/a&gt; (essential reading!)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/ele.12048/abstract&quot; rel=&quot;nofollow&quot; title=&quot;Chave. 2013. The problem of pattern and scale in ecology: what have we learned in 20 years? Ecology letters 16(s1): 4–16&quot;&gt;Chave. 2013. The problem of pattern and scale in ecology: what have we&#xA;learned in 20 years?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1461-0248.2003.00527.x/abstract&quot; rel=&quot;nofollow&quot; title=&quot;Venevsky &amp;amp; Veneskaia. 2003. Large-scale energetic and landscape factors of vegetation diversity. Ecology Letters 6(11): 1004–1016&quot;&gt;Venevsky &amp;amp; Veneskaia. 2003. Large-scale energetic and landscape factors of vegetation diversity&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2007.01020.x/abstract&quot; rel=&quot;nofollow&quot; title=&quot;Mittelbach et al. 2007. Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecology letters 10(4): 315–331&quot;&gt;Mittelbach et al. 2007. Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.paleolab.cl/isi/Marquet%20et%20al%202005%20JEB.pdf&quot; rel=&quot;nofollow&quot; title=&quot;Marquet et al. 2005. Scaling and power-laws in ecological systems. The Journal of Experimental Biology 208: 1749-1769&quot;&gt;Marquet et al. 2005. Scaling and power-laws in ecological systems&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;A couple of caveats/ideas though; first of all, it has been argued that the latitudinal gradient of species richness is likely to be due to many different mechanisms in different taxa (see &lt;a href=&quot;http://www.nature.com/nature/journal/v405/n6783/full/405220a0.html&quot; rel=&quot;nofollow&quot; title=&quot;Gaston. 2000. Global patterns in biodiversity. Nature 405: 220-227&quot;&gt;Gaston, 2000&lt;/a&gt;). Here you are looking for a hypothesis to explain not only this single pattern, but all three of them, which makes a single explanation even less likely. Second, many non-exclusive explanations have been put forward for the latitudinal gradient. Even if we don't know which ones of these that are the true mechanisms, some are clearly incompatible with being explanations for all the three patterns you mention, while others might be applicable to all of them. For instance, environmental stability in the tropics is one suggested mechanism for the latitudinal gradient, but this doesn't make much sense for a gradient along ocean depth (deep sea has arguably been a more stable environment both over shorter and longer time-frames). It might be relevant for an altitude gradient though. Going through different hypothesised explanations for the latitudinal gradient in this way (from what I know, the best studied of these gradients) could give you a list of ideas that are most interesting to target (maybe somebody has already done this though). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-01-15T15:35:35.170" LastActivityDate="2014-01-15T15:35:35.170" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14481" PostTypeId="1" AcceptedAnswerId="14492" CreationDate="2014-01-15T13:29:16.390" Score="3" ViewCount="4834" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Three loci C, D and E are located on the same chromosome in this&#xA;  order. We found that the frequency of recombinants between C and D is&#xA;  10% and that between D and E it is 20%. Assuming that crossing over&#xA;  occurs randomly on the chromosome, what is the expected frequency of&#xA;  recombinants between C and E?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I know that it should be less than 30% (10%+20%) but the answer given is 26%. I don't understand how they figured that out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The frequency of recombination is &amp;lt;30% because of the chance that a crossover happens between C and D &amp;amp; also between D and E. The probability of that to happen is 2% (10/100 X 20/ 100)&#xA;So, why is it 26% instead of 28% ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another posssibility : Am I totally off the track ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2014-01-15T14:26:51.900" LastActivityDate="2015-11-27T11:50:10.333" Title="recombination frequency problem" Tags="&lt;homework&gt;&lt;genetics&gt;&lt;chromosome&gt;&lt;recombination&gt;&lt;genetic-linkage&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14483" PostTypeId="1" CreationDate="2014-01-15T16:15:14.747" Score="3" ViewCount="71" Body="&lt;p&gt;Is it possible for a human and another species to reproduce?&lt;/p&gt;&#xA;" OwnerUserId="5430" LastEditorUserId="3624" LastEditDate="2014-01-15T19:56:52.620" LastActivityDate="2014-01-15T19:56:52.620" Title="Is it possible for a human and another ape species to reproduce?" Tags="&lt;human-biology&gt;&lt;genetics&gt;" AnswerCount="0" CommentCount="6" ClosedDate="2014-01-16T05:10:33.040" ContentLicense="CC BY-SA 3.0" />
  <row Id="14484" PostTypeId="1" CreationDate="2014-01-15T16:59:35.367" Score="3" ViewCount="8988" Body="&lt;p&gt;There are two pathways in blood clot fromation; the extrinsic pathway and the intrinsic pathway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The extrinsic pathway is faster than intrinsic pathway because it has less number of steps. So, why do we need intrinsic pathway then? &lt;/p&gt;&#xA;" OwnerUserId="1765" LastActivityDate="2018-11-25T19:20:52.553" Title="Why do you need the intrinsic pathway when you have faster extrinsic pathway?" Tags="&lt;hematology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14485" PostTypeId="2" ParentId="14484" CreationDate="2014-01-15T17:23:15.687" Score="3" Body="&lt;p&gt;In short: The extrinsic cascade reacts to damages of the blood vessel, the intrinsic pathway reacts to damages of the walls. But as with all things, the long version is ways more complicated:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The extrinsic pathway is activated when you damage tissue and factor VII come in contact with tissue factor (also known as factor III). Tissue factor is located in the membrane of the cells and is only released when the cells are damaged. &#xA;Then the cascade starts and delivers a very fast large amounts of active thrombin, which then converts fibrinogen to fibrin to build a block of the damaged blood vessel. The step from the thrombin is common between both pathways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The intric pathway is also called the &quot;contact pathway&quot;, which starts when the factor VII comes in contact with collagen or anionic surfaces. &#xA;The main advantage of this pathway is the strong amplification of the initial signal from the intrinsic pathway by a factor of about 1000 fold. The intrinsic pathway is also co-activated by active thrombin (which stands at the end of the cascade) meaning it is also a powerfull feedback loop to make the initial reaction much stronger. This also overcomes weak activation which where the active thrombin will be inactivated by Tissue Factor Pathway Inhibitor.&#xA;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Coagulation&quot; rel=&quot;nofollow&quot;&gt;coagulation cascade&lt;/a&gt; has a pretty nice article in the Wikipedia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly it is now believed, that the start of the intrinsic pathway plays no or almost no role in vivo. There are people which &quot;suffer&quot; from a deficiency in factor XII which is necessary to start the intrisic cascade. These people have absolutely no problems with their coagulation, so the first steps are not necessary (any more?). This article presents findings, that it stabilizes a thrombus:&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16466946&quot; rel=&quot;nofollow&quot;&gt;The intrinsic pathway of coagulation is essential for thrombus stability in mice.&lt;/a&gt;&quot;&#xA;Here are some further articles about the intrinsic pathway:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22993391&quot; rel=&quot;nofollow&quot;&gt;In vivo roles of factor XII.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20022081&quot; rel=&quot;nofollow&quot;&gt;Factor XII: what does it contribute to our understanding of the&#xA;physiology and pathophysiology of hemostasis &amp;amp; thrombosis.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-01-15T19:35:05.020" LastActivityDate="2014-01-15T19:35:05.020" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14486" PostTypeId="1" AcceptedAnswerId="14490" CreationDate="2014-01-15T17:49:35.913" Score="3" ViewCount="720" Body="&lt;p&gt;Why is it that natural things like farts, poop, halitosis etc., from which we are always surrounded smell &quot;bad&quot;; whereas manufactured products, such as perfume or glue smell &quot;good&quot; to most of us?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my understanding, things smell &quot;bad&quot;, because they are not good for us. But how are farts not good? And shouldn't artificial things like perfume or glue, which are relatively new to us, smell &quot;bad&quot;?&lt;/p&gt;&#xA;" OwnerUserId="5101" LastEditorUserId="1855" LastEditDate="2014-01-15T19:38:09.340" LastActivityDate="2014-01-16T12:28:55.640" Title="Why do farts stink, but perfume does not?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14488" PostTypeId="1" AcceptedAnswerId="14495" CreationDate="2014-01-15T19:41:44.317" Score="4" ViewCount="229" Body="&lt;p&gt;Some time ago, I read in a newspaper--though I can't recall the details--a list of (mostly artificial) sweeteners and a list comparing how many times sweeter each was than sugar. How is relative sweetness quantified? Is there a standard method?&lt;/p&gt;&#xA;" OwnerUserId="5431" LastEditorUserId="1855" LastEditDate="2014-01-15T19:49:27.570" LastActivityDate="2014-01-16T10:25:21.070" Title="How is sweetness measured?" Tags="&lt;perception&gt;&lt;measurement&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14490" PostTypeId="2" ParentId="14486" CreationDate="2014-01-15T23:45:35.260" Score="9" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Why is it that natural things like farts, poop, halitosis etc., from&#xA;  which we are always surrounded smell &quot;bad&quot;; whereas manufactured&#xA;  products, such as perfume or glue smell &quot;good&quot; to most of us?&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In my understanding, things smell &quot;bad&quot;, because they are not good for&#xA;  us. But how are farts not good? And shouldn't artificial things like&#xA;  perfume or glue, which are relatively new to us, smell &quot;bad&quot;?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Kind of a strange question but here is a quick and rough answer... There are at least three things to think of here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, yes often natural things that are good for you have evolved to smell attractive, but not all natural things are good for you. Therefore a fart should not smell good just because it is natural. And it is likely that breathing farts non stop is not good for you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, perfumes etc. have been chemically manipulated or designed to smell nice by human manufacturers - the preference for such smells existed before the specific perfume, the manufacturer simply designed a fragrance that was attractive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And Finally... &lt;strong&gt;Not everything exists because of selection.&lt;/strong&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/Flatulence#Production.2C_composition.2C_and_smell&quot; rel=&quot;noreferrer&quot;&gt;Farts probably smell as a by-product of process of digestion&lt;/a&gt; rather than selection for avoiding them. Gas is produced during the digestion processes, the amount and odor (determined by the constituents of the gas) of gas will likely depend the efficiency of digestion and what is being digested. The dominant selection force affecting the odor is then probably related to digestive efficacy and selection against odor would only be (relatively) very weak. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's better to digest food and fart a bit than it is to not digest but smell nice, digestion is quite important!&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-01-16T12:28:55.640" LastActivityDate="2014-01-16T12:28:55.640" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14491" PostTypeId="2" ParentId="1037" CreationDate="2014-01-16T05:13:18.910" Score="5" Body="&lt;p&gt;Shown to be in mice &amp;amp; rats (and sick humans), the cell-cell interaction between a macrophage (this is a big engulfing cell required for immunity) and young red blood cells (RBC), is known as the erythroblastic island (commonly known as EBI). If you googled it, there is a scientific review in 2008 that describes this structure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the embryonic stage (in humans), we still retain our RBC nuclei. But as we developed into fetus and adult, we no longer have RBC nuclei. This is thought to be related to the EBI present (in the fetal liver and adult bone marrow respectively). Currently, there is a lack of information of the EBI in other mammals. The only proven ones are mice, rats and sick humans. It is widely assumed (not proven) that mammals have EBIs. Besides mammals, some other animals (e.g. birds) have enucleated RBC, and some don't. It is unclear why is it so. Our lab thinks that it might be related to the formation of the EBI. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to engulfing the RBC nuclei, it is believed that the macrophage acts as a &quot;nurse&quot; cell as proposed in the 50s. In other words, possibly providing iron, and possibly providing some proteins required for young RBC to mature. In early 2013, for the first time, it was showed that these macrophages are important in animal models (published by 2 research groups in nature medicine journal). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for enucleation (the removal of erythroid nuclei), the exact mechanisms are unknown. But cytoskeleton proteins are important players in enucleation. However, there isn't enough information, as these proteins are essential for other important cellular activities as well. For example, bringing in nutrients, development and cellular migration. Most animal models that lack these proteins are unavailable for studies, and these animals usually die at the embryonic stage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The research mentioned by EdoDodo is a proposed model on how enucleation takes place, and is a widely accepted model. Currently, our lab are working on another model that could partially explain how enucleation is being triggered.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Advantages of enucleation&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;In addition to better oxygen diffusion across the membranes, some older scientific papers mentioned that it lightened the cardiac workload. Each extruded RBC nuclei is approximately 40 picograms. A normal healthy adult individual would produce about 2 million RBC per second. That would be 0.08 milligrams of weight per second are required to be removed. However, I couldn't trace the scientific evidence for this claim, but this have been cited by some scientific papers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other advantage would be to reduce risk of hemolysis when transversing through the microvasculature. In other words, mature RBC can move along tiny blood capillaries by changing their biconcave shape (to bell-shaped I think), so that they will not rupture (and die).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, not all RBCs have similar shapes and sizes. You might want to google it for more information. I think camels have slightly different RBC morphology.&lt;/p&gt;&#xA;" OwnerUserId="5434" LastEditorDisplayName="user13145" LastEditDate="2016-10-23T00:16:22.383" LastActivityDate="2016-10-23T00:16:22.383" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14492" PostTypeId="2" ParentId="14481" CreationDate="2014-01-16T05:23:46.927" Score="7" Body="&lt;p&gt;I got $26$% as the answer.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To get a recombination between C and E, there are two possible mechanisms:-   &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;C and D produce a recombinant, but D and E remain linked, therefore the final genotype will be a recombinant considering C and E(Chiasmata between C and D). Here $P_1=P_{CD}\times P'_{DE}$ where $P$ is the probability of recombination and $P'=1-P$ is the probability of linkage.Hence $P_1=0.08$&lt;/li&gt;&#xA;&lt;li&gt;C and D remain linked but D and E undergo recombination (Chiasmata between D and E). Here, $P_2=P'_{CD}\times P_{DE}=0.18$ &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;If there is a chiasmata between both C and D, and D and E, the resultant will not have a recombination in C and E locus due to double crossing over. If there is no crossing over, there will be no recombination at either loci.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The net probability of recombination $P_{CE}$ will be the sum of these two, as any of these possibilities can occur to give a recombination between C and E. $P_{CE}=P_1+P_2=0.26$  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And Biogirllajja, your calculation (the Edit) was almost correct, but you have to subtract $2$% from both $10$% and $20$%, because, both of them include the probability of crossover at one loci, including the case where the other loci has also crossed over. Hence, you need to subtract it from both, and then add to get $26$%. Tell me if you want me to expand on my explanation or provide some clarifications.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we simply add the map distances, we get the actual map distance which disregards the possibility of double recombinations. All map units greater than 10cM have significant chances of double crossovers between them, and hence, the observed recombination frequency would be less than the expected 0.1. Hence, for distances greater than 10cM, the observed frequency of recombination will not be the same as (map distance/100).&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2014-01-16T18:15:01.663" LastActivityDate="2014-01-16T18:15:01.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14493" PostTypeId="1" AcceptedAnswerId="14500" CreationDate="2014-01-16T06:41:58.050" Score="2" ViewCount="416" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Macroevolution&quot; rel=&quot;nofollow&quot;&gt;This Wikipedia article states&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Macroevolution is evolution on a scale of separated gene pools. Macroevolutionary studies focus on change that occurs at or above the level of species, in contrast with microevolution, which refers to smaller evolutionary changes (typically described as changes in allele frequencies) within a species or population. ... &lt;strong&gt;macro and microevolution describe fundamentally identical processes on different time scales.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My question is: &lt;strong&gt;Is this a valid claim? Can we say that creating the genetic information for a feather is not qualitatively different from changing the colour of that feather?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5417" LastEditorUserId="3624" LastEditDate="2014-01-16T08:44:15.897" LastActivityDate="2014-01-17T00:30:55.340" Title="Can we say that microevolution and macroevolution is fundamentally the same thing over different time scales?" Tags="&lt;evolution&gt;&lt;speciation&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14494" PostTypeId="2" ParentId="14275" CreationDate="2014-01-16T08:18:29.217" Score="1" Body="&lt;p&gt;We can somewhat rule out reason 1 because fingertips are also highly sensitive to sensory stimulus. Moreover innervation is not solely about sensory inputs but also motor functions, visceral control etc. All the nerves required for the motor function and a significant portion of visceral control nerves connect to spinal cord.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore in my opinion reason 2 is the most appropriate which automatically rules out reason 3. &#xA;Spinal cord is an advancement of neural organization in the chordates. Spinal cord can be viewed as a central cable in which all power lines merge (they still maintain their individuality [the spinal tracts]; they just get clustered to form an organized bundle). Evolution of spinal reflexes must have been a secondary event. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The case of vagus nerve and cranioaccessory nerve suggests that this is an ancient pathway to control the heart. Heart with a closed circulatory system is found in molluscs as well. Apart from the functional significance of the heart (which might to some extent justify direct cranial innervation), it is decently proximal to the brain as well. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-01-16T08:18:29.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14495" PostTypeId="2" ParentId="14488" CreationDate="2014-01-16T10:25:21.070" Score="3" Body="&lt;p&gt;Response of the gustatory receptor neurons can be measured using standard electrophysiological techniques, under different conditions(exposure to substances). For example see &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/neu.20063/full&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it is difficult to say if a person feels sweetness or not or how the substance produces complex taste perceptions in some people.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-01-16T10:25:21.070" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14496" PostTypeId="1" AcceptedAnswerId="14514" CreationDate="2014-01-16T11:40:00.897" Score="7" ViewCount="6063" Body="&lt;p&gt;I have lots of pieces of pine furniture which have different colours depending on how old they are. So, I just wondered why that is. I guess it has something to do with structures and chemical compounds that were already in the wood when it was still alive, so I hope this is not off-topic here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What processes take place in dead wood when it ages? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What determines the colour it will have? For example, pine and spruce wood looks very similar when freshly cut, but will develop very distinct colours afterwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there also wood that does not become darker? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it something to do with the processing of wood, or will that happen to any stick you leave lying around in your room (so it doesn't rot)?&lt;/p&gt;&#xA;" OwnerUserId="5439" LastActivityDate="2018-11-13T16:39:37.620" Title="Why does wood become darker when it ages?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14497" PostTypeId="1" CreationDate="2014-01-16T13:19:51.477" Score="3" ViewCount="676" Body="&lt;p&gt;I've been trying to test for significant phylogenetic conservatism in some plant traits. So far I used R-package picante (Blomberg's K) and AOT in Phylocom. So far these two methods yield completely opposite results for the same traits, and I'm confused. Is it possible to get such very contrasting outputs from these two methods?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, one trait shows Blomberg's K = 0.2892 (P = 0.001), suggesting that the evolution of this trait overall has not been greatly constrained by phylogenetic relatedness. In contrast, for the same trait AOT yields variance of standardized contrasts across tree = 0.006, significance of contrast variance relative to null model (low rank) = 1, and significance of contrast variance relative to null model (high rank) = 1000 (i.e., P = 0.002), suggesting that treewise phylogenetic conservatism is significantly greater than the expectations of random tip swapping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've just started looking at these phylogenetic signals, so I may be overlooking something critical. I will greatly appreciate if you could kindly give me directions, thank you very much!&lt;/p&gt;&#xA;" OwnerUserId="5253" LastActivityDate="2015-06-19T03:20:52.073" Title="Opposite results between Blomberg's K and phylogenetic signal in Phylocom (AOT)" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14500" PostTypeId="2" ParentId="14493" CreationDate="2014-01-16T19:32:51.497" Score="4" Body="&lt;p&gt;You are mixing up two different things in your question: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;the mechanisms (processes) that cause micro- and macroevolution, and &lt;/li&gt;&#xA;&lt;li&gt;the genetic basis for different types of traits. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The processes of evolution (selection &amp;amp; drift acting on genetic variation) are the same for both micro- and macroevolution, and this what the Wikipedia article is stating. The second question is dealing with the amount of cumulative genetic change that is needed for different types of traits. This naturally differs dramatically between traits (the accumulated genetic change that is), and is also reflected by the different scopes of micro- and macroevolution. Macroevolution is usually studying problems above the species level, and therefore often larger morphological changes, while microevolution is dealing with smaller changes within species and populations. The macro/micro division is also artificial and should be seen as a continuum.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-01-17T00:30:55.340" LastActivityDate="2014-01-17T00:30:55.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14501" PostTypeId="1" CreationDate="2014-01-16T19:59:12.177" Score="2" ViewCount="17678" Body="&lt;p&gt;I'm planning a science project about gel electrophoresis, and I'd like to know if there are any &lt;em&gt;measurable, quantifiable&lt;/em&gt; (for example, things I could represent in a graph or chart) differences between the behavior of protein and DNA during agarose gel electrophoresis.&#xA;Detailed inputs and useful links are greatly appreciated.&lt;/p&gt;&#xA;" OwnerUserId="5443" LastActivityDate="2018-04-22T21:23:50.457" Title="What's the difference between protein and DNA behaviour during agarose gel electrophoresis?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="14502" PostTypeId="2" ParentId="14497" CreationDate="2014-01-17T02:56:38.120" Score="2" Body="&lt;p&gt;I think I figured. Someone told me that the above results are the same. The absolute value of K = 0.29 indicates the magnitude of the signal is less than expected under a Brownian motion process, but it’s still more than random expectation (according to the P-value,P = 0.001). So both methods suggest that treewise phylogenetic conservatism is significantly greater than random expectations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually the meanings of K statistic and P-value were clearly stated in the original paper (Blomberg et al. 2003). I should have looked at it first... but anyway, I think it is solved now.&lt;/p&gt;&#xA;" OwnerUserId="5253" LastActivityDate="2014-01-17T02:56:38.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14503" PostTypeId="1" CreationDate="2014-01-17T05:49:33.130" Score="2" ViewCount="313" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Animals can use their circadian clocks to determine direction from the&#xA;  position of the sun. In a particular experiment conducted in Iceland,&#xA;  a bird, kept in a cage open to the sky, was trained to seek food on&#xA;  the western side. Its circadian rhythm was then phase-delayed by 6&#xA;  hours and after phase shifting, the bird was returned to its open cage&#xA;  at 12.00 noon real time. It was observed to seek food in the:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;a. north.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;b. south.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;c. east.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;d. west.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think that if its circadian rhythm was phase delayed by six hours, at noon, it will feel that it is still 6 a.m. So, the sun will be located in its &quot;east&quot; and it will try to seek food in the &quot;west&quot; but its&quot;west&quot; will be our south. So, answer should be south. Is my reasoning correct ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2020-03-26T02:50:46.547" Title="Circadian rhythm in birds" Tags="&lt;ethology&gt;&lt;circadian-rhythms&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14504" PostTypeId="1" CreationDate="2014-01-17T07:15:43.197" Score="1" ViewCount="7610" Body="&lt;p&gt;I am trying to understand Variations, adaptations and selective advantages  and how they are all related. &#xA;Feel free to add or correct me if I'm wrong- Variations are structural, functional, or physiological differences between individual's within a species that result from mutations.  If the variation provides a selective advantage (genetic advantage) the organism's chances of survival in terms of both survival in a changing environment and reproduction increases. The variation is then considered an adaptation. So basically adaptations are variations which provide a genetic advantage and give some organisms within a species a better chance of survival than those without the adaptations. This survival advantage allows those organisms to reproduce and pass on their adaptation more frequently than those who do not possess these adaptations. &lt;/p&gt;&#xA;" OwnerUserId="5275" LastActivityDate="2014-01-17T10:38:59.737" Title="Evolution- Variations, adaptations and selective advantages" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14505" PostTypeId="2" ParentId="14504" CreationDate="2014-01-17T08:41:24.140" Score="3" Body="&lt;p&gt;I would define &lt;strong&gt;variation&lt;/strong&gt; as something a little less specific. When talking about evolution I would consider it to mean any phenotypic variation that exists. I say phenotype because that is what selection &amp;quot;sees&amp;quot; but there can be genetic variation without phenotypic variation (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Synonymous_substitution&quot; rel=&quot;nofollow noreferrer&quot;&gt;synonymous mutations&lt;/a&gt;). The trait could be physiological, morphological, behavioral or a life history trait (a trait which, all else remaining constant, affects fitness e.g. Lifespan or development time). This is also not necessarily just within species too, comparing homologous trait between two species could reveal between-species variation. For example, in one species every individual might day at exactly 100 days old, in another it may be 102 days, there is no variance within species but there is variance between. The phenotypic variation can be a result of &lt;a href=&quot;http://dendrome.ucdavis.edu/help/tutorials/quantitative.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;genotype, environment, or a genotype-environment interaction&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;If a trait positively affects fitness it is an &lt;strong&gt;adaptation&lt;/strong&gt;, it is a trait that offers some kind of benefit over other current or previous incarnations of the trait. The variance for that trait can be zero - a highly adaptive trait is likely to spread rapidly and variation for that trait would zero if it was entirely genetically defined and fixed in the population but that trait would still be considered an adaptation. I would define fitness as the lifetime reproductive success of your evolutionary unit, &lt;a href=&quot;http://en.wikipedia.org/wiki/Unit_of_selection#Selection_at_the_level_of_the_gene&quot; rel=&quot;nofollow noreferrer&quot;&gt;commonly thought to be the gene.&lt;/a&gt; If a variant of a trait increases relative fitness it provides a &lt;strong&gt;selective advantage&lt;/strong&gt;, and any genes (alleles) causing that trait should spread through the population at the expense of other alleles.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;It is important to remember that not every biologist will define these in the same way, there is some debate about definitions in biology.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-01-17T10:38:59.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14506" PostTypeId="2" ParentId="1037" CreationDate="2014-01-17T09:09:06.427" Score="0" Body="&lt;p&gt;The only function of the red blood cell is to transport oxygen,&amp;nbsp;and nothing else. Its concave shape is to increase its surface area, so more oxygen can be transported per cell. The absence of a nucleus means it can be significantly more concave than an other cell of analogous size, meaning it can carry more oxygen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other answers are more detailed, but this is the main reason that there is an absence of a nucleus.  &lt;/p&gt;&#xA;" OwnerUserId="5444" LastEditorUserId="17117" LastEditDate="2015-10-10T18:12:38.050" LastActivityDate="2015-10-10T18:12:38.050" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14507" PostTypeId="2" ParentId="14501" CreationDate="2014-01-17T09:51:43.323" Score="3" Body="&lt;p&gt;There are two important properties that determine how a molecule will move during gel electrophoresis:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;size and shape of the molecule&lt;/li&gt;&#xA;&lt;li&gt;charge of the molecule&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You're applying an electric field, and all molecules will move according to their charge. The gel itself hinders the movement of larger molecules. This means that small molecules will move further than large molecules. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nucleic acids like RNA and DNA have a uniform negative charge from the phosphate backbone. This means that they will generally separate according to their size and shape (plasmids can be present in different forms like supercoiled, circular or linearized). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Proteins have different charges, some have a positive charge at the pH typically used for gel electrophoresis, some have a negative charge, and some have no charge at that pH. So if you would simply run proteins on a gel, some would move backwards, some forward and some not at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To make the proteins separate according to their size we use the detergent SDS to denature the proteins, and to give them a uniform charge (SDS is negatively charged). Proteins are also run on polyacrylamide gels and not agarose as the size of the pores in agarose is a bad fit for the typical sized of proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While I've never seen anyone using agarose for proteins, it seems that it is possible and sometimes used for larger proteins. I found &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0003269787900200#&quot; rel=&quot;nofollow&quot;&gt;one paper describing a protocol&lt;/a&gt;, they used very high concentrations of agarose in the range of 4-5%. I suspect that they won't handle well, but you should try that out yourself. If the proteins you're examining are a bit larger, using agarose should be possible.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-01-17T09:51:43.323" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14513" PostTypeId="1" AcceptedAnswerId="14515" CreationDate="2014-01-17T23:04:39.033" Score="3" ViewCount="138" Body="&lt;p&gt;I cannot find a clear explanation of what is mRNA expression level, and how to measure it. I would appreciate if someone explained it or gave a reference.&lt;/p&gt;&#xA;" OwnerUserId="4791" LastEditorUserId="49230" LastEditDate="2019-03-11T22:54:27.837" LastActivityDate="2019-03-11T22:54:27.837" Title="What is mRNA expression level?" Tags="&lt;genetics&gt;&lt;rna&gt;&lt;dna-sequencing&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="14514" PostTypeId="2" ParentId="14496" CreationDate="2014-01-17T23:15:38.177" Score="4" Body="&lt;p&gt;While most wood we see comes from stain or oils, wood left on its own will darken.  As far as this &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0031942200896466&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; suggests, this is caused by the polymerization of polyphenols from lignin into tannins which are dark red or brown in color when they are highly polymerized.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The specific content of the lignin in different woods will affect the density, strength and color of the wood.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.tanninglamps4less.com/uvcurecabinets.html&quot; rel=&quot;nofollow&quot;&gt;woodworking reference&lt;/a&gt; shows that intense UV exposure to wood will darken it to give it an aged look. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-01-17T23:15:38.177" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14515" PostTypeId="2" ParentId="14513" CreationDate="2014-01-17T23:17:39.107" Score="4" Body="&lt;p&gt;The RNA expression level is an estimate of the amount or proportion a given gene's RNA found in a sample of cells (such as a tissue sample) or even a single cell.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Expression is used because the RNA sequence is translated from DNA to RNA according to the signals within the cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are various means of estimating this.  They often involve a sequence specific probe - a short length of DNA usually - which will bind specifically to the RNA in question.  The exclusiveness of the probe sequence, which is usually 20-45 bases long, to the RNA in question can vary and so this is a bit of an art sometimes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples are &lt;a href=&quot;http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction&quot; rel=&quot;nofollow&quot;&gt;qPCR&lt;/a&gt; (quantitative PCR), &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_microarray&quot; rel=&quot;nofollow&quot;&gt;expression microarrays&lt;/a&gt;.  Both of these technologies have  many flavors and variants. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another category of expression estimation include RNASeq - which will sequence all the RNA polymers in a sample and estimate all the sequences at one time.  The result is similar to a microarray, but RNASeq does not necessarily require the use of specific probes to an RNA to measure it, though it can. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These estimates are usually relative - except for careful qPCR perhaps.  The numbers are not usually interpreted as &quot;X copies of the RNA&quot; in the sample. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-01-17T23:35:33.627" LastActivityDate="2014-01-17T23:35:33.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14516" PostTypeId="1" AcceptedAnswerId="19741" CreationDate="2014-01-17T23:53:11.337" Score="5" ViewCount="1196" Body="&lt;p&gt;Does a mould make a beetroot poisonous or inedible ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lemon's mould for instance, makes penicillin, but it's green there, and I'm allergic to penicillin, would the white mould produce penicillin too?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/A1k34.jpg&quot; alt=&quot;https://fbcdn-sphotos-a-a.akamaihd.net/hphotos-ak-ash3/1525171_10202386003147724_827086259_n.jpg&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5447" LastEditorUserId="25568" LastEditDate="2016-09-10T16:54:21.887" LastActivityDate="2016-09-10T16:54:21.887" Title="Beetroot white skin mould" Tags="&lt;microbiology&gt;&lt;species-identification&gt;&lt;toxicology&gt;&lt;mycology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14517" PostTypeId="1" CreationDate="2014-01-18T06:59:59.560" Score="0" ViewCount="28" Body="&lt;p&gt;Why do our limbs (legs, arms) get numb/feelingless when they are under prolonged pressure or when one has crossed his/her leg while sitting for a long period?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After we move it to a more relaxed or natural position numbness goes away and we get the really strange and hard to bear tickles. Why does the numbness go away by doing this and why do why get these odd tickles?&lt;/p&gt;&#xA;" OwnerUserId="5431" LastActivityDate="2014-01-18T06:59:59.560" Title="Why do our limbs and other body parts get numb/feelingless and then they start to tickle?" Tags="&lt;human-biology&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-01-19T04:16:41.703" ContentLicense="CC BY-SA 3.0" />
  <row Id="14518" PostTypeId="1" AcceptedAnswerId="14520" CreationDate="2014-01-18T11:43:46.897" Score="3" ViewCount="64" Body="&lt;p&gt;During the process of &lt;strong&gt;Conversion to Ribonucleoside Monophosphates&lt;/strong&gt; the various ribonucleoside triphosphates break off their high energy bonds after linkage to the DNA.But the &lt;em&gt;first&lt;/em&gt; ribonucleotide triphosphate retains all the phosphates thus chemically distinct from the rest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now my question is:&#xA;Why does it retain the phosphates?&lt;/p&gt;&#xA;" OwnerDisplayName="user3800" LastEditorDisplayName="user3800" LastEditDate="2014-01-18T13:09:27.227" LastActivityDate="2014-01-18T13:09:27.227" Title="Process of Transcription" Tags="&lt;molecular-genetics&gt;&lt;rna&gt;&lt;transcription&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14520" PostTypeId="2" ParentId="14518" CreationDate="2014-01-18T13:01:20.743" Score="2" Body="&lt;p&gt;There is a useful diagram at &lt;a href=&quot;http://www.nbs.csudh.edu/chemistry/faculty/nsturm/CHEMXL153/RNASynthesisProcessing.htm&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During RNA synthesis &lt;em&gt;in vivo&lt;/em&gt; the 3'-OH oxygen atom of the growing chain reacts with the &amp;alpha; 5'-phosphate of the incoming ribonucleotide (nucleophilic attack), displacing the &amp;beta; + &amp;gamma; phosphates as a pyrophosphate group. This results in a 3'-5' bond between the prexisting oligoribonucleotide and the incoming ribonucleotide. In other words the loss of the pyrophosphate group is an inevitable consequence of the elongation reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At initiation, however, the first ribonucleotide has not been the subject of a nucleophilic attack, because it is first in the chain. Its 3'-OH will carry out the nucleophilic attack descibed above when the next ribonucleotide is added to the chain.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-01-18T13:01:20.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14521" PostTypeId="1" AcceptedAnswerId="14522" CreationDate="2014-01-18T13:11:38.493" Score="0" ViewCount="801" Body="&lt;p&gt;Could someone help me out with a basic example of the interactions of 2 or more non-identical alleles leading to an advantageous outcome for an individual organism? Based on empirical research OR on a theoretical model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of 2 or more non-identical alleles cooperating across replication iterations/generations between individual organisms would be even beter. I somehow find this more spectacular :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please let me know if I'm not mentioning enough elements to answer the question. It's a very broad question and I accept very broad answers - semantically and across scientific branches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All the best,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Flo&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personal background: I am new to the scientific field of biology. I think I caught up on some of the basic principles of genetics, allellomorphs, loci and DNA replication and I've gotten interested in the workings of alleles.&lt;/p&gt;&#xA;" OwnerUserId="5453" LastEditorUserId="5453" LastEditDate="2014-01-18T14:51:39.603" LastActivityDate="2014-01-18T15:34:51.633" Title="A basic example of the interactions of 2 or more non-identical alleles leading to an advantageous outcome for an individual organism" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;rna&gt;&lt;allele&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14522" PostTypeId="2" ParentId="14521" CreationDate="2014-01-18T15:15:54.257" Score="1" Body="&lt;p&gt;Reading your updated question, I think you are interested about &lt;a href=&quot;http://en.wikipedia.org/wiki/Epistasis%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;epistasis&lt;/a&gt;. Let me know if I am mistaken.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concept of epistasis might be confused with the one of &lt;a href=&quot;http://en.wikipedia.org/wiki/Pleiotropy&quot; rel=&quot;nofollow noreferrer&quot;&gt;pleyotropy&lt;/a&gt;, so I will define both terms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pleyotropy occurs when one gene influences multiple &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenotype&quot; rel=&quot;nofollow noreferrer&quot;&gt;phenotypic&lt;/a&gt; traits. Note: the phenotype, to make it simply is what a living things look like (its cells, proteins, shape of the face, size of the leaves, etc…). It is often thought in duality with the genotype which is the total genetic information contained in an individual that codes for the phenotype (Be careful, the environment is also an important factor influencing the phenotype, if you make sports you will have big muscles!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Epistasis is when the effect on the phenotype of one gene depends on the presence of several (or only one) other genes. Wikipedia gives this (simplistic) example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1aj31m.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here, two bi-allelic genes are involved. One gene that determines the hair color. The two alleles influence the phenotype such: one allele gives red hair and the other allele gives blond hair. Now There's another bi-allelic gene coding for baldness. One allele causes the bearer to be hairy and the other one causes the bearer to be bald. Therefore, if an individual carries the allele &quot;Bald&quot; in the &quot;Baldness&quot; loci, what this individual carries on the other loci is not important because it will result into the same phenotype anyway, he is bald. Now if in the baldness loci, the allele is &quot;Hairy&quot;, then the expression of the other gene &quot;Hair color&quot; matters and therefore if the allele is &quot;blond&quot;, the bearer has blond hair and if the allele is &quot;red&quot; the bearer has red hair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;Baldness&quot; gene is called a modifier. One can also say that the expression the &quot;Hair color&quot; gene depends on the genetic background of the individual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now cases of epistasis are not always that easy and if they influence the fitness, this kind of epistatic interaction might have implications for their evolution.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-01-18T15:34:51.633" LastActivityDate="2014-01-18T15:34:51.633" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14523" PostTypeId="1" AcceptedAnswerId="15518" CreationDate="2014-01-18T16:25:11.040" Score="4" ViewCount="479" Body="&lt;p&gt;Many eukaryotic organisms like yeasts, hydras , planarias, plants etc reproduce asexually.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Replication of End of linear DNA pose a limit to the number of cell divisions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question : Do asexually reproducing organisms have telomerase in all their cells ? Is the telomerase activated at specific times at specific places ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If they don't, how can they reproduce infinitely ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2014-01-28T08:58:40.660" LastActivityDate="2014-03-05T23:06:28.543" Title="Asexual reproduction and Telomeres" Tags="&lt;reproduction&gt;&lt;telomere&gt;&lt;eukaryotic-cells&gt;&lt;cell-division&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14525" PostTypeId="1" CreationDate="2014-01-18T18:49:46.240" Score="4" ViewCount="246" Body="&lt;p&gt;In some animals (like dogs) size seems like it's controlled mostly by just a few genes (IGF1, and the genes that repress it). I'm curious:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) Does other miniaturization takes a similar route (for example, with pygmy hippos).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) Do we have the technology / knowledge to deliberately create &quot;pygmy&quot; animals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3) Is it possible that miniaturization could be a way to protect endangered large species? For example, we shrink them down so they need less room but they could still breed and preserve biodiversity. Also, later on there's always the possibility that we could gradually un-shrink the species if we get our act together and free up more habitat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note:&lt;/strong&gt; I realize that they wouldn't be able to fill the same ecological niche at half the size. &lt;/p&gt;&#xA;" OwnerUserId="5457" LastEditorUserId="3624" LastEditDate="2014-01-19T18:46:48.433" LastActivityDate="2017-01-24T05:24:23.030" Title="Could miniaturization be used to protect endangered large species?" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;genomes&gt;&lt;conservation-biology&gt;" AnswerCount="0" CommentCount="6" ClosedDate="2017-01-24T11:06:54.800" ContentLicense="CC BY-SA 3.0" />
  <row Id="14528" PostTypeId="1" AcceptedAnswerId="14575" CreationDate="2014-01-19T15:53:13.177" Score="7" ViewCount="460" Body="&lt;p&gt;Can you tell whether a salix alba tree will produce male flowers or female flowers by looking at it, touching it or generally using your unaided senses? If not, is there any way to do that without specialized equipment or lots of expertise?&lt;/p&gt;&#xA;" OwnerUserId="1278" LastActivityDate="2021-01-15T16:03:26.133" Title="Can you tell the sex of a white willow when it's not flowering?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14529" PostTypeId="1" CreationDate="2014-01-19T16:49:35.537" Score="1" ViewCount="448" Body="&lt;p&gt;I was searching for an answer that &quot;why do we need intrinsic pathway when there is fast extrinsic pathway&quot; and i found the answer in the following link:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pathologystudent.com/?p=3197&quot; rel=&quot;nofollow&quot;&gt;http://www.pathologystudent.com/?p=3197&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It says that the factor X produced in the extrinsic pathway turns off the extrinsic pathway and activates the intrinsic pathway. As the extrinsic pathway is turned off so, we need intrinsic pathway to continue the clotting process. But if the extrinsic pathway is stopped then how do we get prothormbin time because prothrombin time is for extrinsic pathway?&lt;/p&gt;&#xA;" OwnerUserId="1765" LastActivityDate="2014-01-31T11:14:41.760" Title="Prothrombin time when extrinsic pathway is turned off" Tags="&lt;hematology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14530" PostTypeId="2" ParentId="5751" CreationDate="2014-01-19T17:12:15.583" Score="0" Body="&lt;p&gt;Meiosis starts with a somatic (diploid) cell. To make a long story very, very short, this one cell undergoes cytokinesis twice. You end up with four haploid cells, called gametes or sex cells.&lt;/p&gt;&#xA;" OwnerUserId="5466" LastActivityDate="2014-01-19T17:12:15.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14531" PostTypeId="1" CreationDate="2014-01-20T03:08:10.597" Score="0" ViewCount="48" Body="&lt;p&gt;If there is bacteria, lets say &lt;code&gt;Enterococci&lt;/code&gt; that is sensitive to:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Amoxycillin-Clavulinic acid &lt;/li&gt;&#xA;&lt;li&gt;Ampicillin-Sulbactam &lt;/li&gt;&#xA;&lt;li&gt;Ofloxacin&lt;/li&gt;&#xA;&lt;li&gt;Ciprofloxacin&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Is it possible to become resistance to &lt;code&gt;Ampicillin-Sulbactam&lt;/code&gt; by using &lt;code&gt;Amoxycillin-Clavulinic acid&lt;/code&gt; ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to become resistance to &lt;code&gt;Ofloxacin&lt;/code&gt; by using &lt;code&gt;Ciprofloxacin&lt;/code&gt; ?&lt;/p&gt;&#xA;" OwnerUserId="3350" LastActivityDate="2014-08-02T07:27:50.873" Title="Is it possible for bacteria to acquire family-wide antibiotic resistance?" Tags="&lt;evolution&gt;&lt;bacteriology&gt;&lt;antibiotics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14532" PostTypeId="1" AcceptedAnswerId="14536" CreationDate="2014-01-20T06:28:29.657" Score="2" ViewCount="186" Body="&lt;p&gt;Germs can develop antimicrobial resistance. It is a problem serious enough to deserve an FAQ page on the WHO website (&lt;a href=&quot;http://www.who.int/mediacentre/factsheets/fs194/en/&quot; rel=&quot;nofollow&quot;&gt;http://www.who.int/mediacentre/factsheets/fs194/en/&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But how about surfactant resistance? We wash our body, our dishes, our clothes, and pretty much anything that is washable with soap/detergent, which means surfactants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So can germs develop surfactant resistance in a way that is harmful to human health? If so, is there any recorded experiment about it? If not, why not?&lt;/p&gt;&#xA;" OwnerUserId="1114" LastActivityDate="2020-07-24T17:15:24.503" Title="Can germs develop surfactant resistance in a harmful way?" Tags="&lt;microbiology&gt;&lt;hygiene&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14533" PostTypeId="1" CreationDate="2014-01-20T07:16:23.167" Score="3" ViewCount="149" Body="&lt;p&gt;I'm preparing for a debate (just between friends) on evolution (I'm in support), and one of the points I plan to bring up is the Chromosome 2 evidence.  I'm now trying to predict their potential rebuttals.  The common statement I've seen is that since the apes have 48 chromosomes and humans have 46, then there are two possibilities: either we &quot;lost&quot; a chromosome, which would be fatal, or there was fusion.  This, I believe, was an actual prediction prior to the answer of Chromosome 2 being identified.  But couldn't there have been a third possibility - that the apes gained a pair of chromosomes, perhaps thru splitting of some kind?  This seems reasonable to me due to the other claim that we didn't evolve &lt;em&gt;from&lt;/em&gt; apes but that we share a common ancestor, and so the ape lineage could have acquired the extra chromosome after the split.  (Note I'm a total biology noob, so if this doesn't even make sense, then please tell me.)  I understand that this isn't the way it turned out, that Chr 2 looks exactly as we would expect from fusion, but prior to this discovery, couldn't the apes gaining a chromosome have been a possible reason?  TIA.&lt;/p&gt;&#xA;" OwnerUserId="5468" LastEditorUserId="5468" LastEditDate="2014-01-20T07:31:43.337" LastActivityDate="2014-03-22T19:55:26.450" Title="Chromosome 2 alternate explanation - apes gaining a set of chromosomes?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14535" PostTypeId="1" AcceptedAnswerId="14537" CreationDate="2014-01-20T10:09:42.053" Score="2" ViewCount="157" Body="&lt;p&gt;How quickly can the loss of lactose tolerance onset in an adult?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such as being able to process lactose normally to having notice symptoms associated with the inability to process lactose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not asking how long it takes to digest food, but rather how long it takes for lactose intolerance to become noticeable (hours, days, weeks, months, years).&lt;/p&gt;&#xA;" OwnerUserId="4022" LastEditorUserId="4022" LastEditDate="2014-01-20T11:19:49.063" LastActivityDate="2014-01-22T16:41:42.737" Title="How suddenly does lactose-intolerance onset?" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14536" PostTypeId="2" ParentId="14532" CreationDate="2014-01-20T11:16:43.930" Score="2" Body="&lt;p&gt;Never say never indeed!&lt;/p&gt;&#xA;&lt;p&gt;a three part answer to the question:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Bacteria can develop resistance.&lt;/strong&gt;  &lt;a href=&quot;http://www.terrapub.co.jp/onlineproceedings/ec/03/pdf/BR_03089.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;These researchers&lt;/a&gt; did a screen for Staph and Pseudomonas which survived a detergent/soap treatment and indeed were able to select for many strains.  I'm not sure that their explanation of why they are resistant is a final answer, especially for the Pseudomonas strains which have no hypothesis at all.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Nearly all bacteria do this all the time #1&lt;/strong&gt;  Most bacteria can go into spore or plaque forms which basically hibernate.  These plaque colonies are matrices of crosslinked bacteria and are resistant to extremes of conditions in the environment or lack of food.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Even Normal Resistance is a relative thing.&lt;/strong&gt;  Alcohol sanitizers kill 99.9% of bacteria.  That sounds like a lot but that 0.1% can come back to full strength in a relatively short period of time.  0.1% is still millions of individuals surviving after a shower.  Resistant bacteria have a higher proportion of survivors and should improve the bounce back rate.  So resistance is a term which you need to define for a given situation.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;Surfactant (soap) resistant bacteria can be nearly any sort of bacteria and a certain percentage of them are ready for a scrub down at any given time.  To get a surface completely free of bacteria takes a good deal of work.&lt;/p&gt;&#xA;&lt;p&gt;As far as a danger to human health - resistance to being killed by soap is a real problem because the few of them which also have resistance to antibiotics and are pathogenic will be pretty much unstoppable.  Its not likely that surfactant resistance will itself make a bacteria pathogenic (never say never!) but if such a 'triple threat' emerges we'd all be in trouble.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2020-07-24T17:15:24.503" LastActivityDate="2020-07-24T17:15:24.503" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="14537" PostTypeId="2" ParentId="14535" CreationDate="2014-01-20T17:42:45.300" Score="1" Body="&lt;p&gt;&lt;strong&gt;Disclaimer: I am not medically qualified, and this answer must not be construed as being medical advice of any kind.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Primary adult hypolactasia is the most common cause of lactose intolerance. The majority of the world's population have this phenotype. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In these individuals, at weaning, there is a reduction in the level of the enzyme lactase, which is responsible for digesting lactose to galactose and glucose in the small intestine. Undigested lactose can create symptoms via osmotic effects (causing diarrhoea) and because it is metabolised by bacteria in the colon, producing gas and thus abdominal bloating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About 35% of adults have a genetic variant in an region upstream of the lactase gene which results in the expression of lactase continuing into adult life. These individuals are lactose tolerant. This trait is most common in Northern Europe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to references cited in  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ingram, CJE et al. (2009) Lactose digestion and the evolutionary genetics of lactase persistence Hum Genet (2009) 124:579–591 &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(I have removed citations from the passage for clarity.)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;most lactase non-persistent individuals can tolerate small amounts of lactose (as in tea or coffee), and some can consume a lot without ill effects. Variation in the composition of the gut flora between individuals, as well as a psychosomatic component may account for some of the interindividual variation in symptoms.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The clear implication is that there is a lot of variation in the tolerance of lactose amongst those lacking the lactase persistence trait. Given the contribution of the gut flora to the symptoms these could presumably vary as a result of, for example, antibiotic treatment. Also I imagine that the effects of undigested lactose could be synergistic with some other gut disturbance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Added in response to comment from the OP:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In someone with the (common) genotype that corresponds to 'no persistence of lactase' the possibility of showing symptoms will be present from a young age. Apparently there is a lot of variation in the severity of symptoms. If an adult suddenly exhibits symptoms then I am suggesting that this could be due to an interaction of non-persistence with some other gut disturbance - I imagine this could happen quite quickly. Alternatively I suppose that a change in diet could trigger symptoms. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-01-22T16:41:42.737" LastActivityDate="2014-01-22T16:41:42.737" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14539" PostTypeId="2" ParentId="14529" CreationDate="2014-01-20T23:15:13.933" Score="2" Body="&lt;p&gt;In order to understand the importance of both pathways, you first need to be clear about what is meant by them respectively. Clotting activation from tissue factor (TF) is known as the extrinsic pathway, so you've got that one right. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The intrinsic pathway doesn't involve FX&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The intrinsic pathway does not (as often misunderstood) refer to the clotting cascade downstream of factor X (FX) which involves FV, FVIII and thrombin. Rather, the intrinsic pathway is a system which is able to initiate the clotting cascade without any tissue factor being present. It is triggered by the assembly of high molecular weight kininogen, prekallikrein and FXII on collagen. This is also known as &lt;em&gt;contact activation&lt;/em&gt;, and sets off a small cascade producing active FIX (FIXa), which can then assemble with circulating FVIIa in order to produce FXa and thereby set off the rest of the clotting system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The extrinsic and intrinsic pathway are separate ways towards a &quot;common pathway&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So think of it this way: The extrinsic pathway produces FXa in one way (TF), the intrinsic pathway produces FXa in a different way (HMWK+prekallikrein+FXII). There isn't really any interaction between these two. Once FXa is produced from either of these two, it will start to set off what you could call the &quot;common pathway&quot;, i.e. it will produce thrombin, which will activate co-factors that will then lead to more production of FXa and propel the entire thing forward faster and faster until it reaches what we know as the thrombin peak.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The intrinsic pathway is not important for haemostasis in humans&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aside from this, you should know that the intrinsic pathway exists, but it doesn't bear much significance in a living human. This is demonstrated by genetic FXII deficiency - you would expect it to produce haemophilia if FXII and therefore the intrinsic pathway was important (just like FVIII and FIX), but it doesn't (read here: &lt;a href=&quot;http://en.wikipedia.org/wiki/Factor_XII#Role_in_disease&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Factor_XII#Role_in_disease&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The principle behind the initiation pathways and the common pathway&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to summarise: You fell victim to a misunderstanding and a bad explanation on that site you linked. The extrinsic pathway doesn't &quot;turn itself off&quot;, and the intrinsic pathway doesn't &quot;take over&quot;. What really happens in a human is that the intrisic pathway doesn't really do anything. Rather, the extrinsic pathway will produce a little bit of active FXa. But that is enough to produce a little bit of thrombin. And that bit of thrombin will then produce small amounts of FIXa and co-factors (FV and FVIII). These will start to produce more FXa, which will produce more thrombin, which will produce more FIXa and co-factors, and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What the article you refer to is trying to mention are the inhibitory systems that will be set off alongside all of this. Think about it - if thrombin increases its own production perpetually, how does it know when to stop? These systems which ensure that clotting does stop are known as anticoagulation pathways. They are just as amazing as the coagulation pathways themselves, and they are extremely well-geared towards shutting off exactly the right clotting factors at exactly the right time, to ensure that a clot forms in the wound but only there and nowhere else.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;: It turns out people do use more complicated definitions of &quot;intrinsic&quot; and &quot;extrinsic&quot; - the problem being once again that everybody can define words as they like. This is rather based on the distinguishing of the two ten-ases, TF-FVII (extrinsic tenase) and FIX-FVIII (intrinsic tenase). In this understanding, the physiological process does indeed start off by the extrinsic pathway (i.e. mechanisms which generate extrinsic tenase), which will kick off the amplification cascade of the intrinsic pathway (i.e. which produces intrinsic tenase). It is true that this way, the contribution of the &quot;extrinsic pathway&quot; is minor once the &quot;intrinsic pathway&quot; is active, but even so, it does not &quot;shut itself off&quot;. What turns the extrinsic pathway off is the layer of material which gets deposited on top of the exposed subendothelial surface, preventing access to TF!&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2014-01-31T11:14:41.760" LastActivityDate="2014-01-31T11:14:41.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14540" PostTypeId="1" AcceptedAnswerId="14541" CreationDate="2014-01-20T23:35:52.967" Score="5" ViewCount="262" Body="&lt;p&gt;As far as I know, the DNA sequence becomes shorter every time a cell divides.&lt;br&gt;&#xA;A shorter sequence results in information loss and aging characteristics.&lt;br&gt;&#xA;&lt;br&gt;&#xA;As a countermeasure, shouldn't one stay young and healthy at least longer, if the DNA in a cell is changed with a &quot;better&quot; DNA (from years ago... let's say your DNA was extracted with the age of 20 and you reinsert it every 10 years or so)?&#xA;&lt;br&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is true, then (as for today's technology)&lt;br&gt;&#xA;- is it already possible to perfectly reproduce the DNA? (I only found articles about XNA)&lt;br&gt;&#xA;- is it possible to easily replace the DNA in all human cells? (I found articles about bacteria inserting pieces of DNA into human cells)&lt;/p&gt;&#xA;" OwnerUserId="5475" LastActivityDate="2014-01-21T18:30:09.790" Title="Stay young by reinserting own DNA from years ago?" Tags="&lt;dna&gt;&lt;reproduction&gt;&lt;dna-damage&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14541" PostTypeId="2" ParentId="14540" CreationDate="2014-01-21T00:51:23.730" Score="1" Body="&lt;p&gt;Lots of questions here. I recommend taking college level courses in Biochemistry, Molecular Biology, and Medical Physiology, and Geriatrics. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other issues than just DNA. Systemic failure is system-wide, and probably most of the issues are still yet undiscovered. Good news I guess if you want to be a researcher in this exciting field! As for DNA-ends, read up on Telomerase. As for DNA copying learn about PCR and sequencing methods. Generally speaking, reverse transcription can be dangerous. Please see many of diseases we are having a hard-time solving, which often use these pathways. Seriously avoid that one. Not everything in DNA is used by the organism at any given time, and some information is elsewhere. Moreover, what if we use DNA as DATA storage besides blueprint information? Hint: while the jury may be still out on Neurons, environmental factors may be passed as epigenetic traits by not just primary shape such as DNA methylation but by obstructing access via conformation and histone wrapping. Not even mentioning mitochondrial dna or prenatal development factors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead: A good diet and exercise. &lt;/p&gt;&#xA;" OwnerUserId="5187" LastEditorUserId="5187" LastEditDate="2014-01-21T01:32:56.497" LastActivityDate="2014-01-21T01:32:56.497" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14543" PostTypeId="1" AcceptedAnswerId="14545" CreationDate="2014-01-21T11:39:25.027" Score="7" ViewCount="2285" Body="&lt;p&gt;I saw a concept on the Internet that says &quot;the strength of genetic drift is inversely proportional to the population size&quot;. I don't know why they are &lt;strong&gt;inversely proportional&lt;/strong&gt;? Can somebody explain? Thank you all! &lt;/p&gt;&#xA;" OwnerDisplayName="user5407" LastEditorUserId="3624" LastEditDate="2014-11-03T09:08:31.050" LastActivityDate="2019-05-13T20:44:29.217" Title="Why is the strength of genetic drift inversely proportional to the population size?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;population-genetics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14544" PostTypeId="2" ParentId="14543" CreationDate="2014-01-21T12:13:00.410" Score="8" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_drift&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Genetic drift&lt;/strong&gt;&lt;/a&gt; refers to changes in allele frequencies that are due to random sampling effects, and not selection. If you sample alleles from a finite population (e.g. caused by the fact that only some individuals in the population reproduce each year), the resulting frequencies will deviate from the original frequencies due to random chance. If your sample is large (a large population) this deviation will be small, and if your sample is small the effect will be substantial. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is exactly the same process as flipping a coin. If you flip a coin 10 times there is a large probability that the outcome will deviate a lot from 50% heads/tails (the outcome will follow the &lt;a href=&quot;http://en.wikipedia.org/wiki/Binomial_distribution&quot; rel=&quot;nofollow noreferrer&quot;&gt;binomial distribution&lt;/a&gt;). This is analogous to the deviation in allele frequency due to genetic drift. If you flip the coin 10000 times the outcome will deviate little from the expected 50% distribution of heads/tail. Therefore the effect is described as &lt;em&gt;inversely proportional&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There exist several models of genetic drift, but one way to look at it is as for how the variance in allele frequency changes over time, which can be described by: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$ V_t \approx p*q(1-e^{-t/2N_e}) $$&lt;/span&gt;&#xA;where &lt;span class=&quot;math-container&quot;&gt;$p$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$q$&lt;/span&gt; are the allele frequencies and &lt;span class=&quot;math-container&quot;&gt;$N_e$&lt;/span&gt; is the effective population size. Alternatively, the change in heterozygozity (&lt;span class=&quot;math-container&quot;&gt;$H$&lt;/span&gt;) over time due to drift is described by (&lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/1932846123&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Crow &amp;amp; Kimura. 1970. An introduction to population genetics. Harper &amp;amp; Row&quot;&gt;Crow &amp;amp; Kimura, 1970&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$ H_t = H_{t0}\left( 1-\frac{1}{2N_e} \right)^t$$&lt;/span&gt; &#xA;In both these functions, the inverse relationship between genetic drift and population size is seen clearly (population size is found in the denominator in both equations). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concept of genetic drift is closely related to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Founder_effect&quot; rel=&quot;nofollow noreferrer&quot;&gt;founder effect&lt;/a&gt;, but in that case, the sampling is only done once, when a small subpopulation of individuals establishes a new population.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="49230" LastEditDate="2019-03-28T23:09:25.340" LastActivityDate="2019-03-28T23:09:25.340" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="14545" PostTypeId="2" ParentId="14543" CreationDate="2014-01-21T12:14:03.310" Score="14" Body="&lt;p&gt;&lt;strong&gt;Plane Crash Analogy&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;4 people in a plane crash&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a small aeroplane, there are 2 people that wear a blue shirt and 2 people that wear a green shirt. The plane crashes, half of the people died. The 2 survivors are those wearing the green shirt… well, nothing so surprising!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;400 people in a plane crash&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a very big aeroplane, there are 200 people that wear a blue shirt and 200 people that wear a green shirt. The plane crashes, half of the people died. The 200 survivors are those wearing green shirt… This is quite surprising!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Genetic Drift&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same logic applies to genetic drift. Genetic drift is caused by events that modify the reproductive success of individuals in a random way (independently of their genotype). We usually referred to this as random sampling. At each generation, individuals are randomly chosen to reproduce and some genotypes might just happen to be chosen more often than others at a given draw (=at a given generation). Genetic drift pushes the frequency of allele slightly away from what would be predicted. According to the Wright-Fisher model, the frequency of alleles (of a bi-allelic gene) in a haploid population (to make it easier) in the next time step is given by:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$p' = \frac{p \cdot WA}{p \cdot WA + (1-p) \cdot Wa}$$&lt;/span&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where &lt;span class=&quot;math-container&quot;&gt;$p$&lt;/span&gt; is there frequency of an allele at time = &lt;span class=&quot;math-container&quot;&gt;$t$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$p'$&lt;/span&gt; is the frequency at time = &lt;span class=&quot;math-container&quot;&gt;$t+1$&lt;/span&gt;. &lt;span class=&quot;math-container&quot;&gt;$WA$&lt;/span&gt; is the fitness of the genotype which frequency is &lt;span class=&quot;math-container&quot;&gt;$p$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$Wa$&lt;/span&gt; is the fitness of the genotype which frequency is &lt;span class=&quot;math-container&quot;&gt;$1-p$&lt;/span&gt;. If the population is infinite, the predictions of this equation are exactly correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now if we say that meteorites fall and half of the individual get killed. The probability of getting killed by a meteorite obviously does not depend on genetic predisposition, it is a question of chance! If you look at a population of 1 million individuals, half of them having the genotype &lt;span class=&quot;math-container&quot;&gt;$A$&lt;/span&gt;, the other half having the genotype &lt;span class=&quot;math-container&quot;&gt;$a$&lt;/span&gt;. It is very unlikely that more than 60% of all individuals that get killed are of the same genotype. Therefore, the meteorites won't change much the frequency of the genotypes. If you look at a population of 4 individuals 2 are &lt;span class=&quot;math-container&quot;&gt;$a$&lt;/span&gt; and 2 are &lt;span class=&quot;math-container&quot;&gt;$A$&lt;/span&gt;, 2 of them get killed by a meteorite. Well, you have a probability of one half that the two survivors are of the same genotype and that the genotypes frequency would have changed drastically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetic drift refers to these changes in allele frequency which are due to random events (such as meteorites) and the strength of genetic drift indeed depends on the population size for probabilistic reasons. The greatest the population size, the lowest is the strength (or the relative importance) of genetic drift.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How to model genetic drift&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are three famous models of genetic drift that all lead to very similar expectations. I shall just name them here but I will not develop the underlying mathematics.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Wright-Fisher model of genetic drift&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Not to confuse with the Wright-Fisher model of selection written above&lt;/li&gt;&#xA;&lt;li&gt;It models genetic drift as a random sample of the previous generation and hence uses a binomial distribution.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Moran model&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;It is based on a birth-death model (a type of Markov model).&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Kimura's diffusion equation model&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;It is an extension of the above two models for a case of continuous time.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2019-05-13T20:44:29.217" LastActivityDate="2019-05-13T20:44:29.217" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="14546" PostTypeId="1" CreationDate="2014-01-21T15:11:32.700" Score="2" ViewCount="60" Body="&lt;p&gt;While this topic has virtually no real life application and has never been examined due to obvious reasons, it is quite intriguing to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've read a lot of speculations and claims about the world's quietest room (-8.7 decibel at Orfield Laboratories in South Mineapolis) including loss/deterioration of hearing, hallucinations etc. What I was wondering about is if any of the human self-preservance reflexes would kick in once an individual hears his own bodily fluids and organs expanding/retracting? Since, as far as I know, there aren't any scientific proofs or thesis on this subject, what are your thoughts based on your knowledge on regular body functions and reflexes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Third-party links: &lt;a href=&quot;http://www.thedailyswarm.com/headlines/worlds-quietest-room-breeds-insanity/&quot; rel=&quot;nofollow&quot;&gt;TheDailySwarm's post&lt;/a&gt;, &lt;a href=&quot;http://www.cbc.ca/strombo/news/the-sound-of-silence-a.html&quot; rel=&quot;nofollow&quot;&gt;CBC's post&lt;/a&gt;, &lt;a href=&quot;http://awesomefacts.quora.com/The-Worlds-Quietest-room-can-drive-you-crazy&quot; rel=&quot;nofollow&quot;&gt;Quora's post&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5477" LastEditorUserId="3340" LastEditDate="2014-01-22T04:45:40.607" LastActivityDate="2014-01-22T04:45:40.607" Title="Could below zero decibel environment cause arrhythmia?" Tags="&lt;cardiology&gt;&lt;reflexes&gt;" AnswerCount="0" CommentCount="8" ClosedDate="2015-01-07T05:33:51.570" ContentLicense="CC BY-SA 3.0" />
  <row Id="14548" PostTypeId="2" ParentId="14540" CreationDate="2014-01-21T18:18:25.800" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;As far as I know, the DNA sequence becomes shorter every time a cell&#xA;  divides. A shorter sequence results in information loss and aging&#xA;  characteristics.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Neither telomeres nor aging are nearly that simple.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;is it already possible to perfectly reproduce the DNA?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No.  &lt;strong&gt;Any&lt;/strong&gt; method that would be used to replicate DNA requires using enzymes, and they always have a non zero failure rate.  You could use whole genome amplification to make a pile of DNA that was on average the right sequence, but each individual chromosome would have errors.  And forget copying over epigenetic modifications.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are ways to get cells to incorporate new DNA, but every cell in an organ of a living organism?  And a whole mammalian genome's worth?  And to magically tell the cell that the new genome should replace the old one?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;None of that is feasible.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(I found articles about bacteria inserting pieces of DNA into human&#xA;  cells)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Okay, let's get some scale here.  Most bacteria have a genome of 5-10 million bases.  Humans have a genome of 3 billion bases.  Even if a bacteria can transduce a small plasmid into a human cell, that doesn't scale up to bacteria replacing the whole genome of every cell in an organ.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And because there's always a relevant xkcd comic&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://xkcd.com/793/&quot; rel=&quot;nofollow&quot;&gt;http://xkcd.com/793/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5148" LastEditorUserId="5148" LastEditDate="2014-01-21T18:30:09.790" LastActivityDate="2014-01-21T18:30:09.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14549" PostTypeId="2" ParentId="14533" CreationDate="2014-01-21T18:36:43.173" Score="1" Body="&lt;p&gt;I guess part of the question is...what exactly are you bring up Chromosome 2 as evidence of, exactly?  It's evidence of that chromosomal rearrangements are possible, but that isn't terribly helpful to you, so I'm not sure why you are bringing it up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the fusion is a rebuttal to a claim that the disparate # of chromosome is a problem for the claims of common ancestry between humans and other apes, but if they don't mention it, I'm not sure why you would need to use that particular fact.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have you consulted talkorigin's 29 evidences of macroevolution?  Lots of good stuff there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.talkorigins.org/faqs/comdesc/&quot; rel=&quot;nofollow&quot;&gt;http://www.talkorigins.org/faqs/comdesc/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-01-21T18:36:43.173" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14551" PostTypeId="1" CreationDate="2014-01-21T20:15:17.287" Score="2" ViewCount="2470" Body="&lt;p&gt;I am reading a paper on a certain marine microorganism that can eat alkanes and therefore might be useful for cleaning up oil spills, etc. This sentence struck me as odd (although I am sure that the answer is pretty simple):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Using the same probe, Southern blotting analysis showed that there was only one copy of alkB1 in the B-5 chromosome.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I realized that I don't know how Southern blotting can tell you about copy number. Can someone help me on this?&lt;/p&gt;&#xA;" OwnerUserId="5441" LastActivityDate="2014-01-23T04:45:15.637" Title="How can Southern blotting be used to establish gene copy number?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;marine-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14553" PostTypeId="1" CreationDate="2014-01-22T05:39:32.663" Score="4" ViewCount="139" Body="&lt;p&gt;The first electron source for plants was H2S, but now most modern plants use H2O as an electron source.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the advantage of using H2O instead of H2S?&lt;/p&gt;&#xA;" OwnerUserId="5481" LastEditorUserId="3340" LastEditDate="2014-10-09T13:31:07.807" LastActivityDate="2014-10-09T13:31:07.807" Title="H₂S as a source of electrons for plants" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14554" PostTypeId="1" AcceptedAnswerId="14558" CreationDate="2014-01-22T05:49:05.477" Score="2" ViewCount="179" Body="&lt;p&gt;I'm looking at this &lt;a href=&quot;http://www.nytimes.com/2014/01/12/opinion/sunday/goodnight-sleep-clean.html&quot; rel=&quot;nofollow&quot;&gt;article on the possible mechanism of detoxifying brain during sleep using cerebrospinal fluid&lt;/a&gt;. It states that at night, the space between neurons may allow better (up to 20x) circulation of cerebrospinal fluid within the brain to clean out metabolic by products of daytime activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is if this may also work in reverse and allow to deliver drugs within the fluid to the brain.  &lt;strong&gt;If a person ingests a drug or nutrient before sleep, would the increase in circulation of cerebrospinal fluid deliver the drug to deep regions of the brain?&lt;/strong&gt; Or does the blood-brain barrier prevent drugs from entering cerebrospinal fluid?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2014-01-22T17:12:10.747" Title="Can cerebrospinal fluid deliver nutrients/drugs to neurons during sleep?" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;&lt;brain&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14556" PostTypeId="1" CreationDate="2014-01-22T09:03:06.967" Score="1" ViewCount="81" Body="&lt;p&gt;Since most of the cerebrovascular accident are ischemic ones, would it be usefull to have anticoagulant everywhere (we already have  AEDs everywhere) so that everytime someone would have symptoms of a CVA we would be able to destroy the blood clot before any permanent damage to occur ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand may it make the case of ruptured aneurysm getting worse ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what are the potential negative and positive effect of such a policy ?&lt;/p&gt;&#xA;" OwnerUserId="5484" LastEditorUserId="5484" LastEditDate="2014-01-22T10:21:11.133" LastActivityDate="2014-01-22T10:21:11.133" Title="Systematic anticoagulant injection after a CVA" Tags="&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14557" PostTypeId="2" ParentId="14551" CreationDate="2014-01-22T13:18:50.893" Score="2" Body="&lt;p&gt;This method is commonly practiced. Atleast I see the people working with zebrafish transgenics using it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you shear the genomic DNA or do a restriction digestion, you are likely to get fragments of different sizes. &#xA;It is highly probable that the two (or more) locations harboring a copy of the DNA element are a part of fragments with different sizes. So on the blot you'll get two bands.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But as I said this test relies on probability that the two fragments are dissimilar in length. Therefore, southern blot should not be considered as an absolute test to determine copy number. Inverse PCR, FISH, etc can be used to determine copy number. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-01-23T04:45:15.637" LastActivityDate="2014-01-23T04:45:15.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14558" PostTypeId="2" ParentId="14554" CreationDate="2014-01-22T15:11:18.913" Score="3" Body="&lt;p&gt;Only certain drugs can cross the blood brain barrier (BBB). However, there exist techniques to deliver drugs to the brain that otherwise cannot permeate through the BBB.&#xA;One such technique is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Intrathecal&quot; rel=&quot;nofollow&quot;&gt;intrathecal&lt;/a&gt; delivery that injects drugs directly into the cerebrospinal fluid, avoiding the BBB problem and allowing the drug to reach cells, including neurons, in the brain. It has been used for certain kinds of &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemotherapy&quot; rel=&quot;nofollow&quot;&gt;chemotherapy&lt;/a&gt;, pain management, treatment of spastic cerebral palsy, and more recently for &lt;a href=&quot;http://clinicaltrials.gov/ct2/show/NCT01506141&quot; rel=&quot;nofollow&quot;&gt;enzyme replacement therapy&lt;/a&gt;.&#xA;However with intrathecal delivery there is a risk of infection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having said that, if a drug reaches the CSF then your hypothesis should be correct. There is no experimental evidence for it yet.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="3340" LastEditDate="2014-01-22T17:12:10.747" LastActivityDate="2014-01-22T17:12:10.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14560" PostTypeId="1" CreationDate="2014-01-22T15:59:24.737" Score="3" ViewCount="249" Body="&lt;p&gt;I am collecting evidence, even anecdotal, how does single nucleotide deletion or insertion in primer region affect the outcome of real-time PCR. &#xA;I am most interested in how much there is a delay in Cq (treshold cycle value) if compared to perfectly matched primer. But if you do not have Cq data, I also collect &quot;Yes or No&quot; answers, saying, whether there was amplification or no amplification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested specifically in insertion or deletion mismatches. (For substitution mismatches, there is a lot of data.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will appreciate any published or unpublished evidence.&lt;/p&gt;&#xA;" OwnerUserId="5369" LastEditorUserId="5369" LastEditDate="2014-02-02T09:02:39.000" LastActivityDate="2014-02-02T09:02:39.000" Title="Real-time PCR delay in Cq due to insertion SNP in primer" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;pcr&gt;&lt;snp&gt;&lt;primer&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14561" PostTypeId="1" AcceptedAnswerId="14565" CreationDate="2014-01-22T17:24:49.800" Score="3" ViewCount="176" Body="&lt;p&gt;I've been looking through the files available at &lt;a href=&quot;http://www.reactome.org/&quot; rel=&quot;nofollow&quot;&gt;www.reactome.org&lt;/a&gt; along with some others but I only find images/pdfs of metabolic pathway diagrams. Where is the actual data these pathways are drawn from? I imagine there should be some kind of directed graph representation. I'm limited to freely available datasets, so unfortunately I'm not able to check out those such as KEGG.&lt;/p&gt;&#xA;" OwnerUserId="5487" LastActivityDate="2014-01-22T21:32:23.850" Title="Where to obtain metabolic pathway datasets" Tags="&lt;database&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14562" PostTypeId="1" CreationDate="2014-01-22T19:00:14.897" Score="2" ViewCount="137" Body="&lt;p&gt;I want to know the physiological reasons of why the leaves of my study plant got twisted when treated for 10 days with spray of indole acetic acid. I want to treat seeds with IAA, and I'm thinking about testing what will happen when I treat the leaves. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a picture of what the plant looks like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NYx6M.jpg&quot; alt=&quot;twisted leaves&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks &lt;/p&gt;&#xA;" OwnerUserId="5489" LastEditorUserId="3624" LastEditDate="2014-01-23T10:01:34.397" LastActivityDate="2014-01-23T11:04:55.493" Title="Physiological reason why leaves got twisted when treated with indole acetic acid" Tags="&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="14563" PostTypeId="1" CreationDate="2014-01-22T20:54:22.120" Score="2" ViewCount="76" Body="&lt;p&gt;Has there been studies on the difference between the smoke generated from: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;cigarette or cigar manufactured by brands which are proven to contain more than a hundred of dangerous additional components &lt;/li&gt;&#xA;&lt;li&gt;tobacco/marijuana (more or less pure?)/any-plant-dried-leaves made cigarettes.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Apart from the nicotine both contain naturally, are the latter safer to inhale? in which scale?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other question &lt;a href=&quot;https://biology.stackexchange.com/questions/14263/effects-of-smoking-tobacco-compared-to-inhaling-other-smoke&quot;&gt;Effects of smoking tobacco compared to inhaling other smoke&lt;/a&gt;, reminds the danger of all source of intoxication, wall paints are also to consider.. and outdoors gas pipes, etc... But I'm doing a fixation on smoked drugs. I've been living in residences, sharing corridors with flats with more or less important smoke concentration, and had developped &lt;a href=&quot;http://wordinfo.info/unit/4382?letter=C&amp;amp;spage=5&quot; rel=&quot;nofollow noreferrer&quot;&gt;fumiphobia&lt;/a&gt; (but this is out of topic).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is probably psychological but I'd never stay in the same room than someone smoking, but if someone take some dried leaves out of a plant,.. roll them in paper, fire it and inspire it. It never happened but I wouldn't be as much scared by the generated smoke. But if a study would show that manufactured cigarettes are between 1.5 and 3 times more 'toxic' then I would consider both cases dangerous.&lt;/p&gt;&#xA;" OwnerUserId="4447" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-01-22T21:31:58.650" Title="Different level of toxicity between smoke" Tags="&lt;cancer&gt;&lt;respiration&gt;&lt;smoking&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14564" PostTypeId="2" ParentId="14563" CreationDate="2014-01-22T21:31:58.650" Score="1" Body="&lt;p&gt;I am not sure, if any comparisions have been made with other plant leaves, but unless these contain some pharmacologic active substances, I doubt that they are smoked widely.&#xA;There are comparisions between normal smoking and the smoking of marijuana and the short version is: Both are harmful. It depends on the temperature at which they are burned, how they where grown and so on. For smoking marijuana it also depends if you mix it with tobacco...&#xA;This &lt;a href=&quot;http://adai.uw.edu/marijuana/factsheets/respiratoryeffects.htm&quot; rel=&quot;nofollow&quot;&gt;fact sheet&lt;/a&gt; from the University of Washington lists a number of points on marijuana together with proper references.&#xA;Then there are some articles about smoking and marijuana in comparision:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/tx700275p&quot; rel=&quot;nofollow&quot;&gt;A Comparison of Mainstream and Sidestream Marijuana and Tobacco&#xA;Cigarette Smoke Produced under Two Machine Smoking Conditions&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/chapter/10.1007/978-1-4684-0823-2_3&quot; rel=&quot;nofollow&quot;&gt;On the Carcinogenicity of Marijuana Smoke&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/BF01940790&quot; rel=&quot;nofollow&quot;&gt;A possible chemical basis for the higher mutagenicity of marijuana&#xA;smoke as compared to tobacco smoke&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1311802/&quot; rel=&quot;nofollow&quot;&gt;Is frequent marijuana smoking harmful to health?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-01-22T21:31:58.650" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14565" PostTypeId="2" ParentId="14561" CreationDate="2014-01-22T21:32:23.850" Score="2" Body="&lt;p&gt;KEGG is definitely your choice!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible to get the whole list(s) of pathways: &lt;a href=&quot;http://rest.kegg.jp/list/pathway&quot; rel=&quot;nofollow&quot;&gt;http://rest.kegg.jp/list/pathway&lt;/a&gt; (reference pathways) or &lt;a href=&quot;http://rest.kegg.jp/list/pathway/hsa&quot; rel=&quot;nofollow&quot;&gt;http://rest.kegg.jp/list/pathway/hsa&lt;/a&gt; (for human).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then you can use these IDs to retrieve information about individual pathways: &lt;a href=&quot;http://rest.kegg.jp/get/hsa00053&quot; rel=&quot;nofollow&quot;&gt;http://rest.kegg.jp/get/hsa00053&lt;/a&gt; (GeneBank-like format), &lt;a href=&quot;http://rest.kegg.jp/get/hsa00053/image&quot; rel=&quot;nofollow&quot;&gt;http://rest.kegg.jp/get/hsa00053/image&lt;/a&gt; (image), &lt;a href=&quot;http://rest.kegg.jp/get/hsa00053/kgml&quot; rel=&quot;nofollow&quot;&gt;http://rest.kegg.jp/get/hsa00053/kgml&lt;/a&gt; (KEGG xml). It will take a while, of course, and I'd recommend not to overload their server and make delays between queries. With the GeneBank-like format batch querying is also possible: &lt;a href=&quot;http://rest.kegg.jp/get/hsa00053+hsa00061&quot; rel=&quot;nofollow&quot;&gt;http://rest.kegg.jp/get/hsa00053+hsa00061&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This should likely be a one-time or at least rare operation, because of the load on their server (and I don't think they make big changes very often). You can retrieve info for new pathways, once they appear in &lt;a href=&quot;http://rest.kegg.jp/list/pathway/&quot; rel=&quot;nofollow&quot;&gt;http://rest.kegg.jp/list/pathway/&lt;/a&gt;...&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-01-22T21:32:23.850" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14567" PostTypeId="2" ParentId="14440" CreationDate="2014-01-22T22:07:26.693" Score="3" Body="&lt;p&gt;Inhalation and exhalation happen sequentially as Herman stated in the comments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, your general understanding of inhalation is correct. After the air gets into the lungs, the oxygen is diffused into the capillaries covering the alveoli. The now oxygenated blood travels back to the heart to be circulated throughout the body. As this blood enters capillaries in other regions in the body, the oxygen diffuses out of them and into the surrounding cells. Carbon dioxide (CO2) produced by the cells as a waste product then diffuses into the blood vessels. The CO2-rich blood is then circulated back to the heart to be pumped back to the lungs. This blood flows into the capillaries surrounding the alveoli, and diffuses out. &lt;strong&gt;The exchange of carbon dioxide and oxygen occurs simultaneously.&lt;/strong&gt; So, as oxygen is diffused from the lungs into the bloodstream, CO2 in the bloodstream is diffused out into the lungs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are diagrams to depict what is described above. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wqNlx.gif&quot; alt=&quot;This image depicts the exchange of CO2 and O2 in the lungs.&quot;&gt;&#xA; &lt;img src=&quot;https://i.stack.imgur.com/gb8xN.jpg&quot; alt=&quot;This diagram gives an overview of how these gases travel through the body as I described.&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4929" LastEditorUserId="4929" LastEditDate="2014-01-24T00:33:51.700" LastActivityDate="2014-01-24T00:33:51.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14568" PostTypeId="1" CreationDate="2014-01-22T22:38:50.997" Score="2" ViewCount="697" Body="&lt;p&gt;The title says it all. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do natural or human engineered enzymes exist that can speed up the break down kitchen utensils, aluminum cans, wires, etc. into small particles or powders?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be clear I am not talking about chemical transformation (e.g. iron turning to rust).&lt;/p&gt;&#xA;" OwnerUserId="5491" LastEditorUserId="5491" LastEditDate="2014-01-24T15:45:11.843" LastActivityDate="2014-01-24T20:14:18.820" Title="Are there enzymes found in nature or the man made world that can help break down metals?" Tags="&lt;enzymes&gt;" AnswerCount="2" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="14570" PostTypeId="1" AcceptedAnswerId="17951" CreationDate="2014-01-23T04:28:19.147" Score="3" ViewCount="419" Body="&lt;p&gt;&lt;em&gt;&lt;strong&gt;Note&lt;/em&gt;&lt;/strong&gt; : Any answer to this question will not be (and should not be) taken as medical advice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of my friends has allergic rhinitis and has been prescribed an oral vaccine. He is allergic to 3 different classes of substances and so, has been given 3 different types of vaccines. He has to place them below his tongue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am curious about some of the procedures he has to follow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1.How does a vaccine of this type work ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2 He has been given 2 vials for each type of vaccine. First one is labeled SRS and other one as I understand is - it's allergen. So, What is SRS ? What's the requirement of it ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3 It is written in the instructions that he should not eat anything one hour before and one hour after taking the vaccine. Why ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-06-06T19:18:52.260" Title="Allergic rhinitis vaccine" Tags="&lt;immunology&gt;&lt;protocol&gt;&lt;vaccination&gt;&lt;allergies&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14571" PostTypeId="5" CreationDate="2014-01-23T05:20:23.830" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-01-23T05:20:23.830" LastActivityDate="2014-01-23T05:20:23.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14572" PostTypeId="4" CreationDate="2014-01-23T05:20:23.830" Score="0" Body="Biology dealing with study of reproductive process, especially in higher animals. Closely related to reproductive endocrinology. " OwnerUserId="3340" LastEditorUserId="3632" LastEditDate="2014-01-23T05:58:17.623" LastActivityDate="2014-01-23T05:58:17.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14573" PostTypeId="5" CreationDate="2014-01-23T05:21:58.167" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-01-23T05:21:58.167" LastActivityDate="2014-01-23T05:21:58.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14574" PostTypeId="4" CreationDate="2014-01-23T05:21:58.167" Score="0" Body="Basic (positively charged) proteins that help in compacting the genomic DNA in the form of chromatin, by forming nucleosomes. " OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-01-23T07:22:57.180" LastActivityDate="2014-01-23T07:22:57.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14575" PostTypeId="2" ParentId="14528" CreationDate="2014-01-23T09:24:31.560" Score="4" Body="&lt;p&gt;I remember overhearing a botanist some 10 years ago, that he cannot tell male poplar from female when they are not flowering or producing seeds. Poplars and willows are related, so it is a weak indication for you, you will likely not find any visible features in willow neither. But it is an old information, too.   &lt;br/&gt; (Are you interested in DNA sequencing evidence or not ? I can look it up for you, but it seems your statement in comment question was ironical.)&lt;/p&gt;&#xA;&lt;p&gt;EDIT: have just found an article which says: &amp;quot;In Salix viminalis, the sex of plants cannot be confirmed until the first time they flower.&amp;quot; At that time, 1997, there were no DNA markers for plant sex determination, but it is apparent, they did not know how to differentiate the sex of this willow just from morphology. This example is even closer to Salix alba than poplar. I find it even more likely now, that you will not find the morphological features.&lt;/p&gt;&#xA;&lt;p&gt;I took the suggestion of Oreotrephes. This is what to look for under the tree - fruit and seeds:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/J0bvz.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/J0bvz.jpg&quot; alt=&quot;&quot; /&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://acces.ens-lyon.fr/acces/equipes/dyna/travaux/evolbio/phylovegetal/ressources-iconographiques-pour-les-collections-phylogene/photos-jean/Salix%20alba%20fruit%20graine.jpg/view&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;( C. Alström-Rapaport, M. Lascoux, U. Gullberg. Sex determination and sex ratio in the dioecious shrub Salix viminalis L. Theoretical and Applied Genetics 1997, Volume 94, Issue 3-4, pp 493-497).&lt;/p&gt;&#xA;" OwnerUserId="5369" LastEditorUserId="15950" LastEditDate="2021-01-15T16:03:26.133" LastActivityDate="2021-01-15T16:03:26.133" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="14576" PostTypeId="2" ParentId="14562" CreationDate="2014-01-23T10:30:12.147" Score="2" Body="&lt;p&gt;&lt;em&gt;Disclaimer: Not my area of research&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Since IAA (&lt;a href=&quot;http://en.wikipedia.org/wiki/Plant_hormone#Abscisic_acid&quot; rel=&quot;nofollow&quot;&gt;auxins&lt;/a&gt;) can induce growth, partially acting through cell elongation (&lt;a href=&quot;http://www.biosynth.com/index.asp?topic_id=139&quot; rel=&quot;nofollow&quot;&gt;http://www.biosynth.com/index.asp?topic_id=139&lt;/a&gt;), it seems likely that the explanation to your result is differential growth/elongation rates on the upper and lower side of the leaves. This could result from uneven spraying, e.g. by spraying the leaves from the top. Faster growth on the top part of the leaf would lead to downward twisting, which seems to be what is happening most of the time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could test if this is the case by doing a simple experiment where you carefully apply IAA with a brush on both sides of the leaves for some plants, while others are sprayed. If uneven application is the cause you should see twisting when spraying but not when applying with a brush.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, auxin is toxic to plants at high concentrations, so you also need to consider the concentration you are using. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-01-23T11:04:55.493" LastActivityDate="2014-01-23T11:04:55.493" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14577" PostTypeId="1" AcceptedAnswerId="14580" CreationDate="2014-01-23T10:45:43.717" Score="1" ViewCount="2874" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GCdm7.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not understand how to solve this question. I know that RNAse will cut smaller pieces of RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer given is A&lt;/p&gt;&#xA;" OwnerUserId="4058" LastEditorUserId="6" LastEditDate="2014-01-23T11:46:54.377" LastActivityDate="2014-01-23T11:46:54.377" Title="Gel electrophoresis after RNAse treatment" Tags="&lt;dna&gt;&lt;homework&gt;&lt;rna&gt;&lt;gel-electrophoresis&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14578" PostTypeId="2" ParentId="14577" CreationDate="2014-01-23T11:06:37.673" Score="2" Body="&lt;p&gt;RNA can fold and will therefore migrate faster than DNA. So it shows up as the band which is towards the positive front. After RNAse treatment you'll lose that band. So the answer is A&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-01-23T11:06:37.673" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14579" PostTypeId="1" CreationDate="2014-01-23T11:42:03.873" Score="1" ViewCount="363" Body="&lt;p&gt;I've read that in an experiment, a pair of stimulating electrodes were inserted into a blind man's visual cortex, and upon passing electricity, the phosphene phenomenon was produced. Is it the same with memory? Can each and every memory, of an individual be recalled by a similar method? And if so, in which region of the brain will the stimulating electrodes be inserted?&lt;/p&gt;&#xA;" OwnerUserId="5213" LastActivityDate="2014-08-02T09:05:07.220" Title="Recalling memories by electrical impulses?" Tags="&lt;brain&gt;&lt;memory&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14580" PostTypeId="2" ParentId="14577" CreationDate="2014-01-23T11:45:44.450" Score="6" Body="&lt;p&gt;The question is a bit vague in some important parts, so I'll have to make a few assumptions about what the authors likely meant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RNAses are enzymes that degrade RNA. There are a few different ones that lead to different kinds of degradation. The type that you would use in an experiment like this is an RNAse that &lt;em&gt;completely&lt;/em&gt; degrades RNA. The purpose of this is to be able to distinguish RNA from DNA. So whatever is left after the RNAse treatment is DNA, and the bands that vanished are RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you isolate nucleic acids from liver, the major DNA part would be genomic DNA. The major RNA components would be mRNA and rRNA. Genomic DNA is huge compared to mRNA and rRNA. In gel electrophoresis of nucleic acids, the bands that move further are smaller nucleic acids, and the bands that move less far are larger nucleic acids. So the band on the left in your example is likely genomic DNA, and the band to the right is mRNA or rRNA. After RNAse digestion only the left band should remain, which is answer A.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-01-23T11:45:44.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14581" PostTypeId="1" AcceptedAnswerId="14584" CreationDate="2014-01-23T16:45:57.903" Score="0" ViewCount="847" Body="&lt;p&gt;I read &lt;a href=&quot;http://en.wikipedia.org/wiki/SNP_genotyping&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; wikipedia article on SNP genotyping and wasn't able to understand this part :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In examining the results, if a genomic sample is homozygous, then the&#xA;  PCR products that result will be from the primer which matches the SNP&#xA;  location to the &lt;strong&gt;outer, opposite strand&lt;/strong&gt; primer as well from the two&#xA;  opposite, outer primers. If the genomic sample is heterozygous, then&#xA;  products will result from the primer of each allele to their&#xA;  respective outer primer counterparts as well as from the two opposite,&#xA;  outer primers.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Can anyone explain this ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-23T18:39:03.230" Title="SNP genotyping using PCR" Tags="&lt;dna&gt;&lt;pcr&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14582" PostTypeId="1" AcceptedAnswerId="14589" CreationDate="2014-01-23T17:57:16.993" Score="1" ViewCount="35623" Body="&lt;p&gt;We know that a glass gets cracked when it undergoes sudden change in temperature. But what will happen in the case of a human body if it changes from the maximum(&gt;35℃) to the minimum temperature(&amp;lt;35℃) suddenly?&lt;/p&gt;&#xA;" OwnerUserId="5162" LastEditorUserId="19099" LastEditDate="2017-06-11T08:15:33.213" LastActivityDate="2019-01-06T19:32:42.720" Title="What happens to our body when we undergo a sudden temperature change from 40℃ to 20℃?" Tags="&lt;temperature&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14583" PostTypeId="1" AcceptedAnswerId="14585" CreationDate="2014-01-23T18:26:09.870" Score="1" ViewCount="736" Body="&lt;p&gt;What help does goosebumps do to us? I don't think it helps us noticeably when we are scared or shivering.&lt;/p&gt;&#xA;" OwnerUserId="5213" LastActivityDate="2014-01-28T21:10:51.770" Title="Significance of having goosebumps?" Tags="&lt;human-biology&gt;&lt;skin&gt;&lt;hair&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14584" PostTypeId="2" ParentId="14581" CreationDate="2014-01-23T18:39:03.230" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://nar.oxfordjournals.org/content/29/17/e88/F1.large.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Valid XHTML http://nar.oxfordjournals.org/content/29/17/e88/F1.large.jpg&lt;/a&gt;.&#xA;Figure 1. Schematic presentation of the tetra-primer ARMS-PCR method. The single nucleotide polymorphism used here as an example is a G→A substitution, but the method can be used to type other types of single base substitutions. Two allele-specific amplicons are generated using two pairs of primers, one pair (indicated by pink and red arrows, respectively) producing an amplicon representing the G allele and the other pair (indicated by indigo and blue arrows, respectively) producing an amplicon representing the A allele. Allele specificity is conferred by a mismatch between the 3′-terminal base of an inner primer and the template. To enhance allelic specificity, a second deliberate mismatch (indicated by an asterisk) at position –2 from the 3′-terminus is also incorporated in the inner primers. The primers are 26 nt or longer, so as to minimize the difference in stability of primers annealed to the target and non-target alleles, ensuring that allele specificity results from differences in extension rate, rather than hybridisation rate. By positioning the two outer primers at different distances from the polymorphic nucleotide, the two allele-specific amplicons differ in length, allowing them to be discriminated by gel electrophoresis. (&lt;a href=&quot;http://nar.oxfordjournals.org/content/29/17/e88/F1.expansion&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://nar.oxfordjournals.org/content/29/17/e88/F1.expansion&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="5369" LastActivityDate="2014-01-23T18:39:03.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14585" PostTypeId="2" ParentId="14583" CreationDate="2014-01-23T19:16:06.143" Score="4" Body="&lt;p&gt;As a general rule, you might want to check wikipedia before posting here. On the other hand, I am glad you made me look the answer up.   &lt;br/&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Goose-bumps warm you up a little. &quot;During the formation of goose bumps, the body is warmed from the muscle tension in piloerection.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other reasons, which do not directly serve humans, but may be a remnant from evolution. In animals with fur, the erected hair makes thicker insulation and further protection from cold. &quot;Goose bumps can also be a response to anger or fear: the erect hairs make the animal appear larger, in order to intimidate enemies.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More on wikipedia: &lt;a href=&quot;http://en.wikipedia.org/wiki/Goose_bumps&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Goose_bumps&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5369" LastActivityDate="2014-01-23T19:16:06.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14587" PostTypeId="2" ParentId="14583" CreationDate="2014-01-24T05:04:34.267" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The formation of goose bumps in humans under stress is a vestigial&#xA;  reflex; a possible function in human evolutionary ancestors was to&#xA;  raise the body's hair, making the ancestor appear larger and scaring&#xA;  off predators. Raising the hair is also used to trap an extra layer of&#xA;  air, keeping an animal warm. Due to the diminished amount of hair in&#xA;  humans, the reflex formation of goose bumps when cold is also&#xA;  vestigial.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_vestigiality&quot; rel=&quot;nofollow&quot;&gt;wikipedia article on human vestigiality&lt;/a&gt; under Behavioural category.&lt;/p&gt;&#xA;" OwnerUserId="5499" LastEditorUserId="3776" LastEditDate="2014-01-24T05:56:32.053" LastActivityDate="2014-01-24T05:56:32.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14588" PostTypeId="2" ParentId="14568" CreationDate="2014-01-24T09:35:26.710" Score="2" Body="&lt;p&gt;There are bacteria, which can assist the proces of rust.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Some sulfate-reducing bacteria produce hydrogen sulfide, which can cause sulfide stress cracking. &lt;em&gt;Acidithiobacillus&lt;/em&gt; bacteria produce sulfuric acid; &lt;em&gt;Acidothiobacillus thiooxidans&lt;/em&gt; frequently damages sewer pipes. &lt;em&gt;Ferrobacillus ferrooxidans&lt;/em&gt; directly oxidizes iron to iron oxides and iron hydroxides; the rusticles forming on RMS Titanic wreck are caused by bacterial activity. Other bacteria produce various acids, both organic and mineral, or ammonia.&quot; (&lt;a href=&quot;http://en.wikipedia.org/wiki/Microbial_corrosion&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Microbial_corrosion&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you see, many of these active ingredients, like hydrogen sulfide, sulfuric acid, other acids or ammonia are &lt;strong&gt;&lt;em&gt;not enzymes per se&lt;/em&gt;&lt;/strong&gt;, although they are &lt;strong&gt;&lt;em&gt;produced by enzymatic processes&lt;/em&gt;&lt;/strong&gt; in bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Closer to your specification is &lt;em&gt;Ferrobacillus ferrooxidans&lt;/em&gt; (synonyms: &lt;em&gt;Acidithiobacillus ferrooxidans, Thiobacillus ferrooxidans, Ferrobacillus sulfooxidans&lt;/em&gt;), &lt;strong&gt;&lt;em&gt;which directly acts on iron by enzymes&lt;/em&gt;&lt;/strong&gt; associated with the cell membrane: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://c431376.r76.cf2.rackcdn.com/18185/fmicb-03-00096-HTML/image_m/fmicb-03-00096-g001.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Valid XHTML http://c431376.r76.cf2.rackcdn.com/18185/fmicb-03-00096-HTML/image_m/fmicb-03-00096-g001.jpg&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 1. Schematic representation of ferrous iron oxidation by the Gram-negative autotrophic acidophile, At. ferrooxidans. Controlled influx of protons is used to generate ATP via the membrane-bound ATP synthetase complex (ATPase). Iron oxidation is mediated by a cytochrome located on the outer membrane and electrons transferred via periplasmic cytochromes and rusticyanin either to a terminal oxidase (“downhill pathway,” indicated in brown text and by **) where they are used to reduce oxygen, or used to reduce NAD+ (“uphill pathway,” indicated red text and by *) in a reaction also driven by the proton motive force across the inner membrane (Bonnefoy and Holmes, 2011). Source: &lt;a href=&quot;http://www.frontiersin.org/Journal/10.3389/fmicb.2012.00096/full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Johnson et al. 2012&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5369" LastActivityDate="2014-01-24T09:35:26.710" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14589" PostTypeId="2" ParentId="14582" CreationDate="2014-01-24T11:15:32.867" Score="2" Body="&lt;p&gt;&lt;em&gt;Disclaimer: the answer is very broad and covers both the situations I am confident about, as well as those I understand only superficially.&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The outcome depends on particular temperatures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example - &lt;a href=&quot;http://en.wikipedia.org/wiki/Cold_shock#Cold_shock_response_in_bacteria&quot; rel=&quot;nofollow&quot;&gt;cold shock response&lt;/a&gt;: &quot;Cold shock response is the physiological response of organisms to sudden cold, especially cold water. In humans, cold shock response is perhaps the most common cause of death from immersion in very cold water, such as by falling through thin ice. The cold water can cause heart attack due to vasoconstriction, the heart has to work harder to pump the same volume of blood throughout the body. For people with heart disease, this additional workload can cause the heart to go into arrest. Inhalation of water (and thus drowning) may result from hyperventilation. Some people, due to body type or mental conditioning, are much better able to survive swimming in very cold water.&quot; &lt;strong&gt;But&lt;/strong&gt;: &quot; A person who survives the initial minute of trauma (after falling into icy water), can survive for at least thirty minutes provided they don't drown.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sudden heat at entering sauna - I am not sure, but probably it also may cause heart attacks. Recent heart attack is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Sauna#Health_risks_and_benefits&quot; rel=&quot;nofollow&quot;&gt;contraindication for sauna visits.&lt;/a&gt; Healthy individuals do O.K. due to thermoregulation mechanisms in the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As we move to more extreme temperatures, where the thermoregulation of human body simply has no chance at all to keep up, you can percieve the human body as a chunk of meat. The proteins denature, the water in the body gets boiled. The meat gets cooked, turns coal like, burns to ashes... Or by freezing, the water forms crystals, damages and breaks the cells. Eventually the meat freezes to be stone hard and does not change for a long time if kept at such temperature.&lt;/p&gt;&#xA;" OwnerUserId="5369" LastActivityDate="2014-01-24T11:15:32.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14590" PostTypeId="1" AcceptedAnswerId="14591" CreationDate="2014-01-24T11:44:57.990" Score="2" ViewCount="2187" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QDrg1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am unable to understand what happens to the phosphates from  ATP. What are they used for ?Charging 3' end or 5'end ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-24T17:04:07.610" Title="DNA ligase mechanism" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14591" PostTypeId="2" ParentId="14590" CreationDate="2014-01-24T11:56:25.143" Score="3" Body="&lt;p&gt;When you ligate two strands of DNA you build up a phosphodiester bond. To do so, you need energy, and this energy for the DNA ligase comes from the ATP (in bacteria this energy can also come from NAD&lt;sup&gt;+&lt;/sup&gt;.&#xA;The enzyme metabolizes ATP to AMP + PP&lt;sub&gt;i&lt;/sub&gt; and binds the AMP in its active center. Then the AMP is involved in the reaction itself and released afterwards. This &lt;a href=&quot;http://www.biochem.umd.edu/biochem/kahn/molmachines/replication/DNA%20Ligase.htm&quot; rel=&quot;nofollow&quot;&gt;page&lt;/a&gt; has a few illustrations on this process.&#xA;If you want to dive really deep into the topic, have a look at this review:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/pdf/10.1146/annurev.biochem.77.061306.123941&quot; rel=&quot;nofollow&quot;&gt;Eukaryotic DNA Ligases: Structural and Functional Insights&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2014-01-24T17:04:07.610" LastActivityDate="2014-01-24T17:04:07.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14592" PostTypeId="1" CreationDate="2014-01-24T12:35:23.393" Score="3" ViewCount="11017" Body="&lt;p&gt;apart from different fungus causing these diseases in potato, how are Early Blight of potato and Late blight of potato different?&lt;/p&gt;&#xA;" OwnerUserId="5347" LastActivityDate="2018-12-05T17:17:39.143" Title="what is the difference between early blight of potato and late blight of potato?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14593" PostTypeId="1" CreationDate="2014-01-24T13:05:14.317" Score="4" ViewCount="155" Body="&lt;p&gt;In eye-operations such as Lasik and Femto, the thickness of &lt;a href=&quot;http://en.wikipedia.org/wiki/Cornea&quot; rel=&quot;nofollow noreferrer&quot;&gt;cornea&lt;/a&gt; is key decision factor whether the operation is feasible. A normal thickness is between 500-600 µm. Cornea consists of a very special tissue having no blood supply and no vessels so it gets nutrients through diffusion of tear fluid and oxygen directly from air (hence in a way, it has its own respiration system not dependent on lungs).&lt;/p&gt;&#xA;&lt;p&gt;Now I started to think the following questions:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;I. What determines the thickness of cornea?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Helper questions&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;II. Is the thickness of cornea determined genetically so twins have the same cornea thickness?&lt;/p&gt;&#xA;&lt;p&gt;III. Is the thickness determined by the environment and psychological things? Eg. how does diving affect cornea? Look it cannot get oxygen anymore through the air with the mask. What about drying? Does cornea gets too much nutrients all of a sudden from eye fluids?&lt;/p&gt;&#xA;&lt;p&gt;IV. Does Homo Sapiens have more this kind of independent tissues? What about other animials? What determines the thickness of Cornea there?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1705" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-07-06T19:48:41.547" Title="What determines the thickness of Cornea?" Tags="&lt;eyes&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14594" PostTypeId="1" CreationDate="2014-01-24T14:38:21.270" Score="4" ViewCount="206" Body="&lt;p&gt;Single nucleotide polymorphism (SNP) or genetic variation in general, by definition are relative to a reference sequence. When we talk about databases of SNP as in (&quot;dbSNP—Database for Single Nucleotide Polymorphisms and Other Classes of Minor Genetic Variation&quot;, or &quot;A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms&quot; -- titles of well known research papers), what is the reference genome? Similarly for defining a &quot;SNP Map/Profile&quot; of a person (in medical genomics), what is the reference genome sequence? Is there a &lt;em&gt;de facto&lt;/em&gt; reference, or is it context dependent? There is a sentence &quot;Scientists are trying to identify all the different SNPs in the human genome&quot; at &lt;a href=&quot;http://www.cancer.gov/cancertopics/understandingcancer/geneticvariation/page36&quot; rel=&quot;nofollow&quot;&gt;http://www.cancer.gov/cancertopics/understandingcancer/geneticvariation/page36&lt;/a&gt; - &#xA;what is the reference genome here?&lt;/p&gt;&#xA;" OwnerUserId="1800" LastEditorUserId="1320" LastEditDate="2014-01-24T17:01:15.020" LastActivityDate="2014-01-24T22:36:48.337" Title="Reference sequence for defining single nucleotide polymorphisms" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;genomics&gt;&lt;sequence-analysis&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14595" PostTypeId="1" AcceptedAnswerId="14599" CreationDate="2014-01-24T14:39:49.847" Score="1" ViewCount="1531" Body="&lt;p&gt;This is an excerpt from a &lt;a href=&quot;http://www.nature.com/nature/journal/v500/n7463/full/nature12477.html&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;T&gt;C mutations at NpTpN trinucleotides, also found in hepatocellular carcinomas, shows strong transcriptional strand bias with more T&gt;C mutations on the transcribed than untranscribed strands&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What exactly is meant by &quot;transcribed&quot; strand: the sense strand or the template strand ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried looking up for it but couldn't find any definition. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-01-24T17:48:29.730" LastActivityDate="2014-01-24T18:25:17.927" Title="What is &quot;transcribed strand&quot;" Tags="&lt;molecular-genetics&gt;&lt;transcription&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14596" PostTypeId="2" ParentId="14595" CreationDate="2014-01-24T15:43:11.687" Score="2" Body="&lt;p&gt;Remember that DNA is double stranded and each strand has a chemical direction.  Genes are read by the ribosome in the 3' to 5' direction so that the DNA 'forward' direction is defined in this direction.  This is the direction of transcription.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each segment of DNA can therefore be read in 2 directions.  In the direction of transcription each T will have an A on the other strand.  So each letter in the direction of transcription will not be the same if you read the other strand.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Transcription (that which is transcribed) refers to the ribosomal read strand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OvEUF.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-01-24T18:25:17.927" LastActivityDate="2014-01-24T18:25:17.927" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14597" PostTypeId="1" CreationDate="2014-01-24T16:01:23.657" Score="-6" ViewCount="4335" Body="&lt;p&gt;Doesn't make sense. It would be like a human evolving the ability to breathe on the moon without a spacesuit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How would the organism be able to carry out such an evolutionary adaptation, when the evolution of it involves death to the organism, preventing it from ever being able to evolve it to begin with, because the variation cannot develop, or be passed along to the population due to it needing to be functional to survive at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, how does an organism gain the new information necessary to get those land breathing or moon breathing adaptions, from a genome that doesn't already have such an ability encoded in its genetic morphology in the first place?&lt;/p&gt;&#xA;" OwnerUserId="5502" LastActivityDate="2016-08-18T02:06:52.843" Title="How did fish evolve the ability to breathe on land?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14598" PostTypeId="2" ParentId="14597" CreationDate="2014-01-24T16:43:26.520" Score="6" Body="&lt;p&gt;You ask two question. it is always better to restrict a post to only one accurate and narrowed enough question. I will not provide a full review of how did the origin of tetrapods occur. I just give some critics on you question give some words about the evolution of lungs, discuss your comparison with &quot;breathing on the moon&quot; and answer your question concerning the origin of genetic variation.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How did fish evolve the ability to breathe on land?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This question is way too broad, you should narrow it down. You say that this evolution is impossible but you should provide some argument so that we can discuss them. For the moment there is not much to discuss about. The only thing one could si to review tons of article concerning the evolution of tetrapods. I bet you're interested in the evolution of lungs during at the origin of the lineage of the tetrapods. If so… In short, swim bladder and lungs are homologous organs. According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Swim_bladder&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; that at the time tetrapods-like animals evolved, this organs was used to gulp air in oxygen-poor environment. This organs then evolved into various forms of lungs as we know them today in terrestrial and none terrestrial vertebrates. This organ also further evolved in order to control the buoyancy. Note: Several popular sources gives different informations. One would need to go into some articles in order to make sure of details such as &quot;were this organ already used to control buoyancy before the speciation of the tetrapods?&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evograms_04&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; is a simple source that you may like&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You say that evolving abilities to breath in the atmosphere for tetrapods is like evolving abilities to breath on the moon in humans. Well there are several differences that should be considered that make the moon really not a pleasant place to live! The temperature for example spans between 100K and 373K according to this &lt;a href=&quot;http://en.wikipedia.org/wiki/Planetary_equilibrium_temperature&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki&lt;/a&gt;! But let's forget about these other ecological factors. One big difference is that humans do not live in an environment that offers a gradient from earth atmosphere to moon atmosphere while first tetrapods-like animals lived in such a gradient. Also, when you talk about human, it feels like you consider the wrong time-scale. It probably took quite a lot of time to evolve from fish-like to totally terrestrial tetrapods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might want to have a look to &lt;a href=&quot;https://biology.stackexchange.com/questions/937/how-many-times-did-life-emerge-from-the-ocean&quot;&gt;this interesting post&lt;/a&gt;. Life apparently independently emerged out of water at least 9 times.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;How does an organism gain the new information necessary to get those land breathing or moon breathing adaptions, from a genome that doesn't already have such an ability encoded in its genetic morphology in the first place?&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If I understand your point correctly one could rephrase your question into:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;I understand the process of Natural Selection (NS). It selects for some already existing variants but what process creates the variation from which NS makes its selection?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And the answer is: &lt;a href=&quot;http://en.wikipedia.org/wiki/Mutation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mutations&lt;/a&gt;. In the narrow sense (in order to keep it easy), a mutation is a change in a genetic sequence. Such change typically occur during the &lt;a href=&quot;http://en.wikipedia.org/wiki/Meiosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;meiosis&lt;/a&gt;, process that occurs in all sexual reproductions but it also occur during any &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;mitosis&lt;/a&gt; (standard cell division) or other phases of the cell cycle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, mutations create genetic variations and differential reproductive abilities between individuals in a population results in a selection (called Natural Selection) for variants that are the best at reproducing.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2016-08-18T02:06:52.843" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14599" PostTypeId="2" ParentId="14595" CreationDate="2014-01-24T16:59:37.983" Score="5" Body="&lt;p&gt;In my opinion they &lt;strong&gt;should&lt;/strong&gt; mean the template strand, and they probably do. Perhaps if we had a link to the paper we could have examined the language more closely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://mbe.oxfordjournals.org/content/26/1/131.abstract&quot; rel=&quot;noreferrer&quot;&gt;Here is a paper&lt;/a&gt; which uses the term in that sense:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mugal, CF &lt;em&gt;et al&lt;/em&gt;. (2008) Transcription-Induced Mutational Strand Bias and Its Effect on Substitution Rates in Human Genes. Molecular Biology and Evolution 26,131-142&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the abstract (which I have linked to) the authors make a clear reference to the transcribed strand in contrast to the coding strand (i.e. the strand of DNA with the same sequence as the RNA transcript):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;All three [mutational rates] considered are found to be on average higher on the coding strand and lower on the transcribed strand...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are also definitions confirming this at &lt;a href=&quot;http://en.wikipedia.org/wiki/Coding_strand&quot; rel=&quot;noreferrer&quot;&gt;this Wikipedia page&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-01-24T16:59:37.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14600" PostTypeId="1" AcceptedAnswerId="14603" CreationDate="2014-01-24T17:42:53.757" Score="1" ViewCount="410" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2wCp3.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have to classify them either as transported in vesicles or without vesicles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I think - &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Non-vesicular&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;2.vesicular&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3.vesicular&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4.vesicular&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5.non-vesicular&lt;/p&gt;&#xA;&#xA;&lt;p&gt;6.vesicular&lt;/p&gt;&#xA;&#xA;&lt;p&gt;7.vesicular&lt;/p&gt;&#xA;&#xA;&lt;p&gt;8.vesicular&lt;/p&gt;&#xA;&#xA;&lt;p&gt;9.vesicular&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I right ? Is it true that a  protein transported by vesicles is made on ER ribosomes ?&#xA;How are proteins transported non-vesicular transport ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-24T19:16:09.613" Title="Vesicular and non vesicular transport" Tags="&lt;molecular-biology&gt;&lt;homework&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14601" PostTypeId="2" ParentId="14597" CreationDate="2014-01-24T17:50:26.860" Score="16" Body="&lt;p&gt;Air-filled, gut-tube-derived organs (i.e., air bladders, gas bladders, and lungs) have a very wide distribution among fish in general, so the most parsimonious explanation is that the first terrestrial tetrapods already had a lung-like structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image below (from Kardong's &lt;em&gt;Vertebrates&lt;/em&gt;) shows two major clades of fishes, Actinopterygii (ray-finned fishes) and Sarcopyerygii (&quot;fleshy-finned&quot; fishes, which include both lungfish and tetrapods). Given the wide distribution, a homologous organ was almost certainly present at the most recent common ancestor of these two groups. I don't know what the evidence is for lungs further down the tree, so I'm not certain about loss of lungs in Chondrichthyes (sharks, rays, skates).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://2.bp.blogspot.com/-7WI9V1p3EEo/UWs0WxNZcqI/AAAAAAAAATk/sgEPlIOyWJI/s1600/Kardong_fig_11_5%2Blung%2Band%2Bgas%2Bbladder%2Bcladistics.JPG&quot; alt=&quot;Distribution of lungs&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.913" LastActivityDate="2014-01-24T17:50:26.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14603" PostTypeId="2" ParentId="14600" CreationDate="2014-01-24T19:04:29.603" Score="1" Body="&lt;p&gt;Any protein which enters the secretory pathway will proceed via vesicular transport to some point on that pathway. That includes lysosomal proteins, integral plasma membrane proteins and secreted proteins (also, not on your list, resident proteins of the ER, Golgi proteins, some endosomal proteins). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cytoskeletal proteins are cytoplasmic: I suppose you could argue they are 'transported' sometimes, e.g. tubulin treadmilling, motors etc., but no vesicles are involved. Nuclear proteins enter the nucleus from the cytoplasm through nuclear pores. They have nuclear localisation signals; vesicles aren't involved. Mitochondria, chloroplasts and peroxisomes all have their own protein import systems with associated unique signals; again no vesicles are involved.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-01-24T19:16:09.613" LastActivityDate="2014-01-24T19:16:09.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14604" PostTypeId="2" ParentId="14594" CreationDate="2014-01-24T19:44:50.337" Score="1" Body="&lt;p&gt;I don't see your point. If we take e.g. the definition from &lt;a href=&quot;http://en.wikipedia.org/wiki/Single-nucleotide_polymorphism&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;SNP &quot;is a DNA sequence variation occurring when a Single Nucleotide ... in the genome ... differs between members of a biological species or paired chromosomes&quot;,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;there is no place for reference genome. SNP is just a variable position with (commonly) two alternatives in individuals of the same species. In whole-genome sequencing projects some SNPs can be discovered (namely those which are in heterozygous state), but definitely not all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One can investigate SNPs and/or use them as genetic markers irrespective of the availability of the reference genome. That's the way one does it for non-model organisms - e.g. utilizing &lt;a href=&quot;http://en.wikipedia.org/wiki/Restriction_site_associated_DNA_markers&quot; rel=&quot;nofollow&quot;&gt;RAD Seq&lt;/a&gt;: you discover SNPs simultaneously with genotyping.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-01-24T19:44:50.337" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14605" PostTypeId="2" ParentId="14568" CreationDate="2014-01-24T20:14:18.820" Score="0" Body="&lt;p&gt;Non-oxidized metals are rarely substrates for enzymes, although they can be used as &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11206926&quot; rel=&quot;nofollow&quot;&gt;electron donors&lt;/a&gt; in some reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But you are asking about enzymes capable of cleaving &lt;a href=&quot;http://en.wikipedia.org/wiki/Metallic_bonding&quot; rel=&quot;nofollow&quot;&gt;metallic bonds&lt;/a&gt; without oxidation, and neither can I recall something of this kind, nor can imagine a biological role for such a reaction.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-01-24T20:14:18.820" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="14608" PostTypeId="2" ParentId="14594" CreationDate="2014-01-24T22:36:48.337" Score="1" Body="&lt;p&gt;dbSNP actually indexes itself against several reference genome builds including hg19.  you can see this in the ssID records  - we use the bulk downloads and you can see them there as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any difference with respect to any two genome builds is really a variant.  You can see this in the case of tri- and quad- allelic variants. There are cases where entire sequences lengths are added or removed compared to a reference genome build.  These are called insert/delete variants, which can contain short or single nucleotide variants as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;will try to fill this out a bit more later... quick response here. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-01-24T22:36:48.337" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14609" PostTypeId="1" CreationDate="2014-01-25T00:19:22.727" Score="1" ViewCount="30" Body="&lt;p&gt;It's a rather broad question but something I'm curious about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know sulfates tend to be very soluble ions and so don't know nitrates. &#xA;I also know that phosphates are extremely common in biochemistry (e.g. ADP) but they're not very soluble unless they involve group 1 elements, same goes for carbonates. &#xA;I think Carbonates tend to be more common in crustacea, or chicken egg shells. I can't remember if it's found in the Krebb's cycle (don't think so, but maybe in other vitamins?). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Solubility isn't apart of this question, it was just one of the ways I was just trying to pursue an answer. I'm more of a chemist than a biologist...&lt;/p&gt;&#xA;" OwnerUserId="4794" LastActivityDate="2014-01-25T00:19:22.727" Title="Are sulfates or nitrates common ions in biochemistry (specifically of the body)?" Tags="&lt;general-biology&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14610" PostTypeId="2" ParentId="14553" CreationDate="2014-01-25T00:33:20.207" Score="1" Body="&lt;p&gt;The major reason for this is because H20 can cause hydrogen bonding. Hydrogen bonding is what allows for plants to transport &quot;this electron source&quot; from their roots through their stems an further. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The stronger polarity of H20 also allows for stronger interactions. Such as ionic interactions (not fully bound but 2 polar atoms interacting). This kind of ionic interaction also allows for other types of material interactions such as cohesion and adhesion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall, aside from the discussion of abundance as mentioned above (which is a very good point), it also allowed the plants to grow in directions that were more advantageous (darwinian) for their survival.&lt;/p&gt;&#xA;" OwnerUserId="4794" LastActivityDate="2014-01-25T00:33:20.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14611" PostTypeId="1" AcceptedAnswerId="31638" CreationDate="2014-01-25T01:10:41.720" Score="5" ViewCount="1406" Body="&lt;p&gt;I'm curious if HeLa cells are intrinsically poisonous or dangerous to ingest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding is that some of the contamination in HeLa cells such as HPVs are not readily expressed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have no plans to do so, but I'm trying to understand why they might or might not be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MMRTQ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5504" LastActivityDate="2017-10-06T23:20:32.250" Title="Are HeLa cells edible?" Tags="&lt;cell-culture&gt;&lt;eukaryotic-cells&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14612" PostTypeId="2" ParentId="14287" CreationDate="2014-01-25T01:17:53.300" Score="1" Body="&lt;p&gt;Although I found &lt;a href=&quot;http://link.springer.com/article/10.1007/BF01989734&quot; rel=&quot;nofollow&quot;&gt;this study&lt;/a&gt;, where mean and 95% CIs of median time to&#xA;eclosion (h) are provided for some strains of D.m. (with a resolution of 12 h) (in table 3), the moment of eclosion seems to be under &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8695895&quot; rel=&quot;nofollow&quot;&gt;circadian control&lt;/a&gt;: &quot;in Drosophila melanogaster, the emergence of adults from their pupal cases (eclosion) is gated by the circadian clock such that it occurs during a window of approximately 8-10 h starting 1-2 h before lights-on in 12-h light:12-h dark cycles (LD)&quot;. In that particular study Canton-S flies eclosed within 4-5 days after pupation (LD 12:12, 25°C) with the following distribution over day (digitized from Fig. 1A [numbers are approximate, percents don't sum up to 100]):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Hours   % eclosed&#xA;Dark&#xA;12-14   0.5&#xA;14-16   0.4&#xA;16-18   0.6&#xA;18-20   1.1&#xA;20-22   1.4&#xA;22-24   5.6&#xA;&#xA;Light&#xA;0-1     20.4&#xA;1-2     9.3&#xA;2-3     13.7&#xA;3-4     12.0&#xA;4-5     10.3&#xA;5-6     11.3&#xA;6-7     6.6&#xA;7-8     4.9&#xA;8-9     2.1&#xA;9-10    0.8&#xA;10-11   0.8&#xA;11-12   0.4&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-01-25T07:40:06.563" LastActivityDate="2014-01-25T07:40:06.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14613" PostTypeId="2" ParentId="14583" CreationDate="2014-01-25T01:28:29.253" Score="0" Body="&lt;p&gt;My guess was that it was used in the past as a technique to scare predators, seeing as our ancestors had a lot of hair, this could've been a lot of use.&lt;/p&gt;&#xA;" OwnerUserId="5505" LastActivityDate="2014-01-25T01:28:29.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14614" PostTypeId="1" AcceptedAnswerId="14620" CreationDate="2014-01-25T07:41:28.850" Score="0" ViewCount="82" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;If  father has hemophilia, mother is a carrier of the disease, then&#xA;  what is the probability of having a normal daughter ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My question: Should the probability of having a daughter be also multiplied ? Should the answer be 0.5 or should it be 0.25 ?&lt;/p&gt;&#xA;" OwnerUserId="4058" LastActivityDate="2014-01-25T10:43:09.167" Title="probability of having normal daughter" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14615" PostTypeId="1" AcceptedAnswerId="15476" CreationDate="2014-01-25T07:55:24.163" Score="2" ViewCount="275" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Both snake and weasel hibernate. Which of the following is correct? &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;A. They will die when temperature decreases below the critical&#xA;  temperature.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;B. Weasel will die when temperature decreases below the critical&#xA;  temperature.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;C. Snake will die and weasel will wake up when the temperature&#xA;  decreases below the critical temperature.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;D. Weasel keeps low body temperature and slow heart rate during the&#xA;  entire period of hibernation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't think any of them should die, they would have some adaptation to prevent that. So,is the answer (D) ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the snake's adaptation in this situation ?&lt;/p&gt;&#xA;" OwnerUserId="4058" LastActivityDate="2014-03-04T17:53:07.400" Title="Hibernation in ectotherm and endotherm" Tags="&lt;homework&gt;&lt;homeostasis&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14616" PostTypeId="2" ParentId="10842" CreationDate="2014-01-25T07:59:50.570" Score="3" Body="&lt;p&gt;There is a bunch of literature on the topic. A good starting point is probably a short description with lots of references in &lt;a href=&quot;http://indigo.lib.uic.edu/bitstream/handle/10027/8659/Peterson_Bethany.pdf?sequence=1&quot; rel=&quot;nofollow&quot;&gt;this thesis&lt;/a&gt; (page 8), not to talk about other articles, which pop up in &lt;a href=&quot;http://scholar.google.com/scholar?q=turtle%20brain%20more%20resistant%20hypoxia&amp;amp;oi=scholart&quot; rel=&quot;nofollow&quot;&gt;google scholar&lt;/a&gt;: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952077/&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;http://link.springer.com/chapter/10.1007/978-1-4684-5562-5_2&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanisms are multifaceted and involve principally decrease in oxygen and ATP demands: reduced neuronal activity, lower density of ion channels (but hyper-polarization of the membranes) and so on. &lt;a href=&quot;http://link.springer.com/chapter/10.1007/978-1-4684-5562-5_2&quot; rel=&quot;nofollow&quot;&gt;Concerning blood flow&lt;/a&gt;: &quot;Brain blood flow was continued or increased, and oxygen and creatine phosphate (PCr) stores offered some immediate protection. As PCr declined, turtle brain became increasingly reliant upon anaerobic glycolysis.&quot;&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-01-25T07:59:50.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14617" PostTypeId="1" CreationDate="2014-01-25T08:01:57.310" Score="1" ViewCount="947" Body="&lt;p&gt;Do all the arthropods molt ? Which ones do not molt ? Why don't they need to molt ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried googling this - but did not get satisfactory answers.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-25T12:09:47.750" Title="Molting in arthropods" Tags="&lt;entomology&gt;&lt;biodiversity&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14618" PostTypeId="1" AcceptedAnswerId="19949" CreationDate="2014-01-25T08:06:47.797" Score="10" ViewCount="1084" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jVIhq.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that the part E in this graph is definitely the part of refractory period.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question : Will there be any effect on B,C or D if a stimulus is given at  time B,CorD respectively ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2014-01-25T18:38:47.217" LastActivityDate="2014-07-26T07:06:32.457" Title="Refractory period in action potential" Tags="&lt;neuroscience&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14620" PostTypeId="2" ParentId="14614" CreationDate="2014-01-25T10:43:09.167" Score="2" Body="&lt;p&gt;I can't understand what you mean by &quot;Should the probability of having a daughter be multiplied?&quot; But yes, the probability of having a normal daughter is 0.25, but she will be a carrier like her mother.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let H represent normal allele for blood clotting (dominant); h represent allele for hemophilia, XY represent the male chromosomes and XX represent the female chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Parental Phenotypes : &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;   Normal female(carrier) x Hemophiliac male&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Parental Genotypes (2n) :&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;   X(H)X(h)         x     X(h)Y&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Gametes (n) :   &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;   X(H)     X(h)    x   X(h)     Y&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Possible Outcomes :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;X(H)X(h) - A normal female, carrier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;X(H)Y    - A normal male.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;X(h)X(h) - A hemophiliac female.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;X(h)Y    - A hemophiliac male.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So probability of having a normal daughter, that is X(H)X(h) is 0.25.&lt;/p&gt;&#xA;" OwnerUserId="5213" LastActivityDate="2014-01-25T10:43:09.167" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14621" PostTypeId="1" AcceptedAnswerId="14625" CreationDate="2014-01-25T11:00:54.827" Score="2" ViewCount="95" Body="&lt;p&gt;Is there any way of determining which X chromosome a female inherited from her father and which from her mom ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-25T11:53:11.430" Title="Determining whether X chromosome from sperm or egg" Tags="&lt;genetics&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14622" PostTypeId="1" AcceptedAnswerId="14631" CreationDate="2014-01-25T11:05:45.473" Score="3" ViewCount="617" Body="&lt;p&gt;Turner syndrome occurs in 1-1000 to 1-5000 females, and Klinefelter syndrome occurs in 1-500 to 1-1000 males. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is Turner so rare even though they both are caused basically by the same mechanism?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2014-01-25T14:16:20.163" LastActivityDate="2014-01-25T19:30:57.247" Title="Why is Turner syndrome rarer than Klinefelter syndrome?" Tags="&lt;genetics&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14624" PostTypeId="1" AcceptedAnswerId="14626" CreationDate="2014-01-25T11:39:45.620" Score="2" ViewCount="124" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BDbBW.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I understand is- I think this is picture of DNA. But why is it in this conformation ? What types of cells have this type of DNA ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-25T12:00:00.350" Title="What is this image?" Tags="&lt;dna&gt;&lt;microscopy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14625" PostTypeId="2" ParentId="14621" CreationDate="2014-01-25T11:53:11.430" Score="3" Body="&lt;p&gt;yes it is possible... in placenta (trophectoderm) the paternal X is epigenetically silenced &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1377883/&quot; rel=&quot;nofollow&quot;&gt;[ref]&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is if you do the test in the pre/neo-natal stage. Otherwise, at later stages, you have to check by DNA fingerprinting + karyotyping/FISH as Chris suggested. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-01-25T11:53:11.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14626" PostTypeId="2" ParentId="14624" CreationDate="2014-01-25T12:00:00.350" Score="4" Body="&lt;p&gt;It is called a &lt;a href=&quot;http://en.wikipedia.org/wiki/Holliday_junction&quot; rel=&quot;nofollow&quot;&gt;Holliday junction&lt;/a&gt;. It forms during recombination. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-01-25T12:00:00.350" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14627" PostTypeId="2" ParentId="14617" CreationDate="2014-01-25T12:09:47.750" Score="1" Body="&lt;p&gt;in my opinion all arthropods molt. In fact arthropods are a part of clade called ecdysozoa, the members of which undergo ecdysis (molting).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Molting is necessary because arthropods have an exoskeleton which has to be removed if the organism has to grow. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-01-25T12:09:47.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14628" PostTypeId="1" AcceptedAnswerId="14637" CreationDate="2014-01-25T16:45:28.770" Score="2" ViewCount="170" Body="&lt;p&gt;After seeing &lt;a href=&quot;http://www.youtube.com/watch?v=saWSxLU0ME8&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; video I am curious to know why the free living bacteria produce light. What advantage will they have ? Or is it just an &quot;unintentional&quot; result of one of their pathways ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-18T19:01:28.110" Title="Why bacteria produce light?" Tags="&lt;molecular-biology&gt;&lt;microbiology&gt;&lt;bacteriology&gt;&lt;bioluminescence&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14629" PostTypeId="1" CreationDate="2014-01-25T18:16:55.637" Score="2" ViewCount="71" Body="&lt;p&gt;Naïve question - feel free to shoot it down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To the best of my knowledge an infant doesn't really 'shrink' from something without first trying it. Even the action of looking at the fierce expression is undertaken without qualm - squalling comes later (if at all!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are human infants inherently frightened by anything?&lt;/p&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2014-01-25T18:16:55.637" Title="Are human infants inherently frightened by anything?" Tags="&lt;psychology&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14631" PostTypeId="2" ParentId="14622" CreationDate="2014-01-25T19:25:21.723" Score="6" Body="&lt;p&gt;First of all, they are not caused by the same mechanism. They are both &lt;a href=&quot;http://en.wikipedia.org/wiki/Aneuploidy&quot;&gt;aneuploidies&lt;/a&gt;, but the mechanism is different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Turner%27s_Syndrome&quot;&gt;Turner syndrome&lt;/a&gt; happens when one of the gametes (most commonly father's) lacks a copy of X chromosome, or the X chromosome is heavily damaged. This means that while normal women have two X chromosomes, Turner women have only one, and nothing else.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Klinefelter_syndrome&quot;&gt;Klinefelter syndrome&lt;/a&gt; happens when one of the gametes retains an extra copy of the X chromosome. This way a Klinefelter man has two X chromosomes and Y chromosome instead of one X and one Y.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see - the Turner woman is lacking some genetic information, while the Klinefelter man has too much of it. Generally, having too much genetic information is much easier to survive than not having enough of it, so this explains the relative difference on the most basic level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, you might say, what about Barr's bodies? Don't the women use only one X chromosome in each cell? And wasn't Y chromosome almost empty? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, these are an important consideration for these two syndromes. In each cell of a women's body one of the X chromosomes is inactivated and folded into a Barr's body. This inactivation is random, so part of the cells keep mother's and part of the cells keep father's X chromosome active. The trick is that the Barr body is not entirely inactive (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3136209/&quot;&gt;Genes That Escape From X Inactivation&lt;/a&gt;). Only about 15% of the genes are active, but just the lack of them is mostly lethal (Turner fetuses are usually aborted, Wikipedia quotes olny 1% surviving until birth), and accounts for the health problems and deformations in Turner women.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A Klinefelter man has two X chromosomes in addition to his Y chromosome, so one of the chromosomes inactivates into a Barr body. The presence of Y chromosome directs his body to develop into a male pattern, but at the same time, the existence of Barr's body with those still active genes, causes his body to develop also feminine features. There is little to cause spontaneous abortion.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastEditorUserId="1427" LastEditDate="2014-01-25T19:30:57.247" LastActivityDate="2014-01-25T19:30:57.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14634" PostTypeId="1" CreationDate="2014-01-25T22:30:07.560" Score="2" ViewCount="2711" Body="&lt;p&gt;I need help with this practice question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/O75m9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm assuming that would a epsitatic recessive question since the parents are true breeding and then the ratio would be 9.3.4. But I am not so sure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help would be greatly appreciated thanks!&lt;/p&gt;&#xA;" OwnerUserId="5460" LastEditorUserId="1590" LastEditDate="2014-01-26T00:03:44.673" LastActivityDate="2017-07-26T17:30:22.503" Title="Genetic Epistasis Question" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;epigenetics&gt;&lt;allele&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14635" PostTypeId="1" CreationDate="2014-01-26T02:07:35.767" Score="3" ViewCount="541" Body="&lt;p&gt;ethanol then doesn't get converted to acetaldehyde. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;in fact, could someone KO'ed for ADH be resistant to methanol poisoning?&lt;/p&gt;&#xA;" OwnerUserId="103" LastActivityDate="2014-05-26T21:48:15.263" Title="What happens if someone with mutations to alcohol dehydrogenase (ADH) drinks alcohol?" Tags="&lt;toxicology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14636" PostTypeId="2" ParentId="14634" CreationDate="2014-01-26T05:44:42.197" Score="1" Body="&lt;p&gt;The Magenta variety is pure breeding, and hence must be homozygous at both loci, (Dominant at Gene A and recessive at Gene B), otherwise, in some of the generation along the family line, there would have been a non-magenta flower, which contradicts the pure breeding nature. But the same cannot be said for the pure breeding white variety, as it can still be homozygous recessive at Gene A and heterozygous at Gene B, it would still exhibit white flowers in all of its progeny after any number of generations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the fact that all the progeny of the cross between white and the magenta variety turns out to be red, removes the possibility of the white variety being heterozygous, as that would have produced atleast some magenta plants. Since all were red, we can be certain of the genotype of both the parents, and consequently of the F1 progeny.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This solves your first question. The second question needs the extrapolation of the information gathered while solving the first question into a Punnett square and a simple probability calculation. The third question is a factual question, but it must be mentioned, that this particular type of interaction can be classified under more than one type, and hence a single answer would not be possible for your third question.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ADDENDUM&lt;br&gt;&#xA;The third question is actually a bit difficult to answer. The phenotypes will be $\text{A*B*}$=Red, $\text{A*bb}$=Magenta, $\text{aa**}$=white. This gives us $9:3:4$ for Red:Magenta:white. Now the fact that recessive at one locus , Gene A, suppresses the phenotype altogether no matter what the genotype at the other locus, means that one of the phenomenon exhibited is recessive epistasis, where Gene A is the epistatic loci and Gene B is the Hypostatic loci. But, the fact that there are two distinct phenotypes with the epistatic gene dominant, means the interaction is not &lt;a href=&quot;http://www.yourarticlelibrary.com/biology/notes-on-duplicate-polymeric-complementary-and-supplementary-genes/12042/&quot; rel=&quot;nofollow&quot;&gt;complementary ($9:7$) but is supplementary ($9:3:4$)&lt;/a&gt;. This distinction is necessary, and it essentially means that the &quot;intermediate&quot; of the elucidated pathway is also coloured. Otherwise, like in Flower colour in &lt;em&gt;Lathyrus Odoratus&lt;/em&gt;, the phenotypes of $\text{aa**}$ and $\text{A*bb}$ are same, and hence the phenotypic ration remains $9:7$. For a ratio of $13:3$ you need domianant epistasis &lt;em&gt;and&lt;/em&gt; the phenotypes of double recessive and the epistatic recessive must match. Here, it is recessive epistasis, as the recessive condition at one locus suppresses the expression a other, and not dominant. Feel free to seek further clarifications or simplification.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2014-01-27T04:52:30.770" LastActivityDate="2014-01-27T04:52:30.770" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14637" PostTypeId="2" ParentId="14628" CreationDate="2014-01-26T09:11:59.517" Score="1" Body="&lt;p&gt;Go for the  link below, you will find an article on &quot;How do marine bacteria produce light, why are they luminescent, and can we employ bacterial bioluminescence in aquatic biotechnology?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biology-online.org/articles/marine_bacteria_produce_light/bacteria_emit_light.html&quot; rel=&quot;nofollow&quot;&gt;www.biology-online.org/articles/marine_bacteria_produce_light/abstract.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this article :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The question remains whether quorum sensing regulation of bacterial&#xA;  luminescence is a kind of a ‘social behaviour’ in which cells&#xA;  ‘predict’ the possibility of increased mutagenesis where conditions&#xA;  allow for efficient metabolism leading to extensive bacterial growth.&#xA;  Such conditions may cause the appearance of large quantities of&#xA;  metabolites, including mutagenic agents. Thus, one could speculate&#xA;  that enhanced light emission at a high cell density may ensure more&#xA;  efficient DNA repair in response to potentially increased&#xA;  concentrations of mutagens. Alternatively, quorum sensing may be&#xA;  needed for another role of bacterial bioluminescence, besides&#xA;  stimulation of photoreactivation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5499" LastEditorUserId="3615" LastEditDate="2014-03-18T19:01:28.110" LastActivityDate="2014-03-18T19:01:28.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14638" PostTypeId="1" CreationDate="2014-01-26T09:33:07.800" Score="1" ViewCount="59" Body="&lt;p&gt;When people talk about osmosis, they say that when we add a mole of NaCl, then each its molecule gets dissolved into 2 separate particles and therefore we have 2osM/L solution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But both Na &amp;amp; Cl are attached to molecules of water which means that those water molecules are not water anymore and they can't penetrate the membrane. Thus not only the presence of Na &amp;amp; Cl itself changes the concentration of water in solution, but also the number of water molecules &lt;em&gt;taken&lt;/em&gt; by those particles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore if we put 1 particle that binds to 1 water molecule and 1 particle that binds to 5 water molecules - they change the water concentration differently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please somebody tell me where I'm wrong.&lt;/p&gt;&#xA;" OwnerUserId="3793" LastActivityDate="2014-01-26T11:19:08.780" Title="Why all particles have same influence on osmosis" Tags="&lt;osmoregulation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14641" PostTypeId="2" ParentId="14638" CreationDate="2014-01-26T11:19:08.780" Score="1" Body="&lt;p&gt;When you dissolve something in water, you build a solvation shell around this - so each ion (in the case of salts) gets surrounded by a number of water molecules. For more details read this &lt;a href=&quot;http://en.wikipedia.org/wiki/Solvation_shell&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; article.&#xA;The concentration change in free water molecules is usually not taken into account since it can be neglected due to the vast number of &quot;unbound&quot; molecules. So if you have one litre of water, it contains approximately 56 moles of water molecules. If you dissolve 1 mole of sodium chloride in this water, and take in account that this takes quite some water to get solvated, there is ways more water available. So the water concentration is almost constant (especially when you work at physiological osmosis condition).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-01-26T11:19:08.780" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14642" PostTypeId="2" ParentId="14635" CreationDate="2014-01-26T11:40:36.747" Score="1" Body="&lt;p&gt;People, which have no ADH wouldn't be able to process methanol. Since the specificity of the ADH is higher for ethanol you get quite large amounts of ethanol for days (until the methanol level is under a specific level). Another possibility is to treat patient with the ADH inhibitor &lt;a href=&quot;http://en.wikipedia.org/wiki/Fomepizole&quot; rel=&quot;nofollow&quot;&gt;Fomepizole&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This also makes problems for the ethanol metabolization, but according to this paper (&quot;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1016/0307-4412%2890%2990174-M/pdf&quot; rel=&quot;nofollow&quot;&gt;The biochemistry of alcohol metabolism - a brief review&lt;/a&gt;&quot;) there are two other pathways of breakdown. One takes place in the peroxisomes and utilizes catalase and hydrogen peroxide (but is limited by the availability of peroxide), the other take place in the smooth endoplasmatic reticulum and uses the Cytochrome P450 enzyme.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure, if complete losses of ADH really happen (haven't found any reference) but mutations in this enzyme are quite common leading to a lower enzyme activity. &lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-01-26T19:58:24.370" LastActivityDate="2014-01-26T19:58:24.370" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14643" PostTypeId="1" AcceptedAnswerId="14667" CreationDate="2014-01-26T12:43:10.033" Score="5" ViewCount="580" Body="&lt;p&gt;I was just looking at some mouldy ginger found in the fridge under the microscope and was horrified/delighted to find (what looked to be) mites growing in it. I have searched the web and can only find references to red spider mites which these are certainly not. They were clear white and under 40x zoom about less than a mm across - does anyone know what they could be? Furthermore, what are they feeding on (ginger root is only ~15% carbohydrates - is that enough?) and has a minimal (~1%) amount of protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a picture (sorry for the quality but the white thing looks to be a mite).&lt;img src=&quot;https://i.stack.imgur.com/HaPmP.jpg&quot; alt=&quot;mite&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5516" LastEditorUserId="5516" LastEditDate="2014-01-26T16:04:20.380" LastActivityDate="2019-01-05T00:23:12.597" Title="Mites on ginger root" Tags="&lt;nutrition&gt;&lt;microscopy&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14645" PostTypeId="1" CreationDate="2014-01-26T12:55:24.650" Score="2" ViewCount="202" Body="&lt;p&gt;I am trying to figure out if the &lt;a href=&quot;http://genome.cshlp.org/content/20/5/547.full.pdf&quot; rel=&quot;nofollow&quot;&gt;following article&lt;/a&gt; is a primary or secondary source. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm leaning towards secondary but here are my cases for both.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Primary&lt;/strong&gt;: Published in a peer-reviewed journal.   &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Secondary&lt;/strong&gt;: It seems to be mostly a summary of other works so it might&#xA;  not be original research.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Can anyone confirm this for me? Thank you!&lt;/p&gt;&#xA;" OwnerUserId="5518" LastEditorUserId="3776" LastEditDate="2014-01-26T14:21:21.127" LastActivityDate="2014-01-26T14:21:21.127" Title="Need help distinguishing between a primary and secondary source" Tags="&lt;dna&gt;&lt;genomics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14646" PostTypeId="2" ParentId="14645" CreationDate="2014-01-26T13:04:33.583" Score="2" Body="&lt;p&gt;Too long for a comment: Although this is a review article which summarizes the findings of other researchers, considers this as a primary article. The author gives you all the resources he used in the reference section of this article and summarises their finding. Additionally, review articles in renowned journals (and Genome Research is definitely such a journal) are peer-reviewed. Primary vs. secondary sources would be more the comparision of research articles and news articles. In my observation, news articles hardly ever name the sources or the original articles about which they report. Plus they sometimes have problems of getting the message wrong.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-01-26T13:04:33.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14647" PostTypeId="1" CreationDate="2014-01-26T13:34:07.513" Score="1" ViewCount="3360" Body="&lt;p&gt;How does human body deal with inert solid material in the bloodstream? For example, if there is a powder of glass injected into our bloodstream, will the white blood cells do anything or will kidney excrete these materials? Thanks. &lt;/p&gt;&#xA;" OwnerUserId="5519" LastEditorUserId="3776" LastEditDate="2014-01-26T14:20:19.060" LastActivityDate="2017-09-07T14:31:53.083" Title="How does human body deal with inert solid material in the bloodstream?" Tags="&lt;cell-biology&gt;&lt;immunology&gt;&lt;blood-circulation&gt;&lt;kidney&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14650" PostTypeId="1" AcceptedAnswerId="16324" CreationDate="2014-01-26T16:32:15.193" Score="7" ViewCount="1072" Body="&lt;p&gt;I frequently hear expressions like &quot;Dopamine flooding the brain&quot; or &quot;X neurotransmitter flooding the brain&quot; used to communicate with general audiences. For example: &quot;Following [orgasm]? oxytocin floods the brain, causing feeling of deep connectedness between people&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What exactly do they mean by &quot;Oxytocin flooding the brain&quot;?&lt;/strong&gt; I'm interested in where and how it happens. Do they mean that excess neurotransmitters are released in the synaptic cleft? Is it localized to some brain areas, or is it indeed throughout the brain?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If they are indeed talking about the synaptic cleft, then I'm interested in how such &quot;flood&quot; triggers the change in state - &lt;a href=&quot;https://biology.stackexchange.com/questions/5255/is-there-such-thing-as-half-life-of-dopamine&quot;&gt;the answer to this question suggests that the half life of dopamine is only about 2 seconds in prefrontal cortex&lt;/a&gt;. Assuming that the half life of oxytocin is similar, in the &quot;oxytocin floods the brain and produces feeling of connectedness&quot; example, does it mean that a single burst of oxytocin(x seconds in synaptic cleft) is enough to produce such feeling, or are they talking about sustained release or some kind of release loop mechanism?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-04-03T13:43:35.970" Title="What is meant by &quot;neurotransmitters flooding the brain&quot;?" Tags="&lt;brain&gt;&lt;endocrinology&gt;&lt;neurotransmitter&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14651" PostTypeId="1" CreationDate="2014-01-26T18:21:55.287" Score="2" ViewCount="371" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8dDdx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hello! I need help with this exercise question. I am not really sure which pedigree diagram is autosomal and which is not. But, is question b 1/2. Can someone give an explanation? Thanks very much in advance? Appreciate any help!! &lt;/p&gt;&#xA;" OwnerUserId="5460" LastActivityDate="2014-01-26T18:55:49.203" Title="PedigreeAnalysis Genetics" Tags="&lt;homework&gt;&lt;molecular-genetics&gt;&lt;genetics&gt;&lt;epigenetics&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-01-28T02:58:34.270" ContentLicense="CC BY-SA 3.0" />
  <row Id="14652" PostTypeId="2" ParentId="14651" CreationDate="2014-01-26T18:31:52.173" Score="2" Body="&lt;p&gt;According to the key given, the one shaded black on the right is autosomal and one on the left is sex linked.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, the answer to b is half because Maria is XhX ans Peter is XY and so the probability of the child having this disease is 1/2.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2014-01-26T18:55:49.203" LastActivityDate="2014-01-26T18:55:49.203" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="14653" PostTypeId="1" AcceptedAnswerId="14663" CreationDate="2014-01-26T19:01:45.963" Score="1" ViewCount="991" Body="&lt;p&gt;I am doing an experiment on preservation of peas. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first notable change to the peas over a period of one week is that they have changed colour from bright green to a dull colour... Why is this so? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only test tube which did not have peas which changed colour was the one which was kept at 4 degrees Celcius in a fridge, so it probably has some relation to temperature...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many thanks&lt;/p&gt;&#xA;&#xA;&lt;p&gt;N.B.: I know that the bacteria reproduce and could use the pea as their source of food, but how do they have any relation to the colour of the pea? I also put the tag &quot;bacteria&quot; and &quot;thermodynamics&quot; as I couldn't find any other related tags.&lt;/p&gt;&#xA;" OwnerUserId="4819" LastEditorUserId="4819" LastEditDate="2014-01-26T19:15:38.767" LastActivityDate="2014-01-27T11:41:39.513" Title="Why do peas change colour?" Tags="&lt;bacteriology&gt;&lt;thermodynamics&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="14656" PostTypeId="1" CreationDate="2014-01-26T23:15:01.463" Score="1" ViewCount="336" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9ooIe.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am asked to fill the genotypes in the spaces provided but looks like I am aving a little bit of trouble. can anyone help? thanks in advance!&lt;/p&gt;&#xA;" OwnerUserId="5460" LastActivityDate="2014-01-27T02:22:01.710" Title="Pedigree Diagram help" Tags="&lt;homework&gt;&lt;molecular-genetics&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14657" PostTypeId="1" AcceptedAnswerId="14660" CreationDate="2014-01-27T00:53:19.193" Score="17" ViewCount="56728" Body="&lt;p&gt;According to the article &lt;a href=&quot;http://www.google.com/hostednews/afp/article/ALeqM5hFUbEO1ciJQxU6WfzSBwyIHAxfzw?docId=c6a93e4c-3f4c-481e-ba52-eaa180e359d0&quot;&gt;Dark skin and blue eyes: How Europeans once looked&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is widely accepted that Man's oldest common forefather was dark&#xA;  skinned, and that people became more pale as they moved further north&#xA;  out of Africa into colder climates with less sunlight.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I thought that humans' oldest common ancestor was light-skinned, because&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Dark-skinned people have white palms and soles, but light-skinned people have more consistent skin tones. This suggests that light skin is more ancestral and dark skin evolved to protect skin from the sun.&lt;/li&gt;&#xA;&lt;li&gt;Bonobo chimpanzees, our closest primate cousins, look like they have light skin under black hair.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I understand we all originate in Africa, but I thought that the environmental conditions in Africa were different from today. How do we know that the first humans were dark-skinned?&lt;/p&gt;&#xA;" OwnerUserId="5525" LastEditorUserId="3553" LastEditDate="2015-12-13T05:57:53.297" LastActivityDate="2015-12-13T05:57:53.297" Title="Why do we assume that the first humans were dark-skinned?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;gene-expression&gt;&lt;human-genetics&gt;&lt;pigmentation&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14659" PostTypeId="2" ParentId="14656" CreationDate="2014-01-27T02:14:45.357" Score="1" Body="&lt;p&gt;Here are a few hints that might help:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Talking about Maria's pedigree:&#xA;Firstly, it seems as if you have mixed up with $X^a$ and $X^A$, see that the disorder is X-linked DOMINANT. Anyone with either heterozygous or homozygous dominant expression would have the disease expressed. So the first generation male should have a genotype: $X^aY$, because if it were $X^AY$ then Amelogenesis imperfecta would be expressed as his phenotype and the first generation female should have a homozygous recessive genotype. Also no child in the second generation would suffer from the same. &#xA;(&lt;strong&gt;&lt;em&gt;NOTE&lt;/em&gt;&lt;/strong&gt;: The one suffering from Amelogenesis in the second generation would have genotype $X^AY$)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for Gunther disease, both the parent in the first generation should have a &lt;em&gt;heterozygous&lt;/em&gt; dominant expression and the offspring suffering must have a homozygous recessive expression. And you can apply the same basics in Peter's pedigree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this much should be enough to complete the task, but if you still have some doubt you can put it forward in the comments.&lt;/p&gt;&#xA;" OwnerUserId="4947" LastEditorUserId="4947" LastEditDate="2014-01-27T02:22:01.710" LastActivityDate="2014-01-27T02:22:01.710" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14660" PostTypeId="2" ParentId="14657" CreationDate="2014-01-27T03:45:43.000" Score="19" Body="&lt;p&gt;According to &lt;a href=&quot;https://en.wikipedia.org/wiki/Human_skin_color&quot;&gt;wikipedia&lt;/a&gt;, &quot;comparisons between known skin pigmentation genes in chimpanzees and modern Africans show that dark skin evolved along with the loss of body hair about 1.2 million years ago and is the ancestral state of all humans.&quot; This is several million years after after the time estimated for the &lt;a href=&quot;https://en.wikipedia.org/wiki/Chimpanzee-human_last_common_ancestor&quot;&gt;last common human-chimpanzee ancestor&lt;/a&gt;, but at least 1 million years before the emergence of Homo Sapiens. This suggests that the earliest species in &lt;em&gt;Homo&lt;/em&gt; may have had lighter skin, but that the advantageous genes for dark skin were universal by the time of the first true humans.&lt;/p&gt;&#xA;" OwnerUserId="827" LastEditorUserId="827" LastEditDate="2014-01-27T16:51:07.137" LastActivityDate="2014-01-27T16:51:07.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14661" PostTypeId="1" CreationDate="2014-01-27T05:29:14.280" Score="1" ViewCount="20" Body="&lt;p&gt;I'm working on performing phylogentic footprinting to figure out how many TRE sequences there are in the TWIST1 gene. (Sequence motifs). I'm trying to use ENSEMBL to gather orthologues of species in which the gene twist1 is present, compile it into a FASTA file and upload it to MEME SUITE. However, I'm having trouble understanding how to compile the file. I also don't know how to read SEQUENCE LOGOS. If anyone can help me, I would appreciate it SOOOOO much. &lt;/p&gt;&#xA;" OwnerUserId="5526" LastActivityDate="2014-01-27T05:29:14.280" Title="Phylogentic Footprinting Project" Tags="&lt;dna&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14663" PostTypeId="2" ParentId="14653" CreationDate="2014-01-27T09:02:50.260" Score="2" Body="&lt;p&gt;Chlorophyll is a dye that makes leaves green, it plays a key role in photosynthesis. It is present also in unripe fruits, young peas etc. Maybe I should say chlorophylls, because it is a group of similar chemicals. They get &lt;strong&gt;degraded by heat&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(No assistence of microbes needed).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bonus: Chlorophyll contains magnesium at the molecule core, which facilitates the green color. There were some creative people, who were upset, that the canned cucumbers are not green enough, so they added some copper-containing molecule during canning. It replaced magnesium and was more stable, so beautiful bright green cucumbers were on the market for a while. However, they turned out to be slightly poisonous and are not sold anymore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bonus 2: Most varieties of peas change color also naturally as they rippen. The seeds become yellow. The chlorophyll gets degraded in plant metabolism. The chloroplasts, i.e. the cell organelles responsible for photosynthesis change function to become storage organelles called leucoplasts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Edit: Ooops, I first wrote that chlorophyll supposedly contains iron. That was wrong, it is magnesium. Iron is present in a similar die called heme, which makes blood red. Probably I am getting too old :-) )&lt;/p&gt;&#xA;" OwnerUserId="5369" LastEditorUserId="5369" LastEditDate="2014-01-27T11:41:39.513" LastActivityDate="2014-01-27T11:41:39.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14664" PostTypeId="2" ParentId="14657" CreationDate="2014-01-27T09:24:24.120" Score="32" Body="&lt;p&gt;The first modern humans evolved about 200.000 years ago in Africa. When they lost their body hair (or at least most of it), they needed some other protection of their skin from the sun - otherwise they are prone to develop melanoma. Melanin is such a protection, and the rate of melanoma is much lower in dark skinned people. &#xA;There is also a nice correlation between latitude and skin color - the more to the north (and to some degree to the south as well) you get, the lighter the skin color of the population gets. The reason for this is likely the better ability to synthesize Vitamin D (for which you need sunlight on the skin):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10896812&quot;&gt;The evolution of human skin coloration.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://faculty.washington.edu/charles/562_f2011/Week%201/Jablonski%202004.pdf&quot;&gt;The evolution of human skin ans skin color.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19481954&quot;&gt;Development of different human skin colors: a review highlighting&#xA;photobiological and photobiophysical aspects.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.landesbioscience.com/journals/dermatoendocrinology/article/23791/&quot;&gt;North-South gradients of melanomas and non-melanomas: A role of&#xA;vitamin D?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The lightening of the skin occurred after humans moved to Europe:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://mbe.oxfordjournals.org/content/30/1/24&quot;&gt;The Timing of Pigmentation Lightening in Europeans&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And we even know, that this occured more than once, since the genetic reasons for lighter skins are different between europeans and light skinned asians.&#xA;A lot of this we know via sequence comparisions of genes involved in pigmentation, there you can trace mutations and see, where they show up first and how they migrate over time. One very good example is the melanocortin-1-receptor (MC1R), which is mutated pretty often in europeans (mutations in this gene are generally associated with lighter skin and hair color; people with red hair carry certain mutations in this gene) but its under selection pressure to not mutate in africa (there are almost no known mutations in MC1R for africans). Another example would be a mutation in the SLC24A5 gene, which is exclusively found in europeans, but not in asians and which accounts also for lighter skin. I stop here for the moment, if there are more specific question, go ahead.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://hmg.oxfordjournals.org/content/15/suppl_2/R176.full&quot;&gt;The genetic architecture of normal variation in human pigmentation:&#xA;an evolutionary perspective and model&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jstor.org/discover/10.1086/381006?uid=3737864&amp;amp;uid=2&amp;amp;uid=4&amp;amp;sid=21103303964991&quot;&gt;Genetic Variation at the MC1R Locus and the Time since Loss of Human&#xA;Body Hair&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16357253&quot;&gt;SLC24A5, a putative cation exchanger, affects pigmentation in&#xA;zebrafish and humans.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-01-27T09:24:24.120" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14665" PostTypeId="2" ParentId="7652" CreationDate="2014-01-27T10:20:07.590" Score="4" Body="&lt;p&gt;Interesting question, I am not sure if I have a definite answer, but at least some ideas:&#xA;The pigment in the hair is made by specialized cells, the melanocytes. The make the pigment (eumelanin=dark and pheomelanin=red/yellowish) which is then deposited into the growing hair. They are located at the bottom of hair bulb and usually die at the end of each hair cycle. To have the hair of the next hair cycle colored as well, this melanocyte population in the hair bulb needs to be replenished. This is done by melanocate stem cells, which live in the hair bulge and which start to reproduce and differentiate in melanocyte which then migrate down to the hair bulb. There is an excellent article following this process:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15618488&quot; rel=&quot;nofollow&quot;&gt;Mechanisms of hair graying: incomplete melanocyte stem cell&#xA;maintenance in the niche.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The hair later gets grey (low pigment) and white (no pigment) when these melanocytes are not, or not fulley replenished in later hair cycles. Why this happens, there are a few hypothesis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, its possible, that with age the melanocyte stem cell population (which not only need to replenish the melanocytes, but also need to maintain its own population) is getting smaller and disappears over time. This process would explain gradually graying over time. See this reference:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15820674&quot; rel=&quot;nofollow&quot;&gt;Melanocyte stem cell maintenance and hair graying.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Another possibility is the presence of reactive oxigen species (ROS) which occur naturally in melanocytes. Over time, the enzyme which intercepts this ROS (catalase) is getting less active or present in the cells and thus oxidative damage is getting bigger, damaging the melanocytes and their ability to make pigment. It would actually bleach itself...&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.fasebj.org/content/23/7/2065&quot; rel=&quot;nofollow&quot;&gt;Senile hair graying: H2O2-mediated oxidative stress affects human&#xA;hair color by blunting methionine sulfoxide repair&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Melanin has also an important role in intercepting ROS, so in this process less and less pigment is made (as the damage accumulates) and this also leads to hair, which is less pigmented for exogeneous oxidative stress:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16723385&quot; rel=&quot;nofollow&quot;&gt;Towards a &quot;free radical theory of graying&quot;: melanocyte apoptosis in&#xA;the aging human hair follicle is an indicator of oxidative stress&#xA;induced tissue damage.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It could be possible (and this is a wild guess) that the phenomenon of the tips graying first is situated by this. Hair less protected against exogeneous oxidative stress (smoke, UV etc.) so the melanin is &quot;used up&quot; during this until the hair greys at the tip, since its the oldest and most exposed part of the hair. This article by Tobin gives also a nice overview:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21070612&quot; rel=&quot;nofollow&quot;&gt;The cell biology of human hair follicle pigmentation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-01-27T10:26:48.540" LastActivityDate="2014-01-27T10:26:48.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14667" PostTypeId="2" ParentId="14643" CreationDate="2014-01-27T14:27:30.483" Score="5" Body="&lt;p&gt;Does this look like the same bug to you ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cVnMJ.jpg&quot; alt=&quot;bulb mite&quot;&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This one is a bulb mite, &lt;em&gt;Rhizoglyphus robini&lt;/em&gt;, see &lt;a href=&quot;http://ipmworld.umn.edu/chapters/straub.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5369" LastEditorUserId="15950" LastEditDate="2019-01-05T00:23:12.597" LastActivityDate="2019-01-05T00:23:12.597" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="14668" PostTypeId="1" AcceptedAnswerId="14675" CreationDate="2014-01-27T14:42:59.080" Score="3" ViewCount="98" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;List the following proteins in the order of decreasing evolutionary&#xA;  conservativeness of their primary structure:&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;Somatotropin.&lt;/li&gt;&#xA;  &lt;li&gt;Catalytic subunit of a DNA – polymerase.&lt;/li&gt;&#xA;  &lt;li&gt;Histone H1.&lt;/li&gt;&#xA;  &lt;li&gt;Prolamines (storage proteins of cereals).&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What I think : I am sure that 4th one should be last. I believe that H1 sequence is not that important as I had read somewhere that a cell can survive even without H1 histone. I also think that catalytic subunit is most important. So, according to me the order should be : 2,1,3,4.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I right ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-27T22:37:22.723" Title="Evolutionary conservativeness" Tags="&lt;evolution&gt;&lt;homework&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14670" PostTypeId="1" AcceptedAnswerId="14680" CreationDate="2014-01-27T15:28:09.360" Score="1" ViewCount="248" Body="&lt;p&gt;It is found in my apartment in Finland. I had to kill it to stop it from getting away before looking for the camera, but it looked pretty much the same alive and intact. It's length is about half a centimeter, and the younger ones look darker. It is often found in dark. Since their appearance, I often notice red and slightly itchy bug bite in the morning. The question is what is this insect?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/toFXD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZB1aT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5529" LastEditorUserId="3615" LastEditDate="2014-01-27T15:32:01.963" LastActivityDate="2014-01-28T09:18:01.357" Title="Insect identification" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2021-05-03T03:32:56.160" ContentLicense="CC BY-SA 3.0" />
  <row Id="14671" PostTypeId="1" AcceptedAnswerId="25981" CreationDate="2014-01-27T16:36:35.790" Score="4" ViewCount="4006" Body="&lt;p&gt;Is there a publication comparing DNA yield and/or PCR-amplifiability after extraction from fruit flesh (like apples, oranges, cherries etc) in comparison to seeds of the same fruits?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would prefer a reference, but your unpublished experience is also interesting to me. &lt;/p&gt;&#xA;" OwnerUserId="5369" LastEditorUserId="9829" LastEditDate="2015-01-07T06:14:07.490" LastActivityDate="2015-01-07T06:14:07.490" Title="DNA content in plant seeds vs. fruit flesh" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;pcr&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14673" PostTypeId="1" CreationDate="2014-01-27T20:39:21.663" Score="4" ViewCount="1429" Body="&lt;p&gt;It's just a small microbiology lab that currently records everything on paper, and there's quite few mutants as well. Is Excel commonly used for this sort of thing? Or is there a better software to manage a lab?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any help&lt;/p&gt;&#xA;" OwnerUserId="5531" LastEditorUserId="1306" LastEditDate="2014-01-27T22:42:50.660" LastActivityDate="2019-02-21T14:03:45.013" Title="For people who work in microbiology labs, what software do you use to manage your strains?" Tags="&lt;microbiology&gt;&lt;lab-techniques&gt;&lt;software&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14674" PostTypeId="1" CreationDate="2014-01-27T22:09:30.190" Score="3" ViewCount="317" Body="&lt;p&gt;How do surfactants remain on the surface of pneumocytes without  (1) acting as a detergent or (2) the phospholipids getting incorporated into the membranes of pneumocytes... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm guessing the answer has something to with the secretions of clara cells, but I'm curious for a more biophysics-y answer... for example how do the phospholipids that compose surfactant not form miceles or are the miceles simply larger that the individual component phospholipids (I'm basing this off the answer to &quot;how do detergents get in hydrophobic membrane interior&quot;), but even so why wouldn't the micelle simply fuse into the membrane&lt;/p&gt;&#xA;" OwnerUserId="4433" LastActivityDate="2014-01-27T22:09:30.190" Title="Why don't surfactants destroy or incorporate into cell membranes?" Tags="&lt;cell-membrane&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14675" PostTypeId="2" ParentId="14668" CreationDate="2014-01-27T22:37:22.723" Score="3" Body="&lt;p&gt;Even when you can live without Histone H1, its a widely distributed protein which you find in basically all living cells (except for some yeasts if I remember correct). This points to the fact that it must be available for quite a while. The same is true for the catalytic subunit of the DNA polymerase. Somatropin is still pretty important (and can be found in a lot of organisms), prolamines are quite specific to certain cereals. I would group it 2-3-1-4.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-01-27T22:37:22.723" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14678" PostTypeId="2" ParentId="14523" CreationDate="2014-01-28T08:56:09.983" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/early/2012/02/22/1118885109.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a study of planarian worms, which are immortal in asexual reproduction and mortal in sexual reproduction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hydra_%28genus%29#Reproduction_and_life_cycle&quot; rel=&quot;nofollow&quot;&gt;Hydras also become mortal after they reproduce sexually&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Relevant&lt;/strong&gt; to your question: Cells within planarian worm differ in expression of telomerase active subunit depending on body part. Immortal (asexual) worms have more expression in the area around the pharynx, those cells there are &quot;the proliferative stem cells&quot;. There is a nice figure in the article.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume it is similar for hydra, that outer body coat has less expression than the cells inside. &lt;a href=&quot;http://pomona.edu/Magazine/PCMWin09/NKdanielmartinez.shtml&quot; rel=&quot;nofollow&quot;&gt;“Hydra is a bag of stem cells”&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(&lt;strong&gt;Less relevant&lt;/strong&gt; (a version of previous version of my answer. But does not answer the &quot;every cell&quot; inquiry well): In planarian worms &quot;We demonstrate that this difference is reflected in the expression and alternate splicing of the protein subunit of the telomerase enzyme.&quot; The mentioned telomerase &lt;em&gt;subunit&lt;/em&gt; was 1. comparatively more transcribed in immortal (asexual) worm and 2. within the resultant trancripts, there were possibilities of functional and non-functional isoforms due to alternate splicing. Immortal worms had higher ratio of functional isoforms. Summary: immortals have more transcripts and higher proportion of functional versions of them.)&lt;/p&gt;&#xA;" OwnerUserId="5369" LastEditorUserId="5369" LastEditDate="2014-02-02T10:59:14.660" LastActivityDate="2014-02-02T10:59:14.660" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14680" PostTypeId="2" ParentId="14670" CreationDate="2014-01-28T09:18:01.357" Score="3" Body="&lt;p&gt;It reminds me of &lt;a href=&quot;http://en.wikipedia.org/wiki/Silverfish&quot; rel=&quot;nofollow&quot;&gt;silverfish&lt;/a&gt;, a common wingless house insect.&lt;/p&gt;&#xA;" OwnerUserId="1486" LastActivityDate="2014-01-28T09:18:01.357" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14681" PostTypeId="1" AcceptedAnswerId="14682" CreationDate="2014-01-28T09:48:28.370" Score="2" ViewCount="940" Body="&lt;p&gt;If a constitutive mutation happens in the operator of an inducible operon, does that mean that repressors won't be able to bind them ? Or does it mean that even if repressors are bound, they will not have any effect on the gene ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am specifically talking about lac operon.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-28T10:20:12.290" Title="Constitutive mutation in operator gene" Tags="&lt;gene-expression&gt;&lt;mutations&gt;&lt;operons&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14682" PostTypeId="2" ParentId="14681" CreationDate="2014-01-28T09:53:23.777" Score="2" Body="&lt;p&gt;For the lac operon there are two possibilities for constitutive expression mutations:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The operator is never closed.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Reason: Mutation of the repressor, so its not present, doesn't bind or binds only with very low affinity for the operon.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The repressor can not bind.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Reason: The binding site for the repressor is mutated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this &lt;a href=&quot;http://www.ndsu.edu/pubweb/~mcclean/plsc431/prokaryo/prokaryo2.htm&quot; rel=&quot;nofollow&quot;&gt;Website&lt;/a&gt; or this &lt;a href=&quot;http://learning.covcollege.ac.uk/content/Jorum/GMB_Gene-organisation-regulation_LM-1.2/page73.htm&quot; rel=&quot;nofollow&quot;&gt;Website&lt;/a&gt; for more information.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-01-28T10:20:12.290" LastActivityDate="2014-01-28T10:20:12.290" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14688" PostTypeId="1" AcceptedAnswerId="14689" CreationDate="2014-01-28T16:27:04.537" Score="2" ViewCount="109" Body="&lt;p&gt;Assume a sufficiently large population of rats (to allow genetic variation and facilitate inbreeding) in a place with abundant water, sunlight, shelter but no food. For how many generations can this population persist solely by cannibalizing?&lt;/p&gt;&#xA;" OwnerUserId="5547" LastEditorUserId="5547" LastEditDate="2014-01-28T16:34:04.297" LastActivityDate="2014-01-30T07:40:51.390" Title="maximum # of generations possible in a population of cannibalistic rats" Tags="&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14689" PostTypeId="2" ParentId="14688" CreationDate="2014-01-28T18:28:12.680" Score="4" Body="&lt;p&gt;Here's a back of the envelope answer: one generation if you have a LOT of rats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Numbers according to the &lt;a href=&quot;http://www.in.gov/isdh/23256.htm#RATS&quot; rel=&quot;nofollow&quot;&gt;Great State if Indiana&lt;/a&gt;.&#xA;Assuming also that we start with adult breeding rats.  50% females / 50% males.&lt;br&gt;&#xA;The gestation period is 21 days. &#xA;The adult rat can eat 1/3 of its body weight each day. Assuming that the rat is eating about 80% of the 'victim' rat body weight, the colony reduces in size about 40% each day.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lets say the rats are going to be a bit hungry and the colony loses 30% of its size each day. And they don't eat their own feces, which I think they can do, but also assuming that the malnutrition from eating only rat for food will not cause problems. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Over the period of gestation, 21 days the colony will have a final size of 0.3^21 = 0.000559 times its original size.  So in order to have a surviving gestating female you'd have to start with 1791 rats.  Also assuming that the last rat is a very pregnant female who can compete with the male cannibals who are not pregnant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then the average litter is not 1790. So you'd need something like 1790^N rats for N generations.  and they'd have to be pretty lucky rats to boot.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW similar numbers would be true for any animal including human beings. This is one reason that cannibalism is usually only a social ritual, not a means of acquiring nutrition except in extreme cases. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-01-30T07:40:51.390" LastActivityDate="2014-01-30T07:40:51.390" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14691" PostTypeId="2" ParentId="14583" CreationDate="2014-01-28T21:10:51.770" Score="3" Body="&lt;p&gt;Hairs (with their nerve rich follicles) are sense organs, extending our sense of touch beyond the skin. When things disturb our hairs we feel them; bugs, breezes, close encounters. During fright or arousal goosebumps cause the hairs to stand on end, extending our sense of touch to it's furthest distance. In the process the hair shafts that are otherwise laid against each other are separated, reducing the dampening of vibration and movement from shaft to follicle - which increases fine sensitivity. Also during goosebumps the smallest disturbance of hairs causes a reaction in surrounding hairs, amplifying distinguishable sensations into hard to ignore. Goosebumps are sensory enhancers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This goosbumps response predated hairs as fur for insulation and probably mammals as a group. Raising fur to increase insulation, as well as raising hackles to look intimidating almost certainly piggy backed on this pre-existing response.  It is a function that has never been lost and should not be considered vestigial. &lt;/p&gt;&#xA;" OwnerUserId="5551" LastActivityDate="2014-01-28T21:10:51.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14692" PostTypeId="1" AcceptedAnswerId="14717" CreationDate="2014-01-28T21:51:35.580" Score="2" ViewCount="166" Body="&lt;p&gt;I sometimes listen to lectures on my phone using &lt;a href=&quot;http://www.adamvogel.net/wp-content/uploads/2009/11/fab_121.jpg&quot; rel=&quot;nofollow&quot;&gt;ear buds&lt;/a&gt;, but occasionally with only one ear bud in. Is the other half of my brain losing out on any aspect of the lecture? Just how good is the corpus callosum at sharing information between the hemispheres?&lt;/p&gt;&#xA;" OwnerUserId="1289" LastActivityDate="2017-03-12T23:14:29.170" Title="How good is information transfer between the hemispheres of the brain?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;brain&gt;&lt;perception&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14693" PostTypeId="1" AcceptedAnswerId="14694" CreationDate="2014-01-29T02:52:08.063" Score="2" ViewCount="1133" Body="&lt;p&gt;Some time last year, I found an article on Wikipedia about the smallest something to be able to reproduce. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't remember exactly what it was, but I am fairly certain that after the initial discovery another of the previous organism (this one slightly smaller) was discovered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that the smallest something might have been the smallest self-replicating protein, or smallest self-replicating molecule, or something like that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was not mentioned in this thread: &lt;a href=&quot;https://biology.stackexchange.com/questions/1382/which-organism-has-the-smallest-genome-length&quot;&gt;Which organism has the smallest genome length?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It had a strange, stand-out name and I believe it was discovered in the 90s.&lt;/p&gt;&#xA;" OwnerUserId="5553" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2019-06-27T18:18:43.690" Title="What is the name of the smallest self-replicating thing?" Tags="&lt;life&gt;&lt;replication&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14694" PostTypeId="2" ParentId="14693" CreationDate="2014-01-29T03:05:29.583" Score="3" Body="&lt;p&gt;You're probably thinking of the Spiegelman Monster. It was actually discovered in 1965, but it was discovered that it became shorter over time in 1997.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also wasn't included in that thread, and it has a strange name. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Spiegelman_Monster&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Spiegelman_Monster&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5552" LastActivityDate="2014-01-29T03:05:29.583" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14696" PostTypeId="1" AcceptedAnswerId="14730" CreationDate="2014-01-29T03:46:30.260" Score="2" ViewCount="763" Body="&lt;p&gt;I am trying to understand what exactly a phenotype is to try and understand a genetics database. (Ie I don't really know very much about genetics at all)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been reading through &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenotype&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; on what a phenotype is and from what I can gather it is an observable trait which may be impacted by a specific gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I would like to know is if you were looking for the presence of a phenotype such as &lt;code&gt;red hair&lt;/code&gt;, would characteristics like &lt;code&gt;not red hair&lt;/code&gt; and &lt;code&gt;carrier of red hair&lt;/code&gt; also be phenotypes? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example the following table is named Phenotype,&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;+------+------------------+&#xA;| Code |   Description    |&#xA;+------+------------------+&#xA;| RR   | Red Hair         | this makes sense with my understanding of phenotype&#xA;| RN   | Red Hair Carrier | this doesnt&#xA;| NR   | Red Hair Carrier | this doesnt&#xA;| NN   | No Red Hair      | this doesnt&#xA;+------+------------------+&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The whole code column looks like it represents a gene not a phenotype&lt;/p&gt;&#xA;" OwnerUserId="5554" LastEditorUserId="5554" LastEditDate="2014-01-29T09:16:43.193" LastActivityDate="2014-01-30T16:40:23.000" Title="Does a phenotype include the presence of a recessive gene" Tags="&lt;genetics&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14698" PostTypeId="2" ParentId="14696" CreationDate="2014-01-29T06:41:23.987" Score="1" Body="&lt;p&gt;You say it yourself: The phenotype is the observable trait. So this means if you have red hairs, your hair phenotype is red. The most likely reason for it, the mutation of the melanocortin-1-receptor, is the underlying genotype.&#xA;Or: The phenotype of mouse coat color is black, white, brown, speckled, whatever. That what you see, the reasons for that can be (and are) completely different between different mouse strains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first column of the table is the genotype and showing that red hair is a recessive trait (without naming a gene, but this doesn't matter), the second only is a representation of the first and makes actually no statement about the actual phenotype. &lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-01-29T09:51:02.887" LastActivityDate="2014-01-29T09:51:02.887" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14699" PostTypeId="2" ParentId="1827" CreationDate="2014-01-29T10:19:33.810" Score="2" Body="&lt;p&gt;I have found videos of porcupines, armadillos, anteaters.. all swimming.&#xA;The porcupine seemed to have no trouble at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for apes - quite well it seems. &lt;a href=&quot;http://newswatch.nationalgeographic.com/2013/08/20/new-surprising-video-shows-apes-swimming/&quot; rel=&quot;nofollow&quot;&gt;http://newswatch.nationalgeographic.com/2013/08/20/new-surprising-video-shows-apes-swimming/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rhinos: &#xA;www.youtube.com/watch?v=DbqF4AA0Z8U&#xA;The water looks deeper than it's head at times, for sure. But whether it is actually swimming or can just/almost reach the bottom is unclear. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Giraffes:  &lt;a href=&quot;http://www.arkive.org/giraffe/giraffa-camelopardalis/video-ti06.html&quot; rel=&quot;nofollow&quot;&gt;http://www.arkive.org/giraffe/giraffa-camelopardalis/video-ti06.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to me that if these animals couldn't manage at all in the water, that they wouldn't likely do so, from an evolutionary standpoint. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure not all manage terribly well, but the videos seem to show that they managed at least.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pretty cool.  :)&lt;/p&gt;&#xA;" OwnerUserId="5559" LastActivityDate="2014-01-29T10:19:33.810" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14700" PostTypeId="1" CreationDate="2014-01-29T10:58:32.023" Score="5" ViewCount="73" Body="&lt;p&gt;Many women cannot or will not feed their children with breast-milk. It is my understanding breast-milk has many advantages over formula. Some psychological like oxytocin and some physiological like advanced antibodies. Have there been any attempts to create a formula with better psychological and physiological properties? Is it even possible to include antibodies in formula or milk?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2014-01-29T15:54:49.360" LastActivityDate="2014-12-18T16:00:43.857" Title="Are there baby drinks closer to breast-milk?" Tags="&lt;neuroscience&gt;&lt;antibody&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14701" PostTypeId="1" CreationDate="2014-01-29T11:25:22.057" Score="2" ViewCount="500" Body="&lt;p&gt;I realise that the best way to prove the existence of germs or single-celled organisms is by looking at them through a microscope.&#xA;But I don't have a microscope at my home, how can I design an experiment in a normal house environment to show the existence of germs (or other single-celled organisms) without spending too much money?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By &quot;house environment&quot; I mean that I have access to normal stores and the internet. If it's something that can be bought in a &quot;normal&quot; store or on-line without getting me into trouble, and doesn't cost a lot then I can have access to it. I don't have access to lab grade equipment or conditions, so no sterile rooms or special growth environment.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I thought about the following experiment, inspired by the &lt;a href=&quot;http://www.youtube.com/watch?v=Ja09AO5TocA&quot; rel=&quot;nofollow&quot;&gt;mythbusters pyramid power episode&lt;/a&gt;. In the episode they cut an apple in half and put one half under a pyramid and the other not under a pyramid. In the first attempt one of the halfs rotted quicker than the other, they concluded that it happened because the saw they used to cut the apples wasn't sterile.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I thought about taking 3 apples, contaminating a knife (by rubbing human saliva on it). Cutting one apple with the contaminated knife, one apple with a sterile knife (using rubbing alcohol to sterilize it) and one apple by a knife that has 1 contaminated side and one sterile, which is a contaminated knife, that had only 1 side sterilized with rubbing alcohol. Then leaving the 6 halves in separated sealed containers (some tupperware) for a few days and then looking examining the rott. The expected result is that the &quot;contaminated apple&quot; will have a lot of rot on both halves, the &quot;sterile&quot; apple will have no (or close to no) rot, and the half and half apple will have one rotten side and one not rotten side, and the sides will coincide to the contaminated/sterile sides of the knife touching them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Will this experiment work?&lt;/p&gt;&#xA;" OwnerUserId="680" LastEditorUserId="680" LastEditDate="2014-01-29T12:25:44.893" LastActivityDate="2014-01-29T18:17:42.067" Title="Is it possible to create an experiment in house conditions to prove the existence of germs?" Tags="&lt;experimental-design&gt;" AnswerCount="2" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="14702" PostTypeId="2" ParentId="14647" CreationDate="2014-01-29T11:28:08.723" Score="3" Body="&lt;p&gt;Non-opsonized particles (Particles that can't be coated with opsonins like antibodies or complement proteins) can be engulfed by macrophages which could end up, for example, in the lung secretions and be coughed up one day. Note that a cell can only engulf a particle so large, so you'll not feel yourself coughing up anything out of the ordinary. Only tiny particles can be dealt with like this. Bigger particles can become trapped in fine vasculature (small veins; venules, and small arteries;arterioles). This can lead to abscess formation necessitating amputation of the affected limb. &lt;/p&gt;&#xA;" OwnerUserId="5561" LastEditorUserId="20758" LastEditDate="2017-09-07T14:31:53.083" LastActivityDate="2017-09-07T14:31:53.083" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14705" PostTypeId="1" AcceptedAnswerId="14708" CreationDate="2014-01-29T14:05:50.780" Score="1" ViewCount="1371" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;What would you do if you want to &lt;strong&gt;remove&lt;/strong&gt; an EcoRI restriction site&#xA;  and introduce BamHI restriction site at apprx. the same location ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;One of the answers in my textbook was : To construct a DNA fragment with the structure:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;5'AATTGGATCC3'&#xA;    3'CCTAGGTTAA5'&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I understand that this would ligate efficiently to the sticky ends generated by EcoRI cleavage and would introduce a BamHI site but I don't understand how this will remove/not regenerate the EcoRI site.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-01-29T17:14:22.113" Title="Removing a restriction site and introducing other at its place" Tags="&lt;dna&gt;&lt;homework&gt;&lt;genetics&gt;&lt;cloning&gt;&lt;restriction-enzymes&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14706" PostTypeId="2" ParentId="14701" CreationDate="2014-01-29T14:16:54.203" Score="2" Body="&lt;p&gt;You could use Jell-O for growing bacteria if you don't have access to agar ! (I have never tried this but I think it should be possible because the gelatin in Jell-O is like agar.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should first sterilize a small knife on a gas stove or with alcohol and then gently rub it on any surface (where you think bacteria are likely to be found ) and then rub it on Jell-O taken in a dish. You should then place it in an environment similar to the one from where you isolated the bacteria. After one or 2 days the bacteria should grow. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For control : You could simply put a plate of Jell-O in the same place but without inoculation of bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disclaimer : I am not a microbiologist and I am not sure this would work but you could give it a try as it will not be really expensive :)&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2014-01-29T14:56:55.273" LastActivityDate="2014-01-29T14:56:55.273" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14707" PostTypeId="1" CreationDate="2014-01-29T14:37:36.180" Score="0" ViewCount="253" Body="&lt;p&gt;I generally don't care for female perfume. I have very sensitive olfactory receptors and in general, I just find perfume overwhelming.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A couple weeks ago, my wife of almost 14 years and I were shopping. As has happened many times before, she asked me to smell a perfume (Play it Rock by Playboy) to see if I liked it. Shockingly, on first whiff, though still overwhelming, I quite liked it. So she bought it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, when she wears it, I &lt;em&gt;do&lt;/em&gt; find the aroma pleasing, however I find myself getting quite agitated, depressed and even overcome with jealousy and paranoia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously, there are lots of psychological factors in play :&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Perfume's primary purpose &lt;em&gt;is&lt;/em&gt; to arouse and attract men&lt;/li&gt;&#xA;&lt;li&gt;She almost only uses it when there &lt;em&gt;are&lt;/em&gt; going to be other men around&lt;/li&gt;&#xA;&lt;li&gt;It &lt;em&gt;is&lt;/em&gt; playboy, subtly indicating the promotion of promiscuity&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;However my internal reactions are so intense I can't help but conclude there something more physiological triggering/intensifying them.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Could the perfume's pheromones be slightly misformulated to cause&#xA;this reaction?&lt;/li&gt;&#xA;&lt;li&gt;Would the same pheromones that arouse a man also inherently trigger the fear of the arousal of others?&lt;/li&gt;&#xA;&lt;li&gt;Is it possible that my pheromone &quot;sense&quot; is also heightened like my sense of smell, causing an abnormal reaction specifically in me?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;Note : I can't find official documentation that the playboy perfumes apply pheromonology (Yes, I did just make up that word), but I have found them listed by other sources in sections of perfumes that do, but Playboy perfumes seem to be priced drastically less than the rest of the pheromoned perfumes.&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5564" LastActivityDate="2014-01-29T23:04:27.897" Title="Can pheromones in perfume be formulated to cause agitation?" Tags="&lt;physiology&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2014-01-31T02:30:37.063" ContentLicense="CC BY-SA 3.0" />
  <row Id="14708" PostTypeId="2" ParentId="14705" CreationDate="2014-01-29T15:44:45.287" Score="3" Body="&lt;p&gt;The recognition site for EcoRI is &lt;code&gt;GAATTC&lt;/code&gt;, and the enzyme cuts after the first base. See this picture from &lt;a href=&quot;https://www.neb.com/products/r0101-ecori&quot; rel=&quot;nofollow noreferrer&quot;&gt;NEB&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yw70C.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The overhang is: AATT, which is supplied by your oligo and fits into the overhang. If the next nucleotide whould be a &lt;code&gt;C&lt;/code&gt; than the site would be recreated, since its a &lt;code&gt;G&lt;/code&gt; its not. The new sequence of the old EcoRI site is &lt;code&gt;GGATTG&lt;/code&gt; which is not recognized by EcoRI. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One technical note: To avoid religation of the digested DNA which carries this site, I would treat it with alkaline phosphatase to remove the phosphate end at the 5' end of the DNA.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-01-29T17:05:45.077" LastActivityDate="2014-01-29T17:05:45.077" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14709" PostTypeId="2" ParentId="14705" CreationDate="2014-01-29T17:00:56.873" Score="3" Body="&lt;p&gt;Just in case you are having difficulty visualising what happens in the answer from @Chris, here are the steps with the linker shown in lower case&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;...NNNNNGAATTCNNNNN...           ds DNA&#xA;...NNNNNCTTAAGNNNNN...&#xA;&#xA;          |&#xA;          V&#xA;&#xA;...NNNNG          AATTCNNNNN...  after EcoRI digestion&#xA;...NNNNCTTAA          GNNNNN...&#xA;&#xA;          |&#xA;          V&#xA;&#xA;...NNNNG      aattggatcc        AATTCNNNNN...   incoming linker&#xA;...NNNNCTTAA      cctaggttaa        GNNNNN...    &#xA;&#xA;          |&#xA;          V&#xA;&#xA;...NNNNGaattggatccAATTCNNNNN...    after ligation&#xA;...NNNNCTTAAcctaggttaaGNNNNN...&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The left hand &quot;EcoRI&quot; is now GAATTG and the right hand &quot;EcoRI&quot; is CAATTC.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-01-29T17:14:22.113" LastActivityDate="2014-01-29T17:14:22.113" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14710" PostTypeId="1" CreationDate="2014-01-29T17:35:42.693" Score="-2" ViewCount="109" Body="&lt;p&gt;In the modern documentary called &quot;Bi the way&quot;, one American geneticist said that if modern American youngsters may as well be functionally bisexual, then some generations ahead Americans could be possibly born with a strong inclination towards the bisexual lifestyle. If we let aside the futuristic theory according which bisexuality should become an evolutionary norm concerning the human species in the long run, then is there a strong bio-sociological possibility that modern societies could transform normally to sexually fluid homogeneous spaces?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the problem is if humans will naturally evolve to a species which is homogeneous in terms of dynamic bisexual differentiation, while in the meantime producing stable behavioral norms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then it has to be decided if society will integrate this procedure naturally or through competition.&lt;/p&gt;&#xA;" OwnerUserId="5567" LastEditorUserId="5567" LastEditDate="2014-01-30T10:27:16.247" LastActivityDate="2014-01-30T10:27:16.247" Title="Could a normative population ever be non-heterosexual?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="3" ClosedDate="2014-01-30T08:39:04.300" ContentLicense="CC BY-SA 3.0" />
  <row Id="14711" PostTypeId="2" ParentId="14710" CreationDate="2014-01-29T17:45:36.187" Score="0" Body="&lt;p&gt;&quot;one American geneticist&quot;?  You realize that that's how you would describe a crackpot, right?  It's not clear to me at all the American youth are &quot;functionally&quot; bisexual.  For one thing, I don't think American high school culture is all that encouraging of boys experimenting with each other, though I can easily imagine straight girls being under pressure to titillate the boys in their group with lesbian displays.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-01-29T17:45:36.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14712" PostTypeId="2" ParentId="14696" CreationDate="2014-01-29T17:49:45.480" Score="2" Body="&lt;p&gt;I think you are correct, &quot;phenotype&quot; really should be what you observe, or measure in the organism, and genotype is what the underlying genetics is, either inferred, or experimentally determined.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Keep in mind, Mendelian genetics makes for great homework exercises, but there are a million more phenotypes that don't fit the Mendelian paradigm than there are ones that do.  Hair color is a phenotype, but it has a lot more genetic components than the simple &quot;one gene, two alleles, one completely dominant over the other&quot; model that Mendel found applied to his 7 phenotypes.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastEditorUserId="5148" LastEditDate="2014-01-29T19:05:00.270" LastActivityDate="2014-01-29T19:05:00.270" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14713" PostTypeId="2" ParentId="7071" CreationDate="2014-01-29T17:54:59.200" Score="2" Body="&lt;p&gt;That &quot;photosynthetic&quot; salamander is clearly an animal, with smaller photosynthetic organism living in it symbiotically.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And yeah, cladistis is the way to go.  You build your tree based on DNA, and see if the data lets you group organisms in a useful way. You might find a few organisms whose genome makes them edge cases, but this salamander is not one of them.  Yeast very clearly falls way outside both categories.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-01-29T17:54:59.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14714" PostTypeId="2" ParentId="14701" CreationDate="2014-01-29T18:17:42.067" Score="1" Body="&lt;p&gt;I see no reason to restrict yourself to jello or buy agar (its not expensive tho).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Every piece of rotting leftover in the fridge pretty much proves that bacteria and fungi exist....  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can always sterilize any food by boiling it (like jello).   A pressure cooker is better than just boiling it. You will have to boil the dishes you are using too.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then expose one dish  to something that contains germs and compare it to a sealed sterile container of the food.   Breathe on it or put your finger in it - that should be enough. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Seal the exposed container up good after exposure tho - it can get messy!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fruit and even coffee will grow the junk you want pretty quick.  Leave it at room temperature for faster results.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-01-29T18:17:42.067" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14715" PostTypeId="1" AcceptedAnswerId="14725" CreationDate="2014-01-29T19:25:40.477" Score="1" ViewCount="322" Body="&lt;p&gt;I am looking for an algorithm that shows the exact coefficients some variables that have on a hospital patient's chronological age versus their biological age. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand a lot of the variables that go into determining ones biological age (i.e. Blood pressure, diet, family history of disease, obesity etc.) but not the amount of impact that it has on the actual scoring of their age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found many sites that will calculate it, however I need the actual variable coefficients and influence in order to produce a proper score for thousands of patient records. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance for your input! &lt;/p&gt;&#xA;" OwnerUserId="5569" LastActivityDate="2014-01-30T08:37:41.947" Title="Determining a patients biological age?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14717" PostTypeId="2" ParentId="14692" CreationDate="2014-01-29T20:27:32.207" Score="3" Body="&lt;p&gt;Auditory information is routed to &lt;a href=&quot;https://en.wikipedia.org/wiki/Cerebral_hemisphere&quot; rel=&quot;nofollow&quot;&gt;cerebral hemispheres&lt;/a&gt; via the &lt;a href=&quot;https://en.wikipedia.org/wiki/Brain_stem&quot; rel=&quot;nofollow&quot;&gt;brainstem&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Midbrain&quot; rel=&quot;nofollow&quot;&gt;midbrain&lt;/a&gt;.  &lt;a href=&quot;https://en.wikipedia.org/wiki/Medial_geniculate_nucleus&quot; rel=&quot;nofollow&quot;&gt;Structures in the midbrain&lt;/a&gt; receive information from both ears and combine it (including differencing it for spatial location) before sending the combined information on to both cerebral hemispheres.  Usually only the left hemisphere interprets the sound for language content, but it is doing so based on the sounds perceived from both ears.  The &lt;a href=&quot;https://en.wikipedia.org/wiki/Corpus_callosum&quot; rel=&quot;nofollow&quot;&gt;corpus callosum&lt;/a&gt; would not be involved in the hearing pathways.  So sound coming from the left ear should work as well as sound from the other if the perception level is adequate and not interfered with by sounds from the other ear.  It is likely the sound perception is somewhat better if both ears are receiving input from the source.  &lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2014-01-29T20:27:32.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14718" PostTypeId="1" CreationDate="2014-01-29T22:26:31.353" Score="1" ViewCount="127" Body="&lt;p&gt;Is perianth part of the sporophyte or gametophyte in liverworts (Marchantiophyta)?&lt;/p&gt;&#xA;" OwnerUserId="5571" LastActivityDate="2014-01-30T15:57:49.080" Title="Botany related question: liverwort sporophyte" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14719" PostTypeId="2" ParentId="14707" CreationDate="2014-01-29T23:04:27.897" Score="1" Body="&lt;p&gt;Insects generate and respond to pheromones. But despite what sci-fi TV might have told you, there is no evidence that humans make or respond to pheromones like that.  Humans don't have that good sense of smell, for one thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fact that you know it's a Playboy brand of perfume is affecting you?  That's obviously not chemical, is psychological.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, historically, perfume was used just as much to mask unpleasant odors as it was to attract anyone.  When men go through puberty, their sweat changes odor.  That's not to attract other men.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this perfume is affecting you emotionally it's psychological, not chemical.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-01-29T23:04:27.897" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14723" PostTypeId="2" ParentId="14710" CreationDate="2014-01-30T07:07:59.490" Score="1" Body="&lt;p&gt;First, your question makes a few assumptions. We can totally run with those assumptions, but I thought two needed to be noted:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;There is a genetic predisposition to bisexuality.&lt;/li&gt;&#xA;&lt;li&gt;This genetic predisposition does not already dominate the population. (Perhaps suppressed by social pressure)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;A genetic predisposition in a small minority, in order to infiltrate and achieve dominance, would need to either:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Directly possess advantages over the absence of said predisposition&lt;/li&gt;&#xA;&lt;li&gt;Be &quot;luckily&quot; carried by hosts which maintain some other advantage in order to infiltrate the population.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Off the top of my head, some direct advantages of bisexuality could be:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Arousal of opposite gender with homo/bisexual acts or displays&lt;/li&gt;&#xA;&lt;li&gt;Maintenance of psychological and physical fitness during short term gender imbalance&lt;/li&gt;&#xA;&lt;li&gt;Self advancement socially regardless of audience's gender&lt;/li&gt;&#xA;&lt;li&gt;Frequent physical activity (exercise) in a sedentary culture.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I'm sure the list could go on. Specifically with this sample of potential advantages, a cultural stigma would likely both :&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Suppress the fulfillment of this predisposition, thus leaving it unhindered in their offspring&lt;/li&gt;&#xA;&lt;li&gt;Produce reproductive hostility toward those who exhibit signs of this predisposition&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Lifting such stigma, and assuming the advantages somehow outweighed the innumerable disadvantages, I would conclude &quot;yes&quot;, it is possible for a society to be birthed where sexual exclusion by gender was not even considered.  That is, there would be no such thing as &quot;sexual orientation&quot; in the populace's mind share.&lt;/p&gt;&#xA;" OwnerUserId="5564" LastActivityDate="2014-01-30T07:07:59.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14724" PostTypeId="2" ParentId="14718" CreationDate="2014-01-30T07:45:02.467" Score="2" Body="&lt;p&gt;I think it should be a part of the gametophyte because it is formed from the fusion of leaves (which are haploid) and protects the archegonium and the developing capsule.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also can be logically thought out. Since it develops before the sporophyte forms , it should be part of the gametophyte.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3776" LastEditDate="2014-01-30T15:57:49.080" LastActivityDate="2014-01-30T15:57:49.080" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14725" PostTypeId="2" ParentId="14715" CreationDate="2014-01-30T08:37:41.947" Score="3" Body="&lt;p&gt;As the definition of biological age is very ambiguous, I propose that to generate an algorithm, you first need to create a quantifiable definition. I submit:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Biological age is a measure indicating what portion of one's calculated life expectancy is already expended, adjusted proportionately for the average life expectancy of their major demographic.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Wow, that's a mouthful! So, let's break it down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Life expectancy is calculated :&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Ascertain a person's major demographic (Geographic residence, Race, Gender and Generation).&lt;/li&gt;&#xA;&lt;li&gt;Find the average life span of that demographic.&#xA;&lt;ul&gt;&#xA;&lt;li&gt;This is negligibly speculative as a living person's Generation has not yet fully perished&lt;/li&gt;&#xA;&lt;li&gt;Statistical outliers, such as infant mortality, are generally excluded from this calculation&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Adjust for known major factors that have accepted statistical impact.&lt;br /&gt;eg:&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Lifestyle&lt;/li&gt;&#xA;&lt;li&gt;Current medical conditions&lt;/li&gt;&#xA;&lt;li&gt;medical history&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Average Life expectancy of subject's demographic was calculated in #2 above.&#xA;&lt;hr&gt;&#xA;So, now let's throw in some sample numbers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Statistical Facts: (totally made up)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Caucasian males living in the France, born in the 1970s have an average life span of 72 years.&lt;/li&gt;&#xA;&lt;li&gt;Exercising 30 minutes or more daily increases life expectancy 6 years&lt;/li&gt;&#xA;&lt;li&gt;Smoking decreases life expectancy 7 years&lt;/li&gt;&#xA;&lt;li&gt;Not smoking increases life expectancy 2 years&lt;br&gt;&lt;sub&gt;Hold on a second?! Wouldn't not smoking already be accounted for in the &quot;Smoking...&quot; section? Well, no, because our demographic sample are all &quot;unknown&quot; so having specific knowledge would statistically change the results in either direction&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;Heart Disease decreases life expectancy 8 years&lt;/li&gt;&#xA;&lt;li&gt;Devout religious affiliation increases life expectancy 6 years.&lt;/li&gt;&#xA;&lt;li&gt;Family history of diabetes decreases life expectancy 2 years.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Two subjects both Caucasian, french males born in 1974 (40 years old chronologically):&lt;br&gt;Their mom's actually shared a labor and delivery room!&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Beavis - known: Smoker with heart disease.&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Butthead - known: Devout Buddhist, very athletic, non smoker with a family history of diabetes&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beavis' life expectancy is 57 (72-7-8)&lt;br&gt;Butthead's life expectancy is 84 (72+6+2+6-2)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beavis has expended 70.2% (40/57) of his life expectancy&lt;br&gt;Butthead has expended 47.6% (40/84) of his life expectancy&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite sharing a birthday:&lt;br&gt;Bevis' biological age is 50.5 years (.702*72)&lt;br&gt;Butthead's biological age is 34.3 years (.476*72)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;Note: It's almost 6 hours past my bedtime, so please excuse any stupid mistakes or miscalculations.  The general concepts are what is important&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="5564" LastActivityDate="2014-01-30T08:37:41.947" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14727" PostTypeId="2" ParentId="7279" CreationDate="2014-01-30T11:07:51.983" Score="2" Body="&lt;p&gt;Gergana is right about the effects of the Guanidine isothiocyanate, but not the details there of.  Guanidine isothiocyanate absorbs strongly at 260 and NOT 230 (guanidine hcl is the one that absorbs strongly at 230).  As such if your RNA is highly contaminated with guanidine isothiocyanate, which is used in at least one buffer in just about every RNA prep kit, your 260/230 is going to be much larger then 2 (also the &quot;concentration&quot; will be artificially high.  So if you are getting a 260/230 of 25 and have a &quot;concentration&quot; of &quot;1000 ng/µL&quot; you may actually have less then 200 ng/µL of RNA and a ton of Guanidine isothiocyanate throwing everything off.)&lt;/p&gt;&#xA;" OwnerUserId="5577" LastActivityDate="2014-01-30T11:07:51.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14728" PostTypeId="2" ParentId="14696" CreationDate="2014-01-30T14:19:06.083" Score="0" Body="&lt;p&gt;The table in your question is a derivative of a punnett square, which shows how different dominant Vs recessive alleles go on to inform phenotype in a logical way; In this case R is dominant red and r is recessive red.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RR = red : rr = not red :  rR / Rr = carrier of red. Red is the phenotype expression (for red hair).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A carrier can pass on either the (R)ed or the (r)ed during meiosis, whereas a totally dominant (R) or totally recessive (r) will pass on just one type, to be combined with the other contributing parent chromosomes during meiosis 1.&#xA;I hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="5579" LastEditorUserId="5579" LastEditDate="2014-01-30T14:25:47.200" LastActivityDate="2014-01-30T14:25:47.200" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14729" PostTypeId="1" AcceptedAnswerId="14732" CreationDate="2014-01-30T14:20:13.607" Score="4" ViewCount="2142" Body="&lt;p&gt;In the process of studying for my upcoming biochemistry exam, I have stumbled over the classification of glycosidic bonds. I want to be able to distinguish $\alpha$- from $\beta$-glycosidic bonds. Unfortunately, even after reading through &lt;a href=&quot;http://www.chem.qmul.ac.uk/iupac/2carb/06n07.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; page, I don't really understand how to go about classifying the bonds in e.g. an oligosaccharide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/l7XKA.jpg&quot; alt=&quot;Oligosaccharide&quot;&gt;&#xA;(&lt;a href=&quot;http://www.elicityl-oligotech.com/client/cache/produit/500_______GLY058-AP_253.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I am inclined to say that both of these anomeric linkages are of type $\alpha$, because the O-glycosidic bond is axial to the respective sugar rings. Is that a correct way of reasoning?&lt;/p&gt;&#xA;" OwnerUserId="5578" LastEditorUserId="3615" LastEditDate="2014-01-30T15:14:42.103" LastActivityDate="2019-10-07T18:53:25.953" Title="Classification of glycosidic anomeric bonds (alpha vs. beta)" Tags="&lt;biochemistry&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14730" PostTypeId="2" ParentId="14696" CreationDate="2014-01-30T16:40:23.000" Score="5" Body="&lt;p&gt;I agree with one of Alan's comments when he says:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;I think this comes down to whether you include being a carrier of a genetic &quot;condition&quot; a part of your phenotype. It's almost a question of semantics&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To expand on this, I would say there are two major definitions of phenotype, and both are employed by geneticists depending on the context.  Definition one is a bit more naive, and I tend to use it when teaching or trying to explain phenotype to a layman: anything you can observe is a phenotype.  Under this definition, having red hair is a phenotype, not having red hair (or, more directly, having black, brown, blonde, etc. hair) is a phenotype, but carrying the recessive gene for red hair is not a phenotype.  I can observe without checking your genome that you do or don't have red hair, I cannot tell without checking your genome that you have one copy of the recessive gene for red hair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Definition two is more complete, and I tend to use it more in a lab research setting: anything that is the OUTCOME of a genotype can be defined as a phenotype.  Again, red hair and not red hair (meaning brown, black, blonde, etc) are outcomes defined by the genotype.  However, depending on the context (let's say I'm interested in understanding heritable potential and not the color of hair) I'd say that the phenotypes would be 1) the ability to pass on red hair to progeny (outcomes of genotypes RR, RN, RN in your example), and 2) lack of ability to pass on red hair to progeny (outcome of genotype NN in your example).  In both cases, the phenotype is the outcome of the underlying genes, I just have to make sure I frame my scientific context appropriately.&lt;/p&gt;&#xA;" OwnerUserId="5580" LastActivityDate="2014-01-30T16:40:23.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14731" PostTypeId="1" CreationDate="2014-01-30T19:01:34.110" Score="1" ViewCount="81" Body="&lt;p&gt;Does pharmacodynamics of Ethinyl estradiol + Drospirenone in OCP pills like (Yaz, Yasminelle etc.) while using isotretinoin (Axotret, Roaccutane etc.) is changed? &lt;strong&gt;Does isotretinoin weakens the OCP pill by any means in any situation?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know about interaction towards incrase of lipids. The only info I have found is this: &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/15116059&quot; rel=&quot;nofollow&quot;&gt;https://www.ncbi.nlm.nih.gov/pubmed/15116059&lt;/a&gt; and results could be translated: &lt;em&gt;we discovered nothing.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="5534" LastEditorUserId="5534" LastEditDate="2014-01-31T17:13:33.863" LastActivityDate="2014-01-31T17:13:33.863" Title="Pharmacodynamics of Ethinyl estradiol + Drospirenone and interactions with istotertinoin" Tags="&lt;pharmacodynamics&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14732" PostTypeId="2" ParentId="14729" CreationDate="2014-01-30T19:14:32.603" Score="1" Body="&lt;p&gt;Here's my interpretation, as far as I can get, which agrees with your deduction that both of the &lt;em&gt;O&lt;/em&gt;-glycosidic bonds involve &amp;alpha; epimers. (If the epimeric carbon has an -OH in the axial direction then this is the &amp;alpha; anomer.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you have the name of this compound?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's hope that a real glycobiologist comes along.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Supplementary&lt;/strong&gt;&#xA;I'm now not sure that it is even possible to assign an anomeric state to the sugar marked as ?. There is no indication in the diagram of the presence of a -CH&lt;sub&gt;2&lt;/sub&gt;OH substituent on the ring - it appears to have a methyl group instead. If that group &lt;strong&gt;was&lt;/strong&gt; a -CH&lt;sub&gt;2&lt;/sub&gt;OH then the putative anomeric C would indeed be in the &amp;alpha; form since it is pointing in the opposite direction from the &quot;-CH&lt;sub&gt;2&lt;/sub&gt;OH&quot; (c.f. the two galactose residues). If ? is a deoxy- derivative of a sugar then it may be that the convention still holds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WYHMm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-01-31T13:20:42.790" LastActivityDate="2014-01-31T13:20:42.790" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14733" PostTypeId="1" AcceptedAnswerId="20320" CreationDate="2014-01-30T20:35:42.027" Score="5" ViewCount="5477" Body="&lt;p&gt;Is there a generally accepted maximum number of times you should split and reseed mammalian culture cells before restarting cultures from new stock?&lt;/p&gt;&#xA;" OwnerUserId="3001" LastActivityDate="2016-08-15T05:53:08.537" Title="What's the recommended maximum passage number for mammalian cells (NCI-H441)?" Tags="&lt;cell-culture&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14734" PostTypeId="1" AcceptedAnswerId="14741" CreationDate="2014-01-30T22:45:53.517" Score="3" ViewCount="275" Body="&lt;p&gt;It seems that &lt;a href=&quot;http://en.wikipedia.org/wiki/Encephalization_quotient&quot; rel=&quot;nofollow&quot;&gt;dolphins have (among?) the highest encephalization quotients found outside of humans&lt;/a&gt;, higher even than chimpanzees. By the &quot;use it or lose it&quot; principle this indicates that intelligence must be particularly valuable in their niche. Why is that? They are predatory and social, and both of those are associated with intelligence, but why are dolphins smarter than other predatory pack animals? For example, is there something about being an air-breathing organism living in water that makes having a high &lt;a href=&quot;http://en.wikipedia.org/wiki/Encephalization_quotient&quot; rel=&quot;nofollow&quot;&gt;EQ&lt;/a&gt; particularly adaptive?&lt;/p&gt;&#xA;" OwnerUserId="4697" LastActivityDate="2014-01-31T11:05:17.580" Title="Why are dolphins so smart?" Tags="&lt;intelligence&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14735" PostTypeId="2" ParentId="14734" CreationDate="2014-01-31T01:00:22.423" Score="5" Body="&lt;p&gt;It might not fully answer your question…&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cost of having a heavy brain&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally speaking, having a heavy organ is an important cost for flying animals, a medium cost for terrestrial animals and a low cost for marine animals. Loosely speaking, the principle &quot;use it or lose it&quot; does not apply with the same strength in all animals in regards to brain weight. If you create a regression between &quot;intelligence&quot; and &quot;need of being intelligent&quot;(supposing it means something!) in terrestrial mammals and add the dolphin on your graph, you might be surprised that the dolphin does not fit on the regression but it might only be due to the fact that they live in water which is much more dense than air so that it is less costly to carry a big brain. So, yes there might have something to do with &quot;living in the water&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Indexes of intelligence&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EQ does not mean intelligence! It is just an index. And we have to understand that people first were happy to think that humans are very smart because they have a big brain but they were terribly confused when they've learned that sperm whales brain weight 8kg! So they tried finding other indexes. EQ is one of them and we're quite happy to use it because it places humans at the first position. But it does not mean that this index is a good representation of intelligence. Some small birds with their tiny brain were shown to be have a spatial memory that is much more efficient that the one of humans for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something else. When looking at these indexes one should not forget that size (or weight) does not equals efficiency. Let's make an analogy with computers. You can have a good software or a good hardware. Big brains are not necessarily very efficient!&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Now, it is still true that dolphins are good at performing many tasks that we link to the concept of intelligence. Dolphins have complex social organization that is probably link with their intelligence. I would tend to think (just a guess) that there are many social factors involved into the evolution of their cognitive abilities. Because the social structure changes as cognitive abilities evolves, it seems to me quite hard to know what factors made that clever individuals were more fit than stupid ones at every moment during the evolution of dolphins. But I might overlook the complexity of the problem. And I honestly never learned any article concerning the role or the evolution of cognitive abilities in dolphins.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-01-31T01:00:22.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14736" PostTypeId="1" AcceptedAnswerId="14792" CreationDate="2014-01-31T01:16:21.963" Score="3" ViewCount="676" Body="&lt;p&gt;I had a homework question that I could not figure out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It states:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A woman has cystic fibrosis in her family and did not want to have a&#xA;  child that suffered from the disease. She and her spouse went for&#xA;  genetic testing and counselling. She tested positive as a carrier and&#xA;  her spouse tested negative, and their first child was born with cystic&#xA;  fibrosis. Explain how this could happen.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This doesn't make sense because the punnet square would be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;\begin{array}{c|c|c}&#xA;  &amp;amp; A  &amp;amp; A  \\&#xA;\hline&#xA;A &amp;amp; AA &amp;amp; AA \\&#xA;\hline&#xA;a &amp;amp; Aa &amp;amp; Aa  &#xA;\end{array}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This says there are no two recessive alleles which can cause  cystic fibrosis.&lt;/p&gt;&#xA;" OwnerUserId="5584" LastEditorUserId="5584" LastEditDate="2014-02-02T22:12:26.437" LastActivityDate="2014-02-04T17:38:41.237" Title="Question about Autosomal Recessive Alleles" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;homework&gt;&lt;chromosome&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14737" PostTypeId="2" ParentId="14736" CreationDate="2014-01-31T03:45:49.747" Score="6" Body="&lt;p&gt;If really cystic fibrose is expressed only in homozygotes, then here are some possible explanations:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mutation&#xA;&lt;ul&gt;&#xA;&lt;li&gt;very improbable&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Autofecundation&#xA;&lt;ul&gt;&#xA;&lt;li&gt;very improbable&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;False Negative when testing the father&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Because of the test False Negative Rate. @kmm made a very interesting comment below. He said that according to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2014829&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; 75% of the mutations coding for disease correspond to one pattern (3 base pair deletion). The other 25% of the mutations coding for disease might not be detected in the standard test. If so, it is very likely that a the test conducting on the father was a false negative. It would be worth further investigate the test that are usually performed to confirm this.&lt;/li&gt;&#xA;&lt;li&gt;Because of human error. The laboratory operator might accidentally switch two samples or accidentally introduce stranger DNA before PCR (assuming the test is performed through sequencing)&lt;/li&gt;&#xA;&lt;li&gt;I have no idea concerning the probability for such thing to occur! &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;trisomy&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The assumes that a trisomic that have two recessive allele coding for disease and on dominant allele coding for health yield to a individual expressing the disease!&lt;/li&gt;&#xA;&lt;li&gt;The gene for cystic fibrose is on chromosom 7. Trisomy 7 is extremely rare if I'm not mistaken.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;The father is not the father!&#xA;&lt;ul&gt;&#xA;&lt;li&gt;According to different studies between 5% and 20% of the people are not fathered by the man they think is their dad.&lt;/li&gt;&#xA;&lt;li&gt;According to &lt;a href=&quot;http://www.cfmedicine.com/htmldocs/CFText/genetics.htm&quot; rel=&quot;nofollow&quot;&gt;this source&lt;/a&gt; the frequency of the disease is 1/2500 in UK. Assuming Hardy-Weinberg equilibrium the frequency of the allele coding for disease should be $p=0.02$.&lt;/li&gt;&#xA;&lt;li&gt;The probability that the baby comes from another man and that the baby express the disease is $$a \cdot \left(\frac{2\cdot p\cdot (1-p)}{4} + \frac{p^2}{2}\right)$$, where $a$ is the probability that the baby was fathered by another man (let's say 10%) and $p$ is the frequency of the allele coding for the disease (0.02). The division by 2 and 4 are due to the probability that the (real) father and the mother transmit both the alleles coding for the disease.  This probability equals $$0.1 \cdot \left(\frac{2\cdot 0.2\cdot (1-0.2)}{4} + \frac{0.2^2}{2}\right) = 0.01$$ This seems to be from far the most likely explanation! Note: this assumes that the mother is heterozygote (does not express the disease) otherwise, the probability would be 0.02.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-02-04T17:38:41.237" LastActivityDate="2014-02-04T17:38:41.237" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14739" PostTypeId="1" AcceptedAnswerId="14742" CreationDate="2014-01-31T08:41:49.097" Score="0" ViewCount="492" Body="&lt;p&gt;I read an older article where they talk about species being strictly &lt;em&gt;monosexual&lt;/em&gt; as opposite of being &lt;em&gt;hermaphrodite&lt;/em&gt;, etc&lt;a href=&quot;http://link.springer.com/article/10.1007/BF00373213&quot; rel=&quot;nofollow&quot;&gt; [1]&lt;/a&gt;. After an extensive googling and reading about how everybody has to be at least a little bit homosexual, I am still not clear about this. Is monosexual still a valid term to be used in biology? If not, what is the correct term referring to a species that has separate sexes over the entire life-cycle? &lt;/p&gt;&#xA;" OwnerUserId="3302" LastActivityDate="2014-01-31T11:08:26.477" Title="Is &quot;monosexual&quot; still a valid term in biology?" Tags="&lt;reproductive-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14740" PostTypeId="1" CreationDate="2014-01-31T09:34:32.527" Score="4" ViewCount="1995" Body="&lt;p&gt;I'm looking for the whole genome sequences of several human cell lines, e.g., A549 or Ea.hy.926. Is there a database specifically dedicated to human cell lines?&lt;/p&gt;&#xA;" OwnerUserId="852" LastActivityDate="2014-08-07T17:43:35.687" Title="Is there a database containing sequences of human cell lines?" Tags="&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14741" PostTypeId="2" ParentId="14734" CreationDate="2014-01-31T11:05:17.580" Score="2" Body="&lt;p&gt;It's less about the brain size, I think, more about the metabolic cost of brains. Brains are among the most costly organs to keep what it comes to oxygen demand. Air-breathing increases available oxygen for the body, hence mammals have larger brains that for example fish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In diving animals the metabolic cost of brains is connected to the diving time (can't find the reference at the moment). Sperm whales shut down parts of their brains on long dives and do not have particularly active brains in general. Dolphins are mostly shallow diving animals. Maybe the selection favors higher brain metabolism potentially increasing the ability to catch prey and avoid predators? Pure speculation, though.&lt;/p&gt;&#xA;" OwnerUserId="3302" LastActivityDate="2014-01-31T11:05:17.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14742" PostTypeId="2" ParentId="14739" CreationDate="2014-01-31T11:08:26.477" Score="2" Body="&lt;p&gt;I suspect &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Monosexuality&quot; rel=&quot;nofollow&quot;&gt;monosexual&lt;/a&gt;&quot; is a term recruited in sociology, psychology and/or medicine. I haven't ever heard of it in application to biological questions. It's a behavioral habit and doesn't seem to be directly related to the (biological) opposition &quot;separate sexes&quot; vs &quot;hermaphroditism&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In biology:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Animals&lt;/strong&gt; can either be &lt;em&gt;gonochoristic&lt;/em&gt; (separate sexes) or &lt;em&gt;hermaphroditic&lt;/em&gt;. If an animal species reproduces without gametes it's called asexual (in animals asexual reproduction is rarely the only way of propagation), and if only females are present which give birth without fertilization, they are called parthenogenetic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In some cases different modes of reproduction are utilized by different stages (alternate generations) or even phases (larva vs adult, young vs old). In other cases in populations coexist males and hermaphrodites or males and parthenogenetic females. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mammals, including humans, are (nearly) perfect examples of gonochoristic animals: only a male and a female together can produce offspring. If someone is homosexual (it refers to behavior only), he is a dead end in this respect.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-01-31T11:08:26.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14743" PostTypeId="2" ParentId="14334" CreationDate="2014-01-31T13:47:21.227" Score="2" Body="&lt;p&gt;I think at @fileunderwater provides a good explanation of the basics math behind it, and some good references. I would like to go more into detail about the modeling decisions and benefits of assuming weak selection and why it is done in the literature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you are making evolutionary models, especially one in evolutionary game theory, the first place is to &lt;strong&gt;start with a differential equations model of inviscid populations&lt;/strong&gt; (this usually means that you assume very large population size). These models often result in dynamics of the form $\dot{x}_i = x_if_i(\vec{x})$ where $f_i$ is a non-linear function corresponding to the relative fitness but where the non-linearity depends on the strength of selection. Making a weak-selection argument, often &lt;strong&gt;allows you to come close to linearizing $f_i$ using Taylor expansion&lt;/strong&gt;. This reducese your equations to a form like $\frac{dx_i}{dt} = x_i(\vec{c}_i^T\vec{x} - \phi)$ where $\phi$ is an average fitness. Although the transients of this dynamic are still complicated, the equilibrium is usually relatively easy to analyze and reduces to looking at the matrix $C = [\vec{c}_i^T]_{1 \leq i \leq n}$ with its columns given by your linearization of the $f_i$s.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, this is only a first step, and the current trend in the literature is to &lt;strong&gt;move to a setting where you have &lt;a href=&quot;http://egtheory.wordpress.com/2012/03/21/spatial-structure/&quot; rel=&quot;nofollow noreferrer&quot;&gt;spatial structure&lt;/a&gt;&lt;/strong&gt;. Here, weak selection gives you a further bonus because you can use it to separate the timescales of local (dominated by the constant term) and global (dominated by first-order in $w$ -- the selection strength) network dynamics. This allows you to use the powerful &lt;a href=&quot;https://cstheory.stackexchange.com/q/11229/1037&quot;&gt;pair-approximation technique&lt;/a&gt;. A great example of its use is &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022519306002426&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ohtsuki &amp;amp; Nowak's (2006)&lt;/a&gt; solution to the evolutionary dynamics of games on &lt;a href=&quot;http://egtheory.wordpress.com/2012/03/29/random-regular-graphs/&quot; rel=&quot;nofollow noreferrer&quot;&gt;$k$-regular random graphs&lt;/a&gt; (you can find a &lt;a href=&quot;http://egtheory.wordpress.com/2012/10/25/ohtsuki-nowak-transform/&quot; rel=&quot;nofollow noreferrer&quot;&gt;brief overview here&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The final settings where this is useful is for &lt;strong&gt;studying the interaction of mutation and selection in finite populations&lt;/strong&gt;. In this case, weak selection allows you to look at the selective force as a small perturbation of the mutator-balanced steady state. In the setting of EGT this rquires you to define some new solution concepts for what it means for one strategy to be &quot;better&quot; than another but then &lt;a href=&quot;http://egtheory.wordpress.com/2012/10/18/finite-pop-risk-dom/&quot; rel=&quot;nofollow noreferrer&quot;&gt;some interesting connections&lt;/a&gt; (see &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022519308006127&quot; rel=&quot;nofollow noreferrer&quot;&gt;Antal, Nowak, &amp;amp; Traulsen (2009)&lt;/a&gt; for more) and &lt;a href=&quot;http://egtheory.wordpress.com/2012/10/22/evolutionary-games-in-finite-inviscid-populations/&quot; rel=&quot;nofollow noreferrer&quot;&gt;very general analysis&lt;/a&gt; of the mutation-selection equilibrium can be done (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022519309000721&quot; rel=&quot;nofollow noreferrer&quot;&gt;Antal et al., 2009&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2017-04-13T12:32:32.393" LastActivityDate="2014-01-31T13:47:21.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14744" PostTypeId="2" ParentId="14395" CreationDate="2014-01-31T16:12:27.033" Score="1" Body="&lt;p&gt;There are various factors which decide the dominance of one gene over the other. Owing to the complex biochemical pathways it is difficult to predict which gene is dominant unless we know exactly how the gene is translated to protein and how the protein interacts with the body.&#xA;These are the few answers that could help:-&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/7401/what-makes-a-gene-dominant-or-recessive?rq=1&quot;&gt;What makes a gene dominant or recessive&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/11009/what-determines-if-a-gene-is-dominant-or-recessive?rq=1&quot;&gt;What determines if an allele is dominant or recessive?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;As for your question;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two genes:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;D- The allele which is dominant&lt;/li&gt;&#xA;&lt;li&gt;d-The allele which is recessive.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;A &lt;strong&gt;&lt;em&gt;recessive gene&lt;/em&gt;&lt;/strong&gt; is a gene that is nonfunctional or expresses its characteristic phenotype in presence of an identical allele.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a person to have &lt;a href=&quot;http://www.biology.arizona.edu/human_bio/problem_sets/blood_types/rh_factor.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rh negative blood&lt;/a&gt; group he must inherit 'd' allele from both the parents as it is a recessive trait.And as @swbarnes2 mentioned in the comments 'd' allele is more common in &lt;a href=&quot;http://www.madsci.org/posts/archives/2001-03/985200157.Ge.r.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;European&lt;/a&gt; countries leading to a wide range of population possessing Rh negative blood groups.&lt;/p&gt;&#xA;" OwnerUserId="5589" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-02-02T14:34:37.120" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14745" PostTypeId="1" AcceptedAnswerId="14869" CreationDate="2014-01-31T16:39:08.873" Score="3" ViewCount="142" Body="&lt;p&gt;And would a very accurate sensitive system for detecting circulating tumor cells (which detects 1 cell per 50 billion) be useful as a screening tool ?&lt;/p&gt;&#xA;" OwnerUserId="5591" LastEditorUserId="1320" LastEditDate="2014-02-01T13:09:26.193" LastActivityDate="2016-02-03T12:56:04.967" Title="At what cancer stage do tumors release circulating tumor cells into the blood?" Tags="&lt;cancer&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14747" PostTypeId="1" AcceptedAnswerId="14772" CreationDate="2014-01-31T22:07:04.150" Score="4" ViewCount="116" Body="&lt;p&gt;I am not by any means a biologist - so go easy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would be a method for determining whether or not a patient has cancer based only on a genomic sequence?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt; Thanks for the help in revising the questions.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;What information is extractable once a genome has been sequenced?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is it possible to derive whether or not a person has cancer based only on the genome which was sequenced? i.e. Are there anomalies to look out for to detect the cancer.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5594" LastEditorUserId="5594" LastEditDate="2014-02-01T21:45:30.913" LastActivityDate="2014-02-01T22:33:40.863" Title="Detecting cancer or a genetic predisposition based on DNA sequencing" Tags="&lt;dna&gt;&lt;dna-sequencing&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14748" PostTypeId="2" ParentId="14747" CreationDate="2014-01-31T23:24:07.250" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;When sequencing a human's (i hope im stating this correctly) genome is&#xA;  there a difference between the genome before and after the patient is&#xA;  found to have developed some sort of cancer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you are asking if cancer cells have an altered genome as compared to the rest of the organism, yes, this usually is the case.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What would be a method for determining whether or not a patient has&#xA;  cancer based only on a genomic-sequence.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you scrape some cheek cells to do DNA sequencing, you will know what the sequence is in those cheek cells, and you can figure that most of the cells in the rest of the body have that same sequence.  But if some, say, brain cells have acquired genetic errors causing them to start going haywire, that won't magically change the DNA in your cheek cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A genetic predisposition could be identified...if scientists had determined one.  For instance, Angelina Jolie got a double mastectomy because both her family history and her genetics strongly indicated that she would get breast cancer otherwise.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastEditorUserId="5148" LastEditDate="2014-01-31T23:29:15.577" LastActivityDate="2014-01-31T23:29:15.577" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14749" PostTypeId="1" AcceptedAnswerId="14761" CreationDate="2014-02-01T00:49:37.767" Score="2" ViewCount="98" Body="&lt;p&gt;I am reading about a paper about inferencing pathway information in cancer cells. Authors refer to &lt;a href=&quot;http://en.wikipedia.org/wiki/HER2/neu&quot; rel=&quot;nofollow&quot;&gt;ERBB2&lt;/a&gt; as a gene and a pathway. I don't have solid biology background. What exactly means when we refer to ERBB2 as a pathway? Does it refer to activity of a protein encoded by ERBB2?&lt;/p&gt;&#xA;" OwnerUserId="4791" LastActivityDate="2014-02-01T10:31:33.583" Title="Connection between genes and pathways" Tags="&lt;genetics&gt;&lt;cell-biology&gt;&lt;bioinformatics&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14750" PostTypeId="2" ParentId="14749" CreationDate="2014-02-01T01:00:38.157" Score="2" Body="&lt;p&gt;ERBB2 appears to be a (tyrosine kinase) receptor; that is, it lives in the cell membrane; with a part that sticks outside of the cell, and part that sits inside.  When the right molecule attaches to the outside part, the inside part changes shape, which alters its function, causing it to start phosphorylating other proteins, which alters their functions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the ERBB2 pathway is the set of genes/proteins whose behavior is affected by ERBB2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Google &quot;ERBB2 pathway&quot; and &quot;tyrosine kinase receptor&quot; for more info.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-02-01T01:00:38.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14751" PostTypeId="2" ParentId="38" CreationDate="2014-02-01T02:25:23.700" Score="0" Body="&lt;p&gt;To save cost, you can buy spin columns alone from suppliers such as Syd Labs (&lt;a href=&quot;http://www.sydlabs.com/spin-column-for-plasmid-miniprep-p110.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.sydlabs.com/spin-column-for-plasmid-miniprep-p110.htm&lt;/a&gt;) and make home-made buffers. The suppliers normally provide the buffer recipe. &lt;/p&gt;&#xA;" OwnerUserId="5595" LastActivityDate="2014-02-01T02:25:23.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14752" PostTypeId="2" ParentId="14560" CreationDate="2014-02-01T02:57:20.013" Score="1" Body="&lt;p&gt;As @WYSIWYG pointed out, having the indel difference in the &lt;a href=&quot;http://link.springer.com/protocol/10.1007/978-1-62703-493-7_11&quot; rel=&quot;nofollow&quot;&gt;3' end&lt;/a&gt; can be &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0198885912004168&quot; rel=&quot;nofollow&quot;&gt;informative&lt;/a&gt;, but I'm having a harder time finding evidence in the middle of the primer.  Putting the mutation/indel at the &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1537-2995.2006.00992.x/abstract&quot; rel=&quot;nofollow&quot;&gt;3' end&lt;/a&gt; will change the ΔCT.  To &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2607568/&quot; rel=&quot;nofollow&quot;&gt;do it well&lt;/a&gt;, you need wide coverage on your mutation site. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that it is possible that there could be a difference with a mismatch in the middle of a primer, but it wouldn't be as obvious as if it were closer to the 3' end.  Unless there was some serious reason why you couldn't put it there (ie Tm below 45 on the reference) that sounds like poor primer design.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will note I am certainly not a qPCR expert, and I don't think the question has been directly researched (as you surmised).  Again when I've looked for Indels before (was doing some interesting stuff with HLA types...) we used larger primers for the qPCR.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this doesn't answer your question satisfactory, is there an initial reference you would have us look at?  I imagine things like good quenching and other factors could pull out some significance when comparing two templates (one with indel one without), but again, it's kind of odd to put the mutation in the middle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit to comments:&#xA;1: I think the Cq delay is going to depend on things like length, sequence, and mutation.  There may be a grand scheme formula/algorithm to predict the delay, but I don't know of one, and I couldn't find it if it does exist.  Most of the graphs and differences I've seen have been big enough that it convinced me that it was significant.  I don't know if this is like flow where you can sit and argue all day about the biological relevance of 40% to 30% of a particular group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2: Sorry I didn't have time to come in and give an adequate summery of them.  They are, as you pointed out, tangential to what you're trying to do, but do in fact address the problem through their methods.  I will attempt a better summery as I have time (I've got a grant on I'm trying to get done by Tuesday, so probably after that).  If you have any clarifications to the question to add, please do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3: This may have grown from the general perception that it was needed, and that I aim for the highest Tm I can generally manage without structure problems being introduced.  I also have the luxury of not needing to worry over the cost of ulta-mers.  It also could have come from history of working in &lt;a href=&quot;https://en.wikipedia.org/wiki/Bacterial_artificial_chromosome&quot; rel=&quot;nofollow&quot;&gt;BACs&lt;/a&gt; years ago.  Longer primers always increased my success rates when I was knocking out cassettes.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2014-02-02T04:01:20.823" LastActivityDate="2014-02-02T04:01:20.823" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="14753" PostTypeId="1" AcceptedAnswerId="14754" CreationDate="2014-02-01T03:35:25.150" Score="2" ViewCount="494" Body="&lt;p&gt;From &lt;a href=&quot;http://www.mbari.org/staff/conn/botany/phytoplankton/phytoplankton_diatom_asexual.HTM&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; we can see that diatoms reduce their size after asexual reproduction.&lt;img src=&quot;https://i.stack.imgur.com/lgbar.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This would ultimately lead to nonviable small size. Is there any mechanism to avoid this ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-02-01T03:36:53.610" Title="Reduction of size in diatoms due to asexual reproduction" Tags="&lt;reproduction&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14754" PostTypeId="2" ParentId="14753" CreationDate="2014-02-01T03:36:53.610" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;The ability to reproduce sexually is closely associated with cell size&#xA;  of the diatom. It is the most prevalent method of restoring cell size,&#xA;  and it is often triggered when the size of a cell is less than a&#xA;  critical level (usually smaller than half of the original size for&#xA;  most species).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source : &lt;a href=&quot;http://wgbis.ces.iisc.ernet.in/biodiversity/sahyadri_enews/newsletter/issue26/article1/chap4.htm&quot; rel=&quot;nofollow&quot;&gt;Sexual reproduction in diatoms&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-02-01T03:36:53.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14755" PostTypeId="1" AcceptedAnswerId="14757" CreationDate="2014-02-01T03:54:20.460" Score="3" ViewCount="573" Body="&lt;p&gt;I'm taking a bioinformatics class and at this point we are just going over basic stuff about molecular biology. Half of the class is doing reading/research on our own, so there isn't much class time to ask questions or go over examples. One topic is transition/transversion ratio, and I'm not 100% sure I'm understanding it. Do you just compare the first symbol of string 1 to the first symbol of string 2? What if the two symbols you're comparing are the same? Do you just ignore it? Let's say string 1 is ACGATG and string 2 is TCAGTG. Would the ratio be 2/1?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are the comparisons I made.&#xA;Transitions: G--&gt;A, A--&gt;G,&#xA;Transversions: A--&gt;T, &#xA;Neither: C--&gt;C, T--&gt;T, G--&gt;G&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this correct or am I completely on the wrong path?&lt;/p&gt;&#xA;" OwnerUserId="5596" LastEditorUserId="3615" LastEditDate="2014-02-01T04:03:06.040" LastActivityDate="2014-02-01T08:29:21.887" Title="Transition/Transversion ratio" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14756" PostTypeId="1" CreationDate="2014-02-01T04:01:08.263" Score="2" ViewCount="63" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Suppose you are able to observe under a microscope the total number&#xA;  of meiotic divisions occurring in one gonad of a given individual and to&#xA;  outnumber exactly the crossovers between two given loci for which that&#xA;  individual is dihybrid. If the frequency of these particular&#xA;  crossovers is 100% (that is to say that every meiosis exhibits one&#xA;  crossing over between the two loci you consider) you anticipate that&#xA;  the total percentage of recombinant gametes would be equal to: &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't understand how to solve this.&lt;/p&gt;&#xA;" OwnerUserId="4058" LastEditorUserId="3776" LastEditDate="2014-02-01T14:16:06.010" LastActivityDate="2014-02-01T14:16:06.010" Title="recombinant gametes" Tags="&lt;homework&gt;&lt;reproduction&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14757" PostTypeId="2" ParentId="14755" CreationDate="2014-02-01T08:29:21.887" Score="2" Body="&lt;p&gt;You are almost on the right path.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This schematics from Wikipedia is quite clear in my opinion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/3/35/Transitions-transversions-v3.png/480px-Transitions-transversions-v3.png&quot; alt=&quot;Transitions and transversions&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Slightly more chemical explanation (which you do not necessarily need to do bioinformatics, however I think it is always better to know exactly what you are dealing with outside of the computer!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea is that you have four basic nucleotides: cytosine and thymine are called &lt;strong&gt;pyrymidines&lt;/strong&gt; and adenine (A) and guanine (G) which are called &lt;strong&gt;purines&lt;/strong&gt;. Pyrymidines are characterised by a 6 carbon azo-ring which is called a &lt;em&gt;pyridine&lt;/em&gt;, while purines have a larger double ring, formed by a pyridine ring + an imidazole ring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A transition is defined as the passage purine -&gt; purine or pyrimidine -&gt; pyrimidine.&lt;br&gt;&#xA;A transversion is the passage purine -&gt; pyrimidine, or viceversa.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These mutations can be caused for instance by certain chemicals, such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Alkylation#Alkylating_agents&quot; rel=&quot;nofollow noreferrer&quot;&gt;alkylating agents&lt;/a&gt;, or by &lt;a href=&quot;http://en.wikipedia.org/wiki/Ionizing_radiation&quot; rel=&quot;nofollow noreferrer&quot;&gt;ionizing radiations&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;In your specific example, given the sequences&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; ACGATG &#xA; TCAGTG&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;You have 3 mutations:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;A -&amp;gt; T  &#xA;G -&amp;gt; A&#xA;A -&amp;gt; G&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So you have 1 transversion (from the purine A to the pyrimidine T) and two transitions (between the purines A and G).&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.930" LastActivityDate="2014-02-01T08:29:21.887" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14758" PostTypeId="2" ParentId="13853" CreationDate="2014-02-01T08:44:06.190" Score="-3" Body="&lt;p&gt;Biology arises when some molecules begin copying themselves with a certain amount of error: not too much error, or there would be no heritability; but SOME error, or else there would be no evolution at all. Copying, copying, a few molecules become a multitude, and evolution spreads in all directions, to the more and to the less complex. But when a new level of complexity arises, it usually allows a new size, and a bigger organism can, for instance, eat a smaller organism. Once this level is achieved, it tends to be mantained. Again some copies will lead to smaller lineages, but the big ones have founded a niche that will not disappear by itself (it may take an asteroid). So, looking up close, evolution leads to diversity, not only to higher complexity. But since small complexity already existed, and bigger complexity is something new, we tend to perceive evolution as creating complexity - which is not a false point of view.&lt;/p&gt;&#xA;" OwnerUserId="4821" LastActivityDate="2014-02-01T08:44:06.190" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14759" PostTypeId="1" CreationDate="2014-02-01T10:15:53.787" Score="0" ViewCount="78" Body="&lt;p&gt;What are the health effects of being exposed to a very strong electromagnetic field caused by  two resonating superconductive coils (not static magnets) for a period of years?&lt;/p&gt;&#xA;" OwnerUserId="5599" LastEditorUserId="1320" LastEditDate="2014-02-01T13:10:24.463" LastActivityDate="2014-02-05T19:57:09.927" Title="What is the impact of prolonged electromagnetic exposure on human health?" Tags="&lt;human-biology&gt;&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14761" PostTypeId="2" ParentId="14749" CreationDate="2014-02-01T10:31:33.583" Score="1" Body="&lt;p&gt;ErbB2 is a receptor tyrosine kinase. This is a class of receptors, which are located in the membrane ob the cell and which pass signals from the outside of the cell into it, so it can for example react to changing conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ErbB2 (which is also called HER2, which translates into &quot;human epidermal growth factor receptor 2&quot;) normally reacts when it binds it ligand &lt;a href=&quot;http://en.wikipedia.org/wiki/Epidermal_growth_factor&quot; rel=&quot;nofollow noreferrer&quot;&gt;epidermal growth factor&lt;/a&gt; (EGF). Upon binding, ErbB2 changes its conformation, phosphorylates itself (meaning it adds phosphogroups to specific amino acids of the protein) which leads phosphorylation (and therefore activation) of other proteins, which finally results in changed expression of genes, which are involved in cellular proliferation, differentiation, and survival (see this reference: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15142631&quot; rel=&quot;nofollow noreferrer&quot;&gt;Review of epidermal growth factor receptor biology.&lt;/a&gt;&quot;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leads to the second part of your question what pathway means in this context: The sequence of different molecules which start at the receptor and finally induces changes of gene expression in the cells nucleus are called pathway. For members of the Erb-family of receptors there are different possibilites, but the picture below shows how this works in principle:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TDaWd.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image is from the Wikipeadiapage on &lt;a href=&quot;http://en.wikipedia.org/wiki/Epidermal_growth_factor_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;EGFR&lt;/a&gt;.&#xA;You can see, that the ligand binds extracellular to the receptor, which is then phosphorylated, and then passes the signal downstream for example to Ras-Raf-Mek-Erk and then into the nucleur (in fact, activated Erk enters the nucleus).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This cascade also shows, why these receptors are often mutated in cancers: They are involved in the regulation of genes important for survival, proliferation and differentiation, which is very important for cancer cells. ErbB2 for example is mutated in about 30% of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23320171&quot; rel=&quot;nofollow noreferrer&quot;&gt;breast cancers&lt;/a&gt;. These mutations often lead to a constitutive active receptor which is permanently phosphorylated independent of ligand binding. This leads to a permanent activation of the downstream pathways which is obviously not a good thing, since these genes are normally under a very tight regulation.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-01T10:31:33.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14763" PostTypeId="1" AcceptedAnswerId="14765" CreationDate="2014-02-01T13:22:59.463" Score="5" ViewCount="433" Body="&lt;p&gt;I have read that vitamin C is highly sensitive to light. So, how could parsley, for instance keep its vitamin C as it's flooded with sunlight?&lt;/p&gt;&#xA;" OwnerUserId="5603" LastEditorUserId="3776" LastEditDate="2014-02-01T14:13:09.730" LastActivityDate="2014-02-01T15:13:12.097" Title="Why plants (eg. parsley) can keep vitamin C despite all the sun?" Tags="&lt;biochemistry&gt;&lt;plant-physiology&gt;&lt;vitamins&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14765" PostTypeId="2" ParentId="14763" CreationDate="2014-02-01T15:13:12.097" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://prr.hec.gov.pk/Chapters/529S-2.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;UV light promotes the photo-oxidation of ascorbic acid (AsA) to dehydroascorbic acid (DHA).&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TsmQv.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Glutathione_dehydrogenase_(ascorbate)&quot; rel=&quot;nofollow noreferrer&quot;&gt;DHA can be reduced to AsA by a specific dehydrogenase using reduced glutathione as reductant.&lt;/a&gt; I'm pretty sure that all cells are able to carry out this recycling of ascorbate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, in plants it appears that &lt;a href=&quot;http://www.plantphysiol.org/content/early/2011/02/28/pp.110.171918?cited-by=yes&amp;amp;legid=plantphysiol;pp.110.171918v1&quot; rel=&quot;nofollow noreferrer&quot;&gt;ascorbate acts as an electron donor to photosystem II&lt;/a&gt; (which is equivalent to it being oxidised).&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-01T15:13:12.097" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14766" PostTypeId="1" CreationDate="2014-02-01T15:52:35.640" Score="0" ViewCount="933" Body="&lt;p&gt;I found this paragraph in my study materials about implantation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Original&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Simplest trophoblast excretes trypsin related substances and embedding consists of 3 stages:&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;The blastocyst (composed of cytotrophoblast and embryoblast) stick to the uterine wall&lt;/li&gt;&#xA;  &lt;li&gt;Enzymes digest nische (little hole in the endometrium) to the functional layer and the blastocyst deepens in it. The nische is a closed and destroyed functional layer, in it tissue and blood is used for trophic (called a nischtrophic way of feeding)&lt;/li&gt;&#xA;  &lt;li&gt;Implantation ends in 13½ day when the functional layer covers the blastocyst.&#xA;  Implantation normally takes place in anterior and posterior wall of uterus, sometimes in superior or fundus wall.&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My suggestion for corrections&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Syncitiotrophoblast excretes Digestive Enzymes and embedding consists of 3 stages:&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;The blastocyst (composed of cytotrophoblast and embryoblast) stick to the uterine wall&lt;/li&gt;&#xA;  &lt;li&gt;Syncytiotrophoblast expresses digestive enzymes which dig a little hole (nische) into endometrium. The hole is usually filled with maternal tissue (so closed) and blood used by the conceptus for histotrophic feeding (nischtrophic way of feeding)&lt;/li&gt;&#xA;  &lt;li&gt;Implantation should end in 13½ day when the endometrium covers the blastocyst.&#xA;  Implantation normally takes place in anterior and posterior wall of uterus between glands of the hypertrophic endometrium, sometimes in superior or fundus wall.&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I cannot accept the phrase &lt;strong&gt;simplest trophoblast&lt;/strong&gt; and the use of the words &lt;strong&gt;trypsin related substances&lt;/strong&gt;. Really, how can you get trypsin without pancreas? I would not use the word trypsin although the enzymes may have some structural similarities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How would you reformulate the paragraph?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="107" LastEditDate="2014-02-02T17:52:34.520" LastActivityDate="2014-02-02T17:52:34.520" Title="Some trophoblast excreting digestive enzymes in implantation" Tags="&lt;embryology&gt;&lt;implantation&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14767" PostTypeId="1" AcceptedAnswerId="14768" CreationDate="2014-02-01T17:57:09.517" Score="1" ViewCount="180" Body="&lt;p&gt;I have a problem in my bioinformatics class that I thought I was doing right, but someone else is getting a different answer. Here is the problem:  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Given the following DNA sequence, 5'-GGATCGTGCCACCATCCACCATCGTTA-3', if two introns are in bases 3-9 and 15-22, what is the mRNA transcribed? Give the answer 5' to 3'. Note that the first base is base 1.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And here are the steps that I took:  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;5'-GG &lt;strong&gt;ATCGTGC&lt;/strong&gt; CACCA &lt;strong&gt;TCCACCAT&lt;/strong&gt; CGTTA-3' (remove the bolded)&lt;/li&gt;&#xA;&lt;li&gt;5'-GGCACCACGTTA-3' (new string)&lt;/li&gt;&#xA;&lt;li&gt;take reverse complement&lt;/li&gt;&#xA;&lt;li&gt;swap T's with U's&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Is this correct? Or where am I going wrong?&lt;/p&gt;&#xA;" OwnerUserId="5596" LastEditorUserId="1306" LastEditDate="2014-02-02T14:14:17.050" LastActivityDate="2014-02-02T14:14:17.050" Title="Transcribing DNA to mRNA with introns" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14768" PostTypeId="2" ParentId="14767" CreationDate="2014-02-01T18:30:25.517" Score="4" Body="&lt;p&gt;I think the only place you are going wrong is in getting confused about strands (&quot;take reverse complement&quot;).&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;5'-GGATCGTGCCACCATCCACCATCGTTA-3'   &amp;lt;&amp;lt; coding strand&#xA;3'-CCTAGCACGGTGGTAGGTGGTAGCAAT-5'   &amp;lt;&amp;lt; template strand&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The coding strand has the &lt;strong&gt;same sequence&lt;/strong&gt; as the transcribed RNA (apart from T&gt;U), so the primary transcript is:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;5'-GGAUCGUGCCACCAUCCACCAUCGUUA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Then, positions of introns:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;5'-GG AUCGUGC CACCA UCCACCAU CGUUA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and after splicing:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;5'-GGCACCACGUUA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-01T18:30:25.517" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14769" PostTypeId="2" ParentId="14766" CreationDate="2014-02-01T19:00:40.087" Score="2" Body="&lt;p&gt;I have no idea what is meant by 'the simplest trophoblast'. I did, however, find this review, pointing to a role of proteases in the implantation process:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Salamonsen L.A. Salamonsen and Nie, G. (2002) Proteases at the Endometrial–Trophoblast Interface: Their Role in Implantation. Reviews in Endocrine and Metabolic Disorders, 3:133-143&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;which discusses the roles in implantation of three classes of proteases : matrix metalloproteinases, serine proteinases and cystein proteinases. The reference to 'trypsin-like' presumably relates to the serine proteases. The review reports the results of a number of gene knockout experiments in mice in which genes for individual proteases have been disrupted which indicate that no single enzyme is identified as being essential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Referring to &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Afonso S et al (1997) The expression and function of cystatin C and cathepsin B and cathepsin L during mouse embryo implantation and placentation. Development 124:3415-3425.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;the authors of the review state that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[they] demonstrated that cysteine proteases play a critical role in implantation. Cathepsin B mRNA was expressed by mouse trophoblast throughout the invasive period (days 5.5±10.5) while the proteins for cathepsins B and L were localized to the mature invasive trophoblast giant cells; activity of these enzymes was also demonstrated. Cathepsin L was also present within the stroma particularly in the lateral decidualizing zone. Cystatin C, the major inhibitor of cathepsins, was shown to be a major product of the adjacent decidualizing stroma close to the embryo, suggesting a restraining role. After the completion of placental trophoblast invasion (day 11.5) the trophoblast cells express high levels of cystatin C, probably in association with a switch from an invasive cell type to one providing nutrients to the conceptus [35]. In addition, treatment of pregnant mice with E-64, a synthetic cysteine protease inhibitor, resulted in failure of implantation and normal uterine decidualization.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-01T19:00:40.087" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14770" PostTypeId="2" ParentId="9125" CreationDate="2014-02-01T19:58:50.297" Score="2" Body="&lt;p&gt;Here is a report that shows significant increase in transformation efficiency for large plasmids (transformation was by electroporation. However the paper has been cited fewer than ten times so clearly the technique did not catch on.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Zhixing, Y and Nahon, J-L (1995) DNA gyrase improves DNA transformation of E.coli cells with large recombinant plasmids. Nucleic Acids Res. 23:3353-3354&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GCdft.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-01T19:58:50.297" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14772" PostTypeId="2" ParentId="14747" CreationDate="2014-02-01T22:18:11.567" Score="3" Body="&lt;p&gt;Answering your question 2: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is it possible to derive whether or not a person has cancer based only&#xA;  on the genome which was sequenced? i.e. Are there anomalies to look&#xA;  out for to detect the cancer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would say no.&#xA;The problem with mutations is that we still don't know exactly what mutations are needed for a cell to become a primary tumor cell.&#xA;There are anomalies, but we know these in fully developed tumors. I can give an example (I need to explain a bit wider for it) to show this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The expression of genes is dependent on many different signals, some come from the outside of the cell (for example from growth factors) and they are passed down into the nucleus along so called signal transduction pathways.&#xA;For melanoma (skin cancer) mutations in some key elements of this pathways are pretty often mutated, for example we find mutations in one kinase (an enzyme that phosphorylates other proteins) in about 60% of the cases. This kinase is called Braf and it carries a mutations in amino acid 600 changing it from valine to glutamic acid (so call Braf-V600E). This makes the kinase permanently active (also when she shouldn't be activated due to a missing signal) which derugulates otherwise pretty tightly controlled gene expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem with the Braf-V600E mutation is that this is not only found in melanoma cells, but also in benign nevi. Only that these are usually senescent (meaning that they do not divide and only sit on the skin) and harmless. Most of them never transform into melanoma, but some do and here we don't know why. Obviously cells need to pick up other mutations on their way to become cancer cells and there are quite some possibilities for that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cancer is a pretty complex disease, which is under high selection pressure: Cells need to evade the immune system and also be able to survive, proliferate and differentiate. Whole genome sequencing has opened a door to understand cancers better and also to diagnose them better in terms of treatment, but I don't think you can really do this only on the base of a sequence, since there a too many possibilities to bring up false positive (and also negative) results.&#xA;Its possible that the Cancer genome project will change this, but I am doubtful about it.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-02-01T22:33:40.863" LastActivityDate="2014-02-01T22:33:40.863" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14773" PostTypeId="1" AcceptedAnswerId="14822" CreationDate="2014-02-01T22:34:50.213" Score="2" ViewCount="541" Body="&lt;p&gt;I am reading Murray Microbiology book.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some facts&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;M. tuberculosis is an intracellular pathogen.&lt;/li&gt;&#xA;&lt;li&gt;At the time of exposure, M. tuberculosis enters the respiratory airways and infectious particles penetrate to the alveoli where they are phagocytised by alveolar macrophages.&lt;/li&gt;&#xA;&lt;li&gt;In contrast with most phagocytised bacteria, M. tuberculosis &lt;strong&gt;prevents fusion of the phagosome with lysosomes&lt;/strong&gt; (by blocking the specific bridging molecule, early endosomal autoantigen 1 [EEA1]). &lt;strong&gt;NB probably here something relevant&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;At the same time, the phagosome is able to fuse with other intracellular vesicles, permitting access to nutrients and facilitating intravacuole replication.&lt;/li&gt;&#xA;&lt;li&gt;Phagocytised bacteria are also able to evade macrophage killing mediated by reactive nitrogen intermediates formed between nitric oxide and superoxide anions by catalytically catabolising the oxidants that are formed.&lt;/li&gt;&#xA;&lt;li&gt;Dissemination to any body site occurs most commonly in immunocompromised patients, like HIV patient.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-09-04T06:16:28.273" Title="Why HIV patients have greater virulence of M.tuberculosis?" Tags="&lt;microbiology&gt;&lt;hiv&gt;&lt;tuberculosis&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14774" PostTypeId="2" ParentId="14773" CreationDate="2014-02-01T22:34:50.213" Score="1" Body="&lt;p&gt;I think one reason for greater virulence is the fact that M.tuberculosis &lt;strong&gt;prevents fusion of the phagosome with lysosomes&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this picture is little relevant here&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zbfJ0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking what is happening in these two parts here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dKH3R.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This answer does not provide enough support why there is greater virulance in HIV patients than in normal people.&#xA;And particularly why the preventation of the fusion of the phagosome with lysosomes leads to it.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-01T22:34:50.213" CommentCount="0" CommunityOwnedDate="2014-02-01T22:34:50.213" ContentLicense="CC BY-SA 3.0" />
  <row Id="14775" PostTypeId="2" ParentId="9631" CreationDate="2014-02-01T23:21:55.640" Score="2" Body="&lt;p&gt;Even if you have unlimited water available to the plants you'd still have to worry about the high temperatures and light levels of these areas. In the hot periods I would look into any plant that uses &lt;a href=&quot;http://en.wikipedia.org/wiki/C4_carbon_fixation&quot; rel=&quot;nofollow&quot;&gt;c4 carbon fixation&lt;/a&gt; like millet, sorghum, corn, sugar cane... In the cooler periods maybe look into rotating to a cool season legume crop like the cowpea that would help fix nitrogen. Another really important thing to do would be to find &lt;a href=&quot;http://en.wikipedia.org/wiki/Cover_crop&quot; rel=&quot;nofollow&quot;&gt;cover crops&lt;/a&gt; that will hold down the soil and build up some life in the otherwise sterile sands of the desert.&lt;/p&gt;&#xA;" OwnerUserId="5607" LastActivityDate="2014-02-01T23:21:55.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14778" PostTypeId="1" AcceptedAnswerId="14779" CreationDate="2014-02-02T08:37:04.033" Score="1" ViewCount="116" Body="&lt;p&gt;I got this question which I interpret as&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why PPD test in patients without M. tuberculosis often have slightly positive PPD reaction i.e., a lifelong slightly positive skin test reaction?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;because &lt;em&gt;slightly positive&lt;/em&gt; -phrase does not make so much sense to me.&#xA;I first thought it is about false positiveness, but it does not make sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am reading Murray Microbiology book.&#xA;It says there&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[An alternative to the PPD skin test,] is in vitro IFN-gamma release&#xA;  assays. The tests use immunoassays to measure IFN-gamma produced by&#xA;  sensitised T cells stimulated by M.tuberculosis antigens. If an&#xA;  individual was previously infected with M.tuberculosis, exposure of&#xA;  sensitised T cells present in whole blood to M.tuberculosis-specific&#xA;  antigens results in IFN-gamma production.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="86" LastEditorUserId="107" LastEditDate="2014-02-02T17:48:20.783" LastActivityDate="2014-04-03T18:28:11.107" Title="Why PPD test in patients without M.tuberculosis often slightly positive?" Tags="&lt;microbiology&gt;&lt;tuberculosis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14779" PostTypeId="2" ParentId="14778" CreationDate="2014-02-02T08:37:04.033" Score="1" Body="&lt;p&gt;The question asks PPD test in patients without M.tuberculosis.&#xA;It does not say if the patient has previously had infection with M.tuberculosis.&#xA;I think this question implies that the patient has never had before infection with M.tuberculosis.&#xA;I am not sure how it can be in reality possible for adults, since M.tuberculosis spreads in air.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for false positiveness can be that assays that use PPD use unspecific antigens, in contrast to IFN-gamma and second-generation assays.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other reason is that once you get infected you always have some degree positive skin test reaction. &#xA;So to say &lt;strong&gt;patient without M.tuberculosis&lt;/strong&gt; is faulty in a way because I think most people get exposured to this bacteria at least little in life.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-02T08:37:04.033" CommentCount="0" CommunityOwnedDate="2014-02-02T08:37:04.033" ContentLicense="CC BY-SA 3.0" />
  <row Id="14780" PostTypeId="1" AcceptedAnswerId="14784" CreationDate="2014-02-02T10:28:45.347" Score="3" ViewCount="155" Body="&lt;p&gt;The genes of the mitochondrion (kinetoplast) of some &lt;em&gt;Kinetoplastida&lt;/em&gt; - e.g. Trypanosoma brucei, the parasite which causes African sleeping sickness - are &quot;encoded&quot; in a way that the pre mRNA requiries partially heavy editing (insertion and deletion of Uridines) by the editosome (a RNA/Protein complex) until it can be translated to the correct proteins.&#xA;The information where to insert and remove Uridines is contained in small gRNA also part of the mitochondrial genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However this whole thing seems kind of unnecessary to me. Why did evolution not get rid of the surplus/missing Thymidines in those Genes? What's the use of this?&lt;/p&gt;&#xA;" OwnerUserId="3042" LastEditorUserId="1320" LastEditDate="2014-02-02T12:08:06.660" LastActivityDate="2014-02-03T12:21:31.783" Title="What's the use of RNA editing in kinetoplast?" Tags="&lt;evolution&gt;&lt;rna&gt;&lt;parasitism&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14783" PostTypeId="2" ParentId="14395" CreationDate="2014-02-02T16:13:08.893" Score="0" Body="&lt;p&gt;In this specific case the dominant allele is the presence of a gene (RHD), and the recessive allele is (usually) the absence of that gene. This is why you will see the statement &quot;there is no d gene&quot;. There does indeed appear to be an environmental factor which governs the frequency of the various genotypes - &lt;em&gt;Toxoplasma gondii&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I find this topic quite a challenge. Here is a distillation of my research. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is thought that the RHD gene may have arisen through a duplication of the adjacent RHCE gene. It seems that the possession of this gene (a D allele) confers a selective advantage in individuals suffering from toxoplasmosis (infection by the protozoan &lt;em&gt;Toxoplasma gondii&lt;/em&gt;. Toxoplasmosis has an effect upon what is termed psychomotor performance, which is usually measured as reaction time. So, for example, it has been reported that &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2692860/&quot; rel=&quot;nofollow&quot;&gt;there is an increased incidence of road traffic accidents amongst those suffering from (asymptomatic) toxoplasmosis&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://web.natur.cuni.cz/flegr/pdf/rh.pdf&quot; rel=&quot;nofollow&quot;&gt;Heterozygosity at RHD seems to reduce this effect of toxoplasmosis.&lt;/a&gt; So, the current theory is that the D allele appeared in humans because of the prevalence of toxoplasmosis, with the selective disadvantage of haemolytic disease of the newborn being balanced by the heterozygote advantage (similar to the malaria/sickle cell anaemia interaction). There is currently no biochemical explanation of why the RHD gene product has this effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a region with a very low risk of toxoplasmosis there would be a strong selection for the (ancestral?) dd genotype since these individuals have the best reaction time of all (when not infected). The definitive hosts (i.e. where the parasite reproduces) of &lt;em&gt;Toxoplasma gondii&lt;/em&gt; are cats, and these were rare in Europe before the domestication of cats. This could explain why the dd genotype is more frequent in this area.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-02-02T16:31:01.197" LastActivityDate="2014-02-02T16:31:01.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14784" PostTypeId="2" ParentId="14780" CreationDate="2014-02-02T16:52:57.187" Score="3" Body="&lt;p&gt;You could have asked a similar question about splicing. The function of RNA editing seems to be similar: it's one of the ways to trigger production of alternative transcripts and proteins given the same DNA sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is discussed, for example, in &lt;a href=&quot;https://www.landesbioscience.com/journals/rnabiology/HajdukRNA7-2.pdf&quot; rel=&quot;nofollow&quot;&gt;this review&lt;/a&gt;. The authors describe different known effects of alternative RNA editing:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Amino-acid substitutions&lt;/li&gt;&#xA;&lt;li&gt;ORF extension&lt;/li&gt;&#xA;&lt;li&gt;New unique ORFs&lt;/li&gt;&#xA;&lt;li&gt;Alternative UTRs&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Alternative editing is correlated with developmental stage, which is not surprising, given the fact that the parasites switch their energy metabolism in different hosts (&lt;a href=&quot;https://www.landesbioscience.com/journals/rnabiology/HajdukRNA7-2.pdf&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;,&lt;a href=&quot;http://link.springer.com/article/10.1007/BF00763065&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;,&lt;a href=&quot;http://www.kinetoplastids.com/content/2/1/11&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;), with the mitochondria changing their structure accordingly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors seem to be astonished as well and conclude: &quot;RNA editing in kinetoplastid mitochondria is a beautiful example how evolution favors diversifying mechanisms even if they seem to be extremely wasteful from a&#xA;human perspective.&quot;&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-02-03T12:21:31.783" LastActivityDate="2014-02-03T12:21:31.783" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14785" PostTypeId="1" AcceptedAnswerId="14788" CreationDate="2014-02-02T18:36:48.617" Score="1" ViewCount="40149" Body="&lt;p&gt;Please answer in simple terms im only in 9th grade.&lt;/p&gt;&#xA;" OwnerUserId="5616" LastEditorUserId="6307" LastEditDate="2017-03-30T15:08:24.017" LastActivityDate="2017-03-30T15:08:24.017" Title="How would the result of Hershey and Chase experiment been different if protein was the genetic material?" Tags="&lt;homework&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-02-02T21:22:43.070" ContentLicense="CC BY-SA 3.0" />
  <row Id="14788" PostTypeId="2" ParentId="14785" CreationDate="2014-02-02T19:20:21.047" Score="4" Body="&lt;p&gt;Hershey and Chase did two experiments to prove that DNA is the carrier of the genetic information.&#xA;First, they grew phages (viruses which infect bacteria) in a medium containing radioactive sulphur (&lt;sup&gt;35&lt;/sup&gt;S). This marked all the proteins of the phage (the hull) radioactive. They then used this phage to infect bacteria. To do so, the phage attaches to the surface of the bacteria and injects its genetic material. This looks like in this picture from the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Bacteriophage&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bacteriophages&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wzWnJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bacteria with the attached phages are then blended, so they will loose the attachment to the bacterial surface. The mixture of bacteria and phages is then centrifuged, this makes the heavy bacteria sediment at the bottom of the tube, the lighter phages stay in the supernatant. Hershey and Chase then measured where the radioactivity from the marked phage proteins had gone, since they found it in the supernatant, they knew, that no proteins had entered the bacteria.&#xA;If proteins would have been the carrier of the genetic information they would have entered the bacteria and had been found in the sediment inside the bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the second experiment (the proof if you want to say so) they marked the DNA of the phages radioactive (with radioactive phosphorus, &lt;sup&gt;32&lt;/sup&gt;P). They repeated the experiment and found the radioactivity in the sediment with the bacteria, proving, that the DNA had indeed entered the bacteria. &#xA;If the DNA wouldn't be the carrier, it wouldn't have entered the bacteria and would have stayed in solution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The whole experiment is nicely shown in this &lt;a href=&quot;http://en.wikipedia.org/wiki/Hershey%E2%80%93Chase_experiment&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia illustration&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ykPby.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2014-02-02T22:49:59.283" LastActivityDate="2014-02-02T22:49:59.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14789" PostTypeId="1" CreationDate="2014-02-02T19:25:01.510" Score="4" ViewCount="315" Body="&lt;p&gt;Several on-line resources (e.g. &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/003482.htm&quot; rel=&quot;nofollow&quot;&gt;MedlinePlus&lt;/a&gt;) suggest:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Normal range for non-diabetic people who are fasting should range between: 70 and 100 milligrams per deciliter (mg/dL)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Non-diabetic people who are not fasting should have a blood glucose level below 125 mg/dL&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I am interested in however, is the coverage interval of the population that was used to determine these 'normal' values.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also are there differences based on age, sex or any other factors.&lt;/p&gt;&#xA;" OwnerUserId="5619" OwnerDisplayName="Mansoor Nathani" LastEditorUserId="915" LastEditDate="2014-03-09T10:40:06.093" LastActivityDate="2014-03-09T18:04:38.377" Title="What constitutes the determination of a normal blood glucose level?" Tags="&lt;metabolism&gt;&lt;glucose&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14792" PostTypeId="2" ParentId="14736" CreationDate="2014-02-02T22:00:52.983" Score="-1" Body="&lt;p&gt;I asked my Biology teacher and she said that the if the father is not a carrier, he must have the disease. So the father is aa.&lt;/p&gt;&#xA;" OwnerUserId="5584" LastActivityDate="2014-02-02T22:00:52.983" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14793" PostTypeId="1" CreationDate="2014-02-03T03:02:33.233" Score="1" ViewCount="183" Body="&lt;p&gt;There exist a co-ordinate system from chromosomes like &quot;12p11.3&quot;. In this system, first integer range from 1 to 23 i.e it takes homologous chromosomes as a pair. If we want to distinguish among homologous chromosomes, how do we refer to each on of the pair? Is it possible to determine if one chromosome from a pair of homologous chromosomes is from father or mother?&lt;/p&gt;&#xA;" OwnerUserId="1800" LastEditorUserId="3340" LastEditDate="2015-06-03T17:04:41.297" LastActivityDate="2015-07-03T17:12:12.500" Title="Referencing the homologous chromosomes" Tags="&lt;genetics&gt;&lt;cell-biology&gt;&lt;human-genetics&gt;&lt;chromosome&gt;&lt;human-genome&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14794" PostTypeId="1" AcceptedAnswerId="19644" CreationDate="2014-02-03T04:14:11.850" Score="26" ViewCount="36391" Body="&lt;p&gt;I've seen a number of animals - dogs, cats, squirrels, ducks and geese, etc drink from puddles, some of them were muddy, others had green flora growing under water. Same goes for lakes and rivers. A human would not drink that. Do animals experience gastrointestinal discomfort or can they die from drinking water like that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the same time I hear about the problem of &quot;clean water&quot; in 3rd world countries and how diarrhea is the #1 killer of children under 5. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are humans the only animals that require a certain purity of their drinking water?&lt;/strong&gt; Why is it that a dog can drink from a puddle, but a human is likely to get sick from doing the same? Do baby animals get sick from drinking &quot;dirty&quot; water?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2018-04-30T03:39:09.767" Title="Are humans the only animal that requires &quot;clean water&quot;?" Tags="&lt;human-biology&gt;&lt;zoology&gt;&lt;digestive-system&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14795" PostTypeId="1" AcceptedAnswerId="14797" CreationDate="2014-02-03T05:50:34.767" Score="3" ViewCount="569" Body="&lt;p&gt;I have a college level background in Biology, say at the level of Campbell. I am very curious to know why it's extremely difficult to develop vaccines for certain diseases. Two cases which I am really interested in are &lt;strong&gt;Malaria&lt;/strong&gt; and &lt;strong&gt;AIDS&lt;/strong&gt;. It would be great if someone can give a brief sketch of the major issues being faced without getting into extreme technicalities. Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="5604" LastActivityDate="2014-02-03T08:48:00.687" Title="Difficulty in developing certain vaccines" Tags="&lt;microbiology&gt;&lt;vaccination&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14797" PostTypeId="2" ParentId="14795" CreationDate="2014-02-03T08:48:00.687" Score="4" Body="&lt;p&gt;Not an easy question, especially since the reasons for both pathogens are different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For HIV the problems are manyfold:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Insufficient knowledge about required immunity&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Its not known, which parameters are really important to raise an adequate immunity.   &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Variation in HIV strains&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;HIV has a very high mutation rate, which results in many different subtypes. This makes the virus extremely successful, but also causes problems for making vaccines. We have a similiar problem with vaccines for the flu, but there the number of subtypes is known and not very high. Still we need a new vaccine for each season based on the current viruses. For HIV there are no knwon proteins against which immunity can directed like in the case of the flu.&#xA;HIV also recombines very fast, so new variants can come up pretty fast.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;HIV targets the immune system&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The HI virus targets cells of the human immune system (namely CD4 T-cells) which are important for developing a proper response to a vaccination. These cells need to be stimulated, but on the other hand are destroyed and specially targeted by the virus.  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Lack of an effective animal model&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;To develop and test good vaccines, scientists need good animal models to test the pathogen and see the effect of a treatment.&#xA;Chimpanzees show some response to HIV infections, but they are expensive to keep as laboratory animals and also rare to get. The problem is, that HIV is pretty good adapted to its human host.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Human subjects trials&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This is more an ethic problem, but still needs to be adressed. To test the efficiency of new drugs, double-blinded placebo controlled test are done. Afterwards you can compare the placebo group to the treatment group and analyze the outcome. How do you do this with a deadly disease?&#xA;More information can be found on this &lt;a href=&quot;http://www.niaid.nih.gov/topics/hivaids/understanding/prevention/pages/vaccinechallenges.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;webpage&lt;/a&gt; from the NIH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For malaria some of the problems are similiar, others are different. he greatest problem was for years, that not enough money was available for research, which has been overcome only quite recently:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Plasmodium goes through different stages&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The parasite causing malaria goes through three different stages in its development in the human body. With each step it hides again from the immune system. The different stages are also present in different cell types, see this image from JCI (&quot;&lt;a href=&quot;http://www.jci.org/articles/view/44423&quot; rel=&quot;nofollow noreferrer&quot;&gt;Advances and challenges in malaria vaccine development&lt;/a&gt;&quot;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eIMxP.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;antigen&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Its not clear, against which antigens such a vaccine shoud be directed. This is due to the problem with the different stages and hasn't been found yet. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;different pathogens&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are four forms of plasmodium which definitely cause malaria - : Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale and Plasmodium malariae. Newer results suggest, that Plasmodium knowlesi is also a pathogen for humans.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;lack of animal models&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;More information can be found &lt;a href=&quot;http://www.scidev.net/global/policy-brief/malaria-vaccines-research-problems-and-priorities.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-03T08:48:00.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14798" PostTypeId="1" CreationDate="2014-02-03T11:26:39.537" Score="0" ViewCount="163" Body="&lt;p&gt;Human DNA consists of adenine, thymine, guanine and cytosine. Can thymine of other animal can be placed with humans thymine?&lt;/p&gt;&#xA;" OwnerUserId="5343" LastActivityDate="2017-04-13T14:44:43.243" Title="Can a certain part of human dna can be replaced with other animals dna?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14799" PostTypeId="1" AcceptedAnswerId="14801" CreationDate="2014-02-03T12:31:36.960" Score="3" ViewCount="368" Body="&lt;p&gt;I discussed a leather store about the white border aka salt border on leather shoes. They said that it is due to inner features of leather and you could try to add some fat/cream to push it back inside the shoes. I haven't yet understood physiology of skin here, &lt;code&gt;&quot;why does it act like that?&quot;&lt;/code&gt; is the first doubt and then the second &lt;code&gt;&quot;does human skin act the same way?&quot;&lt;/code&gt; -- I can see this kind of salt borders in gym clothes when they cry uncleaned but haven't seen them yet on my skin at least. The extra salty water from legs causes real damage, such as getting the inner fluids out, to the leather. When you do heavy training, the salty sweat in the human skin acts apparently the same way. So:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;how to manage the skin in living human skin and how does it differ from leather maintenance? What is the common physiological background with the different kinds of skins?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I try to answer it myself:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;leather: you can add the fat/cream/etc only externally&lt;/li&gt;&#xA;&lt;li&gt;living human ski: you can add the fat/cream-etc both internally (fatty food) and externally (lotions) &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9OkTm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1705" LastActivityDate="2014-02-03T13:11:08.313" Title="Physiology of skin and leather: why do salt borders occur?" Tags="&lt;physiology&gt;&lt;skin&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14801" PostTypeId="2" ParentId="14799" CreationDate="2014-02-03T13:11:08.313" Score="1" Body="&lt;p&gt;The two processes are quite different: On leather shoes no active transport takes place. The salt either comes with the snow (most likely most of it) when the streets get salted to avoid ice. Your shoe soaks up the salt-water mixture and when the water dries up, the salt stays behind. The other possibility (more for new leather shoes) is that water goes into the leather and dissolves salts, which remain from the tanning process of the leather. With older shoes I have never observed this &quot;snow marks&quot; in the summer when the shoes got wet in rain.&#xA;Using a wet cloth removes the salt, subsequent treatment of the shoe prevents that water can enter the leather.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The skin is quite different: Here we have living cells and an active transport of water through pores when you body get warm. This is to cool you and prevent overheating and since the body fluids contain salt, so does sweat. &lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-03T13:11:08.313" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="14804" PostTypeId="2" ParentId="14794" CreationDate="2014-02-03T16:53:34.853" Score="7" Body="&lt;p&gt;Animals do sometimes experience health problems from microbiologically polluted water. But they drink it, because they probably don't have as many options to choose from as humans have. Additionally, wilderness is very harsh, sick animals get eaten by predators quickly, so the short term evolutionary selection pressure in wilderness works very strongly in favor of good immunities in animals. So yes, I would expect animals would be a little less sensitive than humans, but still susceptible to illnesses. When I searched for examples about &lt;a href=&quot;http://www.theamericandogmag.com/drs-corner/water-borne-illnesses-in-dogs&quot;&gt;dogs&lt;/a&gt; I found:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Giardia and Cryptosporidium [...] can cause inflammation of the intestinal tract and diarrhea when in ­gested by dogs (or people) even in small numbers. Most dogs with healthy immune systems are able to recover from this infection but severe diarrhea may, in some cases, lead to dehydration and significant illness. Puppies and older dogs with other un­derlying health issues may be more severely affected. Leptospirosis is a less common [...] illness transmitted by bacteria. [It] may lead to fever, lethargy, vomiting, kidney failure, liver failure, and even death in some untreated individuals.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www3.ag.purdue.edu/entm/wildlifehotline/Pages/diseaseInfo.aspx&quot;&gt;Another webpage&lt;/a&gt; talks about wildlife water-borne illnesses. Giardiasis, leptospirosis and tularemia affect animals as well as humans.&lt;/p&gt;&#xA;" OwnerUserId="5369" LastEditorUserId="16143" LastEditDate="2015-06-09T12:08:00.393" LastActivityDate="2015-06-09T12:08:00.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14805" PostTypeId="1" AcceptedAnswerId="14867" CreationDate="2014-02-03T16:54:30.280" Score="0" ViewCount="204" Body="&lt;p&gt;I smoke. For some reason, I've always had this idea that the pleasure of smoking works more or less like this: from the lungs, the nicotine reaches the blood, with which it travels to the brain, and there it does some difficult chemical stuff to make me feel all good. But that's also never made sense to me. I mean, the gratification is instant. I don't even inhale very deeply, and, momentarily, I feel the feeling for which I do the thing. I don't know how fast the blood travels -- I only know it varies -- but it seems impossible for it to travel &lt;em&gt;this&lt;/em&gt; fast. Or is it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could you explain to me, a non-biologist, how it works?&lt;/p&gt;&#xA;" OwnerUserId="1278" LastActivityDate="2014-02-05T16:47:52.987" Title="How does a smoker's pleasure work?" Tags="&lt;human-biology&gt;&lt;pharmacology&gt;&lt;brain&gt;&lt;lungs&gt;&lt;smoking&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14808" PostTypeId="1" AcceptedAnswerId="14866" CreationDate="2014-02-03T18:41:55.290" Score="8" ViewCount="4990" Body="&lt;p&gt;It seems so simple that if my brain can tell my right hand to do something, then it should be able to tell equally well to the left ? This seems like a pretty major evolutionary advantage. Why haven't we evolved so during millions of years ?&lt;/p&gt;&#xA;" OwnerUserId="4705" LastActivityDate="2018-06-13T05:09:55.850" Title="Why aren't we ambidextrous?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14810" PostTypeId="1" AcceptedAnswerId="14811" CreationDate="2014-02-03T19:35:07.543" Score="0" ViewCount="219" Body="&lt;p&gt;I found this sentence in my notes which is not exact enough:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Electrical axes&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Excitatory processes have definite direction and magnitude and could therefore be represented as vectors. At any moment there are two&#xA;  points in the heart with the biggest potential difference, which is&#xA;  called electrical axis, characterized by the angel α.&lt;/li&gt;&#xA;  &lt;li&gt;Under normal conditions -&gt; 30°&amp;lt; angel α &amp;lt; 90°&lt;/li&gt;&#xA;  &lt;li&gt;Electrical axis gives information about the position of the heart, where the normal position ([arrow to south-east]) represents the&#xA;  biggest amplitude in the III lead&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the exact electrical axis and of what they are talking about?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-03T19:58:57.233" LastActivityDate="2014-10-04T22:38:02.923" Title="Normal position of Electrical axis only in the III lead?" Tags="&lt;physiology&gt;&lt;electrocardiography&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14811" PostTypeId="2" ParentId="14810" CreationDate="2014-02-03T19:45:34.517" Score="0" Body="&lt;p&gt;Let's consider the definition of the electrical axis.&#xA;The text does not specify which type of electrical axis and of what.&#xA;For instance, Guyton discusses Mean Electrical Axis of the Ventricular QRS only.&#xA;However, Guyton says that the mean electrical axis of the normal ventricle is 59 degrees. &#xA;In many pathological conditions of the heart, this direction changes markedly, sometimes even to opposite poles of the heart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the original author must have considered the Mean Electrical Axis of Ventricular QRS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would change the paragraph to&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mean Electrical axes of the Ventricular QRS&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Excitatory processes have definite direction and magnitude and could&#xA;  therefore be represented as vectors. At any moment there are two&#xA;  points in the heart with the biggest potential difference, which is&#xA;  called electrical axis, characterized by the angel α. &lt;/li&gt;&#xA;  &lt;li&gt;Under normal&#xA;  conditions -&gt; 30°&amp;lt; angel α &amp;lt; 90° &lt;/li&gt;&#xA;  &lt;li&gt;The Mean Electrical axis of normal ventricles is 59 degrees, which gives information&#xA;  about the position of the heart, and it represents the biggest amplitude in the lead III.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-03T19:45:34.517" CommentCount="0" CommunityOwnedDate="2014-02-03T19:45:34.517" ContentLicense="CC BY-SA 3.0" />
  <row Id="14812" PostTypeId="1" CreationDate="2014-02-03T19:47:09.427" Score="1" ViewCount="10271" Body="&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=U0u3-2CGOMQ&quot; rel=&quot;nofollow&quot;&gt;https://www.youtube.com/watch?v=U0u3-2CGOMQ&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's this video on Youtube about biological Evolution that has gone viral. I'll paste it above for your convenience.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To cut to the chase, Ray Comfort asks this question repeatedly to various people, and I guess he never got an answer or a good answer. The question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you think of any observable evidence for Darwinian Evolution where there is a change of kind?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By change of kind, I assume Comfort wants observable evidence of one species/kind morphing into a new or different kind/species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How would you answer this challenge?&lt;/p&gt;&#xA;" OwnerUserId="5502" LastActivityDate="2016-08-18T19:30:49.137" Title="Can you answer Ray Comfort's question on Biological Evolution?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="11" FavoriteCount="1" ClosedDate="2014-02-13T18:50:23.350" ContentLicense="CC BY-SA 3.0" />
  <row Id="14816" PostTypeId="1" AcceptedAnswerId="14818" CreationDate="2014-02-03T20:31:34.750" Score="1" ViewCount="667" Body="&lt;p&gt;I have a basic and probably silly question. I am isolating RNA with TRIzol. I have performed the basic steps and dissolved the pellet in 50 uL water. I ve measured the concentration and it was 3313 ng/uL (Around 165 ug total yield.). Now my next step is DNase treatment. It says 1 unit of enzyme for 1 ug of RNA in 10 ul reaction mix. I would like to dilute my RNA to 100 ug and use 100 units of enzyme in a 1000 uL reaction mix. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this logic true, and if it is how I am going to do the dilution?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="5630" LastEditorUserId="1320" LastEditDate="2014-02-03T21:43:37.197" LastActivityDate="2014-02-03T21:43:37.197" Title="Dilution question about RNA" Tags="&lt;molecular-biology&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14818" PostTypeId="2" ParentId="14816" CreationDate="2014-02-03T21:41:41.313" Score="3" Body="&lt;p&gt;If I understand correctly what you mean by &quot;I would like to dilute my RNA to 100 ug&quot;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your RNA preparation is at 3.3 &amp;mu;g &amp;mu;l&lt;sup&gt;-1&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To add 100 &amp;mu;g to a reaction you need to add 100/3.3 = 30 &amp;mu;l&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then make the total volume up to 1000 &amp;mu;l with enzyme and buffer as appropriate.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-03T21:41:41.313" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14820" PostTypeId="1" CreationDate="2014-02-03T22:08:38.293" Score="1" ViewCount="145" Body="&lt;p&gt;After RNA isolation and before following experiments, I know that RNA quality so called RNA integrity is so important. So why there is a RNA fragmentation kit? Do we need RNA intact or fragmented? (RNA will be used for biotinylation and RT-qPCR afterwards)&lt;/p&gt;&#xA;" OwnerUserId="5630" LastActivityDate="2014-08-18T01:16:09.123" Title="RNA integrity and RNA fragmentation" Tags="&lt;rna&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14822" PostTypeId="2" ParentId="14773" CreationDate="2014-02-03T23:02:35.120" Score="4" Body="&lt;p&gt;If you read &lt;a href=&quot;http://icmr.nic.in/ijmr/2004/1002.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article, you will find that CD4+ and CD8+ T-cells are probably the major mediators of the immune response against &lt;em&gt;M. tuberculosis&lt;/em&gt;. Since HIV severely depletes the number of CD4+ T-cells (and to a lesser extent other kinds of lymphocytes), it stands to reason that the frequency of infection and virulence will be substantially increased in such patients.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastActivityDate="2014-02-03T23:02:35.120" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14823" PostTypeId="2" ParentId="14808" CreationDate="2014-02-04T01:16:55.163" Score="-1" Body="&lt;p&gt;A simple answer to this is that at some point our brain's architecture was wired to have a dominant side, at which point it became too expensive evolutionarily to have drastic brain re-organisation or size changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another answer to this is that the two sides have many different specialisations and functions. While having similar bodily control from both sides might seem to be an advantage, that would mean that one of the hemispheres would have to dedicate more neural circuitry to finer motor control. This means less neural material will be available for other tasks. Alternatively, if you want to be able to do other tasks equally well like now (and keep the specialisation of the hemispheres) , but have ambidextrous ability, you'd possibly need a bigger brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, while it might seem like a good idea to be ambidextrous, it would probably come at a high cost on other brain functions or brain size.&lt;/p&gt;&#xA;" OwnerUserId="5367" LastActivityDate="2014-02-04T01:16:55.163" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14825" PostTypeId="1" AcceptedAnswerId="14829" CreationDate="2014-02-04T01:55:17.250" Score="3" ViewCount="178" Body="&lt;p&gt;I am a mathematician, and I decided to try to model cell division with math and see what conclusions came out of it. I had some questions concerning stem cells that came up in the model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In an extremely simplified model of cell division, each cell decides what cells it will divide into with no output from the outside workd, including from neighboring cells. I also assume the time frame is small enough that cells do not die, and that there are only finitely many 'programs' telling different cells how to divide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given these assumptions, I came to the conclusion that one of two things could happen:&#xA;1. The number of cells grows exponentially, or&#xA;2. Most cells will never divide into other cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, if growth is going to remain constant (e.g. 300,000,000 cells per month, every month in a sample), then eventually there will be two kinds of cells:&#xA;1. Normal cells, which never divide, and&#xA;2. 'Starter cells', which divide into normal cells but NEVER create other starter cells. The number of starter cells is eventually constant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hypothesized that these starter cells would eventually be far outnumbered and become a very small part if the body proportionally. I hypothesized that hair follicles, nail roots, growth plates, and bone marrow contained starter cells. I further hypothesized that these are adult stem cells.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Question 1: Is this what stem cells are? Are they the cells that divide to create other, non-dividing cells?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;After this, I realized that if the starter cells die, they would not be replaced under my model, because no cell is allowed to divide into new starter cells. I hypothesized that stem cell transplants fail because the host body kills off stem cells one by one and they can it be replaced. I also hypothesized that in the host, outside signals like hormones (which weren't allowed in my model) tell the body to create new stem cells as needed.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Question 2: Do stem cell transplants fail because isolated stem cells do not replicate themselves?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Finally, I noted above that the alternative to a bounded amount of stem cells is exponential growth, where stem cells divide into stem cells.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Question 3: Do embryo stem cells divide into other stem cells exponentially? Is this why embryo stem cells are easier to work with?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thanks for your time. Even answers like &quot;no, this is obviously wrong because ...&quot; would be appreciated. &lt;/p&gt;&#xA;" OwnerUserId="5632" LastActivityDate="2014-02-04T09:52:11.773" Title="An over-simplified model of cell division and its relation to stem cells" Tags="&lt;mathematical-models&gt;&lt;stem-cells&gt;&lt;cell-division&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14826" PostTypeId="2" ParentId="14812" CreationDate="2014-02-04T02:11:47.787" Score="4" Body="&lt;p&gt;It depends a lot on the meaning of &quot;Kind.&quot;  An ill-defined term is subject to goal-post-moving, so that if an example is presented of A splitting from B, or A descending from B, the person asking the question can claim that A and B are still the same &quot;Kind&quot;.  With a sufficiently broad definition of &quot;Kind&quot;, you are just a funny kind of fish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It can also be used as a strawman, to ask for evidence of a sort of evolution that nobody accepts, for example, the crocoduck.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, @rg255 is absolutely correct that observable evidence does not have to be &quot;live.&quot;  Archaeologists for example can and do observe evidence of battles without ever being in combat.  For a partial list of evidence for speciation and the common descent of different species from a common ancestor, see &lt;a href=&quot;http://www.talkorigins.org/faqs/comdesc/&quot; rel=&quot;nofollow&quot;&gt;http://www.talkorigins.org/faqs/comdesc/&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5633" LastEditorUserId="1590" LastEditDate="2016-08-17T08:47:11.337" LastActivityDate="2016-08-17T08:47:11.337" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14827" PostTypeId="1" CreationDate="2014-02-04T03:15:58.783" Score="0" ViewCount="173" Body="&lt;p&gt;Is there an example of nature creating codes or specified complexity? It is said by Creationists that codes can only come from minds, and since DNA has a code, it was created by a mind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this true? If false, can you explain how unguided, unintelligent nature could create coded specified information? Just as a note to show where I'm coming from, I am an Evolutionist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I have to admit, this appears to be a very, very strong argument in favor of special creation by an intelligence.&lt;/p&gt;&#xA;" OwnerUserId="5502" LastActivityDate="2014-02-04T11:00:32.070" Title="Can nature create codes and specified complexity?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="6" ClosedDate="2014-02-04T12:03:41.377" ContentLicense="CC BY-SA 3.0" />
  <row Id="14828" PostTypeId="2" ParentId="14773" CreationDate="2014-02-04T08:22:21.613" Score="1" Body="&lt;p&gt;&lt;strong&gt;Extension to Kanchi's answer&lt;/strong&gt; by using Murray Microbiology textbook&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dissemination to any body site occurs most commonly in immunocompromised patients, like HIV patient.&#xA;CD4+ and CD8+ T-cells are the major mediators of the immune response against M.tuberculosis.&#xA;Since HIV severely depletes the number of CD4+ T-cells (and to a lesser extent other kinds of lymphocytes), it stands to reason that the frequency of infection and virulence will be substantially increased in such patients.&#xA;In patients with HIV infection and with a low CD4 T-cell count, the disease usually appears before the onset of other opportunistic infections, is twice as likely to spread to extrapulmonary sites, and can progress rapidly to death. &lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-04T08:22:21.613" CommentCount="0" CommunityOwnedDate="2014-02-04T08:22:21.613" ContentLicense="CC BY-SA 3.0" />
  <row Id="14829" PostTypeId="2" ParentId="14825" CreationDate="2014-02-04T09:52:11.773" Score="3" Body="&lt;p&gt;You have a few misconceptions about stem cells, I will try to explain where they are. &#xA;First of all, cells are not independent. They influence each other with signals and secreted messenger substances. If you look at a human embryo the state of &lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_potency#Totipotency&quot; rel=&quot;nofollow&quot;&gt;totipotency&lt;/a&gt; (where all cells can differentiate into each cell type of the body) ends after 3-4 days when the blastocyte has developed. This structure already has a differentiation into a inner cell mass (embryoblast) and a outer cell layer (tropoblast).&#xA;If all cells would simply divide on their own, this would rather look like bacteria dividing in culture media, but not as a forming, multicellular organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From these few cells in the beginning all cell types of the body have to develop (around 200, if I remember the number correctly). To reach this, the pluripotent stem cells need to proliferate and differentiate (develop into more specialized cell types) quite a lot. So embryonic stem cells do proliferate. Adult stem cells are not proliferating at the same rate a embryonic, but they still do. A good example are the melanocyte stem cells (which are already pretty specialized as they can only further differentiate into melanocytes) which replenish the melanocyte population of the hair bulb at the beginning of each hair cycle. Differentiated cells can divide as well, when necessary, think only about wound healing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Question 2: Stem cells (especially adult stem cells) need very defined living conditions. This includes specific signalling molecules (Oct or nanog are examples for that) to stay stem cells. If this signalling is missing (and it does in the normal human body) then these cells either differentiate or (more likely) die.&#xA;The only stem cell transplant which takes place regulary is the transfer of hematopoietic stem cells to leukemia patients. There the problem is to keep the immune system from atacking these cells as foreign.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-04T09:52:11.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14830" PostTypeId="2" ParentId="14827" CreationDate="2014-02-04T11:00:32.070" Score="1" Body="&lt;p&gt;If you think of laws of nature as being codes, then we've found many instances of such codes that are in some sense not man-made. Of course, you could say that they are of &quot;divine creation&quot; or some such thing, but then you'll probably be ready to label everything seemingly intelligent, interesting or found as such. So let's not go there! These laws can be seen as codes, albeit not intentionally created ones.&lt;/p&gt;&#xA;" OwnerUserId="5367" LastActivityDate="2014-02-04T11:00:32.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14831" PostTypeId="1" AcceptedAnswerId="14886" CreationDate="2014-02-04T11:36:45.560" Score="6" ViewCount="335" Body="&lt;p&gt;&lt;strong&gt;Theoretical question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Can diploidy (or polyploidy) evolve from a haploid lineage in the absence of sexual reproduction ?&lt;/li&gt;&#xA;&lt;li&gt;For what theoretical reason? How can such evolution take place?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Empirical evidence&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beside theoretical answers I'd like to also ask for empirical examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Are there any examples of diploid (or polyploid) species that reproduce exclusively asexually, and for which sexual reproduction never occurred in the evolutionary lineage of this species?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Or in other words,&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Does diploidy (or polyploidy) exist in lineages that has never underwent sexual reproduction?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is my assumption correct?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am assuming that in eukaryotes haploidy appeared before diploidy. Is this assumption correct?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;By sexual reproduction I mean that the genome of the offspring is a combination (with or without recombination/crossover) of two parent individuals. I don't mean reproduction with sexes (or with mating types). I welcome the discussion of self-fertilization if needed.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3624" LastEditDate="2016-01-21T16:09:06.193" LastActivityDate="2017-02-08T13:31:51.607" Title="Can diploidy evolve in absence of sexual reproduction?" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;reproductive-biology&gt;&lt;polyploidy&gt;&lt;sexual-reproduction&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14832" PostTypeId="2" ParentId="14812" CreationDate="2014-02-04T11:59:57.140" Score="8" Body="&lt;p&gt;The question is really not well defined for two reasons:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;What would you accept to consider being an observation? It seems to me that many creationist would accept to consider something to be an observation only if it is extremely simple to understand it. The methodology of observation in evolutionary biology (just like in most science field) are not always very simple to understand for non biologists.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The word &quot;kind&quot; is not define in the sentence &quot;what is a change of kind?&quot;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Because the question is poorly defined, it makes it impossible to answer. And that is the common problem with creationist arguments. Their arguments are not scientific and therefore cannot really been argued for or against. Just want to say also that evolutionary biologist do not need non-scientist to fight against their work. Scientists create their own criticism. Scientists do not form a political party that fight for one point of view just for the purpose of defending it. They think neutrally and objectively (as much as a human can).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Change of kind&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;If change of kind = change in DNA sequence&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's assume change of kind means change in the DNA sequence. Change of kinds have been observed in real time in almost all lineages we looked at (including humans). These changes are not only observable at the genetic level but also at the so-called phenotypic (loosely speaking the phenotype is way the organism looks like) level. We can for example think of disease in humans that are due to de novo mutations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;If change of kind = a population/species adapt to a new environment&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If by change of kind, one mean &quot;adaptation&quot;, then adaptation to new environment have been observed in tons of lineages again. In a lab it can be observed in bacteria within the course of a month. It has been observed in many mammals, birds, plants and unicellular eukaryotes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;If change of kind = one lineage splits and there is reproductive isolation&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If by change of kind, one mean &quot;reproductive isolation&quot;, then reproductive isolation has also been observed in real time and many times in nature and in labs (see &lt;a href=&quot;https://biology.stackexchange.com/questions/17799/have-we-ever-observed-two-drosophila-lineages-that-evolved-reproductive-isolatio&quot;&gt;this post&lt;/a&gt; for example)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;If change of kind = something else&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just tell me what is this something else and we'll let you know if it has ever been observed. We can also let you know if this something is a prediction from the theory of evolution or not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Observation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you accept observation based on slightly more complex method such as molecular clocks and comparative genomics, then you'll find thousands of example of &quot;change of kind&quot;, again in roughly speaking all lineages of the tree of life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Very recently I worked on the speciation of clownfishes. This speciation was dated and we observed morphological and genetic adaptation to specific environments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.s. I haven't looked at the video completely but only some randomly selected part for a total duration of about 30 seconds! At first sight I'd like to say: Please don't fall into the trap of the media. One making interviews of people that are sometimes identified and sometimes not and that select for some part of their answer and that ask poorly defined question can really easily say anything from his records.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I welcome editing and I welcome anybody wanting to add references. One can find tons of them!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2016-08-18T19:30:49.137" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14833" PostTypeId="1" CreationDate="2014-02-04T12:50:37.347" Score="6" ViewCount="176" Body="&lt;p&gt;My query is that as atoms &amp;amp; its molecules have inter &amp;amp; intra molecular forces,like that only what type of force keeps the cells bonded to each other &amp;amp; prevent it from collapsing ever since.&lt;/p&gt;&#xA;" OwnerUserId="5635" LastEditorUserId="948" LastEditDate="2014-02-07T05:03:14.773" LastActivityDate="2014-05-29T09:21:05.870" Title="What type of force holds my body rigid &amp; doesn't make it collapse?" Tags="&lt;physiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14835" PostTypeId="2" ParentId="14833" CreationDate="2014-02-04T13:47:39.213" Score="0" Body="&lt;p&gt;Fundamentally, the most important physical force in everyday life and most cell-to-cell as well as molecule-to-molecule interactions are electromagnetic interactions. It is mainly electrical interactions that turn amino acids into intricate 3-dimensional proteins, as well get molecules attracted and specific for cell receptors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reality is somewhat more complex, as quantum mechanical (e.g. in charge distribution and fluctuations) effects can affect the attraction or repulsion of things temporarily.&lt;/p&gt;&#xA;" OwnerUserId="5367" LastEditorUserId="3624" LastEditDate="2014-02-07T08:58:17.207" LastActivityDate="2014-02-07T08:58:17.207" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14836" PostTypeId="1" CreationDate="2014-02-04T14:03:02.120" Score="3" ViewCount="196" Body="&lt;p&gt;Often we are able to memorize very precise bits of information (exact addresses, birthdays of inlaws, number of dirty socks under the bed), but over time our recollection tends to become fuzzy. We no longer recall the day and month a certain president was killed, only the year, or maybe the decade (despite being straight A students in junior high). Like the smoothing out of a delta function under the heat equation, instead of a pin-sharp value we're left with a range of values where the correct one is likely situated. However, most of the time we are perfectly satisfied with such approximate information and can work with them just fine (except in some extreme cases of function impairment, such as Alzheimer's or the aftermath of binge drinking).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Discrete data must be stored in low entropy structures in the brain that over time spontaneously shift to a higher entropy state. Meanwhile, our biology tries incessantly to slow down the decay by expending energy (with the frequently utilized neural pathways being better maintained than the abandoned ones). Even processes analogous to error correction take place, e.g. when we arrive at a certain lost piece of information by lateral thinking and piecing together available data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is whether the fading of memory exactitude can be explained in terms of the thermalization of the digital-like structures where discrete information is stored, and if anyone can point me to studies in this direction.&lt;/p&gt;&#xA;" OwnerUserId="5636" LastActivityDate="2014-07-13T07:20:59.350" Title="Can 'hardware' thermalization explain memory decay?" Tags="&lt;neuroscience&gt;&lt;memory&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14837" PostTypeId="2" ParentId="14836" CreationDate="2014-02-04T14:22:58.833" Score="1" Body="&lt;p&gt;Interesting point, but I think there is a simpler and possibly more widespread reason for the decay of memories. Namely, as new memories need to be stored in the same neural networks, the weights, timings and other properties of the network links are constantly changed. In other words, there is competition for the limited amount of memory. This re-use of the same networks for multiple functions and memories is the same reason we have redundancy in our brain - it's also largely why they are as fuzzy in remembering as they are. And since memories are recalled associatively, the more connected two networks that encode different memories, the more likely it is that activations of one will activate the other. But that also blurs the boundaries between specific bits of information stored. It's a trade-off between fidelity of the memory stored and recalled and generality of the recall and associations possible.&lt;/p&gt;&#xA;" OwnerUserId="5367" LastActivityDate="2014-02-04T14:22:58.833" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14838" PostTypeId="1" AcceptedAnswerId="15062" CreationDate="2014-02-04T15:26:26.597" Score="1" ViewCount="573" Body="&lt;p&gt;I am reading &lt;a href=&quot;http://apbrwww5.apsu.edu/thompsonj/Anatomy%20&amp;amp;%20Physiology/2020/2020%20Exam%20Reviews/Exam%201/CH18%20Cardiac%20Cycle.htm&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt; and my study materials.&#xA;The end-systolic volume (ESV), 50-60 ml, is the volume of blood found in ventricles after systole and contraction of ventricles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think ESV is the same as residual volume because residual volume is always the volume found in ventricles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is ESV the same as residual volume in normal physiological situations?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-07T20:11:30.873" LastActivityDate="2014-02-15T11:43:22.140" Title="Is end-systolic volume (ESV) the same as residual volume?" Tags="&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14839" PostTypeId="1" CreationDate="2014-02-04T16:11:02.963" Score="4" ViewCount="794" Body="&lt;p&gt;I frequently hear talk about parts of the brain like &quot;Amygdala&quot; or &quot;Hypothalamus&quot;, so I looked them up in an app called &quot;essential anatomy&quot;. What I see is that there's mirror symmetry, and most of these glands/nuclei are actually mirrored in two halves of the brain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I'm trying to understand how two halves of nuclei like amygdala work together.&lt;/strong&gt; For example, it is frequently said that Amygdala processes fear response. If it was a single nucleus, it is conceptually easy to comprehend, but what about a &quot;multi core&quot; nuclei with two halves? Which half would process the fear response?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additional questions to help clarify this question:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Are duplicate nuclei connected through some nerves, making up a single organ?&lt;/li&gt;&#xA;&lt;li&gt;Is there a dominant/non-dominant relationship between halves (like dominant hand)?&lt;/li&gt;&#xA;&lt;li&gt;Or do nuclei fulfill identical role within different brain halves (right half gets scared, then left half gets scared)?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Here's an image that prompted my curiocity - it is a 3D model of nuclei that sit on top of brain stem and under white matter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rj1vh.jpg&quot; alt=&quot;Brain glands mirror image&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2016-04-09T20:45:03.380" Title="How do duplicate brain regions (ex: left/right amygdaloid body) operate together?" Tags="&lt;brain&gt;&lt;human-anatomy&gt;&lt;endocrinology&gt;&lt;neuroanatomy&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14840" PostTypeId="1" AcceptedAnswerId="14881" CreationDate="2014-02-04T16:33:31.753" Score="1" ViewCount="1602" Body="&lt;p&gt;While calculating photosynthetic efficiency, do we take into account the Gross Primary Production or the Net Primary Production ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-02-06T17:20:09.490" Title="Calculating photosynthetic efficiency" Tags="&lt;ecology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14844" PostTypeId="1" AcceptedAnswerId="17859" CreationDate="2014-02-04T17:37:32.563" Score="5" ViewCount="257" Body="&lt;p&gt;Hummingbirds prefer to build their nests with spore-bearing ferns, and mosses. This is helpful for the reproduction of the ferns, which are then better able to spread their seeds. But how is this beneficial for hummingbirds? Building in this manner is more difficult and energy-consuming.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do live ferns make for better building materials? Is there a scent that these ferns are giving off to attract the hummingbirds? What kinds of research exist on this question? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carl Zimmer's National Geographic article, &quot;A Living Nest?&quot; (Feb 4, 2014) &lt;a href=&quot;http://phenomena.nationalgeographic.com/2014/02/04/a-living-nest/&quot; rel=&quot;noreferrer&quot;&gt;http://phenomena.nationalgeographic.com/2014/02/04/a-living-nest/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Question by Twitter-user Jessica: @LadyJaya&lt;/p&gt;&#xA;" OwnerUserId="3271" LastActivityDate="2014-07-04T06:02:26.837" Title="Why do hummingbirds build nests with live ferns instead of dead materials?" Tags="&lt;evolution&gt;&lt;ecology&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14845" PostTypeId="1" AcceptedAnswerId="14846" CreationDate="2014-02-04T18:02:09.850" Score="1" ViewCount="270" Body="&lt;p&gt;I am using a RNA which is in vitro transcripted before I started my project. It turned out it is not prepared properly and has DNA contamination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead of perform the in vitro transcription again, I want to try to clean it with DNase treatment and LiCl precipitation afterwards. Do you think would that work? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And second thing, in vitro transcipted RNA is in different dilutions, so I have a little bit of stock (maybe 5 uL) which is around 200 ng/uL and I have other dilutions 1 and 0.1 ng/uL. I would like to clean all of them. Do you think if I just mix all of the dilutions with the stock and determine the concentration and do the rest? Is it appropriate?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="5630" LastActivityDate="2014-02-04T18:47:51.377" Title="In vitro transcription, contamination problem" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;rna&gt;&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14846" PostTypeId="2" ParentId="14845" CreationDate="2014-02-04T18:47:51.377" Score="2" Body="&lt;p&gt;DNase treatment is actually one of the optional steps if you want to get rid of the original DNA template: &lt;a href=&quot;https://www.neb.com/protocols/2013/04/02/standard-rna-synthesis-e2050&quot; rel=&quot;nofollow&quot;&gt;https://www.neb.com/protocols/2013/04/02/standard-rna-synthesis-e2050&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you know, your the contamination happened after the transcription, DNase treatment should obviously help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Concerning the aliquots: your stock is 200 times more concentrated than the aliquots (so to get equal amounts of RNA as in 1 µl of the stock, you'd need to take 200 µl of the 1 ng/µl aliquot). I don't think it's worth mixing them (and the efficiency of RNA precipitation will likely be decreased), otherwise just make another transcription.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-02-04T18:47:51.377" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14848" PostTypeId="1" AcceptedAnswerId="14850" CreationDate="2014-02-05T04:04:43.757" Score="2" ViewCount="7519" Body="&lt;p&gt;Why is the recombination frequency higher if the genes are farther apart? &lt;/p&gt;&#xA;" OwnerUserId="1800" LastEditorUserId="1320" LastEditDate="2014-02-05T06:05:14.033" LastActivityDate="2018-01-22T12:44:52.717" Title="Gene distance and Recombination Frequency: Mechanism" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14849" PostTypeId="1" AcceptedAnswerId="17000" CreationDate="2014-02-05T04:43:33.083" Score="0" ViewCount="942" Body="&lt;p&gt;I've recently learned that &lt;a href=&quot;http://psychology.about.com/od/memory/ss/ten-facts-about-memory_8.htm&quot; rel=&quot;nofollow&quot;&gt;scents can trigger memory recall in humans&lt;/a&gt;, and am thinking about setting up an experiment where I would attempt to induce memory recall through exposure to scents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to help reduce the amount of experimentation required to actually trigger recall, I'm interested in - &lt;strong&gt;What kinds or qualities of scents have been demonstrated to trigger memory recall in humans?&lt;/strong&gt; Are they pleasant smells/unpleasant,  sharp or subtle?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any information about &lt;strong&gt;how long&lt;/strong&gt; of an exposure is needed to trigger such recall? Is it 2 seconds, 15 seconds, an hour?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="3624" LastEditDate="2014-03-19T09:19:25.717" LastActivityDate="2014-04-29T16:33:08.290" Title="How to design an experiment with scent triggered memory recall in humans?" Tags="&lt;human-biology&gt;&lt;experimental-design&gt;&lt;memory&gt;&lt;olfaction&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14850" PostTypeId="2" ParentId="14848" CreationDate="2014-02-05T06:14:06.453" Score="6" Body="&lt;p&gt;The genetic phenomenon referred to as recombination reflects the process of crossing over which occurs during &lt;a href=&quot;http://en.wikipedia.org/wiki/Meiosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;meiosis&lt;/a&gt;. &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosomal_crossover&quot; rel=&quot;nofollow noreferrer&quot;&gt;Crossing over&lt;/a&gt; creates an exchange of genetic information between homologous chromosomes. To a first approximation cossing over events take place at random positions along the aligned chromosomes. Consequently the further two loci are apart, the more likely that there will be a crossing over event between them. Thus the &lt;a href=&quot;http://en.wikipedia.org/wiki/Recombination_frequency&quot; rel=&quot;nofollow noreferrer&quot;&gt;recombination frequency&lt;/a&gt; can be used to measure the distance between two genetic loci (or genes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Supplement added in response to comment from OP&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mLPZU.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;An analogy&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine a piece of string. It has 6 marks on it (1-6 on the diagram) which divide it into 7 intervals (A-G). We are going to cut the string at one of the marks. We throw a die to decide which position to cut.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the probability that our cut will separate A and G? It's 100% since all single cuts will do this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the probability that our cut will separate A and D? It's 50% since single cuts at 1,2 or 3 will do this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the probability that our cut will separate A and B? It's 16.7% (1/6) since only a cut at position 1 will do this and the probability of throwing a 1 on our die is 1/6.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think of the intervals (A-G) as genes and the cut sites (1-6) as possible crossing over events. If two homologous chromosomes are going to undergo a single crossover somewhere at random, then the closer together are the genes (intervals), the less likely is it that the crossover (cut) will take place between them. This assumes of course that the site of crossing over is chosen at random.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the model presented here, if the order of the letters was scrambled and didn't know what it was but we were told the frequencies of occurrence of the separation of the intervals with random cutting we could deduce the order of the letters.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-02-05T17:15:18.790" LastActivityDate="2014-02-05T17:15:18.790" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14851" PostTypeId="1" AcceptedAnswerId="14852" CreationDate="2014-02-05T08:14:18.487" Score="0" ViewCount="1048" Body="&lt;p&gt;I found this sentence from my notes which I cannot understand&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;PR &amp;lt; CO, CO $\uparrow$, PR &amp;gt; CO $\downarrow$&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;where&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;\item CO = AP / PR, Cardiac Output = Arterial P / Peripheral Resistance&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I cannot understand the first sentence.&#xA;I cannot understand how you can deduce by Ohm's law the relationship.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the point of the first sentence?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-05T08:38:12.130" Title="Can you approximate Cardiac Output by Ohm's law?" Tags="&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14852" PostTypeId="2" ParentId="14851" CreationDate="2014-02-05T08:38:12.130" Score="2" Body="&lt;p&gt;I don't get the first sentence either, since PR and CO in your notation are in fundamentally different units. It's like saying '4 Celsius &amp;lt; 5 meters.' You will have to think about what you are implicitly holding constant and ignoring in that relationship to make it meaningful. I suspect the first sentence is just emphasizing the inverse relationship between CO and PR (PR goes up, CO goes down, etc). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for Ohm's law, absolutely! You have it written right there. I assume Cardiac output is the flow rate of fluid in a blood vessel, and AP is arterial pressure, and PR is peripheral resistance. Stated another way,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\textrm{Flow} = \frac{\textrm{Pressure}}{\textrm{Resistance}}$,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;which is exactly Ohm's law. Frequently electrical current is described with a &lt;a href=&quot;http://en.wikipedia.org/wiki/Ohm%27s_law#Hydraulic_analogy&quot; rel=&quot;nofollow&quot;&gt;Hydraulic analogy&lt;/a&gt;, with pressure$\rightarrow$voltage, fluid flow$\rightarrow$current, and flow resistance$\rightarrow$electrical resistance. It makes a lot of sense, since electric current is literally flow of electrons. &lt;a href=&quot;http://en.wikipedia.org/wiki/Hagen%E2%80%93Poiseuille_equation&quot; rel=&quot;nofollow&quot;&gt;Poiseuille's Law&lt;/a&gt; that makes this analogy rigorous, deriving an Ohmic relationship between those variables. Interestingly enough, Poiseuille derived the law in the context of blood flow, making it particularly applicable. &lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2014-02-05T08:38:12.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14853" PostTypeId="2" ParentId="14849" CreationDate="2014-02-05T09:20:51.813" Score="1" Body="&lt;p&gt;Scents can make memory recalls. We experience this very often, like when we repeatedly smell a good perfume in ,say a shopping mall , and when some person uses it too, we recall the memory of the shopping mall. This hqppens especially when the smell is associated with a very good or very bad incident.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an experiment, you can expose yourself or someone to a particular smell ,either very good or very bad at any one time, like during examination or holidays for a couple of times. Next when the person again smells the scent he/she will be reminded of the previous exposure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As regards to how long the exposure is required to trigger recall,it depends upon how strong the smell is (subtle smell takes ponger time) , how good/bad the memory is (very good or very bad memories will be recalled faster) and ofcourse on the memory associativity power of the person.&lt;/p&gt;&#xA;" OwnerUserId="5549" LastActivityDate="2014-02-05T09:20:51.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14856" PostTypeId="1" AcceptedAnswerId="14865" CreationDate="2014-02-05T09:33:49.573" Score="4" ViewCount="2326" Body="&lt;p&gt;Is there a linear connection between muscle size and the power it can produce?&#xA;If not, why? And what is the true correlation if any, can it be described with an appropriate function? What other factors modify it? (Red/white fiber for instance?)&lt;/p&gt;&#xA;" OwnerUserId="673" LastActivityDate="2014-02-05T15:59:38.953" Title="Correlation between muscle size and absolute strength" Tags="&lt;physiology&gt;&lt;muscles&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14857" PostTypeId="1" CreationDate="2014-02-05T09:38:07.757" Score="1" ViewCount="75" Body="&lt;p&gt;In total how many blood types are there?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And why do people normally know only 8 of them? (A+, B+ , AB+ and O+ and Rh- counterparts)&lt;/p&gt;&#xA;" OwnerUserId="5642" LastEditorUserId="5144" LastEditDate="2014-06-13T21:10:37.163" LastActivityDate="2014-06-13T21:10:37.163" Title="How many blood types are there?" Tags="&lt;human-biology&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="2" ClosedDate="2014-06-03T10:05:33.353" ContentLicense="CC BY-SA 3.0" />
  <row Id="14859" PostTypeId="1" AcceptedAnswerId="14863" CreationDate="2014-02-05T13:07:04.037" Score="0" ViewCount="141" Body="&lt;p&gt;I found this picture in my study materials.&#xA;I think it is too schematic and ignores the big pictures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/V6cgi.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the thing connected to the hormone is receptor.&#xA;The second messanger is then connected to the receptor which stimulates the effector cell in the cytosol. &#xA;The cell then response both to cytosol and to extracellular space.&#xA;&lt;strong&gt;How do you understand this picture?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do you know any similar pictures which present the same thing but clearer and more exactly?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="5144" LastEditDate="2014-02-05T13:17:38.293" LastActivityDate="2014-02-05T15:00:44.493" Title="To understand Second messenger signalling in I/c and E/c" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;signalling&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14860" PostTypeId="2" ParentId="14859" CreationDate="2014-02-05T13:16:48.117" Score="0" Body="&lt;p&gt;I found this picture from my old study materials which I edited little to show the I/e and E/c spaces.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hx5zY.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-05T13:16:48.117" CommentCount="1" CommunityOwnedDate="2014-02-05T13:16:48.117" ContentLicense="CC BY-SA 3.0" />
  <row Id="14862" PostTypeId="2" ParentId="14856" CreationDate="2014-02-05T14:50:38.103" Score="0" Body="&lt;p&gt;The muscular fiber cross section and length would be proportional to its strength, but there are also many &lt;a href=&quot;https://en.wikipedia.org/wiki/Skeletal_striated_muscle&quot; rel=&quot;nofollow&quot;&gt;different kinds of cellular types and structures&lt;/a&gt; which can result in muscles which are quicker or stronger, have better endurance etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedaily.com/releases/2009/03/090330200829.htm&quot; rel=&quot;nofollow&quot;&gt;This post&lt;/a&gt; from 2009 ago puts forward the hypothesis that chimpanzees, who &lt;a href=&quot;http://animals.nationalgeographic.com/animals/mammals/chimpanzee/&quot; rel=&quot;nofollow&quot;&gt;weigh 70 to 130 lbs (32 to 60 kg)&lt;/a&gt; are typically capable of lifting 3-4 times more weight than a human being can. They also put forward that the coordination of the muscle with other muscle fibers makes up the gross difference in strength. Human beings have much better fine motor control for delicate operations than chimps, which might cause the muscles to be less in synch resulting in lower strength despite the fact that we have about the same amount (or less) of muscle tissues in say our arms or legs. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-02-05T14:50:38.103" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14863" PostTypeId="2" ParentId="14859" CreationDate="2014-02-05T15:00:44.493" Score="2" Body="&lt;p&gt;I think the schematic you have there and the one that @Masi posted are pretty good.  A better way of getting a grasp of intercellular signaling would be to study a specific hormone and understand how each of the elements in the block diagrams here could vary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance take a look at this diagram from a &lt;a href=&quot;http://www.nature.com/nprot/journal/v5/n3/full/nprot.2009.239.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;journal article&lt;/a&gt; where they are tinkering with yeast mating factor, one of the first discovered extracellular signaling pathways. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/46ict.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;alpha factor and 'ligand' (I assume its not known at this point) bind to their receptors Ste2 and hGPCR respectively.  They then activate G protein complexes and both activate the same kinase cascade Ste4/18 -&gt; Cdc42 -&gt; Ste20 -&gt; MEKK/MEK/MAPK/Ste5 which then may activate Far1 (or not) and Ste12.  Far1 and Ste12 are migrated into the nucleus to activate genes for cell reproduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By actually filling out the boxes in your diagram you can see dozens of different paradigms for how cell signaling may work, and why the diagram you have needs to be so simple.  Hope this helps. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-02-05T15:00:44.493" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14864" PostTypeId="1" CreationDate="2014-02-05T15:30:49.183" Score="9" ViewCount="390" Body="&lt;h1&gt;Introduction&lt;/h1&gt;&#xA;&lt;p&gt;Standard models in population genetics look up at the evolution of few loci which impact fitness. The variance in fitness is determined by the genetic variance and the environmental variance (and the co-variance between environment and genetics). In this question &lt;strong&gt;I am interested only about genetic variance and about what percentage of the total (additive or not) genetic variance in fitness do &lt;em&gt;'n'&lt;/em&gt; loci explain.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;h1&gt;Question&lt;/h1&gt;&#xA;&lt;p&gt;&lt;strong&gt;In general, in natural populations, what percentage of the total genetic variance is explained by the &lt;em&gt;'n'-&lt;/em&gt; most important loci?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Here, by &amp;quot;most important loci&amp;quot; I mean loci which variance explain much of the total genetic variance.&lt;/p&gt;&#xA;&lt;p&gt;In other words, the subquestions are of the kind:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;how much of the fitness variance does the most important locus explain?&lt;/li&gt;&#xA;&lt;li&gt;How much of the fitness variance do the 3 most important loci explain?&lt;/li&gt;&#xA;&lt;li&gt;How much of the fitness variance do the 100 most important loci explain?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Of course, the answer depends on the population under consideration. Factors that might influence the answers are for example&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;species&lt;/li&gt;&#xA;&lt;li&gt;population size&lt;/li&gt;&#xA;&lt;li&gt;environment stability&lt;/li&gt;&#xA;&lt;li&gt;…&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Beside this question, I also welcome some insights concerning how different factors are likely to influence the answer.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2016-09-18T20:27:40.623" Title="What percentage of the genetic variance is explained by the 'n'- most important loci?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14865" PostTypeId="2" ParentId="14856" CreationDate="2014-02-05T15:59:38.953" Score="2" Body="&lt;p&gt;The short answer to your question is that the work output from a muscle is a combination of physiological cross-sectional area, length, fiber type, and recruitment (how many motor units are activated).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Read on for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Force output (tension) of a muscle is proportional to its physiological cross sectional area (&lt;a href=&quot;http://books.google.com/books?id=Cp5WVLGpyZoC&amp;amp;pg=PT170&amp;amp;lpg=PT170&amp;amp;dq=muscle%20tension%20cross%20sectional%20area&amp;amp;source=bl&amp;amp;ots=Eam1yAxwBQ&amp;amp;sig=_VnoKb4OiqL3vjl4itvmrMxnUEk&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=4FnyUtKtJ6KyyAHZ_oGYDg&amp;amp;ved=0CG4Q6AEwCw#v=onepage&amp;amp;q=muscle%20tension%20cross%20sectional%20area&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fundamental of Medical Physiology&lt;/a&gt;), and shortening is proportional to the length of the muscle. Work output (force X length) is a function of both. Power (work / time) involves both force, length change, and the shortening velocity. Shortening velocity is related to muscle fiber types.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a complex relationship between force output and length. In the graph below, the x-axis is relative length (1.0 being resting). When muscles operate outside a relatively narrow range (gray box), the cross-bridges are either too close together or too far apart to optimally generate force. When the muscle gets really stretched, force goes up, but only because passive tension (the intramuscular connective tissue is getting stretched) increases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7HfZg.png&quot; alt=&quot;Force length curve&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The force-velocity curve below relates relative force output to how fast the muscle is shortening (which can be negative; i.e., lengthening contraction). The green part of the curve is muscle shortening. As velocity approaches 0, the muscle produces maximal shortening force. When the muscle goes into the red part of the curve, force is even higher. In order for a muscle to shorten very quickly, it can't produce a lot of force (far right).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/i6JcV.jpg&quot; alt=&quot;Force velocity curve&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://ptjournal.apta.org/content/81/11/1810.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;Muscle fiber type&lt;/a&gt; generally relates to both the force output of a muscle fiber and it's shortening velocity. There are different ways to classify muscle fibers (enzyme activity, myosin isoform, or the &quot;classical&quot; method):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ssFQK.gif&quot; alt=&quot;Fiber types&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;SO (&quot;slow oxidative&quot;; the dark meat of a chicken) fibers contract slowly, produce lower force but are fuelled by oxidative reactions and thus have good endurance. At the other end of the spectrum, FG (&quot;fast glycolytic&quot;; the white meat of a chicken) fibers contract quickly with high force, but fatigue easily because they get energy from glucose, which is rapidly depleted. FOG fibers are intermediate between the two.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2014-02-05T15:59:38.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14866" PostTypeId="2" ParentId="14808" CreationDate="2014-02-05T16:26:56.450" Score="3" Body="&lt;p&gt;Having a dominant side is advantageous. Instead of seeing it as the brain influences our fine motor skill, think of it the other way round. The way we use our hands or any other part of our body sends feedback to the brain to increase the portion of the brain devoted to that region of the body and of course with disuse the reverse occurs. The more you do a certain task the more that portion of the brain gets better and coordinating the movement. The portion I talk about is the primary and supplementary motor cortices. So basically we are specialising. In the same way a heart doctor is better with treating conditions of the heart than a foot doctor. So we can either devote our experience to the one hand, or both or the other hand. If we use both hands equally our brain adapts so that we are ambidextrous, if instead we use just the one hand our brain develops just that side. But if you do focus on both you are using your dominant hand less so overall same amount of development just over both sides of the brain rather than just one side. You can probably see the benefit of having this plasticity of improving only what is used because why improve what we don't use and waste resources? And you may also see the benefits of higher specialising of one hand rather than having two slightly specialised hands. There are few tasks that require both hands to be very specialised, but if that were the case then the body would go ahead and do that but in spending time training your hands you are probably training your legs or something else less.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;///&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why not have a switch between the two hemispheres to give the hand currently being used the fine motor skill located in the other hemisphere? (from comment)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see. In my answer I only talked about one aspect. The brain doesn't have to learn skills for each hand completely independently. For example imagine if you learn to play a musical piece with your right hand only. If you try it with your left you won't be amazing but you'll definitely be better than a complete novice. Our brain can learn how to do by seeing which is vital for development. But there's a limit to that, your hands aren't completely identical so there's still a portion that needs fine tuning. Your muscles have different stregth, fatigue, resistance, recruitment patterns, places they innervate. Your hands are mirror images. The weight of your hand is different. And not only that but these variables aren't fixed, there's lots of them and they are different for different tasks. So to use your analogy, the more expensive remote can be used but it wasn't bought for use with the black plane. It'll give more control to the black plane but it still won't be the best ever until it learns what the muscle strength is etc. then it will be just as great. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1757" LastEditDate="2014-02-06T19:34:52.500" LastActivityDate="2014-02-06T19:34:52.500" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14867" PostTypeId="2" ParentId="14805" CreationDate="2014-02-05T16:47:52.987" Score="2" Body="&lt;p&gt;20-30 seconds is all it takes to reach the brain, then levels continue to increase with a peak at around 15 minutes and normal levels by about 2 hours (hence the craving). Smoking increases your heart rate directly and also indirectly through reducing the oxygen levels in your blood so your body compensates by increasing heart rate as well as makes each beat stronger, so it pumps more blood with each beat. Nicotine itself is really soluble, it goes straight through the lungs (alveoli) because the lungs get an incredible amount of blood (which they need to do their job) so massive surface for the nicotine to go through so enough nicotine gets into the blood and concentrations are really rapidly high enough for you to feel the nicotine. Carrying on from that, the blood rapidly gets back to the heart and around the body with the brain being practically a direct connection away. Consider the classic cyanide capsule death seen often on TV. The reason people seem to lose consciousness within 30 seconds is because they inhale the cyanide. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nicotine replacement therapy used to stop smoking uses similar mechanisms to give the same speedy delivery of satisfaction without the massive risks of smoking, stopping cravings and really improving one's quality of life. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-05T16:47:52.987" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14868" PostTypeId="2" ParentId="14798" CreationDate="2014-02-05T16:50:13.197" Score="3" Body="&lt;p&gt;Yes. They're identical. When we eat animals or plants we digest their DNA to use to make our own DNA. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-05T16:50:13.197" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14869" PostTypeId="2" ParentId="14745" CreationDate="2014-02-05T16:59:51.297" Score="2" Body="&lt;p&gt;Tumour cells can also metastasise using the lymphatic system. They first need to detach (produce enzymes that break down the extracellular matrix or any adherent molecules etc). Then they need to survive in the blood which is really hard with all the mechanical stress of being pushed around, the completely different nutrients, the different levels of blood gases, the immune cells in the blood and numerous filter mechanisms, then to truly metastasise they need to settle down somewhere and grow in their new environment. That's a lot of things right? So a sensitive assay like one you describe would need to have that tumour cell in the sample (unlikely, and only one cell is required to make a new tumour), is likely to be unable to tell that the cell is a tumour cell, wouldn't be able to differentiate between tumour cells that could or couldn't survive in the blood or differentiate those that could then go on to grow more in a tissue or not. And of course you're missing the entire lymphatic system. Following all of that, why does it matter? See a cancer, cut it out if you can and give chemotherapy to get rid of any possible cells outside of what you cut. If your assay came back negative or positive, treatment wouldn't change. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-05T16:59:51.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14871" PostTypeId="2" ParentId="14759" CreationDate="2014-02-05T19:57:09.927" Score="1" Body="&lt;p&gt;Actually the applications of magnetism to organic systems is new to Science.  Duke Univ in NC is currently experimenting with humans sticking their heads into large electromagnetic coils while electrodes are attached to the outside of the skull. A small amount of research has been done with magnetism and plant physiology (my interest), but in the main very little published research is available on the topic.  I might direct you to use Scholar.Google to find more technical articles rather than just using Google itself.&lt;/p&gt;&#xA;" OwnerUserId="5647" LastActivityDate="2014-02-05T19:57:09.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14872" PostTypeId="1" AcceptedAnswerId="24580" CreationDate="2014-02-05T20:03:22.050" Score="1" ViewCount="35" Body="&lt;p&gt;I found this sentence in my notes interesting&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;E-NOS and n-NOS are Ca-calmodulin dependent ferments.&#xA;  They are synthesized in small concentration as a response to physiological signals which increases the level of Ca&lt;sup&gt;2+&lt;/sup&gt; in cell.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Does it mean that e-NOS and n-NOS are synthesized by mediation of Ca and calmodulin?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I remember how RNS can be derived from nitric oxide and superoxide.&lt;br&gt;&#xA;&lt;strong&gt;Are e-NOS and n-NOS expressed on macrophages after induction by cytokines and microbial products, notably interferon-gamma and lipopolysaccharide?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="3340" LastEditDate="2014-12-05T09:42:12.290" LastActivityDate="2014-12-05T10:00:55.620" Title="To understand synthesis of e-NOS and n-NOS with respect to Ca and calmodulin" Tags="&lt;biochemistry&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14873" PostTypeId="1" CreationDate="2014-02-05T20:50:22.630" Score="4" ViewCount="2367" Body="&lt;p&gt;Several places on the internet seem to purport that animal sacrifice is painless because exsanguination causes no pain. That sounds unscientific to me and an attempt to appease culture than than using science. For instance this question on the se and others like it on the internet. &lt;a href=&quot;https://biology.stackexchange.com/questions/9572/is-there-a-difference-between-pig-and-cow-anatomy-that-makes-religious-slaughter&quot;&gt;Is there a difference between pig and cow anatomy that makes religious slaughter of the latter less painful?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could someone comment on the validity of this research?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Schulze W, Schultze-Petzold H, Hazem AS, Gross R. Experiments for the objectification of pain and consciousness during conventional (captive bolt stunning) and religiously mandated (“ritual cutting”) slaughter procedures for sheep and calves. Deutsche Tierärztliche Wochenschrift 1978 Feb 5;85(2):62-6.&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-06-06T13:31:49.970" Title="Death by exsanguination not painful?" Tags="&lt;pain&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14874" PostTypeId="1" AcceptedAnswerId="14880" CreationDate="2014-02-05T21:22:16.083" Score="2" ViewCount="1932" Body="&lt;p&gt;I am using Neutravidin Agarose beads to isolate biotinylated RNA. The thing is, in the manual it says to use 8M Guanidine-HCl, pH 1.5 for elution biotinylated molecules. As far as I know it is a very harsh elution buffer. Do you think it would effect my RNA? I have isolated my RNA with TRIzol which also contains Guanidine salt but the concentration is not that high.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a second question, do you know other ways to elute my biotinylated RNA from beads?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="5630" LastActivityDate="2014-02-06T13:36:51.487" Title="Elution of biotinylated RNA" Tags="&lt;molecular-biology&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14876" PostTypeId="1" AcceptedAnswerId="21045" CreationDate="2014-02-05T21:31:30.590" Score="1" ViewCount="111" Body="&lt;p&gt;&lt;strong&gt;Which properties do determine the radius of blood vessel?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have these thoughts&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;distension, &lt;/li&gt;&#xA;&lt;li&gt;elasticity, &lt;/li&gt;&#xA;&lt;li&gt;contractility and&lt;/li&gt;&#xA;&lt;li&gt;cross-sectional area of the walls.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any other properties?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-09-05T02:09:43.540" Title="Characteristics of radius of blood vessel" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14877" PostTypeId="1" AcceptedAnswerId="14878" CreationDate="2014-02-06T06:25:48.663" Score="5" ViewCount="3333" Body="&lt;p&gt;This came up in an argument with some friends. I know that birds are direct descendants of dinosaurs, shown pretty clearly through the fossil record. However, is it proper to say that birds &lt;em&gt;are&lt;/em&gt; dinosaurs, or is there an actual distinction?&lt;/p&gt;&#xA;" OwnerUserId="5649" LastEditorUserId="3776" LastEditDate="2014-02-06T11:10:31.880" LastActivityDate="2017-03-07T16:07:16.750" Title="Birds and Dinosaurs" Tags="&lt;evolution&gt;&lt;taxonomy&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14878" PostTypeId="2" ParentId="14877" CreationDate="2014-02-06T11:27:44.117" Score="9" Body="&lt;p&gt;I bet you'll be interested about the concept monophyly. Any human-made group of species (or taxon) like birds dinosaurs, primate, bacteria, angiosperm, reptiles, … are either monophyletic, polyphyletic or paraphyletic. This picture explain the concept When the taxon is monophyletic it is called a clade.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EgjgE.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Monophyletic taxon are those groups of species that can be considered to be objective in the sense that it represents a group of species where each species in the taxon is more related (in terms of time to common ancestor, not according to their genetic similarity) to any other species within the same taxon than to any other species outside this taxon. This is obviously not the case for paraphyletic or polyphyletic taxon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Typically, we do not consider a parrot or a deer to be reptiles. Therefore, the ususal understanding of &quot;reptiles&quot; makes this taxon paraphyletic. Now, one should not confound the common understanding (what is a reptile in our everyday life) with the strict definition of the taxon Reptilia, which is a monophyletic taxon (or a clade in other words). Probably the best source for exploring the tree of life is &lt;a href=&quot;http://tolweb.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;tolweb.org&lt;/a&gt;. Here, you will find the clade &lt;a href=&quot;http://tolweb.org/Amniota/14990&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reptilia&lt;/a&gt; (who include birds, snakes, turtles and lizards). Note: Mammals are within the Reptiliomorpha, not the Reptilia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is exactly the same issue with the dinosaurs. When we talk about dinosaurs in our everyday life we do not mean birds. But there is a clade called &lt;a href=&quot;http://tolweb.org/Dinosauria/14883&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dinosauria&lt;/a&gt;, which include both dinosaurs and birds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, I would say that a bird is a Dinosauria (monophyletic taxon) but is not a dinosaur (paraphyletic taxon). But this little play on word is not a scientific issue but an issue of english usage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will also find in &lt;a href=&quot;https://biology.stackexchange.com/questions/52700/why-do-the-ancestors-of-birds-still-exist/52729#52729&quot;&gt;this post&lt;/a&gt; an introduction to phylogeny&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2017-03-07T16:07:16.750" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="14879" PostTypeId="1" CreationDate="2014-02-06T12:20:32.917" Score="2" ViewCount="112" Body="&lt;p&gt;For the third time in a row, I found a mysterious life-form inside my house. I live in the Netherlands in the Eindhoven region, in a city called &lt;a href=&quot;https://maps.google.nl/maps?q=maps+oss&amp;amp;ie=UTF-8&amp;amp;hq=&amp;amp;hnear=0x47c6fc89edf0a983:0xd870787dc357c409,Oss&amp;amp;gl=nl&amp;amp;ei=TH3zUqWkGsO8ygPV-ILoCA&amp;amp;ved=0CDEQ8gEwAA&quot; rel=&quot;nofollow noreferrer&quot;&gt;Oss near a forest area&lt;/a&gt;. Before I set it free outside, I put it in a jar to make a few pictures for identification purposes. What is this creature?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ypa4W.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/k2P1Y.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/nJ931.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/u0oaT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5650" LastActivityDate="2014-02-06T12:20:32.917" Title="Identification of a mysterious lifeform, what is this?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="1" ClosedDate="2014-02-09T16:13:59.607" ContentLicense="CC BY-SA 3.0" />
  <row Id="14880" PostTypeId="2" ParentId="14874" CreationDate="2014-02-06T13:36:51.487" Score="4" Body="&lt;p&gt;The biotin-streptavidin interaction is extremely strong, one of the strongest (if not &lt;em&gt;the&lt;/em&gt; strongest) non-covalent interaction between biomolecules. So you'll need pretty harsh conditions in any case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Extreme pH values are generally a very bad idea for RNA. I'm pretty sure that the conditions you mentioned are not meant for elution of nucleic acids. Such low pH values (and high pH values as well) lead to a quick hydrolysis of the phosphoester bond of RNA, you can read more about the mechanism of that &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/cr960425x&quot; rel=&quot;nofollow&quot;&gt;in this review&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A quick Google search lead me to &lt;a href=&quot;http://www.lifetechnologies.com/de/de/home/brands/product-brand/dynal/streptavidin-coupled-dynabeads/dynabeads-streptavidin.html#11&quot; rel=&quot;nofollow&quot;&gt;the following protocol&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To dissociate biotinylated nucleic acids from Streptavidin-Coupled&#xA;  Dynabeads®, incubate the beads in 95% formamide + 10mM EDTA, pH 8.2&#xA;  for 5 minutes at 65°C or for 2 minutes at 90°C.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This sounds reasonable to me, as formamide is also commonly used in sample buffer for denaturing gel electrophoresis of RNA. I haven't done anything like that myself, so I can't guarantee that this would work in your case.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-02-06T13:36:51.487" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14881" PostTypeId="2" ParentId="14840" CreationDate="2014-02-06T13:50:18.757" Score="1" Body="&lt;p&gt;We can actually use either depending on the specified convention, but a more convenient way to characterise the photosynthetic efficiency is:-  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Considering the total incident solar radiation instead of that part which is absorbed (so that the calculated efficiency takes into account the total available solar energy on earth)&lt;/li&gt;&#xA;&lt;li&gt;Using Net Primary Productivity instead of Gross PP.(so that the efficiency is characterised by the useful output (product) of photosynthesis by removing the non-useful respiratory losses of plant.)   &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I should also mention that using GPP instead of NPP was the practice followed in a large number of texts I read. But I think using NPP is not only the modern view, but also scientifically more convenient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Photosynthetic_efficiency&quot; rel=&quot;nofollow&quot;&gt;Here is the wikipedia page&lt;/a&gt; on photosynthetic efficiency and &lt;a href=&quot;http://books.google.co.in/books?id=6F7yuf1Sj30C&amp;amp;redir_esc=y&quot; rel=&quot;nofollow&quot;&gt;here is the book&lt;/a&gt; which houses the technicalities of these definitions along with several values of the various efficiencies.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2014-02-06T17:20:09.490" LastActivityDate="2014-02-06T17:20:09.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14882" PostTypeId="1" AcceptedAnswerId="14887" CreationDate="2014-02-06T14:02:19.153" Score="1" ViewCount="65" Body="&lt;p&gt;I found this statement in my study materials in the section of Staphylococcus&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The AG structure: &lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;protein AG (species specific);&lt;/li&gt;&#xA;  &lt;li&gt;polysaccharide AG (serotype specific).&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I know what is Protein A/G, a recombinant fusion protein that combines IgG binding domains of both Protein A and Protein G. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the point of this AG structure thing in the contex of Staphylococcus?&lt;/strong&gt;&#xA;Can we say that staphylococcus have AG structure? &#xA;I think it has properties related to protein A\G and also to polysaccharide A\G.&#xA;I know very little about polysaccharide A\G and not sure how it is related to serotype specificity in the context of staphylococcus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Extension to the question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Antigenic structure of Steptococcus pyogenes: &#xA;the group AG is unique, placing streptococcus in group A.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the AG here?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-06T20:25:56.800" LastActivityDate="2014-02-06T20:25:56.800" Title="Staphylococcus AG structure?" Tags="&lt;microbiology&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14883" PostTypeId="1" AcceptedAnswerId="14885" CreationDate="2014-02-06T14:29:33.097" Score="0" ViewCount="63" Body="&lt;p&gt;I found this sentence confusing&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Transitor carriers of staphylococcal infections 70% because of mupirocin i/n.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Mupirocin is drug which affects some way.&#xA;I am not sure if the statement means inner neuronal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am little confused by the abbreviation &lt;strong&gt;i/n&lt;/strong&gt;.&#xA;&lt;strong&gt;What is the point of the sentence?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-06T14:43:38.420" Title="How does Mupirocin affect in staphylococcal infection?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14884" PostTypeId="2" ParentId="10803" CreationDate="2014-02-06T14:33:51.343" Score="0" Body="&lt;p&gt;This is a very good question! There are many factors there so the list would be very long. There are many kinds of artifacts too, some related to processes and the other on technical devices. Some of the processes we do not know or we have not defined those rigorously mathematically. It depends on the methods used to get the final list. You need to specify exactly the research tool(s) and narrow the scope still to be able to define exactly some artifacts.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-06T14:33:51.343" CommentCount="0" CommunityOwnedDate="2014-02-06T14:33:51.343" ContentLicense="CC BY-SA 3.0" />
  <row Id="14885" PostTypeId="2" ParentId="14883" CreationDate="2014-02-06T14:43:38.420" Score="1" Body="&lt;p&gt;This comes from the usage of the Mupirocin: Its an antibiotic, which is used topically (on the skin, its not taken in form of pills). It binds specifically to the isoleucyl t-RNA synthetase in gram positive bacteria and Streptoccus and Staphylococcus and is used to fight intranasally (that what i/n stands for) infections with these bacteria. It inhibts the introduction of isoleucine into proteins. More informations can be found &lt;a href=&quot;http://en.wikipedia.org/wiki/Mupirocin&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-06T14:43:38.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14886" PostTypeId="2" ParentId="14831" CreationDate="2014-02-06T16:24:45.340" Score="7" Body="&lt;p&gt;I can only offer a partial answer on the &lt;strong&gt;theoretical aspects&lt;/strong&gt;. I don't know if you are familiar with the mid-90s papers by Otto et al. (&lt;a href=&quot;http://www.genetics.org/content/131/3/745&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Otto &amp;amp; Goldstein. 1992. Recombination and the evolution of diploidy. Genetics 131(3)&quot;&gt;Otto &amp;amp; Goldstein,1992&lt;/a&gt;, &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.1996.tb00309.x/abstract&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Otto &amp;amp; Marks. 1996. Mating systems and the evolutionary transition between haploidy and diploidy. Biological Journal of the Linnean Society 57(3)&quot;&gt;Otto &amp;amp; Marks, 1996&lt;/a&gt;), but these are definately relevant to your question. They deal with the &quot;masking hypothesis&quot; of diploidy, i.e. that deleterious mutations can be masked by &quot;healthy&quot; alleles, and the trade-offs between diploidy (ploidy level), recombination rate and purging of deleterious alleles. &lt;a href=&quot;http://www.genetics.org/content/131/3/745&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Otto &amp;amp; Goldstein. 1992. Recombination and the evolution of diploidy. Genetics 131(3)&quot;&gt;Otto &amp;amp; Goldstein (1992)&lt;/a&gt; shows that recombination is essential for the evolution of diploidy, and without recombination haploids will &quot;win&quot; over diploids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.1996.tb00309.x/abstract&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Otto &amp;amp; Marks. 1996. Mating systems and the evolutionary transition between haploidy and diploidy. Biological Journal of the Linnean Society 57(3)&quot;&gt;Otto &amp;amp; Marks (1996)&lt;/a&gt; is a fairly comprehensive paper that builds on the previous one, and looks at how different mating systems interacts with recombination and purging to influence the evolution of ploidy levels. As a general results they predict a correlation between mating system and ploidy level, with sexual reproduction favoring diploidy while asexual reproduction favors haploidy. However, from what I can see after a quick re-read, there is nothing that prohibits asexually reproducing species to be diploid (and vice-versa) - see e.g. page 206 - and the paper includes a condition that must hold for diploids to invade in asexually reproducing or selfing populations. I have not followed this literature closely though, and I imagine that tracing recent papers that cite &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.1996.tb00309.x/abstract&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Otto &amp;amp; Marks. 1996. Mating systems and the evolutionary transition between haploidy and diploidy. Biological Journal of the Linnean Society 57(3)&quot;&gt;Otto &amp;amp; Marks (1996)&lt;/a&gt; can be useful to find further relevant studies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should also consider that ploidy levels can differ between sexes (e.g. bees), which can lead to antagonistic selection which can influence ploidy evolution (see e.g. &lt;a href=&quot;http://www.jstor.org/stable/10.1086/674025&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Immler &amp;amp; Otto. 2014. Driven Apart: The Evolution of Ploidy Differences between the Sexes under Antagonistic Selection. American Naturalist 183(1)&quot;&gt;Immler &amp;amp; Otto, 2014&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the &lt;strong&gt;empirical evidence&lt;/strong&gt; part, I do not have any good examples. However, I imagine that it can be extremely difficult to prove that a lineage have only reproduced asexually (or never asexually), since these things are hard to track in fossils. Also consider that it is common to have both sexual and asexual stages, and many species can have a long asexual diploid stage followed by a shorter sexual haploid stage. From what I know, this is the norm in e.g. &lt;a href=&quot;https://en.wikipedia.org/wiki/Algae#Life-cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;algae&lt;/a&gt; (arguably a group of fairly &quot;basal&quot; taxa). However, I don't know what the ancestral state of algae was (i.e. if they became diploid before having a sexual stage).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the ancestral state of eukaryotes, there seems to be evidence that the ancestral state was in fact facultatively sexual (&lt;a href=&quot;http://link.springer.com/article/10.1007%2FPL00013156&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Dacks &amp;amp; Roger. 1999. The First Sexual Lineage and the Relevance of Facultative Sex. Journal of Molecular Evolution 48(6)&quot;&gt;Dacks &amp;amp; Roger, 1999&lt;/a&gt;), which would &lt;strong&gt;invalidate your assumption&lt;/strong&gt;. However, this is only based on a couple of quick literature searches on my part, and I am in no way an expert in this area. There are probably more recent studies on this topic as well. However, it is clear that you cannot blindly assume that eukaryotic haploid is ancestral. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2017-02-08T13:31:51.607" LastActivityDate="2017-02-08T13:31:51.607" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14887" PostTypeId="2" ParentId="14882" CreationDate="2014-02-06T17:44:43.510" Score="3" Body="&lt;p&gt;After puzzling over this for a while I think I have the answer . It's nothing to do with protein A or protein G. I think that whoever wrote your study materials meant Ag which is a common abbreviation for 'antigen'. I guess this was in the context of immune responses, or strain typing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking back over your last few questions, it seems that you are at the mercy of a teacher who specialises in ambiguity.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-06T17:44:43.510" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14888" PostTypeId="1" AcceptedAnswerId="59068" CreationDate="2014-02-06T18:04:01.437" Score="10" ViewCount="14117" Body="&lt;p&gt;Approximately, how many &lt;a href=&quot;https://en.wikipedia.org/wiki/Family_%28biology%29&quot;&gt;families&lt;/a&gt; have been identified?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've often often come across figures for the total number of species on Earth. Recently, I found myself wondering about the encompassing ranks above them, specifically family, but I can't recall any figures on family and it's a little difficult finding what I want by typing &quot;family&quot; into a Google search. ;)&lt;/p&gt;&#xA;" OwnerUserId="5366" LastActivityDate="2017-05-02T12:08:29.020" Title="How many (taxonomic) families are there?" Tags="&lt;taxonomy&gt;&lt;statistics&gt;&lt;biostatistics&gt;" AnswerCount="5" CommentCount="3" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14889" PostTypeId="1" AcceptedAnswerId="14892" CreationDate="2014-02-06T19:19:13.653" Score="0" ViewCount="632" Body="&lt;p&gt;I am reading my study materials and think what is the systemic POV here&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Regional circulation&lt;/strong&gt; Blood flow within the tissue/organs based on the functional demands of the tissue. &#xA;      E.g. The blood flow to the brain should remain relatively constant from a systemic POV (13% of CO at rest).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the POV here?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Extension to the question and explanation.&lt;/strong&gt;&#xA;The last part is just 13% of maximal cardiac output.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-07T20:46:25.277" LastActivityDate="2014-02-07T20:46:25.277" Title="Regional circulation and Cardiac output?" Tags="&lt;physiology&gt;&lt;homework&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2014-02-08T00:54:52.283" ContentLicense="CC BY-SA 3.0" />
  <row Id="14890" PostTypeId="2" ParentId="14888" CreationDate="2014-02-06T19:22:35.547" Score="5" Body="&lt;p&gt;I don't know about other groups, but about plants, number of families depends on the system you follow. Recent version of The Plant List (1.1) estimates about 352 000 species of Angiosperms and lists over 400 families. See &lt;a href=&quot;http://www.theplantlist.org/1.1/browse/A/&quot; rel=&quot;noreferrer&quot;&gt;http://www.theplantlist.org/1.1/browse/A/&lt;/a&gt; It is very good and reliable source of information. Second very good source about plant systematics is database Tropicos provided by Missouri Botanical Garden and Angiosperm Phylogeny Group. See list of families according to APG3 &lt;a href=&quot;http://www.mobot.org/MOBOT/research/APweb/&quot; rel=&quot;noreferrer&quot;&gt;http://www.mobot.org/MOBOT/research/APweb/&lt;/a&gt; and click to &quot;Families&quot; on the top of the page. Just note, that there are also synonyms, so that You can't just count the rows. ;-)&lt;/p&gt;&#xA;" OwnerUserId="5587" LastActivityDate="2014-02-06T19:22:35.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14892" PostTypeId="2" ParentId="14889" CreationDate="2014-02-06T21:13:44.147" Score="2" Body="&lt;p&gt;It might be as simple as 'point of view'.&lt;/p&gt;&#xA;" OwnerUserId="5657" LastActivityDate="2014-02-06T21:13:44.147" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14893" PostTypeId="1" AcceptedAnswerId="14896" CreationDate="2014-02-06T21:23:40.260" Score="1" ViewCount="1171" Body="&lt;p&gt;When you record a video while pointing the viewfinder towards the screen showing a live preview you create optical feedback: &lt;a href=&quot;http://www.youtube.com/watch?v=CTyH_Q82lIw&quot; rel=&quot;nofollow&quot;&gt;video example&lt;/a&gt;. An anoalogous effect occurs when you turn your microphone towards the speaker.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you look at your own retina with the same eye, does our brain create a similar effect as recorded in the video? Or could it be something different all together?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;Obviously the best way to find out is to 'just go ahead' and see for myself, but it seems as if I don't have the proper conditions to test this at home: The pupil gets too small in the mirror and thus the retina is plain dark. Such an experiment would require eye drops to force widen the pupil and allow for more light onto the retina. &lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5656" LastEditorUserId="5656" LastEditDate="2014-02-06T21:30:07.137" LastActivityDate="2020-11-10T05:35:53.593" Title="What do you see if you look at your own retina with the same eye? (optical feedback)" Tags="&lt;eyes&gt;&lt;human-eye&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14894" PostTypeId="2" ParentId="14831" CreationDate="2014-02-06T21:27:22.737" Score="3" Body="&lt;p&gt;This is not on theoretical grounds, but here is an existence proof: a number of bacteria, which reproduce asexually, are polyploid. &lt;a href=&quot;http://schaechter.asmblog.org/schaechter/2010/11/of-terms-in-biology-bacterial-ploidy.html&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a blog I really like informally discussing the concept of ploidy in bacteria. The example I am familiar with is cyanobacteria, which can have 3-4 all the way up to 142 copies of its genome, according to this paper &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2011.02368.x/pdf&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt;. There are other examples as well, such as &lt;em&gt;Epulopisculum&lt;/em&gt;, a sturgeonfish symbiont &lt;a href=&quot;http://www.pnas.org/content/105/18/6730.full&quot; rel=&quot;nofollow&quot;&gt;(2)&lt;/a&gt;. This paper even reports a diploid bacteria &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812979/&quot; rel=&quot;nofollow&quot;&gt;(3)&lt;/a&gt;. Searching in Pubmed should reveal other interesting cases of this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A more borderline example would be even the most typical bug &lt;em&gt;E. coli&lt;/em&gt;. When &lt;em&gt;E. coli&lt;/em&gt; grows rapidly, it is well known that it has more than one copy of its genome per cell; this allows the organism to be creating the genome for the granddaughters of the current cell, allowing the time between divisions to be shorter than the time it takes to replicate DNA &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0022283668904245&quot; rel=&quot;nofollow&quot;&gt;(4)&lt;/a&gt;. &lt;a href=&quot;http://sandwalk.blogspot.co.uk/2008/05/dna-replication-in-e-coli-solution.html&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is an intuitive explanation of this. Depending on your definition of polyploidy this might not count, but the bacteria presumably are able to make use of this copy number effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2011.02368.x/pdf&quot; rel=&quot;nofollow&quot;&gt;(1) Greise M et al. (2011). Ploidy in cyanobacteria. &lt;em&gt;FEMS Microbiol. Lett.&lt;/em&gt; 323(2):124-31&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/105/18/6730.full&quot; rel=&quot;nofollow&quot;&gt;(2) Mendell JE et al (2008). Extreme polyploidy in a large bacterium. &lt;em&gt;PNAS&lt;/em&gt; 105(18): 6730-34&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812979/&quot; rel=&quot;nofollow&quot;&gt;(3) Michelsen O et al (2010). &lt;em&gt;J. Bacteriol.&lt;/em&gt; 192(4): 1058-65&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0022283668904245&quot; rel=&quot;nofollow&quot;&gt;(4) Helmstetter CE (1968). DNA synthesis during the division cycle of rapidly growing &lt;em&gt;Escherichia coli&lt;/em&gt; B/r. &lt;em&gt;J. Mol. Biol.&lt;/em&gt; 31(3) 507-518&lt;/a&gt; ---non-free, unfortunately, but see also &lt;a href=&quot;http://jb.asm.org/content/189/23/8660.long&quot; rel=&quot;nofollow&quot;&gt;Nielsen HJ et al (2007). &lt;em&gt;J. Bacteriol.&lt;/em&gt; 189(23):8660-6&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2014-02-06T21:27:22.737" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14895" PostTypeId="2" ParentId="14893" CreationDate="2014-02-06T22:24:07.513" Score="2" Body="&lt;p&gt;You would see your retina and that's all. There would have no &quot;&lt;a href=&quot;http://fr.wikipedia.org/wiki/Mise_en_abyme&quot; rel=&quot;nofollow noreferrer&quot;&gt;mise-en-abyme&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to experience this feedback loop you describe, you need to see something which includes the total picture of what you see. For example: You might see a woman holding a frame of the totality of what you see.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PubEQ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you look at your retina, you can't see something which includes the total picture of what you see, you just see your retina! It would probably work if the retina was a mirror (or any output device) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question might not really a good fit for Biology.SE. You might have a chance to make a good fit by asking a question on the mechanistic nature of the process called mise-en-abyme on &lt;a href=&quot;http://philosophy.stackexchange.com&quot;&gt;Phylosophy.SE&lt;/a&gt;. And ask wether one can live this same process with any of their sense (perception). You can ask whether the &lt;a href=&quot;http://en.wikipedia.org/wiki/Audio_feedback&quot; rel=&quot;nofollow noreferrer&quot;&gt;Larsen effect&lt;/a&gt; (audio feedback) is a similar process to the one we experience when looking at this picture and in what terms they are similar and in what terms they differ. If you ask such question, I welcome you to add the link on this post (except if the post get closed)!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-02-10T07:23:01.877" LastActivityDate="2014-02-10T07:23:01.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14896" PostTypeId="2" ParentId="14893" CreationDate="2014-02-06T22:48:02.773" Score="2" Body="&lt;p&gt;There was an answer posted here and deleted again - which I think has found the error my question. Please undelete it :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What the eye observes once it glances at the retina is a physically &lt;strong&gt;constant image&lt;/strong&gt; of the retina.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order for the optical feedback loop to work however, the retina image 'in' the mirror would need to be affected by what is projected onto the retina of the observing eye. Since the retina image in the mirror is constant (there is no link of any kind between whe mirrored retina an the observing retina) the projected image onto the retina of the observing eye is constant as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The loop is broken and there is no optical feedback.&lt;/p&gt;&#xA;" OwnerUserId="5656" LastActivityDate="2014-02-06T22:48:02.773" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14897" PostTypeId="1" CreationDate="2014-02-06T23:04:43.047" Score="8" ViewCount="21397" Body="&lt;p&gt;This is basically a fun question, inspired by this &lt;a href=&quot;https://scifi.stackexchange.com/a/49594/8368&quot;&gt;answer&lt;/a&gt; on scifi.se. So, which cell type will have the greatest number of mitochondria? Obviously, I am talking about wild type, healthy individuals and am looking for a rule of thumb. I realize that the number can change under different conditions/ between different individuals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Off the top of my head, I would say that it's sperm cells given the strenuous exercise they need to perform and their MT-packed axonemes but perhaps there are better contenders?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am primarily interested in human cell types but answers dealing with other mammals are welcome.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2017-04-13T12:43:38.097" LastActivityDate="2015-06-28T15:21:33.037" Title="Which of the cell types commonly found in mammals has the greatest number of mitochondria?" Tags="&lt;cell-biology&gt;&lt;mitochondria&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14899" PostTypeId="1" AcceptedAnswerId="14971" CreationDate="2014-02-07T03:10:59.123" Score="4" ViewCount="624" Body="&lt;p&gt;I've recently heard a podcast, in which &lt;a href=&quot;http://en.wikipedia.org/wiki/Helen_Fisher_%28anthropologist%29#Four_broad_personality_styles&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dr. Helen Fisher suggests that there are &amp;quot;4 broad personality types&amp;quot;&lt;/a&gt;, and each one is associated with a particular neurotransmitter:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The corresponding Platonic thinking style, Keirsey temperament type (according to some readers, not Fisher herself), and color can be seen in parenthesis.&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Explorer (creative; Artisan temperament, yellow) = &lt;strong&gt;dopamine&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;Builder (sensible; Guardian temperament, blue) = &lt;strong&gt;serotonin&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;Director (reasoning; Rational temperament; red) = &lt;strong&gt;testosterone&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;Negotiator (intuitive; Idealist temperament; green) = &lt;strong&gt;estrogen/oxytocin&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I'm interested &lt;strong&gt;if there's indeed scientific evidence&lt;/strong&gt; to support that for different people their &lt;strong&gt;affinity for a certain neurotransmitter&lt;/strong&gt; is increased to such degree that it manifests in a noticeable difference in personality?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-02-12T07:17:53.063" Title="Do humans have a &quot;dominant&quot; neurotransmitter system/sensitivity within their brain?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;endocrinology&gt;&lt;neurotransmitter&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14900" PostTypeId="1" AcceptedAnswerId="20598" CreationDate="2014-02-07T08:55:37.657" Score="1" ViewCount="358" Body="&lt;p&gt;I find this statement that Aorta is called Compression Chamber in my study materials.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aorta can&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;it keeps blood flowing&lt;/li&gt;&#xA;&lt;li&gt;it can accumulate potential energy for bumping and compression &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;However, why aorta is called chamber and particularly compression chamber?&lt;/strong&gt;&#xA;I heard this term today first time.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-07T19:48:29.920" LastActivityDate="2014-08-18T21:02:44.070" Title="Why is Aorta sometimes called Compression chamber?" Tags="&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14902" PostTypeId="1" CreationDate="2014-02-07T10:00:19.743" Score="2" ViewCount="1621" Body="&lt;p&gt;There is one type of potassium voltage-gated channels open in Phase 1 too.&#xA;Some call them early repolarization channels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not convinced that the channels are different in different phases: 0, 2, 3 and 4.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think all these potassium channels are voltage-gated.&#xA;However, they probably differ in some places.&#xA;I am not sure if one type of channel can be open in all these five phases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which types of potassium channels are open during the action potential of cardiomyocyte?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-07T19:46:11.573" LastActivityDate="2015-01-11T15:35:45.940" Title="Voltage-gated Potassium channels in the action potential of cardiomyocyte?" Tags="&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14903" PostTypeId="1" AcceptedAnswerId="19168" CreationDate="2014-02-07T10:16:18.973" Score="7" ViewCount="141" Body="&lt;p&gt;Having DNA samples of all or almost all members of a population of, say, a few hundred or thousand individuals, is it possible to draw the entire family tree of those individuals? (Let's not assume monogamy or any other facilitation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This may be a sum of two different questions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;does comparison of two DNA samples give any information other than topographical distance between individuals? In other words, is it possible to tell two sisters from a mother and a daughter by DNA alone?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;(more a mathematical question than a biological one, maybe) having the relative topographical distance of all members of a group, can their full graph be drawn?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5233" LastEditorUserId="5233" LastEditDate="2014-02-07T18:36:41.173" LastActivityDate="2014-06-17T22:04:02.470" Title="is it possible to completely reconstruct a family tree by DNA comparison alone?" Tags="&lt;dna&gt;&lt;genetic-diagrams&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14905" PostTypeId="1" AcceptedAnswerId="14906" CreationDate="2014-02-07T12:54:48.627" Score="1" ViewCount="1833" Body="&lt;p&gt;Given what we know of the genetics of eye color and their historical distribution, is it possible or at least plausible for a person born in the Horn of Africa during the early Neolithic (ca. 9000 BCE), assuming no recent ancestors from outside this area, to have had amber eyes (or in general anything other than brown?) If so, would one or both parents need to have that color as well, and what of siblings?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that today there is much less isolation and much more crossing of genetic lines, so that pretty much any combination of skin and eye color is likely possible, but no doubt it was different back then.&lt;/p&gt;&#xA;" OwnerDisplayName="user5661" LastActivityDate="2018-07-17T12:23:43.037" Title="Amber eye color in Neolithic Africa" Tags="&lt;eyes&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14906" PostTypeId="2" ParentId="14905" CreationDate="2014-02-07T16:15:14.857" Score="0" Body="&lt;p&gt;There are two possibilities: First, that an individual develops a mutation de novo and is the first to carry it. &#xA;When we talk about recessive expressed allels, than both parents need to have a copy of the allel, otherwise it will not show up in the kids. In this case a mixed population of siblings is to be expected (some carrying both recessive allels, some only one). &#xA;However, its most likely, that the eye color at this time was brown. As far as I know, there has been no evidence so far from ancient DNA that this has been different. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The oldest DNAfrom Europe, which has been analyzed and which showed a difference for the eye color comes from Spain (La Brana-Arintero site in Valdelugueros) and is about 7.000 years old. See this &lt;a href=&quot;http://www.sciencedaily.com/releases/2014/01/140126134643.htm&quot; rel=&quot;nofollow&quot;&gt;report&lt;/a&gt; about it. This individual is thought to have an &quot;african&quot; type of pigmentation but blue eyes. The original publication is called &quot;&lt;a href=&quot;http://bioinfo2.ugr.es/PDFsClase/EvolMol/Cazador%20de%20ojos%20azules%20y%20piel%20oscura_nature12960.pdf&quot; rel=&quot;nofollow&quot;&gt;Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another paper claims that the blue eye color comes from a mutation which occured in a gene called &quot;OCA2&quot; in the black sea region some 6-10.000 years ago. See here: &quot;&lt;a href=&quot;http://link.springer.com/article/10.1007/s00439-007-0460-x&quot; rel=&quot;nofollow&quot;&gt;Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression&lt;/a&gt;&quot;&#xA;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-02-07T17:01:02.020" LastActivityDate="2014-02-07T17:01:02.020" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14907" PostTypeId="1" CreationDate="2014-02-07T19:08:13.150" Score="1" ViewCount="30" Body="&lt;p&gt;There are currently ongoing clinical trials for neurostimulation implants designed to keep the tongue from blocking the airway in obstructive sleep apnea.  The nerves for this are in the neck and surgically accessible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where are the nerves that control the soft-palate, and would it be plausible to implant a similar device for them (given years of development obviously)?&lt;/p&gt;&#xA;" OwnerUserId="5664" LastActivityDate="2014-02-07T19:08:13.150" Title="Is a neurostimulation implant for the soft-palate component of obstructive sleep apnea plausible?" Tags="&lt;biotechnology&gt;&lt;medicine&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14908" PostTypeId="1" CreationDate="2014-02-07T20:21:41.300" Score="2" ViewCount="199" Body="&lt;p&gt;Do you know any program which can compare two and more different RNA secondary structures? I need find some (dis)similarities between lots of predicted secondary structures. And create maybe common sec. structure/shape.&lt;/p&gt;&#xA;" OwnerUserId="5665" LastActivityDate="2014-02-09T21:33:43.533" Title="RNA secondary structure comparison" Tags="&lt;bioinformatics&gt;&lt;rna&gt;&lt;structure-prediction&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14909" PostTypeId="1" AcceptedAnswerId="20596" CreationDate="2014-02-07T20:24:18.167" Score="3" ViewCount="442" Body="&lt;p&gt;My study materials use the word &lt;strong&gt;vesselcompression chamber&lt;/strong&gt; of aorta to emphasize aorta's elastic property.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The arch of the aorta only coils, not its straight part.&#xA;I think the reason why the arch coils is the elasticity of aorta (artery) is high.&#xA;If the elasticity is too low, then the aorta is more stiff.&#xA;This means that heart has to work harder so higher systolic pressure and lower diastolic pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why does the arch of the aorta coils?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-08-19T05:55:39.463" LastActivityDate="2014-08-19T05:55:39.463" Title="Why does the arch of aorta coils?" Tags="&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14910" PostTypeId="1" AcceptedAnswerId="14914" CreationDate="2014-02-07T20:36:09.960" Score="1" ViewCount="88" Body="&lt;p&gt;I am thinking the more reasons why sitting much lead to thrombosis i.e. clotting of blood in blood vessels and then hypoxia in the deep tissues eventually.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the physiological mechanisms for this to happen?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One student said hormones. &#xA;It can be right, but I am thinking how.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-08T01:07:18.563" Title="Sitting much, thrombosis and hypoxia" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14912" PostTypeId="2" ParentId="14899" CreationDate="2014-02-07T22:07:59.293" Score="0" Body="&lt;p&gt;I know that the Keirsey model itself is rather unsubstantiated. It's a sort of simplified version of MBTI. So I am not sure if relating the neurotransmitters to Keirsey temperament would work due to the fallibility of temperaments.&#xA;However, different neurotransmitter levels certainly contribute to different moods. That has been proved. Does that translate to personality? Don't know.&lt;/p&gt;&#xA;" OwnerUserId="5668" LastActivityDate="2014-02-07T22:07:59.293" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14913" PostTypeId="1" CreationDate="2014-02-07T22:25:11.793" Score="2" ViewCount="383" Body="&lt;p&gt;Some systems are in parallel. &#xA;For instance, the resistance of lungs $R_{\text{lungs}}$. &#xA;Assume here for simplicity that these parallel systems can be handled linearly. &#xA;We also consider only Total Vascular Resistance for simplification.&#xA;So we have now only systems in series under consideration. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Linear system  for Systemic Vascular Resistance&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Formula for the total resistance as mechanical definition as assuming linear connections between those systems:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$R_{\text{total}}=R_A+R_a+R_c+R_V+R_v$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where appropriate resistances are&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;$R_c$ capillaries, &lt;/li&gt;&#xA;&lt;li&gt;$R_a$ arterioles,  &lt;/li&gt;&#xA;&lt;li&gt;$R_A$ Small artery,  &lt;/li&gt;&#xA;&lt;li&gt;$R_v$ venules and &lt;/li&gt;&#xA;&lt;li&gt;$R_V$ vein.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Nonlinear system for Systemic Vascular Resistance&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There are many factors involved in these locations:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;permeability&lt;/li&gt;&#xA;&lt;li&gt;vasoconstriction&lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;li&gt;growth factors (FGF) for renewal of the vessel wall&lt;/li&gt;&#xA;&lt;li&gt;different channels (activated, deactivated - mostly potassium channels)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;where I skip the consideration of vasoconstriction, growth factors and different channels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Permeability is one which applies to all types of vessels. &#xA;Change in permeability of one location does not mean a linear change in permeability in another. &#xA;A change in the permeability of small arterioles does not lead to a similar change in the arteries or venules. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The vessel is permeable to gas and liquid. &#xA;Let's consider only these components.&#xA;I want to include these facts into the definition because, in the pathological situations, different state of inflammation for instance can apply to a vessel. &#xA;Let's call total permeability $S$ which is dependent on gas and liquid components, first on liquid component (so inner integral). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could give you the nonlinear formula of the total resistance but I think it goes over the skills most here. &#xA;Let's call the nonlinear resistance dependent on permeability of the vessel, $W(x,y)(t,f)$ in time and space.&#xA;So consider only the nonlinear component of the permeability formula after parametrisation i.e. permeability, let's call it $T$, which is dependent on changes in water (w) and gas (g) components over a path integral. &#xA;The path covers all components in the vascular system that are in series. &#xA;So total resistance defined nonlinearly&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$W(x,y)(t,f) = \int_{\gamma} T(u) \frac{1}{u} \int_{t-u/2}^{t+u/2} T(w) \, S(x,y)(t,f) dw \, du$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where the inner integral corresponds to the water component while the outer integral to the gaseous component. &#xA;There is only an averaging in the inner integral when the width of the window is $u$. &#xA;However, we do not any windowing here actually, just because of this averaging, so we lose no data and can handle the total resistance as a single process. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notice that change in $T(u)$ leads to a change in $T(w)$ nonlinearly.&#xA;I skip the nonlinear definition of $S(x,y)(t,f)$ which stands for the energy in time in each instance - you can think it as the amount of permeability in each position of the vessel.&#xA;Actually, I also skipped the explicit definitions of the water and gaseous components too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have not found any work done on the nonlinear development of the resistance. &#xA;I think this is necessary for defining inflammation explicitly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can you describe the total resistance as an nonlinear operation better?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-05T14:25:06.020" LastActivityDate="2014-12-05T23:25:13.347" Title="To define the total Resistance of Systemic Blood Circulation" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;blood-circulation&gt;&lt;electrophysiology&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14914" PostTypeId="2" ParentId="14910" CreationDate="2014-02-08T01:07:18.563" Score="3" Body="&lt;p&gt;Venous return from the limbs is largely facilitated by the action of neighbouring skeletal muscles compressing the veins and forcing the blood proximally past the valves which prevent back flow.  If you are inactive for a long time by sitting, or are sitting in such a way as to impede blood returning from your calves (i.e. with the back of your knees pressing into the edge of the chair) blood movement in this manner is greatly slowed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Blood that is moving more slowly or turbulently has a greater propensity to coagulate and form a thrombus.  This is similar to the rationale for prescribing anti coagulants to patients with atrial fibrillation - the turbulent and slow movement of blood through their atria leaves them at greater risk of throwing a clot to the brain causing a cerebrovascular accident.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hypoxia isn't really that relevant in the case you describe as arterial supply is unaffected (much higher pressure) meaning tissues do not become ischaemic. There is also collateral venous drainage from the limb although this can subsequently cause problems in the form of post thrombotic syndrome.  The most significant risk would be that of the thrombus breaking off and lodging in the lungs - a pulmonary embolism.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2014-02-08T01:07:18.563" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14918" PostTypeId="1" AcceptedAnswerId="14960" CreationDate="2014-02-08T17:44:14.227" Score="0" ViewCount="7311" Body="&lt;p&gt;The latent period is the time between the start of depolarisation and the start of contraction. &#xA;I know that the contraction of ventricles starts after sufficient influx of Ca2+ and threshold potential is met.&#xA;The influx of Ca2+ is at start of Phase 2, so Phase 0 and 1 are included in the latent period.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Comparing to &lt;strong&gt;electrocardiogram&lt;/strong&gt; is not simple, since there is always at least some time lag between the event and the recording.&#xA;I think there not much sense to compare cellular model events to ECG recordings here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which cellular processes does the latent period include?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-11T17:05:58.873" LastActivityDate="2014-02-15T20:52:12.553" Title="Which processes are during the latent period of ventricular contraction?" Tags="&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14919" PostTypeId="1" AcceptedAnswerId="21174" CreationDate="2014-02-09T13:59:18.213" Score="29" ViewCount="286865" Body="&lt;p&gt;I have learned (probably in high school?) that hairs turning white is caused by the part of the folicle which produces the pigment dying and being replaced by an air bubble. This sounds very irreversible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have long dark brown hair, and since I turned 25, I have had a few white hairs here and there. It is not unusual to find hairs which have a dark tip but are white at the root, which fits the above theory. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I also have hairs which are the opposite: the lower ten centimeters are pure white, but at some point, there is an abrupt transition to dark brown, and the hair is dark again up to the root. This is all a natural phenomenon, I haven't used dyes or bleaches. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what makes white hair white, if it can turn back to dark? Why would a single hair turn back? &lt;/p&gt;&#xA;" OwnerUserId="1578" LastActivityDate="2019-03-22T07:54:38.140" Title="Why can white hairs get dark again?" Tags="&lt;pigmentation&gt;&lt;hair&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="14920" PostTypeId="2" ParentId="14908" CreationDate="2014-02-09T14:25:33.317" Score="3" Body="&lt;p&gt;You can use &lt;a href=&quot;http://tcoffee.crg.cat/apps/tcoffee/do:rcoffee&quot; rel=&quot;nofollow noreferrer&quot;&gt;R-coffee&lt;/a&gt; of the T-coffee suite of tools. In general, the *coffee tools are excellent and work very well if you can get over their author's self obsession&lt;sup&gt;1&lt;/sup&gt;. R-coffee can align RNA sequences taking into account structural information:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/52Pcr.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt; The guy actually adds his name to the output of all his programs! Seriously, he does. Apart from being simply ridiculous, this also affects other programs you might want to pipe your data to. For example, I wanted to pipe t-coffee alignments to an alignment viewer and I had to parse out his effing name in order to be able to do it. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-02-09T14:25:33.317" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14923" PostTypeId="1" AcceptedAnswerId="14925" CreationDate="2014-02-09T15:31:30.697" Score="1" ViewCount="165" Body="&lt;p&gt;I am looking for a statistical amounts which are allowed.&#xA;Some students say it is 0 for all bacteria, which I think is false.&#xA;I found &lt;a href=&quot;http://water.epa.gov/drink/contaminants/&quot; rel=&quot;nofollow&quot;&gt;this USA source&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found there&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Total Coliforms (including fecal coliform and E. Coli) mg/l. No more than 5.0% samples total coliform-positive (TC-positive) in a month.&lt;/li&gt;&#xA;&lt;li&gt;Giardia lamblia: 99.9% removal/inactivation.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the right place to look for such information?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-09T15:45:13.317" LastActivityDate="2014-02-09T17:51:28.130" Title="What is the maximum amount of different bacteria in the drinking water in Europe?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14924" PostTypeId="1" CreationDate="2014-02-09T15:41:17.420" Score="5" ViewCount="1550" Body="&lt;p&gt;I want to know how aquatic animals behave as a natural indicator of the acidity in lakes and rivers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do they tolerate these pH change?&lt;/p&gt;&#xA;" OwnerUserId="5676" LastEditorUserId="20392" LastEditDate="2017-04-01T09:40:32.727" LastActivityDate="2017-04-01T09:40:32.727" Title="How do fish tolerate pH changes in water?" Tags="&lt;ecology&gt;&lt;ichthyology&gt;&lt;biochemistry&gt;&lt;ph&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14925" PostTypeId="2" ParentId="14923" CreationDate="2014-02-09T16:41:13.887" Score="3" Body="&lt;p&gt;No, your colleages are right: There should be no coliforms in drinking water in Europe following the &lt;a href=&quot;http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=CELEX:31980L0777:EN:HTML&quot; rel=&quot;nofollow noreferrer&quot;&gt;Council Directive 80/777/EEC&lt;/a&gt;.&#xA;This PDF from the &lt;a href=&quot;http://www.coralenvironmental.com/wp-content/uploads/European-and-National-Drinking-Water-Quality-Standards.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Northern Ireland Environment Agency&lt;/a&gt; (which follows the directice mentioned above) shows this a bit nicer.&#xA;It makes sense, since coliforms are a sign of mixing sewage and fresh water. Nothing you want to have happening.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the relevant table from the linked PDF:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/4J2GN.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1306" LastEditDate="2014-02-09T17:51:28.130" LastActivityDate="2014-02-09T17:51:28.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14926" PostTypeId="1" AcceptedAnswerId="14927" CreationDate="2014-02-09T16:53:06.270" Score="1" ViewCount="4825" Body="&lt;p&gt;I am trying find explanation for these mechanisms&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Tox plasmid -&gt; exotoxin (enterotoxin) -&gt; activation of adenylcyclase&#xA;  -&gt; \up cAMP enterocytes -&gt; release of H2O, electrolytes in gut lumen -&gt; diarrhea.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Tox plasmid is a toxin generated by the genus enterobacteriaceae.&#xA;I read this as that exotoxin Tox activates adenilciclase enzyme (protein) which increases the amount of cyclic AMP in the enterocytes, and releases water and electrocytes into gut lumen consequently resulting in diarrhea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How does the activation of adenylcyclase lead to increased cAMP heparis and diarrhea?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-09T16:58:24.757" LastActivityDate="2018-12-19T20:03:35.963" Title="How does activation of adenylcyclase lead to increased cAMP and diarrhea?" Tags="&lt;microbiology&gt;&lt;liver&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14927" PostTypeId="2" ParentId="14926" CreationDate="2014-02-09T17:15:57.553" Score="2" Body="&lt;p&gt;The crypt cells of the gut can actively secrete electrolytes (ions) via special channel which finally leads to water secretion. This is usually tightly controlled, since uncontrolled loss of water is obviously not good for the cells.&#xA;Have a look at this schematic figure, (from this &lt;a href=&quot;http://www.vivo.colostate.edu/hbooks/pathphys/digestion/smallgut/secretion.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;webpage&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/H6nCM.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Sodium, Potassium and Chloride ions are co-transported into the cell,&#xA;sodium and potassium are transported back out via other channels.&lt;/li&gt;&#xA;&lt;li&gt;If the adenyl cyclase is activated (for example by bacterial toxins,&#xA;cholera does this), then cAMP is made.&lt;/li&gt;&#xA;&lt;li&gt;cAMP aktivates Protein Kinase A (PKA) which in turn phosphorylates the the Cystic fibrosis transmembrane conductance regulator&#xA;(CFTR)(this channel is also important for cystic fibrosis) which leads&#xA;to the secretion of chloride ions from the cell. This builds up a&#xA;negative potential across the membrane (positively charged ions are&#xA;missing).&lt;/li&gt;&#xA;&lt;li&gt;This leads to the secretion of sodium ions through the tight&#xA;junctions, resulting in the netto secretion of NaCl.&lt;/li&gt;&#xA;&lt;li&gt;The secretion of salt builds up and osmotic gradient across the&#xA;membrane, which leads to water secretion and can also lead to hyponatraemia.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;To overcome this problems, the so called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Oral_rehydration_therapy&quot; rel=&quot;nofollow noreferrer&quot;&gt;oral rehydration therapy&lt;/a&gt;&quot; is used. The solution contains of an isotonic solution of sodium chloride and glucose. This is taken up by the sodium-glucose symporter (a special class of transporter, that transports two molecules in the same direction) and builds up a gradient which is directed in the opposite direction of the diarrhoea, helping to fight dehydration.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2018-12-19T20:03:35.963" LastActivityDate="2018-12-19T20:03:35.963" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="14932" PostTypeId="2" ParentId="14908" CreationDate="2014-02-09T21:33:43.533" Score="2" Body="&lt;p&gt;there a number of tools in the Vienna package (RNAalifold, RNALalifold):&#xA;&lt;a href=&quot;http://www.tbi.univie.ac.at/~ronny/RNA/index.html&quot; rel=&quot;nofollow&quot;&gt;http://www.tbi.univie.ac.at/~ronny/RNA/index.html&lt;/a&gt;&#xA;some other tools are available from Freiburg Univ. such as:&#xA;LocARNA or CARNA (&lt;a href=&quot;http://rna.informatik.uni-freiburg.de/CARNA/Input.jsp&quot; rel=&quot;nofollow&quot;&gt;http://rna.informatik.uni-freiburg.de/CARNA/Input.jsp&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="4453" LastActivityDate="2014-02-09T21:33:43.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14933" PostTypeId="1" CreationDate="2014-02-09T22:12:25.707" Score="3" ViewCount="986" Body="&lt;p&gt;Consider the following question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Piney Woods of Eastern Texas is home to a wide variety of organisms ranging from the grass Longleaf Oats to coyotes. Which of the following best explains why these varied specifies can live together in this particular ecosystem?&#xA;  A.) Each species lives in a slightly different habitat B.) Each spices occupies a different niche C.) Each species functions at a different trophic level D.) A and B   E.) A, B, and C&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I chose answer choice E with the reasoning that: Oats and Coyotes do not share the same habitat; they occupy a different niche -- Coyotes eat organisms, oats use photosynthesis; coyotes are at a completely different trophic level when compared to oats -- oats being primary producers. The answer choice E however is incorrect and I'd like to know why and what the correct answer should be. Is there a flaw in my logic? &lt;/p&gt;&#xA;" OwnerUserId="4890" LastActivityDate="2014-02-10T02:20:53.603" Title="Why Can Varied Species Live Together in Particular Ecosystems?" Tags="&lt;homework&gt;&lt;ecology&gt;&lt;ecosystem&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14937" PostTypeId="1" CreationDate="2014-02-10T00:01:29.517" Score="2" ViewCount="604" Body="&lt;p&gt;I have two biotins--one of which is binding my RNA with cleavable bonds, and the other with irreversible bonds. Does biotin have an effect if it keeps its bonds with RNA? If it does, why is this the case?&lt;/p&gt;&#xA;" OwnerUserId="5630" LastEditorUserId="1855" LastEditDate="2014-02-12T18:14:57.653" LastActivityDate="2014-08-18T01:19:33.763" Title="Does biotin affect downstream experiments, such as RT-qPCR?" Tags="&lt;molecular-biology&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14939" PostTypeId="2" ParentId="14933" CreationDate="2014-02-10T02:20:53.603" Score="1" Body="&lt;p&gt;The answer should be B &quot;Each spices occupies a different niche&quot; because this is the only answer that reflects a model of species coexistence.  Niche theory proposes a mechanism that allows multiple species to occupy the same space and time any yet avoid competition for limited resources.  Briefly, the model says that a species niche is the total suite of resources that it requires to survice and reproduce and that coexisting species will limit their niche overlap to avoid competition (and its requisite reduction in fitness).  Species can limit niche overlap by preferentially using a subset of resources that are not shared with potentially competing species (this is called the realized niche) or by evolving a new niche that does not overlap with the competitor (this is called character displacement).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that your reasoning is incomplete because the question does not specify that the organisms listed are the complete set of organisms  in the community.  For example if the community contained another species of grass, then choice &quot;C&quot; would be false.  Most importantly though, habitat or trophic variation are not mechanisms of coexistence, so they should not be used as general hypotheses explaining coexistence.&lt;/p&gt;&#xA;" OwnerUserId="137" LastActivityDate="2014-02-10T02:20:53.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14940" PostTypeId="1" AcceptedAnswerId="15196" CreationDate="2014-02-10T08:16:52.550" Score="2" ViewCount="299" Body="&lt;p&gt;Trying to find a way to take a cancer drug (from CancerDR, for instance) and infer the metabolic reactions that are affected by it in the Human Metabolic Model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially, I would like to know which HMM reactions are affected by a certain cancer therapy drug, especially the ones found in the Cancer Cell Line Encyclopedia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Example:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Searching for the reactions that are associated with the &lt;code&gt;HSP90&lt;/code&gt; protein, which is targeted (to some extent) by the &lt;code&gt;17-AAG&lt;/code&gt; agent.  That way, I can trace back the relevant section of the HMM and mark it as 'affected' by that agent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This could be a very broad or naïve question, but I am afraid I don't know enough to be able to determine that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If someone can only provide some tip or guidance, that will be greatly appreciated as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks very much!&lt;/p&gt;&#xA;" OwnerUserId="5680" LastEditorUserId="5680" LastEditDate="2014-02-10T08:30:03.960" LastActivityDate="2014-02-20T21:49:23.850" Title="How to relate human metabolic model reactions and cancer drug targets / reactome items?" Tags="&lt;molecular-biology&gt;&lt;pharmacology&gt;&lt;metabolism&gt;&lt;systems-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14941" PostTypeId="1" AcceptedAnswerId="14944" CreationDate="2014-02-10T09:41:30.790" Score="2" ViewCount="118" Body="&lt;p&gt;I am reading about the protein family in relation to the prolongation of cell life.&#xA;It is known that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sirtuins have been implicated in influencing a wide range of cellular&#xA;  processes like ageing, transcription, apoptosis, inflammation and&#xA;  stress resistance, as well as energy efficiency and alertness during&#xA;  low-calorie situations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, I am not sure if these physiologic processes are only during low-calorie situations.&#xA;Alertness is at least.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It says in the original paper only that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our results suggest that in the hypothalamus, SIRT1 functions as a key&#xA;  mediator of the central response to low nutritional availability,&#xA;  providing insight into the role of the hypothalamus in the regulation&#xA;  of metabolism and aging in mammals.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, it does not specify how the Sir2 works to high-calorie diet.&#xA;Therefore, I asked mostly.&#xA;&lt;strong&gt;When is the protein family active?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Does the Sirtuin protein family work mostly during low-calorie diet?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-10T13:49:52.913" LastActivityDate="2014-02-10T18:13:06.163" Title="Does Sirtuin protein family Sir2 work in low-calorie diet mostly?" Tags="&lt;physiology&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14942" PostTypeId="1" AcceptedAnswerId="14947" CreationDate="2014-02-10T10:25:43.327" Score="0" ViewCount="94" Body="&lt;p&gt;I am reading about atrophy and I am thinking to which processes the phrase &lt;strong&gt;cells eating themselves&lt;/strong&gt; refer to.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cells need something to survive these difficult times. To decrease&#xA;  protein synthesis to survive. If insufficient, cells start&#xA;  to eat themselves. Then, ubiquitine-proteosome pathway and autophagy&#xA;  pathway.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am not sure if it is only apoptosis.&#xA;It can refer here to longer cascade.&#xA;I think it can at least refer to autophagy where one cell degrades its components.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which processes does the phrase &lt;em&gt;cells eating themselves&lt;/em&gt; include?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-10T21:08:58.637" Title="Which processes are included in the process called cells eating themselves?" Tags="&lt;physiology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14943" PostTypeId="2" ParentId="9626" CreationDate="2014-02-10T11:20:44.780" Score="1" Body="&lt;p&gt;I agree with @gchadwick that more infor would help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, based on my understanding of what you are trying to do (SNP genotyping on several genes), I suggest. &#xA;1) Enrich your DNA with DNA from the organism you want&#xA;2) Enrich your DNA with DNA in the desired regions (if any).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Solution: Target enrichment. You are probably aware that companies such as agilent, nimblegen and illumina offer target enrichment kist for next generation sequencing.&#xA;However, if your DNA is soooo bad, I suggest performing target selection with PCR.  &lt;/p&gt;&#xA;" OwnerUserId="5297" LastActivityDate="2014-02-10T11:20:44.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14944" PostTypeId="2" ParentId="14941" CreationDate="2014-02-10T14:33:39.760" Score="2" Body="&lt;p&gt;Does sirtuin 1 (&lt;a href=&quot;https://en.wikipedia.org/wiki/Sirtuin&quot; rel=&quot;nofollow&quot;&gt;SIRT1/SIR1&lt;/a&gt;) function to mediate the effects of a low calorie diet? Perhaps, but its really not clear.  Is the function of SIRT1 primarily to mediate low calorie response? Absolutely not.  What does that mean for SIRT2/SIR2 - its probably not more closely associated with calorie restriction signals, though it might be connected in a similar ambiguous way... but see below. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly SIRT1 has also been shown to have &lt;a href=&quot;http://www.omim.org/entry/604479&quot; rel=&quot;nofollow&quot;&gt;many influences in many studies&lt;/a&gt; of conditions such as Alzheimers, anxiety and other neuro-functions.  SIRT1 modifies &lt;a href=&quot;https://en.wikipedia.org/wiki/P53&quot; rel=&quot;nofollow&quot;&gt;p53&lt;/a&gt; - a bottleneck in cellular reproduction and a key regulator in cancer prevention, but which also an important aspect as to why it is active in calorie restriction conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When reading reference like the one you have here its important to remember that correlation is not causality.  Very few genes in animals function only when specific behavior or conditions are experienced, especially signaling genes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examining the OMIM report (see link above) there has been a close examination of the possible role of SIRT1 in calorie restriction since the early 2000s in knockout mice. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;SIRT1 would seem to play an important role in embryonic development for instance - cell growth is so important at that point and 80% of mice who are homozygous SIRT1 (-/-) knockouts die before they are born and even more die in the early natal period.  The mice who do survive have problems generating red blood cells which is another important case of cellular reproduction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet the relationship of the knockout mice to calorie restriction has been debated - its been difficult to interpret the activity and the weight loss or gain of the knockout mice compared to wild type mice since the SIRT1 knockouts are smaller.  They may also have genetic traits that compensate for the absence SIRT1 in order to have survived.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More recently mice where SIRT1 expression in the brain have been produced, but the result has been anxiety or anxiousness as opposed to specific calorie restriction diet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This reminds me of the story of &lt;a href=&quot;http://www.omim.org/entry/164160&quot; rel=&quot;nofollow&quot;&gt;leptin&lt;/a&gt;, in the early 90s they found that leptin deficient mice became quite fat, but despite this obvious linkage to obesity, leptin turned out to mediate a lot of other psychological factors as well - it only caused obesity when its function was blocked.  It did not turn out to be an appetite signal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.omim.org/entry/604480&quot; rel=&quot;nofollow&quot;&gt;SIRT2&lt;/a&gt; seems to have similar roles in calorie restriction.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Rogina et al (2002) found that under 2 life-extending conditions, Rpd3 (601241) mutants fed normal food and wildtype flies fed low calorie food, Sir2 expression was increased 2-fold.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But also has similar relationships to Alzheimers.  SIRT2 has not been followed up on as much as SIRT1.  This correlation might not be causal or should be nuanced in a similar way.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-02-10T18:13:06.163" LastActivityDate="2014-02-10T18:13:06.163" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14946" PostTypeId="1" CreationDate="2014-02-10T20:30:00.047" Score="3" ViewCount="211" Body="&lt;p&gt;Is there a way to measure ATP usage in the brain (or anywhere else) similarly to how fMRI works (measuring changes in iron resonance in oxygenated/deoxygenated blood)? Is there some sort of similar signal that can be used for ATP?&lt;/p&gt;&#xA;" OwnerUserId="5684" LastEditorUserId="3340" LastEditDate="2015-06-04T11:46:28.740" LastActivityDate="2015-06-04T11:46:28.740" Title="Is there a way to measure ATP usage in the brain similarly to fMRI?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14947" PostTypeId="2" ParentId="14942" CreationDate="2014-02-10T21:08:58.637" Score="1" Body="&lt;p&gt;So:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the processes are mentioned in the quote you provided: &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Proteasome#Ubiquitination_and_targeting&quot; rel=&quot;nofollow&quot;&gt;ubiquitine-proteasome pathway&lt;/a&gt; (note: it's proteAsome) and &lt;a href=&quot;http://en.wikipedia.org/wiki/Autophagy&quot; rel=&quot;nofollow&quot;&gt;autophagy pathway&lt;/a&gt;&quot;. As far as I know, apoptosis &lt;em&gt;per se&lt;/em&gt; is not utilized for recycling.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-02-10T21:08:58.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14951" PostTypeId="1" AcceptedAnswerId="24534" CreationDate="2014-02-11T01:51:15.993" Score="3" ViewCount="880" Body="&lt;p&gt;I thought there were only two centrioles per cell, that convert to the basal body at some point during the cell cycle. I also thought there's one basal body per cilium, so I'm not clear on where the other basal bodies are coming from. I'd like to know the distribution of basal bodies and centrioles throughout the cell cycle in multi-ciliated organisms/cells.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3340" LastEditDate="2014-12-04T09:36:44.440" LastActivityDate="2016-01-27T11:00:35.490" Title="How many centrioles/basal bodies are there in multi-ciliated cells throughout the cell cycle?" Tags="&lt;cell-biology&gt;&lt;cell-cycle&gt;&lt;cilia&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14952" PostTypeId="1" CreationDate="2014-02-11T04:32:32.017" Score="0" ViewCount="86" Body="&lt;p&gt;Can we determine the gender of a child now,I mean,not randomly?&lt;br/&gt;&#xA;There are equal amount of sperms with X chromosome and Y chromosome.&lt;br/&gt;&#xA;Can these two kinds of sperms be distinguished easily?&lt;br/&gt;&#xA;If yes,we can choose the kind of sperm to meet the ovum,then the gender of the child can be determined.&lt;br/&gt;&lt;/p&gt;&#xA;" OwnerUserId="5688" LastActivityDate="2014-02-11T19:22:08.700" Title="about the direct intervention of a child's gender" Tags="&lt;chromosome&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14953" PostTypeId="2" ParentId="14952" CreationDate="2014-02-11T06:09:40.003" Score="3" Body="&lt;p&gt;Sperms can and are sorted using &lt;a href=&quot;http://en.wikipedia.org/wiki/Sperm_sorting&quot; rel=&quot;nofollow&quot;&gt;flow cytometry&lt;/a&gt; to attempt to separate sub-populations carrying X or Y chromosomes. The technique isn't perfect but it is undergoing &quot;clinical trials&quot; in the USA.&lt;/p&gt;&#xA;" OwnerUserId="12" LastActivityDate="2014-02-11T06:09:40.003" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14954" PostTypeId="2" ParentId="14368" CreationDate="2014-02-11T06:31:27.590" Score="1" Body="&lt;p&gt;I'm going to hazard turning my comment into an answer....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if the answer might be no, you know this is a good thought and there is something there... lets dig a little. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eusociality in evolutionary biology is by many like Dawkins and Wilson pointing to the evolution of sterile castes of animals, which are very closely related to the breeding caste.  This is how hymenoptera are famed as examples of the importance of &lt;a href=&quot;https://en.wikipedia.org/wiki/Kin_selection&quot; rel=&quot;nofollow&quot;&gt;kin selection&lt;/a&gt;. Worker ants are entirely dependent upon the queen to reproduce the next generation, but they can do so because the queen is close enough to being them so that ants continue to exist as they do.  Not only is this a reasonable way to exist, but kin selection has produced eusocial animals in every &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The application of this definition to mammals has been done, but its not &lt;a href=&quot;https://en.wikipedia.org/wiki/Eusociality#In_mammals&quot; rel=&quot;nofollow&quot;&gt;a universally agreed upon definition of eusociality&lt;/a&gt;.  To a great extent its because the animals can still breed, even if they are inhibited from doing so by a social structure.  Wolf packs and ape troops where the alpha male sires all the offspring are not eusocial - the other males are only deferring mating (sometimes forever) but they are biologically fertile.  This is not eusocial, just social biology.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But to your question, I think the point to be considered is that the dynamic that allows the evolution of eusociality does shape social structures.  Primates are so rational and their brains are so big that their brains allow them to adapt their social matrix such that we can have different roles in our groups depending on the conditions of environment at any given moment, whereas sterility and castes defined by adaptation will change very slowly, we can change our society in just a generation.  Social animals are eusocial in a way, but they are more adaptable by the use of their social reprogrammability.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-02-11T06:31:27.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14955" PostTypeId="2" ParentId="14893" CreationDate="2014-02-11T10:36:55.180" Score="1" Body="&lt;p&gt;&lt;em&gt;Feedback&lt;/em&gt; means that the output from a device is fed back to it as new input. You can feed input to a retina, but cannot take its output.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will get no feedback if the microphone is not linked to a speaker, or cannot hear the speaker.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will get no feedback if the video camera is not pointing to the display.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your eye consumes input, but this input is only used to change the state of your brain in mysterious ways. No output is produced. There is no &quot;Kodak&quot; organ in the human body which reproduces with fidelity the image seen by the retina*. Without output, there is nothing to &lt;em&gt;feed back&lt;/em&gt; - same as how you can't get feedback when a camera is not linked to a display. A display, with human beings, would be analogous to a magic machine that reads your mind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you looked at your retina, you'd see your retina. Just like a camera pointed at a mirror would see a camera.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The closest thing you can do is imagine yourself, imagining yourself, imagining yourself... Although you would probably need to take mind-altering substances to experience this fully.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;*: I say no organ exists, but it &lt;em&gt;is&lt;/em&gt; possible for humans to reproduce an image they've seen. It's called &quot;painting&quot;. Some famous painters apparently have included an image of themselves in their picture, depicted while painting the picture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This isn't really a classical painting, but to give an example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KZkhy.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The trouble is that actually painting a picture takes a long time, so the feedback is very slow - each iteration may take days.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-02-11T10:36:55.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14956" PostTypeId="1" AcceptedAnswerId="16868" CreationDate="2014-02-11T11:47:09.533" Score="4" ViewCount="1590" Body="&lt;p&gt;The very first sentence of the abstract of &lt;a href=&quot;http://www.genetics.org/content/169/4/2353&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;In finite populations subject to selection, genetic drift generates negative linkage disequilibrium, on average, even if selection acts independently (i.e., multiplicatively) upon all loci.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does genetic drift generate negative linkage disequilibrium?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-08-19T17:14:20.540" LastActivityDate="2017-01-13T17:24:20.213" Title="Why do genetic drift generates negative linkage disequilibrium?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;population-biology&gt;&lt;population-dynamics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14957" PostTypeId="1" AcceptedAnswerId="16025" CreationDate="2014-02-11T12:06:35.007" Score="5" ViewCount="1586" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ronald_Fisher&quot; rel=&quot;nofollow&quot;&gt;Ronald Fisher&lt;/a&gt; discovered what he, with humility, called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Fisher%27s_fundamental_theorem_of_natural_selection&quot; rel=&quot;nofollow&quot;&gt;Fundamental Theorem of Natural Selection&lt;/a&gt;. This theorem says (in its modern terminology):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The rate of increase in the mean fitness of any organism at any time ascribable to natural selection acting through changes in gene frequencies is exactly equal to its genetic variance in fitness at that time.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As I understand it, it sounds alike the standard equation that we learn in the first class of &lt;em&gt;Introduction to evolutionary biology&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$R = S \cdot \frac{V_G}{V_p}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In words: the response to selection equals the selection differential times the genetic variance of the trait under consideration divided by the total phenotypic variance of the trait under consideration&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;But how can we prove/demonstrate that Fisher's fundamental theorem of natural selection holds true?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't ask for empirical evidences that support this claim but for a theoretical/mathematical proof/demonstration of this claim.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3624" LastEditDate="2014-02-11T22:29:26.407" LastActivityDate="2017-12-23T18:14:17.360" Title="Fisher's Fundamental Theorem of Natural Selection" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14958" PostTypeId="1" CreationDate="2014-02-11T15:02:51.190" Score="1" ViewCount="181" Body="&lt;p&gt;I want to know what sort of range there is on the number of different chemical species in a typical plant and animal cell. Failing that, some specific examples (with sources please).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="3338" LastEditorUserId="5144" LastEditDate="2014-05-12T20:09:47.253" LastActivityDate="2019-08-24T17:03:00.413" Title="How many chemical species are on average in a typical plant and animal cell?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2019-08-25T03:26:51.387" ContentLicense="CC BY-SA 3.0" />
  <row Id="14959" PostTypeId="2" ParentId="14958" CreationDate="2014-02-11T15:34:40.310" Score="0" Body="&lt;p&gt;There is no average plant cell.  However this article describes a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3793045/&quot; rel=&quot;nofollow&quot;&gt;whole plant flux balance model with 333 metabolites&lt;/a&gt;. This won't describe a lot of the molecules plants make.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I seem to remember a natural product analysis of garlic that had scores of sulphur containing compounds that give its distinctive smell for instance.  This model would be a simplified plant which has no special characteristics like that, which probably doesn't exist.  Its probably not less than half the number of compounds that some plants produce or use. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="5144" LastEditDate="2014-02-11T16:20:32.640" LastActivityDate="2014-02-11T16:20:32.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14960" PostTypeId="2" ParentId="14918" CreationDate="2014-02-11T16:44:39.703" Score="0" Body="&lt;p&gt;During the latent period of ventricular contraction, excitation-contraction coupling takes place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There may be other processes, but I think most are these from &lt;a href=&quot;http://en.wikipedia.org/wiki/Excitation%E2%80%93contraction_coupling&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;An action potential is initiated by pacemaker cells in the Sinoatrial node or Atrioventricular node and conducted to all cells in the heart via gap junctions.&lt;/li&gt;&#xA;&lt;li&gt;The action potential travels along the surface membrane into T-tubules (the latter are not seen in all cardiac cell types) and the depolarisation causes Ca2+&#xA;to enter the cell via L-type calcium channels (also known as Dihydropyridine receptors) and possibly sodium-calcium exchanger during the early part of the plateau phase. This Ca2+&#xA;influx causes a small local increase in intracellular Ca2+&#xA;.&lt;/li&gt;&#xA;&lt;li&gt;The increase in Ca2+&#xA;is detected by ryanodine receptors in the membrane of the sarcoplasmic reticulum which releases Ca2+&#xA;in a positive feedback physiological response. This positive feedback is known as calcium-induced calcium release and gives rise to Calcium sparks.&lt;/li&gt;&#xA;&lt;li&gt;The spatial and temporal summation of ~30,000 Ca2+&#xA;sparks gives a cell-wide increase in cytoplasmic calcium concentration.&lt;/li&gt;&#xA;&lt;li&gt;Contractile mechanism similar as in skeletal muscle about cytoplasmic calcium binding to troponin C and so on. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note that to fully answer this question you should include figures about mechanisms of excitation-contraction coupling, cardiac action potential -figure and permeabilities of different ions.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-15T20:52:12.553" LastActivityDate="2014-02-15T20:52:12.553" CommentCount="0" CommunityOwnedDate="2014-02-11T16:44:39.703" ContentLicense="CC BY-SA 3.0" />
  <row Id="14962" PostTypeId="2" ParentId="14957" CreationDate="2014-02-11T17:53:15.130" Score="1" Body="&lt;p&gt;Here's &lt;a href=&quot;http://www.ias.ac.in/jgenet/Vol74Nos1&amp;amp;2/19.pdf&quot; rel=&quot;nofollow&quot;&gt;a paper with an historical bibliography of mathematical analyses in the introduction&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see when you demand a mathematical treatment of something as poorly understood as the genetic inheritance of traits, the word proof is to be used in a qualified way.  In this case a multilocus fitness with variation in the population with no linkage between the alleles.  Its probably a case that shows up frequently enough, but how many alleles are we talking about?  With large numbers of alleles which are scrambled randomly at each generation (zero linkage) I would imagine that the number of individuals that contain a lot of diversity.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most GWAS studies show lots of less probable variants may contribute to many genetic traits (like height, diabetes, etc).  So this is quite a reasonable number of the cases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fundamental theorem is true for any number of variants involved though, so hopefully this helps. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-02-11T17:53:15.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14963" PostTypeId="2" ParentId="14952" CreationDate="2014-02-11T19:22:08.700" Score="0" Body="&lt;p&gt;&quot;Sex&quot; is the right word when talking about biology.  &quot;Gender&quot; is about the cultural signifiers and differences that a culture puts on people depending on their sex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are transexual people and transgender people and intersexed people...so it's a little rude to them to act like biological sex is a binary thing, or that is it totally the same as gender.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-02-11T19:22:08.700" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14964" PostTypeId="2" ParentId="14957" CreationDate="2014-02-11T20:41:58.657" Score="3" Body="&lt;p&gt;I don't think that you need to look further than &lt;a href=&quot;http://en.wikipedia.org/wiki/Price_equation&quot; rel=&quot;nofollow&quot;&gt;the Price equation&lt;/a&gt;, which is basically a proof of a generalized version of Fisher's fundamental theorem. Price had a series of papers in the 70's that derived and applied the Price equation (e.g. &lt;a href=&quot;http://www.nature.com/nature/journal/v227/n5257/abs/227520a0.html&quot; rel=&quot;nofollow&quot; title=&quot;Price. 1970. Selection and covariance. Nature&quot;&gt;Price, 1970&lt;/a&gt;; &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-1809.1957.tb01874.x/abstract&quot; rel=&quot;nofollow&quot; title=&quot;Price. 1972. Extension of covariance selection mathematics. Annals of Human Genetics 35&quot;&gt;Price, 1972a&lt;/a&gt;), but most relevant for your question in probably &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-1809.1972.tb00764.x/abstract&quot; rel=&quot;nofollow&quot; title=&quot;Price. 1972. Fisher's ‘fundamental theorem’ made clear. Annals of Human Genetics 36(2)&quot;&gt;Price (1972b)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A nice summary of Price's legacy can be found in &lt;a href=&quot;http://stevefrank.org/reprints-pdf/95JTB-Price.pdf&quot; rel=&quot;nofollow&quot; title=&quot;Frank. 1995. George Price's Contributions to Evolutionary Genetics. Journal of Theoretical Biology 175&quot;&gt;Frank (1995)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2014-02-11T20:41:58.657" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14965" PostTypeId="2" ParentId="8897" CreationDate="2014-02-11T21:19:54.407" Score="0" Body="&lt;p&gt;From the &lt;a href=&quot;http://www.scientificamerican.com/article/the-science-behind-dreaming/&quot; rel=&quot;nofollow&quot;&gt;ScientificAmerican&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Yet, given the vast documentation of realistic aspects to human dreaming as well as indirect experimental &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1053810003000199&quot; rel=&quot;nofollow&quot; title=&quot;35.95$&quot;&gt;evidence&lt;/a&gt; that other mammals such as cats also dream, evolutionary psychologists have theorized that dreaming really does serve a purpose.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Although the linked article doesn't look like they were talking about animals. But I wont purchase the article to check that...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your second question, I would say yes, when you would say, making a plan is equivalent to dream of the future. Crows are &lt;a href=&quot;http://www.cracked.com/article_19042_6-terrifying-ways-crows-are-way-smarter-than-you-think_p4.html&quot; rel=&quot;nofollow&quot;&gt;smarter than you think&lt;/a&gt;...&lt;/p&gt;&#xA;" OwnerUserId="5344" LastEditorUserId="5344" LastEditDate="2015-03-27T10:37:22.547" LastActivityDate="2015-03-27T10:37:22.547" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="14966" PostTypeId="1" CreationDate="2014-02-11T23:22:48.880" Score="2" ViewCount="247" Body="&lt;p&gt;Many breeds of dogs are known for a high incidence of genetic disorders. German shepherd and Saint Bernard dogs are predisposed to developing a crippling condition called hip dysplasia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Q: What advice would you give to dog breeders who want to maintain their dogs' purebred pedigrees, but also want their dogs to be as healthy as possible?&lt;/p&gt;&#xA;" OwnerUserId="5584" LastEditorUserId="5584" LastEditDate="2014-02-11T23:28:44.627" LastActivityDate="2014-07-14T10:35:36.580" Title="Maintaining purebred pedigrees and how to lessen chance of getting disease?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;zoology&gt;&lt;homework&gt;&lt;chromosome&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14968" PostTypeId="1" CreationDate="2014-02-12T05:45:43.090" Score="2" ViewCount="345" Body="&lt;p&gt;I'm trying to understand what neuroeconomics is. There are two possibilities for what it might mean. (1) The study of cognitive processes in the brain by applying basic principles of economic theory like concepts of utility, decision making, etc. (2) The study of how a human behaves in an economic setting, somewhat like game theory and so on, which is more economics than brain science. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which one is it?&lt;/p&gt;&#xA;" OwnerUserId="625" LastActivityDate="2014-07-16T10:01:38.007" Title="Does neuroeconomics study the brain or study economics?" Tags="&lt;neuroscience&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14969" PostTypeId="1" AcceptedAnswerId="15107" CreationDate="2014-02-12T05:58:33.063" Score="2" ViewCount="9602" Body="&lt;p&gt;Splicing is a modification of pre mRNA when all introns are removed and exons are joined.&#xA;What is a splice junction pair? It is two exons which connected together?&lt;/p&gt;&#xA;" OwnerUserId="4791" LastActivityDate="2019-01-28T13:38:08.230" Title="What is splice junction pairs?" Tags="&lt;cell-biology&gt;&lt;genomics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="14971" PostTypeId="2" ParentId="14899" CreationDate="2014-02-12T07:17:53.063" Score="4" Body="&lt;p&gt;Dr. Helen Fisher's conclusions are plain bunkum. What does it even mean when she says associated with a particular neurotransmitter? The sheer work required to even get at this question is vast and difficult so it is unsurprising that she is venturing as much as a guess.There is scientific evidence to support different neurotransmitters systems can go awry in diseases but Fisher is overinterpreting the literature. Take a look at the neurotrasmiter table and you can see what each does and how malfunctions can result in certain diseases.&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Neurotransmitter&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Neurotransmitter&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also testosterone and estrogen are thought of primarily as hormones not neurotrasmiters.So Fisher is saying women(who have more estrogen) are better negotiatiors whereas men(more testosterone) are directors. Even these banal conclusions are contentious and debatable.&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-02-12T07:17:53.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14972" PostTypeId="2" ParentId="14966" CreationDate="2014-02-12T07:19:57.607" Score="0" Body="&lt;p&gt;Outbreed your dog every couple of generations with a bloodline that is slightly different or at the very least a similar looking breed.&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-02-12T07:19:57.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14973" PostTypeId="2" ParentId="14836" CreationDate="2014-02-12T07:24:48.003" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Discrete data must be stored in low entropy structures in the brain that over time spontaneously shift to a higher entropy state&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;How on Earth could you possibly know that? You are overextending physics to the workings of the brain and there is nothing that says this is necessarily so. Memory decay is not fully understood but it is known that the more features(i.e sound ,taste) are used when forming the memory and the more it is associated within an existing knowledge framework, the higher the chance that the memory will persist.&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-02-12T07:24:48.003" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14976" PostTypeId="2" ParentId="14966" CreationDate="2014-02-12T09:17:57.023" Score="1" Body="&lt;p&gt;Many races of dogs are relatively new with most of them appearing (were bred) in the last few hundred years. These variations are caused by small mutations in certain genes and this is also the problem. To keep a race pure, it has to be interbred to maintain the special set of mutations. And this makes the dogs vulnerable to collect more damaging mutations, especially when the number of animals used for breeding are too small. This is the same problem, that animal conservation projects face in zoos.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good example for that is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Dalmatian_%28dog%29&quot; rel=&quot;nofollow&quot;&gt;Dalmatian dog&lt;/a&gt;. Its characteristic spotted pattern is caused by genes, that can also cause &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19207931&quot; rel=&quot;nofollow&quot;&gt;sensineural deafness&lt;/a&gt;. To avoid this, deaf dogs are excluded from the breeding and a backcross project was started. &lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5762" LastEditDate="2014-05-15T09:41:17.780" LastActivityDate="2014-05-15T09:41:17.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14979" PostTypeId="1" AcceptedAnswerId="14984" CreationDate="2014-02-12T10:55:13.150" Score="0" ViewCount="101" Body="&lt;p&gt;Assume you have an exam which has 5 extensive questions and 60 minutes.&#xA;You do not have time to cover most if you write everything in essay format.&#xA;If you start to write essays, you do not really have time to cover all mechanisms and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just heard that one student did the exam with by list format, for instance&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;sitting -&gt; venous return down &amp;amp; skeletal muscles not working correctly -&gt; trombus. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and then describing relevant mechanisms similarly and combining the their roles shortly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another morphology of H. pylori&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Curved (spiral shape), Gram-negative, 2-4 micrometer long, coccoid forms in older cultures, &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any official standard or unofficial accepted way how to answer questions in Physiology/Medicine?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-12T12:05:01.757" Title="Is there any format for official Physiological/Medicine answers?" Tags="&lt;physiology&gt;&lt;homework&gt;&lt;microbiology&gt;" AnswerCount="2" CommentCount="0" ClosedDate="2014-02-12T14:44:36.193" ContentLicense="CC BY-SA 3.0" />
  <row Id="14980" PostTypeId="1" CreationDate="2014-02-12T10:59:57.380" Score="1" ViewCount="62" Body="&lt;p&gt;So far I found papers that show studies using RNA arrays on whom they categorized water stress gene markers in root. Water stresses were reproduced by different protocols (manitol...) but always on several week old plants. Does anyone know any study carried on young (6 days more or less) arabidopsis thaliana plants?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastActivityDate="2014-02-12T10:59:57.380" Title="water stress expression markers in arabidopsis thaliana" Tags="&lt;plant-physiology&gt;&lt;gene-expression&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14981" PostTypeId="1" CreationDate="2014-02-12T11:21:35.580" Score="3" ViewCount="200" Body="&lt;p&gt;People who lack the sense of hearing, vision and speaking are called &lt;em&gt;Deaf&lt;/em&gt;, &lt;em&gt;Blind&lt;/em&gt; and &lt;em&gt;Mute&lt;/em&gt;.&#xA;But what is the person called if he/she lacks the sense of smell? Is there any case like that?&lt;/p&gt;&#xA;" OwnerUserId="5162" LastEditorUserId="3624" LastEditDate="2014-02-13T09:58:32.210" LastActivityDate="2014-02-13T12:06:51.723" Title="What is lack in sense of smell called?" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14982" PostTypeId="2" ParentId="14979" CreationDate="2014-02-12T11:24:31.140" Score="1" Body="&lt;p&gt;I usually answer in a extensive and descriptive way, and I try to put as much information as possible. If it's a process I usually add a little diagram. If there are lot of attributes to add sometimes I do lists, but usually teachers don't like them an it's easier to find errors or lacks in lists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no standard answer model at least in my University.&lt;/p&gt;&#xA;" OwnerUserId="5405" LastActivityDate="2014-02-12T11:24:31.140" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14983" PostTypeId="2" ParentId="14981" CreationDate="2014-02-12T11:46:49.663" Score="6" Body="&lt;p&gt;This condition is called 'anosmia', see these two links: &lt;a href=&quot;http://en.wikipedia.org/wiki/Anosmia&quot;&gt;Wikipedia&lt;/a&gt; and from the british &lt;a href=&quot;http://www.nhs.uk/conditions/anosmia/Pages/Introduction.aspx&quot;&gt;National Health Service&lt;/a&gt;. They include a definition and reasons for anosmia.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-12T11:46:49.663" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14984" PostTypeId="2" ParentId="14979" CreationDate="2014-02-12T12:05:01.757" Score="2" Body="&lt;p&gt;Given the highly variable nature of such processes and systems, it's unlikely that a common standard is feasible or sensible. In medical questions, a bottom-up order like in your example usually makes sense, starting with the most specific known cause and deriving from there until you arrive at the symptoms. Treatments can branch off or into the order at the point where they apply logically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your exam instructions ask for flow text, your question is alreay unnecessary - but if you believe you have the choice, use a note format that is appropriate by common sense. You are essentially creating a diagram, and like any diagram you have to ensure that it is self-contained and comprehensive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can shorten the amount of time it takes to write sentences by reducing the literary quality. Of course a well-written text is more pleasing to read and mark, but the main emphasis in your grading will usually be content, meaning that you can afford to form sentences of repetitive structures or lacking logical connection if it is difficult to figure out quickly whether there is one or how to express it etc.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2014-02-12T12:05:01.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14985" PostTypeId="1" CreationDate="2014-02-12T15:57:11.670" Score="1" ViewCount="578" Body="&lt;p&gt;I've seen many times mentioned in textbooks and popular articles that a reason of the Cambrian explosion is an 'evolutionary arms race' between predators and prey. But this isn't really a sufficient reason, since that happens all the time, but evolution seems to happen only at brief intervals separated with long intervals of stasis, which is described extensively in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Punctuated_equilibrium&quot; rel=&quot;nofollow&quot;&gt;Punctuated equilibrium hypothesis&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, my question is, what made the evolutionary arms race of the Cambrian possible?&lt;/p&gt;&#xA;" OwnerUserId="1086" LastActivityDate="2014-02-12T15:57:11.670" Title="Cambrian explosion and evolutionary arms race" Tags="&lt;evolution&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14986" PostTypeId="1" AcceptedAnswerId="16526" CreationDate="2014-02-12T16:00:47.350" Score="4" ViewCount="112" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;When penicillin-resistant bacteria are grown in liquid culture media,&#xA;  &amp;beta;-lactamase is secreted into the medium. The supernatant of such a medium can be assayed for &amp;beta;-lactamase activity. Culture supernatants &#xA;  different organisms , which are suspected to be penicillin-resistant,&#xA;  were obtained and were assayed for &amp;beta;-lactamase activity. The corresponding absorbance value were measured at a certain wavelength.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Let us assume that supernatant from organism 1's culture had absorbance value X and 2 had absorbance value Y.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question : If X&gt;Y, does that mean that more &amp;beta;-lactamase was being produced by organism 1 ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1320" LastEditDate="2014-09-17T21:05:27.103" LastActivityDate="2014-09-17T21:06:10.290" Title="Correlating beta-lactamase expression to absorbance" Tags="&lt;biochemistry&gt;&lt;homework&gt;&lt;bacteriology&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="14987" PostTypeId="1" AcceptedAnswerId="14988" CreationDate="2014-02-12T16:15:27.477" Score="1" ViewCount="45" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Four pesticides P1 to P4 are reversible inhibitors of an enzyme E that&#xA;  is essential for the growth of a bacterium B. Their Ki values are&#xA;  given in the table below. Each of these four pesticides is used in&#xA;  four geographically different regions R1 to R4. The residual&#xA;  concentrations of these four pesticides in the respective regions are&#xA;  also shown in the table below:&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Zcb4X.png&quot; alt=&quot;Table&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Which pesticides will be able to inhibit bacteria ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My question : I know that Ki shows the binding affinity. So, how is that related to residual concentration ? How can I deduce whether it will kill the bacteria or not ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unrelated question : Is it acceptable to use the word &lt;em&gt;pesticide&lt;/em&gt; here ?!&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-02-12T17:02:12.613" Title="Correlating Ki values of pesticides to bacterial growth" Tags="&lt;biochemistry&gt;&lt;homework&gt;&lt;bacteriology&gt;&lt;enzymes&gt;&lt;antibiotics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14988" PostTypeId="2" ParentId="14987" CreationDate="2014-02-12T17:02:12.613" Score="1" Body="&lt;p&gt;Ki is the equilibration dissociation constant. The smaller this constant is, the stronger (more specific) is the binding between the inhibitor and the enzyme. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the residual concentration is now higher than the Ki, for each molecule from the inhibitor which dissociates from the enzyme a new will bind (simply because of the concentration). If the concentration is lower (or much lower), this will not be sufficient to inhibit the enzyme. This assumes that the relation between enzyme, inhibitor and substrate are linear (and we are not getting some kind of saturation here).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under the conditions mentioned above, P1 and P4 will inhibit the enzyme. For P2 and P3 the concentration is to low.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-12T17:02:12.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14990" PostTypeId="1" AcceptedAnswerId="14991" CreationDate="2014-02-12T18:16:40.157" Score="7" ViewCount="439" Body="&lt;p&gt;I have just begun to read about Chaos theory and have come across the statement that &quot;Period three implies chaos.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question: Does any odd period imply chaos or only 3? If so, how can populations of cicadas that cycle every 17 years exist?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3624" LastEditDate="2015-03-02T10:00:16.923" LastActivityDate="2015-03-02T10:00:16.923" Title="Chaos theory and population cycles of odd periodicity" Tags="&lt;ecology&gt;&lt;mathematical-models&gt;&lt;population-dynamics&gt;&lt;theoretical-biology&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14991" PostTypeId="2" ParentId="14990" CreationDate="2014-02-12T18:44:37.710" Score="7" Body="&lt;p&gt;The chaotic behaviour you are referring to (at least the one described in your link in the comments) is a property of the discrete version of the logistic equation, where you get chaotic dynamics at growth rates above ~3.55 (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Logistic_map&quot; rel=&quot;nofollow noreferrer&quot;&gt;the logistic map&lt;/a&gt;). The behaviour of this equation has been described in a classic paper by Robert May &lt;a href=&quot;http://www.nature.com/nature/journal/v261/n5560/abs/261459a0.html&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;May. 1976. Simple mathematical models with very complicated dynamics. Nature 261&quot;&gt;(1976)&lt;/a&gt;. As you increase growth rate (&lt;em&gt;a&lt;/em&gt; in your link) from one you go from a stable attractor (approached directly or by dampened occilations) to cycling behaviour (between 2 to 4 to 8 states as growth rate increase) to chaotic dynamics, which is shown in this bifurcation diagram.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JQdus.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And to be clear, nothing of this has anything to do with period/cycle length per se (in the sense of species interactions or lagging feedback loops), but is a property of the model and the population growth rate. The statement about period 3 implying chaos probably refers to a brief window around r ~3.83 ($1+\sqrt{8})$ where you get cycling between three values, and at higher values then this you only find chaotic behaviour (which you get at lower values as well though).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Addition:&lt;/strong&gt;&#xA;I now realize that the statement &quot;&lt;em&gt;Period three implies chaos&lt;/em&gt;&quot; comes from the theoretical paper with the same name (&lt;a href=&quot;http://www.its.caltech.edu/~matilde/LiYorke.pdf&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Li &amp;amp; Yorke. 1975. Period three implies chaos. The American Mathematical Monthly 82&quot;&gt;Li &amp;amp; Yorke, 1975&lt;/a&gt;). This paper proves that all one-dimensional models (not only the equation above) that has a period 3 cycle will also show chaotic behaviour. This proof is a special case of the &lt;a href=&quot;http://mathworld.wolfram.com/SharkovskysTheorem.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sharkovsky's theorem&lt;/a&gt;, which is older but was unknown to Li &amp;amp; Yorke at the time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also a question at MathSE that deals with the same problem, and some of the answers there link to useful resourses:&lt;br&gt;&#xA;&lt;a href=&quot;https://math.stackexchange.com/questions/2901/period-of-3-implies-chaos&quot;&gt;https://math.stackexchange.com/questions/2901/period-of-3-implies-chaos&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="-1" LastEditDate="2017-04-13T12:19:22.807" LastActivityDate="2014-02-14T12:42:52.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="14993" PostTypeId="1" CreationDate="2014-02-12T19:40:34.880" Score="3" ViewCount="54006" Body="&lt;p&gt;I have a very tricky question....all the veg and fruit &lt;/p&gt;&#xA;&#xA;&lt;p&gt;cells contain cell wall and it is made of cellulose when we eat how our body digest though we &lt;/p&gt;&#xA;&#xA;&lt;p&gt;don't have the enzymes to breakdown 1-4 beta glucose sugar?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastActivityDate="2014-02-12T19:56:27.587" Title="why can't we digest cellulose" Tags="&lt;digestive-system&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-02-12T22:26:49.853" ContentLicense="CC BY-SA 3.0" />
  <row Id="14994" PostTypeId="2" ParentId="14993" CreationDate="2014-02-12T19:56:27.587" Score="1" Body="&lt;p&gt;Humans, unlike cows for ex. don't have the necessary bacteria in their intestines that make the enzymes(cellulases) necessary to breakdown the 1-4 beta glucose bonds. So we cannot break down cellulose into its constituent glucose molecules as we do with starch. Therefore this is secreted as unbroken down chains of glucose called fiber.&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-02-12T19:56:27.587" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14995" PostTypeId="1" AcceptedAnswerId="15001" CreationDate="2014-02-12T21:00:28.867" Score="1" ViewCount="65" Body="&lt;p&gt;Extradistestinal disease seems to prefer to &quot;bowel&quot; diseases, I think this is about diseases outside gastrointestinal tract so stomach.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider diseases ulcerative colitis and Crohn's disease (enteritis) as examples.&#xA;Colitis affects to colon, outside of small intestine, I think extraintestinal therefore.&#xA;Crohn's disease (enteritis) however affects to the small intestine so I would think intestinal disease (but this clause is wrong) - it should be at least have extraintestinal manifestations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the exact definition of the word &lt;em&gt;extra&lt;/em&gt; in intestinal diseases?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-13T06:01:33.007" Title="To understand clearly extraintestinal diseases" Tags="&lt;microbiology&gt;&lt;gastroenterology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="14996" PostTypeId="1" CreationDate="2014-02-12T22:12:57.337" Score="0" ViewCount="579" Body="&lt;p&gt;The problem to be solved is to determine what the flux values are for the different reactions in the human metabolic model.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I understand, a good way to do that would be to use gene expression data to calculate a flux, but I am not sure that is a good idea or if it is even possible.  I am not very sure of what is the correct process to do this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any help or suggestions!&lt;/p&gt;&#xA;" OwnerUserId="5680" LastActivityDate="2014-02-17T16:16:28.110" Title="How to determine the actual flux in the human metabolic model of a cell line?" Tags="&lt;molecular-biology&gt;&lt;metabolism&gt;&lt;rna&gt;&lt;gene-expression&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="14998" PostTypeId="1" CreationDate="2014-02-13T04:24:55.480" Score="5" ViewCount="842" Body="&lt;p&gt;Is there any specific reason behind why we dream? Why do we sometimes get weird and unusual dreams? Sometimes we can't even recall what we dreamt of. Why does this happen?&lt;/p&gt;&#xA;" OwnerUserId="5343" LastEditorUserId="19099" LastEditDate="2017-03-17T11:48:33.810" LastActivityDate="2020-04-23T09:40:23.327" Title="Why do we dream while sleeping?" Tags="&lt;brain&gt;&lt;sleep&gt;&lt;dreaming&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="14999" PostTypeId="1" CreationDate="2014-02-13T05:07:47.693" Score="1" ViewCount="63" Body="&lt;p&gt;I've heard &lt;a href=&quot;http://www.ted.com/talks/sandra_aamodt_why_dieting_doesn_t_usually_work.html&quot; rel=&quot;nofollow&quot;&gt;this TED.com talk about dieting&lt;/a&gt; and it mentions that there's a very definitive setpoint within the human brain about how much a human should weight. The speaker mentions that after as much as 7 years, the body returns to that &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_homeostasis#Sleep&quot; rel=&quot;nofollow&quot;&gt;homeostatic&lt;/a&gt; weight setpoing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested if there's something similar for sleep - &lt;strong&gt;is there a homeostatic setpoint that says that a human should sleep X hours out of 24?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this example by homeostatic I mean:&#xA;If the sleep setpoint is at 9 hours, the human can sleep for 8 hours for some time, but when the artificial sleep restriction is removed, the human would return to 9 hours of sleep naturally. &lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2014-02-13T05:07:47.693" Title="Is there a homeostatic setpoint for number of hours of sleep required by a human?" Tags="&lt;human-biology&gt;&lt;sleep&gt;&lt;homeostasis&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15000" PostTypeId="1" CreationDate="2014-02-13T05:17:06.120" Score="5" ViewCount="310" Body="&lt;p&gt;I've long been interested in the effect of music/sound on dreaming, and even built 2 apps that play music during REM period. Now I'm looking at this article about &lt;a href=&quot;http://www.mpipsykl.mpg.de/en/research/themes/sleep/czisch_02/&quot; rel=&quot;noreferrer&quot;&gt;FMRI studies of a sleeping brain&lt;/a&gt;, and I see that it mentions:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;During wakefulness, acoustic stimulation elicits activation of the&#xA;  auditory cortex (red). Similar stimulation during light NREM sleep&#xA;  stage 2 &lt;strong&gt;evokes transient downregulation of widespread cortical areas&lt;/strong&gt;&#xA;  (blue), supposedly a sleep protective mechanism.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Acoustic stimulation in REM (rapid eye movement) sleep revealed a&#xA;  different brain activation pattern during phasic and tonic REM&#xA;  periods, with &lt;strong&gt;strongest suppression of cortical reactivity&lt;/strong&gt; during&#xA;  phasic REM sleep periods.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can I interpret information on that site to suggest that auditory stimulation during sleep actually makes the brain less active?&lt;/strong&gt; Can one assume that playing audio during REM would disrupt dreaming due to transient downregulation?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2014-02-17T03:31:44.523" Title="Does playing music during sleep actually suppress rather than rouse the brain?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;brain&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15001" PostTypeId="2" ParentId="14995" CreationDate="2014-02-13T06:01:33.007" Score="3" Body="&lt;p&gt;Certain intestinal diseases have symptoms that appear concurrently in other systems of the body, but the bowel diseases &lt;em&gt;themselves&lt;/em&gt; are not extraintestinal.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Extraintestinal manifestations of inflammatory bowel disease are prevalent in both ulcerative colitis and Crohn's disease. The most common manifestations involve the musculoskeletal and dermatologic systems. Other manifestations involve the hepatopan-creatobiliary system (eg, primary sclerosing cholangitis) as well as the ocular, renal, and pulmonary systems&lt;sup&gt;1&lt;/sup&gt;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;One of the key differences between extraintestinal manifestations and comorbid conditions (though seemingly not a necessity, the article cites primary sclerosing cholangitis as an counterexample) is that the extraintestinal effects will subside once the disease of the bowel is treated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt; Levine, J.S., Burakoff, R. (2011). Extraintestinal Manifestations of Inflammatory Bowel Disease. &lt;em&gt;Gastroenterol Hepatol (NY), 7&lt;/em&gt;(4), 235–241. &lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2014-02-13T06:01:33.007" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15003" PostTypeId="1" AcceptedAnswerId="15008" CreationDate="2014-02-13T10:32:53.560" Score="6" ViewCount="135" Body="&lt;p&gt;I recently cut my finger fairly deeply with a box cutter and had to have it stitched. During the healing process I contracted a strong cold/mild flu (a sore throat and runny nose with a high fever, aches and shivering). I doubt the two have anything to do with one another apart from happening to occur at the same time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But they &lt;em&gt;did&lt;/em&gt; occur at the same time. So I'm wondering: what is my body going to do?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I recall my junior high biology, a cut is healed by platelets and [other stuff I can't recall], whereas a virus is fought with antibodies. Presumably in both cases it's a bit more complicated than just that. I'm also not sure if there is any crossover - are antibodies, for example, needed to protect the open wound from bacterial infection? Regardless, my question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Since the resources in the human body are finite, would having to fight off the cold have a detrimental effect on the healing of the cut?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If certain resources are needed for both tasks, would the body divide its resources or give one precedence over the other?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm guessing this is not something that is easy to measure, since it would be difficult to conduct a control experiment given the insane amount of variables. But presumably there is a consensus in the biological community on whether there would be an effect, even if it is not possible to determine the degree of said effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I should mention in closing that I am not remotely worried about any of this; it just piqued my curiosity.&lt;/p&gt;&#xA;" OwnerUserId="5704" LastActivityDate="2014-02-13T13:03:18.217" Title="Healing rate of cut while suffering from a cold" Tags="&lt;human-anatomy&gt;&lt;virus&gt;&lt;healing&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15004" PostTypeId="1" CreationDate="2014-02-13T11:07:11.003" Score="4" ViewCount="774" Body="&lt;p&gt;I have a list of differentially expressed genes from an RNA-Seq experiment in &lt;em&gt;Xenopus laevis&lt;/em&gt; that I'm looking to functionally annotate with GO-terms. As &lt;em&gt;X.laevis&lt;/em&gt; is not listed in DAVID it seems I have 2 options:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;BLAST my DE genes against a database with GO terms (human/mouse) to look for orthologs&lt;/li&gt;&#xA;&lt;li&gt;Use a program that assigns GO from BLAST results, such as Blast2GO&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I've been trying with Blast2GO recently, but find if very slow and generally lacking - does anyone have any experience doing GO in &lt;em&gt;Xenopus&lt;/em&gt; or other non-model organisms?&lt;/p&gt;&#xA;" OwnerUserId="4242" LastActivityDate="2014-04-04T08:09:10.400" Title="GO terms for non-model organisms" Tags="&lt;bioinformatics&gt;&lt;rna-sequencing&gt;&lt;blast&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15006" PostTypeId="1" AcceptedAnswerId="15018" CreationDate="2014-02-13T11:14:40.697" Score="1" ViewCount="313" Body="&lt;p&gt;Research projects with artificial life generally use creatures that are haploid. The offspring randomly inherit some genes from one parent, and some genes from the other parent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Q1: Are there any biological species which reproduce similarly? I.e., they're haploid, but the offspring aren't clones. Perhaps hermaphroditic species like slugs or some plants?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Q2: Is there a name for this type of reproduction? If not, I guess I'll call it &quot;pseudosexual&quot; since it's a simplified form of true sexual reproduction.&lt;/p&gt;&#xA;" OwnerUserId="5706" LastActivityDate="2018-11-13T15:02:43.000" Title="Pseudosexual reproduction" Tags="&lt;genetics&gt;&lt;sex&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15008" PostTypeId="2" ParentId="15003" CreationDate="2014-02-13T13:03:18.217" Score="2" Body="&lt;p&gt;First of all: No, there is no connection between these two incidents, correlation does not imply a causation. Cold and flu viruses affect the respiratory system and the infection route goes via it. A cut is a local wound, which does not affect the respiratory tract.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then: Recovering from an infection is a task for the immune system (its both, the innate and the adaptive immune system, the last involves the antibodies), which is not doing much for wound healing. The wound attracts neutrophils and macrophages which are attracted by factors released by the wound and they react to bacterial infections (when they occur). See this &lt;a href=&quot;http://en.wikipedia.org/wiki/Wound_healing&quot; rel=&quot;nofollow&quot;&gt;Wikipedia article&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ressources of a normally healthy person are quite big. This is demonstrated by the fact that many secondary infections only occur in a opportunistic fashion (for example viruses like Herpes or certain fungi) when the body is weakened by other infections. So there is a limit, but this will certainly not be reached with a severe cold.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-13T13:03:18.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15011" PostTypeId="1" CreationDate="2014-02-13T14:06:55.370" Score="1" ViewCount="88" Body="&lt;p&gt;I'm reading Yang's computational molecular evolution and in the very first chapter it says the &lt;em&gt;P&lt;/em&gt; distance is a &quot;simplistic distance measure&quot; between two sequences. It is the number of different sites / the total number of sites. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, because back mutation and multiple hits cause inaccuracy it become weak over longer distances (large number of generations to most recent common ancestor, MRCA, I guess). &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The raw proportion &lt;em&gt;p&lt;/em&gt; is usable only for highly similar sequences,&#xA;  with &lt;em&gt;p&lt;/em&gt; &amp;lt;0.05 (5%, approximately).&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;How far back in divergence time do we have to go for this &lt;em&gt;p&lt;/em&gt;&amp;lt;5% to be violated? I assume it has to do with the mutation rate right? I'm trying to get a sense of scale on this for myself. Are we talking a distance of just a few generations (within species), the distance between two closely related species, or an even greater distance?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-02-14T08:30:09.563" LastActivityDate="2014-02-14T08:30:09.563" Title="How far in evolutionary distance is the P-distance estimator &quot;accurate&quot;?" Tags="&lt;molecular-evolution&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15012" PostTypeId="1" CreationDate="2014-02-13T14:14:19.803" Score="3" ViewCount="85" Body="&lt;p&gt;I am currently working with a peptide which is an analogue for glp-1, but during invitro studies am not able to detect for the presence of GLP1- receptors.&#xA;The cell line used is Min-6. How do I detect it? &lt;/p&gt;&#xA;" OwnerUserId="5707" LastActivityDate="2014-08-14T09:13:20.333" Title="How do you express and detect GLP-1 receptors?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;endocrinology&gt;&lt;biotechnology&gt;&lt;diabetes-mellitus&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15013" PostTypeId="1" AcceptedAnswerId="15016" CreationDate="2014-02-13T14:33:02.360" Score="1" ViewCount="4976" Body="&lt;p&gt;I have only been sick a few times in my life(I'm 21 and probably 3-4 times) and even when I am sick I don't feel that bad and I am over it within a day or two. My family has always given me slack for never washing my hands but I see no point unless they physically look dirty. Unlike me though my family gets sick around the same amount as other people(a couple times a year).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have this theory that since my body is always exposed to germs and other bacteria that it is stronger and able to fight off most colds before they ever happen. This theory obviously contradicts popular opinion and what doctors recommend but I have always felt fine not washing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do you guys think?&lt;/p&gt;&#xA;" OwnerUserId="5708" LastActivityDate="2014-02-13T17:37:11.887" Title="I don't wash my hands and never get sick. Any theories?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-02-13T18:49:50.567" ContentLicense="CC BY-SA 3.0" />
  <row Id="15014" PostTypeId="1" CreationDate="2014-02-13T14:33:19.297" Score="2" ViewCount="46" Body="&lt;p&gt;I am no biologist, but I have this question buzzing in my mind. It's a matter of curiosity&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens when two nuclei occupy the same cell? Would we expect the embryo (if it lives) to have complex cells (assuming the nuclei are from different species, i.e., genetically incompatible with each other)?&lt;/p&gt;&#xA;" OwnerUserId="5709" LastEditorUserId="107" LastEditDate="2014-02-13T23:44:25.127" LastActivityDate="2014-02-15T20:10:24.317" Title="Dinuclei cellular mechanism" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15015" PostTypeId="1" AcceptedAnswerId="15065" CreationDate="2014-02-13T16:01:42.363" Score="5" ViewCount="507" Body="&lt;p&gt;I have a list of ENA accession numbers and a start and end position in each sequence. In the end I want to align all those sequences, but first I have to fetch them and the list is too long to do that manually.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any existing tool or script that can fetch all those entries from a database and extract the correct subset of the sequence? &lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2015-06-19T07:07:43.803" Title="How can I fetch nucleotide sequences based on ENA accession numbers and positions?" Tags="&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15016" PostTypeId="2" ParentId="15013" CreationDate="2014-02-13T17:37:11.887" Score="3" Body="&lt;p&gt;You may very well be strengthening your immune system, but there are microorganisms that you don't want to get, which can have longer term health consequences. For example, there seems to be a significant increase in developing MS if you've ever had the Epstein-Barr virus. But this is just one case. You also don't want Salmonella, tape worms, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there may be a price to pay for a stronger immune system: namely higher probability of exposing yourself to the more dangerous things out there. &lt;/p&gt;&#xA;" OwnerUserId="5367" LastActivityDate="2014-02-13T17:37:11.887" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15017" PostTypeId="1" AcceptedAnswerId="15020" CreationDate="2014-02-13T17:42:21.937" Score="4" ViewCount="21764" Body="&lt;p&gt;What is the mechanism?&#xA;In other words, how does the tRNA know whether the codon is in 5' to 3' direction? I also heard that anything that is translated from 3' to 5' direction is degraded. Is it true? &lt;/p&gt;&#xA;" OwnerUserId="887" LastActivityDate="2014-02-14T10:05:23.267" Title="Why are transcripts translated from 5' to 3' direction?" Tags="&lt;rna&gt;&lt;translation&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15018" PostTypeId="2" ParentId="15006" CreationDate="2014-02-13T19:08:39.133" Score="3" Body="&lt;p&gt;Generally, all diploid species pass through a haploid phase in their life. This is called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Alternation_of_generations&quot; rel=&quot;nofollow noreferrer&quot;&gt;alternation of generations&lt;/a&gt; and the cycle may be presented like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GL4qC.png&quot; alt=&quot;haploid, then diploid, then haploid and so on&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Commonly we see organisms that spend most of their life in the diploid phase, with greatly reduced haploid phase (e.g. humans &quot;live&quot; in haploid state only as gametes). However, this is not the only way possible. There are organisms, which spend similar amount of time in each phase, which change ploidy depending on the conditions of the environment and, of course, organisms which spend most of their lives as haploids, with only a short diploid stage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a rule, lower plants, fungi and protozoa may exibit this behaviour. Some examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Saccharomyces cerevisiae (yes, baker's yeast) will undergo meiosis and form haploid spores in unfavourable conditions, which then can grow as haploid colonies until they encounter a colony of opposite &quot;sex&quot;&lt;/li&gt;&#xA;&lt;li&gt;Mosses commonly grow larger gametophytes (haploid) than sporophytes (diploid)&lt;/li&gt;&#xA;&lt;li&gt;Some &lt;a href=&quot;http://en.wikipedia.org/wiki/Brown_algae#Life_cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;brown algae&lt;/a&gt; grow sporophytes and gametophytes that are indistinguishable form each other&lt;/li&gt;&#xA;&lt;li&gt;Ferns often grow large sporophytes and small, but &lt;a href=&quot;http://en.wikipedia.org/wiki/Prothallium&quot; rel=&quot;nofollow noreferrer&quot;&gt;self-sufficient gametophytes&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Next question should be &quot;why only lower plants and fungi?&quot; And the shortest answer is that a diploid organism is usually more robust, it can survive more potentially lethal mutations than a haploid.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastActivityDate="2014-02-13T19:08:39.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15019" PostTypeId="2" ParentId="15014" CreationDate="2014-02-13T19:23:42.417" Score="2" Body="&lt;p&gt;It depends on the kind of organism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the cell with two nuclei will try to go through mitosis, the nuclear membranes will fragment, releasing all genetic material to the cytoplasm, where it will behave normally, as if it came from only one nucleus. The DNA will divide and move into two daughter cells, each of which will assemble its one nucleus from the membrane fragmnets. However, each daughter nucleus will have double the normal number of chromosomes - one whole set from each of the old nuclei. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(In fact, this is what happens in humans after fertilization - the male and female pronuclei never merge, they just copy their DNA and divide it simultaneously into two daughter cells. The pronuclei are haploid, so the resulting daughter cells are diploid.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens later, to the tetraploidic cells from your question, when they try to develop into a full organism, may end better or worse.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For exapmple many plants will just grow normally, only form bigger plants (modern &lt;a href=&quot;http://en.wikipedia.org/wiki/Wheat#Genetics&quot; rel=&quot;nofollow&quot;&gt;wheat&lt;/a&gt; is such an example - it may be tetra- or even hexaploidic, meaning it has up to 6 sets of chromosomes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For animals this is usually fatal, but some, like &lt;a href=&quot;http://en.wikipedia.org/wiki/Xenopus_laevis&quot; rel=&quot;nofollow&quot;&gt;the xenopus&lt;/a&gt;, seem to be unaffected.&lt;/p&gt;&#xA;" OwnerUserId="1427" LastEditorUserId="1427" LastEditDate="2014-02-15T20:10:24.317" LastActivityDate="2014-02-15T20:10:24.317" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15020" PostTypeId="2" ParentId="15017" CreationDate="2014-02-13T19:24:41.657" Score="5" Body="&lt;p&gt;The tRNA is not acting alone, it has the help of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Ribosome&quot; rel=&quot;noreferrer&quot;&gt;Ribosome&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vArV7.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Ribosome assembles at the beginning of the transcript and starts the translation at the first AUG codon. It then binds the first tRNA which fits to the mRNA. The tRNA is then moved from the A-position to the P-position and the next tRNA is binding (the move around and bind by chance. A nice animation is found in the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Translation_%28biology%29&quot; rel=&quot;noreferrer&quot;&gt;translation&lt;/a&gt; (which is also the source for the image above). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Translation can't go into the other direction, it is always in 5' -&gt; 3'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To recognize the right direction (and the right starting point) the Ribisome is not simply starting at the 5`end of the mRNA. Before the start codon AUG the mRNA contains a regulatory, untranslated region, the so-called 5'UTR. The end of the 5'UTR of eukaryotes contains the so called methylguanosine cap (and is only present in mature mRNA), in proaryotes this is done by the Shine-Delgano sequence. Both are recognized by the ribosome. After binding to the mRNA, the ribosome slides along the nucleotide chain until it reaches the first AUG to initiate translation. The image is from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK9849/&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; description (which contains a lot more details, if you are interested in it).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TdhC3.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-02-13T22:25:51.313" LastActivityDate="2014-02-13T22:25:51.313" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15021" PostTypeId="1" CreationDate="2014-02-13T19:43:38.383" Score="2" ViewCount="163" Body="&lt;p&gt;Why people should take anti-inflammatory drugs, when inflammation is a physiological way to defend our organism?&lt;/p&gt;&#xA;" OwnerUserId="5714" LastEditorUserId="1320" LastEditDate="2014-02-14T09:56:18.277" LastActivityDate="2014-02-16T16:01:05.883" Title="Why do people use anti-inflammatory drugs?" Tags="&lt;medicine&gt;&lt;infection&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15023" PostTypeId="2" ParentId="15021" CreationDate="2014-02-13T22:05:20.677" Score="3" Body="&lt;p&gt;While inflammation is a natural defensive process, it also does (sometimes severe and/or permanent) damage to tissue. Therefore, when inflammation has been caused by an injury or an auto-immune disease such as rheumatoid arthritis, anti-inflammatory drugs do more good than harm.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastActivityDate="2014-02-13T22:05:20.677" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15025" PostTypeId="1" CreationDate="2014-02-13T22:14:04.143" Score="2" ViewCount="888" Body="&lt;p&gt;My husband had light brown eyes. His father had hazel and his mother, light brown as well. His younger brother however, has blue eyes. Both my children have blue eyes. Is this possible? I thought once the recessive gene was used in my first child, his dominant brown gene would take over?&lt;/p&gt;&#xA;" OwnerUserId="5715" LastActivityDate="2014-02-13T22:36:20.840" Title="2 blue eyed children" Tags="&lt;gene-expression&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15026" PostTypeId="2" ParentId="15025" CreationDate="2014-02-13T22:36:20.840" Score="2" Body="&lt;p&gt;There is some chance for that. Look at this chart with some probabilities:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/guIuv.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its from this &lt;a href=&quot;http://www.dnaexaminers.com/lib/ckeditor/eye-color-paternity-test.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;webpage&lt;/a&gt;, which also gives some background information.&#xA;There is also an online calculation tool available, which takes the grandparents into account as well. It can be found &lt;a href=&quot;http://genetics.thetech.org/online-exhibits/what-color-eyes-will-your-children-have&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-13T22:36:20.840" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15027" PostTypeId="1" AcceptedAnswerId="15314" CreationDate="2014-02-13T22:36:45.123" Score="0" ViewCount="37" Body="&lt;p&gt;I know that it has transcellular activity i.e. it can pass through neighbouring cells.&#xA;However, I am not completely sure if it does not have paracellular activity, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC108731/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;H. pylori did not induce any modification of the paracellular pathway&#xA;  (R = 148 ± 10 versus 174 ± 16 Ω · cm2; JNa = 4.16 ± 0.44 versus 3.51 ±&#xA;  0.41 μEq/h · cm2; JMan = 0.081 ± 0.01 versus 0.058 ± 0.009 μmol/h · cm2), nor did it modify J3H-HRP (2,201 ± 255 versus 2,110 ± 210 ng/h ·&#xA;  cm2 for H. pylori-infected and control cells, respectively). However,&#xA;  in the presence of H. pylori, we observed a significant increase in&#xA;  JHRPi (520 ± 146 versus 171 ± 88 ng/h · cm2). This effect was not&#xA;  dependent of the cag status of the strain and was not reproduced by&#xA;  the sonicates or the culture supernatants.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any evidence that Helicobacter pylori has paracellular activity?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorDisplayName="user38945" LastEditDate="2018-12-17T04:38:10.133" LastActivityDate="2018-12-17T04:38:10.133" Title="Does H. pylori have paracellular activity?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="15028" PostTypeId="1" AcceptedAnswerId="15034" CreationDate="2014-02-14T01:14:02.403" Score="1" ViewCount="88" Body="&lt;p&gt;It can spread in blood (Type III secretion system -&gt; apoptosis).&#xA;I am interested if there is any others ways to move.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do Yersinia spp have anything virulence factors to move?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-14T07:31:26.640" Title="Do Yersinia genus spp have anything movement factors?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15029" PostTypeId="1" CreationDate="2014-02-14T04:15:21.257" Score="2" ViewCount="131" Body="&lt;p&gt;I have rudimentary knowledge of evolution, and biology in general, so bear with me if this question is a bit naive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say we have a particular trait, like highly sensitive peripheral vision. There are two ways to go about explaining how this came about: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One is to say that evolution selected for it over time, because animals with a poor sensitivity to peripheral activity could easily become prey. So there is an advantage to having sensitive peripheral vision, and such a trait is &lt;em&gt;adaptive&lt;/em&gt;. The picture I have in my mind is of an assembly line where there are randomly wired visual cortices and the best ones get selected for automatically. This seems to be the view of the field of evolutionary algorithms, at least to my mind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, if we focus on the random nature of the wiring, we might see that there is an explosion of possibilities in terms of how the visual system can be wired together. After all, evolution is blind, and it doesn't know beforehand which physical signals are of interest. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm trying to think of a more plausible mechanistic explanation. Suppose we &lt;strong&gt;assume&lt;/strong&gt; that given certain reliable properties of the physical world, like permanence of objects for example, evolution has found the optimal way to wire the visual cortex so that peripheral vision (and a host of other good-to-have features) is a natural outcome, then it would give us more focus in what environmental features and algorithms to look for. This can also be thought of as the idea that evolution, over time, has come to assume that certain things in the physical world will be a given and exploits these. (For example, objects in the peripheral areas of vision will tend to have different perceived velocities, so perhaps normalizing velocities across the field of vision automatically results in a need for higher sensitivity in that region. It just so happens that this could also be useful in detecting predators).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question then is, is my assumption in the above paragraph valid? (Of course, the question then gets shifted to &quot;Why normalize velocities across the visual field in the first place?&quot;).&lt;/p&gt;&#xA;" OwnerUserId="625" LastActivityDate="2020-11-04T20:17:43.887" Title="Evolution, self organization and neuroscience" Tags="&lt;evolution&gt;&lt;neuroscience&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15030" PostTypeId="2" ParentId="15015" CreationDate="2014-02-14T04:38:05.163" Score="6" Body="&lt;p&gt;From ENA&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To retrieve results by a single identifier for all records other than&#xA;  Taxon and Project please, use the following URL syntax:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;http://www.ebi.ac.uk/ena/data/view/&quot; rel=&quot;nofollow&quot;&gt;http://www.ebi.ac.uk/ena/data/view/&lt;/a&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;For example, the following URL returns the EMBL-Bank entry with&#xA;  accession number A00145 in HTML format:&#xA;  &lt;a href=&quot;http://www.ebi.ac.uk/ena/data/view/A00145&quot; rel=&quot;nofollow&quot;&gt;http://www.ebi.ac.uk/ena/data/view/A00145&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Check &lt;a href=&quot;https://www.ebi.ac.uk/ena/about/browser#retrieval_single_identifier&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you use a *nix system (such as Linux, Unix, or OSX) then you can do this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[ if &lt;code&gt;list.txt&lt;/code&gt; contains all your ids ]&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;for i in `cat list.txt`; do wget -q -O $i&quot;.fa&quot; &quot;http://www.ebi.ac.uk/ena/data/view/&quot;$i&quot;&amp;amp;display=fasta&quot;; done&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;OR ELSE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Download the entire database and pick up sequences based on your identifiers, offline. You can use your favourite programming language to retrieve sequences. [I prefer awk but python is also good]&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-19T07:07:43.803" LastActivityDate="2015-06-19T07:07:43.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15031" PostTypeId="1" CreationDate="2014-02-14T04:54:07.403" Score="0" ViewCount="3045" Body="&lt;p&gt;Plants has the capacity to take in both CO&lt;sub&gt;2&lt;/sub&gt; and oxygen, that's during day CO&lt;sub&gt;2&lt;/sub&gt; and at night oxygen. Why don't humans have such a capability?&lt;/p&gt;&#xA;" OwnerUserId="5343" LastEditorUserId="1320" LastEditDate="2014-02-14T09:48:19.713" LastActivityDate="2014-10-09T13:58:41.727" Title="Why can we breathe only oxygen?" Tags="&lt;zoology&gt;&lt;botany&gt;&lt;cellular-respiration&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15032" PostTypeId="2" ParentId="15031" CreationDate="2014-02-14T05:38:58.317" Score="0" Body="&lt;p&gt;Humans breathe in air, which contains both oxygen and carbon dioxide. But we do not photosynthesise and so we do not take in CO&lt;sub&gt;2&lt;/sub&gt;. The CO&lt;sub&gt;2&lt;/sub&gt; produced from respiration in our body builds up in the blood and through diffusion escapes into the lungs and out when we exhale.&lt;/p&gt;&#xA;" OwnerUserId="3465" LastEditorUserId="1320" LastEditDate="2014-02-14T09:48:08.277" LastActivityDate="2014-02-14T09:48:08.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15034" PostTypeId="2" ParentId="15028" CreationDate="2014-02-14T07:31:26.640" Score="3" Body="&lt;p&gt;Yersinia enterocolitica does express flagella at a temperature around 25°C, but not at 37°C. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8830263&quot; rel=&quot;nofollow&quot; title=&quot;Kapatral et al.&quot;&gt;Kapatral et al.&lt;/a&gt;&#xA;Besides that it can rely on peristaltic movement in the intestines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yersinia pestis is as far as I know nonmotile in the host, but motile if isolated &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK7798/&quot; rel=&quot;nofollow&quot;&gt;Medical Microbiology&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As there are some other Yersinia species, including Y. pseudotuberculosis of course, I think you cannot totally generalize the answer for Yersinia spp., but searching for the Yersinia of interest with &quot;flagella&quot;, &quot;motility&quot;, &quot;movement&quot; or similar keywords on Pubmed might help.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2014-02-14T07:31:26.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15035" PostTypeId="2" ParentId="15031" CreationDate="2014-02-14T09:48:47.610" Score="1" Body="&lt;p&gt;You should have a look biological processes which are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;cellular respiration&lt;/li&gt;&#xA;&lt;li&gt;photosynthesis&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Loosly speaking, these two processes are just the opposite but deal with the same chemical compunds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$C_6H_{12}O_6 + 6O_2 \xrightleftharpoons\  6CO_2 + 6H_2O (+ Energy)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or in words...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;glucose + Oxygen $\xrightleftharpoons\ $ Carbon Dioxide + Water (+ Energy)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From left to right is the process of respiration and from right to left is the process of photosynthesis.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Respiration releases energy from glucose (sugar). Therefore, animals, plants, fungi respire in order to get their energy from their food. More information on the chemical pathways on  &lt;a href=&quot;http://en.wikipedia.org/wiki/Citric_acid_cycle&quot; rel=&quot;nofollow&quot;&gt;Krebs cycle (or citric acid cycle)&lt;/a&gt;. The main &lt;a href=&quot;http://en.wikipedia.org/wiki/Organelle&quot; rel=&quot;nofollow&quot;&gt;organelle&lt;/a&gt; involved in celullar respiration is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitochondrion&quot; rel=&quot;nofollow&quot;&gt;mitochondrion&lt;/a&gt;. Note: (Loosely speaking) the glucose is the end product of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Digestion&quot; rel=&quot;nofollow&quot;&gt;digestion&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;photosynthesis allows organisms to create its own tissues from water and $CO_2$. But this cost energy. This is why plants use capture the energy form the sun with their leaves. More information on the chemical pathways on &lt;a href=&quot;http://en.wikipedia.org/wiki/Calvin_cycle#Calvin_Cycle&quot; rel=&quot;nofollow&quot;&gt;Calvin Cycle&lt;/a&gt;. The main organelle involved in photosynthesis is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Chloroplast&quot; rel=&quot;nofollow&quot;&gt;chloroplast&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Note: In our lungs comes air which is a mixture of different gases (just like coke (Coca-Cola) is a mixture of different compounds). The two main compounds of air are Nitrogen (~78%) and Oxygen (~21%). We use only Oxygen. More info on the air composition &lt;a href=&quot;http://en.wikipedia.org/wiki/Atmosphere_of_Earth#Composition&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3340" LastEditDate="2014-10-09T13:58:41.727" LastActivityDate="2014-10-09T13:58:41.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15036" PostTypeId="2" ParentId="15017" CreationDate="2014-02-14T10:05:23.267" Score="4" Body="&lt;p&gt;I think that there is no reason in principle why early evolution couldn't have landed on a translation mechanism going 3'&gt;5'. There are, however, clear biochemical reasons why the transcript itself has to be made in a 5'&gt;3' direction. So in this alternative world where the initiation signals would have been at the 3' end of the mRNA, the message would have to be fully transcribed before the anti-ribosome could bind to these initiation signals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In bacteria at least, translation is initiated at the 5' end of the mRNA even as it is being synthesised, and this rapid transcription&gt;translation link may offer some advantages.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-14T10:05:23.267" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15037" PostTypeId="2" ParentId="15029" CreationDate="2014-02-14T10:09:20.120" Score="3" Body="&lt;p&gt;I don't fully understand your question. I hope the following will help a bit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like to pinpoint what seems to me to be one important mistake in your text. Reading you we have the feeling that selection acts on wires so to select the best combination. If this is what you meant, then it is obviously wrong. The thing is that the change that get inherited are alleles. An allele is a variant of a gene. For example: gene codes for eyes color. A bi-allelic gene has an allele which codes for blue eyes while the other codes for brown eyes. Assuming that there is genetic variance underlying the wire connection variance in the population, then yes selection will select for the best genetic variant. This does not necessarily mean that this best genetic variant is the most optimal possible to imagine solution. The most optimal allele might have never been created just because of the randomness nature of mutations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Do natural selection always bring a particular &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenotype&quot; rel=&quot;nofollow&quot;&gt;phenotypic&lt;/a&gt; (loosly speaking, phenotype = morphological) trait to its optimal state?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No! It does not.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The main reason is that the genetic variant coding for this optimal trait does not necessarily exist because of the randomness of mutational process. Also, because of the metabolic pathway bringing some variance to a trait, it is often very hard to even imagine a  mutation that would allow creating a new, more optimal, phenotypic variant. So indeed developmental biology has to be taken in account to.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Because in absence of &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_drift&quot; rel=&quot;nofollow&quot;&gt;genetic drift&lt;/a&gt; (infinite population), selection can only bring genotypes uphill in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Fitness_landscape&quot; rel=&quot;nofollow&quot;&gt;fitness landscape&lt;/a&gt;. If a very high peak exist somewhere in the fitness landscape but in order to reach such peak, 10 mutations are needed were all of them in any other genetic background are deleterious (correspond to valleys in fitness landscape), then the optimal high will probably never be reached (except if all 10 mutations appear suddenly in the same individual).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Because selection might be weaker than genetic drift. Also, different subpopulations might be in different environments were different traits correspond to optimal traits and because of migration (gene flow) between subpopulations, it is possible that no optimal phenotypic trait can be ever seen although all the genotypic variance exist.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The seemingly most optimal trait might actually not be really optimal. For example: Peripheral vision might be limited by the brain rather than by the eye because it would be an important energy cost for the brain to process more information, a cost that might outweight the benefit of having a better peripheral vision.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-02-14T11:55:52.060" LastActivityDate="2014-02-14T11:55:52.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15038" PostTypeId="1" AcceptedAnswerId="15045" CreationDate="2014-02-14T10:17:50.280" Score="1" ViewCount="82" Body="&lt;p&gt;I am looking for a good book in:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Yeast reproduction&#xA;&lt;ul&gt;&#xA;&lt;li&gt;mating types&lt;/li&gt;&#xA;&lt;li&gt;Recombination&lt;/li&gt;&#xA;&lt;li&gt;mating type determination mechanism&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Yeast evolution&lt;/li&gt;&#xA;&lt;li&gt;Yeast as model organism and its use in experimental biology&#xA;&lt;ul&gt;&#xA;&lt;li&gt;It should include common technics used to work with yeast. For example: We can add a plasmid in order to fool yeast and let them think they have another mating type than the actually have.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Note: I am mostly interested in &lt;a href=&quot;http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae&quot; rel=&quot;nofollow&quot;&gt;Saccharomyces cerevisiae&lt;/a&gt; of course.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-02-14T16:41:04.033" Title="Book on yeast reproduction, evolution and on the use of yeast as model organism" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;experimental-design&gt;&lt;book-recommendation&gt;&lt;yeast&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15039" PostTypeId="1" AcceptedAnswerId="15064" CreationDate="2014-02-14T12:29:57.707" Score="1" ViewCount="535" Body="&lt;p&gt;One of the options is correct&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Kidney can be taken from a dying person who has the&lt;/p&gt;&#xA;&lt;p&gt;a) cessation of neurological function only&lt;/p&gt;&#xA;&lt;p&gt;b) cessation of cardiac function only&lt;/p&gt;&#xA;&lt;p&gt;c) cessation of respiratory function only&lt;/p&gt;&#xA;&lt;p&gt;d) cessation of kidney function only&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I think that answer should be b. as if heart stops working then the person is definitely dead. but m not sure if on the cessation of neurological/respiratory function, one still has chance of revivial. Moreover answer is given as A. I don't know how. Could it be that on cessation of cardiac/respiratory function, kidney gets damaged while not so in case of neurological dysfunction?&lt;/p&gt;&#xA;" OwnerUserId="5719" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-02-20T22:18:26.337" Title="Regarding kidney transplant" Tags="&lt;homework&gt;&lt;kidney&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15040" PostTypeId="1" CreationDate="2014-02-14T12:46:55.723" Score="1" ViewCount="158" Body="&lt;p&gt;I am thinking the mechanism is something like first adhesins (mucinase).&#xA;Howevever, this does not seem to be enough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How are the flagella of H. pylori produced?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-14T12:46:55.723" Title="How are lophotrichous flagella of helicobacter pylori produced?" Tags="&lt;microbiology&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15041" PostTypeId="2" ParentId="15021" CreationDate="2014-02-14T13:30:14.953" Score="5" Body="&lt;p&gt;You are correct in that inflammation is a physiological process. It is vital for the correct development and localisation of a strong immune response, and contributes to tissue healing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the beneficial effects are replaced by dangerous processes when they are prolonged or too intense. This includes both effects of leukocyte attraction and invasion, but also deleterious consequences of the accumulated cytokines. For example, TNF-alpha originally contributes to immune cell activation but in prolonged inflammation prevents tissue healing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that &quot;prolonged inflammation&quot; does not necessarily mean that inflammation has been apparent or noticeable for the affected person for a long time. Often by the time symptoms present, the inflammation process has been persistent and become pathological. At this point, anti-inflammatory drugs need to be used as soon as possible to minimise irreversible damage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aside from this, quite often inflammatory and immune processes are triggered without a need for them. Our immune system is quite prone to errors, and cases of misguided immune reactions are actually increasing. Consider for example allergies, which often manifest with skin-symptoms such as eczema that can be treated with anti-inflammatory creams.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2014-02-16T16:01:05.883" LastActivityDate="2014-02-16T16:01:05.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15043" PostTypeId="1" AcceptedAnswerId="15044" CreationDate="2014-02-14T15:30:09.050" Score="1" ViewCount="759" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;&lt;strong&gt;Agglutination test&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Latex agglutination using bound antigens&lt;/strong&gt; : by coating soluble (non - particulate ) antigens on to microscopic latex spheres, their reaction with a particular antibody can be visualized.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Haemagglutination&lt;/strong&gt; : red blood cells can be used as agglutinating particles.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What are non-particulate antigens ? Why are they used instead of particulate ones ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How are red blood cells used as agglutinating particles ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2015-04-19T15:21:28.737" Title="Agglutination test using antibodies" Tags="&lt;immunology&gt;&lt;protocol&gt;&lt;antibody&gt;&lt;antigen&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15044" PostTypeId="2" ParentId="15043" CreationDate="2014-02-14T16:27:36.873" Score="3" Body="&lt;p&gt;If you have an antibody that is directed against, for example, a bacterial surface protein, then by mixing the bacterial cells with the antibody at a suitable stoichiometry you could observe clumping of the cells as the antibody molecules essentially cross link the cells together. This would be an example of using an agglutination (clumping) assay with a particulate antigen. You can also probably see why it is important that each cell (particle) carries many copies of the antigen for cross linking to take place effectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If, however, the antibody of interest is directed against a soluble protein, then mixtures of antigen and antibody are less likely to form cross-linked complexes, although it can happen and can be used for example in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Ouchterlony_double_immunodiffusion&quot; rel=&quot;nofollow&quot;&gt;Ouchterlony technique&lt;/a&gt;. If you want to use an agglutination test (i.e clumping of particles) with a soluble antigen then you can achieve this by attaching multiple copies of the antigen to macroscopic particles. This is what is being described in the definition of Latex agglutination in your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I imagine that there are ways of attaching a soluble antigen to red blood cells (e.g. by chemical cross-linking to the red blood cell surface) in which case you could observe clumping of the red blood cells when you added your antibody. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-14T16:27:36.873" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15045" PostTypeId="2" ParentId="15038" CreationDate="2014-02-14T16:41:04.033" Score="1" Body="&lt;p&gt;Here is my list, in no particular order.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cshlpress.com/default.tpl?cart=13923940041297048&amp;amp;fromlink=T&amp;amp;linkaction=full&amp;amp;linksortby=oop_title&amp;amp;--eqSKUdatarq=526&quot; rel=&quot;nofollow&quot;&gt;Methods in Yeast Genetics&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cshlpress.com/default.tpl?cart=13923940041297048&amp;amp;id1=108&amp;amp;startat=1&amp;amp;--woSECTIONSdatarq=108&amp;amp;--SECTIONSword=ww&amp;amp;sortby_1=recency&quot; rel=&quot;nofollow&quot;&gt;Some other yeast books at CSHL&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fred Sherman's primer, available free at various sites including &lt;a href=&quot;http://www.uni-marburg.de/fb20/cyto/lehre/praktikumsunterlagen/vl/hefe/sherman01&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Freiburg manual &lt;a href=&quot;http://www.unifr.ch/biochem/assets/files/schneiter/cours/Yeast/YeastGenetics.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0879693649&quot; rel=&quot;nofollow&quot;&gt;The timeless classics (link to volume 3 but see all volumes)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.genetics.org/site/misc/yeastbook.xhtml&quot; rel=&quot;nofollow&quot;&gt;YeastBook&lt;/a&gt; is an attempt to build a current encyclopaedia to replace the previous item on my list.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.yeastgenome.org&quot; rel=&quot;nofollow&quot;&gt;Saccharomyces genome database&lt;/a&gt;, probably the best organism-specific resource ever.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-14T16:41:04.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15046" PostTypeId="2" ParentId="14998" CreationDate="2014-02-14T16:48:22.697" Score="4" Body="&lt;p&gt;Recent scientific research suggests that &lt;a href=&quot;http://en.wikipedia.org/wiki/Cognitive_neuroscience_of_dreams#Dopaminergic_activation&quot; rel=&quot;nofollow&quot;&gt;dopaminergic pathways are responsible for dreaming&lt;/a&gt;. According to this theory if something affects your dopamine system, it will also affect dreaming. My personal takeaway from this is that your dreaming can be viewed as an indicator of how your dopaminergic system works. Significant deviations from the baseline dream content may be a reaction to drugs, especially psychiatric drugs or changes in diet. These changes rarely persist for many days, as the brain compensates for the new thing.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A &lt;strong&gt;dopaminergic pathway&lt;/strong&gt; runs from the ventral tegmental area, ascends&#xA;  through the lateral hypothalamus, various basal forebrain areas&#xA;  (nucleus basalis, stria terminalis, shell of nucleus accumbens) and&#xA;  terminates in the amygdala, anterior cingulate gyrus and frontal&#xA;  cortex. Damage to the dopaminergic pathway results in a loss of&#xA;  dreaming. Furthermore, &lt;strong&gt;chemical stimulation of the pathway (with&#xA;  L-DOPA for example) increases the frequency and vividness of dreams&lt;/strong&gt;&#xA;  without affecting REM sleep.[10] It is interesting to note that the&#xA;  mesolimbic and mesocortical pathways are considered the seeking areas&#xA;  or the motivational command centers of the brain.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The evidence of the involvement of mesolimbic and mesocortical&#xA;  dopaminergic pathways suggests that &lt;strong&gt;dreaming occurs when a&#xA;  motivational component is activated&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="577" LastActivityDate="2014-02-14T16:48:22.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15047" PostTypeId="1" AcceptedAnswerId="15048" CreationDate="2014-02-14T16:49:35.843" Score="10" ViewCount="19422" Body="&lt;p&gt;I've been told that the maximum number of cycles in PCR is between 20 and 30.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this true, and what are the reasons for this limitation?&lt;/p&gt;&#xA;" OwnerUserId="5578" LastEditorUserId="948" LastEditDate="2014-02-14T17:18:41.003" LastActivityDate="2015-08-11T11:58:38.030" Title="Why is the number of PCR cycles limited?" Tags="&lt;molecular-biology&gt;&lt;pcr&gt;&lt;experimental&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15048" PostTypeId="2" ParentId="15047" CreationDate="2014-02-14T16:55:24.190" Score="10" Body="&lt;p&gt;I would draw the line beyond 35, but thats a bit cosmetic. &#xA;The reasons are manyfold:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;due to the exponential fashion of the amplification (ideally)&#xA;reagents are used up at some point&lt;/li&gt;&#xA;&lt;li&gt;reagents degrade, this is especially true for the dNTPs&lt;/li&gt;&#xA;&lt;li&gt;the activity of the enzyme, despite being heat-stable is declining&#xA;over time&lt;/li&gt;&#xA;&lt;li&gt;beyond 35 cycles the exponential curve is flattening out (reasons see&#xA;above)&lt;/li&gt;&#xA;&lt;li&gt;if you run the PCR for too long, you will get more and more&#xA;side-products (mostly primer dimers, but mis-aligned primers can also&#xA;make problems), this is more a problem for real-time PCR than for ones run on a gel&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you need a higher sensitivity with more cycles, you can use the technique called &quot;nested PCR&quot;. There you do a first round with a primer pair specific for the region of interest and then do a second round with primers which are located slightly to the inside of the amplified DNA. This is done to avoid the amplification of unwanted contaminations. Since you do some 50-70 rounds of PCR amplification in total, this method is extremely sensitive (also to contaminations). See the image from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nested_PCR&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt; article for details:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CKbPl.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-02-14T17:23:19.753" LastActivityDate="2014-02-14T17:23:19.753" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15049" PostTypeId="1" CreationDate="2014-02-14T17:10:02.527" Score="1" ViewCount="103" Body="&lt;p&gt;In the &lt;a href=&quot;http://en.wikipedia.org/wiki/Jack_Andraka&quot; rel=&quot;nofollow&quot;&gt;wikipedia article about Andraka's pancreatic cancer test&lt;/a&gt; there are some controversial statements.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On one hand there are many glorious words about the method, also some awards, also some astonishing comparisons with other methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, there is no proof, and also some evidence against its efficacy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I can't find any signs of Andraka's test in reality. For example, there is no such product in drug stores.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the proof or evidence that Andraka's method is really working and can feasibly exist in the near future?&lt;/p&gt;&#xA;" OwnerUserId="5720" LastEditorUserId="5144" LastEditDate="2014-02-17T10:25:40.587" LastActivityDate="2014-02-17T10:25:40.587" Title="Is the Andraka pancreatic cancer test real?" Tags="&lt;cancer&gt;&lt;peer-review-journal&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15050" PostTypeId="2" ParentId="15047" CreationDate="2014-02-14T17:30:28.843" Score="7" Body="&lt;p&gt;&lt;strong&gt;How many cycles of PCR before dNTPs run out?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume a 25 &amp;mu;l reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume 200 &amp;mu;M dNTPs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;200 &amp;mu;M dNTPs = 200 pmol  &amp;mu;l &lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so in  25 &amp;mu;l  reaction, there are 5000 pmol of dNTPs&lt;/p&gt;&#xA;&#xA;&lt;p&gt;= 5000 x 10&lt;sup&gt;-12&lt;/sup&gt; x 6 x  10&lt;sup&gt;23&lt;/sup&gt; molecules &lt;/p&gt;&#xA;&#xA;&lt;p&gt;= 3 x 10&lt;sup&gt;15&lt;/sup&gt; molecules dNTP&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume that we start with 1 molecule of a 1000 bp template, 50% GC&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1 kb = 2000 nucleotides&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So , how many of these molecules can we construct using 3 x 10&lt;sup&gt;15&lt;/sup&gt; molecules dNTP?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;= 3 x 10&lt;sup&gt;15&lt;/sup&gt;/2000&lt;/p&gt;&#xA;&#xA;&lt;p&gt;= 1.5 x 10&lt;sup&gt;12&lt;/sup&gt; DNA molecules&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How many cycles of PCR to produce this many from a single template molecule?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2&lt;sup&gt;n&lt;/sup&gt; = 1.5x 10&lt;sup&gt;12&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;nlog2 = log(1.5) + log(10&lt;sup&gt;12&lt;/sup&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;nlog2 =  12.18&lt;/p&gt;&#xA;&#xA;&lt;p&gt;n = 12.18/ log2 = &lt;strong&gt;41 cycles&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course this in an absolute upper limit. The estimate assumes that you start with one template molecule of 1 kb, and that dNTPs aren't being hydrolysed, or otherwise degraded.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-14T17:30:28.843" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15051" PostTypeId="1" CreationDate="2014-02-14T21:00:37.740" Score="29" ViewCount="1401" Body="&lt;p&gt;We can often think of cells as a sort of circuit on macromolecules, and can show that they can &lt;a href=&quot;http://egtheory.wordpress.com/2013/05/29/cells-and-dna/&quot; rel=&quot;noreferrer&quot;&gt;accurately and robustly implement functions&lt;/a&gt; like &lt;span class=&quot;math-container&quot;&gt;$\text{MAJ}(x_1,...,x_n)$&lt;/span&gt; (return &lt;span class=&quot;math-container&quot;&gt;$1$&lt;/span&gt; if more than half of &lt;span class=&quot;math-container&quot;&gt;$x_1,...,x_n$&lt;/span&gt; is &lt;span class=&quot;math-container&quot;&gt;$1$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$0$&lt;/span&gt; otherwise) under natural conditions (Cardell &amp;amp; Csikász-Nagy, 2012).&lt;/p&gt;&#xA;&lt;p&gt;Not all functions are created equal. &lt;span class=&quot;math-container&quot;&gt;$\text{XOR}(x,y)$&lt;/span&gt; is a boolean function that is &lt;span class=&quot;math-container&quot;&gt;$1$&lt;/span&gt; if exactly one of &lt;span class=&quot;math-container&quot;&gt;$x$&lt;/span&gt; or &lt;span class=&quot;math-container&quot;&gt;$y$&lt;/span&gt; is &lt;span class=&quot;math-container&quot;&gt;$1$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$0$&lt;/span&gt; otherwise (i.e, if &lt;span class=&quot;math-container&quot;&gt;$x = y$&lt;/span&gt;). It is often generalized to a multi-input function parity (or odd) as &lt;span class=&quot;math-container&quot;&gt;$\text{ODD}(x_1,...,x_n)$&lt;/span&gt; which returns &lt;span class=&quot;math-container&quot;&gt;$1$&lt;/span&gt; if an odd number of &lt;span class=&quot;math-container&quot;&gt;$x_1,...,x_n$&lt;/span&gt; is &lt;span class=&quot;math-container&quot;&gt;$1$&lt;/span&gt;. Notice that this is superficially similar to &lt;span class=&quot;math-container&quot;&gt;$\text{MAJ}$&lt;/span&gt; but is doing its counting in base 2, which one would expect to be easier for say finite state machines.&lt;/p&gt;&#xA;&lt;p&gt;However, in some ways, this sensitivity makes the function much more difficult to the point that &lt;a href=&quot;http://egtheory.wordpress.com/2014/02/14/evolution-is-machine-learning/&quot; rel=&quot;noreferrer&quot;&gt;Valiant (2009) writes&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;[Parity] appears to be biologically unnatural. That is exactly the prediction of our theory, which asserts that evolution cannot be based on the evolvability of [the class of functions parity belongs to]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Synthetic biologists used to agree to some extent, with Tamsir et al. (2011) writing that the closely related XNOR (i.e. &lt;span class=&quot;math-container&quot;&gt;$\text{XNOR}(x,y) = 1 - \text{XOR}(x,y)$&lt;/span&gt;) is empirically impossible to implement. However, they were &lt;a href=&quot;http://egtheory.wordpress.com/2013/04/08/cell-computer/&quot; rel=&quot;noreferrer&quot;&gt;proven wrong&lt;/a&gt; when Bonnet et al. (2012) implemented XNOR among many other amplifying gates by exploiting the structure and process of transcription. Unfortunately, this is an example from synthetic biology, and I really want to learn ones (if any) that occur naturally.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Are there any examples of XOR or related gates implemented (without human engineering) at the cellular level?&lt;/strong&gt; Are there any naturally occurring molecular pathways that compute something similar to parity? (i.e. something similar to the majority result, but for a more 'sensitive' function) I am primarily interested in empirical demonstrations, but I would be satisfied with theoretical examples that are appealing to biologists (i.e. not something purely comp. sci. like P-systems or something).&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h3&gt;References&lt;/h3&gt;&#xA;&lt;p&gt;Bonnet J, Yin P, Ortiz ME, Subsoontorn P, &amp;amp; Endy D (2013). Amplifying Genetic Logic Gates. &lt;em&gt;Science&lt;/em&gt;, 340(6132): 599-603. PMID: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23539178&quot; rel=&quot;noreferrer&quot;&gt;23539178&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Cardelli L, &amp;amp; Csikász-Nagy A (2012). The cell cycle switch computes approximate majority. &lt;em&gt;Scientific Reports&lt;/em&gt;, 2: 656. PMID: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22977731&quot; rel=&quot;noreferrer&quot;&gt;22977731&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Tamsir, A., Tabor, J. J., &amp;amp; Voigt, C. A. (2011). Robust multicellular computing using genetically encoded NOR gates and chemical wires. &lt;em&gt;Nature&lt;/em&gt;, 469(7329), 212-215.&lt;/p&gt;&#xA;&lt;p&gt;Valiant, L.G. (2009) Evolvability. &lt;em&gt;Journal of the ACM&lt;/em&gt;, 56(1): 3-22.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2018-02-14T20:56:53.520" Title="Natural examples of XOR functions at the cellular level" Tags="&lt;cell-biology&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;experimental&gt;" AnswerCount="1" CommentCount="10" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="15053" PostTypeId="2" ParentId="15051" CreationDate="2014-02-15T02:24:26.703" Score="10" Body="&lt;p&gt;When I think about your question of natural examples of XOR, it pushes me to think about what type of natural environments (i.e., evolutionary pressures) would lead to the selection of an XOR equivalent.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When we implemented a synthetic XOR by &quot;double flipping&quot; one transcription terminator as a type of gene expression &quot;check valve&quot; it was the case that I did not know of any natural examples of flipping terminators, whereas I know of several examples of nature flipping promoters.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do we have plenty of natural examples of flipping promoters but (unknown to me at least) as yet no charismatic examples of naturally flipping terminators?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps we haven't been looking in the right environments to find them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.g., for a terminator to exist in nature, there needs to be something that must  be expressed upstream of the terminator, and also something that should not be expressed downstream of the terminator.  Since there are plenty of terminators there must plenty of examples of nature selecting for terminators.  My favorite example is the &quot;Tø&quot; terminator in phage T7 that is just downstream of the major capsid gene (highly expressed) but just upstream of a minor particle protein (weakly expressed).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But now reason thru what would need to be true in order to select for terminator flipping.  I'd need all the requirements of a static terminator (above), and then another such pairing of selective requirements under different environmental circumstances for additional gene products encoded in the opposite direction on the complementary strand of DNA. Phew! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not saying that it is impossible to imagine such a complicated coupling of selection requirements emerging in nature, but it definitely seems a much more improbable aggregation of selective pressures to co-mingle all within a single genetic loci.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm still nevertheless very curious and would be grateful to learn of any natural examples.  -DE&lt;/p&gt;&#xA;" OwnerUserId="5726" LastActivityDate="2014-02-15T02:24:26.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15054" PostTypeId="1" CreationDate="2014-02-15T05:30:50.753" Score="5" ViewCount="124" Body="&lt;p&gt;I was watching &lt;a href=&quot;http://www.g2conline.org&quot; rel=&quot;nofollow&quot;&gt;a video&lt;/a&gt; where a professor said that according to some experiments, Long Term Potentiation (LTP) is correlated with better learning, while in yet other experiments, LTP is correlated with poorer learning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any models that explain this phenomenon? What's the current theory on this?&lt;/p&gt;&#xA;" OwnerUserId="625" LastEditorUserId="3632" LastEditDate="2014-02-24T21:33:40.037" LastActivityDate="2014-06-28T17:36:58.153" Title="What is the current consensus, if any, about why long term potentiation is not clearly correlated with learning?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15056" PostTypeId="1" AcceptedAnswerId="15057" CreationDate="2014-02-15T08:22:26.750" Score="2" ViewCount="154" Body="&lt;p&gt;Dolly the sheep was a clone. When she was born she was eight years old on her 1st day of birth, her mother (from which she was cloned) was also eight years old. What is a molecular reason behind this - that Dolly was eight years old when she was born?&lt;/p&gt;&#xA;" OwnerUserId="5729" LastEditorUserId="1320" LastEditDate="2014-02-15T10:03:24.203" LastActivityDate="2014-02-15T10:03:46.440" Title="Cloning of a sheep.. Dolly?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15057" PostTypeId="2" ParentId="15056" CreationDate="2014-02-15T08:41:54.540" Score="5" Body="&lt;p&gt;If you look at the replication of end of chromosomes, you will see that one of the strand gets shorter every time. To prevent the genes from being disrupted, the ends of the chromosomes have repetitive sequences called telomeres which shorten with every replication but will prevent the disruption of genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can deduce from the above information, there will be a certain limit to how many times a cell can divide.So, it has been thought that any organism ages because of shortening of telomeres.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gametes have the enzyme telomerase which will lengthen the telomeres to full length so that the zygote formed will have unshortened telomeres. But, in the case of Dolly the nucleus was taken from a somatic cell and so the telomeres did not lengthen. The age of Dolly at the time of birth was thus the age of mother from which the nucleus was taken.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See : &lt;a href=&quot;http://en.wikipedia.org/wiki/Telomere&quot; rel=&quot;nofollow&quot;&gt;Telomere&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1320" LastEditDate="2014-02-15T10:03:46.440" LastActivityDate="2014-02-15T10:03:46.440" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15058" PostTypeId="1" CreationDate="2014-02-15T08:44:37.947" Score="3" ViewCount="256" Body="&lt;p&gt;What do you think are the potential drawbacks/weakness of using ORA to explain distinction between two phenotypes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I identified a few which were the dependencies of DE and the statistical method used to filter the starting DE list.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any other weakness?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="5730" LastActivityDate="2014-04-18T15:04:53.967" Title="Bioinformatics : Drawbacks of using ORA(Overlap Analysis)" Tags="&lt;bioinformatics&gt;&lt;gene-expression&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15059" PostTypeId="1" AcceptedAnswerId="15129" CreationDate="2014-02-15T08:48:32.820" Score="3" ViewCount="420" Body="&lt;p&gt;We inserted an insulin gene from human into bacteria. Will translation of the gene (protein formation) occur in bacteria? If translation occurs then why does it occurs, give a reason for this? &lt;/p&gt;&#xA;" OwnerUserId="5729" LastEditorUserId="1320" LastEditDate="2014-02-15T09:59:49.177" LastActivityDate="2014-02-18T10:07:14.833" Title="Translation of mRNA?" Tags="&lt;molecular-biology&gt;&lt;homework&gt;&lt;biotechnology&gt;" AnswerCount="4" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15060" PostTypeId="2" ParentId="15059" CreationDate="2014-02-15T08:55:11.720" Score="1" Body="&lt;p&gt;All the organisms share a common ancestor and have evolved from it. So they share quite the same machinery for transcription and translation. Codons are also interpreted in the same way in almost all the organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, yes translation should happen ( Assuming that the gene has been cloned in the right way.) &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-02-15T08:55:11.720" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15061" PostTypeId="2" ParentId="15059" CreationDate="2014-02-15T09:00:54.853" Score="1" Body="&lt;p&gt;It works, and is actually done to make all the &quot;human&quot; insulin which is used by diabetes patients today.&#xA;This is because the genetic code is almost completely conserved (with only very few exceptions in nature), so bacteria use the same codons to code for an amino acid as in humans. So with a suitable vector (a ring of DNA which carries extrachromosomal genetic information) which has the ability to replicate independent from the cell and which has the correct promoters (start points) for initiating transcription in bacterial cells, you can basically clone and express any human gene.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2014-02-15T10:01:26.027" LastActivityDate="2014-02-15T10:01:26.027" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15062" PostTypeId="2" ParentId="14838" CreationDate="2014-02-15T11:43:22.140" Score="0" Body="&lt;p&gt;The ESV is the residual volume of blood remaining in the ventricle after ejection. &#xA;It is the minimum volume of blood in the ventricles (residual volume). &#xA;Note that you can also have residual volume of air in the lungs after exhalation.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-15T11:43:22.140" CommentCount="0" CommunityOwnedDate="2014-02-15T11:43:22.140" ContentLicense="CC BY-SA 3.0" />
  <row Id="15063" PostTypeId="2" ParentId="15004" CreationDate="2014-02-15T12:09:16.137" Score="2" Body="&lt;p&gt;I've done a functional annotation of a non-model, and used Blast2Go with fine results.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, I took all of my proteins and queried again the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/refseq/&quot; rel=&quot;nofollow&quot;&gt;NCBI non redundant (nr) protein database&lt;/a&gt; using &lt;a href=&quot;http://www.mpiblast.org/&quot; rel=&quot;nofollow&quot;&gt;mpiBLAST&lt;/a&gt;, then I analyzed this output using Blast2GO (B2G4PIPE) and a local B2G Database.&lt;/p&gt;&#xA;" OwnerUserId="1210" LastActivityDate="2014-02-15T12:09:16.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15064" PostTypeId="2" ParentId="15039" CreationDate="2014-02-15T12:30:54.327" Score="7" Body="&lt;p&gt;There are actually very few situations where organs can be harvested from donors. For all deceased donor transplants, the donor must be confirmed as being brain dead (both brain stem and higher cortical functions).  However, in order for the organs to remain viable they must not become ischaemic - which is obviously a huge problem when the patients heart has stopped beating.  For this reason most patients who die and go on to become organ donors were already on a ventilator in intensive care in order to keep their blood oxygenated and circulating to perfuse their organs.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kidneys are listed by &lt;a href=&quot;http://www.organdonation.nhs.uk/how_to_become_a_donor/questions/index.asp&quot; rel=&quot;nofollow&quot;&gt;NHSBT&lt;/a&gt; as a special case where a ventillator may not be required in advance to maintain viability - offhand I'm not sure why this would be - however to answer your question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A. &lt;strong&gt;Neurological death&lt;/strong&gt; - correct answer - the patient must be deceased without chance of recovery (hence brainstem and cortical death)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B. Cardiac function - were this to stop unilaterally then the patient may still be recoverable whilst the organs may be damaged due to lack of perfusion and thus not be viable for transplant&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C. Respiratory function - almost identical to the cessation of cardiac function (and indeed will lead onto it very quickly)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D. Renal function - there's no point transplanting useless kidneys!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a look through the NHS Blood and Transplant Organ Donation site linked above, it's a great and trustworthy resource.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2014-02-20T22:18:26.337" LastActivityDate="2014-02-20T22:18:26.337" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15065" PostTypeId="2" ParentId="15015" CreationDate="2014-02-15T14:56:57.470" Score="3" Body="&lt;p&gt;I will edit this if you update your question with more information, but for the moment I am assuming you have access to a Linux/Unix system and that your file of accessions looks like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;A00145.1 123  456&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Where the first column is the accession and the next two are the start and end of the region of interest. So, using the same basic approach as WYSIWIG's answer, you can combine this with &lt;code&gt;fastasubseq&lt;/code&gt; from the &lt;a href=&quot;https://www.ebi.ac.uk/~guy/exonerate/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;code&gt;exonerate&lt;/code&gt;&lt;/a&gt; suite of tools (on Debian based systems, which include Ubuntu and Mint, you can install by runnning &lt;code&gt;sudo apt-get install exonerate&lt;/code&gt;). Just copy/paste this into your terminal:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;while read acc start end; do &#xA;  wget -q -O &quot;$acc&quot;.fa &quot;http://www.ebi.ac.uk/ena/data/view/$acc&amp;amp;display=fasta&quot; &amp;amp;&amp;amp;&#xA;  fastasubseq &quot;$acc&quot;.fa $start $end &amp;gt; $acc.$start-$end.fa&#xA;  rm &quot;$acc&quot;.fa &#xA;done &amp;lt; list.txt&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;With the example above, this command will create a file called &lt;code&gt;A00145.1.123-456.fa&lt;/code&gt; which contains the subsequence of &lt;code&gt;A00145.1&lt;/code&gt; from positions 123 to 456. Since it first needs to download the entire sequence, it also creates the temporary file &lt;code&gt;A00145.1.fa&lt;/code&gt; which is deleted by &lt;code&gt;rm &quot;$acc&quot;.fa&lt;/code&gt;. If you want to keep the file, just remove the &lt;code&gt;rm&lt;/code&gt; line.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you can't install &lt;code&gt;exonerate&lt;/code&gt;, you can also extract the subsequence manually but that's a bit more complex:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;while read acc start end; do &#xA; wget -q -O &quot;$acc&quot;.fa &quot;http://www.ebi.ac.uk/ena/data/view/$acc&amp;amp;display=fasta&quot; &amp;amp;&amp;amp; &#xA;awk -v st=$start -v end=$end '{&#xA;                               if($1~/&amp;gt;/){print}else{s=s$0}}END{print substr(s,st,end)&#xA;                          }'  $acc.fa | &#xA; fold -w 60 &amp;gt; &quot;$acc.$start-$end.fa&quot; &amp;amp;&amp;amp; rm &quot;$acc&quot;.fa &#xA;done &amp;lt; list.txt &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I think explaining these scriptlets in detail is not in scope here but I'd be happy to do so if you post a question over on &lt;a href=&quot;https://unix.stackexchange.com/&quot;&gt;unix &amp;amp; linux&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2017-04-13T12:37:21.100" LastActivityDate="2014-02-15T17:14:08.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15066" PostTypeId="1" CreationDate="2014-02-15T15:55:30.353" Score="6" ViewCount="1490" Body="&lt;p&gt;I don't know about all the mankind, but I know enough people, who becomes sleepy after their meals. Also, I'm not sure, what kind of food do they consume, but I personally get sleepy almost from any food: sweet, fat, spicy, salty, liquid, tasty, not tasty, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this phenomenon well known? And, if yes, how does it occur?&lt;/p&gt;&#xA;" OwnerUserId="5732" LastEditorUserId="19099" LastEditDate="2017-11-23T07:41:23.133" LastActivityDate="2017-11-23T07:41:23.133" Title="Why do the humans become sleepy after meals?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;physiology&gt;&lt;nutrition&gt;&lt;sleep&gt;" AnswerCount="5" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15067" PostTypeId="2" ParentId="15066" CreationDate="2014-02-15T16:21:50.397" Score="0" Body="&lt;p&gt;Digestion burns a lot of energy as many muscles enter the mechanism as well as many chemical reactions.&#xA;Therefore, you feel tired as your body has less energy for other functions than it usually do.&#xA;I remember a lecture at the university about sciences' history in which they explained an experiment, a long time ago, led on death sentenced men. After a very good meal, one guy was going out for a ride while the other was going to sleep. After 6 hours, they killed both of them : the one who slept had fully digested the meal whereas, for the other, digestion was not complete. They guessed it did not go as well as part of the energy needed for digestion was used for skeletal muscles and that sleeping afer eating helped for a better digestion.&lt;/p&gt;&#xA;" OwnerUserId="5702" LastActivityDate="2014-02-15T16:21:50.397" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15068" PostTypeId="1" AcceptedAnswerId="15069" CreationDate="2014-02-15T16:52:27.173" Score="1" ViewCount="193" Body="&lt;p&gt;Can the terms &quot;transcription factor binding site&quot; and &quot;operator&quot; be used interchangeably in all contexts when referring to a DNA sequence, e.g. regardless of a cell type, whether or not the binding sequence is synthetic or natural etc.? If not, what are the differences?&lt;/p&gt;&#xA;" OwnerUserId="3583" LastActivityDate="2014-02-16T13:33:21.433" Title="Do &quot;transcription factor binding site&quot; and &quot;operator&quot; mean the same thing?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15069" PostTypeId="2" ParentId="15068" CreationDate="2014-02-15T17:07:05.767" Score="4" Body="&lt;p&gt;As you no doubt know, the term operator was coined by Jacob and Monod as part of the formalism they developed to explain the properties of certain mutants in the &lt;em&gt;lac&lt;/em&gt; operon in &lt;em&gt;E. coli&lt;/em&gt;. In physical terms it is indeed the site of binding of a transcription factor, the &lt;em&gt;lac&lt;/em&gt; repressor. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding is that technically it is best to restrict the use of this terminology to bacterial systems in which the idea of an operon is useful. I don't think it would be wise to extend it to cover any site in eukaryotic DNA where a transcription factor is shown to bind.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-02-16T13:33:21.433" LastActivityDate="2014-02-16T13:33:21.433" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15070" PostTypeId="1" AcceptedAnswerId="15071" CreationDate="2014-02-15T17:15:17.283" Score="1" ViewCount="2094" Body="&lt;p&gt;What would happen if you took the deadliest diseases/viruses in the world and combined them in a single medium (a solution of water or a test subject)? Would the strongest virus defeat the rest or would a  new deadly virus be created?&lt;/p&gt;&#xA;" OwnerUserId="5735" LastEditorUserId="22057" LastEditDate="2017-12-09T07:55:43.250" LastActivityDate="2017-12-16T05:12:43.653" Title="What would happen if you combined the world's deadliest diseases &amp; viruses?" Tags="&lt;virology&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15071" PostTypeId="2" ParentId="15070" CreationDate="2014-02-15T17:32:01.640" Score="5" Body="&lt;p&gt;Viruses in the same cell can recombine (although they don't always do). This can happen by crossing-over of the genomic strands or reassortment of genomic segments. Therefore, you can get a new virus out of the fist two. The new one is not necessarily deadlier than the first two. If there's no recombination, the test subject will enjoy both diseases until the deadliest one kills him.&lt;/p&gt;&#xA;" OwnerUserId="5702" LastEditorUserId="4840" LastEditDate="2014-02-16T02:24:44.360" LastActivityDate="2014-02-16T02:24:44.360" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15072" PostTypeId="1" AcceptedAnswerId="15075" CreationDate="2014-02-15T18:33:53.697" Score="0" ViewCount="1557" Body="&lt;p&gt;If a species has a vestigial anatomical&#xA;structure that it no longer uses, would&#xA;you expect this structure to disappear&#xA;over many generations through the action&#xA;of natural selection? Always, sometimes,&#xA;or never? Explain your answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm having a hard time with this question. I don't know what should I do&lt;/p&gt;&#xA;" OwnerUserId="5736" LastEditorUserId="69" LastEditDate="2014-02-15T19:05:16.227" LastActivityDate="2014-02-15T19:07:57.330" Title="vestigial structure question" Tags="&lt;evolution&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15075" PostTypeId="2" ParentId="15072" CreationDate="2014-02-15T19:07:57.330" Score="1" Body="&lt;p&gt;If a species has a vestigial anatomical structure that it no longer uses, it may or may not disapear through natural selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution is based on four mechanisms :&#xA;- mutation&#xA;- natural selection&#xA;- sexual selection&#xA;- genetic drift&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A no longer used structure can disapear if a mutation makes it to. Then, if it confers a selection advantage (natural or sexual), then individuals without that structure will survive and / or reproduce better than the other. The mutation will spread among the population and structure may finally disapear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it does not confer benefit the individual nor decrease it's chances of survival or reproduce compare to others, mutation may or may not be conserved and so for the structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetic drift can accelerate disapearance of a structure, especially if the population is really small, even if it does not confer any advantages to the individuals. The mutation can rapidly spread through the population just by chance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, in human body, the appendix is no longer used but still remains. It's absence does increase chance of survivol nor is attractive to sexual partners, so it doesn't imply natural or sexual selection structure. Genetic drift may or may not randomly make it disapear one day, no one knows.&lt;/p&gt;&#xA;" OwnerUserId="5702" LastActivityDate="2014-02-15T19:07:57.330" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15076" PostTypeId="1" AcceptedAnswerId="15084" CreationDate="2014-02-15T19:31:27.327" Score="1" ViewCount="1055" Body="&lt;p&gt;Cattle breeders have improved the quality of meat over the years by which process?&#xA;A) artificial selection&#xA;B) directional selection&#xA;C) stabilizing selection&#xA;D) A and B&#xA;E) A and C&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know the answer is D. It is obvious that is artificial selection but WHY is it also directional selection? how do we know? I know the differences between directional, stabilizing and disruptive selection but there is nothing in the question that explains the quality of meat in relation to directional selection. so HELP!&lt;/p&gt;&#xA;" OwnerUserId="5736" LastEditorUserId="4840" LastEditDate="2014-02-16T02:24:53.797" LastActivityDate="2014-02-21T16:35:08.093" Title="question about directional selection" Tags="&lt;homework&gt;&lt;natural-selection&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15080" PostTypeId="2" ParentId="15070" CreationDate="2014-02-15T22:05:49.237" Score="-1" Body="&lt;p&gt;See viruses are made to destroy the host, not other viruses, so putting different types together really wouldn't have much an effect would it? as Manuella answer says, the host cell will simply suffer (or enjoy as he says) with both at once. Viruses don't mate so I sincerely doubt there would be a &quot;combination&quot;. What some [evil] scientists are doing is that they take bacterium or viruses and they genetically modify them, and though this is a seriously tedious process, a bio-weapon could be created. Google bio-weapons and how they are made by governments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, this would probably cost you a TON of money to do such a dangerous and complex project, and I doubt that anyone sensible would sponsor you.&lt;/p&gt;&#xA;" OwnerUserId="5744" LastEditorUserId="-1" LastEditDate="2014-02-16T08:50:59.257" LastActivityDate="2014-02-16T08:50:59.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15082" PostTypeId="1" AcceptedAnswerId="15085" CreationDate="2014-02-16T05:46:55.947" Score="23" ViewCount="428100" Body="&lt;p&gt;What are 5' and 3' in DNA and RNA strands? Please clarify with some images and please use simple English.&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="6" LastEditDate="2014-02-16T09:27:11.090" LastActivityDate="2017-06-23T12:07:25.847" Title="What does 5' and 3' mean in DNA and RNA strands?" Tags="&lt;dna&gt;&lt;ligation&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15084" PostTypeId="2" ParentId="15076" CreationDate="2014-02-16T09:15:00.937" Score="0" Body="&lt;p&gt;There is a small issue in this question that is: everybody does not always use the exact same definition of stabilizing selection and disruptive selection. These two concepts are sometimes used to refer to phenotypic traits or to genes. For example stabilizing selection might either mean,&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;selection for the mean phenotypic trait of the population&#xA;or&lt;/li&gt;&#xA;&lt;li&gt;selection for the wildtype allele, getting rid of all newcoming mutations.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Under simple genetic architecture the two concepts are equal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although for this question I don't think we even need to give a clear definitions between these two words, we'll use the phenotypic based definition (the first one above) in order to ease the intuitive understanding of the answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say the trait breeders select for is mean quality and for ease again, we'll imagine this trait as being one unique trait that we can map on one axis from low quality to high quality. Here is a representation of that where the x-axis represent meat quality (left = low quality) and the y-axis represents the density of cows in the population which has the associated meat quality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RhUqE.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If breeders performed a stabilizing selection, it means that they would not improve the meat but only prevent the meat to change quality. In order to shift the quality of the meat to the right (to better quality), breeders need to perform directional selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the only problem that you had for solving this problem was the conceptual issue of considering meat quality just like any phenotypic trait. And if you want to shift a phenotypic trait on one side or another, you have to apply directive selection.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-02-21T16:35:08.093" LastActivityDate="2014-02-21T16:35:08.093" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15085" PostTypeId="2" ParentId="15082" CreationDate="2014-02-16T10:49:38.470" Score="22" Body="&lt;p&gt;The 5' and 3' mean &quot;five prime&quot; and &quot;three prime&quot;, which indicate the carbon numbers in the DNA's sugar backbone. The 5' carbon has a phosphate group attached to it and the 3' carbon a hydroxyl (-OH) group. This asymmetry gives a DNA strand a &quot;direction&quot;. For example, DNA polymerase works in a 5' -&gt; 3' direction, that is, it adds nucleotides to the 3' end of the molecule (the -OH group is not shown in diagram), thus advancing to that direction (downwards).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6bmHJ.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5032" LastEditorUserId="-1" LastEditDate="2017-06-23T12:07:25.847" LastActivityDate="2017-06-23T12:07:25.847" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15086" PostTypeId="2" ParentId="15082" CreationDate="2014-02-16T11:33:02.927" Score="5" Body="&lt;p&gt;The no 5 and 3 are the carbon no of the carbon skeleton ring of deoxyribose  as similar as any other organic compound. In any nucleic  acid, RNA or DNA 3' refers to the  3rd carbon of sugar ribose or deoxyribose which is linked to OH group and 5' linked to a triple phosphate group. So these  5' and 3' group provide a directional polarity to the DNA or RNA molecule. Now a good question would be y 3' and 5' not 3 and 5. It is simply to differentiate sugar carbons from that of the bases which are also having a carbon skeleton and thus nos for their carbon&lt;/p&gt;&#xA;" OwnerUserId="5741" LastActivityDate="2014-02-16T11:33:02.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15087" PostTypeId="1" AcceptedAnswerId="15105" CreationDate="2014-02-16T14:10:15.223" Score="0" ViewCount="94" Body="&lt;p&gt;I am trying to explain the effect of respiration on arterial pressure.&#xA;I am looking preferably some visual way to show it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can you show the effect of respiration on arterial pressure?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking some kind of figure which has the respiration rate and arterial pressure.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-18T07:41:33.993" Title="Effect of respiration on Arterial pressure" Tags="&lt;physiology&gt;&lt;respiration&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15088" PostTypeId="1" CreationDate="2014-02-16T15:13:33.240" Score="0" ViewCount="133" Body="&lt;p&gt;I first covered the fast and moderate control mechanisms which I think are&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fast control: Baroreceptive reflex (tonus), Chemoreceptive reflex&#xA;  (CO$_2$). &#xA;  Moderate control:  Bicarbonate&#xA;  (ECF), Phosphate buffer (ECF), Proteins (ICF).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;then late control mechanisms about which I am unsure&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Capillary fluid shift mechanisms&lt;/li&gt;&#xA;&lt;li&gt;Stress-relaxation of the vasculature&lt;/li&gt;&#xA;&lt;li&gt;RAA&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the late control mechanisms of blood pressure?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-16T15:23:52.167" LastActivityDate="2014-02-16T16:59:25.630" Title="Late control mechanisms of blood pressure (arterial) level?" Tags="&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ClosedDate="2015-01-24T19:06:42.907" ContentLicense="CC BY-SA 3.0" />
  <row Id="15089" PostTypeId="1" CreationDate="2014-02-16T15:55:23.273" Score="1" ViewCount="1560" Body="&lt;p&gt;I am working with the enzyme Cu/Zn Superoxide (SOD1) and i am quantifying them in ng/ml.&#xA;However, most past studies has SOD1 quantified in unit/mg or unit/ml, and i need to compare the SOD1 level of my study with those past studies. Is there a way to standardize these units?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="5750" LastActivityDate="2014-03-19T13:45:51.177" Title="Converting unit/mg or unit/ml into ng/ml, or vice-versa" Tags="&lt;biochemistry&gt;&lt;physiology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15091" PostTypeId="1" CreationDate="2014-02-16T16:49:07.350" Score="3" ViewCount="41956" Body="&lt;p&gt;I want to get my head round this once and for all so if you guys could help me would really appreciate it! I understand lesions to the optic nerve. It is the other nerves that I find difficult. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far this is my understanding, please correct me if I'm wrong. The cranial nerves do not decussate generally with exceptions being CN2, CN4, CN7 and CN12. That means if a lesion affects Cranial Nerve 1, 5, 8, 9 and 11 or the respective nucleus there is either sensation loss or atrophy of the muscle (dependent on what the nerve does) of the ipsilateral side. For example in a lesion affecting CN6, the eye cannot look out in the side of the lesion. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of CN4, I'm not too sure what happens but I imagine if there is damage to the nucleus the opposite side is affected (meaning superior oblique in the contralateral side will not work). If the nerve is affected, it is typically the ipsilateral side. The same I imagine is true for CN12. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In CN7, the forehead is bilaterally innervated so if the upper motor neurone is affected eyebrows can be raised but the lower side of the face is affected ipsilaterally. In a lower motor neurone lesion, there is complete loss of one side of the face ipsilaterally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I correct?&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2016-08-27T01:54:35.953" Title="Cranial Nerve Decussation" Tags="&lt;cranial-nerves&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15092" PostTypeId="2" ParentId="15088" CreationDate="2014-02-16T16:59:25.630" Score="1" Body="&lt;p&gt;Capillary fluid shift mechanisms&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the pressure of the blood is high, there is high hydrostatic pressure. Simply put, this means fluid exits the capillaries at the arterial side due to this pressure, and less fluid returns at the venous side. With less fluid in the circulation, blood pressure falls. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stress-relaxation of the vasculature&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine the arteries are like springs. The more you pull them the stronger the recoil force. However if you stretch them too much for too long, they stay stretched. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Renin-Angiotensin-Aldosterone system&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the blood pressure is high, there is less release of renin from the kidneys. This means less angiotensin II production. Angiotensin acts to increase blood pressure by increasing vasoconstriction and increasing retention of fluid and salt (via aldosterone). With less RAA system activation, the blood pressure drops. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-16T16:59:25.630" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15093" PostTypeId="2" ParentId="15066" CreationDate="2014-02-16T18:25:08.390" Score="1" Body="&lt;p&gt;As far as I know it happens due the histamine release after meals. It leads to vasorelaxation and blood flow to the gastrointestinal tract. So, brain does not receive enough blood and you feel sleepy.&lt;/p&gt;&#xA;" OwnerUserId="1839" LastActivityDate="2014-02-16T18:25:08.390" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15094" PostTypeId="2" ParentId="15089" CreationDate="2014-02-16T20:52:02.807" Score="1" Body="&lt;p&gt;There is no archaism in measuring enzyme amounts in units. Unit definition for SOD and a protocol can be found here (from Sigma): &lt;a href=&quot;https://www.safcglobal.com/technical-documents/protocols/biology/enzymatic-assay-of-superoxide-dismutase.html&quot; rel=&quot;nofollow&quot;&gt;https://www.safcglobal.com/technical-documents/protocols/biology/enzymatic-assay-of-superoxide-dismutase.html&lt;/a&gt; :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;One unit will inhibit the rate of reduction of cytochrome c by 50% in a coupled system, using xanthine and xanthine oxidase ...&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think, there is a good way to convert ng's to units, since one measures either mass or enzymatic activity, and the correlation between them is not always consistent. Units should be much more reliable in terms of comparisons with other studies, if you are not considering your enzyme as, e.g., a nutritious substance.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-02-17T11:00:57.613" LastActivityDate="2014-02-17T11:00:57.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15095" PostTypeId="1" AcceptedAnswerId="15100" CreationDate="2014-02-16T22:13:42.680" Score="2" ViewCount="120" Body="&lt;p&gt;I'm reading a systems biology paper, and I'm suspecting there's a typo in an equation, but I want to make sure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article is &quot;Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices.&quot; (Famili &amp;amp; Palsson 2003, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12900206&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/12900206&lt;/a&gt; / &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022519303001462&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0022519303001462&lt;/a&gt;). In equation 5, I wonder if the final subscript u_kr shouldn't be u_km, as the vector u_k^T is a column vector in the matrix U, which has dimensions m x m. Of course, some elements in u_k might be zero, in which case there would be less than m products in the sum, but I see no reason why there would be maximally r non-zero elements either (where r is the rank of the matrix S which has been decomposed). I worked out a simple example on paper where r &amp;lt; m and still got vectors with m non-zero elements. Can someone give me a second opinion on this? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: Here are the main equations.&#xA;A model of a metabolic reaction network is described by a stoichiometric matrix S of dimensions m x n and rank r. For the metabolites in the model, changes in metabolite concentrations is equal to S multiplied with the vector of reaction rates, v:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;${\frac{{dx}}{{dt}} = Sv}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The singular value decomposition of S is given by&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$S = U\sum {V^T}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Multiplying on the left side with $U^T$ (The transpose of U) we get:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;${U^T}\frac{{dx}}{{dt}} = \sum {V^T}v$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After matrix multiplication, we have for each row in $U^T$ and $V^T$, where $\sigma_k$ is the k'th singular value&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\frac{{d(u_k^Tx)}}{{dt}} = {\sigma _k}(v_k^Tv){\text{   k   =  1}},...,{\text{r}}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And finally, equation 5:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;${\text{u}}_k^T \cdot x{\text{  =  }}{{\text{u}}_{k1}}{x_1} + {u_{k2}}{x_2} + ... + {u_{kr}}{x_m}{\text{   (5)}}$&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-02-16T23:35:17.753" LastActivityDate="2014-02-17T02:16:18.363" Title="Does this equation have a typo? (Systems Biology, singular value decomposition)" Tags="&lt;systems-biology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ClosedDate="2014-02-18T19:06:42.357" ContentLicense="CC BY-SA 3.0" />
  <row Id="15097" PostTypeId="2" ParentId="14996" CreationDate="2014-02-16T23:38:35.820" Score="2" Body="&lt;p&gt;I am no expert on the field, but quantifying gene expression isn't a simple problem, although it is a possibility.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A solution I know to be used is using radioactive markers. See for example &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805372/#__sec3&quot; rel=&quot;nofollow&quot;&gt;this review&lt;/a&gt; and particularly &quot;The cell-cell lactate shuttle&quot; section, which might give some insights.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can include radioactive tracers (such as [14C]lactate), non-radioactive tracers (with [13C] or [2H]), &quot;net exchange measurements&quot; (I don't really know what this means here, perhaps the kind of exchange calculations they present &lt;a href=&quot;http://jap.physiology.org/content/87/5/1684.long#sec-14&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;), and muscle biopsies (it is then possible to measure the metabolite concentration by enzymatic reaction or spectrophotometry for example).&lt;/p&gt;&#xA;" OwnerUserId="5757" LastEditorUserId="5757" LastEditDate="2014-02-17T01:02:43.597" LastActivityDate="2014-02-17T01:02:43.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15100" PostTypeId="2" ParentId="15095" CreationDate="2014-02-17T02:16:18.363" Score="3" Body="&lt;p&gt;You are right this is a typo. Equation 5 is just a restatement of the definition of the dot product of two vectors:&#xA;$$\mathbf{u}_k^T\cdot \mathbf{x} = \sum_{i=1}^m u_{ki}^Tx_i$$&#xA;or written in another way&#xA;$$\mathbf{u}_k^T\cdot \mathbf{x} = u_{k1}x_1+u_{k2}x_2+\cdots+u_{km}x_m.$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the text Equation 5 is stating that one can find a linear combination of the metabolites described in $\mathbf{x}$ whose time evolution is described simply by a linear combination of the flux rates described in $\mathbf{v}$. The coefficients of the first linear combination are given by a row vector $\mathbf{u}_k^T$ in $U^T$. From this perspective, since there are $m$ possible metabolites ($\mathbf{x}$ is a $m\times 1$ vector), there have to be $m$ coefficients, so that the indices must range from 1 to $m$ in Equation 5. You are correct that $u_{ki}^T$ might be 0 for some $i$. But that doesn't change the fact that there should be $m$ (possibly vanishing) coefficients.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2014-02-17T02:16:18.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15101" PostTypeId="2" ParentId="15000" CreationDate="2014-02-17T03:31:44.523" Score="1" Body="&lt;p&gt;This is a very interesting but difficult to answer question. That is because scientists are still debating about the various stages of consciousness. As it stands, there is evidence that people can learn even though they are asleep indicating that it is likely that sensory channels are open and information is being processed even when asleep. That likely means the brain is behaving as if it were awake at certain times during sleep. In this article they interpret the lack of blood flow seen by fMRI as less active which is mostly correct. Playing audio during REM is a tricky question because as you know dreaming does not require sensory input so that channel(hearing) may be free to receive information although your guess may also be true if if the music was loud enough to interfere with other cognitive processes.&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-02-17T03:31:44.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15102" PostTypeId="2" ParentId="15058" CreationDate="2014-02-17T04:47:47.060" Score="1" Body="&lt;p&gt;It really depends on the specific methods you're using. If you're using a pathway-based methodology, I'd strongly recommend reading Khatri et al (2012) (&lt;a href=&quot;http://www.ploscompbiol.org/article/info%3adoi/10.1371/journal.pcbi.1002375&quot; rel=&quot;nofollow&quot; title=&quot;Khatri et al &amp;#40;2012&amp;#41;&quot;&gt;1&lt;/a&gt;), which provides a good overview. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main issue that's not touched on in that work is that pathway-based methods are highly dependent on the pathway definitions used, and the contents of the pathways are not always what you might expect in terms of their topology (a good example is KEGG's Neuroactive ligand-receptor interaction (&lt;a href=&quot;http://www.genome.jp/kegg-bin/show_pathway?map=hsa04080&amp;amp;show_description=show&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;), which contains a huge number of events that look like 'single ligand binds to receptor', with no downstream events).&lt;/p&gt;&#xA;" OwnerUserId="5761" LastActivityDate="2014-02-17T04:47:47.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15103" PostTypeId="2" ParentId="15049" CreationDate="2014-02-17T05:17:15.070" Score="1" Body="&lt;p&gt;Basically, Andraka's method measures mesothelin. There's two key questions being asked about it (as it stands right now), falling into two categories:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) There is some doubt as to the significance of serum mesothelin levels as a biomarker in pancreatic and biliary cancers. Some studies (e.g. Sharon et al (&lt;a href=&quot;http://www.degruyter.com/view/j/cclm.2012.50.issue-4/cclm.2011.816/cclm.2011.816.xml&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;)) suggest that there is no significant difference in levels - others (e.g. Hassan et al (&lt;a href=&quot;http://ajcp.ascpjournals.org/content/124/6/838.short&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;)) suggest that mesothelin may be a valid biomarker in some conditions but not others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) There are questions around the test itself. Andraka's work is promising and quite impressive. There are, however, some claims about it are being made that there's just not the evidence to support. I suspect that any fault for this lies with the journalists reporting on the story or PR people for various companies or institutions. The device may stand up to clinical trials and testing and be as revolutionary as it's claimed to be, but it does need to be fully tested. &lt;/p&gt;&#xA;" OwnerUserId="5761" LastActivityDate="2014-02-17T05:17:15.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15104" PostTypeId="1" AcceptedAnswerId="15110" CreationDate="2014-02-17T05:45:44.723" Score="1" ViewCount="334" Body="&lt;p&gt;So in short, I did a blastn with standalone blast using all known miRNAs against the EST sequences in a genome (word length 7 and e-value 0.01). Now to confirm one of the next steps would be obtain the pre-miRNA sequence of each hit and do an mFOLD for structural confirmation. Each paper I read always mentions to get a sliding window (of 70 - 100 nt length) but how do you get this sliding window from the BLASTN output.. Do you have to code something yourself or is there an easier way to do it. Thanks. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="1306" LastEditDate="2014-02-17T15:35:34.760" LastActivityDate="2014-04-30T12:40:43.687" Title="How do you find pre-miRNAs from mature miRNA Blast output?" Tags="&lt;bioinformatics&gt;&lt;blast&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15105" PostTypeId="2" ParentId="15087" CreationDate="2014-02-17T05:51:18.693" Score="0" Body="&lt;p&gt;Alan's pointing picture is this&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bXSra.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this picture better&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5VHE9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;but not sure if it is exactly the level respiration to the arterial pressure.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-17T05:51:18.693" CommentCount="0" CommunityOwnedDate="2014-02-17T05:51:18.693" ContentLicense="CC BY-SA 3.0" />
  <row Id="15106" PostTypeId="2" ParentId="15070" CreationDate="2014-02-17T11:21:23.620" Score="-1" Body="&lt;p&gt;Poison + poison = poison. They aren't integers to give you a result of 2poison. Viruses are a gatewat between living and non living organisms so they would barely mate and produce a more deadly virus. You might have been a fan of Umbrella Corporation (the company working as bio-weaponary making company which tests virus and takes over world) but in real life they don't work as we think they should.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some virus would reverse the effect of the bad virus too. Thus as other answers has told you that being evil would cost you much more money than you think. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacterias are living viruses are both, so some would double up the disease whereas some might lessen down the effect of other virus.&lt;/p&gt;&#xA;" OwnerUserId="4674" LastEditorUserId="6194" LastEditDate="2017-12-16T05:12:43.653" LastActivityDate="2017-12-16T05:12:43.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15107" PostTypeId="2" ParentId="14969" CreationDate="2014-02-17T12:07:17.167" Score="3" Body="&lt;p&gt;Splice junctions are the exon-intron junctions, at which splicing takes place. &#xA;Splice junction pairs are the pairs of such junction (to cut an intron you need to splice in two junctions).&#xA;So, you are almost there, since two exons will be joined in correspondence of two subsequent splice junctions.&#xA;You might find these &lt;a href=&quot;http://www2.oakland.edu/biology/chaudhry/pics/chapter24f.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;slides&lt;/a&gt; useful (slide B-6)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As &lt;a href=&quot;https://biology.stackexchange.com/users/2996/adam-kurkiewicz&quot;&gt;Adam&lt;/a&gt; pointed out the slides are no longer available. I have no idea on where they are gone, but I suggest referring to the following wikipedia pages for an introduction:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/RNA_splicing&quot; rel=&quot;nofollow noreferrer&quot;&gt;RNA splicing&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Exon_junction_complex&quot; rel=&quot;nofollow noreferrer&quot;&gt;Exon junctions&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Alternative_splicing&quot; rel=&quot;nofollow noreferrer&quot;&gt;Alternative Splicing&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5297" LastEditorUserId="5297" LastEditDate="2019-01-28T13:38:08.230" LastActivityDate="2019-01-28T13:38:08.230" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="15108" PostTypeId="2" ParentId="15089" CreationDate="2014-02-17T12:50:07.807" Score="0" Body="&lt;p&gt;Quantification is a measure of your protein quantity and units/ml or mg is a unit of protein quantity. These are two different things. You need to set a rxn of SOD with its substrate and get activity which is proportional to your consumption of substrate. Then u will get the activity of your protein which will be in units/mg or ml&lt;/p&gt;&#xA;" OwnerUserId="5741" LastActivityDate="2014-02-17T12:50:07.807" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15110" PostTypeId="2" ParentId="15104" CreationDate="2014-02-17T15:43:50.533" Score="1" Body="&lt;p&gt;DISCLAIMER: I have never worked with miRNAs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, from what little I know, the mature miRNA is produced by modifying the pre-miRNA. This means that you should be able to infer the pre-miRNA by mapping your miRNA to the genome using a tool like &lt;a href=&quot;http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&quot; rel=&quot;nofollow&quot;&gt;BLAT&lt;/a&gt;. Since you already have an EST which represents a transcribed sequence, you can map your EST back to the genome. You can simplify this by using a tool like &lt;a href=&quot;https://www.ebi.ac.uk/~guy/exonerate/&quot; rel=&quot;nofollow&quot;&gt;&lt;code&gt;exonerate&lt;/code&gt;&lt;/a&gt; that also models splicing.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-02-17T15:43:50.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15111" PostTypeId="2" ParentId="14996" CreationDate="2014-02-17T16:16:28.110" Score="2" Body="&lt;p&gt;Summary: Try one of the extensions of FBA which take gene regulation into account, but be aware of the limitations. See below for references.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Long answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two approaches to estimating internal metabolic fluxes: The (primarily) experimental and the (primarily) computational. I say primarily, because even for the experimental approach, a large amount of computation need to be done, and for the computational approach, experimental studies must be consulted in order to set realistic model parameters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Experimental determination of internal metabolic fluxes has been centered around 13C-metabolic flux analysis (13C-MFA) performed through carbon-labelling experiments, as mentioned above. 13C-MFA is complicated and expensive, so there is a relative lack of experimental data, and most experiments cover only a few fluxes when compared to the number of possible reactions, typically several thousand in genome-scale metabolic models. In 13C-MFA, most experiments estimate the fluxes in a much smaller model (for example the central carbon metabolism), avoiding or ignoring other possible reactions, and the set of fluxes that are estimated varies between experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Models which are used in computational approaches to flux analysis are typically larger than the models used in 13C-MFA experiments, and thus it is usually not possible to determine all the fluxes from experimental data alone. Thus, an approach called constraint-based modelling (COBRA) is mainly used. The basic assumption of most current flux analysis methods, both experimental and computational, is that metabolite concentrations are at steady state. Mathematically, this can be described by the equation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$S\overrightarrow v  = 0$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $S$ is a &lt;em&gt;stoichiometric matrix&lt;/em&gt; relating the metabolites and all possible reactions (basically a compact description of the metabolic model), and $\overrightarrow v$ is the &lt;em&gt;flux vector&lt;/em&gt; containing all the flux values. In addition to the steady state requirement, constraints are typically applied to the uptake and excretion rates of various metabolites, limiting them to biologically realistic values. Other requirements, such as requirements for ATP maintenance consumption can also be applied.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because there are typically many possible flux patterns that obey the above constraints, a principle is needed for selecting a biologically realistic solution from the solution space of feasible flux patterns. Assuming that cells optimize their metabolic patterns in some way, different &lt;em&gt;objective functions&lt;/em&gt; are used that attempt to capture the metabolic behaviour for cells. Once an objective function is chosen, the set of possible solutions can be searched for the flux pattern that gives the highest objective value as a function of the flux vector. Given that the objective is linear (simply a weighed sum of fluxes), an optimal solution can be found rapidly. &lt;strong&gt;In general, many different optimal solutions may exist for a given objective function.&lt;/strong&gt; The method of applying an objective function to a constrained metabolic model at steady state is called Flux Balance Analysis (FBA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most basic and a popular objective is maximization of biomass production. While useful for determining maximal growth rates, &lt;strong&gt;this objective is unlikely to be realistic when applied to human cells.&lt;/strong&gt; FBA and related methods is generally well-suited to determining performance limits for single endpoints such as growth rate or production of a single metabolite, but not capable of precisely determining all internal metabolic fluxes. The point that many optimal solutions may exist for a single objective function is important in this regard.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As 13C-MFA and FBA are based on the same concept of metabolite balancing, they can be viewed as different ends of the same spectrum, from purely experimental to purely computational, with 13C-MFA constrained FBA (where 13C-MFA results is used to constrain the possible fluxes in a model before optimizing an objective function, or minimizing the difference between the experimental fluxes and the FBA solution, subject to additional constraints) in the middle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an introduction to Flux Balance Analysis, see  Orth, Thiele &amp;amp; Palsson: &lt;em&gt;&quot;What is flux balance analysis?&quot; Nature Biotechnology 28 245-48 2010.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For performing Flux Balance Analysis, several software packages are available. One of the most used is the COBRA Toolbox for Matlab. A version for Python called CobraPy is also under development. Both are available at &lt;a href=&quot;http://opencobra.sourceforge.net/openCOBRA/Welcome.html&quot; rel=&quot;nofollow&quot;&gt;http://opencobra.sourceforge.net/openCOBRA/Welcome.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that most gene-expression data only shows relative changes in expression between two conditions. Most methods are thus based on comparing two different conditions. More recently, RNA-sequencing (RNAseq) may also be used to obtain more direct measures of gene expression levels. Many extensions and variations on FBA have been published which take into account gene expression. Some of these are regulatory FBA (rFBA, Covert &amp;amp; Palsson: &lt;em&gt;Journal of Biological Chemistry, 2002 277, 28058-28064&lt;/em&gt;), Metabolic Adjustment by Differential Expression (MADE, Jensen &amp;amp; Papin: &lt;em&gt;Bioinformatics. 2011 Feb 15;27(4):541-7&lt;/em&gt; ) and iMAT (Schlomi et al:  &lt;em&gt;Bioinformatics (2010) 26 (24): 3140-3142&lt;/em&gt;.). For a more recent method, gx-FBA (gene expression-FBA), see *Navid &amp;amp; Almaas, BMC Systems Biology 2012, 6:150). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may also want to read this article which deals with construction tissue-specific metabolic models: &lt;em&gt;Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol. 2010 Sep 7;6:401. doi: 10.1038/msb.2010.56.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem with using FBA and related methods to estimate internal fluxes is that validation of the results is difficult because of the mentioned lack of experimental data. I wrote a project report on the topic during the last year of my Master's, which includes a basic description of 13C-MFA. It can be read at &lt;a href=&quot;http://www.slideshare.net/jarlemag/rapport-31295058&quot; rel=&quot;nofollow&quot;&gt;http://www.slideshare.net/jarlemag/rapport-31295058&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-02-17T16:16:28.110" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15112" PostTypeId="1" CreationDate="2014-02-17T16:59:28.467" Score="2" ViewCount="552" Body="&lt;p&gt;I have used DNAStar laser gene and VectorNTI in the past for cloning, primer design, sequence alignments, etc but no longer have access to these. Are there any comparable replacement suites or what stand alone packages would you now recommend?&lt;/p&gt;&#xA;" OwnerUserId="5284" LastActivityDate="2014-05-23T13:07:24.403" Title="Sequence analysis software suites" Tags="&lt;molecular-biology&gt;&lt;software&gt;&lt;sequence-analysis&gt;" AnswerCount="6" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15113" PostTypeId="2" ParentId="15112" CreationDate="2014-02-17T17:27:42.380" Score="0" Body="&lt;p&gt;For primer design you can use the Gene Designer: &lt;a href=&quot;https://www.dna20.com/resources/genedesigner&quot; rel=&quot;nofollow&quot;&gt;https://www.dna20.com/resources/genedesigner&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For sequence alignment you can use BLAST (from the NCBI, also downloadable as a standalone tool)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course there are better options that might be more specific for your situation.&lt;/p&gt;&#xA;" OwnerUserId="5699" LastActivityDate="2014-02-17T17:27:42.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15114" PostTypeId="1" AcceptedAnswerId="15124" CreationDate="2014-02-17T19:34:41.060" Score="2" ViewCount="1084" Body="&lt;p&gt;What modern insects are not flying or descended from flying ancestors?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I read somewhere that 99% are, so of course I instantly became curious which &lt;em&gt;aren't&lt;/em&gt;. xD )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:  Sorry, I should have been clearer: I meant examples of modern insects with &lt;em&gt;no&lt;/em&gt; flying ancestors.&lt;/p&gt;&#xA;" OwnerUserId="5767" LastEditorUserId="5767" LastEditDate="2014-02-17T23:57:37.490" LastActivityDate="2016-03-28T18:22:45.877" Title="What modern insects are not (flying OR descended from flying ancestors)?" Tags="&lt;evolution&gt;&lt;entomology&gt;&lt;flight&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15115" PostTypeId="1" CreationDate="2014-02-17T20:23:47.973" Score="1" ViewCount="209" Body="&lt;p&gt;Where can I find the metabolic network of the human erythrocyte (red blood cell), in SBML format? The red blood cell metabolic network is a model that's usually employed in the literature [see refs below] to demonstrate mathematical techniques of analysis of metabolic networks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite this common use, I haven't been able to find a metabolic network of the human erythrocyte in SBML format, which is commonly employed for these networks (for example, in the BiGG database, &lt;a href=&quot;http://bigg.ucsd.edu/&quot; rel=&quot;nofollow&quot;&gt;http://bigg.ucsd.edu/&lt;/a&gt;) because it is easy to use with the COBRA package (&lt;a href=&quot;http://opencobra.sourceforge.net/&quot; rel=&quot;nofollow&quot;&gt;http://opencobra.sourceforge.net/&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, anyone can tell me where I can find an SBML model of the metabolic network of the human red blood cell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References where the red blood cell metabolic network is used:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Wiback, S. J., Famili, I., Greenberg, H. J., &amp;amp; Palsson, B. Ø. (2004).&#xA;Monte Carlo sampling can be used to determine the size and shape of&#xA;the steady-state flux space. Journal of Theoretical Biology, 228,&#xA;437–447. doi:10.1016/j.jtbi.2004.02.006&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Braunstein, A., Mulet, R., &amp;amp; Pagnani, A. (2008). Estimating the size&#xA;of the solution space of metabolic networks. BMC Bioinformatics, 9, 240. doi:10.1186/1471-2105-9-240&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Jamshidi, N., Edwards, J. S., Fahland, T., Church, G. M., &amp;amp; Palsson,&#xA;B. Ø. (2001). Dynamic simulation of the human red blood cell&#xA;metabolic network. Bioinformatics, 17(3), 286–287.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Kauffman, K. J., Pajerowski, J. D., Jamshidi, N., Palsson, B. Ø., &amp;amp;&#xA;Edwards, J. S. (2002). Description and analysis of metabolic&#xA;connectivity and dynamics in the human red blood cell. Biophysical&#xA;Journal, 83(2), 646–662. doi:10.1016/S0006-3495(02)75198-9&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="561" LastActivityDate="2014-02-17T21:04:31.537" Title="Where can I find the metabolic network for the human erythrocyte?" Tags="&lt;metabolism&gt;&lt;literature&gt;&lt;red-blood-cell&gt;&lt;systems-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15116" PostTypeId="2" ParentId="15114" CreationDate="2014-02-17T20:38:09.997" Score="6" Body="&lt;p&gt;Silverfish, also known as Lepisma (order Zygentoma), does not fly and does not descend from flying ancestors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's close to Archeognatha, which don't fly either nor descend from flying ancestor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/a/a7/Lepisma_saccharina_1a.JPG&quot; alt=&quot;Lepisma saccharina&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5702" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.990" LastActivityDate="2014-02-17T20:38:09.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15117" PostTypeId="2" ParentId="15112" CreationDate="2014-02-17T20:54:00.917" Score="1" Body="&lt;p&gt;I would recommend Galaxy. &lt;a href=&quot;https://usegalaxy.org/&quot; rel=&quot;nofollow&quot;&gt;https://usegalaxy.org/&lt;/a&gt; &#xA;The system does include primer design, sequence alignments and covers many common bioinformatics tasks.&lt;/p&gt;&#xA;" OwnerUserId="3586" LastActivityDate="2014-02-17T20:54:00.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15118" PostTypeId="2" ParentId="15115" CreationDate="2014-02-17T21:04:31.537" Score="4" Body="&lt;p&gt;The model used by Jamshidi et al. can be found in the BioModels database with acession no. MODEL1103210001  &lt;a href=&quot;http://www.ebi.ac.uk/compneur-srv/biomodels-main/MODEL1103210001&quot; rel=&quot;nofollow&quot;&gt;http://www.ebi.ac.uk/compneur-srv/biomodels-main/MODEL1103210001&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A more recent model has also been described in &lt;em&gt;Bordbar et al. iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. BMC Systems Biology 2011, 5:110&lt;/em&gt; The model file in SBML format can be downloaded from the Additional Files section (&lt;a href=&quot;http://www.biomedcentral.com/1752-0509/5/110/additional&quot; rel=&quot;nofollow&quot;&gt;http://www.biomedcentral.com/1752-0509/5/110/additional&lt;/a&gt;) or BioModels (&lt;a href=&quot;http://www.ebi.ac.uk/compneur-srv/biomodels-main/MODEL1106080000&quot; rel=&quot;nofollow&quot;&gt;http://www.ebi.ac.uk/compneur-srv/biomodels-main/MODEL1106080000&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-02-17T21:04:31.537" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15119" PostTypeId="2" ParentId="14330" CreationDate="2014-02-17T21:12:44.450" Score="1" Body="&lt;p&gt;LC-MS map they refer to is the projection of two separation method (Liquid Chromatography - Mass Spectroscopy) results into an imaginary plane. It's a conceptual map. From this map, peptide signals referred to as &quot;features&quot; (article uses this term) are selected for the next level of fragmentation and then MS again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 1 of the article you cite simulates a small fraction of this larger map. &lt;/p&gt;&#xA;" OwnerUserId="3586" LastActivityDate="2014-02-17T21:12:44.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15120" PostTypeId="2" ParentId="15091" CreationDate="2014-02-17T21:18:10.987" Score="1" Body="&lt;p&gt;As you mentioned, the resulting impairment depends on the level of the injury: nuclear, fascicular, central / peripheral. So, you should differentiate lesions inside the brain tissue (which can be at nucleus, at any location of a tract, before crossing or after, and outside. From this, the first thing we should explain is the normal anatomy.  From normal anatomy we can understand the pathology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One interesting fact you probably wanted to know is that Optic Nerve it not a real nerve in a classic definition, because it begins outside the brain as grouping axons of RGCs (retinal ganglion cells) and after leaving the eye becomes a “nerve”. From this, you can understand its damage better, because the damage to the visual fields depends on the level of insult. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;IV nerve is the only cranial nerve that completely crossed (decussated). Thus, the lesion before the crossing/decussation (you were right mentioning the nucleus, but we extend the “region” until the decussation) will cause palsy and consequent atrophy contralaterally to the lesion. After the decussation the palsy and atrophy will be ipsilateral.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering cranial nerve XII we should speak about nuclear-infranuclear and supranuclear damage and with this notion supranuclear damage will cause contralateral transient tongue paresis. Nuclear-infranuclear damage will cause more permanent palsy, which is mostly bilateral because the nuclei are close to each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering VII pair, nuclear-intranuclear damage (“peripheral”) will cause ipsilateral hemifacial palsy including the brow and eyelid, while supranuclear (“central”) lesion will cause contralateral facial palsy with brow/eyelid sparing.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2014-02-17T21:18:10.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15121" PostTypeId="1" CreationDate="2014-02-17T21:26:21.243" Score="2" ViewCount="170" Body="&lt;p&gt;In order to use the Human Metabolic Model for Flux Balance Analysis of specific cancer cell lines, we would like to know what sort of flux values have been determined for the Human Metabolic Model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, how usable is it to predict biomass production in humans (to some extent)?  If it is not very good for this, what other options are there?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks very much!&lt;/p&gt;&#xA;" OwnerUserId="5680" LastActivityDate="2014-02-17T23:05:48.220" Title="How usable is the Human Metabolic Model to predict biomass?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;metabolism&gt;&lt;systems-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15122" PostTypeId="1" CreationDate="2014-02-17T21:31:32.670" Score="1" ViewCount="60" Body="&lt;p&gt;Trying to get a good SBML representation of the Human Metabolic Model for use in Flux Balance Analysis and drug targetting (i.e. gene knockout) simulations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are good sources for these data?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks very much!&lt;/p&gt;&#xA;" OwnerUserId="5680" LastActivityDate="2014-02-17T21:51:07.753" Title="What are good data on the Human Metabolic Model and where can I get them?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;metabolism&gt;&lt;database&gt;&lt;systems-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15123" PostTypeId="2" ParentId="15122" CreationDate="2014-02-17T21:51:07.753" Score="2" Body="&lt;p&gt;As far as I know, there is no one model officially known as &quot;the Human Metabolic Model&quot;, but the Recon 2 model, described as a &quot;consensus&quot; model and the most comprehensive to date in &lt;em&gt;Thiele et al. 2013, A community-driven global reconstruction of human metabolism&lt;/em&gt; (&lt;a href=&quot;http://www.nature.com/nbt/journal/v31/n5/full/nbt.2488.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nbt/journal/v31/n5/full/nbt.2488.html&lt;/a&gt;) is available at &lt;a href=&quot;http://humanmetabolism.org/?page_id=75&quot; rel=&quot;nofollow&quot;&gt;http://humanmetabolism.org/?page_id=75&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tissue-specific models are also available. See for example  &lt;em&gt;Wang et al.:  Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Systems Biology 2012, 6:153:&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-02-17T21:51:07.753" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15124" PostTypeId="2" ParentId="15114" CreationDate="2014-02-17T22:15:56.627" Score="5" Body="&lt;p&gt;Do you ask for examples of non-flying insects which ancestor were flying? In other words do you ask for examples of insect lineages that lost the ability to fly?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ability to fly arose with the clade called the &lt;a href=&quot;http://tolweb.org/Pterygota/8210&quot; rel=&quot;nofollow&quot;&gt;Pterygota&lt;/a&gt;. All species from this monophyletic taxon come from ancestors that had once the ability to fly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For &lt;strong&gt;nonflying species with no flying ancestors&lt;/strong&gt;, you can navigate back in Tree of Life and look at the other two clades in Insecta: Archaeognatha and Thysanura.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For &lt;strong&gt;nonflying species &lt;em&gt;with&lt;/em&gt; flying ancestors&lt;/strong&gt;, you can look within Pterygota on Tree of Life, and you can find many non-flying species in the following clades for example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://tolweb.org/Hemiptera/8239&quot; rel=&quot;nofollow&quot;&gt;Hemiptera&lt;/a&gt; (bugs, aphids)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://tolweb.org/Coleoptera/8221&quot; rel=&quot;nofollow&quot;&gt;Coleoptera&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://tolweb.org/Siphonaptera/8228&quot; rel=&quot;nofollow&quot;&gt;Siphonaptera&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Many &lt;a href=&quot;http://tolweb.org/Vespoidea/11191&quot; rel=&quot;nofollow&quot;&gt;Vespoidae&lt;/a&gt; (clade contained in the &lt;a href=&quot;http://tolweb.org/Hymenoptera/8232&quot; rel=&quot;nofollow&quot;&gt;hymenoptera&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Did Flying only evolved once in insects?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes it did evolve once only. At the start the ancestor had 3 pairs of wings that are though to have evolved from gills &lt;em&gt;or&lt;/em&gt; from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sclerite&quot; rel=&quot;nofollow&quot;&gt;sclerites&lt;/a&gt; (competitive hypotheses) of the prothorax. the most anterior pair of wing was lost. The diptera lost a second pair of wings (the posterior ones) that degenerate into &lt;a href=&quot;http://en.wikipedia.org/wiki/Halteres&quot; rel=&quot;nofollow&quot;&gt;halteres&lt;/a&gt; (particularly easy to see in crane flies). The insects that perform the most &quot;primitive&quot; fly are the &lt;a href=&quot;http://en.wikipedia.org/wiki/Odonata&quot; rel=&quot;nofollow&quot;&gt;Odonata&lt;/a&gt; (dragonflies and damselflies). These insects can move their wings independently which is not the case of other flying insects because the way their wings are attached to the rest of the body has changed.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3952" LastEditDate="2016-03-28T18:22:45.877" LastActivityDate="2016-03-28T18:22:45.877" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="15125" PostTypeId="1" CreationDate="2014-02-17T22:25:43.617" Score="5" ViewCount="157" Body="&lt;p&gt;I know that in E. coli the lactose operon is shut down by CAP protein when binding cAMP. Is this true also for Gram positive bacteria?&lt;/p&gt;&#xA;" OwnerUserId="5686" LastActivityDate="2014-02-18T18:07:04.547" Title="Is the regulation of lactose operon different between Gram + and Gram -?" Tags="&lt;microbiology&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15126" PostTypeId="2" ParentId="15121" CreationDate="2014-02-17T23:05:48.220" Score="2" Body="&lt;p&gt;Firstly, it is important to remember that Flux Balance Analysis computes theoretical performance limits, i.e, the theoretically optimal behaviour of the system with respect to the objective and constraints. When growing bacterial cells growing in culture evolve under selection pressure for biomass production, the theoretical limit on biomass production may indeed be approached, see for example Ibarra et al: &lt;em&gt;Nature. 2002 Nov 14;420(6912):186-9&lt;/em&gt;. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12432395&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/12432395&lt;/a&gt;) and Fong &amp;amp; Palsson: &lt;em&gt;Nat Genet. 2004 Oct;36(10):1056-8&lt;/em&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15448692&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/15448692&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How closely other systems can be expected to approach optimality should be considered on a case-by-case basis, and the constraints should be realistic. In humans, you would for example expect that the physiology of the persons (blood glucose levels, etc.) would greatly affect the growth rate of any cancer cells, in addition to the structure of the tumour (especially blood supply). For cells growing freely in culture, one might expect FBA to be easier to apply.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For HeLa cells growing in culture, the results of at least one study suggests agreement between experimental and FBA-predicted growth rates: See Resendis-Antonio et al: &lt;em&gt;Modeling core metabolism in cancer cells: surveying the topology underlying the Warburg effect. PLoS ONE, 5 (2010), pp. 1–11 (&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012383&quot; rel=&quot;nofollow&quot;&gt;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012383&lt;/a&gt;)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whether the precise biomass production rate is predicted or not may actually not be so important, and there has been considerable interest in applying FBA to studying various aspects of cancer metabolism. Here are some papers that may be of interest:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Ashwini Kumar Sharmaa, Rainer König. Metabolic network modeling approaches for investigating the “hungry cancer”. Seminars in Cancer Biology 23:4,2013, 227–234 (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1044579X13000436&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S1044579X13000436&lt;/a&gt;)&lt;/em&gt; (Review)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Shlomi et al.: Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect. PLoS Coputational Biology 2011 (&lt;a href=&quot;http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002018&quot; rel=&quot;nofollow&quot;&gt;http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002018&lt;/a&gt;).&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Lewis &amp;amp; Abdel-Haleem. The evolution of genome-scale models of cancer metabolism. Front. Physiol., September 2013 (&lt;a href=&quot;http://www.frontiersin.org/Journal/10.3389/fphys.2013.00237/full&quot; rel=&quot;nofollow&quot;&gt;http://www.frontiersin.org/Journal/10.3389/fphys.2013.00237/full&lt;/a&gt;).&lt;/em&gt; (Review)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And a relevant Master's thesis: Computational Metabolic Modeling of&#xA;Cellular Growth: From Bacteria to Cancer. &lt;a href=&quot;http://www.cs.tau.ac.il/thesis/thesis/Benyamini.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.cs.tau.ac.il/thesis/thesis/Benyamini.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-02-17T23:05:48.220" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15128" PostTypeId="2" ParentId="15112" CreationDate="2014-02-18T04:00:05.277" Score="3" Body="&lt;p&gt;I would strongly recommend benchling &lt;a href=&quot;https://benchling.com&quot; rel=&quot;nofollow&quot;&gt;https://benchling.com&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is an awesome web based tool for cloning, primer design, multiple sequence alignments and everything else you are used to doing with the other tools. It is very user friendly, and most importantly you can share designs with your collaborators. Also, the graphics are very beautiful. I recently started using it and I am really impressed with the technical support they offer: you can chat with them and they would reply within minutes. Also, if there is a feature you would like to have implemented they would definitely consider it. Benchling is free, open source and you might be even able to code up some features yourself.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2014-02-18T04:00:05.277" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15129" PostTypeId="2" ParentId="15059" CreationDate="2014-02-18T04:50:44.647" Score="5" Body="&lt;p&gt;Yes, bacteria will produce human (or any organism's) proteins if you introduce their genetic material but there are a few things to consider.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, the introns must be removed from the human genetic sequence. Bacteria do not have the machinery to splice out introns after transcription. This is typically done by using a viral protein to reverse transcribe mRNA, which already have the introns removed, into DNA which you can use to transform bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, you need to insert a Shine-Dalgarno sequence. This allows the bacterial ribosomes to bind to the mRNA they will produce, and translate the protein you desire. This sequence is not found in eukaryotic genes, so you have to make sure it was included either in the vector or in the PCR primers you used to amplify the gene sequence.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastEditorUserId="5144" LastEditDate="2014-02-18T06:36:57.467" LastActivityDate="2014-02-18T06:36:57.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15130" PostTypeId="2" ParentId="15059" CreationDate="2014-02-18T10:07:14.833" Score="3" Body="&lt;p&gt;Although the genetic code is almost conserved among organisms there are some issues to take in account, among which:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Every organism has its own &lt;strong&gt;codon usage&lt;/strong&gt;, i.e. the differences in frequency of occurrence in synonymous codons in coding DNA (that reflect the composition of tRNA abundances). So, for example, the codons UUU and UUC both encode for phenylalanine but - I'm making this up - UUU is common in human but rare in coli while UUC the contrary. If the coding sequence of insuline is rich of UUU, you probably need to change the codon UUU to UUC in order to avoid slow translation.&lt;/li&gt;&#xA;&lt;li&gt;Also the &lt;strong&gt;aminoacid abundance&lt;/strong&gt; can be very variable between two organisms. One of the ways you can handle the differences is by &quot;tuning&quot; the expression of the aminoacids. &lt;a href=&quot;http://en.wikipedia.org/wiki/Proteinogenic_amino_acid#Stoichiometry_and_metabolic_cost_in_cell&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; a table of aminoacids abundance in coli.&lt;/li&gt;&#xA;&lt;li&gt;The &lt;strong&gt;regulatory sequences&lt;/strong&gt; in coli are not the same as in human. In fact, prokaryotic translation initiation needs a purine-rich sequence upstream the (usually) AUG initiation codon called Shine Dalgarno. This sequence is complementary to the 16S RNA in 30S ribosome subunit.&lt;/li&gt;&#xA;&lt;li&gt;Often peptide chains are subjected to various &lt;strong&gt;post-translational modifications&lt;/strong&gt;. The insulin peptide, for example, once synthetized is cleaved by specific peptidases and disulfide bonds are formed. Because human and coli post-translational modification mechanisms are not the same, this can be a difficult problem to handle. Instead of trying to exactly reproduce the protein with all its modifications, often people search for functionally (and not structurally) identical proteins.&lt;/li&gt;&#xA;&lt;li&gt;Also the &lt;strong&gt;folding process&lt;/strong&gt; can be different, both assisted (by chaperones) and spontaneous (withouth chaperones). The folding can be influenced by a number of factors like molecular crowding, pH, ...&lt;/li&gt;&#xA;&lt;li&gt;A lot of eukaryotic genes have &lt;strong&gt;introns&lt;/strong&gt;: sequences removed before translation. Once splicing sites are known, this problem is easily solved by using a sequence withouth introns.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3523" LastActivityDate="2014-02-18T10:07:14.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15131" PostTypeId="1" AcceptedAnswerId="15132" CreationDate="2014-02-18T10:40:26.527" Score="0" ViewCount="2136" Body="&lt;p&gt;I have lets say 10ng/uL of RNA. How can I convert it to picomole?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I need it to calculate how much magnetic beads I need. This is the product: &lt;a href=&quot;http://tools.lifetechnologies.com/content/sfs/manuals/dynabeads_m270_sav_man.pdf&quot; rel=&quot;nofollow&quot;&gt;http://tools.lifetechnologies.com/content/sfs/manuals/dynabeads_m270_sav_man.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not know how much beads should I use.&lt;/p&gt;&#xA;" OwnerUserId="5630" LastActivityDate="2014-10-20T09:36:55.947" Title="How to convert nanogram to picomole?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2014-02-19T12:37:19.103" ContentLicense="CC BY-SA 3.0" />
  <row Id="15132" PostTypeId="2" ParentId="15131" CreationDate="2014-02-18T11:32:55.320" Score="5" Body="&lt;p&gt;&lt;code&gt;Average molecular weight (MW) of a ribonucleotide = 340g/mol&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Size of RNA = x&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;MW of RNA = 340*x g/mol&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;moles of RNA needed = y * 10⁻¹² moles&lt;/code&gt; (&lt;em&gt;1 picomole = 10⁻¹² mol&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;mass of RNA needed = 340*x*y*10⁻¹² g&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Conc of RNA = 10*10⁻⁹ g/µl&lt;/code&gt; `(&lt;em&gt;1ng =10⁻⁹g&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Volume needed for y picomoles = (340*x*y*10⁻¹²)/10*10⁻⁹ = 0.034*x*y µl&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your RNA is biotinylated then add the MW of biotin to MW of RNA&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-10-20T09:36:55.947" LastActivityDate="2014-10-20T09:36:55.947" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15135" PostTypeId="2" ParentId="14998" CreationDate="2014-02-18T14:06:06.107" Score="1" Body="&lt;p&gt;This is a difficult question to answer because we are only aware of basic mechanisms that go on in the brain during dreaming. One theory that is prevalent during sleep is that we may be replaying the day's events in order to extract and store the important information encountered. So if you block sleep after learning you can interfere with it. The function of dreaming itself is more speculative but one idea is that all that replaying back of sensory information along with normal conscious processes creates vivid imagery that is strange and new.As you know during REM the brain is very active so it can &quot;perceive&quot; as if it were awake. This answer is mostly directed at how we dream but hopefully you've gleamed some additional insight from it.&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-02-18T14:06:06.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15137" PostTypeId="1" CreationDate="2014-02-18T16:41:08.700" Score="0" ViewCount="91" Body="&lt;p&gt;Many molecular biology recipes use MgSO&lt;sub&gt;4&lt;/sub&gt; (and not MgCl&lt;sub&gt;2&lt;/sub&gt;). Is there indeed a preference? If so, why? &lt;/p&gt;&#xA;" OwnerUserId="867" LastEditorUserId="5144" LastEditDate="2014-02-19T09:23:32.897" LastActivityDate="2014-02-19T09:23:32.897" Title="Why prefer $MgSO_4$ over $MgCl_2$ in recipies" Tags="&lt;protocol&gt;&lt;biochemistry&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-02-19T10:55:27.483" ContentLicense="CC BY-SA 3.0" />
  <row Id="15139" PostTypeId="2" ParentId="15137" CreationDate="2014-02-18T17:58:42.883" Score="2" Body="&lt;p&gt;My guess is its the solubility properties of the anions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chloride ions can precipitate with some metals that might appear in a complicated buffer or medium. And yes they could even compete with enzyme binding.  Sulfate will remain in solution with just about anything.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are exceptions, but if you're making a buffer you're probably going to do better if you use the &lt;a href=&quot;http://www.csudh.edu/oliver/chemdata/solrules.htm&quot; rel=&quot;nofollow&quot;&gt;general solubility rules&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-02-18T23:21:26.013" LastActivityDate="2014-02-18T23:21:26.013" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15140" PostTypeId="2" ParentId="15125" CreationDate="2014-02-18T18:07:04.547" Score="4" Body="&lt;p&gt;I know it's stupid but I answer my own question, for those who are interested.&#xA;It is different.  CAP protein regulates lactose operon only in Gram -. In Gram + the presence of glucose shuts down the operon with another mechanism: the TCRS that relies to concentration of fructose 1,6 phosphate.&lt;/p&gt;&#xA;" OwnerUserId="5686" LastActivityDate="2014-02-18T18:07:04.547" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15141" PostTypeId="2" ParentId="15112" CreationDate="2014-02-18T20:48:55.000" Score="-1" Body="&lt;p&gt;Geneious is probably the strongest standalone package, but real bionformaticians rarely deal with GUI driven programs. &lt;/p&gt;&#xA;" OwnerUserId="5778" LastActivityDate="2014-02-18T20:48:55.000" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15143" PostTypeId="2" ParentId="10140" CreationDate="2014-02-19T02:19:47.310" Score="8" Body="&lt;p&gt;The answer really depends on how you think of invasive.  One extreme answer is to say that all things are relative, and that the concepts of local and invasive are all relative.  This matters to a certain extent because &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1472-4642.2000.00083.x/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;ecologists draw a fuzzy line between invasive and naturalized&lt;/a&gt;.  You could start with some basic species that we all think of as either good, local, or neutral.  Take the earthworm.  Most people think of it as a common native species, but &lt;a href=&quot;http://www.dnr.state.mn.us/invasives/terrestrialanimals/earthworms/index.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;the earthworm is actually an invasive species that has radically changed much of North America&lt;/a&gt; that came over with the Europeans.  Similarly, &lt;a href=&quot;http://www.dfg.ca.gov/fish/resources/WildTrout/WT_BrownDesc.asp&quot; rel=&quot;nofollow noreferrer&quot;&gt;brown trout are also invasive&lt;/a&gt;, coming to the US in the 1800's.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as why invasive species succeed, it's still an open question.  What you reference is the enemy release hypothesis, but there are others such as disturbance, diversity of the new community, and just the traits.  Here's &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/ece3.431/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;a good review of biological invasions&lt;/a&gt; and &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2009.01418.x/full&quot; rel=&quot;nofollow noreferrer&quot;&gt;a second one&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question about adapting, I wouldn't trust your memory. It's important to keep in mind that most likely your memory is flawed, and you are only observing a very limited number samples with an incomplete sampling methodology.  For instance &lt;a href=&quot;https://link.springer.com/article/10.1007/PL00012004&quot; rel=&quot;nofollow noreferrer&quot;&gt;gypsy moths undergo wild population fluctuations&lt;/a&gt;, and have for over 100 years.  How well do ecosystems bounce back from invasions depends on lots of factors.  Often time the ecosystem can survive, but the some species won't.  An easy example would be Norther Hardwood forests.  Chestnuts (extirpated by an invasive fungus)are mostly gone from the wild, but the forest persists, as well as many of the species that rely on them.  So in part the answer to your question depends on scale.  The forest survived, but an individual species was nearly destroyed.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0921800904003027&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ecological economists have tried to put a value on the destruction that invasive species have caused too&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="1097" LastEditorUserId="3970" LastEditDate="2017-04-12T22:24:16.083" LastActivityDate="2017-04-12T22:24:16.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15144" PostTypeId="1" AcceptedAnswerId="15146" CreationDate="2014-02-19T06:31:11.050" Score="0" ViewCount="853" Body="&lt;p&gt;Someone gives you a short DNA sequence that comes from the middle of a gene.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;5'- TCTAACTGATTAGC -3'&#xA;3'- AGATTGACTAATCG -5'&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;From this sequence, determine the following:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Is the promoter located to the left or right as the sequence is written?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is the sense strand the top or bottom strand?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What amino acids are encoded by this gene fragment?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The only thing I have been able to come up with, is that since this is from the middle of a DNA sequence I need to choose a frame with no stop codons.&lt;/p&gt;&#xA;" OwnerUserId="5781" LastEditorUserId="1320" LastEditDate="2014-02-19T09:26:38.640" LastActivityDate="2014-02-19T09:26:38.640" Title="DNA sequence from the middle of a gene" Tags="&lt;dna&gt;&lt;homework&gt;&lt;dna-replication&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15145" PostTypeId="2" ParentId="15144" CreationDate="2014-02-19T06:41:41.150" Score="2" Body="&lt;p&gt;On the sequence alone, you can answer neither of these questions because:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;from the sequence alone you don't know anything about the gene or the&#xA;promoter.&lt;/li&gt;&#xA;&lt;li&gt;the same is true for the orientation&lt;/li&gt;&#xA;&lt;li&gt;and the codons, since you don't know if the code is in frame or not. &#xA;If one base is cut-off from the original sequence, your codons shift,&#xA;and don't show the original code. The sequence has 14 nucleotides&#xA;which will not ressolve into a short amino acid sequence.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You can probably identify the gene using BLAST and then see, where the sequence is located and answer the questions. I tried to blast the sequence, but it is too short to give a definitive answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the first thing, you need to do is identify the sequence (gene and the organism where it comes from), then you can do the rest of the work.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-19T06:41:41.150" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15146" PostTypeId="2" ParentId="15144" CreationDate="2014-02-19T07:39:58.760" Score="3" Body="&lt;p&gt;TCT AAC &lt;em&gt;TGA&lt;/em&gt; TTA GC&lt;/p&gt;&#xA;&#xA;&lt;p&gt;T CTA ACT GAT &lt;em&gt;TAG&lt;/em&gt; C&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TC &lt;em&gt;TAA&lt;/em&gt; CTG ATT AGC&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AGA TTG ACT AAT CG &amp;lt;&amp;lt;&amp;lt; this is the ORF&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A GAT &lt;em&gt;TGA&lt;/em&gt; CTA ATC G&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AG ATT GAC &lt;em&gt;TAA&lt;/em&gt; TCG&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the sequence comes from the middle of a gene we assume it should encode an open reading frame.&#xA;For this sequence only 1/6 frames does not include a stop codon (shown above in italics). So in standard format, with promoter to the left we can write the ds sequence as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5'-AGATTGACTAATCG&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3'-TCTAACTGATTAGC&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since this is homework I'll leave the rest to you.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-19T07:39:58.760" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="15148" PostTypeId="2" ParentId="13810" CreationDate="2014-02-19T08:36:05.800" Score="2" Body="&lt;h1&gt;Music and Emotions&lt;/h1&gt;&#xA;&lt;p&gt;The most difficult  problem in answering the question of how music creates emotions is likely to be the fact that assignments of musical elements and emotions can never be defined clearly. The solution of this problem is the Theory of Musical Equilibration. It says that music can't convey any emotion at all, but merely volitional processes, the music listener identifies with. Then in the process of identifying the volitional processes are colored with emotions. The same happens when we watch an exciting film and identify with the volitional processes of our favourite figures. Here, too, just the process of identification generates emotions.&lt;/p&gt;&#xA;&lt;p&gt;An example: If you perceive a major chord, you normally identify with the will &amp;quot;Yes, I want to...&amp;quot;. The experience of listening to a minor chord can be compared to the message conveyed when someone says, &amp;quot;No more.&amp;quot; If someone were to say these words slowly and quietly, they would create the impression of being sad, whereas if they were to scream it quickly and loudly, they would be come across as furious. This distinction also applies for the emotional character of a minor chord: if a minor harmony is repeated faster and at greater volume, its sad nature appears to have suddenly turned into fury.&lt;/p&gt;&#xA;&lt;p&gt;Because this detour of emotions via volitional processes was not detected, also all music psychological and neurological experiments, to answer the question of the origin of the emotions in the music, failed.&lt;/p&gt;&#xA;&lt;p&gt;But how music can convey volitional processes? These volitional processes have something to do with the phenomena which early music theorists called &amp;quot;lead&amp;quot;, &amp;quot;leading tone&amp;quot; or &amp;quot;striving effects&amp;quot;. If we reverse this musical phenomena in imagination into its opposite (not the sound wants to change - but the listener identifies with a will not to change the sound) we have found the contents of will, the music listener identifies with. In practice, everything becomes a bit more complicated, so that even more sophisticated volitional processes can be represented musically.&lt;/p&gt;&#xA;&lt;p&gt;Further information is available via the free download of &lt;em&gt;my&lt;/em&gt; e-book &amp;quot;&lt;a href=&quot;http://www.willimekmusic.de/music-and-emotions.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Music and Emotion - Research on the Theory of Musical Equilibration&lt;/a&gt;&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;or on the online journal &lt;a href=&quot;http://www.eunomios.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;EUNOMIOS&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5783" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-02-20T13:20:38.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15149" PostTypeId="2" ParentId="2912" CreationDate="2014-02-19T09:49:57.120" Score="2" Body="&lt;p&gt;I dont understand what you mean by hydrolysis in this context. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The way to go about is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Clone the DNA, that will give rise to the probe, downstream of T7 (or any other) promoter&lt;/li&gt;&#xA;&lt;li&gt;Linearize this plasmid by digesting at (or ahead of) the 3' of cloning site&lt;/li&gt;&#xA;&lt;li&gt;Set up an In-vitro Transcription reaction with T7 polymerase (or whatever corresponds to the promoter you used)&lt;/li&gt;&#xA;&lt;li&gt;Precipitate and purify the RNA (you can use DNAseI to get rid of the DNA).&lt;/li&gt;&#xA;&lt;li&gt;To check the RNA size: mix ~2$\mu$l of RNA (less or more depending on your yield) with equal volume of 2x RNA loading dye (contains formamide 95%, EDTA, SDS, and the dyes). &lt;/li&gt;&#xA;&lt;li&gt;Heat at 85⁰C for 5min. Let it cool and run in 1% TAE/TBE-agarose gel (no need to make MOPS-Formaldehyde gel)&lt;/li&gt;&#xA;&lt;li&gt;dsDNA ladder wont be very accurate but may be used for size estimation (if linear, the mobility of dsDNA and ssDNA/RNA wont be very different. Formamide treatment keeps the RNA linear). Use ssDNA or RNA ladder for better accuracy. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Btw.. the absorbance ratios mentioned are okay.. you don't need an RNA of supreme quality for this application (in fact this suffices for most experiments)&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-02-19T10:47:42.280" LastActivityDate="2014-02-19T10:47:42.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15150" PostTypeId="1" CreationDate="2014-02-19T10:32:57.883" Score="2" ViewCount="63" Body="&lt;p&gt;It is commonly believed that vitamins can help our memory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this really true? What is the biological basis of this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any specific research paper on the subject?&lt;/p&gt;&#xA;" OwnerUserId="5785" LastEditorUserId="115" LastEditDate="2014-02-19T16:43:49.383" LastActivityDate="2014-02-19T18:32:11.497" Title="Do vitamins help our memory?" Tags="&lt;memory&gt;&lt;vitamins&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15151" PostTypeId="1" CreationDate="2014-02-19T12:09:04.907" Score="1" ViewCount="103" Body="&lt;p&gt;Lately, I've become a believer in the limits of reductionist explanations especially in areas like complex systems and biology. So, without wasting any more time, I'll get to my question..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whenever we think of something like cooperation, the most common explanation that comes up is that of genetic fitness. It is said that evolution would have selected for psychological mechanisms of cooperation because it is beneficial in a society in which reciprocity is possible. You scratch my back, and I scratch yours. Add to the mix the ability to name names, and reputation becomes a kind of proxy signal for fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the major problem I have with this is &lt;em&gt;does it all have to boil down to fitness&lt;/em&gt;? Can't it be a phenomenon that is culture-specific? Different cultures go to different lengths to help a stranger. Yet, we all share the same evolutionary history. This seems like a strong indicator that cooperation can't be reduced to one's genetic or reputational fitness alone. Should the study of cooperation be handed off to the anthropologists?&lt;/p&gt;&#xA;" OwnerUserId="625" LastEditorUserId="625" LastEditDate="2014-02-20T02:28:21.013" LastActivityDate="2014-02-20T02:28:21.013" Title="Aren't current explanations for the evolution of human cooperation a little too reductionist?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15152" PostTypeId="2" ParentId="15151" CreationDate="2014-02-19T12:20:20.620" Score="2" Body="&lt;p&gt;Interesting question! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that in terms of 'tribal' fitness, altruism would be strongly selected for, as communities would tend to be quite small (relative to, say, a town today). In modern civilization cultures have developed differing levels of altruism, but I imagine this is a result of upbringing rather than inherent differences in tendency toward altruistic actions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in my opinion you cannot rule out altruism being selected for because it is clearly an advantage (in terms of survival / fitness) in smaller communities - we just don't live in that kind of society any more; people don't have to be altruistic to get by, and this kind of mind-set can 'evolve' culturally, outside genetics. But on the whole I would still argue that most people are inclined toward altruism - ether because they feel naturally inclined to help others, or feel that by helping others some benefit (such a reputation) would be bestowed upon them (the former may be the same as the latter, but at an unconscious level).&lt;/p&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2014-02-19T12:30:56.037" LastActivityDate="2014-02-19T12:30:56.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15153" PostTypeId="2" ParentId="15151" CreationDate="2014-02-19T13:08:41.613" Score="2" Body="&lt;p&gt;There are many various model used in order to explain evolution of cooperation. Here is a small list:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;kin selection&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;group selection (levels of selection)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;lineage selection&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Reciprocity&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;direct&lt;/li&gt;&#xA;&lt;li&gt;indirect&lt;/li&gt;&#xA;&lt;li&gt;network&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Memetics&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;People from many different background study social evolution including&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;mathematicians&lt;/li&gt;&#xA;&lt;li&gt;biologists&lt;/li&gt;&#xA;&lt;li&gt;philosophers&lt;/li&gt;&#xA;&lt;li&gt;computer scientists&lt;/li&gt;&#xA;&lt;li&gt;paleontologists&lt;/li&gt;&#xA;&lt;li&gt;…&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Social evolution is studied through fundamental science (using mathematical modelling and computer simulation) or by looking for common trait among species that are very social. For example, it seems that having a high extrinsic mortality rate &quot;helps&quot; a species evolving altruistic behaviors. Or sex determination mechanism such as haplo-diploidy seem to be important too. There are many experimental studies on human behavior too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The field you referenced to (&quot;Can't it be a phenomenon that is culture-specific&quot;) is called memetics. A meme (named by analogy with the word gene) is a cultural unit which reproduces according to their &quot;memetic fitness&quot; and mutates. There are lots of computer simulations on the subject and there are several empirical observations such as the evolution of a joke.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that none of the field we manage to think it would help explaining the evolution of cooperation is neglected. There are several articles who investigate the co-evolution between genes and memes. I don't know any of them who focused on the question of altruism. I have to confess that I have never read any article who considered the combined effects of several models from several fields in the study of altruism. But I don't think we have a sufficient level of understanding of each field in order to combine these models. For example, it's been argued that kin selection and group selection is actually the same process.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-02-19T13:08:41.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15156" PostTypeId="2" ParentId="15150" CreationDate="2014-02-19T18:32:11.497" Score="2" Body="&lt;p&gt;There seems to be no effect of vitamins. This paper (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23589432&quot; rel=&quot;nofollow&quot;&gt;Preventing cognitive decline in healthy older adults.&lt;/a&gt;&quot; found no evidence for herbal supplements, vitamins or fatty acids improve cognitive functions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There seems to be some evidence (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23690582&quot; rel=&quot;nofollow&quot;&gt;Preventing Alzheimer's disease-related gray matter atrophy by B-vitamin treatment.&lt;/a&gt;&quot;) that a cocktail of hig dosed vitamins including folic acid, Vitamin B6 and Vitamin B12 can slow Alzheimer's disease. But: The benefits were only seen in participants which had high blood levels of homocysteine. This amino acid is linked to a higher risk of heart disease for which the B vitamins are postive for the outcome. So this might only be helpful for people with too high homocysteine levels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And its questionable if high doses of antioxidants (like vitamin A or E) are not only not helpful, but can cause actual damage. This is due to the fact that they catch up reactive oxygen species, which might otherwise trigger the cell to go into apoptosis and prevent it from becoming a cancer cell. Here is the paper: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24477002&quot; rel=&quot;nofollow&quot;&gt;Antioxidants accelerate lung cancer progression in mice.&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-19T18:32:11.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15159" PostTypeId="1" CreationDate="2014-02-19T21:31:56.660" Score="1" ViewCount="59" Body="&lt;p&gt;Is it on the North-South axis, the East-West axis or some other orientation?&lt;/p&gt;&#xA;" OwnerUserId="5014" LastEditorUserId="460" LastEditDate="2014-02-20T05:29:16.277" LastActivityDate="2014-04-21T12:42:34.277" Title="Which direction are wild beehives combs oriented?" Tags="&lt;entomology&gt;&lt;environment&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15160" PostTypeId="1" AcceptedAnswerId="15161" CreationDate="2014-02-19T22:09:55.163" Score="3" ViewCount="337" Body="&lt;p&gt;Mutation rate is a phenotypic trait that evolves. The process of evolution of such kind of traits are often referred to as evolvability. I am wondering about the evolution of the mutation rates in viruses. For the purpose of this question, I'll focus only on viruses that do not possess DNA polymerase. Because the replication of the viral DNA is performed by the molecular machinery of the host cell (eukaryote or not) it seems rather impossible to me for a virus to evolve its mutation rate. Is it correct?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Do we have any evidence of adaptive mutation rate in viruses?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is there a correlation between the mutation rate of the host and the mutation rate of the virus?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Could the virus evolve some structure (or codon bias) of their DNA/RNA in order to adapt their mutation rate?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is there another mechanism allowing a virus lineage to adapt their mutation rate?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-02-19T23:02:35.327" LastActivityDate="2014-02-19T23:09:29.987" Title="Mutation rate in viruses" Tags="&lt;evolution&gt;&lt;mutations&gt;&lt;virus&gt;&lt;molecular-evolution&gt;&lt;retrovirus&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15161" PostTypeId="2" ParentId="15160" CreationDate="2014-02-19T22:29:17.377" Score="3" Body="&lt;p&gt;Really interesting question.&#xA;I am not sure, if the mutation rate is something &quot;actively done&quot; by the virus. I think its more a byproduct of vast replication after taking over the host cell. Mutations with a negative effect are deleted, those with neutral effects will be there, and those with positive mutations will be selected for. This paper looks interesting in this context: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20660197&quot; rel=&quot;nofollow&quot;&gt;Viral Mutation Rates&lt;/a&gt;&quot;. Looking for related publications on the site, I found this two:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18319742&quot; rel=&quot;nofollow&quot;&gt;Rates of evolutionary change in viruses: patterns and determinants.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8828136&quot; rel=&quot;nofollow&quot;&gt;A short introduction to the origin and molecular evolution of&#xA;viruses.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The whole list is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_reviews&amp;amp;from_uid=20660197&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Answering your second question: There is obviously no connection between the mutation rate of the virus and the host. I have found this paper (&quot;&lt;a href=&quot;http://www.genetics.org/content/148/4/1667.full&quot; rel=&quot;nofollow&quot;&gt;Rates of Spontaneous Mutation&lt;/a&gt;&quot;) which gives some pretty interesting numbers. In short: The rate of mutation for DNA viruses is much higher than for eukaryotic cells and for RNA viruses 2-4 orders of magnitude higher than for DNA viruses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At least RNA viruses encode for some own polymerases, the reverse transcriptase. Depending on which these have a proof-reading (exonuclease) function they induce more or less errors.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-02-19T23:09:29.987" LastActivityDate="2014-02-19T23:09:29.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15162" PostTypeId="2" ParentId="7847" CreationDate="2014-02-19T23:40:27.687" Score="1" Body="&lt;p&gt;None of these answers makes sense, and there some minor errors in them. I know that action potentials may continue to fire down the axon. One reason may be because acetylcholinesterase is not coming to the rescue and cleaning up all the acetylcholine in the synaptic cleft. But that usually happens if there are drugs involved. So, in terms of natural muscle cramps, it really does not make any sense whatsoever. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A really good reason is mainly because of a lack of potassium. The function of potassium inside the muscle cell is to repolarize the membrane. However, if there is not enough potassium, the time it takes for it to repolarize is very slow. On the other hand, sodium is used to depolarize the membrane. As a result, since there is an unequal distribution of sodium to potassium, less potassium flows out the membrane while more sodium flows into the membrane, causing it to depolarize faster than it repolarizes. Since the inside of the cell is becoming more positive with the help of sodium, and since the outside of the cell is becoming negative with the help of potassium, the inside of the cell is pulling back the potassium. But, again, there is an unequal distribution of potassium compared to sodium, so it will never achieve that electrochemical equilubrium (resting membrane potential). Since electrochemical equilibrium can not be achieved, sodium is flowing inside the membrane, causing it to depolarize across the membrane and to form an unfused tentanus at a rapid rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rate in which this is happening is so fast that it won't let the myosin head detach from actin for a long period, so it is continuously making the sacromere shorter, causing a pain receptor to travel toward the CNS. This is my hypothesis. &lt;/p&gt;&#xA;" OwnerUserId="5792" LastEditorUserId="-1" LastEditDate="2017-11-11T15:50:43.563" LastActivityDate="2017-11-11T15:50:43.563" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15163" PostTypeId="2" ParentId="7847" CreationDate="2014-02-20T00:26:50.213" Score="0" Body="&lt;p&gt;One of the things that I would like to point out is that ATP detached the myosin head but does not control the powerstroke! If there are no more ATP being produce, then rigor mortis results. You will just be really tense/sore because the myosin head is not being released, and it's staying contracted (perhaps a fused tentanus), but it does not make the sacromere shorter if ATP are no longer able to be produced. And if there are no more ATP being produce, it can't be hydrolyzed into ADP and inorganic phosphate (Pi). &#xA;That would help to create the cross bridge. In addition, inorganic phosphate, not ATP, is the essential compound when you want the power stroke to happen. &lt;/p&gt;&#xA;" OwnerUserId="5792" LastEditorUserId="-1" LastEditDate="2017-11-11T15:50:40.850" LastActivityDate="2017-11-11T15:50:40.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15164" PostTypeId="1" CreationDate="2014-02-20T01:43:00.337" Score="1" ViewCount="846" Body="&lt;p&gt;There is &quot;proof&quot; out there today that suggests smoking is directly linked to cancer. I cannot argue against that, for the evidence in favor appears strong, and the evidence against is lacking. I'll happily sit here and agree that smoking increases the risk of cancer. This question, however, is not about how smoking increases the risk of cancer, rather how stopping smoking might increase the risk of cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider what I know so far:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Cancer is caused by mutant cell growth.&lt;/li&gt;&#xA;&lt;li&gt;Mutant cell growth is believed to be caused by chemicals in the smoke&lt;/li&gt;&#xA;&lt;li&gt;Smoking itself stunts growth, thus slowing the cell growth rate&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If the growth stunt is severe enough that it will reduce the cell growth rate by 20%, one might assume this would take some weeks (let's say 8 weeks, sounds reasonable to me, though I lack knowledge of the subject) to recover. This will likely be some scale and will gradually decrease to somewhere near 0.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further to this, the risk of cancer is not directly related to the lung, but it is believed to be caused by chemicals entering through the lung into the blood, and travelling around the body, causing cancer in various organs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider that the cell growth is probably linked (in the lung, at least) to chemicals &quot;surrounding&quot; the existing cells, this explains why smokers run short of breath. This partially explains the growth stunt side of smoking. Perhaps this happens body-wide, I don't know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then consider what will happen when one stops smoking. The cell growth rate will begin to radically and unexpected increase as the growth stunt is suspended, meanwhile chemicals will still exist in the blood and organs which will be perverting cell growth causing mutant (cancerous) cells. At this point the body is unprepared and settled into its routine of slowly generating cells, but now it is generating them faster and is struggling to keep up. Energy is lacking in areas, and there is further cause of mutant cells to grow and even to be allowed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Surely, given this reasoning, it might be understandable that stopping smoking increases the immediate risk of cancer, though reducing the long term risk?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anybody know, or can anybody find reasonable proof that any part of this argument is flawed? Is there any research to suggest that there is or is not an immediate increased risk? The one thing that people never mention in the side-effects of quitting is the risk of immediate body failure through a variety of means (I've known people to come with flu-like symptoms then find they have cancer weeks later). Is this really unexplored? Or is the nanny state trying to hide it from smokers to prevent them from damaging their health further?&lt;/p&gt;&#xA;" OwnerUserId="5794" LastActivityDate="2014-02-21T08:04:46.253" Title="Smoking, cancer, correlation between quitting smoking and increased immediate risk" Tags="&lt;cell-biology&gt;&lt;cancer&gt;&lt;smoking&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15165" PostTypeId="1" AcceptedAnswerId="15235" CreationDate="2014-02-20T03:25:29.257" Score="12" ViewCount="4201" Body="&lt;p&gt;The wikipedia entry on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Portuguese_Man_o%27_War&quot;&gt;Portuguese man o' war&lt;/a&gt; says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... the Portuguese man o' war is ... not actually a single multicellular organism but a &lt;strong&gt;colonial organism&lt;/strong&gt; made up of many highly specialized minute individuals called zooids. These zooids are &lt;strong&gt;attached to one another&lt;/strong&gt; and &lt;strong&gt;physiologically integrated&lt;/strong&gt; to the extent that they are &lt;strong&gt;incapable of independent survival&lt;/strong&gt;. &lt;em&gt;(emphasis added)&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is contradictory. If it's got multiple cells, and those cells are highly specialized to the point of being incapable of surviving on their own, then how does that differ from a multicellular organism? That last sentence seems like it describes the cells in my body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, the entry &lt;a href=&quot;http://en.wikipedia.org/wiki/Colony_%28biology%29&quot;&gt;colonial organisms&lt;/a&gt; says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The difference between a multicellular organism and a colonial organism is that individual organisms from a colony &lt;strong&gt;can, if separated, survive on their own&lt;/strong&gt;, while cells from a multicellular life form (e.g., cells from a brain) cannot. &lt;em&gt;(emphasis added)&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, is the Portuguese man o' war a colony or a multicellular organism? And if it's a colony, can its zooids survive independently, the wikipedia text notwithstanding?&lt;/p&gt;&#xA;" OwnerUserId="5795" LastEditorUserId="3624" LastEditDate="2014-02-20T10:25:36.197" LastActivityDate="2020-05-25T17:54:50.237" Title="Why is Portuguese man o' war considered a colony?" Tags="&lt;zoology&gt;&lt;taxonomy&gt;&lt;development&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15166" PostTypeId="1" AcceptedAnswerId="15181" CreationDate="2014-02-20T03:28:18.213" Score="4" ViewCount="54" Body="&lt;p&gt;I was wondering if anyone had recommendations for good, large (hopefully 100kDa+), control proteins that would be present in most mammalian cells.  I'm working mostly with tissue samples from humans and mice, and airway epithelium in particular if that matters.  So far the best I've thought of is HSP90, but that is far from ideal for a number of reasons.  My target proteins are between 125 and 210 kDa.  To improve resolution, we've run pretty much everything under 90kDa off the gel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That removes the old standbys like actin or GAPDH.  I understand that the protein levels could vary between cell types for a good loading control target.  Bonus points if you know a good antibody clone to it.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2014-02-20T05:05:14.670" LastActivityDate="2014-02-20T14:49:56.423" Title="Prevalent large (&gt;=90kDa) maintenance protein/loading control" Tags="&lt;lab-techniques&gt;&lt;western-blot&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15167" PostTypeId="2" ParentId="11178" CreationDate="2014-02-20T04:04:38.993" Score="1" Body="&lt;p&gt;So we went ahead and did this.  The efficiency was much lower, which you might expect, and dehydration did aid the process.  We found that taking raw lysates and running them through the linked protocol, had about ~20% the efficiency of conducting it on purified protein.  I assume the majority of the loss was due to reagents being expended on proteins that were not of interest.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2014-02-20T04:04:38.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15168" PostTypeId="1" AcceptedAnswerId="15170" CreationDate="2014-02-20T04:14:23.583" Score="0" ViewCount="96" Body="&lt;p&gt;I just thought about the fact that people move through electrical pulses traveling through neurons in the brain and muscles through the body. Here is what i know: the body is full of 97 or more, percent of water. the thoughts we have and the moves we make are a result of electrical impulses within the neurons and cells.&#xA;  My question is why the water does not disperse the impulse and or make it completely ineffective. My personal guess would be that each neuron is made of or has an outer layer of electric resistance material that( is it conducts) electricity.&lt;/p&gt;&#xA;" OwnerUserId="5796" LastActivityDate="2014-02-20T05:46:07.743" Title="How do neurons send electric pulses even though they are surrounded by liquid which is mostly water?" Tags="&lt;neuroscience&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15170" PostTypeId="2" ParentId="15168" CreationDate="2014-02-20T05:46:07.743" Score="2" Body="&lt;p&gt;Neurons have sodium, potassium, as well as &lt;em&gt;some&lt;/em&gt; calcium channels all over the surface of the cell (I'm giving a very generalized explanation here). The &quot;electric pulses&quot; that you are mentioning is more of electrostatic potentials generated from the interactions of cations and anions flowing in and out of the channels. Water at the specific pH surrounding the cations is a good conductor of these electrostatic interactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You have to remember that there are large negatively charged anion proteins inside the neurons which attract the cations (sodium ions for example) to rush into the cell. Once threshold is reached all gates open and an action potential is produced. &lt;/p&gt;&#xA;" OwnerUserId="5798" LastActivityDate="2014-02-20T05:46:07.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15172" PostTypeId="1" CreationDate="2014-02-20T08:38:13.593" Score="2" ViewCount="420" Body="&lt;p&gt;I am interested in using forskolin in cell culture medium. Does anyone know how to make solution of 10 microM forskolin in 5% ethanol or less. I would like to avoid using DMSO as a solvent.&#xA;Thank you. L.&lt;/p&gt;&#xA;" OwnerUserId="4944" LastActivityDate="2014-04-21T10:42:28.883" Title="Solubility of Forskolin in ethanol" Tags="&lt;neuroscience&gt;&lt;cell-biology&gt;&lt;cell-culture&gt;&lt;stem-cells&gt;&lt;organic-chemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15173" PostTypeId="2" ParentId="15172" CreationDate="2014-02-20T09:21:31.797" Score="1" Body="&lt;p&gt;Sigma gives a solubility of 200 microMole in water containing 2% ethanol.&#xA;They state:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Forskolin is soluble in water (with 2% ethanol) up to 0.2 mM by first&#xA;  dissolving in ethanol at 5 mg/mL and doing subsequent dilutions with&#xA;  water.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The datasheet can be found &lt;a href=&quot;http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Product_Information_Sheet/f6886pis.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-20T09:21:31.797" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15175" PostTypeId="1" AcceptedAnswerId="15211" CreationDate="2014-02-20T10:52:11.917" Score="0" ViewCount="123" Body="&lt;p&gt;This question intrigued me a lot since if animals in the wild did have menstruation with blood flow, wouldn't all that blood be attracting every other predator in the vicinity?&lt;/p&gt;&#xA;" OwnerUserId="5799" LastEditorUserId="5799" LastEditDate="2014-02-21T05:05:39.113" LastActivityDate="2014-02-21T06:43:18.880" Title="Why do mammals in the wild retain the &quot;trait&quot; of menstruating with blood?" Tags="&lt;mammals&gt;&lt;reproductive-biology&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2016-02-16T06:49:57.410" ContentLicense="CC BY-SA 3.0" />
  <row Id="15176" PostTypeId="2" ParentId="15159" CreationDate="2014-02-20T11:04:13.407" Score="1" Body="&lt;p&gt;I've usually observed wild Indian Bees (Apis cerana) orient their hives in an East-West direction. The entrances are usually oriented towards the Sun.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is purely from my own observation (in South India) and not from any research.&lt;/p&gt;&#xA;" OwnerUserId="5799" LastActivityDate="2014-02-20T11:04:13.407" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15177" PostTypeId="1" CreationDate="2014-02-20T13:34:35.450" Score="4" ViewCount="583" Body="&lt;p&gt;I add about 3/4 cups of Blue Diamond almond milk (unsweetened) every morning to a single serving of Cheerios. The milk contains filtered water, and I read that drinking water with food at the same time makes it harder for the small intestine to absorb the nutrients from the food. Has this been verified? &lt;/p&gt;&#xA;" OwnerUserId="5800" LastEditorUserId="3703" LastEditDate="2014-10-19T13:03:46.197" LastActivityDate="2014-10-19T13:03:46.197" Title="Does adding milk to cereal make it harder for our body to absorb the vitamins and minerals from the cereal?" Tags="&lt;digestive-system&gt;&lt;milk&gt;&lt;digestion&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15178" PostTypeId="1" AcceptedAnswerId="15182" CreationDate="2014-02-20T13:41:59.250" Score="0" ViewCount="142" Body="&lt;p&gt;This picture is my drawing about germ layer - not embryonic folding as I wrote initially.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JSwrS.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Where exactly is the endoderm here in the picture?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The known things&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Ectoderm &lt;/li&gt;&#xA;&lt;li&gt;Neural tube&lt;/li&gt;&#xA;&lt;li&gt;Notochord&lt;/li&gt;&#xA;&lt;li&gt;Endoderm - &lt;strong&gt;Where is this?&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;Somite&lt;/li&gt;&#xA;&lt;li&gt;Somite leg&lt;/li&gt;&#xA;&lt;li&gt;Intraembryonic coelom&lt;/li&gt;&#xA;&lt;li&gt;Embryonic somatopleura&lt;/li&gt;&#xA;&lt;li&gt;Embryonic splanchopleura (lateral mesoderm)&lt;/li&gt;&#xA;&lt;li&gt;Endoderm&lt;/li&gt;&#xA;&lt;li&gt;Mesoderm (intraembryonic)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-20T15:08:32.283" LastActivityDate="2014-02-20T15:22:30.280" Title="Is endoderm visible in the germ layer?" Tags="&lt;embryology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15180" PostTypeId="1" CreationDate="2014-02-20T14:32:02.110" Score="0" ViewCount="190" Body="&lt;p&gt;I want to find the conventional phylogenetic tree of human, mouse, C elegans and drosophila, without all the other organisms.&#xA;Do you know where can I get it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks,&#xA;Noga&lt;/p&gt;&#xA;" OwnerUserId="5790" LastActivityDate="2014-02-21T19:21:25.450" Title="Phylogenetic tree" Tags="&lt;evolution&gt;&lt;bioinformatics&gt;&lt;phylogenetics&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15181" PostTypeId="2" ParentId="15166" CreationDate="2014-02-20T14:49:56.423" Score="3" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Vinculin&quot; rel=&quot;nofollow&quot;&gt;Vinculin!&lt;/a&gt;  I love our grad-students, I can't believe I didn't think of it last night.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, &lt;a href=&quot;http://www.abcam.com/primary-antibodies/loading-control-guide&quot; rel=&quot;nofollow&quot;&gt;awesome chart&lt;/a&gt;, even if it's from a company.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2014-02-20T14:49:56.423" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15182" PostTypeId="2" ParentId="15178" CreationDate="2014-02-20T15:22:30.280" Score="1" Body="&lt;p&gt;I think you're going for a view of tube formation, in which case, here's a good image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Xiopy.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Lateral plate mesoderm  &lt;/li&gt;&#xA;&lt;li&gt;Intermediate mesoderm&lt;/li&gt;&#xA;&lt;li&gt;Somite mesoderm&lt;/li&gt;&#xA;&lt;li&gt;Chorda  &lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Endoderm&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.vcbio.science.ru.nl/en/virtuallessons/embryology/chicken-33-36h/&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Reference)&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Again in your drawing I think you correctly have it labeled as 10, and don't really need to put it twice. &lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2014-02-20T15:22:30.280" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15184" PostTypeId="1" CreationDate="2014-02-20T16:52:17.507" Score="2" ViewCount="539" Body="&lt;p&gt;I am trying to figure out how to link Gene Entrez ID with Gene Symbol, for TCGA dataset.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far, I have found &lt;a href=&quot;ftp://ftp.ncbi.nlm.nih.gov/gene/DATA&quot; rel=&quot;nofollow&quot;&gt;this ftp directory&lt;/a&gt; with Gene info updated daily.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, for Entrez ID 728661, I have found two different mappings:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bioinformatics.picr.man.ac.uk/adapt/ProbeToGeneAction.adapt?genes=728661&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; symbol is RP11-345P4.4;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/gene/?term=728661&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, and in gene info downloaded from ftp above, symbol is SLC35E2B while RP11-345P4.4 is in the field 'locus tag'.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Since I am a newbie I am bit confused about this thing. And, while I think they can be synonyms, I need to know if there is a best practice to use in this case, and if I need to implement some script on my own to do it automatically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks &lt;/p&gt;&#xA;" OwnerUserId="3466" LastEditorUserId="14852" LastEditDate="2015-04-24T04:48:38.340" LastActivityDate="2015-04-24T04:48:38.340" Title="Best way to automatically link Gene Entrez ID with Gene Symbol in TCGA" Tags="&lt;genetics&gt;&lt;cancer&gt;&lt;tcga&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15186" PostTypeId="2" ParentId="15180" CreationDate="2014-02-20T17:42:29.973" Score="1" Body="&lt;p&gt;This isn't a complete answer, but to get things rolling.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think I see what you want; a comprehensive &quot;correct&quot; tree you can compare your single alignment tree to?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can think of a couple of responses to this.  Firstly there is no perfect way to make a phylogenetic tree. Aside from all the different distance metrics you could use and algorithms to sort large trees, the data you use can also vary depending on what you want to do.  You can compare some conserved genes for long distance comparisons or highly mutable sequences for close distances, but which are subject to noise. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said a tree comparing ribosomal RNA is a phylogenetic standard.  As are trees derived from multiple genes. If you want to see if your genes are unusual you can run a few other genes through the same comparison and see if the trees vary substantially for your gene. Because the animals you compare are so far apart on the tree the relative comparison will be pretty close to the tree you've made.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are trying to compare the tree quantitatively to some master tree, that will be a demanding task.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-02-20T17:42:29.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15187" PostTypeId="1" AcceptedAnswerId="15190" CreationDate="2014-02-20T18:02:25.410" Score="0" ViewCount="613" Body="&lt;p&gt;what kind of Pathway mediates nitroglycerin-induced relief from angina pectoris,please provide some idea...&lt;/p&gt;&#xA;" OwnerUserId="5164" LastEditorUserId="107" LastEditDate="2014-02-21T14:48:41.900" LastActivityDate="2014-10-31T12:37:08.590" Title="Pathway mediates nitroglycerin-induced relief from angina pectoris" Tags="&lt;biochemistry&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-02-21T14:49:05.320" ContentLicense="CC BY-SA 3.0" />
  <row Id="15188" PostTypeId="1" CreationDate="2014-02-20T18:11:10.790" Score="0" ViewCount="436" Body="&lt;p&gt;How does the closure of M-type potassium channels by muscarinic receptors result in increased excitation of the target neuron?&lt;/p&gt;&#xA;" OwnerUserId="5164" LastEditorUserId="1320" LastEditDate="2014-02-21T13:38:13.653" LastActivityDate="2014-02-21T16:19:11.307" Title="M-type potassium channels by muscarinic receptors" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15189" PostTypeId="1" CreationDate="2014-02-20T19:42:30.903" Score="0" ViewCount="68" Body="&lt;p&gt;It follows from the complication of S.pyogenes' pharyngitis.&#xA;I am thinking how the inflammatory response behaves: acute or chronic or something between.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think chronic disease is better description here than acute, however not sure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the type of inflammatory response in the Rheumatic fever?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-20T19:55:37.640" LastActivityDate="2014-02-20T20:44:51.633" Title="Is Rheumatic fever more Chronic than acute?" Tags="&lt;microbiology&gt;&lt;inflammation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15190" PostTypeId="2" ParentId="15187" CreationDate="2014-02-20T20:16:32.377" Score="3" Body="&lt;p&gt;The effect of nitroglycerin on the cardiac tissue is similar to nitric oxide (NO),  which forms in the endothelium of blood vessels from arginin metabolism products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the general scheme can look like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;R-NO&lt;sub&gt;2&lt;/sub&gt; is converted to R-NO outside of the cell (glutathion-SH-dependent reaction). NO is lipophilic and rapidly penetrates into the cell where it activates guanylate cyclase. From this moment you can see the resulting influence on myosin and actin on this picture:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Gvr6j.png&quot; alt=&quot;muscle relaxation NO related&quot;&gt; &lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="3340" LastEditDate="2014-10-31T12:37:08.590" LastActivityDate="2014-10-31T12:37:08.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15191" PostTypeId="1" AcceptedAnswerId="15199" CreationDate="2014-02-20T20:21:12.197" Score="6" ViewCount="2562" Body="&lt;p&gt;I am an electronic engineer so I am thinking about this from an electronics outlook.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does the addressing system work, As I see it, the nervous system is small parallel branches attached to larger &quot;serial&quot; lines (spinal cord).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The serial line is then attached to the brain, but how does it then figure out where the message came from and then get the message back to the place it came from.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I were to build a robot I would have an addressing system with each message and maybe some kind of error checking to make sure the messages don't become corrupted, but as it's not an electronic system I don't see how the brain could possibly do this. unless it is a fully parallel system and there is a single wire going from every sensor back to the CPU..&lt;/p&gt;&#xA;" OwnerUserId="5804" LastActivityDate="2014-02-20T22:31:26.477" Title="How does the brain know where a signal came from? What is the addressing system" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;neurotransmitter&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15192" PostTypeId="2" ParentId="15191" CreationDate="2014-02-20T20:34:58.303" Score="1" Body="&lt;p&gt;your question is a little bit difficult to answer in the current forum format, however I'd suggest you reading about &lt;a href=&quot;http://en.wikipedia.org/wiki/Reflex_arc&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reflex arc&lt;/a&gt;  - from this you can understand consequence of the events in simple reflex on the level of spinal cord (i.e. monosinaptic pathway) and very complex reflexes managed by multiple neural cells (neurons).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A classic example of the reflex - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qvFE9.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to dive into the very complex explanations you should read some textbook and probably not forums. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably, you'd like to know what the &lt;a href=&quot;http://en.wikipedia.org/wiki/Action_potential&quot; rel=&quot;nofollow noreferrer&quot;&gt;potential of action&lt;/a&gt; is....&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2014-02-20T20:34:58.303" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15193" PostTypeId="1" CreationDate="2014-02-20T20:39:55.813" Score="2" ViewCount="67" Body="&lt;p&gt;I am using a microscope with an LED derived light through the epi-fluorescent port of a microscope.  I know that the &quot;field of view&quot; for a given objective is equal to the field number/magnification but I don't know that this is the actual area of illumination on the sample.  In my case, I am using a 40x objective with field number 26.5. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, if I were to use a pinhole filter between the light source and the back of the objective would this limit the area of illumination so long as the pinhole was smaller than the f.o.v. dimension?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be grateful for any answers, most of the information I can find on beam size at sample is related to spot size calculations of resolution. &lt;/p&gt;&#xA;" OwnerUserId="5805" LastActivityDate="2014-03-28T09:02:20.520" Title="What's the best way to measure/calculate the size of a light beam at the sample of a microscope?" Tags="&lt;neuroscience&gt;&lt;biophysics&gt;&lt;microscopy&gt;&lt;fluorescent-microscopy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15194" PostTypeId="2" ParentId="15189" CreationDate="2014-02-20T20:44:51.633" Score="1" Body="&lt;p&gt;the inflammatory response it autoimmune reaction, thus it occurs 4 weeks after the Strep infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;please, look at the picture from the &quot;&lt;a href=&quot;http://www.nature.com/nrcardio/journal/v10/n3/fig_tab/nrcardio.2012.197_F4.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nature&lt;/a&gt;&quot; - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6seoc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2014-02-20T20:44:51.633" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15195" PostTypeId="1" AcceptedAnswerId="15197" CreationDate="2014-02-20T21:28:39.167" Score="2" ViewCount="289" Body="&lt;p&gt;Fulminant seems to mead rapid.&#xA;There is however some articles with both phrases: &quot;fulminant meningococcecemia&quot; (about 5000 Google matches) and &quot;acute meningococcecemia&quot; (about 3000 Google matches).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking Neisseria meningitidis and its pathogenesis&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Portal entry nasopharynx (pili)-&gt; attach epithelium cells -&gt; bloodstream (bacteremia); upper respiratory tract infection -symptoms; may be asymptomatic in transient flora; fulminant meningocococcemia (regardless of meningitis)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the difference between the two diseases?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="43480" LastEditDate="2018-09-14T21:25:03.930" LastActivityDate="2018-09-14T21:25:03.930" Title="Difference between Fulminant and Acute Meningococcemias" Tags="&lt;human-biology&gt;&lt;microbiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15196" PostTypeId="2" ParentId="14940" CreationDate="2014-02-20T21:49:23.850" Score="1" Body="&lt;h2&gt;Short answer:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;For drugs with targets having a &lt;em&gt;direct&lt;/em&gt; effect on reactions in the model:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Find the gene name for the target protein -&gt; Find the Entrez Gene ID (or other gene identifier, &lt;em&gt;depending on the model&lt;/em&gt;) -&gt; Search the model file or database for reactions having a gene association with the gene identifier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;AND/OR:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Find the EC number for the target protein. -&gt; Search the model file or database for reactions associated with the EC number (likely to miss many reactions or be imprecise).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EC numbers can be found in the UniProt database, while the HGNC database at &lt;a href=&quot;http://www.genenames.org/&quot; rel=&quot;nofollow&quot;&gt;http://www.genenames.org/&lt;/a&gt; can be used to look up genes by name and find their Entrez Gene ID and other resources, including links to UniProt. Many other databases can also be used.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;For drugs with targets having an &lt;em&gt;indirect&lt;/em&gt; effect on reactions in the model:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Model/estimate in-direct metabolic effect yourself by using data on known regulatory effects to create new gene-reaction associations or modify the bounds on reactions affected by the drug.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Long answer:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;To knock out or constrain a reaction based on data about a drug, you have to go from an entry in a drug database to an EC number or gene identifier consistent with the annotation in the model you are using. However, &lt;strong&gt;There is currently no standard annotation nomenclature for gene-protein-reaction (GPR) associations in metabolic models, and in general only direct GPR associations are encoded in model files.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that you have a metabolic model in SBML format (for example the RECON 2 model), reactions may have a gene association and/or be associated with an Enzyme Comission (EC) Number.&lt;a href=&quot;http://en.wikipedia.org/wiki/Enzyme_Commission_number&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt; However, several model reactions catalyzed by distinct isozymes (different enzymes catalyzing the same reaction) may be associated with the same EC number, and many reactions may not be annotated with an EC association. Therefore you might want to use the gene associations directly. Both gene associations and EC numbers are recorded in the &quot;notes&quot; tag for each reaction in the SBML file, and is not part of the SBML specification. (A proposal has been published for improving support for gene associations in the SBML format.&lt;a href=&quot;http://figshare.com/articles/Proposal_Encoding_Gene_Protein_Associations_in_SBML/855490&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Using EC numbers:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Using EC numbers is the simplest, but not the most precise or possibly even usable solution. It is simpler than using gene associations, because genes may described using any of a number of identifiers depending on the database while any reaction is associated with at most one EC number. Once you know the target protein, you can look it up in the UniProt database, and find its EC number (if any) in the field &quot;protein names&quot;. A simple example: The DrugBank entry for the cancer drug Fluorouracil (&lt;a href=&quot;http://www.drugbank.ca/drugs/DB00544&quot; rel=&quot;nofollow&quot;&gt;http://www.drugbank.ca/drugs/DB00544&lt;/a&gt;), links to the UniProt entry for one of its targets, Thymidylate synthase (&lt;a href=&quot;http://www.uniprot.org/uniprot/P04818&quot; rel=&quot;nofollow&quot;&gt;http://www.uniprot.org/uniprot/P04818&lt;/a&gt;), where the EC number is given as 2.1.1.45. Searching the RECON 2 SBML file (or searching in BiGG at &lt;a href=&quot;http://bigg.ucsd.edu/bigg/main.pl&quot; rel=&quot;nofollow&quot;&gt;http://bigg.ucsd.edu/bigg/main.pl&lt;/a&gt;) for occurences of this number will show that it is associated with the &quot;TMDS&quot; reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The IUPHAR database (&lt;a href=&quot;http://www.iuphar-db.org/index.jsp&quot; rel=&quot;nofollow&quot;&gt;http://www.iuphar-db.org/index.jsp&lt;/a&gt;) may also be useful. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Using Gene associations:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Genes are conceptually at least one step removed from the reactions their products catalyze, so one might argue that using EC numbers which actually correspond to reactions would be better. However, it is thinkable that a drug might affect only one of several enzymes which catalyze the same reaction and thus share an EC number. Furthermore,  annotation of reactions with EC numbers in metabolic models may be poor. Thus you may want to use gene associations to determine which reaction are affected by a drug.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, due to the large number of databases, a single gene may be described using many identifiers or symbols in different databases. You thus have to identify the gene coding for the product which is the target of the drug, and obtain the correct identifier for that gene which corresponds to the nomenclature used in the model.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming again that you are using the RECON 2 model, it is an update of RECON1 which was made using the BiGG database&lt;a href=&quot;http://www.biomedcentral.com/1471-2105/11/213&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;. Gene protein reaction (GPR) associations are therefore recorded using the gene names in BiGG. When ignoring the decimal and any following numbers, BiGG gene names &lt;em&gt;appear&lt;/em&gt; to correspond to Gene IDs in the NCBI Gene database.&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene&quot; rel=&quot;nofollow&quot;&gt;5&lt;/a&gt; A question on how to identify BiGG reactions  was also discussed at BioStar.&lt;a href=&quot;http://www.biostars.org/p/9047/&quot; rel=&quot;nofollow&quot;&gt;6&lt;/a&gt; However, you have the opposite problem: Finding a BiGG gene name from another gene identifier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using Fluorouracil as an example again, the DrugBank entry lists &quot;Cytochrome P450 2C9&quot; as a targeted enzyme, with the effect being inhibition. Following the link to the UniProt entry P11712 (&lt;a href=&quot;http://www.uniprot.org/uniprot/P11712&quot; rel=&quot;nofollow&quot;&gt;http://www.uniprot.org/uniprot/P11712&lt;/a&gt;), we find that it has an EC number 1.14.13.- However, this EC number corresponds to a &lt;em&gt;class&lt;/em&gt; of reactions (or rather, enzymes). There are also listed several additional EC number at the single reaction level, but as these may not cover or be associated with all relevant reactions, we'll use the gene association. Going back to the DrugBank entry (or just reading on the UniProt page), we find that the gene name is CYP2C9. Looking up this name at a suitable database, for example the HGNC database of human gene names at &lt;a href=&quot;http://www.genenames.org/&quot; rel=&quot;nofollow&quot;&gt;http://www.genenames.org/&lt;/a&gt;, we find the entry for CYP2C9 (&lt;a href=&quot;http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=2623&quot; rel=&quot;nofollow&quot;&gt;http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=2623&lt;/a&gt;) and that its Entrez Gene ID is 1559. Searching for this gene identifier in the BiGG database, we find that four reactions are associated with this identifier (The actual association is to &quot;1559.1&quot;): P4502C9,P4502C92,P4502C93 and P4502C94. Note that none of these reactions have an associated EC number.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Defining your own GPR associations&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Keep in mind that even in genome-scale metabolic models, a large number of reactions and processes are missing. While the term metabolism in its widest sense may be used to refer to &lt;strong&gt;all&lt;/strong&gt; reactions occuring in a cell, metabolic models have so far been mostly limited to covering transport and inter-conversions of small metabolites. Processes involving signalling molecules and regulation of enzymes have been mostly or completely left out, along with critical processes such as DNA replication, DNA repair and apoptosis.  Because of the limited scope of the models, gene-protein-reaction (GPR) relations do not generally take regulatory effects into account, being limited to describing direct relations between one or more genes encoding (part of) a protein which directly catalyzes a reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One could also model a very large number of &lt;em&gt;indirect&lt;/em&gt; regulatory effects, but as current metabolic models generally do not specify these, you may have to construct them yourself. To find reactions in a metabolic model which are affected by a certain drug, you may have to &quot;travel&quot; several steps of interactions from the original target of the drug. You may consider using protein-protein-interaction network (PIN) data to help in this. You will have to consider the strength/importance of the interactions, something which may require a high degree of manual curation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, if your drug affects HSP90, which is needed for correct folding of certain enzymes, you may consider creating a GPR stating that the gene for HSP90 (or rather, HSP90 itself) is needed for any reactions catalyzed by a specific enzyme to be active. This would be an indirect GPR, as HSP90 does not itself produce any part of the enzyme that catalyzes the reaction. As an alternative to on/off regulation through a GPR, you may consider searching for data on the ratio of correctly folded and misfolded enzymes in the presence and absence of HSP90, and apply bounds on reactions catalyzed by the affected enzyme to reflect this. &lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-02-20T21:49:23.850" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15197" PostTypeId="2" ParentId="15195" CreationDate="2014-02-20T21:49:57.697" Score="2" Body="&lt;p&gt;When we say &quot;Fulminant meningococcemia&quot; we mean failure of adrenal glands due to haemorrhage of infectious origin, or &lt;a href=&quot;http://en.wikipedia.org/wiki/Waterhouse%E2%80%93Friderichsen_syndrome&quot; rel=&quot;nofollow&quot;&gt;Waterhouse–Friderichsen syndrome&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and acute is related to &lt;strong&gt;time&lt;/strong&gt; of signs appearance, opposed to chronic disease.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2014-02-20T21:49:57.697" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15199" PostTypeId="2" ParentId="15191" CreationDate="2014-02-20T22:31:26.477" Score="3" Body="&lt;p&gt;The brain knows where a sensory signal came from by what neuron is doing the signalling.  The incoming neuron is dedicated to signals from one source and, since it is not shared by other sources, does not need to have an encoding as to what the source was. When your toe touches something, the sensation causes a pulse which, amazingly, travels along a single nerve cell (neuron) up to the &lt;a href=&quot;https://en.wikipedia.org/wiki/Brainstem&quot; rel=&quot;nofollow&quot;&gt;brain stem&lt;/a&gt;.  That neuron has its nucleus at a &lt;a href=&quot;https://en.wikipedia.org/wiki/Dorsal_root_ganglion&quot; rel=&quot;nofollow&quot;&gt;dorsal root ganglion&lt;/a&gt; located by the &lt;a href=&quot;https://en.wikipedia.org/wiki/Spinal_cord&quot; rel=&quot;nofollow&quot;&gt;spinal cord&lt;/a&gt;, and has a fiber (axon) that extends to the source (toe) and another extending up to the brain stem.  This pathway is called the PCML pathway and the &lt;a href=&quot;https://en.wikipedia.org/wiki/Posterior_column-medial_lemniscus_pathway&quot; rel=&quot;nofollow&quot;&gt;Wikipedia article&lt;/a&gt; has some readable details.  &lt;a href=&quot;http://www.acbrown.com/neuro/Review/NrRevwSmtc.htm&quot; rel=&quot;nofollow&quot;&gt;This page&lt;/a&gt; has a schematic and tabular summary, while &lt;a href=&quot;http://www.bioon.com/bioline/neurosci/course/bassens.html&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt; has a good descriptive overview.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a robot were built along the same sort of design, to determine what was happening at 1000 places in its body, it would have 1000 wires running to its central computer.  You probably wouldn't choose to use such a design, but then you probably wouldn't be designing a robot that has to build itself from raw materials. &lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2014-02-20T22:31:26.477" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15200" PostTypeId="1" AcceptedAnswerId="15224" CreationDate="2014-02-20T22:48:03.750" Score="0" ViewCount="310" Body="&lt;p&gt;Sometimes when a person gets touched on one part of the body they feel it else where and may think it came from a different part of the body. What causes this? Other examples are similar to why you can trick your self into thinking your arms are heavier than they really are. another would be that you can close your eyes and move in circles up and down your arm slowly and then when you guess where u are touching your hand is higher or lower than expected. What causes these things?&lt;/p&gt;&#xA;" OwnerUserId="5796" LastEditorUserId="5796" LastEditDate="2014-02-21T16:09:15.537" LastActivityDate="2014-02-21T16:09:15.537" Title="Systemic sensory confusion?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;neuroanatomy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15201" PostTypeId="2" ParentId="15200" CreationDate="2014-02-20T23:09:05.920" Score="2" Body="&lt;p&gt;When our brain works out where a part of our body is in relation to another part of our body, or in relation to anything for that matter, we combine:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;visual information&lt;/li&gt;&#xA;&lt;li&gt;information about how much our muscles are contracted&lt;/li&gt;&#xA;&lt;li&gt;how much our joints are contracted&lt;/li&gt;&#xA;&lt;li&gt;different forces being applied on our arms/legs or other body parts&lt;/li&gt;&#xA;&lt;li&gt;where it remembers we used to be&lt;/li&gt;&#xA;&lt;li&gt;how much force we applied to move where we wanted to move&lt;/li&gt;&#xA;&lt;li&gt;where we would therefore expect to be &lt;/li&gt;&#xA;&lt;li&gt;and many other things&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;That's quite a few things that our body relies on! The one that's most fine tuned is our vision. Let's face it, whatever we are actively doing with our hands requires the most skill and knowledge of where our hands etc. are. It is also the system that we rely on the most. But other systems are helpful to make sure we don't fall, grabbing on to things and making sure we reflexively contract the opposite muscles to prevent falling, stop us dropping things and lot's more. It doesn't matter if they're not accurate, they just need to be fast and in doing so they can't be extremely exact. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When we don't use vision, we rely on these other things. They're made to quickly adapt (e.g. hold a shopping bag for a while and when you let go your arm feels light or when you get out of a swimming pool your body feels heavy) and it is important that they do this to allow their functions as listed in the last paragraph. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-20T23:09:05.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15202" PostTypeId="2" ParentId="15177" CreationDate="2014-02-20T23:19:16.683" Score="1" Body="&lt;p&gt;Overall, no it doesn't. Cereal is made in a way that it's expected consumers will consume it with milk. Here's a list of some important fortifications added to cereal and milk effects on absorption. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Riboflavin&lt;/strong&gt;: No. Affected most strongly by light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Iron&lt;/strong&gt;: Yes. Calcium can affect absorption. Milk causing a deficiency is rare unless it is being used as a breast milk substitute in babies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Thiamin&lt;/strong&gt;: No. Unless you are drinking alcohol with your cereal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Folic acid&lt;/strong&gt;: Milk is a source of this!&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-20T23:19:16.683" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15203" PostTypeId="2" ParentId="15164" CreationDate="2014-02-20T23:34:22.490" Score="3" Body="&lt;p&gt;To summarise your argument, cancer is a disease characterised by uncontrolled cell division of mutant cells. Smoking decreases cell division, thereby smoking decreases risk of cancer. Furthermore, stopping smoking increases growth rates, thus there's an immediate rise in risk following smoking cessation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cancer is NOT caused by cell division. Smoking does NOT cause cancer by cell division. That's the flaw in your argument. What's happening is that cell division ISN'T being controlled. Let's propose that smoking does indeed stunt normal cell growth. The carcinogens in tar from smoking are still floating around causing mutations in the DNA. Most of DNA doesn't code for very much, but some parts of it codes for genes which control cell division. If these genes mutate then cell division is no longer controlled by these genes and hence there's uncontrolled cell division a.k.a cancer. Once these cells are dividing in an uncontrolled fashion, smoking isn't going to limit their growth. That's because this cancer has developed in the presence of these toxins that limit it's growth and despite this it's still managed to occur. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And then that cell growth stunting may actually be causing cancer to occur. White blood cell function is impaired by smoking, these cells usually target cancerous cells and destroy them. Without being destroyed, there's a higher chance of cancer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And then I could go further, usually cells grow older and die. Maybe smoking by stunting growth of these cells leads to cells that last longer than they should. These cells accumulate mutations and become cancerous, where else they otherwise would've been recycled. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Smoking however has been linked to improving the symptoms of some diseases. Just not cancer. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-20T23:34:22.490" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15204" PostTypeId="2" ParentId="11385" CreationDate="2014-02-21T00:04:25.420" Score="2" Body="&lt;p&gt;After a couple months I got this working. I ordered the psuedouridine and 5 methylcytidine from Trilink. I also switched from the mMessage mMachine kit the the Megascript kit. Megascript has all the nucleotides separated while mMessage mMachine has them pooled. You have to dissolve Trilink nucleotides so that the concentration is the same as the natural nucleotides in your IVT kit. Then you just use the non-natural nucleotides instead of UTP and CTP. Let the IVT reaction run 4 hours. Be careful about RNAse contamination.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-02-21T00:04:25.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15206" PostTypeId="2" ParentId="15180" CreationDate="2014-02-21T00:40:32.087" Score="1" Body="&lt;p&gt;You can go to &lt;a href=&quot;https://species.wikimedia.org&quot; rel=&quot;nofollow&quot;&gt;Wikispecies&lt;/a&gt; and find the species page for each organism, e.g. &lt;a href=&quot;https://species.wikimedia.org/wiki/Mus_musculus&quot; rel=&quot;nofollow&quot;&gt;the Mouse page&lt;/a&gt;.  On there you can click on the Taxonavigation box Expand button and see the group names for the organism.  Comparing the names for each organism will give the closest common ones, which gives you the tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, for the tree between the mammals and the other two, you might want to have a look at the &lt;a href=&quot;http://tolweb.org/Bilateria/2459&quot; rel=&quot;nofollow&quot;&gt;Tree of Life Web page for Bilateria&lt;/a&gt;.  Your three groups fall into Deuterostomia, Arthropoda, and Nematoda; for these you'll find a tree for these three groups.  (Actually two trees, but for your groups they amount to the same thing.)&lt;/p&gt;&#xA;" OwnerUserId="231" LastEditorUserId="231" LastEditDate="2014-02-21T00:45:32.997" LastActivityDate="2014-02-21T00:45:32.997" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15209" PostTypeId="1" CreationDate="2014-02-21T04:05:04.683" Score="2" ViewCount="102" Body="&lt;p&gt;I'm taking an online bioinformatics class and I am stuck on a problem. The resources I have found don't help that much. Here is the problem: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Assemble the error-free reads from a circular genome on the dataset below. You do not need to consider the reverse complement of the reads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dataset: CGTTCT CTAG GACGT TAGAC&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;As the reads do not have the same length, convert the reads to 4-mers using the approach proposed by Idury and Waterman&lt;/strong&gt;.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe this means I need to convert this into sets of 4 characters each. Do I simply break them up by taking the first 4 characters and last 4 characters like this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CGTTCT: CGTT --&gt; TTCT&lt;br&gt;&#xA;CTAG: CTAG --&gt; CTAG&lt;br&gt;&#xA;GACGT: GACG --&gt; ACGT&lt;br&gt;&#xA;TAGAC: TAGA --&gt; AGAC&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And end up with a new dataset of: &quot;CGTT TTCT CTAG GACG ACGT TAGA AGAC&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is there more to it than that? Thanks for any help.&lt;/p&gt;&#xA;" OwnerUserId="5596" LastActivityDate="2014-08-07T18:36:19.820" Title="Genome Assembly Using Reads" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15211" PostTypeId="2" ParentId="15175" CreationDate="2014-02-21T06:43:18.880" Score="1" Body="&lt;p&gt;I would guess that the answer is something like this: ever since the development of the placenta enabled females to carry their offspring longer and to develop more fully.  Upon birth they were stronger and/or their brains were more fully developed (in the case of humans).  The increased gestation time, made possible by the structures of the womb and placenta is probably an adaptation whose advantages are much greater than the increased risk from menstruation once a month.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some anthropological studies indicate that in preindustrial societies that women do not menstruate very much as adults though.  If you subtract out the time that they are carrying infants and nursing, which both prevent menstrual cycles, females will miss years of menstruation with only a few months in between. I would assume this is a factor in the risk of menstruation for many animals.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-02-21T06:43:18.880" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15212" PostTypeId="2" ParentId="15164" CreationDate="2014-02-21T08:04:46.253" Score="2" Body="&lt;p&gt;One thing is pretty clear and needs not to be debated I think: Smoking is pretty unhealthy and can cause cancer. I see a number of misconceptions here:&#xA;First you assume, that a slower cell division is something you want to have. Most cell of the adult human body do no divide at all (or only at relatively low rates). Some cells have higher proliferation rates belong to the hematopoietic system, the gut, the mucosas of the body and the skin. These cells need to be able to proliferate in order to fulfill their function. Other cells are dividing to replace cells which went into apoptosis or had to be replaced, but this can not be compared like the growing rates of kids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, cell growth is highly restricted and controlled for good reasons. I did a short search for articles describing slower cell growth by smoking. What I found does not favor the idea that slowed cell growth might be beneficial. This paper for example (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643295/&quot; rel=&quot;nofollow&quot;&gt;Cigarette Smoke Induces Cellular Senescence&lt;/a&gt;&quot;), shows that lung fibroblasts are going into senescence and are not able to do necessary proliferation for lung maintanence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, even if cancer is defined (among other things) to be a fast proliferating, uncontrolled growing mass of cells, its not enough to simply let cells grow, to be able to call them cancer cells. To be able to grow as a cancer cell, the cell needs to change genetically and pick up a number of mutations which allows them to escape the security programs of the body. These are apoptosis and the immune system and its not an easy task. Most cells with the potential to become cancer cells get caught on the way. For the way, how cells become cancer cells, this &lt;a href=&quot;http://lungcancer.about.com/od/Biology-of-Cancer/a/Cancer-Cells-Normal-Cells.htm&quot; rel=&quot;nofollow&quot;&gt;webpage&lt;/a&gt; is pretty interesting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stopping to smoke does not cause more problems for you body, it reduces them. The number of dangerous substances delivered to your body is reduced, as is the chance for them to cause harm (lower concentrations). It will take quite a while to get rid of them though, for tar in the lung this can take several years.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-21T08:04:46.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15214" PostTypeId="1" AcceptedAnswerId="20597" CreationDate="2014-02-21T09:03:15.470" Score="3" ViewCount="38562" Body="&lt;p&gt;Laplace law explains why the pressure is the same in aorta and arteries (100).&#xA;I am thinking why there is so big drop in pressure when going from arteries to arterioles (40-60).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why there is a great drop in pressure from arteries to arterioles?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2015-10-13T11:35:16.653" Title="Why there is a very high drop in pressure from arteries to arterioles?" Tags="&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15216" PostTypeId="1" AcceptedAnswerId="15219" CreationDate="2014-02-21T11:44:36.373" Score="0" ViewCount="1596" Body="&lt;p&gt;I normally use Amies medium, but I today heard that Cary-Blair is also possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;When should you use Cary-Blair medium?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1320" LastEditDate="2014-02-21T13:31:34.757" LastActivityDate="2014-02-21T13:35:33.973" Title="Difference between Cary-Blair and Amies transport media for Staphylococcus and Streptococcus?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15217" PostTypeId="1" CreationDate="2014-02-21T12:25:52.627" Score="2" ViewCount="939" Body="&lt;p&gt;When searching for misprimings I have been told that an e value that is higher than 0.01 is ok and will produce no significant amounts of mispriming. Yet I searched some and it would seem that the e value threshold limit is dependent upon the &quot;amount of information&quot; in the database.  Indeed I found that some papers cite as values lower than 0.07 to be significant already. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the criteria you use at times to judge this issue, and how do I know when to lower or increase my stringency when running a routine BLAST for the purposes of designing primers?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="1320" LastEditDate="2014-02-21T16:37:42.143" LastActivityDate="2014-03-23T16:58:04.500" Title="Primer design and BLAST E value stringency" Tags="&lt;blast&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15218" PostTypeId="2" ParentId="14998" CreationDate="2014-02-21T13:24:26.217" Score="2" Body="&lt;p&gt;Well i will like to contribute a fact which might seem a little bit out of context.&#xA;R P Feynman, the famous physicist, in his semi-autobiographical book mentioned his experiments with his consciousness and also 'dreams'. He reported that he was actually able to alter his dreams, with a little bit of practice, while he was experiencing them. Well after reading that i was quite fascinated with the possibilities and tried it myself to a fair amount of success.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover although the exact mechanism or motivation of sleep hasn't been understood it is generally accepted that 'dreams' always occur in the REM stage of sleeping. In light of the 'Restorative theory of sleep',which basically says that sleep happens to make up for all we lose during daytime, i can say that dreams are actually a byproduct of the fact that maintenance of brain cells occurs by a different pathway than normal body maintenance. So all in all saying that the 'Waking up' part of our body isn't perfect and almost everytime one part of brain 'Wakes up' before the other and contributes to the bizarre yet frequent phenomena of 'Dreams'.&lt;/p&gt;&#xA;" OwnerUserId="5808" LastActivityDate="2014-02-21T13:24:26.217" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15219" PostTypeId="2" ParentId="15216" CreationDate="2014-02-21T13:35:33.973" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.copanusa.com/products/history_of_transport/&quot; rel=&quot;nofollow&quot;&gt;This site&lt;/a&gt; (no connection) states (my emphasis):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Unlike &lt;strong&gt;Cary-Blair Medium, which is almost exclusively associated with enteric transport&lt;/strong&gt;, both Stuart and Amies Medium have been widely used for the transportation of a diverse range of clinical swab samples from sites including the eye, ear, nose, throat, skin, genital tract and wounds.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-21T13:35:33.973" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15220" PostTypeId="1" AcceptedAnswerId="15227" CreationDate="2014-02-21T13:43:32.610" Score="9" ViewCount="31882" Body="&lt;p&gt;On average, how many cells divide each day in a human being? &#xA;How long does a cell wait before dividing itself ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried to look on the internet but surprisingly the answer is difficult to find..&lt;/p&gt;&#xA;" OwnerUserId="4746" LastEditorUserId="1320" LastEditDate="2014-02-21T19:23:24.833" LastActivityDate="2017-10-05T22:22:36.593" Title="Rate of cell division in humans" Tags="&lt;cell-division&gt;&lt;cell&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15222" PostTypeId="1" AcceptedAnswerId="15240" CreationDate="2014-02-21T15:20:45.437" Score="2" ViewCount="59" Body="&lt;p&gt;We usually talk of smooth or rugged fitness landscape.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Are there any (standard) indices to measure the &quot;structure&quot; of fitness landscapes?&#xA;&lt;ul&gt;&#xA;&lt;li&gt;For example, one might consider the mean epistatic interactions (over all possible combination of loci)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-02-21T20:17:36.773" LastActivityDate="2014-02-21T22:21:09.903" Title="What indices can we use to describe fitness landscapes?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;&lt;fitness&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15223" PostTypeId="2" ParentId="15217" CreationDate="2014-02-21T15:31:34.840" Score="1" Body="&lt;p&gt;I never used BLAST for primer design, but often for finding out where a sequence came from. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the FAQ of the NCBI:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&amp;amp;PAGE_TYPE=BlastDocs&amp;amp;DOC_TYPE=FAQ&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&amp;amp;PAGE_TYPE=BlastDocs&amp;amp;DOC_TYPE=FAQ&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The lower the E-value, or the closer it is to zero, the more &quot;significant&quot; the match is. However, keep in mind that virtually identical short alignments have relatively high E values. This is because the calculation of the E value takes into account the length of the query sequence. These high E values make sense because shorter sequences have a higher probability of occurring in the database purely by chance. For more details please see the calculations in the BLAST Course.&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What they say in the papers is true, the size of your database matters in deciding how significant the match is. I can imagine that for primer design you want to be more careful with the E-values, as they often fall under: &quot;because shorter sequences have a higher probability of occurring in the database purely by chance&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps to make your decision for deciding your threshold, otherwise please give more information. &lt;/p&gt;&#xA;" OwnerUserId="5699" LastActivityDate="2014-02-21T15:31:34.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15224" PostTypeId="2" ParentId="15200" CreationDate="2014-02-21T15:45:34.680" Score="2" Body="&lt;p&gt;The situations you describe involve what is called proprioception or the feedback to the brain of where your arms and limbs are in space. As APengioun mentioned, this is a complicated undertaking and if information is restricted, for example eyes are closed then the sense of where your limbs are gets messed up. As for your title, it's not really neuronal confusion as it is confusion of the sensory system if you can call it that. This includes sensory neurons from your limbs as well as central neurons in the brain that further process your information. &lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-02-21T15:45:34.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15225" PostTypeId="2" ParentId="15188" CreationDate="2014-02-21T16:19:11.307" Score="1" Body="&lt;p&gt;Closing of the channel through muscarinic receptors involves activation of phospoholipase C and depletion of membrane phosphatidyilinositol-4,5-bisphospate which is needed for the channel to stay open. Once the channel is closed,  potassium, which is a positive ion accumulates inside the cell eventually depolarizing it or lowering its threshold for activation. Thus, blocking the extrusion of K ions results in excitation of the target neuron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this for more:&#xA;Brown, D. A., and Constanti, A. (1980). Intracellular observations on the effects of muscarinic agonists on rat sympathetic neurones. Br. J. Pharmacol. 70, 593–608.&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-02-21T16:19:11.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15226" PostTypeId="1" CreationDate="2014-02-21T16:32:28.113" Score="2" ViewCount="401" Body="&lt;p&gt;On &lt;a href=&quot;http://www.nature.com/nature/journal/v443/n7107/abs/nature05049.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt;, first column, eighth line of the introduction:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;By bringing together favourable alleles from different chromosomes, sex and recombination increase the additive genetic variance for fitness [..]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Can you please help me understanding &lt;strong&gt;why does recombination increase the additive genetic variance for fitness&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: In reaction @mgkrebbs comment, I think that given the subject of this article, when talking about different chromosomes, the authors actually referred exclusively to homologues chromosomes. My question concerns the second part of this sentence anyway: &quot;Why does sex and recombination increase the additive genetic variance for fitness&quot;?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/15239/network-of-gene-interactions&quot;&gt;Here&lt;/a&gt; is another question on the same article&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-04-14T19:50:12.840" Title="Does recombination increase the additive genetic variance for fitness?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;&lt;sex&gt;&lt;recombination&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15227" PostTypeId="2" ParentId="15220" CreationDate="2014-02-21T16:36:29.920" Score="11" Body="&lt;p&gt;My first thought was this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Apoptosis&quot;&gt;According to Wikipedia&lt;/a&gt; (citation provided)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Between 50 and 70 billion cells die each day due to apoptosis in the average human adult. For an average child between the ages of 8 and 14, approximately 20 billion to 30 billion cells die a day.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For every cell that dies a new one must be born, so there must be at least between 50 and 70 billion cell divisions to replenish these cells in an adult human (no net growth).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;But then I remembered erythrocytes&lt;/strong&gt;. &lt;a href=&quot;http://en.wikipedia.org/wiki/Red_blood_cell&quot;&gt;Wikipedia again&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Adult humans have roughly 2–3 × 10&lt;sup&gt;13&lt;/sup&gt; (20–30 trillion) red blood cells at any given time, comprising approximately one quarter of the total human body cell number&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;these cells live in blood circulation for about 100 to 120 days&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So approximately 1% of erythrocytes are destroyed every day and must be replaced. That's 2-3 x 10&lt;sup&gt;11&lt;/sup&gt; cells formed every day, which dwarfs the cells replenished due to apoptosis (5 - 7 x 10&lt;sup&gt;9&lt;/sup&gt;). &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Through this process [erythropoiesis] erythrocytes are continuously produced in the red bone marrow of large bones, at a rate of about 2 million per second in a healthy adult. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-02-21T19:22:46.357" LastActivityDate="2014-02-21T19:22:46.357" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15228" PostTypeId="2" ParentId="15217" CreationDate="2014-02-21T16:40:58.453" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/tools/primer-blast/&quot; rel=&quot;nofollow&quot;&gt;This NCBI page&lt;/a&gt; offers a primer design tool which appears to incorporate a specificity check run via BLAST. However it seems to base stringency upon degree of mismatch rather than an e value.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-21T16:40:58.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15229" PostTypeId="1" CreationDate="2014-02-21T17:24:28.920" Score="5" ViewCount="1062" Body="&lt;p&gt;Meiosis is a type of cell division that reduces the chromosome number from 2n to n to make gametes viable for reproduction in humans. I know that during meiosis, there is independent assortment and crossing over that occurs, which help to make more genetically individual organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, why don't haploid gametes go through mitosis to reproduce instead of diploid germ cells going through meiosis to create more gametes, without considering crossing over and independent assortment? This is just my opinion, but meiosis seems like a much more energy intensive process. After the germ cells go through meiosis once to create the gametes, I do not see why the gametes don't then just multiply via mitosis (again, not considering crossing over/independent assortment.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any specific reason, other than to create more genetically diverse people, that gametes do not undergo mitosis to multiply rather than germ cells undergoing meiosis to make more gametes? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry if my question is confusing, I'm just curious to what the reason is. It's probably something obvious I'm not seeing myself. :)&lt;/p&gt;&#xA;" OwnerUserId="4929" LastEditorUserId="1320" LastEditDate="2014-02-21T19:25:07.877" LastActivityDate="2018-12-12T00:10:19.667" Title="Meiosis vs. Mitosis" Tags="&lt;reproduction&gt;&lt;meiosis&gt;&lt;mitosis&gt;&lt;cell-division&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15230" PostTypeId="2" ParentId="15229" CreationDate="2014-02-21T17:38:16.907" Score="2" Body="&lt;p&gt;Couldn't fit in a comment...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To me, your question sounds like &quot;what are the possible advantages of sexual reproduction over asexual reproduction?&quot; but in the meantime you're saying that you're not interested neither in the advantage of recombination nor in the advantage of &quot;independent assortment&quot;. I don't quite see what you mean by &quot;independent assortment&quot; in this context.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just want to say some words about some &quot;proximate&quot; possible explanations of the evolution of sex. It's been suggested that meiosis have evolved in order to repair damage in double stranded DNA. Also, it's been suggested that meiosis is important for the problems of telomere length also.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might be interested to have a look to the evolution of bi-phasic life cycles and, more globally speaking to the evolution of sex.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-03-23T20:05:23.120" LastActivityDate="2014-03-23T20:05:23.120" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15231" PostTypeId="2" ParentId="15214" CreationDate="2014-02-21T18:10:38.120" Score="2" Body="&lt;p&gt;The vessel diameter is the most principal determinant to control resistance. Compared to other smaller vessels in the body, the artery has a much bigger diameter (4 mm), therefore the resistance is low.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, flow rate (Q) is also the product of the cross-sectional area of the vessel and the average velocity (Q=AV). Flow rate is directly proportional to the pressure drop in a tube or in this case a vessels, although there are other factors of blood vessels that contribute towards the difference in pressure drop in bifurcations of blood vessels. These include viscosity, length of the vessel, and radius of the vessel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Factors that determine the flow's resistance as described by Poiseuille’s relationship: ∆P=8µlQ/πr4:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;∆P: Pressure drop/gradient µ: Viscosity l: length of tube. In the case of vessels with infinitely long lengths, l is replaced with diameter of the vessel. Q: flow rate of the blood in the vessel r: radius of the vessel &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming steady, laminar flow in the vessel, the blood vessels behavior is similar to that of a pipe. For instance if p1 and p2 are pressures are at the ends of the tube, the pressure drop/gradient is (p1−p2)/l =∆P.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the arterioles blood pressure is lower than in the major arteries. This is because velocity of flow is increased with decrease in diameter and vice versa.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Blood_pressure_drop_across_major_arteries_to_capillaries&quot; rel=&quot;nofollow&quot;&gt;http://en.m.wikipedia.org/wiki/Blood_pressure_drop_across_major_arteries_to_capillaries&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is important as for efficient exchange at the capillary bed pressure and flow need to be much lower. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-21T18:10:38.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15232" PostTypeId="2" ParentId="15226" CreationDate="2014-02-21T18:43:47.677" Score="4" Body="&lt;p&gt;This is a little tricky. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all lets be clear about 'bringing together favorable alleles' (or any alleles) represented by site mutations on 2 chromosomes:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;--------A------------------&#xA;             X     &#xA;------------------B--------&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;If the two dashed lines are two copies of the same chromosome, then a recombination event at X may produce: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;--------A---------B--------&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Allowing both A and B to be passed along to offspring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any given case of recombination might actually harm resulting offspring. But in cases where A and B together are beneficial, over the course of generations you will find AB genotype combinations show up more frequently in the population because of selection and competition. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly each individual variant experiences some selection for fitness and many are lost.  Because of this, recombination will typically put two or more such variants together onto a single chromosome.  Recombination allows for individual mutations of benefit to pool together and collect into a single place.  This multiplies the chance that stronger combinations of mutations will show in the gene pool.  This increases the fitness variance - the most powerful combinations are more beneficial than any single variant alone.  On the other end detrimental combinations will also make some individuals exceptionally weak.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So its not just recombination, but recombination &lt;em&gt;and&lt;/em&gt; selection which create favorable combinations of alleles in populations.  The link you give discusses how when selection is not strong, recombination is not so great, but we never seem to lose recombination where these conditions don't hold sway. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By comparison, consider a simple case where recombination does not occur where there is an A genotype and then one waits for B to show up on the same chromosome by random mutation.  That would take perhaps thousands or even millions of generations before such a thing happens at random.  Recombination is a powerful accelerator of evolution. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-04-14T19:50:12.840" LastActivityDate="2014-04-14T19:50:12.840" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="15233" PostTypeId="2" ParentId="15180" CreationDate="2014-02-21T19:21:25.450" Score="1" Body="&lt;p&gt;If you accept the nowadays prevailing &lt;a href=&quot;http://en.wikipedia.org/wiki/Ecdysozoa&quot; rel=&quot;nofollow&quot;&gt;Ecdysozoa&lt;/a&gt;-hypothesis the relationships are as follows:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;               ____ Drosophila&#xA;              |&#xA;        ______|&#xA;       |      |____ C. elegans&#xA;       |&#xA;  -----|       ____ Human&#xA;       |      |&#xA;       |______|&#xA;              |____ Mouse&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;According to the more traditional views (the &lt;a href=&quot;http://en.wikipedia.org/wiki/Ecdysozoa#Coelomata_Hypothesis&quot; rel=&quot;nofollow&quot;&gt;Coelomata&lt;/a&gt;-hypothesis):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;         _______________ C. elegans&#xA;        |&#xA;    ----|     __________ Drosophila&#xA;        |    |&#xA;        |____|       ____ Human&#xA;             |      |&#xA;             |______|&#xA;                    |____ Mouse&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;(Note that these trees have the same unrooted topologies)&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-02-21T19:21:25.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15234" PostTypeId="2" ParentId="15112" CreationDate="2014-02-21T19:29:47.860" Score="2" Body="&lt;p&gt;I personally use more frequently Geneious for most of the basic every-day manipulations (my university bought a license), but I would recommend &lt;a href=&quot;http://ugene.unipro.ru/&quot; rel=&quot;nofollow&quot;&gt;Ugene&lt;/a&gt;: it's free, open-source, cross-platform and supports batching and scenarios.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-02-22T21:33:04.427" LastActivityDate="2014-02-22T21:33:04.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15235" PostTypeId="2" ParentId="15165" CreationDate="2014-02-21T19:37:37.563" Score="6" Body="&lt;p&gt;Physalia and &lt;a href=&quot;http://en.wikipedia.org/wiki/Siphonophorae&quot; rel=&quot;noreferrer&quot;&gt;Siphonophorans&lt;/a&gt; in general are multicellular Metazoans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the whole discussion is about modularity on the level of individuals: Siphonophorans are colonial organisms, which means they are composed of multiple individual polyps and medusae. This is in fact quite common among &lt;a href=&quot;http://en.wikipedia.org/wiki/Hydrozoa&quot; rel=&quot;noreferrer&quot;&gt;Hydrozoa&lt;/a&gt;, but in Siphonophora the degree of integrity and function division among the components is of extraordinary level.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-02-21T19:37:37.563" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15236" PostTypeId="1" AcceptedAnswerId="15237" CreationDate="2014-02-21T20:32:51.140" Score="3" ViewCount="9547" Body="&lt;p&gt;DNA prep protocols often include a final precipitation step with alcohol, often isopropanol, where the DNA must be kept in the alcohol, at a low temperature such as -20C or -70C, often overnight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the point of keeping it at low temperature? Is lower better? At what point do you see diminishing returns?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about the time? Is overnight really necessary, or would, say, an hour suffice? Do lower temperatures result in quicker precipitation?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-02-21T20:59:12.717" Title="Isopropanol precipitation of DNA - duration and magnitude of cold storage" Tags="&lt;biochemistry&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15237" PostTypeId="2" ParentId="15236" CreationDate="2014-02-21T20:50:13.913" Score="4" Body="&lt;p&gt;For the precipitation you use different reagents: First you add salt under slightly acidic conditions to make sure that the DNA precipitates in a less polar environment. This is achieved by adding alcoholes like ethanol or isopropanol.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is commonly thought that a incubation at low temperatures enhances the results, but this is interestingly not true. There is a paper from the Bethesda Research Laboratories which is called &quot;&lt;a href=&quot;http://www.lifetechnologies.com/content/dam/LifeTech/migration/en/filelibrary/pdf/focus.par.56415.file.dat/focus%20volume%207%20issue%204.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ethanol Precipitation of DNA.&lt;/a&gt;&quot; which analyzes these relationships (temperature, time and alcohol concentration) in great detail, its definitely worth reading.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 1-3 from this paper shows the influence for Ethanol (but I am pretty sure that this is not much different for isopropanol):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/C8i8r.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would prefer ethanol precipitation to ispropanol whenever possible. Isopropanol co-precipates salts, so you have to wash a few times with 70% ethanol and it is less volatile than ethanol, so the drying step takes longer. Its also less effective cleaning organic compounds like phenol away and sometimes the pellets are harder to see.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other it can be useful when you have to deal with large volumes, since you only need 0,7 volumes of isopropanol compared with 2,5 volumes of ethanol. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Precipitations with Isopropanol are usually not incubated but centrifuged directly after mixing. Here is a protocol from my lab (which originally came from Qiagen, if I remember correct):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Adjust the salt concentration, for example, with sodium acetate (0.3&#xA;   M, pH 5.2, final concentration) or ammonium acetate (2.0–2.5 M,&#xA;   final concentration).&lt;/li&gt;&#xA;&lt;li&gt;Add 0.6–0.7 volumes of room-temperature isopropanol to the DNA&#xA;       solution and mix well.&lt;/li&gt;&#xA;&lt;li&gt;Centrifuge the sample immediately at 10,000–15,000 x g for 15–30 min&#xA;   at 4°C&lt;/li&gt;&#xA;&lt;li&gt;Carefully decant the supernatant without disturbing the pellet.&lt;/li&gt;&#xA;&lt;li&gt;Wash the DNA pellet by adding 1–10 ml (depending on the size of the&#xA;preparation) of room-temperature 70% ethanol. This removes&#xA;co-precipitated salt and replaces the isopropanol with the more&#xA;volatile ethanol, making the DNA easier to redissolve.&lt;/li&gt;&#xA;&lt;li&gt;Centrifuge at 10,000–15,000 x g for 5–15 min at 4°C&lt;/li&gt;&#xA;&lt;li&gt;Repeat the washing and centrifugation steps once more.&lt;/li&gt;&#xA;&lt;li&gt;Carefully decant the supernatant without disturbing the pellet.&lt;/li&gt;&#xA;&lt;li&gt;Air-dry the pellet for 5–20 min (depending on the size of the&#xA;pellet).&lt;/li&gt;&#xA;&lt;li&gt;Redissolve the DNA in a suitable buffer.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-02-21T20:59:12.717" LastActivityDate="2014-02-21T20:59:12.717" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="15238" PostTypeId="1" CreationDate="2014-02-21T22:00:06.400" Score="1" ViewCount="118" Body="&lt;p&gt;I read that one hard step in algae oil extraction is to rupture (or fracture) the cell walls to get the contents inside. Some people use chemical methods; some use sonication or mechanical forces.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder why nobody is talking about using viruses to accomplish this task? Viruses destroy the cells and release clones of itself. Some article states that there are plenty of unknown viruses in seawater. I'm sure a major part of it infects algae.&lt;/p&gt;&#xA;" OwnerUserId="5819" LastEditorUserId="3340" LastEditDate="2015-06-04T11:46:09.557" LastActivityDate="2015-06-04T11:46:09.557" Title="Can viruses be used to extract oil from algae?" Tags="&lt;marine-biology&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15239" PostTypeId="1" AcceptedAnswerId="16279" CreationDate="2014-02-21T22:08:21.577" Score="7" ViewCount="269" Body="&lt;p&gt;From &lt;a href=&quot;http://www.nature.com/nature/journal/v443/n7107/abs/nature05049.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt;, first page, middle of the second column:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Even if harmful alleles do not become fixed, they can still reduce the efficacy of selection on neighbouring loci through a process called Hill–Robertson interference. This effect occurs because individuals bearing deleterious mutations are less likely to survive and reproduce, reducing the number of individuals that contribute genetically to the future population. This reduces the effective population size witnessed by a focal locus&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't understand the link between the Hill-Robertson effects and the effective population size. Why would the effective population size be greater in absence of Hill-Robertson effects? Can you please make this link clear to me?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/15226/does-recombination-increase-the-additive-genetic-variance-for-fitness&quot;&gt;Here&lt;/a&gt; is another question on the same article.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-11-03T09:10:50.203" Title="Hill-Roberston effects and effective population size" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;population-dynamics&gt;&lt;population-genetics&gt;&lt;recombination&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15240" PostTypeId="2" ParentId="15222" CreationDate="2014-02-21T22:21:09.903" Score="2" Body="&lt;p&gt;This paper uses 4 metrics for discreet landscapes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240586/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240586/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Deviation from additivity: How much your genes interact (normalized). Fitness in a purely additive landscape with three genes, for example, is F=f(x)+g(y)+h(z) where f,g, and h are each functions of one variable (the x,y, and z &quot;genes&quot;/coordinates). Deviation measures how far from additivity the fitness is. Higher is not always rougher but it is &quot;trickier&quot; since the effects of changing a gene depend on other genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Peak fraction: The % of points that are local peaks (discreet landscapes only), higher is rougher.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tree component: The % of points that have at most one neighbor of higher fitness. Lower is rougher and indicates that there is a choice as to which direction to travel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;% monotonic paths: The fraction of paths (of all &lt;em&gt;possible shortest&lt;/em&gt; paths from a given point to the peak) that don't go downhill. This calculation is averaged over all starting points in the landscape (excluding the peak). Lower is rougher.&lt;/p&gt;&#xA;" OwnerUserId="4321" LastActivityDate="2014-02-21T22:21:09.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15241" PostTypeId="2" ParentId="15238" CreationDate="2014-02-21T22:50:52.223" Score="1" Body="&lt;p&gt;A virus has to infect the cell, take over the cell machinery to make more virus, and then is might lyse the cell.  And then you have to wait for more virus to do that again to more cells, and you have to keep the algae alive all that time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chemical or mechanical shearing would be much faster, and you don't have to run the risk of virus floating around and getting into stocks that you don't want to kill right now.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-02-21T22:50:52.223" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15242" PostTypeId="2" ParentId="15238" CreationDate="2014-02-21T23:21:52.277" Score="5" Body="&lt;p&gt;Viruses hijack the hosts translational machinery, forcing the host to downregulate translation of other proteins in favor of viral proteins. Your cells will eventually lyse, but in the meantime they would not be producing the enzymes required to make whatever product it is you're trying to get, likely resulting in low yields that are contaminated with virus.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-02-21T23:21:52.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15244" PostTypeId="2" ParentId="13841" CreationDate="2014-02-22T00:12:15.530" Score="2" Body="&lt;p&gt;In short, yes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best way to think about ageing is as an accumulation of age-related disorders. Telomere loss is one of many cellular defects that accumulate with age. Other defects include oxidative stress, accumulation of amyloid proteins and metabolic dysfunction. While these are all likely related in some way, there is no evidence that specifically preventing telomere shortening would stop ageing. In fact, while telomere length is roughly correlated with age, it is not well correlated with such age-related disorders as &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278593/&quot; rel=&quot;nofollow&quot;&gt;Alzheimer's disease&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it is clear that loss of telomeres is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21113150&quot; rel=&quot;nofollow&quot;&gt;a problem&lt;/a&gt;. Therapies that restore telomerase function will always run the risk of causing cancer. Most cells in the human body &lt;a href=&quot;http://jco.ascopubs.org/content/18/13/2626.long&quot; rel=&quot;nofollow&quot;&gt;do not express telomerase&lt;/a&gt;, and those that do often do so transiently during times of replication. Introducing functional telomerase into new cells could only increase the risk of developing cancer. A generalized cure for cancer would make designing anti-telomere shortening therapies much easier, because listing cancer as a side effect would not be as ridiculous as it is today.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The way I see it is that cancer is just one of those many age-related disorders that comprises the term &quot;ageing.&quot; Especially colorectal cancers have a &lt;a href=&quot;http://www.cancer.org/cancer/colonandrectumcancer/detailedguide/colorectal-cancer-risk-factors&quot; rel=&quot;nofollow&quot;&gt;strong association&lt;/a&gt; between onset and age, hence all the colonoscopies recommended after age 50. If colorectal cancer is so well associated with age, and there is a mechanism that ties the formation of cancer to the passage of time (the build up of deleterious mutations during the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK1566/&quot; rel=&quot;nofollow&quot;&gt;many divisions&lt;/a&gt; that occur in colonic crypts), then I think its safe to consider it a part of ageing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to stop ageing, you have to stop all of the age-related disorders, and that includes cancer.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-02-22T00:12:15.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15245" PostTypeId="1" CreationDate="2014-02-22T02:52:01.127" Score="0" ViewCount="40" Body="&lt;p&gt;How can we define ageing from a biological standpoint without making an appeal to chronological age?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Related, but less important, are there any metrics we can use to determine someone's biological age other than their chronological age?&#xA;Telomere length is an obvious candidate, but &lt;a href=&quot;http://biomedgerontology.oxfordjournals.org/content/66A/2/202.full&quot; rel=&quot;nofollow&quot;&gt;it is imperfect&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-02-22T02:52:01.127" Title="Can we define biological age?" Tags="&lt;senescence&gt;&lt;telomere&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2014-12-03T11:17:51.877" ContentLicense="CC BY-SA 3.0" />
  <row Id="15247" PostTypeId="1" AcceptedAnswerId="15251" CreationDate="2014-02-22T08:49:02.217" Score="4" ViewCount="184" Body="&lt;p&gt;I am not a biology student, but just want to know if GULO gene are present only in mammals or all species possess it ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And is GULO gene active in human fetus?&lt;/p&gt;&#xA;" OwnerUserId="5823" LastEditorUserId="5823" LastEditDate="2014-02-22T09:07:13.467" LastActivityDate="2020-05-12T20:32:55.823" Title="GULO only for mammals?" Tags="&lt;genetics&gt;&lt;mammals&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15248" PostTypeId="1" CreationDate="2014-02-22T09:31:24.583" Score="0" ViewCount="184" Body="&lt;p&gt;The O antigen is synthesised by Pathology islands (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2223840/&quot; rel=&quot;nofollow&quot;&gt;PAI&lt;/a&gt;).&#xA;O antigen may be a factor why Shigella survives the passage through host defences.&#xA;I am interested in which step of pathogenesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are Bacterial ATPase (actin tail, intracellular movement), M-cell (enter) ...-&gt; extracellular movement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Where can the O antigen affect in Shigella?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1320" LastEditDate="2014-02-22T10:00:37.863" LastActivityDate="2014-02-22T10:00:37.863" Title="Shigella's O antigen (PAI synthesised) and passage through host defences" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15249" PostTypeId="2" ParentId="15248" CreationDate="2014-02-22T09:58:55.420" Score="2" Body="&lt;p&gt;The outer layer of the cell envelope of Gram negative bacteria is the outer membrane, and the outer leaflet of that membrane is composed largely of &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipopolysaccharide&quot; rel=&quot;nofollow&quot;&gt;lipopolysaccharide&lt;/a&gt; (LPS). The O antigen is the name given to the outer glycan portion of the LPS - there is a nice diagram at the Wikipedia article I have linked to which makes this clear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because this structure is exposed at the bacterial surface it is a target for the immune response, and the serotyping of many bacterial species incorporates this O serotype information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Table 1 of the review that you link to indicates that PAI SHI-O carries genes &lt;em&gt;gtrA,B,V&lt;/em&gt; (originally derived from a bacteriophage - not unusual for a pathogenicity island). These genes encode enzymes which modify the O-antigen via a glucosylation reaction. Presumably this helps the bacteria adapt to an immune response via a shift in serotype. It may be, for example, that an invading population of &lt;em&gt;Shigella&lt;/em&gt; includes variants which do or do not express these genes so that a subpopulation can arise which is not recognised by an existing immune response. This is what is meant in Table 1 of the article by &quot;evasion of host immune response&quot;. It is a common strategy - examples in &lt;em&gt;Salmonella&lt;/em&gt; (flagellar phase variation) and &lt;em&gt;Helicobacter&lt;/em&gt; (induced transformation) spring to mind.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-22T09:58:55.420" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15250" PostTypeId="1" AcceptedAnswerId="15260" CreationDate="2014-02-22T10:11:00.313" Score="2" ViewCount="4871" Body="&lt;p&gt;I tested this out with my friends, and I find that after they hold their breath and can't hold it anymore, they exhale air, instead of inhaling air.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, they all try to inhale in as much air as possible before starting to hold their breath. When I told them to exhale as much air as possible before starting to hold their breath, they inhaled air after they can't hold it anymore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's understandable that when one exhales then holds his breath, he needs air and thus he inhales afterwards. But when one inhales then holds his breath, shouldn't he inhale again after &quot;using up all that air he inhaled before holding hi breath&quot;?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2015-12-17T00:52:14.520" Title="Why do we exhale after we hold our breath?" Tags="&lt;physiology&gt;&lt;respiration&gt;&lt;breathing&gt;" AnswerCount="3" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15251" PostTypeId="2" ParentId="15247" CreationDate="2014-02-22T10:15:59.330" Score="8" Body="&lt;p&gt;GULO encodes &lt;a href=&quot;http://en.wikipedia.org/wiki/L-gulonolactone_oxidase&quot; rel=&quot;noreferrer&quot;&gt;L-gulonolactone oxidase&lt;/a&gt; which catalyses a step in the biosynthetic pathway to ascorbic acid (vitamin C).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did a BLAST search at NCBI using the mouse GULO protein as probe, excluding mammals, and I saw highly significant hits in reptiles, birds, sea urchins, fungi and bacteria. I conclude that this enzyme, (or very close relatives) is ubiquitous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans (and other primates; also guinea pigs and the Dalmatian coach hound) have a defective GULO gene and so require dietary ascorbate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the gene is non-functional in humans it isn't expressed in the foetus.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-22T10:15:59.330" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15252" PostTypeId="1" CreationDate="2014-02-22T10:18:31.073" Score="11" ViewCount="3770" Body="&lt;p&gt;Most accounts I read involving action potentials and synapses and the like tend to focus mostly on the action potential as a mere automatic reaction to another similar event happening upstream.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a more theoretical point of view, it would be nice to know if (and under what circumstances) a neuron would be able to generate an action potential, &lt;em&gt;in the absence of an upstream neuron firing first&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect that the nervous system, at least in higher animals, is not simply a relay system that processes and transmits information from senses to actuators like the limbs. The relay system picture is fine for short-timescale, reactionary behavior but it is hard to imagine any longer-timescale learning processes happening this way. This is what motivates my question. &lt;/p&gt;&#xA;" OwnerUserId="625" LastEditorUserId="9943" LastEditDate="2015-04-07T14:11:32.670" LastActivityDate="2019-07-27T20:33:37.310" Title="Does a neuron ever generate an action potential without stimuli?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15253" PostTypeId="2" ParentId="15252" CreationDate="2014-02-22T11:39:53.607" Score="7" Body="&lt;p&gt;Neurones fire when they're sufficiently depolarised past their threshold. In the sensory system this is in response to an external stimuli which sets of a chain reaction. Then motor neurones may relay signals back and in this case the signal or initial depolarisation is occurring in the brain. However this is still caused by a stimuli even if indirectly. If we take an action it is generally because we thought which action we should take because of some sort of stimuli e.g. we are cold so we put a coat on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But anything which depolarises neurones can set of an action potential. However there's always something which causes it to depolarise, perhaps a drug or a stimulus or another neurone. If any of these don't count as a stimuli depending on your definition, there's your answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or perhaps if you consider cardiac muscle which can intrinsically depolarise. Not a neurone but there's an action potential. They just naturally depolarise over time and action potentials are set of regularly with no stimulus required. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for learning, where the structure of neurones can change so they connect to new neurones or not to old neurones or vary in the strength of their connection. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-22T11:39:53.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15254" PostTypeId="2" ParentId="15250" CreationDate="2014-02-22T11:46:19.230" Score="3" Body="&lt;p&gt;Good question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you inhale on top of inhaled air this is more work. There is more dead air, air which is not as useful due to the lower concentration gradient. And we breathe more to exhale carbon dioxide than we require oxygen. Low oxygen levels only push us to breathe when oxygen levels are a good deal lower, however tiny changes in carbon dioxide causes changes in our ventilation rate almost immediately. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also more work as our muscles require more energy to inflate an already inflated chest. This is the case in COPD patients. Try this: take a deep breath in and now holding that air in, breathe normally on top of that air. Feel how difficult it is and how breathless you feel. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-22T11:46:19.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15256" PostTypeId="1" AcceptedAnswerId="15258" CreationDate="2014-02-22T12:06:26.357" Score="0" ViewCount="153" Body="&lt;p&gt;I could not spell the agar [gonoline-uroline] which I heard yesterday.&#xA;My spelling is so wrong that I could not find it in Google.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the right spelling for this agar?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-22T14:44:16.497" LastActivityDate="2014-02-23T01:47:55.303" Title="What is the right spelling for this agar?" Tags="&lt;homework&gt;&lt;microbiology&gt;" AnswerCount="2" CommentCount="4" ClosedDate="2014-02-24T15:38:36.117" ContentLicense="CC BY-SA 3.0" />
  <row Id="15257" PostTypeId="1" AcceptedAnswerId="15280" CreationDate="2014-02-22T12:17:09.313" Score="1" ViewCount="56" Body="&lt;p&gt;I heard this fact that you can use some [hypertriade] for vibrio cholera diagnosis which has compontents&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;sucrose (yellow)&lt;/li&gt;&#xA;&lt;li&gt;mannose (yellow)&lt;/li&gt;&#xA;&lt;li&gt;arabinose (do not ferment; stay dark pink)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I did not find this hypertriade agar on Google. &#xA;It reminds me of Egg Yolk Agar, but I think cannot be it because of the arabinose.&#xA;Otherwise, it seems to be similar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the best detection medias for cholera?&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-02-24T14:46:46.860" LastActivityDate="2014-02-24T14:46:46.860" Title="What are the best detection medias for cholera?" Tags="&lt;homework&gt;&lt;microbiology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15258" PostTypeId="2" ParentId="15256" CreationDate="2014-02-22T12:34:44.883" Score="3" Body="&lt;p&gt;The first word is ok, there is agar called Gonoline, the second one is probably Euroline and there is an agar with this word too (Liver IgG Euroline).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've found both of them on the &lt;a href=&quot;http://www.marigoitalia.com/public/reagenti.txt&quot; rel=&quot;nofollow&quot;&gt;Italian site&lt;/a&gt;, probably the are not one, but two agars.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2014-02-22T12:34:44.883" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15259" PostTypeId="2" ParentId="15252" CreationDate="2014-02-22T13:30:31.533" Score="7" Body="&lt;p&gt;There are many spontaneously active neurons. This has been known for many years [1]. There are multiple sources that could make a neuron spontaneously fire. In cortical culture of neurons where there is no external input to the system, neurons are spontaneously active, for example [2]. Of course, there are spontaneous vesicle releases from synapses (miniature EPSC) in this case, so you might say there are still some &quot;input&quot; to each neuron. However, even if you block synaptic transmissions, and some neurons do fire spontaneously [3]. It could be ion channels, or some internal chemical process. If you include the network level spontaneous dynamics, there are even more possible ways to have active neural system without any stimulus.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Alving BO (1968) Spontaneous activity in isolated somata of Aplysia pacemaker neurons. J Gen Physiol 51: 29-45.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Potter, S. M. and Demarse, T. B. (2001). A new approach to neural cell culture for long-term studies. Journal of Neuroscience Methods, 110:17-24.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Häusser, M., Raman, I. M., Otis, T., Smith, S. L., Nelson, A., du Lac, S., Loewenstein, Y., Mahon, S., Pennartz, C., Cohen, I., and Yarom, Y. (2004). The beat goes on: Spontaneous firing in mammalian neuronal microcircuits. The Journal of Neuroscience, 24(42):9215-9219.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2014-10-31T13:53:03.150" LastActivityDate="2014-10-31T13:53:03.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15260" PostTypeId="2" ParentId="15250" CreationDate="2014-02-22T14:04:31.830" Score="6" Body="&lt;p&gt;This is more about basic physics than biology. When you hold your breath, you normally take in one last long breath and keep it in as long as possible, Your lungs are therefore already full of gas (remember that the oxygen used by our lungs is only ~22% of the total volume of air you inhale). Therefore, when you release that breath and want to take in a new one you need to first empty your lungs out in order to refill them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, you need to have your lungs empty in order to be able to expand them and draw in more air. There is no biological reason for any of this, it is the same principle as trying to use a turkey baster:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/6GrOT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you use it once and pull up some liquid into it, you will have to let air out before you can use it again. Your lungs work in the same way. Test this by exhaling all the air from your lungs and then holding your breath without inhaling. When you want to start breathing again, you'll be able to breathe directly in without needing to exhale first.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-02-26T13:01:56.983" LastActivityDate="2014-02-26T13:01:56.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15261" PostTypeId="1" AcceptedAnswerId="15269" CreationDate="2014-02-22T14:45:47.110" Score="0" ViewCount="601" Body="&lt;p&gt;I was heard that this combination first Gonoline and other culture another culture on Euroline is good one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the benefit of using Gonoline-Euroline in combination?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-23T01:58:23.143" Title="What is the benefit of using Gonoline-Euroline in combination?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ClosedDate="2014-02-23T19:21:09.687" ContentLicense="CC BY-SA 3.0" />
  <row Id="15262" PostTypeId="1" AcceptedAnswerId="15263" CreationDate="2014-02-22T15:37:16.937" Score="6" ViewCount="462" Body="&lt;p&gt;Plants transport food mostly in the form of disaccharides like sucrose but humans transport them in the form of a monosaccharide -  glucose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the reason behind this ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1320" LastEditDate="2014-02-22T16:30:08.580" LastActivityDate="2017-03-10T19:01:38.367" Title="Why do humans circulate monosaccharides instead of disaccharides as in plants?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;physiology&gt;&lt;botany&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15263" PostTypeId="2" ParentId="15262" CreationDate="2014-02-22T15:39:18.837" Score="2" Body="&lt;p&gt;One of the reasons could be  -&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;humans and many other animals have active circulatory systems,&#xA;  there is little need for targeting sugars for specific parts of the&#xA;  body. The entire body would rapidly reach equilibrium with the glucose&#xA;  level of the bloodstream, and thus there likely never evolved the need&#xA;  to target specific organs to receive sugars via disaccharides&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source : &lt;a href=&quot;http://www.newton.dep.anl.gov/askasci/mole00/mole00218.htm&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other reason could be that disaccharides are harder to transfer inside the cells than monosaccharides.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1320" LastEditDate="2014-02-22T16:34:59.893" LastActivityDate="2014-02-22T16:34:59.893" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15264" PostTypeId="2" ParentId="3510" CreationDate="2014-02-22T17:03:32.133" Score="4" Body="&lt;p&gt;For two reasons: Women are&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;exposed to estrogen,¹ and&lt;/li&gt;&#xA;&lt;li&gt;the lobules in a woman's breast go through 4 stages:&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;Type 1: prepubescent &amp;amp; Type 2: pubescent&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fghqv.gif&quot; alt=&quot;types 1 &amp;amp; 2 lobules&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Type 3: reproductive &amp;amp; Type 4: lactation lobules²&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ISWz9.gif&quot; alt=&quot;types 3 &amp;amp; 4 lobules&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The sooner a woman progresses to Type 3 and Type 4 lobules, the lower her risk of cancer. An interruption of the progression from Type 1 to Type 4 lobules (such as with a late-term miscarriage or induced abortion) increases the risk of cancer, as cancer generally arises in Type 1 and Type 2 lobules.³&lt;/p&gt;&#xA;&lt;h3&gt;References&lt;/h3&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Miller, Katherine. &lt;a href=&quot;http://jnci.oxfordjournals.org/content/95/2/100.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Estrogen and DNA damage: The silent source of breast cancer?&lt;/a&gt; &lt;em&gt;J Natl Cancer Inst&lt;/em&gt; 2003: 95:100-102.&lt;/li&gt;&#xA;&lt;li&gt;Schwartz, Shires, Spencer, Principles of Surgery (McGraw Hill) Russo J, Tay LK, Russo IH. &lt;a href=&quot;http://link.springer.com/article/10.1007/BF01805718&quot; rel=&quot;nofollow noreferrer&quot;&gt;Differentiation of the mammary gland and susceptibility to carcinogenesis&lt;/a&gt;. &lt;em&gt;Breast Cancer Res &amp;amp; Treatment&lt;/em&gt; 1982;2:5-73.&lt;/li&gt;&#xA;&lt;li&gt;Daling JR, Malone DE, Voigt LF, White E, Weiss NS. &lt;a href=&quot;http://jnci.oxfordjournals.org/content/86/21/1584.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Risk of breast cancer among young women: relationship to induced abortion&lt;/a&gt;. &lt;em&gt;J Natl Cancer Inst&lt;/em&gt; 1994;86:1584-92.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5825" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-02-22T17:17:13.910" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15265" PostTypeId="1" AcceptedAnswerId="15266" CreationDate="2014-02-22T17:14:28.867" Score="0" ViewCount="52" Body="&lt;p&gt;From &lt;a href=&quot;http://www.uptodate.com/contents/multiple-myeloma-treatment-beyond-the-basics&quot; rel=&quot;nofollow&quot;&gt;the UpToDate article on multiple myeloma&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In most people, chemotherapy partially controls multiple myeloma;&#xA;  rarely, chemotherapy leads to complete remission.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Transplantation, when successful, prolongs survival, leads to a&#xA;  remission, and, infrequently, cures multiple myeloma. However,&#xA;  transplantation has several limitations. The high-dose chemotherapy&#xA;  given before transplantation usually fails to kill all of the plasma&#xA;  cells, allowing the condition to relapse after transplantation. Such&#xA;  treatment also puts the patient at risk for serious infections and&#xA;  bleeding, which can be fatal.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.uptodate.com/home/about-us&quot; rel=&quot;nofollow&quot;&gt;UpToDate is used by 700,000+ physicians worldwide&lt;/a&gt;; it's not alternative medicine. Thus, if even mainstream medicine recognizes the relative ineffectiveness of chemo and transplantation for multiple myeloma, why do they do it?&lt;/p&gt;&#xA;" OwnerUserId="5825" LastActivityDate="2014-02-22T18:46:03.723" Title="Why do doctors do chemo or transplantation for cancers that don't respond well to these treatments?" Tags="&lt;cancer&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-02-22T20:18:58.580" ContentLicense="CC BY-SA 3.0" />
  <row Id="15266" PostTypeId="2" ParentId="15265" CreationDate="2014-02-22T18:46:03.723" Score="2" Body="&lt;p&gt;To long for a comment: Its more an ethical thing I would say. &#xA;I do research which is connected to melanoma - a cancer which is notoriously treatment resistant, once it started moving. Until very recently there was only one chemotherapeuticum which has pretty low (around 20%) response rates. It was usually tried anyway because its possible that the patients belong to this 20% which respond. If not, treatment was usually not prolonged. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think its something similiar here. The other problem for chemotherapy is that it is cytotoxic (until we got the small molecule inhibitors which are tested and used today) and the problem is to kill the cancer cells (all when possible) while you leave the rest of the body as unaffected as possible. To get this balance is hard (people tend to react differently to chemotherapy). The other problem is that cancers are not homogenous. So its possible that 99.9% of the cells present respond to chemotherapy and get killed, while a few acquired an additional mutation, which gives them an advantage. The conditions of chemotherapy are very selective.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-22T18:46:03.723" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15268" PostTypeId="2" ParentId="15256" CreationDate="2014-02-23T01:28:19.550" Score="0" Body="&lt;p&gt;Looking at your two questions together, I think you mean gonoline media, followed by blood agar.  To be honest, I feel like this question would be off topic.  You may be referring to a specific blood agar, like Chocolate agar, but that would be wild speculation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gonoline media is often used for Neisseriaceae, so perhaps you are specifically looking at Gonorrhea?&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2014-02-23T01:47:55.303" LastActivityDate="2014-02-23T01:47:55.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15269" PostTypeId="2" ParentId="15261" CreationDate="2014-02-23T01:41:37.557" Score="3" Body="&lt;p&gt;Looking at your other question, I think there's some serious editing that needs to be done to clarify this question.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still I think there is a quick and easy answer to your question.  Gonoline media makes an excellent transfer media.  If you are out in the field some where and want to take a swab for further analysis, you could easily choose a gonoline media for transport.  Then you would want to follow that up with some selective blood agars that might show a pathogenic species that you were looking for.  Thus to use gonoline media with any other medium, is merely to preserve your sample for plating on your diagnostic media/agar later.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, looking at your related question, I could only guess that you meant chocolate agar, because you might be hunting Neisseriaceae (which you should put in the question if you are).&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2014-02-23T01:58:23.143" LastActivityDate="2014-02-23T01:58:23.143" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15270" PostTypeId="1" CreationDate="2014-02-23T04:06:12.263" Score="1" ViewCount="90" Body="&lt;p&gt;Animal -&gt; bacterial gene transfer seems easier than bacteria -&gt; animal (rotifers are an interesting exception); there are bacteria live in close contact to us but our germ-line cells are protected. Given enough time, even free-living bacteria would start to pick up some of our genes (once the introns were lost).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this true? If so, do we see animal/plant genes gradually spreading into single cell organisms as time goes on (although &quot;seeing&quot; this would be difficult)? Is this effect &quot;significant&quot; for evolution in microbes? &lt;/p&gt;&#xA;" OwnerUserId="4321" LastActivityDate="2014-03-25T12:58:30.323" Title="Multicellular organisms as DNA banks" Tags="&lt;horizontal-gene-transfer&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15271" PostTypeId="1" CreationDate="2014-02-23T05:41:42.477" Score="3" ViewCount="283" Body="&lt;p&gt;The following is a minor clarification that I want to make, since it is rarely addressed directly in most of the texts I have gone through.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;strong&gt;C₄&lt;/strong&gt; pathway, the chloroplasts are dimorphic, that is, the bundle sheath chloroplasts contain &lt;strong&gt;RuBisCO&lt;/strong&gt;, but lack grana and can hence perform only the light-independent reactions. The mesophyll chloroplasts lack &lt;strong&gt;RuBisCO&lt;/strong&gt; but contain the granal apparatus to perform light reactions for synthesis of &lt;strong&gt;ATP&lt;/strong&gt; and &lt;strong&gt;NADPH&lt;/strong&gt;. The bundle sheath cells are impervious to gaseous transport (to prevent the entry of &lt;strong&gt;O₂&lt;/strong&gt;), but recieve the required &lt;strong&gt;CO₂&lt;/strong&gt; by the intake of an organic acid produced by &lt;strong&gt;CO₂&lt;/strong&gt; fixation by the mesophyll cells.   &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But, to effect the Calvin cycle in the bundle sheath cells, it&#xA;  requires a high concentration of the light reaction products, i.e.,&#xA;  &lt;strong&gt;ATP&lt;/strong&gt; and &lt;strong&gt;NADPH&lt;/strong&gt;. Since they themselves lack grana, they must obtain the required share from elsewhere. Where do they obtain it&#xA;  from?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My guess is that &lt;strong&gt;NADPH&lt;/strong&gt; enters the bundle sheath cell with the organic acid primarily produced in the mesophyll cells where light reaction occurs. &lt;strong&gt;ATP&lt;/strong&gt; is met by a similar uptake plus the utilisation of the ATP produced by respiration. I need to confirm this as it is usually never addressed in texts.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3340" LastEditDate="2014-10-09T14:43:09.583" LastActivityDate="2014-10-09T14:43:42.417" Title="Clarification on Hatch and slack pathway" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15274" PostTypeId="1" CreationDate="2014-02-23T08:52:38.923" Score="0" ViewCount="37" Body="&lt;p&gt;I have this sentence in my notes&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Inflammation consists of two local reactions and one systemic reactions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;which is difficult for me to accept.&#xA;Two local reactions are vascular and cellular.&#xA;I think there are two systemic reactions too:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;White blood cell response&lt;/li&gt;&#xA;&lt;li&gt;Acute-phase response&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How many systemic reactions there are in the inflammation?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-03-26T14:59:38.797" Title="How many systemic reactions in inflammation?" Tags="&lt;physiology&gt;&lt;pathology&gt;&lt;inflammation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15276" PostTypeId="2" ParentId="15270" CreationDate="2014-02-23T10:13:36.583" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2124629&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; seems relevant. I just found it and don't have access, so I haven't read it. It does seem to suggest that there is evidence for eukaryotic genes being taken up by a prokaryote.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would imagine this is rare, though. Eukaryotic cells don't tend to just spew their genetic material everywhere. Most death pathways involve breaking down any genetic material in the cell, I believe.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-02-23T10:13:36.583" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15277" PostTypeId="1" CreationDate="2014-02-23T10:25:18.750" Score="1" ViewCount="50" Body="&lt;p&gt;Isn't it possible to reverse tomography methods to create means to deliver heat or radiation precisely in 3D? This would be &quot;3D scalpel&quot; i.e. device which would be able to eradicate tumor cells precisely in otherwise unreachable areas?&lt;/p&gt;&#xA;" OwnerUserId="1584" LastActivityDate="2014-03-28T03:02:14.633" Title="Reverse tomography to create 3D scalpel" Tags="&lt;radiation&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15278" PostTypeId="1" CreationDate="2014-02-23T11:56:48.043" Score="1" ViewCount="571" Body="&lt;p&gt;If Pseudomonas is a gram negative bacteria, it does not retain crystal violet but why is it that so many people are using crystal violet staining in theri Microtiter Dish Biofilm Formation Assay?&lt;/p&gt;&#xA;" OwnerUserId="5517" LastEditorUserId="5144" LastEditDate="2014-02-23T12:20:45.600" LastActivityDate="2017-05-15T11:49:58.870" Title="Microtiter Dish Biofilm Formation Assay- Pseudomonas and Crystal Violet" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15279" PostTypeId="2" ParentId="15270" CreationDate="2014-02-23T12:00:34.493" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Elysia_chlorotica&quot; rel=&quot;nofollow&quot;&gt;This sea slug&lt;/a&gt; is one example of prokaryotic genes ending up in an animal. The slug ingests chloroplasts from algae and incorporates them into its own cytoplasm. It has also acquired, presumably through horizontal gene transfer, some or all of those genes necessary to maintain the chloroplast. While this is not a gene transfer from a &lt;em&gt;free-living&lt;/em&gt; prokaryote, chloroplasts are essentially cyanobacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the paper (PDF), see &lt;a href=&quot;http://www.pnas.org/content/105/46/17867.abstract&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also see a more general review &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/281/1777/20132450.abstract&quot; rel=&quot;nofollow&quot;&gt;here (free full text)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastActivityDate="2014-02-23T12:00:34.493" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15280" PostTypeId="2" ParentId="15257" CreationDate="2014-02-23T14:47:26.443" Score="0" Body="&lt;p&gt;You should use &lt;a href=&quot;http://en.wikipedia.org/wiki/Thiosulfate-citrate-bile_salts-sucrose_agar&quot; rel=&quot;nofollow&quot;&gt;Thiosulfate-citrate-bile salts-sucrose agar&lt;/a&gt; for the detection of all vibros, including cholera.  When cholera is presant, you should expect round, largish (not huge), yellow colonies.  This is the CDC &lt;a href=&quot;http://www.cdc.gov/cholera/diagnosis.html&quot; rel=&quot;nofollow&quot;&gt;recommended&lt;/a&gt; diagnoses method.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again this question might be better phrased &quot;what are the best detection medias for cholera,&quot; or &quot;what plate screens should be conducted when vibros are suspected?&quot;&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2014-02-23T14:47:26.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15281" PostTypeId="2" ParentId="15271" CreationDate="2014-02-23T16:34:32.580" Score="2" Body="&lt;p&gt;I am not sure about the source of ATP but I can tell you something about NADPH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The conversion of malate to pyruvate and CO₂ by malic enzyme is carried out in the bundle sheath cell. This process produces NADPH. &lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3340" LastEditDate="2014-10-09T14:43:28.600" LastActivityDate="2014-10-09T14:43:28.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15283" PostTypeId="2" ParentId="15271" CreationDate="2014-02-23T18:36:32.910" Score="1" Body="&lt;p&gt;See the very 1st thing is bundle sheath cell shows very less concentration of Grana, hence we say Grana is absent,  the required amount of ATP &amp;amp; NADPH₂ are also transported from mesophyll cell to bundle sheath cell via plasmodesmata. &lt;/p&gt;&#xA;" OwnerUserId="5832" LastEditorUserId="3340" LastEditDate="2014-10-09T14:43:42.417" LastActivityDate="2014-10-09T14:43:42.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15285" PostTypeId="1" AcceptedAnswerId="15289" CreationDate="2014-02-23T19:43:32.063" Score="0" ViewCount="2178" Body="&lt;p&gt;The ability to taste PTC is due to a single dominant allele &quot;T&quot;. You sampled 215 evolution students, and determined that 150 could detect the bitter taste of PTC and 65 could not. Assuming this trait is in Hardy-Weinberg equilibrium in this population and that there are only two alleles, calculate the number of heterozygotes for this trait there are in the population.&lt;/p&gt;&#xA;" OwnerUserId="5164" LastEditorUserId="107" LastEditDate="2014-02-23T20:39:18.410" LastActivityDate="2014-02-23T21:45:24.570" Title="calculate the number of heterozygotes" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;hardy-weinberg&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2014-03-18T17:59:31.497" ContentLicense="CC BY-SA 3.0" />
  <row Id="15287" PostTypeId="1" AcceptedAnswerId="15311" CreationDate="2014-02-23T20:39:09.647" Score="3" ViewCount="923" Body="&lt;p&gt;Life expectancy for human has significantly increased during the last century or so. We all know that there are many reasons that are not linked with &quot;evolution&quot;, but I am wondering if such change in life expectancy has been observed &quot;naturally&quot; (not counting animals in zoos or domestic ones). Does evolution favor long lasting individuals?&lt;/p&gt;&#xA;" OwnerUserId="5833" LastEditorUserId="1306" LastEditDate="2014-02-24T14:01:34.767" LastActivityDate="2014-02-25T09:43:01.547" Title="Is there any evidence of increased life expectancy for animal species?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15288" PostTypeId="2" ParentId="15287" CreationDate="2014-02-23T21:45:21.130" Score="1" Body="&lt;p&gt;The life expectancy of an animal (or anything) is just one aspect of how 'fit' they are to survive.  having them live too long can be a detriment to the species.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no simple 'better/worse' relationship of fitness to life expectancy.  In simple population models predators which reproduce to much or live too long will tend to eat all the prey and starve to death for instance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most famous example of life extension molecular biology is the discovery of a '&lt;a href=&quot;http://www.scientificamerican.com/article/methuselah-worm-remains-e/&quot; rel=&quot;nofollow&quot;&gt;Methuselah worm&lt;/a&gt;' by Cynthia Kenyon about 10 years ago.  With a &lt;a href=&quot;http://www.nature.com/scitable/topicpage/genetic-control-of-aging-and-life-span-847&quot; rel=&quot;nofollow&quot;&gt;single mutation&lt;/a&gt; these C. elegans worms can live about 50% longer, and seem to be pretty energetic while doing it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be interesting to put some of these Methuselah worms into a wild population and see what happens to their life span as they interbreed.  C elegans is a highly programmed organism - each cell has a predetermined plan for development and lifespan, which made this worm relatively easy to find.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For human beings (the best studied animal on Earth) there i&lt;a href=&quot;http://www.scientificamerican.com/article/genetic-factors-associated-with-increased-longevity-identified/&quot; rel=&quot;nofollow&quot;&gt;s no simple genetic relationship to longevity for most of us, but there appear to be some simple combinations that are responsible for the oldest living humans&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a genetic model comprising 150 SNPs in order to compute the predisposition of an individual toward EL. Their model successfully predicted exceptional longevity in a different sample of centenarians (individuals that live to age 100) with 77 percent accuracy. This demonstrates that EL is strongly associated with complex combinations of genetic variants.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So for humans this experiment has sort of been done.  Longevity phenotypes are possible but don't overall convey a reproductive advantage and so while they hang out in the gene pool,  they aren't enough of an advantage to reproduction to be spread about widely...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-02-24T14:10:03.570" LastActivityDate="2014-02-24T14:10:03.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15289" PostTypeId="2" ParentId="15285" CreationDate="2014-02-23T21:45:24.570" Score="2" Body="&lt;p&gt;Hardy-Weinberg law gives the frequencies of genotypes from allele frequencies: $p^2 + 2pq + q^2$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the allele &quot;T&quot; is dominant, the frequency you're directly measuring through the experiment is the addition of $p^2$ and $2pq$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$p^2 + 2pq = 150/215 ≈ 0.6976$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;solving for $p$ (and replacing $q$ by $1-p$) gives:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$p = 1 - \sqrt{\frac{13}{42}} ≈ 0.45 $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The frequency of heterozygotes is given by:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$2p(1-p) ≈ 0.4950 $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And the number of heterozygotes in a population of 215 individuals is given by:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$215 \cdot 0.4950 = 106.43$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That sounds very alike what you wrote in the comments!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-02-23T21:45:24.570" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15290" PostTypeId="1" AcceptedAnswerId="15300" CreationDate="2014-02-23T21:51:33.023" Score="1" ViewCount="177" Body="&lt;p&gt;I work with RNA and I have some RNase issues. For example I am using RNeasy mini kit and at one step I use 100% EtOH. It does not say it is RNase free or not. Does absolute EtOH inhibits or removes RNase or should I be worried about it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Addition: I am using eppendorfs directly from the bag. So they supposed to be RNase-free, right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="5630" LastActivityDate="2014-02-24T06:48:00.073" Title="RNase and EtOH issue" Tags="&lt;molecular-biology&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15292" PostTypeId="1" AcceptedAnswerId="15294" CreationDate="2014-02-23T23:05:23.770" Score="-1" ViewCount="1675" Body="&lt;p&gt;As a molecular biology graduate student I have decided to learn some basic programming and bioinformatics since everybody says that it is crucial. For example, what would you learn if you need to work with RNA-Seq data, compare and interpret them? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks! &lt;/p&gt;&#xA;" OwnerUserId="5630" LastEditorUserId="5630" LastEditDate="2014-02-24T12:18:40.373" LastActivityDate="2019-03-29T18:41:35.917" Title="basic programming and bioinformatics" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="2" ClosedDate="2014-02-24T06:41:45.010" ContentLicense="CC BY-SA 3.0" />
  <row Id="15293" PostTypeId="1" CreationDate="2014-02-24T00:01:32.463" Score="3" ViewCount="170" Body="&lt;p&gt;I'm looking for a database of nsSNP (non synonymous single nucleotide polymorphisms) and their effects. As I understand, the common methods to predict this are SIFT and PolyPhen, and I want to compare them to other methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The database needs to list the old sequence and the new one (or that I'd be able to infer that somehow), and their effect (whether harmful or not).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are my options?&lt;/p&gt;&#xA;" OwnerUserId="1190" LastActivityDate="2014-08-02T21:13:14.153" Title="Comparing SIFT and PolyPhen to other methods" Tags="&lt;snp&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15294" PostTypeId="2" ParentId="15292" CreationDate="2014-02-24T00:25:56.073" Score="11" Body="&lt;p&gt;Indeed the question is broad and quite hard to answer I think. I'll give a try. I very welcome editing to improve this answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The field of bioinformatics is a big field. Bioinformaticians need basic knowledge in&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;biology&lt;/li&gt;&#xA;&lt;li&gt;molecular genetics&lt;/li&gt;&#xA;&lt;li&gt;Population genetics&lt;/li&gt;&#xA;&lt;li&gt;programming&lt;/li&gt;&#xA;&lt;li&gt;statistics&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You may find courses on statistics applied to bioinformatics &lt;a href=&quot;http://cran.r-project.org/doc/contrib/Krijnen-IntroBioInfStatistics.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;here (R-language)&lt;/a&gt; and &lt;a href=&quot;https://www.coursera.org/course/bioinformatics&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; (I haven't watched these sources).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How to start programming? - Python&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You seem to be mostly interested in is programming. I think that &lt;strong&gt;Python&lt;/strong&gt; is a very good start to get in touch with programming. Programming might look a bit scary when you don't really know what it is about but you can easily, in a few days, acquire basic knowledge in this field and already solve some pretty neat problems. Many people actually have lots of fun learning how to program. And you'll probably be amazed by all the power this tool will offer to you. I personally really enjoyed learning to programming in Python. I did it (I was mostly interested in object-oriented programming, you'll learn what it means) in a day or two with a very good source but unfortunately, this source is not available in English. But there are tons of introductory documents, you'll have no difficulty to find a good one. I'd counsel you to directly &lt;a href=&quot;http://python.org/download/&quot; rel=&quot;nofollow noreferrer&quot;&gt;download Python&lt;/a&gt; and to look at online courses on &lt;a href=&quot;https://en.khanacademy.org/science/computer-science-subject/computer-science&quot; rel=&quot;nofollow noreferrer&quot;&gt;khan academy&lt;/a&gt; or &lt;a href=&quot;https://www.edx.org/course/mitx/mitx-6-00-1x-introduction-computer-1498&quot; rel=&quot;nofollow noreferrer&quot;&gt;EdX&lt;/a&gt; (I haven't watched them).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Data analysis - R&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While Python is very popular, I think that, as a biologist, it is very important that you know about &lt;strong&gt;R&lt;/strong&gt;. R is a programming language which is slow (compare to Python, C, Java, …) but it is very useful for statistical analysis and visual display of data. Also, many people use R in bioinformatics (for phylogenetic analysis typically). I think that acquiring basic knowledge in R takes more time than in Python because we tend to use R because of its huge amount of already existing functions and therefore, we have to learn many of these functions before understanding that R can indeed be much more useful than Python for some tasks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Command line - Shell script&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Shell script&lt;/strong&gt; (BASH for example) is a very specific and very important language too. Very useful for manipulating, transferring files, managing processes or pretty much anything that is happening on your computer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;C&lt;/strong&gt; and &lt;strong&gt;C++&lt;/strong&gt; are very fast and very much used as well. &lt;strong&gt;Perl&lt;/strong&gt; is commonly used for genomic sequence analysis (although Perl is slowly losing users to the advantage of Python).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Usefulness of programming&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You also ask about the usefulness of programming. Well, it is used in pretty much all areas of biology. It is used for analyzing empirical data, computer simulations in population genetics, graph theory, annotating DNA sequences, … I guess that 98% of biologists have at least some basic knowledge in programming. The main point about programming is that it performs calculation much faster than anything you could ever realize with your calculator. Typically, in bioinformatics, analysis of DNA sequences often asks for very intense calculation and asks for big computation power. Processes such as constructing phylogenetic trees, determining a goodness of fit of evolutionary models, annotating DNA, aligning DNA sequences, analyzing microarray and many other things are all sorts of tasks that require programming.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-29T18:41:35.917" LastActivityDate="2019-03-29T18:41:35.917" CommentCount="8" ContentLicense="CC BY-SA 4.0" />
  <row Id="15295" PostTypeId="1" AcceptedAnswerId="15296" CreationDate="2014-02-24T04:29:00.247" Score="1" ViewCount="2593" Body="&lt;p&gt;Succinate dehydrogenase is attached to the inner mitochondrial membrane. All the other enzymes of the Krebs cycle are located within the matrix of mitochondria, though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In biological systems, there is often a relation between structural properties and function. For example, two enzymes that function sequentially in a metabolic pathway are sometimes held in close proximity to one another by a scaffold  (e.g., in fatty acid synthesis). Is there a similar biochemical reason why succinate dehydrogenase is attached to the inner mitochondrial membrane, as opposed to being dissolved in the mitochondrial space?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="9943" LastEditDate="2015-12-31T19:13:10.543" LastActivityDate="2015-12-31T19:13:10.543" Title="Why is succinate dehydrogenase attached to the inner mitochondrial membrane?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;metabolism&gt;&lt;enzymes&gt;&lt;cellular-respiration&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15296" PostTypeId="2" ParentId="15295" CreationDate="2014-02-24T04:32:07.340" Score="1" Body="&lt;p&gt;The reason behind this lies in the properties of FAD+. Unlike NAD+, FAD+ is not free to diffuse within the mitochondrion, it is an integral part of the inner mitochondrial membrane. Its reduced form FADH2 contributes electrons directly to ETC.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-02-24T04:32:07.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15297" PostTypeId="1" AcceptedAnswerId="15321" CreationDate="2014-02-24T04:34:18.363" Score="1" ViewCount="166" Body="&lt;p&gt;Why is NAD+ free to diffuse within the mitochondrion whereas FAD+ is not ? What biochemical properties cause this difference ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-01T19:06:55.050" Title="Diffusion of FAD+" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15298" PostTypeId="2" ParentId="15295" CreationDate="2014-02-24T05:03:20.977" Score="0" Body="&lt;p&gt;Succinate dehydrogenase is also known as Complex II in the electron transport chain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although textbooks often show Complex II as taking FADH&lt;sub&gt;2&lt;/sub&gt; as a substrate, this is a little bit misleading. Succinate is the substrate, the oxidation of which facilitates the reduction of an FAD cofactor, which is already bound to Complex II. The resulting FADH&lt;sub&gt;2&lt;/sub&gt; is then oxidized in order to reduce ubiquinone, and feed electrons to Complex III.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://images.flatworldknowledge.com/ballgob/ballgob-fig20_014.jpg&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; is a pretty good image explaining the electron transport chain.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-02-24T05:03:20.977" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15299" PostTypeId="1" AcceptedAnswerId="15318" CreationDate="2014-02-24T06:11:01.403" Score="1" ViewCount="347" Body="&lt;p&gt;Analysis of the DNA of the Phenylalanine hydroxylase (PAH) gene in a&#xA;patient with phenylketonuria revealed a mutation in the protein coding&#xA;region whose predicted effect would be to replace the amino acid aspartic&#xA;acid, with histidine. Nevertheless, no mutant protein could be found in the&#xA;patient’s cells.How this could be as mutation is in the protein coding region,can anyone explain?&lt;/p&gt;&#xA;" OwnerUserId="5164" LastActivityDate="2014-02-24T15:44:42.757" Title="PAH gene mutation" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15300" PostTypeId="2" ParentId="15290" CreationDate="2014-02-24T06:48:00.073" Score="2" Body="&lt;p&gt;Ethanol is not a problem, we use it without any further precautions and it seems to be RNAse free. You should take the usual precautions you should take with all chemicals when you work with RNA, never use a spatula or spoon to get anything out of the bottle (unless you want to bake your spatulas all the time), always pour them to avoid any contamination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We autoclave the Eppis once, this might be an unnecessary precaution. I think you can also buy them certified RNAse free, but I'm not sure if they are actually treated any different or simply more expensive.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-02-24T06:48:00.073" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15302" PostTypeId="1" CreationDate="2014-02-24T08:38:21.640" Score="3" ViewCount="585" Body="&lt;p&gt;What are the benefits of &lt;a href=&quot;http://www.nature.com/nature/journal/v497/n7449/full/nature12107.html&quot; rel=&quot;nofollow&quot;&gt;CLARITY&lt;/a&gt; over &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3297424/&quot; rel=&quot;nofollow&quot;&gt;this technique&lt;/a&gt; that was published more than a year earlier?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course the second technique needs a fancier microscope that is likely more expensive and requires more technical ability. But CLARITY requires an objective with a very long working distance. I'm no expert in optics, but I'm pretty sure this results in a significant decrease in numerical aperture and therefore resolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems as though the other method is simply better than CLARITY, and that a lab serious about doing whole brain imaging could afford to invest in a setup similar to the one described. Yet this technique received none of hype that was bestowed on CLARITY. Am I missing something?&lt;/p&gt;&#xA;" OwnerUserId="5771" LastEditorUserId="948" LastEditDate="2014-02-24T16:05:56.507" LastActivityDate="2014-02-25T04:33:52.520" Title="Benefits of CLARITY?" Tags="&lt;neuroscience&gt;&lt;cell-biology&gt;&lt;lab-techniques&gt;&lt;microscopy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15303" PostTypeId="1" CreationDate="2014-02-24T09:33:17.550" Score="1" ViewCount="436" Body="&lt;p&gt;I am thinking how thrombus (veins, arteries and heart) can move.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondary mechanisms come to my mind only: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;some enzyme which lyses it, probably adhesion mechanism.&lt;/li&gt;&#xA;&lt;li&gt;Blood circulation (flow rate) is one secondary measure, I think.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am not sure if there exist any primary mechanisms:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;In veins, there are valves which probably can help thrombus go forward by pushing.&lt;/li&gt;&#xA;&lt;li&gt;Veins can also dilate so dilation of vessel can help.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Arteries do net dilate their diameter.&#xA;So aim would be there to maximise laminar flow, and decrease turbulence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So probably the question is related somehow to the laminar flow which could help thrombus to move.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can thrombus move in veins, arteries and heart?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-08-08T09:09:13.670" LastActivityDate="2014-08-08T09:32:11.560" Title="What are the movement mechanisms of thrombus?" Tags="&lt;physiology&gt;&lt;pathology&gt;&lt;blood-circulation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15304" PostTypeId="1" AcceptedAnswerId="15350" CreationDate="2014-02-24T10:31:56.773" Score="1" ViewCount="234" Body="&lt;p&gt;I know for microvasculature&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;New microvasculature (arterioles, venules) are always more permeable&#xA;  as they lack pericytes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and then I have this sentence about new blood vessels (not specific)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;New vessels contain initially only proliferative endothelium, the basement membrane has not formed yet, and pericytes are absent.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, I think pericytes are only around microvasculature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the second statement is correct for microvasculature too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why are new vessels more permeable in microasculature?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-03-14T06:58:03.343" LastActivityDate="2014-03-14T06:58:03.343" Title="Why are new vessels more permeable in microvasculature?" Tags="&lt;physiology&gt;&lt;human-anatomy&gt;&lt;circulatory-system&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15308" PostTypeId="1" AcceptedAnswerId="15312" CreationDate="2014-02-24T13:26:17.333" Score="5" ViewCount="21691" Body="&lt;p&gt;In molecular biology, what's the meaning of the terms &quot;downstream signaling&quot; and &quot;upstream signaling&quot;? What's the difference between them?&lt;/p&gt;&#xA;" OwnerUserId="561" LastEditorUserId="948" LastEditDate="2014-02-24T15:33:51.780" LastActivityDate="2014-02-24T15:41:36.720" Title="Explanation of the terms &quot;downstream signaling&quot; and &quot;upstream signaling&quot;" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;cell-signaling&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15309" PostTypeId="2" ParentId="15308" CreationDate="2014-02-24T13:45:57.793" Score="3" Body="&lt;p&gt;If you think of a transcription factor, than this factor needs to be regulated. This happens either by signalling pathways and also on the gene expression level (how much of the factor is available). So everything what regulates this factor is called upstream (look at the image below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Everything which is regulated by our factor (other genes) is located downstream of it. I think these terms come from the flow diagrams which are pretty usual in this context.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look at the figure (from &lt;a href=&quot;http://www.sabiosciences.com/iapp/ppar.html#animdemo-ppar&quot; rel=&quot;nofollow noreferrer&quot;&gt;SABiosciences&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Yn2ib.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here the signal comes from the membrane and is mediated through different factors until its passed into the nucleus.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-24T13:45:57.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15310" PostTypeId="2" ParentId="15299" CreationDate="2014-02-24T13:48:29.707" Score="2" Body="&lt;p&gt;There are many possible reasons for this, the two most obvious ones are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Alternative_splicing&quot; rel=&quot;nofollow&quot;&gt;Alternative splicing&lt;/a&gt;. Perhaps the mutation is indeed in the coding region but of an exon that is not constitutively expressed. As a result, the majority of transcripts created from this gene would not contain the mutation and neither would their resulting protein.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Posttranslational_modification&quot; rel=&quot;nofollow&quot;&gt;Post translational modifications&lt;/a&gt;. Proteins with the mutation might actually be produced but the histidine is changed to an aspartic acid by post translational modification so the mutation is not detectable in the cell's proteins. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-02-24T13:48:29.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15311" PostTypeId="2" ParentId="15287" CreationDate="2014-02-24T14:08:14.673" Score="2" Body="&lt;p&gt;As far evolution is concerned, there is no benefit whatsoever in having long lived individuals. Evolution only &quot;cares&quot; about individuals while they are capable of reproducing. Survival past the maximum age of reproduction is irrelevant from the evolutionary point of view since it does not make you any better at reproducing, and therefore your genes will not be selected for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is highlighted by the various species that die to give birth to or feed their young. One of my favorite examples is the giant pacific octopus (Enteroctopus dofleini) whose females lay their eggs and then die, leaving their body to feed the emerging young. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, a mutation that makes an individual both longer lived and capable of reproducing at a greater age could well be selected for. It just always needs to be combined with the ability to reproduce. By itself, dying older will confer no selective advantage unless it is combined with producing more offspring. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-02-25T09:43:01.547" LastActivityDate="2014-02-25T09:43:01.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15312" PostTypeId="2" ParentId="15308" CreationDate="2014-02-24T14:15:08.030" Score="4" Body="&lt;p&gt;It simply means &lt;em&gt;after&lt;/em&gt; and &lt;em&gt;before&lt;/em&gt; with respect to the flow of information in a given pathway. For example, consider this schematic representation of a pathway:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;TF1 ==activates==&amp;gt; gene1 ==produces==&amp;gt; Kinase1 ==phosphorylates==&amp;gt; ProtA &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;In this schema, Kinase1 is downstream of TF1 and upstream of ProtA. Or, to take a classic example (&lt;a href=&quot;http://dna.brc.riken.jp/en/GENESETBANK/mapk_ras.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/C7A1Bm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MEK1/2 is downstream of Raf and upstream of ERK1/2.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-02-24T15:41:36.720" LastActivityDate="2014-02-24T15:41:36.720" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15313" PostTypeId="2" ParentId="15274" CreationDate="2014-02-24T14:25:35.897" Score="1" Body="&lt;p&gt;There are two systemic reactions in inflammation too: mediated by leucocytes and acute-phase response (proteins). &lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-24T14:25:35.897" CommentCount="0" CommunityOwnedDate="2014-02-24T14:25:35.897" ContentLicense="CC BY-SA 3.0" />
  <row Id="15314" PostTypeId="2" ParentId="15027" CreationDate="2014-02-24T14:44:06.410" Score="0" Body="&lt;p&gt;I found no evidence for paracellular movement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some notes of mine&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Mucinase $\to$ lophotrichous flagella $\to$ Transcellular (actin fibrils, tails) movement&lt;/li&gt;&#xA;  &lt;li&gt;ICF Vacuolating cytotoxin (VacA) $\to$ altered T-cell function $\to$&#xA;  damages epithelial cells, disrupts tight junctions and causes&#xA;  apoptosis. &lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think the latter point makes transcellular momevment possible.&#xA;I see no way how paracellular movement would be possible.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-24T14:44:06.410" CommentCount="0" CommunityOwnedDate="2014-02-24T14:44:06.410" ContentLicense="CC BY-SA 3.0" />
  <row Id="15316" PostTypeId="1" AcceptedAnswerId="15319" CreationDate="2014-02-24T15:38:36.093" Score="3" ViewCount="87" Body="&lt;p&gt;I heard several times that two SNPs, that have at least 1'000 nucleotides between them, can be seen as 'unlinked' due to frequent recombination events. I also once saw a paper showing a graph &quot;degree of linkage vs. genetic distance&quot;. Unfortunately I can't remember which paper it was. Does anyone know where this number (1000) comes from?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: I'm aware that this topic is much more complex, especially if you are interested selective sweeps.&lt;/p&gt;&#xA;" OwnerUserId="3941" LastActivityDate="2014-02-24T15:52:45.760" Title="What is the genetic distance where linkage can be ignored?" Tags="&lt;dna&gt;&lt;genomics&gt;&lt;snp&gt;&lt;recombination&gt;&lt;genetic-linkage&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15317" PostTypeId="1" AcceptedAnswerId="15334" CreationDate="2014-02-24T15:39:03.583" Score="1" ViewCount="166" Body="&lt;p&gt;I am trying to parse the &lt;a href=&quot;http://scop.mrc-lmb.cam.ac.uk/scop/parse/index.html&quot; rel=&quot;nofollow&quot;&gt;SCOP parseable files&lt;/a&gt;, specifically dir.des.scop.txt ver 1.75. But, I have been facing problems with the PDB residue identifiers in the file. This is a tab limited file and the PDB residue and chain identifier is the 6th column which. An example of this identifier is A:1-28,A:77-837 for domain d1kk8a2.  Hence forward I'll represent that as domain_id (pdb_id chain&amp;amp;range). This particular example is straightforward, which means the domain d1kk8a2 consists of residues 1-28 and 77-837 of chain A of the corresponding PDB entry 1kk8. But some of them are unintuitive and like d3ckra1 (3ckr A:-2-385), what does the negative entry for the start mean? And this example d2p83b1 (2p83 B:61P-385), there is a P in the range (61P-385).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you go to &lt;a href=&quot;http://www.rcsb.org/pdb/home/home.do&quot; rel=&quot;nofollow&quot;&gt;pdb website&lt;/a&gt; and search for the corresponding entries, then go to the sequence tab, you will see the alignment of the PDB chain and the corresponding SCOP domains. The ranges shown there correspond to the entries in SCOP, but it is difficult to make sense of it. Can someone please explain or provide some pointers. Thank you.&lt;/p&gt;&#xA;" OwnerUserId="4279" LastActivityDate="2014-02-25T05:36:30.917" Title="How to parse SCOP parseable files PDB residue identifiers?" Tags="&lt;proteins&gt;&lt;pdb&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15318" PostTypeId="2" ParentId="15299" CreationDate="2014-02-24T15:44:42.757" Score="3" Body="&lt;p&gt;In terms of the way that the question is worded, I imagine the most likely answer would be that the amino acid substitution D &gt; H disrupts the folding of the protein so that it is recognised as being aberrant and is rapidly degraded.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-24T15:44:42.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15319" PostTypeId="2" ParentId="15316" CreationDate="2014-02-24T15:52:45.760" Score="2" Body="&lt;p&gt;I think you must have misremembered what you heard.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cut-off distance for genetic linkage is 50 centimorgans which corresponds to 50% recombination. In the human genome 1 centimorgan is approximately 10&lt;sup&gt;6&lt;/sup&gt; base pairs, so the 'unlinked distance' is 5 * 10&lt;sup&gt;7&lt;/sup&gt; base pairs.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-24T15:52:45.760" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15320" PostTypeId="1" CreationDate="2014-02-24T16:05:32.807" Score="4" ViewCount="2148" Body="&lt;p&gt;I recently heard a claim that Asians in general have more difficult births than Europeans. Is this true?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found a few studies(&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1049386706000557&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;,&lt;a href=&quot;http://europepmc.org/articles/PMC2847630&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;) on the effect of ethnicity on birth outcomes but they seem to be limited to a small geographic area or focus on aspects such as risk of premature birth, neonatal and/or maternal mortality, etc. Those are of course important facts, but I am more interested in whether an &lt;em&gt;otherwise normal&lt;/em&gt; birth is likely to be longer and/or be perceived as more difficult by this specific ethnic group, on basis of their ethnicity alone. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found a few articles dealing with possible effects of specific genes on duration of labor. Debiec et al. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19858874&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;) write that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Asian women had slower active labor than other ethnicities (P &amp;lt; 0.01). Asian women also reported less pain during their labor compared to all other patients (P &amp;lt; 0.001). Slower labor progress was associated with less rapid progression of pain, but this did not obviate the effect of Asian ethnicity on pain.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;According to Reitman et al.(&lt;a href=&quot;http://www.asaabstracts.com/strands/asaabstracts/abstract.htm;jsessionid=A8068074F3D7A7909CB5D56D971EA92E?year=2010&amp;amp;index=14&amp;amp;absnum=1885&quot; rel=&quot;nofollow&quot;&gt;4&lt;/a&gt;,&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3063327/&quot; rel=&quot;nofollow&quot;&gt;5&lt;/a&gt;) the genotype CC at the SNP Rs1042714(&lt;a href=&quot;http://snpedia.com/index.php/Rs1042714&quot; rel=&quot;nofollow&quot;&gt;9&lt;/a&gt;), which is more prevalent in ethnic Asians, is associated with longer duration of first-stage labor. Polymorphisms in the oxytocin receptor (OXTR) gene have also been tied to variations in labor progress (&lt;a href=&quot;http://www.asaabstracts.com/strands/asaabstracts/abstract.htm;jsessionid=E3F44008F278FF674EE3688DDD9F781B?year=2011&amp;amp;index=13&amp;amp;absnum=4335&quot; rel=&quot;nofollow&quot;&gt;6&lt;/a&gt;,&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22939719&quot; rel=&quot;nofollow&quot;&gt;8&lt;/a&gt;), but I haven't found data on the prevalence of these polymorphisms in Asian populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Greenberg et al. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16949407/&quot; rel=&quot;nofollow&quot;&gt;7&lt;/a&gt;) write that &quot;Nulliparous Asian women had a significantly longer second stage and higher rates of prolonged second stage&quot;. However, after controlling for confounding variables the actual increase in mean second-stage duration compared to white women was only  5.2 and 5.9 minutes for nulliparous Asian women with and without epidural analgesia, respectively. They also write that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When the rates of second stage of &gt;3 hours were analyzed by epidural subgroups in the multivariate analysis, black women with epidural analgesia had lower rates than white women, and Asian women with epidural analgesia had higher rates than white women, regardless of parity, although no differences were demonstrated among women without epidural analgesia.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Considering the above sources and any other that may exist, is it reasonable to state that Asian women in general have more difficult births than white/European women?&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2019-01-28T23:49:49.180" Title="Do Asian women have more difficult births than Europeans?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15321" PostTypeId="2" ParentId="15297" CreationDate="2014-02-24T16:07:25.340" Score="3" Body="&lt;p&gt;As explained at &lt;a href=&quot;http://en.wikipedia.org/wiki/Succinate_dehydrogenase#Redox_centers&quot; rel=&quot;nofollow&quot;&gt;the Wikipedia page for succinate dehydrogenase&lt;/a&gt; the FAD is covalently attached to one of the subunits of the protein. It is the first carrier in a short &lt;strong&gt;intramolecular&lt;/strong&gt; redox chain involving Fe-S clusters, and possibly a haem, before the electrons derived from succinate are passed on to ubiquinone and on down the respiratory chain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you say, this contrasts with NAD which is a diffusible coenzyme. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-03-01T19:06:55.050" LastActivityDate="2014-03-01T19:06:55.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15322" PostTypeId="1" AcceptedAnswerId="15323" CreationDate="2014-02-24T18:20:54.413" Score="0" ViewCount="772" Body="&lt;p&gt;this simulation, you sampled the gene pool without replaceing beads in the beakerafter you drew each one. Thus, f(A) and f(a) in the gene pool changed slightly after each bead was drawn. For example, if you begin with 50 light and 50 dark beads, the probability of drawing a dark bead the first time is 50/100 = 0.5. THe beaker would then contain 49 dark beads and 50 light beads, so the probability of drawing a second dark bead becomes 49/99 = 0.495. Does this make your simulation slightly less realistic? In small natural populations, does one mating change the gene pool available for the next mating, or not? What biological factors must be considered in answering this question?&lt;/p&gt;&#xA;" OwnerUserId="5164" LastEditorUserId="3615" LastEditDate="2014-02-25T12:40:12.307" LastActivityDate="2014-02-25T12:40:12.307" Title="Gene pool simulation" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;biostatistics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ClosedDate="2014-02-27T08:04:53.067" ContentLicense="CC BY-SA 3.0" />
  <row Id="15323" PostTypeId="2" ParentId="15322" CreationDate="2014-02-24T18:41:54.643" Score="2" Body="&lt;p&gt;I am not sure I'm answering your question but I hope this will help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two main models of genetic drift in biology: &lt;strong&gt;Moran model&lt;/strong&gt; and Wright-Fisher model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;Wright-Fisher model&lt;/strong&gt; implies picking $N$ beads (where $N$ is the population size) with replacement in order to form the new population. Therefore, the change in allele frequency (due to genetic drift) follows a Poisson distribution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{2N!\cdot p^kq^{2N-k}}{k!(2N-k)!}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;Moran model&lt;/strong&gt; consists of the following: At each time step you draw two beads. One disappear from the population and the other replicate in order to keep a stable population size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two models yield to similar results. Moran model runs twice as fast as Wright-Fisher model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I don't fully understand your model&lt;/strong&gt;. You say that in your model you pick one bead at a time. What do you do with this bead? How do you construct your population at the next time step? Do you allow changes in population size? Can you please try to develop how you defined your model. If it is a computer simulation you might paste the important part of your code, that might help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Haldane and Kimura both worked a lot on these models of genetic drift. For example, they provide different ways of calculating the mean time to fixation of a given allele given their selection coefficient $s$ starting from a given initial frequency $p_0$. Also some work has been done on genetic drift in population where the population size changes over time. Some work have been performed considering more or less complex probability density function for the number of offspring per individual. This kind of literature is very interesting but sometimes ask for quite good knowledge in mathematics (especially for Kimura's articles).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I once asked &lt;a href=&quot;https://biology.stackexchange.com/questions/10195/genetic-drift-models-assumptions-and-empirical-observations&quot;&gt;this question concerning the different models of genetic drift and their assumptions&lt;/a&gt; but I didn't get an answer yet.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-02-24T18:41:54.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15324" PostTypeId="2" ParentId="15302" CreationDate="2014-02-24T19:34:08.590" Score="3" Body="&lt;p&gt;To start with, CLARITY is a whole-brain imaging technique , there is no need for sectioning which destroys connections and can cause the brain slices to warp as they are being cut. The costs for setting up CLARITY are much lower because all that is needed is chemicals to get the prep ready for imaging whereas in the Nat Methods paper you have to set up an automated slicing and imaging system,not an easy task by any means. Therefore an investigator is more likely to use CLARITY due to its easy of setting up and low start up costs. Also, as with any brain slice technique , you lose patterns of connectivity among neurons that are more than the slice distance apart(i.e in the next slice) and you don't look at the &quot;whole picture&quot;. Thus due to the complexity,high start-up costs and specialized machinery STP is a poorer method than CLARITY for whole-brain imaging.As for resolution, I agree with you on principle that CLARITY has worse resolution(I looked through the paper but couldn't find exact figures) although you have to consider this in terms of all the trade-offs.&lt;/p&gt;&#xA;" OwnerUserId="5694" LastEditorUserId="5694" LastEditDate="2014-02-25T04:33:52.520" LastActivityDate="2014-02-25T04:33:52.520" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15326" PostTypeId="2" ParentId="15054" CreationDate="2014-02-24T19:40:48.650" Score="1" Body="&lt;p&gt;I'm going to answer your general inexact question with a general inexact answer. The consensus is that LTP is correlated with learning. &#xA;To clarify in more detail, studies have shown that when an animal performs a learning task that involves the hippocampus(which is important for memory), and the animal effectively learns, less LTP is seen in-vitro in brain slices from these same animals. LTP is said to be occluded or blocked since potentiation of those synapses have already maximized through the in-vivo mechanisms. This can be interpreted as learning affecting LTP or at least both acting on the same basic mechanisms of the synapse(strengthening and weakening).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See for ex.&#xA;Learning induces long-term potentiation in the hippocampus.&quot;, Jonathan R Whitlock, Science (New York, N.Y.), 2006;313(5790):1093-7&lt;/p&gt;&#xA;" OwnerUserId="5694" LastEditorUserId="5694" LastEditDate="2014-02-25T04:28:42.233" LastActivityDate="2014-02-25T04:28:42.233" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15327" PostTypeId="1" CreationDate="2014-02-24T21:03:19.110" Score="1" ViewCount="203" Body="&lt;p&gt;I'm assuming this field of study would focus on motor controls, movement, and exercise, but it could also focus on activities which strengthen the corpus callosum or stimulate a specific half of the brain.&lt;/p&gt;&#xA;" OwnerUserId="5843" LastActivityDate="2014-02-24T21:41:25.827" Title="Is there a scientific name for the field of study focusing on the hemispheres of the brain and their control of opposite sides of the body?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;brain&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15328" PostTypeId="2" ParentId="15327" CreationDate="2014-02-24T21:41:25.827" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Lateralization_of_brain_function&quot; rel=&quot;nofollow&quot;&gt;Lateralization&lt;/a&gt; of brain function...&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2014-02-24T21:41:25.827" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15329" PostTypeId="1" CreationDate="2014-02-24T22:47:17.013" Score="5" ViewCount="171" Body="&lt;p&gt;I have a friend who no longer needs glasses. He previously had myopia in both eyes but over the years it has improved until he no longer needs glasses clinically. He's had glasses for over 30 years since he was around 20. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on the above, I'd like to know if myopia can be improved naturally. Specifically whether not using glasses helps the underlying architecture of the visual system compensate in someway, or perhaps if nutrition can reduce myopia or finally if aging is known to decrease myopia. I'm interested in any biological mechanism at play. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a good understanding of Opthalmology and additionally would like any answers to be evidence based.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="3615" LastEditDate="2014-02-25T12:37:26.463" LastActivityDate="2014-02-26T22:47:11.847" Title="Improving myopia" Tags="&lt;human-biology&gt;&lt;pathology&gt;&lt;vision&gt;&lt;human-eye&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15332" PostTypeId="1" CreationDate="2014-02-25T02:34:30.610" Score="4" ViewCount="62" Body="&lt;p&gt;I was wondering whether anyone has looked at what are the expression changes in yeast when the microtubule or the microfilament polymerization is inhibited? Have there been whole-genome studies?&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="1320" LastEditDate="2014-02-25T12:35:54.190" LastActivityDate="2014-02-25T14:15:53.183" Title="What are the effect of microtubule or microfilament inhibition on yeast expression profile?" Tags="&lt;cell-biology&gt;&lt;gene-expression&gt;&lt;yeast&gt;&lt;cytoskeleton&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15334" PostTypeId="2" ParentId="15317" CreationDate="2014-02-25T05:36:30.917" Score="2" Body="&lt;p&gt;PDB residues are described by the residue number and an insertion code. Residue numbers can be any number, including negative values. In 3CKR the first residue has nr. -6, followed by -5, etc. This might indicate that there are additional residues at the beginning of the sequence, relative to other PDB entries. In 2P83, the first residue has the number 61P. Take a look at &lt;a href=&quot;https://lists.sdsc.edu/pipermail/pdb-l/2004-March/001513.html&quot; rel=&quot;nofollow&quot;&gt;https://lists.sdsc.edu/pipermail/pdb-l/2004-March/001513.html&lt;/a&gt; for an explanation why PDB residue numbers have insertion codes.&lt;/p&gt;&#xA;" OwnerUserId="3150" LastActivityDate="2014-02-25T05:36:30.917" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15335" PostTypeId="1" AcceptedAnswerId="15336" CreationDate="2014-02-25T07:51:50.633" Score="6" ViewCount="789" Body="&lt;p&gt;Suppose I want to create a mutant like &lt;a href=&quot;http://en.wikipedia.org/wiki/Antennapedia&quot; rel=&quot;nofollow&quot;&gt;Antennapaedia&lt;/a&gt; how will I go about accomplishing it ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that radiation and certain chemicals are mutagenic. So do scientists subject animals to such mutagenic chemicals and then wait for their progeny to see what mutation it has got ? Are there any specific protocols to create a specific type(for eg.homeotic) of mutant or is it pure luck ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry if I am being too naive!&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2014-02-25T13:53:11.920" LastActivityDate="2014-02-25T13:53:11.920" Title="How do scientists create specific mutations?" Tags="&lt;dna&gt;&lt;protocol&gt;&lt;mutations&gt;&lt;evo-devo&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15336" PostTypeId="2" ParentId="15335" CreationDate="2014-02-25T08:07:50.573" Score="4" Body="&lt;p&gt;Thats basically the oldest method to induce such mutations. For this purpose either radiation (x-rays) or mutagenic chemicals (like Ethylnitrosourea) have been used for this purpose. This method is undirected, so you never know what the outcome will be untill you see the off-springs. Using this method to get specific mutations is relative difficult. Its used for the detection of genes which deliver visible phenotypes (for example it has widely been used for the analysis of pigmentation in mice, since you can easily spot mutations).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Newer methods can target genes directly and either introduce or remove sequence areas. These techniques make use of homologous recombinases. In short you bring in you gene of interest in the modified version on a plasmid into the cell which you want to change. The plasmid also expresses the recombinase (this can be under a cell specific promoter to target specific cells) which then recombines the DNA between the plasmid and the genomic DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example for that is the FLP-recombinase system (image from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Site-specific_recombinase_technology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia article&lt;/a&gt; on it):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2PMlD.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other examples for site specific altertions are the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cre-Lox_recombination&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cre-LoxP-System&lt;/a&gt; or the &lt;a href=&quot;http://de.wikipedia.org/wiki/CRISPR&quot; rel=&quot;nofollow noreferrer&quot;&gt;Crispr/CAS-System&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-02-25T08:07:50.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15338" PostTypeId="2" ParentId="15329" CreationDate="2014-02-25T11:55:59.627" Score="0" Body="&lt;p&gt;I'll give you an answer based on my personal experience. I know that presbyopia usually increases with aging, so presbyopia and myopia can compensate each other with time. That's maybe what happened to your friend. But I don't know if myopia is related to nutrition or the use of glasses..&lt;/p&gt;&#xA;" OwnerUserId="5686" LastActivityDate="2014-02-25T11:55:59.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15340" PostTypeId="1" AcceptedAnswerId="15341" CreationDate="2014-02-25T12:41:37.560" Score="4" ViewCount="278" Body="&lt;p&gt;I am isolation RNA from Drosophila larvae brain with &lt;a href=&quot;https://en.wikipedia.org/wiki/Trizol&quot; rel=&quot;nofollow&quot;&gt;TRIzol&lt;/a&gt; method. What percentage of extracted RNA will be ribosomal RNA? I am only interested in mRNA, so I am trying to figure out whether I need to get rid of rRNA. Thanks&lt;/p&gt;&#xA;" OwnerUserId="5630" LastEditorUserId="1306" LastEditDate="2014-02-25T13:13:45.167" LastActivityDate="2014-02-26T23:18:13.427" Title="Ribosomal RNA amount in a Drosophila cell" Tags="&lt;molecular-biology&gt;&lt;rna&gt;&lt;mrna&gt;&lt;ribosome&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15341" PostTypeId="2" ParentId="15340" CreationDate="2014-02-25T14:00:02.113" Score="3" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Guanidinium_thiocyanate-phenol-chloroform_extraction&quot; rel=&quot;nofollow&quot;&gt;The protocol you are using&lt;/a&gt; will not only leave the sample with rRNA but also non coding RNA.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many RNA protocols will separate &lt;a href=&quot;http://www.fgsc.net/neurosporaprotocols/HowtoisolatemRNA%20final.pdf&quot; rel=&quot;nofollow&quot;&gt;mRNA by affinity of a carrier to the polyA tail&lt;/a&gt;.  This protocol references an older paper that estimates that &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/158528&quot; rel=&quot;nofollow&quot;&gt;only 5% of RNA is mRNA&lt;/a&gt;.  I'd be surprised if this ratio changed by more than 2-3 fold in drosophila. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume that %age is by weight but it could be a densitometry measurement which is similarly interpreted. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-02-26T23:18:13.427" LastActivityDate="2014-02-26T23:18:13.427" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15342" PostTypeId="2" ParentId="15332" CreationDate="2014-02-25T14:15:53.183" Score="1" Body="&lt;p&gt;Browsing around GEO, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gds/?term=yeast%5BOrganism%5D%20microtubule&quot; rel=&quot;nofollow&quot;&gt;I see 13 experiments&lt;/a&gt; focusing on microtubule disruption in yeast. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7276&quot; rel=&quot;nofollow&quot;&gt;This CHIP-CHP experiment&lt;/a&gt; actually uses nocodazole.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1693&quot; rel=&quot;nofollow&quot;&gt;This is a microarray experiment with benomyl treatment&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rest focus on specific mutants that try to perturb the microtubules in specific ways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's more if you broaden the search there is an &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gds/?term=microtubule&quot; rel=&quot;nofollow&quot;&gt;extensive body of work&lt;/a&gt; including human cell lines work as well... &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-02-25T14:15:53.183" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15343" PostTypeId="1" AcceptedAnswerId="15351" CreationDate="2014-02-25T14:50:59.407" Score="0" ViewCount="277" Body="&lt;p&gt;What is immunosuppression? I know it is used in cancer patients, but why would one want to suppress the immune system?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do homeopathic physicians ever use immunosuppression, or do only allopathic doctors practice this?&lt;/p&gt;&#xA;" OwnerUserId="5825" LastActivityDate="2014-02-25T21:32:49.780" Title="What is immunosuppression? Why would one use it?" Tags="&lt;immunology&gt;&lt;autoimmune&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2014-02-27T02:40:47.903" ContentLicense="CC BY-SA 3.0" />
  <row Id="15344" PostTypeId="1" CreationDate="2014-02-25T14:53:42.347" Score="2" ViewCount="248" Body="&lt;p&gt;I have been thinking about some alternative CO₂ fixation pathways. As almost all of them include ferredoxin reduction I started to wonder where does the ferredoxin comes from. I could not find any of the pathway in databases (ecocyc,kegg). Does any of you know if the biochemical pathway and the genes involved in synthesis are known?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,Martin&lt;/p&gt;&#xA;" OwnerUserId="4860" LastEditorUserId="3340" LastEditDate="2014-10-09T15:01:44.610" LastActivityDate="2016-06-06T17:42:09.423" Title="Ferredoxin synthesis pathways" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15345" PostTypeId="1" AcceptedAnswerId="15347" CreationDate="2014-02-25T15:11:09.120" Score="-2" ViewCount="2314" Body="&lt;p&gt;Are there &quot;essential sugars&quot;? Some have suggested that the 8 principal sugars found in glycoproteins are &quot;essential sugars&quot;:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Galactose&lt;/li&gt;&#xA;&lt;li&gt;Glucose&lt;/li&gt;&#xA;&lt;li&gt;Mannose&lt;/li&gt;&#xA;&lt;li&gt;N-Acetylneuraminic acid&lt;/li&gt;&#xA;&lt;li&gt;Fucose&lt;/li&gt;&#xA;&lt;li&gt;N-Acetylgalactosamine&lt;/li&gt;&#xA;&lt;li&gt;N-Acetylglucosamine&lt;/li&gt;&#xA;&lt;li&gt;Xylose&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I realize the liver can convert glucose to many different sugars, so by &quot;essential sugar&quot; I mean a sugar that is difficult to obtain from diet or that the liver requires much energy to convert from glucose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How difficult is it for the liver to convert glucose to the other sugars listed above?&lt;/p&gt;&#xA;" OwnerUserId="5825" LastEditorUserId="5825" LastEditDate="2014-02-25T20:35:11.567" LastActivityDate="2014-02-25T20:35:11.567" Title="Are the 8 principal sugars in glycoproteins &quot;essential sugars&quot;?" Tags="&lt;nutrition&gt;" AnswerCount="2" CommentCount="3" ClosedDate="2014-02-27T02:38:48.690" ContentLicense="CC BY-SA 3.0" />
  <row Id="15346" PostTypeId="1" AcceptedAnswerId="24324" CreationDate="2014-02-25T15:24:13.240" Score="3" ViewCount="591" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Catnip#Attractant&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;, the active substance is nepetalactone (&lt;span class=&quot;math-container&quot;&gt;$\ce{C_{10}H_{14}O_{2}}$&lt;/span&gt;) which has weak sedative, antispasmodic, febrifuge, and antibacterial effects in humans. Why are cats so fond of it? Why do they seem to get high on it?&lt;/p&gt;&#xA;&lt;p&gt;According to the same wikipedia page, the effect is gene-linked but it does not mention which genes, what they code for or any details whatsoever. Are all felines affected in this way or only &lt;em&gt;Felis catus&lt;/em&gt;? What is the biochemical mechanism by which cats are attracted to catnip?&lt;/p&gt;&#xA;" OwnerUserId="5825" LastEditorUserId="24354" LastEditDate="2021-04-23T16:56:53.597" LastActivityDate="2021-04-23T16:56:53.597" Title="Why are cats attracted to catnip?" Tags="&lt;zoology&gt;&lt;feline&gt;&lt;cat&gt;&lt;addiction&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="15347" PostTypeId="2" ParentId="15345" CreationDate="2014-02-25T16:30:09.280" Score="3" Body="&lt;p&gt;&lt;strong&gt;There are no essential sugars.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the context of nutrition &quot;essential&quot; usually means &quot;must be obtained from the diet&quot;. So for example the amino acid methionine is an essential amino acid (for humans).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within this definition there are &lt;strong&gt;zero&lt;/strong&gt; essential sugars. A Google search for &lt;em&gt;essential sugars&lt;/em&gt; reveals lots of sites like &lt;a href=&quot;http://nutrition-now.com/2010/04/what-are-essential-sugars-and-why-are-they-essential/&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt;. The site lists glucose as the first &quot;essential sugar&quot;. In fact we can make glucose from a range of other nutrients including amino acids, lactic acid and glycerol. The second sugar on the list is galactose - we can make that from glucose. And so on...&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-25T16:30:09.280" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15348" PostTypeId="2" ParentId="15345" CreationDate="2014-02-25T17:26:02.587" Score="2" Body="&lt;p&gt;@AlanBoyd is right that the term 'essential sugar' is not a scientific or biologically defined term and is not true given the meaning of the word essential that is in use in biology. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In alternative health and diet circles, the term 'essential sugars' refers to a set of simple carbohydrates which are hypothesized to be important for good health and nutrition in people.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if this were a valid approach in humans its very unlikely to be the same specific sugars and proportions for other animals and living things. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So given all these caveats the &lt;a href=&quot;http://nutrition-now.com/2010/04/what-are-essential-sugars-and-why-are-they-essential/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt; I found for 'essential sugars' lists these 8: glucose, galactose, fucose, mannose, glucosamine, galactosamine, neuraminic acid, and xylose. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as whether this really helps us, I personally don't think this is the key to good health in and of itself.  It really oversimplifies all of the biomachinery we have to break down and utilize carbohydrates.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the diet recommends the eating of vegetables which aren't too green, avoiding fructose, it doesn't seem to hurt.  Carbohydrates from food are often the product of breaking down complex carbohydrates.  I feel as if watching the glycemic index of your food and avoiding soft drinks and too much fruit juice will get you further in terms of health.  &lt;a href=&quot;http://www.webmd.com/diet/news/20040305/more-carbs-more-exercise-more-weight-loss&quot; rel=&quot;nofollow&quot;&gt;Avoiding simple carbohydrates entirely in your diet&lt;/a&gt; also has advocates and there is some medical research that backs it up. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-02-25T17:31:43.393" LastActivityDate="2014-02-25T17:31:43.393" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15349" PostTypeId="2" ParentId="1526" CreationDate="2014-02-25T20:04:56.540" Score="1" Body="&lt;p&gt;I assume you are talking about the mTAG visualization technique for mRNAs &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19680241&quot; rel=&quot;nofollow noreferrer&quot;&gt;(1)&lt;/a&gt;. You are probably familiar with it, but the OFR of interest is tagged with MS2L sequence downstream of it and upstream of the 3'UTR. There is also a modified version, in which you can visualize both the mRNA of interest, and the protein that is translated, see the figure below &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222136/&quot; rel=&quot;nofollow noreferrer&quot;&gt;(2)&lt;/a&gt;. Haim and colleagues found that yeast expressing mCherry and MS2L tagged ATP2 grew on glycerol-containing media, which would require efficient translation of ATP2. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OowZV.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I would assume that there is no translational repression if you tag the mRNA downstream of the ORF. Unless you have a very good reason to tag the ORF of interest with MS2 upstream of the start codon, I wouldn't do it, because these stem-loop structures would most probably stall translation, as mRNA secondary structure has been implicated in translation initiation efficiency. &lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2014-02-25T20:14:52.253" LastActivityDate="2014-02-25T20:14:52.253" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15350" PostTypeId="2" ParentId="15304" CreationDate="2014-02-25T21:06:24.763" Score="3" Body="&lt;p&gt;In adult/pediatric humans, no they don't.  A good figure to get everyone on the same page was made by &lt;a href=&quot;http://www.nature.com/doifinder/10.1038/nm0603-661&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cleaver &amp;amp; Melton&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/j3vxX.gif&quot; alt=&quot;Comparison of the composition large and small human blood vessels&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important to note that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In fact, endothelial diversity is reflected by vessel size-specific,&#xA;  organ-specific and even age-specific differences. &lt;a href=&quot;http://www.nature.com/doifinder/10.1038/nm0603-661&quot; rel=&quot;nofollow noreferrer&quot;&gt;(1)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Developing blood vessels in the fetus can be a bit of a different story, and highlights the fact the one should loose the &quot;inert plumbing&quot; mentality of the previous century.  &lt;a href=&quot;http://dx.doi.org/10.1126/science.1235249&quot; rel=&quot;nofollow noreferrer&quot;&gt;Modern research&lt;/a&gt; tells us that the epithelium is a very dynamic region that participates heavily with signalling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When large vessels are growing the fetus, &lt;a href=&quot;http://en.wikipedia.org/wiki/Mesenchymal_stem_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;mesenchymal stem cells&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Neural_crest&quot; rel=&quot;nofollow noreferrer&quot;&gt;neural crest cells&lt;/a&gt; are the normal precursors to &lt;a href=&quot;http://en.wikipedia.org/wiki/Pericyte&quot; rel=&quot;nofollow noreferrer&quot;&gt;pericytes&lt;/a&gt;, but depending on exposure the line between pericyte and smooth-muscle cell can be blurred &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1871727/&quot; rel=&quot;nofollow noreferrer&quot;&gt;(2)&lt;/a&gt;.  I'm assuming it's beyond the scope of the answer to go into the signalling differences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good review of &lt;a href=&quot;http://en.wikipedia.org/wiki/Endothelium&quot; rel=&quot;nofollow noreferrer&quot;&gt;endothelium&lt;/a&gt; generation, and the surrounding tissue, can be found &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3697817/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2014-02-25T21:06:24.763" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15351" PostTypeId="2" ParentId="15343" CreationDate="2014-02-25T21:32:49.780" Score="3" Body="&lt;p&gt;Immunosuppression is not used in cancer, in fact it is typically harmful unless of course the cancer is a immune or white blood cell cancer where suppressing their growth may be helpful. What you are perhaps alluding to is that an adverse effect of cytotoxic chemotherapy used in the medical treatment of cancer can cause immunosuppression. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Immunosuppression is helpful when it is causing more harm than good. The immune system is powerful and sometimes when its fighting an infection it can go a little overboard and cause enough damage to harm someone in the long term. In this case immunosuppression is helpful in preventing too high a response. For example in an organ transplant the recipient's immune system may destroy the new organ, but immunosuppression can prevent rejection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another case is when there is an autoimmune or inflammatory condition occurring. Rheumatoid arthritis being an example of the former and asthma being an example of the latter. In these diseases inflammation due to the immune system perhaps targeting our own body cells causes damage to our organs or cells and causes the disease. Immunosuppression here can limit or prevent further degradation or sometimes even reverse damage due to inappropriate immune responses. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly the human body must keep a good balance between being under and overactive. Certain individuals with better ability to control HIV infections or other infections are genetically more likely to also get autoimmune conditions.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-25T21:32:49.780" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15352" PostTypeId="1" CreationDate="2014-02-25T21:41:58.013" Score="2" ViewCount="91" Body="&lt;p&gt;When analyzing how the human species evolved and will continue to evolve over time, what evidence and tools (theory/models) do we have available to derive the rate at which this happens? Is it even possible to set reasonable bounds on such a rate?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, how large is the available dataset? And how does the dataset match with theory? I would especially like to get an idea of how well statistical (Bayesian/likelihood) analysis matches with empirical data and more conceptual models. &lt;/p&gt;&#xA;" OwnerUserId="5850" LastActivityDate="2014-03-11T23:25:04.793" Title="What evidence do we have to derive a rate of evolution?" Tags="&lt;evolution&gt;&lt;mutations&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15353" PostTypeId="2" ParentId="15352" CreationDate="2014-02-25T22:28:19.410" Score="1" Body="&lt;p&gt;Let me expand on my comment...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several such clocks, there are a couple of methods in use. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The oldest and primary methodology is to look at the bodies of the plants and animals and assemble the evolutionary tree by how closely these animals resemble each other (taxonomy).  There are several authoritative databases on this data.  The &lt;a href=&quot;http://eol.org&quot; rel=&quot;nofollow&quot;&gt;encyclopedia of life&lt;/a&gt; is a major aggregator for taxonomic analysis.  They are tied into the &lt;a href=&quot;http://www.itis.gov/&quot; rel=&quot;nofollow&quot;&gt;Integrated Taxonomic Information system&lt;/a&gt; (ITIS).  The millions of species known have not been sequenced and this is probably the most comprehensive overview of life as we know it on earth.  The ITIS data is downloadable.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand the taxonomic record has many known problems.  For example &lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0080282&quot; rel=&quot;nofollow&quot;&gt;Rodentia (rodents) are known to be a bit of a dumping ground&lt;/a&gt; where hard to classify mammals are put because we just don't really know where they go.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In cases where there is money and energy to resolve an issue like this, a main methodology to gauge the evolutionary distance is to observe the number of mutations that appear in genomic dna over time. Their sequence divergence varies over time at varying rates, but overall that's the clock.  This is pretty indisputable, but the coverage over the phylogenetic tree is low.  There are a few databases focused on bacteria for instance and fungi, but you have to know what you are looking for.  Often such evidence is entered into databases such as ITIS over time. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-02-25T22:28:19.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15354" PostTypeId="2" ParentId="15352" CreationDate="2014-02-25T22:38:49.163" Score="3" Body="&lt;p&gt;&lt;strong&gt;This question is very broad&lt;/strong&gt;. And because of its broadness, I am afraid you won't find a database that will give you what you're looking for.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Are you interested in some specific phenotypic traits?&lt;/li&gt;&#xA;&lt;li&gt;Or in some specific genes?&lt;/li&gt;&#xA;&lt;li&gt;What time scale are you interested in?&lt;/li&gt;&#xA;&lt;li&gt;Do you want to know about the time that a given allele needed to reach fixation?&lt;/li&gt;&#xA;&lt;li&gt;Do you want to compare the number of mutations that accumulated in a given DNA sequence between human and close relatives (apes, primates, mammals, ..)?&lt;/li&gt;&#xA;&lt;li&gt;Do you want to compare the evolution of the mitochondrial DNA between human populations that have different mating systems?&lt;/li&gt;&#xA;&lt;li&gt;Evolution in response to HIV?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If there is one specific gene or trait (including traits such as the mutation rate) that interest you, you might want to ask a more specific question on another post.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Concerning the &lt;strong&gt;methodology&lt;/strong&gt;, I agree with shigeta that probably the main methodology you'd be interested in is &lt;strong&gt;molecular clock&lt;/strong&gt;. The &lt;strong&gt;ratio of synonymous over non-synonymous mutations&lt;/strong&gt; are also of interest to compare rates of evolution. &lt;strong&gt;Comparisons of mutations accumulation between different sequences&lt;/strong&gt;. But you might also be interested in &lt;strong&gt;fossil records&lt;/strong&gt; (depending on the trait and the time scale you're interested in). Or more interestingly in &lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Selective_sweep&quot; rel=&quot;nofollow&quot;&gt;selective sweeps&lt;/a&gt;&lt;/strong&gt;. Selective sweep is the reduction in polymorphism and heterozygosity of linked loci to the locus under selection. In humans examples exist in the microcephalin gene or in the lactase gene for example. You might also be interested into &lt;strong&gt;allele frequency cline over spatial distribution&lt;/strong&gt; and things like that. &lt;strong&gt;Comparison of evolutionary rates between populations of different size&lt;/strong&gt; might also give you some insights in how quick does evolution occurs in humans. There are probably tons of other methodologies one could use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You talk about comparisons between empirical data and theoretical model. But again the question is too broad I think. There a tons of different models to be considered depending on what you are interested in.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-02-27T07:17:40.623" LastActivityDate="2014-02-27T07:17:40.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15357" PostTypeId="2" ParentId="15277" CreationDate="2014-02-26T02:08:05.427" Score="1" Body="&lt;p&gt;The principle of targeting cancers with high intensity radiation is already in use. For example: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mayoclinic.org/tests-procedures/gamma-knife-radiosurgery/basics/definition/prc-20014760&quot; rel=&quot;nofollow&quot;&gt;http://www.mayoclinic.org/tests-procedures/gamma-knife-radiosurgery/basics/definition/prc-20014760&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-02-26T02:08:05.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15359" PostTypeId="1" CreationDate="2014-02-26T03:58:29.637" Score="3" ViewCount="552" Body="&lt;p&gt;I am at the verge of submitting a paper on 'scientific explanation of reality' to an international philosophy body. First submitted draft was returned by the evaluation expert, asking me to re-submit it, after re-checking the validity of my  assertion that 'science (biology) believes that neuron firing always precedes thought'. Can any one provide answer on biology's clear stand on above question ?  &lt;/p&gt;&#xA;" OwnerUserId="5852" LastActivityDate="2014-04-19T22:00:21.570" Title="Thoughts precede neuron firing or vise-verse?" Tags="&lt;neuroscience&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15360" PostTypeId="2" ParentId="15359" CreationDate="2014-02-26T04:20:21.273" Score="3" Body="&lt;p&gt;You've stumbled on an old and unanswered question that is still debated--- bordering on the issue of Free Will. The reason it is still in the realm of philosophy is because current experiments don't allow direct testing of which neurons give rise to specific thoughts. This area of consciousness is fraught with difficulties and we just can't get at an answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now for a more philosophical answer.&#xA;All consciousness is generated by the brain so every thought must come from neuronal firing &lt;em&gt;necessarily&lt;/em&gt;. The difficulty lies in the fact that thoughts themselves cause neurons to fire and one is never thoughtless so we are reduced to the chicken and the egg problem if we continue down this path. However, assuming we come from a thought free state- for example deep coma-- the first thoughts we have are indeed generated by neuronal firing so your assertion is correct.&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-02-26T04:20:21.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15361" PostTypeId="2" ParentId="15329" CreationDate="2014-02-26T04:30:41.470" Score="1" Body="&lt;p&gt;Apparently reduction of myopia with age is fairly common. It is thought that the improved vision comes from relaxation of the ciliary muscle as the person ages. Since the lens changes shape the aberrant myopic focusing of light can be corrected to the correct location. While age was found to be the strongest factor influencing myopia progression, other factors like ethnicity and sex also play a role.&#xA;&lt;a href=&quot;http://archopht.jamanetwork.com/article.aspx?articleid=417134#&quot; rel=&quot;nofollow&quot;&gt;http://archopht.jamanetwork.com/article.aspx?articleid=417134#&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For additional info see:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.iovs.org/content/41/8/2103.long&quot; rel=&quot;nofollow&quot;&gt;http://www.iovs.org/content/41/8/2103.long&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.improveeyesight.org/can-myopia-near-sightedness-improve-with-age&quot; rel=&quot;nofollow&quot;&gt;http://www.improveeyesight.org/can-myopia-near-sightedness-improve-with-age&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5694" LastEditorUserId="5694" LastEditDate="2014-02-26T22:47:11.847" LastActivityDate="2014-02-26T22:47:11.847" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15362" PostTypeId="1" CreationDate="2014-02-26T05:12:21.273" Score="5" ViewCount="700" Body="&lt;p&gt;Normal soap requires scrubbing, does anti-bacterial soap require scrubbing too? Since it (I assume) works chemically, can I produce the same cleansing effect without lathering with soap and using anti-bacterial soap instead? It could save me a lot of time showering in the morning.&lt;/p&gt;&#xA;" OwnerUserId="5853" LastEditorDisplayName="user560" LastEditDate="2014-04-15T21:37:09.353" LastActivityDate="2015-05-18T08:51:27.153" Title="Does antibacterial soap work chemically?" Tags="&lt;bacteriology&gt;&lt;antibiotics&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15363" PostTypeId="2" ParentId="15359" CreationDate="2014-02-26T05:36:16.350" Score="4" Body="&lt;p&gt;I think the only way to interpret these kinds of questions biologically is to assume that &quot;thought&quot; means &quot;the perception of a thought occurring.&quot; The perception of a thought, like all perception, arises from neuronal firing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The interesting biological (rather than philosophical) questions arise when we look at the relationship between the neural firing that gives rise to the perception of intent to act and neural firing that carries out the &quot;intended&quot; actions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://diyhpl.us/~bryan/papers2/neuro/Manipulating%20the%20experienced%20onset%20of%20intention%20after%20action%20execution%20by%20TMS.pdf&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; is relevant. The authors are trying to argue that the initiation of a motor action comes before the perception of intent for that action. I'm not a cognitive neuroscience person, though, so I'm not very familiar with their techniques and personally have a hard time determining if they draw valid conclusions.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-02-26T05:36:16.350" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15365" PostTypeId="1" AcceptedAnswerId="19349" CreationDate="2014-02-26T07:59:04.147" Score="1" ViewCount="1485" Body="&lt;p&gt;What is the physiological mechanism behind the occurrence of orthostatic hypertension in the presence of hypovolemia?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2014-06-26T18:47:05.210" Title="Hypovolemia and orthostatic hypertension" Tags="&lt;physiology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15366" PostTypeId="2" ParentId="15193" CreationDate="2014-02-26T08:14:13.813" Score="1" Body="&lt;p&gt;Well you can always use a piece of white circular paper and draw the outline of the light onto it since it should be visible. This is a quick and dirty method that can be improved by taking a photo of the light with a camera if you have one and then comparing the distance of the edge of the paper measured with a ruler to that of the circle of light.&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-02-26T08:14:13.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15367" PostTypeId="1" CreationDate="2014-02-26T08:14:40.447" Score="0" ViewCount="83" Body="&lt;p&gt;I am thinking the pathogenesis of the C5a in GBS.&#xA;I think the pathogenesis happens like&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;C5a-peptidase in acid environment (Sialic acid, capsule) $\to$ cleaves C'-derived Neu chemoattractant C5a $\to \downarrow$ alternative pathway of Complement.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, this part &lt;strong&gt;cleaves C'-derived Neu chemoattractant C5a&lt;/strong&gt; is not clear to me.&#xA;I think this means that C5a-peptidase cleaves Neu C5a from the previous complement reaction that inhibits the next coming alternative pathway of complement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How does this pathogenesis of GBS happen?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-26T14:12:43.897" Title="Pathogenesis of Group B Streptococci and C5a" Tags="&lt;microbiology&gt;&lt;pathogenesis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15369" PostTypeId="1" CreationDate="2014-02-26T12:47:53.823" Score="0" ViewCount="1124" Body="&lt;p&gt;I know that low oncotic pressure is associated with many pathologies.&#xA;I am interested how it is associated with Third spacing.&#xA;My professor says that it can permit edema formation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The opposing pressure of oncotic pressure is hydrostatic pressure.&#xA;So that would suggests mean that the blood pressure is too high if low oncotic pressure and thus fluid would like to go to the third spacing (not sure) and edema.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can too low colloid oncotic pressure lead to Third spacing?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-02-26T16:41:08.250" Title="Can too low oncotic pressure lead to Third spacing and Edema?" Tags="&lt;physiology&gt;&lt;blood-pressure&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15370" PostTypeId="2" ParentId="10195" CreationDate="2014-02-26T13:48:16.880" Score="4" Body="&lt;p&gt;This question has been around for a while, so I'll try to start with a partial answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The basic assumptions of the standard &lt;strong&gt;Wright-Fisher-Model&lt;/strong&gt; are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Constant population size $N$.&lt;/li&gt;&#xA;&lt;li&gt;Discrete, non-overlapping generations.&lt;/li&gt;&#xA;&lt;li&gt;Neutrality (e.g. all individuals are equally likely to reproduce)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I prefer looking at the model for haploid/chromosomes. If you bundle up chromosomes to polyploids, then you get the additional assumption of random mating, e.g. all pairs of individuals are equally likely to reproduce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I might have missed something, but these assumptions should be sufficient to generate the Wright-Fisher-Dynamics: When we build a new generation, we have to fill $N$ spots again (follows from the first two assumptions). As each old individual is equally likely to reproduce (third assumption), e.g. to become parent of a new individual, we get the multinomial offspring distribution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main difference in the &lt;strong&gt;Moran model&lt;/strong&gt; is that it assumes overlapping generations. Main assumptions here are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Again constant population size.&lt;/li&gt;&#xA;&lt;li&gt;Individuals reproduce at a constant rate.&lt;/li&gt;&#xA;&lt;li&gt;Neutrality (however the Moran model can relatively easily be adapted to incorporate positive selection).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Every time an individual reproduces, another one instantly dies to maintain the constant population size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, the models have the same diffusion limit, e.g. they behave similarly for large populations (and identically for an 'infinitely large population'). If you trace the ancestry of a sample back in a large population, you will get close to &lt;a href=&quot;https://en.wikipedia.org/wiki/Coalescent_theory&quot; rel=&quot;nofollow&quot;&gt;Kingman's Coalescent&lt;/a&gt; under both models.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the two models exist more because of their distinct mathematical properties, than because one fits better to certain natural populations than the other. I'm not aware of any experiments that have shown how well they fit, maybe someone else can jump in here.&lt;/p&gt;&#xA;" OwnerUserId="5644" LastEditorUserId="948" LastEditDate="2014-02-26T21:18:19.997" LastActivityDate="2014-02-26T21:18:19.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15371" PostTypeId="2" ParentId="15367" CreationDate="2014-02-26T14:12:43.897" Score="1" Body="&lt;p&gt;I think &quot;neu&quot; must be an abbreviation for &quot;neutrophil&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;C3a and C5a are both chemotactic peptides that recruit cells to sites where &lt;a href=&quot;http://en.wikipedia.org/wiki/Complement_system&quot; rel=&quot;nofollow&quot;&gt;complement activation&lt;/a&gt; is occurring. C5 is a substrate for the C5 convertases formed in one of the three complement pathways (classical, lectin, alternative). C5b, the other product of this cleavage goes on to form the membrane attack complex. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;C5a peptidase is a Streptococcal product which destroys the C5a peptide before it can recruit neutrophils and other agents of cell-mediated immunity. Streptococci also produce an inhibitor of the membrane attack complex.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-02-26T14:12:43.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15372" PostTypeId="1" AcceptedAnswerId="15373" CreationDate="2014-02-26T14:35:31.467" Score="6" ViewCount="999" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;---- &lt;em&gt;Notations and assumptions&lt;/em&gt; ----&lt;/p&gt;&#xA;&#xA;&lt;p&gt;let $W_{ij}$ be the fitness associated to the genotype $AiAj$. $x$ is the frequency of the allele $A1$ in the population. The frequency of the allele $A2$ is $1-x$ because we'll consider only the case of a bi-allelic locus. Also, we consider that only one locus influence the random variable $W$ (the fitness). We will assume that the environment does not influence the fitness. We also assume random mating in order to use hardy-Weinberg equilibrium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;---- &lt;em&gt;calculations&lt;/em&gt; ----&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mean fitness is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\bar W = x^2W_{11} + 2x(1-x)W_{12} + (1-x)^2W_{22}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The variance of fitness is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma^2 = x^2(W_{11}-\bar W)^2 + 2x(1-x)(W_{12}-\bar W)^2 + (1-x)^2(W_{22}-\bar W)^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We then want to calculate the covariance between father and son with respect to fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose first that the father is $A_1A_1$ Then the son will be $A_1A_1$ if the mother transmits an $A_1$ gene to him, an event with probability x. Similarly the son will be $A_1A_2$ with probability $1-x$. The father himself will be $A_1A_1$ with probability $x^2$. Continuing this wa it is possible to draw up a table of the probabilities of the various father-son combinations in genotype and hence fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, assuming no change in frequency of $A1$ between the two generations, the covariance father-son is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$cov = x^3W_{11}^2 + 2x^2(1-x)W_{11}W_{12} + x(1-x)W_{12}^2 + 2x(1-x)^2W_{12}W_{22} + (1-x)^3W_{22}^2-\bar W^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;which also equals&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$cov = x(1-x)(xW_{11} + (1-2x)W_{12} - (1-x)W_{22})^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The correlation between the two fitnesses is found by dividing the co-variance by the variance (since the variance of sons is the same as that for fathers):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$cor = \frac{x(1-x)(xW_{11} + (1-2x)W_{12} - (1-x)W_{22})^2}{\sigma ^2}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We then define dominance and additive variance:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma_D^2 = x^2(1-x)^2(2*W_{12} - W_{11} - W_{22})^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma_A^2 = 2x(1-x)(xW_{11}+(1-2x)W_{12} - (1-x)W_{22})^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;such as&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma_D^2 + \sigma_A^2  = \sigma$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The slope of a parent-offspring regression equals the heritability in the narrow sense $h^2_N$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heritability in the narrow sense is defined as $h_N^2 = \frac{\sigma_A^2}{\sigma}$ (see &lt;a href=&quot;https://biology.stackexchange.com/questions/42273/why-is-a-heritability-coefficient-not-an-index-of-how-genetic-something-is&quot;&gt;Why is a heritability coefficient not an index of how “genetic” something is?&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We defined above that the correlation between parents and offspring is $cor = \frac{cov}{\sigma}$. So &lt;strong&gt;I'd expect the slope of the parent-offsprings regression to equal $cor = \frac{cov}{\sigma}$ and not $h_N^2 = \frac{\sigma_A^2}{\sigma}$&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What am I missing? Is there a mistake in my background calculations? Is there a mistake in the way I defined some concepts?&lt;/strong&gt; The answer might be much simpler than it looks like!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2018-03-04T21:06:21.440" LastActivityDate="2018-03-04T21:06:21.440" Title="Why does the slope of parent-offspring regression equals the heritability in the narrow sense?" Tags="&lt;genetics&gt;&lt;evolution&gt;&lt;population-genetics&gt;&lt;theoretical-biology&gt;&lt;natural-selection&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15373" PostTypeId="2" ParentId="15372" CreationDate="2014-02-26T15:01:00.417" Score="6" Body="&lt;p&gt;Well, I think I found the very simple mistake I made…&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking again in my equations, I realize that (for some reason) $cor = 2 \cdot \frac{\sigma_A^2}{\sigma}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And looking at &lt;a href=&quot;http://userwww.sfsu.edu/efc/classes/biol710/heritability/heritability.htm&quot;&gt;this website&lt;/a&gt;, I see that the slope of the parent-offspring regression is $\frac{h_N^2}{2} = slope$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here was my mistake!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-02-26T15:01:00.417" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15374" PostTypeId="2" ParentId="15369" CreationDate="2014-02-26T16:41:08.250" Score="2" Body="&lt;p&gt;Yes it can! Its a very important cause of third spacing a.k.a. peripheral oedema, mainly due to decreased protein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below is a list of causes of peripheral oedema due to fluid moving from the vascular bed to the peripheral spaces gathered from the following source: &lt;a href=&quot;http://www.patient.co.uk/doctor/Peripheral-Oedema.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.patient.co.uk/doctor/Peripheral-Oedema.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Immobility: Increased fluid pressure from venous stasis. Varicose veins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obesity: Increased fluid pressure from sodium and water retention; should not to be confused with non-pitting lymphoedema.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cardiac: Increased fluid pressure: right heart failure, constrictive pericarditis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Drugs: Increased fluid pressure from sodium and water retention: calcium antagonists, non-steroidal anti-inflammatory drugs (NSAIDs), prolonged steroid therapy, insulin.[1]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hepatic: Decreased oncotic pressure: cirrhosis causing hypoalbuminaemia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Renal: Decreased oncotic pressure from protein loss, and increased fluid pressure from sodium and water retention: acute nephritic syndrome, nephrotic syndrome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gastrointestinal: Decreased oncotic pressure: starvation, malabsorption, protein-losing enteropathy (eg Crohn's disease, ulcerative colitis, tumours of stomach and colon, coeliac disease and other intestinal allergies).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pregnancy: Increased fluid pressure both from sodium and water retention and venous stasis from pelvic obstruction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;High-altitude illness: Oedema of face, hands and ankles may occur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Idiopathic oedema: Associated with cyclical high lymph volume overload, or dynamic insufficiency: usually in a woman aged 20-40 years. Variable and not related to menstrual periods. Diagnosis is based on the exclusion of other causes of oedema.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Post-thrombotic syndrome: Late complication of deep vein thrombosis (DVT) which occurs in up to two-thirds of patients. May present with pain, oedema, hyperpigmentation, and even skin ulceration. May result from remaining venous obstructions, from reflux, or both. Rate of reflux is highest during the 6-12 months after an acute DVT. It may be temporary and self-limiting or not resolve and persist at variable severity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pitting localised limb oedema:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DVT: Compression of large veins by tumour or lymph nodes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following hip replacement or knee replacement. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Local infection, trauma (including burns, which may also cause generalised oedema because of protein loss), animal bites or stings.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-26T16:41:08.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15375" PostTypeId="2" ParentId="15250" CreationDate="2014-02-26T16:47:19.717" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;It's understandable that when one exhales then holds his breath, he needs air and thus he inhales afterwards. But when one inhales then holds his breath, shouldn't he inhale again after &quot;using up all that air he inhaled before holding hi breath&quot;?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Before we hold our breathe we first inhale some air inside.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, after holding it for some times, carbondioxide (CO2) which can be toxic to our body will be released after completing metabolic processes inside our body which will be pushed to our thorax, ready to be expelled. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The partial pressure of this gas (pCO2), is the primary fast (minutes or hours) trigger for breath; where partial pressure of Oxygen (pO2) is a slow trigger (hours or days). This explains why patients with severe re-acutized cronic obstructive pulmonary disease (COPD) stop spontaneous breathing, even if their pO2 falls, because of augmented pCO2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pCO2 is sensed in the human body in the Central Nervous System (CNS), precisely in the ponto-bulbar centers of breathing. The pO2 is sensed at periferical strucrures as the &lt;em&gt;glomi aorticus&lt;/em&gt; and &lt;em&gt;carotideus&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5855" LastEditorUserId="16651" LastEditDate="2015-12-17T00:52:14.520" LastActivityDate="2015-12-17T00:52:14.520" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15376" PostTypeId="2" ParentId="15365" CreationDate="2014-02-26T16:49:57.567" Score="0" Body="&lt;p&gt;I presumed you meant orthostatic hypotension. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Blood pressure falls on standing and is caused primarily by increased gravity causing blood pooling in the legs. This reduces venous return and subsequently cardiac output and therefore arterial blood pressure. Usually however standing doesn't usually cause a massive fall in blood pressure as standing immediately triggers vasoconstriction (baroreceptor reflex), pressing the blood up into the body again. However when there's a secondary factor reducing blood pressure such as hypovolaemia, the fall in pressure is higher than the body may sometimes be able to compensate for. This causes symptomatic orthostatic hypotension.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-26T16:49:57.567" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15378" PostTypeId="1" AcceptedAnswerId="16649" CreationDate="2014-02-26T20:21:12.017" Score="6" ViewCount="564" Body="&lt;p&gt;I have been trying to find out which sigma factor is responsible for the transcription of RNA polymerase subunits $\alpha$ (rpoA) and $\beta ^{\prime}$ (rpoC) in &lt;em&gt;Bacillus subtilis&lt;/em&gt;. I would expect it to be the housekeeping $\sigma^A$. However I have found out from the &lt;a href=&quot;http://dbtbs.hgc.jp/&quot;&gt;Bacillus subtilis transcription factor database&lt;/a&gt;, that $\sigma^A$ binding sites have been found in the promoters of $\beta$ (rpoB) and $\delta$ (rpoE) subunits, and a whole bunch of alternative $\sigma$ factors, but it says nothing about $\alpha$ or $\beta ^{\prime}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I want to know if there is a way for me to find out, without entering a wet lab!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly; how do we know that something is a transcription/sigma factor binding site? What is it about the region? And how do we know which TF/SF it is a binding site for? Could the same transcription/sigma factor have multiple different binding site motifs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly; Since the genome for &lt;em&gt;B. subtilis&lt;/em&gt; is available, would I be able to find out binding site motifs for all the sigma factors, and then determine which is/are contained within the promoter for the $\alpha$ subunit? &lt;em&gt;I.e.&lt;/em&gt; if I know the TF/SF sequence, is there a way of finding out which promoters it can bind to?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally; the main purpose of this question is to find out how rpoA is transcribed, and I know that in general sigma factors are required in bacteria for specific transcription initiation, but could it be that rpoA transcription is non-specific, and that the sigma factor is just not involved in its transcription?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please let me know if there is anything I can do to improve my question, I can provide references if it would be a good idea. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="445" LastActivityDate="2014-04-18T06:36:31.723" Title="How can promoter binding sites be determined?" Tags="&lt;bioinformatics&gt;&lt;bacteriology&gt;&lt;transcription&gt;&lt;binding-sites&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15379" PostTypeId="2" ParentId="15352" CreationDate="2014-02-26T23:07:39.410" Score="0" Body="&lt;p&gt;There are currently 7 billion human organisms on the planet.  We each have genome of about 3 billion letters, and we all  have millions of differences in our DNA from each other.  Some of these differences are private, only found in one individual, some are found in only one family, some only found in some larger kin groups.  Over time, more novel polymorphisms will arise, and those and the existing ones will change proportion in sub populations, and in the human species as a whole.  Some will have phenotype effects that we can measure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You think the changing of those millions of DNA sequences in a population of 7 billion can be meaningfully summed up in some single measurement?&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-02-26T23:07:39.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15381" PostTypeId="1" AcceptedAnswerId="15382" CreationDate="2014-02-27T00:11:56.097" Score="1" ViewCount="3748" Body="&lt;p&gt;The most I've been able to come up with is that fetuses are embryos slightly farther along in their development. Is that correct?&lt;/p&gt;&#xA;" OwnerUserId="5466" LastEditorUserId="13252" LastEditDate="2018-01-27T06:24:57.740" LastActivityDate="2018-01-27T06:24:57.740" Title="What's the difference between an embryo and a fetus?" Tags="&lt;embryology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15382" PostTypeId="2" ParentId="15381" CreationDate="2014-02-27T00:19:59.270" Score="3" Body="&lt;p&gt;Yes, you are correct. You can read the &lt;a href=&quot;http://en.wikipedia.org/wiki/Embryo&quot; rel=&quot;nofollow&quot;&gt;wikipedia article&lt;/a&gt; about an embryo:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the &gt;time of first cell division until birth, hatching, or germination. In humans, it is called an &gt;embryo until about eight weeks after fertilization (i.e. ten weeks after the last menstrual &gt;period or LMP), and from then it is instead called a fetus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="28" LastEditorUserId="5466" LastEditDate="2014-02-27T00:45:45.527" LastActivityDate="2014-02-27T00:45:45.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15383" PostTypeId="1" AcceptedAnswerId="15385" CreationDate="2014-02-27T02:00:49.593" Score="5" ViewCount="7404" Body="&lt;p&gt;How do we know that everybody's DNA fingerprint is unique?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know, I know, everybody's DNA is unique. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But when we do DNA fingerprinting, we're looking at very specific regions of high variability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do we know that just by chance, two people's DNA could be the exact same in the spot(s) we're observing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With real fingerprints, uniqueness is (almost) guaranteed (I believe it's a 1 in 64 billion chance) because they are developed by physical stresses on the fetus in the womb. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any similar mechanism/affect that acts on these non-coding/highly variable sections of DNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;evamvid&lt;/p&gt;&#xA;" OwnerUserId="5466" LastEditorUserId="5466" LastEditDate="2014-02-27T02:49:48.940" LastActivityDate="2016-03-23T01:46:20.930" Title="How do we know that everybody's DNA fingerprint is unique?" Tags="&lt;human-biology&gt;&lt;dna&gt;&lt;homework&gt;&lt;dna-sequencing&gt;&lt;gel-electrophoresis&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15384" PostTypeId="1" CreationDate="2014-02-27T02:35:19.657" Score="7" ViewCount="336" Body="&lt;p&gt;Gap junction proteins, connexins, are known to form intercellular hemichannels, between two adjacent cells. These junctions are maintained cell adhesion proteins (cadherins), yet the turnover of connexins is fairly rapid. As these connexins are being turned over, do the replacement connexins re-form the channel at the same location as previously existing channels, or is the pattern stochastic? Put another way, if we know cells in culture have formed gap junctions, and for any one cell, does it have different connected neighbours with time?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-03-03T20:16:46.797" Title="Gap junction turnover" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15385" PostTypeId="2" ParentId="15383" CreationDate="2014-02-27T02:46:47.917" Score="5" Body="&lt;p&gt;First, remember that identical twins actually have the same genotype. So its not exactly true that everyone has a unique genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But to get at the heart of it, you're asking how I can be sure that I have a different genome than you, or even than say my brother. And moreover you're asking how these differences are obvious enough that they can be detected &lt;em&gt;without&lt;/em&gt; whole genome sequencing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer is that there is no mechanism to ensure differences, but that the differences arise from the enormous variability of our genome. Look at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Major_histocompatibility_complex&quot; rel=&quot;nofollow&quot;&gt;major histocompatibility complex&lt;/a&gt;, or &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK27156/&quot; rel=&quot;nofollow&quot;&gt;MHC&lt;/a&gt;, a cluster of genes that affect our immune system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just to simplify things, lets focus in on four genes in this cluster: HLA-A, HLA-B, HLA-C and HLA-DRB1. According to &lt;a href=&quot;http://www.ebi.ac.uk/ipd/imgt/hla/stats.html&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt; there are 2579, 3285, 2133 and 1411 alleles for each, respectively. If we make a naive assumption that each of us received a random assortment of these genes, that makes 2579 x 3285 x 2133 x 1411 = 25,549,791,000,000 possible combinations. The chance that we both have the same combination is then about 1 in 25 trillion, just considering 4 genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But wait, you say, surely some of these genes are not equally likely and surely they segregate together, making this chance much smaller. You would be right. But this consideration stops mattering very much when you account for the rest of the variable regions. They combine multiplicatively, so considering a fifth gene with only 2 possible alleles brings the possible combinations to 50 trillion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you consider just a few more genes, the numbers get unthinkably high. This pretty much ensures that, even considering a small sequence, we can be sure that the genetic fingerprint is unique.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastEditorUserId="22057" LastEditDate="2016-03-23T01:46:20.930" LastActivityDate="2016-03-23T01:46:20.930" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15386" PostTypeId="1" AcceptedAnswerId="15391" CreationDate="2014-02-27T02:55:55.080" Score="7" ViewCount="1404" Body="&lt;p&gt;In gel electrophoresis, what causes effects like these (see column 11 in the first one, and column 6 in the second)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gnhLX.gif&quot; alt=&quot;this&quot;&gt; &#xA;&lt;img src=&quot;https://i.stack.imgur.com/whngD.gif&quot; alt=&quot;this&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(These images were samples that I took from an online activity we did for class)&lt;/p&gt;&#xA;" OwnerUserId="5466" LastEditorUserId="15950" LastEditDate="2019-01-07T06:05:07.180" LastActivityDate="2019-01-07T06:05:07.180" Title="What causes skewed lanes in a DNA gel electrophoresis experiment?" Tags="&lt;human-biology&gt;&lt;dna&gt;&lt;dna-sequencing&gt;&lt;gel-electrophoresis&gt;&lt;human-genome&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="15387" PostTypeId="2" ParentId="15362" CreationDate="2014-02-27T03:36:04.247" Score="8" Body="&lt;p&gt;What the comments are trying to say might go something like this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The antibiotic &lt;a href=&quot;https://en.wikipedia.org/wiki/Triclosan&quot;&gt;triclosan&lt;/a&gt; that's used in almost all 'antibacterial' products works pretty quickly - by interfering with several processes in the bacterial and fungal membrane.  It doesn't need much more than contact to work.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, the longer your exposure to the antibiotic, the more thoroughly it will work.  Triclosan can penetrate the blood stream through the skin.  If you have soap suds scrubbing may or may not get the triclosan into more contact with a greater surface area as it diffuses into the skin, but probably won't affect the substantial effect it has killing surface bacteria and fungi/yeasts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its worth noting that the FDA &lt;a href=&quot;http://www.fda.gov/ForConsumers/ConsumerUpdates/ucm205999.htm&quot;&gt;doesn't recommend the use of antibacterial soap or other antibacterial products&lt;/a&gt;.  Soap itself is a powerful agent for killing bacteria and other microorganisms and biocides like triclosan probably encourage the &lt;a href=&quot;http://www.nytimes.com/2013/09/18/opinion/the-antibiotic-resistance-crisis.html?_r=0&quot;&gt;emergence of antibiotic resistant strains which present a medical risk to people&lt;/a&gt;.   &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-02-27T03:36:04.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15388" PostTypeId="1" AcceptedAnswerId="15389" CreationDate="2014-02-27T05:18:14.677" Score="-2" ViewCount="198" Body="&lt;pre&gt;&lt;code&gt;&amp;gt;&amp;gt;&amp;gt; from Bio import SeqIO&#xA;&amp;gt;&amp;gt;&amp;gt; for seq_record in SeqIO.parse(&quot;ls_orchid.fasta&quot;, &quot;fasta&quot;):&#xA;... print(seq_record.id)&#xA;  File &quot;&amp;lt;stdin&amp;gt;&quot;, line 2&#xA;    print(seq_record.id)&#xA;        ^&#xA;IndentationError: expected an indented block&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;First I import the sequence and then whenever i try to print using this &#xA;&quot; print(seq_record.id)&quot;&#xA;        ^&#xA;I get this error&#xA;&lt;strong&gt;IndentationError: expected an indented block&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;how can I preent that need help..&lt;/p&gt;&#xA;" OwnerUserId="5164" LastEditorUserId="948" LastEditDate="2014-12-08T02:43:10.020" LastActivityDate="2014-12-08T02:43:10.020" Title="Biopython error" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-02-27T06:54:00.247" ContentLicense="CC BY-SA 3.0" />
  <row Id="15389" PostTypeId="2" ParentId="15388" CreationDate="2014-02-27T05:56:49.217" Score="2" Body="&lt;p&gt;Biopython is a module of python and the language is structured in the same way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This particular example does not make it clear how and where to find the files and extract the data you want. First, you need to download the file and put it in a place where python will find it. Below I have an example where I was able to extract the record id. I first set up a fasta file for my code to go through and then it adds the data to a list (seq = []). The &quot;with open&quot; line joins my data files together. The line ends with a &quot;:&quot; to signal to the program that there is a block of something to do in the next line. Indentation is important in python and after a &quot;:&quot; the next line is indented 4 spaces.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;from Bio import SeqIO&#xA;&#xA;data_dir = 'data' #folder where my data files are&#xA;data_file = 'ampk.fasta' #name of file I want to get data from&#xA;&#xA;seqs = []&#xA;&#xA;with open(os.path.join(data_dir, data_file), &quot;rU&quot;) as f:&#xA;    for record in SeqIO.parse(f, &quot;fasta&quot;) :&#xA;        seqs.append(record)&#xA;        print(record.id)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="5861" LastActivityDate="2014-02-27T05:56:49.217" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15390" PostTypeId="1" AcceptedAnswerId="15393" CreationDate="2014-02-27T06:37:41.587" Score="3" ViewCount="252" Body="&lt;p&gt;I know B cells found in bone marrow produce immunoglobin G.  But IgM is produced in mucosal cells at least in the gut.  Can you find immunoglobin expressing cells in other tissues in the human body?  Are B cells or IgG mRNA ever found in blood or tissues? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-02-27T18:53:39.603" LastActivityDate="2014-02-27T18:53:39.603" Title="What cell types produce immunoglobins and where are those cells found?" Tags="&lt;immunology&gt;&lt;immunoglobin&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15391" PostTypeId="2" ParentId="15386" CreationDate="2014-02-27T06:40:33.297" Score="8" Body="&lt;p&gt;These are sequencing gels (in the cases here even radioactive ones) - they are run a lot longer than ordinary agarose gels and they are made from polyacrylamide. Im my experience, the most likely cause for skewing of lanes (not only bands) are samples, which still contain too much salts from the PCR reactions. This can also happen to only a few bands as seen here. Overall these are still pretty nice and clean gels, I have seen much worse.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other reasons which cause uneven gels are cases where the acrylamide is not mixed good enough (causing the gel to have different concentration and thus causing different running conditions), uneven warming (although this was usually preventing by the gel heating system) and leaky gels where the electric field was not completely even.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-02-27T07:17:23.793" LastActivityDate="2014-02-27T07:17:23.793" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15392" PostTypeId="2" ParentId="15383" CreationDate="2014-02-27T08:07:34.743" Score="3" Body="&lt;p&gt;Possibly partly offtopic, but I'd like to add that when using dna fingerprint as evidence of identity in a legal investigation, the odds become smaller due to combination of human factors and reduced accuracy. There is the twin issue already mentioned, but in addition &lt;a href=&quot;https://www.apa.org/monitor/jun07/problem.aspx&quot; rel=&quot;nofollow&quot;&gt;there are laboratory errors and the possibility of contamination with other evidence&lt;/a&gt;. Samples may be damaged in other ways as well, and dna samples &lt;a href=&quot;http://science.howstuffworks.com/life/genetic/dna-evidence6.htm&quot; rel=&quot;nofollow&quot;&gt;can be planted&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the analysis done by Jonathan Koehler, it was &lt;a href=&quot;http://www.theguardian.com/uk/2002/jan/27/ukcrime.research&quot; rel=&quot;nofollow&quot;&gt;found that around 1.2% of tests used in this context gave out an incorrect match&lt;/a&gt;. Additionally, in this &lt;a href=&quot;http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1469627&quot; rel=&quot;nofollow&quot;&gt;other study&lt;/a&gt; by him it was found that the way results are presented has a considerable impact as well.&lt;/p&gt;&#xA;" OwnerUserId="5863" LastEditorUserId="5863" LastEditDate="2014-02-27T10:33:06.880" LastActivityDate="2014-02-27T10:33:06.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15393" PostTypeId="2" ParentId="15390" CreationDate="2014-02-27T08:18:14.643" Score="6" Body="&lt;p&gt;First: B cells do not produce antibodies, but rather they synthesise the B cell receptor. This may sound a bit picky, but is not, since the B cell receptor is anchored in the membrane of B cells and not secreted. Its this receptor which recognizes antigens and causes the production of highly specific antibodies (including somatic hypermutation and all related processes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antibodies are produced by plasma cells (and that basically the only thing they do), which are differentiated from activated B cells which have undergone the selection process on the given antigen. &#xA;IgM is the first set of antibodies produced by the mature B cell, later on this often changes to IgG (different heavy chain, same antigen recognition site) by class switching.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The secreted antibody is IgA, which is found basically in all body fluids and is also secreted into the different mucosas of the body. It has two subtypes: IgA1 and IgA2 with A1 mostly present in the serum and A2 mostly secreted (see: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7118169&quot;&gt;IgA subclasses in various secretions and in serum.&lt;/a&gt;&quot; for details).&#xA;IgA is made by plasma cells which are located in the lamina propria adjacent to mucosal surfaces. For details see thesetwo papers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12511876&quot;&gt;Intestinal IgA synthesis: regulation of front-line body defences.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1924341&quot;&gt;The polymeric immunoglobulin receptor (secretory component) mediates&#xA;transport of immune complexes across epithelial cells: a local&#xA;defense function for IgA.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;B cells (and also plasma cells) are found in the blood, they are then called peripheral cells. B cells have to be present outside the lymphatic tissues (not only bone marrow but also lymph nodes and the spleen) to be able to get in contact with antigens. Upon contact with an antigen they move into the adjacent lymphatic tissue.&#xA;You will not find IgG mRNA in the blood, as this will trigger immune responses. And it has no function outside of the cell.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2014-02-27T08:45:08.473" LastActivityDate="2014-02-27T08:45:08.473" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="15394" PostTypeId="1" CreationDate="2014-02-27T10:02:18.600" Score="0" ViewCount="99" Body="&lt;p&gt;What can be said on the length differences between interacting proteins? Are they usually of similar sequence lengths or not at all?&lt;/p&gt;&#xA;" OwnerUserId="1190" LastActivityDate="2014-02-28T15:56:39.073" Title="Length differences between physically interacting proteins" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15395" PostTypeId="1" AcceptedAnswerId="15399" CreationDate="2014-02-27T14:27:44.547" Score="0" ViewCount="227" Body="&lt;p&gt;Is cancer due to a defect in the immune system?&lt;/p&gt;&#xA;" OwnerUserId="5825" LastEditorUserId="5825" LastEditDate="2017-12-20T17:05:54.730" LastActivityDate="2017-12-20T17:05:54.730" Title="Is cancer a defect of the immune system?" Tags="&lt;immunology&gt;&lt;cancer&gt;&lt;autoimmune&gt;&lt;immunoglobin&gt;" AnswerCount="1" CommentCount="11" ClosedDate="2014-02-28T18:44:35.983" ContentLicense="CC BY-SA 3.0" />
  <row Id="15396" PostTypeId="1" CreationDate="2014-02-27T17:46:35.683" Score="1" ViewCount="83" Body="&lt;p&gt;We know that the nucleus of the cell is the White House of the cell and its DNA is the president and it commands to make protein. So my question when DNA only codes for protein and enzymes,after the birth of a new cell where does the cell get lipids and carbohydrates to make membranes, organelles, water, ions, plasma membrane etc ...?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="1320" LastEditDate="2014-02-27T20:05:42.923" LastActivityDate="2014-02-27T21:15:52.403" Title="how cells make other macro molecules?" Tags="&lt;cell-biology&gt;&lt;cell-division&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15397" PostTypeId="1" AcceptedAnswerId="15404" CreationDate="2014-02-27T20:03:52.497" Score="3" ViewCount="110" Body="&lt;p&gt;I'm under the impression that nematode worms just perform the same scripted actions over and over again in response to specific stimuli. They have 302 neurons. Chimpanzees display problem solving capabilities, as do other mammals with smaller brains (cats, for instance with ~ 1 billion neurons). You might say that bees demonstrate something more than reflexes when they communicate the location of nectar sources to the hive (~ 960,000 neurons).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the creature with the lowest number of neurons to demonstrate something more than mere scripted actions? I would imagine its somewhere between a bee and a nematode worm...&lt;/p&gt;&#xA;" OwnerUserId="866" LastActivityDate="2014-02-27T22:16:10.507" Title="What is the creature with the lowest neuron count that demonstrates cognition beyond reflexes?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;intelligence&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15398" PostTypeId="2" ParentId="13869" CreationDate="2014-02-27T20:22:26.120" Score="-2" Body="&lt;p&gt;Well, your logic is flawed because it is not proven that humans evolved from chimpanzees. not trying to start another debate with the whole evolution, but even if I did believe in evolution I would suggest before making up your hypothesis of researching a lot more than monkeys. Research things like: ancient brothels, traditional marriage views/ cohabitation views, {things that humans practiced and accepted back in the day} and you will have much more evidence. &lt;/p&gt;&#xA;" OwnerUserId="5870" LastActivityDate="2014-02-27T20:22:26.120" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15399" PostTypeId="2" ParentId="15395" CreationDate="2014-02-27T20:36:03.967" Score="2" Body="&lt;p&gt;Cancer is uncontrolled division of abnormal cells. This is caused by mutations in a cell which causes a cell to divide more frequently and the lack of control by intracellular AND extracellular mechanisms. The extracellular mechanisms include growth inhibition by hormones, local factors, contact and also the immune system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These cancerous cells could be immune system cells and then, in that respect, the cancer could be considered an immune system disorder. Or the cells could be of different origin, but due to the lack of a functioning immune system (particularly NK cells), the cells may divide uncontrollably whereas otherwise they would've been tagged for immune or self destruction. Or a cancer may be caused by a virus; in this situation an immunocompromised patient is more susceptible to a cancer caused by this oncogenic virus. In these cases the risk of cancer is increased due to a compromised immune system. So cancer risk may be increased in these circumstances but cancer still is not an immune disorder.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-02-27T20:36:03.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15400" PostTypeId="2" ParentId="15394" CreationDate="2014-02-27T20:38:39.107" Score="1" Body="&lt;p&gt;At least in a human protein interaction network, it appears that proteins indeed mostly bind to proteins of similar sequence length. Consider the figure below, based on analysis of a human protein interaction network from the Protein Interaction Network Analysis (PINA) platform. In the data set, the median relative protein size (the largest amino acid sequence length divided by the smallest in each interacting pair) was 1.9, the maximum value was 293.6 and the 99th percentile, which is the cutoff for the plot, was at 15.2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sJjSf.png&quot; alt=&quot;Relative sizes of interacting proteins&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: As per stords comment below, you get essentially the same result for a random network: &lt;img src=&quot;https://i.stack.imgur.com/3NRK8.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case, the network was generated by picking two proteins at random from the original network, creating an interaction between them, and repeating until the random network has the same number of interactions as the original. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Immediately, it might look like the PINA PIN is dominated by random interactions. I would run some network analysis to determine its characteristics, but seeing as it's a rather large network it would take more time than I have right now. The results are similar for two additional networks with interactions in Saccharomyces cerevisiae and Caenorhabditis elegans respectively downloaded from PINA. Note that all three networks have been constructed from databases with varying levels of curation (See the original publication for PINA:  &lt;a href=&quot;http://www.nature.com/nmeth/journal/v6/n1/full/nmeth.1282.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.nature.com/nmeth/journal/v6/n1/full/nmeth.1282.html&lt;/a&gt;). As such, many of the interactions might not be biologically meaningful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taking into account the above, you might want to define &quot;interacting proteins&quot; more precisely. One might expect that a better curated network only containing interactions with a known function or effect might give a different picture. However, using a more strigently constructed human &quot;functional interaction&quot; network published by Wu et al. (&lt;a href=&quot;http://genomebiology.com/content/11/5/R53&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://genomebiology.com/content/11/5/R53&lt;/a&gt;, FIs_043009.txt in Additional file #3) still gave a similar result. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Method: I made a Python script to calculate the relative amino acid sequence lengths for all interactions in a human protein-protein interaction network (PIN) available from PINA ((&lt;a href=&quot;http://cbg.garvan.unsw.edu.au/pina/interactome.stat.do&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://cbg.garvan.unsw.edu.au/pina/interactome.stat.do&lt;/a&gt;). The network file is located at: &lt;a href=&quot;http://cbg.garvan.unsw.edu.au/pina/download/Homo%20sapiens-20121210.sif&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://cbg.garvan.unsw.edu.au/pina/download/Homo%20sapiens-20121210.sif&lt;/a&gt;. PINs for other organisms are also available at the same site and many other places. The script can be used with any PIN in SIF format using UniProt identifiers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The script can be downloaded here: &lt;a href=&quot;https://github.com/jarlemag/misc-bioinformatics/blob/master/ProteinInteractionNetwork.py&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://github.com/jarlemag/misc-bioinformatics/blob/master/ProteinInteractionNetwork.py&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most time-consuming part was downloading the sequence lengths from UniProt. To avoid having to do that, the protein sequence lengths can be saved to and loaded from a text file.  The list of protein sequence lengths is here: &lt;a href=&quot;https://github.com/jarlemag/misc-bioinformatics/blob/master/protlengths.txt&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://github.com/jarlemag/misc-bioinformatics/blob/master/protlengths.txt&lt;/a&gt; To create the figure, place all three files in the same directory and run the script using Python 2.7.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Keep in mind that the PIN data may not be entirely reliable.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-02-28T15:56:39.073" LastActivityDate="2014-02-28T15:56:39.073" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15401" PostTypeId="2" ParentId="15396" CreationDate="2014-02-27T20:43:03.040" Score="2" Body="&lt;p&gt;Molecules like complex lipids and carbohydrates are all synthesized by a special class of proteins that catalyze chemical reactions, called enzymes. Since the information of these proteins is coded for in the nucleus, you can imagine that ultimately the synthesis of these molecules does boil down to the genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The basic building blocks that the enzymes use to synthesize complicated molecules come from things you eat. Of course, we eat things that were once alive, and so the molecules that we get have been built up through enzymatic processes in the organisms we eat. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultimately, the &quot;pre-organism&quot; source of most of our molecules is CO&lt;sub&gt;2&lt;/sub&gt; from the air. Plants and photosynthetic algae have proteins that allow them to use the energy of the sun to reduce the carbon, making useful compounds such as glucose.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastEditorUserId="5771" LastEditDate="2014-02-27T21:15:52.403" LastActivityDate="2014-02-27T21:15:52.403" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15402" PostTypeId="2" ParentId="13869" CreationDate="2014-02-27T21:33:12.213" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;My hypothesis is &quot;Yes&quot;, that is &quot;Early human beings are far more&#xA;  promiscuous than we are now&quot;. So how i came up this? Cos Human came&#xA;  from Chimpanzee right?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Also, when human evolved, they started to realized that&#xA;  promiscuousness wss not healthy &amp;amp; not good for society&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm sorry, what ancient society are you claiming cracked down on &lt;strong&gt;male&lt;/strong&gt; promiscuity?  &lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-02-27T21:33:12.213" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15403" PostTypeId="2" ParentId="477" CreationDate="2014-02-27T21:44:19.780" Score="6" Body="&lt;p&gt;Actually there is a polymerase that catalyzes 3' - 5' elongation.  See for example the Thg1 superfamily.  &quot;Doing it in reverse: 3'-to-5' polymerization by the Thg1 superfamily.&quot; Jackman, et al.&lt;/p&gt;&#xA;" OwnerUserId="5871" LastActivityDate="2014-02-27T21:44:19.780" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15404" PostTypeId="2" ParentId="15397" CreationDate="2014-02-27T22:16:10.507" Score="4" Body="&lt;p&gt;Indeed, &lt;i&gt;C. elegans&lt;/i&gt; nematodes (which are the ones you are talking about) do not show cognitive responses. AFAIK, &lt;i&gt;Drosophila melanogaster&lt;/i&gt; is also able to learn and display some quite complex behaviors, but no cognitive functions. I believe the &quot;simplest&quot; organism known to display what could be called &quot;cognitive&quot; functions is the honeybee (see for example &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24107530&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But as to your question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;to demonstrate something more than mere scripted actions&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would also ask &quot;what is a scripted action?&quot; and to what extend a complex, cognitive response from a monkey or a human isn't also scripted (though through many different interacting pathways)?&lt;/p&gt;&#xA;" OwnerUserId="5757" LastActivityDate="2014-02-27T22:16:10.507" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15406" PostTypeId="1" CreationDate="2014-02-28T03:30:36.210" Score="0" ViewCount="6666" Body="&lt;p&gt;I would appreciate it someone could explain clearly how the genes in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Lac_operon&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;lac&lt;/em&gt; operon of E coli&lt;/a&gt; are activated to allow the bacteria to metabolize lactose? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The part that I really don't understand is the activation of the lac operon.  A good answer would make clear to me how the introduction or removal of lactose from the envirnment activates and deactivates the different genes there.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, what are the specific functions of each of the genes (lacA, lacI, lacY, lacZ).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am in AP Biology and I will not see the light of day again if I do poorly on this test. Please help!&lt;/p&gt;&#xA;" OwnerUserId="5859" LastEditorUserId="3632" LastEditDate="2014-02-28T19:37:27.280" LastActivityDate="2014-03-01T08:47:57.600" Title="What is the significance of and biological mechanisms demonstrated in lac operon?" Tags="&lt;gene-expression&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15408" PostTypeId="1" CreationDate="2014-02-28T05:29:44.533" Score="2" ViewCount="338" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/h1bCu.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As indicated in this question, what do you think is is the best explanation for the observed progeny, is it because distance between genes affects recombination frequency? My main concern is question b).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help would be greatly appreciated thanks in advance!!&lt;/p&gt;&#xA;" OwnerUserId="5460" LastActivityDate="2019-02-20T16:02:13.677" Title="Genetics independent assortment?" Tags="&lt;homework&gt;&lt;gene-expression&gt;&lt;genetics&gt;&lt;allele&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15410" PostTypeId="2" ParentId="15408" CreationDate="2014-02-28T07:28:17.800" Score="2" Body="&lt;p&gt;Until now, it looks good. When you are looking at basic mendelian gene linkage problems like these and you find out that the chi square analysis rejects your hypothesis, it means that there is linkage. In that case, you should have a case where your two recombinant genotypes have an approximately equal number of progeny and your two parental genotypes also have an approximately equal number of progeny. In your case, 220 is about 230, and 270 is about 280.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/QXSxe.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/QXSxe.jpg&quot; alt=&quot;testcross&quot; /&gt;&lt;/a&gt;&lt;br /&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;https://greatneck.k12.ny.us/GNPS/SHS/dept/science/krauz/bio_h/images/15_06RecombLinkedGenes_L.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;k12.ny.us&lt;/a&gt;)&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;p&gt;This image is just like your problem. I want you to imagine that b+ and b represent A and a in your problem and that vg+ and vg represent B and b in your problem, respectively. You start out with an AaBb crossed with an aabb. On the gametes line, it lists all of the possible gametes of this cross. On the line where it describes testcross offspring, we see a situation very similar to yours. In this case, AaBb = 965, aabb = 944, Aabb = 206, and aaBb = 185. We have our two pairs: AaBb/aabb and Aabb/aaBb. Sound familiar?&lt;/p&gt;&#xA;&lt;p&gt;The recombinant offspring are defined as the offspring that do not have a genotype of either parents. The reason this is important is because you need a crossover to get a recombinant. The closer two alleles are together on the same chromosome, the harder it is to get one of the alleles to cross over without the other one crossing over with it.&lt;/p&gt;&#xA;&lt;p&gt;Let's clarify. This means that if the alleles are closer, you get less crossovers. All recombinant exist because of a crossover. Therefore, the closer two alleles are, the less recombinants you get.&lt;/p&gt;&#xA;&lt;p&gt;Quick note: the formula for the distance two alleles are from each other is expressed by this formula:&lt;/p&gt;&#xA;&lt;p&gt;100(recombinant frequency) / (total offspring) = distance apart.&lt;/p&gt;&#xA;&lt;p&gt;This is consistant with everything we have said, because as recombinant frequency decreases, distance apart decreases as well.&lt;/p&gt;&#xA;&lt;p&gt;Another way to explain it: on the gametes, AB and ab really like to stay together, as they are LINKED. It is very difficult to separate them. That is why there are more AaBb and aabb; they only require the gametes AB and ab.&lt;/p&gt;&#xA;&lt;p&gt;Apply the formula to find out how far they are apart. I think you can figure out the rest from here. I want you to try and answer the question.&lt;/p&gt;&#xA;&lt;p&gt;Hope this helped! :)&lt;/p&gt;&#xA;" OwnerUserId="5859" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-02-20T16:02:13.677" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="15412" PostTypeId="2" ParentId="14833" CreationDate="2014-02-28T08:25:30.163" Score="1" Body="&lt;p&gt;Adding on to what Martin said. If you imagine an atom to be the size of a football stadium, the nucleus would be the size of a fly on the fifty yard line. The &lt;strong&gt;vast&lt;/strong&gt; majority of an atom is empty space.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the 'classical' view, atoms are mostly empty space and the reason they feel solid is that if you try and push them, the electrons around your atoms bump into the electrons around the other atoms and because they're both negative they repel each other and push away. You feel this force as 'solid'. It's like pushing a really, really stiff spring or trying to force 2 magnets together, except it's electronic in origin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In quantum physics, each particle has a wave function. Wave functions can only exist in certain forms, and when electrons are bound in an atom their waves spread up over a big volume (it's the only way mathematically to get a stable wave, ie an electron that exists. Since it exists, its wave function spreads out much further than the thing you classically think of as an electron). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Electrons have something called antisymmetric wave functions, which means they obey the Pauli exclusion principle: &#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Pauli_exclusion_principle&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Pauli_exclusion_principle&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can't have 2 electrons in the same state (and 'state' includes 'space'. You can have 2 oppositely spinning electrons, but no more in the same place). So atoms spread out because you can't squeeze the wave functions in. The rest of it is electrostatic repulsion just like in the classical model. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sorry if that sounds a little complicated, but it's a combination of quantum physics (which doesn't really make sense, even though it works!) and electronic repulsion (from like-charges-repel).&lt;/p&gt;&#xA;" OwnerUserId="5859" LastActivityDate="2014-02-28T08:25:30.163" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15414" PostTypeId="1" CreationDate="2014-02-28T10:16:40.843" Score="2" ViewCount="2016" Body="&lt;p&gt;Here is the question:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose an experimenter becomes proficient with a technique that allows her to move DNA sequences within a prokaryotic genome. If she moves the promoter for the lac operon to the region between the beta galactosidas gene and the permease gene which of the following would be likely?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the answer: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beta galactosidase will be produced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question to you is: why is this so? I have no idea where this conclusion came from. &#xA;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="5859" LastEditorUserId="5859" LastEditDate="2014-03-01T23:00:19.360" LastActivityDate="2014-03-02T22:43:14.387" Title="Promoter in the lac operon" Tags="&lt;homework&gt;&lt;gene-expression&gt;&lt;genetics&gt;&lt;gene-regulation&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15415" PostTypeId="1" AcceptedAnswerId="15423" CreationDate="2014-02-28T11:35:52.240" Score="1" ViewCount="332" Body="&lt;p&gt;My recent post was tagged as unclear so I wanted to re frame my question. Though I am a layman, I would love to read books and find the stuff, if I get an overall picture of intelligence factor. My question is, how come evolutionary mechanism of protecting ones species made them adapt to their environment ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer comes by the genetic mutation, the switch genes and so on. But how are these cells intelligent to cause such mutation ? For instance, cells don't have intelligence of their own, so presented a situation where in you have to see, but have no eyes, or have to walk but have no legs, how come cells know that they have to work against gravity and develop such structures and hollow bones in birds to make the flight easier ? Does it mean that nature is intelligent ? How come matter itself create gravity, space etc., on one side, and creating beings to overcome it ? Isn't the matter altogether ? If that's the case, imagine a thought experiment, where in we all have dangerous predators which are 4D beings. So since our cognitive and visual percepts  are just designed to perceive 2 dimensions at a time, we being 3D creatures. So over thousands of years, since we have to live and survive, would we develop a vision that can see 3D ? It would be amazing then. It then means that there is an intelligence factor in nature that tells the creatures how to change ! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please do answer, and again repeating I want to hear, how Genes know that they have to work against gravity, or develop a particular efficient thing, that can solve the problem. Otherwise it's as if Genes permute infinitely, and then develop all possible models, and only those which serve the purpose will stay. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please do clarify. &#xA;Thanks !  &lt;/p&gt;&#xA;" OwnerUserId="5874" LastEditorUserId="5144" LastEditDate="2014-03-07T16:58:15.237" LastActivityDate="2014-03-17T17:52:38.457" Title="Evolution (Reductionism)" Tags="&lt;evolution&gt;&lt;mutations&gt;&lt;intelligence&gt;" AnswerCount="3" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="15416" PostTypeId="2" ParentId="15415" CreationDate="2014-02-28T11:44:28.887" Score="5" Body="&lt;p&gt;Too long for a comment:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution and mutation has nothing to do with intelligence and is not influenced by the cells itself. It happens by chance and if the mutation turns out to be beneficial (or at least not harmful for the moment) it will be a selection advantage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something to think about: If a mutation in an enzyme which is responsible for Glucose metabolization allows bacteria to also metabolize another sugar (lets say Galactose) with the same enzyme, this will not change anything for the moment. If these cells are living in a substrate where glucose gets a limiting nutrient but which contains still a lot of galactose, these bacteria will have a growth advantage and overgrow the other strain. Eventually the strain, which can only metabolize glucose will disappear completely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution is also a very gradual and slow process. So it is not &lt;em&gt;boom&lt;/em&gt; suddenly birds appear on the sky, it is a process which took millions of to happen. All the things which allow birds to fly (hollow bones, feathers and so on) developed slowly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genes do not know anything, since they have no consciousness. They are &quot;simply&quot; building blocks. They also don't solve any problems, they are only expressed, not more. &#xA;It is like you write, genes acquire mutations, which allows changes in function or morphology. As stated above: This is a slow and steady process with a lot of dead ends.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-02-28T14:10:29.143" LastActivityDate="2014-02-28T14:10:29.143" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15419" PostTypeId="2" ParentId="15414" CreationDate="2014-02-28T14:10:27.807" Score="1" Body="&lt;p&gt;I believe the answer should be that permease is expressed. &#xA;&lt;img src=&quot;https://i.stack.imgur.com/qB26J.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see from the image, if the operator is moved between Z gene and Y gene, Y gene should be expressed and permease should be made.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-02-28T14:10:27.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15420" PostTypeId="1" AcceptedAnswerId="15421" CreationDate="2014-02-28T14:24:42.753" Score="5" ViewCount="8634" Body="&lt;p&gt;I get air bubbles while pipetting small volumes. How can I avoid them ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="948" LastEditDate="2014-03-03T16:44:21.183" LastActivityDate="2014-03-03T16:44:21.183" Title="How to avoid air bubbles while pipetting?" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;protocol&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15421" PostTypeId="2" ParentId="15420" CreationDate="2014-02-28T14:42:34.247" Score="10" Body="&lt;p&gt;You're still pipetting too fast, you should move the piston slowly and evenly to avoid air bubbles. Also make sure that you wait a second or two for the liquid to rise before moving the tip out of the liquid reservoir. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pipettes can also behave rather weird with any liquid that differs significantly in any physical property from water, e.g. very viscous solutions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find a few more tips &lt;a href=&quot;http://www.eppendorf.com/int/index.php?l=41&amp;amp;action=document&amp;amp;sitemap=1&amp;amp;docnode=53708&quot;&gt;in this document from Eppendorf&lt;/a&gt; or &lt;a href=&quot;http://www.pipettecalibration.net/pipette-calibration-files/Guide-To-Pipetting-2.pdf&quot;&gt;this one from Thermo Scientific&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-02-28T14:42:34.247" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15422" PostTypeId="2" ParentId="15414" CreationDate="2014-02-28T14:54:09.620" Score="2" Body="&lt;p&gt;Since @biogirl has given an answer, I'll add my opinion: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&amp;beta;-galactosidase would be expressed but the permease and transacetylase would not.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The operator lies adjacent to/slightly overlaps the promoter, upstream of the lacZ gene. Binding of the repressor to the operator blocks the promoter, and induction of theoperon involves the repressor leaving the operator unoccupied. If you precisely excised the operator and transplanted it between the lacZ and lacY genes then I think the promoter would be constitutively expressed leading to &amp;beta;-galactosidase synthesis, but the operator would block the polymerase from transcribing the permease gene. In this view the operator would be acting more like a terminator.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, if an inducer was added it would relieve the effect of the transplanted operator and the downstream genes would be transcribed. It's even possible that this experiment has been done sometime in the last three decades.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;added later:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The OP has now edited the question in such a way as to make my answer, and the answer from @biogirl, nonsensical. The original wording referred to moving &quot;the lac operon&quot; not &quot;the lac promoter&quot;, hence my question in a comment asking &lt;em&gt;&quot;operon&quot; or &quot;operator&quot;?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll leave my answer here, but this question is now so compromised that I advise everyone to just forget about it.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-03-02T22:43:14.387" LastActivityDate="2014-03-02T22:43:14.387" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15423" PostTypeId="2" ParentId="15415" CreationDate="2014-02-28T15:07:32.100" Score="10" Body="&lt;p&gt;I think we may be missing a piece from &lt;strong&gt;Darwin's original hypothesis&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An outline of the first 4 chapters of &lt;a href=&quot;http://www.literature.org/authors/darwin-charles/the-origin-of-species/index.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Origin of Species&lt;/a&gt; form the kernel of the Theory of Evolution:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;1: Variation under Domestication &#xA;2: Variation under Nature &#xA;3: Struggle for Existence&#xA;4: Natural Selection&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Really you can't reduce evolution to less than variations; competition (struggle) ; selection.  that's about as far as you can go and still call it evolution.  Even &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_algorithm#Methodology&quot; rel=&quot;nofollow noreferrer&quot;&gt;genetic algorithms&lt;/a&gt; which don't use living organisms at all have these 3 steps.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most people don't have an issues with Variation any more.  At one time it was thought that individual variations were not important, but now most people understand that one water bug might have significant individual differences from other water bugs and its not just people who look at each other and marvel at individual traits.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The struggle for existence was difficult for people to accept at the time, but its simply that most living things don't make it.  Darwin had noticed that each spring that a typical bird pair might have 3-4 eggs in their nest but if you do the numbers it tells a story of how much of a struggle life can be even if we don't see it on a walk in the woods.  If all eggs reached maturity and reproduced, a single pair of birds would generate enough birds to cover England in about 40 years.  That's just a squeak under 3.5^40 without death from old age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The struggle for existence hints how competitive Selection is.  In their breeding lifetime, to have a static population of birds, a breeding pair produces 2 breeding offspring out of perhaps 14 eggs lain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a given that genes don't know that they have to do &lt;em&gt;anything&lt;/em&gt;, but if they don't work well they will not be seen again. Their host dies from a developmental issue, falls and hurts itself doesn't display the right plumage, isn't fast enough to catch its food, is so slow that it gets eaten, its seed falls on soil it cannot germinate in, etc etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The list is endless as to the things that can go wrong in the wild and would cause an individual to be removed from the gene pool and they don't produce offspring. All of the important qualities that genes need to have is mysteriously embedded in what we call the environment - the earth, the air, the water the behavior of other living things decide whether most genes make it or not. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you need any more evidence that intelligence has nothing to do with evolution, then look at human beings... not getting along well with other living things well now - is that smart? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;An example of selection&lt;/strong&gt;&#xA;Since it was requested, let me expand and give a very simple example of random selection that I've always liked (Disclaimer: maybe because I made it up as far as I know!). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take a box of 100 coins.  We want all 100 coins to be heads up, but we can't individually flip any of the coins over: we can only shake the box.  Note that when we shake the box - nothing is thinking or acting consciously.  Genes do permute randomly and, for all reasonable approximations of infinity, infinitely, but they tend to stick around when something works.  This makes evolution seem unnaturally quick to respond.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Method 1: shake the box, looking every time. There are 2^100 combinations.  Getting terribly lucky we'd have to shake the box 2^97 times before we accidentally caught a box of all heads up coins.  That's random chance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Method 2: if we remove the coins that are heads up every time we shake the box, we'll be shaking the box 8 times or so.  That is similar to a strong selection case in evolution: the coins which are heads up are like traits which have an advantage so they stay around.  Its striking how efficient this can be and how many tremendous changes can happen in a short time if there is selection and advantage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that we have plenty of bad traits here (tails up); they show up all the time - with great frequency.  They just don't stick around because the struggle for existence is so challenging. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can further get an idea of weaker selection if you can imagine that instead of the heads always staying heads, you have a little stickiness on the tails of the coins.  80% or 60 or 52% of the time these coins stick and stay as heads.  It still will not be long before you find that the coins are mostly heads.  10 20 or 30 shakes of the box rather than 8.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Where do new traits come from then?&lt;/strong&gt;&#xA;So taking all this and thinking about how new traits like eyes which had not been&#xA;seen before, the same blind and random process applies.  It is better not to think of humans and human traits - we're the product of over a billion years of selection and evolution!   Think how primal traits at the bacterial level emerge.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below is a picture of &lt;a href=&quot;http://www.amusingplanet.com/2012/06/multicolored-salt-ponds-at-san.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;salt pools in the San Francisco Bay&lt;/a&gt;.  Evaporation increases the salt concentration in the pools and as they become inhospitable, &lt;a href=&quot;http://halo.umbi.umd.edu/~dassarma/halophiles.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;halophilic (salt loving) bacteria&lt;/a&gt; take over. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HKgHK.jpg&quot; alt=&quot;salt pools&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pools are colored because these bacteria have an ancient mechanism which allows them to harvest light to pump the salt out of their bodies and help create energy as well.  The light is harvested in one well documented case by a &lt;a href=&quot;https://en.wikipedia.org/wiki/Retinol&quot; rel=&quot;nofollow noreferrer&quot;&gt;retinol&lt;/a&gt; molecule which absorbs blue light.  Retinols are a variation on vitamin A and must be quite ancient.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet a similar molecule, retinal, is used in human eyes as the light sensor there.  A similar protein holds those light sensing molecules in both &lt;a href=&quot;https://en.wikipedia.org/wiki/Rhodopsin&quot; rel=&quot;nofollow noreferrer&quot;&gt;human&lt;/a&gt; and &lt;a href=&quot;http://www.rcsb.org/pdb/101/motm.do?momID=27&quot; rel=&quot;nofollow noreferrer&quot;&gt;halophile&lt;/a&gt; as well. While the structure of the eye and the nervous system that processes information into the brain all came later, you can see at one point the interaction with a bacterium with light became so useful that once it evolved, it has stayed in the gene pool since the days of bacteria to be the light sensor.  Vitamin A is the product of a biosynthetic pathway that very easily makes a variety of molecules.  The light sensing genes that used them evolved once, but variations on it sense light in our eyes today. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-03-17T17:52:38.457" LastActivityDate="2014-03-17T17:52:38.457" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="15424" PostTypeId="1" CreationDate="2014-02-28T16:50:55.603" Score="1" ViewCount="245" Body="&lt;p&gt;I am writing an article where I describe real-time PCR experiments. My collaborator, after reviewing the article, consistently replaced the word &quot;parallels&quot; with &quot;replicates&quot;. Are they not synonymous? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I prefer the word parallel, because, in the context of PCR, it implies that these three identical experiments were performed in the same real-time PCR run (and not consecutively). &lt;/p&gt;&#xA;" OwnerUserId="5369" LastEditorUserId="6" LastEditDate="2014-02-28T18:59:42.640" LastActivityDate="2014-02-28T22:25:38.793" Title="parallels or replicates?" Tags="&lt;terminology&gt;&lt;pcr&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15426" PostTypeId="2" ParentId="15424" CreationDate="2014-02-28T22:25:38.793" Score="2" Body="&lt;p&gt;The explanation I got when learning how to do qPCR was that you need run both replicate experiments and parallel experiments to get publishable data. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Replicates (or biological replicates) would be qPCR runs on independently collected samples. That does not count your control vs your experimental groups. So for my work I had to collect 3 sets of control tissue and 3 sets of experimental tissue from independent sets of animals (in my case 3 generations but for mammalian work I think three different animals would be ok). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Parallel does imply that you ran the the samples together in the qPCR machine. I think the standard is that for each sample in a particular replicate you need to run three qPCR reactions in parallel. So in total you need to run 9 wells of qPCR reactions for each test group.&lt;/p&gt;&#xA;" OwnerUserId="5869" LastActivityDate="2014-02-28T22:25:38.793" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15427" PostTypeId="2" ParentId="14148" CreationDate="2014-02-28T22:26:36.917" Score="5" Body="&lt;p&gt;One thing I think you're missing: a perceptron model and a spiking model aren't mutually exclusive. In fact, in perceptrons, people usually use a sigmoid function. That's not a coincidence: it kind of simulates a spike. If you were to model an organism such as C. elegans, whose neurons aren't spiking (but use &quot;graded action potentials&quot;), you would use another type of activation function (by the way, if you like the Human Brain Project, you should also check the &lt;a href=&quot;https://en.wikipedia.org/wiki/OpenWorm&quot; rel=&quot;noreferrer&quot;&gt;Openworm&lt;/a&gt; project, which is much more realistic and already gives &lt;a href=&quot;https://www.youtube.com/watch?v=D8ogHHwqrkI&quot; rel=&quot;noreferrer&quot;&gt;some interesting outcomes&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, back to the point. When you try to model learning and generation of memory, you often end up dealing with plasticity. Just a quick explanation: a neuron does fire an Action Potential (AP) when its transmembrane potential gets above a limit. The potential itself changes due to the inputs from other neurons. But all the inputs don't have the same weight. Let's say you look at neuron A, which gets synapses from neurons B, C, D... If B fires at the same time as C, it can be enough to create an AP from A. But, even in combination with B or C, D doesn't elicit enough transmembrane potential variation to create an AP; it has to fire exactly at the same time as E, F, G and H to get enough &quot;firepower&quot; to activate A.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if each time D fires, A gets an AP (because of the simultaneous activation of other incoming neurons), then you could say D is &quot;useful&quot; for A, and (depending on the type of neuron and other parameters) the weight of D can increase, so that, after a while, D is able to elicit an AP in A just by firing at the same time as any other incoming neuron. That's a plasticity phenomenon. Note that here, it is a really simple hypothetical example. And also that the idea that learning results from plasticity is more and more being challenged.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if you want to understand how learning and memory happen, you might be interested in the weights of the connections only, and how they evolve depending on the network's activity. In that case, a perceptron model is a good way to go.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Now, the big new thing these days with artificial neural networks is simulating them with biological precision- that is, with spiking&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, as you already mention in your question, this is a matter of choosing a model that you're going to use (as a researcher trying to understand the brain). This is &lt;em&gt;not&lt;/em&gt; trying to give an accurate depiction of how the brain really is. If you're interested in the weights of the connections, you can use a neural networks approach (and this is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3876265/&quot; rel=&quot;noreferrer&quot;&gt;not outdated&lt;/a&gt;), and you don't care about a single ion channel on the membrane of a neuron. But alternatively, you can also dedicate your life to understanding the structure of a single ion channel, and how simple details can determine the whole working of the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Projects such as the Human Brain Project are trying to create a &quot;biologically exact&quot; model of the brain. So, it involves modeling the spikes, as well as the network organization, as well as single ion channels. So, in that case they don't need to use paradigms such as artificial neural networks, since the network's behavior should be a result of the single neurons' modeling: that would be an &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S095943881300189X&quot; rel=&quot;noreferrer&quot;&gt;emergent response&lt;/a&gt;. However, they don't have anymore the simplifications brought by other models, so, they need huge computational power, and they also face new problems: for example they have to give values to all the individual parameters of their models, some of which are currently unknown, and could even not exist at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I think this gives answers your question, in the sense that it is not the brain which evolved to pick a model, but the scientists who try to modelize one particular aspect of the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I see in fact this question is quite old; sorry it was a suggestion on the right which brought me here. But I think my answer can still bring an aspect which wasn't already mentioned in the other answers. So I hope you will see it.&lt;/p&gt;&#xA;" OwnerUserId="5757" LastActivityDate="2014-02-28T22:26:36.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15428" PostTypeId="2" ParentId="15406" CreationDate="2014-03-01T06:16:53.617" Score="1" Body="&lt;p&gt;The &lt;em&gt;lac&lt;/em&gt; operon in E coli is a set of four genes which work together to allow the bacterium to make use of lactose for energy. An &lt;a href=&quot;https://en.wikipedia.org/wiki/Operon&quot; rel=&quot;nofollow noreferrer&quot;&gt;Operon&lt;/a&gt; is a set of genes which are co-transcribed on a single mRNA, controlled from a common promoter.  While operons are nearly always found in bacteria, eukaryotes (and viruses that infect eukaryotes) do have some sets of genes organized into operons. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;lacZ and lacY is the business end of the lac operon. They are the only 2 genes necessary for lactose usage in the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;lacZ&lt;/em&gt; codes for beta-galactosidase, an enzyme that cleaves the lactose disaccharide into D-galactose and D-glucose.  Most of know that glucose is an important source or energy via the glycolysis pathway, which is highly connected energy usage in the cell.  Galactose is readily converted by an enzyme (galactose mutarotase) into glucose, making lactose an efficient source of energy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EXUpt.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;lacY&lt;/em&gt; codes for a protein found in the cell membrane called &lt;a href=&quot;https://en.wikipedia.org/wiki/Lactose_permease&quot; rel=&quot;nofollow noreferrer&quot;&gt;lactose permease&lt;/a&gt; which pumps lactose into the cell from the outside using the proton gradient inside the cell for its motive force.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;lacA&lt;/em&gt; gene codes for an enzyme which transfers an acetyl group to galactose, which may prevent the buildup of galactose in the cell.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The way the operon works is more important than what it does.  the lac operon was one of the first examples of transcription regulation every studied.  lacI is not in the lac operon, but it is the single gene which controls whether the operon is copied to RNA from the chromosome.  lacI is translated to the lac repressor protein (LacI), which binds to one of three sites in front of the lac operon.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;lacI is a repressor gene - when it is active, it prevents the lac operon from being transcribed into RNA.  LacI is a tetramer - four copies of the protein form a complex.  LacI binds to allolactose, a derivative of lactose, when it is present in sufficient quantities, which then causes it to release itself from the chromosomal DNA, allowing transcription to occur and the lac genes may be expressed. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1320" LastEditDate="2014-03-01T08:47:57.600" LastActivityDate="2014-03-01T08:47:57.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15429" PostTypeId="1" CreationDate="2014-03-01T09:47:47.627" Score="1" ViewCount="3112" Body="&lt;p&gt;My question is actually my long term doubt. I have seen most of the flowers turning into fruits. But why not this jasmine flower?&lt;/p&gt;&#xA;" OwnerUserId="5880" LastActivityDate="2014-03-01T15:15:18.013" Title="All flowering plants gives fruits. Why does jasmine flower plant not yield fruits?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15430" PostTypeId="2" ParentId="15429" CreationDate="2014-03-01T15:15:18.013" Score="6" Body="&lt;p&gt;Flower gives rise to seeds and fruits which are the ways through them the plant distributes the seeds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here, one should differentiate botanic term &quot;fruit&quot; and general common meaning of the word &quot;fruit&quot; which are not the same. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Botanic fruit can be subtle, not fleshy and come as a grain or pods. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Jasmine fruits are black berries.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bphxz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2014-03-01T15:15:18.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15431" PostTypeId="1" AcceptedAnswerId="15433" CreationDate="2014-03-01T15:59:33.150" Score="15" ViewCount="5322" Body="&lt;p&gt;I understand there are two kinds of active vaccination&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Injecting complete viruses that are weakened to not cause the disease being vaccinated against&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Injecting only antigen particles of viruses that the body creates antibodies for. So the disease can't arise, not even in a weakened form.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I am wondering how the viruses for vaccination are weakened. Is this simply a process where randomly parts of the virus DNA/RNA are taken out and tested on animals, and as soon as it is sufficiently weakened, it is considered suitable? Or is this an analytical and systematic process?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering because some popular vaccinations (including that against measles) can still (very rarely) cause fatal complications. Which made me think whether it's systematic or just &quot;accelerated mutation and selection&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested in an answer for layman, if that is possible at all.&lt;/p&gt;&#xA;" OwnerUserId="304" LastEditorUserId="3776" LastEditDate="2014-03-01T18:01:02.460" LastActivityDate="2015-11-12T21:22:01.290" Title="How are viruses weakened to be suitable for vaccination?" Tags="&lt;virus&gt;&lt;vaccination&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15432" PostTypeId="1" AcceptedAnswerId="15438" CreationDate="2014-03-01T17:09:24.663" Score="2" ViewCount="1895" Body="&lt;p&gt;I think no, but I am not sure since Listeria is Gram-positive and probably has lipopolysaccharide (exception among Gram positive bacteria).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can Listeria monocytogenes' endotoxin act like exotoxin A-B?&lt;/strong&gt;&#xA;(In which component B lets component A inside the cell and component A causes the toxicity.)&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1320" LastEditDate="2014-03-01T22:50:04.710" LastActivityDate="2014-03-02T22:47:45.003" Title="Can Listeria monocytogenes endotoxin act as an A-B toxin?" Tags="&lt;microbiology&gt;&lt;bacterial-toxins&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15433" PostTypeId="2" ParentId="15431" CreationDate="2014-03-01T17:50:56.707" Score="12" Body="&lt;p&gt;There is a Wikipedia page on the topic of &lt;a href=&quot;http://en.wikipedia.org/wiki/Attenuated_vaccine&quot;&gt;attenuated vaccines&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically the idea is that the virus is grown on some sort of foreign host such as cells in culture, eggs or an animal. This selects for mutant viruses, present in the original population, which are pre-adapted to the new host (so that they grow better). By repeating this process several times it is possible to develop a new variant of the virus which grows poorly in the original host (i.e. humans) but is still able to stimulate an immune response. The resulting antibodies, will recognise a subsequent infection by the original disease-causing virus as long as the viral component responsible for the immune response is still present in the attenuated virus that is used for vaccination.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-01T17:50:56.707" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15434" PostTypeId="2" ParentId="15431" CreationDate="2014-03-01T22:44:49.577" Score="7" Body="&lt;p&gt;There are basically three classical possibilies:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Using an attenuated virus as Alan described in his answer&lt;/li&gt;&#xA;&lt;li&gt;use only parts of viruses (here mostly proteins, which are displayed&#xA;on the surface of the virus and which can be recognized by the immune&#xA;system)&lt;/li&gt;&#xA;&lt;li&gt;inactivated viruses (here often formaldehyde is used, which changes&#xA;parts of the proteins, the formaldehyde is then cleaned away to have&#xA;the vaccine free of it)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The part you describe about using DNA from a virus is done these days. It is called &quot;reverse vaccinology&quot; and uses conservation analysis between different strains (this is also used for bacteria) to get a vaccine which covers as much different strains as possible. For the vaccine, proteins are selected which are conserved as good as possible and which show no similarities to human proteins (you don't want to induce autoimmunity). Candidate proteins for a vaccine are then expressed biotechnically and tested if they work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Complications in vaccinations (which are really rare, for measles the chance for complications is 3-4 orders of magnitude lower than when actually get the disease) are usually due to allergic reactions.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-11-12T21:22:01.290" LastActivityDate="2015-11-12T21:22:01.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15435" PostTypeId="1" AcceptedAnswerId="15437" CreationDate="2014-03-02T01:19:19.113" Score="4" ViewCount="259" Body="&lt;p&gt;In order to initiate glycolysis, 2 ATP are necessary. In the glycolytic process, you generate an additional 4 ATP, which results in a net gain of 2 ATP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you don't undergo glycolysis, however, then you have an extra 2 ATP not being used. If you do glycolysis, you still got only 2 ATP. Am I missing something here?&lt;/p&gt;&#xA;" OwnerUserId="4478" LastEditorUserId="16299" LastEditDate="2015-12-31T19:19:56.457" LastActivityDate="2015-12-31T19:19:56.457" Title="What's the point of glycolysis in fermentation?" Tags="&lt;metabolism&gt;&lt;cellular-respiration&gt;&lt;fermentation&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15436" PostTypeId="2" ParentId="15435" CreationDate="2014-03-02T02:27:37.463" Score="3" Body="&lt;p&gt;Remember that glycolysis yields 2 NADH as well as 2 net ATP. This NADH can be used to a terminal electron acceptor to produce an end product with a net gain of ATP. End-products of fermentation can include lactate, acetate, butyrate, propionate and ethanol, all of which generate different amounts of additional ATP. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact pathways involved vary according to the organism, but anywhere between 1 (or even 0.5) and 4 additional ATPs can be generated, even without the involvement of oxygen. In the case of aerobic respiration of course, the NADH feeds into the electron transport chain and yields ATP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: It's perhaps worth noting that the 2 ATP is &lt;em&gt;gained&lt;/em&gt;. See @SatwikPasani's answer for the math.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastEditorUserId="3631" LastEditDate="2014-03-02T15:03:01.927" LastActivityDate="2014-03-02T15:03:01.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15437" PostTypeId="2" ParentId="15435" CreationDate="2014-03-02T02:42:18.473" Score="3" Body="&lt;p&gt;Suppose the cellular pool has $x$ATP before starting glycolysis. In the initial phosphorylation steps, we use up two ATP to get the total tally at $(x-2)$ATP. The following steps yields $4$ ATP which brings the final total to $(x+2)$ATP.&lt;br&gt;&#xA;Assuming the cell is performing fermentation, the two additional $NADH$ formed will not be contributing to any ATP gain. And hence we &lt;em&gt;earn a total of $2$ ATP in excess of the already existing amount&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2014-03-02T02:42:18.473" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15438" PostTypeId="2" ParentId="15432" CreationDate="2014-03-02T10:29:21.383" Score="6" Body="&lt;p&gt;Considering great research we did after the answer was accepted, I should add important information about the topic. The old (and accepted) answer follows in &quot;&quot; marks for the sake of clarity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We found that in spite of the earlier reports, the newest ones failed to find endotoxin-like structure in the Listeria born material. Most academic discussions about the issue say there is no such thing called &quot;listeric endotoxin&quot;, thus I gave a right answer to a &quot;compromised&quot; question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I should say that question is still brilliant because it promoted great research and should be an important source for everyone looking for information about listeric &quot;endotoxin&quot;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Listeria endotoxin is not a protein. Thus, is lacks enzymatic activity&#xA;  and acts indirectly by binding to sensitive receptors on macrophages. &#xA;  Thus, it can not cause lysis itself.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Considering AB-exotoxins, A-subunit is a protein that has enzymatic&#xA;  activity (responsible for toxin action)  and subunit B has no&#xA;  enzymatic activity (protein responsible for binding to receptors).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Thus, the answer to your brilliant question is NO, Listeria endotoxin&#xA;  cannot act as AB-exotoxin being nonprotein and non enzymatic&#xA;  substance.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Also, don't be confused with Listeriolysin O, which is listeria's&#xA;  eXotoxin protein which is pore-creating protein.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="1320" LastEditDate="2014-03-02T22:47:45.003" LastActivityDate="2014-03-02T22:47:45.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15439" PostTypeId="2" ParentId="15432" CreationDate="2014-03-02T13:09:18.337" Score="5" Body="&lt;p&gt;Just to add some important relevant information to the answer from @Ilan.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;There is no evidence for the presence of &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipopolysaccharide&quot; rel=&quot;nofollow noreferrer&quot;&gt;endotoxin/lipopolysaccharide&lt;/a&gt; in &lt;em&gt;Listeria&lt;/em&gt;.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;There was an early report of the presence of LPS (Wexler &amp;amp; Oppenheim, 1979) but this was contradicted by a later study (Maitra &lt;em&gt;et al&lt;/em&gt;., 1986). The endotoxin activity of Gram negative bacteria is strongly associated with the &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipid_A&quot; rel=&quot;nofollow noreferrer&quot;&gt;lipid A moiety&lt;/a&gt; of the LPS. Lipid A is synthesised from N-acetylglucosamine in a three step pathway encoded by the genes lpxA, lpxC and lpxD. I obtained the sequences for the corresponding &lt;em&gt;E. coli&lt;/em&gt; gene products and conducted BLAST searches against the &lt;em&gt;Listeria monocytogenes&lt;/em&gt; genome with these results:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;lpxA - best hit E=0.11&lt;/p&gt;&#xA;&lt;p&gt;lpxC - no significant hit&lt;/p&gt;&#xA;&lt;p&gt;lpxC - best hit E=1e-04&lt;/p&gt;&#xA;&lt;p&gt;the last hit is to a 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase whereas the &lt;em&gt;E. coli&lt;/em&gt; gene encodes a UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase. The similarity in the sequences seems to be because they are both members of a large superfamily of acyltransferases.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I conclude that &lt;em&gt;Listeria monocytogenes&lt;/em&gt; does not not synthesise lipid A and therefore has no LPS, and no endotoxin.&lt;/p&gt;&#xA;&lt;p&gt;Wexler, H., and J. D. Oppenheim. 1979. Isolation, characterization, and biological properties of an endotoxin-like material from the gram-positive organism Listeria monocytogenes. Infect.Immun. 23:845-857.&lt;/p&gt;&#xA;&lt;p&gt;Maitra, SK et al. (1986) Establishment of beta-hydroxy fatty acids as chemical marker molecules for bacterial endotoxin by gas chromatography-mass spectrometry. Appl. Env. Mic. 52: 510-514&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-03-02T18:13:27.560" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15440" PostTypeId="1" CreationDate="2014-03-02T14:14:36.390" Score="2" ViewCount="430" Body="&lt;p&gt;Is there a condition where myopic power changes with ambient brightness. When I drive in the morning in bright sunlight my power is -4.0; however when I wear the same -4.0 glass in the evening (dusk time and night) I cant see properly. The images are blurred. I have to change to -5.0 glass. However the same situation does not happen in my right eye which has a constant -5.0 power in both daylight and night. I have observed this for many years (15+). &lt;/p&gt;&#xA;" OwnerUserId="5886" LastActivityDate="2014-03-02T18:39:27.470" Title="eye myopia power changes with brightness" Tags="&lt;eyes&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15441" PostTypeId="2" ParentId="15440" CreationDate="2014-03-02T15:37:34.503" Score="1" Body="&lt;p&gt;NIGHT MYOPIA -  is a tendency for eyes to become near-sighted in dim illumination.  There are multiple theories explaining the phenomenon, most of them are related to accommodation or chromatic shift in scotopic light conditions when to light is focused before the fovea thus worsening the existing myopia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Citation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In dark adaptation the eye becomes more sensitive to shorter wave&#xA;  lengths (Purkinje shift- In the light-adapted eye the region of&#xA;  maximal brightness is in the yellow; in the dark adapted eye, the&#xA;  region of maximal brightness is in the green),and visual acuity&#xA;  depends on parafoveal blue cones. Shorter wavelengths come into focus&#xA;  in front of the retina, and this chromatic aberration accounts for&#xA;  some of the relative myopia that a normal eye experiences at night;&#xA;  much of the remainder is due to an increase in accommodative tone in&#xA;  the dark.  It is also called dark focus of accommodation, or tonic&#xA;  accommodation, or resting state of accommodation. Consequently, a&#xA;  measurement of the refraction (i.e. the determination of appropriate&#xA;  optical glasses to obtain good vision on these distant objects) gives&#xA;  the result that the eye is myopic. Night myopia can reach values of up&#xA;  to about - 4.0 D. Night myopia decreases with age31 and therefore it&#xA;  can be of special importance for young drivers at night. In one&#xA;  experiment with people aged 16 to 25 years, 38% had night myopia of -&#xA;  0.75 D or more, and 4% had – 2.50 D or more. Cause of Night Myopia:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Spherical aberration (The optical effect of the larger pupil decreases&#xA;  the depth of focus) Chromatic aberration. Parkinje shift Ciliary spasm&#xA;  At low light levels there is a change of the biochemistry of imaging&#xA;  on the retina: in bright light the receptors in the retina are cones&#xA;  with higher image acuity, and imaging of colors, whereas in low light&#xA;  the receptors in the retina are rods with reduced image acuity, and&#xA;  imaging of black and white only. The transition between both states,&#xA;  i.e. to get maximum sensitivity when moving from the bright to the&#xA;  dark, doesn't happen immediately, but takes some minutes33. This is a&#xA;  problem e.g. when driving a car in sunlight and entering a tunnel. The&#xA;  low light imaging by rods in the retina can be further reduced by a&#xA;  lack of vitamin A and zinc Symptoms:&#xA;  1. Blur vision only in low luminance.&#xA;  2. Feeling discomfort while maintaining fixation in low illumination level.&#xA;  3. Difficulty in night driving.&#xA;  4. Hallows around light.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2014-03-02T18:39:27.470" LastActivityDate="2014-03-02T18:39:27.470" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15443" PostTypeId="2" ParentId="3722" CreationDate="2014-03-02T19:59:44.120" Score="1" Body="&lt;p&gt;i tried this experiment but failed.&#xA;The reason for our failure in this experiment might be as follows:&#xA; 1. The grape coating might be immpermeable.&#xA; 2. It may happen that the solution might not be hypertonic but isotonic(equal concen. of solutes in both)&#xA; 3. The salt solution might be less dilute than the sugar one.&#xA;i am just a student but giving my point of veiw....&lt;/p&gt;&#xA;" OwnerUserId="5889" LastActivityDate="2014-03-02T19:59:44.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15444" PostTypeId="1" CreationDate="2014-03-02T20:44:21.833" Score="3" ViewCount="3746" Body="&lt;p&gt;What are the highest and lowest possible values of pH, $paCO_2$, and $HCO_3$ in the (arterial or venous) blood of a living human being?&lt;/p&gt;&#xA;" OwnerUserId="3475" LastEditorUserId="9268" LastEditDate="2014-09-27T17:21:04.057" LastActivityDate="2014-09-27T23:27:14.590" Title="What are the highest and lowest possible pH, paCO2 and HCO3 in the blood of living human?" Tags="&lt;physiology&gt;&lt;respiration&gt;&lt;ph&gt;&lt;renal-physiology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15445" PostTypeId="2" ParentId="3722" CreationDate="2014-03-02T22:08:02.307" Score="3" Body="&lt;p&gt;It is important to note that osmotic pressure is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Colligative_properties&quot; rel=&quot;nofollow&quot;&gt;colligative property&lt;/a&gt;, which means that it does not depend on the identity of the solutes, but simply their concentration. This also means that in considering the grape, we have to estimate the concentration of all solutes, not just the one you used to make the (possibly) hypertonic solution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll assume the sugar used was sucrose, which is the common table sugar. I guess I should also mention that I'll assume the salt was NaCl, which is the common table salt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sucrose&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; says that the solubility of sucrose is 2000 g/L. As the molar mass is 342.3 g/mol, the concentration is approximately 5.8 M.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sodium_chloride&quot; rel=&quot;nofollow&quot;&gt;NaCl&lt;/a&gt; on the other hand, has a solubility of 359 g/L. At 58.44 g/mol, the concentration is approximately 6.1 M. However, the Na&lt;sup&gt;+&lt;/sup&gt; and the Cl&lt;sup&gt;-&lt;/sup&gt; dissociate in water, so the concentration is effectively double when counting solutes. That gives 12.2 M, which is much higher than a sugar solution. This accounts for why grapes would shrivel in a salt solution more than in a sugar solution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to why the grapes did not shrink in a sugar solution - I don't think it is unreasonable for a grape to have total solute concentration in the range of 5.8 M. Estimates of the sugar concentration in a grape are given in % w/w. Clearly grapes are denser than water (you can test this by putting a grape in water and seeing it sink). Therefore if you were to calculate in % w/v, you would find it to be more concentrated than a the same % w/w solution in water. Moreover, according to &lt;a href=&quot;http://thepaleodiet.com/fruits-and-sugars/&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt; grapes have a significant amount of glucose and fructose. These are monosaccharides, as opposed to sucrose which is a disaccharide. This means for the same mass of &quot;sugars&quot; there are more individual sugar molecules, resulting in more osmotic pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In sum, I think the sugar solution is probably isotonic, not hypertonic.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-03-02T22:08:02.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15446" PostTypeId="1" CreationDate="2014-03-03T02:08:39.043" Score="9" ViewCount="216" Body="&lt;p&gt;Ribosomes can read mRNA and produce proteins, if we somehow make a circular mRNA for the ribosome to bind onto, it will make infinitely long &quot;proteins&quot;, (since ribosomes can make very big proteins, I assume they can bind long enough before disassociating)&#xA;However after doing some search on this topic, it seems that I am able to find only about 2 related papers. One of them seems to be from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1369681/&quot;&gt;1998&lt;/a&gt;, while the other one is more &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/anie.201302044/abstract&quot;&gt;recent&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These articles suggest that it's doable. If this works, we'll be able to produce biopolymers with the sequence exactly as we designed, there would be massive applications, but I'm curious why it's not getting much attention, or why aren't there more papers related to this area? &lt;/p&gt;&#xA;" OwnerUserId="5819" LastEditorUserId="3340" LastEditDate="2014-12-25T12:12:53.350" LastActivityDate="2015-05-29T03:38:49.797" Title="Circular mRNA to produce long proteins" Tags="&lt;proteins&gt;&lt;mrna&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15447" PostTypeId="1" CreationDate="2014-03-03T03:41:16.617" Score="7" ViewCount="160" Body="&lt;p&gt;In a human, if you were to avoid a tympanotomy (surgical examination of the middle ear), how could you distinguish between a blocked Eustachian tube, a ruptured eardrum, or a perilymph fistula?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, take the situation where a young man (suffering from a common cold) blew his nose violently, became dizzy for 1 minute, and then reported loss of hearing in one ear of about 40%.  What would your diagnosis be, possible treatments, and expected outcome?    &lt;/p&gt;&#xA;" OwnerUserId="5891" LastEditorUserId="9943" LastEditDate="2015-05-23T13:20:36.057" LastActivityDate="2015-05-23T13:22:24.327" Title="How can one accurately diagnose the cause of human hearing loss without surgery?" Tags="&lt;human-biology&gt;&lt;hearing&gt;&lt;human-ear&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15448" PostTypeId="1" AcceptedAnswerId="15450" CreationDate="2014-03-03T05:14:00.000" Score="2" ViewCount="110" Body="&lt;p&gt;After HGP, we are not having many databases which consist of several notepad files of ATCG.... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can we distinguish quantitatively a given A,T,C and G stretch as DNA or Gene? &lt;/p&gt;&#xA;" OwnerUserId="5892" LastActivityDate="2014-03-06T15:56:15.507" Title="Quantitative Differences : DNA and Gene" Tags="&lt;dna&gt;&lt;genetics&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15449" PostTypeId="2" ParentId="15384" CreationDate="2014-03-03T09:13:05.540" Score="2" Body="&lt;p&gt;This is an interesting question.&#xA;Reading this two articles linked below, it seems very much that the connexins are turned over and degraded with the channel more or less staying at the same place (the figure is taken from the first paper, but the second has a similar):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ILmPf.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following this, the connexins are synthesized and then subjected into the ER and then the Golgi for proper protein maturation and oligomerization into hemichannels (misfold proteins are subjected to proteasomal degradation). They are then exported from the trans-Golgi in small vesicles to the cell membrane, transported to the sarcolemma where they form complete gap junction channes with hemichannels from another cell. Single channels aggregate into gap junction plaques.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The connexins are degraded in the proteasome and the lysosome. It is discussed that post-translational modifications as phosphorylation and ubiquitination play an important role here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The degradation seems to take place at the formed channels. This was tested in two ways: When the export of new proteins to the membrane is inhibited, then the connexins in the membrane and the junctions get lost over time. If the proteasome is inhibited, the number is growing. And when both pathways are inhibited (export and degradation) the number is approximately constant. See paper 3 for more details. &#xA;This shows that the process of forming the junctions and degrading the connexins is a permanent and that cells, which form junction with each other stay in the same place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://circres.ahajournals.org/content/86/7/723.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Connexin Expression and Turnover&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://cardiovascres.oxfordjournals.org/content/62/2/256.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pathways for degradation of connexins and gap junctions&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9367633&quot; rel=&quot;nofollow noreferrer&quot;&gt;Degradation of connexin43 gap junctions involves both the proteasome&#xA;and the lysosome.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-03T20:16:46.797" LastActivityDate="2014-03-03T20:16:46.797" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15450" PostTypeId="2" ParentId="15448" CreationDate="2014-03-03T09:52:32.407" Score="4" Body="&lt;p&gt;I interpret your question as: Given a stretch of DNA sequence, can we determine if it encodes a gene? My summary of the answer would be: &quot;Sometimes&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem you ask about is called &quot;Gene prediction&quot; and is described in some detail by Wikipedia:  &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene_prediction&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Gene_prediction&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most basic indication that a gene may exist is the presence of an &quot;Open Reading Frame&quot; (ORF). An ORF is a stretch of DNA from which a single protein may be produced.  However, an ORF is not strictly required for a gene (as not all genes encode proteins), and not all ORFs are genes. There are many software tools for gene prediction available which use different rules to predict if a given region of DNA is functional (contains a gene or a regulatory element). They may be usable on any kind of DNA sequence, or on sequences from certain organisms only, depending on the program.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two commmonly used gene prediction tool are GLIMMER (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi&lt;/a&gt;, used for microbial genomes) and GeneMark (&lt;a href=&quot;http://opal.biology.gatech.edu/gmhmm2_prok.cgi&quot; rel=&quot;nofollow&quot;&gt;http://opal.biology.gatech.edu/gmhmm2_prok.cgi&lt;/a&gt;). See also &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene_prediction&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Gene_prediction&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a quick check, you may also use NCBI BLAST (&lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi&quot; rel=&quot;nofollow&quot;&gt;http://blast.ncbi.nlm.nih.gov/Blast.cgi&lt;/a&gt;) to see if your sequence aligns to a known gene.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-03-03T09:52:32.407" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15452" PostTypeId="1" AcceptedAnswerId="15453" CreationDate="2014-03-03T14:06:35.577" Score="1" ViewCount="146" Body="&lt;p&gt;I am wondering if anyone has seen a data of Giardiasis (Giardia Lamblia) cases  in different countries on the world? I have found for different diseases and also for 'diarrhoea diseases' in general, but I need especially for Giardia Lamblia. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any suggestion where I can try to look for this data will be useful. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you very much!&lt;/p&gt;&#xA;" OwnerUserId="4593" LastActivityDate="2014-03-03T15:34:00.593" Title="Giardia lamblia cases of infections" Tags="&lt;parasitology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15453" PostTypeId="2" ParentId="15452" CreationDate="2014-03-03T15:15:59.400" Score="4" Body="&lt;p&gt;If you have or can get access to it, you might try looking in the Incidence and Prevalence database: &lt;a href=&quot;http://thomsonreuters.com/incidence-and-prevalence-database/&quot; rel=&quot;nofollow&quot;&gt;http://thomsonreuters.com/incidence-and-prevalence-database/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another possibility is the GIDEON database: &lt;a href=&quot;http://www.gideononline.com/&quot; rel=&quot;nofollow&quot;&gt;http://www.gideononline.com/&lt;/a&gt;. It is possible to sign up for a 15-day trial.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For Europe, statistics are available from the WHO CISID at &lt;a href=&quot;http://data.euro.who.int/cisid/&quot; rel=&quot;nofollow&quot;&gt;http://data.euro.who.int/cisid/&lt;/a&gt; (select &quot;all infectious diseases&quot;, then &quot;Giardiasis&quot;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The WHO does not have any global statistics available on their website, so otherwise you might have to piece together data from individual publications. Some examples:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thailand, 2005: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16438174&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/16438174&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Germany, 2006: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=19404678&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed?term=19404678&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;United States, 2006-2008: &lt;a href=&quot;http://www.cdc.gov/mmwr/preview/mmwrhtml/ss5906a2.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.cdc.gov/mmwr/preview/mmwrhtml/ss5906a2.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Portugal, 2002-2008: &lt;a href=&quot;http://www.parasitesandvectors.com/content/5/1/22&quot; rel=&quot;nofollow&quot;&gt;http://www.parasitesandvectors.com/content/5/1/22&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quatar, 2008: &lt;a href=&quot;http://www.parasitesandvectors.com/content/4/1/211&quot; rel=&quot;nofollow&quot;&gt;http://www.parasitesandvectors.com/content/4/1/211&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tajikistan, 2009: &lt;a href=&quot;http://www.parasitesandvectors.com/content/4/1/195&quot; rel=&quot;nofollow&quot;&gt;http://www.parasitesandvectors.com/content/4/1/195&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ivory Coast, 2009: &lt;a href=&quot;http://www.parasitesandvectors.com/content/4/1/96&quot; rel=&quot;nofollow&quot;&gt;http://www.parasitesandvectors.com/content/4/1/96&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tanzania, 2011: &lt;a href=&quot;http://www.parasitesandvectors.com/content/6/1/3&quot; rel=&quot;nofollow&quot;&gt;http://www.parasitesandvectors.com/content/6/1/3&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ghana, 2006-2009: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170632/?report=classic&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170632/?report=classic&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Canada, 1999/2002: &lt;a href=&quot;http://www.biomedcentral.com/1471-2334/5/72&quot; rel=&quot;nofollow&quot;&gt;http://www.biomedcentral.com/1471-2334/5/72&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Canada, 1990-1998: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC194172/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC194172/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;China, 2012-2013: &lt;a href=&quot;http://www.biomedcentral.com/1471-2334/14/25&quot; rel=&quot;nofollow&quot;&gt;http://www.biomedcentral.com/1471-2334/14/25&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ethiopia, 2009: &lt;a href=&quot;http://www.biomedcentral.com/1471-2334/13/419&quot; rel=&quot;nofollow&quot;&gt;http://www.biomedcentral.com/1471-2334/13/419&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kenya, 2010-2011: &lt;a href=&quot;http://www.biomedcentral.com/1471-2334/13/243&quot; rel=&quot;nofollow&quot;&gt;http://www.biomedcentral.com/1471-2334/13/243&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-03-03T15:34:00.593" LastActivityDate="2014-03-03T15:34:00.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15454" PostTypeId="1" AcceptedAnswerId="15458" CreationDate="2014-03-03T20:01:48.317" Score="1" ViewCount="2008" Body="&lt;p&gt;Are there any fungi whose spores can survive 100+ degrees for 15 minutes and grow in a sugar-deprived medium?&lt;/p&gt;&#xA;" OwnerUserId="957" LastEditorUserId="1320" LastEditDate="2014-03-03T20:04:18.623" LastActivityDate="2014-03-03T22:53:54.330" Title="What are some of the known fungi with heat resistant spores" Tags="&lt;mycology&gt;&lt;thermophilia&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15455" PostTypeId="1" AcceptedAnswerId="20462" CreationDate="2014-03-03T20:57:01.517" Score="6" ViewCount="125" Body="&lt;p&gt;I am working on phylogeography on one model species and I am a beginner. You can imagine one species that came on locality more than 5 mya (million years ago). It was a good environment, so the species expanded very quickly. After climatic changes this model species split in two refugiums (isolated locations for a once widespread species) and evolved into two species. This happened several times and now we have from that one ancestral species six valid species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have data from MrBayes and BEAST molecular clock. Can you recommend some phylogeographical program which can consider also expansion and contraction of model species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My input data:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;molecular identification (sequences)&#xA;coordinates (lat, lon) for each species&#xA;geographical data of a continent (altitude, precipitation etc.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My goal:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Create a map where will be polygons (areas) of each species. These areas will expand and contract (step-by-step not like a do not want create video).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My problem:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am able to make polygons by MCP, or kernel density, but unable to incorporate barriers into model. For example, polygons of species which lives in mountain region created by MCP include areas of lowland inside...&lt;/p&gt;&#xA;" OwnerUserId="5893" LastEditorUserId="8186" LastEditDate="2014-08-13T20:55:53.543" LastActivityDate="2014-08-13T20:55:53.543" Title="Visualisation of phylogeography" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;phylogenetics&gt;&lt;software&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15456" PostTypeId="1" AcceptedAnswerId="16000" CreationDate="2014-03-03T21:16:13.850" Score="1" ViewCount="291" Body="&lt;p&gt;I heard the phrase &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Neutrophilic leucocytes are kings in the acute inflammation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Neutrophils are granulocytes, while leucocytes are not granulocytes.&#xA;I think this statement refers to the fact that leucocytes have neutrophilic properties, instead of being neutrophils itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Acute inflammation players are, I think&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Granulocytes, monocytes and leucocytes&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;while in chronic inflammation similar player but the main factor is macrophages so the phrase which I heard&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Macrophages are the kings of chronic inflammation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think granulocytes are related to the Healing and Proliferation.&#xA;Eosinophils for instance in the allergic responses of acute inflammation.&#xA;I think granulocytes are phagocytosed by the macrophages and this way spread their functions through macrophages around.&#xA;Probably, neutrophiles are attached to the leucocytes such that they spread their function through leucocytes (so called neutrophilic leucocytes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's cover first this, since we can after understanding it go to the chronic one.&#xA;&lt;strong&gt;What is the purposes of granulocytes in acute inflammation?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-03-22T13:35:52.797" Title="What are the purposes of granulocytes in acute inflammation?" Tags="&lt;immunology&gt;&lt;pathology&gt;&lt;inflammation&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15458" PostTypeId="2" ParentId="15454" CreationDate="2014-03-03T22:53:54.330" Score="2" Body="&lt;p&gt;According to Sterflinger, some black yeasts may qualify: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10081587&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/10081587&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Rock inhabiting meristematic fungi are extremely tolerant against high&#xA;  temperatures, desiccation and osmotic stress. Their temperature&#xA;  tolerance increases with increasing dehydration of the fungal thallus.&#xA;  Air dried mycelia of black yeasts stand temperatures up to 120 degrees&#xA;  C for at least 0.5 hours&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;More recently, Suryanarayanan et al. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21872180&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/21872180&lt;/a&gt;) have published the discovery of several fungal environmental isolates able to survive dry heat sterilization for 2h at 100+ degrees C. Growth testing was done on Potatao Dextrose Agar (PDA). &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Among 25 species of Ascomycota isolated from leaf litter, nine were&#xA;  able to grow after incubation in a drying oven for 2 h at 100 °C; the&#xA;  spores of two of these species survived 2 h incubation at 110 °C, and&#xA;  one survived exposure to 115 °C for 2 h.&quot; (...) Craphigera and Phoma sp.&#xA;  survived 2 h incubation at 110 °C; the conidia of Bartalinia sp. were&#xA;  the most resistant and survived exposure to 115 °C for 2 h&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The isolates which survived at least 2h at 100 C were:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Bartalinia sp. (NFCCI 2307)&lt;/li&gt;&#xA;&lt;li&gt;Chaetomella raphigera (NFCCI 2308)&lt;/li&gt;&#xA;&lt;li&gt;Curvularia sp. isolate 2 (NFCCI 2311)&lt;/li&gt;&#xA;&lt;li&gt;Drechslera halodes (NFCCI 2312)&lt;/li&gt;&#xA;&lt;li&gt;Leptosphaerulina sp. &lt;/li&gt;&#xA;&lt;li&gt;Pestalotiopsis sp. isolate 1 (NFCCI 2309)&lt;/li&gt;&#xA;&lt;li&gt;Pestalotiopsis sp. isolate 2 (NFCCI 2313)&lt;/li&gt;&#xA;&lt;li&gt;Phoma sp. (NFCCI 2310)&lt;/li&gt;&#xA;&lt;li&gt;Pithomyces sp. (IMTECH 9398)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-03-03T22:53:54.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15459" PostTypeId="2" ParentId="15448" CreationDate="2014-03-03T23:55:59.513" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;My conviction is that genes are not randomly arranged as a finite&#xA;  string. There must be a beautiful organization.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In bacteria, you will have a whole series of genes required for a pathway all next to each other, so that their expression can all be controlled from one point upstream of them.  We call that whole suite of genes and the upstream binding site an operon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But in eukaryotes, there is no grand organization of genes with regard to their position on the chromosomes, in general.  Regardless of what you think they should look like, we don't observe a wonderful organization.  Evolution results in things looking pretty haphazard.  Go browse ensembl.org if you want to see for yourself.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastEditorUserId="5148" LastEditDate="2014-03-04T04:23:53.340" LastActivityDate="2014-03-04T04:23:53.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15462" PostTypeId="1" AcceptedAnswerId="15463" CreationDate="2014-03-04T06:54:28.493" Score="0" ViewCount="117" Body="&lt;p&gt;I read about the hidden markov model in bioinformatics. I amn't able to understand what it is.&#xA;Can anyone explain me in brief and in very very simple words what it is ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have NO background in bioinformatics or programming and wikipedia article on it is too scary .&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-04T07:49:20.703" Title="Hidden Markov Model" Tags="&lt;bioinformatics&gt;&lt;computational-model&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15463" PostTypeId="2" ParentId="15462" CreationDate="2014-03-04T07:49:20.703" Score="3" Body="&lt;p&gt;A Markov model is a description of a system that follows a Markov process. In a Markov process the next state of the system is a function of its current state and does not depend on where from and how it started. For example Brownian motion can be called a Markov process. The transition from current state to next state is described by probabilities. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to conclude, a Markov model is a probabilistic model of a system that is assumed to have no memory. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a Hidden Markov Model (HMM) the state(s) of the system are not known (therefore hidden). However, there are some functions that depend on the state and their outputs can be used to approximate the state of the system. There goes the definition- it is not that easy to explain how it is applied to different concepts (not just bioinformatics).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Strictly speaking this is off-topic. HMM is not a biological concept. It is a statistical/computational concept (it is like asking what is Dynamic Programming- which is the underlying concept behind BLAST algorithm). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-03-04T07:49:20.703" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15465" PostTypeId="1" AcceptedAnswerId="15466" CreationDate="2014-03-04T08:54:30.043" Score="2" ViewCount="783" Body="&lt;p&gt;Why is it that, even if we were going to immediately agree that every women will not have more than 2.1 children on average, the world population would continue to grow for another 60 years? I've learned that a TFR of 2.1 means the population is at 0 growth rate. I guessed the answer was the population-lag effect, but since we are assuming that ALL women immediately have only 2.1 children on average, wouldn't there be a 0 population growth immediately and not after 60 years? Thanks in advance!&lt;/p&gt;&#xA;" OwnerDisplayName="user5902" LastActivityDate="2014-03-04T09:38:12.973" Title="Why will world population keep growing if all women have only 2.1 children" Tags="&lt;population-biology&gt;&lt;population-dynamics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15466" PostTypeId="2" ParentId="15465" CreationDate="2014-03-04T09:27:33.790" Score="1" Body="&lt;p&gt;As you mention, the population-lag effect is responsible for this. From The Wikipedia article on TFR: &lt;a href=&quot;http://en.wikipedia.org/wiki/Total_fertility_rate#Population-lag_effect&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Total_fertility_rate#Population-lag_effect&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A population that has recently dropped below replacement-level&#xA;  fertility will continue to grow, because the recent high fertility&#xA;  produced large numbers of young couples who would now be in their&#xA;  childbearing years.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thus, even if the current TFR implies long-term stability, the recent history of TFR values will continue to affect birth rates, and thus population growth/decrease, &lt;em&gt;in the future&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine that you have a stable population, with static birth and death rates. Now imagine that the birth rate during a single year for some reason doubles before dropping back to normal the next year, thus transiently increasing TFR. Now, it is easy to see that when the newly born, larger-than-normal generation reaches reproductive age, the population will increase &lt;em&gt;again&lt;/em&gt; because the birth rate will increase in proportion with the size of the generation, while the death rate is unaffected until the enlarged generation reaches old age and starts dying off. Later, the population will decrease to its long-term stable level, which will be larger than before the TFR spike.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-03-04T09:38:12.973" LastActivityDate="2014-03-04T09:38:12.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15467" PostTypeId="1" AcceptedAnswerId="15470" CreationDate="2014-03-04T09:30:16.827" Score="0" ViewCount="167" Body="&lt;p&gt;&lt;a href=&quot;http://9gag.com/gag/agy2Lxx&quot; rel=&quot;nofollow&quot;&gt;This page&lt;/a&gt; says it won't.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This page says it's the carb again &lt;a href=&quot;http://www.mindbodygreen.com/0-10454/in-defense-of-bacon-why-eating-fat-can-help-you-get-thin.html&quot; rel=&quot;nofollow&quot;&gt;http://www.mindbodygreen.com/0-10454/in-defense-of-bacon-why-eating-fat-can-help-you-get-thin.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't see how eating fat will not make me gain weight while eating carbohydrates will, since fat is made of, well, fat. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It says eating carbs will make us fat. How can this be? Is this true?&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="3632" LastEditDate="2014-03-04T13:39:01.777" LastActivityDate="2014-03-04T13:50:36.123" Title="How can eating bacon not make me fat?" Tags="&lt;diet&gt;&lt;fatty-acid-synthase&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ClosedDate="2014-03-05T22:17:55.970" ContentLicense="CC BY-SA 3.0" />
  <row Id="15468" PostTypeId="1" AcceptedAnswerId="15499" CreationDate="2014-03-04T11:07:44.720" Score="2" ViewCount="1068" Body="&lt;p&gt;Assume some bacteria have capsular antigen.&#xA;&lt;strong&gt;Do these bacteria always have a capsule?&lt;/strong&gt;&#xA;I think not, I think the antigen only makes it possible.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1306" LastEditDate="2014-03-04T16:33:41.053" LastActivityDate="2014-03-05T11:48:58.217" Title="Do bacteria with capsular antigen always have a capsule?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15469" PostTypeId="1" AcceptedAnswerId="23717" CreationDate="2014-03-04T13:03:50.030" Score="3" ViewCount="954" Body="&lt;p&gt;I am thinking why hydrogen sulfide has its effects in the body.&#xA;For instance, it is one Salmonella's virulence factor.&#xA;I am not sure if such a balance equations holds&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;H&lt;sub&gt;2&lt;/sub&gt;O + H&lt;sub&gt;2&lt;/sub&gt;S ←→ ...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually, I miss here some factors because I am not understanding the biochemistry enough to answer this.&#xA;I think H&lt;sub&gt;2&lt;/sub&gt;S can exists in some sort of ionic form.&#xA;Hydrogen sulfide reminds me of ammonia.&#xA;I think it inhibits some systems.&#xA;&lt;strong&gt;By which mechanisms?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is mentioned in many places the empirical effects: signaling functions similar to NO and CO.&#xA;But I am interested in how this happens.&#xA;&lt;strong&gt;What is the rate of adhesion of H&lt;sub&gt;2&lt;/sub&gt;S to hemoglobin for instance?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;H2S can change to sulfite and thiosulfate in mitochondria which are then excreted into urine.&#xA;I think most of the biological effects are done before these forms.&#xA;&lt;strong&gt;But in which forms?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-11-05T08:31:40.857" LastActivityDate="2014-11-14T18:06:53.233" Title="What are the physiological roles of Hydrogen sulfide?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;neuroscience&gt;&lt;neurotransmitter&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15470" PostTypeId="2" ParentId="15467" CreationDate="2014-03-04T13:50:36.123" Score="1" Body="&lt;p&gt;I think this question can also be said to be - how can the &lt;a href=&quot;https://en.wikipedia.org/wiki/Atkins_diet&quot; rel=&quot;nofollow&quot;&gt;Atkins diet work&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Atkins and other low carbohydrate diets sound counterintuitive.  They vary in details, but the basic theme is: cut back on carbohydrates - e.g. bread, sugar, fruit, pasta, milk etc etc.  But eat as much fat and protein as you like - e.g. steak, ham, bacon, eggs, cheese etc etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These diets really do work.  Our metabolism allows us to draw food from two sources.  Glucose or fat. (there is also something called glycogen, but that is only used short term and not relevant for diets long term).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was known in the late 50s that our metabolism will to switch over consuming fat, allowing weight loss, only based on the amount of carbohydrates we consume. low carb diets initiate this change from glucose to fat metabolism because our bodies make the switch based only on the amount of glucose available in the blood.  Our bodies think we are starving even if we are gorging ourselves on food which is has little or no glycemic index.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Low carb diets are not a hoax or snake oil - they really work.  They can be a shock to the system and so one should discuss with your doctor before engaging them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first link you have is also true though.  Eating fat will usually just make you gain weight.  The low carb response has to be induced by basically removing all carbohydrates from the diet.  If you break the low carb regime and eat a large amount of carbs, the body will switch practically instantly out of starvation mode and also take in all the fats you're eating.  Lots of people on low carb diets can gain a lot of weight rapidly if they break the diet. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-03-04T13:50:36.123" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15471" PostTypeId="1" AcceptedAnswerId="15472" CreationDate="2014-03-04T14:12:23.813" Score="2" ViewCount="128" Body="&lt;p&gt;Do you use Pippin prep? We would like to buy it, but we need more info. What is the &lt;strong&gt;expiration date of kits for Pippin prep&lt;/strong&gt;? Thanks!&lt;/p&gt;&#xA;" OwnerUserId="5893" LastActivityDate="2014-03-04T15:10:51.713" Title="Pippin prep kits - expiration date" Tags="&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15472" PostTypeId="2" ParentId="15471" CreationDate="2014-03-04T14:45:10.947" Score="3" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.n-genetics.com/file/Pippin-Prep-Operations-Manual-Rev-6.00-CD6.pdf&quot; rel=&quot;nofollow&quot;&gt;this document&lt;/a&gt; (page 11) the shelf life for the cassettes is 1 year. The other ingredients (running buffer, DNA size markers, loading dye) appear to be standard reagents. Of those, the DNA size marker will probably have the shortest shelf life, but it stands to reason that the reagents should have a shelf life at least as long as the cassettes, seeing as only their shelf life is mentioned. It is possible to buy reagent replacement kits.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-03-04T15:10:51.713" LastActivityDate="2014-03-04T15:10:51.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15474" PostTypeId="1" CreationDate="2014-03-04T16:27:08.980" Score="2" ViewCount="315" Body="&lt;p&gt;When performing PCRs, usually in every protocol enzyme amount is specified as 1.25 U as optimal per 50 uL reaction. Then, when running 25 uL PCR reaction should i use 1/2 he amount the enzyme or should i respect the value on Units thus using the same volume as in 50 uL reaction?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastActivityDate="2014-03-08T16:44:27.330" Title="PCR enzyme units or concentration?" Tags="&lt;pcr&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15475" PostTypeId="2" ParentId="15474" CreationDate="2014-03-04T17:28:23.620" Score="1" Body="&lt;p&gt;You have to scale amounts of all PCR components proportionally depending on the volume of the reaction. The polymerase is no exception in this respect, the only difference is that you measure it in terms of activity - units. So in your protocol you have 0.025 U/µl and you have to maintain this concentration when changing the volume.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-03-04T17:28:23.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15476" PostTypeId="2" ParentId="14615" CreationDate="2014-03-04T17:53:07.400" Score="1" Body="&lt;p&gt;Weasels don't hibernate.  See &lt;a href=&quot;http://icwdm.org/handbook/carnivor/Weasels.asp&quot; rel=&quot;nofollow&quot;&gt;http://icwdm.org/handbook/carnivor/Weasels.asp&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both will die when the temperature falls below a certain level.  The difference between snakes (ectotherms) and weasels (endotherms) is that the snake's body temperature will fluctuate more, depending on the surrounding temperature.&lt;/p&gt;&#xA;" OwnerUserId="5907" LastActivityDate="2014-03-04T17:53:07.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15477" PostTypeId="1" AcceptedAnswerId="15537" CreationDate="2014-03-04T18:08:42.260" Score="5" ViewCount="1078" Body="&lt;p&gt;According to Invasive Species Advisory Committee (ISAC), the definition of the invasive species is “a species that is non-native to the ecosystem under consideration and whose introduction causes or is likely to cause economic or environmental harm or harm to human health.” &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But considering the following facts, why is this species not categorized as an invasive species?&#xA;Homo sapiens:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;is non-native to the most of the ecosystem which it is inhabiting, since it originated from a certain area of Africa and spread quite recently.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;has often caused environmental problems by decreasing the local species after its introduction, as it is known that the number of species in the planet is drastically decreasing ever since the advent of Homo sapiens.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;is likely to cause the same problem after introduced to new environment where homo sapiens hasn't inhabited yet.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.invasivespeciesinfo.gov/docs/council/isacdef.pdf&quot; rel=&quot;noreferrer&quot;&gt;http://www.invasivespeciesinfo.gov/docs/council/isacdef.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4858" LastEditorUserId="1320" LastEditDate="2014-03-04T19:32:28.450" LastActivityDate="2019-06-09T13:48:48.613" Title="Why is Homo sapiens not categorized as an invasive species?" Tags="&lt;environment&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15478" PostTypeId="1" AcceptedAnswerId="15496" CreationDate="2014-03-04T18:18:55.593" Score="3" ViewCount="1949" Body="&lt;p&gt;I understand that the first BLAST yields almost the same results as blastp. The second time the iterated blast generates different results as it uses different matrix based on our first result.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I don't understand how exactly the second matrix is generated. &lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3553" LastEditDate="2016-06-29T06:53:45.577" LastActivityDate="2016-06-29T06:53:45.577" Title="What is happening in each iteration of PSI-BLAST?" Tags="&lt;bioinformatics&gt;&lt;sequence-alignment&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15479" PostTypeId="1" AcceptedAnswerId="15498" CreationDate="2014-03-04T18:21:06.763" Score="0" ViewCount="1912" Body="&lt;p&gt;I wonder if there are any benefits to eat earth. What I mean by earth is the topsoil that is sometimes on vegetable (I eat organic vegetables and some of them like spinach are full of topsoil).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this &lt;a href=&quot;http://www.sciencedaily.com/releases/2011/06/110602162820.htm&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; (a study about why people, in certain culture, eat earth) but it doesn't clearly answer my question as it's about clay and not topsoil. Topsoil has a highest concentration of organic matter than clay.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder if we can digest the soil nutrient (Phosphorus, Potassium, Calcium, Magnesium, Manganese, Zinc, Copper) just as we would if there were coming from vegetable and fruits. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the other pros and cons of eating earth (soil)? (I am aware of the cons about parasite and bacteria but my question is not about these risks. It's about nutritive value of earth.)&lt;/p&gt;&#xA;" OwnerUserId="5908" LastEditorUserId="5908" LastEditDate="2014-03-05T05:04:13.987" LastActivityDate="2017-10-08T06:31:34.257" Title="What are the pros and cons of eating earth (soil)?" Tags="&lt;digestive-system&gt;&lt;nutrition&gt;&lt;soil&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15480" PostTypeId="1" AcceptedAnswerId="15481" CreationDate="2014-03-04T18:44:12.450" Score="0" ViewCount="333" Body="&lt;p&gt;I know that Cl tetani is not invasive and strictly localised.&#xA;I think toxemia means spread in the blood.&#xA;I am thinking this sentence &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The volume of infected tissue is small, and the disease is almost entirely a toxemia.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Cl tetani has spores.&#xA;This suggests me that these spores spread through blood. &#xA;They then open and become pathogenic in some tissues where they remain strictly locally (so small area/volume of infected tissue; I think area is better word, since the disease is not invasive) and pathogenic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How do you understand the quoted sentence about pathogenesis of Cl tetani?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1320" LastEditDate="2014-03-04T19:32:56.427" LastActivityDate="2014-03-04T19:32:56.427" Title="What does this sentence about toxemia and Clostridium tetani mean?" Tags="&lt;microbiology&gt;&lt;pathogenesis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15481" PostTypeId="2" ParentId="15480" CreationDate="2014-03-04T19:08:50.927" Score="5" Body="&lt;p&gt;&lt;em&gt;Clostridium tetani&lt;/em&gt; produces a protein toxin, &lt;a href=&quot;http://en.wikipedia.org/wiki/Tetanospasmin&quot;&gt;tetanospasmin&lt;/a&gt; which causes the major symptom of tetanus, namely involuntary muscle spasms. &lt;em&gt;C. tetani&lt;/em&gt; is an aerobic species, does not infect the blood, and apparently only produces toxin in anaerobic conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a pathogenic bacterium propagates through the bloodstream this condition is referred to as &lt;strong&gt;bacteraemia&lt;/strong&gt;. In the case of &lt;em&gt;C. tetani&lt;/em&gt; it is the toxin which enters the bloodstream, not the bacteria, hence &lt;strong&gt;toxaemia&lt;/strong&gt;. The bacteria, being anaerobic, are inhibited from spreading through aerobic tissues.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-04T19:08:50.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15482" PostTypeId="2" ParentId="15478" CreationDate="2014-03-04T19:31:48.270" Score="3" Body="&lt;p&gt;PSI-BLAST is Position-Specific Iterated BLAST.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm probably out of my depth here, but my understanding is that the results of the first, essentially standard, BLAST search are used to create a multiple sequence alignment. This alignment is then converted to a &lt;a href=&quot;http://en.wikipedia.org/wiki/Position-Specific_Scoring_Matrix&quot; rel=&quot;nofollow&quot;&gt;Position Specific Scoring Matrix (PSSM)&lt;/a&gt;. (The linked Wikipedia entry shows this for DNA sequences, but the principle is exactly the same for protein sequences.) This matrix can then be used as the probe for the next round of BLAST, and the results of that alignment can be used judiciously to improve the matrix, and so on until the results converge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cs.umd.edu/class/fall2011/cmsc858s/PSI-BLAST.pdf&quot; rel=&quot;nofollow&quot;&gt;Here is a link to some slides by Stephen Altschul&lt;/a&gt; which go into lots of detail. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-04T19:31:48.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15483" PostTypeId="1" AcceptedAnswerId="15495" CreationDate="2014-03-04T19:37:49.983" Score="1" ViewCount="101" Body="&lt;p&gt;I am currently doing some research into distributions and probabilities with Mendellian genetics. I came across this problem that I cannot seem to wrap my head around.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that the population has two characteristics, they are color and texture. Supposed two dihybrids reproduce (&lt;code&gt;AaBb x AaBb&lt;/code&gt;) and if the dominant form of the&#xA;color gene is contributed, then the dominant form of the texture gene is three&#xA;times as likely to be contributed as the recessive form. If the recessive color gene is contributed then the dominant and recessive genes for texture are equally likely. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this the geneotypic distribution has to be calculated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know the solution is:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;[9/64   6/64   1/64   3/16   1/4   1/16   1/16   2/16   1/16]&#xA;&#xA; AABB   AABb   AAbb   AaBB   AaBb  Aabb   aaBB   aaBb   aabb&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;When I performed the punnett square I got the distribution of:  &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; [1/16   2/16   1/16   2/16   4/16   2/16   1/16   2/16   1/16]&#xA;&#xA; AABB   AABb   AAbb   AaBB   AaBb  Aabb   aaBB   aaBb   aabb&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and did not know where to go from there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is how did they incorporate the &lt;code&gt;&quot;times as likely&quot;&lt;/code&gt; condition into the solution.&lt;/p&gt;&#xA;" OwnerUserId="5910" LastEditorUserId="5910" LastEditDate="2014-03-05T20:09:32.187" LastActivityDate="2014-03-05T20:09:32.187" Title="Genotypic distribution of a population with two characteristics and linkage" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15484" PostTypeId="1" AcceptedAnswerId="15485" CreationDate="2014-03-04T19:50:26.693" Score="1" ViewCount="43" Body="&lt;p&gt;I am doing some research into Mendelian genetics and came across this phrase called &lt;code&gt;adverse selection.&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found a few questions but I am unsure of the calculations. For example given a distribution &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[0.36 0.48 0.16]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;it is stated that 25% of individuals with &lt;i&gt;Aa(middle)&lt;/i&gt; genotype dies. The distribution changes to &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[0.4091 0.4091 0.1818].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I initially thought to just take off 25% of the middle becoming 0.36 and equally distributing the 0.12 change to the other two geneotypes. Can someone explain how they did this computation.&lt;/p&gt;&#xA;" OwnerUserId="5910" LastActivityDate="2014-03-04T20:09:11.033" Title="Distribution of genotypes after adverse selection" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15485" PostTypeId="2" ParentId="15484" CreationDate="2014-03-04T20:03:48.923" Score="2" Body="&lt;p&gt;If you distribute the 0.12 equally to the two other genotypes you change the relative frequencies. You have to withdraw 0.12 to 0.48 and then set the three frequencies so that they sum up to 1. Therefore, the correct calculation is the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we set $fAA = 0.36$, $fAa = 0.48$ and $faa = 0.16$ and then simulate the death of 25% of the Aa individuals, the same variables at the next time step (without reproduction) will be...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$faa = \frac{0.16}{0.36 + 0.36 + 0.16} ≈ 0.1818$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$fAa = \frac{0.36}{0.36 + 0.36 + 0.16} ≈ 0.4091$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$fAA = \frac{0.36}{0.36 + 0.36 + 0.16} ≈ 0.4091$$&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-03-04T20:09:11.033" LastActivityDate="2014-03-04T20:09:11.033" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15486" PostTypeId="1" AcceptedAnswerId="15489" CreationDate="2014-03-04T20:10:53.243" Score="9" ViewCount="2744" Body="&lt;p&gt;I always wear gloves when I'm doing cell culture. Moreover, I always spray my gloves with ethanol to disinfect, so that I don't contaminate everything.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I recently heard the argument that EtOH could impair the integrity of the glove, making it an unsuitible barrier between your hand and the culture. According to this argument, the best idea is to not wear gloves during cell culture, but instead thoroughly spray your hands with EtOH to ensure decontamination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't believe it, but I'm wondering if anyone else has heard a similar argument and if there is any truth to the claim.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-03-04T20:58:53.047" Title="Gloves for Cell Culture?" Tags="&lt;lab-techniques&gt;&lt;cell-culture&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15487" PostTypeId="1" CreationDate="2014-03-04T20:34:07.280" Score="2" ViewCount="687" Body="&lt;p&gt;Since the precise amount of cells in each well of an MTT assay varies, how can I normalize the results by cell number/concentration?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can I take into account the number of cells that have already disappeared due to the action of a toxin applied previously as part of this assay?&lt;/p&gt;&#xA;" OwnerUserId="5911" LastActivityDate="2014-03-04T20:34:07.280" Title="MTT assay normalization" Tags="&lt;cell-biology&gt;&lt;toxicology&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15488" PostTypeId="2" ParentId="15486" CreationDate="2014-03-04T20:34:25.123" Score="3" Body="&lt;p&gt;Assuming you use latex or nitrile, you're probably good.  Nitrile does hold up better than latex in many situations, so if you're worried about it, switch to nitrile.  &lt;a href=&quot;http://amo-csd.lbl.gov/downloads/Chemical%20Resistance%20of%20Gloves.pdf&quot; rel=&quot;nofollow&quot;&gt;This is a good quick guide&lt;/a&gt; to glove materials and their resistance.  For some of the applications we do in our clinic/lab, we use thick &gt;6mm nitrile gloves.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your needs all really depend on your application.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2014-03-04T20:34:25.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15489" PostTypeId="2" ParentId="15486" CreationDate="2014-03-04T20:47:32.660" Score="9" Body="&lt;p&gt;In my opinion wearing gloves during cell culture is a good idea. It works both ways as a protection: For your cells since you are not loosing small danders from your hand and for you since you are not getting media or chemicals used in cell culture on your skin when you are uncautious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I usually prefer nitrile gloves over latex, since nitrile gloves are ways more stable and pose no risk for allergies (I am not allergic, but minimizing risks is always a good idea). The downside of nitrile is, that they are a bit more expensive (thats the point where you need to argue with some coordinators about what to buy).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I never had problems with desinfectants and gloves, but this is my personal experience and probably not more than an anecdote. I desinfect my gloves, since I touch different things with them, but I usually don't spray everything which comes around with alcohol since this is usually pointless. To be useful, it needs to reach all points of a surface and also needs to stay there for a while. What I make sure is that all the stuff, which goes into the hood is either very clean or packaged sterile anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After my experiences some data, this &lt;a href=&quot;http://amo-csd.lbl.gov/downloads/Chemical%20Resistance%20of%20Gloves.pdf&quot;&gt;PDF&lt;/a&gt; has quite a lot of information. The list below is taken from the PDF:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nitrile gloves:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Acetone - fair&lt;/li&gt;&#xA;&lt;li&gt;Ethanol - excellent&lt;/li&gt;&#xA;&lt;li&gt;Isobutyl - alcohol excellent&lt;/li&gt;&#xA;&lt;li&gt;Isopropyl - alcohol excellent&lt;/li&gt;&#xA;&lt;li&gt;Methanol - fair&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Latex gloves:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Acetone - good&lt;/li&gt;&#xA;&lt;li&gt;Ethanol - excellent&lt;/li&gt;&#xA;&lt;li&gt;Isobutyl - alcohol poor&lt;/li&gt;&#xA;&lt;li&gt;Isopropyl - alcohol excellent&lt;/li&gt;&#xA;&lt;li&gt;Methanol - fair&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-04T20:58:53.047" LastActivityDate="2014-03-04T20:58:53.047" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15490" PostTypeId="1" AcceptedAnswerId="15491" CreationDate="2014-03-04T22:01:52.887" Score="5" ViewCount="180" Body="&lt;p&gt;Suppose a simple synthetic construct, consisting of a constitutive promoter and a single gene:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/BRpvx.png&quot; alt=&quot;construct&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the simplest ways to model GFP transcription is to use an ODE:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\frac{d [GFP_{mRNA}]}{dt} = a - b{\cdot}[GFP_{mRNA}]$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $a$ is GFP transcription rate and $b$ is GFP mRNA degradation rate (both constants). Normally, we assume $a&amp;gt;&amp;gt;b$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose we wish to account for plasmid concentration with the value of transcription rate $a$ - e.g. with higher plasmid concentration, the ratio $a/b$ should increase as the mRNA saturation levels are expected to be reached faster. In other words, suppose we transfect 2 individual constructs depicted above, 10 ng of one and 30 ng of the other - how should this difference in concentration impact the rate constants values, assuming the constructs are otherwise identical?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Assuming this, approximately how does gene transcription rate $a$ change as a function of the amount of transfected plasmid containing the above construct?&lt;/strong&gt; Ideally, I'd be interested in knowing this for HEK 293 cells, but any other decent estimation is acceptable. One simple option is to simply assume linear relation, but I think that's too simplistic: e.g. if we say $a=1$ at 10 ng plasmid concentration, then $a=3$ at 30 ng plasmid concentration. Note that I'm not necessarily limiting myself to ODE models, just looking for some kind of relation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have so far not been able to find anything useful in papers I've examined, so any help would be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="3583" LastEditorUserId="3583" LastEditDate="2014-03-04T22:36:22.363" LastActivityDate="2014-03-04T23:50:01.483" Title="What is the relation between plasmid concentration and mRNA levels?" Tags="&lt;molecular-biology&gt;&lt;gene-expression&gt;&lt;mathematical-models&gt;&lt;transcription&gt;&lt;synthetic-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15491" PostTypeId="2" ParentId="15490" CreationDate="2014-03-04T22:23:15.510" Score="4" Body="&lt;p&gt;The amount of transfected plasmid does not correlate at all with the protein expression level. After transfction, usually each cell is going to get and keep only one copy of the plasmid. Once the plasmid is in the cell, it will be replicated and the cell will contain X copies of it, depending on the plasmid copy number. In general, plasmids with low copy numbers correlate with lower protein expression compared to plasmids with high copy number. But there are also exceptions:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Expression of genes under control of EF1α promoter appears to correlate with plasmid copy number.  In contrast, expression driven by the more traditional CMV immediate early promoter appears less plasmid copy number dose-responsive &lt;a href=&quot;http://home.ccr.cancer.gov/lco/293TT.htm&quot; rel=&quot;nofollow&quot;&gt;(ref)&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="28" LastEditorUserId="3632" LastEditDate="2014-03-04T23:50:01.483" LastActivityDate="2014-03-04T23:50:01.483" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15492" PostTypeId="2" ParentId="15478" CreationDate="2014-03-05T00:06:49.013" Score="3" Body="&lt;p&gt;From Russ Altman (Stanford University) lecture: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Blast takes as an input a sequence, it searches the database, and outputs a set of alignments (a top ranked alignment, followed by a second-top ranked, a third, and so on). Then you take the top scoring sequences (you might use the E-value as a cutoff) and you can create a position-specific scoring matrix (PSSM) based on the occurrences of amino acids in all the columns of these alignments. This is allowed, because there is a high chance that these sequences are homologous to the query sequence and thus looking at the amino acids would give you a good sense of the variability in position that is allowed in the initial query sequence. The next step is to re-search the database for more hits. So now instead of searching with a sequence, you are searching with a profile, and you get another set of hits. You can iterate a few times which would give you a much more sensitive search.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vmzik.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2014-03-05T00:17:22.800" LastActivityDate="2014-03-05T00:17:22.800" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15493" PostTypeId="1" CreationDate="2014-03-05T01:25:42.020" Score="5" ViewCount="120" Body="&lt;p&gt;In a &lt;a href=&quot;http://p-gerlee.blogspot.ca/2014/02/the-role-of-mathematical-oncology.html&quot; rel=&quot;noreferrer&quot;&gt;recent post&lt;/a&gt;, Philip Gerlee highlighted the two biggest contributions of mathematical oncology to cancer research: (1) increasing focus on the progress of cancer as an evolutionary process, and (2) looking at the importance of tumor heterogeneity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the first point, the standard historical reference is: Nowell, P. C. (1976). The clonal evolution of tumor cell populations. &lt;em&gt;Science&lt;/em&gt;, 194(4260): 23-28.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, for the second point, although I am vaguely familiar with &lt;a href=&quot;http://www.pnas.org/content/110/10/4009.full&quot; rel=&quot;noreferrer&quot;&gt;modern work&lt;/a&gt;, I don't know of a historical reference. &lt;strong&gt;When was tumour heterogeneity first recognized as important to cancer dynamics and treatment?&lt;/strong&gt; Was this work related to mathematical or other modeling insights? If not, what is the first important mathematical (or computational) modeling work on tumour heterogeneity?&lt;/p&gt;&#xA;" OwnerUserId="500" LastActivityDate="2014-03-07T00:26:30.957" Title="Is there a standard reference for the importance of tumor heterogeneity?" Tags="&lt;cancer&gt;&lt;mathematical-models&gt;&lt;history&gt;&lt;literature&gt;&lt;medicine&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15494" PostTypeId="2" ParentId="15493" CreationDate="2014-03-05T04:05:37.397" Score="1" Body="&lt;p&gt;It's quite interesting that the first reference that come to mind is not a mathematical/theoretical one (which is, in all likelihood, going to be a lot older than the one I am going to mention) but a clinical one. That would be Gerlinger and Swanton and their paper in the &lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMoa1113205&quot; rel=&quot;nofollow&quot;&gt;New England Journal of Medicine&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="5879" LastEditorUserId="3340" LastEditDate="2014-03-05T04:58:02.320" LastActivityDate="2014-03-05T04:58:02.320" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15495" PostTypeId="2" ParentId="15483" CreationDate="2014-03-05T04:20:29.977" Score="2" Body="&lt;p&gt;You are...  done. You fully answered the question; if I were you, I might just put it in ratio format instead of probability, just to be safe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The three times thing is a bit weird, but I have seen it before. First, let's look at the phenotypic ratio of the progeny: 9:3:3:1 for Dominant Both:Dominant A Recessive B:Recessive A Dominant B: Recessive Both.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's find out how many dominant and recessive there are for each trait. For the dominant A trait, you add up the 9 and 3, because they are the only two types of dominant phenotypes, and find that 12 different organisms of the 16 possible are dominant for Trait A, so the probability of getting trait A is 3/4 or 75%. This means that 4 of the 16 orgamisms are recessive for Trait A, so the probability of being recessive for Trait A is 4/16, or 25%. Therefore, the ratio of Dominant Organism probability:Recessive organism probability is 75% to 25%, or 3:1. This means that it is 3 times as likely to get the dominant trait than the recessive trait. Make sense?&lt;/p&gt;&#xA;" OwnerUserId="5859" LastActivityDate="2014-03-05T04:20:29.977" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15496" PostTypeId="2" ParentId="15478" CreationDate="2014-03-05T04:45:51.117" Score="3" Body="&lt;p&gt;Addition to previous answers: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;PSI-BLAST is a sort of machine learning algorithm which uses the results of the first alignment (PSSM) to score the next iteration of alignment. I would recommend you to refer to the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2590/&quot; rel=&quot;nofollow&quot;&gt;NCBI bookshelf page&lt;/a&gt; on PSI-BLAST. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;PSI-BLAST adopts a scoring scheme (PSSM) that is built based on a given set of data (the aligned sequences), rather than using a generalized scoring matrix. This improvisation updates the prior knowledge of the homologs and helps to detect similar sequences that were otherwise undetectable. With iterations the PSSM keeps getting updated, thereby, making the BLAST more sensitive in finding homologs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How PSSM is constructed&lt;/strong&gt;: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a position in the alignment is conserved (i.e same residue in many sequences), it receives a high score whereas a position with low conservation gets a low score. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Score is based on relative counts of a residue in a position. If you want to know the details see &lt;a href=&quot;http://noble.gs.washington.edu/~zafer/projects/psp/doc/pssm.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-03-05T09:15:24.770" LastActivityDate="2014-03-05T09:15:24.770" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15497" PostTypeId="1" CreationDate="2014-03-05T07:04:39.767" Score="7" ViewCount="105" Body="&lt;p&gt;As there is a potential for them to be more readily purged in hemizygous males (and in cell lineages in females with the deleterious-allele-bearing chromosome activated), I would expect the frequency of deleterious alleles to be lower on this chromosome than in autosomes. Is this information known?&lt;/p&gt;&#xA;" OwnerUserId="1906" LastEditorUserId="4101" LastEditDate="2014-08-27T16:03:20.973" LastActivityDate="2014-08-27T16:03:20.973" Title="Are recessive, deleterious alleles less common on the X chromosome than the autosomes in humans?" Tags="&lt;genetics&gt;&lt;genomics&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15498" PostTypeId="2" ParentId="15479" CreationDate="2014-03-05T08:16:16.513" Score="2" Body="&lt;p&gt;The article (a PDF can be found &lt;a href=&quot;http://www.d.umn.edu/~pfarrell/Soils/Readings/geophagy.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) suggests that this happens neither for feeding reasons (to get your belly filled, when anything else is available) nor that this is done for supplemental reasons. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They suggest that this happens more for protective reasons. In the abstract they write:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our results indicate that human geophagy is best explained as&#xA;  providing protection from dietary chemicals, parasites, and pathogens,&#xA;  whereas animal geophagy may involve both micronutrient acquisition and&#xA;  protection.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the paper they give a few examples for this. First the earth eaten is usually digged up from deeper layers of the ground and sometimes even cooked. Then they bring in the example of people, which eat soil, when they have gastrointestinal problems as a kind of medicine to calm down the problems. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my opinion there is not much nutritional value in eating soil. Organic compounds can usually not be metabolized (for example we don't have the possibility to break down cellulose). I am not sure, if we can get minerals from clay into our body, since a lot of them is present in soil as unsoluble minerals.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-05T08:16:16.513" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15499" PostTypeId="2" ParentId="15468" CreationDate="2014-03-05T11:48:58.217" Score="3" Body="&lt;p&gt;In short: It can depend on your definition of encapsulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the Oxford Dictionary of Biochemistry, a capsular antigen is &lt;a href=&quot;http://www.answers.com/topic/capsular-antigen-biochemistry&quot; rel=&quot;nofollow&quot;&gt;defined&lt;/a&gt; as &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;any of the antigens, usually polysaccharide in nature, that are&#xA;  carried on the surface of bacterial capsules. The term K antigen is&#xA;  used for those that mask somatic (O) antigens.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In general, capsule polysaccharides have complex structures and are produced by a the action of several enzymes, with the genes necessary for production of the capsule typically making up a gene cluster in the genome (see for example Chen et al.: &lt;a href=&quot;http://www.biomedcentral.com/1471-2180/10/274&quot; rel=&quot;nofollow&quot;&gt;http://www.biomedcentral.com/1471-2180/10/274&lt;/a&gt;). On the face of it, it would seem somewhat unlikely that a bacterium would produce a known capsular polysaccharide antigen without retaining the ability to produce a capsule, as the selective advantage of the capsule then would be lost. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In actuality, the answer might depend on how you define &quot;have capsular antigen&quot; and &quot;capsule&quot;. Historically, several methods have been used for demonstrating encapsulation. Methods based on staining microscopy or colony morphology observations tend to identify fewer strains as encapsulaed than does serotyping (reaction of serum with antigen). With this in mind, strains that can be shown to be encapsulated without serotyping are sometimes referred to as &quot;highly encapsulated&quot; to distinguish them from strains that test positive for encapsulation through serotyping only. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For discussions of capsule detection methods as applied to Staphylococcus aureus, see Sutra et al. (&lt;a href=&quot;http://jcm.asm.org/content/28/3/447.full.pdf&quot; rel=&quot;nofollow&quot;&gt;http://jcm.asm.org/content/28/3/447.full.pdf&lt;/a&gt;) and O'riordan and Lee (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC321462/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC321462/&lt;/a&gt;).  O'riordan and Lee writes&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Isolates belonging to the remaning serotypes produce nonmucoid&#xA;  colonies on solid medium, and their colony morphology is&#xA;  indistinguishable from that of strains lacking a capsule. Some&#xA;  investigators have referred to nonmucoid, encapsulated S. aureus&#xA;  isolates as microencapsulated to distinguish them from the atypical&#xA;  mucoid strains.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thus, &lt;strong&gt;if both &quot;have capsular antigen&quot; and &quot;have a capsule&quot; is defined by a positive serotyping result for a capsular antigen, then all strains with a capsular antigen as detected by serotyping have a capsule per definition.&lt;/strong&gt; If on the other hand you define encapsulation based on ink staining microscopy or colony morphology, there are definitely strains that produce K-antigens and don't qualify as &quot;encapsulated&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that while bacterial capsules consist mostly of polysaccharides, capsule proteins make up a second class of capsule antigens. One example is the Caf1 capsule antigen protein produced by &lt;em&gt;Yersinia pestis&lt;/em&gt;: &lt;a href=&quot;http://en.wikipedia.org/wiki/Caf1_capsule_antigen&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Caf1_capsule_antigen&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-03-05T11:48:58.217" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15500" PostTypeId="2" ParentId="14794" CreationDate="2014-03-05T14:31:41.263" Score="2" Body="&lt;p&gt;Also, I guess civilization would have its effects on the human immune system (both positive and negative).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The more exposed you are to microbiological pathogens, the better the chance of developing a more robust immune system.&lt;br&gt;&#xA;In a very civilized (or rather a very clean) environment, humans would not be exposed much to external pathogens and hence would not have developed immunity to many of the diseases caused by those pathogens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In comparison, people who live in &quot;less clean&quot; environments (take some of the 3rd world countries for example), would be exposed to a higher level of pathogens and would naturally develop immunity to more diseases.&#xA;There's a Reddit discussion on &lt;a href=&quot;http://www.reddit.com/r/askscience/comments/1gg0r4/is_it_true_that_people_who_live_in_dirty/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same applies to humans vs animals I guess. Animals don't usually live in artificially clean environments and hence develop a better immunity.&lt;/p&gt;&#xA;" OwnerUserId="5799" LastEditorUserId="-1" LastEditDate="2018-04-30T03:39:09.767" LastActivityDate="2018-04-30T03:39:09.767" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15501" PostTypeId="2" ParentId="13526" CreationDate="2014-03-05T16:30:27.090" Score="2" Body="&lt;p&gt;Unfortunately, the answer depends completely on how stringent you are with &quot;Hamilton's rule&quot;. If you just mean the equation $r \geq c/b$ then it is important to look at modern usages. In modern usage, all three of the terms $r$, $c$, and $b$ can be arbitrarily complicated. &lt;a href=&quot;http://egtheory.wordpress.com/2013/03/25/if-vs-gs/#comment-1338&quot; rel=&quot;nofollow noreferrer&quot;&gt;My favorite&lt;/a&gt; examples include when $r$ takes into account spatial structure saying that an agent near you is more &quot;related&quot; than a genetically identical agent far from you. Assumptions like that are a must, if you want to look at things that much of modern research is concerned with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For this &quot;most general&quot; interpretation of Hamilton's rule, only one property is required and this property does not appear on your list: &lt;strong&gt;linearity&lt;/strong&gt;. Note that this is not the same thing as the additivity you describe. Linearity means that your equations for small changes in proportions are linear in fitness: i.e. $\dot{p} = pf(E)$ where $E$ is some description of the environment, and $f$ is a linear function of the variables of interest (I used a continuous or large-population limit here, but similar things hold true for distributions over discrete populations). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note, that in the above general and super-vague use of Hamilton's rule, the rule itself is not a biological observation but a simple fact of linear algebra. Of course, if you want to get linearity out as a consequence of some biological assumption, then the most common way to do this is by &lt;a href=&quot;https://biology.stackexchange.com/a/14743/500&quot;&gt;assuming weak selection&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you put restrictions on what kind of features of the population, interaction, and environment structure $r$, $c$, and $b$ are allowed to incorporate then this will result in biological theories which will be mathematically true under only some of the assumptions you list. The subset of required assumptions will depend on what specific restrictions you place on $r$, $b$, and $c$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are no standard assumptions accepted on these parameters, so (unsurprisingly) I can't answer your question further without more specification on your part.&lt;/p&gt;&#xA;" OwnerUserId="500" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-03-05T16:39:31.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15502" PostTypeId="1" AcceptedAnswerId="15908" CreationDate="2014-03-05T17:29:42.213" Score="8" ViewCount="5305" Body="&lt;p&gt;I am trying to check if a fastq file has single or paired end reads. How can I achieve this with an error-proof method?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I checked &lt;a href=&quot;http://en.wikipedia.org/wiki/FASTQ_format&quot; rel=&quot;noreferrer&quot;&gt;wikipedia&lt;/a&gt; and &lt;a href=&quot;http://maq.sourceforge.net/fastq.shtml&quot; rel=&quot;noreferrer&quot;&gt;MAQ&lt;/a&gt; but I want to know if is there a reliable document that describes all possible variants in sequence ID to check for single/paired end reads. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am searching also for a library, better in Python, to achieve this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks &lt;/p&gt;&#xA;" OwnerUserId="3466" LastEditorUserId="3466" LastEditDate="2014-03-05T23:45:58.993" LastActivityDate="2021-01-19T16:05:32.843" Title="How to check if a fastq file has single or paired end reads" Tags="&lt;bioinformatics&gt;&lt;sequence-analysis&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15503" PostTypeId="1" AcceptedAnswerId="15504" CreationDate="2014-03-05T19:17:04.407" Score="1" ViewCount="171" Body="&lt;p&gt;I have obtained some plasmids used as integration vectors, this question may apply to all plasmids. I would like to have a somewhat continuos source for these plasmids, let's say that the origin of replication is e-coli specific and can i then just transform the e-coli with the plasmid, let it grow to some density and then do miniprep? or can i also create glycerol stocks out of the bacteria that contain the plasmids and then harvest more plasmids as needed? i realize that both things are possible, but is this a good reasoning to follow?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="233" LastActivityDate="2014-03-05T19:20:47.953" Title="Plasmid maintenance" Tags="&lt;lab-techniques&gt;&lt;plasmids&gt;&lt;minipreps&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15504" PostTypeId="2" ParentId="15503" CreationDate="2014-03-05T19:20:47.953" Score="4" Body="&lt;p&gt;What I would usually do is transform E. coli with the plasmid, grow an overnight culture and mini prep the plasmid in the morning. Before you do the miniprep save a glycerol stock. Thus, you would have some plasmid to work with in the next couple of weeks, and also a glycerol stock to come back to. You can also keep the plate with your transformants, as you can go back to it within a month.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2014-03-05T19:20:47.953" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15505" PostTypeId="1" AcceptedAnswerId="15506" CreationDate="2014-03-05T19:42:25.000" Score="6" ViewCount="2987" Body="&lt;p&gt;In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to messenger RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is simply how many transcription factors are there in the genomes of: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Humans&lt;/li&gt;&#xA;&lt;li&gt;Anopheles gambiae (or it's close taxonomic relatives)&lt;/li&gt;&#xA;&lt;li&gt;Less prioritized: any other species&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2014-03-21T19:22:53.410" LastActivityDate="2014-03-21T19:22:53.410" Title="How many transcription factors are there?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;transcription&gt;&lt;transcription-factor&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15506" PostTypeId="2" ParentId="15505" CreationDate="2014-03-05T20:00:19.723" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://www.tfcat.ca/&quot;&gt;This&lt;/a&gt; is the Curated database of mouse and human transcription factors. And &lt;a href=&quot;http://genomebiology.com/2009/10/3/R29&quot;&gt;this&lt;/a&gt; is the paper in which they describe how they curated the database. In summary, there are 3230 putative mouse TF, 1200 of which are described in scientific papers.&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2014-03-05T20:08:30.610" LastActivityDate="2014-03-05T20:08:30.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15507" PostTypeId="2" ParentId="15505" CreationDate="2014-03-05T20:06:23.427" Score="4" Body="&lt;p&gt;Pretty interesting question. There are a few numbers out, I remember that round about 10% of the human genes are coding for transcription factors (unfortunately I don'T remember the source for that).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This paper from 2002 estimates between 2000 and 3000 factors:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11823631&quot; rel=&quot;nofollow&quot;&gt;Signal transduction and the control of gene expression.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This paper from 2009 states a number of 1391 manually curated factors and also speculates about a number of 2000 - 3000 factors in total. This is definitely interesting to read.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19274049&quot; rel=&quot;nofollow&quot;&gt;A census of human transcription factors: function, expression and&lt;br&gt;&#xA;evolution.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-05T20:06:23.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15508" PostTypeId="1" AcceptedAnswerId="15511" CreationDate="2014-03-05T20:55:51.117" Score="1" ViewCount="146" Body="&lt;p&gt;The host response involves at least phagocytosis and probably localised acute inflammatory response at least after the colonisation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking how the host can defend against pneumolysin which helps the streptococcus pneumoniae invasion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can the host defend against Streptococcus pneumoniae capsule?&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="5144" LastEditDate="2014-03-07T21:34:20.860" LastActivityDate="2014-03-07T21:34:20.860" Title="How host defends against S. pneumoniae capsule?" Tags="&lt;microbiology&gt;&lt;inflammation&gt;&lt;pathogenesis&gt;&lt;host-pathogen-interaction&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15509" PostTypeId="1" CreationDate="2014-03-05T21:00:05.043" Score="2" ViewCount="478" Body="&lt;p&gt;Recently, I've been reading about the MyD88 dependent signalling pathway, with particular reference to its activation in Macrophages and other cells of the immune system on recognition of a pathogen. I understand that when a PAMP (Pathogen Associated Molecular Pattern) binds with a PRR (Pattern Recognition Receptor), the receptor undergoes a conformational change, which precipitates a cascade of chemical reactions between various proteins, which eventually leads (inter alia) to the translocation of NF-κB to the nucleus, which leads to the production of cytokines. My question is about the finer points, particularly with respect to TLR1 and TLR2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My reading suggests that these generally form a heterodimer - is this always true? Are both required for a pathogen to be recognised and an immune response produced?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Upon the pathogen binding with TLR1 (whether in a complex with TLR2 or not) what precisely happens to the receptor. I understand that MyD88 is, ultimately, recruited, but by what means?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe I understand everything that happens after the recruitment of MyD88, but I am less clear on everything before that. I had initially understood that the recruitment of MyD88 was the immediate next step, but other sources make reference to two proteins which I was initially unaware of: TOLLIP and TIRAP. What, if anything, is their role?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm still a little new to stackexchange so I apologise if this question is not up to standard, in which case, let the question simply be: 'How do TLR1/TLR2 activate the MyD88 dependent pathway?'&lt;/p&gt;&#xA;" OwnerUserId="5263" LastActivityDate="2014-03-05T22:13:52.357" Title="How do TLR1/TLR2 activate the MyD88 dependent pathway" Tags="&lt;immunology&gt;&lt;signalling&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15510" PostTypeId="2" ParentId="15505" CreationDate="2014-03-05T21:02:48.137" Score="2" Body="&lt;p&gt;Amos Bairoch, of SWISSProt/UniProt fame has set up the &lt;a href=&quot;http://www.nextprot.org/&quot; rel=&quot;nofollow&quot;&gt;nextprot&lt;/a&gt; database, a manually curated repository of knowledge for human proteins. While that won't help you get a number for the mosquito, it does make it easy to retrieve &lt;a href=&quot;http://www.nextprot.org/db/search#%7Bf%3afunction,t%3a%22transcription%20factor%22%7D&quot; rel=&quot;nofollow&quot;&gt;a list&lt;/a&gt; of human proteins that are annotated as transcription factors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Searching for &quot;Transcription Factor&quot; in the &quot;Function&quot; tab &lt;a href=&quot;http://www.nextprot.org/db/search#%7Bf%3afunction,t%3a%22transcription%20factor%22%7D&quot; rel=&quot;nofollow&quot;&gt;returns&lt;/a&gt; 1405 hits. You'll notice that most answers are in the same ball park despite small differences, but bear in mind that many of these are assumed TFs and it will be a while before all of them have been experimentally confirmed to act as such &lt;em&gt;in vivo&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-03-05T21:02:48.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15511" PostTypeId="2" ParentId="15508" CreationDate="2014-03-05T21:17:16.037" Score="1" Body="&lt;p&gt;According to the two papers listed below, this is mostly done by a neutrophilic inflammatory response. The response is regulated by mechanisms of the innate immune system and is mediated by receptor like TLR2, TLR4 and SIGN-R1.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jimmunol.org/cgi/content/meeting_abstract/188/1_MeetingAbstracts/45.8&quot; rel=&quot;nofollow&quot;&gt;Role of Dectin-2 in the host defense against Streptococcus&#xA;pneumoniae infection&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24205278&quot; rel=&quot;nofollow&quot;&gt;Dectin-2-dependent NKT cell activation and serotype-specific antibody&#xA;production in mice immunized with pneumococcal polysaccharide&#xA;vaccine.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are a few papers which go deeper (reviews, so you will probably have to go through the reference lists):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1571441&quot; rel=&quot;nofollow&quot;&gt;Mechanisms of host defense against infection with Streptococcus&#xA;pneumoniae.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This paper mentions specific antibodies later on in the reaction and finally the opsonization by immune cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These two papers tal specifically about pneumolysin:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7588820&quot; rel=&quot;nofollow&quot;&gt;Pneumococcal virulence factors and host immune responses to them.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15995579&quot; rel=&quot;nofollow&quot;&gt;Pneumolysin as a vaccine and drug target in the prevention and&#xA;treatment of invasive pneumococcal disease.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-07T21:33:45.743" LastActivityDate="2014-03-07T21:33:45.743" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15512" PostTypeId="2" ParentId="15505" CreationDate="2014-03-05T21:21:11.113" Score="5" Body="&lt;p&gt;As the number of human TFs have been discussed by the previous answers, I'll limit myself to &lt;em&gt;Anopheles gambiae&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the same issue of &lt;em&gt;Science&lt;/em&gt; in which Holt et al. published a genome sequence for &lt;em&gt;Anopheles gambiae&lt;/em&gt; (&lt;a href=&quot;http://www.sciencemag.org/content/298/5591/129.long&quot;&gt;1&lt;/a&gt;), Zdobnov et al. published a comparison of the &lt;em&gt;A. gambiae&lt;/em&gt; and &lt;em&gt;Drosophila melanogaster&lt;/em&gt; genomes.(&lt;a href=&quot;http://www.sciencemag.org/content/298/5591/149.long&quot;&gt;2&lt;/a&gt;) While the two species diverged about 250 million years ago, and the &lt;em&gt;D. melanogaster&lt;/em&gt; genome is about twice the size of the &lt;em&gt;A. gambiae&lt;/em&gt; genome, the two species still show broad similarities and a similar number of proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors identified 6089 protein pairs as &quot;clear orthologs&quot;, corresponding to 47% and 44% of the of the Anophelesand and Drosophila proteins respectively. One might thus be tempted to estimate the number of TFs in &lt;em&gt;A. gambiae&lt;/em&gt; as similar to that in &lt;em&gt;D. melanogaster&lt;/em&gt;. For the latter, the FlyTF database (&lt;a href=&quot;http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/old_index.html&quot;&gt;http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/old_index.html&lt;/a&gt;) currently lists 753 putative site-specific TFs and 454 &quot;well supported&quot; candidates. More recently, Hammonds et al. identified 708 &lt;em&gt;melanogaster&lt;/em&gt; genes &quot;likely to encode sequence-specific DNA-binding TFs&quot;.(&lt;a href=&quot;http://genomebiology.com/2013/14/12/R140&quot;&gt;3&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: You may also want to check out the following question on Biostars: &lt;a href=&quot;http://www.biostars.org/p/53590/&quot;&gt;http://www.biostars.org/p/53590/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-03-05T21:51:49.577" LastActivityDate="2014-03-05T21:51:49.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15513" PostTypeId="2" ParentId="15509" CreationDate="2014-03-05T21:40:00.077" Score="1" Body="&lt;p&gt;The TLR are usually working as homodimers (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0960982211005975&quot; rel=&quot;nofollow noreferrer&quot;&gt;Toll-like receptors&lt;/a&gt;), although TLR2 can cooperate with TLR1 or 6.&#xA;Upon binding of its ligand (this is called pathogen associated molecular pattern) the receptors change their conformation and allow binding of TIRAP (TIR adapter protein) to their Toll-interleukin 1 receptor (TIR) domain. TIRAP then recruits MYD88, which then recruits IRAK1 or 4. The signal is then passed down the pathway as shown in the figure below (taken from the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Toll-like_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;TLR&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7o8zi.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-05T22:13:52.357" LastActivityDate="2014-03-05T22:13:52.357" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15514" PostTypeId="1" AcceptedAnswerId="15516" CreationDate="2014-03-05T22:09:42.440" Score="26" ViewCount="5920" Body="&lt;p&gt;I've often heard that a population, human or otherwise, will continue to grow as long as there is food available (assuming nothing else is killing them off).  It makes sense: if you have food you can live, and if nothing is hunting you you'll survive to reproduce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I recently designed a piece of software to simulate an ecosystem, with groups of creatures of different species eating and hunting and reproducing alongside each other.  It was very simplified (each animal had simple attack/defense/speed/stealth values, etc), but something became rapidly apparent: in every simulation the predators overwhelmed the prey, reproducing until their numbers could not be sustained by the herbivores, and leading to an inevitable die-off of both groups.  I could delay the die-off by adjusting different values and initial population counts, but it would always happen eventually.  The predators would eat and breed and eat and breed until the entire system collapsed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At first I thought it was just the product of my over-simplified system, but it got me thinking: &lt;strong&gt;what prevents predators from overpopulating in real life?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems like the natural tendency would be for (for example) the sharks to continue breeding and eating until all the fish are gone, or the wolves to eat all the deer, etc.  Obviously some predators have predators of their own, but that's just putting off the question: if the hyenas don't overpopulate because the lions eat them, then what's keeping the lions from overpopulating?  I can't come up with anything that would prevent the apex predators from growing too numerous, then fighting each other over a dwindling prey population, then dying off entirely when there was no more food to find.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do predator populations self-regulate to prevent putting undo stress on their prey populations?  Or is there some other mechanism to keep the predator hierarchy from becoming top-heavy?&lt;/p&gt;&#xA;" OwnerUserId="5917" LastEditorUserId="3624" LastEditDate="2015-02-06T12:26:39.333" LastActivityDate="2019-03-19T00:01:33.800" Title="What prevents predator overpopulation?" Tags="&lt;ecology&gt;&lt;population-dynamics&gt;&lt;ecosystem&gt;&lt;antipredator-adaptation&gt;&lt;predation&gt;" AnswerCount="7" CommentCount="9" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="15515" PostTypeId="1" AcceptedAnswerId="15517" CreationDate="2014-03-05T22:56:26.420" Score="3" ViewCount="198" Body="&lt;p&gt;While the vast majority of eukaryotic organisms maintain their chromosome ends (telomeres) via telomerase, an enzyme system that generates short, tandem repeats on the ends of chromosomes, other mechanisms such as the transposition of retrotransposons (e.g. Drosophila) or recombination (e.g. Yeast) can also be used in some species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know of your thoughts on the possible mechanisms that regulate telomere lengths in mosquitoes.&lt;/p&gt;&#xA;" OwnerUserId="5005" LastActivityDate="2014-03-05T23:49:25.567" Title="How do mosquitoes maintain telomere length?" Tags="&lt;genetics&gt;&lt;cell-biology&gt;&lt;dna&gt;&lt;senescence&gt;&lt;telomere&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15516" PostTypeId="2" ParentId="15514" CreationDate="2014-03-05T22:59:40.527" Score="31" Body="&lt;p&gt;No, I don't think auto-regulation explain much in the population sizes of predators. Group selection may explain such auto-regulation but I don't think it is of any considerable importance for this discussion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The short answer is, as @shigeta said&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[predators] tend to starve to death as they are too many!&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To have a better understanding of what @shigeta said, you'll be interested in understanding various model of prey-predator or of consumer-resource interactions. For example the famous Lotka-Volterra equations describe the population dynamics of two co-existing species where one is the prey and the other is a predator. Let's first define some variables…&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;span class=&quot;math-container&quot;&gt;$x$&lt;/span&gt; : Number of preys&lt;/li&gt;&#xA;&lt;li&gt;&lt;span class=&quot;math-container&quot;&gt;$y$&lt;/span&gt; : number of predators&lt;/li&gt;&#xA;&lt;li&gt;&lt;span class=&quot;math-container&quot;&gt;$t$&lt;/span&gt; : time&lt;/li&gt;&#xA;&lt;li&gt;&lt;span class=&quot;math-container&quot;&gt;$\alpha$&lt;/span&gt;, &lt;span class=&quot;math-container&quot;&gt;$\beta$&lt;/span&gt;, &lt;span class=&quot;math-container&quot;&gt;$\xi$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$\gamma$&lt;/span&gt; are parameters describing how one species influence the population size of the other one.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The Lotka-Voltera equations are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$\frac{dx}{dt} = x(\alpha - \beta y)$$&lt;/span&gt;&#xA;&lt;span class=&quot;math-container&quot;&gt;$$\frac{dy}{dt} = -y(\gamma - \xi x)$$&lt;/span&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can show that for some parameters the matrix for these equations have a complex eigenvalue meaning that the long term behavior of this system is cyclic (periodic behavior). If you simulate such systems you'll see that the population sizes of the two species fluctuate like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZRImS.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where the blue line represents the predators and the red line represents the preys.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Representing the same data in phase space, meaning with the population size of the two species on axes &lt;span class=&quot;math-container&quot;&gt;$x$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$y$&lt;/span&gt; you get:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yidcV.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where the arrows shows the direction toward which the system moves. If the population size of the predators (&lt;span class=&quot;math-container&quot;&gt;$y$&lt;/span&gt;) reaches 0 (extinction), then &lt;span class=&quot;math-container&quot;&gt;$\frac{dx}{dt} = x(\alpha - \beta y)\space$&lt;/span&gt; becomes &lt;span class=&quot;math-container&quot;&gt;$\frac{dx}{dt} = x\alpha \space$&lt;/span&gt; (which general solution is &lt;span class=&quot;math-container&quot;&gt;$x_t = e^{\alpha t}x_0$&lt;/span&gt;) and therefore the populations of preys will grow exponentially. If the population size of preys (&lt;span class=&quot;math-container&quot;&gt;$x$&lt;/span&gt;) reaches 0 (extinction), then &lt;span class=&quot;math-container&quot;&gt;$\frac{dy}{dt} = -y(\gamma - \xi x)\space$&lt;/span&gt; becomes &lt;span class=&quot;math-container&quot;&gt;$\frac{dy}{dt} = -y\gamma \space$&lt;/span&gt;, and therefore the population of predators will decrease exponentially.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following this model, your question is actually: Why are the parameters &lt;span class=&quot;math-container&quot;&gt;$\alpha$&lt;/span&gt;, &lt;span class=&quot;math-container&quot;&gt;$\beta$&lt;/span&gt;, &lt;span class=&quot;math-container&quot;&gt;$\xi$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$\gamma$&lt;/span&gt; not &quot;set&quot; in a way that predators cause the extinction of preys (and therefore their own extinction)? One might equivalently ask the opposite question? Why don't preys evolve in order to escape predators so that the population of predators crushes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As showed, you don't need a complex model to allow the co-existence of predators and preys. You could describe your model a bit more accurately in another post and ask why in your model the preys always get extinct. But there are tons of possibilities to render your model more realistic such as adding spatial heterogeneities (places to hide for example as suggested by @AudriusMeškauskas). One can also consider other trophic levels, stochastic effects, varying selection pressure through time (and other types of balancing selection), age, sex or health-specific mortality rate due to predation (e.g. predators may target preferentially young ones or diseased ones), several competing species, etc..&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I would also like to talk about other things that might be of interest in your model (two of them need you to allow evolutionary processes in your model):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) &lt;strong&gt;lineage selection&lt;/strong&gt;: predators that eat too much end up disappearing because they caused their preys to get extinct. This hypothesis has nothing to do with some kind of auto-regulation for the good of species. Of course you'd need several species of predators and preys in your model. This kind of hypothesis are usually considered as very unlikely to have any explanatory power.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) &lt;strong&gt;Life-dinner principle&lt;/strong&gt;. While the wolf runs for its dinner, the rabbit runs for its life. Therefore, there is higher selection pressure on the rabbits which yield the rabbits to run in average slightly faster than wolves. This evolutionary process protects the rabbits from extinction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) You may consider..&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;more than one species of preys or predators&lt;/li&gt;&#xA;&lt;li&gt;environmental heterogeneity&lt;/li&gt;&#xA;&lt;li&gt;partial overlapping of distribution ranges between predators and preys&lt;/li&gt;&#xA;&lt;li&gt;When one species is absent, the model behave just like an exponential model. You might want to make a model of logistic growth for each species by including &lt;span class=&quot;math-container&quot;&gt;$K_x$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$K_y$&lt;/span&gt; the carrying capacity for each species.&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Adding a predator (or parasite) to the predator species of interest&lt;/p&gt;&#xA;&#xA;&lt;p&gt;... and you might get very different results.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="43480" LastEditDate="2019-03-18T23:37:35.610" LastActivityDate="2019-03-18T23:37:35.610" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="15517" PostTypeId="2" ParentId="15515" CreationDate="2014-03-05T23:05:05.570" Score="2" Body="&lt;p&gt;It seems that the current model is that recombination is the mechanism by which telomere length is maintained in the malaria vector &lt;em&gt;Anopheles gambiae&lt;/em&gt;. Here is an exerpt of &lt;a href=&quot;http://mcb.asm.org/content/17/9/5176.short&quot; rel=&quot;nofollow&quot;&gt;Roth &lt;em&gt;et al&lt;/em&gt;&lt;/a&gt; paper that proposed the recombination mechanism:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The insertion of a transgenic pUChsneo plasmid at the left end of chromosome 2 provided a unique marker for measuring the dynamics of the 2L telomere over a period of about 3 years. The terminal length was relatively uniform in the 1993 population with the chromosomes ending within the white gene sequence of the inserted transgene. Cloned terminal chromosome fragments did not end in short repeat sequences that could have been synthesized by telomerase. By late 1995, the chromosome ends had become heterogeneous: some had further shortened while other chromosomes had been elongated by regenerating part of the integrated pUChsneo plasmid. A model is presented for extension of the 2L chromosome by recombination between homologous 2L chromosome ends by using the partial plasmid duplication generated during its original integration.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You might also be interested in this paper: &lt;a href=&quot;http://etheses.nottingham.ac.uk/2589/&quot; rel=&quot;nofollow&quot;&gt;Genes required to maintain telomeres in the absence of telomerase in Saccharomyces cerevisiae&lt;/a&gt; and then look at whether there are mosquito homologs of the identified yeast genes that might be involved in telomere maintance.&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2014-03-05T23:49:25.567" LastActivityDate="2014-03-05T23:49:25.567" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="15518" PostTypeId="2" ParentId="14523" CreationDate="2014-03-05T23:06:28.543" Score="2" Body="&lt;p&gt;&lt;strong&gt;Short answer:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No. Eukaryotes have more ways of maintaining telomere length than via telomerase alone and all organisms with circular genomes do not need to worry about telomere length anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long answer:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, the telomerase system is not the only observed mechanism in Eukaryotes that elongates telomeres. Other mechanisms such as the transposition of retrotransposons (e.g. Drosophila) or recombination (e.g. Yeast) can also be used in some species. Yeast  has been observed to use several of these mechanisms. So no, telomerase itself is not always necessary for immortality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ofcourse prokaryotes do not need to worry about shortening chromosome ends at all since their genome is circular - i.e. it has no ends to shorten with each cell division! &lt;/p&gt;&#xA;" OwnerUserId="5005" LastActivityDate="2014-03-05T23:06:28.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15519" PostTypeId="1" CreationDate="2014-03-05T23:21:09.777" Score="3" ViewCount="339" Body="&lt;p&gt;&lt;strong&gt;Background:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An electronic cigarette (e-cig or e-cigarette) is a battery-powered device which simulates tobacco smoking patented in 1963 by Herbert A. Gilbert. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It generally uses a heating element known as an atomizer, that vaporizes a liquid solution. Some solutions contain a mixture of nicotine and flavorings, while others release a flavored vapor without nicotine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any health risks uniquely associated with e-cigs as compared with normal cigarettes?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MgjQC.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5005" LastActivityDate="2014-03-06T10:52:30.527" Title="Electronic cigarettes (e-cigs), any health risks?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;pathology&gt;&lt;respiration&gt;&lt;health&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15521" PostTypeId="2" ParentId="13665" CreationDate="2014-03-06T01:24:00.330" Score="0" Body="&lt;p&gt;Well... this is true in the same way that books are constricted by letters. We could have more letters and create more combinations with the same length of DNA. But, like books, there are just so many combinations.&lt;/p&gt;&#xA;" OwnerUserId="5859" LastActivityDate="2014-03-06T01:24:00.330" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15522" PostTypeId="1" AcceptedAnswerId="15543" CreationDate="2014-03-06T01:28:06.593" Score="2" ViewCount="745" Body="&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does the telomeric repeating sequence vary in non-vertebrate Eukaryotes? If you know the repeating sequence of a given species I would appreciate hearing it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Telomerase is a ribonucleoprotein enzyme that adds DNA sequence repeats to the 3' end of DNA strands in the telomere regions, which are found at the ends of eukaryotic chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In vertebrates the conserved telomeric repeating sequence is &quot;TTAGGG&quot;.&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2014-03-18T17:55:14.577" LastActivityDate="2014-03-18T17:55:14.577" Title="How does the telomere repeat sequence vary in Eukaryotes?" Tags="&lt;dna&gt;&lt;genomics&gt;&lt;senescence&gt;&lt;telomere&gt;&lt;copy-number-variation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15524" PostTypeId="1" CreationDate="2014-03-06T04:31:55.030" Score="1" ViewCount="503" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MiXqa.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hi everyone! Here is a diagram of a genetics complementation problem. My main concern is regarding number 3d. I'm assuming that in this case, it would be complementary interaction and thus exhibiting a ratio of nine to seven. because if we cross F1, 3 will be mutant while one will exhibit wild-type phenotype. Is this right? Thanks in advance! &lt;/p&gt;&#xA;" OwnerUserId="5460" LastActivityDate="2014-03-06T06:23:04.727" Title="Gene Complementation Question" Tags="&lt;homework&gt;&lt;molecular-genetics&gt;&lt;genetics&gt;&lt;allele&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15525" PostTypeId="2" ParentId="15524" CreationDate="2014-03-06T06:23:04.727" Score="1" Body="&lt;p&gt;Yes 9:7 seems to be the right answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;F1 progeny should be AaGg... and crossing it will give a ratio of 9:7 as is of any complementary genes&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-06T06:23:04.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15526" PostTypeId="1" AcceptedAnswerId="15528" CreationDate="2014-03-06T07:00:46.060" Score="6" ViewCount="721" Body="&lt;p&gt;I was reading &lt;a href=&quot;http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13112.html&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; which states this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Classical Batesian mimicry, in which an undefended mimic evolves to&#xA;  look like a toxic model, is a parasitic relationship in which the&#xA;  mimic gains an advantage at the expense of the model&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't understand why this mimicry is equivalent to parasitism. Do the authors call it parasitic because eventually it may cause threat to the model, as the predator learns that it is being fooled around ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't see a clear and certain antagonistic relationship here. Can someone please explain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it is the case that the mimic reduces the likelihood of the model being preyed then then outcome of this is dependent on multiple parameters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The +/- effect of this interaction is not always certain (which on the other hand is usually certain in the case of a typical parasitism). The uncertainty can arise not just by evolution of the predator but by other factors such as population size and structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering all this is it correct to call a relationship as parasitism just based on one of the many possible outcomes ?&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-03-09T20:21:54.513" LastActivityDate="2015-08-30T06:40:25.400" Title="Parasitism and mimicry" Tags="&lt;evolution&gt;&lt;ecology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15527" PostTypeId="2" ParentId="15519" CreationDate="2014-03-06T07:04:21.170" Score="0" Body="&lt;p&gt;The e-cig possess potential risks for healthy people as well as for a ill ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It contains nicotine which still reaches the lungs and causes its negative effects as oxidative stress. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, because one can smoke e-cig anywhere there is potential risk for nicotine intoxication for smokers using e-cig nonstop.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a risk of paradoxical conversion from e-cigs to regular ones by teenagers/beginners because starting smoking with e-cigs can increase tolerance to nicotine and raise the need to higher concentrations of it to achieve the desired sensation of &quot;smoking&quot;, thus the user can replace the e-cigs to regular and more toxic ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Feb 2014 a special article was published&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ann Am Thorac Soc. 2014 Feb;11(2):236-42. Electronic cigarettes. Potential harms and benefits. Drummond MB1, Upson D which abstract I place here - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Use of electronic cigarettes, devices that deliver a nicotine-containing vapor, has increased rapidly across the country and globally. Perceived and marketed as a &quot;healthier alternative&quot; to conventional cigarettes, few data exist regarding the safety of these devices and their efficacy in harm reduction and treatment of tobacco dependence; even less is known about their overall impact on population health. This review highlights the recent data regarding electronic cigarette toxicity, impact on lung function, and efficacy in smoking reduction and cessation. Studies show that the vapor generated from electronic cigarettes has variable amounts of nicotine and potential harmful toxins, albeit at levels lower than in conventional cigarettes. The long-term carcinogenic and lung function effects of electronic cigarettes are not known. Although some data demonstrate that electronic cigarettes may be effective in reducing conventional cigarette consumption, there are no data demonstrating the efficacy of electronic cigarettes as a tool to achieve cessation. Until robust longitudinal evaluations demonstrate the safety of electronic cigarettes and efficacy in treatment of tobacco dependence, their role as a harm reduction tool is unclear.&quot;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2014-03-06T07:57:46.417" LastActivityDate="2014-03-06T07:57:46.417" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15528" PostTypeId="2" ParentId="15526" CreationDate="2014-03-06T07:34:40.683" Score="8" Body="&lt;p&gt;A parasitic interaction is when one species has a fitness increase (benefit) from the interaction while the other has a fitness decrease (cost). Note: you don't need to have physical contact to have an interaction. As soon as the presence of one specie influence the fitness of the other, it is enough to consider that there is an interaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of Batesian mimicry, I think it is obvious to understand why the non-toxic species gain from this interaction. Let's imagine the toxic (model) species is blue. Predators learn to avoid blue species because they feel very sick right after eating it. In other words, the predators have a bad experience or even better we can say that the predator receives a punishment or a negative reinforcement (&lt;a href=&quot;http://en.wikipedia.org/wiki/Instrumental_conditioning&quot; rel=&quot;nofollow noreferrer&quot;&gt;instrumental conditioning&lt;/a&gt;). In consequence the predator that got this negative reinforcement will probably avoid blue individuals in the future.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a predator eats an individual from the mimic non-toxic species, he got a positive reinforcement. In consequence the predator learns that the prey tastes good and in consequence it is more likely to eat a blue prey next time it encounters one, which obviously has a negative impact on toxic model organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I have two issues with this concept.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The interaction is not one-to-one and we can consider that the presence of a species that use Batesian mimicry influence the variance in fitness of the toxic species only if (actually you might argue differently by not assuming infinite population size) the distribution ranges are not completely overlapping or if there are some kind of population structure.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If the toxic species causes death to the predator, then the predators never get the opportunity to learn. But one can consider the same mechanisms at evolutionary timescale than at the time of the lifespan of the predators. It is also possible that the predators have higher cognitive abilities allowing them to gain insights concerning the toxicity of one species without having to taste it.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;EDIT&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What if predators can tell the difference between the two prey species?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Your point, if I understand it, is that if the predators manage to sense (or to evolve sensing) the two prey species differently (in consequence the non-toxic species does not mimic the other prey species anymore), then the toxic species will not suffer anymore from the mimicry. So in other words, mimicry is a parasitic interaction but predators might evolve ways to sense the two species differently in which case there would have no mimicry anymore. Note: the predator is more likely to evolve good sensing abilities if it forages on few species only.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think your issue is that you should not consider a species to be mimicry if the predator can tell the difference between the two prey species. It is not to the human eyes that the mimicry makes sense but only to those of the predators. So, batesian mimicry is a parasitic interaction and if the predators evolve so that they can sense the difference between the two species, then there is no more Batesian mimicry and there is no more parasitic interactions between the two prey species.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why do you say that  &quot;physical contact&quot; not necessary for two species to have a parasitic interaction?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The interactions between species are defined as follow:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bEY4Z.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The benefits and costs (harmed) are defined in terms of fitness. These definitions do not involve any physical interactions. And to the eyes of the evolutionist at least, that would not make much sense to add a notion of physical interaction into these definitions.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the case of Batesian mimicry the ± effect is not always certain (while it is certain in common parasitic interactions)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The point is interesting. I think it just mean that the non-toxic organism is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Facultative_parasite&quot; rel=&quot;nofollow noreferrer&quot;&gt;facultative parasite&lt;/a&gt; (a species that can live with or without the parasitic interaction). Statistically speaking, if you have enough preys of each species and especially enough predators, then the consequence is certain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider the common Ivy. It is a parasite of other plants but can also live on human-made walls in which case the negative effect on other plants is not always certain either. The difference between the Ivy and the non-toxic prey is that the fitness of the non-toxic prey depends on whether it parasites the other species while the Ivy is doing just fine on human-made walls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can think about the interactions between rabbits and wolves. They share a prey-predator interaction which is a special case of the parasitic interaction according to above diagram. In a particular environment the wolves might be absent and so predation does not occur, just like the non-toxic species might be absent species might be absent and so the parasitic interaction does not occur anymore.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-08-30T06:40:25.400" LastActivityDate="2015-08-30T06:40:25.400" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15529" PostTypeId="1" AcceptedAnswerId="15530" CreationDate="2014-03-06T08:16:29.733" Score="8" ViewCount="782" Body="&lt;p&gt;I am not a biologist. Please pardon me, if my question does not make sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am trying to obtain a DNA sequence for pattern analysis in Matlab. I used to generate random sequence &lt;code&gt;randseq&lt;/code&gt; in Matlab. However, I am trying to obtain some real dataset. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any idea where I can obtain the DNA dataset. I am looking at a dataset having &lt;code&gt;acgt&lt;/code&gt; patterns&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT : Thanks a lot guys, I found it here. : &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nucest?term=((human%5BComponent+Accession%5D)+AND+normal+Breast+gene+sequence)+AND+1000%3A10000%5BSequence+Length%5D&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/nucest?term=((human%5BComponent+Accession%5D)+AND+normal+Breast+gene+sequence)+AND+1000%3A10000%5BSequence+Length%5D&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5919" LastEditorUserId="5919" LastEditDate="2014-03-06T15:29:37.390" LastActivityDate="2014-03-06T15:29:37.390" Title="Looking for a DNA sequence" Tags="&lt;dna&gt;&lt;dna-sequencing&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15530" PostTypeId="2" ParentId="15529" CreationDate="2014-03-06T08:20:02.503" Score="8" Body="&lt;p&gt;There are several nucleotide sequence datbases available. One of the largest is the NCBI GenBank at &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genbank/&quot;&gt;http://www.ncbi.nlm.nih.gov/genbank/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may use the search bar at the top to search for nucleotide sequences belonging to a certain organism or gene. For example, searching for &quot;E coli&quot; will give you the full genome sequences for several bacterial species, with a strain of &lt;em&gt;E. coli&lt;/em&gt; as the top result. The &lt;em&gt;E. coli&lt;/em&gt; genome is about 5 MB large. If you want a single gene sequence, searching for &quot;sonic hedgehog&quot; (without quotes) will return the human hedgehog gene as the top result, which is 1,481 basepairs long.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To get a sequence in raw format, select &quot;FASTA&quot; below the entry. At the page you get sent to  , chose &quot;send&quot; in the upper right corner and under &quot;Choose destination&quot;, &quot;file&quot;. This will give you a .fasta file, the standard raw sequence format. The first line, starting with &quot;&gt;&quot; will be metadata, while the rest of the file consists of the nucleotide letters only.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that in addition to a,t,g and c, you may also find other characters, most often &quot;n&quot;. These characters describe ambiguity in the sequence (meaning that the nucleotide at that position could not be determined). For a full description of the FASTA format sequence representation, see &lt;a href=&quot;http://en.wikipedia.org/wiki/FASTA_format#Sequence_representation&quot;&gt;http://en.wikipedia.org/wiki/FASTA_format#Sequence_representation&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-03-06T08:28:25.697" LastActivityDate="2014-03-06T08:28:25.697" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15531" PostTypeId="2" ParentId="15529" CreationDate="2014-03-06T08:20:58.160" Score="2" Body="&lt;p&gt;you can download real sequences from GENBANK. You can search model organism(s) or genetic marker(s) and download it in *.fasta or other format. Good luck!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genbank/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/genbank/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5893" LastActivityDate="2014-03-06T08:20:58.160" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15532" PostTypeId="1" AcceptedAnswerId="16029" CreationDate="2014-03-06T08:56:30.637" Score="3" ViewCount="1194" Body="&lt;p&gt;I am thinking of why some patients do not have natural immunity after exposure to the A-B toxin of diphthria.&#xA;I think the A-B exotoxin is the key factor causing this disease and should trigger memory cells to form.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DT has both local and systemic effects.&#xA;Locally, its action on epithelial cells leads to necrosis and inflammation, forming a pseudomembrane composed of a coagulum of fibrin, leukocytes and cellular debris.&#xA;Absorption and circulation of DT allow binding throughout the body.&#xA;Local effects produce pseudomembrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The major impact of transduction in pathogens is the introduction and stable inheritance of virulence genes such as those coding for toxins.&#xA;C diphtheriae is lysogenic with a phage containing the diphtheria toxin gene.&#xA;Diphtheria toxin is produced by C diphtheriae only when infected with a bacteriophage that integrates the toxin-encoding genetic elements into the bacteria&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The toxicity for intact cells depends on toxin binding and uptake.&#xA;In other words, the net effect of the toxin depends on the function of the target protein and the function of the cell.&#xA;B subunit binds to receptors that regulate cell growth and differentiation, thus exploiting a normal cell function.&#xA;A subunit inhibits protein synthesis.&#xA;B subunit binding determines cell susceptibility.&#xA;Absorption and circulation of DT allow binding throughout the body.&#xA;&lt;strong&gt;I think this uptake does not occur sufficiently with patients without natural immunity stimulation&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the reason for no natural immunity for some patients after &lt;strong&gt;toxin exposure is that the host does not stimulate enough adaptive immunity and no memory cells are built&lt;/strong&gt;.&#xA;Again, this is because the bacteria has little invasive capacity.&#xA;Diphtheria is due to the local and systemic effects of DT with potent cytotoxic features.&#xA;The uptake of the toxin varies also among some patients.&#xA;So other patients have probably more local effects.&#xA;This would explain partially why the adaptive immunity is not triggered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diphtheria toxin is antigenic itself.&#xA;So it can stimulate the production of protective antitoxin antibodies during natural infection.&#xA;In those patients without development of natural immunity, A subunit fails to bind EF-2, probably.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One reason is that the toxin does not get into bloodstream in 6-8% cases, and so natural immunity is developed. &#xA;So there is too low effective dose of diphtheria for some patients to invade the epithelium and trigger the adaptive immune response and create memory cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources: Murray Microbiology, Sherris Microbiology and Jawetz Microbiology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why do 6-8% of diphtheria patients not develop natural immunity after being infected?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="3971" LastEditDate="2014-03-09T00:51:36.310" LastActivityDate="2014-03-24T11:56:21.000" Title="Why do 6-8% of diphtheria patients do not develop natural immunity after being affected?" Tags="&lt;microbiology&gt;&lt;epidemiology&gt;&lt;infection&gt;&lt;pathogenesis&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15534" PostTypeId="2" ParentId="15522" CreationDate="2014-03-06T10:15:34.487" Score="2" Body="&lt;ul&gt;&#xA;&lt;li&gt;TTAGG telomeric repeats have been found in several insects. From Sahara, Marek &amp;amp; Traut (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10560968/&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;):&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(TTAGG)n-containing telomeres were found in three Lepidoptera species,&#xA;  the silkworm Bombyx mori (in which the telomeric sequence was recently&#xA;  discovered), the flour moth Ephestia kuehniella, and the wax moth&#xA;  Galleria mellonella, in one species of Hymenoptera, the honey bee Apis&#xA;  mellifera, in one species of Coleoptera, the bark beetle Ips&#xA;  typographus, in one species of Orthoptera, the locust Locusta&#xA;  migratoria, and in a crustacean, the amphipod Gammarus pulex&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;C. elegans have TTAGGC repeats.(&lt;a href=&quot;http://www.pnas.org/content/93/17/8983.abstract&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The TTAGGG motif is also common in filamentous fungi, while Saccharomyces cerevisiae telomeres have TG(TG)(TG) repeats. Many plants have TTTAGGG repeats.(&lt;a href=&quot;http://nar.oxfordjournals.org/content/34/17/4685.full&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For additional references, see the introduction in Wu et al.(&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651048/&quot; rel=&quot;nofollow&quot;&gt;4&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-03-06T10:15:34.487" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15535" PostTypeId="1" AcceptedAnswerId="15538" CreationDate="2014-03-06T10:20:15.670" Score="0" ViewCount="126" Body="&lt;p&gt;&lt;em&gt;S. pyogenes&lt;/em&gt; is &quot;flesh-eating&quot; bacteria.&#xA;It results from life-theatening &lt;strong&gt;myonecrosis&lt;/strong&gt; caused by this organism.&#xA;&lt;em&gt;S. pyogenes&lt;/em&gt; avoids phagocytosis (mediated primarily by capsule, M and M-like proteins, C5a peptidase), adhere to and invade host cells (M protein, lipoteichoic, F protein), and produce toxins (streptococcal pyrogenic exotoxins, steptolysin S, streptolsin O, streptokinase, DNases).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppurative diseases: pharyngitis, soft-tissue infections.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Erysipelas&lt;/strong&gt;: localised skin infection with pain, inflammation, lymph node enlargement and systemic symptoms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cellulitis&lt;/strong&gt;: infection of the skin that involves the subcutaneous tissues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Necrotising fasciitis&lt;/strong&gt;: deep infection of skin that involves destruction of muscle and fat layers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think these are most its skin infections. But what about its diagnostics?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think take biopsy from living tissue, not from necrotic.&#xA;If pus, then probably from it.&#xA;I think we can do Gram staining, recognise gram-positive cocci like in a string&#xA;Then, we can do hydrogen peroxide test - if no bubbles, then suspicion to &lt;em&gt;S. pyogenes&lt;/em&gt;, since catalase negative.&#xA;The do optochin test which is positive for &lt;em&gt;S. pyogenes&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the correct procedure for doing skin infection diagnostics for group A streptococci?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="107" LastEditDate="2014-03-06T14:51:34.127" LastActivityDate="2014-03-06T14:51:34.127" Title="S. pyogenes' skin infection diagnostics" Tags="&lt;microbiology&gt;&lt;skin&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15536" PostTypeId="2" ParentId="15519" CreationDate="2014-03-06T10:52:30.527" Score="2" Body="&lt;p&gt;Since the question is about risk specific to e-cigarette as opposed to classic cigarettes, what's left is the potential harm from the chemicals in refill-fluids (apart from nicotine): polyethylene glycol, glycerol, alcohol, linalol, flavours. You can find cytotoxicity experiments (e.g. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0890623812002833&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0890623812002833&lt;/a&gt;), that show that the most harmful components may be the flavouring compounds. Some other articles (I can't find a reference right now) point out that the moderate heating of the fluid might create harmful byproducts, differently from those in regular cigarette: acroleine, formaldehyde. The use of e-cigarette is probably too recent to have long-term studies that answer your question.&lt;/p&gt;&#xA;" OwnerUserId="3394" LastActivityDate="2014-03-06T10:52:30.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15537" PostTypeId="2" ParentId="15477" CreationDate="2014-03-06T11:51:43.107" Score="4" Body="&lt;p&gt;Ignoring for the moment the question of politics, let's consider the various definitions of the term &quot;invasive species&quot; that are in use. Colautti and MacIsaac write in their discussion of invasive species terminology (&lt;a href=&quot;http://www.esf.edu/efb/parry/502_reading/colautti2004.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The greatest confusion [among the discussed ecological terms]&#xA;  surrounds the common term ‘invasive’ and its various derivatives&#xA;  (Richardson et al., 2000a). Explicit or implicit definitions for&#xA;  ‘invasive’ include: (1) a synonym for ‘nonindigenous’ (e.g. Goodwin et&#xA;  al., 1999; Radford &amp;amp;Cousens, 2000); (2) an adjective for native or&#xA;  nonindigenous species (NIS) that have colonized natural areas (e.g.&#xA;  Burke &amp;amp; Grime, 1996); (3) discrimination of NIS established in&#xA;  cultivated habitats (as ‘noninvasive’) from those established in&#xA;  natural habitats (e.g. Reichard &amp;amp; Hamilton, 1997); (4) NIS that are&#xA;  widespread (e.g. van Clef &amp;amp; Stiles, 2001); or (5) widespread NIS that&#xA;  have adverse effects on the invaded habitat (e.g. Davis &amp;amp; Thompson,&#xA;  2000; Mack et al., 2000).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Note that except for #2, all the definitions require that the species is a nonindigenous (non-native) species in the area under consideration. Therefore, while humans may be considered to have been an invasive species for much of our species history, under most definitions of the term &lt;strong&gt;we no longer qualify because&lt;/strong&gt; except in a few places (mainly the arctic, antarctic and marine environments, where human presence is minimal) &lt;strong&gt;we are now a native species.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also &lt;a href=&quot;http://www.smithsonianmag.com/science-nature/are-humans-an-invasive-species-42999965/?no-ist&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.smithsonianmag.com/science-nature/are-humans-an-invasive-species-42999965/?no-ist&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-03-06T11:51:43.107" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15538" PostTypeId="2" ParentId="15535" CreationDate="2014-03-06T13:51:25.137" Score="3" Body="&lt;p&gt;&lt;em&gt;S. pyogenes&lt;/em&gt; cultured on Blood Agar should show beta-hemolysis. B-hemolytic colonies can be further identified as &lt;em&gt;S. pyogenes&lt;/em&gt; by the results of negative catalase (hydrogen peroxide) test, positive L-pyrrolidonyl arylamidase (PYR) reaction (&lt;a href=&quot;http://www.cdc.gov/ncidod/biotech/strep/strep-doc/section1.htm#25&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;) and sensitivity to Bacitracin (&lt;a href=&quot;http://www.cdc.gov/ncidod/biotech/strep/strep-doc/section1.htm#5&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;). See &lt;a href=&quot;https://www.inkling.com/read/medical-microbiology-murray-rosenthal-pfaller-7th/chapter-19/streptococcus-pyogenes&quot; rel=&quot;nofollow&quot;&gt;https://www.inkling.com/read/medical-microbiology-murray-rosenthal-pfaller-7th/chapter-19/streptococcus-pyogenes&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PCR may also be used: &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0923250805000215&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0923250805000215&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-03-06T13:51:25.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15539" PostTypeId="2" ParentId="15529" CreationDate="2014-03-06T14:09:48.230" Score="3" Body="&lt;p&gt;Try Wolfram|Alpha at www.wolframalpha.com.  On the home page is &lt;code&gt;Examples&lt;/code&gt;.   Click it.  One of the boxes on the next screen is &lt;code&gt;Life Sciences&lt;/code&gt;. Within that box is a choice of &lt;code&gt;Human genome&lt;/code&gt;. Click on that. You will then see examples of searches.  Those include sections of the human genome and even sequences for specific genes.   Choose an existing one or modify.  Then submit the query clicking on the &lt;code&gt;=&lt;/code&gt; at the right hand side of the (sample) query.  When you get a result from such a search, mouse over the ATGC sequence and you will see a menu appear. The icon &quot;A&quot; allows you to copy the plaintext.  That should quickly give you sample sequences for further processing.&lt;/p&gt;&#xA;" OwnerUserId="5922" LastEditorUserId="5922" LastEditDate="2014-03-06T14:22:16.973" LastActivityDate="2014-03-06T14:22:16.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15540" PostTypeId="1" AcceptedAnswerId="20306" CreationDate="2014-03-06T14:17:30.780" Score="11" ViewCount="2104" Body="&lt;p&gt;Are any invertebrate nephridia (proto/meta) homologous with vertebrate kidneys in the sense that embryologically they also begin together with the genital system?  When did the embryologic association between reproduction and osmoregulartion/metabolite elimination begin in terms of evolution?&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="107" LastEditDate="2014-03-06T14:49:51.527" LastActivityDate="2014-08-07T13:43:54.960" Title="Beginning of the urogenital system" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;development&gt;&lt;kidney&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15541" PostTypeId="2" ParentId="15529" CreationDate="2014-03-06T15:23:01.193" Score="2" Body="&lt;p&gt;Since you don't seem to care what sequence you have as long as it is a real sequence, here's the (one of them anyway) &lt;a href=&quot;https://en.wikipedia.org/wiki/Messenger_RNA&quot; rel=&quot;nofollow&quot;&gt;mRNA&lt;/a&gt; sequence of the human tumor suppressor &lt;a href=&quot;https://en.wikipedia.org/wiki/P53&quot; rel=&quot;nofollow&quot;&gt;TP53&lt;/a&gt;, perhaps the most studied gene in the world:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/371502115?report=fasta&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/nuccore/371502115?report=fasta&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you prefer genomic sequences as opposed to mRNA:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/383209646?report=fasta&amp;amp;from=5001&amp;amp;to=24149&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/nuccore/383209646?report=fasta&amp;amp;from=5001&amp;amp;to=24149&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if you are looking for a larger sample size, here's the entire sequence of the human 22nd chromosome (careful, largish file, ~30MB)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/568801965?report=fasta&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/nuccore/568801965?report=fasta&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, if you want a &lt;em&gt;lot&lt;/em&gt; of sequence, you can download the entire human genome from here (careful: 905MB):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz&quot; rel=&quot;nofollow&quot;&gt;ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-03-06T15:23:01.193" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15542" PostTypeId="2" ParentId="15448" CreationDate="2014-03-06T15:56:15.507" Score="1" Body="&lt;p&gt;This is possible and is an important topic in bioinformatics. Lots of tools have been written and papers have been published, most important&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A random sequence usually &quot;encodes&quot; only very short protein sequences before the &quot;stop&quot; codon (three nucleotide combination marking the end of the protein) is met just by chance. Coding sequence encodes a reasonably long protein.&lt;/li&gt;&#xA;&lt;li&gt;Same amino acid can usually be encoded by multiple alternative sequences of three nucleotides (codons). In a real coding sequence they are not equally probable, some codons are preferred over others (which ones, is organism-specific).&lt;/li&gt;&#xA;&lt;li&gt;It is possible to find characteristic nucleotide patterns inside or in some cases near the coding sequence. Dropping the coding sequence alone into genome would only result in a non-functional pseudogene.&lt;/li&gt;&#xA;&lt;li&gt;Most often, encoded protein sequence is more or less similar to the sequence of some already known protein.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;.. and so on. Try &lt;a href=&quot;http://genes.mit.edu/GENSCAN.html&quot; rel=&quot;nofollow&quot;&gt;GenScan&lt;/a&gt;, for instance.&lt;/p&gt;&#xA;" OwnerUserId="5924" LastActivityDate="2014-03-06T15:56:15.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15543" PostTypeId="2" ParentId="15522" CreationDate="2014-03-06T16:44:29.523" Score="3" Body="&lt;p&gt;A database that answers the question, charting telomere repeat sequences for all known species, is: &lt;a href=&quot;http://telomerase.asu.edu/sequences_telomere.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://telomerase.asu.edu/sequences_telomere.html&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example in Yeast:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xI581.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5005" LastActivityDate="2014-03-06T16:44:29.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15544" PostTypeId="1" AcceptedAnswerId="15545" CreationDate="2014-03-06T20:00:38.083" Score="5" ViewCount="19095" Body="&lt;p&gt;Why do cells vary in shape and function when they have the same genome and the same organelles. For example: why do all cells have nuclei but red blood cell's don't; why can't the cells of a eye perform the function of the tongue; and the list goes on and on. If you say it is because of gene regulation, so then how does the RNA know to transcribe the specific genes that are necessary to that particular cell?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="1320" LastEditDate="2014-03-06T21:51:26.120" LastActivityDate="2017-01-26T19:50:51.843" Title="Why do cells vary in shape and function when they have the same genome and the same organelles?" Tags="&lt;genomes&gt;&lt;cell&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15545" PostTypeId="2" ParentId="15544" CreationDate="2014-03-06T20:28:00.450" Score="11" Body="&lt;p&gt;Because cells are not only characterized by by their genetic material and other interior components, but also by the genes they express. Cells have to fulfill multiple different functions to be able to build complex multicellular organisms. Differently expressed genes lead to different proteins made in the cell, which leads to different morphology, shape or function. For example melanocytes in the skin are highly specialized cells which mostly make the pigment melanin. Plasma cells on the other are highly specialised for making antibodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is all about regulation of genes. The RNA doesn't know or transcribe anything - &#xA;the DNA is trancribed into the mRNA (which is then further processed) and finally translated into proteins. Cells develop from precursors which proliferate and finally differentiate into highly specific cells. This progress is controlled and activated by specific transcription factors and growth factors. For example: pigment cells only develop, when a specific transcription factor is present. When this factor cannot be expressed, these cells do not develop at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This developmental process is shown schematically in the figure below (the figure is from the NIH website on &lt;a href=&quot;http://stemcells.nih.gov/info/scireport/pages/chapter1.aspx&quot;&gt;stem cells)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/H8qB9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2014-03-06T21:53:30.930" LastActivityDate="2014-03-06T21:53:30.930" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15546" PostTypeId="1" AcceptedAnswerId="15547" CreationDate="2014-03-06T22:13:43.447" Score="4" ViewCount="463" Body="&lt;p&gt;So, I saw a video on YouTube that says the banana we eat today is not what a banana looked like years ago. Since the banana has been genetically modified over the years, does that qualify as evolution?&lt;/p&gt;&#xA;" OwnerUserId="5926" LastActivityDate="2014-03-12T19:21:55.917" Title="Evolution in fruits" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15547" PostTypeId="2" ParentId="15546" CreationDate="2014-03-06T22:25:51.563" Score="5" Body="&lt;p&gt;Yes. Modern domesticated bananas have evolved from ancestral wild species under the influence of humans. Quoting D'Hont et al.: (&lt;a href=&quot;http://www.nature.com/nature/journal/v488/n7410/full/nature11241.html&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The [banana] domestication process started some 7,000 years ago in&#xA;  Southeast Asia. It involved hybridizations between diverse species and&#xA;  subspecies, fostered by human migrations, and selection of diploid and&#xA;  triploid seedless, parthenocarpic hybrids thereafter widely dispersed&#xA;  by vegetative propagation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Modern bananas have undergone extensive evolution from the original wild species. The selection pressure has in part been provided by humans, who have selected the most nutritious/tasty/desirable examplars and facilitated their reproduction. This can be considered &quot;artificial selection&quot; as opposed to &quot;natural selection&quot;, but does not change the fact that an evolutionary process has taken place. The UC Berkeley website &quot;Understanding Evolution&quot; gives the following definition of &quot;artificial selection&quot;.(&lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evo_30&quot; rel=&quot;noreferrer&quot;&gt;2&lt;/a&gt;) &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A process in which humans consciously select for or against particular&#xA;  features in organisms. For example, the human may allow only organisms&#xA;  with the desired feature to reproduce or may provide more resources to&#xA;  the organisms with the desired feature. This process causes&#xA;  evolutionary change in the organism and is analogous to natural&#xA;  selection, only with humans, not nature, doing the selecting.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thus, whether the selection is considered &quot;natural&quot; or &quot;artificial&quot;, the end result is evolution.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-03-12T16:06:57.693" LastActivityDate="2014-03-12T16:06:57.693" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15548" PostTypeId="1" CreationDate="2014-03-06T23:55:02.257" Score="5" ViewCount="27776" Body="&lt;p&gt;I haven't seen any gel lanes in neither my PCR samples nor the marker itself when photographing them.  This is not my first time performing 1.2% agarose gel electrophoresis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see gel lanes when I take the gel out the apparatus, but when I go to photograph them:  nothing shows up.  I only let the samples &quot;run&quot; for 30-40 minutes (when I ran for an hour, the bands almost ran off the gel).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tried using different markers:  no luck.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Re-added some more EtBr to better stain the gel:  no luck. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am also keeping the lights off in the dark room, so I do not think I am exposing the film to light early on (errors still a possibility though). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What could I be doing wrong?  Am I taking the film out too early?&lt;/p&gt;&#xA;" OwnerUserId="5927" LastActivityDate="2017-11-01T03:03:59.107" Title="No bands show up in gel electrophoresis, not even marker" Tags="&lt;pcr&gt;&lt;gel-electrophoresis&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15549" PostTypeId="1" CreationDate="2014-03-07T00:07:43.103" Score="0" ViewCount="68" Body="&lt;p&gt;I was fortunate enough to get a position as a researcher for the Mayo Clinic's SURF Program this year.  My PI's lab focus is on the the immune system's role in CNS axonal and neuronal injury, specifically through the lens of how innate and adaptive immune effectors interact w/ infected neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although I do research under a professor at my college and I volunteered for a state university lab during the previous summer, this is my first REU/SURF opportunity, and I REALLY want to make a good impression.  Here are my questions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the do's and don't's in terms of being a skilled and efficient researcher?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since I am still an undergrad, I know that I will be a less useful asset to the lab than a grad student or post-doc, but what can I do as an undergrad to not burden my colleagues and PI?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you all for your help!  Wishing you all the very best! &lt;/p&gt;&#xA;" OwnerUserId="5927" LastActivityDate="2014-03-07T02:16:16.783" Title="Do's and Don't's of Undergraduate Research?" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-03-07T10:01:47.483" ContentLicense="CC BY-SA 3.0" />
  <row Id="15550" PostTypeId="2" ParentId="15548" CreationDate="2014-03-07T00:22:45.237" Score="6" Body="&lt;p&gt;What I can quickly think of is that you were running the gel incorrectly: instead of from - to + direction,  You ran it the other way around and your DNA went out of the gel. Another thing might be that the UV light was not turned on or is broken.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2014-03-07T00:22:45.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15551" PostTypeId="2" ParentId="15493" CreationDate="2014-03-07T00:26:30.957" Score="1" Body="&lt;p&gt;The idea of tumour heterogeneity has been around for a long time (look at the below review and the refs therein), but the underlying causes have been revised in the light of theoretical advances and the novel (Gerlinger et al.) genetic data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly genetic heterogeneity was largely believed to be the cause of genetic instability (an increased mutation rate), and hence being attributed to drift rather than multiple fitness peaks (i.e. selection).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly there was no evidence to determine if the observed phenotypic heterogeneity (from histology slides) could be attributed to genetic changes, or if it was the cause of phenotypic plasticity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://drive.google.com/file/d/0By7yvhGUfC-peXh1Y0o3aWZUSGc/edit?usp=sharing&quot; rel=&quot;nofollow&quot;&gt;Alexandrova, Tumour Heterogeneity, Exp. Pathol. Parasitol (2001).&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5929" LastActivityDate="2014-03-07T00:26:30.957" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15552" PostTypeId="2" ParentId="15549" CreationDate="2014-03-07T02:16:16.783" Score="1" Body="&lt;p&gt;Ask plenty of questions and &lt;strong&gt;write everything down&lt;/strong&gt;. If you do not write notes when someone is explaining something to you, it will be embarrassing to go back and ask them a second time to explain it again. Before you get to the lab I would locate/Ask for review articles related to the project. Realize that you will likely shadowing a senior person while you are there, adapt to their schedule. Don't spend your incubation times face booking. Use this time to build relationships with others in the lab and on your floor and try to absorb as much information about the way the world of science works. Speaking from personal experience the small things you learn there may be insignificant but may come to be important to you in the future. If you have your own project, realize that it will probably be a small one attached to a bigger project another lab member is working on. Thats a good thing, because your time there is not long enough to get into something complicated. A simple, clear, and focused question will be key to your success. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you should take away from the experience is not necessarily something that will amount to publication, but the actually experience in the actual process of designing experiments, performing them, and analyzing data. Assuming you are doing this to help prepare you to go on to work on a graduate degree in your favorite area of biology then remember that this is here to help you get to the next level. Programs like this allow you to demonstrate that you understand what it takes to perform graduate-level work, and potentially become a successful scientist one day. &lt;/p&gt;&#xA;" OwnerUserId="5284" LastActivityDate="2014-03-07T02:16:16.783" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15553" PostTypeId="1" AcceptedAnswerId="15647" CreationDate="2014-03-07T04:53:26.343" Score="5" ViewCount="2141" Body="&lt;p&gt;What is the evolutionary purpose of the topology of human ears? I understand why the ears may have a funnel-like shape but if the various &quot;hills and valleys&quot; do not amplify incoming sound, what purpose do they have?&lt;/p&gt;&#xA;" OwnerUserId="5930" LastEditorUserId="5930" LastEditDate="2014-03-13T23:09:20.493" LastActivityDate="2016-10-24T20:30:04.440" Title="What is the evolutionary purpose of the topology of the human ear?" Tags="&lt;evolution&gt;&lt;human-anatomy&gt;&lt;hearing&gt;&lt;human-ear&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15554" PostTypeId="1" CreationDate="2014-03-07T05:05:48.793" Score="0" ViewCount="994" Body="&lt;p&gt;in the connective tissue (Bones) we have 3 types  osteoblast, osteocoel,osteocyst what are they and why they differ.&lt;/p&gt;&#xA;" OwnerUserId="5700" LastActivityDate="2014-03-07T05:30:33.497" Title="what these suffixes mean,-coel,-blast,-cyst?" Tags="&lt;histology&gt;&lt;bone-biology&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2014-03-07T12:57:56.877" ContentLicense="CC BY-SA 3.0" />
  <row Id="15555" PostTypeId="1" AcceptedAnswerId="15559" CreationDate="2014-03-07T05:22:15.233" Score="15" ViewCount="2269" Body="&lt;p&gt;So obviously, viruses are nonliving. But when my teacher was teaching viruses in the video (we're doing &quot;flip&quot; learning this semester), the way he described it, it seemed like the viruses responded to their environment in that they moved around until they found a cell of the right type, and then they latched on and hijacked it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I had always thought of it more like that they were just kind of floating around, carried by the host system (blood in animals for example), until they &quot;bumped into&quot; the right kind of cells and both sets of membrane proteins &quot;docked&quot;. But my theory/idea doesn't really make sense because it doesn't account for how viruses would be able to infect bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, the idea that viruses propel themselves doesn't make much sense either, because viruses are nonliving, and one of the characteristics of life that they do not meet is that living things acquire and use energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary my question is, how are viruses propelled? Do they move themselves, or are they moved by external forces?&lt;/p&gt;&#xA;" OwnerUserId="5466" LastEditorUserId="3553" LastEditDate="2016-11-15T07:37:26.373" LastActivityDate="2021-02-25T08:28:31.657" Title="Are viruses self-propelled?" Tags="&lt;microbiology&gt;&lt;virus&gt;&lt;virology&gt;&lt;life&gt;&lt;locomotion&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15556" PostTypeId="2" ParentId="15554" CreationDate="2014-03-07T05:30:33.497" Score="2" Body="&lt;p&gt;You can easily search this on the web. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Osteoblasts are the immature cells of bone which are responsible for the production and mineralization of bone matrix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Osteocytes are the mature cells of bone found in open spaces in bone called lacunae. The functions of osteocytes includes maintenance of bone and  calcium homeostasis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Osteoclasts are responsible for removal of bone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source : Tortora and Derrickson&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-07T05:30:33.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15557" PostTypeId="1" AcceptedAnswerId="15598" CreationDate="2014-03-07T05:44:41.910" Score="1" ViewCount="2462" Body="&lt;p&gt;Let's do some exercise(duh!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ok so lie on the bed. Lift your left leg. Put it down. Lift your right leg.Put it down. Easy?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now lift your left leg and without putting it down, lift your right leg. Easy ? No.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now try to lift both the legs together. Easy ? No.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question : What is the anatomical reason ( arrangement of muscles around the bones etc.) which makes it difficult ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-09T15:50:34.803" Title="Raising two legs together while lying on bed" Tags="&lt;human-biology&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15559" PostTypeId="2" ParentId="15555" CreationDate="2014-03-07T06:13:44.223" Score="14" Body="&lt;p&gt;All of your reasoning is correct - viruses are &lt;strong&gt;not&lt;/strong&gt; motile (i.e. not self-propelled). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't understand why you think this would cause a difficulty in the case of bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit in response to comment @Remi.b&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some cursory research on estimating probabilities of collisions between particles engaged in random walks has revealed some very challenging maths. So I decided to simply look at some data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remarkably there is a fairly recent paper describing investigations of the kinetics of bacteriophage adsorption.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1914437/pdf/303.pdf&quot; rel=&quot;noreferrer&quot;&gt;Moldovan, et al. (2007) On Kinetics of Phage Adsorption. Biophysical Journal 93:303–315&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I didn't realise it was still possible to publish papers like this, but in fact it is very interesting. For our current purposes we only need to consider the data presented in Figure 3, which show that when &lt;em&gt;E. coli&lt;/em&gt; cells at a density of 10&lt;sup&gt;8&lt;/sup&gt; cells ml&lt;sup&gt;-1&lt;/sup&gt; are mixed with bacteriophage &amp;lambda; at a density of 5 x 10&lt;sup&gt;4&lt;/sup&gt; particles ml&lt;sup&gt;-1&lt;/sup&gt;, then 90% of the phage have attached to a bacterial cell within less than 10 min.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just to relate this to a real life situation, it is estimated that sea water contains bacteria at a density of 10&lt;sup&gt;6&lt;/sup&gt; cells ml&lt;sup&gt;-1&lt;/sup&gt; and phage at 5 x 10&lt;sup&gt;7&lt;/sup&gt; particles ml&lt;sup&gt;-1&lt;/sup&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-03-07T18:17:38.933" LastActivityDate="2014-03-07T18:17:38.933" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15562" PostTypeId="2" ParentId="15555" CreationDate="2014-03-07T07:30:05.070" Score="5" Body="&lt;p&gt;You are right, viruses are neither alive, nor are they moving by themselves. They are moved by passive movements (e.g. the bloodstream or movements of the air) until they meet their target cells. This can be either a cell in the human body (for flu viruses these are cells of the respiratory tract for example) or bacteria (for bacteriophages). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For bacteria both can happen, viruses floating around meet a bacteria they can infect or the other way that moving bacteria meet the virus.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="-1" LastEditDate="2017-08-30T19:39:21.057" LastActivityDate="2017-08-30T19:39:21.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15563" PostTypeId="1" CreationDate="2014-03-07T09:41:25.507" Score="0" ViewCount="119" Body="&lt;p&gt;I need the genetic regulatory network of TAG synthesis (Kennedy pathway) of Jatropha plant??&#xA;Or is there any way to convert metabolic pathway into genetic regulatory network?&lt;/p&gt;&#xA;" OwnerUserId="5933" LastEditorUserId="3632" LastEditDate="2014-03-07T12:50:57.283" LastActivityDate="2014-03-10T01:13:21.817" Title="Systems Biology of triacylglycerol (TAG) synthesis in Jatropha" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;&lt;biotechnology&gt;&lt;systems-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15566" PostTypeId="2" ParentId="15563" CreationDate="2014-03-07T12:49:39.417" Score="1" Body="&lt;p&gt;Triacylglycerol synthesis in plants is probably highly conserved.  The metabolic pathway is &lt;a href=&quot;http://www.wikipathways.org/index.php/Pathway%3aWP627&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://dnaresearch.oxfordjournals.org/content/early/2010/12/08/dnares.dsq030.full&quot; rel=&quot;nofollow&quot;&gt;Jatropha genome sequence&lt;/a&gt; is also available. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given this some effort has been made to figure out how these genes are regulated.  This is a &lt;a href=&quot;http://www.researchgate.net/publication/228476071_Expression_profiles_of_genes_involved_in_fatty_acid_and_triacylglycerol_synthesis_in_developing_seeds_of_Jatropha_%28Jatropha_curcas_L.%29&quot; rel=&quot;nofollow&quot;&gt;microarray study&lt;/a&gt; of Jatropha focusing on fatty acid and TAG biosynthesis.   This gives some idea of how TAG genes respond to one another, but of course will not find the promoter sequences or the transcription factors themselves. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having spent a summer going over fatty acid synthesis, I can only say that there has been a lot of wet lab work done on these pathways which would probably be conserved in the Jatropha plant.  The literature would be quite extensive.  Integrating all of that is more like a paper for publication than an answer on stackexchange.  This sort of outlines the procedure... do you have a more focused question? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll outline one way of approaching this - there are an uncountable number of variants if you tweak it.  There are other ways to get this, most notably looking for defective mutants, the method which is still used in plants quite a bit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway here is a genome based approach:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) &lt;strong&gt;Identify genes in the pathway of interest.&lt;/strong&gt; choose 10 or so genes that you think constitute your network.  This is an editorial decision. Ultimately if you start looking at genes regulated by the same transcription factors as being included in your network, you will eventually take in the entire genome and the work will be impossible to accomplish. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) &lt;strong&gt;find candidate promotor binding sites&lt;/strong&gt;. look at the &lt;a href=&quot;https://en.wikipedia.org/wiki/Promoter_%28genetics%29#Eukaryotic_promoters&quot; rel=&quot;nofollow&quot;&gt;upstream promotor regions&lt;/a&gt; for all these genes.  you can look at how these are conserved between similar plants by examining the same gene promotor regions aligned against each other.  This doesn't work very well.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2b) Another way of finding these is to do a &lt;strong&gt;pull down experiment&lt;/strong&gt; where transcription factors are bound to DNA and a DNAse digestion is done and remaining fragments identify the binding sites.  All this somewhat assumes that you kind of know which transcription factors are responsible for each gene. That is probably not the case here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) find the transcription factors important for the plant pathway.  this is not easy - one way is to try knock outs of the TF genes.  I imagine this plant has 4000 + of these genes.  around 1-2% may be involved.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far these methods have been use for the ENCODE project as well as some bacterial genomes.  a plant is a new scenario which will have issues of its own. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-03-10T01:13:21.817" LastActivityDate="2014-03-10T01:13:21.817" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15567" PostTypeId="1" AcceptedAnswerId="15570" CreationDate="2014-03-07T14:29:15.857" Score="29" ViewCount="28824" Body="&lt;p&gt;Can a human eat grass and digest it?&#xA;Could it be possible to use it as food just like other plants such as wheat or beans?&lt;/p&gt;&#xA;" OwnerUserId="5925" LastEditorUserId="-1" LastEditDate="2014-03-07T18:58:22.267" LastActivityDate="2015-05-12T17:14:32.013" Title="Can humans eat grass?" Tags="&lt;human-biology&gt;&lt;food&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="15568" PostTypeId="1" CreationDate="2014-03-07T14:35:41.210" Score="6" ViewCount="370" Body="&lt;p&gt;Clearly, creatures such as us humans, after vastly increasing the entropy of our food, expel most of the mass that we consume. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some creatures, however, do NOT get the opportunity to eat nearly as often, even though these creatures are if anything more competitive (and perhaps cannibalistic!) than we are - snakes come to mind here, as do spiders.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such a lifestyle implies that growing large - or at least to adult form - quickly has a huge advantage evolutionary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the awkward question that arises is thus: do such animals have a higher &quot;absorption rate&quot;, if you will, then humans and other frequent feeders?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, do such animals maximize their diet by incorporating more of the mass of their food and expelling less of it, or is there some physics/chemistry which makes this difficult?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="5936" LastEditorUserId="5936" LastEditDate="2014-03-07T14:43:07.880" LastActivityDate="2014-07-19T21:31:24.940" Title="Absorption rate of Infrequently eating animals?" Tags="&lt;digestive-system&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15569" PostTypeId="2" ParentId="15567" CreationDate="2014-03-07T14:42:07.690" Score="8" Body="&lt;p&gt;Well, humans can eat grass, but it will not be digested. Cause to digest grass our body needs different kind of enzymes, which lack in humans so they can't digest grass directly although humans can eat grass, but not recommended.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly our body has different enzymes to digest wheat and beans etc. Also remember rice, wheat and beans are fruit, not plant. Although we can digest some of the plant.&lt;/p&gt;&#xA;" OwnerUserId="5937" LastEditorUserId="5925" LastEditDate="2014-03-07T14:46:46.467" LastActivityDate="2014-03-07T14:46:46.467" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15570" PostTypeId="2" ParentId="15567" CreationDate="2014-03-07T14:52:41.397" Score="31" Body="&lt;p&gt;To elaborate on A random zoologist's answer, the problem is that the human digestive system does not contain any cellulase enzymes. &lt;a href=&quot;http://en.wikipedia.org/wiki/Cellulase&quot;&gt;Cellulases&lt;/a&gt; are a class of enzymes that break down cellulose, the chief structural component of plants.  You might be able to obtain a small amount of nutrition from grass or other cellulose-rich materials, but as the plant cell walls are made of cellulose, most of the plant material will be indigestible.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="260" LastEditDate="2014-03-08T16:39:57.920" LastActivityDate="2014-03-08T16:39:57.920" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="15571" PostTypeId="1" AcceptedAnswerId="15572" CreationDate="2014-03-07T15:19:07.980" Score="2" ViewCount="4977" Body="&lt;p&gt;Human urine is sterile as long as it is in the human body. But is it dirty after leaving the human body? Could you get sick from it, if you drink it or don't wash your hands, for example?&lt;/p&gt;&#xA;" OwnerUserId="5925" LastActivityDate="2014-03-07T16:00:03.757" Title="Is urine dirty as soon as it leaves the human body?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15572" PostTypeId="2" ParentId="15571" CreationDate="2014-03-07T15:54:23.597" Score="6" Body="&lt;p&gt;It was believed for a long time that urine stored in the urinary bladder is sterile. However, Wolfe et al(&lt;a href=&quot;http://jcm.asm.org/content/50/4/1376.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;). recently found evidence of bacterial presence in the urine extracted from bladders of healthy women. In an article just published, Hilt et al. found that at least some bacteria found in the bladder of healthy women are viable and can be grown in a laboratory after extraction from the bladder).&lt;a href=&quot;http://jcm.asm.org/content/52/3/871.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt; (Paywall). They expect that the same is the case for men.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the Hilt et al. paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Thirty-five different genera and 85 different species were identified&#xA;  by EQUC. The most prevalent genera isolated were Lactobacillus (15%),&#xA;  followed by Corynebacterium (14.2%), Streptococcus (11.9%),&#xA;  Actinomyces (6.9%), and Staphylococcus (6.9%). Other genera commonly&#xA;  isolated include Aerococcus, Gardnerella, Bifidobacterium, and&#xA;  Actinobaculum.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Note that these species for the most part (Actinobaculum being one exception, as a possible uropathogen) appear to be part of the normal microbiome (collection of microorganisms) in healthy people in the same way as bacteria inhabit other parts of healthy persons. Additionally, the recovered organisms required special care to achieve growth:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Most of the bacteria isolated required either increased CO2 or&#xA;  anaerobic conditions for growth, along with prolonged incubation, and&#xA;  they often were present in numbers below the threshold of detection&#xA;  used in routine diagnostic urine culture protocols.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thus, fresh urine is non-sterile but probably unlikely to cause infection in healthy persons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the process of leaving the body, there is a chance of contamination from organisms living in the urinary tract or on the surface of the body. However, if organisms picked up from the urinary tract made you sick, I except that you would already be having symptoms of an urinary tract infection, as the stomach is hardly a more forgiving environment. The risk of contamination from the surface of the body would depend on personal hygiene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also this question on &lt;a href=&quot;https://outdoors.stackexchange.com/questions/264/is-drinking-urine-safe&quot;&gt;https://outdoors.stackexchange.com/questions/264/is-drinking-urine-safe&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: This might go without saying, but apart from possible pathogens, there are of course other aspects of urine which makes it unfit for general consumption.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:01.470" LastActivityDate="2014-03-07T16:00:03.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15573" PostTypeId="1" AcceptedAnswerId="15583" CreationDate="2014-03-07T17:50:56.867" Score="2" ViewCount="147" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rO5z0.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a figure summarising the quorum sensing mechanism in &lt;em&gt;Vibrio cholerae&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://www.youtube.com/watch?v=k-CkqIePaqI&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; video by Bonnie Bassler, she explains how quorum sensing can be targeted to control infections.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At 15:09 she explains why cqsA&lt;sup&gt;-&lt;/sup&gt; mutants show more dramatic effect when external CAI1 is added - &lt;em&gt;because we are not fighting against the endogenously produced autoinducer1.&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question : But won't endogenously produced autoinducer help in controlling virulence, as the more the auto inducer lesser the virulence ? Why should we be fighting against endogenously produced autoinducer 1 ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1320" LastEditDate="2014-03-07T18:22:42.233" LastActivityDate="2014-03-08T04:20:56.757" Title="Quorum Sensing in Vibrio cholerae" Tags="&lt;biochemistry&gt;&lt;bacteriology&gt;&lt;mutations&gt;&lt;antibiotics&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="15574" PostTypeId="2" ParentId="1910" CreationDate="2014-03-07T18:24:01.047" Score="15" Body="&lt;p&gt;Yes.  Rob Rhinehart has developed what he refers to as &amp;quot;a food substitute intended to supply all of a human body's daily nutritional needs, made from powdered starch, rice protein, olive oil, and raw chemical powders&amp;quot; which he calls &lt;a href=&quot;https://campaign.soylent.me/soylent-free-your-body&quot; rel=&quot;noreferrer&quot;&gt;Soylent&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;It was developed and tested largely in 2013, crowdfunded late 2013, and is expected to start shipping in 2014. Tests of at least 30 days with no other food intake have been performed, though this is being marketed as a food and not a medical aid of any sort, so does not require FDA testing.&lt;/p&gt;&#xA;&lt;p&gt;Even if this didn't exist, there are numerous &amp;quot;complete&amp;quot; human diet foods meant for medical use.  These are mentioned in &lt;a href=&quot;http://www.washingtonpost.com/blogs/wonkblog/wp/2013/03/14/rob-rhinehart-has-a-crazy-plan-to-let-you-go-without-food-forever-it-just-might-work/&quot; rel=&quot;noreferrer&quot;&gt;an article about soylent&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Jay Mirtallo is a professor of pharmacy at Ohio State and the immediate past president of American Society for Parental Enteral Nutrition, which focuses on the science and practice of providing food to patients through both intravenous injections and feeding tubes. His main concern with Rhinehart's plan is that he's making the concoction himself, rather than buying it from reputable suppliers.&lt;/p&gt;&#xA;&lt;p&gt;&amp;quot;He basically made medical food,&amp;quot; Mirtallo says. &amp;quot;If he wanted to switch to a liquid diet, those are already available.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;Indeed they are. Companies like Abbott Nutrition and NestléHealthScience sell dozens of medical food products, intended to be used by patients under medical supervision and administered intravenously, orally, or through an incision in the stomach.&lt;/p&gt;&#xA;&lt;p&gt;&amp;quot;They’re very complex products, in terms of making sure you get them in a form that’s palatable but that stays in a form that’s bioavailable to the body,&amp;quot; Mirtallo says. &amp;quot;Some of the products are very difficult to get into a liquid form and may lose their potency when they do that, or could interact with other substances that keep them from being absorbed completely.&amp;quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Rob appears to be attempting to make a consumer version, and so far &lt;a href=&quot;http://motherboard.vice.com/blog/soylent-no-food-for-30-days&quot; rel=&quot;noreferrer&quot;&gt;reports are positive&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;But even if you don't trust Rob's mixture, there are countless medically complete nutritional foods that are FDA approved, though not generally available at the supermarket.&lt;/p&gt;&#xA;" OwnerUserId="5940" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-03-07T18:24:01.047" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15576" PostTypeId="1" AcceptedAnswerId="15580" CreationDate="2014-03-07T19:38:46.950" Score="1" ViewCount="11438" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;In a given population under Hardy Weinberg equilibrium, 40.0% of men have hemophilia. What is the probability that a random man and random woman will have a daughter with haemophilia?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think the answer is 16%, but the answer given is 9.6%. According to  Hardy-Weinberg principle, p&lt;sup&gt;2&lt;/sup&gt; + 2pq + q&lt;sup&gt;2&lt;/sup&gt; = 1. In order to inherit the disease, the mother must either be a carrier of have the disease, which occurs with probability 1-q&lt;sup&gt;2&lt;/sup&gt; = 0.72&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, the odds of having a child with the disease is (0.84)(0.4). Since it asks for the probability of a girl, the total must be divided by two, so the answer is 0.168&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where am I wrong?&lt;/p&gt;&#xA;" OwnerUserId="5945" LastEditorUserId="3340" LastEditDate="2015-04-03T08:36:02.510" LastActivityDate="2018-04-05T04:40:03.667" Title="X Linked Hardy Weinberg Equilibrium Problem" Tags="&lt;genetics&gt;&lt;hardy-weinberg&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15577" PostTypeId="1" AcceptedAnswerId="15579" CreationDate="2014-03-07T19:40:58.840" Score="2" ViewCount="223" Body="&lt;p&gt;The wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Gestational_carrier&quot; rel=&quot;nofollow&quot;&gt;surrogacy&lt;/a&gt; highlights two main forms of surrogacy: Traditional Surrogacy and Gestational Surrogacy. Traditional surrogacy inseminates the surrogate mother with sperm, while gestational surrogacy uses in vitro fertilization to form an embryo from egg and sperm, which is then transferred into the surrogate mother. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It does not discuss whether surrogacy is possible after a natural fertilization has already taken place, such as if a woman becomes pregnant and then wishes, for whatever reason, to have a surrogate take the baby to term. Is this biologically possible? If it is possible, what is the mechanism? Also, if possible, is heightened risk a major reason it is not more common?&lt;/p&gt;&#xA;" OwnerUserId="5944" LastActivityDate="2019-01-31T22:35:27.777" Title="Surrogacy Post Fertilization" Tags="&lt;human-biology&gt;&lt;reproduction&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15578" PostTypeId="2" ParentId="15567" CreationDate="2014-03-07T19:43:17.213" Score="7" Body="&lt;p&gt;Even in times of famine, when people are literally dying from hunger, they do not eat grass - it is not digestible. But they eat cooked &lt;a href=&quot;http://en.wikipedia.org/wiki/Atriplex_hortensis&quot; rel=&quot;nofollow&quot;&gt;artiplex&lt;/a&gt;, which commonly grows by roadsides.&lt;/p&gt;&#xA;" OwnerUserId="5946" LastEditorUserId="5958" LastEditDate="2014-03-08T10:20:55.203" LastActivityDate="2014-03-08T10:20:55.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15579" PostTypeId="2" ParentId="15577" CreationDate="2014-03-07T21:08:43.080" Score="4" Body="&lt;p&gt;No, it is not possible. The problem is the fertilization which takes place near the ovary. It takes the new forming blastocyst about 4-5 days to wander through the fallopian tube to reach the uterus and 8-9 days in total to implant itself into the uterine wall. See the picture below (from the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Fertilisation&quot; rel=&quot;nofollow noreferrer&quot;&gt;fertilization&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UjjhO.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You would have to get the blastocyst out of the right fallopian tube, make sure it survives the procedure and then implant it into the uterus of a woman which is about in the same phase of their period (otherwise the uterus is not ready to allow implantation).&#xA;It is already hard enough to do in vitro fertilization where you can control the environment.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2014-03-07T22:08:16.727" LastActivityDate="2014-03-07T22:08:16.727" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15580" PostTypeId="2" ParentId="15576" CreationDate="2014-03-07T21:22:47.457" Score="4" Body="&lt;p&gt;I make it 8%. Here is my reasoning.&lt;/p&gt;&#xA;&lt;p&gt;The gene is X-linked.&lt;/p&gt;&#xA;&lt;p&gt;40% mutant males, so freq(mutant allele) = p = 0.4, and freq(wt allele) = q = 0.6&lt;/p&gt;&#xA;&lt;p&gt;To get a mutant female we have to have a mutant male parent, probability = 0.4&#xA;Of these matings one half will produce a female offspring so 0.4*0.5 = 0.2&lt;/p&gt;&#xA;&lt;p&gt;i.e. 20% of matings derive from a mutant male and produce a female offspring.&lt;/p&gt;&#xA;&lt;p&gt;Now look at the female mate:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;probability(mutant) = p&lt;sup&gt;2&lt;/sup&gt; = 0.16&lt;/p&gt;&#xA;&lt;p&gt;probability(carrier) = 2pq = 0.48&lt;/p&gt;&#xA;&lt;p&gt;probability(wt) = q&lt;sup&gt;2&lt;/sup&gt; = 0.36&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;so our 20% of matings that have the potential to produce a mutant female offspring partition as:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;mating with a mutant female:&lt;/strong&gt; 0.2 x 0.16 = &lt;em&gt;0.032 mutant female offspring&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;mating with a carrier female:&lt;/strong&gt; 0.2 x 0.48 = 0.096 of which:&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;0.048 mutant female offspring&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;0.048 carrier female offspring&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;mating with wt female:&lt;/strong&gt; 0.2 x 0.36 = 0.072 carrier female offspring&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;(sanity check - 0.032 + 0.096 + 0.072 = 0.2)&lt;/p&gt;&#xA;&lt;p&gt;Thus the probability of random mating producing a mutant female is 0.032 + 0.048 = 0.08 (8%)&lt;/p&gt;&#xA;&lt;p&gt;Incidentally there is another way of thinking about this. Note that the H-W frequency of mutant females in the population is 16%. One of the assumptions of H-W is random mating. So the probability of a random mating producing a mutant female = p(female) * p(mutant if female) = 0.5 x 0.16 = 0.08&lt;/p&gt;&#xA;&lt;p&gt;So - where have I gone wrong?&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-03-08T23:41:29.667" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15581" PostTypeId="2" ParentId="15567" CreationDate="2014-03-07T23:12:36.153" Score="14" Body="&lt;p&gt;Wheat and other grasses are very significant sources for human nutrition.  Grass seeds are digestible; seeds have to digest themselves to sprout, with very little biochemical machinery.  Human civilization is founded on the ability to cultivate grass to eat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is due to pepsin that a cellulase supplement would not help to digest grass stems and leaves.  Pepsin is the enzyme in the stomach that breaks peptide bonds and from its perspective, cellulase is just another peptide chain (pepsin is so effective, the stomach has to prevent itself from being digested while at the same time maintaining enough pepsin to digest food — because pepsin digests pepsin).  Cellulose is a tough sugar polymer (as is chitin, which forms insect and fungus exoskeletons), so after all the cellulase was digested by pepsin only bacteria from the intestine could process the remaining cellulose.  What the bacteria convert it to might make one ill.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans &lt;em&gt;can&lt;/em&gt; derive significant nutrition from bamboo shoots, which have less robust cellulose than in mature plants, and bamboo is a grass.  Pandas also cannot digest cellulose effectively, but that doesn't stop them from trying.  They might eventually develop a cellulase gene by sheer willpower and tenacity.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;@jarlemag: inhaling sugar water could quickly become a &lt;em&gt;very bad idea&lt;/em&gt;.  Encouraging microbes to colonize near the brain may result in them converting neurons into more microbes.  The &lt;em&gt;Naegleria&lt;/em&gt; amoebae can be very aggressive.  In Pakistan and India it is somehow traditional to treat illness by putting water up one's nose; when it is not recognized how clean the water must be to do that safely, people die.&lt;/p&gt;&#xA;" OwnerUserId="5951" LastActivityDate="2014-03-07T23:12:36.153" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15582" PostTypeId="1" AcceptedAnswerId="15584" CreationDate="2014-03-08T02:03:18.433" Score="8" ViewCount="3116" Body="&lt;p&gt;Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an activator binding site and a promoter - would placing the binding site closer to the promoter lead to significantly stronger activation, or more robust system behavior? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In some genomics-related models I saw authors assigned weights to binding sites based on position (orientation and distance from the promoter); the general idea was that binding sites farther away could have a weaker influence on transcription. This can be modeled e.g. by decreasing the binding affinity. But that was genomics, and I'm unsure how much of that has any relevance in smaller scale plasmid constructs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, suppose we have a highly specific binding site (e.g. a TALE binding site) upstream of the promoter:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/t1zVC.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Fig.1, the binding site &lt;em&gt;A&lt;/em&gt; is only e.g. 40 bp away from the promoter. In Fig.2, it is e.g. 5000-7000 bp away. Should I expect this to make a noticeable difference? Would the same apply if it would be a constitutive promoter, with a repressor instead of an activator? What about more complex networks, could the answer change?&lt;/p&gt;&#xA;" OwnerUserId="3583" LastEditorUserId="3583" LastEditDate="2014-03-16T00:27:23.193" LastActivityDate="2014-03-16T00:27:23.193" Title="How much does the distance between a transcription factor binding site and a promoter influence transcription?" Tags="&lt;molecular-biology&gt;&lt;gene-expression&gt;&lt;mathematical-models&gt;&lt;transcription&gt;&lt;binding-sites&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15583" PostTypeId="2" ParentId="15573" CreationDate="2014-03-08T04:20:56.757" Score="3" Body="&lt;p&gt;First of all I find quorum sensing to be generally facinating, so I'm happy to see the topic brought up here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dr. Bassler has many papers on the subject, but I think one of the most relevant ones to this question is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077805/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding your question, you have the right idea, but you're missing the point of her comment.  The Western shows a more dramatic difference in cqsA- bacteria because they are not inhibiting themseleves (as you suggested).  Thus the lower concentrations have much higher levels of the toxin produced because the only CAI-1 being provided is the synthetic one.  This makes the ramp up in administered CAI-1 seem more drastic because you start at a higher level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope that makes since, if I can find an open writes version of the Western, I'll come back and give further analysis on it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding @AlanBoyd 's comments, V. cholerae is different because it seeks to create an acute infection, not a persistent one.  &lt;a href=&quot;https://en.wikipedia.org/wiki/Cholera_toxin&quot; rel=&quot;nofollow&quot;&gt;Cholera toxin&lt;/a&gt; is what causes the majority of diarrhea and virulence from cholera.  V. cholera produces the toxin until it's inhibited by ether auto-inducer (which should be after the pt already has massive diarrhea), then it switches to produce enzymes which detach it from the gut.  The pt still has diarrhea at this point, cholera just doesn't need to make any more toxin for it to continue.  To do so would probably waste energy, and not help the bacteria make it back to a water supply.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2014-03-08T04:20:56.757" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15584" PostTypeId="2" ParentId="15582" CreationDate="2014-03-08T10:21:32.883" Score="7" Body="&lt;p&gt;That really depends on your system. At least for yeast the difference influences the strength of the activation (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952096/&quot; rel=&quot;noreferrer&quot;&gt;Analysis of Transcriptional Activation at a Distance in Saccharomyces cerevisiae&lt;/a&gt;&quot;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For bacteria such long distance regulations have recently been identified. Before that it was thought that this does happen only in eukaryotes. See the paper: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11282468&quot; rel=&quot;noreferrer&quot;&gt;Long distance relationships: enhancer-promoter communication and dynamic gene transcription.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I eukariotic cells the regulatory sequences (transcription factor binding sites and enhancers as well as silencers) can be really far away. An example for this would be the rs12913832 in intron 86 of HERC2, which influences the expression of the OCA2 gene, which is about 21 kB away. Both genes are not related in their functions. Normally three transcription factors interact here in the regulation of OCA2, HLTF, LEF1 and MITF, which leads to the formation of a DNA loop between the enhancer in HERC2 and the promoter in OCA2. The polymorphism reduces the binding of HLTF to the enhancer and hinders the formation of the loop which results in reduced expression of OCA2 (the whole story can be found here: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22234890&quot; rel=&quot;noreferrer&quot;&gt;HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter.&lt;/a&gt;&quot;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This paper (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21258399&quot; rel=&quot;noreferrer&quot;&gt;Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma.&lt;/a&gt;&quot;)analyzed (among other things) the binding sites for the microphthalmia-associated transcription factor (MITF) and their distance from the transcription start site. Figure 1 a/b of the paper is shown below. Interestingly a lot of the binding sites where pretty distant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qlqnX.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To go deeper into the topic, the following reviews are interesting to read:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23124110&quot; rel=&quot;noreferrer&quot;&gt;Long distance relationships: enhancer-promoter communication and&#xA;dynamic gene transcription.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22169023&quot; rel=&quot;noreferrer&quot;&gt;Enhancer and promoter interactions-long distance calls.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-08T10:21:32.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15585" PostTypeId="1" AcceptedAnswerId="15586" CreationDate="2014-03-08T15:13:17.647" Score="3" ViewCount="1331" Body="&lt;p&gt;This question may seem illogical to some, but I seriously have this doubt. I searched google for some proofs but they were extremely complex and I couldn't understand anything.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was just wondering whether we really have recessive allele or not? Is it like there are only dominant allele present, and when dominant allele isn't present we consider it recessive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it like there is a place reserved for dominant allele and if that place is empty it turns out to be recessive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although this thought is vague but then if you take this example, it probably would make sense:&#xA;Let's say there are two allele : T and t for tall and short respectively. Now, because TT, Tt, tT are tall, they all lead to the formation of specific hormone due to the presence of dominant allele. But the plant with genotype tt is short, hence the &quot;extra&quot; hormone for &quot;excessive&quot; tallness is missing in tt plant because the dominant gene isn't present. Can we say that that place for two allele (dominant allele) is actually empty in the plant with genotype tt?&lt;/p&gt;&#xA;" OwnerUserId="5963" LastEditorUserId="1320" LastEditDate="2014-03-08T17:37:31.930" LastActivityDate="2015-10-30T14:11:01.983" Title="Do recessive alleles really exist?" Tags="&lt;genetics&gt;&lt;gene-synthesis&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15586" PostTypeId="2" ParentId="15585" CreationDate="2014-03-08T16:32:25.107" Score="10" Body="&lt;p&gt;This is a good question. Firstly, let's get the terminology straightened out: The terms recessive and dominant are not actually used to describe genes, but rather &lt;em&gt;alleles&lt;/em&gt;. The term allele is used for alternative forms of the same gene.(&lt;a href=&quot;http://en.wikipedia.org/wiki/Allele&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;) Many genes have two or more alleles, and &lt;em&gt;some&lt;/em&gt; genes have alleles that can be described as dominant or recessive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also useful to be familiar with the terms &lt;em&gt;genotype&lt;/em&gt; and &lt;em&gt;phenotype&lt;/em&gt;. Genotype refers to the form of the genetic material (DNA), while phenotype refers to the observed &lt;em&gt;effect&lt;/em&gt; of the genotype. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, it's important to realize that the concept of &quot;dominant&quot; and &quot;recessive&quot; is a human-made &lt;em&gt;abstraction&lt;/em&gt;. The concept of dominant and recessive genes were invented (or discovered, if you like) before we reached a good undertanding of how genetics works at the molecular level. Thus, genetics in the early days had a much cruder understanding of how different phenotypes depend on the genotype. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The dominant/recessive concept is useful in cases where there is a limited number of possible allele pairs and one or several alleles can &lt;em&gt;mask&lt;/em&gt; the effect of other alleles. This is a very limited set of cases. Many genes have &lt;em&gt;many&lt;/em&gt; different alleles, and it's hard to account for all of them. Many alleles also do not have a clear observable effect, in which case any &quot;masking&quot; effect is not prominent. To quote Wikipedia (&lt;a href=&quot;http://en.wikipedia.org/wiki/Dominance_%28genetics%29&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The most common basis of dominance and recessiveness is that the&#xA;  dominant allele codes for a functional protein and the recessive&#xA;  allele for a mutant, non-functional protein.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A further important point is made in the following passage:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dominance is not inherent to an allele. It is a relationship between&#xA;  alleles; one allele can be dominant over a second allele, recessive to&#xA;  a third allele, and codominant to a fourth. Dominance should be&#xA;  distinguished from epistasis, a relationship in which an allele of one&#xA;  gene affects the expression of an allele at a different gene.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Let's consider your example: A single gene with two different &lt;em&gt;alleles&lt;/em&gt;, T and t. Let's assume the T allele codes for a more powerful version of the growth hormone than the t allele, or that the t allele produces a non-functional hormone. Furthermore, we assume that production of the T hormone from a single allele is enough to make the plant grow tall, and that production of T &lt;em&gt;or t&lt;/em&gt; from a second allele has no further effect. Then, we can say that the T allele masks the effect of the t allele. However, as you can probably imagine, one allele fully masking the effect of another is rather rare. So recessive/dominant allele pairs are rather the exception than the norm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, the that place for the two &lt;em&gt;alleles&lt;/em&gt; in the genome of the plant is definitely not empty. Note that a mutation &lt;em&gt;could&lt;/em&gt; in principle cause one of the genes to be deleted in its entirety from one of the chromosomes of the plant during reproduction. The &quot;place&quot; for the &lt;em&gt;gene&lt;/em&gt; on that chromosome would then indeed be empty. This has nothing to do with how dominance and recessiveness usually works, except that a recessive gene could become expressed if the dominant allele is deleted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, &lt;strong&gt;at the molecular level there is no concept of recessive or dominant alleles. Some genes have allele pairs that can be described as dominant/recessive in relation to each other, most others do not.&lt;/strong&gt; The &lt;em&gt;effect&lt;/em&gt; of different combinations of alleles determines whether the relationship between the alleles is described in terms of dominant/recessive.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="-1" LastEditDate="2014-03-09T06:45:24.737" LastActivityDate="2014-03-09T06:45:24.737" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="15588" PostTypeId="2" ParentId="15585" CreationDate="2014-03-08T17:36:43.770" Score="2" Body="&lt;p&gt;I'm having real difficulty understanding the original question. We know that a diploid organism has two copies of a gene because we can sequence them, and if they are different alleles we can point to the difference in their sequences. Then through genetic crosses we can follow the two alleles and look at the association between genotype and phenotype, thus deciding on the nature of any dominance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also we can create a mutation in a gene by inserting another piece of DNA with its own associated phenotype (drug resistance for example). In this situation we would normally see a dominant phenotype associated with the undisrupted gene, but we would know that the recessive (disrupted) allele was also present because of the associated drug resistance. Certainly this is done all of the time in yeast genetics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the problem is that you are treating genes as abstract entities in some sort of 19th century theoretical framework, disregarding over a century of genetic studies and, as @jarlemag has so eloquently explained, the physical reality of genes (as DNA sequences).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Final thought: the situation that you are describing (a &quot;space&quot;) does exist in the special case of  males for X-lined genes, where only one allele is present. This is the explanation for the genetic properties of sex-linked diseases like haemophilia.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-08T17:36:43.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15589" PostTypeId="1" AcceptedAnswerId="15591" CreationDate="2014-03-08T18:31:03.240" Score="5" ViewCount="420" Body="&lt;p&gt;Are there any commercially available fluorescent dyes that will bind only to double stranded DNA (not RNA, single stranded DNA etc.) for studying &lt;em&gt;in vitro&lt;/em&gt; using confocal microscopy?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2016-11-01T13:35:26.583" LastActivityDate="2016-11-01T13:35:26.583" Title="Dyes to bind to double stranded DNA?" Tags="&lt;biochemistry&gt;&lt;microscopy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15591" PostTypeId="2" ParentId="15589" CreationDate="2014-03-08T18:52:16.667" Score="4" Body="&lt;p&gt;Most of the dyes used for visualization bind with a much higher affinity to dsDNA. This would be SybrGreen, EtBr (although this will bind RNA as well).&#xA;There is a pretty comprehensive website from Life Technologies about &lt;a href=&quot;http://www.lifetechnologies.com/de/de/home/references/molecular-probes-the-handbook/nucleic-acid-detection-and-genomics-technology/nucleic-acid-stains.html&quot; rel=&quot;nofollow&quot;&gt;Nucleic acid stains&lt;/a&gt; that is worth a look.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is as well a publication on this topic: &quot;&lt;a href=&quot;https://workspace.imperial.ac.uk/imagingfacility/Public/DNA%20Staining%20for%20Fluorescence%20and%20Laser%20Confocal%20Microscopy.pdf&quot; rel=&quot;nofollow&quot;&gt;DNA Staining for Fluorescence and Laser Confocal Microscopy&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-08T18:52:16.667" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15596" PostTypeId="1" CreationDate="2014-03-09T11:20:38.503" Score="0" ViewCount="1142" Body="&lt;p&gt;I am always confused about this...so when one cell which has 23 pairs of chromosomes undergoes the two meiotic divisions it produces four cells containing 1 chromatid of every chromosome pair so when this fertilizes the opposite gamete (of course it has also one chromatid of each chromosome pair) when they are fertilized they make one 23 chromosomes because 23 chromatid from one and 23 from other and they will form 23 chromosomes not 23 pairs of it, so my question is how they form 23 pair of it or to make it homologue..please clarify with some pics??...tnx&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="1320" LastEditDate="2014-03-09T15:36:43.423" LastActivityDate="2015-04-01T09:06:59.187" Title="How does a fertilized egg form 23 pairs of chromosomes?" Tags="&lt;cell-division&gt;&lt;cell&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15597" PostTypeId="2" ParentId="15596" CreationDate="2014-03-09T15:34:42.557" Score="1" Body="&lt;p&gt;After fertilisation the zygote has two copies of each of the chromosomes (not worrying about sex chromosomes). When each of these is replicated the cells will have chromosome pairs, which will then divide in mitosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The classical chromosome image of pairs of X-shaped chromosomes relates to the situation at mitotic metaphase when each of the chromosomes has replicated and consists of two sister chromatids. As anaphase proceeds the splitting of the centromeres means that each of the sister chromatids becomes a chromosome, and each cell ends up with a pair of each chromosome type, just like a zygote. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-09T15:34:42.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15598" PostTypeId="2" ParentId="15557" CreationDate="2014-03-09T15:42:06.130" Score="4" Body="&lt;p&gt;I suspect it is just physics. Each of your legs makes up about 1/6 of body mass, leaving about 2/3 of your mass superior to your hips.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Raising one leg requires action of the hip flexors (i.e., iliopsoas complex) but also activity in the anterior abdominal wall muscles (rectus abdominis, obliques) and back muscles to stabilize your abdomen. To raise the other leg simultaneously, you recruit the ipsilateral hip flexors. But, importantly, you probably have already maximally recruited most of your abdominal and back muscles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine the body as a lever system. With one leg raised, you have 1/6 of body mass balanced against 2/3. With both legs up, you have 1/3 vs. 2/3 and with potentially increased torque, because your legs are long (a force acting at a larger distance). The muscle forces to stabilize that must be larger, but the additional muscles are not there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can raise both legs with difficulty (admittedly, $n=1$).&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2014-03-09T15:50:34.803" LastActivityDate="2014-03-09T15:50:34.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15599" PostTypeId="2" ParentId="7344" CreationDate="2014-03-09T16:16:17.143" Score="3" Body="&lt;p&gt;Synthesizing spider silk seems to be developing quickly, but for 3D printing we need not just synthetic spider silk, but a liquid form that can solidify once printed. I would imagine it is going to be two or more liquids mixing together at the printhead and then bonding and solidifying with the adjacent layers, like spider silk epoxy.&lt;/p&gt;&#xA;" OwnerUserId="5980" LastActivityDate="2014-03-09T16:16:17.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15600" PostTypeId="1" AcceptedAnswerId="15604" CreationDate="2014-03-09T16:21:55.643" Score="0" ViewCount="1628" Body="&lt;p&gt;The primary parameters of heart pumping are&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;strength of contractility (inotropic positive; Frank-Starling relationship)&lt;/li&gt;&#xA;&lt;li&gt;rate of relaxation (lusitropic positive)&lt;/li&gt;&#xA;&lt;li&gt;heart rate (chronotropic positive)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;which change the secondary parameters according to the marginals&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Heart rate&lt;/li&gt;&#xA;&lt;li&gt;Stroke volume &#xA;&lt;ul&gt;&#xA;&lt;li&gt;Contractility &lt;/li&gt;&#xA;&lt;li&gt;Starling relationship&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which of these paramecers are controlled intracardiacally and which extracardiacally?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-03-09T18:44:19.143" Title="What is the difference between intracardiac and extracardiac reflexes in cardiac regulation?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;reflexes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15601" PostTypeId="2" ParentId="875" CreationDate="2014-03-09T17:51:18.177" Score="10" Body="&lt;p&gt;When females are in their mother's womb all their Oogonium (plural Oogonia) are being made, they they undergo mitotic divisions to become a primary oocyte. Then, the primary oocytes start to undergo meiosis I -  but meiosis I is arrested. This is the first meiotic arrest. Meiosis I continues when a female hits puberty, every month one or more primary oocytes undergo meiosis I and create secondary oocytes. These secondary oocytes will then  start the second meiotic division, but this second meiotic division is arrested as well. It is arrested for about 24 hours, waiting for a sperm to fertilise it in the Fallopian tubes. The only time an egg (or in medical terms - secondary oocyte) will complete meiosis II is if a sperm penetrates the egg, and then it is called an ovum, which develops into a zygote and a then foetus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, the answer to your question will be - the first meiotic arrest in oogenesis will occur from the time the primary oocytes are created in the womb, until a female reaches  puberty. starting puberty until menopause every month one or more primary oocytes will mature and complete the first meiotic division.&lt;/p&gt;&#xA;" OwnerUserId="5981" LastEditorUserId="3553" LastEditDate="2016-06-07T04:11:43.417" LastActivityDate="2016-06-07T04:11:43.417" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15602" PostTypeId="2" ParentId="14789" CreationDate="2014-03-09T18:04:38.377" Score="1" Body="&lt;p&gt;Determining what is considered to be &quot;normal&quot; is quite challenging indeed. Both the ADA and the WHO look at upgrading diagnosis limits and both have a conservative approach, primarily due to the difficulties in conducting large scale studies and the anomalies between assumptions of plasma glucose distribution and what is probably actually present in populations. Digging through, I found a very good WHO document here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.who.int/diabetes/publications/Definition%20and%20diagnosis%20of%20diabetes_new.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.who.int/diabetes/publications/Definition%20and%20diagnosis%20of%20diabetes_new.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not going to regurgitate from this document, but I believe Issue 2 provides a detailed answer to your question detailing several determination methodologies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to your second question on age/sex variations, are you asking if the criteria are different? At least with reference to FPG, they don't appear to be so. &lt;/p&gt;&#xA;" OwnerUserId="1521" LastActivityDate="2014-03-09T18:04:38.377" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15603" PostTypeId="1" CreationDate="2014-03-09T18:20:39.190" Score="2" ViewCount="155" Body="&lt;p&gt;Which databases contain the metabolic pathway of human diseases?&#xA;I have searched Metacyc and KEGG but didn't find the appropriate metabolic pathway.&lt;/p&gt;&#xA;" OwnerUserId="5933" LastEditorUserId="948" LastEditDate="2014-03-09T18:23:51.457" LastActivityDate="2014-06-11T09:15:38.543" Title="Databases for metabolic pathways of human disease" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;&lt;biotechnology&gt;&lt;systems-biology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15604" PostTypeId="2" ParentId="15600" CreationDate="2014-03-09T18:44:19.143" Score="2" Body="&lt;p&gt;Rate is controlled outside the heart by the Vagus Nerve having parasympathetic activity on the sinoatrial nerve.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stroke volume (taking contractility and Starling's law as one) are factors from the cardiac tissue itself - &quot;intracardiac&quot;.  &lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2014-03-09T18:44:19.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15605" PostTypeId="1" AcceptedAnswerId="16913" CreationDate="2014-03-09T18:50:24.250" Score="2" ViewCount="162" Body="&lt;p&gt;While looking at (daylight) color perception I came across a paper by Jeremy Nathans (et al., Proc. Nat. Acad. Sci., vol. 100 no. 20, 2003, full text &lt;a href=&quot;http://www.pnas.org/content/100/20/11706.full&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) in which he describes the creation of a mouse with genetically modified vision. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My threshold question is just about the mechanics of the process, which he characterizes as &quot;site-directed mutagenesis.&quot; My understanding (a guess, really) is that embryonic stem cells are induced to assimilate homologous human DNA sequences and these cells are injected into mouse blastocysts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In outline I understand the idea of the DNA construct but wonder physically how the stem cell initially acquires the knock-in construct. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any enlightenment.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: I see that there are several ways to do this and that the paper's &quot;Materials and Methods&quot; section focuses on the molecular genetic details. Maybe we can't get the information from the four corners of the document? If so I'd still be interested in whatever process seems likely given the sort of mouse they made. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-03-11T03:08:19.660" LastActivityDate="2014-04-28T03:52:47.140" Title="How is a stem-cell induced to assimilate a knock-in DNA construct?" Tags="&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="15607" PostTypeId="1" AcceptedAnswerId="15609" CreationDate="2014-03-09T19:47:50.953" Score="5" ViewCount="1618" Body="&lt;p&gt;Methionine and Cysteine are the two amino acids containing sulfur. &lt;a href=&quot;https://en.wikipedia.org/wiki/Cysteine&quot; rel=&quot;nofollow&quot;&gt;According to wikipedia, cysteine&lt;/a&gt; is built from methionine. However, the wikipedia also claims that &lt;a href=&quot;https://en.wikipedia.org/wiki/Methionine#Biosynthesis&quot; rel=&quot;nofollow&quot;&gt;methionine is synthesized from cysteine&lt;/a&gt;.&lt;br&gt;&#xA;So, a chicken and egg problem (esp. since eggs are a rich source for those proteins). Where do living things get their sulfur to build these amino acids in the first place, in what forms is sulfur available biologically?&lt;/p&gt;&#xA;" OwnerUserId="3037" LastEditorUserId="5144" LastEditDate="2014-03-09T21:07:16.030" LastActivityDate="2014-03-09T21:07:16.030" Title="In biosynthesis of cysteine and methionine, where does the sulfur come from?" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15608" PostTypeId="2" ParentId="15607" CreationDate="2014-03-09T21:03:56.633" Score="5" Body="&lt;p&gt;First of all, the wikipedia article you quote states that methionine is synthesized from cysteine in &lt;em&gt;plants and microorganisms&lt;/em&gt;, not in humans. In humans, both cysteine and methionine are &lt;a href=&quot;https://en.wikipedia.org/wiki/Essential_amino_acid&quot; rel=&quot;noreferrer&quot;&gt;essential amino acids&lt;/a&gt; which means that they cannot be produced by the human body but need to be acquired elsewhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, this is mostly done by eating proteins that contain these amino acids. The proteins are broken down and the amino acids (or their constituents, such as sulfur) are reused. In mammals, cysteine is produced from serine but the sulfur comes from methionine via homocysteine:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BSeUV.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, methionine comes from the diet and it is then used to produce cysteine. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-03-09T21:03:56.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15609" PostTypeId="2" ParentId="15607" CreationDate="2014-03-09T21:05:40.193" Score="6" Body="&lt;p&gt;Microorganisms (and plants) make cysteine from serine using H&lt;sub&gt;2&lt;/sub&gt;S as the sulphur source. Condensation of these two directly gives cysteine in some bacteria, but most often the reaction sequence is:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;serine + acetyl-CoA &amp;gt;&amp;gt;&amp;gt; O-acetylserine + CoA-SH&lt;/p&gt;&#xA;&lt;p&gt;O-acetylserine + H&lt;sub&gt;2&lt;/sub&gt;S &amp;gt;&amp;gt;&amp;gt; cysteine + acetate + H&lt;sub&gt;2&lt;/sub&gt;O&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;As you say, in terms of the sulphur, cysteine and methionine are interconvertible.&lt;/p&gt;&#xA;&lt;p&gt;Animals rely upon their diet for methionine, and can make cysteine from that methionine.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-03-09T21:05:40.193" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15610" PostTypeId="1" AcceptedAnswerId="15619" CreationDate="2014-03-10T01:23:35.827" Score="2" ViewCount="655" Body="&lt;p&gt;So in the video my instructor sent on viruses, he said that for lytic viruses, new viruses manufactured by the host cell could get out of the cell in one of two ways.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The new viruses would leave by exocytosis.&#xA;or,&lt;/li&gt;&#xA;&lt;li&gt;The cell would be &quot;ruptured&quot; and the new viruses would &quot;erupt out of the cell&quot;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In the rupturing option, is the cell destroyed? The way he phrased it as well as his tone of voice brought to mind an image of the cell &lt;em&gt;bursting&lt;/em&gt; and the viruses spilling out....but the diagram showed a little gap in the cell membrane, and the viruses leaving from that one exit point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which is more accurate?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;evamvid&lt;/p&gt;&#xA;" OwnerUserId="5466" LastEditorUserId="3624" LastEditDate="2014-03-10T12:00:18.713" LastActivityDate="2014-03-10T12:00:18.713" Title="Lytic Viruses -- Cell lysis?" Tags="&lt;homework&gt;&lt;virology&gt;&lt;virus&gt;&lt;cycle&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15611" PostTypeId="1" CreationDate="2014-03-10T01:30:20.073" Score="2" ViewCount="1839" Body="&lt;p&gt;In the video sent by my teacher on viruses, the example he used for lysogenic viruses was a bacteriophage infecting a bacteria. When he was describing how the genetic material was incorporated into the host cell's genetic material, he said something along the lines of:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Now the genetic material is incorporated into the cell's chromosome.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My question is, did he describe it as one main chromosome because that was the example being used? Or do lysogenic viruses only infect bacteria?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess a better way of phrasing this would be, are bacteriophages the only type of lysogenic viruses?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;evamvid&lt;/p&gt;&#xA;" OwnerUserId="5466" LastActivityDate="2014-03-10T13:28:50.527" Title="Do lysogenic viruses only infect bacteria?" Tags="&lt;bacteriology&gt;&lt;virology&gt;&lt;virus&gt;&lt;infection&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15612" PostTypeId="1" AcceptedAnswerId="15624" CreationDate="2014-03-10T01:41:30.290" Score="3" ViewCount="2372" Body="&lt;p&gt;After a virus (one of the varieties which infects the cell via injection and not endocytosis) injects its genetic material into the host cell, what happens to its protein coat? I would guess that it just falls off. However, since it is now outside of a cell, there are no protein-digesting enzymes -- or are there? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens to it now? I'm guessing it doesn't just float around for all eternity.&lt;/p&gt;&#xA;" OwnerUserId="5466" LastEditorUserId="7974" LastEditDate="2014-06-09T03:04:24.857" LastActivityDate="2014-06-09T03:04:24.857" Title="What happen's to a virus's capsid after it injects its genetic material into the host cell?" Tags="&lt;proteins&gt;&lt;enzymes&gt;&lt;virology&gt;&lt;virus&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15613" PostTypeId="1" AcceptedAnswerId="15621" CreationDate="2014-03-10T01:53:29.740" Score="1" ViewCount="188" Body="&lt;p&gt;In a diagram of the lysogenic cycle sent by my instructor in a video, it shows the provirus splitting from the cell's main DNA when the dormancy period ends and the viral DNA is &quot;activated&quot;. Is this how it happens, or was he just trying to illustrate the activation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess a better way of phrasing this would be, is the viral DNA replicated as part of the cell's normal DNA, or is it replicated separately?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;evamvid&lt;/p&gt;&#xA;" OwnerUserId="5466" LastEditorUserId="5144" LastEditDate="2014-03-10T07:36:20.700" LastActivityDate="2014-03-10T08:03:05.283" Title="In the lysogenic cycle, does the provirus split from the cell's main genetic material for replication?" Tags="&lt;virology&gt;&lt;virus&gt;&lt;replication&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15614" PostTypeId="1" AcceptedAnswerId="15620" CreationDate="2014-03-10T01:58:34.850" Score="2" ViewCount="5110" Body="&lt;p&gt;Is it impossible for retroviruses to be lysogenic? In the lysogenic cycle, the viral genetic material is incorporated into the host cell's DNA. Because retroviruses have RNA, it would be impossible for their genetic material to be incorporated into the host cell's DNA, unless the RNA is reverse-transcribed or something. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this the case? How does this work?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;evamvid&lt;/p&gt;&#xA;" OwnerUserId="5466" LastEditorUserId="5466" LastEditDate="2014-03-10T17:31:44.950" LastActivityDate="2014-03-10T17:31:44.950" Title="Is it impossible for a retrovirus to be lysogenic?" Tags="&lt;virology&gt;&lt;virus&gt;&lt;retrovirus&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15615" PostTypeId="1" AcceptedAnswerId="16926" CreationDate="2014-03-10T04:45:48.663" Score="2" ViewCount="47" Body="&lt;p&gt;I am thinking this question.&#xA;Thrombosis can result in&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;organisation of thrombus,&lt;/li&gt;&#xA;&lt;li&gt;sepsis&lt;/li&gt;&#xA;&lt;li&gt;thromboembolism, &lt;/li&gt;&#xA;&lt;li&gt;fibrinoid swelling&lt;/li&gt;&#xA;&lt;li&gt;adiposity.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I fibrinoid swelling (edema) (4) can occur.&#xA;Also, I think (3) thromboembolism can occur and also (1) organisation of thrombus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What can thrombosis result in?&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-03-10T05:42:58.767" LastActivityDate="2014-04-27T16:23:24.977" Title="What can thrombosis lead to?" Tags="&lt;cell-biology&gt;&lt;homework&gt;&lt;pathology&gt;&lt;pathogenesis&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15616" PostTypeId="1" AcceptedAnswerId="15626" CreationDate="2014-03-10T05:47:54.553" Score="1" ViewCount="179" Body="&lt;p&gt;I think it is decreased blood supply to organs and tissues.&#xA;I also think it is the stopped circulation.&#xA;However, both ones cannot be right, I think.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is ischaemia exactly? &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1320" LastEditDate="2014-03-10T12:53:00.013" LastActivityDate="2014-03-10T12:53:00.013" Title="What is ischaemia exactly?" Tags="&lt;physiology&gt;&lt;homework&gt;&lt;pathology&gt;&lt;pathophysiology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15617" PostTypeId="1" AcceptedAnswerId="16927" CreationDate="2014-03-10T06:01:49.550" Score="0" ViewCount="50" Body="&lt;p&gt;I am thinking, if 1) little compressed superior caval vena and 2) some vein compression by tumor, can cause systemic venous congestion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this is only in rare occasions.&#xA;However, the question is if this is possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can systemic venous congestion caused by these two factors?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-04-27T16:31:04.207" LastActivityDate="2014-05-27T20:04:11.520" Title="Can systemic venous congestion caused by tumor?" Tags="&lt;pathogenesis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15618" PostTypeId="1" AcceptedAnswerId="15628" CreationDate="2014-03-10T06:32:24.983" Score="0" ViewCount="58" Body="&lt;p&gt;If we eat fat:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the fat go into heart, arteries and fat cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;OR&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the fat digested, following which our body creates fat that goes into heart, arteries and fat cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which one is right?&lt;/p&gt;&#xA;" OwnerUserId="554" LastEditorUserId="1320" LastEditDate="2014-03-10T12:49:42.093" LastActivityDate="2014-03-11T17:54:53.967" Title="Does fat on our heart come from the fat that we eat?" Tags="&lt;fatty-acid-synthase&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15619" PostTypeId="2" ParentId="15610" CreationDate="2014-03-10T07:35:54.593" Score="2" Body="&lt;p&gt;Yes, ruptured here means that the host cell is destroyed. The virus &quot;hijacks&quot; the cell anyway and uses its protein production machinery to make as much virus particles and its transcription enzymes to makes as many viral genomes as possible. If the ressources of the cell are exhausted, it get destroyed and the viruses are set free.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this image (from the &lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Lytischer_zyklus.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt; article on the lytic process). It actually doesn't matter, if the virus infects the cell from the outside or if it comes from the genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qn5Vr.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Adsorption of the virus to the cell.&lt;/li&gt;&#xA;&lt;li&gt;Injection of its genetic material into the cell.&lt;/li&gt;&#xA;&lt;li&gt;Production of new viruses (hull and genome).&lt;/li&gt;&#xA;&lt;li&gt;Rupture of the cell and release of the viruses.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-10T07:59:52.550" LastActivityDate="2014-03-10T07:59:52.550" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="15620" PostTypeId="2" ParentId="15614" CreationDate="2014-03-10T07:47:55.830" Score="2" Body="&lt;p&gt;Both things are not exclusive of each other. Retroviruses are RNA-based viruses which need to reverse transcribe their RNA genome into DNA before they can multiply. This is done by the reverse transcriptase enzyme, which is part of the virus and is incorporated into the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once the reverse transcriptase has been active and made the DNA, this DNA can also be incorporated into the hosts genome. If you look into the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Bacteriophage&quot; rel=&quot;nofollow&quot;&gt;Bacteriophages&lt;/a&gt;, you will find a list of different bacteriophages, with all kind of genomes, among them as well a number of RNA-based viruses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RNA-based viruses which enter the lysogenic pathway are obviously either pretty rare or they haven't been discovered yet in bigger numbers. Two examples are the phages &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/895846&quot; rel=&quot;nofollow&quot;&gt;F2&lt;/a&gt; and &lt;a href=&quot;http://scholar.google.de/scholar_host?q=info%3aV2sLS1EKAgcJ%3ascholar.google.com/&amp;amp;hl=de&amp;amp;as_sdt=0,5&amp;amp;as_vis=1&amp;amp;output=viewport&amp;amp;pg=61&quot; rel=&quot;nofollow&quot;&gt;MS2&lt;/a&gt; (which are closely related).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-10T13:53:02.130" LastActivityDate="2014-03-10T13:53:02.130" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15621" PostTypeId="2" ParentId="15613" CreationDate="2014-03-10T08:03:05.283" Score="1" Body="&lt;p&gt;When the virus is integrated into the hosts genome (and becomes a provirus) it is replicated with the cell genome, since it is now part of it. When the provirus gets activated (this happens by changes in the host's environmental conditions or health), it will get transcribed.&#xA;This is followed by the translation of the viral proteins which then leads to a cell which exclusively produces viruses until its resources are exhausted and the cell gets destroyed.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-10T08:03:05.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15622" PostTypeId="2" ParentId="15611" CreationDate="2014-03-10T08:23:41.680" Score="5" Body="&lt;p&gt;Bacteriophages are the only viruses where this phenomenon is called lytic and lysogenic cycle. There is a similiar phenomenon in humans (and other mammals as well) which is called &quot;endogenous retrovirus&quot; and is pretty common.&#xA;For humans, there are estimations that something between 5 and 8% of the human genome are made of endogeneous retroviruses. See these two references:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15044706&quot; rel=&quot;noreferrer&quot;&gt;Long-term reinfection of the human genome by endogenous retroviruses.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.hindawi.com/journals/ijg/2002/265325/abs/&quot; rel=&quot;noreferrer&quot;&gt;Endogenous Retroviruses and Human Evolution&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Otherwise I can recommend reading the article on &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Endogenous_retrovirus&quot; rel=&quot;noreferrer&quot;&gt;Endogeneous retroviruses&lt;/a&gt;&quot; in the Wikipedia, it is pretty extensive and has a lot of references.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-10T13:28:50.527" LastActivityDate="2014-03-10T13:28:50.527" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15623" PostTypeId="1" AcceptedAnswerId="16928" CreationDate="2014-03-10T09:26:20.353" Score="1" ViewCount="45" Body="&lt;p&gt;I think hypertrophy happens in most of the cases. However, I am not sure if hypertrophy always happens. I started to think about wet lungs (pulmonary reason for the left-sided heart failure).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can the decrease of cell size occur in the heart failure?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="107" LastEditDate="2014-03-10T14:10:55.360" LastActivityDate="2014-04-27T16:30:14.650" Title="Are there any forms of heart failure where cell size decreases?" Tags="&lt;physiology&gt;&lt;pathology&gt;&lt;cardiology&gt;&lt;pathogenesis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15624" PostTypeId="2" ParentId="15612" CreationDate="2014-03-10T09:30:36.240" Score="1" Body="&lt;p&gt;Interesting question and actually I haven't found a real answer here yet. The phages seem to bind rather hard, since the need to be blended (subjected to relatively high forces) to shear off. This was used in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hershey_chase&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hershey-Chase-Experimen&lt;/a&gt;t to find out what the genetic material of the cell is. It doesn't matter though, since most of the cells which are infected get destroyed anyway. If not, they are most likely taken up and broken down inside the cell, as it happens with other membrane proteins.&#xA;This is only valid for viruses which inject their genetic material into the host cell, while the capsid stays outside. This happens mostly for Bacteriophages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a few other possibilities for viruses to enter cells where this is no problem:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Viruses which have a membrane envelope can enter the cell via membrane fusion. To make the fusion happen, either the membranes have to get very close, or the virus first binds receptors on the cell surface and then fuses its membrane with the cell. This causes the interior of the virus to be released into the cell. The picture below shows the fusion (from the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Interbilayer_forces_in_membrane_fusion&quot; rel=&quot;nofollow noreferrer&quot;&gt;membrane fusion&lt;/a&gt;). An interesting article on this topic is: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12383801&quot; rel=&quot;nofollow noreferrer&quot;&gt;Membrane fusion.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XSHVm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another possibility for a virus to enter a host cell is via endocytosis. Here the virus uses the uptake of material from the surrounding of the cell to get inside. This can either happen together with resources inside a vacuole. &#xA;Or it happens via the binding of specific receptors, which are internalized into the cell upon binding of the specific ligand. Here the virus mimics the ligand of the receptor to get internalized into the cell.&#xA;In both cases the virus needs to escape from the vacuole before it get broken down because the vacuole is turned into a lysosome.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2014-03-10T13:12:17.807" LastActivityDate="2014-03-10T13:12:17.807" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15626" PostTypeId="2" ParentId="15616" CreationDate="2014-03-10T11:15:40.883" Score="4" Body="&lt;p&gt;Ischaemia is lack of sufficient &lt;strong&gt;perfusion&lt;/strong&gt; to a tissue.  Reduced perfusion could therefore mean decreased blood supply to organs and tissues &lt;em&gt;and could also mean&lt;/em&gt; a complete cessation of blood flow to an area - therefore both can be correct as they are on a continuum.  &lt;strong&gt;Infarction&lt;/strong&gt; is tissue death due to hypoxia which can result from ischaemia that is not swiftly resolved.&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2014-03-10T11:15:40.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15627" PostTypeId="2" ParentId="15603" CreationDate="2014-03-10T13:06:58.973" Score="1" Body="&lt;p&gt;NCBI BioSystems help file contains a list of their sources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_help.html#SourceDatabases&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_help.html#SourceDatabases&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please specify what you need as stated in the comments as it is almost impossible to give you more (relevant) information then this. &lt;/p&gt;&#xA;" OwnerUserId="5699" LastActivityDate="2014-03-10T13:06:58.973" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15628" PostTypeId="2" ParentId="15618" CreationDate="2014-03-10T13:07:34.210" Score="6" Body="&lt;p&gt;Fat is, in molecular terms, triacylglcerol. In order to be absorbed in the small intestine triacylglycerol molecules are broken down by lipases into fatty acids and monoacylglycerols. Once these have got across the enterocyte membrane they are reassembled into triacylglycerols and packed up into a special class of lipoprotein particle, a chylomicron, which enters the bloodstream via the lymphatic system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The triacylglycerols in the chylomicrons are then able to be passed around through the system of lipoproteins (LDL, VLDL etc.) and pretty much can end up anywhere, including fat cells (adipocytes) or they can be metabolised as fuel molecules&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, because of that initial digestive step I would say that a single intact dietary fat molecule cannot end up as a body component directly, but complete metabolism of the components of the fat molecule is not necessary for these to contribute to body fat.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-10T13:07:34.210" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15629" PostTypeId="1" CreationDate="2014-03-10T16:08:17.363" Score="5" ViewCount="1087" Body="&lt;p&gt;I need to isolate RNA from Drosophila head. I basically chop the head off and first homogenize it with a homogenizer (similar to this: &lt;a href=&quot;http://www.omni-inc.com/omni-tissue-homogenizer-th-package-p-11.html&quot;&gt;http://www.omni-inc.com/omni-tissue-homogenizer-th-package-p-11.html&lt;/a&gt;) and further homogenize it with 22G needle in TRIzol reagent. I use TRIzol RNA isolation for larvae brain a lot and have no problem with the method itself. However, with adult I got really low RNA concentration which is weird. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought that maybe I have problem with homogenization itself, or I overlook something (such as extra centrifugation or different kind of homogenization etc). Does anybody have experience with it? &#xA;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="5630" LastActivityDate="2016-08-17T08:49:25.950" Title="RNA isolation from Drosophila head" Tags="&lt;molecular-biology&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15631" PostTypeId="1" CreationDate="2014-03-10T18:57:42.333" Score="1" ViewCount="156" Body="&lt;p&gt;I know that this is true of (roasted) coffee but haven't been able to find any reliable information about mate in its smoked or steamed state.  Thank you.&lt;/p&gt;&#xA;" OwnerUserId="5989" LastEditorUserId="5989" LastEditDate="2014-03-10T19:06:11.457" LastActivityDate="2014-06-30T21:58:33.873" Title="Does Yerba Mate contain Beta carbolines like harman and norharman?" Tags="&lt;botany&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15632" PostTypeId="1" CreationDate="2014-03-10T19:03:06.110" Score="2" ViewCount="959" Body="&lt;p&gt;Why do men produce so much spermatozoa, that will get discarded, but women, just one ovulum, which is a good one.&lt;/p&gt;&#xA;&lt;p&gt;Couldn't men produce good spermatozoa as a limited edition?&lt;/p&gt;&#xA;&lt;p&gt;Where is the evolutionary advantage of things being like they are?&lt;/p&gt;&#xA;" OwnerUserId="4419" LastEditorUserId="4419" LastEditDate="2020-07-15T17:31:47.660" LastActivityDate="2020-07-15T17:31:47.660" Title="Many spermatozoa, but just one ovulum" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;reproduction&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="15633" PostTypeId="2" ParentId="15632" CreationDate="2014-03-10T19:10:54.913" Score="0" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;As spermatozoa need to be transported therefore in order to increase the chances of successful transportation (and fertilization) the number may be high.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Also, there is only one ovum probably because more cytoplasm is required in the creation of an ovum, which is evident from its size. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5963" LastActivityDate="2014-03-10T19:10:54.913" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15634" PostTypeId="1" CreationDate="2014-03-10T19:30:44.967" Score="3" ViewCount="185" Body="&lt;p&gt;Imagine a lineage of multicellular organisms that had mating types and evolved their mating types into sexes. &lt;strong&gt;What are the possible mechanisms that might have brought this lineage to evolve sexes from mating types?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To my understanding of the definitions of sexes and mating types, the only diffenece between the two is that sexes imply gametes of different sizes. Is it correct?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-04-10T21:51:07.873" Title="Evolution from Mating types to different sexes" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;theoretical-biology&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15635" PostTypeId="1" AcceptedAnswerId="15639" CreationDate="2014-03-10T21:49:55.050" Score="0" ViewCount="850" Body="&lt;p&gt;What organ can be conserved outside of the body for the longest time and still function when reimplanted?&lt;/p&gt;&#xA;" OwnerUserId="5990" LastEditorUserId="1757" LastEditDate="2014-03-12T15:08:47.930" LastActivityDate="2014-03-12T15:08:47.930" Title="Organs lifespan out of the body" Tags="&lt;organs&gt;&lt;lifespan&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2014-03-13T19:41:23.490" ContentLicense="CC BY-SA 3.0" />
  <row Id="15636" PostTypeId="2" ParentId="15632" CreationDate="2014-03-10T22:41:52.873" Score="2" Body="&lt;p&gt;I think the asymmetry allows for a stronger selection process.  Sperm competition is a powerful force in evolution.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is useful since sperm &lt;a href=&quot;http://www.vivo.colostate.edu/hbooks/pathphys/reprod/semeneval/motility.html&quot; rel=&quot;nofollow&quot;&gt;vary wildly in quality&lt;/a&gt; - for healthy human males only 50% might not be normally motile. Other animals can have a higher percentage, but there are always a significant number of floaters... This means that the fertilization via sperm takes out a lot of the less functional sperm.  Since these are in many cases the same genes we use as diploid organisms later, sperm competition really tames a lot of problems which might be produced in meiosis.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many animals have multiple mating events from multiple males at just about the same time - when the female is in heat.  This gives a larger role for sperm competition - literally different sires are competing as sperm to fertilize the egg.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In females it is a different process of choosing the cells.  Ova are mostly eliminated in women by the time they reach reproductive age.  I think that this is not well understood biologically... references are hard to find.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The differences in the morphology and roles of the gametes, which goes back to the most primitive of animals has a strong role in selection of healthy offspring through a diverse set of mechanical and biochemical conditions experienced during fertilization. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Added Note: I ran across this reference for &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973204/&quot; rel=&quot;nofollow&quot;&gt;how ova are selected for presentation by the ovaries&lt;/a&gt;.  Its not really a review, but maybe a lead reference on how selection works in the female reproductive system - its also picky:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In mammals, ovarian folliculogenesis is a process regulated by complex networks composed of various endocrine, paracrine and autocrine factors that interact coordinately.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Its no cake walk to being an egg either...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-04-25T19:13:00.137" LastActivityDate="2014-04-25T19:13:00.137" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15637" PostTypeId="1" AcceptedAnswerId="15638" CreationDate="2014-03-11T01:21:45.323" Score="11" ViewCount="9532" Body="&lt;p&gt;Is it a viral vs. bacterial thing?&#xA;Is there just more variety among types of flu than other diseases, so that this year's vaccines don't cover next year's flu?&lt;/p&gt;&#xA;" OwnerUserId="4697" LastEditorUserId="4101" LastEditDate="2015-06-02T14:34:44.597" LastActivityDate="2015-06-02T14:34:44.597" Title="Why do I need a flu shot every year, while many other vaccinations last years or even a lifetime?" Tags="&lt;immunology&gt;&lt;virology&gt;&lt;vaccination&gt;&lt;influenza&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15638" PostTypeId="2" ParentId="15637" CreationDate="2014-03-11T01:39:07.977" Score="24" Body="&lt;p&gt;The flu virus changes rapidly so that the current vaccine doesn't work against the new strains. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The way vaccines work is that they teach our immune system what to look out for. The vaccine contains bits of the virus but in a form that can't cause a proper infection, the body learns what to look for and next time before the virus can really get going the immune system kills it off first. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of flu, every year it looks different enough that the targeting mechanisms of our body don't recognise it. Flu being a RNA virus frequently mutates until it is slightly different. This is called antigenic drift, the changing of the antigens or the parts our body recognises. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On top of that there's lots and lots of types of the influenza virus, that can not only infect humans but others which affect other animals. Occasionally the virus might combine with a random other strain making it completely new: an animal flu and human flu hybrid. These are the epidemics of swine or avian flu etc. This recombination is called antigenic shift.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So each year scientists predict which viruses will affect us this coming year and grow them ready for vaccines. Of course there's some of the old virus floating around looking for someone to infect, but those infected can't be infected by it again if the immune system is working. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-03-11T01:39:07.977" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15639" PostTypeId="2" ParentId="15635" CreationDate="2014-03-11T01:42:55.133" Score="1" Body="&lt;p&gt;Depends what you consider an organ. Typically though it's the cells which require the most metabolic activity which have the shortest life span. The kidney is the most of the major internal organs with up to 36 hours with liver coming second at up to 16 hours. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-03-11T01:42:55.133" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15640" PostTypeId="1" AcceptedAnswerId="15644" CreationDate="2014-03-11T02:29:50.370" Score="1" ViewCount="1401" Body="&lt;p&gt;So according to a PPT I'm reading, bacterial conjugation works by the two bacteria joining pili and exchanging plasmids. So how exactly do the plasmids get across the gap? If I understand this correctly, the pili are little hair-like things on the outside of the bacteria -- so unless the plasmids were actually able to somehow be pushed &lt;em&gt;through&lt;/em&gt; the pili, there would be gap. Right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only other possibility I can think of would be that the membranes fused or something like that. But that comes with it's own whole set of problems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this work?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;evamvid&lt;/p&gt;&#xA;" OwnerUserId="5466" LastEditorUserId="5466" LastEditDate="2014-03-11T02:54:36.880" LastActivityDate="2014-03-11T07:33:38.967" Title="Bacterial Conjugation/Horizontal Gene Transfer -- how does the plasmid exchange work?" Tags="&lt;bacteriology&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15642" PostTypeId="1" CreationDate="2014-03-11T05:57:10.317" Score="2" ViewCount="44" Body="&lt;p&gt;This is a follow up to this previous question: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/15607/in-biosynthesis-of-cysteine-and-methionine-where-does-the-sulfur-come-from&quot;&gt;In biosynthesis of cysteine and methionine, where does the sulfur come from?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can animals use gaesous H&lt;sub&gt;2&lt;/sub&gt;S in the atmosphere, say for instance from a sulfur rich hot springs, to aquire sulfur? &lt;/p&gt;&#xA;" OwnerUserId="5991" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-03-11T08:11:47.020" Title="Can animals absorb atmospheric sulfur?" Tags="&lt;homocysteine&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15643" PostTypeId="1" CreationDate="2014-03-11T06:27:08.120" Score="9" ViewCount="34874" Body="&lt;p&gt;I can see the chain of spreading disease: Humans usually get rabies from domestic animals, those usually get it from wild animals, wild animals in their turn get from the other wild animals and here I'm stuck. Well, so where do wild animals get it from initially?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that rabies is a virus and it needs warm-blooded animals to live out. Also according to &lt;a href=&quot;http://en.wikipedia.org/wiki/Rabies_in_animals&quot;&gt;Wikipedia&lt;/a&gt; once an animal is effected it lasts, let's say, no longer than for 2 weeks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, does it mean that there is a constant population of rabid animals that exists in order to pass this virus from one animal to another every 2 week on the average?&lt;/p&gt;&#xA;" OwnerUserId="5992" LastEditorUserId="5754" LastEditDate="2014-03-11T08:38:01.033" LastActivityDate="2017-05-02T17:14:19.133" Title="How do wild animals get rabies?" Tags="&lt;virus&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15644" PostTypeId="2" ParentId="15640" CreationDate="2014-03-11T07:33:38.967" Score="1" Body="&lt;p&gt;The donor cell retracts it pilus upon contact with another cell and both cells form a pore between the two cells, which allows the transfer of DNA. &#xA;Take a look at the image, I think this makes it clearer (from the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Pilus&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pili&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YhWY0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has even be seen in an electron microscope:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QKeNf.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-11T07:33:38.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15645" PostTypeId="2" ParentId="15643" CreationDate="2014-03-11T07:45:17.457" Score="13" Body="&lt;p&gt;Such viruses have a natural host, which might get sick, but is usually not killed by the virus. From there, the virus can get zoonotic (jump over species barriers) and infect other animals when it comes to contact. For Rabies the reservoir hosts are different, for the US these are bats, skunks and racoons. For more details, have a look on this &lt;a href=&quot;http://www.nimbios.org/workshops/talks/WS_cats_rabies_New.pdf&quot;&gt;PDF&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example for this is the SARS virus (a corona virus) which most likely lives in bats naturally and has jumped from there onto birds and from there infected humans. &lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-11T07:45:17.457" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="15646" PostTypeId="2" ParentId="15642" CreationDate="2014-03-11T07:53:53.630" Score="2" Body="&lt;p&gt;No, they can not do this. We don't have the enzymes to metabolize H&lt;suB&gt;2&lt;/suB&gt;S, besides that, it is highly toxic. H&lt;suB&gt;2&lt;/suB&gt;S can be used by some bacteria and archea (so called &lt;a href=&quot;http://en.wikipedia.org/wiki/Lithotrophic&quot; rel=&quot;nofollow noreferrer&quot;&gt;lithotrophic bacteria&lt;/a&gt;), but they are relatively rare.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sulfur is reduced by plants, which take it up in the form of sulfates and subsequently reduce it to form different sulphur compounds. Animals are dependent on the uptake of sulphur from plant sources, as the sulphur containing amino acids are essential (meaning the cannot be synthesized by themself). The pathway is relatively complex. The image below is from the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Sulfur_assimilation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sulphur assimilation&lt;/a&gt;, which I can also recommend, if you want to know all the details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3CvS4.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-11T08:11:47.020" LastActivityDate="2014-03-11T08:11:47.020" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15647" PostTypeId="2" ParentId="15553" CreationDate="2014-03-11T09:52:30.890" Score="2" Body="&lt;p&gt;Humans do not have the ability to move their outer ear in response to sound. Many animals can do that, and use it to determine the source of the sound waves. Thus, human outer ears are equipped with many &quot;hills and valleys&quot;. It does not provide amplification (because the waves can lose their energy bouncing around the ridges), but rather gives the brain more information about the sources' location in space. The brain calculates that location by determining minute differences in the time it takes for the sound to reach sensory cells in the inner ear on both sides. The shape basically attenuates the raw information. That way you get different properties of the sound wave that enters your ear depending on the angle at which it fell on you outer ear.&lt;/p&gt;&#xA;" OwnerUserId="5995" LastActivityDate="2014-03-11T09:52:30.890" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15648" PostTypeId="1" CreationDate="2014-03-11T10:46:05.573" Score="4" ViewCount="78" Body="&lt;p&gt;I am looking for a molecular tech' which could result in transient gene silencing in plants. The objective is to not make transgenic plant, but to use these tech' to silence a gene of interest for a short time. From my limited knowledge, I found that virus induced gene silencing (VIGS) may be an option, I wonder how easy and how long such silencing last? Is there any alternative method?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't have any candidate gene to be silenced at this moment, but the tissue will be flower. so it would be nice if the protocol works for flower.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance&lt;/p&gt;&#xA;" OwnerUserId="5997" LastEditorUserId="9079" LastEditDate="2014-09-04T16:27:27.177" LastActivityDate="2014-10-04T16:37:57.703" Title="Is it possible to elicit transient gene silencing by using virus induced gene silencing (VIGS) in plants?" Tags="&lt;gene-expression&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15649" PostTypeId="1" CreationDate="2014-03-11T11:15:20.653" Score="3" ViewCount="2944" Body="&lt;p&gt;There is hardly any subject as contested in the media as what humans should eat. Usually, such discussions are devoid of actual scientific reasoning, though they all claim to be backed by scientific studies (typically without naming those studies). The colorful spectrum of suggestions ranges from eating only bananas, to avoiding &quot;refined&quot; sugars and red meats, to avoiding meat altogether, to eating as much meat as possible etc. Clearly, many of them are completely contradictory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a purely biological, evidence-based perspective, how does an optimal human diet look? In particular, I'm interested in the following questions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Is there a single diet that can be recommended to all humans, regardless of lifestyle, which only needs to be scaled in quantity&lt;/strong&gt; (i.e. more physically active people should eat more of it) &lt;strong&gt;but not content?&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;Excluding diseases, &lt;strong&gt;does the optimal diet for an individual depend not only on their lifestyle but also on their genetic makeup?&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Knowing nothing about their genetic makeup and living an average industrialized-society lifestyle, what is the best guess for what a human should eat?&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Answers should be backed by solid reasoning and (ideally) references to verified (meta-)studies published in actual scientific journals supporting the claim. It seems strange to have to ask such a question, as one might expect it to have been answered thousands of times already, and of course it has, but the answers vary so wildly that I suspect I'm being fed hogwash mostly.&lt;/p&gt;&#xA;" OwnerUserId="6000" LastActivityDate="2014-03-11T16:55:09.177" Title="From a purely biological perspective, how does an optimal human diet look?" Tags="&lt;human-biology&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-03-12T06:38:33.933" ContentLicense="CC BY-SA 3.0" />
  <row Id="15650" PostTypeId="2" ParentId="15637" CreationDate="2014-03-11T16:28:04.413" Score="3" Body="&lt;p&gt;What you call influenza isn't a specific virus which is always the same, but a virus that has numerous different strains. Flu virus is constantly alive on this planet, and there are numerous different types, such as the ones which infect humans, the ones that infect birds, and occasionally a virus that mutates to infect humans although it shouldn't as it infects birds only.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Viruses evolve very quickly. The strain of flu virus which was rampant last year definitely won't be the one to look out for this year. What scientists are doing is a very difficult job - they're tracking the progress of different flu virus strains and trying to make an educated guess about the strain or strains which might spread the most during the flu season. And then they come up with a flu vaccine which is a mix that targets the several strains that were identified as being the biggest threat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a hit or miss kind of thing, and it's quite possible that the scientists get it wrong, or not necessarily wrong, but something happens in the virus evolution process that renders this year's vaccine useless.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, it's possible to get a flu vaccine and still get flu - if you happen to come in contact with a strain that wasn't targeted by the vaccine. Viruses evolve very very quickly, so vaccine isn't failsafe, virus can evolve in some other person, you come in contact with the virus and get infected despite being vaccined against the original strain.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2014-03-11T16:28:04.413" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15652" PostTypeId="2" ParentId="15649" CreationDate="2014-03-11T16:55:09.177" Score="3" Body="&lt;p&gt;No, there isn't a single diet that can be recommended from a biological perspective.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most popular diet from a pseudo-scientific perspective is the Paleo diet, saying we should eat what our ancestors in the Paleolithic were eating, but it makes a mistake of forgetting that our metabolism has evolved since then. There are also numerous other flaws in the Paleo diet but I won't go through them all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most notable example to use here would be dairy products, as we're among the few species that can drink milk at adult age. Drinking milk as an adult isn't normal, and yet we evolved the ability to do so. Some individuals can't drink milk, same goes for consuming gluten, nuts, and several other things, but the species as a whole can consume all of the above. Some people must avoid certain foods because of their individual genetic makeup though. Most evolved to process gluten and this ability is greatly responsible for the fact that there are 7 billion of us now. If you read an article &quot;gluten is bad&quot;, remember that gluten grew the human race and without it at least a third of the world's population would die through starvation. If you read an article about the Paleo diet, remember we wouldn't be here if the agricultural revolution didn't happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The correct answer would be - humans can consume everything that isn't toxic and provides them with energy. We're very capable omnivores, which is probably one of the reasons why we've done so well as a species. In other words, you won't die from eating processed sugar. There are healthier and less healthy foods, but none will kill you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are correct, there are numerous answers (or attempts to answer) to this question, and the way the research is concluded definitely doesn't help. Research is mostly conducted through polls designed to prove the scientist's original unverified claim, and virtually no research is conducted on the biological level, e.g. what happens to the body when you consume a certain carbohydrate. The whole field became pseudoscientific. The &quot;food pyramid&quot; is...pretty much wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Body needs proteins, body needs carbohydrates, body needs fat. You could come up with a vague answer if you eliminate the foods that body doesn't need, such as processed sugars, but it's still energy and you won't die from consuming it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no scientific research that consumation of any food, or elimination of any food, affects life span. Meaning, there's no differential survival rate depending on what you eat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To put things in perspective, imagine a lion preoccupied with attempting to answer whether it would be better for his body to eat an antilope or a gazelle. 10.000 calories is 10.000 calories and if he eats either he'll live another day.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2014-03-11T16:55:09.177" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15653" PostTypeId="2" ParentId="3610" CreationDate="2014-03-11T17:16:57.483" Score="1" Body="&lt;p&gt;Human life span is too long and not suitable for such studies, so mice are used pretty much because their life span is much shorter and because they're already used for pretty much everything.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mice and men as mammals have the same heritage and a metabolism which is very, very similar, almost identical - compared to the metabolism of insects, for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the millions of years of separate evolution made us the most capable omnivores on the planet, who learned to cook, became monogamous, evolved intelligence and grand-paternal care etc. We even evolved to drink milk as adults and eat gluten. So you can't possibly come up with conclusions about such complex species by looking at a simple creature that is an evolutionary dead end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're using mice for your study, you can find out how something affects a mammalian species in general, e.g. radiation, but not how nutrition affects humans - because human nutrition is unique. The scientists basically don't know much about nutrition to begin with, and I suppose they're trying to figure out the basics for now, some general rules which apply to all mammals, and that's why they're using mice. A less complex organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But you'll get nowhere if you're researching traits unique to the human race by looking at another species which doesn't have those traits.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2014-03-11T17:16:57.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15654" PostTypeId="2" ParentId="554" CreationDate="2014-03-11T17:29:55.290" Score="0" Body="&lt;p&gt;You'd be deprived of the vitamins and minerals which are found only in vegetables, but you'd live. There are vitamins and minerals in meat and other foods, plenty of them, and your metabolism would adapt to produce the proteins which are missing. Human body is a wonderful organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You wouldn't have a higher risk of cancer because cancer is a byproduct of life (the DNA repair mechanism and programmed cell death) and you can't get it by consuming meat or by not consuming vegetables.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You wouldn't gain weight if you're not consuming too much food. The math is simple, if you need 2000 calories, you'll gain weight if you're consuming 2050 calories of vegetables and lose weight if you're consuming 1950 calories of meat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your risk of heart disease wouldn't increase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only things which would change in this case would be the ones directly related to the nature of carbohydrates, proteins and fat. The carbohydrates in vegetables release energy slowly over a longer period of time, so if you'd eliminate vegetables you'd possibly be hungry more often. However, fat - and the glucose produced from it - would keep you going.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And you might have digestion problems because of lowered intake of fibers until your metabolism adapts.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2014-03-11T17:29:55.290" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15655" PostTypeId="2" ParentId="15553" CreationDate="2014-03-11T17:39:02.010" Score="-2" Body="&lt;p&gt;Evolution doesn't have a purpose. In that light, it's quite possible for an ear to be poorly adapted to hearing - which in fact it is compared to other species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stereo hearing (two ears, so you can better detect where the sound is coming from) is heritage from our ancestors, and I know for a fact it didn't evolve further in humans because there was no evolutionary pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, the topology isn't exclusive to our species and is heritage from our mammalian lineage. At some point in our lineage, the species/individuals who had this topology of the ear were able to gather sound waves better and that affected their survival so they passed on the trait to their offspring. Ear topology didn't evolve in humans.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2014-03-11T17:39:02.010" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15656" PostTypeId="1" CreationDate="2014-03-11T17:45:13.580" Score="3" ViewCount="66" Body="&lt;p&gt;I've reading about proteomics and how it can be used with mass spectrometry to sequence digested peptides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reading this &lt;a href=&quot;http://www.nature.com/nrm/journal/v5/n9/full/nrm1468.html&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; the author states (in box 2):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;peptide fragmentation induced by collisions with residual gas, and&#xA;  bond breakage mainly occurs through the lowest energy pathways - that&#xA;  is, cleavage of the amide bonds&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why is cleavage predominately at the amide bond? What makes the amide bond the lowest energy pathway?&lt;/p&gt;&#xA;" OwnerUserId="158" LastEditorUserId="3340" LastEditDate="2014-11-26T13:04:57.653" LastActivityDate="2014-11-26T13:04:57.653" Title="What makes the amide bond the lowest energy pathway?" Tags="&lt;energy&gt;&lt;mass-spec&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-12-08T16:34:05.870" ContentLicense="CC BY-SA 3.0" />
  <row Id="15658" PostTypeId="2" ParentId="15415" CreationDate="2014-03-11T17:45:48.860" Score="3" Body="&lt;p&gt;Nature isn't intelligent, genes aren't intelligent, and evolution doesn't have a purpose or a goal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations are random, and roughly 97% of them are deleterious while roughly 0.03% are advantageous for the species. This is the first prerequisite of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second one is differential survival. An organism with a better chance to survive or reproduce (because of a random mutation which was advantageous) will have a better chance of passing on that trait to his offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We're talking about billions of years, and billions and billions of organisms, and that's how complex structures evolve. The most notable example would be the eye. First, by random chance, an organism evolved a light receptor cell and had a better chance to survive. Then there were several light receptor cells, then there was a chamber, and so forth. Eventually you have the eye as we know it. It took billions of years.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2014-03-11T17:45:48.860" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15660" PostTypeId="2" ParentId="15618" CreationDate="2014-03-11T17:54:53.967" Score="0" Body="&lt;p&gt;Fat is digested just like any other food you consume, and eventually the energy you do not expend ends up as an energy reserve in shape of fat cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the second statement is right.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2014-03-11T17:54:53.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15664" PostTypeId="2" ParentId="15634" CreationDate="2014-03-11T21:32:06.637" Score="2" Body="&lt;p&gt;Another important reason to have mating types is to prevent self-fertilization or self-polination that produces less capable offspring. Because of this requirement, &lt;a href=&quot;http://en.wikipedia.org/wiki/Mating_type&quot; rel=&quot;nofollow&quot;&gt;mating types&lt;/a&gt; may evolve also for species that produce both types of gametes, or does not differentiate them into male and female gametes. Fertilization is only possible if gametes have different mating types.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It may be more than two mating types, but if there are only two, they are probably similar to &quot;sexes&quot; even if gametes do not look different.&lt;/p&gt;&#xA;" OwnerUserId="5924" LastActivityDate="2014-03-11T21:32:06.637" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15665" PostTypeId="2" ParentId="15546" CreationDate="2014-03-11T23:10:39.550" Score="-1" Body="&lt;p&gt;You could say it clasiffies as evolution only if you accept that the artificial things humans have done to bananas are actually natural occurences. I personally don't think they are, because intent is at play here, and evolution is a natural process without intent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution is not when something gets better. That's the misconception behind your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If humans would just happen to eat the tasty bananas first, what would happen is negative selection and all the remaining bananas (which lived long enough to reproduce) wouldn't be tasty. Bananas would get less tasty in order to survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What actually happened goes against the natural process of selection, and is something completely different to the concepts of evolution which led to us evolving intelligence, for example. This is just selective breeding. Nothing as grand as evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution is a natural process which led to intelligent species from single-cell organisms, and is a continuous process of random mutations being selected for or against by natural causes. Evolution has no intent and is a natural random process. A grand one, as all biology depends on it, and we depend on it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetic engineering, on the other hand, has intent to improve things, and happens on a much smaller scale than the natural process of evolution. Genetic engineering of any kind, whether it be tinkering with the genes or just inbreeding to create a new breed, is artificial and is being done by an intelligent creature as opposed to nature. Calling genetic engineering a tool for evolution is the same mistake that eugenics proponents made.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastEditorUserId="6003" LastEditDate="2014-03-12T19:21:55.917" LastActivityDate="2014-03-12T19:21:55.917" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15666" PostTypeId="2" ParentId="15352" CreationDate="2014-03-11T23:25:04.793" Score="0" Body="&lt;p&gt;I'd argue against using models of any sort, because the answer will be way off even if you use it on existing hard facts. Common sense is required here, I personally think it's silly to be trying to find a model for evolution when it is known evolution isn't a constant process and has no intent. Also, evolution can lead to a dead end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main reason why common sense is needed is that only then you can know when a species stopped evolving because there's no selective pressure. There are very few human groups today which are still evolving, but the species as a whole isn't evolving anymore and it won't in the future. There - just saved you the trouble of modeling future evolution because there won't be any.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2014-03-11T23:25:04.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15668" PostTypeId="2" ParentId="14216" CreationDate="2014-03-11T23:34:05.403" Score="0" Body="&lt;p&gt;It didn't have to benefit them, evolution has no intent and not all traits are advantageous. Not every thing we have in our bodies is there &quot;for a reason&quot;, some things are just there, others evolved, and some are vestigial (inherited from our ancestors).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A whale can move his tail up-down only because he's a mammal and can't ever be anything else, while fish move their tails left-right because they're fish and that's their heritage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Constantly growing nails never helped a single human, but they sure did help our ancestors which had claws and needed them for survival. We lost the claws but didn't lose the constantly growing trait. Basically, next time you trim your nails remember they (in shape of claws) saved your ancestor's life a long time ago and that's why you have them although you don't need them. He needed them.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2014-03-11T23:34:05.403" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15669" PostTypeId="2" ParentId="9342" CreationDate="2014-03-11T23:58:06.613" Score="2" Body="&lt;p&gt;Interesting question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The organism would have to be monogamous, that's for sure, otherwise it would be too competitive and it would be a beast - as chimps are. Chimps couldn't integrate into the modern society.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, monogamy is the prime prerequisite as it's also prerequisite for intelligence. Bipedalism is another obvious prerequisite, as you need an organism with fine motorics of front limbs - and fingers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For &quot;modern language&quot; you need high intelligence and the ability of abstract thinking. Same goes for reading and writing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans split from great apes between 8 and 4 million years ago. Problem here is that every new piece of fossil of a human ancestor is classified as a new species, so there's very little we're certain of. I'd say the first organism capable of doing the above things existed around 200.000 years ago. Either homo erectus or, more likely, a Neanderthal.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2014-03-11T23:58:06.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15672" PostTypeId="2" ParentId="14216" CreationDate="2014-03-12T02:05:05.747" Score="4" Body="&lt;p&gt;I can't say anything for sure (and, with questions like this, it's rare that anyone can), but my guess would be that human nails grow constantly for the same reason as the (analogous) claws of most mammals do: to keep them from accumulating damage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your bones, if they suffer mild to moderate damage, are &lt;a href=&quot;//en.wikipedia.org/wiki/Bone_healing&quot; rel=&quot;nofollow&quot;&gt;capable of healing&lt;/a&gt; through the concerted action of several specialized cell types in your body.  This healing process, however, is only possible because the bones are &lt;em&gt;inside&lt;/em&gt; the body, surrounded and permeated by living tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your nails, however, are simple sheets of &lt;a href=&quot;//en.wikipedia.org/wiki/Keratin&quot; rel=&quot;nofollow&quot;&gt;keratin&lt;/a&gt;, and contain no living cells that could heal them, nor any blood vessels that could keep such cells alive.  Being exposed to the outside of the body, outside the skin barrier, they cannot really support living tissue that could heal them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead, the way human nails (and animal claws, more generally) &quot;heal&quot; is by growing.  Since the nail itself cannot contain cells that would rebuild it, those cells are instead located in the &lt;a href=&quot;//en.wikipedia.org/wiki/Nail_matrix&quot; rel=&quot;nofollow&quot;&gt;nail matrix&lt;/a&gt;, which is located under the nail and from which the exposed part of the nail continually grows out of.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Indeed, the same is true of most of the exposed parts of your body: your hair and even the surface of your skin itself are also composed of non-living keratin constantly growing from an underlying matrix.  This is necessary to maintain the &lt;a href=&quot;//en.wikipedia.org/wiki/Skin_barrier&quot; rel=&quot;nofollow&quot;&gt;skin barrier&lt;/a&gt; between the interior and the exterior of the body.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason human nails must keep growing all the time is that they do continually wear down and suffer damage from various causes (and would surely have worn down much faster yet for our primitive ancestors, who had to sustain themselves through hard manual labor with few or no tools).  If your nails just stopped growing after you reached adulthood, they'd be in &lt;em&gt;horrible&lt;/em&gt; shape even just a few years down the road, not to mention decades later.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the rate at which human nails do grow is pretty slow &amp;mdash; it takes several months for a damaged fingernail to fully regrow, and up to a year for a toenail (a fact I can confirm from personal experience, having broken my toenail last summer) &amp;mdash; it's still enough to ensure that your nails will only bear less than a year's cumulative damage at any moment, rather than every nick and scratch and cut they've suffered during your entire lifetime so far.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a relatively sheltered modern lifestyle, it's quite likely that even this moderate growth rate may exceed normal wear on your nails, requiring them to be clipped regularly.  Still, the fact that you &lt;em&gt;can&lt;/em&gt; clip your nails (or, in a pre-modern society, just bite or scrape or cut them down) reduces the selection pressure against excessive nail growth.  On the other hand, &lt;em&gt;not&lt;/em&gt; having your nails grow back as fast as you wear them down through hard manual work could be quite bad for your fingers, and could easily reduce your working ability or even lead to harmful infections.  Thus, it makes sense that evolution has optimized out nails to grow at a rate that, on average, tends to somewhat exceed the typical rate of wear.&lt;/p&gt;&#xA;" OwnerUserId="239" LastActivityDate="2014-03-12T02:05:05.747" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15673" PostTypeId="2" ParentId="10008" CreationDate="2014-03-12T02:31:39.333" Score="9" Body="&lt;p&gt;Wild ducklings, like these &lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Female_Mallard_and_ducklings_in_Golden_Gate_Park.jpg&quot; rel=&quot;noreferrer&quot;&gt;baby Mallard ducks&lt;/a&gt;, are in fact typically only partly yellow:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Female_Mallard_and_ducklings_in_Golden_Gate_Park.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/3/3b/Female_Mallard_and_ducklings_in_Golden_Gate_Park.jpg/640px-Female_Mallard_and_ducklings_in_Golden_Gate_Park.jpg&quot; alt=&quot;Picture&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sup&gt;Photo by &lt;a href=&quot;https://sites.google.com/site/thebrockeninglory/&quot; rel=&quot;noreferrer&quot;&gt;TheBrockenInaGlory&lt;/a&gt; via Wikimedia Commons, used under the &lt;a href=&quot;https://creativecommons.org/licenses/by-sa/3.0/deed.en&quot; rel=&quot;noreferrer&quot;&gt;CC-By-SA 3.0&lt;/a&gt; license.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While I'm no expert, I would guess that the mottled yellow-brown coloring of the juveniles is, at least partially, protective coloration, just like the somewhat similar pattern on the adult female's feathers.  While it may appear conspicuous on open water, ducks in their natural habitat will often seek shelter among reeds and other vegetation, where the irregular pattern of light and shadow would create a very effective camouflage for the ducklings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the all-yellow ducklings of &lt;a href=&quot;https://en.wikipedia.org/wiki/Domestic_duck&quot; rel=&quot;noreferrer&quot;&gt;domestic ducks&lt;/a&gt;, these presumably arose via elimination of the darker parts of the coloring as a result of selective breeding, perhaps as a side effect of artificial selection for the white adult plumage found in many domestic ducks today.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, according to &lt;a href=&quot;https://doi.org/10.1038/s41467-018-04868-4&quot; rel=&quot;noreferrer&quot;&gt;a recent study of domestic duck genetics&lt;/a&gt;, it appears that the all-white plumage of domestic Pekin ducks is caused by a single recessive mutation to the &lt;a href=&quot;https://en.wikipedia.org/wiki/Microphthalmia-associated_transcription_factor&quot; rel=&quot;noreferrer&quot;&gt;MITF&lt;/a&gt; gene, which regulates melanin production.  The mutation, when homozygous, causes the normal melanin production pathway in the skin to be almost entirely shut off, so that the adult plumage is pure white regardless of what other plumage color genes the bird may be carrying (a fact apparently &lt;a href=&quot;http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC1208485&amp;amp;blobtype=pdf&quot; rel=&quot;noreferrer&quot;&gt;known for a long time&lt;/a&gt; from cross-breeding experiments, even though the specific mutation behind this effect was not determined until recently).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently, however, the yellow base pigmentation in young ducklings is &lt;em&gt;not&lt;/em&gt; affected by the MITF mutation, and thus appears even in individuals homozygous for it.  Presumably this is because the yellow color is produced via some other pathway, which is active in young ducks but gets shut off as they develop their adult plumage.  The brown pigmentation pattern overlaid on top of it in wild-type ducklings, however, &lt;em&gt;is&lt;/em&gt; controlled by MITF, and thus fails to appear in ducklings with two copies of the mutated version of the gene, leaving their juvenile plumage pure yellow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I can tell, the specific reason &lt;em&gt;why&lt;/em&gt; the yellow pigmentation in ducklings is not controlled by the MITF gene still remains unknown.  Or, if it is known, my Google search skills were not good enough to find it.&lt;/p&gt;&#xA;" OwnerUserId="239" LastEditorUserId="239" LastEditDate="2018-12-17T16:23:24.663" LastActivityDate="2018-12-17T16:23:24.663" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="15674" PostTypeId="1" CreationDate="2014-03-12T02:40:01.050" Score="5" ViewCount="1649" Body="&lt;p&gt;What is the minimum length of a DNA molecule for the ends to come in close enough contact that they can ligate. Assume there are free divalent cations in solution. Does anyone have any idea?&lt;/p&gt;&#xA;" OwnerUserId="3619" LastActivityDate="2014-03-12T03:30:31.853" Title="What is the minimum length required for a circular DNA ligation?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;plasmids&gt;&lt;ligation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15675" PostTypeId="2" ParentId="15674" CreationDate="2014-03-12T03:30:31.853" Score="5" Body="&lt;p&gt;I stumbled across this paper demonstrating it is between 150-200 base pairs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA flexibility studied by covalent closure of short fragments into circles&#xA;D Shore, J Langowski, and R L Baldwin&#xA;PNAS 1981 78 (8) 4833-4837&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/78/8/4833.full.pdf&quot;&gt;http://www.pnas.org/content/78/8/4833.full.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3619" LastActivityDate="2014-03-12T03:30:31.853" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15676" PostTypeId="1" CreationDate="2014-03-12T09:02:23.780" Score="1" ViewCount="236" Body="&lt;p&gt;My question is:-&lt;br&gt;&#xA;&lt;strong&gt;Only liquid water supports almost every living organism's metabolism, neither the vapour nor the condensed form of water does so. What is the chemical &amp;amp; the biological reason behind this fact?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5635" LastEditorUserId="3776" LastEditDate="2014-03-12T09:56:56.047" LastActivityDate="2014-03-12T10:00:35.733" Title="Why only water in liquid form is essential to live?" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15677" PostTypeId="2" ParentId="15676" CreationDate="2014-03-12T09:55:14.690" Score="1" Body="&lt;p&gt;A layman's view of the problem : &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's assume that water in liquid form was not necessary and organisms could survive on solid or gaseous water. What would some of the difficulties be to sustain such a life form?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Solid Form of water&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;How would the organism move without breaking or tearing itself apart? How would essential substances be transported from one part to another of the organism body?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Gaseous form&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;What would be the size of the organism? Gas has a much bigger volume than water.&lt;/li&gt;&#xA;&lt;li&gt;In order to transport nutrient molecules within the a gaseous body, a huge air pressure needs to be generated. Also, how will gravity be overcome while transporting these molecules? A lot of energy will be required to maintain such pressures.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I guess nature (which always takes an optimal path) asked such questions and found that water in it's liquid form was the most suited to support life on Earth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It need not be water alone. Other liquids &lt;strong&gt;&lt;em&gt;may&lt;/em&gt;&lt;/strong&gt; be able to support life as well. Only, we haven't discovered them yet. But whatever the substance, it's liquid form would seem to be an optimal solution for life.&lt;/p&gt;&#xA;" OwnerUserId="5799" LastActivityDate="2014-03-12T09:55:14.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15678" PostTypeId="2" ParentId="15676" CreationDate="2014-03-12T10:00:35.733" Score="1" Body="&lt;p&gt;Organisms evolve to fit the environment they are in and all of earths organisms have a typical body temperature of above 0C and 100C, the freezing and boiling points of water respectively. So water at this temperature is liquid and we have evolved to carry out reactions at this temperature and use water as the solution for many reactions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But why couldn't we have just done the same for water as a gas or a solid. Well as a gas it takes up a much larger volume, phenomenally higher and therefore we would either need to be massive or use high pressures. Additionally, containing reactions that carried out at this temperature with probably huge releases of energy is incredibly difficult. As a solid it is difficult to mobilise. As we dissolve essentially all of our bodies nutrients in water, or use the hydrophobic properties of fats to mobilise lipid soluble things, it would be incompatible with life. We rely very strongly on the ability of water to flow. Solids can't. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An interesting question is why water and not another liquid?&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-03-12T10:00:35.733" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15679" PostTypeId="1" AcceptedAnswerId="15696" CreationDate="2014-03-12T10:03:41.307" Score="1" ViewCount="136" Body="&lt;p&gt;I have 2 transgenic lines of Drosophila. I would like to cross them and get both transgene in the same fly. To start this cross, does it matter which fly is female or male? Or as long as the female is virgin, it does not matter?&lt;/p&gt;&#xA;" OwnerUserId="5630" LastActivityDate="2014-03-13T07:23:44.607" Title="Drosophila Crosses" Tags="&lt;genetics&gt;&lt;drosophila&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15680" PostTypeId="1" AcceptedAnswerId="15682" CreationDate="2014-03-12T11:58:04.097" Score="0" ViewCount="232" Body="&lt;p&gt;Please, see the picture where the areas (1,2,3) look little yellow:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Xz3r1.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think these areas are fat, platelets and/or air.&#xA;I think 3 is fat/platelets while 1 is air/platelets.&#xA;There also exists white thrombosis, which can explain something here.&#xA;However, I do not it is that because those white areas do not contain thrombocytes or leucocytes (not sure, since I have no more closer picture; probably you can see it from this).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think at the moment that these white areas are endothelium-lined spaces.&#xA;However, I am not sure about (3).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What can these three areas be in the coronary thrombosis?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-03-12T13:09:24.470" Title="What are these white areas of coronary thrombosis?" Tags="&lt;pathology&gt;&lt;red-blood-cell&gt;&lt;pathogenesis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15681" PostTypeId="2" ParentId="15514" CreationDate="2014-03-12T12:36:19.750" Score="9" Body="&lt;p&gt;One of the possible adjustments of these mathematical models is to introduce a &quot;place to hide&quot;, making some (small) percent of the prey population not accessible (or much more difficult to access) for predators. After the number of predators decreases from starvation, prey individuals are relatively safer outside the &quot;place to hide&quot; and can grow over this limit before the number of predators increases again. &lt;/p&gt;&#xA;" OwnerUserId="5924" LastEditorUserId="5924" LastEditDate="2014-03-13T08:53:42.017" LastActivityDate="2014-03-13T08:53:42.017" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15682" PostTypeId="2" ParentId="15680" CreationDate="2014-03-12T13:09:24.470" Score="2" Body="&lt;p&gt;Low density lipoproteins can be taken up by the macrophages under a number of circumstances (typically high circulating levels is the most important). These macrophages are called foam cells. The macrophage can then die and deposit this cholesterol and fatty material onto a vessel wall in the context of atherosclerosis. Additionally tissue damage as a result of release of damaging chemicals from the macrophage can induce an inflammatory response recruiting more macrophages (worsening the problem in a cyclical manner) and result in fibrosis and platelet activation. I think this would cause the white stuff you point to. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary I think you're right, it's a combination of fat, cholesterol, fibrotic tissue and platelets. 3 is more likely macrophages and platelets whilst 1 and 2 are more likely a combination of all the above. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-03-12T13:09:24.470" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15683" PostTypeId="1" AcceptedAnswerId="15684" CreationDate="2014-03-12T17:46:48.443" Score="6" ViewCount="5544" Body="&lt;p&gt;When I did a research, most of the sources say that &lt;strong&gt;orca&lt;/strong&gt; is &lt;strong&gt;one of&lt;/strong&gt; the fastest. But I could not find a source that says it is actually the fastest. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some sources say that &lt;strong&gt;Dall's porpoises&lt;/strong&gt; rival orcas in speed. And there are other kinds of porpoises and dolphins that comes into question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any scientific research with measurements? Or does anyone have any detailed knowledge about this topic?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Also it would be nice to know top 10 fastest marine mammals, so the question becomes: what are the fastest marine mammals?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: This scientific research might be difficult to conduct also so you can explain the situation as well.&lt;/p&gt;&#xA;" OwnerUserId="6019" LastActivityDate="2018-12-11T14:07:52.887" Title="What is the fastest marine mammal?" Tags="&lt;zoology&gt;&lt;mammals&gt;&lt;marine-biology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15684" PostTypeId="2" ParentId="15683" CreationDate="2014-03-12T18:41:57.587" Score="5" Body="&lt;p&gt;According to the &lt;a href=&quot;http://marinebio.org/oceans/marine-mammals.asp&quot; rel=&quot;noreferrer&quot;&gt;MarineBio conservation society&lt;/a&gt;, the fastest marine mammal is the &lt;a href=&quot;http://marinebio.org/species.asp?id=32%20Common%20Dolphin&quot; rel=&quot;noreferrer&quot;&gt;Common Dolphin&lt;/a&gt;, with a top speed of 64 km/h. That places it just above the Zebra on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Fastest_animals#Mammals%20Wikipedia%20list%20of%20fastest%20mammals&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia list of fastest mammals&lt;/a&gt;. (I wasn't able to find a primary source for this immediately, so take it with a pinch of salt.)&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="6019" LastEditDate="2014-03-14T18:27:19.727" LastActivityDate="2014-03-14T18:27:19.727" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15685" PostTypeId="1" CreationDate="2014-03-12T19:47:05.610" Score="1" ViewCount="4221" Body="&lt;p&gt;&lt;strong&gt;How deadly is a stab in the back?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Video games, movies, and other fiction would have us believe that a backstab against a foe with a modestly-sized blade leads to immediate and certain death, having a 100% success rate and causing death virtually instantaneously.  How close is this to reality?  How does the lethality of a puncture wound to the back compare to such wounds delivered to other areas of the body?  What is the primary target in such an attack in terms of internal organs, and what variables effect its projected success?&lt;/p&gt;&#xA;" OwnerUserId="3713" LastEditorUserId="16651" LastEditDate="2015-12-31T20:01:42.410" LastActivityDate="2015-12-31T20:01:42.410" Title="Is a stab wound to the back lethal?" Tags="&lt;death&gt;&lt;injury&gt;&lt;surgery&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ClosedDate="2016-01-02T00:45:58.727" ContentLicense="CC BY-SA 3.0" />
  <row Id="15686" PostTypeId="2" ParentId="5524" CreationDate="2014-03-12T19:50:48.043" Score="-3" Body="&lt;p&gt;Inbreeding isn't negative at all, so one couple would suffice for colonization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Inbreeding fixes recessive traits and the ones displaying unwanted traits can be culled. Actually, inbreeding is one of the most potent weapons of evolution, it speeds things up greatly. We went through a major bottleneck event ourselves and lived to tell the tale.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact number of individuals needed for a healthy species that will survive X number of generations depends on the species though. To maintain healthy genetic diversity and establish enough different alleles to allow for sustainability of the species. I don't remember the exact number but I think for humans it was something between 1000 or 10000, and if you get below that number the species will likely go extinct by natural causes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, everything is completely different when you have full control over who mates with who. But still, in the above example of 1 couple, they can successfully start a seemingly healthy population, but due to low genetic diversity they - as a species - won't be able to respond to, say, increased radiation, changes in atmosphere, a virus, bacteria, shortage of food, etc. That's why 1 couple is basically enough, but to ensure longetivity of the species 25 couples is far from enough.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2014-03-12T19:50:48.043" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="15688" PostTypeId="1" AcceptedAnswerId="15689" CreationDate="2014-03-12T21:24:08.860" Score="0" ViewCount="98" Body="&lt;p&gt;Are there resources for interesting or fun facts about biology, for example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;fastest animal/bird/insect&lt;/li&gt;&#xA;&lt;li&gt;largest organ in human body&lt;/li&gt;&#xA;&lt;li&gt;largest virus&lt;/li&gt;&#xA;&lt;li&gt;largest genome&lt;/li&gt;&#xA;&lt;li&gt;largest de novo synthesized genome &lt;/li&gt;&#xA;&lt;li&gt;largest protein&lt;/li&gt;&#xA;&lt;li&gt;longest experiment done so far&lt;/li&gt;&#xA;&lt;li&gt;most expensive experiment done so far&lt;/li&gt;&#xA;&lt;li&gt;biggest discovery by luck&lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You get the idea. It would be nice if these is a curated &quot;database&quot; for all these interesting facts that might be fascinating to lay people as well.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2014-03-12T21:48:50.733" Title="Resources for interesting facts about biology" Tags="&lt;general-biology&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-03-13T18:23:22.437" ContentLicense="CC BY-SA 3.0" />
  <row Id="15689" PostTypeId="2" ParentId="15688" CreationDate="2014-03-12T21:35:41.757" Score="3" Body="&lt;p&gt;Whether you find the content interesting or not I can't say, but you might want to check out the &lt;a href=&quot;http://bionumbers.hms.harvard.edu&quot; rel=&quot;nofollow&quot;&gt;BioNumbers&lt;/a&gt; database. It has a category for &lt;a href=&quot;http://bionumbers.hms.harvard.edu/search.aspx?task=searchbyamaz&quot; rel=&quot;nofollow&quot;&gt;&quot;Amazing bionumbers&quot;&lt;/a&gt; and a &lt;a href=&quot;http://www.weizmann.ac.il/plants/Milo/index.php?page_name=BioNumberOfTheMonth&quot; rel=&quot;nofollow&quot;&gt;&quot;BioNumber of the Month&quot;&lt;/a&gt; section.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-03-12T21:48:50.733" LastActivityDate="2014-03-12T21:48:50.733" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15690" PostTypeId="1" AcceptedAnswerId="15706" CreationDate="2014-03-13T01:16:31.810" Score="0" ViewCount="36" Body="&lt;p&gt;Are animals able to plan hunts, give tasks if they do it in groups and fulfil it adapted to the current situation? Do they use unique tactics for special circumstances (e.g. based on experiences)  or they just act from instincts?&lt;/p&gt;&#xA;" OwnerUserId="6024" LastActivityDate="2014-03-13T15:25:58.667" Title="Do animals follow tactics?" Tags="&lt;ethology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15691" PostTypeId="1" AcceptedAnswerId="15692" CreationDate="2014-03-13T01:53:29.597" Score="1" ViewCount="687" Body="&lt;p&gt;I am stuck on a Homework Question. It says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Evaluate the following statement: “Natural selection works like a copy&#xA;  editor; it works only with&#xA;  what is already present in a population.” (Note: Copy editors check&#xA;  written material before it is set into type, to correct errors in&#xA;  spelling, grammar, usage, and style.)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I thick that Natural Selection is not like a Copy editor because:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Natural Selection has no set direction, which means it does not decide on anything. A weak organism might be able to survive by luck. While a copy editor knows the mistakes and eliminates them instantly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can I get some help on this. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="5584" LastEditorUserId="5584" LastEditDate="2014-03-13T02:36:26.023" LastActivityDate="2014-03-13T02:53:53.367" Title="Is Natural Selection like a Copy Editor?" Tags="&lt;evolution&gt;&lt;homework&gt;&lt;natural-selection&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="15692" PostTypeId="2" ParentId="15691" CreationDate="2014-03-13T02:53:53.367" Score="3" Body="&lt;p&gt;Evolution, in the Darwinian sense, can be broadly described as the interaction of three processes: inheritance, mutation and selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of those three processes, &lt;strong&gt;mutation&lt;/strong&gt; is the one that produces novel innovation, by occasionally producing new alleles that did not exist in the parent population.  It is, however, a blind innovator &amp;mdash; the novel genotypes produced by mutation are essentially random, and no more likely to be advantageous to the organisms carrying them than one would expect by change (i.e. not very likely at all).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Selection&lt;/strong&gt;, whether natural or artificial, is what happens when the organisms carrying the diverse genomes produced by mutation end up competing for survival and reproductive opportunities against each other and against their environment.  It acts on the diversity generated and replenished by mutation, favoring those mutations that happen to confer a survival advantage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, &lt;strong&gt;inheritance&lt;/strong&gt; ensures that the beneficial alleles generated by mutation and filtered by selection get passed on to successive generations, allowing them to spread in the population and to be further modified by successive mutations.  In a sense, inheritance and mutation can be seen as opposite sides of the same coin: the more faithfully genes are inherited, the less mutations there are.  Yet both are necessary for evolution; an organism that never mutates obviously could not evolve, but neither could one that mutated so much that all of its genes were totally scrambled in each generation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, this whole process is stochastic in nature &amp;mdash; even the best adapted individual may die without offspring due to simple bad luck, just as even a maladapted individual may get lucky and prosper.  But over generations, there is nonetheless a statistical tendency for individuals carrying certain alleles, or combinations of them, to be more fecund than others, and those will be the alleles that will eventually come to dominate the population (assuming they're not it turn displaced by even more successful mutants).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, I would personally say that, of these three components of evolution, (natural) selection indeed &quot;works only with what is already present in a population.&quot;  However, it's not really like a copy editor, since it does not seek to &quot;correct errors&quot; in the genome; it's more akin to a &lt;a href=&quot;//en.wikipedia.org/wiki/Slush_pile&quot; rel=&quot;nofollow&quot;&gt;slush reader&lt;/a&gt;, who just sorts the incoming texts into ones to keep and ones to throw away.&lt;/p&gt;&#xA;" OwnerUserId="239" LastActivityDate="2014-03-13T02:53:53.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15695" PostTypeId="2" ParentId="15603" CreationDate="2014-03-13T07:10:27.183" Score="0" Body="&lt;p&gt;You can try Disgene package in Cytoscape.&lt;/p&gt;&#xA;" OwnerDisplayName="user6026" LastActivityDate="2014-03-13T07:10:27.183" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15696" PostTypeId="2" ParentId="15679" CreationDate="2014-03-13T07:23:44.607" Score="1" Body="&lt;p&gt;As long as none of your genes are X-linked and you use virgins it shouldn't matter and you'd get the same proportion of double homozygotes. You may want to perform a reciprocal cross (&lt;a href=&quot;https://en.wikipedia.org/wiki/Reciprocal_cross&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Reciprocal_cross&lt;/a&gt;) if you don't know what chromosome these genes are on (though flybase.org is useful too). &lt;/p&gt;&#xA;" OwnerUserId="6027" LastActivityDate="2014-03-13T07:23:44.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15699" PostTypeId="1" AcceptedAnswerId="16930" CreationDate="2014-03-13T13:41:52.167" Score="0" ViewCount="152" Body="&lt;p&gt;Autoregulation is the maintenance of constant blood flow to an organ in spite of fluctuations in Blood pressure.&#xA;It involves the relaxation of myocardium and contraction.&#xA;It is local.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that autoregulation is best done in the brain, well in kidneys and badly in skeletal muscle.&#xA;I am interested how it is in the heart.&#xA;I think it should be at least good.&#xA;Brain can be thought more important.&#xA;However, I am not sure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How good is the autoregulation of the blood flow in the heart?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-12-26T09:22:05.610" Title="What is the quality rate of intrinsic autoregulation in the heart?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;blood-circulation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15700" PostTypeId="1" AcceptedAnswerId="15702" CreationDate="2014-03-13T14:37:27.383" Score="1" ViewCount="612" Body="&lt;p&gt;When puting a real time PCR, parameter CT, which means threshold cycle, is used. What does it mean really? according to wikipedia &quot;The number of cycles at which the fluorescence exceeds the threshold is called the threshold cycle (Ct)&quot;&#xA;could anyone put it in conext?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="3657" LastEditDate="2014-03-13T17:28:15.640" LastActivityDate="2014-03-13T17:28:15.640" Title="Real time PCR parameter CT" Tags="&lt;pcr&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15701" PostTypeId="1" AcceptedAnswerId="15716" CreationDate="2014-03-13T14:39:20.963" Score="2" ViewCount="13443" Body="&lt;p&gt;I would like to study cells and looking for a microscope that would allow me to see:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;groups of cells&lt;/li&gt;&#xA;&lt;li&gt;individual cell&lt;/li&gt;&#xA;&lt;li&gt;cells organelles&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I would like to target insects and mammal tissue.&lt;br&gt;&#xA;I would be very grateful for info in magnification ranges that I need and maybe some popular models of microscopes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a difference between digital and non-digital microscopes for that purpose? &lt;/p&gt;&#xA;" OwnerUserId="6031" LastActivityDate="2014-03-14T06:57:10.567" Title="What kind of a microscope do I need to see cell organelles?" Tags="&lt;cell-biology&gt;&lt;microbiology&gt;&lt;cell&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15702" PostTypeId="2" ParentId="15700" CreationDate="2014-03-13T14:47:53.713" Score="2" Body="&lt;p&gt;Realtime PCR uses a fluorescent dye which binds to double-stranded DNA and thus allows to measure the growing amount of DNA by each cycle. The DNA added to the reaction also binds the fluorescent dye and makes some part of the fluorescent background. When the PCR reaction starts, it takes a while until enough DNA is synthesized to go over the background and to be able to reliable distinguish the signal from the noise. I think this becomes clearer, when you look at the image below (from the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/probe/doc/TechQPCR.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;NIH&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/z3jh2.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Ct is the point where the signal can be distinguished from the background when it enters the exponential grwoth phase. The no template control stays below this threshold.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-13T16:11:53.787" LastActivityDate="2014-03-13T16:11:53.787" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15703" PostTypeId="1" AcceptedAnswerId="16931" CreationDate="2014-03-13T15:06:08.750" Score="0" ViewCount="108" Body="&lt;p&gt;I know that there exist Continuous capillaries (skeletal muscle, adipose tissue, connective tissue, pulmonary circulation), Fenestrated capillaries (small intestine, renal glomerulus, exocrine glands), and Discontinuous capillaries (sinusoids; liver, spleen, bone marrow and hypophysis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I am not sure how to characterise these.&#xA;The diameter of capillaries is different for each.&#xA;I have not managed to find any figure which present the relationship of diameter of these capillaries.&#xA;I have reviewed books Guyton, Pocock and Lange.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the diameters of capillaries in different organs?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-27T16:40:25.403" Title="To characterise diameter of capillaries in organs" Tags="&lt;physiology&gt;&lt;blood-circulation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15706" PostTypeId="2" ParentId="15690" CreationDate="2014-03-13T15:25:58.667" Score="3" Body="&lt;p&gt;Do some research on wolves hunting. They certainly have tactics that change depending on the prey that they're hunting, the terrain, danger posed by other members of the prey's herd or family (if any), etc. They're very capable of learning, and use fairly complex communications. They run in packs, live with their mother for a number of years, and have a rather involved family structure that allows for the passing on of behaviors learned from previous generations. It would be difficult to tease out exactly which behaviors are instinctual, and which are learned, but you could say the same of humans as well.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-03-13T15:25:58.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15708" PostTypeId="1" AcceptedAnswerId="15725" CreationDate="2014-03-13T20:11:00.040" Score="8" ViewCount="194" Body="&lt;p&gt;Every once in a while, there is an official announce that a new species has been discovered. For example, paleontologists have &lt;a href=&quot;http://blogs.discovermagazine.com/d-brief/2014/03/12/pygmy-dinosaur-cousin-of-t-rex-roamed-the-arctic/#.UyJEl4UVAVM&quot; rel=&quot;noreferrer&quot;&gt;recently discovered&lt;/a&gt; a dinosaur they named &lt;em&gt;Nanuqsaurus hoglundi&lt;/em&gt;, which really resembles Tyrannosaurus Rex, but in a smaller version. It also lived during the same era. Is there something that indicates it's a cousin of the T-Rex, and not Mr. Rex's son?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other small dinosaurs include the &lt;a href=&quot;http://en.wikipedia.org/wiki/Compsognathus&quot; rel=&quot;noreferrer&quot;&gt;Compsognathus&lt;/a&gt;, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Microraptor&quot; rel=&quot;noreferrer&quot;&gt;Microraptor&lt;/a&gt; and &lt;a href=&quot;http://dinosaurs.about.com/od/typesofdinosaurs/tp/Five-Smallest-Dinosaurs.htm&quot; rel=&quot;noreferrer&quot;&gt;others&lt;/a&gt;. Why were they classified as new species when they were discovered?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering evolution over a few million years, my guess is that some earlier species may have been smaller and evolved into more complex animals, bigger bodies, horns, frills, etc.&lt;/p&gt;&#xA;" OwnerUserId="6033" LastEditorUserId="6033" LastEditDate="2014-03-14T12:32:42.093" LastActivityDate="2015-01-07T21:33:12.120" Title="How to determine whether a newly discovered dinosaur is not a young one and not an entirely different species?" Tags="&lt;taxonomy&gt;&lt;palaeontology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15709" PostTypeId="1" CreationDate="2014-03-13T22:46:22.547" Score="2" ViewCount="162" Body="&lt;p&gt;Say someone eats 100 calories of chocolate vs. 100 calories of carrots. Something tells me that eating the chocolate will lead to you generating more fat. Will it? Is it harder to burn the calories that you consumed from the chocolate?&lt;/p&gt;&#xA;" OwnerUserId="6035" LastEditorUserId="6035" LastEditDate="2014-03-13T23:34:08.493" LastActivityDate="2014-03-13T23:41:58.050" Title="Is it easier to burn a calorie of fat or a calorie of a carbohydrate?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;nutrition&gt;&lt;fitness&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15710" PostTypeId="2" ParentId="15709" CreationDate="2014-03-13T23:41:58.050" Score="4" Body="&lt;p&gt;It isn't burning of the calorie you should consider as once digested different calories are stored in the same manner, it is actually the digestion itself. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Proteins are by far the most energy requiring foods to digest such that around 20% of the calories in proteins are used in extracting them. In comparison carbohydrates are much easier at around 5-10% whilst fats are even easier to digest. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But think of it in simple terms, chewing a vegetable and digesting it down and the relatively sheer quantity of mass you need to make it calorifically the same value as chocolate means that yes 100 calories isn't 100 calories.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All then in terms of real life application, our bodies respond to how much we eat. If we eat a large volume of low calorie food we will eat less calories in total. This also plays an important role.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20613890&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/20613890&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-03-13T23:41:58.050" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15711" PostTypeId="1" CreationDate="2014-03-14T02:17:03.217" Score="3" ViewCount="107" Body="&lt;p&gt;Just curious, how much solar energy can power an (herbivore) animal? Specifically, is it enough sunlight on Mercury (4 to 10 times brighter than on Earth) to &quot;feed&quot; a zebra? Will it be sufficient at 10x more effective photosynthesis? Notwithstanding lack of atmosphere, water being buried deep and other minor problems, of course :)&lt;/p&gt;&#xA;" OwnerUserId="6036" LastEditorUserId="22057" LastEditDate="2019-01-26T23:41:36.867" LastActivityDate="2019-01-26T23:41:36.867" Title="How much solar energy required to produce enough food for a herbivore?" Tags="&lt;metabolism&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="15712" PostTypeId="1" AcceptedAnswerId="15717" CreationDate="2014-03-14T02:43:04.737" Score="2" ViewCount="8934" Body="&lt;p&gt;Say I cough on my table, then someone else touches it and picks up something I've got... how is it that these things can live outside the body, how long can they manage it, and how long is generally 'safe' to consider something no longer carrying these germs?&lt;/p&gt;&#xA;" OwnerUserId="6037" LastEditorUserId="6037" LastEditDate="2016-02-17T18:00:10.997" LastActivityDate="2018-12-10T14:30:20.747" Title="How do viruses or bacteria survive outside the body long enough to spread?" Tags="&lt;bacteriology&gt;&lt;pathology&gt;&lt;virus&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15714" PostTypeId="2" ParentId="15712" CreationDate="2014-03-14T03:32:12.267" Score="1" Body="&lt;p&gt;Viruses really take to heart the idea of &quot;quantity, not quality.&quot; Like animals and plants, viruses and bacteria are a &lt;strong&gt;Completely&lt;/strong&gt; different ball game (even more so than animals and plants). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you maybe know, you have bacteria floating around you in the air right now. Realistically, a single T4 bacteriophage (a type of virus) has a life cycle of about 20-30 minutes at 37 &amp;deg;C. However, in this time period, it often reproduces in a bacterium and creates tens if not hundreds more phage particles using the bacterium like a machine that was hacked to do its bidding. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only way to prevent a virus from attacking is through vaccinations and other preemptive measures, as it is so difficult to prevent reproduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria are so different they, for all intensive purposes, cannot be approximated. For a &lt;strong&gt;rough&lt;/strong&gt; approximation, somewhere from hours to weeks.&lt;/p&gt;&#xA;" OwnerUserId="5859" LastEditorUserId="1320" LastEditDate="2014-03-14T14:10:40.420" LastActivityDate="2014-03-14T14:10:40.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15715" PostTypeId="2" ParentId="15711" CreationDate="2014-03-14T05:29:45.860" Score="5" Body="&lt;p&gt;BMR is the amount of energy an animal uses just by being alive. BMR is proportional to the mammal's mass. More precisely, BMR is proportional to the mammal's mass to the power of 3/4. A 0.1 kg mammal has a BRM of 10 kcal/day. Using the aforementioned proportionality, a 600 kg mammal (average mass of a cow) will have a BMR of 6800 kcal/day.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that a cow would need about 6800 kcal of energy per 24 hours (1440 minutes) to survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The amount of solar energy reaching the earth’s atmosphere is 0.00194 kcal per square centimeter per minute. Since, according to you, there is 10 times the amount of sun in Mercury, there should be 0.0194 kcal per square centimeter per minute hitting Mercury. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;0.0194 kcal per minute for 720 minutes (counting only day - since there is no sun during the night) equals 13.968 kcal per square centimeter per day. At this rate, the sun has to hit an area of 486 cm squared to harness enough energy for the cow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The average cow needs about 6800 kcal per day to survive (BMR)&lt;/li&gt;&#xA;&lt;li&gt;On Mercury, the sun generates 13.968 kcal per square cm&lt;/li&gt;&#xA;&lt;li&gt;Which means, the sun has to hit an area of 486 square cm&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In one sentence:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;In order to power a cow on Mercury, the sun has to hit an area of 486 cm for 720 minutes.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;To learn more:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Kleiber%27s_law&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Kleiber%27s_law&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ase.org/resources/measuring-number-calories-sunlight&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ase.org/resources/measuring-number-calories-sunlight&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6038" LastEditorUserId="27918" LastEditDate="2019-01-26T17:14:08.217" LastActivityDate="2019-01-26T17:14:08.217" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="15716" PostTypeId="2" ParentId="15701" CreationDate="2014-03-14T06:51:07.513" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;groups of cells&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A normal light microscope. 4x-20x magnification&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;individual cell&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Lo resolution: Light microscope with 40x magnification. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;High resolution: Confocal microscope with 40-100x magnification. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;cell organelles&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Low resolution: Confocal microscope with &gt;=60x magnification. &#xA;Note: some organelles are easier to visualize while others are difficult. With confocal you can manage to see almost all of them with low resolution i.e you will be able to detect their location and distribution but wont be able view their fine structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To view the structure of organelles you would definitely need an Electron Microscope.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there a difference between digital and non-digital microscopes for that purpose? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you are not too much into the optics of it then I guess it wont matter. I prefer if it has an analog mode along with a digital mode. Image acquisition is anyways digital. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Popular models: Leica, Zeiss and Olympus are popular brands. You select the model as per your requirements. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-03-14T06:57:10.567" LastActivityDate="2014-03-14T06:57:10.567" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15717" PostTypeId="2" ParentId="15712" CreationDate="2014-03-14T11:24:57.833" Score="4" Body="&lt;p&gt;It depends entirely on the environment the virus or bacterium is in and also the size of it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Virus&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regards to viruses, the most important thing is typically whether or not the virus has an outer membrane or envelope.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Non-enveloped viruses such as rhinoviruses, noroviruses and adenoviruses can in fact survive for long periods outside the host (up to several days) whereas viruses with membranes such as HIV, influenza and the herpes viruses which do well in the host survive for shorter time periods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Experiments with rhinoviruses and influenza viruses have shown potential survival times ranging from a few minutes to 48 hours or more.  They remain active longer on stainless steel, plastic and similar hard surfaces than on fabric and other soft surfaces. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is because many enveloped viruses rely on the proteins on the surface of the membrane to attach to the host cell, this envelope is generally sensitive to degradation to sunlight and normal cleaning procedures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Outbreaks associated with the non-enveloped viruses can continue for many months due to their relative stability in the environment, think of winter vomiting outbreaks, hand foot and mouth in animals as good examples of this phenomenon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Bacteria&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because bacteria can undergo metabolism, synthesise proteins etc. for themselves, their life span is usually longer. If we split them into gram positive and gram negative its easier to discuss. Gram positive bacteria have a protein coat that prevents drying allowing them to survive longer. An example is the bacteria Staphylococcus aureus, which is responsible for toxic shock syndrome, food poisoning, and wound infections. With its protein coat it can withstand temperature and humidity extremes. The spore may survive for weeks on dry clothing using sloughed skin cells for food. The Bacillus anthracis, the anthrax bacteria, can also form spores and survive tens to hundreds of years. This is in comparison to gram negative which need humidity. An infamous example is Escherichia coli which survives typically only a few hours at best. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1320" LastEditDate="2014-03-14T14:09:07.673" LastActivityDate="2014-03-14T14:09:07.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15718" PostTypeId="1" CreationDate="2014-03-14T14:07:14.413" Score="3" ViewCount="307" Body="&lt;p&gt;I am a statistician and I'd like to test my new method on biological data. For this I am looking for genotype data for a number of individuals. That is, I am looking for something like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&#xA;                    | Individual 1 | Individual 2 | Individual 3 | Individual 4 | ....&#xA;Chromosome 1 SNP 1  | AA           | BA           | AB           | BB           |&#xA;Chromosome 1 SNP 2  | AB           | AA           | AB           | BA           |&#xA;Chromosome 2 SNP 1  | BB           | AB           | BB           | AB           |&#xA;etc.                    &#xA;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I don't really care about the species. Ideally I'd like to have data for complex and less complex genotypes (different number of chromosomes and number of SNP's). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any publicly available data sets like this? I have been searching the internet, but I can't find any.&lt;/p&gt;&#xA;" OwnerUserId="6039" LastActivityDate="2014-04-21T13:42:31.327" Title="Publicly available genotype data?" Tags="&lt;genetics&gt;&lt;genomics&gt;&lt;genomes&gt;&lt;snp&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15719" PostTypeId="2" ParentId="15718" CreationDate="2014-03-14T14:25:58.897" Score="1" Body="&lt;p&gt;How about the allele frequency database?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://alfred.med.yale.edu/alfred/index.asp&quot; rel=&quot;nofollow&quot;&gt;http://alfred.med.yale.edu/alfred/index.asp&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the main problems with SNP databases is that there are a lot of them so you can get lost quickly. This sight gives some overview on the available resources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.humgen.nl/SNP_databases.html&quot; rel=&quot;nofollow&quot;&gt;http://www.humgen.nl/SNP_databases.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="5699" LastActivityDate="2014-03-14T14:25:58.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15720" PostTypeId="1" AcceptedAnswerId="15722" CreationDate="2014-03-14T15:05:21.707" Score="1" ViewCount="2292" Body="&lt;p&gt;I have been reading about next-generation sequencing technologies that can sequence long reads. Even though the origin of my question is sequencing technologies, the question I am asking is about the basics of DNA biochemistry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the issues in manipulating DNA samples seems to be the ability to circularize long linear DNA molecules into circular DNA molecules. What are the technical challenges of circularising DNA molecules longer than 50Kbp?&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="658" LastEditDate="2014-03-15T11:30:22.297" LastActivityDate="2014-03-15T11:30:22.297" Title="circularizing DNA molecules?" Tags="&lt;dna&gt;&lt;protocol&gt;&lt;ligation&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15721" PostTypeId="1" AcceptedAnswerId="15731" CreationDate="2014-03-14T15:12:52.927" Score="2" ViewCount="356" Body="&lt;p&gt;I just read an article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Homo_%28genus%29&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; and noticed that some similarities between &lt;em&gt;Homo Erectus&lt;/em&gt; and &lt;em&gt;Homo Sapiens&lt;/em&gt; in the &quot;Comparative table of Homo species&quot;. My question is;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to say that some members of &lt;em&gt;Homo Erectus&lt;/em&gt; species&#xA;have survived up to now and they are living in modern world as members&#xA;of &lt;em&gt;Homo Sapiens&lt;/em&gt;?&lt;/p&gt;&#xA;" OwnerUserId="6041" LastEditorUserId="3340" LastEditDate="2014-03-15T07:17:50.440" LastActivityDate="2014-03-15T07:17:50.440" Title="Evolution of Homo Erectus to Homo Sapiens" Tags="&lt;human-biology&gt;&lt;evolution&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15722" PostTypeId="2" ParentId="15720" CreationDate="2014-03-14T15:48:14.983" Score="2" Body="&lt;p&gt;For ligation of a linear molecule to occur, the two ends must come together at the active site of the DNA ligase. In a simple molecular cloning experiment the aim is usually to avoid recircularisation of a cut plasmid vector, and instead to get a new fragment of DNA inserted into the vector. However because the ends of the linearised circular plasmid are tethered together (by being ends of the same molecule) they are more likely to encounter each other than they are to encounter the end of an incoming fragment. This is usually overcome, in part, by increasing the relative concentration of the target fragment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are aiming to recircularise a long fragment then the opposite effect will come into play: the ends of individual long molecules will be much more independent and so the end of another molecule will be likely to compete successfully for ligation. In theory this effect could be overcome by reducing the DNA concentration, but I assume that this is impractical for other reasons.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-14T15:48:14.983" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15724" PostTypeId="2" ParentId="15718" CreationDate="2014-03-14T17:22:31.393" Score="2" Body="&lt;p&gt;that's the stated purpose of the thousand genomes project. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;the thousand genomes project has.. 1000 genomes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;its all downloadable. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.1000genomes.org/&quot; rel=&quot;nofollow&quot;&gt;http://www.1000genomes.org/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-03-14T17:22:31.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15725" PostTypeId="2" ParentId="15708" CreationDate="2014-03-14T18:16:10.533" Score="6" Body="&lt;p&gt;Diagnosing extinct species is even more difficult than extant taxa (see &lt;a href=&quot;https://biology.stackexchange.com/questions/11240/transitivity-of-species-definitions/11243&quot;&gt;this question&lt;/a&gt;). Because systematists describing fossil species (usually) only have skeletons, they compare to other fossils. You are correct that diagnosing a species from only a skeleton can be tricky. What defines what you call a genus, a species, etc.? How morphologically &lt;em&gt;dis&lt;/em&gt;similar can two skeletons be before you call them different species? The running joke is that if you found fossils of a chihuahua skeleton and a great dane skeleton, you would certainly call them different species. But by modern biological species concepts, they are the same species. Then there are extant species that are essentially indistinguishable in terms of their skeletons, but do not interbreed, and so are probably different species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes there is consensus, and sometimes there is not. This disagreement can lead to a description of a new species by one person being reclassified (&quot;revised&quot; is the term used) as another species. There are lots of examples of this among dinosaurs. Most famously, &lt;em&gt;Brontosaurus&lt;/em&gt; was revised as &lt;a href=&quot;http://www.npr.org/2012/12/09/166665795/forget-extinct-the-brontosaurus-never-even-existed&quot; rel=&quot;nofollow noreferrer&quot;&gt;actually being Apatosaurus&lt;/a&gt;. More recently, and relevant to your question, &lt;em&gt;&lt;a href=&quot;http://www.smithsonianmag.com/science-nature/montanas-dueling-dinosaurs-134669023/?no-ist=&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nanotyrannus&lt;/a&gt;&lt;/em&gt; is thought by some to be a juvenile &lt;em&gt;Tyrannosaurus rex&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So then how did Fiorillo and Tykowski, who described &lt;em&gt;Nanuqsaurus hoglundi&lt;/em&gt;, decide that it was (1) not just a juvenile T. rex and (2) that it was a new species? Their rationale is laid out really well in their paper, primarily in the sections &quot;Diagnosis&quot; and &quot;Description&quot;. You rightly picked out the two questions that paleontologists reading this paper would want to know.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;&lt;em&gt;Nanuqsaurus&lt;/em&gt; is not a juvenile:&lt;/h3&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The dorsomedial edge of the maxilla is marked by deep pockets separated by pronounced transverse ridges. These together formed a strong peg-in-socket articulation between the dorsal margin of the maxilla and the ventrolateral edge of the nasal. The same kind of deeply interlocking naso-maxillary contact is a well-documented character that is also present only in developmentally mature individuals of the derived tyrannosaurines &lt;em&gt;Daspletosaurus torosus&lt;/em&gt;, &lt;em&gt;Tarbosaurus bataar&lt;/em&gt;, and &lt;em&gt;Tyrannosaurus rex&lt;/em&gt; &lt;a href=&quot;http://www.npr.org/2012/12/09/166665795/forget-extinct-the-brontosaurus-never-even-existed&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;, [6], [20], [21], [22]. The nasal-maxilla contact is either smoothly grooved or bears only weak scalloping in immature individuals and more basal tyrannosauroids &lt;a href=&quot;http://www.npr.org/2012/12/09/166665795/forget-extinct-the-brontosaurus-never-even-existed&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;, [6]. The presence of this feature in DMNH 21461 is evidence that the material also represents a developmentally mature individual.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What they are saying here is that maxilla (part of the front of the upper jaw) in &lt;em&gt;Nanuqsaurus&lt;/em&gt; has a very characteristic relationship to the nasal bone in which they form a peg-and-socket joint. This relationship is found in tyrannosaurine dinosaurs like &lt;em&gt;Tyrannosaurus&lt;/em&gt;, &lt;em&gt;Daspletosaurus&lt;/em&gt;, and &lt;em&gt;Tarbosaurus&lt;/em&gt;. But more importantly, it is only found in adult tyrannosaurines. So they conclude that &lt;em&gt;Nanuqsaurus&lt;/em&gt; is an adult.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;&lt;em&gt;Nanuqsaurus&lt;/em&gt; is a distinct species from &lt;em&gt;Tyrannosaurus&lt;/em&gt; and other tyrannosaurines&lt;/h3&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In all three hypotheses of phylogeny, &lt;em&gt;Nanuqsaurus hoglundi&lt;/em&gt; was found to be a derived tyrannosaurine, the sister taxon to the &lt;em&gt;Tarbosaurus&lt;/em&gt; + &lt;em&gt;Tyrannosaurus&lt;/em&gt; clade (Figure 6). This node was supported by a single unambiguous character, the presence of a dorsoventrally tall, paired sagittal crest on the frontal. The age of &lt;em&gt;Nanuqsaurus hoglundi&lt;/em&gt; (70-69Ma) is consistent with its place in the recovered hypothesis of tyrannosauroid phylogeny, positioned in time between the more basal &lt;em&gt;Daspletosaurus torosus&lt;/em&gt; (Middle to Late Campanian) and the more derived &lt;em&gt;Tyrannosaurus rex&lt;/em&gt; (latest Maastrichtian) among other North American tyrannosaurines.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors ran a phylogenetic analysis of characters coded for &lt;em&gt;Nanuqsaurus&lt;/em&gt; and about 20 other taxa. &lt;em&gt;Nanuqsaurus&lt;/em&gt; has enough shared characteristics to put to solidly among tyrannosaurine (near &lt;em&gt;Tyrannosaurus&lt;/em&gt;, &lt;em&gt;Daspletosaurus&lt;/em&gt;, and &lt;em&gt;Tarbosaurus&lt;/em&gt;). But, importantly, it has a characteristic that none of these others have: &quot;the presence of a dorsoventrally tall, paired sagittal crest on the frontal.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on its being an adult and having a character that is not found anywhere else among tyrannosaurines, Fiorillo and Tykowski name a new species. I'm simplifying what they did, but that's the general idea. To their credit, they acknowledge that there is not a lot distinguishing the new species and discuss in much more detail their rationale and the implications of their results. &lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-01-07T21:33:12.120" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15726" PostTypeId="1" AcceptedAnswerId="15728" CreationDate="2014-03-14T22:19:03.057" Score="5" ViewCount="2273" Body="&lt;p&gt;According to this article, &lt;a href=&quot;http://www.nature.com/news/dna-has-a-521-year-half-life-1.11555&quot; rel=&quot;nofollow&quot;&gt;DNA has a half life of 512 years&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Oldest_viable_seed&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; claims that there are seeds planted as old as 31000 years&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Doing the basic math $100 / (2^{30000/512})$ we get that only about &#xA;$2.2989191*10^{-16}%$ of the DNA would be left&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how do these plants still grow when replanted?&lt;/p&gt;&#xA;" OwnerUserId="1625" LastEditorUserId="115" LastEditDate="2014-03-16T10:00:46.683" LastActivityDate="2014-03-16T10:00:46.683" Title="If DNA has a half life of about 500 years, how can old seeds be planted?" Tags="&lt;dna&gt;&lt;seeds&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15727" PostTypeId="1" AcceptedAnswerId="15749" CreationDate="2014-03-14T22:29:51.010" Score="5" ViewCount="5947" Body="&lt;p&gt;When I was first started to write this question, I wanted to know how species evolve to have a different chromosomal arrangement, such as having two pairs of chromosomes instead of one? However, I think I have resolved my misunderstanding by reading:&#xA;&lt;a href=&quot;http://scienceblogs.com/pharyngula/2008/04/21/basics-how-can-chromosome-numb/&quot; rel=&quot;noreferrer&quot;&gt;http://scienceblogs.com/pharyngula/2008/04/21/basics-how-can-chromosome-numb/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My basic misunderstanding was that I thought animals with a different number of chromosomes couldn't reproduce, which appears to be wrong. My question is now, are there examples of animals that can interbreed that have a different number of chromosomes (particularly offspring that are not sterile)? Is there a species that is known to have a variation in the number of chromosomes (yet, somehow, hasn't yet resulted in complete speciation); or are there two species that can be interbred and result in fertile offspring?&lt;/p&gt;&#xA;" OwnerUserId="6043" LastActivityDate="2018-07-14T00:06:50.987" Title="Examples of animals with different number of chromosomes that can interbreed?" Tags="&lt;genetics&gt;&lt;chromosome&gt;&lt;speciation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15728" PostTypeId="2" ParentId="15726" CreationDate="2014-03-14T22:33:20.790" Score="13" Body="&lt;p&gt;That half-life was for temperatures of 13.1ºC. In more ideal conditions, such as for temperature of −5 ºC or drier conditions, the half-life would be longer. The Wikpedia article in fact states that the seeds that were 31,000 years old were frozen under permafrost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The original article estimates that the half-life at −5 ºC (for a 30 bp fragment of mtDNA from bone) would be 158,000 years. I'm not sure how well this data can be extrapolated to seeds.&lt;/p&gt;&#xA;" OwnerUserId="6043" LastEditorUserId="6043" LastEditDate="2014-03-14T22:54:43.507" LastActivityDate="2014-03-14T22:54:43.507" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15729" PostTypeId="1" AcceptedAnswerId="15734" CreationDate="2014-03-14T22:52:34.257" Score="1" ViewCount="140" Body="&lt;p&gt;Let's say that I have a population of &lt;em&gt;Mus musculus&lt;/em&gt; in the lab. I divide it in a control group and a test group. The test group is constantly subjected to a stress (example: elevated UV radiation). Both groups are allowed to reproduce for 20 generations.&#xA;I want to fully characterize and compare what changed in each offspring (control vs test group) by using omics. The objective is then to integrate all these information in a new database with the pathways that change and by what magnitude.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Should I use genomics or/and exomics or/and epigenomics?&lt;/li&gt;&#xA;&lt;li&gt;If I do one of the above and proteomics, why could I need the transcriptomics for?&lt;/li&gt;&#xA;&lt;li&gt;Would the metabolomics, which are mainly punctual measures, add any valuable information?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This is a purely didatic exercise.&lt;/p&gt;&#xA;" OwnerUserId="6044" LastEditorUserId="3340" LastEditDate="2014-03-15T06:05:39.327" LastActivityDate="2014-03-15T06:22:44.460" Title="Omics integration questions" Tags="&lt;genomics&gt;&lt;transcription&gt;&lt;epigenetics&gt;&lt;exons&gt;&lt;metabolomics&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-03-16T22:35:32.847" ContentLicense="CC BY-SA 3.0" />
  <row Id="15730" PostTypeId="1" AcceptedAnswerId="17712" CreationDate="2014-03-15T01:29:28.467" Score="4" ViewCount="2987" Body="&lt;p&gt;Mother kangaroos are able to rear multiple joeys (young kangaroos) at different stages of development at the same time. According to Wikipedia, &quot;the mother is able to produce two different kinds of milk simultaneously for the newborn and the older joey still in the pouch.&quot; What biological mechanisms are able to ensure that the correct joey gets the correct kind of milk? Do different teats produce different types of milk and somehow the joeys know which teat to suck from; or is each teat able to deliver both types of milk and the teat is able to tell from the mouth conformation (or something else) which type of milk to deliver?&lt;/p&gt;&#xA;" OwnerUserId="6043" LastActivityDate="2014-05-28T06:16:53.223" Title="How do Kangaroo mothers deliver the correct kind of milk to the correct joey?" Tags="&lt;mammals&gt;&lt;milk&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15731" PostTypeId="2" ParentId="15721" CreationDate="2014-03-15T01:44:34.960" Score="1" Body="&lt;p&gt;It is not plausible that members of Homo erectus would survive and remain a separate species from Homo sapiens. For members of Homo erectus to survive implies that there wasn't significant interbreeding with Homo sapiens, which would require a significant population of Homo erectus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is some evidence that Homo erectus and other hominids interbred with Homo sapiens. So it is more likely that there may be some people with more genetic traits from Homo erectus than others. However, by significant interbreeding, there currently only exists a single species that may contain ancestors from multiple hominid species.&lt;/p&gt;&#xA;" OwnerUserId="6043" LastActivityDate="2014-03-15T01:44:34.960" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15733" PostTypeId="1" AcceptedAnswerId="15735" CreationDate="2014-03-15T06:08:03.790" Score="2" ViewCount="75" Body="&lt;p&gt;Would expression of GroEL and GroES in erythrocytes be a potentially effective therapeutic strategy for sickle cell disease? Why or why not?&lt;/p&gt;&#xA;" OwnerUserId="5164" LastEditorUserId="1320" LastEditDate="2014-03-15T07:25:31.087" LastActivityDate="2014-03-15T07:25:31.087" Title="Would expression of GroEL and GroES in erythrocytes be a potentially effective therapy for sickle cell disease?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15734" PostTypeId="2" ParentId="15729" CreationDate="2014-03-15T06:22:44.460" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Should I use genomics or/and exomics or/and epigenomics?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Depends on what you want to look at. Whole genome sequencing will give you all the mutations. If you are interested only in the coding part of the genome then you can go for exome sequencing. Though, exome sequencing will save your time and resources considerably, you may lose out a lot of relevant information from the non-coding and regulatory part of the genome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Epigenomics is a very broad term. There are several aspects to it. You can go for the DNA methylome, Nucleosome positioning, or ChIP-Seq for Histone modification/variants. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would suggest that if you can afford it then go for whole genome sequencing. Next choice would be exome sequencing. Once you have these data it might be relevant to add the third layer of DNA methylome. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If I do one of the above and proteomics, why could I need the transcriptomics for?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Transcriptomics is easier and better standardized than proteomics. There are also many good analysis tools. &lt;/li&gt;&#xA;&lt;li&gt;There are several ncRNA, which has been shown to play important role in cellular homeostasis and gene regulation. You will miss out those. &lt;/li&gt;&#xA;&lt;li&gt;You will save money. The reagents used for the transcriptomics experiments are the same as the ones used for the genomics experiments. Proteomics is a different domain altogether. You might need to look for collaborators. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Would the metabolomics, which are mainly punctual measures, add any valuable information?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Sure, they do add information. Whether of great value or not depends on the study that you are carrying out. For e.g if you are studying the role of stress in diabetes then doing a metabolomics study may be of great value. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-03-15T06:22:44.460" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15735" PostTypeId="2" ParentId="15733" CreationDate="2014-03-15T06:32:40.750" Score="3" Body="&lt;ol&gt;&#xA;&lt;li&gt;GroEL and GroES are multiprotein chaperonin complexes: Not so easy to ectopically express&lt;/li&gt;&#xA;&lt;li&gt;Erythrocytes do not have nucleus: you cannot stably express anything in mature erythrocytes.&lt;/li&gt;&#xA;&lt;li&gt;If your aim is to do a stable gene expression (which would require genomic integration), the better way is to do a gene therapy: culture haematopoetic stem cells, Correct the mutation by homologous recombination. Put the cells back into the bone marrow.   &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-03-15T06:32:40.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15736" PostTypeId="1" AcceptedAnswerId="15902" CreationDate="2014-03-15T08:19:51.773" Score="13" ViewCount="22679" Body="&lt;p&gt;I had laser eye surgery a decade ago, but in recent years my eyesight has become significantly myopic. I consulted an ophthalmologist to see if this was eye strain because I work at computers a lot, or part of a natural degradation of the eye over time, or both. My ophthalmologist seems to believe that in my case I'm youngish enough that the natural degradation with age is minimal, and that it's mostly eye strain that is my problem. She believes I can get my eyesight back to roughly 90% of my post-surgery sight ability, if I can reduce eye strain. She gave me some eye drops to help with dryness, and recommended various ways to for me to help my eyes recuperate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I decided to look into eye strain to learn more about what conditions cause it and what can alleviate it. What I learned is that the lens of &lt;a href=&quot;http://en.wikipedia.org/wiki/Accommodation_of_the_eye#Theories_of_mechanism&quot; rel=&quot;noreferrer&quot;&gt;the eye needs to be flatter to accommodate focusing on far objects&lt;/a&gt;, and rounded to focus on near objects. The way the lens becomes flat is by using spring-like connective tissue called &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Choroid&quot; rel=&quot;noreferrer&quot;&gt;choroids&lt;/a&gt;&lt;/em&gt; that pull it taught. Attached to these choroids are muscles called &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ciliary_muscle&quot; rel=&quot;noreferrer&quot;&gt;ciliary muscles&lt;/a&gt;&lt;/em&gt; that stretch the choroids out when they contract. This action causes the choroids to stop pulling on the lens, and the lens will retract into a more rounded shape. So, when the ciliary muscles are relaxed, you can see far. When the ciliary muscles are contracted, you can see close up. &lt;a href=&quot;http://www.yorku.ca/eye/ciliary.htm&quot; rel=&quot;noreferrer&quot;&gt;This diagram from the York University website&lt;/a&gt; was the clearest explanation I have come across:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tM4cr.gif&quot; alt=&quot;ciliary muscles and choroids&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, the reason for my current inability to focus on far objects is that so much focusing on close objects, mainly computer monitors, is straining my eyes. In order to regain the ability to focus on far objects, I need to reduce strain and allow the muscles to relax. If they relax, the choroids can pull the eye to the flatter shape needed to see far.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I can't reconcile that model with how I understand the mechanics of the other muscles in my body. If I go to the gym and run or lift weights, or in any way expose my muscles to work, they respond by getting stronger without sacrificing the ability to stop contracting. The muscles in my body don't lose the ability to relax, no matter how much I train them. I have never heard of anyone who worked out too hard or too long such that their bicep would remain in a permanent state of contraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, in my experience, after a hard workout, it's &lt;em&gt;impossible&lt;/em&gt; to prevent my muscles from relaxing and resisting doing more work. When I do a bicep curl at the gym, and I do it to the point that I can't lift the weight anymore, my muscle gives up and I drop the weight. Similarly, if I've spent a long time looking at close up objects, shouldn't my ciliary muscles give up, allowing the choroids to take over, making clear far vision the unavoidable outcome?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea that my ciliary muscles need to relax in order to see far also seems to contradict my personal anecdotal experience. Sometimes I am able to see far away, but I can't hold it for more than a few seconds. If I try to maintain focus on far objects for too long, I get an uncomfortable feeling in my eyes that is hard to describe, but it's a form of pain that forces me to give up. My vision goes blurry, and I can only see close objects again. If my bicep worked the same way, it would be as if it hurt to let my arm hang straight down with a weight, and the only way to alleviate it would be to raise the weight, which makes no sense. I feel like the effort is in seeing far, and that when I'm tired, I can only see close up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's not that the case that I think that all medical research on the eye has it backwards, it must be that there is some aspect of this that I am not seeing (pun intended).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can it be that the ciliary muscles, unlike other muscles, lose their ability to relax?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is it that my ciliary muscles don't become exhausted and allow the choroids to take over by default?&lt;/p&gt;&#xA;" OwnerUserId="6047" LastEditorUserId="6047" LastEditDate="2014-03-17T07:48:22.710" LastActivityDate="2018-06-15T08:47:11.983" Title="Why can't ciliary muscles in the human eye relax like other muscles?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="5" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15737" PostTypeId="1" CreationDate="2014-03-15T11:43:40.143" Score="5" ViewCount="325" Body="&lt;p&gt;As a follow-up of a &lt;a href=&quot;https://biology.stackexchange.com/q/15720/658&quot;&gt;previous question&lt;/a&gt;, I would like to know what enzymes or protein complexes have been used to manipulate DNA samples into stabilizing DNA loops.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read that cohesin is one of such enzymes, but works as a transcription factor by binding specific DNA motifs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hR6hv.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My interest is in knowing what other enzymes will create DNA loops with no DNA motif biases from a DNA extraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a follow-up question to &lt;a href=&quot;https://biology.stackexchange.com/q/15720/658&quot;&gt;this one&lt;/a&gt;, as ultimately I would like to know if there could be any ways of optimizing the process of DNA circularization of very long stretches of human (or mammalian) double-stranded DNA, from several kilobases to megabases, by first creating stable DNA loops that leave two DNA ends close by for a more effective ligation process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any ideas?&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2016-04-12T10:47:07.967" Title="enzymes that stabilize DNA loops" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15739" PostTypeId="2" ParentId="15726" CreationDate="2014-03-15T14:00:18.870" Score="7" Body="&lt;p&gt;The source paper for the article is this one: &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/279/1748/4724&quot;&gt;The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils&lt;/a&gt; (available for free). The crux of their methodology is given in the abstract &quot;By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa...&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the article you linked is talking about DNA survival &lt;em&gt;after cell death&lt;/em&gt; in fossilised bones. Seeds have not undergone cell death; they're still a small collection of living cells designed to survive in a state of near inactivity until the conditions are suitable for them to germinate. It's therefore not at all clear that we should expect the results from this experiment to generalise to seeds. Doubly so given that, as pointed out by Jonathan, the fossils were effectively held at around 13.1ºC whereas the seeds in the study you mention were found in the permafrost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, the seeds &lt;em&gt;weren't&lt;/em&gt; viable on their own. It was only with significant intervention that scientists were able to get the embryos contained within the seeds to grow.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2014-03-15T14:00:18.870" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15740" PostTypeId="1" AcceptedAnswerId="15748" CreationDate="2014-03-15T15:10:01.503" Score="1" ViewCount="717" Body="&lt;p&gt;I read that protein interactions found using high throughput methods are less trustable than those found using low throughput methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, searching for interaction of BRCA2 on BioGRID, I got &lt;a href=&quot;http://thebiogrid.org/107142/summary/homo-sapiens/brca2.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; result. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, we won't be sure about the interaction of BRCA2 with SIRT1 as it has been found with a high throughput method.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question: Could you give me a very simple explanation of what is the meaning of high and low throughput techniques ? (I have a vague idea reading it on web but I am not satisfied with my understanding.) Why is high throughput not reliable in this case?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One reason I can think is that they involve mostly in vitro studies.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2014-03-15T21:27:03.943" LastActivityDate="2014-03-16T14:04:22.913" Title="Why are low throughput methods more trustable for protein interaction?" Tags="&lt;bioinformatics&gt;&lt;database&gt;&lt;protein-interaction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15741" PostTypeId="1" AcceptedAnswerId="15758" CreationDate="2014-03-15T15:41:41.003" Score="0" ViewCount="7329" Body="&lt;p&gt;Imagine you swallow something up and not everything gets out of the windpipe (this is possible right?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would it be possible for the lung to handle with the rest implying that it is organic? Would it slowing absorb it?&lt;/p&gt;&#xA;" OwnerUserId="6050" LastActivityDate="2019-07-05T16:45:39.827" Title="Does the lung absorb organic food?" Tags="&lt;food&gt;&lt;lungs&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15742" PostTypeId="1" AcceptedAnswerId="20344" CreationDate="2014-03-15T16:16:46.833" Score="7" ViewCount="142" Body="&lt;p&gt;Let’s consider two linked loci $A$ and $B$ that are both bi-allelic. In consequence, we have four different possible &lt;a href=&quot;http://en.wikipedia.org/wiki/Haplotype&quot; rel=&quot;nofollow&quot;&gt;haplotypes&lt;/a&gt; $A_1B_1$, $A_1B_2$, $A_2B_1$, $A_2B_2$, which frequencies are $X_1$, $X_2$, $X_3$, $X_4$ respectively. Let the linkage disequilibrium $D$ be defined as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$D=X_1X_4 - X_2X_3$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The change in haplotype frequencies through time is given by:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\delta X_1 = \frac{X_1(w_1 - \bar w) - Drw_{14}}{\bar w}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\delta X_2 = \frac{X_2(w_2 - \bar w) - Drw_{14}}{\bar w}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\delta X_3 = \frac{X_3(w_3 - \bar w) - Drw_{14}}{\bar w}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\delta X_4 = \frac{X_4(w_4 - \bar w) - Drw_{14}}{\bar w}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;$r$ is the recombination rate between the loci $A$ and $B$&lt;/li&gt;&#xA;&lt;li&gt;$\bar w$ is the mean fitness (sum of the fitnesses of each haplotype weighted by their relative frequencies)&lt;/li&gt;&#xA;&lt;li&gt;$w_{14}$ is the fitness of the (diploid) individual that has the 1st and the 4th haplotypes&lt;/li&gt;&#xA;&lt;li&gt;$w_i = X_1w_{i1} + X_2w_{i2} + X_3w_{i3} + X_4w_{i4}$&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The change in allele frequency of locus $A$ is $x$ and $1-x$. The change of allele frequency of locus $B$ is $y$ and $1-y$. Those changes are given by the addition of haplotypes frequencies:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\delta x = \delta X_1 + \delta X_2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\delta y = \delta X_1 + \delta X_3$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don’t fully understand these formulae! Could you please help me making sense of them. Especially of the presence of the expression $-Drw_{14}$.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0199661731&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-05-02T14:41:10.873" LastActivityDate="2014-08-08T15:33:41.153" Title="Selection on linked loci in a diploid population" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;molecular-biology&gt;&lt;population-dynamics&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15743" PostTypeId="1" AcceptedAnswerId="24072" CreationDate="2014-03-15T16:22:46.993" Score="5" ViewCount="762" Body="&lt;p&gt;Linkage disequilibrium $\left(D\right)$ for two bi-allelic loci is defined as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$D=X_{11}X_{22} - X_{12}X_{21}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $X_{11},\ X_{12},\ X_{21},\ X_{22}$ are the frequencies of the haplotypes $A_1B_1$, $A_1B_2$, $A_2B_1$, $A_2B_2$ respectively (the subscript number correspond to the two different alleles and $A$ and $B$ correspond to the two different loci)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My questions are&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;How is $D$ defined for more loci and a greater number of alleles?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How is $D$ defined when the number of alleles differ from locus to locus?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3340" LastEditDate="2014-11-14T16:44:37.960" LastActivityDate="2014-11-21T16:44:47.623" Title="Linkage disequilibrium with multiple alleles and loci" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15744" PostTypeId="1" AcceptedAnswerId="15754" CreationDate="2014-03-15T17:04:56.613" Score="-2" ViewCount="89" Body="&lt;p&gt;I am thinking which hormonal and chemical effects from:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;catecholamines&lt;/li&gt;&#xA;&lt;li&gt;thyroxin&lt;/li&gt;&#xA;&lt;li&gt;corticosteroids&lt;/li&gt;&#xA;&lt;li&gt;sex hormones&lt;/li&gt;&#xA;&lt;li&gt;prostaglandins&lt;/li&gt;&#xA;&lt;li&gt;Ca2+&lt;/li&gt;&#xA;&lt;li&gt;Na+&lt;/li&gt;&#xA;&lt;li&gt;K+&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;can be be regarded as metabolites i.e. intermediates or products of metabolism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I got this question&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Account for chemical and hormonal effects on the heart.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and I am thinking if I should include metabolites as a factor as&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Metabolites by intrinsic autoregulative system locally&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;because the autoregulation of heart is very important factor in the physiology of the heart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can you regard some metabolites as having hormonal and chemical effects?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-03-16T17:30:58.140" LastActivityDate="2014-03-16T17:30:58.140" Title="Which chemical and hormonal effects on heart are by metabolites?" Tags="&lt;physiology&gt;&lt;endocrinology&gt;&lt;cardiology&gt;&lt;blood-circulation&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ClosedDate="2014-11-26T04:50:22.523" ContentLicense="CC BY-SA 3.0" />
  <row Id="15745" PostTypeId="1" AcceptedAnswerId="15751" CreationDate="2014-03-15T17:10:21.073" Score="2" ViewCount="119" Body="&lt;p&gt;Let's think of a species which has four generations per year and which population size changes from season to season so that the population size is 100 in summer, 200 in spring, 50 in autumn and 20 in winter for example. In such case, the effective population size $N_e$ can be calculated by:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$N_e = \frac{n}{\sum_{i=1}^n\frac{1}{N_i}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $n$ is the number of generation per year (4 in my example) and each $N_i$ correspond to the population size in one season.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you please provide an explanation of why this formula (based on the harmonic mean) holds true to define the effective population size?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0199661731&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3624" LastEditDate="2014-03-15T23:55:30.060" LastActivityDate="2014-03-15T23:55:30.060" Title="Effective population size when the population sizes varies from season to season" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;population-dynamics&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15746" PostTypeId="1" AcceptedAnswerId="23108" CreationDate="2014-03-15T18:39:53.920" Score="4" ViewCount="513" Body="&lt;p&gt;From this &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0199661731&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;: If &lt;a href=&quot;http://en.wikipedia.org/wiki/Overlapping_generations_model&quot; rel=&quot;nofollow noreferrer&quot;&gt;generations are overlapping&lt;/a&gt;, then the effective population size $N_e$ does not equal the population size $N$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know mathematical formulations in order to find the effective population size $N_e$ when the sex-ratio is biased &lt;a href=&quot;http://en.wikipedia.org/wiki/Effective_population_size#Non-Fisherian_sex-ratios&quot; rel=&quot;nofollow noreferrer&quot;&gt;$\left(N_e = \frac{4N_mN_f}{N_m+N_f}\right)$&lt;/a&gt; or when the population size varies cyclically through time &lt;a href=&quot;https://biology.stackexchange.com/questions/15745/effective-population-size-when-the-population-sizes-varies-from-season-to-season&quot;&gt;$\left(N_e = \frac{n}{\sum_{i=1}^n\frac{1}{N_i}}\right)$&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the effective population size in a population with overlapping generations?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-01-12T12:18:18.100" Title="How to calculate the effective population size ($N_e$) with overlapping generations?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15748" PostTypeId="2" ParentId="15740" CreationDate="2014-03-15T19:41:11.850" Score="1" Body="&lt;p&gt;This article is a bad example, it has been retracted. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24201285&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&#xA;But this doesn't matter for the methods.&#xA;This is usually done by so called &quot;genome wide association studies&quot;. There you compare the regulation of your group of interest with a &quot;normal&quot; group to find genes which are differently expressed. This is something we did: We overexpressed a transcription factor in a cell line and compared it to the untransfected cell line, which doesn't have this factor. The comparision brings up differently expressed genes. This is either done with microarrays or today more like by ChIP-sequencing (let me know, if you want to know more, I can go into the details).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you analyze such data, you first cut-off all data, which is below a certain threshold to be sure, that you reduce the number of false positives. A low threshold for the recognition of changes means that you are more likely to have false positive genes in your final list. This might happen due to changes in the cell or the conditions, secondary effects and so on. And you will also have signals, which appear statistically and which are false positive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you choose your threshold too high, you will reduce the number of false positives, but on the downside you will also generate false negatives, since you refuse genes which only have a relatively low change but are real. The balance between this is not always easy. As a rule of thumb usually everything which changes at least twofold in expression is used (unless you control better).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even when filtered, the output of the experiment will still contain some false positives. Then you will also record some secondary effects, meaning that you gene of interest regulates a second, which regulates a third. Since both will come up in the analysis, it will look like that the third gene is regulated by the first (and not the second, as it would be correct). And these are the reasons why usually every intereaction between two genes (or better: Between a protein and a gene when talking about a transcription factor or two proteins) needs to be verified in the wet lab. And this is work, which can be pretty hard.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-16T14:04:22.913" LastActivityDate="2014-03-16T14:04:22.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15749" PostTypeId="2" ParentId="15727" CreationDate="2014-03-15T20:29:56.830" Score="4" Body="&lt;p&gt;Such examples are not that rare: multiple species are polymorphic for &lt;a href=&quot;https://en.wikipedia.org/wiki/B_chromosome&quot; rel=&quot;nofollow noreferrer&quot;&gt;supernumerary (B-chromosomes)&lt;/a&gt;, others are known to show intra-specific Robertsonian polymorphism (fusions of acrocentric/separation of metacentric chromosomes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One very well studied example, which covers both intra- and inter-specific crossings, are isopod crustaceans from the Jaera albifrons complex. They show Robertsonian variation (and additionally sometimes B-chromosomes):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;different species in the same location normally have different chromosomal numbers;&lt;/li&gt;&#xA;&lt;li&gt;on the macrogeographical level at least some species show certain gradients in chromosomal numbers;&lt;/li&gt;&#xA;&lt;li&gt;sometimes the same variation can be observed on the level of local populations.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Hybrids &lt;strong&gt;between species&lt;/strong&gt; are viable and not sterile, but rare in nature. Fecundity of hybrids is lower than that of the parental species, and this seems to serve as an additional post-zygotic mechanism of species isolation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Crossings between specimens of &lt;strong&gt;the same species&lt;/strong&gt; with different numbers of chromosomes do occur in mixed populations and are also possible for parents coming from different extremities of the above mentioned chromosomal cline. In the case of mixed populations frequency of these hetezygotes is less than expected by Hardy-Weinberg. Such offspring is fertile, and its lowered frequency is associated with higher incidence of abnormal meiosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the cytological level (normal) meiosis in a heterozygote individual is remarkable in showing trivalents instead of bivalents for the polymorphic chromosomes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1u5NQ.png&quot; alt=&quot;Autosomal trivalent in Jaera albifrons&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(a metaphase with a trivalent in the center and two bivalents) (from Staiger &amp;amp; Bocquet 1956)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, in four out of five species of the complex chromosomal sex determination is of the following uncommon type: males are homogametic with sex chromosomes ZZ, while females are heterogametic with ZW&lt;sub&gt;1&lt;/sub&gt;W&lt;sub&gt;2&lt;/sub&gt; chromosomes. So, females normally have in total an odd number of chromosomes and in their meiosis one observes a trivalent similar to the one shown above: the metacentric Z-chromosome conjugates with the two acrocentrix W-chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some references available on-line:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://decapoda.nhm.org/pdfs/30504/30504.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lécher &amp;amp; Prunus 1971&lt;/a&gt; (in French)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://decapoda.nhm.org/pdfs/22748/22748.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Solignac 1981&lt;/a&gt; (English, on isolating mechanisms in general)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.tandfonline.com/doi/abs/10.1080/07924259.1995.9672440&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lécher et al 1995&lt;/a&gt; (a review in English)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://books.google.de/books?id=0aLWAQAAQBAJ&amp;amp;pg=PA3&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kappas et al 2013&lt;/a&gt; (a review in English - see pages 23-26)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;These are highly relevant to the question, but not accessible on the web:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Lécher 1967 (Cytogénétique de l'hybridation expérimentale et naturelle chez l'Isopode Jaera (albifrons) syei Bocquet)&lt;/li&gt;&#xA;&lt;li&gt;Lécher 1967 (Polysomie autosomique chez l'Isopode Jaera albifrons syei Bocquet)&lt;/li&gt;&#xA;&lt;li&gt;Staiger &amp;amp; Bocquet 1956 (Les chromosomes de la super-espèce Jaera marina (Fabr.) et de quelques autres Janiridae (Isopodes Asellotes))&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-03-15T20:29:56.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15750" PostTypeId="1" CreationDate="2014-03-15T21:34:04.327" Score="2" ViewCount="1127" Body="&lt;p&gt;What does &quot;oleracea&quot;, as appears in numerous plant species (scientific) names, mean? Examples: &lt;em&gt;Euterpa oleracea, Brassica oleracea, Portulaca oleracea, Acmella oleracea, Spilanthes oleracea&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6051" LastEditorUserId="16866" LastEditDate="2020-04-15T13:09:51.263" LastActivityDate="2020-04-15T13:09:51.263" Title="Meaning of the word Oleracea" Tags="&lt;taxonomy&gt;&lt;nomenclature&gt;&lt;etymology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="15751" PostTypeId="2" ParentId="15745" CreationDate="2014-03-15T22:19:47.540" Score="4" Body="&lt;p&gt;This is derived from studying how heterozygosity changes over time. The standard equation for change in heterozygosity ($H$) with constant population size ($N$) is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$H_t = \left(1 - \frac{1}{2N}\right)^tH_0$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When $N$ varies between generations you use the product of this formula:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$H_t = \left(1 - \frac{1}{2N_0}\right)\left(1 - \frac{1}{2N_1}\right)...\left(1 - \frac{1}{2N_{t-1}}\right)H_0 = \prod_{i=0}^{t-1}\left(1 - \frac{1}{2N_{i}}\right)H_0$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To get the overall $N_e$ you need to find the population size that gives the corresponding decrease in heterozygocity over t generations i.e:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\left(1 - \frac{1}{2N_{e}}\right)^t = \prod_{i=0}^{t-1}\left(1 - \frac{1}{2N_{i}}\right)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rearranging gives:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$N_e = \frac{1}{2\left[1-\left[\prod_{i=0}^{t-1}\left(1 -\frac{1}{2N_{i}}\right)\right]^{1/t}\right]}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This expression can be approximated by the harmonic mean, which is easy to verify with some toy data (you get small deviations if yearly population sizes are very small). The explanation given above can also be found in &lt;a href=&quot;http://books.google.no/books?id=pBq69Luwf7UC&amp;amp;pg=PA217#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot; title=&quot;Hedrick. 2019. Genetics of populations 4th ed. Jones &amp;amp; Bartlett Learning&quot;&gt;Hedrick (2009, p217ff)&lt;/a&gt;, along with some nice examples that integrates the effects on effective population size from several factors.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-03-15T23:12:28.117" LastActivityDate="2014-03-15T23:12:28.117" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15752" PostTypeId="2" ParentId="3455" CreationDate="2014-03-16T03:16:15.633" Score="1" Body="&lt;p&gt;I think its related to structure, like the noncoding (junk) DNA contributes to structure my guess would be that the Linear genome &quot;just happend&quot; and there was no way of going back.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That could have been because of Phage/Viral predation radical changes in genome structure will make it certainly very hard for viruses to adept. So in the early days of the eukaryotes the different genome would have provided a very strong protection against viral predation and thus would have allowed those organisms to reproduce nearly inhindered from the selective pressure of viruses. Which allowed for evolution to take place structures developed that make a step back impossible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;but yeah those are just WILD guesses&lt;/p&gt;&#xA;" OwnerUserId="6054" LastActivityDate="2014-03-16T03:16:15.633" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15753" PostTypeId="2" ParentId="15712" CreationDate="2014-03-16T03:53:19.520" Score="1" Body="&lt;p&gt;Virus particles (virions) are not alive. They are just a Genome Delivery Vehicle. They are essentially like landmines. However like different types of landmines different types of viruses can remain &quot;active&quot; for longer or shorter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Those depend as explained above on the virion structure but also on Humidity and temperature, the fomite (surface) and the ammount of virions. Some viruses need up to 10k Virons to cause disease. The higher this &quot;Particle to PFU ratio&quot; is the lower the chance they can remain active outside the body for long. So if the Virus in question needs few particles, is not enveloped then this one can in theory live for quite a while outside, Norovirus for example is one of those.&lt;/p&gt;&#xA;" OwnerUserId="6054" LastActivityDate="2014-03-16T03:53:19.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15754" PostTypeId="2" ParentId="15744" CreationDate="2014-03-16T07:13:31.293" Score="2" Body="&lt;p&gt;Ions are not hormones. Ions are not metabolites either. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Technically, anything that is not directly absorbed from environment but is synthesized/modified in the body is a metabolite. &#xA;Even if you don't consider polypeptides as metabolites (which for some reason are not classified as metabolites in scientific parlance), all the molecules that you mention are metabolites with known biosynthetic pathways. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-03-16T07:13:31.293" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15755" PostTypeId="1" AcceptedAnswerId="15757" CreationDate="2014-03-16T08:40:05.400" Score="1" ViewCount="377" Body="&lt;p&gt;I read that proteins that have been highly conserved are non-immunogenic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is it so ? What is the special thing that makes it non immunogenic(antibodies against them are hard to make) ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-16T11:10:11.187" Title="Conserved proteins are non immunogenic" Tags="&lt;proteins&gt;&lt;immunology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15756" PostTypeId="2" ParentId="15755" CreationDate="2014-03-16T09:54:22.247" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Immunogenicity&quot; rel=&quot;nofollow&quot;&gt;Immunogenicity&lt;/a&gt; is&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the ability of a particular substance, such as an antigen or epitope, to provoke an immune response in the body of a human or animal. In other words, immunogenecity is the ability to induce a humoral or/and cell mediated immune response.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If a protein is highly conserved between species it means that its epitopes will be recognised as &lt;em&gt;self&lt;/em&gt; by most species, hence the organism will avoid producing antibodies against them to prevent &lt;a href=&quot;http://en.wikipedia.org/wiki/Autoimmunity&quot; rel=&quot;nofollow&quot;&gt;autoimmunity&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may want to read about &lt;a href=&quot;http://en.wikipedia.org/wiki/Central_tolerance&quot; rel=&quot;nofollow&quot;&gt;central tolerance&lt;/a&gt; to see how T cells and B cells are rendered non-reactive to self.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2014-03-16T09:54:22.247" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15757" PostTypeId="2" ParentId="15755" CreationDate="2014-03-16T10:28:10.180" Score="2" Body="&lt;p&gt;Immunogenicity has nothing to do with how conserved a protein is. As nico already pointed out, it is a mechanism to prevent autoimmunity. But this is only valid for proteins which are similar to human proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you design a vaccine, you try to choose proteins as vaccine candidates, which are as conserved as possible. This makes the vaccine more universal (since conserved proteins are shared between different strains of a bacterium or a virus) and also prevents it from getting ineffective when the target protein mutates. An example would be the flu virus where you need to predict the strains which will be in circulation to formulate a vaccine. If it would be possible to find a conserved protein, which is shared between all viruses (and of course has no similarities to human proteins) than you would have a universal flu vaccine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antibodies can (and are) be designed artificially, this is for example done for capsulated bacteria like Menningococcus B, where so far no vaccine was available. These vaccines are either relatively short peptides or single proteins from the from the pathogen. The proteins for the vaccine are then usually made in a biotechnological way, purified and can be used as a vaccine. This approach is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Reverse_vaccinology&quot; rel=&quot;nofollow&quot;&gt;reverse vaccinology&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-16T11:10:11.187" LastActivityDate="2014-03-16T11:10:11.187" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15758" PostTypeId="2" ParentId="15741" CreationDate="2014-03-16T10:29:10.517" Score="3" Body="&lt;p&gt;When we eat the architecture makes sure most if not all the food ends up in our foodpipe rather than our windpipe. This is aided by a structure called the epiglottis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However frequently foods may be inhaled, for example if a drink is sucked through a straw more if it gets into the lungs compared to if we drink it. Occasionally we will inhale a peanut or something else which typically occurs due to abnormal relaxation or muscular problems in the structures involved. This may be due to a neurological disease (e.g. myasthenia gravis) or because simply drinking too much and inhaling peanuts or vomit (aspiration). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the inhaled substance is small and lipid soluble e.g. alcohol, it can pass through the alveoli at the end of the lung to the rich blood supply. If it doesn't we rely on macrophages to digest the food. They aren't frequent enough to digest anything substantial. Bacteria however are great at munching this up and increase substantially in number. Typically your lowest airways are sterile but food can interfere with clearance mechanisms and provide a home. The part of the lung blocked (distal to the foreign object) can collapse and frequently does. In the long run this may cause bronchiectasis, where an infection recurrently affects the area due to permanent damage done during the initial event resulting in widened airways and an ongoing inflammatory response. The inflammatory response reveals even more receptors for bacteria to latch on to. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-03-16T10:29:10.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15759" PostTypeId="1" AcceptedAnswerId="16332" CreationDate="2014-03-16T11:21:59.120" Score="4" ViewCount="168" Body="&lt;p&gt;In &lt;a href=&quot;http://www.ibiology.org/ibioseminars/genetics-gene-regulation/elizabeth-blackburn-part-1.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; amazing video, at 26:03 we see this image&lt;img src=&quot;https://i.stack.imgur.com/g3rGI.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We now know that the telomerase contains a sequence complementary to the telomere sequence and so is able to do what it is capable of doing in this image.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions : What if we make a piece of dna with  five GGGGG at the 3' end ? Will the telomerase not work, as the RNA in telomerase has the sequence AACCCC and so won't be able to form complementary strand ? If so, has such a mutation been detected in any organism ie it's telomerase is unable to work just because it has a random insertion(maybe during replication) of one of the nucleotides in the telomere at the 3' end ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-04T04:25:10.080" Title="Telomerase in tetrahymena" Tags="&lt;dna&gt;&lt;rna&gt;&lt;enzymes&gt;&lt;telomere&gt;&lt;protein-binding&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15760" PostTypeId="2" ParentId="15750" CreationDate="2014-03-16T12:07:10.807" Score="3" Body="&lt;p&gt;It means &lt;a href=&quot;http://www.wordsense.eu/holeraceus/&quot; rel=&quot;nofollow&quot;&gt;&quot;vegetable&quot;&lt;/a&gt;.&#xA;I think it's because people use those plants for food&lt;/p&gt;&#xA;" OwnerUserId="1839" LastActivityDate="2014-03-16T12:07:10.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15761" PostTypeId="1" AcceptedAnswerId="15766" CreationDate="2014-03-16T14:12:01.813" Score="1" ViewCount="36" Body="&lt;p&gt;As telomerase works by adding new nucleotides complementary to the RNA it contains, it cannot work for the complementary strand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Say telomerase X has RNA complementary to the 5' to 3' strand it cannot elongate he telomere for the 3'to 5' strand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So does a cell have 2 types of telomerases ? One for 5' to 3' and another for 3' to 5' ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-16T17:07:49.813" Title="2 types of telomerases?" Tags="&lt;dna&gt;&lt;rna&gt;&lt;enzymes&gt;&lt;telomere&gt;&lt;protein-binding&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15762" PostTypeId="1" AcceptedAnswerId="15765" CreationDate="2014-03-16T14:18:01.633" Score="4" ViewCount="258" Body="&lt;p&gt;The telomerase is an enzyme that adds telomeres. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What stops the telomerase from adding too many telomere sequences ? What's the regulating mechanism ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-16T14:47:17.597" Title="What stops telomerase?" Tags="&lt;enzymes&gt;&lt;telomere&gt;&lt;protein-binding&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15763" PostTypeId="1" CreationDate="2014-03-16T14:29:45.317" Score="3" ViewCount="246" Body="&lt;p&gt;Jimbo suffers a lesion to the entire right half of the spinal cord at the T6 level. A few weeks after his injury, his doctor tests his right and left legs for somatic sensation and tone.  fill out her chart concerning the absence or presence of different sensations and muscle tone in the lower limbs.&#xA;Mark a for absent, P for present&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Right leg: Light touch, Pain, Proprioception, Temperature, Hypertonicity, Hypotonicity&#xA;Left Leg: Light touch, Pain, Proprioception, Temperature, Hypertonicity, Hypotonicity&lt;/p&gt;&#xA;&#xA;&lt;p&gt;what about if the lesion is in C1 or L5? where would it affect (leg/hand..) and fill out the above chart?&lt;/p&gt;&#xA;" OwnerUserId="6056" LastEditorUserId="9943" LastEditDate="2016-03-10T20:57:34.867" LastActivityDate="2016-03-10T20:57:34.867" Title="spinal cord lesion and result in somatic sensation" Tags="&lt;neuroscience&gt;&lt;homework&gt;&lt;medicine&gt;&lt;touch&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15764" PostTypeId="1" CreationDate="2014-03-16T14:45:41.383" Score="2" ViewCount="63" Body="&lt;p&gt;Let’s say an experimenter has an electrode that can give a shock to a single axon. She takes that electrode and zaps an axon connected to thermoreceptors in the hand of her subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I) What would the subject’s perception of the stimulus be? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;II) Why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;III) If she zaps that axon AND ONLY THAT AXON so hard that it destroys the axon, would the subject feel pain?&lt;/p&gt;&#xA;" OwnerUserId="6056" LastEditorUserId="3615" LastEditDate="2014-03-16T15:51:57.383" LastActivityDate="2014-10-01T16:23:57.307" Title="Neuroscience: zapping an axon connected to thermoreceptor" Tags="&lt;neuroscience&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15765" PostTypeId="2" ParentId="15762" CreationDate="2014-03-16T14:47:17.597" Score="4" Body="&lt;p&gt;Telomerases are tightly controlled on all level: Expression, post-translational modifications and by external factors. I think for this the external factors, a protein class called telomeric proteins. They bind to the end of the telomere and regulate the telomerase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/byjcR.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The figure is from this paper, which looks into the topic quite extensively:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://delangelab.rockefeller.edu/pubs/78_Smogorzewska_Ann_Rev_Biochem_2004.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Regulation of telomerase by telomeric proteins.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-16T14:47:17.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15766" PostTypeId="2" ParentId="15761" CreationDate="2014-03-16T17:07:49.813" Score="2" Body="&lt;p&gt;A second telomerase is not necessary, as the lagging strand is filled in by the DNA-Polymerase, see this &lt;a href=&quot;http://en.wikipedia.org/wiki/Telomerase&quot; rel=&quot;nofollow noreferrer&quot;&gt;figure&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IKmx0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-16T17:07:49.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15767" PostTypeId="1" AcceptedAnswerId="15768" CreationDate="2014-03-16T17:14:09.390" Score="1" ViewCount="142" Body="&lt;p&gt;I am thinking about inflammation process with Cytomegalovirus infection.&#xA;I first thought it is about chronic inflammation, but then changed my mind because of virus infection.&#xA;I think cytokines must be there in activation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking which of these is right mechanism for both of these&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;mononuclear cells and granulocytes (I think this must be chronic inflammation)&lt;/li&gt;&#xA;&lt;li&gt;granulocytes with scar formation (I think no scar)&lt;/li&gt;&#xA;&lt;li&gt;cytopathic cytoproliferation inflammation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I think the cytopathic cytoproliferation inflammation is the right one because cytokines are activating the inflammatory response in virus infection.&#xA;However, I am not sure if this inflammation is of chronic type.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which type of inflammation can cytomegalovirus infection lead to?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-03-16T17:24:19.533" Title="Which inflammatory response with Cytomegalovirus infection?" Tags="&lt;pathology&gt;&lt;virus&gt;&lt;inflammation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15768" PostTypeId="2" ParentId="15767" CreationDate="2014-03-16T17:24:19.533" Score="1" Body="&lt;p&gt;According to this paper the virus triggers the innate immune system and induces inflammatory cytokines as well as interferon stimulated genes (which is a response to a viral infection).&#xA;It seems to be recognized by the cells via the Toll-like receptor 2 and CD14, which subsequently trigger the cytokine production. A schematic view comes from the second paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TnxU9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These two articles are interesting in this context, the first addresses CMV in special,&#xA;the second is a pretty recent review about how viruses are recognized and how cytokines are involved:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12663765&quot; rel=&quot;nofollow noreferrer&quot;&gt;Human cytomegalovirus activates inflammatory cytokine responses via&#xA;CD14 and Toll-like receptor 2.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23435233&quot; rel=&quot;nofollow noreferrer&quot;&gt;Learning from the messengers: innate sensing of viruses and cytokine&#xA;regulation of immunity - clues for treatments and vaccines.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-16T17:24:19.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15769" PostTypeId="1" AcceptedAnswerId="15795" CreationDate="2014-03-16T20:09:07.597" Score="2" ViewCount="817" Body="&lt;p&gt;You need a solution containing 1000 buccal cells/mL. You count that you have 125 buccal cells in 50uL, from a total solution of 8 mL. How much of your stock solution should you take to make the 1000 cells/mL mixture? How much solvent if you would like a total volume of 5mL?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't even know how to approach this!!!&#xA;Help??&lt;/p&gt;&#xA;" OwnerUserId="6058" LastActivityDate="2014-03-17T07:36:23.737" Title="How much of your stock solution should you take to make the 1000 cells/mL mixture?" Tags="&lt;homework&gt;" AnswerCount="2" CommentCount="1" ClosedDate="2014-03-18T17:59:42.303" ContentLicense="CC BY-SA 3.0" />
  <row Id="15770" PostTypeId="2" ParentId="15769" CreationDate="2014-03-16T20:23:57.580" Score="1" Body="&lt;p&gt;Oh, come on, thats simple math.&#xA;First calculate how many cells you have per ml: 50$\mu$l are $\frac{1}{20}$ of 1 ml. So multiply 125 with 20 to get the concentration per ml: $125 \times 20 = 2500 \frac{cells}{ml}$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to know how many cells you have in total, multiply by 8 (for the 8ml you have) and you come to 20.000 cells in your 8ml solution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you want to know, how much of your solution you need, you calculate: $\frac{2500 \frac{cells}{ml}}{1000 cells} = \frac{1 ml}{x}$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can be transformed into $x = \frac{1}{2,5} ml = 400 \mu l$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you need 400 $\mu$l for each ml of your final cell solution. So if you want to have 5ml with 1000 cells/ml you need $5 \times 400 \mu l = 2000 \mu l = 2 ml$ of your cell solution. To reach 5 ml add 3 ml of your solvent/media.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T07:36:23.737" LastActivityDate="2014-03-17T07:36:23.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15772" PostTypeId="2" ParentId="2915" CreationDate="2014-03-16T21:59:39.670" Score="1" Body="&lt;p&gt;Embed the tissue in OCT first (roughly cut to remove everything what is not needed) and the flash freeze it. Then you can cut your sections.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first protocol describes it in detail, the second gives some additional information:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.thelabrat.com/protocols/prepfrozensections.shtml&quot; rel=&quot;nofollow&quot;&gt;Protocol for Preparation of Frozen Tissues for Sectioning&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://mhpl.facilities.northwestern.edu/files/2013/10/Tissue-Freezing-Presentation-5-26-20111.pdf&quot; rel=&quot;nofollow&quot;&gt;Tissue freezing methods for cryostat sectioning&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-16T21:59:39.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15774" PostTypeId="5" CreationDate="2014-03-16T22:16:54.713" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-16T22:16:54.713" LastActivityDate="2014-03-16T22:16:54.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15775" PostTypeId="4" CreationDate="2014-03-16T22:16:54.713" Score="0" Body="Nutrient solution for the growth of eukariotic cells or bacteria. It can contain everything the cell needs for its growth (complete media) or can be incomplete (selective media) to select for cells that are able to synthesize specific nutrients." OwnerUserId="5144" LastEditorUserId="69" LastEditDate="2014-03-16T22:19:51.847" LastActivityDate="2014-03-16T22:19:51.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15776" PostTypeId="5" CreationDate="2014-03-16T22:18:47.657" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-16T22:18:47.657" LastActivityDate="2014-03-16T22:18:47.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15777" PostTypeId="4" CreationDate="2014-03-16T22:18:47.657" Score="0" Body="Is the process of covalently link two DNA ends. The process is usually done by the enzyme class of ligases." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T00:34:04.300" LastActivityDate="2014-03-17T00:34:04.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15778" PostTypeId="5" CreationDate="2014-03-16T22:21:48.203" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-16T22:21:48.203" LastActivityDate="2014-03-16T22:21:48.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15779" PostTypeId="4" CreationDate="2014-03-16T22:21:48.203" Score="0" Body="A primer is short oligo made from nucleic acids. It is the starting point for DNA polymerases to start DNA synthesis. DNA polymerases can only synthesize enlarge existing nucleic but not generate new ones 'de novo'. Primers can be made of DNA (for PCR) or RNA (naturally occuring)." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T00:34:18.173" LastActivityDate="2014-03-17T00:34:18.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15780" PostTypeId="5" CreationDate="2014-03-16T22:28:47.120" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-16T22:28:47.120" LastActivityDate="2014-03-16T22:28:47.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15781" PostTypeId="4" CreationDate="2014-03-16T22:28:47.120" Score="0" Body="Journal where experts from the field (peers) of a submitted article review the article prior to publication. They decide what happens to the article, if it needs to be supplemented with further experiments, re-phrased or be rejected. When the article needs to be revised they decide if the revision is ok and recommend the acceptance or rejection to the journal." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T00:34:24.330" LastActivityDate="2014-03-17T00:34:24.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15782" PostTypeId="5" CreationDate="2014-03-16T22:31:06.877" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-16T22:31:06.877" LastActivityDate="2014-03-16T22:31:06.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15783" PostTypeId="4" CreationDate="2014-03-16T22:31:06.877" Score="0" Body="pH is a measure of the acidity of a solution. It is defined as the negative logarithm (base 10) of the concentration of hydronium ions in a solution." OwnerUserId="5144" LastEditorUserId="948" LastEditDate="2016-07-15T20:51:04.323" LastActivityDate="2016-07-15T20:51:04.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15784" PostTypeId="5" CreationDate="2014-03-16T22:32:42.213" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-16T22:32:42.213" LastActivityDate="2014-03-16T22:32:42.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15785" PostTypeId="4" CreationDate="2014-03-16T22:32:42.213" Score="0" Body="Hormone responsible for controlling the circadian rhythym." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-16T23:45:52.580" LastActivityDate="2014-03-16T23:45:52.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15786" PostTypeId="5" CreationDate="2014-03-16T22:35:34.967" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-16T22:35:34.967" LastActivityDate="2014-03-16T22:35:34.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15787" PostTypeId="4" CreationDate="2014-03-16T22:35:34.967" Score="0" Body="A cell is the smallest functional unit of life." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T00:33:57.063" LastActivityDate="2014-03-17T00:33:57.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15788" PostTypeId="5" CreationDate="2014-03-16T22:44:52.643" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-16T22:44:52.643" LastActivityDate="2014-03-16T22:44:52.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15789" PostTypeId="4" CreationDate="2014-03-16T22:44:52.643" Score="0" Body="ELISA stands for enyzme-linked immunosorbent assay. It is analytical method which binds an antigen to an antibody in a microreaction plate und uses a second, enzyme-linked antibody for the detection." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-16T23:44:45.307" LastActivityDate="2014-03-16T23:44:45.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15790" PostTypeId="5" CreationDate="2014-03-16T23:01:52.040" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-16T23:01:52.040" LastActivityDate="2014-03-16T23:01:52.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15791" PostTypeId="4" CreationDate="2014-03-16T23:01:52.040" Score="0" Body="Differentiation describes the process in the development from more general cell types into higher specialized cell types." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-16T23:28:45.583" LastActivityDate="2014-03-16T23:28:45.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15792" PostTypeId="5" CreationDate="2014-03-16T23:04:11.123" Score="0" Body="&lt;p&gt;Melanin is the biopigment which protects the skin from ultraviolet radiation and colors skin and hair. It is made in a special cell type, the melanocytes. The synthesis take place in a special lysosome-derived organelle, the melanosome. Melanocytes export melanin into the surrounding keratinocytes.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-16T23:45:40.290" LastActivityDate="2014-03-16T23:45:40.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15793" PostTypeId="4" CreationDate="2014-03-16T23:04:11.123" Score="0" Body="Biopigment, present in the skin and hair of humans." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-16T23:44:03.330" LastActivityDate="2014-03-16T23:44:03.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15795" PostTypeId="2" ParentId="15769" CreationDate="2014-03-17T03:12:45.227" Score="1" Body="&lt;p&gt;welcome to cell culture &amp;amp; dimensional analysis&lt;/p&gt;&#xA;&#xA;&lt;p&gt;125/50µl or 2.5 cells/µl is your concentration (better way of expressing it)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2.5 * 8000µl = 20,000 total cells you have. 1000µl in 1ml that's why the 8000µl&lt;/p&gt;&#xA;&#xA;&lt;p&gt;20,000 cells / 1000 cells/ml = 20mls final culture volume to reach desired concentration&lt;/p&gt;&#xA;&#xA;&lt;p&gt;20mls - 8mls = 12mls   so you need to add 12mls of medium / saline / whatever to your 8mls to dilute it to the correct concentration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;when you ask about solvent to ADD to make 5mls. Prob with this question is you don't state the desired concentration. So assuming its still 1000 cells/ml kinda go backwards,&#xA;1000 cells/ml * 5mls = 5000 cells is what you want to get&lt;/p&gt;&#xA;&#xA;&lt;p&gt;to get it:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5000 / 2.5 cells/µl = 2000µl or 2mls of your culture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So take 2mls of your culture and mix it with 3mls of solvent / medium  (5mls - 2mls).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm quite certain chris below is not correct.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-03-17T03:12:45.227" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15796" PostTypeId="2" ParentId="2915" CreationDate="2014-03-17T03:19:35.960" Score="1" Body="&lt;p&gt;do not place it directly in the N2 unless it's clean. and high grade liquid N2 costs an arm and leg. put the tissue in the oct in a conical vial and that in the N2. don't use polycarbonate it may crack. check with the OCT manufacturers suggestions first though. I've followed this BD protocol before&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bdbiosciences.com/resources/protocols/frozen_tissue.jsp&quot; rel=&quot;nofollow&quot;&gt;http://www.bdbiosciences.com/resources/protocols/frozen_tissue.jsp&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-03-17T03:19:35.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15797" PostTypeId="1" CreationDate="2014-03-17T03:29:44.413" Score="3" ViewCount="121" Body="&lt;p&gt;I've been doing a lot of live cell imaging lately mostly using hela cells expressing some EYFP based chimeric proteins. I'm building a video library for an art student here at the university who is going to create an exposition using the videos. I need a lot of content to make this sucessful and rather than requiring much scientific merit these videos need to be &quot;busy&quot; and look good. I'm looking for suggestions as to any dyes or fluorophores, drug treatments or conditions someone has worked with that will show significant movement/change of/in the cell, change in intracellular localization....doesn't matter it just needs to be a significant alteration for the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm still really optimizing the system with the CO₂ etc.. and the longest aquisition i have taken is about 8 hours - after that either the cells are dead or the focal drift becomes too much of a problem. I am hoping to see some division once I can get the system recording long enough. Until then was looking for some suggestions as to other possibilities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The various dyes I have been using include:  hoechst, dapi, mito-tracker, draq5, er-red, rox-red. also eyfp/tubulin, eyfy/mito, eyfp/golgi, draq5. These dyes aren't cheap and I'm only one i know doing this so I'm checking here.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="3340" LastEditDate="2014-10-09T15:46:44.270" LastActivityDate="2014-10-09T15:46:44.270" Title="Hela live cell confocal laser scanning - reccommendations for good fluorophore that will show good movement" Tags="&lt;cell-culture&gt;&lt;fluorescent-microscopy&gt;&lt;cell&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15799" PostTypeId="2" ParentId="257" CreationDate="2014-03-17T03:56:23.023" Score="0" Body="&lt;p&gt;The Journal of Visualized Experiments (&lt;a href=&quot;http://www.jove.com/&quot; rel=&quot;nofollow&quot;&gt;jove.com&lt;/a&gt;) is excellent but based on experimental protocols.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.apple.com/apps/itunes-u/&quot; rel=&quot;nofollow&quot;&gt;ItunesU&lt;/a&gt; also has great resources. Stay away from youtube - a lot of people there don't know what they are talking about.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="3624" LastEditDate="2014-03-18T09:58:42.647" LastActivityDate="2014-03-18T09:58:42.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15800" PostTypeId="1" AcceptedAnswerId="15803" CreationDate="2014-03-17T04:23:14.017" Score="1" ViewCount="3058" Body="&lt;p&gt;When there is an error in copying DNA (a mutation), what exactly goes wrong?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If G goes with C and A goes with T, I don't see how that part can mess up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the idea that when the double helix is split, an A gets ruined and replaced with a G by mistake, which then pairs with a C in one of the copies? So something that was &lt;em&gt;supposed&lt;/em&gt; to be AT is now GC.&lt;/p&gt;&#xA;" OwnerUserId="6062" LastEditorUserId="16651" LastEditDate="2015-12-26T23:41:01.440" LastActivityDate="2015-12-26T23:41:01.440" Title="What errors can occur during DNA replication?" Tags="&lt;dna&gt;&lt;mutations&gt;&lt;dna-replication&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15801" PostTypeId="1" CreationDate="2014-03-17T04:40:33.500" Score="0" ViewCount="224" Body="&lt;p&gt;So I'm new to the dimensional analysis world and I'm little confused and the answers I'm getting are not convincing :(&lt;/p&gt;&#xA;&#xA;&lt;p&gt;if the concentration of hemoglobin in a 5ml sample of blood is 34 g/dL. and red blood cells are 31.45 hemoglobin, what is the mass of red blood cells in the sample?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So.. any thoughts on how to do it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you so much&lt;/p&gt;&#xA;" OwnerUserId="6058" LastActivityDate="2014-03-17T05:27:36.703" Title="Dimensional analysis Question" Tags="&lt;homework&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15802" PostTypeId="2" ParentId="15801" CreationDate="2014-03-17T05:27:36.703" Score="1" Body="&lt;p&gt;It doesn't seem like you need the 31.45 hemoglobin number (which is good because no units are given:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5ml * 34g rbc /dL * 1 dL/ 100 ml = 1.7 g rbc&lt;/p&gt;&#xA;&#xA;&lt;p&gt;would fall out from unit analysis&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-03-17T05:27:36.703" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15803" PostTypeId="2" ParentId="15800" CreationDate="2014-03-17T07:33:26.710" Score="4" Body="&lt;p&gt;There are many way in which DNA can be damaged. As already pointed out in the comment by @skymninge, the &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_repair&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia page on DNA repair&lt;/a&gt;, as well as the &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_error&quot; rel=&quot;nofollow noreferrer&quot;&gt;mutation page&lt;/a&gt; detail some of the things that can go wrong. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If G goes with C and A goes with T, I don't see how that part can mess up.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This, however, would imply that the four bases are completely different so that mispairing cannot exist. This is (may I add luckily?) not true.&lt;br&gt;&#xA;Indeed the chemical structure of the bases is very similar, and changes between one base and another (transversions and transitions) are common.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/3/35/Transitions-transversions-v3.png/480px-Transitions-transversions-v3.png&quot; alt=&quot;Transversions and transitions&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These can result for instance from exposure to external agents such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Ionizing_radiation&quot; rel=&quot;nofollow noreferrer&quot;&gt;ionizing radiation&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Alkylating_agent#Alkylating_agents&quot; rel=&quot;nofollow noreferrer&quot;&gt;alkylating agents&lt;/a&gt;, or from exposure to endogenous products such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Reactive_oxygen_species&quot; rel=&quot;nofollow noreferrer&quot;&gt;reactive oxygen species&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, the enzyme synthetizing DNA, called &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_polymerase&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA polymerase&lt;/a&gt;, can insert the wrong base, although most of these errors can be corrected by its &quot;proof-reading mechanisms&quot;. However, it is estimated that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the frequency at which human DNA undergoes lasting, uncorrected errors range from $1 * 10^{-4}$ to $1 * 10^{-6}$ mutations per gamete for a given gene.  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.nature.com/scitable/topicpage/dna-damage-repair-mechanisms-for-maintaining-dna-344&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nature Scitable&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in summary, the system is not perfect, and mutation can be introduced even endogenously. This may seem bad, but, at least for relatively small rates of mutation, is not, as it allows change in the population, which is the &lt;a href=&quot;http://www.nature.com/scitable/knowledge/library/mutations-are-the-raw-materials-of-evolution-17395346&quot; rel=&quot;nofollow noreferrer&quot;&gt;basis for evolution&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:47.930" LastActivityDate="2014-03-17T07:33:26.710" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15804" PostTypeId="5" CreationDate="2014-03-17T07:55:39.710" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T07:55:39.710" LastActivityDate="2014-03-17T07:55:39.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15805" PostTypeId="4" CreationDate="2014-03-17T07:55:39.710" Score="0" Body="Analysis of DNA, RNA or protein (amino acid) sequences. Here sequences are compared so analyze similarities and conserved regions. Sequence analysis is usually done by specialized software." OwnerUserId="5144" LastEditorUserId="5857" LastEditDate="2015-03-23T15:36:56.727" LastActivityDate="2015-03-23T15:36:56.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15806" PostTypeId="5" CreationDate="2014-03-17T07:59:46.680" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T07:59:46.680" LastActivityDate="2014-03-17T07:59:46.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15807" PostTypeId="4" CreationDate="2014-03-17T07:59:46.680" Score="0" Body="Medicine is the doctrine of prevention, diagnosis and treatment of diseases and injuries in humans and animals.&#xD;&#xA;&#xD;&#xA;Health and medicine questions are off-topic unless dealing with the biology underlying health and medicine. Please carefully explore the tour, help centre, and meta before posting health and medicine questions.&#xD;&#xA;" OwnerUserId="5144" LastEditorUserId="1590" LastEditDate="2016-03-15T12:14:27.003" LastActivityDate="2016-03-15T12:14:27.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15808" PostTypeId="5" CreationDate="2014-03-17T08:03:01.270" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T08:03:01.270" LastActivityDate="2014-03-17T08:03:01.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15809" PostTypeId="4" CreationDate="2014-03-17T08:03:01.270" Score="0" Body="Scientific procedure to test a hypothesis. The outcome of the experiment either confirms or denies the hypothesis." OwnerUserId="5144" LastEditorUserId="3632" LastEditDate="2014-03-17T10:50:23.357" LastActivityDate="2014-03-17T10:50:23.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15810" PostTypeId="5" CreationDate="2014-03-17T08:04:39.217" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T08:04:39.217" LastActivityDate="2014-03-17T08:04:39.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15811" PostTypeId="4" CreationDate="2014-03-17T08:04:39.217" Score="0" Body="Hair is a biopolymer mostly made from keratin, which grows from the skin. Hair is exclusively found in mammals." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T08:45:46.047" LastActivityDate="2014-03-17T08:45:46.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15812" PostTypeId="5" CreationDate="2014-03-17T08:07:32.587" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T08:07:32.587" LastActivityDate="2014-03-17T08:07:32.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15813" PostTypeId="4" CreationDate="2014-03-17T08:07:32.587" Score="0" Body="Cell devision is the process in which one parent cell divides into two daughter cells. The interiour (cytoplasm, DNA, mitchondria etc.) of the parent cell is divided between the two new cells." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T10:49:18.417" LastActivityDate="2014-03-17T10:49:18.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15814" PostTypeId="1" AcceptedAnswerId="35069" CreationDate="2014-03-17T08:12:24.790" Score="3" ViewCount="268" Body="&lt;p&gt;I wonder if the thrombus can pass through the brain-blood barrier because I think small molecules like O&lt;sub&gt;2&lt;/sub&gt;, CO&lt;sub&gt;2&lt;/sub&gt; and ethanol can pass it.&#xA;Probably, in some diseases where the permeability of the barrier changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can systemic intravascular thrombosis cause brain infarction?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2015-05-23T08:23:02.110" LastActivityDate="2019-05-05T20:58:02.023" Title="Can systemic intravascular thrombosis cause brain infarction?" Tags="&lt;cardiology&gt;&lt;blood-circulation&gt;&lt;pathogenesis&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15815" PostTypeId="5" CreationDate="2014-03-17T08:19:02.370" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T08:19:02.370" LastActivityDate="2014-03-17T08:19:02.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15816" PostTypeId="4" CreationDate="2014-03-17T08:19:02.370" Score="0" Body="Internal organ of vertebrate species which is important for a lot of biochemical functions including production of molecules, detoxification and production of glycogen." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T08:46:07.253" LastActivityDate="2014-03-17T08:46:07.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15817" PostTypeId="1" AcceptedAnswerId="15869" CreationDate="2014-03-17T08:20:59.020" Score="0" ViewCount="191" Body="&lt;p&gt;I think CVC cannot lead to heart failure primarily.&#xA;So let's think its pathogenesis in skin now only.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the pathogenesis is like this&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;dilation of veins and capillaries due to impaired venous drainage&lt;/li&gt;&#xA;&lt;li&gt;reduced outflow of blood from a tissue&lt;/li&gt;&#xA;&lt;li&gt;passive process&lt;/li&gt;&#xA;&lt;li&gt;$\to$ local increase in blood volumes&lt;/li&gt;&#xA;&lt;li&gt;$\to$ local increase in venous pressure&lt;/li&gt;&#xA;&lt;li&gt;pathological&lt;/li&gt;&#xA;&lt;li&gt;$\to$ shortage of oxygen and built-up metabolic waste&lt;/li&gt;&#xA;&lt;li&gt;$\to$ structural changes in microvasculature&lt;/li&gt;&#xA;&lt;li&gt;$\to$ increased venous permeability % hallmark of acute inflammation&lt;/li&gt;&#xA;&lt;li&gt;$\to$ increased size of venous caliber&lt;/li&gt;&#xA;&lt;li&gt;$\to$ emigration of leucocytes&lt;/li&gt;&#xA;&lt;li&gt;$\to$ accumulation at site of injury&lt;/li&gt;&#xA;&lt;li&gt;activation of acute inflammation&lt;/li&gt;&#xA;&lt;li&gt;$\to$ protein into extravascular space&lt;/li&gt;&#xA;&lt;li&gt;$\to$ increased viscosity of blood &lt;/li&gt;&#xA;&lt;li&gt;$\to$ deoxygenated blood blood stasis&lt;/li&gt;&#xA;&lt;li&gt;$\to$ congested tissue&lt;/li&gt;&#xA;&lt;li&gt;$\to$ leucocytes move to endothelial wall (selectins)&lt;/li&gt;&#xA;&lt;li&gt;$\to$ roll&lt;/li&gt;&#xA;&lt;li&gt;$\to$ adhere (integrin to stop)&lt;/li&gt;&#xA;&lt;li&gt;$\to$ migrate&lt;/li&gt;&#xA;&lt;li&gt;$\to$ dysky reddish-bluish skin (cyanotic)&lt;/li&gt;&#xA;&lt;li&gt;$\to$ healing via fibrosis&lt;/li&gt;&#xA;&lt;li&gt;$\to$ scar&lt;/li&gt;&#xA;&lt;li&gt;Causes: venous thrombosis; venous compression; heart failure; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am not sure about the role of leucocytes exactly in this process.&#xA;I am not sure if they play a big role in the formation of cyanotic skin.&#xA;I think the outcome is mostly because of increased vascular permeability and its deoxygenated blood in extracellular space.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the right pathogenesis of chronic venous congestion in skin?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="5144" LastEditDate="2017-03-13T15:21:41.207" LastActivityDate="2017-03-13T15:21:41.207" Title="Pathogenesis of chronic venous congestion in skin?" Tags="&lt;blood-circulation&gt;&lt;skin&gt;&lt;pathogenesis&gt;&lt;congestion&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15818" PostTypeId="5" CreationDate="2014-03-17T08:26:44.670" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T08:26:44.670" LastActivityDate="2014-03-17T08:26:44.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15819" PostTypeId="4" CreationDate="2014-03-17T08:26:44.670" Score="0" Body="Fruits develop from the flower of plants and hold the seeds. They are the way of plants to distribute their seeds." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T08:46:20.390" LastActivityDate="2014-03-17T08:46:20.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15820" PostTypeId="5" CreationDate="2014-03-17T08:29:37.057" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T08:29:37.057" LastActivityDate="2014-03-17T08:29:37.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15821" PostTypeId="4" CreationDate="2014-03-17T08:29:37.057" Score="0" Body="Homocyteine is a naturally occurring, non-proteinogenic alpha-amino acid." OwnerUserId="5144" LastEditorUserId="62413" LastEditDate="2020-10-26T10:04:27.040" LastActivityDate="2020-10-26T10:04:27.040" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="15822" PostTypeId="5" CreationDate="2014-03-17T08:31:26.063" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T08:31:26.063" LastActivityDate="2014-03-17T08:31:26.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15823" PostTypeId="4" CreationDate="2014-03-17T08:31:26.063" Score="0" Body="Milk is a nutrional white liquid produced by the mammary glands of mammals to feed their offsprings." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T08:45:28.463" LastActivityDate="2014-03-17T08:45:28.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15825" PostTypeId="5" CreationDate="2014-03-17T08:39:20.207" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T08:39:20.207" LastActivityDate="2014-03-17T08:39:20.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15826" PostTypeId="4" CreationDate="2014-03-17T08:39:20.207" Score="0" Body="Toxins secreted by bacteria. Toxins are the agents which cause most of the toxicity of bacteria and are often highly toxic. Examples include the tetanus and the diptheria toxins." OwnerUserId="5144" LastEditorUserId="1590" LastEditDate="2014-03-17T09:47:47.223" LastActivityDate="2014-03-17T09:47:47.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15827" PostTypeId="2" ParentId="14968" CreationDate="2014-03-17T09:11:55.870" Score="1" Body="&lt;p&gt;As @Kyle beautifully summed-up, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Neuroeconomics is the study of the neural basis of economic behavior. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The terms applies to studies concerning the appeal of new logos for marketing purposes to the understanding of the neural correlate of subjective value. The term neuroeconomics has been subject to some debate which made it sometimes unclear. In particular, the term is ambiguous with regards to its applications. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are the theories that are built upon these studies used for marketing purposes (some would say &quot;to optimize brain washing you in the necessity of buying a 7 blade razor&quot;) or for the sake of knowing how the brain may be better understood and to the therapeutical applications of these new theories.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My answer would therefore be this: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the brain is a complex system for which science often used analogies to make progress. It has been compared as steam machines in the 1800s, electricity in the 1900s, or to computers in the this century. &lt;/li&gt;&#xA;&lt;li&gt;The complex interactions present in an economic system -as studied by game theory for instance- present a powerful analogy to understand the brain. &lt;/li&gt;&#xA;&lt;li&gt;Of course, it thus impacts our knowledge on economics as these are often based on our knowledge of decision making. Thus, your two options are (1) and (2) are interconnected.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6065" LastActivityDate="2014-03-17T09:11:55.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15828" PostTypeId="1" AcceptedAnswerId="16934" CreationDate="2014-03-17T09:12:22.643" Score="1" ViewCount="318" Body="&lt;p&gt;I think it is autophagy. Lysosomal degradation. Autophagocytosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example of the brown pigment (lipofuscin) here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/y3uVR.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure if autophagy is the right answer to the &quot;pathogenic&quot; mechanism of atrophy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is autophagy the pathogenic mechanism of atrophy?&lt;/strong&gt;&#xA;Or &lt;strong&gt;what pathogenic mechanism is involved if you see lipofuscin in the histologic slide?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="107" LastEditDate="2014-04-27T16:48:00.670" LastActivityDate="2014-04-27T16:48:00.670" Title="What is the pathogenuc mechanism of brown pigment lipofuscin in muscle atrophy?" Tags="&lt;muscles&gt;&lt;pathogenesis&gt;&lt;autophagy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15829" PostTypeId="5" CreationDate="2014-03-17T09:17:13.353" Score="0" Body="&lt;p&gt;Minipreps (=small preparations of plasmid DNA) are usually done using the alkaline lysis method:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Cells are lysed with a basic buffer containing detergents&lt;/li&gt;&#xA;&lt;li&gt;Proteins and genomic DNA of the bacteria are precipitated and then&#xA;pelleted using centrifugation&lt;/li&gt;&#xA;&lt;li&gt;The plasmid DNA is either precipitated with Ethanol or bound to the&#xA;silica membrane of a flow-through column&lt;/li&gt;&#xA;&lt;li&gt;On the column the DNA is washed, if precipitated, the pellet is&#xA;washed to get rid of the salts used in the process&lt;/li&gt;&#xA;&lt;li&gt;The pure DNA is either eluted from the column or dissolved from the&#xA;pellet&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:41:58.400" LastActivityDate="2014-03-17T12:41:58.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15830" PostTypeId="4" CreationDate="2014-03-17T09:17:13.353" Score="0" Body="A method to purify small amounts of bacterial plasmids from the cells to get purified DNA at the end." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:41:23.897" LastActivityDate="2014-03-17T12:41:23.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15831" PostTypeId="5" CreationDate="2014-03-17T09:20:49.290" Score="0" Body="&lt;p&gt;Competent cells are chemicalls treated bacteria which can take up external DNA. This can either happen with a heat-shock (incubating the cells for a short while at 42°C) or by electroporation (subjecting the cells to an electric shock). Both procedures open up pores in the cell membrane which the DNA can pass.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:40:54.363" LastActivityDate="2014-03-17T12:40:54.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15832" PostTypeId="4" CreationDate="2014-03-17T09:20:49.290" Score="0" Body="Competent cells are bacteria which have been treated with chemicals and which are able to take up external DNA. " OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:41:49.900" LastActivityDate="2014-03-17T12:41:49.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15833" PostTypeId="5" CreationDate="2014-03-17T09:32:50.683" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T09:32:50.683" LastActivityDate="2014-03-17T09:32:50.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15834" PostTypeId="4" CreationDate="2014-03-17T09:32:50.683" Score="0" Body="Ribosomal RNA - builds together with the protein subunits the Ribosome. It is the most predominant material of the ribosome, approximately 60% of the weight are made of rRNA and 40% of proteins.&#xD;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:41:18.867" LastActivityDate="2014-03-17T12:41:18.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15835" PostTypeId="5" CreationDate="2014-03-17T09:44:26.467" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T09:44:26.467" LastActivityDate="2014-03-17T09:44:26.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15836" PostTypeId="4" CreationDate="2014-03-17T09:44:26.467" Score="0" Body="Promoter from the bateriophage T7. The promoter is highly specific for the T7-RNA polymerase and widely used in the field of molecular biology as promoter for controlled gene expression." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:41:39.147" LastActivityDate="2014-03-17T12:41:39.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15837" PostTypeId="5" CreationDate="2014-03-17T09:46:42.180" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T09:46:42.180" LastActivityDate="2014-03-17T09:46:42.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15838" PostTypeId="4" CreationDate="2014-03-17T09:46:42.180" Score="0" Body="Biosynthesis is the process in which living organism synthesize molecules and substances they need. Examples would be the photosynthesis where in the end glucose is synthesized or melanin as the result of the melanin biosynthesis." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:20:44.500" LastActivityDate="2014-03-17T12:20:44.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15839" PostTypeId="5" CreationDate="2014-03-17T09:51:12.607" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T09:51:12.607" LastActivityDate="2014-03-17T09:51:12.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15840" PostTypeId="4" CreationDate="2014-03-17T09:51:12.607" Score="0" Body="A scientific article which summarizes the knowledge of a field. It takes small bits from single research papers and organizes them in a &quot;bigger picture&quot;. Reference articles cite the original articles." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T11:09:17.917" LastActivityDate="2014-03-17T11:09:17.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15841" PostTypeId="5" CreationDate="2014-03-17T09:53:12.100" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T09:53:12.100" LastActivityDate="2014-03-17T09:53:12.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15842" PostTypeId="4" CreationDate="2014-03-17T09:53:12.100" Score="0" Body="Immunoglobulins are also known as antibodies. They are Y-shaped proteins which are build up from four subunits and which bind to an antigen. Upon antigen binding they recruit the immune system for additional help (recognition of an antigen, endocytosis by macrophages etc.)." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:20:58.847" LastActivityDate="2014-03-17T12:20:58.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15843" PostTypeId="5" CreationDate="2014-03-17T10:00:55.240" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T10:00:55.240" LastActivityDate="2014-03-17T10:00:55.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15844" PostTypeId="4" CreationDate="2014-03-17T10:00:55.240" Score="0" Body="Green fluorescent protein is a protein of the jellyfish Aequorea victoria which emits bright green light when it excited with blue to ultraviolet light. The protein is widely used in cell biology to tag proteins and to follow up their localization in the cell." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:16:57.890" LastActivityDate="2014-03-17T12:16:57.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15845" PostTypeId="1" CreationDate="2014-03-17T10:05:16.583" Score="13" ViewCount="1525" Body="&lt;p&gt;Can anyone tell me what kind of insect (if it is one) is this...!! Or is it the pupa of some insect?&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5KciD.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Well I don't think that the whole big thing is the insect itself, it appears to be just a kind of protection or shelter which moves along with the tiny little thing that keeps on popping out and going it so as to move.&lt;/p&gt;&#xA;&lt;p&gt;Location:  India&lt;/p&gt;&#xA;" OwnerUserId="4947" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2017-04-02T14:08:29.987" Title="What insect is this? (India)" Tags="&lt;entomology&gt;&lt;species-identification&gt;&lt;taxonomy&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15846" PostTypeId="5" CreationDate="2014-03-17T10:05:20.790" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T10:05:20.790" LastActivityDate="2014-03-17T10:05:20.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15847" PostTypeId="4" CreationDate="2014-03-17T10:05:20.790" Score="0" Body="Micro RNA (miRNA) are a class of small (22 nucleotide in the mature form) non-coding RNA. They are present in plants and animals and function as transcriptional and post-transcriptional regulators of genes. They bind to a complementary region in the transcribed gene to form doublestanded RNA molecules. These are silenced since they cannot be translated and often subsequently degraded by the cell." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:20:37.483" LastActivityDate="2014-03-17T12:20:37.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15848" PostTypeId="5" CreationDate="2014-03-17T11:19:41.403" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T11:19:41.403" LastActivityDate="2014-03-17T11:19:41.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15849" PostTypeId="4" CreationDate="2014-03-17T11:19:41.403" Score="0" Body="Transcription factors are proteins which regulate the expression of genes. They are divided into two groups: The group of the general transcription factors which are present in every transcription and the special transcription factors, which are present in specific tissues or cells." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:17:48.717" LastActivityDate="2014-03-17T12:17:48.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15850" PostTypeId="5" CreationDate="2014-03-17T11:26:13.430" Score="0" Body="&lt;p&gt;FRET describes the transfer of energy between two closely located chromophores. When the first chromophores gets excited, it will emit energy at a certain wavelength (different from the excitation wavelength). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This emitted wavelenth of the first chromophore will excite the second chromophore, when this is physically close to the first. It will then get excited and emit light at another (different) wavelength. This technique is used to detect interactions of proteins.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:41:13.553" LastActivityDate="2014-03-17T12:41:13.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15851" PostTypeId="4" CreationDate="2014-03-17T11:26:13.430" Score="0" Body="FRET is the abbreviation of Fluorescence resonance energy transfer. " OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:40:42.740" LastActivityDate="2014-03-17T12:40:42.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15852" PostTypeId="5" CreationDate="2014-03-17T11:28:29.940" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T11:28:29.940" LastActivityDate="2014-03-17T11:28:29.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15853" PostTypeId="4" CreationDate="2014-03-17T11:28:29.940" Score="0" Body="CoA is the short form for Coenzyme A. It is a coenzyme which is important in the oxidation of pyruvate in the citric acid cycle. It is also important for the oxidation and synthesis of fatty acids. " OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:17:28.477" LastActivityDate="2014-03-17T12:17:28.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15854" PostTypeId="5" CreationDate="2014-03-17T11:31:54.330" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T11:31:54.330" LastActivityDate="2014-03-17T11:31:54.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15855" PostTypeId="4" CreationDate="2014-03-17T11:31:54.330" Score="0" Body="HLA stands for human leukocyte antigen. It is the name for gene loci which encode the major histocompatibility complex in humans. This locus is important for the function of the immune system in humans." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:41:09.333" LastActivityDate="2014-03-17T12:41:09.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15856" PostTypeId="2" ParentId="15845" CreationDate="2014-03-17T11:36:54.917" Score="18" Body="&lt;p&gt;This is mostly a guess and loose suggestion, since the picture is not very clear (would need to see the larvae in more detail). However, &lt;a href=&quot;http://en.wikipedia.org/wiki/Bagworm_moth&quot;&gt;Bagworm moths&lt;/a&gt; (Psychidae), &lt;a href=&quot;http://en.wikipedia.org/wiki/Case-bearer&quot;&gt;Case moths&lt;/a&gt; (Coleophoridae) and &lt;a href=&quot;http://en.wikipedia.org/wiki/Caddisfly&quot;&gt;Caddisfly larvae&lt;/a&gt; (Trichoptera, almost exclusively aquatic) all build similar cases. They construct their cases out if silk and often include debris, pebbles and other materials. I wouldn't be surprised if the larvae in your picture belongs to one of the first two taxa. Bagworm moths and Caddisflies generally include lots of external materials in their larval cases, which could point to Case moths for your specimen (which seems to have a weaker case mostly made of silk).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are two pictures of first a UK Case moth larvae (&lt;a href=&quot;http://ukmoths.org.uk/showzoom.php?id=5907&quot;&gt;&lt;em&gt;Coleophora deauratella&lt;/em&gt;&lt;/a&gt;) followed by a Bagworm moth (&lt;a href=&quot;http://xenogere.com/2010/04/28/rainy-day-on-the-patio/&quot;&gt;&lt;em&gt;Dahlica triquetrella&lt;/em&gt;&lt;/a&gt;), just as comparisons. If you do google image searches of &quot;group name + larvae&quot; you will see many examples of what they can look like.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/y0o7o.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/DyMRO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And just as a cool example - the larvae often use random material lying around to build their cases, which can give the following result, if caddisfly larvae are bred in a tank containing pieces if gold and pearls. For further information see &lt;a href=&quot;http://marginalrevolution.com/marginalrevolution/2013/02/french-artist-gives-caddisfly-larvae-gold-jewels-to-build-their-protective-cases.html&quot;&gt;this link&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jSihG.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-03-18T09:38:35.563" LastActivityDate="2014-03-18T09:38:35.563" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="15857" PostTypeId="5" CreationDate="2014-03-17T11:48:13.680" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T11:48:13.680" LastActivityDate="2014-03-17T11:48:13.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15858" PostTypeId="4" CreationDate="2014-03-17T11:48:13.680" Score="0" Body="A tumour is a mass of cells which are the result of abnormal growth or cell division. &#xD;&#xA;" OwnerUserId="5144" LastEditorUserId="69" LastEditDate="2014-03-17T12:18:48.453" LastActivityDate="2014-03-17T12:18:48.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15859" PostTypeId="5" CreationDate="2014-03-17T11:51:06.350" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T11:51:06.350" LastActivityDate="2014-03-17T11:51:06.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15860" PostTypeId="4" CreationDate="2014-03-17T11:51:06.350" Score="0" Body="Thermophilia are bacteria (or archea) which are a subgroup of the extremophils. Thermophilia live in hot water between 45°C and 122°C." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:18:08.657" LastActivityDate="2014-03-17T12:18:08.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15861" PostTypeId="5" CreationDate="2014-03-17T11:52:42.670" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T11:52:42.670" LastActivityDate="2014-03-17T11:52:42.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15862" PostTypeId="4" CreationDate="2014-03-17T11:52:42.670" Score="0" Body="Phosphates are salts of phosphoric acid. Monophosphate (or inorganic phosphate) is composed of one central phosphorus atom which is bound to four oxygen atoms. " OwnerUserId="5144" LastEditorUserId="948" LastEditDate="2017-01-01T07:04:05.967" LastActivityDate="2017-01-01T07:04:05.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15863" PostTypeId="5" CreationDate="2014-03-17T11:58:03.727" Score="0" Body="&lt;p&gt;New drugs are tested in controlled clinical trial. To be accepted by the medical regulation bodies, they have to fulfill certain criteria. First, the new drug is either tested against a placebo or against the current best treatment for a disease. Then, all participants including doctors and nurses are so called double-blinded, which means no participant knows who gets the new medication and who belongs to the control group.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:18:59.963" LastActivityDate="2014-03-17T12:18:59.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15864" PostTypeId="4" CreationDate="2014-03-17T11:58:03.727" Score="0" Body="A clinical trial is the process in which new drugs are tested under controlled conditions. " OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:21:34.700" LastActivityDate="2014-03-17T12:21:34.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15865" PostTypeId="5" CreationDate="2014-03-17T12:00:40.420" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T12:00:40.420" LastActivityDate="2014-03-17T12:00:40.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15866" PostTypeId="4" CreationDate="2014-03-17T12:00:40.420" Score="0" Body="Dopamine is a neuotransmitter which is secreted by dopamine-secreting neurons. It is released in the brain by nerve cells to send signals over the synaptic gap to other nerve cells." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:17:58.057" LastActivityDate="2014-03-17T12:17:58.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15867" PostTypeId="5" CreationDate="2014-03-17T12:03:39.777" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T12:03:39.777" LastActivityDate="2014-03-17T12:03:39.777" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15868" PostTypeId="4" CreationDate="2014-03-17T12:03:39.777" Score="0" Body="Atoms are the smallest unit of elements. They are build up by a core of neutrons and protons and are surrounded by a electron hull. Electrons are not charged as the single charges of the elementary particles is neutralized by each other." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:41:27.930" LastActivityDate="2014-03-17T12:41:27.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15869" PostTypeId="2" ParentId="15817" CreationDate="2014-03-17T12:16:26.087" Score="-1" Body="&lt;p&gt;Probably so simple answer is enough&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;acrocyanosis (manifestation of heart failure) which lead to distant (acro - distant) cyanosis, bluish skin. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-03-17T12:16:26.087" CommentCount="0" CommunityOwnedDate="2014-03-17T12:16:26.087" ContentLicense="CC BY-SA 3.0" />
  <row Id="15870" PostTypeId="5" CreationDate="2014-03-17T12:23:04.517" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T12:23:04.517" LastActivityDate="2014-03-17T12:23:04.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15871" PostTypeId="4" CreationDate="2014-03-17T12:23:04.517" Score="0" Body="Pathogenesis is the mechanism by which a disease is causing the disease.  For bacteria this can be the secretion of a toxin which is toxic for the host." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:41:04.413" LastActivityDate="2014-03-17T12:41:04.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15872" PostTypeId="5" CreationDate="2014-03-17T12:25:48.200" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T12:25:48.200" LastActivityDate="2014-03-17T12:25:48.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15873" PostTypeId="4" CreationDate="2014-03-17T12:25:48.200" Score="0" Body="An infection is caused by the invasion of by pathogenic organisms (bacteria, viruses or worms) into a host. These pathogenic organisms live and multiply in its host and cause diseases by this." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T12:41:45.210" LastActivityDate="2014-03-17T12:41:45.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15874" PostTypeId="1" AcceptedAnswerId="15875" CreationDate="2014-03-17T12:52:35.660" Score="1" ViewCount="2136" Body="&lt;p&gt;I am thinking how CVC in lungs lead to the left-sided heart failure.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-16T14:26:22.660" Title="Pathogenesis of Chronic Venous Congestion in Lungs?" Tags="&lt;pathogenesis&gt;&lt;lungs&gt;&lt;congestion&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15875" PostTypeId="2" ParentId="15874" CreationDate="2014-03-17T12:52:35.660" Score="1" Body="&lt;p&gt;I think CVC lead to Pulmonary congestion and edema.&#xA;They produce heavy, wet lungs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pulmonary changes include &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;perivascular and interstitial edema, particularly in the interlobular septa;&lt;/li&gt;&#xA;&lt;li&gt;progessive edematous widening of alveolar septa; and &lt;/li&gt;&#xA;&lt;li&gt;accumulation of edema fluid in alveolar spaces which contain Hemosiderin and microhemorrhages&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Now, the progression of the disease to heart should be discussed.&#xA;I am not sure if hemosiderin can go directly from lungs to heart or if it has to travel through circulation and then to left-side of lung.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-03-17T13:50:26.597" LastActivityDate="2014-03-17T13:50:26.597" CommentCount="0" CommunityOwnedDate="2014-03-17T12:52:35.660" ContentLicense="CC BY-SA 3.0" />
  <row Id="15876" PostTypeId="5" CreationDate="2014-03-17T13:04:43.303" Score="0" Body="&lt;p&gt;Fluorescent microscopy uses the emissions of fluorescently labelled probes to generate an image. &lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-27T12:19:31.840" LastActivityDate="2017-03-27T12:19:31.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15877" PostTypeId="4" CreationDate="2014-03-17T13:04:43.303" Score="0" Body="Fluorescent microscopy uses the emissions of fluorescently labelled probes to generate an image. " OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T14:06:34.047" LastActivityDate="2014-03-17T14:06:34.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15878" PostTypeId="5" CreationDate="2014-03-17T13:11:55.990" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T13:11:55.990" LastActivityDate="2014-03-17T13:11:55.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15879" PostTypeId="4" CreationDate="2014-03-17T13:11:55.990" Score="0" Body="Binding sites are sites in proteins or on DNA where other proteins or DNA can bind. Binding sites are usually conserved." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T14:05:16.387" LastActivityDate="2014-03-17T14:05:16.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15880" PostTypeId="5" CreationDate="2014-03-17T13:15:05.657" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T13:15:05.657" LastActivityDate="2014-03-17T13:15:05.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15881" PostTypeId="4" CreationDate="2014-03-17T13:15:05.657" Score="0" Body="The kidney is an internal, bean shaped organ of vertebrates. Kidneys are responsible for secreting urine, regulate the electrolytes of the body and filter the blood." OwnerUserId="5144" LastEditorUserId="107" LastEditDate="2014-03-17T14:06:55.643" LastActivityDate="2014-03-17T14:06:55.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15882" PostTypeId="5" CreationDate="2014-03-17T13:17:32.530" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T13:17:32.530" LastActivityDate="2014-03-17T13:17:32.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15883" PostTypeId="4" CreationDate="2014-03-17T13:17:32.530" Score="0" Body="Olfactory describes the sense of smell." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T14:05:54.203" LastActivityDate="2014-03-17T14:05:54.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15884" PostTypeId="5" CreationDate="2014-03-17T13:19:14.737" Score="0" Body="&lt;p&gt;The different eye colors are for example different alleles of the genes that make the eye color.&lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="16866" LastEditDate="2019-09-13T02:51:52.853" LastActivityDate="2019-09-13T02:51:52.853" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="15885" PostTypeId="4" CreationDate="2014-03-17T13:19:14.737" Score="0" Body="Alleles are different forms (among many possible alternative forms) of the same gene." OwnerUserId="5144" LastEditorUserId="16866" LastEditDate="2019-09-13T02:51:52.853" LastActivityDate="2019-09-13T02:51:52.853" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="15887" PostTypeId="5" CreationDate="2014-03-17T13:26:49.213" Score="0" Body="&lt;p&gt;Related tags: &lt;a href=&quot;/questions/tagged/respiration&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;respiration&amp;#39;&quot; rel=&quot;tag&quot;&gt;respiration&lt;/a&gt;, &lt;a href=&quot;/questions/tagged/breathing&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;breathing&amp;#39;&quot; rel=&quot;tag&quot;&gt;breathing&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="16866" LastEditDate="2020-01-02T19:42:25.093" LastActivityDate="2020-01-02T19:42:25.093" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="15888" PostTypeId="4" CreationDate="2014-03-17T13:26:49.213" Score="0" Body="The lungs are the respiratory organ which allows the take-up of oxygen and the release of CO2. They are present in most animals which breathe air including many fish species." OwnerUserId="5144" LastEditorUserId="107" LastEditDate="2014-03-17T14:05:42.747" LastActivityDate="2014-03-17T14:05:42.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15889" PostTypeId="5" CreationDate="2014-03-17T13:32:12.420" Score="0" Body="&lt;p&gt;Glucose is a monosaccheride which is build up by plants during photosynthesis.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-29T13:59:53.630" LastActivityDate="2017-03-29T13:59:53.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15890" PostTypeId="4" CreationDate="2014-03-17T13:32:12.420" Score="0" Body="Glucose is a monosaccheride which is build up by plants during photosynthesis. " OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T14:05:47.373" LastActivityDate="2014-03-17T14:05:47.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15891" PostTypeId="5" CreationDate="2014-03-17T13:40:13.367" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T13:40:13.367" LastActivityDate="2014-03-17T13:40:13.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15892" PostTypeId="4" CreationDate="2014-03-17T13:40:13.367" Score="0" Body="An antigen is a substance which causes the the body to produce a reaction of the adaptive immune system. Contact of the immune system to antigens results in the production of highly specific (antigen specific) antibodies." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T14:05:06.917" LastActivityDate="2014-03-17T14:05:06.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15893" PostTypeId="5" CreationDate="2014-03-17T13:43:47.240" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T13:43:47.240" LastActivityDate="2014-03-17T13:43:47.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15894" PostTypeId="4" CreationDate="2014-03-17T13:43:47.240" Score="0" Body="Tuberculosis is a disease caused by the bacterium Mycobacterium tuberculosis. It infects mainly the lungs, but can be found in other parts of the body. Untreated tuberculosis ends fatal." OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-17T14:05:03.403" LastActivityDate="2014-03-17T14:05:03.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15895" PostTypeId="5" CreationDate="2014-03-17T13:44:43.950" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-17T13:44:43.950" LastActivityDate="2014-03-17T13:44:43.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15896" PostTypeId="4" CreationDate="2014-03-17T13:44:43.950" Score="0" Body="Enzyme kinetics is the study of the rates of enzyme-catalysed reactions" OwnerUserId="5144" LastEditorUserId="22057" LastEditDate="2020-12-11T10:29:38.820" LastActivityDate="2020-12-11T10:29:38.820" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="15897" PostTypeId="1" CreationDate="2014-03-17T15:10:15.133" Score="2" ViewCount="521" Body="&lt;p&gt;I performed real-time PCR and I was looking for expression fold changes for 2 genes and I had two sample pools, one treated and the other not treated (for each gene). The problem is that my housekeeping gene (UBQ 30) got a fold change on the treatment. Therefore, what is the correct interpretation and data treatment?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I mean, is it correct to use each control and treatment I got for UBQ CT values to normalize the other two genes corresponding CT, as housekeeping genes are &quot;by definition&quot; expected not to change? (and that is why indeed they are used to normalize)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or should I rather make a mean of my whole UBQ CT-s and normalize all other genes CT values with that mean?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="9943" LastEditDate="2015-05-28T06:05:54.423" LastActivityDate="2015-05-28T07:05:23.713" Title="Real-time PCR result interpretation" Tags="&lt;pcr&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15898" PostTypeId="1" AcceptedAnswerId="15906" CreationDate="2014-03-17T16:17:44.793" Score="3" ViewCount="90" Body="&lt;p&gt;I am working with a set of DNA motifs that are predicted as potential regulatory motifs (e.g. transcription factor binding sites).&#xA;The motifs belong to several species, and I wanted to cluster these motifs via their Position Weight Matrices (PWMs) (also known as PSSMs) to collapse similar motifs together into groups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a tool called MATLIGN (&lt;a href=&quot;http://ekhidna.biocenter.helsinki.fi/poxo/matlign/help#p0&quot; rel=&quot;nofollow&quot;&gt;website here&lt;/a&gt;) that does what I need, but their required format for the PWMs are different to what I have, they claim:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Matrices must be in the frequency matrix format (only integer numbers&#xA;  are acceptable)&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The problem is that my PWM matrices do not have integer numbers but decimals instead. e.g.:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;     A        C        G        T&#xA;1    0.000000 1.000000 0.000000 0.000000&#xA;2    1.000000 0.000000 0.000000 0.000000&#xA;3    0.000000 0.000000 1.000000 0.000000&#xA;4    0.000000 0.421755 0.000000 0.578245&#xA;5    0.289407 0.000000 0.282556 0.428038&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;In other words, instead of the decimal values I have in my matrix I need to have integer counts. Could anybody suggest what I can do? Would I need to create artificial &quot;pseudo-counts&quot;?&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="3624" LastEditDate="2014-03-18T10:27:01.150" LastActivityDate="2014-03-18T18:01:31.403" Title="How can I re-format my DNA motifs' position weight matrices?" Tags="&lt;dna&gt;&lt;transcription&gt;&lt;software&gt;&lt;gene-regulation&gt;&lt;transcription-factor&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15899" PostTypeId="1" AcceptedAnswerId="15976" CreationDate="2014-03-17T17:06:52.050" Score="2" ViewCount="776" Body="&lt;p&gt;A friend used potassium permanganate solution to treat tinea on the hands/feet but after some initial success, the tinea seems to be making a comeback. Could the fungus develop resistance to potassium permanganate?&lt;/p&gt;&#xA;" OwnerUserId="1524" LastEditorUserId="1524" LastEditDate="2014-03-17T17:16:00.193" LastActivityDate="2015-06-25T08:15:46.653" Title="Can a fungus become resistant to a chemical such as Potassium Permanganate?" Tags="&lt;microbiology&gt;&lt;pharmacology&gt;&lt;pathology&gt;&lt;toxicology&gt;&lt;mycology&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="15901" PostTypeId="1" CreationDate="2014-03-17T19:26:06.717" Score="0" ViewCount="34" Body="&lt;p&gt;I'm going to engage into making florariums (a garden in the bottle). I've heard, that violets die in closed space. Do anyone have an idea, what is the reason for that? Lack of oxygen or CO2 or moisture control issues?&lt;/p&gt;&#xA;" OwnerUserId="6070" LastActivityDate="2014-03-18T16:52:55.473" Title="Why violets die in closed space?" Tags="&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15902" PostTypeId="2" ParentId="15736" CreationDate="2014-03-17T19:59:59.383" Score="11" Body="&lt;p&gt;First of all, I should correct some points that were misunderstood. &#xA;Don't change the question because this will lead to confusion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The way the lens becomes flat is by using spring-like connective tissue called choroids that pull it taught.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In classic ophthalmology you don't need to think about choroid in direct relation to accommodation: choroid is a sponge-like layer between the sclera and retina and in general it is consisted of blood vessels. The anterior part of the choroid continues anteriorly to became a ciliary body which in turn contains ciliary muscle - one circular muscle per eye. From the ciliary body/muscle spread zonules (zonule fibers) and they are fixed on the lens equator. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Physiology: contraction of &lt;strong&gt;ciliary muscle&lt;/strong&gt; causes &lt;strong&gt;zonules&lt;/strong&gt; to became loosen and &lt;strong&gt;&quot;free&quot; the lens&lt;/strong&gt; to became more convex and move the focus anteriorly (&lt;em&gt;not choroid contracts itself&lt;/em&gt;). If the ciliary muscle relaxes then zonules are tighten up and the lens consequently becomes more flat (less convex) moving the focus posteriorly. In other words you can say it in the terms of depth of focus - convex lens gives less depth, less convex gives more depth of focus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, the classical choroid layer does not perform any action (look at your choroid related link - there are almost nothing about accommodation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Permanent state of contraction&quot; can be physiological (=normal) as well as abnormal one, and it is very common in some conditions (muscles spasms). One example is priapism, where corporal smooth muscle contraction causes permanent and dangerous penile erection which can be medical emergency (priapism is by far more complex, so take the explanation like a metaphor). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we refer to &quot;accommodation spasm&quot; there is analogy to &quot;muscle spasm&quot; (and partially to priapism), but I should state we believe that spasm of ciliary muscle exists - since we don't see it directly. Probably (and take this sentence as speculation, since I cannot give you reference right now) the causes of this is not a muscle spasm itself, but the state of zonular fibers which cannot come back to their base state. I like the example with iron rod - if you will contract it fast and many times, at some point it can be &quot;loosen&quot; as well as fractured (and probably it does happens to zonules too). Probably (I say &quot;probably&quot; to underline the point we do not exactly know this), the &quot;accommodation spasm&quot; is partially misname and in future the investigations will clarify that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably, you will learn some interesting facts from definition of &quot;pseudoexfoliation&quot; syndrome, but I do not explain it here because it is not related directly to the question. From &lt;a href=&quot;http://en.wikipedia.org/wiki/Pseudoexfoliation_syndrome&quot; rel=&quot;noreferrer&quot;&gt;wiki&lt;/a&gt; &quot;has been known to cause a weakening of structures within the eye which help hold the eye's lens in place, called lens zonules&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example for analogy for continued &quot;spasm&quot; is the situation when one should care something heavy for a long distance without releasing the grasp - finally one can get not only spastic contraction but also severe ischemic damage to the fingers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering your case, you should know about pathological (degenerative) myopia where the eye expands posteriorly and consequently the focus is before the retina which should be corrected by minus lenses. It is well known fact that myopic eyes have longer axial length then normal eyes. Probably, it is your case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, as you can see, the answer to your question is not a clear cut, but assumption. The ciliary muscle does can relax, but probably the problem is more complex then only ciliary muscle related issue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS The image you reposted is a little bitconfusing one and is not exact. This one is classical and gives better understanding of the anatomy - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4Bvku.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2014-03-17T20:31:24.203" LastActivityDate="2014-03-17T20:31:24.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15904" PostTypeId="1" AcceptedAnswerId="15912" CreationDate="2014-03-18T03:15:02.207" Score="4" ViewCount="311" Body="&lt;p&gt;I really like this plant--I'm just wondering what its name is (perhaps genus+species). I think this plant grows in the tropical rainforest in Malaysia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QAlZd.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any suggestions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="6072" LastEditorUserId="3624" LastEditDate="2014-03-18T11:06:36.783" LastActivityDate="2014-03-18T15:22:41.753" Title="What is this plant?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15906" PostTypeId="2" ParentId="15898" CreationDate="2014-03-18T09:08:53.750" Score="3" Body="&lt;p&gt;So what you need is basically your data expressed as counts instead of proportions. Even if you do not have the matrix of counts as raw data, these proportions only needs to be multiplied by the total number of binding sites used in the study (e.g. the number of sequences that have been analysed) to get the counts (since proportion = count/total number of binding sites). You should have that information somewhere. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;@hello_there_andy: indeed there was this missing piece of information available to me, it came in the form of a variable called &lt;strong&gt;nsites&lt;/strong&gt; which equates to the total number of DNA sites that the PWM was generated from.  &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="5005" LastEditDate="2014-03-18T18:01:31.403" LastActivityDate="2014-03-18T18:01:31.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15907" PostTypeId="1" AcceptedAnswerId="15920" CreationDate="2014-03-18T10:50:07.423" Score="4" ViewCount="945" Body="&lt;p&gt;In monoecious plants having unisexual flowers (eg &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Maize&quot; rel=&quot;nofollow&quot;&gt;Zea Mays&lt;/a&gt;&lt;/em&gt;, &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Castor_oil_plant&quot; rel=&quot;nofollow&quot;&gt;Ricinus Communis&lt;/a&gt;&lt;/em&gt; etc), there must be some mechanism as to produce two sexually distinct flowers from the same genotype. Since both the type of flowers are placed on the same plant, the genetic constitution of the cells of both the type of flowers will be similar. &lt;strong&gt;What is the mechanism by which the development of two sexually distinct flowers is carried out in such plants?&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the mechanism similar to the mechanism for differential gene expression in case of embryonic development (&lt;a href=&quot;http://en.wikipedia.org/wiki/Homeobox&quot; rel=&quot;nofollow&quot;&gt;Homeobox genes&lt;/a&gt;)? And moreover, &lt;strong&gt;is the genetic constitution of the pollen produced by the male flower similar to that of the egg produced by the female flower, with respect to the composition of autosomes and allosomes (if any)?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3615" LastEditDate="2014-03-18T17:35:10.817" LastActivityDate="2014-03-20T03:30:16.393" Title="Sexual Differentiation in Monoecious plants with unisexual flowers" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;molecular-genetics&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15908" PostTypeId="2" ParentId="15502" CreationDate="2014-03-18T11:33:44.630" Score="8" Body="&lt;p&gt;By now I got some interesting answers in &lt;a href=&quot;http://www.biostars.org/p/95310/#95310&quot; rel=&quot;noreferrer&quot;&gt;this question on Biostars&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically what I did is the following:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;First of all, I checked if Sequence Id contains paired end notation. As described in &lt;a href=&quot;http://en.wikipedia.org/wiki/FASTQ_format&quot; rel=&quot;noreferrer&quot;&gt;this wikipedia page&lt;/a&gt;, for Illumina reads there are two possible notation for single/paired end reads:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;@HWUSI-EAS100R:6:73:941:1973#0/1&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the last number is &lt;code&gt;/2&lt;/code&gt; in some reads then the reads are paired end; otherwise they can be single end. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second notation is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the first number in the second group is &lt;code&gt;2&lt;/code&gt; in some reads then the reads are paired end; otherwise they can be single end;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Then I checked for multiple files. If a sample has two fastq files it is likely that the reads are paired end. It is to note however that with a single file it is not possible to exclude that paired end reads can be interleaved in one single file, even if it is not common (in my opinion);&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The most general method is to cross check each single reads with the whole set of reads. If the first part of the sequence ID (in this case the field starting from &lt;code&gt;@&lt;/code&gt; and ending before the &lt;code&gt;#&lt;/code&gt; - in the first notation - or the whitespace - in the second notation) is unique among all the reads (for each read) it is likely that the reads are single reads, otherwise - if can be found a duplicate for each reads - the reads are paired end.&#xA;In this case, on *nix systems it can be achieved with the following command (thanks to the biostars answers):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;grep --no-filename @HWUSI-EAS100R:6:73:941:1973 *.fastq | cut -d' ' -f1 | sort | uniq -c | sort -rgk 1,1 | head&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the result shows in the first lines a result like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1        read1_ID&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1        read2_ID&lt;/p&gt;&#xA;&#xA;&lt;p&gt;...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is likely it is single end. Otherwise:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2        read1_ID&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2        read2_ID&lt;/p&gt;&#xA;&#xA;&lt;p&gt;...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;it is paired end.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I skim read BioPython API documentation but I cannot find something useful to do it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suggestions and corrections are welcomed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="3466" LastActivityDate="2014-03-18T11:33:44.630" CommentCount="0" CommunityOwnedDate="2014-03-18T11:33:44.630" ContentLicense="CC BY-SA 3.0" />
  <row Id="15910" PostTypeId="1" AcceptedAnswerId="15911" CreationDate="2014-03-18T13:30:45.943" Score="1" ViewCount="50" Body="&lt;p&gt;From &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12573379&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Those with shorter telomeres in blood DNA had poorer survival,&#xA;  attributable in part to a 3.18-fold higher mortality rate from heart&#xA;  disease (95% CI 1(.)36-7.45, p=0.0079), and an 8.54-fold higher&#xA;  mortality rate from infectious disease (1.52-47.9, p=0.015).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What is the connection between shorter telomeres and heart disease ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-18T14:52:44.957" Title="Association of shorter telomeres with heart disease" Tags="&lt;human-biology&gt;&lt;dna&gt;&lt;cardiology&gt;&lt;hematology&gt;&lt;telomere&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15911" PostTypeId="2" ParentId="15910" CreationDate="2014-03-18T14:52:44.957" Score="2" Body="&lt;p&gt;This seems a bit like a hen and egg problem. Telomere length is both associated with age and with heart diseases, but heart disease is also associated with age. The question here is, is one really causing the other here (short telomeres heart problems) or do they occur simultaneously? The other problem with heart disease is that it is a multi-risk disease, with many risks accumulating with age. The figure below sums this up, it is from the first paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LvjZH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a look on these articles:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://eurjhf.oxfordjournals.org/content/10/11/1049.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Telomere biology in heart failure&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20532978&quot; rel=&quot;nofollow noreferrer&quot;&gt;Aging, telomeres and heart failure.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://circres.ahajournals.org/content/94/5/575.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Telomeres and Cardiovascular Disease&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-18T14:52:44.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15912" PostTypeId="2" ParentId="15904" CreationDate="2014-03-18T14:55:19.047" Score="5" Body="&lt;p&gt;I'm no botanist, but this looks very similar to a young banana plant (&lt;a href=&quot;https://en.wikipedia.org/wiki/Musa_%28genus%29&quot; rel=&quot;noreferrer&quot;&gt;Musa sp.&lt;/a&gt;) to me. The genus is native to south east asia, and there are many wild species. There are also a couple of other similarly looking genera in the banana family (&lt;a href=&quot;http://en.wikipedia.org/wiki/Musaceae&quot; rel=&quot;noreferrer&quot;&gt;Musaceae&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reasons why I'm thinking banana: the plant has tongue-shaped leafs with fairly short petioles, and the leaves have clear horizontal, unbranched veins and horizontal tears (common on banana plants). The leaves come from a single apical meristem and are scattered (not in e.g. distinct rows). Banana plants also have pseudostems, made out of packed leaf sheaths, but the stem cannot be seen in your picture. &lt;a href=&quot;http://www.promusa.org/tiki-index.php?page=Morphology+of+banana+plant&quot; rel=&quot;noreferrer&quot;&gt;Here&lt;/a&gt; is a webpage on banana morphology, if you want to get some further information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some examples:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GNLr0.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/tSAXo.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-03-18T15:22:41.753" LastActivityDate="2014-03-18T15:22:41.753" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15913" PostTypeId="1" CreationDate="2014-03-18T15:12:16.313" Score="2" ViewCount="4766" Body="&lt;p&gt;I am confused about relationship between isoelectric point and pH in context of ion exchange protein purification. Why we cannot use this method for protein with pI below 7? Thank you very much for any tips.&lt;/p&gt;&#xA;" OwnerUserId="4593" LastActivityDate="2014-03-18T16:57:53.303" Title="pI and pH relationship in context of ion exchange protein purification" Tags="&lt;proteins&gt;&lt;purification&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15915" PostTypeId="1" CreationDate="2014-03-18T15:43:05.007" Score="1" ViewCount="2175" Body="&lt;p&gt;A very smart friend of mine seems to get taken in by junk science. He started telling me last night that the electromagnetic field of the heart can be detected beyond 30 feet. What is the actual distance? Thank you.&lt;/p&gt;&#xA;" OwnerUserId="6079" LastActivityDate="2020-09-14T16:03:55.357" Title="The distance the electromagnetic field of the heart can be detected" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15916" PostTypeId="2" ParentId="15913" CreationDate="2014-03-18T16:10:30.160" Score="1" Body="&lt;p&gt;Have a look at this table, it really depends on the buffers you use:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9e4vg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The table is from this &lt;a href=&quot;http://www.reachdevices.com/Protein/ProteinPurification.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;website&lt;/a&gt;, which is definitely worth reading when you are interested (or work) with ion exchange chromatography.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-18T16:10:30.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15917" PostTypeId="2" ParentId="15901" CreationDate="2014-03-18T16:52:55.473" Score="1" Body="&lt;p&gt;I believe it is because of the violets' propensity to collect mould. They seem to like warm, humid space, but in a closed-air type system, it is a breeding ground for mould. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There could be another reason as to why they die, but I would assume it would be an infection. &lt;/p&gt;&#xA;" OwnerUserId="6080" LastActivityDate="2014-03-18T16:52:55.473" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15918" PostTypeId="2" ParentId="15913" CreationDate="2014-03-18T16:57:53.303" Score="1" Body="&lt;p&gt;The pI (iso-electric point) is the pH at which the protein (or other molecule), overall has a net zero charge. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As @Chris points out, the buffer you are using will change the pH the protein finds itself in.  This will change the charge of the protein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In ion exchange chromatography, there are charged chemical groups on the resin and these can cause a protein to be retained on the resin if the protein is complementary (opposite charged)  to the resin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if you have a protein with a pI of 5 say, it would neutral with the presence of excess H+.  This implies that the protein has an overall negative charge.  A cationic resin would tend to retain this protein in a pH 7 buffer.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope that makes sense. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In most cases, ion exchange chromatography is used when most of the protein is separated out and there are a few proteins (maybe a couple of hundred) mixed together.  It can get tricky if you see that the protein is mixed in with something that is also negatively charged.  In that case you might change the pH of the buffer so that other negatively charged proteins are closer to their isoelectric point and come through the column faster than the one you desire to purify.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-03-18T16:57:53.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15919" PostTypeId="1" AcceptedAnswerId="16935" CreationDate="2014-03-18T17:17:26.823" Score="0" ViewCount="36" Body="&lt;p&gt;I think it can because there are many parts in lungs.&#xA;Like for some COPD patients.&#xA;However, I am not sure if COPD patients can have infarction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lungs have parallel circulation.&#xA;Red infarct is possible there.&#xA;Blood can flow there.&#xA;One symptom should be at least pain.&#xA;So now, I think no asymptomatic possible.&#xA;But still, I am not sure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can pulmonary infarction be asymptomatic?&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-27T16:46:27.867" Title="Can pulmonary infarction be asymptomatic?" Tags="&lt;pathology&gt;&lt;pathogenesis&gt;&lt;lungs&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15920" PostTypeId="2" ParentId="15907" CreationDate="2014-03-18T17:24:19.313" Score="3" Body="&lt;p&gt;I will be able to answer only a part of the question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Sex determination in Zea Mays&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Initially, all the flowers in the plant are perfect, ie they have both the male and the female&#xA;flowers. This is followed by abortion of stamen or pistil resulting in unisexual flowers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which part of the flower undergoes abortion is determined according to the location of the flower. The florets in the tassel undergo the suppression of the pistil primordia resulting in staminate flowers, while the florets in the ear undergo suppression of stamen primordia resulting in female flowers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rgC6b.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hormone Gibberelic Acid seems to play a role in sex determination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source and other useful links :&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://books.google.co.in/books?id=MmO6rXOyvasC&amp;amp;pg=PA185&amp;amp;lpg=PA185&amp;amp;dq=sex+determination+in+maize&amp;amp;source=bl&amp;amp;ots=Kj40YQXMkd&amp;amp;sig=Ju6hXdfvUqueRhipncX5NlM3u-w&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=DqYpU4TJM8OOrQfF_YGIDA&amp;amp;ved=0CGAQ6AEwBQ#v=onepage&amp;amp;q=sex%20determination%20in%20maize&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sex determination in Plants by CC Ainsworth.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.amjbot.org/content/94/2/141.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sex chromsomes in flowering plants&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC159810/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sex determination in monoecious and dioecious plants&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.sciencemag.org/content/266/5190/1501&quot; rel=&quot;nofollow noreferrer&quot;&gt;The sex determination process in maize&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3776" LastEditDate="2014-03-20T03:30:16.393" LastActivityDate="2014-03-20T03:30:16.393" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="15921" PostTypeId="1" AcceptedAnswerId="15923" CreationDate="2014-03-18T18:00:15.103" Score="2" ViewCount="87" Body="&lt;p&gt;I know that &lt;a href=&quot;http://en.wikipedia.org/wiki/BRCA2&quot; rel=&quot;nofollow&quot;&gt;BRCA2&lt;/a&gt; interacts with RAD51 to repair DNA damage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But how exactly does it function ? What are the other proteins that interact with it ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-19T18:37:06.470" Title="Functioning of BRCA2" Tags="&lt;dna&gt;&lt;genetics&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15923" PostTypeId="2" ParentId="15921" CreationDate="2014-03-18T18:33:27.370" Score="3" Body="&lt;p&gt;I'm just skimming through it now, but &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22193408&quot; rel=&quot;nofollow&quot;&gt;this 2011 review&lt;/a&gt; in Nature Reviews Cancer looks like it has everything you could possibly want to know about the BRCA1/BRCA2 pathway. If you don't have access to the journal, the first page of &lt;a href=&quot;https://www.google.com/#q=brca2+pathway&quot; rel=&quot;nofollow&quot;&gt;this Google search&lt;/a&gt; should have a PDF link to Researchgate down near the bottom, or you can try &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=14&amp;amp;ved=0CI4BEBYwDQ&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fpublication%2F224824106_BRCA1_and_BRCA2_important_differences_with_common_interests%2Ffile%2F79e415106a30cd771d.pdf&amp;amp;ei=6IooU7G3A67I0AHa64HYDA&amp;amp;usg=AFQjCNHvfWpRjQ-ERgdGv9NWcrX4aZnB2Q&amp;amp;sig2=CDBUO42tsTHJ0cymbm5AVg&amp;amp;bvm=bv.62922401,d.dmQ&amp;amp;cad=rja&quot; rel=&quot;nofollow&quot;&gt;this direct link&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I apologize for the &quot;link-only&quot; answer, but there is a ton of info in the paper, and it would be rather difficult to summarize it in just a few paragraphs. This is a rather broad question, so perhaps you could read through the review and references, and if you still have specific questions about the pathways or interactions you can ask another question.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="3615" LastEditDate="2014-03-19T18:09:32.267" LastActivityDate="2014-03-19T18:09:32.267" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15924" PostTypeId="2" ParentId="13997" CreationDate="2014-03-18T19:43:01.073" Score="2" Body="&lt;p&gt;The progenitor cells of T-cells (they do not develop into T-cells and show their characteristics before reaching the thymus) are mobilized into the bloodstream and enter the thymus from it by crossing the endothelial barrier. The figure shows schematically the development of the precursor cells from hematopoietic stem cells (HSC) and the migration of the precursor cells (it is from the paper linked below):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HS0Zo.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this review for the details (if you have problems accessing the article, let me know):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18925398&quot; rel=&quot;nofollow noreferrer&quot;&gt;The long road to the thymus: the generation, mobilization, and&#xA;circulation of T-cell progenitors in mouse and man.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-18T19:43:01.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15926" PostTypeId="1" CreationDate="2014-03-18T20:21:41.453" Score="3" ViewCount="264" Body="&lt;p&gt;I am supposed to construct a plasmid that contains features from two other plasmids. &#xA;My strategy is to generate three fragments form the two other plasmids. I was encouraged to try Gibson assembly, so I went to NeBuilder entered my sequences and got I list of primers with overhangs and ordered them… But now I am I bit unsure about the linearization of the backbone and insert into that fragment.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In NeBuilder you can choose &quot;by sequence position&quot; in for the insert in the backbone the description reads &lt;em&gt;“Entering the sequence positions of the bases immediately flanking the insert site. Primers for inverse PCR terminating at these endpoints will be calculated automatically”&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have experience using NeBuilder? i am completely unfamiliar with inverse PCR ? &#xA;also my regular software package Geneious is unable to comprehend the two primers for the inverse PCR reaction&lt;/p&gt;&#xA;" OwnerUserId="6082" LastActivityDate="2014-03-18T20:21:41.453" Title="Gibson assembly using NeBuilder" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;lab-techniques&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15927" PostTypeId="1" AcceptedAnswerId="39948" CreationDate="2014-03-18T20:35:01.463" Score="0" ViewCount="3667" Body="&lt;p&gt;Fibrosis is the formation of excess fibrous connective tissue in an organ or tissue in a reparative or reactive process.&#xA;I used the word &quot;fibrogenesis&quot; as the outcome of acute inflammation (healing).&#xA;My colleges use the word &quot;fibrosis&quot;.&#xA;The fibrogenesis seems to be used with the emphasises of the genetic part.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the difference between fibrogenesis and fibrosis?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2015-10-26T02:35:06.440" Title="What is the difference between fibrogenesis and fibrosis?" Tags="&lt;pathology&gt;&lt;pathogenesis&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15928" PostTypeId="1" AcceptedAnswerId="15930" CreationDate="2014-03-18T21:06:24.117" Score="8" ViewCount="2499" Body="&lt;p&gt;I would imagine the bacterial genome is highly conserved and limited in its space, but maybe I am wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you were to take a strain of antibiotic resistant bacteria and kept them isolated, but fed well and so forth, how long would it take for them to lose their resistance? A year? A decade? 100 years? 1000 years? At some point it seems like that trait would disappear, but I have no feeling for how long. Please support your answer with a relevant citation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My purpose is simple: I am thinking about a strategy for dealing with antibiotic resistance. If we were to ban them across the entire world (could be impossible) how long would we need to wait before they would be usable again. If it was a matter of years, then we could almost do a rotation of existing antibiotics (if we had enough) because I would rather not live in post-antiobitic world.&lt;/p&gt;&#xA;" OwnerUserId="6084" LastEditorUserId="3624" LastEditDate="2014-03-20T09:53:48.737" LastActivityDate="2017-04-19T23:54:21.853" Title="How quickly is antibiotic resistance lost?" Tags="&lt;bacteriology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15929" PostTypeId="1" AcceptedAnswerId="15933" CreationDate="2014-03-18T21:46:00.917" Score="5" ViewCount="21444" Body="&lt;p&gt;I have a question about the role of NaCl in the DNA extraction process. So for NaCl concentrations under 0.5M, CTAB and DNA molecules can create complexes. &#xA;In those concentrations, proteins and other hydrocarbons are still soluble in water except the DNA-CTAB complex. If we raise the concentration of NaCl then the complex of CTAB-DNA will be soluble to water too. Correct me if I'm wrong until now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I don't understand something. Why do we use NaCl?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's assume that we don't add NaCl. Will the CTAB create complex with DNA or not? As I read CTAB creates ionic bonds with DNA (phosphate groups). So in this situation (without NaCl) CTAB must be able to create complex with DNA too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why did we use NaCl? Just to keep proteins and other hydrocarbons soluble in the water or there is something else that NaCl helps in this complex creation?&lt;/p&gt;&#xA;" OwnerUserId="6032" LastEditorUserId="107" LastEditDate="2014-03-18T23:53:42.000" LastActivityDate="2014-12-09T02:16:35.780" Title="NaCl role in CTAB - DNA complex in DNA extraction" Tags="&lt;lab-techniques&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15930" PostTypeId="2" ParentId="15928" CreationDate="2014-03-18T21:52:52.327" Score="10" Body="&lt;p&gt;Antibiotic resistances in bacteria is commonly encoded by extrachromosomal DNA, the plasmids. These are circular pieces of DNA, which are much smaller than the hosts genome and which replicate independently from it. See the image from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Plasmid&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YQ1az.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These plasmids can be transfered between different bacterial cells, which then also get resistant. Plasmids are divided between daughter cells, when the parent cell divides. One of the few exceptions seems to be Mycobacterium tuberculosis, which does not seem to carry plasmids but also develops resistances. It has been hypothesized that they contain extrachromosomal single-stranded DNA (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2115217&quot; rel=&quot;noreferrer&quot;&gt;Does Mycobacterium tuberculosis have plasmids?&lt;/a&gt;&quot;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding your question: Plasmids which carry antibiotic resistances will only disappear, when the antibiotic is not seen for a while, since the cells, which don't carry it, have a growth advantage over cells who are still carriers (since they save the energy of forming the plasmid). However, these resistance plasmids are nothing new, evolutionary speaking. They appeared as a countermeasure against fungal toxins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the lab, bacterial strains loose plasmids within a few days, when not kept under selection pressure according to my experience. There are a few paper who looked into it:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10924453&quot; rel=&quot;noreferrer&quot;&gt;Natural selection, infectious transfer and the existence conditions&#xA;for bacterial plasmids.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17890367&quot; rel=&quot;noreferrer&quot;&gt;The persistence of parasitic plasmids.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.biomedcentral.com/1471-2148/11/130&quot; rel=&quot;noreferrer&quot;&gt;The evolution of plasmid-carried antibiotic resistance&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-18T22:28:54.897" LastActivityDate="2014-03-18T22:28:54.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15931" PostTypeId="2" ParentId="15928" CreationDate="2014-03-18T21:54:00.477" Score="2" Body="&lt;p&gt;Lab strains of &lt;em&gt;E. coli&lt;/em&gt; have been in use for many decades now. They have all retained a large number of genes encoding subunits of the flagellar apparatus and the chemotaxis system which confer absolutely no advantage under normal culture conditions. I conclude from this that the selective advantage conferred by losing &quot;unused&quot; genes must be very weak.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, most antibiotic resistance is encoded on plasmids. As @Chris points out, these can be lost easily.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-18T21:54:00.477" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="15932" PostTypeId="1" CreationDate="2014-03-18T22:21:19.570" Score="2" ViewCount="47" Body="&lt;p&gt;Tumor cells are able to migrate due to specific migration proteins.&#xA;What is their evolutionary origin?&#xA;Or are they simply deregulated?&lt;/p&gt;&#xA;" OwnerUserId="6044" LastActivityDate="2014-05-10T17:44:23.217" Title="Evolutionary rationale behind migration proteins" Tags="&lt;proteins&gt;&lt;cancer&gt;&lt;protein-evolution&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15933" PostTypeId="2" ParentId="15929" CreationDate="2014-03-18T22:27:40.283" Score="3" Body="&lt;p&gt;CTAB forms insoluble complexes with nucleic acids and can be used to selectively precipitate them from solutions, see this reference: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0006300253903047&quot; rel=&quot;nofollow&quot;&gt;The isolation of bacterial nucleic acids using cetyltrimethylammonium&#xA;bromide (Cetavlon)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;When you add NaCl in a concentration between 0.4 - 0.7M, the nucleic acids stay in solution, while polysaccharides and other substances, which may interfere with the DNA preparation do not. See this paper: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC324241/&quot; rel=&quot;nofollow&quot;&gt;Rapid isolation of high molecular weight plant DNA.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="9943" LastEditDate="2014-12-09T02:16:35.780" LastActivityDate="2014-12-09T02:16:35.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15934" PostTypeId="2" ParentId="15928" CreationDate="2014-03-18T22:43:43.683" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;If you were to take antibiotic resistant bacteria and kept them&#xA;  isolated, but fed well and so forth, how long would it take for them&#xA;  &quot;forget&quot; their resistance?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's not a matter of &quot;forgetting&quot;.  Bacteria are resistant if their DNA is such that it gives them a biology that renders the antibiotic non-lethal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You put a resistant bacteria in glycerol stocks, you can freeze them for years, maybe longer, and when you revive the population, and get it growing again, the resulting population will still be resistant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, when we talk about bacteria, or any kind of evolution, &lt;strong&gt;single organisms don't change their DNA&lt;/strong&gt;.  Populations change their proportion of different alleles.  Any allele might drift out of a population, and if the resistance-granting mutation is deleterious, natural selection might speed that along, but not all resistance-granting alleles are deleterious enough for that.  If a resistance-granting allele is survival neutral in the absence of the antibiotic, or another mutation somewhere else restores the bacterias' survivability absent antibiotic to what the sensitive genotype's fitness is, the resistance-granting allele might not drift out of the population for a long time.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastEditorUserId="3340" LastEditDate="2014-03-20T10:51:23.640" LastActivityDate="2014-03-20T10:51:23.640" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15937" PostTypeId="1" AcceptedAnswerId="15951" CreationDate="2014-03-18T17:49:28.237" Score="11" ViewCount="17070" Body="&lt;p&gt;While I know that in nature, carnivorous animals are poorly suited to eat plants (largely due to having sharp teeth, not grinding teeth, as far as I know), I was wondering if, in an emergency situation such as imminent starvation, &lt;strong&gt;could a carnivorous animal such as a wolf survive &lt;em&gt;solely&lt;/em&gt; on plant life&lt;/strong&gt;, maybe requiring it to be ground up before hand? &lt;strong&gt;Could an herbivore survive on meat, if the meat was prepared in a manner that would allow the herbivore to eat it?&lt;/strong&gt; Would a wild animal voluntarily consume food that it is not suited for if it would stave off certain death, or would it require force feeding or training?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I am interested in the other side of this question: &lt;em&gt;if an animal cannot safely consume food outside of its normal diet&lt;/em&gt; (carnivore eating plants, herbivores consuming meat), &lt;strong&gt;what negative effects would this action have on the animal?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Just a note, this is purely a hypothetical question, and I am only asking out of curiosity. I am in no way planning on doing this, nor do I advise anyone else doing this if there is a high chance of it harming the animal.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="6087" OwnerDisplayName="The Ugly" LastActivityDate="2018-06-15T10:22:40.040" Title="Can a carnivorous animal consume plants with no adverse effects?" Tags="&lt;diet&gt;&lt;safety&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15939" PostTypeId="2" ParentId="15897" CreationDate="2014-03-19T03:16:21.720" Score="5" Body="&lt;p&gt;You should try another housekeeping gene like GAPDH since the very definition of these genes is that they &lt;em&gt;shouldn't&lt;/em&gt; change with your treatment&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-03-19T03:16:21.720" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15940" PostTypeId="1" AcceptedAnswerId="15941" CreationDate="2014-03-19T09:38:37.113" Score="2" ViewCount="14776" Body="&lt;p&gt;Is inbreeding the same as interbreeding?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On this site &lt;em&gt;interbreeding&lt;/em&gt; is defined as (&lt;a href=&quot;http://www.thefreedictionary.com/interbreeding&quot; rel=&quot;nofollow&quot;&gt;http://www.thefreedictionary.com/interbreeding&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;To breed with another kind or species; hybridize.&lt;/li&gt;&#xA;  &lt;li&gt;To breed within a narrow range or with closely related types or individuals; inbreed.&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But I am sure that interbreeding is not the same as inbreeding. Inbreeding would be between genetically related members of a species and interbreeding would be between genetically un-related members of the same or different species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;after looking at wikepedia pages for both terms as well as searching the english oxford dictionar I am certain they are different&lt;/p&gt;&#xA;" OwnerUserId="6088" LastEditorUserId="3624" LastEditDate="2016-02-17T15:38:57.403" LastActivityDate="2016-02-17T15:38:57.403" Title="Difference between inbreeding and interbreeding" Tags="&lt;terminology&gt;&lt;reproductive-biology&gt;&lt;sexual-reproduction&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15941" PostTypeId="2" ParentId="15940" CreationDate="2014-03-19T10:26:53.057" Score="3" Body="&lt;p&gt;You are basically correct. Most common usage in my experience:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Inbreeding&quot; rel=&quot;nofollow&quot;&gt;Inbreeding&lt;/a&gt;&lt;/strong&gt; refers to sexual reproduction between genetically closely related individuals, within a species. Inbreeding will increase the relatedness between individuals in a population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Interbreeding&quot; rel=&quot;nofollow&quot;&gt;Interbreeding&lt;/a&gt;&lt;/strong&gt; refers to reproduction with another species (or race), and is often used as a synonym to &lt;em&gt;crossbreeding&lt;/em&gt; or &lt;em&gt;hybridization&lt;/em&gt; (when referring to hybrid offspring from two different species/races/breeds, not DNA hybridization). This is also how '&lt;em&gt;Interbreeding&lt;/em&gt;' is defined in the &lt;a href=&quot;http://www.oed.com/view/Entry/97546?redirectedFrom=interbreed#eid&quot; rel=&quot;nofollow&quot;&gt;Oxford English Dictionary&lt;/a&gt;. However, '&lt;em&gt;Interbreeding&lt;/em&gt;' is sometimes used just to signify that two individuals can breed and have viable offspring (&quot;&lt;em&gt;...these two individuals can interbreed...&lt;/em&gt;&quot;), and under this usage this can also include/overlap with inbreeding.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The latter usage can be seen in the &lt;em&gt;Species&lt;/em&gt; article in &lt;a href=&quot;http://www.britannica.com/EBchecked/topic/558649/species?anchor=ref76052&quot; rel=&quot;nofollow&quot;&gt;Encyclopædia Britannica, online&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Species&lt;/strong&gt;, in biology, classification comprising related organisms that share common characteristics and are capable of interbreeding.&lt;br&gt;&#xA;  ...&lt;br&gt;&#xA;  Interbreeding only within the species is of great importance for evolution in that individuals of one species share a common gene pool that members of other species do not.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-03-19T16:20:50.363" LastActivityDate="2014-03-19T16:20:50.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15944" PostTypeId="2" ParentId="13776" CreationDate="2014-03-19T13:24:14.450" Score="4" Body="&lt;p&gt;This is at least doing some confusion, probably also harm. A lot of wildlife conservationists warn about using smartphone apps which replay bird songs, as they are confusing the animals. An example is the &lt;a href=&quot;http://www.dorsetwildlifetrust.org.uk/bird-apps-warning&quot; rel=&quot;nofollow&quot;&gt;Dorset Wildlifetrust&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This phenomenon has even be analyzed scientifically, and the results show that birds are irritated. Territorial birds seem to be affected more and it has been shown that, when a fake call was replayed to them, they sang more often and longer. In the first paper they speculate that this will drain too much energy and prevent the birds from doing other important things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second paper looks at zebra finches, which are not territorial. Here they find that birds pay less attention, the more often the song is replayed.&#xA;The articles:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077902&quot; rel=&quot;nofollow&quot;&gt;Simulated Birdwatchers’ Playback Affects the Behavior of Two Tropical&#xA;Birds&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18845267&quot; rel=&quot;nofollow&quot;&gt;Habituation in songbirds.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="6928" LastEditDate="2016-05-17T18:08:37.410" LastActivityDate="2016-05-17T18:08:37.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15945" PostTypeId="1" CreationDate="2014-03-19T13:52:06.577" Score="3" ViewCount="103" Body="&lt;p&gt;I want to learn more about the data analysis and statistics on transcriptome sequencing data. I would like to read some important papers of the field and books and maybe some MOOCS, if they are available. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More precisely I have data of differentially expressed genes across different groups of individuals and I want to test, if the genes are more expressed in one group are the genes also more polymorphic?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any ideas?&lt;/p&gt;&#xA;" OwnerUserId="5486" LastActivityDate="2014-03-19T13:52:06.577" Title="Data analysis of transcriptome sequencing data" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;statistics&gt;&lt;rna-sequencing&gt;&lt;sequence-analysis&gt;" AnswerCount="0" CommentCount="6" ClosedDate="2014-11-13T13:52:39.543" ContentLicense="CC BY-SA 3.0" />
  <row Id="15946" PostTypeId="2" ParentId="10934" CreationDate="2014-03-19T14:50:05.247" Score="2" Body="&lt;p&gt;I have to add that the authors do not show &lt;em&gt;any&lt;/em&gt; evidence for cell shrinkage. In fact, the word shrink is not mentioned even once in the article. Therefore the BBC article is not correct. To answer your question, all we know is that there is more fluid clearance; the authors &lt;em&gt;do not&lt;/em&gt; show the mechanisms for this.  &lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-03-19T14:50:05.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15947" PostTypeId="1" CreationDate="2014-03-19T18:25:22.837" Score="2" ViewCount="136" Body="&lt;p&gt;When Lions roar, or Dogs show aggression, they do that snort-roar thing. They're producing sound while inhaling. How did that come to be when all (?) other forms of sound involve exhaling?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans do produce sound while snoring, but that's merely a by-product of it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And while people could very well speak by inhaling, they don't do that in their regular communication. Lions and Dogs do. Why/when did they decide that (inhaling sound production) was a better/more effective means of making sound?&lt;/p&gt;&#xA;" OwnerUserId="3141" LastEditorUserId="3141" LastEditDate="2014-03-19T18:36:25.047" LastActivityDate="2014-03-19T18:36:25.047" Title="How did the roar evolve from snort?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;dogs&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15948" PostTypeId="2" ParentId="15921" CreationDate="2014-03-19T18:37:06.470" Score="0" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bwgpE.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is an image of BRCA2 and RAD51 oriented.( I produced this using PyMOL!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The chocolate coloured part is some BRCA repeats. You can see how BRCA repeats and RAD51 are oriented. Here, the association is shown only for one of the 7 subunits of RAD51&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact mechanism in brief :&#xA;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ylmOW.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;BRCA2 binds to RAD51 subunits within the ring via BRC repeat mimicry of the RAD51 polymerization motif.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;2.BRC repeats disassembles the ring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3.The RAD51:BRCA2 comple is recruited to a DNA double strand break.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4.BRCA2 helps displace a protective protein, Replication protein A- RPA, and binds the primary ssDNA substrate by its B folds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5.It loads RAD51 onto DNA. The handoff reaction might be facilitated by attraction of DNA by the positively charged BRC repeat helical arches.The BRCA2 helix-turn-helix domain(red) at the end of the tower may bind dsDNA in cis at the ssDNA/dsDNA intra-DNA junction (3) or in trans to the dsDNA that later serves as the homologous DNA template (6) and the positively charged arch may also help to attract the dsDNA template. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source : Yang etal. 2002 , Shin et al 2003&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks to Nicholas Provert for teaching me basics of PyMOL on Coursera.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-19T18:37:06.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15951" PostTypeId="2" ParentId="15937" CreationDate="2014-03-20T01:11:33.803" Score="6" Body="&lt;p&gt;This is kind of a weird/trick question.  How long do you want the animal to live?  If the lifespan is shortened or compromised does that fit....   Obligate carnivores (cats, dogs) do eat plant material.  In the wild cats mainly eat grass to get rid of hairballs.  Cats are more impacted by phytotoxins than dogs.  However, both, are extremely vulnerable to compounds that don't bother humans (xanthines like theobromine, caffine, compounds in garlic, onions, broccoli, mushrooms).  Cats can't convert plant fats into what they need (we can) as a result they can go blind if they don't get the animal fats they need.  Likewise, herbivores will suffer increased cancer, heart disease, renal failure from diets with animal fats / protein.  Your mention of &quot;wolf&quot; is interesting because there is a South American wolf that supplements its diet with a tomato relative (called something like &quot;fruit for wolves&quot; in Spanish).  This is probably only &quot;good&quot; for it in that it keeps the wolf from otherwise starving.  I don't know that it has a strong deleterious effect (probably not, but it could be more sensitive to trace alkaloids in the fruit) but it could hurt it in a minor way.&lt;/p&gt;&#xA;" OwnerUserId="6093" LastActivityDate="2014-03-20T01:11:33.803" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15952" PostTypeId="1" CreationDate="2014-03-20T06:43:18.817" Score="3" ViewCount="109" Body="&lt;p&gt;How do cellphones calculate heart rate ? I understand that the cameras there try to count undulation in blood flow, but is the method of calculation same as that of professional SpO2 monitors ?&lt;/p&gt;&#xA;" OwnerUserId="4720" LastEditorUserId="4720" LastEditDate="2014-03-20T11:01:47.413" LastActivityDate="2014-03-20T11:01:47.413" Title="How do cellphones calculate heart rate?" Tags="&lt;cardiology&gt;&lt;blood-pressure&gt;" AnswerCount="0" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="15953" PostTypeId="1" CreationDate="2014-03-20T13:39:41.083" Score="1" ViewCount="619" Body="&lt;p&gt;At what height blood can eject from human vein ? &#xA;I see, sometime there is direct blood transfer from one person to patient.&#xA;So sometime blood bottle is kept at certain height and blood is transfered from person to upper bottle and then from that bottle to patient directly.&#xA;At what height blood can go ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, I had not mentioned before,&#xA;What would be the blood pressure outside from body after cutting certain nerve or vein or whatever which carries blood-speedily, when we go inside vacuum chamber ?&lt;br&gt;&#xA;Consider any chamber where you will be able to remove air/atmosphere inside it and a person is provided with oxygen cylinder. Now what will be the blood ejection speed outward from the body ? At what height ? You will have to consider atmospheric pressure also when we leave normally on earth. So question is, at what height in vacuum (where there is no pressure from outside world) ?&lt;/p&gt;&#xA;" OwnerUserId="6096" LastEditorUserId="6096" LastEditDate="2015-03-23T16:59:59.300" LastActivityDate="2015-03-23T16:59:59.300" Title="What is the blood ejection speed outward from human body vein?" Tags="&lt;blood-circulation&gt;&lt;blood-pressure&gt;" AnswerCount="1" CommentCount="11" ClosedDate="2014-04-06T00:31:43.327" ContentLicense="CC BY-SA 3.0" />
  <row Id="15954" PostTypeId="1" AcceptedAnswerId="15957" CreationDate="2014-03-20T14:58:49.810" Score="4" ViewCount="253" Body="&lt;p&gt;I  read (from &lt;a href=&quot;http://www.nature.com/nature/journal/v507/n7490_supp/full/507S4a.html?WT.ec_id=NATURE-20140306&quot; rel=&quot;nofollow&quot;&gt;Nature&lt;/a&gt; Volume507, S4–S7 (06 March 2014) :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For reasons that are poorly understood, BCG protects only infants; it&#xA;  is ineffective in older children and adults. Its efficacy also depends&#xA;  on latitude. BCG works better, and protects people at later ages,&#xA;  farther from the equator. Both effects may result from interfering&#xA;  exposure to noninfectious mycobacteria that are closely related to&#xA;  both BCG and TB. These bacteria are more abundant closer to the&#xA;  equator, and while infants are unlikely to have encountered them,&#xA;  children and adults have more exposure over time.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am unable to understand the relation between exposure to noninfectious mycobacteria and lessening of efficacy of BCG vacccine. What exactly is the &quot;interference&quot; caused by the noninfectious mycobacteria ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="5144" LastEditDate="2014-03-20T15:19:15.763" LastActivityDate="2014-03-20T15:35:11.307" Title="Functioning of BCG vaccine" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;bacteriology&gt;&lt;pathology&gt;&lt;vaccination&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15955" PostTypeId="1" CreationDate="2014-03-20T15:00:10.717" Score="1" ViewCount="362" Body="&lt;p&gt;My colleague and I are working on a project involving data produced at a glycan microarray facility. The array data that came back to us were a list of glycan names (in IUPAC condensed format). We would like to parse the list of 610 names into the graphical representation of the glycan.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To clarify, I wanted to take a list of glycans, written in the IUPAC condensed nomenclature, and return an image for each glycan. Here, each image would be the &quot;graph&quot; representation (nodes + edges). Ideally, I would like to be able to write a Python script to get this done, so we wouldn't have to do this by hand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this possible? If so, what tools are available to get this done?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="1536" LastEditorUserId="1536" LastEditDate="2014-03-21T04:53:51.820" LastActivityDate="2014-09-03T08:59:31.100" Title="Are there tools for automatically parsing glycan names into tree structures?" Tags="&lt;bioinformatics&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15956" PostTypeId="2" ParentId="15953" CreationDate="2014-03-20T15:01:32.230" Score="2" Body="&lt;p&gt;Ah, I'm afraid there are a near infinite number of variables that will make a general answer impossible.  Factors such as: age, sex, weight, which vein, additional damage, heart condition, cholesterol level, body position, body temperature, and how the vein was cut and exposed will all lead to different answers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A general answer from someone with lots of trauma experience, not very far.  Rarely if ever greater than 10cm.  Veins just don't have the pressure that arteries do.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2014-03-20T15:01:32.230" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="15957" PostTypeId="2" ParentId="15954" CreationDate="2014-03-20T15:35:11.307" Score="3" Body="&lt;p&gt;The exposure to environentally occurring Mycobacteria causes a immune response to these (mostly unspecific, since no real infections occur). It seems that immunizations with BCG in these individuals is causing either no, or only a very attenuated immune response&#xA;This is shown in this (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11978337&quot; rel=&quot;nofollow&quot;&gt;BCG-induced increase in interferon-gamma response to mycobacterial antigens and efficacy of BCG vaccination in Malawi and the UK: two randomised controlled studies.&lt;/a&gt;&quot;) in which individuals with a high environmental exposure to mycobycteria showed only a very small response to this vaccination. If this natural level of immunity is enough to produce immunity to tuberculosis is unknown (and can not be tested for obvious reasons).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another possibility is that the natural occurring immunity blocks the vaccine strains so they get eliminated before they induce an immune response. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11796598&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&#xA;This is called the masking theory,if you want to read further, have a look at this three reviews, they give a good overview over the field:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11286732&quot; rel=&quot;nofollow&quot;&gt;TB vaccines: progress and problems.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12443657&quot; rel=&quot;nofollow&quot;&gt;A novel TB vaccine; towards a strategy based on our understanding of&#xA;BCG failure.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16012514&quot; rel=&quot;nofollow&quot;&gt;The success and failure of BCG - implications for a novel&#xA;tuberculosis vaccine.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-20T15:35:11.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15958" PostTypeId="1" AcceptedAnswerId="15962" CreationDate="2014-03-20T16:19:34.087" Score="7" ViewCount="9889" Body="&lt;p&gt;I am reading &lt;a href=&quot;http://www.nature.com/nrg/journal/v6/n2/full/nrg1523.html&quot; rel=&quot;noreferrer&quot;&gt;this review&lt;/a&gt;. In the first part, the author introduces Standing Genetic Variation, described as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;STANDING GENETIC VARIATION Allelic variation that is currently&#xA;  segregating within a population; as opposed to alleles that appear by&#xA;  new mutation events&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Does it mean that in adaptation the allelic variation is already present (not created by mutations) and in adaptation it prevails over the others?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="3466" LastActivityDate="2014-03-20T17:56:16.293" Title="What is the standing genetic variation?" Tags="&lt;genetics&gt;&lt;mutations&gt;&lt;adaptation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15959" PostTypeId="1" AcceptedAnswerId="15960" CreationDate="2014-03-20T16:28:43.010" Score="1" ViewCount="2341" Body="&lt;p&gt;We know that everybody's DNA pattern is different in the world. Then how can ´we transfer blood from one person to another person and this person can survive ?&lt;/p&gt;&#xA;" OwnerUserId="6096" LastEditorUserId="5144" LastEditDate="2014-03-20T16:31:40.040" LastActivityDate="2014-03-20T22:30:24.787" Title="If everybody DNA is different then how blood can match even with matching blood group?" Tags="&lt;dna&gt;&lt;red-blood-cell&gt;&lt;dna-damage&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15960" PostTypeId="2" ParentId="15959" CreationDate="2014-03-20T16:34:38.897" Score="8" Body="&lt;p&gt;A few components to my answer.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Red blood cells do not contain a nucleus, therefore, they do not harbour DNA.&lt;/li&gt;&#xA;&lt;li&gt;The major determinant of blood compatibility is the blood antigen. There are only 4 types: O, A, B, AB. This is genetically encoded, and is expressed as a set of sugar coats on the blood cell membrane. However, the enzymes that encode for A or B should be identical from person to person.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I hope this gives you a preliminary answer to work off.&lt;/p&gt;&#xA;" OwnerUserId="1536" LastActivityDate="2014-03-20T16:34:38.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15961" PostTypeId="2" ParentId="15927" CreationDate="2014-03-20T16:52:58.350" Score="1" Body="&lt;p&gt;I would say fibrosis represents an abnormal accumulation of fibrous tissue usually collagen fibres. Where as fibrogenesis is the process of formation of fibrous tissues be it collagen, reticulin, elastic, oxytalan.. &lt;/p&gt;&#xA;" OwnerUserId="4216" LastActivityDate="2014-03-20T16:52:58.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15962" PostTypeId="2" ParentId="15958" CreationDate="2014-03-20T17:56:16.293" Score="7" Body="&lt;p&gt;Standing genetic variation is when there is more than one allele at locus in the population at the time-point in question. When an allele goes to fixation there is no standing genetic variation at the locus until new mutations occur. Loci where alleles are not fixed are described as having standing genetic variation.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Standing genetic variation: the presence of more than one allele at a locus in a&#xA;  population.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;from &lt;a href=&quot;http://webpages.icav.up.pt/SAPINTO2/8.pdf&quot;&gt;Barrett and Schluter 2007&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-03-20T17:56:16.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15963" PostTypeId="2" ParentId="15955" CreationDate="2014-03-20T19:09:10.090" Score="2" Body="&lt;p&gt;&lt;strong&gt;Edit: C# Functions used in our system, slightly paired down for to simplfy&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;using Microsoft.VisualBasic;&#xA;using System;&#xA;using System.Collections;&#xA;using System.Collections.Generic;&#xA;using System.Data;&#xA;using System.Diagnostics;&#xA;using System.Web;&#xA;using System.Net;&#xA;using System.IO;&#xA;using System.Text.RegularExpressions;&#xA;&#xA;public class KEGGCaller&#xA;{&#xA;    public object ReturnKEGGgif(string GlycanMonoCode, System.Web.HttpServerUtility HTTPUtilityHolder)&#xA;    {&#xA;&#xA;        string CallURL = &quot;http://www.genome.jp/dbget-bin/www_bfind_sub?dbkey=glycan&amp;amp;keywords=&quot;;&#xA;        string GlycanURL = HTTPUtilityHolder.HtmlEncode(GlycanMonoCode);&#xA;        WebClient wc = new WebClient();&#xA;        System.Drawing.Image GlycanGif = default(System.Drawing.Image);&#xA;        CallURL += GlycanURL + &quot;&amp;amp;mode=bfind&amp;amp;max_hit=1&quot;;&#xA;        StreamReader reader = new StreamReader(wc.OpenRead(CallURL));&#xA;        string Gcode = FetchGcode(reader.ReadToEnd());&#xA;        if (Gcode == &quot;Failed&quot;) {&#xA;            return 0;&#xA;        } else {&#xA;            System.Net.HttpWebRequest Request = default(System.Net.HttpWebRequest);&#xA;            System.Net.HttpWebResponse Response = default(System.Net.HttpWebResponse);&#xA;            Request = System.Net.WebRequest.Create(&quot;http://www.genome.jp/dbget-bin/www_bget?gl:&quot; + Gcode + &quot;.gif&quot;);&#xA;            Response = (System.Net.WebResponse)Request.GetResponse;&#xA;            if (Request.HaveResponse) {&#xA;                if (Response.StatusCode == HttpStatusCode.OK) {&#xA;                    GlycanGif = System.Drawing.Image.FromStream(Response.GetResponseStream);&#xA;                    return GlycanGif;&#xA;                } else {&#xA;                    return 2;&#xA;                }&#xA;            } else {&#xA;                return 1;&#xA;            }&#xA;&#xA;        }&#xA;&#xA;    }&#xA;    public object FetchGcode(string PageBlock)&#xA;    {&#xA;        string MatchURLString = &quot;?gl:G\d\d\d\d\d&quot;;&#xA;        Match URLMatch = Regex.Match(PageBlock, MatchURLString);&#xA;        if (URLMatch.Success) {&#xA;            return Strings.Right(URLMatch.Value, 6);&#xA;        } else {&#xA;            return &quot;Failed&quot;;&#xA;        }&#xA;    }&#xA;&#xA;}&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Remainder of the Answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://co.mbine.org/standards/qualifiers&quot; rel=&quot;nofollow&quot;&gt;Biomodels.Net&lt;/a&gt; is a great resource to begin with and familiarize yourself with the field and get ideas of how to tackle your qualification needs.  We used it when we were doing drug screens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More specifically for glycans, you're going to be looking at &lt;a href=&quot;http://www.genome.jp/kegg/glycan/&quot; rel=&quot;nofollow&quot;&gt;KEGG&lt;/a&gt;.  Then use KEGG draw for your visual application.  If you actually just want to parse them, &lt;a href=&quot;http://www.genome.jp/kegg/catalog/codes2.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; is the table on the monosaccharides used (most places).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.kegg.jp/kegg/download/kegtools.html&quot; rel=&quot;nofollow&quot;&gt;Here's a better link&lt;/a&gt; right to the download in case you didn't find it.  The script we wrote was pretty simple, here is the basic logic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Start with the &lt;a href=&quot;http://www.genome.jp/kegg/catalog/codes2.html&quot; rel=&quot;nofollow&quot;&gt;monosaccharide code&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Call a single return of DBGET to GenomeNet pulling from KEGG Glycan.  For example:&#xA;(GlcNAc)6 (Man)3 (Asn)1&#xA;would be called:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; http://www.genome.jp/dbget-bin/www_bfind_sub?dbkey=glycan&amp;amp;keywords=%28GlcNAc%296+%28Man%293+%28Asn%291&amp;amp;mode=bfind&amp;amp;max_hit=1&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Where &lt;code&gt;http://www.genome.jp/dbget-bin/www_bfind_sub?dbkey=glycan&amp;amp;keywords=&lt;/code&gt; and &lt;code&gt;&amp;amp;mode=bfind&amp;amp;max_hit=1&lt;/code&gt; are going to be constant and the middle part is going to be your search.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You need to change your monosaccharide to standard &lt;a href=&quot;http://www.w3schools.com/charsets/ref_html_ascii.asp&quot; rel=&quot;nofollow&quot;&gt;URL ASCII Reference&lt;/a&gt;, concatenating each monosaccharide with a &quot;+&quot;.  Thus &lt;code&gt;(GlcNAc)6 (Man)3 (Asn)1&lt;/code&gt; becomes &lt;code&gt;%28GlcNAc%296+%28Man%293+%28Asn%291&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That will give you one hit with the link to your exact match if there is one.  There will be one link on the returned page in the format of &lt;code&gt;http://www.genome.jp/dbget-bin/www_bget?gl:G#####&lt;/code&gt;, where G##### is your glycan number (in our example G00021).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you have the glycan number you're good to go.  All of the structure images can be found at:&#xA;&lt;code&gt;http://www.genome.jp/Fig/glycan/G#####.gif&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And then you just download your GIF.  The way we did our batches was to do each step for all the hits then move to the next step.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps more.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2014-03-21T19:53:44.980" LastActivityDate="2014-03-21T19:53:44.980" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="15964" PostTypeId="2" ParentId="15959" CreationDate="2014-03-20T20:19:45.380" Score="3" Body="&lt;p&gt;Because one's DNA doesn't have to exactly match another person at all 3 billion locations for the transfusion to be successful.  As it turns out, there are only a few proteins that determine whether a person's blood is a match to someone else's.  And as it turns out, in the vast majority of the human population, there are only three alleles of the ABO gene, and only two alleles for the Rh gene, and for the vast majority of cases, compatibility of those two proteins is all that you need.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-03-20T20:19:45.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15966" PostTypeId="2" ParentId="15959" CreationDate="2014-03-20T22:30:24.787" Score="2" Body="&lt;p&gt;It is critical for you to realize that one's DNA is &lt;strong&gt;not&lt;/strong&gt; the determining factor when it comes to a blood transfusion. Rather, what you have to look at is the &lt;em&gt;proteins being expressed by the DNA coding for blood-associated proteins, as it is these proteins that are the determinant of blood acception or rejection&lt;/em&gt;.In other words, the key question is whether or not the blood being transfused harbors antigens -- specific blood proteins associated with a given blood genotype like A &amp;amp; B -- that are &lt;em&gt;foreign&lt;/em&gt; to the recipient. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Individuals that have type A blood express A-type antigens, but also house anti-B antibodies which specifically bind to blood with the B antigen. For a person with type A blood (AO or AA), transfusing either AB or A type blood would be dangerous. The RBC in both cases would house B antigens, which the recipient would respond to the transfusion by initiation an immune response against the blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to touch up one more time on your connection of DNA to rejection of blood. Please be careful with this as different DNA really does not mean much in this case OR in many other biological cases. You have to be much more specific and ask what is the DNA encoding, what is is transcribing and eventually translating and how that relates to the biological process in question. For blood type, although every individual has 'different' DNA, their DNA for blood type has 3 distinct alleles to consider --iO, iA and iB. These alleles are located only within a small region of a person's overall DNA and the difference are 3 discrete categories, as opposed to every person having a different allele and expressing a different protein. If every person different over this small segment of DNA, in the DNA coding for blood type, then indeed it would be possible for each person to make unique antigens and thus for all transfusions to be rejected. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, since the differences  encompass only 3 allele types, people can only have a limited range of genotypes (aO, aa, bo, bb, ab, oo) which connect to only 4 distinct phenotypes (A, B, AB, O). So there is different in DNA, but the difference is defined and limited, so that overlap of genotypes between is possible and compatibility is quite common. So yes people differ in that DNA, but you have to ask if those differences are significant for a particular biological phenomenon.&lt;/p&gt;&#xA;" OwnerUserId="6099" LastActivityDate="2014-03-20T22:30:24.787" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15968" PostTypeId="1" AcceptedAnswerId="15970" CreationDate="2014-03-21T01:37:18.443" Score="5" ViewCount="115" Body="&lt;p&gt;I'm not a parasitologist, and I was wondering about the current state of malaria research. For instance, is it possible to culture P. &lt;em&gt;falciparum&lt;/em&gt;? Are there techniques for genetic manipulation, editing or transfection (analogous to &lt;em&gt;in vitro&lt;/em&gt; cell culture) ? Are there any major limitations to studying these parasites in culture?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-03-22T04:41:24.150" Title="Can P. falciparum and other malaria parasites be cultured and genetically engineered?" Tags="&lt;parasitology&gt;&lt;malaria&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15970" PostTypeId="2" ParentId="15968" CreationDate="2014-03-21T04:30:23.107" Score="8" Body="&lt;p&gt;Yes it is possible to culture plasmodia but they don't grow in a simple constituted medium. Usually RPMI supplemented with serum and erythrocytes is used for growing plasmodia ex-vivo. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC118084/&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; discusses the issues related to plasmodial culture in detail. The authors say that sometimes a certain growth stage (in particular gametocyte) is lost on prolonged cultivation. &#xA;In the same paper it is discussed that the exo-erythrocytic (liver stage) plasmodia can be grown on cultured hepatoma cell lines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several transfection methods also exist. However, culturing is not a mandatory prerequisite for transfection. Usual methods like electroporation work for a wide spectrum of cell types (in-vivo electroporation is also becoming popular). You can refer to &lt;a href=&quot;http://www.malariajournal.com/content/2/1/19&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; for a summary on different transfection methods for plasmodia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A major limitation, in my opinion would be that the different life stages may not be reproduced in a single culture (as you can see that each stage thrives in a very different type of milieu). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-03-22T04:41:24.150" LastActivityDate="2014-03-22T04:41:24.150" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15972" PostTypeId="1" AcceptedAnswerId="15975" CreationDate="2014-03-21T04:52:23.013" Score="3" ViewCount="195" Body="&lt;p&gt;Can someone please explain how different protein chains occur exactly? I'm not talking about the side chain, but the protein chain which is typically labelled as A,B,C etc in the PDB. I'm curious as to how they are first found and what causes them? As far as I understand, the protein backbone could be in any of several conformations and each conformation has a label? Is that correct?&lt;/p&gt;&#xA;" OwnerUserId="3500" LastActivityDate="2014-03-22T05:34:50.653" Title="how do they identify different protein chains?" Tags="&lt;proteins&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15973" PostTypeId="2" ParentId="15955" CreationDate="2014-03-21T05:13:35.100" Score="1" Body="&lt;p&gt;I don't know if this works out for glycans but &lt;a href=&quot;http://opsin.ch.cam.ac.uk/&quot; rel=&quot;nofollow&quot;&gt;this tool&lt;/a&gt; converts IUPAC name to SMILES format. SMILES is a text based structure notation which can be converted to graphical structure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also check these out:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.openmolecules.org/name2structure&quot; rel=&quot;nofollow&quot;&gt;http://www.openmolecules.org/name2structure&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.iupac.org/home/publications/e-resources/inchi.html&quot; rel=&quot;nofollow&quot;&gt;http://www.iupac.org/home/publications/e-resources/inchi.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am still not sure what you are really asking. It would be easy if you give a dummy example. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-03-21T05:13:35.100" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15975" PostTypeId="2" ParentId="15972" CreationDate="2014-03-21T06:24:12.937" Score="5" Body="&lt;p&gt;Chains are individual polypeptides that make up a multimeric protein complex. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I'm curious as to how they are first found and what causes them?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;SDS-PAGE will resolve all the different chains (if they are different in molecular weight). Chains are products of translation (and some modifications such as clipping and/or other PTMs etc) and they assemble to form final protein complex. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As far as I understand, the protein backbone could be in any of&#xA;  several conformations and each conformation has a label? Is that&#xA;  correct?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes. The labels are assigned as per the reported conformation.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is one chain more common than the other? What causes translation to&#xA;  produce different chains in this case? And finally, during the x-ray&#xA;  crystallography, how do they identify them when they grow the crystal?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There can be different kinds of multimers. There can be homomultimer or a heteromultimer or a multimer of this configuration $(XX)_2$-$(YY)_2$ (a heterodimer of homodimers- just one arbitrary case) etc.&#xA;Each chain is a polypeptide and is encoded by a distinct gene. It is possible that in a multimer there are more number of a certain chain than the other for e.g. $X_3$$Y$. This is not because $X$ is produced more then $Y$ but rather because of the way the multimer is assembled. &#xA;In X-ray crystallography you basically get the arrangement of atoms. You can also understand which atom is what and similarly the termini can be found out. In any case people don't just proceed to crystallography without understanding the subunits and other biochemical properties. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-03-22T05:34:50.653" LastActivityDate="2014-03-22T05:34:50.653" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="15976" PostTypeId="2" ParentId="15899" CreationDate="2014-03-21T08:39:22.180" Score="4" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;I don't think a fungus would develop resistance to something so quickly. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;As Chris suggested in the comments, it could be because &quot;&lt;em&gt;The disinfective effect is based on the production of reactive oxygen species. The problem is that the solutions used for this purposes are not very stable.&lt;/em&gt;&quot; So, if fresh solution haven't been used, it may be ineffective.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;As commented by @inf3rno, fungal infections could be much deeper and hence, &quot;treating&quot; them superficially may not help much.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3340" LastEditDate="2015-06-25T06:49:59.070" LastActivityDate="2015-06-25T06:49:59.070" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15977" PostTypeId="2" ParentId="10212" CreationDate="2014-03-21T09:02:00.093" Score="0" Body="&lt;p&gt;From the comments by Shigeta and WYSIWYG :-&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1.They are easy to get and they can be preserved and used over time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2.They can be differentiated easily.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3.Due to historic reasons - someone getting lucky and finding a protocol for these cells.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-21T09:02:00.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15979" PostTypeId="1" AcceptedAnswerId="15988" CreationDate="2014-03-21T10:55:21.930" Score="2" ViewCount="70" Body="&lt;p&gt;From Solomon et al, 2013 ACC Synthetic biology and from &lt;a href=&quot;http://www.ibiology.org/ibioseminars/biophysics-chemical-biology/kristala-l-j-prather-part-2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; video :&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/T5jly.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Here, there are 2 competing reactions for glucose - one with glk as enzyme and other with gdh as enzyme.&lt;/p&gt;&#xA;&lt;p&gt;In the graph, y axis is gluconate yield and x axis is glk activity. Logically, as glk activity increases, gluconate yield should decrease.&lt;/p&gt;&#xA;&lt;p&gt;This is the case for most of the graph. But why is there an increase in gluconate production initially(when glk activity is somewhere between 0.2 and 0.27 )?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-03-21T20:48:18.707" Title="Activity of glucokinase" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;&lt;synthetic-biology&gt;&lt;enzyme-kinetics&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15980" PostTypeId="2" ParentId="9304" CreationDate="2014-03-21T11:15:56.310" Score="1" Body="&lt;p&gt;[ &lt;em&gt;For the sake of answering a question that is long unanswered&lt;/em&gt; ]&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Can two hammerhead ribozymes simultaneously cleave each other?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, in principle they can.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;two hammerhead ribozymes simultaneously cleave each other when both&#xA;  are expressed, but have these ribozymes cleave a target transcript&#xA;  when expressed alone.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This may be realized only when ribosomes have higher affinity for each other than for the target. As you said in the comment, inserting few mismatches in the ribozyme-target interaction may work. You may need to notice that since the two ribozymes are complementary to each other but cleave the same target, the target sequences will form a set of two mutually complementary regions. If separated well enough, there may not be much of a problem. From your design strategy I guess that UTRs are the best place to keep the ribozyme target sequence. If you keep both the target sequences in the 3'UTR (lets say), then they may form a hairpin structure, which may interfere in the targeting. So you can insert mismatches that also destabilize the possible hairpin. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Has it ever been shown in the literature that a hammerhead ribozyme&#xA;  was able to cleave the flanking arms of another ribozyme?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not yet. Self cleaving examples are there but not mutually cleaving ones. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-03-21T11:15:56.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15981" PostTypeId="1" AcceptedAnswerId="15994" CreationDate="2014-03-21T11:36:42.657" Score="11" ViewCount="26565" Body="&lt;p&gt;According to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Accommodation_%28eye%29&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia article on eye accomodation&lt;/a&gt;, the range in which a human eye can focus is from 7 centimetres away up to essentially an infinite distance. Of course, people can't see things an infinite distance away, but at a certain point the light reflected off an object will come at the eye in effectively parallel paths.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an eye focuses on objects progressively farther away, it seems to me there would be a point when the lens hits maximum flatness, after which it everything will be equally sharp in focus. Looking at an object 500 metres away or 1000 metres away probably doesn't require any change in the lens. However, going from one metre away to seven requires the ciliary muscles adjust to just the right amount.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, &lt;strong&gt;what is a normal minimum distance from the eye at which the lens will reach maximum flatness?&lt;/strong&gt; Everything else in this question is just for context, so an answer to this, stated in metres from the eye, is all I am seeking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article I linked to above mentioned the human eye seeing &quot;13 dioptres&quot;, and I have tried to understand &lt;a href=&quot;http://en.wikipedia.org/wiki/Diopter&quot; rel=&quot;noreferrer&quot;&gt;dioptres&lt;/a&gt;, but it's a little confusing for me. If I understand correctly, the higher the dioptre, the closer you focus, so the 13 dioptres refers to how close the human eye can see. If I have this backwards, please let me know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, my purpose in asking is to determine the range in which ciliary muscles would be required to do more nuanced work in order to hold the lens at in the right shape. Focusing on something 7 centimetres away, the ciliary muscles are at maximum exertion, and at a certain point and beyond the ciliary muscles are completely relaxed. To hold somewhere in between would require more subtly nuanced, and, I suspect, more difficult work on the part of the ciliary muscles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At least, I assume that to be the case because I am hypothesizing that the act of contraction for the ciliary muscles would be similar to other muscles. For example, it is easier to do a bicep curl with weight when going from full resting position to maximum contraction, as opposed to stopping at a particular spot somewhere in the middle of the motion. To stop mid-motion requires more muscle control, and, depending on how fast you wanted to do it, can be difficult to be exact.&lt;/p&gt;&#xA;" OwnerUserId="6047" LastEditorUserId="6047" LastEditDate="2014-03-22T02:23:42.673" LastActivityDate="2015-01-19T06:29:14.640" Title="What's the minimum distance of focus for the lens of a human eye to reach maximum flatness?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15982" PostTypeId="1" CreationDate="2014-03-21T14:37:21.470" Score="2" ViewCount="94" Body="&lt;p&gt;What is the mechanism for transport of insulin in mammalian cells?&lt;/p&gt;&#xA;" OwnerUserId="6106" LastEditorUserId="16299" LastEditDate="2015-12-31T19:13:17.810" LastActivityDate="2015-12-31T19:13:17.810" Title="How is insulin transported in vivo in mammals?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15984" PostTypeId="1" AcceptedAnswerId="15986" CreationDate="2014-03-21T17:13:30.790" Score="5" ViewCount="3675" Body="&lt;p&gt;From this &lt;a href=&quot;http://www.amazon.fr/Mutation-Driven-Evolution-Masatoshi-Nei/dp/0199661731&quot; rel=&quot;nofollow noreferrer&quot;&gt;book&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;For simplicity, let us consider a haploid organism and assume that the frequencies of alleles &lt;span class=&quot;math-container&quot;&gt;$A_1$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$A_2$&lt;/span&gt; are given by &lt;span class=&quot;math-container&quot;&gt;$x$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$y=1-x$&lt;/span&gt;, respectively. We also assume that the fitnesses of &lt;span class=&quot;math-container&quot;&gt;$A_1$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$A_2$&lt;/span&gt; are &lt;span class=&quot;math-container&quot;&gt;$w_1 = 1$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$w_2 = 1-s$&lt;/span&gt;, respectively. In this case the mean fitness &lt;span class=&quot;math-container&quot;&gt;$\bar w$&lt;/span&gt; is given by &lt;span class=&quot;math-container&quot;&gt;$x + (1-x)(1-s)= 1-sy$&lt;/span&gt;, and the allele frequency change per generation becomes&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$\Delta x =  \frac{dx}{dt} = \frac{sxy}{1-sy}$$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;If I would have to find what &lt;span class=&quot;math-container&quot;&gt;$\frac{dx}{dt}$&lt;/span&gt; equals I would use the Wright-Fisher equation and find that:&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$\frac{dx}{dt} = \frac{w_1 \cdot x}{\bar w} = \frac{x}{1-sy}$$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;, which is obviously not the same result as what the author found...&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;What am I missing? How did the author find out this result &lt;span class=&quot;math-container&quot;&gt;$\frac{dx}{dt} = \frac{sxy}{1-sy}$&lt;/span&gt;?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-11-03T09:11:47.973" Title="How do I calculate the change in allele frequency in a haploid population under selection?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15986" PostTypeId="2" ParentId="15984" CreationDate="2014-03-21T19:59:54.880" Score="7" Body="&lt;p&gt;Here is my full derivation to the book example you gave, hopefully it'll help you clear up what went wrong:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dMBkR.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You need to remember that after there is selection acting on the population, you no longer have a total of 1 after selection. Think of selection as &quot;killing&quot; individuals, which means the total is now 1 minus what has been &quot;selected out&quot;. s&lt;em&gt;y is what is selected out, therefore the new total is 1-s&lt;/em&gt;y. Which means you now divide each of your frequencies by 1-s*y (see picture).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please comment if you need more explaining.&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2014-03-26T10:38:27.643" LastActivityDate="2014-03-26T10:38:27.643" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15987" PostTypeId="1" AcceptedAnswerId="15989" CreationDate="2014-03-21T20:36:35.373" Score="2" ViewCount="89" Body="&lt;p&gt;I'm thinking in particular of wings on birds that would - I'm guessing - have to progress through stages during which they confer no particular advantage. Or is it that all evolved features must have followed a path of incremental benefit therefore imposing a fundamental limit on what evolution through natural selection can &quot;achieve&quot;? (features that are not beneficial while gradually appearing cannot be evolved)&lt;/p&gt;&#xA;" OwnerUserId="6110" LastActivityDate="2017-10-02T12:46:07.703" Title="How do beneficial features evolve in species without progressing through detrimental stages?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15988" PostTypeId="2" ParentId="15979" CreationDate="2014-03-21T20:48:18.707" Score="1" Body="&lt;p&gt;First of all lets have a look, what these guys want to accomplish: They want to use bacteria to make certain products. To do so, they want to exploit the bacterial metabolism at steps where no alternative pathways are available. One of these steps is the first step of glycolysis, when Glucose gets phosphorylated to glucose-6-phosphate (G6P). In bacteria the phosphorylation is done during the import of glucose into the cell by the &quot;phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system&quot;, which uses Phosphorenolpyruvate as a phosphate source. This has the disadvantage, that there is almost no free glucose inside the cell, but mostly G6P.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To overcome this problem, the group expressed alternative transporters (which transport glucose into the cell) and Glucokinase (Glk) to allow the cells to survive. This steps decoupled import and phosphorylation of the glucose and resulted in free glucose inside the cell. This free glucose can now be used by different proceses. It also allows glycolysis, since the Glk phosphorylates the glucose which then enters the glycolysis pathway. The Glk was put under different promoters to make different mutants in order to test how the different expression of Glk affects the cells viability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To bring in another enzyme which also metabolizes glucose, they used glucose dehydrogenase (Gdh) which was expressed from a plasmid with a strong, IPTG inducible promoter. They then used different concentrations of IPTG to test the effect on the production of gluconate and cell viability (I am not going into this).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VmyfV.jpg&quot; alt=&quot;enter preformatted text here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The figure above is figure 5 from the paper and shows the effect of the three different IPTG concentrations used to induce the expression of the Gdh. For 10 and 25uM IPTG the yield of gluconate is getting smaller, the higher the Glk activity gets. Only the smalled activity shows a lower yield. This is complete different for the highest concentration, but here the cells get probably messed up by the high expression of the Gdh (which also consumes a lot of energy).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the paper they give no explanation or at least discuss the behaviour of the gluconate yield at the smallest Glk activity (I would like to read the reviewers comments on that). From the data I would expect a higher production. It is possible that the lower energy production (low amounts of G6P means little glycolysis) has negative side effects on the cells. It is also possible, that the Gdh is inhibited at lower Glk activities by some other substances in the cell. Gdh activity is for example inhibited by higher concentrations of nucleotidtriphosphates (ATP and so on), see &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/bi00805a023&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;. Since Glk needs ATP as a cofactor it would be possible that the ATP concentration at lower Glk activities has a negative effect on the Gdh activity (my own speculation). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or it is simply some artefact from the experiment. This has some points which can be critisized (I would like to see the reviewers comments here as well). First the error bars are pretty big, so this can also be somewhat different. In the text they mention that the data was acquired by &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;at least 2 parallel cultures in a representative experiment&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would expect some more repetitions (at least three independent experiments), which would make the data more reliable. Then (and this point is much more important) they can not measure the activity of Glk and Gdh in the same culture due to restrictions in the detection system. Glk activity measurements use a coupled system which in the end measure the concentration change in NADH, while Gdh uses NADPH as a co-factor. Both versions can not be differentiated by measuring a spectrum, so activity measurements of Glk can only take place in untransfected cells. Since the expression changes conditions in the cell (and we don't know how), I would expect at least some discussion about it, but it is missing.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-21T20:48:18.707" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15989" PostTypeId="2" ParentId="15987" CreationDate="2014-03-21T20:53:41.783" Score="1" Body="&lt;p&gt;Features can evolve (or change already present features) which have no negative effect under the current conditions. You can very well have neutral changes which have no purpose. They can then prove positive later (or in a different environment). Changes are usually small and take place over very long time periods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example would be bacteria which mutated one of their enzymes for a energy pathway. Before the mutation the enzyme could only metabolize nutrient A, after it, it is a bit less specific for A, but can also metabolize B. As long as the living conditions are so, that only A is present, this will not change anything. If the conditions are so, that A and B are present and A gets limited, these cells will have a profound advantage over cells, which can only utilize A.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-21T20:53:41.783" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15990" PostTypeId="1" AcceptedAnswerId="16014" CreationDate="2014-03-21T21:14:32.983" Score="2" ViewCount="1205" Body="&lt;p&gt;I am more or less familiar with the evolution theory based on mutations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, starting with a nonsexual being, how did the first organism that reproduces sexually come to exist. &lt;/p&gt;&#xA;" OwnerUserId="5966" LastActivityDate="2014-03-23T13:33:07.123" Title="How did the first sexual animal come to exist?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ClosedDate="2014-03-26T01:12:46.523" ContentLicense="CC BY-SA 3.0" />
  <row Id="15991" PostTypeId="1" AcceptedAnswerId="15993" CreationDate="2014-03-21T21:32:18.320" Score="1" ViewCount="44" Body="&lt;p&gt;The diploid chromosomal architecture is rather interesting. For example, because of diploidy we Humans have to mate. Of course in that sense, because diploid organisms often have mate, this has led to emergence of sexual organs as novel features etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, what I am interested in, is the prospect of recombination and mating being able to lead to drastically novel evolutionary traits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, if a remote tribesman from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Pygmy_peoples&quot; rel=&quot;nofollow&quot;&gt;Pygmy peoples&lt;/a&gt; of Central Africa were to mate with an urban dweller, one theoretical example of a novel feature could emerge in the offspring are new inter-gene/protein interactions between these &quot;never met before&quot; sets of alleles. Recombination would then &quot;seal the deal&quot; by shuffling these allele sets between the maternal/paternal chromosomes, such an individual's offspring would now become a mosaic of their hybrid parent. Just imagine cross-over events occurring between two very divergent promoters of the same loci.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Could the unison of such divergent sets of alleles theoretically lead to unique phenotype and features that bear little resemblance to any features belonging to the parents?&lt;/li&gt;&#xA;&lt;li&gt;Are there any real examples of morphological/physiological features such as that I have tried to describe?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2014-03-21T21:38:59.307" LastActivityDate="2014-03-22T05:04:48.790" Title="Could mating/recombination be responsible for evolution of entirely novel features?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;&lt;sex&gt;&lt;recombination&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15993" PostTypeId="2" ParentId="15991" CreationDate="2014-03-22T05:04:48.790" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Could the unison of such divergent sets of alleles theoretically lead&#xA;  to unique phenotype and features that bear little resemblance to any&#xA;  features belonging to the parents?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Though it is possible that some unique characteristics may emerge but it is very less likely that the offspring will bear no resemblance to the parents. You start with an example of humans. In this case it is, in my opinion, very unlikely because there is not so much of genomic diversity yet that may lead to such an outcome as you ask about. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some examples exist, such as the liger (offspring of a male lion and female tiger) that is bigger than both the species. This happens because of improper growth regulation because of interspecies differences. This could happen because the divergence between lion and tiger is much more than the intraspecific variations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just a speculation : perhaps the offspring of &lt;em&gt;H.sapiens&lt;/em&gt; and &lt;em&gt;H.neanderthalis&lt;/em&gt; could have had such a feature but it seems unlikely for the current population of &lt;em&gt;H.sapiens&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-03-22T05:04:48.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15994" PostTypeId="2" ParentId="15981" CreationDate="2014-03-22T10:56:36.777" Score="5" Body="&lt;p&gt;There are practical questions in ophthalmology and you've asked someone that has a common theoretical answer: 6 meters. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, you should know that from the same theoretical point the far the object the less accommodation we need, so the second answer is - infinity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the difference? From the practical point the accommodation between this two points is negligible and does not have to be taken into account when we correct the refraction error.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Small theory - to see an object placed at a distance of 1 meter we need 1D of accommodation power (1/1meter=1D), to see an object placed at a distance of 30cm we need 3D of accommodation power (1/0.3meter=3D), for an object at a distance of 10cm we need 10 diopters and finally for an object at the distance of a 6 meter we need accommodate 0.16 diopter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus between 6 meter and infinity the accommodation is very low and this is why the distant visual acuity is checked at this distance. Consequently, the lens convexity difference between 6 meters gaze and infinity is negligible and this is why the answer to your question is between 6 meters and infinity (zero accommodation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this explanation you can calculate the dioptric add for any reading distance  and understand how the reading spectacles correct the loss of accommodative power (=presbyopia, the vision of older people).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to know how much the crystalline lens changes its dimensions during accommodation, the answer is near 7% for diameter and near 10% for thickness, so the lens as was convex, stays convex and the visible changes are minimal.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2014-03-22T16:25:49.433" LastActivityDate="2014-03-22T16:25:49.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15995" PostTypeId="1" AcceptedAnswerId="15998" CreationDate="2014-03-22T11:38:06.860" Score="0" ViewCount="1161" Body="&lt;p&gt;I am thinking how clot retraction and fibrinolysis work together.&#xA;I think that clot retraction is a process that gets clot towards fibrinolysis process.&#xA;Fibrinolysis process then lyses the clot.&#xA;However, I am not sure if it is so simple.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some seems to be discussing about how to differentiate start of fibrinolysis from clot retraction morphologically.&#xA;So they probably seem to be at this stage similar processes visually, but not functionally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the function of clot retraction?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-03-22T12:56:30.743" Title="What is the function of clot retraction?" Tags="&lt;physiology&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="15996" PostTypeId="2" ParentId="15718" CreationDate="2014-03-22T12:25:36.530" Score="0" Body="&lt;p&gt;There is a vast amount of genotype data available at &lt;a href=&quot;https://www.vectorbase.org/popbio/project/?id=VBP0000001&quot; rel=&quot;nofollow&quot;&gt;VectorBase's&lt;/a&gt; population biology browser, it is a database of insects which behave according to many mathematical assumptions - e.g. the non-overlapping discrete generations and homogeneous mating landscape.&lt;/p&gt;&#xA;" OwnerUserId="5005" LastActivityDate="2014-03-22T12:25:36.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15997" PostTypeId="2" ParentId="15982" CreationDate="2014-03-22T12:40:23.913" Score="1" Body="&lt;p&gt;The process is described &lt;a href=&quot;http://en.wikipedia.org/wiki/Insulin#Synthesis&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. This is my summary, plus a few extra details:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The primary gene product of the &lt;em&gt;INS&lt;/em&gt; gene is preproinsulin. As the N-terminal signal sequence (pre-) emerges from the ribosome during polypeptide elongation the signal sequence binds to a signal recognition particle which arrests elongation until the nascent chain has engaged with the translocation apparatus in the membrane of the endoplasmic reticulum (ER). The preproinsulin polypeptide is translocated across the ER membrane in a cotranslational process, and the signal sequence is cleaved off by signal peptidase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The proinsulin molecule folds in the ER lumen, assisted by various chaperones and, in particular, by protein disulphide isomerase, which ensures that the correct disulphide bonds form. The correctly-folded proinsulin polypeptide is exported from the ER in COPII-coated vesicles which deliver it to the Golgi. At this stage the proinsulin is cleaved by furin-type proteases (pro-hormone convertases; cleave at pairs of basic residues), removing the internal C-peptide (pro-) and after a little C-terminal trimming, leaving the insulin A and B peptides covalently attached via disulphides. This is mature insulin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mature insulin leaves the Golgi in secretory vesicles. Since insulin secretion is &lt;em&gt;regulated&lt;/em&gt;, these vesicles do not fuse with the cell membrane constitutively, they are stimulated to fuse by a Ca&lt;sup&gt;2+&lt;/sup&gt;-dependent signalling pathway. Vesicle-membrane fusion is mediated by SNARE proteins. At this stage the insulin has been released from the pancreatic &amp;beta; cell. Notice, however, that the insulin has been extracytoplasmic since it was translocated into the ER: all other steps in the transport process are achieved by rounds of vesicle formation and fusion.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-22T12:40:23.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="15998" PostTypeId="2" ParentId="15995" CreationDate="2014-03-22T12:56:30.743" Score="1" Body="&lt;p&gt;The platelets in the clot contain contractile proteins. They bring the edges of the wound together, which also reduces the chance of further bleeding. The contraction process also supports the wound healing process as it brings the ends of the wound together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information see this article: &quot;&lt;a href=&quot;http://www.nature.com/nmat/journal/v10/n1/abs/nmat2903.html&quot; rel=&quot;nofollow&quot;&gt;Mechanics and contraction dynamics of single platelets and implications for clot stiffening&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-22T12:56:30.743" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="15999" PostTypeId="2" ParentId="15469" CreationDate="2014-03-22T13:33:51.740" Score="0" Body="&lt;p&gt;Alan Boyd's answer&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Production of hydrogen sulphide is used as a convenient method for&#xA;  detecting the presence of pathogenic Salmonella, there is nothing to&#xA;  link this with virulence.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;which I agree with.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-03-22T13:33:51.740" CommentCount="0" CommunityOwnedDate="2014-03-22T13:33:51.740" ContentLicense="CC BY-SA 3.0" />
  <row Id="16000" PostTypeId="2" ParentId="15456" CreationDate="2014-03-22T13:35:52.797" Score="0" Body="&lt;p&gt;MattDMo's answer&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Essentially, [neutrophilic granulocytes] are the first infiltrating&#xA;  cells to arrive at the site of injury at the beginning of acute&#xA;  inflammation (bacterial infection, environmental exposure, etc.).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;which I agree with.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-03-22T13:35:52.797" CommentCount="0" CommunityOwnedDate="2014-03-22T13:35:52.797" ContentLicense="CC BY-SA 3.0" />
  <row Id="16001" PostTypeId="1" CreationDate="2014-03-22T15:17:17.743" Score="1" ViewCount="181" Body="&lt;p&gt;I am trying to figure out how prostaglandins in the semen relate to the female reproductive tract.&#xA;More specifically,&#xA;How does prostaglandins in semen help the female reproductive tract increase the chance for fertilization?&lt;/p&gt;&#xA;" OwnerUserId="584" LastActivityDate="2014-03-22T15:17:17.743" Title="Significance of prostaglandins in semen?" Tags="&lt;endocrinology&gt;&lt;embryology&gt;&lt;reproductive-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16002" PostTypeId="2" ParentId="16001" CreationDate="2014-03-22T15:17:17.743" Score="1" Body="&lt;p&gt;Nevermind. While writing out the question I found the answer on wikipedia.&#xA;Prostaglandin type PGF2α will act on the FP receptor to initiate uterus contraction which will help propel sperm further into the reproductive tract.&lt;/p&gt;&#xA;" OwnerUserId="584" LastActivityDate="2014-03-22T15:17:17.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16003" PostTypeId="1" CreationDate="2014-03-22T16:11:01.753" Score="1" ViewCount="95" Body="&lt;p&gt;I was wondering if anybody knew of the &lt;strong&gt;function and process&lt;/strong&gt; of the TCTE-1 receptor during the binding of a sperm with an egg. The only think I know of TCTE-1 is that it is a species-specific receptor.&#xA;I also know that it's removal will render homozygous males infertile. I know that researchers are experimenting with mice to study TCTE-1.&lt;/p&gt;&#xA;" OwnerUserId="584" LastActivityDate="2014-03-22T20:55:54.877" Title="Function and process of TCTE-1 receptor" Tags="&lt;endocrinology&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16005" PostTypeId="1" AcceptedAnswerId="16936" CreationDate="2014-03-22T16:55:46.790" Score="0" ViewCount="30" Body="&lt;p&gt;I am thinking how the nutrient absorption differs between between patients with allergies (Hypersensitivity I) and those not. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The current guideline about number of eggs in diet is one daily regularly.&#xA;My professor says that 1-4 eggs daily can be also ok because cholesterol is inhibited.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I am thinking if we have Hypersensitive (allergic) person, what the recommendation should be then.&#xA;My hypothesis says that more cholesterol would be absorbed and less inhibited.&#xA;However, I cannot find any evidence for this hypothesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hypersensitive response is fast. &#xA;I am interested in many responses during long term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How does nutrient absorption differ in hypersensitive patient and normal patient?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-27T16:49:28.320" Title="Is nutrient absorption different in Hypersensitive I patients?" Tags="&lt;diet&gt;&lt;allergies&gt;&lt;eggs&gt;&lt;hypersensitivity&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16007" PostTypeId="2" ParentId="15990" CreationDate="2014-03-22T18:23:38.933" Score="3" Body="&lt;p&gt;This is a very broad field, with many complementing, overlapping, and contrasting theories. I suggest that you read this part of the Wikipedia article on this topic:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_sexual_reproduction#Origin_of_sexual_reproduction&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Evolution_of_sexual_reproduction#Origin_of_sexual_reproduction&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is what I got from the Wikipedia article (this is just one hypothesis, read the article for all the others):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many advantages to sexual reproduction, two main ones are greater genetic variation and recombinational DNA repair (occurs during meiosis). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are certain species that can reproduce both sexually and asexually. They choose to reproduce sexually during times when the environment is uncertain (changing). This provides evidence that greater variation is one reason for sexual reproduction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Asexual organisms only have one copy of each gene, therefore if this copy is mutated in a bad way, they are out of luck. Organisms that sexually reproduce have two copies of each gene, when one goes bad, they can use the other copy to repair the original copy, during meiosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you may know, stress has many harmful effects, one being that it leads to DNA damage. There are certain species of bacteria who, in response to stress, uptake/integrate nearby bacteria cell's DNA into their own. They can then use this new copy to repair their own copy in case they experience DNA damage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &quot;trait&quot; of up taking/integrating other's DNA may have been evolutionary selected for (because these organisms repaired their DNA, they survived and passed on their genes), therefore eventually leading to organisms that sexually reproduce.&lt;/p&gt;&#xA;" OwnerUserId="6038" LastEditorUserId="166" LastEditDate="2014-03-23T13:03:44.810" LastActivityDate="2014-03-23T13:03:44.810" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16009" PostTypeId="1" AcceptedAnswerId="16010" CreationDate="2014-03-22T19:43:38.400" Score="2" ViewCount="3721" Body="&lt;p&gt;Why carbohydrates and lipids basically used as a sources of energy? Why only proteins are used as building blocks of all the creations? Yes there are some parts of cells like cell walls in which carbohydrates are used but 98% portion of cell is made up of proteins? Why it so? &lt;/p&gt;&#xA;" OwnerUserId="5729" LastActivityDate="2014-03-24T09:22:08.490" Title="carbohydrates and lipids as a source of energy? why?" Tags="&lt;metabolism&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16010" PostTypeId="2" ParentId="16009" CreationDate="2014-03-22T20:05:12.460" Score="4" Body="&lt;p&gt;First, it is a matter of the energy that food can provide. Here fat wins clearly (from the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Food_energy&quot; rel=&quot;nofollow&quot;&gt;Food Energy&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Fat: 37 kJ/g&lt;/li&gt;&#xA;&lt;li&gt;Ethanol (drinking alcohol): 29 kJ/g&lt;/li&gt;&#xA;&lt;li&gt;Proteins: 17 kJ/g&lt;/li&gt;&#xA;&lt;li&gt;Carbohydrates: 17 kJ/g&lt;/li&gt;&#xA;&lt;li&gt;Organic acids: 13 kJ/g&lt;/li&gt;&#xA;&lt;li&gt;Polyols (sugar alcohols, sweeteners): 10 kJ/g&lt;/li&gt;&#xA;&lt;li&gt;Fiber: 8 kJ/g&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Proteins and Carbohydrates have approximately the same energy content. But the advantage of carbohydrates (and especially glucose) is that is can be taken up by the body and the cells pretty fast, while proteins need to be digested and broken up, before they can metabolized further. Also plants make primarily sugars (or derivated polymers like starch), so carbohydrates are readily available in the food.&#xA;Fat and sugars are chosen for nutritional reasons, since they have a higher energy content and are available for it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Structural components are build by proteins, since the 20 amino acids allow a much greater diversity in the protein chains than it would be possible for fats or carbohydrates. The building blocks are relatively small and simple but they all have the same basic structure (carbogroup, aminogroup and the sidechain) which allows linking via the functional group and the sidechain influencing their behavior (hydrophobic, hydrophilic, charged, etc.).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-23T08:22:03.310" LastActivityDate="2014-03-23T08:22:03.310" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16012" PostTypeId="2" ParentId="16003" CreationDate="2014-03-22T20:55:54.877" Score="1" Body="&lt;p&gt;This is by far too long for a comment, so as an answer: I spend now quite a while using Pubmed and other search tools, to find more information. The most recent article I found over and over again was the one from Juneja and colleagues: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9570741&quot; rel=&quot;nofollow&quot;&gt;Sequence divergence within the sperm-specific polypeptide TCTE1 is correlated with species-specific differences in sperm binding to zona-intact eggs.&lt;/a&gt;&quot; (which you probably also found). This article has only been cited two times, which is a bad sign for an article making so important connections. My guess is that no further research in this area either happened or has at least not been published. So beyond this I am afraid that there is no other information available (I am happy to change this, if there is any other information available).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-22T20:55:54.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16014" PostTypeId="2" ParentId="15990" CreationDate="2014-03-22T21:24:17.413" Score="2" Body="&lt;p&gt;Big topic yes, but lets hit some high points. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, sexual reproduction is a no brainer in evolution.   In its basis, sex only requires a segment of the chromosome to be heterogamous - that it will not be recombined.  In male humans this is both X and Y chromosomes, in other animals it is the female which has heterogamy.  Its not the entire chromosome either - the pseudo-autosomal regions of X and Y in humans do recombine.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sexual reproduction allows some individuals to combine their genomes by donating some but not all chromosomes to offspring. The heterogamous regions are always donated by one parent and the same sex is not allowed to combine with others. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sexual reproduction is found in plants, single celled eukaryotes as well as animals.  The forces that drive the emergence of sex show up frequently enough and are persistent enough for sexual chromosomes to have &lt;a href=&quot;http://www.nature.com/hdy/journal/v88/n2/full/6800016a.html&quot; rel=&quot;nofollow&quot;&gt;evolved hundreds of times in plants&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even in animals, where asexual reproduction is very rare there are multiple configurations of sex determining chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sex goes back to a very ancient trait in eukaryotes related to the haploid / diploid life cycle.  In fungi, who are related to the original metazoans, &lt;a href=&quot;http://mmbr.asm.org/content/74/2/298.full&quot; rel=&quot;nofollow&quot;&gt;sex shows up when its needed&lt;/a&gt;.  There the combination of haploid phases may be limited by more than one combination of specific elements.  Fungi can have many genders (mating types) - each of may only allow mating to specific types.  Others like Saccharomyces allow recombination between any two different mating types.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The earliest single celled eukaryotes related to animals show mating types.  The various sexual characteristics related to sexual reproduction, such as placentas, eggs, sperm form &#xA;and function are all embellishments from sexual selection which vary tremendously from one form of animal to another.  The chromosomal functions which became sexual traits are ancient and predate metazoans.  They are not necessarily conserved though - they are simple enough to reproduce that they change their characteristics often in evolutionary history. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I should say that all this doesn't apply to bacteria and eubacteria.  Why?  Because bacteria are much older and have their own systems of gene transfer and recombination with their own rules.  They usually have a single copy of their genome (I'd like to hear about exceptions - I think I know of maybe one) which makes quite gender different.  The do have something called 'sex' where a pili gene can be found on a plasmid which allows the bacteria to transfer DNA directly, which is like a sex determining locus.  But a bacteria may catch gender like a cold - it can not have it, it can get it, it can lose it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria are also capable of &lt;a href=&quot;http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Avery.html&quot; rel=&quot;nofollow&quot;&gt;transferring a single gene or a segment of DNA by various means&lt;/a&gt;, including pili, plasmids, phage, and &lt;a href=&quot;http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_6-2-2013-10-18-30&quot; rel=&quot;nofollow&quot;&gt;simply taking in the naked DNA&lt;/a&gt; that they find laying around.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-03-23T13:33:07.123" LastActivityDate="2014-03-23T13:33:07.123" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16016" PostTypeId="2" ParentId="15532" CreationDate="2014-03-23T00:42:50.183" Score="1" Body="&lt;p&gt;In this article they look at the development of natural immunity to diptheria in those who were vaccinated. I could not find any studies on people who had acquired it naturally. &#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0264410X97001485&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0264410X97001485&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They found that the development of immunity to diptheria vaccine depended on several factors:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Time lapsed since last vaccination&lt;/li&gt;&#xA;&lt;li&gt;Females had lower immunity rates&lt;/li&gt;&#xA;&lt;li&gt;Number of previous vaccinations&lt;/li&gt;&#xA;&lt;li&gt;Last vaccination within the first 3 years of life&lt;/li&gt;&#xA;&lt;li&gt;Age&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;What this may mean for individuals who are affected is that similar factors could play a role preventing them from acquiring immmunity to diptheria. Indeed, some of the factors like last immunization and number of vaccinations are logical since diptheria may evolve or there may be different strains so the body needs to have the lastest antibodies for immunity.&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-03-23T00:42:50.183" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16021" PostTypeId="1" CreationDate="2014-03-23T03:15:14.870" Score="2" ViewCount="40" Body="&lt;p&gt;I'm trying to come up with an idea for a school project (a hypothetical research study).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking at depression and the serotonin transporter gene, which is highly expressed in the human cerebellum. There are 2 common alleles of this gene, a &quot;long&quot; and &quot;short&quot; version. &lt;a href=&quot;http://en.wikipedia.org/wiki/Serotonin_transporter&quot; rel=&quot;nofollow&quot;&gt;The difference is that the long version has 16 repeats of a certain sequence in the promoter, and the short has only 14 repeats&lt;/a&gt;. Though there have been some controversial findings, the short genotype has been linked to patients with depression, suicide, less serotonin uptake, and less localization of the serotonin transporter at the cell membrane (synapse).&#xA;My hypothesis is that RNA polymerase binds preferentially/more strongly to the long allele's promoter over the short allele's promoter in human cerebellum neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This would explain higher levels of transcription of the serotonin transporter gene (though this hasn't actually been shown) and increased serotonin uptake (has been shown), resulting in lowered susceptibility to depression.&#xA;I was thinking I would do this using &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromatin_immunoprecipitation&quot; rel=&quot;nofollow&quot;&gt;ChIP&lt;/a&gt;. I would get cerebellum tissue from deceased patients of each genotype (long/long, long/short, short/short) and compare bound RNA-pol in the different genotypes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My two questions are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Is this a reasonable hypothesis (does it make sense based on what I have described)?&lt;/li&gt;&#xA;&lt;li&gt;Hypothetically, is it possible to do ChIP on dead brain tissue?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6117" LastEditorUserId="948" LastEditDate="2014-04-20T04:20:05.627" LastActivityDate="2014-04-20T04:20:05.627" Title="Is it reasonable to assume that RNA polymerase would bind preferentially to the promoter of the long allele of the SERT gene?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;neurotransmitter&gt;&lt;chip&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16022" PostTypeId="1" AcceptedAnswerId="16023" CreationDate="2014-03-23T13:57:32.763" Score="3" ViewCount="1249" Body="&lt;p&gt;From my understanding, in the sodium-potassium pump we have Na&lt;sup&gt;+&lt;/sup&gt; inside the cell and K&lt;sup&gt;+&lt;/sup&gt; outside the cell, thus forming a so called &quot;salted banana.&quot; After reading my textbook I found many statements saying that &quot;potassium ions tend to diffuse out of the cell...sodium ions tend to flow into the cell.&quot; I initially thought that when the action potential hits Na&lt;sup&gt;+&lt;/sup&gt; leaves the cell and K&lt;sup&gt;+&lt;/sup&gt; enters the cell, which to me contradicts the previous statement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone please clarify this and differentiate between the two?&#xA;I am trying to understand the action potential process as a whole.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you !&lt;/p&gt;&#xA;" OwnerUserId="4562" LastEditorUserId="1320" LastEditDate="2014-03-23T19:04:19.457" LastActivityDate="2014-03-23T19:04:19.457" Title="Sodium-Potassium Pump" Tags="&lt;cell-biology&gt;&lt;cell-membrane&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16023" PostTypeId="2" ParentId="16022" CreationDate="2014-03-23T14:41:02.700" Score="4" Body="&lt;p&gt;Your confusion is caused by the assumption that Na&lt;sup&gt;+&lt;/sup&gt; always leaves the cell and K&lt;sup&gt;+&lt;/sup&gt; always enters. The Na&lt;sup&gt;+&lt;/sup&gt;/K&lt;sup&gt;+&lt;/sup&gt; pump is there to maintain membrane potential and relative Na&lt;sup&gt;+&lt;/sup&gt; and K&lt;sup&gt;+&lt;/sup&gt; ion concentrations stable inside. When an action potential (AP) is generated, sodium channels open and sodium rushes inside to depolarize the cell( 1st phase of AP). Next, the sodium channels close and K&lt;sup&gt;+&lt;/sup&gt; begins to leave the cell (since the inside of the cell contains too many positive charges and the cell would remain depolarized if nothing was changed). Potassium leaves through leak channels. So in summary, Na&lt;sup&gt;+&lt;/sup&gt;/K&lt;sup&gt;+&lt;/sup&gt; pump and the channels that are part of AP generation result in different movement of Na&lt;sup&gt;+&lt;/sup&gt; and K&lt;sup&gt;+&lt;/sup&gt; across the cell membrane. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a nice review of Na&lt;sup&gt;+&lt;/sup&gt;/K&lt;sup&gt;+&lt;/sup&gt; pump and action potential generation. &#xA;&lt;a href=&quot;https://www.khanacademy.org/science/biology/human-biology/neuron-nervous-system/v/sodium-potassium-pump&quot; rel=&quot;nofollow&quot;&gt;https://www.khanacademy.org/science/biology/human-biology/neuron-nervous-system/v/sodium-potassium-pump&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5694" LastEditorUserId="1320" LastEditDate="2014-03-23T19:03:21.747" LastActivityDate="2014-03-23T19:03:21.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16024" PostTypeId="1" CreationDate="2014-03-23T15:31:17.540" Score="0" ViewCount="30" Body="&lt;p&gt;I am trying to find some figure(s) to explain this.&#xA;There is probably better name for &quot;bronchomotor&quot; reaction.&#xA;They seem to opposite terms and actually affecting same things (alveolar diameter/tone); one increasing, while the other decreasing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am been reading Pocock and Guyton but I am not happy in any any figures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which figures can you use to answers this question?&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-03-23T15:31:17.540" Title="How does vasomotor and bronchomotor reactions equilibrate local blood flow to correspond local ventilation?" Tags="&lt;physiology&gt;&lt;blood-circulation&gt;&lt;respiration&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16025" PostTypeId="2" ParentId="14957" CreationDate="2014-03-23T15:33:22.637" Score="1" Body="&lt;p&gt;The following answer is not complete and only give some intuitive grasp on Fisher's fundamental theorem of Natural Selection. A better devlopment can be found in &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0387201912&quot; rel=&quot;nofollow&quot;&gt;Ewen's book&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's first define what is the &lt;strong&gt;Additive Genetic Variance&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider a quantitative character that is determined entirely by a locus $A$ which two alleles are $A_1$ and $A_2$. the measurement $m$ of this quantitative character for an individual is given by their genotypes so that the genotypes $A_1A_1$, $A_1A_2$ and $A_2A_2$ have measurements $m_{11}$, $m_{12}$ and $m_{22}$ respectively. Suppose that random mating obtains with respect to this character and that the frequencies of $A_1A_1$, $A_1A_2$ and $A_2A_2$ are $x^2$, $2x(1-x)$ and $(1-x)^2$, respectively. Then, the mean value $\bar m$ of this measurement is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\bar m = x^2m_{11} + 2x(1-x)m_{12} + (1-x)^2m_{22}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and the variance in the measurement is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma ^2 = x^2(m_{11} - \bar m) + 2x(1-x) (m_{12} - \bar m) + (1-x)^2 (m_{22} - \bar m)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The covariance between the fathers and the sons (assuming no change in allele frequency) is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$x(1-x)\left(xm_{11} + (1-2x)m_{12} - (1-x)m_{22}\right)^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The correlation between the fathers and the sons is found by dividing the covariance by the variance (since the variance of fathers equal the variance of sons) is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{x(1-x)\left(xm_{11} + (1-2x)m_{12} - (1-x)m_{22}\right)^2}{\sigma ^2}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;which can be decomposed into dominance and additive variance&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma _A ^2 = 2x(1-x) (xm_{11} + (1-2x)m_{12} - (1-x)m_{22})^2$$&#xA;$$\sigma _D ^2 = x^2(1-x)^2 (2xm_{12} - m_{11} - m_{22})^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Replacing the measurement by the fitness, you get the additive genetic variance in fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma _A ^2 = 2x(1-x) (xw_{11} + (1-2x)w_{12} - (1-x)w_{22})^2$$&#xA;$$\sigma _D ^2 = x^2(1-x)^2 (2xw_{12} - w_{11} - w_{22})^2$$&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Now, the &lt;strong&gt;mean fitness&lt;/strong&gt; in the population is given by (as already said)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\bar w = x^2w_{11} + 2x(1-x)w_{12} + (1-x)^2w_{22}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using Wright-Fisher equation, the &lt;strong&gt;change in mean fitness&lt;/strong&gt; is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\Delta \bar w = 2x(1-x) (xw_{11} + (1-2x)w_{12} - (1-x)w_{22})^2 \cdot (w_{11}x^2 + (w_{12} + \frac{w_{11} + w_{22}}{2})x(1-x) + w_{22}(1-x)^2)\bar w ^{-2}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;which can be approximated &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\Delta \bar w ≈ 2x(1-x) (xw_{11} + (1-2x)w_{12} - (1-x)w_{22})^2 = \sigma _A ^2$$&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.fr/Mathematical-Population-Genetics-Theoretical-Introduction/dp/0387201912/ref=sr_1_1?ie=UTF8&amp;amp;qid=1395587215&amp;amp;sr=8-1&amp;amp;keywords=mathematical%20population%20genetics&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-04-01T14:24:22.573" LastActivityDate="2014-04-01T14:24:22.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16026" PostTypeId="1" AcceptedAnswerId="16027" CreationDate="2014-03-23T16:58:42.067" Score="1" ViewCount="115" Body="&lt;p&gt;I am trying to find animations which can anonymous or generalised for Embryology.&#xA;However, I have not find any single good source.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any bank of animations for generalised embryos?&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-03-28T07:04:39.513" Title="Is there any bank of animations for Embryology?" Tags="&lt;embryology&gt;&lt;database&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16027" PostTypeId="2" ParentId="16026" CreationDate="2014-03-23T17:07:48.493" Score="2" Body="&lt;p&gt;I don't know of any database, but a short search brought up a few candidates. Depending on what you would like to see, they should be a good start:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.indiana.edu/~anat550/embryo_main/&quot; rel=&quot;nofollow&quot;&gt;Human Embryology Animations&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;S&lt;a href=&quot;http://meded.duke.edu/symbrio/&quot; rel=&quot;nofollow&quot;&gt;imbryo (Flash based)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://embryology.med.unsw.edu.au/embryology/index.php?title=Movies&quot; rel=&quot;nofollow&quot;&gt;UNSW Embryology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.uic.edu/com/surgery/embryo/animation.htm&quot; rel=&quot;nofollow&quot;&gt;Embryological Development of the human&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://embryodynamics.com/?page_id=553&quot; rel=&quot;nofollow&quot;&gt;Embryodynamics&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-23T21:43:04.457" LastActivityDate="2014-03-23T21:43:04.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16029" PostTypeId="2" ParentId="15532" CreationDate="2014-03-23T19:54:02.037" Score="2" Body="&lt;p&gt;There are two other, but rather exotic possibilites which explain why people do not develop immunity after an diphtheria infection. These are unlikely to get to 6-8% of the cases which @Masi writes, but I am missing the reference here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first possibility are people with chronic renal failure. They have problems with their immune responses since their antigenpresenting cells do not get the necessary co-stimulatory signal by the T-cells. See this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10195626&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt;. People with other problems in their T-cells or the co-stimulatory signal would have this problem, too. See this &lt;a href=&quot;http://www.jci.org/articles/view/113129&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other possibility would be the distribution of the antibodies. The diphteria toxin is made out of two subunits, A and B. B is important for making the way of A into the cell, A gets cleaved in this process and fully active. When the antibodies made in the process are mostly against A (and then against parts, which change their conformation after the cleavage), this antibodies are mostly useless to fight the toxin. See this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6164646&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One (but is complete speculative) possibility is on the toxin itself. It could be possible, that some people are more sensitive to the diphtheria toxin, so that the amounts necessary for the negative effects are too small to trigger an adequate immune response. This is known for the tetanus toxin, where even a survived infection doesn't provide immunity (except when people are vaccinated afterwards) as the toxin is so toxic, that it doesn't trigger the immune system. The caveat is, that the diphteria toxin is about 3 orders of magnitude less toxic than the tetanus toxin.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-23T19:54:02.037" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="16031" PostTypeId="2" ParentId="15532" CreationDate="2014-03-23T23:52:15.493" Score="1" Body="&lt;p&gt;Just wanted to add that this is a &lt;a href=&quot;http://www.immunizationinfo.org/parents/why-immunize&quot; rel=&quot;nofollow&quot;&gt;common problem with vaccines&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...consider an actual measles outbreak in Colorado in December 1994.5 Out of 625 children exposed to the disease, 17 got measles. Of those 609 who had previously been vaccinated, only 10 (or 1.6%) developed measles. Of the 16 children who were not immunized, 7 (or 44%) developed measles. Thus, the risk for immunized children was less than 2% while the risk for unimmunized children was 44%.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Most vaccine development struggles to reach high immune efficacy; You usually can't just inject some dead bacteria or virus and expect to get an immune response.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular I think there has been adaptations in the immune system to DT such that it tends to stimulate an immune response.  This is pretty much a reaction to the peptide sequence itself.  We know this because since the 1980s there has been concern that the live toxins in DPT vaccines might be causing health problems with young children.  (&lt;a href=&quot;http://www.cdc.gov/vaccinesafety/vaccines/dtap/dtapindex.html&quot; rel=&quot;nofollow&quot;&gt;They don't&lt;/a&gt;).  As such, acellular vaccines were developed where just a few proteins were included - the cell was not used, and DT was produced where only a fragment was added or the toxin was rendered inactive by mutagenesis. DT is such a reliable component that by itself &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0264410X9900568X&quot; rel=&quot;nofollow&quot;&gt;it can illicit an 88% immunity rate&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These DT fragments are formulated with other bacterial components to &lt;a href=&quot;http://pediatrics.aappublications.org/content/86/4/617.short&quot; rel=&quot;nofollow&quot;&gt;create new vaccines&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The failure of the vaccine on occasion is most likely the result of individual variations in immune loci. The immune system is highly complex and also highly variable from individual to individual even amongst close relatives.  their immune activation or their defenses (complement and immunoglobin pathways) may make some individuals more susceptible to diphtheria than others. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The science of vaccine formulation is highly empirical; I don't think it is understood why some molecules evoke a broadly distributed reaction and others do not.  Even so the diphtheria toxin is one of the more universal immune stimulants known.  I don't think that a completely universal adjuvant (something added to a vaccine to stimulate an immune response) is known. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-03-24T11:56:21.000" LastActivityDate="2014-03-24T11:56:21.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16032" PostTypeId="1" AcceptedAnswerId="16082" CreationDate="2014-03-24T07:13:55.247" Score="9" ViewCount="1317" Body="&lt;p&gt;I've looked it up in plenty of places like the Wikipedia page and such, and it is clear that the most common cause of Paresthesia is either a fair amount of pressure on a specific patch of skin causing lack of blood flow to the specific nerve endings in that limb (not to be confused with a stop in blood flow to the limb altogether) or a much stronger amount of pressure on that patch of skin for a shorter amount of time. This, although the most common cause, is not nearly the only one, which could be anywhere from simply sleeping on the wrong side of the bed to a lethal injection. I'm wondering what happens to the nerve cells that are affected at a cellular level, and what causes it at a cellular level. The level at which pounds per square inch aren't what is being noticed.&lt;/p&gt;&#xA;" OwnerUserId="6120" LastActivityDate="2015-09-06T19:15:40.257" Title="What causes Paresthesia (Pins and Needles) at a cellular level?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;cell-biology&gt;&lt;sleep&gt;&lt;blood-circulation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16033" PostTypeId="2" ParentId="16009" CreationDate="2014-03-24T09:22:08.490" Score="1" Body="&lt;p&gt;There can be many reasons for why proteins are chosen as building blocks. Apart from what Chris said, I would add some points:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Amide bond in proteins is quite strong and thus provides a stable backbone&lt;/li&gt;&#xA;&lt;li&gt;Because of different amino acids proteins can be versatile&lt;/li&gt;&#xA;&lt;li&gt;Functionality comes first and then storage (assuming that initially there was just harvesting and no storage). Considering this and the composition of earth at that time, hydrophobic lipids don't seem to have been functional molecules in the aqueous solvent. Carbohydrates on the other are quite complex. You may argue that nucleotides have sugar backbone so sugar must have existed. I don't have an explanation of why polysaccharides could &lt;strong&gt;never&lt;/strong&gt; be functional molecules: perhaps because they are more structurally complex than proteins but could not adopt stable structures such as helices etc. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;But having chosen proteins as the functional molecules it won't be a nice idea to use them for energy storage unless there is extreme need (such as starvation). Fats being hydrophobic wont easily suffer attack from the regular reactive species in aqueous solvent; this makes them good storage molecules. Same case with carbohydrates, which arise from carbon fixation. Despite the existence several types of sugars the chemical spectrum is much less compared to amino acids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And then there is the reason that Chris pointed out based on calorific value. But I would add a point on this regard: the energy in a food cannot be just measured by their absolute thermodynamic calorific value. For e.g. cellulose (which is present in fibers) has the same constitution as starch but provides practically no energy to humans because it cannot be digested. And in plants it plays a structural rather than functional role. So exceptions exist at least in the case of carbohydrates. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-03-24T09:22:08.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16034" PostTypeId="1" CreationDate="2014-03-24T10:31:08.453" Score="1" ViewCount="259" Body="&lt;p&gt;Sulfur is part of the amino acids cystein and methionin, plants take up sulfur &lt;a href=&quot;https://biology.stackexchange.com/questions/15607/in-biosynthesis-of-cysteine-and-methionine-where-does-the-sulfur-come-from&quot;&gt;in the form of $H_2S$&lt;/a&gt;. These organisms will also need a way to get rid of excess sulfur, how? In what compounds?&lt;br&gt;&#xA;Judging by the smell of some farts, I guess $H_2SO_4$ plays a role, but I can't imagine that one get'S rid of all the sulfur this way.&lt;/p&gt;&#xA;" OwnerUserId="3037" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-08-05T12:28:34.047" Title="In what forms do plants and animals excrete sulfur?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16035" PostTypeId="1" AcceptedAnswerId="16038" CreationDate="2014-03-24T12:26:30.947" Score="2" ViewCount="1500" Body="&lt;p&gt;As blunt as possible: when performing real time PCR it is a routine step to run one PCR in order to plot a &quot;standard curve&quot; with several decreasing dilution ratios from your sample. what is the real purpose of this?&#xA;how should results be used/interpreted?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastActivityDate="2014-03-25T08:33:36.860" Title="Real time PCR standard curve" Tags="&lt;pcr&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16036" PostTypeId="1" AcceptedAnswerId="16090" CreationDate="2014-03-24T12:52:14.197" Score="1" ViewCount="1058" Body="&lt;p&gt;It's common that human females have a more flexible body than males, (but I don't know why, so it'd be helpful if someone answers why so as well!) but does this apply to all mammals?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2014-03-26T10:37:09.583" Title="Are females more flexible than males in all mammals?" Tags="&lt;physiology&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16037" PostTypeId="2" ParentId="16035" CreationDate="2014-03-24T13:27:52.803" Score="1" Body="&lt;p&gt;Because the purpose of the standard curve (which actually results in a standard line) needs to be linear. If it is not linear (because of not enough values which are not linear distributed), then you quantification will be wrong.&#xA;Ideally the line should look like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6iRcV.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This picture is taken from this &lt;a href=&quot;http://pathmicro.med.sc.edu/pcr/realtime-home.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;website&lt;/a&gt;, which gives a nice introduction into the topic.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-24T13:27:52.803" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16038" PostTypeId="2" ParentId="16035" CreationDate="2014-03-24T13:49:43.177" Score="2" Body="&lt;p&gt;You can use 3 or 4 dilutions- 1:1, 1:5, 1:25, 1:125&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Purpose of doing this is to calculate the primer efficiency. Ideally primer efficiency should be 2 i.e. two molecules of DNA are formed in a round of PCR. So after n-rounds of PCR there should be $2^n$ DNA. However, this may not be the case always. You calculate primer efficiency like this:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Plot $Ct$ vs $log_2(Conc)$&lt;/li&gt;&#xA;&lt;li&gt;Get the trendline (in excel) or use a linear regression command for other applications&lt;/li&gt;&#xA;&lt;li&gt;Get the slope ($s$) of the trendline &lt;/li&gt;&#xA;&lt;li&gt;Efficiency in this case would be $2^{-s}$.  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Some people use base of 10 in the log instead of 2 (for which you have to do $10^{-s}$ instead.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This, you can directly use to find out how many copies are produced after n cycles i.e instead of $2^n$ it will be $x^n$  where $x$ is the calculated efficiency. This is particularly useful when you are calculating the fold changes using the comparative Ct method. For details see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11328886&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-03-25T08:33:36.860" LastActivityDate="2014-03-25T08:33:36.860" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="16039" PostTypeId="1" CreationDate="2014-03-24T14:03:49.970" Score="7" ViewCount="695" Body="&lt;p&gt;I'm wondering how can very uncommon diseases remain in a relatively stable equilibrium. For example, if it started to spread, the spread could accelerate and become an epidemic. However, if it doesn't spread, why doesn't it wither away?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I understand, the ebola for example, is highly contagious, nearly always fatal, and kills quickly. So quickly, hat the target has not much time to pass it on to others. If it spread just a little better, it would become an epidemic, just a little slower and it would disappear. How is it possible, that its spread did not change significantly in the last couple of decades? It kills a few dozen, maybe a few hundred people per year, these numbers remain largely unchanged.&lt;/p&gt;&#xA;" OwnerUserId="3798" LastActivityDate="2014-04-29T19:48:15.360" Title="How can highly virulent but uncommon diseases (like ebola) maintain a stable equilibrium?" Tags="&lt;virology&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="16040" PostTypeId="2" ParentId="16039" CreationDate="2014-03-24T15:29:09.507" Score="10" Body="&lt;p&gt;Viruses and other disease causing organisms are usually in an ecological steady state in different organism, called a vector.  When they start to infect another organism similar enough that they can reproduce, they may turn out to be more virulent or fatal than is optimal for the organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The classic example is the case of influenza outbreaks, the flu virus is causing mild infections in other animals such as birds or pigs and then a human being catches it and it may be serious or even fatal.  This is classically because the viruses lytic cycle (where it reproduces and then kills host cells) is not tuned to the equilibrium ideal for viruses in the new human environment, which is not fatal which gives the virus the best chance of reproduction and retransmission.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of Ebola and Marburg viruses the &lt;a href=&quot;http://www.cdc.gov/ncidod/dvrd/spb/mnpages/dispages/vhf.htm&quot; rel=&quot;nofollow&quot;&gt;vector is not known&lt;/a&gt; but there is &lt;a href=&quot;http://www.stanford.edu/group/virus/filo/bats.html&quot; rel=&quot;nofollow&quot;&gt;speculation and research going on&lt;/a&gt;. So in the extremely rare handful of events where these hemorrhagic fevers have been caught by people they fatal.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its the non-equilibrium case where the virus is not adjusted to human hosts and adjusted for its vector population where it is usually most dangerous. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If these viruses were allowed to persist they would theoretically come to the point where it wasn't fatal.  The problem being that people would die and there is always the risk that the virus would burn through all possible human hosts before it adjusts... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to say that this is all driven by evolutionary forces.  If the environment encourages pathogenic characteristics then human pathogens can persist forever.  Flesh eating bacteria and MRSA and other antibiotic resistant bacteria have found a competitive environment where causing disease and death are the only way to go - &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/news/080401_mrsa&quot; rel=&quot;nofollow&quot;&gt;hospitals with antibiotics&lt;/a&gt;. In the case of Ebola/Marburg, there may be a disease reservoir of monkeys acting as a pool for the high fatality strain.  Anything can happen with the right geography and dynamics. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you've been thinking to yourself, 'what are the odds that a virus or bacterium would be extra virulent versus not infectious at all?', you are right. One should also note that fatal outbreaks are rare and exceptional.  There are clearly plenty of cases where viruses or pathogens from other organisms can't get any traction at all in humans.  We are practically swimming in viruses and bacteria all the time.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-04-29T19:48:15.360" LastActivityDate="2014-04-29T19:48:15.360" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16041" PostTypeId="1" AcceptedAnswerId="24779" CreationDate="2014-03-24T16:24:15.587" Score="13" ViewCount="713" Body="&lt;p&gt;I've recently heard a podcast, in which a professor describes &lt;a href=&quot;http://careersuicideblog.wordpress.com/2012/11/14/how-abstract-art-attracts-the-chicks/&quot; rel=&quot;noreferrer&quot;&gt;one of the theories as to why we like abstract art&lt;/a&gt;. In his talk, he mentions an experiment with seagull chicks, in which the seagull chicks mistake a stick with a red dot for their mother's beak, and &lt;strong&gt;in the case of stick with 3 stripes actually preferred it to their mother's beak.&lt;/strong&gt; When a stick like that is waved around a chick, it starts to peck at it, believing it is mother bird:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2GTzO.jpg&quot; alt=&quot;chick beak stick seagull&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This experiment suggests that birds are imprinted to recognize specific patterns and interpret them as mother.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm in trying to create a similar experiment for cats. To do so I'm trying to understand if cats other small predators (ferrets,etc) are imprinted in a similar way - &lt;strong&gt;do cats recognize specific features of a bird to identify it as &quot;bird&quot;, &quot;prey&quot; or &quot;can hunt and eat&quot;?&lt;/strong&gt; I'm talking about stuff like - do they recognize eyes, beaks, wings or tail in a special way?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To paraphrase the question: &lt;strong&gt;If I'm to create a stick like above, but for cats, what features would be painted on the stick?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that butterflies, caterpillars and other insects have evolved to mimick &quot;eyes&quot; on non-vital organs to confuse birds. I'm interested if same stuff exists for small mammal predators.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/FWQrB.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2014-12-11T15:40:41.653" Title="Are there specific features of birds that cats/small predators are attracted to?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;development&gt;&lt;sensation&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16042" PostTypeId="1" AcceptedAnswerId="16053" CreationDate="2014-03-24T18:55:15.753" Score="1" ViewCount="340" Body="&lt;p&gt;If you injected a tumor with epithelial cells infected with the Rhinovirus, would this still evoke an immune response as it would with the respiratory system? Secondly, what is the specific reason the Rhinovirus is only attracted to the epithelial cells in the respiratory system.  Do these cells give off a specific chemical signature in which the virus is attracted to?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastEditorDisplayName="user6116" LastEditDate="2014-03-24T19:20:46.377" LastActivityDate="2014-03-26T08:12:10.820" Title="Epithelial cells and Rhinovirus" Tags="&lt;cancer&gt;&lt;virus&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16043" PostTypeId="1" AcceptedAnswerId="26175" CreationDate="2014-03-24T19:12:35.163" Score="0" ViewCount="447" Body="&lt;p&gt;I have a set of nucleotide sequences for which I have aligned using Clustal Omega. In particular, I performed a full alignment, and obtained a full distance matrix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The distance matrix scores range between 0 and 1. I am looking to use this score to back-compute the number of different positions present in the alignment. Is this possible? If possible, I'm looking to avoid using code (my own or otherwise) to re-compute the number of positions differing between each pair of segments, and instead compute it directly from the distance score.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a toy example of what I am receiving from ClustalOmega:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Sequence    1    2    3    4&#xA;1           0    0.1  0.06 0.1&#xA;2                0    0.4  0.23&#xA;3                     0    0.05&#xA;4                          0&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The numbers are the &quot;distances&quot; as calculated by ClustalOmega. According to the README file, they are computed by the k-tuple measure. I tried parsing the original paper (published in 1983 in PNAS), but I could not figure out how k-tuple distances are computed, and I could not figure out how the distance metric (as reported like above) is computed from k-tuple distances.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to convert those numbers into the &lt;code&gt;number of positions that differ between each pair of sequences when the two are aligned&lt;/code&gt;. This includes substitutions, insertions, deletions. I am currently doing this for 520 sets of virus sequences. Is this possible?&lt;/p&gt;&#xA;" OwnerUserId="1536" LastEditorUserId="1536" LastEditDate="2014-03-24T22:40:48.660" LastActivityDate="2014-12-25T08:39:55.497" Title="Clustal Omega - convert from distance into # of substitutions" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="16044" PostTypeId="2" ParentId="16042" CreationDate="2014-03-24T19:38:20.877" Score="1" Body="&lt;p&gt;The virus has some molecules on it surface, which fit to receptors on the surface of their host cells. In the case of rhinoviruses there are three receptors possible. The viruses of the so called major group (or HRV-A species) dock to ICAM1, the minor group (or HRV-B species) to the LDLR (low density lipid receptor), and the relatively recent group of HRV-C dock to the HRVC receptor. See the image below. It is taken from this article (&quot;&lt;a href=&quot;http://cmr.asm.org/content/26/1/135.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Human Rhinoviruses&lt;/a&gt;&quot;), which give a pretty nice overview of the field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bqUZF.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the injection question: You will provoke an immune reactions against the epithelial cells, if the are from a different person. If they are not, these cells will simply die and nothing else will happen.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-26T08:12:10.820" LastActivityDate="2014-03-26T08:12:10.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16045" PostTypeId="1" CreationDate="2014-03-24T20:01:59.897" Score="3" ViewCount="100" Body="&lt;p&gt;When the spinal cord is damaged, the connection between the brain and some part of the body may be lost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To restore this connection, researches are considering either:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Repairing the damaged area so that the spinal cord works again.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Bypassing the spinal cord by connecting the brain directly to the affected part of the body.  This is done by implants in the brain connected directly to electrodes in the muscles creating a new circuit in parallel.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My question is has there been any attempt to bypass only the damaged part of the spinal cord?  To create a bridge over the damaged tissue? &lt;/p&gt;&#xA;" OwnerUserId="5484" LastEditorUserId="9943" LastEditDate="2014-12-18T00:11:36.657" LastActivityDate="2014-12-18T00:11:36.657" Title="Spinal cord injury bypass" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;neuroanatomy&gt;&lt;neural-engineering&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16046" PostTypeId="1" AcceptedAnswerId="16048" CreationDate="2014-03-24T20:04:58.493" Score="2" ViewCount="114" Body="&lt;p&gt;Integral membrane proteins have functional asymmetry i.e. they have two different domains of proteins performing different functions. these proteins have Tyr and Trp amino acid residues at the interface between the lipid and water.Because these amino acids have dual nature that their side chains can interact with both extracellular aqueous environment as well as hydrophobic lipid phase and another generalization about amino acid location relative to bilayer is described by &quot;positive inside rule&quot;: The positively charged Lys,His, and Arg residues of membrane proteins occur more commonly on the cytoplasmic phase of membranes.My question is that why only positively charged amino acids are faced towards cytoplasm why not negatively charged amino acids or other amino acids are favoured here?&lt;/p&gt;&#xA;" OwnerUserId="5729" LastActivityDate="2014-03-24T20:31:03.833" Title="Structure of biological membranes?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;cell-signaling&gt;&lt;cell&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16048" PostTypeId="2" ParentId="16046" CreationDate="2014-03-24T20:31:03.833" Score="4" Body="&lt;p&gt;Some thoughts on this. First of all, the positive-inside rule, proposed by Gunnar von Heijne, is an empirical rule based upon observations, not one derived from theoretical considerations, so any explanation is simply an attempt at a rationalisation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having said that, here are three of those rationalisations:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;the membrane potential is usually negative inside. This will create an electrostatic tendency for basic amino acid side chains to stay inside.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;most phospholipid head groups are either neutral or anionic (phosphatidylserine, when the phosphate is included). Again an electrostatic force favouring basic residues inside since to move them out would require overcoming their interaction with the negatively-charged membrane surface&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the pK values of the basic side chains (lysine and arginine) are much further from 7 than are those of the acidic side chains, so,  since charged residues must be neutralised to get them through the bilayer, it is more energetically unfavourable to deprotonate basic side chains than it is to protonate acidic ones.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-24T20:31:03.833" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16049" PostTypeId="1" AcceptedAnswerId="16050" CreationDate="2014-03-24T22:12:53.197" Score="0" ViewCount="562" Body="&lt;p&gt;Does our DNA adapt by human lifetime? Or do we have the same genetic information from birth to death?&#xA;I mean: What is usually called &quot;evolution&quot; means &quot;natural selection&quot; like this:&#xA;&lt;a href=&quot;http://www.youtube.com/watch?v=hOfRN0KihOU&amp;amp;list=UUsXVk37bltHxD1rDPwtNM8Q&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=hOfRN0KihOU&amp;amp;list=UUsXVk37bltHxD1rDPwtNM8Q&lt;/a&gt;&#xA;-stronger animals have more descendants, so they make bigger percent of strong animals.&#xA;But does evolution work by some primitive genetics-engineering too? Thank you.&lt;/p&gt;&#xA;" OwnerUserId="6124" LastActivityDate="2015-10-01T21:27:06.677" Title="DNA adaptation in human life" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16050" PostTypeId="2" ParentId="16049" CreationDate="2014-03-24T22:32:45.397" Score="2" Body="&lt;p&gt;&lt;strong&gt;Lewontin's recipe&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A very nice way to consider natural selection is through the lense of Lewontin's recipe. Evolution of a given trait (tail length for example) through natural selection occurs whenever the three following conditions are met:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;There is variation for this trait in the population&lt;/strong&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;This variation is caused by mutations&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Part (or the totality) of this variation is &lt;a href=&quot;http://en.wikipedia.org/wiki/Heritability&quot; rel=&quot;nofollow&quot;&gt;heritable&lt;/a&gt;&lt;/strong&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Heritability is the part of the variance in a trait that is explained by genes. It can be measured as a parent-offspring correlation.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;The variation of this trait is correlated with &lt;a href=&quot;http://en.wikipedia.org/wiki/Fitness_%28biology%29&quot; rel=&quot;nofollow&quot;&gt;fitness&lt;/a&gt;&lt;/strong&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;loosely speaking, fitness is an index of both fecundity and survival&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;You can take two minutes to think about how logical it is that changes in frequency of variants (natural selection) occurs whenever these three conditions are met. You can imagine any objects you want (pencils of colors for example) and simulate these three steps:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Variation&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;different pencils have different colors&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Heritability&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;simulate that your pencils reproduce (asexual reproduction is conceptually easier to understand) and offsprings have similar (or even the same) color than parents&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Correlation between trait and fitness&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Pencils of different colors have different fitness.&lt;/li&gt;&#xA;&lt;li&gt;For example each red pencils create two red pencils the next generation while blue pencils do not manage to replicate at all.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;You can quickly see how the red pencils become more frequent in your pencil population through time. If you wait long enough your pencil population will be totally composed of red pencils. And you'll need to simulate a mutation in order to create a blue pencil. I think you understand the how different are the roles of mutations and natural selection in evolution with this example.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Genetic Adaptation During Lifetime of a multicellular organism&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a beginner in evolutionary biology, saying that a &lt;a href=&quot;http://en.wikipedia.org/wiki/Multicellular_organism&quot; rel=&quot;nofollow&quot;&gt;multicellular&lt;/a&gt; individual's genome does not change during its lifetime might be considered satisfying. In reality it is slightly more complicated. Two elements that are mostly influent very early in the lifetime of an individual have to be considered.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;While most mutations occurs during reproduction, some mutations does also occurs during body growth or stated differently during cell reproduction (&lt;a href=&quot;http://en.wikipedia.org/wiki/Mitosis&quot; rel=&quot;nofollow&quot;&gt;Mitosis&lt;/a&gt;). In consequence, some pairs of your cells share exactly the same genome while other pairs of cells have a sligthly different genome.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Moreover, once some mutations had occurred within the development of an individual, these mutations might influence the fitness of the cells and therefore some &lt;a href=&quot;http://en.wikipedia.org/wiki/Allele&quot; rel=&quot;nofollow&quot;&gt;alleles&lt;/a&gt; (variant of a &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene&quot; rel=&quot;nofollow&quot;&gt;gene&lt;/a&gt;) might raise in frequency while others decrease in frequency (Natural selection). It is important to understand that this process of natural selection select for cells that have a higher fitness and therefore do not necessarily select for the cells that allows the individual to increase its own fitness.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I don't fully understand what you mean when saying: &quot;But does evolution work by some primitive genetics-engineering too?&quot; Could you try to rephrase this question?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please, let me know if I answered your question!&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Note:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a good way to understand the difference between &quot;gene&quot; and &quot;allele&quot;. A gene might be a called the &quot;eyes color&quot; gene for example, while the three alleles of the &quot;eyes color&quot;  gene might be callsed &quot;blue eyes&quot;, &quot;brown eyes&quot; and &quot;green eyes&quot;. In this sense, the alleles are the different variants of a gene. Mutations increase the number of alleles and natural selection reduces the number of alleles by selecting for the allele that cause its holder to have the greatest fitness. If you understood that, it is already good!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: Natural selection does not necessarily reduce the number of alleles, several alleles might be kept (&lt;a href=&quot;http://en.wikipedia.org/wiki/Polymorphism_%28biology%29&quot; rel=&quot;nofollow&quot;&gt;polymorphism&lt;/a&gt;) in certain &quot;types&quot; of natural selection (&lt;a href=&quot;http://en.wikipedia.org/wiki/Frequency-dependent_selection&quot; rel=&quot;nofollow&quot;&gt;frequency dependent selection&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Heterozygote_advantage&quot; rel=&quot;nofollow&quot;&gt;overdominance (heterozygote advantage)&lt;/a&gt;, fitness varies in space and/or time, selection acts on different levels). The &quot;type&quot; of Natural selection that reduces the number of alleles after some time is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Directional_selection&quot; rel=&quot;nofollow&quot;&gt;directional selection&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-10-01T21:27:06.677" LastActivityDate="2015-10-01T21:27:06.677" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16051" PostTypeId="1" CreationDate="2014-03-24T22:42:16.213" Score="3" ViewCount="190" Body="&lt;p&gt;How do the instinct to create a hive appeared in bees? Is there some evidence of&lt;br&gt;&#xA;&quot;intermediate&quot; hives? With this questions i mean all the factors necessary to build a hive, including the social structure, the producing of beeswax and architecture.&lt;/p&gt;&#xA;" OwnerUserId="6122" LastEditorUserId="6122" LastEditDate="2014-03-27T02:10:05.880" LastActivityDate="2014-03-27T02:10:05.880" Title="Evolution of bee hives" Tags="&lt;evolution&gt;&lt;sociality&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16052" PostTypeId="2" ParentId="16051" CreationDate="2014-03-24T23:40:48.793" Score="3" Body="&lt;p&gt;I'm assuming you mean the distinct architecture and regular hexagonal shapes in bee honeycombs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, Charles Darwin spent a &lt;a href=&quot;http://www.darwinproject.ac.uk/the-evolution-of-honey-comb&quot; rel=&quot;nofollow&quot;&gt;good bit of time with honeycombs&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all bees and wasps have a common progenitor and wasps also build combs and nests, albeit of paper/celluose as opposed to wax.  He was interested in how the perfect hexagonal lattice formed in the wax.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Darwin tried three different experiments with bees’ cells at Down that he reported in Origin. In one, he put a thick block of wax into the hive. ‘The bees instantly began to excavate minute circular pits in it: and as they deepened these little pits, they made them wider and wider until they were converted into shallow basins, appearing to the eye perfectly true or parts of a sphere, and of about the diameter of a cell. It was most interesting to me to observe that wherever several bees had begun to excavate these basins near together, they had begun their work at such a distance from each other, that by the time the basins had acquired the above stated width (i.e. about the width of an ordinary cell), and were in depth about one sixth of the diameter of the sphere of which they formed a part, the rims of the basins intersected or broke into each other. As soon as this occurred, the bees ceased to excavate, and began to build up flat walls of wax on the lines of intersection between the basins, so that each hexagonal prism was built upon the festooned edge of a smooth basin, instead of on the straight edges of a three-sided pyramid as in the case of ordinary cells.’ (Origin, p. 223.) The cells were built up in a hexagonal shape when their bases intersected with those of other cells; but the pyramidal bases were apparently not built, since there was no pressure to accommodate cells on the other side of the wax, which was a thick block.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This seems to have a built in burrowing behavior in how the lattice forms that eventually turns into hexagonal shapes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW this topic is very similar to the &lt;a href=&quot;http://www.jstor.org/discover/10.2307/3881292?uid=3739560&amp;amp;uid=2&amp;amp;uid=4&amp;amp;uid=3739256&amp;amp;sid=21103845260603&quot; rel=&quot;nofollow&quot;&gt;evolution of spider webs&lt;/a&gt;, which is also fascinating. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-03-24T23:49:28.210" LastActivityDate="2014-03-24T23:49:28.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16053" PostTypeId="2" ParentId="16042" CreationDate="2014-03-25T00:05:19.487" Score="4" Body="&lt;p&gt;Infecting tumor cells with viruses to provoke an immune response used to be  termed (tumor / immune ) 'xenogenization'.  The approach may now fall under the general headings of tumor immunology, immune modifiers or &lt;a href=&quot;http://en.wikipedia.org/wiki/Cancer_vaccine&quot; rel=&quot;nofollow&quot;&gt;tumor vaccines&lt;/a&gt;.   Xenogenization been explored for decades (with only moderate success).  Some modern approaches include adding immune stimulating genes to the viral 'vector' &lt;a href=&quot;http://en.wikipedia.org/wiki/Talimogene_laherparepvec&quot; rel=&quot;nofollow&quot;&gt;(e.g GM-CSF)&lt;/a&gt; to try and improve an immune response.  Xenogenization is usually intended for use with the patients own (autologous) tumor cells.   Other approaches that use viruses include delivering &lt;a href=&quot;http://en.wikipedia.org/wiki/Oncolytic_adenovirus&quot; rel=&quot;nofollow&quot;&gt;genes that preferentially act in tumor cells&lt;/a&gt; or &lt;a href=&quot;http://ci.bavarian-nordic.com/pipeline/technology-platform/poxvirus-based-immunotherapies.aspx&quot; rel=&quot;nofollow&quot;&gt;&quot;tumor antigens&quot;&lt;/a&gt;.  Some of these modified viruses may have been engineered to have low, or no, ability to replicate in the body.   Note that some viruses, such as &lt;a href=&quot;http://pathmicro.med.sc.edu/mhunt/flu.htm&quot; rel=&quot;nofollow&quot;&gt;influenza&lt;/a&gt; or &lt;a href=&quot;http://books.google.com/books?id=4il2mF7JG1sC&amp;amp;pg=PA493&amp;amp;lpg=PA493&amp;amp;dq=lack+of+viremia+rhinovirus&amp;amp;source=bl&amp;amp;ots=NAMosWBeGN&amp;amp;sig=k5an8t0c4oUOQn8Jqg8vrVDVBX8&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=DogxU-HIBejhyQG5kYGYBg&amp;amp;ved=0CCgQ6AEwADgU#v=onepage&amp;amp;q=lack%20of%20viremia%20rhinovirus&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;rhinoviruses&lt;/a&gt; are not (generally) able to circulate in the bloodstream (viremia) to infect distant tumor cells.  Instead, the goal of using such viruses is to provoke an immune response against tumor antigens expressed on the 'original infected' cells at the site of injection and hope that the immune system goes on to attack distant masses/metastases.&lt;/p&gt;&#xA;" OwnerUserId="5922" LastEditorUserId="5922" LastEditDate="2014-03-25T13:51:38.070" LastActivityDate="2014-03-25T13:51:38.070" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16054" PostTypeId="1" CreationDate="2014-03-25T00:17:03.920" Score="3" ViewCount="125" Body="&lt;p&gt;This is the title of this &lt;a href=&quot;http://www.myhealthbeijing.com/china-public-health/a-day-in-beijing-is-like-smoking-only-one-sixth-of-a-cigarette-its-almost-disappointing/&quot; rel=&quot;nofollow noreferrer&quot;&gt;blog post&lt;/a&gt; followed by &lt;a href=&quot;http://www.myhealthbeijing.com/pollution/is-pm2-5-from-air-pollution-the-same-as-from-smoking/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this other good post&lt;/a&gt;.&#xA;I'm particularly anti-tobacco-smoke, at the point of not always considering other pollution, and this article shows how this kind of domestic pollution (main domestic pollution is usually heating) is probably no insignificant in the global air pollution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The weight of this pollution is also maybe increased since people tend to be nearer from potential smokers than from cars (e.g. near entrances).&#xA;I've not known the period of the past, without the smoke-free laws in buildings, but it seems in my country, that it has just moved the problem, possibly reinforced smokers reflex to smoke when outside&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The author shows useful references, that all measure second-hand smoking in terms of PM2.5 which is the common indicator with PM10 for air pollution [car traffic,domestic heating,industry,coal combustion,construction,quarry,waste treatment].&lt;br&gt;&#xA;The results are interesting showing the important rate of PM2.5 in second-hand smoke, it would even be very useful to indicate air pollution levels in terms of cigarette inhalation. 0.17 cigarette/day is quite more insightful than 150μm of PM2.5, at least to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I'm still skeptic and think the effects of second-hand smoke are more important (second-hand smoke is smaller in size than 1μm, considering not only cigarette from manufacturers which include many brute carcinogens and poisons (arsenic, hydrogen cyanide,..), but other tobacco/or drug smoking &lt;a href=&quot;http://www.huffingtonpost.com/2013/04/23/hookah-not-less-harmful-than-cigarettes-_n_3133590.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;that are different but considerably noxious too&lt;/a&gt;)) and this &lt;a href=&quot;http://tobaccocontrol.bmj.com/content/13/3/219.full.pdf+html?ijkey=330b5aea15a8e36fcc2f4208cf99da58d84150f3&quot; rel=&quot;nofollow noreferrer&quot;&gt;study&lt;/a&gt; is quite informative too, comparing diesel car exhaust to cigarette combustion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm wondering:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;is the pollution from cigarettes as volatile as the rest of air pollution?    &lt;/li&gt;&#xA;&lt;li&gt;is the concentration of second-hand cigarette global pollution not insignificant compared to the rest of pollution (in countries with high smoking rates)?  &lt;/li&gt;&#xA;&lt;li&gt;does it go in higher layers of the atmosphere, lower layers (more critical), or does it blend uniformly?  &lt;/li&gt;&#xA;&lt;li&gt;can air pollution mask (with PM2.5, and PM10 reduction filter) protect as well from it?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;particles size in micrometer, from &lt;a href=&quot;http://en.wikipedia.org/wiki/Particulates&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Particulates&lt;/a&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/snj7W.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;edit:&lt;/em&gt; this &lt;a href=&quot;http://ash.org/CAEPAProposal.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://ash.org/CAEPAProposal.pdf&lt;/a&gt; report is particularly interesting&lt;/p&gt;&#xA;" OwnerUserId="4447" LastEditorUserId="4447" LastEditDate="2014-03-25T13:35:18.330" LastActivityDate="2014-03-25T13:35:18.330" Title="A day in Beijing is like smoking Only one sixth of a cigarette" Tags="&lt;physiology&gt;&lt;breathing&gt;&lt;smoking&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16055" PostTypeId="2" ParentId="16049" CreationDate="2014-03-25T01:10:24.190" Score="1" Body="&lt;p&gt;The concept that the environment directly &lt;em&gt;changes&lt;/em&gt; DNA and alters the characteristics of the offspring falls under the heading of &lt;a href=&quot;http://en.wikipedia.org/wiki/Lamarckism&quot; rel=&quot;nofollow&quot;&gt;Lamarkism&lt;/a&gt;. In the context of DNA the  Lamarkian view would be that the giraffe got its long neck by stretching its neck cells reaching up to tall trees for leaves, which then (somehow) changed the DNA in its gametes and thus produced offspring with longer necks.   There's &lt;strong&gt;no compelling evidence&lt;/strong&gt; for Lamarkism and &lt;strong&gt;Remi.b 's  nice answer&lt;/strong&gt; describes DNA and evolution/selection/adaptation in its standard form and how giraffes would evolve such features.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;OP initially asked 'does our DNA adapt during our lifetime'.  Certain regions of the DNA in each of our immune T-cells and B-cells change (recombine) to code for specific protein molecules that bind to antigens.  These are the genes for the &lt;strong&gt;T-cell receptor&lt;/strong&gt; in T-cells and &lt;strong&gt;antibodies&lt;/strong&gt; in the case of B-cells.  So the DNA in a T-cell or B-cell is different compared to other cells in the body including the gametes.  These regions of altered DNA help us fight infection.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can easily imagine that an individuals ability to fight infection may affect whether they can survive to reproductive age.  Genes involved in immune system function might be selected for during &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/news/081001_hivmalaria&quot; rel=&quot;nofollow&quot;&gt;deadly epidemics&lt;/a&gt;. And paradoxically, some genes responsible for debilitating or deadly diseases can persist in human society due to their &lt;a href=&quot;http://en.wikipedia.org/wiki/Sickle-cell_disease#Genetics&quot; rel=&quot;nofollow&quot;&gt;protective effect against other diseases&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For completeness there is also some emerging data that &lt;a href=&quot;http://www.salk.edu/news/pressrelease_details.php?press_id=647&quot; rel=&quot;nofollow&quot;&gt;neurons have some alterations in their DNA&lt;/a&gt; but its not clear what, if anything, that means and whether its of functional significance.  Unless similar types of changes are made in gametes,  DNA altered by this mechanism will not be passed on to offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, DNA in cells can be &lt;em&gt;modified&lt;/em&gt; by a process called &lt;strong&gt;epigenetics&lt;/strong&gt;.  Epi- means 'around'. In &lt;a href=&quot;http://en.wikipedia.org/wiki/Epigenetics&quot; rel=&quot;nofollow&quot;&gt;epigenetics&lt;/a&gt; various regions of the DNA strand (and some related proteins that keep DNA coiled up called histones) are chemically modified by a set of enzymes.  Epigenetics affects how certain genes are switched on and off and is perhaps best known for inactivating one of the two X chromosomes in female cells.  In epigenetic modifications the DNA sequence remains the same but the epigenetic 'decorations' around the DNA can vary and this process can be influenced by the cells environment. &lt;/p&gt;&#xA;" OwnerUserId="5922" LastEditorUserId="5922" LastEditDate="2014-03-25T14:17:01.817" LastActivityDate="2014-03-25T14:17:01.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16057" PostTypeId="1" AcceptedAnswerId="16058" CreationDate="2014-03-25T03:49:28.087" Score="1" ViewCount="175" Body="&lt;p&gt;Where can I buy paracoccus denitrificans? I need it for an experiment. I cannot find online where I can purchase this.&lt;/p&gt;&#xA;" OwnerUserId="6125" LastActivityDate="2014-03-25T04:33:37.660" Title="Buy bacteria for experiment?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16058" PostTypeId="2" ParentId="16057" CreationDate="2014-03-25T04:22:22.590" Score="4" Body="&lt;p&gt;ATCC- you can get most bacterial strains and cell lines there. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Find &lt;em&gt;P. denitrificans&lt;/em&gt; &lt;a href=&quot;http://www.atcc.org/products/all/13543.aspx&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;www.atcc.org/products/all/13543.aspx&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3632" LastEditDate="2014-03-25T04:33:37.660" LastActivityDate="2014-03-25T04:33:37.660" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16060" PostTypeId="1" CreationDate="2014-03-25T06:35:50.743" Score="2" ViewCount="88" Body="&lt;p&gt;Blood donation involving apheresis is becoming increasingly common. It looks like the process involves centrifuging blood at very high speeds* before removing the desired fraction and returning the rest to the donor. Is there good reason to believe that the centrifuging process is harmless to all the various cells, proteins, lipids, and other substances in whole blood? Or is it possible that some blood constituents are damaged or altered?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;* I don't know if the speeds are particularly high compared to other biomedical processes, but they're drastically outside the conditions in which biological products evolved to function, hence my question. &lt;/p&gt;&#xA;" OwnerUserId="827" LastActivityDate="2014-03-25T06:35:50.743" Title="Does apheresis damage any components of blood? If not, why not?" Tags="&lt;hematology&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="16061" PostTypeId="1" AcceptedAnswerId="16071" CreationDate="2014-03-25T12:19:49.887" Score="12" ViewCount="2656" Body="&lt;p&gt;I thought of this question yesterday and it turns out it's surprisingly hard to Google.&lt;/p&gt;&#xA;" OwnerUserId="6128" LastActivityDate="2014-03-27T11:30:51.037" Title="Do any organisms recycle their own waste internally?" Tags="&lt;metabolism&gt;" AnswerCount="4" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16062" PostTypeId="2" ParentId="16061" CreationDate="2014-03-25T14:41:47.483" Score="12" Body="&lt;p&gt;&lt;strong&gt;All&lt;/strong&gt; organisms recycle their waste internally. Every cell of every living organisms is constantly breaking things down and re-using the components so produced. But you're presumably wondering about things such as carbon dioxide, urine and faeces? These are not recycled because the benefits of doing so are not worth the costs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's consider carbon dioxide as an example. We know that carbon dioxide can be usefully converted into energy-holding molecules using readily available sources of water, oxygen and sunlight. So why do animals** &quot;wastefully&quot; breathe it out? Because the energetic benefits of respiration are high compared to the energetic benefits of photosynthesis and so photosynthesis is unable to make a useful contribution to the overall energy balance of an animal while the costs of the effectively photosynthesising are quite high (e.g. having leaf-like protrusions, synthesizing chlorophyll and so on).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, it must always be true that there are processes which are not energetically worthwhile because of entropy. An organism that could perpetually recycle its waste would be a perpetual motion machine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;** - and many microbes and, in fact, plants - although their intake of carbon dioxide is typically higher over the solar cycle.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2014-03-25T14:41:47.483" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16063" PostTypeId="1" AcceptedAnswerId="16073" CreationDate="2014-03-25T16:12:59.190" Score="1" ViewCount="157" Body="&lt;p&gt;What is the current explanation of what causes the different sexual orientations in humans.&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2014-03-25T21:47:41.203" Title="What is the current theory of sexual orientations in Biology?" Tags="&lt;sex&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16064" PostTypeId="1" CreationDate="2014-03-25T16:20:11.347" Score="1" ViewCount="41" Body="&lt;p&gt;Does it matter at all in determining the traits of a baby what the current health of the father is? For example, let's say I got diabetes at the age of 40 because of the poor lifestyle choices. Will the baby be any different from how it would be if it was when I was say 26?&lt;/p&gt;&#xA;" OwnerUserId="6130" LastEditorUserId="6130" LastEditDate="2014-04-24T18:27:00.217" LastActivityDate="2014-04-24T18:27:00.217" Title="Effect of the health of the male parent at the time of conceiving" Tags="&lt;genetics&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16065" PostTypeId="2" ParentId="16064" CreationDate="2014-03-25T16:43:29.517" Score="1" Body="&lt;p&gt;It &lt;em&gt;can&lt;/em&gt; matter, though at this point we are just starting to understand how much. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Men can typically have children much later in life than women, but there are costs as time goes on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Epigenetics has shown us that what happens to the parents in their lifetime can affect his offspring.  Obesity especially has been shown to affect the offspring, &lt;a href=&quot;http://www.nature.com/news/epigenetics-the-sins-of-the-father-1.14816&quot; rel=&quot;nofollow&quot;&gt;producing a higher risk of diabetes for two generations&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is thought that this is not going to affect fathers who develop diabetes at a later age, but primarily those who are obese around 9-12 y.o. when the spermatogenic cells are produced in the testes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens to men as they get older though is that their ability to produce healthy sperm starts to degrade.  They can &lt;a href=&quot;http://en.wikipedia.org/wiki/Paternal_age_effect#Semen_and_sperm_abnormalities&quot; rel=&quot;nofollow&quot;&gt;lose fertility and produce more birth defects&lt;/a&gt; typically as early as age 35.  Given this there are probably a lot of habits or events that can adversely affect fertility. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lifestyle choices as simple as &lt;a href=&quot;http://www.webmd.com/infertility-and-reproduction/features/boxers-vs-briefs-increasing-sperm-count&quot; rel=&quot;nofollow&quot;&gt;tight underwear which might block blood flow to the testes&lt;/a&gt; is sometimes cited.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given all this DNA or cellular damage from chemicals or diet or poor health certainly would also affect male fertility. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-03-25T16:43:29.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16066" PostTypeId="2" ParentId="16061" CreationDate="2014-03-25T17:33:38.110" Score="6" Body="&lt;p&gt;If an organism recycles some material, by definition, it is not waste.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though some animals will eat feces.(For eg.Rabbits) It's a way to double-digest something that was not fully broken down or absorbed the first round.&lt;/p&gt;&#xA;" OwnerUserId="6131" LastEditorUserId="3615" LastEditDate="2014-03-26T04:01:56.147" LastActivityDate="2014-03-26T04:01:56.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16067" PostTypeId="1" AcceptedAnswerId="16068" CreationDate="2014-03-25T17:39:25.973" Score="1" ViewCount="212" Body="&lt;p&gt;I saw on TV that not all sperm are the same. Some have mutations like 2 and 3 tails?  There were other mutations as well.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If one of these mutated sperm actually fertilized an egg, would the embryo be mutated in some form or fashion?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2014-03-25T18:53:27.130" Title="Mutated Sperm - What happens?" Tags="&lt;reproduction&gt;&lt;embryology&gt;&lt;pregnancy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16068" PostTypeId="2" ParentId="16067" CreationDate="2014-03-25T18:53:27.130" Score="0" Body="&lt;p&gt;Yes, the embryo would get that DNA mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both sperm and egg are haploid, meaning they only have 1 copy of each gene. When the sperm fertilizes the egg, the resulting child is a diploid, meaning he/she has two copies of each gene. However, if the sperm was mutated, then child has one mutated copy of some gene(s). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending on the gene(s) that are mutated and the sequence of the mutated gene(s), this could result in non existent to severe consequences.&lt;/p&gt;&#xA;" OwnerUserId="6038" LastActivityDate="2014-03-25T18:53:27.130" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16069" PostTypeId="1" AcceptedAnswerId="16070" CreationDate="2014-03-25T19:04:33.247" Score="1" ViewCount="1016" Body="&lt;p&gt;What happens when two sperm fertilize an egg?  This can be either naturally or by experiment.&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2020-07-16T05:10:56.047" Title="Fertilization of an egg by two sperm" Tags="&lt;reproduction&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16070" PostTypeId="2" ParentId="16069" CreationDate="2014-03-25T19:12:59.967" Score="2" Body="&lt;p&gt;This phenomenon is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Polyspermy&quot; rel=&quot;nofollow&quot;&gt;polyspermy&lt;/a&gt; and results in an embryo which is not viable. This is because it has more than the usual two sets of chromosomes (one from each parent), but one from the mother and multiple (depending on how much spermcells enter the egg) from the father.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To avoid this, most species (including mammals) have protective mechanisms against it. The so called &lt;a href=&quot;http://en.wikipedia.org/wiki/Cortical_reaction&quot; rel=&quot;nofollow&quot;&gt;cortical reaction&lt;/a&gt; which starts upon fertilization (the first sperm penetrating the zona pellicula) and releases cortical granules to prevent further sperm cells from entering.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-25T19:12:59.967" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16071" PostTypeId="2" ParentId="16061" CreationDate="2014-03-25T19:14:14.570" Score="5" Body="&lt;p&gt;Hibernating bears have an ingeneous way of recycling their urine (urea) while they hibernate. Also turtles and frogs in the bottom of ponds deal in unique ways during hibernation.. This should get you started.&#xA;recycling waste externally is done by rabbits who will pass pellets through their system twice, the firsttime to partially digest, the second time to extract nutrients.&lt;/p&gt;&#xA;" OwnerUserId="6133" LastActivityDate="2014-03-25T19:14:14.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16072" PostTypeId="2" ParentId="7267" CreationDate="2014-03-25T20:03:59.053" Score="3" Body="&lt;p&gt;This phenomena is known as achiasmy, where recombination is absent in one sex in a species. The Haldane Huxley rule states that in achiasmic species, the sex without recombination will always be the heterogametic sex (XY or ZW). This is basically the only consistent rule relating to recombination. There seem to be exceptions to every other theory and pattern observed. &#xA;The Haldane Huxley rule supports the theory that achiasmy evolved to prevent non-homologous recombination between X and Y. However there are species (most mammals) where the X and Y do experience recombination, but recombination is limited to a small part of the chromosomes called the psudo-autosomal region.&lt;/p&gt;&#xA;" OwnerUserId="6134" LastActivityDate="2014-03-25T20:03:59.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16073" PostTypeId="2" ParentId="16063" CreationDate="2014-03-25T21:47:41.203" Score="1" Body="&lt;p&gt;It seems we have more hypothesis than theories.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a book called &quot;The Moral Animal&quot;, by Robert Wright, where he cites some researches relating order of birth with sexual orientation (of course, not a 100% direct relationship). That's for the proximal cause. For the distal cause (evolutive) it makes sense to me that we are a sort of &quot;eusocial&quot; species, with homosexuality having evolved for the fitness it adds to the family: having lots of offspring, it's benefitial for the family if a few of them don't reproduce, investing instead in other fields of knowledge, like medical herbs, technology, weapons, etc. This may explain why this behavior evolved in first place, and why it's so widespread in virtually every known human culture, and almost all families.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biologist Alfred Kinsey founded the Kinsey Institute (kinseyinstitute.org) for the study of human sexuality. His theory (that also appears in the movie Kinsey) was that there is a gradient from totally homosexual to totally heterosexual, with many intermediary degrees. Our religious culture tries to &quot;erase&quot; this diversity because of platonic ideals of &quot;perfect male&quot; and &quot;perfect female&quot;, but in Amazon I saw that people are much more &quot;plastic&quot; than that, probably because of the lack of power of such religious traditions. Historians also talk about homosexuality as a &quot;usual practice&quot; in pre-Colombian America. And it is said that China have no problem with homosexuality before the arrival of monotheists. In India, homosexuality became a crime only 3 years after the british invasion (so it seems it was very common there, too).&lt;/p&gt;&#xA;" OwnerUserId="4821" LastActivityDate="2014-03-25T21:47:41.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16074" PostTypeId="1" CreationDate="2014-03-25T22:14:07.890" Score="3" ViewCount="186" Body="&lt;p&gt;My text book doesn't say anything about how B memory cells actually ensure a faster response the second time the antigen is encountered. My guess is that they differentiate into plasma cells which produce antibodies, and release cytokines to cause clonal expansion of the correct T killer cells, but I'm not sure...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance for any responses ^_^&lt;/p&gt;&#xA;" OwnerUserId="6136" LastActivityDate="2014-03-26T01:07:22.563" Title="How do B memory cells provide immunological memory? Do they differentiate into plasma cells?" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16075" PostTypeId="1" AcceptedAnswerId="16078" CreationDate="2014-03-25T23:12:49.647" Score="1" ViewCount="234" Body="&lt;p&gt;When a human dreams does the brain activate the cones and rods in the eyes creating the images we see in dreams?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2014-04-17T23:36:07.207" Title="What happens when we dream?" Tags="&lt;brain&gt;&lt;eyes&gt;&lt;dreaming&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16077" PostTypeId="2" ParentId="16074" CreationDate="2014-03-26T01:07:22.563" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15771579&quot;&gt;This 2005 review&lt;/a&gt; in the &lt;em&gt;Annual Review of Immunology&lt;/em&gt; entitled &quot;Antigen-specific memory B cell development&quot; would be a great first resource in answering your question in great detail. Briefly, memory B cells (MBC), upon re-exposure to the same antigen, very rapidly expand and differentiate into antibody-producing plasma cells (PC), with the help of memory T helper cells (Th). However, more MBC are still produced by this reaction, so that a second challenge with antigen doesn't deplete the memory population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PC are geared towards producing gobs of antibody, and not much else. Upon stimulation with antigen, MBC will produce some cytokines to attract the Th cells that are required for costimulation and regulation, but to my understanding it is the Th cells that manage the whole response, activating effector T cells (&quot;killer&quot; T cells), NK cells, dendritic cells, etc., and not the MBC themselves.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-03-26T01:07:22.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16078" PostTypeId="2" ParentId="16075" CreationDate="2014-03-26T01:13:38.367" Score="1" Body="&lt;p&gt;The cones and rods would not contain the images from our dreams. Visual scenes get transferred from the eye to the thalamus (which serves as a relay to the cortex) by optical fibers that are overwhelmingly uni-directional (information is carried from the eyes to the thalamus and not vice-versa).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dreams do, however, activate the thalamus, the visual cortex, and the visual regions that control eye movements (see refs 1,2). I don't believe there has been successful attempts to decode the activation, mainly, I think, because fMRI would be the best that we could use for humans and it does not have good temporal or spatial resolution.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Hong, Charles Chong‐Hwa, et al. &quot;fMRI evidence for multisensory recruitment associated with rapid eye movements during sleep.&quot; Human brain mapping 30.5 (2009): 1705-1722.&lt;/li&gt;&#xA;&lt;li&gt;Dresler, Martin, et al. &quot;Neural correlates of dream lucidity obtained from contrasting lucid versus non-lucid REM sleep: a combined EEG/fMRI case study.&quot; Sleep 35.7 (2012): 1017.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6043" LastEditorUserId="6043" LastEditDate="2014-04-17T23:36:07.207" LastActivityDate="2014-04-17T23:36:07.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16079" PostTypeId="1" AcceptedAnswerId="16084" CreationDate="2014-03-26T01:38:35.140" Score="2" ViewCount="902" Body="&lt;p&gt;I want to know if, as a baby chick grows inside the egg, does it excrete waste?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it does excrete waste, does the waste just sit inside the egg with the chick, until the chick cracks open the egg and gets out?&lt;/p&gt;&#xA;" OwnerUserId="6142" LastEditorUserId="3340" LastEditDate="2014-03-26T11:24:42.200" LastActivityDate="2014-03-26T11:24:42.200" Title="Do chicks in eggs excrete?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16080" PostTypeId="2" ParentId="16061" CreationDate="2014-03-26T01:46:57.793" Score="2" Body="&lt;p&gt;Bears &lt;a href=&quot;http://www.thenakedscientists.com/forum/index.php?topic=6812.0&quot; rel=&quot;nofollow&quot;&gt;recycle their urine while hibernating&lt;/a&gt;, unlike most other mammals. &lt;/p&gt;&#xA;" OwnerUserId="6144" LastEditorUserId="1043" LastEditDate="2014-03-26T08:39:00.883" LastActivityDate="2014-03-26T08:39:00.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16082" PostTypeId="2" ParentId="16032" CreationDate="2014-03-26T03:30:21.293" Score="3" Body="&lt;p&gt;Underneath the superficial layers of your skin there are receptors which sense pressure, temperature and pain. These receptors are part of the peripheral nervous system which senses stimuli and they take the message conveying details about the stimulus to the somatosensory cortex of the brain. Here is where the perception of pain, burning, pressure etc is ultimately made. To take the simplest example, if you stop blood flow for a short amount of time in a limb, these receptors are activated, and will send signals to the brain that are interpreted as tingling or numbness. With more severe pain, different receptors are activated which , again, project to the same brain area but a different message is read out. If the pressure from one limb is removed, the receptors will go back to normal function as blood flow is restored.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Nociceptor&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Nociceptor&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.scholarpedia.org/article/Mammalian_mechanoreception&quot; rel=&quot;nofollow&quot;&gt;http://www.scholarpedia.org/article/Mammalian_mechanoreception&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5694" LastEditorUserId="5694" LastEditDate="2015-09-06T19:15:40.257" LastActivityDate="2015-09-06T19:15:40.257" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16083" PostTypeId="2" ParentId="5144" CreationDate="2014-03-26T03:40:06.750" Score="0" Body="&lt;p&gt;I just came across this answer when I was answering another related question. Although this is closed there is a strong claim from the accepted answer which needs to be toned down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cessation of stimulation does not &lt;em&gt;always&lt;/em&gt; mean cessation of propagation. Once an action potential(AP) is fired it does not necessarily stop its propagation in the next cell. Also cells can make synapses onto themselves which can cause further AP firing without stimulation.&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-03-26T03:40:06.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16084" PostTypeId="2" ParentId="16079" CreationDate="2014-03-26T03:42:48.737" Score="3" Body="&lt;p&gt;Yes they excrete uric acid which is stored in the allantois of the embryo; which acts as a reservoir of nitrogenous waste.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Uric acid is not very soluble in water, so it stays as a small solid mass.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-26T03:42:48.737" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16085" PostTypeId="1" CreationDate="2014-03-26T03:43:20.827" Score="1" ViewCount="330" Body="&lt;p&gt;Why do we value species?  What is so bad about invasive species?  Why value biodiversity?&lt;/p&gt;&#xA;" OwnerUserId="6147" LastEditorUserId="3340" LastEditDate="2014-03-26T09:22:01.323" LastActivityDate="2016-05-26T10:09:52.180" Title="What problems do invasive species cause ?" Tags="&lt;biodiversity&gt;&lt;species&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ClosedDate="2016-05-26T18:04:40.173" ContentLicense="CC BY-SA 3.0" />
  <row Id="16086" PostTypeId="2" ParentId="16085" CreationDate="2014-03-26T03:51:44.047" Score="1" Body="&lt;p&gt;Here is an attempt at a partial answer.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What is so bad about invasive species ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Invasive species have been introduced to a new habitat by humans (or by natural means). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They usually do not have a predator in a new area nor are the pathogens in the area very adept at infecting them. So, they may proliferate rapidly and compete with the native species. They may also be ferocious predators as their preys do not have defenses against them.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-26T03:51:44.047" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16087" PostTypeId="2" ParentId="16085" CreationDate="2014-03-26T08:48:24.740" Score="1" Body="&lt;p&gt;Biodiversity=ecosystem&lt;/p&gt;&#xA;&#xA;&lt;p&gt;system= more than one species&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Advanced creatures such as us cannot live without other creatures, like plants and bacteria to support us. (yet)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to see what invasive species can do watch this video, &lt;a href=&quot;http://www.youtube.com/watch?v=Bk-9ndL3ykM&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=Bk-9ndL3ykM&lt;/a&gt; it has some descriptions on what the invasive species homo sapiens and their domesticated cows do to their planet earth. Wasting resources basically. Displacing other animals and plants, monopolizing the earth. Monopoly or monoculture is not good. For if the monoculture fails all is lost. If you have diversity if one harvest goes bad it's not over yet. It's basically all about stability and sustainability. Without either advanced lifeforms cannot exist.&lt;/p&gt;&#xA;" OwnerUserId="6137" LastEditorUserId="6137" LastEditDate="2014-03-28T14:21:21.847" LastActivityDate="2014-03-28T14:21:21.847" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16088" PostTypeId="2" ParentId="16051" CreationDate="2014-03-26T08:55:03.037" Score="0" Body="&lt;p&gt;I remember an episode of a German science show talking about this. If you do an experiment with bubbles. Eventually several bubbles will share boundaries and a hexagonal form will emerge. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following this it is no instinct but the best way to create boundaries.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They had a more scientific explanation for this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There you go:&#xA;&lt;a href=&quot;http://www.exploratorium.edu/ronh/bubbles/bubble_meets_bubble.html&quot; rel=&quot;nofollow&quot;&gt;http://www.exploratorium.edu/ronh/bubbles/bubble_meets_bubble.html&lt;/a&gt;&#xA;And I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If you take two sheets of clear glass or plastic separated by about one-half inch, soak them in soapy solution and then blow bubbles between the sheets, you will get many bubble walls. If you look closely, you will notice that all of the vertices where three bubble walls meet (and there are always three,) form 120 degree angles. If your bubbles are of uniform size, you will notice that the cells form hexagons and start to look much like the cells of a beehive. Bees, like bubbles, try to be as efficient as possible when making the comb. They want to use the minimum possible amount of wax to get the job done. Hexagonal cells are the ticket.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;-&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just noticed I was answering to an answer. My answer to the question would be that almost every animal on the planet builds nests. If you are a termite you can use mud. If you are a wasp or a bee you build nests in the air or at least not in the mud. That means you have to carry your material through the air. The less the better. Efficiency dictates that you build your &quot;hive&quot; or nest as compact as possible. That means spherical shape which has the most volume vs surface ratio and the hexagons inside follow the same rule. Use as little material as possible or you are outcompeted by bees that do. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also it's a lot more efficient to &quot;manage&quot; a cluster vs nests cluttered all over the place. Again no instinct just necessity which eventually evolved into instinct. Because all other instincts became extinct.&lt;/p&gt;&#xA;" OwnerUserId="6137" LastEditorUserId="6137" LastEditDate="2014-03-26T09:01:29.580" LastActivityDate="2014-03-26T09:01:29.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16089" PostTypeId="2" ParentId="9467" CreationDate="2014-03-26T09:05:25.483" Score="0" Body="&lt;p&gt;What is a lip(s)? A set of muscles around an orifice that can close said orifice. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How about a way to close a hole so that not everything can get in but what we want - to eat, breathe, drink?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fact that they are also sensitive is just needed so that you can more precisely operate them for whatever need you have.&lt;/p&gt;&#xA;" OwnerUserId="6137" LastActivityDate="2014-03-26T09:05:25.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16090" PostTypeId="2" ParentId="16036" CreationDate="2014-03-26T09:08:33.113" Score="1" Body="&lt;p&gt;Try birthing a child for once. You need to be flexible to accommodate the growth of another organism inside you. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take a look at some pictures of the mothers spine during the course of a pregnancy, you will have no further questions. Same with belly size, breast size and vagina size upon birth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This video is a nice explanation of this. Also includes the different centers of gravity for males and females (human).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=WO8DtsZO1nA&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=WO8DtsZO1nA&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6137" LastEditorUserId="6137" LastEditDate="2014-03-26T10:37:09.583" LastActivityDate="2014-03-26T10:37:09.583" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16091" PostTypeId="1" AcceptedAnswerId="16111" CreationDate="2014-03-26T12:27:00.643" Score="6" ViewCount="15264" Body="&lt;p&gt;Why does ear wax taste sour?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested in both the physiochemical mechanisms and the evolutionary reasons behind the sour taste of earwax.&lt;/p&gt;&#xA;" OwnerUserId="6153" LastActivityDate="2015-04-08T16:52:11.917" Title="Why does ear wax taste sour?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;food&gt;&lt;perception&gt;&lt;sensation&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16092" PostTypeId="2" ParentId="13924" CreationDate="2014-03-26T12:31:52.360" Score="1" Body="&lt;p&gt;A more abstract idea for a Bioweapon species could be one that targets key organisms required for completing the &lt;strong&gt;nitrogen&lt;/strong&gt; or &lt;strong&gt;carbon&lt;/strong&gt; cycle. This would likely cause the entire biosphere to collapse though.&lt;/p&gt;&#xA;" OwnerUserId="6153" LastActivityDate="2014-03-26T12:31:52.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16093" PostTypeId="1" AcceptedAnswerId="16103" CreationDate="2014-03-26T12:32:02.183" Score="1" ViewCount="1371" Body="&lt;p&gt;I know that EDTA chelates metal ions. It weakens bacterial cell wall and inactivates the DNases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the reason why it can do so ? I guess it can inactivate DNases by altering the microenvironment. What exactly happens ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-26T16:31:18.147" Title="Functioning of EDTA" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;cell-biology&gt;&lt;bacteriology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16094" PostTypeId="1" AcceptedAnswerId="16095" CreationDate="2014-03-26T12:37:15.073" Score="1" ViewCount="123" Body="&lt;p&gt;I have read that DNA can be concentrated by addition of isopropanol. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does &quot;concentrated&quot; mean? What does isopropanol do on a molecular level to concentrate DNA?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="6" LastEditDate="2014-03-27T13:00:35.143" LastActivityDate="2014-03-27T13:00:35.143" Title="Concentration of DNA by isopropanol" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;protocol&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16095" PostTypeId="2" ParentId="16094" CreationDate="2014-03-26T12:55:02.940" Score="2" Body="&lt;p&gt;What you are asking about is the precipitation of DNA (or any other nucleic acid) by isopropanol (or ethanol, which is more common). To do so, you add salt (usually slightly acidic sodium acetate) which makes sure that the phosphate backbone of the DNA is saturated with sodium ions to make it less soluble. Then you add the organic solvent, which precipitates the DNA from the solution by changing the polarity of the solution. This makes the ions form salts and the DNA precipites. The principle is explained in the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Ethanol_precipitation&quot; rel=&quot;nofollow&quot;&gt;ethanol precipitation&lt;/a&gt;. Finally the solution is centrifuged to collect the DNA at the bottom of your reaction tube and to be able to take off the supernatant.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-26T12:55:02.940" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="16096" PostTypeId="2" ParentId="16093" CreationDate="2014-03-26T13:10:47.960" Score="4" Body="&lt;p&gt;A lot of enzymes need metal ion in their active center (it is actually the metal ion which is taking part in the catalyzed reaction). These are manganese, magnesium, copper and so on. For DNAses the metal in the active center is magnesium and EDTA simply chelates this ions, making them unavailable for the enzyme and thus hinders the enzyme from working.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Chelation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chelation&lt;/a&gt; is the process in which metal ions are coordinated in molecules and form coordinate bonds to the chelating agent. &lt;a href=&quot;http://en.wikipedia.org/wiki/Ethylenediaminetetraacetic_acid&quot; rel=&quot;nofollow noreferrer&quot;&gt;EDTA&lt;/a&gt; looks like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JWM81.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The 3d structure while chelating a metal ions like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CiVsN.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see, that the metal ion is nicely located between the negatively charged oxygen atoms and the nitrogen atoms. These complexes are fairly stable and the metal ions do not escape.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-26T16:31:18.147" LastActivityDate="2014-03-26T16:31:18.147" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16098" PostTypeId="2" ParentId="5148" CreationDate="2014-03-26T13:42:00.733" Score="3" Body="&lt;p&gt;I'm not at a biologist, but I have a pet theory I'd like to throw into the ring: hermaphroditism tends to be unstable in a similar way to strong sex skews.  Imagine species A where 90% of offspring are female; at moderate population density, the 10% male population will be more than sufficient to maintain the females, and having 90% of the population able to breed will out-compete another species with a 50/50 distribution.  However, a mutation which tends to produce more males will tend to become more common, because the males of species A reproduce much more often than the females.  Eventually, this stabilizes at roughly equal frequencies for the sexes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Back to the hermaphroditic species C, imagine that a mutation led to a variant which had a flawed female reproductive system, meaning it could not lay as many eggs when fertilized, but it had some other advantage which made it better at mating: perhaps by diverting energy from the female systems, it was slightly larger and stronger and could intimidate others, or perhaps it put this energy into a stronger immune system.  Eventually, the population evolving in this direction could lose its ability to lay eggs or birth young entirely, and instead focus entirely on being better at finding mates to impregnate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at it from the other side, if some individuals de-prioritize that side of things and instead concentrate on being the best egg-layers and care-providers possible, that could be a stronger evolutionary position than trying to be equally good at both roles.  Eventually, this split would produce recognizably male and female subgroups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this idea has already been proposed and either taken seriously or shot down, I'd appreciate any pointers to further reading.&lt;/p&gt;&#xA;" OwnerUserId="6154" LastActivityDate="2014-03-26T13:42:00.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16099" PostTypeId="1" CreationDate="2014-03-26T13:44:39.707" Score="1" ViewCount="9987" Body="&lt;p&gt;I accidently touched formaldehyde some days ago. Skin on my hand got dehydrated as if I had placed it in salt solution. I washed it with water and it returned to normal state after 5 minutes.&lt;/p&gt;&#xA;&lt;p&gt;But now whenever I wash my hands with water my skin gets dehydrated again, but returns to normal state after some time .&#xA;What's the reason behind it getting dehydrated again when exposed to water ? Will it return to normal state when new skin grows back ?&lt;/p&gt;&#xA;&lt;p&gt;By dehydration, I mean something like this.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bwaqQ.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-04-01T02:34:04.333" Title="Consequence of touching Formaldehyde" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;skin&gt;&lt;osmoregulation&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16100" PostTypeId="1" AcceptedAnswerId="16101" CreationDate="2014-03-26T14:06:44.247" Score="0" ViewCount="64" Body="&lt;p&gt;If we want to design a bilayer from Myristic acid (14 carbon fatty acid). The average bond length between C-C is 1.5 A. What will be average thickness of the membrane?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edited to include the OP attempt that was posted in a comment:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are 13 C-C bonds in Myristic acid, 13*1.5=19.5A. 1A=o.1nm.. so 19.5A=1.95nm, so the average thickness would be 1.95nm. As membrane is bilayer it will be 3.9nm&lt;/p&gt;&#xA;" OwnerUserId="5729" LastEditorUserId="1320" LastEditDate="2014-03-28T08:29:30.720" LastActivityDate="2014-03-28T08:29:30.720" Title="Bilayer synthesis?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;homework&gt;&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-03-27T21:45:34.907" ContentLicense="CC BY-SA 3.0" />
  <row Id="16101" PostTypeId="2" ParentId="16100" CreationDate="2014-03-26T14:26:08.347" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://engelman.csb.yale.edu/PDF/Lewis-1983-1.pdf&quot; rel=&quot;nofollow&quot;&gt;Lewis &amp;amp; Engelman (1983) Lipid bilayer thickness varies linearly with acyl chain length in fluid phosphatidylcholine vesicles. J. Mol. Biol. 166: 211 - 217.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Table 1 and Figure 3 have the information that you need. For C14:0 the thickness of the hydrocarbon bilayer is given as 23 &amp;Aring;. Just in case this is homework, I'll leave you to convert that to nm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;added later&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just to follow up on the comments, as hinted at by Shigeta, if you wanted to calculate an estimated bilayer thickness you would have to take into account the C-C-C bond angle which for tetrahedral carbon is 109.46&amp;deg;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus the distance between two C atoms in an extended C chain is 2 x 1.5 x sin(109.46/2) = 2.45 &amp;Aring;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For C14:0 the length is then 6.5 x 2.45 = 15.9 Å (from methyl C to carbonyl C).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, calculated bilayer thickness = 31.8 Å plus any distance between the two C chains in the centre of the bilayer. This is still a lot bigger than the reported 23 &amp;Aring;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clearly the bilayer does not consist of extended hydrocarbon chains. The chains are presumably partially collapsed (on average) and may also interdigitate to some extent.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-03-27T06:00:16.160" LastActivityDate="2014-03-27T06:00:16.160" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16102" PostTypeId="1" AcceptedAnswerId="16104" CreationDate="2014-03-26T14:27:00.890" Score="4" ViewCount="114" Body="&lt;p&gt;Do the people who have been blind all their lives dream and do they experience or report &quot;imagery&quot; in the dreams?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastEditorDisplayName="user6116" LastEditDate="2014-03-26T14:54:06.883" LastActivityDate="2014-03-26T14:57:47.833" Title="Do people who have been blind all their lives dream?" Tags="&lt;brain&gt;&lt;dreaming&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16103" PostTypeId="2" ParentId="16093" CreationDate="2014-03-26T14:31:07.287" Score="4" Body="&lt;p&gt;The lipopolysaccharide layer of the Gram-negative bacterial cell wall is stabilised by divalent cations. Most recipes for disrupting &lt;em&gt;E. coli&lt;/em&gt; cells include Tris-EDTA for this reason. I seem to just &lt;strong&gt;know&lt;/strong&gt; this, so no reference at the moment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All nucleases require Mg&lt;sup&gt;2+&lt;/sup&gt;, which is why there is EDTA in the stop buffer added to restriction digests. Carry-over of EDTA in DNA pellets can sometimes inhibit digests.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-26T14:31:07.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16104" PostTypeId="2" ParentId="16102" CreationDate="2014-03-26T14:49:27.747" Score="4" Body="&lt;p&gt;Yes, they do. A blog post on the National Geographic website describes the results of a study about how blind people dream.(&lt;a href=&quot;http://phenomena.nationalgeographic.com/2014/02/26/how-the-blind-dream/&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;) The participants who were born blind did not report any visual impressions. Among those who previously had sight, the number of visual impressions reported decreased with the time since loss of sight.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Just as there are many ways to take in the world, there are many ways&#xA;  to dream about it. Blind people dream, just as they live, with a rich&#xA;  mix of sensory information.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;About 18 percent of the blind participants (both congenital and&#xA;  later-onset) reported tasting in at least one dream, compared with 7&#xA;  percent of controls. Nearly 30 percent of the blind reported smelling&#xA;  in at least one dream, compared with 15 percent of controls. Almost 70&#xA;  percent of the blind reported a touch sensation, compared to 45&#xA;  percent of controls. And 86 percent of the blind reported hearing,&#xA;  compared with 64 percent of controls.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(...)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Despite these sensory differences, the emotional and thematic content&#xA;  of dreams isn’t much different in the blind and the sighted. Both&#xA;  groups reported about the same number of social interactions,&#xA;  successes, and failures in their dreams. They had the same&#xA;  distribution of emotions, and the same level of bizarreness.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-03-26T14:57:47.833" LastActivityDate="2014-03-26T14:57:47.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16105" PostTypeId="1" CreationDate="2014-03-26T14:51:07.793" Score="-1" ViewCount="1559" Body="&lt;p&gt;Most people I know find nature beautiful and holidays generally involve a place that has 'natural beauty'. &lt;/p&gt;&#xA;" OwnerUserId="6155" LastActivityDate="2018-03-24T19:54:49.350" Title="Why do we find nature 'beautiful', from an evolutionary perspective?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16106" PostTypeId="1" CreationDate="2014-03-26T15:25:25.837" Score="2" ViewCount="1410" Body="&lt;p&gt;In order for nature to go from microbes to man, there needs to be new information. Where does this new information come from?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is understood that Evolution basically involves three elements. Natural selection, genetic mutation, and time. The problem for Evolution, is that none of those three elements are creative. Natural selection is basically just a pruning process. It selects from what is there and advantageous, and prunes off what is deleterious to the organism as far as its fitness. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetic mutation is just errors in replication. So it creates nothing. It simply degrades. We have no new information, just an erroneous replication, and degradation of what was there before.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is still true of gene duplication. We have an error that repeats the same information/genes. So we have two copies of something but there is still no new information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This brings us to the second problem. What mechanism or process of nature/Evolution, carries out the instructions. What I mean by this, is that it essentially has to work like a computer. If I want my computer to have a more advanced program, I need to input new information, and its often codified in the form of say a disk, or installation file. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the equivalent of this installation file for Evolution?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example. Say I'm a cephalopod. And I'm getting environmental pressure from predators and I want, or need, to advance my defenses, so I want to built some spikes on a hard outer shell. Where does the cephalopod get the new information, or rather, instructions, to know how to do this new feature? &lt;/p&gt;&#xA;" OwnerUserId="5502" LastEditorUserId="5502" LastEditDate="2014-03-28T13:03:45.357" LastActivityDate="2018-09-23T14:12:33.790" Title="How does the creative process of Biological Evolution work?" Tags="&lt;evolution&gt;" AnswerCount="8" CommentCount="18" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16108" PostTypeId="2" ParentId="16106" CreationDate="2014-03-26T15:34:46.470" Score="2" Body="&lt;p&gt;I think this is a little like writing a book.  The most common advice is for aspiring writers to write every day and write a decent amount.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution creates by testing everything against its fitness - its ability to survive and reproduce.  If something is advantageous, it stays in the corpus of genes and genetic solutions to problems.  If something is not working well or even not as well, it may be lost and forgotten - dropped out of the gene pool.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So just as a writer may throw out 90% of their writing to get to their published novel, 90+% of biological experiments are thrown out and don't have long lasting repercussions in the biosphere.  its probably more like 99.9999999% really. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The creation of information you are talking about are all inherent in the physical universe.  Just as every computer program is potentially existant in the laws of logic and mathematics, all the potential mechanical and informational and configurational advantages of living things are embedded in the physical laws in which they operate.  It is not an event of creation, but an event of discovery when a new biological function appears. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-03-26T15:34:46.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16110" PostTypeId="2" ParentId="16099" CreationDate="2014-03-26T15:47:29.587" Score="3" Body="&lt;p&gt;cool pics! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, Formadahyde is a &lt;a href=&quot;http://www.ccohs.ca/oshanswers/chemicals/chem_profiles/formaldehyde.html&quot; rel=&quot;nofollow&quot;&gt;terribly toxic substance.&lt;/a&gt;  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Skin Contact: CORROSIVE. Contact can cause pain, redness, burns, and blistering. Permanent scarring can result. Can be absorbed through the skin.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Formaldehyde causes organ failure and scarring if ingested.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case, since you don't have burning or blistering, it seems like a reasonably low exposure. You should nonetheless call your doctor to check in or drop by the campus infirmary or what you have. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good experience to remind you to wear gloves when working with chemically active reagents or solvents (DMSO for instance!) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not a doctor, but as a non professional and informal opinion, your finger will probably become normal again, eventually all the cells will do their best to repair themselves. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="19521" LastEditDate="2016-09-29T06:22:39.073" LastActivityDate="2016-09-29T06:22:39.073" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="16111" PostTypeId="2" ParentId="16091" CreationDate="2014-03-26T15:51:23.283" Score="7" Body="&lt;p&gt;Earwax, also called cerumen, is slightly acidic (&lt;a href=&quot;http://en.wikipedia.org/wiki/Earwax&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;), with a pH of about 6,  and acidic foods or substances taste &lt;a href=&quot;http://en.wikipedia.org/wiki/Sourness#Sourness%20sour&quot; rel=&quot;nofollow&quot;&gt;sour&lt;/a&gt;. The composition of earwax, upon which its taste depends, is related to its functions. Earwax aids in cleaning and lubrication of the ear canal and has an antimicrobial effect. The antimicrobial effect is in part attributed to its acidity, which might give an evolutionary reason for the sour taste.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Sourness#Sourness%20sour&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cerumen is produced in the outer third of the cartilaginous portion of&#xA;  the ear canal. It is a mixture of viscous secretions from sebaceous&#xA;  glands and less-viscous ones from modified apocrine sweat glands.[4]&#xA;  The primary components of earwax are shed layers of skin, with 60% of&#xA;  the earwax consisting of keratin, 12–20% saturated and unsaturated&#xA;  long-chain fatty acids, alcohols, squalene and 6–9% cholesterol.[5]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(...)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;While studies conducted up until the 1960s found little evidence&#xA;  supporting antibacterial activity for cerumen,[15] more recent studies&#xA;  have found that cerumen has a bactericidal effect on some strains of&#xA;  bacteria. These antimicrobial properties are due principally to the&#xA;  presence of saturated fatty acids, lysozyme and, especially, to the&#xA;  slight acidity of cerumen.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-03-27T08:10:39.567" LastActivityDate="2014-03-27T08:10:39.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16112" PostTypeId="2" ParentId="16106" CreationDate="2014-03-26T16:45:40.553" Score="6" Body="&lt;p&gt;It's seems to me you forget something pretty important about evolution : it has nothing to do with improvement. All living organisms have the exact same time of evolution as they all derive from a common ancestor. They simply evolved through different paths, that's what explain the biodiversity we can observe today and no organism is better than others, not even human.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;New functions are not created just like that, because a species need it. To take your cephalopod's example : if there's pressure from predators, they won't simply grow spikes in order to protect themselves. However, if mutations (one or many) appear in the DNA sequence that make spikes instead of, say, skin, then this particular cephalopod will have better chances of surviving than others and so, better chances to reproduce and pass his new genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations do not necessarily imply degradation -just as the los of one function is not necessarily a degradation. Every organs appeared thanks to mutations and / or duplications. For example, the humans' ability to see colors is due to 3 types of pigments (blue, red, green) named opsine S (blue), opsine M (green), opsine L (red). You add rhodopsine which is sensible to light to see clearly. If you study a mouse's eye, you'll only find 2 opsines + rhodophsine. Scientists have been able to recreate evolution's story : you start with an ancestral gene for opsine. The gene is duplicated and the copy is translocated on another chromosome. You now have 2 copies of the gene on 2 different chromosomes. They both mutate as mutations occur all of the time. You end up with 2 new genes. Then, duplication will happen again (no particular reason). You now have 4 genes, identical two by two. Three genes stay where they are, one of them is translocated on another chromosome and they'll all mutate. You finally get 4 genes on 3 different chromosomes (opsine M, L, S and rhodopsine). New genes and new ability appeared thanks to mutation, duplication and translocation. It just took millions of years of evolution and probably an impressive amount of tests. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Shigeta wrote, everything potentially exists. Some of the possibilities have been discovered, some have not. Evolution applies on hundreds millions of years and billions of living organisms and it process accidents after accidents. If what appears is selected, it stays, if not, it disappears.&lt;/p&gt;&#xA;" OwnerUserId="5702" LastEditorUserId="1306" LastEditDate="2014-03-26T22:19:04.613" LastActivityDate="2014-03-26T22:19:04.613" CommentCount="16" ContentLicense="CC BY-SA 3.0" />
  <row Id="16114" PostTypeId="2" ParentId="16106" CreationDate="2014-03-26T17:04:36.867" Score="11" Body="&lt;p&gt;Your question, I'm afraid, betrays a deep misunderstanding of evolution. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Genetic mutation is just errors in replication. So it creates nothing. It simply degrades.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is patently false. The vast majority of mutations are &quot;errors&quot;, in that they produce a less fit organism. But once in a while, a mutation will confer an advantage, rather than an disadvantage. This, I suppose, is where &quot;new information&quot; comes from, though I would not use those terms. Your metaphor with software is not very accurate. If you want to &quot;evolve&quot; a piece of software through evolution, you do not insert new functionality into the source code. Instead, you would make a number of copies of the source code, each with a small, random alteration. Then you make the software available to all. The version that is most highly used on the market is then taken and the process is repeated. But good software is not developed in this way, for reasons that I hope are obvious. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would highly recommend reading &quot;The Selfish Gene&quot; or &quot;The Extended Phenotype&quot; by Richard Dawkins. &lt;/p&gt;&#xA;" OwnerUserId="6131" LastEditorUserId="6131" LastEditDate="2016-08-26T18:38:14.667" LastActivityDate="2016-08-26T18:38:14.667" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="16116" PostTypeId="1" AcceptedAnswerId="16129" CreationDate="2014-03-26T19:07:40.333" Score="3" ViewCount="302" Body="&lt;p&gt;When interpreting qRT-PCR results, which results are acceptable as fold changes, which are acceptable for housekeeping genes? e.j. a values of 0.8 raw fold changes for a &quot;housekeeping&quot; gene is acceptable as such? and conversely which is the threshold to say that there was &quot;fold change&quot;?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastActivityDate="2014-03-27T06:25:23.110" Title="gene expression fold change threshold limit" Tags="&lt;pcr&gt;" AnswerCount="1" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="16117" PostTypeId="1" CreationDate="2014-03-26T20:05:58.557" Score="1" ViewCount="100" Body="&lt;p&gt;Apologies for weirdness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of the various legal methods of disposing of a human corpse, which one ensures the nutrients which compose the body get back into the wider ecosystem the fastest?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unless I've overlooked something (which is likely) the answer would seem to boil down to:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Burial, in which case soil microbes have relatively free access to the body but will initially restrict their nutrients to the sub-soil ecosystem.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Cremation, in which case most of the nutrients are converted into heat and light energy by the furnace, although this energy, and the remaining nutrients, are then made available to the wider environment much more rapidly.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5083" LastActivityDate="2014-03-27T16:26:30.840" Title="What's the fastest legal way for the nutrients in a dead body to re-enter the ecosystem?" Tags="&lt;microbiology&gt;&lt;ecology&gt;&lt;decay&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16118" PostTypeId="2" ParentId="16105" CreationDate="2014-03-26T21:16:03.713" Score="-2" Body="&lt;p&gt;Bright colors can attract a sexual partner as they are beautiful and are often a sign of good health. So, if you have bright and beautiful colors, you'll attract a partner to reproduce more easily than other and your genes will pass to the next generations. So, some animals are &quot;beautiful&quot; because of sexual selection.&#xA;For flowers, bright colors and perfume attract pollinators, so the brighter the better to reproduce. &#xA;Of course, as beauty is all relative, not all flowers or animals are &quot;beautiful&quot; according to humans' tastes. But they suit the environnement the organism lives in and whatever is needed to get to reproduce.&#xA;Sexual selection is not the answer to everything you find beautiful but it explains some.&lt;/p&gt;&#xA;" OwnerUserId="5702" LastActivityDate="2014-03-26T21:16:03.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16119" PostTypeId="2" ParentId="16106" CreationDate="2014-03-26T21:51:15.727" Score="15" Body="&lt;p&gt;Your basic problem is indeed a fundamental misunderstanding of how DNA and by extension its evolution works. First of all, there is no such thing as &quot;correct&quot; or &quot;error&quot;, there are only changes, some of them are better for the individual and some are worse. You also have a basic misunderstanding of the concept of information. An error does not decrease the amount of information, it just alters that information. For example, consider this sentence:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The book is read&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Say I make a simple error when I transcribe it:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The book is red&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The two statements contain the same amount of information. Nothing has been lost, only changed. &lt;strong&gt;But that change created new information&lt;/strong&gt;. Now what if I try a different change:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The book is rled&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now, this one is nonsensical, indeed, but how does that translate into DNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The computer analogy is a bad one. Programming languages have a very specific set of rules and anything outside those rules results in an error. For example, while this is a perfectly valid statement in many scripting languages:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;print &quot;Hello World&quot;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This one is not:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;priint &quot;Hello World&quot;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;That, however, is not the way that DNA works. DNA is read in words of three characters, the codons. Every single possible &#xA;combination of those characters actually has a meaning. Therefore, a mutation like that above which would decrease the information content of the sentence (here, the gene) is not possible. Let's quantify. The DNA sequence consists of a long series of chemicals, commonly known as A, C, T and G. Since these are read in &quot;words&quot; of three &quot;letters&quot;, this means you have:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$4^{3} = 64$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;64 possible combinations. Of these 64, 61 &lt;a href=&quot;https://en.wikipedia.org/wiki/DNA_Codon_Table&quot; rel=&quot;nofollow noreferrer&quot;&gt;are words with a specific meaning&lt;/a&gt; and 3, the STOP codons, are punctuation marks, full stops if you will. In other words, &lt;strong&gt;all possible combinations of letters have meaning in DNA&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because all possible 3-letter combinations have meaning, no change will affect the information content of the &quot;sentence&quot;. All it can do is change it. Now, changing the information can indeed result in &quot;sentences&quot; that make no sense. In the DNA world, this most often results in what are known as deleterious mutations. These happen all the time, but the result is usually a dead individual. Those with such mutations are not even born (speaking of mammals).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, other mutations, such as the change from &lt;code&gt;read&lt;/code&gt; to &lt;code&gt;red&lt;/code&gt; that I mentioned before, can give rise to a change of meaning, this change, if it turns out that it makes the individual carrying it more likely to reproduce, will spread across the population and will be &lt;em&gt;selected for&lt;/em&gt;. That is how new traits can arise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In closing, another point that you have misunderstood is that evolution is not a path from the least to the most complex. In many ways it is the inverse. In fact, by any measure that counts, bacteria are &lt;em&gt;far&lt;/em&gt; more &quot;evolved&quot; than humans for the very simple reason that the only way you can measure evolution is in terms of numbers of generations. Think of evolution as happening every time a species reproduces, this means that bacteria have had orders of magnitude more time to evolve than mammals have. Still, this is a useless comparison which is why nobody compares species by how &quot;evolved&quot; they are. For a discussion on that, have a look &lt;a href=&quot;https://biology.stackexchange.com/q/832/1306&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2018-09-23T14:12:33.790" LastActivityDate="2018-09-23T14:12:33.790" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="16120" PostTypeId="1" CreationDate="2014-03-26T22:39:44.720" Score="4" ViewCount="492" Body="&lt;p&gt;If our DNA determines certain patterns within the human body such as hair color and eye color, if scientists were able to &quot;turn off&quot; such as the gene for eye color after the pattern was established, what would happen?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2014-03-28T18:52:43.813" Title="DNA of the human body?" Tags="&lt;dna&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16121" PostTypeId="2" ParentId="16120" CreationDate="2014-03-26T23:53:24.507" Score="5" Body="&lt;p&gt;The classic analogy here is that of a blueprint. For example this one I found &lt;a href=&quot;http://bioshock.wikia.com/wiki/File:Blueprint_Little_Sister.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; which is kind of relevant:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/SlHXmm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you use the blueprint above to make yourself a little sister and later change the blueprint, the sister you built will not be affected. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is only part of the story though, the analogy can only go so far. DNA is constantly &quot;read&quot;, what this means is that genes are transcribed to RNA which in turn is translated into proteins. To use a horrible simplification, genes are the blueprints for proteins. Therefore, if you change the gene, and the cell then reads from it to create a protein, it will indeed create a different protein than what the original gene would have coded for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The point I am trying to make is that &lt;em&gt;depending on which genes are changed, you can either have no effect or a huge one&lt;/em&gt;. Some genes are only read once when the cells are reproducing, others are read constantly as the proteins they code for are used up and then produced anew. So, if the gene you change is one that will be read again during the cell's lifetime, then you will see a change. A classic example of this is cancer. If, on the other hand, it is a gene that will not be read again, then the changes will not have any effect.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-03-26T23:53:24.507" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16122" PostTypeId="2" ParentId="16106" CreationDate="2014-03-27T00:00:21.163" Score="1" Body="&lt;p&gt;evolution means unrolling &lt;a href=&quot;http://www.etymonline.com/index.php?term=evolution&quot; rel=&quot;nofollow&quot;&gt;http://www.etymonline.com/index.php?term=evolution&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now if you imagine a tree with one root then the stem rolls out, branches roll out twigs and leaves roll out etc. Same with the roots on the other and to balance it out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And that's it. Evolution does not happen in a vacuum. It happens in and together with an environment. If the environment changes and you have unrolled something that helps you cope with that change then you can continue to procreate so that your offspring also have a chance to test any eventual new unrollings in the constantly changing environment. If they die then the branch or twig that was unrolled is cut off and might unroll again later and be cut off again until maybe, just maybe some sunlight will reach it and it can survive. Until night falls again.&lt;/p&gt;&#xA;" OwnerUserId="6137" LastActivityDate="2014-03-27T00:00:21.163" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16123" PostTypeId="2" ParentId="16105" CreationDate="2014-03-27T00:05:57.893" Score="-2" Body="&lt;p&gt;We find valleys pretty. We find mountains pretty. We like sunshine and clouds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd say all these have some advantages. Trees you can climb. In valleys you have protection. From mountains you have a good view across the landscape. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes it does make sense that we like nature. We like things that are good for us. Like fertile land and food.&lt;/p&gt;&#xA;" OwnerUserId="6137" LastActivityDate="2014-03-27T00:05:57.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16124" PostTypeId="1" AcceptedAnswerId="16128" CreationDate="2014-03-27T02:18:20.320" Score="1" ViewCount="122" Body="&lt;p&gt;In the above title question, can the protein thats altered not be isolated (to separate out from other proteins) somehow?  Is there nothing that can bind to the specific cancer proteins that will not bind to other proteins?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastEditorDisplayName="user6116" LastEditDate="2014-03-27T02:53:21.010" LastActivityDate="2014-03-27T03:46:12.740" Title="If a gene altered causes cancer and creates a protein for cancer can the new protein be isolated in some way?" Tags="&lt;dna&gt;&lt;proteins&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="16126" PostTypeId="1" AcceptedAnswerId="16130" CreationDate="2014-03-27T02:54:45.757" Score="1" ViewCount="157" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IiBSG.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone please help with this question? I'm not so sure whether part A should be 11 inches or something else. Also, is part B correct &lt;/p&gt;&#xA;" OwnerUserId="5460" LastActivityDate="2014-03-27T08:32:00.833" Title="Quantitative Traits Genetics" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;gene-expression&gt;&lt;allele&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16127" PostTypeId="1" AcceptedAnswerId="16152" CreationDate="2014-03-27T03:14:35.813" Score="6" ViewCount="950" Body="&lt;p&gt;Do cancer cells give off specific chemical signatures?   Are these signatures different from normal cells?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2014-03-27T20:49:33.243" Title="Do cancer cells give off specific chemical signatures?" Tags="&lt;cancer&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16128" PostTypeId="2" ParentId="16124" CreationDate="2014-03-27T03:46:12.740" Score="0" Body="&lt;p&gt;From how I read your question, you're wondering if there is some technology to somehow isolate oncogenic proteins inside the cell so they don't do harm, is that correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer is somewhat complicated, as it depends on the protein. First, though, you need to understand that cancer is a very complex disease, and cancer is not caused by a single mutation alone. The &quot;multiple-hit&quot; or &lt;a href=&quot;http://en.wikipedia.org/wiki/Knudson_hypothesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Knudson hypothesis&lt;/a&gt; essentially states that a cell &lt;strong&gt;progresses&lt;/strong&gt; from a normal cell to a cancerous one, accumulating multiple mutations along the way. In pretty much all cases, at least two specific mutations are needed - the constitutive activation of a &lt;a href=&quot;http://en.wikipedia.org/wiki/Proto-oncogene&quot; rel=&quot;nofollow noreferrer&quot;&gt;proto-oncogene&lt;/a&gt;, a group of proteins responsible for cell growth and proliferation, and the deletion or inactivation of one or more &lt;a href=&quot;http://en.wikipedia.org/wiki/Tumor_suppressor_gene&quot; rel=&quot;nofollow noreferrer&quot;&gt;tumor suppressor genes&lt;/a&gt;, which are used to keep growth and proliferation under control. This way, you have a tumor driver (often this is a single protein, like a &lt;a href=&quot;http://en.wikipedia.org/wiki/Growth_factor_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;growth factor receptor&lt;/a&gt;) &quot;driving&quot; the &lt;a href=&quot;http://en.wikipedia.org/wiki/Oncogenesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;oncogenic process&lt;/a&gt;, with no &quot;brake&quot; or regulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I said, mutations in tumor suppressor genes generally result in loss-of-function changes, or complete deletion/inactivation of the gene altogether, so &quot;isolating&quot; these proteins in the cell wouldn't do much good. The focus of many tumor therapies is to down-regulate, inhibit, destroy, or otherwise remove the function of the protein that is driving the uncontrolled growth and proliferation of cells, forming &lt;a href=&quot;http://en.wikipedia.org/wiki/Tumor&quot; rel=&quot;nofollow noreferrer&quot;&gt;tumors&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Metastasis&quot; rel=&quot;nofollow noreferrer&quot;&gt;metastases&lt;/a&gt;. If we're lucky, the tumor driver is an &lt;a href=&quot;http://en.wikipedia.org/wiki/Extracellular_domain&quot; rel=&quot;nofollow noreferrer&quot;&gt;extracellular domain&lt;/a&gt;-containing protein (like a cell-surface receptor) that can be identified and targeted from outside the cell. Once this has occurred, scientists and doctors can use specially-derived &lt;a href=&quot;http://en.wikipedia.org/wiki/Monoclonal_antibody_therapy&quot; rel=&quot;nofollow noreferrer&quot;&gt;monoclonal antibodies&lt;/a&gt; to target and kill the cells containing these proteins:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/6/66/Monoclonal_antibodies.svg/700px-Monoclonal_antibodies.svg.png&quot; alt=&quot;therapeutic monoclonal antibodies&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Monoclonal antibodies for cancer.&lt;/strong&gt; ADEPT, antibody directed enzyme prodrug therapy; ADCC, antibody dependent cell-mediated cytotoxicity; CDC, complement dependent cytotoxicity; MAb, monoclonal antibody; scFv, single-chain variable fragment.&lt;/sub&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;From &lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Monoclonal_antibodies.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;WikiMedia Commons&lt;/a&gt;, released into the public domain.&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a number of ways the cancer cells can be killed, from delivery of radiation or other &lt;a href=&quot;http://en.wikipedia.org/wiki/Cytotoxicity&quot; rel=&quot;nofollow noreferrer&quot;&gt;cytotoxic&lt;/a&gt; compounds, to attracting killer cells from the immune system, to activating the &lt;a href=&quot;http://en.wikipedia.org/wiki/Complement_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;complement system&lt;/a&gt;. However, all of these depend on the surface presence of &lt;a href=&quot;http://en.wikipedia.org/wiki/Biomarker&quot; rel=&quot;nofollow noreferrer&quot;&gt;biomarkers&lt;/a&gt; for the cancerous cells, so as to avoid non-specific killing or off-target effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason so much focus is put on killing the cancerous cells instead of trying to isolate the &quot;bad guys&quot; inside the cells is that by the time the cell has become cancerous, it already has accumulated so many mutations that &lt;strong&gt;&lt;em&gt;a&lt;/em&gt;&lt;/strong&gt;) the cell isn't really worth saving, and &lt;strong&gt;&lt;em&gt;b&lt;/em&gt;&lt;/strong&gt;) it would take an extraordinary amount of effort to corral all the mutated proteins together, and leave whatever unaffected or &quot;wild-type&quot; proteins were left to do their jobs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may recall that each gene we have (except for some on the X and Y chromosomes) is present in duplicate, one copy from our mother and one from our father. The initial mutations that begin the progression to the fully cancerous state may at first only affect one of those two copies of the gene, leaving a working version around for a while. However, as oncogenesis progresses, and more and more regulatory proteins are inactivated, chromosomal damage grows, and frequently the surviving &quot;normal&quot; copy is either mutated itself or completely destroyed. Once this occurs, even if you could isolate the misbehaving proteins, there would be no good proteins left to do the jobs of the cell. Therefore, killing is really the only option.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope I've covered what you were interested in. Please let me know if you don't understand any of it, or you can always &lt;a href=&quot;https://biology.stackexchange.com/questions/ask&quot;&gt;ask a new question&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-03-27T03:46:12.740" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16129" PostTypeId="2" ParentId="16116" CreationDate="2014-03-27T06:25:23.110" Score="2" Body="&lt;p&gt;As I mentioned in your previous post. If your reference gene undergoes changes then replace it with another reference and if even that doesn't work out then use a spike in. You &lt;strong&gt;must&lt;/strong&gt; normalize. Interpreting the raw values can be erroneous- there could be a loading bias. Don't think much- repeating RNA isolation and/or qPCR is not a very hard job. And as Chris said, use two references if you can.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;BTW, if you are fine with it then can you tell what is the gene that you are studying and what is the treatment&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;w.r.t what is a significant fold change.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;There is no hard and fast rule to determine what is an acceptable fold change. In some robust systems a minor perturbation in the gene expression will not translate to any great biological outcome whereas there can be sensitive systems in which minor changes can affect the cell state. These things depend on how the gene is integrated in the regulatory network.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-03-27T06:25:23.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16130" PostTypeId="2" ParentId="16126" CreationDate="2014-03-27T08:32:00.833" Score="2" Body="&lt;p&gt;&lt;strong&gt;Question a&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The only possible genotype that brings a phenotype of 12 inches is: $AABBCC$. Similarly the only possible genotype that bring a phenotype of 6 inches is: $aabbcc$. In consequence the offsprings can only be: $AaBbCc$ which measure $2+1+2+1+2+1 = 9$ inches.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question b&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Now the question is: if we breed two $AaBbCc$ how many offsprings measure 11 inches? Because there are three bi-allelic genotypes you have $2^3=8$ possible gametes and therefore you have to draw a 8x8 punnett square. Doing so, just count the proportion of offsprings that measure 11 inches. You can reason slightly more logically and get a faster answer. To measure 11 inches you need to have only capital letters in your genome except at one position. In consequence, if your father gives the gamete $ABC$, you mother should give the gamete $ABc$, $AbC$ or $aBC$. You can inverse the role of the father and the mother and it works as well. Therefore, you have 6 possible combinations that give rise to an offspring that measure 11 inches. Because there are $8 \cdot 8 = 64$ possible combinations, the proportion of offspring that are 11 inch-long is $\frac{6}{64} = \frac{3}{32} = 0.09375 ≈ 0.1$. About 10% of your F2 individuals are 11 inch long.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-03-27T08:32:00.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16131" PostTypeId="2" ParentId="16106" CreationDate="2014-03-27T08:33:07.760" Score="4" Body="&lt;p&gt;&lt;strong&gt;Where does the information come from?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the environment, and the previous history of interactions in that environment. The process of evolution can be viewed as an undirected search for &quot;good&quot; solutions (i.e. those that better support replication) to problems presented by the environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a large amount of information (in the information-theory sense) in a differentiated environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that information content of the whole system &lt;em&gt;is&lt;/em&gt; preserved when this happens. Partly the misunderstanding of &quot;information is being created&quot; is not seeing what a &lt;strong&gt;huge&lt;/strong&gt; resource of information (in the same sense used with information theory that says it may not be created or destroyed) is available from the environment. It is many many orders of magnitude greater than anything stored in genetic codes.&lt;/p&gt;&#xA;" OwnerUserId="6167" LastEditorUserId="6167" LastEditDate="2014-03-28T13:29:43.170" LastActivityDate="2014-03-28T13:29:43.170" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16132" PostTypeId="2" ParentId="16106" CreationDate="2014-03-27T08:47:47.500" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;It is understood that Evolution basically involves three elements. Natural selection, genetic mutation, and time. The problem for Evolution, is that none of those three elements are creative.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They absolutely are creative in that they create something new. Mutation introduces random errors, some of which may never have existed before in that combination of genes. Now &lt;em&gt;usually&lt;/em&gt; errors are bad, and natural selection prunes the result, but every once in a while, you accidentally stumble upon something new that provides an advantage, and now natural selection means it gets kept and passed on to the next generation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So on their own, it might seem that mutation doesn't add information and natural selection doesn't create anything new, but together, natural selection adds information to the randomness of mutation: it selects what works and what doesn't.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine you're rolling a die &lt;em&gt;(warning! simplified analogies don't accurately reflect the complexities of evolution)&lt;/em&gt;. What are the chances of you rolling 10 sixes in a row? Vanishingly small of course. But that's not what evolution does. What it does is in every phase (generation), it rolls 10 dice, and only keeps the sixes. What is the chance of getting a six in every phase now? Quite a lot bigger. All through randomness and selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(In fact, have you ever played Yahtzee? How can you get the right patterns there if you're just rolling dice and selecting some of them?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take your analogy with the sentence &quot;Make an eye that is compound&quot;. A mutation might turn that into &quot;Make an eyye that is compound&quot; which is useless. But another mutation might turn it into &quot;Bake an eye that is compound&quot; which is grammatically correct though nonsensical. Yet another mutation might create &quot;Make an eyr that is compound&quot;, and if that one happens to survive a generation, you might get &quot;Make an ear that is compound&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thing is, there are a &lt;em&gt;lot&lt;/em&gt; of mutations. Really a lot. Most of them have no measurable effect. Of the remainder, the vast majority breaks something, which means they automatically get weeded out by natural selection. A tiny fraction accidentally adds something useful. If you look at any single mutation, it's impossible to imagine how that could ever result in anything useful, but there's a lot of them. Every generation again, over thousands and millions of years, and eventually, those very few positive mutations start to add up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's impossible to fully grasp how evolution can introduce totally new species without first grasping the enormous time scale on which evolution works. And we humans are limited beings and bad at truly understanding such enormous scales. But it clearly works. We can see the results all around us. We can run simulations on computers that show that the process really does work. I consider it one of God's greatest miracles &lt;em&gt;(warning! personal opinion might not reflect those of others)&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6165" LastActivityDate="2014-03-27T08:47:47.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16133" PostTypeId="1" AcceptedAnswerId="16134" CreationDate="2014-03-27T09:11:20.547" Score="2" ViewCount="1348" Body="&lt;p&gt;While trying to understand DNA supercoiling, I came across these lines in the book &lt;em&gt;Genetics by Ursula Goodenough&lt;/em&gt; :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;All natural DNA is superhelical. The axis of the duplex itself follows&#xA;  a helical path in space. For virtually all DNA, the sense of the&#xA;  superhelical turns is opposite to that of duplex, thereofer, they are&#xA;  negative supertwists.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am unable to understand these lines. Specially, the second one.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="16460" LastEditDate="2017-04-01T08:13:21.333" LastActivityDate="2020-04-11T08:59:43.253" Title="Understanding DNA supercoiling" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;molecular-genetics&gt;&lt;supercoiling&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16134" PostTypeId="2" ParentId="16133" CreationDate="2014-03-27T09:22:05.353" Score="4" Body="&lt;p&gt;It means that the direction in which the normal double-strand is wound up (which is also helical) and the direction on which the double helix itself is twited to reach the supercoils are opposite to each other. Have a look at this image from the &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_supercoil&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;, I think it makes this clearer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/D6KNy.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first show a DNA ring with the normal helix-coiling. The second show the supercoiling of the coiled ring molecule. Imagine a rubber band. This you can twist around its band axis to get the coiling and around its vertical axis to get the supercoiling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For linear DNA molecules, this looks like this (taken from &lt;a href=&quot;http://apbrwww5.apsu.edu/thompsonj/Anatomy%20&amp;amp;%20Physiology/2010/2010%20Exam%20Reviews/Exam%201%20Review/Ch02%20Nucleic%20Acids%20and%20ATP.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KJ9wf.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-27T09:22:05.353" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16135" PostTypeId="2" ParentId="16106" CreationDate="2014-03-27T09:34:26.257" Score="1" Body="&lt;p&gt;Another important point about evolution is, that rhere are many, many small steps - not huge leaps.&#xA;E.g. going from a bacteria to something with four legs in one step will not happen - that is simply too much change at once, and it's probabillity is close to zero.&#xA;But small steps happen all the time - if we take your example with a cephalopod: Imagine that there are some individual cephalopods who have a harder skin. Without predatory pressure this is next to useless: the cephalopod are investing energy on something which brings no benefit. So they are less fit and will probably have fewer offspring than the original ones. Now a predator kill many soft-skinned cephalopods but sometimes fails to eat their harder skinned brethren. The hard-skin variant will producre more offspring and theier genes spread. Then the next round happens: cephalopods with the hard skin might have another mutation which hardens the shell even more - or the predators might get better teeth.&#xA;But be aware that this most not happen: maybe no variant with harder skin exists or the genetic error is not present at the time and the whole race simply dies - this happens a lot. Look at dinosaurs or the polar bear (is under pressure because the polar ice melts) etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some fun fact: since each step is random and has a low probabillity, you willl never get the same reult twice. If you start the evoluation again, the world would look completely different because the steps would look different.&lt;/p&gt;&#xA;" OwnerUserId="6170" LastActivityDate="2014-03-27T09:34:26.257" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16137" PostTypeId="1" AcceptedAnswerId="16140" CreationDate="2014-03-27T10:26:03.560" Score="1" ViewCount="1041" Body="&lt;p&gt;I am thinking this figure&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mWEIA.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;which can also be drawn like this&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DIY1V.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How does HBeAg change to Anti-HBe?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some triggers that stimulate Anti-HBe production after HBeAg level is done. &#xA;I think they can Anti-HBc.&#xA;There must be other mechanisms too.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-03-27T12:03:52.193" Title="How does HBeAg change to Anti-HBe in acute hepatitis" Tags="&lt;microbiology&gt;&lt;antibody&gt;&lt;antigen&gt;&lt;hepatitis&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16140" PostTypeId="2" ParentId="16137" CreationDate="2014-03-27T12:03:52.193" Score="1" Body="&lt;p&gt;I'm not sure that I have understood the question but ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HbeAg is a secreted variant of HbcAg (the core antigen of HBV). Unlike HbcAg, HbeAg is found in the blood. I believe that it is produced as a result of a splice variant of the corresponding RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The phenomenon described in these Figures is an example of &lt;a href=&quot;http://en.wikipedia.org/wiki/Seroconversion&quot; rel=&quot;nofollow&quot;&gt;seroconversion&lt;/a&gt;. Before seroconversion the antigen is detectable in the blood but there is no antibody directed against it; after seroconversion there is antibody but no antigen.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-27T12:03:52.193" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16141" PostTypeId="1" AcceptedAnswerId="16161" CreationDate="2014-03-27T13:16:00.113" Score="1" ViewCount="921" Body="&lt;p&gt;What does single channel microarray mean?&#xA;When is it used?&#xA; Thank you for your case in advance.&lt;/p&gt;&#xA;" OwnerUserId="6175" LastActivityDate="2014-03-28T01:17:44.593" Title="Single channel micro arrays" Tags="&lt;bioinformatics&gt;&lt;microarray&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16142" PostTypeId="5" CreationDate="2014-03-27T14:02:39.117" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-03-27T14:02:39.117" LastActivityDate="2014-03-27T14:02:39.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16143" PostTypeId="4" CreationDate="2014-03-27T14:02:39.117" Score="0" Body="The study of reptiles and amphibians, and a subarea of zoology." OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-03-27T16:59:48.387" LastActivityDate="2014-03-27T16:59:48.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16144" PostTypeId="1" AcceptedAnswerId="16164" CreationDate="2014-03-27T15:13:51.657" Score="2" ViewCount="58" Body="&lt;p&gt;Is there any measurement I could perform after RT that allows me to check the efficiency that the procedure had? Nanodrop cannot be used as remnants of RNA and poly T primers mask measure, or? &lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="6" LastEditDate="2014-03-28T08:54:11.100" LastActivityDate="2014-03-28T22:19:17.793" Title="Measuring reverse transcription yield?" Tags="&lt;reverse-transcription&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16145" PostTypeId="2" ParentId="16117" CreationDate="2014-03-27T15:45:03.673" Score="0" Body="&lt;p&gt;Well, with cremation comes also a lot of harmful gasses entering the atmosphere as well, and from your question, I'm assuming you're interested in eco-friendly alternatives.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've heard of organic embalming fluids, so it might be interesting to you to look into that. Also a lot of steel and cement go into a traditional burial; if you were to be buried in a plain pine box with no fancy coatings or finishings, that would certainly speed up decomposition. If you look at traditional Jewish burial customs, you may find a bit of what you're looking for.&lt;/p&gt;&#xA;" OwnerUserId="6178" LastActivityDate="2014-03-27T15:45:03.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16146" PostTypeId="1" CreationDate="2014-03-27T16:03:55.217" Score="1" ViewCount="238" Body="&lt;p&gt;It seems like every disease we ever hear about is something that's been around since ancient times, since thousands of years ago. Of course new diseases were catalogued over the course of the past couple hundred years, but they weren't actually &lt;em&gt;new&lt;/em&gt; diseases-- they just hadn't been previously classified/identified.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that (in my understanding) viruses and microbial lifeforms can evolve and change considerably more rapidly than higher order organisms, why don't we often/ever hear about completely new diseases that have never been seen before? Diseases that may have only just been born.&lt;/p&gt;&#xA;" OwnerUserId="3830" LastActivityDate="2017-06-30T07:41:13.503" Title="Why don't we see new diseases more often? Or, ever?" Tags="&lt;pathology&gt;&lt;virology&gt;" AnswerCount="3" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16147" PostTypeId="1" AcceptedAnswerId="16149" CreationDate="2014-03-27T16:16:57.873" Score="4" ViewCount="1394" Body="&lt;p&gt;My question is dealing with how many ancestors it took to produce &lt;strong&gt;me&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;--&gt; to produce me it took 2 people (my parents) = ($2^1$) people = 2&lt;/li&gt;&#xA;&lt;li&gt;--&gt; one generation further included = ($2^1 + 2^2$) people = 6&lt;/li&gt;&#xA;&lt;li&gt;--&gt; in the past 500 years my pedigree chart contains 15 generations, so $2^{16}$ people = 65.532 people to produce &lt;strong&gt;me&lt;/strong&gt; (-2 to be completely correct)&lt;/li&gt;&#xA;&lt;li&gt;--&gt; when i calculate back to 35.000 year ago I get a larger number *)&lt;/li&gt;&#xA;&lt;li&gt;--&gt; when i calculate to all humans 2.400.000 ago I get a ridiculous large number *)&lt;/li&gt;&#xA;&lt;li&gt;--&gt; when i include up to all mammal grandfathers and grandmothers 60.000.000 years ago the total number takes pages to scroll *)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;*) see: &lt;a href=&quot;http://ed.je/2L6&quot; rel=&quot;nofollow&quot;&gt;http://ed.je/2L6&lt;/a&gt; for the actual numbers did not want to clutter here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*) I took 3 generations per 100 years to let the numbers be small as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I think I'm making a mistake somewhere. Only I don't know where: to create a child you need 2 parents. And to create a parent you need 2 further parents. But somehow calculating back to &quot;all mammals&quot; just related directly to me would mean $2^{1.800.001}$ mammals walking around 60 millions years ago being my direct predecessor back then. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So where am I going wrong? Somehow I can't figure out where my error lies (I've not studied Biology though).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I visualize a pedigree tree (reverse pyramid) starting with me and then logically each parent needs to be born out of 2 other parents just calculating my way up.&lt;/p&gt;&#xA;" OwnerUserId="6176" LastEditorUserId="3624" LastEditDate="2014-05-26T16:36:50.753" LastActivityDate="2014-05-26T16:36:50.753" Title="Initial population when i count backwards?" Tags="&lt;human-genetics&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16148" PostTypeId="2" ParentId="16117" CreationDate="2014-03-27T16:26:30.840" Score="1" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Parsi&quot; rel=&quot;nofollow&quot;&gt;Parsis&lt;/a&gt; and other &lt;a href=&quot;http://en.wikipedia.org/wiki/Zoroastrianism&quot; rel=&quot;nofollow&quot;&gt;Zoroastrians&lt;/a&gt; dispose of their dead in a so-called &lt;a href=&quot;http://en.wikipedia.org/wiki/Tower_of_Silence&quot; rel=&quot;nofollow&quot;&gt;Tower of Silence&lt;/a&gt;, where the body is left on a raised platform to be eaten by scavengers, particularly birds such as vultures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is possibly (probably?) the quickest way for nutrients to re-enter the wider ecosystem, as scavengers usually work a whole lot quicker than microbes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tibetan tradition also contains a ritual known as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sky_burial&quot; rel=&quot;nofollow&quot;&gt;Sky Burial&lt;/a&gt;, which achieves the same sort of thing. The Tibetan version may be even quicker, as once the scavengers have stripped the body, the bones are ground into a paste along with flour and yak's milk/butter to be fed to a second round of scavenging birds.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastActivityDate="2014-03-27T16:26:30.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16149" PostTypeId="2" ParentId="16147" CreationDate="2014-03-27T16:31:50.550" Score="6" Body="&lt;p&gt;Your calculations are the following. Assuming non-overlapping generations, the number of ancestors you have in the last $t$ generation is given by:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sum_{i=1}^t 2^t$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This sounds correct. But there are some very strong assumptions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Generations are non-overlapping&lt;/strong&gt;. A more realistic model would need to consider $t$ as a continuous variable a give a probability of reproducing which depend on the age of the individual.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Never two related individuals mate together&lt;/strong&gt;. Otherwise, you paternal grandfather might be your maternal grandfather. In reality we are all somehow related, we have a common ancestor (Hey Bro). For example if you consider that your parents are siblings and that their parents are siblings and so forth… then you don't need more than 2 great-great-great-great-grandparents. In order to keep track of such events (inbreeding), you need a stochastic model and you would need to know the population size $N(t)$ as a function of $t$. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Tracking the change of population size through time is part of a very big in biology which is called population biology. For example you will find &lt;a href=&quot;https://biology.stackexchange.com/questions/15514/what-prevents-predator-overpopulation/15516#15516&quot;&gt;in this post&lt;/a&gt; a model of population growth of two interacting species (prey-predator)&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-03-27T16:58:03.333" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16150" PostTypeId="1" CreationDate="2014-03-27T16:32:10.237" Score="9" ViewCount="1163" Body="&lt;p&gt;I've seen videos of hundreds of birds flying in the same general direction but creating incredible patterns in the sky seemingly instantaneously! How do they all know in what direction to turn at the same time? Is there a &quot;Lead&quot; bird dictating this somehow?&lt;/p&gt;&#xA;" OwnerUserId="6179" LastEditorUserId="1320" LastEditDate="2014-03-28T12:54:49.620" LastActivityDate="2015-03-24T22:16:03.067" Title="Why don't birds in flocks fly into each other?" Tags="&lt;ethology&gt;&lt;ornithology&gt;&lt;communication&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="16152" PostTypeId="2" ParentId="16127" CreationDate="2014-03-27T19:16:35.127" Score="4" Body="&lt;p&gt;The answer is &lt;em&gt;it depends&lt;/em&gt;.  First, take a step back from the definitions of &quot;cancer&quot; versus &quot;normal&quot; cell and recognize that cells and tissues can undergo a variety of changes in their growth.  A solid cancer/tumor (as its usually defined) is something that grows and invades the surrounding tissue.   A spectrum of possible cell growth can be :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;normal -&gt; hypertrophy -&gt; hyperplasia or dysplasia -&gt; hamartoma -&gt; benign tumor -&gt; carcinoma in situ -&gt; invasive cancer -&gt; metastais&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(this list is &lt;strong&gt;NOT&lt;/strong&gt; suggesting these are the actual steps to cancer, but instead they are useful for the next paragraph): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The point of this list is that from a &lt;em&gt;human&lt;/em&gt; perspective &lt;strong&gt;we&lt;/strong&gt; can see something odd happening when we see a tumor, but the view from inside a cancer cell is basically &quot;things are fine, I'm just doing my cell thing&quot;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, that said...when a tumor grows and cancer cells invade tissues a few things happen which can give rise to differences between cancer cells and normal tissues and which can be detected.&lt;br&gt;&#xA;First, it needs energy, and cancer cells often switch to aerobic glycolysis (a phenomenon called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Warburg_effect#Oncology&quot; rel=&quot;nofollow&quot;&gt;Warburg effect&lt;/a&gt;). As the link shows, a special form of labelled glucose can be used to detect this in the body.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, a tumor invades the surrounding tissue and generates new blood vessels, and so enzymes that break down &lt;a href=&quot;http://en.wikipedia.org/wiki/Proteases_in_angiogenesis&quot; rel=&quot;nofollow&quot;&gt;extracellular matrix &lt;/a&gt; are released.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some tumors over-express and secrete markers (usually proteins) that can be detected.  The &lt;a href=&quot;http://en.wikipedia.org/wiki/Prostate-specific_antigen&quot; rel=&quot;nofollow&quot;&gt;prostate specific antigen&lt;/a&gt; (PSA) and &lt;a href=&quot;http://en.wikipedia.org/wiki/Carcinoembryonic_antigen&quot; rel=&quot;nofollow&quot;&gt;carcinoembryonic antigen&lt;/a&gt; are two examples.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other things secreted by certain tumors may &lt;a href=&quot;http://en.wikipedia.org/wiki/Canine_cancer_detection&quot; rel=&quot;nofollow&quot;&gt;include volatiles that can be detected by dogs&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The challenge with any 'signature' detection is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sensitivity_and_specificity&quot; rel=&quot;nofollow&quot;&gt;sensitivity and specificity &lt;/a&gt; which often limits the use of tests that show some early promise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cancer cells &lt;strong&gt;DO&lt;/strong&gt; have specific changes to their &lt;a href=&quot;http://www.cancer.gov/cancertopics/understandingcancer/cancergenomics/AllPages&quot; rel=&quot;nofollow&quot;&gt;DNA&lt;/a&gt; that can be used as very specific signatures for detection.  Tumor DNA is shed into the blood and possibly the urine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, tumor biology overlaps with many aspects of normal biology, including wound healing and pregnancy and this continues to make it challenging to identify &lt;em&gt;tumor specific markers&lt;/em&gt; that have high sensitivity and specificity.&lt;/p&gt;&#xA;" OwnerUserId="5922" LastEditorUserId="5922" LastEditDate="2014-03-27T20:49:33.243" LastActivityDate="2014-03-27T20:49:33.243" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16156" PostTypeId="1" AcceptedAnswerId="16298" CreationDate="2014-03-27T21:48:56.613" Score="1" ViewCount="1467" Body="&lt;p&gt;I am thinking this figure&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ghXbR.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It suggests me that there has to be Sepsis that infection can lead to SIRS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking particularly the pathogenesis of Cryptococcus neoformans where&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;respiratory tract $\to$ pulmonary infection $\to$&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;asymptomatic and nonspecific pulmonary signs in normal patients&lt;/li&gt;&#xA;&lt;li&gt;progressive systemic disease in immunocompromised patients&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and the last row.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can SIRS occur without preceding or simultaneous Sepsis?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-02T10:41:28.460" Title="Can SIRS occur without Sepsis from Infection?" Tags="&lt;microbiology&gt;&lt;mycology&gt;&lt;infection&gt;&lt;sepsis&gt;&lt;sirs&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16158" PostTypeId="1" AcceptedAnswerId="16159" CreationDate="2014-03-27T22:23:43.427" Score="2" ViewCount="1480" Body="&lt;p&gt;I am thinking what can cause the swelling of gastrointestinal system i.e. bloating after high protein diet of Whey proteins.&#xA;Liver does breaks those proteins to branched chain amino acids (BCAA), which can cause this swelling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I am not sure if this is the reason.&#xA;It may be the carbohydrates which are broken to enable this BCAA synthesis.&#xA;If you take the protein diet with carbohydrates, there seem to be less swelling.&#xA;So apparently easier energy for BCAA synthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The combination of proteins, carbohydrates and lipids seem to be important.&#xA;Creatine should also be mentioned.&#xA;Fat burner thing is also important here, I think.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What can cause the swelling of gastrointestinal system after high protein diet of Whey proteins?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-08-07T07:38:58.273" LastActivityDate="2014-12-26T09:24:15.033" Title="What can cause the bloating in high protein diet of Whey proteins?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;lipids&gt;&lt;carbohydrates&gt;" AnswerCount="1" CommentCount="10" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16159" PostTypeId="2" ParentId="16158" CreationDate="2014-03-27T22:43:34.300" Score="3" Body="&lt;p&gt;The cause of the swelling is &lt;strong&gt;lack of lymphatic carriage capability&lt;/strong&gt; of proteins to the muscles, because of systemic conditions affecting the circulation of proteins through your lymphatic system.&#xA;There will be edema extracellularly because of insufficient carriage of proteins through lymphatic system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My schematic drawing about the fluid movement between these spaces&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Bm7s9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I started to think why some people do not observe so much swelling.&#xA;I discussed with a few and come to conclusion that the main difference between those people who did not have noticeable swelling was that that they did &lt;em&gt;lymphatic system massage&lt;/em&gt; by maximising &lt;em&gt;abdominal breathing&lt;/em&gt; after taking whey proteins (before training and after training).&#xA;I think it sounds sensible to some extent. &#xA;Those people also included lymphatic system massage in their recovery after training.&#xA;One video &lt;a href=&quot;https://www.youtube.com/watch?v=rMljOuz_l_Q&amp;amp;list=PLDEF532905455E4CD&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; Lymphatic Drainage for Abdomen and Trunk.&#xA;So another reason what may cause the swelling is &lt;strong&gt;insufficient drainage of lymphatic system&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The swelling does not happen to the same extent in all people.&#xA;Some people swell much after one intake of protein drink.&#xA;Some people also do not have to do lymphatic massage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My conjecture:&lt;/strong&gt; The reason to this is most probably one glue-gene-group.&#xA;Those people who have this genome have other systemic diseases that causes the lymphatic drainage have high proportion of proteins already:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;for instance, uncontrolled &lt;strong&gt;asthma patients&lt;/strong&gt;, who are circulating lysed DNAs of lymphocytes from small bronchial tree through the lymphatic circulation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Lymphatic circulation is the system which circulates the proteins to the muscles.&#xA;After absorption from the digestive tract, lymphatic circulation carries proteins systemically.&#xA;However, since there is already a high proportion of proteins, lymphatic circulation cannot take much more proteins to carry. &#xA;Our body has to remove toxic wastes before it can build new materials.&#xA;Catabolism then conquers anabolism in some situations.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-26T09:24:15.033" LastActivityDate="2014-12-26T09:24:15.033" CommentCount="0" CommunityOwnedDate="2014-03-27T22:43:34.300" ContentLicense="CC BY-SA 3.0" />
  <row Id="16160" PostTypeId="2" ParentId="16147" CreationDate="2014-03-28T00:37:07.563" Score="4" Body="&lt;p&gt;An easy way to visualize the mistake in your thought experiment is to consider a &lt;a href=&quot;http://en.wikipedia.org/wiki/Population_bottleneck&quot; rel=&quot;nofollow noreferrer&quot;&gt;bottleneck event&lt;/a&gt;, when the ancestral population was very small, maybe just a few individuals. This would mean that the entire current population is descending from just a few individuals. Your thought experiment is assuming that the &quot;pyramid&quot; of your ancentors is expanding all the time, while the bottleneck event will essentially result in the opposite situation with an inversion of the pyramid, such as:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Your assumption:            Bottleneck:  &#xA;&#xA; xx xx xx xx                     x&#xA;   xx xx                        x x&#xA;    x x                        xx xx     &#xA;     x                      xx xx xx xx&#xA;           (present time)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The reason why the number of ancestors is smaller in the bottleneck event is naturally that the population is inbred (all individuals are related). In contrast, your thought experiment is assuming that all individuals forming the pyramid of your ancestors have completely unrelated ancestry. This is equivalent to assuming that the subpyramids for all ancestors never overlap.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your assumption is unreasonable since human generations are overlapping, the fecundity distribution of individuals is skewed, inbreeding is common and reproduction between more distantly related individuals will happen by pure chance. We also know that humans have historically gone through several population bottlenecks, see e.g. &lt;a href=&quot;http://mbe.oxfordjournals.org/content/17/1/2.full&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Hawks et al. 2000. Population Bottlenecks and Pleistocene Human Evolution. Molecular Biology &amp;amp; Evolution 17(1): 2-22&quot;&gt;Hawks et al. (2000)&lt;/a&gt; and &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0002929707631310&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Liu et al. 2006. A Geographically Explicit Genetic Model of Worldwide Human-Settlement History. Am. J. Hum. Genet 79: 230–237&quot;&gt;Lui et al. (2006)&lt;/a&gt; for an overview. An realistic model of your ancestry is more likely to be (highly idealized and compacted):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;       x&#xA;      x x&#xA;     xx xx&#xA;  xx xx xx xx&#xA;  xx xx xx xx&#xA;     xx xx&#xA;      x x&#xA;       x&#xA;     (you)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The issue we are discussing here is actually known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Pedigree_collapse&quot; rel=&quot;nofollow noreferrer&quot;&gt;pedigree collapse&lt;/a&gt;, where you will eventually find overlap between your ancestors, which will mean that the pedigree collapses instead of growing exponentially. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beside historical bottlenecks, there are also modern examples of extreme human inbreeding. Even if this is not directly related to your thought experiment, you might for instance want to look the pedigree of the &lt;a href=&quot;http://en.wikipedia.org/wiki/House_of_Habsburg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Habsburg royal family&lt;/a&gt;. Here is the genealogy of &lt;a href=&quot;http://en.wikipedia.org/wiki/Charles_II_of_Spain&quot; rel=&quot;nofollow noreferrer&quot;&gt;Charles II&lt;/a&gt; - remember, narrow loops in pedigrees are seldom a good idea:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/C0pK3.jpg&quot; alt=&quot;genealogy of Charles II&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here you can for instance see that Charles' father is also the uncle of his own wife. You can also see that only 5 persons enter in the family tree from the outside through marriages, which means that Charles only had 7 completely independent ancestors (ignoring relationships further back, outside of this tree). Going back 3 generations (sort of - hard to count with overlap), it is also apparent that Charles had a total of 8 ancestors instead of the 14 expected under your model. Another modern example of extreme human inbreeding is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Fundamentalist_Church_of_Jesus_Christ_of_Latter_Day_Saints#Birth_defects&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fundamentalist Church of Jesus Christ of Latter-Day Saints&lt;/a&gt;, where marriages between close relatives have been common along with &lt;a href=&quot;http://www.reuters.com/article/2007/06/14/us-usa-mormons-genes-idUSN0727298120070614&quot; rel=&quot;nofollow noreferrer&quot;&gt;high levels of rare birth defects&lt;/a&gt;. Both these examples definately show, in an extreme way, that you cannot assume that all your ancestors are unrelated.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-03-28T11:22:09.527" LastActivityDate="2014-03-28T11:22:09.527" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16161" PostTypeId="2" ParentId="16141" CreationDate="2014-03-28T01:17:44.593" Score="3" Body="&lt;p&gt;Single channel refers to the system used to detect the labelled probes.  A single channel array, as shown in this &lt;a href=&quot;http://faculty.ucr.edu/~tgirke/HTML_Presentations/Manuals/Microarray/arrayBasics.pdf&quot; rel=&quot;nofollow&quot;&gt;slidedeck&lt;/a&gt; (slides 6-8) uses one type of molecule for detection.  In the example, (slide 8) the optical label is phycoerythrin.   Contrast that to a double channel array (e.g slide 7) that uses a &quot;green&quot; or &quot;red&quot; molecule used to label probes.  Detecting two different labels requires two channels, one to detect red and one the the green.   The key to using two (or more) labeling molecules is to ensure that your detection system can discriminate between the light spectrum emitted by each of the labels.   Many modern microarray readers have designs that handle multiple labels.&lt;br&gt;&#xA;When you see single channel results, they often have colors.  The color is a pseudo color representation of the intensity of the emission of single-color label, which is due to how much probe has bound to the array at that spot. &lt;/p&gt;&#xA;" OwnerUserId="5922" LastActivityDate="2014-03-28T01:17:44.593" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16162" PostTypeId="2" ParentId="16120" CreationDate="2014-03-28T04:25:51.137" Score="2" Body="&lt;p&gt;I'll just extend terdon's answer into more concrete terms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of a gene that is constantly read would probably be the one that determines hair colour. If you were able wave a wand over the head of someone with blonde hair, replacing all their DNA with a different version of the gene, say, the one for brown hair, then chances are that as their hair grows, you would see that it was now brown at the roots! Something like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gy3dvm.jpg&quot; alt=&quot;Dyed hair colour change&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that this picture is evidence of hair dye, not my magic wand. ;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Every time the cells try to produce a pigment, they read that particular gene. But now, they find the &quot;brown version&quot;, and produce a brown pigment instead of a blonde one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, if you replace the gene affecting the length of a person's fingers, they may not just sprout a couple of extra centimetres over the next few months. Those genes may only be read at a particular time of life, such as during puberty or as a child, so they have to be in place at that moment to have much of an effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, that idea of replacing all the copies of your DNA with a different version is roughly called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Gene_therapy&quot; rel=&quot;nofollow noreferrer&quot;&gt;gene therapy&lt;/a&gt;&quot;, and we're still really in the investigation stage of research (to my knowledge).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully that helps to solidify your understanding. :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(And just to add yet another note for this, most traits in humans, like finger length and hair colour, are not the result of just one single gene. They tend to result from a number of factors, but the general idea still applies.)&lt;/p&gt;&#xA;" OwnerUserId="1289" LastEditorUserId="1289" LastEditDate="2014-03-28T18:52:43.813" LastActivityDate="2014-03-28T18:52:43.813" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16163" PostTypeId="1" CreationDate="2014-03-28T04:29:39.410" Score="2" ViewCount="81" Body="&lt;p&gt;Is there a database where I might list the phenotype of a certain rat knockout and/or search for other similar phenotypes? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a &lt;a href=&quot;http://en.wikipedia.org/wiki/International_Mouse_Phenotyping_Consortium&quot; rel=&quot;nofollow&quot;&gt;International Mouse Phenotyping Consortium&lt;/a&gt;, which has the goal of characterizing the phenotypical changes of homozygous knockouts for each of the 20,000 genes in the isogenic mouse line C57BL/6.  The &lt;a href=&quot;http://en.wikipedia.org/wiki/International_Knockout_Mouse_Consortium&quot; rel=&quot;nofollow&quot;&gt;International Knockout Mouse Consortium&lt;/a&gt; is responsible for creating the knockouts and the two consortiums work together closely. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also a Knockout Rat Consortium, but I haven't found a Phenotype Change database for rats. &lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="146" LastEditDate="2014-03-28T18:15:51.890" LastActivityDate="2014-03-29T21:02:05.120" Title="Knockout Rat Phenotype Database?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16164" PostTypeId="2" ParentId="16144" CreationDate="2014-03-28T04:31:22.173" Score="1" Body="&lt;p&gt;Nanodrop may be fine for the volumes but as you rightly guessed it is not so easy to distinguish DNA from RNA (and primers). &lt;a href=&quot;http://wetlab.izzid.com/2008/Feb/Review_of_Qubit/&quot; rel=&quot;nofollow&quot;&gt;Qubit&lt;/a&gt; (invitrogen) is a sensitive, dye based quantification assay. You can use that for estimating cDNA yield. The kit contains different dyes for DNA, RNA and protein estimation.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-03-28T04:31:22.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16167" PostTypeId="1" AcceptedAnswerId="16168" CreationDate="2014-03-28T09:45:39.160" Score="3" ViewCount="1950" Body="&lt;p&gt;I am not a biologist, so please bear with me for this basic question. Although I tried googling, I am confused.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;What is the difference between plastids, chloroplasts and mitochondria?&lt;/li&gt;&#xA;&lt;li&gt;Are there any plant sequence databases for each of them (plastid, chloroplast and mitochondria)?&lt;/li&gt;&#xA;&lt;li&gt;Can we separate chloroplast, mitochondria, plastid sequences from whole genome assemblies?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6188" LastEditorUserId="22033" LastEditDate="2016-03-22T03:46:08.743" LastActivityDate="2016-03-22T03:46:08.743" Title="Plastid and mitochondria" Tags="&lt;cell-biology&gt;&lt;bioinformatics&gt;&lt;mitochondria&gt;&lt;chloroplasts&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16168" PostTypeId="2" ParentId="16167" CreationDate="2014-03-28T11:08:03.297" Score="7" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;What is difference between plastid, chloroplast and mitochondira?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Plastid is a general term for an organelle which consists of Chloroplasts, Chromoplasts, Leukoplasts/Amyloplasts and Apicoplasts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chloroplasts (&lt;em&gt;Chloro = green&lt;/em&gt;) are involved in photosynthesis; they express Chlorophylls and have the thylakoid structures which are involved in the electron transport chain that results in ATP formation during the light reactions of photosynthesis. As it is obvious chloroplasts are found in the green parts of the plants such as leaves. Chloroplasts also have the enzymes of biosynthetic pathways involved in carbon fixation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chromoplasts (&lt;em&gt;Chromo = colored&lt;/em&gt;) express more of other pigments and less of chlorophyll. Neither do they have thylakoid structures. Therefore they are not involved in photosynthesis. When fruits ripen, the chloroplasts differentiate to chromoplasts. Flowers also contain a lot of chromoplasts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Leukoplasts (&lt;em&gt;Leuko = white&lt;/em&gt;) do not have any pigments and usually carry out biosynthetic processes. When they store starch they are called amyloplasts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apicoplasts are found in parasites like plasmodia (causes malaria) and are vital for their survival. The Apicoplast is involved in biosynthetic pathways but the precise importance of it remains unknown.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mitochondrion is a very different organelle and has a different evolutionary origin. Mitochondria, like Chloroplasts, produce ATP from an electron transport chain but use chemical substrates (NADH, flavin etc) rather than light as a source of initial energy. Mitochondria are thought to be an outcome of an endosymbiosis between an ancestral eukaryotic cell and an $\alpha$-proteobacterium. Chloroplasts, on the other hand have descended from a Cyanobacterial endosymbiont. Therefore the structure of mitochondria is very different from that of chloroplasts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chromoplasts, leukoplasts, amyloplasts and apicoplasts have lost the photosynthetic ability. Similarly, there are variants of mitochondria which use different electron acceptors (other than oxygen) and some are just incapable of ATP synthesis. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Are there any plant sequence database for each of them (plastid,&#xA;  chloroplast and mitochondira)?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Chloroplast genome database: &lt;a href=&quot;http://chloroplast.cbio.psu.edu/&quot;&gt;{link}&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know of a separate plant mitochondrial database but you can see this resource called &lt;a href=&quot;http://nar.oxfordjournals.org/content/27/1/128.full&quot;&gt;MitBASE&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NCBI also has the organellar DNA sequences. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Can we separate as chloroplast, mitochondria, platid sequence from&#xA;  whole genome assembly?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Usually the organellar genomes will assemble as separate contigs when you sequence from the whole cell DNA prep. By homology it is possible to say if the contig is a mitochondrial or chloroplast DNA. But the best way would be to experimentally isolate the organelles and sequence their DNA. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-03-28T12:55:52.527" LastActivityDate="2014-03-28T12:55:52.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16169" PostTypeId="2" ParentId="16146" CreationDate="2014-03-28T13:06:21.220" Score="5" Body="&lt;p&gt;The first thing to note is that nothing is truly new, everything is a slightly different version of what existed previously, it's only on the very long term that you can see major change. Mutations occur continuously and new variants arise often. For example you need a new flu shot every year due to the &lt;a href=&quot;http://jvi.asm.org/content/80/7/3675.full&quot; rel=&quot;noreferrer&quot;&gt;high mutation rate of the influenza virus&lt;/a&gt; but we still call it flu because it's only a little different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While disease causing organisms evolve at a relatively slow rate new diseases can appear suddenly when the effect on humans suddenly changes; the most obvious example of which is when a disease changes host species. For example the sudden appearance of HIV when Simian immunodeficiency virus (SIV) &quot;jumped species&quot; to infect human, most likely through &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367631/&quot; rel=&quot;noreferrer&quot;&gt;the consumption and processing of Primate meat&lt;/a&gt;. While HIV appears new it is again ancient in the sense that it has caused a similar condition to HIV/AIDS in many African non-human primates for a significant period.&lt;/p&gt;&#xA;" OwnerUserId="6151" LastActivityDate="2014-03-28T13:06:21.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16170" PostTypeId="1" CreationDate="2014-03-28T15:07:38.230" Score="5" ViewCount="159" Body="&lt;p&gt;What's the most likely mouse species Robert Burns is referring to in his poem &quot;To a Mouse, on Turning Her Up in Her Nest with the Plough&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Burns farmed near Ayr, which is on the Firth of Clyde in Scotland. So the mouse of his poem would have to live in that area in the late 18th century. The creature obviously was living in an open field in December in a nest made of &quot;leaves an' stibble [stubble]&quot;. From the poem's title it appears like the nest was constructed underground. &quot;Sleekit&quot; refers to sleek coated as in shiny fur. A clue to the mouse's diet is given by &quot;A daimen icker in a thrave&quot;, ie grain. According to Wikipedia: &quot;Scotland has no population of the Edible or Hazel Dormouse, or of the Yellow-necked Mouse, and the Harvest Mouse's range is limited to the southern part of the country.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The poem is here: &lt;a href=&quot;http://en.wikipedia.org/wiki/To_a_Mouse&quot;&gt;http://en.wikipedia.org/wiki/To_a_Mouse&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6189" LastEditorUserId="6189" LastEditDate="2014-03-28T16:52:25.477" LastActivityDate="2014-07-29T11:15:47.813" Title="Burns' &quot;To a mouse&quot; - what species of mouse?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16172" PostTypeId="1" CreationDate="2014-03-28T17:54:57.323" Score="1" ViewCount="39" Body="&lt;p&gt;I'm looking to extract DNA for sequencing from FFPE (Formalin fixed paraffin-embedded) tissue samples. I'd like to use a commercial kit that provides a high yield of good quality DNA.&lt;/p&gt;&#xA;" OwnerUserId="6191" LastActivityDate="2014-03-28T17:54:57.323" Title="Which kit provides the highest yield and purity of extracted DNA from FFPE tissue samples?" Tags="&lt;biotechnology&gt;&lt;dna-isolation&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16175" PostTypeId="1" AcceptedAnswerId="16925" CreationDate="2014-03-28T20:38:22.127" Score="0" ViewCount="408" Body="&lt;p&gt;I have palpated many hard organs during my work and studies.&#xA;I have seen many young and old people who have hard organs, like very hard shoulder - very common.&#xA;I have interviewed some of them, some points&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;only one type of weight lifting&lt;/li&gt;&#xA;&lt;li&gt;no running&lt;/li&gt;&#xA;&lt;li&gt;no stretching&lt;/li&gt;&#xA;&lt;li&gt;no stretching before training&lt;/li&gt;&#xA;&lt;li&gt;no stretching after training &lt;/li&gt;&#xA;&lt;li&gt;not age dependent only - very old can be healthy&lt;/li&gt;&#xA;&lt;li&gt;dynamical movement dependent&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are two mechanisms of fibrinous inflammation&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;trigger the release of fibrinogen &lt;/li&gt;&#xA;&lt;li&gt;trigger release of fibrinogen-to-fibrin reaction&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which both result in the production fibrin in the interstitium:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ypduv.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The area may also be mixed with serous so two variations of fibrinous inflammation&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;serofibrinous&lt;/li&gt;&#xA;&lt;li&gt;fibrinous.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am interested in the mechanism that leads to this hard tissue throughout the organ.&#xA;This raised to me an idea about Fibrinous inflammation in the shoulder.&#xA;Robbins say that if the exudate cannot be sucked out, it leads to scarring.&#xA;I think this is what is making the organ feel hard.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the pathogenesis in such monotonous movements without stretching?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-04-27T16:14:15.867" LastActivityDate="2014-04-27T16:14:15.867" Title="Fibrinous inflammation, exudate and scarring in monotonous movements and ageing" Tags="&lt;physiology&gt;&lt;senescence&gt;&lt;pathogenesis&gt;&lt;adaptation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16176" PostTypeId="1" CreationDate="2014-03-28T21:17:22.717" Score="1" ViewCount="123" Body="&lt;p&gt;I am not a biologist, but I have always wondered why my body hasn't learnt to deal with the HSV-1 virus. I understand it reamins dormant for a while and things like stress or the common cold can trigger it. I get cold sores about twice to even four times a year and I have had them since being quite young.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why hasn't my immune system learnt to recognise it and eliminate it?&lt;/p&gt;&#xA;" OwnerDisplayName="user6193" LastActivityDate="2014-03-30T21:33:25.800" Title="Why can't my body deal with cold-sores" Tags="&lt;virus&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16177" PostTypeId="2" ParentId="16163" CreationDate="2014-03-28T22:06:50.487" Score="1" Body="&lt;p&gt;Opinion:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the Jackson laboratory&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jaxmice.jax.org/&quot; rel=&quot;nofollow&quot;&gt;http://jaxmice.jax.org/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the industry leader in transgenic mouse production. Their list of mouse strains is almost a db in itself but currently no db exists that I'm aware of. I take it your looking for something similar to what's available for c elegans:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.celeganskoconsortium.omrf.org/&quot; rel=&quot;nofollow&quot;&gt;http://www.celeganskoconsortium.omrf.org/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-03-29T21:02:05.120" LastActivityDate="2014-03-29T21:02:05.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16178" PostTypeId="2" ParentId="16144" CreationDate="2014-03-28T22:19:17.793" Score="0" Body="&lt;p&gt;Treat with RNAse and spec at 260.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A spec can definitely be used. The extinction coefficient (Beers Lamberts Law) will not  be calculating measuring  NTPs, just intact dsDNA.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-03-28T22:19:17.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16179" PostTypeId="1" CreationDate="2014-03-28T22:20:54.980" Score="3" ViewCount="2742" Body="&lt;p&gt;I would like to grow E coli cells on cellophane on top of LB plate, and then grow yeast cells on the same LB plate. Does (or how well) yeast grow on LB plates? Is there a composition media that can be good for both E. coli and yeast? Has anyone done this experiment?&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2014-03-29T22:00:04.020" Title="Does yeast grow on LB agar plates?" Tags="&lt;yeast&gt;&lt;growth-media&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16180" PostTypeId="1" AcceptedAnswerId="20060" CreationDate="2014-03-28T22:29:29.963" Score="10" ViewCount="2643" Body="&lt;p&gt;What is the E coli transformation efficiency for 2 plasmids? Are any studies that have looked at the correlation between number of plasmids transformed and transformation efficiency? Is there a commercial E coli strain that is better at co-transformation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, electroporation with single plasmid yields around 1 × 10^10 cfu/μg. I would like to know what is the limit for co-transformation and whether it can be or has been improved.&lt;/p&gt;&#xA;" OwnerUserId="28" LastEditorUserId="28" LastEditDate="2014-07-29T19:12:01.883" LastActivityDate="2014-07-29T20:25:54.867" Title="E coli cotransformation efficiency" Tags="&lt;transformation&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16181" PostTypeId="1" AcceptedAnswerId="16188" CreationDate="2014-03-28T23:47:51.167" Score="4" ViewCount="424" Body="&lt;p&gt;This may be anecdotal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the pharmacy earlier, the prescription called for a drug with X mg of the target chemical. The pharmacy however only had stock of a higher potency of the same brand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.g. A prescription may call for 25mg of a particular chemical, whereas the pharmacy could only service a request for 50mg of that chemical in the &lt;strong&gt;same brand&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;According to the pharmacist, and the medic - a proportional fraction of higher potency drug of the same brand may be substituted for the lower potency. Thus in the example above, half-a-tablet of 50mg may serve in lieu of a single tablet of 25mg.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a given brand &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Is half-a-tablet of X a substitute for a full tablet of X/2? &lt;/li&gt;&#xA;&lt;li&gt;Does the corollary scale upwards too?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1005" LastActivityDate="2014-03-29T08:09:55.957" Title="Is half-a-tablet of X a substitute for a tablet of X/2?" Tags="&lt;pharmacology&gt;&lt;medicine&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16182" PostTypeId="2" ParentId="16181" CreationDate="2014-03-29T00:48:21.197" Score="3" Body="&lt;p&gt;This &lt;a href=&quot;http://www.webmd.com/healthy-aging/guide-to-pill-splitting&quot; rel=&quot;nofollow&quot;&gt;website&lt;/a&gt; gives a nice overview, including how the FDA approve drugs that they expect will be spit and some practical issues of pill cutting. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, half a tablet of (2x dose) is, absent other issues, equivalent to one intact tablet of (1x) dose.  The main exceptions are practical ones.. where the tablet cannot easily be cut; where the dosing is so specific that slight variations of dose (uneven tablet fragments) matter, or where the dose is in a capsule or has some special coating so that cleavage might alter the release of drug into the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, dosing scales upwards.  Two pills give twice the total dose of one pill.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All prescriptions are dispensed with specific dosing regimens (i.e how much you take and when you take them) to ensure the drug reaches effective concentrations in the body. You should not try to 'boost' the drugs effectiveness by taking &lt;em&gt;more drug&lt;/em&gt;, or taking &lt;em&gt;drug more frequently&lt;/em&gt; than your physician has prescribed.  As noted in the weblink above, it can be tricky to keep track of dosing and timing if your pill bottle contains whole and cut pills.  (i.e what does &quot;take one pill every NN hours&quot; mean ?). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is &lt;strong&gt;NOT MEDICAL ADVICE&lt;/strong&gt; . Always consult your physician and/or pharmacist for your particular case. &lt;/p&gt;&#xA;" OwnerUserId="5922" LastEditorUserId="5922" LastEditDate="2014-03-29T02:46:56.817" LastActivityDate="2014-03-29T02:46:56.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16183" PostTypeId="1" CreationDate="2014-03-29T01:06:13.880" Score="1" ViewCount="45" Body="&lt;p&gt;What if cellular growth and repair is 'forced' to occur repeatedly in a region where it wouldn't normally happen , if the biological area was 'healthier'. Could this more aggressive cellular growth and repair cause any apoptosis mechanisms to shut down permanently?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastActivityDate="2014-03-29T20:46:09.850" Title="Concerning Apoptosis" Tags="&lt;cancer&gt;&lt;apoptosis&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16184" PostTypeId="2" ParentId="16176" CreationDate="2014-03-29T01:40:33.250" Score="3" Body="&lt;p&gt;HSV-1 has evolved mechanisms to thwart the &lt;a href=&quot;http://en.wikipedia.org/wiki/Herpesviridae#Immune_system_evasions&quot; rel=&quot;nofollow&quot;&gt;immune system's surveillance&lt;/a&gt;.  A number of genes in the viruses genetic material code for proteins that can &lt;a href=&quot;http://www.bio.davidson.edu/people/sosarafova/assets/bio307/jehodge/page05.html&quot; rel=&quot;nofollow&quot;&gt;disrupt the process by which a cell alerts the immune system that it has a foreign virus within in it&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For technical readers, the reasons are described in the links above in detail. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the non-biologist....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;PART ONE&lt;/strong&gt;  As you note in the question, HSV-1 can remain dormant in an infected cells for a long time.  In general, there is nothing for the immune system to respond to at this time.  So the infection persists in a dormant state.  Whats more, when it spreads, it can &lt;a href=&quot;http://pathmicro.med.sc.edu/virol/herpes.htm&quot; rel=&quot;nofollow&quot;&gt;spread between cells, without entering the bloodstream&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;PART TWO&lt;/strong&gt; If the virus re-activates. In order for cells of the immune system to recognize and destroy a cell infected with a virus, the infected cell first chops up bits of the virus that are inside the cell and transfers these pieces (called antigens) to the outside of the cell so they may be &lt;em&gt;presented&lt;/em&gt;  to immune system cells. At the same time, the infected cell attracts and activates immune system cells using 'distress' molecules.    However, HSV carries genes that make proteins that can thwart the presentation of antigens by a cell as well inhibiting the distress molecules that help activate an immune response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;PART THREE&lt;/strong&gt;  What about antibodies ?  During the body's response to an HSV infection, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2650866/&quot; rel=&quot;nofollow&quot;&gt;antibodies can be produced and persist&lt;/a&gt;.  In many infectious diseases, antibodies can be protective as they mop-up any circulating virus and may prevent re-infection.  However, since HSV is already present inside cells, antibodies may have little effect in the reducing the amount of virus-infected cells in the body and may not prevent flare-ups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Paradoxically, some of the symptoms of HSV flare-ups are due to the immune system's response!  &lt;em&gt;(looking for a good reference)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The good news is that &lt;a href=&quot;http://www.webmd.com/skin-problems-and-treatments/understanding-cold-sores-treatment&quot; rel=&quot;nofollow&quot;&gt;drug options to treat HSV have improved&lt;/a&gt;.   &lt;/p&gt;&#xA;" OwnerUserId="5922" LastEditorUserId="5922" LastEditDate="2014-03-30T21:33:25.800" LastActivityDate="2014-03-30T21:33:25.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16185" PostTypeId="2" ParentId="16183" CreationDate="2014-03-29T02:24:25.913" Score="1" Body="&lt;p&gt;One long standing hypothesis of cancer formation is that it originates in a 'wound that never heals'.  I was about to add that there is little hard evidence for wounding as a significant cause of cancers but Google found this fascinating report on &lt;a href=&quot;https://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=58&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CFwQFjAHODI&amp;amp;url=http%3A%2F%2Fwww.ajol.info%2Findex.php%2Fnhj%2Farticle%2Fdownload%2F90533%2F79951&amp;amp;ei=qis2U5T-Ee_fsASqpYLoCQ&amp;amp;usg=AFQjCNEZq8gnYgP-wEM7emhqVm_2lld_pQ&amp;amp;sig2=VX3fN7VS5UjWZyxH7vpcfA&quot; rel=&quot;nofollow&quot;&gt;Marjolin's Ulcers&lt;/a&gt;&#xA; which I had never heard of.   Whether it was the wound or a comorbid virus or something else.....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may also want to search the current thinking of how a chemically inert 'irritant' - an asbestos fibre - &lt;a href=&quot;https://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=58&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CFwQFjAHODI&amp;amp;url=http%3A%2F%2Fwww.ajol.info%2Findex.php%2Fnhj%2Farticle%2Fdownload%2F90533%2F79951&amp;amp;ei=qis2U5T-Ee_fsASqpYLoCQ&amp;amp;usg=AFQjCNEZq8gnYgP-wEM7emhqVm_2lld_pQ&amp;amp;sig2=VX3fN7VS5UjWZyxH7vpcfA&quot; rel=&quot;nofollow&quot;&gt;can cause mesothelioma&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="5922" LastActivityDate="2014-03-29T02:24:25.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16186" PostTypeId="1" AcceptedAnswerId="16187" CreationDate="2014-03-29T02:41:27.960" Score="1" ViewCount="793" Body="&lt;p&gt;Frequently I have experienced sore joints during a bad bout of influenza. I understand that during time of sickness, white blood cells are deployed in the blood stream. I also believe that white blood cells originate or relate to bone marrow. I'm wondering if there is a relationship between each of these&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: &lt;strong&gt;What is the biological reason that some viruses cause sore joints (eg flu)?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5417" LastActivityDate="2014-03-29T03:09:52.860" Title="What is the biological reason that some viruses cause sore joints (eg flu)?" Tags="&lt;virus&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16187" PostTypeId="2" ParentId="16186" CreationDate="2014-03-29T03:09:52.860" Score="4" Body="&lt;p&gt;Almost certainly what is causing the joint pain isn't the virus, but rather its the body's response to the infection.   Cells that are infected with viruses can release proteins called &lt;strong&gt;interferons&lt;/strong&gt;. Interferons can act on surrounding cells and cause them to become less susceptible to viral infection.  Other cells, including your immune cells respond to a virus by releasing other proteins into the blood called &lt;strong&gt;cytokines&lt;/strong&gt;.  Cytokines activate other immune cells and can stimulate the body to generate a fever and 'lock up' molecules of iron so they are not available to invading bacteria.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some cytokines act on the bone marrow and cause the pool of 'reserve' neutrophils (a type of white blood cell) to move into the bloodstream.  Other cytokines shut down the lymphatic vessels, causing lymph nodes to swell up.   And other molecules such as &lt;strong&gt;histamine&lt;/strong&gt; and &lt;strong&gt;prostaglandins&lt;/strong&gt; are released and also play a role.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;SO what you are feeling when you get ill from a virus (or a bacteria or parasite) is the effect of this 'soup' of cytokines, interferons and other 'mediators'.  You may have some combination of fever, muscle/joint pain, runny nose, malaise, fatigue etc.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the US you'll see TV adverts for drugs used to treat Rheumatoid Arthritis.  These drugs include synthetic proteins that bind to a cytokine called TNF-alpha and  block its role in inflammation.  &lt;/p&gt;&#xA;" OwnerUserId="5922" LastActivityDate="2014-03-29T03:09:52.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16188" PostTypeId="2" ParentId="16181" CreationDate="2014-03-29T07:53:57.993" Score="3" Body="&lt;p&gt;&lt;em&gt;Disclaimer: all of this is not to be considered medical advice but rather a general explanation. You should talk with your physician and/or pharmacist on a case by case basis when determining whether to take a drug and how to dose it.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;We should consider that most pharmaceutical forms are made up from two main components: the active ingredient(s) and the excipients.&lt;/p&gt;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Active_ingredient&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;active pharmaceutical ingredient&lt;/strong&gt;&lt;/a&gt; is:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;the substance in a pharmaceutical drug or a pesticide that is biologically active.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;That is, the part of the drug that actually &amp;quot;does the job&amp;quot;. Note that the dosage on the package refer to this, not the weight of the pill! For instance 500mg aspirin will contain 500mg of the active principle (acetylsalicylic acid) but the pill itself will weight more than 500mg.&lt;/p&gt;&#xA;&lt;p&gt;An &lt;a href=&quot;http://en.wikipedia.org/wiki/Excipient&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;excipient&lt;/strong&gt;&lt;/a&gt; is:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;an inactive substance formulated alongside the active ingredient (&amp;quot;API&amp;quot;) of a medication, for the purpose of bulking-up formulations that contain potent active ingredients (thus often referred to as &amp;quot;bulking agents,&amp;quot; &amp;quot;fillers,&amp;quot; or &amp;quot;diluents&amp;quot;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This does not normally have biological effects, but allows you, for instance, to have a pill that is of sufficient size to be easy to take in your hand.&lt;/p&gt;&#xA;&lt;p&gt;When you split a pill in half &lt;strong&gt;you are assuming that each half contains the same amount of active ingredient&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;p&gt;This is regulated by the Pharmacopoeia*. In particular when looking at the &lt;a href=&quot;http://apps.who.int/phint/en/d/Jb.6.2.1.7/#docfirsthighlight&quot; rel=&quot;nofollow noreferrer&quot;&gt;monograph for tablets&lt;/a&gt; we can read (bold is mine):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Tablets are solid dosage forms usually obtained by single or multiple compression of powders or granules. In certain cases tablets may be obtained by moulding or extrusion techniques. They are uncoated or coated.&lt;/p&gt;&#xA;&lt;p&gt;Tablets are normally right circular solid cylinders, the end surfaces of which are flat or convex and the edges of which may be bevelled. &lt;strong&gt;They may have lines or break-marks&lt;/strong&gt; (scoring), symbols or other markings.&lt;/p&gt;&#xA;&lt;p&gt;If the break-mark(s) is/are intended to facilitate breaking the tablet for ease of swallowing a dose consisting of one or more whole tablets, the scoring is not critical. However, &lt;strong&gt;if the break-mark(s) is/are intended to permit accurate subdivision of the tablet in order to provide doses of less than one tablet, the scoring is critical. Tablets containing active ingredients having a narrow therapeutic window should generally not be presented with break-marks for subdivision.&lt;/strong&gt; Non-functional break-marks should be avoided.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The point about the &lt;a href=&quot;http://en.wikipedia.org/wiki/Therapeutic_window&quot; rel=&quot;nofollow noreferrer&quot;&gt;therapeutic window&lt;/a&gt; shows why splitting pills may be dangerous. The therapeutic window is the range of concentration of a drug which treats disease whilst staying within the safety range.&lt;/p&gt;&#xA;&lt;p&gt;If this window is narrow, minimal changes in the dose can cause the treatment to be ineffective -if there is too few of the active ingredient- or toxic -if there is too much.&lt;/p&gt;&#xA;&lt;p&gt;The Pharmacopoeia also lists several tests to be done on tablets. In particular, in the presence of break-marks, the manufacturer should&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;ensure the effectiveness of break-marks with respect to the uniformity of mass or content, as appropriate, of the subdivided parts so that the patient receives the intended dose.&lt;/p&gt;&#xA;&lt;p&gt;A suitable test to assess the uniformity of mass during development is as follows:&lt;/p&gt;&#xA;&lt;p&gt;Take 30 tablets at random. Break each tablet by hand and take one part for the test and reject the other part(s). Weigh each of the 30 parts thus obtained and calculate the average mass. No individual mass is outside the limits of 75% to 125% and not more than one individual mass is outside the limits of 85% to 115% of the average mass.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I will not go into further details, but there are, for instance, other tests to be done to ensure uniformity of mass and content from tablet to tablet, as well as their physical stability (i.e.: they don't have to fall apart in the box).&lt;/p&gt;&#xA;&lt;p&gt;Note that the packaging should generally include instructions about whether it is safe to split the tablet and how to store (and how long) unused pieces.&lt;/p&gt;&#xA;&lt;p&gt;This is for splitting tablets. The opposite situation may also arise. Are 2x2mg tablets equivalent to 1x4mg one (speaking of weigth of the active compound in the tablet, not the weight of the tablet itself)? The same reasonings as above apply, however, because tablets should be uniform and no breaking is involved, this is generally safer than the previous case.&lt;/p&gt;&#xA;&lt;p&gt;All of this applied to a single dose of a drug. Now I would just add a word about repeated doses. I cannot stress this enough: always refer to your physician about drug dosing. Taking a pill in the morning and one in the evening is NOT the same thing as taking two in the morning and none in the evening or taking four halves during the day. Self-dosing &lt;strong&gt;is dangerous and should never be done&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Taking half the dose may result in sub-optimal concentration of the drug (so it won't work as expected). Taking twice the dose may result in a toxic peak concentration, which is obviously not something that you want.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;sub&gt;* note that there are multiple Pharmacopoeias, and the exact directives may vary. For simplicity I will refer to the &lt;a href=&quot;http://apps.who.int/phint/en/p/docf/&quot; rel=&quot;nofollow noreferrer&quot;&gt;International Pharmacopoeia, 4th Edition, 3rd supplement&lt;/a&gt;, published by the World Health Organization, and available online. There are others, such as the &lt;a href=&quot;https://www.edqm.eu/en/european-pharmacopoeia-8th-edition-1563.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;European Pharmacopoeia&lt;/a&gt; (apparently not freely available?) or the &lt;a href=&quot;http://www.pmda.go.jp/english/pharmacopoeia/online.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Japanese Pharmacopoeia&lt;/a&gt;, but I guess that goes beyond the scope of this answer.&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-03-29T08:09:55.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16189" PostTypeId="1" CreationDate="2014-03-29T08:12:53.297" Score="3" ViewCount="233" Body="&lt;p&gt;I having trouble understanding the equation of the cellular respiration. The thing that bothers me is the number of $\ce{H_2O}$ molecules. Generally, cellular respiration is written thus :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\ce{C_6H_{12}O_6 + 6O_2 + 6H_2O -&amp;gt; 6CO_2 + 12H_2O}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet studying the reaction on a molecular level, I realized that the water molecules just don't add up to be six! (on the left side) What I obtained from my textbook and Wikipedia is that (per 1 glucose molecule)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;(Glycolysis) (in the reaction that 2-Phosphoglycerate(2PG) forms Phosphoenolpyruvate(PEP)) 2 molecules of $\ce{H_2O}$ are out of the reaction &lt;/li&gt;&#xA;&lt;li&gt;(TCA cycle) (in the reaction that combines Oxaloacetate and Acetyl-CoA to form Citrate) 2 molecules of $\ce{H_2O}$ are into the reaction&lt;/li&gt;&#xA;&lt;li&gt;(TCA cycle) (in the reaction that Citrate form Cis-Aconitate) 2 molecules of $\ce{H_2O}$ are out of the reaction &lt;/li&gt;&#xA;&lt;li&gt;(TCA cycle) (in the reaction that Cis-Aconitate form D-Isocitrate) 2 molecules of $\ce{H_2O}$ are into the reaction &lt;/li&gt;&#xA;&lt;li&gt;(TCA cycle) (in the reaction from Fumarate to Malate) 2 molecules of $\ce{H_2O}$ are into the reaction &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;These sums up to a net of (only) 2 molecules of $\ce{H_2O}$ into the process of glycolysis and TCA cycle... additional 6 molecules of $\ce{H_2O}$ comes from oxidative phosphorylation. Then, where can the remaining 4 molecules of $\ce{H_2O}$ possibly be?&lt;/p&gt;&#xA;" OwnerUserId="6196" LastEditorUserId="16985" LastEditDate="2016-07-25T20:19:36.777" LastActivityDate="2016-07-25T20:19:41.947" Title="Missing 4 $\ce{H_2O}$ (per glucose) in Cellular Respiration... Where can they be?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;physiology&gt;&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16190" PostTypeId="2" ParentId="16085" CreationDate="2014-03-29T08:58:21.047" Score="0" Body="&lt;p&gt;I don't know much about the field of conservation but I'm giving a try...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the following, when I say conservation I mean: &quot;Human decisions and actions in order to protect the ecosystems&quot;. It has not to be confused with the science of conservation biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that the question you're raising shows the paradox of conservation. The maintenance of Biodiversity occurs through a dynamic process of speciations and extinctions allowed thanks to mutations, selection, population structure and movements. Standard ideas of conservation is not to preserve these processes but to prevent extinctions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quite a lot of many in conservation is aimed to save some big and representative species. Species for which we, as humans, feel some tenderness, love and pity for their fate. I am not saying it is bad to protect this kind of species I just want to emphasize that if we conserve it is not only for economic issues (or for the survival of our species) but also because we have ethics,  because we feel compassion  and guiltiness with nature of with some species such as the panda, the deers, the lynx, the wolves or because we feel compassion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also think that our categorization of living things into species (which is quite an subjective categorization) might bring us to take some decisions that do not fit economic issues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For those who speak french well enough, &lt;a href=&quot;http://podcast.unil.ch/#&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; is a serie of podcasts (follow: &quot;La biodiversité - plus qu'une simple question de conservation/&quot;) that might interest you. Especially the one given by Pierre-Henry Gouyon, which pretty much explain (much better than I did) most of the ideas of the last two paragraphs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question of invasive species is particularly interesting I think because there are especially a lot of invasive species today, first because ecosystems of changing (mostly because of human's activities) but also because human means of transport allow species to travel very far and become invasive. I assume (although I have no reference!) that the current number of invasive species is particularly high and just like any other disturbance in ecosystem, we can hardly predict what will the consequences. So shouldn't we make sure to keep this number of invasive species to a level which is closer to what would be found in nature in absence of human?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-03-29T08:58:21.047" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16191" PostTypeId="1" AcceptedAnswerId="16193" CreationDate="2014-03-29T11:53:25.493" Score="3" ViewCount="200" Body="&lt;p&gt;Inspired by &lt;a href=&quot;https://biology.stackexchange.com/questions/16181/is-half-a-tablet-of-x-a-substitute-for-a-tablet-of-x-2&quot;&gt;this&lt;/a&gt; question, I want to ask a question about centrifugation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose a protocol says : 10 min at 2500 rpm . Can we instead centifuge for 5 min at 5000 rpm or 20 min at 1250 rpm ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-03-29T12:39:01.087" Title="Changing time and rpm of centifuge" Tags="&lt;lab-techniques&gt;&lt;protocol&gt;&lt;centrifugation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16192" PostTypeId="1" AcceptedAnswerId="16194" CreationDate="2014-03-29T12:11:46.913" Score="3" ViewCount="491" Body="&lt;p&gt;From &lt;a href=&quot;http://www.pnas.org/content/74/11/4937.full.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The reaction was terminated and the histones, and most nonhistones,&#xA;  were removed by adding the nuclease-treated chromosomes to a solution&#xA;  containing dextran sulfate (2 mg/ml) (Pharmacia), heparin (0.2 mg/ml)&#xA;  (Sigma), 10 mM Tris (pH 9.0), 10 mM EDTA, 0.1% Nonidet P40, and 1 mM&#xA;  phenylmethylsulfonyl fluoride (PMSF) at a ratio of 1 volume of&#xA;  chromosomes to 3 volumes of solution.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What is the function of  dextran sulfate and heparin in removing the proteins ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-03-29T12:51:38.570" Title="Function of heparin and dextran sulfate for removing proteins" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;protocol&gt;&lt;protein-binding&gt;&lt;histone&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16193" PostTypeId="2" ParentId="16191" CreationDate="2014-03-29T12:39:01.087" Score="5" Body="&lt;p&gt;No, it isn't that simple, because centrifugal force varies with the square of the rotor speed. Have a look at the Wikipedia page for &lt;a href=&quot;http://en.wikipedia.org/wiki/Clearing_factor&quot;&gt;clearing factor&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Those equations are usually used to determine what you need to do if you are going to use a different rotor, but they can also be used to solve your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because you are looking at a situation where the same particles are being centrifuged, the sedimentation coefficient &lt;em&gt;s&lt;/em&gt; is the same in both centrifuge runs. Also all of the factors relating to the rotor properties are the same (r&lt;sub&gt;max&lt;/sub&gt; etc.). So, if you have a set of conditions that work, t&lt;sub&gt;1&lt;/sub&gt; and RPM&lt;sub&gt;1&lt;/sub&gt;, and you want to choose new conditions t&lt;sub&gt;2&lt;/sub&gt; and RPM&lt;sub&gt;2&lt;/sub&gt;, you can use the equation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RPM&lt;sub&gt;2&lt;/sub&gt; = SQRT(t&lt;sub&gt;1&lt;/sub&gt;/t&lt;sub&gt;2&lt;/sub&gt;) x RPM&lt;sub&gt;1&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the example you mention t&lt;sub&gt;1&lt;/sub&gt; = 10 min and RPM&lt;sub&gt;1&lt;/sub&gt; = 2500 rpm. If you change the time to 5 min:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RPM&lt;sub&gt;2&lt;/sub&gt; = SQRT(10/5) x 2500 = 3536 rpm&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the centrifugal force varies with the square of the rotor speed you don't need to double the speed if you halve the time. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-29T12:39:01.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16194" PostTypeId="2" ParentId="16192" CreationDate="2014-03-29T12:51:38.570" Score="5" Body="&lt;p&gt;See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6500254&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Histones are basic proteins (cationic, high pI) because they are required to interact with polyanionic DNA at physiological pH. Heparin and dextran are polyanions which form insoluble salts with the cationic histones.(Dextran is a polymer of glucose. In dextran sulphate it is derivatised with sulphonate groups creating a polyanionic material.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Immobilised heparin is sometimes used as an affinity matrix for purification of DNA-binding proteins like transcription factors.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-29T12:51:38.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16195" PostTypeId="1" CreationDate="2014-03-29T13:57:52.097" Score="1" ViewCount="80" Body="&lt;p&gt;I remember reading that scientist were making cells (I assume bacteria), that used differently oriented proteins to create a whole new class of life. Because apparently right and left aligned proteins don't interact in same way, cells made in such manner would behave similarly but couldn't be interacted with differently aligned bacteria/virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However I can't find any proof this story was true? I could be wrong about details. Is there a similar mechanism that would allow a whole case of twin (contain DNA, and most molecules that regular cells posses) cells that couldn't interact with existing bacteria?&lt;/p&gt;&#xA;" OwnerUserId="6197" LastActivityDate="2019-01-07T15:12:34.300" Title="Cells created using differently aligned proteins" Tags="&lt;biochemistry&gt;&lt;microbiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16196" PostTypeId="1" AcceptedAnswerId="16205" CreationDate="2014-03-29T15:35:11.020" Score="0" ViewCount="149" Body="&lt;p&gt;Suppose a specific gene has two possible alleles. In a given population all members have only the dominant one. By a mutation on member receives the first recessive allele of that population. Is it possible that one day the descendants of this population have this allele manifested? I think it's very unlikely that this allele survive until another similar mutation occurs and they get manifested in the phenotype.&lt;/p&gt;&#xA;" OwnerUserId="1395" LastEditorUserId="3632" LastEditDate="2014-03-29T16:18:50.983" LastActivityDate="2014-03-30T15:40:11.433" Title="How can a recessive allele propagate until they manifest?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;allele&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16197" PostTypeId="1" AcceptedAnswerId="16230" CreationDate="2014-03-29T16:07:24.177" Score="0" ViewCount="101" Body="&lt;p&gt;Here is the original slide:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://dl.dropboxusercontent.com/u/62073194/Screen%20Shot%202014-03-30%20at%2015.42.20.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking about the &quot;cord factor&quot; sentence in a more general case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume you inhibit Leucocytes migration.&#xA;&lt;strong&gt;How does this lead to accumulation of macrophages in the site of infection?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="5144" LastEditDate="2017-03-13T15:21:27.727" LastActivityDate="2017-03-13T15:21:27.727" Title="Can inhibition of lymphocytes migration be a direct cause of chronic inflammation?" Tags="&lt;microbiology&gt;&lt;pathogenesis&gt;&lt;inflammation&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16198" PostTypeId="1" AcceptedAnswerId="16200" CreationDate="2014-03-29T18:14:59.477" Score="4" ViewCount="988" Body="&lt;p&gt;Membranes are specifically designed by lipids to maintain internal hydrophilic environment in narrow range.There are hydrophobic amino acids among naturally occurring 20 amino acids and as well as there are also number of water insoluble polysaccharides like cellulose. These hydrophobic and water insoluble materials can also be used to build membranes but why not? Why lipids are only choice?&lt;/p&gt;&#xA;" OwnerUserId="5729" LastActivityDate="2014-03-30T09:23:20.333" Title="Significance of lipids in biological membranes...?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16199" PostTypeId="1" CreationDate="2014-03-29T19:44:05.623" Score="4" ViewCount="1846" Body="&lt;p&gt;The hazards of congenital insensitivity to pain (CIP) are well-known. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question is about the obverse: what selective advantage, if any, does the normal sensation of pain confer? I'm thinking of severe pain such as that associated with back injury, burns, and some intestinal problems in which the pain seems to serve no function other than to incapacitate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A related question is whether there is a spectrum of sensitivity to pain, ranging from CIP to heightened sensitivity, what the distribution looks like, and whether this is a genetically plastic trait (like color perception)? If the distribution were sensitive to selective pressure then naively I would guess it serves our needs well, but we spend a lot of our collective time trying to dial it back, hence my question.    &lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2021-05-20T11:00:25.037" Title="Advantages of pain sensation?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;pain&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16200" PostTypeId="2" ParentId="16198" CreationDate="2014-03-29T20:21:57.630" Score="5" Body="&lt;p&gt;Membranes are built from a specific class of lipids, namely phospholipids, whose key property is that they are amphiphilic and so can self-organise to form bilayers. Not all amphiphiles do this, some prefer to adopt a micellar organisation. A bilayer composed of phospholipids produces the ideal combination of a hydrophobic barrier with a hydrophilic surface.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although there are clearly amino acids with hydrophobic side chains, it is difficult to conceive of a proteinaceous barrier that would reproduce the properties of a phospholipid bilayer since it would not have a continuous hydrophobic phase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cellulose may be insoluble, but is full of polar groups so again would not create a hydrophobic barrier - I'm sure that ions can diffuse through a cellulose structure for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;added later&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;@WYSIWYG raises an excellent point in the comments. &lt;a href=&quot;http://en.wikipedia.org/wiki/Archea#Membranes&quot; rel=&quot;nofollow&quot;&gt;Archeal membranes&lt;/a&gt; are composed of a different class of amphiphile in which the hydrocarbon tails (branched; derived from isoprenoids) are attached to glycerol by an ether linkage. It's instructive to note that the overall design principles are retained however, suggesting that the self-organising properties of these molecules was the key to the &quot;invention&quot; of biological membranes.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-03-30T09:23:20.333" LastActivityDate="2014-03-30T09:23:20.333" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16203" PostTypeId="2" ParentId="16183" CreationDate="2014-03-29T20:46:09.850" Score="1" Body="&lt;p&gt;The definition of a tumor is a population of cells that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Divides out-of-control&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;2.. Does not exhibit apoptosis&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3.. Does not differentiate&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally the two-hit hypothesis states that at least two genes need to be involved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many genes,  predominantly involved in the regulation of the cell cycle, that when their function is disrupted the cell exhibit uncontrolled replication. Attenuated expression or constitutive activation of the genes does not necessarily affect apoptosis. However, and to give you the quick answer – it depends on the gene involved. Some genes are involved both physiologies. Check out the protein AKT.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-03-29T20:46:09.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16204" PostTypeId="2" ParentId="16199" CreationDate="2014-03-29T20:56:19.373" Score="-1" Body="&lt;p&gt;In terms of inflammation, the purpose of pain is to force the organism to rest the area that is inflamed. Thus promoting healing. In terms of chronic pain, this is the same thing. However I think that if the pain will not cease regardless of protection of the affected area, and say if the underlying cause of the pain is ultimately fatal, then the pain is subordinate. The phenotype is already being selected out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the concept shows a lot of parallel to the underlying concept of hypersensitivity (allergy).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remember that over generations as all different things that can cause and prevent pain in our bodies are evolving, So too is the pain mechanism itself evolving.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2019-05-01T06:33:03.163" LastActivityDate="2019-05-01T06:33:03.163" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="16205" PostTypeId="2" ParentId="16196" CreationDate="2014-03-29T21:59:30.563" Score="3" Body="&lt;p&gt;The short answer is: Because of &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_drift&quot; rel=&quot;nofollow&quot;&gt;genetic drift&lt;/a&gt;. If a mutation does not influence the fitness in heterozygote individuals, then its frequency varies only through genetic drift while it reaches some high enough frequency. If by chance, the frequency of this new allele achieve a high enough level so that the homozygous for this allele given by $x^2$ where $x$ is the frequency of the new allele is high enough to have considerable effect, then the selection coefficient $s$ between the recess if homozygote and the two other genotypes matters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps you. Don't hesitate to ask further more accurate question if you need more details. Or let us know if this does not answer your question.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-03-30T15:40:11.433" LastActivityDate="2014-03-30T15:40:11.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16206" PostTypeId="2" ParentId="16179" CreationDate="2014-03-29T22:00:04.020" Score="3" Body="&lt;p&gt;Not well, they need  dextrose. Use YBT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;20 g Casein Peptone Tpe-M&#xA;10 g Yeast Extract&#xA;20 g Dextrose&#xA;17 g Agar&lt;/p&gt;&#xA;&#xA;&lt;p&gt;q.s. to 975 mls in di-water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;pH to 6.2 w 5M NaOH&lt;/p&gt;&#xA;&#xA;&lt;p&gt;q.s. to 1L with di-water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Autoclave for 45 min at 121C&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aseptically dispense in Petri dishes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Store at 4C for up to 12 weeks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to grow Co-culture do so in LB supplemented with 20g/L Dex.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-03-29T22:00:04.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16207" PostTypeId="1" AcceptedAnswerId="16229" CreationDate="2014-03-29T23:12:53.393" Score="2" ViewCount="225" Body="&lt;p&gt;When you have a stomach virus and it causes extreme bowel movements to the point of almost pure stomach acid, does this kill off the bacteria in our intestinal tracks?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2014-03-30T19:11:55.257" Title="Stomach Virus : How does it affect the bacteria of the intestines?" Tags="&lt;stomach&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16208" PostTypeId="1" AcceptedAnswerId="16209" CreationDate="2014-03-29T23:38:40.400" Score="2" ViewCount="378" Body="&lt;p&gt;I need to make a solution of multiple compounds, one of them is dNTPs. The recipe calls for 20 μl 25 mM dNTPs in a 1250 μL master mix. Unfortunately I do not have it available at that concentration, can I substitute 25mM dNTP mix with 10mM mix? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;TECHNICAL DETAILS&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;$dATP: C_{10}H_{13}N_5O_{12}P_3Na_3 - MW=557.2$    &lt;/li&gt;&#xA;&lt;li&gt;$dCTP: C_9H_{13}N_3O_{13}P_3Na_3 - MW=533.1$    &lt;/li&gt;&#xA;&lt;li&gt;$dGTP: C_{10}H_{13}N_5O_{13}P_3Na_3-MW=573.2$&lt;/li&gt;&#xA;&lt;li&gt;$dTTP: C_{10}H_{14}N_2O_{14}P_3Na_3-MW=548.1$&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Would it be 50μL of 10mM dNTPs to substitute the 20μL of 25mM dNTPs? &lt;/p&gt;&#xA;" OwnerUserId="6082" LastEditorUserId="6" LastEditDate="2014-03-30T09:45:49.013" LastActivityDate="2014-03-30T09:45:49.013" Title="Substitute 25mM dNTPs mix with 10mM dNTPs" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;lab-reagents&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16209" PostTypeId="2" ParentId="16208" CreationDate="2014-03-30T00:08:17.527" Score="5" Body="&lt;p&gt;Yes, you can do this. As long as the final mix has the proper concentrations of everything, its fine. Just make sure you compensate the by adding 30 uL (the extra volume) less of water to the master mix.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-03-30T00:08:17.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16211" PostTypeId="1" AcceptedAnswerId="16214" CreationDate="2014-03-30T04:22:07.213" Score="3" ViewCount="4884" Body="&lt;p&gt;On hot summer nights we get flocks of ants that have grown wings (from what I know to migrate nests). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears the wings are not permanent, but are grown for a temporary purpose. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I know these events are triggered by climatic conditions (warm evenings). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other species, wings seem like a really big deal and are grown from birth - wheras ants seem to just grow them 'on the spur of the moment'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is &lt;strong&gt;How do ants spontaneously grow wings?&lt;/strong&gt; Are they a spare layer of skin that is normally discarded and only comes into action when necessary?&lt;/p&gt;&#xA;" OwnerUserId="5417" LastActivityDate="2014-03-30T07:14:58.533" Title="How do ants spontaneously grow wings?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16212" PostTypeId="1" CreationDate="2014-03-30T05:24:13.590" Score="3" ViewCount="253" Body="&lt;p&gt;In order to build an intelligent design such as a bridge or a mechanical watch, you need a series of non useful steps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I understand, in random evolution theory, the &quot;intelligence&quot; involved is the process of natural selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem with this is that natural selection requires that each step be advantageous right away. If I want to build a bridge, I need many steps which would be disadvantageous until the final product which would be advantageous. This would be like trying to write a computer program where each line of code must be advantageous to the program. An intelligent design just cannot be done like this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does modern biology deal with this problem? To say it all happened at once, is not possible since the probabilities against this are simply outside the capabilities of a random system. Furthermore even if by some freak monumental event it happened, it would need to happen again many times since there is a huge diversity of intelligent designs in life forms such as lungs in birds vs gills in fish, or sexless reproduction in bacteria versus male/female reproduction in animals (which are fundamentally different).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Also, as side question has there been ANY experiment demonstrating that such a thing is even possible? I mean for example, to have a computer simulation of random self-replicating molecules, then having an intelligent human being picking out the best version and eliminating the others, then repeating, etc. until you have an intelligent design.)&lt;/p&gt;&#xA;" OwnerUserId="6202" LastEditorUserId="6202" LastEditDate="2014-03-30T06:06:48.690" LastActivityDate="2016-01-09T09:28:37.007" Title="building intelligent structure with random evolution requires series of non useful steps" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16213" PostTypeId="2" ParentId="16212" CreationDate="2014-03-30T06:33:47.883" Score="1" Body="&lt;p&gt;What you say is true, but the answer as to how modern evolutionary theory understand this considers other ideas about living things which seem to allow so called 'neutral traits'.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neutral traits being those phenotypes which seem to have no particular relationship to fitness. Toungue rolling is an often mentioned example.  &lt;a href=&quot;http://sandwalk.blogspot.com/2011/02/dawkins-darwin-drift-and-neutral-theory.html&quot; rel=&quot;nofollow&quot;&gt;Some folks argue that there is only adaptive changes and phenotype, others like Gould and Lewontin argue that some traits can be the result of pleiotropy&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So first of all this sort of discussion can tell us that the question is argued both ways in a convincing enough way that it is not resolved in biology - some argue quite confidently that all traits are selected for and things like flagellar motors and upright ambulation and eyeballs evolve because of and experiencing constant evolutionary pressure.  Others argue that these genes that produce these things are doing something else useful while they are becoming these later more useful traits. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The common twist here is &lt;a href=&quot;http://www.genetics.org/content/186/3/767.full&quot; rel=&quot;nofollow&quot;&gt;plieotropy&lt;/a&gt;.  That the genes that are producing the phenotype one is observing is also participating in one or more other biological traits that may is being positively selected for.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A more interesting example of how this works is &lt;a href=&quot;https://en.wikipedia.org/wiki/Domesticated_silver_fox&quot; rel=&quot;nofollow&quot;&gt;the domesticated silver fox experiment&lt;/a&gt;. Foxes which have had domestication bred into them (just to show that it can be done by selection) lose their red color and their ears are softer and fuzzier.  Nobody tried to select for these traits, but they come associated with each fox that is domesticated.  Are these traits plieotropic or only very tightly linked?  So far they have not been exhibited separately.  In any case I think its fair to say that the experiment didn't care about the color of the fox - only its meekness towards people.  These traits come along for the ride. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it might be with any other desirable genetic trait.  If a gene becomes closer to producing a lung from a gill, if that gene is sticking around it must be because there is positive selection for that trait, even if the lung like gill is not particularly useful for that fish. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry but I actually disagree that it is obvious that non-useful steps must be had for any such complicated trait.  If that were true then you would have a point, but not every biologist would give that to you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It might be a bit surprising that such discussions are and continue to be matters of faith in science, but I hope you don't dismiss it because of this either.  All sciences do assume some things that make their view of the world make more sense.  But there are also other components of these theories which are consistently observed and understood that demand them... until they don't.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't give really any credence whatsoever when someone says 'this is a widely accepted theory by the scientific community'.  This in itself is not a scientific statement, but more the hope that someone else has one somewhere.  But a refutation must also take under consideration what is being refuted.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-03-30T06:33:47.883" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16214" PostTypeId="2" ParentId="16211" CreationDate="2014-03-30T07:14:58.533" Score="4" Body="&lt;p&gt;See the Wikipedia entry for &lt;a href=&quot;http://en.wikipedia.org/wiki/Nuptial_flight&quot; rel=&quot;nofollow&quot;&gt;nuptual flight&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ants that you see most often are (wingless) female workers. The winged ants that you see are male drones whose only role is to fly with young queens for mating. The drones follow a different developmental pathway, emerge from the pupa as winged ants, and then wait in the nest until conditions are right for the big event.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-30T07:14:58.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16217" PostTypeId="1" AcceptedAnswerId="16219" CreationDate="2014-03-30T11:50:37.093" Score="1" ViewCount="165" Body="&lt;p&gt;&lt;a href=&quot;http://de.wikipedia.org/wiki/H%C3%BChnerei&quot; rel=&quot;nofollow&quot;&gt;http://de.wikipedia.org/wiki/Hühnerei&lt;/a&gt; says it takes up to 24 h for a chicken to produce an egg.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is that dependent on the chickens nutrition, i.e., if it does not get enough food or the wrong kind, meaning it can survive on the food but it does not have everything to produce an egg?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do we have data on this?&lt;/p&gt;&#xA;" OwnerUserId="6137" LastEditorUserId="3624" LastEditDate="2014-03-30T18:49:22.543" LastActivityDate="2017-06-14T11:35:49.343" Title="Do chickens always lay eggs?" Tags="&lt;reproduction&gt;&lt;nutrition&gt;&lt;ornithology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16219" PostTypeId="2" ParentId="16217" CreationDate="2014-03-30T13:50:15.710" Score="4" Body="&lt;p&gt;In short; yes. It depends on the breed (not all lay up to 1 egg/day), the age of the bird and on nutrition. High yielding breeds of chicken are e.g. dependent on supplements of calcium to be able to produce new shells rapidly (e.g. in the form of ground-up shells). Some information on the nutrient requirements of chicken can be found at &lt;a href=&quot;http://www.hyline.com/aspx/redbook/redbook.aspx?s=6&amp;amp;p=53&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Feeding the Laying Hen&lt;/em&gt;&lt;/a&gt;. Egg production will also fluctuate over the year, and will generally decrease e.g. during molting, since energy and nutrients are then diverted to the production of feathers (see info at e.g. &lt;a href=&quot;http://www.thepoultrysite.com/articles/450/several-reasons-why-your-hens-may-stop-laying-eggs&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;The Poultry site&lt;/em&gt;&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-03-30T14:46:09.727" LastActivityDate="2014-03-30T14:46:09.727" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16220" PostTypeId="1" CreationDate="2014-03-30T14:58:36.020" Score="2" ViewCount="157" Body="&lt;p&gt;What would be the best protocol to clone a gene about 5kb in size? The genome is not sequenced, but the gene itself very similar to orthologous genes of organisms with known sequences.&lt;/p&gt;&#xA;" OwnerUserId="5995" LastActivityDate="2014-12-03T09:40:50.010" Title="Cloning a gene of an organism with an nonsequenced genome" Tags="&lt;molecular-genetics&gt;&lt;cloning&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16222" PostTypeId="1" AcceptedAnswerId="16242" CreationDate="2014-03-30T16:02:40.077" Score="1" ViewCount="167" Body="&lt;p&gt;If you have a constant pain in your body, why does a greater pain or pleasure make you not feel the original pain?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastEditorUserId="86" LastEditDate="2014-03-30T16:29:56.373" LastActivityDate="2014-03-30T23:33:56.127" Title="Nervous system: Pain and Pleasure?" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;pathophysiology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16224" PostTypeId="1" AcceptedAnswerId="16243" CreationDate="2014-03-30T17:42:32.450" Score="2" ViewCount="69" Body="&lt;p&gt;If the electrical signals from all the various organs throughout the body eventually connect to the nerves in the spinal column traveling up to the brain, how does the brain differentiate the different signals.  Is the nerve in the spinal column like an electrical conduit with many wires inside?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2014-03-30T23:41:43.153" Title="Nervous system : Nerve signals" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-04-01T04:03:55.077" ContentLicense="CC BY-SA 3.0" />
  <row Id="16225" PostTypeId="1" AcceptedAnswerId="16226" CreationDate="2014-03-30T17:57:27.177" Score="2" ViewCount="43" Body="&lt;p&gt;If a device were created to monitor the nervous  signals from the heart, including stable heartbeats, rapid heartbeats, etc., and this device were capable of transmitting the &quot;stable heartbeat&quot; to the heart, would this have any adverse or advantagious effects for medical science?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2014-03-31T10:05:09.053" Title="Nervous System : Signal Translation" Tags="&lt;theoretical-biology&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16226" PostTypeId="2" ParentId="16225" CreationDate="2014-03-30T18:22:01.337" Score="2" Body="&lt;p&gt;Measuring the electrical signals (=nerve signals) from the heart is frequently done in medicine, it is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Electrocardiography&quot; rel=&quot;nofollow noreferrer&quot;&gt;electrocardiography&lt;/a&gt;. It looks like this (from the same article):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WC7JY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Influencing the heartbear can also be done and is done by &lt;a href=&quot;http://en.wikipedia.org/wiki/Artificial_cardiac_pacemaker&quot; rel=&quot;nofollow noreferrer&quot;&gt;pacemakers&lt;/a&gt;. Depending on the patients necessities the can permanently stimulate the heart or do this only, when certain criteria are met which makes an intervention necessary to prevent cardiac arrest. Wrong stimulation can in fact kill people, since they go into cardiac arrest when the stimulation of the heart is not correct. This is why pacemaker patients have to stay away from strong magnetic fields which make their pacemakers fail and leave them without proper stimulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This technique of influencing the heart from outside is used by &lt;a href=&quot;http://en.wikipedia.org/wiki/Defibrillation&quot; rel=&quot;nofollow noreferrer&quot;&gt;defibrillators&lt;/a&gt;, which use an electric shock to influence the heart beat. It is used for treating cardiac dysrhythmias, ventricular fibrillation and pulseless ventricular tachycardia, which all lead to death if left untreated. A special form are &lt;a href=&quot;http://en.wikipedia.org/wiki/Defibrillation#Automated_external_defibrillator_.28AED.29&quot; rel=&quot;nofollow noreferrer&quot;&gt;automated external defibrillators&lt;/a&gt;, which measure the an electrocardiogram and then decide by the form of it, if an electric shock is needed.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-03-31T10:05:09.053" LastActivityDate="2014-03-31T10:05:09.053" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16227" PostTypeId="1" AcceptedAnswerId="16241" CreationDate="2014-03-30T18:34:50.560" Score="1" ViewCount="163" Body="&lt;p&gt;If an organ was to start failing, not total failure, such as the thyroid gland, is it possible that the fault may not lie in the failure of the organ but in the nerve signals coming from the brain?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2016-09-26T23:40:32.163" Title="Nervous System : Organ or Gland Failure" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16228" PostTypeId="1" AcceptedAnswerId="16247" CreationDate="2014-03-30T19:03:46.247" Score="6" ViewCount="609" Body="&lt;p&gt;When performing normalization of real time PCR results, I found two ways of doing it:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;In my lab they follow the next layout: $\text{Efficiency}^{-(CT\ _{\large\text{interest gene}} - CT _{\large\text{ housekeeping}})}$ each time controls with controls and treatments with treatments. Then they divide the all values (treated and controls) each with controls.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;On the other hand I found another way to normalize that follows this steps: $\text{Efficiency}^{(CT_{\large\text{control}} - CT_{\large\text{treated}})}$. Then you make the same for the normalizing gene and divide the first by the last.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The values obtained are similar but not exact. Also I noticed that first algorithm gives rather different values for most diluted when performing a standard curve.&#xA;Which is correct? &lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="3340" LastEditDate="2015-04-17T12:45:49.933" LastActivityDate="2015-04-17T12:45:49.933" Title="Real time PCR normalization algorithm" Tags="&lt;pcr&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16229" PostTypeId="2" ParentId="16207" CreationDate="2014-03-30T19:11:55.257" Score="1" Body="&lt;p&gt;No, since the pH and the conditions are different in the different compartments (stomach, small intestine, colon) of the bowel.&#xA;See this figure (taken from this &lt;a href=&quot;http://altered-states.net/barry/update178/&quot; rel=&quot;nofollow noreferrer&quot;&gt;website&lt;/a&gt;) for the differences:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JipUR.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are not that much bacteria in the stomach, so even even nothing else than acidic stuff comes out, the bacteria are not affected. And even when you have a severe diarrhea, there are still enough bacteria left to keep it colonized. &lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-03-30T19:11:55.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16230" PostTypeId="2" ParentId="16197" CreationDate="2014-03-30T19:23:00.760" Score="1" Body="&lt;p&gt;The mechanism is likely very straightforward. Activated macrophages already in the area are releasing pro-inflammatory cytokines like TNFα, IL-1β, IL-6, IL-12, MIP-2, etc. These are not only important for granuloma formation, but they also recruit other immune cells to the area. However, since cord factor has this anti-migratory effect, once the cells get there they can't leave. This is important because activated macrophages are key antigen-presenting cells (once they kill and break down the antigen, in this case Mycobacteria), and they need to move to the spleen to assist in the upregulation of the adaptive immune response. By preventing this, mycobacteria can evade part of the immune system - part of the reason why TB is so hard to clear once acquired.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-03-30T19:23:00.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16231" PostTypeId="2" ParentId="16195" CreationDate="2014-03-30T19:57:29.603" Score="1" Body="&lt;p&gt;The problem with this is something called the &lt;em&gt;structure-function relationship&lt;/em&gt;. The function of a protein or enzyme is completely dependent on its structure. For example, take a look at this representation of the active site of &lt;a href=&quot;http://en.wikipedia.org/wiki/Chymotrypsin&quot; rel=&quot;nofollow noreferrer&quot;&gt;chymotrypsin&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hqr26.gif&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The side chains of D102, H57, and S195 all need to be in a perfect conformation in order for the enzyme to function properly, with the hydrogen bonds being essential. If any one of those amino acids was in the D-form, the enzyme would lose its activity completely. Having every single amino acid in the D-form wouldn't help either, as the entire protein's structure (and hence its function) would be altered.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="15950" LastEditDate="2019-01-07T15:12:34.300" LastActivityDate="2019-01-07T15:12:34.300" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="16232" PostTypeId="1" CreationDate="2014-03-30T20:14:13.847" Score="1" ViewCount="167" Body="&lt;p&gt;I know that we age because of errors in the cell replication process and these errors eventually leads to death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we exclude environmental factors, are there any other factors that can cause these errors? Is there for instance some kind of &quot;programming&quot; in our DNA of our death? &lt;/p&gt;&#xA;" OwnerUserId="6208" LastEditorUserId="3624" LastEditDate="2014-03-30T23:23:28.913" LastActivityDate="2015-10-18T21:40:17.060" Title="Does DNA influence death (e.g. by cell aging)" Tags="&lt;dna&gt;&lt;senescence&gt;&lt;death&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16233" PostTypeId="1" AcceptedAnswerId="16552" CreationDate="2014-03-30T20:21:35.130" Score="2" ViewCount="591" Body="&lt;p&gt;Melatonin regulates the wake-sleep cycle by causing drowsiness and lowering body temperature, but which specific chemical pathways lead to this drowsiness?&lt;/p&gt;&#xA;" OwnerUserId="5179" LastActivityDate="2014-04-14T19:40:57.293" Title="Role of Melatonin in Circadian Rhythm" Tags="&lt;melatonin&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16234" PostTypeId="1" CreationDate="2014-03-30T20:40:24.717" Score="1" ViewCount="432" Body="&lt;p&gt;I know what the cardiac cycle is. There are two phases diastole and systole. One is the relaxed, and the other is the contracted form of the heart. The diastole is where blood is pumped to the ventricles and systole is when blood goes to the aorta, and lungs. But what is the connection to blood pressure?&lt;/p&gt;&#xA;" OwnerUserId="5616" LastEditorUserId="5616" LastEditDate="2014-03-31T22:39:24.153" LastActivityDate="2014-07-23T10:56:49.843" Title="People say the cardiac cycle depends on blood pressure? How so?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;cardiology&gt;&lt;blood-circulation&gt;&lt;blood-pressure&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16235" PostTypeId="2" ParentId="16228" CreationDate="2014-03-30T20:54:17.990" Score="2" Body="&lt;p&gt;This topic could probably have it's own StackExchange, there is so much info and trial and error done with rtPCR. Here's my 2 cents:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your adjusted calculation does not normalize your data, it just subtracts the 'background' or control. For expression studies this is not good enough. Normalizing data for gene expression must involve setting it to a scale of another gene whose expression should be not only present but consistent between your treated and untreated samples. House keeping genes (you are probably using GAPDH) make good candidates for this because their expression &lt;em&gt;rarely&lt;/em&gt; changes. If you don't normalize than you don't know if your your expression is actually changing, or if it's simply due to a larger input of mRNA. However it must be shown that the housekeeping gene's expression is also not changing, this is usually accomplished using a different sample set. Take if from me, I've done a lot of this and this step is one of the most important in your experiment. Any reviewer who knows what he's doing will reject a paper using rtPCR without the proper statistics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have had a lot of success using Applied Biosystems StepOne software to provide you with accurate Ct values. Generating the variable is complication, use software to do it right every time:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_042380.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_042380.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What method/system are you using?&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-03-30T20:54:17.990" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16236" PostTypeId="1" AcceptedAnswerId="16244" CreationDate="2014-03-30T21:34:39.137" Score="1" ViewCount="119" Body="&lt;p&gt;How many ways can an Apoptosis mechanism be made disfunctional or irreparably damaged? If a cell has damaged Apoptosis mechanisms and it divides will its daughter cells have such damage?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastEditorUserId="3624" LastEditDate="2014-03-30T23:27:09.660" LastActivityDate="2014-03-31T00:00:55.263" Title="In what ways can mechanisms of apoptosis be damaged?" Tags="&lt;cancer&gt;&lt;senescence&gt;&lt;theoretical-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16237" PostTypeId="2" ParentId="16232" CreationDate="2014-03-30T22:05:38.860" Score="1" Body="&lt;p&gt;Perhaps the best type of study to examine the role of genes (DNA) in human aging are &lt;a href=&quot;http://ageing.oxfordjournals.org/content/41/5/581.long&quot; rel=&quot;nofollow&quot;&gt;twin studies&lt;/a&gt;.  They have either: the same DNA (monozygotic, one egg, &quot;identical&quot; twins (MZ) ) or similar DNA (dizygotic twins, two eggs (DZ) ) and are perhaps exposed the same, or different environments.   I won't repeat the information in the link, above, but studies of this type guide that our DNA is &lt;strong&gt;not&lt;/strong&gt; an absolute roadmap of our future.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA damage can be caused by exposure to excessive radiation, viruses, chemicals and just 'random events'.  Cells and tissues can also be damaged by &lt;a href=&quot;http://en.wikipedia.org/wiki/Free-radical_theory_of_aging&quot; rel=&quot;nofollow&quot;&gt;oxidative damage&lt;/a&gt; - literally oxygen and related molecules that are produced within the body and can react with components of cells (e.g DNA, proteins and the lipid cell membrane).   The accumulation of these oxidized products in and around the cell disrupts tissue function and leads to many of the symptoms of aging, a process called &lt;a href=&quot;http://en.wikipedia.org/wiki/Senescence&quot; rel=&quot;nofollow&quot;&gt;sensescence&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We obviously cannot avoid having oxygen around us.  In the same way, our cells need the sugar glucose as a source of energy. Glucose can spontaneously react with proteins and lipids to form &lt;a href=&quot;http://en.wikipedia.org/wiki/Advanced_glycation_end-product&quot; rel=&quot;nofollow&quot;&gt;advanced glycation endproducts (AGEs)&lt;/a&gt;.&#xA; AGEs are pro-inflammatory.  In diabetes, where blood glucose levels may remain at higher than normal for extended periods, the formation of AGEs can lead to nerve and kidney damage.   &lt;a href=&quot;http://en.wikipedia.org/wiki/Maillard_reaction&quot; rel=&quot;nofollow&quot;&gt;The chemical reaction that is occurring&lt;/a&gt; is the same as when you toast a piece of bread or fry a steak.  So paradoxically, two of the ingredients essential for life - oxygen and glucose - are slowly but surely disrupting our body's function over the course of decades.   Although the body can replace some of these damaged proteins, they accumulate over time, as evidenced by the increasing lack of elasticity of older skin as collagen proteins are cross-linked. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regular exercise, good diet and friendships all add to mental and physical health, quality of life and longevity.  So, to live a long time, don't stress, have ONE slice of cake and make new friends who will exercise with you.&lt;/p&gt;&#xA;" OwnerUserId="5922" LastEditorUserId="5922" LastEditDate="2014-03-30T22:58:22.130" LastActivityDate="2014-03-30T22:58:22.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16238" PostTypeId="2" ParentId="16232" CreationDate="2014-03-30T22:56:18.770" Score="0" Body="&lt;p&gt;It is important for organisms to be renewed. These organisms have less wear and tear, they are modified through evolution to better fit the current environment, they are more likely to have healthy offspring that they can look after. It must also be considered that genetically we must be optimal in anyway that confers our continued survival as a species. So we should remain alive only for as long as it benefits the species (i.e. raising our young) and die once we are less help and more burden. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So with all that in mind, why do errors or mutations occur? Well we need optimal amount of mutations that allow us to constantly evolve to adapt to the newest environment. If we don't evolve, we die. Keeping our DNA mutation free is too costly anyway for it to confer a survival benefit of the species (rather than the individual). It would require far too many error checking pathways which themselves would be in need of being checked. So yes our cells have programming to allow mutations (by not having completely successful countering techniques) as it is beneficial.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our cells themselves can only replicate so many times due to the length of telomeres. These are little bits of DNA at the end which after each cycle shorten (as we can't replicate DNA at the end efficiently). After a certain amount of replications a cell is destined to die. An enzyme exists, telomerase, which resets this by lengthening the telomeres. However over expression of this enzyme leads to cancer. Again, it is important for us to mutate in order to evolve but too much is harmful. The same argument applying that it is too costly to be perfect and not mutate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Logic dictates that if humans survived for much longer, over population would impact on our own survival. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-03-30T22:56:18.770" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16239" PostTypeId="2" ParentId="16236" CreationDate="2014-03-30T23:10:05.020" Score="1" Body="&lt;p&gt;Lot's of ways. Apoptosis is complex, but falls under two pathways ending up at caspase 3. Anywhere in the pathway may there be a problem but also in things that trigger the pathway. For example in cancer there is loss of tumour suppressors which ensure a damaged cell undergoes apoptosis or prevents replication and oncogenes which allow controlled replication. Damage to these genes allows a cell to divide in the absence of signals to divide and also forget to check that it's DNA isn't damaged before replicating. This is then passed on to the daughter cancer cells. As each check is removed the cell permits more and more mutations meaning more and more likelihood for the next mutation to occur. Cancer is caused literally by one cell having defects and every daughter cell also possess the defects. Those that have defects which accidentally kill the cell are selected out. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-03-30T23:10:05.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16240" PostTypeId="1" CreationDate="2014-03-30T23:23:47.740" Score="3" ViewCount="123" Body="&lt;p&gt;I have this picture describing the Brainbow system here: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.imgur.com/LgD5et4.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper I am reading says it uses Cre-lox recombination to express a certain color. If the cell in question was expressing a yellow fluorescence then what would the construct in that cell look like in terms of the picture given? Would it just be a single line with the UAS, EGFP, and mKO2 in that order or would it be two lines, wone with the UAS and EGFP and on with the UAS and mKO2? &lt;/p&gt;&#xA;" OwnerUserId="6209" LastEditorUserId="948" LastEditDate="2014-03-31T14:41:14.447" LastActivityDate="2014-03-31T14:41:14.447" Title="Brainbow fluorescence labeling technique" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16241" PostTypeId="2" ParentId="16227" CreationDate="2014-03-30T23:24:39.993" Score="2" Body="&lt;p&gt;In many hormonrs, the hypothalamus produces a hormone which acts on the pituitary gland which subsequently acts on an end organ. Taking your example of the thyroid gland let's take a look at it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hypothalamus produces TRH which acts on the anterior pituitary causing it to release TSH which in turn stimulates the thyroid gland to make thyroid hormones T3 and T4. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abnormal levels of thyroid hormone may be caused by problems in any one of the three stages. Problems on the end organ are termed primary, in the pituitary gland are termed secondary and in the hypothalamus tertiary. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For simplicity let's look at abnormally high levels of thyroid hormones called hyperthyroidism. In a patient with a primary or thyroid gland problem we expect high levels of thyroid hormones but low levels of TSH. The pituitary gland is trying its best to tell the thyroid gland, &quot;No more!&quot; but it won't listen. In secondary or pituitary disease, the pituitary gland is the bully pushing the thyroid gland to make lots of thyroid hormone by over production of TSH. Usually there are other hormone disturbances too in this case as the pituitary gland has a range of hormones it secretes. Also the swollen pituitary gland puts pressure on the nerves carrying vision leading to visual loss (specifically in the temporal fields). In this case the hypothalamus will be secreting low levels of TRH (which isn't routinely measured) trying to get the pituitary gland to stop acting out. The rarest situation is when the hypothalamus has the problem where every hormone is increased. However again this will be causes by something or the other detectable usually on imaging. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the short answer is yes, but there will be other features. Primary or end organ dysfunction is most common and will cause characteristic findings in blood tests and examination (e.g. swollen thyroid gland) but secondary and tertiary disease can be figured out when other features are found in association. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-03-30T23:24:39.993" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="16242" PostTypeId="2" ParentId="16222" CreationDate="2014-03-30T23:33:56.127" Score="1" Body="&lt;p&gt;I'm not sure if why is referring to the biological basis or the reasoning for why it is beneficial but I've briefly summarised both. If you'd like more detail just accept and ask again clarifying your exact interest in this broad question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pain is taken up through the spinothalamic pathway but at may opportunities it may be blocked. It may be blocked by other ascending pathways or by descending pathways. There are a number of structures involved in this including endorphins and Interneurones which are part of the gate control theory of pain. Basically ascending sensory information is blocked when other sensory information is more acute or more pertinent. This is important for survival e.g. when feeling a lion it is important not to feel pain. That same endorphin pathway is highjacked by drugs such as morphine. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-03-30T23:33:56.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16243" PostTypeId="2" ParentId="16224" CreationDate="2014-03-30T23:41:43.153" Score="3" Body="&lt;p&gt;Yes is the simple answer. A nerve will go up to a specific part of the brain which the brain knows corresponds to a certain region of the body. It isn't perfect though e.g. pain in the diaphragm confuses the brain which doesn't recognise that pain must be coming from there so instead tells the body there is shoulder pain, however this is useful in medicine. Another infamous example is pain from heart disease (angina) which causes pain in the jaw and arm. Perhaps even more interestingly, if a nerve is cut and then grows back linking to the wrong nerve it may lead to the completely wrong part of the body being identified when touched. Also if the brain itself is stimulated in these corresponding areas, a person will feel he or she is indeed being touched in a certain part of the body. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-03-30T23:41:43.153" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16244" PostTypeId="2" ParentId="16236" CreationDate="2014-03-30T23:55:33.237" Score="1" Body="&lt;p&gt;Most of us have had the apoptotic process in our B-lymphocytes disrupted when we had &lt;a href=&quot;http://en.wikipedia.org/wiki/Epstein%E2%80%93Barr_virus&quot; rel=&quot;nofollow&quot;&gt;infectious mononucleosis, caused by the EBV virus&lt;/a&gt;.  The EBV virus (pardon the virus-virus) encodes proteins, including one that mimics a host cell protein, Bcl-2, which plays an important role in apoptosis.  &lt;a href=&quot;http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0030404&quot; rel=&quot;nofollow&quot;&gt;The set of virus 'decoy' proteins &lt;/a&gt; forces the infected cell to survive and be a host to produce new virus, whereas the cell's normal response would be to apoptose.&#xA;&lt;a href=&quot;http://www.virologyj.com/content/10/1/182&quot; rel=&quot;nofollow&quot;&gt;Wart viruses such as HPV&lt;/a&gt; may have similar mechanisms.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in summary, excessive growth or transformation to an immortal cell typically requires &lt;em&gt;activation of mechanisms that promote cell growth&lt;/em&gt; &lt;strong&gt;and&lt;/strong&gt; &lt;em&gt;the inibition of mechanisms that promote cell death&lt;/em&gt;.  &quot;Transforming viruses' often have mechanisms to affect both cell growth and cell death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This answer isn't to the question 'how many ways can [the] apoptosis mechanism [..] be damaged ', but answers 'what's a common way that apoptosis pathways can be disrupted'.... large DNA transforming viruses. &lt;/p&gt;&#xA;" OwnerUserId="5922" LastEditorUserId="5922" LastEditDate="2014-03-31T00:00:55.263" LastActivityDate="2014-03-31T00:00:55.263" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16245" PostTypeId="2" ParentId="16240" CreationDate="2014-03-30T23:57:23.580" Score="1" Body="&lt;p&gt;Yellow would need the expression of red and green so that would mean the excision of the blue fluorophore. It would be one line with egfp and the other line with mKO2--- the order doesn't matter-- these represent chromosomes. &lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-03-30T23:57:23.580" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16247" PostTypeId="2" ParentId="16228" CreationDate="2014-03-31T08:31:58.367" Score="4" Body="&lt;p&gt;First step is the calculation of efficiency, denoted by lets say $E_{gene}$. See &lt;a href=&quot;https://biology.stackexchange.com/questions/16035/real-time-pcr-standard-curve/16038#16038&quot;&gt;this post&lt;/a&gt; for calculation of primer efficiency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the fold change for that gene will be calculated by $E_{gene}^{-\Delta Ct_{gene}}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\Delta Ct  = Ct^{treated} -Ct^{control}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But these Ct values are not normalized. For normalization, you take some reference gene which &lt;strong&gt;need not&lt;/strong&gt; be a housekeeping gene. Reference gene should chosen such that it is not affected by the treatment. In some cases usual housekeeping genes can also get affected for e.g. in treatments affecting cell cycle or differentiation. In such cases you should use a spike-in (an artificial RNA bearing low resemblance with any known gene).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can either normalize the fold change (&lt;strong&gt;Case A&lt;/strong&gt;) or find fold change of the normalized expression (&lt;strong&gt;Case B&lt;/strong&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Means the same mathematically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Case A&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$E_{gene}^{-\Delta Ct_{gene}} / E_{ref}^{-\Delta Ct_{ref}}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Case B&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\large\frac{[E_{gene}^{-Ct^{treated}_{gene}}]/[E_{ref}^{-Ct^{treated}_{ref}}]} {[E_{gene}^{-Ct^{control}_{gene}}]/[E_{ref}^{-Ct^{control}_{ref}}]}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can rearrange the numerator and denominator to get &lt;strong&gt;Case A&lt;/strong&gt; from &lt;strong&gt;Case B&lt;/strong&gt;. I'm not sure how you are ending up getting different values. Recheck once. It &lt;em&gt;may&lt;/em&gt; be because of numerical approximation errors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Case A&lt;/strong&gt; looks much neater; so it is best to calculate that way :)&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-03-31T13:16:47.433" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16248" PostTypeId="1" AcceptedAnswerId="16294" CreationDate="2014-03-31T10:25:59.067" Score="2" ViewCount="147" Body="&lt;p&gt;The genetic variance of a quantitative trait (the quantitative trait in question is fitness) can be express as the sum of two components, the dominance and additive variance:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma_D^2 + \sigma_A^2  = \sigma^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $\sigma$ is the genetic variance, $\sigma_D^2$ is the dominance variance and $\sigma_A^2$ is the additive variance. $\sigma_D^2$  and $\sigma_A^2$ are given by&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma_D^2 = x^2(1-x)^2(2\cdot W_{12} - W_{11} - W_{22})^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma_A^2 = 2x(1-x)(xW_{11}+(1-2x)W_{12} - (1-x)W_{22})^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $W_{11}$, $W_{12}$ and $W_{22}$ are the fitness of the three possible genotypes and $x$ and $1-x$ give the allele frequencies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above definition makes sense for one bi-allelic locus.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;How are $\sigma_D^2$, $\sigma_A^2$ and $\sigma^2$ defined for a locus that have $n$ alleles?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/16249/additive-genetic-variance-with-n-loci&quot;&gt;Here&lt;/a&gt; is a related question&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-04-02T03:46:46.207" Title="Additive genetic variance with $n$ alleles" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;natural-selection&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16249" PostTypeId="1" CreationDate="2014-03-31T10:27:03.967" Score="2" ViewCount="97" Body="&lt;p&gt;The genetic variance of a quantitative trait (the quantitative trait in question is fitness) can be express as the sum of two components, the dominance and additive variance:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma_D^2 + \sigma_A^2  = \sigma^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $\sigma$ is the genetic variance, $\sigma_D^2$ is the dominance variance and $\sigma_A^2$ is the additive variance. $\sigma_D^2$  and $\sigma_A^2$ are given by&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma_D^2 = x^2(1-x)^2(2 \cdot W_{12} - W_{11} - W_{22})^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma_A^2 = 2x(1-x)(xW_{11}+(1-2x)W_{12} - (1-x)W_{22})^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $W_{11}$, $W_{12}$ and $W_{22}$ are the fitness of the three possible genotypes and $x$ and $1-x$ give the allele frequencies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above definition makes sense for one bi-allelic locus only.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;How are $\sigma_D^2$, $\sigma_A^2$ and $\sigma^2$ defined for $n$ bi-allelic loci? Is it:&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;$$\sigma^2 = \sum_{i=1}^n \sigma_i^2$$ $$\sigma_A^2= \sum_{i=1}^n \sigma_{Ai}^2$$ $$\sigma_D^2  = \sum_{i=1}^n \sigma_{Di}^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/16248/additive-genetic-variance-with-n-alleles&quot;&gt;Here&lt;/a&gt; is a related question&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-04-12T05:47:49.033" Title="Additive genetic variance with $n$ loci" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;natural-selection&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16250" PostTypeId="1" AcceptedAnswerId="16254" CreationDate="2014-03-31T10:45:11.020" Score="1" ViewCount="51" Body="&lt;p&gt;&lt;strong&gt;What is the distribution/probability density function (&lt;a href=&quot;http://en.wikipedia.org/wiki/Probability_density_function&quot; rel=&quot;nofollow noreferrer&quot;&gt;PDF&lt;/a&gt;) of recessivity/dominance of new mutations?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I very welcome any partial answer that does not give the whole PDF but just some information about the expected value or the variance of this distribution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/16251/effect-on-fitness-of-mutations&quot;&gt;Here&lt;/a&gt; is a related question&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-03-31T12:59:23.067" Title="Dominance/recessivity of new mutations" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;mutations&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16251" PostTypeId="1" AcceptedAnswerId="16257" CreationDate="2014-03-31T10:46:41.590" Score="1" ViewCount="192" Body="&lt;p&gt;&lt;strong&gt;What is the distribution/probability density function (&lt;a href=&quot;http://en.wikipedia.org/wiki/Probability_density_function&quot; rel=&quot;nofollow noreferrer&quot;&gt;PDF&lt;/a&gt;) of impacts on fitness of new mutations?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I very welcome any partial answer that does not give the whole PDF but just some information about the expected value or the variance of this distribution. Information of the kind: &quot;If we consider only beneficial mutations, then the PDF is $P(X=x) = f(x)$&quot; are also welcome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I say mutations, one might have want to reduce the concept of mutations only to indels and point mutations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course the answer will depend on the species under consideration and from population to population but I welcome any answer that could give some insights. Eventually, some information according to what is generally assumed to be the PDF of effects on fitness of new mutations might be useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/16250/dominance-recessivity-of-new-mutations&quot;&gt;Here&lt;/a&gt; is a related question&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.genetics.org/content/163/4/1519.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; is an article that assumes an exponential distribution of effects on fitness of beneficial mutations.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-03-31T22:23:50.513" Title="Effect on fitness of mutations" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;mutations&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16252" PostTypeId="2" ParentId="16251" CreationDate="2014-03-31T11:55:55.750" Score="1" Body="&lt;p&gt;&lt;em&gt;&lt;strong&gt;[This is purely speculative]&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assumptions: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;impact on fitness is measured by survival chance&lt;/li&gt;&#xA;&lt;li&gt;impact is because of protein coding genes&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Probability of a mutation at position $i$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$P(m=i\ |\ g)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $g$ is the genome with its annotations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probability that activity of some protein changes by X-fold given mutation at $i^{th}$  position(s) in the genome:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\sum\limits_{i}\sum\limits_{gene} P(a_{gene}= X\ |\ m=i)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;sum over all genes that occupy that locus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probability that on a given selection pressure $S$ and protein activity change $X$, the individual survives the selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\sum\limits_{i}\sum\limits_{gene}P(1\ |\ a_{gene}=X,S)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not an expert at Bayesian modeling. But I guess this is one way to go about obtaining the PDF. Each step has to be expanded and combined to get an equation for PDF. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure if this is of any help at all. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-03-31T12:18:01.390" LastActivityDate="2014-03-31T12:18:01.390" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16253" PostTypeId="1" AcceptedAnswerId="16256" CreationDate="2014-03-31T12:32:38.827" Score="1" ViewCount="39" Body="&lt;p&gt;From &lt;em&gt;Genetics by Ursula Goodenough&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;E.coli harboring an F element are endowed with a number of phenotypic&#xA;  traits :&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;1.They are sensitive to infection by ssRNA phages and certain ssDNA phages.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;2.They resist the growth of female specific phages as T3 and T7.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What is the molecular mechanism behind this sensitivity and resistance ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="6860" LastEditDate="2014-05-28T07:14:05.207" LastActivityDate="2014-05-28T07:14:05.207" Title="Property of E.coli harboring F element" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;bacteriology&gt;&lt;molecular-genetics&gt;&lt;virus&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16254" PostTypeId="2" ParentId="16250" CreationDate="2014-03-31T12:59:23.067" Score="3" Body="&lt;p&gt;I don't believe you can produce a general function for this. It will depend on the exact gene and organism you are considering.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a molecular point of view, the vast majority of recessive mutations result from a change producing either a non-functional protein product or a truncated product that is cleaned up by the cell. We can reasonably assume that most modifications significant enough to produce a phenotype will be of this class since there are more mutational sites which can produce a non-functioning product than can produce a product of changed function but the exact ratio of one to the other is not going to be equal across different genes and organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note as well that the whole notion of recessive and dominant traits is probably an over-simplification and, in fact, there are subtle differences between homozygotes and heterozygotes in many, perhaps most, cases so I'm not sure how useful an estimate would be even if you had one.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2014-03-31T12:59:23.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16255" PostTypeId="2" ParentId="7770" CreationDate="2014-03-31T13:00:08.487" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00180642&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; is a study on the O&lt;sub&gt;2&lt;/sub&gt; production rate of one of the fastest growing species of cyanobacteria. The theory is not just someone's idea, it's a conclusion made from trends which were discovered during the course of conducting countless experiments.&lt;/p&gt;&#xA;" OwnerUserId="6211" LastEditorUserId="3340" LastEditDate="2016-05-09T11:36:45.460" LastActivityDate="2016-05-09T11:36:45.460" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16256" PostTypeId="2" ParentId="16253" CreationDate="2014-03-31T13:09:28.480" Score="2" Body="&lt;ol&gt;&#xA;&lt;li&gt;Some bacteriophages adsorb on the pili. So the individuals carrying the F-element will be susceptible to these.&lt;/li&gt;&#xA;&lt;li&gt;F-plasmid encoded membrane protein PifA is responsible for the T7 resistance [See &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0042682204003824&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;]. The exact mechanism is not known&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;If you see the list of references in the textbook chapter you will be able to trace the reference for a certain quoted fact&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-03-31T13:09:28.480" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16257" PostTypeId="2" ParentId="16251" CreationDate="2014-03-31T13:10:59.060" Score="3" Body="&lt;p&gt;To a good first approximation $\overline{\Delta f} = 0$. Where $\overline{\Delta f}$ is the mean change in fitness down to any point or indel mutation. The reasons for this are as follows:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;In the genome of higher organisms, most of the genome is non-functional (&quot;junk&quot;) so most mutations will not have any effect regardless of the change made.&lt;/li&gt;&#xA;&lt;li&gt;A substantial proportion of in-frame point mutations will be synonymous mutations that result in the same amino acid being coded for (actually this can have an effect on protein expression but I don't believe anyone has - yet - shown a fitness difference?)&lt;/li&gt;&#xA;&lt;li&gt;Even where a mutation &lt;em&gt;does&lt;/em&gt; alter an amino acid many amino acid changes have no measurable effect on the protein produced. Especially where the new amino acid has similar properties to the one it has replaced.&lt;/li&gt;&#xA;&lt;li&gt;Even when a mutation does alter the protein function, or render the product non-functional, in many cases this will not impact fitness since fitness is conditional on the environment in which it is measured and not all genes impact all environments.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So the distribution, whatever it is, will have a large spike at 0. Probably this spike is several orders of magnitude higher than the next highest value. Further, we can be reasonably certain that $\overline{\Delta f} &amp;lt; 0$ since there are more possible ways to break a Gene through a point or indel mutation than there are to improve it. If this is the case, so that there is a large excess of mutations with a negative effect on fitness, we can conclude that the distribution of mutational changes in fitness will be non-normal (negative skew and spike at zero), and that the normal distribution will be a poor approximation.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="3624" LastEditDate="2014-03-31T22:23:50.513" LastActivityDate="2014-03-31T22:23:50.513" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16258" PostTypeId="1" AcceptedAnswerId="16261" CreationDate="2014-03-31T14:22:06.393" Score="3" ViewCount="1310" Body="&lt;p&gt;Does anyone know of any papers showing how Gram positive Fermiculates or Actinobacteria use  a H&lt;sup&gt;+&lt;/sup&gt; gradient for an F-type ATPase, It seems impossible since there is no outer LPS membrane to maintain the protons in a periplasmic space. Is the use of ATPase for production of ATP exclusively a Gram negative thing?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this question &quot;Production of ATP in Lactobacilli&quot; but no answers:&#xA;&lt;a href=&quot;https://biology.stackexchange.com/questions/14669/production-of-atp-in-lactobacilli&quot;&gt;https://biology.stackexchange.com/questions/14669/production-of-atp-in-lactobacilli&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-04-01T17:18:20.010" Title="How do Gram + bacteria use a proton gradient for F-type ATPase?" Tags="&lt;microbiology&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16261" PostTypeId="2" ParentId="16258" CreationDate="2014-03-31T18:38:05.110" Score="3" Body="&lt;p&gt;Protons are pumped out of the bacterial cell by the electron tansport chain. This creates a &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemiosmosis#In_prokaryotes&quot; rel=&quot;nofollow&quot;&gt;protonmotive force&lt;/a&gt; with two components, one due to the difference in proton concentration, the other due to the membrane potential that is created. In bacteria and mitochondria it is the membrane potential component that provides most of the driving force to pull protons back in through the ATP synthase. Thus the fate of the protons outside the cell doesn't matter too much. Even if you were to buffer the exterior absolutely, the fact that charge had moved out would drive ATP synthesis.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-03-31T18:38:05.110" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16268" PostTypeId="1" AcceptedAnswerId="16277" CreationDate="2014-04-01T03:06:50.947" Score="1" ViewCount="460" Body="&lt;p&gt;I read that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;trp operon is located at 27 &lt;strong&gt;min&lt;/strong&gt; on E.coli chromosome.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What does &quot;min&quot; mean ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="69" LastEditDate="2014-04-01T09:30:13.803" LastActivityDate="2014-04-01T09:47:57.803" Title="What does min mean?" Tags="&lt;genetics&gt;&lt;terminology&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16271" PostTypeId="1" AcceptedAnswerId="16273" CreationDate="2014-04-01T04:21:43.130" Score="4" ViewCount="153" Body="&lt;p&gt;first of all I'm not sure if I should post this here or in the astronomy stack. I think biologist are more likely to answer my question. To make it short:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why when looking for any sort of life on other planets, we keep looking for similar conditions we call &quot;life friendly&quot;, like nice temperature, oxygen level, pressure etc...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there some rule in biology that says life can only exists under these conditions? Why nobody supposes that evolution did not have enough time yet on our planet to generate other living mechanisms, and that on other planets even if the conditions are not suitable for us, there might be something well evolved through time there. After all if we can conceive electric robots that can survive to radioactivity and to high pressures and temperatures, why nature shouldn't be able to?&lt;/p&gt;&#xA;" OwnerUserId="6213" LastEditorUserId="3624" LastEditDate="2014-04-01T06:34:29.387" LastActivityDate="2014-04-01T06:34:29.387" Title="Life on other planets" Tags="&lt;evolution&gt;&lt;life&gt;&lt;abiogenesis&gt;&lt;astrobiology&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2014-04-01T15:36:40.753" ContentLicense="CC BY-SA 3.0" />
  <row Id="16272" PostTypeId="1" AcceptedAnswerId="16280" CreationDate="2014-04-01T05:01:32.070" Score="15" ViewCount="26293" Body="&lt;p&gt;I still don't  know if the mitochondrion or chloroplast was first? I've looked for it on the internet and in various books but haven't found anything. Does anyone have the answer and a theory which backs up this answer? &lt;/p&gt;&#xA;" OwnerUserId="6214" LastEditorUserId="3340" LastEditDate="2014-11-11T07:21:34.677" LastActivityDate="2018-09-23T15:22:00.133" Title="Was the mitochondrion or chloroplast first?" Tags="&lt;cell-biology&gt;&lt;mitochondria&gt;&lt;chloroplasts&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16273" PostTypeId="2" ParentId="16271" CreationDate="2014-04-01T05:08:50.523" Score="3" Body="&lt;p&gt;We might imagine living things that are very different from what we know. There is no conceptual reason for limiting life in its relation to water for example. Moreover, the definition of what is alive is really unclear. We classified more or less arbitrarily objects we know on earth as being living or not living but this does not give any clear definition of what is life and therefore it would not allow an exobiologist to even know what he's looking for!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if you had to seek in billion of planets/natural satellite a living creature somewhere where what planets would start looking at? Probably those that look alike yours because you already know that life is possible the kind of conditions these planets offer. I think the answer is as easy as that.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-04-01T05:08:50.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16274" PostTypeId="2" ParentId="16272" CreationDate="2014-04-01T06:22:07.813" Score="7" Body="&lt;p&gt;I do not have a definitive answer but I can argue that mitochondria came into existence before chloroplasts despite the fact that, between their free living ancestors- $\alpha$-proteobacterium and Cyanobacteria, the latter seems to be older in evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have following points to support this argument:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The organisms that have chloroplasts also have mitochondria but the converse is not true.&lt;/li&gt;&#xA;&lt;li&gt;There have been events of secondary endosymbiosis (especially in the &lt;em&gt;Chromaveolata&lt;/em&gt;) in which organisms that already contained chloroplasts became endosymbiotic organelles in another host.&lt;/li&gt;&#xA;&lt;li&gt;There is a very recent case of endosymbiosis of a chloroplast like organelle called spheroid bodies in the diatom &lt;em&gt;Rhopallodia gibba&lt;/em&gt; which already has a secondary plastid. See &lt;a href=&quot;http://mbe.oxfordjournals.org/content/21/8/1477.full&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Usually a cell has many mitochondria but fewer chloroplasts. Though this doesn't say much about the evolutionary age but higher number allows more organelle to nuclear gene transfer, considering the limited transfer window hypothesis. More the transfer, more &quot;dependent&quot; will the organelle become on the host.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even though I claim in the first paragraph that Cyanobacteria is older than $\alpha$-proteobacterium (In fact I dont have a strong reason to support that claim), it doesn't mean that photosynthesis has an older origin. Chemosynthetic pathway and membrane bioenergetics have evolved very early on. Coupling of light to assist these processes, most likely came later when organisms surfaced to the limnetic zone. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-05-01T10:35:37.973" LastActivityDate="2014-05-01T10:35:37.973" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16275" PostTypeId="2" ParentId="16272" CreationDate="2014-04-01T07:42:12.950" Score="7" Body="&lt;p&gt;According to my knowledge, this was the molecular and cellular evolutionary path of life.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Synthesis of essential building blocks (fatty acids, aminoacids, cofactors...)&lt;/li&gt;&#xA;&lt;li&gt;Condensation of building blocks&lt;/li&gt;&#xA;&lt;li&gt;First RNA replicase; RNA genomes (differentiation between genomic and&lt;br&gt;&#xA;functional RNA, primitive metabolism) &lt;/li&gt;&#xA;&lt;li&gt;Ribosomes and first matrix dependent translational machinery&lt;/li&gt;&#xA;&lt;li&gt;Copying RNA into DNK (rNDP reductase, reverse transcriptase)&lt;/li&gt;&#xA;&lt;li&gt;PROGENOTES (DNA genome, introns in genes, slow growth, &lt;strong&gt;anaerobic&#xA;heterotrophs&lt;/strong&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;From here you have two main branches, organisms with branched lipids, and with unbranched lipids (the first will become archaea, and the latter urkaryotes and Bacteria)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the Urkaryotes, you have selection of complexity. Their growths is inefficient, and they tolerate extra DNA. Bacteria favored efficient growth, autotrophy and loss of extra DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At this point the endosymbiosis occurred (presumably), and the bacteria became a very specialized parasite. Mitochondria as you probably know, have their own genome which replicates independently from the nuclear genome. Cells and mitochondria became permanently linked when the mitochondria &quot;decided&quot; to relocate parts of it's genome to the nucleus, incorporating it's genome in the host's.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now we have the first Eukaryotic organisms that are similar to today's. They were heterotrophic, but one more event of endosymbiosis occurred. That was the formation of chloroplasts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many people think that autotrophy is more primitive compared to heterotrophy. That simply isn't true. The conditions when these organisms arose were quite different. Building blocks were readily available and plentiful, so the organisms were all &quot;friends&quot; with each other. It is when food became scarce that selective pressure started nudging species into different directions (autotrophy).&lt;/p&gt;&#xA;" OwnerUserId="5995" LastActivityDate="2014-04-01T07:42:12.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16277" PostTypeId="2" ParentId="16268" CreationDate="2014-04-01T09:11:27.817" Score="2" Body="&lt;p&gt;&lt;em&gt;Min&lt;/em&gt; means minutes. Minutes are counted for interruption points since onset of DNA transfer in F-pili-mediated conjugation. The point &quot;0&quot; is not associated with &lt;em&gt;ori&lt;/em&gt;, but is close to &lt;em&gt;thr&lt;/em&gt;. The total chromosome size is 100 min (time taken for conjugation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98936/&quot; rel=&quot;nofollow&quot;&gt;Linkage Map of Escherichia coli K-12, Edition 10: The Traditional Map&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98936/&quot; rel=&quot;nofollow&quot;&gt;Recalibrated linkage map of Escherichia coli K-12&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-04-01T09:47:57.803" LastActivityDate="2014-04-01T09:47:57.803" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16278" PostTypeId="2" ParentId="1034" CreationDate="2014-04-01T12:07:23.580" Score="3" Body="&lt;p&gt;Question is two years old, and the answer is approx 20 yo, but I believe both are still pertinent: According to Jared Diamond on pg 12 of his Harper paper version (1993 -- but reissued in 2006) of The Third Chimpanzee, we replace intestinal lining epithelium every few days, urinary bladder lining every two months, and replace every red blood cell about every four months. So though blood cells are fast (and probably more numerous) they are slow compared to the intestinal cells!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems amazing that the telomeres of the intestinal walls' cells don't wear out and begin cancerous changes much earlier than they do...if the statements above are all accurate. I do find Diamond an incredibly insightful writer and think you can trust him.&lt;/p&gt;&#xA;" OwnerUserId="6217" LastActivityDate="2014-04-01T12:07:23.580" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16279" PostTypeId="2" ParentId="15239" CreationDate="2014-04-01T13:35:03.737" Score="4" Body="&lt;p&gt;Hopefully this syllogism will answer your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given the following premises:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;In the absence of selection, fitness of individuals are at a theoretical maximum.&lt;/li&gt;&#xA;&lt;li&gt;If a theoretical maximum fitness is achieved then effective population size is maximum.&lt;/li&gt;&#xA;&lt;li&gt;If there is an allele that confers both increased &lt;em&gt;and&lt;/em&gt; decreased fitness you have a genetic conflict (e.g. an allele that turns you green gives you good woodland camouflage but is un-attractive).&lt;/li&gt;&#xA;&lt;li&gt;If a deleterious allele is linked to a beneficial allele this is similar to having a genetic conflict.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The conclusion follows: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Strong linkage between beneficial alleles and deleterious alleles (Hill Robertson effects, i.e. 3. and 4.) prevents a theoretically maximum fitness to be attained (1.) and thus a reduced effective population size (2.). Which can only be overcome by high levels of recombination and mating (i.e. by separating deleterious and beneficial alleles).&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2014-04-01T15:51:28.767" LastActivityDate="2014-04-01T15:51:28.767" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16280" PostTypeId="2" ParentId="16272" CreationDate="2014-04-01T14:44:23.663" Score="19" Body="&lt;p&gt;Mitochondria evolved before chloroplasts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We know this because Mitochondria form a monophyletic group: e.g. all life with mitochondria traces back to a single common ancestor (&lt;a href=&quot;http://www.nature.com/scitable/topicpage/the-origin-of-mitochondria-14232356#&quot;&gt;source&lt;/a&gt;). Since the group with chloroplasts groups within this clade, it must be the case that either (a) chloroplasts were obtained by an organism that already had mitochondria or (b) chloroplasts were independently lost by multiple lineages within the Eukaryotic clade and then many of these lineages re-acquired chloroplasts by secondary endosymbiosis. Since (a) is a (much) more parsimonious explanation it is the one it makes sense to accept.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2014-04-01T14:44:23.663" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16282" PostTypeId="1" CreationDate="2014-04-01T17:16:22.333" Score="6" ViewCount="12564" Body="&lt;p&gt;I'm trying to understand how exactly the binding to silica gel (in kits) step works and I cannot find any papers which provide an explanation of the physics or chemistry; especially on the way that Guanidine-HCl works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So lets get them from the beginning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, we adjust DNA binding conditions by adding a buffer which includes &#xA;Guanidine-HCl and ethanol and then we centrifuge our sample. I knew that Guanidine-HCl destroys the tertiary structure of proteins but somewhere I read that also it helps the DNA to bind to a silica column. I searched to find the way that it works but I couldn't find a paper. Also what is the role of ethanol in this step? Is it just to remove proteins and polysaccharides from the sample? &lt;/p&gt;&#xA;" OwnerUserId="6032" LastEditorUserId="16866" LastEditDate="2017-04-04T20:19:31.147" LastActivityDate="2017-04-13T04:32:34.980" Title="What are the roles of guanidine-HCl and ethanol in binding of DNA to silica?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;lab-techniques&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16284" PostTypeId="1" CreationDate="2014-04-01T20:15:47.840" Score="5" ViewCount="766" Body="&lt;p&gt;Standard protocol states having two compatible vectors being transformed simultaneously during the same procedure. I've come across a situation in which transforming one vector, obtaining results, and then transforming the other is preferable. &lt;strong&gt;Is there any reason to think that this wouldn't work? Do I risk losing my first vector upon transformation of the second?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="307" LastActivityDate="2014-04-01T20:56:28.230" Title="Is a sequential double transformation acceptable?" Tags="&lt;microbiology&gt;&lt;protocol&gt;&lt;plasmids&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16285" PostTypeId="2" ParentId="10982" CreationDate="2014-04-01T20:48:34.897" Score="1" Body="&lt;p&gt;Pavement cells should content you:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/SzRon.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://dev.biologists.org/content/131/21/5215.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://dev.biologists.org/content/131/21/5215.full&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6224" LastActivityDate="2014-04-01T20:48:34.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16286" PostTypeId="2" ParentId="16284" CreationDate="2014-04-01T20:56:28.230" Score="4" Body="&lt;p&gt;If the plasmids you wish to transform are very big (more than 20kb), the co-transformation might not be very efficient (you might not get any colonies). Electroporation should work though, as electrocompetent cells are more efficient than chemically competent cells. Alternatively, as you have read, you could transform your first plasmid and select for it, and then make these cell that harbor it competent and transform the second plasmid. As long as you select for the plasmids (with kan/carb/etc resistance marker), the cells that grow on the selective media will keep both of them. If I were you, I would try the co-transformation and then if it doesn't work I would do the sequential transformation.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2014-04-01T20:56:28.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16287" PostTypeId="1" CreationDate="2014-04-01T21:12:41.033" Score="2" ViewCount="1589" Body="&lt;p&gt;Why is it inevitable that evolution by mutations alone should be a common cause of evolutionary change in most natural populations? And do you expect mutation-driven evolution to be more common in typical protists or typical prokaryotes? Why? &lt;/p&gt;&#xA;" OwnerDisplayName="user6225" LastEditorUserId="3632" LastEditDate="2014-05-25T04:04:43.303" LastActivityDate="2015-01-03T23:39:40.040" Title="How does mutation cause natural selection? and is it common in protists or prokaryotes?" Tags="&lt;mutations&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16288" PostTypeId="1" AcceptedAnswerId="17052" CreationDate="2014-04-01T22:25:48.407" Score="2" ViewCount="80" Body="&lt;p&gt;Which usage is better for referring to a &quot;cosmid library of genomic DNA fragments&quot;?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-05-01T10:29:52.963" Title="Cosmid genomic library, or genomic cosmid library?" Tags="&lt;genetics&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16289" PostTypeId="1" AcceptedAnswerId="16296" CreationDate="2014-04-01T22:38:26.120" Score="2" ViewCount="135" Body="&lt;p&gt;I am reading &lt;em&gt;fw2.2: A Quantitative Trait Locus Key to the Evolution of Tomato Fruit Size&lt;/em&gt; (doi: 10.1126/science.289.5476.85).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors are trying to find the gene that makes tomatoes bigger. As far as I understand, previous research had narrowed it down to &quot;something&quot; in the region of the genome called &lt;em&gt;fw2.2&lt;/em&gt;. They are trying to determine the actual genetic elements responsible (which turns out to be a gene similar to human &lt;em&gt;HRAS&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Supposedly, the big-fruit allele is recessive and the small-fruit allele is dominant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They say (in section &lt;em&gt;Genetic complementation with fw2.2&lt;/em&gt;) that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;They got a YAC containing the &lt;em&gt;fw2.2&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;li&gt;They &quot;screened a cDNA library&quot; with the YAC to find transcripts that were potentially relevant. (&lt;strong&gt;&lt;em&gt;How?&lt;/em&gt;&lt;/strong&gt;)&lt;/li&gt;&#xA;&lt;li&gt;They &quot;screened a cosmid library&quot; of genomic fragments to find the stretch of genome that the cosmid came from. (&lt;strong&gt;&lt;em&gt;How?&lt;/em&gt;&lt;/strong&gt;)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;It is unclear to me how steps 2 and 3 work. Can someone explain how you can take a YAC, cDNA library and cosmid library to find the gene inside the region responsible for your trait, as these researchers describe?&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="3624" LastEditDate="2014-04-02T19:53:38.870" LastActivityDate="2014-04-02T19:53:38.870" Title="How can a YAC be screened against a cDNA library and a cosmid library of genomic DNA to find a gene?" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;forward-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16290" PostTypeId="1" AcceptedAnswerId="16291" CreationDate="2014-04-01T22:50:46.463" Score="3" ViewCount="5734" Body="&lt;p&gt;I've been trying to a good contrast for my DNA bands, however I haven't been so successful. I've been running the ladders only to make sure I get a good contrast before further experimentation.&#xA;I created the gel using 70mL 1X TAE buffer, 0.84g of agarose (so about 1.2% gel), and 28ul EtBr.&#xA;I set the electrophoresis box at 90V for about 1 hour hoping to get a better gel but the results came out looking the same as if I had ran it at 110V.&#xA;I've attached a picture of my gel. It was taken with a DSLR, no flash, 20 seconds exposure time.&#xA;Any tips would help. Thanks&#xA;&lt;img src=&quot;https://i.stack.imgur.com/2jvk1.jpg&quot; alt=&quot;Picture of Gel with ladder&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6183" LastActivityDate="2015-11-23T18:32:17.600" Title="How do I get a brighter DNA bands" Tags="&lt;gel-electrophoresis&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16291" PostTypeId="2" ParentId="16290" CreationDate="2014-04-01T23:14:13.280" Score="4" Body="&lt;p&gt;I normally use 1-2 ul (depending on whether my gut tells me I have a lot of DNA, or a little that day) in a 70 ml 1% gel (which is probably 60-65 ml after boiling in the microwave). I have no trouble whatsoever seeing ladders and DNA samples of down to 100 ug in wells not much bigger than about 4 mm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are the factors that you can manipulate to alter the brightness:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Amount of EtBr. More is brighter. (However, you already use a lot - using less may even be better because it would reduce background while still saturating the DNA with EtBr)&lt;/li&gt;&#xA;&lt;li&gt;Amount of DNA. More is brighter. To avoid guesswork, use a ladder and consult the instructions in its manual or spec sheet. They usually have an example picture of a gel, and say exactly how they obtained it.&lt;/li&gt;&#xA;&lt;li&gt;You messed up. Do other people in the lab get good gels? Ask them to do the protocol with you.&lt;/li&gt;&#xA;&lt;li&gt;Sample preparation. Are you using a loading dye in the correct amount? Is the DNA diffusing out of the wells? Are you spilling a lot of it when you load?&lt;/li&gt;&#xA;&lt;li&gt;Band width. Obviously if you load the same amount of DNA in a well 4 times as wide, it will be 4 times fainter.&lt;/li&gt;&#xA;&lt;li&gt;Strength of UV light. Many illuminators have a knob to adjust the intensity, people turn it down to avoid damaging DNA when gel-purifying restriction fragments. You can also play with intensity, gamma and exposure in a geldoc machine.&lt;/li&gt;&#xA;&lt;li&gt;Quality of EtBr. I've never actually had this happen, but your stock may be bad for some reason. Ask another lab for a ul or two to easily control for this.&lt;/li&gt;&#xA;&lt;li&gt;Quality of DNA. Obviously, your sample must actually have DNA in it, and not be degraded. You can check amount and purity easily with a spectrophotometer, but it will not tell you if the DNA has been digested into its component nucleotides (that is usually checked with a gel).&lt;/li&gt;&#xA;&lt;li&gt;Amount of gel. The crucial variable is obviously not total amount of EtBr, but concentration. Less gel, brighter bands - but you seem to be using a standard gel amount.&lt;/li&gt;&#xA;&lt;li&gt;Quality of gel. Again, never had this happen, but try making the gel with someone else's reagents.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I can see that you have a ladder in the middle, so at least some DNA is definitely there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, keep in mind that off-the-shelf cameras are not good at imaging the EtBr fluorescence, because the wavelength is a bit unusual. The nice pictures you see in papers are taken with a specialized geldoc machine or a camera with an appropriate filter.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-04-01T23:14:13.280" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16292" PostTypeId="2" ParentId="16232" CreationDate="2014-04-01T23:40:39.987" Score="0" Body="&lt;p&gt;Obviously, it is conceivable that DNA could be so damaged that the organism dies. Trivially, blasting cells with radiation will cause rampant DNA damage, which will trigger p53 and lead to the cells suiciding (apoptosis), this is a &quot;deliberate&quot; (so to speak) mechanism to manage cancer risk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practice, the reason DNA damage leads to death is usually not because the information is corrupted and important functions are abrogated, but because the mutations lead to cancer, and the cancer leads to death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, most people don't die of cancer. A lot do, especially in developed countries, but &lt;a href=&quot;https://en.wikipedia.org/wiki/List_of_causes_of_death_by_rate&quot; rel=&quot;nofollow&quot;&gt;most often&lt;/a&gt; people die because of infection or heart failure. Other major causes include neurodegenerative disease (neurons dying) and diabetes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are asking whether in some part of the DNA, there is a bit saying &lt;code&gt;Maximum_Age = 85&lt;/code&gt; (by analogy to programming constants), I don't think anything of the sort has been found. The body naturally has finite lifespan because things break, this is extended up to a point because the body also has mechanisms to repair some kinds of damage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why not repair all kinds of damage? Why are the repair processes imperfect, and cannot maintain the organism indefinitely? Good questions, without good answers known to science.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-04-01T23:40:39.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16293" PostTypeId="2" ParentId="16287" CreationDate="2014-04-01T23:41:05.493" Score="1" Body="&lt;p&gt;Your question, as I understand it, concerns the relative role (compare to natural selection and drift probably) of mutation in evolution. But evolution is not one process. Mutation and natural selection are processes that influence populations in very a different manners. At first sight, it seems to me that it does not make sense to weight the important of mutation versus other processes such as selection. But again, in what term would weight these processes?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-04-01T23:41:05.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16294" PostTypeId="2" ParentId="16248" CreationDate="2014-04-02T03:46:46.207" Score="1" Body="&lt;p&gt;Well, the total genetic variance is just, by the definition of the variance,&#xA;$$&#xA;\sigma^2 =\sum_{i,j} f_i f_j (w_{ij}-\bar{w})^2&#xA;$$&#xA;(using $f_i$ and $w_{ij}$ for frequency and fitness, respectively), and&#xA;$$\bar{w} = \sum_{i,j} f_i f_j w_{ij}$$ is just the average fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can calculate the additive genetic variance for different loci by simply assuming that there is no dominance effect, i.e. the alleles are independent. If it helps, think of it as a quantitative trait in a haploid organism. Thus,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;\sigma^2_A =\sum_{i,j} f_i f_j (w_iw_j-\bar{w}')^2 = \sum_i f_i(w_i-\bar{w}')^2.&#xA;$$&#xA;with &#xA;$$&#xA;f_i=\sum_jf_{ij};  w_i=\sum_j f_{ij}w_{ij}; \bar{w}' = \sum_i f_i w_i; &#xA;$$&lt;/p&gt;&#xA;" OwnerUserId="3029" LastActivityDate="2014-04-02T03:46:46.207" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16295" PostTypeId="1" CreationDate="2014-04-02T05:08:02.107" Score="6" ViewCount="727" Body="&lt;p&gt;If there is more dopamine action in the mesocortical pathway in schizophrenia, then schizophrenics should always be in euphoric state. Instead, schizophrenics often lack motivation and do not experience pleasure. Why?&lt;/p&gt;&#xA;" OwnerUserId="6229" LastEditorUserId="9943" LastEditDate="2016-03-30T12:20:07.933" LastActivityDate="2016-03-30T13:15:02.933" Title="Dopamine paradox in schizophrenia" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16296" PostTypeId="2" ParentId="16289" CreationDate="2014-04-02T06:22:57.063" Score="2" Body="&lt;p&gt;The YAC contains a segment of chromosomal DNA. By using it as a probe they could screen the cDNA library to find cDNAs derived from that genomic region. This would be done by plaque or colony hybridisation. The cDNA clones thus identified represent the &quot;candidate genes&quot; . &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The last step is a little unclear. Clearly they are identifying cosmid clones that map to the segment of interest, but they could be using either the YAC or relevant cDNA clones (could be pooled for this step depending upon their aim) as probes. My guess is that they used individual cDNA clones to find corresponding cosmid fragments so that they could home in on the regions encoding the identified cDNAs.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-04-02T06:22:57.063" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16297" PostTypeId="1" AcceptedAnswerId="16299" CreationDate="2014-04-02T10:14:56.830" Score="3" ViewCount="625" Body="&lt;p&gt;I would like to mesure DNA. I quantify the concentration with Qubit fluorometer, but I would like to know also quality of DNA. I try BioAnalyzer (Agilent),but without success. Bioanalyzer measure DNA samples from 100 to 7 000 bp (12 000 bp). Problem is that my DNA is not sheared, I would like to quantify whole mouse DNA. Have you any idea? Thanks!&lt;/p&gt;&#xA;" OwnerUserId="5893" LastActivityDate="2014-04-02T17:25:41.820" Title="How to measure quality and quantity of DNA?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16298" PostTypeId="2" ParentId="16156" CreationDate="2014-04-02T10:41:28.460" Score="1" Body="&lt;p&gt;According to the classification of sepsis, it is SIRS with a suspected or known source of infection. By definition therefore, sepsis without SIRS is not sepsis but SIRS can exist without sepsis. In all fairness though, SIRS can exist if you run for a while (elevated heart rate and respiratory rate by themselves qualify for a diagnosis of SIRS). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sepsis is however not the same as a bacteraemia which may be caused even by brushing your teeth (although the bacteraemia in this case is transient). &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-04-02T10:41:28.460" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16299" PostTypeId="2" ParentId="16297" CreationDate="2014-04-02T12:48:31.010" Score="7" Body="&lt;p&gt;You can run your DNA sample on agarose gel to see, whether you have significant degradation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in contamination, you can make a standard photometric analysis to assess the &lt;a href=&quot;https://en.wikipedia.org/wiki/Nucleic_acid_quantitation#Spectrophotometric_analysis&quot;&gt;260/280 and 260/230 ratios&lt;/a&gt; and absorbance at 320 nm on NanoDrop or even something similar to Eppendorf's BioPhotometer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case RNA may be an obstacle for some down-stream procedures, with Qubit you can also measure separately DNA and RNA concentrations and then decide if you have too much RNA and it's worth treating your sample with RNase.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-04-02T17:25:41.820" LastActivityDate="2014-04-02T17:25:41.820" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16300" PostTypeId="1" AcceptedAnswerId="16301" CreationDate="2014-04-02T13:07:25.690" Score="3" ViewCount="2087" Body="&lt;p&gt;In many papers the MAPK pathway, (along with many others) is referred to as being conserved: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www3.aiche.org/Proceedings/Abstract.aspx?PaperID=133783&quot; rel=&quot;nofollow&quot;&gt;Example&lt;/a&gt;: &quot;The mitogen-activated protein kinase (MAPK) cascades are ubiquitous in eukaryotic signal transduction, and these pathways are conserved in cells from yeast to mammals&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hippo_signaling_pathway&quot; rel=&quot;nofollow&quot;&gt;example 2&lt;/a&gt; &quot;The Hippo signaling pathway appears to be highly conserved.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does it mean for a pathway to be conserved?&lt;/p&gt;&#xA;" OwnerUserId="3338" LastEditorUserId="3338" LastEditDate="2014-04-02T13:20:12.730" LastActivityDate="2014-04-02T13:40:07.653" Title="What does it mean for a chemical pathway to be conserved?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16301" PostTypeId="2" ParentId="16300" CreationDate="2014-04-02T13:31:28.807" Score="5" Body="&lt;p&gt;A conserved pathway is a pathway that exists in a variety of species, by virtue of that pathway being conserved throughout the evolution of those species. A pathway must by neccessity have appeared for the first time in one particular species. If that species gives rise to new species, but the pathway in question is identical or very similar in all the new species, it is sensible to say that pathway has been evolutionary conserved. This may imply that the pathway in its conserved form is important for the fitness of those species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For some examples, here is a page on evolutionary conserved pathways in Drosophila: &lt;a href=&quot;http://www.sdbonline.org/sites/fly/aimain/aadevinx.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.sdbonline.org/sites/fly/aimain/aadevinx.htm&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-04-02T13:40:07.653" LastActivityDate="2014-04-02T13:40:07.653" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16305" PostTypeId="1" CreationDate="2014-04-02T18:37:28.120" Score="3" ViewCount="1623" Body="&lt;p&gt;I have intuition that sepsis with infection can cause:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;spastic functioning of heart during systole&lt;/li&gt;&#xA;&lt;li&gt;heart working spontaneously in snatches during systole&lt;/li&gt;&#xA;&lt;li&gt;atrial fibrillation&lt;/li&gt;&#xA;&lt;li&gt;first contraction of ventricles ends earlier&lt;/li&gt;&#xA;&lt;li&gt;which follows Action potential from A-V node during relative refractory period&lt;/li&gt;&#xA;&lt;li&gt;weak second contraction&lt;/li&gt;&#xA;&lt;li&gt;long compensatory pause&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which can be recorded as spikes in the time axis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With arrhythmic (earlier myocardial infarction) patients, sepsis seems to also cause leaking of valves, weakened compliance of vessels and structure of the heart. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there are creaking sounds in the spectrum spaces.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do the symptoms of sepsis affect heart function?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking if it is possible that this leakiness of valves and weakened compliance last only for short term and occurs periodically, during which also the heart pumps more frequently load during extrasystoles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume that everything listed above is possible. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can temporary acute/chronic inflammation in the heart cause such symptoms such as sudden weakening of valves and only temporary weakened compliance of coronary vessels?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the reason can be thromboembolism which is causing the sudden spastic function and weakened function of vessels and heart structures.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="107" LastEditDate="2016-01-09T01:49:07.170" LastActivityDate="2016-01-09T01:49:07.170" Title="How does sepsis affect heart function?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;electrocardiography&gt;&lt;sepsis&gt;&lt;sirs&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16306" PostTypeId="1" CreationDate="2014-04-02T19:32:19.547" Score="0" ViewCount="99" Body="&lt;p&gt;I am trying to visualise possible ranges of frequencies from different structures of heart:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;different valves and their possible frequencies&lt;/li&gt;&#xA;&lt;li&gt;heart sounds I - IV and their normal frequencties&lt;/li&gt;&#xA;&lt;li&gt;what can frequencies be in healthy situation for adult&lt;/li&gt;&#xA;&lt;li&gt;what can frequencies be in healthy situation for children 4-9 years old&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I searched meta-analysis, clinical trials and reviews in PubMed unsuccessfully.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any review article or book about the frequencies from different structures of heart?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Search terms used&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;frequency heart&lt;/li&gt;&#xA;&lt;li&gt;frequency heart valve&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="86" LastEditorUserId="69" LastEditDate="2014-04-03T18:33:44.890" LastActivityDate="2014-09-28T11:13:29.840" Title="Normal Frequencies in Heart" Tags="&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16307" PostTypeId="2" ParentId="10654" CreationDate="2014-04-02T21:26:07.403" Score="1" Body="&lt;p&gt;BioGRID is an interaction database, and they catalogue interactions by (among other things) the class of experiment that discovered them. See &lt;a href=&quot;http://wiki.thebiogrid.org/doku.php/experimental_systems#genetic_interactions&quot; rel=&quot;nofollow&quot;&gt;http://wiki.thebiogrid.org/doku.php/experimental_systems#genetic_interactions&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other than that, you should look at recent reviews and publications, but you will easily get lost unless you figure out some important particulars, like:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What species? Yeast, worm, human, cell line?&lt;/li&gt;&#xA;&lt;li&gt;What sort of interaction? Synthetic lethality? Complicated, fancy epistasis?&lt;/li&gt;&#xA;&lt;li&gt;How much? Genome-wide? 2-3 genes?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-04-02T21:26:07.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16308" PostTypeId="5" CreationDate="2014-04-02T21:49:08.067" Score="0" Body="&lt;p&gt;It is a common and basic question of biology to ask, &quot;What causes this trait?&quot;. The biologist could then employ a variety of methods to find the genetic elements which influence this trait. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Simple examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Repeated breeding to determine if the trait is Mendelian (which implies a single gene that causes it)&lt;/li&gt;&#xA;&lt;li&gt;Looking at how different traits assort to determine which chromosomes they are on&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;More complicated examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;GWAS&lt;/li&gt;&#xA;&lt;li&gt;Isolating most and least fit of members of a population of cancer cells, then comparing their genomes&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The tag applies to question where the trait is known, and the desire is to find what genes are responsible for it. For example, questions about finding genetic causes of a disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This does not necessarily apply to all questions about causes of a trait. Forward genetics is a &lt;em&gt;research strategy&lt;/em&gt; for investigating a trait, not the body of knowledge about the genetic basis of traits. So, the tag is appropriate for &quot;&lt;em&gt;What experiments can I do to figure out what causes trait X?&lt;/em&gt;&quot; or even &quot;&lt;em&gt;Are there any published experiments that tried to find the cause for trait X?&lt;/em&gt;&quot; but &lt;strong&gt;not&lt;/strong&gt; &quot;&lt;em&gt;What causes trait X?&lt;/em&gt;&quot;.&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-04-02T22:06:46.880" LastActivityDate="2014-04-02T22:06:46.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16309" PostTypeId="4" CreationDate="2014-04-02T21:49:08.067" Score="0" Body="Start with a phenotype, and try to figure out the genotype that causes it. GWAS, linkage disequilibrium mapping, etc." OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-04-02T22:06:36.763" LastActivityDate="2014-04-02T22:06:36.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16310" PostTypeId="1" CreationDate="2014-04-02T21:55:37.790" Score="2" ViewCount="125" Body="&lt;p&gt;How does TILLING (Targeting Induced Local Lesions in Genomes) work? What is needed to perform a TILLING experiment, and what kind of information can we get out of it?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-04-02T21:55:37.790" Title="What is TILLING?" Tags="&lt;genetics&gt;&lt;mutations&gt;&lt;reverse-genetics&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16311" PostTypeId="5" CreationDate="2014-04-02T22:07:39.773" Score="0" Body="&lt;p&gt;As sequencing became cheaper and easier, biologists were often faced with the problem of having an expressed ORF but no information on its function. Reverse genetics refers to the family of methodologies for manipulating a gene and in order to study its phenotypic effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Knockout mutations and transgenic animals (if done to understand the resulting phenotype), mutation screens and TILLING are all examples of reverse genetics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This tag applies to questions which are about studying the function of a gene by manipulating it genetically. For instance, &quot;&lt;em&gt;How can I mutate an ORF of unknown function to understand what it does?&lt;/em&gt;&quot; but not &quot;&lt;em&gt;What is the function of gene X?&lt;/em&gt;&quot;. Using bioinformatics techniques to infer the function of a gene in silico based on the sequence is usually not considered reverse genetics, reverse genetics involve introducing mutations into the gene.&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-04-03T01:00:07.053" LastActivityDate="2014-04-03T01:00:07.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16312" PostTypeId="4" CreationDate="2014-04-02T22:07:39.773" Score="0" Body="Utilize gene sequencing to determine the phenotypic effect of a particular genetic sequence." OwnerUserId="-1" LastEditorUserId="4101" LastEditDate="2014-04-03T00:23:52.263" LastActivityDate="2014-04-03T00:23:52.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16313" PostTypeId="1" AcceptedAnswerId="16347" CreationDate="2014-04-03T02:30:10.963" Score="2" ViewCount="1427" Body="&lt;p&gt;We generally have a good idea of how DNA separates using agarose gel electrophoresis, how well does DNA resolve on a SEC resin like superose? I get the impression that salt influences where it elutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to compare the molecular weight of DNA and where it elutes to the molecular weight of proteins and peptides and where that elutes?&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2014-04-04T21:05:08.063" Title="How does DNA resolve on size exclusion resin?" Tags="&lt;dna&gt;&lt;purification&gt;&lt;chromatography&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16314" PostTypeId="1" CreationDate="2014-04-03T04:05:52.740" Score="1" ViewCount="136" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/93UMh.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone please help with this question? Here is my working (just in case it is not clear: 1/300*1/30*1/2) but is this actually correct or do I need to multiply by 0.5 once again? I appreciate any help! &lt;/p&gt;&#xA;" OwnerUserId="5460" LastActivityDate="2014-04-03T18:36:22.087" Title="Population Genetics Question" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;mutations&gt;&lt;allele&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16316" PostTypeId="1" AcceptedAnswerId="16323" CreationDate="2014-04-03T08:58:36.297" Score="3" ViewCount="228" Body="&lt;p&gt;What is the energy consumption of the brain, and is there a difference in consumption when waking and sleeping?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastEditorUserId="3624" LastEditDate="2014-04-03T18:03:59.187" LastActivityDate="2014-04-03T18:03:59.187" Title="What is the energy consumption of the brain?" Tags="&lt;neuroscience&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16319" PostTypeId="1" AcceptedAnswerId="16322" CreationDate="2014-04-03T11:29:48.620" Score="0" ViewCount="2404" Body="&lt;p&gt;I've recently had a blood test and the results displayed elevated levels of erythrocytes as well as hemoglobin. (As a result my hematocrit levels were also above average)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At my workplace there is a water cooler which also has an option to dispense carbonated water (this is just regular ol' carbonated tap water) and usually over the course of the day I tend to drink quite a lot of the stuff.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since erythrocytes/hemoglobin deals with O&lt;sub&gt;2&lt;/sub&gt; and CO&lt;sub&gt;2&lt;/sub&gt; transport, I was wondering if my daily consumption of carbonated water is a plausible cause for the additional erythrocytes that are being pumped out?&lt;/p&gt;&#xA;" OwnerUserId="6236" LastActivityDate="2017-08-19T01:52:30.047" Title="Can excessive carbonated drink consumption lead to elevated red blood cell levels?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;red-blood-cell&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16320" PostTypeId="2" ParentId="16319" CreationDate="2014-04-03T12:08:37.023" Score="1" Body="&lt;p&gt;Answer: No. How should the CO&lt;sub&gt;2&lt;/sub&gt; from you stomach get into your blood? &#xA;And: Most of the CO&lt;sub&gt;2&lt;/sub&gt;  is removed (by burping) from the solution in your stomach anyway due to the conditions there.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="3340" LastEditDate="2014-12-31T07:14:14.670" LastActivityDate="2014-12-31T07:14:14.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16321" PostTypeId="1" AcceptedAnswerId="16328" CreationDate="2014-04-03T12:49:11.670" Score="3" ViewCount="151" Body="&lt;p&gt;Can someone point me out to literature (reviews or better workbooks) describing industrial chemical reactions catalysed by enzymes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm most interested in are case studies of how the output of a reaction on a big scale is optimized with respect to enzyme activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the literature I'm finding is about optimization of cell growth, which is not what I'm looking for.&lt;/p&gt;&#xA;" OwnerUserId="4971" LastActivityDate="2014-04-04T21:50:59.747" Title="Literature about industrial enzyme application" Tags="&lt;enzymes&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16322" PostTypeId="2" ParentId="16319" CreationDate="2014-04-03T12:52:05.397" Score="3" Body="&lt;p&gt;The main regulatory input into erythrocyte production is hypoxia. The response to elevated CO&lt;sub&gt;2&lt;/sub&gt; levels in the blood (&lt;a href=&quot;http://en.wikipedia.org/wiki/Hypercarbia&quot; rel=&quot;nofollow&quot;&gt;hypercapnia&lt;/a&gt;) is mainly to increase ventilation (i.e. more and/or deeper breaths) so that the excess can be &quot;blown off&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that some carbon dioxide could pass into the bloodstream from the stomach since gases tend to be quite good at diffusing across membranes, but this would be easily dealt with by the physiological mechanism described above.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-04-03T15:44:35.943" LastActivityDate="2014-04-03T15:44:35.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16323" PostTypeId="2" ParentId="16316" CreationDate="2014-04-03T13:04:52.330" Score="1" Body="&lt;p&gt;I assume that you mean energy consumption.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Talking in round numbers the daily energy requirement of a sedentary human is 2,500 kcal. It's usually said that the brain uses 20% of this energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does this mean in terms of power consumption?&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;500 kcal = 500 x 1000 x 4.2 J  -[1]&#xA;24 h = 24 x 60 x 60 s          -[2]   &#xA;&#xA;1 W = 1 J/s&#xA;&#xA;therefore brain power  = [1]/[2] = approximately 24 W&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Most of the energy consumed by the brain is used in maintaining membrane potentials so energy is used continuously. I would think that there will be very little difference between waking and sleeping.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-04-03T13:04:52.330" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16324" PostTypeId="2" ParentId="14650" CreationDate="2014-04-03T13:41:15.080" Score="2" Body="&lt;p&gt;It is very likely what they mean by &quot;neurotransmitters flooding the brain&quot; is the phenomenon called &lt;strong&gt;Volume Transmission&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I paraphrase from &lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Chemical_synapse#Volume_transmission&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;&lt;/strong&gt; source:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When a neurotransmitter is released at a synapse, it reaches its&#xA;  highest concentration inside the narrow space of the synaptic cleft,&#xA;  but some of it is certain to diffuse away before being reabsorbed or&#xA;  broken down. If it diffuses away, it has the potential to activate&#xA;  receptors that are located either at other synapses or on the membrane&#xA;  away from any synapse. The extrasynaptic activity of a&#xA;  neurotransmitter is known as volume transmission. It is well&#xA;  established that such effects occur to some degree, but their&#xA;  functional importance has long been a matter of controversy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5005" LastActivityDate="2014-04-03T13:41:15.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16325" PostTypeId="1" CreationDate="2014-04-03T18:06:49.480" Score="1" ViewCount="49" Body="&lt;p&gt;I have heard about the triune brain model in biology class, but my teacher does not know much about it. What I'm curious about, is this model accepted by most of the neuroscientists, or is it just a mere hypothesis? And should I learn more about it? Although I think it's an interesting topic, I won't put efforts in finding all the info on the net, if not necessary. &lt;/p&gt;&#xA;" OwnerUserId="6241" LastActivityDate="2014-04-03T18:06:49.480" Title="Triune brain model" Tags="&lt;evolution&gt;&lt;brain&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16326" PostTypeId="2" ParentId="16314" CreationDate="2014-04-03T18:36:22.087" Score="1" Body="&lt;p&gt;Question is: If an Ashkenazi(1/30) and(multiply) French-Canadian(1/30) ....&#xA;Where 1/300 came from ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I duno, I may missing something - but may it be like  that&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Parrent1(=1/30 * 1/2)*Parrent2(=1/30 * 1/2) = P(child with both mutations)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="6240" LastActivityDate="2014-04-03T18:36:22.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16327" PostTypeId="1" CreationDate="2014-04-03T20:30:11.393" Score="7" ViewCount="945" Body="&lt;p&gt;What exactly is tinnitus? What is it's cause, and why do some people hear it and others don't?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2015-04-30T15:09:13.300" Title="What exactly is Tinnitus?" Tags="&lt;neuroanatomy&gt;&lt;hearing&gt;&lt;human-ear&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16328" PostTypeId="2" ParentId="16321" CreationDate="2014-04-03T22:32:44.273" Score="2" Body="&lt;p&gt;I'll give you examples I have encountered in talks. There are too many variations and types of applications for me to break out in a comprehensive way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example 1: enzyme production.  this sort of application is about optimizing the amount of a desirable enzyme or protein produced from a liquid culture.  Sorry if this is too close to cell growth, but its terribly important.  Small cell cultures are used in research and the genetics of the cells (usually e coli or yeast, but also often a fungus that's been found somewhere) to improve the amount of the desired protein.  The protein may be secreted, which makes it much easier to purify.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once a good strain is found, the culture is scaled up to thousands of liters, often many kilos of pure enzyme can be produced this way.  Examples: the enzymes that break down fabric for acid washed jeans, the proteases and cutinases which are included in laundry detergent&#xA;and insulin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example 2: glucose isomerase.  &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bit.260300715/abstract&quot; rel=&quot;nofollow&quot;&gt;This enzyme is used to produce high fructose corn syrup&lt;/a&gt;.  The enzyme itself actually changes fructose into glucose, but by &lt;a href=&quot;http://www.chemguide.co.uk/physical/equilibria/lechatelier.html&quot; rel=&quot;nofollow&quot;&gt;le Chatlier's principle&lt;/a&gt;, a glucose syrup under high pressure will be converted to fructose by the enzyme.  This enzyme, produced by an industrial process like that described in example 1 is immobilized onto a resin and packed into large industrial sized columns.  I seem to remember from the talk that they were similar in size to an oil barrel.  Large amounts of glucose rich corn syrup are passed through the column; it comes out about 40% fructose. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example (3)  along those lines might be how to use an enzyme with a product.  In an industrial manufacturing process like &lt;a href=&quot;http://www.abenzymes.com/products/technical-enzymes/denim-wash-and-bio-finishing&quot; rel=&quot;nofollow&quot;&gt;enzyme denim treatment&lt;/a&gt;, the fabric may be washed in a solution including the enzyme.  The process has to be careful to control the amount of enzyme the denim is exposed to and to optimize the conditions so that none of the fabric is ruined but comes out consistently.  The enzyme might be killed by a pH change or heating.  This is essentially chemical engineering and there are courses about this sort of thing at &lt;a href=&quot;http://scpd.stanford.edu/public/category/courseCategoryCertificateProfile.do?method=load&amp;amp;certificateId=15533128&quot; rel=&quot;nofollow&quot;&gt;most major chemE departments now&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-04-04T21:50:59.747" LastActivityDate="2014-04-04T21:50:59.747" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16330" PostTypeId="1" CreationDate="2014-04-03T23:45:50.227" Score="4" ViewCount="325" Body="&lt;p&gt;I am looking for a good book that gives a nice overview of the science and technics of selective breeding. I am particularly interested in the use of population genetics to support decision in this applied field. So do you have any suggestions?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Below are some examples of question that I would hope that book answers.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;If the artificial selection is too strong, it is very likely that some beneficial alleles will disappear. How strong do we decide artificial selection to be?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How do we deal with various lifetime?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How do we deal with species that can have only few babies so that we are obliged to limit the strength of selection to keep a stable population size?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How do we make sure to not reduce the immunologic genetic diversity within the population to zero but only to reduce the diversity of genes that influence the trait of interest?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is it better to wait to be able to measure the quantity of milk in the sisters of a bull in order to infer about the quality of the bull or is it wiser to directly allow the bull to reproduce to speed things up? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How are the estimations of heritability performed?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How do we measure the impact of various environment of the trait of interest?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Which cultural traits should we allow to spread and which should we stop?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How can we use a correlated trait to infer more simply or more rapidly of the amplitude of the trait of interest?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How much outbreeding should we allow?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When is mutation breeding preferable?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and more globally some questions of the kind:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;What are the different solution to artificially inseminate?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Can we select on the spermatozoids?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What financial elements should be taken into before creating a breeding plan?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;GWA's studies in selective breeding&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What is the relative importance of selective breeding and GMO in current economy and in our current ability to improve strains for our purposes?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-04-06T20:45:07.537" LastActivityDate="2014-08-14T15:55:37.097" Title="Book recommendation on selective breeding?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;food&gt;&lt;population-biology&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16332" PostTypeId="2" ParentId="15759" CreationDate="2014-04-04T04:25:10.080" Score="1" Body="&lt;p&gt;This is speculation, as I haven't done or read of the required experiment. However, I imagine that this would not be a problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You're right that the RNA template (&lt;a href=&quot;http://en.wikipedia.org/wiki/Telomerase_RNA_component&quot; rel=&quot;nofollow&quot;&gt;TERC&lt;/a&gt;) would not hybridize with a poly-G sequence, and so the telomerase would not be able to add more telomere repeats. You can imagine that the poly-G sequence is a cap, preventing telomerase activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, without the telomere repeats other proteins are likely to recognize the chromosome end as a DNA break. Exonucleases would likely chew at the end of the chromosome until they got to the actual telomere sequence, which is bound by protective proteins (namely &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16166375&quot; rel=&quot;nofollow&quot;&gt;Shelterin&lt;/a&gt;). With the poly-G region degraded, the end of the chromosome would now have the true telomere repeats, and telomerase would be able to add even more repeats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if the poly-G region was bound by protective proteins, the telomeres naturally shorten with each replication cycle, due to the nature of &lt;a href=&quot;http://en.wikipedia.org/wiki/Okazaki_fragment&quot; rel=&quot;nofollow&quot;&gt;5' to 3' DNA replication&lt;/a&gt;. Therefore, the poly-G region would eventually be removed revealing the true telomere repeats and allowing telomerase to extend the chromosome once again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a worst case scenario, rather than degrade the poly-G region the cell undergoes recombination between poly-G regions on multiple chromosomes, leading to either massive chromosomes or circular chromosomes. However, I'm sure these cells would die with some kind of massive mitotic failure.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-04-04T04:25:10.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16333" PostTypeId="2" ParentId="14946" CreationDate="2014-04-04T05:12:50.600" Score="3" Body="&lt;p&gt;I'm pretty sure this doesn't exist. If it did, that would be awesome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following is 100% pure speculation with nothing to back this up at all (as a disclaimer).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phosphorus-31 (the stable isotope) is NMR active, which means that you could theoretically use an MRI machine to visualize phosphorus. A quick google search shows scientists attempting to use phosphorus MRI for &lt;a href=&quot;http://www.pnas.org/content/early/2012/03/12/1117293109.abstract?sid=96fad806-6097-413d-af31-bed001ea5804http://www.pnas.org/content/early/2012/03/12/1117293109.abstract?sid=96fad806-6097-413d-af31-bed001ea5804&quot; rel=&quot;nofollow&quot;&gt;visualizing bone structure&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't really know much about MRI, but I do know some about small molecule NMR, which is based on the same principles. This is a pretty cool paper showing phosphorus-31 NMR used to &lt;a href=&quot;http://www.pnas.org/content/97/12/6880&quot; rel=&quot;nofollow&quot;&gt;measure ATP synthesis&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe in the distant future it could be possible to use phosphorus-31 MRI to visualize ATP/ADP ratios in various tissues, including the brain. But that would be some amazing sci-fi stuff.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastEditorUserId="5771" LastEditDate="2014-04-05T20:59:47.007" LastActivityDate="2014-04-05T20:59:47.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16334" PostTypeId="2" ParentId="15797" CreationDate="2014-04-04T05:27:58.610" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.lifetechnologies.com/order/catalog/product/M36008?CID=search-M36008&quot; rel=&quot;nofollow&quot;&gt;MitoSOX&lt;/a&gt; looks pretty cool. I've never used it myself, but I'm sure you could see some cool mitochondrial dynamics going on. Its a bit pricey though, but all dyes are going to be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even at only 8 hours you should probably be able to see a few divisions, which would be cool with hoechst.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-04-04T05:27:58.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16335" PostTypeId="1" AcceptedAnswerId="16337" CreationDate="2014-04-04T06:46:55.517" Score="2" ViewCount="91" Body="&lt;p&gt;I prepare a experiment and I found $PacBio SMRT$ as the great way to sequence my PCR products. I find the cost: library preparation 655 dollars + sequencing 435 dollars. It seems very low. Do you have some experience how much of sample can I sequence in one run (by coverage around 30) and if it is really for this price? &lt;/p&gt;&#xA;" OwnerUserId="5893" LastActivityDate="2014-04-04T09:50:18.907" Title="Do you have experience with PacBio?" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16336" PostTypeId="2" ParentId="15004" CreationDate="2014-04-04T08:09:10.400" Score="2" Body="&lt;p&gt;blast2go is on the verge of getting commercialized (as they have started selling PRO versions) and my previous experience was not so good with it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I used IntrProScan to associate GO terms with the transcripts, it ran long but it reported all the possible sequence features.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To use these custom annotation was tricky for visualization, but thanks to BiNGO, I was able to do it flawlessly. For future use I have documented it here, &lt;a href=&quot;http://infoplatter.blogspot.in/2014/04/gene-ontology-go-enrichment-analysis-in.html&quot; rel=&quot;nofollow&quot;&gt;http://infoplatter.blogspot.in/2014/04/gene-ontology-go-enrichment-analysis-in.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good luck!!&lt;/p&gt;&#xA;" OwnerUserId="6247" LastActivityDate="2014-04-04T08:09:10.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16337" PostTypeId="2" ParentId="16335" CreationDate="2014-04-04T09:50:18.907" Score="3" Body="&lt;p&gt;If it is a good idea to use PacBio depends a lot on what you want to sequence and what you want to do with the data you get. In short: you get longer reads but about 15% error per base. This means, you will have to cope with those errors, there are possibilities to do that. How much coverage you will get of you sample I cannot tell you, as I do not know what kind of sample you want to sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much data you get out of one SMRTcell depends also on the chemistry, I think it currently is between 275 Mb and 375 Mb, depending on chemistry. They have a nice &lt;a href=&quot;http://files.pacb.com/pdf/PacBio_RS_II_Brochure.pdf&quot; rel=&quot;nofollow&quot;&gt;brochure&lt;/a&gt; you could look at.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, you probably will have to get some advice by a bioinformatician of you choice on how to design and analyse your sequencing experiment. &lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2014-04-04T09:50:18.907" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16340" PostTypeId="1" CreationDate="2014-04-04T15:12:25.297" Score="1" ViewCount="56" Body="&lt;p&gt;Anyone have a short &amp;amp; sweet protocol for PCR amplifying a region of human DNA (chromosomal or mt, I don't care) extracted from a buccal sample: including validated primer sequences and preferred method of DNA isolation from a buccal swab. I'm looking for a new exercise to run in my classroom. We would be able to follow the amplification up with Sanger sequencing, done in-house.  &lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-04-04T15:12:25.297" Title="condensed protocol for sequencing a portion of human DNA from buccal sample" Tags="&lt;dna&gt;&lt;dna-sequencing&gt;&lt;pcr&gt;&lt;human-genome&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16343" PostTypeId="1" AcceptedAnswerId="16346" CreationDate="2014-04-04T16:29:03.860" Score="4" ViewCount="150" Body="&lt;p&gt;I've read that some people in some countries actually use tapeworms as a form of losing weight.  What are the dangers to these people?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2014-04-06T11:02:35.440" Title="Tapeworms and their effect on humans" Tags="&lt;parasitology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16344" PostTypeId="1" AcceptedAnswerId="16402" CreationDate="2014-04-04T16:48:55.977" Score="1" ViewCount="130" Body="&lt;p&gt;Floating substances in the marine or freshwater environment often carry hitch hiking organisms. It is argued that many species may use this dispersal vector to reach new habitats, however to my knowledge there is no hard evidence / no documented case. This may be because of the difficulty to associate an established species with a certain vector of introduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By floating substances I refer to natural floating substances such as detached algae, trees or pumice and those of anthropogenic origin such as litter items, detached buoys, etc. (in whatever aquatic environment: sea, lakes, rivers)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help to find a reference / documented case study is very welcome!&lt;/p&gt;&#xA;" OwnerUserId="3258" LastActivityDate="2014-04-08T09:10:52.407" Title="Is there any documented case in which floating substances led to the introduction of a new species?" Tags="&lt;marine-biology&gt;&lt;invasive-species&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16346" PostTypeId="2" ParentId="16343" CreationDate="2014-04-04T20:58:46.710" Score="3" Body="&lt;p&gt;I haven't really found much on this topic (besides popular sites) but I can summarize it here:&#xA;There are quite some tapeworms (or cestoda), I found numbers of up to 3500 species. They attach to the intestinal wall of the humans and then start to take up predigested food through their skin. With that, they reduce food from their host and start to grow, some get as long as 15 meters!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the worms seem to be relatively harmless (besides stealing food), but this is more true for the first world. In poor countries, where there is not enough food, tapeworms can cause severe malnutrition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some tapeworms can migrate into the blood stream and from there into other tissues or organs like muscles, eye and brain. There they can cause cysts which can lead to organ failure and death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information see this &lt;a href=&quot;http://www.cdc.gov/parasites/taeniasis/gen_info/faqs.html&quot; rel=&quot;nofollow&quot;&gt;CDC webpage&lt;/a&gt; and this article: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/13973386&quot; rel=&quot;nofollow&quot;&gt;Biochemistry and physiology of tapeworms.&lt;/a&gt;&quot;. This popular &lt;a href=&quot;http://www.today.com/health/iowa-woman-tries-tapeworm-diet-prompts-doctor-warning-6C10935746&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; is probably also interesting.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-04T20:58:46.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16347" PostTypeId="2" ParentId="16313" CreationDate="2014-04-04T21:05:08.063" Score="1" Body="&lt;p&gt;It works pretty well and can be used to desalt DNA. The DNA runs a bit different than proteins since it is more a long stretched molecule while a lot of proteins are globular. See this references (the first is about the behaviour of DNA on superose):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2568993&quot; rel=&quot;nofollow&quot;&gt;Size-exclusion chromatography of DNA restriction fragments. Fragment&#xA;length determinations and a comparison with the behaviour of proteins&#xA;in size-exclusion chromatography.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ma00018a008&quot; rel=&quot;nofollow&quot;&gt;Size exclusion chromatography of DNA and viruses: properties of&#xA;spherical and asymmetric molecules in porous networks&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0021967309010450&quot; rel=&quot;nofollow&quot;&gt;Size exclusion chromatography of plasmid DNA isoforms&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-04T21:05:08.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16348" PostTypeId="2" ParentId="16327" CreationDate="2014-04-04T23:22:29.323" Score="8" Body="&lt;p&gt;Although tinnitus is usually described as a ringing in the ear, there's a whole range of tunes, buzzes, whooshing sounds, humming and hissing sounds that are described of as tinnitus. The sounds can either genuinely be there or be perceived to be there. If it is genuinely there it suggests muscles ate at play or some blood vessel disease if the sounds are in time with your pulse, but usually its the latter perceived to be there that presents. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tinnitus that is perceived and permanent usually suggests damage to your hearing nerve (called the auditory nerve or cranial nerve 8 or vestibulocochlear nerve). The common cause for this we see is patients that have been exposed to loud noises or drugs like certain strong antibiotics which cause damage to the nerve. Other drugs also have a side effect of causing tinnitus. However any ear problems really may cause tinnitus including ear infections, too much wax, getting older, a disease called Mennieres, tumours, neurological diseases, vitamin deficiencies and lots more. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're really interested, keep reading. There's a number of reasons why it might occur. Usually patients presenting with it have some degree of hearing loss. Its thought that somewhere along the line the structures are getting more sensitive to sound because through a feedback mechanism. Think of it this way, you speak to someone but they can't hear you so you speak louder and louder until they can. In the same way its thought that the sensitivity is increased and increased to try to restore hearing but the result is audible nonsense sound from abnormal activity i.e. tinnitus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If anything doesn't make sense, please do say :)&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-04-04T23:22:29.323" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="16349" PostTypeId="2" ParentId="16199" CreationDate="2014-04-04T23:46:35.917" Score="0" Body="&lt;p&gt;Yes a range of pain exists. This can be seen probably in your friends who all probably have a completely different threshold for pain. When doctors ask patients to rate their pain it's usually to establish a baseline so after treatment we can see if there's a decrease. The different thresholds have so many factors from general health to receptors to brain activity to emotional state. You name it! Often just focussing on a pain makes it more painful. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's definitely an unpleasant sensation pain but it's our way of our body saying &quot;hey, you need to pay attention&quot;. Usually the response required is rest or to identify what might be there causing the pain. For example pain means we will withdraw very quickly from a hot surface. Doesn't even require the brain as it is a reflex arc which minimises the time we spend burning that part of our body. And as it continues to hurt we use the arm less letting it recover and protecting it from infection by doing so. &#xA;As these hazards of being cut, burnt, bit, knocked, fractured are very common there is a survival advantage to be the individual that is alerted to these hazards and take the necessary actions. Particularly in children where pain is necessary as it makes the baby know it needs to eat (or the mother) or that something isn't a good idea (putting hands on something hot).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However as you say there are times when the pain itself is more crippling than anything else and in that situation we have a problem. Childbirth, backache and in cancer or in tension headaches are just some examples. As being able to feel pain is pretty much required for a long life, the disadvantage of having pains like the above is less and doesn't outweigh the benefits. Pain is always going to be necessary. They also usually don't interfere with reproduction and so genes are passed on. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-04-04T23:46:35.917" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16351" PostTypeId="1" AcceptedAnswerId="16362" CreationDate="2014-04-05T10:44:13.117" Score="2" ViewCount="697" Body="&lt;p&gt;I learn about the brain right now, and there are crossing of neuron pathways everywhere; in the thalamus, the medulla oblongata, the pyramidal tract... And I don't understand why? What is the reason to connect - for example - the right foot to the left part of your brain? &lt;/p&gt;&#xA;" OwnerUserId="6241" LastEditorUserId="3615" LastEditDate="2014-04-06T15:41:44.173" LastActivityDate="2014-04-06T15:41:44.173" Title="Why do the neuron pathways decussate?" Tags="&lt;evolution&gt;&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16352" PostTypeId="1" CreationDate="2014-04-05T12:46:14.730" Score="5" ViewCount="417" Body="&lt;p&gt;Do we know of any living forms on Earth that could continue to live on Mars? &lt;/p&gt;&#xA;" OwnerUserId="5978" LastActivityDate="2014-09-25T04:14:33.993" Title="Any examples of life forms on Earth that could have survived on Mars or Moon?" Tags="&lt;life&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16353" PostTypeId="1" CreationDate="2014-04-05T13:39:05.300" Score="2" ViewCount="849" Body="&lt;p&gt;Looking at &lt;a href=&quot;https://biology.stackexchange.com/questions/16330/book-recommendation-on-selective-breeding&quot;&gt;this question&lt;/a&gt;, I've been wondering, What are the biggest private companies which work in both animal and non-animal selective breeding?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me know if Biology.SE is not appropriate for this kind of question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you&lt;/p&gt;&#xA;" OwnerUserId="4113" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2017-10-17T17:38:58.753" Title="List of the biggest companies that work in selective breeding" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;natural-selection&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16354" PostTypeId="1" AcceptedAnswerId="16361" CreationDate="2014-04-05T14:00:45.667" Score="1" ViewCount="90" Body="&lt;p&gt;If left glossopharyngeal nerve and right vagus nerve are intact, but there is a lesion at left vagus nerve, would stimulating the left side of pharynx elicit a gag reflex?&lt;/p&gt;&#xA;" OwnerUserId="566" LastActivityDate="2014-04-06T00:23:07.527" Title="A question about gag reflex" Tags="&lt;neurology&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16356" PostTypeId="2" ParentId="16353" CreationDate="2014-04-05T14:41:58.837" Score="4" Body="&lt;p&gt;This varies by the kind of animal or plant. I think one company would rarely do both.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For plants Monsanto comes to mind.  And Syngenta. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure for animals.  For beef cattle in the US, this is done by individual ranchers (who may be corporations) that &lt;a href=&quot;http://animalfrontiers.org/content/1/2/53.full&quot; rel=&quot;nofollow&quot;&gt;collectively share their genetic data&lt;/a&gt; creating a market which can &lt;a href=&quot;http://www.theatlantic.com/technology/archive/2012/05/the-perfect-milk-machine-how-big-data-transformed-the-dairy-industry/256423/&quot; rel=&quot;nofollow&quot;&gt;predict the value of a bull&lt;/a&gt;.  The market for bull semen can be worth hundreds of dollars per impregnation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why are bulls valued at such a greater rate than cows?  Because semen can be preserved, transported and used thousands of times while a cow can only calf one at a time.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-04-05T14:41:58.837" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16357" PostTypeId="1" AcceptedAnswerId="16359" CreationDate="2014-04-05T18:11:06.030" Score="2" ViewCount="746" Body="&lt;p&gt;What are mast cell membranes made out of? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would weaken or strengthen them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Web searches bring up a lot of information about mast cells but very little on the membrane. And the Wikipedia page is not clear as to whether or not additional calcium or sodium fluoride would improve/weaken mast cell wall strength.&lt;/p&gt;&#xA;" OwnerUserId="6258" LastActivityDate="2018-04-10T14:53:02.290" Title="What are mast cell membranes made out of?" Tags="&lt;cell-membrane&gt;&lt;histamine&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16359" PostTypeId="2" ParentId="16357" CreationDate="2014-04-05T18:30:21.223" Score="2" Body="&lt;p&gt;Cell membranes (not cell walls) are composed of a double layer of phospholipids. The lipids are orientated in the way, that the hydrophilic part of the molecule is oriented to the outside and the inside of the cell and the hydrophobic tail to the inside of the membrane.&#xA;See the figure from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_membrane&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/o5aK0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Embedded in the bilayer are transport proteins, receptor and so on. Calcium and sodium fluoride have no effect on the integrity of the membrane.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-05T18:30:21.223" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16361" PostTypeId="2" ParentId="16354" CreationDate="2014-04-06T00:23:07.527" Score="1" Body="&lt;p&gt;The sensory and motor components are  required (GP and vagus respectively). Similar to the corneal reflex and cranial nerve 5 and 7, if a lesion exists in either the sensory or motor component there will be a defect. In your case, there is no motor innervation on the left due to the lack of the vagus nerve so there is no vagus nerve response. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-04-06T00:23:07.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16362" PostTypeId="2" ParentId="16351" CreationDate="2014-04-06T00:29:17.780" Score="3" Body="&lt;p&gt;Crossing or decussation is a lot more robust against wiring errors than their seemingly simpler same-sided wiring counterparts. See &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/ar.20731/pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for the research carried out to establish this and for more detail.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-04-06T00:29:17.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16363" PostTypeId="2" ParentId="6915" CreationDate="2014-04-06T00:59:16.597" Score="2" Body="&lt;p&gt;Here's an armchair evolutionary explanation. In nature, running water tends to be cold whereas tepid water tends to be lukewarm. And for reasons having nothing to do with temperature, running water tends to contain less harmful bacteria. Therefore, our ancestors who preferred to drink cold water over lukewarm had an evolutionary advantage over those who preferred the opposite. &lt;/p&gt;&#xA;" OwnerUserId="6261" LastActivityDate="2014-04-06T00:59:16.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16364" PostTypeId="2" ParentId="9414" CreationDate="2014-04-06T01:43:28.220" Score="1" Body="&lt;p&gt;I would assume that the labeling occurs in the reduction of NTPs to form dNTPS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This process (catalyzed by &lt;a href=&quot;http://en.wikipedia.org/wiki/Ribonucleotide_reductase&quot; rel=&quot;nofollow&quot;&gt;ribonucleotide reductase&lt;/a&gt;) involves protonating the hydroxyl group on the 2' carbon, allowing it to leave as water, and then adding a hydride to the newly formed carbocation. The two hydrogen atoms (the proton and the hydride) come from two thiols on the enzyme, which in the process are oxidized to form a disulfide bond.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The crux is that, in the presence of heavy water, the two thiols would rapidly exchange their hydrogen for deuterium. That means that the hydride that gets added to the carbocation would be a deuterium, and the resulting dNTP would be deuterium labeled.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the only step that I can imagine the labeling working for, as a carbon-hydrogen bond is formed (which doesn't exchange rapidly with the solvent) using the hydrogen from a sulfer-hydrogen bond (which does exchange rapidly with the solvent). &lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-04-06T01:43:28.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16365" PostTypeId="1" AcceptedAnswerId="16369" CreationDate="2014-04-06T03:53:34.720" Score="0" ViewCount="88" Body="&lt;p&gt;Please feel free to construe this question broadly--I don't see why the question would not apply to branches of biology other than mycology. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the goal of taxonomy is to create classification of fungi that reflect evolutionary relationships, and if this results in a more or less unmanageable proliferation of names, might it not be a good idea to use a numeric or alpha-numeric system instead of a verbal one? One author estimates there may be as many as 5 million species of fungi (and it may take 1000 years to catalog them). If we did manage to note them all would the result really be useable? The ease of storage and retrieval alone would seem to commend a numerical approach. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume someone has thought of this before and I guess viral taxonomy does this to some extent. Are there any proposals like this afoot?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any insights.  &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-04-06T12:32:17.813" LastActivityDate="2014-04-06T12:32:17.813" Title="Could alpha-numeric taxonomy of fungi make things simpler?" Tags="&lt;taxonomy&gt;&lt;mycology&gt;&lt;phylogenetics&gt;&lt;nomenclature&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16366" PostTypeId="2" ParentId="16357" CreationDate="2014-04-06T08:22:06.150" Score="4" Body="&lt;p&gt;Although the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Dermatographism&quot; rel=&quot;nofollow&quot;&gt;dermatographism&lt;/a&gt; refers to &quot;weak membranes&quot; it cites no source for this, and like Chris, I haven't found any mention of this in a quick look at the literature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Histamine is usually released from mast cells in response to specific stimuli by a degranulation reaction (internal vesicles fusing with the surface membrane to release their contents) and I would guess that abnormal degranulation is a more likely cause than cell lysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a recent paper &lt;em&gt;(Ralph, JW (2013) Evidence for a role of neural pathways in dermographism. Brit. J. Dermatology 169, 1357–1374)&lt;/em&gt; a case is reported of a man who combines dermatographism with a syndrome called &quot;stocking-glove neuropathy&quot;. This latter syndrome results in a pattern of loss of sensation in the lower arm. When the dermatographic reaction is triggered in this patient the resulting weal does not extend into the affected part of the arm, suggesting that neural activity is part of the trigger for dermatographism. In other words, in those suffering from dermatographism, sensory nerve activation would somehow result in cross-talk into the pathway for stimulating mast cell degranulation.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-04-06T09:21:21.193" LastActivityDate="2014-04-06T09:21:21.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16367" PostTypeId="1" CreationDate="2014-04-06T08:44:47.547" Score="9" ViewCount="216" Body="&lt;p&gt;I've written a paper about DNA sequence analysis. This paper attempts&#xA;to use Bayesian modelling for a set of DNA sequences. It will probably&#xA;end up either in a statistics journal, or, more likely, in a&#xA;bioinformatics journal. My concern is that biologists may take&#xA;exception to some of the language in the introduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm attempting to make a connection between De Novo motif discovery,&#xA;and modelling the sequences. Maybe it is a bit of a&#xA;stretch. E.g. I use language like &quot;analyzing a set of DNA sequences&#xA;with biological significance solely by focusing on the motifs&#xA;contained within them potentially discards valuable information, for&#xA;example, possible long-range correlations between nucleotide&#xA;positions in the sequences.&quot; Also, &quot;An alternative, and possibly&#xA;complementary approach, is to consider a sequence as a single unit,&#xA;and try to do direct statistical analysis on it... This approach is&#xA;used in this paper, which does not use Markovian techniques. Instead,&#xA;it tries to model correlation structure across the sequence.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the question is whether it is better to try to make an explicit&#xA;connection at the risk of saying things that are incorrect and&#xA;generally over-stretching, rather than just saying (which seems a&#xA;little lame) that this sequence classification problem is related to&#xA;De Novo motif discovery problem and leaving it at that. Comments?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I include the first few paragraphs of the introduction below. This&#xA;includes all the relevant language.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm willing to send my current draft to anyone who is interested in&#xA;knowing more about the context. I don't want to post a public link to&#xA;it, though.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;DNA sequence motifs are nucleotide sequence patterns that are&#xA;  conjectured to have a biological significance. Often they indicate&#xA;  sequence-specific binding sites for proteins such as nucleases and&#xA;  transcription factors (TF). Others are involved in important processes&#xA;  at the RNA level, including ribosome binding, mRNA processing&#xA;  (splicing, editing, polyadenylation) and transcription termination.&#xA;  Motif discovery is a very active area of research interest. So-called&#xA;  “De novo computational discovery” is perhaps the most popular, where&#xA;  given only a set of DNA sequences, an algorithm is used to identify&#xA;  candidate shared motifs. This can be thought of as the task of finding&#xA;  a set of non- overlapping, approximately matching substrings given a&#xA;  starting set of strings. This is a very difficult problem.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;From a more general perspective, DNA sequence analysis is often done&#xA;  using DNA sequence motifs. It is reasonable to ask the question - what&#xA;  makes a sequence a motif? From a biological perspective, a motif is&#xA;  simply the smallest identifiable sequence sub- component of something&#xA;  larger.  This subcomponent can be thought of as the smallest&#xA;  identifiable piece of functionality related to the underlying biology,&#xA;  Therefore, sequence analysis often focuses on identifying these&#xA;  motifs. However, these motifs are typically very short, so analyzing a&#xA;  set of DNA sequences with biological significance solely by focusing&#xA;  on the motifs contained within them potentially discards valuable&#xA;  information, for example, possible long-range correlelations between&#xA;  nucleotide positions in the sequences.  Note also that the statistical&#xA;  methods used to identify motifs are typically Markovian, like Hidden&#xA;  Markov Models (HMM), which are naturally tailored towards looking at&#xA;  small sequences.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;An alternative, and possibly complementary approach, is to consider a&#xA;  sequence as a single unit, and try to do direct statistical analysis&#xA;  on it. This approach is less often used. One reason is that such&#xA;  sequences can quickly grow too large, and are not well suited to&#xA;  Markovian approaches. This approach is used in this paper, which does&#xA;  not use Markovian techniques. Instead, it tries to model correlation&#xA;  structure across the sequence.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;We do this by fitting a suitable Bayesian model to that set using&#xA;  Bayesian model selection. As noted above, our major rationale for this&#xA;  model is the assumption that the nucleotide locations of this set are&#xA;  correlated among themselves. With this assumption in mind, we&#xA;  construct a family of probability distributions to capture this&#xA;  correlation information, described in Subsection 2.1.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="284" LastEditorUserId="284" LastEditDate="2014-04-06T08:57:41.250" LastActivityDate="2014-10-06T06:42:18.607" Title="Comment on the introduction to a bioinformatics paper" Tags="&lt;bioinformatics&gt;&lt;sequence-analysis&gt;&lt;publishing&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16368" PostTypeId="2" ParentId="16365" CreationDate="2014-04-06T08:48:30.180" Score="2" Body="&lt;p&gt;This is actually already done in some contexts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance: yeast (a fungus) is a pretty extensively studied organism, and this means that there are a vast number of yeast strains which are know/used by biologists.  Many of these strains are referred to simply by an alphanumeric string rather than a &quot;verbal&quot; name.  (some examples in link &lt;a href=&quot;http://wiki.yeastgenome.org/index.php/Commonly_used_strains&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is also the case for bacteria, and maybe most of microbiology.&lt;/p&gt;&#xA;" OwnerUserId="4973" LastActivityDate="2014-04-06T08:48:30.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16369" PostTypeId="2" ParentId="16365" CreationDate="2014-04-06T10:25:49.777" Score="1" Body="&lt;p&gt;(First of all the term &lt;a href=&quot;http://en.wikipedia.org/wiki/Numerical_taxonomy&quot; rel=&quot;nofollow&quot;&gt;numerical taxonomy&lt;/a&gt; has a completely different meaning. Here you are talking about nomenclature.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(To make it clear: you are talking about species.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Simpler for whom?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For humans numbers are much less memorizable than pronounceable and often meaningful words. For database management identification numbers are unavoidable - that's true, because numbers require less disk space and lead to smaller indices and faster access, but that doesn't mean that the text field &quot;title&quot; should be abandoned.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In IndexFungorum, for example, they have id's for every name: e.g. www.indexfungorum.org/Names/NamesRecord.asp?RecordID=&lt;strong&gt;228098&lt;/strong&gt; for &lt;a href=&quot;http://www.indexfungorum.org/Names/NamesRecord.asp?RecordID=228098&quot; rel=&quot;nofollow&quot;&gt;Boletus edulis&lt;/a&gt;, but they do not expect the user to use 228098 in place of the name, because that would be inconvenient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On Mycobank different id's are used: www.mycobank.org/Biolomics.aspx?Table=Mycobank&amp;amp;MycoBankNr_=&lt;strong&gt;356530&lt;/strong&gt;. I'd agree, that would be good to have the same id everywhere, but database managers nicely trace these numbers for us (see e.g. the &lt;a href=&quot;http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&amp;amp;MycoBankNr_=356530&quot; rel=&quot;nofollow&quot;&gt;&quot;Other fungal links&quot;&lt;/a&gt; section).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, nomenclature of Fungi is controlled by the &lt;a href=&quot;http://www.iapt-taxon.org/nomen/main.php&quot; rel=&quot;nofollow&quot;&gt;International Code of Nomenclature for algae, fungi, and plants&lt;/a&gt;. &lt;a href=&quot;http://www.ictvonline.org/codeOfVirusClassification.asp&quot; rel=&quot;nofollow&quot;&gt;Nomenclature of viral species&lt;/a&gt; is still based on memorizable names.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-04-06T10:25:49.777" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16370" PostTypeId="2" ParentId="16343" CreationDate="2014-04-06T11:02:35.440" Score="3" Body="&lt;p&gt;An addition to the answer by Chris.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably the most dangerous tapeworms for humans are &lt;a href=&quot;http://en.wikipedia.org/wiki/Echinococcus&quot; rel=&quot;nofollow&quot;&gt;Echinococcus&lt;/a&gt;. In humans they form cysts (in a variety of organs including brain) [it's because humans are &quot;interpreted&quot; as intermediate hosts], which can become very large and can cause death when untreated or disrupted.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-04-06T11:02:35.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16371" PostTypeId="1" CreationDate="2014-04-06T11:16:29.000" Score="2" ViewCount="2944" Body="&lt;p&gt;what is the effect of soda water on the process of digestion? As it has been seen that after drinking soda the process is increased...I just want to know that what is the chemistry behind this?&lt;/p&gt;&#xA;" OwnerUserId="6095" LastActivityDate="2019-08-23T13:43:04.767" Title="what is the effect of soda water on digestion?" Tags="&lt;digestive-system&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16372" PostTypeId="1" AcceptedAnswerId="16375" CreationDate="2014-04-06T15:21:31.053" Score="5" ViewCount="1928" Body="&lt;p&gt;I read in the book &quot;Why we get sick.&quot; by Nesse and Williams that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Steady detective work and fabulous luck have enabled geneticists to&#xA;  pinpoint the Huntington's gene on the short arm of chromosome 4.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I want to know what was the &quot;detective&quot; work and the fabulous luck - the whole story of the discovery of the location of the gene.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="1320" LastEditDate="2014-04-06T17:27:54.600" LastActivityDate="2014-04-07T13:42:46.670" Title="How was the Huntington's disease gene's location found?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;pathology&gt;&lt;chromosome&gt;&lt;history&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16373" PostTypeId="1" AcceptedAnswerId="16376" CreationDate="2014-04-06T15:27:21.287" Score="4" ViewCount="18535" Body="&lt;p&gt;Suppose a person wears the specs of power -6D, the far point for that person is 16cm.&#xA;But the near point of normal eye is 25cm. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, is the near point of a  person with myopia (having far point less than the near point of normal person) also changed ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2014-04-06T17:21:24.337" LastActivityDate="2018-10-18T21:04:33.800" Title="Near point and far point of myopic eye" Tags="&lt;human-biology&gt;&lt;pathology&gt;&lt;human-anatomy&gt;&lt;eyes&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16374" PostTypeId="2" ParentId="16372" CreationDate="2014-04-06T16:09:19.097" Score="1" Body="&lt;p&gt;It was fascinating because Huntington himself described what we now call genetics before the field existed. Then to locate the gene scientists used essentially trial and error. They took enzymes that cut different parts of the DNA and looked at which of these were inherited. If it were inherited then there would be cuts made, otherwise not. Then they matched it up to who had the disease. Of course with 46 chromosomes there were thousands and thousands of places to check but they somehow luckily managed to find it on their twelfth try! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The full story can be found here: &lt;a href=&quot;http://www.dana.org/Cerebrum/Default.aspx?id=39308&quot; rel=&quot;nofollow&quot;&gt;http://www.dana.org/Cerebrum/Default.aspx?id=39308&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-04-06T16:09:19.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16375" PostTypeId="2" ParentId="16372" CreationDate="2014-04-06T16:14:22.723" Score="5" Body="&lt;p&gt;A Google search for &quot;Huntingtons disease gene discovery&quot; yielded &lt;a href=&quot;http://www.nature.com/scitable/topicpage/huntington-s-disease-the-discovery-of-the-851&quot; rel=&quot;noreferrer&quot;&gt;this page&lt;/a&gt; at the Nature Education Scitable website. The following citations are provided regarding the molecular basis of HD:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Huntingtin (HTT) was the first disease-associated gene to be&#xA;  molecularly mapped to a human chromosome (Gusella et al., 1983)&lt;a href=&quot;http://www.nature.com/scitable/content/A-polymorphic-DNA-marker-genetically-linked-to-11360&quot; rel=&quot;noreferrer&quot;&gt;2&lt;/a&gt;. Ten&#xA;  years later, scientists identified the DNA sequence and determined the&#xA;  precise nature of the HD-associated mutation in HTT (MacDonald et al.,&#xA;  1993).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Gusella et al. used restriction fragment length polymorphism (RFLP) analysis to locate a RFLP marker linked to Huntington's disease on chromosome 4. From the introduction of their paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We have now identified an anonymous DNA fragment from human chromosome&#xA;  4 that detects two different RFLPs in a HindIII digest of human&#xA;  genomic DNA. This polymorphic DNA marker shows close genetic linkage&#xA;  to the Huntington's disease gene in two separate families, although a&#xA;  different haplotype of the marker segregates with the Huntington's&#xA;  disease gene in each family. We infer that the Huntington's disease&#xA;  locus resides on human chromosome 4.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Further details given in the paper might justify the description given in the question. &quot;Fabolous luck&quot; could refer to the discovery or availability of suitable families and pedigrees for the genetic studies. The &quot;steady detective work&quot; would be the genetic mapping and fieldwork required to establish the link. The following quotes describe some of the efforts spent on the project:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The success of any genetic linkage project depends in large part on&#xA;  the quality of family material available for study. We initially&#xA;  invested considerable effort in identifying a useful family from the&#xA;  National Research Roster for Huntington's Disease Patients and&#xA;  Families at Indiana University. An American family of reasonable size&#xA;  was selected and blood samples were obtained (...). Subsequently, a&#xA;  substantially larger Huntington's disease family was located. This&#xA;  pedigree stem from a unique community of interrelated Huntington's&#xA;  disease gene carriers living along the shores of Lake Maracaibo,&#xA;  Venezuela. (...)For the past three years an expedition has spent one&#xA;  month annually in Venezuela collecting pedigree information, tissue&#xA;  samples, and clinical data. (...) In Venezuela, many family members&#xA;  were examined for three consectuvie years. Permanent lymphoblastoid cell lines were &#xA;  again established for each individual to act as a permanent source of&#xA;  genomic DNA. In both families each individual was examined by at least&#xA;  one neurologist experienced and knowledgable about Huntington's&#xA;  disease.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The Scitable page also summarizes the approach and results described in the paper. For the RFLP analysis, several DNA probes were tried, of which one, &quot;G8&quot;, resulted in a HD-linked pattern:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;James F. Gusella and colleagues carried out a study to determine&#xA;  whether they could identify a DNA probe that would show an&#xA;  HD-associated restriction fragment length polymorphism (RFLP) when&#xA;  used in Southern blot analyses of chromosomal DNA digested with the&#xA;  restriction enzyme HindIII (palindromic recognition sequence&#xA;  5'-AAGCTT-3'). The team identified one probe out of 12 tested, called&#xA;  G8, that showed a specific RFLP pattern associated with HD in two&#xA;  large families with a history of the disease (Gusella et al., 1983).&#xA;  Using the G8 probe, they next identified two HindIII sites (called H1&#xA;  and H2) that were palindromic within this chromosomal region. DNA&#xA;  fragments at these sites vary in length among different HD lineages.&#xA;  Because researchers used two large pedigrees in these experiments,&#xA;  they were able to obtain statistical support for their discovery&#xA;  (Figure 3).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, at the time the origin of the G8 probe DNA in the human genome was not known, so human-mouse somatic cell hybrids were made to identify where the G8 probe DNA belonged. This showed that the G8 probe corresponded to chromosome 4, and indicated that the HD gene would be found there:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Researchers found that the G8 DNA probe hybridized only to Southern&#xA;  blots using chromosomal DNA from human-mouse somatic cell hybrid lines&#xA;  that contained human chromosome 4. Therefore, researchers determined&#xA;  that the G8 DNA probe is located on human chromosome 4, and they&#xA;  concluded that the HD gene is located on chromosome 4 near the region&#xA;  corresponding to the G8 DNA probe (Figure 5; Gusella et al., 1983).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-04-06T16:30:03.530" LastActivityDate="2014-04-06T16:30:03.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16376" PostTypeId="2" ParentId="16373" CreationDate="2014-04-06T20:52:42.447" Score="4" Body="&lt;p&gt;Let us say this myopic patient has amplitude of accommodation of 8D.  The patient accommodates 8D beyond far point, thus his near point is 1/6+8=0.07m (7.1cm).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we compare the case with emmetropic eye with accommodation amplitude of 8D, the near point is 1/8=0.12m (12cm).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, yes, near point of myopic person is different from an emmetropic one. But, you are wrong thinking that near point of &quot;normal&quot; eye is 25cm. The near point is age-and-lens dependent, thus near point is individual one and should be calculated considering amplitude of accommodation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look at this picture of age-related accommodation changes - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sCgym.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look at the scheme of far/near points (near point here is just an example)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6huda.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2014-04-06T21:03:21.993" LastActivityDate="2014-04-06T21:03:21.993" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16378" PostTypeId="2" ParentId="14189" CreationDate="2014-04-07T03:45:38.047" Score="2" Body="&lt;p&gt;It's not 2D: Tactile perception can very simply understand a ring around your finger. If you projected the skin of your body onto a 2D plane there would be a way to represent this sensation, but only as an irregular shape. So you need a third dimension to cognitively process this sensation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But &lt;a href=&quot;http://en.wikipedia.org/wiki/Phantom_pain&quot; rel=&quot;nofollow&quot;&gt;Phantom pain&lt;/a&gt; tells us the brain doesn't always register tactile perception from a true 3D mapping. For example a person without an arm could feel pain in a finger that doesn't exist. Not always, but sometimes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it's greater than two, and sometimes three doesn't fully describe the known phenomena. Therefore it's (at least) 4-D.&lt;/p&gt;&#xA;" OwnerUserId="5277" LastActivityDate="2014-04-07T03:45:38.047" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16379" PostTypeId="2" ParentId="16327" CreationDate="2014-04-07T05:16:44.260" Score="5" Body="&lt;p&gt;+1 for giving a solid answer to @AP, but being older I've had friends who have had tinnitus and I'd like to add some notes to try to flesh this out a bit. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0003534/&quot;&gt;tinnitus&lt;/a&gt; is the result of nerve damage usually.  Nearly everybody experiences episodic tinnitus at one point or another.  When exposed to a loud sound or a blow to the head can cause it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chronic tinnitus occurs when the sound does not go away and is heard all the time.  This is annoying but incredibly common - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0010394/&quot;&gt;nearly 1 to 2 in ten people have an extended period and about 0.5% of people experience tinnitus to the point where it affects their daily life and it doesn't seem to ever go away&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like headaches, schitzophrenia, depression, and other neurological conditions, the specific cause of tinnitus is not really understood and explanations which are really satisfying are hard to imagine.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While a loud noise could possibly cause nerve damage in the auditory system, it sounds more often the cause is related to a vulnerability in the auditory system that allows the generation of these sounds in such a way that they cannot be tuned out. There have been &lt;a href=&quot;http://omim.org/entry/606554&quot;&gt;genetic factors associated with the tendency to tinnitus&lt;/a&gt;, implying that physiological factors are in play. Tinnitis can be aggravated by stress, caffeine and smoking, which further implies that nerve physiology has a lot to do with the condition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Much of the treatment for tinnitus involves amplifying other sounds in other parts of the sound spectrum so that the ringing sound tunes itself out - that the nervous system actually attenuates the sound as it should so that the patient does not consciously register it. Hypnosis and cognitive behavioral therapy have also been touted as well as herbal remedies, diet changes, but attenuation is all the result that is typically expected.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a class of tinnitus where a pulsating sound from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18302544&quot;&gt;vasculature near the auditory nerves appears to be a cause&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-04-07T05:16:44.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16380" PostTypeId="2" ParentId="16327" CreationDate="2014-04-07T06:35:47.717" Score="2" Body="&lt;p&gt;Apparently some (small amount of) tinnitus is caused by, or at least associated with, &lt;a href=&quot;http://en.wikipedia.org/wiki/Otoacoustic_emission&quot; rel=&quot;nofollow&quot;&gt;otoacoustic emissions&lt;/a&gt;. This &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2340968&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; covers the link if you are interested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want a great talk that generally covers the molecular mechanisms behind hearing, I highly recommend &lt;a href=&quot;http://www.cornell.edu/video/james-hudspeth-how-hearing-happens&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt; by James Hudspeth. This covers a ton of material, including otoacoustic emissions, and is very interesting.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-04-07T06:35:47.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16381" PostTypeId="1" CreationDate="2014-04-07T07:17:32.210" Score="3" ViewCount="54" Body="&lt;p&gt;I'm researching phosphorous uptake in monocots to develop planting mixes for riparian planting. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I recently saw a paper suggesting (the author lacked proof) that &lt;strong&gt;root zone mycorrhizae&lt;/strong&gt; may &lt;strong&gt;solubilize phosphorous&lt;/strong&gt; from the soil solution &lt;strong&gt;out of phase with the parent plant's ability to take up the phosphate&lt;/strong&gt;, resulting in P loss from the system. Sadly I didn't save the paper and so it is still out there on the net. If this is the true, and the loss significant, then it would be an argument against using mycorrhizal plants in stream-side planting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this ring a bell with anyone? Failing that, what is known about the relative phasing of mycorrhizal phosphorous release and timing of plant uptake, especially in monocots? &lt;/p&gt;&#xA;" OwnerUserId="5260" LastEditorUserId="6307" LastEditDate="2017-04-11T05:35:06.347" LastActivityDate="2017-04-11T05:35:06.347" Title="phosphorous availability to mycorrhizae and parent plant, timing - paper search" Tags="&lt;ecology&gt;&lt;mycology&gt;&lt;literature&gt;&lt;symbiosis&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16382" PostTypeId="1" CreationDate="2014-04-07T07:18:18.110" Score="1" ViewCount="26" Body="&lt;p&gt;There are several famous cases of great apes demonstrating a surprising degree of wherewithal in communication and tool use - even monkeys can learn some tool use from each other observationally, even if &quot;teaching&quot; would be an exaggeration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ready availability of this information will preclude me from bothering to cite a palate of examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has anyone ever considered, as an experiment, taking such primates which display exemplary tool use in the lab and (at least partially) reintroducing them into the wild and seeing if (perhaps specially crafted) tool lessons learned form us humans propagates among their fellows?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, why not?&lt;/p&gt;&#xA;" OwnerUserId="5936" LastActivityDate="2014-04-07T07:18:18.110" Title="Propagation of tool use in primates?" Tags="&lt;evolution&gt;&lt;intelligence&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16383" PostTypeId="1" AcceptedAnswerId="16392" CreationDate="2014-04-07T08:00:21.737" Score="0" ViewCount="79" Body="&lt;p&gt;In the 2nd episode of the new Cosmos series, the host Neil deGrasse Tyson shows how the white-furred bear could have evolved (reasonable scientific speculation, of course).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you haven't seen that episode, &lt;a href=&quot;http://www.cosmosontv.com/watch/195050051992&quot; rel=&quot;nofollow&quot;&gt;here's the link&lt;/a&gt;. Great show, by the way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, it shows the bears eggs, and then goes on to show how there can happen an error in the DNA copying, that leads to the brown pigment production malfunction. Here's an excerpt from the subtitles text:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;- great bears roamed the frozen wastes of Ireland.&#xA;- This might look like an ordinary bear,&#xA;- but something extraordinary is happening inside her.&#xA;- Something that will give rise to a new species.&#xA;- In order to see it, we'll need to descend down to a much smaller scale, to     the cellular level, so that we can explore the bear's reproductive system.&#xA;..&#xA;- Those are some of her eggs.&#xA;- To see what's going on in one of them,&#xA;- we'll have to get even smaller.&#xA;- We'll have to shrink down to the molecular level.&#xA;..&#xA;- When a living cell divides in two,&#xA;- each one takes away with it a complete copy of the DNA.&#xA;- A specialized protein proofreads to make sure&#xA;- that only the right letters are accepted&#xA;- so that the DNA is accurately copied.&#xA;- But nobody's perfect.&#xA;- Occasionally, a proofreading error slips through,&#xA;- making a small, random change in the genetic instructions.&#xA;- A mutation has occurred in the bear's egg cell.&#xA;- A random event as tiny as this one can have consequences on a far grander scale.&#xA;- That mutation altered the gene that controls fur color.&#xA;- It will affect the production of dark pigment in the fur&#xA;- of the bear's offspring.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;From my (not professional but kind of passionate amateur) knowledge of biology, I I was under impression that all of the mammalian eggs are present at birth. But the story depicted in the show involves the (erroneous) DNA copying. I see dissonance there, and I'd like to solve it.&lt;/p&gt;&#xA;" OwnerUserId="6269" LastEditorUserId="6269" LastEditDate="2014-04-07T12:25:38.273" LastActivityDate="2014-04-07T14:25:39.863" Title="In what circumstances does a mammalian egg copy its DNA?" Tags="&lt;dna&gt;&lt;mammals&gt;&lt;eggs&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16384" PostTypeId="1" CreationDate="2014-04-07T08:05:11.390" Score="2" ViewCount="258" Body="&lt;p&gt;The color of a person's eyes are genetically predetermined. If I knew how and in which gene(s) colors are encoded, I could change these genes in the ovary and sperm and thus change the eye color of the new human being. I only had to work on one or two cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would I need to do to change the eye color of an &lt;em&gt;adult&lt;/em&gt; human? Manipulate the genes in &lt;em&gt;all&lt;/em&gt; body cells? Or would a limited number of cells suffice (e.g. those in the eye)?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Eye color is just an example. Your answer does not have to deal with this trait.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user6268" LastEditorDisplayName="user6268" LastEditDate="2014-04-07T13:17:12.240" LastActivityDate="2014-04-07T13:17:12.240" Title="How does gene expression work in an adult organism? Is everything encoded everywhere?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="16385" PostTypeId="1" AcceptedAnswerId="16387" CreationDate="2014-04-07T08:15:55.530" Score="6" ViewCount="13176" Body="&lt;p&gt;Although farmers appear to be able to tell their cows apart, cows look very much alike to me. And this similarity in appearance seems to be a general trait across the animal kingdom: one individual of one animal species looks much like another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why do human facial and body shapes vary so much?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that human beings live in many different environments (e.g. hot and cold) and have adapted to these (e.g. through lighter or darker skin color), but there seems to be much variation that has no apparent evolutionary purpose. So does the difference have a purpose in itself? That is, did we evlove to vary in appearance, and what is the purpose of this variation?&lt;/p&gt;&#xA;" OwnerDisplayName="user6268" LastEditorDisplayName="user6268" LastEditDate="2016-01-04T08:57:40.397" LastActivityDate="2016-09-04T10:50:32.473" Title="Why do different humans look different?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16386" PostTypeId="2" ParentId="16384" CreationDate="2014-04-07T10:00:40.383" Score="3" Body="&lt;p&gt;With some exceptions (one being red blood cells), all cells in the body contain the complete genome of the individual. The expression of the genes however is, as mentioned in the comments, heavily regulated and different in various tissues. Early efforts at gene therapy have had mixed results, including some fatalities, and the field is still highly experimental.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending on the trait you want to change, you might have to manipulate the genes and/or gene expression in just a particular tissue, or in several. The rates of cell death and replenismhent varies between tissues, and will affect the stability of any introduced mutation. Some traits may depend on too many genes to effectively manipulate with current technology, and eye color does depend on several genes. From the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Eye_color&quot; rel=&quot;nofollow&quot;&gt;Eye color&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Eye color is an inherited trait influenced by more than one gene.&#xA;  These genes are sought using associations to small changes in the&#xA;  genes themselves and in neighboring genes. These changes are known as&#xA;  single-nucleotide polymorphisms or SNPs. (...) There is evidence that&#xA;  as many as 16 different genes could be responsible for eye color in&#xA;  humans; however, the main two genes associated with eye color&#xA;  variation are OCA2 and HERC2, and both are localized in Chromosome 15.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So depending on the original and desired color, you may or may not get away with changing a single gene. However, the pigments that determine eye color are produced in two separate tissues in the eye, making matters a bit more complicated:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In humans, the pigmentation of the iris varies from light brown to&#xA;  black, depending on the concentration of melanin in the iris pigment&#xA;  epithelium (located on the back of the iris), the melanin content&#xA;  within the iris stroma (located at the front of the iris), and the&#xA;  cellular density of the stroma&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Note that cellular density also plays a role, and this presents a much harder property to change with gene therapy, if it is at all possible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eye diseases have been a popular field for gene therapy research and trials lately, and there seems too have been quite some progress. However, the possiblity of using gene therapy for changing eye color has understandably not received much attention, and so there are few if any papers to consult. What can be said though, is that eye color is a complex trait, with a partially known genetic basis. &lt;strong&gt;It is &lt;em&gt;plausible&lt;/em&gt; that gene therapy can be used to change pigment production and thus eye color&lt;/strong&gt;, but even so there would likely to be &lt;strong&gt;many limitations.&lt;/strong&gt; on the changes that can be made.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-07T10:00:40.383" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16387" PostTypeId="2" ParentId="16385" CreationDate="2014-04-07T11:50:07.997" Score="9" Body="&lt;p&gt;There is a substantial variation in some human traits: hair colour, eye colour, height, weight, skin colour, build etc. etc. &lt;strong&gt;HOWEVER&lt;/strong&gt; there is also considerable variation within other species, to suggest otherwise is naive (though quite common). We often feel like there is more variation within our own species because we are more aware of the subtle differences within our own species (we have evolved to be able to recognise those that are more similar to us). Cows for example also have a lot of variation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fSWI6.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5GcGs.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5vmjo.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;But to answer the question of why traits vary so much generally...&lt;/strong&gt; There are two principle reasons that demographic patterns might evolve in traits (for example, &quot;Why do Scandinavians tend to have blonde hair?&quot; - [this is just an example, I'm not sure if blonde hair is actually more common in Scandinavia, it could just be a stereotype])&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly there is the &lt;strong&gt;selectionists&lt;/strong&gt; view. This is the view that traits tend to evolve for some kind of adaptive reason, therefore most traits (and demographic patterns of variation) exist for some kind of purpose. A selectionist would argue that blonde hair offers some kind of advantage in Scandinavia, over other hair colours, that it doesn't in others. It could be a naturally or sexually selected advantage (perhaps blonde hair is more useful when hunting prey in snow, or there is mate preference for blonde individuals etc.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the 1960's though a scientist called Motoo Kimura proposed the neutral theory, a theory that most variation and traits have evolved by neutral processes. For example, scandinavians might be blonde because the humans that colonized Scandinavia were, coincidentally, blondes. &lt;strong&gt;Neutralists&lt;/strong&gt; would argue that the demographic variance we see in humans, and within animal species, is due mainly to random genetic drift.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is some more on &lt;a href=&quot;http://www.nature.com/scitable/topicpage/neutral-theory-the-null-hypothesis-of-molecular-839&quot; rel=&quot;noreferrer&quot;&gt;neutralist vs selectionist&lt;/a&gt;, and some on &lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/IIIDGeneticdrift.shtml&quot; rel=&quot;noreferrer&quot;&gt;genetic drift&lt;/a&gt;. And just to show that other animal species also vary:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are some dogs (which have come under a lot of artificial selection specific to generating different physical variants)...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BGfLF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And here are some apes...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ShzKS.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-01-02T08:36:49.047" LastActivityDate="2016-01-02T08:36:49.047" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="16388" PostTypeId="1" AcceptedAnswerId="16390" CreationDate="2014-04-07T12:04:27.607" Score="5" ViewCount="59479" Body="&lt;p&gt;I am currently studying biology and would like to know why enzymes work best in a particular narrow range of pH (the so-called pH optimum).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unlike temperature change, I do not think this has much to do with energy. Do pH-related changes in enzymatic activity have anything to do with the active site? &lt;/p&gt;&#xA;" OwnerUserId="6271" LastEditorUserId="22057" LastEditDate="2018-02-02T15:59:53.583" LastActivityDate="2018-09-13T00:13:44.403" Title="Why does pH have an effect on enzymes?" Tags="&lt;enzymes&gt;&lt;ph&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16389" PostTypeId="1" AcceptedAnswerId="16401" CreationDate="2014-04-07T12:26:37.233" Score="3" ViewCount="7751" Body="&lt;p&gt;I understand the basics of digestion. I know that nutrients get absorbed by the microvilli, enter the bloodstream and travel to the liver but after all that, what is the biological mechanism that guides these nutrients to the proper receiving location?&lt;/p&gt;&#xA;" OwnerUserId="5491" LastActivityDate="2017-12-20T02:46:45.777" Title="How do nutrients get to the cells they need to get to?" Tags="&lt;cell-biology&gt;&lt;nutrition&gt;&lt;blood-circulation&gt;&lt;liver&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16390" PostTypeId="2" ParentId="16388" CreationDate="2014-04-07T13:11:03.207" Score="3" Body="&lt;p&gt;Enzymes have a more or less narrow optimal pH at which they work, depending on the conditions of their environment. Pepsin for example is active in the stomach which is pretty acidic and has an optimal pH of 2.0, while Trypsin, which is active in the small intestine has an optimal pH around 8.5.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Changes in the pH first affect the form of the protein, hydrogen bonds between the amino acids of the molecule and so on and also the form of the active center of the enzyme. Small changes in pH do little or nothing, then reversible changes occur and finally the enzyme gets irreversibly denaturated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The relationship between enzyme activity and pH always looks like this (the curve can be steeper, if the optimal range is small and broader if the range is wider):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FsMkz.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is taken from this &lt;a href=&quot;http://alevelnotes.com/Factors-affecting-Enzyme-Activity/146?tree=&quot; rel=&quot;nofollow noreferrer&quot;&gt;website&lt;/a&gt;, which is a nice introduction to enzymes. Another one is &lt;a href=&quot;http://www.worthington-biochem.com/introbiochem/default.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the optimal pH for the enzyme the conformation of the protein is as it should be (in the ideal state) while this changes when the pH is not optimal. This can lead to improper substrate binding, changes in the active center and so on.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2014-04-07T13:59:30.190" LastActivityDate="2014-04-07T13:59:30.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16392" PostTypeId="2" ParentId="16383" CreationDate="2014-04-07T14:25:39.863" Score="1" Body="&lt;p&gt;The writers of the show may have been somewhat imprecise either by accident or intentionally to avoid excessive details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several different stages of egg cells, with distinct names for each and for the process that leads from one to the next. The whole process of egg cell creation is called [Oogenesis].&lt;a href=&quot;http://en.wikipedia.org/wiki/Oogenesis&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt; To quote Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Oogenesis starts with the process of developing oogonia, which occurs&#xA;  via the transformation of primordial follicles into primary oocytes, a&#xA;  process called oocytogenesis.[4] Oocytogenesis is complete either&#xA;  before or shortly after birth.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To our current knowledge all primary &lt;a href=&quot;http://en.wikipedia.org/wiki/Oocyte&quot; rel=&quot;nofollow&quot;&gt;Oocytes&lt;/a&gt; are present at birth. The next stage in the maturing process is called ootidogenesis, which produces an ootid. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The succeeding phase of ootidogenesis occurs when the primary oocyte&#xA;  develops into an ootid. This is achieved by the process of meiosis. In&#xA;  fact, a primary oocyte is, by its biological definition, a cell whose&#xA;  primary function is to divide by the process of meiosis.[8]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;However, although this process begins at prenatal age, it stops at&#xA;  prophase I. In late fetal life, all oocytes, still primary oocytes,&#xA;  have halted at this stage of development, called the dictyate. After&#xA;  menarche, these cells then continue to develop, although only a few do&#xA;  so every menstrual cycle.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Meiosis I of ootidogenesis begins during embryonic development, but&#xA;  halts in the diplotene stage of prophase I until puberty. The mouse&#xA;  oocyte in the dictyate (prolonged diplotene) stage actively repairs&#xA;  DNA damage, whereas DNA repair is not detectable in the pre-dictyate&#xA;  (leptotene, zygotene and pachytene) stages of meiosis&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;DNA replication is completed before Meiosis occurs. So oocytes do not replicate DNA after birth, but they do &lt;em&gt;repair&lt;/em&gt; DNA to fix mutations that may occour after birth but before conception. If DNA repair fails, then mutations may persist. So the show would appear to be wrong about egg cells copying DNA in an adult bear, but right in that mutations might occur during its lifetime affecting its offspring.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-07T14:25:39.863" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16394" PostTypeId="1" CreationDate="2014-04-07T15:56:45.407" Score="2" ViewCount="1510" Body="&lt;p&gt;Most of my body hair is black however my lip hair is light brown/blonde the rest of my beard region is black. Since hair color is genetic what causes this?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="4562" LastEditDate="2014-04-08T00:29:33.577" LastActivityDate="2014-04-08T12:53:18.173" Title="Why is the human body hair not uniformly colored?" Tags="&lt;genetics&gt;&lt;epigenetics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16396" PostTypeId="2" ParentId="16388" CreationDate="2014-04-07T19:32:44.623" Score="1" Body="&lt;p&gt;Enzyme function is largely determined by its 3-D shape. Enzyme shape is affected by pH among a couple other things. The enzyme only retains its optimal shape at the optimal pH, as you creep outside of it the enzymes shape changes and hence so does its function.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="22057" LastEditDate="2018-03-07T19:19:06.267" LastActivityDate="2018-03-07T19:19:06.267" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16397" PostTypeId="2" ParentId="16371" CreationDate="2014-04-07T19:36:51.630" Score="1" Body="&lt;p&gt;Soda, anything carbonated causes bloating, which stretches the stomach. Mechanoreceptors in stomach detect the stretching resulting in parasympathetic innervation to GI smooth muscle. This causes an increase in GI motility.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-04-07T19:36:51.630" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16398" PostTypeId="1" AcceptedAnswerId="16399" CreationDate="2014-04-07T20:07:39.650" Score="0" ViewCount="230" Body="&lt;p&gt;I have this sentence in my notes&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ovary is surrounded by tunica albuginea and the cortex keeps the primordial follicles. The medulla containing CT and blood vessels develop from mesonephros. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I have these words in my mind about CT&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;tunica&lt;/li&gt;&#xA;&lt;li&gt;cyto- (maybe cytotrophoblast)&lt;/li&gt;&#xA;&lt;li&gt;corona (no other than corona radiata so not)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What can CT be here?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2018-06-27T22:33:43.287" Title="What is this abbreviation CT in female reproductive system" Tags="&lt;human-biology&gt;&lt;homework&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ClosedDate="2014-04-27T16:40:53.007" ContentLicense="CC BY-SA 3.0" />
  <row Id="16399" PostTypeId="2" ParentId="16398" CreationDate="2014-04-07T20:33:05.483" Score="4" Body="&lt;p&gt;I think CT is an abbreviation for &lt;strong&gt;connective tissue&lt;/strong&gt;. Some examples of its use in that fashion:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Connective_tissue&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Connective_tissue&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://web.archive.org/web/20151024041339/http://www.vetmed.vt.edu/education/curriculum/vm8054/Labs/Lab5/Lab5.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://web.archive.org/web/20151024041339/http://www.vetmed.vt.edu/education/curriculum/vm8054/Labs/Lab5/Lab5.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pitt.edu/~sshostak/biosci1450/hislec03.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.pitt.edu/~sshostak/biosci1450/hislec03.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="9686" LastEditDate="2018-06-27T22:33:43.287" LastActivityDate="2018-06-27T22:33:43.287" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="16400" PostTypeId="2" ParentId="14189" CreationDate="2014-04-07T21:25:28.707" Score="1" Body="&lt;p&gt;Well, vision is 2D * 2 (two retinae) but visual perception is 3D, auditory signal is 1D * 2 (two ears), but its perception is 3D. The 3D perception in these senses are results of analysis of the lower dimensional sensory signal combined with various other internal states. (Internal states can integrate information over time to produce better percepts.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Likewise, each tactile sensor is a point source, but the percept of the total tactile sensory stimuli is 3D; I can tell where the source of the sense is in 3D space relative to my body position. The signals will have to be combined with the proprioception and state information in the brain to do so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that these 3D percepts don't always work perfectly. Sometimes we form the wrong percept or fail to get a percept.&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2014-04-07T21:25:28.707" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16401" PostTypeId="2" ParentId="16389" CreationDate="2014-04-07T21:27:13.747" Score="4" Body="&lt;p&gt;Broadly speaking, nutrients that enter the blood from the gut, and those that are released into the blood by the liver, are available to any cells that require them. So there is no &quot;guiding to the correct location&quot; in the sense that you suggest. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lipids for example are present in the various lipoproteins and can be acquired from these by all cells. Iron is bound to transferrin, and any cell with transferrin receptors can internalise the transferrin and take the iron. Glucose is available in solution in the plasma, and free fatty acids are bound to serum albumin in the blood. During starvation the liver produces ketones (&quot;ketone bodies&quot;) which are taken up by many different tissues/cell types.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-04-07T21:27:13.747" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16402" PostTypeId="2" ParentId="16344" CreationDate="2014-04-07T22:29:25.640" Score="4" Body="&lt;p&gt;There is a number of reported cases of marine species reaching new locations through &quot;hitchhiking&quot; in recent times. However, it seems harder to find reports of species actually becoming &lt;em&gt;established&lt;/em&gt; in a new location through this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following articles describe examples of species transported with ocean debris:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In an early study on the dispersal of plastic pellets (&lt;a href=&quot;http://dx.doi.org/10.1080/00288330.1978.9515768&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;), it was suggested that pellets encrusted with the bryozoan &lt;em&gt;Membranipora tuberculata&lt;/em&gt; was transported to New Zealand across the Tasman Sea from Australia. Barring one exception, this was the first time the species was observed in New Zealand waters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Appendix A of a later article by the same author (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873013/&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;) contains 13 examples of species transported by sea (not necessarily through debris, or invasive), including the previous example. Of it, the author writes that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Later, L. M. Stevens (1992, unpublished data) was to report that [&lt;em&gt;Membranipora tuberculata&lt;/em&gt;]&#xA;  was abundant on both eastern and western shores around northernmost&#xA;  New Zealand.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thus, this is possibly a case of a species transported on floating debris and subsequently becoming established in a new habitat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Jose Derraik also deals with the topic in a review (&lt;a href=&quot;http://www.caseinlet.org/uploads/Moore--Derraik_1_.pdf&quot; rel=&quot;nofollow&quot;&gt;4&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Plastics floating at sea may acquire a fauna of various encrusting&#xA;  organisms such as bacteria, diatoms, algae, barnacles, hydroids and&#xA;  tunicates (Carpenter et al., 1972; Carpenter and Smith, 1972; Minchin,&#xA;  1996; Clark, 1997). The bryozoan Membranipora tuberculata, for&#xA;  instance, is believed to have crossed the Tasman Sea, from Australia&#xA;  to New Zealand, encrusted on plastic pellets (Gregory, 1978). The same&#xA;  species together with another bryozoan (Electra tenella) were found on&#xA;  plastics washed ashore on the Florida coast, USA, and they seem to be&#xA;  increasingtheir abundance in the region by driftingon plastic debris&#xA;  from the Caribbean area (Winston, 1982; Winston et al., 1997). Minchin&#xA;  (1996) also describes barnacles that crossed the North Atlantic Ocean&#xA;  attached to plastic debris. Drift plastics can therefore increase the&#xA;  range of certain marine organisms or introduce species into an&#xA;  environment where they were previously absent (Winston, 1982).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Finally, the book Marine Pollution: New Research (&lt;a href=&quot;http://books.google.no/books?id=a4sIbHJ8AVsC&amp;amp;pg=PA81&amp;amp;lpg=PA81&amp;amp;dq=Membranipora+tuberculata+new+zealand&amp;amp;source=bl&amp;amp;ots=5q_H5b54qA&amp;amp;sig=rToDhugayBWrM_9l8cdOcbIZxRA&amp;amp;hl=no&amp;amp;sa=X&amp;amp;ei=ldhCU_fYHcikyAPq7oCwBg&amp;amp;ved=0CD8Q6AEwAg#v=onepage&amp;amp;q=Membranipora%20tuberculata%20new%20zealand&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;) contains the following passage which ends with the observation that conclusive proof is difficult to obtain:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Drift plastics are known to have introduced exotic marine species to&#xA;  several areas (Winston et al., 1997; Deraik, 2002). Winston et al.&#xA;  (1997) reported that the non-indegenous oyster Lopha cristagalli was&#xA;  fond on plastics wshed ashore in southern New Zealand, and that the&#xA;  exotic bryozoan &lt;em&gt;Thalamoperella evelinae&lt;/em&gt; was found on plastics washed&#xA;  ashore in Florida. Barnes and Milnder (2005) fond the exotic barnacle&#xA;  &lt;em&gt;Elminius modestus&lt;/em&gt; on plastic debris in the Shetland Islands (Atlantic&#xA;  Ocean). The bryozoaen &lt;em&gt;Membranipora tuberculate&lt;/em&gt; is believed to have&#xA;  crossed the Tasman Sea from Australia to New Zealand rafting on&#xA;  plastic pellets (Gregory, 1978). M Tuberculate and the bryozan Electra&#xA;  tenella seem to be increasing their abundance on the Florida coast by&#xA;  drifting on plastic debris from the Caribbean sea (Winston, 1982&#xA;  Winston et al, 1997). Maso et al. (2003) (...) However, attributing a&#xA;  marine biological invasion to floating marine debris and not to other&#xA;  mechanisms is very difficult in most cases, and available data are&#xA;  generally insufficient.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-04-08T09:10:52.407" LastActivityDate="2014-04-08T09:10:52.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16403" PostTypeId="1" AcceptedAnswerId="16407" CreationDate="2014-04-07T22:49:36.733" Score="14" ViewCount="7955" Body="&lt;p&gt;Within a single species, how does the relative number of cells in the body relate to the relative size of the organism?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say we take two humans, one of them is 6 feet tall and the other one is 5 feet tall.  They have similar BMI, age, physical condition, genetic background (aside from height) and are the same sex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the tall one have more cells? Or does he have bigger cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;PS:&lt;/em&gt;&lt;/strong&gt; Ideally, answers should be backed up by appropriate sources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;PPS:&lt;/em&gt;&lt;/strong&gt; While I'm grateful to everyone for the very nice answers I got, I should point out that I'm waiting for an answer which includes references to accept it.&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-04-18T20:34:56.220" LastActivityDate="2020-01-28T21:35:04.603" Title="Do tall people have more cells?" Tags="&lt;physiology&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16404" PostTypeId="1" AcceptedAnswerId="16405" CreationDate="2014-04-07T23:28:34.303" Score="8" ViewCount="9947" Body="&lt;p&gt;There are reactions with large Delta G negative values. Why these reactions are irreversible? As in: out of 10 steps of Glycolysis, 3 are irreversible steps. I need an explanation for why they are irreversible.&lt;/p&gt;&#xA;" OwnerUserId="5729" LastEditorUserId="107" LastEditDate="2014-04-09T17:51:37.270" LastActivityDate="2014-09-16T19:14:41.163" Title="What is an irreversible reaction?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;thermodynamics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16405" PostTypeId="2" ParentId="16404" CreationDate="2014-04-07T23:53:23.650" Score="10" Body="&lt;p&gt;The term &quot;irreversible&quot; means that the reverse reaction occurs so rarely that it is considered negligible. This means that you do not have to consider equilibrium, as you have to for reversible reactions. Instead, you can assume that all of the reactants will eventually become product.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you stated, this is true for reactions that have a very negative Gibbs free energy.  Remember the formulation of the Gibbs free energy in terms of the equilibrium constant:&lt;br&gt;&#xA;$$&#xA;\Delta G^o =  -RTln(K)&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can be rewritten as follows:&#xA;$$&#xA;K = e^{-\Delta G^o/RT}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As $\Delta G^o$ gets very negative, you can see that $K$ gets very positive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The equlibrium constant has two definitions that are both useful. First, it is the ratio of the products to the reactants. Therefore as $K$ gets very positive, the equilibrium ratio of products to reactants approaches infinity, implying that all of the reactants will be consumed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More useful is the definition of the equilibrium constant as the ratio of the rates of the forward and reverse reaction. From this definition we can see that as $K$ gets very large, the ratio of the rates of the forward and reverse reaction approaches infinity. This means that &lt;em&gt;the rate of the reverse reaction becomes negligible compared to the rate of the forward reaction.&lt;/em&gt; This is exactly what it means to be irreversible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that it is possible to make (what I think is) a more convincing argument using the concept of activation energy, using &lt;a href=&quot;http://en.wikipedia.org/wiki/Hammond%27s_postulate&quot;&gt;Hammond's Postulate&lt;/a&gt; to describe the character of the transition state. If you'd like, I can write this out. However, I think the argument given above is more easily understood with a basic chemistry background.&lt;/p&gt;&#xA;" OwnerUserId="5771" LastEditorUserId="5771" LastEditDate="2014-04-09T02:34:00.643" LastActivityDate="2014-04-09T02:34:00.643" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16406" PostTypeId="2" ParentId="16403" CreationDate="2014-04-08T00:19:08.843" Score="0" Body="&lt;p&gt;The taller person has more cells. Most cells can only lengthen up to a certain point. Whilst the neuronal cells will be longer and likely some others, the rest of the cells will just be of larger number. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-04-08T00:19:08.843" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16407" PostTypeId="2" ParentId="16403" CreationDate="2014-04-08T00:28:58.733" Score="10" Body="&lt;p&gt;This is really the most fundamental concept of Cell Biology, so good question. If you look at the size of a any cell from a whale and compare it to the size of any of cells from a mouse, they are in fact quite similar, despite the extreme difference in the overall size of the organisms they are from. There is a reason why cells are small, and it has to do with the fact that they survive based on their ability to absorb enough nutrients from their environment. As a cell gets larger it needs more to survive (because it has a bigger mass). A bigger cell has also has a larger surface area around it (so it can absorb more nutrients).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HOWEVER, there gets to be a point where the mass of the cell is too large for the surface area to compensate for. Mathematically this is shown by what is called the &quot;surface-area-to-volume ratio&quot;. Basically, it states that as a a sphere gets larger, the volume increases at a higher RATE than the surface area. So there is a reason cells get only so big, the 60's horror movie The Blob was not scientifically accurate, a single-cell that large (the blob) would not have enough surface area to absorb enough nutrients to sustain itself. Taller (or bigger) people have more cells (not bigger ones) than others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Effects of osmotic pressure can alter cell size slightly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you are talking about taller individuals, you are (I think) really meaning larger people, people with a higher mass. And yes, they have more cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another topic of Cell Biology you may want to explore is apoptosis. Let's say you have two individuals both 180 lbs. one of them is 5' tall and the other 7'. Both these individuals have the same number of cells, but the taller one has a higher percentage of them in the superior and inferior regions of the body. It is the process of apoptosis that sculps an organisms shape.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-06-30T22:22:18.213" LastActivityDate="2014-06-30T22:22:18.213" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16408" PostTypeId="1" CreationDate="2014-04-08T00:31:38.517" Score="0" ViewCount="1771" Body="&lt;p&gt;Please consider the following question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genes A and B are located on the same chromosome. If two individuals with the genotype shown below are crossed, which genotype could be formed?&#xA;&lt;img src=&quot;https://i.stack.imgur.com/V9fXI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;Let / represent the line in the image above.&#xA;a.)AB/ab&#xA;b.)Ab/Ab&#xA;c.)aB/aB&#xA;d.)AB/Ab&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why can't the answer to this question be all of the choices? I thought that recombination was completely randomized through the process of crossing over. Why is only one of the choices correct and how would I go about doing this on my own?&lt;/p&gt;&#xA;" OwnerUserId="4890" LastActivityDate="2015-11-13T01:33:51.627" Title="Possible Genotypes -- Linked Genes" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;recombination&gt;&lt;genetic-linkage&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16409" PostTypeId="2" ParentId="16394" CreationDate="2014-04-08T00:36:12.110" Score="0" Body="&lt;p&gt;I've heard it mentioned that gene dosage is implicated in this. Gene dosage is the number of the alleles present in the cell.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-04-08T00:36:12.110" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16410" PostTypeId="1" AcceptedAnswerId="16413" CreationDate="2014-04-08T06:21:15.297" Score="4" ViewCount="2297" Body="&lt;p&gt;Antioxidants reduce damage to tissue (by scavenging the free radicals) and thus may reduce ageing.It is known that Uric acid is a very good antioxidant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;People with gout have excess accumulation of uric acid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering the above information the authors of the book  &quot;Why we get sick?&quot; put up an interesting question : Do people with gout live longer ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know if there are any studies done to answer the question.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2016-02-15T00:21:55.023" Title="Do people with gout live longer?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;pathology&gt;&lt;senescence&gt;&lt;life&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16411" PostTypeId="2" ParentId="16408" CreationDate="2014-04-08T06:31:30.793" Score="2" Body="&lt;p&gt;One of the alleles for each gene must come from the parent on the right hand side. That parent only has a and b alleles (is homozygous) - meiotic crossing over will not change this. So the offspring must inherit at least one a and one b. That should point you to the answer.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-04-08T06:31:30.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16412" PostTypeId="1" CreationDate="2014-04-08T09:26:12.897" Score="2" ViewCount="65" Body="&lt;p&gt;I'm interested in learning about computational modeling in biophysics. I have heard some amount about people modeling proteins as a network of ideal springs to examine things like conformation switching. I was thinking it would be cool to try to make a very simple model of a small motif undergoing denaturation at certain temperatures while being stable at others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know of a good reference about protein modeling that would be understandable to someone who is decent with math/physics/programming but is in no way a mathematician/physicist/computer scientist?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, if you have a better idea of a simple project for me to practice computational modeling in biophysics (or even just any biology) I would appreciate hearing it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="5771" LastActivityDate="2014-05-10T17:29:43.950" Title="Protein Conformation Modeling" Tags="&lt;proteins&gt;&lt;biophysics&gt;&lt;literature&gt;&lt;computational-model&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16413" PostTypeId="2" ParentId="16410" CreationDate="2014-04-08T09:30:58.663" Score="5" Body="&lt;p&gt;In men, gout is associated with a higher risk of death from all causes. This would imply that their life expectancy is shorter. From a review by Kim et al. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19026153&quot;&gt;1&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Among men who did not have pre-existing coronary heart disease, the&#xA;  increased mortality risk is due primarily to an elevated risk of&#xA;  cardiovascular death, particularly from coronary heart disease. Also,&#xA;  an extension study of a large clinical trial among men with&#xA;  above-average risk for coronary heart disease found that a diagnosis&#xA;  of gout accompanied by an elevated uric acid level is associated with&#xA;  increased long-term (approximately 17 years) risk of all-cause&#xA;  mortality that arises largely from an increased risk of cardiovascular&#xA;  disease (CVD) mortality.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This does not rule out that some subset of people with gout (patients with less severe symptoms?) might benefit in some way from an antioxidant effect, but in general gout is obviously not good for life expectancy.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-08T09:30:58.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16414" PostTypeId="1" AcceptedAnswerId="16482" CreationDate="2014-04-08T09:59:08.763" Score="1" ViewCount="118" Body="&lt;p&gt;I read that foramen ovale opens in 30% of adults.&#xA;I do not know how much of these openings can then close again.&#xA;Probably, none.&#xA;It is not pathogenic if no symptoms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It allows blood to enter from right atrium to left atrium (fetal), but from left atrium to right atrium in adults.&#xA;Assume that 50% of blood is doing so in adults.&#xA;This means that 50% of blood is not oxygenated.&#xA;Heart has to pump stronger to get some level of oxygenated blood as before.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some thoughts about manifestations of open foramen ovale&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;hypertension&lt;/li&gt;&#xA;&lt;li&gt;ischemic hypoxia&lt;/li&gt;&#xA;&lt;li&gt;Clubbing&lt;/li&gt;&#xA;&lt;li&gt;possible organ failures&lt;/li&gt;&#xA;&lt;li&gt;higher risk for infections, SIRS and sepsis&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Therefore, I think open foramen ovale can be a risk factor for myocardial infarction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the manifestations of an open foramen ovale in adults?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="16866" LastEditDate="2017-04-13T04:10:49.133" LastActivityDate="2017-04-13T04:10:49.133" Title="Manifestations of open foramen ovale in adults" Tags="&lt;cardiology&gt;&lt;embryology&gt;&lt;blood-circulation&gt;&lt;pathophysiology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16415" PostTypeId="1" CreationDate="2014-04-08T12:32:06.363" Score="3" ViewCount="682" Body="&lt;p&gt;I am a HS Bio teacher and doing a microevolution lab involving candy. Essentially students use four candy types and push them together until one cracks (Nat Sel). They also do simulations of migration, mutation and genetic drift. They then calculate the &quot;allele frequency&quot; of each type per generation and look for changes. I want to have my students do a simple statistical test to see whether the change was significant or not from each evolutionary factor. I was going to do a chi square test, but someone told me that is not appropriate to this type of experiment. &#xA;So, can anyone confirm, is chi square inappropriate, and if it is..&#xA;Can anyone point me to a more appropriate test. These are high school kids with no stats background (and I have forgotten virtually all the stats I learned 20 years ago)...&lt;/p&gt;&#xA;" OwnerUserId="1710" LastActivityDate="2014-04-08T13:03:55.710" Title="Appropriate statistical test for a student lab?" Tags="&lt;statistics&gt;&lt;experiment&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16416" PostTypeId="2" ParentId="16394" CreationDate="2014-04-08T12:53:18.173" Score="3" Body="&lt;p&gt;The hairs you mention are also called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Androgenic_hair&quot; rel=&quot;nofollow&quot;&gt;androgenic hairs&lt;/a&gt;&quot;, meaning their growth and pigmentation is influenced by androgens. These include pubic hair, the hairs on the breast and shoulders (almost exclusively for men) and the beard.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems, that these hair bulbs have different sensibilities (number and expression of androgen receptors) so they react differently to androgen levels. This includes balding, pigmentation, growth and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These articles should be a good starting point, if you want to dive deeper into the topic:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23016593&quot; rel=&quot;nofollow&quot;&gt;Androgen actions on the human hair follicle: perspectives.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10439260&quot; rel=&quot;nofollow&quot;&gt;Mechanism of action of androgen in human hair follicle.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-08T12:53:18.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16417" PostTypeId="2" ParentId="16415" CreationDate="2014-04-08T13:03:55.710" Score="5" Body="&lt;p&gt;To choose the right statistical method (it is more than just saying &quot;use the t-test&quot;) you need to think about your experiment. A good starting point is this figure from Bitesizebio:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Fmy77.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two relevant articles on that website:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bitesizebio.com/19298/a-basic-guide-to-stats-comparing-two-sets-of-data/&quot; rel=&quot;noreferrer&quot;&gt;Let’s Talk About Stats: Comparing Two Sets of Data&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bitesizebio.com/19315/lets-talk-about-stats-comparing-multiple-datasets/&quot; rel=&quot;noreferrer&quot;&gt;Let’s Talk About Stats: Comparing Multiple Datasets&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Probably also interesting is the definition of statistical terms:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bitesizebio.com/19291/a-basic-guide-to-stats-understanding-the-lingo/&quot; rel=&quot;noreferrer&quot;&gt;Let’s Talk About Stats: Understanding the Lingo&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-08T13:03:55.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16418" PostTypeId="1" AcceptedAnswerId="16420" CreationDate="2014-04-08T13:16:12.200" Score="2" ViewCount="340" Body="&lt;p&gt;In common lab sessions to extract DNA from strawberry or cheek cells, will there be protein contaminating the DNA extract in alcohol? If so, how can we prevent protein from precipitating out of the solution?&lt;/p&gt;&#xA;" OwnerUserId="6281" LastActivityDate="2014-04-08T13:36:35.667" Title="Can protein precipitate out in alcohol during DNA extraction?" Tags="&lt;dna&gt;&lt;proteins&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16419" PostTypeId="2" ParentId="16418" CreationDate="2014-04-08T13:28:49.963" Score="0" Body="&lt;p&gt;A proteinase eg.proteinase K is usually added when extracting dna.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-08T13:28:49.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16420" PostTypeId="2" ParentId="16418" CreationDate="2014-04-08T13:36:35.667" Score="3" Body="&lt;p&gt;Yes, Ethanol can precipitate proteins during a DNA precipitation as well, although Acetone will be more efficient. Usually you do a proteinase K digest or a proteinase K digest followed by a Phenol/Chloroform extraction to avoid this problem. I was usually doing the later, I can post my protocol if you are interested.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-08T13:36:35.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16421" PostTypeId="2" ParentId="16403" CreationDate="2014-04-08T13:54:53.983" Score="2" Body="&lt;p&gt;Not sure it is proven, but this paper makes use of the assumption: West et al, PNAS 99:2473, &lt;a href=&quot;http://www.pnas.org/content/99/suppl_1/2473.full&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/99/suppl_1/2473.full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Btw, this paper may be relevant for you as it focuses on the metabolic activity, which is not quite propotional to body mass (power 3/4: it's growing slower)&lt;/p&gt;&#xA;" OwnerUserId="6224" LastActivityDate="2014-04-08T13:54:53.983" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16423" PostTypeId="1" CreationDate="2014-04-08T15:56:36.870" Score="2" ViewCount="62" Body="&lt;p&gt;Experiment: deep sequencing for mutants in 700nt fragment.&#xA;the fragment of dna was preamplified by primers flanking the fragment followed by hiseq.&#xA;per base coverage was calculated by coverageBed -d -abam in.bam -b ref.bed &gt; out.cov&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Observation: two distinct peaks in coverage at the ends as below plot.. coverage vs positions&#xA;&lt;img src=&quot;https://i.stack.imgur.com/QyKOf.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;the peaks are made from reads having part of primers..thus also show soft clipping at ends..&#xA;there is a huge difference in the calculations if i include such reads And if I exclude them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Question: is there anyone who knows how to handle such a situation?&lt;/p&gt;&#xA;" OwnerUserId="6254" LastActivityDate="2014-04-08T15:56:36.870" Title="coverage calculations approach for clipped reads" Tags="&lt;dna-sequencing&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2014-04-15T14:41:48.133" ContentLicense="CC BY-SA 3.0" />
  <row Id="16424" PostTypeId="2" ParentId="10372" CreationDate="2014-04-08T17:09:15.360" Score="0" Body="&lt;p&gt;From the source that Amory cites :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;You know that the number of offspring is shown by Pascal's triangle,&#xA;  right?&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;For two alleles you have 1 : 2 : 1&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;For three alleles 1 : 3 : 3 : 1 &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;For four 1 : 4 : 6 : 4 : 1 etc. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;So, if 4 in 1000 are 12 and 36 cm&#xA;  tall, that means that every in 250 plants is tall like that. And on&#xA;  which level of Pascal's triangle you have sum of 250? For two alleles:&#xA;  1 + 2 + 1 = 4 For threee: 1 + 3 + 3 + 1 = 8 For four: 1 + 4 + 6 + 4 +&#xA;  1 = 16 etc. until 1 : 8 : 28 : 56 : 70 : 56 : 28 : 8 : 1 Here you see&#xA;  that you have 9 options of height. The difference is 36 cm - 12 cm =&#xA;  24 cm. 24 cm /9 = 3 cm, so 1 plant will 12 cm, 8 plants will be 15 cm,&#xA;  28 plants will be 18 cm, 56 plants will be 21 cm, 70 plants will be 24&#xA;  cm (i.e. &quot;the majority of F2 are like P1 and F1&quot;) and 56 plants will&#xA;  be 27 cm tall out of 250 plants. Thus C is the closest.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-08T17:09:15.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16425" PostTypeId="2" ParentId="9798" CreationDate="2014-04-08T17:13:14.060" Score="0" Body="&lt;p&gt;It is also an interesting thought that plasmids may be pieces of DNA that light be &quot;parasites&quot; on the bacterial cell which they use to provide resources for replicating themselves.  &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-08T17:13:14.060" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16426" PostTypeId="2" ParentId="13488" CreationDate="2014-04-08T18:57:23.427" Score="1" Body="&lt;p&gt;Practically speaking I have never seen a difference, but the agarose gels usually used in the lab do not have the highest resolution. There is one paper showing that the form (A- or B- form) and the GC-content play a role since DNA molecules of higher GC content are less flexible and therefore have more problems getting through the agarose matrix. Interesting paper, but probably not very relevant in the lab (under &quot;related publications&quot; on the right side of the PubMed site you can find more on this topic):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21504736&quot; rel=&quot;nofollow&quot;&gt;Mechanical Properties of High-G⋅C Content DNA with A-Type&#xA;Base-Stacking&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There is however a technique, which makes use of the different GC content of DNA samples. It is called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Temperature_gradient_gel_electrophoresis&quot; rel=&quot;nofollow&quot;&gt;Denaturing Gradient Gel Electrophoresis&lt;/a&gt;&quot; and makes use of gradients (either chemical or temperature) to denaturate DNA on the gel. Depending on the GC content, this happens earlier or later, which influences the migration pattern (denaturated DNA is much bigger and slower). See &lt;a href=&quot;http://bccm.belspo.be/newsletter/17-05/bccm02.htm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for more details.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-08T18:57:23.427" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16427" PostTypeId="2" ParentId="13998" CreationDate="2014-04-08T19:22:16.193" Score="1" Body="&lt;p&gt;Molecules are antigenic if they are able to elicit an immune response. Let's incorrectly equate &quot;antigenic&quot; with &quot;elicits antibody response&quot;. It's conceivable that a molecule might elicit an immune response, but not generate antibodies - this nuance is not particularly helpful for answering the question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antibodies are proteins which recognize antigens. Exactly which antigen they will recognize depends on the exact sequence of the antibody. This sequence is generated by chance, but it is generated by recombining an array of pre-existing sequences: This means that not every conceivable antibody sequence can be generated by the immune system. Moreover, it is also possible that no antibody at all can be generated for a given substance. So, no, it is not guaranteed that you will be able to generate antibodies for every possible substance. In fact, companies which sell monoclonal antibodies for Western blots often find the occasional substance which will not generate antibodies from their animals (rabbits, mice, goats, and so on).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A second complication is that many molecules are very weakly immunogenic and rely on adjuvants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, there is a simple counter example to your question: There are many foreign molecules, both LPS and peptide, produced by bacteria which do not trigger the immune system at all. This applies to all the species that make up our gut flora, since it would counter productive for the body to attack its own symbiotes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, the immune cells at some stage learn which molecules are &quot;own&quot; molecules, so that they do not attack their own body. If the &quot;foreign&quot; molecule is presented to them at that learning stage, they will not recognize it as an antigen in the future.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-04-08T19:22:16.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16428" PostTypeId="2" ParentId="13998" CreationDate="2014-04-08T19:36:29.153" Score="1" Body="&lt;p&gt;In principle every molecule above a certain size (single amino acids for example can not) can be immunogenic. A very important function of the immune system is to differentiate between molecules, which are foreign and which should raise an immune response and those, which are not and which therefore have to be tolerated. If this differentiation doesn't work, this lead to autoimmunic diseases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two processes which are important here: self-tolerance and tolerance against foreign (or peripheral) antigens. Basically said for self-tolerance autoreactive lymphocites (B- and T-cells) are eliminated from the pool of developing cells, before they can fully differentiate. Only 1-2% of the cells which start developing go get through this selection process. Peripheral antigens (for example from food) are usually tolerated when there is not other immunologic process in the peripheral lymphoid tissues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The process looks in principle like this (image taken from the second review listed below):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hcRJi.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will not write the whole process here, but the &lt;a href=&quot;http://en.wikipedia.org/wiki/Immune_tolerance&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt; article on this topic is a good start. What I can also recommend is the Immunology book written by Janeway and colleagues (if you can get it via a library) and you can have a look on this two reviews:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://immuneweb.xxmu.edu.cn/reading/adative/8.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Immunological Tolerance: Mechanisms&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16932651&quot; rel=&quot;nofollow noreferrer&quot;&gt;Primer: mechanisms of immunologic tolerance.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you have problems accessing the articles, let me know.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-08T19:36:29.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16429" PostTypeId="2" ParentId="13488" CreationDate="2014-04-08T19:38:46.977" Score="2" Body="&lt;p&gt;It does make a difference on polyacrylamide. A and C are faster while G and T are slower.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/?cmd=Search&amp;amp;term=461182%5Bpmid%5D&quot; rel=&quot;nofollow noreferrer&quot;&gt;publication&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YFo84.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;standards&quot; are AAA/TTT/GGG/CCC molecules.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-04-08T19:38:46.977" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16431" PostTypeId="1" AcceptedAnswerId="16434" CreationDate="2014-04-08T22:06:53.940" Score="11" ViewCount="8123" Body="&lt;p&gt;Step 7 of the glycolysis pathway is the conversion of 1,3-bisphosphoglycerate into 3-phosphoglycerate by the action of the enzyme phosphoglycerate kinase, resulting in the production of 2 ATP molecules (per glucose). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This reaction has a large negative value of &amp;Delta;G (-18.5 kJ/mol). If reactions having large negative value of &amp;Delta;G are classed as being irreversible, then why is Step 7 of Glycolysis reversible?&lt;/p&gt;&#xA;" OwnerUserId="5729" LastEditorUserId="1320" LastEditDate="2014-04-09T08:45:07.483" LastActivityDate="2017-07-16T16:06:20.503" Title="Why isn't the phosphoglycerate kinase reaction of the glycolysis pathway irreversible?" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;thermodynamics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16432" PostTypeId="1" CreationDate="2014-04-09T01:59:27.333" Score="3" ViewCount="1060" Body="&lt;p&gt;Is there a reason that oil (e.g., vegetable or clear mineral) is not used to make wet mounts in microscopy? I am not referring to oil immersion technique but substituting oil for water in wet mounts in bright field microscopy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is mostly about moss or mold, things that appear plantlike on a slide. The optical properties may be good and the viscosity, as with glycerine, gives a little depth to the slide. Maybe it causes some sort of distortion? I don't see this listed as a suggestion on microscopy sites. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks. &lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2014-04-11T15:23:40.070" Title="Can oil be used instead of water in preparing wet mounts for microscopy?" Tags="&lt;mycology&gt;&lt;microscopy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16433" PostTypeId="2" ParentId="16431" CreationDate="2014-04-09T07:15:24.723" Score="4" Body="&lt;p&gt;You have to look at the complete reaction including the cofactors. In general, you can drive a chemical reaction into directions which are not favorable by:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;removing products from the environment (if they are gaseous for&#xA;example or react further)&lt;/li&gt;&#xA;&lt;li&gt;having a huge excess of substrates (and thus making the back reaction&#xA;less likely to happen)&lt;/li&gt;&#xA;&lt;li&gt;and by coupling the main reaction to a second, which provides the&#xA;necessary energy for the main reaction to happen&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you look at the reaction of 1,3-BPG to 3-PG this looks like the following (picture from &lt;a href=&quot;http://en.wikipedia.org/wiki/Glycolysis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cYOGV.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The back reaction to 1,3-BPG needs ATP as a co-factor, so that the enzyme has the necessary phosphate group to add. The lysis of  the phosphor diester bond from ATP to ADP delivers the energy to make the reaction possible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This reaction is the control point in either generating ATP (glycolysis), when there is little ATP and much ADP present or generating glucose (gluconeogenesis) when there is much ATP and little ADP. This makes sense when you consider that ATP is a rather instable molecule with its high energy diester bonds, while ADP is more stable.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-04-09T10:27:54.303" LastActivityDate="2014-04-09T10:27:54.303" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16434" PostTypeId="2" ParentId="16431" CreationDate="2014-04-09T08:43:55.507" Score="9" Body="&lt;p&gt;The free energy change that you quote for the phosphoglycerate kinase (PGK) forward reaction is, of course, the &lt;strong&gt;standard free energy change&lt;/strong&gt; (&amp;Delta;G&lt;sup&gt;0&lt;/sup&gt;') for the overall reaction. The standard free energy change is defined for all reactants at a concentration of 1M. Note that this value includes the formation of ATP -  the free energy of hydrolysis of 1,3-BPG would be much larger, and some of that energy is 'captured' in the ATP product.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The actual free energy change for the PGK reaction, &amp;Delta;G,  will differ from this value because of the fact that the actual reactant concentrations are very far from the idealised 1M. You can &lt;a href=&quot;http://en.wikipedia.org/wiki/Glycolysis#Free_energy_changes&quot; rel=&quot;nofollow noreferrer&quot;&gt;find a Table here&lt;/a&gt; which compares, for each step in glycolysis, the standard free energy change with a true free energy change, calculated on the basis of cellular conditions in erythrocytes (also shown). You will see that for the PGK step the actual free energy change is 0.09 kJ mol&lt;sup&gt;-1&lt;/sup&gt; rather than the -18.9 kJ mol&lt;sup&gt;-1&lt;/sup&gt; that you quote in your question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also see from the Table that there are only two reactions in the glycolytic pathway with large negative values for &amp;Delta;G: those catalysed by phosphofructokinase and by pyruvate kinase. These are of course the two steps that are bypassed in gluconeogenesis because they are essentially irreversible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So - your reasoning was correct, but it was based on the wrong &amp;Delta;G values.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;added much later&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As pointed out in the comments, the 1st step in glycolysis also has a large negative value for &amp;Delta;G and is also bypassed. Not sure how I forgot to include that!&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2017-07-16T16:06:20.503" LastActivityDate="2017-07-16T16:06:20.503" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16435" PostTypeId="1" CreationDate="2014-04-09T09:49:25.740" Score="2" ViewCount="579" Body="&lt;p&gt;While studying I read that sperm needs alkaline medium for its survival.But when I studied the composition of semen it revealed that semen contains citric acid which acts as a sperm nutrient along with fructose.It also contain acid phosphatases.So in such sitution how can the sperm survive?&lt;/p&gt;&#xA;" OwnerUserId="6284" LastActivityDate="2014-04-09T13:08:55.527" Title="Why doesn't the sperm die if there is citric acid and acid phosphatases in the semen?" Tags="&lt;reproductive-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16436" PostTypeId="1" CreationDate="2014-04-08T18:48:25.933" Score="5" ViewCount="15555" Body="&lt;p&gt;I asked some of my friends and we all agree that teeth feel funny after drinking Coca-Cola. Other similar soft drinks also cause this effect, but this one most noticeably. It's like teeth become sticky and moving them against each other (by moving jaw) creates rubbery feeling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What ingredient in this soft drink makes teeth like that?&lt;/p&gt;&#xA;" OwnerUserId="1373" OwnerDisplayName="user1306322" LastEditorUserId="1306" LastEditDate="2014-04-09T16:07:10.303" LastActivityDate="2014-12-31T23:50:34.743" Title="What makes teeth feel sticky after drinking Coca-Cola?" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="16438" PostTypeId="2" ParentId="10256" CreationDate="2014-04-09T11:12:27.333" Score="0" Body="&lt;p&gt;You should look at Lehninger's Principles of Biochemistry. Just search for Acetyl-coa in the index, and you will find it's roles in different aspects of the metabolism.&lt;/p&gt;&#xA;" OwnerUserId="5995" LastActivityDate="2014-04-09T11:12:27.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16439" PostTypeId="1" CreationDate="2014-04-09T11:42:41.067" Score="1" ViewCount="55" Body="&lt;p&gt;My thought was to cut all buds of a deciduous tree at spring and see if it can survive a year and develop new buds and leaves next spring. Assuming the tree is already grown and not a sapling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the loss of all buds would be to fatal, how many would a tree need to recover?&lt;/p&gt;&#xA;" OwnerUserId="1807" LastActivityDate="2014-04-09T11:42:41.067" Title="Can a tree survive if someone cuts all buds?" Tags="&lt;plant-physiology&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16440" PostTypeId="2" ParentId="16435" CreationDate="2014-04-09T13:08:55.527" Score="2" Body="&lt;p&gt;Citric acid is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Weak_acid#Weak_acids&quot; rel=&quot;nofollow&quot;&gt;weak acid&lt;/a&gt; so in the context of a buffered physiological medium (semen pH 7.7) it will not cause any significant acidification. Acid phosphatases are enzymes with a pH optimum below 7 (as distinct from alkaline pho sphatases). Their presence has no implications for the pH of semen, although it is interesting to speculate why an alkaline fluid would contain an acid phosphatase.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-04-09T13:08:55.527" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16441" PostTypeId="1" AcceptedAnswerId="16446" CreationDate="2014-04-09T13:55:25.247" Score="9" ViewCount="386" Body="&lt;p&gt;Historically women had a relatively high chance of dying while giving birth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At first thought it seems to me that this would be a disadvantage for the species for the obvious reason that a dead person can no longer give birth (and can't care for her offspring).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this outweighed by some advantages? I can imagine that there would be some evolutionary advantage to have the &quot;weaker&quot; women die during child birth and let the &quot;stronger&quot; ones live to produce more children with &quot;stronger&quot; genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is the high mortality rate in humans during child birth a result of civilization (pre-moderne civilization of course, with the general lack of hygiene/medical knowledge)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is it like for the relatively un-civilized tribes around the world?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is it compared to other closely related mammals?&lt;/p&gt;&#xA;" OwnerUserId="6286" LastEditorUserId="6286" LastEditDate="2014-04-09T14:06:23.360" LastActivityDate="2016-03-12T02:09:02.677" Title="Why did women historically have such a high mortality rate during birth?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16442" PostTypeId="1" AcceptedAnswerId="16443" CreationDate="2014-04-09T14:25:37.733" Score="3" ViewCount="1091" Body="&lt;p&gt;More specifically, if a human subject was exposed to, say, a human cancerous cell line (via intravenous injection or through an open wound, for example), is it possible that they would develop any conditions associated with the cell line?&lt;/p&gt;&#xA;" OwnerUserId="6288" LastActivityDate="2015-03-16T03:39:29.650" Title="Are cell lines potentially dangerous?" Tags="&lt;cell-biology&gt;&lt;cancer&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16443" PostTypeId="2" ParentId="16442" CreationDate="2014-04-09T15:31:05.773" Score="2" Body="&lt;p&gt;This is highly unlikely because the immune system would detect these cells and atack them as foreign. There is at least one case described in the literature in which a woman died of lung cancer after receiving a donor organ from a smoker. This is due to the fact that after transplantations people have to take drugs to suppress their immune system to avoid an immune reaction against the transplanted organ. This allows tumor cells to survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same problem is true in research animals. For the transplantation of tumor cells you need mice with a severely deficient immune system (so called &quot;SCID&quot; (Severe Combined Immunodeficiency) mice) to allow tumor cells to grow. This is different when you work with viruses (like the human papilloma virus) which can cause cancer. Here you have to take appropriate safety measures.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-09T15:31:05.773" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="16444" PostTypeId="1" CreationDate="2014-04-09T16:34:37.297" Score="6" ViewCount="518" Body="&lt;p&gt;Why would things self-organize in such a manner? I'm a mathematician and I have no baggage in ecology or biology. If the question is too broad maybe someone can point me to formal sources where this type of issues are tackled.&lt;/p&gt;&#xA;" OwnerUserId="3487" LastActivityDate="2014-04-10T00:10:28.337" Title="Why are there ecosystems?" Tags="&lt;zoology&gt;&lt;botany&gt;&lt;ecology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16446" PostTypeId="2" ParentId="16441" CreationDate="2014-04-09T17:56:11.610" Score="3" Body="&lt;p&gt;That's an interesting question. And it is also a common misunderstanding of evolutionary processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks to @Chris comment, we know/can assume that high mortality rate is not a consequence of industrialization but has ever been before the era of modern medicine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Women don't let themselves die in order to improve the species. Those women that carry a gene forcing them to commit suicide in order to improve the species won't pass on their genes, and in consequence no women will ever suicide in order to improve the species. In other words, altruistic behavior cannot appear and spread over time. This is the standard view of selection (and probably the good explanation in our case).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I have to say that I lied in the previous paragraph! There is a field of study called &lt;a href=&quot;http://en.wikipedia.org/wiki/Social_evolution&quot; rel=&quot;nofollow noreferrer&quot;&gt;social evolution&lt;/a&gt; which aims to study social traits. Social traits are those traits which influence not only the fitness of the individual carrying the trait but also the fitness of other individuals in the population. Theoretically all traits are somehow social traits! Typically altruistic behavior is among those social traits that cause a decrease (a cost) in the carrier fitness for an advantage (a benefit) for one or several other individuals in the population. There are several models (which are still debated in particular concerning the assumptions of these models) to explain the evolution of such traits. The most famous, most commonly used and most theoretically studied one is Kin selection/Hamilton's rule. You'll find some explanations about this rule on &lt;a href=&quot;https://biology.stackexchange.com/questions/10742/what-if-rb-c-in-hamiltons-rule/10756#10756&quot;&gt;this post&lt;/a&gt;. The concept of population structure is key in the understanding of Hamilton's rule. Also important are the concept of levels of selection, which gives a possible explanation for the evolution of altruism, the concept of lineage selection, and finally the concept of reciprocity (but that doesn't make much sense in the current context!). Some people would not classify these models as I did, some would add other models, some would melt two models into one…&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For one of these models to be correct we would need high lineage split and extinctions in human history which I don't think is really the case. Or we'd need that the death of a woman is particularly benefit to her family. I don't think first human were cannibals. Women were probably very often pregnant and males had to fight to be the father. So dying would probably not free much opportunities for the sisters and brothers…. One would need to write some equations and gather more information than what I have but intuitively I don't think that high mortality rate in women while giving birth is an altruistic behavior.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2016-03-12T02:09:02.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16447" PostTypeId="1" AcceptedAnswerId="16530" CreationDate="2014-04-09T18:00:27.030" Score="3" ViewCount="1582" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/GC-content&quot; rel=&quot;nofollow&quot;&gt;GC-content&lt;/a&gt; refers to the frequency of base pairs that are either C or G in the genome, or in other words the number of GC base pairs divided by the addition of the number of GC base pairs plus the number of AT base pairs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$GCcontent = \frac{N_{GC}}{N_{AT}+N_{GC}}$$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does the GC-content evolve and why does the GC-content differ between populations/species/lineages? Does it evolve under Genetic drift only? Under selection? Intuitively, I'd say that the ratio of the probabilities of mutating from A or T to G or C should be an important factor driving the evolution of the GC-content. Does it? Does the overall mutation rate influence the GC-content? What other traits/forces influence the evolution of the GC-content?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-04-13T19:38:39.900" LastActivityDate="2014-04-14T17:25:32.017" Title="How does GC-content evolve?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;dna&gt;&lt;molecular-genetics&gt;&lt;natural-selection&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16448" PostTypeId="1" AcceptedAnswerId="16487" CreationDate="2014-04-09T18:09:13.890" Score="3" ViewCount="121" Body="&lt;p&gt;The wright-Fisher model of genetic drift is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$p_{ij} = \binom{2N}{j}\left(\frac{i}{2N}\right)^j \left(1- \frac{i}{2N}\right)^{2N-j} $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;,where $\binom{2N}{j}$ is a binomial coefficient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this equation one can infer that the expected heterozygostiy should decrease by $1-\frac{1}{2N}$ at each time step because:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$E[x_{t+1}(1-x_{t+1}) \space|\space x_t] = (1-\frac{1}{2N})x_t(1-x_t)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't understand this equality. That might be very simple though! Can you help me making sense of it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://books.google.ch/books/about/Mathematical_Population_Genetics_1.html?id=twXIyXyod2MC&amp;amp;redir_esc=y&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-04-12T10:29:50.090" LastActivityDate="2014-04-14T06:41:23.147" Title="Heterozygosity under genetic drift" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;&lt;mathematical-models&gt;&lt;population-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16449" PostTypeId="2" ParentId="16444" CreationDate="2014-04-09T18:42:31.260" Score="9" Body="&lt;p&gt;Basically, they don't. Ecosystems are pretty much either &lt;em&gt;de facto&lt;/em&gt;, delimited by geographical boundaries, or defined by us. For example, an underground lake would be an ecosystem and it is organized in such a way for the simple reason that there is no communication between it and any other system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most ecosystems however, do communicate. For example, we call a desert an ecosystem but what of creatures living in the borders? That can survive both the harsh desert and the milder outskirts. Do they belong to the desert ecosystem? To the surrounding one? To both?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, we divide nature into ecosystems because we can study them better that way. Species that form part of the same ecosystem tend to interact in one way or another and species from completely separate ecosystems tend not to. This is not some kind of rule however, it is simply the way &lt;em&gt;we&lt;/em&gt; categorize things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To take a different example, how would you define a city? Where does a city end and the countryside begin? Ecosystems are similar, there are seldom very clear cut lines separating them, they sort of bleed into one another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, your question is moot, ecosystems don't really self organize as such. The organization that does exist is between the different species and is an emergent quality of the complex system that is the ecosystem. Thinking of ecosystems, however, as distinct and well defined entities is generally wrong. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-04-09T18:42:31.260" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16450" PostTypeId="1" CreationDate="2014-04-09T19:40:36.573" Score="1" ViewCount="71" Body="&lt;p&gt;I work in neuroscience, mostly Alzheimer's disease (AD), with some work in autism spectrum disorder (ASD). The work is in gene regulation and epigenomics. I'm familiar with monozygotic twin (MZ) discordance for AD and ASD and the methylome studies done in discordant MZ for those disorders. I began to become curious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What disorders have never had MZ discordance reported in the literature? Even sickle cell has MZ discordant progression (Amin et al. 1991. Hemoglobin. 15:247-56). Do any disorders lack MZ discordance?&lt;/p&gt;&#xA;" OwnerUserId="4032" LastActivityDate="2016-03-18T14:52:50.237" Title="Which disorders are fully concordant?" Tags="&lt;genetics&gt;&lt;pathology&gt;&lt;human-genetics&gt;&lt;twins&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16451" PostTypeId="2" ParentId="16444" CreationDate="2014-04-09T19:53:21.600" Score="2" Body="&lt;p&gt;An ecosystem is a community of living things that exist in conjunction with and rely on nonliving things like a rock, a sandy beach, air, or water. Each organism has an ideal environment, and they may not be able to survive outside that environment. Thus you see a pond with fish living it in next to a forest with squirrels. The division and self organization is natural: the fish do not do so well on land and the squirrels have trouble surviving underwater so they stay in their own ecosystems. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your question is more along the lines of &quot;why is there a desert here next to a mountain with a forest on the other side of the mountain.&quot; This organization occurs due to chance mitigated by the physical laws of the universe based on things like planetary geography / climate, tectonics, and astrophysics.  &lt;/p&gt;&#xA;" OwnerUserId="6291" LastEditorUserId="6291" LastEditDate="2014-04-09T22:15:42.133" LastActivityDate="2014-04-09T22:15:42.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16453" PostTypeId="1" AcceptedAnswerId="16455" CreationDate="2014-04-09T21:06:11.287" Score="5" ViewCount="13967" Body="&lt;p&gt;My son is doing a science research project at school, and he's chosen to research what happens when seeds are refrigerated before planting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I cannot provide any information in regards to background research (I couldn't find any), but I want to know if refrigerating seeds before planting them will have &lt;strong&gt;any&lt;/strong&gt; effect at all on the seed (so that my son's experiment can be interesting).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="1470" LastActivityDate="2018-06-15T21:26:03.407" Title="What happens when seeds are refrigerated before planting?" Tags="&lt;botany&gt;&lt;seeds&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16454" PostTypeId="1" CreationDate="2014-04-09T22:49:20.637" Score="3" ViewCount="6470" Body="&lt;p&gt;Looking at my computer's fan I can say that a lot of dust is collected on it not less dust should be collected in the lungs, not to mention some inhaled parts of food. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How the lungs clear themselves from dust, smoke, food particles?&lt;/p&gt;&#xA;" OwnerUserId="408" LastActivityDate="2014-04-12T08:44:34.427" Title="How the lungs clear themselves?" Tags="&lt;human-biology&gt;&lt;lungs&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16455" PostTypeId="2" ParentId="16453" CreationDate="2014-04-09T23:22:21.227" Score="6" Body="&lt;p&gt;That might be a good experiment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that before planting bulbs you want to put them in the refrigerator or even the freezer sometimes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact this process of cold treating seeds has a name: &lt;a href=&quot;http://www.successwithseed.org/getting-started/367-do-some-seed-need-special-treatments-to-germinate&quot; rel=&quot;noreferrer&quot;&gt;Stratification&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To paraphrase: some seeds become inactivated at higher temperatures like lettuce and delphinium.  You can place the seeds in medium and put them in the fridge or freezer for a day or two. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see how this makes sense.  The seeds have adapted to start growing when they are freezing because the timing results in the plants breaking ground as early as possible when the temperature is warm enough in the spring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A quick search doesn't seem to imply that silverbeet needs to be stratified before planting.  The result might be negative, but there is definitely some good expectation that it makes a difference to some plants. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-04-09T23:22:21.227" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16456" PostTypeId="2" ParentId="16444" CreationDate="2014-04-09T23:40:38.627" Score="3" Body="&lt;p&gt;The definition of ecosystem here is missing, but if you mean &quot;an inter-dependency of different organisms that all live in the same geographic region&quot; then I think that competition and cooperation are big drivers of the establishment of these roles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some animals and plants are so interdependent that they evolve together despite being different species.  The hawk moths have terribly long probiscus which are co-evolved with flowers with deep cup shapes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IXN6r.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The flowers and the moths create more exclusive relationships - the flowers are more reliable food sources for the adult moths when other pollinators can't get to them and the flowers are more likely to succeed in pollination with the moth feeding of fewer kinds of flowers.  Cooperation of this nature tends to be show up spontaneously in the ecological milieu because of the utility and stability it can bring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Competition is the other side to this side of ecosystem evolution.  Because living things reproduce to the point where nutrition and security are scarce (meaning that there isn't enough for every plant/animal) cooperation becomes an important advantage.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-04-09T23:40:38.627" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16457" PostTypeId="2" ParentId="16454" CreationDate="2014-04-09T23:47:10.797" Score="1" Body="&lt;p&gt;Our respiratory tract is lined with &lt;a href=&quot;http://www.ciliopathyalliance.org/cilia/structure-and-function-of-cilia.html&quot; rel=&quot;nofollow&quot;&gt;cilia&lt;/a&gt;, which are hair-like structure that extend from the outside of the cells. They wave back and forth and act like brushes to catch dust particles before they enter the lungs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some particles do get past these cilia and enter the lungs, however. The lungs will secrete mucus that collects the dust. You then cough up the mucus to get rid of the dust particles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mucus your lungs excrete also help against pathogens you inhale. Bacteria and viruses are also collected in the mucus, and then removed via coughing. This is why you may cough up phlegm when you're sick.&lt;/p&gt;&#xA;" OwnerUserId="4929" LastActivityDate="2014-04-09T23:47:10.797" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16459" PostTypeId="2" ParentId="16441" CreationDate="2014-04-10T05:41:05.137" Score="3" Body="&lt;p&gt;Human females have one of the worst  chidbirth experiences. This is because of our extremely high cranial capacity compared to the apes. This had an obvious evolutionary advantage and made us what we are today. However this creates problems as the braincase has to pass the pelvic cavity during childbirth. The wider hips in women compensate for this but still it is much harder than in case of other apes. Shorter women are in greater danger. Much easier for our closest cousins the chimps or gorillas. Compared to tribal women the civilised lineages have survived with more assistance... &lt;/p&gt;&#xA;" OwnerUserId="6298" LastActivityDate="2014-04-10T05:41:05.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16460" PostTypeId="1" AcceptedAnswerId="16467" CreationDate="2014-04-10T06:27:05.053" Score="1" ViewCount="522" Body="&lt;p&gt;Excluding situations where you die from accidents, the main reason for death is -generaly- &lt;a href=&quot;http://www.who.int/mediacentre/factsheets/fs310/en/&quot; rel=&quot;nofollow noreferrer&quot;&gt;diseases&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And usually it is about an organ which becomes &quot;tired&quot; after many years. These results are all from experience and statistics:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4Gvot.png&quot; alt=&quot;Top 10 causes for death&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I've never heard of any study that said: &quot;people can't live longer than x age because the heart can't live longer than that&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From my point of view, I think it's us who control the way we live and consequently someone can live longer than the other. For example, &lt;a href=&quot;http://www.lung.org/stop-smoking/about-smoking/facts-figures/general-smoking-facts.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;smokers die at an early age.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But even the &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_the_verified_oldest_people&quot; rel=&quot;nofollow noreferrer&quot;&gt;oldest person in the world&lt;/a&gt;, lived for 122 years and 164 days. For me this isn't enough. It seems that someone can't control his age after all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically my question is: Does science provide any limit that a person isn't able to live more than it? For instance can someone live more than 1000 years?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;sub&gt;Note: I don't think someone is able to do this because simply even our healthiest habits are not &quot;so&quot; healthy. But imagine someone who doesn't live like any of us as humans, i.e. Can have a very healthy and natural life &lt;/sub&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="6256" LastActivityDate="2014-04-11T06:40:16.473" Title="Does Science Say That We Should Die?" Tags="&lt;human-biology&gt;&lt;mammals&gt;&lt;speculative&gt;&lt;organs&gt;" AnswerCount="2" CommentCount="0" ClosedDate="2014-04-15T01:06:42.303" ContentLicense="CC BY-SA 3.0" />
  <row Id="16465" PostTypeId="2" ParentId="16460" CreationDate="2014-04-10T15:16:15.597" Score="0" Body="&lt;p&gt;Your body knows it should die. Science discovered the details for us to understand. It is called apoptosis: pre-programmed cell death. The DNA in our cells is encoded to replicate only a certain number of times. Thus organs wear out as the cells are not being faithfully replaced (there are other factors to aging as well).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[link] &lt;a href=&quot;http://en.wikipedia.org/wiki/Apoptosis&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Apoptosis&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It probably evolved since a population of organism that do not die will become overpopulated, consume all the food and all die out. Imagine how many people there would be if we never died due to cancer or organ failure. Would we be stacked a mile deep?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conversely cancer is a phenomenon when one or more of the mechanisms (genes) involved with apoptosis are turned off due to damage or mutation of the DNA. Cancer cells then become immortal, replicating indefinitely and continuing to mutate. This causes tumors and problems as there are large masses of non-productive cells taking up space and consuming nutrients.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes there is a limit. A 1000 year old person would not be possible unless someone developed a way to control apoptosis while at the same time not producing a cancer, preventing normal genetic drift, and eliminating other aging factors. Naturally there is a lot of money to be made in extending life so this field is being researched. A near immortal creature could also spontaneously evolve due to random mutation. Similar to someone with a mutation for three perfectly functional arms, or the ability to shock people like an eel, a viable person with genetic near immortally would be highly improbable. &lt;/p&gt;&#xA;" OwnerUserId="6291" LastEditorUserId="6291" LastEditDate="2014-04-10T16:04:36.233" LastActivityDate="2014-04-10T16:04:36.233" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16467" PostTypeId="2" ParentId="16460" CreationDate="2014-04-10T16:09:41.160" Score="3" Body="&lt;p&gt;Quoting a great biologist Peter Medawar :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is by no means difficult to imagine a genetic endowment which can&#xA;  favor young animals only at the expense of their elders; or rather at&#xA;  their own expense when they, themselves, grow old. A gene or&#xA;  combination of genes that promotes this state of affairs will, under&#xA;  certain numerically definable conditions, spread throughout a&#xA;  population simply because the younger animals it favors have, as a&#xA;  group, a relatively large contribution to make to the ancestry of the&#xA;  future population.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From Why We Get Sick :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Imagine that there is a gene that changes calcium metabolism so that&#xA;  bone heals faster, but the same gene also causes slow and steady&#xA;  calcium deposition in the arteries. Such a gene might well be selected&#xA;  for, because many individuals will benefit from its advantages in&#xA;  youth, while few will live long enough to experience the disadvantage&#xA;  of arterial disease in old age. Even if the gene caused everyone to&#xA;  die by age 100, it would still spread if it offered even minor&#xA;  benefits in youth. This argument does not depend on the prior&#xA;  existence of senescence. Other causes of death—accidents, pneumonia,&#xA;  and all the rest—are sufficient to reduce the population at older&#xA;  ages. Nor does the theory depend, like Haldane’s, on cessation of&#xA;  reproduction.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The message I am trying to get across is that - As organisms are like vehicles which carry DNA and DNA just &quot;madly&quot; wants to replicate itself and pass itself from generation to generation, Natural Selection will favour those traits that maximise reproductive success. These may be traits that provide maximum benefit in youth but cause gradual damage and lead to senescence and death. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could also think like this - Every machine has wear and tear and must be thrown away after it is irreparable. Same is with our body, it is the most beautiful machine in the world but it is also subject to the same wear and tear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also there is the end replication problem. See telomeres if you dont know what I am talking about. There is a limit to number of times a cell can divide. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So all in all I would say that there is a biological limit - a certain age up to which a person may live.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2014-04-11T06:40:16.473" LastActivityDate="2014-04-11T06:40:16.473" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16469" PostTypeId="2" ParentId="11134" CreationDate="2014-04-10T17:19:34.660" Score="1" Body="&lt;p&gt;In general fungal cell walls are resistant to whatever enzymes or compounds they are excreting to break material down for consumption. Conceptually, it is a little like your stomach lining being resistant to stomach acid. For a more detailed answer you may have to head over to your local university and find a Mycologist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is ongoing research on how fungi actually &quot;eat.&quot; You can look up fungal endocytosis if you wish to research it more. There may be other mechanisms as Shigeta mentions.&lt;/p&gt;&#xA;" OwnerUserId="6291" LastActivityDate="2014-04-10T17:19:34.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16470" PostTypeId="1" AcceptedAnswerId="16474" CreationDate="2014-04-10T18:26:37.957" Score="31" ViewCount="5743" Body="&lt;p&gt;I have recently been involved in collaborations that require me to model the population genetics of eukaryotic populations. I fear I may either be &quot;re-inventing the wheel&quot; or making conceptual mistakes (e.g. simplifying assumptions) in many of the techniques and decisions so far.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I would very much appreciate recommendations of books about population/evolutionary genetics or micro evolution to deal with these fears. Preferable criteria are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Intuitively introduces key concepts.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Emphasis on modelling with examples of problems and their solutions.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Relatively short (I'm planning to read from cover to cover).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="3624" LastEditDate="2017-03-22T13:39:44.087" LastActivityDate="2020-12-06T06:25:16.547" Title="Books on population or evolutionary genetics?" Tags="&lt;genetics&gt;&lt;evolution&gt;&lt;population-genetics&gt;&lt;book-recommendation&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="16" ContentLicense="CC BY-SA 3.0" />
  <row Id="16471" PostTypeId="2" ParentId="8098" CreationDate="2014-04-10T18:36:25.103" Score="1" Body="&lt;p&gt;I got .59. In response to WYSIWYG:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Note: I'm using A and a for the two alleles. My copy of Bulmer uses B for the second, which makes a little more sense if the alleles are codominant.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a.) The AA x aa cross should be twice as common as the AA x AA and aa x aa crosses, just as HT is more common than HH or TT when we toss a pair of identical coins. In particular, this cross should occur with frequency 2*(.25*.25)= .125. Same goes for AA x Aa, AA x aa, and Aa x aa.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b.) In an Aa x Aa cross, there is a 3/8 probability that two offspring will have the same genotype. I reasoned as follows:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;There is a 0.5 probability that the first offspring will be heterozygous (Aa). In that case, there is a 0.5 probability that the second offspring will also be heterozygous.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There is a 0.25 probability that the first offspring will be homozygous AA: In that case there is a 0.25 probability that the second offspring will also be AA. Likewise for aa.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Summing these: (1/2)^2 + (1/4)^2 +(1/4)^2 = 1/4 + 2/16 = 3/8.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I believe that resolves the issue. Apologies if I've missed something.&lt;/p&gt;&#xA;" OwnerUserId="6306" LastActivityDate="2014-04-10T18:36:25.103" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16472" PostTypeId="1" CreationDate="2014-04-10T18:41:15.527" Score="3" ViewCount="129" Body="&lt;p&gt;Why are many anti-malaria drugs gap junction antagonists?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My professor recently just mentioned that many of the anti-malaria drugs block gap junctions. i am wondering if this blocking is important for stopping malaria, and how blocking gap junctions is anti-malarial. How does this effect connect to the mechanism of malaria?&lt;/p&gt;&#xA;" OwnerUserId="6099" LastEditorUserId="57" LastEditDate="2014-04-10T20:11:27.443" LastActivityDate="2014-04-15T03:09:33.617" Title="Why are many anti-malaria drugs gap junction antagonists?" Tags="&lt;human-biology&gt;&lt;pharmacology&gt;&lt;malaria&gt;&lt;pharmacodynamics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16473" PostTypeId="1" CreationDate="2014-04-10T20:31:17.983" Score="1" ViewCount="290" Body="&lt;p&gt;I meat a overtrained friend (25 years old) who cannot rest.&#xA;He has all muscles and most of the skin very tense.&#xA;He is practising  regularly in gym and sleep badly.&#xA;He moves like a stick figure and has complained pains systemically.&#xA;The tenseness have now been some years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have met once before such a person who was about 90-year old body builder (male) who never run and did no stretching.&#xA;Ageing is not necessarily linked to this kind of tenseness.&#xA;I have not seen such tenseness in women.&#xA;So I think it is related to the muscles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Possible pathogenesis&lt;/strong&gt;. Probable causes of this kind of systemic tension&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;fibrinous inflammation starting from upper body &#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;etc posterior, medial scapula; &lt;/li&gt;&#xA;&lt;li&gt;middle inferior posterior clavicula&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;starting as membranous inflammation&lt;/li&gt;&#xA;&lt;li&gt;long-term accumulation of fibrin and proteins in lymphatic system in interstitial spaces&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;proceeding on muscular membranes and through lymphatic system into axillary zone&lt;/li&gt;&#xA;&lt;li&gt;axillary lymph nodes&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;deep injury of lymph conduction system as a consequence of decreased lymphatic drainage&lt;/li&gt;&#xA;&lt;li&gt;proceeding into pseudomembranous inflammation in the upper body&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;starting from axillary lymphatic system&lt;/li&gt;&#xA;&lt;li&gt;proceeding back to to the origin through fibrinous membranes as pseudomembranous to other parts (clavicula and scapula)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;step by step proceeding into extremities and to lower body&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;eventually achilles tendon and foot Thian point glympadenopathy&lt;/li&gt;&#xA;&lt;li&gt;hardening of foot muscles similarly as through upper body&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Schematic drawing about the fibrinous inflammation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WmOWB.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Possible other causes&lt;/strong&gt; without citings to literature&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;right heart failure&lt;/li&gt;&#xA;&lt;li&gt;systemic hypertension and defect in heart (etc fully patent foramen ovale; got idea from &lt;a href=&quot;https://biology.stackexchange.com/a/16482/86&quot;&gt;this discussion&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am interested what is name of this kind of systemic tenseness, probably muscular origin.&#xA;&lt;strong&gt;What is the pathogenesis of this kind of tenseness?&lt;/strong&gt;&#xA;Why is it systemic? &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-04-12T11:12:59.270" Title="What is the name of systemic tension of muscles?" Tags="&lt;pathology&gt;&lt;senescence&gt;&lt;pathogenesis&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16474" PostTypeId="2" ParentId="16470" CreationDate="2014-04-10T21:56:19.767" Score="32" Body="&lt;p&gt;&lt;strong&gt;TL;DR&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;I'd recommend &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0801880092&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Population Genetics: A Concise Guide (Gillespie)&lt;/a&gt; for an introduction to population/evolutionary genetics (thanks AGS for highlighting this big miss of mine on the first version of my answer).&lt;/p&gt;&#xA;&lt;p&gt;I'd recommend &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0691123446&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;A Biologist's guide to mathematical modelling in evolution and ecology (Otto and Day)&lt;/a&gt; if you want to ensure your knowledge in mathematics by learning their application to evolutionary biology.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;General Entry Books to Population Genetics&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;There are several books that offer an introduction to population genetics. I read &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0878933085&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Principles of Population Genetics (Hartl &amp;amp; Clarke)&lt;/a&gt;. I appreciated it but if I were you I think I would rather try &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0981519423&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Elements of population genetics (Charlesworth)&lt;/a&gt; or &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/1405132779&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Population Genetics (Hamilton)&lt;/a&gt;. There is also &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0763757373&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Genetics of Populations (Hedrick)&lt;/a&gt;. I would tend to think that this last book presents lots of empirical population genetics data and doesn't take as much focus as the others in theoretical concepts (but I might be wrong). Gillespie's book &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0801880092&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Population Genetics: A Concise Guide&lt;/a&gt; is a classic. It is short, very easy to follow and pleasant to read. Gillespie's book might eventually be a little bit outdated but I would still highly recommend it.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Emphasis on Analytical Modelling&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0691123446&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;A Biologist's guide to mathematical modelling in evolution and ecology (Otto and Day)&lt;/a&gt; is a very good and very accessible book. It makes a good review about all subjects that are usually taught to first year students in Biology such as linear algebra for example. It is highly accessible and in the meantime it goes pretty far as it ends up talking about the application of diffusion equation in population genetics (Kimura's work among others). This book presents some important models in population genetics but as it aims to provide the tools for mathematical modelling in ecology and evolution it may under-considerate some fields of ecology and evolutionary biology. For example, the book does not talk about population structure nor about evolutionary game theory and there is little about Coalescent theory.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Other books treating specific subjects within population genetics&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0974707759&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Coalescent Theory: an Introduction (John Wakeley)&lt;/a&gt; is a good book. I haven't read it completely for both time issues and because the math are a bit complicated for me. Coalescent theory offers a very important set of mathematical tools in evolutionary biology.&lt;/p&gt;&#xA;&lt;p&gt;There's also &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0387201912&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mathematical population genetics (Ewens)&lt;/a&gt;. I am currently reading it. It is definitely not an introductory book and it really doesn't cover much of the most common fields in population genetics.&lt;/p&gt;&#xA;&lt;p&gt;If you are particularly interested in age-structured population, &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0521459672&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evolution in age-structured populations (Charlesworth)&lt;/a&gt; is a very good book.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/B005OKYTXU&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Modeling evolution (Roff)&lt;/a&gt; offers some discussion on how to mathematically define fitness from phenotypic traits. While it is interesting I would not counsel you to buy it. Moreover, all the mathematics are quite basic and it aims to explain how to perform mathematical modelling with R which is to my opinion not essential to learn as other languages make a better job at dealing with math (Mathematica for example).&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0521116082&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evolutionary Conservation Biology (Ferrière, Couvet and Dieckmann)&lt;/a&gt; is a very good book of conservation and conservation genetics. It develop some mathematical models that are of special interest to conservation of populations and communities.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.fr/Ecology-Genetics-Evolution-Metapopulations-Hanski/dp/0123234484/ref=sr_1_5?ie=UTF8&amp;amp;qid=1406725307&amp;amp;sr=8-5&amp;amp;keywords=mutational%20meltdown&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ecology, Genetics and Evolution in Metapopulations (Hanski and Gaggiotti)&lt;/a&gt; is a book that may interest you as well. However it focuses much more on ecology than the other ones I cited above. Note: I haven't read it entirely.&lt;/p&gt;&#xA;&lt;p&gt;If you are interested in kin selection and level of selection, you might want to have a look at &lt;a href=&quot;https://www.amazon.ca/Major-Transitions-Evolution-Maynard-Smith/dp/019850294X/ref=sr_1_1?ie=UTF8&amp;amp;qid=1505925039&amp;amp;sr=8-1&amp;amp;keywords=major%20transitions%20in%20evolution&quot; rel=&quot;nofollow noreferrer&quot;&gt;Major Transitions In Evolution (Maynard Smith and Szathmary)&lt;/a&gt; which is a classic (I have not read it though) or &lt;a href=&quot;https://www.amazon.ca/Major-Transitions-Evolution-Revisited/dp/0262015242/ref=sr_1_2?ie=UTF8&amp;amp;qid=1505925039&amp;amp;sr=8-2&amp;amp;keywords=major%20transitions%20in%20evolution&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Major Transitions in Evolution Revisited (Calcott and Sterelny)&lt;/a&gt; who encompass the opinion of many authors on the subject. &lt;a href=&quot;https://www.amazon.ca/Evolutionary-Dynamics-Exploring-Equations-Life/dp/0674023382/ref=sr_1_1?ie=UTF8&amp;amp;qid=1505925119&amp;amp;sr=8-1&amp;amp;keywords=nowak%20dynamic&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evolutionary Dynamics: Exploring the Equations of Life (Nowak)&lt;/a&gt; is also of interest esp. for those interested in epidemiology. Finally, you might want to have a look at the extremely well written and easy to read books by Dawkins such as &lt;a href=&quot;https://www.amazon.ca/Extended-Phenotype-Long-Reach-Gene/dp/0192880519&quot; rel=&quot;nofollow noreferrer&quot;&gt;The extended phenotype (Dawkins)&lt;/a&gt; for example. The Dawkins book are very popular and very very introductory. It offers more a way to think than the actual science behind evolutionary biology.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2020-12-06T06:25:16.547" LastActivityDate="2020-12-06T06:25:16.547" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="16475" PostTypeId="2" ParentId="16388" CreationDate="2014-04-10T23:41:00.007" Score="5" Body="&lt;p&gt;Proteins are polymers of amino acids. Each amino acid has a side chain. Many of these side chains contain ionisable groups. The ionization state of these groups is dependent on the pH. A group that is protonated at pH=2 and neutral, for example, may become deprotonated at pH=8 and become negative. See the Henderson-Hasselbalch equation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Protein structure is held together by many intermolecular interactions: dipole-dipole, hydrophobic, electrostatic, etc. The correct protein structure is necessary for function. At different pH levels, the protonation and deprotonation of ionisable amino acids affects the intermolecular interactions within the protein and its conformation will change. At a certain pH, the conformation of the protein will be optimal for its function and this is where it will have maximum activity. As pH deviates to either side of the optimum, the conformation changes and the structure will no longer be correct for proper function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ionization state of amino acids is also important in the active site but not only because of conformational changes. Catalytic residues must have certain properties to catalyze their specific reactions. As an example, two Asp residues (which have carboxylates on their side chains) in the active site of DNA polymerase are responsible for coordinating two magnesium ions that promote polymerization. If the pH were to decrease to a point where the Asp residues were protonated, they could no longer bind the Mg2+ ions and the enzyme would not function.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-04-10T23:41:00.007" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16477" PostTypeId="2" ParentId="16448" CreationDate="2014-04-11T09:32:30.910" Score="1" Body="&lt;p&gt;The notation at &lt;a href=&quot;http://www.stat.berkeley.edu/users/terry/Classes/s260.1998/Week13a/week13a/node9.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; site resembles that in your question but preserves the $\frac{x_t}{2N}$ notation for probability of selecting an allele. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$E[\frac{x_{t+1}}{2N})(1 - \frac{x_{t+1}}{2N} )|x_t] = (\frac{x_{t}}{2N})(1 - \frac{x_{t}}{2N}) (1 - \frac{1}{2N})  $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The expression $(\frac{x_{t}}{2N})(1 - \frac{x_{t}}{2N}) $ is the probability of heterozygosity at step $t.$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your expression says that the expected heterozygosity at step $(t+1)$ is equal to the heterozygosity at step at $t$ multiplied by $(1-\frac{1}{2N}).$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a population of size $2N,~(1-\frac{1}{2N})^{2N}\approx 1/e,$ so large populations are insulated from this effect and small ones may lose genetic diversity rapidly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A typical explanation can be found &lt;a href=&quot;http://www.math.ubc.ca/~db5d/SummerSchool09/lectures-dd/lectures6-7.pdf&quot; rel=&quot;nofollow&quot;&gt;here.&lt;/a&gt; The notation at this site condenses the expression $(\frac{x_{t}}{2N})(1 - \frac{x_{t}}{2N}) $ to $H_n$ and explicitly says it is $1 - F_n, $ in which $F_n$ is the probability of homozygous at step $n.$&lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-04-12T01:20:31.977" LastActivityDate="2014-04-12T01:20:31.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16478" PostTypeId="1" AcceptedAnswerId="19876" CreationDate="2014-04-11T10:08:25.900" Score="11" ViewCount="4526" Body="&lt;p&gt;Did the killing or sterilisation of people considered as living a &quot;life unworthy of life&quot; in Nazi Germany have any measurable effect on the &quot;average health&quot; of Germany? Is there any statistical evidence that the rate of (a specific) mental or physical illness is lower in Germany compared to other countries that were not affected by the Nazis  (I guess you would need to have data on the rate of that illness from before the eugenics program as well)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. Please note, I'm neither interested in discussing the ethics of eugenics, nor in condoning what has happened in its name under the Nazis. I just want to know what the result on average health (if there is such a thing) was.&lt;/p&gt;&#xA;" OwnerUserId="6309" LastActivityDate="2019-02-27T16:01:11.423" Title="Did the eugenics program in Nazi Germany have a measurable effect?" Tags="&lt;genetics&gt;&lt;human-genetics&gt;&lt;history&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="2" ClosedDate="2014-07-24T10:05:45.230" ContentLicense="CC BY-SA 3.0" />
  <row Id="16480" PostTypeId="2" ParentId="16432" CreationDate="2014-04-11T15:23:40.070" Score="2" Body="&lt;p&gt;Typically wet mounts are used to observe the mobility and behavior of microorganisms. A classical use for a wet mount would be to study something like pond water were you could see all the different organisms swimming around like they would in their natural environment. Oils are more viscus and would impede mobility and might impact behavior or even be toxic to the microorganisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you were an olive oil manufacturer, and you thought you had some odd microbial contamination of your olive oil you might look at a drop of your olive oil between a slide and cover slip thus using an oil based wet mount like you are describing. You might also do this if you were studying the microbiology of an oil spill in water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is nothing saying you could not suspend a sample in oil. There may even be a unknown benefit of using this method in certain circumstances, that is waiting to be discovered.&lt;/p&gt;&#xA;" OwnerUserId="6291" LastActivityDate="2014-04-11T15:23:40.070" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16481" PostTypeId="1" AcceptedAnswerId="16544" CreationDate="2014-04-11T18:34:17.627" Score="0" ViewCount="106" Body="&lt;p&gt;Many trees survive centuries and die only in disasters like&#xA;storms and lightnings or infections. So do they have no set&#xA;life span? Are they exceptionally resistant to genetic&#xA;mutations and have very less cell cycle regulations which&#xA;keep them 'forever young'?&lt;/p&gt;&#xA;" OwnerUserId="6298" LastActivityDate="2014-04-14T16:15:08.820" Title="Do trees have no set lifespan and&#xA;&quot;quite&quot;immortal?" Tags="&lt;lifespan&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16482" PostTypeId="2" ParentId="16414" CreationDate="2014-04-11T21:00:53.187" Score="2" Body="&lt;p&gt;A fully patent foramen ovale (pfo) is rare however a partial or small pfo is present in about 30% of the population. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the manifestations you described are partially correct. A pfo causes a left to right shunt in the adult whilst a right to left shunt in the fetus. In the fetus this is normal. In the adult, it is left to right because the left atrium is at higher pressure than the right. Due to this some of your manifestations are the wrong way round but still correct. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example you mentioned hypertension, but presumably you meant systemic hypertension. It is more common at least in the early stages to get pulmonary hypertension. The pressures in the left atrium cause the pressures in the right atrium to increase when there is shunting. This is frequently seen when pressures in the left are increased due to factors like systemic hypertension. Coronary artery disease can also worsen the shunt and increase pressures in the right atrium and pulmonary pressures because the left ventricle can be stiffer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite all this the more common presentation of a clinically significant pfo is right heart failure. Volume overloaded,the right heart dilates and fails. This will cause the usual presentation of right heart failure i.e. peripheral oedema, ascites and hepatomegaly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course increased pulmonary pressures also causes strain to the right heart and can also cause right heart failure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They then may go on to develop congestive cardiac failure and the exertional dyspnoea that comes with it. The inadequacy of the right heart can lead to excess strain to the left heart through a number of mechanisms that leads to it also failing. Dilation of the right heart can also lead to atrial fibrillation which in turn leads to stroke all being other possible presentations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cyanosis usually doesn't occur at least early in the disease as there isn't a shift from right to left (unoxygenated to oxygenated) but the other way round. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The severity of the pfo will lead to the severity of the clinical manifestation and how early it is picked up. Most people have routine checks of their heart (the murmur is usually pretty loud) so it is frequently corrected before any clinical disease manifests. In patients with small pfos they may never notice unless they become hypertensive or put strain on their heart during pregnancy. Yes they have a slight disadvantage as they lose some oxygenated blood but not anything noticeable. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If anything is unclear or you have more questions, please ask. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-04-11T21:00:53.187" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16483" PostTypeId="1" AcceptedAnswerId="16508" CreationDate="2014-04-11T22:01:09.853" Score="4" ViewCount="125" Body="&lt;p&gt;I am supposed to calculate the relative rate of evolution of two sequences (human and sheep) with a chicken serving as the outgroup. The sequences are pretty long, so I will just create a short example since I just want to learn the process (we are expected to use online resources to figure out our homework problems since it is an online class, but I can't find any examples).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human:   GGATGCGCCT &lt;br&gt;&#xA;Sheep:   GGACGCGCCT &lt;br&gt;&#xA;Chicken: GGACACGCCT &lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone show me how to do this? Here is my guess from the limited info I found, but I have little to no confidence that it is correct:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;p-distance of human/chicken = 2&lt;br&gt;&#xA;p-distance of sheep/chicken = 1&lt;br&gt;&#xA;relative rate of evolution = 2/1 = 2&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this correct? If not, can someone show me how to do it correctly?&lt;/p&gt;&#xA;" OwnerUserId="5596" LastEditorUserId="4108" LastEditDate="2014-04-11T23:54:57.330" LastActivityDate="2014-04-12T19:00:25.287" Title="relative-rate of evolution" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;homework&gt;&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16484" PostTypeId="1" CreationDate="2014-04-12T00:28:00.440" Score="4" ViewCount="986" Body="&lt;p&gt;I think this problem should be asked in a physiology forum rather than biology@ stackex but I'll give it a try.&#xA;So my question is simple - why a mosquito bite is usually confined to a certain shape (shape = red area) and not just disappearing continuously? Can our body cells tolerate some level of antigens without changing color from that?&lt;/p&gt;&#xA;" OwnerUserId="5203" LastEditorUserId="5203" LastEditDate="2014-04-14T23:24:01.840" LastActivityDate="2014-04-14T23:24:01.840" Title="Why mosquito bite is confined to a certain shape?" Tags="&lt;cell-biology&gt;&lt;physiology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16485" PostTypeId="1" AcceptedAnswerId="16502" CreationDate="2014-04-12T04:05:34.023" Score="2" ViewCount="240" Body="&lt;p&gt;According to ITIS the classification &lt;a href=&quot;http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&amp;amp;search_value=180614&quot; rel=&quot;nofollow&quot;&gt;Pinnipedia is  invalid&lt;/a&gt;, and it is proposed to rather use &lt;a href=&quot;http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&amp;amp;search_value=552303&quot; rel=&quot;nofollow&quot;&gt;Caniformia&lt;/a&gt;. The later group however includes a range of terrestrial animals as opposed to the pinnipeds (the seals), which only include marine mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the term Pinnipedia nevertheless still accepted and used in scientific media? Is there any debate whether to use one and not the other?&lt;/p&gt;&#xA;" OwnerUserId="3258" LastEditorUserId="107" LastEditDate="2014-04-12T13:03:02.700" LastActivityDate="2014-04-12T13:03:02.700" Title="Usage of the taxonomic classification &quot;Pinnipedia&quot;" Tags="&lt;taxonomy&gt;&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16486" PostTypeId="2" ParentId="16472" CreationDate="2014-04-12T05:25:10.023" Score="2" Body="&lt;p&gt;I wasn't sure when I first read this, but this is actually a very interesting question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Right now there seem to be two completely divorced lines of inquiry that researchers are pursuing with respect to the antimalarial drugs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One group of researchers is working on working out the mechanism by which say, chloroquine and its ilk bind to and  interfere with the formation of hemazoin (a parasite-friendly form of red blood cell proteins) in the vacuoles of the plasmodium (the parasite that causes malaria). Some folks have recently gotten some pretty reasonable &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0162013408001141&quot; rel=&quot;nofollow&quot;&gt;crystals&lt;/a&gt; of chloroquine interacting directly with hemazoin. This all provides strong evidence for the view that, as regards killing plasmodium, the most significant interaction for an antimalarial is the one between it and hemazoin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In (probably) unrelated news it was discovered that many of these antimalarials are also potent &lt;a href=&quot;http://www.pnas.org/content/98/19/10942.full.pdf&quot; rel=&quot;nofollow&quot;&gt;channel blockers&lt;/a&gt; of various kinds. I haven't dug into this too deeply yet, but most antimalarial people seem to view the channel blocking activity as a side effect. There are a number of other studies underway right now evaluating the psychological effect of the channel blocking activity of the antimalarials. There's &lt;a href=&quot;http://www.jbiomedsci.com/content/20/1/77&quot; rel=&quot;nofollow&quot;&gt;one out of Iran&lt;/a&gt; that says that the blocking activity of Mefloquine can be used to ease the symptoms of morphine withdrawal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another thing to keep in mind is that Mefloquine fell out of favor not due to a decrease in efficacy, but was instead mostly taken out of circulation due to it's (justified) reputation for causing psychotic episodes in patients. So maybe this gap junction blocking stuff could be used to explain Mefloquine psychological side-effects. That would be neat!&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2014-04-15T03:09:33.617" LastActivityDate="2014-04-15T03:09:33.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16487" PostTypeId="2" ParentId="16448" CreationDate="2014-04-12T05:33:17.990" Score="1" Body="&lt;p&gt;To derive it, first use that $E[x(1-x)]= E[x-x^2]=E[x]-E[x^2]$ and that $E[x^2]=\text{Var}[x]+E[x]^2$ to rewrite the left-hand side:&#xA;$$E\left[x_{t+1}(1-x_{t+1})\right] = E\left[x_{t+1}\right](1-E\left[x_{t+1}\right])-\text{Var}\left[x_{t+1}\right].$$&#xA;The equation for $p_{ij}$ is just saying that $2Nx_{t+1}$ is binomially distributed with $2N$ trials with success probability $x_t$, so $E[x_{t+1}]=x_t$ and $\text{Var}[x_{t+1}]=x_t(1-x_t)/(2N)$. (Note that $\text{Var}[\alpha x]=\alpha^2\text{Var}[x]$.) Plugging these values into the equation above gives the form you're looking for.&lt;/p&gt;&#xA;" OwnerUserId="6313" LastEditorUserId="6313" LastEditDate="2014-04-14T06:41:23.147" LastActivityDate="2014-04-14T06:41:23.147" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16489" PostTypeId="2" ParentId="16249" CreationDate="2014-04-12T05:47:49.033" Score="1" Body="&lt;p&gt;Not in general -- there can be linkage disequilibrium among the loci. For instance, say that there are two di-allelic loci, $A/a$ and $B/b$, and that the frequencies of the $A$ and $B$ alleles are both $1/2$ and that they have the same effect on the trait, with no dominance. If all haplotypes in the population are either $Ab$ or $aB$ (with no $AB$ or $ab$ haplotypes), then the genetic variance at each locus is high, but the total genetic variance for the trait is 0!&lt;/p&gt;&#xA;" OwnerUserId="6313" LastActivityDate="2014-04-12T05:47:49.033" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16491" PostTypeId="1" AcceptedAnswerId="16494" CreationDate="2014-04-12T06:54:59.073" Score="2" ViewCount="2011" Body="&lt;p&gt;Assume a patient with previous cardial infaction which SA node not possible to activate action potential anymore.&#xA;However, SA trying to beat unsuccessfully repeatedly waisting energy.&#xA;Therefore, I thought in &lt;a href=&quot;https://biology.stackexchange.com/questions/16490/laser-surgery-to-stop-damaged-sinus-node-from-beating&quot;&gt;this discussion&lt;/a&gt; about the possibility to stop Sinus node from trying to start action potential; which was deleted but the &lt;a href=&quot;http://www.jafib.com/published/webFormat/Fisher/fisher.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;article&lt;/a&gt; about the SSS (sick SA) and remodelling is about its goal. The proposed treatment (laser ablation) of AF/AFL can backfire and cause SN (Sick Node) through remodeling. Assume there is no bypass of impulses through SA node.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Can the heart still beat through AV node and bundle? Yes. &lt;/li&gt;&#xA;&lt;li&gt;Do you have any evidence that [heart] can &quot;beat&quot; properly on just the AVN? Yes, see &lt;a href=&quot;http://www.jafib.com/published/webFormat/Fisher/fisher.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;article&lt;/a&gt;. Short-term mechanisms where electrical/metabolic remodeling. Long-term mechanisms where irregular rhythms and complete heart block can occur because of anatomical remodeling. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I want to know if these pacemakers are in series or parallel.&#xA;If they are in series, then laser operation can be dangerous to the SA node.&#xA;The series connection is however the idea which I get from many schematic drawings:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0XV3r.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2016-07-06T20:36:12.457" Title="Is Sinus node conduction necessary for heart beating?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;electrocardiography&gt;&lt;pathophysiology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16493" PostTypeId="1" AcceptedAnswerId="16498" CreationDate="2014-04-12T07:37:09.047" Score="2" ViewCount="241" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Humic_acid&quot; rel=&quot;nofollow&quot;&gt;Humic acids&lt;/a&gt; are a complex group of organic substances, that are generally known to be hardly biodegradable. Fungi as agroup are known for breaking down complex organic matter like cellulose or lignin. But are there any that beak down humic acids as a major contributor to their energy needs?&lt;/p&gt;&#xA;" OwnerUserId="3037" LastActivityDate="2014-04-12T11:12:54.003" Title="Are there any fungi that can digest humic acids?" Tags="&lt;digestive-system&gt;&lt;mycology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16494" PostTypeId="2" ParentId="16491" CreationDate="2014-04-12T08:34:22.493" Score="3" Body="&lt;p&gt;The SA node is not necessary for contraction of the heart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason that this works is exactly what you mentioned: schematics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are in sequence, but within that sequence, there are multiple &lt;strong&gt;autonomous&lt;/strong&gt; signal generators in the heart, where spontaneous depolarization occurs to initiate contraction: the &lt;strong&gt;SA&lt;/strong&gt; node, the &lt;strong&gt;AV&lt;/strong&gt; node, and the &lt;strong&gt;purkinje&lt;/strong&gt; fibers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;SA&lt;/strong&gt; node fires the most rapidly, 60-90 times per minute - which is the average normal heartrate, because in most people the signal for contraction arises from the SA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;AV&lt;/strong&gt; node fires at 46-60 times per minute.  If it receives the signal from the SA node then it depolarizes in sequence like the normal sequence we learn.  But if there is no SA node signal received, the AV node will depolarize on its own.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The last &quot;generator&quot; are the &lt;strong&gt;perkinje&lt;/strong&gt; fibers.  If there is no signal from previous nodes, they will spontaneously depolarize.  However, they depolarize VERY slowly, at a rate usually under 40 bpm.  This severe bradycardia is potentially life-threatening, but allows the heart to keep some circulation going if there is a sudden complete AV node block - but prompt treatment is critical.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the lack of necessity of the SA node: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, in some cases of supraventricular tachycardia (for example IST, see &lt;a href=&quot;http://en.wikipedia.org/wiki/Inappropriate_sinus_tachycardia&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) that are not responsive to conservative treatment, they will actually &lt;strong&gt;ablate&lt;/strong&gt; (surgically destroy) the SA node in order to slow the heartrate down because a persistently extremely high heart rate can be dangerous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good question!&lt;/p&gt;&#xA;" OwnerUserId="6314" LastActivityDate="2014-04-12T08:34:22.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16495" PostTypeId="2" ParentId="16454" CreationDate="2014-04-12T08:44:34.427" Score="4" Body="&lt;p&gt;nuhcole is mostly correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Airborne particles first pass through the nasal passageways and/or mouth and throat and many are caught, but those that enter the lungs become trapped in mucus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your cilia act like a constant escalator, bringing up that mucus from your lungs 24/7.  You reflexively swallow it without even realizing it.  That is why when you are healthy, you might not even notice.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are sick (or asthma/allergies), more mucus is produced.  That is when you may notice the increased quantity coming up, and may need to cough to bring more up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your cilia are damaged (like in smokers), then mucus does not clear well from the lungs. In this case, people must cough more in order to bring it up.&lt;/p&gt;&#xA;" OwnerUserId="6314" LastActivityDate="2014-04-12T08:44:34.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16496" PostTypeId="1" CreationDate="2014-04-12T08:47:39.590" Score="2" ViewCount="906" Body="&lt;p&gt;SI ran my 2% agarose gel on constant voltage (100 V). For a few times it worked at CV but, after a week or so the machine would automatically switch to constant current by itself. And this only happens when I try to increase the voltage to 100 V. It works fine between 50-80 V. Beyond 80 V it keeps fluctuating between CV and CC.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a problem in my power supply (GENEI electrophoresis power supply) or is the TE buffer that I am using? Although I checked its pH and it's fine.&lt;/p&gt;&#xA;" OwnerUserId="6315" LastEditorUserId="107" LastEditDate="2014-04-12T13:04:18.123" LastActivityDate="2014-04-12T13:04:18.123" Title="Troubleshooting for Agarose Gel Electrophoresis" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16497" PostTypeId="2" ParentId="16496" CreationDate="2014-04-12T10:16:04.677" Score="2" Body="&lt;p&gt;I haven't found a manual for this machine, but my guess is that you exceed the maximum current which the power supply can provide. This is something I have experienced myself for electrophoresis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually power supplies then switch into the constant current mode at the maximum current they can deliver, which I think is what happens here. If the voltage you choose is lower, you do not run into this limitation, thats why it is working without problems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you can either run your gels at constant current, which makes them run faster but also produces more heat, which can make your gel blurry. Or you live with a slightly smaller constant voltage, have your gels run a bit slower, but probably have a bit better resolution. I have to say that I have never had any problems with the resolution, even when I ran my gels really fast.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-12T10:16:04.677" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16498" PostTypeId="2" ParentId="16493" CreationDate="2014-04-12T11:12:54.003" Score="2" Body="&lt;p&gt;According to Wikipedia, &lt;a href=&quot;http://en.wikipedia.org/wiki/Humic_acid&quot; rel=&quot;nofollow noreferrer&quot;&gt;humic acid (HA)&lt;/a&gt; is a product of the biodegradation of dead organic matter. Shown below is a representative structure, but it important to understand that humic acid is a name given to a family of loosely related polymers of the products of biodegradation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although HA is resistant to further biodegradation, there are indeed fungi that are able to break it down further.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nAeaQ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is evidence that fungi can break down HA:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Grinhut et al (2011) Mechanisms of Humic Acids Degradation by White Rot Fungi Explored Using 1H NMR Spectroscopy and FTICR Mass Spectrometry Env Sci &amp;amp; Technol 45, 2784-2754&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This paper reports studies of the mechanism of HA degradation by Trametes and Phanerochaete fungi (Basidiomycetes). This degradative property is attributed to the secretion of non-specific oxidising enzymes: manganese peroxidase, lignin peroxidase and laccase. the authors report evidence for &quot;oxidation, a decrease in the aromatic content, and indication of demethylation of the HA during biodegradation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper is also a source of references to earlier work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The indications are however that these fungi carry out this degradation in the presence of other nutrients, i.e they cannot utilise HA as a major carbon/energy source.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-04-12T11:12:54.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16499" PostTypeId="2" ParentId="16491" CreationDate="2014-04-12T11:33:53.003" Score="1" Body="&lt;p&gt;&lt;strong&gt;Extension to Doctor Whom's clear answer.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clearer problem&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is debated whether the pathophysiology of IST and POTS results from&#xA;  abnormal autonomic regulation or abnormal sinus node function.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;h2&gt;&lt;a href=&quot;http://circ.ahajournals.org/content/92/10/2919.long&quot; rel=&quot;nofollow&quot;&gt;Radiofrequency Catheter Modification of the Sinus Node for “Inappropriate” Sinus Tachycardia&lt;/a&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Location modification: Superior aspect of the crista terminalis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Benefits&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;presyncope can resolve with sotalol&lt;/li&gt;&#xA;&lt;li&gt;palpitation can resolve with β-adrenergic blockers&lt;/li&gt;&#xA;&lt;li&gt;some patients (about 1/3) did not require any medication after operation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and other highlights&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;superior vena cava syndrome and dual-chamber pacemaker with patient with earlier A-V ablation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;&lt;a href=&quot;http://jaha.ahajournals.org/content/3/2/e000700.full&quot; rel=&quot;nofollow&quot;&gt;Postural Tachycardia Syndrome and Inappropriate Sinus Tachycardia: Role of Autonomic Modulation and Sinus Node Automaticity&lt;/a&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Ceteris paribus condition&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;have IHR condition (Intravenous propranolol and atropine were given to block the sympathetic and parasympathetic limbs)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Findings&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Treatment of IST and POTS should focus on sympatholysis, reserving sinus node modification for patients with continued debilitating symptoms after beta‐blockade and possibly ivabradine.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It is open research topic how the SA node should be ablated (removed) and how much.&#xA;I did not find any meta-analysis about the issue.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-04-12T12:23:23.247" LastActivityDate="2014-04-12T12:23:23.247" CommentCount="0" CommunityOwnedDate="2014-04-12T11:33:53.003" ContentLicense="CC BY-SA 3.0" />
  <row Id="16500" PostTypeId="1" AcceptedAnswerId="44653" CreationDate="2014-04-12T11:37:20.363" Score="3" ViewCount="1385" Body="&lt;p&gt;When reading &lt;a href=&quot;https://en.wikipedia.org/wiki/Pistachio&quot; rel=&quot;nofollow&quot;&gt;the Wikipedia entry on pistachio&lt;/a&gt;, I noticed that IUCN has classified the plant under &quot;Near Threatened&quot;. On looking up &lt;a href=&quot;http://www.iucnredlist.org/details/summary/63497/0&quot; rel=&quot;nofollow&quot;&gt;its entry at IUCN&lt;/a&gt;, I see that its population is trending downwards, and it is &quot;threatened by fruit collection, livestock grazing and cutting&quot;. The treat seems to have nothing to do with the &lt;a href=&quot;http://www.prnewswire.com/news-releases/california-pistachio-industry-threatened-by-potentially-devastating-disease-58854062.html&quot; rel=&quot;nofollow&quot;&gt;often reported fungus&lt;/a&gt;. Looking up the yearly yields at &lt;a href=&quot;http://www.acpistachios.org/statistics.htm&quot; rel=&quot;nofollow&quot;&gt;Administrative Committee for Pistachios&lt;/a&gt;, I see that 2010 and 2012 were bumper years, but otherwise, I see no real trend of a decrease. Quite the contrary, I get the impression that the yearly yield is increasing. It's not as if the tree is difficult to grow, and we rely on trees growing in the wild; these trees are grown in orchards. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what's going on? Why would IUCN say that pistachio is Near Threatened? &lt;/p&gt;&#xA;" OwnerUserId="3479" LastActivityDate="2016-03-27T22:36:55.850" Title="Why does IUCN classify pistachio as a &quot;Near Threatened&quot; species?" Tags="&lt;conservation-biology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16502" PostTypeId="2" ParentId="16485" CreationDate="2014-04-12T12:57:43.913" Score="3" Body="&lt;p&gt;The Comments section of that page has the explanation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Wilson &amp;amp; Reeder (eds., 1993) note that &quot;the pinnipeds (otariids,&#xA;  odobenids, and phocids) are included within the suborder Caniformia;&#xA;  placing them in a separate Order would make the Carnivora&#xA;  paraphyletic.&quot; This arrangement continues to be followed in Wilson &amp;amp;&#xA;  Reeder (eds., 2005)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If both Carnivora (Bowdich, 1821) and Pinnipedia (Illiger, 1811) are orders in the traditional Linnean taxonomic sense, then one cannot be nested within the other. If this were to happen, then Carnivora would be paraphyletic because it would exclude some of its members. The same argument is made when discussion &lt;a href=&quot;http://www.ucmp.berkeley.edu/diapsids/avians.html&quot; rel=&quot;nofollow&quot;&gt;birds as dinosaurs&lt;/a&gt; (you can't talk about Dinosauria that doesn't include Aves).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem arises when phylogenetic systematics (clade names) meets traditional Linnean systematics (orders, suborders, etc.). &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01&quot; rel=&quot;nofollow&quot;&gt;Phylogenetic systematics&lt;/a&gt; does not distinguish these higher taxonomic groups. Clades are just nested groups of monophyletic taxa.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So then to answer your last question, Pinnipedia does appear to be in common usage (&lt;a href=&quot;http://scholar.google.com/scholar?as_ylo=2013&amp;amp;q=Pinnipedia&amp;amp;hl=en&amp;amp;as_sdt=0,26&quot; rel=&quot;nofollow&quot;&gt;Google Scholar reports several hundred citations&lt;/a&gt; in the past few years). The key is to distinguish Pinnipedia as a traditional Linnean order (not valid) and Pinnipedia as a monophyletic clade that includes seals, walrus, and sea lions (perfectly fine). Seals, walrus, and sea lions are all more closely related to each other than to other Carnivora, so they are monophyletic, and the name for that grouping is Pinnipedia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the &lt;a href=&quot;http://tolweb.org/Carnivora/15971&quot; rel=&quot;nofollow&quot;&gt;Tree of Life page&lt;/a&gt; that has all the clade names.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2014-04-12T12:57:43.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16503" PostTypeId="1" AcceptedAnswerId="16504" CreationDate="2014-04-12T13:24:43.363" Score="5" ViewCount="1172" Body="&lt;p&gt;I have a basic question about evolution, for which I never found an answer. I understand how evolution works if we focus on one specific organ or trait. With each generation, some organism is more likely to reproduce, so the trait that leads to success gets more frequent. My problem is understanding how all the traits can evolve simultaneously. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking back to our ancestors, we evolved many different kinds of adaptations (in unrelated areas like eyesight, kidney efficiency or a healthy fear of predators, digestion of certain nutrients, balanced walking etc.).&#xA;Natural selection can only work with what's there, so mutations are important. But if  mutations are rare, it seems unlikely that many (thousands of) properties of organisms get improved in a single generation. You'd need to get very lucky to randomly improve all the genes responsible for it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if we look back to our ancestors again, did they just improve on a single or a handful of traits in each generation? In that case we would need hundreds of generations before we have improved somewhat on each &quot;front&quot;. By then, the other properties could &quot;drift&quot; back to a not-so-advantageous version. (This was supposing that each generation improves on a random trait, as opposed to long sequences of generations each improving on the same).&#xA;Or were there always some super lucky organisms that randomly got an improvement on almost all different traits? But just having some of those super lucky ones is not enough. The good traits don't guarantee success, just improve the odds. So we'd need many very lucky ones in each generation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has anyone calculated or simulated how the adaptation for many different traits can happen &lt;em&gt;simultaneously&lt;/em&gt;?&lt;/p&gt;&#xA;" OwnerUserId="6316" LastActivityDate="2014-04-14T06:53:17.573" Title="Evolution: How could all useful traits evolve simultaneously?" Tags="&lt;evolution&gt;&lt;adaptation&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16504" PostTypeId="2" ParentId="16503" CreationDate="2014-04-12T14:04:03.230" Score="7" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Has anyone calculated or simulated how the adaptation for many different traits can happen simultaneously?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are a lots of studies on the subject but I don't fully understand what is your issue. So I'll try to give some words hoping that helps a bit but it is possible that I'll totally miss the point you want to make.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mutation rate in humans is around $1.25 \cdot 10^{-8}$ per base pair per individual per generation. The human genome contains about 3400 Mpb, meaning that you probably carry $1.25 \cdot 10^{-8} * 3.4*10^9 = 42.5$ mutations that none of your parents had in their genome. Now if you consider the population size, you'll see that a fairly big amount of mutations occurs each generation in the human population. So mutations are not that rare! It might unfair to take human as an example though as human's population size is very big. Anyway, the great majority of mutations are deleterious. In consequence, you are right, probably not many beneficial mutations will occur in a given population at one given generation and especially not in the same individual (except if you think of viruses!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, depending on how beneficial is the mutation you are considering (selection coefficient), depending on its dominance, depending on the (effective) population size, your new mutations might take quite a bit of generations before reaching fixation in the population. In this time other mutations might occur. And then, the question is very interesting. Imagine a population of asexual individuals where two beneficial mutations exist (at two different loci [=position on a chromosome]). Because there is no recombination (by definition of what is an asexual population) never these two mutations will be found in the same individuals and in consequence if one mutation reaches fixation, it necessarily mean that the other mutation would have disappear. In sexual population it is different. Recombination allow that the two mutations, once they reaches a sufficient frequency will probably be found in the same organism and therefore, the two mutations can reach fixation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helped a bit&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-04-12T16:55:58.857" LastActivityDate="2014-04-12T16:55:58.857" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16505" PostTypeId="1" CreationDate="2014-04-12T14:49:50.150" Score="3" ViewCount="18019" Body="&lt;p&gt;We all know why there are 3-base codons, and why there aren't any 2-base codons. But why is there not a 4-base a 5-base codon? &lt;/p&gt;&#xA;" OwnerUserId="6318" LastEditorUserId="1306" LastEditDate="2014-04-12T17:13:34.997" LastActivityDate="2014-04-12T18:30:41.997" Title="Why do three nucleotides code for one amino acid? Why not 5 nucleotides?" Tags="&lt;dna&gt;&lt;proteins&gt;&lt;amino-acids&gt;&lt;genetic-code&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ClosedDate="2014-04-14T08:38:19.643" ContentLicense="CC BY-SA 3.0" />
  <row Id="16506" PostTypeId="2" ParentId="16505" CreationDate="2014-04-12T15:04:08.207" Score="5" Body="&lt;p&gt;The more bases there are per codon the more information you can code for. There are only 22 different amino acids, in consequence we need minimum 3 bases per codon.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1 base-codon --&gt; 4^1 = 4 possible codes which are:&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A / T / C / G &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;2 base-codon --&gt; 4^2 = 16 possible codes which are:&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;AA / AT / AC / AG / TT / TA / TC / TG / CC / CA / CG / CT / GG / GC / GT / GA&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;3 base-codon --&gt; 4^3 = 64 possible codes which are:&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;AAA / AAT / AAC / AAG / ACA / ACT / ACG / ACC / AGA / AGT / etc...&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;4 base-codon --&gt; 4^4 = 256 possible codes which are:&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;AAAA / AAAT / AAAC / AAAG / AATA / AATC / AATG / etc..&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;5 base codon --&gt; 4^5 = 1024 possible codes&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If we had only 2 bases per codon we couldn't code for all of the possible different amino-acids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand there are several costs associated with carrying lots of DNA. It takes space, it takes energy and matter to get copied, it takes time to copy it (generation time might be limited by copying time), … I have just asked &lt;a href=&quot;https://biology.stackexchange.com/questions/16509/what-are-the-costs-associated-with-carrying-lots-of-genetic-material&quot;&gt;this question&lt;/a&gt; hoping to make things clear about the possible costs. If there is a cost associated with having a 4-base codon system compare to a 3-base codon system but there is no associated benefit. Such trait (that has a cost with no benefit) are not expected to evolve (counter-selected).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You'll notice that there are 64-22=42 extra possibilities. In consequence the genetic code is redundant. Meaning that several codon codes for the exact same amino-acid. And interestingly, it is often a the last of the three bases of the codon the does no yield to any change in the coding sequence as you can see here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iBV9Q.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/10009/how-does-the-genetic-code-evolve&quot;&gt;This post&lt;/a&gt; about the evolution of genetic code might interest you.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-04-12T18:30:41.997" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="16507" PostTypeId="2" ParentId="16503" CreationDate="2014-04-12T16:25:27.753" Score="2" Body="&lt;p&gt;I think the main issue you have is in this paragraph:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But if mutations are rare, it seems unlikely that many (thousands of) properties of organisms get improved in a single generation. You'd need to get very lucky to randomly improve all the genes responsible for it.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are two basic misconceptions there:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Mutations are &lt;em&gt;not&lt;/em&gt; rare. They're actually very common. One of the cells in your body probably just developed one while you were reading this answer. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It is indeed unlikely that thousands of properties get &quot;improved&quot; in a single generation. That is not how evolution works. You need to remember that &lt;em&gt;species&lt;/em&gt; evolve, not individuals. So, say I have been selected for because I run faster and my mate has been selected for because she's smarter, our child might incorporate both characteristics. Now extrapolate that to all individuals of a species and add a few million years and you get both intelligence and speed selected for.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Finally, luck has very little to do with it. We're talking about a very slow process that works over millions of years. Evolution does not occur over single generations, the mutations driving it might but not the evolutionary process by which these mutations become incorporated into the genome of the population at large.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-04-12T16:25:27.753" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16508" PostTypeId="2" ParentId="16483" CreationDate="2014-04-12T17:34:07.450" Score="2" Body="&lt;p&gt;This kind of thing is normally calculated using the &lt;a href=&quot;https://en.wikipedia.org/wiki/Ka/Ks_ratio&quot; rel=&quot;nofollow&quot;&gt;$K_{a}/K_{s}$ ratio&lt;/a&gt;, the ratio of synonymous to non-synonymous substitutions. It is not enough to count mutations for coding sequences, you should also take into account whether or not that mutation will actually change the resulting product.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are various online tools that can help you do this, for example Phylemon:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://phylemon.bioinfo.cipf.es/evolutionary.html&quot; rel=&quot;nofollow&quot;&gt;http://phylemon.bioinfo.cipf.es/evolutionary.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-04-12T19:00:25.287" LastActivityDate="2014-04-12T19:00:25.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16509" PostTypeId="1" AcceptedAnswerId="16765" CreationDate="2014-04-12T18:29:03.803" Score="11" ViewCount="253" Body="&lt;p&gt;What are the costs (if any) associated with carrying lots of genetic material (Big genome size)? &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;energy for copying?&lt;/li&gt;&#xA;&lt;li&gt;raw material for copying?&lt;/li&gt;&#xA;&lt;li&gt;space in the cell?&lt;/li&gt;&#xA;&lt;li&gt;Maintenance cost (matter and energy)?&lt;/li&gt;&#xA;&lt;li&gt;time to copy is a limiting factor for the minimum generation time?&lt;/li&gt;&#xA;&lt;li&gt;Less &lt;a href=&quot;http://en.wikipedia.org/wiki/Robustness_%28evolution%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;robustness&lt;/a&gt;?&lt;/li&gt;&#xA;&lt;li&gt;More likely to evolve a gene that spreads well but has a negative fitness impact on the rest of the genome (selfish gene or outlaw)?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The answer probably depends on the organism. I am interested about any information concerning uni- or multi-cellular eukaryotes, bacteria or viruses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do we have any knowledge about how important are these costs or is it pure guesses?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;This post comes in reaction to @AlanBoyd comments on &lt;a href=&quot;https://biology.stackexchange.com/questions/16505/why-do-three-nucleotides-code-for-one-amino-acid-why-not-5-nucleotides/16506?noredirect=1#comment22278_16506&quot;&gt;this post&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-11-06T16:19:13.390" Title="What are the costs associated with carrying lots of genetic material" Tags="&lt;evolution&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;cytogenetics&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16510" PostTypeId="1" AcceptedAnswerId="16593" CreationDate="2014-04-12T18:43:16.593" Score="7" ViewCount="461" Body="&lt;p&gt;I am right-handed. Which means that when I hammer down a nail, I hold the nail in my left hand, with which I can hold it straight and at a controlled position.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is true in situations where the task of holding something in place is  simultaneous with a more complex task, such has hammering, done with the right hand. But I note that even when there is no other task, I personally use my left hand to hold in place, e.g., a  bottle that I am filling up in a stream of water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To generalize a little, it seems to me that while I use my right hand for precise motion or applying a force, I'll use my left hand to maintain a position against forces.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this behaviour something documented? Does one develop specific brain control to implement this controlled-position tasks?&lt;/p&gt;&#xA;" OwnerUserId="6224" LastEditorUserId="6224" LastEditDate="2014-04-15T07:21:30.637" LastActivityDate="2014-04-16T09:13:59.273" Title="Task-dependent &quot;reversed&quot; handedness: why use left hand for some tasks? How is it controlled by the brain?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;physiology&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16511" PostTypeId="2" ParentId="10009" CreationDate="2014-04-12T20:36:44.307" Score="3" Body="&lt;p&gt;Some elements of response to your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, something about tRNA frequency. Even if there are six codons for a given amino acid, they are not equivalent because some will correspond to abundant tRNA, while others correspond to very minor tRNA. This has significant influence on the traduction speed, as the traduction will dramatically slow down on minor tRNA (while the ribosome waits for the proper tRNA). This may have very important impact on the folding of proteins (see for instance this paper: &lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0002189&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1371/journal.pone.0002189&lt;/a&gt;). Having several codons for common amino-acids may actually be a powerful fine-tuning too for the folding of proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, as in some cases (splicing, selenocysteine insertion, what else ?), the secondary structure of the mRNA produced is extremely important, the organisms must be able to tweak the sequence of RNA to leave room for that to happen, and that can only happen if there are lots of amino acids for which there is latitude to tweak the produced mRNA sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Third, it is false that the genetic code is universal. There are some evolutions of the genetic code, see for instance the specific case of methionine in mitochondria: &lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0802779105&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1073/pnas.0802779105&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6319" LastActivityDate="2014-04-12T20:36:44.307" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16512" PostTypeId="1" CreationDate="2014-04-12T23:20:47.180" Score="7" ViewCount="499" Body="&lt;p&gt;I keep hearing over an over how humans can satisfy their entire daily caloric need in one sitting at a fast food restaurant. At the same time I'm looking at the kitchen plates, cups, etc, and they also seem to be getting bigger. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This makes me ask the question - &lt;strong&gt;was breakfast-lunch-dinner a concept invented because people:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Could not make enough food?&lt;/li&gt;&#xA;&lt;li&gt;Could not make food fast enough?&lt;/li&gt;&#xA;&lt;li&gt;Could not make food with high enough caloric intake?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I'm thinking along the lines of: you can make only so much tasteless porridge and stuff it in your mouth before it gets cold. At the same time I know that gorillas and some other primates have a very long (8 hours?) feeding session of eating raw vegetation throughout the day.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there a biological explanation why human food intake should be spread into X distinct sittings?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="5144" LastEditDate="2014-04-13T10:17:47.707" LastActivityDate="2014-06-28T12:18:47.973" Title="Is there a biological reason for spreading food intake into breakfast-lunch-dinner?" Tags="&lt;human-biology&gt;&lt;food&gt;&lt;digestive-system&gt;&lt;nutrition&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16513" PostTypeId="1" AcceptedAnswerId="16514" CreationDate="2014-04-13T06:07:14.973" Score="1" ViewCount="45" Body="&lt;p&gt;At frequency 0-3 Hz.&#xA;Like computer processors which can work at low frequencies and controlling under- and overvoltage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Normal most significant channels are Ca2+ and K+ that are changing.&#xA;However, I am not convinced that they can work with such a low frequencies.&#xA;There must be some other channels that are triggering the extrasystole on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which ionic channels of Pacemakers can work in 2-3 Hz triggering extrasystole?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-13T06:14:43.030" Title="Which ionic channels of Pacemakers can work in very low frequencies in extrasystole?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;electrocardiography&gt;&lt;pathophysiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16514" PostTypeId="2" ParentId="16513" CreationDate="2014-04-13T06:14:43.030" Score="0" Body="&lt;p&gt;I think none.&#xA;It is so specific frequency range that the possible sources are&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;autonomic nervous system and&lt;/li&gt;&#xA;&lt;li&gt;some reflex arch.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Also, the frequency is logically low with autonomic triggering.&#xA;My conjecture is that sympaticus starts up extrasystoles.&#xA;I think it must go through some reflex arch to be so specific.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-13T06:14:43.030" CommentCount="0" CommunityOwnedDate="2014-04-13T06:14:43.030" ContentLicense="CC BY-SA 3.0" />
  <row Id="16515" PostTypeId="1" CreationDate="2014-04-13T06:27:36.120" Score="1" ViewCount="83" Body="&lt;p&gt;I am researching what is triggering the extrasystoles - initial idea from &lt;a href=&quot;https://biology.stackexchange.com/questions/16513/which-ionic-channels-of-pacemakers-can-work-in-very-low-frequencies-in-extrasyst&quot;&gt;this thread&lt;/a&gt; about &lt;em&gt;Which ionic channels of Pacemakers can work in very low frequencies in extrasystole?&lt;/em&gt;&#xA;I am interested in the reflex arc with extrasystoles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not completely sure if the intrinsic regulation of the heart can start specific stimuli.&#xA;I have now intuition that not possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the reflex arcs of the heart?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-04-13T06:32:26.977" Title="Which reflex arcs work in Heart with extrasystoles?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;reflexes&gt;&lt;electrocardiography&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16517" PostTypeId="1" AcceptedAnswerId="16529" CreationDate="2014-04-13T09:01:08.943" Score="5" ViewCount="727" Body="&lt;p&gt;I just got struck by curiosity now: Intuition says no, but I've never had confirmation of it. &lt;/p&gt;&#xA;" OwnerUserId="783" LastEditorUserId="3952" LastEditDate="2014-04-16T19:24:58.767" LastActivityDate="2014-04-18T17:57:10.767" Title="Is it possible to have life in vacuum?" Tags="&lt;physiology&gt;&lt;speculative&gt;&lt;extremophiles&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16519" PostTypeId="2" ParentId="16517" CreationDate="2014-04-13T10:19:35.357" Score="6" Body="&lt;p&gt;No, it is not. Or at least not in the form we know life. The reason is that water (which is essential for life) boils at low pressures at room temperature. This makes life impossible in the form we live it on earth.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-13T10:19:35.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16520" PostTypeId="1" CreationDate="2014-04-13T10:43:13.087" Score="1" ViewCount="238" Body="&lt;p&gt;I started this thread by thinking this question but I developed it further below&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What is the mechanism maintaining refractory period of pacemakers?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My conjecture is that the mechanism is the simultaneous depolarisation of at least SA node and AV node. &#xA;I am not convinced yet about the Purkinje fibers' participation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bigger question from this is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How do pacemakers work under threshold without action potential?&lt;/strong&gt;&#xA;There are continually leaking Funny channels (Na+) in pacemakers.&#xA;There has to be chemical changes &lt;strong&gt;intrinsic&lt;/strong&gt; changes&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;change in the permeability of Funny channels or&lt;/li&gt;&#xA;&lt;li&gt;active pumping of Na+ out OR pumping something negative inside the cell (probably Cl-, not sure) and&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;extrinsic changes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;reflex arch blocking the action potential of pacemakers when enough preceeding sensitisation of AV node&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I have no evidence for that this kind of sensitisation would happen in SA node or in Purkinje fibers.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which all seem to be working together in firing recovery mechanism through AV node without specific SA node stimulation.&#xA;Example logic tree for a myocardial infarction patient of 68 years old:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;R wave of atrial fibrillation and flutter&lt;/li&gt;&#xA;&lt;li&gt;extrinsic stimulus to start sensitisation of AV node&lt;/li&gt;&#xA;&lt;li&gt;intrinsic sensitisation of AV node&lt;/li&gt;&#xA;&lt;li&gt;extrinsic stimulus through reflex arch&lt;/li&gt;&#xA;&lt;li&gt;systole and upper-systole of AV node starting&lt;/li&gt;&#xA;&lt;li&gt;lower-systole of AV node&#xA;&lt;ul&gt;&#xA;&lt;li&gt;intersection of upper- and lower-systoles&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;unstable end of lower-systole&lt;/li&gt;&#xA;&lt;li&gt;unstable systole&lt;/li&gt;&#xA;&lt;li&gt;extrinsic firing simultaneous SA and AV node (similar extrinsic regulation as in the beginning of this logic tree)&lt;/li&gt;&#xA;&lt;li&gt;prolonged and stable refractory period and long compensatory pause&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is debated whether the pathophysiology of IST and POTS results from abnormal autonomic regulation or abnormal sinus node function.  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My conjectures based on my logic tree&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Pathophysiology of IST results from normal extrinsic (recovery) mechanism of autonomic regulation which body uses to recover from abnormal stimuli (etc atrial fibrillation and flutter)&lt;/li&gt;&#xA;&lt;li&gt;Pathophysiology of POTS results from abnormal extrinsic mechanism of autonomic regulation when there is no stimuli after abnormal stimuli&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is causing the abnormal autonomic mechanism in POTS?&lt;/strong&gt;&#xA;I would say that IST precedes POTS.&#xA;Prolonged IST seems to be going to POTS.&#xA;Physical explanation is that the body cannot last regular IST so it goes to POTS, since losing its normal extrinsic regulation.&#xA;&lt;strong&gt;What is this (apparently cumulative, not necessarily long-term) trigger of disabling the extrinsic autonomic regulation of the heart?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-26T09:23:17.687" LastActivityDate="2014-12-26T09:23:17.687" Title="What are the mechanisms of disabling extrinsic control of heart?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;electrocardiography&gt;&lt;pathophysiology&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16521" PostTypeId="1" AcceptedAnswerId="16522" CreationDate="2014-04-13T13:39:18.000" Score="3" ViewCount="1172" Body="&lt;p&gt;Dont tell me the &quot;function&quot; of IgE is to cause allergy ! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In whatever texts I have seen it is  written that IgE is important to cause allergies but what is the beneficial function of IgE ? Why was it ever created ? Did it have an advantage in the pre historic ages but now causes allergies ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-13T15:20:19.183" Title="What is the beneficial function of IgE antibody?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;immunology&gt;&lt;antibody&gt;&lt;allergies&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16522" PostTypeId="2" ParentId="16521" CreationDate="2014-04-13T14:37:30.057" Score="7" Body="&lt;p&gt;No, they are of course not there to cause allergies.&#xA;It is thought (although not directly proven in human) that IgE is important to fight parasites and worms. They bind to antigens from the parasites, which leads to the secretion of histamines. This causes a local immune reaction (which also is a problem in allergies) which is helpful to fight the parasites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FDNR1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See these papers for example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8872184&quot; rel=&quot;nofollow noreferrer&quot;&gt;IgE, allergies and helminth parasites: a new perspective on an old&#xA;conundrum.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jimmunol.org/content/172/2/1139.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;IgE Enhances Parasite Clearance and Regulates Mast Cell Responses in&#xA;Mice Infected with Trichinella spiralis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://iai.asm.org/content/70/2/427.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Immunology of Parasitic Helminth Infections&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There is also some evidence, that IgE is involved in the immunological response to cancers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12672069&quot; rel=&quot;nofollow noreferrer&quot;&gt;Activity of human monocytes in IgE antibody-dependent surveillance&#xA;and killing of ovarian tumor cells.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22193986&quot; rel=&quot;nofollow noreferrer&quot;&gt;Animal models for IgE-meditated cancer immunotherapy&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1306" LastEditDate="2014-04-13T15:20:19.183" LastActivityDate="2014-04-13T15:20:19.183" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16523" PostTypeId="1" AcceptedAnswerId="16524" CreationDate="2014-04-13T16:47:13.310" Score="8" ViewCount="1585" Body="&lt;p&gt;I know that often oxidation processes are mentioned when referring to the color change from yellow to brown in bananas (specifically: those that you get everywhere in supermarkets, with no seeds).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I am really interested if there is a specific oxidative pathway that is generally followed in this process, and whether it has been examined.&lt;/p&gt;&#xA;" OwnerUserId="5578" LastActivityDate="2014-04-13T18:19:48.763" Title="What exactly makes bananas go brown?" Tags="&lt;biochemistry&gt;&lt;food&gt;&lt;fruit&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16524" PostTypeId="2" ParentId="16523" CreationDate="2014-04-13T17:04:37.377" Score="9" Body="&lt;p&gt;The reason for this is the oxidation of phenol residues in the banana (for example in the yellow color) which get oxidized by the enzyme Polyphenol oxidase (PPO) to melanins. The scheme (the image is from this &lt;a href=&quot;http://www.food-info.net/uk/colour/enzymaticbrowning.htm&quot; rel=&quot;noreferrer&quot;&gt;website&lt;/a&gt; on food browning) looks like this (you can of course also use more complicated substrates):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Jdfk6.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For further information, see these references:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC549964/&quot; rel=&quot;noreferrer&quot;&gt;Banana Polyphenoloxidase. Preparation and Properties.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/s004250100553&quot; rel=&quot;noreferrer&quot;&gt;Molecular cloning and characterisation of banana fruit polyphenol&#xA;oxidase&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Polyphenol oxidases are widely found in fruits and cause most of the oxidative browning. See these articles:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16973188&quot; rel=&quot;noreferrer&quot;&gt;Polyphenol oxidases in plants and fungi: going places? A review.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://hortsci.ashspublications.org/content/45/8/1150.full&quot; rel=&quot;noreferrer&quot;&gt;Enzymatic Browning, Polyphenol Oxidase Activity, and Polyphenols in&#xA;Four Apple Cultivars: Dynamics during Fruit Development&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-04-13T18:19:48.763" LastActivityDate="2014-04-13T18:19:48.763" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16525" PostTypeId="1" CreationDate="2014-04-13T17:45:46.710" Score="3" ViewCount="11805" Body="&lt;ol&gt;&#xA;&lt;li&gt;It could be the tidal volume because it affects how a person inhales and exhales normally.&lt;/li&gt;&#xA;&lt;li&gt;It could be the residual volume and functional residual volume, because it increases its amount. Because it traps air. &lt;/li&gt;&#xA;&lt;li&gt;On the other hand it also affects the Forced vital capacity because it decreases the amount of air that can be forcibly exhaled immediately after one inhalation.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5616" LastEditorUserId="231" LastEditDate="2018-02-24T21:24:40.220" LastActivityDate="2018-10-09T18:49:47.003" Title="For emphysema, which of the respiratory volumes is affected?" Tags="&lt;human-biology&gt;&lt;breathing&gt;&lt;lungs&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16526" PostTypeId="2" ParentId="14986" CreationDate="2014-04-13T18:25:04.083" Score="4" Body="&lt;p&gt;In the &amp;beta;-lactamase test, an inhibitor of &amp;beta;-lactamase is added to a sample of the culture medium. The inhibitor binds to the enzyme and changes its color, which is in direct correlation to the concentration of the &amp;beta;-lactamase. More &amp;beta;-lactamase means more inhibitor binding and this results in more color development leading to a higher absorption. So higher absorption means more &amp;beta;-lactamase in the supernatant.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2014-09-17T21:06:10.290" LastActivityDate="2014-09-17T21:06:10.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16528" PostTypeId="1" AcceptedAnswerId="16535" CreationDate="2014-04-13T20:26:57.870" Score="2" ViewCount="6116" Body="&lt;p&gt;Something I have wondered for a while is why have two different primary defense mediums, ie earwax and mucus, that perform the same function?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I know, mucus and earwax are both part of the primary defense of an organism against disease and foreign particles, by trapping any pathogens or dust that enters the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is; Why does the body use earwax for ears and mucus for the lining of other entrances to the body, why not have mucus in the ears or earwax everywhere else? is there an advantage to have each medium in their respective places?&lt;/p&gt;&#xA;" OwnerUserId="6330" LastActivityDate="2014-04-14T07:15:57.477" Title="Earwax versus Mucus" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16529" PostTypeId="2" ParentId="16517" CreationDate="2014-04-14T01:27:49.983" Score="8" Body="&lt;p&gt;As @terdon comments, dormant organisms can survive in vacuum. This includes lichens, bacteria, and even an animal: the ever-amazing and adorable tardigrade (&lt;a href=&quot;http://dx.doi.org/10.1016/j.cub.2008.06.048&quot; rel=&quot;noreferrer&quot;&gt;Jönnson et al 2008&lt;/a&gt;). In 2006, tardigrades survived exposure to the vacuum of outer space with &lt;strong&gt;no appreciable difference in mortality&lt;/strong&gt; compared to controls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eRGom.jpg&quot; alt=&quot;CC by-nc-ca by Goldstein lab - tardigrades&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tardigrade &lt;em&gt;Hypsibius dujardini&lt;/em&gt;, a different genus than the ones sent into space, but probably equally hardy. Photo by Bob Goldstein &amp;amp; Vicky Madden (CC by-nc-ca via &lt;a href=&quot;https://www.flickr.com/photos/waterbears/2851666759/&quot; rel=&quot;noreferrer&quot;&gt;Goldstein lab - tardigrades on flickr&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.cub.2008.06.048&quot; rel=&quot;noreferrer&quot;&gt;Jönsson, K. I. et al (2008). Tardigrades survive exposure to space in low Earth orbit. Current Biology 18(17):R729–R731&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2014-04-14T01:27:49.983" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16530" PostTypeId="2" ParentId="16447" CreationDate="2014-04-14T02:56:06.497" Score="1" Body="&lt;p&gt;I think the key work here is 'evolve'.  Overall GC/AT ratios change by mutations, whose rate is constant.  The probability that given a mutation event that one base will be substituted by another one has been modeled in several ways where the probabilities of different mutations may or &lt;a href=&quot;https://www.mun.ca/biology/scarr/Transitions_vs_Transversions.html&quot; rel=&quot;nofollow&quot;&gt;may not be the same&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall the GC content will tend to close to 50%.  What causes GC rich genomes to become GC rich (60-70%) are that mutations to GC base pairs have selective advantages either in &lt;a href=&quot;http://www.plosgenetics.org/article/info%3adoi/10.1371/journal.pgen.1001107&quot; rel=&quot;nofollow&quot;&gt;regions&lt;/a&gt; or in the genome overall that &lt;em&gt;cause them to be retained&lt;/em&gt;. The mutation rate may be no different (or even lower) in GC rich organism (many of them are deep underground or deep underwater.  GC rich genomes occur because AT-&gt;GC mutations convey an advantage and they stick around. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reasons that the GC content migrates away from 50% fall into two categories I will call entropic and selective.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By &lt;em&gt;entropic&lt;/em&gt; I mean specifically that coding sequences for genes and other features such as binding sites on the DNA or other features such as centromeres, which will cause the overall ratio to vary from 1 because the sequence is constrained by the information it contains.  While &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8703087&quot; rel=&quot;nofollow&quot;&gt;coding regions have a ratio higher than 1&lt;/a&gt;, &lt;a href=&quot;http://www.researchgate.net/publication/14499424_A_relationship_between_GC_content_and_coding-sequence_length/file/79e4150bb1dd6c5e51.pdf&quot; rel=&quot;nofollow&quot;&gt;GC content tends to hover around 54%&lt;/a&gt;.  Eukaryotes have GC islands and etc, but this also does not overall change the GC content &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So gene rich genomes and typical functional features of the genome do not really explain some of the spectacularly high GC contents found; up to the 70% range.  While the link above looks at GC bias in coding regions, its a given that any part of the genome that is merely a spacer between elements with specific functions will freely vary to GC if it is useful.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Selective&lt;/em&gt; factors for high GC content include high pressure and temperature environments for instance, which usually strongly bias to high GC content by this mechanism.  You can imagine how this works: high GC content genomes are thermodynamically more stable and can survive the extra molecular collisions of higher energy of those environments more readily. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;GC rich genomes are not simple adaptations to live with.  All the genes for DNA oriented processes such as transcription, chromosome packing, DNA polymerase have to adjust a lot. As the organism adapts to hotter temperatures or higher pressures, &lt;a href=&quot;http://www.ploscompbiol.org/article/info%3adoi/10.1371/journal.pcbi.0030005&quot; rel=&quot;nofollow&quot;&gt;each individual protein produced will have to also change to be stable and function in the new conditions&lt;/a&gt;.  As such, these changes happen only over long evolutionary times.  This is probably a good part of the reason why the archaea niches have not been superseded by eubacteria in all 1+ billion years since life has been on Earth.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-04-14T17:25:32.017" LastActivityDate="2014-04-14T17:25:32.017" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16531" PostTypeId="1" AcceptedAnswerId="16538" CreationDate="2014-04-14T04:02:30.407" Score="2" ViewCount="320" Body="&lt;p&gt;At 10.000 BC (12 ka), we became the last of the &lt;em&gt;Homo&lt;/em&gt; species on Earth. In evolutionary terms this is a very little time range to something happen, but I'm wondering anyway, in this meantime which are the most significant changes in our species? Were there any?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I've heard something about how our body hair and nails will be gone 'soon', there's any estimation of when such a thing could happen?! &lt;/p&gt;&#xA;" OwnerUserId="6334" LastEditorUserId="107" LastEditDate="2014-04-27T18:59:27.887" LastActivityDate="2014-04-27T20:08:12.757" Title="Which was the last significant event in human evolution? What's next?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;human-genetics&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16533" PostTypeId="1" CreationDate="2014-04-14T06:12:59.070" Score="7" ViewCount="745" Body="&lt;p&gt;Some species have different numbers of chromosomes, as we all know. Throughout evolution, how was a species able to survive with an extra chromosome? How was this organism able to breed successfully to form offspring with the additional chromosome?&lt;/p&gt;&#xA;" OwnerUserId="6336" LastActivityDate="2014-05-20T06:59:46.313" Title="Evolution of Chromosome Numbers" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16534" PostTypeId="2" ParentId="16503" CreationDate="2014-04-14T06:53:17.573" Score="1" Body="&lt;p&gt;The basic idea is that mutations improving different traits can occur in different individuals, and then be brought together by recombination. So the frequency of recombination roughly sets the maximum rate at which the population can acquire good mutations. Nick Barton and I calculated it, and found that a population can gain about one good mutation per chromosome per generation:&#xA;&lt;a href=&quot;http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002740#pgen-1002740-g008&quot; rel=&quot;nofollow&quot;&gt;http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002740#pgen-1002740-g008&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6313" LastActivityDate="2014-04-14T06:53:17.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16535" PostTypeId="2" ParentId="16528" CreationDate="2014-04-14T07:08:25.403" Score="1" Body="&lt;p&gt;Unique and interesting question.  It's hard to give a firm &quot;why,&quot; but we can discuss the ways that the ear and other &quot;holes&quot; differ.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mucous membranes line every tract into/out of the human body.  Technically the ear is not a point of entry, as the tympanic membrane makes the external auditory canal a sort of blind pouch.  The skin lining the ear is keratinzed skin.  Most skin has keratin and is difficult to permeate.  But mucous membranes are moist, thin, usually highly vascular, and generally easier to permeate.  Disease often takes hold or gains entry at mucous membranes (respiratory infections, GI infections, etc). That is why mucus is so critical as it is protective and acts as a barrier and flushing-system.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mucus requires some form of circulation, as it is a fluid.  Once produced, usually at least some of the fluid is reabsorbed, and the remaining material is passed along until it exits the body.  In the lungs, cilia bring it up to the throat and it is swallowed into the GI tract.  In the nose, it drains down the back of the throat and is swallowed.  In the eye, the fluid (which has mucus components to it) drains into a small tract that runs into the nasal passageway, which drains along with the other nasal mucus.  Obviously saliva, which also has mucus components, is swallowed (2 liters a day of it, actually).  In the genito-urinary tract, there is both reabsorption of some of the fluid components, but mainly flushing outwards when urinating.  The GI tract reabsorbs almost all water components and the remnants pass with stool.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mucus is produced by mucus glands.  Cerumen (ear wax) is produced by sebaceous (oil) glands and apocrine (sweat) glands, but is primarily composed of shed skin cells from the ear canal.  Sebaceous and apocrine glands are all over most of our exposed skin (except palms etc) so it stands to reason that they would be present in our ears as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cerumen exits the ear several ways: all skin on the body sheds the top layers as new skin grows from underneath, and in the ear, the skin cells also migrate with a directionality from the tympanic membrane outwards.  Head movements (like chewing) help dislodge things stuck to the walls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I'll put in my plug here about NOT using cotton swabs (aka Q-tips) to clear your ears.  It generally just pushes the wax deeper, except for the tiny bit you manage to get out.  I've cleaned out tons of wax-impacted ear canals from people who use Qtips on themselves or their kids!!&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the ear were to use a mucous membrane system, the lower viscosity fluid would have to go somewhere.  We would be weeping mucus from our ears unless there were a drainage system into the sinus passageways.  The body conserves liquid, so we couldn't afford the constant fluid loss otherwise. The middle ear has a canal - the eustachean tube - which leads into the nasal sinus (although primarily to equalize pressure).  But the external ear does not, so it's probably a good thing that we don't have mucous membranes in our ears.&lt;/p&gt;&#xA;" OwnerUserId="6314" LastEditorUserId="6314" LastEditDate="2014-04-14T07:15:57.477" LastActivityDate="2014-04-14T07:15:57.477" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16536" PostTypeId="2" ParentId="16525" CreationDate="2014-04-14T07:48:38.230" Score="7" Body="&lt;p&gt;To learn obstructive/restrictive lung diseases, I find it easiest to think in extremes at first, with vivid descriptions of why.  So in obstructive lung diseases, like COPD/emphysema:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Total volume increases because so many of the walls of the alveoli have been destroyed, they are like giant floppy bags instead of nice firm bubbles.  There's more empty space, and total volume is therefore increased.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reserve Volume and End Respiration Volume increase because these alveoli are large and stretched and floppy and can't push as much air out, even when you try.  (Decreased elastic recoil.)  They also flop shut often before the air is expelled - trapping air in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tidal volume may not change at all, but it takes longer to exhale than with normal lungs.  That is why FEV1 and FVC are lower, for the same reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Residual volume&#xA;&lt;img src=&quot;https://i.stack.imgur.com/R2nLS.png&quot; alt=&quot;enter image description here&quot;&gt; &#xA;&lt;img src=&quot;https://i.stack.imgur.com/Z4G7Y.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6314" LastActivityDate="2014-04-14T07:48:38.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16537" PostTypeId="1" AcceptedAnswerId="16819" CreationDate="2014-04-14T08:01:55.393" Score="3" ViewCount="83" Body="&lt;p&gt;Suppose we have a network with &lt;strong&gt;N*&lt;/strong&gt; nodes (N* is the number of internal nodes). Every directed link in this network exists with probability &lt;strong&gt;p&lt;/strong&gt;. What would be the number of:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;motifs that are auto-regulatory?&lt;/li&gt;&#xA;&lt;li&gt;feed-forward loop motifs&lt;/li&gt;&#xA;&lt;li&gt;feed-back loop motifs&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6016" LastEditorUserId="-1" LastEditDate="2014-04-14T10:43:51.157" LastActivityDate="2014-04-24T07:10:23.153" Title="Number of autoregulation and FFL motifs in a network" Tags="&lt;bioinformatics&gt;&lt;transcription-factor&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16538" PostTypeId="2" ParentId="16531" CreationDate="2014-04-14T08:27:37.810" Score="4" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like to start by saying that &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenotype&quot; rel=&quot;nofollow&quot;&gt;phenotypic&lt;/a&gt; (loosely speaking phenotypic mean morphological) traits evolve because their variance in the population is correlated with some genetic variance. If most of the phenotypic variance is genetically coded, you'd expect that the trait will change through if different variant of the trait influence fitness (which is a function of both survival and reproductive success). Stated differently and more accurately the change in mean value of a given trait $R$ in the population is given by:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$R=S\frac{V_{Ga}}{V_{P}} = S\frac{V_{Ga}}{V_{G}+V_{E}} =  S\frac{V_{Ga}}{V_{Ga} + V_{Gd}+V_{E}} $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $S$ is the selection differential, $V_{G} = V_{Ga}+ V_{Gd}$ is the genetic variance where its two components are the additive and dominance genetic variance respectively. $V_P  = V_G + V_E$ is the phenotypic variance which two components are the genetic and environmental variances. The ratio $\frac{V_{Ga}}{V_{P}}$ has a name; it is called the heritability in the narrow sense symbolized by $h_N$ Note: I present here a simplified version of the reality! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if the trait you consider has genetic variance in the population and that this trait influence the fitness with a given selection differential you can provide estimates of how the trait will change through time in the human population. Now if the variance does not already exist in the population but you have to wait for mutations to occur, then you cannot really provide an estimate of when will this occur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Discussion on the future evolution of nail size&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, when you think about some traits such as our nails. You may consider that they are of no use but do you really think that those people that have no nail would really have a better fitness. At first I would tend to think that I would rather chose a partner that have nails, it is much more sexy! If many people are like me and appreciate nails, nailless people will have difficulties to reproduce or in other words, they will have a lower fitness that nailed people.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think we have data on what &lt;a href=&quot;http://en.wikipedia.org/wiki/Locus_%28genetics%29&quot; rel=&quot;nofollow&quot;&gt;loci&lt;/a&gt; (positions on the chromosomes) influence the size of the nails and about how much of the variance in nail size is explained by the genetic additive variance. And how do the size of our nails influence fitness. So we don't know about how this trait will evolve through time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Future evolution of other traits&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several traits that we can/could more or less predict their evolution. Those are the traits for which we know the ratio of the genetic additive variance over the phenotypic variance and how it influences fitness. I can think of genes that are linked with resistance to new diseases such as HIV for example. If malaria comes to a new area you might expect the &lt;a href=&quot;http://en.wikipedia.org/wiki/Allele&quot; rel=&quot;nofollow&quot;&gt;allele&lt;/a&gt; (=variant of a gene) allowing a better resistance to malaria will increase in frequency (note that this allele is advantageous in heterozyotes (protects from malaria) but it is highly disadvantegous in homozygote because it causes &lt;a href=&quot;http://en.wikipedia.org/wiki/Sickle-cell_disease&quot; rel=&quot;nofollow&quot;&gt;sickle-cel disease&lt;/a&gt;). We could estimate the change in frequency of alleles linked with obesity in some countries also. Probably several studies exist on the subject but I don't know them. One might improve this answer by giving some information about how HIV resistant variants is likely to change in frequency through time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What were the last evolutionary changes in human history?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can think of the impressive frequency of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Tay%E2%80%93Sachs_disease&quot; rel=&quot;nofollow&quot;&gt;Tay-Sachs disease&lt;/a&gt; in french canadian due to a &lt;a href=&quot;http://en.wikipedia.org/wiki/Population_bottleneck&quot; rel=&quot;nofollow&quot;&gt;bottleneck effect&lt;/a&gt;. Or you may think of the evolution of height, about the evolution of the shape of the skull or the evolution of feet. You can think of the reduction of our gut. etc… Your question is not well enough define so that we know if you consider the raise in frequency of Tay-Sachs disease is sufficient for you to be called a significant evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-04-27T20:08:12.757" LastActivityDate="2014-04-27T20:08:12.757" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16540" PostTypeId="1" CreationDate="2014-04-14T11:14:23.790" Score="7" ViewCount="179" Body="&lt;p&gt;I'm currently reading &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0198567022&quot; rel=&quot;nofollow&quot;&gt;Computational Molecular Evolution&lt;/a&gt; by Yang. Can you recommend alternative books?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am finding it to be lacking on conceptual discussion (it's more focussed on the mathematics and statistical intricacies). I'd like to find something which discusses why we do the things, and the strengths and weaknesses of the ideas, which are presented in the Yang book whilst not being overly specialist - more of an introductory text to the field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any introduction to phylogenetics books??&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-11-03T09:49:56.480" LastActivityDate="2014-11-03T09:49:56.480" Title="Book suggestion on computational molecular evolution" Tags="&lt;bioinformatics&gt;&lt;book-recommendation&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16541" PostTypeId="1" CreationDate="2014-04-14T13:27:39.903" Score="9" ViewCount="7646" Body="&lt;p&gt;Does the size of the eye increase as we develop from the stage the complete eye first forms to infancy and then to adulthood ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2014-04-15T13:19:24.920" LastActivityDate="2018-05-21T07:21:18.240" Title="Does our eyeball increase in size as we grow?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;&lt;eyes&gt;&lt;embryology&gt;&lt;development&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16542" PostTypeId="1" AcceptedAnswerId="16543" CreationDate="2014-04-14T14:31:50.540" Score="14" ViewCount="1397" Body="&lt;p&gt;When learning about the immune response, my teacher mentioned that all the bodies B cells are present at birth, and there is one to counter every disease. But if this is the case, why should the primary response take a long time? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I know, the primary response involves the non-specific response followed by the specific response, where APCs cause the activation of T cells resulting in clonal selection and expansion of T and B cells. The B cells then differentiate into plasma cells and produce antibodies. It results in the memory cells being produced, which can quickly reengage the specific response the next time the pathogen enters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why doesn't the body just make memory cells to begin with? As if it has already encountered every possible pathogen. I presume it is just a lack of specificity in the A level teaching, but I am curious to know what I am missing here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,&#xA;Jamie&lt;/p&gt;&#xA;" OwnerUserId="6330" LastActivityDate="2015-08-12T16:47:34.017" Title="If all B cells are present at birth, why should the primary response to an infection take longer than the secondary response?" Tags="&lt;immunology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16543" PostTypeId="2" ParentId="16542" CreationDate="2014-04-14T15:52:49.830" Score="10" Body="&lt;p&gt;These so called virgin B-cells (becase they never had contact with their antigen) which are present in your body only have random B-cell receptors (when secreted, these are the antibodies), mostly of a relatively low binding affinity. These B-cells undergo division, &lt;a href=&quot;http://en.wikipedia.org/wiki/V%28D%29J_recombination&quot; rel=&quot;nofollow noreferrer&quot;&gt;re-arrangement&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Somatic_hypermutation&quot; rel=&quot;nofollow noreferrer&quot;&gt;somatic hypermutation&lt;/a&gt; of the B-cell receptor and clonal selection. Only cells producing high-affinity antibodies survive this selection process and build later the pool for the memory cells and the plasma cells. It is like in the image below (from &lt;a href=&quot;http://www.nature.com/nrc/journal/v12/n5/fig_tab/nrc3257_F1.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yMsd2.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using this approach we have a big pool of low affinity antibodies (which somewhat fit). These are then used as the basis for the elaboration of a population of high affinity (perfectly fitting) antibodies, which target only the pathogen. And the antibodies are available relatively fast.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="4139" LastEditDate="2015-08-12T13:48:00.373" LastActivityDate="2015-08-12T13:48:00.373" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16544" PostTypeId="2" ParentId="16481" CreationDate="2014-04-14T16:15:08.820" Score="1" Body="&lt;p&gt;There are certain annual(eg.peas) and biennial plants(eg.carrot) also which die at fixed times.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But for perennial plants :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.straightdope.com/columns/read/849/do-trees-ever-die-of-old-age&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Trees endure as long as they do basically because they're&#xA;  nonhierarchical organisms. In animals, all vital functions are&#xA;  controlled by the central nervous system, the guiding element of which&#xA;  is the brain. When the brain dies, so does the animal. By contrast,&#xA;  vital functions in trees are decentralized. A large part of the tree&#xA;  can die, and indeed routinely does die, without killing off the tree&#xA;  as a whole. Most of a mature tree is dead except for a few layers&#xA;  under the bark.....&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;All trees die eventually, of course. Four thousand years is old&#xA;  compared to the life spans of gossamer creatures like ourselves, but&#xA;  in the context of geologic time it's the blink of an eye. As they get&#xA;  older trees become more susceptible to disease, pests, and other&#xA;  perils, and inevitably these take their toll.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-14T16:15:08.820" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16545" PostTypeId="2" ParentId="16233" CreationDate="2014-04-14T16:31:19.520" Score="0" Body="&lt;p&gt;From wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Melatonin_receptor&quot; rel=&quot;nofollow&quot;&gt;melatonin receptors&lt;/a&gt; (with some modifications) :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In mammals, melatonin receptors, which are G protein coupled receptors, are found in the brain and some&#xA;  peripheral organs. However, there is considerable variation in the&#xA;  density and location of MT receptor expression between species.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;MT1&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In humans, The MT1 subtype is expressed in the pars tuberalis of the&#xA;  pituitary gland and the suprachiasmatic nuclei of the&#xA;  hypothalamus....This is indicative of its role in circadian and&#xA;  reproductive function.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;MT2&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The MT2 subtype is expressed in the retina. MT2 receptor mRNA has not&#xA;  been detected by in situ hybridization in the rat suprachiasmatic&#xA;  nucleo or pars tubealis. This receptor may have a role in light&#xA;  dependent functions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-14T16:31:19.520" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16547" PostTypeId="2" ParentId="16541" CreationDate="2014-04-14T17:29:54.673" Score="7" Body="&lt;p&gt;No. In fact the lens of the eye, which is nearly optically perfect in humans, &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/002398.htm&quot;&gt;does not change or grow after it is fully formed around week 26 of gestation&lt;/a&gt;.  Interestingly this is why one of the cues for identifying young children is having small faces with large eyes.  This also the case for puppies and cats and other animals, who are mostly cuter when they are small with large eyes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Lens_%28anatomy%29#Development_and_growth&quot;&gt;The eye lens is composed of dead cells whose remains are almost entirely a single protein called a crystallin&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This doesn't apply to compound eyes though. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-04-14T17:36:24.177" LastActivityDate="2014-04-14T17:36:24.177" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16548" PostTypeId="2" ParentId="16189" CreationDate="2014-04-14T17:42:37.127" Score="3" Body="&lt;p&gt;First thing to make clear is that net $6 \, \ce{H_2O}$ go out of the reaction.($12 \,\ce{H_2O}-6\,\ce{H_2O}$)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me tell you my calculation, you should then be able to figure out what went wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the Left hand Side, $6\,\ce{H_2O}$ are accounted here :&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;$2\,\ce{H_2O}$ go in conversion of 2-Phosphoglycertae to phosphoenolpyruvate.&lt;/li&gt;&#xA;&lt;li&gt;$2\,\ce{H_2O}$ in TCA from conversion of Oxoloacetate to Citrat by combining with Acetyl CoA.(One for each Acetyl CoA molecule)&lt;/li&gt;&#xA;&lt;li&gt;The aconitase -cis-aconitase-isocitrate water molecules cancel out. Equal no go in and out.&lt;/li&gt;&#xA;&lt;li&gt;$2\,\ce{H_2O}$ in TCA from conversion of fumarate to Malate.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For the right hnd side, if we calculate the no. of NADH formed = 10 and assume that each participates in respiratory chain, we have $10\,\ce{H_2O}$ from there. The other $2$ will be from the $2$ FADH produced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So we have 6 on the LHS and 12 on the RHS. Hope this makes sense !&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="16985" LastEditDate="2016-07-25T20:19:41.947" LastActivityDate="2016-07-25T20:19:41.947" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16549" PostTypeId="2" ParentId="16484" CreationDate="2014-04-14T17:57:34.050" Score="2" Body="&lt;p&gt;What you're referring to as a mosquito bite is actually the &quot;wheal&quot; (red swollen bump in the skin) that forms from an immune system reaction to antigens (foreign molecules) in the saliva of the mosquito that it leaves behind inside the bite.  It's not technically a toxin, just something that causes an immune reaction.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also not an infection, it's inflammation.  Infection might set in if the skin is scratched open and bacteria move in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason it's red is that immune cells release cytokines (like histamine and that cause cause edema that leads to swelling, heat, itching, etc - and recruit other cells to do the same.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cytokines that act locally have a range of effect, especially histamine.  The degree of immune reaction determines the size of the wheal and how long it lasts.  Scratching it contributes to irritation and can prolong resolution.  Scratching it open can lead to infection.&lt;/p&gt;&#xA;" OwnerUserId="6314" LastActivityDate="2014-04-14T17:57:34.050" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16550" PostTypeId="2" ParentId="15066" CreationDate="2014-04-14T18:00:29.473" Score="0" Body="&lt;p&gt;Source : &lt;a href=&quot;http://www.howitworksdaily.com/science/why-do-we-feel-sleepy-after-eating/&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sugary foods lead to the production of insulin. Insulin stimulates cells to take up glucose from blood. It also mobilizes tryptophan to brain. Once in brain, tryptophan triggers formation of serotonin, a hormone involved in controlling mood and slumber.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-14T18:00:29.473" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16551" PostTypeId="1" AcceptedAnswerId="16553" CreationDate="2014-04-14T19:28:58.303" Score="4" ViewCount="113" Body="&lt;p&gt;Each Spring, our local health unit begins its campaign of Lyme disease and tick-bite awareness. I was wondering if there has ever been a vaccine available, and if so, what antigen does it target?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-04-14T20:02:13.877" Title="Is there a Lyme disease vaccine?" Tags="&lt;pathology&gt;&lt;vaccination&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16552" PostTypeId="2" ParentId="16233" CreationDate="2014-04-14T19:40:57.293" Score="2" Body="&lt;p&gt;This is a quite complicated question, as melatonin has quite a range of effects on the cells. First, melatonin binds to three different melatonin receptors, which are found in a wide variety of tissues or organs including brain and retina, cardiovascular system, liver and gallbladder, intestine, kidney, immune cells, adipocytes, prostate and breast epithelial cells, ovary/granulosa cells, myometrium, and skin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two of the receptors a G-protein coupled receptors (GPCR), the MT1 and MT2 receptors. The third is a quinone reductase called QR2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more details, see this papers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16527442&quot; rel=&quot;nofollow noreferrer&quot;&gt;Melatonin receptors in humans: biological role and clinical&#xA;relevance.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12628439&quot; rel=&quot;nofollow noreferrer&quot;&gt;Melatonin receptors and their regulation: biochemical and structural&#xA;mechanisms.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The role of melatonin is pretty broad, see the figure (from this article:&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16817850&quot; rel=&quot;nofollow noreferrer&quot;&gt;Melatonin: Nature's most versatile biological signal?&lt;/a&gt;&quot;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fiWzr.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The receptors transport the outside chemical signal (the melatonin) to the inside and activate (or repress) a number of different signal transduction pathways. See the figure below (taken from &lt;a href=&quot;http://www.qiagen.com/products/genes%20and%20pathways/pathway%20details?pwid=288&quot; rel=&quot;nofollow noreferrer&quot;&gt;Qiagen&lt;/a&gt;): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VOFPY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This includes MAP-Kinase pathways, proteinkinase C, IP3, adenyl cyclase and so on. This is quite complicated and I recommend reading some of the following articles if you are interested in a deeper insight. Finally these signals are transmitted into the nucleus and result in a changed gene regulation/expression.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18493248&quot; rel=&quot;nofollow noreferrer&quot;&gt;Melatonin receptors, heterodimerization, signal transduction and&#xA;binding sites: what's new?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18571301&quot; rel=&quot;nofollow noreferrer&quot;&gt;Physiological effects of melatonin: role of melatonin receptors and&#xA;signal transduction pathways.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-14T19:40:57.293" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16553" PostTypeId="2" ParentId="16551" CreationDate="2014-04-14T20:02:13.877" Score="3" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Lyme_disease#Vaccination&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; in 1998 a vaccine was approved by the FDA. It was directed against the outer surface protein A (OspA) of B. burgdorferi, but was taken from the market in 2002 after a large number of recipients reported the development of autoimmune diseases. An investigation of the FDA and the CDC found no connection to these claims, but afterwards the sales went to the bottom until the vaccine was withdrawn from the market. An interesting article on this story (with a number of references) can be found &lt;a href=&quot;http://www.historyofvaccines.org/content/articles/history-lyme-disease-vaccine&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two new approaches to develop vaccine candidates. One is directed against the outer surface protein C (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17921702&quot; rel=&quot;nofollow&quot;&gt;An octavalent lyme disease vaccine induces antibodies that recognize all incorporated OspC type-specific sequences.&lt;/a&gt;&quot;, another against glycolipoproteins on the bacterias surface (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17182019&quot; rel=&quot;nofollow&quot;&gt;Synthesis of an experimental glycolipoprotein vaccine against Lyme disease.&lt;/a&gt;&quot;). As far as I see, none of these vaccine candidates is already licensed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another approach is to vaccinate the animal reservoir hosts, as this has been done successfully for rabies. Here either vaccinated baits (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3209012/&quot; rel=&quot;nofollow&quot;&gt;Reservoir Targeted Vaccine for Lyme Borreliosis Induces a Yearlong, Neutralizing Antibody Response to OspA in White-Footed Mice&lt;/a&gt;&quot;) or recombinant vaccines (&quot;&lt;a href=&quot;http://www.pnas.org/content/101/52/18159.full&quot; rel=&quot;nofollow&quot;&gt;An ecological approach to preventing human infection: Vaccinating wild mouse reservoirs intervenes in the Lyme disease cycle&lt;/a&gt;&quot;) were used with good results. Neither of these methods is already been used, as far as I see.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-14T20:02:13.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16554" PostTypeId="1" CreationDate="2014-04-14T20:12:27.173" Score="6" ViewCount="1657" Body="&lt;p&gt;Basically, what I'm asking is, is the actual sperm cell built from the blueprint in the DNA of the man or is it itself also a consequence of the DNA it carries?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like to know a few more things related to this. For example, which DNA is in the nucleus of a sperm? Is it the same as the DNA of other bodily cells in the man's body, or is it just the DNA it's delivering? Can the sperm's performance be affected by any specific genetic traits that can be observed in a potential human the sperm could make? For example, a sperm swims faster if it's carrying the genetic material that would result in a tall person (probably a silly question).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The original question I had is if the statement that female sperm live longer is true. If it turns out that the man's body makes all the sperm more or less the same and they're just boxes that can swim, then I would guess the answer is no.&lt;/p&gt;&#xA;" OwnerUserId="6340" LastEditorUserId="948" LastEditDate="2015-08-31T18:46:09.130" LastActivityDate="2015-08-31T18:46:09.130" Title="Does the genetic material the sperm carries affect its physical properties" Tags="&lt;dna&gt;&lt;reproduction&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16555" PostTypeId="1" CreationDate="2014-04-14T21:18:36.967" Score="2" ViewCount="846" Body="&lt;p&gt;I'm confused about the fate map of a human embryo. Is it just a particular part of the embryo development or does it include everything, from the conception (germinal stage) to the day the baby is born? &lt;/p&gt;&#xA;" OwnerUserId="6341" LastActivityDate="2014-04-16T08:55:12.553" Title="Where does the fate map of a human embryo end?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16556" PostTypeId="2" ParentId="15066" CreationDate="2014-04-14T21:56:15.300" Score="7" Body="&lt;p&gt;The name used frequently for this phenomenon is &quot;Post-lunch dip&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The post-lunch dip is a real phenomenon that can occur even when the individual has had no lunch and is unaware of the time of day. This dip has its roots in human biology, and may be linked to the size of the 12-hour harmonic in the circadian system. It is certainly exacerbated by a high-carbohydrate lunch, and may be more likely to occur in extreme morning-type individuals.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15892914&quot; rel=&quot;noreferrer&quot;&gt;PubMed Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another PubMed &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22155490&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;&#xA;&quot;The 'post-lunch' dip is a bi-circadian phenomenon, largely unrelated to lunch, and worsened by a disturbed prior night's sleep. Despite anecdotal claims of adverse effects of larger lunches on afternoon driving ability, there is little actual driving data to support this belief.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=post-lunch%20dip&quot; rel=&quot;noreferrer&quot;&gt;For other reading and research...&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2014-04-14T21:56:15.300" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16557" PostTypeId="1" AcceptedAnswerId="16983" CreationDate="2014-04-14T22:00:52.567" Score="5" ViewCount="212" Body="&lt;p&gt;I'm curious to learn about the 'most human' teratoma ever recorded. By that I mean a teratoma which most resembles the form of a human being.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suppose there are several factors which would contribute to this criteria:&#xA;-Most organs, and components found in a human (e.g. brain, teeth, organs, etc.)&#xA;-Most closely organized structurally like a developing human.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also I was wondering. Given the right conditions could a teratoma grow into a living being? Could they theoretically develop the necessary organs to be excised from their host and sustain the functions necessary for survival.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically I am curious to learn about the possibility of teratoma maturing into a bonafide organism.&lt;/p&gt;&#xA;" OwnerUserId="6342" LastEditorUserId="6342" LastEditDate="2016-02-20T00:47:18.623" LastActivityDate="2016-02-20T00:47:18.623" Title="Most human-like teratoma ever recorded?" Tags="&lt;cancer&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16558" PostTypeId="2" ParentId="16554" CreationDate="2014-04-14T23:08:54.730" Score="4" Body="&lt;p&gt;I think there is a strong driving force for sperm to be free living haploid versions of human beings.  Since they are a &lt;a href=&quot;http://en.wikipedia.org/wiki/Meiosis&quot; rel=&quot;nofollow&quot;&gt;product of meiosis&lt;/a&gt; sperm are the product of recombination of both the male chromosome sets. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While I'm sure that if we look closely enough, the germline cells that produce the sperm are contributing some protein and structure to the sperm, the life cycle of the sperm is mostly the result of the genome that it contains within itself.  Sperm are prone to defects.  On the average in human beings about &lt;a href=&quot;http://en.wikipedia.org/wiki/Semen_analysis#Motility&quot; rel=&quot;nofollow&quot;&gt;half of sperm are non-motile&lt;/a&gt;: simply unable to form the flagellum or power its motion adequately for motility. That's a pretty strong selective force in the life of our other, 'half genome' selves.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sperm selection - the sorting of which sperm from a single male achieves fertilization is pretty rigorous.  It can take &lt;a href=&quot;http://www.newhealthguide.org/How-Long-Does-It-Take-To-Fertilize-An-Egg.html&quot; rel=&quot;nofollow&quot;&gt;30 minutes to days&lt;/a&gt;.  Once in contact with the ovum, the sperm executes a &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_fertilization&quot; rel=&quot;nofollow&quot;&gt;critical set of transformations and biochemical activations&lt;/a&gt; to get past the various layers of the cell.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sperm are from the man, but they are each living creatures on their own which we hope will deliver themselves up to the ovum to create another human being.  They vary in their genetic quality and effectiveness and this is highly related to their genetic make up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because each sperm is the product of two stages of Meiosis, they can be full of genetic defects, most of which would be fatal in a diploid human being.  The functions of the sperm as it goes through its short but competitive life weed out genetic abberations and help assure that the next generation of diploid human beings is as healthy as they can.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So they are not DNA boxes that swim.  I'd be hard pressed to think of a passive role for a cell in biology - they are all working pretty hard... I'd be interested in a comment with suggestions of something that is not under selective pressure in biology.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It sort of reminds me of the old argument about passive mating in females. Behavioral biologists used to think that female animals had little or no active role in mating.   That &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3826201/&quot; rel=&quot;nofollow&quot;&gt;myth was retired about 30 years ago now&lt;/a&gt;.  That link points to an introduction to an &lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/368/1631.toc&quot; rel=&quot;nofollow&quot;&gt;entire volume reviewing that whole discussion of active female roles in reproduction&lt;/a&gt; in case anyone reading is interested. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW I'm not an expert on gametes, but I'd be surprised if the ova also didn't have a complimentary but quite different selective process they had to get through to become a fully presented candidate for fertilization.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just to add a note about how the functioning sperm genes affect the diploid organism: This is one of the most important things that sperm does.  The genes that function in the living spermatazoan are the &lt;em&gt;same genes&lt;/em&gt; the diploid organism uses, or at least a substantial number of them.  Further, these genes are scattered across all the chromosomes and so major chromosomal defects and important genes are functional if fertilization is completed.  As an example here's a cool blog post about how &lt;a href=&quot;http://nittygrittyscience.com/2014/04/14/mosquito-sperm-need-to-smell-to-swim/&quot; rel=&quot;nofollow&quot;&gt;mosquito sperm have been shown to use odorant receptors to orient themselves in the fertilziation process&lt;/a&gt;. Those same receptors and the signalling genes that link that signal to the sperm behavior are probably quite useful to the adult mosquito.  I'd be surprised if human sperm also did not use similar pathways to function. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not to beat a dead horse, but the recent nature has a report of &lt;a href=&quot;http://www.nature.com/news/sperm-rna-carries-marks-of-trauma-1.15049&quot; rel=&quot;nofollow&quot;&gt;small RNAs in mouse sperm as being an epigenetic carrier for stress&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-04-16T17:38:55.560" LastActivityDate="2014-04-16T17:38:55.560" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="16561" PostTypeId="2" ParentId="16554" CreationDate="2014-04-15T04:58:59.350" Score="2" Body="&lt;p&gt;Shigeta, you have some good points there.  I wanted to clarify some things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sperm and ova are considered tissues, not &lt;a href=&quot;http://en.wikipedia.org/wiki/Life#Biology&quot; rel=&quot;nofollow&quot;&gt;individual living creatures&lt;/a&gt;.  They are not individually capable of cell division nor production of offspring.  They are specialized cells with specific functions that are created by a multicellular organism as a means of transferring DNA.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sperm carries 1/2 of a chromosome set from the male's own DNA, after cross-overs during meiosis (meaning that the DNA in a sperm has some different combinations than the parent DNA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Metabolism primarily occurs at the mitochondria.  Protein synthesis does occur in the sperm, using nucleus-encoded mRNA.  What I was unable to find an answer to was whether this mRNA was transcribed from the nucleus of that same sperm, or whether it was from the primary spermatocyte DNA (diploid) or from the sperm nucleus (haploid).  The chromatin in the sperm nucleus is several times more tightly wound than in a somatic cell, so I am not sure how it would be accessible to transcription, nor am I sure that the full set of enzymes required for transcription, modification, and translation is present in the spermatozoa.  I'll be very interested in hearing if anyone is able to find this information!&lt;/p&gt;&#xA;" OwnerUserId="6314" LastActivityDate="2014-04-15T04:58:59.350" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16563" PostTypeId="2" ParentId="16541" CreationDate="2014-04-15T07:19:48.407" Score="10" Body="&lt;p&gt;First of all, I should quote the sentence from the MOST reliable ophthalmology sourcing in the world - &lt;a href=&quot;http://www.aao.org/&quot;&gt;American Academy of Ophthalmology&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Section 11 - &quot;&lt;a href=&quot;http://store.aao.org/clinical-education/product-line/basic-and-clinical-science-course-bcsc/2013-2014-basic-and-clinical-science-course-section-11-lens-and-cataract.html&quot;&gt;Lens and Cataract&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The equatorial diameter of the unfixed human lens measures 2 mm at 12 weeks and 6 mm at 35 weeks. Both the growth and the maturation of lenticular fibers continue throughout life.&quot; The antero-posterior dimensions of the lens enlarge from 3 mm at infancy to 6 and even more in adult years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The lens continues to grow throughout life (page 7 the same source)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, the growth of the eye continues after birth - at the beginning the growth is fast and later the growth is much slower but still - there is GROWTH of the eye after the birth.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2014-04-15T07:19:48.407" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="16564" PostTypeId="1" AcceptedAnswerId="16586" CreationDate="2014-04-15T07:40:33.660" Score="2" ViewCount="56" Body="&lt;p&gt;I think they are not inputs from maternal placenta.&#xA;I think they are the results of foetus metabolism.&#xA;However, I do not understand it how and where exactly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the roles of creatine and bilirubin in foetus circulation?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-16T07:04:08.823" Title="Roles of creatine and bilirubin in foetus circulation" Tags="&lt;biochemistry&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16566" PostTypeId="2" ParentId="16531" CreationDate="2014-04-15T09:30:00.303" Score="1" Body="&lt;p&gt;One example of an active selection pressure's effect on human phenotype is in areas where malaria is endemic, the prevalence of sickle cell anemia is higher.  Sickle cell anemia is highly protective against malaria, and less people die from sickle cell than die from malaria, so you see a rise of sickle cell in the population.  This is a small degree of phenotype selection compared to the sort of selective pressure that would be required to cause the degree of evolution you are talking about, but it's one of the few things that can be readily seen in the modern world.  Most people in the modern world live long enough to reproduce, and survival of the fittest has less influence on us than it did in our tribal days.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To wax philosophical, one might argue that the media (e.g. Hollywood) has exerted a selective pressure over our evolution, as it has significant influence over what people deem &quot;beautiful&quot; and &quot;attractive,&quot; thereby altering our ultimate mating selection behaviors.&lt;/p&gt;&#xA;" OwnerUserId="6314" LastActivityDate="2014-04-15T09:30:00.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16568" PostTypeId="1" AcceptedAnswerId="16574" CreationDate="2014-04-15T10:45:49.403" Score="2" ViewCount="134" Body="&lt;p&gt;From &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0878933085&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; textbook&lt;/p&gt;&#xA;&lt;p&gt;Under the wright-Fisher model of genetic drift and under the assumption that all alleles are neutral, the probability that &lt;span class=&quot;math-container&quot;&gt;$k$&lt;/span&gt; alleles had &lt;span class=&quot;math-container&quot;&gt;$k$&lt;/span&gt; distinct parent alleles the previous generation is&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$Pr(k) = \prod_{i=1}^{k-1}1-\frac{i}{2N} ≈ 1-\frac{{k \choose 2}}{2N} $$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;The chance of two alleles not coalescing for &lt;span class=&quot;math-container&quot;&gt;$t$&lt;/span&gt; generations is &lt;span class=&quot;math-container&quot;&gt;$\left(1-\frac{1}{2N}\right)^t$&lt;/span&gt; , and the chance that they coalesce in the next generation is &lt;span class=&quot;math-container&quot;&gt;$\frac{1}{2N}$&lt;/span&gt;. Therefore, the probability that 2 alleles had a common ancestor t+1 generations ago is&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$\frac{1}{2N}\left(  1-\frac{1}{2N} \right)^t ≈ \frac{1}{2N}e^{\frac{-t}{2N}}$$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;I understand up to this point!&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;The probability that the &lt;span class=&quot;math-container&quot;&gt;$k$&lt;/span&gt; alleles do not coalesce for &lt;span class=&quot;math-container&quot;&gt;$t$&lt;/span&gt; generations, and then one pair coalesce to give &lt;span class=&quot;math-container&quot;&gt;$k-1$&lt;/span&gt; alleles at &lt;span class=&quot;math-container&quot;&gt;$t+1$&lt;/span&gt; generations ago is as follows:&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$Pr(k)^t \left[ 1-Pr(k) \right] ≈ \frac{{k \choose 2}}{2N}exp\left[ -\frac{{k \choose 2}}{2N}t \right] $$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Can you help me to understand this last part?&lt;/strong&gt; (both the left and right part of the equation)&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-04-15T15:12:00.883" Title="Coalescent Theory - Probability for $k$ alleles that of one coalescence event occured $t+1$ generations ago" Tags="&lt;evolution&gt;&lt;population-biology&gt;&lt;population-dynamics&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16570" PostTypeId="1" AcceptedAnswerId="17504" CreationDate="2014-04-15T12:39:17.943" Score="2" ViewCount="2211" Body="&lt;p&gt;I'm trying to use the TCGA data portal to get gene expression data for cancer tissues, but I'm not sure what &quot;Tumor matched normal&quot; means.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is unclear to me if the values are already compared to a control (non cancerous) tissue or there is another sample which gives the healthy tissue values. Assuming it is the latter, I don't see these samples anywhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a screenshot of my filter&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.clipular.com/c/5452873408184320.png?k=rlA9jy3Kb2U47JT7GrXBTzdsln4&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.clipular.com/c/5452873408184320.png?k=rlA9jy3Kb2U47JT7GrXBTzdsln4&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And here is a picture of the result (only TNs appear).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qLptI.png&quot; alt=&quot;Only TNs appear&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1190" LastEditorUserId="14852" LastEditDate="2015-04-24T04:08:35.970" LastActivityDate="2015-04-24T04:08:35.970" Title="TCGA gene expression data are missing matched normal" Tags="&lt;bioinformatics&gt;&lt;cancer&gt;&lt;tcga&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16571" PostTypeId="1" CreationDate="2014-04-15T13:18:43.020" Score="3" ViewCount="1061" Body="&lt;p&gt;I have tried reading about development of vitreous humor but it is all very confusing. When does it first developed ? Does it renew itself ? Please provide reliable sources..&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-07-14T15:49:42.947" Title="Development of vitreous humor" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;embryology&gt;&lt;development&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16572" PostTypeId="1" AcceptedAnswerId="16758" CreationDate="2014-04-15T13:19:31.980" Score="3" ViewCount="222" Body="&lt;p&gt;I am doing face detection application where every face detected is inside a rectangle. The rectangle always contains some background behind the face and now I need to extract as much of the face as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also the method should be fast so I've decided to extract just some basic shape from the rectangle, like an inscribed circle. This circle unfortunately also doesn't fit so well. The best shape I've tried right now is ellipse:  &lt;code&gt;(2*width of the rectangle)/3 x height&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So right now I am looking for some better ratio between the width and height of the face maybe the best would be if you could point me to some research papers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="6348" LastEditorUserId="43" LastEditDate="2014-04-15T14:45:47.297" LastActivityDate="2014-04-22T06:50:57.077" Title="Average face shape" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16573" PostTypeId="2" ParentId="16571" CreationDate="2014-04-15T13:52:25.287" Score="2" Body="&lt;p&gt;Look at this scheme - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/K7jMc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I stated before, vitreous is 99% water and is &lt;strong&gt;not an organ itself&lt;/strong&gt;, thus the &quot;replacement of vitreous&quot; is actually = 99% water re-production and the only organ inside the eye which can perform this - ciliary body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consequently, if the vitreous was removed and replaced by gas or saline it will be replaced by aqueous which produced by ciliary body - this process takes 8 weeks to completely replace foreign substance as a gas by aqueous. &lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2014-04-15T13:52:25.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16574" PostTypeId="2" ParentId="16568" CreationDate="2014-04-15T14:27:25.517" Score="2" Body="&lt;p&gt;Is this the exact text from the book? The left side seems to represent the probability for &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;No coalescence in $k$ lines in $t$ generations (i.e. the $Pr(k)^t$ term), and &lt;strong&gt;at least one&lt;/strong&gt; coalescence among those lines in generation $t+1$ (the $1-Pr(k)$ term)&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;which is the same event as&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;First coalescence event in $k$ lines is exactly in generation $t+1$&quot;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The right hand side is derived analogous to the second equation, with $1-\frac{1}{2N}$ (&quot;no coalescence in two lines&quot;) replaced by $1-\frac{k\choose2}{2N}$ (approximation for &quot;no coalescence in $k$ lines):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;\begin{align}&#xA;Pr(k)^t \left[ 1-Pr(k) \right] &amp;amp;≈ \left( 1-\frac{k\choose2}{2N} \right)^t \left [1 - 1 +  \frac{k\choose2}{2N} \right] \\&#xA;&amp;amp;\approx \exp\left( - \frac{k\choose2}{2N} t \right) \frac{k\choose2}{2N}&#xA;\end{align}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;were is first approximation is due to your first calculation. The second one seems to use a first order Tailor approximation of $\exp(x)$:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;\exp(-xt) = exp(-x)^t \approx (1-x)^t&#xA;$$&lt;/p&gt;&#xA;" OwnerUserId="5644" LastEditorUserId="5644" LastEditDate="2014-04-15T15:12:00.883" LastActivityDate="2014-04-15T15:12:00.883" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16575" PostTypeId="2" ParentId="16554" CreationDate="2014-04-15T20:53:32.233" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;For example, a sperm swims faster if it's carrying the genetic&#xA;  material that would result in a tall person&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and in the comments&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It seems to me that there would have to be some defined standard of a&#xA;  normal DNA that the sperm would check against to determine how&#xA;  &quot;broken&quot; it is, and I doubt there's something like that&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If some aspects of sperm cells indirectly connected with some parts of phenotype, so we can expect that result, but not because of sperm cell carries that noble phenotype gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA in sperm cell is packed and not expressing (not transcribed).&lt;br&gt;&#xA;Because DNA is packed and because test checks consuming energy, which sperm needs for another tasks - pretty wise to shut down checks, repairs.&lt;br&gt;&#xA;Also DNA is not like ZIP archive, where cell can check the check sum, to make shure it works witch &lt;em&gt;good DNA&lt;/em&gt;. Cell have difficulties working with information, if it needs to connect information results from distance sources. (Let say as example: if gene A have mutation A* and gene B have mutation B* then do X).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also there is big big difficulties with that mater: &lt;em&gt;some defined standard of a normal DNA&lt;/em&gt; - all DNA that leads to organism which is able to procreate, to survive - is good enough for nature. Thats Evolution spirit). And who can, who not - will be sorted out, later and with 100% accuracy.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For example, humans with mental retardation often have above average strength.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Our DNA actually consists from imperfections, which showed up long ago and became standard &lt;em&gt;de facto&lt;/em&gt;, some are compensated at the moment and are RFC(Request for Comments). This or another set of genes is a balanced system. Balance can be shifted and that will have some consequences, actually thats how another system is prepared for testing by Evolution factors. By shifting balance far enough, for making some things at extreme, we may expect that another things have to break. But strength is not because of mental retardation, or vice verse. (It may be connected, may be not; also I would not trow away, some ontogenesis matter in that case) They both are results, not cause. But there are some reasons to be connected, if you take look on apes behavior as example.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;just boxes that can swim&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Man it's a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26914/&quot; rel=&quot;nofollow&quot;&gt;Rocket&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6240" LastEditorUserId="6240" LastEditDate="2014-04-15T21:16:00.313" LastActivityDate="2014-04-15T21:16:00.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16576" PostTypeId="1" CreationDate="2014-04-15T21:53:13.643" Score="6" ViewCount="154" Body="&lt;p&gt;I actually have algae growing in water in a container. I was thinking if it was possible to filter the water so that all the small cells will be filtered out and only the bigger ones will remain to reproduce cells that tend to be bigger.&#xA;Is that possible? &#xA;What type of filter should I use?&lt;/p&gt;&#xA;" OwnerUserId="6352" LastActivityDate="2015-01-04T22:27:40.247" Title="Can I force evolution in a group of cells by removing all the smaller cells?" Tags="&lt;evolution&gt;&lt;cell-biology&gt;&lt;zoology&gt;&lt;natural-selection&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16577" PostTypeId="1" AcceptedAnswerId="16579" CreationDate="2014-04-15T22:14:51.190" Score="4" ViewCount="407" Body="&lt;p&gt;I was recently working on getting a statistical model of a DNA sequence. To do this I found that understanding evolution quantitatively seems to be quite important. I would really appreciate any book recommendations on the basics of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I come from an Electrical Engineering background and have a limited knowledge of evolution and biology.&lt;/p&gt;&#xA;" OwnerUserId="6353" LastEditorUserId="6353" LastEditDate="2014-04-15T22:21:32.557" LastActivityDate="2015-03-03T14:22:01.117" Title="Book recommendations for evolutionary models" Tags="&lt;evolution&gt;&lt;theoretical-biology&gt;&lt;book-recommendation&gt;&lt;molecular-evolution&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16578" PostTypeId="2" ParentId="16576" CreationDate="2014-04-15T22:24:50.417" Score="6" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes that would work in the condition that the trait you select for (size) is heritable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The kind of selection you would apply is called truncated selection because you fix a limit in size (depends on your filter) under which individuals do not survive and above which individuals survive and reproduce equally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The response to selection ($R$) is given by the breeder's equation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$R = h_N S$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $S$ is the selection you apply. In your case, $S$ is the difference between the mean size of the parent generations and the mean size of those you allow to reproduce in the parent generations. $h_N$ is the heritability (more info in additional info).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if you measure the mean size of your cells, filter them, measure their size again (or infer their size based on previous measurement and the size of you filter) and calculate the difference between the two measurements you get $S$. Then you let your filtered individuals to reproduce and you measure the size of their offspring which is $R$. By dividing $R$ by $S$ you get the heritability $h_N$. If you do not observe any difference in size between your two generations it means that the heritability is 0 ($\space h_N = 0\space$). Of course, you'll need a population that is composed of enough cells in order to have a good estimate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Additional info&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be a bit more accurate $h_N$ is the heritability in the narrow sense. It represents the part of variance in the population that has to be accounted to additive genetic variance. The word additive genetic variance might seem obscure. In other words&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$h_N = \frac{V_{Ga}}{V_{P}} = \frac{V_{Ga}}{V_{G}+V_{E}} =  \frac{V_{Ga}}{V_{Ga} + V_{Gd}+V_{E}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $V_{GA}$ is the additive genetic variance, $V_{GD}$ is the dominance genetic variance, $V_E$ is the variance due to environmental variance and $V_P$ is the total variance (phenotypic variance)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps. Do not hesitate to ask further question if something is unclear or if I missed one of your point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Filter&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The filter you need should allow you to discriminate the cells based on their size. Therefore, it should be relatively accurate. It is common to classify the phytoplankton based on their size, see &lt;a href=&quot;http://en.wikipedia.org/wiki/Plankton#Size_groups&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;. You should try different filters and see what filter allows a good discrimination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;EDIT&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assumed your cells were all of the same species. Is it the case? If you just sampled them from a lake and let them grow in a container then you very probably have various species. Therefore, you would select (based on their size) for species with your filter rather than selecting individuals within a species (based on their size again). It is kind of the same process anyway and the breeder's equation still holds.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-01-04T22:27:40.247" LastActivityDate="2015-01-04T22:27:40.247" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16579" PostTypeId="2" ParentId="16577" CreationDate="2014-04-15T22:49:49.633" Score="7" Body="&lt;p&gt;You either want a introductory book in evolutionary biology or a book that offers mathematical models of evolutionary processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my first class of evolutionary biology I had this textbook: &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0878931872&quot; rel=&quot;nofollow noreferrer&quot;&gt;Futuyama, Evolution&lt;/a&gt; I think it gives a good start to the field and offers a good overview of the difference subfields.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you think you already know enough about the concepts selection, genetic drift, molecular evolution, etc… and you want a book that provides mathematical formulations of evolution, then you might want to have a look into the field of population genetics. On &lt;a href=&quot;https://biology.stackexchange.com/questions/16470/book-recommendation-on-population-evolutionary-genetics/16474#16474&quot;&gt;this post&lt;/a&gt; you'll find some book-recommendations&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are particularly interested into molecular evolution, I'd suggest: &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0198567022&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yang, Computational molecular evolution&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe you are particularly interested into the statistical methodology used in DNA annotation or in phylogeny. Then…. I don't know! It's not quite my field!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-03-03T14:22:01.117" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16580" PostTypeId="2" ParentId="16470" CreationDate="2014-04-16T02:16:21.873" Score="20" Body="&lt;p&gt;@Remi.b's list is excellent, but it should also include &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0801880092&quot;&gt;Gillespie's Population Genetics: A Concise Guide&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1210" LastActivityDate="2014-04-16T02:16:21.873" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16582" PostTypeId="1" CreationDate="2014-04-16T06:14:08.377" Score="2" ViewCount="413" Body="&lt;p&gt;Why doesn't the avocado turn brown when its kept with its seed?&#xA;What does the seed release that slows down the oxidation process?&lt;/p&gt;&#xA;" OwnerUserId="6355" LastEditorUserId="43" LastEditDate="2014-05-17T02:20:04.730" LastActivityDate="2014-05-17T02:20:04.730" Title="Why doesn't the avocado turn brown when it is kept with its seed?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16583" PostTypeId="2" ParentId="15362" CreationDate="2014-04-16T06:29:38.257" Score="1" Body="&lt;p&gt;This is a very good question, and a very important topic in the healthcare and biological world.  It is something that everyone should consider, as the answer is not as self-evident as it may appear.  The responses here are excellent.  I would like to add a few things from a healthcare perspective.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.who.int/gpsc/clean_hands_protection/en/&quot; rel=&quot;nofollow noreferrer&quot;&gt;This is the WHO recommendation&lt;/a&gt; on how to wash your hands.  It is in agreement with the CDC recommendations. This includes use of antibacterial soaps.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for friction in handwashing is as Chris and WYSIWYG said: removal of oils, dirt, bacteria and other things accumulated in the crevasses of your skin and nails (including microbes and biological residues). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regular soap on its own is a surfactant; it is a molecule with a polar end (and a non-polar end.  It basically dissolves in both oils and waters.  It is perfect for removing oils and rinsing them off in water.  Detergents such as soaps are cell membrane disrupters, and as such, it is capable of rupturing cell membranes of many microbes on its own.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Shigeta is right-on with the FDA recommendations to not use antibacterial soaps.  They are completely unnecessary is most situations and actually do harm by putting selective pressure on bacteria strains to become stronger by killing off all but the most resistant ones, which then breed and overgrow.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In daily use, alcohol foams are a convenient way to sanitize if soap and water are unavailable, but it's often overused.  Soap and water are better in the daily environment, and always better before eating, because alcohol does not kill spores nor denature toxins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overuse of antibiotics in general is the reason why MRSA and other multi-drug resistant bacteria have emerged, and these are extremely dangerous because they are so difficult to treat.  We're struggling to catch up with antibiotics to kill the newly emerging strands.  There are cases I have seen where all efforts to treat an infection failed due to resistance.  So I guess I'm saying all this to emphasize that yeah, it's important to not go overboard on antibacterial cleansing :)  /end soapbox.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well, one more quick thing - I do want to add that healthcare settings are slightly different.  The use of antibacterial soap in hospitals is approved for the purpose of reducing the microbial load on skin between patients, to reduce transmission as much as possible.  Alcohol foams have been found to be comparable, but are insufficient in several cases (such as spores). (See the CDC for more info on alcohol foams: &lt;a href=&quot;http://www.cdc.gov/oralhealth/infectioncontrol/faq/hand.htm#a3&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.cdc.gov/oralhealth/infectioncontrol/faq/hand.htm#a3&lt;/a&gt;).&#xA;In daily use, alcohol foams are a convenient way to sanitize if soap and water are unavailable, but it's often overused.  Soap and water are better in the daily environment, and always better before eating, because alcohol does not kill spores nor denature toxins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;References for following information:  I personally have been involved in patient counseling discussions in clinic with a patient and an attending physician (a supervisory teaching doctor) discussing best practices in hygiene.  This includes two dermatologists, two Emergency physicians, an OB/Gyn physician, and a pediatrician - and all concur:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For general washing in the shower, unless you sweat a great deal or are exposed to dirt and chemicals, the majority of your exposed skin does not require extensive scrubbing to become clean.  In fact, scrubbing can irritate skin, worsen dry skin, or exacerbate conditions such as eczema.   Warm water, normal soap (or even better for sensitive skin / eczema, moisturizing body wash like Dove), and a soft washcloth are completely sufficient. If using a pouf or exfoliator, only apply light pressure, never aggressive. Armpits, groin, and feet do require more attention, but hard scrubbing is unnecessary.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly (and hopefully not TMI in this post), I learned from the OB/Gyn's patient counseling that it is unnecessary (and actually irritating to the mucous membranes) for women to use more than warm water to clean between the labia majora. I looked this up and found supporting information for this. Other genital surfaces should be washed well, but as mucous membranes, that area has a self-cleaning system of secretions.  This is similar to the strong recommendation for women not to use vaginal douching - it upsets the balance of natural bacteria (flora) in the vaginal canal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The WHO handwashing instructions:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/cUF62.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6314" LastEditorUserId="6314" LastEditDate="2014-04-16T06:36:25.917" LastActivityDate="2014-04-16T06:36:25.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16585" PostTypeId="2" ParentId="16582" CreationDate="2014-04-16T06:36:50.363" Score="3" Body="&lt;p&gt;This is actually only partly true: When you cut the avocado in half, only the part where the seed really sits stays green, while the surrounding cut area gets brown over time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Avocados turn brown because of an enzyme called polyphenol oxidase, which oxidizes the green contents of the avocado upon contact with oxygen. The seed blocks the access to oxygen, thats why it helps here (but only where it makes close contact). See &lt;a href=&quot;http://www.straightdope.com/columns/read/2210/does-leaving-the-avocado-pit-in-the-guacamole-keep-the-stuff-from-turning-brown&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; and this &lt;a href=&quot;http://www.livescience.com/33660-guacamole-avocado-pit-prevent-brown.html&quot; rel=&quot;nofollow&quot;&gt;links&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two ways of preventing the browning of cut avocados (besides avoiding oxygen contact): Use either lemon juice, which inhibits the enzyme (by chelating the metal ion from its active center) or keep it cooled to slow down the procession rate of the enzyme (which will only work for some time).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-16T06:36:50.363" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16586" PostTypeId="2" ParentId="16564" CreationDate="2014-04-16T07:04:08.823" Score="2" Body="&lt;p&gt;Creatine is an important energy source for body, especially for the muscles, so it is no wonder you can finde it there. I don't think it has a special role besides that. See the &lt;a href=&quot;http://en.wikipedia.org/wiki/Creatine&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; article for more information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For bilirubin this is different, this substance is a breakdown product of the heme metabolism (basically hemoglobine). It is not water soluble and needs to be conjugated to a carrier protein (albumin). In this way it is transported to the liver, where the glucuronyltransferase conjugates it to glucuronic acid. This step makes the bilirubin water soluble and it can be excreted from the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Newborns have a higher bilirubin level, since their glucuronyltransferase activity is at about 0.1% of that of adults. This can lead to the typical newborn jaundice. For more details about bilirubin, see &lt;a href=&quot;http://en.wikipedia.org/wiki/Bilirubin&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-16T07:04:08.823" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16589" PostTypeId="1" AcceptedAnswerId="16634" CreationDate="2014-04-16T07:43:02.990" Score="2" ViewCount="598" Body="&lt;p&gt;Many people on this site ask questions that directly or indirectly have to do with heritability in human.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do you know a list of estimates of heritability of various traits in humans? Or could you try to create such list?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That might be great to have various kind of traits, personality traits, life-history traits, morphological traits, …&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not necessarily asking for &lt;a href=&quot;http://en.wikipedia.org/wiki/Genome-wide_association_study&quot; rel=&quot;nofollow&quot;&gt;GWA&lt;/a&gt; studies that inform about what genes explain the observed variance (although that would be really great) but just some estimates of heritability and eventually information about the method used (parent-offspring regression, twins, ...) and which population was studied. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-04-16T11:46:09.587" LastActivityDate="2014-04-17T18:01:14.010" Title="List of heritability estimates in humans?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;genetics&gt;&lt;human-genetics&gt;&lt;human-genome&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16590" PostTypeId="1" AcceptedAnswerId="41115" CreationDate="2014-04-16T08:05:38.380" Score="9" ViewCount="333" Body="&lt;p&gt;More than 50 years after hormonal contraception for women was invented, a contraceptive pill for males is still not available. With the obvious major biological differences in mind, why does it appear more difficult to create a chemical contraceptive for males? What are the main challenges that must be overcome to create a viable, reliable and marketable contraceptive pill for men?&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2015-12-02T12:31:48.777" Title="What is the main challenge in creating a chemical male contraceptive?" Tags="&lt;human-biology&gt;&lt;reproductive-biology&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16592" PostTypeId="2" ParentId="16555" CreationDate="2014-04-16T08:55:12.553" Score="2" Body="&lt;p&gt;In the developing embryo you have the three germ layers: Endoderm, mesoderm and ectoderm. From these layers all cell lineages of the body develop and can be traced back through their differentiation and migration to this three layers.&#xA;Have a look on the image below, which illustrates this pretty nicely:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/R5VXU.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The figure is part of &lt;a href=&quot;http://pqdtopen.proquest.com/pqdtopen/doc/305016519.html?FMT=ABS&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; PhD thesis, which also seems worth reading when you are interested in this topic.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-16T08:55:12.553" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16593" PostTypeId="2" ParentId="16510" CreationDate="2014-04-16T09:13:59.273" Score="7" Body="&lt;p&gt;The dynamic-dominance hypothesis of handedness states that the essential factor that distinguishes dominant from nondominant arm performance is the facility governing the control of limb dynamics. Sainburg (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11807578&quot;&gt;1&lt;/a&gt;) writes that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It should be noted that dominant arm advantages do not apply to all&#xA;  tasks, or all aspects of tasks. Healey et al. (1986) examined an&#xA;  extensive range of tasks and found that four factors or groups of&#xA;  tasks accounted for 80% of the variance in hand preference among the&#xA;  110 subjects tested. Tasks that were almost exclusively associated&#xA;  with dominant arm use included activities requiring precision in&#xA;  interjoint coordination and trajectory formation. (...) In contrast,&#xA;  tasks that involved spatially orienting a body segment posture were&#xA;  more often performed with the nondominant arm. These tasks included&#xA;  posturing the hand to point toward a distant object, which is similar&#xA;  to other functional tasks such as holding a piece of paper that is&#xA;  being cut with scissors, or orienting the hand in space for catching a&#xA;  baseball. Such postural orientation tasks are less dependent on&#xA;  intersegmental dynamics, since the trajectory used to attain the&#xA;  posture is not critical for task success. The dynamic dominance&#xA;  hypothesis thus appears to account for the extent to which hand&#xA;  preferences for specific activities are lateralized.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This appears to be consistent with your experience.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-16T09:13:59.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16595" PostTypeId="2" ParentId="3645" CreationDate="2014-04-16T10:00:52.360" Score="14" Body="&lt;p&gt;Sneezing does not occur during REM sleep, due to REM atonia.(&lt;a href=&quot;http://scienceillustrated.com.au/blog/science/ask-us-can-humans-sneeze-while-sleeping/&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The coughing reflex is  also suppressed during sleep, but coughing may still occur occasionally during sleep. (&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/19823913&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2018-07-24T09:03:48.227" LastActivityDate="2018-07-24T09:03:48.227" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="16596" PostTypeId="1" CreationDate="2014-04-16T12:58:20.347" Score="3" ViewCount="2052" Body="&lt;p&gt;Why does methylation not occur in viral DNA? Can viral DNA undergo the process of methylation? If not then why does this process does not occur in viruses?&lt;/p&gt;&#xA;" OwnerUserId="6095" LastEditorUserId="5144" LastEditDate="2014-04-16T15:05:44.583" LastActivityDate="2017-09-28T12:57:17.860" Title="Why does methylation not occur in viral DNA?" Tags="&lt;molecular-biology&gt;&lt;virus&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16597" PostTypeId="2" ParentId="13711" CreationDate="2014-04-16T13:26:18.517" Score="5" Body="&lt;p&gt;There are regulatory mechanisms that may prevent moderate hypoglycemia to progress to a more severe state, however these mechanisms act before lack of conciousness sets in. The progression of hypoglycemia may depend on overall health and medical status and vary between healthy and diabetic persons, for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rosenthal et al. (&lt;a href=&quot;http://diabetes.diabetesjournals.org/content/50/7/1618.full&quot;&gt;1&lt;/a&gt;) write that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The brain is normally dependent on glucose for oxidative metabolism&#xA;  and function. Acute iatrogenic hypoglycemia, occurring as a result of&#xA;  insulin excess during the treatment of type 1 diabetes, can cause&#xA;  clinically significant cognitive impairment. In health, such&#xA;  hypoglycemic cognitive dysfunction does not occur. Endogenous&#xA;  counterregulatory mechanisms are activated in response to a small&#xA;  reduction in circulating glucose, preventing more profound&#xA;  hypoglycemia. In diabetes, the inability to reduce circulating insulin&#xA;  levels (1), the failure of glucagon responses (2), sometimes&#xA;  accompanied by defective autonomic and adrenergic responses (3), can&#xA;  allow plasma glucose levels to fall low enough to result in detectable&#xA;  disturbance of cognitive function, ranging from a subtle slowing of&#xA;  reaction times (3) to coma (4).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In short, the brain malfunctions due to lack of glucose (the sole energy source for the brain). Note that cognitive impairment and unconciousness can also occur in otherwise healthy persons, for example in the case of prolonged exercise combined with lack of nutrition. The exact cause of cortical dysfunction is not known:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Impairment of brain function is a recognized consequence of acute&#xA;  hypoglycemia. It is known that different brain functions have&#xA;  different susceptibilities to acute hypoglycemia; for example, the&#xA;  triggering of autonomic activation, a hypothalamic function, occurs in&#xA;  response to quite modest decrements in circulating glucose&#xA;  concentrations (5,6,7), whereas significant cortical dysfunction&#xA;  requires more profound glucose deprivation (3). Even within different&#xA;  cortical functions, there is variation in hypoglycemia susceptibility&#xA;  (26). The mechanisms of cortical dysfunction during hypoglycemia are&#xA;  not known.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-16T13:26:18.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16599" PostTypeId="2" ParentId="16596" CreationDate="2014-04-16T15:31:04.810" Score="4" Body="&lt;p&gt;Contrary to the question title, viral DNA can be methylated.  See for example Bonvicini et al. 2012. (&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0033316&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;) and Hoelzer et al. 2008 (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2396429/&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hoelzer et al. give a review of the presence and role of cytosine methylation in DNA viruses of animals:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To understand the impact of cytosine methylation on the viral life&#xA;  cycle and the evolution of base composition, the particularities of&#xA;  each virus will need to be considered. Differences will inevitably&#xA;  exist between actively replicating viral DNA and that which is&#xA;  integrated into the host genome. The type of viral persistence will&#xA;  also be of importance. The integration of adeno- or polyomavirus DNA&#xA;  into the host genome is usually a terminal process since the viruses&#xA;  cannot liberate their genomes and are therefore no longer infectious.&#xA;  The evolutionary roles of methylation in these cases will likely&#xA;  differ from those seen in other viruses, such as Herpesviruses, which&#xA;  can liberate their genome after periods of latency. But differences&#xA;  may also exist between large and small viruses—with many larger&#xA;  viruses encoding their own replication machinery and additional&#xA;  proteins which modify host cell processes and immune responses. The&#xA;  susceptibility of the viral genome to methylation and immune&#xA;  recognition will also be affected by other factors, such as the&#xA;  location of replication within the cell and the specific intracellular&#xA;  trafficking route.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Viral DNA methylation has mostly been studied in large DNA virii, and the extent of methylation may be related to repression of viral replication. Bonvicini et al. writes that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Epigenetic mechanisms, and in particular the impact of cytosine&#xA;  methylation at CpG dinucleotides on the viral life cycle have been&#xA;  mainly studied for viruses that can establish latency and undergo&#xA;  reactivation, such as viruses in the Herpesviridae family, or for&#xA;  viruses that can integrate their genome into the host genome such as&#xA;  Retroviridae or Papillomaviridae. In general, a correlation has been&#xA;  found between the extent of CpG dinucleotides methylation of viral&#xA;  genomes and viral quiescence [24]. Scarce information is on the&#xA;  contrary available on the possible occurrence and role of methylation&#xA;  for actively replicating viruses&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-16T15:31:04.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16600" PostTypeId="1" CreationDate="2014-04-16T16:09:30.203" Score="0" ViewCount="88" Body="&lt;p&gt;Eukaryotes have ER which manufactures plasma membrane of cells. How is prokaryotic plasma membrane made ? What is the pathway and which enzymes are involved ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-16T17:14:25.027" Title="How is bacterial plasma membrane made?" Tags="&lt;cell-biology&gt;&lt;bacteriology&gt;&lt;enzymes&gt;&lt;cell-membrane&gt;&lt;prokaryotes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16601" PostTypeId="2" ParentId="10184" CreationDate="2014-04-16T16:34:15.583" Score="2" Body="&lt;p&gt;I think any discussion of this question can benefit from a historical perspective. For a long time, it was in fact believed that proteins was the hereditary material. The Nature Scitable page on the discovery of DNA (&lt;a href=&quot;http://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;) starts with the following passage:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the first half of the twentieth century, Gregor Mendel's principles&#xA;  of genetic inheritance became widely accepted, but the chemical nature&#xA;  of the hereditary material remained unknown. Scientists did know that&#xA;  genes were located on chromosomes and that chromosomes consisted of&#xA;  DNA and proteins. At the time, however, proteins seemed to be a better&#xA;  choice for the genetic material, because chemical analyses had shown&#xA;  that proteins are more varied than DNA in their chemical composition,&#xA;  as well as in their physical properties.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;While perhaps easy to dismiss in hindsight, it is possible to understand the reasoning of the day. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology&quot; rel=&quot;nofollow&quot;&gt;&quot;central dogma&quot;&lt;/a&gt; of molecular biology, that genetic information flows from DNA to RNA to proteins was only described later, and explained how the production of complex proteins consisting of 20-odd amino acids can be directed by a polymer consisting of only four nucleotides. This allows great complexity and variety in phenotypes while maintaining simplicity of the genetic material. The central dogma also facilitates the seperation of the &lt;em&gt;use&lt;/em&gt; (through protein expression) and &lt;em&gt;storage&lt;/em&gt; (as DNA) of genetic material.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Watson and Crick noted in their &lt;a href=&quot;http://www.nature.com/nature/dna50/watsoncrick.pdf&quot; rel=&quot;nofollow&quot;&gt;famous paper&lt;/a&gt;, the double helix of DNA, when discovered, immediately suggested how the genetic material could be elegantly copied. While the more complex structure of proteins would likely require a more complex copying mechanism, the specification of amino acids through three-nucleotide codons in DNA allows the regularity of the DNA material to be retained for easy replication while allowing complex proteins to be produced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, even though DNA is the primary genetic material today, the situation may have been different at the time life first appeared. According to the &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_world_hypothesis&quot; rel=&quot;nofollow&quot;&gt;RNA world hypothesis&lt;/a&gt;, RNA may have been the original genetic material and that DNA is a variation of RNA, not the other way around as it is commonly seen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a fuller historical perspective, I recommend the book &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1107604664&quot; rel=&quot;nofollow&quot;&gt;&quot;What is Life?&quot;&lt;/a&gt; by Erwin Schrödinger, which was written before the discovery of DNA as the genetic material.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-16T16:34:15.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16602" PostTypeId="1" CreationDate="2014-04-16T16:49:01.543" Score="2" ViewCount="105" Body="&lt;p&gt;I've read that ebola is an effective killer in humans because it has the ability to interrupt dendritic cells from manufacturing proteins that cause the immune system to destroy the dendritic cells when they're infected. Do any other animal species have different kinds of dendritic cells that don't get thus interrupted by ebola?&lt;/p&gt;&#xA;" OwnerUserId="263" LastActivityDate="2014-04-16T16:57:52.487" Title="Do any nonhuman species have effective ebola immunity?" Tags="&lt;immunology&gt;&lt;pathology&gt;&lt;virology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16603" PostTypeId="2" ParentId="16602" CreationDate="2014-04-16T16:57:52.487" Score="1" Body="&lt;p&gt;While at least some other primates are suspectible to Ebola, pigs appear to be immune. From the WHO factsheet on Ebola (&lt;a href=&quot;http://www.who.int/mediacentre/factsheets/fs103/en/&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Although non-human primates have been a source of infection for&#xA;  humans, they are not thought to be the reservoir but rather an&#xA;  accidental host like human beings. Since 1994, Ebola outbreaks from&#xA;  the EBOV and TAFV species have been observed in chimpanzees and&#xA;  gorillas.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;RESTV has caused severe EVD outbreaks in macaque monkeys (Macaca&#xA;  fascicularis) farmed in Philippines and detected in monkeys imported&#xA;  into the USA in 1989, 1990 and 1996, and in monkeys imported to Italy&#xA;  from Philippines in 1992.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Since 2008, RESTV viruses have been detected during several outbreaks&#xA;  of a deadly disease in pigs in People’s Republic of China and&#xA;  Philippines. Asymptomatic infection in pigs has been reported and&#xA;  experimental inoculations have shown that RESTV cannot cause disease&#xA;  in pigs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-16T16:57:52.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16604" PostTypeId="2" ParentId="16600" CreationDate="2014-04-16T17:14:25.027" Score="1" Body="&lt;p&gt;The processes that occur at the ER membrane in eukaryotic cells take place directly at the bacterial plasma membrane. Phospholipids are synthesised and inserted at the plasma membrane, and there is a protein translocation apparatus for translocation of proteins into the periplasmic space and insertion of transmembrane proteins into the plasma membrane.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-04-16T17:14:25.027" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16605" PostTypeId="1" AcceptedAnswerId="16915" CreationDate="2014-04-16T18:46:04.473" Score="3" ViewCount="452" Body="&lt;p&gt;Lymphatic drainage occurs from many portions of the body:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To venous angle:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;head &lt;/li&gt;&#xA;&lt;li&gt;axillary lymph nodes&#xA;&lt;ul&gt;&#xA;&lt;li&gt;hands &lt;/li&gt;&#xA;&lt;li&gt;abdomen&#xA;&lt;ul&gt;&#xA;&lt;li&gt;legs (I think legs' drainage goes through abdomen)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The speed of the lymph drainage is different in each part of the body depending on the situation at hand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume you have tense muscles in the hand (biceps and trieps).&#xA;The lymphatic drainage there can be lowered and be the limiting factor in the system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think lowered lymphatic drainage in one part of the body causes more lymph goes to other parts of the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the negative results of too high lymphatic drainage in an organ?&lt;/strong&gt;&#xA;My intuition&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;edema&lt;/li&gt;&#xA;&lt;li&gt;hypertrophy in some cases (excess of nutrients)&lt;/li&gt;&#xA;&lt;li&gt;hypertension&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Negative results of too slow lymphatic drainage are the prolonged intoxication times of &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;biological, &lt;/li&gt;&#xA;&lt;li&gt;chemical and &lt;/li&gt;&#xA;&lt;li&gt;physical factors.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am trying to find any studies about the effective speed of lymphatic drainage.&#xA;I have an intuition that the lowest drainage of one section is the limiting factor in the whole system.&#xA;&lt;strong&gt;Is there any studies about how to quantify the speed of lymphatic drainage from one part of the body?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heart pumps (blood) and sucks (lymph).&#xA;So probably some cardiovascular study relates the pumping to the lymphatic drainage.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2015-01-28T08:36:44.493" Title="Speed of effective lymphatic drainage?" Tags="&lt;cardiology&gt;&lt;blood-circulation&gt;&lt;lymphatic-system&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16606" PostTypeId="1" CreationDate="2014-04-16T19:07:02.897" Score="0" ViewCount="476" Body="&lt;p&gt;Do nerve pills actually suppress the nervous system and how would that effect the Shingles virus which is known to activate under large amounts of stress?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2015-06-28T15:27:47.867" Title="Effect of nerve pills and relationship to Shingles" Tags="&lt;human-biology&gt;&lt;virus&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-06-28T15:39:50.377" ContentLicense="CC BY-SA 3.0" />
  <row Id="16607" PostTypeId="1" AcceptedAnswerId="16623" CreationDate="2014-04-16T19:18:22.647" Score="2" ViewCount="797" Body="&lt;p&gt;I want to know what's the approximate percentage of understood human DNA, as in, which part does what. I'm not asking for details, just the amount.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="6363" LastActivityDate="2014-04-17T07:03:34.560" Title="Percentage of understood human DNA" Tags="&lt;dna&gt;&lt;human-genome&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ClosedDate="2014-04-21T10:44:59.473" ContentLicense="CC BY-SA 3.0" />
  <row Id="16610" PostTypeId="1" CreationDate="2014-04-16T20:35:30.733" Score="-1" ViewCount="902" Body="&lt;p&gt;A plant breeder crossed two plants, one with red flowers, and the other with white flowers. Red is dominant. Calculate the phenotype and genotype ratios of the F2 generation of this cross. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this a monohybrid or dihybrid cross? &lt;/p&gt;&#xA;" OwnerUserId="6364" LastEditorUserId="86" LastEditDate="2014-04-17T11:51:25.403" LastActivityDate="2014-04-17T11:51:25.403" Title="Punnett square and hybrid cross" Tags="&lt;genetics&gt;&lt;cell-biology&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-04-17T16:17:33.237" ContentLicense="CC BY-SA 3.0" />
  <row Id="16611" PostTypeId="1" AcceptedAnswerId="16616" CreationDate="2014-04-16T22:47:19.550" Score="7" ViewCount="5163" Body="&lt;p&gt;I'm reading &lt;a href=&quot;http://www.jbioleng.org/content/6/1/9&quot; rel=&quot;nofollow noreferrer&quot;&gt;a paper&lt;/a&gt; where the authors constructed a toggle switch that uses bidirectional &lt;span class=&quot;math-container&quot;&gt;$P_R/P_{RM}$&lt;/span&gt; promoter found in the &lt;span class=&quot;math-container&quot;&gt;$\lambda$&lt;/span&gt; phage. There are 3 binding sites - &lt;span class=&quot;math-container&quot;&gt;$O_{R1}$&lt;/span&gt;, &lt;span class=&quot;math-container&quot;&gt;$O_{R2}$&lt;/span&gt;, &lt;span class=&quot;math-container&quot;&gt;$O_{R3}$&lt;/span&gt; - located between the two promoters. CI is expressed by &lt;span class=&quot;math-container&quot;&gt;$P_{RM}$&lt;/span&gt; and CI dimers bind to these binding sites:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/R3NZt.png&quot; alt=&quot;Bidirectional lambda phage promoters&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;What I don't get is that &lt;strong&gt;CI seems to function as both an activator and a repressor of &lt;span class=&quot;math-container&quot;&gt;$P_{RM}$&lt;/span&gt;&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;p&gt;First, my understanding was that &lt;span class=&quot;math-container&quot;&gt;$P_{RM}$&lt;/span&gt; is an inducible promoter activated by CI which also represses a constitutive promoter &lt;span class=&quot;math-container&quot;&gt;$P_R$&lt;/span&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;CI is a transcriptional activator of &lt;span class=&quot;math-container&quot;&gt;$P_{RM}$&lt;/span&gt;, thus producing positive feedback.&lt;/p&gt;&#xA;&lt;p&gt;CI preferentially binds to &lt;span class=&quot;math-container&quot;&gt;$O_{R1}$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$O_{R2}$&lt;/span&gt;, repressing the constitutive promoter, &lt;span class=&quot;math-container&quot;&gt;$P_R$&lt;/span&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However, it is also stated:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In high concentrations, CI binds to &lt;span class=&quot;math-container&quot;&gt;$O_{R3}$&lt;/span&gt; and acts as a repressor to &lt;span class=&quot;math-container&quot;&gt;$P_{RM}$&lt;/span&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This seems to suggest that the CI can function either as an activator or as a repressor depending on the binding site bound; specifically, CI dimer binding to &lt;span class=&quot;math-container&quot;&gt;$O_{R1}$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$O_{R2}$&lt;/span&gt; will repress &lt;span class=&quot;math-container&quot;&gt;$P_R$&lt;/span&gt; and at the same time activate &lt;span class=&quot;math-container&quot;&gt;$P_{RM}$&lt;/span&gt;, while CI dimer binding to &lt;span class=&quot;math-container&quot;&gt;$O_{R3}$&lt;/span&gt; will repress &lt;span class=&quot;math-container&quot;&gt;$P_{RM}$&lt;/span&gt;. Is this correct?&lt;/p&gt;&#xA;&lt;p&gt;I (a computer scientist by training) was always given the impression that a transcription factor is either inherently a repressor or an activator of a promoter, but this doesn't seem to be the case here. I would expect that e.g. CI would act as a repressor to &lt;span class=&quot;math-container&quot;&gt;$P_R$&lt;/span&gt; and an activator to &lt;span class=&quot;math-container&quot;&gt;$P_{RM}$&lt;/span&gt; regardless of the binding site. So why does CI binding to &lt;span class=&quot;math-container&quot;&gt;$O_{R2}$&lt;/span&gt; (and &lt;span class=&quot;math-container&quot;&gt;$O_{R1}$&lt;/span&gt; as well?) activate &lt;span class=&quot;math-container&quot;&gt;$P_{RM}$&lt;/span&gt;, while binding to &lt;span class=&quot;math-container&quot;&gt;$O_{R3}$&lt;/span&gt; represses it - why the inconsistency? Note that I'm primarily interested in this from the modeling perspective.&lt;/p&gt;&#xA;&lt;p&gt;What I also don't understand is whether or not &lt;span class=&quot;math-container&quot;&gt;$P_{RM}$&lt;/span&gt; promoter is inducible or constitutive (e.g. in the absence of bound transcription factors, how leaky is it)?&lt;/p&gt;&#xA;" OwnerUserId="3583" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-27T12:13:38.067" Title="How can CI repressor both activate and repress $P_{RM}$ promoter found in $\lambda$ phage?" Tags="&lt;molecular-biology&gt;&lt;gene-expression&gt;&lt;synthetic-biology&gt;&lt;gene-regulation&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16612" PostTypeId="2" ParentId="16576" CreationDate="2014-04-16T23:28:28.663" Score="1" Body="&lt;p&gt;I think one would not have a lot of success using a filter to do this, rather using a centrifugal gradient and comparing the fractions to a standard I think would be preferable. Nitrocellulose filters are made with precision but not very astounding accuracy which is the main reason they are commonly used at set sizes (like 0.2 and 0.4 microns) and not often in between. Good question though&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-04-16T23:28:28.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16613" PostTypeId="2" ParentId="16611" CreationDate="2014-04-17T01:57:40.037" Score="5" Body="&lt;p&gt;I'm tempted to say, &quot;It's complicated.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CI does indeed act as both a repressor and activator. Transcription regulation in the lambda bacteriophage is quite complex for such a small system, so some confusion is understandable. Lewis et al. gives a rough description in a relatively recent paper (&lt;a href=&quot;http://www.pnas.org/content/early/2011/08/18/1111221108.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The CI protein autoregulates its synthesis. At low cellular CI concentration, CI enhances its own synthesis from PRM; when high, CI&#xA;  represses PRM (1, 8, 9). It was originally believed that both positive&#xA;  and negative autoregulations are achieved exclusively by the action of&#xA;  CI dimers at the PRM-OR-PR sequence of the phage genome (1, 10) (Fig.&#xA;  1A), based on the following observations. (i) There is a hierarchy of&#xA;  intrinsic binding affinities of a CI dimer to individual operators&#xA;  sites: OR1 &gt; OR2 &gt; OR3 (11–17); (ii) CI bound to the intrinsically&#xA;  weak OR2 site is strengthened by cooperative interactions with CI&#xA;  bound to the stronger adjacent OR1 site, and the ensemble of two CI&#xA;  dimers at the OR1 ∼ OR2 sites represses PR and activates PRM (13, 16)&#xA;  (Fig. 1A); (iii) at high CI concentrations, a CI dimer can bind to the&#xA;  weakest operator site, OR3, repressing PRM (1, 2) (Fig. 1C).&#xA;  Incidentally, a second pair of CI dimers binds cooperatively to OL1 ∼&#xA;  OL2, and represses PL (7).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;CI binding affects transcription of Lambda phage DNA through several mechanisms, including DNA looping between the OR operator sites at the Prm/Pr promoters and OL operator sites at the Pl promoter. The behaviour of an engineered transcription system derived from Lambda phage thus depends on whether the possibility of DNA looping between these sites are retained.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The discussion section gives addditional exposition:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our study confirmed several predictions of previous investigators&#xA;  discussed above about the mechanism of autoactivation and&#xA;  autorepression of PRM by measuring in vitro transcription on&#xA;  supercoiled DNA templates containing different combinations of&#xA;  operator mutations. Our transcription data support the model that&#xA;  autoactivation requires CI binding to OR2, and that activation is&#xA;  stimulated by cooperative dimer–dimer and tetramer– tetramer&#xA;  interactions between CI molecules at OR2 and those bound to other&#xA;  operator subsites. First, cooperative interactions of CI not only&#xA;  occur between OR1 and OR2 in cis, as reported previously, but also&#xA;  between OR1 ∼ OR2 and OL1 ∼ OL2 in trans, resulting in individual site&#xA;  occupancies at lower CI concentrations as judged by their effects on&#xA;  PRM activation. The trans-cooperativity by octamer formation requires&#xA;  adjacent CI binding sites between OR1 ∼ OR2∕OL1 ∼ OL2 or OR1 ∼ OR2∕OL2&#xA;  ∼ OL3 and not OR1 ∼ OR2 and OL1 ∼ OL3 (Fig. S3 F and J). Similar&#xA;  trans-cooperativity between OR3 and OL3 is inferred from PRM&#xA;  repression at lower CI concentrations. Cooperative interactions lead&#xA;  to DNA looping when they occur between CI at OL and OR sites. PRM is&#xA;  autorepressed by the binding of CI to OR3 as reported previously&#xA;  (1–3), and this is stimulated by dimer–dimer and tetramer–tetramer&#xA;  interactions that occur through DNA looping. Our results are in&#xA;  agreement with Revet et al. (18) that looping per se strengthens the&#xA;  binding of CI to the suboperators (Fig. 5). Our work provided&#xA;  quantitative evaluation of the contribution of each operator to&#xA;  autoregulation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Phew!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you wish to accurately model the system described by Huang et al., I would look very closely at the circuit sequence and determine which parts of the lambda phage system are actually present. They may not have taken into account the latest knowledge about regulation of the Pr and Prm promoters when discussing their system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On to the second question: When isolated and with no CI present, the Prm promoter may be used as a constitutive promoter (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564261/&quot; rel=&quot;noreferrer&quot;&gt;2&lt;/a&gt;). Under such conditions, the Prm promoter showed similar rates of transcription as the constitutive promoter ptet.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-17T01:57:40.037" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16614" PostTypeId="1" AcceptedAnswerId="16618" CreationDate="2014-04-17T02:05:18.067" Score="0" ViewCount="2347" Body="&lt;p&gt;In the mollusks section, the powerpoint mentioned that gastropods and bivalves have an &lt;em&gt;open circulatory system&lt;/em&gt;. According to the note, this means that the blood does not travel in vessels. How, then, does blood move? Does that mean that these organisms are simple enough to be able to survive by just pumping blood straight out into the body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this type of circulatory system work?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;evamvid&lt;/p&gt;&#xA;" OwnerUserId="5466" LastActivityDate="2014-04-17T03:33:31.150" Title="In an open circulatory system, how is blood moved?" Tags="&lt;zoology&gt;&lt;cardiology&gt;&lt;blood-circulation&gt;&lt;circulatory-system&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16615" PostTypeId="2" ParentId="16606" CreationDate="2014-04-17T02:53:06.837" Score="1" Body="&lt;p&gt;I gather you are talking about anti-axiety drugs (&lt;a href=&quot;http://en.wikipedia.org/wiki/Anxiolytic&quot; rel=&quot;nofollow&quot;&gt;anxiolytics&lt;/a&gt;). &lt;a href=&quot;http://en.wikipedia.org/wiki/Benzodiazepine&quot; rel=&quot;nofollow&quot;&gt;Benzodiazepines&lt;/a&gt; is one of the major groups of anxiolytics, and includes Xanax. Benzodiazepines are &lt;a href=&quot;http://en.wikipedia.org/wiki/Central_nervous_system_depressants&quot; rel=&quot;nofollow&quot;&gt;central nervous depressants&lt;/a&gt;, meaning that they reduce the activity of &lt;a href=&quot;http://en.wikipedia.org/wiki/Neurotransmitter&quot; rel=&quot;nofollow&quot;&gt;neurotransmitters&lt;/a&gt; in the brain. They do this by binding to the GABA-A receptor and enhancing the effect of the inhibitory neurotransmitter &lt;a href=&quot;http://en.wikipedia.org/wiki/Gamma-Aminobutyric_acid&quot; rel=&quot;nofollow&quot;&gt;GABA&lt;/a&gt; when it binds to the same receptor. The binding of GABA to a GABA receptor on a neuron causes hyperpolarization of the neuron by ion flow through the cellular membrane and decreases the chance of an &lt;a href=&quot;http://en.wikipedia.org/wiki/Action_potential&quot; rel=&quot;nofollow&quot;&gt;action potential&lt;/a&gt;. So yes, nerve pills act by supressing the nervous system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your question about interaction with Shingles, I think that's considered off-topic under the personal medical questions policy.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-17T02:53:06.837" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16616" PostTypeId="2" ParentId="16611" CreationDate="2014-04-17T02:53:21.120" Score="6" Body="&lt;p&gt;There's no rule that says a transcription factor must be either a repressor or an activator. The lambda repressor (CI) is in fact a repressor and activator of transcription, depending on where it is bound and to what promoter you are referring to. I know your question isn't directly about lambda phage, but I think this mechanism may be best explained in the context of where it was first invented: nature. So, I will try to briefly explain how the lambda repressor's dual role allows regulation of its own expression and controls lysogenic induction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cI gene is under the control of the PRM promoter. The PRM promoter is weak because the sigma factor of RNA polymerase (RNAP) holoenzyme has low affinity for it. Binding of RNAP to PRM, and thus transcription from there, at a reasonable level requires an activator. There is another protein involved in this process as well, called Cro, that can also bind the OR operators. The cro gene is under the control of the PR promoter. PRM is not a constitutive promoter because it requires an activator. I have heard PR called constitutive because it is a strong promoter and can bind RNAP without an activator. But, at the same time, it is under the control of the lambda repressor. I suppose it depends on which definition of 'constitutive promoter' you use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The OR operators are not identical and thus CI and Cro bind them with different affinities: CI has the highest affinity for OR1, followed distantly by OR2 and OR3, while Cro binds OR3 with highest affinity. Binding (of any two molecules) is dependent on both their affinity to each other as well as their effective concentration. At lower concentrations, CI can only bind OR1 and OR2 cooperatively. That is, each lambda repressor dimer binds to another, forming a tetramer, with one half binding OR1 and the other binding OR2. Binding both operators as tetramer allows for a stronger interaction. At higher concentrations, CI can bind OR3. Furthermore, OR1 and OR2 are located in the PR promoter, while OR3 is located in the PRM promoter.*&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most lambda genes are under the control, directly or indirectly, of the PR and PL promoters (PL is similar to PR, but the promoter itself is not directly involved in cI regulation). When lambda exists as a prophage, its DNA is integrated into the host genome and most of its gene expression is repressed. This requires CI repression of PL and PR. When the viral DNA is first integrated, there is no CI in the cell (because it is a phage gene). Expression of cI is initially dependent on a different promoter (PRE), but I won't get into this here. Once CI concentration is high enough, it can bind to OR1 and OR2 as a tetramer. Binding here physically blocks the PR promoter and prevents expression of cro (CI acts as a repressor of PR here). It also interacts with RNAP (actually the sigma factor) and facilitates is binding to the PRM promoter, which leads to further cI expression. This process is commonly called recruitment: since CI is bound tightly to the DNA and has some affinity for RNAP, it can create a stronger interaction between the DNA and the RNAP-CI complex. Simply put, it induces the PRM promoter and is thus functioning as an activator of cI transcription. As CI concentration increases, it will bind OR3 more (which is located in the PRM promoter) and repress the PRM promoter by physically blocking RNAP from binding. In these ways, cI can autoregulate its expression level, both positively and negatively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the lysogen is in some kind of stressful condition, normal host processes will result in proteolysis of CI and its DNA/sigma binding domain is cleaved from the dimer- and tetramerization domains. This means that CI can no longer oligomerize and is no longer able to bind cooperatively to OR1 and OR2. The result is loss of PRM activation (leading to vastly reduced cI expression) and also a loss of PR repression (leading to cro expression). Cro can then bind OR3 and represses PRM. Lack of PR repression also allows expression of early phage genes (which are under the control of PR).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that a similar situation occurs at the PL promoter region, and binding of CI to both OR and OL as well as CI octomerization is important in prophage regulation, but that seems even further out of the scope of your question. Hopefully you can see how he lambda &quot;repressor&quot; actually functions as both a repressor and activator of transcription. If this kind of stuff interests you, I highly recommend a textbook called Molecular Biology of the Gene by Watson et al.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*See comments. Upon further research, the PRM and PR promoters both overlap OR2 (Autoregulation and Function of a Repressor in Bacteriophage Lambda, Ptashne et al.), as the diagram in the OP shows. It appears that the -35 region of both PRM and PR overlap OR2 by 2 and 3 base pairs, respectively. That led me to wonder that if CI binds to OR2, which is in PRM, wouldn't it physically inhibit RNAP binding and thus repress transcription? Well it appears that CI interacts with the same region of sigma that is responsible for binding the -35 region of PRM (Amino acid substitutions in the -35 recognition motif of sigma 70 that result in defects in phage lambda repressor-stimulated transcription, Kuldell and Hochschild). So instead of blocking sigma binding here, it enhances it.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-04-18T02:17:33.597" LastActivityDate="2014-04-18T02:17:33.597" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16618" PostTypeId="2" ParentId="16614" CreationDate="2014-04-17T03:33:31.150" Score="3" Body="&lt;p&gt;In a closed circulatory system, all of the blood stays within blood vessels or the heart itself. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Organisms that have open circulatory systems, such as arthropods, have hemolymph (a fluid that is essentially a mixture of blood and interstitial fluid). The hemolymph actually does travel in vessels for a very short amount of time, as it is leaving the heart. After this, it goes to the body cavities of the animal and directly bathes the tissues in the fluid in order to deliver oxygen, nutrients, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hemolymph moves throughout the body when the animal moves. Also, when the heart relaxes, hemolymph is drawn back toward the heart through ostia, or open-ended pores. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to answer your question, yes, these animals can survive just by pumping hemolymph straight into the body. This is only effective because their body cavities are very small. In humans, an open circulatory system would never work because it would require an enormous amount of work to pump and circulate blood throughout our entire body cavity. &lt;/p&gt;&#xA;" OwnerUserId="6367" LastActivityDate="2014-04-17T03:33:31.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16620" PostTypeId="1" AcceptedAnswerId="16624" CreationDate="2014-04-17T04:22:05.477" Score="7" ViewCount="468" Body="&lt;p&gt;A smallish insect hive has been forming on the grill of my balcony in the last month or two, and I wanted to know should I be worried or can I just let it be. Its 13th floor in Singapore, if the height helps in ID. So far they have not been very aggressive, and have not bothered us even if we get within few feet of it, but want to know if that can change in horror movie style..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find the pictures below, both are pretty much the same, but with some flash tweaking. For a size estimate, they appear to be between half and 1 cm long, and the distance between the bars of the grill is about 12 cm or so. Are they some kind of bees? Would they leave eventually or is this a long term thing. Also, the length of the hive appears to be growing at ~ 1-2 cm per week.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/Q7a0b.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/Q7a0b.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;(crop of larger picture found below)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/aIOs1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mhrCW.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6368" LastEditorUserId="3624" LastEditDate="2016-06-16T08:05:30.730" LastActivityDate="2017-11-28T10:24:17.437" Title="Could someone Identify this Insect Hive on my Balcony Grill" Tags="&lt;species-identification&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16621" PostTypeId="1" CreationDate="2014-04-17T04:37:47.187" Score="17" ViewCount="2859" Body="&lt;p&gt;I'm not sure if this is the right place for this but...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for a list of computationally &quot;hard&quot; problems such that if a problem from this list could be solved effectively, it would be (significantly, or otherwise) beneficial in some form or another to the biology community.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some examples I have found (or atleast were tagged as &quot;np-hard&quot; problems):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Multiple sequence alignment problem&#xA;Protein threading / design problem&#xA;Map / sequence assembly problem&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The list does not have to be extensive, but hopefully more than a few.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Also, I couldn't think of any more tags to add so feel free to help out there as well.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note:&#xA;Same question at biostars: &lt;a href=&quot;https://www.biostars.org/p/98112/&quot;&gt;https://www.biostars.org/p/98112/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6369" LastEditorUserId="6369" LastEditDate="2014-05-17T18:08:45.183" LastActivityDate="2019-07-29T18:55:05.930" Title="List of np-hard problems in biology/bioinformatics" Tags="&lt;bioinformatics&gt;" AnswerCount="3" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16622" PostTypeId="2" ParentId="16610" CreationDate="2014-04-17T06:39:47.397" Score="3" Body="&lt;p&gt;Unfortunately, that isn't a very well-written problem, but I think I can help. If we assume simple Mendelian genetics, this would be a monohybrid cross, as you're only examining one trait (flower color).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You have a pure-breeding white flower and a pure-breeding red flower. These make up the P (parental) generation. Their offspring will be the F1 (first filial) generation. A cross of two plants from the F1 generation produces the F2 (second filial) generation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since each P-generation plant in the has only one possible allele to give, each of the F1 plants will inherit one red and one white allele. Because red is dominant, all F1 plants's phenotypes will be red.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you cross two F1 plants, each has a 50% chance to pass on either the red or the white allele.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using Punnett Squares:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/N0uX6.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6371" LastActivityDate="2014-04-17T06:39:47.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16623" PostTypeId="2" ParentId="16607" CreationDate="2014-04-17T07:03:34.560" Score="3" Body="&lt;p&gt;The devil is in the details, and therefore we cannot just state that we have understood X% of the DNA. We know e.g. that 2% of the human DNA encode proteins. And for a good number of proteins we know what they do. So you might know that a particular codon AGT &lt;a href=&quot;https://en.wikipedia.org/wiki/DNA_codon_table&quot; rel=&quot;nofollow&quot;&gt;encodes&lt;/a&gt; a serine residue in a protein, which could have a catalytic activity. Or it has a structural activity. Or we are not sure what it does. Sometimes &lt;a href=&quot;http://www.bacteriatobonobos.com/1/post/2013/12/go-home-pr-team-youre-drunk.html&quot; rel=&quot;nofollow&quot;&gt;protein-coding and regulatory sequences overlap&lt;/a&gt;. So even if we first understood the protein-coding function, there was still the regulatory function to be discovered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The upshot is that there are multiple levels of understanding, and big controversies of what they actually imply (see e.g. &lt;a href=&quot;http://evmedreview.com/?p=1644&quot; rel=&quot;nofollow&quot;&gt;the ENCODE saga&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2014-04-17T07:03:34.560" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16624" PostTypeId="2" ParentId="16620" CreationDate="2014-04-17T11:34:55.493" Score="11" Body="&lt;p&gt;These are certainly &lt;a href=&quot;https://en.wikipedia.org/wiki/Paper_wasp&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper wasps&lt;/a&gt; (Vespidae) building their paper nest. Looks like a species of &lt;a href=&quot;http://www.vespa-bicolor.net/main/vespid/ropalidia.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ropalidia&lt;/a&gt;, which are known from Singapore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know little about Ropalidia, it seems to be rather small and probably harmless, but our larger European wasps can sting and bite and are sometimes quite aggressive (this refers first of all to &lt;em&gt;Vespula germanica&lt;/em&gt;).&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2017-11-28T10:24:17.437" LastActivityDate="2017-11-28T10:24:17.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16625" PostTypeId="1" AcceptedAnswerId="16630" CreationDate="2014-04-17T12:48:57.073" Score="4" ViewCount="106" Body="&lt;p&gt;If an individual has a new chromosome, which is very unlikely to happen, he will not have any luck in finding a sexual partner with this same trait. How will the offspring inherit this trait. And given that extra/fewer chromosomes are often undesirable traits (e.g. Turner Syndrome) how can it propagate?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume that humans and rats have different number of chromosomes, so a common ancestor must give a lineage where some individuals had a different number of chromosomes than their parents.&lt;/p&gt;&#xA;" OwnerUserId="6372" LastActivityDate="2014-04-17T16:19:41.317" Title="How are new chromosomes replicated into the next generation via sexual reproduction?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16626" PostTypeId="1" AcceptedAnswerId="16628" CreationDate="2014-04-17T14:54:00.300" Score="9" ViewCount="1032" Body="&lt;p&gt;It occurred to me (while urinating) that this would seem to be selected against because water is a scarce resource.   Why are we constantly losing water we don't need to through urination?   What is it about the chemistry of urine and the waste products eliminated that make urination necessary as opposed to eliminating them through defecation and recovering the water on the way out?&lt;/p&gt;&#xA;" OwnerUserId="6374" LastActivityDate="2019-03-28T21:36:59.753" Title="Why haven't land animals evolved beyond urination?" Tags="&lt;evolution&gt;&lt;mammals&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16627" PostTypeId="1" AcceptedAnswerId="16678" CreationDate="2014-04-17T15:16:36.637" Score="1" ViewCount="191" Body="&lt;p&gt;Consider $m$ loci with heterozygote advantage (overdominance) such that the fitness of the two homozygotes is $1-\frac{s}{2}$ and the fitness of the heterozygotes is $1+\frac{s}{2}$, where $s&amp;gt;0$. We'll assume that the fitness of an individual is given by the multiplication of the fitness component on each locus. In consequence, the fitness of the best possible genotype is given by $\left(1+\frac{s}{2}\right)^m$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0387201912&quot; rel=&quot;nofollow&quot;&gt;this book&lt;/a&gt;, an individual is heterozygote at $j$ of these $m$ loci with probability&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$${m\choose j}\left(\frac{1}{2}\right)^m$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and the equilibrium population mean fitness $\hat w$ is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\hat w = \sum_{j=0}^m {m\choose j}\left(\frac{1}{2}\right)^m  \left(1+\frac{s}{2}\right)^j  \left(1-\frac{s}{2}\right)^{m-j} = 1$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I don't understand any of these two equations! Can you help me to understand how they have been calculated?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;For the moment I just enjoyed proving that $\hat w = 1$. We can reformulate $\hat w$ as&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\hat w = \left(\frac{1}{2}\right)^m  \sum_{j=0}^m {m\choose j} \left(1+\frac{s}{2}\right)^j  \left(1-\frac{s}{2}\right)^{m-j} = 1$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;,then using the &lt;a href=&quot;http://en.wikipedia.org/wiki/Binomial_theorem&quot; rel=&quot;nofollow&quot;&gt;binomial identity&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ \hat w = \left(\frac{1}{2}\right)^m \left(\left(1+\frac{s}{2}\right) + \left(1-\frac{s}{2}\right)\right)^{\space m}$$&#xA;$$\hat w = \left(\frac{1}{2}\right)^m 2^m$$&#xA;$$ \hat w = 1 $$&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-04-25T12:34:16.020" Title="Heterozygosity and overdominance" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;population-biology&gt;&lt;population-dynamics&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16628" PostTypeId="2" ParentId="16626" CreationDate="2014-04-17T15:48:07.190" Score="15" Body="&lt;p&gt;It is probably true that toilets and other resting-ish area are always a great place to think about biology, I agree &lt;span class=&quot;math-container&quot;&gt;$\ddot \smile$&lt;/span&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why do we urinate?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, urine contains the waste from our blood while defecation is just the stuff that we haven't digested. Kidneys are the organs responsible for draining wastes (mostly nitrogen-containing, or nitrogenous, wastes) from our blood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Trade-off: energy cost vs. water loss&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You're correct that the loss of water through urination is a considerable cost for an organism (especially those living in dry environments). But the amount of water used to excrete nitrogenous wastes is negatively correlated with the energy it costs to perform this excretion. In other words, there is a trade-off between water and energy loss during nitrogen excretion. Also, the question of toxicity is important.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Three ways to excrete nitrogenous wastes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Animals basically have three choices to excrete nitrogenous wastes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Uric acid (excreted by uricotelic organisms)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Solid (crystal) with low water solubility&lt;/li&gt;&#xA;&lt;li&gt;Low toxicity&lt;/li&gt;&#xA;&lt;li&gt;Little water is needed&lt;/li&gt;&#xA;&lt;li&gt;Lots of energy is needed&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Ammonia (excreted by aminotelic organisms)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Highly soluble in water&lt;/li&gt;&#xA;&lt;li&gt;High toxicity&lt;/li&gt;&#xA;&lt;li&gt;Lots of water is needed to dilute it because of the toxicity&lt;/li&gt;&#xA;&lt;li&gt;Not much energy is needed&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Urea (excreted by ureotelic organisms)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Solid but highly soluble in water&lt;/li&gt;&#xA;&lt;li&gt;&quot;medium&quot; amount of water is needed&lt;/li&gt;&#xA;&lt;li&gt;&quot;medium&quot; toxicity&lt;/li&gt;&#xA;&lt;li&gt;&quot;medium&quot; amount of energy is needed&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What method is most beneficial for a given individual?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The amount of energy and the availability of water are very important aspects to understand whether a species is ureotelic, aminotelic or uricotelic. Another developmental constraint must be considered too. For example, birds are uricotelic (uric acid) probably because during the development of the embryo the wastes cannot be excreted outside the egg and therefore, excreting uric acid allows to greatly decrease the toxicity of the embryo's environment. In short, we must consider&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Water availability&lt;/li&gt;&#xA;&lt;li&gt;energy loss&lt;/li&gt;&#xA;&lt;li&gt;developmental constraints&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note&lt;/strong&gt;: This domain is not at all my field of study and I have no reference, typically for what concerns the toxicity, water amount and energy amount. One should not take my words for granted! &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-28T21:36:59.753" LastActivityDate="2019-03-28T21:36:59.753" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="16629" PostTypeId="1" CreationDate="2014-04-17T16:05:20.010" Score="1" ViewCount="147" Body="&lt;p&gt;By this I mean in cases where tandem exons are introduced by &lt;a href=&quot;https://en.wikipedia.org/wiki/Replication_slippage&quot; rel=&quot;nofollow&quot;&gt;replication slippage&lt;/a&gt; how would a DNA polymerase by chance duplicate an entire exon cleanly (i.e. from exact start to exact end) when it doesn't even know what an exon is?&lt;/p&gt;&#xA;" OwnerUserId="1241" LastActivityDate="2014-04-21T16:37:12.407" Title="How do exon tandem exon duplications occur in the genome?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16630" PostTypeId="2" ParentId="16625" CreationDate="2014-04-17T16:06:47.660" Score="1" Body="&lt;p&gt;You are right that a person with an abnormal number of chromosomes will be unlikely to find an &quot;equal&quot; partner to mate with. This does not prevent a chromosome aberration from spreading though, and it is not necessary that the mutation is initially beneficial for it to spread. While it is true that many chromosomal aberrations may be detrimental and cause various syndromes, a chromosome split or multiplication may also be netural except for the matter of reproduction. A change in chromsome number will not be inherited deterministically, but can give rise to various new permutations in the offspring due to the mechanics of chromosome segregation during meiosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find a good explanation at Scienceblogs.com: &lt;a href=&quot;http://scienceblogs.com/pharyngula/2008/04/21/basics-how-can-chromosome-numb/&quot; rel=&quot;nofollow&quot;&gt;http://scienceblogs.com/pharyngula/2008/04/21/basics-how-can-chromosome-numb/&lt;/a&gt; :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The net result [of a chromosome split] is that although this&#xA;  individual is fine and healthy, a significant number of his or her&#xA;  gametes may carry serious chromosomal errors, which means they may&#xA;  have reduced fertility. They aren’t sterile, though; some of their&#xA;  gametes will have the full complement of genes, and can similarly&#xA;  produce new healthy individuals who will probably have fertility&#xA;  problems. (...)&#xA;  So our two chromosome individual will have a reduced fertility as long&#xA;  as he or she is breeding with the normal one chromosome organisms, but&#xA;  those split chromosomes can continue to spread through the population.&#xA;  They are not certain to spread — they’re more likely to eventually go&#xA;  extinct — but by chance alone there can be continued propagation of&#xA;  the two chromosome variant. Which leads to another misconception in&#xA;  the question: something doesn’t have to provide a benefit to spread&#xA;  through a population! Chance alone can do it. We don’t have to argue&#xA;  for a benefit of chromosome fission at all in order for it to happen.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-04-17T16:19:41.317" LastActivityDate="2014-04-17T16:19:41.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16631" PostTypeId="1" AcceptedAnswerId="16632" CreationDate="2014-04-17T16:09:02.220" Score="1" ViewCount="38" Body="&lt;p&gt;I was just wondering wether it would be possible to detect if the body is in a &quot;fasting&quot; state, via lasers attached to the body. If it is possible, what sort of laser would be needed?&lt;/p&gt;&#xA;" OwnerUserId="6376" LastActivityDate="2014-04-17T16:40:42.663" Title="Detecting a Fasting State in the Body via Lasers" Tags="&lt;hematology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16632" PostTypeId="2" ParentId="16631" CreationDate="2014-04-17T16:30:34.277" Score="3" Body="&lt;p&gt;If by a fasting state, you mean blood glucose levels, researchers seem to think it is feasible. See for example Pleitez et al. (&lt;a href=&quot;http://scitation.aip.org/content/aip/journal/rsi/84/8/10.1063/1.4816723&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;) and Guo et al. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3493219/&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;). Their designs both utilize infrared IR laser light to measure glucose levels in the skin.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-04-17T16:40:42.663" LastActivityDate="2014-04-17T16:40:42.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16633" PostTypeId="2" ParentId="16570" CreationDate="2014-04-17T17:53:06.373" Score="2" Body="&lt;p&gt;The TCGA Project has been collecting primary tumors and matched normals per patient per cancer indication and has been exome (WXS) profiling those samples, and genome (WGS) profiling a subset of them. In those cases, the primary tumor is tissue collected from the primary tumor and the matched normal is usually a blood samples, but could be derived from a buccal swab or some other source. As you can imagine, it would make less sense in terms of expression to assay matched control that derives from another tissue type such as blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the expression data, the majority of the data comes from RNA-Seq and array-based profiling of the primary tumor data, and in some cases where adjacent normal tissue was collected and submitted, the TCGA has also profiled those samples. These are probably what you are seeing with your TN filter, and generally why you are having trouble finding equivalent amounts of matched normals as compared to primary tumor samples for the expression projects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incidentally, the company I work for has recently launched a free genomics data portal for the research community called GeenPool Reference. As part of it, we have deposited all of the publicly available TCGA RNA-Seq. The data along with all the associated clinical metadata is readily available for navigating and data mining. You'll easily be able to figure out the quantity of samples, and their matched pairs. If you're interested, you can take a look at the data projects available in GenePool Reference here: &lt;a href=&quot;http://www.stationxinc.com/reference-library&quot; rel=&quot;nofollow&quot;&gt;http://www.stationxinc.com/reference-library&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;~Sandeep&lt;/p&gt;&#xA;" OwnerUserId="6378" LastActivityDate="2014-04-17T17:53:06.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16634" PostTypeId="2" ParentId="16589" CreationDate="2014-04-17T18:01:14.010" Score="3" Body="&lt;p&gt;You may consider consulting the &lt;a href=&quot;http://tga.nig.ac.jp/h2db/&quot; rel=&quot;nofollow&quot;&gt;H2DB&lt;/a&gt; database. The database is quite new, so the number of heritability estimates is not very high at the moment (currently 225 estimates for human, 838 estimates in total), but it's a start. The database is described in a paper by Kaminuma et al.(&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23193255&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-17T18:01:14.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16635" PostTypeId="1" CreationDate="2014-04-17T18:10:57.333" Score="4" ViewCount="1308" Body="&lt;p&gt;After thinking about it, I'm confused by what the reaction barrier of an enzyme actually means.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine a reactor containing enzyme and substrate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the enzyme in the reactor has a reaction barrier of 15 kcal/mol, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) then when 1 mole of product has formed, that means 15 kcal have been consumed, independent of how much enzyme is present in the reactor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) then when 1 mole of enzyme is present in the reactor and 1 mole of product is formed, 15 kcal have been consumed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it option a), b) or otherwise?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Let us imagine two companies A and B.&#xA;Both companies use very similar technical equipment to carry out a biotechnological process where a chemical reaction is catalyzed by an enzyme.&#xA;Company A uses an enzyme with a reaction barrier of, say, 15 kcal/mol, while company B uses an enzyme to catalyze the same reaction but this enzyme has an activation energy of only, say 12 kcal/mol.&#xA;For every Mole of product, company B saves 3 kcal worth of energy needed to drive the factory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does that make sense?&lt;/p&gt;&#xA;" OwnerUserId="4971" LastEditorUserId="4971" LastEditDate="2014-04-17T19:04:41.440" LastActivityDate="2014-04-17T19:04:41.440" Title="What does &quot;kcal/mol&quot; mean when speaking of enzyme catalysis?" Tags="&lt;enzymes&gt;" AnswerCount="3" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16636" PostTypeId="2" ParentId="16635" CreationDate="2014-04-17T18:24:25.420" Score="3" Body="&lt;p&gt;The reaction barrier (also termed activation energy) is the energy that is needed for the reaction to take place. An enzyme is &quot;only&quot; a catalysator which lowers the necessary energy (and/or makes the reaction possible under the conditions) but some energy to start a chemical reaction is still needed. See this image (from &lt;a href=&quot;http://blogs.scientificamerican.com/WSS/post.php?blog=49&amp;amp;post=4438&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/y72Xa.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To your questions: A and B are essentially the same - but the reaction time necessary with small amounts of enzyme is much longer than when 1 mole of enzyme is present. The amount of energy needed to catalyze the production of 1 mole of product stays the same.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-17T18:24:25.420" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16637" PostTypeId="2" ParentId="16635" CreationDate="2014-04-17T18:27:52.327" Score="2" Body="&lt;p&gt;The activation energy for a reaction is given for a given extent of reaction, typically per mole of product formed. In general, the amount of enzyme present in the reactor is irrelevant with respect to the activation energy. So option a) is closest to correct. However, note that the activation energy &lt;strong&gt;does not&lt;/strong&gt; tell you how much energy is consumed taken up during the reaction, only how much energy is needed for the activation energy to be exceeded and the reaction to proceed. The kinetics of a reaction, is a separate issue from the thermodynamics of the reaction, which determines the equilibrium concentrations of substrate and product. What the enzyme does is lowering the activation energy, thus speeding up the kinetics of the reaction and allowing equilibrium to be reached. In practice, the activation energy in the absence of the enzyme may be so high that the reaction would not proceed at all, and thus equilibrium would not be reached.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-17T18:27:52.327" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16638" PostTypeId="2" ParentId="16635" CreationDate="2014-04-17T18:32:21.447" Score="2" Body="&lt;p&gt;To better understand the activation energy concept my teacher had given us an excellent example.  Suppose you are driving a car and want to cross a mountain. You could either go to the mountain summit and then come down or you could directly cross it through a tunnel. What enzyme does is to construct a tunnel for the reaction to proceed.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-17T18:32:21.447" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16639" PostTypeId="2" ParentId="14924" CreationDate="2014-04-17T19:21:18.073" Score="3" Body="&lt;p&gt;Often, in terms of a water body becoming acidified, it depends on the rate of acidification.  Fish and other aquatic species, such as invertebrates, are fairly resilient to miniscule changes, but they also have a threshold at which not a lot of them, adapted or no, can survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the U.S. Environmental Protection Agency (&lt;a href=&quot;http://www.epa.gov/acidrain/effects/surface_water.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.epa.gov/acidrain/effects/surface_water.html&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Acid rain causes a cascade of effects that harm or kill individual fish, reduce fish population numbers, completely eliminate fish species from a waterbody, and decrease biodiversity.  Low pH [...] is directly toxic to fish. In addition, low pH and increased aluminum levels cause chronic stress that may not kill individual fish, but leads to lower body weight and smaller size and makes fish less able to compete for food and habitat.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Some types of plants and animals are able to tolerate acidic waters. Others, however, are acid-sensitive and will be lost as the pH declines. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Commonly, benthic invertebrates (including insects, crustacean and molluscs) are used as indicators for ecosystem health.  Invertebrates that need a high amount of calcium, such as crayfish (for their exoskeleton), are typically not found even in slightly acidified lakes.  Other invertebrates can be used as indicator species because they respond to changes in water conditions, such as pH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YNeIi.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good example of this is the acid rain that occurred in Sudbury, Ontario, Canada as a result of sulfur dioxide emissions from mining activities, which were especially high in the 1970s.  This affected the lakes in the area not only from acid rain, but the runoff as well as there were no trees left.  The pH was so low that it effectively made all lakes in the area sterile. Since then, a lot of effort has been put into bringing back the native aquatic species, such as liming the lakes and restocking them with species such as Brook Trout (&lt;em&gt;Salvelinus fontinalis&lt;/em&gt;).  More information can be found here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00160348&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://link.springer.com/article/10.1007%2FBF00160348&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, I do not know that aquatic animals necessarily behave a certain way as a natural indicator of acidity, however it is more of their presence or absence that biologists use to determine acidity and the overall ecosystem health in lakes and rivers.&lt;/p&gt;&#xA;" OwnerUserId="6380" LastEditorUserId="20392" LastEditDate="2017-03-12T11:07:19.100" LastActivityDate="2017-03-12T11:07:19.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16640" PostTypeId="1" CreationDate="2014-04-17T20:13:08.640" Score="19" ViewCount="364" Body="&lt;p&gt;I am trying to understand the effect of aging on the sympathetic fibers of &lt;a href=&quot;http://www.medicinenet.com/script/main/mobileart.asp?articlekey=5402&quot; rel=&quot;noreferrer&quot;&gt;SA node.&lt;/a&gt;&#xA;I know that aging shifts the vagal curve to left in frequency due to aging.&#xA;However, I am interested if aging has similar effect on sympathetic fibers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In young heart, heart's intrinsic functions can work with simultaneous parasympathetic and sympathetic processes.&#xA;If there is no change in the sympathetic function, then those processes have to happen at different times. &#xA;I am having this kind of schematic picture in my mind:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BG6dN.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where intrinsic functions occur in 100-110 BPM normally.&#xA;However, aging shifts V1 to V2, no intersection anymore between V2 and S1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the effect of aging on the sympathetic fibers of SA node?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1590" LastEditDate="2016-08-20T10:12:00.900" LastActivityDate="2021-05-11T13:18:47.950" Title="Effect of Aging on SA node's sympathetic fibers" Tags="&lt;cardiology&gt;&lt;senescence&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="16642" PostTypeId="1" CreationDate="2014-04-17T22:48:57.067" Score="6" ViewCount="471" Body="&lt;p&gt;You sleep at night and are active during the day that's how things work for humans, but theoretically if a human whose parents lived on earth were to be born in another planet resembling earth but the difference was that this planet has an 8.5 hour day, what kind of changes will this person undergo?if a human who grew up on earth suddenly had to move to this planet how would his body adapt? what would be the difference between a person who moves to this 8.5 hour day planet with the person that was born there? and would the person who was born on this planet be active for 4.25 hours and then sleep for the other 4.25?&lt;/p&gt;&#xA;" OwnerUserId="6383" LastEditorUserId="3952" LastEditDate="2014-05-22T01:41:09.523" LastActivityDate="2014-07-25T17:08:05.753" Title="How would the human body adjust to sleep times if we were to live in a place with different day lengths?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;brain&gt;&lt;sleep&gt;&lt;speculative&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16643" PostTypeId="1" AcceptedAnswerId="16656" CreationDate="2014-04-17T23:06:23.583" Score="2" ViewCount="110" Body="&lt;p&gt;This is mostly a question about usage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a probability-related idea that has been used in at least two biological contexts. The idea is that if something happened, it was &lt;em&gt;probably&lt;/em&gt; likely to do so. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has been used in discussions about evolution, in which it is said that while we have trouble imagining circumstances in which self-replicating forms arise, the odds were probably in favor of their emergence when it actually occurred. And in discussions of the existence of intelligent life--it may be prevalent if we make the somewhat natural assumption (among others) that our own emergence was not highly improbable, given the existence of a suitable planet and so on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a name for this principle? I am familiar with the idea in the context of probability but have thought of it as an 'argument from likelihood' in biology. Also if there is a good description of the idea in a biological context a reference would be appreciated.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The tag is a little arbitrary. Thanks for any suggestions.  &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="3952" LastEditDate="2014-04-18T19:18:36.563" LastActivityDate="2014-05-04T00:56:18.407" Title="Is there a name for this principle in biological contexts?" Tags="&lt;terminology&gt;&lt;literature&gt;&lt;molecular-evolution&gt;&lt;philosophy-of-science&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16644" PostTypeId="2" ParentId="16642" CreationDate="2014-04-17T23:49:39.613" Score="3" Body="&lt;p&gt;Humans have evolved for 24 hour days and our bodies would not adapt well to this short of sleep/wake cycles (whether or not they were born there, unless they have been there for many generations and have been able to evolve for the new time). Our bodies would still want to spend about the same amount of time sleeping and being awake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we tried to adjust our sleep cycles to this planet with 8.5 hour days, we would experience many of the stresses that occur during jet lag (&lt;a href=&quot;http://scholar.google.com/scholar?hl=en&amp;amp;q=jet%20lag%20stresses&amp;amp;btnG=&amp;amp;as_sdt=1,21&amp;amp;as_sdtp=&quot; rel=&quot;nofollow&quot;&gt;Google Scholar search&lt;/a&gt;), which can cause depression. Jet lag is identical to experiencing one day which is shorter or longer than the typical 24 hours.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sunlight helps set our circadian rhythm, but 8.5 hours would be too fast. I thought I heard for an experiment that used mice that supports this, but I still haven't found the reference yet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nbogard referenced the article &lt;a href=&quot;http://ncbi.nlm.nih.gov/pmc/articles/PMC1934931&quot; rel=&quot;nofollow&quot;&gt;Plasticity of the Intrinsic Period of the Human Circadian Timing System&lt;/a&gt;, which showed that the circadian rhythm in humans can be altered by up to 0.65 hours by the use of lights. This is consistent with what I mentioned that the sunlight helps to set our circadian rhythm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best way to adapt would be to use artificial lighting to keep your days about 24 hour days (artificial light during waking hours, heavy curtains during sleeping hours), as mentioned in ThePopMachine's answer.&lt;/p&gt;&#xA;" OwnerUserId="6043" LastEditorUserId="6043" LastEditDate="2014-07-25T17:08:05.753" LastActivityDate="2014-07-25T17:08:05.753" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="16645" PostTypeId="1" AcceptedAnswerId="16770" CreationDate="2014-04-18T00:13:21.800" Score="3" ViewCount="1910" Body="&lt;p&gt;Found in central florida in the bath tub. Its about the size of a pencil marking, very small. What is it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CQGFB.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6384" LastEditorUserId="22628" LastEditDate="2016-06-12T03:16:56.293" LastActivityDate="2016-06-12T03:16:56.293" Title="What kind of small insect is this?" Tags="&lt;species-identification&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16649" PostTypeId="2" ParentId="15378" CreationDate="2014-04-18T06:36:31.723" Score="3" Body="&lt;p&gt;I don't have a definitive answer, but I can perhaps offer some insight. Given the necessary function of rpoA, I would be willing to bet that SigA is the factor responsible for its transcription, so I will focus my discussion there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Predicting promoters without experimentation can be very challenging given their immense variability. The &lt;em&gt;idealized&lt;/em&gt; core promoter consists of a -10 region, a spacer and a -35 region. Recognition of the promoter by a sigma factor is done at the -10 and -35 regions: each sigma factor recognizes a different consensus sequence. &lt;em&gt;Bacillus subtilis&lt;/em&gt; SigA recognizes the consensus sequences TTGACA (-35) and TATAAT (-10). They key word there is consensus however, as it is rare that a promoter will actually contain these exact sequences. In reality, 3/6 nucleotides matching could be considered reasonable. Between the -10 and -35 regions is a spacer with conserved length. In the absence of transcription activators, SigA requires a 17 +/- 1 nucleotide spacer. This is due to thermodynamic constraints. Very briefly, promoter melting (at -10) is dependent the angle between the -10 and -35 regions. Given the helical nature of DNA, this angle is in turn dependent on the distance between the -10 and -35 regions. If the angle is just right, the untwisting of the DNA to align the promoter elements and thus allow sigma binding provides the energy to melt the promoter. If the angle is too large, the regions can never align. If the angle is to small, alignment will not provide enough energy for melting. Complicating this are non-standard core promoters and various flanking sequences that all play a role in transcription initiation. As a direct answer to one of your question, a single sigma factor can bind to many different DNA sequences with some conserved regions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/255767013?report=graph&amp;amp;tracks=%5Bkey%3agene_model_track,name%3aGenes---Unnamed,display_name%3aGenes,id%3aSTD3,category%3aGenes,annots%3aUnnamed,Options%3aMergePairs,SNPs%3afalse,CDSProductFeats%3atrue,ShowLabelsForAllFeatures%3atrue,HighlightMode:2%5D&amp;amp;appname=ncbientreznuccore&amp;amp;color=0&amp;amp;label=0&amp;amp;decor=0&amp;amp;spacing=0&amp;amp;v=148789.25:150016.75&amp;amp;c=FFFF00&amp;amp;gflip=false&amp;amp;select=gi%7C255767013-000245c2-00024972-0101-6f461356-ffea8d58&quot; rel=&quot;nofollow&quot;&gt;Fortunately, the &lt;em&gt;B. subtilis&lt;/em&gt; genome has been sequenced.&lt;/a&gt; Your search for the promoter might involve looking for the -10 and -35 regions 5' to the rpoA gene. This however doesn't take into account that rpoA might be part of a polycistronic operon and thus under the control of a promoter further upstream. &lt;a href=&quot;http://jb.asm.org/content/168/1/65.short&quot; rel=&quot;nofollow&quot;&gt;Suh et al. (1986)&lt;/a&gt; did basically this and reported:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our DNA sequence analysis suggests further experiments to study regulation within the rpoA region. Because inhibition of polycistronic message translation by free protein S4 is one of the chief controls of alpha operon expression in E. coli (16, 23), the apparent absence of S4 from the B. subtilis alpha region suggests different regulation. Although the close coupling of the rpsM and rpsK genes in our sequence (Fig. 3) supports the notion of a translational coupling similar to E. coli, the putative rpoA promoters in the relatively large intercistronic distance following rpsK are also different (28, 29). However, the apparent absence of a rho-independent terminator in this region could indicate that significant transcription occurs from additional upstream promoters in B. subtilis as well as in E. coli (28).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Albeit this is an old paper, but I was unable to find more recent studies in my quick research. Basically they compared the &lt;em&gt;B. subtilis&lt;/em&gt; rpoA gene to that of &lt;em&gt;Escherichia coli&lt;/em&gt;, where it is located in an operon with ribosomal proteins rpsM, rpsK, rpsD and rplQ (under the control of a single promoter). They found both similarities and differences. They were able to find two possible SigA core promoters in the region between rpoA and rpsK (the next gene 5' to rpoA in &lt;em&gt;B subtilis&lt;/em&gt;). There was also a relatively large distance between the two genes, suggesting that they are not part of the same operon. Furthermore, they were able to find a ribosome binding site (Shine-Dalgarno sequence) between the hypothetical promoters and the translation start site. On the other hand there is no transcription terminator between rpsK and rpoA which suggested that a promoter further upstream regulated rpoA expression. After their sequence analysis, they suggested that further experimentation was required.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion, it's hard to find promoters just by looking at the sequence. Even if you do find a possible promoter, it's impossible to say whether or not it is utilized without experimentation. That said, given that the alpha subunit is necessary for cell function, that the rpoA gene appears to be transcriptionally tied to ribosomal proteins (which are also necessary for cell function) and that SigA is the predominant factor in log phase &lt;em&gt;B. subtilis&lt;/em&gt;, I feel that it is very likely that SigA is ultimately the factor responsible for rpoA expression&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also thought I'd mention that there are various online bioinformatics tools that attempt to predict promoters, but I will not comment more on them because I have not used them.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-04-18T06:36:31.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16650" PostTypeId="2" ParentId="16642" CreationDate="2014-04-18T06:52:31.347" Score="2" Body="&lt;p&gt;Actually, for your example it would be pretty easy to adapt.  You just have a 25.5 hour day with 12.75 hours of day and 12.75 hours of night.  Except you have a 4.25 hour period in the middle of the day where you stay inside and use lights (like in the evening for most people on Earth) and a 4.25 hour period at night where you make sure your eye mask is on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Added convenience: there are three different choices of when to call day so it's good for shift work and there's no problem with traffic.  Let's move there!&lt;/p&gt;&#xA;" OwnerUserId="6374" LastActivityDate="2014-04-18T06:52:31.347" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16653" PostTypeId="2" ParentId="16643" CreationDate="2014-04-18T11:33:48.837" Score="1" Body="&lt;p&gt;The principle of least effort / path of least resistance fit pretty well: animals, people, and systems (like evolution or a mechanical system like a machine) will naturally choose the path of least resistance or effort. The principal applies to chemistry (low energy states) and physics (the path an electrical current takes) as well. Occam's Razor fits somewhat too in an abstract sense in that nature favors simple solutions over complex ones. You may find something in thermodynamics as well.&lt;/p&gt;&#xA;" OwnerUserId="6291" LastEditorUserId="6291" LastEditDate="2014-04-18T18:03:08.367" LastActivityDate="2014-04-18T18:03:08.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16654" PostTypeId="1" AcceptedAnswerId="16657" CreationDate="2014-04-18T14:12:52.993" Score="4" ViewCount="718" Body="&lt;p&gt;Can identical twins have different genders (as in &lt;strong&gt;biological sex&lt;/strong&gt;)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought they should have absolutely the same genes. If they can, what caused it? I'd assume it MAY be because of errors in cellular division at conception.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="6363" LastEditorUserId="-1" LastEditDate="2014-12-03T20:41:46.893" LastActivityDate="2014-12-03T20:41:46.893" Title="Identical twins' biological sexes" Tags="&lt;twins&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16655" PostTypeId="2" ParentId="15058" CreationDate="2014-04-18T15:04:53.967" Score="1" Body="&lt;p&gt;Like Liam said, this sort of analysis is dependent on the database you use, which may not be adequate for what you are trying to accomplish. And as far as I know, these databases are at the gene, not isoform, level. So if a change in two conditions is a result of a change in which isoform is expressed, rather than the amount of expression, you will not detect it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also it treats genes as equals that are independent of each other but thats usually not the case. For example if p53, at the top of a pathway, is expressed differently,  that has much stronger implications than if a gene at the bottom of the pathway was expressed differently. Additionally, it treats each pathway as independent of each other, but again that is usually not that case and there usually is some overlap between pathways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read more here &lt;a href=&quot;http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002375&quot; rel=&quot;nofollow&quot;&gt;http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002375&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2014-04-18T15:04:53.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16656" PostTypeId="2" ParentId="16643" CreationDate="2014-04-18T15:32:56.307" Score="2" Body="&lt;p&gt;It may also be called as Idea of maximum parsimony. It is used in phylogenetics to construct phylogenetic trees which require the least number of evolutionary events.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-18T15:32:56.307" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16657" PostTypeId="2" ParentId="16654" CreationDate="2014-04-18T15:34:40.730" Score="7" Body="&lt;p&gt;Identical twins occur when a single egg is fertilized to form one zygote, which then divides into two separate embryos. Thus, identical twins are always the same sex unless there has been a mutation during development. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, two identical twins expressing different sexual phenotypes does happen in some extremely rare cases due to environmental factors, deactivation of different X chromosomes in females, or aneuploidy. This is normally because an &lt;a href=&quot;http://en.wikipedia.org/wiki/Klinefelter_syndrome#Diagnosis&quot;&gt;XXY Klinefelter syndrome&lt;/a&gt; zygote has split unevenly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are correct though, in that identical twins usually have hundreds of genetic differences early in fetal development which can be attributed to mutations in the DNA. But usually these differences do not result in twins with different sexual phenotypes, though it is possible.&lt;/p&gt;&#xA;" OwnerUserId="6367" LastActivityDate="2014-04-18T15:34:40.730" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16658" PostTypeId="1" CreationDate="2014-04-18T15:51:53.490" Score="0" ViewCount="1495" Body="&lt;p&gt;What is accumulation and release centre of neurohormones?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it hypothalamus?&lt;/p&gt;&#xA;" OwnerUserId="6390" LastActivityDate="2014-04-19T04:02:00.920" Title="What is accumulation and release centre of neurohormones?" Tags="&lt;neuroscience&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16660" PostTypeId="2" ParentId="16517" CreationDate="2014-04-18T17:57:10.767" Score="1" Body="&lt;p&gt;No, because some kind of fluid (liquid or gas) is necessary to supply resources and carry away wastes. Bacterial spores, tardigrades, etc. are in a dormant state when in a vacuum.&lt;/p&gt;&#xA;" OwnerUserId="5985" LastActivityDate="2014-04-18T17:57:10.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16661" PostTypeId="1" AcceptedAnswerId="16663" CreationDate="2014-04-18T18:45:26.453" Score="2" ViewCount="3441" Body="&lt;p&gt;Just like the title says: Strictly from a biological perspective, what is the functional expectation of a human being. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;No religious or philosophy-based answers will be accepted, we are talking biology not religion or philosophy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Answers involving excessive psychology will be frowned upon unless found to be exceedingly insightful. (The brain is a biological entity)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are considering claiming this to be too broad or unanswerable consider the hypothetical question &quot;what are the functional expectations of human feet&quot; which can be answered fairly easily by a child with no formal training in biology. In my actual question I simply ask about the feet and the other parts attached to them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: Originally this question was titled &quot;Strictly from a biological perspective, what is the purpose of a human existence.&quot; To clarify the question i have changed it to &quot;Strictly from a biological perspective, what is the functional expectation of a human being.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite the concerns raised with the use of the word &quot;purpose&quot; the question was serving its purpose with the answers I am seeing.  I did have  some reservations about the word &quot;purpose&quot; as well, but I thought I would try it and see what others thought. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if a human stomach has the overall functional expectation of mechanically and chemically breaking down and digesting food, what would be the overall functional expectation of a human as a whole? I am looking for not so much of psychologically specific functional expectations and more of physical functional expectations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance a house cat's functional expectations are generally considered to be sleeping, eating, reproducing, socializing, hunting, etc. &lt;/p&gt;&#xA;" OwnerUserId="6291" LastEditorUserId="6291" LastEditDate="2014-04-19T09:17:01.230" LastActivityDate="2014-04-19T09:17:01.230" Title="Strictly from a biological perspective, what is the functional expectation of a human being" Tags="&lt;human-biology&gt;" AnswerCount="4" CommentCount="5" ClosedDate="2014-04-19T11:49:04.617" ContentLicense="CC BY-SA 3.0" />
  <row Id="16663" PostTypeId="2" ParentId="16661" CreationDate="2014-04-18T19:23:38.813" Score="13" Body="&lt;p&gt;I will start with a quote from François Jacob, a French geneticist:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The sole ambition of a bacterium is to make two bacteria.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The same reasoning can be extended to all life on Earth, including humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no purpose to human existence, in the same way that there is no purpose for life at all. Life is there because it can. It works, chemically, physically and thermodynamically, given the physical conditions present on Earth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biology does not give any moral reason for our existence. It only describes what is there. Using experimental techniques we can infer the purpose of the human feet. All we need to do is to remove the feet of a human subject and see what happens. The subject will be unable to walk, and therefore we will be able to infer that the feet's purpose is to enable locomotion. In biological research, we usually remove or silence genes or proteins from an organism to infer their purpose. We then observe the phenotype. Most of the time however, such an experiment does not give any information on the purpose of the gene because its function is not obvious enough to be observed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the same vein, one could remove humans from the Earth and see what happens. If something changes for the worse on Earth, then we would be able to infer that our purpose was to prevent such event from happening. Obviously, such an experiment is impossible to perform, therefore we will never know what is our purpose, neither will we know whether we actually have a purpose.&lt;/p&gt;&#xA;" OwnerUserId="6395" LastActivityDate="2014-04-18T19:23:38.813" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16664" PostTypeId="2" ParentId="16661" CreationDate="2014-04-18T20:03:27.917" Score="3" Body="&lt;p&gt;Purpose requires a sentient being to have intent.  There is no biological reason to suppose there is any purposeful intent behind life.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you hold otherwise, perhaps inquire of the fellow or lady or other you suppose is responsible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just because a child can give an answer to a question doesn't mean that the answer is accurate, or that the question truly is well-formed enough to answer well.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-04-18T20:03:27.917" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16666" PostTypeId="2" ParentId="5171" CreationDate="2014-04-18T21:45:14.643" Score="0" Body="&lt;p&gt;Our bodies work in cycles.. Circadian cycles that refer to our daily routines. We need sleep every night, eating at night affects us differently than if eating in the morning, etc... all because our bodies functions work in these 24 hour cycles... &#xA;Now, beside the circadian cycles, our bodies also have circaceptan (or 7 day) rythms. For example, our immune system picks every 7 days (reason why the 7th day after a transplant is the most likely one may reject the organ). This 7-day cycle is also observed in other life forms... &#xA;But, read for yourself:&#xA; a seven-day cycle has been found in fluctuations of blood pressure, acid content in blood, red blood cells, heartbeat, oral temperature, female breast temperature, urine chemistry and volume, the ratio between two important neurotransmitters, norepinephrine and epinephrine, and the rise and fall of several body chemicals such as the stress coping hormone, cortisol. &quot;In fact,&quot; Perry and Dawson note, &quot;weekly rhythms appear easiest to detect when the body is under stress, such as when it is defending itself against a virus, bacterium, or other harmful intruder. For example, cold symptoms (which are really signs of the body defending itself against the cold virus) last about a week. Chickenpox symptoms (a high fever and small red spots) usually appear almost exactly two weeks after exposure to the illness.:&quot; [Susan Perry and Jim Davson, The Secrets Our Body Clocks Reveal, (New York: Rawson Associates, 1988) p. 22.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Doctors have long observed that response to malaria infection and pneumonia crisis peaked at seven days. Organ transplants face similar crises as the body's immune system attack the foreign organ. Campbell explains: &quot;When a human patient receives a kidney transplant, there is a rhythm of about seven days, a predictable rise and fall in the probability that the body's immune system will reject the new kidney. A major peak of rejection occurs seven days after the operation, and when a serum is given to suppress the immune reaction, a series of peaks occurs, with increasing risk of rejection, at one week, two weeks, three weeks and at four weeks, the time of the highest of all.&quot; [Jeremy Campbell, Winston Churchill's Afternoon Nap, (New York: Simon and Schuster, 1986). p. 76]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in answer to your question... it makes a lot of sense that if so many of our body functions have 7-day rythms, we would feel a biological need to slow down and allow our bodies to rest, rejuvenate.... &lt;/p&gt;&#xA;" OwnerUserId="6399" LastActivityDate="2014-04-18T21:45:14.643" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16668" PostTypeId="1" AcceptedAnswerId="16692" CreationDate="2014-04-19T00:35:45.010" Score="4" ViewCount="243" Body="&lt;p&gt;In immunotherapy a person is regularly exposed to an allergen to decrease the allergy. Yet apparently &quot;repeated intranasal challenges ... induces robust allergic airway inflammation, &quot; [0]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when does exposure to an allergen cause allergy induction vs hyposensitization?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[0] &lt;a href=&quot;http://www.researchgate.net/post/Which_is_the_best_way_to_sensitize_mice_to_house_dust_mites&quot; rel=&quot;nofollow&quot;&gt;http://www.researchgate.net/post/Which_is_the_best_way_to_sensitize_mice_to_house_dust_mites&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6402" LastActivityDate="2014-04-19T20:13:19.680" Title="When does exposure to an allergen increase / decrease allergy?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;allergies&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16669" PostTypeId="2" ParentId="16661" CreationDate="2014-04-19T02:23:04.803" Score="1" Body="&lt;p&gt;That all depends on the perspective from which you view the question. For example, from the perspective of a human being the purpose of human existence may be to make more humans. From the perspective of a herd of goats the purpose for human existence is for the humans to bring food and water, care for kids, shovel out the barn, talk nicely to them, scratch them behind the horns where they can't reach, and give them something to snicker at. Cats are much the same but will sometimes allow their bellies to be scratched, don't have horns, and are to the best of my knowledge unable to snicker.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And of course all &lt;em&gt;this&lt;/em&gt; assumes, on what only be termed hear-say evidence, that humans exist. &quot;Ah&quot;, you say, &quot;but I am real - I have form - I have substance - of &lt;em&gt;course&lt;/em&gt; I, and by extension the entire human race, and in fact the entire universe, exist!&quot;. Perhaps, but then again perhaps not. What if what you perceive as existence is merely the by-product of intestinal gas disturbing the slumbers of a god-like creature whose vagrant dreams can morph into something approaching reality, but which vanish like a popping soap bubble when the god awakes?&lt;/p&gt;&#xA;" OwnerUserId="6403" LastActivityDate="2014-04-19T02:23:04.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16670" PostTypeId="2" ParentId="16661" CreationDate="2014-04-19T03:41:24.380" Score="2" Body="&lt;p&gt;In the context of evolution, the only &quot;purpose&quot; that a thing can serve is the role it plays in the process of reproduction, selection and mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, &quot;what purpose do feet serve&quot;? Naively: the formation of part of the human body as feet serves to increase the likelihood of the survival and reproduction of humans, by supporting the way we move and stand. Even more naively, the child wouldn't talk about survival and reproduction -- to a child the purpose of something is whatever benefit it is seen to cause, so the purpose of feet would be &quot;walking&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;What purpose do humans serve&quot;? Naively: to survive and reproduce. With more nuance, since we know about symbiotic evolution: to increase the likelihood of the survival and reproduction of various species, including but not limited to humans. For example humans have been pretty bad news for North American magafauna, but pretty good news for wheat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On this basis of symbiosis you could reasonably conclude that the &quot;purpose&quot; of animals (or at any rate most bilateral animals) is to serve as a habitat and food-gathering mechanism for their gut-flora. Or that the &quot;purpose&quot; of most eukaryotes is to do the same for mitochondria. Or less fancifully, that the &quot;purpose&quot; of living organisms is to provide a stable environment for RNA and DNA to reproduce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's ultimately a question of perspective and as such subjective. &quot;Purpose&quot; really implies intent, which absent religion or philosophy is pretty hard to pin down. But when talking about feet and other biological characteristics we use &quot;purpose&quot; as a shorthand for &quot;benefit which explains their being selected for&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As such, providing an environment for DNA to reproduce is right up there as a candidate for the purpose of life in general, including humans. Humans then are a variation within this general goal, that seems to be doing OK for the time being. This is more or less the theme of &lt;em&gt;The Selfish Gene&lt;/em&gt;. You can easily question Dawkins's views on religion and philosophy, but (despite some disagreement) his ideas on genetics were pretty well received as far as they went.&lt;/p&gt;&#xA;" OwnerUserId="6132" LastEditorUserId="6132" LastEditDate="2014-04-19T04:04:16.673" LastActivityDate="2014-04-19T04:04:16.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16671" PostTypeId="2" ParentId="16658" CreationDate="2014-04-19T04:02:00.920" Score="5" Body="&lt;p&gt;The &lt;a href=&quot;http://www.britannica.com/EBchecked/topic/410635/neurohormone&quot;&gt;neurohormones&lt;/a&gt; in most mammals include oxytocin and vasopressin, both of which are &lt;strong&gt;produced in the hypothalamic region&lt;/strong&gt; of the brain and &lt;strong&gt;secreted into the blood by the neurohypophysis (part of the pituitary gland)&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A second group of neurohormones, called releasing hormones, also originates in the hypothalamus. The members of this group, however, are transmitted within the neural cells to a second locus in the brain, from which they pass in the bloodstream to the &lt;strong&gt;adenohypophysis&lt;/strong&gt;, which also is a part of the pituitary gland. There they either stimulate or inhibit the release of the various adenohypophysial hormones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A third group of neurohormones includes the enkephalins and other endorphins. The endorphins are effective in relieving pain, a property apparently related to their function as neurotransmitters, passing nerve impulses from one neuron to another. Their neurohormonal activity is manifested by their stimulation of the secretion of somatotropin and vasopressin by an indirect process &lt;strong&gt;involving a site (other than the secretory neuron) in the central nervous system.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="6367" LastActivityDate="2014-04-19T04:02:00.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16672" PostTypeId="1" AcceptedAnswerId="16676" CreationDate="2014-04-19T08:06:53.707" Score="3" ViewCount="608" Body="&lt;p&gt;Ruminants are known for their regurgitation of food; the food goes through the 1st and 2nd stomach chambers, then returns to the oral cavity in cuds. The cuds then come back into the stomach, but this time they go through the 3rd and 4th chambers, instead of going to the 1st and 2nd again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is it ensured that the regurgitated food doesn't go through the 1st and 2nd chamber by a mistake?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2014-04-20T19:02:08.010" Title="How does regurgitated food go to the 3rd stomach chamber instead of going to the 1st?" Tags="&lt;physiology&gt;&lt;digestion&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16673" PostTypeId="1" AcceptedAnswerId="16677" CreationDate="2014-04-19T08:25:31.980" Score="5" ViewCount="2936" Body="&lt;p&gt;I keep reading about how primers are useful in pcr -- they allow you to select a specific dna region. Similarly, in NGS or Sanger sequencing they give you a starting point. The primers I see are about 20-30 bases long.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, how were the first primers developed? Somewhere, someone needed to come up with a 20-base sequence that bound to a specific part. Aren't there 4^20 such combinations? That's a lot of potential options to test.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How was that done?&lt;/p&gt;&#xA;" OwnerUserId="3500" LastEditorUserId="22057" LastEditDate="2017-05-09T19:35:24.447" LastActivityDate="2017-05-09T19:35:24.447" Title="How were the first primers made?" Tags="&lt;dna-sequencing&gt;&lt;genomics&gt;&lt;rna-sequencing&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16674" PostTypeId="1" AcceptedAnswerId="16675" CreationDate="2014-04-19T08:27:31.497" Score="3" ViewCount="380" Body="&lt;p&gt;When sequencing papers refer to single molecule sequencing, what is their definition of a &quot;molecule&quot;. Are they saying base by base? The entire DNA chain in a chromosome can also be though of as a &quot;molecule&quot;. In that case, that's a much larger read. What's the default interpretation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, is the Illumina sequencing &quot;single molecule&quot; as they fluoresce one base at a time?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="3500" LastEditorUserId="1320" LastEditDate="2014-04-21T07:10:06.260" LastActivityDate="2014-04-21T07:10:06.260" Title="What is meant by single molecule sequencing?" Tags="&lt;dna-sequencing&gt;&lt;human-genome&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16675" PostTypeId="2" ParentId="16674" CreationDate="2014-04-19T09:26:59.593" Score="2" Body="&lt;p&gt;For the classic Sanger sequencing you need quite large amounts of DNA to be able to run the sequence reaction. This is a problem when you want to sequence whole genome since the DNA needs to be amplified then, which for some sequences can cause problems, introduce errors or cause bias.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Single molecule sequencing is a huge step forward here, since only one molecule of DNA is used for sequencing. There are different sequencing technologies based on this principle. &#xA;The system of pacific biosciences uses a polymerase bound to a small well which binds a singlestranded DNA and begins to make the opposite strand, when nucleotides are present.&#xA;See the image below or this &lt;a href=&quot;http://www.youtube.com/watch?v=v8p4ph2MAvI&quot; rel=&quot;nofollow noreferrer&quot;&gt;video&lt;/a&gt;, which explains the technique quite nicely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vE3wo.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Illumina binds singlestranded DNA molecules to the surface of the reaction chamber and starts amplifying them there. The use of fluorescently labelled nucleotide allows to monitor the reaction. This looks like the following (left side of the figure from the review mentioned below):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FXHxO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An illustration from Illumina which is more detailed, can be found &lt;a href=&quot;http://res.illumina.com/documents/products/techspotlights/techspotlight_sequencing.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&#xA;Although it is a bit older (and the technology develops fast), this review is a nice introduction: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19997069&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sequencing technologies - the next generation.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-04-19T13:49:53.700" LastActivityDate="2014-04-19T13:49:53.700" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="16676" PostTypeId="2" ParentId="16672" CreationDate="2014-04-19T13:08:15.820" Score="5" Body="&lt;p&gt;Your question supposes a very linear version of the flow of stomach contents of:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1-&gt;2-&gt;mouth-&gt;3-&gt;4&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In reality, it is not so linear. Firstly some background: The rumen and reticulum form the first two parts of the four, and are in fact a single chamber/organ (collectively known as the reticulorumen). They have different wall structures, and perform initial digestion of different particles (mostly heavier particles in the rumen such as grain and more digested hay). This reticulorumen chamber is where the initial microbial fermentation of the feed occurs. Matter passes from rumen to reticulum and back regularly by means of two distinct muscle contractions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To aid in the breakdown of the feed, the cud is regularly regurgitated, chewed and then re-ingested. The re-ingested cud returns to the reticulorumen. From there, in order to advance down into the later stages of the digestive tract, it must pass through the reticulorumen orifice into the third compartment - the omasum. The orifice allows particles up to 4mm in size in cattle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The omasum chamber removes water and some nutrients. The contractions of the omasum remove water and move solids through the system, and the contractions are speculated to filter out any larger particles and return them to the reticulorumen. Matter that has been processed by the omasum is passed along to the fourth chamber, the abomasum. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to answer your question in brief, after mastication the cud returns to chambers one and two, potentially going round this loop several times until it is sufficiently broken down by chewing, saliva and bacterial action, and then it can proceed from there to the third chamber.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;digesta circulation and reticulo rumen motility in the ruminent&quot; paper (C. Poncet, C.H. Malbert, R. Baumont) has this to say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The outflow of digesta, allowed by the opening of the ROO [reticulorumen orifice] during the second phase of the reticular contraction, is highly selective. The effluent does not contain particles greater than 2mm in sheep and 4mm in cattle. This is due to the buoyancy of the large particles in the reticulum, to the self filtration of the digesta during the passage through the ROO and perhaps to backflows from the omasum to the reticulum.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You may find it useful to get a copy of this collection of papers (quote from p.366): &lt;a href=&quot;http://books.google.co.uk/books?id=Bcsa8Z4u-E4C&amp;amp;printsec=frontcover#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;http://books.google.co.uk/books?id=Bcsa8Z4u-E4C&amp;amp;printsec=frontcover#v=onepage&amp;amp;q&amp;amp;f=false&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="6406" LastEditorUserId="6406" LastEditDate="2014-04-20T19:02:08.010" LastActivityDate="2014-04-20T19:02:08.010" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16677" PostTypeId="2" ParentId="16673" CreationDate="2014-04-19T14:16:43.627" Score="11" Body="&lt;p&gt;The MIT synthetic chemist &lt;a href=&quot;https://en.wikipedia.org/wiki/Har_Gobind_Khorana&quot; rel=&quot;noreferrer&quot;&gt;Gobind Khorana&lt;/a&gt; won the 1968 Nobel Prize in Chemistry for his work which successfully was able to make chains of Ribonucleic acids.  The chemistry was difficult at the time but he won the prize for making specific sequences of RNA bases which were then fed to cells, resulting in specific amino acid chains, which ultimately deciphered the specific base to amino acid correspondence of the genetic code. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Oligonucleotide_synthesis&quot; rel=&quot;noreferrer&quot;&gt;Khorana was only one of the chemists who worked on nucelotide synthesis&lt;/a&gt;, but the technique overall is simple and since nucleic acid polymers are only unbranched polymers, &#xA;any sequence combination is easily obtained.  Each sequential reaction adds one base.  Repeat the reaction as many times as needed.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BlADi.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The chemistry Khorana devised was refined and easily extended to DNA polymers since the linkages are identical, the difference between DNA and RNA is only a single alcohol (-OH) group, which is not directly involved in the bond between the nucleotide bases.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By 1983 when Kary Mullis concieved the idea of PCR, short sequences of DNA and RNA could be synthesized on commercially available machines.  In fact &lt;a href=&quot;http://www.karymullis.com/pcr.shtml&quot; rel=&quot;noreferrer&quot;&gt;Mullis was responsible for just such a machine&lt;/a&gt; at Cetus Pharmaceuticals and had been trying to find a way to increase demand for his services.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The PCR oligos were the easy part of the operation.  To prove the concept, the team at Cetus used a conventional DNA polymerase and add it to the PCR mix after every cycle.  &lt;a href=&quot;http://molecular.roche.com/pcr/Pages/History.aspx&quot; rel=&quot;noreferrer&quot;&gt;By 1986 the Cetus team had succeeded in performing PCR a heat tolerant DNA polymerase&lt;/a&gt; from Thermus aquaticus, a bacterium from a hot spring, which basically made it the technique we still use today. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-04-19T14:21:57.697" LastActivityDate="2014-04-19T14:21:57.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16678" PostTypeId="2" ParentId="16627" CreationDate="2014-04-19T14:28:08.750" Score="1" Body="&lt;p&gt;If the fitness of a heterozygote is $(1+s/2)$ and of a homozygote is $(1-s/2)$ then why is the probability for a given state $(1+s/2)^j(1-s/2)^{m-k}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\binom mj (1/2)^j(1/2)^{m-j}= \binom mj (1/2)^m~~ ?$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you pointed out earlier, in the general case it need not be true that $p = q = 1/2$ but that is what the form of the probability above implies. So the threshold question is why this particular heterozygous-dominant model implies equilibrium probabilities $p = q = 1/2.$ I think the ideas below begin to address this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The simplest case is for one locus, two alleles, and there are many good derivations online. I think if you understand the situation for one locus you can generalize to higher numbers. (Hopefully I will supplement this answer, time allowing. I think a shortcut would be to assume $p = q = 1/2$ and use your fitness weights. That gives us $\bar{w}=1$ as a denominator. Now for reasons of symmetry I think you can show that the relative frequencies of $p$ and $q$ are equal and so $p' = p.$ Then you have to show that this equilibrium solution is unique.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a single locus the derivations of `heterozygote advantage' I have found,&lt;a href=&quot;http://w3.ualg.pt/~rcastil/GPE/Main_files/0_Tamarin_Processes_change_book_chapter.pdf&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt;&lt;a href=&quot;http://evol.bio.lmu.de/_teaching/evogen/Evo7-Summary.pdf&quot; rel=&quot;nofollow&quot;&gt;(2)&lt;/a&gt;, assign fitness weights as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AA = (1 - s),     Aa = 1,       aa = (1 - t )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;in which $s,t &amp;gt; 0, s \neq t$ in general, from which they derive as a condition for equilibrium &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\Delta q = \frac{pq(sp-tq)}{\bar{W}}  = 0$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\hat{p} = \frac{t}{s+t} ~~~\text{and}~~~ \hat{q} = \frac{s }{s+t}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;in which $\hat{p}, \hat{q}$ are equilibrum frequencies for each allele, respectively, and s and t are rates of mutation. Nowhere did I see a model in which they had assigned the same fitness to both homozygous cases (AA, aa) but it's just a special case of the heterozygote advantage model. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;fitness (AA) = fitness(aa) = (1 - s/2), fitness(Aa) = (1+ s/2). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if we subtract s/2 from each fitness score (or normalize with respect to Aa to the same effect), we get: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;fitness(AA) = fitness (aa) = (1- s ) and fitness (Aa) = 1 as in the two references above, except that now the two homozygous states have equal fitness. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But then we have $$\Delta q = \frac{pq(sp-sq)}{\bar{W}} =  \frac{pqs(p - q)}{\bar{W}} $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and the only nontrivial solution is $p = q = 1/2.$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what I am suggesting is that when you assign the same fitness to both $AA$ and $aa$ you no longer have the general case. As for the value of s being forced, the following seems relevant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The full expression from (2) for the equilibrium condition is &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$p' = \frac{p^2 W_{AA}+ pq W_{Aa}}{\bar{W}} \hspace{10mm}(1)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;in which$ W_{AA} = W_{aa} =  1- s$ and $W_{Aa} = 1$ and &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\bar{W} = p^2 W_{AA}+2pqW_{Aa}+q^2W_{aa}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the homozygotes are assigned the same fitness and $p = q = 1/2$ , equation (1) above becomes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$p' = \frac{\frac{1}{4} + \frac{1}{4}(1-s)}{\frac{1}{2} + \frac{1}{2}(1-s)} $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The program on page 583 of (1) is helpful. Let h:= heterozygous and m:= homozygous. If $p = q = 1/2$ then as long as fitness(h) and fitness(m) are equal the system is in equilibrium immediately. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If $p\neq 1/2$ then as long as f(h) = f(m) the system reaches equilibrium at $p = 1/2$ asymtotically. If $p = 1/2$ but f(h) $\neq$ f(m) the asymtotic limit has to be calculated.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also &lt;a href=&quot;http://evol.bio.lmu.de/_teaching/evogen/Evo8-Summary.pdf&quot; rel=&quot;nofollow&quot;&gt;http://evol.bio.lmu.de/_teaching/evogen/Evo8-Summary.pdf&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-04-25T12:34:16.020" LastActivityDate="2014-04-25T12:34:16.020" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16679" PostTypeId="1" CreationDate="2014-04-19T14:51:24.477" Score="4" ViewCount="112" Body="&lt;p&gt;There are many claims made about nutrient absorption, eg &lt;a href=&quot;http://articles.mercola.com/sites/articles/archive/2014/04/19/juicing-benefits.aspx#&quot; rel=&quot;nofollow&quot;&gt;&quot;Juicing helps you absorb all the nutrients from the vegetables&quot;&lt;/a&gt;.  I'm curious to know how nutrient uptake is measured.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eg is it a pure nutrients in vs nutrients out equation?  Or are blood levels of nutrients measured before and after consumption?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What ever the methods, are they reliable enough to support claims made about relative absorption rates of certain diets or eating practices?&lt;/p&gt;&#xA;" OwnerUserId="6408" LastActivityDate="2014-04-19T14:51:24.477" Title="How is nutrient uptake in humans measured?" Tags="&lt;food&gt;&lt;diet&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2014-12-08T16:55:16.027" ContentLicense="CC BY-SA 3.0" />
  <row Id="16680" PostTypeId="1" CreationDate="2014-04-19T15:31:48.920" Score="2" ViewCount="191" Body="&lt;p&gt;This is a variation of the &quot;does the immune system run out of memory&quot; question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a (possibly imperfect) thought experiment: You take two twins. One of them lives in a bubble from birth. One of them is Mike Rowe from Dirty Jobs, and gets exposed to all sorts of antigens as well as vaccines. When they are 30 years old, you expose both of them to an antigen that neither has seen before. What happens?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;PS:&lt;/strong&gt; Note that while this example is illustrative, my question is really about whether there is any way at all in which the response of a naive immune system to a novel antigen is different from that of a very educated immune system (which has also not seen the antigen before). For instance, would the same amount of antigen be required to stimulate the immune system? Would the antibody count several months or years post-exposure differ?&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-04-19T21:43:22.390" LastActivityDate="2014-04-19T21:43:22.390" Title="Is a naive immune system equally able to handle new antigens as an educated one?" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16681" PostTypeId="1" CreationDate="2014-04-19T18:10:50.730" Score="2" ViewCount="10769" Body="&lt;p&gt;I'm a student new to molecular biology coming in from an eco-evo background looking for tips from you molecular pros! It seems that I'm running quite a few gels. The loading dye I'm using is Gel Loading Dye, blue (6X). The supporting document calls for 5uL:25uL reaction and 10uL dye:50uL reaction. Here's the problem: I'm trying to get my PCR to work and so I'm doing a lot of 'just checking' trials where I only load 2uL of reaction to each well from different 20uL PCR reactions. &lt;strong&gt;What volume of Gel Loading Dye, blue (6X) should I use when running only 2uL of PCR product&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My goal now is to learn to do a DIG in situ hybridization to localize the distribution of mRNA of a gene I'm interested in so any tricks and tips would be greatly appreciated!&lt;/p&gt;&#xA;" OwnerUserId="6412" LastEditorUserId="6" LastEditDate="2014-04-19T18:20:53.650" LastActivityDate="2014-04-19T18:20:53.650" Title="Gel Electrophoresis - loading dye and more" Tags="&lt;gel-electrophoresis&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16682" PostTypeId="2" ParentId="16681" CreationDate="2014-04-19T18:17:19.113" Score="1" Body="&lt;p&gt;When using small sample volumes, it is advisable to use water to increase the volume and make handling and mixing with loading dye easier. For example, you may mix 2 uL of your sample with 1 uL 6X loading dye and 3 uL water for a final volume of 6 uL. &lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-19T18:17:19.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16683" PostTypeId="2" ParentId="16681" CreationDate="2014-04-19T18:20:13.650" Score="2" Body="&lt;p&gt;The loading buffer you add to your samples for gel electrophoresis has a few different purposes, but the exact amount does not really matter. The purpose of the loading buffer is&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;to make the sample heavier so it is easy to get into the pocket and stays there&lt;/li&gt;&#xA;&lt;li&gt;to visualize how far the gel has run&lt;/li&gt;&#xA;&lt;li&gt;to denature the sample (only for denaturing gels)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Sample buffers for agarose gels usually use something heavier than water like glycerol or sucrose together with a tiny amount of a dye like bromophenol blue. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in general there is no issue with using too much dye, but using not enough could lead to the sample being not heavy enough and problematic to pipet, or the sample not being properly denatured. I'd either use 1 ul of the sample buffer (smaller amounts can be annoying to pipett) for your sample, or dilute the sample to 5-10 ul and use the regular amount. &lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-04-19T18:20:13.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16685" PostTypeId="1" CreationDate="2014-04-19T18:40:32.313" Score="5" ViewCount="485" Body="&lt;p&gt;This probably sounds pretty dumb, but wouldn't algae blooms produce a lot of oxygen? Although they would die out and decomposers would use up oxygen, is that more than what the algae produced?&lt;/p&gt;&#xA;" OwnerUserId="6413" LastActivityDate="2016-07-11T17:05:30.667" Title="Why is oxygen used up in eutrophication?" Tags="&lt;marine-biology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16686" PostTypeId="2" ParentId="16685" CreationDate="2014-04-19T18:54:13.713" Score="2" Body="&lt;p&gt;As you surmise, the oxygen is consumed by decomposers. From the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Eutrophication&quot; rel=&quot;nofollow&quot;&gt;Eutrophication&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Phosphorus is a necessary nutrient for plants to live, and is the&#xA;  limiting factor for plant growth in many freshwater ecosystems. The&#xA;  addition of phosphorus increases algal growth, but not all phosphates&#xA;  actually feed algae.[2] These algae assimilate the other necessary&#xA;  nutrients needed for plants and animals. When algae die they sink to&#xA;  the bottom where they are decomposed and the nutrients contained in&#xA;  organic matter are converted into inorganic form by bacteria. The&#xA;  decomposition process uses oxygen and deprives the deeper waters of&#xA;  oxygen which can kill fish and other organisms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-19T18:54:13.713" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16687" PostTypeId="2" ParentId="16680" CreationDate="2014-04-19T19:05:54.397" Score="3" Body="&lt;p&gt;They will both go through a primary and secondary immune response. So first low affinity antibodies will bind, the corresponding b cells will undergo affinity maturation, somatic hypermutation until high affinity (perfectly fitting) antibodies are available and these antibodies will finally undergo class switching.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending on the antigen an innate immune response will also be triggered as part of the first line of defense. There is no difference in the immune response between these two hypothetical brothers.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-19T19:05:54.397" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16688" PostTypeId="1" AcceptedAnswerId="16690" CreationDate="2014-04-19T19:08:50.247" Score="3" ViewCount="553" Body="&lt;p&gt;I am running PCR reactions with different sets of degenerate primers and I want to know what should go into the master mix&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;My usual master mix: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;DEPC water&lt;/li&gt;&#xA;&lt;li&gt;PCR buffer (-Mg)&lt;/li&gt;&#xA;&lt;li&gt;25mM MgCl2&lt;/li&gt;&#xA;&lt;li&gt;10mM dNTPmix&lt;/li&gt;&#xA;&lt;li&gt;cDNA&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;On ice I add my forward and reverse primers to the appropriate PCR tubes, add master mix to each PCR tube, then right before I pop them into the thermal cycler I add taq and mix.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Is this a proper way of doing it? I get product but I'm thinking maybe I can improve it by changing what I add to the master mix. For example, &lt;strong&gt;is it better to add taq instead of cDNA to the master mix and then add cDNA before I start the PCR? Is it okay to add both cDNA and taq to the master mix together?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="6412" LastActivityDate="2014-04-19T19:18:40.630" Title="PCR master mix contents" Tags="&lt;lab-techniques&gt;&lt;pcr&gt;&lt;lab-reagents&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16690" PostTypeId="2" ParentId="16688" CreationDate="2014-04-19T19:18:40.630" Score="2" Body="&lt;p&gt;I always add the Taq to the mastermix. First it makes the handling easier and it avoids pipetting steps which can cause contamination and can also be forgot. Then the enzyme is very stable and will even tolerate room temperature without problem. Since we are going to heat this 30-40 up to 95°C, so this is clearly not problematic. Since the reaction mix is cooled, you reaction will not start. And even if it does, there wouldn't be much amplification due to the low temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I usually add everything which is the same for all reactions to the mastermix (this can include the DNA as well). If I use more than one DNA I split the mastermix in half. This way you are not going to make different pipette errors for the template, which is especially important for realtime-PCR. I usually dilute the primers slightly so I can pipett bigger volumes (simply use a part of the water used to balance the PCR reaction). You can also premix primer pairs, if you want, I have never seen problems doing this.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-19T19:18:40.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16691" PostTypeId="1" AcceptedAnswerId="16693" CreationDate="2014-04-19T19:51:19.623" Score="0" ViewCount="155" Body="&lt;p&gt;The word seems to be of German origin.&#xA;I have it here&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Saccus lymphaticus inguinalis,&#xA;  Saccus lymphaticus jugularis,&#xA;  Saccus lymphaticus posterior,&#xA;  Saccus lymphaticus retroperitonaealis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would like to use the word &quot;sinus&quot; instead.&#xA;However, Google search does not give good results for it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the meaning of the word &quot;saccus&quot; here?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="16866" LastEditDate="2020-04-16T04:49:38.187" LastActivityDate="2020-04-16T04:49:38.187" Title="What is Saccus in Embryology?" Tags="&lt;homework&gt;&lt;embryology&gt;&lt;etymology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16692" PostTypeId="2" ParentId="16668" CreationDate="2014-04-19T20:13:19.680" Score="2" Body="&lt;p&gt;Small or relatively small amounts of the antigen can cause an allergy, when you have IgE antibodies which fit to this antigen. They will then cause a local immune reaction and cause the secretion of histamine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the desensitation therapy large amounts of antigen are given (which is not without risk). The mechanism behind this therapy is not completely understood, but there are some good points.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The immunetherapy seems to induce class switching from the IgE antibodies which can trigger allergic reaction to IgG who can not do this. Furthermore the IgG will mark the antigen for uptake and degradation by the mast cells.&#xA;This seems to be induced by a shift from a Th2 immune response over to a Th1 response. This also leads to the production of a different set of cytokines which are anti-inflammatory (IL-10 for example) and the already mentioned different secondary immune response. The immunetherapy reduces the amount of mast cells, basophils and eosinophils which are recruited into skin, nose, eye and the bronchial mucosa. These cell usually support the reaction to allergens in this tissues after the exposure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See these papers for more information:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20176266&quot; rel=&quot;nofollow&quot;&gt;Allergen immunotherapy.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.aacijournal.com/content/7/S1/S5&quot; rel=&quot;nofollow&quot;&gt;Allergen-specific immunotherapy&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-19T20:13:19.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16693" PostTypeId="2" ParentId="16691" CreationDate="2014-04-19T20:26:37.733" Score="3" Body="&lt;p&gt;Saccus simply means sac or bag and is is closed cavity. The lymph nodes develop from the structures, see this image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JWHGT.gif&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Superior cardinal vein (jugular vein)&lt;/li&gt;&#xA;&lt;li&gt;Jugular lymphatic sacs&lt;/li&gt;&#xA;&lt;li&gt;Right subclavian vein&lt;/li&gt;&#xA;&lt;li&gt;Axillary lymphatic sacs&lt;/li&gt;&#xA;&lt;li&gt;Left brachiocephalic vein&lt;/li&gt;&#xA;&lt;li&gt;Thoracic duct (bilateral)&lt;/li&gt;&#xA;&lt;li&gt;Lumbar lymphatic sacs&lt;/li&gt;&#xA;&lt;li&gt;Iliac lymphatic sacs&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The image is taken from this &lt;a href=&quot;http://www.embryology.ch/anglais/pcardio/lymph01.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;webpage&lt;/a&gt;, which should be interesting for you.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-19T20:26:37.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16694" PostTypeId="1" CreationDate="2014-04-19T21:53:45.740" Score="4" ViewCount="480" Body="&lt;p&gt;There is both long and short limb gastric bypass surgeries (along with several other variations on intestinal bypass procedures). How much of the jejunum is bypassed with a long-limb and short-limb gastric bypass?&lt;/p&gt;&#xA;" OwnerUserId="6415" LastEditorUserId="16299" LastEditDate="2015-12-31T19:13:34.320" LastActivityDate="2015-12-31T19:13:34.320" Title="How much of the jejunum is bypassed during gastric bypass?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;surgery&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16698" PostTypeId="2" ParentId="16577" CreationDate="2014-04-19T23:26:45.253" Score="2" Body="&lt;p&gt;I really good intro to evolution book is The Evolution of Vertebrate Design by Leonard Radinski. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, for a more math based approach you could look into Narrow Roads of Gene Land. These are collected papers of W.D Hamilton. &lt;/p&gt;&#xA;" OwnerUserId="6412" LastActivityDate="2014-04-19T23:26:45.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16699" PostTypeId="1" AcceptedAnswerId="16713" CreationDate="2014-04-19T23:49:08.200" Score="2" ViewCount="1441" Body="&lt;p&gt;Mold spores sometimes have the same shape as platelets in blood. If I were designing a spore it would probably be spherical. Is there any advantage to this cup-like shape? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe there is some advantage in flow properties in fluid or air? And maybe the physics of structures on that scale differ from that of everyday objects?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks. &lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2014-04-20T13:17:01.377" Title="Advantage of cup-like shape of blood cells, spores?" Tags="&lt;cell-biology&gt;&lt;physiology&gt;&lt;mycology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16700" PostTypeId="1" AcceptedAnswerId="57873" CreationDate="2014-04-20T00:29:36.840" Score="5" ViewCount="562" Body="&lt;p&gt;I'm using Alconox powder detergent to clean my laboratory glassware, the powder is a pain to store near the sink and to use. Would like to make a   concentrated liquid to use in its stead. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried a few things, obviously just water and mixing, even up to overnight. It really doesn't go into solution very well, even at seemingly low concentrations. Ive got it up to about 20% w/v but I've tried heat, glycerin, adjusting pH to ~8.8, adding EDTA. I have not added these things in any scientific way, just kind of pouring glycerol or EDTA in. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wondering if anyone in here has experience with detergents like this , or has done something like this before. Thanks in advance!&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6307" LastEditDate="2017-03-30T20:03:49.667" LastActivityDate="2017-03-31T15:00:18.553" Title="Ideal lab glassware cleaner for molecular biologist" Tags="&lt;lab-techniques&gt;&lt;materials&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16701" PostTypeId="1" AcceptedAnswerId="16706" CreationDate="2014-04-20T01:59:03.443" Score="7" ViewCount="990" Body="&lt;p&gt;I hope this question is suitable for this site. I am concerned about the Chip experiment part so I think it should be okay. I am a Applied Math student starting to get into bioinformatics and so I've been looking at Chip Seq data. But to make sense of the Chip Seq data I wish to understand how the experiment is first performed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically my question relates to step 1 of the following diagram:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ocBEJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now my main question is &lt;strong&gt;how come the reads are overlapped?&lt;/strong&gt; Where did we get so many of the (almost the) same reads? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My &quot;understanding&quot; is that:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) They take a DNA sequence and crosslink the protien of interest. Then they get rid of the DNA sequence surrounding this area of interest so now we have a &quot;small&quot; sequence of DNA and in this small DNA is somewhere where our TF binds. Now we make copies of this small DNA seq and run it through a sequencing machine. Is this correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) They take a bunch of cells = bunch of DNA sequences. Then they do the same procedure above (by crosslinking and getting a &quot;smaller&quot; DNA sequence of interest). Since they had many cells to begin with, this means they had many DNA seq to begin with. Now they shear the DNA seq and we have fragments. Then we align these up with the reference genome.&lt;/p&gt;&#xA;" OwnerUserId="6416" LastEditorUserId="948" LastEditDate="2014-04-20T04:17:04.810" LastActivityDate="2014-04-30T04:55:51.793" Title="introduction to Chip Seq" Tags="&lt;bioinformatics&gt;&lt;lab-techniques&gt;&lt;dna-sequencing&gt;&lt;chip&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16702" PostTypeId="2" ParentId="16701" CreationDate="2014-04-20T03:52:38.033" Score="5" Body="&lt;p&gt;So that's not quite how ChIP-Seq (Chromatin ImmunoPrecipitation and Sequencing) works. First, you start out with a large number of cells per sample (preferably on the order of 10&lt;sup&gt;7&lt;/sup&gt; or more - the more sample, the more &lt;a href=&quot;http://en.wikipedia.org/wiki/Immunoprecipitation&quot; rel=&quot;noreferrer&quot;&gt;immunoprecipitations&lt;/a&gt; you can do to different targets) and do whatever it is that you're going to do to induce &lt;a href=&quot;http://en.wikipedia.org/wiki/Transcription_factor&quot; rel=&quot;noreferrer&quot;&gt;transcription factor&lt;/a&gt; binding - expose cells to drugs, treat with &lt;a href=&quot;http://en.wikipedia.org/wiki/Cytokine&quot; rel=&quot;noreferrer&quot;&gt;cytokines&lt;/a&gt;, grow in different conditions, or simply compare two types of cell populations - normal vs. cancer, etc. After a certain period of time, determined by your experimental setup, you cross-link the cells with 1% formaldehyde, which fixes everything in place, including transcription factors bound to DNA. The cells are then broken apart by incubation in a detergent-containing buffer, and nuclei are harvested. After washing, the nuclei are either incubated with micrococcal nuclease (MNase) to digest DNA into strands of 1-5 &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleosome&quot; rel=&quot;noreferrer&quot;&gt;nucleosomes&lt;/a&gt; in length (150-900 bp), or sheared by mechanical &lt;a href=&quot;http://en.wikipedia.org/wiki/Sonication&quot; rel=&quot;noreferrer&quot;&gt;ultrasonication&lt;/a&gt;, hopefully leaving strands of the same length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you have your DNA strands, you add &lt;a href=&quot;http://en.wikipedia.org/wiki/Antibody&quot; rel=&quot;noreferrer&quot;&gt;antibodies&lt;/a&gt; to specific targets - either certain forms/&lt;a href=&quot;http://www.cellsignal.com/common/content/content.jsp?id=science-tables-histone&quot; rel=&quot;noreferrer&quot;&gt;post-translational modifications of the histone proteins&lt;/a&gt; that make up the nucleosome, or to specific transcription factors or TF families. The antibodies bind to their targets, and are enriched by incubating with (generally magnetic) beads that have the antibody-binding protein &lt;a href=&quot;http://en.wikipedia.org/wiki/Protein_G&quot; rel=&quot;noreferrer&quot;&gt;Protein G&lt;/a&gt; covalently attached to their surfaces. The beads are washed with low-salt and high-salt washes, then the formaldehyde cross-links are reversed and the chromatin is eluted from the beads in an elution buffer at high temperature (65°C) with vortexing in a thermomixer. Any remaining protein is removed by digesting with Proteinase K, the DNA is purified using a spin column, and you now have your enriched, purified DNA sample ready for sequencing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2Wka6.gif&quot; alt=&quot;ChIP method overview from CST&quot;&gt;&#xA;&lt;sup&gt;&lt;a href=&quot;http://www.cellsignal.com/common/content/content.jsp?id=chip-assay-overview&quot; rel=&quot;noreferrer&quot;&gt;Source&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antibody binding and enrichment of known sequences is often first analyzed by regular &lt;a href=&quot;http://en.wikipedia.org/wiki/PCR&quot; rel=&quot;noreferrer&quot;&gt;PCR&lt;/a&gt;, just to ensure that everything worked. Once your sample has been validated, it is then prepared for &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_sequencing#Next-generation_methods&quot; rel=&quot;noreferrer&quot;&gt;next-gen sequencing&lt;/a&gt;. We are now near Step 1 of your illustration above. The read lengths of some instruments may be shorter than the average length of the fragments you prepared during the ChIP step (150-900 bp), so during the library construction phase they are further broken down into shorter strands before having the common primer templates ligated to them (if that's the technology you're using). Even if the instrument allows you to use the full length of your DNA strands, you need to remember that the sample is the aggregate DNA from millions of cells, and they didn't all break after MNase digestion in exactly the same way. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After amplification and reading, you are then left a large number of short sequences, which need to be compared to a reference genome and aligned: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BrSFY.png&quot; alt=&quot;Mapping reads&quot;&gt;&#xA;&lt;sup&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/File:Mapping_Reads.png&quot; rel=&quot;noreferrer&quot;&gt;Source&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since we've already enriched for certain regions of DNA by using the antibodies which bind to DNA-bound or -associated proteins, there will be a larger number of similar overlapping reads in enriched areas, allowing us to tell where the histone, transcription factor, or other protein was bound when the sample was originally cross-linked.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully this all makes sense to you. I based my description of the ChIP protocol on Cell Signaling's &lt;a href=&quot;http://www.cellsignal.com/common/content/content.jsp?id=apps-chromatin-immunoprecipitation&quot; rel=&quot;noreferrer&quot;&gt;SimpleChIP&lt;/a&gt; products, which I've found to be of quite good quality and reproducibility (no, I don't work for them!).&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-04-20T03:52:38.033" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16703" PostTypeId="2" ParentId="9556" CreationDate="2014-04-20T04:07:41.620" Score="0" Body="&lt;p&gt;It's simplest to think about a haploid population with size $N$. Say there are two alleles, $A$ and $a$, with $A$ having frequency $p$ in this generation. Each $A$ individual will have some realized fitness (i.e., number of offspring) in this generation; let's call this number $w_A^{(i)}$ for the $i^\text{th}$ individual. The total number of $A$ individuals in the next generation is then $\sum_{i=1}^{Np}w_A^{(i)}=Npw_A$, where $w_A$ is the arithmetic mean of the fitness distribution, $w_A\equiv\sum_{i=1}^{Np}w_A^{(i)}/(Np)$. So regardless of how weird the distribution of the $w_A^{(i)}$ was, all that matters (in the large-$N$ limit) is the arithmetic mean.&lt;/p&gt;&#xA;" OwnerUserId="6313" LastActivityDate="2014-04-20T04:07:41.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16704" PostTypeId="5" CreationDate="2014-04-20T04:14:41.057" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-04-20T04:14:41.057" LastActivityDate="2014-04-20T04:14:41.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16705" PostTypeId="4" CreationDate="2014-04-20T04:14:41.057" Score="0" Body="ChIP, or Chromatin ImmunoPrecipitation, is a molecular biology technique used to study protein-DNA interactions in the natural context of the cell. It is performed by cross-linking proteins and DNA, cleaving the chromatin into short strands, enriching for certain regions using antibodies specific to DNA-binding proteins, and studying the sequences and/or epigenetic markers of the DNA." OwnerUserId="948" LastEditorUserId="948" LastEditDate="2014-04-20T09:22:10.900" LastActivityDate="2014-04-20T09:22:10.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16706" PostTypeId="2" ParentId="16701" CreationDate="2014-04-20T04:22:45.997" Score="6" Body="&lt;p&gt;The basic steps of ChIP-Seq are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Crosslinking proteins to DNA - this fixes the proteins in their natural positions&lt;/li&gt;&#xA;&lt;li&gt;Nuclease digestion - this removes regions that are unbound to protein; nucleases are sterically hindered from digesting protein-bound DNA&lt;/li&gt;&#xA;&lt;li&gt;Immunoprecipitation - this allows isolation of the target protein by binding it to a selective antibody&lt;/li&gt;&#xA;&lt;li&gt;Sequencing to determine the bound DNA sequence&lt;/li&gt;&#xA;&lt;li&gt;Mapping the reads to the reference genome&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Why so many reads? They are taking many reads from different cells. Why are the reads so short? Many modern next-gen sequencing methods are limited to ~30 bp reads. Thus, the reads you see are not actually the entire protected sequence but rather just a shorter fragment from the 5' end (where sequencing starts from). The why behind this is explained by Jiang and Pugh, 2009 (Nucleosome positioning and gene regulation: advances through genomics):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Three DNA sequencing technologies have been used to map nucleosomes. Pyrosequencing using the Roche 454 GS20/FLX&#xA;  sequences nucleosomel DNA end-to-end, allowing both nucleosome&#xA;  borders to be linked in a single sequence. This method provides the&#xA;  greatest mapping accuracy, particularly in genomic regions of low&#xA;  complexity. By contrast, other platforms, such as those provided by&#xA;  the Illumina-Solexa Genome Analyzer and Applied Biosystems SOLiD,&#xA;  generate only 25-35 by sequence tags, requiring both nucleosome&#xA;  borders to be inferred. Nonetheless, these short-read technologies&#xA;  produce &gt;100 times the number of sequence tags at a similar cost as&#xA;  the long-read technologies, and so the short-read technology is&#xA;  currently the only practical technology for mapping nucleosomes in&#xA;  large genomes. The higher tag count of the short-read technology&#xA;  enhances mapping accuracy and thus provides a practical way of&#xA;  mapping nucleosomes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why are the reads overlapped? I can think of a few explanation for that. For starters, Protein-DNA binding is variable in its specificity. In other words, a given protein might bind at the exact same site every time or it may bind 'around' a site or it may bind randomly. A protein that binds an exact sequence would be expected to produce reads that are more in phase that one that binds more variably. Next, the nuclease digestion process is random (or at least expected to be). Thus the DNA cleavage point relative to the protein is variable and your reads start from different points. Again, from Jiang and Pugh:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At any given genomic locus, the preferential positioning of nucleosomes--called phasing--can be described. At most loci, there is an approximately Gaussian (normal) distribution of nucleosome positions around particular genomic coordinates, ranging from ~30 by for highly phased nucleosomes to a random continuous distribution throughout an array. How much of this variation is due to genuine positional heterogeneity and how much is an artefact that is caused by overtrimming or undertrimming of the DNA at nucleosome borders by micrococcal nuclease during sample preparation remains to be determined. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Does that answer your question? Basically the reads are overlapped because there are many of them and they may differ either because of actual variance in the DNA binding site (which is biologically significant) or because of variance in the DNA digestion site (which is a methodological flaw). As with any biological experiment, you must perform many replicates to statistically determine the source of the variance and this is done by taking many reads. I recommend you read the article I quoted from, it is a good overview of histone mapping with ChIP and is likely also applicable to what you're studying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, do you know why there are two sets of reads (red and blue)? I would venture a guess that they are taken from opposite strands. In other words, they are reads of the same DNA region taken from different directions. That might help clarify what's going on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;To conclude:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;DNA is not extracted from a single cell. In usual procedures it is&#xA;always from a collection of cells or from tissues.&lt;/li&gt;&#xA;&lt;li&gt;The overlap in TF associated reads arises because of the TF bound&#xA;sequence coming from different cells in this collection.&lt;/li&gt;&#xA;&lt;li&gt;Each DNA piece is amplified and clusters are formed in the NGS&#xA;sequencers (for the ease of detection);&lt;/li&gt;&#xA;&lt;li&gt;In a homogeneous cell collection i.e. all cells are of same type, the&#xA;variability in the read position usually arises because of&#xA;flexibility of binding sites (i.e TF wont &lt;strong&gt;exactly&lt;/strong&gt; bind to at a&#xA;certain locus). Also, as previously mentioned the variability can&#xA;arise during the technical procedures.&lt;/li&gt;&#xA;&lt;li&gt;In case of heterogeneous tissues the variability arises because of&#xA;different biochemical status of different cells. Strictly speaking&#xA;there is always some heterogeneity even in an apparently homogeneous&#xA;tissue but tissues such as brain are highly heterogeneous&lt;/li&gt;&#xA;&lt;li&gt;In the case of nucleosomes the positioning is not exact because the&#xA;sequence contribution to the position is very minimal. Certain&#xA;nucleosome positions are tightly maintained for e.g. around the TSS&#xA;(transcription start sites) whereas in other regions the positioning&#xA;is fuzzy because of the dynamic nature of the chromatin.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-04-30T04:55:51.793" LastActivityDate="2014-04-30T04:55:51.793" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16707" PostTypeId="1" CreationDate="2014-04-20T05:37:04.090" Score="3" ViewCount="3533" Body="&lt;p&gt;In plasmid isolation, isopropanol is used to renature only the plasmid macromolecules after we precipitate all macromolecules(DNA, RNA, plasmids) using sodium acetate solution. How does it do that? How does it not renature every other macromolecule?&lt;/p&gt;&#xA;" OwnerDisplayName="user6417" LastActivityDate="2016-11-28T09:02:21.147" Title="Role of isopropanol in plasmid isolation" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16708" PostTypeId="2" ParentId="16707" CreationDate="2014-04-20T06:09:01.150" Score="4" Body="&lt;p&gt;In a standard DNA preparatory procedure, isopropanol is used to precipitate the DNA. Nucleic acids are insoluble in alcohols, and bulk or stick together. This sticking together can be further enhanced by increasing the ionic strength such as through addition of sodium acetate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;alcohols in fact don't really denature the DNA.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-04-20T06:09:01.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16709" PostTypeId="1" AcceptedAnswerId="16712" CreationDate="2014-04-20T07:57:30.113" Score="2" ViewCount="2209" Body="&lt;p&gt;we know that cytoplasm of cells are filled with water molecules and other hydrophilic molecules so my question is why the water of cytosol doesn't dissolve the ionic part of the lipid bilayer or why it doesn't dissolve the proteins and enzymes which are most polar and ionic and they still form structures,organelle and function and suspended in water?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="1320" LastEditDate="2014-04-21T09:28:20.000" LastActivityDate="2014-04-21T09:39:00.930" Title="Why doesn't the cytosol dissolve the polar structures?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;cell&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16711" PostTypeId="1" CreationDate="2014-04-20T09:26:53.903" Score="1" ViewCount="541" Body="&lt;p&gt;I am working on my bachelors thesis, where one part of it is to find width of vein in fingertip. I use database images and extract vein patterns from it, but i have to calculate the width of vein and I have no comparison of how many pixels in pic refers to how many milimeters in real.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to ask how wide is the vein approximately in fingertip or in finger. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks a lot, it would be really helpful.&lt;/p&gt;&#xA;" OwnerUserId="6419" LastActivityDate="2014-04-20T09:26:53.903" Title="Width of vein in finger" Tags="&lt;human-biology&gt;&lt;bioinformatics&gt;&lt;physiology&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16712" PostTypeId="2" ParentId="16709" CreationDate="2014-04-20T12:40:17.060" Score="4" Body="&lt;p&gt;Many cell components are not simply hydrophobic or hydrophilic, but have dual affinities. Proteins typically have structures which result in the interior of the protein being hydrophobic and the exterior, which is exposed to the water in the cytosol, being hydrophilic. Thus, differences in polarity between different regions allow proteins to be dissolved in the cytosol while still maintaining a stable structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, the lipid bilayer is composed of phospholipids, which can be described as &quot;tails&quot; of hydrophobic carbon chains connected to hydrophilic phosphate &quot;heads&quot;. The phospholipid bilayer is organized so that the phosphate heads are on the surface of each side of the bilayer, with the carbon chains from each side of the bilayer intertwined with each other in the interior.&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="3340" LastEditDate="2014-04-21T08:11:41.060" LastActivityDate="2014-04-21T08:11:41.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16713" PostTypeId="2" ParentId="16699" CreationDate="2014-04-20T13:17:01.377" Score="3" Body="&lt;p&gt;The functional implications of the biconcave shape of human red blood cells are not fully understood. Several hypotheses have been suggested as explanations, including bending energy (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022519370800327&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;) and effects on oxygen transport (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/002555649390062F&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;). More recently, it has been hypothesized that the shape is important for the flow properties of the blood cells in capillaries. Uzoigwe (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16797867&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;) states that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The deleterious nature of turbulent flow on the cardiovascular system&#xA;  suggests that the biconcave disc form has evolved out of a necessity&#xA;  to maximise laminar flow, minimise platelet scatter which in turn&#xA;  suppress atherogenic activity in the large vessels.(...) The biconcave&#xA;  profile of the discocyte means that much of the mass is distributed in&#xA;  the periphery. This increases the moment of inertia of the cell and&#xA;  subsequently renders the erythrocyte less prone to rotation during&#xA;  flow in the large vessels. Here it is suggest that this reduction in&#xA;  rotation promotes laminar flow and discourages platelet scattering by&#xA;  minimising the &quot;Eddy currents&quot; and it thus anti-atherogenic. A number&#xA;  of pathological mutations result in the red blood cell adopting a&#xA;  spherical shape as opposed to the biconcave disc profile. The sphere&#xA;  has a smaller moment of inertia when compared to the discocyte, as&#xA;  much of the mass is distributed round the centre. The spherocyte is&#xA;  hence much more prone to rotation during flow in the large vessels.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The advantages of various structures do depend on the scale of the system, as you say. For red blood cells, the size of capillaries and veins are of importance. The shape of red blood cells differ in animals that have blood transport systems with different structures than humans. Thus, the red blood cell shape is likely optimized with respect to movement in the human blood transport system, with oxygen diffusion also being a possible factor. To determine what advantages a specific shape of spores would give, you would need to consider the expected environment the spores would live in and their typical lifecycle.  &lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-20T13:17:01.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16714" PostTypeId="2" ParentId="16673" CreationDate="2014-04-20T13:39:34.600" Score="4" Body="&lt;p&gt;The process of sequencing was, and can be, assisted by cloning a DNA fragment into a known site in a plasmid designed to help sequencing. That cloning site is flanked by a known sequence(s) that can use standard primers&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/fUPm7.jpg&quot; alt=&quot;What happens at the cloning site of sequencing vector&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the figure &quot;A&quot; and &quot;B&quot; are just reference points on either side of the Cloning site.  Of course, the plasmid extends on either side of the shown region.  The plasmid is first cut open at the cloning site (upper step) and the unknown DNA fragment ligated in (middle step). Then the known 'forward' sequence can be used, with a complementary primer (shown as the arrow), to prime a sequencing reaction (lower step, dashed line).&#xA;Additional modifications include (per @Chris) preparing the insert with adapters or using a plasmid with sequence that binds a 'reverse' primer (on this figure, that would be an arrow on the right hand side of &quot;B&quot; and pointing to the left).   The reverse primer allows sequencing of the opposite strand to the forward primer and gives access to the 3' end of the inserted unknown sequence.   In the early days of Sanger sequencing read lengths were quite short and often were unable to run the length of a larger insert.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sequencing plasmids are designed so that their forward and reverse primer binding sites are unlikely to contain any sequences that may be found in the insert.   Because these known primers can be used in this manner to sequence almost any insert, they are often called &lt;em&gt;Universal Primers&lt;/em&gt; (per @AlanBoyd).   &lt;/p&gt;&#xA;" OwnerUserId="5922" LastEditorUserId="5922" LastEditDate="2014-04-20T14:08:25.417" LastActivityDate="2014-04-20T14:08:25.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16715" PostTypeId="1" AcceptedAnswerId="16716" CreationDate="2014-04-20T18:16:25.793" Score="4" ViewCount="4902" Body="&lt;p&gt;I understand that when naive B cells are exposed to antigens, they become memory B cells, but what is the functional difference between the two? I've looked at the quite a few article on B cells, but none of them stated the difference clearly enough for me to understand.&lt;/p&gt;&#xA;" OwnerUserId="6423" LastEditorUserId="1081" LastEditDate="2014-04-20T22:07:35.047" LastActivityDate="2014-06-26T17:33:13.887" Title="What's the difference between naive and memory B cells?" Tags="&lt;immunology&gt;&lt;cell&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16716" PostTypeId="2" ParentId="16715" CreationDate="2014-04-20T18:42:02.260" Score="4" Body="&lt;p&gt;The main difference is that memory B cells start an immune reaction much more effective and faster than naive B cells. The reaction is also specific towards the antigen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The memory B cell has a specific membrane receptor for an antigen. It produces specific antibodies only when exposed to the antigen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Tangye SG, Avery DT, Deenick EK, Hodgkin PD. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12517929&quot; rel=&quot;nofollow&quot;&gt;Intrinsic differences in the proliferation of naive and memory human B cells as a mechanism for enhanced secondary immune responses.&lt;/a&gt; J. Immunol. 2003 Jan 15;170(2):686-94. PubMed PMID: 12517929. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;B cell,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=B_cell&amp;amp;oldid=612990219&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=B_cell&amp;amp;oldid=612990219&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-26T17:33:13.887" LastActivityDate="2014-06-26T17:33:13.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16717" PostTypeId="1" CreationDate="2014-04-20T21:26:54.110" Score="1" ViewCount="1421" Body="&lt;p&gt;&lt;a href=&quot;https://www.dbfz.de/web/fileadmin/user_upload/Vortraege/BiogasWorld2014/18_Kovacs_ENG.pdf&quot; rel=&quot;nofollow&quot;&gt;This presentation on anaerobic digestion mentions (pg. 19)&lt;/a&gt; two major pathways for the digestion of amino acids: Stickland reaction and reductive deamination. While I find some info on the former, what is reductive deamination? What is a representative reaction and what partners are needed?&lt;/p&gt;&#xA;" OwnerUserId="3037" LastEditorUserId="3340" LastEditDate="2014-04-21T09:24:09.320" LastActivityDate="2014-04-21T10:21:37.103" Title="What is reductive deamination?" Tags="&lt;biochemistry&gt;&lt;digestion&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16719" PostTypeId="1" AcceptedAnswerId="16720" CreationDate="2014-04-21T00:55:03.330" Score="8" ViewCount="914" Body="&lt;p&gt;My friend made the claim that there exists a protein in your eye responsible for vision. This protein is sensitive to different wavelengths of light, and when it gets hit by the right wavelength, it kinks. In order to be un-kinked, he claimed, it has to be shipped down to the liver, and then back up to the eye. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;He teaches organic chemistry at UCLA, so I trust him a little bit. But I couldn't find this with a quick search. Anyone know if this is legit?&lt;/p&gt;&#xA;" OwnerUserId="6426" LastEditorUserId="1320" LastEditDate="2014-04-21T07:11:23.473" LastActivityDate="2014-04-22T05:34:25.323" Title="Is there a protein in the eye that gets kinked by photons and shipped down to the liver to get un-kinked?" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16720" PostTypeId="2" ParentId="16719" CreationDate="2014-04-21T01:41:10.450" Score="13" Body="&lt;p&gt;The protein is called &lt;a href=&quot;https://en.wikipedia.org/wiki/Rhodopsin#Phototransduction&quot; rel=&quot;nofollow noreferrer&quot;&gt;rhodopsin&lt;/a&gt; and the bit that gets kinked up is called &lt;a href=&quot;https://en.wikipedia.org/wiki/Retinol#Vision&quot; rel=&quot;nofollow noreferrer&quot;&gt;retinol&lt;/a&gt;.   Normally when light hits it, it does trans to cis isomerization at the 11th carbon.  'kinks up' is a pretty apt way of describing it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/G38tJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not familiar with the shipped down to the liver part, but I'm guessing that the photo reaction of the retinol with itself or the protein must occasionally make the rhodopsin-retinol complex unfunctional - perhaps by the double bonds cross linking to other atoms in the retinol or to the protein.  As I understood it the retinol just straightens out again.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9562631&quot; rel=&quot;nofollow noreferrer&quot;&gt;This reference shows that in the presence of rhodopsin, 11-cis retinol will become all trans again normally&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There should be enzymes in the liver that can recycle some messed up retinol configurations.  Its probably not the main route through your body. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23105095&quot; rel=&quot;nofollow noreferrer&quot;&gt;Retinol is stored in the liver from dietary intake&lt;/a&gt;, and then shipped via retinol binding proteins to the eye. So that is the organ which is the source of retinol in the human body (and probably most animals).  It should catch damaged retinols and refurbish them the same way it does those taken in via the diet.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-04-22T05:34:25.323" LastActivityDate="2014-04-22T05:34:25.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16721" PostTypeId="1" AcceptedAnswerId="16795" CreationDate="2014-04-21T04:39:15.270" Score="0" ViewCount="740" Body="&lt;p&gt;I would like to download all the gene pathways and genes of each pathway. Preferably, gene length of each gene as well. It would be a lot more convenient if there is an R package. &lt;/p&gt;&#xA;" OwnerUserId="6428" LastActivityDate="2014-07-04T07:11:04.577" Title="is there a way to do batch download for all gene pathways?" Tags="&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16722" PostTypeId="2" ParentId="16709" CreationDate="2014-04-21T08:12:46.363" Score="1" Body="&lt;p&gt;&lt;strong&gt;ADDENDUM&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Water can disrupt the intramolecular hydrogen bonds by bonding to the donors/acceptors. However, water in many cases can also act like a bridge and stabilize the protein structures. As already pointed out by jarlemag, the hydrophobic residues can &lt;em&gt;push&lt;/em&gt; the water out of the pockets where intramolecular hydrogen bonds are to be formed. You may notice that the cores of the proteins are mostly hydrophobic while the surface is hydrophilic. So water plays an important role in the maintenance of the structure. Therefore many proteins need the assistance of chaperones to fold into a stable structure; once folded they maintain their structure while remaining suspended in water (I use the term suspended because proteins don't form true solutions: they form colloidal mixture). Chaotropic agents like urea exert their denaturating effect by disrupting hydrogen bonds as well as by increasing the entropy of the water molecules around the hydrophobic regions and thereby reducing the net hydrophobicity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;(I hope it is clear now)&lt;/em&gt; &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-04-21T08:12:46.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16723" PostTypeId="2" ParentId="16709" CreationDate="2014-04-21T09:39:00.930" Score="1" Body="&lt;p&gt;This answer doesn't add anything to the others, but is an attempt to explain using different language.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&quot;my question is why the water of cytosol doesn't dissolve the ionic part of the lipid bilayer&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a sense, it does. See my diagram below The bilayer is composed of phospholipids, classic amphiphiles with a polar head group and a nonpolar tail group. The polar head group can interact favourably (in a thermodynamic sense) with the cytosol through hydrogen bonds. In contrast the hydrocarbon tails cannot interact with water through hydrogen bonds. This means that they force a structure on the surrounding water which decreases entropy of the system (unfavourable). The thermodynamic solution to this is for the bilayer to form - this maximises the interactions between the head groups and the aqueous surroundings and minimises the unfavourable interactions between the tail groups and the solvent. A beneficial side effect is tha the close packing of the tail groups maximises van der Waals interactions between them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On balance the 'ordered' nature of the bilayer is stable because it is paid for by increased disorder of the solvent and favourable interactions between the hydrocarbon tails.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exactly the same arguments apply to proteins: proteins fold to minimise the exposure of nonpolar amino acid side chains.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pMbKm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-04-21T09:39:00.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16724" PostTypeId="1" CreationDate="2014-04-21T10:00:50.187" Score="3" ViewCount="141" Body="&lt;p&gt;I have a dataset containing morphological and performance measures of species from various groups, including insects, lizards, frogs, spiders etc, and want to analyse the relationship between these measures and the animal's body size  via regression methods, while controlling for common ancestry, similar to what has been done in this work:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Peattie, A. M. &amp;amp; Full, R. J. Phylogenetic analysis of the scaling of wet and dry biological fibrillar adhesives PNAS, 2007, 104, 18595-18600&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/104/47/18595.abstract&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/104/47/18595.abstract&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For most of my species, statistically supported branch lengths are lacking, and I was thus wondering what the best way to conduct my analysis would be, and I would be grateful for any hint.&lt;/p&gt;&#xA;" OwnerUserId="6431" LastActivityDate="2014-04-27T14:40:05.307" Title="phylogenetic Independent contrasts with unresolved tree" Tags="&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16725" PostTypeId="2" ParentId="16717" CreationDate="2014-04-21T10:21:37.103" Score="2" Body="&lt;p&gt;Amine is already a reduced state and therefore the reduction part is not of the amine. In chemical process of reductive deamination the arylamine is first converted to an intermediate, usually by sulphonylation of the amine nitrogen &lt;a href=&quot;http://pubs.acs.org/doi/full/10.1021/jo010681w&quot; rel=&quot;nofollow&quot;&gt;[ref]&lt;/a&gt;, which in turn is reduced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$ArNH_2 + CH_3SO_2Cl \ \ \  _{\overrightarrow{pyridine}}\ \ \  ArNHSO_2CH_3 \ \ \  _{\overrightarrow{NaH+NH_2Cl}}  \ \ \ ArH$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biochemical anaerobic reductive deamination is reported but not for amino acids (I couldn't find any). It is reported for anilines which probably proceeds via a carboxyl intermediate [&lt;a href=&quot;http://kops.ub.uni-konstanz.de/handle/urn%3anbn%3ade%3absz:352-opus-25611&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2002.tb11149.x/pdf&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC252412/&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; article says that the non-classical amino acid $ornithine\ \ $ is converted to $\delta-aminovaleric acid\ \ $ via a $\ proline\ $ intermediate but no mechanism is described.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think this answers your question completely; the best solution would be to ask the author of the presentation for the exact reference.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-04-21T10:21:37.103" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16727" PostTypeId="1" AcceptedAnswerId="16728" CreationDate="2014-04-21T12:05:03.347" Score="3" ViewCount="490" Body="&lt;p&gt;In Ross's book of histology it says that the mesothelium that includes all body cavities is made of simple squamous epithelium but in other places it says that in the gastrointestinal tract it is made of simple columnar epithelium. Is it that the trachea and the the gastrointestinal tract are not classed as cavities?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="1320" LastEditDate="2014-04-21T13:48:27.523" LastActivityDate="2014-06-26T17:43:10.563" Title="What are the internal surfaces of body cavities actually made of?" Tags="&lt;histology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16728" PostTypeId="2" ParentId="16727" CreationDate="2014-04-21T13:27:09.650" Score="4" Body="&lt;p&gt;The peritoneum, the pleura, the pericardium, the tunica vaginalis testis and the tunica serosa uteri are made of mesothelium (simple squamous epithelium) &lt;sup&gt;[1]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The GI tube is made of a specialized tissue composed from four layers: mucosa, submucosa, muscularis externa and adventitia. The innermost layer (mucosa) has an epithelium that is stratified, squamous and non-keratinising, for protective purposes. The internal organs in the peritoneal cavity are covered with the visceral sheet of peritoneum which is the adventita layer &lt;sup&gt;[2]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trachea is made of respiratory epithelium, which serves to moisten and protect the airways. It is lined with pseudostratified columnar epithelium with goblet cells that produce mucus &lt;sup&gt;[3]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trachea, stomach and intestines are considered cavitary organs as opposed to parenchymatous organs (lung, kidney, liver).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Mesothelium,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Mesothelium&amp;amp;oldid=598055771&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Mesothelium&amp;amp;oldid=598055771&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Gastrointestinal wall,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Gastrointestinal_wall&amp;amp;oldid=598338180&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Gastrointestinal_wall&amp;amp;oldid=598338180&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Trachea,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Trachea&amp;amp;oldid=613017631&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Trachea&amp;amp;oldid=613017631&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-26T17:43:10.563" LastActivityDate="2014-06-26T17:43:10.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16729" PostTypeId="2" ParentId="16629" CreationDate="2014-04-21T14:12:26.370" Score="0" Body="&lt;p&gt;I'm going to speculate that exons that are not cleanly duplicated activate the cell death machinery. We see the clean exon duplications because they are able to survive.&lt;/p&gt;&#xA;" OwnerUserId="1241" LastActivityDate="2014-04-21T14:12:26.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16731" PostTypeId="1" CreationDate="2014-04-21T15:39:39.780" Score="3" ViewCount="1779" Body="&lt;p&gt;This is from SAT subject biology test practice question. The answer it gave me was both chiasmata and centromeres. I can understand they are held by chiasmata but why also centromeres? I looked it up, I didn't find anywhere mentioned that they are held by centromeres also, only synaptonemal complex and chiasmata. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;tetrads are truly held by spindle fibers on centromeres too, but isn't the question asking what hold them together? Even without spindle fibers, they can still be held by chiasmata I guess.&lt;/p&gt;&#xA;" OwnerUserId="5834" LastActivityDate="2015-09-18T01:24:32.463" Title="tetrads in meiosis are held together by what" Tags="&lt;homework&gt;&lt;meiosis&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16732" PostTypeId="1" CreationDate="2014-04-21T15:51:53.193" Score="4" ViewCount="250" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dream#Dreams_in_animals&quot;&gt;From Wikipedia:&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Studies have observed dreaming in mammals such as monkeys, dogs, cats,&#xA;  rats, elephants and shrews. There have also been signs of dreaming in&#xA;  birds and reptiles.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Have there been such signs in any invertebrate species?&lt;/p&gt;&#xA;" OwnerDisplayName="user4810" LastActivityDate="2014-04-22T00:49:28.470" Title="Do invertebrates dream?" Tags="&lt;sleep&gt;&lt;dreaming&gt;&lt;invertebrates&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2014-05-30T04:39:19.770" ContentLicense="CC BY-SA 3.0" />
  <row Id="16733" PostTypeId="1" AcceptedAnswerId="16734" CreationDate="2014-04-21T16:14:17.133" Score="0" ViewCount="97" Body="&lt;p&gt;I have been reading blogs, Guyton and Pocock about what triggers the feeling of thirsty.&#xA;I am not convinced that is the fact of&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;warm water&lt;/li&gt;&#xA;&lt;li&gt;time is short so not much water lost&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Assume that the water's temperature is the same as body's temperature.&#xA;Of course, there is little temperature change caused by air and water, but I think it is not that much.&#xA;I think more important is the steady, continous irritation of skin as a mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wrote my suggestion for the answer below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do sympaticus and stimulation of lymphatic circulation cause feeling of thirsty?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-21T16:30:17.423" Title="Does Sympaticus and lymphatic circulation cause feeling of thirsty after short shower?" Tags="&lt;physiology&gt;&lt;lymphatic-system&gt;&lt;hypothalamus&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16734" PostTypeId="2" ParentId="16733" CreationDate="2014-04-21T16:14:17.133" Score="1" Body="&lt;p&gt;I think the mechanism is the &lt;strong&gt;stimulation of the skin&lt;/strong&gt; systemically i.e. the most important endocrine organ which we have.&#xA;The irritation of skin in the shower is&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;mechanical turbulent stream of water in acceleration&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1) hitting (start) your skin from different directions (many flows) in many different flows &lt;/li&gt;&#xA;&lt;li&gt;it's you who causes the systemic stimulation effect!&lt;/li&gt;&#xA;&lt;li&gt;water steam in acceleration all the time; moving its direction; in ellipsoidal tracts&lt;/li&gt;&#xA;&lt;li&gt;water stream flowing slowly on your skin towards periphery mostly&lt;/li&gt;&#xA;&lt;li&gt;causing smooth but continuos irritation of your skin&#xA;&lt;ul&gt;&#xA;&lt;li&gt;activation of smooth muscles in synchronous order which boost lymphatic circulation&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;mechanical turbulent stream of air (temperature change of skin)&#xA;&lt;ul&gt;&#xA;&lt;li&gt;this one is not in accelerative move, since there is no forces which keep the subsequent air and skin together&lt;/li&gt;&#xA;&lt;li&gt;very little impact, unless extreme situation (etc in Alaska)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I would think that the increased lymphatic circulation irritates the walls of lymphatic circulation which causes an increase in the need of water there.&#xA;So water would diffuse from vascular space inside blood vessels (extravascular space) into the lymphatic system.&#xA;The decrease in blood pressure through baroreflexive arch and hypothalamus (some nuclei too) would then be sensed as the feeling of thirsty.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Water in shower on the skin &lt;strong&gt;accelerates&lt;/strong&gt;, since it changes its direction all the time from the beginning of the stream until the end.&#xA;I think it is the steady change of irritation's location in ellipsoidal tracts that stimulates hypothalamus.&#xA;I think it is not the strength of the stream but the changing direction that is cause of the irritation.&#xA;Of course, there is little changes in the strength of the total stream. &#xA;I think this is not so significant than the change of the direction of the water flow causing the irritation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, I say that accelerative water streams massage lymphatic system in ellipsoidal tracts.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-04-21T16:30:17.423" LastActivityDate="2014-04-21T16:30:17.423" CommentCount="0" CommunityOwnedDate="2014-04-21T16:14:17.133" ContentLicense="CC BY-SA 3.0" />
  <row Id="16735" PostTypeId="2" ParentId="16629" CreationDate="2014-04-21T16:37:12.407" Score="1" Body="&lt;p&gt;There is a section in the Human Molecular Genetics textbook about how such repeats do occur. Like the commentor said, it is likely a result of recombination. If there are repeats flanking a gene or an exon there can be paring between sister chromatids / chromosomes, which can result in the duplication. See Figure 9.7 here &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK7566/#A1095&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK7566/#A1095&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for how does it &quot;know&quot;: It doesnt. Its not just the exon that is duplicated though. It is also the DNA before and after the exon, which contains cis-elements that splicing factors bind to, which results in the exon being spliced into the transcript.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Splicing is pretty complicated but if just 50 bp upstream and downstream of the exon was also duplicated, it would probably be enough to cause some splicing of the exon. U1 and U2 snRNP bind immediately at the exon-intron junction, and the polypyrimadine tract is about 30 bp or so upstream from the exon. U1 and U2 and the polypyrimadine tract are all vital to splicing. I dont know of any work that shows the minimum requirement for splicing but if you have those 3 you will probably splice the exon at least part of the time. So in sum, its probably not just the exon that is duplicated. It is probably the exon plus the cis elements involved in splicing. &lt;/p&gt;&#xA;" OwnerUserId="4199" LastActivityDate="2014-04-21T16:37:12.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16736" PostTypeId="2" ParentId="16724" CreationDate="2014-04-21T18:13:03.490" Score="2" Body="&lt;p&gt;Look also into PGLS. Either way, one thing you could do--it would be ugly--would be to set all branch lengths to 1. Additionally, you could smooth the tree with penalized likelihood, e.g. &lt;code&gt;chronopl()&lt;/code&gt; function in ape package in R. Again, this is an ugly solution and look into PGLS (it won't solve the ugly phylogeny part).&lt;/p&gt;&#xA;" OwnerUserId="6435" LastEditorUserId="107" LastEditDate="2014-04-27T14:40:05.307" LastActivityDate="2014-04-27T14:40:05.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16737" PostTypeId="2" ParentId="16694" CreationDate="2014-04-21T19:58:29.740" Score="3" Body="&lt;p&gt;One of the most used surgical technique is Roux en-Y where the small intestine is divided approximately 40-50 cm below the lower stomach outlet and is re-arranged into a Y-configuration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The portion of intestine (jejunum) from the upper stomach is called the &quot;Roux limb&quot;. It has a total length of 80 - 150 cm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the Roux en-Y technique &quot;bypasses&quot; only the duodenum and a small portion of jejunum - no more than 50 cm, that's about 7-10% of total length of small intestine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Total_gastrectomy_with_Roux-en-Y.png#mediaviewer/File:Total_gastrectomy_with_Roux-en-Y.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/1/16/Total_gastrectomy_with_Roux-en-Y.png&quot; alt=&quot;Total gastrectomy with Roux-en-Y.png&quot;&gt;&lt;/a&gt;&lt;br&gt;&quot;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Total_gastrectomy_with_Roux-en-Y.png#mediaviewer/File:Total_gastrectomy_with_Roux-en-Y.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;Total gastrectomy with Roux-en-Y&lt;/a&gt;&quot; by &lt;a href=&quot;//commons.wikimedia.org/wiki/User:Ignis&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;User:Ignis&quot;&gt;ignis&lt;/a&gt; - Own work. licensed &lt;a href=&quot;http://creativecommons.org/licenses/by-sa/3.0/&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Creative Commons Attribution-Share Alike 3.0&quot;&gt;CC BY-SA 3.0&lt;/a&gt; via &lt;a href=&quot;//commons.wikimedia.org/wiki/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikimedia Commons&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference:&lt;/strong&gt; Wikipedia contributors, &quot;Gastric bypass surgery,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Gastric_bypass_surgery&amp;amp;oldid=606081291&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Gastric_bypass_surgery&amp;amp;oldid=606081291&lt;/a&gt; (accessed June 27, 2014).&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.053" LastActivityDate="2014-06-27T15:10:41.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16739" PostTypeId="1" AcceptedAnswerId="16743" CreationDate="2014-04-21T20:46:16.797" Score="7" ViewCount="1109" Body="&lt;p&gt;Often, after waking up from a night's sleep hard, flaky, pale yellow crystals are deposited around the eyelids (which easily wash off with water).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are these? Why are they yellow? What are they made of? Is their amount proportional to the length of sleep?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-04-22T03:28:05.713" Title="Crusty eyes in the morning" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16741" PostTypeId="1" AcceptedAnswerId="40505" CreationDate="2014-04-21T21:52:39.653" Score="11" ViewCount="51496" Body="&lt;p&gt;Disregarding hypoxia, what is the minimum air pressure that the human body can tolerate?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(i.e. at what air pressure would the blood start to boil, or skin start to burst, or whatever else might happen that would kill you but isn't related to oxygen?)&lt;/p&gt;&#xA;" OwnerUserId="243" LastActivityDate="2017-04-29T04:48:40.043" Title="What is the minimum air pressure the human body can tolerate if oxygen supply is not an issue?" Tags="&lt;human-biology&gt;" AnswerCount="3" CommentCount="11" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16742" PostTypeId="2" ParentId="16741" CreationDate="2014-04-21T22:23:21.050" Score="4" Body="&lt;p&gt;At sea level, where atmospheric pressure is 1 atm and oxygen is about 21% the partial pressure of oxygen is enough to saturate hemoglobin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lowest tolerable pressure of air is about 0.47 atm (475 millibars of atmospheric pressure) - recorded at &lt;a href=&quot;https://biology.stackexchange.com/questions/16741/what-is-the-minimum-air-pressure-the-human-body-can-tolerate-if-oxygen-supply-is/16742?noredirect=1#comment22653_16742&quot;&gt;5950m&lt;/a&gt; altitude.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At about 0.35 atm (less than 356 millibars at around 8000m) life is impossible. Pulmonary and cerebral edema lead to death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: Wikipedia, &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Effects_of_high_altitude_on_humans&quot; rel=&quot;nofollow noreferrer&quot;&gt;Effects of high altitude on humans&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-06-04T16:43:20.783" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16743" PostTypeId="2" ParentId="16739" CreationDate="2014-04-21T22:29:15.283" Score="8" Body="&lt;p&gt;This is quite common. It is most likely dried &lt;strong&gt;rheum&lt;/strong&gt; (also know by slang terms such as &quot;sleep&quot;, &quot;eye boogers&quot;, &quot;eye crusties&quot;, etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Rheum&lt;/strong&gt; is the result of dried &lt;strong&gt;mucus&lt;/strong&gt;, &lt;strong&gt;tears&lt;/strong&gt; (and the &lt;strong&gt;salt&lt;/strong&gt; and &lt;strong&gt;minerals&lt;/strong&gt; therein), as well as dead &lt;strong&gt;blood&lt;/strong&gt; and &lt;strong&gt;skin cells&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially it is all the stuff that’s normally in your eye that eventually dries up making the contents more condensed giving it a light yellow color. When all that stuff is in your tears it is spread out enough that your tears are still mostly clear. &lt;/p&gt;&#xA;" OwnerUserId="6438" LastEditorUserId="6440" LastEditDate="2014-04-22T03:28:05.713" LastActivityDate="2014-04-22T03:28:05.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16744" PostTypeId="2" ParentId="16731" CreationDate="2014-04-21T23:10:08.943" Score="1" Body="&lt;p&gt;A recombinase only active during meiosis - Dmc1 and a general recombinase Rad51 coat the single-stranded DNA to form nucleoprotein filaments. These filaments hold the homologs together at the chiasma, the point of attachment during crossing over.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-04-22T05:10:03.453" LastActivityDate="2014-04-22T05:10:03.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16746" PostTypeId="1" AcceptedAnswerId="16748" CreationDate="2014-04-21T23:57:33.187" Score="3" ViewCount="188" Body="&lt;p&gt;What is the film that covers the tongue in the mornings, even after brushing the teeth and tongue the night before and why does it have color variations?  Do the different colors mean anything?&lt;/p&gt;&#xA;" OwnerDisplayName="user6116" LastActivityDate="2014-04-22T02:20:13.560" Title="What is the film that covers the tongue?" Tags="&lt;biochemistry&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16748" PostTypeId="2" ParentId="16746" CreationDate="2014-04-22T02:20:13.560" Score="2" Body="&lt;p&gt;It isn't really a film. The tiny bumps that cover your tongue are called papillae, and are normally pink in color. However, they can become inflamed and white when irritated. The appearance of the white &quot;coating&quot; is caused by debris, bacteria and dead cells getting lodged between the papillae. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may be breathing through your mouth when you sleep, which is drying it out. Bacteria may also still be the cause; you may not be brushing well enough or your toothpaste may not be correctly doing its job.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The color variations may be due to different types or amounts of debris, or the color may vary with different conditions &lt;a href=&quot;http://www.mayoclinic.org/symptoms/white-tongue/basics/causes/sym-20050676&quot; rel=&quot;nofollow&quot;&gt;listed here&lt;/a&gt;. Tongue color changes also often occur with glossitis (inflammation of the tongue itself).&lt;/p&gt;&#xA;" OwnerUserId="6441" LastActivityDate="2014-04-22T02:20:13.560" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16749" PostTypeId="1" AcceptedAnswerId="16750" CreationDate="2014-04-22T04:12:50.527" Score="16" ViewCount="61874" Body="&lt;p&gt;What feature of rabies pathophysiology causes hydrophobia? Why is hydrophobia unique to this one particular type of viral infection? &lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2018-10-25T03:05:01.087" Title="Why does rabies cause hydrophobia?" Tags="&lt;virus&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16750" PostTypeId="2" ParentId="16749" CreationDate="2014-04-22T04:48:25.820" Score="11" Body="&lt;p&gt;Rabies causes hydrophobia in the encephalitic stage which means when it affects the brain and causes swelling and inflammation of multiple areas of the brain. Hence, it affects the complex areas in the brain needed for swallowing. Initially into the course of the disease, the patient has involuntary contractions of neck muscles when he drinks water.  At later stages of disease, the patient starts contracting his muscles even at the thought of water. Rabies virus is a neurotropic virus which means that it travels through nerves because of its preference to attach to acetylcholine receptors in the neurons.  That is how the virus spreads from the bite site to the brain(via the nerves).&lt;/p&gt;&#xA;" OwnerUserId="6442" LastEditorUserId="6442" LastEditDate="2018-10-25T03:05:01.087" LastActivityDate="2018-10-25T03:05:01.087" CommentCount="7" ContentLicense="CC BY-SA 4.0" />
  <row Id="16752" PostTypeId="1" CreationDate="2014-04-22T04:52:25.987" Score="2" ViewCount="2122" Body="&lt;p&gt;I have never felt after drinking tea that I can have the power of being able to work late at night. Neither have I felt that it helps me to be awake while working or keeping eyes opened while I am not in mood for sleeping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Drinking tea, then, does not helps me to stay awake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it the nature of the tea itself, or does it have to do with how the body processes caffeine? &lt;/p&gt;&#xA;" OwnerUserId="6443" LastEditorUserId="1320" LastEditDate="2014-04-22T07:37:51.513" LastActivityDate="2014-04-26T13:38:24.357" Title="Why is it that drinking caffeinated tea does not help one to stay awake?" Tags="&lt;pharmacology&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16753" PostTypeId="1" AcceptedAnswerId="16769" CreationDate="2014-04-22T04:56:16.630" Score="2" ViewCount="103" Body="&lt;p&gt;Why do oranges in the US have a small separate detachable part at the tip which is separate from the other pods? It looks like a tiny orange itself and has a long fiber attached to it.&lt;/p&gt;&#xA;" OwnerUserId="6442" LastEditorUserId="1320" LastEditDate="2014-04-22T07:38:49.243" LastActivityDate="2014-04-22T14:44:00.413" Title="Why do oranges in the US have a small separate part?" Tags="&lt;botany&gt;&lt;fruit&gt;&lt;agriculture&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16754" PostTypeId="1" AcceptedAnswerId="16767" CreationDate="2014-04-22T05:02:41.597" Score="2" ViewCount="348" Body="&lt;p&gt;How are oranges in the US or anywhere made seedless? Please explain the broad principles and not the technicalities.&lt;/p&gt;&#xA;" OwnerUserId="6442" LastEditorUserId="3952" LastEditDate="2014-04-22T14:10:46.817" LastActivityDate="2014-04-22T14:35:27.123" Title="How are oranges in the US or anywhere made seedless?" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;food&gt;&lt;ethnobiology&gt;&lt;seeds&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16755" PostTypeId="2" ParentId="16752" CreationDate="2014-04-22T05:08:26.517" Score="0" Body="&lt;p&gt;What is happening to you is 'tolerance'. It is a term used in pharmacology. It is a phenomenon by which a drug/medicine becomes less effective the body gets used to it. One explanation is less receptors for that drug are manufactured because of negative feedback.  You may have developed tolerance to tea.&lt;/p&gt;&#xA;" OwnerUserId="6442" LastActivityDate="2014-04-22T05:08:26.517" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16757" PostTypeId="1" CreationDate="2014-04-22T06:44:53.473" Score="0" ViewCount="4111" Body="&lt;p&gt;Why cold water helps to overcome from high fever in body? As fever is inside the body and we're applying cold water over the body!&lt;/p&gt;&#xA;" OwnerUserId="6443" LastEditorUserId="1320" LastEditDate="2014-04-22T07:39:30.040" LastActivityDate="2014-06-27T14:01:23.457" Title="How does cold water help to overcome high fever?" Tags="&lt;infection&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16758" PostTypeId="2" ParentId="16572" CreationDate="2014-04-22T06:50:57.077" Score="2" Body="&lt;p&gt;According to an article in &lt;em&gt;Vision Research&lt;/em&gt; Volume 50 issue 2 :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The face’s vertical distance between the eyes and the mouth is approximately 36% of its length, and the horizontal distance between the eyes is approximately 46% of the face’s width.&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The article can be found at:&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0042698909005045&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0042698909005045&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6438" LastActivityDate="2014-04-22T06:50:57.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16759" PostTypeId="1" CreationDate="2014-04-22T09:15:04.627" Score="1" ViewCount="2032" Body="&lt;p&gt;If someone falls 30,000 feet without a parachute; what are the chances of survival if they landed in the water?&lt;/p&gt;&#xA;" OwnerUserId="6445" LastEditorUserId="6289" LastEditDate="2014-11-14T16:52:33.590" LastActivityDate="2014-11-14T16:52:33.590" Title="Can human survive falling from 30,000 ft without a chute?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16761" PostTypeId="2" ParentId="16757" CreationDate="2014-04-22T09:55:18.780" Score="2" Body="&lt;p&gt;Fever is triggered when pyrogens cause release of prostaglandin that acts on hypothalamus (which is the center of thermoregulation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fever assists in the healing process by:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;enhancing phagocytosis&lt;/li&gt;&#xA;&lt;li&gt;decreasing negative effects of endotoxins&lt;/li&gt;&#xA;&lt;li&gt;stimulates proliferation of lymphocytes&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Although is a good reaction, when the temperature gets too high it could determine negative effects, like convulsions at children. Brain damage appears when the temperature rises as much as 42 degrees Celsius, and most febrile conditions go up to 40.6 degrees Celsius.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So fever must be kept under control, and cold water helps lowering body temperature. Lowering the temperature will prevent negative effects of fever. Cold water is a symptomatic treatment for fever. Most important is to determine cause of fever and do an ethiological treatment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Source:&lt;/strong&gt; Wikipedia contributors, &quot;Fever,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Fever&amp;amp;oldid=614212619&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Fever&amp;amp;oldid=614212619&lt;/a&gt; (accessed June 27, 2014).&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-27T14:01:23.457" LastActivityDate="2014-06-27T14:01:23.457" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16762" PostTypeId="1" AcceptedAnswerId="16763" CreationDate="2014-04-22T11:44:05.947" Score="5" ViewCount="4901" Body="&lt;p&gt;Untreated diabetes mellitus may lead to blindness and kidney failure because the basement membrane of small blood vessels in these organs thickens due to increased production of collagen and laminin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions : why are these organs most susceptible ? Why will collagen and laminin production increase in diabetes mellitus ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-25T15:07:06.417" Title="Why basement membrane thickens in diabetes mellitus?" Tags="&lt;human-biology&gt;&lt;pathology&gt;&lt;eyes&gt;&lt;histology&gt;&lt;diabetes-mellitus&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16763" PostTypeId="2" ParentId="16762" CreationDate="2014-04-22T13:18:54.850" Score="6" Body="&lt;p&gt;The endothelial cells in small blood vessels take in more glucose (as glucose levels in blood are high due to diabetes.) Thus they form surface glycoproteins which causes the basement membrane to become thicker yet less strong. This leads to blood and protein leakage from the blood stream in other tissues in the space between cells. Blood leakage alters cellular blood supply for all cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Less blood means less oxygen and less nutrients. As you probably know nervous tissue gets damaged fastest without oxygen thus explaining diabetic neuropathy. Also retina and kidney contain cells that get easily damaged when there is not enough blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably the worst complication is neuropathy, because the person suffering from it may suffer a heart attack (caused by the accelerated process of atherosclerosis in diabetes) and feel &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000693.htm&quot; rel=&quot;nofollow&quot;&gt;less pain&lt;/a&gt; (&lt;a href=&quot;http://medlineplus.gov&quot; rel=&quot;nofollow&quot;&gt;http://medlineplus.gov&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Collagen and laminin poduction increases as a result of the fibrosis process that takes place when a tissue gets less nutrients than it needs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diabetes affects all blood vessels, even the larger ones. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Macroangiopathy&quot; rel=&quot;nofollow&quot;&gt;macroangiopaty&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Microangiopathy&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Microangiopathy&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="3615" LastEditDate="2014-04-25T15:07:06.417" LastActivityDate="2014-04-25T15:07:06.417" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16764" PostTypeId="2" ParentId="16759" CreationDate="2014-04-22T13:35:24.347" Score="9" Body="&lt;p&gt;&lt;em&gt;Summary: A fall from &quot;any height&quot; may be survivable, depending on what you hit, but with an expectation of severe injuries. A water impact at terminal velocity will in all likelyhood result in immediate death.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Serbian Flight attendant &lt;a href=&quot;http://en.wikipedia.org/wiki/Vesna_Vulovi%C4%87&quot;&gt;Vesna Vulović&lt;/a&gt; holds the Guiness World Record for surviving a fall without a parchute with an estimated fall height 10,160 metres. However, some doubts have been cast on the accuracy of the record, with claims that the fall was actually only several hundred meters. Vulovic was found partly in the wreckage of the plane, so it can be discussed whether she had a truly &quot;free fall&quot; for the purposes of this question. However, several other persons have been known to survive completely &quot;free&quot; falls from great heights. Although it is hard to verify the exact altitudes, the WW2 aviators &lt;a href=&quot;http://en.wikipedia.org/wiki/Alan_Magee&quot;&gt;Alan Magee&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Nicholas_Alkemade&quot;&gt;Nicholas Alkemade&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Ivan_Chisov&quot;&gt;Ivan Chisov&lt;/a&gt; are reported to have survived falls of about 6700 m, 5500 m and 7000 m, respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact altitudes are in any case not necessarily of interest, as it can be assumed that all persons falling from a height of more than about 500 meters will reach &lt;a href=&quot;http://en.wikipedia.org/wiki/Terminal_velocity&quot;&gt;terminal velocity&lt;/a&gt;, the velocity where air resistance prevents the fall speed from increasing, before hitting the ground. As such, above a certain height, other factors become determining for the survivability of a fall. As has been demonstrated by the listed examples, it is clearly &lt;em&gt;possible&lt;/em&gt; to survive a fall at terminal velocity. However, this requires favorable conditions at the site of impact, and will likely result in severe injuries. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Due to the flat surface and the surface tension of water, it is hard to imagine an unprotected impact with water being survivable at terminal velocity. The best chances for survival will likely be in areas with foliage, snow and/or a hilly landscape allowing the kinetic energy to be dissipated through rolling downhill. Of the listed aviators above, Nicholas Alkemade appears to have been the least injured. About him, it is reported that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;His fall was broken by pine trees and a soft snow cover on the ground.&#xA;  He was able to move his arms and legs and suffered only a sprained leg&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-04-22T13:44:49.377" LastActivityDate="2014-04-22T13:44:49.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16765" PostTypeId="2" ParentId="16509" CreationDate="2014-04-22T14:11:18.990" Score="1" Body="&lt;p&gt;It is generally known that the smaller (or less complex) an organism is, the more &quot;condensed&quot; it's genome is. For example, bacteria (or some eukaryotes) have operons (&lt;a href=&quot;http://en.wikipedia.org/wiki/Operon&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Operon&lt;/a&gt;) or overlapping genes using different and they don't have introns, which alltogether saves a lot of space. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many reasons for that. Available space in the cell is definitely not one if it, however. Energy for copying and maintenance is a good point, but you have to keep in mind how evolution works. Bacteria and unicellular eukaryotes are usually adapted to a very specific environment in which they can reproduce rapidly. This means, they only need a small set of genes, specific for this environment and they have to reproduce very frequent, which means they are very prone to mistakes during DNA-copying. Such a mistake can lead to the death of the cell, which in this case equals the death of the organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In higher organisms however, the advantages of a bigger genome outweigh the disadvantages by far. Evolution can happen much faster because and mistake while copying does not necessarily lead to the death of the whole organism. Adaptation to a much greater variety of conditions is also necessary, e.g. when you look at plants: Their genomes are (on avarage) much bigger than the ones we mammals have, because they cannot move if the conditions around them become unpleasent. Instead, they need to find a way to adapt. This means, a big genome is in this case a fitness bonus. More interestingly, plant genoms are highly mutable (&lt;a href=&quot;http://en.wikipedia.org/wiki/Transposable_element&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Transposable_element&lt;/a&gt;), which was originally thought to be a huge disadvantage.&lt;/p&gt;&#xA;" OwnerUserId="6446" LastActivityDate="2014-04-22T14:11:18.990" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16766" PostTypeId="1" CreationDate="2014-04-22T14:27:34.613" Score="1" ViewCount="128" Body="&lt;p&gt;New to molecular and have learned to design primers from google/youtube so any info would help&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Would someone be willing to share their protocol for degenerate primer design?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Breakdown:&#xA;Trying to design degenerate primers to amplify/clone specific GPCR genes from an unsequenced genome of a particular fish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm using Ensembl and Genbank for sequences of closely related fish but the complete gene has only been sequenced in 2 other fish species. &#xA;I use ClustalOmega for alignment. Is it okay to just use 2 other species for generating degenerates?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) are there any other good databases for gene sequences?&lt;/p&gt;&#xA;" OwnerUserId="6412" LastEditorUserId="3340" LastEditDate="2014-12-05T10:34:51.887" LastActivityDate="2014-12-05T10:34:51.887" Title="Degenerate primer design for DIG in situ hybridization" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;experimental-design&gt;&lt;primer&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16767" PostTypeId="2" ParentId="16754" CreationDate="2014-04-22T14:35:27.123" Score="3" Body="&lt;p&gt;Oranges and other fruits are generally not actively made seedless. Rather, seeds may fail to develop due to either lack of fertilization (pollination) or a natural tendency. The natural production of unfertilized and thus seedless fruit is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Parthenocarpy&quot; rel=&quot;nofollow&quot;&gt;Parthenocarpy&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To quote the Scientific American article (&lt;a href=&quot;http://www.scientificamerican.com/article/how-do-seedless-fruits-ar/&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;) mentioned by Oreotrephes:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fruit development normally begins when one or more egg cells in the&#xA;  ovular compartment of the flower are fertilized by sperm nuclei from&#xA;  pollen. In some plants, however, fruit develops without fertilization,&#xA;  a phenomenon known as parthenocarpy. Parthenocarpic fruit has&#xA;  advantages over seeded fruit: longer shelf life and greater consumer&#xA;  appeal.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The most frequent reasons for lack of seed development are pollination&#xA;  failure, or nonfunctional eggs or sperm. In many plants,&#xA;  self-incompatibility genes limit successful fertilization to&#xA;  cross-pollination between genetically different male and female&#xA;  parents. This property is exploited by citrus farmers who grow&#xA;  seedless fruits, such as navel oranges and clementines. Because these&#xA;  cultivars are self-incompatible, they fail to set seed when they are&#xA;  planted in orchards of identical plants (clones). These plants have a&#xA;  high frequency of parthenocarpy, however, so they still produce fruit.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Parthenocarpic varieties may arise from a lack of pollinators. From the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Parthenocarpy&quot; rel=&quot;nofollow&quot;&gt;Parthenocarpy&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Plants moved from one area of the world to another may not always be&#xA;  accompanied by their pollinating partner and the lack of pollinators&#xA;  has spurred human cultivation of parthenocarpic varieties. Some&#xA;  parthenocarpic varieties have been developed as genetically modified&#xA;  organisms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To preserve the seedless trait, parthenocarpic trees can be propagated by &lt;a href=&quot;http://en.wikipedia.org/wiki/Grafting&quot; rel=&quot;nofollow&quot;&gt;grafting&lt;/a&gt;. It is possible that more kinds of seedless fruits will be engineered in the future (&lt;a href=&quot;http://www.scientificamerican.com/article/how-do-seedless-fruits-ar/&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Plant biologists have learned that if the plant hormone auxin is&#xA;  produced early in ovule development, parthenocarpic fruit can grow on&#xA;  plants that do not usually exhibit this property. Thus, genetic&#xA;  engineering will most likely give consumers parthenocarpic fruit in&#xA;  many other species in the near future.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-22T14:35:27.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16768" PostTypeId="2" ParentId="2891" CreationDate="2014-04-22T14:40:21.857" Score="1" Body="&lt;p&gt;Yes, it's possible to damage dark-adapted ecosystems this way, and there are at least a few examples of it happening:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Deep sea Norwegian Lobsters were blinded by being brought to the surface as bycatch by fishermen (or by scientists tagging them). The original paper is &lt;a href=&quot;http://www.jstor.org/stable/77175&quot; rel=&quot;nofollow&quot;&gt;Loew 1976&lt;/a&gt;, a more recent paper (&lt;a href=&quot;http://dx.doi.org/10.1007/s002270050681&quot; rel=&quot;nofollow&quot;&gt;Chapman et al. 2000&lt;/a&gt;) suggests that even a &amp;lt;1 minute light exposure could cause significant harm, which suggests a camera flash could certainly have an effect.&lt;/li&gt;&#xA;&lt;li&gt;There is evidence that shrimp that live by deep-sea hydrothermal vents have been blinded by the floodlights of exploratory vehicles (&lt;a href=&quot;http://dx.doi.org/10.1038/18142&quot; rel=&quot;nofollow&quot;&gt;Herring et al. 1999&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s002270050681&quot; rel=&quot;nofollow&quot;&gt;Chapman, CJ et al. (2000). Survival and growth of the Norway lobster Nephrops norvegicus in relation to light-induced eye damage. &lt;em&gt;Marine Biology&lt;/em&gt; &lt;strong&gt;136&lt;/strong&gt;:233-241 doi:10.1007/s002270050681&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/18142&quot; rel=&quot;nofollow&quot;&gt;Herring, PJ et al. (1999). Are vent shrimps blinded by science? &lt;em&gt;Nature&lt;/em&gt; &lt;strong&gt;398&lt;/strong&gt;:116 doi:10.1038/18142&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jstor.org/stable/77175&quot; rel=&quot;nofollow&quot;&gt;Loew, ER (1976). Light, and Photoreceptor Degeneration in the Norway Lobster, Nephrops norvegicus (L.) &lt;em&gt;Proceedings of the Royal Society of London. Series B, Biological Sciences&lt;/em&gt; &lt;strong&gt;193&lt;/strong&gt;:31-44&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2014-04-22T14:40:21.857" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16769" PostTypeId="2" ParentId="16753" CreationDate="2014-04-22T14:44:00.413" Score="2" Body="&lt;p&gt;This is specific to navel oranges, which have a conjoined twin fruit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.npr.org/templates/story/story.php?storyId=103250589&quot; rel=&quot;nofollow&quot;&gt;blog&lt;/a&gt; gives an account of this.&lt;/p&gt;&#xA;" OwnerUserId="6224" LastActivityDate="2014-04-22T14:44:00.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16770" PostTypeId="2" ParentId="16645" CreationDate="2014-04-22T15:04:57.083" Score="6" Body="&lt;p&gt;This small hexapod appears to be a species of Springtail (or Collembola).  It is similar to the one below, with slightly different markings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4eftL.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the &lt;a href=&quot;http://edis.ifas.ufl.edu/ig124&quot; rel=&quot;noreferrer&quot;&gt;University of Florida&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Springtails are minute insects without wings in the Order Collembola. They occur in large numbers in moist soil and can be found in homes with high humidity, organic debris, or mold. Homeowners sometimes discover these insects occurring in large numbers in swimming pools, potted plants, or in moist soil and mulch. They feed on fungi, fungal spores, and decaying, damp vegetation, causing organic material and other nutrients to return to the soil; these nutrients are later used by plants. Occasionally, springtails attack young seedlings and may damage the roots and stems.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;More information can also be found at NC State University Entomology Website:&#xA;&lt;a href=&quot;http://www.cals.ncsu.edu/course/ent425/library/compendium/collembola.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.cals.ncsu.edu/course/ent425/library/compendium/collembola.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is hard to say what species it could be, but it looks most similar to:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Isotomurus plumosus&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/h6M8y.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or &lt;em&gt;Isotomurus tricolour&lt;/em&gt; from &lt;a href=&quot;https://www.flickr.com/photos/7535699@N03/sets/72157604086534455/&quot; rel=&quot;noreferrer&quot;&gt;Rick Cowen&lt;/a&gt;: &#xA;&lt;img src=&quot;https://i.stack.imgur.com/4mivr.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is hard to tell but it seems to be part of this genera, or is at least in the family &lt;a href=&quot;http://bugguide.net/node/view/61599/bgimage&quot; rel=&quot;noreferrer&quot;&gt;Isotomidae&lt;/a&gt;, if not the exact species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their taxonomy is actually under debate, and they are in a group of hexapods that are &lt;a href=&quot;http://en.wikipedia.org/wiki/Springtail&quot; rel=&quot;noreferrer&quot;&gt;no longer considered insects&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6380" LastActivityDate="2014-04-22T15:04:57.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16771" PostTypeId="2" ParentId="16752" CreationDate="2014-04-22T15:25:13.217" Score="1" Body="&lt;p&gt;It could be tolerance if other caffeinated beverages are usually consumed, however it also depends on the type of tea itself, and other properties, such as how long the tea has steeped for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, brewed black tea can have anywhere from 14-61 mg of caffeine, which is a large range and depends on which tea you are drinking specifically.  Whereas if you were drinking green tea that has not been steeped for long, it can have 24-40 mg of caffeine, which at the lower range will probably not help you stay awake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.mayoclinic.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;MayoClinic.Org&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The actual caffeine content of the same coffee drink can vary from day to day — even at the same coffee shop — because of various factors, such as roasting and grinding, as well as brewing time. The caffeine content of tea also is affected by how long it's brewed. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Caffeine beverage levels can be found here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mayoclinic.org/healthy-living/nutrition-and-healthy-eating/in-depth/caffeine/art-20049372&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.mayoclinic.org/healthy-living/nutrition-and-healthy-eating/in-depth/caffeine/art-20049372&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GVhD9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6380" LastActivityDate="2014-04-22T15:25:13.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16772" PostTypeId="2" ParentId="16757" CreationDate="2014-04-22T15:37:43.340" Score="2" Body="&lt;p&gt;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;As far as &lt;strong&gt;how&lt;/strong&gt; the water cools the body it's simply a matter of physics. Water has a higher &lt;em&gt;specific heat&lt;/em&gt; also called &lt;em&gt;heat capacity&lt;/em&gt; than the air, clothes, or other matter that normally surrounds the body. &lt;/p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;em&gt;Specific heat&lt;/em&gt; refers to the amount of heat (keep in mind that heat is essentially the measure of the average movements of the molecules in a substance) per unit of mass it would take to raise it's temperature by 1 degree Celsius. Water is useful for temperature regulation because it takes so much energy for it to change temperatures. Metals tend to have low &lt;em&gt;specific heats&lt;/em&gt; which is why we make frying pans out of metals like iron. They take less energy to become hot.&lt;/p&gt; &lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;As systems naturally fall back to equilibrium, if the body is hotter than the water heat will be transferred from the body into the water until they are the same temperature which will be a lot closer to the temperature of the water (compared to the initial temp of the body) because changing the temperature of water 1 degree takes more heat energy than changing the same mass of human to change 1 degree in temperature.&lt;/p&gt;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; While this primarily acts on the outer portions of the body, the process continues into the core of the body as now instead of having hot skin and cold water, you have hot muscles and cold skin, from there you have hot organs and cold muscles, and so on and so on.&lt;/p&gt;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; I hope this is helpful! For more information on &lt;em&gt;specific heat&lt;/em&gt; you can check out: &lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/thermo/spht.html&quot; rel=&quot;nofollow&quot;&gt;http://hyperphysics.phy-astr.gsu.edu/hbase/thermo/spht.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6438" LastActivityDate="2014-04-22T15:37:43.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16773" PostTypeId="1" AcceptedAnswerId="16775" CreationDate="2014-04-22T15:39:13.930" Score="4" ViewCount="9573" Body="&lt;p&gt;When transcription factors attach to the DNA strand - How do they know in which direction they have to initialize the transcription by rna polymerase? Is it always read in the same direction anyway? What about those 'promoters'? Do they influence the transcription direction?&lt;/p&gt;&#xA;" OwnerUserId="6449" LastActivityDate="2014-06-18T21:30:48.403" Title="How is the transcription direction of RNA polymerase determined?" Tags="&lt;dna&gt;&lt;rna&gt;&lt;transcription&gt;&lt;polymerase&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16774" PostTypeId="1" CreationDate="2014-04-22T16:17:21.997" Score="0" ViewCount="39" Body="&lt;p&gt;What nutrients do I lose in the water when I boil vegetables. Has to be some water-soluble and heat labile ones right? Which ones?&lt;/p&gt;&#xA;" OwnerUserId="6442" LastActivityDate="2014-04-22T20:28:21.713" Title="What nutrients do I lose in the water when I boil vegetables?" Tags="&lt;vegetable&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16775" PostTypeId="2" ParentId="16773" CreationDate="2014-04-22T16:32:55.793" Score="3" Body="&lt;p&gt;Transcription always proceeds in the direction 5' (5-prime) to 3' (3-prime) on the coding strand of DNA. Binding of both transcription factors and RNA polymerase to DNA depends on sequence motifs in the DNA. Transcription always happens in the same direction with respect to the chemical structure of the coding DNA strand, while the transcription direction with respect to the structure of the chromosome depends on which strand the coding sequence is found on (and thus which strand is defined as the coding strand for that gene).&lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-22T16:32:55.793" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="16776" PostTypeId="1" AcceptedAnswerId="16796" CreationDate="2014-04-22T16:51:05.750" Score="2" ViewCount="233" Body="&lt;p&gt;I'm programming an implementation of an algorithm for pattern matching in RNA structures.&#xA;The algorithm assumes the following types of base pairs:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Plain&lt;/em&gt;: No base pairs (just the primary structure of the RNA)&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Single&lt;/em&gt;: Each base can be connected to at most one other base&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Multiple&lt;/em&gt;: Each base can be maximally connected to a number of other bases (where 'number' can be constant or infinite)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Although there is no problem with the implementation of the above types of base pairs (apart from the probable high computation complexity), I wonder if all of them were observed in real RNAs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, I'm interested in the following cases:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A base pair between two &lt;strong&gt;adjacent&lt;/strong&gt; bases i,j.&lt;/li&gt;&#xA;&lt;li&gt;One base (i) which connected to two different bases (j,k) (i is not adjacent to j or/and k).&lt;/li&gt;&#xA;&lt;li&gt;One base (i) which connected to more than two different bases, all of them not adjacent to i.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Can these exist? Some of them?&#xA;If they can, how common is their existence?&lt;/p&gt;&#xA;" OwnerUserId="246" LastEditorUserId="3340" LastEditDate="2014-04-23T05:36:07.030" LastActivityDate="2014-04-23T05:36:07.030" Title="Which types of hydrogen bonds are known to exist in RNA secondary structures?" Tags="&lt;bioinformatics&gt;&lt;rna&gt;&lt;biophysics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16777" PostTypeId="2" ParentId="16776" CreationDate="2014-04-22T17:02:40.687" Score="3" Body="&lt;p&gt;By far the most common type of base pair is the Watson-Crick base pair in an RNA helix. Those are comparably easy to predict, e.g. Mfold and the Vienna RNA package can do this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Base triples, three nucleobases that form hydrogen bonds to each other are not uncommon in RNAs with a complex tertiary structure. There is even &lt;a href=&quot;http://rna.bgsu.edu/Triples/triples.php?version=v1.4&quot; rel=&quot;nofollow&quot;&gt;a database of RNA triples&lt;/a&gt;, though this one also contains triples where not all three bases make contact with each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleic_acid_tertiary_structure&quot; rel=&quot;nofollow&quot;&gt;quadruplexes&lt;/a&gt;, but there each base only makes contact with two other bases. I don't know if there are any structures where one base makes contact with more than two other ones.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2014-04-22T17:13:31.017" LastActivityDate="2014-04-22T17:13:31.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16778" PostTypeId="1" AcceptedAnswerId="16779" CreationDate="2014-04-22T17:39:45.700" Score="1" ViewCount="185" Body="&lt;p&gt;Beginner question here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The definition of decussation I see is the crossing through the midline of a bunch of neurons.  But I was wondering if there was a little more to it than this, because I'm given the impression in readings that this is a somewhat difficult task to perform developmentally, like the body might have to take extra effort to regulate the crossing so that the neurons do not interfere.  So when nerves from both eyes cross, for example, do they pass AROUND each other or do the bundles of nerves all weave through each other?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="6450" LastActivityDate="2014-04-22T18:24:41.163" Title="Specifics of decussation" Tags="&lt;neuroscience&gt;&lt;human-anatomy&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16779" PostTypeId="2" ParentId="16778" CreationDate="2014-04-22T18:24:41.163" Score="2" Body="&lt;p&gt;The optic nerve fibers cross inside the optic chiasm sharing the same shell:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xDLrC.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The crossing fibers go ones between others, like on this classical picture - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6BEM5.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2014-04-22T18:24:41.163" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16780" PostTypeId="1" CreationDate="2014-04-22T19:21:19.740" Score="3" ViewCount="150" Body="&lt;p&gt;If I have a predicted RNA stem-loop of energy -0.30 kcal/mol, and another of -4.9 kcal/mol, how do I tell whether such a structure is a significantly stable structure or not? Our two competing hypotheses are that there is some structure with sufficient energetic stability to fold inside a cell, versus the one that there is not.&lt;/p&gt;&#xA;" OwnerUserId="1536" LastEditorUserId="1536" LastEditDate="2014-04-23T00:46:53.613" LastActivityDate="2014-08-31T04:02:01.367" Title="How to determine whether the energy of a stem-loop fold is significant or not?" Tags="&lt;biochemistry&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="16781" PostTypeId="1" CreationDate="2014-04-22T19:54:30.537" Score="1" ViewCount="790" Body="&lt;p&gt;My conjecture is that the natures of sympathetic and parasympathetic action potentials are different.&#xA;My findings propose me that&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;sympathetic action potential is little longer lasting than parasympathetic &#xA;&lt;ul&gt;&#xA;&lt;li&gt;there may be another mechanism in sympathetic action potential - some sort of plateau phase which does not exist in parasympathetic action potential&lt;/li&gt;&#xA;&lt;li&gt;however, I have not managed to gather any convincing evidence on this claim&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;parasympathetic action potential has greater energy per one time instance, while the energy of sympathetic AP is distributed along wider time space&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My hypothesis is that the &lt;strong&gt;energy of parasympathetic and sympathetic action potentials is equal&lt;/strong&gt;.&#xA;This would suggest me that the action potentials of the autonomic nervous system are coming from the same source.&#xA;Their nature is just different.&#xA;&lt;strong&gt;What can this source be exactly?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read the recent Physiology and Pathophysiology books where this topic was not covered rigorously.&#xA;I did not manage to find any good publication about the topic, probably, I missed something.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the nature of autonomic nervous system action potentials?&lt;/strong&gt;&#xA;You can select what ever condition you want and see if you can get some findings as I have got.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-26T09:22:39.643" LastActivityDate="2014-12-26T09:22:39.643" Title="What is the nature of action potentials in autonomic nervous system?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;action-potential&gt;&lt;autonomic-nervous-system&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16782" PostTypeId="2" ParentId="16774" CreationDate="2014-04-22T20:28:21.713" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.medicinenet.com/script/main/art.asp?articlekey=10736&quot; rel=&quot;nofollow&quot;&gt;Vitamin C and the B complex vitamins are water soluble&lt;/a&gt;.   &lt;a href=&quot;http://www.beyondveg.com/tu-j-l/raw-cooked/raw-cooked-2e.shtml&quot; rel=&quot;nofollow&quot;&gt;Thiamine and folate are also heat labile&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall there are hundreds or often thousands of kinds of small molecules (not protein or DNA) in the cell and many of them are water soluble or heat labile.  Plants especially have many unusual small molecules.  Its not known how many of them affect human health, but may affect factors like the gut microbiome quite a bit and have an effect on well being if not mortality. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some people think that live uncooked vegetables have enzymes and other proteins which are good for you since cooked proteins are denatured and may be taken in differently.  At the very least they are probably easier to digest when they are not heat denatured. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-04-22T20:28:21.713" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16784" PostTypeId="1" AcceptedAnswerId="16794" CreationDate="2014-04-22T21:34:33.807" Score="1" ViewCount="185" Body="&lt;p&gt;To my knowledge plants do not have an uncontrolled growth disease similar to cancer. Is the function by which they avoid uncontrolled growth related to their cell wall and preventing damage to DNA/RNA? Is their telomerase special in some way in that it does not indefinitely replicate? &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="3340" LastEditDate="2014-04-23T03:25:05.493" LastActivityDate="2014-04-23T05:13:36.190" Title="Do cell walls prevent cancer?" Tags="&lt;molecular-genetics&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16785" PostTypeId="1" CreationDate="2014-04-22T21:54:11.083" Score="1" ViewCount="896" Body="&lt;p&gt;I have noticed that in infrared film, people's eyes reflect that light within their eyes much like nocturnal animals (and many other animals for that matter) do with regular light. I know that this is in order to maximize their night vision capabilities by reflecting more light onto the retina.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is this: &lt;strong&gt;&lt;em&gt;If&lt;/em&gt;&lt;/strong&gt; a human had the nerves in our eyes to process infrared light, would someone with these 'special' eyes be able to see better than someone with 'regular' eyes? What would they see? What about in low-light conditions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/A3Xnw.jpg&quot; alt=&quot;Example of what I am talking about:&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;...Infra-red illumination of the eye produces the 'bright pupil' effect&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.museumsandtheweb.com/mw2003/papers/milekic/milekic.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.museumsandtheweb.com/mw2003/papers/milekic/milekic.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(most of the way down the page)&lt;/p&gt;&#xA;" OwnerUserId="6452" LastEditorUserId="6452" LastEditDate="2014-04-22T23:08:51.063" LastActivityDate="2019-12-27T19:47:31.433" Title="Could humans theoretically see infrared better than regular light?" Tags="&lt;human-anatomy&gt;&lt;human-eye&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16786" PostTypeId="2" ParentId="16785" CreationDate="2014-04-22T22:05:28.790" Score="-2" Body="&lt;p&gt;Infrared light is emitted by warm things, like our head.  We'd be detecting it ambiantly all the time.  That's why animals that can detect infrared are not warm-blooded.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-04-22T22:05:28.790" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16787" PostTypeId="2" ParentId="16785" CreationDate="2014-04-22T22:10:03.387" Score="2" Body="&lt;p&gt;No, retina doesn't have or has too few infrared receptors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Practical example:&lt;/strong&gt; most remote controls use IR LEDs (infra red light emitting diodes) to send commands to a receiver device. So take a remote control, keep pressing a button and look at its front. Do you see any flashing light? Now take a camera (phone camera, photo camera or video camcorder) and look with it at the remote while pressing a button. Now you see it producing white light. The camera sensor detects IR. That is how night vision in cameras work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you read in that article is about how light is reflected by the eye (the pupil). There is nothing to do with the retina which is on the 'back wall' of the eye ball.&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-04-22T22:17:06.173" LastActivityDate="2014-04-22T22:17:06.173" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16788" PostTypeId="1" CreationDate="2014-04-23T01:50:18.760" Score="3" ViewCount="197" Body="&lt;p&gt;I just want to confirm the species of the tree in the middle of the picture. Is it the &quot;Flame of the Forest&quot;? This is taken in my school campus. Thanks in advance!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3GM3H.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6454" LastActivityDate="2016-08-10T16:33:54.790" Title="identification of species of tree" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16789" PostTypeId="1" CreationDate="2014-04-23T01:55:49.500" Score="6" ViewCount="213" Body="&lt;p&gt;Hi I saw this bird near my school canteen in Singapore in Spring. Can anyone identify the species of this bird? Thanks in advance!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vduBp.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6454" LastEditorUserId="107" LastEditDate="2014-04-23T16:03:08.110" LastActivityDate="2014-04-23T16:03:08.110" Title="identification of species of this bird" Tags="&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="0" ClosedDate="2014-07-22T04:19:06.180" ContentLicense="CC BY-SA 3.0" />
  <row Id="16791" PostTypeId="1" CreationDate="2014-04-23T02:08:01.497" Score="5" ViewCount="165" Body="&lt;p&gt;I saw this flower in Pulau Ubin in Singapore. Can anyone identify the species of this flower? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dJksq.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6454" LastEditorUserId="6561" LastEditDate="2015-10-12T23:37:15.740" LastActivityDate="2015-10-12T23:37:15.740" Title="identification of this flower" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16792" PostTypeId="1" AcceptedAnswerId="21041" CreationDate="2014-04-23T02:13:19.773" Score="3" ViewCount="943" Body="&lt;p&gt;What method of breathing provides a sudden surge of oxygen into the lungs filling it as full as possible in volume and density. Deep breaths? Shallow breaths? Breaths taken while bent over? Deep inhales followed by further inhales. Breaths held? Movement while breaths are held?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="3340" LastEditDate="2014-04-23T06:03:26.580" LastActivityDate="2015-01-21T23:50:34.970" Title="How to maximize lung oxygen intake?" Tags="&lt;human-anatomy&gt;&lt;lungs&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16793" PostTypeId="1" AcceptedAnswerId="16797" CreationDate="2014-04-23T03:05:10.210" Score="3" ViewCount="225" Body="&lt;p&gt;Can anyone identify this colorful snake found at Pulau Ubin in Singapore? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/c3xtd.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6454" LastEditorUserId="6561" LastEditDate="2015-10-12T23:36:24.497" LastActivityDate="2015-10-12T23:36:24.497" Title="identification of species of snake" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16794" PostTypeId="2" ParentId="16784" CreationDate="2014-04-23T03:46:52.313" Score="2" Body="&lt;p&gt;Plants do have uncontrolled tumorous growth. Though in almost all known cases, it is pathogen induced; such as in the case of the bacterium- &lt;em&gt;Agrobacterium tumefaciens&lt;/em&gt;. Viruses can also induce plant tumors. Theoretically, the cell wall will pose a mechanical barrier to cell division. Also, cell wall synthesis is an extra biochemical step during cell division. Surely, the presence of a cell wall will disallow any metastasis if it might occur. There is &lt;a href=&quot;http://www.sciencemag.org/content/199/4333/1075.short&quot; rel=&quot;nofollow&quot;&gt;an old article&lt;/a&gt; which says that cell wall structure differs between the normal plant tissue and the crown galls (tumor). However, this is with respect to Agrobacterium adsorption sites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not aware of any natural plant tumor or the role of telomerase in plant tumorigenesis. However, there is &lt;a href=&quot;http://www.sciencemag.org/content/291/5509/1797.short&quot; rel=&quot;nofollow&quot;&gt;one paper&lt;/a&gt; that says that telomerase dysfunction leads to disorganized growth.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-04-23T05:13:36.190" LastActivityDate="2014-04-23T05:13:36.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16795" PostTypeId="2" ParentId="16721" CreationDate="2014-04-23T05:29:14.393" Score="1" Body="&lt;p&gt;Try using KEGG &lt;a href=&quot;http://www.kegg.jp/kegg/docs/keggapi.html&quot; rel=&quot;nofollow&quot;&gt;REST&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rest.kegg.jp/link/pathway/hsa&quot; rel=&quot;nofollow&quot;&gt;http://rest.kegg.jp/link/pathway/hsa&lt;/a&gt; ## list of all genes and pathways in Humans&lt;/p&gt;&#xA;" OwnerUserId="6455" LastActivityDate="2014-04-23T05:29:14.393" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16796" PostTypeId="2" ParentId="16776" CreationDate="2014-04-23T05:32:50.447" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;A base pair between two adjacent bases i,j.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is not possible. To form an intramolecular hydrogen bond, the RNA has to bend. The persistence length i.e. the minimum length of the chain required for bending, is around 4 bases for ssRNA (I am not very sure about this number. At this moment I am not able to locate the exact reference. I remember this number from the back of my head which I heard somewhere).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One base (i) which connected to two different bases (j,k) (i is not adjacent to j or/and k).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is definitely possible for one pair after considering the persistence length. If a single base is bound to more than two bases then atleast one interaction should have to form a non Watson-Crick type bonding, as indicated by Mad Scientist. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One base (i) which connected to more than two different bases, all of&#xA;  them not adjacent to i&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Very less likely. There are no known reports. Even if it happens, the bond will be weak because of limitation in the number of H-bond donor/acceptor sites in the bases. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-04-23T05:32:50.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16797" PostTypeId="2" ParentId="16793" CreationDate="2014-04-23T05:42:12.647" Score="4" Body="&lt;p&gt;It is the paradise tree snake (&lt;a href=&quot;http://en.wikipedia.org/wiki/Chrysopelea_paradisi&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Chrysopelea paradisi&lt;/em&gt;&lt;/a&gt;). It is a colubrid snake and is common in south-east asia. See &lt;a href=&quot;http://www.blogiversity.org/blogs/cstanton/archive/2010/04/24/7-spectacular-gliding-animals.aspx&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt; for a better image.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-04-23T05:42:12.647" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16798" PostTypeId="2" ParentId="16780" CreationDate="2014-04-23T06:21:32.630" Score="3" Body="&lt;p&gt;You can convert the $\Delta G$ values into equilibrium constants $K$ using the formula&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ \Delta G = R T \ln K $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This might help you understand what those energies roughly mean.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the more important and also more difficult part is judging how good your predicted free energies actually are. I assume you used a secondary structure prediction program like Mfold to calculate this. They typically have a several parameters you can adjust like ion concentrations and temperature, you should make sure that you have some appropriate values here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Without knowing anything more about your system or data I'd ignore the -0.3 kcal/mole result, the -4.9 kcal/mole structure could be formed, but I wouldn't regard this as certain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, in the &lt;em&gt;in vivo&lt;/em&gt; situation the whole thing gets far more complicated. The presence of RNA binding proteins, helicases and the generally rather complex environment in the cell makes it much harder to predict which secondary structures will actually form. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you wanted to know for sure you could e.g. do SHAPE experiments on your RNA. This is a technique that also works &lt;em&gt;in vivo&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-04-23T06:21:32.630" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16800" PostTypeId="1" CreationDate="2014-04-23T10:23:19.967" Score="3" ViewCount="68" Body="&lt;p&gt;When considering the introduction of 4CMenB vaccine, &lt;a href=&quot;https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/225004/Minutes_Meningococcal_sub-committee_meeting_April_2013_-_final.pdf&quot; rel=&quot;nofollow&quot;&gt;the Joint Committee on Vaccination and Immunisation said&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The sub-committee noted that the clinical trials data suggest that&#xA;  when  4CMenB vaccine is given concomitantly with other routine&#xA;  childhood  immunisations a substantially increased frequency of&#xA;  vaccine-induced  fevers should be expected. Vaccine-induced fever&#xA;  rates may be similar to  those associated with whole cell pertussis&#xA;  vaccine used in the past.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What is the likely explanation for the higher rate of fever for 4CMenB in comparison with other vaccines?&lt;/p&gt;&#xA;" OwnerUserId="6458" LastEditorUserId="6458" LastEditDate="2014-04-25T10:11:13.040" LastActivityDate="2014-04-25T10:11:13.040" Title="Why is post-vaccination fever for 4CMenB so frequent?" Tags="&lt;vaccination&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16801" PostTypeId="1" AcceptedAnswerId="16802" CreationDate="2014-04-23T12:57:13.087" Score="1" ViewCount="49" Body="&lt;p&gt;Some proteins are &quot;activated&quot;, like fibrinogens; they are turned into fibrins by thrombins, and then the fibrins can aid in blood clotting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are fibrinogens and fibrins the same molecule, just in different states? If so, are all &quot;-ogen&quot; ending proteins and their activated forms the same as well?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If they are different molecules, why do us even bother to convert a protein into anotherto work, instead of simply activating a protein?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastEditorUserId="3632" LastEditDate="2014-04-23T13:11:11.133" LastActivityDate="2014-04-23T15:00:03.367" Title="fibrinogens and fibrins - are they the same molecule?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16802" PostTypeId="2" ParentId="16801" CreationDate="2014-04-23T13:18:41.603" Score="1" Body="&lt;p&gt;You could say they are the same molecule, but a molecule whose function is to change its state and properties very quickly when activated by thrombin.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Fibrinogen#Physiology&quot; rel=&quot;nofollow&quot;&gt;Fibrinogen&lt;/a&gt; is a soluble protein - a complex of six protein chains.&lt;br&gt;&#xA;&lt;a href=&quot;https://en.wikipedia.org/wiki/Thrombin&quot; rel=&quot;nofollow&quot;&gt;Thrombin&lt;/a&gt; is an enzyme called a protease which very specifically cuts the ends off of two of those protein chains.&lt;br&gt;&#xA;Once those bits are removed from Fibrinogen, the resulting molecule creates fibers very quickly to form clots.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could also say that fibrin is a different molecule than fibrin because it really consists of many fibrinogen fragments. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1320" LastEditDate="2014-04-23T15:00:03.367" LastActivityDate="2014-04-23T15:00:03.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16803" PostTypeId="1" AcceptedAnswerId="16804" CreationDate="2014-04-23T13:42:07.753" Score="0" ViewCount="2980" Body="&lt;p&gt;i was reading &lt;a href=&quot;http://wiki.answers.com/Q/What_is_time_required_for_human_digestion&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;&#xA;and want to know &lt;/p&gt;&#xA;&#xA;&lt;p&gt;excerpt from the above link&lt;code&gt;Thus, the time for food to travel from one end to the other probably ranges from about 20 to 30 hours&lt;/code&gt;&#xA;I believe it's 24 hours for a normal person going for poop every morning, But I was curoius if anybody could increase the rate of absorption making my digestive and defacaeting system better performing.&lt;/p&gt;&#xA;" OwnerUserId="5008" LastEditorUserId="16299" LastEditDate="2015-11-25T21:27:00.110" LastActivityDate="2015-11-25T21:27:00.110" Title="How to increase the rate of absorption and assimilation of food?" Tags="&lt;digestion&gt;&lt;bile&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-04-23T14:17:14.807" ContentLicense="CC BY-SA 3.0" />
  <row Id="16804" PostTypeId="2" ParentId="16803" CreationDate="2014-04-23T14:00:13.147" Score="1" Body="&lt;p&gt;The rate of absorption is controlled by two essential physical factors:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Contact &lt;strong&gt;surface&lt;/strong&gt; between intestinal content and intestinal mucosa.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Time&lt;/strong&gt; of contact.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;There are many other factors including intestinal peristalsis, gastric, pancreatic and bile secretions that stimulate/help absorption.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So increasing or accelerating intestinal passage of food won't do any good (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Diarrhea&quot; rel=&quot;nofollow&quot;&gt;diarrhea&lt;/a&gt;). Water will not be absorbed into the blood flow thus leading to dehydration and hypovolemia. Also the alimentary principles, vitamins, essential aminoacids won't be absorbed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, slowing down the passage has negative effects. It allows bacterial saprophytic flora to multiply so much that those microorganisms become pathogenic by producing toxins. And increased contact time equals increased absorption both of toxins and food principles. &lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-04-23T14:00:13.147" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16806" PostTypeId="1" CreationDate="2014-04-23T15:56:03.407" Score="3" ViewCount="7232" Body="&lt;p&gt;The univariate breeders equation is defined as,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\ R = h^2 s$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $\ R $ is the response, $\ h^2 $ is the heritability (additive genetic variation), $\ s $ is the selection differential. The multivariate equation is similar to this in principle but includes a multiple trait variance-covariance matrix and multiple selection differentials. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially the breeders equation tells us how strong the response to selection will be as a result of the additive genetic variance within a trait (and between traits in the multivariate) and the selection applied to that variation ($\ s = cov (w,x) $ = the covariance between fitness ($w$) and the trait $x$). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, in trait $x$, $s$ = 0.8 and $h^2$ = 0.5 the value of the response for $x$ is $R$ = 0.4. Compared to another trait, $y$, where $s$ = 0.8 and $h^2$ = 0.1 and thus $R$ = 0.08.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, if we look at a trait in a population, measure it's population mean and define $h^2$ and $s$ values, &lt;strong&gt;can we then predict the change in the population?&lt;/strong&gt; IE. can we predict (with the values of $s,  h^2$  and the population mean) what the mean population mean trait will be in the next generation directly from the result of the breeders equation? Does the value of $R$ give us anything of use?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following from the example above, I examine a trait (wing length in chickens) and find the mean to be 24 cm. I select birds to start my next generation in a way that causes $s$ = 0.8. The additive genetic variance for the wing length is quite high, $h^2$ = 0.5. The predicted response is $R$ = 0.8 x 0.5 = 0.4. What does this tell me about the next generation?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-04-23T16:14:42.707" LastActivityDate="2018-01-22T23:24:50.400" Title="How to interpret the breeders equation?" Tags="&lt;mathematical-models&gt;&lt;population-genetics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16807" PostTypeId="2" ParentId="16806" CreationDate="2014-04-23T16:15:37.787" Score="3" Body="&lt;p&gt;The breeder's equation as you wrote it:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$R = h^2S$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heritability that is the ratio of additive genetic variance over the total phenotypic variance is called the heritability in the narrow sense and is noted $h_N^2 = \frac{V_a}{V_P}$, where $V_A$ and $V_P$ are the additive genetic and phenotypic variance respectively. In contrast the heritability that consider the total genetic variance is called the heritability in the broad sense and is noted $h_B^2 = \frac{V_G}{V_P} = \frac{V_A + V_D}{V_P}$, where $V_G$ is the total genetic variance and is equal the sum of the additive genetic variance $V_A$ and the genetic dominance variance $V_D$. We can rewrite the breeder's equation using the standard notation for the heritability in the narrow sense:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$R = h_N^2S$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The so-called response to selection $R$ is the mean deviation of the trait in the next generation. In other words, $R$ is the difference between the mean trait of the parents and the mean trait of the offspring, &lt;em&gt;So to answer your question, yes, the breeder's equation gives the value of the mean trait in the following generation&lt;/em&gt;. It does not give any information about the frequency and number of alleles though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$S$ is the the mean trait of the individuals which reproduce weighted by their reproductive success minus the mean trait of the parents. In other words, it is &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$S=\frac{1}{\bar w}\sum_{i=1}^{\text{nb inds}}m_iw_i - \bar m$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $m_i$ is the trait measurement and $w_i$ is the fitness of this individual, $\bar m$ is the mean trait of the parents and $\bar w$ is the mean fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mean trait of the parent generation does not appear in the breeder's equation but only their mean trait weighted by their reproductive success. In the standard case of truncated selection (common in artificial selection programs) all $w_i$ are equal and $S$ becomes the mean trait of the individuals that we allow to reproduce in the parent population. And it is exactly the same thing for the multivariate case except that the variance-covariance matrix should be taken into account.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-11-08T17:13:11.300" LastActivityDate="2015-11-08T17:13:11.300" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16809" PostTypeId="1" CreationDate="2014-04-23T17:50:52.153" Score="2" ViewCount="207" Body="&lt;p&gt;Do you know a good review (published peer-reviewed or an online course or whatever) that offers a good overview of all hypothesis explaining the various patterns linked with aging?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like this review to make the following things clear; antagonist pleiotropy, Gompertz and Weibull models and what theoretical explanations are underlying these models, mutation accumulation, reliability theory, eventually group selection, age-specific efficiency of natural selection, telomere length, the definition of senescence, and all not-cited hypothesis to explain the patterns of aging/senescence.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2017-03-12T09:13:59.383" Title="Source of information on the evolution of aging/senescence" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;senescence&gt;&lt;theoretical-biology&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16810" PostTypeId="1" CreationDate="2014-04-23T18:08:04.680" Score="2" ViewCount="109" Body="&lt;p&gt;If I want to measure the exact glucose concentration in a human brain then how can I proceed to do that? Is there any technique or assay to do that?&lt;/p&gt;&#xA;" OwnerUserId="6463" LastEditorUserId="6" LastEditDate="2014-04-23T19:01:32.890" LastActivityDate="2014-06-27T15:12:18.823" Title="Measurement of glucose concentration in the human brain" Tags="&lt;biochemistry&gt;&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16811" PostTypeId="2" ParentId="16810" CreationDate="2014-04-23T18:25:15.140" Score="3" Body="&lt;p&gt;It is possible by using &lt;sup&gt;13&lt;/sup&gt;C NMR Spectroscopy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has been done after infusing enriched D-[1-&lt;sup&gt;13&lt;/sup&gt;C]glucose in six healthy children. The results showed that at euglycemia glucose concentration is about 1 micromol/ml.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Source:&lt;/strong&gt; Gruetter R, Novotny EJ, Boulware SD, Rothman DL, Mason GF, Shulman GI, Shulman RG, Tamborlane WV. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1736294&quot; rel=&quot;nofollow&quot;&gt;Direct measurement of brain glucose concentrations in humans by 13C NMR spectroscopy.&lt;/a&gt; Proc. Natl. Acad. Sci. U.S.A. 1992 Feb 1;89(3):1109-12. PubMed PMID: 1736294. &lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-27T15:12:18.823" LastActivityDate="2014-06-27T15:12:18.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16813" PostTypeId="1" AcceptedAnswerId="16878" CreationDate="2014-04-23T20:11:53.487" Score="8" ViewCount="691" Body="&lt;p&gt;As I know evolution comes bit by bit mutation by mutation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How sex evolved which requires a major change in at least two individuals one to become male and one to become female ?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When that happened as we can see sex in all animals and most plants? &lt;/p&gt;&#xA;" OwnerUserId="6464" LastEditorUserId="1590" LastEditDate="2016-08-20T08:19:30.497" LastActivityDate="2016-08-20T08:19:30.497" Title="How and when did sex evolve?" Tags="&lt;evolution&gt;&lt;bacteriology&gt;&lt;sex&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16814" PostTypeId="1" CreationDate="2014-04-24T02:52:37.830" Score="1" ViewCount="24" Body="&lt;p&gt;I have just aligned 9 paralogous genes from human, uploaded them into MEGA and calculated  negative selection. Can there be negative selection acting in between paralogous genes? Or how should I interpret this result?&lt;/p&gt;&#xA;" OwnerUserId="6466" LastActivityDate="2014-04-24T02:52:37.830" Title="Can paralogous genes be under negative selection?" Tags="&lt;selection&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16815" PostTypeId="1" CreationDate="2014-04-24T03:04:06.163" Score="1" ViewCount="927" Body="&lt;p&gt;When large fast-twitch motor units are temporarily fatigued, non-fatigue small motor units in the same muscle are impaired for small delicate tasks. Why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When impulses from the brain comes down, the impulses from interneuron goes to small diameter motor neuron, which are associated with non-fatigue motor units, and large diameter motor neurons, which are associated with fast-twitch motor units. More impulse is necessary to activate the fast twitch-muscles because the larger neurons have higher leak current and capacitance. Thus, we have an ascending activation of muscle units, from least forceful units to most forceful. Now my question is, if the fast-twitch muscle units are fatigued, why cant we perform delicate movement/ task?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fatigue is mainly caused when the motor unit runs out of ATP. So, is that the bridge between these to things, or is it something else?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or, is it related to how motor units are used is a fixed ascending order for completing tasks? If so, how?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for all the help!&lt;/p&gt;&#xA;" OwnerUserId="5659" LastEditorUserId="5659" LastEditDate="2014-04-24T04:04:04.700" LastActivityDate="2014-04-25T04:45:15.173" Title="Relationship between small and large fast-twitch motor units" Tags="&lt;human-biology&gt;&lt;muscles&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16816" PostTypeId="1" CreationDate="2014-04-24T03:31:15.177" Score="1" ViewCount="105" Body="&lt;p&gt;I have had a few difficulties finding answers for the questions below. I have tried answering the first two myself; but, I am not sure they are correct or not. And I am not too sure about the third one.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;In which structure of the brain does the axon from the spinocerebellum tract synapese? Is it the cerebellum?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are the cell bodies of axon in the gracile tract located at the dorsal root, tectospinal tract located in cerebral cortex?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Which region  of spinal cord carries feed-forward information to help accommodate for upcoming motor movement?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6056" LastEditorUserId="6289" LastEditDate="2014-05-24T22:22:51.993" LastActivityDate="2014-07-05T16:33:27.507" Title="Neurology: spinal tract" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16817" PostTypeId="2" ParentId="16788" CreationDate="2014-04-24T05:27:16.703" Score="3" Body="&lt;p&gt;It looks like a Royal Poinciana tree with the scientific name Delonix regia.. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TBSzF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please refer to &lt;a href=&quot;http://en.wikipedia.org/wiki/Delonix_regia&quot; rel=&quot;nofollow noreferrer&quot;&gt;this link&lt;/a&gt; for more info &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-04-24T05:27:16.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16818" PostTypeId="2" ParentId="16791" CreationDate="2014-04-24T05:30:20.630" Score="4" Body="&lt;p&gt;It is indeed the Nerium oleander.. For more info refer to &lt;a href=&quot;http://en.wikipedia.org/wiki/Oleander&quot; rel=&quot;nofollow&quot;&gt;this link&lt;/a&gt; and also &lt;a href=&quot;http://www.clemson.edu/extension/hgic/plants/landscape/shrubs/hgic1079.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-04-24T05:39:51.843" LastActivityDate="2014-04-24T05:39:51.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16819" PostTypeId="2" ParentId="16537" CreationDate="2014-04-24T06:48:24.010" Score="4" Body="&lt;ol&gt;&#xA;&lt;li&gt;The average number of auto-regulatory motifs (self-edges), is equal to the number of edges &lt;strong&gt;E&lt;/strong&gt; times the probability that an edge is a self-edge which is $p_{self}=1/N$, with &lt;strong&gt;N&lt;/strong&gt; being the total number of nodes. Therefore, $&amp;lt;N_{self}&amp;gt;_{rand} \approx E/N$&lt;/li&gt;&#xA;&lt;li&gt;&amp;amp; 3. According to U.Alon's book (&lt;a href=&quot;http://www.weizmann.ac.il/mcb/UriAlon/introduction-systems-biology-design-principles-biological-circuits&quot; rel=&quot;nofollow&quot;&gt;&quot;Introduction to Systems Biology&quot;&lt;/a&gt;), the mean number of times that a subgraph G occurs in a random network is given by the following formula: $&amp;lt;N_G&amp;gt;\approx a^{-1}N^n p^g$.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Explaining what each term of the formula means:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;α&lt;/strong&gt;: is a number that includes combinatorial factors related to the structure and symmetry of each subgraph, equal to 1 for feed-forward loop (FFL) and equal to 3 for feed-back loop (FBL)&lt;/li&gt;&#xA;&lt;li&gt;$N^n$: is the number of ways of choosing a set of &lt;strong&gt;n&lt;/strong&gt; nodes out of &lt;strong&gt;N&lt;/strong&gt;. Because there are N ways of choosing the first one, times N-1$\approx$N ways of choosing the second one, and so on..(this approximation is true for large networks)&lt;/li&gt;&#xA;&lt;li&gt;$p^g$ : is the probability to get the g edges in the appropriate places (each with probability p)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6016" LastEditorUserId="6016" LastEditDate="2014-04-24T07:10:23.153" LastActivityDate="2014-04-24T07:10:23.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16820" PostTypeId="2" ParentId="9638" CreationDate="2014-04-24T06:59:51.530" Score="8" Body="&lt;p&gt;This is a really old thread but just in case someone happens upon it, this isn't a bed bug.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not an expert but it looks like it's likely a book louse or psocid.&#xA;See comparison photos of unfed first instar bed bug nymphs vs. psocids/booklice here: &lt;a href=&quot;http://bedbugger.com/2008/03/04/booklice/&quot;&gt;http://bedbugger.com/2008/03/04/booklice/&lt;/a&gt;&#xA;It's all about the shape of the head and body.   &lt;/p&gt;&#xA;" OwnerUserId="6467" LastActivityDate="2014-04-24T06:59:51.530" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16821" PostTypeId="1" AcceptedAnswerId="16823" CreationDate="2014-04-24T07:07:56.573" Score="2" ViewCount="1374" Body="&lt;p&gt;I recall reading about a 20th century scientist who made a life-saving drug that could have patented it and made millions. He chose not to and saved the lives of millions around the globe. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought it was &lt;a href=&quot;http://www.scienceheroes.com/index.php?option=com_content&amp;amp;view=article&amp;amp;id=80&amp;amp;Itemid=115&quot; rel=&quot;nofollow&quot;&gt;Frederick Banting&lt;/a&gt; - but it doesn't sound quite right. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;None of the others &lt;a href=&quot;http://www.scienceheroes.com/index.php?option=com_content&amp;amp;view=article&amp;amp;id=258&amp;amp;Itemid=232&quot; rel=&quot;nofollow&quot;&gt;in this list&lt;/a&gt; seem quite right. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: &lt;strong&gt;What is the name of scientist who discovered lifesaving drug and chose not to patent it?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5417" LastActivityDate="2014-04-24T12:15:25.923" Title="Name of scientist who discovered lifesaving drug and chose not to patent it?" Tags="&lt;pharmacology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16822" PostTypeId="1" AcceptedAnswerId="16846" CreationDate="2014-04-24T08:07:57.397" Score="1" ViewCount="45" Body="&lt;p&gt;My assistant says that if you have asthmatic symptoms you cannot have TBE (Tick Born Encephalitis) vaccine, although you are living in the active zone of TBE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cases&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;mild allergic symptoms&lt;/li&gt;&#xA;&lt;li&gt;allergic symptoms under control of Montelukast (asthma in control)&lt;/li&gt;&#xA;&lt;li&gt;asthmatic symptoms (bronchitis, rhinosinutis, repeated cough)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the risks of having this vaccine during allergic symptoms when you have mild asthma medication (Montelukast)?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I still think the risk of encephalitis is higher if you get TBE from nature than from vaccine.&#xA;&lt;strong&gt;Are there really some cases where encephalitis is caused by the TBE vaccine?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-04-26T06:16:27.477" LastActivityDate="2014-04-26T06:16:27.477" Title="To have TBE vaccine during allergic times with mild asthmatic symptoms?" Tags="&lt;microbiology&gt;&lt;vaccination&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16823" PostTypeId="2" ParentId="16821" CreationDate="2014-04-24T09:24:37.430" Score="5" Body="&lt;p&gt;Dr Jonas Salk or Dr Albert Sabin who did not patent their respective polio vaccines. There are some more such researchers so I am not sure who exactly you are looking for but this would be a start. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-04-24T09:24:37.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16824" PostTypeId="1" AcceptedAnswerId="16828" CreationDate="2014-04-24T10:22:25.220" Score="0" ViewCount="576" Body="&lt;p&gt;I am thinking this picture which shows proximal muscles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/J46cR.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why for instance pectoralis major, subclavius and rectus abdominalis are not included in proximal muscles?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-24T12:08:41.873" Title="Why rectus abdominis is not proximal muscle?" Tags="&lt;muscles&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16825" PostTypeId="1" CreationDate="2014-04-24T10:48:05.603" Score="1" ViewCount="302" Body="&lt;p&gt;Which parts of respiratory apparatus are covered by respiratory epithelium and which are covered by other kinds of epithelium?&lt;/p&gt;&#xA;" OwnerUserId="6470" LastActivityDate="2014-04-24T16:18:08.043" Title="Are bronchioles and alveoli covered by respiratory epithelium?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16828" PostTypeId="2" ParentId="16824" CreationDate="2014-04-24T12:08:41.873" Score="2" Body="&lt;p&gt;It's not clear what &quot;proximal&quot; means in this context. It's not a standard use of that anatomical term in English. I'd also say that the figure on the left actually does show the pectoralis major.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The author of this figure might be trying to show the muscles that cross the proximal joints in the upper and lower limbs. For example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Upper limb&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Pectoralis major&lt;/li&gt;&#xA;&lt;li&gt;Biceps brachii&lt;/li&gt;&#xA;&lt;li&gt;Triceps brachii&lt;/li&gt;&#xA;&lt;li&gt;Latissimus dorsi&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Lower limb&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Adductors (brevis, longus, magnus)&lt;/li&gt;&#xA;&lt;li&gt;Rectus femoris&lt;/li&gt;&#xA;&lt;li&gt;Semimembranosus, semitendinosus, biceps femoris (long head)&lt;/li&gt;&#xA;&lt;li&gt;Gluteals (maximus, medius, minimus)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Muscles that do not cross the shoulder or hip are not included. This explains the lack of rectus abdominis or subclavius. Though it is not clear to me which the paired muscles in the posterior view are running craniocaudally from the thorax to the gluteal region. &lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2014-04-24T12:08:41.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16829" PostTypeId="2" ParentId="16821" CreationDate="2014-04-24T12:15:25.923" Score="2" Body="&lt;p&gt;You could've been thinking correctly. Banting did patent insulin but felt it was unethical to profit from such a critical drug. He sold the patent for a dollar to a (now nonexistent) pharmaceutical company.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-04-24T12:15:25.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16830" PostTypeId="2" ParentId="16825" CreationDate="2014-04-24T12:20:16.467" Score="1" Body="&lt;p&gt;&lt;em&gt;From the nose to the pharynx and larynx&lt;/em&gt;: &lt;strong&gt;stratified squamous epithelium&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;From the end of larynx to the bronchi&lt;/em&gt;: &lt;strong&gt;pseudostratified columnar ciliated epithelial cells&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the small bronchi cartilage is being replaced by elastic tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Bronchioles&lt;/em&gt;: &lt;strong&gt;ciliated simple epithelium with &lt;a href=&quot;http://en.wikipedia.org/wiki/Club_cell&quot; rel=&quot;nofollow&quot;&gt;club cells&lt;/a&gt;&lt;/strong&gt; (known as Clara cells). Also they lack cartilage and glands.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Alveoli&lt;/em&gt; are covered with &lt;strong&gt;squamous alveolar cells&lt;/strong&gt; which form the wall (also known as type I pneumocytes). They also contain great alveolar cells (which produce surfactant) or type II pneumocytes and macrophages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Respiratory_tract&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Respiratory_tract&lt;/a&gt; , &lt;a href=&quot;http://en.wikipedia.org/wiki/Pulmonary_alveolus&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Pulmonary_alveolus&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Pharynx&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Pharynx&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-04-24T16:18:08.043" LastActivityDate="2014-04-24T16:18:08.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16831" PostTypeId="2" ParentId="16816" CreationDate="2014-04-24T12:34:15.493" Score="1" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Yes, the spinocerebellar tract ends in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Spinocerebellar_tract&quot; rel=&quot;nofollow&quot;&gt;ipsilateral cerebellum&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The gracile tract is a bundle of axon fibers in the dorsal root. The neural cell bodies are in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Dorsal_root_ganglion&quot; rel=&quot;nofollow&quot;&gt;dorsal root ganglions&lt;/a&gt;. The tectospinal tract is part of extrapyramidal tract that connects midbrain (mesencephalon) with the spinal cord.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Didin't get exactly what you meant but: the lateral corticospinal tract (part of pyramidal tracts) controls fine movement of ipsilateral limbs, while the anterior corticospinal tract (part of the pyramidal tracts) conducts voluntary motor impulses from the precentral gyrus.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Source: Wikipedia: &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Tectospinal_tract&quot; rel=&quot;nofollow&quot;&gt;Tectospinal tract&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Spinocerebellar_tract&quot; rel=&quot;nofollow&quot;&gt;Spinocerebellar tract&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Dorsal_root_ganglion&quot; rel=&quot;nofollow&quot;&gt;Dorsal root ganglion&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Pyramidal_tracts&quot; rel=&quot;nofollow&quot;&gt;Pyramidal tracts&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Anterior_corticospinal_tract&quot; rel=&quot;nofollow&quot;&gt;Anterior corticospinal tract&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Lateral_corticospinal_tract&quot; rel=&quot;nofollow&quot;&gt;Lateral corticospinal tract&lt;/a&gt;.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-05T16:24:56.350" LastActivityDate="2014-06-05T16:24:56.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16832" PostTypeId="1" AcceptedAnswerId="16833" CreationDate="2014-04-24T13:34:22.130" Score="3" ViewCount="109" Body="&lt;p&gt;In regards to a published paper of a spider about to make a meal out of a parasitic wasp (&lt;a href=&quot;http://www.tandfonline.com/doi/abs/10.1080/08912963.2011.640399#.U1kSV14gVBU&quot; rel=&quot;nofollow&quot;&gt;http://www.tandfonline.com/doi/abs/10.1080/08912963.2011.640399#.U1kSV14gVBU&lt;/a&gt;), it reminded me of a issue I've often contemplating for some time:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isn't tree resin very slow moving, for instance maple sap has an extremely high viscosity and therefore how does the resin engulf both an arthropod, such as a spider, quick enough for it to not move away from the slowly moving amber?&lt;/p&gt;&#xA;" OwnerUserId="3056" LastActivityDate="2014-04-24T15:19:47.307" Title="How does tree resin capture arthropods?" Tags="&lt;palaeontology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16833" PostTypeId="2" ParentId="16832" CreationDate="2014-04-24T15:19:47.307" Score="5" Body="&lt;p&gt;I believe it is more of the fact that the organism gets stuck to the residual resin on the plant itself, and becomes encased and later fossilised in the amber.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.livescience.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;LiveScience.Com&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A host of bugs, fungus and other life forms have been found trapped in amber from the time of the dinosaurs.  Bugs can become encased in amber if, while alive, they get stuck in the resin. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Although plant resin is slow-moving, the bug stands to be encased in it if it is already stuck to the tree itself, as there is a large amount of resin on the surface of the plant.  If they are crawling over the plant, or land on the surface, they would become stuck and later encased. It would be similar with other organisms as well, as plants and &lt;a href=&quot;http://www.livescience.com/6316-life-trapped-amber-age-dinosaurs.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;other organisms have been discovered &lt;/a&gt;preserved in this way.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These fossils represent some of the earliest African fossil records for a variety of arthropods, including wasps, barklice, moths, beetles, a primitive ant, a rare insect called a zorapteran, and a sheet-web weaving spider. Parasitic fungi that lived on the resin-bearing trees were also found, as well as filaments of bacteria and the remains of flowering plants and ferns. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RRjOe.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6380" LastActivityDate="2014-04-24T15:19:47.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16835" PostTypeId="1" AcceptedAnswerId="16839" CreationDate="2014-04-24T15:57:37.853" Score="2" ViewCount="128" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Linkage_disequilibrium&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;, linkage disequilibrium $D$ equals&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$D = x_{11} - p_1\cdot q_1$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;        \begin{matrix}&#xA;        \text{Haplotype} &amp;amp; \text{Frequency}\\&#xA;        A_1B_1 &amp;amp; x_{11}\\&#xA;        A_{1}B_{2} &amp;amp; x_{12} \\&#xA;        A_{2}B_{1} &amp;amp; x_{21} \\&#xA;        A_{2}B_{2} &amp;amp; x_{22} \\&#xA;        \end{matrix}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;        \begin{matrix}&#xA;        \text{Allele} &amp;amp; \text{Frequency}\\&#xA;    A_{1} &amp;amp; p_{1}=x_{11}+x_{12} \\&#xA;    A_{2} &amp;amp; p_{2}=x_{21}+x_{22} \\&#xA;    B_{1} &amp;amp; q_{1}=x_{11}+x_{21} \\&#xA;    B_{2} &amp;amp; q_{2}=x_{12}+x_{22} \\&#xA;        \end{matrix}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://books.google.ca/books/about/Principles_of_Population_Genetics.html?id=4ypuQgAACAAJ&amp;amp;redir_esc=y&quot; rel=&quot;nofollow&quot;&gt;Hartl and Clark&lt;/a&gt;, linkage disequilibrium $D$ equals:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$D = x_{11}x_{22}-x_{12}x_{21}$$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you please prove that these two formulations of linkage disequilibrium are equivalent (assuming that they are equivalent)? If they're not… Do we use different definitions? What are their respective meanings?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-08-24T15:25:27.097" LastActivityDate="2014-08-24T15:25:27.097" Title="Definition of Linkage Desiquilibrium (LD)" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;mathematical-models&gt;&lt;population-dynamics&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16836" PostTypeId="1" AcceptedAnswerId="16840" CreationDate="2014-04-24T16:38:55.540" Score="1" ViewCount="1686" Body="&lt;p&gt;I am reading &lt;a href=&quot;http://www.jstor.org/stable/2400177?__redirected&quot; rel=&quot;nofollow&quot;&gt;Punctuated Equilibria: The Tempo and Mode of Evolution Reconsidered&lt;/a&gt;, which mentions the &quot;tempo&quot; and &quot;mode&quot; of evolution. I'm not familiar with the related literature and when I google the concept, what I got is something like: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One general topic, suggested by the word &quot;tempo,&quot; has to do with &quot;evolutionary rates..., their acceleration and deceleration, the conditions of exceptionally slow or rapid evolutions, and phenomena suggestive of inertia and momentum.&quot; A group of related problems, implied by the word &quot;mode,&quot; involves &quot;the study of the way, manner, or pattern of evolution, a study in which tempo is a basic factor, but which embraces considerably more than tempo''&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is as elusive as a definition can be. A clear definition should be something like &quot;tempo is ....&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what are the definitions of mode and tempo in evolution?&lt;/p&gt;&#xA;" OwnerUserId="6473" LastActivityDate="2014-04-24T19:37:01.677" Title="definition of tempo and mode in evolution" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16837" PostTypeId="1" AcceptedAnswerId="21452" CreationDate="2014-04-24T17:13:12.397" Score="2" ViewCount="22773" Body="&lt;p&gt;I am reading an article (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596711/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596711/&lt;/a&gt;) wherein a TOPflash/FOPflash assay is used to detect beta-catenin protein levels in a COS-7 cell line. I can't find a good explanation in the article, or in any other article, as to how this assay works. I understand the cells are transfected with TOPflash/FOPflash reporter plasmids, but that's about it. Any insight or redirection would be much appreciated.&lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2014-09-18T20:53:42.517" Title="How does a TOPflash/FOPflash assay work to detect beta-catenin protein expression?" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16839" PostTypeId="2" ParentId="16835" CreationDate="2014-04-24T19:25:12.523" Score="5" Body="&lt;p&gt;Just need to solve the equation. p1 = X11 + X12; q1 = X11 + X21; 1 = X11 + X12 + X21 + X22.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D = X11 - (X11 + X12) * (X11 + X21)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D = X11 - (X11X11 + X11X21 + X11X12 + X12X21)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D = X11 - X11X11 - X11X21 - X11X12 - X12X21&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D = X11 * (1 - X11) - X11X21 - X11X12 - X12X21&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D = X11 * (X11 + X12 + X21 + X22 - X11) - X11X21 - X11X12 - X12X21&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D = X11 * (X12 + X21 + X22) - X11X21 - X11X12 - X12X21&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D = X11X12 + X11X21 + X11X22 - X11X21 - X11X12 - X12X21&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D = X11X22 - X12X21&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry for the very long answer, but I thought it would be more clear if I wrote everything out.&lt;/p&gt;&#xA;" OwnerUserId="5909" LastActivityDate="2014-04-24T19:25:12.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16840" PostTypeId="2" ParentId="16836" CreationDate="2014-04-24T19:37:01.677" Score="3" Body="&lt;p&gt;Actually, we can go right to the source on this: &lt;a href=&quot;http://people.ucsc.edu/~laporte/simpson/Index.html&quot; rel=&quot;nofollow&quot;&gt;George Gaylord Simpson&lt;/a&gt;'s &lt;em&gt;&lt;a href=&quot;https://www.worldcat.org/title/tempo-and-mode-in-evolution/oclc/993515&quot; rel=&quot;nofollow&quot;&gt;Tempo and Mode in Evolution&lt;/a&gt;&lt;/em&gt; (1944).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Tempo&lt;/strong&gt; is the rate of evolution. Simpson was a paleontologist, so he was trying to answer questions like &quot;what is the percent change in the size of this tooth per million years?&quot; He has a chapter estimating these rates for various characters in horses, which have a very good North American fossil record.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Mode&lt;/strong&gt; encompasses the mechanisms responsible for evolution and their patterns. Simpson was working at the time of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Modern_evolutionary_synthesis&quot; rel=&quot;nofollow&quot;&gt;Modern Synthesis&lt;/a&gt; (the wikipedia page is decent and brief enough on the topic, about which books are written), coming from the perspective of a paleontologist trying to reconcile genetic evolution with the macroevolutionary patterns he was seeing in the fossil record.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Simpson was really the first paleontologist to look at fossils in a quantitative way, trying to understand of connections between microevolutionary processes and macroevolutionary patterns. He even co-authored one of the first quantitative and statistical methods books for &quot;organismal&quot; biologists: &lt;a href=&quot;http://books.google.com/books?id=z-FmQ8l-SZ4C&quot; rel=&quot;nofollow&quot;&gt;Quantitative Zoology&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, of &lt;strong&gt;tempo&lt;/strong&gt;, he says (p. xvii):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;...evolutionary rates under natural conditions, their acceleration and deceration, the conditions of exceptionally slow or rapid evolutions, and phenomena suggestive of inertia and momentum.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Of &lt;strong&gt;mode&lt;/strong&gt;, he says (p. xviii)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;...the study of the way, manner, or pattern of evolution, a study in which tempo is a basic factor, but which embraces considerably more than tempo. The purpose is to determine how populations became genetically and morphologically differentiated, to see how they passed from one way of living to another or failed to do so, to examine the figurative outline of the stream of life and the circumstances surrounding each characteristic element in that pattern.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Mode basically encompasses all the processes of evolution. Tempo is the subset of mode that concerns how fast evolution is (or is not) happening.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The great thing is that 70 years after Simpson's book, biologists are still trying to understand tempo and mode of evolution.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2014-04-24T19:37:01.677" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16841" PostTypeId="2" ParentId="7208" CreationDate="2014-04-24T21:56:08.437" Score="1" Body="&lt;p&gt;you can use something like &lt;a href=&quot;https://www.synbiota.com/&quot; rel=&quot;nofollow&quot;&gt;https://www.synbiota.com/&lt;/a&gt; where you can store and share your protocols with collaborators. If you make your project open, then anyone in the world can view your protocols.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nice thing about this is you can reference actual experiments that made use of the protocol (and literature) and this gives better context and understanding about the protocols...&lt;/p&gt;&#xA;" OwnerUserId="6478" LastActivityDate="2014-04-24T21:56:08.437" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16844" PostTypeId="1" AcceptedAnswerId="16853" CreationDate="2014-04-24T22:14:38.240" Score="2" ViewCount="128" Body="&lt;p&gt;As far as I know, roots of plants grow to the direction of Earth's gravity - this is called gravitropism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what happens if plants are in space? Are they able to perceive gravity in state of weightlessness? Either way, where do they grow their roots in those circumstances?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Note: this question may fit better either to Space.SE or to Astronomy.SE, but I was not sure about it.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="6024" LastActivityDate="2014-04-26T03:15:45.790" Title="In which direction plants' root grow in weightlessness?" Tags="&lt;botany&gt;" AnswerCount="2" CommentCount="1" ClosedDate="2014-07-09T17:32:31.370" ContentLicense="CC BY-SA 3.0" />
  <row Id="16845" PostTypeId="1" CreationDate="2014-04-24T22:53:40.243" Score="3" ViewCount="114" Body="&lt;p&gt;Paracetamol overdose is one of the most common drug toxicities. It may be treated by intravenous N-acetylcysteine which replaces the glutathione that is used up in paracetamol metabolism to prevent the harmful effects of NAQBI. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why can glutathione, NAC nor an inhibitor of the alternate cytochrome metabolism be added to paracetamol to prevent the possibility of acute liver failure? I imagine there is a reason as this is too obvious a solution.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-07-17T04:51:44.133" Title="Preventing paracetamol overdose" Tags="&lt;pharmacology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16846" PostTypeId="2" ParentId="16822" CreationDate="2014-04-24T23:07:25.390" Score="2" Body="&lt;p&gt;Interesting question! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Tick Borne encephalitis vaccine is an inactivated vaccine. It is therefore impossible to get the infection from the vaccine. Reports of fever have been noted but that is due to the body mounting an immune response not due to infection. There are therefore no reports of encephalitis or other markers of infection following the vaccine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not only may you have the TBE vaccine if you are asthmatic, but if you are at risk due to your lifestyle and location then, particularly if you have chronic asthma, the TBE vaccine might be a good idea. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Asthma is usually treated by inhalers and montelukast is reserved for uncontrolled/severe asthma. However in the rarer case of aspirin induced asthma, it is much more first line and used for mild asthma. Montelukast is not considered a mild medication. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this answers your question :) if not, comment below!&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-04-24T23:07:25.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16849" PostTypeId="1" AcceptedAnswerId="16860" CreationDate="2014-04-24T23:47:18.897" Score="1" ViewCount="374" Body="&lt;p&gt;With reference to the simplest Punnet square for Mendel's pea plant experiments it occurred to me that I could not connect the little I know about genetics to the little I know about molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mathematical model assumes that there are two factors (alleles) involved. With respect to Mendel's pea flower colors, to what do those alleles correspond at the molecular level? Genes--minimally it might be two codons, each with binary states so that a protein involved in the manufacture of color molecules changes at two specific amino acids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course it is not so simple. But it must be true that there are two physical objects which in the aggregate have two binary states for &lt;em&gt;this particular case&lt;/em&gt;. Do we know what they are, exactly, for Mendel's peas?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any insight. &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-04-24T23:59:32.497" LastActivityDate="2014-04-25T06:50:28.380" Title="What is the current molecular explanation of Mendel's pea cross?" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16850" PostTypeId="1" CreationDate="2014-04-25T01:45:55.233" Score="3" ViewCount="166" Body="&lt;p&gt;What is wrong with the following chain of reasoning?&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Nearly all cancer cells rely on high rates of glucose uptake (upto 200 times more than normal cells). This is known as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Warburg_effect&quot; rel=&quot;nofollow&quot;&gt;the Warburg effect&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;There is only one cell type in the human body that is obligated to use glucose - red blood cells (erythrocytes).&lt;/li&gt;&#xA;&lt;li&gt;Starve cancer cells of their only energy source by inducing hypoglycaemia in the patient, preserving red blood cells using, for example, erythrocytapheresis or an &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood_substitute#Oxygen-carrying_substitutes&quot; rel=&quot;nofollow&quot;&gt;oxygen-carrying substitute&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I understand that to completely eliminate a tumour such a regime would need to be in place for an extended period, but would like to know why such a treatment isn't feasible in theory?&lt;/p&gt;&#xA;" OwnerUserId="6480" LastActivityDate="2017-11-29T09:34:21.093" Title="Could the Warburg effect be used to starve cancer cells in situ?" Tags="&lt;metabolism&gt;&lt;cancer&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16853" PostTypeId="2" ParentId="16844" CreationDate="2014-04-25T04:24:14.337" Score="2" Body="&lt;p&gt;Astronomers on the International space station have done exactly that and grown Arabidopsis Thaliana in space. You can read the whole article &lt;a href=&quot;http://news.nationalgeographic.co.in/news/2012/121207-plants-grow-space-station-science/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&#xA;Plant roots apparently grow away from the seed exactly like on earth seeking out nutrients. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-04-25T04:24:14.337" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16854" PostTypeId="1" AcceptedAnswerId="16864" CreationDate="2014-04-25T04:34:40.227" Score="13" ViewCount="75375" Body="&lt;p&gt;Why don't we breathe nitrogen while it makes most of the air?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do we always tend to breathe oxygen, not hydrogen and nitrogen?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="22057" LastEditDate="2017-03-06T17:29:04.753" LastActivityDate="2017-03-29T22:51:05.610" Title="Why don't we breathe nitrogen when it makes up most of the air?" Tags="&lt;cellular-respiration&gt;&lt;respiration&gt;" AnswerCount="8" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16855" PostTypeId="2" ParentId="16850" CreationDate="2014-04-25T04:35:38.113" Score="1" Body="&lt;p&gt;The human body needs energy (ATP) for even the most basic function. I guess when you decrease glucose levels (which is broken down for ATP), you will be in affect taking away the ability of the body to function normally by depriving it of energy. This is my theory so I would be happy to if someone with more information on the topic could tell me if I am right or wrong.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-04-25T04:47:59.633" LastActivityDate="2014-04-25T04:47:59.633" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16856" PostTypeId="2" ParentId="16854" CreationDate="2014-04-25T04:43:30.727" Score="0" Body="&lt;p&gt;Basically when air fills our alveoli, by the process of diffusion, only oxygen in the air is taken into the blood stream while the other gases along with the waste CO2 is exhaled. So you do breathe in nitrogen, but it is exhaled as it is by the body. The whole process of the respiratory system is explained &lt;a href=&quot;http://www.patient.co.uk/health/the-lungs-and-respiratory-tract&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; with diagrams. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-04-25T04:43:30.727" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16858" PostTypeId="1" CreationDate="2014-04-25T05:01:19.310" Score="4" ViewCount="313" Body="&lt;p&gt;I'm not sure if I formulated my question well, but I'm curious about a couple statements made by Steven Pinker and and James Heckman.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this interview: &lt;a href=&quot;http://www.youtube.com/watch?v=KJ9Ad6s8g7I&amp;amp;t=7m51s&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=KJ9Ad6s8g7I&amp;amp;t=7m51s&lt;/a&gt; Steven Pinker says &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;there'd be a wide variety of families I could have grown up with and&#xA;  had the same kinds of interests&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and in this interview with James Heckman, he says: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But anyway, Smith says people are basically born the same and at age 8 one can't really see much difference among them. But then starting at age 8, 9, 10, they pursue different fields, they specialize and they diverge. In his mind, the butcher and the lawyer and the journalist and the professor and the mechanic, all are basically the same person at age 8.&#xA;  This is wrong. IQ is basically formed by age 8, and there are huge differences in IQ among people. Smith was right that people specialize after 8, but they started specializing before 8.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Can anyone explain Heckman's statement that people &quot;start specializing before 8&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do we know about genetic influence on interests? (Is this the right stackexchange to ask this on?)&lt;/p&gt;&#xA;" OwnerUserId="6482" LastEditorUserId="3340" LastEditDate="2014-04-25T05:20:01.303" LastActivityDate="2014-04-25T08:57:45.470" Title="Are people genetically predisposed to being interested in specific fields/ideas? How does specialization occur?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16859" PostTypeId="2" ParentId="16854" CreationDate="2014-04-25T06:10:43.230" Score="24" Body="&lt;p&gt;Animals use oxygen as a chemical energy source because oxygen gas can react with many other compounds to form oxides, which releases energy and happen spontaneously.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both carbon and nitrogen can be made to react with oxygen, but otherwise they are pretty inert.  So of all the gasses in the air present at over a fraction of a percent, oxygen is the only one we can use for energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hydrogen (and sulfer) are both possible substitutes for oxygen in the role of redox energy source, but are normally pretty small components of our environment.  On another planet they might well be the basis of biometabolism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course the fact that plants can use carbon dioxide to fix carbon is a different case of biology using a gas out of the air.  Its the defining quality of plants!   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The energetics of using CO2 is endothermic - it requires energy input. They have to use sunlight to get the energy to utilize this energy and its very costly energetically.  Animals can afford to move and grow because they use oxygen while they eat plants. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2017-03-06T03:50:26.850" LastActivityDate="2017-03-06T03:50:26.850" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16860" PostTypeId="2" ParentId="16849" CreationDate="2014-04-25T06:50:28.380" Score="4" Body="&lt;p&gt;The article you have linked to does explain everything thoroughly, though in a somewhat complex way. I did not know how much genetics you actually know, so I tried to answer very thoroughly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the article states that the gene Mendel studied and that was responsible for the white color of the pea flower is &lt;strong&gt;ANTHOCYANIN1&lt;/strong&gt; (in the article it is also called - bHLH, that is the name of the protein family that ANTHOCYANIN1 belongs to). So, ANTHOCYANIN1 is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Transcription_factor&quot; rel=&quot;nofollow&quot;&gt;transcription factor&lt;/a&gt; - a molecule that activates the transcription (making of mRNA) of other genes, basically it activates other genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The white flowered peas have a mutation (Guanine to Adenine transition) in the sixed intron of the gene ANTHOCYANIN1. &lt;a href=&quot;http://en.wikipedia.org/wiki/Intron&quot; rel=&quot;nofollow&quot;&gt;Introns&lt;/a&gt; are sequences of non-coding DNA, that does not encode amino acids, and is removed from the RNA transcript by a process called splicing. The mutation occurs at a binding site for the &lt;a href=&quot;http://en.wikipedia.org/wiki/Spliceosome&quot; rel=&quot;nofollow&quot;&gt;Spliceosome&lt;/a&gt; (a protein and RNA molecule) that splices the RNA, because of this the RNA transcript is not spliced correctly. The faulty RNA transcript for the gene ANTHOCYANIN1 contains 8 extra nucleotides and because the genetic code is a triplet, a &lt;a href=&quot;http://en.wikipedia.org/wiki/Frameshift_mutation&quot; rel=&quot;nofollow&quot;&gt;frame shift occurs&lt;/a&gt;. When a frame shift occurs all of the codons bellow the frame shift sight get changed. In this case, this leads to a premature stop codon. The translation of the ANTHOCYANIN1 RNA get stopped before a full protein can get synthesized and a non-functional protein is made.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If ANTHOCYANIN1 does not function, no genes are activated and no pigment is synthesized. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To summarize - the white pea flower color is a consequence of a nucleotide mutation (Guanine to Adenine) in a intron sequence of the gene ANTHOCYANIN1, this leads to incorrect splicing of the ANTHOCYANIN1 RNA (a frame shift) and to the production of a shorter protein that is non-functional.&lt;/p&gt;&#xA;" OwnerUserId="5909" LastActivityDate="2014-04-25T06:50:28.380" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16861" PostTypeId="1" CreationDate="2014-04-25T07:01:09.190" Score="1" ViewCount="47" Body="&lt;p&gt;I'm looking for an epigenetic database which includes for each example the psychological history of the persons DNA. Right now I can only find DNA and epigenetic databases. Sadly none of the databases provide &quot;thick data&quot; (qualitative data eg. history of person) to the sequenced DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to investigate the effects of psychology on epigenetic and vice versa.&lt;/p&gt;&#xA;" OwnerUserId="6484" LastActivityDate="2014-07-11T14:56:34.503" Title="psychological database with sequenced DNA records" Tags="&lt;genetics&gt;&lt;behaviour&gt;&lt;epigenetics&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16862" PostTypeId="2" ParentId="16858" CreationDate="2014-04-25T07:04:43.123" Score="2" Body="&lt;p&gt;I think the concept you are looking for is the one of heritability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, heritability represents the part of the variance for a trait that is caused by the genetic variance only. For more information, you can refer to &lt;a href=&quot;https://biology.stackexchange.com/questions/13669/do-genes-play-a-role-in-the-athleticism-and-shape-of-a-person/13670#13670&quot;&gt;this&lt;/a&gt;, &lt;a href=&quot;https://biology.stackexchange.com/questions/11402/will-i-grow-taller-how-can-i-tell/12405#12405&quot;&gt;this&lt;/a&gt;, &lt;a href=&quot;https://biology.stackexchange.com/questions/16531/which-was-the-last-significant-event-in-human-evolution-whats-next/16538#16538&quot;&gt;this&lt;/a&gt; or &lt;a href=&quot;https://biology.stackexchange.com/questions/16587/regarding-the-relation-of-observed-human-nature-with-evolution-and-or-genetics/16588#16588&quot;&gt;this&lt;/a&gt; post or to &lt;a href=&quot;http://en.wikipedia.org/wiki/Heritability&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Heritability_of_IQ&quot; rel=&quot;nofollow noreferrer&quot;&gt;This&lt;/a&gt; wikipedia article talks about the heritability of IQ in human. It has been measured to be around 0.7.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, heritability in IQ is not the same as heritability of &quot;interests&quot;. But I don't know about any measure concerning the heritability of &quot;interests&quot;. Such measure will be highly dependent on how you classify interests together. Does a mathematician specialist of probability theory have the same interests than a mathematician specialist of non-linear algebra? Does a Mathematician have the same interests than a chemist? and of a engineer? and of an electrician? Does a butcher have the same interests than a backer? and of a waiter? and of a bricklayer? .. Does anyone who work in business have the same interests? The fewer groups you make, the higher will the correlation between parents and offsprings and the higher is the part of the genetic variance that explain the variance in interests choice.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-04-25T08:57:45.470" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16863" PostTypeId="1" CreationDate="2014-04-25T10:07:36.810" Score="6" ViewCount="516" Body="&lt;p&gt;Donald Hebb states it as follows:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Let us assume that the persistence or repetition of a reverberatory activity (or &quot;trace&quot;) tends to induce lasting cellular changes that add to its stability.… When an axon of cell A is near enough to excite a cell B and repeatedly or persistently takes part in firing it, some growth process or metabolic change takes place in one or both cells such that A's efficiency, as one of the cells firing B, is increased.&quot;&#xA;  &lt;em&gt;Or we can conclude in short: &quot;Neurons that fire together, wire together&quot;.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As I understand it, this means that synapses that already exist become stronger between neurons.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Could new synapses form between neighboring neurons that &quot;fire together&quot;, but are not necessarily directly connected through an axon?&lt;/li&gt;&#xA;&lt;li&gt;And if so, what is the mechanism to direct the new synapse formation towards that other neighboring neuron that &quot;fires together&quot;?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6016" LastEditorUserId="107" LastEditDate="2014-04-25T13:30:30.367" LastActivityDate="2017-10-28T21:40:12.940" Title="Hebbian theory &quot;fire together&quot; clarification" Tags="&lt;molecular-biology&gt;&lt;neuroscience&gt;&lt;neurotransmitter&gt;&lt;neuroanatomy&gt;&lt;neurology&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16864" PostTypeId="2" ParentId="16854" CreationDate="2014-04-25T13:29:42.570" Score="18" Body="&lt;p&gt;I'd argue that we do &quot;breathe&quot; all those gases. Air that we inhale (at sea level) is about 78% N$_2$, 20.9% O$_2$, 1% argon, and smaller percentages of CO$_2$, neon, methane, etc. So all those gases are going into the lungs with every breath in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We take up oxygen preferentially because we have &lt;a href=&quot;http://proteopedia.org/wiki/index.php/Tutorial%3aHow_do_we_get_the_oxygen_we_breathe&quot;&gt;hemoglobin&lt;/a&gt; to bind O$_2$. When hemoglobin binds the oxygen, it upsets the balance and pulls more oxygen across the alveolar membrane. This is aided by pulmonary circulation which carries the blood away. &lt;a href=&quot;http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf%3a:640%3a:480%3a:/sites/dl/free/0077290828/811360/Hemoglobin_Causes_Net_Diffusion_of_Oxygen.swf%3a%3aHemoglobin%20Causes%20Net%20Diffusion%20of%20Oxygen&quot;&gt;Here's a demo&lt;/a&gt; of the diffusion process.  &lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2014-04-25T14:32:27.923" LastActivityDate="2014-04-25T14:32:27.923" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16865" PostTypeId="1" AcceptedAnswerId="16866" CreationDate="2014-04-25T14:39:28.077" Score="2" ViewCount="85" Body="&lt;p&gt;I always had this question why dental cavities cause pain. I stumbled on &lt;a href=&quot;https://biology.stackexchange.com/questions/9876/why-does-it-hurt-when-you-take-sweets-if-you-have-cavities-in-your-teeth&quot;&gt;this&lt;/a&gt; question on the reasons why dental cavities are painful. I have a followup question on how dental cavities are different from bodily injuries. I was under the impression that pain causes inflammation which in turn triggers something like mitosis that causes healing. Why does the same not happen with the dental cavities? Why are they not treated like the bodily injuries?  &lt;/p&gt;&#xA;" OwnerUserId="6488" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-07-02T22:40:29.990" Title="How are dental cavities different from body injuries?" Tags="&lt;pain&gt;&lt;injury&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16866" PostTypeId="2" ParentId="16865" CreationDate="2014-04-25T15:47:10.800" Score="1" Body="&lt;p&gt;I disagree with some of these statements. Dental cavities are injuries and are treated like injuries warrent. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unlike maybe trauma or cancer, dental cavities are a injury caused by decay of the enamel (the protective hard shell of the tooth). The decay is a result of the proliferation of bacteria, streptococcus mutants which releases an acid and breaks down the tooth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you have perforated enamel, other particles like food can get caught in the tooth and give rise to the growth of other bacteria. At this point you have a cavity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Infection, the presence of certain toxins, and trauma all causes inflammation, a type of non specific immune reaction characterized by increased blood flow to the site of injury (which causes swelling, pain, redness).&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-07-02T22:40:29.990" LastActivityDate="2014-07-02T22:40:29.990" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16867" PostTypeId="2" ParentId="16854" CreationDate="2014-04-25T16:14:40.627" Score="2" Body="&lt;p&gt;The bond in oxygen molecules is high energy, and ready to undergo an energy-yielding reaction with other molecules like sugar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bond in nitrogen not chemical useful to us...other organisms use energy to &quot;fix&quot; nitrogen to make energy rich nitrogen compounds that we &lt;strong&gt;can&lt;/strong&gt; use.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-04-25T16:14:40.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16868" PostTypeId="2" ParentId="14956" CreationDate="2014-04-25T16:56:43.107" Score="4" Body="&lt;p&gt;Genetic drift is the change of allele frequencies in a population due to random sampling during reproduction. This can cause some allele combinations to become more or less common than would be expected without drift, thus creating a disequilibrium. However, it's the combination of genetic drift AND selection that generates negative (instead of positive) disequilibria. From the discussion of the article you linked to:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Selection eliminates positive disequilibria more efficiently than it eliminates negative disequilibria, because negative disequilibrium reduces the genetic variance upon which selection acts. Consequently, the average disequilibrium over loci ... becomes negative over time.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-04-25T16:56:43.107" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16870" PostTypeId="1" AcceptedAnswerId="16875" CreationDate="2014-04-25T18:21:11.243" Score="10" ViewCount="1293" Body="&lt;p&gt;I was wondering if a neuron can make a synapse to itself? I suspect that it would be extremely unusual for a neuron to do this. Anyway, has anyone seen even a single instance of this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the process by which a neuron 'knows' not to make a synapse onto itself is known?&lt;/p&gt;&#xA;" OwnerUserId="6228" LastActivityDate="2014-04-26T22:32:45.743" Title="Can a neuron make a synapse onto itself?" Tags="&lt;synapses&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16871" PostTypeId="1" AcceptedAnswerId="16873" CreationDate="2014-04-25T18:29:27.170" Score="1" ViewCount="40" Body="&lt;p&gt;I'm currently planning out an RPG based on Misfits. Basically young offenders get super powers. I want one of the villains to have a really lame power that they use to become incredibly dangerous. I thought about using a power to caffeinate drinks. If someone used that to super-caffeinate somebody's bloodstream, could that hurt or kill somebody? Or would it not cause any real damage?&lt;/p&gt;&#xA;" OwnerUserId="6491" LastActivityDate="2014-04-25T19:12:02.127" Title="Could super-caffeinating somebody's bloodstream be dangerous?" Tags="&lt;pharmacology&gt;&lt;dose&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16872" PostTypeId="2" ParentId="14107" CreationDate="2014-04-25T18:40:20.493" Score="1" Body="&lt;p&gt;Free electron is just one type of charge-carrier. Once can also have other types: such as anions and cations to carry charge from one place to another. Therefore causing a current to flow. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if skin and hair lack &quot;free electrons&quot; like metal and semiconductor, we definitely have a great amount of anions and cations in our body. One example would be -- as krushna mentioned in his answer -- is $Na^+$ and $Cl^-$ ions from common salt in our body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, not all (type) potential can cause a great deal of current to flow in our body. The 12V lead-acid DC battery definitely does not cause any perceptible current to flow through our body; no matter how many free ions we have on our skin. On the other hand, 440V AC live wire will cause a great harm if we touch it even with dry hands. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I were to model my skin, I would go for a RC circuit with high R and high C attached in series. Put the appropriate values and simulate this circuit using a circuit simulator after applying test voltage across it. The Human Body Model for capacitance, as defined by the Electrostatic Discharge Association (ESDA) is a 100pF capacitor in series with a 1.5kΩ resistor. Since we have a capacitor in series, it prohibits DC current to flow through it. This is one reason why X Volt of AC is much more harmful than X volt of DC voltage (AC passes through capacitor easily).&lt;/p&gt;&#xA;" OwnerUserId="6228" LastEditorUserId="6228" LastEditDate="2014-04-26T07:29:36.013" LastActivityDate="2014-04-26T07:29:36.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16873" PostTypeId="2" ParentId="16871" CreationDate="2014-04-25T19:12:02.127" Score="6" Body="&lt;p&gt;In extreme doses, caffeine can - like almost any substance - cause death. &lt;a href=&quot;http://en.wikipedia.org/wiki/Caffeine#Caffeine_toxicity&quot;&gt;Wikipedia&lt;/a&gt; has this to say on the subject: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Extreme overdose can result in death.[59][60] The median lethal dose&#xA;  (LD50) given orally is 192 milligrams per kilogram in rats. The LD50&#xA;  of caffeine in humans is dependent on individual sensitivity, but is&#xA;  estimated to be about 150 to 200 milligrams per kilogram of body mass&#xA;  or roughly 80 to 100 cups of coffee for an average adult.[61] Though&#xA;  achieving lethal dose of caffeine would be difficult with regular&#xA;  coffee, it is easier to reach high doses with caffeine pills, and the&#xA;  lethal dose can be lower in individuals whose ability to metabolize&#xA;  caffeine is impaired.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You may wish to consult the references mentioned in the Wikipedia article for further details (As we all know, one should not trust Wikipedia too much). Note that caffeine administrated directly to the bloodstream will be more dangerous than the same amounted ingested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Information on caffeine toxicity can also be found at &lt;a href=&quot;http://emedicine.medscape.com/article/821863-overview&quot;&gt;Medscape&lt;/a&gt;. I you need concrete examples, Holmgreen, Norden-Petterson and Ahlner have published case reports on four recent cases of coffeine-related fatalities. (&lt;a href=&quot;http://www.erowid.org/references/refs_view.php?A=ShowDocPartFrame&amp;amp;ID=6702&amp;amp;DocPartID=6209&quot;&gt;3&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To cover all bases, it should be said that &lt;strong&gt;none of the information mentioned should be used to estimate a safe level of caffeine intake.&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-25T19:12:02.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16874" PostTypeId="2" ParentId="16863" CreationDate="2014-04-25T19:14:16.397" Score="1" Body="&lt;p&gt;It probably depends on what stage of development the neurons are in and what region of the brain.  If there's not branching still going on, then probably not.  Hebbian learning is generally considered a concept of neuron connections &lt;em&gt;strengthening&lt;/em&gt; (more synapses forming and dendritic spines growing larger) and not the initial formation, particularly in artificial neural networks, where a non-zero weight is already assigned to the neurons, and it's just a matter of strong vs. weak connections.&lt;/p&gt;&#xA;" OwnerUserId="1853" LastActivityDate="2014-04-25T19:14:16.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16875" PostTypeId="2" ParentId="16870" CreationDate="2014-04-25T19:20:06.133" Score="14" Body="&lt;p&gt;A synapse from a neuron unto itself is called an &lt;a href=&quot;http://en.wikipedia.org/wiki/Autapse&quot;&gt;Autapse&lt;/a&gt;. Not a whole lot is known about them. Tamas et al. (&lt;a href=&quot;http://en.wikipedia.org/wiki/Autapse&quot;&gt;1&lt;/a&gt;) give a summary:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Van der Loos and Glaser (1972)proposed the word “autapse” to describe&#xA;  a transmitter release site made by the axon of a neuron and its own&#xA;  somatodendritic domain. In addition to their original Golgi study in&#xA;  rabbit neocortex predicting the existence of autapses, possible&#xA;  autaptic contacts have been described in dog (Shkol’nik-Yarros, 1971)&#xA;  and rat (Peters and Proskauer, 1980; Preston et al., 1980) cerebral&#xA;  cortex, monkey neostriatum (DiFiglia et al., 1976), and cat spinal&#xA;  cord (Scheibel and Scheibel, 1971). (...)&#xA;  Although autapses formed in cell cultures have been used extensively&#xA;  to study the physiology of synaptic mechanisms (Segal, 1991; Pan et&#xA;  al., 1993;Shi and Rayport, 1994), few proposals have been made for the&#xA;  functional significance of inhibitory autaptic innervation in&#xA;  vivo(neostriatum, Park et al., 1980; Aplysia buccal ganglia,White and&#xA;  Gardner, 1981).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5754" LastActivityDate="2014-04-25T19:20:06.133" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16878" PostTypeId="2" ParentId="16813" CreationDate="2014-04-25T20:33:31.750" Score="4" Body="&lt;p&gt;Sex (depending on how you define it), evolved very early (more than a billion years ago). Even species like yeast have a type of &quot;sex&quot; (see below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, this doesn't mean there is necessarily a big difference between the two sexes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The yeast Saccharomyces cerevisiae, for example, also has two &quot;sexes&quot;, called &lt;em&gt;mating types&lt;/em&gt;. One is called &lt;em&gt;alpha&lt;/em&gt; and the other is called &lt;em&gt;a&lt;/em&gt;. They can only mate if they have different mating types, so it is analogous in a way to mammalian sex. However, the genetic difference between these two types is tiny. There's a specific location in the genome that's called the MAT locus. This location can have either an &lt;em&gt;alpha&lt;/em&gt; sequence or an &lt;em&gt;a&lt;/em&gt; sequence, an that will determine the sex. The rest of the genome will be the same between sexes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it really doesn't seem like it is a huge evolutionary step to go from no sex to some simple version of sex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See more details about yeast mating &lt;a href=&quot;http://en.wikipedia.org/wiki/Mating_of_yeast&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also see &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_sexual_reproduction&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; wikipedia article on the evolution of sexual reproduction.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2014-04-28T18:09:55.937" LastActivityDate="2014-04-28T18:09:55.937" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16879" PostTypeId="1" CreationDate="2014-04-25T21:01:37.110" Score="1" ViewCount="5636" Body="&lt;p&gt;I know that one is a female chicken and the other is male chicken. Are the chickens laying eggs considered the same species as those that we use for poultry meat? Or, are they different sub-species, analogous to how there are multiple breeds of dogs?&lt;/p&gt;&#xA;" OwnerUserId="6492" LastEditorDisplayName="user560" LastEditDate="2014-04-25T23:54:57.190" LastActivityDate="2016-09-30T17:23:24.570" Title="Are hens and roosters the same species?" Tags="&lt;evolution&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16880" PostTypeId="2" ParentId="16879" CreationDate="2014-04-25T21:06:29.370" Score="3" Body="&lt;p&gt;The main difference between a rooster and a hen is that the former is male and the latter is female. Their appearance differs in several ways &lt;sup&gt;[1]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A rooster also known as a cockerel or cock, is a male gallinaceous bird. The term usually refers to a male &lt;strong&gt;chicken&lt;/strong&gt; &lt;sup&gt;[2]&lt;/sup&gt;. The hen or the &lt;strong&gt;chicken&lt;/strong&gt; (&lt;em&gt;Gallus gallus domesticus&lt;/em&gt;) is a domesticated fowl, a subspecies of the Red Junglefowl &lt;sup&gt;[3]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And yes, the chickens laying eggs could be the same as the chickens that we use for poultry meat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Anjus Chiedozie. &lt;em&gt;&lt;a href=&quot;http://www.ehow.com/facts_5541597_rooster-vs-hen.html&quot; rel=&quot;nofollow&quot;&gt;Rooster Vs. Hen on eHow.com&lt;/a&gt;&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia. &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Rooster&quot; rel=&quot;nofollow&quot;&gt;Rooster&lt;/a&gt;&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia. &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Chicken&quot; rel=&quot;nofollow&quot;&gt;Chicken&lt;/a&gt;&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-05T16:29:38.180" LastActivityDate="2014-06-05T16:29:38.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16881" PostTypeId="2" ParentId="16879" CreationDate="2014-04-25T21:18:51.130" Score="0" Body="&lt;p&gt;There are probably different breeds that are commercially preferred for egg laying versus eating.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-04-25T21:18:51.130" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16882" PostTypeId="1" CreationDate="2014-04-25T22:53:11.177" Score="3" ViewCount="172" Body="&lt;p&gt;The following table is from Deonier's text Computational Gene Analysis at p. 152. &#xA;This is an exercise in global sequence alignment and scoring of alternative sequences.&#xA;The text proposed a solution (in parentheses). Setting aside the upper left hand portion of the table it seems there may be a better path. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's more likely I  misunderstand the idea than that there is a typo.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\begin{array}{c | c | c | c | c | c | c |}- &amp;amp; -&amp;amp; T &amp;amp; G &amp;amp; G &amp;amp; T &amp;amp; G\\ \hline  - &amp;amp; (0 ) &amp;amp; -2 &amp;amp; -4 &amp;amp; -6  &amp;amp;-8  &amp;amp; -10 \\ \hline&#xA;A &amp;amp;(-2)  &amp;amp; -1 &amp;amp; -3 &amp;amp; -5 &amp;amp; -7 &amp;amp; -9 \\ \hline&#xA;T &amp;amp;-4 &amp;amp; (-1)  &amp;amp; -2 &amp;amp; -4 &amp;amp; -4 &amp;amp; -6  \\ \hline&#xA;C &amp;amp;-6 &amp;amp; -3  &amp;amp; (-2)  &amp;amp; -3 &amp;amp; -5 &amp;amp; -5  \\ \hline&#xA;G &amp;amp;-8 &amp;amp; -5 &amp;amp; -2 &amp;amp; (-1) &amp;amp; -3 &amp;amp; -4 \\ \hline&#xA;T &amp;amp;-10 &amp;amp; -7 &amp;amp; -4 &amp;amp;-3 &amp;amp; (0)  &amp;amp; (-2 )\\ \hline  \end{array}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just looking at the upper left corner, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\begin{array}{c | c | c |} (0) &amp;amp; -2 &amp;amp; -4...\\ \hline -2 &amp;amp; (-1) &amp;amp; -3...\\ \hline  -4 &amp;amp; (-1) &amp;amp; -2...\\ \hline  -6 &amp;amp; -3 &amp;amp; (-2)...\\ \hline  \end{array}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;which seems to give -7 versus -8 for the book's path. Below are the book's alignment and the one corresponding to my scoring, which may reveal my error. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\begin{array}{c | c | c | c | c | c | c |} A: &amp;amp; A &amp;amp; T &amp;amp; C &amp;amp; G &amp;amp; T &amp;amp; - \\ \hline&#xA;B: &amp;amp; - &amp;amp; T &amp;amp; G &amp;amp; G &amp;amp; T &amp;amp; G  \\ \hline&#xA;\end{array}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\begin{array}{c | c | c | c | c | c | c |}&#xA;A: &amp;amp; A &amp;amp; T &amp;amp; C &amp;amp; G &amp;amp; T &amp;amp; - \\ \hline&#xA;B: &amp;amp; T &amp;amp;  - &amp;amp; G &amp;amp; G &amp;amp; T &amp;amp; G  \\ \hline&#xA; \end{array}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I had no trouble constructing the matrix just scoring it. it's a small point but I don't like to move on without understanding it.  Thanks for any assistance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: Both current answer seem clear on this but just for completeness: a match = 1; mismatch = -1; indel = -2.&lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-04-27T00:14:33.553" LastActivityDate="2014-07-26T01:21:56.853" Title="Sequence alignment scoring" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;&lt;sequence-alignment&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16883" PostTypeId="1" CreationDate="2014-04-25T22:58:12.797" Score="2" ViewCount="250" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Yawn&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;, the jury is still out on the &lt;em&gt;function&lt;/em&gt; a yawn serves. The article referenced above however writes to say &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Yawning most often occurs in adults immediately before and after sleep, during tedious activities and as a result of its infectious quality. It is commonly associated with tiredness, stress, overwork, lack of stimulation and boredom, though studies show it may be linked to the cooling of the brain&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The first sentence there draws my attention. Given a yawn is almost definitely associated with sleep - being expected to occur immediately before, and after. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it follow that an insomniac does not yawn? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a corollary, are there any &lt;strong&gt;known medical conditions&lt;/strong&gt; which preclude the act of yawning? For instance, a comatose person &lt;em&gt;probably&lt;/em&gt; does not yawn.&lt;/p&gt;&#xA;" OwnerUserId="1005" LastEditorUserId="1005" LastEditDate="2014-04-25T23:08:30.983" LastActivityDate="2014-06-25T18:57:44.680" Title="Do insomniacs yawn?" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;behaviour&gt;&lt;neurodegenerative-disorders&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16884" PostTypeId="2" ParentId="16844" CreationDate="2014-04-26T03:15:45.790" Score="0" Body="&lt;p&gt;Roots are negatively phototropic in addition to being positively gravitropic. Both growth patterns are mediated by the same hormone, auxin. Removing one factor or the other will not prevent roots from growing &quot;down.&quot;&lt;/p&gt;&#xA;" OwnerUserId="6371" LastActivityDate="2014-04-26T03:15:45.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16885" PostTypeId="2" ParentId="16882" CreationDate="2014-04-26T05:19:18.063" Score="1" Body="&lt;p&gt;If I am myself not mistaken, the table shows the paths of least resistance. There are many paths through this table and all of them are not shown only the ones that cost the least. You need to understand that a mismatch between the letters costs -1 (eg - AT), but an empty square  costs -2 (-A or -T). So your solution would cost = -1-3-4-3-2-4 which sums up too -17.&lt;/p&gt;&#xA;&lt;p&gt;This is a full alignment table. The top value is going diagonal, the second value is going down and the third value is going right.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/indgM.png&quot; alt=&quot;A full alignment table&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="5909" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-04-26T05:40:26.993" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16887" PostTypeId="1" AcceptedAnswerId="17336" CreationDate="2014-04-26T06:57:53.943" Score="2" ViewCount="545" Body="&lt;p&gt;I understand that chimeric sequence identification is done in results of sequencing projects to remove them and improve the quality of the output. I am unsure as to how they show up during sequencing. Any explanation is appreciated. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-04T10:50:19.487" LastActivityDate="2014-07-04T10:50:19.487" Title="chimeric sequences" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;chimerism&gt;" AnswerCount="2" CommentCount="2" ClosedDate="2014-05-11T19:37:40.230" ContentLicense="CC BY-SA 3.0" />
  <row Id="16888" PostTypeId="1" CreationDate="2014-04-26T07:23:06.540" Score="4" ViewCount="324" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;You are studying cellular signalling through a newly identified GPCR.&#xA;   Specifically you’re working on a pair of newly identified GPCRs, &#xA;  GPCR-A and GPCR-B. Each binds the same small ligand, but activates different &#xA;  heterotrimeric G-proteins that act on adenylyl cyclase.&lt;br&gt;&#xA;  Your grad student mentor explains that both the receptors and the &#xA;  Gα and Gβγ subunits of the heterotrimeric G-proteins are membrane associated.  You examine the sequences of the seven predicted &#xA;  transmembrane α-helices of GPCR-B. You’re surprised to find that there are &#xA;  hydrophilic amino acid residues in these helices. How can you explain this &#xA;  observation?  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This was an MIT quiz question.I have my guesses. But I wanted to know the correct answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well, since GPCRs are transmembrane proteins, normally the transmembrane helices have higher hydrophobic amino acids or only hydrophobic, non-polar aa . Here it says they saw some polar residues. Well my guess is that, since there are two GPCRs a and b that bind to the same ligand, it could be that one activates a stimulatory G protein and the other an inhibitory G protein Gi . So probably the polar amino acids which are in the transmembrane alpha helical segment of the stimulatory GPCR is slightly displaced and is in the intracellular region of the inhibitory GPCR (Gpcr that activates inhibitory G protein ). To be in the intracellular region, it has to be hydrophilic.&#xA;This is all I can think of. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help with this question is much appreciated. It is not a homework question for me. I don't go to MIT. I just wanted to reinforce my concepts.&lt;/p&gt;&#xA;" OwnerUserId="6497" LastEditorUserId="6497" LastEditDate="2014-04-27T14:59:01.650" LastActivityDate="2014-04-27T23:24:36.057" Title="Amino acid profile of GPCRs" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;homework&gt;&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16889" PostTypeId="2" ParentId="15632" CreationDate="2014-04-26T08:56:26.540" Score="2" Body="&lt;p&gt;Shigeta's answer is excellent.  I also agree with Chris in his discussion of ova, upon which I want to expand.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is in part speculation, but I believe that the answer to producing (usually) only one ovum lies in the development of animal &lt;a href=&quot;http://en.wikipedia.org/wiki/Viviparous#In_animals&quot; rel=&quot;nofollow&quot;&gt;viviparity&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many animals (especially aquatic animals) currently and historically have reproduced via &lt;a href=&quot;http://en.wikipedia.org/wiki/Oviparity&quot; rel=&quot;nofollow&quot;&gt;oviparity&lt;/a&gt; - the female producing a multitude of ova and allowing the male to shower them with spermatozoa.  The general style of males producing a large number of spermatozoa seems to not have changed greatly (aside from location of sperm deposition) through evolution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, &lt;a href=&quot;http://en.wikipedia.org/wiki/Viviparous#In_animals&quot; rel=&quot;nofollow&quot;&gt;viviparous&lt;/a&gt; animals must by necessity have some sort of limit on the number of simultaneous offspring, as the females carry offspring within their own bodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In animals who reproduce with &lt;a href=&quot;http://en.wikipedia.org/wiki/Viviparous#In_animals&quot; rel=&quot;nofollow&quot;&gt;hemotrophic viviparity,&lt;/a&gt; the embryos are provided nutrients from the mother through a placental organ that interfaces with the maternal bloodstream; the biological cost of having many offspring depends on how long they are carried and how large they are at term.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most mammals carry a litter and develop small, underdeveloped young, but hominids evolved to carry (usually) one.  There's an interesting discussion to be had on the different reproductive strategies (very careful rearing of one versus attention divided over many) but I don't have sources at the moment for those.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the cost of having more than one embryo must have been significant enough in our own past evolutionary process to have eliminated &lt;em&gt;most&lt;/em&gt; women who produced multiple ova.  Maternal mortality rates have &lt;a href=&quot;http://en.wikipedia.org/wiki/Maternal_death#Prevention&quot; rel=&quot;nofollow&quot;&gt;historically been MUCH higher than they are now&lt;/a&gt;, and risk is higher with twins (or more).  There are still times when more than one ovum reaches maturation and ovulates, resulting in &lt;a href=&quot;http://en.wikipedia.org/wiki/Twins#Fraternal_.28sororal.3B_dizygotic.29_twins&quot; rel=&quot;nofollow&quot;&gt;dizygotic twins&lt;/a&gt;, but it's fairly rare (between 6 and 14 per thousand births).&lt;/p&gt;&#xA;" OwnerUserId="6314" LastActivityDate="2014-04-26T08:56:26.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16890" PostTypeId="1" AcceptedAnswerId="16950" CreationDate="2014-04-26T10:38:15.130" Score="0" ViewCount="53" Body="&lt;p&gt;What book would you recommend me to study:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the dynamics of metapopulations, &lt;/li&gt;&#xA;&lt;li&gt;the structure of metapopulations, &lt;/li&gt;&#xA;&lt;li&gt;the evolution in structured metapopulations?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am not looking for an introduction but for a book that offers good and extensive mathematical formulations.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3624" LastEditDate="2014-05-24T19:48:35.333" LastActivityDate="2014-05-24T19:48:35.333" Title="Metapopulation structure - book recommendations" Tags="&lt;evolution&gt;&lt;ecology&gt;&lt;population-dynamics&gt;&lt;book-recommendation&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16892" PostTypeId="1" AcceptedAnswerId="16901" CreationDate="2014-04-26T11:59:22.557" Score="1" ViewCount="135" Body="&lt;p&gt;I know that viruses and sharp forces can stimulate mast cells by cut or by a virus infecting them and then release histamine. How can blunt force do this and cause inflammation? It doesn't have the above process. And how will the macrophages, neutrophils and plasma cells  react to this type of inflammation when there is no bacteria or viruses to swallow and create antibodies for?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="107" LastEditDate="2014-04-26T16:39:28.767" LastActivityDate="2014-06-05T16:31:21.700" Title="How does a blunt force stimulate histamine to develop early stages of inflammation?" Tags="&lt;physiology&gt;&lt;inflammation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16893" PostTypeId="2" ParentId="16882" CreationDate="2014-04-26T12:08:12.277" Score="1" Body="&lt;p&gt;The problem is that you are using the &lt;code&gt;T&lt;/code&gt; twice. Let's build the alignment manually, we have two sequences:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt;seq1&#xA;ATCGT&#xA;&amp;gt;seq2&#xA;TGGTG&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So, to build the alignment using your approach, we would take the first nt of seq1, the &lt;code&gt;A&lt;/code&gt; and choose the highest scoring nt from seq2 to align it against. In your example, that would be the &lt;code&gt;T&lt;/code&gt; (-1) which produces:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;A&#xA;T&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;OK, now we move to the next nt of seq1, the &lt;code&gt;T&lt;/code&gt;. Now, in your table, the highest score is indeed for &lt;code&gt;TT&lt;/code&gt; &lt;strong&gt;but we have already used the &lt;code&gt;T&lt;/code&gt; from seq2&lt;/strong&gt;, we can't use it again! In your alignment, you used a &lt;code&gt;-&lt;/code&gt;. The score for &lt;code&gt;T-&lt;/code&gt; at position 2 is -4. This means that your alignment:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ATCGT-&#xA;T-GGTG&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Has a score of:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$(AT)_{pos1} + (T-)_{pos2} + (CG)_{pos3} + (GG)_{pos4} + (TT)_{pos5} + (-G)_{pos6}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$-1-4-2-1-10 = -18 $&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the book's alignment is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$(A-)_{pos1} + (TT)_{pos2} + (CG)_{pos3} + (GG)_{pos4} + (TT)_{pos5} + (-G)_{pos6}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$-2 -1 -2 -1 -10 = -16 $&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-04-26T12:08:12.277" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16894" PostTypeId="1" AcceptedAnswerId="16895" CreationDate="2014-04-26T12:08:36.283" Score="3" ViewCount="1086" Body="&lt;p&gt;I have heard that during meiosis, homologous chromosomes from each parent &quot;cross-over&quot;, which enables the off-spring to inherit some alleles from the mother and some alleles from the father.  The picture below illustrates this &quot;cross-over&quot;, but of course this must occur at multiple sites, rather than just the one shown in the picture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/acSvZ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now my question is what causes the chromosomes to align perfectly during cross-over so that the loci of a particular gene will substitute for the corresponding loci on the homologous chromosome, as opposed to being substituted with a completely random locus?  Does each gene have a unique non coding sequence before it specifying what gene it is to enable this process to occur?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2014-04-26T14:09:24.447" Title="How does chromosome cross-over occur?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16895" PostTypeId="2" ParentId="16894" CreationDate="2014-04-26T13:19:36.150" Score="4" Body="&lt;p&gt;Quite simply, because chromosome pairing is sequence specific. Holliday Junctions, which are the functional structures of a cross-over, occur through a process called &quot;strand invasion,&quot; during which a region of one chromosome physically base-pairs with that of another.  Thus one locus cannot pair with a random locus, as there is generally insufficient sequence complimentarity between two random regions to form a functional Holliday Junction.  One interesting consequence of this mechanism is gene duplication and deletion in repetitious regions of the chromosome.  For example, genes with large repeated regions, such as the &lt;a href=&quot;http://ghr.nlm.nih.gov/condition/huntington-disease&quot;&gt;gene responsible for Huntington's disease&lt;/a&gt;, can expand and contract during homologous recombination due to strand invasion occurring at non-equivalent, but still homologous, sites.  Wikipedia does a nice job going over homologous recombination.  I also recommend looking over the relevant sections in Molecular Biology of the Cell, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26840/&quot;&gt;available&lt;/a&gt; on the PubMed Bookshelf.&lt;/p&gt;&#xA;" OwnerUserId="6501" LastEditorUserId="6501" LastEditDate="2014-04-26T14:09:24.447" LastActivityDate="2014-04-26T14:09:24.447" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16897" PostTypeId="2" ParentId="16752" CreationDate="2014-04-26T13:38:24.357" Score="1" Body="&lt;p&gt;Another idea I have come across is that caffeine absorption is much slower with tea, though my source is a &lt;a href=&quot;https://www.youtube.com/watch?v=7UXqfp8tL90&quot; rel=&quot;nofollow&quot;&gt;Good Eats Episode&lt;/a&gt;.  The relevant information can be found at approximately 19 min.  Maybe it's true, maybe it's not, but regardless, it's a great episode to watch if you are into tea.&lt;/p&gt;&#xA;" OwnerUserId="6501" LastActivityDate="2014-04-26T13:38:24.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16899" PostTypeId="1" AcceptedAnswerId="16923" CreationDate="2014-04-26T14:29:35.123" Score="7" ViewCount="1852" Body="&lt;p&gt;I'm trying to look at relationships between parasite and host phylogenetic trees. I have done a bit of searching for software with which to do this, and I have tried using Dendroscope and TreeMap, but can't get to grips with them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to produce something along the lines of this;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XXsaO.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3382" LastEditorUserId="22057" LastEditDate="2018-04-29T17:27:19.873" LastActivityDate="2020-05-28T20:58:32.147" Title="Does anyone know good software for producing tanglegrams?" Tags="&lt;bioinformatics&gt;&lt;phylogenetics&gt;" AnswerCount="5" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16900" PostTypeId="2" ParentId="16899" CreationDate="2014-04-26T15:01:21.317" Score="4" Body="&lt;p&gt;I have to confess that I know nothing about phylogenetics and the associated software but according to the abstract of &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/zoj.12027/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt; it seems that they used &lt;a href=&quot;http://beast.bio.ed.ac.uk/&quot; rel=&quot;nofollow noreferrer&quot;&gt;BEAST&lt;/a&gt; to map coalescence of co-evolving hosts and parasites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also &lt;a href=&quot;http://bioinformatics.oxfordjournals.org/content/27/13/i248.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt; is probably of highest interest to you as it compares the efficiency of different software to construct tanglegrams&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="22057" LastEditDate="2018-04-29T17:30:02.573" LastActivityDate="2018-04-29T17:30:02.573" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16901" PostTypeId="2" ParentId="16892" CreationDate="2014-04-26T16:35:56.067" Score="2" Body="&lt;p&gt;An brunt force (trauma) may destroy cells and tissues by mechanical action. It simply squashes them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cells contain different kinds of chemical substances in specific cellular organelles. The most important in this context are enzymes from lysozyme.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once enzymes are released (by squashing the cell) they induce irritating reactions to other cells and activate specific receptors found on immunitary system cells. This is how non-infectious inflammation occurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cell components act as inflammatory mediators responsible for the clinical signs of inflammation. Here are some examples &lt;sup&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Inflammatory_mediators#Cell-derived_mediators&quot; rel=&quot;nofollow&quot;&gt; [Wikipedia]&lt;/a&gt;&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Lysosome granules from destroyed cells&lt;/li&gt;&#xA;&lt;li&gt;NO (Nitric oxide) from endothelial cells and some neurons&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Other inflammatory mediators are produced by macrophages, neutrophiles and plasma cells, thus leading to a chain reaction, in which immunitary system cells activate one by another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Macrophages have enough to 'swallow': all the destroyed cells which must be removed from the tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antibodies are produced because altered cell structures are considered non-self and gain antigen properties.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: Wikipedia, &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Inflammation&quot; rel=&quot;nofollow&quot;&gt;Inflammation&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-05T16:31:21.700" LastActivityDate="2014-06-05T16:31:21.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16903" PostTypeId="2" ParentId="16883" CreationDate="2014-04-26T18:35:11.340" Score="2" Body="&lt;p&gt;Of course. As you quoted from &lt;a href=&quot;http://en.wikipedia.org/wiki/Yawn&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is commonly associated with &lt;strong&gt;tiredness, stress&lt;/strong&gt;, overwork, lack of stimulation and boredom.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Insomniacs, because they can't get a good sleep, are more tired and stressed than the others.&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-04-26T18:35:11.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16904" PostTypeId="2" ParentId="16879" CreationDate="2014-04-26T19:02:17.337" Score="-2" Body="&lt;p&gt;Yes, they are the same species. Meat birds and layers are the same species, they have just been bred differently to produce a certain result. (Along these lines, you may wish to picture a tomato, there are many different shapes and colors. However, they are all the same thing.).&#xA;As with humans, certain chickens have certain characteristics. And to an extent &quot;personalities&quot;. &#xA;It does appear, based on this link, that chickens are a subspecies of Red Junglefowl. However, chickens themselves do not appear to have an subspecies within them. Sorry I had to use &lt;a href=&quot;https://en.wikipedia.org/wiki/Chicken&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6289" LastEditorUserId="6289" LastEditDate="2016-09-30T17:23:24.570" LastActivityDate="2016-09-30T17:23:24.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16905" PostTypeId="1" AcceptedAnswerId="16906" CreationDate="2014-04-26T10:59:33.117" Score="14" ViewCount="658" Body="&lt;p&gt;I have noticed that if you look directly at tubelight (I have only white ones in my home) and close your eyes little, you see little random shaped colourless things sometimes with slow speed and sometimes with falling down. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are shaped like circles with something in between and in chains of random length. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My father has also seen them. So, I am sure I am not imagining things. What the hell are they?&lt;/p&gt;&#xA;" OwnerUserId="19517" OwnerDisplayName="Awesome" LastActivityDate="2017-01-11T14:03:10.197" Title="Seeing strange things in light" Tags="&lt;vision&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16906" PostTypeId="2" ParentId="16905" CreationDate="2014-04-26T11:11:04.613" Score="16" Body="&lt;p&gt;Those are &lt;a href=&quot;http://en.wikipedia.org/wiki/Floater&quot; rel=&quot;nofollow noreferrer&quot;&gt;floaters&lt;/a&gt;. These are objects floating in the vitreous humour that fills the eyeball. They typically look like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/c4K1H.png&quot; alt=&quot;Floaters&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3220" OwnerDisplayName="John Rennie" LastActivityDate="2014-04-26T11:11:04.613" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="16907" PostTypeId="2" ParentId="7259" CreationDate="2014-04-26T20:06:42.623" Score="20" Body="&lt;p&gt;I know of an ER doctor who had a patient who removed (by biting and pulling) every last part of her tongue, she survived that (although, her ability to speak was probably shot). The stump of her tongue clotted before she could even go into shock (at least where it was really serious). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a quote from &lt;a href=&quot;http://www.robertlesslie.com/angelsintheer.htm&quot;&gt;the book &lt;em&gt;Angels in the ER&lt;/em&gt;&lt;/a&gt;  (this is a paramedic speaking with the doc):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Every bit of it. Gone. And the funny thing, Doc, is it didn't even&#xA;  bleed very much.&quot;&lt;br&gt;&#xA;  The doctor then asked his patient to open her&#xA;  mouth... &quot;it &lt;em&gt;was&lt;/em&gt; gone!&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&#xA;It would certainly be possible to commit suicide doing this if one was a hemophiliac or continued to remove the clot from the hole(s) in their tongue (although the latter could be a potentially painful and I have a feeling that it would take a very, very long time!).&lt;/p&gt;&#xA;" OwnerUserId="6289" LastEditorUserId="3117" LastEditDate="2014-05-30T05:01:32.323" LastActivityDate="2014-05-30T05:01:32.323" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16908" PostTypeId="2" ParentId="4926" CreationDate="2014-04-26T20:18:12.590" Score="-1" Body="&lt;p&gt;This isn't quite the same; however, children can have parts of their brains removed and then the remaining parts of the brain can take over for that removed part. There are not also lasting effects of this even.&#xA;&lt;/p&gt;&#xA;There is a neurosurgeon by the name of Benjamin Carson who has done a procedure called a hemispherectomy. A hemispherectomy is the act of removing one side of the person's brain. This procedure can only be done in children under the age of either 10 or 12 (I am so sorry, I can't remember right now).&#xA;&lt;p&gt;&#xA;The reason this can only be done in children is because the side of the brain &lt;em&gt;not&lt;/em&gt; removed is able to take over for the removed side, this &lt;em&gt;cannot&lt;/em&gt; occur in adults.&lt;/p&gt;&#xA;" OwnerUserId="6289" LastActivityDate="2014-04-26T20:18:12.590" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16909" PostTypeId="2" ParentId="16870" CreationDate="2014-04-26T22:32:45.743" Score="5" Body="&lt;p&gt;There isn't enough research out there to explain the role of autapses however having read a selection of the latest research I can perhaps explain some of the proposed theory. Autapses may self inhibit or self excite. In the latter, one of their roles is thought to be to make a rhythmic action potential. This allows the brain to have an action potential which fires rhythmically if needed. Autapses of this nature have been identified in Interneurones for this purpose of continual activity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there is even less researched areas. Imagine you need a neurone to fire twice to certain neurones but once to others or other similar requirements. A mixture of autapses with self inhibition and self stimulation properties can achieve this elegantly in a short space. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Things like this however aren't required frequently. Usually interconnecting neurones is sufficient, however possibly in places of high rhythmic activity or fine control these autapses may be helpful. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0960982203003634&quot; rel=&quot;noreferrer&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0960982203003634&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-04-26T22:32:45.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16910" PostTypeId="1" AcceptedAnswerId="16971" CreationDate="2014-04-26T23:00:13.343" Score="10" ViewCount="297" Body="&lt;p&gt;Please forgive me in case my question wouldn't make much sense. I was reading about ABO blood groups &lt;a href=&quot;https://en.wikipedia.org/wiki/ABO_blood_group_system&quot;&gt;on Wikipedia,&lt;/a&gt; where I learnt that O is a recessive allele, and that it seems the A allele predates the O allele. My question is, therefore, how is it possible that almost half of the human population is group O?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, I would expect (quite naively I reckon), if only alleles A and O existed, that around 75% of the population should be A, and 25% should be O.&lt;/p&gt;&#xA;" OwnerUserId="6504" LastActivityDate="2014-04-28T23:54:45.490" Title="Why do so many people have group O blood?" Tags="&lt;human-genetics&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16911" PostTypeId="1" CreationDate="2014-04-27T01:06:05.817" Score="14" ViewCount="45051" Body="&lt;p&gt;&lt;em&gt;(careful, disturbing!)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was experimenting with some stray cockroaches that ended up falling in my bath tub overnight (there is currently an infestation undergoing in my apartment building) and I found out that they are very easily killed by simply soaking them in soapy water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read that soap blocks some pores in insects' bodies which leads to suffocation, which appears to be the cause of death for my test cockroaches. But what I don't get is why about a half of them died with their innards bursting from their tail end. The water wasn't too hot to make them boil. Is it that they suffocate so hard that attempting to breathe they blow out their insides? Or is it the soap's reaction with the cockroach's bodily materials? Or is something else causing this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I remember watching a documentary on injecting various insects with hydrogen peroxide which caused much more dramatic explosions, but it's not like I was injecting cockroaches, I just sprinkled them with soap water.&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2019-05-16T16:55:13.843" Title="Why do cockroaches burst from soapy water?" Tags="&lt;entomology&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16912" PostTypeId="2" ParentId="9893" CreationDate="2014-04-27T03:32:31.153" Score="4" Body="&lt;p&gt;Blood from a cut or a wound is tainted with bacteria from the surrounding environment. To a mosquito from an evolutionary perspective it would be like eating off the floor. The blood which flows through your veins is clean(er) due to your immune system and so evolution selected a pathway based on insertion into the skin in order to obtain the meal. &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-04-27T03:32:31.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16913" PostTypeId="2" ParentId="15605" CreationDate="2014-04-27T03:53:46.453" Score="1" Body="&lt;p&gt;There are two ways to introduce genetic material past a cell membrane. Infection and generation of a porous cytoplasm. Viruses and bacteria generally are used. Retroviruses tend to cause leukemia so they are avoided however they are the only way to get past the nucleus in vivo of multicellular life. Electroporation and needles generate a porous cytoplasm allowing genetic material to seap or be inserted into the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once the genetic material is in the cell it has to have contained site specific oligonucleotides to hybridize with the strand of interest. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mfMdL.png&quot; alt=&quot;http://en.wikipedia.org/wiki/Knockout_mouse&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Procedure&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The procedure for making mixed-genotype blastocyst.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Breeding scheme for producing knockout mice. Blastocysts containing cells, that are both wildtype and knockout cells, are injected into the uterus of a foster mother. This produces offspring that are either wildtype and coloured the same colour as the blastocyst donor (grey) or chimera (mixed) and partially knocked out. The chimera mice are crossed with a normal wildtype mouse (grey). This produces offspring that are either white and heterozygous for the knocked out gene or grey and wildtype. White heterozygous mice can subsequently be crossed to produce mice that are homozygous for the knocked out gene.&#xA;  There are several variations to the procedure of producing knockout mice; the following is a typical example.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The gene to be knocked out is isolated from a mouse gene library. Then a new DNA sequence is engineered which is very similar to the original gene and its immediate neighbour sequence, except that it is changed sufficiently to make the gene inoperable. Usually, the new sequence is also given a marker gene, a gene that normal mice don't have and that confers resistance to a certain toxic agent or that produces an observable change (e.g. colour or fluorescence).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Stem cells are isolated from a mouse blastocyst (a very young embryo) and grown in vitro. For this example, we will take stem cells from a white mouse.&#xA;  The new sequence from step 1 is introduced into the stem cells from step 2 by electroporation. By the natural process of homologous recombination some of the electroporated stem cells will incorporate the new sequence with the knocked-out gene into their chromosomes in place of the original gene. The chances of a successful recombination event are relatively low, so the majority of altered cells will have the new sequence in only one of the two relevant chromosomes - they are said to be heterozygous.&#xA;  The stem cells that incorporated the knocked-out gene are isolated from the unaltered cells using the marker gene from step 1. For example, the unaltered cells can be killed using a toxic agent to which the altered cells are resistant.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The knocked-out stem cells from step 4 are inserted into a mouse blastocyst. For this example, we use blastocysts from a grey mouse. The blastocysts now contain two types of stem cells: the original ones (from the grey mouse), and the knocked-out cells (from the white mouse). These blastocysts are then implanted into the uterus of female mice, where they develop. The newborn mice will therefore be chimeras: some parts of their bodies result from the original stem cells, other parts from the knocked-out stem cells. Their fur will show patches of white and grey, with white patches derived from the knocked-out stem cells and grey patches from the recipient blastocyst.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Some of the newborn chimera mice will have gonads derived from knocked-out stem cells, and will therefore produce eggs or sperm containing the knocked-out gene. When these chimera mice are crossbred with others of the wild type, some of their offspring will have one copy of the knocked-out gene in all their cells. These mice will be entirely white and are not chimeras, however they are still heterozygous.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;When these heterozygous offspring are interbred, some of their offspring will inherit the knocked-out gene from both parents; they carry no functional copy of the original unaltered gene (i.e. they are homozygous for that allele).&#xA;  A detailed explanation of how knockout (KO) mice are created is located at the website of the Nobel Prize in Physiology or Medicine 2007.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;-&lt;a href=&quot;http://en.wikipedia.org/wiki/Knockout_mouse&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2014-04-28T03:52:47.140" LastActivityDate="2014-04-28T03:52:47.140" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16915" PostTypeId="2" ParentId="16605" CreationDate="2014-04-27T08:06:49.933" Score="0" Body="&lt;p&gt;Leonardo's answer:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Animal study on sheep - &lt;a href=&quot;http://ncbi.nlm.nih.gov/pubmed/3444363&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;where&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[L]ymphatic flow in sheep, and&#xA;  the range being very heterogeneous (virtually no flow at the lower&#xA;  bound). I would agree that, in general, this is a very heterogeneous&#xA;  effect subject to many chemical (hydration, osmotic balance, blood&#xA;  pressure modifying drugs) and physical (cardiovascular tone, posture,&#xA;  activity level) factors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-27T08:06:49.933" CommentCount="0" CommunityOwnedDate="2014-04-27T08:06:49.933" ContentLicense="CC BY-SA 3.0" />
  <row Id="16919" PostTypeId="1" AcceptedAnswerId="16920" CreationDate="2014-04-27T11:42:28.860" Score="15" ViewCount="1184" Body="&lt;p&gt;I am inquisitive to know about how a person contracts AIDS.&#xA;Among the common masses it's still the belief that having sex with multiple partners causes the disease but that is not the case when read online that it can come only from persons carrying the virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if a person (male or female) is carrying the virus (HIV positive) does it mean that he/she is suffering from the disease or the person may be carrying the HIV disease and still be free from AIDS. If so how did this chain reaction of spreading the virus start?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also is it true that immune systems of some rare people in this world can fight with this disease.&lt;/p&gt;&#xA;" OwnerUserId="5008" LastEditorUserId="3340" LastEditDate="2014-11-12T06:12:13.050" LastActivityDate="2016-04-11T11:06:03.423" Title="How does a person get AIDS?" Tags="&lt;human-biology&gt;&lt;hiv&gt;&lt;aids&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16920" PostTypeId="2" ParentId="16919" CreationDate="2014-04-27T12:21:03.793" Score="9" Body="&lt;p&gt;You read right: it can only come from people already infected through:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;sexual contact&lt;/li&gt;&#xA;&lt;li&gt;contact with an infected person's body fluids (blood transfusions), although not all fluids carry HIV (saliva, tears)&lt;/li&gt;&#xA;&lt;li&gt;from mother to child (pregnancy, breast feeding)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Having unprotected sex with multiple partners statistically increases the risk of stumbling upon someone infected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A person carrying the HIV virus may not show symptoms of AIDS, because the HIV infection passes through a stage of clinical and symptomatic latency (the asymptomatic HIV or chronic HIV) which can last up 20 years (average of 8 years) when only uncommon symptoms like fever and weight loss show up. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where it started? It is believed that HIV originated in non-human primates in West-central Africa and were transferred to humans in the early 20th century. The virus adapted and became strong, because the virus from primates is typically suppressed by the human immune system within weeks of infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HIV is a retrovirus that primarily infects components of the human immune system such as &lt;strong&gt;CD4+ T cells, macrophages and dendritic cells&lt;/strong&gt;. &lt;strong&gt;It directly and indirectly destroys CD4+ T cells.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it destroys the cells reponsible of its removal from the human body. Hard to believe that there are people whose immune can really destroy the virus. A virus lives inside the cell it parasite, so the immune cells must destroy one the other. Also the virus infects and kills them (the good ones). However, as &lt;a href=&quot;https://biology.stackexchange.com/posts/comments/22865?noredirect=1&quot;&gt;MattDMo suggested&lt;/a&gt; an infected person may take antiretroviral drugs and the disease progression can be slowed down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: Wikipedia - &lt;a href=&quot;http://en.wikipedia.org/wiki/HIV/AIDS&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;HIV, AIDS&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-06-04T16:33:58.843" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16921" PostTypeId="1" AcceptedAnswerId="17252" CreationDate="2014-04-27T12:40:09.773" Score="3" ViewCount="377" Body="&lt;p&gt;I have been looking for some time to find an answer to the following question. I would be grateful for any help/advice or directions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I work very frequently with large number of proteins and assess their importance in a biological network. Traditionally there are two methods used to visualise proteins in a network and withdraw conclusions purely on network architecture bases, before one looks at the top hits in details using databases. One is degree and the other is clustering coefficience. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Degree refers to a node being connected to edges. The higher the degree, the more nodes are connected to a given node. Traditionally people interpret nodes with high degree as being biologically important, so called hubs. Since hubs are so highly connected it means that a failure of a biological hub has catastrophic consequences since the functions of many proteins are related/dependent on hubs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However what confuses me is the biological meaning of clustering coefficient of a node in a given network. I’m aware that clustering coefficience refers to the tendency of a nodes neighbours to connect to each other; however, I was unsure as to what it means biologically and whether that means a node with a high clustering coefficience is more “important” than a node with low clustering coefficience. This just seems unlikely to me because hub proteins, are considered important proteins; however, hubs usually have low clustering coefficience but that doesn’t mean they are less important since they are highly connected (high degree). Therefore to put it in plain english, why do people use clustering coeffience in biological networks and what biological information is it providing them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I would appreciate any explanation/advice and references you could provide that would help me understand the biological meaning/interpretation of clustering coefficience.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-08T14:47:48.437" Title="Biological meaning/interpretation of clustering coefficience" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;network&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16922" PostTypeId="1" AcceptedAnswerId="16946" CreationDate="2014-04-27T13:24:42.013" Score="6" ViewCount="16980" Body="&lt;p&gt;Let's take a quote from Wikipedia about zebroids.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Donkeys are closely related to zebras and both animals belong to the horse family. These zebra donkey hybrids are very rare. In South Africa, they occur where zebras and donkeys are found in proximity to each other. Like mules, however, they are generally genetically unable to breed, due to an odd number of chromosomes disrupting meiosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;First, if I understand meiosis, the resulting cells don't actually end up with half the number of chromosomes, but closer to a full set of halves of chromosomes. How is the meiotic process disrupted?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A donkey has 62 chromosomes; the zebra has between 32 and 46 chromosomes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Apparently this difference doesn't obstruct producing (infertile) offspring. How comes the process of recombination of such vastly different number of chromosomes in gametes is viable? What happens to chromosomes that don't find their 'pair'?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And then,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Horses have 64 chromosomes, while most zebroids end up with 54 chromosomes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;54 is an even number. How comes zebroids can't just normally produce fertile offspring with other zebroids of the same number of chromosomes?&lt;/p&gt;&#xA;" OwnerUserId="6512" LastActivityDate="2017-11-24T12:25:34.637" Title="Why are hybrids infertile?" Tags="&lt;genetics&gt;&lt;hybridization&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16923" PostTypeId="2" ParentId="16899" CreationDate="2014-04-27T14:38:44.037" Score="11" Body="&lt;h1&gt;Dendroscope&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;Using &lt;a href=&quot;http://ab.inf.uni-tuebingen.de/software/dendroscope/&quot; rel=&quot;noreferrer&quot;&gt;Dendroscope&lt;/a&gt;, I opened the provided example file &lt;code&gt;trees.new&lt;/code&gt;. This opens a new window with 16 trees in it.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Shift click on the first two trees (&lt;code&gt;Tree1&lt;/code&gt; and &lt;code&gt;Tree2&lt;/code&gt;).&lt;/li&gt;&#xA;&lt;li&gt;Choose &lt;code&gt;Algorithms&lt;/code&gt; $\rightarrow$ &lt;code&gt;Tanglegram...&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;This will compute the tanglegram and open a new window.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;At this point, I get:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4V2KM.jpg&quot; alt=&quot;Tanglegram&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is nothing special in the &lt;code&gt;trees.new&lt;/code&gt; file, just 16 Newick trees. So it looks like all you need is to have your trees in the same file or use &lt;code&gt;File&lt;/code&gt; $\rightarrow$ &lt;code&gt;Add from file&lt;/code&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that the tricky part is that your trees have to have the same tip labels, so that they can be lined up optimally. So in your example, &lt;em&gt;Phalacrocorax pygmaeus&lt;/em&gt; and &lt;em&gt;Pectinopygus excornis&lt;/em&gt; must have been named the same in the original Nexus file and then modified to produce the final figure.&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;TreeMap 3&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://sydney.edu.au/engineering/it/~mcharles/software/treemap/treemap3.html&quot; rel=&quot;noreferrer&quot;&gt;TreeMap&lt;/a&gt; requires some preliminary setup. Basically you create a Nexus file manually. Using the &lt;code&gt;4taxonmatch&lt;/code&gt; file from the &lt;a href=&quot;https://sites.google.com/site/cophylogeny/example-data-files&quot; rel=&quot;noreferrer&quot;&gt;examples&lt;/a&gt;, you can get the basic layout. You have a &lt;code&gt;HOST&lt;/code&gt; block and a &lt;code&gt;PARASITE&lt;/code&gt; block. Within each one of those is a &lt;code&gt;TREE&lt;/code&gt; block, which contains the Newick formatted tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;code&gt;RANGE&lt;/code&gt; block inside the &lt;code&gt;DISTRIBUTION&lt;/code&gt; block contains the mapping table. Here &lt;code&gt;p&lt;/code&gt; maps to &lt;code&gt;u&lt;/code&gt;, etc. This is the connection between host and parasite.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;#NEXUS&#xA;BEGIN HOST; &#xA;TREE * Host1 = (u, (v, (w, x))); &#xA;ENDBLOCK; &#xA;&#xA;BEGIN PARASITE;&#xA;TREE * Para1 = (p, (q, (r, s))); &#xA;ENDBLOCK; &#xA;&#xA;BEGIN DISTRIBUTION; &#xA;RANGE &#xA;    p: u, &#xA;    q: v, &#xA;    r: w, &#xA;    s: x&#xA;; &#xA;END;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;In contrast, you get the correctly labelled tree directly. See below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6G1eD.jpg&quot; alt=&quot;Tanglegram 2&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2014-04-27T14:38:44.037" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16924" PostTypeId="1" AcceptedAnswerId="16940" CreationDate="2014-04-27T15:30:40.887" Score="2" ViewCount="314" Body="&lt;p&gt;I am trying to find some reliable gene kit by which you can rapidly test Toxoplasma gondii.&#xA;I am not sure if it exists.&#xA;I have an intuition that some tests done during 90s-00s on this species had high false negatives.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which genes should you detect to find Toxoplasma gondii in a gene kit?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-27T17:01:16.130" Title="Saliva test for Toxoplasma gondii?" Tags="&lt;parasitology&gt;&lt;saliva&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16925" PostTypeId="2" ParentId="16175" CreationDate="2014-04-27T16:12:19.667" Score="0" Body="&lt;p&gt;I would now say that the hardening is just &lt;strong&gt;local acute venous congestion&lt;/strong&gt; if in the short term.&#xA;Without stretching after practice, it just takes more days to recover.&#xA;So lymphatic drainage is the one which helps the muscle get its needs and nutrients.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this happens during years, it is difficult to say what is the causal factor.&#xA;It depends on many factors. &#xA;One key factor is how well the lymphatic circulation can recover the body back.&#xA;So genomics of the patient comes in the picture.&#xA;Many other factors too like anatomical structure of chest.&#xA;Then, depending on these factors and other pathological processes may happen many processes like&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;accumulation of fibrinoid&lt;/li&gt;&#xA;&lt;li&gt;accumulation of calcium deposits&lt;/li&gt;&#xA;&lt;li&gt;shorter diffuse distances&lt;/li&gt;&#xA;&lt;li&gt;smaller total area of cells&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which are some adaptation processes to the ageing (also of prolonged monotonous weight lifting).&#xA;They can lead to&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;acute lymphangitis (reddening of the skin)&lt;/li&gt;&#xA;&lt;li&gt;Chronic lymphangitis&lt;/li&gt;&#xA;&lt;li&gt;Chronic Granulomatous Lymphadenitis (fibrosis happening between muscles and connection points - not in all cases granulomatous - rare only)&lt;/li&gt;&#xA;&lt;li&gt;lymphadenopathy (very, very late - after many years)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;during ageing (adaptation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Better question would probably be: &lt;strong&gt;what are processes happening during ageing?&lt;/strong&gt;&#xA;And then cover pathologies of ageing separately and also the physiological processes on the weight lifting separately. &lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-27T16:12:19.667" CommentCount="0" CommunityOwnedDate="2014-04-27T16:12:19.667" ContentLicense="CC BY-SA 3.0" />
  <row Id="16926" PostTypeId="2" ParentId="15615" CreationDate="2014-04-27T16:23:24.977" Score="0" Body="&lt;p&gt;Fibrinoid swelling involves necrosis and swelling so no.&#xA;Organisation of thrombus refers to some very large space of organising thrombus in different ways - so no, since there is an exact mechanism under.&#xA;Based on my interpretation of Robbins -book.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The correct answer is 3. thromboembolism.&#xA;Thromboembolism is a combination of thrombosis and its main complication, &lt;strong&gt;embolism&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-27T16:23:24.977" CommentCount="0" CommunityOwnedDate="2014-04-27T16:23:24.977" ContentLicense="CC BY-SA 3.0" />
  <row Id="16927" PostTypeId="2" ParentId="15617" CreationDate="2014-04-27T16:24:44.903" Score="0" Body="&lt;p&gt;No. They increase the risk, but are not the causes.&#xA;There must be other factors involved which triggers the systemic venous congestion.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-27T16:24:44.903" CommentCount="0" CommunityOwnedDate="2014-04-27T16:24:44.903" ContentLicense="CC BY-SA 3.0" />
  <row Id="16928" PostTypeId="2" ParentId="15623" CreationDate="2014-04-27T16:30:14.650" Score="1" Body="&lt;p&gt;Literature covers only hypertrophy of the heart.&#xA;Atrophy not mentioned.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Theoretically atrophy of the heart would require some factors&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;mutations (which can destroy the gene to build up the organ), &lt;/li&gt;&#xA;&lt;li&gt;poor nourishment, &lt;/li&gt;&#xA;&lt;li&gt;poor circulation, &lt;/li&gt;&#xA;&lt;li&gt;loss of hormonal support, &lt;/li&gt;&#xA;&lt;li&gt;loss of nerve supply to the target organ, &lt;/li&gt;&#xA;&lt;li&gt;excessive amount of apoptosis of cells, and &lt;/li&gt;&#xA;&lt;li&gt;disuse or lack of exercise or disease intrinsic to the tissue itself. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Atrophy can happen locally in some part of the heart only, like in some parts of myocardial infarction.&#xA;However, the surrounding healthy tissue then undergoes hypertrophy so the total heart undergoes hypertrophy.&#xA;Some discussion about &lt;em&gt;Cardiac atrophy&lt;/em&gt; &lt;a href=&quot;http://www.abcam.com/index.html?pageconfig=resource&amp;amp;rid=12408#3&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-27T16:30:14.650" CommentCount="0" CommunityOwnedDate="2014-04-27T16:30:14.650" ContentLicense="CC BY-SA 3.0" />
  <row Id="16929" PostTypeId="1" CreationDate="2014-04-27T16:35:23.497" Score="2" ViewCount="350" Body="&lt;p&gt;&lt;strong&gt;Note : Images displayed below might be disturbing to some people.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have dissected a fish for the first time ! I have some idea of what some of the structures might be but I am not sure and so would like your help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1.Here is the fish I dissected. Are the white structures (towards the dorsal surface) muscles ? They are beautifully arranged. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Qcphn.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2.I want to know what the yellow coloured structure (towards the ventral side) is. I guess it's the intestine. It looks &quot;noodly&quot;. Here is a close up.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/dJyvo.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3.I have pointed at two different parts in the following images. I want to know whether they are part of the same structure - ie swim bladder or whether they are two different structures altogether. When I poked one of the parts the other part increased in size ,so I guess it's one structure but I just wanna make sure.&lt;img src=&quot;https://i.stack.imgur.com/pJDME.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/2DaRy.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-07-26T19:23:16.693" Title="Identifying internal structures of dissected fish" Tags="&lt;zoology&gt;&lt;anatomy&gt;&lt;ichthyology&gt;&lt;dissection&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16930" PostTypeId="2" ParentId="15699" CreationDate="2014-04-27T16:36:51.870" Score="0" Body="&lt;p&gt;&lt;strong&gt;My conjecture&lt;/strong&gt;: Intrinsic regulation is done in the heart the second best, after the brain.&#xA;This idea is based on the fact that the brain controls heart's some autonomic functions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is an open research question how the autonomic nervous system affects the intrinsic functions of the heart - and the reverse is true too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer this question, we need to understand the autonomic regulation of the heart better i.e. the inner-physiology of the heart's electrical activity.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-26T09:22:05.610" LastActivityDate="2014-12-26T09:22:05.610" CommentCount="0" CommunityOwnedDate="2014-04-27T16:36:51.870" ContentLicense="CC BY-SA 3.0" />
  <row Id="16931" PostTypeId="2" ParentId="15703" CreationDate="2014-04-27T16:40:25.403" Score="0" Body="&lt;p&gt;This question is dependent on the specific patient at hand.&#xA;I think in the normal situation the diameter of the capillaries is about the same in each organ.&#xA;Better question would be: how does the diameter changes in relation to the venous and arterial ends of the capillaries?&#xA;Then, think about how big portion of the capillaries are in the venous end in the organ.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I cannot say that 50% of capillaries are on the venous end of the organ and 50% on the arterial side.&#xA;This is again an open research question.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-27T16:40:25.403" CommentCount="0" CommunityOwnedDate="2014-04-27T16:40:25.403" ContentLicense="CC BY-SA 3.0" />
  <row Id="16932" PostTypeId="1" CreationDate="2014-04-27T16:41:40.077" Score="3" ViewCount="161" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YKRQO.jpg&quot; alt=&quot;myst![mystery bug&quot;&gt;ery bug 1]&lt;a href=&quot;https://i.stack.imgur.com/YKRQO.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What insect are these? Found them indoors. No wings, just crawling on the walls. &lt;/p&gt;&#xA;" OwnerUserId="6514" LastActivityDate="2014-06-20T15:01:33.440" Title="What type of insect is this?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-11-24T15:16:13.427" ContentLicense="CC BY-SA 3.0" />
  <row Id="16933" PostTypeId="2" ParentId="15814" CreationDate="2014-04-27T16:42:44.737" Score="1" Body="&lt;p&gt;The question has a vague term &lt;em&gt;cause&lt;/em&gt; which is confusing people here. &#xA;For me, it means that the event increases the risk of the outcome. &#xA;For some others, it means the event is a definite factor in resulting in the outcome. &#xA;So I avoid answering to the question Yes or No because of different interpretations of the term. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The systemic intravascular thombosis increases the risk of stroke, for example, through the two situations as described in Raoul's answer &lt;a href=&quot;https://biology.stackexchange.com/a/34460/86&quot;&gt;here&lt;/a&gt; but those are not sufficient for the accurate risk score of the stroke risk. &#xA;The factors of stroke risk interact with each other so we cannot leave this question just only about intravascular thombosis and stroke risk, but must consider stroke risk more generally. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;CHA2VASc Score for General Stroke score&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.medscape.org/viewarticle/803859&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Role of the Left Atrial Appendage in AF-Related Strokes&lt;/a&gt;, 2013.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Chads-Vasc score. CHA2 DS2-VASc. &#xA;                        SCORE&#xA;C    CHF or LVEF &amp;lt; 40\%  1&#xA;H    Hypertension        1&#xA;A    Age &amp;gt; 75            2&#xA;D    Diabetes            1&#xA;S    Stroke/TIA/ HF&#xA;    thromboembolism/     2&#xA;V    Vascular disease    1&#xA;A    Age 65-74           1&#xA;S    Sex Category female 1&#xA;                        Max points 9. &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;which specificity and sensitivity are not so high which has resulted in many variations of the initial CHAD VASc score, for example in this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23566635&quot; rel=&quot;nofollow noreferrer&quot;&gt;study&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We studied 94 patients, 66.0% male, mean age 64.4 years (standard&#xA;  deviation 14.2). A cardioembolic source was detected in 20 patients.&#xA;  ROC curve analysis identified as predictors of cardioembolic source&#xA;  CHADS2 score ≥4 (sensitivity of 75.0%, specificity of 66.0%, p=0.014)&#xA;  and CHA2DS2-VASc score ≥5 (sensitivity of 83.3%, specificity of 58.0%,&#xA;  p=0.009).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To improve this score is ongoing research:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;CHADS2 as well as the CHA2DS2VASc risk score can exclude a large proportion of patients from having high risk of stroke or death, &lt;a href=&quot;http://spo.escardio.org/eslides/view.aspx?eevtid=48&amp;amp;fp=131&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Negative predictive value for zero as cut off value for the endpoint Stroke between CHADS2 (solid dots) and CHA2DS2VASc (circles) in Figure 1&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Figure 1: CHADS2 (solid dots) and CHA2DS2VASc (circles). &#xA;&lt;img src=&quot;https://i.stack.imgur.com/mHd6z.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sources of thrombosis&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Atrial fibrillation and Left atrial appendix is the source where thrombus can spread into the great circulation&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://circ.ahajournals.org/content/112/7/1063.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Patent Foramen Ovale and Stroke&lt;/a&gt; where risk factors &lt;em&gt;anatomic variation (PFO size, ASA, eustachian valve anatomy), hemodynamic parameters, presence of venous thrombus identified through higher-sensitivity tests such as lower extremity/abdominal/pelvic MRI, and the presence of hypercoagulable genetic variables&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;BBB's permeability and Stroke risk&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The interaction of the permeability of the brain-blood barrier with the stroke risk is much unknown. &#xA;The following factors interact with the BBB's permeability&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Montelukast (increases)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Cerebral Blood Flow (CBF) and stroke and Stroke Risk&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;CBF interaction with the risk of stroke is unknown field&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Alcohol effects on CBF in subjects with low and high responses to alcohol, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21332525&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;carbonated water increases CBF &lt;/li&gt;&#xA;&lt;li&gt;aging decreases CBF (standard textbook MRI pictures)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Sources&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Stoll, Guido. Molecular mechanisms of thrombus formation in ischemic stroke: novel insights and targets for treatment. 2009. Online &lt;a href=&quot;http://www.bloodjournal.org/content/bloodjournal/112/9/3555.full.pdf?sso-checked=true&quot; rel=&quot;nofollow noreferrer&quot;&gt;available&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Homma, Shunichi, et al. Foramen Ovale and Stroke. 2005. Online &lt;a href=&quot;http://circ.ahajournals.org/content/112/7/1063.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;available&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Citings in the body of this question. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="86" LastEditorUserId="15950" LastEditDate="2019-05-05T20:58:02.023" LastActivityDate="2019-05-05T20:58:02.023" CommentCount="3" CommunityOwnedDate="2014-04-27T16:42:44.737" ContentLicense="CC BY-SA 4.0" />
  <row Id="16934" PostTypeId="2" ParentId="15828" CreationDate="2014-04-27T16:45:25.633" Score="-1" Body="&lt;p&gt;Simple answer: Atrophy through autophagy.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-27T16:45:25.633" CommentCount="1" CommunityOwnedDate="2014-04-27T16:45:25.633" ContentLicense="CC BY-SA 3.0" />
  <row Id="16935" PostTypeId="2" ParentId="15919" CreationDate="2014-04-27T16:46:27.867" Score="-3" Body="&lt;p&gt;No. Based on experience. Lungs are very active organs.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-27T16:46:27.867" CommentCount="0" CommunityOwnedDate="2014-04-27T16:46:27.867" ContentLicense="CC BY-SA 3.0" />
  <row Id="16936" PostTypeId="2" ParentId="16005" CreationDate="2014-04-27T16:49:28.320" Score="0" Body="&lt;p&gt;The absorption is itself not different, but the rate of absorbed substances is different because of greater amounts of proteins in the allergic lymphatic circulation. &#xA;So less capacity stays for circulation of nutrients and so less absorption in time.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-04-27T16:49:28.320" CommentCount="0" CommunityOwnedDate="2014-04-27T16:49:28.320" ContentLicense="CC BY-SA 3.0" />
  <row Id="16937" PostTypeId="2" ParentId="16929" CreationDate="2014-04-27T16:52:05.017" Score="1" Body="&lt;p&gt;Since I can't actually look at and handle the yellow structures, it is difficult for me to provide any information on them. &#xA;&lt;p&gt;&#xA;As far as the white structures you mention on the first picture, I believe those are most likely muscles. &#xA;As for your third question. That does appear to be all one structure; and yes, going on that assumption, the entire structure would be the swim bladder.&lt;/p&gt;&#xA;" OwnerUserId="6289" LastEditorUserId="6289" LastEditDate="2014-04-27T17:12:09.593" LastActivityDate="2014-04-27T17:12:09.593" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16938" PostTypeId="1" CreationDate="2014-04-27T16:54:31.480" Score="0" ViewCount="3330" Body="&lt;p&gt;&lt;strong&gt;Note: Some of the images might be disturbing.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have dissected prawn for the first time. Would like your help in identifying some structures&#xA;.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;This is the dissection of the posterior part of the prawn. What is this blackish structure in the middle ? This structure becomes whitish farther down. Then, it forms a small sac like structure and then becomes thin again. This whole structure appeared just after I cut the exoskeleton. It is directly above the muscles.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/w3YZn.jpg&quot; alt=&quot;enter image description here&quot;&gt; &#xA;&lt;img src=&quot;https://i.stack.imgur.com/6UZ5i.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XrKVj.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/W8D5H.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that this is it's alimentary canal and the black area has digested food in it. The sac like structure might be the rectum.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-04-28T21:14:03.370" Title="Identifying internal structure of dissected prawn" Tags="&lt;zoology&gt;&lt;anatomy&gt;&lt;organs&gt;&lt;dissection&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16939" PostTypeId="1" AcceptedAnswerId="16958" CreationDate="2014-04-27T16:59:57.037" Score="1" ViewCount="117" Body="&lt;p&gt;I am aware of the fact that there are several different types of pneumonia.&#xA;&lt;p&gt;&#xA;However, I am wondering if any of these types of pneumonia are contagious from person to person. &#xA;Is this possible?&lt;/p&gt;&#xA;" OwnerUserId="6289" LastActivityDate="2014-04-28T06:45:49.840" Title="Any forms of pneumonia that can be caught?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16940" PostTypeId="2" ParentId="16924" CreationDate="2014-04-27T17:01:16.130" Score="3" Body="&lt;p&gt;All research on saliva tests I've found involve antibody detection which, as you suspected, can produce false negatives depending on the disease process or the presence of immune disfunction (such as due to AIDS). Thus, if you can isolate &lt;em&gt;T. gondii&lt;/em&gt; gDNA from the saliva, a genetic assay may be more sensitive. However, &lt;a href=&quot;http://europepmc.org/abstract/MED/2135828&quot; rel=&quot;nofollow&quot;&gt;Amato Neto et al.&lt;/a&gt; report:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In 26 patients with AIDS, including six with tomographical evidence suggesting cerebral abscess caused by Toxoplasma gondii, no parasites were found in the saliva by the use of the mouse inoculation model. This trial [suggests] that the search for Toxoplasma gondii in the saliva is not an alternative method for the diagnosis of toxoplasmosis in patients with AIDS. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So perhaps the most difficult aspect of generating a gene based saliva test is actually isolating the parasite from the saliva. I was unable to find other isolation attempts, but my research was very brief.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for which genes to detect, studies involving human blood samples have found that PCR amplification of B1 paralogs provides a sensitive and selective method for detecting &lt;em&gt;T. gondii&lt;/em&gt;. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC267672/&quot; rel=&quot;nofollow&quot;&gt;Burg et al&lt;/a&gt; found that there are about 35 copies of the B1 gene in &lt;em&gt;T. gondii&lt;/em&gt; and also state that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because of its repetitive nature, the B1 gene is an attractive target for detecting T. gondii parasites through amplification of B1-specific DNA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They were able to amplify and detect the gene from crude cell lysate as well as from purified DNA samples containing a 1:10 000 ratio of parasite to leukocyte. Furthermore, they could not detect the gene when assaying other organisms. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC495065/&quot; rel=&quot;nofollow&quot;&gt;Ho-Yen et al.&lt;/a&gt; later attempted PCR amplification of the same genes in human blood from patients with suspected toxoplasmosis and found that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;PCR can be reliably used on human blood samples. For a reference laboratory, this is a valuable addition to its array of diagnostic tests, and provides a more rapid assay than animal culture. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10711675&quot; rel=&quot;nofollow&quot;&gt;Jones et al.&lt;/a&gt; compared detection of the B1 genes with P30 and 18S rRNA genes in aqueous humour. They were able to detect 50 fg of gDNA using the B1 assay, which is equivalent to a single parasite. They concluded that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The B1 PCR protocol appears to be the most sensitive protocol in the detection of T. gondii DNA and has been successful in identification of T. gondii DNA in ocular fluids and retinal sections.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-04-27T17:01:16.130" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16941" PostTypeId="1" CreationDate="2014-04-27T17:03:12.870" Score="1" ViewCount="1273" Body="&lt;p&gt;&lt;strong&gt;Note: This image might be disturbing.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know what the red and the black structures (directly posterior to the red structure) are. I guess it's the heart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WDsUC.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-07-27T07:32:55.830" Title="Identifying structures from anterior end of dissected prawn" Tags="&lt;zoology&gt;&lt;anatomy&gt;&lt;dissection&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16942" PostTypeId="2" ParentId="16759" CreationDate="2014-04-27T17:34:08.763" Score="0" Body="&lt;p&gt;To put it simply... NOT GOOD!!! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&#xA;US Coast Guard rescue swimmers will not do a free fall deployment from above 200 ft (actually, I think it is less, I cannot remember right now) into water, this is too dangerous.&#xA;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I personally think you'd be better off trying to find about fifteen feet of soft snow to land in! In reading trying to find additional information with which to answer this question, I stumbled upon someone who said they knew of a pilot in Vietnam who's 'chute didn't open when he ejected. He survived with &quot;only&quot; broken bones and a ruptured spleen. I have included a link that I hope is helpful!&#xA;&lt;/p&gt;&#xA;&lt;a href=&quot;https://physics.stackexchange.com/questions/9059/jumping-into-water&quot;&gt;https://physics.stackexchange.com/questions/9059/jumping-into-water&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6289" LastEditorUserId="-1" LastEditDate="2017-04-13T12:40:13.457" LastActivityDate="2014-04-27T17:34:08.763" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16946" PostTypeId="2" ParentId="16922" CreationDate="2014-04-27T23:23:38.390" Score="8" Body="&lt;p&gt;A critical step in meiosis is the formation of tetrads. In diploid organisms like donkeys, they have a paternal version and a maternal version of each chromosome. Two chromosomes 2, for instance. During prophase 1, these two &quot;matching&quot; or homologous chromosomes form a tetrad and cross over, swapping alelles. There is no recombination and no tetrad formation in mitosis, which is used for growth and daily living.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How is the meiotic process disrupted?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In a hybrid, there are no matching maternal and paternal chromosomes. In the zebroid testes or ovary, a lonely donkey chromosome 2 is wandering around, looking for another donkey chromosome 2, and &lt;strong&gt;there isn't a homologous chromosome&lt;/strong&gt;. This mucks up Prophase 1, and the first division pulls crazy numbers of chromosomes to each daughter cell, and the gametes from this division are likely full of extra chromosomes and missing some critical ones.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Apparently this difference doesn't obstruct producing (infertile) offspring. How comes the process of recombination of such vastly&#xA;  different number of chromosomes in gametes is viable?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;An embryo needs a solid set of genes to grow up, but chromosomes don't have to be homologous for mitosis, and organisms use &lt;strong&gt;mitosis&lt;/strong&gt; for growth and living, not meiosis. As long as the crazy mis-matched chromosomes in a zebroid have everything needed for a healthy organism, the hybrid will be healthy. It isn't until the zebroid starts to make gametes via meiosis that a problem occurs, as the homologues ONLY form tetrads in making eggs and sperm. The inability to recombine only occurs in the making of gametes.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;54 is an even number. How comes zebroids can't just normally produce&#xA;  fertile offspring with other zebroids of the same number of&#xA;  chromosomes?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Because even chromosome number doesn't help if they are not each homologous with another chromosome.&lt;/p&gt;&#xA;" OwnerUserId="6517" LastActivityDate="2014-04-27T23:23:38.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16947" PostTypeId="2" ParentId="16888" CreationDate="2014-04-27T23:24:36.057" Score="4" Body="&lt;p&gt;Polar amino acids in this case stabilize the helical structure within the apolar milieu of the membrane by making intra- and inter-helical connections. Thus the side chains of polar amino acids turn to one another while apolars face the apolar membrane. This would be definitely supported if you could find alternating apolar - polar segments in the sequence of helices.&lt;/p&gt;&#xA;" OwnerUserId="6518" LastActivityDate="2014-04-27T23:24:36.057" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16949" PostTypeId="1" AcceptedAnswerId="16951" CreationDate="2014-04-28T02:15:34.303" Score="3" ViewCount="41" Body="&lt;p&gt;I'm trying to learn more about polarized epithelial cells of the gut. I am familiar with classic brush border transporters localized to the apical memebrane to facilitate nutrient absorption. I am wondering though, where are ion channels located? I would guess basolaterally since they would be exposed to the extracellular space. I would appreciate a primary reference showing the location of voltage-gated channels in particular as I could not find them myself.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-04-28T03:31:59.260" Title="Polarized epithelium and localization of ion channels" Tags="&lt;physiology&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16950" PostTypeId="2" ParentId="16890" CreationDate="2014-04-28T02:24:33.397" Score="5" Body="&lt;p&gt;Probably the best source to start would be Ilkka Hanksi's work, you can find a full list here: &lt;a href=&quot;http://www.helsinki.fi/science/metapop/People/IlkkaPub2.htm&quot; rel=&quot;noreferrer&quot;&gt;http://www.helsinki.fi/science/metapop/People/IlkkaPub2.htm&lt;/a&gt;.  The seminal work would be &quot;Ecology, Genetics and Evolution of Metapopulations&quot;  It gives a strong mathematical treatment&lt;/p&gt;&#xA;" OwnerUserId="1097" LastActivityDate="2014-04-28T02:24:33.397" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16951" PostTypeId="2" ParentId="16949" CreationDate="2014-04-28T03:31:59.260" Score="3" Body="&lt;p&gt;Well, that's a first for me. I wouldn't have guessed gut cells would have voltage-gated channels.&#xA;This article describes voltage-gated sodium channels on both the luminal and basolateral membranes: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Barshack, I., Levite, M., Lang, A., Fudim, E., Picard, O., Ben Horin, S., &amp;amp; Chowers, Y. (2008). Functional voltage-gated sodium channels are expressed in human intestinal epithelial cells. Digestion, 77(2), 108-117.&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18391489&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/18391489&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6517" LastActivityDate="2014-04-28T03:31:59.260" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16952" PostTypeId="1" AcceptedAnswerId="16955" CreationDate="2014-04-28T05:06:02.620" Score="2" ViewCount="155" Body="&lt;p&gt;Do stem cells have an apoptosis mechanism and , if they do could this be used to repair the  cell self-destruction pathways in a cancer cell?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastActivityDate="2018-09-08T14:20:28.913" Title="About stem cells and Cancer" Tags="&lt;cancer&gt;&lt;apoptosis&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16953" PostTypeId="1" AcceptedAnswerId="16960" CreationDate="2014-04-28T05:30:51.290" Score="4" ViewCount="1234" Body="&lt;p&gt;How are two species with similar phenotypes identified as different? Have two different individuals  that were thought to be different species ever been determined  to be from the same species ( or one a subspecies of the other's species ) ?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastEditorUserId="107" LastEditDate="2014-04-28T13:24:52.193" LastActivityDate="2014-04-28T14:55:51.183" Title="How are two species with similar phenotypes identified as different?" Tags="&lt;evolution&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16954" PostTypeId="2" ParentId="16953" CreationDate="2014-04-28T05:55:50.550" Score="1" Body="&lt;p&gt;Genotypes are used to differentiate when phenotypes are identical. In Bacteria the 16S rRNA sequence is particularly useful in helping to identify which population is present in what percentage. In fungal its ITS and in mammals its 18S. &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-04-28T05:55:50.550" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="16955" PostTypeId="2" ParentId="16952" CreationDate="2014-04-28T06:02:58.110" Score="2" Body="&lt;p&gt;No but they can be used as part of a gene therapy to induce cellular death in cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/gt/journal/v21/n3/full/gt201388a.html&quot; rel=&quot;nofollow&quot;&gt;TRAIL-secreting mesenchymal stem cells promote apoptosis in heat-shock-treated liver cancer cells and inhibit tumor growth in nude mice&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Liver cancer is one of the top six leading causes of cancer-related death. Radiofrequency ablation (RFA) is an important means of treating liver cancer. Residual cancer after RFA is the most frequent cause of recurrence in cases of liver cancer. The main difference between residual cancer cells and ordinary liver cancer cells is that residual cancer cells experience heat shock. The secretable form of trimeric human tumor necrosis factor-related apoptosis-inducing ligand (stTRAIL) induces apoptosis in a variety of human cancers but not in normal tissues. It has shown potent cancer-selective killing activity and has drawn considerable attention as a possible cancer therapy. In the present work, the therapeutic potential of this stTRAIL-based gene therapy was evaluated in hepatocellular carcinoma subjected to RFA. Rat bone marrow mesenchymal stem cells (BM-MSCs) were isolated and transduced with a lentiviral vector encoding stTRAIL (stTRAIL-MSCs, T-MSCs). Cells treated with heat treatment at 43 °C for 45 min served as simulated residual cancer cells. After treatment with T-MSCs, apoptosis in heat-shock-treated liver cancer cells increased significantly, and caspase-3 was upregulated. When T-MSCs were subcutaneously injected into nude mice, they localized to the tumors and inhibited tumor growth, significantly increasing survival. Collectively, the results of the present study indicate that BM-MSC can provide a steady source of stTRAIL and may be suitable for use in the prevention of the recurrence of hepatocellular carcinoma after RFA with secretable trimeric TRAIL.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2014-04-28T15:19:51.930" LastActivityDate="2014-04-28T15:19:51.930" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16957" PostTypeId="2" ParentId="16941" CreationDate="2014-04-28T06:21:59.937" Score="1" Body="&lt;p&gt;I guess you got your antero-posterior axis wrong. If I am correct then anterior is right and posterior is left in your image. In that case the black structure should be the cerebral ganglion and the red should be the heart. See the image below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Up93p.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-04-28T06:21:59.937" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="16958" PostTypeId="2" ParentId="16939" CreationDate="2014-04-28T06:45:49.840" Score="3" Body="&lt;p&gt;Pneumonia means inflammation of lungs- especially alveoli. &#xA;There can be many causes of it including infectious agents, autoimmune condition and  chemical irritants. Pneumonitis is a more accurate word for lung inflammation, the causes of which includes the abovementioned agents; Pneumonia in common usage refers to the condition due to infectious agents such as bacteria, viruses and fungi.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In almost all the cases the infectious agents are airborne in the form of aerosols (spread by cough) and infect the respiratory tract directly. Some cases of fungal pneumonia (&lt;em&gt;Pneumocystis, Penicillium&lt;/em&gt;) are observed more commonly in immunocompromised individuals, such as AIDS patients, and dissemination happens via spores. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can intuitively figure out the infectivity is different for different pathogens. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-04-28T06:45:49.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16959" PostTypeId="2" ParentId="16919" CreationDate="2014-04-28T07:07:03.310" Score="8" Body="&lt;p&gt;Being HIV+ and having AIDS are slightly different terminologies:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the virus is detectable in an individual by existing medical techniques he/she is called HIV+. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A HIV+ person is said to have progressed to AIDS only when the CD4+ T-lymphocyte count drops below 200 cells per ml of blood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cornelius has nicely summarized the infection routes so I wont touch on that. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Also is it true that immune systems of some rare people in this world&#xA;  can fight with this disease.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes. In some people the progression from HIV+ to AIDS is very slow and they practically lead a normal life. Such individuals are called long term non progressors (&lt;a href=&quot;http://en.wikipedia.org/wiki/Long-term_nonprogressors&quot; rel=&quot;nofollow&quot;&gt;LTNP&lt;/a&gt;). Some genetic reasons for having an LTNP phenotype is summarized in the link, however, this topic is still under active research. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some individuals just don't acquire HIV. This is because they lack the CCR5 chemokine receptor which is essential for HIV entry into the cells. Deleting this receptor is also being considered to cure AIDS via a stem cell therapy. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-07-22T05:27:15.680" LastActivityDate="2014-07-22T05:27:15.680" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16960" PostTypeId="2" ParentId="16953" CreationDate="2014-04-28T08:21:44.447" Score="8" Body="&lt;p&gt;&lt;strong&gt;Species are difficult to define.&lt;/strong&gt; This is because they form over a gradual continuous spectrum via evolution, one species does not suddenly become two, but lineages diverge (perhaps because there is some kind of barrier - like a mountain range - in the way) eventually reaching a point where we class them as separate species. How we define species is debated but the most generally accepted definition is the &lt;strong&gt;Biological Species Concept&lt;/strong&gt; (BSC). Roughly the BSC defines a species as &quot;a group of individuals that do, or could, successfully breed.&quot; &lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/VA2OtherSpeciesConcept.shtml&quot; rel=&quot;nofollow&quot;&gt;Other species concepts&lt;/a&gt; do exist, some have their merits, but the BSC is most widely accepted and normally taken with a pinch of salt - it's not always possible to perfectly define a species because evolution and speciation are ongoing processes. Therefore, according to the BSC, &lt;strong&gt;two groups can be called different species even if the individuals look identical&lt;/strong&gt; as long as there is true reproductive isolation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reproductive isolation can occur because of physical barriers such as rivers, oceans, mountains, environmental change. This is the cause of &lt;a href=&quot;http://en.wikipedia.org/wiki/Allopatric_speciation&quot; rel=&quot;nofollow&quot;&gt;allopatric speciation.&lt;/a&gt; One species could become split when a subpopulation forms on an island (e.g. if humans take them to an island). If enough time passes without migration they will become reproductively incompatible. Another mechanism is &lt;a href=&quot;http://en.wikipedia.org/wiki/Sympatric_speciation&quot; rel=&quot;nofollow&quot;&gt;sympatric speciation&lt;/a&gt;, when two species form without geographic isolation. This could be by the evolution of new behavioural, morphological or physiological forms which create division within the initial meta-population in to distinct sub-populations which over time become more reproductively isolated. Traits related to reproduction are amongst the fastest evolving and can quickly reinforce speciation (e.g. sperm morphology is extremely varied between species, see &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/B003GGST30&quot; rel=&quot;nofollow&quot;&gt;Sperm Biology: An evolutionary perspective&lt;/a&gt;, chapter 3).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The higher up the &lt;a href=&quot;http://en.wikipedia.org/wiki/File%3aBiological_classification_L_Pengo_vflip.svg&quot; rel=&quot;nofollow&quot;&gt;tree of biological classification&lt;/a&gt; you go the easier it becomes to classify things in to distinct groups, e.g. An oak tree is clearly a plant, and a whale is clearly and animal; further towards species definitions a whale is a mammal and a sparrow is a bird and both are animals; and perhaps less clearly, carrion crows and hooded crows are two different bird species in the &lt;em&gt;Corvus&lt;/em&gt; genus. (Formerly these two were considered the same species!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously problems begin to occur when we consider species that reproduce through means other than sexual reproduction - e.g. bacteria which clonally reproduce. Traditionally this has been done by phenotypic information. We are now in the genomics era which opens new possibilities. &lt;a href=&quot;http://www.biomedcentral.com/1471-2180/12/302&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; discusses modern techniques by which utilise genetic similarity &amp;amp; difference between cells to define species and they suggest it to be a good method. However, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764935/&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; seems to suggest that genomic methods need some refining first before we start classifying species with them.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Currently, it appears more pragmatic and efficient to preserve the current species definition than to replace it, because it is serviceable as a first level of screening and current phylogenetic knowledge is too limited for a universal and sound change in the definition.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As for whether two species have been reclassified in to one I know there are examples but Google is not throwing up anything and there's nothing I can remember off of the top of my head - if I remember correctly the male and female mallard were once considered separate species because they look so different but I can't find anything to back this up. Species formerly described as one have been split in to two as well - &lt;a href=&quot;http://www.endangeredspeciesinternational.org/gorillas.html&quot; rel=&quot;nofollow&quot;&gt;gorilla's are one such example.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-04-28T14:55:51.183" LastActivityDate="2014-04-28T14:55:51.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16961" PostTypeId="1" CreationDate="2014-04-28T12:27:04.640" Score="1" ViewCount="264" Body="&lt;p&gt;I am looking for PDB file for Osteopontin (SPP1). The entry- &lt;a href=&quot;http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3CXD&quot; rel=&quot;nofollow&quot;&gt;3CXD&lt;/a&gt; shows the structure of an Osteopontin antibody, not of the protein itself. &#xA;Thanks&lt;/p&gt;&#xA;" OwnerUserId="6523" LastEditorUserId="3340" LastEditDate="2014-04-28T13:57:32.143" LastActivityDate="2014-05-06T06:35:32.463" Title="PDB file for Osteopontin (SPP1)" Tags="&lt;pdb&gt;&lt;3d-structure&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16962" PostTypeId="1" CreationDate="2014-04-28T12:30:51.590" Score="6" ViewCount="1589" Body="&lt;p&gt;I know that animals can't make poly-unsaturated fatty acids (PUFA) and so require them from dietary sources. For eg.Omega -3 and Omega 6 fatty acids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions : Can animals synthesize other unsaturated fatty acids from scratch? If not, does the unsaturated fatty acids in the phospholipids of plasma membrane of animals come only from dietary sources? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="948" LastEditDate="2014-04-29T02:56:51.830" LastActivityDate="2018-03-18T23:59:48.340" Title="Can animals make their own unsaturated fatty acids?" Tags="&lt;metabolism&gt;&lt;lipids&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16963" PostTypeId="2" ParentId="16961" CreationDate="2014-04-28T12:45:33.197" Score="4" Body="&lt;p&gt;There doesn't seem to be a 3D structure of Osteopontin available, and after looking a bit at the literature about this protein I'm not really surprised.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Osteopontin is hypothesized to assume an elongated and flexible structure (&lt;a href=&quot;http://cro.sagepub.com/content/11/3/279.long&quot; rel=&quot;nofollow&quot;&gt;Sodek et al., 2000&lt;/a&gt;). Flexible proteins are very hard to impossible to crystallize, typically the flexible parts are either removed or stabilized in some way. I'm not a crystallographer, but this protein doesn't look like it can be crystallized in the full form.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For NMR it is a bit on the large side, a full structure would likely be not feasible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also has extensive posttranslational modifications, which makes it much harder to produce in large amounts as needed for crystallography, and extremely expensive for NMR where you would have to isotope-label the protein as well.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-04-28T12:45:33.197" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16964" PostTypeId="2" ParentId="16962" CreationDate="2014-04-28T13:35:17.083" Score="7" Body="&lt;p&gt;Yes, animals can make their own unsaturated fatty acids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mammalian fatty acyl desaturases can introduce double bonds at the &amp;Delta;5, &amp;Delta;6 and &amp;Delta;9 positions (i.e. numbering from the functional group). As shown in the diagram below, this means that we cannot introduce double bonds at the &amp;omega;3 or &amp;omega;6 positions (i.e. numbering from the methyl end of the molecule) in fatty acids of a reasonable length (see any Biochemistry textbook for confirmation). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've illustrated the impossibility of us making &amp;alpha;-linolenic acid as an example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iioZv.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-04-28T13:35:17.083" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16965" PostTypeId="2" ParentId="16962" CreationDate="2014-04-28T13:41:10.077" Score="1" Body="&lt;p&gt;Only linoleic acid ($\omega 6$) and $\alpha$-linolenic acid ($\omega 3$) are essential. Other PUFAs are synthesized from these by desaturases (as Alan Boyd pointed out). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't come across any study that reports de-novo synthesis of $\alpha$-linolenic acid in animals. However, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0965174813001495&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; study reports that mites can synthesize linoleic acid. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-04-28T13:41:10.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16966" PostTypeId="1" AcceptedAnswerId="20556" CreationDate="2014-04-28T15:41:17.747" Score="3" ViewCount="202" Body="&lt;p&gt;I've recently heard a podcast which explained teenage impulsivity and novelty seeking in part by &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;Lowering the baseline dopamine activity in the reward system&quot;&lt;/li&gt;&#xA;&lt;li&gt;&quot;Increase in dopaminergic reward in response to novelty&quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I assume that by reward system the author means &lt;a href=&quot;http://en.wikipedia.org/wiki/Mesolimbic_pathway&quot; rel=&quot;nofollow noreferrer&quot;&gt;mesolimbic&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Mesocortical_pathway&quot; rel=&quot;nofollow noreferrer&quot;&gt;mesocortical&lt;/a&gt; dompaminergic pathways in the brain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.theatlantic.com/health/archive/2014/01/dopamine-and-teenage-logic/282895/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here's an article that seems to state similar findings&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Starting in early adolescence and peaking midway through, this&#xA;  enhanced dopamine release causes adolescents to gravitate toward&#xA;  thrilling experiences and exhilarating sensations. Research even&#xA;  suggests that the &lt;strong&gt;baseline level of dopamine is lower—but its release&#xA;  in response to experience is higher&lt;/strong&gt;—which can explain why teens may&#xA;  report a feeling of being “bored” unless they are engaging in some&#xA;  stimulating and novel activities.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The dopamine system here is being compared to the child's dopamine system. I'm interested in &lt;strong&gt;what happens to the dopaminergic system once a teenager/adolescent becomes an adult at around the age of 24-25?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking for insight along these lines - does the reward system of an adult &quot;settle down&quot; and no longer respond to novelty as strongly? Is the baseline dopamine level higher?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="32436" LastEditDate="2017-06-04T08:20:08.557" LastActivityDate="2017-06-04T08:20:08.557" Title="What happens to human dopaminergic reward system once a teenager becomes adult?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;development&gt;&lt;behaviour&gt;&lt;dopamine&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16967" PostTypeId="1" CreationDate="2014-04-28T16:18:20.533" Score="1" ViewCount="378" Body="&lt;p&gt;Since DNA footprinting is an old method I thought there may be some more recent and effective methods to identify a DNA sequence, do you know any of them?&lt;/p&gt;&#xA;" OwnerUserId="1843" LastActivityDate="2014-04-30T15:24:47.263" Title="Modern alternatives of DNA footprinting" Tags="&lt;molecular-biology&gt;&lt;biotechnology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16968" PostTypeId="1" CreationDate="2014-04-28T16:32:27.063" Score="3" ViewCount="4477" Body="&lt;p&gt;I have a few questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;What is an OD value?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Why do we use blank solution in Lowry's protein estimation method?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If The OD of a protein is 0.01, what does it mean?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="6524" LastEditorUserId="1320" LastEditDate="2014-04-28T18:14:49.090" LastActivityDate="2014-04-28T18:18:43.843" Title="What is optical density in Lowry's protein estimation method?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16969" PostTypeId="2" ParentId="16968" CreationDate="2014-04-28T16:38:38.947" Score="4" Body="&lt;ol&gt;&#xA;&lt;li&gt;The OD measurement is the output of what the photometer measures. It is actually the amount of light which is scattered or absorbed by your sample - scientifically called extinction.&lt;/li&gt;&#xA;&lt;li&gt;A blank is used to be able to substract the influence of reagents, light that is scattered on the surfaces of the cuvette (which is probably also not completely clean) and so on. Every of this influences reduces the amount of light which should reach the detector on the other side of the probe and give you false extinction readings. If you are using a colored detection sample (which colors deeper or looses color during the reaction) this is more obvious. The solution already has an extinction on its own which is not of interest. So you make a blank (which basically substracts all these influences from you sample reading) to correct for this. How this is done depends on the photometer. Some make a correction reading at the beginning, while others use a second cuvette (a blank cuvette) which is permanently measured.&lt;/li&gt;&#xA;&lt;li&gt;It means that the protein gives you this extinction. Without a calibration curve (made from serial dilutions with known protein concentrations) it is impossible to make any further comment on this number.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2014-04-28T18:18:43.843" LastActivityDate="2014-04-28T18:18:43.843" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16971" PostTypeId="2" ParentId="16910" CreationDate="2014-04-28T18:34:05.710" Score="8" Body="&lt;p&gt;There are many different variants of O (all loss-of-function) indicating that this mutation has arisen many times in the human population. The prevalence of O is indeed taken as evidence of balancing selection. Various pathogens use the A or B antigens as receptors. The cited paper presents evidence about the phylogeny of the ABO gene in human populations and reports that there is clear evidence of balancing selection.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;We propose several hypotheses for the cause of [balancing selection], which most likely involved interactions with multiple pathogens at different geographic regions and timescales.&lt;/p&gt;&#xA;&lt;p&gt;Calafell et al (2008) &lt;a href=&quot;http://www.saitou-naruya-laboratory.org/assets/files/pdf/Calafell_HG08.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evolutionary dynamics of the human ABO gene.&lt;/a&gt; Human Genetics 124: 123-135&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-04-28T23:54:45.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16972" PostTypeId="1" AcceptedAnswerId="17004" CreationDate="2014-04-28T19:08:24.887" Score="7" ViewCount="572" Body="&lt;p&gt;A friend told me, during a 3 minute discussion, that viruses that are endemic in host $A$ and make repeated jumps to host $B$ but can't be transmitted between individuals of species $B$, may slowly adapt (through these repeated jumps) to be able to be transmitted between individuals of host $B$ and become epidemic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know much about epidemiology. I don't understand how a virus population that is endemic to host $A$ may adapt to host $B$ with repeated jumps while the viruses that jump to host $B$ are dead end because they cannot be transmitted further more. Or Are these viruses able to jump back to host $A$ to bring back their newly acquired adaptations to host $B$?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I might misunderstand the meaning of &quot;repeated host jumps transmission&quot;. I first thought it meant repeated jumps from a reservoir population in host $A$ to host $B$, but it is also possible that it describes the dynamic of a virus population that is adapted to jump from species to species and they actually gain this ability by keeping jumping and jumping. But then, how could a virus species get adapted to jump from species to species? I'm a bit confused…. Can you give me some hints about this process of cross-species transmission through repeated jumps?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-04-30T15:12:25.687" LastActivityDate="2014-04-30T15:12:25.687" Title="Viruses: Adaptation to a new host through repeated host jumps" Tags="&lt;evolution&gt;&lt;virology&gt;&lt;virus&gt;&lt;medicine&gt;&lt;epidemiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16973" PostTypeId="1" CreationDate="2014-04-28T20:58:49.963" Score="1" ViewCount="416" Body="&lt;p&gt;Has anyone theorized how evolution would be affected by a different length of solar day, what were the conclusions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thought came from thinking about life on other planets/moons, but I'm initially thinking about it from the frame of &quot;How would life on earth and humans specifically have evolved (or if they would have) if a day were 12 hours or 48 hours?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I imagine the actual effects on evolution and lifestyle would be extensive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: this question &lt;a href=&quot;https://biology.stackexchange.com/questions/16642/how-would-the-human-body-adjust-to-sleep-times-if-we-were-to-live-in-a-place-wit&quot;&gt;How would the human body adjust to sleep times if we were to live in a place with different day lengths?&lt;/a&gt; is slightly related, but just to clarify I'm intersted in effect on evolution, not adaptation if an indivdual moved between planets.&lt;/p&gt;&#xA;" OwnerUserId="4884" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-08-11T19:20:07.853" Title="How would a different solar day affect evolution?" Tags="&lt;evolution&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="16975" PostTypeId="2" ParentId="16938" CreationDate="2014-04-28T21:14:03.370" Score="2" Body="&lt;p&gt;It is, indeed, the alimentary canal. It is actually this canal that it's important for one to remove when &quot;de-veining&quot; shrimp, rather than the vein itself, which lies immediately dorsal to the digestive tract.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;In the future, I might suggest doing a little more research prior to asking the stack exchange, as frequent users of the site do like to see evidence of effort on the part of the user to find their own answers. A quick search for &quot;alimentary canal prawn&quot; or &quot;arthropod anatomy&quot; would likely have turned up your answer.&lt;/p&gt;&#xA;" OwnerUserId="6371" LastActivityDate="2014-04-28T21:14:03.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16980" PostTypeId="2" ParentId="16972" CreationDate="2014-04-29T07:04:34.960" Score="2" Body="&lt;p&gt;A quick answer for now (I'll add details as I find):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The infection of &lt;strong&gt;B&lt;/strong&gt; from &lt;strong&gt;A&lt;/strong&gt; would be zoonosis. This transfer may not have followed a classical route of infection. For example the case of hantavirus pulmonary syndrome (HPS), the zoonosis occurs throuch the rodent (primary host) droppings. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other example is that of avian influenza- the zoonosis doesn't happen via the respiratory route but by contact with body fluids of infected birds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also dead end can be achieved in the case of vector borne diseases especially those of Arboviruses. There is no mechanism of spread other than through a vector. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other cases the virus may not be produced in high titres in the secondary host to cause infections, but enough to cause mild symptoms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is interesting to know how the pathogen can propagate in &lt;strong&gt;B&lt;/strong&gt; but cannot infect: I dont have a definitive answer for this. If a receptor/viral adsorption site is similar between the two hosts but interaction with virus is much stronger in &lt;strong&gt;A&lt;/strong&gt;, then &lt;strong&gt;B&lt;/strong&gt; cannot be infected unless there are loads of virions. However once adsorbed, they can propagate within the cell and go from cell to cell with a relative ease, may be by using a different mechanism. For e.g. , in case of plants the viruses can go through plasmodesmata. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Back jump should be possible unless the pathogen has mutated to fit the new host. In such cases a enzootic infection might happen and &lt;strong&gt;A&lt;/strong&gt; will be dead end. For e.g. in influenza.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/275/1643/1611.full&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; article says that dead-end host (dragonfly) behavior can be manipulated by a certain parasite (&lt;em&gt;Acanthocephalus lucii&lt;/em&gt;) to increase transmission probability to original host (perch).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: influenza is a very unique case as you might be aware of the genetic drifts/shifts that make it highly adaptable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Refer &lt;a href=&quot;http://www.nature.com/nature/journal/v430/n6996/full/nature02759.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article for some details, It has a section on dead-end transmissions.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-04-29T07:24:53.723" LastActivityDate="2014-04-29T07:24:53.723" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16981" PostTypeId="1" AcceptedAnswerId="20156" CreationDate="2014-04-29T07:32:40.933" Score="1" ViewCount="55" Body="&lt;p&gt;Are cancer cells destabilized if near a strong electromagnetic field over a long period of time? I read this technique of using radio-frequency ablation and heat shock to kill cancer cells. I don't know if this is viable but maybe a person could wear a device like a pacemaker right over the area of a tumor that emits  strong E.M. pulses over say a month or a year. Could this destabilize the tumor ?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastEditorUserId="1320" LastEditDate="2014-08-02T07:55:27.970" LastActivityDate="2014-08-02T07:55:27.970" Title="Regarding cancer cells and radio-frequency ablation" Tags="&lt;cancer&gt;&lt;homeostasis&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="16982" PostTypeId="1" CreationDate="2014-04-29T07:56:36.463" Score="0" ViewCount="306" Body="&lt;p&gt;I'm in my last year of high school and doing a research assignment on thermoregulation. In the excellence level exemplar for the standard, a student made the statement: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Once the body's internal temperature is well above the optimum range, important enzymes start to denature, phospholipids start to destabilise, and cell membrane lipids begin to dissolve. As a result of this, important organs in the trunk of the body are unable to carry out important metabolic processes. If the temperature continues to rise it causes tissue damage which could cause disability depending on its severity. It also causes the hypothalamic thermostat to break down, meaning the body can no longer have control of the core temperature.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, I have been unable to find any sources which mention destabilisation of phospholipids or the dissolving of membrane lipids. I have also not found anything on tissue damage or the cessation of the hypothalamic thermostat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these things true? And if so, could someone please direct me to a reliable source which states this?&lt;/p&gt;&#xA;" OwnerUserId="6529" LastEditorUserId="948" LastEditDate="2014-04-29T15:31:53.777" LastActivityDate="2015-01-14T08:32:28.800" Title="Hypothalamic breakdown and effect of temperature on membrane lipids" Tags="&lt;homework&gt;&lt;homeostasis&gt;&lt;hypothalamus&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16983" PostTypeId="2" ParentId="16557" CreationDate="2014-04-29T08:10:02.380" Score="7" Body="&lt;p&gt;There's a 2003 paper published in the Journal of Korean Medical Science describing a case of a 'homunculus' within a teratoma: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055135/&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055135/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It contained some hair, brain tissues, cranial and other bones, but no internal organs.&lt;/p&gt;&#xA;" OwnerUserId="6530" LastActivityDate="2014-04-29T08:10:02.380" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16984" PostTypeId="2" ParentId="1573" CreationDate="2014-04-29T08:11:40.027" Score="7" Body="&lt;p&gt;There are different causes and mechanisms behind runny and stuffy nose.&#xA;I cover them separately below.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Runny nose&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;My professor of pathoanatomy and pathophysiology says that the correct answer here is &lt;strong&gt;serous inflammation&lt;/strong&gt; to the runny nose.&#xA;Serous inflammation&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Marked exudation by relatively thin fluid&lt;/li&gt;&#xA;&lt;li&gt;Cold is caused by Acute respiratory viral infections &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Acute viral respiratory infection&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Exudate is very watery and clear - &lt;em&gt;serous inflammation&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;li&gt;At 3rd day, whitish mucose excretion - &lt;em&gt;catarrhal inflammation&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;li&gt;At 5th day, greenish colour - a lot of neutrophils and mucose. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The other answers mostly discusses about the mechanisms (secondary), but not the cause itself. &#xA;The most upvoted answer describes factors affecting the inflammation but not explicitly mention serous inflammation and its factors.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Stuffy nose&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Congestion in nose is a passive and local process resulting from reduced outflow of blood from a nasal tissue.&#xA;The nasal epithelium is very thin which makes it vulnerable to flu and cold.&#xA;The viral particle passes through the membrane (often because of scarring) and causes the change in the vascular permeability of the surrounding big vein.&#xA;Mechanisms of stuffy nose are covered partially by Ram and Aleadam:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;local edema &lt;/li&gt;&#xA;&lt;li&gt;because of changed vascular permeability of large veins surrounding the nose&lt;/li&gt;&#xA;&lt;li&gt;bradykinin&lt;/li&gt;&#xA;&lt;li&gt;histamine (cetiritzin)&lt;/li&gt;&#xA;&lt;li&gt;counteracted by epinephrine&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which respond against viral particles and cause&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;atrophy &lt;/li&gt;&#xA;&lt;li&gt;dryness of nose.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Stuffy nose is about the reduced outflow of blood from a nasal tissue i.e. &lt;strong&gt;isolated venous obstruction&lt;/strong&gt;.&#xA;Even small obstruction (scarring) can lead to it. &#xA;I know no safe systemic medication that can prevent the change of vascular permeability of the nasal big vein.&#xA;Local steroids like Nasonex improve the recovery time by reducing the congestion when taken during long term - however, it cannot prevent the vascular permeability change of the large vein.&#xA;I have an intuition that the the nasal venous congestion can be relieved by the &lt;strong&gt;systemic lymphatic drainage massage&lt;/strong&gt; by special movements involving&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;abdomen (attention to deep breathing with abdomen and exhale too)&lt;/li&gt;&#xA;&lt;li&gt;supraclaviculus&lt;/li&gt;&#xA;&lt;li&gt;under medial occipitalis&lt;/li&gt;&#xA;&lt;li&gt;under auricles&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which help to drain the accumulated fluid from the nasal tissues.&#xA;I know no substitute or medication to replace the stimulation of lymphatic drainage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Prophylactics for the symptoms&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can oil your membranes but to oil them all even at the back side is difficult - even more difficult if have to have them oiled continuously.&#xA;So there remains some membranes unoiled.&#xA;I think it takes rather much time for the venous side to recover.&#xA;Therefore, you feel stuffy nose long time after the runny nose has ended.&#xA;Local oiling is not enough during cold and allergic times for many patients.&#xA;Some medicines for Prophylactics&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Xylometazoline (Olynth) - cause atrophy and dryness, but good for stuffy nose &lt;/li&gt;&#xA;&lt;li&gt;Quixx - sea water&lt;/li&gt;&#xA;&lt;li&gt;Eucalyptus and vitamin E (Coldises spray for instance)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2016-06-28T11:52:57.890" LastActivityDate="2016-06-28T11:52:57.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16985" PostTypeId="1" CreationDate="2014-04-29T08:29:55.023" Score="0" ViewCount="272" Body="&lt;p&gt;I describe &lt;a href=&quot;https://biology.stackexchange.com/a/16984/86&quot;&gt;here&lt;/a&gt; the serous inflammation of runny nose.&#xA;Cough is mediated by Cough center.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think Runny nose is also controlled by the autonomic nervous system and probably by some reflex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume you have mild runny nose under Montelukast medication.&#xA;You have &lt;strong&gt;irritated cough&lt;/strong&gt; (coughing so much you cannot sleep).&#xA;You stop the cough by codeine before sleeping.&#xA;You sleep at 30 degree angle.&#xA;Sometimes, you also feel that the runny nose stops i.e. &lt;strong&gt;complete relieve of runny nose in both nostrils and whole nose&lt;/strong&gt; for about 30 seconds to a minute - perfectly clear nose and no serous inflammation - no symptoms of imflammation in the nose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, it (serous inflammation) starts again - not like mucose running back - but the feeling of uneasiness in the whole nose starts again - then mucose can also continue to migrate from one nostril to another.&#xA;&lt;strong&gt;What is causing this kind of behaviour i.e complete relieve of of runny nose for about 30 seconds?&lt;/strong&gt;&#xA;&lt;strong&gt;What is causing the stopping of serous inflammation in the nose?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the Runny nose can also be controlled by medulla oblongata because Codeine is blocking the cough center there. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried to achieve this behaviour by stimulating by lymphatic system in regulating breathing by abdominal muscles - lymphatic drainage massage - breathing inside with abdomen (not with thorax) and deeply exhale with abdomen).&#xA;At that time, I did not hear any creaky sounds in my throat.&#xA;After trying to stop the serous inflammation again, I heard them without managing to stop serous inflammation in both nostrils at the same time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How is the control of Cough and Runny nose regulated by the autonomic nervous system?&lt;/strong&gt;&#xA;Probably, some parallelism there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Processes going on regulating Cough and Runny nose&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;reflex from medulla oblongata&lt;/li&gt;&#xA;&lt;li&gt;sympaticus and parasympaticus (not sure about these)&lt;/li&gt;&#xA;&lt;li&gt;possible parallelism of irritated cough and runny nose control&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-12-26T09:23:56.813" Title="Parallel Autonomic regulation of Cough and Runny Nose" Tags="&lt;pathophysiology&gt;&lt;autonomic-nervous-system&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16986" PostTypeId="1" AcceptedAnswerId="16991" CreationDate="2014-04-29T08:53:42.737" Score="1" ViewCount="86" Body="&lt;p&gt;Where can I compare the C-peptide sequence of guinea pig with human or mouse?&#xA;I am also interested in finding whether the guinea pig has insulin 1 and 2 to know whether I could use an anti-C-peptide 1 and 2?&lt;/p&gt;&#xA;" OwnerUserId="126" LastActivityDate="2014-04-29T13:50:43.043" Title="conservation of C-peptide sequence in the guinea pig" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="16987" PostTypeId="1" AcceptedAnswerId="16989" CreationDate="2014-04-29T10:20:22.350" Score="8" ViewCount="2613" Body="&lt;p&gt;How does the ebola virus attack and how do some people get away with it? Normally any virus would attack a cell with some kind of receptors and some kind of lock and key mechanism entering the cell and then multiplying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens to the virus if a person manages to live through it, does the virus die and is thrown out or still remains inside the host?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure about a normal virus attack i tried to explain please correct on that also.&lt;/p&gt;&#xA;" OwnerUserId="5008" LastEditorUserId="2949" LastEditDate="2014-10-24T18:14:12.707" LastActivityDate="2015-10-22T07:11:09.067" Title="How does the ebola virus attack?" Tags="&lt;virus&gt;&lt;ebola&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16988" PostTypeId="2" ParentId="16813" CreationDate="2014-04-29T11:19:49.780" Score="1" Body="&lt;p&gt;The oldest evidence we have of sex comes from the fossil record which shows it was present more than &lt;a href=&quot;http://paleobiol.geoscienceworld.org/content/26/3/386.abstract&quot; rel=&quot;nofollow&quot;&gt;one billion years ago&lt;/a&gt; - it could be even longer (it would be naive to think we have found all fossils or that all organisms that ever existed became fossilized). Sexual reproduction introduces potential benefits because it allows recombination meaning useful gene combinations are created more regularly and deleterious mutations are lost more efficiently (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Muller%27s_ratchet&quot; rel=&quot;nofollow&quot;&gt;Muller's Ratchet&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is thought that sexual reproduction &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/037570261X&quot; rel=&quot;nofollow&quot;&gt;first occurred in single celled eukaryotes&lt;/a&gt;. In bacteria it has been shown that stress can induce the process of &lt;a href=&quot;http://en.wikipedia.org/wiki/Transformation_%28genetics%29&quot; rel=&quot;nofollow&quot;&gt;transformation&lt;/a&gt;. Transformation is a sex-like process in bacteria where one bacterial cell takes DNA from a donor bacterial cell and incorporates it in to it's own cell, it could help to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203263/&quot; rel=&quot;nofollow&quot;&gt;repair DNA damage&lt;/a&gt; caused by stress. Transformation could represent one early form of sex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is difficult to put a timeline on it because it can only be seen from fossil data. But from early primitive haploid organisms we would need the evolution of diploidy, some sex-determining mechanisms, anisogamy, and reproductive physiology for basic recognisable sexes. From transformation you could get early eukaryotes that take up extra copies of genes from donors, leading to primitive diploidy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To put down some unsupported thoughts (because this question is very hard to answer - there is no really firm consensus)... Once diploidy (having more than one copy of a section of DNA) is established it may be possible to form some gamete type functions, and anisogamy, where donors can more actively package, send, and receive large sections of DNA. From there anisogamy could encourage the specialization of gamete cells more similar to what we are familiar with (eggs and sperm). One likely next step would be through hermaphroditism - the ability to be produce both gamete types simultaneously or sequentially. Then some individuals would specialize in being one or the other (sex-determination). Continued evolution would lead to more distinct male and female phenotypes.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-04-29T11:19:49.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16989" PostTypeId="2" ParentId="16987" CreationDate="2014-04-29T12:48:23.143" Score="15" Body="&lt;p&gt;It is known that Ebola uses at least one cholesterol transporter called &quot;Niemann-Pick C1&quot; (NPC1) to enter its host cells. Cells with a mutated form of this transporter were not infected by the virus (this extends to other viruses from the Filovirus group as well), which seems like a proof that this can make people &quot;immune&quot; to the virus. However, these are only experiments in cell culture. Other experiments show that a small molecule inhibitor that mimics the transporter can inhibit Ebola from entering cells and infecting them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two papers on this topic:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3175325/&quot;&gt;Ebola virus entry requires the cholesterol transporter Niemann-Pick&#xA;C1&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230319/&quot;&gt;Small molecule inhibitors reveal Niemann-Pick C1 is essential for&#xA;Ebola virus infection&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If a person manages to survive an Ebola infection the immune system fights the virus by making highly specific antibodies against it. These antibodies bind to the viruses and mark them for the immune system (mainly through mast cells) for take-up and degradation while inhibiting them from infecting other cells. Serum from Ebola survivors has been used as experimental treatment for infected people (here mainly the antibodies can be helpful). People who survive the infection are immune against another infection of the same virus strain.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="231" LastEditDate="2014-04-30T04:07:53.773" LastActivityDate="2014-04-30T04:07:53.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16990" PostTypeId="1" AcceptedAnswerId="16996" CreationDate="2014-04-29T12:48:24.860" Score="2" ViewCount="439" Body="&lt;p&gt;How do we define the fields that are &lt;strong&gt;Evolutionary (quantitative) genetics&lt;/strong&gt; and &lt;strong&gt;population genetics&lt;/strong&gt;. What set these two fields apart? Can you try to provide definitions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To my intuitive understanding, I'd tend to think that population genetics is a subfield of evolutionary genetics.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-04-29T13:24:19.397" LastActivityDate="2014-04-29T15:18:50.247" Title="Defining: Evolutionary (quantitative) Genetics and Population Genetics" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16991" PostTypeId="2" ParentId="16986" CreationDate="2014-04-29T13:17:52.987" Score="1" Body="&lt;p&gt;The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nucleotide&quot; rel=&quot;nofollow&quot;&gt;NCBI Nucleotide&lt;/a&gt; database can be used to search for coding sequences (mRNA and translated protein) of genes. You need to enter the name of the gene (INS) or protein (insulin) and then species (use either the common name, &quot;guinea pig&quot; or the scientific name, &quot;&lt;em&gt;Cavla porcellus&lt;/em&gt;&quot;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Filter the results to show you only mRNA coding sequences (sometimes abbreviated as &quot;complete CDS&quot;). These entries are annotated with the regions that account for the signal peptide, mature peptide(s) and prodomain(s). In &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/K02233.1&quot; rel=&quot;nofollow&quot;&gt;your case&lt;/a&gt;, the full proinsulin is annotated as mature peptide and the B and A chains. The C peptide connects the A and B chains, located between the only two dibasic sites (R55R56 and K88R89).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another useful database is the &lt;a href=&quot;http://www.uniprot.org&quot; rel=&quot;nofollow&quot;&gt;UniProt Protein Knowledge Base&lt;/a&gt; which presents similar information in a slightly more graphical presentation. Here is &lt;a href=&quot;http://www.uniprot.org/uniprot/P01329&quot; rel=&quot;nofollow&quot;&gt;guinea pig insulin&lt;/a&gt; in this database.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you happen to compile a whole list of C-peptide domains from other mammals, then you can use an alignment tool like &lt;a href=&quot;https://www.ebi.ac.uk/Tools/msa/clustalo/&quot; rel=&quot;nofollow&quot;&gt;ClustalOmega&lt;/a&gt; to align the peptide sequences to look for commonalities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for guinea pigs, there is only a single insulin gene (like most mammals). Only mice and rats have a two gene insulin system, Ins1 and Ins2. Generally speaking, there is &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0052847&quot; rel=&quot;nofollow&quot;&gt;poor conservation&lt;/a&gt; of the C peptide domain across mammals, in part because it only serves to link the A and B chains together to form the necessary disulfide bridges.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are wondering whether an anti-guinea pig antibody will cross react with another species' epitope, that information is listed on the antibody specification sheet under species cross-reactivity. Some antibodies are more cross-reactive than others, and you will need to refer to the specific manufacturer's information to be sure. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0052847&quot; rel=&quot;nofollow&quot;&gt;Wang S, Wei W, Zheng Y, Hou J, Dou Y, et al. (2012) The Role of Insulin C-Peptide in the Coevolution Analyses of the Insulin Signaling Pathway: A Hint for Its Functions. PLoS ONE 7(12): e52847. doi:10.1371/journal.pone.0052847&lt;/a&gt; A note on this paper, I would not take the conclusions that C-peptide has a physiological role in intracellular or endocrine signalling because it is still quite a controversial issue. I used this article because it was open access and to demonstrate in Figure 1 the variability of the C-peptide domain across selected mammals.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2014-04-29T13:50:43.043" LastActivityDate="2014-04-29T13:50:43.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16992" PostTypeId="1" CreationDate="2014-04-29T14:10:49.587" Score="4" ViewCount="209" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Why are covalently closed circular plasmid DNAs naturally found in an underwound state ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is it because this makes it easier for the DNA replication machinery to access and unwind DNA ? Or is it because underwound state is energetically more favourable than an overwound state ?&lt;/p&gt;&#xA;" OwnerUserId="6497" LastEditorUserId="5144" LastEditDate="2014-04-29T14:26:56.033" LastActivityDate="2014-04-29T18:04:26.090" Title="Topology of closed circular DNA" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16993" PostTypeId="1" CreationDate="2014-04-29T14:21:55.297" Score="3" ViewCount="76" Body="&lt;p&gt;I am looking for a book (or any good source of information) that offers an in-depth discussion and models about the evolution and analysis of complex traits and complex genetic architecture. Do you have any suggestions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd define complex traits as those traits whose variance in the population is explained by quite a lot of various genetic loci and environmental factors.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-04-29T17:50:15.277" LastActivityDate="2016-08-17T08:45:53.403" Title="Book Recommendation: Complex Traits and Complex Genetic Architecture" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;book-recommendation&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="16994" PostTypeId="2" ParentId="16992" CreationDate="2014-04-29T14:31:36.177" Score="5" Body="&lt;p&gt;DNA is not always negatively supercoiled naturally. It is important to keep in mind that different regions of topologically constrained DNA can have different supercoiling values. For example, the action of unwinding DNA for transcription or replication introduces positive supercoils ahead of the polymerase and negative supercoils behind it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, supercoiling is present in DNA normally. Supercoiling is the result of more or less twist in a DNA helix, which is most stable when it has ~10.5 bp/turn (for B-DNA). Supercoiling allows under- or overwound DNA to return to its most stable twist. Negative supercoiling is the result of underwound DNA. Underwound DNA is not thremodynamically favourable and will actually lower the melting point of DNA (the point where strand separation occurs). This can be compensated by introducing supercoils but it is also important for processes such transcription, which require ssDNA. Negative supercoils and ssDNA can be thought of as interchangeable. Negative supercoils are also used to package DNA around histones in eukaryotes and archaea. On the other hand, positive supercoiling is the result of overwound DNA (also not thermodynamically favourable) and will increase the melting point of DNA. Positive supercoiling is often found in thermophiles which live at higher temperatures and need to prevent their DNA from melting excessively. It has also been suggested that positive supercoiling can play a role in regulation of gene expression (by inhibiting promoter melting). Organisms like to keep an approximately constant amount of supercoiling in their DNA for the above reasons; this is called the superhelical density and is characteristic of different classes of organisms.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-04-29T18:04:26.090" LastActivityDate="2014-04-29T18:04:26.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16995" PostTypeId="1" CreationDate="2014-04-29T14:58:38.320" Score="5" ViewCount="296" Body="&lt;p&gt;I am growing algae in a container in my roof. It gets sunlight for the whole day as there are no clouds nowadays in my area. There is no lack of nutrients as I am constantly adding water mixed with organic waste. The dirt visible in the photos is from manure, which I added as fertilizer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The water has become green and algae is deposited on top covering almost all of the surface area. There are no threads, so it is not filamentous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since there are probably several species of algae in it which I don't know, please tell me the doubling time of most common species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, is there anything I can do to hasten the production of cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below are pictures of the culture, as asked for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UqXpI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/tsiwh.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/tIUKK.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/EsFwv.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6352" LastEditorUserId="338" LastEditDate="2014-07-09T00:30:40.183" LastActivityDate="2019-03-12T18:26:32.730" Title="With an excess supply of nutrients, in how much time will the number of algae cells double in full sun?" Tags="&lt;cell-division&gt;&lt;growth&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="16996" PostTypeId="2" ParentId="16990" CreationDate="2014-04-29T15:18:50.247" Score="5" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.sinauer.com/principles-of-population-genetics.html&quot; rel=&quot;noreferrer&quot;&gt;Hartl &amp;amp; Clark&lt;/a&gt; on population genetics:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Population genetics deals with Mendel's laws and other genetic&#xA;  principles as they apply to entire populations of organisms.... also&#xA;  includes the study of the various forces that result in evolutionary&#xA;  changes in species through time.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.sinauer.com/a-primer-of-ecological-genetics.html&quot; rel=&quot;noreferrer&quot;&gt;Conner &amp;amp; Hartl&lt;/a&gt; also on population genetics:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Population genetics is the study of naturally occurring genetic&#xA;  differences between organisms; these differences are called genetic&#xA;  variation. Genetic variation is important because it is the raw&#xA;  material for evolution... to understand the purview of population&#xA;  genetics, we need to have a better understanding of populations and&#xA;  genetic variation&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.sinauer.com/a-primer-of-ecological-genetics.html&quot; rel=&quot;noreferrer&quot;&gt;Conner &amp;amp; Hartl&lt;/a&gt; on quantitative genetics:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Most phenotypic traits do not fall in to distinct categories, but&#xA;  rather are continuously distributed... These traits are called&#xA;  quantitative or metric traits because they need to be measured not&#xA;  just scored.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0582243025&quot; rel=&quot;noreferrer&quot;&gt;Falconer &amp;amp; Mackay&lt;/a&gt; on quantitative genetics (my personal favourite book on quant gen, which spends the first 5 chapters going through population genetics):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Quantitative genetics is concerned with the inheritance of those&#xA;  differences between individuals that of degree rather than of kind,&#xA;  quantitative rather than qualitative.... It is nevertheless a basic&#xA;  premise of quantitative genetics that the inheritance of quantitative&#xA;  differences depends on genes subject to the same laws of transmission&#xA;  and having the same general properties as the genes whose transmission&#xA;  and properties are displayed by qualitative differences.&#xA;  &lt;strong&gt;Quantitative genetics is therefore an extension of Mendelian genetics, resting squarely on Mendelian principles as its&#xA;  foundation.&lt;/strong&gt;&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Personally I would say that evolution is inescapably a population genetics process and (&lt;em&gt;virtually&lt;/em&gt;) no study of it can be done without some understanding of population genetic principles. Many evolutionary genetics problems can be best dealt with using quantitative methods, and quantitative genetics is an extension of population genetic principles. Population genetics relies on selection, drift, mutation and gene flow - these are all key quantitative genetics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Population genetics study focuses then on the four basic principles above from a (simplified) Mendelian view, while quantitative genetics deals with more realistic evolutionary genetic phenomena by allowing for, and assessing, genetic variance from many loci influenced by additivity, dominance, and environmental factors. Both fields are studies of evolutionary genetics, population genetics can be studied whilst ignoring quantitative genetics, but quantitative genetics relies on population genetics principles so I would call it an extension of - but not sub-field - of population genetics.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-04-29T15:18:50.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16997" PostTypeId="2" ParentId="13867" CreationDate="2014-04-29T15:52:23.973" Score="4" Body="&lt;p&gt;The position of a gene is not always fixed neither within nor between species. There are &lt;a href=&quot;http://en.wikipedia.org/wiki/Copy-number_variation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Copy Number Variation&lt;/a&gt; for example. A great part of the variation within humans is due to CNV. I agree that it is important to consider other genetic variations than only the alleles though. CNV, position of genes, regulatory sequences and other stuff are important too in the description and the functionality of a lineage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concept of species is a poor concept which is old as Aristotle and important in the christian culture but we have to accept that this concept is not a natural category. For french speaker people &lt;a href=&quot;http://podcast.unil.ch/#&quot; rel=&quot;nofollow noreferrer&quot;&gt;this podcast&lt;/a&gt;(Follow: Biodiversité: Plus qu'une simple histoire de conservation/Pierre-Henry Gouyon) is of interest. You won't find the perfect objective definition of what is a species. &lt;a href=&quot;https://biology.stackexchange.com/questions/16953/how-are-two-species-with-similar-phenotypes-identified-as-different&quot;&gt;Here&lt;/a&gt; and &lt;a href=&quot;https://biology.stackexchange.com/questions/11240/transitivity-of-species-definitions&quot;&gt;here&lt;/a&gt; are posts that discuss the definition of species.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-04-29T15:52:23.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16998" PostTypeId="1" AcceptedAnswerId="17024" CreationDate="2014-04-29T16:18:17.470" Score="1" ViewCount="58" Body="&lt;p&gt;When performing a standard curve for some new primers to test for fold change, is it necessary to run the standard curve? I mean, in case your experiment has several genotypes for the same ecotype background, with correspondent control and treatments, must I run the standard curves for all this scenarios, or rather may I pick, just to say a random genotype of treated ones, see that it R=0.99 is or higher and efficiency 2? &#xA;It is in order to not to waste material.&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="107" LastEditDate="2014-04-30T00:56:11.810" LastActivityDate="2014-04-30T13:02:55.710" Title="Standard curve for real time" Tags="&lt;pcr&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="16999" PostTypeId="2" ParentId="8995" CreationDate="2014-04-29T16:27:39.830" Score="2" Body="&lt;p&gt;Reading K&amp;amp;R &quot;Principles and practice of sleep medicine&quot; 4th edition, on page 15, under sleep onset I've noticed the following paragraph:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Is &quot;falling asleep&quot; a unitary event? Our observations suggest that it&#xA;  is not.&lt;/strong&gt; Different functions, such as sensory awareness, memory,&#xA;  self-consciousness, continuity of logical thought, latency of response&#xA;  to a stimulus and alterations in the pattern of brain potentials all&#xA;  go in parallel in a general way, but there are exceptions to every&#xA;  rule.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The book continues to mention that it is possible to drift in and out of sleep for a few seconds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've became aware of experiments on split brain patients (severed corpus colossum) which revealed that two brain hemispheres have their own conscious awareness. Some experiments even paralyzed one hemisphere to see how the other one responds. As such, it appears that a human can function with only one hemisphere active at a time. &lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="577" LastEditDate="2016-06-29T20:11:38.200" LastActivityDate="2016-06-29T20:11:38.200" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17000" PostTypeId="2" ParentId="14849" CreationDate="2014-04-29T16:33:08.290" Score="1" Body="&lt;p&gt;Originally I wanted to try this experiment during sleep, however, the K&amp;amp;R &quot;Principles and practice of sleep medicine&quot; 4th edition, on page 16, under &quot;Olfactory system&quot; mentions that both pleasant (peppermint) and unpleasant (pyridine) smells were poorly recognized during sleep:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Both well recognized during stage 1 sleep&lt;/li&gt;&#xA;&lt;li&gt;Peppermint not consciously smelled in stage 2, stage 4 and REM sleep.&lt;/li&gt;&#xA;&lt;li&gt;Pyridine not smelled in Stage 2 sleep&lt;/li&gt;&#xA;&lt;li&gt;Pyridine occasionally smelled in Stage 2 and 4 sleep&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It suggests that one conclusion would be that &lt;strong&gt;olfactory system of humans is not a good sentinel during sleep.&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2014-04-29T16:33:08.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17001" PostTypeId="1" AcceptedAnswerId="17003" CreationDate="2014-04-29T16:33:56.837" Score="6" ViewCount="2180" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Virophage&quot;&gt;Wikipedia&lt;/a&gt; states &quot;Virophages are satellite viruses that inhibit or impair the reproduction of the auxiliary virus.&quot;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it theoretically possible for a virophage that doesn't hurt the human body to attach itself to a more serious virus like the AIDS virus for example and be used to wipe out the virus, or at least inhibit it's reproduction?  I'm completely ignorant of the virophage relationship, so feel free to inform me as needed. &lt;/p&gt;&#xA;" OwnerUserId="6534" LastEditorUserId="4108" LastEditDate="2014-04-29T16:45:39.683" LastActivityDate="2014-08-11T23:24:38.110" Title="Can a virophage potentially be used to cure a viral disease?" Tags="&lt;human-biology&gt;&lt;virology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17002" PostTypeId="2" ParentId="8895" CreationDate="2014-04-29T17:29:24.293" Score="1" Body="&lt;p&gt;The virus must be present in one partner's body for transmission to occur.&lt;/p&gt;&#xA;&lt;p&gt;&#xA;Also, HIV can be transmitted through blood to blood contact. &#xA;&lt;/p&gt;&#xA;&lt;p&gt;There is currently a similar question/conversation that I have provided a link for here. It may provide some slightly more scientific answers than what I can:)&#xA;&lt;a href=&quot;https://biology.stackexchange.com/questions/16919/how-does-a-person-get-aids&quot;&gt;How does a person get AIDS?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6289" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-04-29T17:29:24.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17003" PostTypeId="2" ParentId="17001" CreationDate="2014-04-29T18:22:47.083" Score="5" Body="&lt;p&gt;There are few enough virophages occurring in nature that I don't know if there's a clear and compelling case for them being potentially therapeutic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;em&gt;principle&lt;/em&gt; however, the answer is yes, though they may suffer from the same problems that bacteriophage treatments have suffered during their history - difficulty in preparation, extreme species specificity, and fairly daunting regulatory hurdles. While viral diseases don't have the &quot;Or we could just use antibiotics, which work&quot; out which made bacteriophages less popular, as far as I know there's not been a suggestion of widespread virophages against human pathogens.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2014-04-29T18:22:47.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17004" PostTypeId="2" ParentId="16972" CreationDate="2014-04-29T18:30:10.610" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;A friend told me, during a 3 minute discussion, that viruses that are&#xA;  endemic in host A and make repeated jumps to host B but can't be&#xA;  transmitted between individuals of species B, may slowly adapt&#xA;  (through these repeated jumps) to be able to be transmitted between&#xA;  individuals of host B and become epidemic.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is...mostly true. A good example is avian influenza - there are a number of human infections linked to contact with infected poultry, but the virus is not particularly good at sustaining long chains of human-to-human transmission, likely due to differences in the respiratory tract between humans and birds.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I don't know much about epidemiology. I don't understand how a virus&#xA;  population that is endemic to host A may adapt to host B with repeated&#xA;  jumps while the viruses that jump to host B are dead end because they&#xA;  cannot be transmitted further more. Or Are these viruses able to jump&#xA;  back to host A to bring back their newly acquired adaptations to host&#xA;  B?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What they mean by repeated jumps, or what they should mean, is not a virus hopping back and forth, but a virus going from A to B many times. This is my problem with your friend's statement, it's not so much a &quot;slow adaptation&quot; as, well, random chance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine that there's a mutation in Virus A, which lives in chickens, that will make it well adapted to live in human beings. It's an extremely rare mutation, so the dominant strain of Virus A is maladapted for human to human transmission. That means &lt;em&gt;most&lt;/em&gt; Virus A infections in humans will be the non-productive kind, that will infect a person, but not go on to infect other people. But, with enough rolls of the dice, a human might get the human-favored Virus A, and since there's now intense selective pressure &lt;em&gt;for&lt;/em&gt; that strain of the virus within its new human host, it might establish itself and take off.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2014-04-29T18:30:10.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17005" PostTypeId="2" ParentId="16985" CreationDate="2014-04-29T18:36:36.983" Score="1" Body="&lt;p&gt;Skymninge mentioned opioidreceptors and the withdrawal symptom of opiods as a runny nose: codein binds to opioidreceptors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think now that the cough can trigger runny nose.&#xA;I breathed with empty nose some 15 minutes.&#xA;Then, I had a deep dry cough and right after it a stuffy nose.&#xA;I really felt this time the negative gradient at the level of kidneys and also posteriorly.&#xA;I do not know how this kind of pain was felt, I think, near or on the kidneys.&#xA;I do not understand the effects of deep dry coughs.&#xA;They seem to be linked to several processes and locations in the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After this deep dry cough, I did some abdominal breathes and this way massaging the lymphatic circulation systemically, the stuffy nose disappeared.&#xA;My thorax is opposite of astonic person (say if you remember the name in Propedeutics).&#xA;This can be a restricting factor in the circulation of the lymph.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My conjecture is that the people with big chests (opposite of astonic) need to concentrate more on abdominal breathing such that to keep out of stuffy noses.&#xA;Restricted lymphatic circulation causes less wastes returned to the blood circulation.&#xA;Thus, accumulation of bacteria in the larynges which increases the risk of a dry cough.&#xA;Good lymphatic circulation ensures that bacteria is not congested in the larynx.&#xA;So &lt;strong&gt;cough seems to be a mechanism to start a runny nose&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This all is finely regulated.&#xA;There are several receptors in the body.&#xA;The deep cough however seems to be linked to a reflex which causes a runny nose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some studies about opiates and respiratory activity&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1890632&quot; rel=&quot;nofollow&quot;&gt;The effects of opiates on the respiratory activity of thoracic motoneurones in the anaesthetized and decerebrate rabbit.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-26T09:23:56.813" LastActivityDate="2014-12-26T09:23:56.813" CommentCount="0" CommunityOwnedDate="2014-04-29T18:36:36.983" ContentLicense="CC BY-SA 3.0" />
  <row Id="17006" PostTypeId="2" ParentId="17001" CreationDate="2014-04-29T18:42:05.693" Score="3" Body="&lt;p&gt;In theory it should be possible, though this approach seems to be limited by the nature of the virophages known today. They seem to &quot;infect&quot; (this is actually wrong, since they take use of some of the proteins produced by the mama virus and do not infect these viruses) only very big DNA viruses. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://scienceblogs.com/notrocketscience/2008/08/07/the-virophage-a-virus-that-infects-other-viruses/&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; (which is interesting to read in this context) talks about 400nm for the mimivirus, which is quite a lot. The problem is that many of the viruses which are interesting are fast mutating RNA viruses like HIV and the Ebola virus.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-04-29T18:42:05.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17007" PostTypeId="1" CreationDate="2014-04-29T19:51:12.547" Score="6" ViewCount="16622" Body="&lt;p&gt;Everyone knows what a lip is but I'm asking from a technical and anatomical standpoint.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually what we call &quot;lip&quot; is &lt;strong&gt;&quot;vermilion&quot;&lt;/strong&gt; in medical terminology. But I want to ask if my understanding is right or not regarding to surface anatomy of the lip.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lip consists of two parts called upper lip and lower lip. And upper lip and lower lip consists of two parts: skin (cutaneous) part and vermilion part  (vermilion is a special kind of skin also but we do not call it skin). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus: &lt;br&gt;&#xA;&lt;strong&gt;Lip = upper lip (upper cutaneous lip + upper vermilion) + lower lip (lower cutaneous lip + lower vermilion)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a diagram that depicts the upper lip portion:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/z1HzF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;Source: &lt;a href=&quot;http://elementsofmorphology.nih.gov/anatomy-oral.shtml&quot; rel=&quot;noreferrer&quot;&gt;http://elementsofmorphology.nih.gov/anatomy-oral.shtml&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I right so far? Did I miss any points?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the term &quot;upper lip&quot; ever used for the skin (cutaneous) part only? (especially in surgical terminology and reconstruction surgeries)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are the &quot;upper cutaneous lip&quot; and &quot;lower cutaneous lip&quot; terms established terms in medicine? Are there any other names or latin names for those?  (I also see the usage of &quot;cutaneous upper lip&quot; and &quot;cutaneous lower lip&quot;)&lt;/p&gt;&#xA;" OwnerUserId="6019" LastActivityDate="2019-01-24T12:26:42.817" Title="What is a lip? (upper lip and lower lip)" Tags="&lt;human-anatomy&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17008" PostTypeId="1" CreationDate="2014-04-29T20:24:22.480" Score="-1" ViewCount="825" Body="&lt;p&gt;How do the DNA modules tell the cell what to do? &lt;/p&gt;&#xA;" OwnerUserId="6537" LastEditorUserId="6537" LastEditDate="2014-04-30T14:43:14.633" LastActivityDate="2014-04-30T14:43:14.633" Title="how does DNA and RNA work" Tags="&lt;dna&gt;" AnswerCount="2" CommentCount="1" ClosedDate="2014-04-30T00:56:42.997" ContentLicense="CC BY-SA 3.0" />
  <row Id="17009" PostTypeId="1" AcceptedAnswerId="17025" CreationDate="2014-04-29T16:17:00.363" Score="1" ViewCount="9597" Body="&lt;p&gt;I often hear from many people saying to waiters - &quot;Please, don't put oil to salad&quot;. They probably believe the fat from vegetables has the same impact on the weight as an &quot;animal&quot; fat (meat, eggs, butter).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions are - &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Are these two types of fat have equal influence considering their converting to fat tissue in humans?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What are the pathways for conversion of vegetable oil fats to adipose tissue storage, in humans?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If one eats $X$ grams of either saturated or unsaturated fats, will they (in equal conditions) gain equal weight ($Y$ grams) in both the cases ?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5755" OwnerDisplayName="Ilan" LastEditorUserId="3340" LastEditDate="2014-04-30T08:08:24.763" LastActivityDate="2014-04-30T08:08:24.763" Title="What is the difference between vegetable and animal fats?" Tags="&lt;biochemistry&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17010" PostTypeId="2" ParentId="17008" CreationDate="2014-04-29T21:02:08.887" Score="2" Body="&lt;p&gt;This question is too broad (and also a bit poorly defined). I will try to give few concepts to help you in your exploration of wikipedia articles. If then you have more specific question, we'll be delighted to help you answering them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In very short...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genetic information contained in DNA in coded through codons, which are series of three base pairs, there are 4 different base pairs, namely, A,T,C,G. Therefore, there are $4^4 = 64$  but these 64 codons codes for only 20 amino acids (in most species). By analogy you may consider a base pair as a letter, a codon as a word (all words are made of 3 letters) and genes are sentences. But many words are synonymous. The genetic code is said to be redundant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA is a double stranded molecule, which splits in two around a coding region so that a RNA molecule can be created by copying the DNA template. This process is called transcription. This RNA is called pre mRNA. It is then spliced to become a mRNA (messenger RNA). The mRNA exit the nucleus. Two rRNA (ribosomial) RNA (which forms the so called ribosome) attach to the mRNA and tRNA (transfer RNA) will recognize the RNA sequence and paste amino-acids the ones to the others according to RNA sequence. This process is called translation. The molecule that is constructed is a polypetpide (a protein).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The quantity of proteins that are produced can be regulated by various mechanisms at different &quot;moments&quot;: pre-transcription, pre-translation, post-translation. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-04-29T21:02:08.887" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17012" PostTypeId="1" AcceptedAnswerId="17029" CreationDate="2014-04-29T21:23:08.047" Score="1" ViewCount="489" Body="&lt;p&gt;I am interested in the mechanism between the dry cough and runny nose (serous inflammation) &lt;a href=&quot;https://biology.stackexchange.com/q/16985/86&quot;&gt;here&lt;/a&gt;.&#xA;I started to think how Acute respiratory viral infection is causing the dry cough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The serous membrane, pleura pulmonalis, connects diaphragma to pars basalis pulmonalis. &#xA;It can be the source of the serous inflammatory response spreading to the nose probably.&#xA;There must be some source of inflammatory responses such that reflex arches can use them fast, thinking physically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume medication Montelukast (stop asthmatic symptoms), codeine (to stop irritated dry cough) Flixotide (with Montelukast).&#xA;Assume that there is a diaphragm press on pars basalis pulmonalis.&#xA;Assume you breath mostly by abdomen 15 minutes in the supine position.&#xA;Assume opposite-astonic person in thorax.&#xA;You then feel that you exhale too much - the serous membrane pushing on pars basalis pulmonalis - serous inflammatory response in pleura pulmanalis.&#xA;The breathing process moves thoracic muscles and thoracic cavity gets shortly extended only little.&#xA;Negative tensor on lungs i.e. the volume of the lungs is getting smaller.&#xA;Consequently, a cough reflex arch and sympaticus start a deep dry cough to protect lungs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Characteristics of the pathway against Acute respiratory viral infection&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;serous inflammation on pleura pulmonalis&lt;/li&gt;&#xA;&lt;li&gt;serous membrane pleura pulmonalis presses on pars basalis pulmonalis&lt;/li&gt;&#xA;&lt;li&gt;negative tensor on lungs&lt;/li&gt;&#xA;&lt;li&gt;cough reflex arch and sympaticus&lt;/li&gt;&#xA;&lt;li&gt;dry cough&lt;/li&gt;&#xA;&lt;li&gt;positive gradient on the pleura spreads inflammatory response through the surrounding lymphatic system is sensed as dry in larynx&lt;/li&gt;&#xA;&lt;li&gt;negative gradient is sensed on the nasal mucosa membranes as serous inflammation (runny nose)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can the serous inflammation of plera pulmonalis cause a deep dry cough and runny nose?&lt;/strong&gt;&#xA;The cause of this inflammatory response can then be Acute viral respiratory infection in some part of the lungs.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-04-30T10:38:42.637" Title="Can Serous inflammation on pleura pulmonalis cause dry cough and runny nouse?" Tags="&lt;pathophysiology&gt;&lt;lungs&gt;&lt;autonomic-nervous-system&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17013" PostTypeId="1" CreationDate="2014-04-29T21:47:01.100" Score="5" ViewCount="1623" Body="&lt;p&gt;Ever since learning that the shortening of telomeres is linked to aging I've tried to figure out what causes cells to divide, and if it's possible to slow down the rate of cell division through life style changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How would, for example, increased or decreased metabolism affect the cell cycle? If we exercise a lot, would it tear on the cells in any way, forcing faster cell division?&lt;/p&gt;&#xA;" OwnerUserId="6311" LastActivityDate="2018-11-07T23:21:18.057" Title="Does increased physical activity increase the rate of cell division?" Tags="&lt;senescence&gt;&lt;cell&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17014" PostTypeId="1" AcceptedAnswerId="20226" CreationDate="2014-04-29T22:08:58.167" Score="0" ViewCount="56" Body="&lt;p&gt;I am trying to find any recent study on pattern recognition in nerve signals. It does not really matter the part of the body where the research is focused on. It can be anything from studying activity of one group of nerves to signals coming from an entire limb.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was only able to find old (1996) research, which could be much more complete with the modern advancements in computing and manufacturing of micro-instruments. Here is an example of an old &lt;a href=&quot;http://ieeexplore.ieee.org/xpl/login.jsp?tp=&amp;amp;arnumber=647523&amp;amp;url=http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=647523&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. I am generally looking for information on how nerve signals differ within multiple subjects of same specie. For example, how would nerve response to a stimuli differ for two mice from same offspring and how will they differ from it's parents.&lt;/p&gt;&#xA;" OwnerUserId="4421" LastActivityDate="2014-08-04T20:57:11.260" Title="Modern research or study on patterns in nerve signals" Tags="&lt;neurotransmitter&gt;&lt;neurology&gt;&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17015" PostTypeId="2" ParentId="17008" CreationDate="2014-04-29T22:20:18.053" Score="0" Body="&lt;p&gt;I agree with Chris that this is way too broad a question.  But if you want a very broad answer...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA is a long molecule consisting of a sequence of 4 different subunits.  The sequence of those subunits determines the shape of the DNA, and its shape determined how it interacts with other molecules, based on their shapes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Computer code doesn't work like that at all, so I think you need to really strongly question your premise that knowing anything about computers is going to tell you much about biology.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-04-29T22:20:18.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17018" PostTypeId="2" ParentId="5166" CreationDate="2014-04-29T22:52:16.747" Score="3" Body="&lt;p&gt;Myoepithelial cell contraction initiates glandular release from most exocrine glands developed from the ectoderm. These are the cells that exist in the glandular epithelium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the distal end of the glanduar coil, an isotonic plasma filtrate gets actively transported into its lumen. As you move down the coil, close to where it connects to the duct, absorptive cells remove NaCl to make sure the sweat is hypotonic when it reaches the surface of the skin. If you view these cells where staining for alpha tubulin or beta actin, you will see they have abundant levels of myofillaments, something uncharacteristic of epithelial cells. Hence Myoepithelial. &lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-04-29T22:52:16.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17019" PostTypeId="2" ParentId="16967" CreationDate="2014-04-29T22:58:21.677" Score="1" Body="&lt;p&gt;DNA sequencing, RFLP, IHC, &lt;em&gt;In Situ&lt;/em&gt; Hybridization, Southern Blotting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the technique you are looking for (what you are talking about), is an Electro Mobility Shift Assay or EMSA&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-04-29T22:58:21.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17020" PostTypeId="2" ParentId="17013" CreationDate="2014-04-30T00:38:13.087" Score="3" Body="&lt;p&gt;My understanding is that telomeres are linked to cell senescence, which is not necessarily the same thing as &lt;em&gt;organism&lt;/em&gt; senescence. So even if you could track down a method to slow cell division, it would more likely mess with organ function now rather than extend life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a nice summary of cell senescence: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26877/#A3266&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK26877/#A3266&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did look into cell division in muscle, and new muscle cells come from &lt;a href=&quot;http://en.wikipedia.org/wiki/Myosatellite_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;satellite cells&lt;/a&gt;, rather than from mitotic division of currently active muscle cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Caloric restriction was the hot new way to live longer for a while, but studies in primates found that a sensible diet and good genetics have a bigger effect. Which is pretty much the T-shirt in medical science.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/7418/exercise-causes-number-of-cell-divisions-to-approach-hayflick-limit-faster-and?rq=1&quot;&gt;This question&lt;/a&gt; was asked last spring as well. Coincidence? Homework?&lt;/p&gt;&#xA;" OwnerUserId="6517" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-04-30T00:38:13.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17023" PostTypeId="2" ParentId="17013" CreationDate="2014-04-30T04:27:52.570" Score="0" Body="&lt;p&gt;Metabolism does affect cell cycle. Stress is known to affect ageing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1073/pnas.1404293111&quot; rel=&quot;nofollow&quot;&gt;Mitchell et al., (2014)&lt;/a&gt; report that there is a telomere shortening in kids who grow up in &lt;em&gt;disadvantaged&lt;/em&gt; social environments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Metabolism and stress are known to affect longevity and general health. After much research on genomic associations of diabetes, people have come to the conclusion that physical exercise helps. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Physical exercise is also known to stimulate neurogenesis in the hippocampus; the causes are not well understood (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18286389&quot; rel=&quot;nofollow&quot;&gt;van Praag, 2008&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are more of such reports. If you search you'll find.  &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-09-18T14:07:01.740" LastActivityDate="2016-09-18T14:07:01.740" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17024" PostTypeId="2" ParentId="16998" CreationDate="2014-04-30T04:36:27.637" Score="2" Body="&lt;p&gt;Do the standard curve once for each primer pair to determine efficiencies. You can use the efficiency values for any number of replicates with any template.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think we have somewhat discussed this issue in your &lt;a href=&quot;https://biology.stackexchange.com/questions/16035/real-time-pcr-standard-curve?rq=1&quot;&gt;previous post&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-04-30T13:02:55.710" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17025" PostTypeId="2" ParentId="17009" CreationDate="2014-04-30T05:04:02.157" Score="1" Body="&lt;p&gt;There is a subtle difference between oils and fats- oils are generally unsaturated (Carbon-Carbon double bonds) whereas fats are saturated (all single bonds).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Are these two types of fat have equal influence considering their converting to fat tissue in humans?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No. There are some kinds of fatty acids that are synthesized only by plants (Essential fatty acids). However, these can be obtained indirectly from animal sources such as fish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fats have multiple roles- not just storage. They are also critical for making up the cell membrane. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What are the converting pathways for vegetable oil fats to adipose tissue in humans?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The fatty acids in oils are absorbed in the intestine and esterified (wit glycerol) to form triglycerides. Then, they are incoporated in lipoprotein complexes. There are different types of lipoproteins- VLDL (Very Low Density Lipoprotein), LDL (Low Density Lipoprotein) and HDL (High Density Lipoprotein) which have different sizes and compositions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When lipoprotein comes in contact with lipoprotein lipase in capillaries, the free fatty acids are liberated from trigycerides, which is taken up by adipose tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fats stored in adipose tissue depends on diet. This has been &lt;a href=&quot;http://ajcn.nutrition.org/content/58/2/174.short&quot; rel=&quot;nofollow&quot;&gt;studied in rabbit&lt;/a&gt; but similar principles may apply to humans too. Fats can also be synthesized in the body. It is always saturated fat and is synthesized by the fatty acid synthase complex. The starting substance is Acetyl-CoA which is produced during catabolism of both carbohydrates and fats. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;if one eat Y of 2 meal if saturated and unsaturated fats, he/she (in equal conditions) will gain X gram if they were saturated fat and Z in a case of unsaturated fats?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;By principles of mass balance, if both have equal rates of absorption and degradation then there will be equal gain. According to &lt;a href=&quot;http://www.gastrojournal.org/article/S0016-5085%2872%2980115-X/abstract&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; study, absorption rate of unsaturated fats is higher. In that case if you eat $X$ grams of both types then the absorbed amount should be $Y_{sat}$ &amp;lt; $Y_{unsat}$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure about the degradation rates but I think it is higher for saturated fats because unsaturated has to be reduced to saturated before metabolizing via $\beta$-oxidation. Determining the exact steady state values will be tricky without a mathematical model. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;NOTE&lt;/strong&gt;: Dont confuse this with body weight gain (in the sense of obesity); it is a complex phenomenon. You have to consider a lot of things when predicting weight gain. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-04-30T05:53:49.687" LastActivityDate="2014-04-30T05:53:49.687" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17026" PostTypeId="1" AcceptedAnswerId="17028" CreationDate="2014-04-30T07:10:57.083" Score="7" ViewCount="612" Body="&lt;p&gt;Has there ever been incidences of one or more cancerous cells having all it's cell-death pathways and apoptosis mechanisms intact and functional?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastEditorUserId="5563" LastEditDate="2014-04-30T14:48:53.570" LastActivityDate="2014-04-30T14:48:53.570" Title="Can oncogenesis happen without apoptosis pathway being affected?" Tags="&lt;cancer&gt;&lt;apoptosis&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17027" PostTypeId="2" ParentId="17026" CreationDate="2014-04-30T08:37:05.767" Score="3" Body="&lt;p&gt;This is pretty unlikely, since one of the most important steps for cancer cells is to shut off apoptosis and proteins which control it (like p53, BCL2 and so on). Cancer cells (especially when they are genetically unstable) acquire so much mutations and misregulations, that these would otherwise trigger apoptosis which would result in the removal of the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can look like the following (figure taken from &lt;a href=&quot;http://www.molecular-cancer.com/content/9/1/144/figure/F3&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;), when you compare normal and cancer cell:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yFaWS.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-04-30T09:17:57.140" LastActivityDate="2014-04-30T09:17:57.140" CommentCount="19" ContentLicense="CC BY-SA 3.0" />
  <row Id="17028" PostTypeId="2" ParentId="17026" CreationDate="2014-04-30T08:38:18.997" Score="5" Body="&lt;p&gt;Usually the cell death mechanisms are overridden and therefore oncogenesis. The pathway components themselves are not mutated. One classical case I can cite is that of Ras-oncogene. See this &lt;a href=&quot;http://cancerres.aacrjournals.org/content/72/10/2457.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;article&lt;/a&gt; for details. Usually the survival/growth signals (MAP-kinase) are activated with simultaneous inactivation of apoptotic regulators (Akt-pathway). A mutation of MAP-kinase component ERK can also cause cancer but apoptosis is nonetheless supressed because of the interconnections of these tow pathways in the gene regulatory network. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whereas in the case of tumor suppressors, the cause of cancer is genomic instability and failure to initiate apoptosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xhrVT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-04-30T08:57:49.883" LastActivityDate="2014-04-30T08:57:49.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17029" PostTypeId="2" ParentId="17012" CreationDate="2014-04-30T08:50:47.370" Score="1" Body="&lt;p&gt;If &lt;a href=&quot;http://en.wikipedia.org/wiki/Inflammation#Morphologic_patterns&quot; rel=&quot;nofollow&quot;&gt;serous inflammation&lt;/a&gt; produces a large amount of serous fluid this leads to lung compression and limitation of respiratory movement. This, as you said produces dry cough by means of reflex arch.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However lung compression leads to alveolar collapse or &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001130/&quot; rel=&quot;nofollow&quot;&gt;atelectasis through pleural effusion&lt;/a&gt;. After atelectasis, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001130/&quot; rel=&quot;nofollow&quot;&gt;pneumonia can develop quickly&lt;/a&gt; as a complication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And nasal congestion is a symptom of pneumonia. Also if pneumonia develops, the cough, initially dry and reflex, will turn to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001200/&quot; rel=&quot;nofollow&quot;&gt;cough with mucus expectoration&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cough stimulates nasal congestion when it brings up mucus from the lungs and extends the alveolar inflammation up to the nose by taking and concentrating all the bacteria in the upper airway (pharynx and larynx bacteria gets in the nasal sinuses) - and in case of bacterial pneumonia mucus also contains the etiologic agent of that pneumonia (so not only from the upper airway).&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-04-30T10:38:42.637" LastActivityDate="2014-04-30T10:38:42.637" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17031" PostTypeId="2" ParentId="15104" CreationDate="2014-04-30T12:40:43.687" Score="1" Body="&lt;p&gt;A BLASTN would work for mapping the mature miRNA but you should correct some parameters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E-value is fine but increase the word length. Keep it close to 17 because you are interested in perfect matches. With miRNA small mismatches can mean a different miRNA altogether. Also run for only plus/plus alignments. (You can see &lt;a href=&quot;https://www.biostars.org/p/51697/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; post on biostar for details on how to do it) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you can also do is to use &lt;code&gt;bowtie&lt;/code&gt; (sometimes BLAST is very slow and though BLAST allows multiple threads there is no option for utilize multiple cores i.e true parallelization). Again use the option &lt;code&gt;--norc&lt;/code&gt; to avoid plus-minus alignments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Use &lt;code&gt;bowtie-build&lt;/code&gt; on your EST sequences to make an index.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there is one more problem; it is unlikely that you'll get pre-miRNA sequences in your EST collection. This is because the stable form is mature miRNA and pre is generally too shortlived to be sequenced properly without appropriate selective measures. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Capturing small RNAs by sequencing is also not that straightforward. It needs size fractionation of RNA and subsequent library preparation from the small RNA fraction. So I guess you will not discover miRNAs from ESTs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have small RNA sequences then you can align it to the genome and then select the $\pm 70$ nt to find the hairpin. &#xA;In fact there is an algorithm called mirdeep which does that; you can use it and avoid writing your own codes. If you are good at perl then you can modify it to suit your specific needs if any.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-04-30T12:40:43.687" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17032" PostTypeId="1" AcceptedAnswerId="17034" CreationDate="2014-04-30T13:07:11.977" Score="10" ViewCount="15275" Body="&lt;p&gt;Why is it that when a bee stings, a little area around it gets swelled?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it is some sort of defense mechanism of the body.  But how does it help?&lt;/p&gt;&#xA;" OwnerUserId="3881" LastEditorUserId="460" LastEditDate="2014-04-30T14:47:02.460" LastActivityDate="2016-12-13T02:40:21.400" Title="Why do Bee stings cause swelling?" Tags="&lt;health&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17033" PostTypeId="1" AcceptedAnswerId="17038" CreationDate="2014-04-30T13:22:14.583" Score="2" ViewCount="8299" Body="&lt;p&gt;What is the function of the auricles (conical appendages through the atria) present in the heart?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do they have any other function than increasing the volume of blood the heart can hold?&lt;/p&gt;&#xA;" OwnerUserId="3881" LastEditorUserId="6422" LastEditDate="2014-06-27T19:25:50.983" LastActivityDate="2014-06-27T19:25:50.983" Title="Function of the Auricle in heart" Tags="&lt;human-anatomy&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17034" PostTypeId="2" ParentId="17032" CreationDate="2014-04-30T14:00:56.353" Score="13" Body="&lt;p&gt;Bee, or other insect stings/bites, will cause a reaction to occur due to chemicals being released from your immune system.  This can result in anywhere from a small bump to anaphylaxis, which can be life-threatening if not treated right away.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kyqQF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;https://www.southerncross.co.nz/AboutTheGroup/HealthResources/MedicalLibrary/tabid/178/vw/1/ItemID/97/Bee-wasp-sting-allergies-and-analphylaxis.aspx&quot; rel=&quot;noreferrer&quot;&gt;Southern Cross Medical Library&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An anaphylactic reaction occurs when the body's antibodies respond to the insect venom by releasing chemicals such as histamine and serotonin that trigger the allergic reaction. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Whatever the reaction, it is correct to say that the reaction to an insect sting/bite is a defense mechanism of the body.  An interesting study done by Stanford University School of Medicine was done and discusses these &lt;a href=&quot;http://www.redorbit.com/news/health/1112985062/allergy-to-bee-stings-a-defense-mechanism-102513/&quot; rel=&quot;noreferrer&quot;&gt;immune mechanisms&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Innate immune responses occur in subjects exposed to a foreign substance, such as a pathogen or a toxic material like venom, for the first time. [...] Immune cells called mast cells, which reside in most of the body’s tissues, are poised to unleash signals that turn on defense responses when a pathogen or toxin intrudes.  Prior immunization is not required for these types of innate immune responses, nor is the development of specific antibodies. In contrast, during an adaptive immune response, the immune system creates antibodies that can recognize the toxin or pathogen that is invading the animal’s system. Adaptive immunity is typically a faster, more specified and more effective form of defense than innate immunity, the research team explained.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LkJeF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More explanation of the &lt;a href=&quot;http://www.walgreens.com/adamHtml/bodyguides/reftext/html/immu_sys_fin.html&quot; rel=&quot;noreferrer&quot;&gt;non-specific immune response&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If a bee stings you, the presence of the bee venom triggers a nonspecific immune response. White blood cells arrive first on the scene to rid the body of bee venom antigens. As war wages between antigens and white blood cells, battle signs may appear on the affected skin. Inflammation (redness, swelling, heat, and pain) results as the body wards off invaders.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oNIH8.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If the body detects an antigen that it previously met, a specific immune response occurs. In this response, the body has been trained to recognize and neutralize a familiar specific antigen; its immune system &quot;remembers&quot; the antigen. Such systemic (not restricted to the initial infection site) immunity enables a faster, longer lasting immune response than does a nonspecific response.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Therefore, these reactions to bee stings and other foreign toxins help us to better develop our immune system to protect against potential future encounters with these insects.&lt;/p&gt;&#xA;" OwnerUserId="6380" LastActivityDate="2014-04-30T14:00:56.353" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17035" PostTypeId="1" AcceptedAnswerId="17036" CreationDate="2014-04-30T14:06:39.780" Score="1" ViewCount="389" Body="&lt;p&gt;I was working through a previous exam and came across the following question (with reference to the picture shown below):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;What MS ionization method was employed (MALDI or ESI)?&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I cannot seem to find the answer, so I'm guessing it is not possible to tell, but if there is a way to see which one was used, please enlighten me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xd3Mp.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6544" LastActivityDate="2014-05-01T04:23:12.147" Title="How do I tell whether a mass spectrum was made with ESI or MALDI?" Tags="&lt;mass-spec&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17036" PostTypeId="2" ParentId="17035" CreationDate="2014-04-30T15:12:21.200" Score="2" Body="&lt;p&gt;I am not an expert in this topic but from what I have heard ESI generates multiply charged ions but MALDI usually does't. It is possible to find multiply charged species in the spectrum. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-05-01T04:23:12.147" LastActivityDate="2014-05-01T04:23:12.147" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17037" PostTypeId="2" ParentId="16967" CreationDate="2014-04-30T15:24:47.263" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/DNase-Seq&quot; rel=&quot;nofollow&quot;&gt;DNAse-seq&lt;/a&gt; is the most obvious choice. It uses the same idea as DNAse footprinting but measures output using high-throughput sequencing, so it can be done on a whole genome in one shot.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastActivityDate="2014-04-30T15:24:47.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17038" PostTypeId="2" ParentId="17033" CreationDate="2014-04-30T15:59:24.387" Score="2" Body="&lt;p&gt;The left auricle is a decompression chamber when atrial blood pressure is high (in systole or in some pathological conditions) [1, 2]. Some research claims it also plays a role in cardiac regeneration because it contains cardiac progenitor cells [3].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably the right auricle has less important function; also there are fewer studies about it.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Al-Saady NM, Obel OA, Camm AJ. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10525506&quot; rel=&quot;nofollow&quot;&gt;Left atrial appendage: structure, function, and role in thromboembolism.&lt;/a&gt; Heart. 1999 Nov;82(5):547-54. PubMed PMID: 10525506. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Bansal M, Kasliwal RR. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23102384&quot; rel=&quot;nofollow&quot;&gt;Echocardiography for left atrial appendage structure and function.&lt;/a&gt; Indian Heart J. 2012 Jul 27;64(5):469-75. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.ihj.2012.07.020&quot; rel=&quot;nofollow&quot;&gt;10.1016/j.ihj.2012.07.020&lt;/a&gt;. PubMed PMID: 23102384. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Leinonen JV, Emanuelov AK, Platt Y, Helman Y, Feinberg Y, Lotan C, Beeri R. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23555001&quot; rel=&quot;nofollow&quot;&gt;Left atrial appendages from adult hearts contain a reservoir of diverse cardiac progenitor cells.&lt;/a&gt; PLoS ONE. 2013 Mar 12;8(3):e59228. doi: &lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0059228&quot; rel=&quot;nofollow&quot;&gt;10.1371/journal.pone.0059228&lt;/a&gt;. PubMed PMID: 23555001. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-27T15:27:09.767" LastActivityDate="2014-06-27T15:27:09.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17039" PostTypeId="1" CreationDate="2014-04-30T16:07:22.057" Score="1" ViewCount="26" Body="&lt;p&gt;I have learnt that the brain provides a perception of image due to previous memory and experience. Then how does a blind person attain vision after cornea replacement?&lt;/p&gt;&#xA;" OwnerUserId="6390" LastActivityDate="2014-04-30T16:07:22.057" Title="Image formation" Tags="&lt;neurology&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17040" PostTypeId="2" ParentId="417" CreationDate="2014-04-30T18:26:11.580" Score="0" Body="&lt;p&gt;Failure of maintaining atonia does not lead to sleep-walking but to REM sleep behavior disorder. Sleep-walking is a mixture of NREM and wakefulness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mahowald, M. W., &amp;amp; Schenck, C. H. (2005). Insights from studying human sleep disorders. Nature, 437(7063), 1279–85. doi:10.1038/nature04287&lt;/p&gt;&#xA;" OwnerUserId="6547" LastActivityDate="2014-04-30T18:26:11.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17041" PostTypeId="1" AcceptedAnswerId="17042" CreationDate="2014-04-30T20:27:54.610" Score="3" ViewCount="267" Body="&lt;p&gt;I have a question, maybe a naive one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's assume that we isolated some RNA from a tissue. Do RNA molecules can bind each other if they have the complementary sequence? I know that some small RNA molecules can bind other RNAs and regulate them but I do not know it is possible in this case? It is like 2 different mRNA can bind each other or not?&lt;/p&gt;&#xA;" OwnerUserId="5630" LastActivityDate="2014-04-30T22:19:03.900" Title="Do RNA molecules bind each other?" Tags="&lt;molecular-biology&gt;&lt;rna&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17042" PostTypeId="2" ParentId="17041" CreationDate="2014-04-30T20:35:18.713" Score="4" Body="&lt;p&gt;The difference between RNA and DNA is rather small, and both can form a double-helix structure. So if you had two sequences of RNA complementary to each other they would basepair and form a helix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There were also some ideas to use this for therapeutic purposes, &lt;a href=&quot;http://en.wikipedia.org/wiki/Antisense_RNA&quot; rel=&quot;nofollow&quot;&gt;antisense RNA&lt;/a&gt;, an RNA oligo complementary to a messenger RNA, can theoretically be used to silence gene expression by base-pairing to the mRNA.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-04-30T20:35:18.713" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="17043" PostTypeId="2" ParentId="17041" CreationDate="2014-04-30T22:19:03.900" Score="3" Body="&lt;p&gt;@MadScientist answer is very good. I just want to add a detail that could not fit in a comment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Double stranded RNA is nothing exceptional. You can see an RNA strand that binds to its antisense in &lt;a href=&quot;http://en.wikipedia.org/wiki/Transfer_RNA&quot; rel=&quot;nofollow noreferrer&quot;&gt;tRNA&lt;/a&gt; and in &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_interference&quot; rel=&quot;nofollow noreferrer&quot;&gt;RNAi&lt;/a&gt; for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;tRNA&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UVMIo.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;RNAi&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/K776R.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-04-30T22:19:03.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17044" PostTypeId="1" AcceptedAnswerId="17045" CreationDate="2014-05-01T03:41:06.887" Score="1" ViewCount="47" Body="&lt;p&gt;I saw a news story a few years ago (I think) about a girl with a poor heart having a device implant that took over only some of the functioning of her heart ( I think they called it a piggy-back device , or something like that). The extraordinary thing is that it not only helped her live but all the heart functions started to improve. It was as if giving part of the heart a chance to 'rest'  allowed the whole heart to improve. If this procedure works could it be applied to other organs? Could a Piggy-Back device be made for the liver taking over only some of its functions for instance?  Could such a thing help the liver functions to 'regenerate'?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastActivityDate="2014-05-01T08:54:34.717" Title="About a mechanical aid to the heart" Tags="&lt;cardiology&gt;&lt;implantation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17045" PostTypeId="2" ParentId="17044" CreationDate="2014-05-01T04:45:18.673" Score="3" Body="&lt;p&gt;The function of heart is just to pump blood and nothing else. Though, it is a vital organ, its functions are limited. The device that you are talking about is a battery powered mechanical pump that performs the same function as heart. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Liver, however has a more complex function. One of its function is to synthesize and secrete certain molecules. A small artificial device cannot do that (you would need a bioreactor !!!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We still haven't developed and artificial cell. Perhaps a consortium of bacteria can do some of the liver's functions but to culture them in right proportions and implant them without the risk of infection or their elimination is almost impossible as of now. You can clearly see that there are too many steps to be optimized.  &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-05-01T08:54:34.717" LastActivityDate="2014-05-01T08:54:34.717" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="17048" PostTypeId="1" AcceptedAnswerId="17051" CreationDate="2014-05-01T10:10:57.063" Score="0" ViewCount="50" Body="&lt;p&gt;I presume microorganisms would have very short life span and they would multiply more creating millions of their kind. Is it really a threat to consider when we use anibiotics and other stuff more making these creatures becoming resilient to the medicines. On the other hand bodies becoming dependent on the medicine making us weaker .we clean our office spaces homes etc with bleaching agents, acids killing microorganisms and thus making our body unaware of these and letting these organisms survive and create more deadly strains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe there are examples like malaria microbes becoming resistant to &lt;code&gt;quinine&lt;/code&gt; perhaps many more.  If someone tries not to take medicines when he suffers from common cold and small fevers and let the body fight but is it right to do so considering that mecines are available and one should take them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an &lt;a href=&quot;http://www.dailymail.co.uk/health/article-2616794/Antibiotic-resistance-needs-taken-seriously-AIDS-Implications-bacteria-evading-drugs-devastating-says-landmark-report.html&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; also published today.&lt;/p&gt;&#xA;" OwnerUserId="5008" LastEditorUserId="1320" LastEditDate="2014-05-01T12:36:21.120" LastActivityDate="2014-05-01T18:46:42.863" Title="evolution and mutation of microrganisms against medicines?" Tags="&lt;evolution&gt;&lt;adaptation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17049" PostTypeId="1" CreationDate="2014-05-01T10:14:37.113" Score="7" ViewCount="10232" Body="&lt;p&gt;This picture shows the development inside a bird egg:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/awuI5.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;This shows the connection of the embryo to the yolk sac.  Does this mean birds have navels?  And if so, what happens to the umbilical cord once the bird hatches?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-12-03T22:06:24.560" Title="Do birds have navels?" Tags="&lt;embryology&gt;&lt;ornithology&gt;&lt;eggs&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17051" PostTypeId="2" ParentId="17048" CreationDate="2014-05-01T10:19:22.453" Score="3" Body="&lt;p&gt;A few throughts about this: Microorganisms have a short life span but they replicate very fast with a short generation time. So this create vast amounts of &quot;offsprings&quot; with some mutations naturally occurring. Due to this large numbers the chance of developing resistances is much higher than for slowly replicating species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is especially true, when the selection pressure is high, as this is the case when you treat with drugs which usually kill these microbes efficiently. When people are not taking these drugs (antibiotics for example) according to the necessary scheme, the concentration of the drug in the body is lower than necessary to kill of all microorganisms. This leads to the survival of microorganisms which are a bit adapted to survive the drug and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The real problem are people who are not following their treatment regime necessary and thus causing resistancies. A case for this is tuberculosis. Regarding taking medication: Always take them when necessary and leave them out when not. A simple cold for example can not be treated antibiotics since it is viral, the secondary middle ear infection usually can.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-05-01T18:46:42.863" LastActivityDate="2014-05-01T18:46:42.863" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17052" PostTypeId="2" ParentId="16288" CreationDate="2014-05-01T10:29:52.963" Score="1" Body="&lt;p&gt;I've always used Cosmid Library but Cosmid Genomic Library is better than Genomic Cosmid Library. &lt;/p&gt;&#xA;" OwnerUserId="6557" LastActivityDate="2014-05-01T10:29:52.963" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17053" PostTypeId="1" CreationDate="2014-05-01T10:30:28.817" Score="0" ViewCount="129" Body="&lt;p&gt;I can't understand how to study enzyme kinetics. Say I have a lipase and want to study the kinetics of this lipase using a fluorogenic substrate, how would I do this? From what I understand I would use a 96 or so well plate and in each increase the amount of substrate or increase the amount of enzyme and use a fluorescence microscope or a spectrophotometer? &lt;/p&gt;&#xA;" OwnerUserId="6557" LastEditorUserId="1320" LastEditDate="2014-05-01T12:34:44.347" LastActivityDate="2014-05-11T14:04:42.783" Title="Enzyme kinetics" Tags="&lt;enzymes&gt;&lt;fluorescent-microscopy&gt;&lt;kinetics&gt;&lt;enzyme-kinetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ClosedDate="2014-05-12T10:43:30.173" ContentLicense="CC BY-SA 3.0" />
  <row Id="17054" PostTypeId="2" ParentId="11159" CreationDate="2014-05-01T10:42:41.853" Score="2" Body="&lt;p&gt;I think telomere shortening largely accounts for the replicative cell aging.&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22901253&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/22901253&lt;/a&gt;&#xA;The increase in no. of mutations with age surely does affect the tissue/organism survival too. There's a recent study that I'd like to share here. It is quite interesting and informative.&#xA;&lt;a href=&quot;http://www.iflscience.com/health-and-medicine/mutations-found-115-year-old-womans-blood-could-help-unlock-secrets-aging&quot; rel=&quot;nofollow&quot;&gt;http://www.iflscience.com/health-and-medicine/mutations-found-115-year-old-womans-blood-could-help-unlock-secrets-aging&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6349" LastActivityDate="2014-05-01T10:42:41.853" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17055" PostTypeId="1" AcceptedAnswerId="17069" CreationDate="2014-05-01T10:51:37.703" Score="1" ViewCount="508" Body="&lt;p&gt;Expressed in number of Base Pairs or Bytes, about how large is the simplest eukaryotic genome?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much of this is 'junk-DNA' (non-coding)?&lt;/p&gt;&#xA;" OwnerUserId="6499" LastEditorUserId="1320" LastEditDate="2014-09-04T21:57:15.130" LastActivityDate="2014-09-06T20:22:10.953" Title="What is most simple eukaryotic genome?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;bioinformatics&gt;&lt;eukaryotic-cells&gt;" AnswerCount="2" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="17057" PostTypeId="1" AcceptedAnswerId="17068" CreationDate="2014-05-01T12:50:39.980" Score="2" ViewCount="940" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;Also, transplants from one identical twin to another are &lt;strong&gt;almost never&lt;/strong&gt; rejected.&lt;br /&gt;&#xA;&lt;sub&gt;[ Source: &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000815.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Medline Plus&lt;/a&gt; ]&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Why can a tissue from an &lt;em&gt;identical&lt;/em&gt; twin be rejected ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="24354" LastEditDate="2020-07-16T19:35:33.303" LastActivityDate="2020-07-16T19:35:33.303" Title="Why will tissue from identical twin be rejected in some cases?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;tissue&gt;&lt;transplantation&gt;&lt;twins&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="17058" PostTypeId="2" ParentId="17049" CreationDate="2014-05-01T13:57:27.893" Score="9" Body="&lt;p&gt;All animals develop in this way, whether they are oviparous (developing in an egg) or viviparous (developing inside their mother, or live-birth).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://lansingwbu.blogspot.ca/2012/02/do-birds-have-belly-buttons.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wild Birds Unlimited&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;All mammals have navels or belly buttons where the umbilical cord distributes nutrients between a mother and her fetus. After birth, the umbilical cord is cut and a scar develops on the abdomen where the hole closes. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Of course avians or birds hatch from eggs which are virtually self-contained life-support systems that only require warmth and oxygen to develop properly. Instead of an umbilical cord scar, birds have yolk sac scars at hatching. This is where the chick embryo is attached to the yolk sac. But don’t look for any bird belly button rings. The scars usually heal and become virtually invisible.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5Y8Vj.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for their &lt;a href=&quot;http://mag.audubon.org/articles/birds/question-do-birds-have-belly-buttons&quot; rel=&quot;nofollow noreferrer&quot;&gt;umbilical cord&lt;/a&gt;, it looks like it falls off when the chick hatches if it is not fully absorbed along with the yolk sac, along with everything else contained in the egg (although there is not a lot of material left within the egg by the time the chick is &lt;a href=&quot;http://www.shmoop.com/animal-reproduction/birth-hatching.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;ready to hatch&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Inside a bird's egg there is a tiny cord that connects the developing embryo to the yolk sac. When the egg cracks open, the hatchling does in fact have a miniscule residual scar where the cord was. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6380" LastEditorUserId="6380" LastEditDate="2014-08-14T20:09:06.843" LastActivityDate="2014-08-14T20:09:06.843" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17059" PostTypeId="2" ParentId="17057" CreationDate="2014-05-01T15:49:01.990" Score="2" Body="&lt;p&gt;This was too long for a comment, but I have absolutely no evidence for what I'm about to say :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It looks like that sentence was a little bit of hand-waving, as the author didn't want to categorically state that identical twin tissue would &lt;strong&gt;never&lt;/strong&gt; be rejected. I suspect that in the early days there may have been reports of organ failure (esp. kidneys) in the recipient that were incorrectly identified as rejection episodes. I suppose there's also the slight possibility that one twin could have a mutation event very shortly after the separation of the twins &lt;em&gt;in utero&lt;/em&gt; (when all the cells are still pluripotent) that could somehow change or (more likely) silence one or more of the HLA or other surface antigens involved in transplant rejection. This would almost certainly have to happen when the separated twin was a single cell. The mutated twin would therefore not express an antigen the non-mutated twin did, and if the non-mutated twin donated a kidney or other organ to the mutated one, its immune system wouldn't recognize the silenced antigen and could potentially result in rejection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like I said earlier, all pure conjecture :) &lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-05-01T15:49:01.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17060" PostTypeId="1" CreationDate="2014-05-01T17:09:16.367" Score="7" ViewCount="28593" Body="&lt;p&gt;When using the latin nomenclature for a fish in printed materials (such as &lt;em&gt;Sander vitreus&lt;/em&gt; for walleye), what is the correct capitalization of each word? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this example, should 'S' be uppercase only, or both 'S' and 'V' be upper/lower case?  &lt;/p&gt;&#xA;" OwnerUserId="6559" LastEditorUserId="3624" LastEditDate="2015-04-01T08:36:58.303" LastActivityDate="2015-04-01T08:36:58.303" Title="What is the proper format for genus and species names in latin?" Tags="&lt;taxonomy&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17061" PostTypeId="2" ParentId="13864" CreationDate="2014-05-01T17:21:02.020" Score="3" Body="&lt;p&gt;The chance of having a child with Down's Syndrome does not only have to do with cell division, but the mechanism that allows spontaneous abortion to occur &lt;a href=&quot;http://www.sciencedaily.com/releases/2006/10/061012184355.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;within the uterus of the mother&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;There is strong evidence for uterine selection against genetically disadvantaged embryos.  However, as women approach the menopause and the risk of future infertility increases, this selection, or filtering stringency, is expected to relax.&lt;/p&gt;&#xA;&lt;p&gt;Neuhäuser and Krackow’s paper provides evidence that older mothers, who give birth to children with Down Syndrome, have a relaxed stringency of quality control of embryos (or relaxed filtering stringency), which increases the probability that these women will bring children with developmental defects to full term.  They believe that this relaxed filtering stringency is an adaptive maternal response and it might explain why the rate of Down Syndrome accelerates with increasing maternal age.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Basically, the mechanism that allows for the uterus to select against 'genetically disadvantaged embryos' (which can be Down's Syndrome, or other genetic deficiencies) is not as good at detecting these problems, &lt;strong&gt;OR&lt;/strong&gt; as this paper suggests, is 'less picky' about the genetic quality of the fertilized egg, and will allow it to implant in the uterine walls.&lt;/p&gt;&#xA;&lt;p&gt;It is also important to note that these studies are all ongoing, and many different reasons for the development of Down's Syndrome are unknown.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Neuhäuser M &amp;amp; Krackow S (2006).  Adaptive-filtering of trisomy 21: risk of Down Syndrome depends on family size and age of previous child.  (Naturwissenschaften, DOI 10.1007/s00114-006-0165-3)&lt;/p&gt;&#xA;" OwnerUserId="6380" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-05-01T19:34:32.323" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17062" PostTypeId="2" ParentId="17060" CreationDate="2014-05-01T17:28:44.943" Score="9" Body="&lt;p&gt;The correct latin nomenclature is &lt;em&gt;Sander vitreus&lt;/em&gt;, with the genus capitalized and the species name in lowercase.  This is known as &lt;a href=&quot;http://www.princeton.edu/~achaney/tmve/wiki100k/docs/Binomial_nomenclature.html&quot; rel=&quot;noreferrer&quot;&gt;binomial nomenclature&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Carl Linnaeus chose to use a two-word naming system [...] binomial nomenclature scheme, using only the genus name and the specific name or epithet which together form the whole name of the species. For example, humans belong to genus &lt;em&gt;Homo&lt;/em&gt; and their specific name is &lt;em&gt;sapiens&lt;/em&gt;.  The first letter of the first name, the genus, is always capitalized, while that of the second is not, even when derived from a proper noun such as the name of a person or place. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Some scientific &lt;a href=&quot;http://www.expertsmind.com/questions/conventions-for-using-binomial-nomenclature-30127486.aspx&quot; rel=&quot;noreferrer&quot;&gt;naming conventions&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Pf5bj.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Classification example (for &lt;em&gt;Homo sapiens&lt;/em&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3e3Cr.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6380" LastEditorUserId="6380" LastEditDate="2014-05-01T19:39:14.393" LastActivityDate="2014-05-01T19:39:14.393" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17063" PostTypeId="1" AcceptedAnswerId="17070" CreationDate="2014-05-01T17:41:49.423" Score="2" ViewCount="131" Body="&lt;p&gt;I have read that DNA(after recombination) is packaged in bacteriophages lambda only if it's between 40000 and 53000 bp long. This constraint can be used to ensure packaging of recombinant DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't understand why shorter DNA can not be packaged.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source : Lehninger Principles of Biochemistry &lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2014-05-02T16:11:57.123" LastActivityDate="2014-05-02T16:11:57.123" Title="Size of DNA in phage" Tags="&lt;dna&gt;&lt;virus&gt;&lt;recombination&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17064" PostTypeId="1" AcceptedAnswerId="24744" CreationDate="2014-05-01T17:45:00.093" Score="2" ViewCount="183" Body="&lt;p&gt;From Lehninger Principles of Biochemistry :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The stability of YAC increases with size (up to a limit). Those with&#xA;  inserts of less than 100000 are gradually lost during mitosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why does this happen ? (YAC refers to yeast artificial chromosome )&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2014-12-10T06:43:49.940" LastActivityDate="2014-12-10T06:43:49.940" Title="Why does the stability of YAC increase with size?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;molecular-genetics&gt;&lt;yeast&gt;&lt;recombination&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17065" PostTypeId="1" AcceptedAnswerId="17067" CreationDate="2014-05-01T19:02:39.143" Score="4" ViewCount="975" Body="&lt;p&gt;In math, there are special numbers, like Pi (3.14159...) and e (2.71828...). In chemistry, there's numbers like avogadro's number (6.0221413e+23). For example a circle can be defined in terms of 2 * Pi.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are there any significant constant numbers in biology that define the shape of an organism&lt;/strong&gt; (ex: mammal)? I'm talking about stuff like shoulder to hip ratio or length of an organism, etc? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's an example that came to mind - different fetuses developing into different organisms. Is there any constant that is the same for these at some stage of development? Like the ratio of head to tail?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Zc2Lj.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="577" LastEditDate="2014-05-01T19:14:54.740" LastActivityDate="2014-05-02T13:18:25.540" Title="Are there special constants in biology that define organism's morphology?" Tags="&lt;development&gt;&lt;morphology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17066" PostTypeId="2" ParentId="17055" CreationDate="2014-05-01T19:06:31.340" Score="-1" Body="&lt;p&gt;According to this:&#xA;&lt;a href=&quot;http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/G/GenomeSizes.html&quot; rel=&quot;nofollow&quot;&gt;http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/G/GenomeSizes.html&lt;/a&gt;&#xA;The shortest DNA of a individually living cell is that of Mycoplasma genitalium at about 580000 base pairs. -But it's not eucariotic!&lt;/p&gt;&#xA;" OwnerUserId="6499" LastEditorUserId="6499" LastEditDate="2014-09-06T20:22:10.953" LastActivityDate="2014-09-06T20:22:10.953" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17067" PostTypeId="2" ParentId="17065" CreationDate="2014-05-01T19:11:36.997" Score="5" Body="&lt;p&gt;I don't know if this is what you mean, but take a look at &lt;a href=&quot;http://bionumbers.hms.harvard.edu/&quot; rel=&quot;nofollow&quot;&gt;BioNumbers&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, mathematical constants like pi are different from physical constants. Mathematical constants are true in a mathematical (logic) sense, and do not need to be related to any physical quantity. They are derived by &lt;strong&gt;logic&lt;/strong&gt;. Physical constants, on the other hand, typically describe an observed relation between two types of quantities. They are derived by &lt;strong&gt;measurement&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2014-05-02T00:16:21.543" LastActivityDate="2014-05-02T00:16:21.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17068" PostTypeId="2" ParentId="17057" CreationDate="2014-05-01T19:18:15.700" Score="1" Body="&lt;p&gt;MattDMo, I think you're right on.  Also remember the &lt;a href=&quot;http://en.wikipedia.org/wiki/Thymus&quot; rel=&quot;nofollow&quot;&gt;thymus&lt;/a&gt; is where T-cell recombination and maturation occurs during fetal development, and rates are highest during neonatal period through pre-adolescent childhood - long after sharing a womb.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The immune system keeps developing during childhood.  It's the immune system that's responsible for tissue rejection in transplant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In our immune system, T cells attack and kill foreign cells in the body.  They're supposed &#xA;to ignore cells that carry molecules belonging to their own body.&#xA;T cells go through selection in the thymus during these years to eliminate the T cells that attack their own molecules;the rest of the T cells that recognize foreign molecules are allowed to live.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next, consider that environmentally-induced &lt;a href=&quot;http://en.wikipedia.org/wiki/Epigenetics&quot; rel=&quot;nofollow&quot;&gt;epigenetics&lt;/a&gt; influence the expression of proteins and other products.  Even twins have different experiences and exposures, so there may be a difference in protein components in their bodies.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, this is conjecture, but the same concepts involved in autoimmune disorders (which are another topic entirely) might also be involved in some of these situations as well.&lt;/p&gt;&#xA;" OwnerUserId="6314" LastActivityDate="2014-05-01T19:18:15.700" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17069" PostTypeId="2" ParentId="17055" CreationDate="2014-05-01T19:59:23.657" Score="4" Body="&lt;p&gt;You asked about eukaryotes. The genome of the yeast &lt;em&gt;Saccharomyces cerevisiae&lt;/em&gt; is 12.2 Mb.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genome of the smallest free-living eukaryote, &lt;em&gt;Ostreococcus tauri&lt;/em&gt; (a unicellular green alga) &lt;a href=&quot;http://www.pnas.org/content/103/31/11647.abstract&quot; rel=&quot;nofollow&quot;&gt;is 12.6 Mb&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are smaller eukaryotic genomes, but these are not free-living organisms they are intracellular parasites.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-01T19:59:23.657" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17070" PostTypeId="2" ParentId="17063" CreationDate="2014-05-01T20:08:30.680" Score="2" Body="&lt;p&gt;For lambda:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If the distance between the two &lt;em&gt;cos&lt;/em&gt; sites is less than ~37 kb, the resulting phage particle will be unstable. When the DNA is inside the capsid, it exerts pressure on the capsid. Likewise the capsid exerts an inward force on the DNA. If there is not enough DNA inside the capsid, it will implode from the inward force of the capsid. If the distance between the two cos sites is too far (~52 kb), then the capsid will be filled before the second cos is reached. The tail cannot be added because the DNA hanging out of the capsid is in the way and no infectious phage particle is produced.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.microinmuno.qb.fcen.uba.ar/03-Bacteriophage.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.microinmuno.qb.fcen.uba.ar/03-Bacteriophage.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In contrast filamentous phage like M13 have no upper size limit, but since they get longer with more DNA they become physically fragile. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-01T20:08:30.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17074" PostTypeId="1" AcceptedAnswerId="17075" CreationDate="2014-05-02T03:50:14.330" Score="2" ViewCount="88" Body="&lt;p&gt;From what I &lt;a href=&quot;http://www.sciencemag.org/content/316/5825/750.full&quot; rel=&quot;nofollow&quot;&gt;read&lt;/a&gt;, A-beta plaques inhibit microtubule based transport of mitochondria when &lt;a href=&quot;http://en.wikipedia.org/wiki/Tau_protein&quot; rel=&quot;nofollow&quot;&gt;tau protein&lt;/a&gt; is present in the cell. How would I be able to do a test to see if one isoform of tau is more effective at conferring this A-beta sensitivity than another isofrom? &lt;/p&gt;&#xA;" OwnerUserId="6209" LastEditorUserId="3340" LastEditDate="2014-05-02T07:28:46.727" LastActivityDate="2014-05-03T04:07:14.617" Title="How to study the effect on tau protein isoforms on microtubule based transport?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17075" PostTypeId="2" ParentId="17074" CreationDate="2014-05-02T04:37:59.627" Score="3" Body="&lt;p&gt;You can do a microscopy based assay to quantify the transport rate (both retrograde and anterograde). Mitochondria can be labeled with fluorescent proteins such as &lt;a href=&quot;http://www.clontech.com/US/Products/Fluorescent_Proteins_and_Reporters/Fluorescent_Proteins_by_Name/DsRed2_Fluorescent_Protein&quot; rel=&quot;nofollow&quot;&gt;mito-dsRed&lt;/a&gt;, and its movement along the axon can be tracked by live cell imaging. You can check &lt;a href=&quot;http://www.cell.com/abstract/S0092-8674%2813%2901277-4&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;; they have done this experiment. (&lt;em&gt;Others have also done it but I remember this paper because someone told me about it recently&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do you plan to see the effect of different isoforms? It may not be that easy. You will have to replace the common isoform with the others. It is not very easy to control splicing. So you may have to make lines that express only one variant (exon deletion). Though this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1784105/&quot; rel=&quot;nofollow&quot;&gt;study&lt;/a&gt; reports that alternative splicing can be controlled by using antisense oligonucleotides, the technology is not standardized yet; you can try it nonetheless, because making knockouts is difficult (you would have to make KO mice and then culture neurons from it).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-05-03T04:07:14.617" LastActivityDate="2014-05-03T04:07:14.617" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17077" PostTypeId="1" AcceptedAnswerId="17091" CreationDate="2014-05-02T05:33:54.220" Score="64" ViewCount="10946" Body="&lt;p&gt;Why does evolution not make life longer for humans or any other species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wouldn't evolution favour a long life?&lt;/p&gt;&#xA;" OwnerUserId="6563" LastEditorUserId="1590" LastEditDate="2016-02-28T22:23:14.877" LastActivityDate="2019-03-18T21:52:38.060" Title="Why does evolution not make our life longer?" Tags="&lt;evolution&gt;&lt;senescence&gt;&lt;life&gt;&lt;environment&gt;" AnswerCount="8" CommentCount="20" FavoriteCount="34" ContentLicense="CC BY-SA 3.0" />
  <row Id="17078" PostTypeId="2" ParentId="17077" CreationDate="2014-05-02T07:47:03.153" Score="22" Body="&lt;p&gt;This is a very good question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a big ongoing field of research called &quot;evolution of aging/senescence&quot; that tackles this question. I won't give you a complete overview of the different hypothesis the could explain why we age but here is a fundamental concept that is to know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We'll assume that there is some extrinsic mortality, mortality against which a lineage won't ever be able to escape and I think it is not an assumption that is hard to meet. Therefore, an allele that has age-specific effect such as decreasing the fecundity at age 3 will undergo a higher selection pressure and will faster get eliminated from the population than another allele causing the same decrease in fecundity but at age 4 because some individuals would have died between age 3 and age 4. In other words, natural selection is more efficient at lower age than at higher age. Now, imagine in humans an allele that increases the reproductive success of an individual at age 20 by decreasing the survival at age 78. This allele will easily spread in the population. Such alleles are said to have &lt;em&gt;age-specific antagonist pleiotropic&lt;/em&gt; effect. And empirical studies have shown that alleles that have antagonist age-specific antagonist pleiotropic exist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, it is because there is some extrinsic mortality that natural selection acts with a different strength at different ages allowing some deleterious allele at old age to fix in the population especially if those alleles have age-specific antagonist pleiotropic effect. You'll find in &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0521459672&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;this book&lt;/a&gt; mathematical formulation and more complete discussion of this effect&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other hypotheses exist which are based on lineage selection, group selection or on the mutation-selection balance.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="16866" LastEditDate="2019-03-18T21:52:38.060" LastActivityDate="2019-03-18T21:52:38.060" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="17079" PostTypeId="1" CreationDate="2014-05-02T08:17:46.237" Score="9" ViewCount="12230" Body="&lt;p&gt;When a pine cone is wet, it remains closed. However, when it's dry it opens again. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the perspective of physics or biomechanics, what is the mechanism that allows a pine cone to open and close as I've described?&lt;/p&gt;&#xA;" OwnerUserId="6552" LastEditorUserId="6380" LastEditDate="2014-05-02T15:39:17.753" LastActivityDate="2018-01-12T17:08:25.603" Title="How does a pine cone open?" Tags="&lt;physiology&gt;&lt;botany&gt;&lt;ecology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17081" PostTypeId="1" AcceptedAnswerId="17083" CreationDate="2014-05-02T09:20:41.783" Score="1" ViewCount="133" Body="&lt;p&gt;In his song &lt;a href=&quot;https://www.youtube.com/watch?v=ESFANzZTdYM&quot; rel=&quot;nofollow&quot;&gt;Lullaby&lt;/a&gt;, Tim Minchin &lt;a href=&quot;https://www.youtube.com/watch?v=ESFANzZTdYM?t=57s&quot; rel=&quot;nofollow&quot;&gt;sings&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Your nappy is dry and your tummy is full&lt;br&gt;&#xA;  Of enough antihistamine to chill out a bull&lt;br&gt;&#xA;  Yet still all this gringing&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;According to Wikipedia, antihistamines are used against allergies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, why is there antihistamine in his baby's tummy and why is it supposed to make her sleepy?&lt;/p&gt;&#xA;" OwnerUserId="6565" LastEditorUserId="6565" LastEditDate="2014-05-02T13:21:57.663" LastActivityDate="2014-05-02T13:21:57.663" Title="What are Antihistamines doing in a baby?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17082" PostTypeId="2" ParentId="17081" CreationDate="2014-05-02T10:31:19.173" Score="3" Body="&lt;p&gt;This is not only happening in babies...&#xA;In short (I will look for some references later and edit the post) the antihistamines are effective in the whole body and block the histamines there. The antihistamines which cross the blood-brain barrier do the same in the brain and hinder the small amounts of histamines which stimulate the nerve cells there from doing so. This results in the typical sleepyness.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-02T10:31:19.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17083" PostTypeId="2" ParentId="17081" CreationDate="2014-05-02T11:32:33.910" Score="8" Body="&lt;p&gt;This song most likely refers to an &lt;strong&gt;off-label&lt;/strong&gt; (&lt;em&gt;and usually &lt;strong&gt;inappropriate&lt;/em&gt;&lt;/strong&gt;) use for certain antihistamines like &lt;strong&gt;Benadryl&lt;/strong&gt;. They are sometimes used by parents to &lt;strong&gt;sedate their children&lt;/strong&gt;, functioning through the exact physiological mechanisms @Chris describes.  Parents use it &lt;strong&gt;inappropriately&lt;/strong&gt; as a means of &lt;strong&gt;behavioral control&lt;/strong&gt; for active or upset children to make them more docile or sleepy, such as for airplane rides, etc.  &lt;a href=&quot;https://www.rnzcgp.org.nz/assets/documents/Publications/JPHC/June-2013/JPHCNuggetsJune2013.pdf&quot;&gt;&lt;strong&gt;It's not recommended by most pediatricians&lt;/strong&gt;&lt;/a&gt;, because even though adverse (bad) side effects are usually rare, it is an actual medication with another primary mechanism of action having effects on many body functions, not a medication designed as a sedative.  &lt;/p&gt;&#xA;" OwnerUserId="6314" LastEditorUserId="6314" LastEditDate="2014-05-02T11:43:04.943" LastActivityDate="2014-05-02T11:43:04.943" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17085" PostTypeId="1" AcceptedAnswerId="39601" CreationDate="2014-05-02T12:28:27.720" Score="3" ViewCount="781" Body="&lt;p&gt;In a class that I'm taking we were presented 3 types of stem cells.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Adult stem cells which come from bone marrow&lt;/li&gt;&#xA;&lt;li&gt;Embryonic stem cells which come from embryos&lt;/li&gt;&#xA;&lt;li&gt;Embryonic germ cells which come from testes&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I understand that adult stem cells are a bit more specialized than embryonic stem cells, but I'm confused why embryonic germ cells are considered stem cells. From Wikipedia, the definition of stem cells is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Undifferentiated biological cells that can differentiate into&#xA;  specialized cells and can divide (through mitosis) to produce more&#xA;  stem cells&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But from my limited understanding of biology embryonic germ cells can't specialize into any other cells unless they fuse with another gamete, so why would they be considered stem cells? What am I missing here?&lt;/p&gt;&#xA;" OwnerUserId="5427" LastActivityDate="2015-10-17T19:45:42.403" Title="Why are embryonic germ cells considered stem cells?" Tags="&lt;cell-biology&gt;&lt;stem-cells&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17086" PostTypeId="1" AcceptedAnswerId="17092" CreationDate="2014-05-02T13:07:22.293" Score="4" ViewCount="2254" Body="&lt;p&gt;I would like to know the specific determinants for formation of IgG dimers. My understanding is the stem of the antibody is a homodimer of two heavy chains, covalently bonded through two disulfide bridges called the hinge region. Is there any association between the constant region? My reading would suggest no but I have not found a specific reference as such.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="948" LastEditDate="2014-05-02T14:40:12.683" LastActivityDate="2014-05-02T16:06:48.280" Title="Dimerization of Immunoglobulin G" Tags="&lt;biochemistry&gt;&lt;immunology&gt;&lt;antibody&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17087" PostTypeId="2" ParentId="17079" CreationDate="2014-05-02T13:09:59.067" Score="8" Body="&lt;p&gt;From &lt;a href=&quot;http://www.nature.com/nature/journal/v390/n6661/abs/390668a0.html&quot; rel=&quot;noreferrer&quot;&gt;How Do Pine Cones Open&lt;/a&gt; (&lt;em&gt;Nature&lt;/em&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The scales of seed-bearing pine cones move in response to changes in relative humidity. The scales gape open when it is dry, releasing the cone's seeds. When it is damp, the scales close up. The cells in a mature cone are dead, so the mechanism is passive: the structure of the scale and the walls of the cells composing the scale respond to changing relative humidity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5qCk2.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the &lt;a href=&quot;http://www.ask.com/question/why-do-pine-cones-open-and-close&quot; rel=&quot;noreferrer&quot;&gt;reasons why&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pine cones usually appear open because this is considered a more favourable condition for the seed dispersal and germination. This usually happens when the weather is warm and when they touch water or in cold conditions, they tend to close to avoid destruction. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As to the physics/biomechanics of the pine cone opening/closing, there is an interesting article titled &lt;a href=&quot;http://www.researchgate.net/publication/26334411_Hygromorphs_from_pine_cones_to_biomimetic_bilayers&quot; rel=&quot;noreferrer&quot;&gt;Hygromorphs: from pine cones to biomimetic bilayers&lt;/a&gt; that discusses objects that respond to environmental humidity to change their shape.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Using the pine cone as an example that opens when dried and closes when wet, we quantify the geometry, mechanics and dynamics of closure and opening at the cell, tissue and organ levels, building on our prior structural knowledge.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6380" LastActivityDate="2014-05-02T13:09:59.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17088" PostTypeId="2" ParentId="17065" CreationDate="2014-05-02T13:18:25.540" Score="2" Body="&lt;p&gt;I think you have the direction of causality reversed. Due to either physical, chemical or dynamical properties of cells and organisms, it would certainly be possible to see patterns of constants emerge when making some measurements. I don't think you can say that the mathematical constants define any aspect of an organism. The Golden Ratio, or phi, was brought up as a recurring pattern in nature (e.g., the spiral pattern of snail. shells and sunflower seeds) but these are emergent properties of a physical system bound by physical constraints, and it so happens some pattern is used because it is efficient (in whatever sense that may mean).&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-05-02T13:18:25.540" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17089" PostTypeId="1" CreationDate="2014-05-02T13:25:30.363" Score="2" ViewCount="66" Body="&lt;p&gt;Are there any examples in animals where individuals survive having no copies of their sexual chromosomes?&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2014-05-02T13:25:30.363" Title="examples of chromosomal aberrations with lack of sexual chromosomes?" Tags="&lt;genetics&gt;&lt;chromosome&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17090" PostTypeId="2" ParentId="17077" CreationDate="2014-05-02T14:02:04.203" Score="5" Body="&lt;p&gt;There is no selection mechanism that would favor high age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the time it's apparent whether or not an individual can reach a high age healthily, they'll have ceased all reproductive activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conversely, people who get cancer at 45 will have likely reproduced already.&lt;/p&gt;&#xA;" OwnerUserId="6566" LastActivityDate="2014-05-02T14:02:04.203" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17091" PostTypeId="2" ParentId="17077" CreationDate="2014-05-02T14:20:09.697" Score="74" Body="&lt;p&gt;Why do we age is a classical question in Evolutionary Biology. There are several things to consider when we think of how genes that cause disease, aging, and death to evolve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One explanation for the evolution of aging is the &lt;a href=&quot;http://www.programmed-aging.org/theories/mutation_accumulation.html&quot;&gt;&lt;strong&gt;mutation accumulation&lt;/strong&gt; (&lt;strong&gt;MA&lt;/strong&gt;)&lt;/a&gt; hypothesis. This hypothesis by P. Medawar states that mutations causing late life deleterious (damaging) effects can build up in the genome more than diseases that cause early life disease. This is because selection on late acting mutations is weaker. Mutations that cause early life disease will more severely reduce the fitness of its carrier than late acting mutations. For example, if we said in an imaginary species that all individuals cease to reproduce at 40 years old and a mutation arises that causes a fatal disease at 50 years old then selection can not remove it from the population - carriers will have as many children as those who do not have the gene. Under the mutation accumulation hypothesis it is then possible for mutations to &lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/IIIDGeneticdrift.shtml&quot;&gt;drift&lt;/a&gt; through the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another hypothesis which could contribute to aging is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Antagonistic_pleiotropy_hypothesis&quot;&gt;&lt;strong&gt;antagonistic pleiotropy&lt;/strong&gt; (&lt;strong&gt;AP&lt;/strong&gt;)&lt;/a&gt; hypothesis of G.C. Williams. &lt;a href=&quot;http://en.wikipedia.org/wiki/Pleiotropy&quot;&gt;Pleiotropy&lt;/a&gt; is when genes have more than one effect, such genes tend to cause correlations between traits, height and arm length probably have many of the same genes affecting them, otherwise there would be no &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8793422&quot;&gt;correlation between arm length and height&lt;/a&gt; (though environment and linkage can also cause these patterns)... Back to AP as an explanation for aging, if a gene improves fitness early in life, but causes late life disease it can spread through the population via selection. The favourable early effect spreads well because of selection and, just as with MA, selection can not &quot;see&quot; the late acting disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under both MA and AP the key point is that selection is less efficient at removing late acting deleterious mutations, and they may spread more rapidly thanks to beneficial early life effects. Also if there is extrinsic mortality (predation etc.) then the effect of selection is also weakened on alleles that affect late life. The same late-life reduction in the efficacy of selection also slows the rate at which alleles increasing lifespan spread.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A third consideration is the &lt;a href=&quot;http://www.programmed-aging.org/theories/disposable_soma.html&quot;&gt;&lt;strong&gt;disposable-soma model&lt;/strong&gt;&lt;/a&gt;, a description by T. Kirkwood of life-history trade-offs which might explain why aging and earlier death could be favoured. The idea is that individuals have a limited amount of resources available to them - perhaps because of environmental constraints or ability to acquire/allocate the resources. If we then assume that individuals have to use their energy for two things, staying alive via repair and maintenance (somatic-maintenance) and making offspring (reproductive-investment), then any energy devoted to one will take away from the other. If an individual carries a gene that makes it devote all of its energy to somatic maintenance then its fitness will be very low (probably 0!) and that gene will not spread. If the level of maintenance required to live forever costs more energy than an individual can spare without suffering from low fitness (very likely) or can even acquire and efficiently convert in the first place (also very likely) then high-maintenance alleles will not spread (and aging &amp;amp; death will continue to occur). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To go a little further, it is common for sexes to age differently (this is what I work on) and one possible explanation is that the sexes favour different balances of the trade off between somatic-maintenance and reproductive investment, this can lead to conflict over the evolution of genes affecting this balance and slow the rates of evolution to sex specific optima. &lt;a href=&quot;http://www.cosmoid.de/zajitschek/papers/Bonduriansky2008FunctionalEcology.pdf&quot;&gt;This paper&lt;/a&gt; provides a good review of the area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;To summarise&lt;/strong&gt;, evolution has not managed to get rid of death via genetic disease etc. (intrinsic mortality) because the effect is only weakly selected against, and those alleles may provide some early life benefit, and resource limitation may also reduce the potential to increase lifespan due to trade-offs with reproductive effort. Adaptive evolution is not about the &lt;em&gt;survival&lt;/em&gt; of the fittest but the &lt;em&gt;reproduction&lt;/em&gt; of the fittest - the fittest allele is the one which spreads the most effectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt; Thanks to Remi.b for also pointing out some other considerations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another thought is that of altruistic aging - aging for the good of the population (the population is likely to contain related individuals, &lt;em&gt;you&lt;/em&gt; are related to all other humans to some degree). In this model aging is an adaptive process (unlike in MA where it is just a consequence of weak selection). By dying an individual makes space for it's offspring/relatives to survive (because resources are then less likely to limit populations). This will stop excessive population growth which could lead to crashes in the population and so, by dying earlier, an individual promotes the likelihood that its progeny will survive. Arguments of altruistic sacrifice are often hard to promote but &lt;a href=&quot;http://www.researchgate.net/publication/255170953_Viscous_populations_evolve_altruistic_programmed_aging_in_ability_conflict_in_a_changing_environment&quot;&gt;recent work suggests that this is a more plausible model than once thought&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.programmed-aging.org/theories/evolvability_theories.html&quot;&gt;Evolvabilty theories&lt;/a&gt; also suggest that aging is an adaptive process. These suggest that populations, composed of a mixture of young and old, have biases in how well adapted the members of the population are - where younger individuals are better adapted (because they were produced more recently it is likely that the environment is similar to the environment they are favoured in). Thus by removing the less well adapted individuals from a population via senescence and freeing up resources for younger better adapted individuals, a population evolves more rapidly towards it optimal state.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-01-27T11:44:59.510" LastActivityDate="2016-01-27T11:44:59.510" CommentCount="19" ContentLicense="CC BY-SA 3.0" />
  <row Id="17092" PostTypeId="2" ParentId="17086" CreationDate="2014-05-02T14:28:46.417" Score="2" Body="&lt;p&gt;For human IgG1 and 4, the only inter-heavy chain disulfide bonds are the two in the hinge region. IgG2 has 4 disulfides in the hinge, and IgG3 has 11:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/m695j.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are intra-heavy chain disulfides in the Fc region, and of course there are non-covalent bonds between the two heavy chains (as well as the light chains) to maintain structure, but aside from the hinge region the only other inter-chain disulfides are between heavy and light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22327427&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; is an interesting review of classical (determined in the 1960s) and non-classical (more recently discovered) disulfide bond formation and structure in human IgGs.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2014-05-02T16:06:48.280" LastActivityDate="2014-05-02T16:06:48.280" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17095" PostTypeId="2" ParentId="17077" CreationDate="2014-05-02T15:53:25.087" Score="7" Body="&lt;p&gt;If you take the line of &quot;The Selfish Gene - Richard Dawkins&quot;. Evolution doesn't care about individuals, it cares about genes. So as long as the genes are passed along reliably into the future, evolution may do it with 4 generations per 100 years or 100 generations per 100 years.&lt;/p&gt;&#xA;" OwnerUserId="6571" LastActivityDate="2014-05-02T15:53:25.087" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="17096" PostTypeId="1" AcceptedAnswerId="17111" CreationDate="2014-05-02T16:26:00.343" Score="2" ViewCount="457" Body="&lt;p&gt;The &lt;a href=&quot;http://www.lifetechnologies.com/us/en/home/life-science/cloning/gateway-cloning/clonase-enzyme.html&quot; rel=&quot;nofollow&quot;&gt;Gateway cloning system&lt;/a&gt; utilizes what Life Technologies refers to as &quot;Clonase enzyme mix&quot; to catalyze the BP and LR reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is in this enzyme mix? Is there a sequence for them?&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-05-03T04:27:54.467" LastActivityDate="2014-05-03T19:17:13.293" Title="What are the Gateway clonase enzymes?" Tags="&lt;molecular-biology&gt;&lt;enzymes&gt;&lt;cloning&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17097" PostTypeId="2" ParentId="17077" CreationDate="2014-05-02T16:41:08.613" Score="13" Body="&lt;p&gt;Actually, genetically, there is no reason for animals to continue to exist after they have procreated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at salmon, they die immediately after procreating, which is probably the most efficient way to carry the best genes to the next generation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of mammals, they need to teach their offspring where to find food, where to find water and how to avoid dangers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of humans, that goes into the third generation, so most humans know their parents and their grandparents, and even they live with them in some cultures, since their experiences and ideas are taken as very important.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So maybe the question should be the opposite, why do we live to see our grandchildren grow?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taking your same question to the opposite: why do people die? Why don't they live forever instead of reproducing? I can think of various reasons for this. Imagine a race that lives forever and another race who have a lot of children early on and then die. Now imagine a contagious disease that spreads among both populations. Which race has the most probability of survival?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, the race that reproduces rapidly has a better chance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And also, evolution works wonders for the race that reproduces rapidly instead of the race that lives forever. Meaning the number of years a species live has carefully been &quot;designed out&quot; by evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution would not work if it didn't stabilize around the best genes. And that's exactly what happens with humans. Most humans have the same traits: live around the same number of years, and have more or less the same abilities, most differences are almost irrelevant.&lt;/p&gt;&#xA;" OwnerUserId="6572" LastEditorUserId="49230" LastEditDate="2019-03-18T21:46:05.310" LastActivityDate="2019-03-18T21:46:05.310" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="17098" PostTypeId="2" ParentId="17077" CreationDate="2014-05-02T17:24:39.080" Score="14" Body="&lt;p&gt;Because evolution isn't about individuals: it's about species. What matters to natural selection isn't how long you live, but how many grandchildren you have. A long lifespan &lt;em&gt;can&lt;/em&gt; be an evolutionary advantage, but like any trait, it's only an advantage to the extent that allows you to reproduce more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would seem that a longer lifespan would be advantageous anyway, because it would give you more time to reproduce. However, for reasons we don't yet fully understand, it doesn't seem to work out that way in practice. Most organisms (assuming they live long enough) eventually reach an age where they stop reproducing. Even humans do this, and although we've managed to increase the average lifespan quite a bit over the course of recorded human history (to say nothing of the millennia before that), the average age at which people stop reproducing apparently hasn't changed very much.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why not? What makes &lt;em&gt;this&lt;/em&gt; an evolutionary advantage over having more reproductive years? This is one of those things that we haven't really figured out yet. There are a number of competing theories, and the other answers here go into some of them. But the most direct way to answer your question is fairly simple: longer lifespans (and/or reproductive years) haven't given us, or our children, any more success at reproducing. Thus, there is no pressure on the species to live longer, and so it doesn't happen.&lt;/p&gt;&#xA;" OwnerUserId="6574" LastActivityDate="2014-05-02T17:24:39.080" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="17100" PostTypeId="1" AcceptedAnswerId="17102" CreationDate="2014-05-02T19:56:59.890" Score="4" ViewCount="495" Body="&lt;p&gt;I understand that someones genetic makeup at an allele is usually denoted as (AA,Aa,aa).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That means that instead of an A-T pair you get a C-G pair on none, 1 or 2 copies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, what exactly happens when you have a tri-allele (as in blood type). Are they looking at two base positions? Or is it instead of an A -&gt; C mutation, you get something weirder like an A-&gt;G mutation (and thus you need to account for directionality) etc?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="3500" LastActivityDate="2014-05-03T21:39:04.680" Title="Help explain multi alleles in terms of actual genetic code" Tags="&lt;genetics&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17102" PostTypeId="2" ParentId="17100" CreationDate="2014-05-02T20:17:55.283" Score="2" Body="&lt;p&gt;All of these things happen, but triallelic SNPs (single nucleotide polymorphisms) refer to the case where a single specific base in the genome may have one of three bases. e.g.: A/G/C &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cases where more than one base in a sequence that changes.  This doesn't really have a name though: (e.g. AA -&gt; GC ).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These can be called a/b/c alleles I guess.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for this not having a name is probably because two bases don't really change at the same time as a common event.  If two SNPs are next to each other they probably changed at different times, which means that if you look around enough you will find AA, GC, and GA because the A-&gt;G happened first and then a few dozen generations the second A-&gt;C mutation happened. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-05-02T20:17:55.283" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="17103" PostTypeId="2" ParentId="17100" CreationDate="2014-05-02T21:16:39.310" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I understand that someones genetic makeup at an allele is usually&#xA;  denoted as (AA,Aa,aa).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No. That's what you learn in high school, because it's easy, and because it's what Mendel worked out for the 7 traits he studied in pea plants.  Real life is a &lt;strong&gt;lot&lt;/strong&gt; more complex.  Most phenotypic differences cannot be explained in terms of exactly two alleles, one of which is classically dominant to the other.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;That means that instead of an A-T pair you get a C-G pair on none, 1&#xA;  or 2 copies.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not necessarily.  Two alleles might differ at many many points in their sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And you seem to be a bit confused about how people write out DNA sequence.  Even though DNA is a double helix, when we talk about what the sequence is, we refer only to one strand, like this&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GAGCCATGGGGCGCCATGTTGCCACCAGCTGCCACGTGGCCTGGCTTTTGGTGCTGATCT&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A mutation might turn that last T into an A, but we don't say &quot;oh, nothing happened, it's still an A-T pair&quot; because it matters which strand has which letter.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Now, what exactly happens when you have a tri-allele (as in blood&#xA;  type).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, blood type is more complicated that just ABO...but here's a pretty old paper with some helpful details&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2333095&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/2333095&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Here we present a molecular basis for the ABO genotypes. The A and B genes differ in a few single-base substitutions, changing four amino-acid residues that may cause differences in A and B transferase specificity.  A critical single-base deletion was found in the O gene, which results in an entirely different, inactive protein incapable of modifying the H antigen.&quot;&lt;/p&gt;&#xA;" OwnerUserId="5148" LastEditorUserId="4108" LastEditDate="2014-05-02T21:27:31.153" LastActivityDate="2014-05-02T21:27:31.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17104" PostTypeId="1" AcceptedAnswerId="17291" CreationDate="2014-05-02T22:26:56.887" Score="16" ViewCount="781" Body="&lt;p&gt;I recently read about an experiment where they removed the dendrites and axons from rat neurons and placed them on a grid. After a while they started reconnecting and were able to learn things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since I'm trying to create a model simulating this, I'd like to know (as much as is needed to make it look at least a little bit realistic) how they reconnected. As far as I know some molecules are secreted attracting or repelling axon growth cones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think I can model that part, but the problem is that the axons can easily grow back to where they came from, so how do the axons in a brain 'know' they are not growing back to the neuron they originated from.&lt;/p&gt;&#xA;" OwnerUserId="6580" LastEditorUserId="948" LastEditDate="2014-05-09T19:57:40.693" LastActivityDate="2014-12-17T12:51:04.730" Title="How does an axon &quot;know&quot; it's not connecting to its own neuron?" Tags="&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17109" PostTypeId="1" CreationDate="2014-05-03T07:43:19.070" Score="4" ViewCount="194" Body="&lt;p&gt;Living in northern latitudes, I have always wondered why do migratory birds invest so much time and energy to travel twice a year the vast distances between their breeding grounds and wintering areas. The most commonly found explanation, and the one I am grown accustomed to, is the scarcity of resources, resources meaning food and nesting places. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For years I have considered this a quite convenient explanation but recently I came to rethink it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you know, many of the longest migrating birds are insectivorous such as European Pied Flycatcher that breeds in much of Europe and western Asia but spends winters in western Africa. While it is easy to see the scarcity of food (insects) in northern breeding areas during winters, it is more difficult for me to see the scarcity of food in southern wintering areas during summers. - Take, for example, ants, that I expect, are abundant in those places all year around. Considering their total biomass, they would seem to hold a potential for a stable food source for masses of insect eaters with minimal food gathering effort required. So why migrate?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it that ants (or any other seemingly overly abundant invertebrates such as termites and mosquitoes) are not nutritious enough? Or are they too stingy and poisonous perhaps?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for nesting places, I am aware that many birds defend their home range (thereby setting an upper limit for population density), but I imagine that such behaviour could be subject to change (or never had emerged in the first place) if there was no need to compete for other resources (mainly for food).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or are the primary constraining factors disease and predation that would follow from a larger population density?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in short, my question is, what is (/are) the primary reasons(s) for insectivorous birds to migrate instead of staying in their wintering areas and feeding on (seemingly abundant) local resources such as ants?&lt;/p&gt;&#xA;" OwnerUserId="6585" LastEditorUserId="6585" LastEditDate="2014-05-03T08:17:04.210" LastActivityDate="2014-07-29T12:20:11.307" Title="Why do insectivorous birds migrate?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17110" PostTypeId="1" AcceptedAnswerId="17126" CreationDate="2014-05-03T08:15:43.750" Score="2" ViewCount="103" Body="&lt;p&gt;Suppose I filled an oceangoing container with rice and sunk it to the bottom of the ocean… say, a kilometer or so, then brought it back up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would it be edible?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would it retain nutrients?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do these things depend on how long it's been down there (at very low temperatures, mind you).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Asking for myself because, you know, I think ocean-bottom rice would be tasty.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit (after Doctor Whom's answer): I guess I should have mentioned that wrapping it in plastic is an option.  The pressure is what I was most interested in but I did a really poor job conveying that.&lt;/p&gt;&#xA;" OwnerUserId="6586" LastEditorUserId="6586" LastEditDate="2014-05-04T08:30:26.283" LastActivityDate="2014-05-04T08:30:26.283" Title="If I sent a bag of rice to the bottom of the ocean and brought it back, could I eat it?" Tags="&lt;vegetable&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17111" PostTypeId="2" ParentId="17096" CreationDate="2014-05-03T08:50:59.067" Score="3" Body="&lt;p&gt;The prototypes for these proteins are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the bacteriophage &amp;lambda; proteins Int and Xis, required for, respectively the integration and excision of prophages. They are, as mentioned by @WYSIWYG, recombinases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/K1lA8.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Genetic map of bacteriophage &amp;lambda;&lt;/strong&gt; (&lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/9/97/LambdaPhage_Genome_Linear.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;source of image&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the original Ihf (integrative/integration host factor) was identified as an &lt;em&gt;E. coli&lt;/em&gt; protein required for prophage integration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you might expect Int and Xis proteins occur in many phage genomes, and in integrated prophages in bacterial genomes, and Ihf, because it is involved in bacterial DNA replication, is ubiquitous. I imagine the actual source of the proteins used by Life Technologies could be a trade secret. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-05-03T19:17:13.293" LastActivityDate="2014-05-03T19:17:13.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17113" PostTypeId="1" CreationDate="2014-05-03T10:27:00.133" Score="3" ViewCount="165" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Coefficient_of_relationship&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; gives the following formula to calculate a &quot;path of coefficient of relationship&quot; between an ancestor $A$ and an offspring $O$:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\rho_{AO} = 2^{-n} \left( \frac{1+f_A}{1+f_O} \right)^{1/2} = \left( \frac{1}{2}\right)^n \sqrt { \frac{1+f_A}{1+f_O}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $f_A$ and $f_O$ are the coefficient of inbreeding of the ancestor and the offspring respectively.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where does the term $\sqrt { \frac{1+f_A}{1+f_O}}$ comes from? Please explain why this multiplicative term is $\sqrt { \frac{1+f_A}{1+f_O}}$ and not something different such as $\frac{f_A f_O}{2}$ for example.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-05-03T10:44:49.983" LastActivityDate="2014-08-01T19:51:51.180" Title="Inbreeding Coefficient and Coefficient of Relationship" Tags="&lt;evolution&gt;&lt;molecular-genetics&gt;&lt;population-dynamics&gt;&lt;molecular-evolution&gt;&lt;population-genetics&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17114" PostTypeId="1" CreationDate="2014-05-03T10:43:44.253" Score="1" ViewCount="89" Body="&lt;p&gt;&lt;em&gt;- Background -&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Talking about one phenotypic trait, the total phenotypic variance $V_p$ is decomposed into genetic and environmental variance for this trait, represented by the symbols $V_G$ and $V_E$ respectively. Also the covariance between genes and environment affect $V_p$ but we'll ignore it for the purpose of this question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$V_p = V_E + V_G + O(Cov(E,G))$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genetic variance $V_G$ can be further decomposed into dominance and additive variance. Similarly the environmental variance can be further decomposed into for example, for the mammals, the variance in the womb $V_W$ and the other environmental variance $V_{OE}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$V_p = V_w + V_{OE} + V_A + V_D$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$h_N^2 = \frac{V_A}{V_p} = \frac{V_A}{V_w + V_{OE}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One could measure $V_W$ by looking at correlation between dizygotic twins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;- Question -&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What part of the environmental variance in phenotype is explained by the variance in wombs' environments? i.e. what are the estimates of $\frac{V_w}{V_e}$ or what are the estimates of $\frac{V_w}{V_p} = \frac{V_w}{V_w + V_{OE}}$?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course the answer will depends on the trait and on the species. I welcome either a general idea/estimation or any such measure for any specific trait.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-12-25T10:35:37.507" LastActivityDate="2014-12-25T10:35:37.507" Title="How important is the womb's environment?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;mammals&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;" AnswerCount="0" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="17115" PostTypeId="1" AcceptedAnswerId="17118" CreationDate="2014-05-03T11:00:30.617" Score="2" ViewCount="118" Body="&lt;p&gt;A path of coefficient of relationship is defined as&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\rho_{AO} = \left( \frac{1}{2}\right)^n \sqrt { \frac{1+f_A}{1+f_O}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/17113/inbreeding-coefficient-and-coefficient-of-relationship&quot;&gt;This SE post&lt;/a&gt; discusses this definition&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this, the coefficient of relatedness between two individuals $B$ and $C$ is defined as&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$R_{BC} = \sum \rho_{AB} \rho_{AC}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $A$ is (I think) the last common ancestor of $B$ and $C$. The sum is over all possible path coefficients.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://en.wikipedia.org/wiki/Coefficient_of_relationship&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I am a little bit confused, I don't really understand this formula. One reason is the following. Let's assume that  $B$ has 2 paths and $C$ has 3 paths to go to $A$. If we denote $\rho_{AB,i}$, the path $i$ (or the $i^{th}$ if you prefer) between $A$ and $B$, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$R_{BC} = \rho_{AB,i} \rho_{AC,i} + \rho_{AB,j} \rho_{AC,j} + \rho_{AB,k} \rho_{AC,k}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the path $\rho_{AB,k}$ does not exist because there are only 2 paths between $A$ and $B$ (which are denoted $i$ and $j$). Also, there is no reason to count the path in a specific order and not another one. If we change the order we count the paths between $C$ and $A$, we can get:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$R_{BC} = \rho_{AB,i} \rho_{AC,j} + \rho_{AB,j} \rho_{AC,i} + \rho_{AB,k} \rho_{AC,k}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, which is obviously different from the previous calculation of $R_{BC}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you help me making sense of these formulas?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-05-03T20:59:12.570" Title="Coefficient of relationship and path of coefficient" Tags="&lt;evolution&gt;&lt;molecular-genetics&gt;&lt;population-dynamics&gt;&lt;molecular-evolution&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17116" PostTypeId="1" AcceptedAnswerId="25788" CreationDate="2014-05-03T11:19:48.573" Score="3" ViewCount="216" Body="&lt;p&gt;From &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.es.18.110187.001321?journalCode=ecolsys.1&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;,  second paragraph of the second page&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A classic theoretical result is that the mean of a character controlled by a single locus &lt;strong&gt;&lt;em&gt;i&lt;/em&gt;&lt;/strong&gt; with two alleles &lt;strong&gt;&lt;em&gt;A&lt;sub&gt;i1&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; and &lt;strong&gt;&lt;em&gt;A&lt;sub&gt;i2&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; is only affected by the value of &lt;strong&gt;&lt;em&gt;f&lt;/em&gt;&lt;/strong&gt; if there is some degree of dominance.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;where &lt;strong&gt;&lt;em&gt;f&lt;/em&gt;&lt;/strong&gt; is the Wright's inbreeding coefficient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors then add: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Assume that the trait is scaled such that the values for the genotypes &lt;strong&gt;&lt;em&gt;A&lt;sub&gt;i1&lt;/sub&gt;A&lt;sub&gt;i1&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt;, &lt;strong&gt;&lt;em&gt;A&lt;sub&gt;i1&lt;/sub&gt;A&lt;sub&gt;i2&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt;, and &lt;strong&gt;&lt;em&gt;A&lt;sub&gt;i2&lt;/sub&gt;A&lt;sub&gt;i2&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; are &lt;strong&gt;&lt;em&gt;-a&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt;, &lt;strong&gt;&lt;em&gt;d&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt;, and &lt;strong&gt;&lt;em&gt;a&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; respectively. The quantities &lt;strong&gt;&lt;em&gt;a&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; and &lt;strong&gt;&lt;em&gt;d&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; measure the effect of the locus on the character and the degree of dominance of the locus, respectively. With two alleles, there is a linear decline in the mean of a trait&#xA;  with increasing &lt;strong&gt;&lt;em&gt;f&lt;/em&gt;&lt;/strong&gt; either with overdominance (&lt;strong&gt;&lt;em&gt;d&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; &gt; &lt;strong&gt;&lt;em&gt;a&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt;) or if the allele associated with an increased value of the trait is dominant or partially dominant (&lt;strong&gt;&lt;em&gt;a&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; ≥ &lt;strong&gt;&lt;em&gt;d&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; &gt; &lt;strong&gt;&lt;em&gt;0&lt;/em&gt;&lt;/strong&gt;). With additive joint effects of different loci on the trait, this conclusion can be extended to a polygenic character; inbreeding decline occurs if the average value of &lt;strong&gt;&lt;em&gt;d&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; over all &lt;strong&gt;&lt;em&gt;i&lt;/em&gt;&lt;/strong&gt; is positive.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't understand why &quot;[..] there is a linear decline in the mean of a trait&#xA;with increasing &lt;strong&gt;&lt;em&gt;f&lt;/em&gt;&lt;/strong&gt; either with overdominance (&lt;strong&gt;&lt;em&gt;d&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; &gt; &lt;strong&gt;&lt;em&gt;a&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt;) or if the allele associated with an increased value of the trait is dominant or partially dominant (&lt;strong&gt;&lt;em&gt;a&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; ≥ &lt;strong&gt;&lt;em&gt;d&lt;sub&gt;i&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; &gt; &lt;strong&gt;&lt;em&gt;0&lt;/em&gt;&lt;/strong&gt;)&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you please explain why the mean of a character controlled by a single locus is only affected by the value of &lt;strong&gt;&lt;em&gt;&quot;f&quot;&lt;/em&gt;&lt;/strong&gt; if there is some degree of dominance.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3340" LastEditDate="2014-12-03T17:49:09.550" LastActivityDate="2014-12-12T08:50:33.610" Title="Inbreeding depression and dominance" Tags="&lt;evolution&gt;&lt;molecular-genetics&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17117" PostTypeId="1" CreationDate="2014-05-03T16:20:19.013" Score="2" ViewCount="305" Body="&lt;p&gt;A toddler's food intake seems very little: only milk and water and some solid food. Therefore, from where does this energy come?&lt;/p&gt;&#xA;" OwnerUserId="6589" LastEditorUserId="3340" LastEditDate="2015-06-04T11:45:39.590" LastActivityDate="2015-06-04T11:45:39.590" Title="How can toddlers expend seemingly boundless energy when they eat so little?" Tags="&lt;food&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17118" PostTypeId="2" ParentId="17115" CreationDate="2014-05-03T17:27:41.180" Score="2" Body="&lt;p&gt;The expression $f = 2h-1,$ coefficient of inbreeding (COI) is a measure of homozygosity. Since in a randomly breeding herd (of cattle) we expect 50 per cent heterozygous and 50 per cent homozygous, the minimum for $2h-1 $ is 0. If the cattle's genome is purely homozygous (aa, AA) we have $2h-1 = 1.$ (h is total homozygosity--see Wright's paper, linked below.)  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As we can see from this &lt;a href=&quot;http://www.genetic-genealogy.co.uk/Toc115570135.html&quot; rel=&quot;nofollow&quot;&gt;site&lt;/a&gt;, a basic calculation of relationship coefficient may not deal with f at all. For two descendants B, C, the quantities $f_B,f_C$ are an attempt to factor in existing relative homozygosity that the coefficient of relation (COR) would otherwise not capture. Likewise $f_A$ measures preexisting homozygosity in the common ancestor of B and C. If animal A is the product of siblings then the homozygosity could already be quite high and this would maybe have measurable effects on the vitality of a cross between B and C.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now $f_A$ and $f_B$ vary between 0 and 1 so $s = (\frac{1+f_A}{1+f_B})^{1/2}$ varies between $(1/2)^{1/2}$ and $(2)^{1/2}.$ Note that the important thing here is &lt;em&gt;relative&lt;/em&gt; homozygosity of an animal and its ancestor:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a. If the ancestor A and descendent B have the same known preexisting burden of heterozygosity we can disregard s (and f) entirely. Their COR will depend only on path distance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;b. The homozygosity of the ancestor A  tends to increase COR while that of B tends to decrease COR.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The expression $r_{BC }= \sum p_{AB }\cdot p_{AC}$ is somewhat confusing. On page 334 of one of Wright's earlier &lt;a href=&quot;http://aipl.arsusda.gov/publish/other/wright1922.pdf&quot; rel=&quot;nofollow&quot;&gt;papers&lt;/a&gt; we can get a clear idea of the use of the coefficient. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;He defines $p_{BA} = (1/2)^n (\frac{1+f_A}{1+f_B})^{1/2}.$ If the path from C to A is $p_{CA} = (1/2)^m (\frac{1+f_A}{1+f_C})^{1/2}$ then the total path BAC would be  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ p_{AB,AC} = (1/2)^{n+m}(\frac{1+f_A}{1+f_B})^{1/2}(\frac{1+f_A}{1+f_C})^{1/2} $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$= (1/2)^{n+m}\frac{1+f_A}{[(1+f_B)(1+f_C)]^{1/2}}  $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the expression for the sum of such paths would be &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$r_{BC} = \sum_i p_{AB,AC} = \sum_i (1/2)^{k_i}\frac{1+f_{A_i}}{[(1+f_B)(1+f_C)]^{1/2}}   $$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;in which $A_i$ is the ith ancestor through whom B and C are related. The total path length for a given term is $(n_i+m_i)$ which I abbreviated $k_i.$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So a less confusing expression for $r_{BC}$ might be: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$r_{BC }= \sum_i p_{A_iB}p_{A_iC}. $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the sum is over all common ancestors back to some arbitrary generation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good example of this is Figure 11 at link &lt;a href=&quot;http://www.genetic-genealogy.co.uk/Toc115570135.html&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt; above. &#xA;It's really not ``dumbed down'' at all, it just leaves out the factor s, which for a carefully maintained herd may be close to 1 anyway. &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-05-03T20:59:12.570" LastActivityDate="2014-05-03T20:59:12.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17119" PostTypeId="2" ParentId="17077" CreationDate="2014-05-03T18:34:29.193" Score="5" Body="&lt;p&gt;To an extent it does; in that we live longer than our mouse-like ancestors. So the question becomes: why not keep extending it to immortality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key thing is that evolution &lt;em&gt;cares&lt;/em&gt; only about the survival of your genes; so if you live for 1000 years or if 10 generations of your family have 1 individual's worth of your genes in each generation (each living for 100 years) this is equivalently successful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But this assumes it's either-or that an organism can reproduce or live a long time, could it not do both? &lt;a href=&quot;http://www.washingtonpost.com/wp-srv/national/horizon/june98/microbes.htm&quot; rel=&quot;noreferrer&quot;&gt;In principle it could but the resources of a particular niche are limited so in order to avoid mass starvation the reproductive rate must reduce as the average age of the individuals go up&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So this suggests having very long lived individuals is no better than having short lived individuals, but is it at least equal? Sadly not, if fewer new individuals are born then the rate of evolution of that species is reduced. A very long lived species is less able to respond to environmental changes. As such over an evolutionary timescale an extraordinarily long lived animal is likely to be outcompeted by a shorter lived species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course there is a natural breakeven point; there is a considerable cost in bringing an individual from infant to reproductive adult so once they've got there it makes sense to keep them around for a while, but not indefinitely.&lt;/p&gt;&#xA;" OwnerUserId="6151" LastActivityDate="2014-05-03T18:34:29.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17120" PostTypeId="2" ParentId="10264" CreationDate="2014-05-03T19:07:23.233" Score="0" Body="&lt;p&gt;Your method seems overly complicated to me. Surely you have a control virus? I would recommend a constitutively expressed GFP construct to make it compatible with FACS analysis. Use the GFP virus to directly calculate viral titre by FACS, then verify your other viruses by plaque assay.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-05-03T19:07:23.233" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17121" PostTypeId="1" AcceptedAnswerId="17129" CreationDate="2014-05-03T20:37:52.067" Score="2" ViewCount="1514" Body="&lt;p&gt;I first thought this question in the case of &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the cause of dry throat after 3-day recovery of dry cough?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;but then I realised that the cause of dry cough can be a general thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume the person had three days recovery of dry cough under Montelukast and codeine (tablet).&#xA;He visited gym with little cardiotraining just after the catarrhal inflammation ended (no yellow mucose from throat during mornings anymore. &#xA;Just after the training, he felt dry throat after very weak coughs (no codeine medication when doing sport).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure if the dry throat is caused by&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;atrophy of the membranes in the throat&lt;/li&gt;&#xA;&lt;li&gt;or dry cough by Acute respiratory viral infection (possibly through reflex arch; cannot be sure this because no codeine medication).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Let's assume that the dry throat is caused by dry cough (although weak) because virus particle can pass easily the scarring of the mucose membrane in the throat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the atrophy of the membranes in the throat are NOT felt as dry.&#xA;Dry cough of the infection is felt shortly as dry.&#xA;The sympaticus activity clears the mucose membrane from the throat which alleviated the pain and also irritated the scarring.&#xA;Acute virus infection stimulates serous inflammation (as described &lt;a href=&quot;https://biology.stackexchange.com/a/16984/86&quot;&gt;here&lt;/a&gt;) which in the scarred tissue is felt once again as catarrhal inflammation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I think the cause of dry cough is &lt;strong&gt;catarrhal inflammation&lt;/strong&gt;.&#xA;The localisation of the inflammation is essential to determine the type of inflammation, I think.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the cause of dry cough?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-05-04T07:09:29.750" Title="What is the cause of dry cough?" Tags="&lt;pathophysiology&gt;&lt;lungs&gt;&lt;autonomic-nervous-system&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17122" PostTypeId="1" CreationDate="2014-05-03T21:04:07.840" Score="1" ViewCount="2459" Body="&lt;p&gt;I was thinking about how when people say: &lt;em&gt;&quot;Nerve cells don't regenerate&quot;&lt;/em&gt; (which is, &lt;a href=&quot;http://en.wikipedia.org/wiki/Neuroregeneration&quot; rel=&quot;nofollow&quot;&gt;apparently&lt;/a&gt;, not true at least for some kinds of nerves) and &lt;em&gt;&quot;You're making me nervous&quot;&lt;/em&gt; they might not refer to the same &quot;nerves&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What makes a person &quot;feel nervous&quot;? Does it have anything to do with nervous system?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bonus question: How did people come up with the thought that nerve cells don't regenerate?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2017-03-28T18:41:22.463" Title="What do nerves have to do with feeling nervous?" Tags="&lt;neuroscience&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17123" PostTypeId="2" ParentId="10422" CreationDate="2014-05-03T21:35:13.117" Score="0" Body="&lt;p&gt;If I got your question correctly, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;you were aware that humans in some way, shape or form have descended from a common ancestor shared with other primates;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You then realized the relative 'distance' of modern Homo Sapiens from these other primates;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You concluded (or know) that there have been various morphological stages in between, none of which has survived until today;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You were basically puzzled by the question why no intermittent evolutionary stages exist of say the human species. Actually, this is not a bad question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it can be explained with population growth. The modern species has just multiplied so dramatically, continuously selecting for certain features, that there was ultimately less and less room for &lt;em&gt;older&lt;/em&gt; forms which have not been able to &lt;em&gt;survive into today&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Monkeys also exist today, which means they have 'survived', but their populations are relatively smaller, and in their case, selection has not emphasized too many new features (correct me if I'm totally wrong).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think especially when selection is fueled by intelligent awareness, its evolutionary momentum increases dramatically. Our older ancestors (early hominid stages) have then simply been outnumbered by the newer ones, dwindled in numbers and simply become extinct whereas the entire monkey-, or for that matter alligator population has selected relatively more traditionally and remained more homogenous (over-simplification!) - so they're still around, too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, today there are in fact many different types of homo sapiens around with somewhat distinct features, but they're all able to reproduce interracially without much of a problem. In the last few hundred thousand years I'd say there was not enough &lt;em&gt;change&lt;/em&gt; to reproductively cut off any (isolated?) group from the main gene pool. Just our common, older ancestors were unable to catch up. This could &lt;em&gt;theoretically&lt;/em&gt; happen again in the future, maybe not on this interconnected world, but with different human space colonies. &lt;/p&gt;&#xA;" OwnerUserId="6593" LastActivityDate="2014-05-03T21:35:13.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17124" PostTypeId="2" ParentId="17100" CreationDate="2014-05-03T21:39:04.680" Score="2" Body="&lt;p&gt;I'm not sure you've got a really solid understanding of what an allele is, so let me blather a bit and see if it helps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The gene that codes for the enzyme that puts the &quot;A&quot; type of carbohydrate on a red blood cell is called the &quot;IA&quot; allele of the gene.  This gene is about 1065 base pairs long. If you were to spell it out, it would look like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CAATGGCCGGGTAATTAAAATTGACGAC... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;GTTACCGGCCCATTAATTTTAACTGCTG... (keep going to 1065 letters)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most common O allele has the same series of base pairs, except one base pair (G_C) is lost at the 261 position. This is a deletion mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most common B allele is the same gene sequence, except there are seven single base substitutions within the coding sequence at base pairs 297, 526, 657, 703, 796, 803 and 930. These are substitution mutations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does that make sense? The basic ABO blood-type gene is almost the same in each allele, but has slight changes that result in different phenotypes.  And this is the simple version. Now that we can easily sequence genes, we can look in lots of people, and see that there are at least TWENTY different gene sequences with small changes in base pairs that still result in type &quot;A&quot; blood. You can see a figure with examples in this paper: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12014997&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/12014997&lt;/a&gt; (open-source)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, since one gene has hundreds of base pairs, there are often many more than two, three or four alleles for that gene. You can add base pairs, delete them, change them, switch them in chunks from other chromosomes -- all kinds of stuff happens.&lt;/p&gt;&#xA;" OwnerUserId="6517" LastActivityDate="2014-05-03T21:39:04.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17125" PostTypeId="2" ParentId="17122" CreationDate="2014-05-04T02:15:23.940" Score="1" Body="&lt;p&gt;Yes, it's a response caused by a division of the autonomic nervous system, called the sympathetic autonomic nervous system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding nerve cell regeneration, it's not a thought it's proven. Primary neurons are not readily mitotic.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-05-04T02:15:23.940" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17126" PostTypeId="2" ParentId="17110" CreationDate="2014-05-04T02:16:13.993" Score="4" Body="&lt;p&gt;Depends on the container.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Mariana_Trench&quot; rel=&quot;nofollow&quot;&gt;The bottom of the ocean&lt;/a&gt; has three main properties that would affect the rice:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Water &lt;/li&gt;&#xA;&lt;li&gt;Salt and floating materials &lt;/li&gt;&#xA;&lt;li&gt;Pressure - at the bottom of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Mariana_Trench&quot; rel=&quot;nofollow&quot;&gt;Mariana Trench&lt;/a&gt;, the pressure is 1000x that standard atmospheric pressure at sea level.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Rice is absorbent.  Depending on the container, if it is permeable to water, then both seawater and pressure will affect the rice.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rice + Water = soggy rice with a different texture than cooked rice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rice + Brine in Seawater = soggy rice that absorbed salt and fine particulate materials from the surrounding water.  (Cooking this would probably taste just like using seawater to cook rice.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rice + Intense pressure = the water, salt, and other materials would be absorbed on its way down more quickly due to the increased pressure, and any air within the grains would be replaced with water as the grain is compressed.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not believe it would work at all like a pressure cooker does due to the cold temperature; I am fairly certain that it would be only the grainy soggy rice - cooked rice is different from dry rice because of changes to the starches by the heat when cooking (and obviously the absorption of water).  The rice itself is a starch, so the carbohydrates would not likely respond differently to the pressure in the absence of heat.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am curious if anyone might come up with anything on the chemistry of carbohydrates under pressure at near-freezing temperatures - whether any chemical bonds may be altered (like deformation of the beta-1-4 glycosidic linkage).  That's beyond my level of chemistry/physics knowledge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the duration of the journey would likely result in mush by the time it came up.  There are not many nutrients to white rice in the first place, other than the carbohydrates, so the nutrient change would be what it gains in the brine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I am missing something, please point it out.  But I believe this is the extent of the effects on the rice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your rice were in a sealed container capable of withstanding the pressure without collapse or leaking, I am fairly certain that the rice would arrive back to the surface completely unchanged.  &lt;em&gt;Humans&lt;/em&gt; are able to go down to the sea bottom in specially designed vehicles.&lt;/p&gt;&#xA;" OwnerUserId="6314" LastEditorUserId="6314" LastEditDate="2014-05-04T06:52:08.047" LastActivityDate="2014-05-04T06:52:08.047" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17127" PostTypeId="2" ParentId="17117" CreationDate="2014-05-04T02:21:41.130" Score="10" Body="&lt;p&gt;They don't eat little. Consider the volume of milk / food they consume as a ratio of their weight. Quite the contrary they are ravenous machines and their consumption is much higher than an average adult. All cellular energy comes from the hydrolysis of ATP, and the production of ATP comes from the breakdown of glucose. The glucose comes from a sugar found in breast milk, called lactose.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-05-04T02:21:41.130" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17128" PostTypeId="2" ParentId="10422" CreationDate="2014-05-04T06:32:51.540" Score="0" Body="&lt;p&gt;This is another one of those question where the premise is so crazy wrong, it's hard to answer well without writing a thousand words to explain why every sentence is wrong, wrong wrong.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why does evolution (namely the evolution of primates into humans) take&#xA;  place both uniformly and universally on the earth?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That's ridiculous.  Most of the earth doesn't have primates, and 2 million years ago, most of the ones that did exist weren't evolving into humans.  The ancestors of today's New World monkeys didn't evolve into humans.  The ancestors of today's lemurs didn't evolve into humans.       &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why aren't there any creatures who have not taken the same&#xA;  evolutionary steps as their same species elsewhere on earth?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't think this makes any sense as written.  We do observe different species sometimes evolving the same response to pretty similar environments, like cacti on different continents evolving in to similar-looking forms, despite being far apart evolutionary.  But we don't expect every population to evolve the same way, because &lt;strong&gt;evolution builds on the random changes that came before in that population&lt;/strong&gt;.  That's the basic premise of evolution, that's the premise that explains what we see very well, and if you think some other wildly different premise is in effect, and insist on forcing explanations and data to fit something that is just wrong, nothing in biology will make sense to you.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-05-04T06:32:51.540" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17129" PostTypeId="2" ParentId="17121" CreationDate="2014-05-04T07:09:29.750" Score="3" Body="&lt;p&gt;&lt;a href=&quot;https://www.google.com/search?q=asthma%20variants&amp;amp;oq=asthma%20variants&amp;amp;aqs=chrome..69i57j0l5.2591j0j7&amp;amp;sourceid=chrome&amp;amp;es_sm=122&amp;amp;ie=UTF-8&quot; rel=&quot;nofollow&quot;&gt;Cough-variant asthma&lt;/a&gt; is a common cause for a non-productive dry cough.  Asthma is not a single condition involving bronchospasm and with associated wheezing - there is a variant that is primarily or only coughing.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are different inciting factors that bring on symptoms cough-variant asthma.  Most commonly they are exercise-induced, cold-induced, allergy-induced, or quite commonly it happens following a viral respiratory infection (post-viral-URI).  Symptoms can be acute (exercise or cold) lasting minutes, or chronic lasting days-weeks or even indefinitely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pathophysiology for each is different.  The latter 2 are inflammatory processes, as you mentioned, each a little different (hypersensitivity versus residual infectious inflammation).  I am a little uncertain about the mechanisms you described, and I am not sure the correct thing to focus on is scarring.  I would focus primarily on the inflammation.  Inflamed mucous membranes are extremely sensitive, reacting to even dry or cold air.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using a long-term steroid inhaler is a preferred method of handling chronic cough-variant asthma, as it reduces airway inflammation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There can be other causes of cough such as postnasal drip, chronic rhinitis, sinusitis, or gastroesophageal reflux disease (GERD or heartburn).  &lt;/p&gt;&#xA;" OwnerUserId="6314" LastActivityDate="2014-05-04T07:09:29.750" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17130" PostTypeId="2" ParentId="17122" CreationDate="2014-05-04T07:31:05.963" Score="5" Body="&lt;p&gt;As buzrw's first comment states, most nervousness is primarily a sympathetic nervous system response.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also neurotransmitter imbalances involved with anxiety, especially in &lt;a href=&quot;http://en.wikipedia.org/wiki/Anxiety_disorder&quot; rel=&quot;nofollow&quot;&gt;anxiety disorders.&lt;/a&gt;  The NT are dopamine, serotonin, and norepinephrine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to clarify buzrw's comment on nerve cell regeneration, as I am unsure if he is stating it's proven to exist or to not exist.  &quot;Primary neurons are not readily mitotic...&quot; makes me think it's the latter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Neuroregeneration&quot; rel=&quot;nofollow&quot;&gt;Neuroregeneration &lt;em&gt;is&lt;/em&gt; proven.&lt;/a&gt; Mayo Clinic has good information &lt;a href=&quot;http://www.mayo.edu/research/centers-programs/center-regenerative-medicine/focus-areas/neuroregeneration&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and this is a well-phrased simplified answer &lt;a href=&quot;http://askabiologist.asu.edu/regeneration&quot; rel=&quot;nofollow&quot;&gt;here.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Neuroregeneration&quot; rel=&quot;nofollow&quot;&gt;It is more commonly seen in peripheral nervous system&lt;/a&gt;, as the central nervous system has limited capabilities to regenerate.  Mostly it is regrowth of severed axons of  cells, and differs between different nerve cell types.  There are other types of regeneration as well.  They involve &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23292211&quot; rel=&quot;nofollow&quot;&gt;many physiological processes we're only starting to understand,&lt;/a&gt; such as the role of &lt;a href=&quot;http://en.wikipedia.org/wiki/Neuroligin&quot; rel=&quot;nofollow&quot;&gt;neuroligin&lt;/a&gt;.  Without getting too technical, there is a lot that can be done to help stimulate and guide the regrowth of some neural damage, but there are still chasms in our knowledge in the fields of neurology and psychiatry.&lt;/p&gt;&#xA;" OwnerUserId="6314" LastEditorUserId="6314" LastEditDate="2014-05-04T07:46:46.397" LastActivityDate="2014-05-04T07:46:46.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17131" PostTypeId="2" ParentId="17117" CreationDate="2014-05-04T08:08:39.633" Score="7" Body="&lt;p&gt;Just to add to the answer from @buzrw:&lt;/p&gt;&#xA;&lt;p&gt;Using data from &lt;a href=&quot;http://www.webmd.com/diet/features/estimated-calorie-requirement&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.who.int/childgrowth/standards/wfa_boys_z_exp.txt&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; I have estimated recommended calorie intake per kg for a 2 yr old and for an adult. I've used figures for males and assumed 70 kg for the adult weight which is the &amp;quot;international standard man&amp;quot;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;toddler: 120 Cal kg&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;p&gt;adult: 40 Cal kg&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So yes, the energy intake of toddlers is higher than that of an adult.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-05-04T08:08:39.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17132" PostTypeId="1" AcceptedAnswerId="17155" CreationDate="2014-05-04T09:45:17.563" Score="0" ViewCount="62" Body="&lt;p&gt;I am not sure which project database to use UCSC or Ensembl for my asthma study about ADRB2 gene (Arg/Arg-16 genotype).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am using the original Human Genome Project database at the moment.&#xA;However, I think Ensembl may be better suited for me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which genome database is good for Asthma research for Single Nucleotide Polymorphism (SNP variations)?&lt;/strong&gt;&#xA;I am looking for something which has existing visualisation tools or one where you can easily write one yourself.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-05-05T08:36:48.237" LastActivityDate="2014-05-05T09:01:52.307" Title="Genome Project Focusing on gene ADRB2?" Tags="&lt;genomes&gt;&lt;human-genome&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17133" PostTypeId="2" ParentId="10264" CreationDate="2014-05-04T14:10:59.300" Score="0" Body="&lt;p&gt;Having gained a lot more experience with how research works, I can actually answer myself now:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) beta-actin quantity is divided by 2 because it is a human gene and hence present twice in mammalian cells, dividing it by 2 gives an estimate of the number of cells present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) The result gives an estimate of how many viral copies will end up in cells from &lt;em&gt;the amount of virus solution used&lt;/em&gt; - thus if it was 10 uL of a 1:100 dilution this represents 0.1uL of neat virus solution. So the result's unit in this case would be &quot;viral infections per 0.1uL&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c) The number of beta-actin copies doesn't correspond to the number of cells initially seeded. 400k cells which double once per roughly 24h would make 3.2m cells after 72h (3.2x10&lt;sup&gt;6&lt;/sup&gt;) so that's not all too far off the copy number.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2014-05-04T14:10:59.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17135" PostTypeId="1" CreationDate="2014-05-04T16:20:06.497" Score="1" ViewCount="174" Body="&lt;p&gt;Is there a generally accepted &quot;gold standard&quot; for testing the performance of CNV detection methods?  I'm interested both in learning about existing datasets that may serve as gold standards for CNV detection, as well in methods for producing such datasets in the first place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(In case it matters, I'm primarily interested in the evaluation of CNV detection methods in laboratory mice.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="3778" LastActivityDate="2015-02-26T11:46:00.497" Title="&quot;Gold standard&quot; for CNV detection methods?" Tags="&lt;genomics&gt;&lt;statistics&gt;&lt;copy-number-variation&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17140" PostTypeId="1" CreationDate="2014-05-04T18:58:57.257" Score="0" ViewCount="85" Body="&lt;p&gt;Dogs shed their fur twice a year, so I assume this is the same with cats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the mechanism whereby the change in temperature (assuming this is what causes the shedding) leads to the falling off of fur? Is it the same mechanism as balding?&lt;/p&gt;&#xA;" OwnerUserId="1667" LastActivityDate="2014-05-05T06:35:45.213" Title="How do cats shed their fur?" Tags="&lt;zoology&gt;&lt;hair&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17141" PostTypeId="1" CreationDate="2014-05-04T20:14:41.093" Score="4" ViewCount="6270" Body="&lt;p&gt;I would like to get the gene length information of all the human genes. Is there a quick way to get this information? Thank you!&lt;/p&gt;&#xA;" OwnerUserId="6428" LastEditorUserId="3340" LastEditDate="2014-05-05T09:29:18.237" LastActivityDate="2015-12-09T09:19:13.367" Title="How do download a list of the gene length of all genes?" Tags="&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17142" PostTypeId="1" CreationDate="2014-05-04T20:44:42.053" Score="1" ViewCount="1704" Body="&lt;p&gt;Eye-dominance is a critical thing with bows: right-eye-dominant is recommended to do the aiming on the right eye &lt;a href=&quot;https://www.youtube.com/watch/?v=aGfI8IqVVfY&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; otherwise inaccuracy. This made me think whether all people are even able to do this. I have seen people who can only close one eye or two eyes at the same time but not two eyes separately. What is the factor determining this? Is this determined by genes, learning or by something else? Is it possible that the other side of the eye muscles are missing because they have not been needed for the survival? I discussed missing muscles with my medical friends and they mentioned that there are muscles that some people do miss such as in hands because they are not essential for survival. I don't know whether certain muscles in face could be missing with some people or is this just learning thing?&lt;/p&gt;&#xA;" OwnerUserId="1705" LastEditorUserId="1705" LastEditDate="2014-05-04T20:56:22.677" LastActivityDate="2014-05-04T20:56:22.677" Title="Why only able to close one eyelid? Genetic reason?" Tags="&lt;genetics&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17144" PostTypeId="1" CreationDate="2014-05-04T22:34:56.503" Score="-3" ViewCount="872" Body="&lt;p&gt;In the popular culture, Intelligent Design is often portrayed as trying to be an alternate theory to evolution.  However, as the following question points out, it is not scientific, and so cannot be an alternative theory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/9085/what-is-the-viability-of-intelligent-design-as-a-supplement-to-chemical-abiogene&quot;&gt;What is the viability of Intelligent Design as a supplement to chemical abiogenesis and Darwinian Evolution?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, this also puts evolution in a tight spot.  Science progresses by competing theories.  Yet, there is no competing theory to evolution as a whole, only variations within the theory (e.g. Neo-Darwinism vs Punctuated Equilibrium).  So, if there are no scientific alternatives to evolution, does that make it unscientific as well?  If there are no proposed alternatives, how do we know evolution got it right?  And finally, what would a non-ID alternative to evolution look like?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Full disclosure: I am quite interested in ID, and do believe it is scientific and testable, but that is not what I am addressing with this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE: For those downvoting this question, how do you suggest I improve it?  Is it not a valid question?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To use an evolutionary analogy, without a diversity of theories our understanding of where we came from will not evolve and remain fit.  Shouldn't evolutionary theory apply to evolutionary theory itself?&lt;/p&gt;&#xA;" OwnerUserId="6607" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-05-06T03:54:16.747" Title="If not intelligent design, what is an alternative scientific theory to evolution?" Tags="&lt;evolution&gt;&lt;philosophy-of-science&gt;" AnswerCount="2" CommentCount="5" ClosedDate="2014-05-06T13:59:20.073" ContentLicense="CC BY-SA 3.0" />
  <row Id="17146" PostTypeId="2" ParentId="17144" CreationDate="2014-05-04T22:42:30.237" Score="10" Body="&lt;p&gt;Too long for a comment: You have a misconception about scientific theories: They are not competing what is wrong or right. They are set up, tested, corrected if necessary or discarded if they can not be proven. Science (or more Scientists) has no problem with rejecting a theory when no other is available. There are always things which can not be explained with the current knowledge, but this is the way this process works. And scientists have no problems admitting this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW: It is not theoretical because it is called a theory. Darwin's theory has been proven quite a number of times and works pretty well - but it has its limitations because of findings he couldn't know of, but this doesn't make it wrong. It is a bit like Newton's theory of gravity and Einstein's general theory of relativity. The first cannot explain certain phenomena that the later can, which doesn't make Newton wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other thing is, that ID is in fact no scientific theory. A theory makes a prediction, has some foundation on earlier work and can be falsified/proven. It will be corrected if it has minor loopholes and discarded if completely incorrect (For example, see Lamarck's theory of evolution, that was once discarded but is being revisited in the light of the recently discovered phenomenon of transgenerational epigenetic inheritance). &#xA;ID is built just on beliefs and is nothing but a refined form of creationism; it doesn't make predictions and can not be falsified or tested (because it is just a &lt;em&gt;belief&lt;/em&gt;). This makes it completely unscientific.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="3340" LastEditDate="2014-05-06T03:54:16.747" LastActivityDate="2014-05-06T03:54:16.747" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="17147" PostTypeId="1" AcceptedAnswerId="59089" CreationDate="2014-05-05T03:18:47.170" Score="4" ViewCount="1984" Body="&lt;p&gt;The post-apocalyptic science fiction novel &lt;a href=&quot;http://en.wikipedia.org/wiki/Dark_Universe_%28novel%29&quot; rel=&quot;nofollow&quot;&gt;Dark Universe&lt;/a&gt; by Daniel F. Galouye has some plants living inside bunkers that use infrared light for photosynthesis. There are &lt;a href=&quot;http://blog.physicsworld.com/tag/plants/&quot; rel=&quot;nofollow&quot;&gt;speculations&lt;/a&gt; that extraterrestrial plants might use the same trick on planets orbiting red dwarfs and that their leaves would be totally black. Would this type of photosynthesis be possible and are there any plants on low-light environments from Earth that might do this already?&lt;/p&gt;&#xA;" OwnerUserId="6608" LastActivityDate="2018-11-24T08:28:02.290" Title="Is infrared photosynthesis possible?" Tags="&lt;plant-physiology&gt;&lt;photosynthesis&gt;&lt;extremophiles&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17148" PostTypeId="1" CreationDate="2014-05-05T04:57:23.783" Score="4" ViewCount="1118" Body="&lt;p&gt;If we consider an analogy between a wire and a neuron there may be some resemblance between the factors controlling the data flow rate. For example the increased width of wire leads to decreased resistance etc; similarly increasing or decreasing the thickness of myelin sheath may have an effect on the conductivity or data transfer between neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there additional factors that can control the speed of nervous conduction? &lt;/p&gt;&#xA;" OwnerUserId="5008" LastEditorUserId="8495" LastEditDate="2014-08-25T14:02:28.950" LastActivityDate="2014-08-25T14:02:28.950" Title="What are the factors that control the speed of propagation of neuronal signals?" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;brain&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17149" PostTypeId="1" CreationDate="2014-05-05T05:45:44.807" Score="4" ViewCount="192" Body="&lt;p&gt;A benign tumor  has an outer layer of cancerous cells beyond which are regular cells (I Think).  The Tumor must have some kind of boundary layer like a wall where somehow the cancerous cells can't affect any more normal cells outside the &lt;em&gt;wall&lt;/em&gt;. A Benign Tumor I think can be inactive for many months; it might never grow anymore. Might it be that the cancer cells at this &lt;em&gt;Benign Tumor Wall&lt;/em&gt; are inhibited from affecting any more cells? Could there be an Apoptosis shut-off inhibitor or a cell-death pathway shutting-off inhibitor in this case? &lt;/p&gt;&#xA;" OwnerUserId="6195" LastEditorUserId="3340" LastEditDate="2014-05-05T09:46:47.127" LastActivityDate="2014-12-31T12:03:45.193" Title="How is the growth of benign tumors suppressed?" Tags="&lt;cell-biology&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17150" PostTypeId="2" ParentId="17147" CreationDate="2014-05-05T06:14:54.300" Score="3" Body="&lt;p&gt;I would hardly ever say never where biology is concerned.  In this case that utilizing red rather than blue light for a plant would require many of the basic assumptions of photosynthesis in terrestrial plants to be revised, but since we're talking about another planet, that might not really be an issue.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we are asking only about how we could change our plants to work with IR light, I'd say that might take a few hundred million years of selection and its harder to imagine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly photosynthesis in another planet doesn't have to fix carbon or produce oxygen - both of these chemical processes utilize the relatively greater energy produced in blue and red light photosynthesis we see in plants here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly using IR would have its particular questions associated with it.  In this case the energy quanta are very small and in fact in the same range as chemical bond vibrational energies.  Such energy might be hard to capture with any efficiency since simple heat would tend to compete with the photon, so this would work better if the entire system were at a relatively low temperature.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The leaves could be black or they could be completely clear by the way. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-05-05T06:14:54.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17151" PostTypeId="2" ParentId="17140" CreationDate="2014-05-05T06:35:45.213" Score="1" Body="&lt;p&gt;Basic reasons as to why cats shed fur can be found in &lt;a href=&quot;http://www.cozycatfurniture.com/cat_newsletters/catnewsletter13.html&quot; rel=&quot;nofollow&quot;&gt;this link&lt;/a&gt; and &lt;a href=&quot;http://www.aspca.org/pet-care/cat-care/shedding&quot; rel=&quot;nofollow&quot;&gt;this link&lt;/a&gt;. &#xA;An elaborate understanding of shedding in animals including cats can be obtained from &lt;a href=&quot;http://www.furminator.com/why-do-dogs-cats-and-rabbits-shed.aspx&quot; rel=&quot;nofollow&quot;&gt;this link&lt;/a&gt;. Hope that helps.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-05T06:35:45.213" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17152" PostTypeId="2" ParentId="17141" CreationDate="2014-05-05T07:40:46.183" Score="3" Body="&lt;p&gt;Some basic information like length can be obtained in the &lt;a href=&quot;http://www.gencodegenes.org/gencodeformat.html&quot; rel=&quot;nofollow&quot;&gt;GTF file&lt;/a&gt; (you can get the latest ENCODE GTF from the UCSC genome browser).&#xA;Other information are also available and obtainable from the UCSC genome browser → &lt;a href=&quot;http://genome.ucsc.edu/cgi-bin/hgTables?command=start&quot; rel=&quot;nofollow&quot;&gt;table browser&lt;/a&gt;. Select the group and tracks that you want from the corresponding dropdown boxes. You can export the data as a text file or forward it to the galaxy interface for analysis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are familiar with some programming then you can pull out the lengths (it is not explicitly given in the output or in the GTF). Also, the gene length may be different from the mRNA length because of the presence of introns in the former. The third field in the GTF file denotes the feature (gene, transcript, exon, etc); you can parse the GTF for picking up only desired features, lets say the mRNAs.&#xA;The fourth and fifth fields denote start and end positions respectively; all you have to do is &lt;code&gt;end - start&lt;/code&gt; to obtain the length. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A small scriptlet such as this would work in linux/cygwin terminal (I wont go in detail because this is not the scope of this forum):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;awk -F &quot;\t&quot; '$3==&quot;transcript&quot;{print $9, $5-$4}' file.gtf &amp;gt; output.txt&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The &lt;code&gt;$9&lt;/code&gt; refers to the ninth field which holds information about that feature including the gene name, gene id etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first link that I mentioned also shows some basic methods of extracting information from GTF.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-12-09T09:19:13.367" LastActivityDate="2015-12-09T09:19:13.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17154" PostTypeId="2" ParentId="17148" CreationDate="2014-05-05T08:57:39.153" Score="3" Body="&lt;p&gt;The myelin sheath of a neuron affects conduction of action potentials. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Things to read through at wikipedia for example are the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nodes_of_Ranvier&quot; rel=&quot;nofollow&quot; title=&quot;Nodes of Ranvier&quot;&gt;Nodes of Ranvier&lt;/a&gt;, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Saltatory_conduction&quot; rel=&quot;nofollow&quot;&gt;saltatory conduction&lt;/a&gt; and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Schwann_cell&quot; rel=&quot;nofollow&quot;&gt;Schwann cells&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There might be other features changing nervous conduction, but those are the ones I remember from my study times.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastEditorUserId="3340" LastEditDate="2014-05-05T09:13:01.553" LastActivityDate="2014-05-05T09:13:01.553" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17155" PostTypeId="2" ParentId="17132" CreationDate="2014-05-05T09:01:52.307" Score="2" Body="&lt;p&gt;If you are looking for variations in a gene, there are a few databases you an consult. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can of course use the usual genome browsers, search for your gene and then select the variations listed. For ADRB2 this looks like &lt;a href=&quot;http://www.ensembl.org/Human/Search/Results?q=adrb2;site=ensembl;facet_feature_type=;facet_species=Human&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; on Ensembl. If you plan to retrieve and compare data from different genomes/genes, I really recommend learning how to use &lt;a href=&quot;http://www.ensembl.org/biomart/&quot; rel=&quot;nofollow&quot;&gt;Biomart&lt;/a&gt;, as this is a very powerful tool.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then you can use specific databases or search engines, which only target SNP's. Examples would be: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/projects/SNP/&quot; rel=&quot;nofollow&quot;&gt;DBSnp&lt;/a&gt; and &lt;a href=&quot;http://spsmart.cesga.es/&quot; rel=&quot;nofollow&quot;&gt;SPSmart&lt;/a&gt; (which queries different databases).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-05T09:01:52.307" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17156" PostTypeId="5" CreationDate="2014-05-05T10:07:54.500" Score="0" Body="" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-05-05T10:07:54.500" LastActivityDate="2014-05-05T10:07:54.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17157" PostTypeId="4" CreationDate="2014-05-05T10:07:54.500" Score="0" Body="Acquired ImmunoDeficiency Syndrome (AIDS) is a disease caused by the Human Immunodeficiency Virus (HIV), that results in loss of CD4+ T-Lymphocyte thereby leading to a loss of immune function. " OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-05-05T10:07:54.500" LastActivityDate="2014-05-05T10:07:54.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17159" PostTypeId="1" AcceptedAnswerId="17161" CreationDate="2014-05-05T10:28:38.683" Score="9" ViewCount="23904" Body="&lt;p&gt;What is the difference between transformation and transfection? How do both of these methods work?&lt;/p&gt;&#xA;" OwnerUserId="3751" LastActivityDate="2016-05-15T18:43:57.957" Title="What is the difference between transformation and transfection?" Tags="&lt;molecular-biology&gt;&lt;transformation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17160" PostTypeId="2" ParentId="17159" CreationDate="2014-05-05T10:40:05.663" Score="2" Body="&lt;p&gt;As far as I know (and I haven't found no evidence against it) this is mostly a semantic difference. Both processes describe the addition of genetic material into cells using various techniques. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Transformation is here mostly used for bacterial work (transforming plasmids for example), while transfection is almost exclusively used for eukaryotic cells. The reason may be, that the term transformation is used in eukaryotic cells as well to describe the progresion of cells into cancer cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The techniques are not very different and there are a lot of them. Transfections often use transfection agents, which form pores in the cell membrane through which the DNA can enter the cell. This can also be done by using a short electropulse. A lot of transformations are done using &quot;chemically treated&quot; cells, where the cells are brought into a state in which they take up DNA which adheres to their outside. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Wikipedia articles on &lt;a href=&quot;http://en.wikipedia.org/wiki/Transfection&quot; rel=&quot;nofollow&quot;&gt;Transfection&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Transformation_%28genetics%29&quot; rel=&quot;nofollow&quot;&gt;Transformation&lt;/a&gt; gives you more details on the methods.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-05T10:40:05.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17161" PostTypeId="2" ParentId="17159" CreationDate="2014-05-05T10:42:33.113" Score="8" Body="&lt;p&gt;If you are interested in the history of molecular biology this is an interesting question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically transformation came to be used to describe experiments in which the phenotype of an organism was changed by the uptake of DNA, and because of the way this developed in  bacterial systems this DNA was usually a plasmid. Then it became possible to use purified phage DNA to infect cells, whereupon the 'transformed' cells produced phage particles - for obvious reasons this was called transfection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When efforts turned to getting the same techniques working with cultured animal cells many of the vectors were based on viral genomes (e.g. SV40) and these workers referred to this as transfection. At this point the distinction between the two terms became meaningless, and usage tends to be for historical reasons. Interestingly in molecular manipulations of yeast, where there are no viruses, the transfection word is rarely used.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="5754" LastEditDate="2014-05-05T17:29:25.447" LastActivityDate="2014-05-05T17:29:25.447" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17162" PostTypeId="2" ParentId="17144" CreationDate="2014-05-05T10:57:28.760" Score="4" Body="&lt;p&gt;I try to avoid getting involved in these debates, but I feel the need to point out that if you &lt;em&gt;are&lt;/em&gt; going to debate these issues you must make sure that you use terms correctly. Here is the first paragraph from the WP entry for &lt;em&gt;Evolution&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Evolution is the change in the inherited characteristics of biological populations over successive generations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;None of this is theoretical - it is observable. In my opinion the term &lt;em&gt;Theory of Evolution&lt;/em&gt; is so broad as to be meaningless. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-05T10:57:28.760" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17163" PostTypeId="1" AcceptedAnswerId="17165" CreationDate="2014-05-05T14:07:05.960" Score="0" ViewCount="44" Body="&lt;p&gt;I am reading this paragraph about RS killed-vaccine in &lt;em&gt;Encyclopedia of Virology, Third Edition (2008), vol. 3, pp. 70-77&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fFlUA.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is this data called by which you can say that the frequencies of eosinophils and neutrophils increased within airways?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think sample is first taken from throat and cultivated on some general culture (blood agar).&#xA;Then, specimen is looked under microscope.&#xA;Similarly done for the sample after vaccine.&#xA;Then, visual comparison with identifying visually eosinophils and neutrophils.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is the conclusion made based on culturing, microscopy and visual sampling by eye?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Mass spectrometry&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I am not sure anymore if this technique is useful at all.&#xA;Mass spectrometry can give different intensities and masses.&#xA;If so, the intensity of the corresponding peaks should be greater after the vaccine.&#xA;&lt;strong&gt;Can this kind of conclusion be made based on mass spectrometry?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interesting would be to know the exact spectrum of eosinophils and neutrophils after the vaccine. I think they do not increase proportionally. &#xA;The one increases more than the other.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1320" LastEditDate="2014-05-05T15:15:41.290" LastActivityDate="2014-05-05T15:15:41.290" Title="To measure frequencies of eosinophils and neutrophils in airways" Tags="&lt;mass-spectrometry&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17164" PostTypeId="2" ParentId="8649" CreationDate="2014-05-05T14:53:29.203" Score="2" Body="&lt;p&gt;Have you looked into trying the DropArray microplates? They're a new technology where you don't need to centrifuge your cells to wash them...an old colleague of mine works for the company and they're pretty cool about demoing the products/instruments for you. It's &lt;a href=&quot;http://www.curiox.com/&quot; rel=&quot;nofollow&quot;&gt;http://www.curiox.com/&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think most people that use the system are using suspension cells- because of the challenges you listed above, so may be worth a look!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good luck!&lt;/p&gt;&#xA;" OwnerUserId="6616" LastActivityDate="2014-05-05T14:53:29.203" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17165" PostTypeId="2" ParentId="17163" CreationDate="2014-05-05T15:12:30.937" Score="2" Body="&lt;p&gt;The original tests where done with blood and then:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An eosinophillc index was calculated by multiplying the percentage of&#xA;  eosinophiles found in the routine white blood count by the total white&#xA;  blood count. An index of greater than 250 was considered positive.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;See table 8 in this paper: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4305200/&quot; rel=&quot;nofollow&quot;&gt;Field evaluation of a respiratory syncytial virus vaccine and a trivalent parainfluenza virus vaccine in a pediatric population.&lt;/a&gt;&quot; So they measure the eosinophils in the periphery not in the airways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This article used histologic techniques: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4305198&quot; rel=&quot;nofollow&quot;&gt;Respiratory syncytial virus disease in infants despite prior administration of antigenic inactivated vaccine.&lt;/a&gt;&quot; Both articles are from 1969.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Newer studies used micropical techniques and FACS analysis, but these experiments were done with mice: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4305198/&quot; rel=&quot;nofollow&quot;&gt;Respiratory synctial virus infection in BALB/c mice previously immunized with formalin-inactivated virus induces enhanced pulmonary inflammatory response with a predominant Th2-like cytokine pattern.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-05T15:12:30.937" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17167" PostTypeId="2" ParentId="17141" CreationDate="2014-05-05T16:46:44.463" Score="3" Body="&lt;p&gt;I'd use Ensembl's BioMart.  It's not connecting for me right this second, but it should have that information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ensembl.org/index.html&quot; rel=&quot;nofollow&quot;&gt;http://www.ensembl.org/index.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-05-05T16:46:44.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17168" PostTypeId="1" AcceptedAnswerId="17218" CreationDate="2014-05-05T17:24:40.080" Score="3" ViewCount="149" Body="&lt;p&gt;Let $T_i$ be the time to coalesce from $n(t)=i+1$ to $n(t)=i$, where $n(t)$ is the number of sites that have not coalesced yet. In the below example the maximum $n(0)=6$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6gAIJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I understand it, many mathematical developments in coalescent theory depends on the fact that the random variables $T_i$ are independent (but not identically distributed). In other words...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$f_{T_n, T_{n-1}, …. T_3, T_2}(t_n, t_{n-1},….,t_3, t_2) = \prod_{i=2}^n f_{T_i}(t_i)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the assumptions for this equation to hold true?&lt;/strong&gt; Below are some suggestions&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;No selection&lt;/li&gt;&#xA;&lt;li&gt;Selection is not varying through time&lt;/li&gt;&#xA;&lt;li&gt;Stable population size&lt;/li&gt;&#xA;&lt;li&gt;Random mating&lt;/li&gt;&#xA;&lt;li&gt;Both sexes have the same genetic background&lt;/li&gt;&#xA;&lt;li&gt;Both sexes have the same variance in fitness&lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0974707759&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2020-08-16T16:59:30.810" Title="Coalescent theory - independence of coalescent times" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17169" PostTypeId="1" AcceptedAnswerId="17171" CreationDate="2014-05-05T20:04:12.080" Score="8" ViewCount="867" Body="&lt;p&gt;I saw a mammal that looked like a large squirrel. I haven't seen anything quite like it. Can you help me identify it?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Squirrel-like, &quot;hunched over&quot; posture.&lt;/li&gt;&#xA;&lt;li&gt;It was too large to be an eastern squirrel&amp;mdash;approximately 2.5 feet, from nose to tail.&lt;/li&gt;&#xA;&lt;li&gt;It had a fluffy tail like an eastern squirrel, not short and rat-like like a ferret.&lt;/li&gt;&#xA;&lt;li&gt;Black face with white nose, body was chestnut-brown.&lt;/li&gt;&#xA;&lt;li&gt;I saw this on the ground, not in a tree.&lt;/li&gt;&#xA;&lt;li&gt;I saw it in a pine forest in east-central Alabama.&lt;/li&gt;&#xA;&lt;li&gt;At one point, it sat up on its hind legs.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6617" LastEditorUserId="6703" LastEditDate="2014-05-22T22:16:27.260" LastActivityDate="2014-05-22T22:16:27.260" Title="What species is this mammal?" Tags="&lt;species-identification&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17170" PostTypeId="1" CreationDate="2014-05-05T20:29:40.057" Score="3" ViewCount="4953" Body="&lt;p&gt;I am trying to determine the &quot;translated&quot; meanings (not seeking the common names) of different insects, (presently some bees and wasps).  Does anyone know of a printed or internet resource that defines the various names. I have one for plants, but not for animals.  Knowing the (English) meaning of the Latin / Greek/ etc. is often very informative -- IF I can find it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can give more specifics if you want.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glen B&#xA;Olympia WA, USA&lt;/p&gt;&#xA;" OwnerUserId="6619" LastEditorUserId="16866" LastEditDate="2017-04-26T19:49:25.303" LastActivityDate="2017-04-26T19:49:25.303" Title="translation of scientific names" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;terminology&gt;&lt;nomenclature&gt;&lt;etymology&gt;" AnswerCount="2" CommentCount="3" ClosedDate="2014-05-07T09:02:06.010" ContentLicense="CC BY-SA 3.0" />
  <row Id="17171" PostTypeId="2" ParentId="17169" CreationDate="2014-05-05T20:34:47.930" Score="6" Body="&lt;p&gt;It sounds pretty much like a fox squirrel (or better: as masked face fox squirrel which are found in Alabama).&#xA;They look like this (taken from this &lt;a href=&quot;http://gardeningsoul.blogspot.de/2011/05/masked-face-fox-squirrel.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;website&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NfGSU.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There seems to be quite some variation in terms of fur color, some animals are more greyish:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/H2Exa.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taken from &lt;a href=&quot;http://www.outdooralabama.com/watchable-wildlife/what/Mammals/Rodents/fs.cfm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;, this website also contains some additional information.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-05T20:34:47.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17173" PostTypeId="2" ParentId="7087" CreationDate="2014-05-05T23:27:03.543" Score="12" Body="&lt;p&gt;I confirm rg255's answer: it is a &lt;em&gt;Picus viridis&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally we can see it is a young male (immature). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Young because the spots; picture of an adult &lt;a href=&quot;http://fabrice.henon.oiseaux.net/european.green.woodpecker.32.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; and young &lt;a href=&quot;http://vdrtol.oiseaux.net/european.green.woodpecker.2.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Male because the red spot under the cheeks, the &lt;a href=&quot;http://pat.marques.oiseaux.net/european.green.woodpecker.4.html&quot; rel=&quot;noreferrer&quot;&gt;females&lt;/a&gt; get this part only black.&lt;/p&gt;&#xA;" OwnerUserId="6561" LastEditorUserId="6561" LastEditDate="2015-10-09T21:27:30.687" LastActivityDate="2015-10-09T21:27:30.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17174" PostTypeId="2" ParentId="11250" CreationDate="2014-05-06T03:12:58.633" Score="3" Body="&lt;p&gt;Bradwell et al. report RNA viruses with the smallest genome may have particularly high mutation rates. A particular bug was shown to have about 1.4 x $10^{-4}$ substitutions per nucleotide per round of copying (high for viruses generally) and the authors suggest this is to optimize adaptibility. Correlation Between Mutation Rate and Genome Size in Riboviruses: Mutation Rate of Bacteriophage $Q \beta$, Genetics, vol.195 no. 1 243-51 (2013). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cuevas et al. report a phage with 1.0 x $10^{-6}$ mutations per base per round of copying (m/b/r), which conforms (they state) to Drake's rule of 0.003 mutations per genome per round of copying in DNA-based microorganisms. They indicate that DNA-based microorganisms range between $10^{-10}$ to $10^{-6}$ m/b/r. They state that RNA viruses vary between $10^{-6}$ and $10^{-4}$ m/b/r, consistent with the result above. Point Mutation Rate of Bacteriophage $\Phi X174,$ Genetics, vol. 183 no 2 (2009).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Drake's paper often-cited paper (one of them) is available at &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC52253/pdf/pnas01066-0270.pdf&quot; rel=&quot;nofollow&quot;&gt;this link.&lt;/a&gt; &#xA;He has a remarkable graph on p. 7163 of this paper in which based on his observation of seven microorganisms with a wide range of genome size (bp) he plots the log of the mutation rate per base pair against the log of genome size (bp). The resulting (fitted) line has a slope of roughly negative one. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In a nutshell, Drake shows that over a wide range of genome size, as the genome size climbs exponentially the mutations per base per round of copying drops exponentially. This relationship is roughly log-log linear.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In his discussion he says that the factors influencing mutation rates (in either direction) are so general that they seem to have imposed a small range of variation of mutation rate per genome in microbes that have a large range in genome size and mutation rate per base pair.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for more complex organisms, I have read very little. There is a recent review article in Nature about a report that a hypothesized inverse correlation between genome size and mutation rates in certain plants (angiosperms) is untrue. Genome size is positively correlated with genome size. Plants with the larger genomes have higher mutation rates than those with smaller than average genomes. I don't have access to this pay-walled article or the methods involved so I am quoting the abstract. Tasci, Nature Reviews Genetics 13, 148 (March 2012).     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As usual an expert in this area could correct/expand these few details I've found but it's an interesting question. Drake's paper gives a remarkable result. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the question about correlation coefficient, I think that Drake's graph suggests a strong correlation between linearized functions over a certain range. &#xA;I suppose we could attach a number to that... &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-05-06T03:30:37.760" LastActivityDate="2014-05-06T03:30:37.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17176" PostTypeId="2" ParentId="7748" CreationDate="2014-05-06T03:46:31.793" Score="4" Body="&lt;p&gt;Also, tears are an intrinsic pain response and considering the dermal-derivative nature of hair, there are loose nerve endings ensnaring the follicular area, so the sensory neurons detect pain and tears are a physical manifestation of the pain, cuing the body to avoid that stimulus again. &lt;/p&gt;&#xA;" OwnerUserId="6622" LastActivityDate="2014-05-06T03:46:31.793" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17177" PostTypeId="2" ParentId="17170" CreationDate="2014-05-06T04:36:44.880" Score="1" Body="&lt;p&gt;Glen, sometimes there are many species that have same colloquial name. For e.g. &lt;em&gt;frog&lt;/em&gt; includes hundreds of species. If you require high level of detail, you may need to look for more comprehensive lists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are zoology dictionaries such as &lt;a href=&quot;http://www.oxfordreference.com/view/10.1093/acref/9780199233410.001.0001/acref-9780199233410&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;. I think it should serve your purpose. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-05-06T04:36:44.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17178" PostTypeId="2" ParentId="11250" CreationDate="2014-05-06T04:41:19.203" Score="2" Body="&lt;p&gt;I'd clarify the above that the mutation rate is probably linear with the number of bases in the cell, since they are caused by random collision with ionizing radiation most of the time.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The number of mutations retained will vary though by organism which may reflect the trend that @daniel is describing.  Certainly larger prokaryotes will start to have more DNA and mutation repair genes when they have larger genomes, on the average.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eukaryotes, including metazoans will have more elaborate selection mechanisms such as diploid recombination and social selection to throw out mutations for many of the genes.  This may explain the additional dropoffs for even larger genomes, who tend to be eukaryotes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an example of the points above, take a look at &lt;em&gt;Deinococcus radiodurans&lt;/em&gt;, a &lt;a href=&quot;https://en.wikipedia.org/wiki/Deinococcus_radiodurans&quot; rel=&quot;nofollow&quot;&gt;prokaryote found in cans irradiated with gamma radiation as a means of sterilizing and preserving the food&lt;/a&gt;.  This bacterium can withstand a half million rad of gamma radiation - one thousand times the human lethal dose.  &lt;a href=&quot;https://en.wikipedia.org/wiki/Deinococcus_radiodurans#Ionizing_radiation_resistance_mechanisms&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;D radiodurans&lt;/em&gt; has multiple copies of its genome and several times the number of DNA repair pathways, and probably all the tricks in the book to keep its DNA intact and break/mutation resistant&lt;/a&gt;.  It would be way off the mean slope in your chart. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-05-06T04:41:19.203" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17179" PostTypeId="1" CreationDate="2014-05-06T04:41:25.547" Score="0" ViewCount="184" Body="&lt;p&gt;My internet is slow and I have only 1GB data usage allowed for this month. And I want to make maximum out of it for learning some basics of computational biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which are the best online course (freely available lectures) suggestions for me?&lt;/p&gt;&#xA;" OwnerUserId="5669" LastActivityDate="2014-06-26T10:57:48.910" Title="Can someone suggest me good opencourseware links for learning computational biology basics?" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17181" PostTypeId="2" ParentId="16961" CreationDate="2014-05-06T06:35:32.463" Score="1" Body="&lt;p&gt;only a small peptide of Osteopontin is available currently&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.rcsb.org/pdb/protein/P10451&quot; rel=&quot;nofollow&quot;&gt;http://www.rcsb.org/pdb/protein/P10451&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3150" LastActivityDate="2014-05-06T06:35:32.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17182" PostTypeId="1" AcceptedAnswerId="17236" CreationDate="2014-05-06T07:44:55.667" Score="5" ViewCount="1347" Body="&lt;p&gt;Editing a manuscript of mine, a co-author changes &quot;selection pressure&quot; to &quot;selective pressure&quot;. Are those two terms interchangeable? Or are there subtle differences that I'm not aware of?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sentence under consideration: &quot;In contrast, gene expression changes during development and tissue formation are under high selection/selective pressure.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;FWIW, &quot;selection pressure&quot; is a &lt;a href=&quot;https://books.google.com/ngrams/graph?content=selection%20pressure,selective%20pressure&amp;amp;year_start=1900&amp;amp;year_end=2000&amp;amp;corpus=15&amp;amp;smoothing=3&amp;amp;share=&amp;amp;direct_url=t1;,selection%20pressure;,c0;.t1;,selective%20pressure;,c0&quot; rel=&quot;nofollow&quot;&gt;bit more popular&lt;/a&gt; in the literature. &lt;/p&gt;&#xA;" OwnerUserId="112" LastEditorUserId="112" LastEditDate="2014-05-07T15:37:58.217" LastActivityDate="2016-08-17T08:46:42.507" Title="&quot;selective pressure&quot; or &quot;selection pressure&quot;?" Tags="&lt;evolution&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17183" PostTypeId="1" AcceptedAnswerId="17242" CreationDate="2014-05-06T08:32:14.400" Score="6" ViewCount="1780" Body="&lt;p&gt;I can get goosebumps at will, regardless of the environment. Its mostly visible on my arms, and I can feel it on my head. It requires some level of concentration to achieve this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions are : what biological mechanisms are involved in doing this ? Is it common ? Is it useful ?&lt;/p&gt;&#xA;" OwnerUserId="6624" LastActivityDate="2017-11-16T21:20:37.737" Title="Getting goosebumps at will" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17184" PostTypeId="2" ParentId="17170" CreationDate="2014-05-06T09:19:41.730" Score="1" Body="&lt;p&gt;There are multiple resources that are in use as far as I can see from a quick google search. You would find the Integrated Taxonomic Information System &lt;a href=&quot;http://www.itis.gov/&quot; rel=&quot;nofollow&quot;&gt;(ITIS)&lt;/a&gt; quite useful. It includes details on scientific papers published about a specific species. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-05-07T05:04:57.050" LastActivityDate="2014-05-07T05:04:57.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17185" PostTypeId="1" AcceptedAnswerId="20273" CreationDate="2014-05-06T11:18:54.780" Score="2" ViewCount="3682" Body="&lt;p&gt;I need to draw simple, phylogenetic tree for kids lecture.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for an online tool where I can enter organisms (e.g., human, wasp, fungus) and get figure of a phylogenetic tree. Tree should be based on how close those organisms are (I don't need genome alignments).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similar figure producing tool would be perfect. &#xA;&lt;img src=&quot;https://i.stack.imgur.com/rSi0A.jpg&quot; alt=&quot;## Heading ##&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="744" LastEditorUserId="3615" LastEditDate="2014-05-06T12:41:30.247" LastActivityDate="2019-01-31T02:09:18.910" Title="Draw simplified phylogenetic tree for kids" Tags="&lt;bioinformatics&gt;&lt;phylogenetics&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17186" PostTypeId="1" AcceptedAnswerId="17188" CreationDate="2014-05-06T11:43:37.003" Score="4" ViewCount="17606" Body="&lt;p&gt;What are the functions of disulphide bonds between amino acids in proteins or peptides?&lt;/p&gt;&#xA;" OwnerUserId="3751" LastEditorUserId="3340" LastEditDate="2014-05-06T12:28:16.823" LastActivityDate="2014-05-06T12:28:16.823" Title="What are the functions of disulphide bonds?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;amino-acids&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17187" PostTypeId="2" ParentId="17186" CreationDate="2014-05-06T11:55:48.360" Score="6" Body="&lt;p&gt;Disulphide bonds occur in proteins, not amino acids, although they involve a covalent bond between two amino acids (both cysteine).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The received wisdom is that disulphides are used as extra stabilisation of the structure of proteins which are secreted, or which have an extracellular domain. It's important to get hold of the idea that they do not occur in the cytoplasm, but are only formed in proteins which pass through the secretory pathway: they are formed in the endoplasmic reticulum (ER), and there are resident ER proteins (protein disulphide isomerases) whose function is to assist in their formation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Classical examples of disulphide-bonded proteins are insulin (where the A and B chains are linked by disulphides) and immunoglobulin G where each Ig domain has an intradomain disulphide, and where the heavy chains are linked by disulphides. There are, of course, many others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cells also contain the tripeptide glutathione which includes a cysteine residue. the ratio of oxidised (disulphide bonded dimers) to reduced (monomers) glutathione helps to set the redox state of the cytoplasm and the lumen of the endoplasmic reticulum.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-06T11:55:48.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17188" PostTypeId="2" ParentId="17186" CreationDate="2014-05-06T11:57:54.443" Score="6" Body="&lt;p&gt;Disulfide bonds form between different amino acids of a protein chain and the help to stabilize and maintain a distinct three dimensional form. In principle this looks like this (pipcture from the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Disulphide_bond&quot; rel=&quot;noreferrer&quot;&gt;Disulfide bonds&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JrFuA.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disulphide bonds (or bridges) can also hold different subunits of larger protein complexes together, one example for this would be antibodies. Here the light and the heavy chains are connected by disulfide bonds, they also play a role for maintaining the structure of the single protein chains (image from &lt;a href=&quot;http://dxline.info/diseases/antibody&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2DGzI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-06T11:57:54.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17189" PostTypeId="1" AcceptedAnswerId="17196" CreationDate="2014-05-06T12:38:45.537" Score="3" ViewCount="2326" Body="&lt;p&gt;I read in Tortora and Derrickson Anatomy and Physiology that :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Another type, called brown adipose tissue obtains its darker color&#xA;  from a very rich blood supply , along with numerous pigmented&#xA;  mitochondria that participate in aerobic cellular respiration.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Brown_adipose_tissue&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...brown adipocytes contain numerous smaller droplets and a much&#xA;  higher number of (iron-containing) mitochondria, which make it brown.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The conclusion seems to be that there should be some iron containing pigment in the mitochondria of  BAT which (along with a rich blood supply) gives brown colour to the BAT.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the brown pigment present in the mitochondria of BAT ? Is it the uncoupler protein - thermogenin ?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-05-06T16:30:03.733" Title="Why is brown fat brown?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;mitochondria&gt;&lt;tissue&gt;&lt;lipids&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17190" PostTypeId="1" CreationDate="2014-05-06T12:55:21.250" Score="2" ViewCount="1229" Body="&lt;p&gt;I am currently studying color blindness, and there is no medicine that can help it. Is it possible nonetheless for someone who is color blind to have their eyes restored to normal color vision by replacing the patient's eyes with donor eyes? Please explain any answer. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="6625" LastEditorUserId="1368" LastEditDate="2014-06-16T00:18:16.090" LastActivityDate="2018-02-26T06:24:53.707" Title="Can someone who is color blind recover color vision by surgical means?" Tags="&lt;genetics&gt;&lt;eyes&gt;&lt;health&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17191" PostTypeId="1" CreationDate="2014-05-06T14:02:39.257" Score="1" ViewCount="114" Body="&lt;p&gt;Someone claimed that the dinosaurs could only live because back then athmospheric density was around 650 kg/m³, providing some buyoncy, this claim is &lt;a href=&quot;https://skeptics.stackexchange.com/questions/19073/what-was-the-density-of-prehistoric-earth-atmosphere-dinosaurs-buoyancy-theory/20516&quot;&gt;checked on Skeptics SE&lt;/a&gt;. The claim itself is beside the point now. A simple calculation shows us that an atmsphere with this density would be &lt;a href=&quot;http://en.wikipedia.org/wiki/Supercritical_fluid&quot; rel=&quot;nofollow noreferrer&quot;&gt;supercritical&lt;/a&gt; in underwise normal conditions, the pressure would be increased by a factor of roughly 520. See my &lt;a href=&quot;https://skeptics.stackexchange.com/a/20516/16410&quot;&gt;answer to the skeptics question&lt;/a&gt; for a bit more explanation. I would say that a supercritical air atmosphere rules out life for several reasons:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The high effusity of the fluid may mean that cell membranes don't work&lt;/li&gt;&#xA;&lt;li&gt;Proteins fold differently under high pressure, requiring specific adaptions&lt;/li&gt;&#xA;&lt;li&gt;If the partial pressure of oxygen is increased proportionally, the atmosphere is highly toxic&lt;/li&gt;&#xA;&lt;li&gt;If the partial pressure of oxygen remains at current levels, it is a trace gas and reactions relying on oxygen may run into kinetic problems (There may be a sweet spot between the last two issues)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Anyway, those are just my hunches, I never heard of experiments about life in supercritical fluids and I'm no biologist so my hunches may be totally wrong. My question is: &lt;strong&gt;Can we rule out life in supercritical fluids;&lt;/strong&gt; if not &lt;strong&gt;can we rule out air breathing, multi cellular animal life?&lt;/strong&gt;&lt;br&gt;&#xA;Or has any life been shown to thrive in a supercritical fluid?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To stress again, the part with buoyant dinosaurs was given for background (and amusement), I'm only asking here to check my hunch that suprecriticality rules out life.&lt;/p&gt;&#xA;" OwnerUserId="3037" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2014-05-06T14:44:17.870" Title="Is life in a supercritical fluid possible?" Tags="&lt;biochemistry&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17192" PostTypeId="1" AcceptedAnswerId="17195" CreationDate="2014-05-06T14:17:22.240" Score="0" ViewCount="183" Body="&lt;p&gt;Here's my thought process, correct me where I'm wrong.  It seems the human body has thresholds.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples: You lift too much weight, and the muscles and tendons risk serious injury, but otherwise they tend to rebuild stronger to handle more weight.  Too much sun can lead to sunburn or worse, but moderate UVB exposure can lead to melanogenesis and increase protection to UV damage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do the lungs behave in a similar manner where a small amount of smoking might actually strengthen your lungs before reaching the threshold where you're causing severe damage?  My guess is the answer is &quot;probably/somewhat&quot; but that there haven't been any studies since it'd be difficult to analyze and quantify, but maybe somebody has an answer based on theory.  &lt;/p&gt;&#xA;" OwnerUserId="6534" LastActivityDate="2014-05-06T14:52:48.983" Title="Could light/occasional smoking strengthen the lungs?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;lungs&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17193" PostTypeId="1" AcceptedAnswerId="17201" CreationDate="2014-05-06T14:24:42.893" Score="3" ViewCount="100" Body="&lt;p&gt;I am in great need of help in order to infer the statistical hypothesis tests performed in an old paper. However I need to make some reasonable guesses only from the abstract of the paper since the original text is in chinese which i can not understand (after extensive search i was also unable to find the original text even in chinese)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The title of the paper is:&#xA;&lt;strong&gt;“Detection of sister chromatic exchange in workers exposed to coal tar pitch and to coke oven volatiles&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The abstract of the paper (which was published in 1998 is the following):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to know the changes of genetic toxicological effects on workers occupationally exposed to polycyclic aromatic hydrocarbons (PAHs), sister chromatic exchange(SCE) was detected by the methods of peripheral lymphocyte culture in 23 workers exposed to coal tar pitch (CTP) and in 19 workers exposed to coke oven volatiles (COV) and 12 normal controls. The results suggested that the SCE in occupational workers was significantly higher than that in controls (11.31 vs 6.37, P &amp;lt; 0.001). The SCE in workers exposed to CTP and to COV was higher than that of control (10.27 and 12.58 vs 6.37) respectively. In workers exposed to CTP and COV, there were no differences of SCE for smokers and nonsmokers (P &gt; 0.05). It is indicated that CTP and COV caused strong genetic toxicity and injury to chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your opinion how do you think that the above reasarch was organized&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example: a) What types of statistical hypothesis testing was performed by the reasearchers b) What kind of data was collected and used for each statistical hypothesis test c) What methods were employed for the each hypothesis test ?&lt;/p&gt;&#xA;" OwnerDisplayName="user6628" LastEditorDisplayName="user6628" LastEditDate="2014-05-06T17:02:44.613" LastActivityDate="2014-05-06T19:41:37.627" Title="Needing help in order to infer the statistical hypothesis tests performed in an old paper" Tags="&lt;bioinformatics&gt;&lt;statistics&gt;&lt;biostatistics&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17194" PostTypeId="1" CreationDate="2014-05-06T14:50:41.977" Score="1" ViewCount="44" Body="&lt;p&gt;I would like to know the initial conditions and locations of the chemical reagents in the MAPK cascasde. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm going to plug this information into a reaction diffusion simulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From reading various papers I have gleaned the following:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;[MKKK]total = 100nm; [MKK]total = 300nm; [MAPK]total = 300nm&#xA;&#xA;MKKK]total = [MKKK] + [MKKK-P]&#xA;[MKK]total = [MKK] + [MKK-P] + [MKK-PP]&#xA;[MAPK]total = [MAPK] + [MAPK-P] + [MAPK-PP]&#xA;&#xA;Ras-GTP seems to have an initial concentration of 30 nM and seems to start at the nucleus.&#xA;&#xA;ppMAPK seems to have an initial concentration of 0.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I can't figure out where the rest of the reagents start and what thier concentrations are. People always seem to miss this out from their work...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="3338" LastActivityDate="2014-05-06T14:50:41.977" Title="MAPK signalling pathway initial conditions" Tags="&lt;cell-biology&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17195" PostTypeId="2" ParentId="17192" CreationDate="2014-05-06T14:52:48.983" Score="3" Body="&lt;p&gt;From your examples only the first is really true. Exercise leads to better physical abilities (within some boundaries).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sunlight on the other hand is always potentially dangerous, depending on the dose. But the damages accumulate over the years which finally lead to the so called senile lentigos (others call them aging spots) occuring in sun exposed skin from the age of 50.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And the same is true for cigarette smoke. Here you expose yourself to a nasty cocktail of potentially harmful to cancerogenous substances (tar, polycyclic aromatic hydrocarbons, benzene, nicotine and much more). These do potential harm to your lungs depending on the dose (meaning how many cigarettes you smoke a day), but there is nothing like a harmless amount. Your lungs will eventually recover from this (tar takes the longest to be removed), but it is definitely not good.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-06T14:52:48.983" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17196" PostTypeId="2" ParentId="17189" CreationDate="2014-05-06T16:30:03.733" Score="3" Body="&lt;p&gt;Brown fat is so-called because it contains a large number of mitochondria, certainly greater than its white fat counterpart. The reason for the excess in mitochondria is to participate in thermogenesis (incidentally, brown fat is also called thermogenic adipose tissue). Nearly all mammals have brown fat (excluding pigs), especially those that hibernate. Brown fat require larger numbers of mitochondria in order for the fat to be used in beta oxidation (which is carried out directly by mitochondria), and subsequently produces heat via the electron transport chain. This also requires greater access to oxygen from the blood, and as a result, greater capillary density also darkens the appearance of the gross tissue. Mitochondria themselves are dark because of the iron content; vitamins B2, B6 and B12; as well as the pigmented flavins (FADx).&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-05-06T16:30:03.733" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17200" PostTypeId="2" ParentId="17190" CreationDate="2014-05-06T17:56:52.093" Score="1" Body="&lt;p&gt;Most forms of color blindness are caused by defects in the eyes, not the brain.  Usually the receptors in they eye that are supposed to be sensitive to one fraction of the visible spectrum don't work properly.  So yes, replacing the whole eye (I don't know if that's possible now) would in theory fix those forms of color blindness, thought it's likely that the brain would be confused getting a new kind of signal that it had never received before.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-05-06T17:56:52.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17201" PostTypeId="2" ParentId="17193" CreationDate="2014-05-06T18:02:22.513" Score="2" Body="&lt;p&gt;Someone else can probably elaborate on how &quot;peripheral lymphocyte culture&quot; works, but this is what the statistical results suggest to me:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The results suggested that the SCE in occupational workers was significantly higher than that in controls (11.31 vs 6.37, P &amp;lt; 0.001).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is a two-sample t-test. Occupational workers were pooled into one group and the mean value of SCE for those workers (11.31) was compared to controls (6.37). The null hypothesis is that the means are not different. They reject the null hypothesis. It would be nice if they included the standard errors for the means, so that you would have a sense for the amount of variation within the groups.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The SCE in workers exposed to CTP and to COV was higher than that of control (10.27 and 12.58 vs 6.37) respectively.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is likely an ANOVA with three groups (CTP, COV, and control). This test is kind of redundant with the first test, since the appropriate post-hoc test will tell you that CTP and COV are both significantly higher than control. But since they report only one P-value, then this is probably the overall F-test for the ANOVA. So all they can say with this test is &quot;at least one group is different.&quot; You don't know if, for example, CTP and COV are different from one another. It's not clear from the text that they did a posthoc test (Tukey's HSD, for example), but I doubt it.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In workers exposed to CTP and COV, there were no differences of SCE for smokers and nonsmokers (P &gt; 0.05).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Considering only the occupational groups, the sample is divided into smokers and non-smokers. There was no significant difference in mean SCE between the groups. This is a two-sample t-test like the first one. The null hypothesis is that the means are not different. They fail to reject the null hypothesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also possible (but impossible to determine from the abstract alone) that they did a single, larger multiple regression. Properly coded, they would be able to, at once, test for occupational vs. control, CTP vs. COV vs. control, and smoker vs. non-smoker. It would be pretty dicey with such a small sample, so they probably didn't take that approach.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Why do we perform t-tests?&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;The null hypothesis of a two-sample t-test is that the means of two groups are not different from one another.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;How do we know that our data follows a normal distribution? Shouldn't we perform tests in order to decide whether our data follows normal distribution and is of equal variance?&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.csic.cornell.edu/Elrod/t-test/t-test-assumptions.html&quot; rel=&quot;nofollow&quot;&gt;Assumptions of t-tests&lt;/a&gt; include normal distributions within groups and equal variance between groups. These should be checked prior to carrying out the test. We can assume that the authors did these tests, but they are very rarely reported.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;In case the criteria needed to perform a t-test are not fulfilled should we choose a non parametric equivalent?&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Non-parametric alternatives should be considered when the assumptions are not met. That being said, t-tests are pretty robust to violations of these assumptions.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Also the anova mentioned in the answer above is an N-way anova?&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;ANOVA in general is a test of equality among N groups. So you could think of a t-test as just a special kind of ANOVA on two groups (indeed, they are numerically equal).&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2014-05-06T19:41:37.627" LastActivityDate="2014-05-06T19:41:37.627" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17202" PostTypeId="1" CreationDate="2014-05-06T18:41:28.453" Score="2" ViewCount="49" Body="&lt;p&gt;In the study of supercentenarian woman &lt;a href=&quot;http://www.iflscience.com/health-and-medicine/mutations-found-115-year-old-womans-blood-could-help-unlock-secrets-aging&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, it was found that all her blood cells are formed from only two stem cells (ancestor stem cells).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How scientists can distinguish cell ancestors?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aren't all genes of one body identical?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there are somatic mutations, which are increasing while lifetime, then how they could know, that there are more ancestor stem cells in childhood? Shouldn't it be less mutations and cell lines less distinguishable? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;May be stem cells only can be counted in oldness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then how is it possible to know, that there are 20000 of stem cells at birth?&lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="948" LastEditDate="2014-05-07T14:00:16.020" LastActivityDate="2014-05-07T14:00:16.020" Title="How can stem cells be counted in body?" Tags="&lt;senescence&gt;&lt;human-genome&gt;&lt;stem-cells&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17203" PostTypeId="1" AcceptedAnswerId="17206" CreationDate="2014-05-06T18:48:07.543" Score="3" ViewCount="136" Body="&lt;p&gt;It is evident for scientists, that all cancer cells have some mutated genes. Say mutations in general.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But this evidence means necessary condition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what about sufficient conditions? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible, that mutations are necessary but insufficient for cancer?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I.e. may be other factors exist, which are probably more important? &lt;/p&gt;&#xA;" OwnerUserId="1584" LastActivityDate="2014-05-06T19:23:29.613" Title="Is it firmly established, that mutations are sufficient for cancer?" Tags="&lt;cancer&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17204" PostTypeId="1" CreationDate="2014-05-06T18:54:08.407" Score="1" ViewCount="61" Body="&lt;p&gt;Every animal born small, then grow larger and larger.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same is true for parts of the animal bodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any cases, when body or part of the body diminishes in size and mass, while staying healthy? &lt;/p&gt;&#xA;" OwnerUserId="1584" LastActivityDate="2014-05-09T21:40:08.853" Title="Is process, opposite for growth, known for mammals?" Tags="&lt;growth&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17206" PostTypeId="2" ParentId="17203" CreationDate="2014-05-06T19:23:29.613" Score="2" Body="&lt;p&gt;Acquiring mutations (more than one) are the necessary (and sufficient) steps on the way to cancer. The current opinion is that cells need &quot;multiple hits&quot; to fully transform into a cancer cell. It is also called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Knudson_hypothesis&quot; rel=&quot;nofollow&quot;&gt;Knudson hypothesis&lt;/a&gt;, the original paper is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/5279523&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example melanocytes (the pigment cells in the body) which acquire the activating BRAF V600E mutation (which is an important step in getting a melanoma cell, this mutation is found in about 70% of all melanoma) is not enough to transform the cell. Other mutations are necessary to do this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Among the things important for cells to become malignant are to escape the apoptosis mechanisms of the cells and also the immune system. Both are linked to the mutation, inactivation or epigenetic silencing of genes, so I would say genes are the key to cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For further readings these two articles should be interesting:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996413/&quot; rel=&quot;nofollow&quot;&gt;Are oncogenes sufficient to cause human cancer?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://carcin.oxfordjournals.org/content/21/3/379.long&quot; rel=&quot;nofollow&quot;&gt;Significance of multiple mutations in cancer&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-06T19:23:29.613" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17207" PostTypeId="1" AcceptedAnswerId="35153" CreationDate="2014-05-06T19:26:16.393" Score="3" ViewCount="318" Body="&lt;p&gt;I was at the park lying on the grass and its the third time I have seen them, I used to think they were parasites when I was like 7. It is the very small brown worm on the green leaf. It moves by squiggling. It comes in different colors but same size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://postimg.org/image/ea3x2nw95/&quot; rel=&quot;nofollow&quot;&gt;http://postimg.org/image/ea3x2nw95/&lt;/a&gt;&#xA;&lt;a href=&quot;http://postimg.org/image/zfawh9pr1/&quot; rel=&quot;nofollow&quot;&gt;http://postimg.org/image/zfawh9pr1/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4652" LastEditorUserId="9943" LastEditDate="2015-06-12T00:27:54.797" LastActivityDate="2015-06-12T00:27:54.797" Title="What species is this worm?" Tags="&lt;species-identification&gt;" AnswerCount="2" CommentCount="5" ClosedDate="2015-06-13T16:04:36.527" ContentLicense="CC BY-SA 3.0" />
  <row Id="17208" PostTypeId="1" CreationDate="2014-05-06T19:36:54.773" Score="4" ViewCount="1853" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Knudson_hypothesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Knudson hypothesis&lt;/a&gt;, cancer mutations accumulate in order. Statistics says, that cancer probability increases as sixth order of age, which may mean six consequential steps to cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, mutations are random in nature. There is no apparent cause, why mutations ABCDEF can't occur in reverse order, i.e. FEDCBA and any other possible orders.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If unordered, any number of required mutations should cause flat age dependency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, something is ordering these mutations, i.e. making mutation B impossible until A occurs and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cancer incidence dependency on age:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FeZRC.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The graph is not linear, which means that mutations are not independent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE 2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's regard some cancer, which requires 6 mutations. It's incidence distribution should be like shown above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now suppose we knew the distribution of all precancer stages, i.e. the distribution of people with 1, 2, 3 and so on mutations. These distributions should look similar to final distribution&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KxJKP.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now let's regard only one (first) mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is it's incidence age dependent?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations are random. They should not depend on age. If they do depend on age, then they are not random. If &quot;they&quot; are not random, then &quot;they&quot; are not mutations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or, in other words, the cause of progression is not a mutation itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isn't it true?&lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="1584" LastEditDate="2014-05-08T05:19:46.450" LastActivityDate="2018-11-19T12:56:19.720" Title="Why cancer mutations do accumulate sequentially?" Tags="&lt;cancer&gt;&lt;mutations&gt;&lt;statistics&gt;" AnswerCount="4" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17209" PostTypeId="2" ParentId="17208" CreationDate="2014-05-06T19:46:52.703" Score="3" Body="&lt;p&gt;Mutations occur indeed randomly. Most of them are either repaired or the cells go either into senescence or apoptosis and will cause no harm. Some mutations are harmless while others are among the ones which can cause cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These genes, which are often mutated in cancers are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Oncogene&quot; rel=&quot;nofollow&quot;&gt;oncogenes&lt;/a&gt; and they are either mutated (permanently activated or inactivated) or misregulated (up- or downregulated, amplified etc.) in many cancers. These are preferrably genes which are involved in the regulation of cell cycle (which is usually halted if cells acquire mutations, something that the cell has to overcome), growth, division, differentiation and also apoptosis (genes which are regulating apoptosis are very often affected).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These mutation doesn't have to occur in a certain order, they need to overcome some &quot;threshold&quot; to transform the cell. During this whole process the tanforming cell has to escape the checks of the body which eliminates these cells.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-06T19:46:52.703" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="17210" PostTypeId="1" CreationDate="2014-05-06T20:54:11.333" Score="1" ViewCount="55" Body="&lt;p&gt;I've been told some interesting facts about &lt;a href=&quot;http://en.wikipedia.org/wiki/Oenothera&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;oenothera&lt;/em&gt;&lt;/a&gt;. Apparently in this species some lineages have been through some translocations and in results to these translocations and in consequence, some chromosomes are inherited exclusively through the female function while some other chromosomes are inherited only through the male function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you please provide a summary description of how things work in this species concerning the meiosis, the haplo-diplontic life cycle and the recombination?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-05-12T18:43:31.943" LastActivityDate="2020-07-07T21:41:23.810" Title="Study case of the inheritance system of Oenothera" Tags="&lt;evolution&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;meiosis&gt;&lt;recombination&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17212" PostTypeId="2" ParentId="17204" CreationDate="2014-05-06T23:51:44.583" Score="3" Body="&lt;p&gt;In humans at least (I'm not sure about other mammals), the thymus grown until puberty and then shrinks gradually, a process called &lt;a href=&quot;http://en.wikipedia.org/wiki/Thymus#Involution&quot; rel=&quot;nofollow&quot;&gt;involution&lt;/a&gt;. I'm not sure if this meets your criteria. The thymus remains &quot;healthy,&quot; but it's function greatly diminishes over time.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2014-05-07T14:01:18.193" LastActivityDate="2014-05-07T14:01:18.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17213" PostTypeId="1" AcceptedAnswerId="17221" CreationDate="2014-05-07T00:24:08.463" Score="4" ViewCount="161" Body="&lt;p&gt;There's undoubtedly more than one way to do this, but if a DIY biologist were to attempt to detect food fraud (e.g. as done by students from &lt;a href=&quot;http://conservationmagazine.org/2008/09/impostor-fish/&quot; rel=&quot;nofollow&quot;&gt;Stanford University&lt;/a&gt; and &lt;a href=&quot;http://www.nytimes.com/2008/08/22/science/22fish.html?_r=0&quot; rel=&quot;nofollow&quot;&gt;Trinity School, Manhattan&lt;/a&gt; with respect to fish samples from markets and sushi restaurants), then what would be the minimum steps and equipment?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;(I know barely anything about molecular genetics, but have been reading about DremelFuge, OpenPCR, and Blue Transilluminator, and wondered whether they - or things like them - might get such an investigator some of the way towards the goal above; and what else would be required.)&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user6636" LastEditorUserId="5144" LastEditDate="2014-05-07T07:19:14.857" LastActivityDate="2014-05-09T03:15:23.707" Title="Detecting food fraud" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;food&gt;&lt;diy-biology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17214" PostTypeId="1" AcceptedAnswerId="17220" CreationDate="2014-05-07T01:50:45.780" Score="0" ViewCount="10283" Body="&lt;p&gt;&lt;em&gt;Back story.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Watched an episode of &lt;a href=&quot;https://en.wikipedia.org/wiki/Arctic_Air&quot; rel=&quot;nofollow&quot;&gt;Arctic Air&lt;/a&gt;, (season three episode six), where they are practicing and hoping to become a licensed search and rescue airline.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyhow; two hikers gets attacked by a grizzly bear and whilst one get killed the other manages to throw himself off a cliff and ending up with his leg pinched under a rock. He also has big lacerations on his chest from the grizzly. Finally he manages to send a distress signal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though not licensed a team travels out to asses the situation. As they find the wounded climber they start to help. First they clean the lacerations by pouring alcohol over them, and then lay some bandages on top. After a while the injured man complains he is thirsty, and they give him water.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;TLDR;/Question&lt;/em&gt;&lt;/strong&gt; If I recall correctly one should &lt;em&gt;not&lt;/em&gt; give water to a trauma patient. They can have internal bleeding and/or, as in this case big external wounds which likely has caused quite some blood loss.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Liquid will, IIRC, cause some bad effect on the re-production on blood, and might also affect existing blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I correct in this? If so; &lt;strong&gt;&lt;em&gt;what happens and why should one not give liquid to the patient?&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Guess there could be some situations where liquid is proper. E.g. patient has been laying in exposure to sun for N hours and dehydration might also cause ill effects... ? (Kidneys, blood-pressure, plasma?) But that might be a negative in any case if one suspect internal bleeding?&lt;/p&gt;&#xA;" OwnerUserId="6638" LastEditorUserId="6638" LastEditDate="2014-05-07T05:55:01.087" LastActivityDate="2014-05-07T06:29:09.410" Title="Trauma, blood loss and thirst" Tags="&lt;human-biology&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17218" PostTypeId="2" ParentId="17168" CreationDate="2014-05-07T05:43:08.187" Score="4" Body="&lt;p&gt;As long as members of a generation &amp;quot;randomly choose&amp;quot; their ancestor in the previous generation the law of independent probability (your equation) will hold.&lt;/p&gt;&#xA;&lt;p&gt;Any study of coalescent theory begins with the Wright-Fisher model. The assumptions are:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;finite diploid population of constant size N,&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;non-overlapping generations (simultaneous reproduction),&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;random mating,&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;no mutation, selection, or migration.&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;These assumptions are consistent with independent non-identically distributed waiting times. An example of an assumption under which independence no longer holds:&lt;/p&gt;&#xA;&lt;p&gt;Individual B's random choice in generation 2 of ancestor A in generation 1 reduces the probability that individual C in generation 2 will choose A. In other words, the likelihood that A will give its genes to the next generation falls off with each new recipient. Then the independence no longer holds.&lt;/p&gt;&#xA;&lt;p&gt;See, e.g., Deonier, Computational Genome Analysis (2005, Springer) at pp. 392 ff.&lt;/p&gt;&#xA;&lt;p&gt;J. Wakely's paper &lt;em&gt;Coalescent Theory: An Introduction&lt;/em&gt; (Systematic Biology, 58:1, Feb. 2009) may be one of the best overviews of this immense topic available. He mentions Kingman's 1982 mathematical proof (which I haven't gone through) of the coalescent process (Stochastic Processes and their Applications 13 (1982)--available as a free download from ScienceDirect).&lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2020-08-16T16:59:30.810" LastActivityDate="2020-08-16T16:59:30.810" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="17220" PostTypeId="2" ParentId="17214" CreationDate="2014-05-07T06:29:09.410" Score="3" Body="&lt;p&gt;After some general research there are specifically 3 arguments that I came across that people give for supporting this particular theory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) somebody seriously injured might be given an anesthesia shot by the doctor or whoever that treats him first up for relief from the pain and distress. This would lead to relaxation of the stomach muscles and the contents of your stomach can travel up to your throat and into your lungs which would be fatal. Read about &lt;a href=&quot;http://en.wikipedia.org/wiki/Pulmonary_aspiration&quot; rel=&quot;nofollow&quot;&gt;pulmonary aspiration.&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) the second case is if there is an injury to the gut or the GI tract, then providing water would be counter productive. A layman might not be able to assess the level of injury to someone just by sight. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) the third is that giving water would increase blood pressure and (sometimes) apparently dilute the scars. This could also lead to chances where sutured wounds might reopen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are no real guidelines as to how much water can be given to an injured person. Depends on the situation or how much time he has been bleeding for and the kind of environment that he is subjected to like you pointed out. Some medics have recommended sucking on citrus fruits to prevent dehydration. Also, swabbing the patient all over the body with a cold compress can provide some relief and delay dehydration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Guidelines for bleeding victims are &lt;a href=&quot;http://www.betterhealth.vic.gov.au/bhcv2/bhcarticles.nsf/pages/Bleeding&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-07T06:29:09.410" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17221" PostTypeId="2" ParentId="17213" CreationDate="2014-05-07T07:23:07.310" Score="5" Body="&lt;p&gt;There are several ways you could go about identifying species through DNA. If you want to do everything yourself, the simplest option in terms of equipment needed consists of evaluating fragment lengths observed during gel electrophoresis after amplifying specific DNA sequences using PCR.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are content with some outsourcing, you can also send DNA samples to a commercial company for sequence analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A compromise between these options in terms of information obtained, is to do study &lt;a href=&quot;http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism&quot; rel=&quot;nofollow&quot;&gt;Restriction Fragment Length Polymorphism&lt;/a&gt; (RFLP) by amplifying DNA fragments and using restriction enzymes to cut the fragments, before analyzing the fragmentation pattern using gel electrophoresis. To perform RFLP analysis, you would need to obtain restriction enzymes in addition to the chemicals mentioned below, and they can be a bit pricey.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The minimum equipment would consist of a PCR machine, one or more pipettes with matching pipette tips, a gel electrophoresis tray with power supply and a transilluminator (preferably blue-light/non-UV). A centrifuge is not strictly necessary, but can be useful for processing/filtering your DNA source. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some chemicals will also be needed: Polymerase and dNTPs for the PCR reaction (or a pre-made &quot;master mix&quot; containing both), electrophoresis-grade agarose and running buffer for the electrophoresis, along with a DNA dye specific to the type of transilluminator (Usually UV or blue light). For a blue-light transilluminator, GelGreen is a suitable DNA dye. You will also want to use a &quot;loading dye&quot; to mix in your DNA sample before applying it to the electrophoresis gel. This can either be purchased or prepared yourself by mixing sugar and food coloring in water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You need some form of heating to dissolve the agarose - a microwave oven is convenient for this, but take care to avoid over-heating, glass explosions or flash boiling. It is convenient but not strictly necessary to have some lab glassware. Preferably use a screw-top bottle to mix your agarose solution. Always leave the top off when heating bottles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photographic equipment can be also useful for documenting results of gel electrophoresis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, you will need single-stranded DNA oligomers (primers) specific to the DNA regions you want to amplify. DNA primers can be bought from a number of companies, but it varies how easy it is for non-affiliated individuals to order and make payments. &lt;a href=&quot;http://www.macrogen.com/eng/&quot; rel=&quot;nofollow&quot;&gt;Macrogen&lt;/a&gt; has been my choice: They both deliver DNA primers and perform DNA sequencing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may be interested in the following thread on the DIY Bio e-mail group: &lt;a href=&quot;https://groups.google.com/forum/#!topic/diybio/cPzfEuiZH58&quot; rel=&quot;nofollow&quot;&gt;https://groups.google.com/forum/#!topic/diybio/cPzfEuiZH58&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have collected some of the primer sequences mentioned in the thread on a page on OpenWetware: &lt;a href=&quot;http://openwetware.org/wiki/User%3aJarle_Pahr/Meat&quot; rel=&quot;nofollow&quot;&gt;http://openwetware.org/wiki/User:Jarle_Pahr/Meat&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5754" LastEditorUserId="5754" LastEditDate="2014-05-07T16:58:34.527" LastActivityDate="2014-05-07T16:58:34.527" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17223" PostTypeId="2" ParentId="6933" CreationDate="2014-05-07T08:24:56.233" Score="3" Body="&lt;p&gt;I think a strong case can be made for three nt codons existing already in the primordial genetic code, which included only eight abiotic amino acids (this is still clearly seen today in translation tables where most abiotic amino acids are defined by four or more codons). However, in this primordial genetic code, the last nt was likely meaningless (this has been reinvented in many mitochondrial genomes where a single tRNA, usually thanks to a modified U in the anticodon wobble position, recognizes up to 4 codons). Assuming the three nt codon primordial genetic code existed, we see that the reason for the three nt codon structure was not that two nt codon structure was not enough for coding everything (4^2 &gt; 9, it would have sufficed), but something else. So what could it be? My educated guess is that it has to do with the A,P,E-site structure of the ribosome not fitting into a smaller molecular configuration (i.e. you couldn't have the adjacent A,P,E-sites within the space limited by just five phosphodiester bonds (six nt, three two nt codons) vs. eight phosphodiester bonds (nine nt, three three nt codons)). So in short, my view is that the primordial ribosomal structure was the key factor to the three nt codon structure of the genetic code, it couldn't have worked with anything less and anything more would have been a waste.&lt;/p&gt;&#xA;" OwnerUserId="5784" LastEditorUserId="5784" LastEditDate="2014-05-07T09:01:28.660" LastActivityDate="2014-05-07T09:01:28.660" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17225" PostTypeId="1" CreationDate="2014-05-07T09:07:23.640" Score="4" ViewCount="7222" Body="&lt;p&gt;Are Scientists currently looking into this? &lt;/p&gt;&#xA;" OwnerUserId="6644" LastEditorUserId="5144" LastEditDate="2014-05-07T09:10:05.897" LastActivityDate="2014-10-20T09:43:43.970" Title="How do you increase eumelanin but not pheomelanin?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17226" PostTypeId="2" ParentId="17225" CreationDate="2014-05-07T09:34:12.907" Score="3" Body="&lt;p&gt;I doubt that this will be really successful, since the synthesis is rather complex and can be influenced (positively and negatively) in many ways. First, the synthesis pathways looks roughly like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9QyDk.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first step is identical for both melanin forms, it is the conversion of the amino acid tyrosine into dopaquinone by the enzyme tyrosinase. The next steps are different for each process and only one of the possibilities can happen at any given time. The decision is done by the availibility of the necessary components. When the cysteine concentration in the cell is high, the pathway goes exclusively into the direction of pheomelanin, only when the cyteine concentration is lower than 0,76µM eumelanin is made (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12950725&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18435614&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for details).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But this is not the only influence on the reaction. The availibility of dopaquinone is critical, and the activity of the tyrosinase can be influenced by the pH of the melanosome (the compartiment in which the pigment production takes place). The tyrosinase activity for people with dark skin is about 10 times higher than for people with pale skin (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15265699&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14634018&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for details). The difference here is mainly the pH, which is neutral for dark skinned people and acidic for pale.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there is of course the availibity of tyrosine (which is less of a problem, as this amino acid is not essential) and also the availibity and activity of downstream enzymes for the eumelanin production as tyrosinase-related protein 1 and dopachrome tautomerase. &lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="3340" LastEditDate="2014-10-20T09:43:43.970" LastActivityDate="2014-10-20T09:43:43.970" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17227" PostTypeId="1" AcceptedAnswerId="17228" CreationDate="2014-05-07T10:37:55.497" Score="2" ViewCount="2968" Body="&lt;p&gt;I am not a biologist. But need some genetic data. So I searched internet and reached NCBI's website. I came to know from the FAQ page that I can the complete genome data of organisms from &lt;a href=&quot;ftp://ftp.ncbi.nih.gov/genomes/&quot; rel=&quot;nofollow&quot;&gt;ftp://ftp.ncbi.nih.gov/genomes/&lt;/a&gt;. So I went to the FTP site and opened the homosapien section &lt;a href=&quot;ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/&quot; rel=&quot;nofollow&quot;&gt;ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/&lt;/a&gt;. I found folders CHR_1 to CHR_22, CHR_MT,CHR_Un, CHR_X and CHR_Y.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My doubt is this : Normally there are only 23 pair chromosomes right? 1 to 22 pairs OK. XY make another pair. Then what are MT and Un ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And the folder which I am looking is a genome of male right?&lt;/p&gt;&#xA;" OwnerUserId="5669" LastActivityDate="2014-05-07T17:47:59.287" Title="What does chromosome CHR_Un, CHR_MT in the ftp site of NCBI mean?" Tags="&lt;genetics&gt;&lt;chromosome&gt;&lt;database&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17228" PostTypeId="2" ParentId="17227" CreationDate="2014-05-07T10:51:39.000" Score="4" Body="&lt;p&gt;&lt;strong&gt;chr_MT&lt;/strong&gt;: List of variations that map to the mitochondria &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;chr_Multi.txt.gz&lt;/strong&gt;: List of variations that map to multiple chromosomes&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;chr_UN&lt;/strong&gt;: List of mapped variations that are on unplaced chromosomes&lt;/p&gt;&#xA;&#xA;&lt;p&gt;see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK174586/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for more information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the reference genome for human, as far as I know there is no discrimination for it into male/female.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1306" LastEditDate="2014-05-07T17:47:59.287" LastActivityDate="2014-05-07T17:47:59.287" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="17229" PostTypeId="1" AcceptedAnswerId="17230" CreationDate="2014-05-07T12:12:58.257" Score="2" ViewCount="152" Body="&lt;p&gt;I wonder why Rhesus conflict can happen during pregnancy and mother can make antibodies against Rh protein (I think the correct name is D protein), but it doesn't happen if mother has different ABO type than the child? &lt;/p&gt;&#xA;" OwnerUserId="3793" LastActivityDate="2014-05-07T12:28:19.343" Title="Why Rh conflict happen but no ABO conflicts?" Tags="&lt;immunology&gt;&lt;antibody&gt;&lt;red-blood-cell&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17230" PostTypeId="2" ParentId="17229" CreationDate="2014-05-07T12:28:19.343" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/ABO_blood_group_system#Disease_risks&quot;&gt;It happens&lt;/a&gt;, but it is very rare.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Anti-A&lt;/strong&gt; and &lt;strong&gt;Anti-B&lt;/strong&gt; antibodies are IgM type. They &lt;strong&gt;do no cross the placenta&lt;/strong&gt;. Sometimes IgG can be produced and lead to the hemolytic disease of the newborn.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Anti-D&lt;/strong&gt; antibodies &lt;a href=&quot;http://en.wikipedia.org/wiki/Rhesus_blood_group_system#Hemolytic_disease_of_the_newborn&quot;&gt;are IgG type&lt;/a&gt; and &lt;strong&gt;can pass through the placenta&lt;/strong&gt;. &lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-05-07T12:28:19.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17231" PostTypeId="1" CreationDate="2014-05-07T16:13:24.113" Score="2" ViewCount="947" Body="&lt;p&gt;It is possible that I am overthinking this but I have difficulties relating the neural activation to the amplitude and frequency of EEG recordings. &#xA;For example; if at the EEG location P3/P4 we observe alpha waves at 10Herts, what will that tell us about the action potentials and membrane polarisation within the population of neurons generating the wave at this frequency?&#xA;Also, high amplitude within alpha frequency may indicate attention deficits, but how is the high amplitude related to or explained in terms of electrochemical activity within a neuron?&#xA;Informed replies are very much appreciated!&#xA;Many thanks &lt;/p&gt;&#xA;" OwnerUserId="6648" LastEditorUserId="14852" LastEditDate="2016-05-31T07:04:36.223" LastActivityDate="2016-05-31T07:04:36.223" Title="Relationship between action potentials and EEG recordings" Tags="&lt;neuroscience&gt;&lt;eeg&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17232" PostTypeId="2" ParentId="17231" CreationDate="2014-05-07T17:05:34.120" Score="1" Body="&lt;p&gt;Most of the EEG waves are not directly generated by action potential, because it is too short and has a high frequency. They are generated by synaptic activity (overall propagation potential of axons).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The amplitude of this propagation potential depends on the impedance of the brain. Higher impedance means higher amplitude. Impedance is higher for low frequency signals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The amplitude is also affected by the direction of the EEG vector so parallel axons which go in the same direction should produce a higher wave in amplitude.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference:&lt;/strong&gt; Rudell AP, Fox SE. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1932547&quot; rel=&quot;nofollow&quot;&gt;The propagation potential. An axonal response with implications for scalp-recorded EEG.&lt;/a&gt; Biophys. J. 1991 Sep;60(3):556-67. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/S0006-3495%2891%2982085-9&quot; rel=&quot;nofollow&quot;&gt;10.1016/S0006-3495(91)82085-9&lt;/a&gt;. PubMed PMID: 1932547. &lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-27T15:17:52.870" LastActivityDate="2014-06-27T15:17:52.870" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17233" PostTypeId="1" CreationDate="2014-05-07T10:57:45.283" Score="8" ViewCount="94" Body="&lt;p&gt;This applies to most if not all reptiles, but I'll write about leopard geckos since that's what I know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incubation temperature of the eggs makes a big difference in the development of the gecko. Obviously excessively high or low temperatures will kill the embryo, but inside the safe temperature range there are some interesting effects. The most well-known is Temperature-Dependant Sex Determination (TDSD).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Studies have been done and it is quite well-documented that:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Incubating eggs at the mid-point of the safe range results in predominantly male offspring.&lt;/li&gt;&#xA;&lt;li&gt;Incubating eggs at the high &lt;em&gt;or&lt;/em&gt; low end of the range &lt;em&gt;both&lt;/em&gt; result in predominantly female offspring.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;According to my gecko book, there are also some interesting effects regarding males that hatch from female-biased temperatures being more sexually active but less aggressive to females than the &quot;macho&quot; males produced at male-biased temperatures, females at female-biased temperatures being the most fertile and high-temperature females being more aggressive than lower-temperature females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Incubation temperature also affects colour - specifically melanin production levels. AFAIK it's not known whether this is a direct effect of the temperature or an indirect effect from the changes in sex hormones at the different temperatures. It's probably a different enough issue to warrant a separate question, though.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Going back to TDSD, my question is: &lt;strong&gt;what theories have put forward to &lt;em&gt;explain&lt;/em&gt; this sex determination?&lt;/strong&gt; Evolutionarily speaking, how did this come about? Are males less likely to survive so they are only produced at safe temperatures? Does the optimal male:female ratio for propagating the species change in adverse conditions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I'm not looking for random guesses.&lt;/strong&gt; I'm interested in knowing if there have been any theories put forward from knowledgeable and reputable sources. &lt;/p&gt;&#xA;" OwnerUserId="10482" OwnerDisplayName="starsplusplus" LastActivityDate="2014-05-08T00:07:44.050" Title="Have there been any theories put forward as to the reasons behind Temperature-Dependant Sex Determination in reptiles?" Tags="&lt;eggs&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17234" PostTypeId="2" ParentId="17233" CreationDate="2014-05-07T18:40:19.320" Score="8" Body="&lt;p&gt;Welcome to Biology StackExchange!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Environmental sex determination is tremendously interesting. &#xA;It looks like the most common explanation is that &lt;strong&gt;temperature-dependent sex determination&lt;/strong&gt; (TSD) is the original form of sex determination, and genetic sex determination has evolved multiple times in different animal groups since then. Reptiles are a mish-mash of different mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If TSD came first, then the real question is not why did it evolve, but why is it still around. And the answer is likely because it works well enough. I couldn't find a lot of evidence that females make varying choices for next temperature, so in &quot;real life&quot; it might mostly be that plenty of males and females are always born. There is also recent evidence that genes affect when the temperature has an effect, so again, temperature alone is unlikely to drive sex ratios.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as possible advantages of TSD there is no definitive explanation that has held up to testing. It is possible that ideal female development has slightly different requirements than male development, so nest location choice by the parent may act to produce more females if the current environment supports them more than males. For instance, it has been shown that having more female offspring when temperatures are higher results in larger females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry to not have a simple answer for you. The whole idea is fascinating, along with other environmental triggers to development, like worker ant larvae becoming a winged queen if given the right nutrition, or butterflies that add &quot;eyespot&quot; pigmentation to their wings in wet years with increased predators.&lt;/p&gt;&#xA;" OwnerUserId="6517" LastActivityDate="2014-05-07T18:40:19.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17235" PostTypeId="1" AcceptedAnswerId="17241" CreationDate="2014-05-07T23:45:30.767" Score="0" ViewCount="509" Body="&lt;p&gt;This is somthing that really makes me curious. How is posible that trough a  evolution process the best posible candidate is the one that falls in love whith his progenitor?&lt;/p&gt;&#xA;" OwnerUserId="6649" LastActivityDate="2014-05-08T07:01:41.427" Title="How does Oedipus complex fit in the evolutionary theory?" Tags="&lt;human-biology&gt;&lt;evolution&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-05-08T11:51:10.903" ContentLicense="CC BY-SA 3.0" />
  <row Id="17236" PostTypeId="2" ParentId="17182" CreationDate="2014-05-07T23:49:52.920" Score="5" Body="&lt;p&gt;As far as online references are concerned, they should be equivalent (as &quot;selective&quot; becomes &quot;making a selection&quot;). The important difference in my understanding is that speaking in terms of biology, &quot;selection&quot; triggers associations with evolutionary terminology, whereas &quot;selective&quot; doesn't. Thus, as far as I am concerned, &quot;selective pressure&quot; could be referring to some machine that has a method of applying pressure to one thing but not another, whereas &quot;selection pressure&quot; immediately makes me think of factors benefitting the proliferation of one thing over another. Hence I would personally prefer &quot;selection pressure&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given the ambiguity, you probably won't be able to make all readers happy with either of the two. Thus, it might be best just to use a different phrasing as suggested e.g. by rg255 (&quot;subject to selection&quot;).&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="1590" LastEditDate="2016-08-17T08:46:42.507" LastActivityDate="2016-08-17T08:46:42.507" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17238" PostTypeId="2" ParentId="17208" CreationDate="2014-05-08T00:12:21.140" Score="2" Body="&lt;p&gt;Maybe your question is essentially semantic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You have I think misinterpreted the phrase &quot;sixth order.&quot; A sixth order* polynomial is one of the form $p = k_6 x^6 + k_5x^5+k_4x^4+k_3x^3+k_2x^2+k_1x +k_0.$ The $k_i$ are constants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The graph caption in the first link in your post [Nordling] says that cancer mortality increases as the sixth power of age. You refer to this mathematical modeling idea in your question. This has &lt;em&gt;nothing to do with the number of mutations&lt;/em&gt; or the order in which they occur. It simply means the trend can be modeled with a sixth degree polynomial. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of your graph something like $y = k\cdot x^6 + 2000$ for an appropriate value of k gives an idea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7oWm8.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Knudson's hypothesis, also known as the &quot;multiple hit hypothesis,&quot; says nothing about the order in which mutations occur.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: The word 'random' as applied to mutations (and almost everything else), while still in use, may be incorrect and I removed it from this answer.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;*The reference in the linked article uses the term &quot;power.&quot; The term &quot;order&quot; in this context is a slight abuse of language. The correct term would be &quot;degree,&quot; as in, a &quot;sixth degree polynomial.&quot; Order is related to the highest degree of a set of polynomials spanning a vector space, not the topic here. &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-05-10T22:32:08.907" LastActivityDate="2014-05-10T22:32:08.907" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17239" PostTypeId="1" AcceptedAnswerId="17240" CreationDate="2014-05-08T04:00:39.110" Score="3" ViewCount="187" Body="&lt;p&gt;I would like to explore the genome sequence of a publicly available genome sequences of a family (like mother, father, son, daughter...). If such human genome sequences are not publicly available at least any animal's family data is also OK. :)  I am not a biologist, but aims to just understand things more clearly.&lt;/p&gt;&#xA;" OwnerUserId="5669" LastActivityDate="2020-11-22T11:00:04.213" Title="Do there exist publicly available Genome sequences of a family?" Tags="&lt;genetics&gt;&lt;genomes&gt;&lt;database&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17240" PostTypeId="2" ParentId="17239" CreationDate="2014-05-08T04:38:09.600" Score="6" Body="&lt;p&gt;I know that &lt;a href=&quot;http://www.1000genomes.org/home&quot;&gt;1000 Genomes&lt;/a&gt; has sequenced Mother-Father-Child genomes from populations around the world (I think at least some of these samples were obtained from &lt;a href=&quot;http://hapmap.ncbi.nlm.nih.gov/&quot;&gt;HapMap&lt;/a&gt;) and their data is publicly available by following the links in their website.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-05-08T04:38:09.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17241" PostTypeId="2" ParentId="17235" CreationDate="2014-05-08T06:31:56.927" Score="6" Body="&lt;p&gt;It doesn't.  The Oedipus complex is one of Freud's theories to explain human behavior, not something that is endorsed by the fields of psychology or psychiatry.  Freud had a lot of interesting theories, some of which remain core concepts in psychology, and some of which have been marginalized or rejected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some professionals who feel it has merits for consideration, to one degree or another, but if you look at publications by the APA (American Psychological Association) and Psych.org (American Psychiatric Association), you won't see in their practice guidelines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;APA: &lt;a href=&quot;http://psycnet.apa.org/journals/pst/32/4/535/&quot;&gt;http://psycnet.apa.org/journals/pst/32/4/535/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia: &lt;a href=&quot;http://en.wikipedia.org/wiki/Oedipus_complex#Criticism&quot;&gt;http://en.wikipedia.org/wiki/Oedipus_complex#Criticism&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;If you're asking how &lt;em&gt;might&lt;/em&gt; it fit with evolution if it &lt;em&gt;were&lt;/em&gt; to be true, that's more of a philosophical question - which perhaps is the better angle from which to approach the question.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &quot;survival of the fittest&quot; - &quot;fittest&quot; is better described as &quot;those who most successfully reproduce and produce offspring that are also highly successful in reproducing.&quot;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reproducing with one's immediate family results frequently in severe birth defects, the opposite of &quot;fit.&quot;  Those who want to reproduce with their mother but don't, and reject all other mates, will not reproduce.  Not &quot;fit.&quot;  The only possibility similar to the oedipal complex is that males choose mates that are like their mothers.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is true is that we often marry someone similar to our parent - but it is not a result of an actual oedipal complex.  Freud &lt;em&gt;wrote&lt;/em&gt; the oedipal complex in part to try to explain this phenomenon.  But there are better explanations - we are attracted to that with which we are most familiar, to that which makes us feel comfortable, to that which makes us feel warm and fuzzy.  Our definition of beauty is largely shaped by family faces - because that is what you are surrounded with as your mind develops.  Etc etc.&lt;/p&gt;&#xA;" OwnerUserId="6314" LastEditorUserId="6314" LastEditDate="2014-05-08T07:01:41.427" LastActivityDate="2014-05-08T07:01:41.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17242" PostTypeId="2" ParentId="17183" CreationDate="2014-05-08T07:17:58.797" Score="10" Body="&lt;p&gt;Interesting!  I haven't seen anyone able to do this deliberately.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Goose bumps are caused by the tiny muscles at the base of hair follicles contracting, and the hair stands up.  The skin around it puckers.  It's mediated by the sympathetic nervous system (the &quot;fight-or-flight&quot; aspect of the system).  This is how animals' fur stands up when afraid or upset (think of a scared cat).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's called the pilomotor reflex.  It also helps them keep warm (fur insulates) - so it happens when we're cold too.  But since we have so few hairs, it's not very useful to us. It's more of a vestigial reflex than anything.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It happens for other reasons too.  See the &lt;a href=&quot;http://en.wikipedia.org/wiki/Goose_bumps#Anatomy_and_biology&quot;&gt;wikipedia article,&lt;/a&gt; it's a good place to start.  For more info, look &lt;a href=&quot;http://www.personal.psu.edu/afr3/blogs/SIOW/2011/10/what-are-goosebumps.html&quot;&gt;at this article&lt;/a&gt; or a medical textbook.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you can do it at will, you likely are in tune fairly well with your sympathetic nervous system.  That's excellent.  You may be able to make minor alterations in your pulse and blood pressure through breathing regulation - check out the concept of &lt;a href=&quot;http://en.wikipedia.org/wiki/Biofeedback&quot;&gt;biofeedback&lt;/a&gt;.  It is a way to help manage stress, keep yourself calm in terrible situations, manage anxiety or panic disorders, anger management..... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Being able to use physical self-awareness to affect physiological changes takes practice to develop as a skill.  You've got a great start!&lt;/p&gt;&#xA;" OwnerUserId="6314" LastActivityDate="2014-05-08T07:17:58.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17243" PostTypeId="2" ParentId="9716" CreationDate="2014-05-08T07:36:14.277" Score="6" Body="&lt;p&gt;The medical term is &quot;lagophthalmos&quot; if the person is unable to close their eyes at night.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several factors involved, and unless it's due to physical obstruction, lid archetecture (such as short lid length (due to surgery etc)), or facial nerve (CN VII) problems, it's not well understood.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have seen numerous people with varying degrees of this over the years.  For most of those people, it's an intermittent thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tears are essential for eye tissue health, including cleaning and avoiding infection. People complain of dry or irritated eyes mostly.  But in more extensive cases, keratitis and ulcers can occur, which are bad.  If it's frequent, tell the person to make sure they tell their eye doctor (or if they don't have one, get it checked out sometime) so that the health of their eye tissue can be evaluated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another possibility is Grave's disease - in that condition, the entire eyeball protrudes and sometimes the eyelids aren't long enough to cover them adequately.  But what you're describing is probably not Grave's disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Lagophthalmos#Nocturnal&quot;&gt;Wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.aao.org/publications/eyenet/200804/pearls.cfm&quot;&gt;American Academy of Ophthalmology&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6314" LastActivityDate="2014-05-08T07:36:14.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17244" PostTypeId="2" ParentId="10883" CreationDate="2014-05-08T07:50:06.353" Score="5" Body="&lt;p&gt;I recognize this was asked like 7 months ago, but in case you're still looking for a good resource:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I used a CD of heart sounds that is called something like &quot;Harvey Heart Sounds,&quot; which I got with the purchase of my stethoscope.  If you can find a copy of this, I found it an excellent tool when training to recognize the differences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are good heart sounds: &lt;a href=&quot;http://depts.washington.edu/physdx/heart/demo.html&quot;&gt;http://depts.washington.edu/physdx/heart/demo.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you were looking for something other than the sounds themselves, then I'm not sure if you're asking about.  There are all sorts of good ECG references, especially Dale Dubin's EKG Interpretation book.  And Kablunde was the cardio textbook I used, which I liked.&lt;/p&gt;&#xA;" OwnerUserId="6314" LastActivityDate="2014-05-08T07:50:06.353" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17245" PostTypeId="1" AcceptedAnswerId="17247" CreationDate="2014-05-08T10:32:30.380" Score="5" ViewCount="311" Body="&lt;p&gt;If a person's head was cleanly and rapidly decapitated by a sharp blade slicing through the neck, such as would happen on the guillotine, could that person remain conscious? If so for how long? Long enough to be aware of (the head) falling down and hitting the ground? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously it would be brief due to lack of blood supply, but it seems plausible that it could be a few seconds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is there some inherent neurological shock due to the severing the top of the spinal cord that would cause near instantaneous loss of conciousness?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could Marie Antoinette have seen her own severed neck from the basket below the blade?&lt;/p&gt;&#xA;" OwnerUserId="6657" LastActivityDate="2014-05-08T19:41:11.810" Title="Is it possible to be (briefly) aware you had been decapitated?" Tags="&lt;neurology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17246" PostTypeId="1" CreationDate="2014-05-08T10:54:10.077" Score="8" ViewCount="394" Body="&lt;p&gt;It is obviously very onerous to generate heat at all, although it has advantages. We don't have to lie on the sun like a crocodile to get warmer. And we avoid the freezing of our body water by out own means. But wouldn't just a little of heat be enough? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do humans go as far as 37 C? Couldn't we just have a temperature of 10 C to avoid freezing but stay at it?&lt;/p&gt;&#xA;" OwnerUserId="4419" LastActivityDate="2016-12-26T07:41:31.980" Title="Why humans have the temperature they have?" Tags="&lt;temperature&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17247" PostTypeId="2" ParentId="17245" CreationDate="2014-05-08T11:59:30.057" Score="5" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029360/&quot;&gt;this&lt;/a&gt;, in rats it takes about 17 seconds after decapitation for the EEG to become iso-electric. But there is no known correlation between EEG and consciousness. Also at 50-80 seconds after decapitation, EEG being iso-electric, a very slow, late wave appears on the EEG record.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029360/&quot;&gt;The same article&lt;/a&gt; concludes that it takes about 3-4 seconds after decapitation for the animal to lose conscience and perceive no stress and pain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, dr. Harold Hilman states in &lt;a href=&quot;http://books.google.com/books?id=pKU5MXqo4UYC&quot;&gt;&lt;em&gt;An unnatural way to die&lt;/em&gt;&lt;/a&gt; article from october 1983 issue of &lt;em&gt;New Scientist&lt;/em&gt;, page 277 that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Consciousness is probably lost within 2-3 seconds, due to a rapid fall of intracranial perfusion of blood.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-05-08T12:45:54.250" LastActivityDate="2014-05-08T12:45:54.250" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17249" PostTypeId="2" ParentId="17246" CreationDate="2014-05-08T12:03:33.430" Score="2" Body="&lt;p&gt;It's simply not possible for humans to live with an absolute body temperature below 20 C for the simple biophysical reason that it would prevent flux of protein through the Golgi and therefore biosynthetic and secretory pathways, as well as endocytosis. The lipid membranes become too &quot;stiff&quot; to correctly function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My own sense is that the nominal 37 C body temperature is a result of all of the ATP hydrolysis reactions that happen all the time. The chemical reaction is not efficient, and some of that energy is absorbed, heating the tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are various grades of hypothermia, from mild (33–35 °C) to severe (&amp;lt; 28 °C). Death from hypothermia results only from prolonged exposure, for example, being in ice-cold water results in death after 50-100 minutes. The basic mechanism is that the body dies from a combination of decreased electrical conductance of pacemaker nerves in the heart, and a slowed heart rate incompatible with sustaining life. Ultimately, hypothermic death is a dysregulation of the body's thermoregulatory mechanism, rather than an immediate biochemical problem as I've pointed out above. For a &lt;a href=&quot;http://qjmed.oxfordjournals.org/content/95/12/775.full&quot; rel=&quot;nofollow&quot;&gt;detailed review&lt;/a&gt;, there is an open access article detailing hypothermic etiology and pathophysiology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://qjmed.oxfordjournals.org/content/95/12/775.full&quot; rel=&quot;nofollow&quot;&gt;M.L. Mallet. Pathophysiology of accidental hypothermia. QJM (2002) 95 (12): 775-785.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2014-05-08T15:17:50.920" LastActivityDate="2014-05-08T15:17:50.920" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17250" PostTypeId="1" CreationDate="2014-05-08T13:48:10.493" Score="3" ViewCount="883" Body="&lt;p&gt;Hi could anyone explain the biological basis behind romantic love. What is the biological basis of falling in love?I know that serotonin and dopamine are secreted when we first fall in love. What happens after that as we move on to the more advanced stages of love. Why is it that after some time, we no longer feel the initial feelings of love. What is the biological basis behind it. And also why do we feel so heartbroken if we happen to fall out of love? What is the biological basis behind it?&lt;/p&gt;&#xA;" OwnerUserId="6659" LastActivityDate="2016-09-16T02:59:07.107" Title="Biology in romantic love" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17251" PostTypeId="2" ParentId="17250" CreationDate="2014-05-08T14:19:53.170" Score="7" Body="&lt;p&gt;&lt;a href=&quot;http://www.asdn.net/asdn/chemistry/chemistry_of_love.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dopamine, norepinephrine, and serotonin&lt;/a&gt; are more commonly found during the &lt;strong&gt;attraction&lt;/strong&gt; phase of a relationship.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All these chemicals stimulate the brain's pleasure center. But this stage only lasts 1.5 - 3 years &lt;sup&gt;[2]&lt;/sup&gt;. That's why &lt;em&gt;'we no longer feel the initial feelings of love'&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oxytocin and vasopressin seemed to be more closely linked to long term bonding and relationships characterized by strong &lt;strong&gt;attachments&lt;/strong&gt; &lt;sup&gt;[1]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Attachment makes relationships last for years and decades. It is based on commitment and mutual friendship. Oxytocin and vasopressin are at higher levels &lt;sup&gt;[2]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The neurological process involved in the perception of &lt;strong&gt;heartache&lt;/strong&gt; is not known, but is thought to involve the anterior cingulate cortex of the brain, which during stress may overstimulate the vagus nerve causing pain, nausea or muscle tightness in the chest &lt;sup&gt;[3]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CqlfV.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;Image from Wikipedia &lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Biological basis of love,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Biological_basis_of_love&amp;amp;oldid=613867553&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Biological_basis_of_love&amp;amp;oldid=613867553&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Love,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Love&amp;amp;oldid=614240299&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Love&amp;amp;oldid=614240299&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Broken heart,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Broken_heart&amp;amp;oldid=613979584&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Broken_heart&amp;amp;oldid=613979584&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-26T17:41:18.927" LastActivityDate="2014-06-26T17:41:18.927" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17252" PostTypeId="2" ParentId="16921" CreationDate="2014-05-08T14:47:48.437" Score="1" Body="&lt;p&gt;First of all, I find this an interesting question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Clustering coefficience is widely used&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It is widely accepted that hub genes are more essential than poorly connected genes&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;but research is not always interested in the hub genes / proteins / molecules (for example most metabolic pathways involve water)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Answering your question, why people would want to use this kind of method:&#xA;If you would take a random model (pathway) most of the lines will be equally distributed between the nodes. This is not the case for most biological networks. Because of this, the global clustering coeffiecence can be used to see if a network could be biological. Clustering coeffiecence can also be used to find out about more specific nodes. For example if a protein has a relationship with two other proteins (binding, regulation, etc.), the two other proteins are also more likely to have a relationship with each other (similar to a social network).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Clustering_coefficient&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Clustering_coefficient&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biomedcentral.com/1752-0509/6/34&quot; rel=&quot;nofollow&quot;&gt;http://www.biomedcentral.com/1752-0509/6/34&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/99/12/7821.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/99/12/7821.full.pdf+html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5699" LastActivityDate="2014-05-08T14:47:48.437" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17253" PostTypeId="1" CreationDate="2014-05-08T15:27:19.683" Score="10" ViewCount="30833" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Premature_ejaculation&quot;&gt;Wikipedia&lt;/a&gt; is saying:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Men's typical ejaculatory latency is approximately 4–8 minutes&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;How the researchers measured this? How did they know if the test subjects weren't suffering from premature ejaculation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And is this measured from the start of erection or from the start of penetration?&lt;/p&gt;&#xA;" OwnerUserId="6660" LastEditorUserId="1368" LastEditDate="2014-06-08T06:46:47.827" LastActivityDate="2015-11-04T04:37:14.437" Title="What is the normal duration of human sexual intercourse?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17255" PostTypeId="1" AcceptedAnswerId="17256" CreationDate="2014-05-08T16:15:45.993" Score="9" ViewCount="3935" Body="&lt;p&gt;I have a plant on my desk, and it got me to wondering: Can my plant use the light from my monitors to photosynthesize? If so, what light (apart from green light, to a degree) can't plants use to perform photosynthesis? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that plants have the photosynthetic pigments to absorb many different wavelengths of light (primarily red and blue) but would there be certain types of light it can't use?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(The specific plant by the way is &lt;em&gt;Schlumbergera truncata&lt;/em&gt;)&lt;/p&gt;&#xA;" OwnerUserId="6330" LastActivityDate="2018-01-10T08:10:46.827" Title="What types of light can't a plant photosynthesize in?" Tags="&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17256" PostTypeId="2" ParentId="17255" CreationDate="2014-05-08T16:22:22.383" Score="9" Body="&lt;p&gt;Chlorophyll can use a quite broad range of light for photosynthesis, the only range where it is not working is approximately between 500 and 620nm. See this adsorption spectrum of chlorophyll (from the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Chlorophyll&quot; rel=&quot;noreferrer&quot;&gt;Chlorophyll&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WAZfw.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lack of chlorophyll to absorb light between 500 and 620nm (roughly) results in the green color of leafs, because this light is reflected.&#xA;Besides the wavelength also the energy of the light is important, so plants will grow better in sunlight than in the light of your monitor. This &lt;a href=&quot;http://scienceline.ucsb.edu/getkey.php?key=1668&quot; rel=&quot;noreferrer&quot;&gt;link&lt;/a&gt; about the maximum effectiveness of photosynthesis is also interesting.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-05-08T16:40:59.903" LastActivityDate="2014-05-08T16:40:59.903" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17258" PostTypeId="2" ParentId="13615" CreationDate="2014-05-08T17:05:51.153" Score="3" Body="&lt;p&gt;Chandra's Textbook of Dental and Oral Histology and Embryology with MCQs p40-42 explains the complexity of enamel, and provides diagrams and images of real enamel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I didn't know before was that the hydroxyapatite is in the form of very small crystallites packed inside the key-like structure of the rods. The rods are packed together with a cement-like material. The rods themselves are segmented.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This small design and lack of vital parts suggest to me that bioglasses like Novamin would at least not recreate the natural enamel structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What isn't so easy to guess is whether crystallites from the components of the bioglass are formed on the existing crystallites, and if so, whether this can continue indefinitely, and with what qualities.&lt;/p&gt;&#xA;" OwnerUserId="4983" LastActivityDate="2014-05-08T17:05:51.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17260" PostTypeId="2" ParentId="17253" CreationDate="2014-05-08T18:20:01.350" Score="14" Body="&lt;p&gt;First, &quot;premature ejaculation&quot; is a matter of definition. Here is an authoritative source. From the American Urological Association's news site, a 2008 notice:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;'The ISSM [Int'l Soc. for Sexual Med.] has defined premature ejaculation as “a male sexual dysfunction characterized by ejaculation which always or nearly always occurs prior to or within about one minute of vaginal penetration; and, inability to delay ejaculation on all or nearly all vaginal penetrations; and, negative personal consequences, such as distress, bother, frustration and/or the avoidance of sexual intimacy.”'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main author of the ISSM paper was Sharlip. Sharlip ID, Hellstrom WJG, Broderick GA: The ISSM definition of premature ejaculation: a contemporary, evidence-based definition. J Urol, suppl., 2008; 179: 340, abstract 988.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is the threshold for PE then it is not a stretch to say that almost anything else is within normal limits. If &quot;typical latency is 4-8 minutes&quot; then 1.5 minutes would be near the low extreme of normal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the issue of stress is at least as important as duration. If something isn't bothersome it never becomes a medical issue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A nice study involving 491 men is reviewed &lt;a href=&quot;http://www.medicine.ox.ac.uk/bandolier/band137/b137-4.html&quot;&gt;here&lt;/a&gt;. The mean IELT (intravaginal ejaculatory latency time) is 5.4 minutes. As you can see from the graph on the site, most of the results are contained in the first few minutes with a tail of longer times to the right. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The original source for that information is MC Waldinger et al. A multinational population survey on intravaginal ejaculation latency time. Journal of Sexual Medicine 2005 2: 492-497. This also addresses your question about the timing of measurement--it's post-entry. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An expert in this area could update my information but it's a recent average so I don't think things have changed much.&lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2014-05-08T18:20:01.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17262" PostTypeId="2" ParentId="17208" CreationDate="2014-05-08T19:31:42.280" Score="5" Body="&lt;p&gt;&lt;strong&gt;TL;DR:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;A sixth order probability curve of cancer does not mean six steps. The order of the curve has nothing to do with the number or sequence of mutations.&lt;/li&gt;&#xA;&lt;li&gt;Causes why ABCD could be more likely than DABC exist and have been extensively studied&lt;/li&gt;&#xA;&lt;li&gt;Repair and control (&quot;defence&quot;) mechanisms are what does the 'ordering' of steps by selecting for mutations which can circumvent them&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The sigmoidal shape of the curve thus reflects the slow accumulation of &quot;defence&quot;-damaging mutations, which increase their own probability and thus the slope of the curve. I don't know if the slight decrease in slope towards the end reflects a real limit to the incidence of cancers, or if it's an issue related to the data, its availability or the way it is gathered (but has no basis in substance i.e. there isn't actually a limit).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;To elaborate:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many biological factors which play into helping you understand the problem you are wondering about, and the fact that different cancers work differently does not make it easier. I would &lt;em&gt;highly&lt;/em&gt; recommend that you check out &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Hallmarks_of_Cancer&quot; rel=&quot;nofollow&quot; title=&quot;Hallmarks of Cancer&quot;&gt;Hallmarks of Cancer&lt;/a&gt;, the Wikipedia article also cites the interesting original publication. Basically, certain principles underly all cancers, but different cancers have different tendencies to develop certain hallmarks in a particular order.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Randomness of mutations:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations are not random. The nature of DNA sequences affects their susceptibility to DNA &lt;em&gt;lesions&lt;/em&gt;, i.e. damage caused by chemical processes such as a nucleotide losing its base, dimerisation of thymidine, single or double strand breaks and so on. Lesions occur all the time, so there are mechanisms in place to fix all types of DNA lesions. Occasionally however, the circumstances will permit e.g. two lesions to coincide or the repair process itself to make an error, which then leads to a permanent change of the DNA sequence that cannot be fixed anymore because the original sequence has been lost. This is a &lt;em&gt;mutation&lt;/em&gt;, and mutations are also not random because the nature of DNA sequences affects the chancefor them to incur lesions that cannot be repaired.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, one reason why certain mutations occur more frequently than others is because they are actually more likely to occur. But this isn't the main reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cell self-control&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are higher levels of control than DNA repair. Various mechanisms in the cell exist to detect malfunctioning proteins (due to mutations in their gene) and degrade them - though sometimes malfunctioning proteins can still escape these mechanisms. Even in this case, there is an additional safety layer created by various mechanisms which lead a cell to kill itself (apoptosis). These are triggered for example if excessive DNA damage is detected, or if the cell-internal signals for and against proliferation are conflicting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sequential accumulation of mutations&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The result of repair and control mechanisms (which I will now call &quot;defence mechanisms&quot;) is on the one hand that we are far more resistant to mutations than we would be without them. On the other hand however, they create &lt;strong&gt;selection for mutations which are not affected&lt;/strong&gt; by them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is where multi-hit models of cancer come from. A &quot;first hit&quot;, &quot;enabling mutation&quot; or whatever you want to call it would be a mutation which itself is not affected by defence mechanisms - and simultaneously impairs the defence against other mutation(s). The &quot;second hit&quot;, &quot;initiating mutation&quot;,... would be a mutation which causes cancerous cell behaviour, but would be eliminated by a defence mechanism without the first hit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that mutations do not always occur in the same sequence but rather, they occur in all sequences and sequences other than those that we find in cancer cells are eliminated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that not all cancers have several mutations or a sequence. For example, chronic myeloid leukaemia (CML, a blood cancer) in the vast majority of cases is caused by a translocation from chromosome 19 to chromosome 22 which results in the famous Philadelphia chromosome and produces the BCR-ABL fusion gene. This single mutation is sufficient to cause CML.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Age-dependency of mutations:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations can affect all parts of a cell's machinery, including the lesion repair mechanisms. This means that throughout its life time, a cell can (and will) accumulate mutations which increase the likelihood of further mutations. Mature cells usually have short life spans and mutations to their DNA repair machinery die with them relatively soon (days or weeks). However, pluripotent stem cells (PSC) in the tissues are just as likely to develop these mutations as mature cells - and PSCs are the ones which renew the tissue throughout life by differentiating into mature cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, a mutation in a PSC remains for life, and the longer you live, the higher the chance that one mutation will affect the chance for gaining further mutations. This is why for all cancer types, the risk to develop them increases with age (though there are a few which are most likely at young age!)&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2014-05-08T20:55:26.717" LastActivityDate="2014-05-08T20:55:26.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17263" PostTypeId="2" ParentId="17245" CreationDate="2014-05-08T19:41:11.810" Score="0" Body="&lt;p&gt;I remember reading that during the French Revolution Antoine Lavoisier arranged with his assistant condemned to death to blink after the cut off if he still had conscience (Lavoisier was to call his name first to limit automatisms). He reported a possibility that the assistant did hear him (the blinking was apparently not that obvious) &lt;/p&gt;&#xA;" OwnerUserId="4016" LastActivityDate="2014-05-08T19:41:11.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17264" PostTypeId="1" AcceptedAnswerId="17287" CreationDate="2014-05-08T23:28:06.703" Score="3" ViewCount="985" Body="&lt;p&gt;I couldn't seem to find one elsewhere, at least not with a scientific source.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would seem as it's quite a striking feature there would be an advantage it would infer.&lt;/p&gt;&#xA;" OwnerUserId="1763" LastActivityDate="2014-05-14T11:10:46.920" Title="Is there an evolutionary explanation for the black spots around a pandas eyes?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17265" PostTypeId="1" AcceptedAnswerId="17285" CreationDate="2014-05-08T23:51:48.357" Score="7" ViewCount="2286" Body="&lt;p&gt;Let first state that I understand natural selection. I am not asking if evolution happened. I see evolution as a fact, but I do not assume the &lt;strong&gt;current&lt;/strong&gt; theory of natural selection as fact.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder if there has been enough &quot;time&quot;, or number of generations, needed to create enough mutations that lead to the known genetic complexity of all species today (or even just until dinosaurs), since the Last Universal Ancestor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to prove, or estimate this time?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: There was obviously enough time for evolution to occur. My question is if, the known mechanisms of mutation and theory of natural selection, are enough to justify the evolution in this amount of time.&lt;/p&gt;&#xA;" OwnerUserId="6665" LastActivityDate="2017-05-15T02:24:04.373" Title="Has it been enough time for evolution through simple natural selection?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17266" PostTypeId="1" CreationDate="2014-05-09T02:57:59.817" Score="5" ViewCount="447" Body="&lt;p&gt;The main cause for diabetes is lack of insulin in the body. Insulin is the hormone that allows body cells to absorb glucose from the blood. With out insulin, the body cells can't get glucose from the blood. So, why doesn't diabetes cause death by starvation?&lt;/p&gt;&#xA;" OwnerUserId="1003" LastEditorUserId="1003" LastEditDate="2014-05-09T03:23:44.257" LastActivityDate="2016-10-19T06:58:58.743" Title="Why doesn't Diabetes cause death by starvation?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;pathology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17267" PostTypeId="2" ParentId="17213" CreationDate="2014-05-09T03:15:23.707" Score="1" Body="&lt;p&gt;This can in principle be done at least partly with DIY methods, by using PCR followed by gel electrophoresis. The DremelFuge, OpenPCR, and Blue Transilluminator would be the primary tools, along with pipettes, test tubes, autoclave (or equivalent), etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a clear video demonstration of using PCR to amplify DNA from various samples, as well as a PDF containing the details of the protocol used, see &lt;a href=&quot;http://www.dnabarcoding101.org/&quot; rel=&quot;nofollow&quot;&gt;www.dnabarcoding101.org&lt;/a&gt;. That procedure would be followed by using gel electrophoresis on a small portion of the amplified product, to check that the product appears to be of &lt;a href=&quot;http://www.biotechlearn.org.nz/themes/dna_lab/video_clips/using_gel_electrophoresis_to_check_a_pcr_reaction_v0036&quot; rel=&quot;nofollow&quot;&gt;adequate quality for sequencing&lt;/a&gt;. If so, then the remaining portion of the product can be sent to a lab for sequencing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, by using a suitable primer for each species one wishes to test for, one could check for the presence of that species using &lt;a href=&quot;http://journals.tubitak.gov.tr/veterinary/issues/vet-07-31-3/vet-31-3-3-0601-30.pdf&quot; rel=&quot;nofollow&quot;&gt;PCR and gel electrophoresis alone&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerDisplayName="user6636" LastActivityDate="2014-05-09T03:15:23.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17271" PostTypeId="1" CreationDate="2014-05-09T06:50:57.473" Score="2" ViewCount="3331" Body="&lt;p&gt;Human blood groups are of 4 types with negative and positive of each types &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood_type&quot; rel=&quot;nofollow&quot;&gt;(Wikipedia)&lt;/a&gt;. But according to &lt;a href=&quot;http://wordpress.org/support/topic/plugin-for-blood-donor-data-bank&quot; rel=&quot;nofollow&quot;&gt;this forum thread&lt;/a&gt; there are some other types too:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A+,A-,B+,B-,O+,O-,AB+,AB-,A1+,A1-,A2+,A2-,A1B+,A1B-,A2B+,A2B-&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm going to make software for blood donation, where I need to put a dropdown list of actual blood types. I had intended to use:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&#xA;[ Select Blood Group V ]&#xA;[ O Negative           ]&#xA;[ O Positive           ]&#xA;[ A Negative           ]&#xA;[ A Positive           ]&#xA;[ B Negative           ]&#xA;[ B Positive           ]&#xA;[ AB Negative          ]&#xA;[ AB Positive          ]&#xA;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;But now I am uncertain whether this is appropriate. What is the most suitable list of blood types for donors?&lt;/p&gt;&#xA;" OwnerUserId="6669" LastEditorUserId="22057" LastEditDate="2016-08-20T13:49:02.963" LastActivityDate="2016-08-20T13:49:02.963" Title="What are the blood groups for human beings?" Tags="&lt;hematology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17272" PostTypeId="1" CreationDate="2014-05-09T06:54:38.280" Score="0" ViewCount="84" Body="&lt;p&gt;What is in compound &quot;Brazzein&quot; that it makes it 2000 times more sweeter than sugar?&#xA;Can anyone please explain the science behind it? &lt;/p&gt;&#xA;" OwnerUserId="6671" LastActivityDate="2014-05-09T17:02:10.963" Title="Curious about Brazzein" Tags="&lt;proteins&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17273" PostTypeId="1" AcceptedAnswerId="17274" CreationDate="2014-05-09T08:38:51.597" Score="5" ViewCount="360" Body="&lt;p&gt;Reading Okasha's &quot;Evolution and the levels of selection&quot; he talks about &quot;the levels of selection problem.&quot; There is a bit of a problem with this opening chapter because, while he talks about why the levels of selection problem is a problem, he doesn't define what the levels of selection problem &lt;em&gt;is&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The opening line from the book.. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The levels of selection problem is one of the most fundamental in&#xA;  evolutionary biology, for it arises directly from the underlying logic&#xA;  of Darwinism. The problem can be seen as the upshot of three&#xA;  factors...&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think what he means by the &quot;levels of selection problem&quot; is that selection acts on many levels, and what is adaptive at one level may be maladaptive at another. Therefore we can not define selection as acting at one single level, and studying it as such is likely to lead to incorrect conclusions - studying selection is not a simple process. &lt;strong&gt;Can anyone provide a firm definition of what Okasha, and the general community on the matter, mean by the &quot;levels of selection problem&quot;?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Note: The factors are the abstract nature of the principles of selection, the hierarchical nature of biological organisation, and the process of adaptation via natural selection).&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-05-10T13:55:59.100" Title="Evolution and the levels of selection" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;philosophy-of-science&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17274" PostTypeId="2" ParentId="17273" CreationDate="2014-05-09T10:05:16.593" Score="4" Body="&lt;p&gt;Reeve and Keller in the &lt;a href=&quot;http://press.princeton.edu/chapters/s6703.html&quot; rel=&quot;nofollow&quot;&gt;first chapter&lt;/a&gt; of &lt;em&gt;Levels of Selection in Evolution&lt;/em&gt; (Princeton Univ. Press,1999) seem to address this question in the second item in the following paragraph. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The purpose of this volume is to sample current theoretical and empirical research on (1) how natural selection among lower-level biological units (e.g., organisms) creates higher-level units (e.g., societies), and (2) given that multiple levels exist, &lt;strong&gt;how natural selection at one biological level affects selection at lower or higher levels&lt;/strong&gt; [boldface added]. These two problems together constitute what Leigh (chap. 2) calls the &quot;fundamental problem of ethology.&quot; Indeed, as Leigh further suggests, they could be viewed jointly as the &quot;fundamental problem of biology,&quot; when genes and organisms are also included as adjacent levels in the biological hierarchy. This generalization has the desirable property of immediately removing the long-standing conceptual chasm between organismal and molecular biologists.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors suggest definitions of fitness that account for hierarchical relationships (the level of selection problem) by considering the effect of a trait (nepotism among social insects) on &quot;adjacent&quot; biological levels, such as individual and colony. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By measuring what they call 'absolute fitness force' they propose to eclipse what they see as spurious debate over the fundamental level of selection (genes vs. individuals, say). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A somewhat surprising aspect of their discussion emerges here: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;It is still embarrassingly common to read inaccurate statements...that frogs have to produce many eggs to ensure the survival of the species because tadpoles suffer extremely high rates of predation, or that wolves have evolved ritualized displays to establish dominance hierarchies because physical combats would be too disadvantageous for the species. These naive statements betray a widespread and persistent misunderstanding of the level at which natural selection most commonly operates.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their point is that such statements focus on the wrong level of selection (group), and that stronger selection may occur at the individual level; their overall argument being that both levels should be factored in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I cannot present this as a 'community definition' but it may be a representative example.   &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-05-10T13:55:59.100" LastActivityDate="2014-05-10T13:55:59.100" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17275" PostTypeId="2" ParentId="17271" CreationDate="2014-05-09T12:14:54.110" Score="5" Body="&lt;p&gt;As far as I am aware it is the RhD and ABO blood groups that matter with blood donation - though you may wish to contact a blood donation organisation for more specific information on how they handle &amp;amp; categorise the blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But using just RhD and ABO gives 8 combinations, positive and negative of A, B, AB, and O. You can find out more about the blood groups, blood donation, and the characteristics of blood groups &lt;a href=&quot;http://www.blood.co.uk/about-blood/blood-group-basics/&quot;&gt;here&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The subgroups you allude to are due to differences in the number of the antigens on the surface of the blood cell, for example the &lt;a href=&quot;https://web.archive.org/web/20080802232301/http://www.owenfoundation.com/Health_Science/Blood_Group_A_Subtypes.html&quot;&gt;A1 group have ~1,000,000 A antigens per cell whereas A2 variants have ~250,000&lt;/a&gt;. The A group has ~20 subgroups, the vast majority of people are A1 (~80%) or A2 (~20%), and the other groups make up less than 1% of the population.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/ABO_blood_group_system&quot;&gt;These two subgroups are interchangeable as far as transfusion is concerned, but complications can sometimes arise in rare cases when typing the blood.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-05-09T12:28:23.817" LastActivityDate="2014-05-09T12:28:23.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17276" PostTypeId="1" AcceptedAnswerId="17414" CreationDate="2014-05-09T12:38:12.137" Score="4" ViewCount="507" Body="&lt;p&gt;There are two different cell lines but we do not know that these cell lines have Gs or Gi proteins, associated with their G-protein coupled receptors. If we wants to know about this. Can we design a experiment through which we would be able to identify specific Gs or Gi proteins in cell lines?&lt;/p&gt;&#xA;" OwnerUserId="5729" LastActivityDate="2014-05-18T18:41:13.887" Title="Signaling through G protein Coupled Receptors?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-signaling&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17278" PostTypeId="2" ParentId="3807" CreationDate="2014-05-09T13:39:18.500" Score="0" Body="&lt;p&gt;It is simple.  The brain through evolution split into two hemispheres when binocular vision was evolving.  If you follow the neurons from the eye, the lateral neurons travel to the ipsilateral hemisphere.  The medial neurons cross to the contralateral hemisphere.  I would bet the protopathic pathways were around in evolutionary terms before binocular vision and the epicritic pathways developed after binary vision.  Vision drove the hemispheres into two compartments. I could draw the diagram but unable to do so on this response&lt;/p&gt;&#xA;" OwnerUserId="6673" LastActivityDate="2014-05-09T13:39:18.500" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17279" PostTypeId="1" AcceptedAnswerId="17286" CreationDate="2014-05-09T13:46:55.317" Score="9" ViewCount="356" Body="&lt;p&gt;I just found this in my &lt;em&gt;Drosophila&lt;/em&gt; lab (within a closed vial) - unfortunately it was dead having been frozen for two weeks. Can anyone help &lt;strong&gt;id what it is&lt;/strong&gt;, and &lt;strong&gt;whether it poses a risk to my flies&lt;/strong&gt; (like mites do)? My inclination is that it is some kind of (moth?) larvae. Note the awesome corkscrew tail...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Found in Uppsala, Sweden, May 2014 in a vial of &lt;em&gt;Drosophila&lt;/em&gt; with food (a yeast, sugar, and agar mix). Length is about 3-4mm excl. tail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5TW7s.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8T92o.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mVW9e.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-05-09T19:36:40.227" Title="Identification of species found in fly lab" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17281" PostTypeId="2" ParentId="17265" CreationDate="2014-05-09T15:25:07.487" Score="4" Body="&lt;p&gt;What's your average contemporary DNA pol error rate? Something like 10^-9 errors per bp? Your average prokaryote generation time is maybe something like 10 days. LUCA is thought to be about 3.5 billion years old. However, it would be expected that DNA pol error rates were far higher in the past. In fact, if RNA + protein world existed (I think a strong case can be made for it), we're looking at multiple orders of magnitude faster change. Eukaryotes with their longer generation times don't pose much problems to the calculations, since the vast majority of domains in Eukaryote proteins were prokaryotic inventions and Eukaryote proteins are mostly just prokaryotic domains shuffled around. I agree with the above answer of there being way too many variables involved (that we would basically have to guess) for robust calculations..&lt;/p&gt;&#xA;" OwnerUserId="5784" LastActivityDate="2014-05-09T15:25:07.487" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17282" PostTypeId="2" ParentId="17266" CreationDate="2014-05-09T15:58:36.427" Score="4" Body="&lt;p&gt;Not all cells depend on insulin to take in glucose from blood (e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Microangiopathy&quot; rel=&quot;nofollow&quot;&gt;vascular endothelial cells&lt;/a&gt;). But the majority do (muscle tissue and fat tissue).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lack of insulin causes the cell to use &lt;em&gt;auxiliary&lt;/em&gt; metabolic pathways to generate its energy &lt;sup&gt;[1]&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;in muscle, the &lt;strong&gt;protein breakdown&lt;/strong&gt; is stimulated&lt;/li&gt;&#xA;&lt;li&gt;liver &lt;strong&gt;gluconeogenesis&lt;/strong&gt; is stimulated by low insulin levels and high amino acid levels in blood and using substrate from muscle and fat tissue&lt;/li&gt;&#xA;&lt;li&gt;glucocorticoids stimulate &lt;strong&gt;lipolysis&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;liver starts &lt;strong&gt;ketone body&lt;/strong&gt; synthesis, which along with medium chain fatty acids prove to be quite a good alternative &lt;a href=&quot;http://en.wikipedia.org/wiki/Brain#Metabolism&quot; rel=&quot;nofollow&quot;&gt;energy source for the brain&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Food_energy#Nutrition_labels&quot; rel=&quot;nofollow&quot;&gt;Energy from nutritional principles&lt;/a&gt; is as follows:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Lipolysis&quot; rel=&quot;nofollow&quot;&gt;Lipids&lt;/a&gt; = 9 kcal/g&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Gluconeogenesis&quot; rel=&quot;nofollow&quot;&gt;Proteins&lt;/a&gt; = 4 kcal/g&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Carbohydrates = 4 kcal/g&lt;/strong&gt; - the most important because &lt;a href=&quot;http://en.wikipedia.org/wiki/Food_energy&quot; rel=&quot;nofollow&quot;&gt;they are used as is&lt;/a&gt;. Lipids and proteins require energy from other sources to start chemical reactions which yield energy.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Mark Brandt, Ph.D. &lt;a href=&quot;http://www.rose-hulman.edu/~brandt/Chem330/EndocrineNotes/Chapter_6_Diabetes.pdf&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Endocrine Notes Supplement&lt;/em&gt;&lt;/a&gt; from &lt;a href=&quot;http://www.rose-hulman.edu/&quot; rel=&quot;nofollow&quot;&gt;Rose Hulman Institute of Technology&lt;/a&gt;, pages 78-80  &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; (links)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-27T15:03:38.533" LastActivityDate="2014-06-27T15:03:38.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17283" PostTypeId="2" ParentId="17271" CreationDate="2014-05-09T16:39:07.290" Score="2" Body="&lt;p&gt;If the blood donor is filling out the info, I recommend you have one dropdown that offers: A, B, O, AB, don't know....  And a second dropdown that offers Rh +, Rh -, don't know. And be aware that the average person is not likely to correctly know their blood type.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actual laboratory blood typing checks for a large number of possible differences between blood cells beyond just ABO types. The clinician or technician will not use anything as simple as either your drop-down OR the slightly more complex drop-down in the referenced forum post.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you &lt;strong&gt;still&lt;/strong&gt; want to know more about &quot;what the actual blood types are,&quot; recognize that there are LOTS of blood types, including the MNS system, the Kell system, and the Lewis system: &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood_typing&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Blood_typing&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6517" LastEditorUserId="6517" LastEditDate="2014-05-09T20:20:17.297" LastActivityDate="2014-05-09T20:20:17.297" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17284" PostTypeId="2" ParentId="17272" CreationDate="2014-05-09T17:02:10.963" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Brazzein&quot; rel=&quot;nofollow&quot;&gt;Brazzein&lt;/a&gt; is not even a sugar - its a protein that comes from Oubli, a West African climbing plant.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While I think nearly every living thing from bacteria up to large animals can perceive some carbohydrates as a food source, the mechanisms vary over the tree of life.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of this the taste of sweetness in animals varies a lot.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Aspartame&quot; rel=&quot;nofollow&quot;&gt;Aspartame&lt;/a&gt;, a non carbohydrate sweetener &lt;a href=&quot;http://chemse.oxfordjournals.org/content/36/5/453.short&quot; rel=&quot;nofollow&quot;&gt;does not register as sweet in all the primates&lt;/a&gt;.  Brazzein and aspartame as capable of activating one or more of the human taste receptors.  Receptors are just proteins which sense a stimulus.  They can be activated by other compounds - this is how most pharmaceuticals work.  Sweeteners which are not glucose/sucrose can bind more tightly or affect the structure of the receptors, causing them to send a sweetness signal. Often these compounds also register with other sense receptors and so the sweetness is accompanied by other tastes as well.  It sounds like Brazzein is a clean taste, less likely to have such side effects.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've not dug fully into this - its clear that some human sweetness receptors are known, but I'm not sure they are all known.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-05-09T17:02:10.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17285" PostTypeId="2" ParentId="17265" CreationDate="2014-05-09T17:13:49.280" Score="11" Body="&lt;p&gt;The evolution to the current state of life on earth has occurred through some &lt;a href=&quot;http://www.bbc.co.uk/nature/history_of_the_earth&quot;&gt;3.8 billion years&lt;/a&gt;. During this time it has gone from the most basic forms of life, simple self-replicating units, to the complex beings we see today. Evolution, the process of change within a collection of units, is caused by 4 factors, mutation, selection, drift, and gene flow. So firstly, the current state is not thought to just be the result of natural selection but instead a result of all the mechanisms of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Selection can itself be subdivided in to two types, natural and sexual selection. Therefore &quot;natural selection&quot; does not even contain all types of selection. Selection is not a simple process, but occurs in a very complex manner, simultaneously affecting the &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/B005FOHQMG&quot;&gt;many levels upon which selection can act&lt;/a&gt; (nucleotide, gene, organelle, cell, organs, organism, population, species, ecosystem etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a number of things to consider when discussing whether enough time has elapsed for the mechanisms of evolution to produce the variation we see today, a primary concern is quantifying how much variation there is in the world that has evolved. Here are &lt;em&gt;some&lt;/em&gt; other factors which would determine the likelihood at arriving at that level of genetic variation:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mutation rates (per generation)&lt;/li&gt;&#xA;&lt;li&gt;Generation times&lt;/li&gt;&#xA;&lt;li&gt;Offspring per generation (affects the number of potentially new lineages per generation)&lt;/li&gt;&#xA;&lt;li&gt;Genome size (number of potential sites)&lt;/li&gt;&#xA;&lt;li&gt;Complexity and strength of selection&lt;/li&gt;&#xA;&lt;li&gt;Population size (affecting drift and the efficacy of selection)&lt;/li&gt;&#xA;&lt;li&gt;Genetic admixture/inbreeding/potential gene flow&lt;/li&gt;&#xA;&lt;li&gt;Recombination rates&lt;/li&gt;&#xA;&lt;li&gt;Social structure&lt;/li&gt;&#xA;&lt;li&gt;Environmental variation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;These all vary wildly in contemporary populations and would also have varied in ancestral lineages too, this makes it, in my opinion, &lt;strong&gt;near impossible to even get a rough estimate of how likely our current state of variation evolved via the known mechanisms of evolution&lt;/strong&gt;. But there is a simple answer, all variation you see today arose from simple life and evolved in the last 4 billion years via the four known mechanisms of evolution - which, in part, includes natural selection. The proof is in its existence and the absence of other possible (plausible) mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;To illustrate the complexity of the problem and the high likelihood of these mechanisms leading to substantial genetic variation (this is highly unscientific):&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd suggest a very conservative estimate of just mutation rates and time since life began (3.8 billion years, Last universal common ancestor [LUCA]), using approximate human mutation rates (&lt;a href=&quot;http://www.genetics.org/content/156/1/297.abstract&quot;&gt;175 per generation&lt;/a&gt; and 25 years per generation = 7 bp mutations per year), would suggest a single lineage from LUCA to now could have had some 26 billion mutations, an average of 8 mutations per site in the human genome (this would assume constant mutation and generation rates, and starting genome size of 3 billion BP in LUCA - obviously completely ridiculous, but it's just an illustration and assumes evolution purely by drift and mutation).&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-05-09T17:35:47.693" LastActivityDate="2014-05-09T17:35:47.693" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17286" PostTypeId="2" ParentId="17279" CreationDate="2014-05-09T17:18:31.510" Score="6" Body="&lt;p&gt;I'd guess it's a &lt;a href=&quot;https://www.google.com/search?tbm=isch&amp;amp;q=Dermestidae%20Larva&quot; rel=&quot;nofollow&quot;&gt;larva&lt;/a&gt; of one of the carpet beetles (&lt;a href=&quot;https://en.wikipedia.org/wiki/Dermestidae&quot; rel=&quot;nofollow&quot;&gt;Dermestidae&lt;/a&gt;), some of which are synanthropic. They probably would be interested not in live flies, but in their food and cadavers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its appearance seems to be very characteristic - someone would be able to identify it to generic or even specific level.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-05-09T19:36:40.227" LastActivityDate="2014-05-09T19:36:40.227" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17287" PostTypeId="2" ParentId="17264" CreationDate="2014-05-09T17:37:30.313" Score="5" Body="&lt;p&gt;As your commenters have suggested, no.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order for an explanation to be a &lt;strong&gt;good&lt;/strong&gt; evolutionary explanation, it needs to have a testable hypothesis and a mechanism to test it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most common mechanism for testing the crypsis (camouflage) hypothesis is to take a large number of closely-related species, and see if their coloration differences are correlated to a particular habitat. Since pandas have few black-and-white relatives, there is no statistical power in this analysis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another option is to take a large number of pandas, create a treatment and control group and bleach the treatment group (or their eyespots) white, and compare survival or visual acuity. Unsurprisingly, this has not been done. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a nice article to animal coloration for those that have access: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Caro, T. I. M. (2005). The adaptive significance of coloration in mammals. Bioscience, 55(2), 125-136.&lt;/p&gt;&#xA;" OwnerUserId="6517" LastActivityDate="2014-05-09T17:37:30.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17288" PostTypeId="1" CreationDate="2014-05-09T20:35:35.917" Score="2" ViewCount="1120" Body="&lt;p&gt;Is the following statement in agreement with Darwin's theory of evolution?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The number of offspring is not related to fitness.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If so, why? This is not a homework assignment, I just want to justify the reason for which this statment is in agreement (which I really hope it is).&lt;/p&gt;&#xA;" OwnerUserId="6679" LastActivityDate="2014-07-07T06:19:02.983" Title="Is this statement in agreement with Darwin's theory of evolution?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="17290" PostTypeId="2" ParentId="17204" CreationDate="2014-05-09T21:40:08.853" Score="2" Body="&lt;p&gt;Not a mammal, but the &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Pseudis_paradoxa&quot; rel=&quot;nofollow&quot;&gt;paradoxical frog&lt;/a&gt; (&lt;em&gt;Pseudis paradoxa&lt;/em&gt;) starts life as a small tadpole that grows into a large tadpole and ends up as a much smaller frog. There are bound to be other examples of this phenomenon, but this is the one that immediately sprang to mind.&lt;/p&gt;&#xA;" OwnerUserId="3631" LastActivityDate="2014-05-09T21:40:08.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17291" PostTypeId="2" ParentId="17104" CreationDate="2014-05-09T21:53:16.800" Score="9" Body="&lt;p&gt;I think I can partially answer you question. As far as I'm aware, there are many surface receptor molecules such as ephrins that are responsible for axonal guidance and dendritic repulsion in developing organisms such as flies (Drosophila). As you can tell this is extremely crucial since its important for neurons to spread their dendrites and axons as far as possible, evenly spaced out with axons bifurcating (separating) correctly and not sticking together. This is for example important in the Drosophila brain for axonal projections into different lobes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One such surface receptor, which helps achieving the above is Dscam (Down syndrome cell adhesion molecule) (schmucker et al 2000 Cell). Dscam gene is expressed in over 38000 isoforms (through complex alternative splicing of Dscam mRNA) in flies. It is the homophilic binding and subsequent repulsion of Dscam protein isoforms that enables an intrinsic self-recognition for repulsion of same-cell axon. As far as I understand it, if a number of similar Dscam isoforms are present on axons or dendrites of a neuron, this is self recognised and the dendrites and axons get repelled from one another. This is the molecular pathway that ensures sister dendrites are not adhered together or become concentrated in one area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the absence of Dscam or when Dscam protein isoform diversity is removed flies die during larval stages and the early embryonic axonal patterning of the fly nervous system is clearly disrupted. In the absence of Dscam protein, Bolwig's axons exhibit frequent axon pathfinding errors at a specific intermediate target. Most of these processes are conserved in mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For further information please look at Schmucker &amp;amp; chen, 2009 Genes and Dev&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="3340" LastEditDate="2014-12-17T12:51:04.730" LastActivityDate="2014-12-17T12:51:04.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17292" PostTypeId="2" ParentId="10474" CreationDate="2014-05-10T00:07:35.553" Score="2" Body="&lt;p&gt;I will attempt to answer the question. Allele is defined, in simple terms, variation of a given gene, e.g. through deletions, SNPs etc. Humans are diploid organisms, meaning we have two sets of chromosomes, one from mother and one from father. Now since we have two sister chromosome, we can only have (share) two alleles of a given gene (one from mother and one from father) unless there are multiple copies of a gene or chromosome, which is mostly observed in disease conditions but that's not what we are talking about. Now since every humans have SNPs at roughly 1 every 1000 base pair, there are genetic variations between sequences of genes between humans, although there are some hot spots, which are more varied and some genes are very highly conserved due to their critical function such as cytochrome C. This just means that parents of the child you are describing (if not related to each other) are not likely to share the exact same, sequence wise, genetic code for a given gene selected at random.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The inheritance of a given allele of a gene on a chromosome happens through independent assortment (a process which happens maternally and paternally), meaning a child (offspring/zygote) would get one copy of a gene/allele (from the possible two that each parent themselves have) from maternal and one copy from paternal side at random. This is one source of genetic variation in a zygote. The other source of genetic variation is gene cross-over (through homologous recombination) meaning bits of the maternal or paternal chromosomes swap at gamete stage before the gametes are fused together to form a zygote, which makes the offspring unique and no offspring alike (except MZ twins but thats another discussion). This overall means that you can inherit a maximum of two alleles of a given gene (assuming again the parents of the child are not closely related) and even then the sequence of the offspring genes are not likely to be exactly the same as their parents, which makes every human unique. But saying that, you have a much higher gene sequence match to your parents than any other non-related human selected at random.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One thing worth noting here is that mitochondrial genes, are inherited exclusively from you mother (through the egg) and males inherit the Y chromosomes paternally so there are circumstances I guess you could say you inherit certain gene/alleles paternally or maternally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I speculate you might be thinking about is how many homologues (similar versions) of a given genes humans have and I think the average in the human genome is 3 but do check this! Flies (Drosophila) tends to have one, which is why its such a great model organism to study genetics and genetic interactions with as you do not tend to get redundancies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this answers your question&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-05-17T00:11:15.297" LastActivityDate="2014-05-17T00:11:15.297" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17294" PostTypeId="2" ParentId="14409" CreationDate="2014-05-10T01:18:28.507" Score="5" Body="&lt;p&gt;Your question has several parts to it so I will attempt to address them one-by-one. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of protein stability and turnover, this is a nice paper describing how human cell (HeLa) line, although this is a cancerous cell line, is used to measure the turnover of proteins (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3316722/?report=classic&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3316722/?report=classic&lt;/a&gt;). They have used labelled amino acid technique and mass spectrometry (SILAC) to make measurements of protein turnover. It is concluded that on average the turnover is 20 hours, which is correct in my experience when doing gene knockdowns in Drosophila (S2) cells using RNAis as we incubate the RNAi with cells for 72 hours to ensure most proteins that we targeting are degraded and we can see the desired effects in cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now getting to your questions regarding organelle turnover, you have to consider that cellular organells are very precious to the cells as most of them consume a lot of energy to build hence they are maintained unless they suffer critical damage, and they would become detrimental to the cellular integrity. In that case organells such as mitochondria undergo a specific type of degradation called mitophagy, which is a subtype of autophagy. Now I'm sure there are specific average times for the so called turn-over of cellular organelle under &quot;normal&quot; conditions but thats a slightly misleading view since the turnover can be tipped through reactive oxygen species (ROS) or ageing leading to less efficient cellular maintenance and buildup of toxic aggregated proteins or ROS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now just to clarify the use of the word half-life in you last paragraph, half-life normally refers to the time it takes for half the molecules in a given system to degrade (or to be more correct Half-life is the amount of time required for a quantity to fall to half its value as measured at the beginning of the time period) so I do not agree with your use of the word half-life in the last paragraph of above question although human DNA does have a replication limit (Hayflick limit) of roughly 40-60 due to telomer shortening and afterwards the cells (due to the DNA) that no longer replicates will enter senescence and eventually die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now getting to non-replicating, highly differentiated cells such as neurons, it still remains a mystery as to how neuronal DNA remains so highly stable (although DNA is a highly stable molecule (compared to RNA) and its further stabilised through histones), while undergoing many dynamic processes such as transcription (since if anything goes wrong the cells cannot be replaced at least in CNS) and how axons of some neurone that can reach over a meter in length are maintained so well for decades. There is a lively argument amongst the scientific community about this, which you can find out about if you simply search for axonal maintenance in a search engine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this answers some of your questions.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-10T01:18:28.507" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17295" PostTypeId="1" AcceptedAnswerId="17298" CreationDate="2014-05-10T02:18:54.820" Score="7" ViewCount="14426" Body="&lt;p&gt;Wikipedia states that a cell is &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the basic structural, functional and biological unit of all known living organisms. Cells are the smallest unit of life that can &lt;strong&gt;replicate independently&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It then goes on to state that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;All cells (&lt;strong&gt;except red blood cells&lt;/strong&gt; which lack a cell nucleus and most organelles to accommodate maximum space for hemoglobin) possess DNA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Then why are red blood cells still considered cells, while they can't replicate? Is the definition on Wikipedia just a bad definition? Or are red blood cells wrongly considered cells, but remain so for historical reasons? Or are they considered cells for some other reason, such as &lt;a href=&quot;https://biology.stackexchange.com/a/1039/611&quot;&gt;this answer&lt;/a&gt; which states that red blood cells do contain a nucleus at some point?&lt;/p&gt;&#xA;" OwnerUserId="611" LastEditorUserId="24354" LastEditDate="2020-07-16T19:35:38.020" LastActivityDate="2020-07-16T19:35:38.020" Title="Why are red blood cells considered to be cells?" Tags="&lt;cell-biology&gt;&lt;hematology&gt;&lt;red-blood-cell&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17296" PostTypeId="1" CreationDate="2014-05-10T02:27:52.877" Score="7" ViewCount="504" Body="&lt;p&gt;We've known for a long time now how to &quot;add a new entry to the database,&quot; as it were, of immune responses.  It's called &lt;em&gt;vaccination,&lt;/em&gt; and it's been one of the greatest success stories in the history of medicine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And yet, allergies and autoimmune disorders, both caused by an immune system gone rogue, are still serious problems today.  If it's so easy to add a new immune response, why don't we have any way of deleting one?&lt;/p&gt;&#xA;" OwnerUserId="6683" LastActivityDate="2014-05-10T09:03:44.533" Title="Why is there no way to remove an immune response?" Tags="&lt;immunology&gt;&lt;autoimmune&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17297" PostTypeId="2" ParentId="8834" CreationDate="2014-05-10T02:40:41.187" Score="1" Body="&lt;p&gt;I think the statement above is slightly misleading. There are many many types of cell signalling, anything from RTK (at the cell surface or when its endocytosed), to steroid receptors, which operate on different time scales and produce different results depending on the type of signalling. Also it depends on what you are measuring/defining as a signal/response in lets say &quot;cell signalling&quot; because you could define cell signalling response as protein phosphorylation at any point in a signalling cascade or it could be the transcriptional activation itself (consider the MAPK pathway in Drosophila, at which point do you consider a response is produced? when Raf is activated? or when transcription factors such as pointed bind to their ETS binding site and start to transcribe as measured by luciferase? as you can tell the time difference between the two is quite large, well as far as I know after RTK activation in Drosophila it takes ERK 20 minutes just to translocate to the nucleus). A cell signalling response could also constitute changes in the rate of cell migration, cell shape etc, which can either be slow or fast depending on the signal in question. so I think the above question needs major rethinking and redefining.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now getting back to your questions about key search terms, in my experience, over time you just end up developing a knack for what you consider to be key words after you carefully define the question and think bout its different aspects. A rule of thumb that I use is typing at name of proteins (e.g. JNK or RAS etc) or processes (transcription, phosphorylation etc) and use a word like rate, time-scale, half-life, turn-over or something like that if its measuring changes in time you are interested in. Just play around with words.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also as a general advice you don't have to reference every snippet of every fact like &quot;water is liquid at RT in standard atmospheric pressure&quot; etc. References are meant to be there to acknowledge the work of others like &quot;how DNA was discovered&quot; so that people can't just lift paragraphs or pages out os someones research without acknowledging them and passing it as their own work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-10T02:40:41.187" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17298" PostTypeId="2" ParentId="17295" CreationDate="2014-05-10T05:36:34.163" Score="9" Body="&lt;p&gt;A very good question, and it is most likely because of the last option.  It had a nucleus for part of its life. After the RBC jettisons its nucleus, it still remains very metabolically active for approximately 3 months.  It maintains its cell membrane integrity, it metabolizes glucose, it interacts constantly with its environment, numerous cellular functions and structure remain intact...  It is extremely specialized for a primary purpose, and no longer requires the nucleus to provide more proteins.  It has limited capacity to heal from injury, so it has a limited life span.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Speculation:  I wonder if it might lose the nucleus early on so that when it is destroyed in the spleen at the end of its life as RBCs are, the spleen macrophages are not overwhelmed with additional processing of nucleic acids?  Macrophage type cells are already working hard in there to clear infectious agents and some immune cells from the blood.&lt;/p&gt;&#xA;" OwnerUserId="6314" LastEditorUserId="6314" LastEditDate="2014-05-10T05:42:03.340" LastActivityDate="2014-05-10T05:42:03.340" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17299" PostTypeId="2" ParentId="17296" CreationDate="2014-05-10T07:12:50.657" Score="3" Body="&lt;p&gt;Too long for a comment: Because we don't know how to do this. &#xA;The immune system is an extremely complex and highly regulated function of the human body and it is not easy to shut down single pieces of it without affecting the whole rest. We can completely block immune responses (more or less), which is beneficial for people who got a transplant. These people couldn't survive without this intervention, since their immune system would otherwise turn against their transplant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The downside for them is, that they are more likely to get severe infections. A friend of mine, which got a kidney transplanted has to be very careful to not get pneumonia, since his immune system can barely fight this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other problem with fighting of these immune responses is that they are widely distributed. Lets take allergies as an example: Here you make antibodies which are highly specific for the antigen. This means that you make relative short living plasma cells which actively make large amounts of this antibody and long living memory cells which keep this memory alive. The later are then homing into the bone marrow and wait for another exposure to make them proliferating into more plasma cells and a few memory cells again. This process works for every antigen for which we acquire immunity, including vaccinations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How should we selectively delete one subgroup of memory cells from the bone marrow without affecting all others? How do we find all versions (one protein, which causes an immune reaction has a lot more than one antigenic peptides) of it? And what else do we mess up, when we try to do so?&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-10T07:12:50.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17300" PostTypeId="2" ParentId="17296" CreationDate="2014-05-10T07:21:03.450" Score="5" Body="&lt;p&gt;It is an interesting question. The reason for why new immune responses can be launched but the memory of old ones are not deleted is based on the concept of irreversibility of certain chemical reactions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Launching an immune response involves clonal expansion of cells expressing the epitope sensors such as the immunoglobins and T-cell receptors, accompanied by maturation of these receptors. Some of the reactions involved in this process are irreversible, which include VDJ recombinations, class switching and affinity maturation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In an overall sense, immune response is analogous to natural selection- in the presence of the antigen the best binders are selected and expanded. Now to make a species extinct you would have to find each individual and kill it. Or you may have to develop a technology that will identify and kill a certain species in an automated manner. This is difficult to implement; how to engineer a mechanism that will precisely seek and destroy &lt;em&gt;all the epitope sensors&lt;/em&gt; for a particular antigen. In contrast selection happens spontaneously because it does not proceed with a reason. It just selects the best from available stock. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-05-10T09:03:44.533" LastActivityDate="2014-05-10T09:03:44.533" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17301" PostTypeId="2" ParentId="17288" CreationDate="2014-05-10T09:44:42.733" Score="3" Body="&lt;p&gt;&lt;strong&gt;Short Answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The statement &quot;The number of offspring is not related to fitness.&quot; is wrong! In other words, The number of offspring &lt;strong&gt;is&lt;/strong&gt; related to fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Various definitions of fitness exist depending on the model you want to use but whatever is the model you want to use the number of offspring is always related to fitness. For the purpose of a beginner in evolutionary biology, it is probably enough to assume that the number of offsprings that managed to survive to some adult age and fitness are actually the exact same thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long Answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Darwin's theory of evolution?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do you call Darwin's theory of evolution? Do you mean the theory of evolution as it was formulated by Charles Darwin at its time or do you mean the current theory of evolution? Charles Darwin never used the word fitness (if I am not mistaken), so I will talk about the modern theory of evolution only.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Generalities&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For most of the purpose it is enough to consider fitness as being the expected number of offsprings that manage to survive to some adult age of an individual given its environment and its genotype. The word &quot;expected&quot; used above refers to the first statistical moment (mean) of the random variable which is the number of offspring of an individual given its genotype and its environment. In other words, &lt;strong&gt;the number of offsprings is &quot;related&quot; to fitness&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Absolute versus Relative fitness&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, we talk about absolute and relative fitness, where the absolute fitness of an individual is its number of offsprings and the relative fitness of an individual is its absolute fitness divided by either the mean fitness of the population or more often divided by the absolute fitness of the fittest individual in the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Fitness is a function of fecundity and survival&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be a bit more accurate, fitness is a function of both age-specific survival and age-specific fecundity. A very good measure of fitness is given be the elements of leading eigenvalue of the Leslie matrix $L$ in $\overrightarrow n_{t+1} = L \overrightarrow n_t $ where $\overrightarrow n_t$ is a vector that gives the number of individuals of a given genotype of each age living at time $t$. $\overrightarrow n_t = (n_{1t}, n_{2t}, …, n_{nt})^T$, where $T$ indicates transpose and $n_{xt}$ is the number of individuals of age classe $x$ at time $t$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Definitions of fitness slightly varies depending on the model you want to use&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One may want to use an even more complex definitions of fitness, typically when using models that apply to species that have an &lt;a href=&quot;http://en.wikipedia.org/wiki/Alternation_of_generations&quot; rel=&quot;nofollow&quot;&gt;alternation of generation&lt;/a&gt;. Or when considering, genotypes that have different &lt;a href=&quot;http://en.wikipedia.org/wiki/Norms_of_reaction&quot; rel=&quot;nofollow&quot;&gt;norms of reactions&lt;/a&gt; and considering a changing environment through time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, whatever is the model you want to apply, fitness is always related to the expected number of offsprings. It would be wrong though to reduce fitness to the expected number of offsprings only, because a more complex definition might be necessary in some special cases. In any case, fitness is always an index of how much will a variant spread in a population and is therefore closely linked to the number of offsprings.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-07-07T06:19:02.983" LastActivityDate="2014-07-07T06:19:02.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17302" PostTypeId="2" ParentId="17104" CreationDate="2014-05-10T10:38:57.847" Score="5" Body="&lt;p&gt;In cases of severe head injury where a large portion of neurons and their connections get shredded. I don't think a neuron would be very choosy  when presented with quite a few axons and lots of intracellular fluid &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are coup and the contra coup (p silent) brain injuries that occur because the brain bounces back and forth in the skull. The contra coup, other side contusion (bruise) is usually worse. A lot of axonal injury occurs in the brain stem and since the basics of life (breathing centers) a severe injury to the brain stem can cause not surviving the injury.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably speed of healing I is the priority. I forgot which journal it was in but those with a college education were 60% more likely to have a good recovery while those with just a high school diploma have only 10-20% chance of having a good recovery. It's a similar ranking when it comes to neuronal connections. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for answering my curiosities on how indeed does one heal from Diffuse Axonal Injury (DAI) on a molecular basis. I was a 1sr yr. radiology resident when I had a severe TBI or Traumatic Brain Injury. TBI is the fancy way of saying brain damaged. But now we know victims of severe head injury can recover and even grow new neurons until old age.&lt;/p&gt;&#xA;" OwnerUserId="6685" LastActivityDate="2014-05-10T10:38:57.847" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17303" PostTypeId="1" AcceptedAnswerId="17722" CreationDate="2014-05-10T10:40:43.840" Score="3" ViewCount="314" Body="&lt;p&gt;It's known for some scorpion species such as Pandinus imperator, Heterometrus Petersii etc. to be shining under UV light. That makes them easier to capture and collect by humans. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any evolutionary advantage for this property? &#xA;Usually, in articles you stumble upon the phrase &quot;It is not known&quot; for this matter (&lt;a href=&quot;http://www.wired.com/2011/12/scorpion-fluorescence/&quot; rel=&quot;nofollow&quot;&gt;example&lt;/a&gt;). Maybe someone knows of recent discoveries.&lt;/p&gt;&#xA;" OwnerUserId="6016" LastEditorUserId="6016" LastEditDate="2014-05-10T10:50:15.163" LastActivityDate="2014-05-28T15:22:15.877" Title="Why are some scorpion species fluorescent under UV light?" Tags="&lt;evolution&gt;&lt;cell-biology&gt;&lt;zoology&gt;&lt;fluorescent-microscopy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17304" PostTypeId="2" ParentId="7778" CreationDate="2014-05-10T11:32:15.483" Score="1" Body="&lt;p&gt;If i were to have a blind attempt at your question, it is never a good idea to freeze thaw any protein, not even cell lysates. Thats the whole point of glycerol use, which we use in our lab at 50% (v/v) to store bead bound proteins. Thats also why antibodies and restriction enzymes are stored in glycerol since freeze thawing antibodies dissolved in water often leads to their degradation, although you only tend to store stuff in glycerol, like restriction enzymes, if the concentration of the protein is very very high. One golden trick I use is aliquoting my samples and snap freeze them in liquid nitrogen and store in -80 freezer. I'm curious as to what happens with your protein, does it degrade after a freeze thaw cycle? (I'm aware that transmembrane proteins are notorious when it comes to storage/maintenance due to their awkward hydrophobic transmembrane region so its best to speak to an x-ray crystallography expert, if there is some one like that roaming around your research lab :), since they have face problems like this quite frequently and have excellent suggestions). Are your proteins GST tagged and bound to glutathione agarose beads? or you use HIS tags and nickel beads and elute the purified protein through imidazole? i suspect it is GST in which case its probably not a good idea to snap freeze although I have (somehow) had frozen glycerol beads at -20 and they were fine after use. I have had a friend talking about protein purification and the fact that protein isolation has to be done fresh so you might have to go down that root if your current method is not ideal. Also one last question, are you purifying you protein bacterially or they get secreted into the media? I suspect if its a membrane protein you are using the cell based system since if it was E. coli you were using (as suggested above) you could have just had your protein expressed through IPTG and just washed you cell pellet in STE buffer and spun it down hard and stored the pellet at -20, in which case would save you some time in the purification process. The use of Na azide is a good idea too but I only use it for primary antibody storage which is already dissolved in the block buffer such as 5%-BSA-TBST for WB and store the whole thing at 4 oC and Na azide is there to prevent BSA and the Ab going off.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main problem many many people have, including my self is that the majority of times, over expressed protein is insoluble or just doesn't get expressed in certain systems so you are very lucky to have a working system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is all I know about protein storage. I hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-10T11:32:15.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17305" PostTypeId="1" AcceptedAnswerId="17307" CreationDate="2014-05-10T11:38:10.423" Score="1" ViewCount="1550" Body="&lt;p&gt;I know that it decreases the amount of leucotrienes in blood.&#xA;I saw a patient with high IgE altough under Montelukast medication.&#xA;This suggests me that Montelukast does not affect the immunoglobulins, but somehow restrict the allergic reaction indirectly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the effect of Montelukast on the amount of IgE in blood?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-05-10T15:03:02.600" Title="What is the effect of Montelukast on the amount of IgE in blood?" Tags="&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17306" PostTypeId="1" AcceptedAnswerId="17311" CreationDate="2014-05-10T14:13:29.503" Score="2" ViewCount="311" Body="&lt;p&gt;I mean, saving sick people means that they possibly can propagate something that nature does not allow. I know that there is already something that operate at genetical level producing alteration, i.e. genetical mutation. And i am well aware that natural selection and genetical mutations take place really slowly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;p.s. i really want medicine to work!!&lt;/p&gt;&#xA;" OwnerUserId="6627" LastActivityDate="2014-05-10T15:52:16.763" Title="Is there a possibility that medicine will affect the efficiency of natural selection?" Tags="&lt;genetics&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17307" PostTypeId="2" ParentId="17305" CreationDate="2014-05-10T15:03:02.600" Score="3" Body="&lt;p&gt;I was interested in this question because I have always been a little confused about allergic responses, so I did some rather superficial research (i.e. I looked at some Wikipedia pages). As far as I can see there is no reason to think that Montelukast will have any effect upon IgE levels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Montelukast&quot; rel=&quot;nofollow&quot;&gt;Montelukast&lt;/a&gt; is a leukotriene receptor antagonist. It is used to treat allergies and asthma.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Leukotrienes are lipid signalling molecules that are used by cells to regulate immune responses. One role of leukotrienes is to promote contractions in the smooth muscles lining the bronchioles. If they are over-produced they can cause inflammation in the airways leading to symptoms of asthma. Since leukotrienes act through a receptor, an antagonist of that receptor such as montelukast can reduce their effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/IgE&quot; rel=&quot;nofollow&quot;&gt;IgE&lt;/a&gt; is involved in allergic responses because it interacts with Fc receptors on the surface of certain cells such as mast cells. If the IgE molecules are associated with one another through Ig-antigen interactions this leads to clustering of the Fc receptors which triggers an intracellular signalling pathway leading to mast cell degranulation - the release of histamine by fusion of storage vesicles with the cell membrane (i.e. exocytosis). &lt;a href=&quot;http://en.wikipedia.org/wiki/Histamine&quot; rel=&quot;nofollow&quot;&gt;Histamine&lt;/a&gt; causes constriction of the bronchioles via effects on smooth muscle, just like leukotrienes.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-10T15:03:02.600" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17308" PostTypeId="1" CreationDate="2014-05-10T15:19:30.017" Score="2" ViewCount="509" Body="&lt;p&gt;As per title: If fertilized, is a double-yolk egg capable of producing two viable chicks (that could survive to adulthood)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have there been any reported cases of such (presumably) fraternal twins?&lt;/p&gt;&#xA;" OwnerUserId="6657" LastActivityDate="2014-05-10T15:41:57.483" Title="Is a double-yolk egg capable of producing two viable chicks?" Tags="&lt;twins&gt;&lt;eggs&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17309" PostTypeId="2" ParentId="17308" CreationDate="2014-05-10T15:41:57.483" Score="2" Body="&lt;p&gt;According to the discussion &lt;a href=&quot;http://www.homesteadingtoday.com/livestock-forums/poultry/446574-two-chicks-one-egg.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; they normally fail to hatch because the chicks cannot get enough leverage to break the shell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=S1ZeEY-kt7A&quot; rel=&quot;nofollow&quot;&gt;Here is a video&lt;/a&gt; of an assisted hatching. It is claimed that these two survived.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-10T15:41:57.483" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17311" PostTypeId="2" ParentId="17306" CreationDate="2014-05-10T15:52:16.763" Score="3" Body="&lt;p&gt;Summary:  Yes it can, but not the way you might think.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans aren't under a lot of selective pressure on a large scale right now.  We have a lot of control over our environment, and you're accurate that disease (or I'd add massive, fatal natural disasters) are the biggest ways we would see a large genetic shift.  (Or genocide, which is an extremely unnatural, artificial selection, but some of our species have historically been horrific enough to try to do this.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Small &lt;a href=&quot;http://en.wikipedia.org/wiki/Sickle_cell_trait#Association_with_malaria&quot; rel=&quot;nofollow&quot;&gt;local natural selection has happened in areas where Malaria is endemic&lt;/a&gt;: many people die from malaria. some people die early from homozygous &lt;a href=&quot;https://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CFAQFjAB&amp;amp;url=http://www.nlm.nih.gov/medlineplus/ency/article/000527.htm&amp;amp;ei=b0duU-qYK5XQsQSAtoCQDw&amp;amp;usg=AFQjCNE7Ftnvhbck4kn_I58OJ-v46q0W7w&amp;amp;sig2=qB5x3LsiDOIYM8IO4EfTyg&amp;amp;bvm=bv.66111022,d.cWc&quot; rel=&quot;nofollow&quot;&gt;sickle cell anemia&lt;/a&gt;, but those who are heterozygous have &quot;sickle cell trait&quot; (because of incomplete dominance) and have deformed enough RBC that malaria isn't able to infect them well.  So the survival advantage is enough that the prevalence of sickle cell alleles in these areas is higher.  There's a similar story with &lt;a href=&quot;https://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCsQFjAA&amp;amp;url=http://en.wikipedia.org/wiki/Glucose-6-phosphate_dehydrogenase_deficiency&amp;amp;ei=UUduU-38BcjlsASquYGYDw&amp;amp;usg=AFQjCNHsEepdc75X-I-BMMcEHNcEoBK9oA&amp;amp;sig2=WvWZxNS-ndGAuRgqDz6F9Q&amp;amp;bvm=bv.66111022,d.cWc&quot; rel=&quot;nofollow&quot;&gt;Glucose-6-phosphate dehydrogenase deficiency&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But on a scale you might be thinking of, the primary mechanism would be a global pandemic infection that targets people with a specific trait.  For example, if suddenly an incurable contagious, virulent, highly pathogenic, and fatal virus/bacteria that was only fatal to those with an allele for blood type A were to emerge.  Theoretically it would cause a genetic shift to eliminate type A blood from the gene pool, and reduce prevalence of type B (by eliminating AB due to the A).  Or if it attacked only one location of the world, but that's highly unlikely due to global travel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Medicine could theoretically catch it in time - mitigate impact and prevent a large shift by creating a vaccine or cure that is effective and easily mass-produced.  The most likely to succeed would be a vaccine (yay for public health!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Variations on this have happened to reduce or eliminate pathogens (such as polio and smallpox because of the vaccine) and their effect on mankind, but those have little to do with selection for human traits that would cause genetic shift.&lt;/p&gt;&#xA;" OwnerUserId="6314" LastActivityDate="2014-05-10T15:52:16.763" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17312" PostTypeId="2" ParentId="14048" CreationDate="2014-05-10T15:53:28.697" Score="4" Body="&lt;p&gt;As a Drosophila biologist, I will attempt to address the above question by giving an examples from the Drosophila field. When this paper (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7720066&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/7720066&lt;/a&gt;) in Cell came out, it sent shockwaves around the world since it showed a molecular mechanism by which production of cAMP and activation PKA, effects CREB transcriptional activation and in turn formation of the long-term memory (LTM) in flies. Some of these CREB over expressing flies could learn a task after simply one try whereas wild-types had to do it several times! This work was later followed by mouse studies (&lt;a href=&quot;http://www.pnas.org/content/100/18/10518.full.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/100/18/10518.full.pdf&lt;/a&gt;) and comparisons to RTS patients were made. At that time there were discussions of CREB being responsible for intelligence however now there is nice nature review/meta-analysis paper (&lt;a href=&quot;http://www.nature.com/srep/2014/140225/srep04176/pdf/srep04176.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/srep/2014/140225/srep04176/pdf/srep04176.pdf&lt;/a&gt;), which says there are no evidence connecting CREB and IQ. This paper performs a literature based investigation and identifies several candidates that are testable and can act as biomarkers for intelligence related therapeutic approach to mental retardation. According to their screen dopamine and norepinephrine pathways seems to be important in IQ-related biological processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-10T15:53:28.697" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17313" PostTypeId="2" ParentId="5470" CreationDate="2014-05-10T17:00:51.523" Score="7" Body="&lt;p&gt;Well it depends on the application. First you have to determine what it is that you want to view under the microscope e.g. an organism such as &lt;em&gt;Drosophila&lt;/em&gt; or you want to see microscope slides? In the first case you need to by a dissecting microscope, otherwise you need to by an upright light microscope with the appropriate objective lenses, again depending on the application. If you are viewing cells in a flask/dish/plate in a cell culture setting or if viewing a haemocytometer (although not necessarily in the case of haemocytometer), you need to buy an inverted light microscope with phase contrast since you wouldn't be able to view the cells very well with an upright microscope since the goal is to reduce the distance between the objective and the sample for a better view of the samples in cases of dishes or plates. Again the choice of equipment depends on the application. But as correctly said above you need to clarify what you mean in the question.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-11-09T21:41:55.273" LastActivityDate="2014-11-09T21:41:55.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17314" PostTypeId="2" ParentId="16887" CreationDate="2014-05-10T17:17:42.443" Score="0" Body="&lt;p&gt;My understanding of chimeric sequences is that they are produced as the result of inserting two different cDNAs (usually from different species) into a backbone such as pUAST to make a protein that is partly from one species and partly from another species. Sometimes you want to do this because for example the ligand for a receptor in lets say Drosophila is very difficult to produce but the ligand for the mammalian receptor is easily available so what scientists do is that they attach the human cDNA corresponding to the extracellular side of the receptor to the Drosophila intercellular portion of the Drosophila receptor. Now you can intracellularly activate a Drosophila receptor using a human ligand for a receptor. Now I have never seen/heard of chimeric in vivo sequences and that just doesn't seem possible but what I imagine can happen when viewing sequencing data for a species that are not fully sequences is that the search engines says a particular sequence is from a different species that you have sequenced. This is because the database will try to find the closest match to the sequence. NCBI BLAST for example can do this but usually it gives you a percentage sequence matching/probability. Otherwise I'm not sure what you mean by the word sequencing projects. Could you provide an example/reference?&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-10T17:17:42.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17315" PostTypeId="2" ParentId="16412" CreationDate="2014-05-10T17:29:43.950" Score="1" Body="&lt;p&gt;Well I sometimes use PDB files from proteins whose structure has been identified and study them. I use swiss PDB viewer software to do this and its pretty neat! I haven't looked at the biophysical data associated with a PDB file but I'm pretty sure they are there since you wouldn't be able to make the calculations and resolve the protein structure and confirmation without that kind of data. All you need is to download the software, go to Uniprot database and use the accession number of a protein you are interested in, see if its structure is resolved and either download the PDB file or use the accession number to download the file inside the software.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-10T17:29:43.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17316" PostTypeId="2" ParentId="15932" CreationDate="2014-05-10T17:44:23.217" Score="1" Body="&lt;p&gt;This would be a very long answer but just to give you some hints, the migrational mechanisms are already there and the cancerous cells makes use of them to metastasise. So in short its deregulation. What is under selection pressure tho are cancerous cells themselves to constantly change and evade cellular fail safes which kill (apoptosis) uncontrollably replicating cells. You can find out about this here (&lt;a href=&quot;http://www.nature.com/onc/journal/v22/n42/abs/1206757a.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/onc/journal/v22/n42/abs/1206757a.html&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-10T17:44:23.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17317" PostTypeId="2" ParentId="11200" CreationDate="2014-05-10T18:17:19.390" Score="2" Body="&lt;p&gt;You could do negative geotaxis (climbing) assay, (larval or adult) locomotion assays, % brain vacuolisation (after the flies die), maze tests. There are probably much more but these are all I can think of that are no-lethal and can be applied to males and females and some larval work too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could maybe consider doing starvation assays and longevity in some of your populations.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-10T18:17:19.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17318" PostTypeId="2" ParentId="11351" CreationDate="2014-05-10T18:48:33.897" Score="1" Body="&lt;p&gt;I haven't done LRS but I don't see a reason why you couldn't make that measurement over only a few days, if you keep this method consistent through out all your populations. Just as a control you might have to do a complete LRS to see if you get any patterns in their egg laying behaviour, which I assume/believe is a decreasing pattern over time but just check the pattern of your WT and make sure your food is the same throughout all your experiments as changes in yeast % can completely distort your results as fly lay eggs like crazy when given yeast!! so use the same batch of fly food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although I'm no expert at this, if you look at female ovaries and do some molecular/phenotypic characterisations, you might get some interesting data if you are already observing a huge difference between your populations although you would have to look at the literature for this but having played around with these stuff a little, you find a surprising amount of data! This is in a way nice since you take the males out of the equation as the reproductive fitness could be compromised by either males or females in a population. To determine this you need to cross the males and females of your population of interest to WT flies and count the embryos (although this is slightly dangerous since if males are not performing well, females can lay lots of unfertilised eggs, blanks, and they are indistinguishable from fertilised egg so maybe count the hatched offspring and immediately discard them although that presents its own set of challenges and variables and to be honest its not likely to happen since you usually get this blanks in virgin females that have not yet courtshiped). If you observe lets say no changes in embryo numbers when your male populations are crossed to WT females but significant changes when females are crossed to the WT males, you would know the problem is with the males in your population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: So I looked a bit further into this and came across this paper (&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024560&quot; rel=&quot;nofollow&quot;&gt;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024560&lt;/a&gt;). If you look at Fig 6, I think it answers your question. I'm basically quoting the paper here. They measured the correlations between adult LRS and cumulative and short-time measures of fecundity and offspring production. Correlations of the short-time measures of fecundity and offspring production with adult LRS were highly dependent on the time of measurement. For young females the correlations were low, but when measured from older females, the correlations were much higher (up to 0.67 for short-time fecundity and 0.83 for short-time offspring production). For both short-time fecundity and short-time offspring production the highest correlations with adult LRS were reached when the female age was about 50 to 80 days. The length of the time frame had only a minor effect: the correlation of the 10-day measure with adult LRS was generally only slightly higher than that of the 2-day measure. The short-time measures performed well in comparison to the cumulative measures of fecundity and offspring production. So in short if you let your females age a bit and measure their fecundity, then it should be representative of their LRS.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-05-12T09:52:05.173" LastActivityDate="2014-05-12T09:52:05.173" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17319" PostTypeId="2" ParentId="7137" CreationDate="2014-05-10T19:09:30.020" Score="1" Body="&lt;p&gt;The standard when purifying GST with Glutathione agarose beads is to use STE buffer (10 mM Tris-HCl (pH 7-7.5), 150 mM NaCl and 1 mM EDTA) for washes and we have had no problem with this in our lab!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-05-11T10:01:21.803" LastActivityDate="2014-05-11T10:01:21.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17320" PostTypeId="1" AcceptedAnswerId="17321" CreationDate="2014-05-10T22:09:52.723" Score="4" ViewCount="8845" Body="&lt;p&gt;I thought that the definition of a definitive host was that the parasite had to sexually reproduce in that particular host. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been told that mosquitoes are the definitive host for the plasmodium parasite, but I thought that the fertilization (and thus the sexual reproduction) takes place in the human?&lt;/p&gt;&#xA;" OwnerUserId="3382" LastActivityDate="2017-03-02T11:23:50.160" Title="Why is the mosquito a definitive host in malaria?" Tags="&lt;entomology&gt;&lt;parasitology&gt;&lt;parasitism&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17321" PostTypeId="2" ParentId="17320" CreationDate="2014-05-10T23:38:02.167" Score="10" Body="&lt;p&gt;&lt;em&gt;Plasmodium falciparum&lt;/em&gt; (the main causative agent of malaria) and other &lt;em&gt;Plasmodium&lt;/em&gt; species have a very complex life cycle, with stages in the female host &lt;a href=&quot;http://en.wikipedia.org/wiki/Anopheles&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Anopheles&lt;/em&gt;&lt;/a&gt; mosquito, in the human liver, and in the human circulatory system, where it primarily resides in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Erythrocyte&quot; rel=&quot;nofollow noreferrer&quot;&gt;erythrocytes&lt;/a&gt; (red blood cells, or RBCs):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://www.cdc.gov/dpdx/images/malaria/malaria_LifeCycle.gif&quot; alt=&quot;Plasmodium spp. life cycle&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During a blood meal, a malaria-infected mosquito injects sporozoites in its saliva into the human host (&lt;strong&gt;&lt;em&gt;1&lt;/em&gt;&lt;/strong&gt;). Sporozoites travel through the circulatory system and first infect &lt;a href=&quot;http://en.wikipedia.org/wiki/Hepatocyte&quot; rel=&quot;nofollow noreferrer&quot;&gt;hepatocytes&lt;/a&gt; (liver cells) (&lt;strong&gt;&lt;em&gt;2&lt;/em&gt;&lt;/strong&gt;, stage &lt;strong&gt;&lt;em&gt;A&lt;/em&gt;&lt;/strong&gt;) and mature into schizonts (&lt;strong&gt;&lt;em&gt;3&lt;/em&gt;&lt;/strong&gt;), which rupture and release merozoites (&lt;strong&gt;&lt;em&gt;4&lt;/em&gt;&lt;/strong&gt;). After this initial replication in the liver (exo-erythrocytic schizogony (&lt;strong&gt;&lt;em&gt;A&lt;/em&gt;&lt;/strong&gt;), which can last a minimum of 5.5 days), the parasites undergo asexual multiplication in the erythrocytes (erythrocytic schizogony (stage &lt;strong&gt;&lt;em&gt;B&lt;/em&gt;&lt;/strong&gt;)). Merozoites leave the liver and enter the circulatory system where they infect red blood cells (&lt;strong&gt;&lt;em&gt;5&lt;/em&gt;&lt;/strong&gt;). The ring stage trophozoites mature into schizonts, which rupture releasing more merozoites, which continue the cycle of infection of RBCs (&lt;strong&gt;&lt;em&gt;6&lt;/em&gt;&lt;/strong&gt;). Some immature trophozoites, in the so-called &quot;ring stage,&quot; differentiate into sexual erythrocytic stages (gametocytes) (&lt;strong&gt;&lt;em&gt;7&lt;/em&gt;&lt;/strong&gt;). Blood stage parasites are responsible for the clinical manifestations of the disease. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important to note here (in answer to your question) that while the male and female gametocytes are formed at this stage in the human (the equivalent of meiosis), sexual reproduction does not occur until the micro and macrogametocytes are taken up by a mosquito.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The male (microgametocytes) and female (macrogametocytes) gametocytes are ingested by a female &lt;em&gt;Anopheles&lt;/em&gt; mosquito during a blood meal (&lt;strong&gt;&lt;em&gt;8&lt;/em&gt;&lt;/strong&gt;) - only female mosquitoes (of pretty much any species) drink blood. The parasites' multiplication in the mosquito is known as the sporogonic cycle (stage &lt;strong&gt;&lt;em&gt;C&lt;/em&gt;&lt;/strong&gt;). While in the mosquito's stomach, the microgametes penetrate the macrogametes generating zygotes (&lt;strong&gt;&lt;em&gt;9&lt;/em&gt;&lt;/strong&gt;). The zygotes in turn become motile and elongated (ookinetes) (&lt;strong&gt;&lt;em&gt;10&lt;/em&gt;&lt;/strong&gt;) which invade the midgut wall of the mosquito where they develop into oocysts (&lt;strong&gt;&lt;em&gt;11&lt;/em&gt;&lt;/strong&gt;). The oocysts grow, rupture, and release sporozoites (&lt;strong&gt;&lt;em&gt;12&lt;/em&gt;&lt;/strong&gt;), which make their way to the mosquito's salivary glands. Inoculation of the sporozoites into a new human host perpetuates the malaria life cycle (&lt;strong&gt;&lt;em&gt;1&lt;/em&gt;&lt;/strong&gt;).&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Sources&lt;/h3&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The Centers for Disease Control and Prevention: &lt;a href=&quot;https://www.cdc.gov/dpdx/malaria/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Malaria&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia: &lt;a href=&quot;http://en.wikipedia.org/wiki/Plasmodium_falciparum_biology&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Plasmodium falciparum&lt;/em&gt; biology&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="948" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.070" LastActivityDate="2014-05-10T23:38:02.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17322" PostTypeId="1" AcceptedAnswerId="17338" CreationDate="2014-05-11T08:29:00.530" Score="1" ViewCount="1607" Body="&lt;p&gt;When our instructor asked us about the speed of action potentials in cells, I told him that action potentials and two-wheelers travels at similar speeds. He thought that this is an 'interesting' way of looking at it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Needless to say after the class I tried to figure out the minimum, average and maximum speed of action potentials in neurons. &lt;a href=&quot;http://en.wikipedia.org/wiki/Conduction_velocity&quot; rel=&quot;nofollow&quot;&gt;Wiki helped&lt;/a&gt; but its not authoritative. Some place it says that the fastest is 110 m/s and other place it is 120 m/s. While slowest one varies between 7 m/s (in Rana frog) to 0.5 m/s (Nociceptors) on Wiki. The average speed would be hard to calculate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for any references where slowest and fasted action potentials are described. They would be interesting cases to write a note for classromm.&lt;/p&gt;&#xA;" OwnerUserId="6228" LastActivityDate="2014-05-11T17:08:19.003" Title="Fastest and slowest action potential" Tags="&lt;neuroscience&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17323" PostTypeId="1" AcceptedAnswerId="17329" CreationDate="2014-05-11T09:57:44.110" Score="2" ViewCount="118" Body="&lt;p&gt;I am trying to find data and some method by which I can see and say that there are some cardiomyocytes not working.&#xA;I have reviewed many arrythmia data where I think I can see much cardiomyocetes there and there which are not beating at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any method with available data for the recognisition of cardiomyocytes without beating?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am particularly interested in the paediatric data.&#xA;I am using at the moment ECG data after cardiac infarction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the name of this video record?&lt;/strong&gt;&#xA;Picture from House season 3 episode 2:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/o6eRe.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="9943" LastEditDate="2016-02-23T12:55:20.933" LastActivityDate="2016-02-23T12:55:20.933" Title="To determine no beating cardiomyocytes from ECG or video recording" Tags="&lt;cardiology&gt;&lt;signal-processing&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17324" PostTypeId="1" AcceptedAnswerId="17893" CreationDate="2014-05-11T10:18:47.360" Score="8" ViewCount="2903" Body="&lt;p&gt;It looks like a simple problem, affecting almost half of the population at the post-pubertal age and of any gender and ethnicity [wikipedia]. What is so complex about finding a cure? Also, if you know some of the most effective treatments, they're welcome.&lt;/p&gt;&#xA;" OwnerUserId="6016" LastActivityDate="2015-12-08T01:35:05.230" Title="Why is there no cure for Dandruff?" Tags="&lt;human-biology&gt;&lt;pathology&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17327" PostTypeId="1" CreationDate="2014-05-11T12:31:16.570" Score="5" ViewCount="6040" Body="&lt;p&gt;Are there any animal species that have two sexes and a kind of different internal diversification in two genders or more? I don't mean something like different-task-based diversity, but something biological? &#xA;For example let's imagine a species with:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2 sexes (male and female)&lt;/li&gt;&#xA;&lt;li&gt;2 gender (A and B)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and individuals can match iff they are not only of different sex but also of different gender.&#xA;So you can only have Ma-Fb, Mb-Fa.&lt;/p&gt;&#xA;" OwnerUserId="6693" LastEditorUserId="28125" LastEditDate="2017-07-22T20:07:49.797" LastActivityDate="2017-07-23T01:40:54.123" Title="Does any animal species have two sexes and more genders?" Tags="&lt;reproduction&gt;&lt;ethology&gt;&lt;sex&gt;&lt;sexual-selection&gt;" AnswerCount="8" CommentCount="9" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17328" PostTypeId="1" CreationDate="2014-05-11T13:37:29.840" Score="4" ViewCount="2705" Body="&lt;p&gt;Don't they both just disrupt RNA so it can't make a protein? If so, then what is the difference between the 2?&lt;/p&gt;&#xA;" OwnerUserId="6413" LastActivityDate="2014-05-11T17:21:35.697" Title="Do miRNA and antisense RNA do essentially the same thing?" Tags="&lt;rna&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17329" PostTypeId="2" ParentId="17323" CreationDate="2014-05-11T13:47:09.420" Score="2" Body="&lt;p&gt;A number of cardiomyocytes is lost during an infarction. Instead, fibrous tissue forms, but it only preserves structural integrity, having no contractile function &lt;sup&gt;[1]&lt;/sup&gt;. Myocardial infarction is an uncommon condition in pediatrics, happening very rare, when embolization occurs due to blood coagulation affections or heart congenital defects &lt;sup&gt;[2]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fibrous tissue has different properties, thus modifying:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;MDE-MRI images &lt;sup&gt;[3]&lt;/sup&gt;&lt;/li&gt;&#xA;&lt;li&gt;ECG: deep Q wave &lt;sup&gt;[4]&lt;/sup&gt;&lt;/li&gt;&#xA;&lt;li&gt;echocardiography: hypoechoic and hyperdense echoes inside the fibrotic material (the latter compatible with calcium) &lt;sup&gt;[5]&lt;/sup&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;That video record is probably about 3D Echocardiography (look &lt;a href=&quot;http://www.escardio.org/communities/EACVI/CasePortal/Pages/multiplanar--3d-echocardiographic-analysis-of--a-subaortic-membrane.aspx&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; at Video 2 and figure 2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Yao Sun, &lt;a href=&quot;http://cardiovascres.oxfordjournals.org/content/81/3/482.full.pdf&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Myocardial repair/remodelling following infarction: roles of local factors&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Nicola Carano &lt;em&gt;et al.&lt;/em&gt;, &lt;a href=&quot;http://pediatrics.aappublications.org/content/114/2/e255.full&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Acute Myocardial Infarction in a Child: Possible Pathogenic Role of Patent Foramen Ovale Associated With Heritable Thrombophilia&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Harikrishna Tandri &lt;em&gt;et al.&lt;/em&gt;, &lt;a href=&quot;http://content.onlinejacc.org/article.aspx?articleid=1136198&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Noninvasive detection of myocardial fibrosis in arrhythmogenic right ventricular cardiomyopathy using delayed-enhancement magnetic resonance imaging&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;ECGpedia - &lt;a href=&quot;http://en.ecgpedia.org/wiki/Pathologic_Q_Waves&quot; rel=&quot;nofollow&quot;&gt;Pathologic Q Waves&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Berenzstein CS &lt;em&gt;et al.&lt;/em&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10804436&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Usefulness of echocardiography and doppler echocardiography in endomyocardial fibrosis&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-05-11T13:47:09.420" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17330" PostTypeId="2" ParentId="17327" CreationDate="2014-05-11T13:51:36.067" Score="3" Body="&lt;p&gt;There are &lt;a href=&quot;http://animals.pawnation.com/list-hermaphrodite-animals-2829.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;hermaphrodites&lt;/a&gt; and &lt;a href=&quot;http://evolutionfaq.com/articles/sex-change-nature-coral-reef-fish&quot; rel=&quot;nofollow noreferrer&quot;&gt;gender changing&lt;/a&gt; (M-&gt;F, F-&gt;M) fish.  Also occasionally, there are also individuals who are neither male nor female, which may or may not count here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I haven't seen 3+ separate genders except for fungi, which might occasionally be multicellular, but probably not what you are thinking of. Fungal genders are so many because they define combinations where mating is compatible.  &lt;a href=&quot;http://www.independent.co.uk/news/scientists-discover-why-fungi-have-36000-sexes-1119181.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;This news story&lt;/a&gt; has a decent summary of why as far as gametes goes, larger animals are known to have only 2 gametic genders, while fungi can have thousands.  You might say that bacteria have gender when they want it (when they have a pili-containing plasmid) and otherwise they have none - any individual may transfer DNA to another under the right conditions (like death).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know this isn't what you are asking about, but this is the closest I can find. Digging around, biologist Joan Roughgarden has written a book &lt;a href=&quot;http://www.crossdreamers.com/2009/12/transgender-animals.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;Evolution's Rainbow&quot;&lt;/a&gt; about cases where there may be more than one social role in a given species for biologically male or females - dominance, display, homosexuality and behaviors like this.  Social gender roles has been a way of talking about the biological nature of human social roles since the 1970s - see also Sarah Hrdy. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2016-12-21T23:59:26.840" LastActivityDate="2016-12-21T23:59:26.840" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17331" PostTypeId="1" CreationDate="2014-05-11T13:58:34.197" Score="3" ViewCount="325" Body="&lt;p&gt;It can either go to the smooth ER then to the Golgi or it can go directly to the Golgi, right? Also, the smooth ER gets all of its material to synthesize things from the rough ER, right? Sorry, I looked around but couldn't really find a direct answer to my question. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="6413" LastActivityDate="2014-07-10T19:30:06.457" Title="In the endomembrane system, after a protein leaves the rough ER, where does it go?" Tags="&lt;intracellular-transport&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17332" PostTypeId="2" ParentId="17053" CreationDate="2014-05-11T14:04:42.783" Score="1" Body="&lt;p&gt;I'm going to try to lay out some basic definitions here in as plain language as I can find.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its difficult to study enzymes when they are outside the cell, where they may behave quite differently in different contexts.  We categorize a given enzyme in its class by &lt;em&gt;kcat&lt;/em&gt;, &lt;em&gt;Km&lt;/em&gt; and by mechanism (the sort of reaction they catalyze.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;kcat&lt;/em&gt; is sort of a maximum velocity of the enzyme - when there is a lot of substrate around - what is the rate of catalysis.  Ideally there will be zero product present.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Km&lt;/em&gt; is sort of the inverse affinity of the enzyme for its substrate, but at half the maximum velocity of the reaction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanism, which has a couple of definition basically asks how many substrates are bound and in what order, which products are released and in what order, and any intermediates in the reaction which might appear, and in what order.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;e.g.: A -&gt; A* -&gt; B* -&gt; B&#xA;  A + B -&gt; C + D &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I say 'sort of' because you might never see an enzyme operate at maximum rate in living cells.  Substrates are usually rate controlled there - they only have enough of any given compound as they need. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The context that all of these numbers and designations are used is often taxonomical - that is to say you can categorize and sort, and describe what the enzyme does.  In practice large differences in the numbers can describe how useful one enzyme is over another, but it doesn't necessarily tell you how an enzyme will definitely behave &lt;em&gt;in vivo&lt;/em&gt; or entirely how it will work in an industrial application.  Its just a start.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-05-11T14:04:42.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17333" PostTypeId="1" CreationDate="2014-05-11T14:43:52.250" Score="4" ViewCount="258" Body="&lt;p&gt;I have a .map file which contains x-ray crystallography data of a bacteriophage. The format of the file is CCP4. I can open the file using VMD. However, I am unable to get the xyz co-ordinates. It shows the following error when I click on the option of saving data in xyz format:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;`No timesteps selected; trajectory file will not be written.'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is a big file of 64MB. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The file I am referring to may be downloaded at:&#xA;&lt;a href=&quot;ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1086/map/emd_1086.map.gz&quot; rel=&quot;nofollow&quot;&gt;ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1086/map/emd_1086.map.gz&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can't we save xyz co-ordinates for CCP4 files? Or is it possible to extract any other form of data?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am new to VMD and these formats.&#xA;Any help would be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="6694" LastEditorUserId="6694" LastEditDate="2014-05-12T08:54:12.757" LastActivityDate="2014-07-11T12:00:16.557" Title="Getting xyz co-ordinates from a .map file (CCP4 format) in VMD" Tags="&lt;xray-crystallography&gt;&lt;ccp4&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17334" PostTypeId="2" ParentId="17328" CreationDate="2014-05-11T15:34:24.060" Score="4" Body="&lt;p&gt;Antisense simply means that a sequence is the complement of another. miRNAs are naturally occurring antisense RNAs yes. The &quot;difference&quot; is that &lt;em&gt;antisense RNA&lt;/em&gt; is often used for sequences developed in the lab and used for processes such as &lt;a href=&quot;https://en.wikipedia.org/wiki/RNA_interference&quot; rel=&quot;nofollow&quot;&gt;RNAi&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;miRNAs, on the other hand, are encoded by the genome and are used by the cell for regulating gene expression. They do this through the &lt;a href=&quot;https://en.wikipedia.org/wiki/RNA-induced_silencing_complex&quot; rel=&quot;nofollow&quot;&gt;RISC complex&lt;/a&gt;, just like artificial antisense RNAs such as &lt;a href=&quot;https://en.wikipedia.org/wiki/Small_interfering_RNA&quot; rel=&quot;nofollow&quot;&gt;siRNAs&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, &lt;em&gt;antisense&lt;/em&gt; is the general term, and can be applied to any sequence whose complement exists in the genome. miRNAs are a particular class of antisense RNAs. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-05-11T16:59:57.657" LastActivityDate="2014-05-11T16:59:57.657" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17335" PostTypeId="2" ParentId="17328" CreationDate="2014-05-11T15:46:31.053" Score="2" Body="&lt;p&gt;Antisense RNA is any RNA that is complementary to another RNA. Therefore, miRNA is a type of antisense RNA. Antisense RNA can inhibit translation of mRNA by hybridizing and preventing ribosomal binding/translocation. Antisense RNA in this context could be any length and bind anywhere between the RBS and end of the CDS. miRNA also prevents translation but it does so through the RNAi pathway by facilitating binding of the RISC complex to mRNA (often in the 3'-UTR, which is after the CDS). miRNA are around 22 nts long (but it is species dependent). &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-05-11T17:21:35.697" LastActivityDate="2014-05-11T17:21:35.697" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17336" PostTypeId="2" ParentId="16887" CreationDate="2014-05-11T16:11:43.903" Score="3" Body="&lt;p&gt;Chimeric sequences show up in sequencing projects a lot and you always have to watch for them. They show up a lot for a couple of reasons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, sequencers are not perfect and generate sequences with errors.  Also they produce a lot of data but often not quite enough.  There are usually thin spots in the sequence assembly - regions which are not covered very well.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a sequencing error coincides with a gap in the sequencing, the two ends of a sequence alignment can align to two unrelated or distant segments of sequence, creating an alignment assembly which has two unrelated portions - a chimera. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is especially the case in EST and RnaSeq runs where long scaffold sequences and higher coverage might not help as much. It does have an impact in Chromosomal sequencing as well.  There's some interest in how often &lt;a href=&quot;http://gettinggeneticsdone.blogspot.com/2014/05/mycoplasma-contamination-in-cell-line.html&quot; rel=&quot;nofollow&quot;&gt;contaminating DNA get included into sequencing output&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-05-11T16:11:43.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17337" PostTypeId="2" ParentId="17276" CreationDate="2014-05-11T16:41:30.270" Score="3" Body="&lt;p&gt;EDITED ANSWER&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on comments and responses my original answer to this question received I have decided to edit the answer and respond to some questions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since I work on proteins, I tend to favour protein based approaches specially when wondering about the presence of a protein. This is simply the case because protein is what is important functionally (purely talking about protein based problems/questions here and not talking about RNAi stuff here) so what I have experienced editors require for majority of papers, they want to see some sort of protein work. Now I'm aware that is not always possible since the antibody (Ab) might not be very specific or sensitive specially for low expressing proteins. If a protein is highly transient that makes the problem even worse, which is why many people resort to mRNA expression to make deductive reasoning for the presence of proteins although that makes a number of assumptions about how the mRNA is processed and whether the relationship between mRNA expression and protein expression level is linear but thats another discussion. So all I'm trying to say is that it's important check for the presence of a protein using Ab based techniques, which are immunohistochemistry (IHC) and western-blot (WB).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my primary recommendation is to use Gi and Gs species specific (non-cross reactive) antibodies to check for the presence of your proteins of interest and always use Ab heavy chain control for IHC and a negative control for your WB using a sample that you know doesn't express your proteins of interest, if thats available. IHC also tells you some spatial information and whether Gs and Gi are both present in the same cell line or not and if they co-localise etc etc! Obviously check for Ab availability and if its compatible for IHC or WB procedures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other method that is feasible is if you know your two different cells express only one of the Gs or Gi exclusively, you can look at their specific inhibitors and add it to some of your cells and the chances are if the dose is high enough it will cause the cells to die since Gs or Gi are crucial for cell function. You can probably get away with an experiment like this using wells in a 24 well dish so you don't have to use that much media or drugs. But with stuff like this it might not work and you might get off-target effects so just do this as a complementary test. For your drug test always do a DMSO control since the chances are that's what the drugs are dissolved in and if not just use whatever solvent the drugs are dissolved in and add them to your cells in your control experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the other possible and commonly used method to check for the gene expression of protein and subsequently infer its presence as a protein is to use a reverse transcription based PCR, such as RT-PCR although it doesn't have to be real-time as correctly mentioned in the comments. Please note that I'm not at all an expert in this and do check my answer in this section since I haven't personally done reverse transcription based PCR. As far as I'm aware, the basic procedure is to extract cellular mRNA, which can be performed using kits such as RNeasy or a similar product (I'm not promoting any products here and these are just what I have came across!). The protocols come with the kits and available online, and tells you exactly what min/max cell number/RNA levels should be present and how your cells should be (pelleted) before processing. Another method for RNA extraction is CsCl but thats pretty messy and complicated and requires high expertise to get it right but I know its inevitable for certain situations but for cell processing, a kit will do. At least RNeasy protocol states it enriches for mRNA and selectively exclude other types of RNA. Once you have your cellular mRNA you can proceed to reverse transcription using the appropriately designed primers for your gene of interest using a thermocycler. Again I'm not sure what tools to use for designing the primers for making cDNA from mRNA and what to look for (apart from the fact that make sure your primers are specific) as I only do regular PCR but would welcome any edits! Once you get from mRNA to cDNA, you can then run them on your (Ethidium Bromide or whatever DNA staining based) agarose gel and see if your amplicon is present and is the correct size (again based on the primers you have chosen you would know what the correct size is) and hence whether your gene is expressed or not. At least RNeasy kit says you do not need to use DNase digestion to get rid of any DNA before reverse transcribing your mRNA as most of it gets cleaned up when using the kit but you have that option. Now regarding the next-generation RNA sequencing I do not know anything about them so would again welcome any edits but seems unnecessary since you only want to know if the gene of interest is expressed so don't need any sequence info but thats an option too (although I imagine a little expensive?). Just to mention something very obvious, it's important that the species, which your lines have been generated from are sequenced or you have good sequence information about the Gs and Gi genes in your lines otherwise designing primers would be guess work. Its always best to see if anyone has done what you are trying to do and ask for their primers as most people are happy to share reagents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now you have probably noticed so far that my methods are quite biased towards molecular biology approaches and that's simply because that's what I know more about, however a great suggestion was to use cAMP levels as an indicator for Gs or Gi expression. Again I'm not an expert in this since I haven't ever analysed small molecules but I imagine that involves something like a HPLC, which you need to discuss with a chemist/biochemist how to extract and clean up your cells from everything and leave only the cAMP. There is probably a procedure/kit/biosensor for it but I will avoid getting into it as I know virtually nothing about this. However I have a note of caution for these types of indirect experiments. I have no idea what your cell lines are and how well they are characterised but since lines have all sorts of mutations and deletions and insertions in them, it's not a good idea to make inferences from cAMP levels. Since considering cAMP presence is quite important for cellular function, their absolute levels in a cell line is not necessarily a good indicator of whether one cAMP production regulator is present or not and I'm sure if you do something like this you open yourself to major criticism by any journal editor/referee. What will be a good idea though in any future experiments you do with these cells is to over express Gs or Gi and see their effects on cAMP production but I just don't recommend using cAMP levels as a sole indicator as to whether Gs or Gi is expressed or not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If everything else fails and you got tired and wanted to wash your hands off this identification task, you can always lyse your cells and send them for mass spectrometry (MS) if there is such a facility at your institute. It's crucial that the species, which your lines originate from are characterised in terms of their global protein sequences since programs such as Mascot query the raw spectral data against databases such as UniProt to get protein coverage and subsequently protein hits. Also before you go ahead with you MS experiments, just speak to the facility manager and ask for guidance as to what lysis buffer is best to lyse your cells in and what components should not be in your lysis buffer and how sensitive their machines are and how likely you are to get detection and what your protein concentration should be. I think the best machine to use is Orbitrap and as a general rule, the higher the protein amount, the more likely you are to detect it. Since cell lysate is pretty messy and the MS machine columns can get saturated by abundant proteins such as actin, it would be best to run your lysates on an SDS-PAGE gel under reducing conditions (you can even do multiple loads by running your samples in the gel, switching off the WB machine, loading more samples and running them in the gel and continue doing this a few times. It works, I have done it myself but for pulled down samples which are a bit cleaner (less contaminants/unwanted proteins) in general). Once your gel runs through just cut the region of the gel corresponding to the molecular weights of Gs and Gi and send that for MS identification. This method (running your lysate through SDS-PAGE gel) gets rid of unwanted proteins that can interfere with the identification process. But MS is very expensive!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again I would highly welcome any edits to my own edited reply! I'm here to help and learn.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-05-12T22:50:42.970" LastActivityDate="2014-05-12T22:50:42.970" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17338" PostTypeId="2" ParentId="17322" CreationDate="2014-05-11T17:08:19.003" Score="1" Body="&lt;p&gt;You can search on &lt;strong&gt;&lt;a href=&quot;http://bionumbers.hms.harvard.edu/&quot; rel=&quot;nofollow&quot;&gt;Bionumbers&lt;/a&gt;&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is what I got after searching &lt;a href=&quot;http://bionumbers.hms.harvard.edu/search.aspx?log=y&amp;amp;task=searchbytrmorg&amp;amp;trm=action%20potential&amp;amp;org=&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;action potential&lt;/em&gt;&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Speed of action potential along non-myelinated invertebrate axons of ~10μm diameter = less than 1 m/s&lt;/li&gt;&#xA;&lt;li&gt;Action potential speed in myelinated axon = 50 ... 100 m/s&lt;/li&gt;&#xA;&lt;li&gt;Velocity of action potential in pyramidal tract at 37°C (in Cat Felis) = 164 m/s&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It offers you references for every number.&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-05-11T17:08:19.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17340" PostTypeId="1" CreationDate="2014-05-11T17:41:58.920" Score="2" ViewCount="667" Body="&lt;p&gt;During the acrosome reaction, the activation enzyme present in the sperm dissolves the corona radiata and zona pellucida enabling the sperm to reach the plasma membrane of the egg.&#xA;Also calcium and magnesium ions play an important role in acrosome reaction &lt;sup&gt;[&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jez.1401980312/abstract&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;ref&lt;/strong&gt;&lt;/a&gt;]&lt;/sup&gt;.&#xA;What I fail to understand is how exactly do calcium and magnesium ions play a key role in acrosome reaction?&lt;/p&gt;&#xA;" OwnerDisplayName="user3800" LastEditorUserId="3340" LastEditDate="2014-12-24T13:34:43.593" LastActivityDate="2015-03-26T10:27:17.990" Title="Role of Calcium and Magnesium in capacitation/acrosome reaction" Tags="&lt;human-biology&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17341" PostTypeId="1" CreationDate="2014-05-11T17:47:54.750" Score="2" ViewCount="5137" Body="&lt;p&gt;Why does the affinity of haemoglobin for oxygen increase if an organism lives at a higher elevation where the oxygen pressure is lower?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wouldn’t its affinity for oxygen decrease because the acidity of the body would increase with the lack of oxygen? The textbook said otherwise though and I don't understand.&lt;/p&gt;&#xA;" OwnerUserId="6413" LastEditorUserId="22057" LastEditDate="2018-01-26T22:37:25.913" LastActivityDate="2018-01-26T22:37:25.913" Title="Why does the affinity of haemoglobin for oxygen increase at higher elevations?" Tags="&lt;hematology&gt;&lt;haemoglobin&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17342" PostTypeId="2" ParentId="17331" CreationDate="2014-05-11T18:11:49.337" Score="2" Body="&lt;p&gt;I'm no expert at this but will do my best to answer your question based on the title. It depends on the protein! proteins can either be cytoplasmic, nuclear, transmembrane or secretory. Cytoplasmic proteins (as far as I know) get released to the cytoplasm after they have been folded correctly (through chaperones) and gone through the quality control mechanism. Nuclear proteins get transported through the nuclear pores, across the nuclear envelope through chaperones. Now for the transmembrane or secretory proteins, the fate of these proteins and where they go is decided by the ER (but obviously the information is there in the protein sequence). Transmembrane proteins have a signalling peptide and a transmembrane domain signal anchor sequence which ER recognises and through fancy looping and elongation across the ER membrane, the proteins is further translated by the ribosomes and eventually gets translocated to the cell membrane. There is very very nice nature review paper (Rapoport, 2007) about this and if you look at Figure 5, you will get a good ideas as to what goes on. For the secretory protein again its the interaction of the protein sequence with the ER membrane, helped with the ribosomes (in fact the groves in the ribosomes are key for making these fancy looping happen as the protein residues in ribosomes interact with peptide residues (amino acids) that are being produced on the fly), that processes it and sends it for secretion (Rapoport, 2007) and trans-golgi network is also important in the secretion process (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1424219/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1424219/&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully these information would provide you with some hints.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-11T18:11:49.337" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17343" PostTypeId="2" ParentId="17341" CreationDate="2014-05-11T18:14:19.857" Score="3" Body="&lt;p&gt;The question seems to be based on the idea that there would be physiological adaptation to low oxygen, possibly through the Bohr effect. In fact the usual mechanism of adaptation is through genetic change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a lot of examples of animals which live (or fly) at high altitude and which have a haemoglobin with a higher oxygen affinity. Examples which spring to mind are the bar-headed goose and the camelids of South America (llamas, alpacas etc.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Haemoglobin has evolved as an efficient oxygen-delivery protein by having a variable affinity for oxygen: low affinity at low oxygen concentration, high affinity at high oxygen concentration. This is achieved through co-operative binding (allostery), and it ensures that the protein loads up with oxygen in the pulmonary circulation but releases oxygen in the peripheral tissues. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At high altitude, where the partial pressure of oxygen is lower, the haemoglobin of humans, for example, will not be fully saturated, impairing the delivery of oxygen to the body. Haemoglobin variants with an increase in the overall affinity for oxygen can achieve full loading at the expense of slightly less release in the tissues - overall a better oxygen delivery function. This is what happens in the camelids, but there is no such adaptation in humans living at high altitudes.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-11T18:14:19.857" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17344" PostTypeId="1" CreationDate="2014-05-11T19:13:24.053" Score="0" ViewCount="42" Body="&lt;p&gt;I started a thread about &lt;em&gt;Nasal chronic Inflammation after influenza virus&lt;/em&gt; &lt;a href=&quot;https://biology.stackexchange.com/questions/17325/nasal-chronic-inflammation-after-influenza-virus&quot;&gt;here&lt;/a&gt;.&#xA;However, I do not understand enough well the structure of the nose to answer the questions there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that the lysed DNA (proteins) of small bronchial tree are circulated on the nasal epithelium.&#xA;I am not sure how this happens but my intuition is&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;first through lymphatic circulation&lt;/li&gt;&#xA;&lt;li&gt;then on posterior nasalis membrane upward progression on the nasal membrane in the nares.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Picture about the nasal membrane. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ovu9z.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Better pictures about the linkage of lymphatic circulation from the small bronchial trees into posterior nasal membrane are wanted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I am not completely sure how this organisation occurs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How is the nasal secretion system of local immunity (IgA) coupled with the lymphatic circulation around the back of the nose?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-05-11T19:13:24.053" Title="How is the nasal secretion system of local immunity coupled with lymphatic circulation?" Tags="&lt;lymphatic-system&gt;&lt;nose&gt;&lt;immunity&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17345" PostTypeId="1" AcceptedAnswerId="17347" CreationDate="2014-05-11T19:39:19.213" Score="3" ViewCount="1080" Body="&lt;p&gt;Are there any advantages of bisexual reproduction over asexual one towards species conservation and promotion? Do animals that have two or more sexes have more chances to reproduce?&#xA;Does anybody had a quantitative account of this fact? &lt;/p&gt;&#xA;" OwnerUserId="6693" LastActivityDate="2014-12-31T09:25:57.093" Title="Advantages of bisexual reproduction over asexual one toward species promotion?" Tags="&lt;reproduction&gt;&lt;sex&gt;&lt;sexual-selection&gt;&lt;conservation-biology&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-05-12T14:57:10.717" ContentLicense="CC BY-SA 3.0" />
  <row Id="17346" PostTypeId="1" CreationDate="2014-05-11T20:06:27.327" Score="2" ViewCount="107" Body="&lt;p&gt;In the following scenario: You were given short sequence reads of plant RNA obtained from a next-generation sequencing machine (fragments of 20–30 nucleotides in length). You attempt to map them back to the genome, but a significant proportion of them do not align.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is: give some obvious explanations why the alignment of short sequences can fail, apart from possible contamination or technical difficulties during the preparation of the RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I would answer it as because reads are short, and because of introns(since it is RNA)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another scenario: There are some indications that the problematic sequences come from an uncharacterised plant RNA virus. What would you do next? What are the specific caveats with short sequence reads?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I got the above questions, I am a computer science student doing bioinformatics, any biologist could answer it will be well appreciated&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="6678" LastEditorUserId="6678" LastEditDate="2014-05-11T20:54:21.663" LastActivityDate="2014-05-12T17:11:16.560" Title="In genome research, what is the problem in Mapping that may be caused by reads being too short?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;dna-sequencing&gt;&lt;genomics&gt;&lt;rna-sequencing&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17347" PostTypeId="2" ParentId="17345" CreationDate="2014-05-11T20:22:55.053" Score="2" Body="&lt;p&gt;Those are very good questions. Unfortunately answers are not easy and ask for writing a lot! But maybe someone else will give it a try and make it better than I can. Note that the evolution of recombination and of sexual reproduction are not quite the same thing. Also, evolution of sexual reproduction is not the same than evolution from various reproductive system. Finally there are also questions concerning the evolution of sexual determination system. You might have more chance to get useful answers  by splitting up your question and to ask for evolution between different reproductive system. Hermaphroditism vs Bisexual reproduction. Asexual vs sexual. And finally on another post you may add the &quot;conservation&quot; part of your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do you mean &quot;animals that have two or more sexes&quot;? Do you mean hermaphrodites?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may have a look to other posts on this sites that discuss the question. I don't think there is one post yet that really goes in depth though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that would be great if someone could post an easy-to-read source of information on the subject. &lt;a href=&quot;http://www.lecactusheuristique.com/article-26225719.html&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is one but it is in french only. &lt;a href=&quot;https://www.youtube.com/watch?v=AKEZH2-frxw&quot; rel=&quot;nofollow&quot;&gt;This presentation&lt;/a&gt; by Sally Otto will probably interests you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some hints in very short: One issue with hermaphroditism is selfing and its associated concept inbreeding depression. For conservation purposes, note that if one beneficial mutation occurs (at any locus) before another beneficial mutation had time to reach fixation, then  the frequency of one of the two beneficial mutations will necessarily goes to zero. You may be interested in the two-fold cost of sex. &lt;a href=&quot;http://en.wikipedia.org/wiki/Muller%27s_ratchet&quot; rel=&quot;nofollow&quot;&gt;Müller's ratchet&lt;/a&gt; is also a concept you may want to learn about. There are several very interesting quantitative models on the subject and it is still an ongoing debate. You may be interested in the work of S. Otto and B.&amp;amp; D. Charlesworth. You may be interested in &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0691083126&quot; rel=&quot;nofollow&quot;&gt;E. Charnov's book&lt;/a&gt; although it is a bit old now. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-12-31T09:25:57.093" LastActivityDate="2014-12-31T09:25:57.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17348" PostTypeId="1" CreationDate="2014-05-11T20:57:25.797" Score="3" ViewCount="2254" Body="&lt;p&gt;In nursing school, they advice for people with upper respiratory infections to be in a slightly elevated position at the head region when sleeping.&#xA;My intuition of the reason is that the lymphatic drainage to the venous arch works better; gravity helps to drain the lymph to the venous system; not only the heart.&#xA;Bacterial infection of the pharynx occurs in a prolonged exposure of the concentrated lymph.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I got today exact information about exact positions to relieve the body most when sleeping:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;5-10 % angle to relieve body most, while gravity helping to suck the lymph from the throat; can be helped with the hormone motilium (domperidone)&lt;/li&gt;&#xA;&lt;li&gt;more than 10 % is for other conditions&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any studies about the effect of elevated sleeping position on the recovery time from the upper respiratory infection?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-07T20:22:04.927" LastActivityDate="2014-12-26T09:33:29.717" Title="Elevated position effect on recovery times from upper respiratory infections at rest?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;pharmacology&gt;&lt;cardiology&gt;&lt;infection&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17349" PostTypeId="1" CreationDate="2014-05-11T22:00:00.517" Score="6" ViewCount="441" Body="&lt;p&gt;I've been doing a bit of reading about mast cell degranulation and have become thoroughly lost while trying to understand how the secretory granules are actually secreted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that there are many ways in which mast cells can be stimulated to degranulate, but I have been focusing on the example of IgE bound to FcεRI receptors. I believe I'm right in saying that antigen binding causes cross-linking of FcεRI receptors (since the antigen epitopes bind with the IgE paratopes and the IgE antibodies are themselves bound to the FcεRI receptors.) This recruits Lyn which phosphorylates ITAM motifs on the β and γ chains of the FcεRI receptors. This recruits Syk which is phosphorylated and activates LAT. This phosphorylates PLCγ which catalyzes the breakdown of PIP2 into IP3 and DAG.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of this leads to the activation of PKC. I understand that PKC is (at least in part) responsible for the exoctyosis of SG but my question is by what means? &lt;a href=&quot;http://en.wikipedia.org/wiki/Mast_cell#Degranulation_and_fusion&quot;&gt;Wikipedia&lt;/a&gt;, &lt;a href=&quot;http://www.kegg.jp/kegg-bin/show_pathway?hsa04664&quot;&gt;KEGG&lt;/a&gt; and &lt;a href=&quot;http://wenliang.myweb.uga.edu/mystudy/immunology/ScienceOfImmunology/Hypersensitivitydiseases.html&quot;&gt;this handy resource&lt;/a&gt; are all very cursory, whereas the academic papers which google turns up are way over my head.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if I might, what is it that PKC does and, in general, how are the secretory granules transferred from within the cell to the plasma membrane and out into the environment around the cell?&lt;/p&gt;&#xA;" OwnerUserId="5263" LastActivityDate="2014-05-31T02:17:49.970" Title="Exocytosis of mast cell secretory granules" Tags="&lt;cell-biology&gt;&lt;immunology&gt;&lt;cell-signaling&gt;" AnswerCount="4" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17350" PostTypeId="2" ParentId="3181" CreationDate="2014-05-11T23:11:29.167" Score="1" Body="&lt;p&gt;I'm going to give this question a blind attempt, assuming you are talking about PCR (since you are talking about genomic DNA and cDNA) and not RT-PCR or qPCR, since I know very little about them. This answer is not necessarily optimisation for annealing but checking some basics and potential solutions. In my work I had to do a lot of site directed mutagenesis and genotyping and there are some important rules you have to follow in your primer design. First try to keep your primer length between 25-30 for sequencing (at least thats what I do) and for site-directed mutagenesis between 25-45 since anything above 45 bases increases the likelihood of secondary structure formation. Primer melting temperature (Tm) should be &gt;=78 oC (Tm= 81.5 + 0.41(%GC)-675/N [with N being primer length in bases]). Also primers should have a minimum CG content of 40% and should ideally start and end with a C or G. So check your primer CG% since if its too high then it will make a few problems including increased Tm and possibility of primer-dimer formation due to CG triple hydrogen binding. This document has some nice information (&lt;a href=&quot;http://www.genomics.agilent.com/files/Manual/210518.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.genomics.agilent.com/files/Manual/210518.pdf&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my opinion if all else fails and you are still struggling with your primers, then re-design a new primer set, if possible. Now getting back to the annealing temperature issue, in my experience for cDNA, annealing temp of 50 oC works best and for genomic DNA, annealing temp of 55 oC works best, which is about the range most people work with and I have so far had no problems. I'm more than happy to share my genomic DNA PCR cycle information with you if you wish through an edit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-11T23:11:29.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17351" PostTypeId="1" CreationDate="2014-05-11T23:20:24.693" Score="5" ViewCount="474" Body="&lt;p&gt;This &lt;a href=&quot;http://www.cell.com/cell/abstract/S0092-8674%2814%2900340-7?cc=y?cc=y&quot;&gt;recent paper in Cell&lt;/a&gt; describes a cancer cell using osmotic pressure to move in confined spaces. The cell preferentially inserts Na+/H+ antiporters in the leading membrane. I want someone to double-check my osmosis before I make students reason it out:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The normal Na+/K+ pumps cause an increase in Na+ ions outside the cell, but little change in osmotic pressure across the membrane.&lt;/li&gt;&#xA;&lt;li&gt;Increased Na+/H+ antiporters will allow Na+ in while pushing H+ out at the &quot;front&quot; end of the traveling cell.&lt;/li&gt;&#xA;&lt;li&gt;While this causes little net solute change, it increases water flow into the cell via aquaporins (?? this part I find mysterious)&lt;/li&gt;&#xA;&lt;li&gt;Na+ continues to be pumped out of the cell by the Na+/K+ pump at the &quot;back&quot; end of the cell&lt;/li&gt;&#xA;&lt;li&gt;Water follows the Na+ through aquaporins out the &quot;back&quot; of the cell, moving the cell forward&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I don't feel convinced that moving ions around like this is causing osmotic gradients. Can anyone convince me?&lt;/p&gt;&#xA;" OwnerUserId="6517" LastActivityDate="2014-07-29T19:24:25.253" Title="How does a Na+/H+ antiporter drive osmosis in this &quot;osmotic motor&quot;?" Tags="&lt;physiology&gt;&lt;cell-biology&gt;&lt;osmosis&gt;&lt;membrane-transport&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17352" PostTypeId="1" CreationDate="2014-05-12T03:08:02.967" Score="2" ViewCount="224" Body="&lt;p&gt;I am in the process of creating a poster for the phage that I recently annotated. The phage is an A4 and the portion of the poster I am working on is analyzing the data that we have collected. I have an excel sheet that has all the Shine Dalgarno scores for each gene that we annotated and decided was the best. Using mathematica I tallied all the data into a table and this is what I got (The x value of the list shows the score, the y value shows the amount of genes that had this score): &lt;img src=&quot;https://i.stack.imgur.com/Zu4Ug.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can I create a distribution from this data? Would I need to use a Histogram, a plot, or some other graphic to represent the data? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biologically speaking, can we make any observations about the genome from these scores?&lt;/p&gt;&#xA;" OwnerUserId="6689" LastEditorUserId="1306" LastEditDate="2014-05-13T14:59:52.330" LastActivityDate="2014-07-16T13:05:38.500" Title="Comparing Shine Dalgarno scores, creating a distribution" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17353" PostTypeId="1" AcceptedAnswerId="17355" CreationDate="2014-05-12T06:22:53.397" Score="2" ViewCount="127" Body="&lt;p&gt;Assume you suspect amyloidosis because of the history of the patient: problem with vertebral column and &quot;purulent&quot; (serous, fibrous, or hemorrhagic) inflammation when patient very young.&#xA;Now, the patient has a chronic renal failure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any other method to diagnose the fracture of some bone than röntgen?&lt;/strong&gt;&#xA;Assume you do not know where the fracture is exactly.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="3624" LastEditDate="2017-03-13T13:50:25.470" LastActivityDate="2017-03-13T13:50:25.470" Title="To diagnose osteomyelitis of vertebral column in chronic kidney failure" Tags="&lt;pathophysiology&gt;&lt;kidney&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17354" PostTypeId="2" ParentId="17346" CreationDate="2014-05-12T06:54:08.737" Score="2" Body="&lt;p&gt;Being a bioinformatician as well, I am not really what you asked for, but I work with plant genetics so I'll try and answer anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you are mapping is RNA. So, as you already figured out, &lt;strong&gt;splicing events&lt;/strong&gt; will be a problem for end-to-end mapping of the reads. There are tools managing that, though, so let's assume you used one of them and still a lot of your reads do not map. To put in WYSIWIG's good point: Another event that can mess up with your alignments is &lt;strong&gt;RNA editing&lt;/strong&gt;, although this is not too likely to cause a high proportion of reads to not align at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some aligners might &lt;strong&gt;filter&lt;/strong&gt; out &quot;too short&quot; queries, so make sure you are not using one of them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, have you &lt;strong&gt;preprocessed&lt;/strong&gt; your reads? If you have not, there might be adaptor sequences left. Or may reads have very poor quality, thus are also aligned with poor quality, thus might be counted as unaligned.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And then check what you are aligning to. Many published plant genomes are also of &lt;strong&gt;minor quality&lt;/strong&gt;, including lots of unassigned bases. So, there could be large proportions of your reference genome that count in the genome length, but are only Ns and nothing will align there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Last but not least, your thought about a virus could also be right. Depending on the experiment, there might be &lt;strong&gt;pathogenic RNA&lt;/strong&gt; in your sample, so check against a suitable database.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the problem is only that the reads are &quot;too short&quot; for whatever reason, try doing &lt;strong&gt;transcriptome assembly&lt;/strong&gt; before comparing to your reference.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastEditorUserId="3827" LastEditDate="2014-05-12T10:46:08.137" LastActivityDate="2014-05-12T10:46:08.137" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17355" PostTypeId="2" ParentId="17353" CreationDate="2014-05-12T08:45:28.603" Score="1" Body="&lt;p&gt;Osteomyelitis can be diagnosed with the following imaging techniques &lt;sup&gt;[1]&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;first of all: &lt;strong&gt;radiography&lt;/strong&gt; to view the anatomy of the bone&lt;/li&gt;&#xA;&lt;li&gt;the sonography can be used to diagnose fluid collections, periosteal involvement. It is also the most useful procedure for kidney assessment &lt;sup&gt;[2]&lt;/sup&gt;.&lt;/li&gt;&#xA;&lt;li&gt;CT is also useful to detect early osseous erosion, but is less sensitive when it comes to bone infection&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;MRI&lt;/strong&gt; is the most sensitive and specific for osteomyelitis&lt;/li&gt;&#xA;&lt;li&gt;Nuclear imaging can be used to identify multifocal osseous involvement. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Carlos Pineda &lt;em&gt;et al.&lt;/em&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2884903/&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Radiographic Imaging in Osteomyelitis: The Role of Plain Radiography, Computed Tomography, Ultrasonography, Magnetic Resonance Imaging, and Scintigraphy&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;American College of Radiology, &lt;a href=&quot;http://www.acr.org/~/media/cfbe883c503c45e982d4b722de80230b.pdf&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Renal failure&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-05-12T10:29:22.203" LastActivityDate="2014-05-12T10:29:22.203" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17359" PostTypeId="1" AcceptedAnswerId="17375" CreationDate="2014-05-12T11:50:37.027" Score="6" ViewCount="201" Body="&lt;p&gt;Is it possible that an insect poisons itself while eating &quot;wrong&quot; plants/fruits/... and have symptoms like pain (may hard to measure or detect) or orientation disorder?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Background:&#xA;I observed a physically apparently healthy caterpillar moving in circles (or rather changing its direction constantly and end up at the same point again) on the street and falling over in middle of moving or standing. My first and a bit naive thought was, that it may have eaten something wrong...&lt;/p&gt;&#xA;" OwnerUserId="1807" LastEditorUserId="3952" LastEditDate="2014-05-12T19:26:29.810" LastActivityDate="2014-10-06T17:51:42.247" Title="Can an insect poison itself with food?" Tags="&lt;entomology&gt;&lt;food&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17360" PostTypeId="1" AcceptedAnswerId="17367" CreationDate="2014-05-12T12:18:27.843" Score="0" ViewCount="88" Body="&lt;p&gt;OK I have read that a cell generates 4 kinds of digital (to be precise discrete) data namely DNA, RNA, Protein (sequences that can be encoded as string sequences of nucleotides/ amino acids) and micro array image. I am not a biologist, but my interest is in the statistics and information theory of these data. I would like to know what information do DNA micro array image convey? For example after processing it with the aid of a suitable software, what sort of information we do obtain?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sample micro array image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HmPRm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5669" LastActivityDate="2014-05-12T14:57:38.060" Title="What information do microarray image convey?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;rna&gt;&lt;gene-expression&gt;&lt;microarray&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17361" PostTypeId="1" AcceptedAnswerId="17474" CreationDate="2014-05-12T12:58:30.107" Score="3" ViewCount="881" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Neurons were kept in a physiological solution. During the resting&#xA;  phase, the membrane potential in the axoplasm of neurons was negative&#xA;  compared to the extracellular space and a potential difference of -70&#xA;  mV was observed in this phase. Neurons were then treated in two&#xA;  different experiments with either gamma-amino butyric acid (GABA; an&#xA;  inhibitory neurotransmitter) or glutamate (an excitatory&#xA;  neurotransmitter) and the membrane potentials were recorded. Choose&#xA;  the correct statement/s:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(A) The resting membrane potential of -70 mV would not change with&#xA;  either GABA or glutamate treatments.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(B) The membrane potential would be even more negative than resting&#xA;  phase with GABA treatment.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(C) The membrane potential would be positive when the neuron was&#xA;  exposed to glutamate.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(D) The membrane potential would be more negative than resting&#xA;  potential after glutamate treatment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I feel, since, glutamate is excitatory, so resting potential should decrease when exposed to glutamate and increase when exposed to GABA. So (A)&amp;amp;(D) automatically gets eliminated and (B) is correct answer. I am confused at (C)&lt;/p&gt;&#xA;" OwnerUserId="6390" LastEditorUserId="806" LastEditDate="2014-05-15T18:37:12.440" LastActivityDate="2014-08-22T04:28:42.627" Title="Membrane potential after exposure to glutamate" Tags="&lt;neuroscience&gt;&lt;homework&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17362" PostTypeId="1" CreationDate="2014-05-12T13:19:25.080" Score="2" ViewCount="25" Body="&lt;p&gt;Six independent transformation experiments of tobacco leaf explants were carried out using&#xA;two different constructs - (1) construct I containing only a Hygromycin-resistance gene&#xA;$(HYG^R)$ as a selection marker and (2) construct II with the $(HYG^R)$ gene as a selection&#xA;marker and a passenger gene encoding a dephosphorylase enzyme $(DEP)$ that inhibits&#xA;phosphorylation in cells in which it is expressed. The marker as well as passenger genes&#xA;were placed under transcriptional control of a constitutive promoter $(CaMV35S)$, which&#xA;expresses in all cells/tissues. The results obtained are tabulated below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/aT1At.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Explain how The $HYG^R$ gene used in construct II lost its functionality probably due to&#xA;mutation(s) either in the gene or in the promoter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My approach: There is a probability that Expression of the $DEP$ gene is lethal to the transformed cells.&lt;/p&gt;&#xA;" OwnerUserId="6390" LastActivityDate="2014-07-11T14:39:42.577" Title="Question regarding 2 constructs of tobacco plant" Tags="&lt;homework&gt;&lt;gene-expression&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17363" PostTypeId="2" ParentId="17362" CreationDate="2014-05-12T13:27:45.160" Score="1" Body="&lt;p&gt;Having a toxic product for the cell in an expression vector is a not uncommon problem when overexpressing proteins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other possibility is that the selection marker itself is the problem. Here you can have mutations either in the promoter of the gene as well as in the gene itself resulting in a protein which is not capable of protecting the cells from the selection. Both possibilities (no expression and mutated protein) leave to the death of the transfected cells, since there is no protection of them by the resistance protein.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-12T13:27:45.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17364" PostTypeId="2" ParentId="17349" CreationDate="2014-05-12T14:16:49.580" Score="3" Body="&lt;p&gt;Mast cells contain a number of large, granular structures that are regarded as “secretory lysosomes,” yet they share several features in common with large dense-core vesicles, particularly with respect to the mechanisms of exocytosis. Upon activation, mast cells &quot;degranulate&quot; and exotcytose the contents of granules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;SNARE-dependent mechanism mediates exocytosis of neurotransmitters, hormones, and cytokines. Exocytosis of MCG is also SNARE-dependent. SNARE proteins are a family of evolutionarily conserved proteins that facilitate docking of apposing membranes and facilitate the fusion of membranes to accomplish exocytosis. The characteristic feature is a SNARE motif, a stretch of 60-70 amino acids, arranged in heptad repeat. This feature allows SNARE motifs of the individual SNARE proteins (from opposing membranes)  to zipper together, forming a core complex of a four helix bundle. The major SNARE proteins involved in mast cell degranulation include VAMP-8 (integrated in mast cell membrane), SNAP-23 and syntaxin-4 (both plasma membrane bound)⁠. There are other layers of regulation of course. The SNARE accessory proteins synaptotagmin 2 (a calcium sensor), Munc13-1/2, Munc18-2 and complexin-2, exert negative or positive modulatory effects on mast cell granule exocytosis &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.2011.01443.x/abstract&quot; rel=&quot;nofollow&quot;&gt;(Woska &amp;amp; Gillespie 2012)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt; I don't know about PKC's involvement, but I can speculate that it's part of the signalling pathway after activation of the Fc receptor and upstream of events that initiate mobilization of intracellular calcium, which would then immediately trigger exocytosis. As for movement, if they're like dense-core vesicles, move along actin filaments using a myosin motor (Va or Vb, for example), and in association with Rab-3. This is speculation though, and I'd suggest looking into the literature for more detailed analyses as you are asking for a broad literature review. &lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2014-05-13T00:21:36.757" LastActivityDate="2014-05-13T00:21:36.757" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17367" PostTypeId="2" ParentId="17360" CreationDate="2014-05-12T14:57:38.060" Score="1" Body="&lt;p&gt;Each spot overlaps with an oligonucleotide &lt;em&gt;probe&lt;/em&gt;, that is designed to identify a specific nucleic acid sequence. Gene expression arrays have probes which are complementary to sequences derived from the exons; therefore they will hybridize with these sequences. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before hybridization the cDNA (in this case) is labeled with a fluorescent molecule such as Cy3 or Cy5 (two dyes can be used to differentiate treated and control). Note that each spot will have many probe molecules. &#xA;Fluorescent intensity is proportional to number of hybridized DNA strands, which in turn is proportional to its expression in the sample.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Extensive amount of texts are available on microarray data analysis which you can find quite easily. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-05-12T14:57:38.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17368" PostTypeId="1" AcceptedAnswerId="17385" CreationDate="2014-05-12T16:44:12.260" Score="4" ViewCount="271" Body="&lt;p&gt;Imagine a typical situation that is likely to give rise to a bad temper within an individual: a person is awoken very early in the morning by a sound of a lawn being mowed next door.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unlike expected awakening by an alarm clock, such unexpected awakening by a lawn mower is likely to leave the person in a bad temper, feeling grumpy or sulky. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I'm interested if there's a specific hormone or process that makes a person experience the feeling of grumpiness?&lt;/strong&gt; Is it related to adrenaline and fight or flight instinct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, can experience of grumpiness be induced under laboratory conditions by using some combination of hormones/drugs?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2015-07-29T18:04:51.097" Title="Is there a hormone combination that makes humans grumpy?" Tags="&lt;human-biology&gt;&lt;brain&gt;&lt;endocrinology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17369" PostTypeId="2" ParentId="17346" CreationDate="2014-05-12T17:11:16.560" Score="0" Body="&lt;p&gt;I don't think it's possible to answer part 1 without more information.  Specifically, are you using a splice aware mapper, like Tophat?  Are you using a predetermined gtf with putative exon coordinates?  If so, is it for an extremely well studied plant, like Arabidopsis, or something brand new?  Your answer isn't right, introns would align to the genome fine.  The aligner doesn't know or care that those sequence shouldn't be in the sample, that won't affect mapping.  Personally, I don't think there is a very good answer to the question.  Short reads aren't more likely to fail than longer reads.  They are more likely to map to the wrong place, but that's not failure to map.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-05-12T17:11:16.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17370" PostTypeId="1" AcceptedAnswerId="17477" CreationDate="2014-05-12T17:16:39.250" Score="11" ViewCount="108062" Body="&lt;p&gt;An &lt;a href=&quot;https://pets.stackexchange.com/questions/3159/what-is-an-acceptable-flea-treatment-for-kittens/3176#3176&quot;&gt;answer at Pets&lt;/a&gt; suggested using dawn dish soap to kill fleas. I did a little looking around, and found several references supporting the idea.  Most of what I found was in 'selfhelp' and 'save a dime' type books and web sites. So while it seems to be a popular idea, I am unsure if it is an effective idea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any reliable science supporting the use of dish soap to kill fleas and/or ticks? If so what points in the life cycle would it be effective?  If it does work, how often would I need to use it to be relatively sure all the fleas/ticks have been through the appropriate life cycle and are dead?&lt;/p&gt;&#xA;" OwnerUserId="4240" LastEditorUserId="-1" LastEditDate="2017-04-13T12:59:17.050" LastActivityDate="2016-06-07T19:05:35.813" Title="Can dish soap really be used to kill ticks and fleas?" Tags="&lt;parasitology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17372" PostTypeId="1" AcceptedAnswerId="17408" CreationDate="2014-05-12T17:45:16.720" Score="5" ViewCount="110" Body="&lt;p&gt;In Felsenstein's 1981 Paper &lt;em&gt;&lt;a href=&quot;http://loco.biosci.arizona.edu/PDG/pdfs/Felsenstein1981.pdf&quot; rel=&quot;nofollow&quot;&gt;Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach&lt;/a&gt;&lt;/em&gt;, he describes (in equations (6) and (7)) a derivation of the equation of the probability of a particular base substitution.  I am having trouble making the connection between equations 6 and 7.  That is, going from &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$P_{ij}(dt) = (1- u\  dt)\ \delta_{ij} + u\ dt \ \pi_j \quad\quad [6]$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;to&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$P_{ij}(t) = e^{-ut}\ \delta_{ij} + (1- e^{-ut}) \pi_j \quad\quad [7]$$   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $u$ is the rate of base substitution per unit time, $\pi_j$ is the probabiltiy of observing a particular base and $\delta_{ij}$ is the Kronecker delta function (1 if i=j, 0 if i != j).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the paragraph that follows these equations there is an explanation as to why the exponential term makes sense (if you already know thats what it is), but I'm not understanding how to get from the first equation to the second. Any insights?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case anyone is ever interested (or perhaps if I eventually forget), it appears that Felsenstein is using a Poisson Process approximation for equation [7], although even with this new information I still do no see the connection between equations [6] and [7].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Page 9 of this &lt;a href=&quot;http://scholarship.claremont.edu/cgi/viewcontent.cgi?article=1047&amp;amp;context=scripps_theses&quot; rel=&quot;nofollow&quot;&gt;thesis&lt;/a&gt; had a pretty good explanation of this.&lt;/p&gt;&#xA;" OwnerUserId="6701" LastEditorUserId="6701" LastEditDate="2014-05-14T15:58:53.777" LastActivityDate="2014-05-17T02:05:50.853" Title="Base Substitution Probabilities Derivation" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17373" PostTypeId="1" AcceptedAnswerId="17374" CreationDate="2014-05-12T17:58:55.967" Score="4" ViewCount="27138" Body="&lt;p&gt;What is a suicide plasmid?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2737453/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2737453/&lt;/a&gt; mentions a &quot;suicide vector&quot;. See also &lt;a href=&quot;http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/plasmids/allele-exchange.html&quot; rel=&quot;nofollow&quot;&gt;http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/plasmids/allele-exchange.html&lt;/a&gt; which also mentions them.&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-05-12T19:20:15.793" LastActivityDate="2014-05-12T19:20:15.793" Title="What is a suicide plasmid?" Tags="&lt;cloning&gt;&lt;plasmids&gt;&lt;definitions&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17374" PostTypeId="2" ParentId="17373" CreationDate="2014-05-12T18:05:39.000" Score="6" Body="&lt;p&gt;As can be inferred from the Shanks et al. paper linked in the question: In molecular biology, &quot;suicide plasmid&quot; is a term that refers to a plasmid which is &lt;strong&gt;replication incompetent&lt;/strong&gt;.*&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plasmids normally bear a sequence called &quot;origin of replication&quot; &lt;code&gt;Ori&lt;/code&gt; which marks the plasmid for replication by the host cell. Plasmids that lack this &lt;code&gt;Ori&lt;/code&gt; will not be replicated during cell division, and will become diluted away and/or degraded after a few generations. Hence the name: The plasmid will &quot;commit suicide&quot; by promptly becoming eliminated from the population of DNA molecules inside each cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that because not all &lt;code&gt;Ori&lt;/code&gt;s are universal, the same exact plasmid may be a normal vector in one species (eg. E. coli) and a suicide vector in another species (eg. P. aeruginosa) - which is logical: If a vector can't replicate in any species at all, how do you produce this vector in the first place? (there are ways, but they are laborious)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;*: I am unable to find an authoritative source for this definition. The other two paragraphs are common knowledge.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-05-12T18:05:39.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17375" PostTypeId="2" ParentId="17359" CreationDate="2014-05-12T19:07:31.743" Score="8" Body="&lt;p&gt;Indeed, many plants produce molecules which are poisonous to things that eat that plant (insect, mammal, bird) in the &quot;hopes&quot; of preventing that animal from eating them. In this sense, even eating the &quot;right&quot; fruit may be dangerous (if that individual plant happens to be an exceptionally vigorous producer of the poison, or because the eater is weakened for some other reason, or simply ate too much). I doubt insects would eat the wrong fruit that much, because evolution favors insects that can precisely recognize correct prey plants, at least in indigenous surroundings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed, many plant &quot;flavors&quot; that we humans enjoy (such as garlic and peppers) are likely such herbivore poisons that we happen to be immune to. In fact, &lt;a href=&quot;http://youtu.be/6ClQXwkkH8A&quot; rel=&quot;noreferrer&quot;&gt;almost every plant is actually poisonous&lt;/a&gt; - the question is, poisonous &lt;em&gt;to which species&lt;/em&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plant defense is a very actively researched topic these days, since it relates to things like agricultural efficiency and global food shortages (and besides, it's a very interesting phenomenon). Here is a review discussing what you ask about in more detail: &lt;a href=&quot;http://www.plantphysiology.org/content/121/2/325.full&quot; rel=&quot;noreferrer&quot;&gt;http://www.plantphysiology.org/content/121/2/325.full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An addendum upon reading this question many months later: While evolution has perfected the ability of insects to recognize correct food, this has not been the case for man-made pesticides. I would guess that the caterpillar you saw is more likely to have eaten an artificial chemical (either pesticide or pollutant) than a &quot;wrong fruit&quot;.&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-10-06T17:51:42.247" LastActivityDate="2014-10-06T17:51:42.247" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17376" PostTypeId="2" ParentId="17327" CreationDate="2014-05-12T19:32:15.150" Score="7" Body="&lt;p&gt;Many organisms have multiple &lt;em&gt;sexes&lt;/em&gt;. For instance, here is one which &lt;a href=&quot;http://www.csuohio.edu/sciences/dept/biology/BGESweb09/BGESFaculty/doerder/index_files/Mating_types.htm&quot;&gt;apparently has 7&lt;/a&gt; (and each sex, or &quot;mating type&quot; can only mate with the others). The &quot;gotcha&quot; is that, mostly, they're unicellular organisms where mating in itself is weird to begin with. I haven't ever heard of a metazoan which truly has more than one sex (there may be variation within the males or females, but I think the sperms or eggs are always interchangeable).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Gender&lt;/em&gt;, I think, is more of a social term relevant to human behavior. Especially nowadays, so much of the literature and understanding of what is referred to as &quot;gender&quot; is closely linked to things such as gender identity, sexuality, gender roles and personality that is difficult to see how you could meaningfully speak about the &quot;gender&quot; of (non-human) animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's analogous to the idea of &quot;animal language&quot; - certainly some animals may be said to behave in stereotypical ways which influence their mating behavior. Does that mean that what is written about human gender applies? I suspect precious little of it would. I would be quite skeptical of someone discussing gender (in the modern sense) for even uncivilized humans, let alone non-human animals.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-05-12T19:32:15.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17377" PostTypeId="1" AcceptedAnswerId="17469" CreationDate="2014-05-12T19:38:55.463" Score="1" ViewCount="403" Body="&lt;p&gt;The membrane of a human erythrocyte has polarity:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Phosphatidylethanolamine and phosphatidylserine are predominantly on the inner side.&lt;/li&gt;&#xA;&lt;li&gt;Phosphatidylcholine and sphingomyelin are predominantly on the outer side.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Although these can diffuse in the lipid bilayer, they stay on only one side of it. How is this sidedness preserved?&lt;/p&gt;&#xA;" OwnerUserId="5729" LastEditorUserId="540" LastEditDate="2014-05-12T20:04:17.107" LastActivityDate="2014-05-22T11:47:54.100" Title="Transverse diffusion of lipids in red blood cells" Tags="&lt;biochemistry&gt;&lt;homework&gt;&lt;cell-signaling&gt;&lt;lipids&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17379" PostTypeId="2" ParentId="17207" CreationDate="2014-05-12T20:20:54.737" Score="3" Body="&lt;p&gt;Is this what you mean? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/popbq.png&quot; alt=&quot;wireworm&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's pretty hard to tell from this photo, and I'm no entemologist, but to me, it looks like it may be a &lt;strong&gt;wireworm&lt;/strong&gt;, a larvae of a &lt;a href=&quot;http://en.wikipedia.org/wiki/Click_beetle&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;click beetle&lt;/strong&gt;&lt;/a&gt;. This is a diverse group, so I think it would be pretty difficult to give a specific identification. (&lt;a href=&quot;https://www.google.com/search?q=Wireworms&amp;amp;tbm=isch&quot; rel=&quot;nofollow noreferrer&quot;&gt;More images&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="6703" LastActivityDate="2014-05-12T20:20:54.737" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17381" PostTypeId="1" AcceptedAnswerId="17443" CreationDate="2014-05-12T20:35:50.203" Score="3" ViewCount="96" Body="&lt;p&gt;I have very limited knowledge of how the human memory works as I think, at this time, most people do. However, I have been reading and some &lt;a href=&quot;http://www.iflscience.com/brain/watch-chemicals-turn-memories-first-time-has-ever-been-recorded&quot; rel=&quot;nofollow&quot;&gt;articles&lt;/a&gt; which say, and I quote the article just linked &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Memories are made by messenger RNA (mRNA) that encode β-actin protein.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now, correct me if I'm wrong but proteins of any sort have mass. So, why following this rule of proteins being used to create the memory does our brain not grow in mass with each memory we create/ encode. And also, if our memories &lt;strong&gt;are&lt;/strong&gt; encoded using proteins, why can neurodegen­erative  (E.g. Alzheimer's) cannot be cured by artificial proteins in the same way we use insulin. I quote again, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;memories were merely out of reach &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.technologyreview.com/article/408075/memories-misplaced-not-lost/&quot; rel=&quot;nofollow&quot;&gt;full article&lt;/a&gt;&#xA;Surely this means that, it is possible to, by using artificial proteins or possibly electrical stimuli we could recover memories. Or have I wandered off on a wrong track here? Am I correct? Or are my concepts of memory slightly wrong?  &lt;/p&gt;&#xA;" OwnerUserId="6704" LastEditorUserId="6704" LastEditDate="2014-05-12T20:43:57.567" LastActivityDate="2014-05-15T17:17:36.007" Title="The use of proteins in memory creation" Tags="&lt;neuroscience&gt;&lt;proteins&gt;&lt;memory&gt;&lt;neurodegenerative-disorders&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17383" PostTypeId="2" ParentId="17327" CreationDate="2014-05-12T21:59:31.677" Score="3" Body="&lt;p&gt;I'm not sure what you mean by &quot;gender&quot; in the context of non-human organisms.  Gender is usually defined as the intersection between biologically determined sex, and the surrounding culture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe you could argue that in social insects like, say, ants, the fertile queen and the infertile female workers diverge so much in behavior and gene expression that they aren't the same &quot;sex&quot;, or that they could be considered different &quot;genders&quot;, but I  think that is really stretching the usual definitions of those terms.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastEditorUserId="3952" LastEditDate="2015-05-08T15:51:37.890" LastActivityDate="2015-05-08T15:51:37.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17384" PostTypeId="1" CreationDate="2014-05-12T22:27:47.343" Score="1" ViewCount="2764" Body="&lt;p&gt;I am trying to build a gene regulation network, and I need some basic knowledge of it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in gene research, we perturb genes. Such as knock down them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can people tell 2 or 3 experiment methods to perturb genes? &#xA;And 3 or more observations (phenotypes) after perturbation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it could be explained in the context of Microarray, it will be well appreciated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is not that organised, if you can tell a whole story before the computational work started, I will thank you so much.&lt;/p&gt;&#xA;" OwnerUserId="6678" LastEditorUserId="6678" LastEditDate="2014-05-13T19:09:48.440" LastActivityDate="2014-05-14T20:56:09.620" Title="Gene perturbation, what is it used for, explain to computer scientists?" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;gene-expression&gt;&lt;gene-regulation&gt;&lt;microarray&gt;" AnswerCount="2" CommentCount="5" ClosedDate="2014-05-19T19:59:40.743" ContentLicense="CC BY-SA 3.0" />
  <row Id="17385" PostTypeId="2" ParentId="17368" CreationDate="2014-05-12T23:49:52.760" Score="5" Body="&lt;p&gt;This is a hard question to respond to.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many things might make someone grumpy.  There are also individual temperaments, making grumpy hard to quantify - a Grumpy to one person might barely be a blip on another individual's scale.  Hormones like cortisol reflect stress, and can make people in general irritable, but I doubt any one combination of hormones would always cause grumpiness. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I thought I'd venture an answer since I did see this paper today:  &lt;a href=&quot;http://www.pnas.org/content/111/17/6254.short?rss=1&amp;amp;ssource=mfr&quot; rel=&quot;nofollow&quot;&gt;&quot;Low glucose relates to greater aggression in married couples&quot;&lt;/a&gt; doi: 10.1073/pnas.1400619111&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Being hungry will do this for lots of people, so maybe a bit of an answer for you. There are lots of different kinds of signals that mediate hunger though, so still a tough call. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update: here's an additional article that specifically talks about &lt;a href=&quot;http://www.iflscience.com/health-and-medicine/science-hangry-or-why-some-people-get-grumpy-when-they-re-hungry&quot; rel=&quot;nofollow&quot;&gt;parts of the brain involved in aggression and grumpiness as response to a drop in glucose&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="577" LastEditDate="2015-07-29T18:04:51.097" LastActivityDate="2015-07-29T18:04:51.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17386" PostTypeId="1" CreationDate="2014-05-13T00:38:30.760" Score="6" ViewCount="25051" Body="&lt;p&gt;Why do our eyes close when we sleep? Is it to relax our eye muscles? How can it be explained from an evolutionary point of view?&lt;/p&gt;&#xA;" OwnerUserId="6442" LastActivityDate="2017-10-25T03:08:38.640" Title="Why do our eyes close when we sleep?" Tags="&lt;evolution&gt;&lt;eyes&gt;&lt;sleep&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17387" PostTypeId="2" ParentId="17386" CreationDate="2014-05-13T01:32:50.223" Score="10" Body="&lt;p&gt;Our eyelids close when we sleep probably for the obvious reason that it prevents the sclera and cornea from drying out, becoming accidentally scratched (such as blowing dust) and allowing oxygen diffusion from the inside of the eyelid (to the sclera and cornea). Fragile corneas are a requirement for our vision. Thick corneas are much less fragile but then attenuates more light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From terdon:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) blinking requires muscle movement which sort of defeats the purpose of resting &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) closed eyelids offer much better protection than periodic blinking &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) if you can blink, you have eyelids.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2014-05-14T21:47:26.253" LastActivityDate="2014-05-14T21:47:26.253" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="17388" PostTypeId="2" ParentId="17349" CreationDate="2014-05-13T04:15:37.637" Score="1" Body="&lt;p&gt;You've already learned much more than I know about cellular cascades in mast cells, but I wanted to be sure you knew about this handy resource - a free, searchable &quot;Molecular Biology of the Cell&quot; textbook: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21054/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK21054/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For general explanations about cell biology, it's thorough and readable. For instance:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26892/&quot; rel=&quot;nofollow&quot;&gt;Transport from the Trans Golgi Network to the Cell Exterior: Exocytosis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26884/&quot; rel=&quot;nofollow&quot;&gt;B Cells and Antibodies&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Carry on learning.&lt;/p&gt;&#xA;" OwnerUserId="6517" LastActivityDate="2014-05-13T04:15:37.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17389" PostTypeId="2" ParentId="10739" CreationDate="2014-05-13T06:22:19.060" Score="1" Body="&lt;p&gt;I can't say for sure but it looks like a species of the Laetiporus mushrooms. Please refer to its &lt;a href=&quot;http://en.wikipedia.org/wiki/Laetiporus&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; page for the full info. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;edit:&lt;/strong&gt; I did not read your question fully and now I see that you reached the same conclusion. Just ignore my answer. As to the second part of your question asking if it could be anything else, that is quite hard to visually determine as there are many look alikes in the mushroom kingdom. &lt;a href=&quot;http://www.first-nature.com/fungi/facts/imposters.php&quot; rel=&quot;nofollow&quot;&gt;Read this&lt;/a&gt; for some imposters. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-05-13T11:07:24.823" LastActivityDate="2014-05-13T11:07:24.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17391" PostTypeId="1" AcceptedAnswerId="17442" CreationDate="2014-05-13T09:57:58.083" Score="0" ViewCount="227" Body="&lt;p&gt;I'm trying to color certain amino acid's van der waals bonds as in the following picture:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Vogl9.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;can anybody please describe the steps to accomplish that? &lt;/p&gt;&#xA;" OwnerUserId="3739" LastActivityDate="2014-05-15T13:42:16.660" Title="Color van der waals bonds in swiss PdbViewer" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;pdb&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17394" PostTypeId="2" ParentId="10468" CreationDate="2014-05-13T11:19:39.010" Score="2" Body="&lt;p&gt;It's with noting that just because something is evolutionary diverged sequentially through specialization does not mean that that function has not been to the same degree conserved. For instance non coding RNA are not characterized by sequential homology alone but through structural conservation. To a greater degree even this structure function relationship exists in other parts of the genome with retro elements and beyond the genome with proteins especially antibodies. &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-05-13T11:19:39.010" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17398" PostTypeId="2" ParentId="15548" CreationDate="2014-05-13T13:49:07.467" Score="5" Body="&lt;p&gt;Here's my $0.02 at troubleshooting:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I see gel lanes when I take the gel out the apparatus,&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Good, you're loading your gel correctly and the density is correct so the DNA sits at the bottom of the wells.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;but when I go to photograph them: nothing shows up. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This points to a problem with image formation: not enough EtBr, not enough DNA, burnt out UV bulb, incorrect UV filter, or incorrect imaging station settings.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I only let the samples &quot;run&quot; for 30-40 minutes (when I ran for an hour, the bands almost ran off the gel).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You've run the electrophoresis in the correct direction and not long enough to run the bands completely out of the gel.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Tried using different markers: no luck.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Are you loading enough DNA with these markers?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Re-added some more EtBr to better stain the gel: no luck.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I suspect a problem with the gel documentation system.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I am also keeping the lights off in the dark room, so I do not think I am exposing the film to light early on (errors still a possibility though). Am I taking the film out too early?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't know what you're talking about here. EtBr is a fluorescent dye under UV illumination, and doesn't normally require photographic film. Some systems will capture an image of the gel using a &quot;Polaroid&quot; sort of camera, but that works because the gel was exposed to UV light and the incoming light was filtered accordingly. Most systems however use a gel documentation system with a transilluminating tray and digital camera system to take an image.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some things to try:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Prepare two samples: a standard marker lane, and a DNA lane of known concentration (load up a lot of DNA, like 1-2 ug of plasmid to know that you can't miss the band).  Add 1 uL stock EtBr to each lane's sample, mix, then load on the gel. Run the gel using your usual parameters, keeping a eye on the migrating dye front the make sure you don't run the DNA off the gel. This will make sure that you have two good samples that should appear on the gel, and that they are plenty bright by having excess EtBr.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Image the gel. Things to double check here:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;is the emission wavelength correct? EtBr requires short or medium wave UV illumination (250-300 nm), but some systems have long wave illumination as well. Long wave will not work.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;is there filter setting correct? EtBr fluoresces with a red peak (595 nm max), and if a filter is in place to remove this band, you won't see anything either. Usually there is no filter, or an &quot;EtBr/UV&quot; filter option. Here's a &lt;a href=&quot;http://www.syngene.com/assets/doc/Technical-notes/Imaging-Ethidium-bromide-48.pdf&quot; rel=&quot;nofollow&quot;&gt;technical document&lt;/a&gt; with an example of setting up for EtBr capture.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;is the camera set with an appropriate shutter speed/exposure time? Try experimenting with 20 ms to 200 ms. On our system, 40 ms is ideal. Too short an exposure time means that you won't see anything.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;is the camera iris set the maximally open? If the iris is closed too much, it restricts the incoming light for image formation and eiter no image or a weak image will form. This will also impact ideal exposure time (see above).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;is the camera in focus and operational? Can you image an object like your gloved hand or the physical gel before getting the EtBr settings correct?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-05-13T13:49:07.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17399" PostTypeId="2" ParentId="17349" CreationDate="2014-05-13T14:28:48.277" Score="1" Body="&lt;p&gt;Here is a paper reviewing PKC action in exocytosis. Although it dates from several years ago it should be a good start for accessing the literature on this topic since it has been cited 90 times.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Morgan A. &lt;em&gt;et al&lt;/em&gt;. (2005) Regulation of exocytosis by protein kinase C. Biochem Soc Trans. &lt;strong&gt;33&lt;/strong&gt;:1341-4.&lt;/p&gt;&#xA;&lt;p&gt;PKC (protein kinase C) has been known for many years to modulate regulated exocytosis in a wide variety of cell types. In neurons and neuroendocrine cells, PKC regulates several different stages of the exocytotic process, suggesting that these multiple actions of PKC are mediated by phosphorylation of distinct protein targets. In recent years, a variety of exocytotic proteins have been identified as PKC substrates, the best characterized of which are SNAP-25 (25 kDa synaptosome-associated protein) and Munc18. In the present study, we review recent evidence suggesting that site-specific phosphorylation of SNAP-25 and Munc18 by PKC regulates distinct stages of exocytosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-05-13T14:28:48.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17400" PostTypeId="1" CreationDate="2014-05-13T14:34:16.580" Score="6" ViewCount="13419" Body="&lt;p&gt;I have just read this post at researchgate: &quot;&lt;a href=&quot;http://www.researchgate.net/post/How_to_calculate_experimental_binding_free_energy_from_the_IC50_value&quot; rel=&quot;noreferrer&quot;&gt;How to calculate experimental binding free energy from the IC50 value&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not be very sure about what the difference is between K&lt;sub&gt;i&lt;/sub&gt; and IC&lt;sub&gt;50&lt;/sub&gt;. Could anybody explain?&lt;/p&gt;&#xA;" OwnerUserId="4971" LastEditorUserId="5144" LastEditDate="2014-12-17T20:57:26.230" LastActivityDate="2014-12-17T20:57:26.230" Title="What's the difference between Ki and IC50?" Tags="&lt;biochemistry&gt;&lt;enzyme-kinetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17402" PostTypeId="2" ParentId="17361" CreationDate="2014-05-13T15:32:20.727" Score="4" Body="&lt;p&gt;I believe C is also correct. The excitatory neurotransmitters open $\ce{Na}$ channels which makes the cell membrane more permeable to sodium as compared to potasium and therefore the equilibrium membrane potential would be much closer to the nernst potential for sodium. Now, since the concentration of sodium outside is much greater than inside, the nernst potential for sodium is positive with respect to the inside of the membrane. This makes the overall potential also positive.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want further clarifications regarding the calculation of the equilibrium and the nernst potential across the membrane, feel free to ask.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ADDENDUM  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The approximate concentrations of sodium and potassium inside and outside a cell are :-&lt;br&gt;&#xA;$$\ce {Na+_{in}}=10 \text{mmoll}^{-1}$$&#xA;$$\ce {K+_{in}}=105 \text{mmoll}^{-1}$$&#xA;$$\ce {Na+_{out}}=140 \text{mmoll}^{-1}$$&#xA;$$\ce {K+_{out}}=5 \text{mmoll}^{-1}$$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Nernst potential is given by $E=-\frac{RT}{nF}\ln\frac{\text{in}}{\text{out}}$  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which for the given concentrations comes out to be $+67.7mV$ for sodium and $-78.1mV$ for potassium. During a sufficiently strong action potential, the relative permeability of sodium with respect to potassium becomes $10$. Using the &lt;a href=&quot;http://www.nernstgoldman.physiology.arizona.edu/launch/&quot; rel=&quot;nofollow noreferrer&quot;&gt;GHK equation&lt;/a&gt;(ignoring the contribution of chlorine) gives us a net potential of $+47.5mV$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The graph of the action potential clearly indicates that at the peak of the AP, the membrane potential is positive. Source : &lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/biology/imgbio/actpot4.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;Graph of action potential&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oiryS.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3615" LastEditDate="2014-05-15T15:26:27.757" LastActivityDate="2014-05-15T15:26:27.757" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17403" PostTypeId="1" AcceptedAnswerId="17405" CreationDate="2014-05-13T15:50:14.753" Score="2" ViewCount="441" Body="&lt;p&gt;I am studying biology by myself &lt;em&gt;via&lt;/em&gt; distance-learning. I have been trying to solve the following problem for a while now and hoped you could help me. As this is &quot;homework&quot; I would appreciate hints rather than solutions.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Drosophila has a gene &quot;yellow body&quot;, &lt;span class=&quot;math-container&quot;&gt;$y$&lt;/span&gt;, on the X chromosome. The other, dominant, allele is &quot;grey body&quot;, &lt;span class=&quot;math-container&quot;&gt;$y^+$&lt;/span&gt;.&#xA;When crossing female grey bodies  with male grey bodies we get 50% grey females, 22% grey males and 28% yellow males.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the genotype of the parents?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;My work so far:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genotype must be &lt;span class=&quot;math-container&quot;&gt;$Xy^+X?$&lt;/span&gt; for the female and &lt;span class=&quot;math-container&quot;&gt;$Xy^+Y$&lt;/span&gt; for the male.&#xA;There are two cases to consider: &lt;span class=&quot;math-container&quot;&gt;$?=y^+$&lt;/span&gt; or &lt;span class=&quot;math-container&quot;&gt;$?=y$&lt;/span&gt;. &#xA;In the former we get &lt;span class=&quot;math-container&quot;&gt;$\frac{3}{8}$&lt;/span&gt; grey females and &lt;span class=&quot;math-container&quot;&gt;$\frac{1}{8}$&lt;/span&gt; yellow females and &lt;span class=&quot;math-container&quot;&gt;$\frac{2}{8}$&lt;/span&gt; grey and yellow males each; that seems correct except for the yellow females.&#xA;In the latter, we get twice as many yellow females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps the XXyy (yellow females) genotype is lethal but this doesn't help in determining the parents' genotypes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If &lt;span class=&quot;math-container&quot;&gt;$? = y$&lt;/span&gt; then cross-over from &lt;span class=&quot;math-container&quot;&gt;$Xy^+\mathbf{Xy} \; x \; \mathbf{Xy^+}Y$&lt;/span&gt; would not eliminate yellow females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know of other effects to take into account, so I am stuck.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$ $&lt;/span&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you'd like to suggest resources (websites, textbooks &lt;span class=&quot;math-container&quot;&gt;$\ldots$&lt;/span&gt;) pertaining to this subject or on biology at this level in general, I would very much appreciate it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Edit: I'd like to add an image for anyone having a similar problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hTr9H.jpg&quot; alt=&quot;?=y&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6715" LastEditorUserId="15950" LastEditDate="2019-01-09T10:00:20.463" LastActivityDate="2019-01-09T10:00:20.463" Title="Drosophila grey / yellow" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="17405" PostTypeId="2" ParentId="17403" CreationDate="2014-05-13T17:16:20.197" Score="1" Body="&lt;p&gt;Since Drosophila have &lt;a href=&quot;http://en.wikipedia.org/wiki/XY_sex-determination_system&quot; rel=&quot;nofollow&quot;&gt;the same system of sex chromosomes as human beings&lt;/a&gt;, (XY males and XX females).  Its clear that the sex determination is important - no females have yellow bodies. This is the key observation.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Amongst the males you have about 50%/50% Y/y phenotype.  This appears to be a classic sex chromosome related trait.  Does this help?  I can go further, but this should get you there. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-05-13T17:16:20.197" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17406" PostTypeId="1" CreationDate="2014-05-13T19:07:48.757" Score="1" ViewCount="58" Body="&lt;p&gt;all&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am a little bit confused about using the related genome or reference genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;When we have a reference genome, we can do alignment. Also we can do the assembly.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you give some more reason why a related genome can help to improve gene model ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if we do use a related genome, what kind of problems or caveats may occur there ?&lt;/p&gt;&#xA;" OwnerUserId="6678" LastActivityDate="2014-06-13T04:12:42.033" Title="What is the close and related genome used for in Gene models?" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;molecular-genetics&gt;&lt;genomics&gt;&lt;sequence-analysis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17408" PostTypeId="2" ParentId="17372" CreationDate="2014-05-14T02:00:22.327" Score="2" Body="&lt;p&gt;&lt;strong&gt;(1) There are two cases.&lt;/strong&gt; For the first equation (6), the case $i \neq j,$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$(1) \hspace{13mm} P_{ij}(dt) = u~dt ~\pi_j $$ if we have a transition from one base to another (for example G to C). In the case $i = j,$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$(2)\hspace{10mm} P_{jj}(dt) = (1 - u~dt) + u~dt~\pi_j $$ holds for a same-base transition (G to G) or a non-transition (say, G and no change). Intuitively, we expect that, all things being equal, the probability of a base to same-base situation is slightly higher: it is the sum of probability that the base changes to itself plus the probability the base sits and does nothing in time $dt$ (with the same net result). &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(2) Now we look at the equation(s)&lt;/strong&gt; (7). Again there are two cases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$(1a) \hspace{10mm} P_{ij}(t) = (1 - e^{-ut})\pi_j $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For case 2 (base to same base transition, $i = j$): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$(2a)\hspace{13mm} P_{jj}(t) = e^{-ut} + (1 - e^{-ut})\pi_j. $$&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(3) The author uses&lt;/strong&gt;  $P(dt),$ $P$ at a very small (infinitesimal) quantity $dt.$ He tells us the leap from (1) to (1a) follows &quot;almost immediately&quot; when we see that $e^{-ut}$ is the probability that no base transition occurs. Well, then $(1 - e^{-ut})$ is the probability that a transition occurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now $e^{-ut} \approx (1 - ut) $ (a truncated Taylor series) or $ut\approx (1 - e^{ut}).$ So for short times $dt$ we have $u~dt \approx (1 - e^{-u dt})$ and this explains his first equality $P(dt) = u~dt~\pi_j.$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So we have to recognize when he tells us about $e^{-ut}$ that $u t$ is the [truncated] Taylor series representation of $(1-e^{-ut})$ for $t$ very near 0. That is how he gets from 1 to 1a and (6) to (7). &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(4) $(1 - u)$ is the probability&lt;/strong&gt; that no transition from one base to another occurs in some short time $t_i.$ The probability that this happens over n consecutive time intervals is $(1 - u)^{(nt_i)}.$ Let $nt_i = T.$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that  $u \ll 1.$ We can write $(1 - u)^T = (1 - \frac{uT}{T})^T $ and &#xA;$$\lim_{T \to \infty} (1 - \frac{uT}{T})^T= e^{-uT}.  $$ This reasoning comes directly from that used to derive the Poisson distribution which is used to study rare events. See, for example, Deonier, &lt;em&gt;Computational Genome Analysis,&lt;/em&gt; p.74.&lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-05-17T02:05:50.853" LastActivityDate="2014-05-17T02:05:50.853" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17409" PostTypeId="2" ParentId="17384" CreationDate="2014-05-14T02:04:49.707" Score="4" Body="&lt;p&gt;Here are 3:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) gene knockout.  Just delete the gene from the genome.  The function is gone - useful for demonstrating a direct involvement of the gene in the phenotype.  As a phenotype, the microarray will register all sorts of reactions to the loss of the gene in addition to the RNA in question being gone. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) use selection to find mutants for the gene.  Expose the organism to a mutagen or high amounts of UV radiation.  Useful mutants vary by what the function of the genes are.  Temperature sensitivity - the gene doesn't function above 30 deg C is an &lt;em&gt;example of a phenotype for a mutant&lt;/em&gt; that has been used classically.  In this case the functioning of the gene itself is a phenotype.  This is an example of a weaker perturbation.  Can be used when knockouts are fatal or when the system is too sensitive for a knockout. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) change the environmental conditions. increase the concentration of a substrate or lower the availability of nutrients.  Phenotypes can be rate of growth/division, production of a given metabolite from the cells, but it goes on and on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The affect on whole genome microarray data can be quite complex in such perturbation experiments because the coupling of many genes, even in bacteria can be broad and significant.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-05-14T20:56:09.620" LastActivityDate="2014-05-14T20:56:09.620" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17410" PostTypeId="1" CreationDate="2014-05-14T05:39:42.060" Score="10" ViewCount="1896" Body="&lt;p&gt;While discussing with a friend a while back on the likelihood a futanari (a woman with both fully developed and functioning sets of genitalia) existing in real life, we got into a discussion of whether a child could carry the genetics over from 2 months.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Currently (to my knowledge), for a female same-sex couple to conceive a child and for both women to be involved, one would donate an egg, the other actually gives birth, and the sperm is donated by a third party. However, this means that the child will carry over the genetics of one women in the couple and the unknown male.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering if there is a way for sperm to contain the genetic information so that way both women in a same-sex relationship could be genetically related to the child.&lt;/p&gt;&#xA;" OwnerUserId="4378" LastEditorUserId="9694" LastEditDate="2016-11-09T19:49:53.987" LastActivityDate="2016-11-09T19:49:53.987" Title="Could a sperm be altered to contain a female's genetics?" Tags="&lt;genetics&gt;&lt;reproduction&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17411" PostTypeId="2" ParentId="477" CreationDate="2014-05-14T05:46:36.633" Score="16" Body="&lt;p&gt;In my opinion, Prof. Allen Gathman's &quot;great 10-minutes video on Youtube&quot; is a pretty waste of time if you already know how hydrolysis happens. In fact, he has not considered the 3'-&gt;5' route in an unbiased manner; he doesn't seem to look at the possibility of a triphosphate appearing at the growing 5' tip of the strand in the 3'-&gt;5' case. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually, the only difference between the two routes (5'-&gt;3' and 3'-&gt;5') is that the reacting triphosphate appears in different places. In the usual case, the triphosphate which is hydrolysed belongs to the added nucleotide, while in the latter case, the triphosphate which is hydrolysed belongs to the nucleotide on the growing strand. Both are feasible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, it is known that &lt;em&gt;RNA&lt;/em&gt; polymerase has dual activity, but you see, RNA polymerase doesn't have proofreading activity!.  Proofreading requires removal of the mismatched base, but in the 3'-&gt;5 direction the base's attachment had consumed the triphosphate at the 5' tip of the strand, so it is no longer available to add the replacement base. &lt;em&gt;3'-&gt;5' activity readily destroys  proofreading capability of a polymerase&lt;/em&gt;  So, basically, &lt;em&gt;it is the need for proofreading that restricts the synthesis of DNA strands to 5'-&gt;3'&lt;/em&gt;. Why it is so, would need a lot more explanation (if in words) but I think a picture has far better explanatory power than a thousand words. I've added a picture from &lt;em&gt;Essential Cell Biology&lt;/em&gt; that shows the answer to the 'WHY' question:&lt;img src=&quot;https://i.stack.imgur.com/rE2WN.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other important consideration is repair. If one or more nucleotide is missing in one strand, repair of the missing nucleotide would be impossible for 3' to 5' synthesis, because no 5'-triphosphate is present. On the other hand, 5' to 3' synthesis does not require a 3'-triphosphate present at the repair site. This is important. That is 3' to 5' synthesis does not allow nucleotide repair.&lt;/p&gt;&#xA;" OwnerUserId="6723" LastEditorUserId="231" LastEditDate="2018-05-05T22:33:14.900" LastActivityDate="2018-05-05T22:33:14.900" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="17412" PostTypeId="2" ParentId="17410" CreationDate="2014-05-14T05:52:10.910" Score="0" Body="&lt;p&gt;You could maybe generate sperm cells from the other woman and use those to impregnate the other. This is biologically possible, but not a technical reality yet, and I doubt we'll ever go there. Given the lack of Y-chromosomes, the couple could obviously have only female children.&lt;/p&gt;&#xA;" OwnerUserId="5784" LastActivityDate="2014-05-14T05:52:10.910" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="17413" PostTypeId="2" ParentId="16295" CreationDate="2014-05-14T06:13:42.167" Score="2" Body="&lt;p&gt;No. Schizophrenia isn't a single disease. It is &lt;a href=&quot;http://psychcentral.com/lib/types-of-schizophrenia/000714&quot; rel=&quot;nofollow&quot;&gt;class of psychotic disorders&lt;/a&gt;. &lt;a href=&quot;http://en.wikipedia.org/wiki/Dopamine_hypothesis_of_schizophrenia&quot; rel=&quot;nofollow&quot;&gt;Dopamine&lt;/a&gt; isn't the single cause of psychotic type diseases including schizotype. Many other pathways play a part in the various diseases; &lt;a href=&quot;http://blogs.discovermagazine.com/neuroskeptic/2009/03/26/serotonin-hallucinations-psychosis/&quot; rel=&quot;nofollow&quot;&gt;Serotonin&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Glutamate_hypothesis_of_schizophrenia&quot; rel=&quot;nofollow&quot;&gt;Glutamate&lt;/a&gt;, &lt;a href=&quot;http://link.springer.com/article/10.2165/00023210-199708040-00002#page-1&quot; rel=&quot;nofollow&quot;&gt;Histamine&lt;/a&gt;...ect.ect.ect. Genetic, Expressive and developmental factors are all known to play a role too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover you're not even describing typical symptomatic schizophrenia but a version of schizo that contains depressive features as well. Apathy caused by schizophrenia is a negative symptom a lack of interest in this life. Often we become preoccupied with the pleasures of delusions or hallucinations. The large dose of dopamine associate with a not &quot;evil&quot; hallucination is pleasurable on the order of cocaine. Delusions feel like antidepressants. Apathy caused by antipsychotics is entirely different. &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2014-05-14T07:47:54.037" LastActivityDate="2014-05-14T07:47:54.037" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17414" PostTypeId="2" ParentId="17276" CreationDate="2014-05-14T08:48:23.220" Score="2" Body="&lt;p&gt;Bez experiments are too difficult and costly you don't need to do that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take, label samples then apply ligands and sustenance. The inhibitory will have have a slower rate of &lt;strong&gt;&lt;em&gt;growth&lt;/em&gt;&lt;/strong&gt; not death and use a control with replicates. Also if you have the money buy an epac FRET to measure cAMP. Find someone to do the FRET if you can't. It will take a longer than a day but you avoid the whole I gave it too much it was going to die anyways. If you did not initially separate your cell lines by proteins and have a mix of Gs Gi within the cell lines and you need to find which ligand causes a dominant response then you will have to do individuals of these test. There are companies that specialize in growth response. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not FRET. Find some business with an &lt;a href=&quot;http://allseq.com/knowledgebank/sequencing-platforms/life-technologies-ion-torrent&quot; rel=&quot;nofollow&quot;&gt;ION torrent&lt;/a&gt; and sequence the &lt;strong&gt;&lt;em&gt;genome&lt;/em&gt;&lt;/strong&gt; its really really cheap. If your proteins have known homology to Gs or Gi this will give the best results quickest. If you're proteins function is novel add ligands and the Gi will have less PCR amp than the Gs. Don't do your own NA extraction just let them. I've seen so many samples go bad in delivery because people tried to save a buck. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also since you had trouble designing this experiment find a company which will run the whole of the experiment for you. Most places with ION torrents have the whole lab setup to run such an experiment and do so on a weekly basis. &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2014-05-14T10:31:03.107" LastActivityDate="2014-05-14T10:31:03.107" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17417" PostTypeId="2" ParentId="17264" CreationDate="2014-05-14T10:30:03.190" Score="0" Body="&lt;p&gt;I quite like the explanation I found on the website of &quot;Exploring the BioEdge&quot;. Robin and Honeybadger explain the black and white colouration as follows: To minimize the risk of being attacked by the tiger, the colouration of the giant panda is aposematic, warning would-be predators of its vice-like hug and bite. This warning signal, visible even in poor light, consists of a black-and-white contrast on the face (ears and eyes) as well as the body as a whole.”&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://explorebioedge.com/bio-bullets/item/43-warning-colouration-in-the-giant-panda.html&quot; rel=&quot;nofollow&quot;&gt;http://explorebioedge.com/bio-bullets/item/43-warning-colouration-in-the-giant-panda.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6725" LastEditorUserId="6725" LastEditDate="2014-05-14T11:10:46.920" LastActivityDate="2014-05-14T11:10:46.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17418" PostTypeId="1" AcceptedAnswerId="17421" CreationDate="2014-05-14T10:40:32.010" Score="2" ViewCount="412" Body="&lt;p&gt;For example the pectoralis muscle starts from sternum region and ends on the acromion or coracoid process. Why you can't say that it starts acromion process and ends on the sternum?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="107" LastEditDate="2014-06-13T13:34:40.277" LastActivityDate="2014-06-13T13:34:40.277" Title="What are the criteria for determining the origin and end of muscle anatomically?" Tags="&lt;homework&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17420" PostTypeId="2" ParentId="13867" CreationDate="2014-05-14T11:02:11.047" Score="1" Body="&lt;p&gt;As Remi points out you are generally incorrect but the locality idea is specifically ok. The positions and types of mutations and divergence for specialization in certain genes regardless of their place in the genome is key in determining homology which is used for species determination at the molecular level. The drawback is: its rather expensive when most species differences are obvious at the phenotypic level.&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-05-14T11:02:11.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17421" PostTypeId="2" ParentId="17418" CreationDate="2014-05-14T11:06:36.107" Score="1" Body="&lt;p&gt;This is more of a convention.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The start point or &lt;strong&gt;origin&lt;/strong&gt; is considered to be:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;bone which is proximal&lt;/li&gt;&#xA;&lt;li&gt;bone with higher mass&lt;/li&gt;&#xA;&lt;li&gt;bone with higher stability during muscle contraction&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The end point or &lt;strong&gt;insertion&lt;/strong&gt; is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the structure that tends to be moved by contraction&lt;/li&gt;&#xA;&lt;li&gt;tendon&lt;/li&gt;&#xA;&lt;li&gt;distal end of a bone&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Reference: Wikipedia - &lt;a href=&quot;http://en.wikipedia.org/wiki/Anatomical_terms_of_muscle#Insertion_and_origin&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Anatomical terms of muscle&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-05-14T11:06:36.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17424" PostTypeId="2" ParentId="17384" CreationDate="2014-05-14T13:46:35.867" Score="0" Body="&lt;p&gt;Perturbation is when you either introduce a gene or gene product or inhibit it using a variety of approaches to see what other genes show changes in expression or other epigenetic modifications, which can be measured using a microarray.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If genes A,B,C,D,E are expressed more due to the activity of Gene X while F,G,H are unaffected, when you compare microarray data from samples where X has been turned off to those where it hasn't, you will see decreased expression of A,B,C,D and E - you can represent this as a graph with Gene X being the hub.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps,&#xA;Ankur.&lt;/p&gt;&#xA;" OwnerUserId="6726" LastActivityDate="2014-05-14T13:46:35.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17425" PostTypeId="2" ParentId="10468" CreationDate="2014-05-14T13:52:47.337" Score="0" Body="&lt;p&gt;Conservation might indicate selective pressure as a general rule, but this isn't a given; you can delete some ultraconserved elements and still get viable mice...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0050234&quot; rel=&quot;nofollow&quot;&gt;http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0050234&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6726" LastActivityDate="2014-05-14T13:52:47.337" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17426" PostTypeId="2" ParentId="17148" CreationDate="2014-05-14T15:00:11.823" Score="4" Body="&lt;p&gt;The diameter of axons also makes a difference, the thicker the axon, the faster the rate of action potential conduction. This is seen in invertebrates, such as squid. Squid have giant axons (up to 2mm in diameter), which exhibit rapid conduction rates. See Wikipedia 'squid giant axon', in which it says up to 1mm, but I have measured 2mm myself. These are not found in mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Original research on squid giant axon  was by Cole &amp;amp; Curtis (The Journal of general physiology, 1939). For more recent research see Hartline &amp;amp; Colman (Curr Biol. 2007 Jan 9;17(1):R29-35.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Work by Hodgkin, Huxley and Katz (The Journal of physiology, 1952,  116(4): 424–448) using squid giant axons lead to the elucidation of the mechanism of action potential conduction and a Nobel prize. Academic summary here: &lt;a href=&quot;http://jp.physoc.org/content/538/1/2.full&quot; rel=&quot;nofollow&quot;&gt;http://jp.physoc.org/content/538/1/2.full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia: see the Goldman equation (Goldman shared the Nobel Prize with Hodgkins and Katz). This is more frequently known as the Goldman-Hodgkin-Katz  equation in UK publications.&lt;/p&gt;&#xA;" OwnerUserId="6727" LastEditorUserId="6727" LastEditDate="2014-05-14T15:44:04.073" LastActivityDate="2014-05-14T15:44:04.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17427" PostTypeId="1" AcceptedAnswerId="17439" CreationDate="2014-05-14T15:08:26.033" Score="1" ViewCount="132" Body="&lt;p&gt;I had a dental problem when my first molar broke some months ago and after some decay and pain I am undergoing a dental treatment. The doctor was performing a root canal and kept on talking about calcified stones being formed and looking for a 'tak' sound inspite of having x-rays. Doctor did not point to the calcified stones earlier and suddenly came out with this new issue. In the mean time when looking for stones doctor actually managed to break my tooth and has blamed grinding and clenching for a crack that caused the tooth to break.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am shocked that neither the calcified stone nor the crack showed up in x-ray and the preliminary examination. With current technology, can the cracks in tooth and calcified stones not be detected. &lt;/p&gt;&#xA;" OwnerUserId="6488" LastActivityDate="2014-05-15T09:10:31.503" Title="Detecting Calcified stones and cracks in tooth" Tags="&lt;teeth&gt;&lt;hygiene&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17429" PostTypeId="1" CreationDate="2014-05-14T19:27:36.427" Score="2" ViewCount="109" Body="&lt;p&gt;There is a neuromorphic vision sensor that is generating some interesting research these days that is called the &lt;a href=&quot;http://www.inilabs.com/products/dynamic-vision-sensors&quot; rel=&quot;nofollow&quot;&gt;Dynamic Vision Sensor&lt;/a&gt;. One of the claims of this sensor is good approximation of the conventional retina. However, there's no detail on the website in what way this is true or to what degree this is true.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It does not detect colour, so obviously it isn't an accurate approximation of the cones found in the retina. Additionally, the function of the cornea is fulfilled by the lens of the camera, so this input isn't totally approximated. Consequently, the only significant component that remains to be evaluated is the rods of the retina?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the similarities and differences between a retina and the DVS sensor?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, let me save you some reading by explaining how the DVS sensor is different from a typical camera. Instead of synchronously sending frames with data about every pixel, the DVS is event driven. That means, when a light intensity change occurs, an event is fired with the address of that change, a time-stamp and whether the pixel observed an increase or a decrease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do rods also encode changes in light intensity in the same manner? If not, what is the difference?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5427" LastEditorUserId="5427" LastEditDate="2014-05-17T13:14:29.330" LastActivityDate="2014-05-17T13:14:29.330" Title="How well does the event-driven DVS sensor approximate the rods of the retina?" Tags="&lt;vision&gt;&lt;neurology&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17431" PostTypeId="2" ParentId="17386" CreationDate="2014-05-14T22:09:05.610" Score="3" Body="&lt;p&gt;There's definitely something to the fact that eyes work better when they are closed periodically and don't work well when they are open constantly, but there is another angle to this topic.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think its worth adding that not all animals sleep with their eyes closed.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is because some animals sleep with only half of their brain at once.  Ducks, some birds, aquatic mammals like whales dolphis and seals engage &lt;a href=&quot;http://en.wikipedia.org/wiki/Unihemispheric_slow-wave_sleep&quot; rel=&quot;nofollow noreferrer&quot;&gt;Unihemispheric sleep&lt;/a&gt;.  In Unihemispheric sleep, half the brain is asleep and the other is awake.  Not necessarily fully awake, but enough that one eye is open and watching for predators or other threats.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One might ask - didn't we all have predators and threats?  Why don't we all sleep half the brain at a time?  The answer is not clear, but it appears that unihemispheric sleep is not a trait that is maintained easily.  Very few animals really have the ability.  As such there must be some advantages physiologically to closing both eyes at once and experiencing total sleep.  Once the threat is not so great from being sleeping prey, animals start to close both eyes pretty quickly.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2017-10-25T03:08:38.640" LastActivityDate="2017-10-25T03:08:38.640" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17432" PostTypeId="2" ParentId="10294" CreationDate="2014-05-15T00:44:50.497" Score="-1" Body="&lt;p&gt;From my own point of view, I think the answer to no. 1 is a 50% chance i.e. 2 out of 4. My reason is because, IV-1 could be a carrier of the trait and since the IV-2 is affected that means 2 will be affected.&#xA;No 2. For the second question, the answer is 1 out of 4, because it's obvious both (IV-1 and IV-2) would be carriers of the trait from their family pedigree, and have 1 in a 4 chance of developing an offspring with the trait.&lt;/p&gt;&#xA;" OwnerUserId="6732" LastEditorUserId="806" LastEditDate="2014-05-15T19:17:51.240" LastActivityDate="2014-05-15T19:17:51.240" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17433" PostTypeId="2" ParentId="13867" CreationDate="2014-05-15T01:46:09.547" Score="0" Body="&lt;p&gt;I would add:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most categories in sciencie (species, order, living, planets, moons, stars, organs, fruits, etc.) are not &quot;real&quot;. We (humans) create categories and attach objets to them in order to make general assumptions, so we can say things like &quot;Most objects of category X have Y property.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, the way we define categories it's mainly the most practical way. And sometimes we addapt definitions, when there are practical motivations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the motivation to define species related to the usual intra reproduction hability (and usual inter reproduction inhability) it's because that mantains certain homogeinity. Maybe a better definition would be something like &quot;two groups of individuals belongs to the same specie if the rate of fertility among their individuals is &gt; x %&quot;.&lt;/p&gt;&#xA;" OwnerUserId="6733" LastActivityDate="2014-05-15T01:46:09.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17434" PostTypeId="2" ParentId="17410" CreationDate="2014-05-15T02:11:32.510" Score="0" Body="&lt;p&gt;Yes, it is scientifically possible. Though a third party (male sperm donor) is still required. Scientists working for a British biotechnology company, as well as doctors at Oregon Health and Sciences University have been working on complex procedures but are fighting the ethical red tape and are not currently using the techniques on patients.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the basics of the procedure being used by the doctors in Britain &quot;The nuclei from the father's sperm and the mother's egg, which contain the parents' DNA, were removed. The nuclei were put into another egg from which the nucleus had been removed, but which retained its mitochondria. This new embryo contained the genes from both parents plus a tiny amount of mitochondrial DNA from the donor egg.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The scientists in Oregon have a similar yet slightly different approach with procedure explained as &quot;Doctors would remove the nucleus DNA from the donor eggs and replace it with nucleus DNA from the patient's eggs. So, they would end up with eggs that have the prospective mother's nucleus DNA, but the donor's healthy mitochondrial DNA.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This approach can easily be modified to fit a lesbian couples desire to have a child that is related to both of them. Scientifically it is possible for two mothers to be directly related to a child, but the sperm is still a relevant part of the equation. It is not possible, so far, to create a functioning embryo without male sperm. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources: &#xA;&lt;a href=&quot;http://digitaljournal.com/article/290608&quot; rel=&quot;nofollow&quot;&gt;http://digitaljournal.com/article/290608&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.huffingtonpost.com/2012/10/24/3-person-ivf-embryos-women-man_n_2011546.html&quot; rel=&quot;nofollow&quot;&gt;http://www.huffingtonpost.com/2012/10/24/3-person-ivf-embryos-women-man_n_2011546.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And my reproductive biology book and studies: &lt;em&gt;Trends in Endocrinology and Metabolism&lt;/em&gt; by Claire Bourgain.  &lt;/p&gt;&#xA;" OwnerUserId="6684" LastActivityDate="2014-05-15T02:11:32.510" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17435" PostTypeId="2" ParentId="17410" CreationDate="2014-05-15T04:27:18.307" Score="9" Body="&lt;p&gt;You might be interested in &lt;a href=&quot;http://www.nature.com/nature/journal/v479/n7371/full/nature10448.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; article. In this study they created haploid ES cells from artificially activating an unfertilized oocyte and growing the haploid cells. These cells, when introduced in the ICM, give rise to viable chimeras. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In another &lt;a href=&quot;http://www.nature.com/nature/journal/v490/n7420/full/nature11435.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;study&lt;/a&gt;, haploid androgenetic ES cells were created by injecting a sperm into an enucleated oocyte. These cells also are capable of creating offspring when fused with another oocyte. [See &lt;a href=&quot;https://biology.stackexchange.com/questions/8223/are-any-organisms-known-to-use-meiosis-i-to-create-non-identical-offspring-asexu/8224#8224&quot;&gt;this&lt;/a&gt; post also]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, since these cells can be cultured, they can be genetically modified. However, they undergo spontaneous diploidization and lose reproductive potential after a few rounds of division. This is related to the alteration of epigenetic status of these cells on certain imprinted loci. Others have also indicated the importance of both paternal and maternal imprinting in the viability of embryos which might be a problem in oocyte-oocyte derived hES cell fusions (See cross references). [Check &lt;a href=&quot;http://ac.els-cdn.com/S0092867412004217/1-s2.0-S0092867412004217-main.pdf?_tid=e772b464-dbe9-11e3-8bec-00000aab0f01&amp;amp;acdnat=1400128521_54f5ed0f06d70dba66ac17ea7f184a93&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; article too].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It can be concluded that oocyte$-$oocyte-hES fusions are not observed because of same imprint status (Also mentioned by Chris in the comments). AD-hES also lose their paternal imprints on prolonged culture (but retain maternal imprints). It is to be ascertained if paternal imprints are more unstable compared to maternal imprints under these conditions. It may be possible to optimize the culture conditions such that oocyte derived hES lose their maternal marks: would that lead to incorporation of paternal marks post-fusion is debatable. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-02-17T09:40:54.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17437" PostTypeId="2" ParentId="17288" CreationDate="2014-05-15T07:44:28.597" Score="2" Body="&lt;p&gt;It is definitely in line with Darwin's theory.  You can look at living things as having two sorts of reproduction strategies (for the sake of this question - of course there are many diverse strategies, but this is just one dimension of it).  &lt;a href=&quot;https://en.wikipedia.org/wiki/R/K_selection_theory&quot; rel=&quot;nofollow&quot;&gt;r and K strategies&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;K-selective strategies try to select the best mates and produce the strongest offspring, which they invest a lot of resources in so a to maximize their chances of reproducing.  Human beings are a classic example of K-selective evolution.  A human child will take a decade or even two before it is independent.  Birds might give their offspring a few weeks.  That is why as a person you might tend to think that all animals succeed by investing in offspring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;r- selective strategies do not value their offspring at all.  They produce hundreds or thousands of offspring and don't invest in any of them at all.  A common example of this is cockaroaches or guppies, which are as likely to eat their offspring as acknowledge it, having thousands or hundreds of eggs in one clutch respectively.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For these animals, life is cheap, the fit and the unfit all come out together, but those who survive are the strongest.    &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-05-15T07:44:28.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17438" PostTypeId="1" AcceptedAnswerId="17470" CreationDate="2014-05-15T09:09:25.070" Score="3" ViewCount="424" Body="&lt;p&gt;Let us assume that in a human body, a mitochondrial DNA is released to extracellular environment.&#xA;We know that mtDNA inheritance is solely matrilineal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the question is, If your mitochondrial DNA is released to the extracellular environment (or into&#xA;cell cytoplasm) due to cellular and/or mitochondrial damage, what could be the&#xA;ramification of this released DNA if your immune system cells (such as macrophages,&#xA;dendritic cells or B cells) pick up and sense these DNA as a danger signal?&#xA;Is there any chance for mtDNA to survive by establishing a new mtDNA ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking, macrophages engulf and destroy them but cannot provide sufficient evidence.&lt;/p&gt;&#xA;" OwnerUserId="6735" LastEditorUserId="6735" LastEditDate="2014-05-15T09:18:44.973" LastActivityDate="2014-05-19T13:09:24.273" Title="Do macrophages engulf mtDNA?" Tags="&lt;human-biology&gt;&lt;molecular-biology&gt;&lt;mitochondria&gt;&lt;autoimmune&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17439" PostTypeId="2" ParentId="17427" CreationDate="2014-05-15T09:10:31.503" Score="1" Body="&lt;p&gt;Cracks on your teeth are hard to detect if they are cracks on the mesial or distal surfaces (surface of the tooth closest to and farthest from the midline respectively) through x-rays. Please check &lt;a href=&quot;http://www.dental.umaryland.edu/dentalstudent/download/Introduction_to_Dental_Terms_2.pdf&quot; rel=&quot;nofollow&quot;&gt;this link&lt;/a&gt; for illustrations and very good explanations from the University of Maryland dentistry department. The different methods on the detection of cracks as well as the uses of radiographic evidence can be found in &lt;a href=&quot;http://www.aae.org/uploadedfiles/publications_and_research/endodontics_colleagues_for_excellence_newsletter/ltfbonusmaterial_c.pdf&quot; rel=&quot;nofollow&quot;&gt;this link.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now pulp stones can be identified through x-rays unless they are too small or not too dense. There has been researches done specifically using radiographs for detection like &lt;a href=&quot;http://www.researchgate.net/publication/11336590_A_radiographic_assessment_of_the_prevalence_of_pulp_stones_in_Australians&quot; rel=&quot;nofollow&quot;&gt;&quot;A radiographic assessment of the prevalence of pulp stones in Australians&quot;&lt;/a&gt;. It could also be human error that your doctor was unable to detect it. A small explanation on pulp stones can be found &lt;a href=&quot;http://www.breadentistry.com/files/pdf/OPG_pul_sto.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-15T09:10:31.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17441" PostTypeId="1" AcceptedAnswerId="17478" CreationDate="2014-05-15T11:45:30.567" Score="0" ViewCount="4992" Body="&lt;p&gt;It is said that genes define how we look physically and psychologically; so for example if a male human sperm carries a certain number of genes, say x, and a female carries y, then mathematically there would be m genes from the male and n from the female, and a finite total available. Could there be people identical in appearance if the same genetic combinations recur?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also we find similar-looking people with perhaps similar behaviour accross diferent geographic locations; does this means that they have similar genetic make-up, up to some percentage?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please correct my biology and share the possiblity of having genetically identical people across different geographic locations.&lt;/p&gt;&#xA;" OwnerUserId="5008" LastEditorUserId="1368" LastEditDate="2014-05-17T07:37:19.360" LastActivityDate="2014-05-17T12:06:45.477" Title="What makes us all different and similar to some extent?" Tags="&lt;human-genetics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ClosedDate="2014-05-19T13:58:01.347" ContentLicense="CC BY-SA 3.0" />
  <row Id="17442" PostTypeId="2" ParentId="17391" CreationDate="2014-05-15T13:21:06.333" Score="0" Body="&lt;p&gt;If I'm right in assuming you are trying to get colouring like the purple AA VDW bonds then I can only specifically colour VDW bonds in solid 3D view (under display, Render in solid 3D) in SPDBV but not when solid 3D view is not activated, as in the example in your picture. One option is to use POV-Ray but I haven't worked with it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the purple colouring is not photoshoped by the authors of the paper you got the picture from, then the chances are they have written a custom script for it in the software, which allows them to do this. So I would just contact the corresponding author and ask them how they managed it and if they have done it through a script or some other software. Most of the time people are happy to share their methodology once they have published it!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also have you tried the Jalview software? Although it's designed primarily as an alignment tool but it has a nice 3D Jmol view. You can load up your sequence and the associated PDB file and you can play around with it. The graphics output are quite publication friendly. I'm not an expert at it and I've only been playing around with it for a bit but when you get the hang of it, it's quite nice graphically. Although the VDW view is still space fill 3D but it's a bit nicer as it has opacity etc etc. Just download it and as soon as you open it up, you are presented with an example alignment and Jmol view. Just play around with the alignment section and the Jmol view and see if you like the aesthetics. The only tricky part in the software is getting the residues you want selected but once you manage that, you can get the program to display VDW only for the selected residues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-05-15T13:42:16.660" LastActivityDate="2014-05-15T13:42:16.660" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17443" PostTypeId="2" ParentId="17381" CreationDate="2014-05-15T17:17:36.007" Score="0" Body="&lt;p&gt;I think its important to mention that the particulars of memory storage in the brain are still being worked out.  I think what we do know about it is that memory storage depends a lot on the physical configuration of the neurons in the brain.  They move about and make new connections as they process information (and probably also when they are not processing information!).  Different regions of the brain store short vs long term memory and different sorts of memories.  They neurons themselves have a lot of internal cell physiology that can change as well - there are many different neuroreceptors that constitute the synaptic junctions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All these things may not be a comprehensive list.  But at the basis of all these processes, the cell expresses new proteins in mRNA and these proteins are doing all this work.  beta-actin and histone de-acetylase, as mentioned in your link, are responsible for the cell rearranging itself in the cell shape and in terms of its internal transport processes and in the nucleus respectively.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm pretty sure that exactly what is happening here is not really well understood.  monitoring the interior of the cell is difficult.  The &lt;a href=&quot;http://www.technologyreview.com/article/408075/memories-misplaced-not-lost/&quot; rel=&quot;nofollow&quot;&gt;work where histone deacetylase is inhibited&lt;/a&gt; is a fresh new thought, showing that the arrangement of the chromosomes in the nucleus is involved in hiding memories.  Its still the equivalent to getting a stopped watch to start again by shaking it - there are parts there that fell into place and started ticking again, but we don't really know what the parts are doing in any detail yet.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This hints that if you were to disrupt the cells in some ways you might be able to free up memory, but its a long way from guaranteeing that any given approach will work.  I'd be surprised even if Dr Tsai's cell treatment worked even 70% of the time in her experiment.  Hypnosis or a focused meditation session might still be just as effective.  I think that its a bit too much to expect that Alzheimer's memories are completely preserved and recoverable.  In some cases probably, but categorical statements rarely hold in bioscience. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like a lot of neuroscience, this work is suggestive, but still just progress towards a clearer understanding of these processes.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-05-15T17:17:36.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17445" PostTypeId="1" CreationDate="2014-05-15T18:10:00.133" Score="1" ViewCount="36" Body="&lt;p&gt;Do people with an hyperkinetic dysfuntion have a better endurance?  Are they fitter in cause of their Dopamine-overdose or any other reason? I have a case, where someone does not do any sports, but has an endurance way better than most of others who does no sports. He even can compete with some amateur athletes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just for comprehension: He does not eat well, sits most of the time (during work, at home), does not do any other activities except eSports (onlinegames). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe someone has an answer, at least I hope you have.&lt;/p&gt;&#xA;" OwnerUserId="6740" LastEditorUserId="806" LastEditDate="2014-05-15T18:37:04.293" LastActivityDate="2014-05-15T18:37:04.293" Title="Prenatal hyperkinetic dysfunction and its effect on endurace" Tags="&lt;physiology&gt;&lt;muscles&gt;&lt;kinetics&gt;&lt;health&gt;&lt;dopamine&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17446" PostTypeId="1" AcceptedAnswerId="17717" CreationDate="2014-05-15T19:02:51.047" Score="2" ViewCount="258" Body="&lt;p&gt;I read Wikipedia claiming 52.&#xA;I heard that this can be extended to 54.&#xA;I see there is no limit of having more areas - just better understanding of the neuroblast migration and fibroblast too, probably.&#xA;&lt;strong&gt;How is this newer classification of Brodmann map done?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-05-28T06:55:22.297" LastActivityDate="2014-05-28T07:06:12.263" Title="How many areas are there in Brodmann map?" Tags="&lt;embryology&gt;&lt;histology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17447" PostTypeId="1" AcceptedAnswerId="17450" CreationDate="2014-05-15T19:08:17.540" Score="3" ViewCount="552" Body="&lt;p&gt;Most organic structures built from hydrogen, oxygen, nitrogen and carbon. They are represent 1-,2-,3-,4- bond relations (chemical valence) which allow to build variety of chain structures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there exist some replacements for these elements to create complex structures that theoretically can create life (self-reproduced or be a part of cell as organelle)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.thewestheimerinstitute.org/pubs/Is%20there%20a%20common%20chemical%20model%20for%20life%20in%20the%20universe%3F.pdf&quot; rel=&quot;nofollow&quot;&gt;Is there a common chemical model for life in the universe?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/news/2010/101202/full/news.2010.645.html&quot; rel=&quot;nofollow&quot;&gt;Arsenic-eating microbe may redefine chemistry of life&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencemag.org/content/332/6034/1163.full&quot; rel=&quot;nofollow&quot;&gt;A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/DNA#Alternate_DNA_structures&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/DNA#Alternate_DNA_structures&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Arsenic_DNA&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Arsenic_DNA&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6738" LastEditorUserId="6738" LastEditDate="2014-05-18T10:57:51.160" LastActivityDate="2014-05-18T10:57:51.160" Title="H O N C alternatives for organic life?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;life&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17448" PostTypeId="1" CreationDate="2014-05-15T19:58:12.017" Score="1" ViewCount="108" Body="&lt;p&gt;Several factors affecting vitamin D and its active form absorption and storage&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;acidity of stomach (not significant effect)&lt;/li&gt;&#xA;&lt;li&gt;cytopathic effects of viruses&lt;/li&gt;&#xA;&lt;li&gt;cytopathic effects of bacteria&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;where the last two reasons can be some reasons which may explain why vitamin D should be administered with bread; to make a surface covering around out vitamin D molecules. &#xA;Probably, the fibers also work in some short of transport media.&#xA;They can also partially explain why big dose of vitamin D does not last long time in the normostenic body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Summary of procedures in administrating vitamin D orally&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;with bread (carbohydrates; fibers) - possible protection, better transportation and more to absorbtion&lt;/li&gt;&#xA;&lt;li&gt;with oils (fat metabolism could help in destroying extra free radicals; but I see no other sense in administrating vitamin D with fish oils)&lt;/li&gt;&#xA;&lt;li&gt;daily (not weekly)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why does the lipid-soluble vitamin D not last in the body long time?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-05-16T05:15:52.517" LastActivityDate="2014-05-16T16:01:35.477" Title="Vitamin D oral intake, transportation and absorption" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;microbiology&gt;&lt;vitamins&gt;&lt;fat-metabolism&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17449" PostTypeId="1" CreationDate="2014-05-15T20:12:20.890" Score="2" ViewCount="168" Body="&lt;p&gt;I have Ensembl compara gene tree alignments (Compara.gene_trees.57.fasta.gz downloaded from &lt;a href=&quot;ftp://ftp.ensembl.org/pub/release-57/emf/ensembl-compara/homologies/&quot; rel=&quot;nofollow&quot;&gt;ftp://ftp.ensembl.org/pub/release-57/emf/ensembl-compara/homologies/&lt;/a&gt;) in nucleotide format. According to documentation, it says that the file &quot;contains the peptide alignment for every genetree in fasta format&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering what might be a handy tool to obtain the corresponding amino acid alignments from the file.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ikram&lt;/p&gt;&#xA;" OwnerUserId="6741" LastActivityDate="2014-07-15T01:52:15.980" Title="Converting Ensembl Compara gene tree DNA alignment to corresponding amino acid alignment" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;amino-acids&gt;&lt;molecular-evolution&gt;&lt;sequence-alignment&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17450" PostTypeId="2" ParentId="17447" CreationDate="2014-05-15T21:15:29.497" Score="4" Body="&lt;p&gt;Its not scientifically or logically possible to say 'this is impossible' but since this is a speculative question, I'll hazard an opinion.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like to argue that, at Earth standard pressure temperature and atmospheric conditions, C H O and N are not really replaceable.  Throw water into the mix as the most common liquid and replacing any or all of these elements is hard to imagine.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One can think about this by looking at the formation of long hydrocarbon chains.  &lt;a href=&quot;http://www.elmhurst.edu/~chm/vchembook/404silicone.html&quot; rel=&quot;nofollow&quot;&gt;Silicon can form polymers, but they tend to fall apart&lt;/a&gt;. Silcone-oxide polymers [SiR2-O-SiR2-O-] are more stable, but do not resemble hydrocarbon polymers as readily.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carbon is much more versatile, capable of forming either chain, or including sulfur, nitrogen in stable chains that don't seem to really have any length limitations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At thousands of atmosphere's pressure, temperatures of 70 Kelvin or in a sea of sulfuric acid, its easy to imagine other sorts of chemistry would dominate - phosphate , arsenic chains or germainium lattices, but on Earth most of these would fall apart.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if/when life is discovered elsewhere , it will certainly feature chemistry that will completely amaze us; unlike anything here.  But even so, its hard for me to imagine it being completely exclusive of these four elements.  I just want to point out that by a wide margin, &lt;a href=&quot;http://en.wikipedia.org/wiki/Abundance_of_the_chemical_elements&quot; rel=&quot;nofollow&quot;&gt;hydrogen is the most common element of the universe.   Nearly all the other light elements like C, O and N are the next most common.  This is simply because they take fewer nuclear fusion events to create&lt;/a&gt;.  Hydrogen is pretty useful no matter what chemistry you are looking at.  These four are probably going to be there somewhere - most planetary atmospheres have Ammonia, CO2 and methane in them as well - at least as far as we've seen.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-05-16T21:27:44.240" LastActivityDate="2014-05-16T21:27:44.240" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17451" PostTypeId="2" ParentId="10294" CreationDate="2014-05-15T22:17:16.493" Score="0" Body="&lt;p&gt;Rory gave a good answer to part 1.  Your main problem is that you have written Aa for III-7, and that's not the right call.  III-7 is not in the family (maybe you missed that detail in the tree), so their odds of carrying a bad allele in the same gene that this family carries a broken gene in is very very small.  So III-7 is AA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the III-6,7 mating is AA x Aa.  That means the odds of their kid also being a carrier is 50/50, the odds of the kid passing on the bad allele to her kid is also 50/50, so the odds of V being affected are .25.  (when you have a probability question in the form of &quot;What are the odds of this, then that happening&quot;, you multiple the probabilities to get the answer)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Part 2, if IV-2 is unaffected, then the odds are 2/3 that their genotype is Aa, and 1/3rd that their genotype is AA.  (See the Punnett Square, and notice that you disregard the box that leads to an affected phenotype)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for V to be affected, we need &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) III-6 to have passed on the bad allele to IV 1(50%)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) IV-1 to have passed on the bad allele (50%)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) IV-2 to be heterozygous (66.6%)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) IV-2 to have passed on the bad allele (50%)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The odds of all of that happening is 1/12&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-05-15T22:17:16.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17453" PostTypeId="2" ParentId="17449" CreationDate="2014-05-16T00:26:54.600" Score="1" Body="&lt;p&gt;As a general rule, both within and without the world of bioinformatics, public FTP sites contain README files tat explain what each file offered by the FTP server contains. The file &lt;a href=&quot;ftp://ftp.ensembl.org/pub/release-57/emf/ensembl-compara/homologies/README.protein_trees&quot; rel=&quot;nofollow noreferrer&quot;&gt;README.protein_trees&lt;/a&gt; states:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Compara.gene_trees.{release}.emf.gz&lt;/p&gt;&#xA;&lt;p&gt;                        contains the peptide alignment for every genetree in emf alignment format&lt;/p&gt;&#xA;&lt;p&gt;Compara.gene_trees.{release}.fasta.gz&lt;/p&gt;&#xA;&lt;p&gt;                      contains the peptide alignment for every genetree in fasta format&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This means that both &lt;a href=&quot;ftp://ftp.ensembl.org/pub/release-57/emf/ensembl-compara/homologies/Compara.newick_trees.57.emf.gz&quot; rel=&quot;nofollow noreferrer&quot;&gt;Compara.gene_trees.57.emf.gz&lt;/a&gt; and &lt;a href=&quot;ftp://ftp.ensembl.org/pub/release-57/emf/ensembl-compara/homologies/Compara.gene_trees.57.fasta.gz&quot; rel=&quot;nofollow noreferrer&quot;&gt;Compara.gene_trees.57.fasta.gz&lt;/a&gt; contain the protein alignments. I had a quick look at the files and it looks like &lt;code&gt;Compara.gene_trees.57.fasta.gz&lt;/code&gt; actually contains nucleototide sequences but &lt;code&gt;Compara.gene_trees.57.emf.gz&lt;/code&gt; does indeed contain a protein alignment:&lt;/p&gt;&#xA;&lt;pre&gt;&lt;code&gt;$ zgrep -m 1 AAAAASAAAT Compara.gene_trees.57.emf.gz.crdownload &#xA;SAAA-AHS-AGTAAAAA--AA--AAAAASAAAT-ASAATAI-SASSA-ASAAT-V----AAASVAA-HAFAS---ASAAASAAAAA-TIVAAAAX-SAASIYSAAAA-YAA--AASAS-ASAASAS-ASAASSSSSARS-AAS&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;p&gt;So, to answer your question, the file you want is the &lt;code&gt;.emf.gz&lt;/code&gt; one.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-05-16T00:26:54.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17454" PostTypeId="1" AcceptedAnswerId="17456" CreationDate="2014-05-16T06:14:40.137" Score="3" ViewCount="476" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23496758&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; cites a bunch of articles (I haven't been through them) that the effect of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_sexual_reproduction#Two-fold_cost_of_sex&quot; rel=&quot;nofollow&quot;&gt;two-fold cost of sex&lt;/a&gt; is &quot;reduced&quot; in stable environment or in K-selected environment. It says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[..] the infamous ‘two-fold’ cost may be reduced or, perhaps more accurately, more easily balanced in K-selected species. The ‘cost of males’ is with respect to reproduction. Abugov (1985) argued from life history theory principles that the two-fold cost of sex might be easier to pay with K-selection. The two-fold fecundity advantage of asexual reproduction is always a two-fold fitness advantage, regardless of whether it is in a K- or r-selected environment. However, a survival advantage is worth more under K-selection than under r-selection. Consequently, it is easier to balance the two-fold cost under K-selection if sexually derived genotypes have a survival advantage.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think that k-selection, k-selected environment and stable environment describe (more or less) the same kind of environment. Let me know if this sounds wrong to you. &lt;a href=&quot;http://en.wikipedia.org/wiki/R/K_selection_theory&quot; rel=&quot;nofollow&quot;&gt;Here is wiki for r/K selection theory&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the same article K-selection is defined as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;K-selection might favour slower development, greater competitive ability, delayed reproduction, higher survival rates, lower resource thresholds, leading to ‘efficiency’ (rather than productivity) and constant population sizes at or near carrying capacity of the environment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It sounds really strange to me. &lt;strong&gt;Can you please help me to understand why the two-fold cost of sex is lower in stable environment than in unstable environment?&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-07-30T17:57:36.360" Title="Two-fold cost of sex and r/K selection theory" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;ecology&gt;&lt;natural-selection&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17456" PostTypeId="2" ParentId="17454" CreationDate="2014-05-16T14:27:49.543" Score="3" Body="&lt;p&gt;r/K selection has become &lt;a href=&quot;https://en.wikipedia.org/wiki/R/K_selection_theory&quot; rel=&quot;nofollow&quot;&gt;more of an heuristic for characterizing a species' strategy of reproduction&lt;/a&gt; and less a matter of predicting what sort of species will emerge from a given environment as it had originally been proposed by MacArthur and Wilson in 1967. The paper you cite tries to determine whether rotifers become more r or more K selective in different environments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thought here on k-selection is not almost from the definitions of the term, which is why it isn't explained in the paper.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In R-selected strategies, many more offspring are produced, but less investment is made in each one.  Think about a cockaroach laying thousands of tiny eggs.  The hatchlings might be eaten by their own mother; they are so 'cheap' the insect who layed the eggs doesn't have any anxiety about their survival.  In extreme cases, most of these hatchlings will not reproduce, they may even be a bit of food for the ones which do reach maturity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In k-selected strategies, very few offspring are produced.  In addition to the 'cost of sex' limitation, they are invested in so heavily that the female may stop being fertile for a while.  An example would be how female mammals which are lactating are not fertile or seasonal mating like many birds do; the females turn off reproduction so that they can focus on the success of one or two produced offspring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;k-selection is advantageous over R-selection when more of their investment pays off.  If one out of ten R-offspring survive and one out of four k-selected offspring survive, then for these competing rotifers, the k-selected strategy is advantageous. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cost of sex is that its half as efficient as asexual reproduction because males don't really reproduce - they only provide genetic material for females.  You can argue r/K selection independently of this factor, but the article is suggesting that k-selection can be so advantageous as to also give sexual selection an advantage over asexual selection.  I think asexual reproduction could be k-selected as well, but that seems to be the point being made here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason that k/R has toned down in importance in the past couple of decades is that it has been found that individual species can adapt to shift their k/R strategems. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-07-30T17:57:36.360" LastActivityDate="2014-07-30T17:57:36.360" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17457" PostTypeId="1" AcceptedAnswerId="17464" CreationDate="2014-05-16T15:22:22.883" Score="14" ViewCount="2429" Body="&lt;p&gt;Let's say you're a 23-year-old man who impregnates a woman. Will your genes be the same if you were to impregnate another woman at age 35? Will your genes in those 12 years have changed/mutated/become smarter? &lt;/p&gt;&#xA;" OwnerUserId="6744" LastEditorUserId="49230" LastEditDate="2019-03-28T17:58:55.763" LastActivityDate="2019-03-28T17:58:55.763" Title="Can genes change as we age?" Tags="&lt;genetics&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="17458" PostTypeId="1" AcceptedAnswerId="17463" CreationDate="2014-05-16T16:08:29.400" Score="2" ViewCount="105" Body="&lt;p&gt;I saw there was another question about vitamin D; however, I do not believe this is a repeat.&#xA;What are some of the effects/side effects of having too much vitamin D in your body?&lt;/p&gt;&#xA;" OwnerUserId="6289" LastActivityDate="2014-05-16T16:29:50.283" Title="Effects of having too much vitamin D?" Tags="&lt;human-biology&gt;&lt;vitamins&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17459" PostTypeId="2" ParentId="17457" CreationDate="2014-05-16T16:08:46.173" Score="2" Body="&lt;p&gt;Genes can get mutated in one's lifetime. They gene altering agents are mutagens. Some common mutagens are X-ray, UV-ray, tobacco. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recent studies have yielded results which state that some behavioral actions may cause gene mutations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, yes in twelve years gene can mutate. Moreover as a man ages his efficiency of meiosis division is affected. So, genes may differently get expressed in his progenies.&lt;/p&gt;&#xA;" OwnerUserId="6390" LastActivityDate="2014-05-16T16:08:46.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17460" PostTypeId="1" AcceptedAnswerId="17503" CreationDate="2014-05-16T16:10:38.743" Score="3" ViewCount="992" Body="&lt;p&gt;In population genetics, we talk about several types of &lt;em&gt;genetic loads&lt;/em&gt; (also called just &lt;em&gt;loads&lt;/em&gt;). I am asking for a exhaustive list and a short definition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are for example some &lt;em&gt;genetic loads&lt;/em&gt; that come to my mind..&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mutation load&lt;/li&gt;&#xA;&lt;li&gt;Segregation load&lt;/li&gt;&#xA;&lt;li&gt;Drift load&lt;/li&gt;&#xA;&lt;li&gt;Lag load&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-05-17T18:18:31.907" LastActivityDate="2016-08-17T08:48:29.083" Title="Various Genetic Loads and their Definitions" Tags="&lt;evolution&gt;&lt;molecular-genetics&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17462" PostTypeId="2" ParentId="17457" CreationDate="2014-05-16T16:27:59.863" Score="5" Body="&lt;p&gt;Pre-sperm cells divide constantly, and will have more mutations in 12 years. Unfortunately, neither the genes (nor the father) are likely to be smarter. There is some evidence that children from older fathers are more prone to diseases like autism and schizophrenia. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A very nice, short overview of the current research is in this (open-source) &lt;a href=&quot;http://www.nature.com/nm/journal/v14/n11/full/nm1108-1170a.html&quot; rel=&quot;noreferrer&quot;&gt;Nature article&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6517" LastActivityDate="2014-05-16T16:27:59.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17463" PostTypeId="2" ParentId="17458" CreationDate="2014-05-16T16:29:50.283" Score="1" Body="&lt;p&gt;That is a rare condition that can only occur when taking too much doses of vitamin D. It has nothing to do with sun exposure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;High levels of vitamin D stimulate hypercalcemia and all its &lt;a href=&quot;http://en.wikipedia.org/wiki/Hypercalcaemia#Signs_and_symptoms&quot; rel=&quot;nofollow&quot;&gt;negative consequences&lt;/a&gt;. It can also exacerbate liver and kidney chronic diseases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference: Katherine Zeratsky, &lt;a href=&quot;http://www.mayoclinic.org/healthy-living/nutrition-and-healthy-eating/expert-answers/vitamin-d-toxicity/faq-20058108&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;What is vitamin D toxicity, and should I worry about it since I take supplements?&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-05-16T16:29:50.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17464" PostTypeId="2" ParentId="17457" CreationDate="2014-05-16T16:30:26.840" Score="15" Body="&lt;p&gt;Yes, there are some differences between the gametes that a parent produces at different ages!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Mutations in the germline during mitosis&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Every time a cell replicates some mutations may occur (even through &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;mitosis&lt;/a&gt;). Of course, any mutation that occurs in cells are located in your hand or in your brain, for example, will not be transmitted to the offsprings. Only mutations occurring in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Germline&quot; rel=&quot;nofollow noreferrer&quot;&gt;germline&lt;/a&gt; (cells in the testis and in the ovaries whose descendent or themselves go through meiosis) are possibly passed to the offsprings. Interestingly, because of the developmental pathways of sperm cells and ovules, sperm cells go through a lot more mitosis than ovules do, resulting in more mutations in the sperms than in the ovules. Therefore, if you look at a mutation in an individual and assuming you know that the mutation occurred during the lifetime of the parents, then you are more likely that the mutation comes from the father than from the mother.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As reviewed by &lt;a href=&quot;http://digitalcommons.wayne.edu/humbiol/vol85/iss4/1/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cochran and Harpending (2013)&lt;/a&gt;, mothers transmit on average a number x of new mutations to their offspring. This number x is independent of the age of the Mother. Fathers, however, transmit a number of new mutations to their offsprings that is very much dependent on the age of the father for developmental reasons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, as it has been pointed out there are various environmental factors that may increase or diminish the mutation rate (such as the mutagens (Tobacco, X-ray, ..))&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note on the process of adaptation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important to know that a vast majority of mutations are deleterious (impact negatively the reproductive success and survival of the individual carrying it). If we assume that no selection occurs between the cells of the germline, then no adaptation is possible. And in average sperm cells of an old guy should have lower fitness than the sperm cells of the same guy when he was younger. This process is referred to as mutation accumulation (mutation accumulation is not a concept that is specific to somatic lines mutations). However, one may argue the opposite! One might think that the cells that carry the new mutations (the mutation that occurred during the lifetime of the man) may be selected for or counter-selected. In such a case, the few beneficial mutations might be enough to make our cell lineages more fit with age. Whether the fitness of cells increase or decrease through our lifetime is dependent on the effective population size, the mutation rate and distribution of mutational effects. One can calculate the critical parameters yielding to one (mutation accumulation and fitness decrease) or the other (fitness increase through age) thanks to the &lt;a href=&quot;https://en.wikipedia.org/wiki/Mutational_meltdown&quot; rel=&quot;nofollow noreferrer&quot;&gt;mutational meltdown&lt;/a&gt; literature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important to note however that what increase the fitness of a cell might decrease the fitness of its carrier. Knowing the joint distribution of mutational effect for both the carrier and the cells should allow us to calculate if reproducing late in life allows transmitting better genes than reproducing early in life. Intuitively, I would expect that reproducing early in life would allow a parent to transmit better genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Epigenetics&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We have to talk about &lt;a href=&quot;http://en.wikipedia.org/wiki/Epigenetics&quot; rel=&quot;nofollow noreferrer&quot;&gt;epigenetics&lt;/a&gt; also. Epigenetics refers to all the modification that occur &quot;around&quot; or &quot;on&quot; the DNA but which are not the modification of the sequence of nucleotides. It is possible that the transmission of epigenetic modification is dependent on the age of the parents. But I have never heard of any case where this happens.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-28T17:46:26.490" LastActivityDate="2019-03-28T17:46:26.490" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="17467" PostTypeId="1" AcceptedAnswerId="17472" CreationDate="2014-05-16T17:25:30.517" Score="0" ViewCount="512" Body="&lt;p&gt;Tc is T cell which can give T killer cells and T helper cells.&#xA;T helper cells (Th1) see the pathogen presented by antigen presenting cells (dendritic cells and macrophages).&#xA;They then secrete antigens to kill the pathogen.&#xA;If there is memory from previous interaction, then it will be easier to protect.&#xA;However, since some viruses replicate fast (RNA particularly), this memory benefit is often lost, like in the case of influenza virus A and B types.&#xA;However, I am uncertain how to explain this immunology with viruses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can you explain this general viral interaction better in the immune response?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have these pictures in mind:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BLbWh.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3YYK0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-05-17T06:24:43.257" Title="Tc and Th1 interaction and viral immune response" Tags="&lt;microbiology&gt;&lt;immunology&gt;&lt;virus&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17469" PostTypeId="2" ParentId="17377" CreationDate="2014-05-16T18:53:58.743" Score="4" Body="&lt;p&gt;There are two reasons for the asymmetry for the lipid composition of membranes in cells usually.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first which was mentioned by @Superbest is proteins which are called 'flippases' which describes &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0005273608001090&quot; rel=&quot;nofollow&quot;&gt;three broad categories of proteins&lt;/a&gt; which facilitate the translocation of the lipids through the membrane, despite the fact that they all have polar or even charged head groups. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not really an answer to your question here though - they will have little to do with asymmetry of lipids in erythrocytes I think because the these proteins will only allow lipid diffusion to equilibrium on either side of the membrane.  To force an energetically unfavorable mixture of lipids they would require the use of energy.  While some lipid translocases can force the composition to change against the equilibrium, these seem to require ATP and &lt;a href=&quot;http://pimm.wordpress.com/2007/01/19/are-there-any-mitochondria-in-our-red-blood-cells/&quot; rel=&quot;nofollow&quot;&gt;human erythrocytes do not have mitochondria&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second, probably better answer is that the &lt;a href=&quot;http://www.pnas.org/content/82/11/3665.full.pdf&quot; rel=&quot;nofollow&quot;&gt;lipid composition of a membrane at equilibrium is dictated by of the curvature of the membrane&lt;/a&gt;.  The outside of a membrane takes lipids with larger head groups and shorter or fewer chains, the interior will compose more of lipids with smaller head groups and longer and more aliphatic chains.&lt;br&gt;&#xA;This capacity of a lipid to take up a greater volume in its head group vs its non-polar end is called its 'intrinsic curvature'.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Erythrocytes have some cytoskeletal structures such as &lt;a href=&quot;https://en.wikipedia.org/wiki/Ankyrin#ANK1&quot; rel=&quot;nofollow&quot;&gt;ankyrins&lt;/a&gt; which give the cell its characteristic curvy 'dented lozenge' shape, which must also drive some of the lipid composition in some parts of the cell. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1320" LastEditDate="2014-05-22T11:47:54.100" LastActivityDate="2014-05-22T11:47:54.100" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17470" PostTypeId="2" ParentId="17438" CreationDate="2014-05-16T23:51:14.920" Score="3" Body="&lt;p&gt;&lt;strong&gt;EDITS&lt;/strong&gt; &lt;em&gt;- I appreciate the comments and have incorporated them here.  Thanks to    @Superbest and @user22406 for raising them.  I hope this makes a better answer for the community.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under &lt;em&gt;normal&lt;/em&gt; circumstances, genomic (self) or mtDNA released into your cell or body cause absolutely no (known) problems.   I'll explain why that is, how the body can detect bacterial DNA, and finally the circumstances in which DNA can cause problems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Self-DNA generally causes no problems&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Almost from conception, cells in your body die.  Sometimes as part of pre-programmed sequence (eg inter-digital cells of the fetal limb paddle die and form fingers) or normal replenishment of cells such as the white blood cell (hundreds of millions of neutrophils die each day) or your gut epithelium.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Macrophages consume liberated DNA, and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Reticuloendothelial&quot; rel=&quot;nofollow&quot;&gt;reticulo-endothelial system in the spleen, liver and lungs&lt;/a&gt; filters the blood for cellular fragments.  &lt;a href=&quot;http://www.jimmunol.org/content/157/5/2116.short&quot; rel=&quot;nofollow&quot;&gt;This paper (from @Superbest)&lt;/a&gt; shows that bacterial DNA, and not normal human genomic DNA, can activate macrophages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So your immune system develops, and is constantly being exposed to, virtually every cell type and cell component (proteins, lipids, DNA and RNA etc).  If self-DNA could spark an immune reaction, normal life would be difficult.  We don't make antibodies (from B-cells) or T-cells that react with self-components due to a process called &lt;em&gt;anergy&lt;/em&gt; in which any developing T- or B- cells that could react to self-components during their maturation are instructed to shut down and/or die.   Yes, mitochondrial are inherited matrilinearly, but they still lyse and cause anergy, preventing an auto-immune response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Not all cell death is harmless- @Superbest's comment reminds us that apoptosis (involved in finger formation and other tissue remodelling and cell turnover) can package cellular components into self-contained vesicles.  On the other hand, damaged or lysed cells can liberate cytoplasmic components that can be pro-inflammatory or pro-coagulant.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Macrophages' vacuoles contain DNAse II, an enzyme that degrades DNA it encounters following phagocytosing/endocytosing fragments of dead cells.  More about that later....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Our bodies can detect bacterial DNA.  Same DNA, different decoration&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, invaders (bacterial, viruses, worms etc) may activate a family of receptors called &lt;a href=&quot;http://en.wikipedia.org/wiki/Toll-like_receptor&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Toll-like receptors&lt;/em&gt; (TLRs)&lt;/a&gt;.   TLRs have evolved to have specificity for antigens not seen in mammals e.g &lt;a href=&quot;http://en.wikipedia.org/wiki/Toll-like_receptor#Summary_of_known_mammalian_TLRs&quot; rel=&quot;nofollow&quot;&gt;cell walls, bacterial flagella and so on&lt;/a&gt;.  Some TLRs &lt;em&gt;do&lt;/em&gt; recognise DNA or RNA.  You may know that DNA contains 4 nucleotide bases, A,T,G and C.  In mammals, special sequences of two bases, C-G, (called &quot;CpG&quot;s) can be enzymatically modified by a methyl group.  In bacterial CpGs are not typically methylated and so a TLR (e.g TLR-9) that detects un-methylated CpGs is generally detecting bacterial DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Mitochondria are different&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mitochondria have features that resemble bacteria: a cell wall, a genome and the production of proteins that begin with the amino acid N-formyl-Methionine (f-Met).  Mammalian proteins don't have f-Met at the start (&quot;N-terminus&quot;).  Macrophages have a receptor that can recognize f-Met sequences (especially f-Met-Leu-Phe, fMLP) and activation of the fMLP receptor stimulates phagocytosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23804556&quot; rel=&quot;nofollow&quot;&gt;2013 paper&lt;/a&gt; describes the controversy whether mammalian  mtDNA is methylated (at CpGs) and offers strong evidence that it &lt;strong&gt;is&lt;/strong&gt; methylated.    In contrast, the &lt;a href=&quot;http://www.nature.com/nature/journal/v485/n7397/full/nature10992.html#supplementary-information&quot; rel=&quot;nofollow&quot;&gt;Oka paper&lt;/a&gt;  gives 5 citations where mtDNA &lt;strong&gt;is not&lt;/strong&gt; CpG-methylated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So..do mitochondria look like bacteria to our innate immune system?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;@user22406 flagged &lt;a href=&quot;http://www.nature.com/nature/journal/v485/n7397/full/nature10992.html#supplementary-information&quot; rel=&quot;nofollow&quot;&gt;this paper by Oka &lt;em&gt;et al&lt;/em&gt;&lt;/a&gt; which cites &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20203610&quot; rel=&quot;nofollow&quot;&gt;this paper by Zhang &lt;em&gt;et al&lt;/em&gt;&lt;/a&gt; as evidence that mtDNA can be pro-inflammatory.  The &lt;em&gt;Zhang paper&lt;/em&gt; provides evidence that mitochondria can stimulate the immune system's receptors for (1) f-Met-peptides (i.e detecting mitochondrial proteins that look 'bacterial&quot;) and (2) receptors for un-methylated CpGs, the TLR-9 receptor.  The Commentary on the article has a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2857339/figure/F1/&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;great figure of how mito components might promote inflammation&lt;/strong&gt;&lt;/a&gt; which copyright prevents me adding. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;Oka paper&lt;/em&gt; uses 2 key techniques: (1) surgical constriction of the aorta to cause heart enlargement (cardiac hypertrophy) and (2) a mouse strain with the gene for DNAse II deleted (noted as -/-, two minuses, both alleles gone).  In the hearts of DNAse II -/- mice, they observe higher levels of deposition of mtDNA in the damaged heart (Supplemental Fig 2), greater heart damage and many animals die.  This &lt;em&gt;suggests&lt;/em&gt; that excessive levels of DNA (not degraded in these DNAse -/-  mice) may be driving the damage. (The general phenotype of DNAse -/- mice was studied by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17066036&quot; rel=&quot;nofollow&quot;&gt;Kawane &lt;em&gt;et al&lt;/em&gt;&lt;/a&gt;  and the mice get an arthritis).  In Oka's DNAse II -/- mice, the degree of heart damage can be reduced by blocking TLR-9 (using an inhibitory oligo).  In aortic constricted mice where the DNAse II gene is intact (+/+), adding the TLR-9 blocking oligo gave some improvement, suggesting that the level of unmethylated DNA liberated in tissue damage &lt;strong&gt;may stimulate TLR-9 in normal animals.&lt;/strong&gt; &#xA;The authors also examined aortic constriction in TLR-9 -/- mice and found they had less lung and heart damage compared to controls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, the &lt;em&gt;Oka&lt;/em&gt; paper suggests something is signalling  via TLR-9 to drive inflammation and damage in this model and implies (but does not prove) that the 'something' is mtDNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;mtDNA in the plasma&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2843437/#&quot; rel=&quot;nofollow&quot;&gt;Zhang paper&lt;/a&gt;  detects up to 1ug/ml of mtDNA in the blood following major trauma (car and motorcycle crashes, falling 4 stories etc).  Their paper shows that this level of liberated mitochondria could stimulate immune cells (via TLR-9 and f-Met receptor).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;mtDNA won't get back inside the cell&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Extracellular DNA and RNA is generally broken down and cleared rapidly.  DNA, being a large, negatively charged molecule, will have extreme difficulty passing through an intact cell membrane.  In the laboratory, cells need to be exposed to high voltage electric shocks to make transient 'pores' in the cell membrane to allow DNA to enter or have the DNA formulated in liposomes.  Even if endocytosed, there is no known pathway to direct endocytosed DNA to the nucleus or an new mitochondrial 'host'.  So mtDNA would be extremely unlikely to re-seed into a new cell or a mitochondria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;But self-DNA can be harmful if released in large quantities&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;During successful cancer chemotherapy, large numbers of tumor cells lyse and may give rise to &lt;a href=&quot;http://en.wikipedia.org/wiki/Tumor_lysis_syndrome&quot; rel=&quot;nofollow&quot;&gt;tumor lysis syndrome&lt;/a&gt;.  Among the products released when a tumor is killed is DNA. A and G - the 'purine bases' - can be further &lt;a href=&quot;http://en.wikipedia.org/wiki/Purine_metabolism#Adenine&quot; rel=&quot;nofollow&quot;&gt;metabolized into uric acid&lt;/a&gt;.    Uric acid can crystallize in the kidney and cause damage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Summary&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mitochondria may be the remnants of &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitochondrion#Origin&quot; rel=&quot;nofollow&quot;&gt;endosymbiotic bacteria&lt;/a&gt; but, absent major trauma or mutations in both of your DNAse II genes, mitochondria come (and stay) in peace.     &lt;/p&gt;&#xA;" OwnerUserId="5922" LastEditorUserId="5922" LastEditDate="2014-05-19T13:09:24.273" LastActivityDate="2014-05-19T13:09:24.273" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="17471" PostTypeId="2" ParentId="14951" CreationDate="2014-05-17T04:27:09.633" Score="1" Body="&lt;p&gt;It seems that there is one basal body per cilium in multiciliated cells. Centriole duplication (as far as I understand, a basal body is just a different name for a centriole that is attached to a cilium) is tightly coupled to the cell-cycle. There is always one pair of centrioles that are at the base of the primary cilium (of which there is exactly one in most cells).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But not in multiciliated cells. These cells are differentiated and can no longer divide, and their centriole duplication process is decoupled from the cell cycle. In fact, they aren't, strictly speaking, &quot;duplicating&quot;, since many procentriolar bodies may form around one cylinder. Indeed, each cilium has its own basal body; thus a cell with hundreds of cilia has hundreds of basal bodies.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nrm/journal/v12/n4/pdf/nrm3085.pdf&quot; rel=&quot;nofollow&quot;&gt;Ishikawa 2011&lt;/a&gt; is a review that examines the structure of primary and motile cilia, and ciliogenesis. It does not spell out how the basal body gets there.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://jcb.rupress.org/content/50/1/10.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Anderson 1971&lt;/a&gt; describes the formation of new cilia in monkey oviduct. They first remove the ovaries of these monkeys to prevent cells from differentiating (this apparently requires estrogen), then administer estrogen and look at EM images of the cells over the following 6 days. They describe at length the processes of basal body formation.&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.biolcell.org/boc/072/0031/boc0720031.pdf&quot; rel=&quot;nofollow&quot;&gt;Dirksen 1991&lt;/a&gt; is another review focusing specifically on basal body formation during ciliogenesis. From their introduction:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;In order for the 200-300 cilia to form that the fully differentiated cell will need, production of that many centrioles is required first.&#xA;  The cell, after the last division, has usually retained a pair of&#xA;  centrioles. To what extent these mature centrioles are involved in the&#xA;  earlier stages of centriole formation, in which centriole precursor&#xA;  structures of varying sizes and shapes are generated and proceed to&#xA;  undergo transformational changes of great complexity, is largely&#xA;  unknown.&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://jcs.biologists.org/content/3/2/207.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Sorokin 1968&lt;/a&gt; is apparently a classic text which goes over EM images of ciliogenesis at various stages, and proposes a series of events describing what is happening. This is probably what you want, re: where are the other basal bodies coming from.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nrm/journal/v8/n6/pdf/nrm2180.pdf&quot; rel=&quot;nofollow&quot;&gt;Bettencourt-Dias 2007&lt;/a&gt; reviews the research on the formation of new basal bodies. This is another publication that answers your question very directly: &#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Many ciliated cells, such as those in vertebrate respiratory and&#xA;  reproductive tracts, can have 200–300 cilia per cell. This requires&#xA;  the generation of multiple centrioles during ciliogenesis. Here,&#xA;  centrioles are generated by two pathways, a centriolar and an&#xA;  acentriolar mechanism. In the first one, a parent centriole usually&#xA;  produces one daughter at a time; however, in certain cases several&#xA;  centrioles have been observed to develop simultaneously around one&#xA;  parent centriole, with the daughter centrioles being released into the&#xA;  cytoplasm to mature. The acentriolar pathway is the major pathway for&#xA;  basal body production. In this pathway, fibrous granules 124 that are&#xA;  70–100 nm in diameter first appear in the cytoplasm and subse quently&#xA;  move to the apical cytoplasm. Deuterosomes appear within the area.&#xA;  (...) Multiple procentrioles can grow out from deuterosomes, and&#xA;  mature daughter centrioles travel towards the apical region where they&#xA;  form ciliary basal bodies.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="540" LastEditorUserId="3340" LastEditDate="2016-01-27T11:00:35.490" LastActivityDate="2016-01-27T11:00:35.490" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17472" PostTypeId="2" ParentId="17467" CreationDate="2014-05-17T06:18:32.620" Score="1" Body="&lt;p&gt;PlaysDice's answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antigen presenting cells migrate from skin/mucosa to secondary lymphoid organs like lymph nodes/spleen/GALT and drive T cell activation and maturation.&#xA;T helper cells with CD8 and MHCII complex recognise the virus and kill it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this is what is happening, for instance in HIV infection:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QIOb8.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;dendritic cell (ADCC) presentation of HIV infected CD4+ to MHCII and T helper cell&lt;/li&gt;&#xA;&lt;li&gt;T helper cell activates cytokine release&lt;/li&gt;&#xA;&lt;li&gt;Natural killer cells come and lyse the HIV infected CD4+ T lymphocyte&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-05-17T06:24:43.257" LastActivityDate="2014-05-17T06:24:43.257" CommentCount="0" CommunityOwnedDate="2014-05-17T06:18:32.620" ContentLicense="CC BY-SA 3.0" />
  <row Id="17473" PostTypeId="2" ParentId="14968" CreationDate="2014-05-17T08:14:17.683" Score="1" Body="&lt;p&gt;My initial reaction is that (1) is preposterous, because there is no economics of the brain, as it is not made up of rational actors who trade or manage resources as individuals. Therefore it must be (2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I happen to know from experience that there is much said and written about (2) and less about (1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is some evidence supporting this:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dibs.duke.edu/research/d-cides/research/neuroeconomics/&quot; rel=&quot;nofollow&quot;&gt;Duke University's Center for Neuroeconomic Studies&lt;/a&gt; states that they apply &quot;&lt;em&gt;the techniques of cognitive and systems neuroscience – along with computational modeling – to understand economic decision making and related behavior&lt;/em&gt;&quot;.&lt;/li&gt;&#xA;&lt;li&gt;The &lt;a href=&quot;http://www.neuroeconomics.nyu.edu/mission/&quot; rel=&quot;nofollow&quot;&gt;IISDM at NYU&lt;/a&gt; (who have a program in neuroeconomics) says their goal is to &quot;&lt;em&gt;better understand the mechanisms, predict the impacts, and shape the policies that will define the study of decision-making tomorrow (...) by developing novel research infrastructures to support the propagation of neurobiological insights about the human animal into the policy domain&lt;/em&gt;&quot;..&lt;/li&gt;&#xA;&lt;li&gt;The &lt;a href=&quot;http://neuroeconomics.org/about-the-society/&quot; rel=&quot;nofollow&quot;&gt;Society for Neuroeconomics&lt;/a&gt; says their mission is to &quot;&lt;em&gt;foster research on the foundations of economic behavior by promoting collaboration and discussion among scholars from the psychological, economic, and neural sciences&lt;/em&gt;&quot;.&lt;/li&gt;&#xA;&lt;li&gt;The most highly cited result on Google Scholar for &quot;neuroeconomics&quot; is titled &quot;&lt;em&gt;&lt;a href=&quot;http://authors.library.caltech.edu/22006/2/0022051053737843.pdf&quot; rel=&quot;nofollow&quot;&gt;Neuroeconomics: How Neuroscience&#xA;Can Inform Economics&lt;/a&gt;&lt;/em&gt;&quot;. The &lt;a href=&quot;http://mail.physiol.gu.se/medfys/kogvt07/Articles/Sci%20Oct04%20Cog06.pdf&quot; rel=&quot;nofollow&quot;&gt;third hit's&lt;/a&gt; abstract says &quot;&lt;em&gt;Economics, psychology, and neuroscience are [aiming to provide] a single, general theory of human behavior. This is the emerging field of neuroeconomics (...) The goal of this discipline is thus to understand the processes that connect sensation and action by revealing the neurobiological mechanisms by which decisions are made.&lt;/em&gt;&quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So I would conclude from this that neuroeconomics is the study of human decision making, by application of neuroscience.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Granted, at this point I feel compelled to admit that perhaps I was too quick in my initial reaction: Is it really possible to isolate the study of the human brain from the study of human decision making? There is just so much overlap that even a &quot;pure&quot; neuroscientist will inevitably generate research which bears much relevance to economics. And with economics, the only way to &quot;escape&quot; neuroscience is to assume that all actors are perfectly rational, which is almost certainly at least a little bit untrue (although a staple of classical economics). It's probably a bit of loop, and I'd favor NYU's emphasis on it being interdisciplinary field rather than &quot;field X applied to field Y&quot;. That said, indeed, most neuroeconomics studies appear to be interested in solving economics problems, and not neuroscience problems.&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-05-17T08:21:29.977" LastActivityDate="2014-05-17T08:21:29.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17474" PostTypeId="2" ParentId="17361" CreationDate="2014-05-17T09:40:32.290" Score="2" Body="&lt;p&gt;It is more correct to call it &quot;resting potential difference&quot; (like your question), because electrical potential is relative, not absolute.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That phrasing exposes a crucial point: The difference of &lt;em&gt;what&lt;/em&gt;? Cell cytoplasms are negatively charged (to remember this, it helps to remember that protons are usually pumped out of the cytosol either into the periplasm, vesicles, mitochondrial intermemberane space, or outside of the cell). If you subtract the potential of the outside from the inside, you'll get +70. If you do it the other way around, you'll get -70. By convention, the (+) probe of the voltmeter is stuck inside the cell, and the (-) is stuck outside, so we end up with the &quot;official&quot; figure of -70 mV.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nature obviously does not like this potential difference, and wants to neutralize it by pushing current across the membrane. Luckily the membrane is not very conductive, and the cell can expend energy to undo the effects of any leaking and prevent the potential [difference] from drifting toward 0 (it would actually drift toward a number above 0 because potential difference isn't the only factor, there is also the concentration difference).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the cell is like a battery that keeps itself charged. It also has a threshold, and it will only empty itself if it has discharged at least to a certain point. That point depends on the cell, but a typical value is -55 mV (so closer to equilibrium point than the resting -70 mV).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What will an inhibitory chemical like GABA do? It will pull the cell further away from the threshold, so it's harder to overcome it. Bringing -70 mV to -90 mV would be lowering it (because the number goes down).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What will an excitatory chemical like glutamate do? It will bring the cell closer to the threshold, so it's easier to overcome it. Bringing -70 mV to -55 mV would be raising it (because the number goes up).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question, unfortunately, does not specify whether the action potential fires. Typically, the peak of the AP is +40 mV. In theory, you could have a threshold say, at +20 mV, and then perhaps the potential could go positive (eg. +10 mv) and stay there. But I really, really doubt you could find a cell with a threshold above 0. If the threshold is below zero, then the cell &lt;em&gt;will&lt;/em&gt; reach a positive potential difference (if you use enough glutamate to elicit the AP), but it will only stay there momentarily before collapsing back to -80 mV (the refractory state).&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-05-17T09:40:32.290" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17475" PostTypeId="2" ParentId="17441" CreationDate="2014-05-17T11:00:53.470" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;It is said that genes define how we look physically and psychologically&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would be skeptical of anyone saying this. Nature vs. nurture is far from settled, especially in psychology. The trend seems to be that many behavioral traits have a large heritable component, but are far from being determined only by heritable traits.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;if a male human sperm carries a certain number of genes, say x, and a female carries y, then mathematically there would be m genes from the male and n from the female&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think you are confused. If a sperm carries $x$ genes and an egg carries $y$ genes, the resulting zygote will have $x+y$ genes. If the male had $m$ and the female had $n$ genes, $x+y\approx m+n$ and $m \approx 2x$, $n \approx 2y$.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Could there be people identical in appearance if they end up with identical combinations of genes?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, we call these people identical twins. It could also occur by chance in unrelated individuals (well, everyone is somewhat related...) but this is extremely rare. There is just that too much variation in the human genome. There are literally tens of millions of points in the genome where some people have one version and others have another, and this person would have to happen to have the exact same version at each one as you do. This is an order of $10^{-8}$, if we consider humanity completely homogenous (and it isn't, so the probability is even lower).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;we find similar-looking people with perhaps similar behaviour accross diferent geographic locations; does this means that they have similar genetic make-up, up to some percentage?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The genes may be different and still lead to the same phenotype. Say one person has the set of genes that result in red hair, another one has the set that results in brown hair. They are both albinos. They'd look the same, but have different genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, genes are not the only thing that determines how people look or behave.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the fact that two people are phenotypically identical does not imply they are genetically identical. You can come up with a Bayesian probability that says they are more likely to have similar genes if they look similar, but how do you calculate the priors? Worse, how are you even going to measure how &quot;similar&quot; people look, or behave?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-05-17T11:00:53.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17476" PostTypeId="2" ParentId="17352" CreationDate="2014-05-17T11:23:21.343" Score="1" Body="&lt;p&gt;I would expect to see if every gene has a strong SDS, and that every strong SDS is in a gene (and if not, an explanation of why).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematically, that can be calculated using Fisher's Exact Test (since I don't see any p-values for your scores).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should also provide a diagram of the genome showing coding sequences or genes, and mark each SDS on it.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-05-17T11:23:21.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17477" PostTypeId="2" ParentId="17370" CreationDate="2014-05-17T11:34:31.123" Score="14" Body="&lt;p&gt;First part of the answer - Yes fleas (Siphonaptera) can be drowned. But not as easily as the internet would lead you to believe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many claims on the internet (and printed works) expounding on how simple it is to drown fleas.  The best science I found so far on the topic is in &lt;a href=&quot;http://books.google.com/books?id=c4FNatmAE48C&amp;amp;pg=PT101&amp;amp;dq=drown+Siphonaptera&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=Az93U66IKMjRsASn8IDwBQ&amp;amp;ved=0CEwQ6AEwBg#v=onepage&amp;amp;q=drown%20Siphonaptera&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Forensic Entomology: An Introduction By Dorothy Gennard; John Wiley &amp;amp; Sons, Apr 30, 2013; section 4.3&lt;/a&gt; which reflects a 1985 work by Simpson K. (&lt;em&gt;Journal of the New York Entomological Society 76: 253-265, not finding this online&lt;/em&gt;). Gennard is using the fleas present on a human body at death to determine how long the body had been submerged.  Findings - &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A flea submerged for up to 12 hours will appear to dead, but can revive in about 60 minutes after being removed from the water&lt;/li&gt;&#xA;&lt;li&gt;A flea submerged for 18 - 20 hours will appear to dead, but can revive in  4- 5 hours after being removed from the water&lt;/li&gt;&#xA;&lt;li&gt;It takes 24 hours of full submersion to fatally drown a flea &#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Side note; lice (Phthiraptera) can be fatally drowned in about 12 hours.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Second part of the answer - Yes soap can facilitate the death of fleas in bathing&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far the best I have is &lt;a href=&quot;http://books.google.com/books?id=T8CWvVGwKhoC&amp;amp;pg=PT404&amp;amp;dq=drown+flea&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=oz13U9OoE8uosQSZ_ID4Cw&amp;amp;ved=0CEkQ6AEwAg#v=onepage&amp;amp;q=drown%20flea&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Medical and Veterinary Entomology by Gary R. Mullen, Lance A. Durden Academic Press, Apr 22, 2009&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;This work suggests the process of washing the flea (and the pet) removes integumental waxes on the fleas body and they die from desiccation (dehydration).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;More Research&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been unable to find solid research specific to fleas (Siphonaptera) and soap (surfactants), so I had to reach in to the general insect works for answers.  There are a number of pesticides which include surfactants in their make up to increase effectiveness but these seem to be to an aid in the delivery of the pesticide not because the surfactant has any additional killing power.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a surfactant may affect the efficacy of an insecticide by its influence on wetting, spreading and run-off rather than by its influence on cuticular penetration&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://books.google.com/books?id=_AUQ_wntE8gC&amp;amp;pg=PA335&amp;amp;dq=surfactant+insects&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=xup_U9XQA_DNsQTlr4E4&amp;amp;ved=0CDIQ6AEwAQ#v=onepage&amp;amp;q=surfactant%20insects&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Physiology of Insecta, Volume 6 edited by Morris Rockstein&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is some science suggesting soaps can help break down cell membranes but they seem to be most effective on soft bodied insects (which fleas are not)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Soaps... kill insects by disrupting the exoskeleton and breaking down cell membranes.  Soaps generally work best against small soft bodied insects such as aphids, scale crawlers, meatybugs, and young caterpillars as well as spider mites.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://books.google.com/books?id=zMJ4MSKG9-AC&amp;amp;pg=PA67&amp;amp;dq=surfactant+insects&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=iOt_U42uAtDIsAST-4DgBg&amp;amp;ved=0CCoQ6AEwADgU#v=onepage&amp;amp;q=surfactant%20insects&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Destructive Turfgrass Insects: Biology, Diagnosis, and Control By Daniel A. Potter&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Summary&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are multiple online reports of &quot;drowning fleas&quot; and killing them with soapy water.  After looking for the science there does not seem to be much support for these fatal claims. There is little doubt that giving your pet a soapy bath in the tub will help remove the fleas, they may even appear dead.  But in all likelihood these fleas are just waiting to dry out and be revived, hopefully in the city sewer.  If you bath your pet in the yard, and than let the dry pet in the yard again the next day the clean pet and clean revived fleas will likely reunite. Soapy water is more likely to facilitate removal of the comatose flea from the pet and carry it down the drain. So it is reasonable to have noticeable decrease in the flea population after a bath.  But &lt;a href=&quot;https://pets.stackexchange.com/questions/196/&quot;&gt;excessive bathing has it's own risks&lt;/a&gt; and given the &lt;a href=&quot;https://en.wikipedia.org/wiki/Flea#Life_cycle_and_habitat&quot; rel=&quot;nofollow noreferrer&quot;&gt;life cycle of a flea&lt;/a&gt; soapy baths alone are unlikely to be a final solution.&lt;/p&gt;&#xA;" OwnerUserId="4240" LastEditorUserId="-1" LastEditDate="2017-04-13T12:59:17.050" LastActivityDate="2014-05-24T01:40:31.247" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17478" PostTypeId="2" ParentId="17441" CreationDate="2014-05-17T12:06:45.477" Score="2" Body="&lt;p&gt;For ease of explanation let me first tell you that the &quot;genetic makeup&quot; is called &quot;genotype&quot; and that &quot;how we look physically and psychologically&quot; is known as &quot;phenotype&quot;. These are not complete definitions of the terms but this should help you understand what we're talking about. I also apologise for the lack of detail or inaccuracies which many fellow contributors may find aggravating, but the question calls for keeping things down to the most important aspects :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do genes define how we look?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genotype defines &lt;em&gt;to some extent&lt;/em&gt; the human phenotype, but we don't know exactly to what extent regarding most aspects of the phenotype. This is called the &quot;nature vs. nurture&quot; debate and is concerned with the effects of genotype itself on phenotype vs. the effects of non-genetic influences after fertilisation (such as chemical surroundings during embryonal growth, experiences at young age etc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Numbers of genes from males and females&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another misunderstanding is that a sperm carries a certain number of genes which it combines with a number of genes from the egg. While this is strictly true, the number isn't what matters because &lt;strong&gt;we all carry the same number of genes&lt;/strong&gt; (*). The genotype doesn't depend on the &lt;em&gt;number&lt;/em&gt; of genes, but rather, almost all genes exist in several &lt;em&gt;variants&lt;/em&gt; within the human population. So the genotype is actually about which variants an individual carries, not about the number of genes. In biology, we use the term &quot;allele&quot; to refer to variants in this context. So in other words, each gene can have different alleles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;People with identical appearance&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If two people have identical alleles for all genes (i.e. identical genotype), then they can indeed look almost identical. However, because of the vast number of genes and alleles present in the human population, it is practically impossible for the same alleles to come together in two humans. With only one exception: if two individuals result from the same combination of sperm and egg cell, they will be identical, and this is exactly what happens in monozygotic twins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Similarities by geographical region&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the total number of genes and alleles is limited (**). This concept is what people call the &quot;gene pool&quot; and is the reason why humans are still always humans and share certain similarities. In particular, for most of human history our geographical movement has been limited (most of the time), creating geographical &quot;sub-gene pools&quot; (to keep it simple). This is why people from the same geographical region are more likely to look similar; they have a higher chance to share the same alleles of genes that determine appearance. In terms of behaviour - to whatever degree genotype influences behaviour, peopel from the same geographical region will be more likely to be similar in these regards than people from different geographical regions. However, you can now hopefully understand why this &quot;degree of similarity&quot; is next to impossible to quantify (lack of knowledge: which genes determine what, how many alleles exist of them, how many people have which allele, how much and how far do people travel,...).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;(*) Ok, not quite - it is possible for an individual to have the odd gene actually completely missing, but for the sake of simplicity we all have the same number.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(**) Again, not strictly, because new alleles and possibly even entire genes can result from mutation, but this is relatively rare and on the large scale you can work on the assumption that they are limited in number.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2014-05-17T12:06:45.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17479" PostTypeId="1" CreationDate="2014-05-17T12:11:56.903" Score="3" ViewCount="8331" Body="&lt;p&gt;Sedimentation coefficients, using a centrifuge, are expressed using Svedberg unit (symbol S, sometimes Sv). Wikipedia states that $S = 10^{-13}$ sec but I also saw in a book that actually $S = 10^{-13}$ sec/$\text{rad}^2$. Which of these is correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that a 50S ribosome has higher molecular weight than a 30S ribosome and for that reason the 50S would travel faster (on a test tube placed in the centrifuge) than a 30S, but if substitute S by $10^{-13}$ sec, for me it's a little bit-non intuitive, because 50S would be $50\cdot{10^-13}$ sec (and that is greater than $30\cdot{10^-13}$ sec), which means it takes more time to travel? Obviously not, so what's the physical meaning of time in this situation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In response to Alan Boyd:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;&lt;em&gt;In other words, at 1x g a 1S particle will travel at &lt;strong&gt;$10^{-13} m\cdot s^{-1}$&lt;/strong&gt;&lt;/em&gt;&quot; or &lt;strong&gt;$10^{-12}$&lt;/strong&gt;? &#xA;Indeed 5.5h is a reasonable value but I still cannot understand the significance of the ratio between velocity and acceleration which corresponds to Svedberg units (in seconds). &#xA;Maybe $50\cdot{10^-13}$ sec is the time that our ribosome takes to reach the terminal velocity in the fluid? That would make some sense, for example, if I drop an unfolded A4 paper to the ground the time it will take to reach terminal velocity will be lower than the time a A4 folded paper will take to reach it's specific terminal velocity, which is higher than the velocity from the unfolded A4 paper, because the area is larger (the friction force acting on it will be very high) which is consistent with the observations that are made (in centrifugation objects with larger surface area will travel at a slower terminal velocity). What do you think ?&lt;/p&gt;&#xA;" OwnerUserId="6753" LastEditorUserId="6753" LastEditDate="2014-05-17T15:40:05.853" LastActivityDate="2016-04-15T07:18:55.633" Title="What's the physical meaning of Svedberg unit?" Tags="&lt;molecular-biology&gt;&lt;centrifugation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17480" PostTypeId="2" ParentId="13888" CreationDate="2014-05-17T12:17:35.540" Score="2" Body="&lt;p&gt;I have looked at this ECG using &lt;a href=&quot;http://physionet.org/lightwave/&quot; rel=&quot;nofollow noreferrer&quot;&gt;LightWAVE&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first part is showing &lt;a href=&quot;http://www.learntheheart.com/ecg-review/ecg-topic-reviews-and-criteria/atrial-fibrillation-review/&quot; rel=&quot;nofollow noreferrer&quot;&gt;atrial fibrillation&lt;/a&gt; or flutter with variable conduction because:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;arrhytmia&lt;/li&gt;&#xA;&lt;li&gt;no P waves or coarse fibrillatory waves&lt;/li&gt;&#xA;&lt;li&gt;tachycardia at about 95-100 beats/minute&lt;/li&gt;&#xA;&lt;li&gt;can be seen better in V1&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/A5vcP.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;Sample from 00:00:40&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second part is showing &lt;a href=&quot;http://www.learntheheart.com/ecg-review/ecg-topic-reviews-and-criteria/premature-ventricular-contractions-review/&quot; rel=&quot;nofollow noreferrer&quot;&gt;premature ventricular contractions&lt;/a&gt; with trigeminy because:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;different morphology of QRS - ectopic &lt;/li&gt;&#xA;&lt;li&gt;wide QRS&lt;/li&gt;&#xA;&lt;li&gt;two normal complexes followed by one ectopic&lt;/li&gt;&#xA;&lt;li&gt;presence of the compensatory pause after PVC&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tcrgO.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;Sample from 00:09:20&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;ECG data: &lt;a href=&quot;http://physionet.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;PhysioNET&lt;/a&gt; &lt;a href=&quot;http://www.physionet.org/physiobank/database/mitdb/&quot; rel=&quot;nofollow noreferrer&quot;&gt;MIT-BIH Arrhythmia Database&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;ECG criteria: &lt;a href=&quot;http://www.learntheheart.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;LearnTheHeart.com&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-05-17T12:17:35.540" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17481" PostTypeId="2" ParentId="17479" CreationDate="2014-05-17T14:35:27.753" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Svedberg&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The sedimentation coefficient is the ratio of the speed of a substance in a centrifuge to its acceleration in comparable units. A substance with a sedimentation coefficient of 26S (26×10−13 s) will travel at 26 micrometers per second (26×10−6 m/s) under the influence of an acceleration of a million gravities (107 m/s2). Centrifugal acceleration is given as rω2; where r is the radial distance from the rotation axis and ω is the angular velocity in radians per second.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In other words, at 1x g a 1S particle will travel at 10&lt;sup&gt;-13&lt;/sup&gt; m s&lt;sup&gt;-1&lt;/sup&gt; = 0.1 pm s&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Particles with higher values of S will travel proportionately faster, and increasing g force will also increase sedimentation rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's look at the example of a 50S ribosome at 100 000 g:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;rate of sedimentation = 10&lt;sup&gt;-13&lt;/sup&gt; x 10&lt;sup&gt;5&lt;/sup&gt; x 50 m per sec = 50 x 10&lt;sup&gt;-8&lt;/sup&gt; m s&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how long to travel 10 cm = 10&lt;sup&gt;-2&lt;/sup&gt; m?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;=10&lt;sup&gt;-2&lt;/sup&gt;/(50 x 1010&lt;sup&gt;-8&lt;/sup&gt;) s&lt;/p&gt;&#xA;&#xA;&lt;p&gt;= approximately 5.5 h, which seems about right.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-17T14:35:27.753" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17482" PostTypeId="1" AcceptedAnswerId="17494" CreationDate="2014-05-17T17:42:52.877" Score="2" ViewCount="2035" Body="&lt;p&gt;Antihistamines are known to cause tiredness. &#xA;The essential hormones of the body are insulin (glucose), parathyroid hormone (calcium) and aldosterone (Na-K ATPase, sodium).&#xA;I am thinking how this tiredness symptom can come.&#xA;There are so many different antihistamines so I am confused about the mechanism how they cause tiredness.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Histamine acts on parietal cells of stomach via H2 receptors to stimulate hydrogen ion secretion - cephalic phase.&#xA;Excess of antihistamines can lead to decreased acidity of stomach so change in conversion of pepsinogen into pepsin. &#xA;So less pepsin breaking down peptides and proteins.&#xA;Body has to do something else to break those components - and this consumes much energy and makes you tired.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Small mucus food mass stays in the intestines.&#xA;Delayed absorption.&#xA;Nutrients needed so liver has to work and make essential things - amino acids and something else.&#xA;Some waste management also may happen - because of tiredness.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Changes in blood sugar level.&#xA;Delayed most probably after food intake.&#xA;Very fast and fast insulin secretion mechanism starting during wrong times - all of the sudden.&#xA;So less insulin secretion cumulatively:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;very fast mechanism - change of permeability of membranes (Na-K ATPase and sodium channels) reacting during times when not suitable - long after food intake&lt;/li&gt;&#xA;&lt;li&gt;fast mechanism (phosphorylation of different things) happening more, since sympaticus apparently is not so inhibiting here&lt;/li&gt;&#xA;&lt;li&gt;slow and very slow mechanisms however preferable (increased permeability of amino acids and mitoses)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So I think the tiredness of antihistamines is because of the increased amount of active fast mechanisms of insulin secretion, while less very fast mechanisms.&#xA;To carry the raw food mass in the intestines also require much energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the physiological mechanism behind the tiredness of excess antihistamines?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2016-07-02T20:48:45.843" LastActivityDate="2016-07-02T20:48:45.843" Title="Antihistamine's effect on insulin secretion and tiredness?" Tags="&lt;physiology&gt;&lt;cell-membrane&gt;&lt;blood-sugar&gt;&lt;antihistamines&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17483" PostTypeId="1" CreationDate="2014-05-17T19:07:11.370" Score="1" ViewCount="72" Body="&lt;p&gt;I built a script to detect microsatellites in a FASTA file. However, there are thousands of possibilities. &#xA;So, my question is: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;what are the markers of a &quot;good&quot; or &quot;useful&quot; microsatellite? &#xA;- How many base pairs, how many repetitions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And, are there any other heuristics that can be run to further detect usefulness of the microsatellite?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks.&lt;/p&gt;&#xA;" OwnerUserId="6755" LastActivityDate="2014-07-13T04:20:59.467" Title="About the quality of microsatellites" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17484" PostTypeId="1" AcceptedAnswerId="17486" CreationDate="2014-05-17T19:11:35.937" Score="1" ViewCount="98" Body="&lt;p&gt;What does the term &quot;&lt;em&gt;developmentally programmed&lt;/em&gt;&quot; mean? I can't seem to find a definition anywhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would the alternative (i.e. not developmentally programmed) imply?&lt;/p&gt;&#xA;" OwnerUserId="6756" LastEditorUserId="6703" LastEditDate="2014-05-18T02:23:12.990" LastActivityDate="2014-05-18T10:56:14.533" Title="What does &quot;developmentally programmed&quot; mean?" Tags="&lt;terminology&gt;&lt;development&gt;&lt;definitions&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="17485" PostTypeId="2" ParentId="7492" CreationDate="2014-05-17T22:18:01.687" Score="2" Body="&lt;p&gt;In bright light, a cat can also squint, thus approximating a circle with a square-like aperture. So a vertical pupil is not that much of a liability to focusing. The same cannot be said of a horizontal pupil (unless the eyelids are vertical). Additionally, a vertical pupil might optimize detection of horizontal movement, which is likely an advantage in hunting prey on the savannah.&lt;/p&gt;&#xA;" OwnerUserId="6758" LastActivityDate="2014-05-17T22:18:01.687" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17486" PostTypeId="2" ParentId="17484" CreationDate="2014-05-17T22:46:18.007" Score="1" Body="&lt;p&gt;The term could mean two things depending on the emphasis:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;developmentally &lt;em&gt;programmed&lt;/em&gt;&quot; would seem to emphasise the &quot;programmed&quot; nature of the development of something, implying that it is under specific regulation and the result of targeted energy expenditure (&quot;Here, we describe widespread developmentally programmed nuclear destruction (PND) events that occur during yeast gametogenesis&quot;).&lt;/li&gt;&#xA;&lt;li&gt;&quot;&lt;em&gt;developmentally&lt;/em&gt; programmed&quot; would be intending to distinguish from other means of being programmed, i.e. this would go in the direction of a nature vs. nurture statement (&quot;Hair colour is &lt;em&gt;developmentally&lt;/em&gt; programmed and does not depend on external influences after fertilisation&quot;).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The first of the two appears to be the more common use of this phrasing if one wants to trust Google to be representative. Something along these lines might be intended in your example, though I don't see why this statement is necessary as it seems quite obvious that any organ that develops during embryogenesis is &quot;developmentally programmed&quot;...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suppose the alternative (&quot;not developmentally programmed&quot;) would imply that the development of secondary lymphoid organs is an accident which is not driven by specific mechanisms that exist for the particular purpose of developing them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, there is no magical scientific meaning to either of these two words, to me your example seems to be rather a mishap of phrasing.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2014-05-18T10:56:14.533" LastActivityDate="2014-05-18T10:56:14.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17487" PostTypeId="1" CreationDate="2014-05-17T22:55:45.167" Score="9" ViewCount="576" Body="&lt;p&gt;What is the mechanism by which &lt;a href=&quot;http://en.wikipedia.org/wiki/Aminoglycoside&quot;&gt;aminoglycoside&lt;/a&gt; antibiotics (such as streptomycin and gentamicin) damage the mechano-sensory hair cells of the auditory and vestibular system? (Could this be seen as evidence for &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20203251&quot;&gt;Lynn Margulis' theory that these cilia are descended from bacteria&lt;/a&gt;?) &lt;/p&gt;&#xA;" OwnerUserId="6760" LastEditorUserId="6760" LastEditDate="2014-05-20T15:41:54.300" LastActivityDate="2014-05-22T07:38:19.420" Title="How can antibiotics damage the ear?" Tags="&lt;antibiotics&gt;&lt;hearing&gt;&lt;human-ear&gt;&lt;cilia&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17488" PostTypeId="1" CreationDate="2014-05-17T23:09:05.430" Score="3" ViewCount="2236" Body="&lt;p&gt;From my understanding, the increase in atmospheric carbon dioxide will also increase oxygen levels. That makes me wonder if in the near future insects will grow larger than they are today, since their maximum size is limited by how deeply oxygen is able to diffuse into their body.&lt;/p&gt;&#xA;" OwnerUserId="6758" LastActivityDate="2014-05-17T23:53:49.567" Title="Will the increase in atmospheric carbon dioxide lead to larger insects?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17489" PostTypeId="1" CreationDate="2014-05-17T23:31:36.663" Score="5" ViewCount="165" Body="&lt;p&gt;I'm trying to do some rough figuring to calculating efficiencies of various light sources for growing plants.  I'm hampered, however, by the lack of a curve to multiply by the spectrum of light sources to determine the amount of photosynthetically active radiation that a typical plant will absorb and use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can find curves like below all over, but I can't get numerical data in the form of tables. Is there some source from where I can get such data?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/7/72/Par_action_spectrum.gif&quot; alt=&quot;PAR curve&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="25" LastEditorUserId="3340" LastEditDate="2014-12-25T12:09:42.117" LastActivityDate="2014-12-25T12:09:42.117" Title="Where can I get numerical data for the PAR (photosynthetically active radiation) curve?" Tags="&lt;photosynthesis&gt;&lt;literature&gt;&lt;light&gt;" AnswerCount="0" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="17490" PostTypeId="2" ParentId="17488" CreationDate="2014-05-17T23:48:26.727" Score="8" Body="&lt;p&gt;There is the supported theory that insects during the Paleozoic period were larger in size because of the &lt;a href=&quot;http://www.sciencedaily.com/releases/2006/10/061012093716.htm&quot; rel=&quot;noreferrer&quot;&gt;increased oxygen content&lt;/a&gt; in the air.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The study adds support to the theory that some insects were much larger during the late Paleozoic period because they had a much richer oxygen supply.&lt;/p&gt;&#xA;&lt;p&gt;The Paleozoic period, about 300 million years ago, was a time of huge and abundant plant life and rather large insects - dragonflies had two-and-a-half-foot wing spans, for example. The air's oxygen content was 35% during this period, compared to the 21% we breathe now, Kaiser said. Researchers have speculated that the higher oxygen concentration allowed insects to grow much bigger.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This article is based on a paper published in the &lt;em&gt;American Physiological Society&lt;/em&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;It is because when the oxygen concentration in the atmosphere is high, the insect needs smaller quantities of air to meet its oxygen demands. The tracheal diameter can be narrower and still deliver enough oxygen for a much larger insect, Kaiser concluded.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MTDGR.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;There are similar papers that investigate the relationship between oxygen and &lt;strong&gt;maximum potential size&lt;/strong&gt;, such as this &lt;a href=&quot;http://www.nature.com/nature/journal/v399/n6732/abs/399114b0.html&quot; rel=&quot;noreferrer&quot;&gt;article&lt;/a&gt; published in &lt;em&gt;Nature&lt;/em&gt; (1999):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The tendency of some animals to be larger at higher latitudes ('polar gigantism') has not been explained, although it has often been attributed to low temperature and metabolism. [...] We have analysed length data for 1,853 species of benthic amphipod crustaceans from 12 sites worldwide, from polar to tropical and marine (continental shelf) to freshwater environments. We find that maximum potential size (MPS) is limited by oxygen availability.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Another &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/early/2010/03/04/rspb.2010.0001.full&quot; rel=&quot;noreferrer&quot;&gt;paper&lt;/a&gt; published in &lt;em&gt;Proceedings&lt;/em&gt; further supports this theory:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;[...] A variety of recent empirical findings support a link between oxygen and insect size, including: (i) most insects develop smaller body sizes in hypoxia, and some develop and evolve larger sizes in hyperoxia; (ii) insects developmentally and evolutionarily reduce their proportional investment in the tracheal system when living in higher PO2, suggesting that there are significant costs associated with tracheal system structure and function; and (iii) larger insects invest more of their body in the tracheal system, potentially leading to greater effects of a PO2 on larger insects.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The question you propose is very interesting, although I am sure it would take thousands of years for these insects to adapt to this oxygen level change (which in itself, to reach prehistoric levels, would take a long time) and in turn become larger.&lt;/p&gt;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.livescience.com/1083-oxygen-giant-bugs.html&quot; rel=&quot;noreferrer&quot;&gt;article&lt;/a&gt;, based on the original &lt;em&gt;APS&lt;/em&gt; paper, seems to think larger insects could appear in the future if the limiting factor (in this case low oxygen levels) is removed.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Xvrgx.gif&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Image from &lt;a href=&quot;http://www.pnas.org/content/109/27/10745.full&quot; rel=&quot;noreferrer&quot;&gt;Biotic interactions modify the effects of oxygen on insect gigantism&lt;/a&gt; (&lt;em&gt;PNAS&lt;/em&gt;, Chown 2012).&lt;/p&gt;&#xA;" OwnerUserId="6380" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-05-17T23:53:49.567" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17494" PostTypeId="2" ParentId="17482" CreationDate="2014-05-18T09:10:49.623" Score="3" Body="&lt;p&gt;Thanks to studies on animal behavior and on histamine dection in the Central Nervous System, researchers found out the &quot;histaminergic system&quot;.&#xA;It's thought that histamine-containing neurons regulate sleep-wake cyrcle, immunity, memory, body temperature, drinking, feeding rhythms. By the way, knockout rats who lack of histamine system don't show big defects in any function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;H1-Receptors for Histamine are distributed in the CNS and in the rest of the body. H1-antagonists (such as Promethazine, Chlorcyclizine, Loratadine...) have different effects on CNS, depending on dose. At conventional doses central depression appears and patients are sedated. They can even experience an antihistamine &quot;hangover&quot; in the morning, even if they take these drugs at bedtime. By the way, antihistamine overdose typically shows with convulsions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;non-sedating&quot; H1-antagonists, or &quot;second generation&quot; have a lot less effects on CNS. They have polar chemical structure: they can not cross the blood-brain barrier.&#xA;By the way, a lot of typical and atypical anti-psychotic drugs have H1-antagonism effects on the brain (with H2 and H4 antagonism): their main goal is sedation to stop the patient from hurting himself (or others) during manic episodes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I think the last two sentences explain that sedation is almost a totally CNS-mediated side effect of antihistamine drugs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;H1-antagonists don't suppress gastic secretion, do not inhibit salivary, lacrimal or other exocrine secretions. Older H1-antagonists have an anti-colinergic effect on muscarinic receptors: they may reduce ACh-mediated secretions, typically in mouth and in the respiratory tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;H2-antagonists are used to treat acid-peptic desease (as PPIs, proton pump inhibitors). CNS-related side effects are not commons, and include: confusion, delirium, hallucinations, slurred speech and headaches. These effects are mostly related with IV infusion of the H2-antagonist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just made a very small research on PubMed. I found this:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3529778&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/3529778&lt;/a&gt;&#xA;as you can see it is a study (on only 9 patients, in 1986), about insuline-glucose-Cpeptide and ranitidine (H2-antagonist) relations. Their conclusion is &quot;Ranitidine significantly increased the area under concentration/time curves for glucose and insulin but not that of C-peptide. Our data indicate that ranitidine does not affect pancreatic insulin release nor peripheral glucose utilization and are consistent with the hypothesis that ranitidine influences the hepatic clearance of glucose and insulin both of which undergo high first-pass liver extraction.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that tiredness is a typical CNS-mediated side effects of H1-antagonists (anti-allergic) but is not a side effect of H2-antagonists (anti-acid). Maybe H2-antagonists affects insulin action via hepatic effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*I'm italian (sorry for any english mistake) and I am a last-year medicine college student.&#xA;I wrote trying to summarize some chapters (8, 32 and 45) of:&#xA;- &quot;Goodman &amp;amp; Gilman's The Pharmacological Basis of Therapeutics&quot; - L. Brunton, B. Chabner, B. Knollman - 12th edition; McGrawth Hill 2011 &lt;/p&gt;&#xA;" OwnerUserId="6762" LastActivityDate="2014-05-18T09:10:49.623" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17496" PostTypeId="1" CreationDate="2014-05-18T10:11:19.137" Score="4" ViewCount="1515" Body="&lt;p&gt;When the vesicle is swallowed of course the lipid layer internalizes. My question is how will the top segment of membrane will bind back together when that vesicle took the membrane with it inside cytoplasm. Will the plasma of the cell decrease or they will repair back and how does the membrane know that a certain substance is outside and i have to internalize myself in order to swallow. The same thing with exocytosis: How does the membrane open itself and repair back and what will happen to the membrane of the vesicle which went out? &lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="3632" LastEditDate="2014-05-18T14:50:30.223" LastActivityDate="2014-05-18T14:50:30.223" Title="how is the plasma membrane repaired after endocytosis?" Tags="&lt;molecular-biology&gt;&lt;membrane-transport&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17497" PostTypeId="2" ParentId="17496" CreationDate="2014-05-18T13:09:48.530" Score="6" Body="&lt;p&gt;You have one misconception about the endocytosis: In the process no hole in the membrane is generated. It works in principle like in the figure below (it is of course more complicated, but this should explain it): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vm03P.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The membrane forms a vesicle around the particle which shall be integrated until it is completely surrounded by a membrane. At this point the vesicle is detached from the cell membrane and inside the cell. To accomplish internalization, the particle binds to certain receptors which regulate this process. See the &lt;a href=&quot;http://en.wikipedia.org/wiki/Endocytosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt; for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exocytosis works in principle the other way round. Here are the visicles detached from the Golgi apparatus (mostly at least) and are directed to the cell membrane. Here the fuse with the membrane and form a pit which has its opening to the outside, releasing what was in the vesicle. It works like this (image from &lt;a href=&quot;http://www.histology-world.com/photoalbum/displayimage.php?album=70&amp;amp;pid=3703&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kaYiN.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this process you have to differentiate between permanent unregulated exocytosis and regulated endocytosis (for example for the release of hormones) which are regulated by signal transduction pathways.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-05-18T13:54:12.370" LastActivityDate="2014-05-18T13:54:12.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17498" PostTypeId="1" AcceptedAnswerId="17555" CreationDate="2014-05-18T14:35:02.637" Score="5" ViewCount="1278" Body="&lt;p&gt;I am wondering exactly what a-fib is (causes and symptoms).&#xA;&lt;p&gt;&#xA;I would really appreciate having a sample of an EKG with it (because in my limited research, I have found it nearly impossible to find just a sample piece of an EKG that has a-fib on it) with your answer, so I can actually get an idea of what it looks like. With the sample EKG, I would love to have a normal one beside it so I can kind of analyze the differences between the two.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note:&lt;/strong&gt; This is not and never was a homework question! &lt;/p&gt;&#xA;" OwnerUserId="6289" LastEditorUserId="6289" LastEditorDisplayName="user12874" LastEditDate="2016-08-24T15:12:02.113" LastActivityDate="2016-08-24T15:12:02.113" Title="What is atrial fibrillation?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;&lt;electrocardiography&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="2" ClosedDate="2015-01-19T06:39:28.087" ContentLicense="CC BY-SA 3.0" />
  <row Id="17499" PostTypeId="1" CreationDate="2014-05-18T16:34:30.280" Score="5" ViewCount="69" Body="&lt;p&gt;Humans don't digest fibre, and nor do any animals, but some creatures have micro-organisms (bacteria, I'm guessing) in their gut which digest fibre for them.  My question is, could humans take some sort of pill and establish our own fibre-digesting colonies in our intestines?  Has this been tried?  Supposing it could be done, would you suppose it would have any negative effects on our health?  (i.e.. would those whose gut digested fibre for them be stuck on a low-fibre diet?).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Purpose of question: just wondering.  It would be cool to be able to eat bark.  &lt;/p&gt;&#xA;" OwnerUserId="6767" LastActivityDate="2014-05-19T12:29:39.200" Title="Could humans choose to establish fibre digesting colonies in our guts?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17500" PostTypeId="2" ParentId="17499" CreationDate="2014-05-18T17:17:37.220" Score="6" Body="&lt;p&gt;Probably not without some substantial evolution to change our physiology, depending on what you are wanting.  If you just want to digest fibre, that might be done, but if you wanted to see nutritional value out of it, its not clear that's going to be worth it..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Soluable fibre is currently used by the human body, so you are probably be asking about insoluble fibre.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It might be possible to do a little of this experimentation - I'm not recommending this - but there would be several likely issues depending on your goals in such a project, which could vary.  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;the human gut microenvironment probably will not accommodate the bacteria you need and they might not grow in significant quantity.&lt;/li&gt;&#xA;&lt;li&gt;the human gut is not physiologically arranged for digesting such fibre - &lt;a href=&quot;http://www.ultimateungulate.com/cetartiodactyla/Rumination.html&quot; rel=&quot;noreferrer&quot;&gt;ungulates generally have four stomach chambers&lt;/a&gt; that they can use to store some of the hard for the longer time it takes to break the fibre down. &lt;/li&gt;&#xA;&lt;li&gt;the nutritional value of plant fibre is low XKCD has some numbers on this and &lt;a href=&quot;http://what-if.xkcd.com/17/&quot; rel=&quot;noreferrer&quot;&gt;a cow can eat 10kg of plant matter a day&lt;/a&gt; and in doing so they don't tend to move that much.  Humans have to eat a greater volume of vegetables to get the calories they need.  Is getting that last 2-5% or so of the energy from digesting fibre worth the trouble? Eat one more apple or a handful of grain.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Lastly, there would likely be some impact on human health - if you succeed then you would be modifying &lt;a href=&quot;http://www.nhs.uk/chq/Pages/1141.aspx?CategoryID=51&amp;amp;SubCategoryID=167&quot; rel=&quot;noreferrer&quot;&gt;fibre's role in human diet as it stands&lt;/a&gt; - which is to help keep the intestines cleaned out. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-05-19T00:08:33.627" LastActivityDate="2014-05-19T00:08:33.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17503" PostTypeId="2" ParentId="17460" CreationDate="2014-05-18T18:02:44.577" Score="4" Body="&lt;p&gt;The genetic load is a population construct, a way of quantifying the fitness reduction in a population due deviations from the optimal genotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One type of load comprises all the others, namely genetic load.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Genetic load is just the loss of mean fitness relative to the ideal fitness.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You forgot to include substitution load in your list, but otherwise I think you included all the main ones.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Substitution load is the total loss of mean fitness caused because favorable alleles substitute gradually by selection rather than&#xA;  instantaneously.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As for the ones you mentioned:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Mutational load is just the accumulation of deleterious alleles in a population.&lt;/li&gt;&#xA;  &lt;li&gt;Segregating load is the decrease in fitness in a population due to homozygotes being less fit.&lt;/li&gt;&#xA;  &lt;li&gt;Drift load is the fixation of deleterious alleles due to small population size. The smaller the population, the greater the risk of&#xA;  this happening.&lt;/li&gt;&#xA;  &lt;li&gt;Lag load is the loss of fitness due to a change in environment.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Another type, mentioned by rg255:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Gender load, which is the deviation from the optimum due to an allele drifting back and forth because the version that is optimal in one sex is not the one that is optimal in another. &lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6768" LastEditorUserId="1590" LastEditDate="2016-08-17T08:48:29.083" LastActivityDate="2016-08-17T08:48:29.083" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17504" PostTypeId="2" ParentId="16570" CreationDate="2014-05-18T19:00:27.730" Score="2" Body="&lt;p&gt;These values are not already normalised to normal tissue controls. That a tumour is marked as tumour with matched normal doesn't mean that all of the platforms used by the TCGA (Expression, CNV, protein and methylation) have normal tissues available - in most cases Tumours with Matched Normals are annotated thusly because mutation calling was performed using tumour vs normal comparisons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are looking for normal tissue controls for your given platform type (RPPA in your screenshot) you will find them labelled NT or N. If you don't see any that are labelled with those descriptions it means normal tissue samples have not been processed using that platform.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The TCGA doesn't do loads of normal tissue analysis for anything other than mutation calling because the project is focused on classifying tumours into subgroups using unsupervised approaches, primarily, and therefore all comparisons that get heavily used are tumour vs tumour after allocation to subtypes. &lt;/p&gt;&#xA;" OwnerUserId="6726" LastActivityDate="2014-05-18T19:00:27.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17508" PostTypeId="1" CreationDate="2014-05-19T12:25:06.457" Score="4" ViewCount="301" Body="&lt;p&gt;Why are the lengths the way they are with middle finger the longest?&lt;/p&gt;&#xA;" OwnerUserId="6772" LastActivityDate="2016-05-06T15:03:40.817" Title="What is the evolutionary cause for various finger lengths?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;human-anatomy&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17509" PostTypeId="2" ParentId="17499" CreationDate="2014-05-19T12:29:39.200" Score="2" Body="&lt;p&gt;Just to add something to the answer from @shigeta - even assuming that you did manage to establish a gut microbiome that was capable of metabolising fibre, this wouldn't be a source of glucose: in ruminants the gut bacteria ferment the sugars released from the cellulose, releasing short chain fatty acids (&lt;a href=&quot;http://en.wikipedia.org/wiki/Volatile_fatty_acids&quot; rel=&quot;nofollow&quot;&gt;a.k.a. volatile fatty acids, &lt;/a&gt; e.g. propionic acid). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These compounds are used to fuel gluconeogenesis in the liver of the animal: in  a lactating cow this can amount to kilograms of glucose synthesised per day. Although you wouldn't be aiming to eat that much fibre, the release of these VFAs into your bloodstream might still cause some metabolic problems.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-19T12:29:39.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17511" PostTypeId="1" AcceptedAnswerId="17518" CreationDate="2014-05-19T16:34:06.287" Score="12" ViewCount="3574" Body="&lt;p&gt;This is my first question here, so I apologize for all mistakes I could have possibly made.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm a high school student in East-Central Europe and I need to complete some research for a biology contest (asking for advice is accepted, so I'm not cheating). My task is to analyze the influence of certain environmental factors (temperature etc., it's not that important for my question) on the activity of bees. The method is pretty simple: once a week I record the entrance to the bee hive (I do it on four hives), play it in slow-mo (It's impossible to count them properly without doing so) and simply count the number of bees entering or leaving.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Problem is, I don't know how long the observation should take. I play it in like X1/8, you need to play it twice (entering/leaving), so it takes a lot of time to gather one piece of information for a certain day. Till now I've been doing it for one minute - and there seems to be some kind of pattern to their activity analyzed that way. Yet, I'm not sure if it's actually eligible. I can't do the observation for hours - I still need to learn and have other duties.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what should I do? Could anyone give me some advice? Is one minute (several, like 6 times a day per hive) legitimate enough?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance.&lt;/p&gt;&#xA;" OwnerUserId="6774" LastEditorUserId="2938" LastEditDate="2014-05-20T10:56:36.083" LastActivityDate="2014-05-20T10:56:36.083" Title="How best to count bees entering and leaving a hive to measure hive activity?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;statistics&gt;&lt;research-design&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17512" PostTypeId="2" ParentId="17511" CreationDate="2014-05-19T17:00:41.910" Score="9" Body="&lt;p&gt;One thing that's certain is that the activity of bees varies according to time of day, so more important than &lt;em&gt;how long&lt;/em&gt; you record for is probably &lt;em&gt;at what time&lt;/em&gt; you record. If you always record at the same time of day, this should allow a reasonable comparison between results of different days. For example, recording from time 14:30 to 14:35 every day could be fine. You could then record conditions at this time each day (temperature, weather, etc.) along with this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the exact length of your recordings: Of course, the longer they are, the better. More samples usually increases reliability and representativeness of your results. However, more importantly you want a practically useful time as well. This really depends on the actual number of bees entering into the hive within different time frames, as well as the baseline variability between days irrespective of the conditions you are investigating. I don't know anything about either of these :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You want the number of entrances in your recording to be at a level where you will notice if there is a meaningful difference between days, and the only way of going about this is usually to start with a guess and then change if you notice that you can't really make sense of your results.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2014-05-19T17:00:41.910" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17513" PostTypeId="1" AcceptedAnswerId="17516" CreationDate="2014-05-19T18:46:54.293" Score="2" ViewCount="388" Body="&lt;p&gt;&lt;em&gt;Extensor digitorum&lt;/em&gt; and &lt;em&gt;extensor digiti minimi&lt;/em&gt; both insert into the extensor hoods of digits 2-5 (or just 5 in the case of &lt;em&gt;e. digiti minimi&lt;/em&gt;).  In every source that I can find, &lt;em&gt;extensor pollicis longus&lt;/em&gt; &amp;amp; &lt;em&gt;brevis&lt;/em&gt; insert &lt;strong&gt;directly&lt;/strong&gt; into the base of the distal and proximal phalanxes respectively.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this indicate that the thumb does not have an extensor sheath as the remainder of the digits do?&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2014-05-19T19:31:42.153" Title="Does digit 1 have an extensor sheath?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17514" PostTypeId="2" ParentId="16533" CreationDate="2014-05-19T19:04:44.273" Score="2" Body="&lt;p&gt;Chromosome splits (or fusions for that matter) might not mean that much for reproductive success since genes can still line up and recombine. To quote the science blogger &lt;a href=&quot;http://scienceblogs.com/pharyngula/2008/04/21/basics-how-can-chromosome-numb/&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;P.Z. Myers&quot;&gt;P.Z. Myers&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[C]hromosome numbers can change dramatically with no obvious effect&#xA;  on the phenotype of the organism.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;He illustrates it thusly:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8uncT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to answer your first question, changes in the number of chromosomes aren't always fatally deleterious (as you seem to think).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for how a change in chromosome number might spread, the explanation is likely random drift and inbreeding. To quote P.Z. Myers again:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So our two chromosome individual will have a reduced fertility as long&#xA;  as he or she is breeding with the normal one chromosome organisms, but&#xA;  those split chromosomes can continue to spread through the population.&#xA;  They are not certain to spread — they’re more likely to eventually go&#xA;  extinct — but by chance alone there can be continued propagation of&#xA;  the two chromosome variant.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://books.google.no/books/about/Evolution.html?id=HCh7n6zuWeUC&amp;amp;redir_esc=y&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Evolution&quot;&gt;&quot;Evolution&quot;&lt;/a&gt; by Mark Ridley, p. 361 similarly points out that reproduction will be an uphill battle until the new variant becomes more common (often through inbreeding or drift in small populations):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When a new chromosomal fusion mutation arises, it will be selected&#xA;  against because of its disadvantage in heterozygous form. But if it&#xA;  drifts up to a locally high frequency, as may easily happen in a&#xA;  local, small, and perhaps inbreeding, mouse population, natural&#xA;  selection will favor it. Natural selection favors whichever&#xA;  chromosomal form is locally common[.]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This might in the end lead to speciation due to the two populations becoming incompatible.&lt;/p&gt;&#xA;" OwnerUserId="6768" LastEditorUserId="6768" LastEditDate="2014-05-20T06:59:46.313" LastActivityDate="2014-05-20T06:59:46.313" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17515" PostTypeId="2" ParentId="17508" CreationDate="2014-05-19T19:20:41.253" Score="8" Body="&lt;p&gt;When you bend your fingers, they all arrive at the same height. I would tend to think that their lengths differ when you keep them straight because they need to have similar length when you bend them. And I guess that there is some optimal length (when bended) for fingers to grasp things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is nothing but a quick hypothesis. But it sounds quite plausible to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As @JordiZambrino commented, it is possible also that middle fingers evolved to be longer in reaction for the need for throwing things.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2016-05-06T15:03:40.817" LastActivityDate="2016-05-06T15:03:40.817" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17516" PostTypeId="2" ParentId="17513" CreationDate="2014-05-19T19:31:42.153" Score="1" Body="&lt;p&gt;From $n=2$ textbooks, the results are equivocal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.lww.co.uk/clinically-oriented-anatomy&quot; rel=&quot;nofollow&quot;&gt;Moore et al. (2013)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;There is no mention of an extensor expansion associated with the pollex.&lt;/li&gt;&#xA;&lt;li&gt;EPL and EPB are listed as inserting on the distal and proximal phalanges, respectively.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.lww.co.uk/color-atlas-of-anatomy&quot; rel=&quot;nofollow&quot;&gt;Rohen et al. (2010)&lt;/a&gt; (p. 394)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;Extensor expansion of extensor of thumb&quot; The label points to the middle of the diaphysis of the proximal phalanx. It's odd that extensor is singular here, given that there are two extensors.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;However, &lt;a href=&quot;http://czasopisma.viamedica.pl/fm/article/view/FM.2013.0040/25861&quot; rel=&quot;nofollow&quot;&gt;Abdel-Hamid et al. (2013)&lt;/a&gt; present data from dissection of 95 limbs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Extensor pollicis longus:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;EPL tendon was attached to both proximal (PP) and distal (DP) phalanx through the extensor expansion in 94.7% of specimens (Figs. 1A, B; 2A). In 5.3% of upper limbs, the EPL tendon was attached to the DP through its extensor expansion (Fig. 2B; Table 2).&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Extensor pollicis brevis:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In 55.8% of upper limbs, [EPB] was attached distally to the base of the [proximal phalanx] of the thumb (Fig. 1B). While in 41%, EPB tendon was attached to the extensor expansion of the thumb at the level of the base of [proximal phalanx] (Fig. 2A). However, in 3.2% of specimens its tendon was inserted into the extensor expansion of the thumb at the level of the base of [distal phalanx].&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And the answer appears to still be equivocal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abdel-Hamid GA, El-Beshbishy RA, Abdel Aal IH. 2013. Anatomical variations of the hand extensors. &lt;em&gt;Folia Morphol&lt;/em&gt; 72:249–257.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2014-05-19T19:31:42.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17518" PostTypeId="2" ParentId="17511" CreationDate="2014-05-19T20:40:10.573" Score="2" Body="&lt;p&gt;I'm no expert at this but these are some of the things that I would consider thinking about. How practical is it for you to count the total number of bees in the hive, based on lets say hive weight or the number of bees on one rack in the hive (then multiply by the total number of racks to give you an estimate of the total bee numbers in a hive) before you start collecting video data? This will at least put your influx/outflow number into some sort of prospective if you are counting in different times of days or if there are different wheather conditions in different days. This is easily achieved if you divide your influx and outflow numbers by the total (estimated) number of bees. This gets you two numbers (ratios) which you plot on the Y-axis. On the x-axis you can plot the passage of time and even colour code different days based on average (lets say) temperature to see if temperature had an obvious effects on your observations. But obviously all your instances of recording and time intervals between recordings needs to be constant!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in many fly behavioural or locomotion function assays, scientists record fly movements at certain fps and analyse the videos. Now most of this video data analysis  is done using scripting in Matlab which is (I know to be) the tool choice for motion analysis. Now since you say you are at high school, this would probably be quite a challenge since the program is costly and scripting is not that easy (at least for me), so see if you can utilise the help of someone to get over this barrier. Once you do then you can analyse much longer videos at much higher frequencies, which will give you a better resolution on your data. If you could't then consider looking through web sites using search engines such as google for Matlab codes for motion tracking analysis scripts. I did this some time ago and there are wealth of information out there and once you do that you can get the communities help in websites such as stack overflow to help you refine your codes or any problems you may have with it, so long as you show evidence of your work. This is a great option since you can add variety of data (or different data aspects) to your project such as what is the average speed/velocity which your bees travel at in different times when entering/exiting the hive, is there a pattern to their travelling (e.g. straight line, zig-zag etc) and much more. I'm aware that this is beginning to sound like a PhD project and not a high school project but these are some things to consider. If programming is totally out of the question then you can look on internet to see what free programs are out there to aid you with your data collection. I briefly looked and saw this (&lt;a href=&quot;http://www.youtube.com/watch?v=jWD8CHW06Ks&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=jWD8CHW06Ks&lt;/a&gt;) and this (&lt;a href=&quot;http://www.researchgate.net/post/Does_anyone_know_of_FREE_software_for_motion_capture&quot; rel=&quot;nofollow&quot;&gt;http://www.researchgate.net/post/Does_anyone_know_of_FREE_software_for_motion_capture&lt;/a&gt;) just by simply typing into google &quot;video motion tracking software&quot; so look around and see if you can find anything which you can tailor for your own need.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now regarding video length time, as correctly mentioned in Armatus response (if I'm not wrong and correct me if I am) it shouldn't matter for how long or how frequent you are recording so long as you keep the variables (i.e. time of recording, frequency of recording etc) to the minimum (i.e. not change them), or in other words keep your observation methodology constant through time, and try to come up with a practical schedule and if you explain your thought rational (experimental design) in your report, even a professor (i dare to say) wouldn't be able to argue with it but you always have to talk about the limitations of your study and that is key and that's where peoples project falls apart when an expert reviews it and finds holes and criticises claims made, which can not be backed up by the data/types of analysis gathered/performed!!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Just to address some statistics issues, I would make your recordings from minimum of three hives per recording time-interval/point since in science n (number of observations) should be &gt;= 3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyways I hope my ramblings have been somewhat useful.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-05-19T21:20:06.557" LastActivityDate="2014-05-19T21:20:06.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17519" PostTypeId="1" AcceptedAnswerId="17521" CreationDate="2014-05-19T20:43:37.740" Score="1" ViewCount="423" Body="&lt;p&gt;Here is the thing. I am using a method, called TU-Tagging, to isolate cell type specific RNA. You can find more about the method here: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783170/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783170/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To explain it very briefly, there is an enzyme called UPRT (Uracil Phosphoribosyltransferase) which is expressed in &lt;em&gt;Toxoplasma gondii&lt;/em&gt;. Under normal circumstances UPRT creates UMP from host cells' uracil and this UMP incorporated in RNA. However, they found that this enzyme cannot distinguish uracil and uracil analog 4-Thiouracil (Basically has thio on 4th position of the uracil). So, when 4-TU provided externally, UPRT incorporates 4-TU into RNA and you get thio-RNA. Then with basic biotinylation and streptaividin isolation you can get thio-RNA from your total RNA isolate. (Of course UPRT should be put to specific cell types of your interest)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, after the explanation (maybe it was unnecessary though) here is my question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After I isolate my so called specific RNA, I check the purity by qPCR by using cell type specific markers. I do not have a reference gene. The only thing I am interested in is the presence or absence of markers (and also the fold change of course). Now, I have some data but I do not know how to present them (There is nobody in my lab experienced with qPCR and my experience is just so limited).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you have an idea how I can overcome this issue? I looked into some calculations but most of them are needed for reference genes or some other stuff. The only thing that I have is cycle numbers and my primers' efficiency. Do you think I can do something with these inputs? (I know that cycle numbers mean nothing in a plot, so I do not want to put cycle numbers basically.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for reading it. Any help/idea would be very appreciated. I am so desperate. Thank you.&lt;/p&gt;&#xA;" OwnerUserId="5630" LastActivityDate="2014-05-19T23:28:33.910" Title="A question related to qPCR analysis" Tags="&lt;molecular-biology&gt;&lt;rna&gt;&lt;pcr&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17520" PostTypeId="2" ParentId="17511" CreationDate="2014-05-19T21:21:13.410" Score="4" Body="&lt;p&gt;Ideally, you would gather preliminary statistics to design the experiment. If you have a high variability, and your observation window is short, then small effects will be swamped by the variability. However, if what you are looking for has a big effect in the number of bees, then counting for a shorter time is going to be fine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A rule of thumb would be to try recording 5 to 10 segments of 1 minute analysis and see what the variability is. If the standard deviation is small compared to the effects you are seeing, then 1 minute is fine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want a more theoretical justification, &lt;a href=&quot;http://en.wikipedia.org/wiki/Poisson_distribution&quot; rel=&quot;nofollow&quot;&gt;Poisson distribution&lt;/a&gt; could be used as a first order approximation of the distribution. I don't know much about statistics specific for this kind of insect behaviors though.&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2014-05-19T21:21:13.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17521" PostTypeId="2" ParentId="17519" CreationDate="2014-05-19T23:28:33.910" Score="4" Body="&lt;p&gt;OK, let us start from the beginning. We know what makes one cell type different from another cell type is its expression - i.e. what genes are actually being transcribed into RNA. Therefore, there should be certain RNA in one cell type that should not exit in another cell type. If you isolate RNA from a certain cell type, say a neuron and you want to show that your sample RNA contains only neuronal RNA, than you have to prove 2 things:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;That your sample contains certain RNA sequences that are known to be in neurons&lt;/li&gt;&#xA;&lt;li&gt;That your sample does NOT contain certain RNA sequences that are known NOT to be in neurons&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;There are several lab procedures for identifying the presence/absence of certain RNA sequences in a sample, your chosen technique is qPCR. Here is a brief explanation of how qPCR works. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You put your RNA sample along with a sequence specific primer in the qPCR machine. The primer will bind to a specific sequence and then that strand will be replicated. This will keep on repeating, cycle after cycle. So if you start with 1 sequence of say sequenceA, after cycle 1, you will end up with 2, then 4, then 8 and so on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyways, if your goal is to use qPCR to prove your RNA sample comes from a neuron then you must find some sequences that are known to be specific to neurons. Then find primers for these sequences. Then use these primers to amplify some RNA from your sample. If you get amplification, then you must have had that sequence in your RNA sample. To further support yourself, you may also want to look up a few sequences that are known NOT to be expressed in neurons and using the same principle prove that these sequences are NOT in your sample.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above will give you qualitative data, it will simply tell you if a certain sequence exits or does not exist in your RNA sample. Since you are only interested in the presence or absence of markers, this should be sufficient. Howver, if you would like to quantify your data, i.e. find out how much a certain sequence is expressed then read on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also get quantitative data from qPCR (after all qPCR stands for quantitative PCR). The number of copies of an RNA sequence after a certain number of cycles is proportional to the initial number of copies of that sequence in your sample. In other words, if your initial RNA sample has a lot of sequenceA and a little sequenceB, then at any cycle, you should see more sequenceA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can take advantage of this relationship. There are two general methods you can use to quantify your results. One is called Absolute quantification and the other Relative quantification. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea behind absolute quantification is that you run two qPCRs. In one, you do your RNA sample. In the second, you run a standard sample, for which a standard curve is available. You can then compare your RNA sample results with the standard's results to get an idea of the number of copies in your sample.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea behind relative quantification is that you compare the qPCR results for your sequence of interest with the qPCR results of a refrence gene. This will only give you an idea of how many times more or less your sequence of interest if expressed than the reference gene. Since you do not have a refrence gene you cannot use this method, but you can use the absolute quantification method explained in the paragraph above!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are very useful links on quantifying using qPCR:&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction#Quantification_of_gene_expression&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction#Quantification_of_gene_expression&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://relative.gene-quantification.info/&quot; rel=&quot;nofollow&quot;&gt;http://relative.gene-quantification.info/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me know if you need further clarifications.&lt;/p&gt;&#xA;" OwnerUserId="6038" LastActivityDate="2014-05-19T23:28:33.910" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17522" PostTypeId="1" AcceptedAnswerId="17534" CreationDate="2014-05-20T01:52:52.917" Score="2" ViewCount="899" Body="&lt;p&gt;It is &lt;a href=&quot;http://www.nature.com/nrm/journal/v12/n4/abs/nrm3085.html&quot; rel=&quot;nofollow&quot;&gt;often stated&lt;/a&gt; that most cells in the human body have a primary cilium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which ones don't? For which cells is it unknown?&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="231" LastEditDate="2014-05-20T16:34:40.333" LastActivityDate="2014-05-20T17:46:56.347" Title="What cells don't have a primary cilium?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;cilia&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17524" PostTypeId="1" AcceptedAnswerId="17530" CreationDate="2014-05-20T02:52:03.007" Score="5" ViewCount="1124" Body="&lt;h1&gt;My Data&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;I have a 23andMe file listing SNPs in the form:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;rsid       chromosome      position        genotype&#xA;rsXXXXX         1           PPPPPP          CT&#xA;rsXXXXX         1           PPPPPP          GG&#xA;&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fields are TAB-separated and each line corresponds to a single SNP. For each SNP, four fields of data are supplied. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;An identifier (an rsid or an internal id)&lt;/li&gt;&#xA;&lt;li&gt;Its location on the reference genome.&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The chromosome it is located on.&lt;/li&gt;&#xA;&lt;li&gt;The position within the chromosome is is located on.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;The genotype call oriented with respect to the plus strand on the human reference sequence.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The reference genome is the human assembly build 37 (also known as Annotation Release 104).&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;My Question&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;How do I merge the SNPs into the reference genome?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, take the first line in my SNP file:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;rsXXXXX        1           PPPPPP          CT&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Part 1&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;I can see that I need to replace the nucleotide at position PPPPPP on chomosome 1 of the reference genome with a nucleotide from the genotype field, but which nucleotide am I supposed to use? C or T? And why?&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Part 2&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Where am I supposed to start counting from on the reference genome? Looking at chromosome 1 of the human assembly build 37, the first ~10,000 characters (excluding the first line description) are &lt;code&gt;N&lt;/code&gt;. Is the first N number 1? eg. If PPPPPP was 100,000 would I replace the 100,000th character in the reference genome with the correct nucleotide from &lt;strong&gt;Part 1&lt;/strong&gt; of this question? Or should I start counting from the first non-N character in the fasta file?&lt;/p&gt;&#xA;" OwnerUserId="6780" LastActivityDate="2014-05-20T10:39:10.493" Title="How do you merge SNP data with a reference genome?" Tags="&lt;genetics&gt;&lt;human-genome&gt;&lt;snp&gt;&lt;nucleic-acids&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17525" PostTypeId="2" ParentId="17524" CreationDate="2014-05-20T03:17:21.997" Score="0" Body="&lt;p&gt;Genetics 101, you have 2 copies of all your DNA at every position, one copy from your mother, one from your father.  So for the &quot;CT&quot; one, you have one copy with a C, and one with a T.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And yea, it's normal for the first several thousand, or million letters to be N's.  The genome is repetitive and yucky there, but it's counted for numbering purposes anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Honestly, I wouldn't do this with a giant text file of the genome.  Just search for your SNP in ensembl.org using the rs number, and you'll get the SNP, and some flanking sequence, and some context.  Search it in PubMed if you want to see if it's ever turned up in any publication&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-05-20T03:17:21.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17526" PostTypeId="2" ParentId="17524" CreationDate="2014-05-20T05:27:00.670" Score="0" Body="&lt;p&gt;&lt;strong&gt;Part 1:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://liorpachter.wordpress.com/2013/11/30/23andme-genotypes-are-all-wrong/&quot; rel=&quot;nofollow&quot;&gt;Lior Pachter&lt;/a&gt;, 23andme data are not phased. Which means that for each entry in the genotype field, you do not know which chromosome copy it came from. This happens since modern microarray platforms are not able to tell which of the two copies of a chromosome a snp came from. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can solve this problem for most snps by comparing your alleles to the reference genome, but this would take some programming chops. You could use &lt;a href=&quot;https://github.com/endrebak/qc_gwas&quot; rel=&quot;nofollow&quot;&gt;https://github.com/endrebak/qc_gwas&lt;/a&gt; as an example, which does the same thing, but for plink files. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Part 2:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm assuming that you would like to do this programatically, and not by copying and pasting the snps into the reference genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The short answer is that the first N is the first nucleotide. But, you should rather use a package such as &lt;a href=&quot;http://biopython.org/wiki/SeqIO#Sequence_Input&quot; rel=&quot;nofollow&quot;&gt;Biopython&lt;/a&gt; to do the counting for you, it might be knottier than you think (you need to adjust for line endings in the fasta file, for example). &lt;/p&gt;&#xA;" OwnerUserId="6768" LastActivityDate="2014-05-20T05:27:00.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17528" PostTypeId="1" CreationDate="2014-05-20T08:14:24.930" Score="1" ViewCount="62" Body="&lt;p&gt;I need to know the correct term(s) which are usually used in the parlance of both biology and bioinformatics for this study approach:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About 11 transcripts were investigated using qPCR for a number of samples (about 200) and then  the gene expression data were subjected to data mining tools: principal component analysis (PCA), cluster analysis (CA) and the results were interpreted using other supportive data that were not included in PCA in order to reveal the nature of acquired clusters.&#xA;Clusters obtained were then predicted from the gene expression data using machine learning classifiers. In short, it is a blend of molecular biology, data mining tools, and machine learning classification (predictive modeling).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please if you have ever done this kind of data analysis, what should be the appropriate term to describe this approach?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Likely candidates&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Gene expression profiling study&lt;/code&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Transcript profiling study&lt;/code&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Transcript Wide Analysis Study&lt;/code&gt; or &lt;code&gt;TWAS&lt;/code&gt; for short  &lt;/p&gt;&#xA;" OwnerUserId="3320" LastActivityDate="2014-05-20T08:14:24.930" Title="What is the suitable terminology to describe this study approach?" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;pcr&gt;&lt;transcription&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17529" PostTypeId="1" CreationDate="2014-05-20T08:40:05.360" Score="2" ViewCount="79" Body="&lt;p&gt;What are the known natural biochemical reasons for a dead human's body not fully decaying (decomposing)?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&#xA;I am interested in a scientific explanation of those cases, in which human body would not fully decay, for example, some parts of skin and hair would still be there, and I am not talking about such cases like hand-made mummification (like, say, those Pharaoh's mummies in Egypt). &lt;/p&gt;&#xA;" OwnerUserId="6783" LastEditorUserId="6783" LastEditDate="2014-05-20T12:23:24.273" LastActivityDate="2014-05-20T12:23:24.273" Title="What are the known natural biochemical reasons for a dead human's body not fully decaying?" Tags="&lt;decay&gt;" AnswerCount="0" CommentCount="7" ClosedDate="2014-08-08T04:17:41.450" ContentLicense="CC BY-SA 3.0" />
  <row Id="17530" PostTypeId="2" ParentId="17524" CreationDate="2014-05-20T10:39:10.493" Score="3" Body="&lt;p&gt;First, you need to know which genome sequence does the SNP file refer to. They must have mentioned the reference sequence that they used. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As others mentioned the case of &lt;code&gt;CT&lt;/code&gt; is heterozygosity. If you just want to mark the changes then discard the residue that is already present in the reference genome and use the other allele. However, you want to keep a track of the haplotype then you have make sure that a set of SNPs come from the same chromatid. This is difficult- you might still be able to know it for SNPs that are close enough to be mapped by a single read but it is almost impossible for SNPs that are separated well enough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Endre said, you have to start from the first nucleotide. However, it seems dubious that you are getting $\ (NNNN)_n$ in the beginning of chromosome 1. Complete assembled chromosomes do not have such stretches. Below are the first 10 lines of the chromosome 1 fasta file. See for yourself.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt;gi|568815364|ref|NT_077402.3| Homo sapiens chromosome 1 genomic scaffold, GRCh38 Primary Assembly HSCHR1_CTG1&#xA;TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC&#xA;CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACCCTAACCCTAACCCTAA&#xA;CCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCT&#xA;AACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTAAACCCTAACCCTAACCCTAACCCTA&#xA;ACCCTAACCCCAACCCCAACCCCAACCCCAACCCCAACCCCAACCCTAACCCCTAACCCTAACCCTAACC&#xA;CTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCCTAACCCTAACCCTAACCCTA&#xA;ACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTCGCGGTACCCTCAGCCGGCCCG&#xA;CCCGCCCGGGTCTGACCTGAGGAGAACTGTGCTCCGCCTTCAGAGTACCACCGAAATCTGTGCAGAGGAC&#xA;AACGCAGCTCCGCCCTCGCGGTGCTCTCCGGGTCTGTGCTGAGGAGAACGCAACTCCGCCGTTGCAAAGG&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;How to replace $N^{th}$ residue is quite a straightforward task. But that is a programming question and not the scope of this forum. Assuming that you have solved the part 1 problem and have a tab separated &lt;strong&gt;sorted&lt;/strong&gt; file like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;chromosome  position    residue&#xA; 1           79989           G&#xA; 1           100232          T&#xA; 3           341342          A&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This script may not be the best but would work in a linux/*nix/Cygwin terminal, to replace the residues (ensure that you have &lt;code&gt;gawk version &amp;gt;=4.0&lt;/code&gt;):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;gawk -F &quot;\t&quot; '(FNR==1){x++} (x==1){a[$1][$2]=$3;next} (x==2){if($0~/&amp;gt;/){h=$0;sub(/^.*chromosome /,&quot;&quot;,h);sub(/ .*/,&quot;&quot;,h)} else{seq[h]=seq[h]$0}} END{for(i in a){s=0; for(j in a[i]){m=m substr(seq[i],s,j-1) a[i][j];s=j+1} m=m substr(seq[i],s); print &quot;&amp;gt;Chr&quot;i&quot;\n&quot;m}}' SNP_file Genome.fa | fold -w 60&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-05-20T10:39:10.493" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17531" PostTypeId="1" CreationDate="2014-05-20T12:46:05.463" Score="3" ViewCount="345" Body="&lt;p&gt;As far as we know, sleep seems to be the part of the daily cycle when executive functions are resting and memories are fortifying. Many, but not all, of the functions that become dysfunctional upon sleep deprivation seem to be situated in the frontal lobe or associated with the neocortex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is whether there is a correlation between percentage of the day spent sleeping and brain size (either the whole brain, or a part of the brain such as the neocortex or frontal lobe). How do other species correlate compared to us? Either in absolute brain size, or in brain size relative to body size.&lt;/p&gt;&#xA;" OwnerUserId="4336" LastEditorUserId="1306" LastEditDate="2014-05-20T18:45:21.813" LastActivityDate="2014-05-20T18:45:21.813" Title="Is there a correlation between brain size and amount of sleep?" Tags="&lt;brain&gt;&lt;sleep&gt;&lt;circadian-rhythms&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-05-20T19:58:51.017" ContentLicense="CC BY-SA 3.0" />
  <row Id="17532" PostTypeId="1" AcceptedAnswerId="17560" CreationDate="2014-05-20T14:44:43.680" Score="7" ViewCount="890" Body="&lt;p&gt;The Price equation describes mathematically the evolution of a population of units from one generation to the next. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;$\bar{w}\Delta \bar{z}$ = $Cov (w_i,z_i) $+$ E(w_i\Delta z_i)$&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would like to know how to actually employ the equation to some data. Perhaps a simple online &quot;walk-through&quot; type guide of the Price equation would help. It should simply show the calculation of the Price equation using numbers from an example population. For example, I'd like to see how the Price equation is applied to the following scenario:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A population, $P$, of 5 individuals reproduces to produce population&#xA;  $P'$. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The trait value of the $i^{th}$ individual is $z_{i}$ where $z_1$,&#xA;  $z_2$ and $z_3$ all = 1 and where $z_4$ and $z_5$ both = 2 and $\bar{z}$ = 1.4. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Absolute fitness is $w_i$ for the $i^{th}$ individual where $w_1$,&#xA;  $w_2$ and $w_3$ all = 1, and $w_4$ and $w_5$ both = 5. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Relative fitnesses, $\omega_i$, are $\omega_{z=1}$ = 0.077, and $\omega_{z=2}$ = 0.385.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Thus the population $P'$ has $n$ = 13, with 3 individuals where $z$ = 1&#xA;  and 10 individuals where $z$ = 2 and $\bar{z}'$ = 1.769. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;$\Delta z $ is the transmission bias and is equal to 0 in this case&#xA;  (perfect transmission of the trait score $z$)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The value $\Delta \bar{z}$ = $Cov (w,z)/ \bar{w}$ = ....&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here's an R script to create the above information:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;# Define two trait values:&#xA;z1 = 1&#xA;z2 = 2&#xA;&#xA;# Define two fitness values:&#xA;w1 = 1&#xA;w2 = 5&#xA;&#xA;# Set number of units possesing each trait in P population:&#xA;n1 = 3&#xA;n2 = 2&#xA;&#xA;# Create data&#xA;df = data.frame(c(rep(z1,n1),rep(z2,n2)),c(rep(w1,n1),rep(w2,n2)))&#xA;colnames(df) = c(&quot;z&quot;,&quot;w&quot;)&#xA;&#xA;df$omega = df$w / sum(df$w)&#xA;&#xA;n_P = length(df$z)&#xA;    n_O = sum(df$w)&#xA;z_P_bar = mean(df$z)&#xA;    z_O_bar = sum(df$w*df$z) / sum(df$w)&#xA;omega_z1 = mean(df$omega[df$z==z1])&#xA;omega_z2 = mean(df$omega[df$z==z2])&#xA;&#xA;# Parental population size:&#xA;n_P&#xA;# Offspring population size:&#xA;n_O&#xA;# Parental mean trait:&#xA;z_P_bar&#xA;# Offspring mean trait:&#xA;z_O_bar&#xA;# Realtive fitnesses:&#xA;omega_z1&#xA;omega_z2&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-05-21T08:23:07.590" LastActivityDate="2016-01-05T14:37:59.163" Title="Help with the Price equation" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;population-genetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17533" PostTypeId="2" ParentId="17532" CreationDate="2014-05-20T15:27:21.330" Score="2" Body="&lt;p&gt;This is a nice numerical walk-through and explanation, see this &lt;a href=&quot;http://www.tedpavlic.com/post_price_equation.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;webpage&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;As requested I've sketched out a solution to the specific case above.&lt;/p&gt;&#xA;&lt;p&gt;A nicer way for caclulations is to rewrite the price equation as:&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$ \Delta z = Cov(w_i/\bar{w}, z_i) +E(w_i/\bar{w}, \Delta z_i) $$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;So lets draw out some important terms.&lt;/p&gt;&#xA;&lt;p&gt;In the current population average for &lt;span class=&quot;math-container&quot;&gt;$z$&lt;/span&gt;, the average trait value in the second generation &lt;span class=&quot;math-container&quot;&gt;$z'$&lt;/span&gt;  and, the average relative fitness of the parents &lt;span class=&quot;math-container&quot;&gt;$\bar{w}$&lt;/span&gt; are:&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$\bar{z} = 1.4$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$z' = 1.769$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$\bar{w} = 0.2002$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;So we an brute force the &lt;span class=&quot;math-container&quot;&gt;$\Delta z$&lt;/span&gt; by doing &lt;span class=&quot;math-container&quot;&gt;$1.769-1.4 = 0.369$&lt;/span&gt;. However we shall also show this using the price equation (note for sample data the correction is &lt;span class=&quot;math-container&quot;&gt;$n-1$&lt;/span&gt; not &lt;span class=&quot;math-container&quot;&gt;$n$&lt;/span&gt; as shown below).&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$Cov(x,y) = ((x_1 - \bar{x})*(y_2 - \bar{y})+(x_2 - \bar{x})*(y_1 - \bar{y})+ ... (x_n - \bar{x})*(y_n - \bar{y}))/n$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;Using the data provided we can say:&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$Cov(w_i/\bar{w}, z_i)= ((3 * (0.077 - 0.2002)*(1-1.769)) + (2 * (0.385-0.2002)*(2-1.769)))/5 = 0.07392 $&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;This is a per capita change. &lt;span class=&quot;math-container&quot;&gt;$0.07392 * 5 = 0.3696$&lt;/span&gt; (rounding error).&lt;/p&gt;&#xA;&lt;h1&gt;Expectation&lt;/h1&gt;&#xA;&lt;p&gt;So the OP identifies a situation where transmission effects are non zero. Lets just consider that the mutation that causes z=2 is a  super-synergistic and causes its offspring to be z=4. The expectation term in this case is:&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$E(w_i/\bar{w}, \Delta z_i)= ((w_4/\bar{w})*(z'_4-z_4) + (w_5/\bar{w})*(z'_5-z_5)) /5$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;I've ignored the first 3 individuals because the transmission effect will make their terms 0 (1-1=0).&lt;/p&gt;&#xA;" OwnerUserId="5311" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2016-01-05T14:37:59.163" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17534" PostTypeId="2" ParentId="17522" CreationDate="2014-05-20T17:46:56.347" Score="1" Body="&lt;p&gt;It seems that, by and large, most animal and plant cells have primary cilia. To quote from &lt;a href=&quot;http://www.landesbioscience.com/journals/organogenesis/article/28910/&quot; rel=&quot;nofollow&quot;&gt;this open access paper&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;.[..] organisms that form cilia have a basal body or centriole-like structure as their microtubule-organizing center, whereas those that do not [e.g., yeast, higher plants] use morphologically distinct structures for organization of their microtubule cytoskeleton.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Other cases where cells lack primary cilia are when they possess motile cilia (e.g., sperm are mono-ciliated, respiratory epithelia are multi-cilliated).&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.landesbioscience.com/journals/organogenesis/article/28910/&quot; rel=&quot;nofollow&quot;&gt;Fry AM, Leaper MJ, Bayliss R. The primary cilium: Guardian of organ development and homeostasis. Organogenesis. 2014 Jan 1;10(1):62-68. Epub 2014 Apr 17.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-05-20T17:46:56.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17535" PostTypeId="2" ParentId="17487" CreationDate="2014-05-20T21:52:05.027" Score="3" Body="&lt;p&gt;This phenomenon is called Ototoxicity, which literally means &quot;toxic for the ear&quot;. Mostly the cochlea or the auditory nerve are affected and almost all these cases are connected to medications as gentamicin or cisplatin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reasons for this are that the cells are either driven into apoptosis or necrosis. This is caused by destroying mitochondria and releasing calcium and cytochrome c which triggers apoptosis or by deregulating the the JNK-signal transduction pathway and causing necrosis. This image gives a nice overview:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qpIbE.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For further reading you can start with the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Ototoxicity&quot; rel=&quot;nofollow noreferrer&quot;&gt;ototoxicity&lt;/a&gt; and then also read these two papers which are both freely available (the figure above is from the first):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21799993&quot; rel=&quot;nofollow noreferrer&quot;&gt;Intracellular mechanisms of aminoglycoside-induced cytotoxicity.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22715386&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gentamicin rapidly inhibits mitochondrial metabolism in&#xA;high-frequency cochlear outer hair cells.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;To answer the question why this occurs in the ear, it seems that there is some genetic predisposition for this, see this paper: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17266591&quot; rel=&quot;nofollow noreferrer&quot;&gt;Aminoglycoside-induced ototoxicity.&lt;/a&gt;&quot; Mitochondrial damages leading to hearing loss is also not uncommin, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1376819/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;. Noise seems to play an additional role here and is probably the &quot;last drop&quot; to cause hearing loss.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-05-22T07:38:19.420" LastActivityDate="2014-05-22T07:38:19.420" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17537" PostTypeId="1" CreationDate="2014-05-21T07:34:04.480" Score="0" ViewCount="111" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qiKRD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This picture shows one of the steps of heme synthesis. In this step two propanoate groups of coproporphyrinogen III are decarboxylated to form protoporphyrinogen IX. The enzyme that catalyses this step is an oxidase. Oxidase enzymes catalyze the removal of hydrogen  in the presence of oxygen to form water or hydrogen peroxdide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, will a water molecule form in this step? 2H&lt;sup&gt;+&lt;/sup&gt; will come from the two carboxylate groups and oxygen will combine with it to form water. Will a water molecule form in this way?&lt;/p&gt;&#xA;" OwnerUserId="1765" LastEditorUserId="3632" LastEditDate="2014-05-22T23:58:48.690" LastActivityDate="2014-05-22T23:58:48.690" Title="Protoporphyrinogen (IX) formation in heme synthesis" Tags="&lt;hematology&gt;&lt;biosynthesis&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17539" PostTypeId="1" CreationDate="2014-05-21T10:48:29.953" Score="1" ViewCount="197" Body="&lt;p&gt;I fail to see how natural selection can build any kind of new functionality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;New functionality in a design requires sacrificing a complex series of meanwhile useless steps before the new functionality works and becomes advantageous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, if I want to upgrade a stationary chair to a wheelchair, there are many intermediate steps that must be done (which are not advantageous) before the added functionality becomes advantageous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a human being sits there and tries to intelligently assemble the wheelchair in such a way that it will be advantageous at each step, he will not be able to do it. it just doesn't work like this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone fill me in as to how this works and whether there have been experiments that demonstrate this, for example, having someone assemble a simple functional design with the limitation that every few step adds advantageous functionality.&lt;/p&gt;&#xA;" OwnerUserId="6202" LastActivityDate="2014-05-21T16:24:05.000" Title="problem with natural selection" Tags="&lt;natural-selection&gt;" AnswerCount="2" CommentCount="9" ClosedDate="2014-05-21T16:56:26.897" ContentLicense="CC BY-SA 3.0" />
  <row Id="17540" PostTypeId="2" ParentId="17539" CreationDate="2014-05-21T12:03:09.360" Score="3" Body="&lt;p&gt;This is fundamentally a teleological argument. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The error is in assuming that the intermediate steps were a precursor to the present functionality. For example, interpreting an 'intermediate' bird wing as a fully functional wing, intended for flight. In fact, there is no prerequisite that present characteristics or functions have evolved from intermediates that were intended FOR that characteristic or function.&lt;/p&gt;&#xA;" OwnerUserId="6787" LastActivityDate="2014-05-21T12:03:09.360" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17541" PostTypeId="1" CreationDate="2014-05-21T12:06:47.953" Score="14" ViewCount="2313" Body="&lt;p&gt;I'm planning to scale up a PCR reaction, and I'm wondering if filling the PCR tubes to the maximum volume of 200 ul would be a problem. It would mean a lot less pipetting as I would only need 1/4 of the tubes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The typical protocols I've seen always use 50 ul for a PCR reaction, I'm wondering if there are any issues with larger volumes, e.g. differences in heat transfer, that could cause issues if I scale up the volume in one tube.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is scaling up the volume problematic? Any specific aspects I should consider?&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-05-25T10:08:19.100" Title="Are there issues with filling PCR tubes to capacity?" Tags="&lt;lab-techniques&gt;&lt;pcr&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17542" PostTypeId="2" ParentId="17541" CreationDate="2014-05-21T12:24:57.750" Score="12" Body="&lt;p&gt;Too long for a comment: I would say it depends on the PCR. I have personally used maximum volumes of 50ul, if I needed to prepare higher volumes, I made one mix which subsequently got distributed to more tubes with 50ul max. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem with big volumes is to get a fast and homogeneous heating and cooling. If the outside of the tube is faster, the reaction there starts already while this may not be the case in the middle. This can lead to uneven denaturation and amplification of your template. The later is especially problematic when you amplify short sequences. There the amplification time might already be over and the PCR program is moving on before the template is finished, which will result in less of your full-length product and the enrichment of shorter versions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is another problem that might occur in big reactions: Due to gradients in reactivity because of temperature gradients I think it is possible that reagents (dNTPs, Mg-ions) can form gradients which further inhibit a good yield.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally I tested one thing on one of our PCR machines: The PCR tube is set into the heating/cooling block. It is not completely set into the block but stick out partly, so if you fill it up to maximum capacity, the upper 75-100ul (approximately) would be outside the heating block and we have a thermal problem. The reaction mix there would only heat up due convection.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-05-25T10:08:19.100" LastActivityDate="2014-05-25T10:08:19.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17543" PostTypeId="2" ParentId="17541" CreationDate="2014-05-21T12:44:32.807" Score="12" Body="&lt;p&gt;(Also too long for a comment.) This question reminded me about an anecdote told by Arthur Kornberg concerning the approach to scaling up that was adopted by Reiji Okazaki (discoverer of &lt;a href=&quot;http://en.wikipedia.org/wiki/Okazaki_fragment&quot;&gt;Okazaki fragments&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a quotation taken from &lt;strong&gt;For the Love of Enzymes: The Odyssey of a Biochemist by Arthur Kornberg&lt;/strong&gt;&#xA; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Reiji’s research style is not readily gleaned from his publications,&#xA;  but it is vivid in my memory. One example I call the Okazaki maneuver. In purifying an enyme, he used a heating step: 10 milliliters of&#xA;  the enzyme solution was held in a test tube at 70°C for ﬁve minutes;&#xA;  then the coagulated impurities were removed by centrifugation.&#xA;  When he came to the point of scaling up the procedure to several&#xA;  liters, he simply repeated the original heating procedure several&#xA;  hundred times. I was embarrassed to have to report such an unsophisticated procedure in our publication. But then I realized that&#xA;  he was able to complete this step in a few hours and saw no point in&#xA;  wasting precious time and material in learning how to do the heating in a large beaker or flask. Later, when another of my students&#xA;  puriﬁed an enzyme with a heating step and had to scale up his&#xA;  procedure 2,000-fold from 3 milliliters to 6 liters, I advised the&#xA;  Okazaki maneuver: he added 3 milliliters to each of 200 test tubes to&#xA;  carry out the heating and centrifugation step, repeating the procedure nine times. Another student who tried heating a large volume&#xA;  of this enzyme in a single step lost it in a thick coagulum.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-05-21T14:15:13.853" LastActivityDate="2014-05-21T14:15:13.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17544" PostTypeId="2" ParentId="16932" CreationDate="2014-05-21T14:05:43.073" Score="0" Body="&lt;p&gt;Looks like a termite; male; after loss of wings.&lt;/p&gt;&#xA;" OwnerUserId="6787" LastActivityDate="2014-05-21T14:05:43.073" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17545" PostTypeId="2" ParentId="10457" CreationDate="2014-05-21T14:12:03.983" Score="1" Body="&lt;p&gt;The simple explanation is that there are three (or more) traits drawing from the pool, and you're only looking for trade-offs between two of them. The unobserved third may show the effect of a trade-off.&lt;/p&gt;&#xA;" OwnerUserId="6787" LastEditorUserId="6787" LastEditDate="2014-05-21T15:08:11.480" LastActivityDate="2014-05-21T15:08:11.480" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17546" PostTypeId="1" AcceptedAnswerId="17549" CreationDate="2014-05-21T16:13:02.330" Score="31" ViewCount="4711" Body="&lt;p&gt;I've seen some articles which came in contradiction with each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first article was talking about flying dinosaurs, dinosaurs with feathers and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A couple of other articles are talking about misconceptions about dinosaurs one of them being that there are no flying dinosaurs but just flying reptiles (from &lt;a href=&quot;http://www.scholastic.com/teachers/article/dinosaurs-flying-reptiles&quot;&gt;scholastic.com&lt;/a&gt; and &lt;a href=&quot;http://www.livescience.com/24071-pterodactyl-pteranodon-flying-dinosaurs.html&quot;&gt;livescience.com&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, which one is right?&#xA;Also if possible please provide a source for argument.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I cannot find the first article again.&lt;/p&gt;&#xA;" OwnerUserId="6788" LastEditorUserId="42780" LastEditDate="2018-05-28T20:08:14.637" LastActivityDate="2019-06-03T10:07:12.700" Title="Were there any flying dinosaurs?" Tags="&lt;evolution&gt;&lt;ornithology&gt;&lt;palaeontology&gt;&lt;herpetology&gt;&lt;dinosaurs&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17547" PostTypeId="2" ParentId="17539" CreationDate="2014-05-21T16:24:05.000" Score="3" Body="&lt;p&gt;There are so many wrong-headed premises here, one hardly knows where to start.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, natural selection is the process of changing the frequency of alleles in a population, &lt;strong&gt;mutation&lt;/strong&gt; is what creates new ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, just because &lt;strong&gt;you&lt;/strong&gt; can't think of every intermediate step doesn't mean it's impossible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Third, you are assuming that natural selection is so uber powerful that every single stop must be beneficial, and there's no evidence that that's the case.  Evolution preserves lots of neutral and nearly neutral mutations.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fourth, you are assuming that each step in some kind of path way can only possibly be used for the pathway it's in today.  That's not true either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want somewhere to start in the literature, try some papers by Lenski:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22992527&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/22992527&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23918358&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/23918358&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you really want to argue that it's impossible for, say, E.coli to evolve the ability to metabolize citrate, because it's too hard to get from here to there, you need to address the empirical fact that these bacteria did just that.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-05-21T16:24:05.000" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17548" PostTypeId="2" ParentId="17546" CreationDate="2014-05-21T16:25:18.903" Score="8" Body="&lt;p&gt;I'm not an expert, but I think that you have to be specific about the flying animals to which you are referring. &lt;a href=&quot;http://en.wikipedia.org/wiki/Pterosaur&quot;&gt;Pterosaurs&lt;/a&gt; are not classed as dinosaurs, whereas modern &lt;a href=&quot;http://en.wikipedia.org/wiki/Avialae&quot;&gt;birds&lt;/a&gt; are descended from &lt;a href=&quot;http://en.wikipedia.org/wiki/Theropod&quot;&gt;theropod dinosaurs&lt;/a&gt; which is where feathers appeared.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-21T16:25:18.903" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17549" PostTypeId="2" ParentId="17546" CreationDate="2014-05-21T16:50:54.773" Score="49" Body="&lt;p&gt;Birds are both flying dinosaurs &lt;em&gt;and&lt;/em&gt; flying reptiles. Yes, that's potentially confusing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To understand the apparent contradiction, you have to understand how modern classification of organisms works (&lt;a href=&quot;http://www.ucmp.berkeley.edu/clad/clad4.html&quot; rel=&quot;noreferrer&quot;&gt;phylogenetic systematics&lt;/a&gt;). Under the old (Linnean) classification system, Reptilia (reptiles) was an order and Aves (birds) was a separate order. Phylogenetic systematics, which has completely replaced the Linnean system, views all organisms as interrelated in a nested set of &lt;a href=&quot;https://biology.stackexchange.com/questions/14877/birds-and-dinosaurs/14878#14878&quot;&gt;monophyletic&lt;/a&gt; groups (clades). It's like a set of venn diagrams, where all organisms fall into a giant circle and then successively smaller circles classify more and more specific groups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The clade Reptilia includes snakes, lizards, crocodiles, and lots of extinct groups, including dinosaurs. So all dinosaurs are reptiles. The clade Dinosauria includes all the extinct dinosaurs (&lt;em&gt;Stegosaurus&lt;/em&gt;, &lt;em&gt;Triceratops&lt;/em&gt;, sauropods, etc.), including theropod dinosaurs, which include well known dinosaurs like &lt;em&gt;Tyrannosaurus&lt;/em&gt; and &lt;em&gt;Allosaurus&lt;/em&gt;. Based on a mountain on anatomical evidence, including lots of transitional fossils, living &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evograms_06&quot; rel=&quot;noreferrer&quot;&gt;birds are a sub-group of theropod dinosaurs&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So all birds (Aves) are theropod dinosaurs (Dinosauria: Theropoda). All dinosaurs are reptiles. Therefore, birds are dinosaurs and reptiles. They are just more closely related to dinosaurs than to other reptiles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The tricky part is that most people have an intuitive idea of what &quot;reptiles&quot; and &quot;dinosaurs&quot; are. To a systematist, whose job it is to classify organisms, these terms don't mean the same thing as they do to most people. Systematists think about groups like Reptilia and Dinosauria and how those groups are related to one another. So they have no problem saying that birds are dinosaurs &lt;em&gt;and&lt;/em&gt; reptiles, because birds are nested within both of those groups.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;A few words about pterosaurs&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Along with birds and bats, pterosaurs are the other clade of vertebrates capable of powered, flapping flight. Pterosaurs fall within Reptilia (and Diapsida and Archosauria) along with Dinosauria, which includes birds. There are a lot of other extinct lineages in the tree that are not shown, e.g., ornithodirans that are not dinosaurs and not pterosaurs. Pterosaurs and birds share anatomical features that all reptiles, diapsids, archosaurs, and ornithodirans have, which is how we know that they are more closely related to each other than to other groups, like crocodiles. But their flight structures evolved independently and are anatomically distinct fro one another. So pterosaurs &lt;em&gt;are&lt;/em&gt; flying reptiles but &lt;em&gt;not&lt;/em&gt; flying dinosaurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These images might help you understand the above explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nPg3f.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MpU6G.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-05-23T00:46:20.570" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="17550" PostTypeId="1" CreationDate="2014-05-21T16:52:45.883" Score="7" ViewCount="424" Body="&lt;p&gt;A recent flurry of &quot;fluoride is bad!&quot; posts are appearing on my social network news feeds.  Usually I can simply ignore them after a brief look, but this one, stemming from a recent article in The Lancet, isn't easy enough for me to understand and apply or ignore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The posts link to a March, 2014 article, &lt;a href=&quot;http://www.thelancet.com/journals/laneur/article/PIIS1474-4422%2813%2970278-3/fulltext#article_upsell&quot;&gt;Neurobehavioural effects of developmental toxicity&lt;/a&gt;, from The Lancet Neurology, Volume 13, Issue 3, which has the summary (emphasis added):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Neurodevelopmental disabilities, including autism, attention-deficit hyperactivity disorder, dyslexia, and other cognitive impairments, affect millions of children worldwide, and some diagnoses seem to be increasing in frequency. Industrial chemicals that injure the developing brain are among the known causes for this rise in prevalence. In 2006, we did a systematic review and identified five industrial chemicals as developmental neurotoxicants: lead, methylmercury, polychlorinated biphenyls, arsenic, and toluene. &lt;strong&gt;Since 2006, epidemiological studies have documented six additional developmental neurotoxicants&lt;/strong&gt;—manganese, &lt;strong&gt;fluoride&lt;/strong&gt;, chlorpyrifos, dichlorodiphenyltrichloroethane, tetrachloroethylene, and the polybrominated diphenyl ethers. We postulate that even more neurotoxicants remain undiscovered. To control the pandemic of developmental neurotoxicity, we propose a global prevention strategy. Untested chemicals should not be presumed to be safe to brain development, and chemicals in existing use and all new chemicals must therefore be tested for developmental neurotoxicity. To coordinate these efforts and to accelerate translation of science into prevention, we propose the urgent formation of a new international clearinghouse.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't have full access to the article, so I can't refer to the epidemiological study it says shows fluoride to be a developmental neurotoxicant.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What is a developmental neurotoxicant?&lt;/li&gt;&#xA;&lt;li&gt;How strong is the research that claims fluoride is a developmental neurotoxicant?&lt;/li&gt;&#xA;&lt;li&gt;What relationship, if any, does this report or research have with typical &lt;a href=&quot;http://en.wikipedia.org/wiki/Water_fluoridation&quot;&gt;fluoride compounds used in US water treatment&lt;/a&gt; at the levels typically present in US water (sodium fluoride, fluorosilicic acid, or sodium fluorosilicate at 0.7 mg/L)? &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5940" LastEditorUserId="1320" LastEditDate="2014-05-21T17:28:04.587" LastActivityDate="2014-05-22T07:19:07.030" Title="Is fluoride toxic, and how worried should I be about it?" Tags="&lt;biochemistry&gt;&lt;development&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="17551" PostTypeId="1" AcceptedAnswerId="17552" CreationDate="2014-05-21T17:29:33.957" Score="2" ViewCount="431" Body="&lt;p&gt;From Molecular Biology of the Cell (4th edition) by Bruce Alberts et al. (Chp 6, Pg 338) :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Both bacterial and eucaryotic tRNAs are typically synthesized as&#xA;  larger precursor tRNAs, and these are then trimmed to produce the&#xA;  mature tRNA. In addition, some tRNA precursors (from both bacteria and&#xA;  eucaryotes) contain introns that must be spliced out.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What's the difference between the two statements (and between trimming and splicing) ? &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-05-21T17:58:20.600" Title="Trimming of tRNA precursors" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;rna&gt;&lt;splicing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17552" PostTypeId="2" ParentId="17551" CreationDate="2014-05-21T17:58:20.600" Score="4" Body="&lt;p&gt;Trimming = removing RNA sequences from one end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wsQSu.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_splicing&quot; rel=&quot;nofollow noreferrer&quot;&gt;Splicing&lt;/a&gt; = removing introns and joining exons back together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vavyV.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-05-21T17:58:20.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17554" PostTypeId="2" ParentId="17550" CreationDate="2014-05-21T18:49:36.347" Score="12" Body="&lt;p&gt;First of all: Yes, fluoride is toxic, but the toxicity depends largely on the form (soluble vs. unsoluble, which fluoride salt etc.) occurs. It also depends on the environment since insoluble salts which are subjected to strong acids can release fluorine ions.&#xA;The certain toxic dose for adults is 32-64mg/kg body weight, a 75kg adult needs to take up between 2,4 and 4,8 grams of fluoride ions (for sodium fluoride this would be between 5,3 and 10,6 gr of the salt). For children this is about 5mg/kg body weight.&#xA;For the water the added dose of fluorine is much lower, somewhere between 0,7 and 1.2 mg/l. Other sources of fluroride are food (especially sea food) and also black tea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The toxicity of fluoride is mediated by different ways: First it forms an insoluble salt with calcium in the cells, effectively causing hypocalcemia. Calcium is an important second messenger in different signal transduction pathways as well as highly important for the functioning of nerve cells (which also explains why it is neurotoxic in the development of nerve and brain cells). It also causes the inhibition of a number of different enzymes as enolase (disturbs the glycolysis) but also phosphatases and katalase. For all of this have a look into the &lt;a href=&quot;http://en.wikipedia.org/wiki/Fluoride&quot;&gt;Wikipedia&lt;/a&gt; if you want to know more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About the paper: It is a review of published research articles which sums up the situation in this field. The paper mentions fluoride only twice: Once on the abstract and once in a table about newly identified developmental neurotoxins (table 2 to be precise). It references only one meta-analysis on this topic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cited meta-analysis (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22820538&quot;&gt;Developmental fluoride neurotoxicity: a systematic review and meta-analysis&lt;/a&gt;&quot;) which did a statistical meta-analysis of published papers and their data. They find a significant relation between the fluoride content of the drinking water and the IQ of the children.&#xA;However this is not undisputed (to say it mildly), since while a finding can be statistically significant, it doesn't necessarily mean that there is clinical importance. The other important point which @Doctor Whom mentioned is that a correlation doesn't imply a causation. So even if there seems to be a correlation between two things, they are not necessarily connected (see the famous example of storchs and birth rates). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This paper (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23455234&quot;&gt;Developmental fluoride neurotoxicity: clinical importance versus statistical significance.&lt;/a&gt;&quot;) is published as a comment on the original paper and claims exactly this. They say the the mean difference in IQ is about 7 points, which is not of clinical importance. Another paper critizes the relatively low quality of the original papers used for the study (&quot;&lt;a href=&quot;http://journal.nzma.org.nz/journal/126-1375/5664/&quot;&gt;Fluoride and children's IQ.&lt;/a&gt;&quot;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They also mention a low consensus about what is a high concentration of fluoride in the drinking water and also show the very wide variation of the fluoride concentration in the original studies. The highest concentrations mentioned are around 10mg/l which is about 10x the concentration used for adding fluoride to the water. Even if we take in account that children are more sensitive to fluoride and also need lower fluoride concentrations to cuse some developmental damages (below the fatal concentration) this would still add up to quite absurd amounts of water they have to drink.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding your questions: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;A developmental neurotoxin is a substance which interferes with developing neurons or nerve cells. It either inhibits their growth completely or at least impairs the cells.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Given on the articles I found (and cited above) I would say that fluoride is a developmental neurotoxin. Nevertheless it seems to me that it is not very strong in this context as the current studies are contradictory. Thinking about the amounts of fluoride present in water (even if the concentration is much higher than recommended) makes me doubt if this is really the causative agent.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-05-22T07:19:07.030" LastActivityDate="2014-05-22T07:19:07.030" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17555" PostTypeId="2" ParentId="17498" CreationDate="2014-05-21T20:02:56.657" Score="5" Body="&lt;p&gt;A human heart can be viewed as 2 hearts, the left and the right heart, each consisting of an atrium and a ventricle. The atrium's function is to fill the ventricle with as much blood as it can and the ventricle then pump the blood away. Also there is a system of valves to control blood flow on each side. Basically this is how our heart works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, to make this system work we need to have a coordinated movement of atrium and ventricle, that is, first atrium is filled, then it pumps blood into ventricle, valve closes and then ventricle compresses. &#xA;The movement of heart muscle causes currents that can be measured (this is the ECG pronounced EKG). These currents are representative of the movements of atrium and ventricles are expressed respectively as p waves (for atria) and qrs (for ventricles). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is the case that atria are not very important and sometimes they can stop working properly. They now longer have coherent movement and stop helping to pump blood into the ventricles, but they still move. This event is called atrial fibrillation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this explanation one can expect that no longer p waves will be identifiable in the ecg, but instead a random noise overlapping with &quot;normal&quot; qrs representing normal ventricular movement. The movement is actually not exactly normal, because the ventricular contraction due to atrial fibrillation now occurs at random times, that is qrs complexes occur with random spaces between them. The explanation for this is rather more complex: there are bundles of specialized cardiomyocites with different frequencies of depolarization. The fastest ones are on SAN and basically guide the whole heart rhythm through specialized bundles. When you have atrial fibrillation, the depolarization signals no longer come from these preferential bundles, but from any part of the atria at random. This causes the ventricles to initiate motion at irregularly spaced intervals.&#xA;I've included a photo of a normal rhythm and a atrial fibrillation side by side, but I hope you can use this explanation to find better ones by yourself in the web.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: don't confuse atrial fibrillation with atrial flutter. Flutter is a faster paced regular (therefore organized) atrial movement. It will appear as a saw-tooth shaped wave with regularly spaced qrs complexes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cUhHR.jpg&quot; alt=&quot;a-fib&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Causes of atrial fibrillation are numerous, bur mainly high blood pressure, vascular disease, heart and lung disease among others. It can be asymptomatic in most cases or presenting with the symptoms of its underlying cause.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please refer to &lt;a href=&quot;http://www.webmd.com/heart-disease/atrial-fibrillation/heart-disease-atrial-fibrillation-basics&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.webmd.com/heart-disease/atrial-fibrillation/heart-disease-atrial-fibrillation-basics&lt;/a&gt; for a quick overview.&lt;/p&gt;&#xA;" OwnerUserId="4036" LastEditorUserId="4036" LastEditDate="2014-11-09T00:18:36.720" LastActivityDate="2014-11-09T00:18:36.720" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17557" PostTypeId="1" AcceptedAnswerId="25991" CreationDate="2014-05-21T22:28:41.863" Score="6" ViewCount="323" Body="&lt;p&gt;Beside many anaerobic &lt;a href=&quot;http://en.wikipedia.org/wiki/Obligate_anaerobe#Examples&quot;&gt;single cell organisms&lt;/a&gt;, there are some &lt;a href=&quot;http://en.wikipedia.org/wiki/Polychaete&quot;&gt;annelid worms&lt;/a&gt; that are obligate anaerobic at least in their early development stages. Probably, due to low concentration levels in nature, some of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Anaerobic_respiration#Examples_of_respiration&quot;&gt;other respiration methods&lt;/a&gt; (like uranium or iron reduction) can limit the maximum size an organism will grow. Given the lower energy level extracted compared to the oxygen respiration, what size limits enforces the sulfate, sulfur or methanogenesis respiration? What's the biggest discovered organism, extinct or alive, that is obligate anaerobic?&lt;/p&gt;&#xA;" OwnerUserId="6608" LastActivityDate="2014-12-17T20:10:22.540" Title="What's the biggest obligate anaerobic organism discovered till now?" Tags="&lt;extremophiles&gt;&lt;anaerobic-respiration&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17558" PostTypeId="1" AcceptedAnswerId="17588" CreationDate="2014-05-21T22:50:15.240" Score="3" ViewCount="1606" Body="&lt;p&gt;Nitrogen and Phosphorus are usually the limiting nutrient for plants, especially for algae.  Phosphorus is used for DNA, ATP and phospholipids, and Nitrogen is used for pretty much every protein a cell might want to produce.  That is, their need for biological processes is not tied specifically to photosynthesis: anything that lives is going to need them, pretty much for anything it might want to do.  It would make sense for them to be a limiting nutrient for almost anything that's trying to grow, plant or animal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet for animals the limiting &quot;nutrient&quot; seems to always be energy, ie: food.  Why aren't animals limited by lack of nutrients in the same way that plants are?  Obviously animals need these nutrients, too.  Or to reverse the question, why do plants need so much more phosphorus/nitrogen than animals do?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My best guess is that an animal's digestion of plant material is relatively inefficient energy-wise but relatively efficient nutrient-wise.  So for an animal to eat enough food to have sufficient energy to survive, it's probably eaten more than enough Nitrogen and Phosphorus for its needs.  But I'm just guessing and I can't find any data that would back up that guess.&lt;/p&gt;&#xA;" OwnerUserId="6793" LastEditorUserId="6793" LastEditDate="2014-05-21T23:00:46.253" LastActivityDate="2014-05-23T09:35:52.063" Title="Why isn't phosphorus or nitrogen a limiting nutrient for animals?" Tags="&lt;metabolism&gt;&lt;ecology&gt;&lt;photosynthesis&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17559" PostTypeId="2" ParentId="14096" CreationDate="2014-05-21T23:01:46.280" Score="1" Body="&lt;p&gt;This is a very large topic but I will try to partially provide an answer. Now your question has three parts as far as I understand it.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Do phospho-protein binding domains only bind to phosphorylated proteins i.e. is that their sole (observed) function.&lt;/li&gt;&#xA;&lt;li&gt;What roles do phospho-protein binding domains mediate.&lt;/li&gt;&#xA;&lt;li&gt;Function of BRCA1 phosphorylation/phospho-protein binding&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Just to get some basics out of the way, there are three amino-acid residues in a protein that can become post-translationally modified by phosphorylation, including serine, threonine and tyrosine. Now the purpose of protein phosphorylation ranges from activation/deactivation signals to binding and changing cellular localisation i.e. recruiting a protein to different part of a cell. Now tyrosine phosphorylation, which I know by far the most about is capable of all the above. So if you think about a receptor tyrosine kinase (RTK) such as epidermal growth factor receptor (EGFR), once a ligand such as EGF binds to it, it becomes tyrosine phosphorylated (activated) through its intrinsic tyrosine kinase activity. Once tyrosine phosphorylated, many proteins are capable of binding to tyrosine-phosphorylated RTKs such as Grb2 to induce a signal downstream of RTKs. So as you can see, phosphorylation of RTK affected cellular localisation of GRB2. Excellent Ras signalling review by Karnoub &amp;amp; Weinberg, 2008 Nature reviews (Fig 5). Grb2 binds to phospho-RTKs through a specific domain called Src-homology 2 (SH2) domain, which provides a platform for other proteins such as Son of sevenless (SOS) which is a GEF to bind to it and induce RTK signalling through Ras. So in the above case the role of phospho-protein binding domain (SH2) is to change cellular localisation of multiple proteins and mediate signalling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now I'm no expert in BRCA1 but just had a quick look and it seems serine phosphorylation of BRCA1 may be responsible for its recruitment to the DNA site of damage and if serine residues in BRCA1 are mutated, the protein will no longer get phosphorylated, which may effect its recruitment to the DNA sites of damage, which may affect its DNA damage response function (Clark et al 2012 Comput Struct Biotechnol J). Now BRCA has a phospho-protein binding domain called BRCT, and that is also thought to mediate DNA binding and binds to phosphorylated and non-phosphorylated proteins. So BRCA1 phosphorylation and phospho-protein binding is though to be important in its function (Clark et al 2012 Comput Struct Biotechnol J). So to answer your question in short, phospho-protein binding domains such as BRCT do not necessarily bind to their target proteins through phosphorylation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-21T23:01:46.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17560" PostTypeId="2" ParentId="17532" CreationDate="2014-05-22T02:00:17.460" Score="3" Body="&lt;p&gt;Here is a simple example using your data in which both terms of the Price equation are needed, since the value of the character for $z_2 $ changes in the second generation. I used your suggested change $z_2'=(9\cdot 2 + 1\cdot 3)/10 = 2.1$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Price equation or theorem is:&#xA;$$(1)\hspace{10mm}w\cdot \Delta z =  \text{cov}(z_i,w_i) + E(w_i\Delta z_i)  $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the idea here is just to give a credible calculation using both terms in the right side of the equation, and while the intuition behind the equation is essentially mathematical (or is it? $^1$), Steven Franks' paper, 'George Price's Contribution to Evolutionary Genetics', J. Theor. Biol. 175 (1995), 373-88, is a good introduction. His characterization of the right side may be the best one can do: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The two terms may be thought of as changes due to selection and transmission, respectively. The covariance between fitness and character value gives the change in the character caused by differential reproductive success. The expectation term is a fitness weighted measure of the change in character values between ancestor and descendant. The full equation describes both selective changes within a generation and the response to selection...&quot; p. 376. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;We work with reference to the following data and will define variables below. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\begin{array}{c | c | c | }  n_i &amp;amp; 3 &amp;amp; 2  \\ \hline&#xA;z_i &amp;amp;1  &amp;amp; 2  \\ \hline&#xA;w_i &amp;amp;1&amp;amp; 5   \\ \hline&#xA;n_i' &amp;amp; 3 &amp;amp; 10  \\ \hline &#xA;z_i' &amp;amp; 1 &amp;amp; 2.1  \\ \hline \end{array}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All cites WK are to the Wiki page on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Price_equation&quot; rel=&quot;nofollow&quot;&gt;Price equation&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(1) We can write&lt;/strong&gt; $\text{cov} (w_i, z_i)$ as $E(w_iz_i) - wz.\hspace{10mm}$ WK eq. (7).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Explicitly: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ \text{Cov}(w_i,z_i) = E(w_iz_i)- wz = \frac{ w_1z_1n_1 + w_2z_2n_2}{n_1+n_2} - wz $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ = \frac{1\cdot1\cdot3 + 5\cdot2\cdot2}{3+2} - (2.6)(1.4) =\frac{23}{5} - (2.6)(1.4)= 0.96$$&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(2) We can write&lt;/strong&gt; $E(w_i\Delta z_i) = E(w_i z_i') - E(w_i z_i).\hspace{10mm}$ WK eq. (8).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now $E(w_i z_i') = \frac{1}{n}\sum w_iz_i'n_i\hspace{40mm} $ WK eq. (9a). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$ = \frac{1}{2 + 3}(1\cdot 1\cdot 3 + 5\cdot(2.1)\cdot 2) = 24/5.$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$E(w_iz_i) = 23/5$ from (1) above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So  $ E(w_i z_i') - E(w_i z_i) = \frac{24}{5} - \frac{23}{5} = 1/5$&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(3) Finally&lt;/strong&gt; we have $\Delta z =  z' - z = \frac{2.1(10) + 3(1)}{13}-\frac{3\cdot 1+2\cdot 2}{5} = \frac{29}{65} $&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and $w = \frac{3\cdot 1+ 2\cdot 5}{3+2} = \frac{13}{5} = 2.6$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So $$w \Delta z = (2.6) \frac{29}{65} = 1.16 $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$= \text{cov}(z_i,w_i) + E(w_i \Delta z_i) = 0.96 + .2 = 1.16 $$&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;$n_i$ is the number of elements in group $i.$ &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;$n_i'$ is the same for the filial generation.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;$z_i$ is the value of a character for group $i.$&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;$z_i'$ is the same for offspring of $z_i.$&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;$w_i$ is a fitness weight, often the number of offspring an element $z_i$ will have. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;$w$ is the average fitness for the parental generation.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;$z$ is the average value of z for parental generation;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;$z'$ is the average of z for the filial generation.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;$z_2' - z_2$ (for example) is the average value of $z_2$ in the second filial &#xA;  generation minus the average of $z_2$ in the parent's generation.  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;$^1$ This &lt;a href=&quot;http://evolutionandgames.nl/wiki/index.php?title=Price_3.0&quot; rel=&quot;nofollow&quot;&gt;site&lt;/a&gt; condenses some critical discussion of the Price equation. I have not worked through it yet but it addresses some lingering doubts I have about just what this equation means. Strongly recommended. &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-05-31T01:24:23.253" LastActivityDate="2014-05-31T01:24:23.253" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17561" PostTypeId="1" AcceptedAnswerId="17562" CreationDate="2014-05-22T04:06:02.077" Score="0" ViewCount="9259" Body="&lt;p&gt;Why do bananas turn black after some time? Please don't just give hypotheses but concrete references to experiments&lt;/p&gt;&#xA;" OwnerUserId="6442" LastActivityDate="2014-05-22T04:24:35.840" Title="Why do bananas turn black after some time?" Tags="&lt;fruit&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-05-22T15:48:33.920" ContentLicense="CC BY-SA 3.0" />
  <row Id="17562" PostTypeId="2" ParentId="17561" CreationDate="2014-05-22T04:24:35.840" Score="3" Body="&lt;p&gt;Banana skin consists of plant cells and cellular tissue. This tissue contains phenolic compounds. On getting old, the cell membranes of the banana get weak. When the membranes weaken, the phenolic compounds mix with polyphenol oxidase (an enzyme present in the cells cytoplasm). As a result of this interaction, the phelonic compounds oxidize and produce a brown compound called melanin which results in the colour of the peel turning black. Also, the green skin of banana contains a gaseous plant hormone, ethylene, which diffuses into the fruit and hastens the process of ripening. It is yellow when the fruit is ripe and turns black with the production of more and more ethylene. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-22T04:24:35.840" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17564" PostTypeId="2" ParentId="17546" CreationDate="2014-05-22T07:03:05.253" Score="24" Body="&lt;p&gt;In addition to &lt;a href=&quot;https://biology.stackexchange.com/a/17549&quot;&gt;kmm's excellent answer&lt;/a&gt;, I'd like to present &lt;a href=&quot;http://xkcd.com/1211/&quot; rel=&quot;nofollow noreferrer&quot;&gt;the xkcd point of view&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://xkcd.com/1211/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://imgs.xkcd.com/comics/birds_and_dinosaurs.png&quot; alt=&quot;xkcd/1211&quot; title=&quot;Sure, T. rex is closer in height to Stegosaurus than a sparrow. But that doesn&amp;#39;t tell you much; &amp;#39;Dinosaur Comics&amp;#39; author Ryan North is closer in height to certain dinosaurs than to the average human.&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;By any reasonable definition, &lt;em&gt;T. Rex&lt;/em&gt; is more closely related to sparrows than to &lt;em&gt;Stegosaurus&lt;/em&gt;.&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Separation by time&lt;/li&gt;&#xA;  &lt;li&gt;Phylogenetic distance&lt;/li&gt;&#xA;  &lt;li&gt;Physical similarity&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;  &#xA;  &lt;p&gt;Birds aren't &lt;em&gt;descended&lt;/em&gt; from dinosaurs, they &lt;em&gt;are&lt;/em&gt; dinosaurs.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Which means the fastest animal alive today is a small carnivorous dinosaur, &lt;em&gt;Falco Peregrinus&lt;/em&gt;.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;It preys mainly on other dinosaurs, which it strikes and kills in midair with its claws.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This is a good world.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6800" LastEditorUserId="6800" LastEditDate="2018-07-05T07:50:34.430" LastActivityDate="2018-07-05T07:50:34.430" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="17565" PostTypeId="1" AcceptedAnswerId="17566" CreationDate="2014-05-22T08:50:14.247" Score="9" ViewCount="2944" Body="&lt;p&gt;I am a bit confused with the notion that &quot;&lt;strong&gt;walking after meals helps you in digestion&lt;/strong&gt; &quot;,  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some say that it helps, whereas others oppose it. Can someone come up with a valid explanation for this?&lt;/p&gt;&#xA;" OwnerUserId="6802" LastEditorUserId="1320" LastEditDate="2014-05-22T09:39:05.027" LastActivityDate="2015-06-22T13:58:47.520" Title="Does a walk after a meal help with digestion?" Tags="&lt;digestion&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17566" PostTypeId="2" ParentId="17565" CreationDate="2014-05-22T09:16:48.327" Score="10" Body="&lt;p&gt;apparently walking helps in the movement of food into the stomach and improves digestion. Also helps in decreasing blood sugar after meals, which decreases cardiovascular risk and potential signal diabetes by helping muscles absorb glucose in the blood. Here is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18392240&quot;&gt;the link&lt;/a&gt; to a study done comparing the results of walking after food and after a drink. Also a study &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19560716&quot;&gt;was conducted&lt;/a&gt; where when people with Type 2 diabetes took a 20 minute walk just 15 minutes after eating, their post-meal blood sugar levels were lower than if they had walked before dinner or not walked at all. Here is &lt;a href=&quot;http://care.diabetesjournals.org/content/early/2013/06/03/dc13-0084.abstract&quot;&gt;the link&lt;/a&gt; to another similar study.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-05-22T09:21:55.697" LastActivityDate="2014-05-22T09:21:55.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17567" PostTypeId="1" AcceptedAnswerId="17608" CreationDate="2014-05-22T12:30:02.717" Score="2" ViewCount="526" Body="&lt;p&gt;Stimulants are the first choice for treating ADHD. But we also know that exercise helps to improve concentration. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We know that both stimulants and exercise increase bloodflow to muscles and to the brain by activating the sympathetic nervous system. Is this is the MAIN cause of the effect of improved concentration, rather than, say, specific activation of parts of the brain responsible for learning or planning or something similar? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm asking is, do drugs and exercise have different effects on the brain, what are the differences, and what are the consequences of these differences on concentration and learning? Which is more effective for promoting concentration and why? &lt;/p&gt;&#xA;" OwnerUserId="6805" LastActivityDate="2014-05-24T06:53:09.350" Title="Exercise vs stimulants, which is more effective for promoting concentration?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17568" PostTypeId="1" AcceptedAnswerId="17569" CreationDate="2014-05-22T13:49:47.747" Score="8" ViewCount="320" Body="&lt;p&gt;To what extent do brains (e.g. of humans) contain &lt;a href=&quot;http://en.wikipedia.org/wiki/Recurrent_neural_network&quot;&gt;recurrent &lt;/a&gt; connections? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am studying artificial neuronal networks and frequently encountered the statement, that recurrent neural networks are closer to biological neuronal networks than for example &lt;a href=&quot;http://en.wikipedia.org/wiki/Feedforward_neural_networks&quot;&gt;feed forward networks&lt;/a&gt;. But I didn't find information on the question if feed forward or recurrent architectures dominate the brain architecture.&lt;/p&gt;&#xA;" OwnerUserId="6806" LastEditorUserId="3340" LastEditDate="2014-05-22T18:03:32.153" LastActivityDate="2014-08-25T12:31:04.290" Title="Neuronal Architecture of the Brain" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;biological-networks&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17569" PostTypeId="2" ParentId="17568" CreationDate="2014-05-22T14:01:33.960" Score="6" Body="&lt;p&gt;The recurrent patterns of connections in a network are known as network motifs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can check &lt;a href=&quot;http://www.sciencemag.org/content/298/5594/824.full&quot;&gt;this&lt;/a&gt; paper out. They have identified common network motifs in different types of real networks including neural networks (of C.elegans though). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from feed forward loops, bi-fan is also a common network motif in neural networks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps the &lt;a href=&quot;http://www.humanconnectomeproject.org/&quot;&gt;connectome project&lt;/a&gt; has data for human brain which you can analyze for identifying network motifs. You would have to request for the data, though.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-05-22T14:01:33.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17571" PostTypeId="1" AcceptedAnswerId="17575" CreationDate="2014-05-22T16:09:27.877" Score="5" ViewCount="366" Body="&lt;p&gt;Biology is so exciting! Answering a question leads to  thousand more questions! There is no limit to how much one kind find out about a phenomena&amp;hellip;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I have always wondered how someone can decide that it is time to publish some fixed amount of research they have done. How do biologists decide when to publish a paper? How do biologists know that results are sufficient enough for a publication?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="107" LastEditDate="2014-05-23T00:41:23.817" LastActivityDate="2014-05-23T00:41:23.817" Title="How does a biologist decide when she has enough results to publish a paper?" Tags="&lt;publishing&gt;&lt;research-process&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17572" PostTypeId="2" ParentId="17571" CreationDate="2014-05-22T16:16:20.257" Score="3" Body="&lt;p&gt;When you do science you start with a question or a hypothesis. How is Gene A regulated? Or &quot;does hormone B have an effect on the immune system&quot;. Or whatever.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then you start by thinking how you can prove or disprove your question/hypothesis with experiments. You then do your experiments and see if they are enough to prove your question. It often happens that you have to do additional experiments to cover side-questions which appear during the work or to exclude some side-effects which may also be important. If you have done all this (with replicates) and looked from different angles on your problem, then you can start writing an article.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This includes some introduction from the literature and a classification of your results into the things already known. If you make strong claims, then you will need a lot of arguments (=results) to prove your point. It is quite hard to argue against &quot;common knowledge&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question of how much research is enough is quite philosophical, since you usually don't &quot;finish&quot; a topic. You look only at certain aspects from a certain angle. This can be quite different for other researchers.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-22T16:16:20.257" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17573" PostTypeId="2" ParentId="17571" CreationDate="2014-05-22T16:40:57.600" Score="2" Body="&lt;p&gt;It's all about &quot;Is this paper interesting enough to get published?&quot;  And people just get a feel for that when they are reading papers all the time, and submitting papers frequently.  For instance, maybe publicizing a big cool dataset was useful enough a few years ago to be published as is, but now, you might need a good finding that you found from that dataset, and followed up on, before the paper will be considered by your journal of choice.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-05-22T16:40:57.600" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17574" PostTypeId="2" ParentId="17558" CreationDate="2014-05-22T18:13:21.827" Score="0" Body="&lt;p&gt;Off the top of my head:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Plants are photosynthetic so have unlimited access to energy.&lt;/strong&gt; If an animal had unlimited access to energy it would likely have Nitrogen or Phosphorous or something else as the limiting nutrient. &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Animals eat plants and/or each other.&lt;/strong&gt; Whatever animals eat will have to a greater or lesser degree sufficient protein/fat/nucleic acids etc to satisfy minimum nutritional requirements. As noted in Chris' comment there can be some species-specific limitations like availability of salt in a herbivore diet, or the human requirement of an external source of vitamin C.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6810" LastActivityDate="2014-05-22T18:13:21.827" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17575" PostTypeId="2" ParentId="17571" CreationDate="2014-05-22T18:18:35.510" Score="1" Body="&lt;p&gt;I agree with all the responses so far; however I thought I should add that to publish a paper in a decent internationally peer-reviwed journal, more often than not, a paper has to tell a story, ideally a novel story and not just the same data that has been published before or at least address an old question in a new manner, that provides a fresh insight into the field or the question. A publication can't just be a bunch of random small and unrelated questions and experiments, at least not in any peer-reviewed journal. The key to a successful paper is that it should have ideally one message, which can be identified in the title, since believe it or not thats how most scientists vet whether a paper (abstract/summary) worth looking at or not. So as correctly mentioned, you identify a gap in the knowledge and attempt to address it having considered what is know about it so far, if any. Writing a paper follows a global formula, which has been elaborated in Chris response. Hence the key is that the paper has to tell ideally one story and the experiments used to address it has to make a logical progression to address the question. So you can't just jump from a small preliminary experiment which is questionable in its reliability into a large scale experiment. Some times you have to make the leap of &quot;faith&quot; in your experimentations and just do a certain experiment but the chances are your previous experiments have given you an indication as to whether its going to work or not. Be very mindful that most of the time the order in which you do your experiments is not the order in which you put them in the paper so what usually happens is that you have a central question, you do a bunch of experiments to address it and then you shuffle them around to tell the story in the most concise way and again the key word here is story.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now not only a paper has to tell a concise story but it has to be of general interest to the scientific community, specially in high impact journals. You probably know a recent paper about STAP cell lines that got into Nature and attracted world-wide attention in which the authors described how exposing the cells to stimulus/stressors such as acid or pressure can turn it pluripotent, which the media linked to personalised treatments. Now I don't want to get into all the controversy that followed it but its just to make the point that a research like this is not only of interest to the scientific community but also the public hence it got published in a highly respectable journal. Now whether thats the right thing for scientists to do and send important research to the top journals, which is hard to access by many countries is a whole different argument but I hope you can begin to see publishing a paper in a journal is not only related to its scientific merits but also to what extent it is of interest to the general or scientific community and what story is it telling or implying (to put it a bit more crudely). Now not every paper makes it to Nature and most of the time publications are highly specialised work which not everyone on the planet might be interested in them but they still follow the points I talked about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-05-22T18:23:52.807" LastActivityDate="2014-05-22T18:23:52.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17576" PostTypeId="1" AcceptedAnswerId="43823" CreationDate="2014-05-22T18:22:24.787" Score="3" ViewCount="68" Body="&lt;p&gt;Do axon grows after cutting of some of its part to near original place?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do axon restores after local damaging of some of its part?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I take &lt;a href=&quot;https://class.coursera.org/neurobio-001/&quot; rel=&quot;nofollow&quot;&gt;https://class.coursera.org/neurobio-001/&lt;/a&gt; classes and learn that axons are very long. So it is interesting if they able to restore connection to far places parts of body...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Axon_guidance&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Axon_guidance&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6738" LastEditorUserId="6738" LastEditDate="2014-05-22T18:28:05.183" LastActivityDate="2016-02-29T21:35:33.787" Title="Do axon grows after cutting/damaging of some of its part?" Tags="&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17577" PostTypeId="2" ParentId="17537" CreationDate="2014-05-22T19:19:06.157" Score="1" Body="&lt;p&gt;Seemingly the enzyme uses molecular oxygen in the reaction and one of the end products is water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This reaction scheme is more detailed and presumably accurate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.hmdb.ca/reactions/3063&quot; rel=&quot;nofollow&quot;&gt;http://www.hmdb.ca/reactions/3063&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition there is also a set of papers detailing coproporphyrinogen oxidase which was also on the website, hopefully one goes into more detail on the reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.hmdb.ca/proteins/HMDBP00251&quot; rel=&quot;nofollow&quot;&gt;http://www.hmdb.ca/proteins/HMDBP00251&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6811" LastActivityDate="2014-05-22T19:19:06.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17578" PostTypeId="1" AcceptedAnswerId="19701" CreationDate="2014-05-22T19:21:53.793" Score="10" ViewCount="437" Body="&lt;p&gt;I took a picture of this snake in Switzerland (Geneva Area):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SvnwV.jpg&quot; alt=&quot;Snake&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It looks to be an adder but cannot be sure about which species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Switzerland we have two kinds of adder: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Vipera_berus&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Vipera berus&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Vipera_aspis&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Vipera aspis&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;For me it looks like a &lt;em&gt;Vipera berus&lt;/em&gt;, but all the images I saw from both species (and the variations) I cannot be sure.&lt;/p&gt;&#xA;" OwnerUserId="6561" LastEditorUserId="6561" LastEditDate="2020-06-15T20:28:01.497" LastActivityDate="2020-06-15T20:28:01.497" Title="What is this snake" Tags="&lt;species-identification&gt;&lt;herpetology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17579" PostTypeId="1" AcceptedAnswerId="17587" CreationDate="2014-05-22T20:09:13.867" Score="3" ViewCount="1184" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UVyic.png&quot; alt=&quot;picture 1 (left upper corner) is the FAS or fatty acid synthase. It&amp;#39;s the multifunctional proteïn that has all the necessary enzymes in one complex consisting of 2 monomers. (And for example; CE is the condensing enzyme). Picture 2 (at the right) is the steps you do when you are at the reduction part (green part on picture 1) And picture 3 (left bottom corner) is another scheme that shows the condensation, reduction and translocation and so on. This last picture confuses me a little.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a problem in my reasoning on the fatty acid synthesis in the human body.&#xA;In the synthesis process you have this homodimer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the synthesis starts with the transfer of a acetyl group from acetyl-CoA to the sulfhydrylgroup of the condensing enzyme (CE) with help of the acetyltransferase enzyme (AT) and this on 1 of the 2 monomers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the same time a malonyl group from malonyl-CoA is transfered to the sulfhydryl terminus of phosphopantotheine from the ACP, and this on the other monomer and with help of the malonyltransferase (MT) enzyme.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;AND HERE THE PROBLEM STARTS&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The acetyl residue will be condensing with the malonylACP and at the same time there will be a decarboxylation (CO2 goes off) and CE goes off from acetyl. At the end acetoacetyl-ACP is formed. So if I got it right; the acetyl residue is being 'cut off' from the CE from the first monomere and binds to the malonylACP on the other monomere. Right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And after that the acetoacetyl-ACP will be swept back to the other monomer (to the reduction part), is this also right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then the reduction-dehydration-reduction steps are happening and at the end of the road you will get butyryl-ACP which will cut off from the ACP and migrate on the same monomer to the cysteine residue at the condensing enzyme (CE) (= translocation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And after that you can start a new condensation-reduction-translocation cycle and go on until you end up at palmitoyl-ACP. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the actual question is; is my reasoning right about how the product is going from one monomer to the other several times?&#xA;In my book it's a pretty messy explanation and so I want to be sure I'm right.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope somebody can help me out =)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Greetings&lt;/p&gt;&#xA;" OwnerUserId="6812" LastEditorUserId="3340" LastEditDate="2014-10-09T16:48:37.373" LastActivityDate="2014-10-09T16:48:37.373" Title="Fatty Acid Synthesis" Tags="&lt;lipids&gt;&lt;biochemistry&gt;&lt;fatty-acid-synthase&gt;&lt;fat-metabolism&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17580" PostTypeId="1" CreationDate="2014-05-22T21:44:42.650" Score="3" ViewCount="65" Body="&lt;p&gt;Biologists researching diseases will frequently use animal models. The way I understand it, there are species of animals, such as &quot;mouse&quot;, and lines of mice, such as &lt;code&gt;Black six&lt;/code&gt;, &lt;code&gt;NMRI&lt;/code&gt; or also genetically engineered lines like &lt;code&gt;B6.Cg-Tg(CAG-cre/Esr1*)5Amc/J&lt;/code&gt;. But they also sometimes take cell lines such as &lt;code&gt;HeLa&lt;/code&gt; and transplant them into animals, or treat them in vitro. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a word which covers both &quot;animal line&quot; and &quot;cell line&quot; and is in widespread use? I thought that &quot;model organism&quot; would be a good way to express it, but a biologist working in disease models told me that when she hears that, she only thinks of animals, never of cell lines. She wasn't able to come up with a term which covers both. Her best try was &quot;experimental system&quot;, but she conceded that, if used out of context, no biologist would recognize that it is about animal and cell lines. &lt;/p&gt;&#xA;" OwnerUserId="1578" LastEditorUserId="107" LastEditDate="2014-05-23T00:40:49.187" LastActivityDate="2014-05-23T00:40:49.187" Title="Is there a superterm combining &quot;animal line&quot; and &quot;cell line&quot; in disease models?" Tags="&lt;terminology&gt;&lt;animal-models&gt;&lt;research-tools&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17581" PostTypeId="2" ParentId="17580" CreationDate="2014-05-22T22:45:08.810" Score="2" Body="&lt;p&gt;There is no super-term that I can think of but you could say genetically modified (mouse) samples/specimens?&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-22T22:45:08.810" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17584" PostTypeId="1" AcceptedAnswerId="20249" CreationDate="2014-05-23T07:20:49.820" Score="2" ViewCount="472" Body="&lt;p&gt;&lt;strong&gt;How do you define Sexual Selection (SS)?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(One might want to subdivide SS into intra- and inter- SS to answer)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Is SS clearly different from Natural Selection (NS)?&lt;/li&gt;&#xA;&lt;li&gt;Is SS nested within NS or are NS and SS two different and (anti- or not) parallel processes?&lt;/li&gt;&#xA;&lt;li&gt;Is the evolutionary processes due to sexual conflict are SS processes?&#xA;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sexual conflict arises when the reproductive interests of males and females are not aligned, generating sex-specific selection on shared traits such as mating rate (from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20059540&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;)&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;(One may want to subdivise sexual conflict into intralocus and interloci conlict to answer)&lt;/li&gt;&#xA;  &lt;/ul&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Are the evolutionary processes of sexually antagonist genes SS processes?&lt;/p&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sexually antagonist genes are those genes where one allele is favored in females while another allele is favored in males (my own definition)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;li&gt;Can SS be accurately defined or is there a continuum of kinds or processes from complete SS processes to complete NS processes?&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Stated differently, is SS defined as the color orange (it is a continum) or like a square and a rtiangle (no continuum)&lt;/li&gt;&#xA;&lt;li&gt;(I talk here about kinds of processes, not about the relative importance of SS and NS in explaining the evolutionary dynamic of a trait or a locus)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you define SS based on some other concepts that might be subject to various definition, please define this other concept. For example, if one says &quot;SS occurs on a trait whenever this trait undergoes directional selection due to sexual competition&quot;, he will necessarily need to define &quot;sexual competition&quot; as well.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Below is a list of scenarios where you can answer by yes or no whether SS is involved in the evolution of some feature. In all of these scenarios, we'll consider cases where the males have to find a mate…&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The males need good ears to find the females before other males. Is SS involved in the adaptation of ears abilities?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The males need good flying abilities (supposing we talk about flying animals) to have access to females before another male. Is SS  involved in the adaptation to good flying abilities?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The males need good flying abilities  to have access to females although there is not much between male competition because the vast majority of females won't never be fertilized. Is SS is involved in the adaptation to good flying abilities?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The males need good flying abilities to be able to fly a long time without spending to much energy otherwise they will die before finding a female. Is SS is involved in the adaptation to good flying abilities?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The males need good flying abilities to be able to fly a long time without spending to much energy otherwise they will die before finding a female. There are quite a few females but there the competition is so rough to find a female that is still unmated Is SS is involved in the adaptation to good flying abilities?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The males need good camouflage because when they fly to find a mate they may get eaten by a predator and die before reproducing. Is SS is involved in the adaptation to good flying abilities?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The males need good camouflage because when they fly to find a mate they may get eaten by a predator and die before reproducing. Here the difference is that the predators are attracted to the spot if they can sense many males. So the presence of the other males influence the probability of finding a mate of a given male. Is SS is involved in the adaptation to good flying abilities?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-05-24T08:13:34.277" LastActivityDate="2014-08-05T17:20:12.153" Title="Definition of Sexual Selection?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;&lt;sexual-selection&gt;&lt;definitions&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17585" PostTypeId="1" AcceptedAnswerId="20250" CreationDate="2014-05-23T07:24:54.073" Score="1" ViewCount="668" Body="&lt;p&gt;How do you define a male-biased gene and a female-biased gene as they are found in the abstract of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20059540&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-05-24T08:08:29.197" LastActivityDate="2014-08-05T17:40:08.197" Title="What is a sex-biased gene?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;&lt;sexual-selection&gt;&lt;definitions&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17586" PostTypeId="1" AcceptedAnswerId="17589" CreationDate="2014-05-23T07:28:56.723" Score="1" ViewCount="77" Body="&lt;p&gt;If I get out in the wild observe wild populations and measure the distribution of fitness $f(w)$ in a given population. What will I find out? Will I observe a Gaussian distribution, a Poisson distribution, an exponential distribution, ….?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It probably depends on the species under consideration, typically it may depend on whether there is an sexual selection in this species. I welcome any insights!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-05-24T11:08:50.487" Title="Distribution of fitness in wild populations" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;&lt;sexual-selection&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17587" PostTypeId="2" ParentId="17579" CreationDate="2014-05-23T09:02:40.483" Score="2" Body="&lt;p&gt;The textbook descriptions of fatty acid synthesis can be confusing because although the underlying chemistry of the process is universal, the way that it is organised is different in the systems that have been characterised, which include &lt;em&gt;E. coli&lt;/em&gt;, yeast and vertebrates.&lt;/p&gt;&#xA;&lt;p&gt;In vertebrates:&#xA;The fatty acid synthase is a dimer of identical multifunctional single polypeptides. The synthesis process involves two -SH groups: one is the terminal group of the pantothenate of the acyl carrier protein domain (Pan-SH) and the other is an -SH group of the condensing enzyme (CE-SH).&lt;/p&gt;&#xA;&lt;p&gt;For the first condensation step the initiating acetyl group is attached to the CE-SH of one monomer and the incoming unit (malonyl CoA) is attached to the Pan-SH of the other monomer.&lt;/p&gt;&#xA;&lt;p&gt;The condensation reaction between these two results in the new elongated unit being attached to the Pan-SH. This unit then goes through the reductase/dehydratase/reductase steps to form the new acyl CoA which is finally transferred to an CE-SH group, opening up the Pan-SH for the next incoming malonyl CoA.&lt;/p&gt;&#xA;&lt;p&gt;This will happen repeatedly in each cycle of the process. Obviously since each monomer has both -SH groups a single fatty acid synthase dimer can be engaged in two elongations at the same time, but these will always include a transfer. It is thought that the initiating acetyl group comes in via the Pan-SH group.&lt;/p&gt;&#xA;&lt;p&gt;You say:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;And after that the acetoacetylACP will be swept back to the other monomere (to the reduction part), is this also right?&#xA;Then the reduction-dehydration-reduction steps are happening and at the end of the road you will get butyrylACP which will cut off from the ACP and migrate on the same monomere to the cysteïnresidu at the condensing enzyme (CE) (= translocation).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The diagram that you included clearly shows that the acetoacetyl group is formed via the reduction-dehydration-reduction steps on the same Pan-SH where its precursor was formed by condensation. Only then is it transferred to the CE-SH group. The diagram also indicates that the acetoacetyl group is transferred to the CE-SH of the same monomer. This implies that a growing chain never transfers from one monomer to the other. I have seen other sources which seem to suggest that this step does involve a transfer between monomers.&lt;/p&gt;&#xA;&lt;p&gt;In fact it would appear from the discussion on the WP page for &lt;a href=&quot;http://en.wikipedia.org/wiki/Fatty_acid_synthase&quot; rel=&quot;nofollow noreferrer&quot;&gt;fatty acid synthase&lt;/a&gt; that this is an unresolved issue - see for example:&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Joshi et al. (2003) Engineering of an Active Animal Fatty Acid Synthase Dimer with Only One Competent Subunit Chemistry &amp;amp; Biology 10:169 - 173&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Abstract&lt;/p&gt;&#xA;&lt;p&gt;Animal fatty acid synthases are large polypeptides containing seven functional domains that are active only in the dimeric form. Inactivity of the monomeric form has long been attributed to the obligatory participation of domains from both subunits in catalysis of substrate loading and condensation reactions. However, we have engineered a fatty acid synthase containing one wild-type subunit and one subunit compromised by mutations in all seven functional domains that is active in fatty acid synthesis. This finding indicates that a single subunit, in the context of a dimer, is able to catalyze the entire biosynthetic pathway and suggests that, in the natural complex, each of the two subunits forms a scaffold that optimizes the conformation of the companion subunit.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-05-23T09:02:40.483" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17588" PostTypeId="2" ParentId="17558" CreationDate="2014-05-23T09:35:52.063" Score="2" Body="&lt;p&gt;&lt;strong&gt;Phosphorus&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your suggestion that if we are meeting our calorific requirement we will be getting enough is true for phosphorus.&#xA;Most foods contain lots of phosphorus. The maximum dietary requirement occurs during adolescent growth, estimated at 1250 mg per day. Assuming a calorie intake of 2500 kcal we can calculate a 2500 kcal equivalent phosphorus content for various foods:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;skimmed milk contains 7,400 mg phosphorus per 2500 kcal&lt;/p&gt;&#xA;&#xA;&lt;p&gt;roasted chicken breast contains 7,500 mg phosphorus per 2500 kcal&lt;/p&gt;&#xA;&#xA;&lt;p&gt;cooked white rice contains 3840 mg per 2500 kcal&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Calculations are based upon values obtained via &lt;a href=&quot;http://webprod3.hc-sc.gc.ca/cnf-fce/index-eng.jsp&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Nitrogen&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our requirement for nitrogen is met by our protein intake: inadequate protein intake manifests as &lt;a href=&quot;http://en.wikipedia.org/wiki/Kwashiorkor&quot; rel=&quot;nofollow&quot;&gt;kwashiorkor&lt;/a&gt; which is essentially due to a dietary deficiency of essential amino acids. In other words, the only way to achieve a nitrogen-deficient diet is to not eat protein, and this would not be alleviated by any inorganic source of nitrogen, even if we could consume enough of such a N source.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-23T09:35:52.063" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17589" PostTypeId="2" ParentId="17586" CreationDate="2014-05-23T10:06:29.420" Score="2" Body="&lt;p&gt;Long for a comment but consider this to be an extended comment and not an exact answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At least for Poisson I can say that the random variable should fit the three Poisson postulates. Poisson RV generally describe discrete events in continuous intervals. A fitness function doesn't seem to be such a type of RV; it is a property of a population rather than an event.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would also not expect it to be exponentially distributed which would mean that probability is highest for the most fit (or most unfit) individual i.e the more fit are more frequent. I assume that it cannot be decided who is the most fit until selection happens. This &lt;em&gt;may&lt;/em&gt; still be the case just after a selection event but not otherwise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that this function should be Gaussian: assuming that there is little variability between individuals and what exists is because of independent events of mutation, these should converge to Gaussian as per the central limit theorem. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But generally the term that best describes this RV is a performance function. Fitness would always be a conditional RV. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For e.g. I would very roughly define fitness like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$f(X) = P(m(X)\ |\ p(X),S)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $f(x)$ is the fitness of $X$, $m(X)$ is the survival probability of $X$, $p(X)$ is performance in different tasks and $S$ is selection event. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-05-24T11:08:50.487" LastActivityDate="2014-05-24T11:08:50.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17590" PostTypeId="1" AcceptedAnswerId="17592" CreationDate="2014-05-23T10:15:21.477" Score="4" ViewCount="21716" Body="&lt;p&gt;Wikipedia definitions for these terms are pretty similar:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Clade&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Clade&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Monophyletic_group&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Monophyletic_group&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Taxon&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Taxon&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;They sound like the terms are synonyms. Why there are separate articles for them then?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it true that every person is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Reptiliomorpha&quot; rel=&quot;nofollow&quot;&gt;reptilomorph&lt;/a&gt; and an &lt;a href=&quot;http://en.wikipedia.org/wiki/Eupelycosauria&quot; rel=&quot;nofollow&quot;&gt;eupelycosaur&lt;/a&gt; just like he/she is a mammal?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bonus question: what is the difference between a &lt;a href=&quot;http://en.wikipedia.org/wiki/Cladogram&quot; rel=&quot;nofollow&quot;&gt;cladogram&lt;/a&gt; and a &lt;a href=&quot;http://en.wikipedia.org/wiki/Phylogenetic_tree&quot; rel=&quot;nofollow&quot;&gt;phylogenetic tree&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS Please don't just give definitions and/or quote Wikipedia. Point out the &lt;em&gt;differences&lt;/em&gt;, if any. Even better, provide examples that can be considered one but not the other.&lt;/p&gt;&#xA;" OwnerUserId="6820" LastEditorUserId="6820" LastEditDate="2014-05-23T10:37:17.453" LastActivityDate="2014-05-23T10:59:43.490" Title="What is the difference between these terms: clade, monophyletic group and taxon?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;taxonomy&gt;&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17591" PostTypeId="1" AcceptedAnswerId="17654" CreationDate="2014-05-23T10:34:15.720" Score="3" ViewCount="39499" Body="&lt;p&gt;If the squamous (top) layer of epidermis, or skin, is burned or damaged in another way, will it then be replaced by the next layer of below?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, from where does the basal membrane originate? Does it regenerate from a different layer of cells? &lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="6380" LastEditDate="2014-05-26T02:46:45.880" LastActivityDate="2016-04-19T13:03:35.427" Title="If the top epidermal layer is burned away, what is it replaced with?" Tags="&lt;human-biology&gt;&lt;histology&gt;&lt;tissue-repair&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17592" PostTypeId="2" ParentId="17590" CreationDate="2014-05-23T10:51:57.853" Score="8" Body="&lt;p&gt;A taxon (Plur. taxa) is any (monophyletic or not) group of species. For example the group of yellow flowers is a taxon. The group of primates is a taxon. The taxon of aquatic animals is a taxon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A clade is a monophyletic taxon or monophyletic group if you prefer. A monophyletic taxon (or a clade) is defined as a taxon that contains only all descendants of a common ancestor and the common ancestor. On the following picture, only the Taxon 1 is a clade.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KG9my.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To cite few examples of clades: Primates, &lt;a href=&quot;http://tolweb.org/Life_on_Earth/1&quot; rel=&quot;noreferrer&quot;&gt;Eukaryotes&lt;/a&gt;, &lt;a href=&quot;http://tolweb.org/Rosales/21029&quot; rel=&quot;noreferrer&quot;&gt;Rosacea&lt;/a&gt;, &lt;a href=&quot;http://tolweb.org/Terrestrial_Vertebrates/14952&quot; rel=&quot;noreferrer&quot;&gt;Reptilomorpha&lt;/a&gt;, &lt;a href=&quot;http://tolweb.org/Eutheria/15997&quot; rel=&quot;noreferrer&quot;&gt;Rodentia&lt;/a&gt;. (The links yield to tolweb.org. See below for more info about this site)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A cladogram is some kind of reduced evolutionary tree that only shows the branching pattern but the length of the branches does not carry any information. At the opposite on a evolutionary tree the lengths of branches usually indicate the inferred time from the divergence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the best tree you can find online is &lt;a href=&quot;http://tolweb.org&quot; rel=&quot;noreferrer&quot;&gt;tolweb.org&lt;/a&gt;. You can find &lt;a href=&quot;http://tolweb.org/Terrestrial_Vertebrates/14952&quot; rel=&quot;noreferrer&quot;&gt;here the clade of Reptilomorpha&lt;/a&gt; and here the clade of &lt;a href=&quot;http://tolweb.org/Synapsida/14845&quot; rel=&quot;noreferrer&quot;&gt;Eupelycosaur&lt;/a&gt;. As you can see from these links, the mammals form a clade within the Eupelycosaur which itself is a clade within the Reptilomorpha. So yes, every human being is a Reptiliomorpha/Eupelycosaur/Mammalia. You can have fun going through this evolutionary tree and see what are the common ancestors between human and other mammals, human and turtles, human and jellyfish, human and plants, etc… to cite just a few relationships you might be interested to look at.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-05-23T10:59:43.490" LastActivityDate="2014-05-23T10:59:43.490" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17593" PostTypeId="2" ParentId="15112" CreationDate="2014-05-23T13:07:24.403" Score="0" Body="&lt;p&gt;If it's not loo late to contribute, CLC workbench is nice too (&lt;a href=&quot;http://www.clcbio.com/products/clc-main-workbench/&quot; rel=&quot;nofollow&quot;&gt;http://www.clcbio.com/products/clc-main-workbench/&lt;/a&gt;). I only use the free version (&lt;a href=&quot;http://www.clcbio.com/products/clc-sequence-viewer/&quot; rel=&quot;nofollow&quot;&gt;http://www.clcbio.com/products/clc-sequence-viewer/&lt;/a&gt;) but its very user friendly in terms of the features I have worked with.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-23T13:07:24.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17594" PostTypeId="1" CreationDate="2014-05-23T13:32:20.777" Score="2" ViewCount="246" Body="&lt;p&gt;It's been established that &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9216570&quot; rel=&quot;nofollow&quot;&gt;food palatability is related to it's caloric density&lt;/a&gt;. This hypothesis is used to explain why humans are partial to sugar and fat. But it is also said that humans are partial to salt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that salt has no calories, are there evolutionary reasons that explain why humans have a preference for salty foods?&lt;/p&gt;&#xA;" OwnerUserId="6821" LastActivityDate="2014-05-23T14:32:27.297" Title="What is the evolutionary reason behind human preference for salty foods?" Tags="&lt;evolution&gt;&lt;food&gt;&lt;diet&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17595" PostTypeId="2" ParentId="17594" CreationDate="2014-05-23T13:41:02.693" Score="4" Body="&lt;p&gt;The body needs more than energy to survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Salt is vital to the body's function. Ions of sodium and calcium perform numerous vital functions, but are particularly related to the function of the nervous system and contraction of muscles. Accordingly, seeking out sources of salt makes sense in a natural environment in which salt is relatively unavailable.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2014-05-23T13:41:02.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17597" PostTypeId="1" AcceptedAnswerId="17605" CreationDate="2014-05-23T14:15:17.160" Score="3" ViewCount="242" Body="&lt;p&gt;Quoting from : Scientific American July 1975 &lt;em&gt;The Manipulation of genes&lt;/em&gt; by Stanley Cohen :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Restriction endonucleases (and modification methylases) are widespread&#xA;  in microorganisms; genes for &lt;strong&gt;making&lt;/strong&gt; them were found on &lt;strong&gt;viral&#xA;  chromosomes&lt;/strong&gt; and extrachromosomal plasmid DNA as well as on many&#xA;  bacterial chromosomes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why would the genes for making RE be found on viral chromosomes ? Also, could you give some examples where they are found on plasmids ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-05-23T20:06:12.660" Title="Restriction endonucleases are found in?" Tags="&lt;bacteriology&gt;&lt;molecular-genetics&gt;&lt;virus&gt;&lt;plasmids&gt;&lt;restriction-enzymes&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17598" PostTypeId="1" AcceptedAnswerId="17603" CreationDate="2014-05-23T14:29:17.470" Score="2" ViewCount="164" Body="&lt;p&gt;The sequence of restriction site of EcoRI - GAATTC was identified in the early 1970s, before Sanger Sequencing was invented.(1977)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How was the restriction site of EcoRI sequenced ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2014-05-23T16:23:01.357" LastActivityDate="2014-05-24T18:45:26.877" Title="How was Restriction Site of EcoRI sequenced?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;dna-sequencing&gt;&lt;history&gt;&lt;restriction-enzymes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17599" PostTypeId="1" AcceptedAnswerId="60503" CreationDate="2014-05-23T15:35:53.320" Score="11" ViewCount="592" Body="&lt;p&gt;I'd appreciate some help identifying these three corvids I photographed in Austria during the Summer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/AIyuO.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/AIyuO.jpg&quot; alt=&quot;corvids&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know identifying corvids can be difficult and I'm not an ornithologist -- just an amateur bird watcher. After looking through many images of various crow species and their hybrids, I've tentatively identified these as:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Carrion crow (&lt;em&gt;Corvus corone&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Carrion crow × Hooded crow (&lt;em&gt;Corvus corone × Corvus cornix&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Carrion crow × Hooded crow (&lt;em&gt;Corvus corone × Corvus cornix&lt;/em&gt;)&lt;br&gt;&#xA;I initially believed this to be a Hooded crow (&lt;em&gt;Corvus cornix&lt;/em&gt;), but the broken coloration on the wings made me think it might actually be a hybrid as well.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Can someone here either confirm my identification or provide a more informed identification?&lt;/p&gt;&#xA;" OwnerUserId="6703" LastEditorUserId="16866" LastEditDate="2017-06-07T18:30:30.903" LastActivityDate="2019-02-04T06:12:50.697" Title="Help Needed Identifying Corvids" Tags="&lt;zoology&gt;&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17600" PostTypeId="2" ParentId="17597" CreationDate="2014-05-23T15:50:51.700" Score="2" Body="&lt;p&gt;If you have a dsDNA genome and replicate it by rolling circle like most bacteriophages and many plasmids do, an endonuclease is pretty much a necessity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hiycs.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5784" LastEditorUserId="5784" LastEditDate="2014-05-23T16:04:55.017" LastActivityDate="2014-05-23T16:04:55.017" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="17601" PostTypeId="2" ParentId="15683" CreationDate="2014-05-23T16:33:26.627" Score="6" Body="&lt;p&gt;&lt;a href=&quot;http://www.elasmo-research.org/education/topics/r_haulin%27_bass.htm&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; by R. Aiden Martin doesn't have citations, but is a great read with a lot of detail on observations and mechanics of animals moving in water. If you trust the numbers the author gives, the top 10 marine mammals in terms of speed (in mph = 1.6 km/h) are:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dall's Porpoise (&lt;em&gt;Phocaenoides dalli&lt;/em&gt;), leaping   34.5 mph&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Killer Whale (&lt;em&gt;Orcinus orca&lt;/em&gt;)  34.5 mph&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Shortfin Pilot Whale (&lt;em&gt;Globicephala macrorhynchus&lt;/em&gt;)   30.4 mph&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Blue Whale (&lt;em&gt;Balaenopterus musculus&lt;/em&gt;) 29.76 mph&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Fin Whale (&lt;em&gt;Balaenoptera physalus&lt;/em&gt;)   25.42 mph&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;California Sea Lion (&lt;em&gt;Zalophus californianus&lt;/em&gt;)    25 mph&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Pacific Spotted Dolphin (&lt;em&gt;Stenella attenuata&lt;/em&gt;)    24.7 mph&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Common Dolphin (&lt;em&gt;Delphinus delphis&lt;/em&gt;)  23.6 mph&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Bottlenose Dolphin (&lt;em&gt;Tursiops truncatus&lt;/em&gt;) 17 mph&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Pacific Whitesided Dolphin (&lt;em&gt;Lagenorhynchus obliquidens&lt;/em&gt;) 17 mph&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As noted in the article, higher estimates of speed for, for instance, the common dolphin may be in fact records of them 'surfing' on the bow wave of boats (not propelling themselves through the water).&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="19468" LastEditDate="2016-07-09T16:27:29.677" LastActivityDate="2016-07-09T16:27:29.677" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17602" PostTypeId="1" AcceptedAnswerId="17606" CreationDate="2014-05-23T17:34:15.483" Score="3" ViewCount="49591" Body="&lt;p&gt;You also realize probably, when we get so much anger or high levels of stress, after some point we have terrible stomach ache, like really heavy pain. Why is that? How stress or anger can effect our stomach? What is the mechanism?&lt;/p&gt;&#xA;" OwnerUserId="5630" LastActivityDate="2016-07-04T20:41:52.577" Title="Why do we suffer abdominal pain after we get very angry or stress?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;pain&gt;&lt;stomach&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17603" PostTypeId="2" ParentId="17598" CreationDate="2014-05-23T17:59:39.000" Score="7" Body="&lt;p&gt;The first determination of a recognition site for a restriction endonulease was reported in:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Kelly &amp;amp; Smith (1970) A restriction enzyme from Hemophilus influenzae II. Base sequence of the recognition site. J Mol. Biol. 51: 393-409&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The enzyme was then called endonuclease R, but is now known as HindII (or HincII). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The method used was to cut DNA with the enzyme and then remove the exposed terminal phosphates with alkaline phosphatase. These ends could then be labelled with &lt;sup&gt;32&lt;/sup&gt;P using polynucleotide kinase and &amp;gamma;-labelled ATP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The end-labelled DNA was then treated with nucleases in three different ways to release mononucleotides, dinucleotides, and a mixture enriched for trinucleotides. In each case the labelled products were identified by their behaviour in 2D thin-layer chromatography, and were  further characterised for their total base composition after digestion to mononucleotides where appropriate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The deduced site was/is &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;5'----GTY RAC----3'&#xA;3'----CAR YTG----5'&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Thus the labelled mononucleotides were found to be A and G (purine=R), the dinucleotides were found to be GA and AA and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The EcoRI sequence was determined by essentially the same methodology and was reported by &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hedgpeth et al (1972) DNA nucleotide sequence restricted by the RI endonuclease. Proc. Natl. Acad. Sci USA 69:3448 - 3452&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Addendum:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although Sanger sequencing (the plus-minus method) may have been developed through the 1970s, it really didn't catch on until the early 80s. So for example the first complete plasmid sequence to be determined was pBR322 in 1979:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sutcliffe (1979) Complete nucleotide sequence of the Escherichia coli plasmid pBR322. CSH Symp. Quant. Biol. 43: 77 - 90&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&quot;I have determined the 4362-nucleotide-pair sequence of the plasmid cloning vector pBR322 using the DNA-sequencing technique of Maxam and Gilbert (1977). The DNA structure has several interesting features that lead to testable predictions.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The standard sequencing method in use at that time was chemical sequencing using the Maxam-Gilbert methodology. When I started a postdoc in the USA in 1979 M-G sequencing was the standard method. Sanger sequencing really only took off following the development of the M13 mp vectors (and later the pUC plasmids) by J Messing in the early 80s. And what a relief it was: M-G sequencing was extremely laborious, as anyone who ever did it will testify.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-05-24T18:45:26.877" LastActivityDate="2014-05-24T18:45:26.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17604" PostTypeId="2" ParentId="17597" CreationDate="2014-05-23T18:10:46.977" Score="2" Body="&lt;p&gt;The familiar restriction enzyme EcoRI is plasmid encoded.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Betlach et al. (1976) A restriction endonuclease analysis of the bacterial plasmid controlling the EcoRI restriction and modification of DNA. Fed. Proc. 35:2037 - 43.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For an example of a phage encoded system see:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dempsey et al. (2005) Sau421, a BcgI-like restriction-modification system encoded by the Staphylococcus aureus quadruple-converting phage Phi42. Microbiology 151: 1301-1311&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This second paper suggests an answer to why a phage would have such a system: lysogens of Phi42 are resistant to infection by all 23 members of a standard set of &lt;em&gt;S. aureus&lt;/em&gt; phages. Once a phage has lysogenised it is in its interest to prevent lysis of its host.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-23T18:10:46.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17605" PostTypeId="2" ParentId="17597" CreationDate="2014-05-23T19:58:51.313" Score="2" Body="&lt;p&gt;There are many proposals for the ecological role of restriction-modification (RM) systems, and why they would exist on mobile genetic elements (e.g. plasmids and viruses). In this case, I am specifically talking about the viruses that infect bacteria (aka, bacteriophage).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) RM systems may have an anti-viral function. Normally we would think of such systems as being part of the host chromosome, but as Alan Boyd suggested, once a temperate phage has integrated itself into the chromosome, its fitness is tied to its host. Therefore, a RM system found in a prophage could prevent infections by additional phage. See here for a discussion of this issue:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23471617&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/23471617&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) RM systems may have &quot;addictive&quot; properties by acting as toxin-antitoxin systems. Basically, this means that if the genes for the RM system are lost, the host cell dies. This can provide selection for the maintenance of plasmids and prophage inside of the host cell. See here for a discussion of this issue:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874152/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874152/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Finally, viruses need to destroy the host genome -- both to suppress any anti-viral response and to release nutrients for viral replication. While this is typically achieved with nucleases other than restriction endonucleases, there is at least one situation where a RE seems to be involved. This is discussed in the first link above (see the section entitled &quot;Role in Nutrition&quot;)&lt;/p&gt;&#xA;" OwnerUserId="5006" LastEditorUserId="5006" LastEditDate="2014-05-23T20:06:12.660" LastActivityDate="2014-05-23T20:06:12.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17606" PostTypeId="2" ParentId="17602" CreationDate="2014-05-23T22:04:01.077" Score="4" Body="&lt;p&gt;Cortisol produced from the zona fasciculata of the adrenal cortex is directly caused by stress.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Cortisol&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Cortisol&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cortisol stimulates gastric-acid secretion. Cortisol's only direct effect on the hydrogen ion excretion of the kidneys is to stimulate the excretion of ammonium ions by deactivating the renal glutaminase enzyme. Net chloride secretion in the intestines is inversely decreased by cortisol in vitro.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This increase in gastric-acid secretion can irritate the lining of the GI tract, especially if there are ulcers or inflammation, resulting in pain. In addition, the fight-or-flight response causes &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;inhibition of stomach and upper-intestinal action to the point where digestion slows down or stops.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(see &lt;a href=&quot;http://en.wikipedia.org/wiki/Fight-or-flight_response&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Fight-or-flight_response&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Those things, paired with increased muscle tension and vasoconstriction cause pressure changes in the GI tract, which can cause pain.&lt;/p&gt;&#xA;" OwnerUserId="6828" LastActivityDate="2014-05-23T22:04:01.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17607" PostTypeId="1" AcceptedAnswerId="17609" CreationDate="2014-05-24T04:35:22.350" Score="3" ViewCount="344" Body="&lt;p&gt;So, after starting to gain weight on sitting in front of my computer too long, I have decided to take the plunge and maybe stick to an exercise regimen. As has been reported by &lt;a href=&quot;http://www.doctoroz.com/videos/what-s-best-time-exercise&quot; rel=&quot;nofollow&quot;&gt;some studies&lt;/a&gt;, exercising in the morning can be more beneficial than doing so in the evening. Now, personally, waking up in the morning is a huge chore for me. Furthermore, I have people advising me to hit the loo (toilet) before exercising as it may not be good for my health and leads to waste accumulation in the body. Now, search as I may, I cant find any basis that supports this theory. I understand that hygiene might be a factor but does exercising in the morning before going to the loo have any effects on health in general? Thanks.  &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2016-08-07T09:13:01.717" Title="What is the best time to exercise" Tags="&lt;health&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17608" PostTypeId="2" ParentId="17567" CreationDate="2014-05-24T06:53:09.350" Score="0" Body="&lt;p&gt;exercise stimulates brain regions that are involved in memory function to release a chemical called brain-derived neurotrophic factor (&lt;a href=&quot;http://en.wikipedia.org/wiki/Brain-derived_neurotrophic_factor&quot; rel=&quot;nofollow&quot;&gt;BDNF&lt;/a&gt;) which is a protein that helps in the survival of neurons and promotes the growth of new neurons. BDNF rewires memory circuits so they work better. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Memory enhancers or smart drugs or &lt;a href=&quot;http://en.wikipedia.org/wiki/Nootropic&quot; rel=&quot;nofollow&quot;&gt;Nootropics&lt;/a&gt; as they are called help in improving the efficiency of neurotransmitters and its associated receptors in cognitive function. Three systems that are stimulated by these drugs which I could find are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Cholineric System&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Glutamatergic System&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Dopaminergic &amp;amp; Serotonergic Systems&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read about about &lt;a href=&quot;http://peaknootropics.com/how-do-nootropics-work/&quot; rel=&quot;nofollow&quot;&gt;them here&lt;/a&gt; along with links to published articles on their effects. Details of different nootropic drugs are mentioned in &lt;a href=&quot;http://www.thinkinginanutshell.com/nootropics&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; along with their effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course naturally improving concentration would be the way to go considering the hazards of long term use of drugs. Some links to the side effects are &lt;a href=&quot;http://www.livescience.com/45621-students-risk-brain-problems-from-smart-drugs.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; and &lt;a href=&quot;http://www.sciencedaily.com/videos/618790.htm&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-24T06:53:09.350" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17609" PostTypeId="2" ParentId="17607" CreationDate="2014-05-24T06:55:16.057" Score="4" Body="&lt;p&gt;WHO's definition about Health&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Health is a state of complete physical, mental and social well-being and not merely the absence of disease or infirmity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In other words, Good health means active life where you can express yourself freely, you can succeed and can make mistakes, can reach your goals, can understand your body and others, and can say &lt;strong&gt;no&lt;/strong&gt; when you see your limit to yourself and others - and can set new targets to yourself, feel accepted in your society and accept &lt;strong&gt;yourself&lt;/strong&gt; as you are.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Best time to Exercise for successful results in competitions - dependent on Age&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Endurance atletes during ages 25-30 years in this answer about &lt;a href=&quot;https://biology.stackexchange.com/a/19268/86&quot;&gt;Why does max heart rate decrease with age?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Short-term and long-term effects of exercise on Vitality&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There are many stages in your question in Physiology, Pathophysiology and Microbiology, for instance.&#xA;I can cover here only the surface:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;very short effect of short exercise (20 min) on brain &lt;/li&gt;&#xA;&lt;li&gt;long term effect of regular short exercise (20 min) on brain, hypothalamus and biologic clock - wakefulness (limbic system)&lt;/li&gt;&#xA;&lt;li&gt;long-term effect of regular weekly exercise (3.5 h) on brain&lt;/li&gt;&#xA;&lt;li&gt;long-term effect of regular weekly exercise (3.5 h) on body muscles&lt;/li&gt;&#xA;&lt;li&gt;long-term effect of careful regular stretching and appropriate resting on congestion of body&lt;/li&gt;&#xA;&lt;li&gt;long-term effect of regular weekly exercise (3.5 h) on metabolism &lt;/li&gt;&#xA;&lt;li&gt;effect of regular exercise on circulation system (blood and lymph) - known to increase i.e. include temperature distribution and defence bodies distribution&lt;/li&gt;&#xA;&lt;li&gt;short-term effect of short exercise on PTH secretion (calcium); autoregulation of renal blood flow with two major theories: myogenic mechanism and tubuloglomerular effect&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;where I only briefly cover one term in Pathology.&#xA;There are two unanswered questions about the renal function [Costanzo, 2013]&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(1) What component of tubular fluid is sensed at the macula densa? The&#xA;  major candidates are luminal Na+ and Cl−. (2) What vasoactive&#xA;  substance is secreted by the juxtaglomerular apparatus to act locally&#xA;  on afferent arterioles? Here, the candidates are adenosine, ATP, and&#xA;  thromboxane.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;so to understand the effect of short-term morning training on PTH secretion, we should understand the two questions first.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Evidences to some things&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/x8z5A.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Short-term exercise can work sometimes as prophylactics for allergic symptoms.&#xA;I think the most important thing is the irritation of your skin which is the most important endocrine organ in our body.&#xA;Skin's temperature change secretes many hormones than help us to stand irritations from the environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the effects of short-term exercise in the morning depends on the patient at hand.&#xA;I cannot say much general.&#xA;For instance, if your heart is not strained; that it has too high T peak, too heavy exercise can cause you harm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My personal experience&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Short-term exercise suited to a person with no deficits in sleeping can help to alleviate symptoms of allergies and decrease stress in a normally physiological balances without viral infections,&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;but the real world is not that nice.&#xA;The problem comes if the patient has any disease that uses our immune system against us such as some &lt;strong&gt;viral infection&lt;/strong&gt;.&#xA;The immune response is also the source of pathogenesis for many viral diseases.&#xA;Unlike for a bacterial infection, the ultimate goal of the immune response in a viral infection is to eliminate both the virus and the host cells harbouring or replicating the virus, [Murray, Medical Microbiology, 6th ed].&#xA;Actually, some drugs are immunosuppressant like cortisone, and some procedures like radiation therapy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, with some medication plans, you should avoid drugs, living styles and habits that immunosuppresses your body. &#xA;For instance, HIV patients with HAART medication plan (medication combination is antiretroviral but possible immunosuppressive pathways may exist in different conditions) that involves a strategy depending on the condition, since HAART medications are life-long and cannot be stop, so other conditions etc TBC must be treated first, to avoid too much burden on the body at the same time.&#xA;In a similar way, avoiding living style or habits that puts immunosystem down can help with HIV.&#xA;Doing sport when you have slept badly many days and feel exhausted, puts your body under immunosuppression. &#xA;So the state of the disease or your physical wellbeing determines when sport is useful and when not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other part of your question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To hit toiled before exercise is good because then&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;you decrease the risk of gastrointestinal bleeding and venous congestion. &lt;/li&gt;&#xA;&lt;li&gt;effect of exercise on constipation is one topic here; depends on you, since there are many types&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The more stuff you have in your colon and gastrointestinal system, the harder it is to use fully your muscles of your body. &#xA;Try pull-ups with more empty colon vs full one.&#xA;Pull-ups require many muscles from upper trunk and lower trunk. &#xA;You cannot use all your stomach muscles if something is blocking your middle body muscles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good Hygiene is the easiest way to decrease the risk of any infections caused by many factors.&#xA;I estimate that 2-5 % of people visiting public toilets wash hands correctly; one video &lt;a href=&quot;https://www.youtube.com/watch?v=0at_jtzJCDM&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; about how one should do it.&#xA;Many people leave their hands wet.&#xA;If you have infection in your body, you should not exercise because failure to resolve the infection may lead to persistent or chronic infection or death.&#xA;It takes much energy from our body to handle with infections.&#xA;To recover from training, it requires good balance of many factors.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Summary&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The best time to do sport when you are healthy &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;you do not have any infections (viral particularly) because a failure to resolve the infection can lead to persistent or chronic infection or death&lt;/li&gt;&#xA;&lt;li&gt;when you have prepared early enough for the exercise with enough sleep&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;where pathologies and/or teratologies are not limiting your process.&#xA;You compete only against yourself and then grow from that to see you how good person you are really. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The morning exercise in a body which has rested well before the exercise and prepared accordingly to the exercise can be useful because &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;short-term effects on the brain (process things during exercise) (See Figure 1)&lt;/li&gt;&#xA;&lt;li&gt;possible short-term effects during day after the exercise&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and if the exercise becomes a habit in a healthy person, then &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;long-term effects: increased metabolism and many other positive effects described above&lt;/li&gt;&#xA;&lt;li&gt;and many other possible reasons from social to better self-esteem&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;when the the person listens to his body and stops when it hurts or something goes over; can rest accordingly.&#xA;Good motivation is useful in gaining good health.&#xA;Motivation is the strength and direction of the effort.&#xA;If you are interested in morning exercise, then you can set target and make a realistic plan.&#xA;Listen your own body and be able to refit your plan accordingly.&#xA;Actually, here is an important step that the consultation of many doctors can be useful; one doctor cannot always see the main problem for instance of prolonged and deepened allergic symptoms.&#xA;Consultation and discussions of other people can also be useful - like discussing where to help for this and this; who has enough capabilities to understand it.&#xA;The person cannot always know himself what is a main disease underneath.&#xA;Anything can come that postpone some training sessions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Infectious disease courses 2015-2016   &lt;/li&gt;&#xA;&lt;li&gt;Gleeson. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1553334/&quot; rel=&quot;nofollow noreferrer&quot;&gt;The effect on immunity of long-term intensive training in elite swimmers&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Anderson. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632802/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Effects of Exercise and Physical Activity on Anxiety&lt;/a&gt;. 2013. &lt;/li&gt;&#xA;&lt;li&gt;Laires. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18705536&quot; rel=&quot;nofollow noreferrer&quot;&gt;Exercise, magnesium and immune function&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Gunzer. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475230/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Exercise-Induced Immunodepression in Endurance Athletes and Nutritional Intervention with Carbohydrate, Protein and Fat—What Is Possible, What Is Not?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;HAART and HIV in DynaMed Plus. Visited 7.8.2016. &lt;/li&gt;&#xA;&lt;li&gt;WHO. &lt;a href=&quot;http://www.who.int/topics/health_education/en/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Health Education&lt;/a&gt;. Visited 7.8.2016. &lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2016-08-07T09:13:01.717" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17611" PostTypeId="1" AcceptedAnswerId="17612" CreationDate="2014-05-24T08:48:11.160" Score="6" ViewCount="10549" Body="&lt;p&gt;The definition of entomology says it is the science of studying insects. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know spiders are not insects but does entomology include studying spiders as well?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise is there any name to the science of studying spiders (class &lt;em&gt;Arachnida&lt;/em&gt;)?&lt;/p&gt;&#xA;" OwnerUserId="6561" LastEditorUserId="948" LastEditDate="2014-05-24T16:53:22.127" LastActivityDate="2019-07-22T20:45:16.183" Title="Are spiders part of the study of entomology?" Tags="&lt;entomology&gt;&lt;definitions&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17612" PostTypeId="2" ParentId="17611" CreationDate="2014-05-24T08:58:42.957" Score="10" Body="&lt;p&gt;Spiders are part of a taxon called &lt;a href=&quot;http://en.wikipedia.org/wiki/Arachnid&quot; rel=&quot;nofollow&quot;&gt;Arachnida&lt;/a&gt;. Arachnida also contain scorpions, Oppiliones, acari, … The science of arachnids is logically called &lt;a href=&quot;http://en.wikipedia.org/wiki/Arachnology&quot; rel=&quot;nofollow&quot;&gt;Arachnology&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, (&lt;a href=&quot;http://en.wikipedia.org/wiki/Entomology&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Entomology (from Greek ἔντομος, entomos, &quot;that which is cut in pieces or engraved/segmented&quot;, hence &quot;insect&quot;; and -λογία, -logia) is the scientific study of insects, a branch of arthropodology. In the past the term &quot;insect&quot; was more vague, and historically the definition of entomology included the study of terrestrial animals in other arthropod groups or other phyla, such as arachnids, myriapods, earthworms, land snails, and slugs. This wider meaning may still be encountered in informal use.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In other words, &lt;strong&gt;in the informal sense entomology include arachnology but the strict definition entomology does not encompass arachnology&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will find &lt;a href=&quot;http://tolweb.org/Arthropoda/2469&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; on tolweb.org more information about the systematics of &lt;a href=&quot;http://en.wikipedia.org/wiki/Arthropod&quot; rel=&quot;nofollow&quot;&gt;Arthropoda&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-09-25T01:36:48.350" LastActivityDate="2015-09-25T01:36:48.350" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17613" PostTypeId="1" CreationDate="2014-05-24T05:23:41.617" Score="0" ViewCount="577" Body="&lt;p&gt;Jellyfish use jet propulsion to move forward, according to &lt;a href=&quot;http://earthsky.org/earth/how-do-jellyfish-swim&quot; rel=&quot;nofollow&quot;&gt;http://earthsky.org/earth/how-do-jellyfish-swim&lt;/a&gt;. Otherwise, they drift with the ocean currents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this mean that, without the presence of water currents, jellyfish cannot swim backwards? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(This question was inspired by watching countless SpongeBob episodes and seeing the efficiency in which SB catches jellyfish).&lt;/p&gt;&#xA;" OwnerDisplayName="geoff" LastEditorUserId="3340" LastEditDate="2014-05-24T10:36:41.010" LastActivityDate="2014-06-10T18:01:10.767" Title="Can jellyfish swim backwards?" Tags="&lt;invertebrates&gt;&lt;bio-mechanics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17614" PostTypeId="2" ParentId="17613" CreationDate="2014-05-24T09:34:30.470" Score="1" Body="&lt;p&gt;Jellyfish move by a form of jet propulsion and it moves in the direction that the head is facing. If it needs to change direction, it just needs to pivot and propel itself in the direction that it needs to move. Comb jellies (which are not really jellyfish) have cilia that beat continuously in the water for it to move forward. So water currents are not necessary. Here is an &lt;a href=&quot;http://earthsky.org/earth/how-do-jellyfish-swim&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; with videos on how jellyfish move.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="948" LastEditDate="2014-05-24T16:46:12.610" LastActivityDate="2014-05-24T16:46:12.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17619" PostTypeId="1" AcceptedAnswerId="17671" CreationDate="2014-05-24T11:27:41.567" Score="3" ViewCount="211" Body="&lt;p&gt;I am studying about the endogene lipidcycle in the human body and I know that VLDL (very low density lipoproteïn) is made in the liver and that it contains triglycerides and cholesterol from your food but also made in the body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next with that, I know that VLDL brings triglycerides to the adipose tissue (or fat tissue) and to the muscles with help of the LPL (lipoproteïnlipase) just as chylomicrons do. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Enclosed; VLDL will go over to IDL (intermediate density lipoproteïn).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what is the definition then from IDL exactly?&#xA;Is IDL just a smaller lipoproteïn then VLDL and does it only contains a sort of 'leftover' of the triglycerides? Or does it also contains cholesterol?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if VLDL brings the triglycerides to the muscles and fat tissue, does it only contains triglycerides then? Or does it also carry cholesterol with it? If yes, what happens with the cholesterol then? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because my book is only telling me about the transport of triglycerides to the fat tissue and muscles, but in the beginning it also says that it carry's cholesterol, and a little further in my book it even tells it can also carry cholesterolesters from HDL...&#xA;It's getting confusing... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope somebody can tell me what is exactly in all the kinds of lipoproteïns, where the lipoproteïns are all made, and where the products they carry come from, and where they go to. Because my book is being very indistinct.&lt;/p&gt;&#xA;" OwnerUserId="6812" LastActivityDate="2014-05-26T17:16:58.673" Title="What is inside IDL (intermediate density lipoproteïn)?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;liver&gt;&lt;lipids&gt;&lt;fat-metabolism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17620" PostTypeId="2" ParentId="17591" CreationDate="2014-05-24T12:19:08.157" Score="0" Body="&lt;p&gt;The Basal Membrane is regenerated by a different layer of cells.&#xA;Not replaced by the skin layer below&#xA;if your epidermis and squamous was shed and the skin below would replace it that layer would soon shed and after a while your skin would have been shed down to your muscle!&#xA;If you want to do a small experiment to see what happens to your epidermis when it is broken try biting the skin of the end of your fingers,&#xA;Then see what happends. &lt;/p&gt;&#xA;" OwnerUserId="6830" LastActivityDate="2014-05-24T12:19:08.157" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17621" PostTypeId="2" ParentId="7457" CreationDate="2014-05-24T19:37:09.290" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Burl&quot; rel=&quot;nofollow&quot;&gt;Burls/Burrs&lt;/a&gt; are often defined as tree tumours, and as analogous to cancer in animals. There seems to be numerous reasons why burls are formed (more research is needed on the topic), which include wounds, insects, fungi, DNA changes, environmental stress and viruses. However, burls are localized and often relatively benign, and since plant cells do not move around they cannot metastasize (see e.g. &lt;a href=&quot;http://www.nytimes.com/2013/07/16/science/can-plants-get-cancer.html?_r=0&quot; rel=&quot;nofollow&quot; title=&quot;Ray. 'Can Plants Get Cancer?'. New York Times. July 15, 2013&quot;&gt;&quot;Can Plants Get Cancer?&quot;&lt;/a&gt; from the &lt;em&gt;New York Times&lt;/em&gt;). Since burls have multipe causes the 'Cancer/tumour' label might not fit very well to all types of burls, and in some cases normal shoots can sprout from burls that have been removed from the tree (indicating that the burl was not caused by damaged DNA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Galls are related tumorous growths that are usually caused by parasites (insects, virus, bacteria, fungi), and are often induced by plant hormones (at least from insects/mites, see &lt;a href=&quot;http://www.ext.colostate.edu/pubs/insect/05557.html&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Insect and mite galls&lt;/em&gt;&lt;/a&gt;). However, in the case of crown gall caused by the bacteria &lt;a href=&quot;http://en.wikipedia.org/wiki/Agrobacterium&quot; rel=&quot;nofollow&quot;&gt;Agrobacterium tumifaciens&lt;/a&gt; the tumorous growth is due to a DNA transfer, which will permanently modify the infected cells (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC299031/&quot; rel=&quot;nofollow&quot; title=&quot;Gheysen et al. 1987. Integration of Agrobacterium tumefaciens transfer DNA (T-DNA) involves rearrangements of target plant DNA sequences. PNAS 84(17): 6169–6173&quot;&gt;Gheysen et al 1987&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, the answer to your question depends on if you are interested in tumorous growths in general (where many types of burls and galls should qualify) or cancer in particular (if defined as unregulated cell growth caused by permanent DNA damage).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2014-05-24T19:37:09.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17622" PostTypeId="2" ParentId="7457" CreationDate="2014-05-24T22:22:24.717" Score="0" Body="&lt;p&gt;Could not fit in a comment. The following is purely intuitive, I have not much knowledge in this field and no reference. I am just guessing and I'd welcome some corrections. I was thinking about three points which effect opposite each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) In plants, there are no cells specialized in transporting stuff throughout the body (I think!) while there are many cells that travels a lot in animals. Therefore, I0d guess that plants cancer are much more likely to only remain localized while animal cancer are more likely to create &lt;a href=&quot;http://en.wikipedia.org/wiki/Metastasis&quot; rel=&quot;nofollow&quot;&gt;metastasis&lt;/a&gt;. As a consequence, I'd expect that cancer would be more lethal in animals than plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The number of mitosis occurring in the lifetime of an individual is probably positively correlated with the occurrence of cancers. Because plants tend to be bigger than animals, I would expect more mitosis in plants and therefore, I would expect that cancer are more common in plants than in animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) According to life history theory, the intensity of selection on a gene decreases as the ratio of the fitness pre- and post- expression of the gene. Because plants never really age and stop reproducing, I would expect that selection against cancer would be stronger in plants than in animals resulting in a less cancer in plants than in animals.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-05-24T22:22:24.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17623" PostTypeId="1" AcceptedAnswerId="17669" CreationDate="2014-05-25T00:36:42.330" Score="0" ViewCount="94" Body="&lt;p&gt;I understand that there are several reserves available to muscle that can be tapped for ATP, and that each reserve is being used to some degree at all times.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these reaction rates purely due to the presence of reactants which are products of myocyte activity?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or are there other controlling reactants involved that determine the rate at which each reserve is consumed?&lt;/p&gt;&#xA;" OwnerUserId="2999" LastActivityDate="2014-05-26T17:43:43.270" Title="Feedback affecting myocyte metabolism in humans" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17624" PostTypeId="1" AcceptedAnswerId="17625" CreationDate="2014-05-25T01:00:31.123" Score="1" ViewCount="4269" Body="&lt;p&gt;I'm looking specifically for examples and comparisons, because the definitions of inverted and everted are remarkably similar; e.g. from Dictionary.com/Reference.com:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;everted&lt;br&gt;&#xA;  verb (used with object) &#xA;  to turn outward or inside out.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dictionary.reference.com/browse/everted&quot; rel=&quot;nofollow&quot;&gt;http://dictionary.reference.com/browse/everted&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;vs. (esp. #5)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;inverted&#xA;  verb (used with object)&#xA;  1. to turn upside down.&#xA;  2. to reverse in position, order, direction, or relationship.&#xA;  3. to turn or change to the opposite or contrary, as in nature, bearing, or effect: to invert a process.&#xA;  4. to turn inward or back upon itself.&#xA;  &lt;strong&gt;5. to turn inside out.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dictionary.reference.com/browse/inverted&quot; rel=&quot;nofollow&quot;&gt;http://dictionary.reference.com/browse/inverted&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm curious because of this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Structurally, the cephalopod eye differs from the vertebrate eye.&#xA;  Cephalopods do not have a cornea, and the retina is &lt;strong&gt;everted&lt;/strong&gt; so that&#xA;  the distal end of photoreceptive cells lies directly behind the lens&#xA;  and points toward incoming light. As a result, photoreceptor cells&#xA;  connect to the optic nerve behind the retina (Packard 1972).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From: Evolution: Education and Outreach&#xA;October 2008, Volume 1, Issue 4, pp 439-447&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs12052-008-0084-1&quot; rel=&quot;nofollow&quot;&gt;http://link.springer.com/article/10.1007%2Fs12052-008-0084-1&lt;/a&gt;&#xA;&lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs12052-008-0084-1/fulltext.html&quot; rel=&quot;nofollow&quot;&gt;http://link.springer.com/article/10.1007%2Fs12052-008-0084-1/fulltext.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;via&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Cephalopod#cite_note-Serb2008-12&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Cephalopod#cite_note-Serb2008-12&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;If you have the rep please tag this with cephalopod; the tag doesn't exist and I don't have enough rep to create it. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="6833" LastActivityDate="2014-05-25T01:38:45.453" Title="What the difference between an inverted and everted retina?" Tags="&lt;definitions&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17625" PostTypeId="2" ParentId="17624" CreationDate="2014-05-25T01:38:45.453" Score="2" Body="&lt;p&gt;Based on your title and description, all that means is that in vertebrates the retina is inverted in a sense that light sensing cells sit at the back of the retina meaning light has to pass through layers of neurons and capillaries before reaching light sensing cells, whereas cephalopod has the photoreceptors at the front side of the retina, with processing neurons and capillaries behind them hence retina is everted i.e. inside out. See this page (&lt;a href=&quot;http://en.wikipedia.org/wiki/Retina&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Retina&lt;/a&gt;) under &quot;In other animals&quot; section.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-25T01:38:45.453" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17626" PostTypeId="2" ParentId="16287" CreationDate="2014-05-25T04:03:17.103" Score="1" Body="&lt;p&gt;Prokaryotes have very high reproductive rate. So, they develop mutants far more faster than multicellular eukaryotes.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-05-25T04:03:17.103" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17627" PostTypeId="1" CreationDate="2014-05-25T04:11:09.543" Score="3" ViewCount="303" Body="&lt;p&gt;I am confused about the prerequisites for cell division and cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which of the following is necessary for the cell cycle to progress?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Hormones&lt;/li&gt;&#xA;&lt;li&gt;Growth factor  &lt;/li&gt;&#xA;&lt;li&gt;Cyclins  &lt;/li&gt;&#xA;&lt;li&gt;Cyclin dependent kinases &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Which of the following is essential for cancer proliferation?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Growth factors&lt;/li&gt;&#xA;&lt;li&gt;Signalling molecules&lt;/li&gt;&#xA;&lt;li&gt;DNA replication &lt;/li&gt;&#xA;&lt;li&gt;A control mechanism&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;How do the cell cycle and cancer relate to each other?&lt;/p&gt;&#xA;" OwnerUserId="6834" LastEditorUserId="540" LastEditDate="2014-05-25T23:32:02.020" LastActivityDate="2014-05-25T23:32:02.020" Title="Cancer growth and cell division" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;cancer&gt;&lt;cell&gt;" AnswerCount="2" CommentCount="10" ClosedDate="2014-05-26T03:31:30.887" ContentLicense="CC BY-SA 3.0" />
  <row Id="17628" PostTypeId="2" ParentId="17627" CreationDate="2014-05-25T05:23:48.013" Score="3" Body="&lt;p&gt;Cyclin dependent kinase is the answer for the first question. Cyclin concentration increases during m phase and falls in g1 s and g2 phase as it is degraded. Cdk is always present in the cell but gets activated during m phase, when cyclin is present. (cyclin dependent)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cancer cells do not require growth factors to stimulate cell division. They have mutations which disrupts the normal cell cycle regulation. Now can you think what should be the answer ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-05-25T05:23:48.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17629" PostTypeId="1" AcceptedAnswerId="17793" CreationDate="2014-05-25T06:28:58.110" Score="11" ViewCount="7391" Body="&lt;p&gt;For maggot therapy, how are maggots disinfected? I'd imagine there's a limited scope of measurements that can be taken to sterilize the maggots - i.e. we don't want to sterilize them and kill them too. &lt;/p&gt;&#xA;" OwnerUserId="6759" LastActivityDate="2015-11-06T08:34:35.090" Title="How are Maggots Sterilized (Disinfected)?" Tags="&lt;medicine&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17630" PostTypeId="1" AcceptedAnswerId="17646" CreationDate="2014-05-25T07:04:22.130" Score="1" ViewCount="184" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iXkAE.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A and B are 2 reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is an excess availability of citrate, then which of the above reactions will prevail?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that citric acid is formed when oxaloacetic acid reacts with acetyl coA. But how does concentration of citric acid influence the above reactions&lt;/p&gt;&#xA;" OwnerUserId="6390" LastEditorUserId="3776" LastEditDate="2014-05-25T13:45:50.053" LastActivityDate="2014-05-26T18:43:58.997" Title="Relation between respiration and concentration of citric acid" Tags="&lt;respiration&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17631" PostTypeId="1" AcceptedAnswerId="28251" CreationDate="2014-05-25T07:28:14.007" Score="25" ViewCount="2856" Body="&lt;p&gt;I have been wondering why would insects in general, not be scared when important changes happen on your monitor where they have landed...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you move even just a finger, they are &lt;em&gt;scared to death&lt;/em&gt; and fly away, but anything on my monitor and they remain completely placid.&lt;/p&gt;&#xA;" OwnerUserId="6835" LastEditorUserId="6835" LastEditDate="2016-08-13T02:42:40.317" LastActivityDate="2016-08-13T04:27:28.970" Title="Why are flies not scared when landing on a monitor with changing graphics?" Tags="&lt;zoology&gt;&lt;ecology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17633" PostTypeId="1" CreationDate="2014-05-25T10:52:59.063" Score="2" ViewCount="151" Body="&lt;p&gt;Catabolite Activator/Repressor, Cra protein (formerly known as Fructure Repressor FruR) plays a significant role in central carbon metabolism of E coli. Its activity is inhibited by fructose-1,6-bisphosphate (FBP); Cra up-regulate gluconeogeneis pathways and down-regulate glycolysis and carbon-uptake pathways. I found enough literature on how Cra plays a regulatory role in metabolism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I am unable to find out explanation of one experimental observation: with increase in glucose uptake rate the transcript level of cra decreases. What is the mechanism for this. Further, are Cra proteins degraded as the glucose uptake rate increase, if so what is the regulatory mechanism?&lt;/p&gt;&#xA;" OwnerUserId="1800" LastActivityDate="2014-05-25T10:52:59.063" Title="Regulation of Cra protein level in E coli" Tags="&lt;microbiology&gt;&lt;metabolism&gt;&lt;ecoli&gt;&lt;gene-regulation&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17634" PostTypeId="1" AcceptedAnswerId="17683" CreationDate="2014-05-25T12:37:29.740" Score="1" ViewCount="638" Body="&lt;p&gt;Why can fish breathe under water but land mammals can't? How can fish extract oxygen straight from water but humans can't?&lt;/p&gt;&#xA;" OwnerUserId="6836" LastActivityDate="2014-05-27T08:44:03.237" Title="Breathing under water" Tags="&lt;respiration&gt;&lt;ichthyology&gt;&lt;breathing&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17635" PostTypeId="1" AcceptedAnswerId="26177" CreationDate="2014-05-25T13:48:57.463" Score="2" ViewCount="338" Body="&lt;p&gt;In the movie- &lt;em&gt;Saw&lt;/em&gt;, for the last trap Bobby was told to insert metallic hooks into his &lt;a href=&quot;https://en.wikipedia.org/wiki/Pectoralis_major_muscle&quot; rel=&quot;nofollow&quot;&gt;pectoralis major muscle&lt;/a&gt;. In his fake story Bobby has raised himself successfully, but when he was &quot;really&quot; trapped, his muscles were broken under his own weight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it true, that muscles can be broken so easy? When human is pulling up on the bar, aren't these muscles undergo much more tension, because of lever effect made by his arms?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, what if Bobby insert hooks under his ribs, would he die immediately due to &lt;a href=&quot;https://en.wikipedia.org/wiki/Pneumothorax&quot; rel=&quot;nofollow&quot;&gt;pneumothorax&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is biological, no interest of how it was possible to overcome trap with mechanical means. &lt;/p&gt;&#xA;" OwnerUserId="5720" LastEditorUserId="3340" LastEditDate="2014-12-25T13:00:40.770" LastActivityDate="2015-06-01T15:54:49.483" Title="How much mechanical stress can a skeletal muscle bear?" Tags="&lt;muscles&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17636" PostTypeId="2" ParentId="16621" CreationDate="2014-05-25T14:07:15.007" Score="3" Body="&lt;p&gt;I'm no expert in computational biology but I am very much interested and do some big data analysis using R for my own projects so I will try to provide some information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK25461/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK25461/&lt;/a&gt;) is an excellent book talking about all the grand challenges in computational biology and the emerging fields so I definitely recommend looking through at least the list on the page, if you don't want to read the entire book. To me all this points to the fact that we are in the big data era, where we have masses of data but making sense of them all and putting them into prospective and analysing them in a way to show us new insights into problems is difficult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might also be interested in BOINC, which runs a few computationally challenging projects through crowd sourcing/grid computing (&lt;a href=&quot;http://boinc.berkeley.edu/projects.php&quot; rel=&quot;nofollow&quot;&gt;http://boinc.berkeley.edu/projects.php&lt;/a&gt;). In more theoretical aspects, here is a list of unsolved problems (&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_unsolved_problems_in_mathematics&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/List_of_unsolved_problems_in_mathematics&lt;/a&gt;), solving of which will excel our understanding of many modelling problems, which percolate in biological problems as well although I'm not at all an expert in biological systems modelling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-05-25T19:45:04.213" LastActivityDate="2014-05-25T19:45:04.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17639" PostTypeId="1" AcceptedAnswerId="17645" CreationDate="2014-05-25T16:50:31.080" Score="9" ViewCount="2417" Body="&lt;p&gt;There's this fascinating &quot;kitchen experiment&quot;. Take a &quot;brick&quot; of baker's yeast (not dry yeast), and a couple teaspoons of sugar, put them together in a cup and stir together. There's no doubt both are solids: yeast is a firm block, you must use quite a bit of force initially to crush it and even then it should remain a rather thick paste. The sugar is crystals, nothing tricky about that. And then, within a minute or so of stirring, your cup contains only liquid - not entirely fluid like water, but not much thicker than cream. Solid+Solid -&gt; Liquid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What process leads to that? What happens with the baking yeast when it comes in contact with sugar, that it turns from solid to liquid, and releasing enough water to dissolve the sugar?&lt;/p&gt;&#xA;" OwnerUserId="6512" LastEditorUserId="5006" LastEditDate="2014-05-29T05:42:03.780" LastActivityDate="2014-08-27T15:37:16.020" Title="How does yeast dissolve in sugar?" Tags="&lt;mycology&gt;&lt;yeast&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17640" PostTypeId="1" CreationDate="2014-05-25T17:03:25.297" Score="0" ViewCount="3171" Body="&lt;p&gt;OK so I'm a bit confused. Does a chromosome consist of genes and do genes consist of DNA? What about the 23 pairs in sexual reproduction? I can't remember what the pairs consist of  &lt;/p&gt;&#xA;" OwnerUserId="6838" LastEditorUserId="86" LastEditDate="2014-05-26T20:32:57.987" LastActivityDate="2014-05-26T20:32:57.987" Title="Genes, chromosomes, base pairs and the 23 pairs" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17642" PostTypeId="1" CreationDate="2014-05-25T18:22:54.830" Score="1" ViewCount="111" Body="&lt;p&gt;Sometimes I'd come across a Lychee or a Naseberry whose seeds are kinda disintegrated.. in a thick powdered form, either completely or partially. What could cause such a thing? And is the fruit with such seed harmful?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wish I had pics to show but it happens rarely. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a normal Lychee with normal seed: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://t3.gstatic.com/images?q=tbn:ANd9GcRHJvK7cp6eFnH3iAuj8hsvzb8rUIFvX6THTefLm59kYnwmAFdd7Q&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And what I sometimes find in place of the solid black seed is something that has the texture like this wet dirt:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://t2.gstatic.com/images?q=tbn:ANd9GcTzmvo4ghmS8DeUSU95H6qJ4pGUExJ5x5C-mwjvmD8VupGDPqhFjQ&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;but obviously more like the seed itself that has disintegrated into a thick wet powder. &lt;/p&gt;&#xA;" OwnerUserId="3141" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.130" LastActivityDate="2014-05-25T22:39:36.583" Title="Why do some fruits have their seeds disintegrated" Tags="&lt;fruit&gt;&lt;seeds&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17643" PostTypeId="2" ParentId="17640" CreationDate="2014-05-25T18:38:31.633" Score="4" Body="&lt;p&gt;I will start from the small and go to the big organisational unit: &#xA;All of this is constructed by &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA&lt;/a&gt;, the sequence of the four bases: adenosine, thymidine, cytidine and guanosine.  They are abbreviated G, A, T and C and are called the letters of DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Gene&quot; rel=&quot;nofollow noreferrer&quot;&gt;Genes&lt;/a&gt; are organisational units formed by a specific sequence of the four &quot;letters&quot;. Genes encode for all the proteins (in fact this is a simple view, but should be enough for the moment) and are the way the information of how the protein sequence looks is conserved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All DNA is organised in the form of a long string of bases, which would be very long in higher organisms. To come around this problem, the DNA is organised in &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosome&quot; rel=&quot;nofollow noreferrer&quot;&gt;chromosomes&lt;/a&gt;, in which the DNA is wound around special proteins (the histones) and further wound up to get a compact form.  The image below (from &lt;a href=&quot;http://elcaminogmi.dnadirect.com/grc/patient-site/array-cgh-for-developmental-abnormalities/index.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;) shows the relationship:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kUMGe.gif&quot; alt=&quot;chromosome-dna-relationship&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The 23 chromosome pairs are the 23 organisational units in humans, in which our genetic information is stored and organised.  A picture of them looks like this (image from the same website as above):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EuF4W.jpg&quot; alt=&quot;chromosomes&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please note that the chromosomes are not X-shaped, although they might look like on the image. They are pairs of long DNA molecules, which are not connected.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-05-26T06:38:31.263" LastActivityDate="2014-05-26T06:38:31.263" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17644" PostTypeId="2" ParentId="16287" CreationDate="2014-05-25T18:41:53.483" Score="1" Body="&lt;p&gt;Your question doesn't make a lot of sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutation is the process whereby new alleles are created, by the DNA chemically changing its sequence.  Natural selection is the process where in a population, alleles change frequency over time due to differing survival rates.  (And there are lots of other kinds of selection, and allele frequencies can change just due to chance, too)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I don't think &quot;evolution by mutation alone&quot; makes much sense.  In sexually reproducing eukaryotes, variety can be created by mixing and matching different alleles in the population in different combinations, which isn't something that prokaryotes really do, so I guess that's a difference in the importance of mutations between sexually reproducing eukaryotes and prokaryotes.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-05-25T18:41:53.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17645" PostTypeId="2" ParentId="17639" CreationDate="2014-05-25T19:05:48.163" Score="16" Body="&lt;p&gt;The whole process is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Osmosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;osmosis&lt;/a&gt;. In it there is the flow of liquid along a concentration gradient. Water then flows from the side which contains the low concentration of dissolved molecules (this can be salts or sugar for example) to the side with the higher concentration until it reached equilibrium. This principle is shown in the image below (all images from the Wikipeadia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Osmosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;osmosis&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/S9abq.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The blue dots are the dissolved material, the concentration is high on the right side and lower on the left. Through the dotted line in the middle (which is a semi-permeable membrane) only the solvent can pass to reach a concentration equilibrium. There is a pretty cool osmotic pressure simulator available on &lt;a href=&quot;http://molo.concord.org/database/activities/72.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Molecular Logic&lt;/a&gt; which can also help understanding the principle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And this is exactly what happens to the yeast cells. The sugar crystalls get dissolved (at least partly) by some of the humidity from the yeast block (this will not work with dried yeast) and form a highly concentrated sugar solution (also called hypertonic). The sugar concentration inside the cells is relatively low (called hypotonic). This leads to the effort to balance the concentration inside the cell and outside of it which then leads to a massive efflux of water from the cells. This goes so far, that the cell membranes break and the interior of the cells is released (nucleus, DNA, proteins and so on) and the sugar is completely dissolved in the released water. The reason why this mixture is so &quot;gooey&quot; afterwards is the DNA, which forms long, thick strains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gv3Y7.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This method can be used in the lab to break up cells relatively gently without applying too much force.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When baking you should make sure, that your yeast is not coming directly into contact with undissolved sugar (or salt which works the same way), as this will kill a part of your yeast cells. However, for baking you usually dissolve the yeast in water or milk, so there is a huge excess of water which dissolves the sugar (or salt) and protects the cells. Addionally your yeast is much better distributed in the dough and gives better results.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-08-27T15:37:16.020" LastActivityDate="2014-08-27T15:37:16.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17646" PostTypeId="2" ParentId="17630" CreationDate="2014-05-25T19:25:25.107" Score="2" Body="&lt;p&gt;This image is a bit misleading since both ways seem to be the reversion of each other, but in fact they are not (although the same metabolites are used).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reaction A takes only place in &lt;a href=&quot;http://en.wikipedia.org/wiki/Gluconeogenesis&quot; rel=&quot;nofollow&quot;&gt;gluconeogenesis&lt;/a&gt; which makes glucose from other metabolites (coming from the metabolism of fatty acids for example) and this pathway is only active when there is an abundance of energy present in the cell. Citrate activates the Fructose-1,6-bisphosphatase. The gluconeogenesis takes only place in liver and kidney. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reaction B takes place in &lt;a href=&quot;http://en.wikipedia.org/wiki/Glycolysis&quot; rel=&quot;nofollow&quot;&gt;glycolysis&lt;/a&gt; and is the rate limiting for the whole pathway. It takes place when glucose is taken up and then used for the production of energy. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphofructokinase_1&quot; rel=&quot;nofollow&quot;&gt;Phosphofructokinase&lt;/a&gt; (PFK) is inhibited by signals of excess energy as ATP (which is an allosteric inhibitor of PFK) as well as citrate and NADH/H+. While citrate is a weak allosteric inhibitor on its own, it acts as a strong inhibitor together with ATP. This makes sense since both molecules are indicators of free energy metabolites in the cell.&#xA;See these two publications for details: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6228716&quot; rel=&quot;nofollow&quot;&gt;&quot;Allosteric regulatory properties of muscle phosphofructokinase.&quot;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1164964/&quot; rel=&quot;nofollow&quot;&gt;Effect of citrate on the activities of 6-phosphofructokinase from&#xA;nervous and muscle tissues from different animals and its&#xA;relationships to the regulation of glycolysis.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If there is an excess of AMP/ADP then the enzyme is activated and phosphorylates Fructose-1-phosphate. &lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-05-26T18:43:58.997" LastActivityDate="2014-05-26T18:43:58.997" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17647" PostTypeId="1" AcceptedAnswerId="17648" CreationDate="2014-05-25T20:02:12.053" Score="2" ViewCount="1669" Body="&lt;p&gt;Why this process called &quot;auto&quot;?&#xA;Is it because each tyrosine kinase receptor subunit of the RTK dimer has the ability to phosphorylate tyrosine or other amino acid residue present in other subunit of the RTK dimer's cytoplasmic tail? Is it because no new set of kinase enzyme is needed to phosphorylate them?&lt;/p&gt;&#xA;" OwnerUserId="6524" LastEditorUserId="16866" LastEditDate="2020-04-15T13:10:29.523" LastActivityDate="2020-04-15T13:10:29.523" Title="Meaning of &quot;auto&quot; in trans autophosphorylation?" Tags="&lt;terminology&gt;&lt;cell-signaling&gt;&lt;etymology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17648" PostTypeId="2" ParentId="17647" CreationDate="2014-05-25T20:14:03.467" Score="6" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Receptor_tyrosine_kinase&quot; rel=&quot;nofollow noreferrer&quot;&gt;Receptor tyrosine kinases&lt;/a&gt; are proteins which float around in the cellular membrane. Upon binding of their ligand, the dimerize (two units form a dimer). This releases the kinase domains and the proteins start phosphorylating themselves over cross (meaning part a phosphylates part b and vice versa). This looks like in this figure below (from &lt;a href=&quot;http://johanneswilbertz.com/2010/09/24/the-most-important-class-of-enzyme-linked-cell-surface-receptors-receptor-tyrosine-kinases/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;, it is an interesting article):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iHRjm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides ATP this process needs no further co-factors so the &quot;auto&quot; refers to the ability of the RTK to phosphorylate itself upon activation. See more about &lt;a href=&quot;http://en.wikipedia.org/wiki/Autophosphorylation&quot; rel=&quot;nofollow noreferrer&quot;&gt;autophosphorylation&lt;/a&gt; here.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-25T20:14:03.467" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17650" PostTypeId="1" AcceptedAnswerId="17662" CreationDate="2014-05-25T21:07:05.127" Score="3" ViewCount="2009" Body="&lt;p&gt;Standard recipes for yeast medium often include &quot;bacto-peptone&quot;. Is this the same as bacteriological peptone? Is there an authoritative source that spells it out?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-05-26T13:26:23.407" Title="What is &quot;bacto&quot; peptone?" Tags="&lt;molecular-biology&gt;&lt;microbiology&gt;&lt;terminology&gt;&lt;protocol&gt;&lt;growth-media&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17651" PostTypeId="2" ParentId="17627" CreationDate="2014-05-25T21:32:54.780" Score="3" Body="&lt;p&gt;There is a wide continuum from &quot;cancer&quot; in the sense of uncontrolled cell division (this could include even things like 2-3 extra cells making an imperceptible, microscopic bulge in your colon) to cancer in the sense of huge lumps of meat growing on your body and killing you painfully within X months. For the latter kind, many &quot;stages&quot; of &quot;evolution&quot; must be completed by &quot;the cancer&quot; (forgive the excessive quotes, but the terminology is a bit nuanced here). For a better idea of the nature of cancer, you could start by reading &lt;a href=&quot;https://en.wikipedia.org/wiki/The_Hallmarks_of_Cancer&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;The Hallmarks of Cancer&lt;/em&gt;&lt;/a&gt; (and reading about it).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Which of the following is always present in the cell cycle?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are eukaryotic cells like yeast which can be cultured in a medium containing only nutrients. Because these are unicellular organisms, there's no reason to expect that they have any growth factors or hormones or extrinsic signal like that (there's a caveat that often even unicellular organism can signal each other, but I believe there are also many that don't). All eukaryotic cells that divide have a cell cycle, so these cells also have it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, hormones and growth factors cannot be required for the cell cycle. Cyclins and Cdks are a fundamental part of virtually any cell cycle ever seen by science, so you could say they are necessary (though I think it is conceivable that an organism could exist which progresses its cell cycle using proteins completely divergent from known cyclins and Cdks, but then again).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Which of the following is essential in cancer growth and division? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Without DNA replication, you obviously cannot make more cells, so that is necessary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are cancer kinds which are dependent on growth factors (perhaps they make their own growth factor) but there are also cancer which simply jam the receptor active, so that they can grow even without the factor. This is discussed in &lt;em&gt;The Hallmarks of Cancer&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Signalling molecules (assuming that extracellular signaling is meant, because if you start taking away signalling molecules &lt;em&gt;inside the cell&lt;/em&gt; like IP3, obviously you can break the cell to the point it won't divide) is just a superset of growth factors; same arguments apply because growth factors &lt;em&gt;are&lt;/em&gt; the most potent &quot;signalling molecules&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Control mechanism is also &quot;obviously unnecessary&quot; and &quot;obviously necessary&quot;. Cancer is uncontrolled division, so if there was control, the cancer wouldn't be there in the first place, duh. But obviously cancer cells also control their own division to some extent - they still have a coherent cell cycle and so on.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Ultimately, the key to understanding cancer is being cognizant of &quot;perspectives&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The body&quot; (actually the wild-type genome) has a certain plan in mind for what each cell should do, and to that end, it has programmed the cells here to divide so many times in so and so fashion and the cells there to not divide unless this event happens and so forth. If those cells are mutated, and that programming is disrupted, they may divide in ways the body &quot;does not want&quot; (ie. they create tissue which has not been evolutionary selected for over previous generations), so from the body's point of view the cancer is indeed out of control.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, the cancer is almost like its own separate organism - for one, it certainly has a different DNA than you, as it has mutated. It undergoes Darwinian evolution and becomes gradually more adept at surviving and spreading inside your body. So from the cancer's point of view, the cancer cells are indeed quite well-controlled, with the goal of that control being to divide as much as possible.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-05-25T21:32:54.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17654" PostTypeId="2" ParentId="17591" CreationDate="2014-05-25T22:57:05.757" Score="4" Body="&lt;p&gt;The epidermis is a four- or five-layered epithelium. The top layers are squamous whereas the bottom ones are more columnar (&lt;a href=&quot;http://en.wikipedia.org/wiki/Epidermis_(skin)&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Epidermis_(skin)&lt;/a&gt;). The lowest layer is separated from the dermis by the basal membrane (a.k.a. basal lamina, basement membrane).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The process of wound healing in skin is extremely complex and obviously depends on the individual wound and how many layers are destroyed. There is a lot of detail on Wikipedia: &lt;a href=&quot;http://en.wikipedia.org/wiki/Wound_healing&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Wound_healing&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the basement membrane is not disrupted, there are two main components as a rule of thumb: 1) outwards-inwards migration, i.e. cells surrounding a wound will migrate into the wound. 2) bottom-upwards differentiation, i.e. the bottom-most layer contains replicating cells which will differentiate and squamify to regenerate upper layers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something like this (picture modified from Wikipedia): &lt;img src=&quot;https://i.stack.imgur.com/Xvd2W.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the wound is bleeding, this means the basement membrane is disrupted and the dermis underneath is also wounded (the epidermis itself contains no blood vessels). In this case, the dermis needs to regenerate first, in a process which is probably similar as described above. Simultaneously, the bottom-most epidermal cell layer will proliferate to close the gap, and then deposit new basement membrane. Remember that the basement membrane is a mesh of proteins, not an actual cell layer.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2014-05-26T12:17:47.320" LastActivityDate="2014-05-26T12:17:47.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17655" PostTypeId="2" ParentId="17591" CreationDate="2014-05-26T00:48:19.277" Score="3" Body="&lt;p&gt;It would first be good to look at the &lt;a href=&quot;http://www.webmd.com/skin-problems-and-treatments/picture-of-the-skin&quot; rel=&quot;nofollow noreferrer&quot;&gt;different layers within the skin &lt;/a&gt; as you mentioned in your question.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The skin is made up of:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Epidermis: the outermost layer of skin, provides a waterproof barrier and creates our skin tone&lt;/li&gt;&#xA;  &lt;li&gt;Dermis: beneath the epidermis, contains tough connective tissue, hair follicles, and sweat glands&lt;/li&gt;&#xA;  &lt;li&gt;Hypodermis: deeper subcutaneous tissue is made of fat and connective tissue&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WUs0I.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Different kinds of damage can occur to the skin, including &lt;strong&gt;burns&lt;/strong&gt;, which have different degrees based on what layer of skin is damaged and how far down the burn goes.  Therefore, it is &lt;a href=&quot;https://umm.edu/health/medical/altmed/condition/burns&quot; rel=&quot;nofollow noreferrer&quot;&gt;not as simple as&lt;/a&gt; the epidermis itself getting burned, it could also be much worse and the healing process may be hindered if too much damage occurs.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Burns can happen when the skin is exposed to heat (from fire or hot liquids), electricity, corrosive chemicals, or radiation (UV rays from the sun or tanning beds, or radiation treatments). &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Burns are classified as follows, according to the severity of tissue damage:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;First degree burns: affect only the outer layer of the skin (epidermis), causing pain and redness. The prototype is mild sunburn&lt;/li&gt;&#xA;  &lt;li&gt;Second degree burns: extend to the second layer of the skin (the dermis), causing pain, redness, and blisters that may ooze; deep second degree burns may progress to third degree burns over the course of several days&lt;/li&gt;&#xA;  &lt;li&gt;Third degree burns: involve both layers of the skin and may also damage the underlying bones, muscles, and tendons; the burn site appears pale, charred, or leathery; there is generally no pain in the area because the nerve endings are destroyed.&lt;/li&gt;&#xA;  &lt;li&gt;Fourth degree burns: extend through the skin and subcutaneous fat into the underlying muscle and bone; are stiff and charred&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Depending on the type of burn, different skin generation occurs.  If it is a really terrible burn, then a &lt;strong&gt;skin graft&lt;/strong&gt; from another area of the body may be needed, as it &lt;a href=&quot;http://faculty.stcc.edu/AandP/AP/AP1pages/Units1to4/skin/repairof.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;cannot regenerate the epidermis layer&lt;/a&gt; due to the excessive damage.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;First degree burns are the easiest from which to recover [...] the dermis remains intact and can support the regeneration of the epidermis.  It may happen that the skin will get inflamed (due to responses in the underlying dermis) during this time; the inflammation is to encourage clean-up cells (macrophages) and nutrients to reach the damaged area.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It appears as though the dermis itself will help with the regeneration of the epidermal cells.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In a second degree burn, the dermis is also affected, at least partially.   But, with a second-degree burn, most (or at least some) skin accessory organs typically remain in tact.  Remember, these accessory organs (like glands and hairs) are built from invaginations of the epidermis, creating the epithelium of the glands or hair follicles.  If these organs survive the burn, the epithelial cells that remain will begin to divide to regenerate a new epidermis.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Third-degree burns are the worst.  In these, even the accessory organs are destroyed.  How can we recover from this?  Skin grafts are about the best way, but they cannot really be done across one's entire body, so a very widespread third-degree burn is not usually something that a person can recover from.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;AND&lt;/strong&gt; although this is a separate question and topic, the basal membrane is thought to be of epithelial origin, but this is very complex and still not completely known.  There is more information about it in &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/aja.1001970404/pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt;; &lt;em&gt;Cellular origin of the dermal-epidermal basement membrane&lt;/em&gt; (Marinkovich et al. 1993).  It is a dated article but has some interesting information.&lt;/p&gt;&#xA;" OwnerUserId="6380" LastActivityDate="2014-05-26T00:48:19.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17656" PostTypeId="1" CreationDate="2014-05-26T04:20:09.200" Score="-2" ViewCount="2001" Body="&lt;p&gt;&lt;strong&gt;I do not understand why individuals with type O- blood are often called universal donors and those with type AB+ blood are called universal recipients.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My thoughts on this are:&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;It should be that because O+ blood has all antibodies but no antigens that all other blood types including O- would be incompatible making O not a universal donor - so &lt;strong&gt;why is O the universal donor?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also if O is the universal donor, it should be O+ that is the universal donor and O- that isn't because Rh+ is compatible with Rh+ and Rh-, not just Rh+ or Rh-.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It should also be that because AB- has all antigens and no antibodies that AB is not the universal recipient - so &lt;strong&gt;why is AB the universal recipient?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is what I would expect from blood group mixtures:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;O-A: A clumping in O&lt;/p&gt;&#xA;&#xA;&lt;p&gt;O-B: B clumping in O&lt;/p&gt;&#xA;&#xA;&lt;p&gt;O-AB: AB clumping in O&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and that being true for the reverse order as well&#xA;AB-A: AB clumping in A&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AB-B: AB clumping in B&lt;/p&gt;&#xA;&#xA;&lt;p&gt;as well as the one that everybody knows which is A-B: A clumping in B and B clumping in A&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would also expect for Rh compatibility:&#xA;Rh- with Rh+: Rh- clumping in Rh+&lt;/p&gt;&#xA;" OwnerUserId="5851" LastEditorUserId="20271" LastEditDate="2019-04-24T18:22:47.110" LastActivityDate="2019-04-24T18:22:47.110" Title="Blood groups - why is O the universal donor and AB the universal recipient?" Tags="&lt;hematology&gt;&lt;red-blood-cell&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ClosedDate="2014-05-26T13:24:43.643" ContentLicense="CC BY-SA 4.0" />
  <row Id="17657" PostTypeId="1" CreationDate="2014-05-25T22:37:56.580" Score="5" ViewCount="33621" Body="&lt;p&gt;In Fullmetal Alchemist when Ed goes to disprove to Rose the Sun God's &quot;miracle&quot; to bring humans back to life by proving that science (in the form of Alchemy) can create people by saying&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Water (35 L), Carbon (20 kg), Ammonia (4 L), Lime (1.5 kg), Phosphorous (800 g), Salt (250 g), Saltpeter (100 g), Sulfur (80 g), Fluorine (7.5 g), Iron (5 g), Silicon (3 g) and trace amounts fifteen other elements.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am wondering, is this composition true in real life? if so what are fifteen trace elements?&lt;/p&gt;&#xA;" OwnerUserId="4378" OwnerDisplayName="Memor-X" LastEditorUserId="4316" LastEditDate="2014-05-26T06:58:01.363" LastActivityDate="2016-05-17T18:38:08.423" Title="Is the human body composition real?" Tags="&lt;human-biology&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17658" PostTypeId="2" ParentId="17656" CreationDate="2014-05-26T07:38:43.087" Score="1" Body="&lt;p&gt;O- should be the universal donor not O+because when rh- blood is given to rh+ person ,the rh+ person can not make antibodies against rh- blood because there are no rh antigens in the rh- blood.(So what will rh antibodies be made against ?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now I think u can figure out about why AB+ is the universal recipient ! &lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-05-26T07:38:43.087" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17659" PostTypeId="2" ParentId="17657" CreationDate="2014-05-26T09:02:26.910" Score="1" Body="&lt;p&gt;Water can be essentially split into hydrogen and oxygen. Also the amount of salt content can be split into calculating the composition of both sodium and chlorine. Almost 99% of the mass of the human body is made up of six elements: oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus. Only about 0.85% is composed of another five elements: potassium, sulfur, sodium, chlorine, and magnesium. The remaining elements are trace elements, of which more than a dozen are thought to be necessary for life, or play a role in good health (e.g., fluorine, which hardens dental enamel). A straightforward elemental composition of the human body with the elements given by weight can be found &lt;a href=&quot;http://chemistry.about.com/od/lecturenoteslab1/a/Elemental-Composition-Of-The-Human-Body-By-Mass.htm&quot; rel=&quot;nofollow&quot;&gt;here.&lt;/a&gt; I would also suggest going through the wikipedia article linked in the comment section.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-01T16:57:16.337" LastActivityDate="2014-07-01T16:57:16.337" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17661" PostTypeId="1" AcceptedAnswerId="17673" CreationDate="2014-05-26T10:35:10.683" Score="3" ViewCount="657" Body="&lt;p&gt;I am trying to predict the secondary structure of certain predicted pre-miRNAs through mFOLD which is the generally accepted technique for structure prediction in most studies. I am finding it hard to interpret the result and accept if the pre-miRNA which I have picked and the miRNA I have can be accepted and included in my result. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is one predicted pre-miRNA structure with the predicted miRNA position shown in green. &#xA;&lt;img src=&quot;https://i.stack.imgur.com/wcs3Z.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is this a good/bad structure and if so, can anyone give me a reason why. Thank you.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;edit: I understand that energy levels are also something that is looked for in the prediction. In this particular figure, ΔG = -75.00 kcal/mol which I think is fine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sequence used for folding is &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;AAAAATAAAAAACAGAACCATGAGGCAGCGCACCAAGAGCGTCGTGAACGTCCGCGAATA CTTCCGCATGGACGGCAGTGGCGCCCCCGAGCAGGAGGACGACGATGACAACGATGACTG GATGGCCATCGCCATGCAGGGCGCACCGCGTAAGGTCAGCGTGGAAGTCGTTAAGCCTGG CAAGAAGGCACGCGCTCGTACGTCGACGTGTGACTCAC&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and the highlighted match area is &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ACGATGACAACGATGAC&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So this structure should be fine because the sequence lies along a stem-loop structure.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/27wDt.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am worried about that bulge on the left top corner though. That doesn't affect the predictability of this structure does it? &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="3340" LastEditDate="2015-06-19T07:19:52.137" LastActivityDate="2015-06-19T07:19:52.137" Title="mFOLD prediction result interpretation" Tags="&lt;bioinformatics&gt;&lt;structure-prediction&gt;&lt;microrna&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17662" PostTypeId="2" ParentId="17650" CreationDate="2014-05-26T10:53:48.290" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.bd.com/ds/productCenter/211820.asp&quot; rel=&quot;nofollow&quot;&gt;See here&lt;/a&gt;. &lt;em&gt;Bacto&lt;/em&gt; is a brand which used to be marketed by Difco. It is a casein (milk protein) hydrolysate.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-26T10:53:48.290" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17663" PostTypeId="1" AcceptedAnswerId="17680" CreationDate="2014-05-26T10:55:15.140" Score="2" ViewCount="225" Body="&lt;p&gt;I aligned all miRNAs available to the supercontigs of a particular genome with certain parameters (e value of 0.01 and a word match of atleast 7 as suggested in &lt;a href=&quot;http://www.hindawi.com/journals/ijg/2012/957607/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper). I have also isolated the pre-miRNAs (+100 nucleotides from either end of the match area). What would you suggest as ideal ab-initio methods to confirm that these miRNAs do exist in that particular genome? Some papers I found use mFOLD like &lt;a href=&quot;http://www.scirp.org/journal/PaperDownload.aspx?paperID=6738&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What would you suggest as best steps to confirm if a predicted miRNA/pre-miRNA is really present in the genome.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="3340" LastEditDate="2014-05-27T09:07:45.437" LastActivityDate="2014-05-27T09:07:45.437" Title="Steps to confirm if predicted miRNA is good or bad" Tags="&lt;bioinformatics&gt;&lt;structure-prediction&gt;&lt;microrna&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17664" PostTypeId="2" ParentId="17656" CreationDate="2014-05-26T12:36:43.297" Score="2" Body="&lt;p&gt;In blood groups you always need to consider two things: The antigens present on red blood cells (RBC) and the antibodies present in plasma, which lead to clumping of RBCs if they match. Don't mix up the words antigen and antibody! A healthy individual will never have antibodies against the antigens on their own RBCs, but they &lt;em&gt;will&lt;/em&gt; have antibodies against antigens which are &lt;em&gt;not present&lt;/em&gt; on their own RBCs. (*)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also always remember that blood transfusions consist only of RBCs! The plasma and antibodies are removed. If you mix blood of two people directly, all combinations will coagulate unless the blood types are identical. Thus, when thinking about donor and acceptor match, you have to consider the &lt;strong&gt;acceptor's antibodies&lt;/strong&gt; and the &lt;strong&gt;donor's antigens&lt;/strong&gt; - nothing else.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, Rh+ means RBCs have the Rh antigen, Rh- means they don't.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A universal acceptor will thus be someone who has no antibodies at all (because their antigens don't matter - they receive no antibodies from the donor). This is the case if the RBCs have all antigens: AB+&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A universal donor will be someone whose RBCs have no antigens at all (because their antibodies don't matter, they get removed before transfusion): O-&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note: The ABO system and Rh are only the two most dangerous blood groups when they are mismatched. There are many more RBC antigen types (around 35) and in fact hospitals will consider several of these when matching donors and acceptors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(*) We don't completely know why we make antibodies against antigens not present on RBCs yet. One hypothesis is that the bacteria in the intestines produce antigens which 'look' similar to our blood antigens. Also, this only applies to the A/B/O antigen. All other antigens work like normal antigens such as bacterial ones - after your immune system has seen them the once, you have antibodies against them.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2014-05-27T18:23:16.743" LastActivityDate="2014-05-27T18:23:16.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17666" PostTypeId="1" CreationDate="2014-05-26T15:39:54.733" Score="5" ViewCount="998" Body="&lt;p&gt;Electric synapses are synapses that do not process information but simply foward one action potential from one neuron to the next. There are no neurotransmitters, no inhibitory and exitatory postsynaptic potentials that would cause different responses in the post-synapse.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I'm wondering: What are the biological advantages over just one long axon? My research has only told me the advantages over &quot;normal&quot; synapses (speed), but I couldn't find any advantage over just using one longer neuron which, I suppose, would be even faster.&lt;/p&gt;&#xA;" OwnerUserId="5660" LastEditorUserId="1320" LastEditDate="2014-05-26T17:00:29.297" LastActivityDate="2017-10-10T14:14:43.133" Title="Biological advantage of electric synapses" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;synapses&gt;&lt;central-nervous-system&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17669" PostTypeId="2" ParentId="17623" CreationDate="2014-05-26T16:57:13.883" Score="1" Body="&lt;p&gt;Well, ATP is replenished from three energy sources, namely:&#xA;1. phosphagen system (very fast, but quickly deprived)&#xA;2. glycolysis (fast, but slower deprived)&#xA;3. oxidative system (slow, 'impossible' to deprive)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When ATP is used, for example for muscle contraction, ADP is formed. The formed ADP can be rephosphorylated to ATP by the enzym creatine kinase, which also requires creatinephosphate (the phosphate attached to the creatine provides the phosphate group for ADP to form ATP). Additionally, ATP can be formed out of 2 ADP molecules by adenylate kinase. The phosphagen system is largely driven by the law of mass action, i.e. the direction of the enzymatic reaction is controlled by the concentration of the products and substrates. In other words; when ATP is low, and ADP is high, the generation of ATP is favored and vice versa. The energy from the phosphagen system is depleted rather quickly tho.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second system, glycolysis, simply refers to the breakdown of carbohydrates (e.g. glucose) to resynthesize ATP from the energy stored in those carbohydrates. Your muscles contain a buffer of glycogen, approx. 300~ gr for the average Joe (give or take). The glycogen can be broken down to glucose-6-phosphate, which can then enter glycolysis. The glucose-6-phosphate is broken down to 2 pyruvate and yields 3 ATP netto (2 when derived from glucose, rather than glycogen, due to a first enzymatic step which requires 1 ATP). The enzymatic steps of glycolysis are controlled by ATP, AMP, ADP and other factors, factually integrating the energy status of the muscle (primarly through allosteric regulation of enzymes, especially phosphofructokinase). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The third system, the oxidative system, refers to the breakdown of carbohydrates and fatty acids, requiring oxygen to 'burn' them (citric acid cycle). The yield of this is much higher than for glycolysis, but the process is way slower. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In essence, all are regulated by the concentration of substrates and products, as well as through allosteric regulation (binding of a molecule at a different site, inhibiting or activating the enzyme, often by intermediates of the pathways themselves). Additionally, there is some long-term regulation through gene expression (e.g. up- or down-regulating expression of genes involved in these pathways), mostly by hormones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&#xA;Well, I guess this is described in any basic biochemistry book (I'm very fund of the book 'Fundamentals of Biochemistry: Life at the Molecular Level'). If you want to see a description of these energy systems in a more exercise related context (since you were aiming at myocytes) I suggest reading Strength and Condition: Biological Principles and Practical Applications from Marco Cardinale et al., and the NSCA book Essentials of Strength and Conditioning. &lt;/p&gt;&#xA;" OwnerUserId="6845" LastEditorUserId="6845" LastEditDate="2014-05-26T17:43:43.270" LastActivityDate="2014-05-26T17:43:43.270" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17670" PostTypeId="2" ParentId="17666" CreationDate="2014-05-26T17:04:05.333" Score="5" Body="&lt;p&gt;Having just read this article (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK11164/&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK11164/&lt;/a&gt;) there are several advantages/functional reasons that seem apparent and important in having electrical synapses with gap junctions compared to just a very long neuron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) signals in electrical synapse can be bidirectional.&#xA;b) electrical synapse synchronize electrical activity among populations of neurons.&#xA;c) The large pores in gap junctions allows passage of ATP and other important intracellular metabolites, such as second messengers between neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure there are plenty of other reasons but these should provide a better picture in terms of the functional significance of having electric synapses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-26T17:04:05.333" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17671" PostTypeId="2" ParentId="17619" CreationDate="2014-05-26T17:16:58.673" Score="0" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ml20I.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taken from Fundamentals of Biochemistry (Voet et al. 2013). Note the differences in apolipoproteins between LDL and IDL, as well as the ratio triacylglycerol : cholesteryl esters between VLDL and IDL. &lt;/p&gt;&#xA;" OwnerUserId="6845" LastActivityDate="2014-05-26T17:16:58.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17673" PostTypeId="2" ParentId="17661" CreationDate="2014-05-26T19:22:14.870" Score="1" Body="&lt;p&gt;The green region will definitely not make an miRNA: It is not a part of a stem loop. See typical miRNA structures from miRbase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bulges can sometimes determine which strand is chosen as mature miRNA. However, this green region is also is unlikely to form miRNA because the stem is just 15bp. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-05-27T11:49:04.163" LastActivityDate="2014-05-27T11:49:04.163" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17674" PostTypeId="1" AcceptedAnswerId="17675" CreationDate="2014-05-26T21:16:06.580" Score="1" ViewCount="142" Body="&lt;p&gt;Coming from a software engineering standpoint, suppose I have a string of code like so:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;... 5'-ATAGAC-3' ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;... 3'-TATCTG-5' ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume the above code is part of a larger segment. Now, reading from 3' to 5', the promoter and operator would be somewhere before the structural gene on the 2nd stand:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Promoter) (Operator) ... 3'-TATCTG-5' ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where would it be on the first strand? From what it looks like, the first strand codes for a completely different protein than the second stand:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;... 5'-ATAGAC-3' ... (Operator) (Promoter)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet, the two strands are complementary.&lt;/p&gt;&#xA;" OwnerUserId="4557" LastEditorUserId="1320" LastEditDate="2014-05-27T08:47:28.467" LastActivityDate="2014-05-27T08:47:28.467" Title="Anti-parallel DNA code operons" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17675" PostTypeId="2" ParentId="17674" CreationDate="2014-05-26T23:42:50.863" Score="1" Body="&lt;p&gt;In your example, yes the two strands do code for different proteins. However, biologically this generally doesn't occur. I say generally because I don't want to rule it out definitively but I don't know of an instance where both strands at a given locus code for a protein and, where it does occur, it is often used as a criterion for annotating one of the elements as dubious. Along with that, there would be no promoter immediately 5' to one of the strands. Even if it does occur biologically, each strand would code for a different protein and would be a different gene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any gene, one of the strands is identical to the RNA transcript (before processing and with T instead of U). This is called the coding or sense strand and runs 5' -&gt; 3'. The other strand is used as a template by RNA polymerase (RNAP) to polymerize the RNA transcript. It runs 3' -&gt; 5' and is called the template or antisense strand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, a note on promoters: promoter consensus sequences by convention are given on the sense strand. However, as far as I know, transcription initiation factors recognize the base pairing between both strands in the major groove of dsDNA because they must bind before promoter melting occurs. Thus, I wouldn't say that a promoter exists only on the template strand.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-05-26T23:42:50.863" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17676" PostTypeId="1" AcceptedAnswerId="17682" CreationDate="2014-05-26T23:52:51.287" Score="7" ViewCount="714" Body="&lt;p&gt;N. Shubin's &lt;em&gt;Your Inner Fish&lt;/em&gt; makes the point several times that there is a lot of functional similarity between some seemingly remote gene cousins. If that needed reinforcing we have the spider-goat, whose milk contains spider's silk, and a knock-in mouse whose vision resembles that of humans. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The last two examples are interesting because, as I recall, nothing beyond the gene insertion (already a feat) had to be done to confer the extra/new capability. The machinery at the cellular level (for the mouse to perceive a new color or for the goat to somehow process the milk) already existed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is whether it might not be possible in theory to create a mammal with the ability to photosynthesize? If this is a polygenic trait perhaps it would be accomplished in multiple stages. I realize an answer here would be highly speculative but a careful answer might cast some light on the process of conferring new traits/abilities in this way. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While I see no obvious benefit of creating a photosynthesizing mouse, at least the food bills for their maintenance might be low. This sounds like a joke but it's not a trivial benefit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any insights.       &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="3340" LastEditDate="2014-05-27T09:11:13.213" LastActivityDate="2021-03-29T09:12:16.377" Title="A photosynthesizing mouse?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17677" PostTypeId="2" ParentId="9051" CreationDate="2014-05-27T02:37:37.123" Score="2" Body="&lt;p&gt;Take a look at the paper by Ojasoo et al. [1] It reports the relative binding affinity for a wide variety of steroids for the AR, PR and GR.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nandrolone (19-nor testosterone) does not have any affinity for the GR, but is a potent activator of the AR. However, it does have some affinity for the progesterone receptor (does this matter for your research?). Additionally, nandrolone bound to the AR also binds estrogen response elements (does this matter for your research?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5a-DHT also is a potent AR activator with no affinity for the GR. Do note that a metabolite of 5a-DHT has significant affinity for the estrogen receptor, might that matter for your research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might also use a strong GR antagonist in conjunction with an androgen which also has some affinity for the GR. Then you can simply use methyltrienolone, as commonly used as AR ligand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a sidenote: do note that androgens usually only lead to significant dissociation of a GR ligand for the GR at very high concentrations. Therefore, androgens most likely act as GR antagonist by heterodimer formation of the AR with GR [2], as well as through squelching [3]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;References&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Ojasoo, T., et al. &quot;Towards the mapping of the progesterone and androgen receptors.&quot; Journal of steroid biochemistry 27.1 (1987): 255-269.&lt;/li&gt;&#xA;&lt;li&gt;Chen, Sei-yu, et al. &quot;Androgen and glucocorticoid receptor heterodimer formation A possible mechanism for mutual inhibition of transcriptional activity.&quot; Journal of Biological Chemistry 272.22 (1997): 14087-14092.&lt;/li&gt;&#xA;&lt;li&gt;Zhao, Jingbo, et al. &quot;Oxandrolone blocks glucocorticoid signaling in an androgen receptor-dependent manner.&quot; Steroids 69.5 (2004): 357-366.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6845" LastEditorUserId="6845" LastEditDate="2014-05-27T02:48:59.647" LastActivityDate="2014-05-27T02:48:59.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17678" PostTypeId="1" CreationDate="2014-05-27T04:15:34.363" Score="8" ViewCount="16696" Body="&lt;p&gt;Why do many humans have bad eyesight, such as near-sightedness, which hampers performance in a wide variety of tasks? Shouldn't there be evolutionary pressure towards better eyesight?&lt;/p&gt;&#xA;" OwnerUserId="6847" LastEditorUserId="6847" LastEditDate="2014-05-27T05:49:30.690" LastActivityDate="2014-05-27T17:02:05.510" Title="Bad Eyesight and Evolution" Tags="&lt;evolution&gt;&lt;human-anatomy&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17679" PostTypeId="2" ParentId="17678" CreationDate="2014-05-27T04:49:34.063" Score="1" Body="&lt;p&gt;Mainly because we haven't been forced to remove the bad genes that cause these defects from our gene pool. In ancient times, a bad gene that causes poor eyesight would have made it difficult for a person to spot prey or escape from a predator. However, we have glasses now which gives the bad eyesight gene as much a chance to propagate as any other gene. it also doesn't really matter since poor eyesight is never a factor for survival in present times. The same with poor hearing which we correct with hearing aid. Please read &lt;a href=&quot;http://www.theguardian.com/notesandqueries/query/0,5753,-20359,00.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; for an article in the guardian and &lt;a href=&quot;http://articles.orlandosentinel.com/1994-01-09/news/9401100448_1_evolution-poor-eyesight-poor-vision&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article in the orlando sentinel. You could also read &lt;a href=&quot;http://www.reddit.com/r/AskReddit/comments/1520pt/from_an_evolutionary_standpoint_why_do_so_many/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; discussion on reddit to see a few fun arguments. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-27T04:49:34.063" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17680" PostTypeId="2" ParentId="17663" CreationDate="2014-05-27T05:29:02.000" Score="1" Body="&lt;p&gt;There won't be any duplicates in miRBase (for a given organism). Choose the taxon nearest to your organism if you are doing homology based discovery. If you want to take all/many organisms then you can use &lt;code&gt;fastx_collapser&lt;/code&gt; to collapse redundant sequences. However you will lose the name of the miRNA. You can use &lt;code&gt;awk&lt;/code&gt; also for this and it will keep the sequence header from the first organism in the list. &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;awk '/&amp;gt;/{$0=h} !(/&amp;gt;/){if($0 in a){next} else{a[$0];print h&quot;\n&quot;$0}}' organism1.fa organism2.fa ... organismN.fa&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Make sure that there are no extra newlines, otherwise you might need a small modification&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To know if something is an expressed miRNA you would need to do a small RNA sequencing. There are some tools like mirdeep and mirSVR which you can use to discover miRNA sequences. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-05-27T08:31:51.440" LastActivityDate="2014-05-27T08:31:51.440" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17681" PostTypeId="2" ParentId="8619" CreationDate="2014-05-27T05:54:58.597" Score="1" Body="&lt;p&gt;Some of it is voluntary and some involuntary and is detailed in this &lt;a href=&quot;http://books.google.co.in/books?id=kYEqWKFuspkC&amp;amp;pg=PA38&amp;amp;lpg=PA38&amp;amp;dq=Is%20the%20color%20change%20of%20chameleon-like%20creatures,%20voluntary%20or%20involuntary?&amp;amp;source=bl&amp;amp;ots=sqxUyzAPnO&amp;amp;sig=cFrS4lgzGFdAK6mmp6DiDfIPEbg&amp;amp;hl=el&amp;amp;ei=RKImSoXyJ4yK_QaTj-ztBw&amp;amp;sa=X&amp;amp;oi=book_result&amp;amp;ct=result&amp;amp;redir_esc=y#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;book&lt;/a&gt;. Chameleons have &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromatophore&quot; rel=&quot;nofollow&quot;&gt;chromatophores&lt;/a&gt; (pigment containing light reflecting organelles in cells) which help in their colour change and many factors like age, health, etc does affect it. And no, they do not form a picture on their head and print it on their bodies.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-27T05:54:58.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17682" PostTypeId="2" ParentId="17676" CreationDate="2014-05-27T06:05:46.487" Score="7" Body="&lt;p&gt;It is almost impossible for following reasons:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;For photosynthesis you need chloroplasts&lt;/li&gt;&#xA;&lt;li&gt;To maintain chloroplasts you need many genes in the nucleus that will support its endosymbiosis&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;I said &lt;em&gt;almost&lt;/em&gt; impossible because there are some natural examples of what you are asking. A sea slug called &lt;a href=&quot;http://en.wikipedia.org/wiki/Elysia_chlorotica&quot; rel=&quot;nofollow noreferrer&quot;&gt;Elysia&lt;/a&gt;  acquires choloplasts from green algae on which it feeds. However, it cannot maintain the chloroplasts and pass them on to the next generation but it acquires enough to appear green and survive on photosynthesis when there is no food.&lt;/p&gt;&#xA;&lt;p&gt;Another example is that of the protist, &lt;em&gt;Rhopalodia gibba&lt;/em&gt;, which acquired a cyanobacteria like organism. This protist already had a red alga derived secondary plastid before it acquired a &amp;quot;&lt;em&gt;green&lt;/em&gt;&amp;quot; cyanobacteria. This acquisition gave the host the ability to fix nitrogen in the presence of light.&lt;/p&gt;&#xA;&lt;p&gt;The case of &lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822%2808%2900237-6&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Paulinella chromatophora&lt;/em&gt;&lt;/a&gt; is very interesting because the acquisition of an endosymbiont happened very recently. The endosymbiont is close to Synechococcus clade of cyanobacteria.&lt;/p&gt;&#xA;&lt;p&gt;Intuitively, it can be understood that these kinds of acquisitions would be quite difficult for a multicellular organism.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;ADDENDUM&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Photosynthesis is a complex reaction which requires a dedicated compartment which not only harvests light and produces ATP but also has enzyme complexes required for anabolism (carbon fixation etc).&#xA;For now we can accept the hypothesis that it would not be possible for a huge eukaryotic cell to perform these functions in absence of a dedicated organelle. For a discussion on why this is so, you can refer &lt;a href=&quot;https://biology.stackexchange.com/questions/14347/the-origin-of-mitochondria/14351#14351&quot;&gt;this&lt;/a&gt; post.&#xA;Having said that, there is an easy way to impart partial &lt;em&gt;photosynthetic ability&lt;/em&gt; to a eukaryotic cell. Some archaea and bacteria employ rhodopsin to pump out protons against its gradient, in the presence of light; this is coupled with ATP-synthase just like the complexes of ETC in mitochondria. In &lt;a href=&quot;http://www.nature.com/srep/2013/130409/srep01635/full/srep01635.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this study&lt;/a&gt;, Hara et al have expressed delta-rhodopsin in mammalian mitochondia which now makes the mitochondria generate ATP in presence of light. Furthermore, these cells were immune to mitochondrial toxins that affect complex-I activity.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;PS: thanks biogirl. I almost forgot about this and I just remembered when I was reading about something else&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2021-03-29T09:12:16.377" LastActivityDate="2021-03-29T09:12:16.377" CommentCount="6" ContentLicense="CC BY-SA 4.0" />
  <row Id="17683" PostTypeId="2" ParentId="17634" CreationDate="2014-05-27T08:44:03.237" Score="4" Body="&lt;p&gt;I'm taking this question at face value. Yes, fish have gills, but we also have a respiratory surface in our lungs so why couldn't we 'breathe' water and extract the oxygen (since extraction is a simple matter of diffusion from the content of the lungs into the blood).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently &lt;a href=&quot;http://health.howstuffworks.com/human-body/systems/respiratory/question98.htm&quot; rel=&quot;nofollow&quot;&gt;we use 550 L of pure O&lt;sub&gt;2&lt;/sub&gt; per day&lt;/a&gt;. This works out as approximately 400 g.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.engineeringtoolbox.com/oxygen-solubility-water-d_841.html&quot; rel=&quot;nofollow&quot;&gt;The solubility of O&lt;sub&gt;2&lt;/sub&gt; in fresh water is around 10 mg L&lt;sup&gt;-1&lt;/sup&gt;.&lt;/a&gt; Assuming a hypothetical situation where we could breathe water and extract all of the O&lt;sub&gt;2&lt;/sub&gt; from each lungful this means that we would need to breathe 28 L of water per minute, compared to the &lt;a href=&quot;http://health.howstuffworks.com/human-body/systems/respiratory/question98.htm&quot; rel=&quot;nofollow&quot;&gt;8 L of air that we breathe&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now of course water has a much higher density than air so that a lot of energy would be expended in moving this much water in and out of the lungs (which in turn would require us to consume more oxygen). Couple this with the fact that realistically we would only be able to use a fraction of the O&lt;sub&gt;2&lt;/sub&gt; dissolved in each lungful and you can begin to see why this is a non-starter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gills allow this problem to be largely circumvented by having a one way flow of water over the respiratory surface, which in the case of fish is often achieved at least in part by moving through the water.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-05-27T08:44:03.237" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17684" PostTypeId="1" AcceptedAnswerId="17685" CreationDate="2014-05-27T08:44:21.770" Score="4" ViewCount="1664" Body="&lt;p&gt;In a standalone blast search, is there a parameter that could be specified to fix the number of mismatches allowed in an alignment. I went through the parameters and I could only find parameters to set score.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-q =&gt; Penalty for a nucleotide mismatch (blastn only) [Integer] default = -3&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-r =&gt; Reward for a nucleotide match (blastn only) [Integer] default = 1&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What do I do if I only require hits with a maximum allowed mismatch or gap of 2 per alignment.&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="3340" LastEditDate="2014-05-27T09:07:01.337" LastActivityDate="2014-06-17T13:17:18.043" Title="The parameter for setting the number of mismatches in standalone blast" Tags="&lt;bioinformatics&gt;&lt;blast&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17685" PostTypeId="2" ParentId="17684" CreationDate="2014-05-27T09:03:55.703" Score="4" Body="&lt;p&gt;There is no direct option like that but you can set percentage identity filter with &lt;code&gt;-perc_identity&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this is only for reporting. BLAST will still perform all the alignments. That is why I suggested you to use bowtie. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT-1&lt;/strong&gt; (getting long for comment)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want a word type of search then use the &lt;code&gt;-n&lt;/code&gt; option. But it always starts from the 5'end which is quite justified in case of miRNA because the seed region is in the 5'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Setting &lt;code&gt;-n&lt;/code&gt; to &lt;code&gt;0&lt;/code&gt; means no mismatch in seed region. &lt;code&gt;-l&lt;/code&gt; option defines the seed length; I would advise that you use something like &lt;code&gt;10&lt;/code&gt;. &lt;code&gt;-e&lt;/code&gt; refers to maximum mismatches in the non seed region but it is not the number of mismatches; it means maximum tolerated sum of phred score of mismatches (fasta files are assigned a default phred score of 40 at all residues. So, for 2 mismatches you have to mention &lt;code&gt;-e 80&lt;/code&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT-2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes. Increasing mismatch and gap penalties would make the search more stringent if you have already specified a cutoff on score.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-06-17T13:17:18.043" LastActivityDate="2014-06-17T13:17:18.043" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17686" PostTypeId="2" ParentId="17678" CreationDate="2014-05-27T09:29:32.917" Score="3" Body="&lt;p&gt;&lt;strong&gt;Maintenance of Polymorphism and Mutation Load&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many possible reasons why some amount of deleterious alleles are maintained in the population. One of which is the mutation-selection-drift balance. In short: Because mutations always occur, there is continually an input of deleterious mutations in populations genome resulting in some fitness decay (called mutation load). While mutations create this polymorphism, processes of selection and genetic drift cause a decrease in polymorphism. At equilibrium there is a balance between mutations, selection and drift called the mutation-selection-drift balance. You may also want to consider various population structure related concepts such as migration between patches. Haldane first explored this mutation load theoretically and estimated that the fitness of an existing individual in a population of perfect (deleteterious-mutations-free) individual is about 80% lower, which is huge! Such mechanism can explain various disease found in a population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Age-specific intensity of selection&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, for the question of disease appearing late in life (which is often the case of eyesight related disease), it is important to realize that those genes which are expressed late in life undergoes a lower selection resulting in a higher mutation-selection-drift balance. See &lt;a href=&quot;https://biology.stackexchange.com/questions/17077/why-does-evolution-not-make-our-life-longer/&quot;&gt;this post&lt;/a&gt; for more info.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Impact of Medicine and social helping on the intensity of selection&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As pointed out by @potterbond007 modern medicine allows to diminish the deleterious effect of some mutations. For example, one that has &lt;a href=&quot;http://en.wikipedia.org/wiki/Club_foot&quot; rel=&quot;nofollow noreferrer&quot;&gt;clubfoot&lt;/a&gt; may be operated and is likely to survive and reproduce and therefore propagating its deleterious alleles. This would be different in some past. Therefore, medicine diminish the selection pressure on deleterious alleles. However, modern medicine probably has a very low effect on our genomes because it is so modern. 100 years ago we could not operate clubfoot and 500 years ago (almost) nobody had glasses to correct for eyesight deficiency. We may go a bit further in the past and also consider that social interactions such as helping weak individuals in a tribe may also have decreases the selection pressure against deleterious alleles (more info in @theBIOguy 's answer). Of course, if selection is diminished the mutation-selcetion-drift balance is increased and deleterious alleles are more common and mutation load is greater.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Further investigations will be needed in Epidemiology&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that eyesights disease are particularly common and deleterious, we should have a closer look to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Epidemiology&quot; rel=&quot;nofollow noreferrer&quot;&gt;epidemiology&lt;/a&gt; of the diseases of interests. If it seems to you that eyesight-related diseases are more common and more important in terms of their effects on fitness than diseases on other traits then, you may want to seek into some physiological and developmental explanations that may tell you why eyes are so likely to be impacted by genetic and/or environmental factors. I personally have absolutely no knowledge about the epidemiology and developmental mechanisms of any eyesight disease! Also considerations of the impact of modern environment should be considered such as the impact of TV and computer screens on our eyes (more info in @biogirl 's answer)&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-05-27T17:02:05.510" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17687" PostTypeId="1" CreationDate="2014-05-27T09:38:51.120" Score="0" ViewCount="78" Body="&lt;p&gt;For a mesophyte growing in a moist soil, water potential of its root sap is -3 atm, then how to find the water potential of moist soil and leaf respectively?&lt;/p&gt;&#xA;" OwnerUserId="6390" LastActivityDate="2014-05-30T04:38:42.277" Title="Calculation of water potential" Tags="&lt;membrane-transport&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17688" PostTypeId="1" CreationDate="2014-05-27T10:22:32.873" Score="1" ViewCount="933" Body="&lt;p&gt;A double stranded DNA was denatured in a mixture that included mRNA from a gene in the segment. The mixture was then cooled to promote RNA and DNA hybridization. The following figure the results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Xtt3g.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which strand is DNA/RNA?&#xA;What is source of the genetic material (Prokaryotic/Eukaryotic)?&#xA;Which segment is exon/intron?&lt;/p&gt;&#xA;" OwnerUserId="6390" LastEditorUserId="3340" LastEditDate="2014-05-27T12:30:49.953" LastActivityDate="2014-05-27T12:30:49.953" Title="Conclusions from hybridization results" Tags="&lt;dna&gt;&lt;homework&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17689" PostTypeId="2" ParentId="8538" CreationDate="2014-05-27T10:28:39.117" Score="2" Body="&lt;p&gt;Tumor ‘budding’ is loosely defined as the presence of individual cells and small clusters of tumor cells at the invasive front of carcinomas. A study of the measure of budding can give an insight into how fast the disease might propogate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/modpathol/journal/v25/n10/full/modpathol201294a.html&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-05-27T11:04:51.850" LastActivityDate="2014-05-27T11:04:51.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17690" PostTypeId="2" ParentId="17688" CreationDate="2014-05-27T10:43:12.740" Score="3" Body="&lt;p&gt;You are almost right. I modified you picture a little bit to answer it:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ldjfW.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Structure I is indeed DNA, structure II is processed RNA. &#xA;This is because in I you see loop structures which have no complementary part in the RNA anymore, these are introns (structure Q and the flanking loop regions to P). P is an exon flanked by two introns.&#xA;The end of the RNA is not complementary to the DNA because the poly-A tail has been added here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The DNA is eukaryotic since you have introns and exons (which are not present in bacteria) and since the processed RNA contains a poly-A tail (which is also not present in bacteria).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="3340" LastEditDate="2014-05-27T12:30:41.897" LastActivityDate="2014-05-27T12:30:41.897" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17692" PostTypeId="2" ParentId="17687" CreationDate="2014-05-27T13:03:41.497" Score="1" Body="&lt;p&gt;I don't know if we can calculate the exact values. The only thing I can say is that the potential of the soil will be less negative than -3 while that of the leaf will be more negative.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You know that water travels from higher potential to lower potential. So, it will travel from a region of less negative water potential to a region of more negative water potential.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3776" LastEditDate="2014-05-30T04:38:42.277" LastActivityDate="2014-05-30T04:38:42.277" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17693" PostTypeId="2" ParentId="17678" CreationDate="2014-05-27T13:15:19.497" Score="4" Body="&lt;p&gt;Remi.b and Potterbond007 have put forward excellent answers. Would like to add something..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the reasons that Myopia (near sightedness) happens is because of use of eye in work like reading, which requires working with close objects. I don't think there was much working with close objects in the past. So very few people with myopia might have been present (and of course, they may have had disadvantages in catching prey.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other common disease is hypermetropia which generally occurs during old age, past the reproductive prime, so it could not have much evolutionary impact.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-05-27T13:15:19.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17694" PostTypeId="1" AcceptedAnswerId="17695" CreationDate="2014-05-27T13:43:21.933" Score="15" ViewCount="2209" Body="&lt;p&gt;For example, there is an incubation period of around 1 to 3 days for common cold, and that of AIDS can range over to decades.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do viruses do actually do during the incubation period?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What triggers them to turn active again?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2014-05-27T15:27:27.557" Title="What do viruses do during incubation period?" Tags="&lt;virology&gt;&lt;virus&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17695" PostTypeId="2" ParentId="17694" CreationDate="2014-05-27T15:27:27.557" Score="15" Body="&lt;p&gt;during the incubation period the virus is typically increasing in numbers and spreading between cells. It takes a while for symptoms to become obvious because it takes time for enough damage to be built up in the tissue to become noticeable.&#xA;Take for instance the Rhinovirus which causes the common cold, once you become infected it is a day or so before enough damage has been caused to the tissue at at the back of the throat to give you a cough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition some of the symptoms of infection are caused by your own immune system as a way of fighting the infection. For instance inflammation is often a sign of infection but is typically caused by the immune system to allow the movement of plasma and leukocytes into the infected tissue. As the immune system requires time to recognise and respond to a pathogen this leads to the delayed onset in symptoms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AIDS is actually a syndrome caused by the HIV virus. the HIV lifecycle occurs CD4+ T-Cells, after infection occurs the immune system tries to cope by destroying the infected cells but over long time the infected population increases. The immune system becomes more and more compromised until the CD4+ cell count drops to a level where the patient is diagnosed with AIDS. At this point the immune system is compromised and the chance of a secondary infection by a different organism increases which the patient can no longer fight off. The actual cause of death for someone infected with HIV is rarely the HIV itself but is quite often a different agent.&lt;/p&gt;&#xA;" OwnerUserId="6811" LastActivityDate="2014-05-27T15:27:27.557" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17696" PostTypeId="1" CreationDate="2014-05-27T15:36:54.180" Score="5" ViewCount="439" Body="&lt;p&gt;I'm a master student working on networks analysis in general. A network is something that has nodes and there are links between the nodes. Nodes and links could have attributes. An evolving network is one that changes overtime (new nodes and links are added..etc). An example of that is Facebook. Nodes are users and links represent the friendship relationship. Users have attributes (gender, age, etc.). A Facebook network as you know is an example of a social network. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The issue is that so many people studied traditional evolving networks like social networks, the web, or transportation networks. Currently I'm looking for novel examples of evolving networks to study them. So I thought there might be some examples in &lt;em&gt;biology&lt;/em&gt; that could represent some kind of an evolving network. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question: Can you give me examples in &lt;em&gt;biology&lt;/em&gt; for evolving networks? I'm aware of metabolic networks, but that is also heavily studied, I need something else.&lt;/p&gt;&#xA;" OwnerUserId="6850" LastEditorUserId="112" LastEditDate="2014-05-28T16:13:55.097" LastActivityDate="2014-06-25T18:21:18.440" Title="What are some examples of evolving networks in biology?" Tags="&lt;evolution&gt;&lt;bioinformatics&gt;&lt;protein-evolution&gt;&lt;network&gt;&lt;biological-networks&gt;" AnswerCount="5" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17697" PostTypeId="2" ParentId="17678" CreationDate="2014-05-27T15:56:52.313" Score="3" Body="&lt;p&gt;With nearly 40,000 years of natural selection on eyesight, prior to the invention of eye glasses, there needs to be a better explanation than the effects of 'modern' technology. There are two likely reasons for the persistence of &quot;poor&quot; eyesight in humans. First, humans are social animals and live in groups. Within groups there is frequently a division of labor. This division of labor deemphasized the importance of vision. Individuals with &quot;poor&quot; eyesight could easily maintain a high fitness (reproductive success) in this social structure. Second, humans have long term parental care (both within and among families - again a function of social living). Most human offspring maintain close familial connections up to and including the age of reproduction. The strength of selection on eyesight diminishes past reproductive age, allowing individual with poor eyesight to have relatively high fitness.&lt;/p&gt;&#xA;" OwnerUserId="6787" LastActivityDate="2014-05-27T15:56:52.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17698" PostTypeId="2" ParentId="17696" CreationDate="2014-05-27T17:20:57.593" Score="1" Body="&lt;p&gt;Not sure if this meets your definition of a network, but there are several kinase cascades which transmit signals. For example, the basic MAPK cascade has evolved to serve different roles via the ERK, JNK, and p38 cascades&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The evolution of the MAP kinase pathways: coduplication of interacting proteins leads to new signaling cascades. Caffrey et al., Journal of molecular evolution, 1997. Link &lt;a href=&quot;http://rd.springer.com/article/10.1007/PL00006578&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ancient signals: comparative genomics of plant MAPK and MAPKK gene families. Link &lt;a href=&quot;http://dx.doi.org/10.1016/S0968-0004%2802%2902179-5&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. Manning et al., Trends in Biochemical Sciences, 2002.&lt;/p&gt;&#xA;" OwnerUserId="6851" LastEditorUserId="6851" LastEditDate="2014-05-28T15:40:57.297" LastActivityDate="2014-05-28T15:40:57.297" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17699" PostTypeId="1" AcceptedAnswerId="17701" CreationDate="2014-05-27T17:23:08.513" Score="3" ViewCount="525" Body="&lt;p&gt;I am trying to understand this statement about the Measles part of the MMR (Mumps, Measles and Rubella) vaccine&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Measles prevention: MMR (AB protect during primary and secondary viremia)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Measles enters from respiratory tract, through mucosa of the upper respiratory tract. The virus passes into cervical lymph nodes. Now, starts first viremia (&lt;strong&gt;MMR somehow helping here&lt;/strong&gt;) which lasts about 5 days. Then antibodies are secreted during 15 days which leads to rash lasting about 3 days. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this second viremia refers to the possible dissemination of the virus to other lymph nodes by blood.&#xA;This suggests me that the vaccine primarily have a mechanism that affects in the lymph nodes or generally in the lymphatic circulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How MMR vaccine affect lymph nodes in preventing measles?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="5144" LastEditDate="2014-05-27T18:07:35.740" LastActivityDate="2016-05-28T05:36:47.410" Title="How does the MMR vaccine affect lymph nodes in preventing measles?" Tags="&lt;microbiology&gt;&lt;virology&gt;&lt;virus&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17700" PostTypeId="2" ParentId="17696" CreationDate="2014-05-27T17:26:57.050" Score="1" Body="&lt;p&gt;The following does not answer the question! It only gives some ideas of where I personnaly found some work involving network analysis in biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the networks I've heard about in biology concern&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;network of species interactions&lt;/li&gt;&#xA;&lt;li&gt;network of individual interactions within a population&lt;/li&gt;&#xA;&lt;li&gt;network of subpopulation interactions within a metapopulation&lt;/li&gt;&#xA;&lt;li&gt;neuronal network&lt;/li&gt;&#xA;&lt;li&gt;anatomy network (blood vessels, skelleton, etc..)&lt;/li&gt;&#xA;&lt;li&gt;network of metabolic pathways. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I give you below a bunch of article title that discuss networks in biology. I'll probably add the links later $ \ddot\smile$ but if you just copy-paste these titles on scholar.google or on WebOfKnowledge you will easily find the articles. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Evolution of a vertebrate social decision-making network&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;climate change, human impacts coral reefs&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;architecture of mutualistic increase biodiviversity&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;variation in migration propensity among individuals maintained by landscape structure&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;skeleton and fractal scaling in complex networks&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Habitat modification alters the structure of tropical host-parasitoid food webs&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This last article concerns the impact of various environment on the network of interactions between host and parasites. Fairly interesting for a biologist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would expect that most evolving networks in biology concerns the impact of environmental changes on the network of species, subpopulations and species interactions. You may have expected some stuff that are more related to evolutionary biology. I think most of this work concers evolutionary ecology and evolutionary processes in metapopulations. Here is a very interesting and very theoretical article (by stuart kauffmann) on evolutionary biology though that has nothing to do with ecology.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;antichaos and adaptation&lt;/em&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-05-27T20:57:02.847" LastActivityDate="2014-05-27T20:57:02.847" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17701" PostTypeId="2" ParentId="17699" CreationDate="2014-05-27T18:06:11.263" Score="3" Body="&lt;p&gt;Lets define &lt;a href=&quot;http://en.wikipedia.org/wiki/Viremia&quot; rel=&quot;nofollow&quot;&gt;viremia&lt;/a&gt; first: The primary viremia occurs in the cells which the virus enters first in the body. There it replicates to high titers before it leaves this cells, spreads through the body and infects other cells. This is then the second viremia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For measles the primary viremia occurs in the respiratory epithelium and in the local lymph nodes. The second viremia then occurs in skin, conjunctiva, respiratory tract, and other distant organs. In this phase also the characteristic rash occurs due to a hypersensitivity reaction of the skin. For details see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4548191&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://ccjm.org/content/77/3/207.full&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The measles vaccine works like any other vaccine: By raising an immune response against the vaccination virus. This leads to a normal immune response which leads to the production of specific antibodies against the measles virus and also to immunologic memory. These antibodies are available to fight the virus when it enters the body of a vaccinated person. This also triggers the proliferation of virus specific memory B cells which then differentiate into plasma cells and produce vast amounts of protective antibodies. So there is no special mechanism involved here beyond immunologic memory.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-27T18:06:11.263" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17703" PostTypeId="2" ParentId="17696" CreationDate="2014-05-27T20:57:15.633" Score="1" Body="&lt;p&gt;I find this a very interesting question as I personally work with networks very frequently!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on your definition of evolving networks, it is feasible to consider protein-protein interaction networks as evolving since over time more and more interactions between different proteins are discovered and more novel proteins (nodes) are tested for their interaction with other proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this meets your definition, then you can use PP interaction databases such as BioGRID and look at the different releases and see what proteins are added over time and what new interactions have been added between different releases. Here is the archives page for BioGRID (&lt;a href=&quot;http://thebiogrid.org/download.php&quot; rel=&quot;nofollow&quot;&gt;http://thebiogrid.org/download.php&lt;/a&gt;). BioGRID has also a Cytoscape plugin which you can use, although I have never worked with dynamic networks in Cytoscape so perhaps have a look at Pavlopoulos et al 2008 BioData Min, which is a survey of visualisation tools for biological network analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-27T20:57:15.633" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17704" PostTypeId="1" CreationDate="2014-05-28T00:00:17.663" Score="1" ViewCount="112" Body="&lt;p&gt;I am currently working through the code example on the &lt;a href=&quot;http://www.mathworks.com/help/bioinfo/examples/exploring-protein-dna-binding-sites-from-paired-end-chip-seq-data.html?prodcode=BI&amp;amp;language=en&quot; rel=&quot;nofollow&quot;&gt;MATLAB website.&lt;/a&gt; It requires me to download the reference genome of &lt;a href=&quot;http://www.genome.jp/kegg-bin/show_organism?org=ath&quot; rel=&quot;nofollow&quot;&gt;Arabidopsis thaliana (thale cress)&lt;/a&gt; so I can use BowTie2 to align the Chip-Seq experiment data. I need it in a .fa file. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since I am very very new to this, what is the database where I can use to download this reference genome? How do I search for something like this? Thanks&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: spoke too soon. I think the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/?term=thale%20cress&quot; rel=&quot;nofollow&quot;&gt;NCBI website&lt;/a&gt; did it for me. Under the &lt;code&gt;Representitive -&amp;gt; Reference genome&lt;/code&gt; section. Is this correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT2: The answer was in the MATLAB page also. The bioinformatics toolbox provides a function: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;% getgenbank('NC_003070','FileFormat','fasta','tofile','ach1.fasta');&#xA;% getgenbank('NC_003071','FileFormat','fasta','tofile','ach2.fasta');&#xA;% getgenbank('NC_003074','FileFormat','fasta','tofile','ach3.fasta');&#xA;% getgenbank('NC_003075','FileFormat','fasta','tofile','ach4.fasta');&#xA;% getgenbank('NC_003076','FileFormat','fasta','tofile','ach5.fasta');&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="6416" LastEditorUserId="6416" LastEditDate="2014-05-28T00:37:17.883" LastActivityDate="2014-05-28T16:47:15.607" Title="downloading a reference genome for alignment" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17706" PostTypeId="1" AcceptedAnswerId="17707" CreationDate="2014-05-28T03:27:57.570" Score="2" ViewCount="120" Body="&lt;p&gt;This incredibly rare animal has been reported to be extinct since 1990, however several cases has been raised that night parrot was spotted in the areas of Australia. What is the cause of their extinction, or in the first place, are they really extinct?&lt;/p&gt;&#xA;" OwnerUserId="4330" LastActivityDate="2014-05-28T05:03:37.513" Title="Are Night Parrots (Pezoporus occidentalis) really extinct?" Tags="&lt;zoology&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17707" PostTypeId="2" ParentId="17706" CreationDate="2014-05-28T05:03:37.513" Score="5" Body="&lt;p&gt;As per &lt;a href=&quot;http://en.wikipedia.org/wiki/Night_Parrot#cite_note-ag-16&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt; it is listed as endangered having been downgraded from critically endangered due to the spread in sightings over the years over a large area. Sightings have been rare with a reported sighting on &lt;a href=&quot;http://www.publish.csiro.au/?paper=MU07058&quot; rel=&quot;noreferrer&quot;&gt;12th April 2005&lt;/a&gt; and a dead specimen found &lt;a href=&quot;http://scienceblogs.com/tetrapodzoology/2009/10/06/2006-dead-night-parrot/&quot; rel=&quot;noreferrer&quot;&gt;in 2006&lt;/a&gt; The first photos and a 17 second video of the bird was taken by a wildlife photographer &lt;a href=&quot;http://en.wikipedia.org/wiki/John_Young_%28cinematographer%29&quot; rel=&quot;noreferrer&quot;&gt;John Young&lt;/a&gt; in 2013. Details can be found in &lt;a href=&quot;http://www.australiangeographic.com.au/news/2013/07/night-parrot-tantalising-clues-revealed/&quot; rel=&quot;noreferrer&quot;&gt;this link&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.birdlife.org/datazone/speciesfactsheet.php?id=1491&quot; rel=&quot;noreferrer&quot;&gt;Birdlife.org&lt;/a&gt; the reason for its population to decrease significantly include predation by feral cats and foxes, altered fire regimes, competition for food, degradation of habitat near water by stock or rabbits, and reduced availability of water as a result of over-use by feral camels.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-28T05:03:37.513" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17708" PostTypeId="2" ParentId="14919" CreationDate="2014-05-28T05:24:05.477" Score="8" Body="&lt;p&gt;Hair colour is maintained by a pigment called &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanin&quot; rel=&quot;noreferrer&quot;&gt;Melanin&lt;/a&gt; which also affects skin colour too. When the melanin content in your hair decreases, it turns grey and eventually white. Multiple factors affect melanin levels in your body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) age&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Genetics&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Diseases&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) Cell Stress&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read about them in a little more detail &lt;a href=&quot;http://www.livestrong.com/article/205518-what-are-the-causes-of-hair-whitening/&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;. I cannot specifically pinpoint if you have deficiency in a particular mineral or the reason for your hair whitening is hereditary from your question. It could be a singular reason or a combination of different problems. Some solutions to treat hair can be found in this &lt;a href=&quot;http://www.home-remedies-for-you.com/articles/903/medicines-and-remedies/controlling-premature-white-hair.html&quot; rel=&quot;noreferrer&quot;&gt;link&lt;/a&gt; (and plenty more if you Google it). If that doesn't work, I would suggest you meet a certified Dermatologist specializing in hair treatment. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-09-10T04:09:21.280" LastActivityDate="2014-09-10T04:09:21.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17710" PostTypeId="2" ParentId="17696" CreationDate="2014-05-28T05:34:16.437" Score="2" Body="&lt;p&gt;Others have nicely summarized to different types of biological networks and how they can evolve. I would like to make a fine distinction between evolution and dynamic adaptation and add some comments about relative evolvabilities of different biological networks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given an architecture, a network can respond dynamically to different inputs. The preferred paths may change and the output characteristics can vary. Example cases include the effect of environment on metabolism. Personally, I would not consider this as network evolution because the architecture remains the same. Network evolution refers to rewiring or addition of new connections. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be apt to classify the biological networks like this: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;molecular networks&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Gene regulatory networks (GRN)&lt;/li&gt;&#xA;&lt;li&gt;Molecular (protein-protein) interaction networks (PPI)&lt;/li&gt;&#xA;&lt;li&gt;Cell signaling networks &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;cellular networks&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Neural networks&lt;/li&gt;&#xA;&lt;li&gt;Biofilms (?)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;organismal networks &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Ecological networks (food webs etc)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are several ways in which a network can evolve: Edge addition, edge deletion, edge modification, node addition, node deletion and node duplication. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In molecular networks &lt;strong&gt;edge modification&lt;/strong&gt; happens when the chemical interaction is affected. For e.g. in a gene regulatory network a promoter-Transcription Factor (TF) interaction can change if there is a mutation in promoter sequence or in the DNA binding domain of TF. Similar situation exists in the cases of PPI and ligand-receptor interactions (Though concept of mutation doesn't apply to ligands). &#xA;Gene (node) &lt;strong&gt;duplications&lt;/strong&gt; are also common mechanism of evolution of GRN. Gene &lt;strong&gt;deletions&lt;/strong&gt;/inactivations also change the network and in some cases result in complex diseases. Metabolic networks evolve if an enzyme mutates and a new pathway is created. &#xA;Usually &lt;strong&gt;node additions&lt;/strong&gt; rarely happen; &lt;strong&gt;node duplications&lt;/strong&gt; and &lt;strong&gt;edge modifications&lt;/strong&gt; are more common in molecular networks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In neural networks the plasticity is higher than molecular networks. There is a basic architecture that is essential to support life but the connections keep changing, nonetheless, in the non-core regions. Since active neurogenesis stops after a certain point, we can assume that number of nodes remains unchanged but &lt;strong&gt;edge addition&lt;/strong&gt; (new synapse), &lt;strong&gt;edge deletion&lt;/strong&gt; (synaptic pruning) and &lt;strong&gt;edge modification&lt;/strong&gt; (long term potentiation/depression) is quite rampant and widespread. In neurodegenerative diseases neurons die and therefore nodes are lost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ecological networks are affected by environment and geological barriers. So there are several subnetworks (ecosystems) that are weakly or strongly connected with each other. Introduction of foreign species (&lt;strong&gt;node addition&lt;/strong&gt;) causes immediate perturbation of the &lt;strong&gt;local&lt;/strong&gt; network architecture. Long term effects arise because of extinction (&lt;strong&gt;node deletions&lt;/strong&gt;), speciation (&lt;strong&gt;node evolution&lt;/strong&gt; leading to &lt;strong&gt;edge modification&lt;/strong&gt; i.e feeding habits etc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also to be noted that in all the cases the effect of a change on a network depends on which node/edge is affected; hubs are under tight scrutiny and are protected from perturbations because any dysregulation can lead to network collapse. Some networks also follow the preferential attachment behavior (which appears contradictory to hub preservation as a mechanism). I &lt;strong&gt;guess&lt;/strong&gt; that molecular networks do not employ preferential attachment whereas ecological networks do. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-05-28T11:29:30.760" LastActivityDate="2014-05-28T11:29:30.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17712" PostTypeId="2" ParentId="15730" CreationDate="2014-05-28T06:16:53.223" Score="3" Body="&lt;p&gt;The younger Joey remains attached to the teat from which it receives its milk for the period of nine months until it leaves the pouch. So that would be teat from which milk suitable for the newborn is available (&lt;a href=&quot;http://www.kidcyber.com.au/topics/kanga.htm&quot; rel=&quot;nofollow&quot;&gt;reference 1&lt;/a&gt; and &lt;a href=&quot;http://www.omgfacts.com/Animals/Kangaroos-can-produce-two-different-type/21148&quot; rel=&quot;nofollow&quot;&gt;reference 2&lt;/a&gt;). The older Joeys also have an incredible sense of smell by which it can detect the teat from which it gets the milk it requires but it stands to reason that they cant get milk from the teat to which the younger joey is attached. (&lt;a href=&quot;https://answersingenesis.org/mammals/australias-amazing-kangaroos-and-the-birth-of-their-young/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-28T06:16:53.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17714" PostTypeId="1" CreationDate="2014-05-28T06:32:43.257" Score="5" ViewCount="927" Body="&lt;p&gt;My son had a &lt;a href=&quot;https://en.wikipedia.org/wiki/Plantar_wart&quot; rel=&quot;nofollow&quot;&gt;plantar wart&lt;/a&gt; on his foot, which (as I understand it) is caused by a virus which only infects skin cells. Once in the skin cell the virus replicates, but when attacked by the immune system prompts the growth of a hard, thick layer of skin (callus). Warts are caused by a &lt;a href=&quot;https://en.wikipedia.org/wiki/Human_papillomavirus&quot; rel=&quot;nofollow&quot;&gt;HPV&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given the wart has infected a skin cell, and skin cells are next to each other in a great big sheet covering the entire human body, why is it that we don't become completely covered in wart?  I assume that it's not the immune system keeping the wart at bay, because the original wart isn't defeated and we can get other spot infections elsewhere.&lt;/p&gt;&#xA;" OwnerUserId="6860" LastEditorUserId="540" LastEditDate="2014-06-01T22:38:06.267" LastActivityDate="2014-06-26T17:48:00.883" Title="Why don't warts caused by HPV spread to the whole body?" Tags="&lt;virus&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17717" PostTypeId="2" ParentId="17446" CreationDate="2014-05-28T07:06:12.263" Score="3" Body="&lt;p&gt;I am no expert on the topic, but according to an &lt;a href=&quot;ftp://ftp.psy.gla.ac.uk/pub/frank/Depression_Wagner/outros/Maxi%20Project%20new/Papers/2010%20Brodmanns%20map%20review.pdf&quot; rel=&quot;nofollow&quot;&gt;article published&lt;/a&gt; on the centenary of his study, it states that the microscopical structure and classification of these areas are in parallel to the evolutionary distinction between old and new cortical subdivisions. So as and when new subdivisions are deduced (&lt;a href=&quot;http://en.wikipedia.org/wiki/Brodmann_area&quot; rel=&quot;nofollow&quot;&gt;based on its function, cytoarchitecture or the structure and organisation of cells&lt;/a&gt;) the map can be extended to include them. There was no upper limit to the number of divisions set in any article I read so it would be nice if you could provide some reference to where it says that the extension can be done to 54. If you are interested, you could have a look at the map published by &lt;a href=&quot;http://en.wikipedia.org/wiki/Constantin_von_Economo&quot; rel=&quot;nofollow&quot;&gt;Constantin von Economo&lt;/a&gt; in 1925.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-28T07:06:12.263" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17719" PostTypeId="1" AcceptedAnswerId="20331" CreationDate="2014-05-28T08:14:17.507" Score="4" ViewCount="133" Body="&lt;p&gt;Is consumption of blood more &lt;i&gt;&quot;dangerous&quot;&lt;/i&gt; compared to meat?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There was a news-article about unnatural chemicals found in the blood of mothers. This reminded me about a question I have pondered upon from time to time. Now, I am not a vampire, but curious as to the nature of blood vs meat in animals. More specifically unhealthy components.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are various examples of viruses being in danger of spreading by consumption of raw blood like ebola, H5N1 etc. (But then also meat etc.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps easier if I throw out some questions to show what I am asking:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Are there more of such in blood then meat? &lt;/li&gt;&#xA;&lt;li&gt;Are there other &lt;em&gt;things&lt;/em&gt; that can be worse in blood even after preparing? Like cooking, conservation etc.&lt;/li&gt;&#xA;&lt;li&gt;Are parasites etc. more frequently found in blood? &lt;/li&gt;&#xA;&lt;li&gt;Are there organisms that are highly resilient to heat treatment found in blood? &lt;/li&gt;&#xA;&lt;li&gt;Are there more heavy metals in blood then meat? (Which I assume cooking does not give much of a difference.) &lt;/li&gt;&#xA;&lt;li&gt;Other toxins?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Some references:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.eufic.org/article/en/food-safety-quality/animal-health/expid/review-animal-diseases/&quot; rel=&quot;nofollow&quot;&gt;http://www.eufic.org/article/en/food-safety-quality/animal-health/expid/review-animal-diseases/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.fao.org/avianflu/en/qanda.html&quot; rel=&quot;nofollow&quot;&gt;http://www.fao.org/avianflu/en/qanda.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6638" LastEditorUserId="6638" LastEditDate="2014-05-28T11:19:27.700" LastActivityDate="2019-03-16T02:56:06.517" Title="Blood consumption" Tags="&lt;bacteriology&gt;&lt;food&gt;&lt;hematology&gt;&lt;toxicology&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17720" PostTypeId="2" ParentId="10034" CreationDate="2014-05-28T08:49:52.393" Score="1" Body="&lt;p&gt;It could be better answered if you specified which species you were interested in. Broadly from &lt;a href=&quot;http://en.wikipedia.org/wiki/Saliva&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;, snakes have venom, some swifts have gummy saliva to help in the building of nests, spiders produce their web from salivary glands etc. This is too broad a topic. The human salivary composition is found on the Wikipedia page I have linked. Salivary compositions can change with habits which have been detailed in &lt;a href=&quot;https://www.google.co.in/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=3&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CEMQFjAC&amp;amp;url=http://oralpathol.dlearn.kmu.edu.tw/case/Journal%2520reading-intern-08-04/Saliva-function-composition-J%2520Comtemp%2520Dent%2520Pract-2008.pdf&amp;amp;ei=YKGFU_iXKs2WuATuuIGQDQ&amp;amp;usg=AFQjCNHyzf9tsFJU7wswS5XzV3r3giGhBQ&amp;amp;sig2=lOLRci0XFxrudih33J4MRg&amp;amp;bvm=bv.67720277,d.c2E&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;. To compare, I am also providing the &lt;a href=&quot;https://www.google.co.in/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=5&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CEgQFjAE&amp;amp;url=http://jeb.biologists.org/content/38/1/61.full.pdf?origin=publication_detail&amp;amp;ei=gaGFU6yrOJSfugTisIGwDg&amp;amp;usg=AFQjCNGEOKV8uPNwF9qPyqFa21P3rzJwFw&amp;amp;sig2=KlA3JbXwFb6Kc69h5RNR8A&amp;amp;bvm=bv.67720277,d.c2E&quot; rel=&quot;nofollow&quot;&gt;link to an article&lt;/a&gt; on the saliva composition of an assassin bug.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-28T08:49:52.393" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17721" PostTypeId="2" ParentId="9724" CreationDate="2014-05-28T09:31:09.070" Score="1" Body="&lt;p&gt;Scientists say that people can have multiple dreams every night and the ones that are not very significant are easily forgotten. Only those experiences that elicit an emotional response (happy, frightened) seem to stick in memory. Suggestions have also been made that being anxious or depressed makes our dreams stick to memory too (&lt;a href=&quot;http://www.everydayhealth.com/news/why-you-remember-or-forget-your-dreams/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). A study suggests that people woken up during &lt;a href=&quot;http://en.wikipedia.org/wiki/Rapid_eye_movement_sleep&quot; rel=&quot;nofollow&quot;&gt;REM sleep&lt;/a&gt; seem to recall their dreams more often (&lt;a href=&quot;http://www.wisegeek.org/why-do-i-sometimes-remember-my-dreams-vividly-and-other-times-not-at-all.htm&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Here is &lt;a href=&quot;http://www.asdreams.org/subidxeduq_and_a.htm&quot; rel=&quot;nofollow&quot;&gt;a link&lt;/a&gt; to some common questions about dreams. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-28T09:31:09.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17722" PostTypeId="2" ParentId="17303" CreationDate="2014-05-28T10:59:01.530" Score="2" Body="&lt;p&gt;As far as I can see from different articles, this seems to be a study in progress. Dr Kloock from the California state University states that scorpions might be more active when not exposed to UV light. If not fluorescing, they know that they are hidden and have a lesser chance of being preyed on. He argues that scorpions are less active on full moon nights rather than other days. (&lt;a href=&quot;http://www.nbcnews.com/id/43027595/ns/technology_and_science-science/t/glow-in-the-dark-scorpions-why-do-they-do-it/#.U4W9Nd_FtTN&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) Dr Kloock has also stated that the pigment could get used up on repeated exposure to UV light. He made an observation that scorpions whose pigments got used up were more active than those still fluorescing when exposed to UV light mimicking the moon and the stars. (&lt;a href=&quot;http://www.newscientist.com/article/mg20827903.700-scorpions-glow-in-the-dark-to-detect-moonlight.html#.U4W80d_FtTM&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) Dr Gaffin from the University of Oklahoma, in his studies have reported that scorpions might be converting UV light to turn it into the colour blue-green which is what they see best effectively turning their body into one big eye. His studies are consistent with Dr Kloock in that scorpions try to hide and avoid UV light (&lt;a href=&quot;http://blogs.discovermagazine.com/notrocketscience/2011/12/23/why-do-scorpions-glow-in-the-dark-and-could-their-whole-bodies-be-one-big-eye/#.U4W71t_FtTM&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Some scientists have also hypothesized that scorpions might glow to warn predators or that the pigments that make it glow are the accidental by products of certain chemical reactions in its body (&lt;a href=&quot;http://en.docsity.com/news/interesting-facts/scorpions-glow-uv-lights/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). There is no definite proof on this subject though.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-05-28T15:22:15.877" LastActivityDate="2014-05-28T15:22:15.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17723" PostTypeId="1" CreationDate="2014-05-28T12:58:56.543" Score="2" ViewCount="2816" Body="&lt;p&gt;I have some questions regarding Satellite chromsomes which could not be resolved by a google search.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Does the satellite consist of telomeric sequences ?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If not, What is the function of a satellite ? And where will the telomeric sequences be present - in the main body ? On the secondary constriction ?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Satellite chromosomes are also known as SAT chromosome which stands for Sino Acid Thymidine. I read in some sources that SAT means without thymidine. But how is that possible, if there is A then obviously there has to be T ? ( in dsDNA)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-05-29T15:07:42.827" Title="Properties of Satellite Chromosomes" Tags="&lt;dna&gt;&lt;chromosome&gt;&lt;chromatin&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17724" PostTypeId="2" ParentId="14673" CreationDate="2014-05-28T12:59:05.137" Score="1" Body="&lt;p&gt;I would go for &lt;a href=&quot;http://www.straincontrol.com&quot; rel=&quot;nofollow&quot;&gt;StrainControl Laboratory Manager.&lt;/a&gt; Works perfect and covers all needs of a lab. Do not go for all the &quot;free&quot; stuff since they rely on a active sponsor and your data is never safe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;StrainControl is free for 3 months and if you want to continue use it you simply purchase the Admin password and all your data is saved.&lt;/p&gt;&#xA;" OwnerUserId="6864" LastEditorUserId="1590" LastEditDate="2016-01-18T15:15:29.623" LastActivityDate="2016-01-18T15:15:29.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17725" PostTypeId="1" AcceptedAnswerId="17772" CreationDate="2014-05-28T13:02:46.750" Score="1" ViewCount="331" Body="&lt;p&gt;I found this claim in my study materials with explanation of amyloi plaques, in comparison to CJD (Creutzfeldt-Jakob Disease).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its characteristic are&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Long doubling time of at least 5.2 days (I think this means the time it takes to double the amount of prions in the target organ)&lt;/li&gt;&#xA;&lt;li&gt;NO Cypopathic Effect (CPE) in vitro&lt;/li&gt;&#xA;&lt;li&gt;Long incubation period (about 30 years)&lt;/li&gt;&#xA;&lt;li&gt;Vacuolation of neurons, amyloid-like plaques&lt;/li&gt;&#xA;&lt;li&gt;Deficient immunity&lt;/li&gt;&#xA;&lt;li&gt;Deficient immunoresponse&lt;/li&gt;&#xA;&lt;li&gt;Deficient Interferen (IFN) production&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;so this suggests me that the person with infection at a young age can have the disease then at an old age.&#xA;Other possible agent could be virus, but it seems that prion is the major one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can Alzheimer's disease be caused primarily by Slow Prion infection?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-05-30T09:10:20.857" Title="Can Alzheimer's disease be caused by Slow Prion infection?" Tags="&lt;microbiology&gt;&lt;prion&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17727" PostTypeId="2" ParentId="17704" CreationDate="2014-05-28T16:47:15.607" Score="1" Body="&lt;p&gt;Since you are using Bowtie, you want the indexed genome, see if that's not available here, instead of downloading the fasta and indexing it yourself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn&quot; rel=&quot;nofollow&quot;&gt;http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-05-28T16:47:15.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17728" PostTypeId="1" AcceptedAnswerId="17822" CreationDate="2014-05-28T17:39:13.333" Score="32" ViewCount="8584" Body="&lt;p&gt;1: There seem to be cases where coma patients with a non-active brain (i.e. flat EEG) have regained full consciousness. =&gt; Apparently memory and knowledge are stored independent of brain activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2: There seem to be animals (e.g. hamsters) that can be frozen to complete organic inactivity and will regain full functionality after being thawed. =&gt; Apparently the stored memory does not depend on blood flow and other support.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3: From this I assume that quickly cooling a human brain to a temperature low enough to avoid decomposition would preserve the state of that brain that corresponds to that human's memories, knowledge, cogntivie abilities, and maybe consciousness at the time of cooling. =&gt; With the proper technology that &quot;content&quot; is theoretically retrievable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Q: &lt;strong&gt;How long would that state remain after death in a brain left at room temperature?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or in other words: How long does it take for decomposition to destroy memory?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Addendum:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fact that the stored memory may not be accessible with current means is not relevant to my question. We cannot access the information stored in &lt;a href=&quot;http://en.wikipedia.org/wiki/Linear_A&quot;&gt;Linear A&lt;/a&gt;, but this unretrievability does not delete the information.&lt;/p&gt;&#xA;" OwnerDisplayName="user6268" LastEditorDisplayName="user6268" LastEditDate="2014-06-02T07:09:01.963" LastActivityDate="2019-03-07T02:40:37.473" Title="How long does it take for memory to disperse after death?" Tags="&lt;brain&gt;&lt;memory&gt;&lt;death&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="17729" PostTypeId="1" CreationDate="2014-05-28T19:03:42.747" Score="3" ViewCount="210" Body="&lt;p&gt;I am looking for professionally used representation of female chest (I know how it sounds ;). Generally - a model comprehensive enough to effectively represent human chest, with focus on breasts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The data it needs to represent are at least: width, height, depth, distance between cardinal points, so on. I do know there's a questionnaire for patients willing to undergo an implant operation - I'm looking around for something similiar. Optimally the model would be directed towards computer represenation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With that in mind, I've checked some computer implementations:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;SOFA (seems promising, but somewhat generic),&lt;/li&gt;&#xA;&lt;li&gt;MakeHuman (nice&#xA;customization, but again, pretty general).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I do not know whether this question is in scope of this site. If it's too specific, then consider the simplified: what are the methods used to describe female chests OR what would be a good source of information about these methods?&lt;/p&gt;&#xA;" OwnerUserId="6867" LastActivityDate="2014-05-28T19:03:42.747" Title="Human female chest model or data representation?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;computational-model&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17730" PostTypeId="1" CreationDate="2014-05-28T20:56:20.720" Score="3" ViewCount="963" Body="&lt;p&gt;I'm really stuck on this question. I'm being asked to find the half life of a drug.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Vd is 50L/kg. The clearance is 0.1 L/hr/kg. The patient weighs 70 kg. &#xA;Equation is:&#xA;T1/2 (halflife) = 0.693 * Vd / Cl.&#xA;I keep getting 0.693 * 50 / 0.1&#xA;               = 346.5&#xA;The right answer is 14.4 days but I can't figure it out.&#xA;Thanks in advance&lt;/p&gt;&#xA;" OwnerUserId="6868" LastActivityDate="2014-05-28T21:48:26.167" Title="Pharmacology Half Life Calculation" Tags="&lt;pharmacology&gt;&lt;pharmacokinetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17731" PostTypeId="2" ParentId="17730" CreationDate="2014-05-28T21:38:04.057" Score="6" Body="&lt;p&gt;You have done the calculation correctly it is just the answer you have is in hours, try dividing by 24. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A  good method of checking answers is to use a trick which is horribly called &quot;Dimensional Analysis&quot;. This basically means writing out your equations but use the units of each value rather than the value itself&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so in this case you have T1/2 = Vd/Cl      (removing the unitless 0.693)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the units for this are then ? = (L/kg)/(L/hr/kg)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;in this case the litres and the kilos cancel to 1/(1/hr) or just hours, comparing this with the correct answer which is in days should then be a little more obvious&lt;/p&gt;&#xA;" OwnerUserId="6811" LastEditorUserId="6811" LastEditDate="2014-05-28T21:48:26.167" LastActivityDate="2014-05-28T21:48:26.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17732" PostTypeId="1" AcceptedAnswerId="17755" CreationDate="2014-05-28T22:33:28.237" Score="2" ViewCount="55" Body="&lt;p&gt;B19 virus (about 20 nm) can; which I think is partially because of its small size; not sure of genomics has something to do with the passing. Rubella's (also called German measles) size is then again minimum 45 nm.&#xA;So I started to think if this virus can pass into the brain stem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can Rubella pass into the brain stem?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some studies are made about Rubella associated hemolysis.&#xA;I think it is not related with this question at all.&#xA;Rubella is diffused along carbon dioxide from capillaries into the brain stem, this is my hypothesis.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-05-29T20:19:03.143" LastActivityDate="2014-05-29T21:02:09.910" Title="Can Rubella virus pass into brain stem?" Tags="&lt;microbiology&gt;&lt;brain-stem&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17734" PostTypeId="2" ParentId="7115" CreationDate="2014-05-28T23:27:31.563" Score="1" Body="&lt;p&gt;Mammals have what are called intrinsically photosensitive retinal ganglion cells (ipRGCs) (&lt;a href=&quot;http://en.wikipedia.org/wiki/Intrinsically_photosensitive_retinal_ganglion_cells&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;), including bats (&lt;a href=&quot;http://a465gilwern2brynmawr.files.wordpress.com/2014/02/dd590-bats-and-light-pollution.pdf&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;). These cells are responsible for modulating mammals circadian rhythms (differently for diurnal and nocturnal species). These cells are interesting because retinal ganglion cells are not normally photosensitive, but receive high acuity images from rods and cones. Interestingly, people with cone-rod retinal dystrophy (including those with complete blindness) still have their circadian rhythms set by ipRGCs in the retina, because these cells are spared. This was unfortunately demonstrated by a doctor that removed the eyes of someone who was blind, which resulted in the patient being unable to have a regular sleep cycle (citation needed).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, even though bats (may?) have poor eyesight, ipRGCs in their retina still set their circadian rhythms. I don't believe they are afraid of the sunlight per se, but the sunlight makes them sleepy. They typically use echolocation at night.&lt;/p&gt;&#xA;" OwnerUserId="6043" LastActivityDate="2014-05-28T23:27:31.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17738" PostTypeId="2" ParentId="8802" CreationDate="2014-05-29T06:03:24.880" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.antweb.org/antblog/2012/11/can-ants-predict-rain-max-gold-coast-australia.html&quot; rel=&quot;nofollow&quot;&gt;An article&lt;/a&gt; suggests that many animals and plants have an instinctual response to seasonal cues like light levels or day length (&lt;a href=&quot;http://en.wikipedia.org/wiki/Photoperiodism&quot; rel=&quot;nofollow&quot;&gt;photoperiod&lt;/a&gt;). Also they may be influenced by &lt;a href=&quot;http://www.springerreference.com/docs/html/chapterdbid/114606.html&quot; rel=&quot;nofollow&quot;&gt;circannual clocks&lt;/a&gt; which depend on factors like temperature, the photoperiod and the increase or decrease in food levels available. There is also some speculation that ants may be influenced by barometric pressure changes though there is no literature available for the same (&lt;a href=&quot;http://www.antweb.org/antblog/2012/01/ants-and-rain-in-australia-roger-new-south-wales-australia.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). There are methods that ants have devised to escape rain some of which are mentioned in this &lt;a href=&quot;http://indianapublicmedia.org/amomentofscience/ants-out-in-the-rain/&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt;. You might be interested in reading &lt;a href=&quot;https://www.google.co.in/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=22&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CC8QFjABOBQ&amp;amp;url=http://web.utk.edu/~nsanders/Pubs/Heller-Oecologia.pdf&amp;amp;ei=xr-GU_OAD8aSuASW7ILQBA&amp;amp;usg=AFQjCNENfwGKnzfx9J4WxsX4Fd_dUIhFwQ&amp;amp;sig2=lBosYt0z5hLM-EunTQY4TQ&amp;amp;bvm=bv.67720277,d.c2E&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; on the spread of Argentine ants being influenced by rain. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-05-31T10:21:59.180" LastActivityDate="2014-05-31T10:21:59.180" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17739" PostTypeId="2" ParentId="16436" CreationDate="2014-05-29T06:43:29.190" Score="3" Body="&lt;p&gt;The sticky feeling comes from the sugars present in soft drinks. The sugar sticking to the surface of the teeth is then broken down into acids by bacteria and this affects the teeth. A list of the amount of sugars in different soft drinks can be found &lt;a href=&quot;http://www.sugarstacks.com/beverages.htm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. Also reading the dental decay section of &lt;a href=&quot;http://en.wikipedia.org/wiki/Soft_drink#Dental_decay&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; gives the info that many carbohydrates are present including glucose, fructose and sucrose. On a dentistry forum (&lt;a href=&quot;http://www.sharecare.com/health/diet-and-teeth/drinking-soft-drinks-oral-health&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;), it says that even artificial sugars can stick to teeth and get metabolized except &lt;a href=&quot;http://en.wikipedia.org/wiki/Xylitol&quot; rel=&quot;nofollow&quot;&gt;xylitol&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-29T06:43:29.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17740" PostTypeId="2" ParentId="16512" CreationDate="2014-05-29T07:03:50.120" Score="2" Body="&lt;p&gt;The answers to your 3 questions are no, no and no. The 3 meal concept is more of a recent concept when you compare that Ancient Romans used to frown upon eating more than once a day. You can read a brief history of how food habits evolved in &lt;a href=&quot;http://www.bbc.com/news/magazine-20243692&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;. Food habits have been variable all throughout history and it still varies by culture. Food habits divided by different eras can be read in &lt;a href=&quot;http://www.foodtimeline.org/foodfaq7.html&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;. In the current age and time, I think we just try to spread our calorie intake over the day and that is why we try to stick to the 3 meal concept.(&lt;a href=&quot;http://www.livestrong.com/article/43876-eat-three-meals-day/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). There is no biological reason as far as I could see (&lt;a href=&quot;http://www.alternet.org/story/152486/there_is_no_biological_reason_to_eat_three_meals_a_day_--_so_why_do_we_do_it&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Just a matter of improved health consciousness and understanding of the human body. This &lt;a href=&quot;http://authoritynutrition.com/how-many-meals-per-day/&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; contain some interesting thoughts on meal timings and optimal intake. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-29T07:03:50.120" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17741" PostTypeId="1" AcceptedAnswerId="17744" CreationDate="2014-05-29T07:40:34.263" Score="2" ViewCount="71" Body="&lt;p&gt;Wikipedia says Caliciviridae Family.&#xA;My notes say that Norovirus includes the following&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Noroviruses&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Norwalk-like viruses&lt;/li&gt;&#xA;&lt;li&gt;Caliciviruses&lt;/li&gt;&#xA;&lt;li&gt;Astroviruses and some small gastroenteroviruses&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which is a larger definition including at least two families than the Wikipedia definition.&#xA;I think &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Caliciviruses $\subset$ Caliciviridae &lt;/li&gt;&#xA;&lt;li&gt;Astroviruses and some small gastroenteroviruses $\subset$ astroviridae&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;so the note is taking subsets among different families and classifying them into abstract class called &lt;strong&gt;Noroviruses&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Extension based by Chris' excellent &lt;a href=&quot;https://biology.stackexchange.com/a/17744/86&quot;&gt;answer&lt;/a&gt;.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Criteria of Noroviruses&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;(+)sense ssRNA viruses&lt;/li&gt;&#xA;&lt;li&gt;Structure and replication: &#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1) only (+)sense ssRNA, &lt;/li&gt;&#xA;&lt;li&gt;2) simple nucleocapsid viruses, &lt;/li&gt;&#xA;&lt;li&gt;3) only viruses transmitted by fecal-oral route, &lt;/li&gt;&#xA;&lt;li&gt;4) size about 30 nm in diameter. &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and then final classification of Noroviruses by these criteria&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Noroviruses&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Noroviruses&lt;/strong&gt; $\subset$ Norwalk-like viruses ($\subset$ F. Caliciviruses)&lt;/li&gt;&#xA;&lt;li&gt;Some Astroviruses ($\subset$ F. astroviridae) and some small gastroenteroviruses (what?)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which, however, does not make sense since Caliciviridae $\not\subset$ Astroviridae.&#xA;I do not understand what is the point of referring to the viruses by the sentence&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Astroviruses and some other round/small gastroenteris viruses&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;which are not part of Astroviridae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which viruses of Caliciviridae are similar to &lt;em&gt;Astroviruses that are apparently round and small gastroenteritis viruses&lt;/em&gt;?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-05-30T13:41:53.637" Title="Do Noroviruses include many families?" Tags="&lt;virus&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17742" PostTypeId="1" AcceptedAnswerId="19139" CreationDate="2014-05-29T09:27:42.727" Score="4" ViewCount="3036" Body="&lt;p&gt;Digesting (trypsin or whatever other proteolytic enzyme) proteins generates multiple peptides  so the degree of complexity of the sample, at the peptide level, increases a lot. In addition there is the problem of infering the original protein from its constituent peptides. &#xA;Why is this digestion step needed when you have to go back to protein level ? Is it just technological limitation? &lt;/p&gt;&#xA;" OwnerUserId="6872" LastActivityDate="2014-06-16T09:41:13.443" Title="Why digest proteins into peptides for Liquid Chromatography - Mass Spectrometry?" Tags="&lt;proteins&gt;&lt;chromatography&gt;&lt;mass-spectrometry&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17743" PostTypeId="2" ParentId="17742" CreationDate="2014-05-29T11:31:33.887" Score="3" Body="&lt;p&gt;This is going to be a very long answer but to give a short response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You have to consider that MS for peptide detection works on the bases/principle of mass to charge (m/z) to detect an AA molecule, which is then normalised and analysed etc etc (&lt;a href=&quot;http://en.wikipedia.org/wiki/Mass_spectrometry&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Mass_spectrometry&lt;/a&gt;). Once you have the amino acids, then you just look at the order in which they get through and then you have your peptide sequence. Please read about the B, A and Y-type ions although this page is slightly technical (&lt;a href=&quot;http://www.matrixscience.com/help/fragmentation_help.html&quot; rel=&quot;nofollow&quot;&gt;http://www.matrixscience.com/help/fragmentation_help.html&lt;/a&gt;). If the proteins was not digested then it would be far too big to be analysed since it would be read as one massive blob of m/z, which could be anything! So once you have your spectra from a peptide, you need to compare it to a model spectra, and based on that you predict what the sequence is as fragmentations peaks can be anything. Look at SEQUEST (&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_mass_spectrometry_software&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/List_of_mass_spectrometry_software&lt;/a&gt;). Now there are tons of correction algorithms that are applied, which you can look up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now RP-LC is carried out before MS to prevent all the sample rushing into the MS machine all at once as the machine can not cope if too much sample is inserted hence the flow rate is controlled. What I think you are thinking in terms of the set machine limit, is the (digested) peptide fragment that enters the machine, before undergoing electrospray. Now the experts that run the MS machines do set a peptide mass upper and lower limit, for what size/mass of fragment to accept and what size/mass to ignore. Look at this theoretical digest example (&lt;a href=&quot;http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msdigest&quot; rel=&quot;nofollow&quot;&gt;http://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msdigest&lt;/a&gt;). This happens frequently with trypsin digest as it recognises specific AA before cleavage (&lt;a href=&quot;http://en.wikipedia.org/wiki/Trypsin&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Trypsin&lt;/a&gt;). Now a days, MS has advanced so much that we have machines such as Orbitrap (&lt;a href=&quot;http://en.wikipedia.org/wiki/Orbitrap&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Orbitrap&lt;/a&gt;), which can cope with peptides, digested with elastase, which cleaves non specifically, which means you are less likely to get peptides that are far too big for analysis, hence increasing the protein coverage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-29T11:31:33.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17744" PostTypeId="2" ParentId="17741" CreationDate="2014-05-29T11:59:18.947" Score="6" Body="&lt;p&gt;You are mixing different things here: Virus are grouped based on their genetic material (dsDNA, ssDNA ssRNA and so on) into several groups (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Virus_classification&quot;&gt;here&lt;/a&gt; for details), then grouped into families, subgrouped into a genus and then into species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it is: Group &gt; Family &gt; Genus &gt; Species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you have here are are different positions in this classification.&#xA;The names you mention belong all to the same tree:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Group: IV (&lt;a href=&quot;http://en.wikipedia.org/wiki/Positive-sense_ssRNA_virus#Group_IV.E2.80.94positive-sense_ssRNA_viruses&quot;&gt;(+)ssRNA-Viruses&lt;/a&gt;) &gt; Family (&lt;a href=&quot;http://en.wikipedia.org/wiki/Caliciviridae&quot;&gt;Caliciviridae&lt;/a&gt;) &gt; Genus (&lt;a href=&quot;http://en.wikipedia.org/wiki/Norovirus&quot;&gt;Norovirus&lt;/a&gt;) &gt; Species (&lt;a href=&quot;http://en.wikipedia.org/wiki/Norwalk_virus&quot;&gt;Norwalk Virus&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Astrovirus&quot;&gt;Astrovirus&lt;/a&gt; belongs into the same group, but then form an own family.&#xA;To answer your question: No, since the Norovirus forms its own genus in the caliciviridae family.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-05-29T19:33:27.400" LastActivityDate="2014-05-29T19:33:27.400" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17745" PostTypeId="2" ParentId="17723" CreationDate="2014-05-29T14:02:11.563" Score="1" Body="&lt;p&gt;If by &quot;satellite chromosomes&quot; you mean &quot;satellite repeats&quot;, then:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Not always. There many types of satellites, such as telomeric, centromeric (like gamma, alpha, beta satellites), simple repeats (CT)n.   &lt;/li&gt;&#xA;&lt;li&gt;It is still an open question. Some say they are important for chromosome structure (e.g., centromeres). Sometimes satellites get transcribed as might act as lncRNAs. And of course, most of them are just junk DNA.&lt;/li&gt;&#xA;&lt;li&gt;If there is &lt;code&gt;T&lt;/code&gt; then there is &lt;code&gt;A&lt;/code&gt; too. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Satellites contain telomeric repeats at their ends as all chromosomes do. But they are more about NOR repeats.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;They are important for the nucleolus functioning. But shorts arms of acrocentric chromosomes are not crucial, take Robertsonian translocation as an example.    &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="744" LastEditorUserId="744" LastEditDate="2014-05-29T15:07:42.827" LastActivityDate="2014-05-29T15:07:42.827" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17747" PostTypeId="1" AcceptedAnswerId="17748" CreationDate="2014-05-29T15:02:36.407" Score="12" ViewCount="466" Body="&lt;p&gt;I have taken this picture of a bird in university zoo in Tel Aviv. It was approximately 25 cm high and seemed to be a flightless species. Can somebody help me identify it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rwTaI.jpg&quot; alt=&quot;A bird&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6875" LastActivityDate="2014-05-29T15:38:19.137" Title="Identify a bird" Tags="&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17748" PostTypeId="2" ParentId="17747" CreationDate="2014-05-29T15:38:19.137" Score="10" Body="&lt;p&gt;It's a Black Crowned Night Heron, &lt;em&gt;Nycticorax nycticorax&lt;/em&gt;, in my opinion - you can read more about it &lt;a href=&quot;http://www.planetofbirds.com/black-crowned-night-heron-nycticorax-nycticorax-2&quot;&gt;here&lt;/a&gt;. Key to it's identification is the shape of the body and bill, it's characteristic of species from the heron family such as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Green_heron&quot;&gt;green heron&lt;/a&gt;. The range is right and the red eye is a good clue too.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-05-29T15:38:19.137" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17750" PostTypeId="2" ParentId="17728" CreationDate="2014-05-29T17:32:19.593" Score="6" Body="&lt;p&gt;Once the thermodynamically irreversible processes we call brain-death have occurred both memories and the machinery to retrieve them are lost. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not an answer but a cavil with the premise of the question. Challenges that do not destroy the brain itself are different from those that do. In particular there may be a big difference between hypoxia during periods of low metabolic rate$^1$ and hypoxia at room temperature without lowering of metabolic rates, which by most accounts leads to brain death in about 6-8 minutes.$^2$ The assumption underlying the title of the question is unsupported and opinion-based.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^1$ See the pretty well-known case of Mitsutaka Uchikoshi, and see News Physiol. Sci. 13: 149-153, 1998, detailing case of a meditation adept who was able to drastically lower metabolic levels.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^2$ See the Wiki page on apnea. Sources avoid putting a time after which brain death is certain, and the definition is not uniform. The one thing they agree on is that it is irreversible; so if someone (or, say, a hamster) recovers from putative brain-death, they were neither factually nor legally dead.        &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-06-02T09:41:28.210" LastActivityDate="2014-06-02T09:41:28.210" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="17751" PostTypeId="1" CreationDate="2014-05-29T18:29:42.930" Score="1" ViewCount="457" Body="&lt;p&gt;This must be an error&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Just as proteins have a polarity defined by the amino and carboxyl&#xA;  termini, oligosaccharides have a polarity defined by their reducing&#xA;  and nonreducing ends. The carbohydrate unit at the reducing end has a&#xA;  free anomeric carbon atom that has reducing activity because it can&#xA;  form the open-chain form, as discussed earlier (p. 325). By&#xA;  convention, this end of the oligosaccharide is still called the&#xA;  &lt;strong&gt;nonreducing&lt;/strong&gt; end even when it is bound to another molecule such as a&#xA;  protein and thus no longer has reducing properties.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In my opinion, this sentence only makes sense if it would read &lt;strong&gt;reducing&lt;/strong&gt;. Can anyone confirm?&lt;/p&gt;&#xA;" OwnerUserId="4971" LastActivityDate="2014-05-30T04:36:14.617" Title="Error in textbook" Tags="&lt;book-recommendation&gt;&lt;carbohydrates&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17752" PostTypeId="2" ParentId="17741" CreationDate="2014-05-29T19:25:10.017" Score="1" Body="&lt;p&gt;I take &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi&quot; rel=&quot;nofollow&quot;&gt;NCBI's taxonomy&lt;/a&gt; any day over what wikipedia says. According to NCBI Caliciviridae includes Lagovirus, Nebovirus, Norovirus, Recovirus, Sapovirus, Vesivirus, Secalivirus, etc. For example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Caliciviridae; Norovirus; Norwalk virus; Chiba virus&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, due to the absence of universal phylogenetic marker genes, viral taxonomy is mostly based on capsid shape and isn't thus very accurate..&lt;/p&gt;&#xA;" OwnerUserId="5784" LastActivityDate="2014-05-29T19:25:10.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17753" PostTypeId="1" CreationDate="2014-05-29T19:54:40.787" Score="1" ViewCount="1067" Body="&lt;p&gt;A motor protein like kinesin-1 cannot use an IF as a track because it lacks polarity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone elaborate on this answer?&lt;/p&gt;&#xA;" OwnerUserId="6524" LastEditorUserId="57" LastEditDate="2014-05-29T20:12:38.803" LastActivityDate="2014-05-30T00:46:35.283" Title="Why can't intermediate filaments be used as tracks by motor proteins?" Tags="&lt;cell-signaling&gt;&lt;cytoskeleton&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17754" PostTypeId="1" CreationDate="2014-05-29T20:32:43.783" Score="5" ViewCount="80" Body="&lt;p&gt;Recently a discovery was made of a ~12,000 year old girl in Hoyo Negro in Mexico.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has been covered by many &lt;a href=&quot;http://www.cnn.com/2014/05/16/world/americas/skeleton-mexico-americans/&quot;&gt;different&lt;/a&gt; &lt;a href=&quot;http://www.nydailynews.com/news/world/scientists-find-12-000-year-old-skeleton-mexican-cave-article-1.1794735&quot;&gt;news&lt;/a&gt; agencies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm confused however by many of the reports.  Does it strengthen the hypothesis that the ancestors to the Native Americans came over the Bering Strait?  Or is there still some doubt on the matter?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, what are the arguments against the Bering Strait migration?&lt;/p&gt;&#xA;" OwnerUserId="6630" LastEditorUserId="6630" LastEditDate="2014-05-29T21:14:04.793" LastActivityDate="2014-07-27T06:23:22.307" Title="Implications of what the discovery of Naia means" Tags="&lt;human-genetics&gt;&lt;anthropology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17755" PostTypeId="2" ParentId="17732" CreationDate="2014-05-29T21:02:09.910" Score="2" Body="&lt;p&gt;It obviously can do that, causing a rubella encephalitis. A specialized form seems to be the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Progressive_rubella_panencephalitis&quot; rel=&quot;nofollow&quot;&gt;Progressive rubella panencephalitis&lt;/a&gt;&quot;, which is very rare with only 20 cases described since its first description in 1974.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About rubella encephalitis more papers are available, see these for a start:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9450233&quot; rel=&quot;nofollow&quot;&gt;Neurological aspects of rubella virus infection.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17609643&quot; rel=&quot;nofollow&quot;&gt;Mumps encephalitis: return with a vengeance.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.karger.com/Article/Abstract/150543&quot; rel=&quot;nofollow&quot;&gt;Neurological Aspects of Rubella Virus Infection&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-29T21:02:09.910" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17756" PostTypeId="1" AcceptedAnswerId="17796" CreationDate="2014-05-29T21:36:11.990" Score="7" ViewCount="1004" Body="&lt;p&gt;I took the following picture of this spider in northern Switzerland (alt: ~700m) with macro flash (then it is not so big: probably around 2-3 cm, including the legs)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8WCUb.jpg&quot; alt=&quot;Spider_night&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This spider made its web on the house and it goes out only during night.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this region we have many &lt;em&gt;Araneus diadematus&lt;/em&gt;, but this one looks totally different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it the same family or another? Does anybody have a clue for the real name?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE: I saw it this afternoon (gave a fly to the web to make it go out), the body is probably around 7-8 mm wide and 9-11 mm long). And now I am sure the colors are more or less right.  &lt;/p&gt;&#xA;" OwnerUserId="6561" LastEditorUserId="6561" LastEditDate="2020-11-16T21:58:41.830" LastActivityDate="2020-11-16T21:58:41.830" Title="What is this spider?" Tags="&lt;species-identification&gt;&lt;arachnology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17757" PostTypeId="1" AcceptedAnswerId="19713" CreationDate="2014-05-29T22:03:10.523" Score="6" ViewCount="376" Body="&lt;p&gt;I took the following picture of this spider in northern Switzerland (alt: ~700m) with macro flash/lense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qSF3J.jpg&quot; alt=&quot;spider in thuja&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The picture was taken during the night in a cedar tree (Thuja occidentalis).&lt;/p&gt;&#xA;" OwnerUserId="6561" LastEditorUserId="5331" LastEditDate="2014-07-16T06:49:54.640" LastActivityDate="2014-07-16T06:49:54.640" Title="What is this spider hunting in the tree in the night?" Tags="&lt;species-identification&gt;&lt;arachnology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17758" PostTypeId="2" ParentId="17753" CreationDate="2014-05-30T00:46:35.283" Score="1" Body="&lt;p&gt;Polarity essentially means a plus end (growing/polymerising) and a minus end (depolymerising). Look at microtubule (MT) (&lt;a href=&quot;http://en.wikipedia.org/wiki/Microtubule&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Microtubule&lt;/a&gt;). So molecules such as Kinesin-1 (&lt;a href=&quot;http://en.wikipedia.org/wiki/Kinesin&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Kinesin&lt;/a&gt;) use the hetero-dimeric nature of MT (alpha and beta subunits) and its polarity to orient themselves and move directionally along MT in an energy dependent manner.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-30T00:46:35.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17759" PostTypeId="1" CreationDate="2014-05-30T02:44:35.427" Score="0" ViewCount="167" Body="&lt;p&gt;Which of the following functions is NOT performed by the liver?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) Storage of vitamins and minerals&#xA;b) converts glucose to glycogen&#xA;c) converts toxins to harmless chemicals&#xA;d) produces bile&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I chose b and got it wrong, any help?&lt;/p&gt;&#xA;" OwnerUserId="6877" LastEditorUserId="10045" LastEditDate="2014-11-08T15:36:47.853" LastActivityDate="2014-11-08T15:36:47.853" Title="Question about what the liver does NOT do" Tags="&lt;homework&gt;&lt;digestive-system&gt;&lt;liver&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17761" PostTypeId="2" ParentId="17751" CreationDate="2014-05-30T04:36:14.617" Score="2" Body="&lt;p&gt;In case of oligosaccharides, only the &lt;em&gt;final&lt;/em&gt; ends matter and not the ends of the individual monosaccharides involved in glycosidic linkage. As a consequence, most oligosaccharides have only one reducing and one non-reducing ends.&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/JWYJH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure what the textbook means by the last line but the following two possibilities seem to be consistent with the understanding of oligosaccharide structure.  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;There is no mistake and the end being talked about is the left end of the monosaccharide on left in the diagram . This monosaccharide has both its ends non-reducing, but only one of these ends will be called the non-reducing end even though the other end(formerly reducing end) is now involved in glycosidic linkage and is hence non-reducing. The &lt;em&gt;it&lt;/em&gt; in the last line in this case refers to the entire monosaccharide (and not the end of concern), which has lost its reducing ability.   &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There is a mistake. And the end being talked about is the right end of the monosaccharide on the left. It is usually not referred to as the reducing end (which is the rightmost end), but for the case of explaining the polarity of the monosaccharide, it can be referred to as the reducing end.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2014-05-30T04:36:14.617" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17762" PostTypeId="2" ParentId="17759" CreationDate="2014-05-30T04:48:24.513" Score="6" Body="&lt;p&gt;Liver does all those functions as far as I know. The liver &lt;a href=&quot;http://en.wikipedia.org/wiki/Hepatocyte&quot;&gt;hepatocyctes&lt;/a&gt; are stimulated to create the enzyme glycogen synthase which promotes the conversion of glucose to glycogen in the presence of insulin. Glycogen is stored in the liver after its production for further use. The whole process is explained in detail in &lt;a href=&quot;http://www.cliffsnotes.com/sciences/biology/biochemistry-i/carbohydrate-metabolism-ii/storage-of-glucose-as-glycogen&quot;&gt;this page&lt;/a&gt;. Regarding the storage of vitamins and minerals, I have a paper which details the &lt;a href=&quot;http://jn.nutrition.org/content/33/1/53.full.pdf&quot;&gt;absorption and storage of Vitamin A in rat liver&lt;/a&gt;.  I am also linking another paper that details the presence of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1413443/&quot;&gt;Vitamin B12 in the human liver&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-30T04:48:24.513" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17763" PostTypeId="1" AcceptedAnswerId="17776" CreationDate="2014-05-30T05:20:24.607" Score="3" ViewCount="255" Body="&lt;p&gt;Since DNA is double stranded and each strand is complementary to the other, the codons on each strand will come out to be different after transcription(depending on the reading frame). Does this mean &quot;each strand of DNA&quot; codes for different set of proteins?&lt;/p&gt;&#xA;" OwnerDisplayName="user6417" LastActivityDate="2021-01-01T11:37:11.157" Title="dsDNA translation" Tags="&lt;dna&gt;&lt;translation&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17764" PostTypeId="2" ParentId="17763" CreationDate="2014-05-30T05:45:57.183" Score="1" Body="&lt;p&gt;DNA is not always double stranded. Anyway, typically, you have islands of protein-coding genes in both strands in all six frames, i.e. a set of genes in the forward strand, then a set of genes in the reverse strand, then again a set of genes in the forward strand, etc.&lt;/p&gt;&#xA;" OwnerUserId="5784" LastActivityDate="2014-05-30T05:45:57.183" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="17765" PostTypeId="1" AcceptedAnswerId="17768" CreationDate="2014-05-30T05:52:30.040" Score="7" ViewCount="1584" Body="&lt;p&gt;I know that veins carry oxygen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Veins look blue because the &lt;strong&gt;oxygen-depleted blood&lt;/strong&gt; in them is blue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this true??&lt;/p&gt;&#xA;" OwnerUserId="6878" LastEditorUserId="1320" LastEditDate="2014-05-30T06:56:05.273" LastActivityDate="2014-05-30T06:56:05.273" Title="Why do veins look blue?" Tags="&lt;human-biology&gt;&lt;blood-circulation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17766" PostTypeId="1" CreationDate="2014-05-30T06:01:49.117" Score="1" ViewCount="135" Body="&lt;p&gt;Plateletpheresis is seperation of platelets from whole blood and putting the leukocytes and erythrocytes back into the blood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the person donating platelets does not have hemophilia than could a hemophilia patient get a periodic transfusion of platelets from a non-hemophiliac platelet donor so that his hemophilia is less severe whether it is hemophilia A or hemophilia B? &lt;/p&gt;&#xA;" OwnerUserId="5851" LastActivityDate="2014-05-30T06:01:49.117" Title="Plateletpheresis for hemophilia" Tags="&lt;pathology&gt;&lt;human-genetics&gt;&lt;hematology&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17768" PostTypeId="2" ParentId="17765" CreationDate="2014-05-30T06:41:16.923" Score="11" Body="&lt;p&gt;Well, even though most people presume that it appears blue (&lt;a href=&quot;http://scienceblogs.com/gregladen/2008/02/11/is-blood-ever-blue-science-tea/&quot;&gt;reference&lt;/a&gt;) is due to the blood being deoxygenated, it is actually not the truth because blood is never blue whether it is deoxygenated or not. In a paper by Dr Alwin Kienle titled &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21085227&quot;&gt;Why do veins appear blue? A new look at an old question&lt;/a&gt;, the authors measured how much light of various wavelengths was reflected from both real blood vessels in skin and imitation vessels in a skin-like environment. The synthetic vessel (which was a capillary tube filled with blood and placed in a milky substance with optical properties similar to skin) allowed the authors to experiment with a variety of parameters (particularly vessel depth and diameter), and they were then able to validate their results by taking measurements on actual vessels in skin. They eventually came to the conclusion that the optical properties of skin and blood is what makes the veins appear blue. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I quote from the paper as to the reason of blood appearing blue. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Blue light does not penetrate as deeply into tissue as red light.&#xA;  Therefore, if the vessel is sufficiently deep, the reflectance in the&#xA;  blue will be affected to a lesser extent. Deoxygenated venous blood&#xA;  has a greater absorption coefficient than oxygenated arterial blood in&#xA;  the red spectral region, and this difference of two, rather small,&#xA;  values is amplified because of the long path length of red light in&#xA;  scattering tissue. As a result, veins are more likely to look blue&#xA;  than arteries at the same diameter and depth. Often arteries are not&#xA;  seen at all because they are generally smaller than veins and have&#xA;  thicker vessel walls. It has been shown that a small vessel will look&#xA;  red when close to the surface. However, if a superficial vessel is&#xA;  large it can still look bluish, particularly in the case of the vein.&#xA;  On the other hand, if the depth of a vessel is large, even red&#xA;  remitted light will not be influenced by the vessel, and it will not&#xA;  be seen.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So in short, the blue appearance could be attributed more to the location of the vein than just the deoxygenation. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-05-30T06:41:16.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17769" PostTypeId="2" ParentId="14126" CreationDate="2014-05-30T07:31:19.150" Score="1" Body="&lt;p&gt;Secondary infection is not rare at all. I mean consider babies. When they get the cold their immune system is weak and focused on the cold virus and they can get viral pneumonia from the flu very easily for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TB is another good example of a disease often weakening the immune system and raising the probability of a secondary infection and HIV is a viral one with the same weakening and higher probability of secondary infection.&lt;/p&gt;&#xA;" OwnerUserId="5851" LastActivityDate="2014-05-30T07:31:19.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17770" PostTypeId="1" AcceptedAnswerId="17771" CreationDate="2014-05-30T07:42:07.310" Score="7" ViewCount="2050" Body="&lt;p&gt;ATP synthase is used by cells to synthesise ATP from ADP using energy from a proton gradient. Depending on which sites I look at, this is either a universal feature of living cells, or it's &quot;almost universal&quot;, used by the vast majority of organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Superbeast points out in a comment, ATP can also be synthesised on the substrate level via the Krebs cycle. However, I would like to know if there are any organisms that &lt;em&gt;only&lt;/em&gt; synthesise ATP this way. In other words, are there any known organisms that entirely lack the ability to produce ATP synthase, and produce ATP entirely through the Krebs cycle, or through some other mechanism not related to ATP synthase?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there are, I would like some information about them. Are there many such species or just a few? Are they all prokaryotes or all eucaryotes, or some of each? What kind of environments do they live in?&lt;/p&gt;&#xA;" OwnerUserId="3347" LastEditorUserId="3347" LastEditDate="2014-06-02T02:50:08.277" LastActivityDate="2014-06-02T02:50:08.277" Title="Are there any organisms that lack ATP synthase?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17771" PostTypeId="2" ParentId="17770" CreationDate="2014-05-30T07:59:11.463" Score="4" Body="&lt;p&gt;As Superbest mentioned, substrate level phosphorylation (SLP) is alternative pathway by which ADP is phosphorylated to ATP. In SLP, phosphorylation is coupled with a highly exergonic chemical reaction. Fermentative organisms (both fully and temporally fermentative) organisms depend on SLP for ATP. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note&lt;/strong&gt;: fermentative $\neq$  anaerobic&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fermentation can either be a temporary situation, depending on the growth substrate (for e.g. yeast) or the only option as in the case of amitochondriate organisms like &lt;em&gt;Entamoeba&lt;/em&gt;. You can refer &lt;a href=&quot;http://www.springer.com/life+sciences/microbiology/book/978-3-540-76732-9&quot; rel=&quot;nofollow&quot;&gt;this book&lt;/a&gt; if it is available to you. See &lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/365/1541/713.long&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also see the wikipedia page on fermentation; it mentions the SLP steps. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-05-30T14:38:50.023" LastActivityDate="2014-05-30T14:38:50.023" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17772" PostTypeId="2" ParentId="17725" CreationDate="2014-05-30T09:01:25.583" Score="2" Body="&lt;p&gt;Dr Yong in the paper titled &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3054270/&quot; rel=&quot;nofollow&quot;&gt;Prion, The unconventional slow Infectious agent&lt;/a&gt; states that the formation of amyloid plaque which is a major contributor to Alzheimer's disease is a unconventionally slow infectious disease (&lt;a href=&quot;http://en.wikipedia.org/wiki/Prion&quot; rel=&quot;nofollow&quot;&gt;Prion&lt;/a&gt;). Some papers have also pointed out the similarities between Alzheimers and prion disorders (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC46935/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) Cerebral amyloid plaques have also been identified in &lt;a href=&quot;http://en.wikipedia.org/wiki/Scrapie&quot; rel=&quot;nofollow&quot;&gt;scrapie&lt;/a&gt; which is caused by a Prion. Discovery of a novel prion disorder (&lt;a href=&quot;http://www.medscape.com/viewarticle/814753&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) with peripheral symptoms have led researchers to believe that protein misfolding, is the basis for most neuro-degenerative diseases, including Alzheimer's disease and Parkinson's disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regard to your question, Alzheimer's has not been completely classified as a prion disorder as of now, but seeing that amyloid plaque formation (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16903146&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) and Creutzfeldt-Jakob disease (CJD) (a form of dementia) (&lt;a href=&quot;http://www.alz.org/dementia/creutzfeldt-jakob-disease-cjd-symptoms.asp&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) have been identified as being part of Prion disorders, it is highly likely that Alzheimer's is too. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-05-30T09:10:20.857" LastActivityDate="2014-05-30T09:10:20.857" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17773" PostTypeId="1" CreationDate="2014-05-30T09:03:03.420" Score="3" ViewCount="756" Body="&lt;p&gt;The basis of this question relies on my understanding of these 2 facts:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;1) A person has a certain number of stem cells from birth &#xA;2) Stem cells are the basis of all cells and are used to repair and replenish&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I read an article about stem cells being found in fat removed by lipsuction and that the trials that has been done on using these stem cells for repair elsewhere in the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, if stem cells are used for repair in the body and you have a certain amount of them, if you &quot;lose&quot; some via liposuction, does this then mean you have less stem cells and therefore less chance of repair and could then theoretically die sooner?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's more than likely my lack of knowledge on the subject but I would like to understand why.&lt;/p&gt;&#xA;" OwnerUserId="6879" LastActivityDate="2014-08-01T04:48:36.427" Title="Does a reduction in stem cells mean possible earlier death?" Tags="&lt;stem-cells&gt;&lt;lipids&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17774" PostTypeId="1" CreationDate="2014-05-30T11:07:25.957" Score="3" ViewCount="92" Body="&lt;p&gt;From &lt;a href=&quot;https://www.youtube.com/watch?v=48afo8ZCC2o&quot; rel=&quot;nofollow&quot;&gt;this video&lt;/a&gt; (21'15''), the speaker gives the following formulae in order to calculate the between and among populations genetic variance from the $F_{ST}$:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$V_{Among Pop} = 2 F_{ST}V_G$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$V_{Within Pop} = (1-F_{ST})V_G$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $V_G$ is the total genetic variance of this population if it was well mixing. $V_{Among Pop}$ is the variance among populations and $V_{Within Pop}$ is the variance within populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this same video, the speaker defines $F_{ST}$ as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$F_{ST} = \frac{\text{Var}(p)}{\bar p (1-\bar p)}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $p$ is a vector of frequencies of a given allele and $\bar p$ and $\text{Var}(p)$ are the mean and variance of this vector.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, consider a metapopulation made of 4 subpopulations. The allele frequencies in these 4 subpopulations are p=[0.2, 0.5, 0.8, 0.3]. $\bar p$ is the mean of $p$ ($\bar p = 0.45$) and $\text{Var}(p)$ is the variance of $p$ ($\text{Var}(p )=0.07 \space$).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can you help me to make sense of the formulas for $V_{Among Pop}$ and $V_{Within Pop}$?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you prove these formulas? I would expect that $V_{Among Pop} + V_{Within Pop} = V_G$ but it doesn't! Maybe the issue has to do with the fact that $V_{Within Pop}$ as defined above fit to haploid population and not diploid populations. Then, I would expect that for diploid populations $V_{Within Pop}$ becomes $(1-2F_{ST})V_G$. Is that correct? Just in order to make it more general, how do you extrapolate these definitions for a tetraploid population? Also maybe I misunderstand the meaning of $V_G$. Is the variance within population the sum of the within populations variance or is it the average (or something else)? Thanks for your help!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-06-05T21:20:42.047" LastActivityDate="2014-06-05T21:20:42.047" Title="$F_{ST}$ and the genetic variance in metapopulations" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;&lt;fst&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17775" PostTypeId="1" AcceptedAnswerId="94488" CreationDate="2014-05-30T11:14:09.610" Score="2" ViewCount="145" Body="&lt;p&gt;Sewall Wright defined the $F_{ST}$ in a metapopulation as being:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$F_{ST} = \frac{\text{Var}(p)}{\bar p (1-\bar p)}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $p$ is a vector of frequencies of a given allele and $\bar p$ and $\text{Var}(p)$ are the mean and variance of this vector.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, consider a metapopulation made of 4 subpopulations. The allele frequencies in these 4 subpopulations are p=[0.2, 0.5, 0.8, 0.3]. $\bar p$ is the mean of $p$ ($\bar p = 0.45$) and $\text{Var}(p)$ is the variance of $p$ ($\text{Var}(p )=0.07 \space$).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can we define $F_{ST}$ for a multiple allele locus? Or should $F_{ST}$ be defined for each allele independently?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-05-30T11:35:53.840" LastActivityDate="2020-07-03T04:44:40.263" Title="$F_{ST}$ when considering a multi-allelic locus" Tags="&lt;evolution&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;&lt;population-genetics&gt;&lt;fst&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17776" PostTypeId="2" ParentId="17763" CreationDate="2014-05-30T11:25:37.037" Score="4" Body="&lt;p&gt;My understanding is that the antisense DNA strand (3'-5') makes the (sense) mRNA hence protein coding DNA strand where as the sense DNA strand (5'-3') is the non-proteins coding DNA strand. Hence the sense DNA produces antisense non-coding RNA, which ultimately acts as a translational regulator (&lt;a href=&quot;http://en.wikipedia.org/wiki/Antisense_strand&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Antisense_strand&lt;/a&gt;). The only reason sense DNA strand is called the the sense strand is because it is complementary to the sense RNA or mRNA.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-05-30T11:25:37.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17777" PostTypeId="2" ParentId="8066" CreationDate="2014-05-30T12:48:41.283" Score="0" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;yes you understand how helper T cells work in the body.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;no. Cytokines are not enough and injecting T cells will just make HIV persist. The only solution to not getting AIDS and having your HIV cured is an HIV vaccine and the people making the vaccines do produce some HIV vaccine.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5851" LastActivityDate="2014-05-30T12:48:41.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17780" PostTypeId="2" ParentId="17773" CreationDate="2014-05-30T14:17:43.180" Score="1" Body="&lt;p&gt;Stem cells persist because they have the capacity to self-renew.  At birth you will have a finite number of each stem cell type (e.g. hematopoietic stem cells that make blood, gut epithelium stem cells that make gut lining etc).  The general picture is that as tissues require replenishment, a stem cell divides. One daughter cell starts to differentiate (and divide) into mature cells required by the tissue, whereas the other daughter cell retains stem cell function.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So a stem cell is typically defined as a cell with the capacity to: (i) self-renew &lt;em&gt;and&lt;/em&gt;  (ii) to give rise to one or more cell types in a tissue. A hematopoietic stem cell can give rise to T-cells, B-cells, neutrophils, red blood cells, platelets etc.  The ability to &lt;em&gt;self-renew&lt;/em&gt; means that, in general, stem cells don't 'run out' during a lifetime.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[ Its important to note that to define a cell as a stem cell, scientists use strange hybrid of: in vitro or animal assays + cell surface markers + location in the tissue + measures of 'having the capacity to make continued contribution to new cells'.  So lets just say that stem cells are only ever as well defined as our choice of assays combined with the interpretation of those results. ]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I mention the challenge of defining stem cells because, in recent years as assays and technologies improved, cells such a oocytes (eggs) or adult neurons, which were once thought to be finite, have been shown to have be replaced/renewed, presumably by some 'stem cell like' cell(s).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As noted above, stem cells are usually involved in the replenishment of a particular tissue type.  So liposuction, which will remove fat cells, should not affect the numbers of hematopoietic or neural stem cells and so on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any claim of clinical benefit of a 'stem cell treatment' using liposuction should be backed by clear data.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A longer answer would get into: &#xA;(i) the concept of 'plasticity' where the classical view - a fixed pathway between a stem cell giving rise to one daughter cell that  gives rise to mature cells and the other returns to a stem cell state - is open for debate, and &#xA;(ii) the idea that since stem cell definitions are only as good as our assays, there may be potential plasticity even among stem cells that we cannot 'detect' yet.&lt;/p&gt;&#xA;" OwnerUserId="5922" LastEditorUserId="5922" LastEditDate="2014-05-31T03:22:25.940" LastActivityDate="2014-05-31T03:22:25.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17781" PostTypeId="1" CreationDate="2014-05-30T14:55:04.277" Score="1" ViewCount="76" Body="&lt;p&gt;Someone told me that primitive lymph nodes do not exist during this week.&#xA;However, others say they can.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a picture about inguinal lymph nodes from &lt;a href=&quot;http://www.embryology.ch/anglais/qblood/lymphat05.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&#xA;No primary lymph nodes are visible (like circular) at 56th day:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rAfJb.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;When are the primitive lymph nodes formed?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="6895" LastEditDate="2014-06-02T12:13:50.943" LastActivityDate="2014-06-02T12:13:50.943" Title="Do primitive lymph nodes exist in 12th week embryo?" Tags="&lt;embryology&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17782" PostTypeId="2" ParentId="17763" CreationDate="2014-05-30T15:25:48.687" Score="5" Body="&lt;p&gt;There are a few confusions here, I will try to get them resolved without adding more:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, a gene is always read in the 5' -&gt; 3' direction, no matter on what strand of the double helix is is located. In the traditional way of writing down DNA the forward (or +) strand is written from left to right, the reverse (or -) strand from right to left. So even is you draw a gene map like the one below, the genes which run on the reverse strand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5nF2o.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the transcription the reverse strand (it doesn't matter if it is the + or - strand) is not important. You can even have different genes on forward and reverse. In many cases the reverse strand doesn't code for any genes though.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-05-30T15:25:48.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17785" PostTypeId="1" AcceptedAnswerId="17786" CreationDate="2014-05-30T19:59:13.020" Score="3" ViewCount="563" Body="&lt;p&gt;How do G-coupled protein receptors (GPCR) transmit signals through the plasma membrane?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Links containing information about this and pictures will be very helpful.     &lt;/p&gt;&#xA;" OwnerUserId="6524" LastEditorUserId="3632" LastEditDate="2014-05-30T21:38:13.113" LastActivityDate="2014-05-30T21:38:13.113" Title="How do GPCRs transmit a signal across the plasma membrane?" Tags="&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17786" PostTypeId="2" ParentId="17785" CreationDate="2014-05-30T20:23:03.937" Score="5" Body="&lt;p&gt;The G-coupled protein receptors (GPCR) transmit signals from outside of the cell into the cell and activate downstream signalling pathways. These change for example the expression of certain genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The whole process is a coorperation between the receptor, a G-protein, GTP as a co-factor and the ligand of the receptor (which starts the whole process). An extensive description (including much more images) is available in the Wikipedia, but in short, it looks like the images below (from the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/GPCR&quot; rel=&quot;nofollow noreferrer&quot;&gt;GPCR&lt;/a&gt;): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9oUZJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer how this signal is tranferred from the outside to the inside look at the first image: Upon ligand binding the conformation of the receptor changes its conformation and brings some of it transmembrane helices together so the G$\alpha$ subunit can bind here and activate downstream signalling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PbtpT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The whole process happens in a few steps:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;In the resting state the receptor has a trimeric G-protein (consisting of the subunits $\alpha, \beta$ and $\gamma$ bound on its cytosolic site. The G-protein also has a GDP molecule bound to it $\alpha$ subunit.&lt;/li&gt;&#xA;&lt;li&gt;Upon binding of the ligand, the receptor changes its conformation, and G$\alpha$ exchanges the GD against GTP, which activates the complex.&lt;/li&gt;&#xA;&lt;li&gt;The G-protein dissociates into the active G$\alpha$ the G$\beta\gamma$ subunits, which signal to downstream signal transduction pathways like the MAP-Kinase pathway.&lt;/li&gt;&#xA;&lt;li&gt;Binding of RGS (regulator of G-protein signalling) to the g$\alpha$ subunit activates the intrinsic GTPase function of the subunit and hydrolyses GTP into GDP and P. The GDP stays bound to the G$\alpha$ subunit, which changes its conformation and forms the G-protein trimer at the receptor. At the receptor itself this induces also a change in conformation which makes the ligand dissociate from the receptor.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;At the end of the fourth step the receptor has returned into its inactive form and stays there until the next ligand binding.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-05-30T20:46:20.633" LastActivityDate="2014-05-30T20:46:20.633" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17789" PostTypeId="2" ParentId="3689" CreationDate="2014-05-31T01:55:06.943" Score="-1" Body="&lt;p&gt;Antibiotics kill bacteria, not virus! So it's just plain wrong. If a bacterial infection appears after the cold, then the antibiotics should be prescribed because of the bacterial infection, not because of the cold. There is a serious concern about misuse of antibiotics promoting hyper-resistant bacteria through natural selection, but doctors keep ignoring alerts from WHO and prescribing antibiotics without even knowing the bacterial strain. It's absurd that a doctor should prescribe an antibiotic just because &quot;the patient needs to get some medicine to be happy&quot;. In this case he/she should prescribe a placebo, not a real antibiotic (and there's still the point that killing most bacteria in our body destroy one of our defensive lines against pathogens). Confirming this point, &lt;a href=&quot;http://www.avaresearch.com/ava-main-website/files/20100401061256.pdf?page=files/20100401061256.pdf&quot; rel=&quot;nofollow&quot;&gt;according to American Medical Association&lt;/a&gt;, medical error is the third death cause in USA. So in many cases, yes, it might just be a medical error.&lt;/p&gt;&#xA;" OwnerUserId="4821" LastActivityDate="2014-05-31T01:55:06.943" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="17790" PostTypeId="1" CreationDate="2014-05-31T02:01:49.833" Score="5" ViewCount="10961" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_membrane&quot; rel=&quot;nofollow&quot;&gt;Cell walls&lt;/a&gt; are selectively permeable to ions and organic molecules. Sometimes the selectivity is passive and a reflection of the physical laws governing diffusion. We can do simple experiments that strengthen intuition about transport across biological membranes. The following homework question concerns a situation which tests understanding of the basic ideas of osmosis and diffusion generally.     &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A bag made of a flexible semipermeable membrane is filled with a 10% glucose and 5% starch solution. This bag is permeable to water and glucose but NOT to starch. The bag is suspended in a a beaker containing a 10% glucose solution. In 30 minutes the bag can be expected to&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;(A) swell&#xA;(B) shrink slightly&#xA;(C) collapse entirely&#xA;(D) become impermeable to glucose&#xA;(E) remain the same&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Since the bag is impermeable to starch, I know that the solution in the bag isn't going to diffuse outside so it won't shrink, but would water from outside flood into the bag to try to dilute the starch concentration to the point that it's isotonic? Or am I not understanding some fundamental principle of diffusion? &lt;/p&gt;&#xA;" OwnerUserId="6882" LastEditorUserId="1368" LastEditDate="2014-07-11T14:48:24.380" LastActivityDate="2015-01-31T03:06:32.573" Title="Diffusion of Hypotonic solution into solution with glucose and starch" Tags="&lt;biochemistry&gt;&lt;homework&gt;&lt;osmosis&gt;" AnswerCount="2" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17791" PostTypeId="2" ParentId="17349" CreationDate="2014-05-31T02:17:49.970" Score="0" Body="&lt;p&gt;Having returned to this topic, I found this very handy journal article:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://journal.frontiersin.org/Journal/10.3389/fimmu.2012.00130/full&quot; rel=&quot;nofollow&quot;&gt;http://journal.frontiersin.org/Journal/10.3389/fimmu.2012.00130/full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Much of it, I'm afraid, is very difficult for me to follow, but I still managed to take a lot from it and I hope others may find it useful. I would summarise what I have found thus:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PKC and the increased levels of Ca&lt;sup&gt;2+&lt;/sup&gt; combine to direct the reorganising of the cytoskeleton through various intermediaries. The cytoskeleton is like the skeleton of the cell and it also provides the structure along which the secretory granules move to the cell membrane. The vesicle will bind with the cell wall and disperses its contents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read &lt;a href=&quot;http://en.wikipedia.org/wiki/Mast_cell#Degranulation_and_fusion&quot; rel=&quot;nofollow&quot;&gt;suggestions&lt;/a&gt; that PKC may be involved in the process of the secretory granules fusing with the cell membrane. Wikipedia suggests that PKC is involved in severing the links between the surface of the secretory granules and the exoskeleton, allowing it to merge with the cell membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any corrections are obviously welcome.&lt;/p&gt;&#xA;" OwnerUserId="5263" LastActivityDate="2014-05-31T02:17:49.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17792" PostTypeId="2" ParentId="17629" CreationDate="2014-05-31T03:17:28.220" Score="8" Body="&lt;p&gt;There is an interesting and authoritative paper on rearing of larvae of blue bottle flies for debridement purposes, cited below. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Essentially the eggs are disinfected (rinsed) using .25 % chloramine solution (NH2Cl), then the larvae are hatched and reared in aseptic conditions and fed sterilized food. There are some additional controls after initial disinfection (eggs are placed in agar and the resulting growth is compared to non-disinfected eggs). The procedure is detailed on page 127-128.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Whether the eggs are perfectly germ-free may be somewhat moot. Historically this was done without disinfecting the eggs (or anything else). Secondary infections were probably not uncommon but the advantages of the technique far outweighed the disadvantages until the advent of antibiotics. Apparently these things are great at debridement of wounds (but shouldn't be used too close to organs or blood vessels).   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;See&lt;/em&gt; Wolff and Hansson, Rearing Larvae of &lt;em&gt;Lucilia sericata&lt;/em&gt; for Chronic Ulcer Treatment--An Improved Method, Acta Derm. Venereol. (2005) 85: 126-131. &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-05-31T12:47:58.637" LastActivityDate="2014-05-31T12:47:58.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17793" PostTypeId="2" ParentId="17629" CreationDate="2014-05-31T05:31:01.300" Score="14" Body="&lt;p&gt;&lt;strong&gt;History&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ambroise_Par%C3%A9&quot; rel=&quot;noreferrer&quot;&gt;Ambroise Paré&lt;/a&gt; is credited with being the first to note his observations on &lt;a href=&quot;http://en.wikipedia.org/wiki/Maggot_therapy&quot; rel=&quot;noreferrer&quot;&gt;Maggot Debridement Therapy&lt;/a&gt; (MDT) in the 1500 though it is a technology that has been used for centuries (&lt;a href=&quot;http://medent.usyd.edu.au/projects/maggott.htm&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;). It wasn't until the 1920's that therapeutic experimentation with maggots was instigated by William Baer, a clinical professor in orthopaedic surgery at the Johns Hopkins University in Baltimore, Maryland, whose unorthodox methods were successful in the treatment of osteomyelitis and pyogenic wounds. He is also considered the father of modern MDT since he was the first to devise a way to sterilize maggots (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048269/&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Procedure&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;In addition to removing necrotic tissue from the wound (a procedure known as debridement) maggots have also been proven to disinfect wounds, promote healing, and inhibit a pesky substance known as biofilm from forming on the wound bed. Maggots are nature’s cleansers, showing up to remove dead tissue and promote healing (&lt;a href=&quot;http://www.thewca.com/blog/201401/%E2%80%9Coh-maggot-where-art-thou%E2%80%9D-quick-history-and-update-maggot-therapy&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;p&gt;Currently &lt;em&gt;Lucilia sericata&lt;/em&gt;, or the greenbottle blowfly larvae is preferred for MDT because&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Firstly, larvae have been shown to debride wounds with extremely low&#xA;probability of &lt;a href=&quot;http://en.wikipedia.org/wiki/Myiasis&quot; rel=&quot;noreferrer&quot;&gt;myiasis&lt;/a&gt; upon clinical application. Larval secretions&#xA;have been shown to help in tissue regeneration. &lt;em&gt;L. sericata&lt;/em&gt; have also&#xA;been shown to lower bacteremia levels in patients infected with &lt;a href=&quot;http://en.wikipedia.org/wiki/Methicillin-resistant_Staphylococcus_aureus&quot; rel=&quot;noreferrer&quot;&gt;MRSA&lt;/a&gt; (&lt;a href=&quot;http://en.wikipedia.org/wiki/Common_green_bottle_fly#Medical_importance&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Sterilizing maggots&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;In early applications, sterilizing the larvae was a major problem. Doctors had to first bathe the eggs in bleach and then soak them in mercuric chloride or formaldehyde. The bandages, gaudy and cumbersome for the patients, were held in place with either surgical tape or Unna’s paste—made of zinc oxide, gelatin, glycerine, and water. Other problems that doctors faced included the maggots escaping during the application process and the leakage of toxic waste secreted by the maggots into the wound, which led to infections such as tetanus. Today, commercial and research laboratories produce sterile larvae. And instead of the bulky gauze bandage, a form-fitting cast with a nylon net to corral the larvae is placed over the wound. An absorbent pad put on top of the netting soaks up the larvae’s toxic waste products. The number of larvae used has also changed. Early prescriptions ranged from 5–6 maggots for a fingertip injury to 500–600 for a more serious wound. Today, the scientific standard of 10 larvae/cm&lt;sup&gt;2&lt;/sup&gt; is used (&lt;a href=&quot;http://pubs.acs.org/subscribe/archive/mdd/v04/i10/html/10health.html&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;p&gt;William Baer proposed a method to produce sterilized maggots and it is understood that sterilization has to start from the egg stage in itself (&lt;a href=&quot;http://jbjs.org/content/16/3/572&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;). The sterilization solution that he proposed was.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Stock Solution of bichloride of mercury, strength one in 1,000 parts.&#xA;Stock Solution of fifty per cent. ethyl alcohol. Take equal volume of&#xA;each Solution, mix, and add one-half of one per cent. chemically pure&#xA;hydrochloric acid. The final Solution will contain bichloride of&#xA;mercury, strength one in 2,000 parts, twenty-five per cent. alcohol,&#xA;and one-half of one per cent. hydrochloric acid.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;He did not sterilize the maggots as such but took care to feed it sterile food. His work can be read &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048276/&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;. Another solution used for sterilization was  5 per cent solution of formalin plus 1 per cent sodium hydroxide (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0002961034901471&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).  Sterilization of maggot larvae in itself was found to be hard with some success being reported (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0002961033904614&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;). Current maggot sterilization techniques include.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;UV Sterilization&lt;/p&gt;&#xA;&lt;p&gt;Rapid washer sterilization&lt;/p&gt;&#xA;&lt;p&gt;Egg to maggot sterilization (&lt;a href=&quot;http://www.researchgate.net/publication/259438977_Development_of_sterilizing_techniques_for_the_production_of_sterile_maggots_used_in_therapy_of_intractable_wounds&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;There is no first generation that has been detailed as such. Mostly sterilization starts from the egg stage. As far as bacteria in the gut is concerned, if sterilization is carried out well, it has been found that there is a significant decrease in any harmful bacteria present (&lt;a href=&quot;http://www.bioone.org/doi/abs/10.1603/0022-2585-38.2.161&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;). Most details of sterilizing maggot larvae is given in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16883286&quot; rel=&quot;noreferrer&quot;&gt;this paper&lt;/a&gt;. Consider reading &lt;a href=&quot;http://www.hkmj.org/article_pdfs/hkm0710p382.pdf&quot; rel=&quot;noreferrer&quot;&gt;this paper&lt;/a&gt; as well.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-11-06T08:34:35.090" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17794" PostTypeId="2" ParentId="16352" CreationDate="2014-05-31T06:24:23.640" Score="3" Body="&lt;p&gt;Yes, research studies that were conducted have found that &lt;a href=&quot;http://en.wikipedia.org/wiki/Methanogen&quot; rel=&quot;nofollow&quot;&gt;methanogens&lt;/a&gt; (microorganisms) are able to survive in conditions similar to Mars (&lt;a href=&quot;http://www.dailymail.co.uk/sciencetech/article-2633741/Could-Earth-superbug-live-MARS-One-planets-simplest-oldest-organisms-survives-Martian-environment.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Another study conducted has also concluded that some lichen and cyanobacteria is also capable of survival.  Surprisingly, they were also found to be active (&lt;a href=&quot;http://www.planetary.org/blogs/guest-blogs/20120515-earth-life-survive-mars.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is speculation now on whether organisms from earth have been accidentally transported to Mars on the Mars Curiosity Rover which would be funny or a cause of concern, depending on how you look at it (&lt;a href=&quot;http://rt.com/usa/160636-mars-curiosity-rover-bacteria/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-09-25T04:14:33.993" LastActivityDate="2014-09-25T04:14:33.993" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17795" PostTypeId="2" ParentId="17790" CreationDate="2014-05-31T08:08:24.300" Score="5" Body="&lt;p&gt;The bag will swell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diffusion results in molecules moving down their concentration gradient. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the set-up described only glucose and water are able to diffuse. Glucose is at the same concentration inside and out so there will be no changes in glucose concentration. Water will move into the bag because it is effectively at a lower concentration (more correctly  - chemical potential) inside due to the presence of the starch. As water moves into the bag, increasing the volume, glucose will also move so that the glucose concentration remains equal on both sides. Thus there will be net movement of water and glucose into the bag.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;@WYSIWYG has raised the spectre of &lt;em&gt;colloids&lt;/em&gt; in the comments. I don't understand colloids so cannot comment, but I think that in the context of problems like this we are usually dealing with &quot;soluble&quot; starch. &lt;a href=&quot;http://books.google.co.uk/books?id=8_7iGj4QLR4C&amp;amp;pg=PA506&amp;amp;lpg=PA506&amp;amp;dq=does+starch+create+osmotic+pressure&amp;amp;source=bl&amp;amp;ots=O9Pb1-kxxG&amp;amp;sig=oa4wRLmUZUtZpxkerzWzoVZvjDk&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=YpyJU-f_NMfdPbbGgYAK&amp;amp;ved=0CDIQ6AEwBA#v=onepage&amp;amp;q=does%20starch%20create%20osmotic%20pressure&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Here is an example of a calculation&lt;/a&gt; in which starch is treated as an osmolyte.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-05-31T09:17:09.483" LastActivityDate="2014-05-31T09:17:09.483" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="17796" PostTypeId="2" ParentId="17756" CreationDate="2014-05-31T08:33:50.667" Score="3" Body="&lt;p&gt;I'd guess it's &lt;em&gt;&lt;a href=&quot;https://www.google.de/search?q=%22Nuctenea%20umbratica%22&amp;amp;tbm=isch&quot; rel=&quot;nofollow&quot;&gt;Nuctenea umbratica&lt;/a&gt;&lt;/em&gt;, or otherwise similar in appearance and coloration pattern, but less frequent &lt;em&gt;&lt;a href=&quot;https://www.google.de/search?q=%22Nuctenea%20silvicultrix%22&amp;amp;tbm=isch&quot; rel=&quot;nofollow&quot;&gt;Nuctenea silvicultrix&lt;/a&gt;&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At least &lt;em&gt;Nuctenea umbratica&lt;/em&gt; was recorded in Switzerland.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-05-31T08:33:50.667" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17797" PostTypeId="1" AcceptedAnswerId="17803" CreationDate="2014-05-31T09:11:06.320" Score="1" ViewCount="50" Body="&lt;p&gt;Generally in miRNA prediction most researchers do as Blast search with a set of miRNAs downloaded from miRBase with the parameters they require. Later on usually custom methods are utilized to get an area around the match area for structure prediction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://bioinformatics.oxfordjournals.org/content/21/18/3610.abstract&quot; rel=&quot;nofollow&quot;&gt;one paper&lt;/a&gt;, I found that ~70 flanking nt of match area was taken as pre-miRNA for structural analysis while in &lt;a href=&quot;http://hindawi.com/journals/ijg/2012/957607&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; ~100 flanking nt of the match area was taken for pre-miRNA structure prediction. Any idea why so?  &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="3340" LastEditDate="2014-05-31T20:32:34.533" LastActivityDate="2014-11-15T10:29:43.323" Title="Why are different lengths of nucleotides taken for structure prediction from an miRNA match area after BLAST analysis?" Tags="&lt;bioinformatics&gt;&lt;structure-prediction&gt;&lt;blast&gt;&lt;microrna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17798" PostTypeId="1" AcceptedAnswerId="17800" CreationDate="2014-05-31T09:11:25.017" Score="1" ViewCount="482" Body="&lt;p&gt;For a bi-allelic locus, the model for haploid Natural Selection is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{dp}{dt} =  \frac{pW_A}{pW_A + (1-p)W_B}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $p$ is the frequency of the allele $A$, which relative fitness is $W_A$. $W_B$ is the fitness of the allele $B$, which frequency is $1-p$. $\frac{dp}{dt}$ is the change in allele frequency through time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same model for diploid selection is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{dp}{dt} = \frac{p^2W_{AA} + p(1-p)W_{AB}}{p^2W_{AA} + 2p(1-p)W_{AB} + (1-p)^2W_{BB}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $W_{AB}$ is the fitness of the diploid genotype carrying the allele $X$ on one chromosome and the allele $Y$ on the other chromosome. We define $W_{AB} = W_{BA}$ and therefore we use only the symbol $W_{AB}$ in the above calculations. Note: This equation assumes &lt;a href=&quot;http://en.wikipedia.org/wiki/Hardy%E2%80%93Weinberg_principle&quot; rel=&quot;nofollow&quot;&gt;Hardy-Weinberg equilibrium&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Those equations can be found in any introductory courses in population genetics. For example, &lt;a href=&quot;http://biomed.brown.edu/Courses/BIO48/6.PopGen1.HW.drift.HTML&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; is a source where you can find this same equation for diploid selection. They just express $q$ instead of $1-p$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Do these models assume constant population size? Why?&lt;/li&gt;&#xA;&lt;li&gt;Do these models assume threshold selection? Why?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="4113" LastEditorUserId="3340" LastEditDate="2014-05-31T13:37:40.737" LastActivityDate="2014-05-31T13:37:40.737" Title="Assumptions of the models for haploid and diploid selection" Tags="&lt;evolution&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17799" PostTypeId="1" AcceptedAnswerId="17801" CreationDate="2014-05-31T09:37:24.763" Score="21" ViewCount="1060" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The standard definition of species refers to the concept of &lt;a href=&quot;http://simple.wikipedia.org/wiki/Reproductive_isolation&quot; rel=&quot;nofollow noreferrer&quot;&gt;reproductive isolation&lt;/a&gt;. If two lineages are found to be reproductively isolated, then we consider these two lineages to belong to different species. My question concerns evolved reproductive isolation in Drosophila sp. following labs due to experimental evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have we ever demonstrated that two Drosophila sp. lineages that could initially interbreed (in nature or in labs) evolved through artificial selection (and drift and mutations) in labs to finally not be able to interbreed anymore either due pre- or post- zygotic isolation (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Reproductive_isolation&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki&lt;/a&gt;)? Or, in other words, have we ever demonstrated that two drosophila lineages evolved to become different species (reproductive isolation definition) in labs experiments?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, have we ever observed some partial reproductive isolation such as inbreeding depression for example?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Note: This question is motivated by @LotusBiology that could not receive the answers she/he was waiting for because he/she failed to ask questions that are possibly answerable! So I wanted to ask this question that somehow addresses &lt;a href=&quot;https://biology.stackexchange.com/questions/17736/if-evolution-is-true-how-would-you-explain-the-fruit-fly-experimentations&quot;&gt;this&lt;/a&gt; question he/she asked (now on-hold)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information about the concept of species, please have a look at &lt;a href=&quot;https://biology.stackexchange.com/questions/39664/how-could-humans-have-interbred-with-neanderthals-if-were-a-different-species&quot;&gt;How could humans have interbred with Neanderthals if we're a different species?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2018-03-07T19:56:09.467" LastActivityDate="2018-03-07T19:56:09.467" Title="Have we ever observed two drosophila lineages that evolved reproductive isolation in labs?" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;speciation&gt;&lt;drosophila&gt;&lt;species&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17800" PostTypeId="2" ParentId="17798" CreationDate="2014-05-31T11:11:57.100" Score="1" Body="&lt;p&gt;Unless I am missing something the equations you have posted are incorrect. The second equation should be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$p' = \frac{p^2 W_{AA} + p(1-p)W_{AB}}{p^2W_{AA}+ 2p(1-p)W_{AB}+(1-p)W_{BB}} $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$p'$ is not interpreted as $\frac{dp}{dt}.$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$p'$ is the frequency of allele A in the next generation. If zygotic frequencies via random mating are &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$p^2(AA) + 2pq(Aa)+q^2(aa) = 1$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;then all of AA individuals and 1/2 the Aa gametes bear the A allele. So we can find $p$ in the next generation as &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$p^2+pq = p^2+p(1-p) = p^2+p-p^2 = p$ which shows that in a Hardy-Weinberg population the frequencies are stable. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The assumptions here are those underlying the HW model, which includes infinite population size (hence constant). &lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2014-05-31T11:11:57.100" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17801" PostTypeId="2" ParentId="17799" CreationDate="2014-05-31T11:49:56.953" Score="20" Body="&lt;p&gt;Rice and Salt$^1$ bred fruit flies for 35 generations and from one line of flies created two groups that were isolated from each other reproductively. They could not interbreed because they no longer bred in the same environment. Depending on one's definition of 'species' this could be a case of artificial speciation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^1$Rice WR, Salt GW (1988), Speciation via disruptive selection on habitat preference: experimental evidence&quot;. The American Naturalist 131 (6): 911–917.&lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2014-05-31T11:49:56.953" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17803" PostTypeId="2" ParentId="17797" CreationDate="2014-05-31T13:54:00.960" Score="1" Body="&lt;p&gt;There is no hard and fast rule for how many nucleotides you have to select. If your miRNA is ~20nt and you take 70nt from both sides (average length of hairpins is ~84nt in humans), your total length will be 160nt. The point of taking $\pm70nt$ is that you don't know if your read is -3p or -5p. So take 70nt from both sides. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The maximum length of a human miRNA hairpin is 180nt for mir-3648 (90nt per half hairpin). In such cases you may take more flanking residues. But these cases are rare. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-05-31T13:54:00.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17804" PostTypeId="1" CreationDate="2014-05-31T15:33:15.723" Score="3" ViewCount="61" Body="&lt;p&gt;I am an amateur interested in neuroscience and was curious whether there is a process by which a neuron or group of neurons would close their receptors and stop receiving signals from specific synapses for a temporary period? &lt;/p&gt;&#xA;" OwnerUserId="6884" LastActivityDate="2014-07-02T11:53:20.490" Title="Can a postsynaptic neuron 'shut itself off?" Tags="&lt;neuroscience&gt;&lt;synapses&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17805" PostTypeId="1" CreationDate="2014-05-31T23:14:30.790" Score="5" ViewCount="17267" Body="&lt;p&gt;Occasionally I will run protein alignments on peptide families and I can never remember what the symbols mean to show degrees of identity. What do they mean?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-05-31T23:14:30.790" Title="What do the Clustal Alignment Symbols Mean?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;homology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17806" PostTypeId="2" ParentId="17805" CreationDate="2014-05-31T23:14:30.790" Score="6" Body="&lt;p&gt;From the &lt;a href=&quot;https://www.ebi.ac.uk/Tools/msa/clustalw2/help/faq.html#23&quot; rel=&quot;noreferrer&quot;&gt;FAQ for the Clustal-W2&lt;/a&gt; program:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;An * (asterisk) indicates positions which have a single, fully conserved residue.&lt;/p&gt;&#xA;&lt;p&gt;A : (colon) indicates conservation between groups of strongly similar properties - scoring &amp;gt; 0.5 in the Gonnet PAM 250 matrix.&lt;/p&gt;&#xA;&lt;p&gt;A . (period) indicates conservation between groups of weakly similar properties - scoring =&amp;lt; 0.5 in the Gonnet PAM 250 matrix.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Therefore the hierchy of conservation using these symbols is * (identical) &amp;gt; : (colon) &amp;gt; . (period).&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-05-31T23:14:30.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17807" PostTypeId="1" AcceptedAnswerId="17814" CreationDate="2014-06-01T02:25:20.023" Score="3" ViewCount="112" Body="&lt;p&gt;When infected with malaria, how many &lt;em&gt;P. falciparum&lt;/em&gt; cells are within a human host? And how does this compare with the average infection parasitemia of &lt;em&gt;A. gambiae&lt;/em&gt;? I can't seem to find a reliable source to guide me on this question.&lt;/p&gt;&#xA;" OwnerUserId="1763" LastActivityDate="2014-06-26T17:37:14.853" Title="When infected with malaria, how many parasites are within a human host?" Tags="&lt;infection&gt;&lt;malaria&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17808" PostTypeId="1" CreationDate="2014-06-01T05:08:08.490" Score="1" ViewCount="93" Body="&lt;p&gt;I can understand the allele notation when is in the form rs8176719(T;T) or rs8176719(G) but recently i found this ones rs8176719(T;-) or rs8176719(-;T). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So im confused, rs8176719(T;-) is the same as rs8176719(T)? or is the location is important ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks .&lt;/p&gt;&#xA;" OwnerUserId="6886" LastActivityDate="2014-07-01T20:51:05.890" Title="Alleles notation in SNPPedia criteria" Tags="&lt;bioinformatics&gt;&lt;human-genetics&gt;&lt;snp&gt;&lt;allele&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17810" PostTypeId="1" AcceptedAnswerId="17820" CreationDate="2014-06-01T11:21:38.260" Score="3" ViewCount="811" Body="&lt;p&gt;I have read about basics of molecular genetics ,although its not a thorough in-depth knowledge. I would like to know about &quot;regulatory genomics&quot;. What is it actually?&lt;/p&gt;&#xA;" OwnerUserId="5669" LastActivityDate="2014-06-01T20:56:52.990" Title="What does &quot;regulatory genomics&quot; mean?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17811" PostTypeId="1" AcceptedAnswerId="17843" CreationDate="2014-06-01T12:28:37.453" Score="8" ViewCount="17120" Body="&lt;p&gt;I have found a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC413948/&quot; rel=&quot;noreferrer&quot;&gt;publication&lt;/a&gt; which proposes some definitions, including a definition for strict and relaxed replication. The definitions are:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Relaxed control of plasmid replication.&lt;/strong&gt; Relaxed control should be used in reference to plasmid replication that is not obligatorily coupled to chromosome-replication.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Stringent control of plasmid replication.&lt;/strong&gt; Stringent control should be used in reference to plasmid replication that is obligatorily coupled to chromosome replication.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However, the publication is from 1976. Are these definitions current? If no, what is the current definition?&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2020-02-28T11:46:11.890" Title="What is the definition of a stringent/relaxed plasmid?" Tags="&lt;molecular-biology&gt;&lt;plasmids&gt;&lt;definitions&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17812" PostTypeId="2" ParentId="17773" CreationDate="2014-06-01T13:37:23.100" Score="-3" Body="&lt;p&gt;Theoretically, yes. Although, to my knowledge it has not been proven. As far as I'm aware there is no known link between liposuction and leukemia, liposuction would most likely not remove enough stem cells to produce such an effect. I've been doing a lot of research into stem cells lately and from what I have found there have not been many, if any, in depth studies on the impact of stem cell removal as the implantation of stem cells is usually the main focus.&lt;/p&gt;&#xA;" OwnerUserId="6889" LastActivityDate="2014-06-01T13:37:23.100" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17813" PostTypeId="1" AcceptedAnswerId="19717" CreationDate="2014-06-01T14:28:30.810" Score="8" ViewCount="163" Body="&lt;p&gt;&lt;strong&gt;&lt;em&gt;Myriapoda&lt;/em&gt;&lt;/strong&gt; (comprising, among others, &lt;strong&gt;millipedes&lt;/strong&gt; and &lt;strong&gt;centipedes&lt;/strong&gt;) can have hundreds of legs (&lt;em&gt;Illacme plenipes&lt;/em&gt; having up to 750 legs). Interestingly, the number of legs (or leg pairs) appears to differ not only between myriapod species, but even between individuals of the same species:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Body light cream-colored, thread-like, extremely narrow and long (max. width: ♂ 0.55, ♀ 0.64; max. length: ♂ 28.16, ♀ 40.40). &lt;strong&gt;Adult individuals with 84 – 192 segments, and with 318 – 750 legs&lt;/strong&gt; (VMNH paratype ♀ with 192 segments and 750 legs, more than any other organism known on Earth).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Source: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3559107/&quot;&gt;A redescription of the leggiest animal, the millipede Illacme plenipes, with notes on its natural history and biogeography&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This raises the question: &lt;strong&gt;Is the number of legs in myriapoda determined entirely by the genome, or do environmental factors play a role in precisely how many legs eventually develop?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Note:&lt;/em&gt; Myriapoda generelly hatch with very few legs, and more legs develop during successive moults. Some examples can be found &lt;a href=&quot;http://en.wikipedia.org/wiki/Centipede#Anamorphy_vs._epimorphy&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerDisplayName="user6890" LastActivityDate="2014-07-16T16:51:22.060" Title="Is the number of legs in myriapoda determined entirely by the genome?" Tags="&lt;genetics&gt;&lt;zoology&gt;&lt;development&gt;&lt;invertebrates&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17814" PostTypeId="2" ParentId="17807" CreationDate="2014-06-01T15:21:46.087" Score="5" Body="&lt;p&gt;The uninucleate sporozoites are injected by the mosquito into a human host. They mature in the liver parenchymal cells in schizonts. Each schizont releases into the blood flow &lt;strong&gt;2,000 to 40,000 uninucleate merozoites&lt;/strong&gt;. Each of them can infect a red blood cell. Here, a merozoite can release other 10 to 36 merozoites &lt;sup&gt;[1]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The numer of injected sporozites depends on the bite and the number of bites &lt;sup&gt;[2]&lt;/sup&gt;. And it seems that a &lt;strong&gt;parasitemia greater than 5000/microliters&lt;/strong&gt; which is usually achieved by 10 infective bites during a 28-day period triggers the signs and symptoms &lt;sup&gt;[3]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I couldn't find any data on the mosquito parasitemia. It has been found that the infected mosquito and the parasite mutually benefit each other and thereby promote transmission of the infection. The Plasmodium-infected mosquitoes have a better survival and show an increased rate of blood-feeding, particularly from an infected host &lt;sup&gt;[4]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;James M. Crutcher and Stephen L. Hoffman. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK8584/&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Medical Microbiology. 4th edition.&lt;/em&gt;&lt;/a&gt; 1996, The University of Texas Medical Branch at Galveston.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Garrett-Jones C, Shidrawi GR. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/5306719&quot; rel=&quot;nofollow&quot;&gt;Malaria vectorial capacity of a population of Anopheles gambiae: an exercise in epidemiological entomology.&lt;/a&gt; Bull. World Health Organ. 1969 Apr;40(4):531-45. PubMed PMID: 5306719. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;McElroy PD, Beier JC, Oster CN, Beadle C, Sherwood JA, Oloo AJ, Hoffman SL. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7985743&quot; rel=&quot;nofollow&quot;&gt;Predicting outcome in malaria: correlation between rate of exposure to infected mosquitoes and level of Plasmodium falciparum parasitemia.&lt;/a&gt; Am. J. Trop. Med. Hyg. 1994 Nov;51(5):523-32. PubMed PMID: 7985743. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Dr. B.S. Kakkilaya's Malaria Web Site. &lt;a href=&quot;http://www.malariasite.com/malaria/LifeCycle.htm&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Life Cycle of Malaria.&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-26T17:37:14.853" LastActivityDate="2014-06-26T17:37:14.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17815" PostTypeId="2" ParentId="17714" CreationDate="2014-06-01T17:03:39.137" Score="4" Body="&lt;p&gt;Plantar warts grow &lt;strong&gt;deep&lt;/strong&gt; into the skin and &lt;strong&gt;slowly&lt;/strong&gt; &lt;sup&gt;[1]&lt;/sup&gt;. It is a common thing for warts to multiply &lt;sup&gt;[1]&lt;/sup&gt;, but because of the slow growth speed, their symptoms &lt;sup&gt;[2]&lt;/sup&gt; and the self clear-up &lt;sup&gt;[1]&lt;/sup&gt; they can't end up by covering the entire skin surface of a previously healthy person.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are cases of generalized warts in patients with immune deficiency like hypogammaglobulinaemia, impairment of cell mediated immunity &lt;sup&gt;[3]&lt;/sup&gt;. The immune system plays an important role in limiting warts. There is also a case of generalized facial warts in a patient with no other known medical condition &lt;sup&gt;[4]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;American College of Foot and Ankle Surgeons, &lt;a href=&quot;http://www.foothealthfacts.org/footankleinfo/Plantar_Wart.htm&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Plantar Wart (Verruca Plantaris)&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;MAYO Clinic, &lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/plantar-warts/basics/symptoms/con-20025706&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Diseases and Conditions - Plantar warts&lt;/em&gt;&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Reid TM, Fraser NG, Kernohan IR. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1086679&quot; rel=&quot;nofollow&quot;&gt;Generalized warts and immune deficiency.&lt;/a&gt; Br. J. Dermatol. 1976 Nov;95(5):559-64. PubMed PMID: 1086679. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Semon H. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19990539&quot; rel=&quot;nofollow&quot;&gt;Papillomatosis: Generalized Facial Warts.&lt;/a&gt; Proc. R. Soc. Med. 1935 Dec;29(2):90. PubMed PMID: 19990539. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-26T17:48:00.883" LastActivityDate="2014-06-26T17:48:00.883" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17816" PostTypeId="1" CreationDate="2014-06-01T20:01:47.423" Score="7" ViewCount="285" Body="&lt;p&gt;I heard a lecture from a supporter of urine therapy and he claimed that urine is not only good disinfection but also as rich source of minerals. To me, these two advice seemed contradictory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, the supporter emphasized one should use his own urine - and yet, as an example of the magical effect of urine therapy we got a story of a boy who was hooked by jellyfish but was saved by a nearby doctor who used urine of his own. Apart from that I see no reason why urine should work against toxins better than a water or a disinfection (they don't).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though, I know a very qualified doctor who advocated this treatment. What do you think?&lt;/p&gt;&#xA;" OwnerUserId="6124" LastEditorUserId="6124" LastEditDate="2016-11-22T12:08:35.487" LastActivityDate="2016-11-22T12:08:35.487" Title="Does urine therapy really work?" Tags="&lt;zoology&gt;&lt;toxicology&gt;&lt;health&gt;&lt;excreta&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17817" PostTypeId="2" ParentId="17808" CreationDate="2014-06-01T20:16:35.763" Score="1" Body="&lt;p&gt;The '-' means that that allele has a single base deletion.  &lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-06-01T20:16:35.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17818" PostTypeId="2" ParentId="17816" CreationDate="2014-06-01T20:16:39.457" Score="9" Body="&lt;p&gt;This is at best anecdotal evidence. First of all, urine is, although it has been thought otherwise for decades, not sterile. The bacteria in it just don't grow under the conditions used in the lab which are used to proof bladder infections. See these two articles:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22278835&quot; rel=&quot;nofollow&quot;&gt;Evidence of uncultivated bacteria in the adult female bladder.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24371246&quot; rel=&quot;nofollow&quot;&gt;Urine is not sterile: use of enhanced urine culture techniques to&#xA;detect resident bacterial flora in the adult female bladder.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;When you take into account that bacteria grow on almost all surfaces which have a connection to the outside (like mouth, stomach, gut and so on) this is not really surprising that this is true for the bladder as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Urine might be a relatively low risk solution of choice to rinse a wound when nothing else is available, but otherwise I wouldn't recommend it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then think of what urine is used for: it is the way our body excretes all the water soluble stuff it doesn't need any more. The body makes a lot of effort here to concentrate the primary urine in our kidneys to recover all the stuff which is still needed and to save water. I wouldn't drink it and make my body go through the whole process of excretion again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About the doctors: is there any hard evidence for that or is this only an anecdote? I get highly skeptical when I hear about such stories.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="284" LastEditDate="2015-04-04T22:18:09.573" LastActivityDate="2015-04-04T22:18:09.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17819" PostTypeId="2" ParentId="17799" CreationDate="2014-06-01T20:40:31.500" Score="10" Body="&lt;p&gt;Diane Dodd's experiments on Drosophila pseudoobscura would be another example of lab-based speciation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jstor.org/stable/2409365?__redirected&quot; rel=&quot;noreferrer&quot;&gt;http://www.jstor.org/stable/2409365?__redirected&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To summarise - four populations each adapted to feeding on a starch-based diet and a maltose-based diet were evolved in the lab to test effects on mating preferences; compared to what is expected by random, using chi-squared tests, 11 of 16 combinations showed greater isolation than expected by chance - strong evidence for assortative mating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An alternate link to the PDF of the paper is here &lt;a href=&quot;http://www.sulfide-life.info/mtobler/images/stories/readings/dodd%201989%20evolution.pdf&quot; rel=&quot;noreferrer&quot;&gt;http://www.sulfide-life.info/mtobler/images/stories/readings/dodd%201989%20evolution.pdf&lt;/a&gt;  &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dodd, Diane M. B. (September 1989). &quot;Reproductive isolation as a consequence of adaptive divergence in &lt;em&gt;Drosophila pseudoobscura&lt;/em&gt;&quot;. &lt;em&gt;Evolution&lt;/em&gt; &lt;strong&gt;43&lt;/strong&gt; (6): 1308–1311. doi:&lt;a href=&quot;https://dx.doi.org/10.2307%2F2409365&quot; rel=&quot;noreferrer&quot;&gt;10.2307/2409365&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6726" LastEditorUserId="3340" LastEditDate="2015-05-28T06:38:30.730" LastActivityDate="2015-05-28T06:38:30.730" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17820" PostTypeId="2" ParentId="17810" CreationDate="2014-06-01T20:56:52.990" Score="5" Body="&lt;p&gt;The genome may be divided into two classes of sequences - those that code for proteins and those that do not. Those that do not code for proteins may be again divided into classes consisting of actively transcribed sequences that have biological activity (such as long noncoding RNA, microRNA, competing endogenous RNA and so on) and those that aren't.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These untranscribed noncoding regions may be involved in regulating the activity of protein coding and actively transcribed regions by binding to transcription factors or transcriptional coactivators/corepressors that control whether certain genes are expressed or not - this can happen close to the start of the gene (i.e, promoters) or far away (at enhancers). Distant enhancers can still affect gene expression because they and the genes they affect can be close together in three-dimensional space (The genome is folded in cells!). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regulatory genomics is, simply put, the study of these regions, which are called genomic &quot;features&quot; and how they regulate genes. A great example of studies in this area are offered by papers published as part of the ENCODE project &lt;a href=&quot;http://www.nature.com/encode/#/threads&quot; rel=&quot;noreferrer&quot;&gt;http://www.nature.com/encode/#/threads&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6726" LastActivityDate="2014-06-01T20:56:52.990" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17821" PostTypeId="1" CreationDate="2014-06-01T22:08:45.117" Score="2" ViewCount="90" Body="&lt;p&gt;I am wondering how DNA glycosylase works from the chemical point of view. Sometimes in papers I can see that they are doing activity assays with 1M NaOH and I am trying to understand why using 1M NaOH is more factual? Thank you for any help. &lt;/p&gt;&#xA;" OwnerUserId="6892" LastActivityDate="2014-06-02T08:05:19.217" Title="Activity of DNA glycosylase" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17822" PostTypeId="2" ParentId="17728" CreationDate="2014-06-01T23:27:26.177" Score="22" Body="&lt;p&gt;There are multiple levels of memory, some of which would die immediately, some of which would take some time. So the answer is: it depends; some immediately, some only very slowly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the highest level, the current neuronal firing state of the brain encodes memory on a very short scale - working memory. The memory held on this level does not have a clear anatomical counterpart (but for the &lt;em&gt;potential&lt;/em&gt; encoded in the synapses). It equals very short-term memory/STM sequences, such as the words you read just before you read the words you're reading right now. This memory is lost immediately when you lose consciousness, at least to some degree; as this memory is hard to even strictly distinguish from consciousness and attention (though see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17854286&quot;&gt;Jonides et al. 2008&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other forms of short-term memory/STM are stored in a slightly different form: short-term potentation, the adaption of neuronal responses following brief and intense stimulation. Spike Frequency Adaption/SFA is at an intermediate stage between this and the previous level. Short-term potentation and SFA decay within minutes or even seconds if they are not transferred into some more durable form of memory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Long-term memory (/LTM) stores have specific anatomical correlates; they are stored in, amongst others, the synaptic weights (i.e. the amount of influence the firing of one neuron has on another). Some forms of LTM are best located in cortical synapses, others in the hippocampus. An even more fundamental, long-term, durable storage form is the wiring itself; not just the weights, but the existence of a synapse between two points, or not. For example, an important part of early learning is synaptic pruning, where synapses which do not play a meaningful role die off, whereas those which connect functionally related brain areas remain.&#xA;This pruning instantiates one form of learning, and the &lt;em&gt;non-existence&lt;/em&gt; of a synapse is a form of memory. Synapses are comparatively stable. Even if the corresponding neurons die, in principle, the synapses still exist - and more importantly, the nonexistence of a synapse is even more durable. This form of memory can be observed in slice preparations of animals long dead.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a simple example, consider any experiment on the neuronal responses in slice preparations, which can be considered a form of (decontextualised) memory access.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the most extreme end, epigenetic adaptions and large-scale brain anatomy (which shows developmental traces) can be considered a form of memory that will remain intact until the whole structure rots away.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the more direct answer to the question the OP is asking is that once a large amount of neurons have died (brain death), there is currently no power on earth that can access a non-trivial amount of memory. As long as this is averted, nontrivial amounts of memory can be recovered.&#xA;For the parts that are lost immediately, see the source by Jonides et al. For more durable memory, you could look at for example &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10799/&quot;&gt;Purves et al, Neuroscience&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6887" LastEditorUserId="6887" LastEditDate="2014-06-02T07:10:19.810" LastActivityDate="2014-06-02T07:10:19.810" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17823" PostTypeId="1" AcceptedAnswerId="17824" CreationDate="2014-06-02T00:14:32.860" Score="6" ViewCount="7505" Body="&lt;p&gt;I read about this &lt;a href=&quot;http://www.instructables.com/id/Mosquito-trap-mosquito-abortion-clinic-or-source-t/&quot;&gt;idea for a mosquito trap&lt;/a&gt; (with a rather tactless name) where the idea seems to be that because the water available for the mosquito eggs is so shallow, they will die somehow or not be viable. Mosquitos are pretty small though, wouldn't they not need much water for the eggs to hatch?&lt;/p&gt;&#xA;" OwnerUserId="6894" LastActivityDate="2018-08-30T03:55:18.567" Title="How deep does water have to be so a mosquito can lay viable eggs in it?" Tags="&lt;physiology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17824" PostTypeId="2" ParentId="17823" CreationDate="2014-06-02T06:18:24.813" Score="7" Body="&lt;p&gt;Many mosquitoes, such as Culex quinquefasciatus, lay their eggs on the surface of fresh or stagnant water. The water may be in tin cans, barrels, horse troughs, ornamental ponds, swimming pools, puddles, creeks, ditches, catch basins or marshy areas. Mosquitoes prefer water sheltered from the wind by grass and weeds (&lt;a href=&quot;http://www.mosquito.org/biology&quot;&gt;reference&lt;/a&gt;). There are mosquitoes like Aedes taeniorhyncus (floodwater mosquitoes) which can even lay eggs in moist soil (because the eggs need to dry out before they can hatch) which then waits for the rainy season for hatching. These eggs are capable of surviving through summer, winter and spring to find the right time to hatch (&lt;a href=&quot;http://mosquito.ifas.ufl.edu/Mosquito_Habitats.htm&quot;&gt;reference&lt;/a&gt;). Water is necessary during the life cycle of a mosquito but how much is never an issue. Even the top of some mushrooms can be a place for mosquitoes to lay eggs (&lt;a href=&quot;http://www.clarku.edu/~tlivdahl/back/index.html&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-02T06:18:24.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17825" PostTypeId="2" ParentId="17821" CreationDate="2014-06-02T06:22:53.530" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_glycosylase&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA glycosylases&lt;/a&gt; bind to dsDNA, flip a base out of the base-paired double-helical structure and cleave it off, leaving the sugar-phosphate backbone intact. This base removal renders the DNA susceptible to alkaline cleavage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this recent paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Miyazono &lt;em&gt;et al.&lt;/em&gt; (2014) A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi. Nature Communications 5: #3178&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;the authors monitor the activity of a DNA glycosylase using this phenomenon: after treating an oligonucleotide with increasing amounts of the enzyme R.PabI they treat the DNA with NaOH so that the oligo is cleaved, allowing detection of the result of enzyme action on a polyacrylamide gel, as you can see from this image, taken from their Figure 3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YLRYI.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incidentally the same phenomenon is exploited when DNA is transferred to a membrane for &lt;a href=&quot;http://ki.mit.edu/sbc/escell/methods/alkaline-transfer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Southern blotting&lt;/a&gt;. After electrophoresis the gel is soaked in acid which causes depurination (analogous to DNA glycosylase). It is then transferred to an alkaline solution. Although protocols often refer to this as a neutralisation step it actually breaks the DNA at the apurinic sites &lt;strong&gt;and&lt;/strong&gt; separates the strands. This cleavage is important for effective transfer of larger fragments from the gel to the membrane.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-06-02T08:05:19.217" LastActivityDate="2014-06-02T08:05:19.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17826" PostTypeId="1" AcceptedAnswerId="17830" CreationDate="2014-06-02T07:32:55.140" Score="5" ViewCount="2321" Body="&lt;p&gt;I was wondering what is in the mosquito bites, which causes the swelling of the skin at the bite and also the itching. I know that the mosquito injects some stuff, but what is it?&lt;/p&gt;&#xA;" OwnerUserId="6895" LastActivityDate="2014-06-02T10:20:53.933" Title="What is in Mosquito bites?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17827" PostTypeId="1" AcceptedAnswerId="17831" CreationDate="2014-06-02T08:13:35.957" Score="3" ViewCount="1717" Body="&lt;p&gt;The movement of ions like sodium into the interstitial space causes water to passively diffuse out the descending loop of Henle. How does this concentrate the urine? The solvent is removed at one place, and the solute at another. Shouldn't the concentration remain the same? Or does the removal of a little solute remove a lot of solvent? Why?&lt;/p&gt;&#xA;" OwnerUserId="6155" LastActivityDate="2014-06-02T10:07:24.567" Title="How does the counter current mechanism concentrate urine?" Tags="&lt;kidney&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17829" PostTypeId="1" AcceptedAnswerId="17833" CreationDate="2014-06-02T09:36:17.343" Score="3" ViewCount="97" Body="&lt;p&gt;Can someone clearly explain me the differences between STRING and I2D(Interlogous interaction database) ? What does each database do best ? Which database is better for what kinds of studies etc ? &lt;/p&gt;&#xA;" OwnerDisplayName="user6417" LastActivityDate="2014-06-02T17:30:43.227" Title="I2D vs STRING for protein-protein interactions" Tags="&lt;bioinformatics&gt;&lt;protein-interaction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17830" PostTypeId="2" ParentId="17826" CreationDate="2014-06-02T09:56:21.437" Score="6" Body="&lt;p&gt;When female mosquitos bite to suck blood, they need to overcome the body reaction against it. So when they found a bood vessel, they inject their saliva into the wound. This saliva contains substances which affect blood clotting and platelet aggregation (so the blood will stay liquid which is essential for sucking) and a vasodilatory substance (which widens the blood vessel and prevents contraction of it). The exact composition depends on the exact mosquito species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These &quot;foreign&quot; substances cause a local immune reaction which results in the release of histamine in the skin. The itching and also the red skin and the swelling are a result of the histamine release. See the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Mosquito&quot;&gt;mosquitos&lt;/a&gt; for more information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in a deeper look on the composition of the mosquito saliva have a look at these two articles and their references (if there is help needed in getting the articles, let me know):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12194906&quot;&gt;Role of arthropod saliva in blood feeding: sialome and post-sialome&#xA;perspectives.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12213246&quot;&gt;Toward a description of the sialome of the adult female mosquito&#xA;Aedes aegypti.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Since the substances affect the blood coagulation cascade, there is some research going on if and how this can be used clinically. See this &lt;a href=&quot;http://www.upf.edu/cexs/actualitat/malaria.html&quot;&gt;article&lt;/a&gt; for an overview or have a look at the original publication here (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23223529&quot;&gt;Unique thrombin&#xA;inhibition mechanism by anophelin, an anticoagulant from the malaria vector&lt;/a&gt;&quot;)&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-06-02T10:20:53.933" LastActivityDate="2014-06-02T10:20:53.933" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17831" PostTypeId="2" ParentId="17827" CreationDate="2014-06-02T10:07:24.567" Score="4" Body="&lt;p&gt;Have a look at this figure (from &lt;a href=&quot;https://ahdc.vet.cornell.edu/clinpath/modules/UA-ROUT/usg.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ip3Ty.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the descending loop the NaCl concentration is lower than in the surrounding tissue which leads to a passive water transport along the gradient, which leads to a concentration effect. In the ascending loop then NaCl is actively transported out of the loop which then prevents the diffusion of water back into the loop. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the collecting tube water is actively transported out leading to an even higher concentration effect. A nice animation of this can be found &lt;a href=&quot;http://www.biologyinmotion.com/nephron/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-02T10:07:24.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17833" PostTypeId="2" ParentId="17829" CreationDate="2014-06-02T10:49:02.273" Score="2" Body="&lt;p&gt;I just looked and it seems I2D use the PPI from 5 organisms to predict interactions in those organisms, which have not yet been experimentally demonstrated, so its interolog PPI prediction tool by design (&lt;a href=&quot;http://genomebiology.com/content/pdf/gb-2007-8-5-r95.pdf&quot; rel=&quot;nofollow&quot;&gt;http://genomebiology.com/content/pdf/gb-2007-8-5-r95.pdf&lt;/a&gt;), where as STRING can be used to see what proteins are known to interact with a given protein, and what evidence is present for a particular interaction, which you then get a (confidence like) score.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-06-02T17:30:43.227" LastActivityDate="2014-06-02T17:30:43.227" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17834" PostTypeId="2" ParentId="17804" CreationDate="2014-06-02T11:07:15.490" Score="1" Body="&lt;p&gt;An example would be the neurons that switch off/switch on based on our sleep cycle. Nerve-signaling chemicals called neurotransmitters control whether we are asleep or awake by acting on different groups of nerve cells, or neurons, in the brain. Neurons in the brainstem, which connects the brain with the spinal cord, produce neurotransmitters such as serotonin and norepinephrine that keep some parts of the brain active while we are awake. Other neurons at the base of the brain begin signaling when we fall asleep. These neurons appear to &quot;switch off&quot; the signals that keep us awake. Research also suggests that a chemical called adenosine builds up in our blood while we are awake and causes drowsiness. This chemical gradually breaks down while we sleep (&lt;a href=&quot;http://www.ninds.nih.gov/disorders/brain_basics/understanding_sleep.htm&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt; and &lt;a href=&quot;http://thebrain.mcgill.ca/flash/i/i_11/i_11_cl/i_11_cl_cyc/i_11_cl_cyc.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Here is a study based on switch on/switch off of fear i mice (&lt;a href=&quot;http://www.nature.com/nature/journal/v454/n7204/full/nature07166.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also artificial ways in which to shut down receptors like our sweet receptors (&lt;a href=&quot;http://lubbockonline.com/stories/032307/lif_032307059.shtml&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). There have also been studies done on other organisms where one particular study showed the switch on/switch off of olfactory receptors in cockroach antenna (&lt;a href=&quot;http://jn.physiology.org/content/105/2/834&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-06-02T11:12:30.423" LastActivityDate="2014-06-02T11:12:30.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17835" PostTypeId="1" CreationDate="2014-06-02T11:10:55.313" Score="2" ViewCount="133" Body="&lt;p&gt;if the evolution makes the species better then why the leaf and trees are not black??&lt;/p&gt;&#xA;&#xA;&lt;p&gt;black colour absorbs more ligth than simply the green color so a black plant should make photosinthesis better then why aren't the plants black ?&lt;/p&gt;&#xA;" OwnerUserId="6900" LastActivityDate="2014-06-02T11:26:31.687" Title="Why the plants are not black but green?" Tags="&lt;botany&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="0" ClosedDate="2014-06-02T17:13:43.340" ContentLicense="CC BY-SA 3.0" />
  <row Id="17836" PostTypeId="2" ParentId="450" CreationDate="2014-06-02T11:26:31.687" Score="11" Body="&lt;p&gt;The biologist John Berman has offered the opinion that evolution is not an engineering process, and so it is often subject to various limitations that an engineer or other designer is not. Even if black leaves were better, evolution's limitations can prevent species from climbing to the absolute highest peak on the fitness landscape. Berman wrote that achieving pigments that work better than chlorophyll could be very difficult. In fact, all higher plants (embryophytes) are thought to have evolved from a common ancestor that is a sort of green alga – with the idea being that chlorophyll has evolved only once. (&lt;a href=&quot;http://en.wikipedia.org/wiki/Chlorophyll#Why_green_and_not_black.3F&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants and other photosynthetic organisms are largely filled with pigment-protein complexes that they produce to absorb sunlight. The part of the photosynthesis yield that they invest in this, therefore, has to be in proportion. The pigment in the lowest layer has to receive enough light to recoup its energy costs, which cannot happen if a black upper layer absorbs all the light. A black system can therefore only be optimal if it does not cost anything (&lt;a href=&quot;http://www.news.leiden.edu/news/why-are-plants-not-black.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Red and yellow light is longer wavelength, lower energy light, while the blue light is higher energy. It seems strange that plants would harvest the lower energy red light instead of the higher energy green light, unless you consider that, like all life, plants first evolved in the ocean. Seawater quickly absorbs the high-energy blue and green light, so that only the lower energy, longer wavelength red light can penetrate into the ocean. Since early plants and still most plant-life today, lived in the ocean, optimizing their pigments to absorb the reds and yellows that were present in ocean water was most effective. While the ability to capture the highest energy blue light was retained, the inability to harvest green light appears to be a consequence of the need to be able to absorb the lower energy of red light (&lt;a href=&quot;http://scienceline.ucsb.edu/getkey.php?key=1668&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some more speculations on the subject: (&lt;a href=&quot;http://thesymbiont.blogspot.in/2010/09/why-arent-plants-black-true-evo.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="49230" LastEditDate="2019-03-19T16:48:46.887" LastActivityDate="2019-03-19T16:48:46.887" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="17837" PostTypeId="1" AcceptedAnswerId="17842" CreationDate="2014-06-02T13:47:07.170" Score="5" ViewCount="44068" Body="&lt;p&gt;Is it true that; when you apply your own saliva to a mosquito bite it would stop itching ?&lt;/p&gt;&#xA;" OwnerUserId="6902" LastActivityDate="2017-06-13T11:51:36.197" Title="Applying saliva to mosquito bites" Tags="&lt;human-biology&gt;&lt;saliva&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17838" PostTypeId="1" AcceptedAnswerId="17844" CreationDate="2014-06-02T13:55:30.137" Score="1" ViewCount="268" Body="&lt;p&gt;I have a question regarding the description of a subset of peptide hormones, called cyclic hormones. Two examples of cyclic hormones would be somatostatin and melanin-concentrating hormones. I know the definition is not applied based on observations of oscillations in biologic levels of the hormones, rather, it is applied to the structure. These hormones possess a single disulfide loop, giving them a cyclic (circular) topology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question relates to the chemical definition of cyclic in this context. Does the word cyclic imply any chemistry that forms a single loop topology, arising from any kind of chemical bond (e.g., C-C bonds in carbon rings, or S-S bonds in these hormones). Or, does the word cycling only apply to S-S bonds in the context of these hormones?  I have not seen it defined in the literature, and my inclination is that it is more a definition of topology than any specific chemistry.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-06-02T23:22:28.020" Title="How are cyclic hormones characterized?" Tags="&lt;physiology&gt;&lt;proteins&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17839" PostTypeId="1" AcceptedAnswerId="17841" CreationDate="2014-06-02T14:03:08.730" Score="2" ViewCount="1373" Body="&lt;p&gt;I'am trying to create a phylogeny tree from some plants, as the post's title says, to help me conclude which of those plants are closer genetically with another one plant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So let's say that this is the plant list:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Nicotiana tabacum , Zea mays, Oryza sativa, Solanum lycopersicum,    Solanum tuberosum, Erythranthe guttata, Hordeum vulgare, Vitis vinifera, Prunus persica, Glycine max, Populus trichocarpa, Medicago truncatula, Phaseolus vulgaris, Morus notabilis, Citrus clementina, Setaria italica, Theobroma cacao, Acacia mangium, Cicer arietinum, Triticum urartu, Brachypodium distachyon, Aegilops tauschii, Panax ginseng&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and i want to see which of those species is closer with &lt;strong&gt;&lt;em&gt;Sorghum bicolor&lt;/em&gt;&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any easy way to conclude something like that or it needs to get results out of bioinformatics using a specific gene , align it , and then see the tree ?&lt;/p&gt;&#xA;" OwnerUserId="6032" LastActivityDate="2014-06-02T19:41:52.990" Title="Plant's phylogeny tree to identify which of them are closer (genetically) with another plant" Tags="&lt;botany&gt;&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17840" PostTypeId="1" AcceptedAnswerId="17869" CreationDate="2014-06-02T17:17:57.923" Score="2" ViewCount="608" Body="&lt;p&gt;In the resting membrane potential of neurons the inside of membrane is kept negative and outside of membrane is kept positive by the utilization of energy through Na-K Atpase pump, While during action membrane potential through the opening of specific gated ion channels inside of membrane is made positive while outside is made negative, What is the significance of specific charges across the membrane, does these specific charges across the membrane play any role in the passage of neurotransmitters ? or these charges are just arbitrary ?does this can happen that during resting membrane potential the inside will become positive and outside will become negative and vice versa, I want to know that what is the significance of these specific charges across the membrane ..?&lt;/p&gt;&#xA;" OwnerUserId="5729" LastActivityDate="2014-06-03T18:34:06.627" Title="Resting and action membrane potential..?" Tags="&lt;neuroscience&gt;&lt;neurotransmitter&gt;&lt;neurology&gt;&lt;signalling&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17841" PostTypeId="2" ParentId="17839" CreationDate="2014-06-02T18:55:51.223" Score="7" Body="&lt;p&gt;In general for plants, before you start trying to make your own phylogeny, you should try to find an existing phylogeny. Phylogenetics is complex, and a lot of people have already done the hard work. You can start by looking at the &lt;a href=&quot;http://www.mobot.org/MOBOT/research/APweb/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Angiosperm Phylogeny&lt;/a&gt; to figure out which species are most closely related. To make use of the tree you will usually have to look up each species to figure out what order or family it is in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VVAPR.gif&quot; alt=&quot;Angiosperm Phylogeny 3 model species tree&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this particular case, &lt;em&gt;Sorghum bicolor&lt;/em&gt; is a grass, so of course it's going to be closed to &lt;em&gt;Zea&lt;/em&gt;, &lt;em&gt;Oryza&lt;/em&gt;, &lt;em&gt;Setaria&lt;/em&gt; and &lt;em&gt;Brachypodium&lt;/em&gt; (all grasses) than any of the others. You can see where it places relative to the other grasses by looking at a grass-specific phylogeny. Because all three are model species, their phylogenetic placement relative to one another is well established. A simple Google image search for [grass model species phylogeny] gives you your answer (from the &lt;a href=&quot;http://www.nature.com/nbt/journal/v30/n6/full/nbt.2196.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Setaria genome paper&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/56Lz4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This shows you that &lt;em&gt;Sorghum&lt;/em&gt; is closest to &lt;em&gt;Zea&lt;/em&gt; out of the species you listed.&lt;/p&gt;&#xA;" OwnerUserId="430" LastEditorUserId="430" LastEditDate="2014-06-02T19:41:52.990" LastActivityDate="2014-06-02T19:41:52.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17842" PostTypeId="2" ParentId="17837" CreationDate="2014-06-02T20:06:52.870" Score="8" Body="&lt;p&gt;There have been many personal experiences documented where people have experienced relief from itching of mosquito bites on the application of their own saliva to the itchy spot (&lt;a href=&quot;http://www.correntewire.com/mosquito_bite_trick&quot;&gt;reference 1&lt;/a&gt;, &lt;a href=&quot;http://www.qryztufre.com/superstitions/saliva.html&quot;&gt;reference 2&lt;/a&gt;) It helps to reduce the itching because saliva has been proven to speed up tissue repair and has antibacterial properties. It also provides a moisturising effect on the itchy spot (&lt;a href=&quot;http://oralpathol.dlearn.kmu.edu.tw/case/Journal%20reading-intern-08-04/Saliva-function-composition-J%20Comtemp%20Dent%20Pract-2008.pdf&quot;&gt;reference&lt;/a&gt;). Salt is also known to provide relief to itching (&lt;a href=&quot;http://www.livestrong.com/article/291635-salt-grains-on-itching-skin/&quot;&gt;reference&lt;/a&gt;) and the slight salt content of saliva helps in that respect too. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-02T20:06:52.870" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17843" PostTypeId="2" ParentId="17811" CreationDate="2014-06-02T20:18:00.077" Score="11" Body="&lt;p&gt;In short, yes, the definitions are still correct:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The number of copies of a plasmid in the cell is determined by the mechanism of its replication: whether it is synchronized with the replication of the bacterial chromosome or is independent of it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the first case, the initiation of replication is performed by the same mechanisms of replication of the bacterial chromosome. This means that the origins of replication, as well as all proteins involved in the initiation of replication, are shared between the plasmid and the bacterial chromosome. For plasmids, which replication is synchronized with the replication of the bacterial chromosome are under &lt;strong&gt;stringent control of replication&lt;/strong&gt;. The stringent control of replication is characteristics of plasmids with low copy number. These plasmids contain DNA regions called &lt;em&gt;par&lt;/em&gt;-locuses (from partition) that control the correct division of the plasmids in the two daughter cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plasmids with high copy number are under &lt;strong&gt;relaxed control of replication&lt;/strong&gt;. These plasmids are replicated independently of the replication of the bacterial chromosome. They have individual mechanisms for initiation of replication. The plasmids themselves encode the initiation factors for replication, which are mainly RNA molecules. Once the plasmid replication is initiated, it continues with the same machinery used by the bacterial chromosome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference (Textbook): Bacterial Genetics, Margarita Pesheva (2000)&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2014-06-02T20:18:00.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17844" PostTypeId="2" ParentId="17838" CreationDate="2014-06-02T21:12:23.243" Score="3" Body="&lt;p&gt;If you look in the &lt;a href=&quot;http://www.jbc.org/content/early/2014/04/29/jbc.M114.548354.full.pdf&quot; rel=&quot;nofollow&quot;&gt;results&lt;/a&gt; section of this paper on somatostatin-14, they explain that s-14 &quot;is a fourteen residue peptide hormone where Cys$^3$ is disulfide bonded with Cys$^{14}$ to form a cyclic structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So your inclination is correct. The structure is cyclic and it is the cyclic structure which is responsible for the terminology. I don't know if there are exactly analogous structures with other than disulfide bonds but they would be cyclic for the same reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://gut.bmj.com/content/35/3_Suppl/S1.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Another paper&lt;/a&gt; at page S1 talks briefly about the linear version of the same hormone, contrasting it with the cyclic form, again confirming that it is the structure that gives rise to the name, and not some other property.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is the second reference that I think also answers the broader question: 'cyclic' is generic usage to describe a (simple or) complicated molecule containing a cyclic structure of joined atoms. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15885114&quot; rel=&quot;nofollow&quot;&gt;Yet another paper&lt;/a&gt; (abstract) talks about cyclic vs. branched in a general way with respect to somatostatin and others:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The aim of this contribution is to offer an unambiguous and general nomenclature system that enables researchers to represent all cyclic and branched homo- and hetero-detic peptides in a coherent manner in one-line text - as long as their as constituents can be represented in (three)-letter codes.&quot;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this somewhat dated &lt;a href=&quot;http://www.iupac.org/publications/pac/1988/pdf/6009x1395.pdf&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; containing proposed IUPAC nomenclature for cyclic organic compounds, in cases in which there is a question whether a molecule is cyclic or not the prefix &quot;cyclo-&quot; enters the formal name. But in the title the origin of the issue is clear: &quot;Nomenclature for cyclic organic compounds...&quot; and again confirms that the usage is not based on the elements bonded but the ringlike structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a &lt;a href=&quot;http://www.newagepublishers.com/samplechapter/001122.pdf&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; in which 'heterocyclic' (vs. 'carbocyclic') is used as a subclass of cyclic to refer to rings containing other than carbon. But the term cyclic applies to both.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally there is &lt;a href=&quot;http://en.wikipedia.org/wiki/Cyclic_peptide&quot; rel=&quot;nofollow&quot;&gt;discussion&lt;/a&gt; of 'cyclic peptides' (wiki entry) generally which are classified 'according to the types of bonds that comprise the ring.' But they are cyclic because of the circular molecular structure notwithstanding considerable variation in the atoms (or multiplicity of bonds) comprising the ring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biochemistry has inherited much nomenclature from organic chemistry, and informal usage in textbook organic chemistry is that ringlike structures are called 'cyclic' whether they are comprised entirely of carbon or contain another element (typically N,O,S, etc.); for example 'cyclic ethers'--oxacyclopentane is a cyclic molecule containing oxygen.   &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-06-02T23:22:28.020" LastActivityDate="2014-06-02T23:22:28.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17845" PostTypeId="1" AcceptedAnswerId="20110" CreationDate="2014-06-02T22:59:09.430" Score="12" ViewCount="1142" Body="&lt;p&gt;There are many combination vaccines available but I've noticed that there don't seem to be any with both live and non-live components, e.g. DTaP/IPV/MMR. Such combinations could be useful in some cases, since most developed countries give a second dose of MMR (or MMRV) at the same time as DTaP/IPV. Is there a biological reason that this is difficult?&lt;/p&gt;&#xA;" OwnerUserId="6458" LastEditorUserId="6458" LastEditDate="2014-06-05T18:04:44.353" LastActivityDate="2014-07-31T20:13:33.483" Title="Is it possible to combine live attenuated and non-live vaccines?" Tags="&lt;vaccination&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17847" PostTypeId="2" ParentId="10492" CreationDate="2014-06-03T00:34:28.283" Score="10" Body="&lt;p&gt;If we define lifespan of a human cell to mean the &lt;em&gt;period during which the cell survives with the same function in a human&lt;/em&gt; then..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;LONGEST (LIFETIME)&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/a/17780/5922&quot;&gt;Stem cells&lt;/a&gt;. Many types of stem cell form during embryogenesis and persist with the same functionality through to death. would be the longest lived (e.g stem cells that form blood cells such as lymphocytes, red blood cells and platelets).  Stem cells are found in many tissues including self-renewing ones such as the blood/bone marrow, gut epithelium and skin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;VERY LONG (YEARS-DECADES)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neurons are long lived and are generally non-mitotic.  However, recent studies are raising questions about the degree of cell division in the 'mature neurons' of the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Memory T-cells and memory B-cell (which can be activated and secrete antibodies as 'plasma cells') can provide long-lasting immunity from exposure to antigens in the environment and vaccines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;LONG (FEWER YEARS-DECADES)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oocytes (eggs)..which are present at birth but which become functionally mature in waves  during puberty.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;RACE FOR THE SHORTEST&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Labeling studies show that mature gastric epithelial cells live for a few days. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The top layer of skin epithelium is sloughed off every few days.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sperm cells live for days and are expended or re-cycled.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mature neutrophils have a &lt;em&gt;circulating half-life of around 8 hours&lt;/em&gt; but they can persist as mature forms within the bone marrow for a few days before entering the circulation and they may exit the circulation into depots such as the lung.  So the 8 hours is too short for their actual lifespan.&lt;/p&gt;&#xA;" OwnerUserId="5922" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-06-03T00:34:28.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17850" PostTypeId="1" AcceptedAnswerId="17872" CreationDate="2014-06-03T06:20:12.490" Score="7" ViewCount="558" Body="&lt;p&gt;A few months ago while backpacking in Taipei I found this very intriguing large bird facing off a curious puppy in a fairly busy pedestrian area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bird did not attempt to fly. None of the Taiwanese locals could tell me what it was and attempts to Google it via description all failed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd appreciate learning the species name, common name in English, and/or common name in Chinese:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WjlmR.jpg&quot; alt=&quot;mystery bird in Taipei, Taiwan&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="224" LastActivityDate="2014-06-03T19:46:41.287" Title="Identify this large exotic bird spotted in Taipei, Taiwan" Tags="&lt;ornithology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17851" PostTypeId="2" ParentId="3619" CreationDate="2014-06-03T06:48:25.210" Score="5" Body="&lt;p&gt;From studies, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;lactic acid bacteria were found to be more resistant to GP (garlic&#xA;  powder) compared to the clostridial members of the gut microbiota.&#xA;  While for most bacteria the antimicrobial effect was transient, the&#xA;  lactobacilli showed a degree of resistance to garlic, indicating that&#xA;  its consumption may favour the growth of these beneficial bacterial&#xA;  species in the gut. Once the strains of other bacteria (eg:&#xA;  Bacteroides ovatus, Bifidobacterium longum DSMZ 20090 and Clostridium&#xA;  nexile A2-232) became resistant, they retained their resistant&#xA;  phenotype upon sub-culturing. Garlic intake has the potential to&#xA;  temporarily modulate the gut microbiota (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22480662&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Overall garlic can prove to be beneficial, because it seems to have more of an effect on detrimental bacteria like Helicobacter pylori (H. pylori), even when its strains were resistant to antibiotics. Overall garlic was found to be more detrimental to pathological bacteria when compared to normal gut flora (&lt;a href=&quot;http://jn.nutrition.org/content/131/3/1106S.fullflora&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;). Garlic’s diallyl disulfide has also been found to effectively cause cell death in &lt;a href=&quot;http://en.wikipedia.org/wiki/Candida_albicans&quot; rel=&quot;noreferrer&quot;&gt;Candida albicans&lt;/a&gt; which is a fungus in our gut which if not kept in check can cause health problems (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17534841&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Inulin&quot; rel=&quot;noreferrer&quot;&gt;Inulin&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Fructooligosaccharide&quot; rel=&quot;noreferrer&quot;&gt;fructooligosaccharides&lt;/a&gt; present in garlic can also serve as nutrients for the probiotics colonizing your body (&lt;a href=&quot;http://www.parentingscience.com/prebiotics.html&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-03T06:48:25.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17852" PostTypeId="1" CreationDate="2014-06-03T07:39:44.583" Score="5" ViewCount="421" Body="&lt;p&gt;There are millions of proteins given in PDB, the sequence for which we can download in FASTA format. There are also hundreds of SNP's given in NCBI dbSNP. My question is whether the proteins in PDB incorporate the SNP's into their structure? If not, is there a way to visualize protein structure using any tool after a SNP on the protein? I know that tools like SIFT exist but they only say whether or not a SNP is harmful or not. They don't comment on the structure of the protein in anyway. &lt;/p&gt;&#xA;" OwnerDisplayName="user6417" LastActivityDate="2014-06-17T23:50:03.960" Title="Protein structures given in PDB and SNP's" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;pdb&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17853" PostTypeId="2" ParentId="17852" CreationDate="2014-06-03T07:58:15.393" Score="5" Body="&lt;p&gt;Solving the 3D structure of a protein is hard and a lot of work, doing that for every common SNP of a protein would be excessive in most cases. So you generally won't find such structures unless the structure of the specific mutated version is particularly interesting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In many cases it is also not structurally interesting what happens, there is no point in trying to get the 3D structure if an SNP leads to a frameshift or an early stop codon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you can do is simply load the PDB structure of the wildtype protein into a viewer like PyMol and look at the amino acid that is changes by the SNP. Read the associated paper to find out if that residue is important in some way. This won't be always possible, but if e.g. the amino acid is in the catalytic center of an enzyme, this would explain how the SNP affect the function of the protein.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-06-03T07:58:15.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17854" PostTypeId="1" CreationDate="2014-06-03T08:37:05.113" Score="1" ViewCount="589" Body="&lt;p&gt;I will soon be receiving Illumina HiSeq 2500 data (150bp PE stranded reads). In the past we have been using Trinity as our assembler of choice, but it uses a default kmer value of 25. I believe this may have been optimal for GAIIx data (35bp) but is it still ok to use such a kmer for 150bp data?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All inputs will be greatly appreciated!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="6905" LastActivityDate="2014-06-03T08:37:05.113" Title="Is the default kmer 25 value in Trinity still ok for assembly of 150bp reads from Illumina HiSeq 2500?" Tags="&lt;rna-sequencing&gt;&lt;sequence-analysis&gt;&lt;sequence-assembly&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="17855" PostTypeId="1" AcceptedAnswerId="17858" CreationDate="2014-06-03T09:01:59.637" Score="2" ViewCount="553" Body="&lt;p&gt;From Fersht, Enzyme Structure and Mechanism p. 87:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Michaelis-Menten mechanism assumes that the enzyme-substrate&#xA;  complex is in thermodynamic equilibrium with free enzyme and&#xA;  substrate.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In my understanding what this means is that the (E-, S- and ES-concentration dependent) rates of association and dissociation have equated.&#xA;So we're kind of in this situation:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Uylnb.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where &quot;product&quot; would be referring to [ES] and &quot;reactant&quot; to [E] and [S]. Does that make sense?&lt;/p&gt;&#xA;" OwnerUserId="4971" LastEditorUserId="1320" LastEditDate="2014-06-04T15:41:50.087" LastActivityDate="2014-06-04T15:41:50.087" Title="What does &quot;thermodynamic equilibrium&quot; mean for an enzyme-substrate complex?" Tags="&lt;enzymes&gt;&lt;enzyme-kinetics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17856" PostTypeId="2" ParentId="17852" CreationDate="2014-06-03T09:03:09.900" Score="6" Body="&lt;p&gt;&lt;a href=&quot;http://spdbv.vital-it.ch&quot;&gt;Swiss PDB Viewer&lt;/a&gt; allows you to mutate residues in an existing structure and explore the effects. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm pretty sure that &lt;a href=&quot;http://www.cgl.ucsf.edu/chimera/&quot;&gt;UCSF Chimera&lt;/a&gt; does too.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-06-03T09:03:09.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17858" PostTypeId="2" ParentId="17855" CreationDate="2014-06-03T09:21:45.747" Score="2" Body="&lt;p&gt;Thermodynamic equilibrium means that:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rate of forward reaction = Rate of backward reaction&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$E + S\xrightleftharpoons[k2]{k1} ES\\ \ \\&#xA; \ \\ \\ at\ equilibrium:\\ \  \ \\ \ k1.[E][S] \tiny{\ (forward\ rate)}\normalsize=  k2.[ES] \tiny\ (backward\ rate)&#xA;$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This was the initial assumption in the Michaelis-Menten model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Later on this was improvised by assuming &lt;strong&gt;pseudo-steady state&lt;/strong&gt; of ES complex. This means that $[ES]$ does not change over time, which is both as a result of its production by the reversible reaction:  $E + S \leftrightharpoons\ ES$ and consumption by the irreversible reaction $\ ES\ \xrightarrow{k3} E+P$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;that is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$k1[E][S]\tiny\ (production)\normalsize=(k2+k3)[ES]\tiny\ (consumption)$&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-06-03T09:34:42.233" LastActivityDate="2014-06-03T09:34:42.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17859" PostTypeId="2" ParentId="14844" CreationDate="2014-06-03T10:36:16.447" Score="4" Body="&lt;p&gt;From the article titled &quot;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0706.2013.01027.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Evidence of mutualistic synzoochory between cryptogams and hummingbirds&lt;/a&gt;&quot;, the specific advantage for the hummingbird is that it gets good nest building material through the selection of &lt;a href=&quot;http://en.wikipedia.org/wiki/Cryptogam&quot; rel=&quot;nofollow&quot;&gt;cryptograms&lt;/a&gt;. The cryptograms though have its seeds dispersed over large distances by birds which is a process called &lt;a href=&quot;http://www.britannica.com/EBchecked/topic/578758/synzoochory&quot; rel=&quot;nofollow&quot;&gt;synzoochory&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-04T06:02:26.837" LastActivityDate="2014-07-04T06:02:26.837" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17860" PostTypeId="2" ParentId="9662" CreationDate="2014-06-03T11:13:58.837" Score="0" Body="&lt;p&gt;You need to have faulty cones or be completely devoid of the cones that help you perceive a particular colour. If you do possess cones to visualize a colour, you aren't technically colour blind because you should still be able to detect the colour slightly (&lt;a href=&quot;https://en.wikipedia.org/wiki/Color_blindness#By_cause&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-03T11:13:58.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17861" PostTypeId="2" ParentId="17840" CreationDate="2014-06-03T14:09:12.413" Score="2" Body="&lt;p&gt;Answering the question: &quot;Why is a negative membrane potential important?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think cells have strong feelings about being slightly negative inside its membrane. I'm guessing these are the driving factors:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the cell membrane is nonpolar, so charged particles can only pass via transport proteins. This makes ion gradients an easy way to maintain a source of (literally, in the physics sense) potential energy.&lt;/li&gt;&#xA;&lt;li&gt;the cell needs to control its environment and send signals to other cells. The particle gradient (sodium, for example), allows it to accomplish these tasks: bring in glucose by co-transporting with sodium, send an action potential by triggering voltage-gated ion channels.&lt;/li&gt;&#xA;&lt;li&gt;Therefore, the Na/K pump is a way to &quot;charge&quot; the ability of the cell to perform various types of work in the future. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;To risk an analogy, a cell having a membrane potential is like &lt;strong&gt;you&lt;/strong&gt; charging your cell in the morning. You aren't quite sure what exactly you'll be doing with your phone all day, but it will be many different tasks and all will be doable because you've got a controlled energy source.&lt;/p&gt;&#xA;" OwnerUserId="6517" LastActivityDate="2014-06-03T14:09:12.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17862" PostTypeId="1" AcceptedAnswerId="17881" CreationDate="2014-06-03T14:14:08.897" Score="0" ViewCount="165" Body="&lt;p&gt;Are there studies that investigate the &lt;a href=&quot;https://biology.stackexchange.com/questions/42273/why-is-a-heritability-coefficient-not-an-index-of-how-genetic-something-is&quot;&gt;heritability&lt;/a&gt; of &quot;believing in supernatural&quot; (or related concepts)?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2018-03-08T07:05:54.647" LastActivityDate="2018-03-08T07:05:54.647" Title="Religion and Genetics" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="17866" PostTypeId="1" CreationDate="2014-06-03T17:00:41.600" Score="2" ViewCount="268" Body="&lt;p&gt;I would like to take an apparatus containing bacteria to another country (Bolivia) from the U.S.. How do I determine whether I am allowed to do this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bacteria are:&#xA;&lt;a href=&quot;http://www.atcc.org/Products/All/49787.aspx&quot; rel=&quot;nofollow&quot;&gt;http://www.atcc.org/Products/All/49787.aspx&lt;/a&gt;,&#xA;&lt;a href=&quot;http://www.atcc.org/Products/All/53774.aspx&quot; rel=&quot;nofollow&quot;&gt;http://www.atcc.org/Products/All/53774.aspx&lt;/a&gt;,&#xA;&lt;a href=&quot;http://www.atcc.org/Products/All/51573.aspx&quot; rel=&quot;nofollow&quot;&gt;http://www.atcc.org/Products/All/51573.aspx&lt;/a&gt;,&#xA;&lt;a href=&quot;http://www.atcc.org/Products/All/700550.aspx&quot; rel=&quot;nofollow&quot;&gt;http://www.atcc.org/Products/All/700550.aspx&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also... What is the best way of transporting bacteria from one country to another?&lt;/p&gt;&#xA;" OwnerUserId="6125" LastActivityDate="2014-06-03T17:00:41.600" Title="Transportation of bacteria" Tags="&lt;bacteriology&gt;" AnswerCount="0" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="17867" PostTypeId="1" CreationDate="2014-06-03T17:08:39.657" Score="6" ViewCount="592" Body="&lt;p&gt;I was told a human should drink a small glass (0,3 liter) of mineral water per day to get the minerals. What is the rationale behind this? What is the difference between tap water and mineral water in terms of nutrition facts and effects on human health?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Values for tap water in my area: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://snag.gy/5A9MV.jpg&quot; alt=&quot;&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How good are the values regarding nutrition facts?&lt;/p&gt;&#xA;" OwnerUserId="5304" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.143" LastActivityDate="2014-08-14T15:34:58.087" Title="Tap vs. mineral water for drinking" Tags="&lt;human-biology&gt;&lt;nutrition&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17868" PostTypeId="2" ParentId="17867" CreationDate="2014-06-03T17:50:21.097" Score="6" Body="&lt;p&gt;The mineral content in tap water differs from area to area as well as the source. The mineral content in bottled water is regulated by the companies that manufacture them, in particular the Mg and Ca content(&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1495189/&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Death rates tend to be lower in areas with tap water containing higher&#xA;  levels of Ca and Mg. It has been shown that deficiencies in magnesium&#xA;  are capable of producing heart disturbances, including 215,000 fatal&#xA;  heart attacks in the U.S. each year, and as many as 20,000,000 fatal&#xA;  heart attacks worldwide (&lt;a href=&quot;http://people.chem.duke.edu/~jds/cruise_chem/water/wattap.html&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Different brands of bottled water will differ in their mineral content as well (&lt;a href=&quot;http://www.google.co.in/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=7&amp;amp;ved=0CEwQFjAG&amp;amp;url=http://www.nuffieldfoundation.org/sites/default/files/files/FSMQ%2520Mineral%2520water%281%29.doc&amp;amp;ei=-AmOU5vpKpe78gX_x4LoBA&amp;amp;usg=AFQjCNGl0GTfR-rGSFwda4tZ_v3pkDWhyg&amp;amp;sig2=T1Yzth_8SbrIWebz9gMS5Q&amp;amp;bvm=bv.68191837,d.dGc&quot;&gt;reference&lt;/a&gt;). The place where you stay might be lacking in a particular mineral that your body requires which is why your doctor has specified the use of a particular brand of mineral water. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-03T17:50:21.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17869" PostTypeId="2" ParentId="17840" CreationDate="2014-06-03T18:34:06.627" Score="2" Body="&lt;p&gt;I've tried to split this into the answer to three questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Why does a membrane potential arise at all?&lt;/li&gt;&#xA;&lt;li&gt;Why does it happen to be around -80mV&lt;/li&gt;&#xA;&lt;li&gt;How does the cell use its membrane potential&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;(1) You've indicated that you know this one already, but I'd still like to point a few things out: The NaK pump not only creates a negative resting potential, it also seriously unbalances the Sodium and Potassium concentrations on each side of the cell. Even without any voltage, diffusion forces would cause an inward sodium current and an outward potassium current if you made holes in the membrane. The NaK pump (and the other active pumps/exchangers) are much slower than the passive currents through ion channels when they open.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) The resting potential is a dynamical equilibrium. This means that the potential you end up with is simply the one where all the opposing forces are equal. If you were designing a new cell from scratch you could put it at other values than around -80mV without too much trouble. In the cells we have, there's this region around -80mV where sodium and calcium channels are closed but a particular Potassium channel is wide open. Because there is much more Potassium inside the cell than out, diffusion drives Potassium out of the channel. However, because K+ has a positive charge the negative potential drives the K+ right back in. These two forces are able to balance each other out at around -80mV.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3) A cell uses its membrane potential in two important ways: Firstly, when you trigger an action potential (AP) in one cell, it almost immediately triggers an AP in its neighbours. This allows rapid communication between neurons in your brain, but also allows for the coordinated contraction of your heart. Secondly, the action potential opens up Calcium channels which let Calcium flow into the cell. The free calcium concentration within a cell acts as a second messenger initiating all sorts of actions. For example, in muscles the increased Calcium triggers a contraction: muscle cells contract during their AP. In neurons, the presence of Ca2+ in a cell strongly increases the release of neurotransmitters.&lt;/p&gt;&#xA;" OwnerUserId="6909" LastActivityDate="2014-06-03T18:34:06.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17872" PostTypeId="2" ParentId="17850" CreationDate="2014-06-03T19:20:57.857" Score="6" Body="&lt;p&gt;For me it looks like a &lt;a href=&quot;http://en.wikipedia.org/wiki/Malayan_night_heron&quot;&gt;Malayan Night Heron&lt;/a&gt;, &lt;em&gt;Gorsachius melanolophus&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They seems to be common in this part of Asia, see the &lt;a href=&quot;http://www.oiseaux.net/birds/malayan.night.heron.html&quot;&gt;distribution&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It looks strange because he probably get scared.&lt;/p&gt;&#xA;" OwnerUserId="6561" LastEditorUserId="107" LastEditDate="2014-06-03T19:46:41.287" LastActivityDate="2014-06-03T19:46:41.287" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17873" PostTypeId="1" CreationDate="2014-06-04T02:32:51.723" Score="5" ViewCount="147" Body="&lt;p&gt;Lambic beers are a Belgian specialty which is still made by open-air &quot;inoculation&quot; by airborne microbiota first, followed by additional yeasts, LAB bacteria and more joining in at the time of transferring to used wine barrels. (No yeast is &quot;pitched&quot; or added intentionally.)  As many as 200 organisms may play a role, and they seem to take turns, partly regulated by rising acidity and alcohol probably, but with some such as Brettanomyces seeming to simply wait their turn compared to what they will do in a single strain fermentation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lambic (or American Coolship Ale hereabouts) fementations can take up to 3 years.  Often a thick fluffy &quot;pellicle&quot; or &quot;film&quot; forms on the top of the barrel, like &quot;flor&quot; on sherry, evidently in response to and protection from oxygen. (Sure seems like a bio film.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(There have been a few studies tracking the staggered blooms of various organisms, including one done 2 years ago at Allagash and one this year at Cantillon, but no discussion about how the sequence is orchestrated. So this is a speculative question about the evolution of these beers.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could interspecies quorum sensing be at work?    How could that be confirmed? &lt;/p&gt;&#xA;" OwnerUserId="6912" LastEditorUserId="3340" LastEditDate="2014-06-05T05:12:57.340" LastActivityDate="2014-06-23T15:29:17.617" Title="Are Lambic beers the product of quorum sensing?" Tags="&lt;microbiology&gt;&lt;fermentation&gt;&lt;quorum-sensing&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17875" PostTypeId="2" ParentId="9374" CreationDate="2014-06-04T07:19:04.873" Score="1" Body="&lt;p&gt;Apart from the way it works and certain structural differences (&lt;a href=&quot;https://www.ntuh.gov.tw/LARD/DocLib1/%E5%80%92%E7%AB%8B%E9%A1%AF%E5%BE%AE%E9%8F%A1%E4%BD%BF%E7%94%A8%E7%94%B3%E8%AB%8B%E8%A1%A8%E6%A0%BC/Microscopy.pdf&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;), the decision of which kind of lens you need to use is left to your own personal choice based on your needs. You can find a list of the different lenses being offered by Olympus in &lt;a href=&quot;https://www.google.co.in/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CDAQFjAB&amp;amp;url=http://www.olympusamerica.com/files/seg_bio/Basics_of_Inv-Microscope.pdf&amp;amp;ei=YMOOU-XWJ4rDkgXizIGYBg&amp;amp;usg=AFQjCNHe05X36DyQXX3dsK0drWK56nUhwg&amp;amp;sig2=k6jGGbw7fDu_LGQBtTzKzg&quot; rel=&quot;nofollow&quot;&gt;this link&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-04T07:19:04.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17876" PostTypeId="1" AcceptedAnswerId="17877" CreationDate="2014-06-04T08:02:29.690" Score="3" ViewCount="181" Body="&lt;p&gt;Is it known which non-venomous snake can attack most quickly? I guess it is a snake that attacks its opponent by bites, and not some kind of constrictor.&lt;/p&gt;&#xA;" OwnerUserId="6914" LastEditorUserId="69" LastEditDate="2014-06-04T14:22:19.907" LastActivityDate="2014-06-04T14:22:19.907" Title="What is the fastest but not venomous snake?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17877" PostTypeId="2" ParentId="17876" CreationDate="2014-06-04T08:37:21.853" Score="3" Body="&lt;p&gt;The fastest non venomous snake is arguably the &lt;a href=&quot;http://en.wikipedia.org/wiki/Masticophis_flagellum_flagellum&quot; rel=&quot;nofollow&quot;&gt;Eastern Coachwhip&lt;/a&gt; with a top speed of upto 10 mph (&lt;a href=&quot;http://entertainment.news-leader.com/outdoors/thisweek/1021-Easterncoa-206629.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). If it feels cornered, it will attack with bites but otherwise, it prefers to flee. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-06-04T09:09:00.477" LastActivityDate="2014-06-04T09:09:00.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17878" PostTypeId="2" ParentId="5089" CreationDate="2014-06-04T10:36:14.173" Score="2" Body="&lt;p&gt;Fish are &lt;a href=&quot;http://en.wikipedia.org/wiki/Ectotherm&quot; rel=&quot;nofollow&quot;&gt;ectothermic&lt;/a&gt;, and so, by definition, cannot hibernate because they cannot actively down-regulate their body temperature or their metabolic rate. However, they can experience decreased metabolic rates associated with colder environments and/or low oxygen availability (hypoxia) and can experience dormancy. For example, epaulette sharks have been known to stay dormant for long periods without oxygen (&lt;a href=&quot;http://en.wikipedia.org/wiki/Hibernation#Dormancy_in_fish&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) Turtles in freshwater lakes have been known to hibernate by burying themselves in mud (&lt;a href=&quot;http://teacher.scholastic.com/activities/explorer/oceanlife/main.asp?template=meet_explorer&amp;amp;article=interview_frank&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). The mechanism through which turtles can experience several months of hypoxia or anoxia is explained in &lt;a href=&quot;http://icb.oxfordjournals.org/content/27/1/59&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;. The Antarctic fish (Notothenia coriiceps) has been found to be able to activate and deactivate their metabolic processes independent of body temperature and hence enter a state of dormancy similar to hibernation through metabolic suppression (&lt;a href=&quot;http://www.plosone.org/article/info%3adoi/10.1371/journal.pone.0001743&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-04T10:36:14.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17881" PostTypeId="2" ParentId="17862" CreationDate="2014-06-04T14:28:26.547" Score="2" Body="&lt;p&gt;There are several twin studies showing, that the tendency to be religious has a genetic component. Not which religion you choose, because that is a cultural thing, but how serious you are abot it. I am lazy for a detailed report, but this blog can lead you to the studies: &lt;a href=&quot;http://www.scilogs.eu/en/blog/biology-of-religion/2011-03-12/religiosity-genes-again-confirmed-by-another-twin-study&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.scilogs.eu/en/blog/biology-of-religion/2011-03-12/religiosity-genes-again-confirmed-by-another-twin-study&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also this article: &lt;a href=&quot;http://www.popsci.com/science/article/2013-08/what-twins-reveal-about-god-gene&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.popsci.com/science/article/2013-08/what-twins-reveal-about-god-gene&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT after a few years - I was informed one link is broken and the other contains no citation. So I checked for new material today and wikipedia has a cool passage how genes and environment affect religion. Wikipedia saves the old version, so this is from March 8 2018, article Religiosity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;&#xA;The contributions of genes and environment to religiosity have been quantified in studies of twins (Bouchard et al., 1999; Kirk et al., 1999) and sociological studies of welfare, availability, and legal regulations [15] (state religions, etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Koenig et al. (2005) report that the contribution of genes to variation in religiosity (called heritability) increases from 12% to 44% and the contribution of shared (family) effects decreases from 56% to 18% between adolescence and adulthood.[16] &quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;15 Nolan, P., &amp;amp; Lenski, G. E. (2010). Human societies: Introduction to macrosociology. Boulder, CO: Paradigm Publisher.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;16 L. B. Koenig, M. McGue, R. F. Krueger and T. J. Bouchard, Jr. (2005). Genetic and environmental influences on religiousness: findings for retrospective and current religiousness ratings. Journal of Personality, 73, 471-88&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.m.wikipedia.org/wiki/Religiosity#Genes_and_environment&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://en.m.wikipedia.org/wiki/Religiosity#Genes_and_environment&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5369" LastEditorUserId="5369" LastEditDate="2018-03-08T04:25:36.813" LastActivityDate="2018-03-08T04:25:36.813" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17883" PostTypeId="1" CreationDate="2014-06-04T15:48:40.767" Score="8" ViewCount="2484" Body="&lt;p&gt;Looking at aerial photos of boreal forests, with dense woods clear-cut by quiet lakes, I wondered why exactly are the woods so clear-cut at the edge of water? Why won't trees develop adaptations that will let them grow from a shallow lake bottom, with the lower part of the trunk in the water and the crown above the water?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to me that this would give them some significant advantages. Lake bottoms are rich in organic nutrition, and insolation will also be plentiful above water, at least at first when there's little competition. So why are lakes' surfaces so clear and open, instead of overgrown? Of course there are aquatic and semi-aquatic plants like water lilies, &lt;a href=&quot;http://en.wikipedia.org/wiki/Scirpus&quot;&gt;Scirpus&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/Typha&quot;&gt;Typha&lt;/a&gt;, but they are a far cry from the nearby terrestrial forests, in terms of biomass. Why don't they develop into large amphibian trees, or why don't terrestrial trees try to re-colonize lakes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://earthdata.nasa.gov/sites/default/files/styles/large/public/2009_forests_landscape.jpg&quot; alt=&quot;Boreal forest lakes&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6917" LastEditorUserId="6917" LastEditDate="2014-06-04T16:20:54.587" LastActivityDate="2014-11-21T12:04:59.970" Title="Why are there no tree-like plants that grow in lakes?" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;ecology&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17889" PostTypeId="1" CreationDate="2014-06-04T17:57:51.070" Score="3" ViewCount="2489" Body="&lt;p&gt;I ask because if you look at a tomato, the way it grows on a vine, its color, the texture, and make up of its skin and internal structure it seems very much like a pepper.  The only thing I can think it lacks that a pepper has is any amount of spice.  I wouldn't be surprised to learn that it has trace amounts of capsaicin.&lt;/p&gt;&#xA;" OwnerUserId="6920" LastActivityDate="2018-01-04T21:40:18.910" Title="Is the tomato a very very close relative of the pepper?" Tags="&lt;taxonomy&gt;&lt;nomenclature&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17890" PostTypeId="1" AcceptedAnswerId="17891" CreationDate="2014-06-04T18:02:14.970" Score="2" ViewCount="4927" Body="&lt;p&gt;i asked this to my anatomy teacher and he said there is no difference but when it comes to specialy in body building when you say to flex their bicep they freeze their upper limb in order to do that but when you say contract your bicep they only isolate it an shortens it. &#xA;am I right with my reason?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastActivityDate="2014-06-26T17:31:22.857" Title="Difference between flexion and contraction?" Tags="&lt;human-anatomy&gt;&lt;movement&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17891" PostTypeId="2" ParentId="17890" CreationDate="2014-06-04T18:09:45.130" Score="6" Body="&lt;p&gt;&lt;strong&gt;Flexion:&lt;/strong&gt; the movement that decreases the angle between two parts [1]. Examples: clenching the hand into fist, sitting down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Contraction&lt;/strong&gt;: the property of muscle to generate tension when actin and myosin filaments are crossing. There are a few types of contractions. The isometric contraction is when the muscle generates tension but its length doesn't change (for example when you try to lift something that you can't). The isotonic contraction is when the muscle changes its length [2]. This kind of contraction leads to movements and can lead to flexion too.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Anatomical terms of motion,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Anatomical_terms_of_motion&amp;amp;oldid=612679254&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Anatomical_terms_of_motion&amp;amp;oldid=612679254&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Muscle contraction,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Muscle_contraction&amp;amp;oldid=609265714&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Muscle_contraction&amp;amp;oldid=609265714&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-26T17:31:22.857" LastActivityDate="2014-06-26T17:31:22.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17892" PostTypeId="2" ParentId="17889" CreationDate="2014-06-04T18:15:51.523" Score="3" Body="&lt;p&gt;They are not related, both plants belong to different taxonomic orders:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Black_pepper&quot; rel=&quot;nofollow&quot;&gt;Pepper&lt;/a&gt; belongs to: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Order: Piperales&lt;/li&gt;&#xA;&lt;li&gt;Family: Piperaceae&lt;/li&gt;&#xA;&lt;li&gt;Genus: Piper&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Tomato&quot; rel=&quot;nofollow&quot;&gt;Tomatoes&lt;/a&gt; belong to the &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Order: Solanales&lt;/li&gt;&#xA;&lt;li&gt;Family: Solanaceae&lt;/li&gt;&#xA;&lt;li&gt;Genus: Solanum&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you look at Capsicum (as MattDmo suggested) then this is different. These peppers belong to the same order (solanales) and family (solanaceae) as tomatoes. They form a different tribe (Capsiceae).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia states on this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The name &quot;pepper&quot; came into use because of their similar flavour to the condiment black &gt;pepper, Piper nigrum, although there is no botanical relationship with this plant, or &gt;with Sichuan pepper.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-06-05T17:50:23.697" LastActivityDate="2014-06-05T17:50:23.697" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17893" PostTypeId="2" ParentId="17324" CreationDate="2014-06-04T19:23:34.170" Score="5" Body="&lt;p&gt;For dandruff caused mainly from dry scalp, I imagine that there is a delicate balance between moisturizing the scalp and getting oily hair. In my uninformed opinion, this is what shampoos like Head and Shoulders attempt to do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taking a more general look at skin health, growing research suggests that the right compilation of microbiota dictates lots of skin health issues. Just like your bowel has an endless supply of mutualistic bacteria, so does your skin. Disruption to this ecosystem (whether genetic, by way of a pathogen, or environmental) could have various negative effects. Dandruff, I imagine, is one of them. It is unfortunately very difficult to understand what a healthy ecosystem looks like, as every person is different both in genetic and environmental factors. This is part of the reason why other dermatological conditions like acne are difficult to treat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may be interested in research done through the &lt;a href=&quot;http://commonfund.nih.gov/hmp/&quot; rel=&quot;noreferrer&quot;&gt;Human Microbiome Project&lt;/a&gt;. Additionally, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535073/&quot; rel=&quot;noreferrer&quot;&gt;this article&lt;/a&gt; includes some discussion of the fungi mentioned above in the comments and postulates the role of microbiota in determining their success.&lt;/p&gt;&#xA;" OwnerUserId="6921" LastActivityDate="2014-06-04T19:23:34.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17894" PostTypeId="2" ParentId="16715" CreationDate="2014-06-04T19:31:22.503" Score="0" Body="&lt;p&gt;Naive B cells have not yet been trained by the immune system to recognize specific antigens -therefore the term &quot;naive&quot;. Prior to antigen exposure, they must be trained in the bone marrow to recognize certain antigens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Memory B cells, on the other hand, are formed after antigen exposure and clonal selection. As stated above, they have specific receptors for antigens and can produce antibodies.&lt;/p&gt;&#xA;" OwnerUserId="6921" LastActivityDate="2014-06-04T19:31:22.503" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17895" PostTypeId="1" AcceptedAnswerId="17950" CreationDate="2014-06-04T20:08:45.427" Score="4" ViewCount="457" Body="&lt;p&gt;The following problem is from Schaum's Outlines on Genetics, 5th edition, by Elrod and Stansfield.  I'm having some trouble solving it.  It is found under a section entitled &quot;Interactions with Three or More Factors&quot; in the problems at the end of the chapter on Epistasis.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Problem 4.30 (pg. 112):  If a pure-white onion strain is crossed to a pure-yellow strain, the&#xA;  F$_2$ ratio is 12 white : 3 red : 1 yellow.  If another pure-white&#xA;  onion is crossed to a pure-red onion, the F$_2$ ratio is 9 red : 3&#xA;  yellow : 4 white.  (a)  What percentage of the white F$_2$ from the&#xA;  second mating would be homozygous for the yellow allele?  (b)  If the&#xA;  white F$_2$ (homozygous for the yellow allele) of part (a) is crossed&#xA;  to the pure-white parent of the first mating mentioned at the&#xA;  beginning of this problem, determine the F$_1$ and F$_2$ phenotypic&#xA;  expectations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the first crossing, it looks like the type of interaction is one of dominant epistasis between two loci.  So, we could call the alleles for the first locus &lt;strong&gt;W&lt;/strong&gt; and &lt;strong&gt;w&lt;/strong&gt; and the alleles for the second locus &lt;strong&gt;A&lt;/strong&gt; and &lt;strong&gt;a&lt;/strong&gt;.  Then &lt;strong&gt;W-A-&lt;/strong&gt; and &lt;strong&gt;W-aa&lt;/strong&gt; would have a white phenotype, &lt;strong&gt;wwA-&lt;/strong&gt; would have a red phenotype, and &lt;strong&gt;wwaa&lt;/strong&gt; would have a yellow phenotype.  This would be consistent with the ratios provided in the problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to explain the 9 red : 3 yellow : 4 white, a third locus can be considered with alleles &lt;strong&gt;B&lt;/strong&gt; and &lt;strong&gt;b&lt;/strong&gt;.  Proceeding as above, where we had the locus for &lt;strong&gt;W&lt;/strong&gt; or &lt;strong&gt;w&lt;/strong&gt; epistatic with respect to the locus for &lt;strong&gt;A&lt;/strong&gt; and &lt;strong&gt;a&lt;/strong&gt;, we could have the same locus for &lt;strong&gt;W&lt;/strong&gt; or &lt;strong&gt;w&lt;/strong&gt; epistatic with respect to the locus for &lt;strong&gt;B&lt;/strong&gt; and &lt;strong&gt;b&lt;/strong&gt;.  This time, &lt;strong&gt;wwB-&lt;/strong&gt; and &lt;strong&gt;wwbb&lt;/strong&gt; would be white, &lt;strong&gt;W-B-&lt;/strong&gt; would be red, and &lt;strong&gt;W-bb&lt;/strong&gt; would be yellow.  This would be consistent with the 9 red : 3 yellow : 4 white ratio.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is where I get stuck.  If the locus for &lt;strong&gt;W&lt;/strong&gt; and &lt;strong&gt;w&lt;/strong&gt; is epistatic in a dominant way with respect to one locus and in a recessive way with respect to another locus, then all onions would be white.  Therefore, I must have done something wrong.  Am I on the right track?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This isn't really a homework problem, despite the &quot;homework&quot; tag.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are the answers provided in the text for the problem:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Problem 4.30 (pg. 115):  (a) 25% (b) F$_1$: all white; F$_2$ : 52&#xA;  white : 9 red : 3 yellow&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="831" LastEditorUserId="831" LastEditDate="2014-06-06T16:30:24.693" LastActivityDate="2014-06-06T19:14:33.820" Title="Epistasis Involving Multiple Loci" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17896" PostTypeId="2" ParentId="9662" CreationDate="2014-06-04T20:43:26.273" Score="1" Body="&lt;p&gt;This is a complicated case, as it can have multiple causes.&#xA;The genes which are coding for the long (L, yellow) and medium (M, green) wavelength photopigments are located head-to-tail on the X chromosome. This is the reason why this colors are affected much more and especially in men (which only have one copy of this chromosome).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What seems to happen mostly is that the photopigment of one type of cone cells (and their neuronal connectivity) is missing, while the density of the cone cells is still the same. This means that the cells are they, but are not functioning. See these publications (when you have problems getting the articles, let me know in the comments, I can help):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0042698989901405&quot; rel=&quot;nofollow&quot;&gt;The density of cones in the fovea centralis of the human dichromat&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20854834&quot; rel=&quot;nofollow&quot;&gt;Color-deficient cone mosaics associated with Xq28 opsin mutations: a&#xA;stop codon versus gene deletions.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15148406&quot; rel=&quot;nofollow&quot;&gt;Functional photoreceptor loss revealed with adaptive optics: an&#xA;alternate cause of color blindness.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;What can additionally happen in some cases is that these cones have a different pigment than they should have. See the third paper above for details.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-06-05T06:19:12.593" LastActivityDate="2014-06-05T06:19:12.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17897" PostTypeId="1" CreationDate="2014-06-04T23:48:28.103" Score="0" ViewCount="42" Body="&lt;p&gt;i was reading &lt;a href=&quot;http://www.cnet.com/au/news/detached-retina-linked-to-overtexting-in-the-dark/&quot; rel=&quot;nofollow&quot;&gt;this artical&lt;/a&gt; after hearing about it on the news, while reading i saw the term &quot;floaters&quot; which made me remember of a recent Family Guy Episode in which there is a joke about them in Peter's vision.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering, what exactly are they? what is their technical term? and is it possible to remove them permanently (apart from the obvious gouging out your eyes).&lt;/p&gt;&#xA;" OwnerUserId="4378" LastActivityDate="2014-06-04T23:48:28.103" Title="What exactly are &quot;floaters&quot;?" Tags="&lt;eyes&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2014-06-05T15:27:23.577" ContentLicense="CC BY-SA 3.0" />
  <row Id="17898" PostTypeId="1" CreationDate="2014-06-05T00:36:35.597" Score="3" ViewCount="151" Body="&lt;p&gt;We have gene expression data (Affimetrix mRNA gene expression results) for several cell lines, over a set of genes.  Our goal would be to be able to compare relative gene expression for genes over the different cell lines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The method we have thought of so far involves calculating some sort of gene-based average (the expression of a particular gene over all the lines) and normalizing our expression data, grouped per gene, based on that.  However, we are not sure that this is a valid method for obtaining relative expression data from our data set, especially so that we can compare the data from several lines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this seem like a valid strategy?  How is this normalization commonly done?  Should we do something differently to get a better comparison?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks so much!&lt;/p&gt;&#xA;" OwnerUserId="5680" LastActivityDate="2014-06-16T01:14:39.677" Title="Valid comparison of gene expression between several genes in several cell lines" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;statistics&gt;&lt;mrna&gt;&lt;systems-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17899" PostTypeId="1" AcceptedAnswerId="17901" CreationDate="2014-06-05T00:36:51.063" Score="9" ViewCount="1390" Body="&lt;p&gt;Some &lt;em&gt;Aspergillus&lt;/em&gt; species appear to like walnuts. My question concerns the association of &lt;em&gt;Penicillium&lt;/em&gt; and &lt;em&gt;Aspergillus&lt;/em&gt;. No sooner does &lt;em&gt;Aspergillus&lt;/em&gt; colonize a walnut (or some other challenging carbon source) than &lt;em&gt;Penicillium&lt;/em&gt; seems to move in, eventually killing the &lt;em&gt;Aspergillus&lt;/em&gt; colony.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A totally unscientific guess is that &lt;em&gt;Aspergillus&lt;/em&gt; is a good colonizer and &lt;em&gt;Penicillium&lt;/em&gt; a good opportunist and that this is a common pattern with these two species. Is there any science in this direction? I do recall a sort of well-known picture from an old text in which &lt;em&gt;Penicillium&lt;/em&gt; is shown more or less strangling a species of &lt;em&gt;Aspergillus&lt;/em&gt;. I didn't think about it much at the time.       &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image attached is not very incriminating but the theme is the same. &lt;em&gt;Penicillium&lt;/em&gt; are the green hand-like structures strewn about the clover-like &lt;em&gt;Aspergillus.&lt;/em&gt; Foot-cell of the latter cropped. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This seems like a simple question but a quick search doesn't reveal a lot, I think in part because this would generally come up as a contamination issue.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hJwq7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-06-05T01:36:54.820" LastActivityDate="2015-11-15T19:14:43.360" Title="Is there an antagonistic association between Penicillium and Aspergillus?" Tags="&lt;ecology&gt;&lt;mycology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17901" PostTypeId="2" ParentId="17899" CreationDate="2014-06-05T01:29:57.873" Score="9" Body="&lt;p&gt;It is hard to find any articles on the &lt;em&gt;association&lt;/em&gt; between &lt;em&gt;Penicillium&lt;/em&gt; and &lt;em&gt;Aspergillus&lt;/em&gt; species, although they are both considered &lt;a href=&quot;http://www.jiaci.org/issues/vol18issue3/2.pdf&quot; rel=&quot;noreferrer&quot;&gt;two of the most common mold species&lt;/a&gt; found indoors.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In this study, the most prevalent spore types detected in both the indoor and outdoor air samples were generally from the &lt;em&gt;Penicillium&lt;/em&gt;/&lt;em&gt;Aspergillus&lt;/em&gt; group [...] these ﬁndings are qualitatively similar to those observed in other geographical locations, conﬁrming the ubiquitous nature of these fungi.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Although these genera seem to be found commonly, it also has to do with environmental factors, and the relative humidity of the area as well.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Geographical location, climate, and short-term meteorological &#xA;  conditions are responsible for outdoor types and levels of fungal &#xA;  spores.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As for the association and apparently colonization/opportunistic behaviour of the genera, it seems like there are not any associations between the two, unless perhaps &lt;a href=&quot;http://www.mycologia.org/content/97/1/202.full&quot; rel=&quot;noreferrer&quot;&gt;environmental conditions are subject to changing&lt;/a&gt;, and different mold species have different moisture/temperature thresholds, although again these mold groups tend to be generalists and do well at a wider range of environmental conditions than other fungi.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A laboratory procedure was developed in which viable peanut seeds were wounded and inoculated with field soil containing natural populations of fungi, then incubated under different conditions of seed water activity and temperature. [...] &lt;em&gt;A. parasiticus&lt;/em&gt; colonized peanut seeds at lower temperatures than &lt;em&gt;A. flavus&lt;/em&gt;, and cool soil temperatures relative to temperatures of aerial crop fruits might explain why &lt;em&gt;A. parasiticus&lt;/em&gt; is found mostly in peanuts. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Other fungi, dominated by the genera &lt;strong&gt;&lt;em&gt;Penicillium&lt;/em&gt;&lt;/strong&gt;, &lt;em&gt;Fusarium&lt;/em&gt; and &lt;em&gt;Clonostachys&lt;/em&gt;, colonized seeds primarily at water activities and temperatures suboptimal for section &lt;em&gt;Flavi&lt;/em&gt; species and &lt;em&gt;A. niger&lt;/em&gt;. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;em&gt;Eupenicillium ochrosalmoneum&lt;/em&gt; frequently sporulated on the conidial heads of section Flavi species and showed specificity for these fungi. The inoculation of wounded viable peanut seeds with soil containing natural populations of fungi provides a model system for studying the infection process, the interactions among fungi and those factors important in aflatoxin formation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Any associations with different fungi species and &lt;a href=&quot;http://www.mycologia.org/content/100/1/12.full&quot; rel=&quot;noreferrer&quot;&gt;their different structures&lt;/a&gt;, including, for example, with the conidial heads of &lt;em&gt;Aspergillus&lt;/em&gt; seem to be currently under study:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The genus &lt;em&gt;Penicillium&lt;/em&gt; comprises species that mostly colonize plant matter. However early reports suggest that several species are capable of parasitizing &lt;em&gt;Aspergillus&lt;/em&gt; and sporulating on the conidial heads of the host. More recently &lt;em&gt;Eupenicillium ochrosalmoneum&lt;/em&gt; and &lt;em&gt;E. cinnamopurpureum&lt;/em&gt;, [...] have been observed sporulating on the heads of &lt;em&gt;Aspergillus&lt;/em&gt; species belonging to section &lt;em&gt;Flavi&lt;/em&gt; during the colonization of peanut seeds.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JmuYD.gif&quot; alt=&quot;*Eupenicillium* and *Penicillium* species sporulating on heads of *Aspergillus*.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Little is known about the host specificity underlying these &lt;em&gt;Aspergillus&lt;/em&gt;-&lt;em&gt;Penicillium&lt;/em&gt; associations&lt;/strong&gt;. [...] all species spread across Aspergillus colonies by means of aerial hyphae that grew from head to head. Additional studies are required to clarify whether &lt;em&gt;Eupenicillium&lt;/em&gt; and &lt;em&gt;Penicillium&lt;/em&gt; species are parasitic or simply epibiotic on their hosts.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6380" LastActivityDate="2014-06-05T01:29:57.873" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17902" PostTypeId="1" AcceptedAnswerId="17903" CreationDate="2014-06-05T07:04:41.793" Score="10" ViewCount="26310" Body="&lt;p&gt;Some peppers, such as the &lt;a href=&quot;https://en.wikipedia.org/wiki/Habanero_chili&quot;&gt;habanero&lt;/a&gt; or &lt;a href=&quot;https://en.wikipedia.org/wiki/Carolina_Reaper&quot;&gt;Carolina reaper&lt;/a&gt; are extremely spicy, and when eaten in larger amounts than one is accustomed to, can cause some discomfort.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've also heard anecdotes claiming that pepper spray, if applied with sufficient intensity, can cause death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What if you were to eat as many spicy peppers as possible, despite the noxious taste? Is it possible to commit suicide in this way (and what would the cause of death)? Would you faint from excessive mouth pain? Would uncontrollable vomiting prevent you from consuming further peppers?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2021-05-15T07:52:54.317" Title="What's the worst that can happen from eating too many spicy peppers? Can you die?" Tags="&lt;botany&gt;&lt;food&gt;&lt;toxicology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17903" PostTypeId="2" ParentId="17902" CreationDate="2014-06-05T07:04:41.793" Score="18" Body="&lt;p&gt;The more &amp;quot;dangerous&amp;quot; properties of spicy peppers are chiefly due to capsaicin.&lt;/p&gt;&#xA;&lt;p&gt;Sigma-Aldrich sells &lt;a href=&quot;http://www.sigmaaldrich.com/catalog/product/sigma/m2028?lang=en&amp;amp;region=US&quot; rel=&quot;noreferrer&quot;&gt;purified capsaicin&lt;/a&gt;, for which they provide safety information, including an MSDS. Most of it is the usual, unsurprising set of warnings about irritation to eyes and the respiratory system. However, there are LD50 numbers:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;LD50 Oral - rat - male - 161.2 mg/kg&lt;/p&gt;&#xA;&lt;p&gt;LD50 Oral - rat - female - 148.1 mg/kg&lt;/p&gt;&#xA;&lt;p&gt;LD50 Dermal - mouse - &amp;gt;512 mg/kg&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;From this, we can conclude that one would have to eat quite a bit of capsaicin to die. If lethality in humans is exactly the same as rat (which it probably isn't),  a 70 kg human would need to consume about 11 g of capsaicin to reach similar levels of lethality.&lt;/p&gt;&#xA;&lt;p&gt;The Carolina Reaper, one of the hottest known peppers, averages about &lt;a href=&quot;https://en.wikipedia.org/wiki/Carolina_Reaper&quot; rel=&quot;noreferrer&quot;&gt;1.6 million&lt;/a&gt; on the Scoville scale. Capsaicin amount is related to &lt;a href=&quot;https://en.wikipedia.org/wiki/Scoville_scale#High-performance_liquid_chromatography&quot; rel=&quot;noreferrer&quot;&gt;Scoville heat units&lt;/a&gt;, so we can make an imprecise conversion from one to the other.&lt;/p&gt;&#xA;&lt;p&gt;Using values given in 2 publications (&lt;a href=&quot;http://www.sciencepub.net/newyork/ny0309/03_3176ny0309_17_21.pdf&quot; rel=&quot;noreferrer&quot;&gt;Nwokem 2010&lt;/a&gt; and &lt;a href=&quot;http://www.mdpi.com/1420-3049/16/10/8919&quot; rel=&quot;noreferrer&quot;&gt;Al Othman 2011&lt;/a&gt;) we can observe the following trend:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jaTOQ.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;So on average, about &lt;span class=&quot;math-container&quot;&gt;$6.25 \cdot 10^{-5}$&lt;/span&gt; mg/g capsaicin per SHU. With this, we get &lt;span class=&quot;math-container&quot;&gt;$(1.6 \cdot 10^5) \cdot (6.25 \cdot 10^{-5}) = 10$&lt;/span&gt; mg/g, or 1% capsaicin for dry Carolina Reapers. To eat the equivalent of 11 g of capsaicin in peppers, you would have to eat 1.1 kg of dry peppers - which should be a couple of dozen.&lt;/p&gt;&#xA;&lt;p&gt;So, I think we can conclude that it is relatively &amp;quot;feasible&amp;quot; to consume a dangerously large amount of capsaicin by eating very spicy peppers. However, there are numerous caveats with my reasoning:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Human LD50 and rat LD50 are not necessarily the same.&lt;/li&gt;&#xA;&lt;li&gt;Toxicity is not necessarily linearly related to body weight.&lt;/li&gt;&#xA;&lt;li&gt;Peppers have compounds besides capsaicin that contribute to hotness.&lt;/li&gt;&#xA;&lt;li&gt;It would be very difficult to eat such a large amount of spicy peppers, and various involuntary reflexes would interfere. Even if one were force fed the peppers, I imagine the body would attempt to vomit it up - which brings up the question of how the toxicologists even managed to feed several milligrams of capsaicin to rats to measure the LD50.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="540" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-06-05T07:04:41.793" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="17904" PostTypeId="2" ParentId="8687" CreationDate="2014-06-05T07:24:28.497" Score="2" Body="&lt;p&gt;Bruises are a type of hematoma of tissue in which capillaries and sometimes venules are damaged by trauma, allowing blood to seep, hemorrhage, or extravasate into the surrounding interstitial tissues (&lt;a href=&quot;http://en.wikipedia.org/wiki/Bruise&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).  From what I read there seems to be two reasons why you notice a reduction in bruising.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first would be because there is a deadening of nerve cells where they get used to the pain and eventually less sensitive. There could also be the development of some scar tissue from the bruising which has irregularly developed nerve endings leading to lesser stimulation. (&lt;a href=&quot;http://www.phoenixgymbkk.com/training-fighting/conditioning-technique-to-strengthen-shins-400.html&quot; rel=&quot;nofollow&quot;&gt;reference 1&lt;/a&gt; and &lt;a href=&quot;http://www.health-news-for-you.com/scar-tissue.html&quot; rel=&quot;nofollow&quot;&gt;reference 2&lt;/a&gt;) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second reason could be because you yourself get stronger. The Wolff's law states that: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bone in a healthy person or animal will adapt to the loads under which&#xA;  it is placed.&lt;a href=&quot;http://en.wikipedia.org/wiki/Bruise&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt; If loading on a particular bone increases, the bone&#xA;  will remodel itself over time to become stronger to resist that sort&#xA;  of loading.&lt;a href=&quot;http://www.phoenixgymbkk.com/training-fighting/conditioning-technique-to-strengthen-shins-400.html&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt; The internal architecture of the trabeculae undergoes&#xA;  adaptive changes, followed by secondary changes to the external&#xA;  cortical portion of the bone,&lt;a href=&quot;http://www.health-news-for-you.com/scar-tissue.html&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt; perhaps becoming thicker as a result (&lt;a href=&quot;http://en.wikipedia.org/wiki/Wolff%27s_law&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, repeated stress on the bones of your face/hands should be make them stronger. I don't think your body can adapt to heal faster in an area from repeated bruising as most likely &lt;a href=&quot;http://en.wikipedia.org/wiki/Scar_tissue&quot; rel=&quot;nofollow&quot;&gt;scar tissue&lt;/a&gt; will develop from repeated stress on the skin. You can however improve your nutrition and diet to help your body heal better (&lt;a href=&quot;http://www.healthline.com/health-slideshow/foods-that-help-you-heal&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-05T07:24:28.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17905" PostTypeId="2" ParentId="17898" CreationDate="2014-06-05T08:31:24.230" Score="1" Body="&lt;p&gt;This is not an easy task, as there are many factors which you have to take in account. First there are intra-essay differences as slightly different conditions for each set of probes for the repetitions. Then, there are inter-assay differences, as differences in the array slides and so on, this paper (&quot;&lt;a href=&quot;http://www-huber.embl.de/pub/pdf/hvhv.pdf&quot; rel=&quot;nofollow&quot;&gt;Analysis of microarray gene expression data&lt;/a&gt;&quot;) goes into more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This articles might be helpful as well:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nmeth/journal/v2/n5/abs/nmeth756.html&quot; rel=&quot;nofollow&quot;&gt;Multiple-laboratory comparison of microarray platforms&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24740471&quot; rel=&quot;nofollow&quot;&gt;Increasing consistency of disease biomarker prediction across&#xA;datasets.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18629271&quot; rel=&quot;nofollow&quot;&gt;The curse of normalization.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18629084&quot; rel=&quot;nofollow&quot;&gt;Microarray probe expression measures, data normalization and&#xA;statistical validation.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;What you could also do is go over the &lt;a href=&quot;http://www.researchgate.net/&quot; rel=&quot;nofollow&quot;&gt;Researchgate&lt;/a&gt;, I think there are more people around with a lot of experience in this field.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-05T08:31:24.230" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17906" PostTypeId="1" AcceptedAnswerId="17909" CreationDate="2014-06-05T09:14:47.097" Score="8" ViewCount="35265" Body="&lt;p&gt;What is the biological function of nose hair? In general, can we consider underarm hair and pubic hair to be vestigial structures?&lt;/p&gt;&#xA;" OwnerUserId="6927" LastEditorUserId="-1" LastEditDate="2019-04-17T11:47:31.740" LastActivityDate="2019-04-17T11:47:31.740" Title="What is the biological function of nose, underarm, and pubic hair?" Tags="&lt;human-biology&gt;&lt;vestigial&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="17908" PostTypeId="2" ParentId="15915" CreationDate="2014-06-05T09:59:57.477" Score="1" Body="&lt;p&gt;The electomagnetic field of the heart actually changes with emotions so there is no fixed range as such (&lt;a href=&quot;http://www.heartmath.org/templates/ihm/articles/infographic/2013/mysteries-of-the-heart/index.php&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). It could also change with temperature and other external magnetic disturbances (&lt;a href=&quot;http://phys.org/news179751368.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). The heart generates the largest electromagnetic field in the body which is up to 50 mV/m, and that of the brain and other vital organs up to 5 mV/m. Here is a paper on the exposure of human beings to electromagnetic waves (&lt;a href=&quot;http://www.academia.edu/2968057/_The_Exposure_of_Humans_to_the_Electromagnetic_Fields_&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). This paper details some of the current medical treatments focusing on the electromagnetic fields (&lt;a href=&quot;http://drpawluk.com/updates/electromagnetic-fields-and-the-heart/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-05T14:29:51.197" LastActivityDate="2014-07-05T14:29:51.197" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17909" PostTypeId="2" ParentId="17906" CreationDate="2014-06-05T10:04:25.443" Score="9" Body="&lt;p&gt;From &lt;a href=&quot;http://www.wisegeek.com/what-is-the-purpose-of-nose-hair.htm&quot; rel=&quot;noreferrer&quot;&gt;this article&lt;/a&gt; I quote &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hair in the nose is one of the body's first lines of defense against&#xA;  harmful environmental pathogens such as germs, fungus, and spores.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Another purpose for nose hair is to provide additional humidity to the&#xA;  inhaled air. As the air passes through the nasal passages, the mucus&#xA;  and hair provide heat and moisture. Humidity is an important factor&#xA;  for the rest of the respiratory system, such as the larynx and lungs.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Hair in the form of tiny cilia also draw solid particles towards the&#xA;  interface between the nose and throat. Harmful debris is generally&#xA;  directed towards the back of the throat and esophagus for swallowing,&#xA;  while the filtered air continues towards the larynx and lungs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you look on an evolutionary perspective, the arm pit hair follicles as well as pubic hair have a type of sweat gland associated with them, called an apocrine gland, that begins to function at puberty and is widely associated with scent-communication via chemicals known as pheromones (&lt;a href=&quot;http://en.wikipedia.org/wiki/Apocrine_sweat_gland&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some other functions that are associated with pubic hair are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Keeping the genitals warm.&lt;/li&gt;&#xA;&lt;li&gt;Drawing attention to the genitalia.&lt;/li&gt;&#xA;&lt;li&gt;It also decreases friction during intercourse (&lt;a href=&quot;http://www.doctoroz.com/blog/lauren-streicher-md/bare-necessities-what-you-should-know-grooming-your-pubic-hair&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The nose hair is definitely not vestigial. As long as the armpit hair (between the body and arm in certain heavyset individuals) and pubic hair serve to reduce friction and male sweat serves to increase female hormones, I wouldn't call them vestigial (&lt;a href=&quot;http://news.cnet.com/Study-Male-sweat-causes-female-hormones-to-rise/2100-11395_3-6157161.html&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="6703" LastEditDate="2014-06-05T15:21:28.907" LastActivityDate="2014-06-05T15:21:28.907" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17910" PostTypeId="2" ParentId="17902" CreationDate="2014-06-05T10:55:00.607" Score="-1" Body="&lt;p&gt;If you have cardiovascular problems, then it should be quite possible for the pain cause by spicy peppers to trigger a heart attack via a spike in blood pressure. A similar scenario might occur with respiratory diseases. And of course an anaphylactic shock, if you are allergic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from such special circumstances, I imagine that it would be nearly impossible to overcome the debilitating effects of capsaicin long enough to consume a lethal dose.&lt;/p&gt;&#xA;" OwnerUserId="4038" LastActivityDate="2014-06-05T10:55:00.607" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17911" PostTypeId="1" AcceptedAnswerId="17959" CreationDate="2014-06-05T11:10:25.590" Score="1" ViewCount="125" Body="&lt;p&gt;Recently I was changing the thermal grease on my PC. I have noticed on the back of box, that the grease is not dangerous when ingested or when touched. But there was specifically stated, that is dangerous to aquatic organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is so special about aquatic chemistry, that the grease is dangerous to them? I would guess that the chemistry of mammals, reptiles, and birds would be quite similar to that of fish.&lt;/p&gt;&#xA;" OwnerUserId="6930" LastEditorUserId="1320" LastEditDate="2014-06-06T08:38:44.677" LastActivityDate="2014-06-07T09:49:54.417" Title="Why are some chemical dangerous to aquatic environment only?" Tags="&lt;environment&gt;&lt;aquaculture&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17912" PostTypeId="1" AcceptedAnswerId="17916" CreationDate="2014-06-05T11:54:56.350" Score="1" ViewCount="158" Body="&lt;p&gt;Hens lay many eggs during their lifetime (at least, I don't know of one which can lay more eggs) and they can't fly. Compared to other domestic animals it seems to me they are the least capable of defending themselves or escape if it comes to be left alone in open wild. What is their evolutionary story?&lt;/p&gt;&#xA;" OwnerUserId="6927" LastEditorUserId="6703" LastEditDate="2014-06-05T15:21:54.320" LastActivityDate="2014-06-05T15:21:54.320" Title="Why are hens so different from other birds?" Tags="&lt;evolution&gt;&lt;zoology&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-06-05T16:36:40.207" ContentLicense="CC BY-SA 3.0" />
  <row Id="17913" PostTypeId="2" ParentId="8257" CreationDate="2014-06-05T12:34:31.330" Score="0" Body="&lt;p&gt;The genus &lt;em&gt;Cenosphaera&lt;/em&gt; has indeed been used to qualify fossils of Spumellarians (an order of polycystine Radiolarians) that consists of a single, hollow, spherical shell. The biological meaningfulness of this definition is however unknown.&lt;br&gt;&#xA;The very small external thorns that one can see on the picture you're showing are thought to be secondary growth and therefore variable with the age of the specimen, the availability of silicon in the specimen water column and the state of preservation (if it is a fossil).&lt;br&gt;&#xA;When alive those species fo course are not hollow inside. The cytology of spumellarians is not as well known as the cytology of Nasselarians (read papers from Cachon, Hollande or Enjumet if you're interested or this nice review from &lt;a href=&quot;http://www.plankton.jp/PBR/issue/vol06_2/0602_069.pdf&quot; rel=&quot;nofollow&quot;&gt;Suzuki &amp;amp; Aita&lt;/a&gt;) but they do possess for sure a cytoplasm separated by a capsular wall into a dense endoplasm and a loose ectoplasm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NB: The &lt;a href=&quot;https://www.kahaku.go.jp/research/db/botany/ehrenberg/contents.html&quot; rel=&quot;nofollow&quot;&gt;reexamination&lt;/a&gt; of the specimens Ehrenberg used to described his first species of &lt;em&gt;Cenosphaera&lt;/em&gt; (&lt;em&gt;Cenosphaera plutonis&lt;/em&gt;, de facto type-species) showed that this specimen was not actually a single-shelled spumellarian, hinting that this genus name have been probably misused in 150 years of radiolarian research.&lt;/p&gt;&#xA;" OwnerUserId="5915" LastEditorUserId="5915" LastEditDate="2014-06-05T12:39:39.613" LastActivityDate="2014-06-05T12:39:39.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17916" PostTypeId="2" ParentId="17912" CreationDate="2014-06-05T14:04:58.657" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Domesticated&quot; rel=&quot;nofollow&quot;&gt;Domestic organisms&lt;/a&gt; are bred to serve specific purposes for humans. Sheep are bred to produce wool; Cows are bred to provide meat and milk for human consumption; dogs are bred for service and companionship. Since domestic animal do &lt;em&gt;need&lt;/em&gt; to survive in the wild in order to reproduce (ignoring &lt;a href=&quot;http://en.wikipedia.org/wiki/Feral&quot; rel=&quot;nofollow&quot;&gt;feral animals&lt;/a&gt;, which is an interesting topic by itself), most of the other aspects of that animal relevant to its survival tend to be minimized. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So one could just as easily point out that there is no other animal that produces as much wool as a sheep, and yet producing copious amounts of wool isn't particularly useful to the animal itself (i.e. other than the fact that humans will tend to select good wool producers for breeding). So sheep are not particularly good at surviving in the wild, and yet they are incredibly successful as a species and are widely distributed, thanks to humans. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, domestic hens evolved to produce many eggs in their lifetime because over the past millennia since humans have started keeping them as livestock, humans tended to preferentially breed those individuals which produced more eggs and to eat those individuals which did not. Chickens tended to be kept in pens and guarded by humans or other animals, so the ability to defend themselves or flee from danger was not important to their survival, and in fact, those that did attack their handlers or escape were probably less likely to be bred. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This process is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Selective_breeding&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;selective breeding&lt;/strong&gt; or &lt;strong&gt;artificial selection&lt;/strong&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6703" LastEditorUserId="6703" LastEditDate="2014-06-05T14:14:19.483" LastActivityDate="2014-06-05T14:14:19.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17918" PostTypeId="2" ParentId="17889" CreationDate="2014-06-05T16:06:45.927" Score="8" Body="&lt;p&gt;There are different unrelated plants called &quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/Pepper&quot; rel=&quot;nofollow&quot;&gt;pepper&lt;/a&gt;&quot; in English. Black pepper (species of the &lt;em&gt;Piper&lt;/em&gt; genus), as indicated by Chris, is not related to tomato and doesn't &quot;look alike&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess the OP meant actually a different plant (&lt;em&gt;Capsicum&lt;/em&gt; genus), to which the common &lt;a href=&quot;https://en.wikipedia.org/wiki/Bell_pepper&quot; rel=&quot;nofollow&quot;&gt;bell pepper&lt;/a&gt; (&lt;em&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Capsicum_annuum&quot; rel=&quot;nofollow&quot;&gt;Capsicum annuum&lt;/a&gt;&lt;/em&gt;) belongs. This one &lt;em&gt;is&lt;/em&gt; similar to tomato and they both belong to Solanaceae, the same subfamily Solanoideae, but different tribes: tomato is classified in Solaneae and &lt;em&gt;Capsicum&lt;/em&gt; in Capsiceae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://biologylabs.utah.edu/bohs/PDFs/Olmstead%20et%20al-2008.pdf&quot; rel=&quot;nofollow&quot;&gt;this study&lt;/a&gt; you can see, how distant phylogenetically the two genera are. Currently accepted classification generally reflects phylogeny, and there are three more tribes that are closer to Capsiceae, to which Solaneae is nevertheless a close relative.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most striking morphological difference between &lt;em&gt;Capsicum&lt;/em&gt; and &lt;em&gt;Solanum&lt;/em&gt; is that the first one is characterized by hollow fruits, while tomato and other &lt;em&gt;Solanum&lt;/em&gt; species have fleshy berry-like fruits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;: It's actually not a difficult task for one's imagination to see that the two types of fruit are structurally very similar. In reality a &lt;a href=&quot;https://www.google.com/search?q=Yellow%20Stuffer&amp;amp;tbm=isch&quot; rel=&quot;nofollow&quot;&gt;pepper-structured tomato cultivar&lt;/a&gt; is known, and even quantitative trait loci underlying this morphological trait were &lt;a href=&quot;http://oardc.osu.edu/vanderknaap/files/stufferms.pdf&quot; rel=&quot;nofollow&quot;&gt;already found&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-06-11T09:14:32.827" LastActivityDate="2014-06-11T09:14:32.827" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17920" PostTypeId="1" AcceptedAnswerId="17922" CreationDate="2014-06-05T18:48:04.060" Score="6" ViewCount="901" Body="&lt;p&gt;After class today, the topic of eating one's one fecal matter came up. There was a sharp divide as to how people thought the defecations would change. I realize this is a bit of an odd question but understanding it would help me understand how our body handles waste. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One theory was that the body would continually reuse some elements of the fecal matter such that, eventually and with no other input, nothing would be defecated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another theory was that there are elements in the fecal matter that the body would never make any use of, so it would continually get excreted (up until the person died, of course). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could someone please explain the likely outcome of continually and only eating your own poop (assuming you could stay alive long enough)?&lt;/p&gt;&#xA;" OwnerUserId="830" LastEditorUserId="16651" LastEditDate="2015-12-11T04:57:54.823" LastActivityDate="2018-04-11T04:09:45.893" Title="What happens to fecal matter if it's continually re-eaten?" Tags="&lt;scatology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17922" PostTypeId="2" ParentId="17920" CreationDate="2014-06-05T19:57:38.503" Score="4" Body="&lt;p&gt;In a healthy person, stool weight depends mainly on the quality and quantity of the diet. The mean stool weight of a normal defecation is about 320 g &lt;sup&gt;[1]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dry weight of fecal matter contains &lt;sup&gt;[2]&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;30 % bacteria&lt;/li&gt;&#xA;&lt;li&gt;30 % undigested food and fiber&lt;/li&gt;&#xA;&lt;li&gt;10-20 % fat&lt;/li&gt;&#xA;&lt;li&gt;2-3% protein&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Let's do the math (the only nutrients in feces are fats and proteins):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;20% * 320g = 64g of fats which can release 64 * 9.3 = 595 kcal of energy&lt;/li&gt;&#xA;&lt;li&gt;3% * 320 = 9.6g of proteins which can release 9.6 * 4.1 = 40 kcal of energy&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;That's about 650 kcal. 2,000 kcal is a rough average of what people eat in a day. But your body might need more or less than 2,000 &lt;sup&gt;[3]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, fecal matter can't supply enough nutrients. Continuously (re)eating feces and only feces will lead to denutrition, less feces and death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Seyed Mohammad Kazem Hosseini Asl MD, Seyed Davood Hosseini MD. &lt;a href=&quot;http://www.ams.ac.ir/AIM/0034/asl0034.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Determination of the Mean Daily Stool Weight, Frequency of Defecation and Bowel Transit Time: Assessment of 1000 Healthy Subjects&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/users/3632/shigeta&quot;&gt;shigeta&lt;/a&gt;'s answer on &lt;em&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/5684/what-is-the-composition-of-human-feces&quot;&gt;What is the composition of human feces?&lt;/a&gt;&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;HowStuffWorks.com. &lt;em&gt;&lt;a href=&quot;http://health.howstuffworks.com/wellness/food-nutrition/facts/question457.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;How many calories does a person need daily?&lt;/a&gt;&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-06-05T19:57:38.503" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17924" PostTypeId="1" AcceptedAnswerId="19297" CreationDate="2014-06-05T20:23:06.810" Score="2" ViewCount="142" Body="&lt;p&gt;I have a question about cancer cure statistics. Many of the cancer literature or databases I have come across speak about 5 year or 10 year survival rates. In this case survival means that the patient with cancer is still alive 5 or 10 years after diagnosis. I am in need of references about the statistics which explain what is the percentage of people in these groups who are in progression-free survival group and disease-free survival group. That is for instance among the cancer patients which survive for some X years, who are completely cured of cancer (which means that the cancer is completely cured and has not reoccured with in this X years).    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update: USA data is preferred&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="5013" LastEditorUserId="5013" LastEditDate="2014-06-06T10:08:26.987" LastActivityDate="2014-07-25T19:29:32.650" Title="Cancer cure statistics questions" Tags="&lt;cancer&gt;&lt;statistics&gt;" AnswerCount="2" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="17925" PostTypeId="2" ParentId="11325" CreationDate="2014-06-05T20:46:25.557" Score="1" Body="&lt;p&gt;The Raynaud phenomenon is a recurrent vasospasm that is associated with cold temperatures and emotional stress [1]. Excessive vasoconstriction leads to hypoxia. The cause of vasoconstriction is a hyperactivation of the sympathetic nervous system [2] and probably the lack of parasympathetic response. The mechanism is thought to involve both central neural issues and peripheral impairment (subclinical polyneuropathy) [3]. The resulted chronic hypoxia leads to pain, atrophy and sometimes even ulceration [2].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Bakst R, Merola JF, Franks AG, Sanchez M. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18656283&quot; rel=&quot;nofollow&quot;&gt;Raynaud's phenomenon: pathogenesis and management.&lt;/a&gt; J. Am. Acad. Dermatol. 2008 Oct;59(4):633-53. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.jaad.2008.06.004&quot; rel=&quot;nofollow&quot;&gt;10.1016/j.jaad.2008.06.004&lt;/a&gt;. PubMed PMID: 18656283. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Raynaud's phenomenon,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Raynaud%27s_phenomenon&amp;amp;oldid=613954124&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Raynaud%27s_phenomenon&amp;amp;oldid=613954124&lt;/a&gt; (accessed June 27, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Koszewicz M, Gosk-Bierska I, Jerzy G, Bilińska M, Podemski R, Budrewicz S, Adamiec R. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21747356&quot; rel=&quot;nofollow&quot;&gt;Peripheral nerve changes assessed by conduction velocity distribution in patients with primary Raynaud's phenomenon and dysautonomia.&lt;/a&gt; Int Angiol. 2011 Aug;30(4):375-9. PubMed PMID: 21747356. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-27T14:56:08.620" LastActivityDate="2014-06-27T14:56:08.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17926" PostTypeId="1" AcceptedAnswerId="17928" CreationDate="2014-06-05T20:48:15.587" Score="6" ViewCount="28807" Body="&lt;p&gt;I received a gift that is a jug of Pure Mexican Vanilla. Having never dealt with large quantities of vanilla, it made me curious as to what would happen if a person had too much vanilla.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that the alcohol has a higher toxicity rate and is probably more fatal than the actual vanilla itself, but I'm curious as to what ratio of mass of pure vanilla to mass of the human would be considered fatal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, what is the physiological effect of a vanilla overdose as it pertains to inhibiting critical bodily functions? That is -- specifically what about a vanilla overdose would cause fatality?&lt;/p&gt;&#xA;" OwnerUserId="6938" LastEditorUserId="6938" LastEditDate="2014-06-06T14:24:52.730" LastActivityDate="2017-09-18T14:34:17.100" Title="How much vanilla will kill a person?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ClosedDate="2017-09-21T07:50:11.087" ContentLicense="CC BY-SA 3.0" />
  <row Id="17927" PostTypeId="2" ParentId="17926" CreationDate="2014-06-05T21:08:04.727" Score="3" Body="&lt;p&gt;Out of interest, I've had a look around a bit and it seems like the most dangerous part of that bottle might be the alcohol.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the &lt;a href=&quot;http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?fr=169.3&quot; rel=&quot;nofollow&quot;&gt;FDA&lt;/a&gt;...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The term unit of vanilla constituent means the total sapid and odorous principles extractable from one unit weight of vanilla beans, as defined in paragraph (b) of this section, by an aqueous alcohol solution in which the content of &lt;strong&gt;ethyl alcohol by volume amounts to not less than 35 percent&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(Emphasis mine.)&lt;/p&gt;&#xA;" OwnerUserId="6939" LastActivityDate="2014-06-05T21:08:04.727" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17928" PostTypeId="2" ParentId="17926" CreationDate="2014-06-05T21:16:06.663" Score="19" Body="&lt;p&gt;Vanillin is the chemical that gives vanilla its flavour and smell &lt;sup&gt;[1]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Vanillin is pharmacologically active, causing depressed blood pressure, increased respiratory rate &amp;amp; death due to cardiovascular collapse &lt;sup&gt;[3]&lt;/sup&gt;.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Non-Human Toxicity Values &lt;sup&gt;[4]&lt;/sup&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;LD50 Rat oral 1580 mg/kg&lt;/li&gt;&#xA;  &lt;li&gt;LD50 Rat ip 1160 mg/kg&lt;/li&gt;&#xA;  &lt;li&gt;LD50 Rat sc 1500 mg/kg&lt;/li&gt;&#xA;  &lt;li&gt;LD50 Mouse ip 475 mg/kg&lt;/li&gt;&#xA;  &lt;li&gt;LD50 Guinea pig oral 1400 mg/kg&lt;/li&gt;&#xA;  &lt;li&gt;LD50 Guinea pig ip 1190 mg/kg&lt;/li&gt;&#xA;  &lt;li&gt;LD50 Rat oral 2.8 g/kg&lt;/li&gt;&#xA;  &lt;li&gt;LD50 Guinea pig oral 1.40 g/kg&lt;/li&gt;&#xA;  &lt;li&gt;LD50 Mouse ip 0.78 g/kg&lt;/li&gt;&#xA;  &lt;li&gt;LD50 Rat sc 1.8 g/kg&lt;/li&gt;&#xA;  &lt;li&gt;LD50 Dog iv 1.32 g/kg slow in fusion.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Vanillin,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Vanillin&amp;amp;oldid=613429267&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Vanillin&amp;amp;oldid=613429267&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;PATTY F. A. 1963. &lt;em&gt;Industrial Hygiene and Toxicology. Volume II Toxicity&lt;/em&gt;, page 1696 (referenced from &lt;a href=&quot;http://toxnet.nlm.nih.gov/cgi-bin/sis/search2/r?dbs+hsdb%3a@term+@rn+@rel+121-33-5&quot; rel=&quot;noreferrer&quot;&gt;TOXNET, &lt;em&gt;Vanillin&lt;/em&gt;&lt;/a&gt; - Human Toxicity Excerpts)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;TOXNET. &lt;a href=&quot;http://toxnet.nlm.nih.gov/cgi-bin/sis/search2/r?dbs+hsdb%3a@term+@rn+@rel+121-33-5&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Vanillin&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-26T16:33:10.613" LastActivityDate="2014-06-26T16:33:10.613" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="17930" PostTypeId="1" AcceptedAnswerId="17937" CreationDate="2014-06-06T04:42:03.593" Score="1" ViewCount="594" Body="&lt;p&gt;Here are some suffixes I want to know their meaning:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;-ium&lt;/em&gt;: trapezium (carpal bone)&lt;br&gt;&#xA;&lt;em&gt;-ius&lt;/em&gt;: trapezius  (column muscle)&lt;br&gt;&#xA;&lt;em&gt;-ous&lt;/em&gt;: Talous and calcanous (tarsal bone)&lt;br&gt;&#xA;&lt;em&gt;-alis&lt;/em&gt;: Acromialis, Ulnaris (shoulder proccess and bone of forearm)&lt;br&gt;&#xA;&lt;em&gt;-ate&lt;/em&gt;: Capitate, Hamate, lunate (carpal bones)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the difference between &lt;em&gt;tuber&lt;/em&gt; and &lt;em&gt;tubercle&lt;/em&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How to know where to use these suffixes, they are randomly given or it has to do with location or something?   &lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="6422" LastEditDate="2014-06-07T08:16:38.030" LastActivityDate="2014-06-07T08:16:38.030" Title="Anatomy suffixes?" Tags="&lt;human-anatomy&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17931" PostTypeId="2" ParentId="9867" CreationDate="2014-06-06T05:00:44.067" Score="1" Body="&lt;p&gt;For a start, you could learn about Bioelectromagnetics which is the study of the interaction between electromagnetic fields and biological entities (&lt;a href=&quot;http://en.wikipedia.org/wiki/Bioelectromagnetics&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Electro-magnetic fields are generated by the heart, brain, tissues and cells. These fields are in-turn affected by temperature and the overall mood of a person (&lt;a href=&quot;http://www.heartmath.org/templates/ihm/articles/infographic/2013/mysteries-of-the-heart/index.php&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a lot of research that is being conducted in the field. You can find a lot of papers relating to the field with a &lt;a href=&quot;http://scholar.google.co.in/scholar?start=0&amp;amp;q=human%20electromagnetic%20fields&amp;amp;hl=en&amp;amp;as_sdt=0,5&amp;amp;as_vis=1&quot; rel=&quot;nofollow&quot;&gt;simple search&lt;/a&gt; on Google Scholar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well technically electromagnetic fields. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are instruments to measure EMF which are detailed in the &lt;a href=&quot;http://en.wikipedia.org/wiki/EMF_measurement&quot; rel=&quot;nofollow&quot;&gt;Wikipedia page&lt;/a&gt;. Here is an article on an instrument made to measure the electromagnetic field of the heart (&lt;a href=&quot;http://phys.org/news179751368.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally, if you have measured the electromagnetic fields in different parts of the body (eg: &lt;a href=&quot;http://www.academia.edu/2968057/_The_Exposure_of_Humans_to_the_Electromagnetic_Fields_&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; states that the electric field of the heart is up to 50 mV/m, and that of the brain and other vital organs up to 5 mV/m) then it shouldn't be too hard to generate them seeing that EMF generated is a low value (&lt;a href=&quot;http://www.ehow.com/how_5135610_create-electromagnetic-field.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-06T05:00:44.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17932" PostTypeId="2" ParentId="14873" CreationDate="2014-06-06T06:37:28.160" Score="2" Body="&lt;p&gt;This is of course a controversial topic with there being supporters for both methods of slaughter. First of all, The research paper that you have mentioned is a highly cited one and it is the foremost study that supporters of &lt;a href=&quot;http://en.wikipedia.org/wiki/Exsanguination#cite_note-schulze_halastudy-2&quot; rel=&quot;nofollow&quot;&gt;exanguination&lt;/a&gt; use to support their method of slaughter. However, the author himself (Wilhelm Schulze) has stated and I quote &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;objective results presented for the captive bolt application in sheep&#xA;  indicates that the captive bolt device used is suspect&quot; and that these&#xA;  initial &quot;scientific findings and the results presented are only a very&#xA;  first contribution&quot; and that they &quot;need to be followed as a high&#xA;  priority by further investigations in the continuation of the&#xA;  scientific clarification of the issues of loss of pain and&#xA;  consciousness during slaughter of this kind with and without stunning&#xA;  using the same experimental approach with a representative number of&#xA;  grown cows of various breeds.&quot; (&lt;a href=&quot;http://en.wikipedia.org/wiki/Wilhelm_Schulze&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Since stunning methods have advanced (&lt;a href=&quot;http://en.wikipedia.org/wiki/Stunning&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) from the time this paper was published (1978), it would probably be a bit unfair to hold onto this paper as proof for supporting exsanguination. Moreover, in another study, in which measurements were done with an electro-corticogram it was found that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Captive bolt stunning followed by sticking one minute later resulted&#xA;  in immediate and irreversible loss of evoked responses after the stun.&#xA;  Spontaneous cortical activity was lost before sticking in three&#xA;  animals, and in an average of 10 seconds after sticking in the&#xA;  remaining five animals. The duration of brain function after &lt;a href=&quot;http://en.wikipedia.org/wiki/Shechita&quot; rel=&quot;nofollow&quot;&gt;shechita&lt;/a&gt;&#xA;  was very variable, and particularly contrasted with captive bolt&#xA;  stunning with respect to the effects on evoked responses. These were&#xA;  lost between 20 and 126 seconds (means of 77 seconds for somatosensory&#xA;  and 55 seconds for visual evoked responses) and spontaneous activity&#xA;  was lost between 19 and 113 seconds (mean 75 seconds) after slaughter (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3381436&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The two questions that have to be answered in exsanguination are&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-- Does the neck cut cause pain?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-- How long does it take for the animal to lose enough blood for insensibility to occur and for any perception of pain or suffering associated with slaughter to disappear?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regard to pain, in the process of cutting the major blood vessels leading to and from the brain a number of other tissues are also severed by the extensive neck cut including muscle, skin, sensory and motor nerves etc. There is a chance that this might cause significant shock and fear to the animal. The time to lose consciousness is highly variable in  exsanguination. (&lt;a href=&quot;http://www.tandfonline.com/doi/abs/10.1080/00480169.2009.36881#.U5FgFN_FtTM&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Very good arguments are presented in &lt;a href=&quot;https://www.livecorp.com.au/rd-report/review-stunning-and-halal-slaughter&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; and I highly recommend that you go through it. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-06-06T13:31:49.970" LastActivityDate="2014-06-06T13:31:49.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17934" PostTypeId="2" ParentId="14245" CreationDate="2014-06-06T07:01:48.133" Score="1" Body="&lt;p&gt;1) According to &lt;a href=&quot;http://www.intervalsforcardio.com/resting-heart-rate.html&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; you should be taking it in the most preferred position you want. It would change according to the position you are in so make yourself comfortable sitting or lying down (&lt;a href=&quot;http://btc.montana.edu/olympics/physiology/cf01.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) You take the number of beats of your heart in a minute. If you take the number of beats for 2 minutes, then average your count by 2. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) One minute (&lt;a href=&quot;http://exercise.about.com/od/cardioworkouts/g/restingheartrat.htm&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) Completely relaxed, most articles recommend taking it in the morning while waking up so you are doing the right thing (&lt;a href=&quot;http://www.huffingtonpost.com/dennis-kravetz/heart-rate_b_4428266.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't understand what you mean by an academic situation so I could try and answer it if you clarified it. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-06T07:01:48.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17935" PostTypeId="2" ParentId="13678" CreationDate="2014-06-06T07:27:00.773" Score="1" Body="&lt;p&gt;Eventhough food contributes the most to flatulance, it can also be caused by swallowing air when you chew gum or smoke. It can also be caused by health conditions like &lt;a href=&quot;http://en.wikipedia.org/wiki/Coeliac_disease&quot; rel=&quot;nofollow&quot;&gt;coeliac disease&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Gastroenteritis&quot; rel=&quot;nofollow&quot;&gt;gastroenteritis&lt;/a&gt; (&lt;a href=&quot;http://www.nhs.uk/Conditions/Flatulence/Pages/Causes.aspx&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). So it is indeed hard to believe when people claim that they never fart.  &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-06T07:27:00.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17936" PostTypeId="2" ParentId="10749" CreationDate="2014-06-06T08:42:29.860" Score="2" Body="&lt;p&gt;Yes, changing the scent has been accepted by most snake breeders as a method to feed stubborn snakes (&lt;a href=&quot;http://www.ehp.qld.gov.au/register/p00061aa.pdf&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). For example, if your snake prefers chicken, and wont accept mice, rub a chick on a pre-killed mouse and this may trick it into eating the mouse (&lt;a href=&quot;http://exoticpets.about.com/od/snakes/f/snakefeeding.htm&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).  With regard to garter snakes, the diet may change based on its habitat, its age and even being kept in captivity can change its diet. This article should provide you information with feeding your garter snake if it is stubborn (&lt;a href=&quot;http://www.gartersnake.info/articles/2004/understanding-garter-snakes-through-their-diets.php&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-07T14:51:26.183" LastActivityDate="2014-07-07T14:51:26.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17937" PostTypeId="2" ParentId="17930" CreationDate="2014-06-06T09:24:42.563" Score="2" Body="&lt;p&gt;These names originate from latin &lt;sup&gt;[1]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;-ium&lt;/em&gt; is the second declension of a noun in accusative (&lt;em&gt;trapezium&lt;/em&gt; refers to a bone thus is a &lt;strong&gt;noun&lt;/strong&gt;)&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;-ius&lt;/em&gt; is a genitive adjective suffix (&lt;em&gt;trapezius&lt;/em&gt; is the name of a muscle thus being an &lt;strong&gt;adjective&lt;/strong&gt;)&lt;/li&gt;&#xA;&lt;li&gt;you have written them wrong: &lt;em&gt;talus&lt;/em&gt; and &lt;em&gt;calcaneus&lt;/em&gt; is correct. They are both nominative &lt;strong&gt;nouns&lt;/strong&gt;.&lt;/li&gt;&#xA;&lt;li&gt;there is no &lt;em&gt;-alis&lt;/em&gt; suffix; it is either &lt;em&gt;-is&lt;/em&gt; or &lt;em&gt;-lis&lt;/em&gt;. They are &lt;strong&gt;adjective&lt;/strong&gt; suffixes.&lt;/li&gt;&#xA;&lt;li&gt;there is no &lt;em&gt;-ate&lt;/em&gt; suffix. Those are &lt;strong&gt;nouns&lt;/strong&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Tuber&lt;/em&gt; is the latin word for &lt;em&gt;tuberosity&lt;/em&gt;. It is the quality or condition of a &lt;em&gt;tubercle&lt;/em&gt; (adjective) &lt;sup&gt;[2]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia, &lt;a href=&quot;http://en.wikipedia.org/wiki/Latin_declension&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Latin declension&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;The Free Dictionary by Farlex, &lt;em&gt;&lt;a href=&quot;http://www.thefreedictionary.com/Tubercle+%28anatomy%29&quot; rel=&quot;nofollow&quot;&gt;Tubercle&lt;/a&gt;&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-06T09:37:41.193" LastActivityDate="2014-06-06T09:37:41.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17938" PostTypeId="2" ParentId="5572" CreationDate="2014-06-06T09:31:40.030" Score="3" Body="&lt;p&gt;Ultrasound is considered a safe procedure (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2678243&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) which is accepted by the WHO as well (&lt;a href=&quot;http://whqlibdoc.who.int/trs/WHO_TRS_875.pdf&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). There have been studies however, that show the link of ultrasound treatment to some undesirable traits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultrasound could be possibly linked to a decrease in body weight on birth of infants (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8105165&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Frequent use of ultrasound may influence babies scanned to grow up left handed (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/uog.9055/abstract&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A significant migration of neurons (change of neurons from their rightful area) has been observed in mice on exposing them to ultrasound at the prenatal stage. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538990/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A study has found detrimental affects to the brains of mice on exposure to ultrasound in the fetal stage (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12034351&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So based on these papers, I wouldn't call them a 100% safe but these tests all relate to repeated usage of ultrasound imaging. Ultrasound usage sparingly and on valid medical indication should not be a matter of concern.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-06T09:31:40.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17939" PostTypeId="1" AcceptedAnswerId="17958" CreationDate="2014-06-06T09:36:44.573" Score="2" ViewCount="3217" Body="&lt;p&gt;Under anaerobic conditions E. &lt;em&gt;coli&lt;/em&gt; has two options to generate ATP: fermentation (substrate-level phosphorylation), and respiration (proton gradient, chemisomotic phosphorylation). Which is favored? What determines the choice? If availability of enzymes required for anaerobic respiration is decisive, what regulates them under anaerobic conditions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I looked into the web but did not find the answer.&lt;/p&gt;&#xA;" OwnerUserId="1800" LastEditorUserId="22057" LastEditDate="2018-09-17T20:54:29.693" LastActivityDate="2018-09-17T20:54:29.693" Title="Anaerobic respiration choice in E. coli" Tags="&lt;biochemistry&gt;&lt;microbiology&gt;&lt;metabolism&gt;&lt;ecoli&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="17940" PostTypeId="1" AcceptedAnswerId="17942" CreationDate="2014-06-06T10:13:06.443" Score="16" ViewCount="39351" Body="&lt;p&gt;In the photosynthesis equation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\ce{6CO2 + 6H2O -&amp;gt;[sunlight] C6H12O6 + 6O2}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only place where we have 6 molecules of $\ce{O2}$ is in $\ce{6CO2}$. Then it reacts with $\ce{6H2O}$ to form $\ce{C6H12O6}$ and $\ce{6O2}$ that apparently comes from $\ce{CO2}$. So why do we say that the $\ce{O2}$ produced by plants comes from $\ce{H2O}$ and not $\ce{CO2}$? I don't know if I'm the one who's understanding something wrong or is it the photosynthesis formula which is wrong?&lt;/p&gt;&#xA;" OwnerUserId="6948" LastEditorUserId="22057" LastEditDate="2017-04-13T15:53:21.867" LastActivityDate="2018-10-29T13:58:54.753" Title="Why does the oxygen produced in the photosynthesis come from water and not carbon dioxide?" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;photosynthesis&gt;" AnswerCount="4" CommentCount="4" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="17941" PostTypeId="1" CreationDate="2014-06-06T10:19:34.610" Score="3" ViewCount="399" Body="&lt;p&gt;I am trying to extract information about SNP data from the FTP server of NCBI. Could someone please explain to me how the directory is organised? There are many many files and folders and I can't figure which contains what. Is there one file which explains the organisation of the ftp site properly? The NCBI help manual did not give much help beyond helping me find species of interest.&lt;/p&gt;&#xA;" OwnerDisplayName="user6417" LastActivityDate="2014-08-02T07:29:52.300" Title="Regarding the NCBI FTP site" Tags="&lt;bioinformatics&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17942" PostTypeId="2" ParentId="17940" CreationDate="2014-06-06T10:32:46.073" Score="15" Body="&lt;p&gt;You are missing some knowledge here for sure, photosynthesis is a little complicated at A level, so I will describe it in brief.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During photosynthesis electrons and protons (A hydrogen atom without the electron) are required for a process called the electron transport chain and proton motive force. This happens during the light dependent stage of photosynthesis, (there is also a second light-independent stage called the Calvin cycle, and that is where the CO$_2$ is used), I won't go into detail about what the protons and electrons do (unless you want me to) but you need to know that these come from a water molecule, the water is split using light (photolysis, literally: cutting with light) into two hydrogens and half an oxygen molecule (or an oxygen atom). The oxygen that was released in photolysis is not required for the rest of the pathway, so it diffuses out of the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For why it doesn't come from carbon dioxide, you need to consider the Calvin cycle. In the Calvin cycle, carbon dioxide is converted to glucose by enzymes, using products from the light dependent stage, so 6CO$_2$ are combined over six cycles to form one molecule of glucose. So that is where the CO$_2$ is used as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helped! If you want me to go into any more detail please ask!&lt;/p&gt;&#xA;" OwnerUserId="6330" LastEditorUserId="6307" LastEditDate="2015-11-03T05:20:07.030" LastActivityDate="2015-11-03T05:20:07.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17943" PostTypeId="1" CreationDate="2014-06-06T10:42:30.133" Score="1" ViewCount="777" Body="&lt;p&gt;In my A level revision guide and places on the internet it states that at low temperatures levels of RuBP, GP and TP all fall. However I don't quite understand how this is the case, because as far as I can see, a reduction in temperature would give the molecules less kinetic energy and reduce the rate of reaction of the enzymes and so there would be no change to relative concentrations, because everything is slower all equally. Could anybody explain to me why all three decrease in concentration at low temperatures?&lt;/p&gt;&#xA;" OwnerUserId="6330" LastActivityDate="2014-06-06T10:42:30.133" Title="Why does low temperature make RuBP, GP and TP concentrations fall in Calvin cycle?" Tags="&lt;photosynthesis&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="17944" PostTypeId="1" AcceptedAnswerId="17945" CreationDate="2014-06-06T11:38:16.183" Score="2" ViewCount="996" Body="&lt;p&gt;My question is: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Where will the new DNA nucleotide connect on the (part of the) DNA shown on the picture? Will it connect to the phosphate group?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What does the 5' --&gt; 3' mean?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VIInt.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance.&lt;/p&gt;&#xA;" OwnerUserId="6950" LastEditorUserId="1320" LastEditDate="2014-06-06T14:34:17.497" LastActivityDate="2014-06-06T14:34:17.497" Title="On which part of the DNA will the new DNA nucleotide connect?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-06-16T21:16:31.000" ContentLicense="CC BY-SA 3.0" />
  <row Id="17945" PostTypeId="2" ParentId="17944" CreationDate="2014-06-06T12:11:33.000" Score="2" Body="&lt;p&gt;The numbers come from the numbering of the carbon atom of the ribose in the backbone of the DNA. The ribose is numbered as shown in the figure below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/So2B5.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the nucleotides the phosphate groups are attached to the 5' carbon atom and new nucleotide will be added at the 3' carbon atom. See the image below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fDDsV.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First you have a OH-group at the 3' position which is then &quot;replaced&quot; by the new nucleotide.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-06T12:11:33.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17946" PostTypeId="2" ParentId="17883" CreationDate="2014-06-06T13:25:38.613" Score="7" Body="&lt;p&gt;&lt;strong&gt;Trees need:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Deep roots to get more water and anchor their growth.&lt;/li&gt;&#xA;&lt;li&gt;Strong trunks to support themselves against gravity.&lt;/li&gt;&#xA;&lt;li&gt;A vascular system to move water and nutrients throughout the tree.&lt;/li&gt;&#xA;&lt;li&gt;Small leaves that can be supported high by the trunk to compete for sunlight.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Water plants need:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Just enough root to anchor its location.&lt;/li&gt;&#xA;&lt;li&gt;No vascular system. Water is everywhere.&lt;/li&gt;&#xA;&lt;li&gt;Leaves that are more substantial than the stems to gather as much sunlight as possible through the cover of water.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So the kind of body that has to develop under water to thrive is in many ways the opposite of the kind of body needed to thrive on land.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Water plants would have to waste energy on&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Vast roots.&lt;/li&gt;&#xA;&lt;li&gt;A strong trunk.&lt;/li&gt;&#xA;&lt;li&gt;A vascular system.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;...Things it wouldn't need till later while receiving little sunlight on small leaves. It would have to shed its thirsty skin like a snake on the above water parts. Too complex and little or no demand for it.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;If water plants had evolved a way to turn oxygen into helium and keep much of it trapped within its leaves, then we'd have tall ocean forests. The plants could grow just like they do now  but with slightly fluffy leaves. As soon as it broke water surface, the abundance of oxygen would ramp up helium production and really fluff them leaves. The slight stems would have to be scrappy instead of massive.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;There would be Greek mythology that Gaia was married to Helios but left him for Poseidon the Gaia-Shaker. Poseidon and Gaia were cursed with children (the vast ocean forests) who rebel against them and adopt a lifestyle where they are always reaching out to Helios and later in life shedd their bodies to be closer to him in spirit. Some early humans tried to rob the Helium spirits of the ocean forests by inhailing them out of their plant bodies. They were cursed and turned into chipmunks with only their hands to remind them of their past humanity.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit to add reference:&lt;/strong&gt; &lt;a href=&quot;http://www.ehow.com/list_5840539_difference-water-plants-land-plants.html&quot;&gt;A piece by Mickey Walburg on eHow.com&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though &lt;strong&gt;I would&lt;/strong&gt; call mangroves amphibian trees, I wouldn't call them large and I was trying to ascertain the spirit of what @kai teorn was asking rather than let the question sit unanswered when I believe I can answer it. &#xA;You learn something new often if you're looking and today @MattDMo introduced mangroves into my awareness. If he thought it was the answer to the spirit of the question post, he might have elaborated on it as an answer instead of a comment. I could be wrong about that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mangrove&quot;&gt;Mangroves are mostly coastal&lt;/a&gt;. They are usually at the edges of the water. The ones that are a few meters in the water are usually more like shrubs than majestic boreal forest trees. They end up shooting roots everywhere and kinda lounge around compared to the typical tree standing straight reaching for the sun. Also the incidences of Mangroves in the ocean away from the shoreline are of maybe a handful bunched up, hardly a species wide return to the the oceans. Seen from aerial photos, Mangrove concentrations look like boreal forests surrounding lakes, not swamp lands.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Why are there no tree-like plants that grow in lakes?&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Looking at aerial photos of boreal forests, with dense woods clear-cut&#xA;  by quiet lakes, I wondered why exactly are the woods so clear-cut at&#xA;  the edge of water?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think the spirit of the next question is about trees in general in lakes. Not the few instances peppered around the world. Also some lakes grow and shrink throughout time, sometimes long enough for trees to gain a little ground and survive lake growth. But I don't think those trees as a species have developed adaptations to grow from shallow lake bottoms.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why won't trees develop adaptations that will let them grow from a&#xA;  shallow lake bottom, with the lower part of the trunk in the water and&#xA;  the crown above the water?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;... and from the end of the post ...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Of course there are aquatic and semi-aquatic plants like water lilies,&#xA;  Scirpus or Typha, but they are a far cry from the nearby terrestrial&#xA;  forests, in terms of biomass. Why don't they develop into large&#xA;  amphibian trees, or why don't terrestrial trees try to re-colonize&#xA;  lakes?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;... I eliminated mangroves from qualification. Interesting but I still don't think it's what @kai teorn had in mind. I think @MattDMo introduced mangroves as a comment to enhance our knowledge.&lt;/p&gt;&#xA;" OwnerUserId="6936" LastEditorUserId="6936" LastEditDate="2014-06-06T17:16:10.037" LastActivityDate="2014-06-06T17:16:10.037" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="17947" PostTypeId="2" ParentId="13678" CreationDate="2014-06-06T13:40:05.710" Score="1" Body="&lt;p&gt;Flatus is a normal product of digestion. To some extent flatus production does not depend on the types of food eaten as some of the gas is nitrogen just from air swallowed while eating. Some of the gas produced may be from bacteria in the intestinal tract. Depending on the species they may not be particularly finicky eaters, and may produce gas from any biodegradable food-item. &lt;/p&gt;&#xA;" OwnerUserId="6291" LastActivityDate="2014-06-06T13:40:05.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17950" PostTypeId="2" ParentId="17895" CreationDate="2014-06-06T19:14:33.820" Score="3" Body="&lt;p&gt;After reading Satwik Pasani's comment to the original problem, I tried using the hypostatic locus as the common locus in the epistatic relationships, instead of the locus causing the onions to be white.  The following solution fits the answers supplied in the book.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Three loci can be used to determine the colors of the onion, the alleles of which can be denoted by &lt;strong&gt;C&lt;/strong&gt;, &lt;strong&gt;D&lt;/strong&gt;, and &lt;strong&gt;E&lt;/strong&gt;.  Suppose that &lt;strong&gt;C&lt;/strong&gt; and &lt;strong&gt;D&lt;/strong&gt; are each epistatic to &lt;strong&gt;E&lt;/strong&gt;, such that the phontypes of the onion are given as:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;cc---- white&#xA;--D--- white&#xA;C-ddE- red&#xA;C-ddee yellow&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Then the first crossing in the problem can be given by &lt;strong&gt;CCDDEE&lt;/strong&gt; x &lt;strong&gt;CCddee&lt;/strong&gt;.  The second crossing could be &lt;strong&gt;ccddee&lt;/strong&gt; x &lt;strong&gt;CCddEE&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="831" LastActivityDate="2014-06-06T19:14:33.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17951" PostTypeId="2" ParentId="14570" CreationDate="2014-06-06T19:18:52.260" Score="2" Body="&lt;p&gt;Rhinitis is irritation and &lt;strong&gt;inflammation of the mucous&lt;/strong&gt; membrane inside the nose. Common symptoms of rhinitis are a stuffy nose, runny nose, and post-nasal drip. The most common kind of rhinitis is allergic rhinitis, which is usually triggered by airborne allergens such as pollen and dander &lt;sup&gt;[1]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many questions regarding sublingual immunization still remain to be addressed, including the use of proper adjuvant and the optimization of vaccine formulation to further enhance the vaccine efficacy &lt;sup&gt;[2]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sublingual immunization can induce both systemic and &lt;strong&gt;mucosal immune responses&lt;/strong&gt; against a variety of antigens, including soluble proteins, inter particulate antigens, and live-attenuated viruses &lt;sup&gt;[2]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sublingual immunization has been shown to be &lt;strong&gt;safe and highly effective&lt;/strong&gt; in generating robust immune responses against the administered antigen. Moreover, it has been shown to confer &lt;strong&gt;protective immunity&lt;/strong&gt; by simultaneously eliciting systemic IgG and mucosal IgA antibodies as well as cytotoxic T lymphocyte responses in the peripheral lymphoid organs and mucosal tissues. Studies also suggest that sublingual immunization could be a better alternative to the traditional parental route of vaccine delivery against both genital and respiratory pathogens &lt;sup&gt;[2]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although the s.l. mucosa does not allow passage of macromolecules into blood, s.l. immunization with ovalbumin, a model soluble protein antigen, administered&#xA;alone or together with cholera toxin adjuvant, induces mucosal antibody responses as well as systemic immune responses in mice. The magnitude of serum antibody responses induced by s.l. immunization was in fact comparable to that seen after intranasal (i.n.) immunization and far superior to that after o.g. (oro-gastric) immunization &lt;sup&gt;[3]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Upon stimulation of mucosal surfaces by foreign antigens, dendritic cells among the antigen presenting cells are immediately processed and transport antigen via afferent lymph to draining lymph node for presentation to T cells. Subsequently they induce secretory IgA antibodies. This suggestive link between trafic pattern of dendritic cells and their functions led to the investigation of the chemokine responsiveness of dendritic cells during their development and maturation. It has been observed that type II mucosa tissues (e.g., skin, vaginal, and buccal), which are covered with stratiﬁed epithelia and devoid of&#xA;mucosa-associated lymphoid tissues, mainly express CCL20, CCL19/CCL21, or CCL27/CCL28 individually &lt;sup&gt;[4]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CCR7 (chemokine receptor) expressed CD8α&lt;sup&gt;-&lt;/sup&gt;CD11c&lt;sup&gt;+&lt;/sup&gt; cells ferry antigens in the sublingual mucosa, migrate into the cervical lymph nodes, and share the antigen with resident CD8α&lt;sup&gt;+&lt;/sup&gt;CD11c&lt;sup&gt;+&lt;/sup&gt; cells for the initiation of antigen-specific T and B cell responses following sublingual challenge. The sublingual mucosa is one of the effective mucosal inductive sites regulated by the CCR7-CCL19/CCL21 pathway &lt;sup&gt;[4]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia, &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Rhinitis&quot; rel=&quot;nofollow&quot;&gt;Rhinitis&lt;/a&gt;&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;Byoung-Shik Shim, Youngjoo Choi, In Su Cheon, and Man Ki Song. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3718922/&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Sublingual Delivery of Vaccines for the Induction of Mucosal Immunity.&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Cecil Czerkinsky, Nicolas Çuburu, Mi-Na Kweon, Fabienne Anjuere and Jan Holmgren. &lt;em&gt;&lt;a href=&quot;http://www.landesbioscience.com/journals/vaccines/CzerkinskyHV7-1.pdf&quot; rel=&quot;nofollow&quot;&gt;Sublingual vaccination.&lt;/a&gt;&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;Joo-Hye Song, Jung-Im Kim, Hyung-Joon Kwon, Doo-Hee Shim, Nirmala Parajuli, Nicolas Cuburu, Cecil Czerkinsky and Mi-Na Kweon. &lt;a href=&quot;http://www.jimmunol.org/content/182/11/6851.short&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;CCR7-CCL19/CCL21-Regulated Dendritic Cells Are Responsible for Effectiveness of Sublingual Vaccination.&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-06-06T19:18:52.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17957" PostTypeId="1" CreationDate="2014-06-07T01:25:16.613" Score="6" ViewCount="130" Body="&lt;p&gt;This virology &lt;a href=&quot;http://www.virology.ws/2013/09/06/how-many-viruses-on-earth/&quot; rel=&quot;nofollow&quot;&gt;[blog]&lt;/a&gt; discusses estimates of the number of mammalian viruses and the costs of 'discovering' 85% of them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is whether this is not a forlorn hope. The &quot;.632 rule&quot; in statistics says roughly that as we approach n random samples from a large population of size n we will see only about 62.3 per cent of the population. After a point we would begin to see the same viruses again and again. This argument is probably stronger with respect to marine viruses, as they may be even more numerous and sampling at depths could be difficult. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder if someone with experience sampling small organisms from large populations or familiarity with the literature has an idea about the plausibility of seeing 85% of a large population, such as mammalian viruses, by sampling? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the samples are really random (in some sense) and the population is large, a few computer simulations reveal the power of this rule of thumb.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit in response to comment/question:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like any such estimate, the blog's estimate of 3.6 million is a guess. I am not reproducing the calculation here because it's just speculation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having said that, if 3.6 million were correct, we would have to draw about 6.8 million samples to find 85% of the existing viruses, 8.2 million to find 90%, and so on. As the blog notes, the PCR approach detects viruses similar to those we know, so the sampling is worse than random. If we look at the difficulty of finding/using a method that has a reasonable chance of capturing any of the extant viruses, the number 3.6 million looks very big. &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-06-08T13:26:03.173" LastActivityDate="2014-06-13T13:08:50.120" Title="Can we really 'discover' 85% of mammalian viruses?" Tags="&lt;virology&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17958" PostTypeId="2" ParentId="17939" CreationDate="2014-06-07T04:39:16.310" Score="4" Body="&lt;p&gt;Let me first clarify the difference between anaerobic respiration and fermentation. &#xA;Literally respiration refers to breathing, but its definition has been extended to include cellular metabolism that leads to ATP generation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fermentation, as you said depends on substrate level phosphorylation. Anaerobic respiration on the other hand just means ATP synthesis in the absence of oxygen- in other words &lt;em&gt;anoxic&lt;/em&gt;. This happens in several cases in which the terminal electron acceptor is not oxygen but some other chemical species such as $Fe^{3+}$ or fumarate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;E.coli&lt;/em&gt; can carry out ETC mediated ATP synthesis both in the presence and absence of oxygen. At high oxygen concentration it uses $O_2$ as electron acceptor, mediated by &lt;em&gt;cytochrome-d&lt;/em&gt;. At low oxygen concentration other kinds of cytochromes accumulate and the cell uses &lt;strong&gt;fumarate&lt;/strong&gt; or &lt;strong&gt;nitrate&lt;/strong&gt; as the terminal electron acceptor with the help of &lt;strong&gt;fumarate reductase&lt;/strong&gt; and &lt;strong&gt;nitrate reductase&lt;/strong&gt; respectively. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373010/&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; is an old article but is still quite informative. Check it out. &#xA;Fumarate and nitrate reductases are regulated as a part of what is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/FNR_regulon&quot; rel=&quot;nofollow&quot;&gt;FNR regulon&lt;/a&gt;. FNR is an oxygen-sensitive transcription regulator. In the presence of oxygen it is inactivated. In the absence of oxygen it activates the fumarate and nitrate reductase genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps in the absence of these alternate electron acceptors, the bacterium totally depends on SLP. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-06-07T08:42:13.913" LastActivityDate="2014-06-07T08:42:13.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17959" PostTypeId="2" ParentId="17911" CreationDate="2014-06-07T09:49:54.417" Score="2" Body="&lt;p&gt;From some of the MSDS (&lt;a href=&quot;http://www.arcticsilver.com/PDF/thermcom/AS5_MSDS_3.pdf&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;http://www.nteinc.com/MSDS/MSDS_NTE303.pdf&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;) I come across, a major component of thermal grease is aluminum oxide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Risk Management for Hazardous Chemicals&lt;/em&gt; by Jeffrey Wayne Vincoli states in page 101 that aluminum oxide has both acute and chronic toxic effects to aquatic life; it also states that aluminum oxide has a half-life longer than 200 days in water; finally, it acknowledges that the short term toxicity data for non-aquatic animals are insufficient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this, the reason thermal greases have special notification regarding to fishes can be attributed to those following points:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The long half life makes fishes exposure to it longer and therefore makes them more susceptible.&lt;/li&gt;&#xA;&lt;li&gt;We simply do not understand how aluminum oxide effect non-aquatic animals.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;(According to &lt;em&gt;Risk Management for Hazardous Chemicals&lt;/em&gt;, bioaccumulation in food chain might not be the concern.)&lt;/p&gt;&#xA;" OwnerUserId="4136" LastActivityDate="2014-06-07T09:49:54.417" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17961" PostTypeId="2" ParentId="9710" CreationDate="2014-06-07T12:06:47.920" Score="1" Body="&lt;p&gt;Because ducks need to float and cows don't. If there was a densely fat duck it wouldn't float or fly very well and it wouldn't survive to reproduce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question, the composition of fat varies because of the different conditions in which the organism needs to thrive. Fur is different as well. Bear in mind nature is a cruel place and any tiny edge you can get is vital for your survival.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My answer is a bit general but I hope it addresses the question.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2014-06-07T12:06:47.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17962" PostTypeId="2" ParentId="15612" CreationDate="2014-06-07T13:00:34.487" Score="-1" Body="&lt;p&gt;I think the external protein coat is degraded as the virus releases it's nucleic acid into the Host' cell. This is due to the fact that a protein is lifeless without the activity of a gene(one gene-one enzyme hypothesis).Since the nucleic acid is composed of genes, when it is injected into the host's cell, the capsid becomes useless and so it is degraded.&lt;/p&gt;&#xA;" OwnerUserId="6960" LastEditorUserId="6960" LastEditDate="2014-06-07T13:09:28.720" LastActivityDate="2014-06-07T13:09:28.720" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17965" PostTypeId="2" ParentId="14459" CreationDate="2014-06-07T14:50:24.893" Score="3" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;The primary activity of the thyroid gland is to concentrate iodine from the blood to make thyroid hormone. The gland cannot make enough thyroid hormone if it does not have enough iodine. Therefore, with iodine deficiency the individual will become hypothyroid. Consequently, the pituitary gland in the brain senses the thyroid hormone level is too low and sends a signal to the thyroid. This signal is called &lt;strong&gt;thyroid stimulating hormone&lt;/strong&gt; (TSH). As the name implies, this hormone &lt;strong&gt;stimulates the thyroid to produce thyroid hormone and to grow in size&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;p&gt;In Graves' disease one’s immune system produces a protein, called &lt;strong&gt;thyroid stimulating immunoglobulin&lt;/strong&gt; (TSI). As with TSH, TSI &lt;strong&gt;stimulates the thyroid gland to enlarge&lt;/strong&gt; producing a goiter. However, TSI &lt;strong&gt;also stimulates the thyroid to make too much thyroid hormone&lt;/strong&gt; (causes hyperthyroidism). Since the pituitary senses too much thyroid hormone, it stops secreting TSH. In spite of this the thyroid gland continues to grow and make thyroid hormone. Therefore, Graves’ disease produces a goiter and hyperthyroidism.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;Source:&lt;/strong&gt;&lt;/em&gt; American Thyroid Association. &lt;a href=&quot;http://www.thyroid.org/what-is-a-goiter/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;What is a Goiter - Causes&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-06-26T17:57:02.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17966" PostTypeId="1" AcceptedAnswerId="17967" CreationDate="2014-06-07T14:52:54.843" Score="12" ViewCount="15199" Body="&lt;p&gt;There was a trail of what are commonly known as sugar ants (small, brown, hyperactive) in my kitchen. Three of them walked onto an ice tray placed in their path.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They only walked a short distance on the ice before being immobilized by cold. I put the tray in the freezer beside a very shallow dish of water. When the water in the dish had frozen (about a half hour later) I removed the tray/ants and let them passively drop onto a warm dry surface. After 2-3 minutes they revived, walked in circles a few times, then headed off to forage (they were released outdoors). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is anecdotal evidence of ants' tolerance of cold but I was a little surprised by this. Do we know the extent of their tolerance of cold?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess it would vary with size and conditions. But an obvious question is whether, having survived freezing at (let's say) 22F, they could survive lower temperatures and/or longer periods of cold if properly handled? There may be cell structures that are sensitive to freezing because they break or change shape but it's already amazing to me that ordinary freezing does not distort water-bound structures in a lethal way. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any insight.   &lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2017-07-09T01:06:44.543" Title="How tolerant are ants to cold?" Tags="&lt;molecular-biology&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17967" PostTypeId="2" ParentId="17966" CreationDate="2014-06-07T15:08:53.240" Score="11" Body="&lt;p&gt;Acclimatization increases cold resistance of ants &lt;sup&gt;[1]&lt;/sup&gt;. They have a strong adaptability to different environments &lt;sup&gt;[2]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When it comes to the &lt;strong&gt;red imported fire ant&lt;/strong&gt; (&lt;em&gt;Solenopsis invicta&lt;/em&gt;) here are some numbers (from [2]):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When the exposure time was 0.5 h, the survival rate of workers was 15.3% at -14°C. At the exposure time of 1, 2 and 4 h, the entire lethal temperatures for &lt;em&gt;S. invicta&lt;/em&gt; were -13°C, -9°C and -9°C, respectively. When the exposure temperature was -10°C, all workers died within 240 min; while at -11°C, it took only 120 min.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Modlmeier AP, Pamminger T, Foitzik S, Scharf I. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22955370&quot; rel=&quot;noreferrer&quot;&gt;Cold resistance depends on acclimation and behavioral caste in a temperate ant.&lt;/a&gt; Naturwissenschaften. 2012 Oct;99(10):811-9. doi: &lt;a href=&quot;http://dx.doi.org/10.1007/s00114-012-0963-8&quot; rel=&quot;noreferrer&quot;&gt;10.1007/s00114-012-0963-8&lt;/a&gt;. PubMed PMID: 22955370. &lt;/li&gt;&#xA;&lt;li&gt;Xu YiJuan; Lu YongYue; Huang Jun; Zeng Ling; Liang GuangWen. &lt;em&gt;&lt;a href=&quot;http://www.cabdirect.org/abstracts/20093321536.html&quot; rel=&quot;noreferrer&quot;&gt;Cold hardiness of natural populations of the red imported fire ant, Solenopsis invicta Buren (Hymenoptera: Formicidae) in Shenzhen, Guangdong.&lt;/a&gt;&lt;/em&gt; Acta Entomologica Sinica 2009 Vol. 52 No. 9 pp. 974-983.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-27T16:53:29.930" LastActivityDate="2014-06-27T16:53:29.930" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17969" PostTypeId="2" ParentId="10096" CreationDate="2014-06-07T18:19:23.077" Score="2" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;For more than 70 years calcium hydroxide has played a major role in endodontic therapy, although many of its functions are now being taken over by the recently introduced material MTA. Calcium hydroxide may be used to preserve the vital pulp if infection and bleeding are controlled; to repair root fractures, perforations, open apices and root resorptions &lt;sup&gt;[1]&lt;/sup&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Calcium ions released from calcium hydroxide stimulates fibronectin synthesis in dental pulp cells. Fibronectin might induce the differentiation of dental pulp cells to mineralized tissue forming cells that are the main cells to form dentine bridges, via contact with cells &lt;sup&gt;[2]&lt;/sup&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Calcium hydroxide (&lt;span class=&quot;math-container&quot;&gt;$Ca(OH)_2$&lt;/span&gt;) is known to cause internal resorption in the deciduous dentition. Though this has been attributed to chronic inflammation and odontoclasts, the exact mechanism has not been elucidated. &lt;span class=&quot;math-container&quot;&gt;$Ca(OH)_2$&lt;/span&gt;-induced odontoclastogenesis could be multifactorial. Odontoclasts may result from fusion of cells of monocyte/macrophage series either due to inflammatory mediators or through stimulation by stromal odontoblasts / fibroblasts. Pre-existing progenitor cells of primary tooth pulp because of their inherent propensity may transform into odontoclasts &lt;sup&gt;[3]&lt;/sup&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Carrotte P. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15608732&quot; rel=&quot;nofollow noreferrer&quot;&gt;Endodontics: Part 9. Calcium hydroxide, root resorption, endo-perio lesions.&lt;/a&gt; Br Dent J. 2004 Dec 25;197(12):735-43. doi: &lt;a href=&quot;http://dx.doi.org/10.1038/sj.bdj.4811897&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1038/sj.bdj.4811897&lt;/a&gt;. PubMed PMID: 15608732.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Mizuno M, Banzai Y. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19133082&quot; rel=&quot;nofollow noreferrer&quot;&gt;Calcium ion release from calcium hydroxide stimulated fibronectin gene expression in dental pulp cells and the differentiation of dental pulp cells to mineralized tissue forming cells by fibronectin.&lt;/a&gt; Int Endod J. 2008 Nov;41(11):933-8. doi: &lt;a href=&quot;http://dx.doi.org/10.1111/j.1365-2591.2008.01420.x&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1111/j.1365-2591.2008.01420.x&lt;/a&gt;. PubMed PMID: 19133082.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Ravi G R, Subramanyam R V. &lt;em&gt;&lt;a href=&quot;http://www.dentalhypotheses.com/text.asp?2012/3/3/90/103910&quot; rel=&quot;nofollow noreferrer&quot;&gt;Calcium hydroxide-induced resorption of deciduous teeth: A possible explanation. Dent Hypotheses&lt;/a&gt;&lt;/em&gt; [serial online] 2012 [cited 2014 Jun 7];3:90-4.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-06-26T18:01:06.007" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17970" PostTypeId="2" ParentId="16919" CreationDate="2014-06-07T20:15:44.143" Score="5" Body="&lt;p&gt;Cornelius covers Primary Infection and some of Dissemination. &#xA;Wysiwyg covers some reasons when HIV cannot proceeds to AIDS. &#xA;Little however is discussed yet exactly about the Pathogenesis - how HIV proceeds into AIDS. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many stages:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Primary infection&lt;/li&gt;&#xA;&lt;li&gt;Dissemination of virus to lymphoid organs&lt;/li&gt;&#xA;&lt;li&gt;Latency&lt;/li&gt;&#xA;&lt;li&gt;Increased HIV expression&lt;/li&gt;&#xA;&lt;li&gt;Constitutional symptoms&lt;/li&gt;&#xA;&lt;li&gt;AIDS&lt;/li&gt;&#xA;&lt;li&gt;opportunistic diseases (etc pneumocystis pneumonia - P. jirovecii for human; HIV-induced thrombocytopenia; ...)&lt;/li&gt;&#xA;&lt;li&gt;death&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Cornelius nicely mentions that HIV infects CD4+ T lymphocytes, macrophages and dendritic cells.&#xA;In other words, HIV infects CD4+ T lymphocytes and the major Antigen Presenting Cells (APC).&#xA;Also monocytes are infected.&#xA;These infected cells play a major role in dissemination and pathogenesis of HIV infection.&#xA;Antigen presentation couples innate and adaptive immune system.&#xA;Any attack on those cells will be difficult to control:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LPHbg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where I left NK cells only to innate immunity because they do not participate in antigen presentation.&#xA;Innate and adaptive immune systems are visualised on the plane. &#xA;You have then humoral immunity working around that plane as circles.&#xA;I emphasize with that the local nature of humoral immune system and how it extends the cell-mediated immune system.&#xA;Any attack on the heart of this system i.e. antigen presentation will also risk the humoral immunity and thus cause fast progression of the disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These APCs act as reservoirs for HIV virus in the body during latent period and after the latent period.&#xA;However, there is very active replication of the virus also during the latent period in these reservoirs.&#xA;The virus replicates actively in lymphatic system.&#xA;This is why you see steady level of HIV virus in blood during first eight years, see Figure below [Fitzpatrick's Color Atlas and Synopsis of Clinical Dermatology, 7e &gt; Section 27. Viral Diseases of Skin and Mucosa].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gJyxW.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The structure of lymph nodes is disrupted eventually.&#xA;There is a degeneration and loss of virus holding function.&#xA;Virus leaks into the blood which can be seen as increased viral load at about 7-8 years after infection when constitutional symptoms start.&#xA;This amount of virus is very large that is released into circulation.&#xA;There is a rise in viremia.&#xA;Now the infection becomes T-tropic (proliferates and replicates actively on CD4+ T lymphocytes), while it was M-tropic (proliferates and replicates actively on APCs in lymphatic circulation) until the start of AIDS.&#xA;Actually, these APCs play a major role in trapping the virus, until their architecture changes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some antiviral drugs work on these CD4+ cells i.e. at least macrophages coupled with MHC II complexes.&#xA;There is still much unknown in the pathogenesis of HIV:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;role of dendritic cells in M-tropic phase&lt;/li&gt;&#xA;&lt;li&gt;role of dendritic cells in T-tropic phase and restricting the functioning of HAART (Highly Active Antiretroviral Therapy) therapy. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and there exist no antiretroviral drug which can target the major antigen presenting cells or use another way - to stop viral replication completely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cornelius writes HIV virus kills CD4+ cells.&#xA;It is better to say HIV virus decreases CD4+ cell count.&#xA;Killing is just one mechanism.&#xA;The mechanisms are&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;HIV can induce apoptosis of CD4+ cells&lt;/li&gt;&#xA;&lt;li&gt;lysis of CD4+ cells&lt;/li&gt;&#xA;&lt;li&gt;killing (natural killers, macrophages)&lt;/li&gt;&#xA;&lt;li&gt;networks (CD4+ cells will bind to other CD4+ cells so cells cannot work)&lt;/li&gt;&#xA;&lt;li&gt;gp120 antigenic - which attach to CD4+ antibodies&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which decreases CD4+ cell count.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sources&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Thomas, C. F, et al. Pneumocystis Pneumonia. The New England Journal of Medicine. 2004. &lt;/li&gt;&#xA;&lt;li&gt;Fitzpatrick's Color Atlas and Synopsis of Clinical Dermatology, 7e &gt; Section 27. Viral Diseases of Skin and Mucosa.&lt;/li&gt;&#xA;&lt;li&gt;My class notes 2014-2016. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2016-04-11T11:06:03.423" LastActivityDate="2016-04-11T11:06:03.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17971" PostTypeId="1" CreationDate="2014-06-08T04:59:03.870" Score="2" ViewCount="3592" Body="&lt;p&gt;From &lt;a href=&quot;http://www.nfstc.org/pdi/Subject05/pdi_s05_m01_01.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.nfstc.org/pdi/Subject05/pdi_s05_m01_01.htm&lt;/a&gt; :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... The separation medium contains a denaturant in order that the&#xA;  electrophoresis is conducted on single-stranded DNA fragments.&#xA;  Single-stranded DNA fragments are more similar to each other than&#xA;  double-stranded DNA fragments are to each other. Double-stranded DNA&#xA;  produces more electrophoretic diversity due to its three-dimensional&#xA;  structure.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Questions :&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;What is the denaturant they are talking about?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It's mentioned that &lt;em&gt;double-stranded DNA&#xA;produces more electrophoretic diversity due to its three-dimensional&#xA;structure&lt;/em&gt;. Why should dsDNA have more 3-D structures than ssDNA? ssDNA can form hairpins and other structures. Which structures can dsDNA form?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3340" LastEditDate="2014-06-08T06:43:54.333" LastActivityDate="2014-06-08T07:23:41.133" Title="Single stranded DNA in gel electrophoresis" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;gel-electrophoresis&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17972" PostTypeId="2" ParentId="17971" CreationDate="2014-06-08T05:23:54.537" Score="1" Body="&lt;ol&gt;&#xA;&lt;li&gt;Formamide and/or urea most likely. They both lower the melting point&#xA;of the ssDNA. This allows the structures to unravel at lower&#xA;temperatures. Typically you want to reach for  melting temperatures&#xA;around 50° C, and then run the gels at that temperature. RNA is&#xA;often denatured with harsher agents, like formaldehyde because RNA&#xA;form stronger structures.&lt;/li&gt;&#xA;&lt;li&gt;ds DNA can exhibit supercoiling which is a very elegant method of&#xA;    packaging DNA. This is a huge topic and mathematically derived. It's&#xA;    important is mostly due to it's role in gene expression via the&#xA;    interaction dsDNA has with proteins it wraps around-his tones.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Note that ds-supercoiled-DNA forms two structures; a plectoneme or a toroid, and can also have combinations of these two. It's interesting stuff. Google &quot;DNA supercoiling&quot; with an image search  and look for a figure that shows the different levels of winding and wrapping:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not very familiar with &lt;a href=&quot;http://click4biology.info/c4b/7/images/7.1/DNAfibre.gif&quot; rel=&quot;nofollow&quot;&gt;this source&lt;/a&gt; but the figure looks to be on the up-and-up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good question&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="3340" LastEditDate="2014-06-08T06:13:07.357" LastActivityDate="2014-06-08T06:13:07.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17973" PostTypeId="2" ParentId="17971" CreationDate="2014-06-08T06:24:06.603" Score="3" Body="&lt;ol&gt;&#xA;&lt;li&gt;As already mentioned formamide can be used. However formamide has to be incubated with the nucleic acid sample and heated. Urea can be included in the gel (8%). DNA can also be denatured using NaOH. NaOH, however, cannot be used for RNA because it will cause alkaline hydrolysis. &lt;/li&gt;&#xA;&lt;li&gt;I don't much agree on this point. Though dsDNA can produce diverse structures, as buzrw mentioned, so can ssDNA (in fact more diverse). Moreover, linearization solves the issue of supercoiling. We never compare circular plasmids with each other on the gel. Long linear dsDNAs can form structures but then in such cases gel electrophoresis is not a very suitable method for comparison. PFGE might be a better option in such cases. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-06-08T07:23:41.133" LastActivityDate="2014-06-08T07:23:41.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17975" PostTypeId="1" CreationDate="2014-06-08T06:55:07.377" Score="1" ViewCount="106" Body="&lt;p&gt;Solunar theory, which states that animal activity in wild (fishes, deer) depends on position of sun and moon in sky. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on the solunar calender, hunters seek for optimal time for hunting fishes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering that how solunar calender is developed from the sun's and moon's rise/set timing or from their positions in sky? For instance if I know the position of sun and moon in sky how would one forecast the animal activity timings of that day? OR the solunar calender is based on some statistical forecasting?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanking you.&lt;/p&gt;&#xA;" OwnerUserId="6963" LastEditorUserId="3340" LastEditDate="2014-06-08T07:13:05.043" LastActivityDate="2014-06-08T07:13:05.043" Title="Solunar theory of animal activity" Tags="&lt;behaviour&gt;" AnswerCount="0" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17976" PostTypeId="1" CreationDate="2014-06-08T06:55:33.190" Score="7" ViewCount="516" Body="&lt;p&gt;If a pregnant women is HIV positive and she is treated with medicines to deliver a normal child,can she transfer the HIV virus back to her normal HIV free child by colostrum?&lt;/p&gt;&#xA;" OwnerUserId="6962" LastEditorUserId="3340" LastEditDate="2014-06-08T07:16:23.513" LastActivityDate="2014-06-08T07:16:23.513" Title="Can HIV be transmitted via breastfeeding?" Tags="&lt;human-biology&gt;&lt;hiv&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="17977" PostTypeId="2" ParentId="17976" CreationDate="2014-06-08T07:09:24.950" Score="8" Body="&lt;p&gt;Yes, it is possible and the chances are pretty high. According to the WHO paper linked below, the rate of partially or completely breastfed children which get infected by this route is about 20-35%, while the rate of children which are not infected and doesn't get breatfed is zero (no surprise here). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanism by which this infection occurs is currently unknown, but it is hypothesized that the virus enters via the mucosa. See these two articles below for more information:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.unaids.org/en/media/unaids/contentassets/dataimport/publications/irc-pub03/jc180-hiv-infantfeeding-3_en.pdf&quot;&gt;A review of HIV transmission through breastfeeding.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.unfpa.org/webdav/site/global/shared/documents/publications/2004/hiv_transmission.pdf&quot;&gt;HIV transmission through breastfeeding : a review.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-08T07:09:24.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17980" PostTypeId="1" AcceptedAnswerId="17981" CreationDate="2014-06-08T10:24:23.493" Score="6" ViewCount="1982" Body="&lt;p&gt;In a documentary on fitness I saw it was stated that women can't get big like men because of their low concentration of testosterone. If it is true that women have testosterone, where is it made? Why do some women, especially later in life, develop facial hair (though obviously not as much as men)? Do men also have &quot;female&quot; hormones in their body? &lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="1590" LastEditDate="2014-06-09T10:00:32.233" LastActivityDate="2014-09-27T22:19:39.910" Title="Do women have testosterone?" Tags="&lt;physiology&gt;&lt;endocrinology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17981" PostTypeId="2" ParentId="17980" CreationDate="2014-06-08T10:29:39.580" Score="14" Body="&lt;p&gt;Yes, they do. The ovaries produce both testosterone and estrogen. Relatively small quantities of testosterone are released into your bloodstream by the ovaries and adrenal glands. Sex hormones are involved in the growth, maintenance, and repair of reproductive tissues &lt;sup&gt;[1]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The serum testosterone level in women with no acne, hirsutism, or menstrual dysfunction is 14.1 +/- 0.9 ng/dL (nanograms per decilitre) &lt;sup&gt;[2]&lt;/sup&gt;. An average adult man has 270-1,070 ng/dL serum testosterone &lt;sup&gt;[3]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Men have female sex hormones too. For a prepubescent male, estrogen levels are expected to be between 1 and 3.7 ng/dL. During puberty, normal levels fall between 2.3 and 8.4 ng/dL. Levels for an adult male should be between 2.5 and 5 ng/dL &lt;sup&gt;[4]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;WebMD, LLC. &lt;a href=&quot;http://www.webmd.com/women/guide/normal-testosterone-and-estrogen-levels-in-women&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Normal Testosterone and Estrogen Levels in Women.&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Ayala C, Steinberger E, Smith KD, Rodriguez-Rigau LJ, Petak SM. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15251653&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Serum testosterone levels and reference ranges in reproductive-age women.&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Alexia Severson. &lt;em&gt;&lt;a href=&quot;http://www.healthline.com/health/low-testosterone/testosterone-levels-by-age&quot; rel=&quot;nofollow&quot;&gt;Testosterone Levels by Age.&lt;/a&gt;&lt;/em&gt; Healthline Networks, Inc.&lt;/li&gt;&#xA;&lt;li&gt;wiseGEEK.com. &lt;a href=&quot;http://www.wisegeek.com/what-are-normal-estrogen-levels-in-men.htm&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;What Are Normal Estrogen Levels in Men?&lt;/em&gt;&lt;/a&gt; (Measurements cited in picograms per millilitre, converted to ng/dL)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2014-06-09T04:12:38.500" LastActivityDate="2014-06-09T04:12:38.500" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="17982" PostTypeId="1" CreationDate="2014-06-08T10:53:19.077" Score="1" ViewCount="702" Body="&lt;p&gt;At the simplest level, we're all just atoms, animals, plants and humans alike. But what I don't understand, is how a particular arrangement of atoms such as us can become self aware, and be able to not only understand our environment, but manipulate it to our will? How is that even possible? &lt;/p&gt;&#xA;" OwnerUserId="6968" LastEditorUserId="3340" LastEditDate="2014-06-08T12:47:30.560" LastActivityDate="2014-06-26T17:55:50.227" Title="How do a particular arrangement of atoms become self aware?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ClosedDate="2014-06-08T14:11:14.927" ContentLicense="CC BY-SA 3.0" />
  <row Id="17983" PostTypeId="2" ParentId="17982" CreationDate="2014-06-08T11:34:38.853" Score="2" Body="&lt;p&gt;You are skipping too many steps.&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$Atom \rightarrow \color{red}{molecule \rightarrow structure \rightarrow cell} \rightarrow organ \rightarrow organism$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;The following is a proposed speculation regarding the steps in red on the above:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;How life originated and how the first cell came into being are matters of speculation, since these events cannot be reproduced in the laboratory. It was first suggested in the 1920s that simple organic molecules could form and spontaneously polymerize into macromolecules under the conditions thought to exist in primitive Earth's atmosphere. At the time life arose, the atmosphere of Earth is thought to have contained little or no free oxygen, instead consisting principally of &lt;span class=&quot;math-container&quot;&gt;$CO_2$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$N_2$&lt;/span&gt; in addition to smaller amounts of gases such as &lt;span class=&quot;math-container&quot;&gt;$H_2$&lt;/span&gt;, &lt;span class=&quot;math-container&quot;&gt;$H_2S$&lt;/span&gt;, and &lt;span class=&quot;math-container&quot;&gt;$CO$&lt;/span&gt;. Such an atmosphere provides reducing conditions in which organic molecules, given a source of energy such as sunlight or electrical discharge, can form spontaneously. The spontaneous formation of organic molecules was first demonstrated experimentally in the 1950s, when Stanley Miller (then a graduate student) showed that the discharge of electric sparks into a mixture of &lt;span class=&quot;math-container&quot;&gt;$H_2$&lt;/span&gt;, &lt;span class=&quot;math-container&quot;&gt;$CH_4$&lt;/span&gt;, and &lt;span class=&quot;math-container&quot;&gt;$NH_3$&lt;/span&gt;, in the presence of water, led to the formation of a variety of organic molecules, including several amino acids.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zQTPp.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Although Miller's experiments did not precisely reproduce the conditions of primitive Earth, they clearly demonstrated the plausibility of the spontaneous synthesis of organic molecules, providing the basic materials from which the first living organisms arose.&lt;/p&gt;&#xA;&lt;p&gt;The next step in evolution was the formation of macromolecules. The monomeric building blocks of macromolecules have been demonstrated to polymerize spontaneously under plausible prebiotic conditions. Heating dry mixtures of amino acids, for example, results in their polymerization to form polypeptides. But the critical characteristic of the macromolecule from which life evolved must have been the ability to replicate itself. Only a macromolecule capable of directing the synthesis of new copies of itself would have been capable of reproduction and further evolution.&lt;/p&gt;&#xA;&lt;p&gt;Of the two major classes of informational macromolecules in present-day cells (nucleic acids and proteins), only the nucleic acids are capable of directing their own self-replication. Nucleic acids can serve as templates for their own synthesis as a result of specific base pairing between complementary nucleotides. A critical step in understanding molecular evolution was thus reached in the early 1980s, when it was discovered in the laboratories of Sid Altman and Tom Cech that RNA is capable of catalyzing a number of chemical reactions, including the polymerization of nucleotides. RNA is thus uniquely able both to serve as a template for and to catalyze its own replication. Consequently, RNA is generally believed to have been the initial genetic system, and an early stage of chemical evolution is thought to have been based on self-replicating RNA molecules—a period of evolution known as the RNA world. Ordered interactions between RNA and amino acids then evolved into the present-day genetic code, and DNA eventually replaced RNA as the genetic material.&lt;/p&gt;&#xA;&lt;p&gt;The first cell is presumed to have arisen by the enclosure of self-replicating RNA in a membrane composed of phospholipids.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Lk7dW.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Phospholipids are the basic components of all present-day biological membranes, including the plasma membranes of both prokaryotic and eukaryotic cells. The key characteristic of the phospholipids that form membranes is that they are amphipathic molecules, meaning that one portion of the molecule is soluble in water and another portion is not. Phospholipids have long, water-insoluble (hydrophobic) hydrocarbon chains joined to water-soluble (hydrophilic) head groups that contain phosphate. When placed in water, phospholipids spontaneously aggregate into a bilayer with their phosphate-containing head groups on the outside in contact with water and their hydrocarbon tails in the interior in contact with each other. Such a phospholipid bilayer forms a stable barrier between two aqueous compartments—for example, separating the interior of the cell from its external environment.&lt;/p&gt;&#xA;&lt;p&gt;The enclosure of self-replicating RNA and associated molecules in a phospholipid membrane would thus have maintained them as a unit, capable of self-reproduction and further evolution. RNA-directed protein synthesis may already have evolved by this time, in which case the first cell would have consisted of self-replicating RNA and its encoded proteins.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;Source:&lt;/strong&gt;&lt;/em&gt; Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000. The Origin and Evolution of Cells. Available from: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK9841/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK9841/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-06-26T17:55:50.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17984" PostTypeId="1" AcceptedAnswerId="17985" CreationDate="2014-06-08T13:36:34.413" Score="1" ViewCount="302" Body="&lt;p&gt;Tubular secretion is : The process in which ions and other waste products are transported into the distal tubules of the nephron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;can it be regarded as local hormone??&lt;/p&gt;&#xA;" OwnerUserId="6524" LastActivityDate="2014-06-26T17:53:53.823" Title="Can tubular secretion regarded as local hormone?" Tags="&lt;physiology&gt;&lt;kidney&gt;&lt;renal-physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="17985" PostTypeId="2" ParentId="17984" CreationDate="2014-06-08T14:16:51.337" Score="2" Body="&lt;p&gt;First of all, I can't understand how can you regard an electrochemical process (tubular secretion) as chemical substance (hormone).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tubular secretion is the transfer of materials from peritubular capillaries to renal tubular lumen. Tubular secretion is caused mainly by &lt;strong&gt;active transport&lt;/strong&gt;.&#xA;Usually only a few substances are secreted. These substances are present in great excess, or are natural poisons. Many drugs are eliminated by tubular secretion &lt;sup&gt;[1]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The substances that are secreted into the tubular fluid (for removal from the body) include &lt;sup&gt;[2]&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Potassium ions (K+),&lt;/li&gt;&#xA;&lt;li&gt;Hydrogen ions (H+),&lt;/li&gt;&#xA;&lt;li&gt;Ammonium ions (NH4+),&lt;/li&gt;&#xA;&lt;li&gt;creatinine,&lt;/li&gt;&#xA;&lt;li&gt;urea,&lt;/li&gt;&#xA;&lt;li&gt;some hormones, and&lt;/li&gt;&#xA;&lt;li&gt;some drugs (e.g. penicillin).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Tubular secretion occurs from the epithelial cells that line the renal tubules and collecting ducts &lt;sup&gt;[2]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Uptake transporters in the basolateral membrane and export transporters in the luminal membrane of renal tubule cells are involved in tubular secretion of their substrates&lt;/strong&gt; (organic anion transporters and organic cation transporters - these are transmembrane proteins) &lt;sup&gt;[3]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite considerable advances in the understanding of basic transport pathways and mechanisms involved in the tubular secretion of organic compounds, there is still relatively little information on the regulation of this transport &lt;sup&gt;[4]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Renal physiology,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Renal_physiology&amp;amp;oldid=608689347&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Renal_physiology&amp;amp;oldid=608689347&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ivy-rose.co.uk/HumanBody/Urinary/Urinary_System_Kidneys_Actions_3.php&quot; rel=&quot;nofollow&quot;&gt;http://www.ivy-rose.co.uk/HumanBody/Urinary/Urinary_System_Kidneys_Actions_3.php&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Müller F, Fromm MF. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21787191&quot; rel=&quot;nofollow&quot;&gt;Transporter-mediated drug-drug interactions.&lt;/a&gt; Pharmacogenomics. 2011 Jul;12(7):1017-37. doi: &lt;a href=&quot;http://dx.doi.org/10.2217/pgs.11.44&quot; rel=&quot;nofollow&quot;&gt;10.2217/pgs.11.44&lt;/a&gt;. PubMed PMID: 21787191. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Berkhin EB, Humphreys MH. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11135053&quot; rel=&quot;nofollow&quot;&gt;Regulation of renal tubular secretion of organic compounds.&lt;/a&gt; Kidney Int. 2001 Jan;59(1):17-30. doi: &lt;a href=&quot;http://dx.doi.org/10.1046/j.1523-1755.2001.00461.x&quot; rel=&quot;nofollow&quot;&gt;10.1046/j.1523-1755.2001.00461.x&lt;/a&gt;. PubMed PMID: 11135053. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-26T17:53:53.823" LastActivityDate="2014-06-26T17:53:53.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="18984" PostTypeId="1" AcceptedAnswerId="18991" CreationDate="2014-06-08T21:09:34.003" Score="5" ViewCount="183" Body="&lt;p&gt;I've thought long and hard about wheter this is the appropriate section for this question, because I guess it's kind of an interdisciplinary subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding of stereopsis (please, correct me if I'm wrong), basically depends of the way we cross our eyes when we attempt to see objects at different distances.&#xA;The more &quot;our eyes are crossed&quot;, the greater the difference between the images we receive in each eye, which it's more effective to look at closer objects. In order for an object to be in focus, it needs to be at the point where the vision of the eyes intersect (including &quot;at infinity&quot; for very far away objects).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, with this mindset, how would such a gadget as &lt;strong&gt;&lt;a href=&quot;http://www.oculusvr.com/&quot; rel=&quot;noreferrer&quot;&gt;Oculus VR&lt;/a&gt;&lt;/strong&gt; work? &#xA;It consists of two separate screens (one for each eye) attached directly on an helmet-like device strapped to the user's head. It is capable of convincing 3D representations and has similar features which make it of close interest for gaming and similar applications.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, my question is: in order to deliver such an illusion of depth, do the users' eyes need to be focused at the screen's distance, or at the represented objects' distance?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry for the long question :P&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance!&lt;/p&gt;&#xA;" OwnerUserId="7970" LastActivityDate="2017-01-12T22:00:57.937" Title="What is the focus distance of a 3D screen?" Tags="&lt;eyes&gt;&lt;vision&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="18985" PostTypeId="1" CreationDate="2014-06-08T21:52:12.843" Score="3" ViewCount="8193" Body="&lt;p&gt;Recently I have just discovered that a certain amount of the mobile phone frequency can be absorbed by human tissues. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, this is the SAR info of iPhone 4s:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&#xA;Head: 1.180 W/kg 1 g&#xA;Body: 0.491 W/kg 1g&#xA;Hotspot: 0.491 W/kg 1 g&#xA;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/IPhone_4S&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/IPhone_4S&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so hotspot means a hot spot on human body right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are hot spots on human body?&lt;/p&gt;&#xA;" OwnerUserId="7971" LastActivityDate="2020-07-28T22:47:00.543" Title="What are hot spots on human body?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="18986" PostTypeId="2" ParentId="14345" CreationDate="2014-06-09T01:22:43.847" Score="6" Body="&lt;p&gt;Assuming the jar is airtight--&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think your oxygen consumption rate may be too high and that 40$\mu l$ per hour$^1$ might be closer but since it's a high figure anyway we can use it. 40 $\mu l$ per minute would be about 2400 $\mu l $/hr. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A 12-ounce jar is about 0.355 liters. At sea level, air contains about 20% oxygen so the volume of oxygen in the jar is about 0.0709 liters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At altitudes which are considered high for humans (17000 feet or higher) the percentage of oxygen falls to about 15%. If a bee is able to get 2400 $ \mu l$ of oxygen per hour from a jar, the volume of oxygen will fall to about 13% after ten hours.$^2$   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on oxygen consumption alone I think a bee would be stressed at this level, especially at temperatures exceeding 32C. I would guess the bee would be stressed well before this, maybe after 5 hours (16.6% oxygen). If we factor in the likelihood that the bee's respiration is up due to the agitation of confinement I think we can shave another hour off. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending on the age, size, species, variety, temperature, location, etc. I think an outside limit of 4 hours in an airtight jar is a good guess. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Toxicity from CO$_2$ may be a problem but bees have a much higher tolerance for CO$_2$ than humans, according to one set of &lt;a href=&quot;https://insects.tamu.edu/continuing_ed/bee_biology/lectures/password/Internal_Anatomy_of_Honey_Bees_PN.pdf&quot; rel=&quot;nofollow&quot;&gt;entomology notes&lt;/a&gt;. At 0.04% the concentration will only increase marginally due to a drop in oxygen alone but the bee itself will produce CO$_2$ and in far greater quantities under stress. A chart &lt;a href=&quot;http://www.coloss.org/beebook/I/physiology/6/1/3&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; shows production of CO$_2$ in reaction to a light being turned on. 400 ppm is 0.04% but in this case it is due to the bee. If the bee during respiration returns CO$_2$ as quickly as it consumes oxygen the jar could reach 7% CO$_2$ in four hours, a level that may be toxic for humans. But we have already suggested the bee is under stress from oxygen depletion at that point. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many assumptions in this note. A conservative estimate might be an hour in an airtight jar. I would not bet on more. There are probably other issues I haven't thought of. Bees are very fragile and the chart linked above suggests they would not fare will in such an environment.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^1$ Respiration of Worker Honeybees of Different Ages and at Different Temperatures, Allen, 1958, J. Experimental Biology 36, 92-101. At page 97 Allen gives a chart showing log $\mu l$ $O_2$/mg body weight/hr. For a 14-23 day old bee at 32C he appears to give about .5 which means 1.65/mg/hr or about 115 $\mu l$ per hour for a 70mg bee. It may be a typo or perhaps I am misreading the chart. Also the study uses an older method of measuring respiration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^2$ This is a simplification. The bee will start breathing a mixture containing falling oxygen levels and this may slow the oxygen depletion a little. But if we say the bee needs what it needs this saves us a differential equation. &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-10-09T16:21:43.377" LastActivityDate="2014-10-09T16:21:43.377" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="18987" PostTypeId="1" AcceptedAnswerId="18989" CreationDate="2014-06-09T01:43:13.113" Score="4" ViewCount="1805" Body="&lt;p&gt;Guanidium salts like (G-isothiocyanate) disrupt the hydrophobic interactions inside a protein or nucleic acid and denature it. What happens when hydrophobic interactions in DNA are broken? (I don't think it should get ssDNA because guanidium doesn't break hydrogen bonds within molecules)&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3340" LastEditDate="2014-06-09T04:49:25.890" LastActivityDate="2014-06-09T05:43:39.750" Title="How does guanidium denature DNA?" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="18989" PostTypeId="2" ParentId="18987" CreationDate="2014-06-09T04:43:48.263" Score="4" Body="&lt;p&gt;Guanidium is a chaotrope i.e it increases the entropy in the solution. It doesn't &lt;em&gt;disrupt&lt;/em&gt; hydrophobic interactions. Guanidium and urea act by forming hydrogen bonds. They can bond with both the dissolved macromolecule and water. The water molecules are arranged as a shell around the hydrophobic regions so as to &lt;em&gt;contain&lt;/em&gt; it, which leads to the reduction of entropy. This containment causes hydrophobic regions to come together and give rise to a pseudo-interaction (hydrophobic interaction. See the figure below). Guanidium interacts with the water shell and disorders it, thereby reducing the hydrophobic effect.&#xA;Guanidium can also interact with macromolecules directly, by forming hydrogen bonds. In this process they can disrupt the normal H-bonds in the macromolecule.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rasQY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-06-09T04:43:48.263" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="18990" PostTypeId="2" ParentId="18987" CreationDate="2014-06-09T05:43:39.750" Score="3" Body="&lt;p&gt;It is important to realize that the hydrophobic effect is largely due to the exclusion of water from non-polar surfaces, which increases entropy. This effect is a major contributor to the helical structure of DNA, which effectively brings the bases closer together and excludes water from contacting their hydrophobic rings. Chaotropic agents like guanidine thiocyanate increase water entropy by disrupting its hydrogen bonding network (decreasing it's order) and this makes it more favourable for hydrophobic surfaces to be exposed to water, thus denaturation can occur. Implicit in that process is that GITC is a hydrogen bond competitor, which is also evident when looking at its structure. So, in fact, GITC can disrupt the hydrogen bonds between base pairs and denature dsDNA at high enough concentrations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That all said, we're ignoring a major component of aqueous solutions that can also form hydrogen bonds with the bases: water itself! So we must ask ourselves that if a compound capable of hydrogen bonding (water) is present, what exactly is it that holds helical DNA together? While base pairing certainly does contribute, the major factors are the hydrophobic and base stacking interactions.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-06-09T05:43:39.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="18991" PostTypeId="2" ParentId="18984" CreationDate="2014-06-09T10:57:50.903" Score="2" Body="&lt;p&gt;There are a number of aspects to the perception of a 3D world. While looking into how cinema and TV 3D systems work recently, I found the following Wikipedia articles useful on how the illusion of a 3D world is generated:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Stereoscopy&quot; rel=&quot;nofollow&quot;&gt;Stereoscopy&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Depth_perception&quot; rel=&quot;nofollow&quot;&gt;Depth perception&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The articles on &lt;a href=&quot;http://en.wikipedia.org/wiki/3d_tv&quot; rel=&quot;nofollow&quot;&gt;3D Television&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/3d_film&quot; rel=&quot;nofollow&quot;&gt;3D film&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Head-mounted_display&quot; rel=&quot;nofollow&quot;&gt;Head-mounted displays&lt;/a&gt; have some coverage of the issues with 3D display systems, since they do not work the same for all individuals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally 3D display systems ignore &lt;a href=&quot;http://en.wikipedia.org/wiki/Convergence_%28eye%29#Convergence&quot; rel=&quot;nofollow&quot;&gt;convergence&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Accommodation_of_the_eye&quot; rel=&quot;nofollow&quot;&gt;accommodation&lt;/a&gt; as a mechanism for generating depth and instead depend on &lt;a href=&quot;http://en.wikipedia.org/wiki/Parallax&quot; rel=&quot;nofollow&quot;&gt;parallax&lt;/a&gt; and the brain being able to assemble an approximation of the 3D scene without the information from those cues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In head-mounted display systems such as the Oculus Rift the image focus is usually at infinity.&lt;/p&gt;&#xA;" OwnerUserId="4117" LastActivityDate="2014-06-09T10:57:50.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="18994" PostTypeId="1" AcceptedAnswerId="19012" CreationDate="2014-06-09T19:56:17.097" Score="1" ViewCount="70" Body="&lt;p&gt;I just started reading about recombination frequencies of genes and related stuff, and can't find an answer to this (possibly naive) question.&#xA;Can recombination possibly &quot;kill off&quot; a gene ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be more specific, say a gene is located at position $x$ to $y$ on some chromosome.  Then, we are so unlucky that recombination decides to cut off the chromosome at location $x + (y - x)/2$, right in the middle of the gene.&#xA;So both halves will get recombined with the other halves of the gene on the homolog chromosome.  If the allele on this chromosome was different, could it result in destroying both alleles of the gene ?  Is there something that prevents this ?&lt;/p&gt;&#xA;" OwnerUserId="4911" LastEditorUserId="10276" LastEditDate="2015-01-16T11:52:54.697" LastActivityDate="2015-01-16T11:52:54.697" Title="Breaking a gene during recombination" Tags="&lt;genetics&gt;&lt;recombination&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="18995" PostTypeId="1" CreationDate="2014-06-09T20:21:05.843" Score="1" ViewCount="38" Body="&lt;p&gt;Why is &lt;em&gt;Silene virginica&lt;/em&gt;, colloquially known as Fire Pink, endangered in Florida? What factors besides human industrialization are affecting its survival there?&lt;/p&gt;&#xA;" OwnerUserId="6622" LastEditorUserId="3624" LastEditDate="2014-06-15T17:39:31.107" LastActivityDate="2014-06-15T17:39:31.107" Title="Silene virginica Endangered in FL" Tags="&lt;botany&gt;&lt;ecology&gt;&lt;conservation-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="18996" PostTypeId="1" CreationDate="2014-06-09T21:09:39.387" Score="0" ViewCount="112" Body="&lt;p&gt;Melatonin (not to be confused with melanin) was sold as a wonder drug during the 90s. I remember images of mice, which supposedly got a more beautiful fur. I would like to know whether the effect is true and whether it also has an effect on humans skin (or appearance in general).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously, googling about melatonin generates a lot of suspicious results.&lt;/p&gt;&#xA;" OwnerUserId="4419" LastActivityDate="2020-07-16T19:35:05.697" Title="Does melatonin change the appearance of humans?" Tags="&lt;melatonin&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="18997" PostTypeId="2" ParentId="5514" CreationDate="2014-06-09T21:57:26.600" Score="2" Body="&lt;p&gt;One olfactory acuity rating method that has found acceptance in some studies (despite the commercial-sounding name) is based on &quot;Sniffin' Sticks,&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;a test of nasal chemosensory performance that is based on penlike odor-dispensing devices. It is comprised of three tests of olfactory function: tests for odor threshold, discrimination and identification. Previous work has already established its test-retest reliability and validity in comparison to established measures of olfactory sensitivity. The results of this test are presented as a composite TDI score--i.e., the sum of results obtained for threshold, discrimination and identification measures.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the paper from which this abstract portion was taken$^1$, subjects were assigned a score based on their thresholds, ability to discriminate, etc., and the findings were said to be internally replicable (consistent from one test to the next).   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is probably not the only rating available but it has been used on &lt;a href=&quot;http://chemse.oxfordjournals.org/content/28/8/691.full#ref-8&quot; rel=&quot;nofollow&quot;&gt;other studies&lt;/a&gt; and seems to be taken seriously by M.D.s and others who measure such things. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no absolute measure of olfactory acuity. People are classed as 'anosmic' if they do poorly enough on the test but that doesn't mean they have no sense of smell (although that might be the case). Likewise people who get a high TDI score are--by definition--people who got the &quot;Sniffin Sticks&quot; right. They might be poor at discriminating a good coffee from a bad one based on smell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The test seems to do what it was intended to do: quantify relative olfactory acuity in a replicable way. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An &lt;a href=&quot;http://chemse.oxfordjournals.org/content/22/1/39.abstract&quot; rel=&quot;nofollow&quot;&gt;earlier study&lt;/a&gt; is somewhat reserved. From an abstract: &quot;It is concluded that ‘Sniffin’ Sticks’ may be suited for the routine clinical assessment of olfactory performance.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^1$ Eur. Arch. Otorhinolaryngol. (2000) 257(4):205-11. Multicenter investigation of 1,036 subjects using a standardized method for the assessment of olfactory function combining tests of odor identification, odor discrimination, and olfactory thresholds. Kobal et al.&lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-06-10T01:31:26.143" LastActivityDate="2014-06-10T01:31:26.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="18998" PostTypeId="2" ParentId="2684" CreationDate="2014-06-09T22:11:20.170" Score="4" Body="&lt;p&gt;Humans do not get an even 1/4 of DNA from each grandparent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main reason is that meiosis is not a precise 50/50 split. Parent cells undergo meiosis to recombine the grandparent chromosomes and produce a set of chromosomes to pass on to a child. This process is not a precise 50/50 split and produced chromosomes will have more of one grandparent DNA than the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second reason is that different chromosomes have different DNA base pair lengths. So, while every human gets exactly 23 nuclear chromosomes from each parent, some of those chromosomes have more DNA base pairs than others, and children receive a different quantity of DNA base pair content from each parent.&lt;/p&gt;&#xA;" OwnerUserId="5100" LastActivityDate="2014-06-09T22:11:20.170" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19001" PostTypeId="1" CreationDate="2014-06-10T02:40:38.357" Score="11" ViewCount="389" Body="&lt;p&gt;From this 2014 &lt;a href=&quot;http://www.simonsfoundation.org/quanta/20140122-a-new-physics-theory-of-life/&quot; rel=&quot;noreferrer&quot;&gt;article&lt;/a&gt; in &lt;em&gt;Quanta&lt;/em&gt; magazine by Natalie Wolchover there is a quote from a physicist with an intriguing idea about evolution: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;“You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant.”&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Jeremy England's idea is that the attributes associated with life have a lot to do with absorbing and dissipating energy. He insists he is not saying Darwin is wrong, and that his thermodynamics-based idea in some sense subsumes Darwinian evolution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(The Quanta article links to a &lt;a href=&quot;http://www.englandlab.com/uploads/7/8/0/3/7803054/2013jcpsrep.pdf&quot; rel=&quot;noreferrer&quot;&gt;recent paper&lt;/a&gt; of England's which is somewhat technical, but deals with bacterial replication and thermodynamics. I include the link to give a sense of his ideas in his own words.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is  whether his idea, taking it at face value, might furnish a better explanation of something already explained in Darwinian terms or fail to account for some detail of current evolutionary theory? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if someone had a lot of examples of different aspects of evolution s/he might be able to say, &quot;Here is a situation in which the thermodynamics do not work out as England suggests but which is explained in evolutionary terms,&quot; or conversely, &quot;Here is something contrary to evolutionists' expectations that seems to be pretty well explained by the thermodynamics.&quot; I suspect that there are several candidates and England's paper gives a hint in one direction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any insights.      &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some helpful reading: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Thermodynamics, Enrico Fermi (1936) [Dover reprint].&lt;/li&gt;&#xA;&lt;li&gt;Understanding Thermodynamics, Ness (1969) [Dover reprint].&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://whatislife.stanford.edu/LoCo_files/What-is-Life.pdf&quot; rel=&quot;noreferrer&quot;&gt;What is Life?&lt;/a&gt;, Schrodinger (1944). &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://arxiv.org/pdf/cond-mat/9901352v4.pdf&quot; rel=&quot;noreferrer&quot;&gt;Entropy Production...&lt;/a&gt;, Crooks (2008).&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://merkury.orconhosting.net.nz/lifeas.pdf&quot; rel=&quot;noreferrer&quot;&gt;Schneider and Kay&lt;/a&gt;, Life as a manifestation of the Second Law of Thermodynamics, Math. and Computer Modeling 19 (6-8): 25-48 (1995).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The last paper is a very readable and non-technical introduction to this topic. If one works through the equations in Chapter 7 of Ness and ref. 4 the idea should be quite clear. Basically, systems (both nonliving and living) which are at some remove from equilibrium devise ways to dissipate energy that involve a decrease in entropy, increasing the entropy of the surrounding system.  &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-06-14T02:06:32.460" LastActivityDate="2014-07-14T02:32:58.070" Title="A question about the intersection of evolution and thermodynamics" Tags="&lt;evolution&gt;&lt;molecular-evolution&gt;&lt;thermodynamics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19002" PostTypeId="1" AcceptedAnswerId="19003" CreationDate="2014-06-10T06:40:18.590" Score="0" ViewCount="179" Body="&lt;p&gt;Is there any academic reference that shows &amp;alpha;-tubulin is around 50-55 kDa? The only thing I found is some data sheets from companies. I need the real reference.&lt;/p&gt;&#xA;" OwnerUserId="5630" LastEditorUserId="1320" LastEditDate="2014-06-11T05:38:41.930" LastActivityDate="2014-06-11T05:38:41.930" Title="alpha tubulin molecular weight problem" Tags="&lt;biochemistry&gt;&lt;homework&gt;&lt;proteins&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19003" PostTypeId="2" ParentId="19002" CreationDate="2014-06-10T06:48:44.547" Score="2" Body="&lt;p&gt;The paper titled &lt;a href=&quot;http://jcs.biologists.org/content/119/5/858.full&quot; rel=&quot;nofollow&quot;&gt;Identification of α-tubulin as a granzyme B substrate during CTL-mediated apoptosis&lt;/a&gt; mentions it as 51KDa and the paper titled &lt;a href=&quot;http://www.nature.com/nature/journal/v282/n5737/abs/282423a0.html&quot; rel=&quot;nofollow&quot;&gt;Carboxy-terminal amino acid sequence of α-tubulin from porcine brain&lt;/a&gt; mentions it as 55,000 Da. Hope that suffices. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-10T06:48:44.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19004" PostTypeId="2" ParentId="19002" CreationDate="2014-06-10T07:06:54.497" Score="3" Body="&lt;p&gt;This is not so easy to answer, since alpha-tubulin has at 10 known genes in this family (data from &lt;a href=&quot;http://www.ensembl.org/Homo_sapiens/Gene/Family/Genes?cdb=compara;db=core;family=ENSFM00250000000217;g=ENSG00000167552;r=12:49578579-49583107&quot; rel=&quot;nofollow&quot;&gt;Ensembl&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;TUBA1A   tubulin, alpha 1a&lt;/li&gt;&#xA;&lt;li&gt;TUBA1B   tubulin, alpha 1b&lt;/li&gt;&#xA;&lt;li&gt;TUBA3E   tubulin, alpha 3e&lt;/li&gt;&#xA;&lt;li&gt;TUBA3D   tubulin, alpha 3d&lt;/li&gt;&#xA;&lt;li&gt;TUBA4A   tubulin, alpha 4a&lt;/li&gt;&#xA;&lt;li&gt;TUBAL3   tubulin, alpha-like 3&lt;/li&gt;&#xA;&lt;li&gt;TUBA1C   tubulin, alpha 1c&lt;/li&gt;&#xA;&lt;li&gt;TUBA3C   tubulin, alpha 3c&lt;/li&gt;&#xA;&lt;li&gt;TUBA8    tubulin, alpha 8&lt;/li&gt;&#xA;&lt;li&gt;TUBAL3   tubulin, alpha-like 3&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You can go on the site linked above and choose any of the proteins. I checked &lt;a href=&quot;http://www.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000167552;r=12:49578579-49583107;t=ENST00000301071&quot; rel=&quot;nofollow&quot;&gt;TUBA1A&lt;/a&gt;, and get a length of 451 amino acids and a weight of approximately 50,1 kDa.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-10T07:06:54.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19005" PostTypeId="1" CreationDate="2014-06-10T07:16:43.827" Score="5" ViewCount="8499" Body="&lt;p&gt;I'm looking for a reference that tells me how many recombenation events occur in humans from one generation to the next.&#xA;Assuming that the human genome is a 3.3 GigaBases long DNA sequence, how many recombination events do you find, and what is he amount of DNA exchanged?&#xA;Is it in the order of 0.1%, 1% oder 10%?&lt;/p&gt;&#xA;" OwnerUserId="3941" LastActivityDate="2018-08-06T21:06:47.087" Title="How many recombination events are there per generation in humans?" Tags="&lt;genomics&gt;&lt;human-genetics&gt;&lt;chromosome&gt;&lt;human-genome&gt;&lt;recombination&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19006" PostTypeId="2" ParentId="19005" CreationDate="2014-06-10T07:26:09.133" Score="2" Body="&lt;p&gt;This is not easy to answer, since it depends on a number of factors. For example it is dependent on the region of the genome (there are hotspots). I found a PhD thesis, which goes into the details here and which also has a ton of interesting references:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://adamauton.com/adam_auton_thesis.pdf&quot; rel=&quot;nofollow&quot;&gt;The Estimation of Recombination Rates from Population Genetic Data&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-10T07:26:09.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19007" PostTypeId="2" ParentId="18995" CreationDate="2014-06-10T08:39:39.937" Score="1" Body="&lt;p&gt;Various factors from different sources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-- Diseases like Anther Smut Disease (&lt;a href=&quot;http://people.virginia.edu/~ja8n/Publications/1996%20Antonovics,%20Stratton,%20Thrall,%20Jarosz%201996.pdf&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-- Rampant use of herbicides. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;-- Invasion of exotic pest species (&lt;a href=&quot;http://www.georgiawildlife.org/sites/default/files/uploads/wildlife/nongame/pdf/accounts/plants/silene_regia.pdf&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-- Spatiotemporal variation in the pollination of Silene virginica by the ruby-throat hummingbird which is its principal pollinator (&lt;a href=&quot;http://www.jstor.org/discover/10.2307/2680202?uid=3737496&amp;amp;uid=2129&amp;amp;uid=2&amp;amp;uid=70&amp;amp;uid=4&amp;amp;sid=21104280742563&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="1320" LastEditDate="2014-06-10T13:13:31.603" LastActivityDate="2014-06-10T13:13:31.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19010" PostTypeId="2" ParentId="18996" CreationDate="2014-06-10T11:23:01.410" Score="4" Body="&lt;p&gt;Melatonin is a hormone produced by the pineal gland located in the brain, and its production is inhibited by light to the retina and permitted by darkness (&lt;a href=&quot;http://en.wikipedia.org/wiki/Melatonin#Humans&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;). It has a lot of effects on the body (&lt;a href=&quot;http://www.lef.org/magazine/mag2012/sep2012_7-Ways-Melatonin-Attacks-Aging-Factors_01.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;) but I will stick to just discussing its apparent effects on aging and skin.&lt;/p&gt;&#xA;&lt;p&gt;Melatonin works as an antioxidant and helps in removing free radicals from the body (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14740000&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;). Research has shown that free radicals could damage the skin (&lt;a href=&quot;http://www.healthy-info.co.uk/skin/How_Free_Radicals_Damage_Skin_Cells.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;), so I would have to conclude that melatonin could have a part to play in maintaining the beauty of your skin.&lt;/p&gt;&#xA;&lt;p&gt;It is a known fact that melatonin levels in the body decrease from age, and its decrease has been correlated with some of the effects of aging (&lt;a href=&quot;http://press.endocrine.org/doi/full/10.1210/jcem.85.6.6660&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;). As you have mentioned in your question, there is research proving that melatonin could decrease the effect of aging in rats (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10650927&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;). Also melatonin was found to increase the youthful rhythmic activity in a shrew (&lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005904&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;). In the paper titled &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23467217&quot; rel=&quot;nofollow noreferrer&quot;&gt;melatonin and skin aging&lt;/a&gt; it has been stated that&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In UV-induced solar damage, melatonin distinctly counteracts massive&#xA;generation of reactive oxygen species, mitochondrial and DNA damage.&#xA;Thus, there is considerable evidence for melatonin to be an effective&#xA;anti-skin aging compound.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Moreover in the paper titled &amp;quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1317110/&quot; rel=&quot;nofollow noreferrer&quot;&gt;On the Role of Melatonin in Skin Physiology and Pathology&lt;/a&gt;&amp;quot;, it has been proposed that&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Melatonin (synthesized locally or delivered topically) could&#xA;counteract or buffer external (environmental) or internal stresses to&#xA;preserve the biological integrity of the skin and to maintain its&#xA;homeostasis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So in conclusion, I would have to say that melatonin does have a lot of positive effects on the skin but, given that it is a hormone and there are side effects (&lt;a href=&quot;http://www.webmd.com/vitamins-supplements/ingredientmono-940-MELATONIN.aspx?activeIngredientId=940&amp;amp;activeIngredientName=MELATONIN&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;), it should be used in moderation.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5119" LastEditDate="2020-07-16T19:35:05.697" LastActivityDate="2020-07-16T19:35:05.697" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="19011" PostTypeId="2" ParentId="19005" CreationDate="2014-06-10T12:58:41.317" Score="4" Body="&lt;p&gt;&lt;strong&gt;Back-of-the-envelope calculation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The definition of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Centimorgan&quot; rel=&quot;nofollow noreferrer&quot;&gt;centimorgan&lt;/a&gt; is that it is the length of DNA in a chromosome corresponding to a 1% chance of crossover occurring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In human chromosomes 1 cM  = approx. 1Mbp.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your value for the length of DNA in the genome = 3.3 Gbp = 3300 MBp&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ignoring complications like the Poisson distribution: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1 cM corresponds to a probability of 1% chance of a detectable crossover. Detectable, because only an odd number of crossing over events between 2 genetic markers can be observed as a recombination, but even numbers instead go unrecognised. Therefore the actual chance of crossing over is doubled relative to the cM value.&#xA;If 1 cM = 2% actual chance of crossover, there will be on average 1 crossover per 50 cM or per 50Mbp&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore crossovers per human genome = 3300/50 = 66  or approx 2-4 per chromosome&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This guess comes near empiric data:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Actual data&lt;/strong&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/w0dTQ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This Table, &lt;a href=&quot;http://books.google.co.uk/books?id=8Q6NrYT470YC&amp;amp;pg=PA21&amp;amp;lpg=PA21&amp;amp;dq=chiasmata+per+chromosome&amp;amp;source=bl&amp;amp;ots=DzWy9rSwRC&amp;amp;sig=fLKeA9K-DMk11U5tSzMkWUGy34g&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=__qWU6uNOsWOO9TwgaAE&amp;amp;ved=0CDEQ6AEwBTgU#v=onepage&amp;amp;q=chiasmata%20per%20chromosome&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;taken from here&lt;/a&gt; shows the number of chiasmata by chromosome for 8 human cells. (Note that it believed that there has to be at least one chiasma per chromatid pair since they have a structural role.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The average chiasmata per chromosome for each chromosome can be estimated by dividing the number in the final column by 8. These vary from (rounding aggressively) 3.5 for Chr 1 and Chr 2, to 1 for Chr 20. So my back-of-the-envelope calculation seems to have produced a reasonable answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the amount of DNA exchanged? I'm not sure this question matches well with the picture that emerges from these numbers. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2018-08-06T21:06:47.087" LastActivityDate="2018-08-06T21:06:47.087" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="19012" PostTypeId="2" ParentId="18994" CreationDate="2014-06-10T13:12:00.520" Score="3" Body="&lt;p&gt;Yes, you could imagine a situation where two functional alleles could produce a recombinant which was non-functional.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;chromosome 1 has A and B at positions &lt;em&gt;x&lt;/em&gt; and &lt;em&gt;y&lt;/em&gt; - functional&lt;/p&gt;&#xA;&lt;p&gt;chromosome 2 has C and D at positions &lt;em&gt;x&lt;/em&gt; and &lt;em&gt;y&lt;/em&gt; - functional&lt;/p&gt;&#xA;&lt;p&gt;Recombination between positions &lt;em&gt;x&lt;/em&gt; and &lt;em&gt;y&lt;/em&gt; produces A/D and C/B versions of the gene. Either or both of these could be non-functional.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Nothing prevents this from happening, but natural selection will act on the recombinants.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-06-10T13:12:00.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19013" PostTypeId="1" AcceptedAnswerId="19015" CreationDate="2014-06-10T13:24:10.813" Score="2" ViewCount="249" Body="&lt;p&gt;Why are some neurons tetraploid, and how does this result from it's ancestor cell ?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="3632" LastEditDate="2014-06-10T16:14:00.703" LastActivityDate="2018-05-07T01:48:34.573" Title="Why some neurons are tetraploid" Tags="&lt;neurology&gt;&lt;histology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19015" PostTypeId="2" ParentId="19013" CreationDate="2014-06-10T16:12:55.647" Score="2" Body="&lt;p&gt;Neurons are tetraploid in pathological situations like Alzheimer disease:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Neurons that duplicate their DNA are rarely observed to undergo mitosis, and they remain for long time as tetraploid cells, in accordance with the chronic course of the disease. We have recently shown that cell cycle re-entry and somatic tetraploidization occurs during normal development in a subpopulation of RGCs (retinal ganglion cells), giving rise to enlarged neurons with extensive dendritic trees. Tetraploization in these neurons occurs in response to the activation of the neurotrophin receptor p75NTR by an endogenous source of NGF (nerve growth factor).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;Source:&lt;/strong&gt;&lt;/em&gt; Frade JM, López-Sánchez N. A novel hypothesis for Alzheimer disease based on neuronal tetraploidy induced by p75NTR. Cell Cycle 2010; 9:1934 - 1941; PMID: 20436277; &lt;a href=&quot;http://dx.doi.org/10.4161/cc.9.10.11582&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://dx.doi.org/10.4161/cc.9.10.11582&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;These neurons are generated in response to nerve growth factor (NGF) acting through the neurotrophin receptor p75 (p75NTR), which induces E2F1 activity and cell cycle re-entry in migrating RGC neuroblasts lacking retinoblastoma (Rb) protein. We have also showed that brain-derived neurotrophic factor (BDNF) prevents G2/M transition in the tetraploid RGCs, thus being crucial for the maintenance of the tetraploid status as well as the survival of these neurons. The realization that tetraploid neurons can be readily observed in the vertebrate nervous system has important physiological consequences.&lt;/p&gt;&#xA;&lt;p&gt;Several eukaryotes are known to undergo endoreduplicative cycles leading to somatic polyploidy, thus increasing cell size in specific tissues. Examples of polyploidy in neurons are known in some invertebrates.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;Source:&lt;/strong&gt;&lt;/em&gt; José María Frade. &lt;em&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889987&quot; rel=&quot;nofollow noreferrer&quot;&gt;Somatic tetraploidy in vertebrate neurons - Implications in physiology and pathology.&lt;/a&gt;&lt;/em&gt; Commun Integr Biol. 2010 Mar-Apr; 3(2): 201–203. PMCID: PMC2889987&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-06-10T16:12:55.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19016" PostTypeId="1" AcceptedAnswerId="19023" CreationDate="2014-06-10T16:16:01.817" Score="0" ViewCount="62" Body="&lt;p&gt;I think this is not possible.&#xA;Conclusion about this preview article &lt;em&gt;TGF-$\beta$ family signaling in stem cells&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;While TGF-$\beta$ family signaling regulates stemness of normal and cancer stem cells, its effects are diverse and depend on the cell types and physiological state of the cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can TGF-$\beta$  induce all somatic stem cells?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1590" LastEditDate="2014-06-10T18:32:03.907" LastActivityDate="2014-06-10T21:44:47.350" Title="Can TGF beta family induce all somatic stem cells?" Tags="&lt;stem-cells&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19017" PostTypeId="2" ParentId="17613" CreationDate="2014-06-10T18:01:10.767" Score="0" Body="&lt;p&gt;No. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They're locomotion only allows for forward/upward motion. That said, their buoyancy control does provide a measure of 'backward' or 'sinking' motion, but it's negligible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But to convert this all into the simplest terms: Jellyfish uses a form of jet propulsion. Ever seen a jet go backwards? (The Harrier does not count.) &lt;/p&gt;&#xA;" OwnerUserId="7985" LastActivityDate="2014-06-10T18:01:10.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19020" PostTypeId="1" CreationDate="2014-06-10T19:40:08.937" Score="3" ViewCount="1333" Body="&lt;p&gt;I have been reading about Maltose Binding Proteins. Mutant forms of the molecule seem to be named MalE_ where the _ represents a number, for example MalE36 or MalE50.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please can someone explain the naming convention for this? i.e. what does the 'E' stand for? Does the number refer to the amino acid that has changed?&lt;/p&gt;&#xA;" OwnerUserId="7988" LastActivityDate="2014-06-10T22:31:19.460" Title="What are the naming conventions for mutations of proteins?" Tags="&lt;proteins&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19021" PostTypeId="2" ParentId="19020" CreationDate="2014-06-10T20:25:11.983" Score="2" Body="&lt;p&gt;What your example is referring to is the change in the glutamic acid (E) amino acid (AA) residue, which is in position 36. This is denoted so that people/scientist would know what has been changed and usually there should be another letter after that number such as Y, which is tyrosine, to denote what it has been changed to, if it is a substitution. Then there is the delta (∆) symbol to denote deletion, and usually a number range e.g. 36-50 or just a number e.g. 70 appears after it to denote if a protein has been truncated in a certain AA range or if the entire protein from that AA is truncated, respectively. Sometimes (quite often now a days) the delta symbol is followed a protein domain name such as SH3 or RA to denote that a protein domain has been deleted and people use all sorts of naming variations for a protein that has been altered from its native sequence, which can be confusing!!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are just some conventions, which isn't documented very well and you just figure them out when reading a few papers but I would welcome any edits for a good source for protein change annotations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since as pointed by Alan Boyd response, MalE is an &lt;em&gt;E. coli&lt;/em&gt; gene encoding Maltose Binding Proteins, then my answer will not apply for any protein AA changes as correctly pointed out and elaborated on in Alan Boyd response.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-06-10T22:31:19.460" LastActivityDate="2014-06-10T22:31:19.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19022" PostTypeId="2" ParentId="19020" CreationDate="2014-06-10T21:34:40.457" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://ecoliwiki.net/colipedia/index.php/malE%3aGene_Product%28s%29&quot; rel=&quot;nofollow&quot;&gt;MalE is the gene that encodes the maltose-binding protein in &lt;em&gt;E. coli&lt;/em&gt;&lt;/a&gt;. If you look at the genotype of any &lt;em&gt;E. coli&lt;/em&gt; strain you will see similar nomenclature. Everything in the answer from @Bez is correct, but in this case the &lt;strong&gt;E&lt;/strong&gt; has nothing to do with glutamate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The numbers are probably just arbitrary numbers that were assigned to the individual mutations, but you would need to provide a link to a source before this could be confirmed. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-06-10T21:34:40.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19023" PostTypeId="2" ParentId="19016" CreationDate="2014-06-10T21:44:47.350" Score="1" Body="&lt;p&gt;Signalling in the TGF&amp;beta; pathway normally puts a brake on the progress of cells through the cell cycle - it counteracts the action of myc for example, partly by regulating the expression of myc. In &lt;a href=&quot;http://en.wikipedia.org/wiki/Burkitt%27s_lymphoma&quot; rel=&quot;nofollow&quot;&gt;Burkitt's lymphoma&lt;/a&gt; myc escapes this regulation because of a chromosomal translocation, tipping the regulatory balance over to uncontrolled cell growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This anti-proliferative action of TGF&amp;beta; signalling is so critical that you might expect it to be ubiquitous in cells, and &lt;a href=&quot;http://en.wikipedia.org/wiki/TGF_beta_receptor_2&quot; rel=&quot;nofollow&quot;&gt;the expression atlas entry for the TGF&amp;beta; receptor&lt;/a&gt; is consistent with this.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-06-10T21:44:47.350" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19024" PostTypeId="1" CreationDate="2014-06-10T22:58:27.480" Score="6" ViewCount="780" Body="&lt;p&gt;I'm trying to purify the protein by Ni-NTA affinity chromatography. It seems that my protein (size about 54 kDa) is co-purified with chaperone protein (probably GroEL  - as the band is around 57kDa). &#xA;I tried the method where 4M glycerol and ATP is added to the wash buffer 1 and then I incubated this with the resin for 2 hrs in 4C, but it did not help. &#xA;Has anyone met such a problem before? I will be grateful for any advices. &lt;/p&gt;&#xA;" OwnerUserId="6892" LastActivityDate="2014-12-19T06:45:30.730" Title="Ni-NTA purification, problem with the chaperone protein" Tags="&lt;chromatography&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19026" PostTypeId="2" ParentId="19024" CreationDate="2014-06-10T23:12:55.107" Score="2" Body="&lt;p&gt;If chaperone proteins are not an expected binding partner to your protein/peptide fragment then you need to use imidazole in your lysis and wash buffer ranging from 1 to 10 mM depending on how stringent you want but 1 mM worked for me. Can go higher than 10 mM if the problem does not resolve but don't go too high since imidazole is also used to get the purified proteins off the nickel beads as an elution buffer!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-06-10T23:12:55.107" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="19028" PostTypeId="2" ParentId="5723" CreationDate="2014-06-10T23:25:06.203" Score="4" Body="&lt;p&gt;There is little hard evidence on whether smoke acts as a mosquitoe repellent. A literature review done by the WHO (&lt;a href=&quot;http://www.who.int/indoorair/publications/smoke_malaria/en/&quot; rel=&quot;nofollow&quot; title=&quot;Biran et al. 2008. Smoke and Malaria. World Health Organization&quot;&gt;Biran et al, 2008&lt;/a&gt;) on smoke and malaria show that evidence is mixed, at least when it comes to long term protection and protection from blood meals from firewood smoke. Their review also notes that few scientific studies have been done on the topic, and they report results from one experimental and a couple of observational studies. However, they do note that burning particular plant materials (based on traditionally used plants) may be effective (see e.g. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0001706X98000837&quot; rel=&quot;nofollow&quot; title=&quot;Pålsson &amp;amp; Jaenson. 1999. Plant products used as mosquito repellents in Guinea Bissau, West Africa. Acta Tropica 72(1)&quot;&gt;Pålsson &amp;amp; Jaenson. 1999&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These results also doesn't preclude that very heavy, temporary, smoke may be effective to get rid of mosquitoes (&quot;&lt;em&gt;... during camping is to stand in the fire's smoke...&lt;/em&gt;&quot;) - that this can be effective is certainly my personal experience as well.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2014-06-10T23:25:06.203" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19030" PostTypeId="1" AcceptedAnswerId="19033" CreationDate="2014-06-11T03:28:01.610" Score="7" ViewCount="509" Body="&lt;p&gt;I store many gel images which are included in my Latex notebooks. The geldoc software normally produces TIFF files, however, Latex only accepts PNG or JPEG.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I am going to store only a single copy of my DNA agarose gel images, which format is a good idea? PNG, or JPEG? Is there a good reason to keep one copy in TIFF and one copy in another format for every gel?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-06-11T09:52:25.957" Title="What is the best file format to store gel images?" Tags="&lt;gel-electrophoresis&gt;&lt;software&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="19031" PostTypeId="2" ParentId="19001" CreationDate="2014-06-11T05:43:56.980" Score="2" Body="&lt;p&gt;&lt;em&gt;Getting long for a comment&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can only comment that evolution &lt;strong&gt;does not&lt;/strong&gt; proceed towards thermodynamic optimum. Adaptation is thermodynamic optimization but evolution is directionless. Otherwise the extant species would not suffer from tradeoffs (which they have even in their usual habitat). Establishment of a self replicating cell may be thermodynamically driven and given the conditions, irreversible; macroscopic evolution is like die roll where some states are randomly⁺ selected and eliminated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;⁺Not really random but a complex non-linear function which seems unpredictable&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can imagine a chamber with particles exhibiting brownian motion. Assume that particles have a random size distribution (lets say they are crystals of different topologies). Now if you keep a separator with few holes wide enough for a just one particle of a given size to pass. Then you'll end up getting only few particles of a narrower size distribution on the other side. This no way ensures that these were the most thermodynamically stable particles. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-06-11T05:52:18.740" LastActivityDate="2014-06-11T05:52:18.740" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19032" PostTypeId="1" AcceptedAnswerId="19045" CreationDate="2014-06-11T05:44:47.027" Score="12" ViewCount="14061" Body="&lt;p&gt;How is the fluoride in toothpaste absorbed by our body? Does the tooth absorb the molecule directly, or is it absorbed by the mouth?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answers to &lt;a href=&quot;https://biology.stackexchange.com/questions/7019/what-nutrients-can-humans-absorb-in-the-mouth&quot;&gt;this question&lt;/a&gt; suggest that some materials can be absorbed by the mouth, but fluoride is absent. Additionally, many municipalities &lt;a href=&quot;http://en.wikipedia.org/wiki/Water_fluoridation&quot; rel=&quot;nofollow noreferrer&quot;&gt;add fluoride to tap water&lt;/a&gt; which I should imagine is actually absorbed in the stomach by a different mechanism than that of toothpaste.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that toothpaste generally comes with stern warnings &lt;a href=&quot;https://web.archive.org/web/20140730000400/http://blog.younglivingcircle.com/wp-content/uploads/2013/02/Toothpaste-Warning-Label-Toxic.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;not to swallow&lt;/a&gt;. Looking at the ingredients it seems the only thing that may be harmful is the fluoride itself. Therefore I &lt;em&gt;suspect&lt;/em&gt; that toothpaste has a much higher fluoride concentration than tap water, which supports the notion that its fluoride is absorbed by a different mechanism than tap water.&lt;/p&gt;&#xA;" OwnerUserId="6967" LastEditorUserId="46087" LastEditDate="2018-09-16T14:08:36.303" LastActivityDate="2018-09-16T14:08:36.303" Title="How is the fluoride in toothpaste absorbed?" Tags="&lt;teeth&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="19033" PostTypeId="2" ParentId="19030" CreationDate="2014-06-11T05:55:27.907" Score="10" Body="&lt;p&gt;&lt;strong&gt;Always keep the raw data files!&lt;/strong&gt; This is always a good idea for scientific data, and the only exception should be if the raw data is prohibitively large and it is not feasible to store it completely. This is not the case for gel images, so I would always keep the originals, and then use a cropped and edited copy in a suitable format for documents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The original image has the full amount of data, any conversion can potentially destroy data. For example, some imaging systems produce images with more than 8 bit color depth. Converting to another format will in many cases reduce the color depth to 8 bit as many programs and some image formats like JPEG don't support higher color depths.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;JPEG is lossy compression, I would always prefer PNG. You might have to use JPEG at some point because of the file size, but that should be at the latest point possible.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2014-06-11T09:52:25.957" LastActivityDate="2014-06-11T09:52:25.957" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19034" PostTypeId="2" ParentId="19032" CreationDate="2014-06-11T06:50:48.170" Score="5" Body="&lt;p&gt;Fluoride is absorbed mostly in the stomach and small intestine.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Several aspects of fluoride metabolism - including gastric absorption, distribution and renal excretion - are pH-dependent because the coefficient of permeability of lipid bilayer membranes to hydrogen fluoride (HF) is 1 million times higher than that of F(-). This means that fluoride readily crosses cell membranes as HF, in response to a pH gradient between adjacent body fluid compartments. After ingestion, plasma fluoride levels increase rapidly due to the rapid absorption from the stomach, an event that is pH-dependent and distinguishes fluoride from other halogens and most other substances. The majority of fluoride not absorbed from the stomach will be absorbed from the small intestine. In this case, absorption is not pH-dependent. Fluoride not absorbed will be excreted in feces. Peak plasma fluoride concentrations are reached within 20-60 min following ingestion. ... Many factors can modify the metabolism and effects of fluoride in the organism, such as chronic and acute acid-base disturbances, hematocrit, altitude, physical activity, circadian rhythm and hormones, nutritional status, diet, and genetic predisposition.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Source:&lt;/em&gt;&lt;/strong&gt; Buzalaf MA, Whitford GM. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21701189&quot;&gt;&lt;em&gt;Fluoride metabolism.&lt;/em&gt;&lt;/a&gt; Monogr Oral Sci. 2011;22:20-36. doi: 10.1159/000325107. Epub 2011 Jun 23.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fluoride concentration:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;tap water: maximum contaminant level goal is 4.0 mg/L or 4.0 ppm &lt;sup&gt;[1]&lt;/sup&gt;&lt;/li&gt;&#xA;&lt;li&gt;optimally fluoridated municipal water: 0.7 parts per million (ppm) of fluoride ion (F) &lt;sup&gt;[2]&lt;/sup&gt;&lt;/li&gt;&#xA;&lt;li&gt;toothpaste for adults: 1000 ppm or 1100 ppm F from three fluoride compounds. These are sodium monofluorophosphate (MFP), sodium fluoride (NaF) and stannous fluoride (SnF2) &lt;sup&gt;[2]&lt;/sup&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;When ingesting toothpaste, fluoride is less absorbed from dicalcium phosphate dihydrate toothpaste &lt;sup&gt;[3]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://water.epa.gov/drink/contaminants/basicinformation/fluoride.cfm&quot;&gt;http://water.epa.gov/drink/contaminants/basicinformation/fluoride.cfm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;American Dental Asociation &lt;a href=&quot;http://www.ada.org/EPUBS/science/2012/may/page.shtml&quot;&gt;http://www.ada.org/EPUBS/science/2012/may/page.shtml&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Drummond BK, Curzon ME, Strong M. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2364407&quot;&gt;&lt;em&gt;Estimation of fluoride absorption from swallowed fluoride toothpastes.&lt;/em&gt;&lt;/a&gt; Caries Res. 1990;24(3):211-5.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-11T06:57:45.567" LastActivityDate="2014-06-11T06:57:45.567" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19035" PostTypeId="2" ParentId="19032" CreationDate="2014-06-11T06:55:54.913" Score="7" Body="&lt;p&gt;From different sources, I think that it can be safely assumed that fluoride stays in the mouth and is absorbed by the teeth while brushing unless ingested (&lt;a href=&quot;http://now.tufts.edu/articles/fluoride-teeth-public-water-supply&quot;&gt;reference&lt;/a&gt;). Most dental doctors agree that the fluoride is not absorbed in the mouth and that it may be retained on the surface of your oral mucosa, where it is then available to help re-mineralize your teeth after acid exposure (&lt;a href=&quot;https://www.healthtap.com/topics/can-fluoride-be-absorbed-through-the-inside-of-the-mouth&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fluoride levels in toothpaste differs according to the company that is producing it.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It may appear after the label &quot;Active ingredient&quot; or as a component&#xA;  under &quot;Ingredients&quot; on the toothpaste tube. Whereas previously&#xA;  fluoride content was given as a percent of volume (% w/v) or weight (%&#xA;  w/w), it is now accepted that the most efficient method of informing&#xA;  people of the amount of fluoride in a toothpaste is to give the &quot;parts&#xA;  per million&quot; fluoride (ppm F). Most manufacturers now give fluoride&#xA;  content in ppm F. The EU has prohibited over the counter sales of&#xA;  toothpastes with a ppm F value of 1500 (&lt;a href=&quot;http://www.dentalhealth.ie/dentalhealth/teeth/fluoridetoothpastes.html&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Of course ingestion of the toothpaste will lead to the fluoride being absorbed by the stomach.This could increase the dietary recommended intake of fluoride leading to fluorosis and many other issues (&lt;a href=&quot;http://cavegirlskincare.com/post/27122721358/are-there-dangers-lurking-in-your-toothpaste&quot;&gt;reference&lt;/a&gt;). There is also a study estimating the fluoride absorbed from toothpastes through ingestion. In the study, it states that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Measuring changing fluoride levels in saliva appears to be an&#xA;  acceptable non-invasive technique for following systemic fluoride&#xA;  absorption(&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2364407&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The 1984 issue of Clinical Toxicology of Commercial Products lists Fluoride as &quot;more poisonous than lead and slightly less poisonous than arsenic&quot;. Lead has a toxicity rating of 3, Fluoride has a toxicity rating of 4 (&lt;a href=&quot;http://voices.yahoo.com/fluoride-other-hidden-toxins-toothpaste-70307.html?cat=5&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence it is recommended that the brushing habits of your young ones be supervised to check ingestion of toothpaste and use the appropriate amounts of toothpaste for brushing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Health effects of fluoride can be read about in &lt;a href=&quot;http://des.nh.gov/organization/commissioner/pip/factsheets/ard/documents/ard-ehp-14.pdf&quot;&gt;this article&lt;/a&gt;.&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The action of fluoride on teeth and treatments with fluoride is very comprehensively given in &lt;a href=&quot;http://lpi.oregonstate.edu/infocenter/minerals/fluoride/&quot;&gt;this article&lt;/a&gt;.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-06-11T07:10:52.120" LastActivityDate="2014-06-11T07:10:52.120" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19036" PostTypeId="1" CreationDate="2014-06-11T08:03:41.783" Score="3" ViewCount="4119" Body="&lt;p&gt;It's not explained on the &lt;a href=&quot;http://en.wikipedia.org/wiki/BamHI&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; page. So if, apparently, 'H' is not relevant, why is it part of the name? And if it is relevant, why is it not explained?&lt;/p&gt;&#xA;" OwnerUserId="4971" LastEditorUserId="1590" LastEditDate="2014-06-11T09:26:30.160" LastActivityDate="2014-06-11T09:26:30.160" Title="What does 'H' in BamHI stand for?" Tags="&lt;restriction-enzymes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19037" PostTypeId="2" ParentId="19036" CreationDate="2014-06-11T08:14:18.097" Score="7" Body="&lt;p&gt;These enzymes are named by the bacteria and the strain from which they are isolated. For BamHI this is Bacillus amyloliquefaciens strain H. In the beginning the enzyme was named BamI, which was later changed to BamHI.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See these two references:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1177312&quot;&gt;Isolation of a sequence-specific endonuclease (BamI) from Bacillus&#xA;amyloliquefaciens H.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/834250&quot;&gt;Recognition sequence of specific endonuclease BamH.I from Bacillus&#xA;amyloliquefaciens H.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The same is true for all the other restriction enzymes, so is EcoRI the first restriction endonuclease isolated from Escherichia coli strain R.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-11T08:14:18.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19038" PostTypeId="1" AcceptedAnswerId="19370" CreationDate="2014-06-11T09:12:07.530" Score="6" ViewCount="30783" Body="&lt;p&gt;What exactly happens when competent cells like DH5ɑ are heatshocked with DNA present? How does the DNA get inside the cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, why are all the steps necessary? What if you heatshock right after adding DNA? What if you don't put on ice after heatshock? What does the calcium chloride do? What actually happens when cells are &quot;competent&quot;? What governs transformation efficiency (besides obvious things like amount of DNA or cells)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To make it clear what I'm talking about, I use a protocol like the following:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Take cells out of -80C and thaw on ice for 5 min.&lt;/li&gt;&#xA;&lt;li&gt;Add 1 ul (~500 ng) plasmid DNA to 50 ul cells, mix gently with pipette tip.&lt;/li&gt;&#xA;&lt;li&gt;Leave on ice for 30 min.&lt;/li&gt;&#xA;&lt;li&gt;Put in 42C water bath for 45 sec.&lt;/li&gt;&#xA;&lt;li&gt;Put on ice for 10 min.&lt;/li&gt;&#xA;&lt;li&gt;Add 950 ul LB, put in 37C for 1 hour.&lt;/li&gt;&#xA;&lt;li&gt;Spread 300 ul of the culture on LB-agar plates with appropriate selection.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I usually get thousands of colonies from this (in fact, often 1:10 or 1:100 dilution is necessary so I can actually get isolated colonies). Even if I skip the outgrowth, I still get hundreds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't have my competent cell protocol, but basically I use that one rubidium chloride that everyone uses: DH5ɑ cells are washed with some buffers, suspended in a solution with CaCl2 and RbCl, then frozen in liquid nitrogen. I never actually measured, but usually the concentration of cells in the frozen aliquots is about 10 times as many as you would get from an overnight liquid culture (they are spun down and resuspended in a small volume).&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-06-11T21:07:20.037" LastActivityDate="2014-06-28T17:49:42.710" Title="How does heat shock transformation work?" Tags="&lt;bacteriology&gt;&lt;transformation&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19040" PostTypeId="1" CreationDate="2014-06-11T09:45:49.300" Score="4" ViewCount="612" Body="&lt;p&gt;My short term goal in a project is to build a local database of the NCBI dbSNP database. The data and schema are available on the FTP site(). I was going to implement the database using MySQL, but I just learnt about MongoDB. Is it possible to somehow convert the sql schema code to mongoDB architecture? Also, are there any real advantages to implementing the dbSNP database as MongoDB?&lt;/p&gt;&#xA;" OwnerDisplayName="user6417" LastActivityDate="2014-06-11T15:35:46.877" Title="Local storage of NCBI database in MongoDB" Tags="&lt;bioinformatics&gt;&lt;database&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2014-06-11T16:38:40.197" ContentLicense="CC BY-SA 3.0" />
  <row Id="19041" PostTypeId="2" ParentId="3743" CreationDate="2014-06-11T10:11:54.850" Score="1" Body="&lt;p&gt;Sleep as you may know is divided into 2 broad categories which are the REM (Rapid Eye movement) and NREM (non rapid eye movement). NREM is further divided into 3 stages (&lt;a href=&quot;http://en.wikipedia.org/wiki/Sleep#Stages&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). You never know which stage of sleep you are in when you are subjected to a particular frequency of sound. Your response to different sounds differ in your different sleep cycles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The present 3 stages in NREM sleep is an update by The American Academy of Sleep Medicine (AASM) in 2007 (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2335403/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).The original 4 stages in the Rechtschaffen and Kales (R&amp;amp;K) standardization of 1968 (&lt;a href=&quot;http://www.scribd.com/doc/51728449/Rechtschaffen-Kales-A-Manual-of-Standardized-Terminology-Techniques-and-Scoring-System-for-Sleep-Stages-of-Human-Subjects&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) has been used to explain the effect of disturbances in different sleep cycles&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Stage 1 is still the phase of sleep from which it is easiest to wake&#xA;  someone up.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;People in Stage 2 sleep are unlikely to react to a light or a noise,&#xA;  unless it is extremely bright or loud.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;During Stage 3, the muscles still have some tonus, and sleepers show&#xA;  very little response to external stimuli unless they are very strong&#xA;  or have a special personal meaning (for example, when someone calls&#xA;  your name, or when a baby cries within earshot of its mother). &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Stage 4 is the stage of sleep that accomplishes most of the body’s&#xA;  repair work and from which it is most difficult to wake someone up (&lt;a href=&quot;http://thebrain.mcgill.ca/flash/a/a_11/a_11_p/a_11_p_cyc/a_11_p_cyc.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A study conducted to measure brain activity while sleeping subjects were subjected to varying degrees of sound found that some people did you wake up after being hit with 70db of sound while others woke up even at sounds between 40 - 50 db (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0960982210007785&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). This could lead to new behavioral or drug therapies for people with sleep disorders.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A review on the affect of low frequency sound on sleep could not reach any significant conclusions warranting that more search needs to be conducted in the field.(&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15273026&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;You will be interested to know that different sounds have been found to wake up men and women. &lt;a href=&quot;http://www.telegraph.co.uk/news/newstopics/howaboutthat/6684362/Buzzing-flies-more-likely-to-wake-men-than-crying-babies-study.html&quot; rel=&quot;nofollow&quot;&gt;A list is available here&lt;/a&gt;. Differences between the sleep of men and women are listed in &lt;a href=&quot;http://www.huffingtonpost.com/dr-michael-j-breus/woman-sleep-different-than-man_b_875285.html&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-06-19T18:45:10.753" LastActivityDate="2014-06-19T18:45:10.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19044" PostTypeId="2" ParentId="15631" CreationDate="2014-06-11T11:08:57.283" Score="2" Body="&lt;p&gt;After a bit of research I can say that Yerba mate does not contain beta-carbolines. Now, I don't know if this makes you happy or sad but the tea has many antioxidant properties which makes it good for health. You can find a list of the components in Yerba mate in &lt;a href=&quot;http://www.scielo.cl/pdf/chiljar/v72n2/at16.pdf&quot; rel=&quot;nofollow&quot;&gt;paper 1&lt;/a&gt; and &lt;a href=&quot;http://www.yerba-mate.com/content/yerbamate.pdf&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-06-30T21:58:33.873" LastActivityDate="2014-06-30T21:58:33.873" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19045" PostTypeId="2" ParentId="19032" CreationDate="2014-06-11T11:48:44.760" Score="13" Body="&lt;p&gt;The chemical mechanism by which fluoride protects teeth is the &lt;a href=&quot;//en.wikipedia.org/wiki/Remineralisation_of_teeth&quot;&gt;remineralization&lt;/a&gt; of hydroxyapatite $\ce{Ca5(PO4)3(OH)}$ in the tooth enamel into fluorapatite $\ce{Ca5(PO4)3F}$:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\ce{Ca5(PO4)3(OH) \ (s) + F- \ (aq) -&amp;gt; Ca5(PO4)3F \ (s) + OH- \ (aq)}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This reaction occurs at the surface of the enamel, i.e. directly within the mouth.  The fluoride ions participating in the reaction are dissolved in the saliva and other fluids present in the mouth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, the fluoride does not need to be absorbed into any part of the body (although, as part of the remineralization process, it can be said to be absorbed directly into the tooth enamel), and, in particular, there is no need for it to be swallowed.  Indeed, because of potential adverse effects of high levels of fluoride when absorbed into the body through the digestive tract, swallowing strongly fluoridated dental care products like toothpaste or mouthwash should be avoided.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, any fluoride that is swallowed and absorbed into the body, e.g. through fluoridated (or naturally fluoride-rich) drinking water, can still contribute to the remineralization of teeth, simply because some of it will be secreted back into the mouth as part of saliva.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the fluoride levels in saliva (assuming a safe level of fluoride intake) are much lower than those in, say, toothpaste, your teeth will be &lt;em&gt;constantly&lt;/em&gt; exposed to the fluoride in saliva, whereas they will only be exposed to toothpaste for a few minutes each day.  Thus, while the rate of remineralization due to systemic fluoride may be much slower than that due to e.g. fluoridated toothpaste, the total amount of remineralization per day may well be of a comparable magnitude.&lt;/p&gt;&#xA;" OwnerUserId="239" LastActivityDate="2014-06-11T11:48:44.760" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19048" PostTypeId="1" CreationDate="2014-06-11T13:07:48.413" Score="1" ViewCount="167" Body="&lt;p&gt;We put 2 flasks inoculated with &lt;em&gt;Bacillus cereus&lt;/em&gt; in 37⁰C: one with 100μg/ml penicillin +  50μg/ml chloramphenicol and the other without penicillin. We found that the OD is higher in the one without the penicillin. These strains are supposedly penicillin resistant as verified by growing them in a test-tube containing penicillin (5mg/ml) at 30⁰C. It contradicts my hypothesis that they should have the same growth rate because of the $\beta$-lactamase secretion that would destroy the penicillin. I can't find any explanation in the web.&#xA;help me&lt;/p&gt;&#xA;" OwnerUserId="7994" LastEditorUserId="3340" LastEditDate="2014-06-12T09:51:07.033" LastActivityDate="2014-06-13T08:21:47.903" Title="How do penicillin resistant bacteria grow slower in the presence of penicillin?" Tags="&lt;cell-biology&gt;&lt;microbiology&gt;&lt;cell&gt;" AnswerCount="1" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="19051" PostTypeId="1" AcceptedAnswerId="19130" CreationDate="2014-06-11T15:06:48.133" Score="5" ViewCount="395" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Botulinum_toxin&quot; rel=&quot;nofollow noreferrer&quot;&gt;Botulinum toxin&lt;/a&gt; is the neurotoxin protein created when botulism spores grow. The requirements for growth and/or for keeping the toxin from denaturing would seem to be very difficult to create in bale of hay.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are well documented &lt;a href=&quot;http://www.omafra.gov.on.ca/english/livestock/horses/facts/info_botulism.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;incidents of botulism in horses&lt;/a&gt; who are eating hay, all the references I found were centered around hay in large plastic wrapped bales.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been &lt;a href=&quot;https://pets.stackexchange.com/questions/4407&quot;&gt;involved in an event&lt;/a&gt; where the presumed DX is botulism secondary to ingestion from hay from last year.  In this case the hay is second cutting timothy hay (making it 6 plus months old), in rectangular 50 pound (22 kg) bales that are not wrapped, have been barn kept, and when purchased from the vendor where stacked in rows 4 feet wide, by 6 feet (2 meters) high. The bale then spent more then a week on an shelf (chrome platted heavy wire) with good air circulation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Three pet &lt;a href=&quot;http://rabbit.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;house rabbits&lt;/a&gt; appear to have been effected. with 2 dead and one recovering from a case of descending paralysis.  Several tests are underway, but my understanding is that it may be difficult to conclusively show either the botulism in the rabbits, or significant presence of 'botulinum toxin' or 'clostridium botulinum' in the hay (samples from the mangers of effected animals are being tested).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to logically conclude that Botulinum toxin could, or could not, be created and/or survive in a bale of hay meeting the above criteria? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is an awareness of a plant based neurotoxin that would cause similar symptoms that may be growing in the hay field please offer that in an answer at &lt;a href=&quot;https://gardening.stackexchange.com/questions/11007&quot;&gt;Gardnening&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="4240" LastEditorUserId="-1" LastEditDate="2017-04-13T12:59:17.050" LastActivityDate="2014-06-16T18:22:15.067" Title="Can botulinum toxin be grown or kept from denaturing in an UNWRAPPED 50 pound hay bale?" Tags="&lt;cell-biology&gt;&lt;toxicology&gt;&lt;growth-media&gt;&lt;bacterial-toxins&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19052" PostTypeId="2" ParentId="19040" CreationDate="2014-06-11T15:35:46.877" Score="2" Body="&lt;p&gt;I've played with mongoDb.  It is a nearly &lt;a href=&quot;http://docs.mongodb.org/manual/core/data-modeling-introduction/&quot; rel=&quot;nofollow&quot;&gt;schemaless data store&lt;/a&gt; - each record (analogous to a row) can have nearly any entry name set except for a unique ID that mongoDb uses.  In practice most of your records will have the same labels and names &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Leaving SQL for noSQL is turning out not to be a great win.  MongoDB will excel in retrieving records quickly and processing records by their content.  It has some constraints too compared to SQL.  It requires that the main index be stored in RAM, which might or not be an issue.   For very large datasets mongoDB can be configured to shard the data automatically - splitting it up over a cluster of machines for high throughput fast processing applications. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you need flexibility in your data record and you have a good machine (or a good cluster) to put it up on it could offer some advantages. We have a reasonable store of dbSNP on a recent MySQL machine and it performs okay.  Not thousands of transactions a second, but we can do reasonable throughput of record processing. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-06-11T15:35:46.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19053" PostTypeId="1" AcceptedAnswerId="19127" CreationDate="2014-06-11T18:25:21.807" Score="4" ViewCount="26339" Body="&lt;p&gt;&lt;a href=&quot;http://f1000.com/prime/reports/m/3/2/&quot; rel=&quot;nofollow&quot;&gt;http://f1000.com/prime/reports/m/3/2/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Filaggrin is a highly abundant protein expressed in the uppermost part of the epidermis that is critical to the formation and hydration of the stratum corneum—the outermost dead cell layers responsible for the barrier function of the skin. Filaggrin deficiency leads to a 'leaky' skin barrier that allows higher than normal water loss (explaining the dry, scaly skin), as well as allowing entry of allergens through the epidermis where they trigger inflammatory and allergic immune responses (atopic eczema and allergies).&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not that such a supplement exists, but is it biologically possible to treat filaggrin deficiency with something taken orally?&lt;/p&gt;&#xA;" OwnerUserId="6534" LastActivityDate="2018-06-21T06:59:55.987" Title="Is it theoretically possible to treat filaggrin deficiency with a dietary supplement?" Tags="&lt;human-biology&gt;&lt;genetics&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19054" PostTypeId="2" ParentId="19053" CreationDate="2014-06-11T18:47:11.127" Score="3" Body="&lt;p&gt;I highly doubt it. &lt;a href=&quot;http://en.wikipedia.org/wiki/Filaggrin&quot; rel=&quot;nofollow&quot;&gt;Filaggrin&lt;/a&gt; is a human protein which is expressed in the skin and stored as profilaggrin. The profilaggrin has a molecular weight of about 350 kDa (which is rather big) and is cut into smaller units of filaggrin, which then crosslinks kreatin fibers of the epidermal keratinocytes. This enhances the durability of the skin. Mutations in the filaggrin gene have been associated with dry skin and excema. See here for more information:&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23517450&quot; rel=&quot;nofollow&quot;&gt;Filaggrin - revisited.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To supplement the profilaggrin, you would have to bring this rather large protein into the skin. You could think about making a cream with the smaller filaggrin in it to promote crosslinking of the upper skin. The question here would be how effective such a treatment ist and how deep the crosslinking would be.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-11T18:47:11.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19055" PostTypeId="1" AcceptedAnswerId="19056" CreationDate="2014-06-11T22:52:44.613" Score="3" ViewCount="10741" Body="&lt;p&gt;A simple question (I could not find it on internet): What is Pan for in pan-caspase? Is it any different from the term 'caspase' ?&lt;/p&gt;&#xA;" OwnerUserId="1843" LastActivityDate="2017-01-22T04:08:59.453" Title="What is Pan for in pan-caspase?" Tags="&lt;molecular-biology&gt;&lt;apoptosis&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19056" PostTypeId="2" ParentId="19055" CreationDate="2014-06-11T23:28:56.427" Score="1" Body="&lt;p&gt;The term pan, in my opinion, is perhaps one of the most vague that exists in science! I can partley answer this question (ironically as vague as the term pan) by referring you to the term pan-neuronal. A pan neuronally expressed genes has features, which include the expression of many &quot;generic&quot; genes required non-specifically for neuronal function, such as components of the synaptic vesicle machinery, so pan-neuronal genes are not neurone class specific (&lt;a href=&quot;http://www.wormbook.org/chapters/www_specnervsys/specnervsys.html&quot; rel=&quot;nofollow&quot;&gt;http://www.wormbook.org/chapters/www_specnervsys/specnervsys.html&lt;/a&gt;). So with that token pan-caspases are a term referring to a general caspase activity/function/structure and not a specific caspase type activity but I would welcome any corrections or edits to this response.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-06-11T23:28:56.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19057" PostTypeId="1" CreationDate="2014-06-11T23:32:02.340" Score="3" ViewCount="148" Body="&lt;p&gt;What is a good recipe for making agar at home for a minimal cost? Are there materials that could be found in the kitchen cabinet?&lt;/p&gt;&#xA;" OwnerUserId="6622" LastEditorUserId="3340" LastEditDate="2014-06-12T09:57:05.397" LastActivityDate="2014-06-12T10:23:54.350" Title="Science experiments at home with Minimal Cost" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19059" PostTypeId="1" CreationDate="2014-06-12T03:14:30.303" Score="3" ViewCount="482" Body="&lt;p&gt;The advent of chlorpromazine in 1955 put an end to one of the more bizarre chapters in American psychiatry.$^1$ Dr. Robert Heath implanted wires or delivered injections of acetylcholine (a neurotransmitter) deep into the 'septal regions' of the brains of men and women with various physical and mental disorders. His discovery of the brain's 'pleasure center' actually preceded the discovery of the same center in rats by about 20 years [Baumeister, below, at 272].    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In one of his papers$^2$ Heath describes intense orgasmic experiences on the part of his patients in response to his treatments, which he dutifully records on EEGs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;His description of Patient b-5 is especially interesting. He relates: &quot;The patient became more attuned to her environment, answered questions more rapidly and accurately, and solved simple mathematical problems with more ease...and in most instances, within another 5 to 10 minutes, this [heightened attunement] culminated in repetitive orgasms.&quot; [Heath, below, at 12].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to refreshing my interest in solving simple mathematical problems, this article made me wonder whether this area of research had been resumed in some form. Many of the ethical and technical problems discussed in Maumeister's article seem surmountable, especially in light of computer-aided visualization of brain structures. Not to mention that a kindred treatment, ECT (electroshock), which can still actually be done involuntarily, has seen something of a comeback in the U.S. since the 1940s. ECT is basically controlled destruction of brain tissue, which seems to cast Heath's work in a kinder light.      &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is whether this thread has been taken up or whether, as one VIP put it, the absence of evidence is evidence of absence. I was unable to turn anything up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any enlightenment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^1$ Baumeister, The Tulane Electrical Brain Stimulation Program: A Historical Case Study in Medical Ethics (2000), J. of the History of the Neurosciences 9 (3): 262-78. See page 270.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^2$Heath, Pleasure and Brain Activity in Man, (1972) Journal of Nervous and Mental Disease 154 (1): 3-17.&lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2014-06-12T03:14:30.303" Title="Electrodes in the brain and 'repetitive orgasms'" Tags="&lt;brain&gt;&lt;neurology&gt;&lt;sex&gt;&lt;psychology&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2014-07-21T23:07:44.037" ContentLicense="CC BY-SA 3.0" />
  <row Id="19063" PostTypeId="2" ParentId="19057" CreationDate="2014-06-12T10:23:54.350" Score="3" Body="&lt;p&gt;Instructions&#xA;1&#xA;Place a coffee filter in a strainer and hang the strainer over the opening of the clear bowl.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2&#xA;Slowly pour the broth into the filter, making sure that the broth doesn't overflow from the sides of the filter. If the filter becomes clogged with particles, remove the used filter, replace with a clean filter and continue pouring the broth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3&#xA;Remove the strainer and filter from the top of the bowl and observe whether the broth appears clear (i.e., there are no suspended particles in the liquid). If particles are floating in the liquid, repeat Steps 1 and 2 using a second clear bowl and a fresh coffee filter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4&#xA;Place the pot on the stove and pour the clear broth into the pot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5&#xA;Add 16 ounces of distilled water to the pot containing the broth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;6&#xA;Turn on the stove and adjust the heat to medium-low. Heat the broth to a simmer (i.e., small bubbles appear near the side of the pot).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;7&#xA;Add 1 teaspoon of the agar-agar powder to the simmering broth (approximately 2.5 grams) and stir the mixture until the powder is dissolved. Make sure to stir the powder to dissolve and prevent the gelatin from sinking to the bottom of the pot (where it can burn).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;8&#xA;Repeat Step 7 until all agar-agar powder has been dissolved in the broth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;9&#xA;Continue stirring the broth for about 1 minute to ensure that all powder is completely dissolved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;10&#xA;Turn off the stove, place the lid on the pot and let the liquid cool for at least 15 minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;11&#xA;Arrange the sterile petri dishes in a row for easy assembly, but do not remove the lids.If desired, place a trivet to hold the warm pot. If you're using lidded custard cups instead of petri dishes, sterilize the custard cups by placing the cups and lids inverted (upside down) on a foil-covered cookie sheet and bake in the oven for at least one hour at 375 degrees Fahrenheit. Make sure the sterilized cups and lids are completely cooled before use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;12&#xA;Carefully touch the outside of the pot to check that it is warm to the touch and place the pot on the trivet. If the pot is too hot to touch, wait at least 10 minutes to let the pot cool.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;13&#xA;Remove the lid and set aside. Place the ladle in the pot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;14&#xA;Remove the lid from one petri dish and dispense nutrient broth to fill the dish halfway. Cover the dish immediately with its cover.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;15&#xA;Repeat Step 14 for each of the petri dishes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;16&#xA;Allow the nutrient broth to solidify in the petri dishes for at least 1 hour, undisturbed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;17&#xA;Gently shake the petri dishes side to side to check that the nutrient broth has completely solidified. If the broth is not completely gelled, wait another 20 minutes before checking again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;18&#xA;Cover a table or flat surface with a roll of paper towels to create a sterile work area. Tear off a sheet of paper towel and fold it four times to create a thick, rectangular wad. Set this wad on one end of the work area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;19&#xA;Transfer one petri dish to the sterile work area and remove the lid. Carefully turn the dish over and place one end on the side of the folded wad, so that it lies inverted and slightly angled (with a slight gap by the paper towel wad).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;20&#xA;Turn the lid over and place it above the petri dish on the sterile work surface. If water droplets appear on the lid, gently shake this moisture off before placing on the covered surface, but do not touch the inside of the lid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;21&#xA;Repeat Steps 19 and 20 for each petri dish, positioning one side of the inverted dish on the side of the previous dish rather than the paper towel wad. The dishes will appear as a staggered set, with gaps on one side so that excess moisture can evaporate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;22&#xA;Look at the inverted petri dishes to check whether the moisture on the sides of the plates evaporated. Once all moisture has cleared, turn the plates right-side up and immediately cover with the lids for use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;23&#xA;Inoculate the nutrient agar on the plate by wiping a swab containing the desired culture on the nutrient agar surface before covering with the lid. Turn the petri dish over so that the solid is on top. Store the inoculated petri dish with the solid on top for culturing and the lid on the bottom to catch any moisture, loose particles or growth.&lt;/p&gt;&#xA;" OwnerUserId="8005" LastActivityDate="2014-06-12T10:23:54.350" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19065" PostTypeId="1" CreationDate="2014-06-12T13:22:42.267" Score="2" ViewCount="109" Body="&lt;p&gt;During bacterial protein synthesis, when ribosomes attach to the cytoplasmic membrane and form a polysome, to what molecule are the ribosomes attaching? Is the polysome held to the cytoplasmic membrane by just a single connection between one ribosome and the particular attachment molecule?&lt;/p&gt;&#xA;" OwnerUserId="6622" LastEditorUserId="948" LastEditDate="2014-06-12T14:48:35.527" LastActivityDate="2014-08-12T10:13:40.767" Title="Prokaryotic Ribosomes" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19066" PostTypeId="1" CreationDate="2014-06-12T13:28:06.377" Score="0" ViewCount="125" Body="&lt;ol&gt;&#xA;&lt;li&gt;Is there any disulphide bond in a quaternary structured protein?&lt;br/&gt;&#xA;If yes, please provide examples.&lt;br/&gt;&lt;/li&gt;&#xA;&lt;li&gt;In tertiary structured proteins, what is(are) the most important characteristic(s)  of tertiary structured proteins?&lt;br/&gt;&#xA;a) globular in shape&#xA;b) have both alpha helix and beta sheet&#xA;or, is there any characteristic that I do not mention? &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8007" LastEditorUserId="3632" LastEditDate="2014-06-12T13:35:30.260" LastActivityDate="2014-06-12T23:02:37.523" Title="level of organisation of proteins" Tags="&lt;human-biology&gt;&lt;proteins&gt;&lt;protein-structure&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19067" PostTypeId="2" ParentId="19066" CreationDate="2014-06-12T13:53:44.417" Score="2" Body="&lt;p&gt;Interesting protein structure trivia question!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disulfide bonds form more or less spontaneously when two sulfhydryl groups from cysteines are close enough to each other in the proper orientation in a reducing environment.  So given this, its possible for them to exist, even though in most cases the distance between the cysteines in a disufide bridge is small and intra-domain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Inter-domain disulfide bonds are rare.  The most common example is that &lt;a href=&quot;http://pathmicro.med.sc.edu/mayer/igstruct2000.htm&quot; rel=&quot;nofollow&quot;&gt;some immunoglobulin domains in antibodies have an intrachain disulfide bridge&lt;/a&gt;.  I also found reference to one in a &lt;a href=&quot;http://www.tandfonline.com/doi/abs/10.1271/bbb.120305#.U5ms95SwLzQ&quot; rel=&quot;nofollow&quot;&gt;starch synthetase from rice&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In tertiary structure, the overall shape is an important one.  Globular shapes are the most common, but &lt;a href=&quot;http://www.rcsb.org/pdb/101/motm.do?momID=88&quot; rel=&quot;nofollow&quot;&gt;elongated protein folds&lt;/a&gt;, &lt;a href=&quot;http://www.rcsb.org/pdb/explore/explore.do?structureId=1EE6&quot; rel=&quot;nofollow&quot;&gt;triangular folds&lt;/a&gt;,  &lt;a href=&quot;http://www.rcsb.org/pdb/explore/jmol.do?structureId=2POL&quot; rel=&quot;nofollow&quot;&gt;rings&lt;/a&gt;, &lt;a href=&quot;http://www.rcsb.org/pdb/explore/explore.do?structureId=3J06&quot; rel=&quot;nofollow&quot;&gt;disk-like structures made out of wedges&lt;/a&gt; are popular examples of how protein structures can do amazing things when selection requires them to. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-06-12T23:02:37.523" LastActivityDate="2014-06-12T23:02:37.523" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19069" PostTypeId="1" AcceptedAnswerId="19070" CreationDate="2014-06-12T16:32:29.370" Score="4" ViewCount="168" Body="&lt;p&gt;Do mitochondria use ATP in order make another ATP from glucose, or does it use another source of energy to convert glucose to ATP?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="3340" LastEditDate="2015-06-04T11:45:21.730" LastActivityDate="2015-06-04T11:45:21.730" Title="Do mitochondria use ATP in order make another ATP from glucose?" Tags="&lt;molecular-biology&gt;&lt;metabolism&gt;&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19070" PostTypeId="2" ParentId="19069" CreationDate="2014-06-12T17:08:24.873" Score="2" Body="&lt;p&gt;During ATP production through the citric acid cycle, some ATP is used to transport necessary molecules for the reactions.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;piruvate molecules are actively transported into the mitochondrial matrix [2]&lt;/li&gt;&#xA;&lt;li&gt;two NADH equivalents from glycolisis are transported into the mitochondrion and consume two molar equivalents ATP [1]&lt;/li&gt;&#xA;&lt;li&gt;protons leakage across the mitochondrial membrane leads to reduced ATP from NADH and FADH&lt;sub&gt;2&lt;/sub&gt; [1]&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In theory, one molar equivalent of glucose can generate 38 equivalents of ATP. The actual number is only 25 [1].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Citric acid cycle,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Citric_acid_cycle&amp;amp;oldid=610117265&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Citric_acid_cycle&amp;amp;oldid=610117265&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Mitochondrion,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Mitochondrion&amp;amp;oldid=614223751&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Mitochondrion&amp;amp;oldid=614223751&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-26T19:45:27.117" LastActivityDate="2014-06-26T19:45:27.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19071" PostTypeId="1" AcceptedAnswerId="19072" CreationDate="2014-06-12T18:08:14.000" Score="9" ViewCount="3773" Body="&lt;p&gt;Lying on my bed, doing nothing I recently noticed flies usually fly in small circles, right under my ceiling lamp. Worth noting - the lamp was off as it was middle of a day. And those flies kept flying like this for hours, not moving anywhere else! Later I noticed it repeated every day, pretty much the same pattern. Why is that?&lt;/p&gt;&#xA;" OwnerUserId="8011" LastEditorUserId="8011" LastEditDate="2018-09-19T08:02:29.457" LastActivityDate="2020-07-24T20:52:24.347" Title="Why do flies fly in circles?" Tags="&lt;entomology&gt;&lt;ethology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="19072" PostTypeId="2" ParentId="19071" CreationDate="2014-06-12T18:21:26.073" Score="13" Body="&lt;p&gt;Flies use any object they can find as a landmark.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The flies patrol &lt;strong&gt;well-defined airspaces underneath landmarks&lt;/strong&gt; like lampshades. ... Male flies approach a landmark from below and, in the absence of other flies, settle to patrol an airspace close to the landmark. A second male approaching the same landmark chases, or is chased away by, the patrolling fly when it comes too close and may eventually settle to patrol 10–30 cm below the airspace occupied by the first fly. ... The position of male patrolling stations relative to the landmark suggests that females might arrive at landmarks from the side (and not from below, as males do), thus crossing the dorsal visual field of patrolling males.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Source:&lt;/em&gt;&lt;/strong&gt; Jochen Zeil. &lt;a href=&quot;http://link.springer.com/article/10.1007/BF00300862&quot;&gt;&lt;em&gt;The territorial flight of male houseflies (Fannia canicularis L.)&lt;/em&gt;&lt;/a&gt; Behavioral Ecology and Sociobiology. August 1986, Volume 19, Issue 3, pp 213-219&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-06-12T18:21:26.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19073" PostTypeId="1" AcceptedAnswerId="19075" CreationDate="2014-06-12T19:50:27.970" Score="5" ViewCount="372" Body="&lt;p&gt;Have 2 organisms ever been introduced to create a symbiotic relationship that doesn't occur in their natural environment?&lt;/p&gt;&#xA;" OwnerUserId="6534" LastActivityDate="2014-06-13T09:34:48.203" Title="Has an artificial symbiotic relationship ever been created?" Tags="&lt;cell-biology&gt;&lt;zoology&gt;&lt;mycology&gt;&lt;parasitology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19075" PostTypeId="2" ParentId="19073" CreationDate="2014-06-12T20:06:19.783" Score="4" Body="&lt;p&gt;Here are some examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;symbiosis between genetic modified yeast cell populations (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17267602&quot; rel=&quot;nofollow&quot;&gt;Shou W et al. 2007&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;symbiosis between green algae and embryonic chick connective tissue (&lt;a href=&quot;http://www.sciencemag.org/content/80/2079/408.short&quot; rel=&quot;nofollow&quot;&gt;Buchsbaum R et al. 1934&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;symbiosis between &lt;a href=&quot;http://en.wikipedia.org/wiki/EcoBot&quot; rel=&quot;nofollow&quot;&gt;EcoBot&lt;/a&gt; II and microbial fuel cells (&lt;a href=&quot;http://www.ias.uwe.ac.uk/pdf%27s/Artificial%20symbiosis.pdf&quot; rel=&quot;nofollow&quot;&gt;Ieropoulos, Ioannis, et al. 2005&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-06-12T20:06:19.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19076" PostTypeId="1" CreationDate="2014-06-12T23:31:06.543" Score="3" ViewCount="312" Body="&lt;p&gt;When you read about the adaptive immune response, you are often told that the response is specific to each pathogen - that the response is tailored. My question is - to what extent is this really true? And if it is true, how is the response tailored?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that the B cell receptors (and, consequently, the antibodies produced by plasma cells in response to a pathogen) are highly specific. A pathogen will bind specifically to a B cell receptor on a particular B cell and particular antibodies will be produced for that pathogen. Again, T cells are specific for each pathogen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, it strikes me that there doesn't seem to be that much variation in what antibodies do. Each antibody is particular to its pathogen, but all antibodies work by doing the same few things, e.g. opsonisation, or inhibiting viruses from infiltrating cells. Yes the antibodies may be specific, but to what extent is it true that the antibody will produce a specific response to a specific pathogen? I mean, does the antibody for staphylococcus affect staphylococcus differently from the way the antibody for listeria affects listeria?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, each CD8+ Tc cell is specific to its pathogen, but they then seem to go about killing their target pathogen in very similar ways - inducing apoptosis or lysis via perforin and various cytotoxins. So, again, would the CD8+ Tc cell for influenza respond differently to the CD8+ Tc cell for norovirus?&lt;/p&gt;&#xA;" OwnerUserId="5263" LastActivityDate="2014-06-13T09:08:54.427" Title="How specific is the adaptive immune response?" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19077" PostTypeId="1" AcceptedAnswerId="19082" CreationDate="2014-06-13T01:36:32.880" Score="5" ViewCount="76" Body="&lt;p&gt;A film clip would be helpful here. A few days ago I noticed a swarm of newly hatched flying bugs about 20 feet away from me with the sun behind them so the shape of swarming (such as it was) was easy to make out. Several times, after creating various spiral shapes or chaotic masses they returned to a sort of 'holding pattern' which I either never noticed or never saw before. To a pretty good approximation the bugs arranged themselves in what seemed like an &quot;oscillating drum head&quot; pattern that is well approximated by a rotated sinc function. The peak at zero is a little exaggerated here but the bugs were more or less dispersed on a shape like: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pi6Ue.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;subject to a light breeze and continuous adjustment. I know that people have studied swarming behavior and made models but are there any that account for this one? It has a lot of significance in ODEs and engineering but I never associated it with swarming behavior. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!    &lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2014-06-13T07:03:39.623" Title="Is there a good explanation for this swarming pattern?" Tags="&lt;entomology&gt;&lt;mathematical-models&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19078" PostTypeId="2" ParentId="17483" CreationDate="2014-06-13T04:04:05.353" Score="1" Body="&lt;p&gt;Try running software like Censor. If checks in the reference repeat databases and detects microsatellites. So, you can most probably be sure of the microsatellites generated. Moreover, the microsatellites have their information present in the GIRI database. So, you can get more information, if you find the microsatellite in your sequences. Hope this helps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;~Rama.&lt;/p&gt;&#xA;" OwnerUserId="6455" LastActivityDate="2014-06-13T04:04:05.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19079" PostTypeId="2" ParentId="17406" CreationDate="2014-06-13T04:12:42.033" Score="1" Body="&lt;p&gt;Why a related genome helps:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Alignment of the reads first and assemble next.&#xA; 2) The gene-space is already predefined ( the genes and their co-ordinates are already known), so if your assembly is fragmented or missing a portion of the gene information, that can be accomodated with reference genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Limitations: Rather than assembling your own genome, you are forcing the reference genome to be part of your genome assembly. If at all, any differences are there, they are washed out, when you do a reference assembly.&lt;/p&gt;&#xA;" OwnerUserId="6455" LastActivityDate="2014-06-13T04:12:42.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19080" PostTypeId="2" ParentId="14836" CreationDate="2014-06-13T06:32:44.710" Score="1" Body="&lt;p&gt;My understanding is that there are two major reasons for not being able to recall where your socks are or when your anniversary is:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The information was not committed to short term memory in the first place when you initially encountered it, so there was never anything to remember.&lt;/li&gt;&#xA;&lt;li&gt;The information is intact, but you are not able to effectively retrieve it, because other memories compete and act as noise when you try to remember a certain specific one.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Neither of these scenarios involves actual loss of long term memory, which is more commonly a result of concussions, or other sorts of serious brain damage.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-06-13T06:32:44.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19081" PostTypeId="1" AcceptedAnswerId="42267" CreationDate="2014-06-13T07:00:27.673" Score="7" ViewCount="17393" Body="&lt;p&gt;It is a cliche of freshman biology labs to point out that &quot;every cycle of PCR doubles the DNA, so the yield will be $2^{cycles}$ times the template amount&quot;. However, if this were true, 1 ng of template would generate about 35 billion ng after 35 cycles, or 35 &lt;em&gt;grams&lt;/em&gt; of DNA. This is clearly absurd and not the case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, the power-of-2 claim is a gross oversimplification (if anything, it is an &lt;em&gt;upper bound&lt;/em&gt; - but even so, a very uninformative one), and in practice, yields will fall far short of it because:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Every single duplex of DNA does not denature at each cycle&lt;/li&gt;&#xA;&lt;li&gt;Primers do not bind to every single molecule of DNA at each cycle&lt;/li&gt;&#xA;&lt;li&gt;Not every DNA strand gets bound by a polymerase at every cycle&lt;/li&gt;&#xA;&lt;li&gt;Not every polymerase that binds manages to complete the entire product in time in every cycle&lt;/li&gt;&#xA;&lt;li&gt;The reaction inhibits itself by depleting dNTPs&lt;/li&gt;&#xA;&lt;li&gt;The heat denatures the reaction by degrading enzyme&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In fact, cursory examination of qPCR output often follows saturation kinetics:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JlTkp.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematical methods for modeling qPCR are obviously well developed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is about ordinary PCR: Is it possible get a reasonable expectation of nanogram yield for an ordinary PCR done in a tabletop cycler, with typical PCR reagents?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, when amplifying from a plasmid, I would like to calculate how many cycles to do, how much template to use, and how much product to load on the agarose gel to ensure that I will be able to clearly distinguish exponential amplification (both primers anneal), linear amplification (only one primer anneals), and no amplification (neither primer can anneal or the reaction did not work).&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-06-13T07:14:00.557" LastActivityDate="2018-05-07T11:11:57.763" Title="Equation for accurate prediction of PCR yield" Tags="&lt;biochemistry&gt;&lt;pcr&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19082" PostTypeId="2" ParentId="19077" CreationDate="2014-06-13T07:03:39.623" Score="1" Body="&lt;p&gt;I watched some youtube videos but couldn't find any swarming that looked like rotated sinc function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following is nothing but the guesses of someone who doesn't know much about swarming!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One pattern that is often found (through computer simulation and empirical observation) in swarming is a simple 2D rotation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/K4T3i.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's first consider only the static form of the shape you observed. This shape might be the consequences of multiple rotating layers. Do you remember what kind of dynamic had the individuals within your sinc function?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oscillation is a pattern that is also sometimes observed in swarming. The oscillating behavior might be the result of inertia. Just like a pendulum, individuals that are far away from the group accelerate continuously in the same direction up to the point they reach the middle of the group. Then they undergo a inverse acceleration up to the point they reach a null speed and then start their cycle again. This inertia depend on the number of neighbors they align their movement on are low. For example, it has been shown in I don't remember which species of birds (I can't find the reference) that each individual align their movement according to only the 6th closest neighbors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information about the 3 basic rules (separation, alignment, cohesion) that allow swarming behavior, have a look to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Boids&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki page&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, I hypothesize that thanks to the underlying 3 basic rules of swarming, the patterns of rotations and inertia together allow to explain your observations.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-06-13T07:03:39.623" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19083" PostTypeId="1" AcceptedAnswerId="19091" CreationDate="2014-06-13T07:13:03.780" Score="1" ViewCount="1676" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Nazi_eugenics&quot; rel=&quot;nofollow&quot;&gt;Nazi eugenics&lt;/a&gt; programs are well known. Despite their &lt;a href=&quot;http://en.wikipedia.org/wiki/Action_T4&quot; rel=&quot;nofollow&quot;&gt;controversy&lt;/a&gt;, I cannot find any indication on their effectiveness. Were there ever and studies done on the (arguably subjective definition of) superiority of German genetics due to (or possibly in spite of) these programs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do we even have a way to objectively measure genetic superiority or fitness? In the case of a lack of such a measurement, the idea could be qualified for purposes of this question as:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Lower instances of genetic disease.&lt;/li&gt;&#xA;&lt;li&gt;Lower instances of mental retardation, criminal tendencies, and mental illness.&lt;/li&gt;&#xA;&lt;li&gt;Higher general academic achievement.&lt;/li&gt;&#xA;&lt;li&gt;Healthier, longer lived population.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Note of course that I am not promoting or condoning eugenics in any way. I am only interested in knowing if the results were effective (i.e. achieved their goals), without comparing the programs' possible benefit against its obvious drawbacks. All contemporary discussion of the programs concentrate only on the drawbacks, unfortunately.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt; Before anyone accuses me of bigotry or crimes against humanity, I will mention that my grandfather lost all seven of his siblings, his parents, and all the rest of his entire family to this same regime. My grandmother lost five of eight siblings, both parents, and all the rest of her entire family to this same regime. What these people did to Jews, Gypsies, and the feeble was terrible and I do not excuse it. This question is intended only to concentrate on the scientific issue of forced, deliberate genetic improvement, a form of &quot;breeding&quot; if you will.&lt;/p&gt;&#xA;" OwnerUserId="6967" LastEditorUserId="6967" LastEditDate="2014-06-13T14:17:13.697" LastActivityDate="2014-06-13T14:17:13.697" Title="Is there any measure by which the Germans today could be called a genetically superior race?" Tags="&lt;human-genetics&gt;" AnswerCount="1" CommentCount="10" ClosedDate="2014-06-14T00:23:53.480" ContentLicense="CC BY-SA 3.0" />
  <row Id="19084" PostTypeId="2" ParentId="19048" CreationDate="2014-06-13T08:21:47.903" Score="1" Body="&lt;p&gt;Your hypothesis is incorrect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You must be assuming that lactamase destroys the antibiotic with perfect efficiency. This is incorrect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You must be assuming that the population will remain genetically stable. This is doubly incorrect. Firstly the penicillin will select highly resistant bacteria which suffer a greater fitness burden from expressing the lactamase. Second, in absence of penicillin, spontaneously arising mutants which suppress the lactamase are free to proliferate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You must be assuming that carrying capacity is identical for Pen+ and Pen- media. Trivially, you claim your experiment disproves this, but the assumption is also baseless since this need not be the case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, your results are inconclusive. You lack crucial controls, such as putting the bacteria from the Pen+ into Pen- and vice versa to see if the growth difference is intrinsic. You have not only failed to provide the error of your measurements, but have failed to provide the quantitative measurements themselves, so we do not even know if the difference is statistically significant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, there are several basic things which you could rightfully expect us to assume, but have nevertheless failed to provide. For instance, you do not say if the populations are clonal.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-06-13T08:21:47.903" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19085" PostTypeId="2" ParentId="19076" CreationDate="2014-06-13T09:08:54.427" Score="2" Body="&lt;p&gt;The adaptive immune response is highly specific and is made to fit a specific antigen. The antigen binding sites are located on the ends of the two short arms of the Y-shaped molecule, as seen in the figure below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pi7lI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The recognition site is made of the ends of one short immunoglobulin chain and one long chain. The ends (shown in yellow in the figure) are also called variable regions and are the key to the big variety of different antibodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When B cells develop, there B cell receptor (which is basically a membrane bound antibody) is tested if it reacts to components from the own organism. If not, they are released into the periphery (blood stream). These B cells are then called naive, since they haven't come in contact with an antigen. They express a B cell receptor which usually only has a weak affinity to an antigen - but the body produces quite a wide variety of these cells. (see the second figure).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zBeFc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the body comes in contact with an antigen (like a virus), it is taken up by the so called professional antigen presenting cells (dendritic cells, macrophages, B cells) of the immune system, broken down into small pieces and these are presented to the immune system. This activates the &lt;a href=&quot;http://en.wikipedia.org/wiki/Affinity_maturation&quot; rel=&quot;nofollow noreferrer&quot;&gt;affinity maturation&lt;/a&gt; of the B cell receptor, &lt;a href=&quot;http://en.wikipedia.org/wiki/Somatic_hypermutation&quot; rel=&quot;nofollow noreferrer&quot;&gt;somatic hypermutation&lt;/a&gt; and finally the clonal selection of the cells, which produce the antibodies with the highest affinity (the strongest binding) to the antigen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are estimates that the human immune system can produce around 10 billion different antibodies. This variability is achieved by the genetic variability of the mutation of the variable region of the antibody (the whole process is nicely explained &lt;a href=&quot;http://en.wikipedia.org/wiki/Antibody&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For further information on this topic I can recommend reading the following articles:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8612345&quot; rel=&quot;nofollow noreferrer&quot;&gt;Development of the immunoglobulin repertoire.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9875841&quot; rel=&quot;nofollow noreferrer&quot;&gt;Immune receptor editing: revise and select.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The reaction of the body afterwards is always the same, as you state yourself. The specificity of the adaptive immune response is &quot;only&quot; mediated by the specificity of the antibodies. This also makes the system very strong against new pathogens, since only one part of the system needs to be adapted, while the cascades behind it (like apoptosis) are always the same and can be activated fastly if needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can cause some problems, too. Think about self-antibodies, which occur in autoimmune diseases. Here the body can not distinguish between a legitimate immune response against a foreign antigen and those, which are from the own body.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-13T09:08:54.427" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19086" PostTypeId="2" ParentId="19065" CreationDate="2014-06-13T09:09:39.613" Score="2" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC411347/&quot; rel=&quot;nofollow&quot;&gt;Smith et al., 1978&lt;/a&gt;, bacterial ribosomes don't necessarily bind directly to the membrane, but through the nascent chain, in which case nothing is truly attaching to anything.. &lt;/p&gt;&#xA;" OwnerUserId="5784" LastActivityDate="2014-06-13T09:09:39.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19087" PostTypeId="2" ParentId="19073" CreationDate="2014-06-13T09:34:48.203" Score="4" Body="&lt;p&gt;Do not forget domesticated animals that we now keep as pets. It's not unreasonable to argue that the relationship between dogs/cats and humans has a symbiotic character. The pet gets foodand shelter whereas the owner benefits in other ways, e.g. companionship, deterrence of enemies, herding,...&lt;/p&gt;&#xA;" OwnerUserId="8015" LastActivityDate="2014-06-13T09:34:48.203" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19090" PostTypeId="2" ParentId="17957" CreationDate="2014-06-13T11:39:05.120" Score="2" Body="&lt;p&gt;For some statistical models, see e.g. &lt;a href=&quot;http://johncarlosbaez.wordpress.com/2012/06/21/the-mathematics-of-biodiversity-part-1/&quot; rel=&quot;nofollow&quot;&gt;The Mathematics of Biodiversity (Part 1) by John Baez&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in terms of new species, such statistical methods may not suffice - usually also our tools for discovering change. So it might be more accurate to extrapolate number of some kind species we know as a function of time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For extrapolations (though not for viruses) see e.g.:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Camilo Mora et al., &lt;a href=&quot;http://dx.doi.org/10.1371/journal.pbio.1001127&quot; rel=&quot;nofollow&quot;&gt;How Many Species Are There on Earth and in the Ocean?&lt;/a&gt;, PLOS Biology (2011).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In any case, for viruses (and many other fast-multiplying asexual creatures) defining number of species can be anywhere from tricky to impossible (for fundamental reasons, not only - practical). At best you can try to estimate their &lt;a href=&quot;http://en.wikipedia.org/wiki/Most_recent_common_ancestor&quot; rel=&quot;nofollow&quot;&gt;time to the last common ancestor&lt;/a&gt;. See also &lt;a href=&quot;http://azimuth.mathforge.org/discussion/1311/quantum-entropy-for-biodiversity/&quot; rel=&quot;nofollow&quot;&gt;links in this discussion on Azimuth&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="129" LastEditorUserId="129" LastEditDate="2014-06-13T13:08:50.120" LastActivityDate="2014-06-13T13:08:50.120" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19091" PostTypeId="2" ParentId="19083" CreationDate="2014-06-13T12:01:06.163" Score="2" Body="&lt;p&gt;I am leaving the word 'superior' aside (it's ill-defined and strongly valuing).&lt;/p&gt;&#xA;&lt;p&gt;In any way - unlikely. If any ethnic group is 'superior' (at least, intellectually) - then, ironically, Nazi main victims - &lt;a href=&quot;http://en.wikipedia.org/wiki/Ashkenazi_Jewish_intelligence&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ashkenazi Jews&lt;/a&gt;. But while there is some genetic component, it is impossible to disentangle it from societal and historical factors. Here are &lt;a href=&quot;https://delicious.com/stared/ashkenazi&quot; rel=&quot;nofollow noreferrer&quot;&gt;some links&lt;/a&gt;, is you are interested.&lt;/p&gt;&#xA;&lt;p&gt;When it comes to Germans, as far as I remember, they are not a group genetically distinct from, say Poles. Yet Slavs were considered by Nazi also an inferior race, to be enslaved or eradicated.&lt;/p&gt;&#xA;&lt;p&gt;In any case, culture and socioeconomic factors seem to be much stronger than (relatively small). In particular, for Germany itself, there was a huge difference between West and East Germany, prior to the fall of Berlin Wall. It can be hardly explained by 'genetical superiority' of West Germans. An excerpt from &lt;a href=&quot;http://www.theamericanconservative.com/articles/race-iq-and-wealth/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Race, IQ, and Wealth by Ron Unz&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Consider, for example, the results from Germany obtained prior to its 1991 reunification. Lynn and Vanhanen present four separate IQ studies from the former West Germany, all quite sizable, which indicate mean IQs in the range 99–107, with the oldest 1970 sample providing the low end of that range. Meanwhile, a 1967 sample of East German children produced a score of just 90, while two later East German studies in 1978 and 1984 came in at 97–99, much closer to the West German numbers.&lt;/p&gt;&#xA;&lt;p&gt;These results seem anomalous from the perspective of strong genetic determinism for IQ. To a very good approximation, East Germans and West Germans are genetically indistinguishable, and an IQ gap as wide as 17 points between the two groups seems inexplicable, while the recorded rise in East German scores of 7–9 points in just half a generation seems even more difficult to explain.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;See also &lt;a href=&quot;http://www.theamericanconservative.com/articles/the-east-asian-exception-to-socio-economic-iq-influences/&quot; rel=&quot;nofollow noreferrer&quot;&gt;The East Asian Exception to Socio-Economic IQ Influences&lt;/a&gt; and &lt;a href=&quot;http://www.theamericanconservative.com/articles/the-myth-of-american-meritocracy/&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Myth of American Meritocracy&lt;/a&gt; (on how ethnicity can affect admission) by the same author.&lt;/p&gt;&#xA;" OwnerUserId="129" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-06-13T12:39:32.847" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19092" PostTypeId="1" CreationDate="2014-06-13T15:36:16.303" Score="3" ViewCount="258" Body="&lt;p&gt;In a jar, where I had some orchid plants, a fungi start growing few days ago. I removed the plants and let the fungi to expand and grow more.  After some days, red drops started to appear on the surface of the fungal body (images below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know what this probably can be or recognize the fungi? Is it an antibiotic or something else?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6EjXn.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vbbML.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xTYXt.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6032" LastEditorUserId="6380" LastEditDate="2014-06-15T00:13:16.453" LastActivityDate="2014-06-15T00:13:16.453" Title="What is this red liquid produced by a fungal colony?" Tags="&lt;mycology&gt;&lt;antibiotics&gt;&lt;experiment&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19093" PostTypeId="1" AcceptedAnswerId="19281" CreationDate="2014-06-13T17:47:56.283" Score="3" ViewCount="142" Body="&lt;p&gt;In general, does seedless grape by definition contains seed or is the seed small enough that the process of ingestion creates the illusion that there is no seed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the latter is true, is the seedless grape capable of germination? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly does the fruit part of the seeded grape function as an incentive for animals to ingest it and provide nutrients for seeds in the form of feces, or can it function as nutrient itself?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="8017" LastActivityDate="2014-06-23T18:19:19.983" Title="Confusion regarding seedless grape and the normal process of germination" Tags="&lt;botany&gt;&lt;reproduction&gt;&lt;plant-physiology&gt;&lt;seeds&gt;&lt;germination&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19094" PostTypeId="2" ParentId="19081" CreationDate="2014-06-13T19:43:39.810" Score="1" Body="&lt;p&gt;The equation is correct, but there's an additional asymptotic limit to a maximum concentration of product depending on the starting concentration of NTPs, template and primer pairs in solution too. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-08-03T01:12:00.737" LastActivityDate="2014-08-03T01:12:00.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19095" PostTypeId="1" AcceptedAnswerId="19097" CreationDate="2014-06-13T19:52:10.320" Score="2" ViewCount="338" Body="&lt;p&gt;For example, what's a $dt^{sz}$ hamster? (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1144494/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1144494/&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's a Rgs9-Cre/+;gtROSA/+ mouse? (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S2212877813000719&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S2212877813000719&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="6759" LastEditorUserId="540" LastEditDate="2014-06-14T19:35:54.820" LastActivityDate="2014-06-14T19:35:54.820" Title="What are these strings used to describe animals?" Tags="&lt;genetics&gt;&lt;nomenclature&gt;&lt;research-design&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19096" PostTypeId="2" ParentId="19095" CreationDate="2014-06-13T20:26:24.910" Score="5" Body="&lt;p&gt;These strings are specific genotypes of these animals. They often denominate mutations or transgenes. &#xA;For the hamster $dt^{sz}$ stands for dystopic, the sz comes from the first denomination of this symptoms as seizure. See &lt;a href=&quot;http://books.google.de/books?id=Qq0SfGR_R_QC&amp;amp;pg=PA459&amp;amp;lpg=PA459&amp;amp;dq=dtsz%20hamster%20seizure&amp;amp;source=bl&amp;amp;ots=HY1P3hOl8V&amp;amp;sig=cDs_cxe1zti-1UYD69fGk4aj01U&amp;amp;hl=de&amp;amp;sa=X&amp;amp;ei=G16bU8eBFobXPeGEgPgE&amp;amp;ved=0CCMQ6AEwAA#v=onepage&amp;amp;q=dtsz%20hamster%20seizure&amp;amp;f=false&quot;&gt;here&lt;/a&gt; for a brief explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the mouse you have both alleles named: Rgs9-cre is a transgene, + in this context always stands for the wildtype. So this mouse has one allele of the transgene Rgs9-cre while the other allele is wildtype for it. Transgene constructs with the cre-recombinase can be inserted into the genome upon induction, which is a useful tool to modify genes. This needs to be done in mice which harbour the gtROSA transgene, which denominates a specific genetic background for the mice.&#xA;See here for more details: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1653172&quot;&gt;Promoter traps in embryonic stem cells: a genetic screen to&#xA;identify and mutate developmental genes in mice.&lt;/a&gt;&quot;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18037879&quot;&gt;Identification and targeting of the ROSA26 locus in human embryonic&#xA;stem cells.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-13T20:26:24.910" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19097" PostTypeId="2" ParentId="19095" CreationDate="2014-06-13T20:40:14.137" Score="8" Body="&lt;p&gt;Those describe the genotype of an animal (or plant, virus etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nomenclature can be very varied and domain-specific, but for those two examples:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$dt^{sz}$ is a Syrian golden hamster model with a spontaneous mutation (i.e. occurred during breeding, without specific human intervention) which gives predisposition to seizures.&lt;br&gt;&#xA;They are described in this paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1270790&quot; rel=&quot;nofollow&quot;&gt;Spontaneous seizures: a new mutation in Syrian golden hamsters. - Yoon et al. - J Hered 1976&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;SPONTANEOUS motor seizures with tonic muscle spasms and severe paralytic states have been observed in inbred line BIO® 86.93 of Syrian hamsters&#xA;  (Mesocricetus auratus auratus). These animals had been inbred for 23 generations and maintained by Bio-Research Consultants. The seizures, which last from 2 to 5 hours, can be precipitated by mild stress, and occur in&#xA;  animals between the ages of 30 days and 60 days. Breeding tests have shown that the condition is transmitted as a simple recessive; accordingly, the gene symbol&#xA;  sz is proposed for this condition.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The lowercase indicates that the mutation is recessive that is, you need to have two copies of the mutation to see its effect (its phenotype).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;dt comes from dystopia, another symptom of the mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for Rgs9-Cre/+;gtROSA/+ mouse, the genotype is a bit more complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whenever you see /+ it means that the animal is heterozygous, that is, it only carries one copy of that specific gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance these are transgenic animals producing the bacterial protein Cre under the Rgs9 promoter. A promoter is a sequence of DNA that controls the expression of a certain gene. In this case the DNA sequence for the promoter of the gene Rgs9 was attached to the DNA sequence for Cre. This new construct was then inserted into the genome of the mouse.&#xA;The result is a mouse in which the cells that normally transcribe the Rgs9 gene also produce Cre.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This mouse line was then crossed with a reporter mouse line called gtROSA26, which expresses a certain protein called $\beta$-galactosidase in a Cre-dependent manner. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The gene for the galactosidase is present in all the cells, but only where Cre is present (in our case the Rgs9 positive cells) it will be transcribed.&#xA;Eventually the crossing leads to the expression of $\beta$-galactosidase in Rgs9 positive cells. &#xA;$\beta$-galactosidase has the nice property that it can change the colour of certain chemicals to blue, which allows to easily visualize the cells that produce it. This can help you answer questions like: &quot;where is the Rgs9 gene transcribed?&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia has a neat &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene_nomenclature&quot; rel=&quot;nofollow&quot;&gt;page on Gene nomenclature&lt;/a&gt; with lots of links to nomenclature guidelines. &lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2014-06-14T08:15:02.993" LastActivityDate="2014-06-14T08:15:02.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19098" PostTypeId="2" ParentId="5680" CreationDate="2014-06-13T23:06:44.550" Score="1" Body="&lt;p&gt;The first part of your second question permits a rough calculation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The second question ( i )&lt;/strong&gt;: For humans the skin has been defined as ending at the hypoderm, which is 2-3mm deep. The average human skin has been estimated to cover an area of 1.5-2 m$^2.$ We can use 2.5 mm and 1.7 m$^2$, respectively. This gives a volume of 0.00425 m$^3$ or 4250 mL in fluid volume. The information for this calculation is at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_skin&quot; rel=&quot;nofollow&quot;&gt;Wiki site&lt;/a&gt; on human skin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Body_water&quot; rel=&quot;nofollow&quot;&gt;One estimate&lt;/a&gt; of the average total volume of fluid in a human body is 40L. Of that, 5L is blood. So roughly 1/8 of the body's fluid is blood. To a good approximation, the body is about &lt;a href=&quot;http://en.wikipedia.org/wiki/Body_fluid&quot; rel=&quot;nofollow&quot;&gt;60% water&lt;/a&gt; by weight. This is presumably a little less than the percentage of fluids generally but since these are rough numbers we can use it. So 60% of the skin is fluid/water, and 1/8$th$ of this is blood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of the 4.250 L of skin, 60% is fluid, of which 1/8 $^{th}$ is blood, so $(4.25) \cdot (0.60) \cdot \frac{1}{8} = 0.3188$ liters of blood at any given moment in the skin, subject to considerable variation no doubt. This sounds a little low but the definition of skin sort of forces this--it is only skin-deep.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://talkingphysics.wordpress.com/2012/03/07/work-done-by-the-human-heart/&quot; rel=&quot;nofollow&quot;&gt;One source&lt;/a&gt; gives an estimate of the energy expended to pump blood in a normal adult heart as &lt;a href=&quot;http://talkingphysics.wordpress.com/2012/03/07/work-done-by-the-human-heart/&quot; rel=&quot;nofollow&quot;&gt;0.5-1.0 Joule per beat&lt;/a&gt; which at 70 beats/minute amounts to 100.8 kJ/day using 1 Joule.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the heart is handling about 5 L of blood of which 0.3188 L is blood in skin, so very roughly we could estimate that $0.3188/5 = 0.0638$ or 6.38% of the work above goes toward supplying skin, i.e. 6.43 kJ/day of energy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a sanity check, if someone burns 1200 [nutritional] calories a day, which is about 5 MJ, we can see that keeping skin supplied with blood represents a small fraction of daily energy expenditure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The title question&lt;/strong&gt;: Like you, I found no study on point but that does not mean one does not exist. I can't see why anyone would do/fund such a study as the answer is unlikely to inform further work, answer any current questions, or solve any problems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The last part of your second question (ii)&lt;/strong&gt; Transporting blood to the capillaries and circulating the blood through capillaries are aspects of the same job. Dividing the work of the heart into skin/non-skin was already artificial. To further divide the work into segments this way requires some motivation because any answer would be a bad approximation. &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-06-14T13:45:34.477" LastActivityDate="2014-06-14T13:45:34.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19099" PostTypeId="1" AcceptedAnswerId="19100" CreationDate="2014-06-13T23:47:18.320" Score="2" ViewCount="79" Body="&lt;p&gt;I'm prepping an activity for my biology students on cystic fibrosis. There are about 2000 different mutations of the CFTR gene that cause CF. Since the final phenotype is pretty much the same, can I still claim that all these mutations represent different &lt;strong&gt;alleles&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I like to point out that genes tend to have more than two alleles - it's something that students really struggle with. But if every allele needs to have a different phenotype based on the standard definition, then this isn't ideal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for the help.&lt;/p&gt;&#xA;" OwnerUserId="6517" LastActivityDate="2014-06-14T08:21:42.157" Title="Does the most common definition of &quot;allele&quot; include a change in phenotype?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19100" PostTypeId="2" ParentId="19099" CreationDate="2014-06-14T00:01:14.753" Score="3" Body="&lt;p&gt;Yes, allele is an alternative form of the same gene which can be produced through any variations/mutations of a gene, such as deletion, segmental duplications, inversions, insertions through transposons, even a SNP or point mutation (&lt;a href=&quot;http://en.wikipedia.org/wiki/Allele&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Allele&lt;/a&gt;) and as correctly stated many alleles do not produce any observable/discernable phenotypic variation. A gene can have many alleles in a given population, but do not confuse allele with gene homologues (which I suspect what you were alluding to above in the second paragraph), which are similar versions of a gene such as RIN1, RIN2 and RIN3 (&lt;a href=&quot;http://homepage.usask.ca/~ctl271/857/def_homolog.shtml&quot; rel=&quot;nofollow&quot;&gt;http://homepage.usask.ca/~ctl271/857/def_homolog.shtml&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="1320" LastEditDate="2014-06-14T08:21:42.157" LastActivityDate="2014-06-14T08:21:42.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19101" PostTypeId="1" CreationDate="2014-06-14T07:43:03.750" Score="5" ViewCount="20175" Body="&lt;p&gt;People in different countries have different average heights. For example, Wikipedia's article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_height#Average_height_around_the_world&quot; rel=&quot;nofollow noreferrer&quot;&gt;human height&lt;/a&gt; states that Australian men have an average height of 177.8 cm, and Australian women 163.8 cm, whereas Japanese men have an average height of 170.7 cm, and Japanese women 158 cm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these differences in height due to environmental differences between people in different countries, or does genetic differences play a role?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, are Asian people (people from Far East countries like Japan) genetically predisposed to be on average shorter than people who are of European descent?&lt;/p&gt;&#xA;" OwnerUserId="576" LastEditorUserId="30328" LastEditDate="2017-05-08T00:19:47.217" LastActivityDate="2017-05-08T00:19:47.217" Title="Are Asian people genetically predisposed to be shorter than Europeans?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19103" PostTypeId="1" CreationDate="2014-06-14T08:25:25.203" Score="3" ViewCount="31" Body="&lt;p&gt;I'm making a thesis about pine processionary moth distribution on the regions of algeria!&#xA;i'm making tests about if there are spatial autocorrelation of this insects on the regions. &#xA;and i'm doing also hierarchical clustering of (degree of infest, small defoliation, medium defoliation, and high defoliation, and lattitude and longitude coordinates ) on each region to see the regions that have the same caracteristics on the variables i muntioned above!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem is that i need some information about the effect of geographical location and climat on this specific insect ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;i have made some statistical tests, and i have found that each year have diffirent cluster caracteristics for this regions, so can anyone help me to know why it's diffirent each year ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the final thing, if anyone could suggest to me some links, to previous some study on another country maybe , so i can take an idea of what do i have to include and do , and to compare also with my results ?&lt;/p&gt;&#xA;" OwnerUserId="8024" LastEditorUserId="3624" LastEditDate="2014-12-03T15:40:57.493" LastActivityDate="2014-12-03T15:40:57.493" Title="Classification of degree of infested areas by pine processionary moth on regions" Tags="&lt;entomology&gt;&lt;ecology&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19104" PostTypeId="1" AcceptedAnswerId="19111" CreationDate="2014-06-14T08:46:26.360" Score="1" ViewCount="178" Body="&lt;p&gt;I often noticed, after (heavy) physical activity like cycling, running, swimming or working an isotonic drink (to recover the electrolyte level) tastes less &quot;salty&quot; compared to when drinking it before the activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this possible or am I just hallucinating?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The object of this (if it's real) could be: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;to save us of taking too much salt&lt;/li&gt;&#xA;&lt;li&gt;to reduce the reluctance against salt if our body is undersupplied (with sodium ions)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My guess is, that the electrolyte or particularly the sodium (chloride) level in our body influences the cells/nerves that sense the taste for salt on our tongue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Taste_bud&quot; rel=&quot;nofollow&quot;&gt;Wikipedia says this&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Salts, sweet, sour and umami tastes causes depolarization of the taste cells, although different mechanisms are applied.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, I imagine it like this: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;If there is enough salt in our body, the cells are saturated with e.g. sodium ions (higher polarization since there are more ions)&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;NaCl&lt;/code&gt; and other salts (probably &lt;code&gt;KCl&lt;/code&gt; too) will then dissociate into &lt;code&gt;Na+&lt;/code&gt; and &lt;code&gt;Cl-&lt;/code&gt; (etc.)&lt;/li&gt;&#xA;&lt;li&gt;The &lt;code&gt;Cl-&lt;/code&gt; will then attract more &lt;code&gt;Na+&lt;/code&gt; from the cells causing deplolarization&lt;/li&gt;&#xA;&lt;li&gt;Our brain converts these signals into the proper perception&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;But maybe I'm just hallucinating... :)&lt;/p&gt;&#xA;" OwnerUserId="8012" LastEditorUserId="8012" LastEditDate="2014-06-14T21:26:15.993" LastActivityDate="2014-06-14T21:26:15.993" Title="Is the sense for salt depending on the electrolyte level in our body?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;nutrition&gt;&lt;sensation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19105" PostTypeId="1" CreationDate="2014-06-14T09:23:08.363" Score="2" ViewCount="663" Body="&lt;p&gt;&lt;a href=&quot;http://www.astrobio.net/news-exclusive/complex-mineral-surfaces-indications-life/&quot; rel=&quot;nofollow&quot;&gt;News to me&lt;/a&gt; is that about 4500 of the 4900 minerals on Earth have been created by life. What are some examples of such processes? Are some minerals formed inside the human body?&lt;/p&gt;&#xA;" OwnerUserId="8025" LastActivityDate="2014-06-14T12:12:55.847" Title="How are minerals formed by biological processes?" Tags="&lt;life&gt;&lt;minerals&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19107" PostTypeId="1" CreationDate="2014-06-14T10:15:53.343" Score="1" ViewCount="275" Body="&lt;p&gt;Ischemia is roughly defined as insufficient blood flow to a specific region of the body and in the literature it is generally considered as causing oxygen and glucose deprivation in the tissue and therefore cells. Can we induce ischemia by depriving cells from oxygen and glucose in the medium or does it require more than that and ischemia is more complicated?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;edit: i know the definition of ischemia maybe i should have said 'mimick' instead of 'induce'. Anyway, here is the better version of my question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ischemia is defined as blood flow shortage in a tissue and it is one of the main causes of non-apoptotic cell death. In an article i was reading, the authors claim that &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006291X10018486&quot; rel=&quot;nofollow&quot;&gt;they induced ischemia in the glucose-serum containing medium&lt;/a&gt;. Does this mean they deprived the cells from oxygen and thus mimicked ischemia? Is this the way to create ischemia in a cell culture? What other ways can there be? Should not cells also be deprived from glucose? &lt;/p&gt;&#xA;" OwnerUserId="1843" LastEditorUserId="1843" LastEditDate="2014-06-16T10:59:44.897" LastActivityDate="2014-06-16T10:59:44.897" Title="difference between ischemia and oxygen-glucose deprived medium" Tags="&lt;molecular-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19108" PostTypeId="2" ParentId="19107" CreationDate="2014-06-14T10:26:13.413" Score="1" Body="&lt;p&gt;&lt;strong&gt;Ischemia&lt;/strong&gt; leads to tissular hypoxia and glycopenia due to an insufficient blood flow (e.g. due to atherosclerosis or thromboembolic diseases). &lt;a href=&quot;http://cvphysiology.com/CAD/CAD005.htm&quot; rel=&quot;nofollow&quot;&gt;Ischemia &lt;strong&gt;always result in hypoxia&lt;/strong&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Hypoxia&lt;/strong&gt; can occur &lt;strong&gt;without ischemia&lt;/strong&gt; (e.g. due to anemia).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tissular &lt;strong&gt;glycopenia&lt;/strong&gt; can occur &lt;strong&gt;without ischemia&lt;/strong&gt; (e.g. due to hypoglicemia).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ischemia&quot; rel=&quot;nofollow&quot;&gt;Ischemia is a shortage in blood supply&lt;/a&gt;. Depriving cells form oxygen and glucose isn't the same as cutting their blood supply.&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-14T10:52:21.910" LastActivityDate="2014-06-14T10:52:21.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19110" PostTypeId="2" ParentId="19105" CreationDate="2014-06-14T12:12:55.847" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;News to me is that about 4500 of the 4900 minerals on Earth have been created by life.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;After reading the article, this isn't what was said.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What was said is that life increases mineral diversity on a planet, most notably through biproducts reacting with existing minerals (like Oxygen - a biproduct of photosynthesis - reacting with iron to create iron-oxide).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, life doesn't &lt;em&gt;create&lt;/em&gt; new minerals, but it does change the abundance of elements at the surface which can undergo reactions with pre-existing minerals to form other minerals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all of the 4500 &quot;new&quot; minerals on the Earth can be attributed to life. We don't know how many new mineral formations have formed because of life, but the article suggests the theory that increased surface diversity of minerals might be a good indicator of life.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2014-06-14T12:12:55.847" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19111" PostTypeId="2" ParentId="19104" CreationDate="2014-06-14T12:25:22.577" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is this possible or am I just hallucinating?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Certainly possible, but I'd peg the mechanism closer to Sensitization or De-sensitization of the neurons involved so that when you finally ingest some salt the sensation is different. The sodium and chloride levels of the ingested material wouldn't have a direct effect on the level of De-/Sensitization, but rather how low your stores are or how long you've gone without.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So, I imagine it like this....&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What you broadly described is how regular sodium receptors work. They will work that way regardless of what you've been doing, and doesn't really explain an increase or decrease in your ability to taste salt - the signals will fire either way. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check out the action of the &lt;a href=&quot;http://en.wikipedia.org/wiki/TRPV1&quot; rel=&quot;nofollow&quot;&gt;Capsaicin receptor&lt;/a&gt; and how it changes sensitivity over short periods of time. I'm betting the phenomenon you're describing will be closer to this (an increase or decrease in the number of sodium receptors in response to the abundance of salts or lack-thereof) than an immediate mechanism from the drink itself.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2014-06-14T12:25:22.577" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19113" PostTypeId="1" AcceptedAnswerId="19120" CreationDate="2014-06-14T16:02:08.410" Score="2" ViewCount="162" Body="&lt;p&gt;This big fellow came to visit my kitchen (in Hong Kong) a bit earlier.&lt;br&gt;&#xA;It is brown with some longitudinal white stripes, banana/boomerang-shaped patterns towards the middle, and an eye-like marking on each forewing tip. Picture below.&lt;br&gt;&#xA;What kind of butterfly is it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CJuTp.jpg&quot; alt=&quot;butterfly&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I helped it find the exit in the meantime, not before taking a lot more pictures.&lt;/p&gt;&#xA;" OwnerUserId="8027" LastEditorUserId="8027" LastEditDate="2014-06-18T09:23:24.550" LastActivityDate="2014-06-18T09:23:24.550" Title="What species of butterfly is this?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19114" PostTypeId="1" CreationDate="2014-06-14T16:37:32.500" Score="4" ViewCount="6163" Body="&lt;p&gt;I don't understand why three bands are found without any restriction digest. Please answer me as soon as possible.&lt;/p&gt;&#xA;" OwnerUserId="8028" LastEditorUserId="5144" LastEditDate="2016-10-10T14:13:22.390" LastActivityDate="2016-10-10T14:13:22.390" Title="Why isolated, recombinant plasmid DNA without any restriction is often detected in agarose gel electrophoresis as three DNA bands?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19115" PostTypeId="1" AcceptedAnswerId="19118" CreationDate="2014-06-14T16:40:48.717" Score="6" ViewCount="2270" Body="&lt;p&gt;Why isn't DNA like RNA; why isn't RNA like DNA, that is, helical? Why are RNA chains straight?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="1368" LastEditDate="2014-06-14T18:34:29.540" LastActivityDate="2021-01-18T08:42:03.830" Title="What makes DNA helical?" Tags="&lt;dna&gt;&lt;rna&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19116" PostTypeId="2" ParentId="19114" CreationDate="2014-06-14T16:49:47.250" Score="6" Body="&lt;p&gt;These are the three forms of the plasmid: supercoiled (smallest 3D-structure, runs fastest), linear (runs in the middle) and relaxed, nicked plasmid (runs highest). You can have another fourth band, which is the circular single stranded plasmid (runs faster than the supercoiled version). See the following figure (from this &lt;a href=&quot;http://bitesizebio.com/13524/how-to-identify-supercoils-nicks-and-circles-in-plasmid-preps/&quot; rel=&quot;nofollow noreferrer&quot;&gt;article&lt;/a&gt;, which I recommend reading):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kmGgM.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-14T16:49:47.250" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19117" PostTypeId="1" CreationDate="2014-06-14T17:04:23.573" Score="2" ViewCount="48" Body="&lt;p&gt;I have statistics on the occurence of the Pine Processionary moth (&lt;em&gt;Thaumetopoea pityocampa&lt;/em&gt;); we have the regions that are located in Algeria, infested area in percent, the defiliation degree (small, medium and high) and we have geographical location (longitude, lattitude).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The table is as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tTwhc.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is there a difference between infested areas, and is there a special pattern for the distribution of this insect? Is it known what the main drivers are for determining the distribution and abundance of this moth, and thereby why some areas are more infested than others?&lt;/p&gt;&#xA;" OwnerUserId="8024" LastEditorUserId="3624" LastEditDate="2014-06-15T19:02:03.497" LastActivityDate="2014-06-15T19:02:03.497" Title="How do climate and location affect the Pine Processionary moth?" Tags="&lt;entomology&gt;&lt;ecology&gt;&lt;environment&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19118" PostTypeId="2" ParentId="19115" CreationDate="2014-06-14T17:09:31.697" Score="10" Body="&lt;p&gt;The helix shape of DNA molecule is a consequence of its secondary structure. This refers to the bases contained in the molecule which pair, thus determining tertiary structure [1].&lt;/p&gt;&#xA;&lt;p&gt;Basepairing also occurs in RNA, so it can form a double helix. In fact, RNA is composed of short helices packed together [2]. Base pairs maintain DNA's helical structure no matter the nucleotide sequence [3].&lt;/p&gt;&#xA;&lt;p&gt;A nucleic acid strand is composed of nucleotides joined together by covalent bonds between the sugar of one nucleotide and the phosphate of the next. Adenine pairs with thymine and cytosine pairs with guanine by hydrogen bonds and form the double-stranded structure [3]. Because covalent bonds are stronger than hydrogen bonds, the double helical structure of DNA is easily broken by heat [4], but the nucleotides remain bonded together.&lt;/p&gt;&#xA;&lt;p&gt;Here is the tRNA molecule (you can see it has short helices):&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:TRNA-Phe_yeast_1ehz.png#mediaviewer/File:TRNA-Phe_yeast_1ehz.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/b/ba/TRNA-Phe_yeast_1ehz.png&quot; alt=&quot;TRNA-Phe yeast 1ehz.png&quot;&gt;&lt;/a&gt;&lt;br&gt;&quot;&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:TRNA-Phe_yeast_1ehz.png#mediaviewer/File:TRNA-Phe_yeast_1ehz.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;TRNA-Phe yeast 1ehz&lt;/a&gt;&quot; by &lt;a href=&quot;//commons.wikimedia.org/wiki/User:Yikrazuul&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;User:Yikrazuul&quot;&gt;Yikrazuul&lt;/a&gt; - Own work. Licensed under &lt;a href=&quot;https://creativecommons.org/licenses/by-sa/3.0/&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Creative Commons Attribution-Share Alike 3.0&quot;&gt;CC BY-SA 3.0&lt;/a&gt; via &lt;a href=&quot;https://commons.wikimedia.org/wiki/Main_Page&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikimedia Commons&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Here is the DNA structure:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:ADN_animation.gif#mediaviewer/File:ADN_animation.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/J3Umv.gif&quot; alt=&quot;ADN animation.gif&quot;&gt;&lt;/a&gt;&lt;br/&gt;&lt;sub&gt;(source: &lt;a href=&quot;https://upload.wikimedia.org/wikipedia/commons/8/81/ADN_animation.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikimedia.org&lt;/a&gt;)&lt;/sub&gt;&lt;br/&gt;&lt;br&gt;&quot;&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:ADN_animation.gif#mediaviewer/File:ADN_animation.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;ADN animation&lt;/a&gt;&quot; by brian0918™ - Own work. Licensed under Public domain via &lt;a href=&quot;https://commons.wikimedia.org/wiki/Main_Page&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikimedia Commons&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &amp;quot;Nucleic acid double helix,&amp;quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Nucleic_acid_double_helix&amp;amp;oldid=609435163&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Nucleic_acid_double_helix&amp;amp;oldid=609435163&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &amp;quot;RNA,&amp;quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=RNA&amp;amp;oldid=612056511&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=RNA&amp;amp;oldid=612056511&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &amp;quot;DNA,&amp;quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=DNA&amp;amp;oldid=611891356&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=DNA&amp;amp;oldid=611891356&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &amp;quot;Nucleic acid thermodynamics,&amp;quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Nucleic_acid_thermodynamics&amp;amp;oldid=606379256&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Nucleic_acid_thermodynamics&amp;amp;oldid=606379256&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="15950" LastEditDate="2021-01-18T08:42:03.830" LastActivityDate="2021-01-18T08:42:03.830" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="19119" PostTypeId="2" ParentId="19115" CreationDate="2014-06-14T18:30:39.673" Score="8" Body="&lt;p&gt;RNA (single or double stranded) actually can and does form a helix in the absence of certain complex 3D structures. The RNA helix is typically A-form, as opposed to B-form for typical DNA. The A-form helix is right-handed like the B-form but is more compact (2.6 Å rise versus 3.4 Å) and wider (26 Å diameter vs 20 Å). The differing helices arise from the 2'-OH present in RNA which sterically hinders the formation of a B-form helix (by constricting the ribose to C-3' endo pucker).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/X84s7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[From Wikipedia. Double stranded DNA helices. A-form is on the left, B-form in the middle and Z-form on the right. There are other forms not illustrated here.]&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/a/a4/Pre-mRNA-1ysv-tubes.png&quot; height=&quot;500&quot; /&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[From Wikipedia. A hairpin loop (the result of intrastrand base pairing in a single RNA molecule) that has adopted an A-form helix.]&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UGljc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[Just emphasizing that a single strand nucleic acid, even without secondary structure, also forms helices.]&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The helices of both DNA and RNA form in aqueous solution because of the hydrophobic and aromatic (which also implies planar) nature of the bases themselves. By forming a helix, the bases within one strand come closer together which is thermodynamically more favourable because of stacking interactions between the conjugated ring systems as well as the exclusion of water from their hydrophobic surfaces (which thus increases entropy). &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.180" LastActivityDate="2015-07-10T06:07:05.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19120" PostTypeId="2" ParentId="19113" CreationDate="2014-06-14T18:35:10.827" Score="6" Body="&lt;p&gt;It isn't a butterfly, it's a saturnid moth -  &lt;a href=&quot;http://en.wikipedia.org/wiki/Samia_canningi&quot;&gt;&lt;em&gt;Samia canningi&lt;/em&gt;&lt;/a&gt;, also known as the wild eri silkworm moth.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a good image on Flickr &lt;a href=&quot;https://www.flickr.com/photos/thomascalame/8407970246/&quot;&gt;here&lt;/a&gt;, and some more information &lt;a href=&quot;http://www.saturniidae-web.de/Samia%20canningi.htm&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-06-14T18:35:10.827" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19121" PostTypeId="1" CreationDate="2014-06-14T20:51:38.903" Score="1" ViewCount="39" Body="&lt;p&gt;Where can I get a good biochemical overview of dystonia? I will be working in a research lab that focuses on dystonia and I would like to not be clueless. &lt;/p&gt;&#xA;" OwnerUserId="6759" LastActivityDate="2014-06-15T00:42:47.467" Title="Primers on Dystonia" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;mice&gt;&lt;research-process&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19123" PostTypeId="1" CreationDate="2014-06-14T23:13:49.460" Score="3" ViewCount="86" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Homozygous DYT1 mutation carriers have not been reported in humans.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Does this mean that the mode of inheritance for dystonia (DYT1) is autosomal dominant? This to me implies that if one has both alleles for dystonia, then one must also have the phenotype, as people with both alleles &lt;em&gt;cannot&lt;/em&gt; be carriers. &lt;/p&gt;&#xA;" OwnerUserId="6759" LastActivityDate="2014-06-15T00:21:12.763" Title="Mode of inheritance - DYT1 Dystonia" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19124" PostTypeId="1" CreationDate="2014-06-07T01:17:02.353" Score="9" ViewCount="94" Body="&lt;p&gt;There are many sources of nitrogen which eventually get deposited out of the atmosphere and onto the land/surface.  Typically higher levels of nitrogen compounds are emitted near urban and roadway locations, raising the levels of nitrogen deposited on the nearby landscape.  &lt;strong&gt;What are the ecological effects of moderately high (at least double background) and prolonged concentrations (10+ years) of nitrogen deposition on an ecosystem?&lt;/strong&gt;  Please be specific about which type of ecosystem your comments are intended.&lt;/p&gt;&#xA;" OwnerUserId="8040" OwnerDisplayName="farrenthorpe" LastEditorUserId="3952" LastEditDate="2014-07-27T20:37:00.203" LastActivityDate="2014-07-27T20:37:00.203" Title="What are the ecological effects of moderately high and prolonged concentrations of nitrogen deposition on an ecosystem?" Tags="&lt;biochemistry&gt;&lt;ecology&gt;&lt;climate-change&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19125" PostTypeId="2" ParentId="19123" CreationDate="2014-06-15T00:21:12.763" Score="3" Body="&lt;p&gt;Your description is correct. Most genes do not show complete dominance as outlined in Mendelian genetics and inheritance is almost always more complicated than a simple 1 gene/2 allele system. The mutation you're studying is classified as autosomal dominant but even heterozygotes may not display the phenotype. The proportion of the population that has the mutation AND displays the mutant phenotype is called the penetrance and, for DYT1, has been estimated at around 30%. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.omim.org/entry/128100?search=Dyt1&amp;amp;highlight=dyt1&quot; rel=&quot;nofollow&quot;&gt;http://www.omim.org/entry/128100?search=Dyt1&amp;amp;highlight=dyt1&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-06-15T00:21:12.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19126" PostTypeId="2" ParentId="19121" CreationDate="2014-06-15T00:42:47.467" Score="2" Body="&lt;p&gt;A good article on the pathophsiology is, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pathophysiological basis of dystonias, Nature Reviews Neuroscience 9, 222-234 (March 2008) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a review of the treatment,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Treatment of dystonia, lancet neurology, Volume 5, Issue 10, October 2006, Pages 864–872.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A comprehensive textbook on movement disorders in general is The oxford textbook of movement disorders&lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-15T00:42:47.467" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19127" PostTypeId="2" ParentId="19053" CreationDate="2014-06-15T11:10:52.643" Score="2" Body="&lt;p&gt;Direct replacement of a protein through oral supplementation is extremely unlikely. Our digestive tract is designed to break down proteins into their constituent amino acids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the stomach pepsin breaks proteins into polypeptides which then pass into the small intestine. At this point (second part of duodenum) multiple enzymes (proteases) enter having been released from the pancreas in response to eating. These enzymes further reduced the polypeptides into smaller components such as you end up with component parts of the original protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These component parts are then transported across the intestine into the blood through cells lining the intestinal lumen (enterocytes). Enterocytes also have proteolytic action on long chains of amino acids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a result of this process, the original structure of the ingested protein is destroyed. However you do end up with the constituent amino acids. If your fillagrin or any other protein deficiency is as a result of lack of nutrients then in response your body may be able to synthesise the required protein. If on the other hand your deficiency is due to a gene defect, despite having the building blocks for the protien you will continue be deficient.&lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-15T11:10:52.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19128" PostTypeId="2" ParentId="17190" CreationDate="2014-06-15T11:40:42.927" Score="3" Body="&lt;p&gt;No this is not currently possible as eye replacement surgery is not possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Colour blindness is either congenital genetic, such as your X linked forms, or due to a degenerative condition such as retinitis pigmentosa. It can also be acquired through retinal damage or brain injury such as stroke effecting specific areas of the visual cortex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the major problems in restoring colour vision would be that the brain itself may not have the required structure to interpret the signals. The visual cortex is 'patterned' as we develop beginning inside the womb and continuing as a baby. During this process neurological connections in the visual cortex are stimulated so that we develop the necessary networks to interpret the signals from our eyes. If we lack the input of our eyes the brain conducts something called neural pruning where the unused neural connections are destroyed never to be regrown. Therefore if you lack visual stimulus for colour you prune these connections. If we were to somehow replace this colour stimulus later our brains would not be able to interpret it. In a somewhat similar circumstance to this it has been found with individuals who are born with congenital cataracts. If they have their cataracts fixed later in life having spent their childhood blind, despite being able to 'see' they cannot interpret the images they receive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In individuals who loose there colour due to degenration of the retina, if we were able to repair the retina, through stem cell or transplant therapy then perhaps colour vision would return.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An individual who lost colour vision due to brain injury cannot have their colour vision returned as we cannot repair such injuries.&lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-15T11:40:42.927" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19129" PostTypeId="2" ParentId="19051" CreationDate="2014-06-15T15:08:43.433" Score="7" Body="&lt;p&gt;Clostridium botulinum toxin is present ubiquitously in soil. As such it is more than plausible that hay bails, which come into contact with soil can and I should expect almost probably will be infected with these bacteria. However it is not the mere presence of the bacteria itself which causes poisoning, it is the toxins they produce when the appropriate conditions are met. These toxins are produced as a consequence of spore formation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Traditionally in human cases, the presence of toxins has been linked to home canned foods, where there is an anaerobic environment with a ph &amp;lt; 4.5 (&lt;a href=&quot;http://cid.oxfordjournals.org/content/41/8/1167.full&quot; rel=&quot;nofollow&quot;&gt;http://cid.oxfordjournals.org/content/41/8/1167.full&lt;/a&gt;). It is conceivable that such an anaerobic environment exists within a hay bail (even if not wrapped). The following site from the ontario minestry agriculture and food (&lt;a href=&quot;http://www.omafra.gov.on.ca/english/livestock/horses/facts/info_haylage.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.omafra.gov.on.ca/english/livestock/horses/facts/info_haylage.htm&lt;/a&gt;) suggest that the pH certain methods of hay bailing have pH &amp;lt; 5. This would seemingly confirm hay as potential source for botulinum toxins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regards to testing the hay for C. botulinum I would expect there to be a very high chance of finding this, due to soil contamination, however this does not imply this was a definite source for poisoning. A more conclusive test would be for the toxin. So in summary it is logical to suggest that hay could be the toxin source, but this does not mean it was the source. &lt;/p&gt;&#xA;" OwnerUserId="8034" LastEditorUserId="8034" LastEditDate="2014-06-16T18:22:15.067" LastActivityDate="2014-06-16T18:22:15.067" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19130" PostTypeId="2" ParentId="19051" CreationDate="2014-06-15T15:46:47.907" Score="5" Body="&lt;p&gt;As an addendum to Spinorial's answer, and after some research, the Center for Food Security and Public Health &lt;em&gt;specifically&lt;/em&gt; lists hay / grass / &lt;strong&gt;decaying vegetable matter&lt;/strong&gt; as a potential source for &lt;em&gt;C. botulinum&lt;/em&gt; growth in their (very informative) &lt;a href=&quot;http://www.cfsph.iastate.edu/Factsheets/pdfs/botulism.pdf&quot; rel=&quot;nofollow&quot;&gt;Botulism PDF&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;All species of Clostridium can produce spores, dormant &#xA;  forms  of  the  organism  that  are  highly  resistant  to &#xA;  disinfectants,  heat  and  environmental  conditions  that  kill &#xA;  vegetative  cells. These  spores  can  survive  for many  years &#xA;  until  favorable  conditions  allow  them  to  germinate  and &#xA;  grow. C. botulinum spores are common in the environment...&lt;br&gt;&#xA;  ...&#xA;  Different  strains  or  groups  of  C.  botulinum  may  have &#xA;  somewhat  different  requirements. For  instance,  the  acidity &#xA;  necessary  to  inhibit C. botulinum  type C strains  is reported &#xA;  to be pH 5.1 to 5.6, but other organisms can survive a lower &#xA;  pH. Each group also has an optimal, minimal and maximal &#xA;  temperature  for  growth.  For  example,  some  group  II &#xA;  organisms  may  be  able  to  grow  in  foods  at  refrigeration &#xA;  temperatures  (3-4°C/ 37-39°F), but group  I organisms  and &#xA;  type  C  toxin-producing  strains  are  inhibited.  Because  C. &#xA;  botulinum  does  not  compete  well  with  other &#xA;  microorganisms,  growth  is  more  likely  to  occur  if  other &#xA;  bacteria  and  molds  have  been  killed  or  inhibited.  C. &#xA;  botulinum  spores  can  survive  cooking  and  some  food-&#xA;  processing  conditions  that  kill  vegetative  cells,  then &#xA;  germinate and grow in the cooked food. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As for your question...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is it possible to logically conclude that Botulinum toxin could, or could not, be created and/or survive in a bale of hay meeting the above criteria? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Could the toxin survive? Probably. The toxin itself isn't particularly hearty, &lt;strong&gt;BUT&lt;/strong&gt;...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could the &lt;em&gt;spores&lt;/em&gt; survive (and go on to create the toxin)? &lt;strong&gt;Definitely&lt;/strong&gt;. The spores survive direct heating/boiling, very low pH environments, and desiccation. For instance, botulism from canned foods &lt;em&gt;can&lt;/em&gt; occur from eating the food (and toxin) directly - but you're supposed to throw it out if it look suspicious because even if you cook it and inactivate the toxin, the spores are still present after cooking. The spores can find anaerobic environments inside the body and germinate, then produce toxin afterwards.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2014-06-15T16:09:55.943" LastActivityDate="2014-06-15T16:09:55.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19131" PostTypeId="2" ParentId="19101" CreationDate="2014-06-15T23:16:41.043" Score="5" Body="&lt;p&gt;&lt;strong&gt;Note:&lt;/strong&gt; This is too long for a comment, so I will post it as an answer, even though it is merely an example and not a full answer to your question. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;An example of the environmental influence on human body height can be found in the statistics assembled by the Swedish conscription service from 1840s to 2010 (when general conscription ended). During this time the average height of Swedish men (aged between 18-21) increased from 167.4 cm (in 1841-45) to 180.2 (in 2004), an increase of 12.8 cm or 7.6% (&lt;a href=&quot;http://pediatrisk-endokrinologi.no/2008/1/Werner_2008_1.pdf&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Werner. 2008. Sekulära förändringar i kroppslängd. Pediatrisk Endokrinologi 2008;6-15&quot;&gt;Werner 2008&lt;/a&gt;, unfortunately in Swedish, but tables 2 and 3 should be understandable). Here is a graph of the data found in the paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uwoh5.png&quot; alt=&quot;Height of Swedish men at conscription&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During this time Sweden has gone from what would have been a bottom-20 position in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_height#Average_height_around_the_world&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia list of average human heights&lt;/a&gt; (close to contemporary India or Mexico) to a top-10 position. This is clearly not due to changes in the genetics of the population, but to changes in the environment (probably mainly due to nutrition). I know that many countries have gone through a similar development, and this is usually refered to as a secular change or trend in body height and weight (see e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/503084&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Roche. 1979. Secular trends in human growth, maturation, and development. Monogr Soc Res Child Dev 44(3-4):1-120&quot;&gt;Roche, 1979&lt;/a&gt; and &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/%28SICI%291096-8644%28200004%29111:4%3C545::AID-AJPA9%3E3.0.CO;2-X/abstract&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Loesch et al. 2000. Secular trend in body height and weight of Australian children and adolescents. American Journal of Physical Anthropology 111(4): 545-56&quot;&gt;Loesch et al., 2000&lt;/a&gt; for further examples).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nothing of this naturally contradicts that genetics is a powerful determinant of human height. However, it shows that the average height in two countries cannot be compared in a meaningful way (at least if you want to infer genetic differences) without knowing something about the nutrition status and the average living conditions in both countries. The situation is rather that genetics is setting the limits of potential height, but that environmental factors will determine the actual outcome. This is also discussed in the paper above, but there are certainly better references to be found in English. In the reference list (#9, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8964861&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Hattori et al. 1996. Decreased insulin-like growth factor I receptor expression and function in immortalized African Pygmy T cells. J Clin Endocrinol Metab 81(6):2257-63.&quot;&gt;#10&lt;/a&gt;) you can also find examples of how there are also well-known genetic determinants of e.g. short stature in some human populations (in this case decreased insulin-like growth factor I receptor expression and function in African Pygmys, see ref &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8964861&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Hattori et al. 1996. Decreased insulin-like growth factor I receptor expression and function in immortalized African Pygmy T cells. J Clin Endocrinol Metab 81(6):2257-63.&quot;&gt;#10&lt;/a&gt;)     &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-10-17T09:28:56.460" LastActivityDate="2014-10-17T09:28:56.460" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19132" PostTypeId="2" ParentId="17898" CreationDate="2014-06-16T01:14:39.677" Score="1" Body="&lt;p&gt;If your data came from a single lab and a standard protocol gcrma normalisation is a good method to use (and comes with the affy R package); if the arrays are of U133A or HGU133plus2 types frozen RMA may be a good method to use. Finally you can check for and control for batch effects using ComBat and use the corrected expression data.&lt;/p&gt;&#xA;" OwnerUserId="6726" LastActivityDate="2014-06-16T01:14:39.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19133" PostTypeId="1" AcceptedAnswerId="19134" CreationDate="2014-06-14T08:50:04.947" Score="1" ViewCount="2615" Body="&lt;p&gt;Most antiandrogens inhibit DHT. DHT is connected to testosterone. [1] shows a beneficial effect on prostate cancer which can be caused by DHT. However, according to [2] garlic also increases testosterone. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the effects of garlic on Dihydrotestosterone (DHT) or 5α-dihydrotestosterone? Can it be used as an antiandrogen?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] Hsing AW, Chokkalingam AP, Gao YT, et al. Allium vegetables and risk of prostate cancer: A population-based study. Journal of the National Cancer Institute 2002; 94(21):1648–1651. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] Oi, Y; Imafuku, M; Shishido, C; Kominato, Y; Nishimura, S; Iwai, K (Aug 2001). &quot;Garlic supplementation increases testicular testosterone and decreases plasma corticosterone in rats fed a high protein diet&quot;. The Journal of nutrition 131 (8): 2150–6.&lt;/p&gt;&#xA;" OwnerUserId="8029" OwnerDisplayName="Alex" LastActivityDate="2014-06-16T03:01:43.487" Title="What are garlic's effects on DHT?" Tags="&lt;cancer&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19134" PostTypeId="2" ParentId="19133" CreationDate="2014-06-14T09:30:58.133" Score="1" Body="&lt;p&gt;Garlic may affect testosterone metabolism. Its beneficial effect on prostate cancer is not attributed to this, but it is attributed to the direct effect on prostate cancer cells.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;What is garlic's connection to DHT?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Cytochrome P450 enzymes.&lt;/strong&gt; Diallylsulfide, a constituent of garlic, suppresses oxidative demethylation by competitively inhibiting cytochrome P450 2E1, an enzyme that activates carcinogens. Since testosterone metabolism occurs through the mixed function oxidase cytochrome P450 system, garlic &lt;em&gt;may&lt;/em&gt; affect the rates of metabolism of testosterone and dihydrotestosterone. The metabolism of testosterone is catalized by inducible P450 1A1, 1A2, 3A3, 3A4 and 3A5 enzymes. These mixed function oxidases can be modulated by a wide variety of environmental facts and dietary constituents. Little is known about the potential for modifying testosterone risk or its treatment modality by administration of garlic constituents &lt;sup&gt;[1]&lt;/sup&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;S-allylcysteine (SAC), a potent compound derived from garlic, suppressed the proliferation of PC-3 cells and led to cell cycle arrest at the G0/G1 phases, as well as induced cell apoptosis, which was accompanied by the decreased expression of Bcl-2 and increased expression of Bax and caspase 8. This demonstrates the chemopreventive activity of SAC in vitro, and that SAC may be a promising candidate for prostate cancer treatment &lt;sup&gt;[2, 4]&lt;/sup&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Diallyl disulfide (DADS) is another major component of an oil-soluble allyl sulfide garlic (Allium sativum) derivative. Inhibitory effects of DADS on prostate carcinoma LNCaP cells motility and invasiveness were found to be associated with increased tightness of the tight junctions (TJ), which was demonstrated by an increase in transepithelial electrical resistance (TER) &lt;sup&gt;[3, 4]&lt;/sup&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Paul A. LaChance. &lt;a href=&quot;http://www.google.com/books?lr=&amp;amp;id=-2cnNsg-hfkC&amp;amp;oi=fnd&amp;amp;pg=PA177&amp;amp;dq=garlic%20Dihydrotestosterone&amp;amp;ots=Dw5wcVdqMZ&amp;amp;sig=epkHiZKLTEieb44k-hNPHNb2cXU&amp;amp;redir_esc=y#v=onepage&amp;amp;q=garlic%20Dihydrotestosterone&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Nutraceuticals: Designer Foods III: Garlic, Soy and Licorice.&lt;/em&gt;&lt;/a&gt; John Wiley &amp;amp; Sons, 2008. Pages 177-180.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Liu Z, Li M, Chen K, Yang J, Chen R, Wang T, Liu J, Yang W, Ye Z. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22052207&quot; rel=&quot;nofollow noreferrer&quot;&gt;S-allylcysteine induces cell cycle arrest and apoptosis in androgen-independent human prostate cancer cells.&lt;/a&gt; Mol Med Rep. 2012 Feb;5(2):439-43. doi: &lt;a href=&quot;http://dx.doi.org/10.3892/mmr.2011.658&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.3892/mmr.2011.658&lt;/a&gt;. PubMed PMID: 22052207.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Shin DY, Kim GY, Kim JI, Yoon MK, Kwon TK, Lee SJ, Choi YW, Kang HS, Yoo YH, Choi YH. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20600798&quot; rel=&quot;nofollow noreferrer&quot;&gt;Anti-invasive activity of diallyl disulfide through tightening of tight junctions and inhibition of matrix metalloproteinase activities in LNCaP prostate cancer cells.&lt;/a&gt; Toxicol In Vitro. 2010 Sep;24(6):1569-76. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.tiv.2010.06.014&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1016/j.tiv.2010.06.014&lt;/a&gt;. PubMed PMID: 20600798.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Bhandari P. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24860728&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dietary botanicals for chemoprevention of prostate cancer.&lt;/a&gt; J Tradit Complement Med. 2014 Apr;4(2):75-6. doi: &lt;a href=&quot;http://dx.doi.org/10.4103/2225-4110.130371&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.4103/2225-4110.130371&lt;/a&gt;. PubMed PMID: 24860728.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" OwnerDisplayName="Cornelius" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-06-14T09:30:58.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19135" PostTypeId="1" CreationDate="2014-06-16T06:08:13.423" Score="1" ViewCount="1605" Body="&lt;p&gt;What is the mechanism of antiperistalsis that occurs during vomiting? Why the peristaltic waves normally don't propagate in anal to oral direction? Please give logical explanation with authentic sources. :)&lt;/p&gt;&#xA;" OwnerUserId="8041" LastActivityDate="2014-06-26T16:01:44.490" Title="Mechanism of antiperistalsis" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19136" PostTypeId="1" AcceptedAnswerId="19145" CreationDate="2014-06-16T06:13:43.003" Score="4" ViewCount="604" Body="&lt;p&gt;Why is there less protein loss via urine in case of nephritic syndrome than in case of nephrotic syndrome?&lt;/p&gt;&#xA;" OwnerUserId="8041" LastActivityDate="2014-06-16T18:53:42.107" Title="What is the reason behind more severe proteinuria in nephrotic syndrome than in nephritic syndrome?" Tags="&lt;physiology&gt;&lt;pathology&gt;&lt;pathophysiology&gt;&lt;kidney&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19137" PostTypeId="1" AcceptedAnswerId="19140" CreationDate="2014-06-16T08:56:56.193" Score="4" ViewCount="310" Body="&lt;p&gt;Several days ago, in a bush I found the fungus as attached which is about 25cm in height and does not look like an edible mushroom:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8jAFO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any one has an idea of its scientific name and other details?&lt;/p&gt;&#xA;" OwnerUserId="8042" LastEditorUserId="8042" LastEditDate="2014-06-21T23:47:22.770" LastActivityDate="2014-06-21T23:47:22.770" Title="What is the scientific name of such a fungus?" Tags="&lt;mycology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19139" PostTypeId="2" ParentId="17742" CreationDate="2014-06-16T09:41:13.443" Score="0" Body="&lt;p&gt;I found the answer to my own question&#xA;It was formulated in a Nature publication by Mathias Mann, a pope in Proteomics:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why are peptides, and not proteins, sequenced?&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;After protein purification, the first step is to convert proteins to a&#xA;  set of peptides using a sequence-specific protease. Even though mass&#xA;  spectrometers can measure the mass of intact proteins, there are a&#xA;  number of reasons why peptides, and not proteins, are analysed in&#xA;  proteomics. Proteins can be difficult to handle and might not all be&#xA;  soluble under the same conditions (it should be noted here that many&#xA;  detergents interfere with MS, because they ionize well and are in a&#xA;  huge excess relative to the proteins). In addition, the sensitivity of&#xA;  the mass spectrometer for proteins is much lower than for peptides,&#xA;  and the protein might be processed and modified such that the&#xA;  combinatorial effect makes determining the masses of the numerous&#xA;  resulting isoforms impossible. Furthermore, it is not easy to predict&#xA;  from the sequence what the mass of a mature, correctly modified&#xA;  protein will be or, conversely, which protein might have given rise to&#xA;  a measured protein mass. Most importantly, if the purpose is to&#xA;  identify the protein, sequence information is needed and the mass&#xA;  spectrometer is most efficient at obtaining sequence information from&#xA;  peptides that are up to approx20 residues long, rather than from whole&#xA;  proteins. Nevertheless, with very specialized equipment, it is&#xA;  becoming possible to derive partial sequence information from intact&#xA;  proteins, which can then be used for identification purposes or the&#xA;  analysis of protein modifications in an approach called 'top-down'&#xA;  protein sequencing&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6872" LastActivityDate="2014-06-16T09:41:13.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19140" PostTypeId="2" ParentId="19137" CreationDate="2014-06-16T09:59:44.223" Score="3" Body="&lt;p&gt;This looks pretty much like a Coprinus comatus (also known as: shaggy ink cap, lawyer's wig, or shaggy mane) to me. You can see the characteristic ring around the stipe of the fungus (see image below from &lt;a href=&quot;http://de.wikipedia.org/wiki/Schopf-Tintling&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;). The fungus is edible and is also cultivated in China for this purpose. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Coprinus_comatus&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CdcYb.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-16T09:59:44.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19141" PostTypeId="1" CreationDate="2014-06-16T10:28:28.123" Score="2" ViewCount="129" Body="&lt;p&gt;I am trying to build a local implementation of dbSNP. I would like to know the descriptions of tables listed on &lt;a href=&quot;ftp://ftp.ncbi.nlm.nih.gov/snp/database/organism_data/human_9606&quot; rel=&quot;nofollow&quot;&gt;ftp://ftp.ncbi.nlm.nih.gov/snp/database/organism_data/human_9606&lt;/a&gt; and on &lt;a href=&quot;ftp://ftp.ncbi.nlm.nih.gov/snp/database/shared_data/&quot; rel=&quot;nofollow&quot;&gt;ftp://ftp.ncbi.nlm.nih.gov/snp/database/shared_data/&lt;/a&gt;. I tried to use the search on this webpage : &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/SNP/snp_db_list_table.cgi&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/SNP/snp_db_list_table.cgi&lt;/a&gt; which is supposed to be a data dictionary for all tables and columns, but I think it is outdated. There are many tables which do not have any definition. Also, there are tables in this dictionary that are not in the ftp site at all. Does anyone know of any better dictionary for the dbSNP database tables?&lt;/p&gt;&#xA;" OwnerDisplayName="user6417" LastActivityDate="2014-06-16T10:28:28.123" Title="dbSNP database table desciptions" Tags="&lt;bioinformatics&gt;&lt;database&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19143" PostTypeId="2" ParentId="3497" CreationDate="2014-06-16T18:17:42.567" Score="2" Body="&lt;p&gt;Torticollis can occur for several reasons, one of which is a side effect of certain drugs. Rather than highlight one specific drug it is perhaps better to talk about the mechanism of action by which this occurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Torticollis in a drug induced form is classed as an extrapyramidial side effect. Classically results from some medications which have anti-dopaminergic effects. The neurotransmitter dopamine is important for the regulation of movement. Different medications have different degrees of anti-dopaminergic effect. To complicate things further there are several different types of dopamine receptors and different drugs have different effects depending on their action on these receptors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Classically drugs that have been associated with extrapyramidial side effects are some of the antipsychotics but there are case reports of this with trycyclics &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC489096/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC489096/&lt;/a&gt; however this appears to be a very rare, see &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0924977X97004057&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0924977X97004057&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paradoxical treatment of torticollis might be dependent on the cause of the condition.  Tricyclic anti-depressants have anti-cholinergic effects, i.e. they block the effects of the neurotransmitter acetylcholine. This neurotransmitter works in opposition to dopamine in the basal ganglia (part of the brain responsible for movement control) as such might be used when the dystonia is as a result of doperminergic disregulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are at all concerned that you may be suffering side effects of any medication, then I highly recommend that you go and discuss this matter with your doctor. The above  is a simplified explanation of some of the reasons why these side effects may occur. It is not intended as information for the purposes of self diagnosis and treatment. &lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-16T18:17:42.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19144" PostTypeId="1" CreationDate="2014-06-16T18:43:24.450" Score="2" ViewCount="451" Body="&lt;p&gt;I'm having little trouble studying general relativity or quantum field theory, but remembering all the amino acids and being able to think about them is something that's completely, utterly and absolutely, defeated me...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do I think about the &lt;a href=&quot;http://en.wikipedia.org/wiki/Amino_acid&quot; rel=&quot;nofollow&quot;&gt;amino acids&lt;/a&gt;, &lt;strong&gt;without any memorization&lt;/strong&gt;, and be able to '&lt;strong&gt;derive&lt;/strong&gt;' all the names, all the categories they fit into, and their important properties? Memorizing some crazy mnemonic is of no help when it says nothing about the amino acids, I can't memorize it without meaning that explains a lot of things. I ultimately just want to be able to read Albert's Molecular Cell Biology and appreciate it, but I can't without conquering this little issue! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a side note regarding memorization tricks: is there a mnemonic scheme for the amino acids analogous to the &lt;a href=&quot;http://web.mit.edu/course/8/8.593/spring10/bk/on_MRS_Thermodynamic_Mnemonic.pdf&quot; rel=&quot;nofollow&quot;&gt;thermodynamical Zhao square&lt;/a&gt;, (which gives all the info you need about basic thermo by drawing lines and squares)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help is greatly appreciated, thank you.&lt;/p&gt;&#xA;" OwnerUserId="8049" LastEditorUserId="8049" LastEditDate="2014-06-17T00:07:59.310" LastActivityDate="2018-06-28T05:50:30.100" Title="Understanding the Amino Acids" Tags="&lt;amino-acids&gt;" AnswerCount="2" CommentCount="10" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19145" PostTypeId="2" ParentId="19136" CreationDate="2014-06-16T18:53:42.107" Score="5" Body="&lt;p&gt;It is to do with the extend of the damage to the glomerulus. In nephrotic syndromes the glomerulus is damaged so that there is death of the podocytes. This happens to sufficiently high number of podocytes so that large proteins such as albumin and clotting factors can leak out causing large proteinuria. Damage to the basement membrane may also occur, such as in minimal change, where there is a loss of charge on the basement membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In nephritic syndrome the damage is as a result of inflammation which does not lead to the same structural damage as in nephrotic syndrome, therefore there is not leakage of protein to the same degree. &lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-16T18:53:42.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19146" PostTypeId="1" AcceptedAnswerId="19528" CreationDate="2014-06-16T19:01:26.093" Score="1" ViewCount="236" Body="&lt;p&gt;I read an argument that 1-3% of lymph is in peripheral blood.&#xA;However, I am not sure if this lymph is about lymphocytes in peripheral blood; not lymph itself.&#xA;Lymph gets exchanged between capillaries through Starling law powered by the heart and Frank-Starling mechanism.&#xA;In this way, it makes sense that some lymph is leaking out from capillaries into the bolod.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can lymph be in the peripheral blood?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-07-08T11:25:19.440" Title="Can lymph be in peripheral blood?" Tags="&lt;physiology&gt;&lt;hematology&gt;&lt;lymphatic-system&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19147" PostTypeId="2" ParentId="19144" CreationDate="2014-06-16T19:09:27.740" Score="5" Body="&lt;p&gt;I'm sure there are lots of ways of handling this, but there are only 20 of them (more or less).  I really wanted to figure out how the amino acids resulted in the resulting protein structure.  So I started to break them down into categories.  The categories cannot draw boundaries exactly since one amino acid might belong to several categories in a unique way, but it starts to give you a sense of what the sidechains do.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Aliphatic : G A L I V M P&lt;br&gt;&#xA;  Aromatic : F Y W H&lt;br&gt;&#xA;  Polarizable : F Y W H M C R&lt;br&gt;&#xA;  Polar: S T Q N D E K C&lt;br&gt;&#xA;  Small: A S T G C&lt;br&gt;&#xA;  Large : F Y W H R K&lt;br&gt;&#xA;  Strong Structural variation: P G&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;you still have to memorize them eventually, but you can make it easier to put them in categories and in these groups its easier to bring them to mind. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-06-16T23:32:14.860" LastActivityDate="2014-06-16T23:32:14.860" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19148" PostTypeId="2" ParentId="19144" CreationDate="2014-06-16T19:13:02.547" Score="3" Body="&lt;p&gt;The question is slightly unclear but will do my best to answer it. I'm not a purist as a biochemist and I can tell you when it comes to biology, there are just certain information you have to memorise and one such instance is AA names. You can drive the AA full chemical name (and its properties such as charge, hydrophilic/hydrophobicity) from its molecular structure but such an approach is far far harder than to remember simple names such as A = alanine, S = serine, P = proline etc! There are some odd ones like Y, which is tyrosine but again the only reason they chose letter Y (second letter in tyrosine) was because (the first) letter T was used for threonine. If you want information on AA and their properties look at this page (&lt;a href=&quot;https://web.archive.org/web/20150302034529/http://www.bio.davidson.edu/biology/aatable.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://web.archive.org/web/20150302034529/http://www.bio.davidson.edu/biology/aatable.html&lt;/a&gt;), but I'm curious as to why you need to know individual AA properties. I don't suggest it is not important but AA property makes more sense in terms of its context in a protein sequence as it interacts with other AA properties and within a 3D protein structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Saying that AA names taken at face value do not make sense since it is not telling information about their property, although true, is broadly similar to saying protein names taken at face value do not make sense, again kind of true, because they do not say anything about their function (not true all the time but mostly true). To me this is the wrong way of looking at it. The designations for AA names were made as they were easier to memorise/refer to (and consequently become aware of their properties e.g. Y is capable of becoming phosphorylated) just as it is easier to refer to protein by its name and not its full AA sequence.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="9686" LastEditDate="2018-06-28T05:50:30.100" LastActivityDate="2018-06-28T05:50:30.100" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="19149" PostTypeId="2" ParentId="19135" CreationDate="2014-06-16T19:24:46.053" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;What is the mechanism of antiperistalsis that occurs during vomiting?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Emetic agents in the bloodstream stimulate chemoreceptors in &lt;a href=&quot;http://en.wikipedia.org/wiki/Area_postrema&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;area postrema&lt;/em&gt;&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Solitary_nucleus&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;nucleus tractus solitarius&lt;/em&gt;&lt;/a&gt; [1]. &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Nucleus tractus solitarius&lt;/em&gt; is connected to motor neurons in ventral medulla and hypothalamus [1].&lt;/li&gt;&#xA;&lt;li&gt;Esophageal and gastric peristalsis is inhibited. Small bowel peristalsis is reversed. Esophagus and stomach don't have antiperistaltic movements [2].&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why the peristaltic waves normally don't propagate in anal to oral direction?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Because of the mechanism of descending inhibition. Distension of the esophagus and intestine causes a reflex action that leads to circular muscular contraction just above the bolus/chymus. Longitudinal muscle also contracts (shortens) [3].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7xIng.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Hornby PJ. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11749934&quot; rel=&quot;nofollow noreferrer&quot;&gt;Central neurocircuitry associated with emesis.&lt;/a&gt; Am. J. Med. 2001 Dec 3;111 Suppl 8A:106S-112S. PubMed PMID: 11749934. &lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Brizzee KR. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2178746&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mechanics of vomiting: a minireview.&lt;/a&gt; Can. J. Physiol. Pharmacol. 1990 Feb;68(2):221-9. PubMed PMID: 2178746. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;AUMSA. &lt;em&gt;&lt;a href=&quot;http://aumsa.wikidot.com/digestive-physiology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Digestive Physiology.&lt;/a&gt;&lt;/em&gt; May 2012. CC-BY-SA-3.0&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-26T16:01:44.490" LastActivityDate="2014-06-26T16:01:44.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19150" PostTypeId="1" CreationDate="2014-06-16T19:52:08.007" Score="0" ViewCount="1020" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/m3yVJ.png&quot; alt=&quot;Pedigree&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried a to decide if this is a autosomal dominant, recessive or a mitochondrial disorder.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to know for sure, or do you have to use probability?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(English is not my native language)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No other pedigrees have had carriers marked so I did not expect this one had it either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Auto dominant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I:1 aa I:2 A-&#xA;II:1 aA II:2 aa II:3 aa II:4 aA&#xA;II:1 children could have got a from him and a from her the the disorder would be gone.&#xA;III:9 children got her dominant A&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recessive&#xA;I:1 A- I:2 aa&#xA;II:1 aa II:2 A- II:3 A- II:4 aa&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mitochondrial disorder&#xA;I read &quot;transmission only accours through females&quot;&lt;/p&gt;&#xA;" OwnerUserId="8050" LastEditorUserId="3615" LastEditDate="2014-06-17T11:15:43.857" LastActivityDate="2014-06-17T11:24:46.737" Title="Pedigree analysis : autosomal or mitochondrial" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19151" PostTypeId="1" CreationDate="2014-06-16T20:46:47.573" Score="2" ViewCount="100" Body="&lt;p&gt;I am struggling with the expression of the certain protein. It seems that it is not properly folded and thus, it is not active. I tried to express it at the lower temperature and for the longer time, but it did not help. Can anyone give me a clue what I can try to do?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The size of the protein is around 55 kDa. I know that I have some soluble protein as I run western blot. The protein contain His-taq on the C-terminus so I started with Ni-NTA column chromatography. Steps of purification: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Incubation the lysate with resin (30 min/4°C)&lt;/li&gt;&#xA;&lt;li&gt;Unbound proteins were collected as the ‘Flow-through’ fraction&lt;/li&gt;&#xA;&lt;li&gt;Wash 1 with buffer: 50 mM NaH2PO4, 1M NaCl, 10 mM Imidazole&lt;/li&gt;&#xA;&lt;li&gt;Wash 2 with 10% buffer B in buffer A&lt;/li&gt;&#xA;&lt;li&gt;Elution with buffer B: 50 mM NaH2PO4, 1M NaCl, 250 mM Imidazole&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Because the protein is co-purified with something else in size around 57 kDa (which might be a chaperone protein) I tried also:&#xA;1. add ATP to first wash in concentartion of 2.5 mM and incubate column for 1h/4C&#xA;2. add ATP to first wash in concentartion of 2.5 mM and incubate column overnight in 4C&#xA;3. add ATP to first wash in concentartion of 2.5 mM and incubate column overnight in room temperature&#xA;4. add ATP and glycerol to first wash in concentartion of 2.5 mM for ATP and  4M for glycerol and incubate column for 2h in 4add ATP to first wash in concentartion of 2.5 mM and incubate column overnight in 4C&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All the method end up with two close to each other bands (only one of them is my protein) and protein is not active. &lt;/p&gt;&#xA;" OwnerUserId="6892" LastEditorUserId="6892" LastEditDate="2014-06-16T21:37:54.967" LastActivityDate="2014-07-16T23:10:50.913" Title="What I can do in order to improve the folding of the protein?" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19152" PostTypeId="2" ParentId="19150" CreationDate="2014-06-16T21:09:41.753" Score="1" Body="&lt;p&gt;Mitochondrial because all the offsprings have the &lt;strong&gt;same&lt;/strong&gt; trait as that of the &lt;strong&gt;female&lt;/strong&gt; &lt;strong&gt;parent&lt;/strong&gt;. Lets go through the possibilities one at a time. Assuming you have no carriers (you do not have any carrier symbols) we can work out the following.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Autosomal Recessive?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This might be the case if we assume the male in the first generation is a carrier. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Autosomal Dominant?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This might be the case but it is unlikely. Looking at the first generation possibly yes, as 50% of offspring have the trait. Looking at the second generation however only 3 out of 9 offspring have the trait. Making autosomal dominant unlikely (but it is still a possibility.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the test, if you have to go with one option, mitochondrial inheritance is the best because there are no assumptions at all but if multiple options may be correct, you can have any of them.&lt;/p&gt;&#xA;" OwnerUserId="8034" LastEditorUserId="3615" LastEditDate="2014-06-17T11:24:46.737" LastActivityDate="2014-06-17T11:24:46.737" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19153" PostTypeId="1" CreationDate="2014-06-16T21:13:05.883" Score="2" ViewCount="431" Body="&lt;p&gt;I found the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hill%27s_muscle_model&quot; rel=&quot;nofollow&quot;&gt;Hill muscle model&lt;/a&gt;, which helps relate the force a muscle can generate to its change in length over time (its &quot;contraction velocity&quot;).  Is there a similar model to get an idea of the energy consumed during a contraction as a function of the force generated?&lt;/p&gt;&#xA;" OwnerUserId="6793" LastActivityDate="2014-07-16T22:10:51.030" Title="Muscle force/energy relationship" Tags="&lt;biophysics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19154" PostTypeId="2" ParentId="19153" CreationDate="2014-06-16T21:25:16.400" Score="1" Body="&lt;p&gt;You can calculate the energy consumption using basic physics formulas. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Work = Force x Distance&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and the unit of work is the Joule. Therefore if force is a function of change in length then substituting this function in for force in the above calculation we have that work is a function of length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to talk about energy consumed in terms of calories rather than joules,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1 calorie = 4.184 joules&lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-16T21:25:16.400" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="19155" PostTypeId="2" ParentId="19151" CreationDate="2014-06-16T21:41:06.683" Score="2" Body="&lt;p&gt;If you have over-expressed an eukaryotic full length protein or the enzymatic part, then &lt;em&gt;E. coli&lt;/em&gt; does not necessarily provide a good environment for its folding so you need to express it in the same system which the original protein came from, e.g. mammalian or Drosophila etc. &lt;em&gt;E. coli&lt;/em&gt; over expression is mostly used to generate wast amounts of protein for the purposes of protein sequence based Ab generation amongst other things. Look at this review for some of the solutions it offers for proteins not folding correctly in &lt;em&gt;E. coli&lt;/em&gt; when over-expressed (&lt;a href=&quot;http://www.biomedcentral.com/1472-6750/4/32&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.biomedcentral.com/1472-6750/4/32&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The remainder of your question is a duplicate of this question (&lt;a href=&quot;https://biology.stackexchange.com/questions/19024/ni-nta-purification-problem-with-the-chaperone-protein&quot;&gt;Ni-NTA purification, problem with the chaperone protein&lt;/a&gt;), which I have provided an extensive answer/comments to!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, since the lack of enzyme functionality is a potential indication of errors in its state/3D structure, it is however not a definitive reason. Could you provide some explanations as to what experiments you have conducted to reach that conclusion and how this second point about chaperone eluding with your protein relevant to the first and the last section of your question?&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-06-16T21:56:24.843" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19156" PostTypeId="1" AcceptedAnswerId="19158" CreationDate="2014-06-16T23:05:00.063" Score="3" ViewCount="283" Body="&lt;p&gt;I have cufflinks data from 18 different RNA-seq experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've noticed that if the sum all the RPKM values for a particular experiment, are vastly different between experiments. How could this be? I was under the impression that RPKM was normalized by the total number of reads. If that is true then the sum of RPKM values for a single experiment should be the same?&lt;/p&gt;&#xA;" OwnerUserId="8052" LastEditorUserId="3340" LastEditDate="2014-06-17T11:29:41.717" LastActivityDate="2014-06-17T12:59:30.223" Title="Should the sum of RPKMs be constant over experiments" Tags="&lt;bioinformatics&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19157" PostTypeId="1" CreationDate="2014-06-17T04:57:34.883" Score="2" ViewCount="166" Body="&lt;p&gt;I'm actually an artist, but I wanted to ask this because it will help a lot in my figure drawings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My artistic anatomy teacher taught me about the Scapulohumeral Rhythm. He said that in during the first 30 degree of rotation of the humerus, neither the scapula nor the clavicle moves. But after that, for the next 60 degree of rotation of the humerus, its rotation is distributed in a 2:1 ratio to the Scapulathoracic joint.&#xA;He said that beyond that, the Humerus is locked into the socket with Acromium and Coracoid Process. So the Glenohumeral Joint is frozen. Additional elevation comes from the Clavicle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My first question is how true is that?&#xA;My second question is what happens to the Scapula after the 90 degrees rotation of the Humerus? I noticed that the Scapula keeps rotating even after the Humerus is rotated beyond 90 degrees, but is there any consistent ratio?&#xA;My third question is what is the maximum elevation of the Humerus in degrees?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Forgive me if I looked liked an annoying dumbass, I'm just an artist. So, please explain in a simple and understandable way.&lt;/p&gt;&#xA;" OwnerUserId="8053" LastEditorUserId="8053" LastEditDate="2014-06-17T05:20:24.687" LastActivityDate="2014-06-17T05:20:24.687" Title="Questions regarding Scapulohumeral Rhythm" Tags="&lt;human-anatomy&gt;&lt;bone-biology&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19158" PostTypeId="2" ParentId="19156" CreationDate="2014-06-17T06:52:13.477" Score="3" Body="&lt;p&gt;I guess this arises because of the default cufflinks option &lt;code&gt;--total-hits-norm&lt;/code&gt; in which it normalizes the FPKMs with total reads including the ones that are not mapped to a known gene or a predicted gene from the assembly. In the &lt;code&gt;genes.fpkm_tracking&lt;/code&gt; file the FPKM values are reported for known/predicted genes. It is certainly possible that the number of genes are different in a certain sample compared to the other and perhaps therefore the sums are different. If you are not interested in finding new transcripts then you can run cufflinks with a reference GTF/GFF file provided using &lt;code&gt;--GFF&lt;/code&gt; along with using &lt;code&gt;--compatible-hits-norm&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also try this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assemble with &lt;strong&gt;cufflinks&lt;/strong&gt;, merge the GTFs with &lt;strong&gt;cuffmerge&lt;/strong&gt; and run &lt;strong&gt;cuffquant&lt;/strong&gt; with the merged GTF. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can subsequently use &lt;strong&gt;cuffnorm&lt;/strong&gt; to normalize the expression values. It has been observed by me and others that the FPKM value reported by cuffdiff and cufflinks are different which is most likely because of differences in default parameters (see &lt;a href=&quot;http://seqanswers.com/forums/showthread.php?t=26041&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;). The inner operations of cufflinks are not very clearly documented; so I cannot conclusively answer your question.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-06-17T12:59:30.223" LastActivityDate="2014-06-17T12:59:30.223" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19159" PostTypeId="1" CreationDate="2014-06-17T06:53:41.823" Score="5" ViewCount="9863" Body="&lt;p&gt;I'm having some trouble understanding the concept of ancestral allele. What exactly does it mean? What does it have to do with Identity by descent/state? What does it have to do(if anything) with SNP's? Also, how is the concept useful in genetics/evolution? I've tried reading these up on various websites, but I'm not satisfied with my understanding yet.&lt;/p&gt;&#xA;" OwnerDisplayName="user6417" LastActivityDate="2015-01-13T08:16:08.140" Title="Ancestral Allele explanation" Tags="&lt;genetics&gt;&lt;snp&gt;&lt;allele&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19160" PostTypeId="2" ParentId="19159" CreationDate="2014-06-17T08:26:55.227" Score="9" Body="&lt;p&gt;&lt;strong&gt;SNP&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's start with the definition that has nothing to do with the rest of the question :). A Single-Nucleotide-Polymorphism (SNP) is a kind of genetic variation that you find in population. This genetic variation is defined as a variation caused by only one single nucleotide (as its name indicates it). For example if you have in the populations the two following variants at the same locus: &lt;code&gt;AGCCGT&lt;/code&gt; and &lt;code&gt;AGCTGT&lt;/code&gt;, then you have a SNP at the position of the C and T. This type of variation is very common. We estimate that there are about 10 millions SNPs in the human genome. We often use these SNPs as genetic markers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Ancestral vs derived alleles&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An ancestral allele or an ancestral trait (depending on whether you look at the phenotype or a t the genotype) is the trait/allele that was carried by the common ancestor of the taxon you consider. For example: as you may know the taxon Reptilia includes lizards, snakes, turtles, birds, mammals and some other lineages. In the taxon Reptilia, the scales is the ancestral state (still exist in lizards for example) and the hairs and feathers are derived states. Usually, the ancestral state is the one that carried by the most basal lineages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Identity by state (IBS) and Identity by descent (IBD)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If two sequences are exactly identical, then we say that they are identical by state (IBS). Such identity can occur either through convergent evolution or through common ancestry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To understand the concept of &quot;identical by descent&quot; (IBD) it is important to understand the concept of coalescence. A coalescent event is, when looking backward in time, an event where two sequences were actually the same sequence. Often IBD is defined relatively to a given threshold in time. If the coalescent event occurs after this event then the two sequences are not IBD. If the two sequences coalesce before this time threshold and that the two sequences are still IBS, then the two sequences are IBD&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Bridging everything together&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if you look at sequences in a given group of lineages and see that they are all exactly the same then they are identical by state. If you know that all these sequences come from a common ancestor and even they all coalesce to a single individual in the common ancestor, then all sequences are identical by descent. But some mutations may have occurred since the last common ancestor resulting in some SNPs, then all the sequences are not IBS anymore and therefore not IBD either. You can use such sequence variance in order to create a phylogeny for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-06-17T18:50:53.933" LastActivityDate="2014-06-17T18:50:53.933" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19161" PostTypeId="2" ParentId="13591" CreationDate="2014-06-17T10:04:22.113" Score="2" Body="&lt;p&gt;The buffer conditions used in the reaction also mitigate against the endonuclease reaction, so it should not be a problem if you stick to the protocols exactly. I've worked on this enzyme since 1988 and was the original &quot;cloner' of the overproducer see &lt;a href=&quot;http://www.sayers.staff.shef.ac.uk/fen/&quot; rel=&quot;nofollow&quot;&gt;http://www.sayers.staff.shef.ac.uk/fen/&lt;/a&gt;   for more information on these enzymes&#xA;Jon Sayers, University of Sheffield. &lt;/p&gt;&#xA;" OwnerUserId="8054" LastActivityDate="2014-06-17T10:04:22.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19162" PostTypeId="1" AcceptedAnswerId="19698" CreationDate="2014-06-17T12:25:12.580" Score="3" ViewCount="384" Body="&lt;p&gt;Once, as a child, I found a spider in my parents' garden. I remember catching it in a jar because I thought it looked unusual, but I never figured out what kind of spider it was and unfortunately didn't get any pictures. I've been looking for it in books and on the Internet since, based on memory, with no luck.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This was twenty years ago now, and I realize my memory of it may not be good enough to identify it now, but here's trying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I remember best was its abdomen, which was a dark metallic blue and sort of rectangular in shape. Its body was probably about 1.5 cm long, without the legs, and maybe 1 cm wide or a little less (I was a child, things look bigger when you're small.) It was found in a garden in the suburbs of Copenhagen, Denmark, sitting on a bed sheet drying in the sun. It left only a few strings of web, almost like a bridge, from the bottom of the jar to the lid where it had escaped during the night because the lid wasn't sealed. I never found it again or saw another spider like it.&lt;/p&gt;&#xA;" OwnerDisplayName="user5661" LastActivityDate="2020-11-30T19:37:29.237" Title="Identifying a spider from my childhood memory" Tags="&lt;species-identification&gt;&lt;arachnology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19165" PostTypeId="1" CreationDate="2014-06-17T19:13:47.503" Score="1" ViewCount="162" Body="&lt;p&gt;Is some part in one hemisphere the decision maker and &quot;calling the shots&quot; - controlling the opposite side's hand &quot;directly&quot; and controlling its own side's hand through the corpus callosum. Or: is there some &quot;Gestalt&quot; of parts in both hemispheres working as one making the decision?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the latter - it would seem counter intuitive to have a deciding part which is not &quot;unified&quot; in one region, having to go back and forth through the corpus callosum for deciding.&lt;/p&gt;&#xA;" OwnerUserId="8055" LastEditorUserId="8055" LastEditDate="2014-06-18T18:17:13.867" LastActivityDate="2014-06-18T18:17:13.867" Title="Simultaneously using both hands - How does that work?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;neuroscience&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19166" PostTypeId="1" AcceptedAnswerId="19173" CreationDate="2014-06-17T20:18:51.573" Score="0" ViewCount="1178" Body="&lt;p&gt;As we all know, harmful gases play a negative role in our society and our environment. Are these gases playing as abiotic or biotic factors in our lives?&lt;/p&gt;&#xA;" OwnerUserId="8057" LastActivityDate="2018-10-22T14:20:04.560" Title="Are harmful gases abiotic or biotic factors in our environment?" Tags="&lt;ecology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19167" PostTypeId="2" ParentId="14399" CreationDate="2014-06-17T21:14:40.863" Score="2" Body="&lt;p&gt;&quot;So my question is, in general, how many different flavors of carcinogens are there?&quot;&#xA;As mentioned in the comments, almost all carcinogens act by damaging DNA.  In general there are three ways to do this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alkylation, a good example is pyridine.  These compounds covalently modify the DNA and either cause a mutation by misincorporation during DNA replication (where the wrong base is incorporated across from the alkylated base), or by generation of double strand breaks during DNA replication that result in a mutations during the repair process (the details of which are not in-scope here).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intercalation, my favourite example being ethidium bromide.  These compounds literally insert themselves between the bases of the double helix, where they cause &quot;fork collapse&quot; during DNA replication, and the ensuing repair process mutates the DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ionization through radicals.  Yes, carcinogens can generate radicals that will generate DNA damage.  A good example is doxorubicin, which is a highly effective chemotherapeutic, but also a carcinogen in its own right.  Some heavy metals can also generate radicals under the right circumstances.  These compounds typically oxidize the bases of DNA, and result in broad misincorporation during DNA replication.  Radicals can also result in breakage of the phosphodiester backbone, which cause mutations during repair. This mechanism is taken advantage of in some methods for studying the primary and secondary structure of RNA molecules, and in &quot;foot printing&quot; methods.  Incidentally, it is this mechanism of carcinogenesis that causes antioxidants to be associated with the prevention of cancer.  Compounds like vitamin C soak up the radicals generated by the carcinogen (or radiation), thereby preventing the damage from occurring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An interesting point: pyrimidine dimers, which are generated whenever you get a sunburn, are a carcinogenic form of DNA damage somewhere between the ionization and alkylation mechanisms.  UV light induces a redox reaction that results in covalent linkage of two neighboring pyrimidines.  A dedicated repair process can cause a mutation at the site of the dimer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the take home point is that the DNA damage itself is not usually the mechanism of mutation!  Mutation occurs when the damage is repaired, either as part of a dedicated repair process, or by (non)homologous recombination after a stall in DNA replication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this answers your question.  It is a complicated subject, and I doubt I covered everything here.&lt;/p&gt;&#xA;" OwnerUserId="6501" LastEditorUserId="6501" LastEditDate="2014-06-17T21:31:35.680" LastActivityDate="2014-06-17T21:31:35.680" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19168" PostTypeId="2" ParentId="14903" CreationDate="2014-06-17T22:04:02.470" Score="1" Body="&lt;p&gt;No, it is not possible to determine ancestry with just two DNA samples, but it is possible with three: &lt;a href=&quot;http://www.nature.com/nature/journal/v487/n7407/full/nature11251.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nature/journal/v487/n7407/full/nature11251.html&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially, each sequence region in the progeny can be traced to either the mother or the father, but you really need both sequences to have any confidence.  That would get you one node on your tree.  You would need additional samples from higher generations to rebuild an entire ancestry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it might be possible with hundreds of samples from laterally related individuals.  In fact, I think this is the fundamental hypothesis of the 1000 genome project, &lt;a href=&quot;http://en.wikipedia.org/wiki/1000_Genomes_Project&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/1000_Genomes_Project&lt;/a&gt;, and it pretty much worked.  Isolated populations can be discriminated by broad DNA sequence analysis.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To reconstruct your tree for a single ancestry, you would just want to use more closely related individuals (many, many of them), and then generate a phylogenetic tree, which should roughly correspond to the family tree you are investigating.&lt;/p&gt;&#xA;" OwnerUserId="6501" LastActivityDate="2014-06-17T22:04:02.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19169" PostTypeId="1" AcceptedAnswerId="19172" CreationDate="2014-06-17T22:42:46.167" Score="5" ViewCount="719" Body="&lt;p&gt;I am trying to find a version of the BLOSUM matrix that has the frequencies instead of the scaled log-odds. i.e. instead of the common version that tells us that the score LEU/ASP is -4, I would like to know the probability of LEU replaced by ASP.&lt;/p&gt;&#xA;" OwnerUserId="8060" LastActivityDate="2014-06-19T19:23:35.817" Title="Blosum matrix with probabilities instead of the positive and negative scores" Tags="&lt;bioinformatics&gt;&lt;sequence-analysis&gt;&lt;sequence-alignment&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19170" PostTypeId="1" AcceptedAnswerId="19188" CreationDate="2014-06-17T22:43:37.550" Score="2" ViewCount="109" Body="&lt;p&gt;I am working on a broad phylogenomic analysis of proteins involved in one particular cellular process.  I have constructed a phylogenetic tree for each protein.  I am now working on comparing those trees in order to extract categories (i. e., allele a of protein a occurs most frequently with allele b of protein b, etc.).  I have attempted to construct a super tree using clann, but the tree is extremely difficult to interpret.  I would therefore like to carryout a quantitative comparison (and subsequent categorisation) of each each tree, but it is unclear to me how to even begin this analysis.  Is there a standardised method for comparison of phylogenetic trees?&lt;/p&gt;&#xA;" OwnerUserId="6501" LastActivityDate="2014-06-18T19:34:06.567" Title="Quantitative Comparisons of Phylogenetic trees" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19171" PostTypeId="2" ParentId="17852" CreationDate="2014-06-17T23:50:03.960" Score="1" Body="&lt;p&gt;check out the sequence page at RCSB PDB, it can show SNPs mapped onto 3D for some of the proteins (you need to enable the SNP annotations in the drop-down)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.rcsb.org/pdb/explore/remediatedSequence.do?params.showJmol=true&amp;amp;structureId=4HHB&quot; rel=&quot;nofollow&quot;&gt;http://www.rcsb.org/pdb/explore/remediatedSequence.do?params.showJmol=true&amp;amp;structureId=4HHB&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3150" LastActivityDate="2014-06-17T23:50:03.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19172" PostTypeId="2" ParentId="19169" CreationDate="2014-06-18T04:27:16.000" Score="4" Body="&lt;p&gt;Download the BLOSUM data and source-code from &lt;a href=&quot;ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blosum/blosum.tar.Z&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. Unzip the archive which has several files.&#xA;The file called &lt;code&gt;blosum'XX'.qij&lt;/code&gt; will have the co-occurence probabilities, and the subsitution probabilities can be calculated from them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also have a look at &lt;a href=&quot;http://www.nature.com/nbt/journal/v26/n3/full/nbt0308-274.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-06-19T19:23:35.817" LastActivityDate="2014-06-19T19:23:35.817" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19173" PostTypeId="2" ParentId="19166" CreationDate="2014-06-18T07:34:38.797" Score="2" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/19166/are-harmful-gases-abiotic-or-biotic-factors-in-our-environment#comment27191_19166&quot;&gt;Bez is correct&lt;/a&gt;, biotic and abiotic refer to the nature of the agent performing the stress. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;biotic = living thing (lion that is actively engaging in catching you as food)&lt;/li&gt;&#xA;&lt;li&gt;abiotic = non-animated (far from optimal temperature)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now the example &quot;shade&quot; is trickier; because it depends on the &lt;strong&gt;perspective&lt;/strong&gt; you choose. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's always a &lt;strong&gt;context&lt;/strong&gt;. Does the element creating the shade matter in your context? &#xA;If so, and this element happens to be animated/living:  stress = biotic (though you should reference at some point that the object at hand is animated).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it doesn't matter what object generates the stress since you are only interested in the effect of the shade on a system: shade = abiotic&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pipeline: Analyze the context, choose and communicate your choice of perspective/angle and then remember what biotic and abiotic literally mean.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coming back to &quot;harmful gases&quot;: What is your context meaning harmful for whom? Specify that first. Carbon Dioxide is an example of something that may be deleterious at a specific concentration for one system and at the same time beneficial for another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it matter how these gases were produced? CO&lt;sub&gt;2&lt;/sub&gt; may be a product of an animated system's metabolism and thus may be called abiotic. It may also be a product of oxidation of a multitude of carbohydrates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know of an example where Carbon Monoxide is produced by living things. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could of course circumvent this discussion by analyzing what harmful effect the gases have on your system of interest. For example: they generate respiratory stress on humans, and then you use the effect of the gases on the system to characterize them.&lt;/p&gt;&#xA;" OwnerUserId="8063" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-06-18T14:45:42.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19174" PostTypeId="1" AcceptedAnswerId="19186" CreationDate="2014-06-18T08:36:02.280" Score="10" ViewCount="14567" Body="&lt;p&gt;I'm asking after reading the cognate wikipedia.en article on &quot;cistron&quot;. I am still not sure about the difference between the two terms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To me it seems valid to picture a &quot;cistron&quot; as the genome wide set of a specific gene's alleles ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus if all copies of a gene bear recessive mutations all generating the same phenotypic trait (not necessarily the same mutation) no complementation is observed in a cis-trans test?&lt;/p&gt;&#xA;" OwnerUserId="8063" LastEditorDisplayName="user38945" LastEditDate="2018-11-29T18:50:13.883" LastActivityDate="2018-11-29T18:50:13.883" Title="What is the difference between &quot;cistron&quot; and &quot;gene&quot;?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="19175" PostTypeId="1" AcceptedAnswerId="24496" CreationDate="2014-06-18T08:47:51.740" Score="4" ViewCount="493" Body="&lt;p&gt;Microarray chips allow us to conduct many expression experiments in parallel to each other but they can be used only once as far as i know. Are there reusable microarray chips? Have people ever tried it? If there are, are they becoming more common? If people do not choose to use them even though they are in the market, what can be the reasons? &lt;/p&gt;&#xA;" OwnerUserId="1843" LastActivityDate="2014-12-03T09:55:04.247" Title="Reusable microarray chips" Tags="&lt;microarray&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19176" PostTypeId="1" AcceptedAnswerId="19177" CreationDate="2014-06-18T09:37:18.730" Score="3" ViewCount="453" Body="&lt;p&gt;Do butterflies (insects) sleep, and if so, where??&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have googled for information but didn't get an exact answer.&lt;/p&gt;&#xA;" OwnerUserId="6878" LastEditorUserId="3624" LastEditDate="2014-06-18T09:46:10.603" LastActivityDate="2014-06-18T10:19:02.253" Title="Where do butterflies sleep?" Tags="&lt;neuroscience&gt;&lt;entomology&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19177" PostTypeId="2" ParentId="19176" CreationDate="2014-06-18T10:19:02.253" Score="6" Body="&lt;p&gt;It would be better to say that they go into an inactive, low metabolic state. This low metabolic state is often driven by the temperature in the air itself; ectothermic butterflies require outside heat-energy to become active. Basically they use this time to digest their food and produce sperm/eggs. (&lt;a href=&quot;http://blog.perunature.com/2013/01/do-butterflies-sleep.html&quot;&gt;reference&lt;/a&gt;). At night, or during inclement weather, most butterflies perch on the underside of a leaf (this provides them with a bit of shelter from the rain and makes them less noticeable to prey), crawl deep between blades of grass or into a crevice in rocks, or find some other shelter to rest (&lt;a href=&quot;http://www.naba.org/qanda.html&quot;&gt;reference&lt;/a&gt;).  In short, I would not call it sleeping but just a state of rest. Butterflies cant even close their eyes from the lack of eyelids (&lt;a href=&quot;http://www.kidsbutterfly.org/faq/behavior/9&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-18T10:19:02.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19178" PostTypeId="1" CreationDate="2014-06-18T10:53:11.853" Score="4" ViewCount="570" Body="&lt;p&gt;I would like to know if there is any research into the latency of human perception.  Particulary:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What is the minimum time for various inputs (vision, touch, sound) to be recognized by the conscious mind?&lt;/li&gt;&#xA;&lt;li&gt;How different are these times?  (Loud sound vs sense of touch in your toe)&lt;/li&gt;&#xA;&lt;li&gt;Given the above, is there a number we can put on how many milliseconds behind reality the human mind is?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8066" LastActivityDate="2014-07-18T13:22:04.353" Title="How Behind is the Human Mind (Latency of the Senses)" Tags="&lt;brain&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19179" PostTypeId="1" CreationDate="2014-06-18T12:42:12.947" Score="4" ViewCount="101" Body="&lt;p&gt;Can treatment of thrombus cause embolism, in case of very high blood pressure, that may even lead to a heart attack ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the very high Blood pressure may cause some of the enzymes not act completely on the thrombus and release emboli in the blood stream ?&lt;/p&gt;&#xA;" OwnerUserId="8067" LastActivityDate="2014-07-26T15:23:18.140" Title="Thrombus and Embolii" Tags="&lt;blood-circulation&gt;&lt;blood-pressure&gt;&lt;circulatory-system&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19180" PostTypeId="2" ParentId="19178" CreationDate="2014-06-18T13:06:35.970" Score="3" Body="&lt;p&gt;There is a huge amount research into this subject. It is vast and nebulous as such I cannot give you an overall picture of this. I can however illustrate some of the complexities to this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly I would say that what you mean by human perception is extremely complex, there are different modalities of perception. For example in terms of a visual stimulus, we may simply perceive its basic shape, outline, colour, whether or not it is moving. We then may also perceive higher levels of information such as the function of the object. Similarly there are different aspects to other stimuli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These different components of perception are transmitted by different neurons leading to the brain and then processed by different areas of the brain suited to specific tasks and then are integrated together to give us a conscious idea of what the object is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore when measuring the latency of human perception you would first have to decide what exactly you mean by this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other aspect is that a lot of study has occurred in this area as we are aware that perception can be altered by states of illness (for example audio evoked responses in schizophrenia, or visual evoke responses in multiple sclerosis). The perception of pain is yet another huge area of study.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again this is such a vast area of research that I wouldn't really know where to point you to. However for a entertaining read on how perception can change in neurology I would recommend reading the books of Oliver Sacks, in particularly &quot;The Man Mistook His Wife for a Hat&quot; and an &quot;Anthropologist on Mars&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am sorry I haven't provided you with more detail but good luck in reading around this subject. If you are more specific about what perceptions, (e.g. perception of faces, perception of danger etc..) then maybe you will receive more specific answers.&lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-18T13:06:35.970" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19181" PostTypeId="2" ParentId="19165" CreationDate="2014-06-18T13:16:35.793" Score="1" Body="&lt;p&gt;I am not sure I fully understand your question, it's a little unclear. But if I understand the question correctly it is how to we coordinate movement on both sides of the body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well this can occur because we have connections between both hemispheres of the brain. The major connection is called the corpus collosum, this is a white matter tract that allows signals from one side of the body to pass to the other side of the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In some rare cases there have been individuals who have had this connection severed, for these individuals each side of the body may perform tasks of which there other side of the body is unaware.&lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-18T13:16:35.793" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19182" PostTypeId="1" CreationDate="2014-06-18T13:56:32.900" Score="3" ViewCount="2056" Body="&lt;p&gt;What's the source of hydrogen in the reduction of oxygen to water in metabolism?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tFMr7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this implying that half the hydrogen comes from NADH and the other half from lone protons?&lt;/p&gt;&#xA;" OwnerUserId="6759" LastActivityDate="2014-07-19T09:56:23.107" Title="Source of hydrogen in reduction of oxygen in electron transport?" Tags="&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19183" PostTypeId="2" ParentId="19179" CreationDate="2014-06-18T16:36:16.153" Score="2" Body="&lt;p&gt;Yes, treatment of thrombus &lt;em&gt;can&lt;/em&gt; cause embolism. Hypertension favors hemorrhagic complications.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Thrombolytics:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, they can cause paradoxical embolism, although it is a rare complication [1]. The most fearful complication of thrombolytic medication is major hemorrhage. And hypertension favors bleeding [2].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Catheter-directed thrombolysis:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hypertension (more than 180 mmHg and associated with congestive heart failure) was found to increase hemorrhagic complications [3]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Angioplasty:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Angioplasty produces some embolic particles [4]. However, using embolic protection is disputed [4, 5].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Liu YF, Bayliss M. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18299379&quot; rel=&quot;nofollow&quot;&gt;Paradoxical embolism: a rare complication of thrombolysis.&lt;/a&gt; Emerg Med J. 2008 Mar;25(3):180-1. doi: &lt;a href=&quot;http://dx.doi.org/10.1136/emj.2007.053934&quot; rel=&quot;nofollow&quot;&gt;10.1136/emj.2007.053934&lt;/a&gt;. PubMed PMID: 18299379.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Meneveau N, Vuillemenot A, Bassand JP. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8815838&quot; rel=&quot;nofollow&quot;&gt;[Complications of thrombolytic therapy in pulmonary embolism].&lt;/a&gt; Arch Mal Coeur Vaiss. 1995 Nov;88(11 Suppl):1769-76. PubMed PMID: 8815838. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Agle SC, McNally MM, Powell CS, Bogey WM, Parker FM, Stoner MC. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20413257&quot; rel=&quot;nofollow&quot;&gt;The association of periprocedural hypertension and adverse outcomes in patients undergoing catheter-directed thrombolysis.&lt;/a&gt; Ann Vasc Surg. 2010 Jul;24(5):609-14. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.avsg.2009.12.011&quot; rel=&quot;nofollow&quot;&gt;10.1016/j.avsg.2009.12.011&lt;/a&gt;. PubMed PMID: 20413257.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Malik RK, Landis GS, Sundick S, Cayne N, Marin M, Faries PL. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20006918&quot; rel=&quot;nofollow&quot;&gt;Predicting embolic potential during carotid angioplasty and stenting: analysis of captured particulate debris, ultrasound characteristics, and prior carotid endarterectomy.&lt;/a&gt; J. Vasc. Surg. 2010 Feb;51(2):317-22. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.jvs.2009.08.063&quot; rel=&quot;nofollow&quot;&gt;10.1016/j.jvs.2009.08.063&lt;/a&gt;. PubMed PMID: 20006918. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Divani AA, Berezina TL, Zhou J, Pakdaman R, Suri MF, Qureshi AI. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18540698&quot; rel=&quot;nofollow&quot;&gt;Microscopic and macroscopic evaluation of emboli captured during angioplasty and stent procedures in extracranial vertebral and internal carotid arteries.&lt;/a&gt; J. Endovasc. Ther. 2008 Jun;15(3):263-9. doi: &lt;a href=&quot;http://dx.doi.org/10.1583/07-2326.1&quot; rel=&quot;nofollow&quot;&gt;10.1583/07-2326.1&lt;/a&gt;. PubMed PMID: 18540698. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-26T14:58:09.690" LastActivityDate="2014-06-26T14:58:09.690" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19185" PostTypeId="1" CreationDate="2014-06-18T17:25:06.147" Score="3" ViewCount="127" Body="&lt;p&gt;I have wifi on at my home almost all the time. I learned that the frequency of visible light is around several hundreds of THz, while the frequency of wifi is only several GHz, which is only 1:100,000. But I'm not sure how the amplitude of wifi wave compares to the amplitude of the visible light? Are the frequency and the amplitude the only concerns when we talk about the radiation? Can someone educate me to quantify the effect wifi radiation could have in our life?&lt;/p&gt;&#xA;" OwnerUserId="8071" LastActivityDate="2014-06-18T17:25:06.147" Title="Is WIFI safe for humans?" Tags="&lt;radiation&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="1" ClosedDate="2014-06-18T17:51:12.590" ContentLicense="CC BY-SA 3.0" />
  <row Id="19186" PostTypeId="2" ParentId="19174" CreationDate="2014-06-18T17:37:43.240" Score="16" Body="&lt;p&gt;A cistron is a gene - here's how the word came about:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's 1955. The proposed double helical structure of DNA has been published and the race is on to understand the implications of this for genetics. Geneticists have been working with genes for decades, but they don't know what genes are. Sanger has sequenced the two polypeptides of insulin, so the idea of a specific sequence of amino acids is established. The emerging molecular geneticists believe that genes will be explained by a feature of DNA, probably a sequence of nucleotides, but they don't know how. Crick and others are theorising about coding (i.e DNA &gt; protein), but at this stage there is no genetic code, no mRNA or tRNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Seymour Benzer, at Purdue, is working on &lt;em&gt;fine structure of a genetic region in bacteriophage&lt;/em&gt; and in this year he publishes a key paper with that phrase as the title. Without going into a lot of detail about his experimental set up, he is studying a region of the bacteriophage T4 genome called rII. Wild-type T4 can form plaques on &lt;em&gt;E. coli&lt;/em&gt; B or &lt;em&gt;E. coli K12&lt;/em&gt;. Mutations in the rII region cause a large plaque phenotype in &lt;em&gt;E. coli&lt;/em&gt; B so it is easy to isolate them, but these phage cannot produce plaques on &lt;em&gt;E. coli&lt;/em&gt; K12 which sets the scene for a powerful assay for rare recombination events.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Benzer used this system to do very fine mapping of thousands of rII mutations because he was able to use the system to measure recombination frequencies, but what matters in the present context is that he was able to do a kind of complementation test (he called this pseudo-allelism). He was able to assign the rII mutants into two groups according to whether, in a mixed infection, they produced lots of progeny. So if he mixed two phage with different mutations and didn't get many progeny he put these in the same group. On the other hand if he did get a lot of progeny he placed the two in different groups. He called this approach a cis-trans test. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The application of the phenotype test to pairs of rII mutants leads to the division of the region into two functionally separable segments.&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is as close as he dared to go to claiming to be studying genes. He refers to 'functional units' but never uses the word 'genes' because at this stage that word belonged to classical genetics in higher organisms. In 1957 he proposed the word &lt;strong&gt;cistron&lt;/strong&gt; for the functional unit defined by this type of test, and the word caught on, particularly because of its incorporation into the operon model with the idea of polycistronic mRNA. His other coinings, &lt;strong&gt;muton&lt;/strong&gt; and &lt;strong&gt;recon&lt;/strong&gt; were not adopted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two T4 genes/cistrons in the rII region of the phage genome are now called rIIA and rIIB.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Benzer, S (1955) Fine structure of a genetic region in bacteriophage Proc. Natl. Acad. Sci. USA 41:344-354&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-06-18T17:37:43.240" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19187" PostTypeId="1" AcceptedAnswerId="19406" CreationDate="2014-06-18T19:17:23.193" Score="2" ViewCount="204" Body="&lt;p&gt;My chives, asparagus, oregano, and rhubarb come back every year like clockwork.  Suppose I want my bok choy to join the party - is there an &quot;I'll be seeing you next year!&quot; gene that can be modified to be turned on to be like my hardy chives, or is it more complicated than that?&lt;/p&gt;&#xA;" OwnerUserId="6534" LastActivityDate="2016-04-07T00:12:33.443" Title="Could an annual plant be genetically modified to be a perennial?" Tags="&lt;genetics&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19188" PostTypeId="2" ParentId="19170" CreationDate="2014-06-18T19:34:06.567" Score="1" Body="&lt;p&gt;I don't know whether it's exactly what you need, but there are formal algorithms for tree comparison.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are basically two approaches: one utilizing tree lengths (branch score distance) and the other one dealing with topologies only (symmetric-difference metric): details and references can be found in the &lt;a href=&quot;http://evolution.genetics.washington.edu/phylip/doc/treedist.html&quot; rel=&quot;nofollow&quot;&gt;manual to treedist from the phylip-package&lt;/a&gt;, which implements both.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://paup.csit.fsu.edu/Cmd_ref_v2.pdf&quot; rel=&quot;nofollow&quot;&gt;PAUP*&lt;/a&gt; has a command under the same name (treedist), which calculates the symmetric-difference metric only. This metric is very intuitive: it describes the total number of partitions (= splits) present only on one of the two trees.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-06-18T19:34:06.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19190" PostTypeId="1" CreationDate="2014-06-18T21:23:21.757" Score="1" ViewCount="178" Body="&lt;p&gt;I have been studying ion channels and there is one thing i am confused about, gating between open and closed states in channels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am i right in thinking gating is so fast that it is effectively always open for ion flow? So that if ten ions flow through a channel, then one can imagine that the channel opens and closes so quickly it is basically always open for the flow of the ten ions, or does a channel open allow one ion through, close and then open again for the next ion?&lt;/p&gt;&#xA;" OwnerUserId="8072" LastActivityDate="2014-06-18T22:27:08.910" Title="Ion Channel gating" Tags="&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19192" PostTypeId="2" ParentId="19190" CreationDate="2014-06-18T22:27:08.910" Score="3" Body="&lt;p&gt;There are several types of channels, but probably the type you are referring to is voltage gated ion channels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The state in which these channels are, open or closed, depends on the action potential across the cell membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the potential is at the correct energy for the channel to be open it will remain open allowing a steady flow of ions through. Once enough ions have passed so that the potential across the membrane changes to meet the deactivation energy, the channel will close. It then enters a refractory period which requires repolarisation across the cell membrane so that the ion is reset ready to open and let ions through again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Different ion channels have different activation potentials, deactivation potentials and different refractory periods. This results in different rates of opening and closing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So based on the above, in answer to your question, no gating is not so fast that it is always open. There are significant periods of time where channels are closed allowing no flow of ions and significant periods of time where they are open allowing continuous flow of ions. &lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-18T22:27:08.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19193" PostTypeId="2" ParentId="19182" CreationDate="2014-06-19T00:09:03.073" Score="1" Body="&lt;p&gt;The equation you've shown is similar to other cellular respiration equations that I've seen, in that, it is trying to simplify a pretty complex process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My guess is that you're doing first year cell biology like I am, so you probably know that there is a difference between the pH of the mitochondrial matrix (7.8 - making it alkaline) and the inter membrane space (roughly that of the cytosol - usually about 7). The lower the pH of a solution, the greater the concentration of H+. My point is that the solutions on either side of the inner mitochondrial membrane both have a concentration of H+.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So even though, when NADH is oxidised, it loses a H+ to solution, thereby contributing to the pH of the mitochondrial matrix, what is the likelihood that that particular H+ will be the H+ that is part of the molecule that takes the electrons at the end of the electron transport chain? I think low.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indirectly, NADH does contribute H+ to the overall pH of the mitochondrial matrix but it doesn't directly give the H+ to &quot;half an oxygen gas molecule&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check the video below which is from the publisher of the textbook my course uses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.garlandscience.com/garlandscience_resources/resource_detail.jsf?landing=student&amp;amp;resource_id=9780815344544_CH14_QTM02&quot; rel=&quot;nofollow&quot;&gt;http://www.garlandscience.com/garlandscience_resources/resource_detail.jsf?landing=student&amp;amp;resource_id=9780815344544_CH14_QTM02&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8051" LastActivityDate="2014-06-19T00:09:03.073" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="19195" PostTypeId="1" CreationDate="2014-06-19T03:06:19.347" Score="3" ViewCount="98" Body="&lt;p&gt;So I'm reading this article to &lt;a href=&quot;http://www.wikihow.com/Treat-Fluid-Retention&quot; rel=&quot;nofollow&quot;&gt;Treat Fluid Retention&lt;/a&gt; and it suggests&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Eat foods with diuretic properties.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;But also &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Avoid drinks that will dehydrate the body such as tea, coffee and alcohol. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;As I understand, tea, coffee and alcohol are plenty diuretic. So what makes those veggies's diuretic nature better than alcohol's?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know alcohol is more harmful than veggies, but I mainly wanted to know &lt;strong&gt;how do diuretic veggies help you&lt;/strong&gt; when infact the diuretic alcohol actually makes you dehyderated? How's veggies' &lt;strong&gt;diuretic nature&lt;/strong&gt; more helpful than the alcohol's (disregarding other side-effects of it)?&lt;/p&gt;&#xA;" OwnerUserId="3141" LastEditorUserId="3141" LastEditDate="2014-06-19T12:06:55.697" LastActivityDate="2014-07-22T07:05:06.823" Title="What's the difference between diuretic veggies and alcohol that make the latter bad?" Tags="&lt;nutrition&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19196" PostTypeId="1" CreationDate="2014-06-19T10:23:00.723" Score="2" ViewCount="393" Body="&lt;p&gt;David Attenborough in his &lt;a href=&quot;http://en.wikipedia.org/wiki/Kingdom_of_Plants_3D&quot; rel=&quot;nofollow&quot;&gt;Kingdom of Plants 3D&lt;/a&gt; said, that flowering plants made two inventions: (1) doubling of genetic material and (2) symbiosis with animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What was meant by &quot;doubling of genetic material&quot;? Appearing of diploidy or something else?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me explain my doubts. Inventing of ploidy I regard as inventing of sex and syngenesis. This was done ~500 million y.a. in Ediacarian, if I am not mistake. Hence, this can't be done 140 m.y.a when flowering appears. I.e. both plats and insects had sex 140 mya.&lt;/p&gt;&#xA;" OwnerUserId="1584" LastEditorUserId="1584" LastEditDate="2014-06-23T08:57:05.260" LastActivityDate="2014-06-23T08:57:05.260" Title="What is doubling of genetic material invented in flowering plants?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;botany&gt;&lt;polyploidy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19197" PostTypeId="2" ParentId="19195" CreationDate="2014-06-19T11:55:47.230" Score="1" Body="&lt;p&gt;Firstly I would suggest if you have concerns about suffering from symptoms fluid overload you should consult your doctor. Self diagnosis and self treatment is not a good option. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of alcohol being used as a diuretic, you have to bear in mind that there are many deleterious effects of excess alcohol. By consuming alcohol as a diuretic you would most likely cause more health problems than you solve. &lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-19T11:55:47.230" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19200" PostTypeId="2" ParentId="19196" CreationDate="2014-06-19T15:02:36.803" Score="4" Body="&lt;p&gt;Yes, D. Attenborough probably refers to ploidy number&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Ploidy number&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans for example are 2N (except during the spermatozoid and ovule phase of human existence) meaning that they carry two copies of each autosome (=non-sexual chromosomes). Some species are 1N (haploid), some are 3N (triploid), etc… It would actually be more correct to talk about the time a species spend in each of its phase or talk about the number of cells in each of its phase because many species undergo change in chromosome number during their existence as it is the case for humans. Humans are 2N most of the time but they are 1N when they are ovules or spermatozoid. The correct word to describe the human &lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_life_cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;lifecycle&lt;/a&gt; is diplontic. Some species are diplontic, some are haplodiplontic and some have phases when they have a greater number of chromosomes. Those species are said to be polyploid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Ploidy number, chromosomes and chromatids&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To make sure one don't mix up things... One chromosome is made of one or two chromatids (depending on the cellular phase). The chromatids of the same chromosome (called sister chromatids) are (almost completely) identical. A given &quot;chromosome type&quot; is either alone (1N) or accompagnied by one very similar chromosome (2N) or two other very similar chromsomes (3N), etc.. Considering the case of a 2N individual: If at a given locus (position in the chromosome) the two alleles (gene variant) are different than the individual is said to be heterozygote for this locus. The ploidy number describe &quot;this number of chromosomes&quot;! Now there may have different number of different &quot;types of chromosomes&quot;. Humans for example have 23 different types of chromosomes and in its haploid phase has therefore 23 chromosomes (23 or 46 chromatids depending on the cellular phase) and has 46 chromosomes (46 or 92 chromatids depending on the cellular phase) in its diploid phase  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Ploidy number in angiosperms and other plants and non-plants organisms&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, D. Attenborough (who I don't know and I haven't read anything of his work) probably means doubling, tripling, quadrupling, .. the number of N of chromosomes. And, yes indeed polyploidy (3N, 4N, 6N, 8N) is relatively often observed in flowering plants. There are many crop species that are polyploid. According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728988/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt; an important part of the speciation that occurred in plants is accompanied by a change in ploidy number but this is not only true for angiosperms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Polyploidy is also found in many fungi species and some animal species as well. There are lots of terminologies linked with the discussion of chromosome number and reproductive system and many articles discuss these mechanisms and also the evolution of polyploidy. I found the work of Sally Otto to be of the greatest interest for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Notes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The words inventions are not really used in evolutionary biology but rather in popular books. Also, there are many non-angiosperm plants that have symbiotic relationship with animals. For examples: some angiosperms and the squirrels or birds. But it is true that angiosperm have particularly important symbiotic relationship with animals, in particular insects and this probably allowed an important diversification in both angiosperms and insects. As already said angiosperms are not the taxon of plants to include polyploid species. There are other characteristics that allow to tell an angiosperm apart from other plants. The number of aperture on pollen grain or the positions of the meristems (tissue where mitotic division of unspecialized cells occur allowing the growth of the plant) for examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may be interested in reading &lt;a href=&quot;https://biology.stackexchange.com/questions/935/why-is-polyploidy-lethal-for-some-organisms-while-for-others-is-not/2552#2552&quot;&gt;this post&lt;/a&gt; on the effect on fitness of ploidy number&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-06-20T05:55:54.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19201" PostTypeId="2" ParentId="6909" CreationDate="2014-06-19T15:02:50.633" Score="2" Body="&lt;p&gt;I do not have a source for the following as it was taught to me in neuroanatomy classes, the explanation given for brain freeze is that it is  referred pain through the trigeminal nerve. The  meninges (the tissue lining the central nervous system) is innervated by the trigeminal nerve in the head. Therefore the pain feels as though it is like a headache from meningeal irritation but is in fact benign.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that the mechanism is through referred pain rather than any vascular event it should not put you at any increased risk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This being said if you experience repeated headaches and are unsure of the cause it would be wise to consult your doctor.&lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-19T15:02:50.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19202" PostTypeId="2" ParentId="2523" CreationDate="2014-06-19T17:10:07.750" Score="2" Body="&lt;p&gt;I would suggest you contact your doctor if you are suffering from tendinitis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;NSAIDs are often used as part of treament for tendinitis, but like all medications they can have side effects. Therefore again if you have concerns about taking NSAIDs contact your doctor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the mechinism of action of NSAIDs they don't constrict vessels but instead reduce the production of inflammatory mediators (prostoglandins) which act to dilate some vessels. These inflammatory mediators also make blood vessels more permeable so that nutrients and cells from the blood can pass through the vessel walls and carry out repairs to damage tissue. The problem however with the bodies inflammatory response is that it can be too severe, so that rather than providing healing it itself can cause damage and pain. For this reason (and many others) NSAIDs may be useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But again if you have concerns about taking NSAIDs or any medical condition these please consult your doctor. The internet is not an appropriate place for medical advice, your doctor is. &lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-19T17:10:07.750" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19204" PostTypeId="1" AcceptedAnswerId="19209" CreationDate="2014-06-19T18:44:58.673" Score="4" ViewCount="1186" Body="&lt;p&gt;Say you have a needle, and you poke a very specific area on your left thumb.&#xA;A signal gets sent from that nerve up your spine and into your brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does the brain know exactly where this signal has come from to such accuracy?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Does each nerve in every conceivable part of the body have a unique path that goes up the spine and into the brain, so that's how the brain knows where it came from?&lt;/li&gt;&#xA;&lt;li&gt;Or does the nerve encode the signal as data which travels up a generic nerve, and the brain decodes the information, which contains the &quot;address&quot; of the particular spot that was stimulated? If this is the case, how are the data encoded? Binary?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8080" LastEditorUserId="9943" LastEditDate="2017-01-20T07:59:01.597" LastActivityDate="2017-01-20T07:59:01.597" Title="How is information sent from the skin to the brain?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;pain&gt;&lt;central-nervous-system&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19205" PostTypeId="2" ParentId="17657" CreationDate="2014-06-19T19:32:15.877" Score="9" Body="&lt;p&gt;&lt;strong&gt;No, it's only a very rough approximation.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I actually made a spreadsheet to figure this out.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/pgMay.png&quot; alt=&quot;human elemental breakdown&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rows represent the composition as described by the quote.  I translated each into its appropriate chemical formula and converted all measurements to grams.  Then I found the atomic weight of each.  The gray area represents the grams of each element made up from that particular description, which are summed up in the first summary line.  The second summary line are the values as specified in &lt;a href=&quot;http://chemistry.about.com/od/lecturenoteslab1/a/Elemental-Composition-Of-The-Human-Body-By-Mass.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Last Word's link&lt;/a&gt;, which are based on a 70 kg (154 lb) person.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see that while some of the numbers are in the right ballpark, most are still off by significant amounts (the bottom row is percentage error - negative means the anime was too low, positive that it was too high).  &lt;/p&gt;&#xA;" OwnerUserId="8079" LastEditorUserId="8079" LastEditDate="2014-07-01T16:01:23.187" LastActivityDate="2014-07-01T16:01:23.187" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19206" PostTypeId="2" ParentId="19204" CreationDate="2014-06-19T21:18:28.847" Score="4" Body="&lt;p&gt;The accuracy of sensation is actually quite variable depending on the region of our body. Highly innervated areas such as our fingers have a higher degree of accuracy than sparsely innervated areas such as our legs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a simple experiment you can do to illustrate this. Close your eyes and then get a friend to lightly and slowly run their finger from your wrist, up towards the bend in your elbow on the inside of your arm. Try to guess at what point the reach the joint of your elbow. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of how the brain knows where it came from,  there is part of your brain called the sensory cortex. This sensory cortex has a pattern that corresponds to areas of the body. This pattern is known as a the sensory homunculus (google images will find this). As signals pass up the various different spinal pathways and into the brain they are sent up to this sensory area and the appropriate region of the homunculus is stimulated thereby giving the sensation in the appropriate body area. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly in some brain surgery a patient may be kept conscious so that these areas can be directly stimulated by electric current and the patient will experience sensations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also a matching area, called the motor cortex, which corresponds to movement rather than sensation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above is a simplified version of what goes on and there is lots more detail which would be covered in neuroanatomy books&lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-19T21:18:28.847" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19207" PostTypeId="2" ParentId="15568" CreationDate="2014-06-19T21:28:19.053" Score="1" Body="&lt;p&gt;I'll take a stab at this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What fraction of your food is absorbed and what fraction is expelled is a function of what kind and how much indigestible material there is in the food, and not related to how often the animal eats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How often an animal eats is a function of its metabolic demands(how many calories it needs) and how many calories it can get in one meal. Reptiles, as ectotherms, have a lower metabolic demand than endotherms. In addition, snakes can swallow huge amounts(relative to body weight) of high-calorie food in one sitting. As a result, snakes eat infrequently. Pet snakes are fed weekly or biweekly, depending on a number of factors. A reticulated python can swallow and digest something &lt;a href=&quot;http://rmbr.nus.edu.sg/rbz/biblio/53/53rbz165-168.pdf&quot; rel=&quot;nofollow&quot;&gt;up to its own body weight&lt;/a&gt;. Ten weeks of digestion gives 1.4% of its own body weight daily, even without fasting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Elephants are a migratory large mammal and eat about 4% of their body weight each day, more or less. This takes about 12-18 hours to collect, according to these &lt;a href=&quot;http://www.nationalelephantcenter.org/learn/&quot; rel=&quot;nofollow&quot;&gt;people&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Elephants eat high-fiber, low-calorie foods, and as a result about &lt;a href=&quot;http://www.elephantdungpaper.com/fact.html&quot; rel=&quot;nofollow&quot;&gt;20% of their food mass is turned directly into poop.&lt;/a&gt; They feed often, and don't absorb much. Hummingbirds eat constantly, consuming their &lt;a href=&quot;http://www.hummingbirds.net/hainsworth.html&quot; rel=&quot;nofollow&quot;&gt;own body weight in food&lt;/a&gt; each day, but &lt;a href=&quot;http://www.hiltonpond.org/ThisWeek040808.html&quot; rel=&quot;nofollow&quot;&gt;poop almost not at all&lt;/a&gt;. Their feces contains the indigestible parts of their food, just as the elephant feces does. The different is that large parts of elephant diet is indigestible fiber, while a tiny part of the hummingbird diet is indigestible insect exoskeletons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All creatures absorb as much nutrition from their food as they can, and expel the remainder. How much remainder there is depends on what kind of food they eat. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Growth rates versus digestion rates and mass intake is a totally different and much more complicated question. Generally speaking, the growth-limiting factor is DNA replication or an essential acid or mineral deficiency and not a raw mass problem. &lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-06-19T21:28:19.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19209" PostTypeId="2" ParentId="19204" CreationDate="2014-06-19T22:11:32.207" Score="3" Body="&lt;p&gt;In addition to what Spinoral has said, and in response to your comment above, I will add a bit more about the mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially, in some form or another it's receptive fields all the way up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A brief outline of the anatomy:&#xA;The cells from the spinal cord are &lt;a href=&quot;http://en.wikipedia.org/wiki/Pseudounipolar_neuron&quot; rel=&quot;nofollow&quot;&gt;pseudounipolar&lt;/a&gt; and have their cell bodies in the dorsal root ganglia in the spinal cord.  The other &quot;leg&quot; of the &lt;a href=&quot;http://blog.ketyov.com/2012/05/what-is-longest-axon.html&quot; rel=&quot;nofollow&quot;&gt;sensory neuron&lt;/a&gt; projects to the medulla, which has cell bodies which send axons to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Ventral_posterolateral_nucleus&quot; rel=&quot;nofollow&quot;&gt;VPL thalamus&lt;/a&gt;, which then has cell bodies that project to the primary somatosensory cortex.  There are points of decussation (crossing over the midline), but I'll ignore those for now. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The receptive fields:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The receptive fields of somatosensory neurons share much in common with the receptive fields of visual neurons. As for visual neurons, the somatosensory receptive fields comprise a restricted 2-dimensional region of space where a stimulus can evoke a neuronal response. In somatosensory neurons, however, space refers to a region of the body and the stimulus can be touch, vibration, temperature or pain&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(from &lt;a href=&quot;http://www.scholarpedia.org/article/Receptive_field#Somatosensory_receptive_fields&quot; rel=&quot;nofollow&quot;&gt;Scholarpedia&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially, the somatosensory input is &quot;filtered&quot; at all of those stops along the way and refined in terms of things such as whether the sensation came from the center or the edges of the receptive field, etc.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cells in the cortex (the waypoint for the sensory information) are organized in &lt;a href=&quot;http://en.wikipedia.org/wiki/Cortical_minicolumn&quot; rel=&quot;nofollow&quot;&gt;microcolumns&lt;/a&gt;, which are representative of a particular location on the body (and arranged topographically into the &quot;homunculus&quot;, as the other answer mentions).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of this follows what is called the &lt;a href=&quot;http://www.d.umn.edu/~jfitzake/Lectures/DMED/SensoryPhysiology/GeneralPrinciples/CodingTheories.html&quot; rel=&quot;nofollow&quot;&gt;&quot;labeled line&quot;&lt;/a&gt; theory, which is getting a bit outmoded due to new knowledge about ensemble coding in neurons, but for purposes of the somatosensory system it still holds up pretty well. &lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2014-06-19T22:11:32.207" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19210" PostTypeId="1" AcceptedAnswerId="19211" CreationDate="2014-06-19T23:38:43.557" Score="3" ViewCount="379" Body="&lt;p&gt;&lt;strong&gt;Background:&lt;/strong&gt; I'm currently performing research in mathematical biology, &#xA;specifically on the treatment dynamics of HIV and TB co-infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt; Can a person infected with TB disease, who are undergoing treatment for it, infect a person with no history of TB bacteria in their body? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reformulation:&lt;/strong&gt; In other words, is there a similar analogue for TB as for HIV, wherein an HIV+ person undergoing treatment for HIV will have a lowered viral load and thus have negligible chances of infecting a person with no history of HIV?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please note that my model does not incorporate latent TB because it would become too complicated to analyze. I am focusing only on TB disease because &lt;strong&gt;only it&lt;/strong&gt; is infectious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any help.&lt;/p&gt;&#xA;" OwnerDisplayName="user4800" LastEditorDisplayName="user4800" LastEditDate="2014-06-19T23:46:46.917" LastActivityDate="2014-07-11T03:55:50.700" Title="TB disease - treatment and infection" Tags="&lt;infection&gt;&lt;tuberculosis&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19211" PostTypeId="2" ParentId="19210" CreationDate="2014-06-20T06:44:02.853" Score="5" Body="&lt;p&gt;First there is one major difference between HIV and TB: As long as the TB bacteria are still susceptible to treatment (which is developing into a major problem in some regions of the world) there is a effective treatment which can eradicate the infection. For HIV this is not possible. Here we can only lower the viral load (sometimes under the detection limit), but when the treatment is stopped, the virus will return.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then it seems that patients under treatment of a drug susceptible TB are infectious for a longer time than previously thought. Until now they have been isolated at the beginning of the treatment (typically around the first two weeks) until three consecutive sputum samples had been negative. Then they were released from isolation and thought to be non-infectious. At this point they are not cured, the treatment has to go on for several weeks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now there is newer research indicating that patients can still be infectious although they are under treatment &lt;em&gt;and&lt;/em&gt; have negative sputum samples. It seems here that the currently used detection method is not sensitive enough. See these references for more information:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23224098&quot;&gt;How Many Sputum Culture Results Do We Need To Monitor&#xA;Multidrug-Resistant-Tuberculosis (MDR-TB) Patients during Treatment?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24278293&quot;&gt;High incidence of tuberculosis, low sensitivity of current diagnostic&#xA;scheme and prolonged culture positivity in four colombian prisons. A&#xA;cohort study.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20624064&quot;&gt;Prolonged infectiousness of tuberculosis patients in a directly&#xA;observed therapy short-course program with standardized therapy.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-20T06:44:02.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19212" PostTypeId="1" CreationDate="2014-06-20T07:05:05.487" Score="8" ViewCount="261" Body="&lt;p&gt;It's a thing of common sense that if you read, drive or look at computer screen for too long your eyes will get tired. They burn, itch and try to close all the time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I was wondering which part(s) of them need rest so much... Blinking muscles? Lense muscles? Or the eyeball is drying out?&lt;/p&gt;&#xA;" OwnerUserId="6918" LastActivityDate="2014-06-20T09:01:53.490" Title="Which part of human eyes is getting tired?" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19213" PostTypeId="2" ParentId="19212" CreationDate="2014-06-20T08:47:50.237" Score="4" Body="&lt;p&gt;These symptoms have a name: Computer vision syndrome.&#xA;Basically our eyes are made to look at longer distances from 1-6 meters without much accommodation. Typically computer screens are located at a much closer distance (30-50cm), which requires constant accommodation by the eye. This leads to high stress on the muscles in the eye which subsequently get tired. Additionally less blinking leads to drier eyes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the common recommendations against this is to regularly focus further located objects to give the eye the chance to relax. This is sometimes called the &quot;20-20-20&quot; rule, every 20 min focus on a 20 feet (about 6 m) far object for 20 seconds. See the article in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Computer_vision_syndrome&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; and &lt;a href=&quot;http://www.public.iastate.edu/~rhetoric/105H16/cofp/smkcofp.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for more information (and probably also the linked references in the articles).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="6918" LastEditDate="2014-06-20T09:01:53.490" LastActivityDate="2014-06-20T09:01:53.490" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="19214" PostTypeId="2" ParentId="19196" CreationDate="2014-06-20T10:40:43.113" Score="3" Body="&lt;p&gt;I haven't seen this particular film, but other documentaries by Dr. Attenborough are very accurate and well done.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In contrast to Remi.b, I'm pretty sure Attenborough referred to the ancient &lt;a href=&quot;http://genome.cshlp.org/content/18/12/1944.long&quot; rel=&quot;nofollow&quot;&gt;whole genome duplication&lt;/a&gt; event in land plants recently discovered in angiosperm genomes by the presence of multiple paralogous genes. The scenario is that at a certain moment either a hexaploidization or a genome fusion event occurred and was followed by gene losses, chromosomal reorganizations and gene diversification. In Selaginella, a spikemoss, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166216/&quot; rel=&quot;nofollow&quot;&gt;no traces&lt;/a&gt; of this event were found.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A similar event, a tetraploidization, &lt;a href=&quot;http://www.nature.com/nature/journal/v453/n7198/abs/nature06967.html&quot; rel=&quot;nofollow&quot;&gt;is hypothesized&lt;/a&gt; for vertebrates.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-06-20T16:59:16.250" LastActivityDate="2014-06-20T16:59:16.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19215" PostTypeId="1" AcceptedAnswerId="19218" CreationDate="2014-06-20T10:54:35.123" Score="2" ViewCount="16917" Body="&lt;p&gt;I have read that epimysium is dense regular connective tissue made covering the a muscle like bicep brachi. at the same time we have fascia that is made of dense regular tissue and covers muscles. so are they same or different how can we describe it and differentiate it?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastActivityDate="2018-02-08T02:53:45.887" Title="Is epimysium same as fascia?" Tags="&lt;histology&gt;&lt;tissue&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19216" PostTypeId="2" ParentId="19215" CreationDate="2014-06-20T11:19:52.703" Score="1" Body="&lt;p&gt;As I understand it epimysium is not only fibrous but also contains more elastic fibres than fascia. As such it is more 'loose' than the 'dense' fascia.  It lies immediately on the surface of the muscle (epi = on, mysium = muscle) below the fascia. The deep fascia which is denser lies on top of this.&lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-20T11:19:52.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19217" PostTypeId="2" ParentId="19210" CreationDate="2014-06-20T12:50:50.723" Score="2" Body="&lt;p&gt;I think its a bit difficult to compare HIV and TB this way because TB is transmitted mainly through respiratory droplets whilst HIV is mainly through contamination of blood products/sex, etc but not via the respiratory route. As far as I know, there's still a likelihood of TB transmission from a treated patient to an untreated patient. TB is quite complex, treated patients can still undergo reactivation later in life and still infect other people-the mechanisms are not fully understood. Treated patients can also develop drug resistance and then relapse which will make them again highly infectious.  &lt;/p&gt;&#xA;" OwnerUserId="3773" LastActivityDate="2014-06-20T12:50:50.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19218" PostTypeId="2" ParentId="19215" CreationDate="2014-06-20T12:58:32.913" Score="2" Body="&lt;p&gt;Epimysium is the specialized fascia located at the muscle. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Epimysium is a layer of connective tissue, which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium &lt;sup&gt;[1]&lt;/sup&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The fascia that covers muscle is named &lt;em&gt;deep fascia&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The deep fasciae envelop all bone (periosteum and endosteum); cartilage (perichondrium), and blood vessels (tunica externa) and become specialized in muscles (epimysium, perimysium, and endomysium) and nerves (epineurium, perineurium, and endoneurium) &lt;sup&gt;[2]&lt;/sup&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Epimysium,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Epimysium&amp;amp;oldid=540536396&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Epimysium&amp;amp;oldid=540536396&lt;/a&gt; (accessed June 27, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Deep fascia,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Deep_fascia&amp;amp;oldid=593605746&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Deep_fascia&amp;amp;oldid=593605746&lt;/a&gt; (accessed June 27, 2014).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-27T16:08:07.937" LastActivityDate="2014-06-27T16:08:07.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19219" PostTypeId="1" CreationDate="2014-06-16T03:56:57.223" Score="5" ViewCount="3350" Body="&lt;p&gt;Does anyone know any good resources dealing with &lt;strong&gt;shapes of trees&lt;/strong&gt;? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, pine trees are cone shaped for optimal absorption of sunlight, but lone pine trees growing in isolation (and other commonly cone shaped conifers) often grow very high above ground and have no well-defined shape. Presumably, when there aren't neighbours to compete with for sunlight or space, the optimal shape is..well, whatever shape absorbs most sunlight; less constraints = more possibilities. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking for an answer that explains this sort of phenomenon. Thanks. &lt;/p&gt;&#xA;" OwnerDisplayName="Bonsai" LastEditorUserId="5144" LastEditDate="2014-06-20T13:50:02.093" LastActivityDate="2014-06-28T16:56:16.330" Title="Where do trees get their shape?" Tags="&lt;botany&gt;&lt;plant-anatomy&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19220" PostTypeId="2" ParentId="19219" CreationDate="2014-06-16T12:30:14.417" Score="3" Body="&lt;p&gt;Plants are genetically programmed to grow in certain shapes; many are subject to apical domination, but it's a very complicated subject, involving exterior influences such as extreme wind causing different growth, and a host of other environmental factors, together with auxin and other plant hormones impacting within the plant itself. The basic tree shapes are columnar, weeping, pyramidal, horizontal branching, vase shaped, round or globular, and all these shapes are programmed in the genetics of the plant. There is a book I know of called Dynamic Models of Plant Growth by Nikolai Bessonov, but it contains an awful lot of scientific biology stuff - I don't know of any simpler books. &lt;/p&gt;&#xA;" OwnerUserId="16674" OwnerDisplayName="Bamboo" LastActivityDate="2014-06-20T13:48:03.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19221" PostTypeId="1" AcceptedAnswerId="19223" CreationDate="2014-06-20T14:32:41.843" Score="1" ViewCount="11215" Body="&lt;p&gt;I recently learned about the concept of &quot;affinity&quot; in regards to hemoglobin. For hemoglobin in humans, carbon dioxide has a lower affinity than oxygen, which allows gas exchange to occur in our lungs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carbon monoxide is problematic for us because it has an even higher affinity to hemoglobin than oxygen does. This means that our red blood cells will not exchange carbon monoxide for oxygen in our lungs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: for high-altitude-adapted organisms such as the bar-headed goose, whose hemoglobin has a higher affinity to oxygen than ours does, is carbon monoxide still poisonous?&lt;/p&gt;&#xA;" OwnerUserId="8084" LastActivityDate="2014-06-20T15:56:42.510" Title="Carbon Monoxide and High-Oxygen-Affinity Varieties of Hemoglobin" Tags="&lt;hematology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19222" PostTypeId="1" CreationDate="2014-06-20T15:10:55.057" Score="3" ViewCount="76" Body="&lt;p&gt;A new study shows strong effects of what should be a negligible CO&lt;sub&gt;2&lt;/sub&gt; concentration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23008272&quot; rel=&quot;nofollow&quot;&gt;Is CO&lt;sub&gt;2&lt;/sub&gt; an Indoor Pollutant? Direct Effects of Low-to-Moderate CO&lt;sub&gt;2&lt;/sub&gt; Concentrations on Human Decision-Making Performance&lt;/a&gt;&quot; exposed people to three levels of CO&lt;sub&gt;2&lt;/sub&gt;: 600, 1000, and 2500 ppm while keeping constant other factors such as ventilation, humidity, temperature, and indoor pollutant concentration. Of course, the participants didn't know how much CO&lt;sub&gt;2&lt;/sub&gt; was in the air.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the 2500 ppm level, most cognitive performance measures were temporally reduced (they used the SMS management test). Some changes were drastic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since normal air is 400 ppm, 2500 ppm sounds like a lot. However, it is dwarfed by internal production. Humans exhale 50,000 ppm CO&lt;sub&gt;2&lt;/sub&gt; in the lungs, meaning that the lung air averages 25,000 ppm (as a rough approximation). The extra 2500 ppm is only a 10% increase in the average &quot;atmosphere&quot; that the blood is exposed to. Furthermore, people partially compensate increased P(CO&lt;sub&gt;2&lt;/sub&gt;) with deeper ventilation (the effect takes much larger concentrations to be noticeable). Why would this extra 10% have such a strong effect?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally I am skeptical. This study has such high impact (millions of people's performance) that it needs replication. Maybe the hissing sound of the injector got people worried (more hissing at a higher concentration!). Maybe an experimenter (who knew the concentration) was watching the people and that subconsciously affected them. &lt;/p&gt;&#xA;" OwnerUserId="4321" LastEditorUserId="11841" LastEditDate="2015-01-07T12:38:17.920" LastActivityDate="2015-01-07T12:38:17.920" Title="Are small CO₂ concentrations devastating to certain cognitive tasks?" Tags="&lt;physiology&gt;&lt;psychology&gt;&lt;respiration&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19223" PostTypeId="2" ParentId="19221" CreationDate="2014-06-20T15:56:42.510" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;My question is: for high-altitude-adapted organisms such as the bar-headed goose, whose hemoglobin has a higher affinity to oxygen than ours does, is carbon monoxide still poisonous?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes. To put out a few other facts from the Stritch School of Medicine:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;CO has 250 times the affinity for hemoglobin than O2&#xA;Hb becomes 100% saturated with CO at PCO = 0.6 mm Hg&#xA;Hb becomes 100% saturated with O2 at PO2 = 600 mm Hg &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;What does that mean? Well, that means that when the partial pressure of CO is 1mmHg, you're well and truly dead. So if the bar headed goose could survive in an environment more than 1% CO its hemoglobin would have to bind to molecular oxygen very, very tightly below 1mmHg. If this was true you would expect their binding curve to reach a high % of O2 saturation below a partial pressure of 1mmHg. Does it exhibit that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TJqa9.jpg&quot; alt=&quot;Bird hemoglobin binding curves&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nope. At 1mmHg (remember, CO has 100% binding at 0.6mmHg) the bar headed goose hemoglobin's saturation is less than 2%. In fact, they're pretty similar to humans:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9D0Gd.gif&quot; alt=&quot;Human hemoglobin curve&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this casual glance conclusive? Well... &lt;em&gt;Not entirely&lt;/em&gt;. I couldn't find any carbon monoxide data for the bar headed goose, but to overcome the 250x higher affinity for CO the goose's hemoglobin would have to be very, very different from that of humans while still exhibiting a similar binding curve. I've not received the education to determine if that's possible or how it would occur, but it is a very remote possibility.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Erring on the side of &quot;most likely&quot;, however, I think it's safe to say that given a room filled with 1% CO you'd end up eventually killing anything that relied on hemoglobin to move necessary oxygen to tissues.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2014-06-20T15:56:42.510" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19226" PostTypeId="1" CreationDate="2014-06-20T18:41:41.880" Score="3" ViewCount="972" Body="&lt;p&gt;I'm a computer science guy, recently crossing over to do some research in computational biology on RNA secondary structure prediction. While looking through the materials I got a crazy idea, what if you could design a synthetic ribosome that acts as a Turing Machine on strings of RNA? (you could do similar things with DNA enzymes)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The immediate applications could be stuff like correcting mutations in RNA to cure genetic diseases, which is a relatively simple computation: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Check if a string is bad. &lt;/li&gt;&#xA;&lt;li&gt;If so, fix bad letter.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Another could be &quot;shredding&quot; DNA/RNA of viruses: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Check if a string is a virus.&lt;/li&gt;&#xA;&lt;li&gt;If so, shred it. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I'm not sure the status of the literature on this is, or synthetic biology's ability to create something like that. Do you think it is a good idea to pursue this idea or not?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize this is a soft question. Perhaps a better one would be, is this possible? &lt;/p&gt;&#xA;" OwnerUserId="8086" LastEditorUserId="6703" LastEditDate="2014-06-20T19:23:30.997" LastActivityDate="2019-01-04T00:41:09.470" Title="Ribosomal Turing Machines, DNA/RNA computation" Tags="&lt;dna&gt;&lt;rna&gt;&lt;synthetic-biology&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="19227" PostTypeId="1" CreationDate="2014-06-21T00:50:16.937" Score="3" ViewCount="584" Body="&lt;p&gt;I am looking for good image repositories for biology teaching. Photos and textbook-like diagrams.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested  in images that can be used commercially without payment, or, at least, that require a small one-time payment. They would be used in videos, not only on lectures, hence the worry about copyright.&lt;/p&gt;&#xA;" OwnerUserId="1167" LastEditorUserId="6422" LastEditDate="2015-09-15T16:54:07.337" LastActivityDate="2015-09-15T16:54:07.337" Title="What are good sources of free-to-use images and diagrams" Tags="&lt;book-recommendation&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19228" PostTypeId="1" CreationDate="2014-06-21T07:56:59.737" Score="1" ViewCount="50" Body="&lt;p&gt;Some days ago, I was thinking (partially) about the complex balance that is needed for an ecosystem to exist. I got curious about the existence of some sort of critical point, something - that when taken out of the system - makes life vanish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a single species that when took out of one ecosystem destroys the life in it? Perhaps there's not a single species, perhaps there could be a minimal set of species in which this could happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Excuse me for the poorly formulated question. I'm not a biology student, I just get random curiosities from time to time. &lt;/p&gt;&#xA;" OwnerUserId="783" LastActivityDate="2014-06-21T07:56:59.737" Title="Are there critical points in ecosystems?" Tags="&lt;ecosystem&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19231" PostTypeId="1" CreationDate="2014-06-21T09:32:17.497" Score="0" ViewCount="71" Body="&lt;p&gt;I wonder how, for purposes of just illustrating some concepts like substrate alignment in the catalytic triad active site, I can quickly and efficiently find a protease structure (irrelevant of what organism exactly) that has a peptide like inhibitor on the PDB database.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hints appreciated.&lt;/p&gt;&#xA;" OwnerUserId="4971" LastActivityDate="2014-06-22T01:33:39.297" Title="How to find a PDB structure of a protease with a peptide like inhibitor" Tags="&lt;pdb&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19232" PostTypeId="1" CreationDate="2014-06-21T09:41:30.387" Score="4" ViewCount="63" Body="&lt;p&gt;How can immune cells produce so many different kinds of antibodies with different variable regions if there are so many mechanisms inside the cells that try to keep the DNA sequence as constant as possible (i.e. prevent mutations, which are actually necessary to create the different kinds of antibodies)?&lt;/p&gt;&#xA;" OwnerUserId="8089" LastActivityDate="2014-06-21T09:41:30.387" Title="How can cells produce antibodies despite error-checking mechanisms in their genomes?" Tags="&lt;antibody&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19233" PostTypeId="2" ParentId="19227" CreationDate="2014-06-21T10:49:50.933" Score="3" Body="&lt;p&gt;You could use &lt;a href=&quot;http://search.creativecommons.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;CC Search&lt;/a&gt;. It allows you to find &lt;a href=&quot;http://creativecommons.org/licenses/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Creative Commons&lt;/a&gt; licensed content that you can use commercially.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ikwPf.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-06-21T10:49:50.933" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19234" PostTypeId="2" ParentId="19231" CreationDate="2014-06-21T11:10:09.357" Score="0" Body="&lt;p&gt;go to &lt;a href=&quot;http://www.uniprot.org&quot; rel=&quot;nofollow&quot;&gt;http://www.uniprot.org&lt;/a&gt; and enter the protease accession number you are interested in and look at the 3D structure databases section to see if its PDB file is deciphered or not. I came across this database (&lt;a href=&quot;http://www.cf.ac.uk/biosi/staffinfo/ehrmann/tools/proteases/allproteases.html&quot; rel=&quot;nofollow&quot;&gt;http://www.cf.ac.uk/biosi/staffinfo/ehrmann/tools/proteases/allproteases.html&lt;/a&gt;) just by typing into google &quot;protease PDB databases&quot;&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-06-21T11:10:09.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19235" PostTypeId="2" ParentId="19227" CreationDate="2014-06-21T12:39:03.593" Score="1" Body="&lt;p&gt;An excellent source for images is the wellcome collections image library &lt;a href=&quot;http://wellcomeimages.org/&quot; rel=&quot;nofollow&quot;&gt;http://wellcomeimages.org/&lt;/a&gt;. You can negotiate commercial use with them, they are very reasonable, especially if it's for teaching purposes.&lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-21T12:39:03.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19237" PostTypeId="2" ParentId="19227" CreationDate="2014-06-21T13:54:57.677" Score="4" Body="&lt;p&gt;I'm guessing the videos are for a flipped/online course and posted on YouTube or Coursera?  I've done this. Biology is hard -- perhaps because I am picky and really want good images. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I used &lt;strong&gt;Wikimedia.com&lt;/strong&gt; to search for many free images. I also contacted the publishers of the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21054/&quot; rel=&quot;nofollow&quot;&gt;free online version&lt;/a&gt; of &lt;strong&gt;Molecular Biology of the Cell&lt;/strong&gt; and asked if I could use up to 20 for my free online course, and they agreed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My university was also able to work out an agreement with the &lt;strong&gt;textbook publisher&lt;/strong&gt; to use 200 of the textbook images for the Coursera course as long as they were credited, and a link to purchasing the textbook was available on the site. They want to keep my university happy as our students buy a truckload of books every year.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've also gotten somewhat decent at using a &lt;strong&gt;drawing tablet and powerpoint&lt;/strong&gt; image (boxes, circles) manipulation to make some of my own cell processes and chromosomes and such.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, &lt;a href=&quot;https://openstaxcollege.org/&quot; rel=&quot;nofollow&quot;&gt;OpenStaxCollege.org&lt;/a&gt; has a wonderful collection of free textbooks for students, and they make their images available to faculty as free powerpoints. They aren't usually &quot;good&quot; enough to satisfy me, but definitely check them out.&lt;/p&gt;&#xA;" OwnerUserId="6517" LastActivityDate="2014-06-21T13:54:57.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19238" PostTypeId="1" AcceptedAnswerId="19241" CreationDate="2014-06-21T23:26:44.207" Score="0" ViewCount="1612" Body="&lt;p&gt;See question title. After doing some looking around on my own I haven't found much so I figured I'd ask some experts.&lt;/p&gt;&#xA;" OwnerUserId="8094" LastActivityDate="2014-06-22T18:09:49.943" Title="What is the smallest known organism with a skeleton?" Tags="&lt;taxonomy&gt;&lt;anatomy&gt;&lt;vertebrates&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2014-06-22T09:09:44.387" ContentLicense="CC BY-SA 3.0" />
  <row Id="19239" PostTypeId="1" AcceptedAnswerId="19240" CreationDate="2014-06-21T23:58:08.937" Score="3" ViewCount="1945" Body="&lt;p&gt;My question is basically out of curiosity and comes from observing how certain plants (such as mangroves or salt cedar) can grow in seawater. If this gives the plant an advantage, why haven't all plants that grow in coastal areas developed a salt tolerance? How can the plants keep from intaking salt, while absorbing other soluble nutrients through the roots?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2014-08-14T03:30:39.450" LastActivityDate="2014-08-14T03:30:39.450" Title="How do some plants grow in salt water, while others die?" Tags="&lt;cell-biology&gt;&lt;botany&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19240" PostTypeId="2" ParentId="19239" CreationDate="2014-06-22T01:23:38.530" Score="2" Body="&lt;p&gt;A few things you have to realize when you ask 'why hasn't species x evolved trait y':&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;What is the cost of evolving this trait? If you gain one trait, you lose another (or others). Everything in evolution is a tradeoff: that's why you're not nine feet tall, you'd be able to beat up all your enemies great, but it would take so much food to sustain you, it wouldn't be worth it.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Not every trait can be easily evolved. When you're starting as a freshwater plant, there are many, many, many, many mutations that have to occur for you to become salt-tolerant. Every one of those mutations would have to give a fitness advantage to be positively selected. The chances of this happening are low, which means if it happens at all, it would take a long time.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Who knows, perhaps these plants are, slowly, becoming more and more salt-tolerant and you're seeing them at an intermediate point in their evolution. Everything is evolving all the time, if these plants were not in a salty environment until recently, mutation and selection haven't had time to work their magic.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update from comment:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Can you flesh out a little on &quot;How can the plants keep from intaking salt, while absorbing other soluble nutrients through the roots?&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Sure! I'll give you the simple answer first: there are different mechanisms for absorbing salt and for absorbing nutrients, so they can function largely independently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the longer explanation: Salt and nutrients don't just diffuse (much) through cell walls, they have to be transported across by what are called transmembrane proteins. Think of the cell membrane (a layer inside the cell wall) as basically something like a layer of oil (it's called a lipid bilayer) -- you know oil and water don't mut, and for the different ions in salt (sodium ion and chloride), neither do oil and salt or oil and many nutrients so they get sort of escorted across that barrier by big proteins that form sort of a tunnel through it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's a different transport protein for different substances; the salt ones will only let salt through, and in fact there are different ones for letting salts in and letting salts out, and for the different ions (sodium and chloride) in salt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update from comment:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This makes me wonder how salt harms most plants, if it can't get in except by 'invitation'&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Quite a bit of salt can diffuse in, the molecules are small enough (unlike most nutrients) to pass through the membrane via the channels that let water in. Every living creature has a quite sophisticated setup of &quot;ion channels&quot; to pump salt out. If suddenly its cells are in a very salty environment, these pumps can't keep up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update from comment:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So if salt can diffuse in, what do salt-tolerant plants have that other plants don't?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Mostly, if I recall correctly, three things: They will have enzymes that have evolved to work in higher salt concentrations, they will have cellular functions to &quot;sequestrate&quot; salt, i.e. store it in organelles called vacuoles instead of leaving it where it can harm other organelles, and of course they will expend more resources on ion pumps to get the salt concentration in the cell to an acceptable level.&lt;/p&gt;&#xA;" OwnerUserId="8095" LastEditorUserId="338" LastEditDate="2014-06-29T02:42:05.410" LastActivityDate="2014-06-29T02:42:05.410" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19241" PostTypeId="2" ParentId="19238" CreationDate="2014-06-22T01:28:51.077" Score="3" Body="&lt;p&gt;The smallest vertebrate (if that's what you mean; there are many invertebrates with endoskeletons that are not made of bone) is &lt;em&gt;Paedophryne amanuensis&lt;/em&gt;, a Papua New Guinea frog that's about 7 mm long.&lt;/p&gt;&#xA;" OwnerUserId="8095" LastEditorUserId="948" LastEditDate="2014-06-22T18:09:49.943" LastActivityDate="2014-06-22T18:09:49.943" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19242" PostTypeId="2" ParentId="19231" CreationDate="2014-06-22T01:33:39.297" Score="1" Body="&lt;p&gt;Here's one: &lt;a href=&quot;http://www.rcsb.org/pdb/explore/explore.do?structureId=2IPH&quot; rel=&quot;nofollow&quot;&gt;http://www.rcsb.org/pdb/explore/explore.do?structureId=2IPH&lt;/a&gt;. It was crystallized with the inhibitor bound to the protein.&lt;/p&gt;&#xA;" OwnerUserId="8095" LastActivityDate="2014-06-22T01:33:39.297" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19244" PostTypeId="1" CreationDate="2014-06-22T05:07:53.020" Score="6" ViewCount="598" Body="&lt;p&gt;What's the smallest organism (animal, insect, or any living creature) that can produce voice. And not just make sound, but has an organ to specifically to create sound, like how us mamals have vocal chords. &lt;/p&gt;&#xA;" OwnerUserId="3141" LastEditorUserId="107" LastEditDate="2014-07-30T00:16:16.190" LastActivityDate="2019-01-22T10:57:19.147" Title="What's the smallest organism that can produce voice?" Tags="&lt;zoology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ClosedDate="2015-01-26T07:30:41.737" ContentLicense="CC BY-SA 3.0" />
  <row Id="19246" PostTypeId="1" CreationDate="2014-06-22T07:51:23.910" Score="11" ViewCount="3754" Body="&lt;p&gt;A virus spreads around and usually attaches itself to the host, multiplies &amp;amp; causes diseases. But is there something like an anti-virus? A single celled entity that does the opposite: spreads around 'kills' other viruses and/or cures diseases. Has anybody discovered something like it or is there any research group working on synthesizing one? If so any links to their publications?&#xA;Forgive me if I got my facts wrong, I am physical sciences person and know nothing about biology. :)&lt;/p&gt;&#xA;" OwnerUserId="8098" LastEditorUserId="8098" LastEditDate="2014-06-22T08:49:25.617" LastActivityDate="2019-12-10T11:01:52.033" Title="Is there an 'anti-virus'?" Tags="&lt;virus&gt;&lt;retrovirus&gt;" AnswerCount="5" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19247" PostTypeId="2" ParentId="510" CreationDate="2014-06-22T08:41:36.220" Score="8" Body="&lt;p&gt;A rule of thumb in optics is that light interacts with materials that have features with  dimensions similar to the wavelength of light. For example, radio waves with large wavelengths interact with large objects like airplanes ,as in the case of radars, and really small wavelengths (x-rays &amp;amp; gamma rays) interact with really small objects like nuclei of atoms. If you take the visible spectrum, light interacts with materials with similar dimensions and/or energies like the C-C, C=O etc that constitute most of the organic compounds. Heck, light with the appropriate wavelength may even interact (or get diffracted in this case) with an organic material that possess many C=O-OH groups spaced with distances similar to the wavelength of light that is shone on it (provided they are regularly spaced and there are lots of them to produce an observable result). Since all organisms are carbon-based the C-C, C=O, C-O, C=_N etc dominate the constituents of the living matter from retina of the human eye to the photosensitive compounds in plants. Hence from the light-matter-interaction perspective all living beings are made up of more or less same materials and this is the reason why plants use the similar wavelength the human eye can detect for photosynthetic processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: just my intuition&lt;/p&gt;&#xA;" OwnerUserId="8098" LastActivityDate="2014-06-22T08:41:36.220" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19248" PostTypeId="2" ParentId="19246" CreationDate="2014-06-22T11:08:15.260" Score="9" Body="&lt;p&gt;There is &lt;strong&gt;no anti-virus&lt;/strong&gt; to all viruses and there is &lt;strong&gt;no such anti-virus&lt;/strong&gt; against a single virus yet, but there is immune response to virus.&#xA;How efficient the immune response is then depends on many things. &#xA;There is no perfect immune response. &#xA;To develop such an antivirus that decreases viral load requires cooperation with the immune response. &#xA;To develop such an antivirus is still in very very early stages, since we do not understand the fine regulation of many processes going on in the viral pathogenesis and how to stop them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There exists in the nature some viruses that attack other viruses. &#xA;However, we do not understand if they attack just one or two viruses. &#xA;See Abraham's good answer &lt;a href=&quot;https://biology.stackexchange.com/a/25950/86&quot;&gt;here&lt;/a&gt; for the latest publications in Nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The immune response tries to eliminate the virus through antigen presentation and cell-mediated immune response. &#xA;The humoral immune response works in the local sides where the cell mediated immune response does not reach.&#xA;However, the immune response is sometimes (and often) insufficient to kill the virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To develop such a general anti-virus is difficult because of a variety of different viruses: (RNA vs DNA; positive sense vs negative sense; single strained vs double stranded; intracellular replication vs extracellular). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is an example of antigen presentation for HIV virus deduced from &lt;a href=&quot;https://biology.stackexchange.com/a/17970/86&quot;&gt;this answer&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7I00C.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where HIV infects the antigen presentation cells (APC) (dendritic cell and macrophages) and monocytes. &#xA;It replicates actively in the lymphatic circulation. &#xA;Since APCs are out, it is difficult to kill the virus. &#xA;To develop such a general anti-virus against HIV would require very specific understanding of many things: probably, iPS cells and development of antigen presentation cells. &#xA;My conjecture is to develop an APC cell that has receptor to HIV virus and so can reach it. &#xA;However, only theory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gamma interferon should be included in the intersection between innate and adaptive immune systems. &#xA;Interferons may play a central role in the future in the development of such anti-viral drugs, because they are specific. &#xA;For instance, the activation of IFN-gamma stimulates the phagocytosis of macrophages against the mycobacteria tuberculosis which is facultatively intracellular (can be intracellular when necessary). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Innate and adaptive immune systems are visualised on the plane in the figure. &#xA;You have then humoral immunity working around that plane as circles. &#xA;I emphasize with that the local nature of humoral immune system and how it extends the cell-mediated immune system. Any attack on the heart of this system i.e. antigen presentation will also risk the humoral immunity and thus cause fast progression of the disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, all measures that are used to decrease the viral load aim to target the immune system to express efficient way of decreasing the viral load (killing is just one of them!). &#xA;This can be done through many ways - most of which we do not know much yet. &#xA;iPS stem cell research and interferon research can be some good ways in the development of good anti-virals. &#xA;However, this will take still many years (probably at least 40-50 years) to have enough control of the specific viral pathways.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-12-26T09:25:09.197" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19250" PostTypeId="1" CreationDate="2014-06-22T13:29:49.550" Score="1" ViewCount="148" Body="&lt;p&gt;Can the &lt;a href=&quot;http://en.wikipedia.org/wiki/Psychology&quot; rel=&quot;nofollow noreferrer&quot;&gt;psychology&lt;/a&gt; of a moderate aged person alter his immune health? because I have read many a times about the different types of linkages between nervous system and immune system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone outline the general facts about what is understood in this relationship from which i would gain some knowledge?&lt;/p&gt;&#xA;" OwnerUserId="8101" LastEditorUserId="50613" LastEditorDisplayName="user8102" LastEditDate="2019-06-20T18:42:20.380" LastActivityDate="2019-06-20T18:42:20.380" Title="Can the psychology of a person alter his immune system and health?" Tags="&lt;immunology&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="19254" PostTypeId="1" AcceptedAnswerId="19274" CreationDate="2014-06-22T16:02:51.867" Score="3" ViewCount="486" Body="&lt;p&gt;This basic evolution theory question has been haunting me since childhood and I'm kind of embarrassed that I can't explain it yet:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider a butterfly. It's wings have evolved to look like the eyes of an owl, so to prevent it's predators who are themselves preys of the owl to attack it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I've learned (and feel free to indulge me in the very basics if I get this wrong), natural selection suggests that the butterflies that didn't have the owl's eyes in their wings would be eaten, leaving the ones with the eyes to survive, right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But that implies that this useful trait appeared in the butterfly's wings by chance. Now, I know trillions of butterflies have been born before this, but trying to figure out the possibility of this to happen by chance doesn't look like it's plausible. Let's go through the things that have to work right before this trait is passed over:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;For a butterfly to be born in a different wing colour, it should be a genetic mutation which doesn't happen this often, for what I know.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The wings are composed of micro-scales. For every scale to compose an image so similar that confuses even us, the margin of error is very slim. It could be anything. It could be a picture of Tom Selleck for all we know. The scales must be in the correct spectrum of colour by a small margin of error. So that is already a very unlikely thing to happen.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Then, this butterfly cannot be eaten out of bad luck (mind you, the wings don't guarantee it will not be eaten, just enlarge her chances).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It has to mate, which also is not a guarantee to happen, since nature deals with competition. If this butterfly we are considering is a male, the female must find the wings hot, instead of being afraid of those creepy eyes.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The genes of this mutations must also be dominant, so when it mates and generates offspring, at least part of the new butterflies inherit this trait.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;And this is a simple example. There are animals that evolved so smartly I can't even start to think of the possibilities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, more precisely, how likely is it for a species to evolve into complex solutions?&lt;/p&gt;&#xA;" OwnerUserId="8104" LastEditorUserId="8104" LastEditDate="2014-06-24T16:51:54.383" LastActivityDate="2014-06-24T16:51:54.383" Title="On evolution statistics" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;biostatistics&gt;" AnswerCount="2" CommentCount="15" FavoriteCount="1" ClosedDate="2014-06-24T11:50:33.257" ContentLicense="CC BY-SA 3.0" />
  <row Id="19255" PostTypeId="2" ParentId="19250" CreationDate="2014-06-22T16:11:56.607" Score="3" Body="&lt;p&gt;I'm not sure what you mean by psychology exactly, but assuming you are referring to a persons mental state there is a known link between stress and immunity. This link occurs through neuro-endocrine pathways. The central nervous system and endocrine (hormonal) systems are linked through the hypothalamus, a key controller of hormone release in the central nervous system. In a state of stress our central nervous system reacts by increasing the release of hormones such as the steroid cortisol and catacholamines such as adrenaline (a.k.a epinephrine in USA). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We know that steroids have an effect of dampening down the immune system (in fact steroids are often used for this intentionally in the case of autoimmune conditions for example). Thus based on this we have a scenario where stress can lead to increase in cortisol (and other hormones) which in turn can have an effect on your immunity. The effect to which this impacts on your life is then further dependent on your psychology and social support.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More generally, the links between illness and psychology are integrated together in what is called the biopsychosocial model of illness. I suggest you look this up to gain a more in depth understanding of this complicated issue. &lt;/p&gt;&#xA;" OwnerUserId="8034" LastEditorUserId="8034" LastEditDate="2014-06-22T17:22:03.840" LastActivityDate="2014-06-22T17:22:03.840" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19256" PostTypeId="1" AcceptedAnswerId="19259" CreationDate="2014-06-22T18:52:33.703" Score="3" ViewCount="183" Body="&lt;p&gt;Let's say that someone uses a needle which has some old blood infected with HIV. In this case, is it possible for them to get infected with HIV?&lt;/p&gt;&#xA;" OwnerUserId="8029" LastEditorUserId="57" LastEditDate="2014-06-22T19:12:20.273" LastActivityDate="2014-06-22T20:40:26.540" Title="Is it possible to get infected with HIV from old blood?" Tags="&lt;hiv&gt;&lt;infection&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19257" PostTypeId="1" CreationDate="2014-06-22T19:06:34.017" Score="4" ViewCount="708" Body="&lt;p&gt;Found in a waterway in Butte County, CA. First thought it was a beaver kit, but it has no&#xA;tail.&#xA;What aquatic mammal has no tail?&#xA;&lt;img src=&quot;https://i.stack.imgur.com/pw0lH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8106" LastEditorUserId="57" LastEditDate="2014-06-22T19:14:18.363" LastActivityDate="2014-07-04T16:31:47.930" Title="What Aquatic Mammal has no Tail?" Tags="&lt;zoology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19258" PostTypeId="1" CreationDate="2014-06-21T20:46:28.013" Score="6" ViewCount="52560" Body="&lt;p&gt;My female cat is a very active hunter and brings me her prey daily. Except for shrews and birds, she always eats them entirely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This afternoon she brought me this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CBnO4.jpg&quot; alt=&quot;Cat with rodent&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was quite large (maybe between half and two thirds of the length of a mole), and I couldn't identify it (I'm in Europe if that matters).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The prey was already dead when my cat brought it to me, and she quickly started eating it. I noticed that she didn't eat this part:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OGwwr.jpg&quot; alt=&quot;rodent Organs&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not a biologist, but I guess this is the stomach of an herbivorous animal?  What's inside looked like wasabi.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why didn't she eat it? She is not so picky with smaller animals. Is it because of the size of this one?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there some organs or parts of the prey that cats usually don't eat ? &lt;/p&gt;&#xA;" OwnerUserId="8133" OwnerDisplayName="user3585425" LastEditorUserId="16866" LastEditDate="2017-03-22T01:10:35.207" LastActivityDate="2017-03-22T01:10:35.207" Title="Which organs do cats not eat on their prey?" Tags="&lt;zoology&gt;&lt;food&gt;&lt;anatomy&gt;&lt;mammals&gt;" AnswerCount="4" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19259" PostTypeId="2" ParentId="19256" CreationDate="2014-06-22T20:40:26.540" Score="4" Body="&lt;p&gt;Yes, you can transmit HIV with infected needles/syringes. This is a quite common mechanism of transmission when drug addicts share and re-use needles and syringes and also in third world hospitals with poor hygiene standards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A drop of blood is considered infectious at least until it has completely dried up (some research showed that it might be contagious for up to 5 days longer when the conditions are right, see reference 1 below). Mostly HIV is senstive against high temperatures (over 60°C), while it is stable at low temperatures. It is very sensitive against shifts in pH (below 7 or above 8) and also against desinfectants like bleach. Have a look at the references below, a lot of research has been done by Abdala et al. in this field. You can find his whole reference list &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=Abdala%20N%5BAuthor%5D&amp;amp;cauthor=true&amp;amp;cauthor_uid=10921429&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; (it contains more articles in this field).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1802953&quot; rel=&quot;nofollow&quot;&gt;Survival of HIV-1 activity after disinfection, temperature and pH&#xA;changes, or drying.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9928733&quot; rel=&quot;nofollow&quot;&gt;Survival of HIV-1 in syringes.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10921429&quot; rel=&quot;nofollow&quot;&gt;Survival of HIV-1 in syringes: effects of temperature during&#xA;storage.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10932845&quot; rel=&quot;nofollow&quot;&gt;Viability of HIV-1 in syringes: implications for interventions among&#xA;injection drug users.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-22T20:40:26.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19260" PostTypeId="2" ParentId="19258" CreationDate="2014-06-22T21:27:55.767" Score="2" Body="&lt;p&gt;I think it depends on hunger, preferences....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Domestic cats can pretty much eat it all.  They might discard items they can't digest like fur, relatively large bones... other than that what they leave behind is rather individual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm guessing this cat doesn't like salads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Typically I haven't seen hunting cats discard digestive organs.  Aside from fur and big bones sometimes they might discard a head (probably because they don't feel like dealing with the skull).&lt;/p&gt;&#xA;" OwnerUserId="6093" LastActivityDate="2014-06-22T21:27:55.767" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19262" PostTypeId="2" ParentId="19258" CreationDate="2014-06-23T02:10:40.563" Score="6" Body="&lt;p&gt;That looks like some sort of rodent.  The rodent stomach, while not as acidic as the human one, is still strongly acidic: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The mouse stomach pH was 3.0 (fed) and 4.0 (fasted), and the corresponding values in the rat were 3.2 (fed) and 3.9 (fasted).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;From &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18088506&quot; rel=&quot;noreferrer&quot;&gt;this article&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since it's clear from the picture that the organism had just eaten (the stomach had not yet emptied), the pH would be on the lower end of that spectrum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In humans, acidic foods often taste &lt;a href=&quot;http://en.wikipedia.org/wiki/Taste#Sourness&quot; rel=&quot;noreferrer&quot;&gt;sour&lt;/a&gt;, so it may be that the cat ran into a terrible taste at the base of the esophagus that caused her to stop there, but I don't know whether the taste buds on the cat are comparable to those in a human. &lt;/p&gt;&#xA;" OwnerUserId="57" LastActivityDate="2014-06-23T02:10:40.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19264" PostTypeId="2" ParentId="19254" CreationDate="2014-06-23T08:46:25.840" Score="6" Body="&lt;p&gt;In your 5 points you basically cover several concepts of evolutionary biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) The number of mutations depend on mutation rate. The mutation rate varies along genome sequences, species and individuals. According to the recent DECODE study (Kong et al., 2012) a human mother transmit on average 15 mutations to her offspring and a human father transmit on average $25 + 2(g-20)$ mutations to his offsprings, where $g$ is the age of the father and where the formula stands only for father older than 20 years old.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Mutations happen by chance and are not directed toward creating some specific feature. But it is much more likely to create a round of color on the wings of a butterfly than creating the picture of Tom Sellek. The reason has to do with the developmental and biochemical pathways linking the given mutation to its phenotypic effect. Looking at a given mutation, you can understand how it yield to the modification of some phenotypic trait by looking at the biochemical and devlopmental pathways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3,4) The third point that you raise is called &quot;genetic drift&quot;. Shortly speaking the concept of genetic drift may be called the good luck/bad luck effects. Stating differently genetic drift is the random sampling of alleles (gene variant) from a population. If some alleles are favored over some others at a given locus, then sampling is not 100% random but is not either 100% deterministic. The only case where genetic drift is absent is in infinite population (which is obviously an unrealistic case). Genetic drift is inversely propotional to population size and you'll understand it better by reading &lt;a href=&quot;https://biology.stackexchange.com/questions/14543/why-is-the-strength-of-genetic-drift-inversely-proportional-to-the-population-si&quot;&gt;this post&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5) When the mutation is at very low frequency, the mutation needs to be dominant in order to be expressed, this is true. But an allele may increase in frequency due to genetic drift up to the point that some individuals are homozygous for this allele and therefore express the trait. Dominance and recessivity are just extreme case of a continuum and most often alleles have intermediate level of dominance. Pleiotropy is also something to consider. Note also thaat the frequency of the three possible genotypes $AA$, $AB$ and $BB$ are given by Hardy-Weinberg law (under some assumptions) $x^2$, $2x(1-x)$ and $(1-x)^2$ respectively, where $x$ is the frequency of the allele $A$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-06-23T12:36:25.767" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19265" PostTypeId="1" AcceptedAnswerId="19271" CreationDate="2014-06-23T09:08:22.157" Score="2" ViewCount="289" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2EzHy.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which of the following demonstrates the pattern of development in Greylag Geese? {Please give specific answers, which among the following gives the best available demonstration?, If needed, have a look at the Paragraph (Image Embedded)}&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(A) Geese reared by humans cannot be taught to respond to its own species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(B) The hatching at an advanced stage is critical for imprinting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(C) The capacity to recognize an adult of its own species is necessarily inherited.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(D) Rearing by humans does not alter the object of the behavioral routine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Option A: “Geese reared by humans cannot be taught to respond to its own species” is correct.&#xA;This is inferred from the 4th paragraph 2nd line: “When young geese are reared wholly by human beings it is towards humans that the young geese direct their behavioural routines”. This line clearly states that geese wholly reared by humans respond only towards humans. Also from the 2nd Paragraph 3rd line It is clear. &#xA;Option B: “The hatching at an advanced stage is critical for imprinting” is false.&#xA;Hatching at an advanced Stage is not shown by Greylag Geese, it is shown by Godwits. (3rd Paragraph, 1st &amp;amp; 2nd Line: The young of Godwits hatch at an advanced stage of development and soon after hatching can recognize the adult bird.) (So the fact is not conclusive from Behavioural Pattern of Greylag Geese) Imprinting can be shown by Greylag Geese, which do not have a prolonged period of hatching, and imprinting totally depends on whatever creature happens to be present at the right moment in their development. &#xA;Options C: “The capacity to recognise an adult of its own species is necessarily inherited” is false. According to the 2nd Paragraph, 2nd line: The capacities to recognise the right stimulus are not always inherited. &#xA;Option D: “Rearing by Humans does not alter the object of the behavioural routine.” is false, as shown in 4th Paragraph 2nd &amp;amp; 3rd line: When young geese are reared wholly by human beings it is towards humans that the young geese direct their behavioural routines.&#xA;Hence, answer should be A.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So Am I correct?&lt;/p&gt;&#xA;" OwnerUserId="8111" LastEditorUserId="8111" LastEditDate="2014-06-23T10:10:09.393" LastActivityDate="2014-06-23T16:14:35.827" Title="Which of the following demonstrates the pattern of development in Greylag Geese?" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19266" PostTypeId="2" ParentId="5558" CreationDate="2014-06-23T10:56:13.537" Score="3" Body="&lt;p&gt;&lt;em&gt;This reply needs to contain a number of links to qualify each of my claims. Unfortunately this site won't allow me to include more than two links because I am a new user. Please see &lt;a href=&quot;http://www.reddit.com/r/NaturalTheology/comments/28v2ib/chromosome_2_fusion_a_response_to_a_question_on/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this post&lt;/a&gt; which contains the same response and all the necessary links as well.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be very careful trusting any claims published by the young earther Jeffrey Tomkins. In my experience, each of his claims needs to be thoroughly researched because I have found him to be less than rigorous (sloppy) in &lt;a href=&quot;http://www.reddit.com/r/NaturalTheology/comments/2625uu/my_first_reply_to_jeffrey_tomkins/&quot; rel=&quot;nofollow noreferrer&quot;&gt;at least one other paper he has published&lt;/a&gt;. He has faced similar accusations from others in the past.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not saying dismiss everything he says: I'm saying take all of his claims with a grain of salt, expect there to be exaggerations, errors and misleading claims (he has a young earth creationist agenda)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are ever concerned about anything he writes, you will need to look at the evidence for yourself. I will attempt to answer your questions here.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In a 30 kb region surrounding the fusion site, there exists a paucity of intact telomere motifs (forward and reverse) and very few of them are in tandem or in frame.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is true, but it isn't surprising (at least not to me). To quote popular science blogger, &lt;a href=&quot;http://blogs.discovermagazine.com/loom/2012/07/23/and-finally-the-hounding-duck-can-rest/#.U6fwp_ldW1c&quot; rel=&quot;nofollow noreferrer&quot;&gt;Carl Zimmer&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The ends of chromosomes are very vulnerable places. If they simply dangle loosely, DNA-cutting enzymes can nibble away at them, destroying the genes they encounter. The dangling end of one chromosome can also get attached to the dangling end of another, fusing chromosomes together. We are mostly protected from such changes thanks to special proteins called telomerases. They tack on little repeating bits of DNA, which form a loop–a telomere–so that chromosomes end as a hairpin curve, rather than dangling ends.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is this loop that prevents chromosomes from undergoing the type of fusion that we see in the second chromosome. Now telomeres naturally shorten and become mutated with age. If we encountered two fused chromosomes (with the telomeres joined end to end) we should expect that this could only happen where the telomeres are short enough and mutated enough to allow this to happen. Only when they can no longer form that protective loop, can they become fused.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Experiments like &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9335332&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; have shown that defective telomeres with few repeats are vulnerable to chromosome fusion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is what the fusion site &lt;a href=&quot;https://i.imgur.com/CJRRUGo.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;actually looks like&lt;/a&gt; - the highlighted repeating elements (TTAGGG and CCCTAA) are those that are still perfectly formed. If I relax my criteria a little and also highlight those repeating elements that have just one single mutation, this is what the fusion &lt;a href=&quot;https://i.imgur.com/r7d0Woa.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;site looks like&lt;/a&gt;. To raise doubts that what we are looking at here are a series of repeats of &quot;TTAGGG&quot; joined to a series of repeats of &quot;CCCTAA&quot; is either asinine or dishonest.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Telomere motifs, both forward and reverse (TTAGGG and CCTAAA), populate both sides of the purported fusion site. Forward motifs should only be found on the left side of the fusion site and reverse motifs on the right side &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;(Note: it is CCCTAA not CCTAAA)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is just pure nonsense, I am tempted even to call it a lie but I can't be sure. I have looked into this claim by searching through the 20,000 bases that surround the fusion site. &#xA;In those 20,000 bases there is exactly 1 instance of TTAGGG that occurs before the fusion site and 1 instance of CCCTAA that occurs before the fusion site (No more than we should expect to occur by chance alone in any sequence this long).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After the fusion site (and away from it), there is 1 more instance of CCCTAA and 3 more instances of TTAGGG (No more than we should expect to occur by chance alone in any sequence this long).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Don't take my word for it. &lt;a href=&quot;https://db.tt/aKV6jN50&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here are 20,023 bases&lt;/a&gt; that surround the fusion site.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The 798-base core fusion-site sequence is not unique to the purported fusion site, but found throughout the genome with 80% or greater identity internally on nearly every chromosome; indicating that it is some type of ubiquitous higher-order repeat.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This sounds like more rubbish (even a lie perhaps). Using BLAT to search for the &lt;a href=&quot;https://db.tt/gqxBG3h8&quot; rel=&quot;nofollow noreferrer&quot;&gt;actual sequence&lt;/a&gt;, there is no location in the human genome except for this place on chromosome 2 where we see a sequence of repeating TTAGGG joined to a sequence of repeating CCCTAA. If the authors claim to have found another site like this, why have they not linked to it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We could also use BLAT to search for an &lt;a href=&quot;https://db.tt/9VqSPWea&quot; rel=&quot;nofollow noreferrer&quot;&gt;idealised sequence&lt;/a&gt; of perfect repeats. Once again, the only hit that includes both the TTAGGG and the CCCTAA is in this exact location on chromosome 2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We do unsurprisingly find sequences of repeating TTAGGG but what makes this fusion site unique is that those repeats are followed by repeating CCCTAA - that isn't found anywhere else in our genome of over 3 billion base pairs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think about that for a moment. A sequence with a signature as unique as this, found in the exact place where scientists expect to find it!&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;No evidence of synteny with chimp for the purported fusion site was found. The 798-base core fusion-site sequence does not align to its predicted orthologous telomeric regions in the chimp genome on chromsomes 2A and 2B.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;First of all, this claim doesn't even make sense. The 798 bases he talks about are just the telomeric repeats. If they are telomeric repeats then they will be found on the telomeres of chromosomes 2A and 2B. Perhaps he made a mistake here and was talking about the wider region surrounding this fusion site? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is true that there is a lack of synteny in the wider region surrounding this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This became well understood with the sequencing of the gorilla genome. There was a &lt;a href=&quot;http://genome.cshlp.org/content/22/6/1036.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper published&lt;/a&gt; explaining how this happened in 2012. If you prefer, here is the &lt;a href=&quot;http://blogs.discovermagazine.com/loom/2012/07/19/the-mystery-of-the-missing-chromosome-with-a-special-guest-appearance-from-facebook-creationists/#.U6QayvldW1d&quot; rel=&quot;nofollow noreferrer&quot;&gt;layman's explanation&lt;/a&gt; with diagrams.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Queries against the chimp genome with the human alphoid sequences found at the purported cryptic centromere site on human 2qfus produced no homologous hits using two different algorithms (BLAT and BLASTN).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This isn't true either. Where does he get this nonsense from? I have downloaded the alphoid sequences from the defunct centromere on human chromosome 2 and used BLAT (against Chimpanzee Feb 2011) to find their homologs in the chimpanzee. Unsurprisingly they are exactly where we expect to find them on chimpanzee chromosome 2B - &lt;em&gt;where there is a functional centromere&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think about that for a moment. The very same sequences that form a functioning centromere on chimpanzee chromosome 2B are found exactly where we expect to find them at a defunct centromere on human chromosome 2. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am busy constructing a detailed write-up on this. I will update this post to provide a link to that.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Alphoid sequences at the putative cryptic centromere site are diverse, form three separate sub-groups in alignment analyses, and do not cluster with known functional human centromeric alphoid elements.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I can't comment on the first claim but it seems irrelevant anyway. I can tell you that these alphoid sequences occur frequently at centromeres all over the human genome from X to 22. More importantly they are appear almost exclusively at centromeres. For example, alphoid 2 appears at centromeres on the following chromosomes: 21, 9 (twice), 11 (twice), 20 (twice), 7 (3x), 22 (5x), 16, 14, 15, 5.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears once at an unexpected location on chromosome 9 where there isn't a centromere, but that exact location is rich in other alphoid sequences suggesting that it too is a defunct centromere (or was perhaps duplicated from another centromere).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This will also be covered in that detailed write-up I mentioned.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;edit (2 Oct 2015):&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I promised to follow up on this post with a detailed write-up on the fossil centromere on chromosome 2. I've done that now (A year and a bit later) - you can find the information I've compiled on the centromere &lt;a href=&quot;https://www.reddit.com/r/junkscience/comments/3n4vim/the_chromosome_2_fusion_site_part_2_the_fossil/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8112" LastEditorUserId="8112" LastEditDate="2015-10-02T11:05:34.427" LastActivityDate="2015-10-02T11:05:34.427" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19267" PostTypeId="1" AcceptedAnswerId="19268" CreationDate="2014-06-23T11:46:57.000" Score="6" ViewCount="7947" Body="&lt;p&gt;I have heard that max heart rate declines steadily with age, and can be approximated by the equation Max Rate = 220 - Age.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the physiological reason for this decline, and how is it consistent with the fact that most endurance athletes reach their peak cardiovascular performance at around age 30?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2014-06-23T12:06:46.707" Title="Why does max heart rate decrease with age?" Tags="&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19268" PostTypeId="2" ParentId="19267" CreationDate="2014-06-23T11:58:17.603" Score="7" Body="&lt;p&gt;There are many reasons why the maximal heart rate decreases with age. &#xA;The most prevalent is the heterogenous thickening of the walls of the heart.&#xA;Cardiac output is stroke volume times heart rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the wall thickens, the heart needs more energy to achieve the same pumping (bigger stroke volume) or it needs to increase heart rate at rest. &#xA;Because of physical limitation, the stroke volume cannot be increased. &#xA;Heart needs to also rest which it does before the action potential reaches the AV conduction system. &#xA;Note the long time just after the action potential reaches AV node. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the heart cannot increase its maximal heart rate if the elasticity of the walls have decreased in ageing. &#xA;Ageing often leads to heterogenous thickening of walls of the heart. &#xA;If this is the case, then T wave gets high fast; which causes the risk of bleeding when exercising. &#xA;Doing sport or just feeling tired can cause a long-standing pain in the heart area in the chest. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sport then again leads to dynamic hypertrophy of the heart tissue, which increases the maximal heart rate. &#xA;Ageing then again does not have such a dynamic changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are secondary reasons caused by ageing&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;hormonal changes&lt;/li&gt;&#xA;&lt;li&gt;decreased metabolism&lt;/li&gt;&#xA;&lt;li&gt;decreased physical activity &lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which are associated with decreased maximal heart rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why most endurance athletes reach their peak cardiovascular performance at around age 30?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human's best age is at about 25 years old physiologically. &#xA;Muscles grow in rest. &#xA;When practicing at that age, recovery time of muscles is short. &#xA;It takes long time to improve cardiovascular performance (1-5 years), since heart muscle improves slowly. &#xA;I think the slow hypertrophy of heart musculature and the best physiological age of human are the reasons why the most successful endurance athletes are about 28-30 years old.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-06-23T12:06:46.707" LastActivityDate="2014-06-23T12:06:46.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19271" PostTypeId="2" ParentId="19265" CreationDate="2014-06-23T15:06:10.600" Score="1" Body="&lt;p&gt;Your logic seems fine to me.. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Option B: The hatching at an advanced stage is critical for imprinting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is wrong because &lt;a href=&quot;http://en.wikipedia.org/wiki/Konrad_Lorenz&quot; rel=&quot;nofollow noreferrer&quot;&gt;Konrad Lorenz&lt;/a&gt; (who rediscovered imprinting) &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;demonstrated how incubator-hatched geese would imprint on the first&#xA;  suitable moving stimulus they saw within what he called a &quot;critical&#xA;  period&quot; between 13–16 hours shortly after hatching (&lt;a href=&quot;http://en.wikipedia.org/wiki/Imprinting_%28psychology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So saying that the hatchling should be at an advanced stage is incorrect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Option C: The capacity to recognize an adult of its own species is necessarily inherited.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again this is incorrect because Lorenz has also stated that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The human-imprinted gosling will unequivocally refuse to follow a&#xA;  goose instead of a human, but it will not differentiate between a&#xA;  petite, slender young girl and a big old man with a beard (Lorenz,&#xA;  1965) (&lt;a href=&quot;http://en.wikibooks.org/wiki/Applied_History_of_Psychology/Attachment&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also in &lt;a href=&quot;http://www.starlingcentral.net/keeping_a_starling.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt; it is implied that starlings that are imprinted to humans do not relate to its own kind. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Option D: Rearing by humans does not alter the object of the behavioral routine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the earlier findings, this is obviously false. Moreover a duck keeper has explained imprinting thus: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An imprinted duck--a duck that was raised from the moment of hatching&#xA;  by a human and so views the human caretaker as a parent or equal--may&#xA;  become accustomed to riding in the car. Imprinted ducks might go&#xA;  camping with you (although you must keep them beside you at all times&#xA;  or in a crate) or go on play dates to a friend's house (you will not&#xA;  want to take them to a farm or a public pond where they may contract&#xA;  diseases). If your duck is in a diaper, you will need to change the&#xA;  diaper every hour or so (&lt;a href=&quot;http://shantiperez.hubpages.com/hub/Keeping-Pet-Ducks-and-Geese&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This shows clear behaviour changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Option A:  Geese reared by humans cannot be taught to respond to its own species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is mostly accepted that it is not with Lorenz himself stating that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;imprinting is irreversible. It is essential in learning that what has&#xA;  been learned can be either forgotten or modified (&lt;a href=&quot;http://www.muskingum.edu/~psych/psycweb/history/lorenz.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However there are claims to the contrary nowadays with it now firmly established that filial and sexual preferences are reversible (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1801945&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;). &lt;a href=&quot;http://www.apa.org/monitor/2011/12/imprinting.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;Another interesting article&lt;/a&gt; by the American Psychological Association with a few links you might want to check out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion, Option A could also have its problems with some response to its species possible, but overall it is the most and best plausible answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fCXtn.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dr Lorenz with his imprinted geese. Also a very interesting read (&lt;a href=&quot;http://www.cerebromente.org.br/n14/experimento/lorenz/index-lorenz.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-06-23T15:28:54.237" LastActivityDate="2014-06-23T15:28:54.237" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="19272" PostTypeId="2" ParentId="17873" CreationDate="2014-06-23T15:29:17.617" Score="2" Body="&lt;p&gt;Almost certainly not. Species occupy different niches due to their differing growth rates and tolerances. Interspecies quorum sensing and the symbiotic relationship that implies do exist(see: lichen), but open-air inoculation is unlikely to produce them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why would the Brettanomyces simply kill time waiting for 'their turn'? It's likely they don't grow as fast as S. cervisiae or other early fermenters, and as a result they're outcompeted until alcohol content rises enough to slow or stop other species. Brettanomyces isn't 'waiting', they're eating and growing as fast as they possibly can. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many microorganisms form spores or simply hibernate until conditions are favorable for growth. For highly acid and alcohol-tolerant species, perhaps they sporulate until the mix is acidic enough to guarantee them habitat. This is a form of quorum sensing, but the transmission medium is pH and alcohol concentration. &lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-06-23T15:29:17.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19273" PostTypeId="1" AcceptedAnswerId="19279" CreationDate="2014-06-23T15:48:17.340" Score="2" ViewCount="323" Body="&lt;p&gt;&lt;strong&gt;margarine&lt;/strong&gt; is commonly used food ingredients that contribute to both inflammation and &lt;/p&gt;&#xA;&#xA;&lt;p&gt;obesity , but actually I want to know the &lt;strong&gt;margarine metabolism&lt;/strong&gt; in the human body &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can find some resources talk about its impact on health but I can't get the idea of its metabolism.&lt;/p&gt;&#xA;" OwnerUserId="8115" LastActivityDate="2014-07-23T18:36:53.873" Title="what is the margarine metabolism in our body?" Tags="&lt;metabolism&gt;&lt;health&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19274" PostTypeId="2" ParentId="19254" CreationDate="2014-06-23T15:54:09.507" Score="6" Body="&lt;p&gt;Remi.b's answer is great, but here's something less technical if that's what you're looking for:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Genetic mutations happen ALL THE TIME. Every time a cell divides, there is an error rate of about one per billion. That's a very low error rate per division, but when you multiply it by the number of divisions, times the number of cells, times the number of individuals, times the number of years the species has existed... well, that's a lot of mutations. Mind you, way fewer mutations will get passed along to offspring, because the vast majority of mutations are non-advantageous (because there a lot more ways to make a bad butterfly than a good one). But that's the job of selection, not mutation.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Evolution is a step-by-step process. There doesn't just have to be mutation and advantage, there has to be an advantage every step of the way. If big circles were selected for, that means intermediate forms (smaller circles, perhaps?) were selected for too. A blob that sort of looks like Tom Selleck will not confer as many fitness advantages as a blob that looks a lot like Tom Selleck (assuming the butterflies' predators hate Magnum P.I., which as far as I'm concerned is a perfectly reasonable assumption ;-)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Lots of butterflies get eaten by bad luck. But it's unlikely any trait was the result of one mutation in one individual (although it does happen sometimes). There are lots of mutations happening, and if one individual doesn't pass it along, another will. Think of this: maybe 100,000,000 years ago some butterfly developed a mutation that would be ten times more effective at discouraging predators than the owl-eye circles ... but then it got stepped on by a dinosaur. You'd never know it happened, and you're left eons later wondering how a way less impressive mutation happened.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There's natural selection, and there's sexual selection. Maybe the females don't like the owl-eye wings so those butterflies mate half as often as their more attractive brethren. But if the resulting offspring is four times more likely to survive, that ugly butterfly just won the gene pool lottery.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;That's a common misconception, traits don't have to be dominant in order to be selected for. Think of this: lactose intolerance is dominant, but in many populations lactose intolerant people are in the minority, because after the domestication of the cow being lactose intolerant was enough of a disadvantage to make those people less likely to have offspring.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;One of the concepts people most often lack when dealing with evolution is of scale. You're looking at a tiny, tiny, tiny fraction of all the mutations that could have possibly happened and thinking, &quot;What are the odds that that happened, it seems so improbable!&quot; But that's because you're not seeing the trillions and trillions and trillions of mutations that could have happened if random chance had taken things in an ever so slightly different direction. SOMETHING had to happen, it's the laws of physics. You're only able to see and be amazed by what did happen... well, because it's the thing that ended up happening. The more you think about it, the easier it is to wrap your mind around.&lt;/p&gt;&#xA;" OwnerUserId="8095" LastActivityDate="2014-06-23T15:54:09.507" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19275" PostTypeId="2" ParentId="10741" CreationDate="2014-06-23T16:01:13.890" Score="2" Body="&lt;p&gt;It is not consistent, and so cannot function as a temporal or generational signal. Not because the telomere shortening is unpredictable, but because of &lt;a href=&quot;http://www4.utsouthwestern.edu/cellbio/shay-wright/publications/Dev%20Gen18.173.1996%20Germline%20Embryonic.pdf&quot; rel=&quot;nofollow&quot;&gt;telomerase activity in the embryo.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it did, gamete production in specialized tissues like the ovaries or testes would have shorter telomeres than the zygote they originated from. Each generation would have shorter telomeres than their parents. They would be genetically 'older', which can't go on forever.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Development is incredibly complicated and mediated by a large number of genes. Try &lt;a href=&quot;http://en.wikipedia.org/wiki/Hox_gene&quot; rel=&quot;nofollow&quot;&gt;homeobox genes&lt;/a&gt; for developmental layout.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-06-23T16:01:13.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19277" PostTypeId="1" AcceptedAnswerId="19278" CreationDate="2014-06-23T17:08:45.353" Score="4" ViewCount="3322" Body="&lt;p&gt;As far as I know TAENIA SOLIUM is an acoelomate which basically means that the space between the alimentary canal and the gut is completely filled [or] occupied by the mesoderm and they do not have primary body cavity as well as secondary body cavity then from where does the space comes in taenia to store that huge amount of eggs &lt;img src=&quot;https://i.stack.imgur.com/RlLMq.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user8102" LastEditorUserId="1320" LastEditDate="2014-06-23T18:53:12.547" LastActivityDate="2014-06-23T18:53:12.547" Title="How can Taenia solium (tapeworm) lay 35,000 eggs per proglottid?" Tags="&lt;reproduction&gt;&lt;eggs&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19278" PostTypeId="2" ParentId="19277" CreationDate="2014-06-23T17:50:05.150" Score="5" Body="&lt;p&gt;The eggs are very small compared to the proglottid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://pathmicro.med.sc.edu/parasitology/cestodes.htm&quot;&gt;this site&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;T. saginata can be up to 4 to 6 meters long and 12 mm broad; it has a pear-shaped head (scolex) with four suckers but no hooks or neck. It has a long flat body with several hundred segments (proglottids). Each segment is about 18 x 6 mm with a branched uterus (15-30 branches). The egg is 35 x 45 micrometers, roundish and yellow-brown. It has peripheral radial striations and contains an embryo with 3 hooklets.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;T. solium is slightly smaller than T. saginata. It has a globular scolex with four suckers and a circular row of hooks (rostellum) that gives it a solar appearance. There is a neck and it has a long flat body (0.1 meter in length). The proglottids are 5 x 10 mm with a 7-12 branch uterus. The eggs of T. solium and T.  saginata are indistinguishable.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I assume that the measurements given for the &lt;em&gt;T. solium&lt;/em&gt; proglottid relate to the dimensions of your diagram, and since this is a tapeworm it is thinner than either of these values, so let's assume 2 mm to make the arithmetic easy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;volume of proglottid = 5 * 10 * 2 * 10&lt;sup&gt;-9&lt;/sup&gt; = 100 * 10&lt;sup&gt;-9&lt;/sup&gt; = 10&lt;sup&gt;-7&lt;/sup&gt; m&lt;sup&gt;3&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The egg approximates to a 40 &amp;micro;m sphere = 33,500 * 10&lt;sup&gt;-18&lt;/sup&gt; m&lt;sup&gt;3&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, volume of 35,000 eggs = 1.2 * 10&lt;sup&gt;-9&lt;/sup&gt; m&lt;sup&gt;3&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, volume occupied by eggs = (1.2 * 1010&lt;sup&gt;-9&lt;/sup&gt; * 100)/1010&lt;sup&gt;-7&lt;/sup&gt; % of proglottid = 1.2 %&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, not much of an accommodation is required for the volume of the eggs, even allowing for errors in this approximation (e.g. I neglected spherical packing which would add somewhat to the volume occupied by the packed eggs).&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-06-23T17:50:05.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19279" PostTypeId="2" ParentId="19273" CreationDate="2014-06-23T18:00:12.363" Score="2" Body="&lt;p&gt;As pointed to by @Chris &lt;a href=&quot;http://en.wikipedia.org/wiki/Margarine&quot; rel=&quot;nofollow&quot;&gt;the Wikipedia link for margarine&lt;/a&gt; explains that these are formulated upon vegetable oil-based fats. Their melting points and other properties are adjusted by industrial hydrogenation of the unsaturated fatty acids in the vegetable oil. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most unsaturated fatty acids present in nature are in the &lt;em&gt;cis&lt;/em&gt; conformation at the double bonds. The hydrogenation process, if it is not carried to completion, produces the &lt;em&gt;trans&lt;/em&gt; isomers of fatty acids. These so-called &lt;a href=&quot;http://en.wikipedia.org/wiki/Trans_fatty_acids&quot; rel=&quot;nofollow&quot;&gt;trans-fats&lt;/a&gt; are blamed for the undesirable side effects of consuming margarine, or other foods containing hydrogenated oils.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the fatty acids present in margarine (i.e. &lt;em&gt;cis&lt;/em&gt; unsaturated and saturated fatty acids) are metabolised by the normal route (&amp;beta; oxidation).&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-06-23T18:00:12.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19280" PostTypeId="2" ParentId="17883" CreationDate="2014-06-23T18:07:33.933" Score="2" Body="&lt;p&gt;The question of &quot;why are there no/few aquatic trees?&quot; can be approached in two ways.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Why are land trees tall? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is it harder to be tall in a lake?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Land trees are tall to shade competitors and &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2011.01867.x/abstract&quot; rel=&quot;nofollow&quot;&gt;spread their seeds and fruits&lt;/a&gt;. To get tall, they need extensive root structures to anchor and provide enough water to the trunk. If there are no competitors to shade out and the water provides long-distance seed dispersal, why bother growing tall?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's much harder to be tall in a lake. &lt;a href=&quot;http://en.wikipedia.org/wiki/Mangrove#Nutrient_uptake&quot; rel=&quot;nofollow&quot;&gt;Nutrient uptake&lt;/a&gt; is a problem, as is proper anchoring. Large amounts of organic biomass may exist, but iron, phosphorus, and other micronutrients are more important. A large oak can be &lt;a href=&quot;http://sylva.org.uk/oneoak/tree_facts.php&quot; rel=&quot;nofollow&quot;&gt;15 tons&lt;/a&gt;, which is harder to support using only sediment on the lakebed. It's also understandably difficult to germinate and sprout if you're an aquatic tree. See mangrove propagules for an example of the problems and how to get around them(sort of). Most mangrove species need lenticels in the trunk to provide enough oxygen, and long roots require periodic pneumatophores to provide oxygen to the roots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at all the pressures on plant life in lakes, it's a lot of work to be a tree, and much easier to be a lilypad. More of the biomass can be concentrated on photosynthesis, and structural concerns are a lot less troublesome. Additionally, many lakes simply do not have the nitrogen or phosphorus content to support tree-sized growth. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Trophic_state_index&quot; rel=&quot;nofollow&quot;&gt;trophic state index&lt;/a&gt; in lakes. If the lake can't support algae, there's no way it can support a tree.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="8244" LastEditDate="2014-11-20T13:29:37.860" LastActivityDate="2014-11-20T13:29:37.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19281" PostTypeId="2" ParentId="19093" CreationDate="2014-06-23T18:19:19.983" Score="1" Body="&lt;p&gt;The seedless grape technically has a seed, but the seed has no hard outer shell and is microscopic/invisible. These seeds aren't viable. Technically you could isolate out the seed tissue from the grape and grow it in specialized germination medium, but that process also works for any other part of the grape plant. Hooray cuttings! Certainly the seedless grape would not grow if you put it in the ground.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fruit part of the seeded grape is 'bait' to get animals to ingest the grape and carry the seeds within inside their digestive tracts. The goal is distance, but the surrounding feces provides bonus nutrients. The fruit is not designed to feed the seedling grape, but instead to act as bait for herbivores. The grape is mostly sugars and water, which makes them excellent bait but not amazing plant food. Plants can make sugar from the sun and pull water from the ground, but nitrogen and phosphorus are harder to come by.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Contrast fruit (which are for animals) with coconuts, which are examples of large fruit storing lots of calories for the seedling itself. The coconut flesh isn't as sweet as fruit, and it's much harder to get at. &lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-06-23T18:19:19.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19282" PostTypeId="1" CreationDate="2014-06-23T18:45:04.897" Score="3" ViewCount="181" Body="&lt;p&gt;Even though your brain can't feel pain, &lt;a href=&quot;https://biology.stackexchange.com/a/3740/6918&quot;&gt;thingies in your head are installed to compensate for that&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Once I thought your head starts to hurt when your brain is tired. I can't believe this any more. Several times I happened to skip sleep completely - while intellectually working (not just watching TV or something like that). The next day I didn't go to sleep to prevent breaking the day/night biorhythm. Yet I don't remember any headaches from not sleeping enough - and working instead.&lt;/p&gt;&#xA;&lt;p&gt;However, when I was worrying about something deeply I often got a headache to the top. Also, you get headache when you're ill. You get them after drinking too much alcohol (or getting poisoned by some other things too as I've heard).&lt;/p&gt;&#xA;&lt;p&gt;As non-biologist I believe that pain receptors are triggered when whatever they're guarding is damaged. Also I thought that they're installed so that you can do something about the cause of the pain - that doesn't seem possible in case of headaches.&lt;/p&gt;&#xA;&lt;p&gt;But I do &lt;strong&gt;hope&lt;/strong&gt; that headache doesn't mean that my brain is sustaining damage.&lt;/p&gt;&#xA;&lt;p&gt;So what's triggering pain sensors? Is it a chemical/hormone that is released when the organism feels endangered (by illness or something else)?&lt;/p&gt;&#xA;" OwnerUserId="6918" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-06-23T21:28:23.320" Title="What causes headaches (biologically)? What does it mean directly?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;human-anatomy&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ClosedDate="2014-06-23T20:47:35.507" ContentLicense="CC BY-SA 3.0" />
  <row Id="19283" PostTypeId="1" CreationDate="2014-06-23T19:43:08.030" Score="3" ViewCount="332" Body="&lt;p&gt;Many have heard about the fabled &quot;immortal&quot; jellyfish, &lt;em&gt;Turritopsis dohrnii&lt;/em&gt;, which doesn't die from aging (senescence) and can revert the aging process indefinitely. It is rather remarkable that only one, or very few species show this type of behavior.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder if at some earlier point in evolution, when life was predominantly simpler and sea based, there were more species with this feature, but this &quot;immortality&quot; caused overpopulation and/or didn't allow for proper action of natural selection, meaning that &quot;immortal&quot; species didn't evolve much and got wiped out almost entirely by whatever phenomenon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this scenario, aging and dying from old age would be an important evolutionary trait which would allow for populations to maintain reasonable sizes and would allow for natural selection to impart changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering how plausible all of this is, since I'm not an expert in the area and know little about the appropriate technical concepts behind these things.&lt;/p&gt;&#xA;" OwnerUserId="8117" LastActivityDate="2014-06-26T16:24:20.733" Title="Senescence, immortality and evolution?" Tags="&lt;evolution&gt;&lt;senescence&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19285" PostTypeId="2" ParentId="3045" CreationDate="2014-06-23T20:45:54.610" Score="1" Body="&lt;p&gt;I'm going to answer the question of whether aestivation/hibernation can be activated in humans or other apes, because it's more interesting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mammals, as a clade, have three major subgroups. Bats, shrew-likes, rodents, and then everything else including primates. One family of the shrew-likes hibernates, some rodents(but not all) and some bats can hibernate or enter a period of extended torpor. The only kind of primate that can hibernate is the dwarf lemur, which does so in a strange way(fully asleep for 6-8 months, little regulation of body temperature). Other hibernating animals regulate their temperature but keep it low, and wake to roll over or whatever every couple of days. Plus lemurs are on the edge of the mammal cladogram, so they're just pretty weird.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phylogenetically, it's not likely(imho, but I'm not a mammalian phylogenetics expert) a primate ancestor of humans has ever had the ability to hibernate. It seems more likely that primates lost the ability if it was a capability of mammalian ancestors and dwarf lemurs re-evolved it. It's possible atavistic remnants of such a system might still exist, but extensive hormonal and possibly surgical treatments would be required to induce it. Not to mention you can wake animals from hibernation by poking them, so it probably would be a substandard anaesthesia method. &lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-06-23T20:45:54.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19287" PostTypeId="2" ParentId="19283" CreationDate="2014-06-23T22:17:39.380" Score="2" Body="&lt;p&gt;You will find &lt;a href=&quot;https://biology.stackexchange.com/questions/17077/why-does-evolution-not-make-our-life-longer?rq=1&quot;&gt;here&lt;/a&gt; a very good overview of the main hypotheses that explain senescence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure I will answer your question but here are some reactions to your post..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you say has to do with species selection. Selection selects between various objects/units that differ. These objects may be genes, individuals, populations, species, etc… In other words, there are various level of selection or different units on which selection acts. &lt;a href=&quot;http://en.wikipedia.org/wiki/Unit_of_selection&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wiki&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally speaking, it is often assumed better to think in terms of selection acting on alleles (gene variants) or on individuals. Therefore, we tend to think that selection acting on genes or on individuals is more effective than selection acting on species. However, selection acts on species and we should not necessarily discard explanation using the concept of species selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you say, if I am not mistaken, if we consider a set of species that are either mortal or immortal, we would predict that selection would benefit the mortal ones. Stating differently, mortal species have some advantage over immortal species that allow them to not get extinct or eventually to speciate more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I don't quite understand the reasons why immortality would be deleterious to species. You say that it leads to overpopulation. So would you expect that a population is lead to overpopulation due to immortality and suddenly disappear because it is overcrowded. It doesn't sound like a well formulated argument to me. You could however argue that mortal species have a much greater individual turnover allowing them to adapt faster to environmental change than would immortal species.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-06-26T16:24:20.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19288" PostTypeId="1" CreationDate="2014-06-23T23:10:52.497" Score="0" ViewCount="117" Body="&lt;p&gt;A &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemostat&quot; rel=&quot;nofollow&quot;&gt;chemostat&lt;/a&gt; is a device to maintain a cell culture in equilibrium, by continually pumping nutrients in and pumping excess cells and nutrients out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the simplest design of a chemostat one can make? Has anyone tried to mount one without pumps?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A particularly sensitive issue here is sample taking, because you risk contamination of the culture.&lt;/p&gt;&#xA;" OwnerUserId="561" LastActivityDate="2014-06-24T13:35:42.423" Title="Simple experimental design of a chemostat without pumps" Tags="&lt;experimental-design&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19290" PostTypeId="2" ParentId="7528" CreationDate="2014-06-23T23:53:18.413" Score="2" Body="&lt;p&gt;I was in a car accident age 19. Jaw was wired shut, food access was limited to one broken front tooth. It was liquid diet or nothing. &#xA; So, I drank a lot of foods in liquid form, ( soups, etc. ) and a lot of Gerber's baby foods, and just about anything that could be pulverized in a blender. &#xA; I gained weight like crazy. About 15 pounds in 2 months. &#xA; The body takes advantage of having the harder work of digestion done for it. One of the advantages of cooking food is it's easier to digest. It is believed by some that such benefits to our life are the reason humans became the dominant force on this planet. &lt;/p&gt;&#xA;" OwnerUserId="8119" LastActivityDate="2014-06-23T23:53:18.413" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19291" PostTypeId="1" AcceptedAnswerId="19296" CreationDate="2014-06-24T03:18:48.237" Score="0" ViewCount="49" Body="&lt;p&gt;Is there an enclosed biosphere that artificially simulates the movement of the sun and moon at increased intervals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is known that &lt;a href=&quot;http://www.howplantswork.com/2009/07/25/does-the-moon-affect-plants-part-2-moonlight-and-biorhythms/&quot; rel=&quot;nofollow&quot;&gt;the sun and moon&lt;/a&gt; alter plant movements therefore I was wondering how far experimentation has gone.  Ideally I am wondering if they have experimented with different speeds of the moon and sun rotation and how it effects plant(and possibly other animal behavior ideas) growth.&lt;/p&gt;&#xA;" OwnerUserId="8120" LastActivityDate="2014-06-24T15:16:54.213" Title="Biosphere that simulates sun and moon shifts" Tags="&lt;human-biology&gt;&lt;biological-networks&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19292" PostTypeId="2" ParentId="10373" CreationDate="2014-06-24T05:28:37.013" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://arohatgi.info/WebPlotDigitizer&quot; rel=&quot;nofollow&quot;&gt;WebPlotDigitizer&lt;/a&gt; is an online application that can also be used to make distance and angle measurements in an image.&lt;/p&gt;&#xA;" OwnerUserId="8121" LastActivityDate="2014-06-24T05:28:37.013" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19293" PostTypeId="1" AcceptedAnswerId="19299" CreationDate="2014-06-24T11:59:24.543" Score="2" ViewCount="96" Body="&lt;p&gt;Beside energy and heat, I don't know any useful physical information of a protein. Can you help me list some of it. Somethings like Fourier-transform infrared spectroscopy to provide protein structure aren't what I'm looking for. &lt;/p&gt;&#xA;" OwnerUserId="6786" LastEditorUserId="6786" LastEditDate="2016-02-19T12:08:57.480" LastActivityDate="2016-02-19T12:08:57.480" Title="What are some useful physical information of a protein?" Tags="&lt;proteins&gt;&lt;biophysics&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19294" PostTypeId="2" ParentId="19288" CreationDate="2014-06-24T13:35:42.423" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.aslo.org/lo/toc/vol_13/issue_4/0720.pdf&quot; rel=&quot;nofollow&quot;&gt;Here is a link&lt;/a&gt; to a design in which electrolysis is used to generate gas which displaces liquid from the reservoir into the culture chamber, which in turn displaces culture into an outflow (where samples could be collected). The design does however require a pump for aeration, and I can't think of a way in which this could be avoided, although there is a reference cited in this article which apparently describes the use of gravity flow (I haven't checked it out).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just for interest, &lt;a href=&quot;http://www.eclf.net/sites/eclf.net/files/file/Tools%20%24%20Info/Chemostat%20Design%20and%20Theory.pdf&quot; rel=&quot;nofollow&quot;&gt;this link&lt;/a&gt; is to a design which does require a peristaltic pump and a vacuum line but it looks to be achievable.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-06-24T13:35:42.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19295" PostTypeId="2" ParentId="19293" CreationDate="2014-06-24T14:10:20.897" Score="2" Body="&lt;p&gt;All the information about a protein, biochemical or functional is encoded in its structure, which are primary (Amino Acid (AA) sequence), secondary (alpha helix or beta pleated sheet), tertiary (overall 3D structure of a single peptide) and quaternary (overall 3D-structure of a protein composed of multiple peptides which are attached together through various different bonds) structures (&lt;a href=&quot;http://en.wikipedia.org/wiki/Protein_structure&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Protein_structure&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously, the key determinants for all these structures is the AA sequence of a protein, since that determines the biochemical property of a protein as well as its function (e.g. enzymatic residues and active sites, functional domains, motifs, whether it is post-translationally modified or not by phosphorylation and whether that causes its activation or inactivation through conformational changes or its interaction with other proteins etc).&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-06-24T14:10:20.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19296" PostTypeId="2" ParentId="19291" CreationDate="2014-06-24T15:16:54.213" Score="2" Body="&lt;p&gt;Sun and moon-faking devices exist. Not sure about 'biosphere'. I have personally observed one for honeybees, but that one was fairly crude(bees are dumb). It was just a big room with a hive stand in the middle and a series of fluorescent lights on the ceiling that turned on one after the other. The goal was to mess with bee circadian rhythms and see which genes became more or less expressed in their brains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's a slightly more sophisticated thing called a 'grow cabinet'. It has expensive lights to produce sun-spectrum light at direct sunlight intensity and humidity and temperature controls. Scientists use them for crop research when the weather is too random and unpredictable and absolute control is required.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe advanced versions simulate moonlight and angle of insolation, but that sort of thing is expensive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know of any full-sized biodomes with fake celestial objects. The cost of such a biodome would be prohibitive, and the experiments it enabled might be easier(certainly cheaper) to do in a smaller container.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-06-24T15:16:54.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19297" PostTypeId="2" ParentId="17924" CreationDate="2014-06-24T17:03:29.523" Score="3" Body="&lt;p&gt;I would caution you against using phrases such as &quot;completely cured&quot; or even &quot;cured&quot;. This goes beyond our technical ability to detect the presence of tumor cells within someone's body. All we can conclude is progression-free survival (i.e. living with cancer that does not get worse) or disease-free survival (i.e.  or no signs or symptoms of the tumor). Many of these data are included in cancer trials along with overall survival rates. Some general statistics for many groups of cancers can be found here: &lt;a href=&quot;http://www.cancer.gov/statistics/find&quot; rel=&quot;nofollow&quot;&gt;http://www.cancer.gov/statistics/find&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And a glossary of terms used in reporting cancer statistics here: &lt;a href=&quot;http://www.cancer.gov/statistics/glossary&quot; rel=&quot;nofollow&quot;&gt;http://www.cancer.gov/statistics/glossary&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5284" LastActivityDate="2014-06-24T17:03:29.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19298" PostTypeId="1" CreationDate="2014-06-24T17:19:13.180" Score="1" ViewCount="110" Body="&lt;p&gt;According to Charles Darwin, as the surrounding environment changes, so changes the anatomy or morphology of a specific organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But nowadays, humans have become very advanced in the technology and when the surrounding temperature changes, humans in turn change the surrounding temperature (e.g. the use of ACs), and maintain the surrounding as they like.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I want to emphasize is can human being evolve with these scopes in mind?&lt;/p&gt;&#xA;" OwnerUserId="8101" LastEditorUserId="6703" LastEditDate="2014-06-25T15:29:20.957" LastActivityDate="2014-06-25T15:29:20.957" Title="Can human change its morphology or anatomy due to ecological changes?" Tags="&lt;evolution&gt;&lt;human-anatomy&gt;&lt;ecology&gt;&lt;adaptation&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19299" PostTypeId="2" ParentId="19293" CreationDate="2014-06-24T17:31:54.613" Score="2" Body="&lt;p&gt;I'll make a list, by wavelength then 'others'.  This is only the most common techniques list.  i'd be here all week if I tried to get all the applications.  Scientists are crafty and are always coming up with stuff.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Electro magnetic protein derived measurements:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;NMR spectroscopy (radio) - can detect the structural variations in&#xA;the individual amino acids allowing a protein structure with the&#xA;dynamics of the peptide chain to be modeled.   &lt;/li&gt;&#xA;&lt;li&gt;IR spectroscopy - can&#xA;look at bond-bond vibrations.  Mostly used to observe for non-peptide&#xA;moities and cofactors of the protein like heme in hemoglobin for&#xA;instance.  &lt;/li&gt;&#xA;&lt;li&gt;RAMAN spectroscopy - also an IR spectroscopy, but which&#xA;can look for dynamic qualities of the interatomic vibrations.  Like&#xA;IR this is used with cofactors usually and not the protein, which&#xA;looks very much the same over most of a peptide.&lt;/li&gt;&#xA;&lt;li&gt;UV/visible spectroscopy - on the low end, examine the behavior or concentration of chromophores associated with the protein.  used for kinetics - study of enzymes in the act of catalysis.  On the high end can also be used for things like watching photon-energy transduction in photosynthetic systems and things like this. The peptide itself has no Visible absorption, but the colored molecules are often used as a probe to watch the peptide in action - like folding.&lt;br&gt;&#xA;FRET is a technique that can measure how far apart two colored labels are - two separate points of a protein are labelled and a distance measurement obtained. &lt;/li&gt;&#xA;&lt;li&gt;UV circular dichroism.  the aromatic side chains of Phe, Trp, Tyr, His etc absorb in the UV and are directly observed to follow folding some times.  Circular dichroism looks for differences in the absorption of right and left circularly polarized light and can show secondary structure.  &lt;/li&gt;&#xA;&lt;li&gt;X-ray.  Scattering of proteins in solution can measure the so called 'radius of gyration' which profiles the overall shape of the protein.  X-ray scattering off of 2D and 3D crystals can reveal the molecular protein structure.  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Others:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Calorimetry.  By tracking the heat capacity/heat given off/taken in by a protein, its folding state, binding and other structural characteristics of a protein sample can be measured. &lt;/li&gt;&#xA;&lt;li&gt;Mass Spectroscopy - generally this just measures whether a protein is present, by fragmenting it and measuring the mass of the fragments.  useful for mixtures of many proteins (like a living cell).&lt;/li&gt;&#xA;&lt;li&gt;Peptide sequencing - like Mass Spec, but often used when there is just one protein in a pure sample.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There's lots more - just depends on where you want to cut off the list.  Hopefully this is a good start. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-06-24T17:31:54.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19302" PostTypeId="2" ParentId="9506" CreationDate="2014-06-25T03:32:59.950" Score="4" Body="&lt;p&gt;Internal or external ears is Not Relavent to an animal giving birth or laying eggs...&#xA;Examples&#xA;Sea Lions - External Ears - Live Birth&#xA;Seal - Internal Ears - Live Birth&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sharks - Internal Ear - Eggs (Oviparous), Live Birth (Viviparious), and Egg cases in mothers womb hatch producing young that feed on siblings before a live birth (Ovoviviparious)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dolphins - Internal Ears - Live Birth&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Frogs - Have an external ear drum - Lay Eggs&#xA;Exhidna (mammal) - Internal Ears - Lay Eggs&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no relation to animal ears being internal(inside)/external(outside) to laying eggs or giving live birth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am a Biologist having worked at with a large variety of animals (egg layers and live birth) for 14 years. Feel free to ask any questions you may have. And by all means please do your own research to see the information I've provided is accurate. &#xA;Great Inquary, I hear of lots of fun facts to remember things...some true,  some not&#xA;True Fact...&#xA;You can SEE a SEA Lions ears but&#xA;A SEALS ears are SEALED up&lt;/p&gt;&#xA;" OwnerUserId="8128" LastEditorUserId="5762" LastEditDate="2014-06-25T04:39:29.900" LastActivityDate="2014-06-25T04:39:29.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19303" PostTypeId="1" AcceptedAnswerId="19306" CreationDate="2014-06-25T07:03:14.340" Score="14" ViewCount="33391" Body="&lt;p&gt;I bought a blood pressure monitor (A&amp;amp;D UA-851) which has the option to measure irregular heartbeat.  I do understand what 'irregular' means, but why do irregular heartbeats happen and what are it's implications short and long term? &lt;/p&gt;&#xA;" OwnerUserId="8129" LastEditorUserId="5762" LastEditDate="2014-06-25T10:54:03.263" LastActivityDate="2016-02-16T15:19:57.003" Title="What does irregular heartbeat mean in simple language?" Tags="&lt;cardiology&gt;&lt;medicine&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19306" PostTypeId="2" ParentId="19303" CreationDate="2014-06-25T11:04:11.260" Score="13" Body="&lt;p&gt;The normal cardiac cycle is comprised of two distinct phases: &lt;strong&gt;the systolic phase&lt;/strong&gt; in which the heart contracts, ejecting the blood, followed by the &lt;strong&gt;the diastolic phase&lt;/strong&gt; when the cardiac muscle relaxes, refilling the heart with blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This cycle is assured by specialised cardiomyocytes (Cardiac muscle cells) that conduct electrical impulses through the heart. When there's interference in this electric activity, the cycle becomes irregular or arrhythmic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Arrhythmias can be divided by their place of origin: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Atrial (atria are the upper chambers of the heart)&lt;/li&gt;&#xA;&lt;li&gt;Ventricular (ventricles are lower chambers of the heart)&lt;/li&gt;&#xA;&lt;li&gt;Junctional (the junction between the two)&lt;/li&gt;&#xA;&lt;li&gt;Heart blocks (caused by a blockade in the conductivity of the electrical specialised cardiomyocytes)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Some arrhythmias are physiological, such as the Respiratory sinus arrhythmia, a naturally occurring variation in heart rate that occurs during a breathing cycle. Also, in healthy individuals, some extra sistoles might occur without being the translation of a subjacent heart condition and have benign prognosis in individuals without other conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, some arrhythmias can have a wide range of health implications, from asymptomatic, to a mild intolerance to exercise, to Cerebrovascular Accident (CVA or stroke) or even sudden death due to cardiac arrest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therapeutic varies with the underlying cause but can be medical (with drugs such as Na+, K+ and Ca+ channel blockers, beta-blockers and Digoxin) or surgical (ie: Artificial pacemaker).&lt;/p&gt;&#xA;" OwnerUserId="6543" LastActivityDate="2014-06-25T11:04:11.260" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="19307" PostTypeId="1" CreationDate="2014-06-25T12:28:38.497" Score="3" ViewCount="1050" Body="&lt;p&gt;I'm looking for a software to calculate Fst from 3 loci DNA data of individuals from a metapopulation. I don't have any prior on the population structure (have no idea of the number of subpopulations for example)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been looking at &lt;a href=&quot;http://www2.unil.ch/popgen/softwares/fstat.htm&quot; rel=&quot;nofollow&quot;&gt;FSTAT&lt;/a&gt; but it doesn't run on MAC. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you have any easy alternative? &lt;/p&gt;&#xA;" OwnerUserId="4113" LastActivityDate="2015-12-17T09:09:46.807" Title="Software to calculate Fst from sequence data" Tags="&lt;bioinformatics&gt;&lt;population-biology&gt;&lt;software&gt;&lt;population-genetics&gt;&lt;fst&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19308" PostTypeId="1" CreationDate="2014-06-25T13:34:47.057" Score="1" ViewCount="112" Body="&lt;p&gt;I'm dealing with MRI DCE maps. Actually I need to find such parameters as the transfer constant &lt;span class=&quot;math-container&quot;&gt;$K^{trans}$&lt;/span&gt; and rate constant &lt;span class=&quot;math-container&quot;&gt;$k^{ep}$&lt;/span&gt; according to the two-compartment model.&#xA;Mathematically, this dynamic system can be described by the following equation:&#xA;&lt;span class=&quot;math-container&quot;&gt;$$C_t(t)=DK^{trans} \sum\limits_{i=1}^2 a_i [exp(-k^{ep}t) - exp(-m_it)]/[m_i-k_{ep}]$$&lt;/span&gt;&#xA;Now if I have contrast agent concentration &lt;span class=&quot;math-container&quot;&gt;$C_t(t)$&lt;/span&gt; time series from experiment I can extract transfer constant &lt;span class=&quot;math-container&quot;&gt;$K^{trans}$&lt;/span&gt;, and rate constant &lt;span class=&quot;math-container&quot;&gt;$k^{ep}$&lt;/span&gt; by least square fitting. The only problem is that I need to know &lt;span class=&quot;math-container&quot;&gt;$a_i$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$m_i$&lt;/span&gt; constants. For this purpose I use the next formula for blood plasma concentration: &lt;span class=&quot;math-container&quot;&gt;$$c_p(t)=D \sum\limits_{i=1}^2 a_i exp(-m_it)$$&lt;/span&gt;&#xA;However I can't find the relation between the blood plasma concentration: &lt;span class=&quot;math-container&quot;&gt;$c_p(t)$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$c_t(t)$&lt;/span&gt;. In the next article:&#xA; Geoff J.M. Parker et. al. &quot;Experimentally-Derived Functional Form for a Population-Averaged High-Temporal-Resolution Arterial Input Function for Dynamic Contrast-Enhanced MRI&quot;&#xA;I have found that biexponential function &lt;span class=&quot;math-container&quot;&gt;$c_p(t)$&lt;/span&gt; is used to describe AIF (arterial input function). It's presented on plot as Weinmann AIF.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/AINI5.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/AINI5.png&quot; alt=&quot;rectangles&quot;&gt;&lt;/a&gt;&#xA;&#xA;QUESTIONS:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) How Weinman AIF and High temporal resolution AIF can describe the same processes, actually from mathematical point of view it's two completely different functions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Do I really can find &lt;span class=&quot;math-container&quot;&gt;$a_i$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$m_i$&lt;/span&gt; parameters by fitting AIF curve with &lt;span class=&quot;math-container&quot;&gt;$C_p(t)$&lt;/span&gt; function?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. I'm just a programmer so I completely unaware in the field of biology and any help is appreciated.&lt;/p&gt;&#xA;" OwnerUserId="8131" LastEditorUserId="15950" LastEditDate="2019-02-21T09:30:59.543" LastActivityDate="2019-02-21T09:30:59.543" Title="Weinman AIF and High temporal resolution AIF difference" Tags="&lt;mri&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="19309" PostTypeId="2" ParentId="17696" CreationDate="2014-06-25T15:00:42.013" Score="1" Body="&lt;p&gt;Ants, slime molds, and brains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0003347205003994&quot; rel=&quot;nofollow&quot;&gt;Ants&lt;/a&gt; and &lt;a href=&quot;http://www.nytimes.com/2012/05/13/opinion/sunday/the-wisdom-of-slime.html?_r=0&amp;amp;adxnnl=1&amp;amp;adxnnlx=1349978684-vFyclEI4pd9lCwS6dI5KJA&quot; rel=&quot;nofollow&quot;&gt;slime&lt;/a&gt; &lt;a href=&quot;http://intl.pnas.org/content/109/43/17490.full&quot; rel=&quot;nofollow&quot;&gt;molds&lt;/a&gt; use simple rules to generate pretty good transportation networks in an emergent way, and brains wire and rewire themselves constantly(adding/removing edges, but not usually nodes). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolutionary networks, metabolic networks, and ecological networks are much harder to get concrete data sets from, because of the time and space scales involved. (I mean the time scale over which node addition/deletion and edge modification takes place, which is in evolutionary time)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Slime mold shapes, ant paths, and neuron traces are all reproducible in the lab, however. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0957417409000384&quot; rel=&quot;nofollow&quot;&gt;Antlike algorithm&lt;/a&gt;s are pretty common, so you could run one of those and then examine the graph it puts out as it works. Those aren't precisely biological networks, but certainly biomimetic. If the subtleties are likely to be important, you might have to physically get some ants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're looking for premade databases of slime mold or ant experiments, you might try contacting the authors of the &lt;a href=&quot;http://intl.pnas.org/content/109/43/17490.full&quot; rel=&quot;nofollow&quot;&gt;PNAS paper&lt;/a&gt;, but I don't think anyone is looking to model slime mold behavior as a graph. You could be the first!&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="4109" LastEditDate="2014-06-25T18:21:18.440" LastActivityDate="2014-06-25T18:21:18.440" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19310" PostTypeId="1" AcceptedAnswerId="19331" CreationDate="2014-06-25T15:32:56.167" Score="12" ViewCount="8346" Body="&lt;p&gt;Not all carcinogens are mutagens. Alcohol and estrogen, for example, does not damage DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's one of the assumptions of the Ames test that mutagenicity implies carcinogenicity, but is this &lt;em&gt;always&lt;/em&gt; the case? I assumed that it was, but then I &lt;a href=&quot;https://biology.stackexchange.com/questions/14399/carcinogens-how-do-they-work?rq=1&quot;&gt;saw one of the comments here&lt;/a&gt;. I did some more research but the internet seems to be reluctant to be definitive on the subject. &lt;a href=&quot;https://answers.yahoo.com/question/index?qid=20120324145935AAa36mO&quot; rel=&quot;nofollow noreferrer&quot;&gt;This guy&lt;/a&gt; claims 'no', but I'd prefer sources or at least a response that handles counterexamples like HPV. &lt;a href=&quot;http://carcin.oxfordjournals.org/content/25/3/299.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;This paper&lt;/a&gt; claims 'yes', but doesn't list any specific examples. Some mutagens might be more specific to genes involved in cell cycle regulation, so I could see how a weak mutagen is a powerful carcinogen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, can you go the other way? Are there mutagens that just do not cause cancer? If they do not exist or are not known to exist, are they even possible?&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="3340" LastEditDate="2019-03-28T13:53:45.913" LastActivityDate="2021-03-18T10:26:57.290" Title="Are all mutagens carcinogens?" Tags="&lt;molecular-genetics&gt;&lt;terminology&gt;&lt;cancer&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19311" PostTypeId="2" ParentId="19310" CreationDate="2014-06-25T15:50:19.750" Score="1" Body="&lt;p&gt;I'm no expert on the matter, but just quoting from &lt;a href=&quot;http://en.wikipedia.org/wiki/Mutagen&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Mutagens are not necessarily carcinogens, and vice versa. Sodium Azide for example may be mutagenic (and highly toxic), but it has not been shown to be carcinogenic.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It cites &lt;a href=&quot;http://ntp.niehs.nih.gov/ntp/htdocs/lt_rpts/tr389.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Toxicology And Carcinogenesis Studies Of Sodium Azide&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;So it would appear the answer is &lt;strong&gt;no&lt;/strong&gt;. Not all mutagens are carcinogens.&lt;/p&gt;&#xA;" OwnerUserId="6703" LastEditorUserId="22057" LastEditDate="2021-03-18T10:26:57.290" LastActivityDate="2021-03-18T10:26:57.290" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="19312" PostTypeId="1" AcceptedAnswerId="19313" CreationDate="2014-06-25T16:16:17.860" Score="2" ViewCount="1916" Body="&lt;p&gt;I am not comparing a cat with leopard.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am just saying that we humans are all one type of creature and we are diverse (I am not saying we are class of mammals and phylum of etc and kingdom etc, because my religion doesn't believe in it).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So consider the class of cats they are one type of species so why aren't they diverse in phenotype like us? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do other animals, plants, unicellular organisms not have diversity in their phenotype and how they can recognize each other, like a bird always brings food to his offspring and it can't make mistake by giving it to other offspring of its own species? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So can I say they aren't diverse because of in their meiosis division their chromosomes don't cross over and random assort (alignment)? &lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="3340" LastEditDate="2014-06-26T11:34:46.070" LastActivityDate="2019-03-28T17:09:10.613" Title="Why aren't animals diverse in phenotype?" Tags="&lt;biodiversity&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ClosedDate="2014-06-26T19:45:12.353" ContentLicense="CC BY-SA 3.0" />
  <row Id="19313" PostTypeId="2" ParentId="19312" CreationDate="2014-06-25T16:42:25.147" Score="16" Body="&lt;p&gt;In your question, your assumption that animal species are less diverse phenotypically than humans is wrong. I am sure you will appreciate @terdon's answer to &lt;a href=&quot;https://biology.stackexchange.com/questions/14414/do-humans-have-enough-biological-differences-to-be-grouped-into-races-or-subspec/&quot;&gt;this post&lt;/a&gt; and @rg255 answer to &lt;a href=&quot;https://biology.stackexchange.com/questions/16385/why-do-different-humans-look-different&quot;&gt;this post&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Don't forget that we are good at detecting differences among humans (because we evolved for this purpose). We are doing much worse at telling apart animals from other species just because we have not evolved for this purpose. This is the reason why we tend to see human faces when looking at clouds but we rarely see sheep faces! Several studies (&lt;a href=&quot;http://www.nature.com/nature/journal/v414/n6860/full/414165a0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/361/1476/2155.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;) showed that sheep are able to recognize each other (and we even know the number of neurones needed to remember one face). They are probably better at telling two sheep apart than telling two human apart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another interesting fact is the so-called &lt;a href=&quot;http://en.wikipedia.org/wiki/Cross-race_effect&quot; rel=&quot;nofollow noreferrer&quot;&gt;cross-race effect&lt;/a&gt;. We, humans, are better at recognizing faces of people from our own ethnic group than faces of people from other ethnic groups. For example, a Japanese is very good at Japanese faces recognition but not good at recognizing European faces. Same is true the other way around.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As @user568459 said in the comments: some people are not able to recognize faces. This is due to a cognitive disease called &lt;a href=&quot;http://en.wikipedia.org/wiki/Prosopagnosia&quot; rel=&quot;nofollow noreferrer&quot;&gt;Prosopagnosia&lt;/a&gt; (also called face blindness). Those suffering from this disease are not better at recognizing sheep faces than human faces.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So consider the class of cats they are one type of species so why aren't they diverse in phenotype like us?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is no good definition I think of what is phenotypic diversity (no accurate and objective index to measure it) but at first sight I would tend to think that cats are more diverse than humans. One of the main features one would probably raise when talking about human diversity is skin color. And in terms of color, cats are much more diverse than humans. You may think of an extraordinary diversity when thinking of Norwegian that are taller than Indonesian (I may not have chosen the two extremes) by several centimeters on average but think about cats! The average cat weight 4 to 5 kg but some cats weight less than 2 kg and some other (like the &lt;a href=&quot;http://en.wikipedia.org/wiki/Maine_Coon&quot; rel=&quot;nofollow noreferrer&quot;&gt;coon cat&lt;/a&gt;) weight more than 10 kg (&lt;a href=&quot;http://www.cat-world.com.au/cat-world-records&quot; rel=&quot;nofollow noreferrer&quot;&gt;World Record&lt;/a&gt;: 21.3 kg). Imagine a human ethnic group that would on average weight 5 times more than another ethnic group! And think also about cats' hair length or tail shape! Humans vary in terms of facial feature (lips size, nose shape, etc.) so do cats. Some look like their face was smashed against a wall while others have a long muffle. Again I welcome you to have a look to &lt;a href=&quot;https://biology.stackexchange.com/questions/14414/do-humans-have-enough-biological-differences-to-be-grouped-into-races-or-subspec/&quot;&gt;this post&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;how they can know each like a bird always brings food to his offspring and it can't make mistake by giving it to other offspring of it's own species?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As I said above humans evolved to recognize their own. Many species also evolved in order to recognize their own. In some species individuals use smell rather than visual features in order to recognize each other (odor is also a kind of phenotypic variation). But still some species are poor to recognize each other. For a bird, it seems rather easy to not feed the wrong individual as all their offspring are usually together in the same nest. However you might be interested the lifestyle of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Common_cuckoo&quot; rel=&quot;nofollow noreferrer&quot;&gt;cuckoo&lt;/a&gt; who parasites nests of other bird species. Cuckoos' babies and particularly the inner beak resemble to the babies of the species they parasite and often the parents (often the mother only is involved in feeding the young) get fooled and feed the cuckoo.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So can i say they aren't diverse because of in their meiosis division their chromosomes don't cross over and random assort (alignment)?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No, you can't say that! Because they are diverse and because for many of the species you may think about, cross-over does occur. Their genetic diversity as well as their phenotypic diversity is as high than in humans. There is nothing extraordinary about humans (except their brain and the related fact that we predigest our food by cooking it) compare to other lineages. And there is nothing extraordinary to have one extraordinary feature (such as a big brain) that you can't find in other lineages! Many lineages are extraordinary in some sense.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2016-08-17T08:50:35.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19314" PostTypeId="1" CreationDate="2014-06-25T18:01:57.413" Score="4" ViewCount="9652" Body="&lt;p&gt;Essential amino acids also have codons.Still they are needed by humans through diet?Will those codons do synthesize amino acids for some other purposes in humans or not?If so, what is the purpose?e.g?&lt;/p&gt;&#xA;" OwnerUserId="8135" LastActivityDate="2014-06-26T07:25:03.637" Title="Essential amino acid codons" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19315" PostTypeId="2" ParentId="19312" CreationDate="2014-06-25T18:05:02.697" Score="6" Body="&lt;p&gt;I'd like to add that the variations in individuals within a species are a fundamental observation upon which modern biology is standing.  Darwin wrote at least &lt;a href=&quot;http://www.markhannam.com/essays/essay5a.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;2 chapters of Origin of Species demonstrating how animals and plants have a lot of individual variations&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Darwin's argument involved four steps.  First, he noted the wide variation between many types of living organisms: between species of plant, fish, bird and mammal; and also between different family groups within the same species; and also between different exemplars within the same family. Wherever we look - and during his five-year voyage on The Beagle in his early twenties, there were few places on earth where Darwin had not looked - we see differences between organisms: different sizes, different colours, different features, different behaviours and, of course, different survival rates. The theory of natural selection takes variation of species and within species as its starting point. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Before that era (he was not the only one who made this argument) pretty much everyone believed that all animals of a given species were the same.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It took quite a while before everyone was convinced, but an entire generation of scientists was won over.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you need a modern confirmation of this, look into cattle breeding. &lt;a href=&quot;http://www.theatlantic.com/technology/archive/2012/05/the-perfect-milk-machine-how-big-data-transformed-the-dairy-industry/256423/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Individual phenotypes make some bulls worth many thousands of dollars/euros&lt;/a&gt;.  Others nothing. Lastly, now that we understand that the basis of inheritance is in the DNA, we can quantitate the specific mutation rates in various genes and segments of DNA and show that &lt;a href=&quot;http://rd.springer.com/article/10.1007%2FBF00393984#page-1&quot; rel=&quot;nofollow noreferrer&quot;&gt;they are comparable from species to species&lt;/a&gt;.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Mutation_rate#Variation_in_mutation_rates&quot; rel=&quot;nofollow noreferrer&quot;&gt;These vary somewhat, but humans are not exceptional&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="49230" LastEditDate="2019-03-28T17:09:10.613" LastActivityDate="2019-03-28T17:09:10.613" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="19316" PostTypeId="1" CreationDate="2014-06-25T18:09:09.250" Score="13" ViewCount="1960" Body="&lt;p&gt;We know that RNA polymerase produces mRNA by reading DNA strand. Which enzyme produces the first RNA polymerase if other RNA polymerases are synthesized in the same way like other enzymes(proteins) ?&lt;/p&gt;&#xA;" OwnerUserId="8135" LastEditorUserId="5762" LastEditDate="2014-07-17T05:16:08.003" LastActivityDate="2016-06-26T23:51:54.840" Title="First RNA polymerase-mRNA" Tags="&lt;rna&gt;&lt;polymerase&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="19317" PostTypeId="2" ParentId="19314" CreationDate="2014-06-25T18:15:30.793" Score="6" Body="&lt;p&gt;You are mixing things. First: Codons have nothing to do with the synthesis of amino acids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A codon is the sequence of nucleotides on the DNA (or RNA) which code for a certain amino acid. For example UGU and UGC code for the amino acid Cysteine and given these codons it will appear in the protein being synthesized. The codons are basically a way to code the sequence of a protein with the smallest amount of information (simply by the sequence of the four nucleotides in DNA/RNA). For further information have a look at the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_code&quot; rel=&quot;nofollow noreferrer&quot;&gt;Codons&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This look like this (image from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_code&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/28NHh.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="4109" LastEditDate="2014-06-25T20:56:58.470" LastActivityDate="2014-06-25T20:56:58.470" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19318" PostTypeId="1" CreationDate="2014-06-25T20:06:29.607" Score="2" ViewCount="8546" Body="&lt;p&gt;The (male) &lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fiddler_crab&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fiddler Crab&lt;/a&gt;&lt;/strong&gt; is a famous example of an animal whose morphology exhibits &lt;strong&gt;neither mirror nor radial symmetry&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/U15Dk.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;(&lt;a href=&quot;http://en.wikipedia.org/wiki/File:Fiddler_crab_anatomy-en.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Image source&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_animals_featuring_external_asymmetry&quot; rel=&quot;nofollow noreferrer&quot;&gt;List of animals featuring external asymmetry&lt;/a&gt; is a Wikipedia article showcasing a few more animals with this property.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there a &lt;em&gt;comprehensive&lt;/em&gt; list of all such animals that have been described?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user6890" LastActivityDate="2014-12-03T02:40:50.100" Title="List of Asymmetric Animals" Tags="&lt;zoology&gt;&lt;literature&gt;&lt;species&gt;&lt;morphology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19320" PostTypeId="1" CreationDate="2014-06-25T23:40:54.690" Score="5" ViewCount="1336" Body="&lt;p&gt;According to &lt;a href=&quot;http://news.nationalgeographic.com/news/2010/05/100513-science-evolution-darwin-single-ancestor/&quot; rel=&quot;nofollow&quot;&gt;National Geographic&lt;/a&gt;, there are 23 proteins that are common to all life forms:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;All species in all three domains share 23 universal proteins, though the proteins' DNA sequences—instructions written in the As, Cs, Gs, and Ts of DNA bases—differ slightly among the three domains&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10485999&quot; rel=&quot;nofollow&quot;&gt;NCBI&lt;/a&gt; there are 324 proteins common to all life forms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How many proteins are common to all life forms, and what are their names? &lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="6" LastEditDate="2014-06-26T07:07:37.527" LastActivityDate="2014-06-26T08:46:37.163" Title="What Proteins Are Universal To All Life Forms?" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19321" PostTypeId="2" ParentId="17883" CreationDate="2014-06-26T00:28:27.377" Score="1" Body="&lt;p&gt;Cypress swamps are an example of tree like plants in lakes. There is even a lake in Louisiana called  &lt;a href=&quot;http://en.wikipedia.org/wiki/Cypress_Lake_%28Lafayette,_Louisiana%29&quot; rel=&quot;nofollow&quot;&gt;Cypress Lake&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8139" LastActivityDate="2014-06-26T00:28:27.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19322" PostTypeId="1" CreationDate="2014-06-26T01:07:35.203" Score="2" ViewCount="273" Body="&lt;p&gt;Is that because of evolution? &#xA;Does it have something to do with its amount in the universe?&#xA;Carbon compounds form the basis of all known life on Earth, and the carbon-nitrogen cycle provides some of the energy produced by the Sun and other stars as I know. &lt;/p&gt;&#xA;" OwnerUserId="8140" LastActivityDate="2014-06-26T08:35:52.417" Title="Why are we carbon-based?" Tags="&lt;carbohydrates&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19325" PostTypeId="2" ParentId="19322" CreationDate="2014-06-26T03:59:18.263" Score="3" Body="&lt;p&gt;We are carbon-based because carbon is the only molecule that is able to form the long, long chains of hundreds of molecules that are required to from proteins, DNA, etc. Absolutely no other molecule will do it. (Whatever you may have heard on Star Trek about Silicon-based life, Silicon doesn't form chains anywhere near as long.) Plus it's very handy in that its oxide is carbon dioxide, which is a gas, so using it and oxygen (another gas) as the end-points of respiration is very handy, you can get rid of a lot of gas very quickly. Silicon's oxide is, well, glass.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to know why only carbon forms long chains, it's because of its size (not too large like silicon), its medium electronegativity (it's in a middle column of the periodic table, so it forms what are called &quot;covalent bonds&quot; very easily, especially with hydrogen, the #1 element in the universe by far; covalent bonds are easy to form and easy to break) and its valence (again, because of its position on the periodic table -- it forms four bonds, the maximum for a smallish molecule, giving it the geometry to form long chains).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For life to be based on anything but carbon, it would have to be made only of smaller molecules, which to our knowledge isn't very likely. Our DNA molecule is made up of billions of atoms; it's difficult to conceive how heredity could work on a small scale.&lt;/p&gt;&#xA;" OwnerUserId="8095" LastActivityDate="2014-06-26T03:59:18.263" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19328" PostTypeId="2" ParentId="17980" CreationDate="2014-06-26T06:10:25.687" Score="1" Body="&lt;p&gt;Healthy young males have estradiol levels in the area of 20-30 pg/ml.&#xA;Also, estrogen is a group of hormones, including estradiol and estrone for example. You shouldn't think of any hormones as women hormones or men hormones really, as both genders have them all, albeit in different proportions, and generated often through different pathways/organs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;this link is the best i could find within a few seconds of a google search:&#xA;&lt;a href=&quot;http://emedicine.medscape.com/article/273153-overview&quot; rel=&quot;nofollow&quot;&gt;http://emedicine.medscape.com/article/273153-overview&lt;/a&gt;&#xA;it will really describe where and what hormones are created where and in what quantities, as well as how and where they can convert within the body into more potent steroids.&lt;/p&gt;&#xA;" OwnerUserId="8143" LastEditorUserId="8143" LastEditDate="2014-06-26T06:16:28.353" LastActivityDate="2014-06-26T06:16:28.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19331" PostTypeId="2" ParentId="19310" CreationDate="2014-06-26T06:37:21.890" Score="13" Body="&lt;h3&gt;Short answer&lt;/h3&gt;&#xA;&lt;p&gt;All mutagens are potential carcinogens unless the mutagen is highly specific to a site. As noted in the question, carcinogens need not be mutagenic.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;HPV causes oncogenic transformation of a cell because of certain proteins that it expresses. HPV is considered a carcinogen by the &lt;a href=&quot;https://monographs.iarc.fr/list-of-classifications-volumes/&quot; rel=&quot;nofollow noreferrer&quot;&gt;IARC&lt;/a&gt;. Some retroviruses are oncogenic: they might carry an oncogene or insert randomly near an endogenous proto-oncogene and cause oncogenic transformation; this phenomenon is called insertional mutagenesis (&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/books/NBK19409/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Coffin JM, Hughes SH, Varmus HE, editors. &lt;em&gt;Retroviruses&lt;/em&gt;&lt;/a&gt;). They can also integrate within a gene and knock it out. Many of these viruses are considered carcinogens by &lt;a href=&quot;https://monographs.iarc.fr/list-of-classifications-volumes/&quot; rel=&quot;nofollow noreferrer&quot;&gt;IARC&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Hepatitis viruses (B &amp;amp; C) can also induce carcinogenesis but insertional mutagenesis is not the sole mechanism (&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/16461228&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cougot et al., 2005&lt;/a&gt;; &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/19874379&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fung et al., 2009&lt;/a&gt;; &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422399/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lemon &amp;amp; McGivern, 2012&lt;/a&gt;). Hepatitis viruses are considered carcinogens by IARC.&lt;/p&gt;&#xA;&lt;p&gt;Ethanol in alcoholic beverages is considered carcinogenic by IARC. There are many substances listed as carcinogens by IARC but they are not mutagenic. The general mechanism of carcinogenesis by these substances may be prolonged inflammation or ROS generation.&lt;/p&gt;&#xA;&lt;p&gt;Loss of function of the tumour suppressor gene p53 leads to cancerous progression (&lt;a href=&quot;https://doi.org/10.1038/onc.2016.396&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chiche et al., 2016&lt;/a&gt;; &lt;a href=&quot;https://doi.org/10.1007/978-1-59259-100-8_14&quot; rel=&quot;nofollow noreferrer&quot;&gt;Venkatachalam et al.&lt;/a&gt; ISBN:978-1-59259-100-8). So an siRNA that targets p53 should be called a carcinogen. It would however not cause any mutations and is hence not a mutagen.&lt;/p&gt;&#xA;&lt;p&gt;If you consider the tools developed for genome editing, such as ZFN, CRISPR-Cas and TALEN as mutagens then they are not carcinogenic. However the term &lt;em&gt;mutagen&lt;/em&gt; is not used for these molecules. Mutagen almost always refers to a molecule that causes random mutagenesis thereby making it a potential carcinogen.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2020-01-13T16:35:00.567" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="19332" PostTypeId="2" ParentId="19314" CreationDate="2014-06-26T06:49:50.463" Score="2" Body="&lt;p&gt;Answer to the comment&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Could you please give me an example of an enzyme or any other protein produced by DNA sequence(mRNA--triplet codons--essential amino acid) with essential amino acids in it?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Partial Amino acid sequence of alpha amylase in Homo sapiens:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;MKLFWLLFTIGF&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Nucleotide sequence:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ATG AAG CTC TTT TGG TTG CTT TTC ACC ATT GGG TTC&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Below s the amino acid single letter representation table that can be referred to understand the amino acid sequence &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zKJW2.png&quot; alt=&quot;This amino acid single letter representation table can be referred to understand the amino acid sequence&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Make sure you follow the reading frame scheme to read the nucleotide sequence. Each time frame should have a triplet codon without including the previous nucleotide. I've represented it for the first few codons. You can observe essential amino acids in this protein. All the amino acids in this partial sequence are essential except glycine. Hope this helps :)&lt;/p&gt;&#xA;" OwnerUserId="8142" LastEditorUserId="3340" LastEditDate="2014-06-26T07:25:03.637" LastActivityDate="2014-06-26T07:25:03.637" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19334" PostTypeId="2" ParentId="19322" CreationDate="2014-06-26T08:35:52.417" Score="3" Body="&lt;p&gt;Too long for a comment. Just extending the answer from @prooffreader slightly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's true that long carbon chains are present in lipids, but in proteins and nucleic acids there are chains of carbon atoms interspersed with other atoms:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;nucleic acids: -C[3']-O-P-O-C[5']-C-C[3']-&#xA;&#xA;protein:       -C[alpha]-C-N-C(alpha)-&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So the ability of C to form stable bonds with N and O (and S) is also important. It is also important that these bonds with heteroatoms are not too stable, thus allowing for making and breaking bonds at physiological temperatures. Then add to this the fact that most carbon atoms in biomolecules are tetravalent so that even when they are part of a chain they can be linked to other functional groups 'hanging off' the chain (such as amino acid side chains).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This combination of properties is unique to carbon.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-06-26T08:35:52.417" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19335" PostTypeId="2" ParentId="19320" CreationDate="2014-06-26T08:46:37.163" Score="9" Body="&lt;p&gt;This question is based upon a wrong inference about the work that forms the basis of the National Geographic article, which includes this statement:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;All species in all three domains share 23 universal proteins, though the proteins' DNA sequences—instructions written in the As, Cs, Gs, and Ts of DNA bases—differ slightly among the three domains (quick genetics overview).&#xA;  The 23 universal proteins perform fundamental cellular activities, such as DNA replication and the translation of DNA into proteins, and are crucial to the survival of all known life-forms—from the smallest microbes to blue whales.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The article is referring to a paper published in Nature in 2010.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20463738&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/20463738&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This paper uses a set of 23 proteins to test the idea that certain genes arose only once.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The data set consists of a subset of the protein alignment data from ref. 27, containing 23 universally conserved proteins for 12 taxa from all three domains of life, including nine proteins thought to have been horizontally transferred early in evolution27. The conserved proteins in this data set were identified based on significant sequence similarity using BLAST searches, and they have consequently been postulated to be orthologues.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is no suggestion that there are only 23 such proteins, it's just that the author chose this subset to test his ideas.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And here they are:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;alanyl-tRNA synthetase, aspartyl-tRNA synthetase, glutamyl-tRNA synthetase, histidyl-tRNA synthetase, isoleucyl-tRNA synthetase, leucyl-tRNA synthetase, methionyl-tRNA synthetase, phenylalanyl-tRNA synthetase &amp;beta; subunit, threonyl-tRNA synthetase, valyl-tRNA synthetase, initiation factor 2, elongation factor G, elongation factor Tu, ribosomal protein L2, ribosomal protein S5, ribosomal protein S8, ribosomal protein S11, aminopeptidase P, DNA-directed RNA polymerase &amp;beta; chain, DNA topoisomerase I, DNA polymerase III &amp;gamma; subunit, signal recognition particle protein and rRNA dimethylase&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-06-26T08:46:37.163" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19336" PostTypeId="1" AcceptedAnswerId="19350" CreationDate="2014-06-25T17:17:55.920" Score="5" ViewCount="3359" Body="&lt;p&gt;Since there seem to be five &lt;a href=&quot;http://en.wikipedia.org/wiki/Bernhard_Caesar_Einstein&quot; rel=&quot;nofollow&quot;&gt;biological descendants&lt;/a&gt; of Albert Einstein, and the original chromosomes of him distributed among them ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is it possible to recover enough DNA of an individual from his progeny and proceed to clone him? Any information would be helpful&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5232" OwnerDisplayName="Fereydoon Shekofte" LastEditorUserId="5762" LastEditDate="2014-06-26T18:13:28.553" LastActivityDate="2017-05-12T19:03:26.887" Title="How much DNA of Albert Einstein is recoverable?" Tags="&lt;dna&gt;&lt;chromosome&gt;&lt;cloning&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19337" PostTypeId="2" ParentId="17179" CreationDate="2014-06-26T10:57:48.910" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://ocw.mit.edu/courses/health-sciences-and-technology/hst-508-genomics-and-computational-biology-fall-2002/audio-lectures/&quot; rel=&quot;nofollow&quot;&gt;http://ocw.mit.edu/courses/health-sciences-and-technology/hst-508-genomics-and-computational-biology-fall-2002/audio-lectures/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Download all the slides if you want good resources.&lt;/p&gt;&#xA;" OwnerUserId="8135" LastActivityDate="2014-06-26T10:57:48.910" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19338" PostTypeId="1" CreationDate="2014-06-26T11:04:23.107" Score="10" ViewCount="33103" Body="&lt;p&gt;What is the best cut-off for e-value in BLAST?&#xA;Some say 0.01 ,others 0.0001?&#xA;Even BLAST tutorials don't give a very clear idea about which cutoff suits which purpose?&#xA;Could some experts give me a clear idea on this.&#xA;Why are we using 0.0001 and not 0.00011?&lt;/p&gt;&#xA;" OwnerUserId="8135" LastEditorUserId="3553" LastEditDate="2016-10-03T07:03:36.550" LastActivityDate="2017-10-03T13:47:56.973" Title="What E-value BLAST cut-off is best?" Tags="&lt;bioinformatics&gt;&lt;sequence-alignment&gt;" AnswerCount="5" CommentCount="3" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19339" PostTypeId="2" ParentId="19338" CreationDate="2014-06-26T11:40:48.907" Score="4" Body="&lt;p&gt;E-value refers to the expected number of random hits for a given &lt;strong&gt;alignment score&lt;/strong&gt;. Smaller it is more reliable is your match. There is no hard and fast rule for e-value cutoff. You can keep whatever you want depending on the level of stringency that you require. But you should note that for smaller sequences (&lt;code&gt;&amp;lt; 30nt&lt;/code&gt;) there is always a higher likelihood of random matches. In such cases it is practical to relax the e-value cutoff. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-06-28T05:04:41.073" LastActivityDate="2014-06-28T05:04:41.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19341" PostTypeId="2" ParentId="19338" CreationDate="2014-06-26T14:01:16.813" Score="5" Body="&lt;p&gt;The e-value is supposed to be a metric for the chance that an alignment could occur at random, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html&quot; rel=&quot;nofollow&quot;&gt;but it is a crude estimate&lt;/a&gt;.  As pointed out in other answers, this significantly does not include the length of the query sequence.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also does not include the conservation of the gene or the frequency of amino acids (in protein blasts).  It does take into account the database of sequences queried, which might be something you know very little about if you didn't make it yourself. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, 1e-5 is a pretty poor score.  Its really awful for nucleotides - maybe a perfect alignment for 10 or 12 bases. So I'm going to assume that you are looking at peptides.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should also look at the coverage statistic.  That is the length of the alignment divided by the query or the hit sequence.  It should be 70%+ depending on what you want. &#xA;If the coverage is good even answers pretty far down the score rankings might be relevant.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarity is usually performed with a BLOSUM matrix.  Regardless, the number of exact matches compared to the number of similar matches of amino acids in an alignment poorly approximates what is going on in evolution.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly protein alignments tend to have gaps - lots of gaps.  The penalty to the scores for allowing gaps might low for long evolutionary distances or completely unreasonable for more recently diverged results.  So you have to look at those qualities of the alignment yourself.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-06-27T22:33:58.003" LastActivityDate="2014-06-27T22:33:58.003" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19342" PostTypeId="1" AcceptedAnswerId="19343" CreationDate="2014-06-26T15:35:32.860" Score="3" ViewCount="76" Body="&lt;p&gt;If we take a male and female, cross them, and collect one son and one daughter to produce the next generation (and continually do this for many generations) - (full-sib mating design) how much genetic variance is lost per generation/how do we calculate this? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume all sites initially have allelic variation, and we imagine a diploid sexual species.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-06-27T16:24:33.880" Title="Loss of allelic variation per generation of full-sib mating" Tags="&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19343" PostTypeId="2" ParentId="19342" CreationDate="2014-06-26T16:14:17.090" Score="2" Body="&lt;p&gt;A classical result from the Wright-Fisher model of genetic drift is that at each generation the heterozygosity ($2x(1-x)$) is expected to decrease by $\frac{1}{2N}$ due to genetic drift. ($x$ is the frequency of one of the two alleles). In your example the expected loss of heterozygosity is $¼$. This same result has been derived from coalescent theory and a similar result is derived from the birth-death Moran model. The issue is that this model assume bi-allelic loci only.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's think of 1 tetra-alellic (4 alleles) locus and let's assume that the 4 alleles in our two original parents are all different. We can draw the 16 possible pairs of offsprings and see the probability to lose 0, 1 or 2 alleles in the next generation&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;lose 0 allele: ¼&#xA;lose 1 allele: ½&#xA;lose 2 alleles: ¼&#xA;lose more than 2 alleles: 0&#xA;Therefore, the expected number of lost alleles is $1$!&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;We can then do the same (calculate the probability mass function) for two parents with 3 alleles and then 2 alleles (with various frequencies). It is not very complicated. But it would be much better to have a general model to describe the loss of heterozygosity through time for more than 2 alleles. &lt;a href=&quot;http://arxiv.org/pdf/1207.6623v1.pdf&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; probably gives this solution but I haven't read it yet. I will probably read it once and I will improve my answer then!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-06-27T16:24:33.880" LastActivityDate="2014-06-27T16:24:33.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19344" PostTypeId="1" CreationDate="2014-06-26T16:43:26.640" Score="3" ViewCount="386" Body="&lt;p&gt;Is it possible that an endothermic physiology can evolve into an ectothermic (poikilothermic) physiology? I have a non-scientific gut feeling that it is irreversible. Whales and dolphins are evolved from land mammals, and they've remained warm blooded. While it doesn't give them any obvious advantage in the water, apparently they've compensated with massive amounts of body fat instead of devolving. If the ocean offers opportunity for mammals, then why haven't fish evolved to be warm blooded directly?&lt;/p&gt;&#xA;" OwnerUserId="8152" LastEditorUserId="107" LastEditDate="2016-09-06T16:40:06.860" LastActivityDate="2016-09-06T16:40:06.860" Title="Is there any evidence for secondarily poikilothermic vertebrate?" Tags="&lt;evolution&gt;&lt;physiology&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-06-27T14:18:43.763" ContentLicense="CC BY-SA 3.0" />
  <row Id="19345" PostTypeId="2" ParentId="19344" CreationDate="2014-06-26T17:27:02.730" Score="6" Body="&lt;p&gt;&lt;strong&gt;What do you mean by cold-blooded?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's an issue with what you mean when saying &quot;cold blooded&quot;. The correct words you may want to use are homeotherm, poikilothermic, ectotherm, and endotherm. In short&amp;hellip;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source of heat &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;endo&lt;/em&gt; = inside&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;exo&lt;/em&gt; = outside&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Variance in warmth&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Poikilo&lt;/em&gt; = varies&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;homeo&lt;/em&gt; = does not vary&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Any combination of these two axes exist. For example: If the temperature in the environment never varies you can be homeotherm without needing to be endotherm. A fun example also are the large dinosaurs that are thought to be homeotherms because their metabolism produce some heat and they are so large that they remain warm thanks to this heat source. However, they were probably not able to regulate actively their temperature. Therefore, I would tend to qualify dinosaurs as homeo-exo-therm but I wouldn't be surprised if someone prefers to call large dinosaur home-endo-therm individuals. Hope that makes sense to you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the terminology might be a bit more complicated in reality as the diversity of mechanisms of body temperature regulation is important.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What did you mean in your question when talking about &quot;cold blooded&quot; species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Transition from endothermy to ectotherm&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks to @tchrist. naked mole rat is ectotherm while its ancestors where endotherm.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2016-09-06T16:39:14.533" LastActivityDate="2016-09-06T16:39:14.533" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19346" PostTypeId="1" AcceptedAnswerId="19351" CreationDate="2014-06-26T17:55:20.297" Score="1" ViewCount="104" Body="&lt;p&gt;From what I understand, one form of cancer is a faulty gene responsible for the programmed death of a cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not long ago, popular wisdom used to say neurons don't regenerate. However that is no longer believed to be true, if I am to believe what the internet says. For me, this begs the question: can neurogenesis result in faulty death genes which in turn result in overgrowth of the number of neurons? Would those neurons be functional? And if so, if theoretically such a brain could be artificially sustained without a body, would its growth be beneficial (in terms of intelligence)?&lt;/p&gt;&#xA;" OwnerUserId="8153" LastActivityDate="2014-06-26T20:04:59.073" Title="Is it possible for neurons themselves to manifest cancerous behavior?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19349" PostTypeId="2" ParentId="15365" CreationDate="2014-06-26T18:47:05.210" Score="1" Body="&lt;p&gt;The pathophysiology of orthostatic hypertension has not been elucidated. It is believed it involves activation of the sympathetic nervous system [1], vascular adrenergic hypersensitivity and diabetic neuropathy [2]. High levels of plasma atrial natriuretic peptide and antidiuretic hormone were observed in children [3].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hypovolemia causes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;baroreflex-mediated increase in muscle sympathetic nerve activity [4]&lt;/li&gt;&#xA;&lt;li&gt;release of epinephrine and norepinephrine [5]&lt;/li&gt;&#xA;&lt;li&gt;activation of renin-angiotensin axis [5], thus increasing ADH levels&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;All these reactions result in vasoconstriction and blood pressure raising. But not up to absolute hypertension.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Orthostatic hypertension is diagnosed by a rise in systolic blood pressure of 20 mmHg or more when standing [6].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is possible. A raise of 20 mmHg from hypotension could result due to vasoconstriction.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Fessel J, Robertson D. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16932477&quot; rel=&quot;nofollow&quot;&gt;Orthostatic hypertension: when pressor reflexes overcompensate.&lt;/a&gt; Nat Clin Pract Nephrol. 2006 Aug;2(8):424-31. doi: &lt;a href=&quot;http://dx.doi.org/10.1038/ncpneph0228&quot; rel=&quot;nofollow&quot;&gt;10.1038/ncpneph0228&lt;/a&gt;. PubMed PMID: 16932477.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Chhabra L, Spodick DH. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23993009&quot; rel=&quot;nofollow&quot;&gt;Orthostatic hypertension: recognizing an underappreciated clinical condition.&lt;/a&gt; Indian Heart J. 2013 Jul 5;65(4):454-6. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.ihj.2013.06.023&quot; rel=&quot;nofollow&quot;&gt;10.1016/j.ihj.2013.06.023&lt;/a&gt;. PubMed PMID: 23993009. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Zhao J, Yang J, Du S, Tang C, Du J, Jin H. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24824244&quot; rel=&quot;nofollow&quot;&gt;Changes of atrial natriuretic peptide and antidiuretic hormone in children with postural tachycardia syndrome and orthostatic hypertension: a case control study.&lt;/a&gt; Chin. Med. J. 2014 May;127(10):1853-7. PubMed PMID: 24824244. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Ryan KL, Rickards CA, Hinojosa-Laborde C, Cooke WH, Convertino VA. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22557974&quot; rel=&quot;nofollow&quot;&gt;Sympathetic responses to central hypovolemia: new insights from microneurographic recordings.&lt;/a&gt; Front Physiol. 2012 Apr 26;3:110. doi: &lt;a href=&quot;http://dx.doi.org/10.3389/fphys.2012.00110&quot; rel=&quot;nofollow&quot;&gt;10.3389/fphys.2012.00110&lt;/a&gt;. PubMed PMID: 22557974. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Shock (circulatory),&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Shock_%28circulatory%29&amp;amp;oldid=612494727&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Shock_(circulatory)&amp;amp;oldid=612494727&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia contributors, &quot;Orthostatic hypertension,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Orthostatic_hypertension&amp;amp;oldid=603984647&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Orthostatic_hypertension&amp;amp;oldid=603984647&lt;/a&gt; (accessed June 26, 2014).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-06-26T18:47:05.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19350" PostTypeId="2" ParentId="19336" CreationDate="2014-06-26T18:48:45.817" Score="10" Body="&lt;p&gt;During the generation of gametes (sperm, eggs), chromosomes can &lt;a href=&quot;http://en.wikipedia.org/wiki/Meiosis&quot;&gt;cross-over&lt;/a&gt; - this swaps paternal and maternally-derived genetic material.  So none of the descendant's chromosomes would be a direct copy of Einstein's, and furthermore, each offspring receives half of its genetic complement from each parent.  This means that if you pool the DNA data from small number of offspring you may not obtain all the elements of one parent's DNA or be able to assign that data back to a specific 'original' chromosome. (On top of this you would have to determine which sequences in the offspring came from the other parent).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I was cloning Einstein, I'd use his DNA.  Is his comb in a museum ? A tooth? A letter he licked?  A large chunk of Einstein still exists &lt;a href=&quot;http://en.wikipedia.org/wiki/Albert_Einstein%27s_brain&quot;&gt;(formalin fixed brain)&lt;/a&gt; and lab protocols can recover DNA from formalin fixed tissues. It wouldn't be easy, but in theory, you could: i) derive its full sequence and ii) synthesize artificial chromosomes with suitable epigenetic modifications, and iii) inject those into enucleated eggs for human cloning or iv) transfect them into enucleated cells from a cell line, make &lt;a href=&quot;http://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell&quot;&gt;iPSCs&lt;/a&gt; and then fuse those with ~8-cell fertilized embryos.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Spoiler - not technically do-able today and almost certainly illegal in most states/countries).&lt;br&gt;&#xA;For a related movie treatment, the &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Boys_from_Brazil_%28film%29&quot;&gt;Boys from Brazil &lt;/a&gt; tells a good story - &lt;strong&gt;warning Nazi content&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5922" LastEditorUserId="5922" LastEditDate="2014-06-26T19:42:01.280" LastActivityDate="2014-06-26T19:42:01.280" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19351" PostTypeId="2" ParentId="19346" CreationDate="2014-06-26T20:04:59.073" Score="4" Body="&lt;p&gt;Yes, but rarely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other types of brain cells are much more likely to form tumors. &lt;a href=&quot;http://en.wikipedia.org/wiki/Oligodendroglioma&quot; rel=&quot;nofollow&quot;&gt;Oligodendrocytes&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Astrocytoma&quot; rel=&quot;nofollow&quot;&gt;astrocytes&lt;/a&gt;, and more generally &lt;a href=&quot;http://en.wikipedia.org/wiki/Glioblastoma_multiforme&quot; rel=&quot;nofollow&quot;&gt;glial cells&lt;/a&gt; all form tumors with some regularity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Neurofibroma&quot; rel=&quot;nofollow&quot;&gt;Nerve sheaths&lt;/a&gt; can also form benign growths.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12235346&quot; rel=&quot;nofollow&quot;&gt;Nerves themselves&lt;/a&gt; can even manifest cancerous behavior, even though they are nearly always benign and very slow growing. Unfortunately, they tend to cause seizures, increased intercranial pressure, and decreased neurological function in affected areas.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-06-26T20:04:59.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19355" PostTypeId="1" AcceptedAnswerId="19359" CreationDate="2014-06-27T16:38:46.533" Score="3" ViewCount="6938" Body="&lt;p&gt;Occasionally I will come across articles that refer to back-crossing mice of one strain onto the background other another strain (e.g., C57Bl6). They do not explicitly state the purpose for doing so, but I can infer that the change of strain is to relate their findings to what is already known using the new strain (e.g., C57Bl6). Usually the back-crosses are performed for 5-10 generations. Is this to try to remove (epi)genetic variation from the original strain relative to the new strain, or is it more about normalizing expression of a particular allelic variant (e.g., knocking-in a transgene)?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-06-27T22:02:05.623" Title="What is the purpose of back-crossing mice for multiple generations?" Tags="&lt;genetics&gt;&lt;experimental-design&gt;&lt;epigenetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19356" PostTypeId="2" ParentId="19338" CreationDate="2014-06-27T18:40:35.883" Score="8" Body="&lt;p&gt;There is no perfect cut-off. It always depends on what you're doing. The e-value is basically a measure of how many such alignments you would expect to find in a database this size by chance. Therefore, e-values greater than 1 mean that you'd expect at least one alignment similar to what you've found by chance alone. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As others have stated, the e-value is not a rigorous measure of significance. It depends on&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The length of your alignment.&lt;/li&gt;&#xA;&lt;li&gt;The alignment's bit-score score (this takes into account amino acid substitution scores based on the matrix being used, &lt;a href=&quot;https://en.wikipedia.org/wiki/BLOSUM&quot;&gt;BLOSUM65&lt;/a&gt; by default).&lt;/li&gt;&#xA;&lt;li&gt;The size of the database you are searching in.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I have at different times and for different projects used e-values ranging from 10 to 1e-100 or less. You always need to take into account what you are looking for. For example, to run a tBLASTn looking for distant homologs, you'd use a relatively high e-value, say 1e-10 or even 1 or greater depending on the details. For example, the default e-value for &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&amp;amp;PAGE_TYPE=BlastSearch&amp;amp;LINK_LOC=blasthome&quot;&gt;ncbi-tBLASTn&lt;/a&gt; is 10.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To find extremely similar sequences in closely related species, you'd use a much smaller one. Say 1e-20 or 1e-50. Normally, you tweak these settings after seeing your results. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After running a few hundred blasts, you get the hang of it and you can have a pretty good estimate of the e-value cutoff you want to use. Until you get that experience, you will have to use trial and error. Just remember that the conclusions you can draw from your data will be heavily influenced by that e-value. Don't try to publish something claiming you've found a homolog if the supporting BLAST hit has an e-value of 45 for example. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally, when looking at BLAST out files, I check the e-value, the alignment's length (as a percentage of the query), the alignment's %id score and the bit score itself. Of these, the most reliable is the bit-score but, again, that too changes depending on what question you are attempting to answer.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-06-27T18:53:18.023" LastActivityDate="2014-06-27T18:53:18.023" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19358" PostTypeId="1" CreationDate="2014-06-27T21:53:01.720" Score="1" ViewCount="95" Body="&lt;p&gt;I'm doing a family study looking for novel cancer-associated variants in germ-line samples; the goal is to find candidate biomarkers which might be used for early detection. At an earlier step our analysis, we eliminated a family that showed a heterozygous mutation known to be associated with our cancer under the premise that this known mutation better explained the presence of the disease than any novel variant we may have found.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've now found another mutation, strongly associated with out cancer, which we does not appear to be heterozygous. 2 out of 3 family members share this mutation with a within-family allele frequency of 0.5. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trying to decide whether this means I need to discard this family from further consideration, adjust my thinking, or not worry about it. My current thinking is that it'd be safest to eliminate the family from consideration because the mutation pathogenic and found in the germline but I can't wrap my head around how the lack of a heterozygous pattern affects things. Does it absolutely mean the variant was not inherited? Can anyone help me get my thoughts straight?&lt;/p&gt;&#xA;" OwnerUserId="8161" LastActivityDate="2014-06-27T21:53:01.720" Title="Can a heterozygous allele show non-heterozygous expression in a family?" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;human-genetics&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19359" PostTypeId="2" ParentId="19355" CreationDate="2014-06-27T22:02:05.623" Score="3" Body="&lt;p&gt;Depending on the exact goal of the experiment, the researchers may back-cross both to smooth out genetic variation between individuals and to potentially normalize expression of a transgene, although once you get past the chimeric stage gene expression should be fairly stable. In my experience, back-crossing allows you to generate a genetically-altered mouse that differs as little as possible from a (generally well-characterized) parent strain, except at the locus of the genetic manipulation. This way, any differences in phenotype can more easily be explained by the knockout/knockin/transgene/what-have-you, and not by any variations in background genetics. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an example, &lt;a href=&quot;http://jaxmice.jax.org/strain/000664.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;C57BL/6&lt;/a&gt; mice, being inbred, have a number of well-known mutations, deficiencies, resistances, etc., and for one reason or another have become one of the most popular and most-characterized mouse strains in biology, so there is a great interest in continuing research using a well-known historical model with so much extant experimental data. These mice are quite different from the &lt;a href=&quot;http://jaxmice.jax.org/strain/002448.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;129&lt;/a&gt; strain, which are frequently used to make initial genetically modified strains due to the large number of embryonic stem cell lines available, and other technical reasons which allow for the relatively easy generation of transgenics, etc. However, for various other reasons, 129s aren't used as often in the type of studies that BL/6s are, so it's preferable to create the mutation in a 129, then back-cross it onto a BL/6 background. Both of these strains are quite homogenous from one individual to another (each sibling is practically a twin of the next), but once you start breeding 129s to BL/6s you can generate all sorts of genetic heterogeneity due to random cross-overs and all the other things we like to talk so much about around here when it comes to mutations and meiosis. As anyone who has worked with genetic diseases in humans will readily tell you, it can be extraordinarily difficult to nail down specific genotypes that lead to specific phenotypes when there are so many other confounding factors present. Backcrossing a mutant 5, 10, or even 20 or more generations back onto a reference strain is one of the best ways we have at the moment of controlling for all the genetic variations that are introduced when two inbred &quot;tool&quot; strains are bred together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And now, cute pictures :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;129 mouse&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oaVno.jpg&quot; alt=&quot;129&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C57BL/6 mouse&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HY3t9.jpg&quot; alt=&quot;C57BL/6&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;both images from &lt;a href=&quot;http://www.criver.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Charles River&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-06-27T22:02:05.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19360" PostTypeId="1" AcceptedAnswerId="19368" CreationDate="2014-06-27T22:41:54.117" Score="2" ViewCount="343" Body="&lt;p&gt;I'm not talking about single celled organisms, but actual cells in your body. Is there any evidence that they can learn to, say, navigate an environment or avoid an aversive stimulus like an animal could? Is their behaviour understood well enough to say that it's entirely mechanistic, or are there things we still don't know?&lt;/p&gt;&#xA;" OwnerUserId="5640" LastActivityDate="2014-06-28T15:42:49.527" Title="Can (any) human cells learn?" Tags="&lt;cell-biology&gt;&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19361" PostTypeId="1" CreationDate="2014-06-27T23:36:52.567" Score="0" ViewCount="330" Body="&lt;p&gt;I heard that after injury or repeated damage bone becomes denser, can skin become denser as well?&lt;/p&gt;&#xA;" OwnerUserId="8162" LastActivityDate="2014-06-28T10:32:28.093" Title="Can skin become denser?" Tags="&lt;skin&gt;&lt;bone-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19362" PostTypeId="1" AcceptedAnswerId="19369" CreationDate="2014-06-28T04:21:51.697" Score="2" ViewCount="334" Body="&lt;p&gt;When we draw a calibration curve for single radial immunodiffusion, the curve does not pass through origin. Instead, there is a y intercept. Why does that happen ? Shouldn't zero antigen give zero ring diameter ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-06-28T17:41:54.653" Title="Calibration curve for single radial immunodiffusion" Tags="&lt;immunology&gt;&lt;antibody&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19364" PostTypeId="1" CreationDate="2014-06-28T07:14:09.840" Score="4" ViewCount="1739" Body="&lt;p&gt;I have seen/read that the Cuttlefish is able to camouflage itself extremely accurately. I have also seen/read that they are completely color-blind, though see with very high contrast. How does the Cuttlefish manage to blend itself so well to its changing surroundings if it is not able to perceive the colors it is changing itself to?&lt;/p&gt;&#xA;" OwnerUserId="8165" LastActivityDate="2014-07-01T04:08:23.987" Title="How does the Cuttlefish camouflage itself accurately despite being color-blind?" Tags="&lt;zoology&gt;&lt;marine-biology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19365" PostTypeId="2" ParentId="19219" CreationDate="2014-06-28T07:20:10.253" Score="4" Body="&lt;p&gt;&lt;a href=&quot;https://plantbio.cals.cornell.edu/people/karl-niklas&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dr Karl Niklas&lt;/a&gt; from the Cornell University has written a book about the effects of factors that influenced the shape of early trees. He created a computer model in which he drew trees in the shape that favored particular characteristics.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When Niklas favored plants that could gather light from the sun, they&#xA;  had non-overlapping horizontal branches. When reproductive success was&#xA;  favored, the plants grew tall, in order to spread their seeds. When&#xA;  the trait selected for was mechanical stability, the plants had few&#xA;  horizontal branches.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;When he combined these three favourable traits, he noticed that most of the trees today are in a form that favors these three traits (&lt;a href=&quot;http://www.pbslearningmedia.org/resource/tdc02.sci.life.evo.shapetrees/shape-of-trees-the-frustration-principle/&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wY6XC.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;L is light favourability, M is mechanical stability and R is the shape of trees that favor reproductive ability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Explanations for a few shapes found commonly with examples can be found in &lt;a href=&quot;http://grounds-mag.com/mag/grounds_maintenance_shape_trees/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt;.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Illustration for the common tree shapes Columnar, Pyramidal,Vase, Round, Spreading, Weeping and umbrella with a few more examples can be found in this article (&lt;a href=&quot;http://www.todayshomeowner.com/guide-to-different-tree-shapes-for-your-yard/&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another interesting thing about trees is the way in which their shapes can be influenced for the purpose of landscaping (&lt;a href=&quot;http://www.telegraph.co.uk/gardening/plants/trees/8774514/Train-your-trees-into-extraordinary-shapes.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you mentioned about pine cones in isolation having no definite shape at all, I would like to see a reference that this is a fact before I can elucidate on it further (I couldn't find any articles that mentioned such a phenomenon). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The reason you felt so could be because it were two completely different species of pines. Counting varieties and subspecies, the plant list of the Royal Botanic Gardens, Kew and Missouri Botanical Garden accepts 175 names of pines as current(&lt;a href=&quot;http://en.wikipedia.org/wiki/Pine&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;). Here is a list of different pine species (&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_Pinus_species&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.clemson.edu/hort/peach/pdfs/acta90.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here is an article&lt;/a&gt; on how tree shape and light available influence yield in cherry trees. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-06-28T16:56:16.330" LastActivityDate="2014-06-28T16:56:16.330" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19366" PostTypeId="2" ParentId="16512" CreationDate="2014-06-28T10:05:26.577" Score="6" Body="&lt;p&gt;The three meals a day seems to be a cultural trait. Then what is the optimal number of meals a day? It is not known. Here are the results of some studies:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reduced meal frequency:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was found that the body can adapt to a single meal a day by modifying circulating hormone levels and glucose tolerance [1]. However it does not modify lipogenesis rates [2]. It may support cardiovascular disease risk factors [8].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Increased meal frequency:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although there are studies that claim 5-6 meals a day help in maintenance of weight loss [3], others claim this habit increases hunger and the desire to eat and has no significant effect on fat oxidation [4]. A higher number of daily meals is recommended to the elderly suffering from cardiovascular diseases [5] because less but square meals lead to a redistribution of blood to the gastro-intestinal tract to increase absorption, which causes reduction of blood pressure [6]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Conclusion:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Energy balance is more important than meal frequency. As this study says [7]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... there is no evidence that weight loss on hypoenergetic regimens is altered by meal frequency. We conclude that any effects of meal pattern on the regulation of body weight are likely to be mediated through effects on the food intake side of the energy balance equation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Carlson O, Martin B, Stote KS, Golden E, Maudsley S, Najjar SS, Ferrucci L, Ingram DK, Longo DL, Rumpler WV, Baer DJ, Egan J, Mattson MP. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17998028&quot; rel=&quot;noreferrer&quot;&gt;Impact of reduced meal frequency without caloric restriction on glucose regulation in healthy, normal-weight middle-aged men and women.&lt;/a&gt; Metab. Clin. Exp. 2007 Dec;56(12):1729-34. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.metabol.2007.07.018&quot; rel=&quot;noreferrer&quot;&gt;10.1016/j.metabol.2007.07.018&lt;/a&gt;. PubMed PMID: 17998028. &lt;/li&gt;&#xA;&lt;li&gt;Jones PJ, Namchuk GL, Pederson RA. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7869919&quot; rel=&quot;noreferrer&quot;&gt;Meal frequency influences circulating hormone levels but not lipogenesis rates in humans.&lt;/a&gt; Metab. Clin. Exp. 1995 Feb;44(2):218-23. PubMed PMID: 7869919. &lt;/li&gt;&#xA;&lt;li&gt;Bachman JL, Phelan S, Wing RR, Raynor HA. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22027056&quot; rel=&quot;noreferrer&quot;&gt;Eating frequency is higher in weight loss maintainers and normal-weight individuals than in overweight individuals.&lt;/a&gt; J Am Diet Assoc. 2011 Nov;111(11):1730-4. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.jada.2011.08.006&quot; rel=&quot;noreferrer&quot;&gt;10.1016/j.jada.2011.08.006&lt;/a&gt;. PubMed PMID: 22027056. &lt;/li&gt;&#xA;&lt;li&gt;Ohkawara K, Cornier MA, Kohrt WM, Melanson EL. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23404961&quot; rel=&quot;noreferrer&quot;&gt;Effects of increased meal frequency on fat oxidation and perceived hunger.&lt;/a&gt; Obesity (Silver Spring). 2013 Feb;21(2):336-43. doi: &lt;a href=&quot;http://dx.doi.org/10.1002/oby.20032&quot; rel=&quot;noreferrer&quot;&gt;10.1002/oby.20032&lt;/a&gt;. PubMed PMID: 23404961. &lt;/li&gt;&#xA;&lt;li&gt;Ortega RM, Redondo MR, Zamora MJ, López-Sobaler AM, Quintas ME, Andrés P, Gaspar MJ, Requejo AM. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9780751&quot; rel=&quot;noreferrer&quot;&gt;[Relationship between the number of daily meals and the energy and nutrient intake in the elderly. Effect on various cardiovascular risk factors].&lt;/a&gt; Nutr Hosp. 1998;13(4):186-92. PubMed PMID: 9780751. &lt;/li&gt;&#xA;&lt;li&gt;Westenend M, Lenders JW, Thien T. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2856754&quot; rel=&quot;noreferrer&quot;&gt;The course of blood pressure after a meal: a difference between young and elderly subjects.&lt;/a&gt; J Hypertens Suppl. 1985 Dec;3(3):S417-9. PubMed PMID: 2856754. &lt;/li&gt;&#xA;&lt;li&gt;Bellisle F, McDevitt R, Prentice AM. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9155494&quot; rel=&quot;noreferrer&quot;&gt;Meal frequency and energy balance.&lt;/a&gt; Br. J. Nutr. 1997 Apr;77 Suppl 1:S57-70. PubMed PMID: 9155494. &lt;/li&gt;&#xA;&lt;li&gt;Stote KS, Baer DJ, Spears K, Paul DR, Harris GK, Rumpler WV, Strycula P, Najjar SS, Ferrucci L, Ingram DK, Longo DL, Mattson MP. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17413096&quot; rel=&quot;noreferrer&quot;&gt;A controlled trial of reduced meal frequency without caloric restriction in healthy, normal-weight, middle-aged adults.&lt;/a&gt; Am. J. Clin. Nutr. 2007 Apr;85(4):981-8. PubMed PMID: 17413096. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-06-28T12:18:47.973" LastActivityDate="2014-06-28T12:18:47.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19367" PostTypeId="2" ParentId="19361" CreationDate="2014-06-28T10:32:28.093" Score="3" Body="&lt;p&gt;The structure of skin (epidermis) can change with damage, when the skin is broken the body repairs this partly by recruiting cells called fibroblasts. These fibroblasts lay down collagen fibres to repair the skin. These fibres a normal component of skin are not as neatly arranged as the original fibres and may also higher in number leading to 'denser' skin. This is essentially what a scar is. In some cases the above process can go awry forming what is known as keloid scars.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other thing that can happen with repeated pressure exposure the skin can become callous, this is when there is thickening of the outer layer formed of cells called keratinocytes increase in number due to recurrent damage. These form typically on pressure points such as balls of feet.&lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-06-28T10:32:28.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19368" PostTypeId="2" ParentId="19360" CreationDate="2014-06-28T15:42:49.527" Score="3" Body="&lt;p&gt;For this specific question, let's divide the cells into two categories: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cells that &lt;em&gt;rarely&lt;/em&gt; &quot;navigate&quot;&lt;/strong&gt; are the cells that are connected to give the tissue its mechanical properties. How do these avoid an &quot;adverse stimulus&quot;? Well, they don't avoid it. But if that stimulus &quot;harms&quot; cells they react in some way:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;if the cell is destructed by the pathogen, it will release chemical compounds that have chemotactic properties and attract specialized cells.&lt;/li&gt;&#xA;&lt;li&gt;if the pathogen has intracellular tropism, the cell may release some chemical compounds (see interferon) to &quot;alert&quot; other cells that something is wrong. Most cells can also present antigens on their surface.&lt;/li&gt;&#xA;&lt;li&gt;there are also some stimuli which change cellular life cycle turning cells into cancerous cells. These cells can gain excretory properties and produce substances that destroy intercellular jonctions. This is how metastases occur.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cells that &quot;navigate&quot;&lt;/strong&gt; are the blood cells. White blood cells respond to different kind of stimuli (chemical) in two ways: either they are attracted (by inflammatory cytokines for example) either they are repelled. Macrophages are attracted by cytokines released when a pathogen agent triggers inflammatory response. They &quot;ingest&quot; that pathogen through phagocytosis and expose some parts of it (the antigens) on their surface receptors. This stimulates lymphocytes which process that antigen and decide if it is self or non-self. If it is non-self, they stimulate proliferation of specialized cells against that antigen. Another type of blood cells, the platelets, although they have no nucleus, have interesting properties: they can adhere to the broken endothelium where they change shape and start to produce different chemical mediators.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Read more on:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Chemotaxis,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Chemotaxis&amp;amp;oldid=600637322&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Chemotaxis&amp;amp;oldid=600637322&lt;/a&gt; (accessed June 28, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Interferon,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Interferon&amp;amp;oldid=608718450&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Interferon&amp;amp;oldid=608718450&lt;/a&gt; (accessed June 28, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Adaptive immune system,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Adaptive_immune_system&amp;amp;oldid=612379171&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Adaptive_immune_system&amp;amp;oldid=612379171&lt;/a&gt; (accessed June 28, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Platelet,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Platelet&amp;amp;oldid=614627651&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Platelet&amp;amp;oldid=614627651&lt;/a&gt; (accessed June 28, 2014).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-06-28T15:42:49.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19369" PostTypeId="2" ParentId="19362" CreationDate="2014-06-28T17:41:54.653" Score="4" Body="&lt;p&gt;When the &lt;a href=&quot;http://en.wikipedia.org/wiki/Radial_immunodiffusion&quot; rel=&quot;nofollow&quot;&gt;radial immunodiffusion method&lt;/a&gt; is used to measure antigen concentrations in samples, a plate or slide is set up using agarose containing an antibody or antiserum. Holes are punched out of the agarose to form wells into which antigen is dispensed. The antigen diffuses out into the agarose and when the antigen/antibody ratio is favourable an immunoprecipitate will form as a ring (immunoprecipitin ring). The final diameter of the ring is proportional to the initial concentration of antigen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Addressing the question: isn't this simply explained because the values on the Y axis are squares of the diameters of the rings, and this includes the well into which the antigen is dispensed?&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-06-28T17:41:54.653" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19370" PostTypeId="2" ParentId="19038" CreationDate="2014-06-28T17:49:42.710" Score="4" Body="&lt;p&gt;Heat shock transformation alters membrane fluidity creating pores:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A sudden increase in temperature creates pores in the plasma membrane of the bacteria and allows for plasmid DNA to enter the bacterial cell.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference:&lt;/strong&gt; Journal of Visualized Experiments. Bacterial Transformation: The Heat Shock Method. 2014. &lt;a href=&quot;http://www.jove.com/science-education/5059/bacterial-transformation-the-heat-shock-method&quot; rel=&quot;nofollow&quot;&gt;http://www.jove.com/science-education/5059/bacterial-transformation-the-heat-shock-method&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The change in temperature alters the fluidity of the semi-crystalline membrane state achieved at 0oC thus allowing the DNA molecule to enter the cell through the zone of adhesion.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference:&lt;/strong&gt; Anh-Hue T. Tu. &lt;a href=&quot;http://www.microbelibrary.org/component/resource/laboratory-test/3152-transformation-of-escherichia-coli-made-competent-by-calcium-chloride-protocol&quot; rel=&quot;nofollow&quot;&gt;Transformation of Escherichia coli Made Competent by Calcium Chloride Protocol.&lt;/a&gt; 2008-2013. American Society for Microbiology&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... heat-pulse (0 degrees C42 degrees C) step of the standard transformation procedure had lowered considerably outer membrane fluidity of cells. The decrease in fluidity was caused by release of lipids from cell surface to extra-cellular medium. A subsequent cold-shock (42 degrees C0 degrees C) to the cells raised the fluidity further to its original value and this was caused by release of membrane proteins to extra-cellular medium.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference:&lt;/strong&gt; Panja S, Aich P, Jana B, Basu T. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18651316&quot; rel=&quot;nofollow&quot;&gt;How does plasmid DNA penetrate cell membranes in artificial transformation process of Escherichia coli?&lt;/a&gt; Mol. Membr. Biol. 2008 Aug;25(5):411-22. doi: &lt;a href=&quot;http://dx.doi.org/10.1080/09687680802187765&quot; rel=&quot;nofollow&quot;&gt;10.1080/09687680802187765&lt;/a&gt;. PubMed PMID: 18651316. &lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-06-28T17:49:42.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19371" PostTypeId="2" ParentId="5324" CreationDate="2014-06-28T18:48:25.323" Score="5" Body="&lt;p&gt;&lt;strong&gt;Vitamin A:&lt;/strong&gt; One study conducted in the 60's claims that vitamin A acid prevents formation of comedones in Acne Vulgaris [1]. Another one conducted in the 70's found no significant improvement of plantar warts when vitamin A acid was applied topically [2].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Vitamin D:&lt;/strong&gt; Agents like calcipotriene associated with topical steroids are effective against psoriazis [3]. They inhibit keratinocyte proliferation, normalize differentiation and modulate the activity of immune cells [4]. Active form of vitamin D is also effective against vitiligo [5].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Vitamin E:&lt;/strong&gt; It reduces skin damage induced by UV [6, 8], but it shouldn't be applied on scars [7].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Vitamin K:&lt;/strong&gt; It prevents bruising after laser treatment and reduces the severity of eventual bruising [9, 10].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Vitamin B12:&lt;/strong&gt; It is an effective treatment for atopic dermatitis [11] and children with eczema [12]. It could also potentially improve olfactory function when associated with corticosteroids [13].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Vitamin B1:&lt;/strong&gt; It doesn't protect you from mosquitoes [14].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Vitamin B3:&lt;/strong&gt; It improves fine lines/wrinkles, hyperpigmentation spots, texture, red blotchiness and sallowness [15, 16].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Vitamin C:&lt;/strong&gt; It improves wrinkling by new collagen formation [17]. It is useful in sun-induced skin ageing [18, 19] where it increases density of dermal papillae [20].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And here are the results of a study [21] which assessed multiple vitamins:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Vitamins A, C, E, and B3 have been shown to have potent antioxidant and anti-inflammatory properties, but to achieve optimal effectiveness, products must be delivered in appropriate formulations. Products containing alpha-tocopherol (vitamin E), L-ascorbic acid (vitamin C), retinol (vitamin A), and niacinamide (vitamin B3), are effective for the treatment of photoaging. These compounds have also shown effectiveness in the treatment of inflammatory dermatoses, acne, and pigmentation disorders and wound healing. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The same study [21] also concludes that combinations are better:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There is emerging evidence that combinations of vitamins have additive effects that provide enhanced efficacy compared with individual compounds.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Kligman AM, Fulton JE, Jr., Plewig G. &lt;a href=&quot;http://archderm.jamanetwork.com/article.aspx?articleid=530928&quot; rel=&quot;noreferrer&quot;&gt;Topical Vitamin A Acid in Acne Vulgaris.&lt;/a&gt; Arch Dermatol. 1969;99(4):469-476. doi:10.1001/archderm.1969.01610220097017.&lt;/li&gt;&#xA;&lt;li&gt;de Bersaques J. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1201813&quot; rel=&quot;noreferrer&quot;&gt;Vitamin A acid in the topic treament of plantar warts.&lt;/a&gt; Dermatologica. 1976;150(6):369-71. PubMed PMID: 1201813. &lt;/li&gt;&#xA;&lt;li&gt;Devaux S, Castela A, Archier E, Gallini A, Joly P, Misery L, Aractingi S, Aubin F, Bachelez H, Cribier B, Jullien D, Le Maître M, Richard MA, Ortonne JP, Paul C. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22512681&quot; rel=&quot;noreferrer&quot;&gt;Topical vitamin D analogues alone or in association with topical steroids for psoriasis: a systematic review.&lt;/a&gt; J Eur Acad Dermatol Venereol. 2012 May;26 Suppl 3:52-60. doi: &lt;a href=&quot;http://dx.doi.org/10.1111/j.1468-3083.2012.04524.x&quot; rel=&quot;noreferrer&quot;&gt;10.1111/j.1468-3083.2012.04524.x&lt;/a&gt;. PubMed PMID: 22512681. &lt;/li&gt;&#xA;&lt;li&gt;Tanghetti EA. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19702030&quot; rel=&quot;noreferrer&quot;&gt;The role of topical vitamin D modulators in psoriasis therapy.&lt;/a&gt; J Drugs Dermatol. 2009 Aug;8(8 Suppl):s4-8. PubMed PMID: 19702030. &lt;/li&gt;&#xA;&lt;li&gt;Gorman S, Judge MA, Hart PH. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20211255&quot; rel=&quot;noreferrer&quot;&gt;Immune-modifying properties of topical vitamin D: Focus on dendritic cells and T cells.&lt;/a&gt; J. Steroid Biochem. Mol. Biol. 2010 Jul;121(1-2):247-9. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.jsbmb.2010.02.034&quot; rel=&quot;noreferrer&quot;&gt;10.1016/j.jsbmb.2010.02.034&lt;/a&gt;. PubMed PMID: 20211255.&lt;/li&gt;&#xA;&lt;li&gt;Burke KE, Clive J, Combs GF, Commisso J, Keen CL, Nakamura RM. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11341050&quot; rel=&quot;noreferrer&quot;&gt;Effects of topical and oral vitamin E on pigmentation and skin cancer induced by ultraviolet irradiation in Skh:2 hairless mice.&lt;/a&gt; Nutr Cancer. 2001;38(1):87-97. doi: &lt;a href=&quot;http://dx.doi.org/10.1207/S15327914NC381_13&quot; rel=&quot;noreferrer&quot;&gt;10.1207/S15327914NC381_13&lt;/a&gt;. PubMed PMID: 11341050.  &lt;/li&gt;&#xA;&lt;li&gt;Baumann LS, Spencer J. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10417589&quot; rel=&quot;noreferrer&quot;&gt;The effects of topical vitamin E on the cosmetic appearance of scars.&lt;/a&gt; Dermatol Surg. 1999 Apr;25(4):311-5. PubMed PMID: 10417589. &lt;/li&gt;&#xA;&lt;li&gt;Krol ES, Kramer-Stickland KA, Liebler DC. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11139138&quot; rel=&quot;noreferrer&quot;&gt;Photoprotective actions of topically applied vitamin E.&lt;/a&gt; Drug Metab. Rev. 2001;32(3-4):413-20. doi: &lt;a href=&quot;http://dx.doi.org/10.1081/DMR-100102343&quot; rel=&quot;noreferrer&quot;&gt;10.1081/DMR-100102343&lt;/a&gt;. PubMed PMID: 11139138. &lt;/li&gt;&#xA;&lt;li&gt;Shah NS, Lazarus MC, Bugdodel R, Hsia SL, He J, Duncan R, Baumann L. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12140470&quot; rel=&quot;noreferrer&quot;&gt;The effects of topical vitamin K on bruising after laser treatment.&lt;/a&gt; J. Am. Acad. Dermatol. 2002 Aug;47(2):241-4. PubMed PMID: 12140470. &lt;/li&gt;&#xA;&lt;li&gt;Cohen JL, Bhatia AC. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19894369&quot; rel=&quot;noreferrer&quot;&gt;The role of topical vitamin K oxide gel in the resolution of postprocedural purpura.&lt;/a&gt; J Drugs Dermatol. 2009 Nov;8(11):1020-4. PubMed PMID: 19894369. &lt;/li&gt;&#xA;&lt;li&gt;Stücker M, Pieck C, Stoerb C, Niedner R, Hartung J, Altmeyer P. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15149512&quot; rel=&quot;noreferrer&quot;&gt;Topical vitamin B12--a new therapeutic approach in atopic dermatitis-evaluation of efficacy and tolerability in a randomized placebo-controlled multicentre clinical trial.&lt;/a&gt; Br. J. Dermatol. 2004 May;150(5):977-83. doi: &lt;a href=&quot;http://dx.doi.org/10.1111/j.1365-2133.2004.05866.x&quot; rel=&quot;noreferrer&quot;&gt;10.1111/j.1365-2133.2004.05866.x&lt;/a&gt;. PubMed PMID: 15149512. &lt;/li&gt;&#xA;&lt;li&gt;Januchowski R. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19368512&quot; rel=&quot;noreferrer&quot;&gt;Evaluation of topical vitamin B(12) for the treatment of childhood eczema.&lt;/a&gt; J Altern Complement Med. 2009 Apr;15(4):387-9. doi: &lt;a href=&quot;http://dx.doi.org/10.1089/acm.2008.0497&quot; rel=&quot;noreferrer&quot;&gt;10.1089/acm.2008.0497&lt;/a&gt;. PubMed PMID: 19368512. &lt;/li&gt;&#xA;&lt;li&gt;Heilmann S, Just T, Göktas O, Hauswald B, Hüttenbrink KB, Hummel T. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15538662&quot; rel=&quot;noreferrer&quot;&gt;[Effects of systemic or topical administration of corticosteroids and vitamin B in patients with olfactory loss].&lt;/a&gt; Laryngorhinootologie. 2004 Nov;83(11):729-34. doi: &lt;a href=&quot;http://dx.doi.org/10.1055/s-2004-825676&quot; rel=&quot;noreferrer&quot;&gt;10.1055/s-2004-825676&lt;/a&gt;. PubMed PMID: 15538662. &lt;/li&gt;&#xA;&lt;li&gt;Holzer RB. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11441693&quot; rel=&quot;noreferrer&quot;&gt;[Protection against biting mosquitoes].&lt;/a&gt; Ther Umsch. 2001 Jun;58(6):341-6. PubMed PMID: 11441693. &lt;/li&gt;&#xA;&lt;li&gt;Bissett DL, Miyamoto K, Sun P, Li J, Berge CA. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18492135&quot; rel=&quot;noreferrer&quot;&gt;Topical niacinamide reduces yellowing, wrinkling, red blotchiness, and hyperpigmented spots in aging facial skin.&lt;/a&gt; Int J Cosmet Sci. 2004 Oct;26(5):231-8. doi: &lt;a href=&quot;http://dx.doi.org/10.1111/j.1467-2494.2004.00228.x&quot; rel=&quot;noreferrer&quot;&gt;10.1111/j.1467-2494.2004.00228.x&lt;/a&gt;. PubMed PMID: 18492135.&lt;/li&gt;&#xA;&lt;li&gt;Bissett DL, Oblong JE, Berge CA. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16029679&quot; rel=&quot;noreferrer&quot;&gt;Niacinamide: A B vitamin that improves aging facial skin appearance.&lt;/a&gt; Dermatol Surg. 2005 Jul;31(7 Pt 2):860-5; discussion 865. PubMed PMID: 16029679.  &lt;/li&gt;&#xA;&lt;li&gt;Fitzpatrick RE, Rostan EF. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11896774&quot; rel=&quot;noreferrer&quot;&gt;Double-blind, half-face study comparing topical vitamin C and vehicle for rejuvenation of photodamage.&lt;/a&gt; Dermatol Surg. 2002 Mar;28(3):231-6. PubMed PMID: 11896774. &lt;/li&gt;&#xA;&lt;li&gt;Humbert PG, Haftek M, Creidi P, Lapière C, Nusgens B, Richard A, Schmitt D, Rougier A, Zahouani H. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12823436&quot; rel=&quot;noreferrer&quot;&gt;Topical ascorbic acid on photoaged skin. Clinical, topographical and ultrastructural evaluation: double-blind study vs. placebo.&lt;/a&gt; Exp. Dermatol. 2003 Jun;12(3):237-44. PubMed PMID: 12823436. &lt;/li&gt;&#xA;&lt;li&gt;Farris PK. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16029672&quot; rel=&quot;noreferrer&quot;&gt;Topical vitamin C: a useful agent for treating photoaging and other dermatologic conditions.&lt;/a&gt; Dermatol Surg. 2005 Jul;31(7 Pt 2):814-7; discussion 818. PubMed PMID: 16029672. &lt;/li&gt;&#xA;&lt;li&gt;Sauermann K, Jaspers S, Koop U, Wenck H. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15456516&quot; rel=&quot;noreferrer&quot;&gt;Topically applied vitamin C increases the density of dermal papillae in aged human skin.&lt;/a&gt; BMC Dermatol. 2004 Sep 29;4(1):13. doi: &lt;a href=&quot;http://dx.doi.org/10.1186/1471-5945-4-13&quot; rel=&quot;noreferrer&quot;&gt;10.1186/1471-5945-4-13&lt;/a&gt;. PubMed PMID: 15456516. &lt;/li&gt;&#xA;&lt;li&gt;Burgess C. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18681152&quot; rel=&quot;noreferrer&quot;&gt;Topical vitamins.&lt;/a&gt; J Drugs Dermatol. 2008 Jul;7(7 Suppl):s2-6. PubMed PMID: 18681152. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-06-28T18:48:25.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19373" PostTypeId="1" AcceptedAnswerId="19376" CreationDate="2014-06-29T00:10:19.770" Score="3" ViewCount="41" Body="&lt;p&gt;I am confused about using the ImageQuantTL application as a tool to analyse the Urea Gel. My problem is that I am not sure if the 'shape' for calculation should be the same for all samples (like on picture A) or as close to the band as possible (like on picture B)? And what about the background subtraction? The `Image Rectangle/Ellipse' option says: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Uses the average pixel intensity in a defined rectangular or elliptical area of the image. To define the area for background calculation, select the background shape in the navigator and then drag with the mouse. Background areas are identified by a broken colored border, and are numbered in the sequence in which they are created. If you have defined several background areas, select the area to use in the Parameters tab.&lt;/em&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Does it mean that the shape for the background subtraction not necessarily has to be exactly the same size as the shape for the band? (See Figure C.) I attach some pictures for your convenience. &lt;img src=&quot;https://i.stack.imgur.com/eJhao.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you very much for any help.&lt;/p&gt;&#xA;" OwnerUserId="4593" LastActivityDate="2014-06-29T11:09:18.197" Title="A question on ImageQuantTL" Tags="&lt;gel-electrophoresis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19374" PostTypeId="1" CreationDate="2014-06-29T05:02:19.760" Score="1" ViewCount="57" Body="&lt;p&gt;If you are investigating low-frequency and rare variants for a complex trait using exome sequencing, why would one consider using different populations (African ancestry and European ancestry) especially considering that the populations have different allele frequencies. Is the main object to see if they're could possibly be novel rare variants in each population at different allele frequencies? &lt;/p&gt;&#xA;" OwnerUserId="8171" LastActivityDate="2014-06-29T07:42:16.557" Title="Investigating rare variants in ethnically different populations (European ancestry &amp; African ancestry)" Tags="&lt;human-genetics&gt;&lt;snp&gt;&lt;population-genetics&gt;&lt;gwas&gt;&lt;exons&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19375" PostTypeId="2" ParentId="19374" CreationDate="2014-06-29T07:42:16.557" Score="1" Body="&lt;p&gt;Too long for a comment, but sort of: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mainly you do this because these populations have segregated long time ago and developed differently, so it is more likely to identify these polymorphisms. It is also helpful to use populations for this which mixed not too much with other populations (thats why north-americans are usually not used here, as America was kind of a melting pot). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will find rare SNPs for pigmentation in europeans that are not present in the more ancient african population (and must therefore be occured after the populations divided), examples are the so called &quot;golden mutation&quot; in SLC24A5 (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16357253&quot; rel=&quot;nofollow&quot;&gt;rs1426654&lt;/a&gt;) or a polymorphism in IRF4 (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18483556&quot; rel=&quot;nofollow&quot;&gt;rs12203592&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-06-29T07:42:16.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19376" PostTypeId="2" ParentId="19373" CreationDate="2014-06-29T11:09:18.197" Score="2" Body="&lt;p&gt;I would definitely go for option A. If you are assuming that the staining in band 6 is all due to whatever you are measuring, there is no reason to think that the signal at the top of lane 1 is not meaningful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, this type of measures is only semi-quantitative, so being too &quot;picky&quot; in how you choose your region probably won't really increase the precision of your result. If you want to get a quantitative measure I am afraid you will have to turn to some other technique.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally note that the area obviously means a lot if you are looking at total intensity of the bands, rather than average intensity.&lt;/p&gt;&#xA;" OwnerUserId="115" LastActivityDate="2014-06-29T11:09:18.197" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19377" PostTypeId="1" AcceptedAnswerId="19379" CreationDate="2014-06-29T11:54:31.430" Score="2" ViewCount="143" Body="&lt;p&gt;I am very curious about this question. I got this doubt when I was studying anatomy and physiology of the earthworm &lt;a href=&quot;http://encyclopedia2.thefreedictionary.com/Lampito+mauritii&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Lampito mauritii&lt;/em&gt;&lt;/a&gt;. It breathes through its skin (cutaneous respiration) and if we cover its body with a wet cloth and all the necessary external openings are left uncovered (such as nephridia and other genital pores) then will the earthworm survive?&lt;/p&gt;&#xA;" OwnerUserId="8101" LastEditorUserId="948" LastEditDate="2014-06-29T16:12:56.840" LastActivityDate="2014-06-30T06:03:58.683" Title="will an earthworm survive after covering its skin with a wet cloth" Tags="&lt;invertebrates&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19378" PostTypeId="1" CreationDate="2014-06-29T23:14:26.280" Score="1" ViewCount="33" Body="&lt;p&gt;I'm reading a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24507774&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; that used whole exome sequencing on an African&#xA; American and European populations to discover novel low frequency and&#xA;rare variants associated with lipid levels &amp;amp; the risk of coronary&#xA;heart disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They used the Illumina Human exome genotyping array that was designed&#xA;based on coding variants discovered from sequencing the exomes of&#xA;12,000 individuals. Therefore, they selected their participants from a&#xA;study who were not among the 12,000 individuals utilized to design the&#xA;array .&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: Why would they select individuals who were not among&#xA;the 12,000 used to design the array? (I'm thinking because maybe it&#xA;could produce false positives associations? bias?)&lt;/p&gt;&#xA;" OwnerUserId="8171" LastEditorUserId="5144" LastEditDate="2014-06-30T19:11:11.430" LastActivityDate="2014-07-01T10:00:11.217" Title="A question on exclusion of study participants for an Exome genotyping array" Tags="&lt;human-genetics&gt;&lt;experimental-design&gt;&lt;population-genetics&gt;&lt;gwas&gt;&lt;exons&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19379" PostTypeId="2" ParentId="19377" CreationDate="2014-06-30T06:03:58.683" Score="3" Body="&lt;p&gt;This is one of those speculative questions where you don't have a definite answer unless you specifically experiment and find out for yourself. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is a known fact that earthworms breathe through diffusion. It has a thin cuticle over its body and requires moist skin which is achieved by a slimy mucous (&lt;a href=&quot;http://www.sas.upenn.edu/~glauren/earthworm.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). It is interesting to note that earthworms are also capable of going into a state of hibernation called &lt;a href=&quot;http://en.wikipedia.org/wiki/Aestivation&quot; rel=&quot;nofollow&quot;&gt;estivation&lt;/a&gt; (in American english) (&lt;a href=&quot;http://www.learner.org/jnorth/search/WormNotes3.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) which helps them maintain a low metabolic state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since you are planning to cover it with a cloth, the material of the cloth also matters. It has to be a material with low &lt;a href=&quot;http://en.wikipedia.org/wiki/Breathability&quot; rel=&quot;nofollow&quot;&gt;breathability&lt;/a&gt;. For eg: the survivability of the worm would depend on if you were using a wool or a silk cloth to cover it. Here is an article on the breathability of different fabrics (&lt;a href=&quot;http://textilelearner.blogspot.in/2013/05/an-overview-of-waterproof-breathable.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion, I would take a guess that it should survive if the material let air pass through and would go into a state of estivation on low availability of oxygen but maybe not die. After all, they are said to be able to survive even in water  if it contains enough available oxygen. (&lt;a href=&quot;http://animals.howstuffworks.com/animal-facts/earthworm2.htm&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-30T06:03:58.683" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19380" PostTypeId="1" AcceptedAnswerId="19386" CreationDate="2014-06-30T08:38:35.823" Score="4" ViewCount="385" Body="&lt;p&gt;I'm writing a novel and i would like to know some of the equipment and techniques involved with modifying a virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it feasible for a virus to be engineered to only affect certain people? It doesn't have to be possible, only sound like i know what i'm talking about. I have been trying to research the subject but nothing i have found will tell me the basics of what is involved with virus modification.&#xA;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="8176" LastEditorUserId="3340" LastEditDate="2014-07-02T05:36:11.557" LastActivityDate="2014-08-01T15:38:28.170" Title="Theoretically, what technique would one use to modify a virus so that it only affected a subset of the population?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;virus&gt;" AnswerCount="4" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19381" PostTypeId="1" AcceptedAnswerId="19382" CreationDate="2014-06-30T09:22:15.923" Score="6" ViewCount="1162" Body="&lt;p&gt;I visited a bird enclosure close to where I live in Australia. The enclosure had several different species. The birds that stood out most were these doves sitting right along the fence railing, making a deep &quot;Wo-wo-wo-woo&quot; sound. That and also I thought they looked and sounded similar to Spotted Doves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/X6Jxl.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/cgtAi.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know what the species of this birds may be?&lt;/p&gt;&#xA;" OwnerUserId="8177" LastActivityDate="2014-06-30T09:57:28.550" Title="Species of this White Dove" Tags="&lt;zoology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19382" PostTypeId="2" ParentId="19381" CreationDate="2014-06-30T09:38:45.447" Score="3" Body="&lt;p&gt;I think this is a Barbary dove (or Ringneck dove). See this image (from the &lt;a href=&quot;http://nzbirdsonline.org.nz/species/barbary-dove&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dFbDY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More information can be found &lt;a href=&quot;http://en.wikipedia.org/wiki/Barbary_dove&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://nzbirdsonline.org.nz/species/barbary-dove&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;. The second pages shows also images of different color variations.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-06-30T09:57:28.550" LastActivityDate="2014-06-30T09:57:28.550" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19383" PostTypeId="2" ParentId="19381" CreationDate="2014-06-30T09:48:40.993" Score="1" Body="&lt;p&gt;it is symi bird and more over it is commonly called as collared dove its a resident of symi and would have brought to australia by other means&#xA;&lt;img src=&quot;https://i.stack.imgur.com/dX223.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;you can find a list off all the symi birds &lt;a href=&quot;http://symifloraandfauna.jigsy.com/symibirdlist&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8101" LastActivityDate="2014-06-30T09:48:40.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19384" PostTypeId="2" ParentId="19364" CreationDate="2014-06-30T10:39:30.690" Score="3" Body="&lt;p&gt;The reason why the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cuttlefish&quot; rel=&quot;nofollow noreferrer&quot;&gt;cuttlefish&lt;/a&gt; is colour blind is because &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;it just has one type of cone cell. Humans have three different types,&#xA;  each sensitive to a different color of light. With only one cone type,&#xA;  you couldn’t differentiate between different colors (&lt;a href=&quot;http://indianapublicmedia.org/amomentofscience/cuttlefish-colorblind-masters-camouflage/&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A study was conducted in the lab of &lt;a href=&quot;http://hermes.mbl.edu/mrc/hanlon/mathger.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dr Lydia M. Mäthger&lt;/a&gt; where two different checkerboards were used to test their colorblindness. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;1) Gray – Green. One green shade, matched to the maximum absorption&#xA;  wavelength of cuttlefish, was combined with 16 different shades of&#xA;  gray. As supposed some shades of gray couldn’t be distinguished from&#xA;  the green by the cuttlefish, which didn’t adapt the body pattern.&#xA;  Experiment one was successful.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;2) Blue – Yellow. A checkerboard of blue and yellow matching in&#xA;  intensity was used for the second experiment. The skin color of the&#xA;  test species didn’t change either and therefore experiment two was&#xA;  also successful (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16376404&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These experiments concluded that it was indeed colourblind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To confirm the effectiveness of the camouflage, HyperSpectral Imaging (HSI) was used to measure the colour match between the cuttlefish and its background. Using this technology it was perceived as to how a predator would view a camouflaged cuttlefish. It was found that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cuttlefish can produce color-coordinated camouflage on natural&#xA;  substrates despite lacking color vision, and that the color aspect of&#xA;  cuttlefish camouflage is highly effective against fish predators. Much&#xA;  of the contrast information (which allows a predator to &quot;pick out&quot; a&#xA;  cuttlefish from the background environment) resides in the brightness&#xA;  (luminance) rather than in the color (chromatic) aspect of the&#xA;  reflected light. What this means is that cuttlefish camouflage&#xA;  strategies take away a tool from predators in their ability to pick&#xA;  out their prey from the background and instead leave them with only&#xA;  brightness as a method for prey identification (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21576487&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference 1&lt;/a&gt; and &lt;a href=&quot;http://www.eurekalert.org/pub_releases/2011-05/mbl-hca051611.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference 2&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And now we get to the main question as to how they do it. Cuttlefish are apparently able to detect the intensity of light reflected from objects in its surroundings. It is able to perceive even a 15% change in contrast. In an experiment, it was found that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The animals did not respond to the checkerboard pattern when placed on&#xA;  substrates whose color intensities were matched to the Sepia visual&#xA;  system, suggesting that these checkerboards appeared to their eyes as&#xA;  uniform backgrounds (&lt;a href=&quot;http://hermes.mbl.edu/news/features-archived/feature_cuttlefish.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In another bit of interesting research done on the ability to copy the patterns on checkerboards (&lt;a href=&quot;http://jeb.biologists.org/content/204/12/2119.figures-only&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;), three inferences were drawn &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first find was that the range (relative to the size of the&#xA;  cuttlefish ‘white square’) for the animal to exhibit disruptive skin&#xA;  patterning had to be withing a certain  narrow range. Secondly, given&#xA;  the appropriate size of checker, cuttlefish regulated their disruptive&#xA;  skin patterns according to the contrast between white and black&#xA;  squares. Third, by manipulating the number of white squares on a board to just  4&#xA;  among 316 black squares (or 1.25 %) produced disruptive patterning,&#xA;  yet increasing the number of white squares to 20, 40 or 80 did not&#xA;  increase the frequency of appearance of the cuttlefish ‘white square’,&#xA;  but only its clarity of expression.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This study shows that the number of white objects in the background significantly influence cuttlefish skin patterns further putting stress on its ability to view the polarization of light (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0960982212000115&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sRGft.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/B46tK.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some cuttlefish camouflage examples&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-01T04:08:23.987" LastActivityDate="2014-07-01T04:08:23.987" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19385" PostTypeId="2" ParentId="7516" CreationDate="2014-06-30T10:41:29.250" Score="1" Body="&lt;p&gt;A couple of months ago I listened to a plant physiologist who strongly recommended recombination-based mapping over sequencing based mapping. The main reason he gave was the error-rate of 2nd generation sequencing. The error rate on Illumina platforms are about 1 % if I recall. In a small genome like that of Arabidopsis thaliana (157 Mbp) that accounts for over 1 million sequencing errors. That can of course be reduced having a proper sequencing depth and using the consensus sequence. But it can still cause problems if you're tracking a phenotype caused by an SNV. In plants like A. thaliana where back crossing can be used to create homozygous plants, recombination-based techniques can be particularily effective.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But he was talking from a plant physiologist's view when working with A. thaliana as a model organism. When working with humans which always are heterozygous, can't be back-crossed, don't have a generation time of six weeks and where samples sizes will probably be small I imagine that the situation is different. The classic geneticists' working with human diseases that I have talked have expressed fear that their work will soon be obsolete due to falling sequencing prices and growing sequence data collections.&lt;/p&gt;&#xA;" OwnerUserId="8179" LastActivityDate="2014-06-30T10:41:29.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19386" PostTypeId="2" ParentId="19380" CreationDate="2014-06-30T11:04:37.580" Score="3" Body="&lt;p&gt;Yes, it is possible and probably you won't need many literary artifices to make it work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially &lt;a href=&quot;http://en.wikipedia.org/wiki/Virus&quot; rel=&quot;nofollow&quot;&gt;viruses&lt;/a&gt; are what is technically called &quot;obligate intracellular parasites&quot;.&lt;br&gt;&#xA;Parasites because they cannot grow by themselves, they need a host cell from which they &quot;steal&quot; the intracellular machinery to replicate; intracellular because they grow inside cells; and obligate because they cannot reproduce outside their target cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, each virus has its &quot;favourite cell&quot; to infect. For instance HIV targets a type of lymphocytes (cells of the immune system), other viruses may only target bacteria (these are called bacteriophages) and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is this specificity achieved? Well, to put it simply, viruses &quot;anchor&quot; to specific &lt;a href=&quot;http://en.wikipedia.org/wiki/Protein&quot; rel=&quot;nofollow&quot;&gt;proteins&lt;/a&gt; (or other molecules) that are sitting on the membrane of their target cells and that allows them to go in. If a cell does not have that specific protein, then the virus cannot infect it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in your story, maybe the target population will have a &lt;a href=&quot;http://en.wikipedia.org/wiki/Mutation&quot; rel=&quot;nofollow&quot;&gt;mutation&lt;/a&gt; in their genome that will modify a certain protein. You could then (fictionally) construct a virus that specifically targets cells expressing that protein and you're set!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The virus construction part is just standard &lt;a href=&quot;http://en.wikipedia.org/wiki/Molecular_biology&quot; rel=&quot;nofollow&quot;&gt;molecular biology&lt;/a&gt;, really.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few things to read:&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_engineering&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Genetic_engineering&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Genetically_modified_virus&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Genetically_modified_virus&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Viruses&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Viruses&lt;/a&gt; &amp;lt;--this explains a lot&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="3340" LastEditDate="2014-06-30T11:10:40.290" LastActivityDate="2014-06-30T11:10:40.290" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="19387" PostTypeId="2" ParentId="8123" CreationDate="2014-06-30T11:14:28.817" Score="5" Body="&lt;p&gt;I cannot find any definite articles on why there would be a reason for this behaviour other than the same ones that you have mentioned in your article. It could be because it wants to mark its territory or the dog wants to hide its scent. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One point that I would also like to add is force of habit. As Charles Darwin (the father of evolutionary biology) had said in his book titled &quot;The expression of emotion in man and animals&quot;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;‘Certain complex actions are of direct or indirect service under&#xA;  certain states of the mind, in order to relieve or gratify certain&#xA;  sensations, desires, etc.; and whenever the same state of mind is&#xA;  induced, however feebly, there is a tendency through the force of&#xA;  habit and association for the same movements to be performed, though&#xA;  they may not then be of the least use’ (&lt;a href=&quot;http://en.wikipedia.org/wiki/The_Expression_of_the_Emotions_in_Man_and_Animals&quot; rel=&quot;noreferrer&quot;&gt;reference 1&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1279921/&quot; rel=&quot;noreferrer&quot;&gt;reference 2&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is more of a guess that we make when we see them hide their faeces but in the end, there may not be a reason at all but a habit that do not serve much purpose passed on through evolution. It is left upto our own liberty as to guess what the exact reason is.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-06-30T11:14:28.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19388" PostTypeId="1" CreationDate="2014-06-30T13:03:10.360" Score="2" ViewCount="446" Body="&lt;p&gt;Would anyone be so kind as to give me a few examples of the equipment involved when modifying a virus? Otherwise my novel may end up reading&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eva entered the lab and modified a virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not much back story there!&lt;/p&gt;&#xA;" OwnerUserId="8176" LastEditorUserId="3340" LastEditDate="2014-07-02T05:25:56.123" LastActivityDate="2014-07-02T05:25:56.123" Title="What equipment would one use to modify a virus?" Tags="&lt;molecular-biology&gt;&lt;virology&gt;" AnswerCount="3" CommentCount="5" ClosedDate="2014-07-02T09:49:16.757" ContentLicense="CC BY-SA 3.0" />
  <row Id="19391" PostTypeId="1" AcceptedAnswerId="19421" CreationDate="2014-06-30T16:14:35.607" Score="3" ViewCount="962" Body="&lt;p&gt;as per &lt;a href=&quot;http://www.practicalscience.com/al.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this site&lt;/a&gt; the dimensions of eggs of &lt;a href=&quot;http://wikipedia.org/wiki/Ascaris_lumbricoides&quot; rel=&quot;nofollow noreferrer&quot;&gt;ascaris lumbricoides&lt;/a&gt; are 78-105 microns and as it is shown in the pic down here only half of the body cavity would be used for storage of all the stages of different sizes of eggs&#xA;&lt;img src=&quot;https://i.stack.imgur.com/3L96A.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;and as we all know pseudo coelomates have very minute width of their body cavity &#xA;and rest of the body cavity is filled with mesoglea &lt;/p&gt;&#xA;&#xA;&lt;p&gt;so my question is how can a round worm accomodate $2$x$10^6$ eggs in its womb before its release&lt;/p&gt;&#xA;" OwnerUserId="8101" LastEditorUserId="3340" LastEditDate="2014-07-01T09:42:33.897" LastActivityDate="2014-08-02T12:48:11.117" Title="how can a pseudo coelomate like ascaris lay 200k eggs in a single day" Tags="&lt;pathology&gt;&lt;eggs&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19392" PostTypeId="1" CreationDate="2014-06-30T17:50:43.053" Score="1" ViewCount="610" Body="&lt;p&gt;Used for instance in this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8219924&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The role of genital mycoplasmas as pathogens - - are&#xA;  generally neglected by diagnostic laboratories in the United Kingdom,&#xA;  possibly due to the lack of a suitable commercially-available culture&#xA;  medium. We have evaluated the bioMerieux Mycoplasma-Lyo system using&#xA;  qualitative and quantitative studies and have found it to have&#xA;  suitable qualities and practical advantages for detection of&#xA;  Ureaplasma urealyticum and Mycoplasma hominis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is Mycoplasma Lyo medium?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it is some sort of anaerobic solid medium for all other mycoplasmas except M. pneumoniae (strict aerobe). &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="3971" LastEditDate="2016-05-27T13:39:08.223" LastActivityDate="2016-05-27T13:39:08.223" Title="What is Mycoplasma Lyo medium?" Tags="&lt;microbiology&gt;&lt;mycoplasma&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19393" PostTypeId="2" ParentId="19388" CreationDate="2014-06-30T18:19:38.667" Score="4" Body="&lt;p&gt;I'm no expert at this and I would welcome any changes to this post. First you need to decide, what your target organism which you want to infect is (e.g. mammalian cells, bacterial cells) and based on that you choose your viral vector as listed in this &lt;a href=&quot;http://en.wikipedia.org/wiki/Viral_vector&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt;. Generally for mammalian cell stable transfection (usually you want the genetic materials you introduced to persist between cell divisions hence stable transfection) and transformation (just a general statement about changing cells as you have introduced, usually foreign genetic material but transformation is not necessarily the same as making something immortalised, which means the cells won't stop dividing i.e. becoming cell lines or in lay term cancerous) scientists tend to use &lt;a href=&quot;http://en.wikipedia.org/wiki/Lentivirus&quot; rel=&quot;nofollow&quot;&gt;lentiviruses&lt;/a&gt;, which are retroviruses, similar to HIV and they can even infect non dividing cells (so this should allow your imagination to run wild!). Once you have decided what the best viral vehicle for targeting your cells of interest is then you essentially transfect the plasmid DNA (packaging vector), which produces the virus protein package, into cells, whose job becomes to produce the virus as those cells have the required cellular machinery for this purpose. These cells are often 293T packaging cells. Along with the plasmid (circular) DNA, which produces the virus package, you co-transfect the packaging (e.g. 293T) cells with another plasmid, called lenti-vector, which does whatever you want it do, such as express a particular protein or microRNA or whatever but the idea is that stuff produces by the lenti-vector should not be toxic to the target cell (i.e. the cells you intend to target), unless thats what you want it to do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now as you can see, you can play around with two things here, first the packaging vector, to change the behaviour of the virus if you wish. And second the lenti-virus vector, to produce whatever you want it to! Once the packaging cells made your viruses, containing your lenti-vector, the virus get secreted into the media, which the packaging cells are in so you have to extract the media, congaing the virus, and concentrate the virus using centrifugation. Once you got the virus then you can use it to transform the (target) cells you wish. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the lab based procedure of how you make the virus and what equipments you use and how to concentrate the virus then please see this &lt;a href=&quot;http://compbio.dfci.harvard.edu/compbio/research/labprotocols/contentBlocks/0/contentBlock_files/file15/Lentivirus_Production_and_Transfection_Protocol.pdf&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt;, although its a little technical. In this case, the packaging vector is fuGENE 6 and the lenti-vector or just plasmids of interests are listed (please not that I do not endorse any products mentioned here and I'm just using it as an example).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now for making the packaging plasmid (making the virus), you often use the genetic materials from a virus and change it through a procedure called polymerase chain reaction (&lt;a href=&quot;http://en.wikipedia.org/wiki/Polymerase_chain_reaction&quot; rel=&quot;nofollow&quot;&gt;PCR&lt;/a&gt;). Same goes for the lenti-vector/plasmid as they are derived from somewhere and then change through time using PCR and &lt;a href=&quot;http://en.wikipedia.org/wiki/Restriction_digest&quot; rel=&quot;nofollow&quot;&gt;restriction digests&lt;/a&gt;, which is an equivalent of genetic material cut and paste, to make the vectors and products of interest. Once all is done the the virus can infect the target cells and effect it based on its designed function (defined by the two vectors I described).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the above response does not answer you question, since it is currently very broad, please make further clarification to the question so that I can modify my response accordingly.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="3340" LastEditDate="2014-07-01T08:10:40.567" LastActivityDate="2014-07-01T08:10:40.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19394" PostTypeId="2" ParentId="19388" CreationDate="2014-06-30T18:55:00.363" Score="1" Body="&lt;p&gt;I would not start from so bottom as Bez in making viruses. &#xA;This is very very long project.&#xA;It is much less cumbersome task to consider modifying virus, since it already occurs passively in real life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would choose equipment based on the characteristics of the virus. &#xA;I would start to develop equipment needed for the specific project, since there is no ready solution for this kind of task. &#xA;The equipment can be targeted to &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;actively changing virus (ss(-) and ss(+) RNA virus)&lt;/li&gt;&#xA;&lt;li&gt;virus not changing so much (here you have to think how you ignite the point mutation and why).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I would use iPS stem cells to as an target but to get this far is very very long process still. &#xA;I would focus on antigen presentation - again very many fine regulation factors in Interferons etc should be considered in the special viral case - note that the interferon research is now in an active phase but early. &#xA;Interferons are specific so specific parts of the equipment should exists to detect them - for instance, IFN-gamma.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Viruses are generally extremely difficult to control - shortly existing in one form. &#xA;You can imagine how difficult they become after editing them real life.&#xA;So the plan would be first to understand some easy virus and its early stages in the replication. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can actually choose a virus that undergoes continuously point mutations (drift mutation) like influenza virus. &#xA;However, I would pick something that is not so changing (not RNA virus). &#xA;There is no good equipment to do regular analysis of the changes in the influenza virus. &#xA;It always requires much work to recognize which genome part has changed and how much internationally. &#xA;The vaccines are made based on reports from many countries about their influenza virus statuses and their genomes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some simple DNA virus with very slow but fixed point mutations in time so you have time to research them and you can estimate when the next change is going to be. &#xA;It would be also useful if you know which part of the virus is going to change (particular plasmid).&#xA;This makes the research much more manageable.&#xA;Sufficient time-series analysis and group of Mathematicians are also needed to understand different data from different stages.&#xA;Actually, your task is extremely broad.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-06-30T19:02:10.913" LastActivityDate="2014-06-30T19:02:10.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19395" PostTypeId="1" CreationDate="2014-06-30T19:11:06.723" Score="1" ViewCount="238" Body="&lt;p&gt;Centromeres move toward the poles as the microtubules that connect them shorten. This shortening is due to the removal of tubulin subunits from the kinetochore ends of the microtubules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm confused as to how the centromeres can be pulled closer to their respective poles while tubulin subunits are being removed. To me, this is similar to pulling an object by a rope while simultaneously cutting pieces of the rope out. How do the centromeres remain connected to the spindles while tubulin subunits are being removed?&lt;/p&gt;&#xA;" OwnerUserId="5179" LastActivityDate="2016-01-12T16:23:41.877" Title="Anaphase Microtubule Disassembly" Tags="&lt;cell&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19396" PostTypeId="1" CreationDate="2014-06-30T20:15:20.437" Score="7" ViewCount="767" Body="&lt;p&gt;Looking at ones that manage well alongside us human animals, such as dogs and cats, we see that this is possible for evolved, distant animals to have heritable, preferable traits around people. However, when especially looking at lions and the like, it doesn't seem to work out as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some people have tigers as pets, but in general it is believed that they are more &quot;wild&quot; and not as tame and domesticated as other animals (such as dogs and cats).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to selectively breed and enable any animal to be more like dogs and cats? Even sharks? Tigers? Alligators? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If domestication worked so well with dogs and cats, such as them living (for the most part) peacefully and well with people, wouldn't the process be beneficial for other animals so we could all live better side-by-side?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, can you theoretically get any animal to have heritable traits?&lt;/p&gt;&#xA;" OwnerUserId="8182" LastEditorUserId="3340" LastEditDate="2014-07-02T05:33:49.690" LastActivityDate="2015-07-01T22:00:43.510" Title="Theoretically, is domestication of (virtually) any animal possible?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;zoology&gt;&lt;behaviour&gt;&lt;artificial-selection&gt;" AnswerCount="5" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19397" PostTypeId="1" CreationDate="2014-06-30T20:55:34.163" Score="4" ViewCount="298" Body="&lt;p&gt;Is there an observed (direct not indirect) speciation on record showing a species shift within the span of history of recorded science?&lt;/p&gt;&#xA;" OwnerUserId="8183" LastEditorUserId="8183" LastEditDate="2014-07-11T20:48:47.410" LastActivityDate="2014-07-11T20:48:47.410" Title="Are there any cases of observed extreme speciation" Tags="&lt;evolution&gt;&lt;speciation&gt;" AnswerCount="1" CommentCount="15" ClosedDate="2014-07-09T16:28:36.267" ContentLicense="CC BY-SA 3.0" />
  <row Id="19398" PostTypeId="2" ParentId="19396" CreationDate="2014-06-30T21:41:24.453" Score="3" Body="&lt;p&gt;I understand the question as &quot;can you get any animal to have heritable traits selected by humans?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This definition of domestication implies that a population of animals can be bred for a sufficiently long period of time, so that humans can select hereditary traits that fit their needs. Humans could provide selective pressure that creates a new variety with different traits. So according to the laws of evolution, I would say it could &lt;em&gt;theoretically&lt;/em&gt; be done for any living being.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But there may be species that could be reluctant to such a control, e.g. animals that we have difficulties to reproduce in captivity for whatever reasons (polar bears?), or isolate from their wild congeners (genetic isolation is a generally a pre-requisite to domestication). For them, domestication could take too much effort or a longer time than humans would be willing to spend.&lt;/p&gt;&#xA;" OwnerUserId="3394" LastEditorUserId="3394" LastEditDate="2014-07-01T08:37:10.487" LastActivityDate="2014-07-01T08:37:10.487" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19399" PostTypeId="2" ParentId="19380" CreationDate="2014-06-30T22:41:08.160" Score="3" Body="&lt;p&gt;Virus is a non-living but infectious structure consisting of a nucleic acid core and envelope covering. The envelope is what determines target specificity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are genetically engineering, lets say a retrovirus (which if you are writing a sci-fi book this is probably the type of virus you are wanting to write about, for many reasons) you would want to use peices of DNA that code for integrated expression cassettes for viral &lt;em&gt;Gag&lt;/em&gt;, &lt;em&gt;Pol&lt;/em&gt;, and &lt;em&gt;Env&lt;/em&gt; proteins, all of which are required in &lt;em&gt;trans&lt;/em&gt; to make virus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These DNA's would be mixed and then put into a living mammalian cell (what we cell biologists call a packaging cell). This packaging cell line transcribes and translates the 3 cassettes and builds the virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;gag&lt;/em&gt; gene encodes internal structural proteins, &lt;em&gt;pol&lt;/em&gt; encodes reverse transcriptase &#xA;and integrase, and the &lt;em&gt;env&lt;/em&gt; gene encodes the viral envelope protein, which &#xA;resides on the viral surface and facilitates infection of target cell by &#xA;direct interaction with cell type-specific receptors; thus the host range of the virus is determined by the design of the envelope proetin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for some example envelopes, the amphotropic envelope protein has historically been the protein of choice for infection of human and other mammalian cell lines. The 10A1 envelope protein has also been used due to its increased versatility relative to the amphotropic &#xA;protein.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-06-30T22:41:08.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19401" PostTypeId="2" ParentId="19395" CreationDate="2014-07-01T04:29:22.390" Score="1" Body="&lt;p&gt;I don't think the microtubules shorten. The disassembly of tubulin (dynamic catastrophe) happens from its + end which in this case is protected by the kinetochore proteins. The separation of chromatids, I &lt;em&gt;guess&lt;/em&gt;, happens via a dynein (and in some cases kinesin) mediated movement. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;https://en.wikipedia.org/wiki/Kinetochore&quot; rel=&quot;nofollow&quot;&gt;wikipedia article&lt;/a&gt; on kinetochore is quite detailed and you can have a look at it.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-01-12T10:23:43.887" LastActivityDate="2016-01-12T10:23:43.887" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19403" PostTypeId="2" ParentId="5401" CreationDate="2014-07-01T05:04:27.263" Score="4" Body="&lt;p&gt;The short answer is that yes, they will grow back. Cats do regularly shed their whiskers and grow them back in time (&lt;a href=&quot;http://avetsguidetolife.blogspot.in/2011/07/do-cat-whiskers-regrow.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). The thing is that if damage has been done to the root of the whisker, it may grow back in an irregular manner (&lt;a href=&quot;http://pets.thenest.com/cat-whiskers-grow-back-pulled-out-11482.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Wish for the best and by now I think the whisker should be back just fine. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-07-01T05:04:27.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19404" PostTypeId="2" ParentId="3694" CreationDate="2014-07-01T05:12:54.973" Score="3" Body="&lt;p&gt;First we will take a look at the lines of resistance of a carrot. There are three&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;The skin&lt;/strong&gt; - The first line of resistance is the outer membrane or skin of the carrot and chemical compounds that are normally present&#xA;  there. Two antifungal polyacetylenes, falcarinol and falcarindiol, and&#xA;  an isocoumarin, 6-methoxymellein, are present in small amounts in a&#xA;  normal carrot and present the first barrier in undamaged carrots.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Post Harvest&lt;/strong&gt; - If during harvest or post harvest handling this barrier is broken, the surface is punctured, scraped or sliced,&#xA;  microorganisms may begin to grow. The carrot at this point begins a&#xA;  wound healing process by accumulating suberin, a complex&#xA;  polysaccharide, at the wound site. Along with suberin, lignin is also&#xA;  accumulated. Suberisation is complete within 48 hours after wounding,&#xA;  and lignification is complete within 168 hours of wounding..&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Phytoalexin barrier&lt;/strong&gt; - The last and most important line of resistance is the phytoalexin barrier. Phytoalexins are chemicals&#xA;  produced by plants that impart disease resistance in response to&#xA;  mechanical injury, physiological stimuli or infection. Scopoletin, a&#xA;  coumarin,and para-hydroxy benzoic acid, a phenol, are apparently early&#xA;  arrivals on the scene but later disappear (&lt;a href=&quot;http://www.carrotmuseum.co.uk/Disease%20Response%20Mechanism.pdf&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are three enemies of carrot storage: wilt, re-growth and rot. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some reasons for carrots rotting faster: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many fruits and vegetables start to produce ethylene gas when they start to ripen. Some foods are extremely sensitive to ethylene gas which makes them rot faster (&lt;a href=&quot;http://www.coreperformance.com/daily/nutrition/why-fresh-produce-goes-bad-so-fast.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). I am guessing that you keep different vegetables close together. Maybe if you stored carrots separately, it might make them last a bit longer.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Major post-harvest losses in carrots are due to Sclerotinia rot,&#xA;  Botrytis rot, Bacterial soft rot (Erwinia) and Sour rot (Geotrichum).&#xA;  Of these, Sclerotinia rot is the most prevalent.The Sclerotinia fungus&#xA;  infects the carrot roots in the field through the crown. During&#xA;  storage, the Sclerotinia fungus produces a white, cottony mycelium&#xA;  which covers the roots. Infected roots are usually soft and watery (&lt;a href=&quot;http://www5.agr.gc.ca/resources/prod/doc/pfra.../carrots-carottes_eng.pdf&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There would definitely be more reasons but I am guessing that these are the major contributors to it rotting faster. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-01T05:37:36.223" LastActivityDate="2014-07-01T05:37:36.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19406" PostTypeId="2" ParentId="19187" CreationDate="2014-07-01T05:57:47.167" Score="2" Body="&lt;p&gt;Researchers at Ghent University have made a discovery that downregulation of the proteins CONSTANS 1 (SOC1) and FRUITFULL (FUL) lead to the development of many perennial traits in annual plants (in the study &lt;em&gt;Arabidopsis thaliana&lt;/em&gt; is used) (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18997783&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The CONSTANS gene controls flowering in &lt;em&gt;Arabidopsis thaliana&lt;/em&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7697715&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;FRUITFULL (FUL) is an MADS box gene that functions early in controlling flowering time, meristem identity and cauline leaf morphology and later in carpel and fruit development in &lt;em&gt;Arabidopsis thaliana&lt;/em&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21284215&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The process is complicated and would need many genes to be manipulated but this research proves that it is possible. &lt;a href=&quot;http://jxb.oxfordjournals.org/content/62/13/4415.full&quot; rel=&quot;nofollow&quot;&gt;Another article of interest&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-02T03:36:15.917" LastActivityDate="2014-07-02T03:36:15.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19407" PostTypeId="1" CreationDate="2014-07-01T07:10:13.053" Score="2" ViewCount="72" Body="&lt;p&gt;Sometimes there are identical sequences in Genbank/Genpept, most often coming from the same species but different strains. Ie if I look up &quot;bacteria chitin synthase&quot;, the 624-aa protein from &lt;em&gt;Dickeya dadantii&lt;/em&gt; shows up three times. There even is an &quot;identical proteins&quot; link.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any filter that I can use to get only one sequence from every group of identical ones? I mean, other than parse downloaded file on my own computer.&lt;/p&gt;&#xA;" OwnerUserId="8185" LastActivityDate="2014-08-01T02:04:51.813" Title="Hiding identical sequences in NCBI web interface" Tags="&lt;bioinformatics&gt;&lt;sequence-analysis&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19408" PostTypeId="2" ParentId="19407" CreationDate="2014-07-01T07:57:17.793" Score="1" Body="&lt;p&gt;I'm not sure if there's a way on GenBank, but UniProt offers &lt;a href=&quot;http://www.uniprot.org/help/uniref&quot; rel=&quot;nofollow&quot;&gt;UniRef&lt;/a&gt; where you can cluster &lt;a href=&quot;http://www.uniprot.org/uniref/?query=uniprot%3A%28bacteria%20chitin%20synthase%29%20identity:1.0&quot; rel=&quot;nofollow&quot;&gt;redundant sequences&lt;/a&gt; or specify a lower cutoff (like &lt;a href=&quot;http://www.uniprot.org/uniref/?query=uniprot%3A%28bacteria%20chitin%20synthase%29%20identity:0.9&quot; rel=&quot;nofollow&quot;&gt;90% identity&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2014-07-01T07:57:17.793" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19409" PostTypeId="2" ParentId="19388" CreationDate="2014-07-01T09:08:34.980" Score="3" Body="&lt;p&gt;&lt;em&gt;Consider this as a summary of the previous answers. Also, I am elaborating more on how to make self-sustaining mutated viruses&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Points to consider before you think about working with viruses:-&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Viruses are pathogenic and the biologist working on them faces a risk of infection. Viral work is always carried out in a protected environment at high &lt;a href=&quot;http://en.wikipedia.org/wiki/Biosafety_level&quot; rel=&quot;nofollow&quot;&gt;biosafety levels&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Viruses need a host to survive. You need to culture host cells or use a live organism to propagate the virus. Generally one goes for the latter only if cell culture methods are unfeasible.&lt;/li&gt;&#xA;&lt;li&gt;Almost all viruses have a very small genome (which can be replicated very fast), that can be either DNA or RNA. The genome has only very few essential genes that are responsible for the virus capsid (external shell) formation and early replication; most other factors required for the propagation are hijacked from the host.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Having identified and obtained a suitable host, one can proceed to genetic manipulation. The lentiviral vectors that Bez described are basically partial viruses. One part codes for the capsid and cannot make active viruses by itself whereas the other holds the genes for replicative function. So in a way the lentiviral vectors are disarmed viruses that are used as molecular biology tools. But what you are looking for is different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To modify a virus you need to make mutations in its genome. Once you have identified what mutations are to be made then as previously mentioned, PCR can be used to incorporate them. This technique is slightly different from a usual PCR (not in principle, though) and is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Site-directed_mutagenesis&quot; rel=&quot;nofollow&quot;&gt;site-directed mutagenesis&lt;/a&gt;. For ease it is always better to clone (fix) the viral genome in a plasmid (circular DNA that can be propagated in a usual lab bacteria- &lt;em&gt;E.Coli&lt;/em&gt;). After mutating the viral genome, you can excise it from the plasmid. Note that PCR is done with DNA. For RNA viruses you need to convert its genome into a DNA sequence before you go for site-directed mutagenesis. Conventional technique would be to reverse-transcribe the viral RNA. But nowadays chemical DNA synthesis has become quite easy and you can synthesize entire viral genome in a &quot;test-tube&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having done this, we proceed to the trickiest part: &lt;em&gt;How to get this genome to form an active virus?&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some viruses, as mentioned before use RNA as their genome (poliovirus, retroviruses, common-cold virus etc) while some use DNA (chickenpox, smallpox, herpes etc). The mutagenesis, however, is performed on the DNA. For DNA viruses, introduction of the viral DNA into the host cell, using the conventional transfection methods, might work. For certain RNA viruses like poliovirus this DNA has to be transcribed to RNA. This can be done using a technique called &lt;a href=&quot;http://openwetware.org/wiki/In_vitro_transcription_with_T7_RNA_polymerase&quot; rel=&quot;nofollow&quot;&gt;in-vitro transcription (IVT)&lt;/a&gt; and the RNA product can be introduced inside the cell. IVT wont work well for long RNAs. In such cases you can use the cell itself to make the RNA instead of doing it in-vitro. Use a plasmid that can transcribe a DNA sequence inside a host cell- this is fairly common and almost all molecular bio labs will have such plasmids. Transfect this plasmid inside the host cell and it will make viral RNA, which in-turn will make active viruses.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Retroviruses work slightly different from other RNA viruses. They have an RNA genome that they convert to a DNA. This DNA gets integrated in the host genome and keeps producing viruses. To make a retroviral DNA integrate you need an enzyme encoded in the virus- &lt;strong&gt;integrase&lt;/strong&gt;. You can clone integrase separately and co-transfect it with the viral genomic DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A couple of final points to consider:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Some viruses such as retroviruses can mutate very fast naturally, because of their error prone replication. They may lose the incorporated mutation unless the mutation provides them a tactical advantage (this is true for all organisms).&lt;/li&gt;&#xA;&lt;li&gt;I share with many others this opinion that that bioterrorism should not be glamorized. So take care to present it well :)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-07-01T10:56:56.067" LastActivityDate="2014-07-01T10:56:56.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19410" PostTypeId="2" ParentId="19378" CreationDate="2014-07-01T10:00:11.217" Score="1" Body="&lt;p&gt;When you design the arrays, you need to have probes on the surface complementary to the sequence you want to detect. Depending on what you want to detect, you need to design these probes with known sequence on a known position.&#xA;If you want to detect single nucleotide polymorphisms (SNP), then you need a library of known SNPs on your ChIP, which are basically the position of the SNP and the surrounding sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;SNPs can be roughly grouped into two subgroups, common (I call them like this) and rare (frequency in the population lower than 0.1%). The problem with this ChIP based method is that it can only detect SNPs which are already known (or at least are located close to known SNPs with which they in linkage disequilibrium). So if you want to detect rare SNPs in your population sample, you need a big group of people from which you take the SNPs into you ChIP design. If you look at the numbers, one rare variant will only be present in about 12 of the 12.000 persons used in the design.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your study group is then different from the group of people, which where used to make the ChIP design. Here you take people with a certain background (high lipid levels for example) and then compare, if people which had coronary heart problems have SNPs in common which might be connected to this disease. This can help to identify a mutation in a protein which is the risk factor.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-01T10:00:11.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19411" PostTypeId="1" AcceptedAnswerId="19413" CreationDate="2014-07-01T11:30:51.060" Score="2" ViewCount="592" Body="&lt;p&gt;I got this doubt when I was studying about &lt;a href=&quot;http://en.wikipedia.org/wiki/Hematocrit&quot; rel=&quot;nofollow&quot;&gt;haematocrit&lt;/a&gt; value. According to my NCERT textbook males have greater number of RBCs than females. But who will have more RBCs when comparing a normal male and a female who lives at a higher altitude?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*edit&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the magnitude of altitude would be less than &lt;a href=&quot;http://en.wikipedia.org/wiki/Kangchenjunga&quot; rel=&quot;nofollow&quot;&gt;8,586 m (28,169 ft&lt;/a&gt;) as the woman I know is not exactly at the top summit of &lt;a href=&quot;http://en.wikipedia.org/wiki/Kangchenjunga&quot; rel=&quot;nofollow&quot;&gt;Kanchenjunga&lt;/a&gt; so what would be the answer then?&lt;/p&gt;&#xA;" OwnerUserId="8101" LastEditorUserId="1320" LastEditDate="2014-07-01T14:35:42.663" LastActivityDate="2014-07-01T14:35:42.663" Title="Do females living on mountains have more RBCs than a normal male" Tags="&lt;hematology&gt;&lt;red-blood-cell&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="1" ClosedDate="2014-07-01T19:07:25.200" ContentLicense="CC BY-SA 3.0" />
  <row Id="19412" PostTypeId="2" ParentId="19411" CreationDate="2014-07-01T12:23:57.223" Score="2" Body="&lt;p&gt;According to the &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/003646.htm&quot; rel=&quot;nofollow&quot;&gt;MedlinePlus site&lt;/a&gt; these are the normal ranges for haematocrit:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Male: 40.7 - 50.3%&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Female: 36.1 - 44.3%&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately it isn't clear if these ranges are for people living at low altitude, but since most people in the USA do, I think this is a safe inference. So clearly there is already some overlap.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper accessible &lt;a href=&quot;http://www.jpp.krakow.pl/journal/archive/11_07_s5/pdf/811_11_07_s5_article.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; reports various changes in haematocrit due to moving between different altitudes. Broadly speaking these changes are in the range of 10 - 15 percentage points (e.g. a change from 39% to 49%).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes, a female who has moved to a high altitude is likely to experience an erythrocytosis (or polycythaemia) which would mean that her haematocrit would exceed that of many males. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-07-01T12:23:57.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19413" PostTypeId="2" ParentId="19411" CreationDate="2014-07-01T12:51:33.860" Score="3" Body="&lt;p&gt;Currently impossible to give a definite answer... It depends what altitude you look at. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Going from @Alan_boyd's answer the normal range is 40-50% for males and 36-44% for females. If the altitude at which a person is acclimatized to correlates well with red blood cell count (RBCC), and this effect is not gender specific (i.e. both sexes are affected similarly), then an average woman from high altitude should have a higher RBCC than an average from low altitude. But whether or not the high altitude female RBCC exceeds that of the male depends on the altitude of the two measured.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This rough graph, &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Altitude_training&quot; rel=&quot;nofollow noreferrer&quot;&gt;assuming RBCC and altitude correlate&lt;/a&gt; and that &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/003646.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;male RBCC is higher than female RBCC&lt;/a&gt;&lt;/em&gt;, shows the problem. Female (red dashed line) A is from a higher altitude than the selected male (blue dashed line) and has lower RBCC. Female (red dashed line) B is from a higher altitude than the selected male (blue dashed line) and has higher RBCC. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oLScX.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Define altitudes and the question may be answerable.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-07-01T12:51:33.860" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19415" PostTypeId="2" ParentId="13568" CreationDate="2014-07-01T15:03:35.920" Score="9" Body="&lt;p&gt;I think that the advantages of using both hands with equal ease is quite evident whether it be sports, at your work or while you are doing your household chores. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Cjkoo.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An obvious advantage is using both hands to write or draw with both at the same time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I would be focusing on the disadvantages that may be faced.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;1) Ambidextrous people are more prone to suffer from &lt;a href=&quot;http://en.wikipedia.org/wiki/Synesthesia&quot; rel=&quot;noreferrer&quot;&gt;Synaesthesia&lt;/a&gt;&#xA;  (&lt;a href=&quot;http://synaesthesia.fws1.com/main.html&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;2) They are likely to possess (not necessarily) the LRRTM1 gene which&#xA;  is linked with Schizophrenia (&lt;a href=&quot;http://somelearning.com/ambidextrous&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;3) They score lesser in intelligence testing (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2831280/&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;4) Mixed handed children are more likely to suffer from ADHD&#xA;  (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20100759&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;5) Mixed handedness is associated with greater age-related decline&#xA;  (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3236539/&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;6) They are easier to anger and influence emotionally (&lt;a href=&quot;http://www.newscientist.com/article/dn20156-ambidextrous-people-easier-to-influence-emotionally.html#.U7LKN7G9tOQ&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are quite a few studies that have pointed out that it may not be all that good a condition but &lt;strong&gt;Leonardo da Vinci&lt;/strong&gt; who was probably the most diversely talented man who ever lived is said to have been ambidextrous. He apparently could draw with one hand and write with the other at the same time, so I would have to say that the positives of the condition are extremely good (&lt;a href=&quot;http://discovermagazine.com/2006/may/10-da-vinci&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;edit:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This probably qualifies as a second question &lt;strong&gt;:-D&lt;/strong&gt; but I just saw a thought by biogirl in the comments section on &lt;strong&gt;&quot;whether our ancestors used both the hands and using just one hand is recently evolved&quot;&lt;/strong&gt; and she has a point there. From a study publlished in 1977 I quote. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The predominance of the right hand over the left was also reported&#xA;  among Egyptian art forms 3,500 to 4,500 years old, where the ratio of&#xA;  left- to right-handers was 9:111 and 5:100, respectively. However,&#xA;  going further back using the &quot;Draw-a-Man Test,&quot; found that ancient&#xA;  paleolithic man, from 1,750,000 to 8,000 years B.C., was probably&#xA;  either more ambidextrous or that there was a greater proportion of&#xA;  left-handers than there are now. (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.1977.tb41927.x/abstract&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also from a study titled &lt;strong&gt;&quot;Evolutionary Back Grounds of Human Left Handedness&quot;&lt;/strong&gt;, the authors concluded that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For most manual tasks, especially those tasks involved in competitive&#xA;  activities, increasing performance by the specialization of one hand&#xA;  is certainly adaptive. Aggressive interactions are responsible for&#xA;  fundamental selection pressures acting during primate and human&#xA;  evolution. The higher prevalence of right-handedness might well be due&#xA;  to a previously existing cerebral bias. But the specialization of one&#xA;  forelimb leading to right or left-handedness is better viewed as the&#xA;  result of natural selection. (&lt;a href=&quot;http://www.medwelljournals.com/fulltext/?doi=rjbsci.2010.36.41&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-03T08:33:50.000" LastActivityDate="2014-07-03T08:33:50.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19416" PostTypeId="1" CreationDate="2014-07-01T17:21:09.133" Score="1" ViewCount="141" Body="&lt;p&gt;FRET only works for interactions between 1nm to 20nm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can you be sure that the interaction that you want to study isn't less than 1 nm/greater than 20nm apart?&lt;/p&gt;&#xA;" OwnerUserId="8189" LastActivityDate="2014-07-03T19:50:56.003" Title="FRET only works for interactions between 1nm to 20nm." Tags="&lt;molecular-biology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19417" PostTypeId="1" AcceptedAnswerId="19434" CreationDate="2014-07-01T18:08:07.100" Score="1" ViewCount="777" Body="&lt;p&gt;I heard that some point mutations in proteins are OK, like from alanine to glycine (I'm not sure, it's just an example), some will change the protein significantly. I want to understand deeper but don't know the right keyword. I have tried some but none of them works. Can you give me a good keyword to start searching? Thank you.&lt;/p&gt;&#xA;" OwnerUserId="6786" LastEditorUserId="1320" LastEditDate="2014-07-02T12:00:12.780" LastActivityDate="2014-07-02T12:00:12.780" Title="Which point mutations in proteins are OK, and which cause significant change?" Tags="&lt;proteins&gt;&lt;mutations&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19418" PostTypeId="2" ParentId="19257" CreationDate="2014-07-01T18:41:39.813" Score="4" Body="&lt;p&gt;Looks like a mountain beaver (&lt;em&gt;Aplodontia rufa&lt;/em&gt;) to me. Location, appearance, and minimal tail all match.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A bit more detail:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where I'm from on Washington's Olympic Peninsula, they're not uncommon, but Butte County is near the southern end of their distribution (&lt;a href=&quot;http://eol.org/pages/34465/maps&quot; rel=&quot;nofollow&quot;&gt;eol map page&lt;/a&gt;) and they may be less common there, and limited to cooler higher elevations (&lt;a href=&quot;https://oak.ucc.nau.edu/pb1/vitae/Beier.1989.Aplodontia.pdf&quot; rel=&quot;nofollow&quot;&gt;Beier 1989&lt;/a&gt;), and to wet habitats (their inability to concentrate urine (!) means they need to drink enormous quantities of water).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This white paper from USDA (&lt;a href=&quot;http://digitalcommons.unl.edu/icwdm_usdanwrc/675&quot; rel=&quot;nofollow&quot;&gt;Arjo 2007&lt;/a&gt;) is a great source, and more comprehensive than the  the &lt;a href=&quot;http://en.wikipedia.org/wiki/Mountain_beaver&quot; rel=&quot;nofollow&quot;&gt;wikipedia page&lt;/a&gt;, which is also good.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Arjo, Wendy M. (2007). &quot;Mountain Beaver: A Primitive Fossorial Rodent&quot;. USDA National Wildlife Research Center - Staff Publications. Paper 675.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beir, Paul (1989). Journal of Wildlife Management 53(3) 649-654&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-07-04T16:31:47.930" LastActivityDate="2014-07-04T16:31:47.930" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19419" PostTypeId="2" ParentId="19417" CreationDate="2014-07-01T18:59:22.870" Score="2" Body="&lt;p&gt;I think you are referring to the concept of conserved substitution, which tends not to change the property/function (&lt;a href=&quot;http://en.wikipedia.org/wiki/Sequence_alignment&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Sequence_alignment&lt;/a&gt;) of a protein although thats not necessarily true if the mutated AA (point mutation) changes a functional residue in an enzymatic domain such as GAP or kinase domains or even certain residues that are important for PP interactions such as tyrosine Y, which can become phosphorylated and thats important at times for its interaction with other proteins or the activation/inactivation status of a protein such as receptor tyrosine kinases (&lt;a href=&quot;http://en.wikipedia.org/wiki/Receptor_tyrosine_kinase&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Receptor_tyrosine_kinase&lt;/a&gt;). But in most cases it depends where the AA is and the role of the AA. For example two AA can have the same charge/polarity but if their sizes are considerably different, then that could interfere with the way protein folds (conformational changes) and end up affecting its function. So AA substitution and its effects is not necessarily straight forward and its very much dependent on other factors!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-07-01T22:40:04.800" LastActivityDate="2014-07-01T22:40:04.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19421" PostTypeId="2" ParentId="19391" CreationDate="2014-07-01T19:06:16.647" Score="2" Body="&lt;p&gt;First of all, the statement that &quot;pseudo coelomates have very minute width of their body cavity and rest of the body cavity is filled with mesoglea&quot; is not correct at least for (large) nematodes and priapulids: they have quiet voluminous body cavity and no mesoglea. In small nematodes (to which &lt;em&gt;Ascaris&lt;/em&gt; doesn't belong) the body cavity is indeed vestigial, but the &quot;space&quot; between the organs is filled with extracellular matrix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another point is that the eggs in nematodes develop not in the body cavity directly, but in the ovaries and uteri (as correctly shown in the picture you provided), which indeed occupy very large part of the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now to the question about the counts: individual capacity of a single female 29 cm long was &lt;a href=&quot;http://books.google.com/books?id=VOvUAAAAMAAJ&amp;amp;q=egg-producing%20capacity&quot; rel=&quot;nofollow&quot;&gt;once&lt;/a&gt; (&lt;a href=&quot;http://www.jstor.org/discover/10.2307/3271720&quot; rel=&quot;nofollow&quot;&gt;see also&lt;/a&gt;) estimated to be ca. 27 mln eggs contained in its ovaries and uteri, which is impressive, but reasonable given the extremely small size of the eggs and extremely large size of the worm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we very coarsely approximate the volume occupied by a single egg with a cube 70x70x70 µm&lt;sup&gt;3&lt;/sup&gt;, we get ca. 9 ml for 27 mln of them, and not much imagination is required to see, how a female ascarid can find room for this volume of relatively loosely packed eggs in its genital system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt;&#xA;To check my statement about &quot;quiet voluminous body cavity and no mesoglea&quot; one can open any modern textbook on invertebrates (or attend a practical course of invertebrate zoology). This is how the nemotode body cavity is described in the monograph &quot;Nematoda&quot; by Vladimir Malakhov (the original I cite is in Russian, but there is also a &lt;a href=&quot;http://books.google.de/books/about/Nematodes.html?id=tHjwAAAAMAAJ&quot; rel=&quot;nofollow&quot;&gt;translation&lt;/a&gt; of the book):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;The presence of a spacious body cavity is considered to be the most characteristic property of the whole class of nematodes&quot;.&lt;/li&gt;&#xA;&lt;li&gt;&quot;Schizocoel [= primary body cavity] doesn't have its own walls made of cellular material and is represented by spaces between organs filled with liquid&quot;.&lt;/li&gt;&#xA;&lt;li&gt;&quot;Nevertheless, it should be stressed, that the opinion of the schizocoel being a voluminous body cavity, appeared as a result of investigations on large parasitic nematodes.&quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-08-02T12:48:11.117" LastActivityDate="2014-08-02T12:48:11.117" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19422" PostTypeId="2" ParentId="14579" CreationDate="2014-07-01T20:14:30.840" Score="1" Body="&lt;p&gt;There have been quite a few studies on stimulating the brain with electrical pulses and it has been found to be successful too. Three papers of particular interest I found were:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) In a study titled &lt;strong&gt;&quot;Explaining How Brain Stimulation Can Evoke Memories&quot;&lt;/strong&gt;, it was found that electrical stimulation in the &lt;strong&gt;temporal neocortex&lt;/strong&gt; can cause neurosurgical patients to spontaneously experience memory retrieval. The subject's brain in the study when stimulated enabled him to recollect memories from the time that he was in high school. They concluded that there are patches of neurons encoding memories for differnt periods (in this case the high school). (&lt;a href=&quot;http://jacobslab.biomed.drexel.edu/pubs/JacoEtal12.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) In the second study titled &lt;strong&gt;&quot;Memory Enhancement and Deep-Brain Stimulation of the Entorhinal Area&quot;&lt;/strong&gt;, it was observed that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;entorhinal stimulation&lt;/strong&gt; applied while subjects learned the locations of&#xA;  landmarks enhanced their subsequent memory of these locations: and the&#xA;  subjects reached these landmarks more quickly and by shorter routes,&#xA;  as compared with locations learned without stimulation. (&lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMoa1107212?query=featured_home&amp;amp;&amp;amp;#t=abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;3) In a third study titled &lt;strong&gt;&quot;Stimulation of Entorhinal Cortex Promotes Adult Neurogenesis and Facilitates Spatial Memory&quot;&lt;/strong&gt;, it was found that stimulating a specific region of the brain leads to the production of new brain cells that enhance memory. (&lt;a href=&quot;http://www.jneurosci.org/content/31/38/13469&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In two on these studies, memory is enhanced by stimulation to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Entorhinal_cortex&quot; rel=&quot;nofollow noreferrer&quot;&gt;entorhinal cortex&lt;/a&gt; and in the first study the &lt;a href=&quot;http://en.wikipedia.org/wiki/Neocortex&quot; rel=&quot;nofollow noreferrer&quot;&gt;neocortex&lt;/a&gt; was stimulated. So, in a broad sense the  cerebral cortex is generally used for these studies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a continuous field of research as a treatment to diseases like Alzheimers (&lt;a href=&quot;http://www.hopkinsmedicine.org/news/media/releases/deep_brain_stimulation_may_hold_promise_for_mild_alzheimers_disease&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VF0VM.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;strong&gt;Gray-Brodman-Entorhinal Cortex&lt;/strong&gt; (Wikipedia)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bMMSH.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Neocortex location&lt;/strong&gt; (&lt;a href=&quot;http://hs.riverdale.k12.or.us/~hfinnert/exhib_05/alexanderm05/meub_paper_physical.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-03T08:32:45.233" LastActivityDate="2014-07-03T08:32:45.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19424" PostTypeId="2" ParentId="19417" CreationDate="2014-07-01T23:14:16.297" Score="4" Body="&lt;p&gt;There are twenty standard amino acids, and some of them are structurally/functionally similar to each other, such as aspartate and glutamate, or asparagine and glutamine, or glycine and alanine. In general, mutations that cause these amino acid switches don't change the function of the protein, but that's just a general rule - it also depends on where these amino acids are in the protein structure. These are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Point_mutation#Functional_categorization&quot; rel=&quot;nofollow&quot;&gt;conservative mutations&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6027" LastActivityDate="2014-07-01T23:14:16.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19425" PostTypeId="2" ParentId="19407" CreationDate="2014-07-02T01:40:35.273" Score="1" Body="&lt;p&gt;I've written a little script to remove identical sequences from fasta to get what I need. To print the list of removed sequences, uncomment line 22&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;#! /usr/bin/python3&#xA;# Removes identical sequences from fasta file&#xA;&#xA;import sys&#xA;from Bio import SeqIO&#xA;sequences={}&#xA;#This is where sequences will be stored&#xA;#likely calling str(seq.seq) on every test will be slower&#xA;with open(sys.argv[1], 'r') as fasta:&#xA;    parser=SeqIO.parse(fasta,'fasta')&#xA;    for seq in parser:&#xA;        sequences[seq.id]=str(seq.seq)&#xA;l=list(sequences.keys())&#xA;for j in range(0,len(l)-1,1):&#xA;    try:&#xA;        s=sequences[l[j]]&#xA;        for k in range(j+1,len(l)-1,1):&#xA;            if sequences[l[k]]==sequences[l[j]]:&#xA;                del sequences[l[k]]&#xA;    except KeyError:&#xA;        pass&#xA;        #print(l[j],file=sys.stderr)&#xA;for j in sequences.keys():&#xA;    print('&amp;gt;',j,'\n',sequences[j])&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="8185" LastActivityDate="2014-07-02T01:40:35.273" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19427" PostTypeId="1" CreationDate="2014-07-02T03:57:53.933" Score="4" ViewCount="4104" Body="&lt;p&gt;Do insects see near infrared light?  If yes, are they attracted to it at night, as they are to visible light sources?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am building something similar to a home-made trailcam &lt;a href=&quot;http://www.raspberrypi.org/pi-noir-infrared-camera-now-available/&quot; rel=&quot;nofollow&quot;&gt;with a Raspberry Pi camera&lt;/a&gt;.  Currently I use an incandescent light source.  Obviously, it attracts lots of bugs.  I was wondering if the same is going to happen when I switch to an infrared light source.  This would be 850 nm or 940 nm, as these types of LEDs are commonly available.&lt;/p&gt;&#xA;" OwnerUserId="8194" LastActivityDate="2017-05-25T15:36:17.993" Title="Are insects attracted to near infrared light?" Tags="&lt;entomology&gt;&lt;vision&gt;&lt;behaviour&gt;&lt;light&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19428" PostTypeId="2" ParentId="10690" CreationDate="2014-07-02T05:58:52.900" Score="3" Body="&lt;p&gt;It is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Torrent_salamander&quot; rel=&quot;nofollow&quot;&gt;torrent salamander&lt;/a&gt;. Most likely this is the southern torrent salamander (&lt;em&gt;Rhyacotriton variegatus&lt;/em&gt;)&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-07-02T05:58:52.900" CommentCount="1" CommunityOwnedDate="2014-07-02T05:58:52.900" ContentLicense="CC BY-SA 3.0" />
  <row Id="19429" PostTypeId="1" AcceptedAnswerId="19432" CreationDate="2014-07-02T06:48:01.197" Score="6" ViewCount="334" Body="&lt;p&gt;In most of the signaling pathways the activated receptor when activates Protein Kinase through the action of secondary messenger, then these protein kinases almost always phosphorylate on the specific Serine, Threonine, or Tyrosine amino acid residues? what is the reason of phosphorylating specifically these amino acid residues. why not other than these amino acid residues are choosen for phosphorylation ? &lt;/p&gt;&#xA;" OwnerUserId="5729" LastActivityDate="2015-01-07T14:31:56.553" Title="Specificity of Protein Kinases in Signaling Pathways..?" Tags="&lt;biochemistry&gt;&lt;amino-acids&gt;&lt;cell-signaling&gt;&lt;signalling&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19430" PostTypeId="2" ParentId="15514" CreationDate="2014-07-02T07:12:20.270" Score="14" Body="&lt;p&gt;Remi.b's answer is an excellent one, and this should be taken as a supplement to it:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;It's possible your simulation is correct&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Lotka-Volterra equations are what is known as a deterministic model, and it describes the behavior of predator-prey systems (in a somewhat simplified fashion) in &lt;em&gt;large populations&lt;/em&gt;. Small populations are subject to what is known as stochastic extinction - as the predator and prey curves approach their minimums, they may predict populations less than 1, which in reality are either 0 &lt;em&gt;or&lt;/em&gt; 1, and when they're 0...well, someone's gone extinct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Odds are your simulation is on a small population, and if its a simulation, rather than calculus, you should be seeing those stochastic effects (to be sure - if your simulation keeps track of integer animals, rather than continuous animals, and random chance is involved, this is going to be something you have to worry about).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a similar model I've been working with, that's a pretty simple adaptation of a L-V model that should, deterministically, result in a stable system like in Remi.b's picture, the predators go extinct 20% of the time, and the prey 80% of the time.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2014-07-02T07:12:20.270" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19431" PostTypeId="2" ParentId="19429" CreationDate="2014-07-02T08:50:00.763" Score="3" Body="&lt;p&gt;Those residues are phosphorylated because they have a free hydroxyl group available to be bonded to a phosphate.  Many other resides can be modified, like acetylation of lysines, but only those residues are chemically compatible with &lt;em&gt;reversible&lt;/em&gt; phosphorylation.&lt;/p&gt;&#xA;" OwnerUserId="6501" LastActivityDate="2014-07-02T08:50:00.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19432" PostTypeId="2" ParentId="19429" CreationDate="2014-07-02T08:55:41.497" Score="6" Body="&lt;p&gt;Phosphorylation requires a nucleophile and hydroxyl oxygen acts like one. Serine, theronine and tyrosine get phosphorylated on the free &lt;strong&gt;OH&lt;/strong&gt; group in their side chains. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nitrogen, in some cases also can act as a nucleophile. In case of histidine, the imidazole nitrogen is phosphorylated during bacterial chemotaxis signaling. As far as I know eukaryotes do not have an enzyme for histidine phosphorylation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carboxylic groups in glutamate and aspartate can technically be phosphorylated as it happens in case of phosphoglycerate. Glutamate is phosphorylatyed by the enzyme glutamine synthase during the synthesis of glutamine. Same happens in the case of aspartate during aspargine synthesis. However, this is a reactive intermediate and the phosphorylation is not stable like that of hydroxyls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other amino acids do not have such nucleophilic groups to render an attack on the phosphorous atom in phosphate- so they are not phosphorylated. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-01-07T14:31:56.553" LastActivityDate="2015-01-07T14:31:56.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19433" PostTypeId="2" ParentId="19429" CreationDate="2014-07-02T09:01:54.690" Score="5" Body="&lt;p&gt;This is mostly because of the nature of the amino acids. You need to have a Hydroxy-group in the sidechain of the amino acid which is the point where the phosphogroup is attached. Since this process needs to be reversible, this can only happen here. See the image below (from &lt;a href=&quot;http://www.piercenet.com/method/peptide-design&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;) about the chemical structure:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RgzCA.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In eukaryotes not only these three are phosphorylated, histidine phosphorylation also occurs (and happens more frequently than tyrosine phosphorylation, see this article:&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21623415&quot; rel=&quot;nofollow noreferrer&quot;&gt;Phosphorylation of basic amino acid residues in proteins: important but easily missed.&lt;/a&gt;&quot;).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-02T09:01:54.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19434" PostTypeId="2" ParentId="19417" CreationDate="2014-07-02T10:14:18.817" Score="3" Body="&lt;p&gt;As others have said, although certain amino acid substitutions are considered to be conservative, the effect of a particular substitution will very much depend upon the context. Here are some examples:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bioc.uzh.ch/plueckthun/pdf/APpub0038.pdf&quot; rel=&quot;nofollow&quot;&gt;gly&gt;ala can change stability of glyceraldehyde-3-phosphate dehydrogenase&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://peds.oxfordjournals.org/content/9/6/499.full.pdf&quot; rel=&quot;nofollow&quot;&gt;gly&gt;ala mutations in a fungal glucoamylase increase thermostability&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8094613&quot; rel=&quot;nofollow&quot;&gt;asp&gt;glu in a lysosomal &amp;alpha;-glucosidase is responsible for a glycogen storage disease&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biochemj.org/bj/301/bj3010275.htm&quot; rel=&quot;nofollow&quot;&gt;asn&gt;gln will abolish glycosylation at NXS/T sites which can have effects on stability and secretion&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.chemistry.montana.edu/~martint/BCHM444/AlkPhosS102Tstruct.ProtSci06.pdf&quot; rel=&quot;nofollow&quot;&gt;ser&gt;thr at the active site has profound effects upon catalytic activity of an alkaline phosphatase&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-07-02T10:14:18.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19435" PostTypeId="1" CreationDate="2014-07-02T11:27:43.470" Score="2" ViewCount="62" Body="&lt;p&gt;Is there some way to experimentally determine the density distribution of Kinesin and Dynein in a Neuron?&#xA;Fluorescence labeling would be impossible(?) as GFP markers would probably alter the motor dynamics.&#xA;Any ideas? Or do any studies exist which looked into this topic?&lt;/p&gt;&#xA;" OwnerUserId="8196" LastEditorUserId="3340" LastEditDate="2014-12-03T11:56:29.323" LastActivityDate="2014-12-03T11:56:51.653" Title="Kinesin-5 / cytoplasmic dynein spatial density distribution in neurons" Tags="&lt;molecular-biology&gt;&lt;neuroscience&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19436" PostTypeId="1" CreationDate="2014-07-02T12:23:36.957" Score="1" ViewCount="156" Body="&lt;p&gt;I am working on a project and I'm trying to find data on the position of genes and heterochromatin binding sites such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Heterochromatin_protein_1&quot; rel=&quot;nofollow&quot;&gt;HP1&lt;/a&gt; in &lt;em&gt;Drosophila melanogaster.&lt;/em&gt; Is this information available for the &lt;a href=&quot;http://dgrp.gnets.ncsu.edu/&quot; rel=&quot;nofollow&quot;&gt;DGRP&lt;/a&gt; lines? Would I be able to measure the distance between a gene and its nearest binding site from such data?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-07-04T18:49:55.880" Title="Heterochromatin binding sites position information" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;molecular-genetics&gt;&lt;drosophila&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19437" PostTypeId="1" CreationDate="2014-07-02T12:31:52.520" Score="3" ViewCount="57" Body="&lt;p&gt;Currently playing with some ideas for a project and needed some guidance. I am wondering, both in &lt;em&gt;Drosophila melanogaster&lt;/em&gt; and in general, is the amount of heterochromatin a cell/nucleus can produce limited/consistent or variable? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does one cell in a &lt;em&gt;D. melanogaster&lt;/em&gt; produce a similar amount of heterochromatin as another cell in the same fly or another fly (assuming same conditions - environment etc.) or is the heterochromatin production quite variable? How is heterochromatin production regulated?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-11-05T06:10:50.520" Title="Heterochromatin production limitations" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;molecular-evolution&gt;&lt;gene-regulation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19438" PostTypeId="1" AcceptedAnswerId="19439" CreationDate="2014-07-02T13:22:29.400" Score="16" ViewCount="119246" Body="&lt;p&gt;If I squash an insect and it produces red &quot;juice&quot;, does it always mean it is a blood-sucking type of insect? Or do some insects have red &quot;juice&quot; themselves, so the color is red on its own and not caused by sucking higher animal's blood?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I squashed a small fly-like insect recently, it produced a red stain, so I am wondering if the stain come from the insect itself or if it has to be some other animal's blood.&lt;/p&gt;&#xA;" OwnerUserId="8198" LastEditorUserId="3340" LastEditDate="2014-07-03T07:03:48.360" LastActivityDate="2016-12-03T06:11:31.040" Title="If I squash an insect and it produces red &quot;juice&quot;, does it always mean it is a blood-sucking type?" Tags="&lt;entomology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19439" PostTypeId="2" ParentId="19438" CreationDate="2014-07-02T13:33:53.473" Score="16" Body="&lt;p&gt;No - &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood#Invertebrates&quot; rel=&quot;noreferrer&quot;&gt;invertebrates don't have &amp;quot;blood&amp;quot; though they do have hemolymph&lt;/a&gt;. Hemolymph flows around the body cavity, rather than through vessels such as veins and capillaries, and comes in to direct contact with tissues and &lt;em&gt;generally&lt;/em&gt; it is not red.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Hemolymph fills all of the interior (the hemocoel) of the animal's&#xA;body and surrounds all cells. It contains hemocyanin, a copper-based&#xA;protein that turns blue in color when oxygenated, instead of the&#xA;iron-based hemoglobin in red blood cells found in vertebrates, thus&#xA;giving hemolymph a blue-green color rather than the red color of&#xA;vertebrate blood. When not oxygenated, hemolymph quickly loses its&#xA;color and appears grey. The hemolymph of lower arthropods, including&#xA;most insects, is not used for oxygen transport because these animals&#xA;respirate directly from their body surfaces (internal and external) to&#xA;air, but it does contain nutrients such as proteins and sugars.&lt;/p&gt;&#xA;&lt;p&gt;~ &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemolymph&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Hemolymph&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The red you see from squashing, depending on the insect, could come from blood of other animals or (eye) pigments produced by the insect. For example, in my lab we have some &lt;em&gt;Drosophila melanogaster&lt;/em&gt; with red eyes and some with white eyes (they carry a genetic mutation which represses the production of pigments in the eye) - if I squash the red eyed fly red &amp;quot;juice&amp;quot; is left on the desk, this doesn't happen with the white eyed flies.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-07-03T15:41:56.553" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19440" PostTypeId="2" ParentId="19438" CreationDate="2014-07-02T13:35:08.507" Score="6" Body="&lt;p&gt;Insects do not have blood as we know it from the higher animals. They have a kind of, which is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemolymph&quot;&gt;hemolymph&lt;/a&gt; and is, compared to human a mixture of blood and the lymphatic fluid. The most important difference is that hemolymph doesn't transport oxygen and thus has no red blood cells. The &quot;breathing&quot; of the insects takes mostly place through passive oxygen diffusion through the &quot;skin&quot; and small openings in it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hemolymph is mostly made of water and contains things like amino acids, carbohydrates, lipids and so on and is very important for the distribution of nutrients in the insect. It also contains &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemocytes&quot;&gt;hemocytes&lt;/a&gt; which are part of the insects immune system and play a role similiar to human phagocytes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The color of the hemolymph comes from pigments and varies quite a lot between insects from green to yellow to red.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-02T13:35:08.507" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19441" PostTypeId="1" CreationDate="2014-07-02T15:41:51.837" Score="6" ViewCount="18812" Body="&lt;p&gt;As is advised with most fish you should avoid sudden changes in water temperature (for example by introducing new water that hasn't been left to come to room temperature). I have, however, never understood why that is the case, in particular given that most fish are cold blooded so there is no issue with needing to &quot;ramp up&quot; the metabolism when in cold water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Say a particular species of fish can survive in water between 20°C and 30°C what causes a fish that was previously in 30°C water to die when suddenly plunged into 20°C water? I understand this effect is called &quot;shock&quot; but I'm looking for the biological reason for it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be clear I'm not looking for &quot;chemical x is released and that leads to the fish dying,  I'm looking for why these chemicals are released at all. So to give an example if my question had of been &quot;why does adrenaline shock kill&quot; I'd be looking for &quot;adrenaline release is usually a good thing, it's released in response to a fright and prepares the body for a fight or flight response. However this heightend preparedness can cause additional strain on the body which can cause death in some cases&quot;&lt;/p&gt;&#xA;" OwnerUserId="6151" LastEditorUserId="6151" LastEditDate="2017-11-06T10:57:52.380" LastActivityDate="2017-12-27T03:48:30.943" Title="Why does temperature shock kill fish?" Tags="&lt;zoology&gt;&lt;ichthyology&gt;&lt;temperature&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19442" PostTypeId="1" AcceptedAnswerId="19447" CreationDate="2014-07-02T15:52:24.293" Score="5" ViewCount="342" Body="&lt;p&gt;I am impressed by the illustrations for the Protein Data Bank ‘Molecule of the month’, e.g. the gorgeous image of &lt;a href=&quot;http://www.rcsb.org/pdb/101/motm.do?momID=168&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA Helicase&lt;/a&gt; below. Does anyone know how they were made or how one might create something similar?&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/GDfyn.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/GDfyn.jpg&quot; alt=&quot;DNA Helicase&quot; /&gt;&lt;/a&gt;&lt;br /&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://www.rcsb.org/pdb/education_discussion/molecule_of_the_month/images/168-DNAHelicase_4esv.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;rcsb.org&lt;/a&gt;)&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="8199" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-02-25T08:09:14.377" Title="How can one create images like those in the PDB ‘Molecule of the month’?" Tags="&lt;molecular-biology&gt;&lt;proteins&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="19444" PostTypeId="2" ParentId="19441" CreationDate="2014-07-02T16:24:13.620" Score="8" Body="&lt;p&gt;This due to a phenomenon called &quot;cold shock&quot;. This induces a number of physiological changes in the fishs metabolism and also in its behaviour and can lead to death. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first paper cites some reasons in table 1:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Brain and central nervous system response: Changes in neuronal&#xA;activity&lt;/li&gt;&#xA;&lt;li&gt;Catecholamine and corticosteroid response: Release of hormones due to&#xA;the shock.&lt;/li&gt;&#xA;&lt;li&gt;Haematological and metabolic response: Changes in red and white blood&#xA;cells and lactic acid in the blood.&lt;/li&gt;&#xA;&lt;li&gt;Protein expression and molecular responses: Changes in the expression&#xA;of proteins of the heat shock family.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;These changes (especially in brain and nerves and also the hormones) can deregulate the fishs metabolism so much that it can die. Shock is a critical condition. Obviously a lot of research is going on, but I recommend reading the two articles below for further details.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.fecpl.ca/wp-content/uploads/2008/09/JFB-Donaldson-etal-2008.pdf&quot;&gt;Cold shock and fish&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.scielo.br/scielo.php?script=sci_arttext&amp;amp;pid=S0044-59672008000400002&quot;&gt;Physiological stress responses in the warm-water fish matrinxã&#xA;(Brycon amazonicus ) subjected to a sudden cold shock&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-02T16:24:13.620" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19446" PostTypeId="1" CreationDate="2014-07-02T20:31:07.103" Score="3" ViewCount="272" Body="&lt;p&gt;Insects do have a nervous system, even if it isn't nearly as complex as that of other animals. Can insects or other arthropods sense pain? Does their aversion to harmful stimuli suggest that they can 'feel' pain in the sense that other animals seem to? &lt;/p&gt;&#xA;" OwnerUserId="6027" LastActivityDate="2014-07-03T04:41:07.177" Title="Can insects feel pain?" Tags="&lt;entomology&gt;&lt;sensation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19447" PostTypeId="2" ParentId="19442" CreationDate="2014-07-02T20:53:29.227" Score="9" Body="&lt;p&gt;Those (really cool) pictures are created by David Goodsell using custom-written software.&lt;/p&gt;&#xA;&lt;p&gt;From an &lt;a href=&quot;http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/about.html&quot; rel=&quot;noreferrer&quot;&gt;interview to the artist&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;PDB&lt;/em&gt;: How do you create the illustrations?&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Goodsell&lt;/em&gt;: Most of the pictures are created with a computer program that I developed back when I was doing postdoctoral work with Dr. Art Olson here at The Scripps Research Institute. I've been using this style of illustration--with flat colors and black outlines--for about 10 years now. I like the way that this style simplifies the molecule, giving a feeling for the overall shape and form of the molecule, but at the same time you can still see all the individual atoms. On the last page of each Molecule of the Month--&amp;quot;Exploring the Structure&amp;quot;--I always use RasMol, to give visitors an idea of the kinds of pictures that they can create themselves with off-the-shelf software.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;There are good tools around if you want to replicate that look. Although it may take a bit of tweaking (and possibly programming) I would surely give &lt;a href=&quot;http://www.pymol.org/&quot; rel=&quot;noreferrer&quot;&gt;PyMOL&lt;/a&gt; and &lt;a href=&quot;http://www.bioblender.eu/&quot; rel=&quot;noreferrer&quot;&gt;Bioblender&lt;/a&gt; a try.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-07-02T20:53:29.227" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19448" PostTypeId="1" CreationDate="2014-07-02T21:30:39.197" Score="11" ViewCount="18096" Body="&lt;p&gt;What are the evolutionary explanations for why women are physically weaker than men (on average), and is this difference adaptive? &lt;a href=&quot;http://jap.physiology.org/content/83/5/1581&quot; rel=&quot;noreferrer&quot;&gt;See figure one here.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suppose that something puts pressure on men to be physically stronger than women, but I don't see what it can be. Why the discrepancy between the sexes? &lt;/p&gt;&#xA;" OwnerUserId="4419" LastEditorUserId="3553" LastEditDate="2016-04-26T09:30:51.823" LastActivityDate="2017-07-06T22:21:39.330" Title="Why are men stronger than women?" Tags="&lt;evolution&gt;&lt;human-genetics&gt;&lt;sexual-selection&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19449" PostTypeId="2" ParentId="19448" CreationDate="2014-07-03T02:21:47.920" Score="9" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;What are the evolutionary explanations for why women are weaker than men (on average), and is this difference adaptive?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;All of the theories surrounding this fact are speculative; it would be difficult to prove &quot;why&quot; men are, on average, stronger than women.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One contributing theory is &lt;a href=&quot;http://adarwinstudygroup.org/sexuality/female-choice/&quot; rel=&quot;noreferrer&quot;&gt;Female-Choice&lt;/a&gt; - basically that women had (or has) the ability to be more selective when it comes to choosing a mate. Over time men will reflect the preferences of women (taller than them, stronger than them, facial hair qualities, etc.). This is superficially supported by casual studies like &lt;a href=&quot;http://blog.okcupid.com/index.php/your-looks-and-online-dating/&quot; rel=&quot;noreferrer&quot;&gt;this study from OkCupid&lt;/a&gt; where the &quot;attractiveness&quot; curve for men is down-shifted, meaning women think the average man looks below average in attractiveness and implying those who are viewed as average ( &lt;em&gt;actually&lt;/em&gt; the top 20% of men or so) would have better reproductive success. Men, in the same casual study, had a nearly perfect bell-curve associated the attractiveness of women, implying that men are excellent at deducing whether a women is below average in attractiveness, average, or above average in attractiveness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another contributing theory is &lt;a href=&quot;http://adarwinstudygroup.org/sexuality/male-competition/&quot; rel=&quot;noreferrer&quot;&gt;Male-Male Competition&lt;/a&gt;. Basically men, at some point (and still might) compete with other men to win over women. The bigger, stronger man would presumably win in a fight and eliminate his competition - directly preventing the production of offspring by the weaker male. The male-male competition also holds true in a more speculative theory in that the winners of wars literally &lt;em&gt;raped&lt;/em&gt; their way to reproductive success.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is worth noting that men, on average, are only about &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8477683&quot; rel=&quot;noreferrer&quot;&gt;30-40% stronger than women&lt;/a&gt; due to the larger muscle fibers in men (as cross-sectional area determines muscle strength, not volume). With training the difference (kg for kg) &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_Olympic_records_in_weightlifting&quot; rel=&quot;noreferrer&quot;&gt;is reduced to 15-20%&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultimately &lt;em&gt;why&lt;/em&gt; women are weaker than men (or men are stronger than women - whichever way you prefer to put it) doesn't have a solid answer beyond &quot;because the stronger, taller men have reproduced&quot;.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="3553" LastEditDate="2016-04-26T09:25:38.803" LastActivityDate="2016-04-26T09:25:38.803" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="19450" PostTypeId="2" ParentId="19437" CreationDate="2014-07-03T04:26:48.627" Score="2" Body="&lt;p&gt;Heterochromatin profile is of course different in different cells but I am not sure if absolute heterochromatin content will vary greatly. &lt;a href=&quot;http://massgenomics.org/2012/09/encode-regulatory-variation-in-the-human-genome.html&quot; rel=&quot;nofollow&quot;&gt;This DNAse hypersensitivity region&lt;/a&gt; data is for human cells but same principles apply to all organisms. If I have to take a guess then I would say that quiescent cells are likely to have more heterochromatin. Heterochromatin production is regulated by different epigenetic mechanisms but I cannot comment (I feel it is unlikely) if there is a mechanism to control absolute heterochromatin content. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-07-03T04:26:48.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19451" PostTypeId="2" ParentId="19436" CreationDate="2014-07-03T04:33:47.330" Score="1" Body="&lt;p&gt;Have a look at these ChIP-seq data for HP1 in Drosophila: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/sra/SRX111799%5Baccn%5D&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/sra/SRX032114%5Baccn%5D&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/sra/SRX032113%5Baccn%5D&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;. From ChIP-seq data you can find the distance between the TFBS peaks and the TSS of the gene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also look for nucleosome positioning and DNAse hypersensitvity regions; for the former, I am sure that data is available for Drosophila. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-07-03T04:33:47.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19452" PostTypeId="2" ParentId="19446" CreationDate="2014-07-03T04:41:07.177" Score="3" Body="&lt;p&gt;This question has been asked in different forums and many of the answers say that there is no nociception in insects. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK5247/&quot; rel=&quot;nofollow&quot;&gt;This book&lt;/a&gt;, however claims that Drosophila do have heat induced nociception and is mediated by TRPA ion channels. Also, there is a gene called &lt;em&gt;painless&lt;/em&gt; whose mutation causes loss of nociception. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-07-03T04:41:07.177" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19453" PostTypeId="2" ParentId="17657" CreationDate="2014-07-03T07:26:35.527" Score="5" Body="&lt;p&gt;Alright, so this answer is partially based off the ideas presented by Bobson above. What i did was take his Excel spreadsheet idea and put that into the upper section. Then, I used the amounts used on the website he linked to check the proper amounts needed in the body. I then used those numbers to reverse engineer how much of each compound would be needed for the measurements to be correct.  Some of the measurements added up while others didn't. The red and blue text are the measurements used for sodium and chlorine, respectively, because they worked against each other. Also, the oxygen and hydrogen didn't add up exactly with the water so that's what the green and yellow text is. From this we see that most of the measurements are off by substantial amounts. This also shows that certain elements exist beyond the compounds stated in the show throughout the body. So although the show is simpler and fun to quote, it's not scientifically correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PiZc3.png&quot; alt=&quot;humanchemicalbreakdown&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;https://i.stack.imgur.com/PiZc3.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Full size image)&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you notice anything that stands out or that I missed, feel free to leave a comment and I'll try to correct myself or see your perspective. And sorry the Excel sheet may seem a bit sloppy, I tried to work quickly late at night.&lt;/p&gt;&#xA;" OwnerUserId="8184" LastEditorUserId="8079" LastEditDate="2014-07-04T15:34:03.703" LastActivityDate="2014-07-04T15:34:03.703" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19455" PostTypeId="1" AcceptedAnswerId="19471" CreationDate="2014-07-03T08:58:01.780" Score="0" ViewCount="1161" Body="&lt;p&gt;I have a list of gene name in a file &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;CHRNB2&#xA;EGR2&#xA;GCK&#xA;KRT14&#xA;LMNA&#xA;FGF3&#xA;TK2&#xA;ABCC8&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;How can I map them to uniprot ID ? &lt;br&gt;&#xA;&lt;strong&gt;P.S&lt;/strong&gt; I tried Uniprot &quot;ID mapping&quot; (from-&quot;GENEID&quot; to-&quot;UNIPROTKB AC&quot;), but it couldn't map.&lt;br&gt;&#xA;Please suggest me what to do.&lt;/p&gt;&#xA;" OwnerUserId="8210" LastEditorUserId="3553" LastEditDate="2017-07-05T06:12:55.367" LastActivityDate="2017-07-05T06:12:55.367" Title="Convert gene name to uniprot ID" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;database&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19456" PostTypeId="2" ParentId="11351" CreationDate="2014-07-03T12:30:51.253" Score="0" Body="&lt;p&gt;Just finished an experiment (yesterday) where I measured lifetime reproductive success (LRS) of a few hundred flies, with measures taken from 24 hours of production every 7 days over the entire life of the fly. From this I can now answer the question.&lt;/p&gt;&#xA;&lt;p&gt;Correlations of time interval to total offspring production (reproductive success [RS]):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Correlation of Week 1 RS         with Total LRS:    &lt;span class=&quot;math-container&quot;&gt;$\rho $&lt;/span&gt; ~ 0.7&lt;/p&gt;&#xA;&lt;p&gt;Correlation of Week 1 + 2 RS     with Total LRS:    &lt;span class=&quot;math-container&quot;&gt;$\rho $&lt;/span&gt; ~ 0.9&lt;/p&gt;&#xA;&lt;p&gt;Correlation of Week 1,2 +3 RS    with Total LRS:    &lt;span class=&quot;math-container&quot;&gt;$\rho $&lt;/span&gt; &amp;gt; 0.9&lt;/p&gt;&#xA;&lt;p&gt;Correlation of Week 1,2,3 + 4 RS with Total LRS:    &lt;span class=&quot;math-container&quot;&gt;$\rho $&lt;/span&gt; &amp;gt; 0.95&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Approximate conclusion (at least from my data - it may vary depending on experimental conditions and specific flies) is that LRS can be well estimated by measuring three to four weekly intervals.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2016-03-31T07:14:58.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19457" PostTypeId="1" CreationDate="2014-07-03T13:10:05.620" Score="5" ViewCount="270" Body="&lt;p&gt;I'm trying to annotate a list of organisms taken from NCBI for cellularity (unicellular or multicellular). Does any of you ever found a database with association between an organisms' name or taxa and whether it is unicellular or multicellular? Desirably, I would like to get information both on species level and on higher taxonomic level (phyla, classes, etc.), but any information on this is welcomed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case it matters, I'm using Perl to do this annotation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance&lt;/p&gt;&#xA;" OwnerUserId="3324" LastActivityDate="2014-07-08T12:18:10.690" Title="Database of Multicellular and Unicellular organisms?" Tags="&lt;cell-biology&gt;&lt;database&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19460" PostTypeId="1" CreationDate="2014-07-03T17:04:03.103" Score="1" ViewCount="326" Body="&lt;p&gt;Imagine a population that has a larger proportion of older individuals than younger ones, what could possible happen to it in the future?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am guessing that if the older individuals reproduce, the population will increase but as the older generation grow older they would eventually perish again decreasing the population. As they form the larger proportion, the net population would eventually grow but decline, but would the population then begin to stabilize or continue declining?&lt;/p&gt;&#xA;" OwnerUserId="8212" LastEditorUserId="69" LastEditDate="2014-07-03T17:45:23.017" LastActivityDate="2014-07-03T22:54:02.690" Title="Does a top heavy population grow, decline or stabilize?" Tags="&lt;population-dynamics&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19461" PostTypeId="2" ParentId="19416" CreationDate="2014-07-03T18:36:52.787" Score="1" Body="&lt;p&gt;To get an elaborate answer on this one, I guess you should ask at &lt;a href=&quot;https://physics.stackexchange.com/&quot;&gt;physics&lt;/a&gt;. Very basically, FRET works by that an excited chromophore transfers energy to a nearby chromophore, through dipole-dipole coupling, which in turn emits energy (light) which can be detected. This is a quantum mechanic effect, i.e. these are very small energies. The emission energy between from the donor to the acceptor chromophore is inversely proportional to the distance between to the power of six according to the equation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/math/b/e/2/be2895beaa166bf3d13d1ae09406dace.png&quot; alt=&quot;equation&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where &lt;em&gt;r&lt;/em&gt; is the distance and &lt;em&gt;R0&lt;/em&gt; the Förster distance between the donor/acceptor-pair (distance which the energy transfer efficiency is 50 %).This means that the energy to be detected very rapidly decreases. The Förster distance is in the range &lt;a href=&quot;http://chemwiki.ucdavis.edu/Theoretical_Chemistry/Fundamentals/Fluorescence_Resonance_Energy_Transfer&quot; rel=&quot;nofollow noreferrer&quot;&gt;2-10 nm&lt;/a&gt; for different chromophore pairs, which leads to the upper limit of FRET use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lower limit I don't know if it's due to steric effects or some quantum mechanical effect I do not know about. But since proteins are in the size range of the lower limit they must be in really close vicinity in order for their interaction to be detected using FRET.&lt;/p&gt;&#xA;" OwnerUserId="8179" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.210" LastActivityDate="2014-07-03T18:36:52.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19462" PostTypeId="2" ParentId="19416" CreationDate="2014-07-03T19:31:05.497" Score="1" Body="&lt;p&gt;The answer is to perform a FRET experiment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;FRET is most commonly used to find out whether something is nearby something else in this range.  Its chosen as a technique when two points of attachment for FRET probes &lt;em&gt;might&lt;/em&gt; be within 20 nm, but are not known to be, or might be only in certain conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some rules of thumb though. 1 nm, or 10 Angstroms, is about the length of 6 chemical bonds.  To be that close the two FRET probes (which are fluorescent molecules) would typically be attached to the same molecule.   3-4 amino acids apart in a peptide, at the opposite ends of a steroid.  These are schemes for a FRET experiment you would typically avoid out of hand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;FRET is often used for proteins, which are often wider than 20 nm.  For instance FRET probes might be attached to specific positions in two proteins which are known to bind to one another.  A FRET signal would indicate whether the two attachment points of the FRET probes are physically in proximity, allowing one to narrow down the orientation of the two proteins which are binding.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So its more or less an educated guess as to whether to do a FRET experiment, but using simple spatial reasoning you make a safe bet.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-07-03T19:31:05.497" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19463" PostTypeId="2" ParentId="19416" CreationDate="2014-07-03T19:50:56.003" Score="1" Body="&lt;p&gt;I'll add on to shigeta's and RickardSjogren's answer. Firstly, I agree that the upper limit for Forster interaction distance is ~ 10-11 nm due to the rapid fall off of the effect. If I infer from your question correctly, you seem to be asking how to confirm a lack of FRET interaction is a result of no interction, or steric hindrance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Classical methods of confirmation can be learned from biochemsitry. For instance, co-immunoprecipitation and intermolecular linkage with pull-down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the FRET interaction doesn't show a positive result, perhaps it's because the interaction is so tight and the probes are so close that they are prohibited from the FRET effect. That would suggest a strong interaction, and a co-immunoprecipitation should readily show you that you can pull down one protein, run the results on a western blot, and probe for the other protein. The second permutation is to pull down protein B, and probe for protein A. This is a confirmation that both proteins exist in complex. Failure to co-immunoprecipitate both proteins (especially when trying both permutations) would likely indicate that proteins A and B do not interact, or that their interaction is highly transient or very weak. Co-IP can be demonstrated in vitro using purified recombinant proteins, or in vivo, in their native state from cell lysates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Enter the second technique. Various small molecule compounds of different molecular length can be used to make inter-molecular, amine-to-amine linkages. &lt;a href=&quot;http://www.piercenet.com/product/bs3&quot; rel=&quot;nofollow&quot;&gt;See BS3 for example&lt;/a&gt;. This works best in vivo, where incubation with a compound such as this would create cross-links between neighbouring proteins only with the reach of the englth of the compounds. If two proteins interact, then by definition they must be spatially close to each other, and therefore some percentage of your proteins should be in complex together. From there, you can run a western blot and show that you can probe for both proteins, that run at the same apparent molecular weight defined by the sum of both proteins molecular weights (and therefore both proteins will run higher than expected because their mass is modified by the addition of the interacting protein + linker). Modern versions of this approach involve using mass spec identification of cross-linked fragments, which is much more sensitive and quantitative that western blotting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A third method could be quantitative colocalization by immunofluorescence microscopy. Prepare cells for immunofluorescence, probing for both proteins of interest, and quantitatively assess whether the proteins co-localize with each other. By eye (and not so rigorously), you would expect that both proteins should exhibit very similar spatial distributions within the cell if they are in fact interacting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Failure of the above two methods strongly supports the idea that the proteins do not interact, or that they do interact in very weak or very transient conditions. The only way to truly exclude the idea that they do interact in a very weak/transient manner is if you know that the protein complex does something in a cell. If they do something while in complex, then you can knock one protein out, or express a recombinant mutated form of the protein, and assay for the lack of the normal action.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-07-03T19:50:56.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19464" PostTypeId="1" CreationDate="2014-07-03T20:31:13.887" Score="2" ViewCount="257" Body="&lt;p&gt;Assume you are 45 minutes on the supine position. Furthermore: you stand all of a sudden and fast and without sympaticus activity. &#xA;The venous return (smooth musculature of vessels) accommodates faster to the change (decrease of venous return) so returns blood to the heart before the sympaticus has accommodated for increased cardiac output.&#xA;This creates a significant increase in the blood volume entering the heart. &#xA;In pathological situation where systemic vasoconstriction not occurring normally, the heart is not capable of handling the overdistension; resulting in a pain during the second cardiac cycle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested in knowing which phase the heart is most vulnerable: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;filling, &lt;/li&gt;&#xA;&lt;li&gt;isovolumetric contraction &lt;/li&gt;&#xA;&lt;li&gt;ejection&lt;/li&gt;&#xA;&lt;li&gt;isovelumetric relaxation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;or more explicitly (from my answer &lt;a href=&quot;https://biology.stackexchange.com/a/19304/86&quot;&gt;here&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Atrial systole&lt;/li&gt;&#xA;&lt;li&gt;Isovolumetric ventricular contraction&lt;/li&gt;&#xA;&lt;li&gt;Rapid ventricular ejection&lt;/li&gt;&#xA;&lt;li&gt;Reduced ventricular ejection&lt;/li&gt;&#xA;&lt;li&gt;Isovolumetric ventricular relaxation&lt;/li&gt;&#xA;&lt;li&gt;Rapid ventricular filling&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I think filling can happen normally, but not with the sudden isovolumetric contraction (most sympathetic innervations here, so therefore I think this is the weak link). &#xA;When there is too much blood in the ventricles, some of the blood is reflected back from the ventricles into the atria causing a painful sensation and possibly tachycardia (as well as an possible increased risk of atrial fibrillation if such events happen regularly).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is the isovolumetric contraction (systole of ventricles) of the cardiac cycle the possible weak link in accommodating a sudden increased venous return?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-12-05T21:39:01.437" Title="Fast standing and the heart's insufficient accommodation of the increased venous return" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;pathophysiology&gt;&lt;ventricles&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19465" PostTypeId="2" ParentId="19460" CreationDate="2014-07-03T21:18:08.807" Score="2" Body="&lt;p&gt;Your question leads to the field of structured population models, and I am afraid the answer is: &lt;strong&gt;It very much depends on the exact Leslie matrix!&lt;/strong&gt;. The population may go extinct, may remain at stable size or may grow indefinitely (theoretically speaking), may increase in size and then go extinct, etc…&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is at least true if you make the assumptions that the rates that govern transitions between age/stage classes (survival, growth, reproduction) are  stable over time. Your scenario is explicitly dealing with transitory population dynamics, i.e. it is asking about the population fluctuations that will happen before the age-structured population stabilizes (assuming it does stabilize at some point). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To understand what will happen to your population you can model your population using a Leslie Matrix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Leslie matrix&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Leslie matrix describes the age-specific survival and fecundity of individuals in a population. Shortly speaking, a population dynamic model using age-specific survival and fecundity looks like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CFnyq.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Renaming the matrix and the two vectors you see above it gives: $n(t+1) = M \cdot n(t)$, where $n(t)$ is the vector of number of individuals in the population at each age and $L$ is the Leslie matrix, where the first row gives the fecundity of each age ($f_2$ is the fecundity of the individuals of age class $s$ where the number of individuals is a given time is given by $n(t)$) and the lower diagonal gives the survival probability ($s_2$ is the probability of surviving from age 2 to age 3).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, basically to answer your question, define your Leslie matrix $L$, define $n(0)$ and iterate (left multiply your vector $n(t)$ several times) to see how the number of individuals change through time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Leslie Matrix and Linear Algebra&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The right leading eigenvector of $L$ gives the stationary distribution and the associated eigenvalue gives the growth rate $R$. If $0&amp;lt;R&amp;lt;1$, then the population size decreases through time if $R&amp;gt;1$, the population size increases through time. $R$ cannot be lower than zero (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Perron%E2%80%93Frobenius_theorem&quot; rel=&quot;nofollow noreferrer&quot;&gt;Perron-Frobenius theorem&lt;/a&gt; to understand why). Many biologically interesting features can be extrapolated from the Leslie matrix such as the average lifespan or wether you'd better to introduce individuals of a age 1 or of age 2 (for examples) in a natural population in order to prevent its extinction. The sensitivity of the population to change in parameter (such as an increasing mortality rate at lower age due to a new predator for example). You will find more information on the Leslie matrix on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Leslie_matrix&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki article&lt;/a&gt; and on many other websites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other ways to model using a Leslie Matrix&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One can also model age-structured population using right matrix multiplication (unlike the above example) and use row vector rather than column vector. The Leslie matrix may also be a function of various variables such as the population size. One can also extend the Leslie matrix to incorporate different class of individuals in the population (different genotypes or different sexes for examples).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Books&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.fr/Evolution-Age-Structured-Populations-Brian-Charlesworth/dp/0521459672/ref=sr_1_3?ie=UTF8&amp;amp;qid=1404421829&amp;amp;sr=8-3&amp;amp;keywords=Brian%20charlesworth&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Charlesworth. 1994. Evolution in Age-Structured Populations. Cambridge University Press.&quot;&gt;Charlesworth (1994)&lt;/a&gt; and &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0878930965&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Caswell. 2001. Matrix Population Models. Sinauer.&quot;&gt;Caswell (2001)&lt;/a&gt; are both excellent books to go deeper into the subject of structured population models, but may be challenging if you lack some background knowledge in linear algebra or population biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps!&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT - R simulation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's been a time I haven't programmed in R. So, I took the advantage of your question to have some fun and write a quick and dirty code. Below you'll find a R code that allows you to see how the age-specific population size varies depending on your initial vector $n$ and the Leslie matrix. I also add some instructions in order to change the number of age classes (because my code is not very flexible).&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;install.packages(&quot;ggplot2&quot;)&#xA;require(ggplot2)&#xA;&#xA;######## Parameters&#xA;&#xA;n = c(2,23,40,300) # initial age-specific population size. MNodify as you which. You can as well change the number of age classes&#xA;&#xA;L = matrix(c(0,0,1,2,0.8,0,0,0,0,0.8,0,0,0,0,0.3,0), byrow=T, ncol=4) # Leslie matrix (Left multiplication). Modify as you wish but make sure it should always be a Leslie matrix. You can modify the number of age classes&#xA;&#xA;nb_generations = 100 # Number of generations you want to compute&#xA;&#xA;############&#xA;&#xA;n_t = data.frame(age1=rep(0,nb_generations), age2=rep(0,nb_generations), age3=rep(0,nb_generations), age4=rep(0,nb_generations), Generation=1:nb_generations) # It is a data frame to keep track of age-specific population size changes through times. You will have to add more `ageX` columns if you want to simulate more than age classes&#xA;&#xA;# print (n)&#xA;for (generation in 1:nb_generations){&#xA;    n_t[generation,1:4] = n&#xA;    n = L %*% n&#xA;#   print (n)&#xA;}&#xA;&#xA;&#xA;n_t2 = reshape(n_t, direction='long', idvar='Generation', v.names='Age_Specific_Number_of_Individuals', varying=c('age1', 'age2', 'age3', 'age4'), timevar='age') # Just to reshape the data for convenience!&#xA;&#xA;ggplot(n_t2, aes(x=Generation, y=Age_Specific_Number_of_Individuals, color=factor(age))) + geom_line() + scale_color_manual(values=colorRampPalette(c(&quot;black&quot;, &quot;grey&quot;))(4)) # change the last number of this line according to your number of age classes.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vfbYm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see that there are important osciliations in the first 30 or so generations just as expected. Then, the population more or less stabilizes. You also see that due to a survival probability that is different from 1 for each age class, there is necessarily at equilibrium more individuals in age class 1 than in age class 2 and more in age class 2 than in age class 3, etc...&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3624" LastEditDate="2014-07-03T22:54:02.690" LastActivityDate="2014-07-03T22:54:02.690" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19466" PostTypeId="1" AcceptedAnswerId="19475" CreationDate="2014-07-03T22:33:39.800" Score="0" ViewCount="1529" Body="&lt;p&gt;Maybe I'm confused by the term &quot;codominance&quot;, but I wondering if codominance only occurs with two dominant alleles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can two recessive alleles produce codominance in an individual?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Likewise, can two recessive alleles produce incomplete dominance?&lt;/p&gt;&#xA;" OwnerUserId="5179" LastActivityDate="2014-07-04T16:27:37.970" Title="can recessive alleles produce codominance?" Tags="&lt;genetics&gt;&lt;allele&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19467" PostTypeId="2" ParentId="19466" CreationDate="2014-07-03T23:39:35.910" Score="1" Body="&lt;p&gt;When two alleles show codiminance, they are not described as dominant or recessive relative to each other. They are simply codiminant to each other. The same applies to incomplete dominance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that all these terms are relative to the alleles you're talking about. An allele that is dominant over one allele may be recessive to another and codiminant with yet another. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-07-03T23:39:35.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19469" PostTypeId="2" ParentId="13812" CreationDate="2014-07-04T04:11:59.373" Score="1" Body="&lt;p&gt;&lt;strong&gt;Rh is just a proteinous(antigenic) factor in red blood cells; not a DISEASE&lt;/strong&gt;.If it is present in blood you are Rh positive. If not Rh negative.An Rh negative person if exposed to Rh positive blood will form specific antibodies against the Rh antigens. In case of pregnancy, Rh antigens of the foetus do not get exposed to the Rh negative blood of the mother during first pregnancyas the two bloods are well separated by the placenta.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However during the delivery of the first child there is a possibility of the exposure of maternal blood to small amounts of Rh positive blood of the foetus.In such cases the mother starts preparing antibodies against Rh antigens in her blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case of her subsequent pregnancies, the Rh antibodies from the Rh negative mother can leak into the blood of the Rh positive foetus and destroy the foetal RBCs. THis could be fatal to the foetus or could cause severe anaemia and jaundice to the baby.A condition called &lt;em&gt;erythroblastosis foetalis&lt;/em&gt; arises.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This condition can be avoided by administering ant- Rh antibodies to the mother immediately after her first delivery.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not a disease but is just as a result of antigen- antibody reaction.As far as Rhesus monkeys are concerned, it is an innate factor in them, common to all.It is quite similar to the case of &lt;em&gt;Bacillus thuringiensis&lt;/em&gt; in biotechnology. When inserted into plant cells these bacterial phytotoxins cause havoc as an insecticidal agent; whereas they seem to have exactly no effect inside bacteria.You may also consider the case of &lt;em&gt;Penicillium notatum&lt;/em&gt;.These organisms are capable of causing harm to other living organisms but are not affected themselves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similar is the case with Rhesus monkeys.&lt;/p&gt;&#xA;" OwnerUserId="8216" LastActivityDate="2014-07-04T04:11:59.373" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19470" PostTypeId="2" ParentId="16721" CreationDate="2014-07-04T07:11:04.577" Score="1" Body="&lt;p&gt;If you're working with BioCyc pathways you can use their &lt;a href=&quot;http://biocyc.org/web-services.shtml&quot; rel=&quot;nofollow&quot;&gt;REST-API&lt;/a&gt; for batch-downloading all genes for their pathways. You can run a wide range of queries including BioVelo-queries for all genes/compounds in a specified pathway, all pathways in organism etc. A query for all the pathways in B. subtilis would look like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://biocyc.org/xmlquery?%5bx%3ax%3C-bsub&quot; rel=&quot;nofollow&quot;&gt;http://biocyc.org/xmlquery?[x:x%3C-bsub&lt;/a&gt;^^pathways]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where you get an XML with the Cyc-IDs for the pathways which can be used to search for the genes. A query for all genes in the Arginine synthesis pathway in B. subtilis would then look like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://biocyc.org/xmlquery?%5bx%3ay%3a=bsub~argsyn-pwy,x%3C-%28genes-of-pathway%20y%29%5d&amp;amp;detail=full&quot; rel=&quot;nofollow&quot;&gt;http://biocyc.org/xmlquery?[x:y:=bsub~argsyn-pwy,x%3C-%28genes-of-pathway%20y%29]&amp;amp;detail=full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which returns an XML with information regarding the genes, start and end positions including (i.e. gene length). Since I don't work very much in R I don't know if there exists an R-package. But it is very straightforward to write Python scripts for downloading and XML-parsing.&lt;/p&gt;&#xA;" OwnerUserId="8179" LastActivityDate="2014-07-04T07:11:04.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19471" PostTypeId="2" ParentId="19455" CreationDate="2014-07-04T07:33:15.330" Score="0" Body="&lt;p&gt;for biomart goto below link&lt;br&gt;&#xA;&lt;a href=&quot;http://central.biomart.org/converter/#!/ID_converter/gene_ensembl_config_2&quot; rel=&quot;nofollow&quot;&gt;http://central.biomart.org/converter/#!/ID_converter/gene_ensembl_config_2&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also there is one more converter which i found pretty useful&lt;br&gt;&#xA;&lt;a href=&quot;http://biodbnet.abcc.ncifcrf.gov/db/db2db.php#biodb&quot; rel=&quot;nofollow&quot;&gt;http://biodbnet.abcc.ncifcrf.gov/db/db2db.php#biodb&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8210" LastActivityDate="2014-07-04T07:33:15.330" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19472" PostTypeId="1" AcceptedAnswerId="19474" CreationDate="2014-07-04T07:41:15.923" Score="14" ViewCount="11690" Body="&lt;p&gt;Last night I laid on my bed and tried to go to sleep with the light off.&#xA;I closed my eyes (but hadn't gone to sleep). My younger brother touched the wireless mouse (which had laser) for the laptop.  He wiggled the mouse and it's laser contacted my closed eye . I knew some light was thrown on my face, and it's color was red. The laser on the mouse was actually red. So my question is, when my eyes are not functioning (not seeing, closed) how did I come to know that there was a light aimed at my eyes, and it was red? &lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="338" LastEditDate="2014-07-04T19:32:16.800" LastActivityDate="2014-10-06T05:24:42.653" Title="How do we know the presence of light when our eyes are closed?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;eyes&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19473" PostTypeId="2" ParentId="19472" CreationDate="2014-07-04T07:53:08.263" Score="22" Body="&lt;p&gt;Short answer, your eyelids does not block all light. Since they are only a thin layer of skin, the light is able to pass through although not completely obviously. Since the eyes are still completely functional when you close them, only covered by the eyelids, you are able to see when light strikes your face. &lt;/p&gt;&#xA;" OwnerUserId="8179" LastActivityDate="2014-07-04T07:53:08.263" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19474" PostTypeId="2" ParentId="19472" CreationDate="2014-07-04T08:51:27.880" Score="16" Body="&lt;p&gt;There are two reasons for light to appear red through the eyelids.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Eyelids get a rich supply of blood which contains iron (in hemoglobin). The iron in blood absorbs all colors of light but reflects red light. (&lt;a href=&quot;http://www.chemistry.wustl.edu/~edudev/LabTutorials/Hemoglobin/MetalComplexinBlood.html&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Our tissue transmits red wavelengths of light very well, but it doesn't transmit blue or wavelengths of light towards the blue end of the spectrum very well. So, the blue light is absorbed by the skin, while the red light travels through. When this light hits our eye through our eyelids, it is mostly red. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8719122&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Also, as Rickard Sjogren said, the eyelid is a thin membrane and allows light to pass through. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5431" LastEditDate="2014-10-06T05:24:42.653" LastActivityDate="2014-10-06T05:24:42.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19475" PostTypeId="2" ParentId="19466" CreationDate="2014-07-04T09:24:51.650" Score="4" Body="&lt;p&gt;An allele is not dominant or recessive by itself. It is dominant or recessive compared to another allele. Therefore, if you consider one locus (position on a sequence) that has two alleles (bi-allelic locus), you cannot have two dominant or two recessive alleles. It is like saying that two things are darker. In reality you can either say that one is darker than the other one or that the color is as dark as the other one. So either one allele is dominant (or partially dominant) and the other is necessarily recessive (or partially recessive) or the two alleles are codominant.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Think of a gene that influence a phenotypic trait such as tail length for example. This locus is bi-allelic (two different alleles (=variant of a gene) exist (=segregate) at this locus). We'll call the two alleles $A$ and $B$. An individual that homozygous $AA$ has trait value $M_{AA}$. The homozygotes $AB$ have trait value $M_{AB}$ and individuals $BB$ have trait values $M_{BB}$. Viewing this in a table it gives:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;\begin{array}{c|lcr}&#xA;\text{Genotype} &amp;amp; \text{Tail length} \\&#xA;\hline&#xA;\text{AA} &amp;amp; M_{AA}\\&#xA;\text{AB} &amp;amp; M_{AB}\\&#xA;\text{BB} &amp;amp; M_{BB}\\&#xA;\end{array}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following table gives the tail length of the different genotypes under the different types of interactions (dominance, partial dominance and co-dominance).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;\begin{array}{c|lcr}&#xA;\text{Interaction} &amp;amp; \text{AA} &amp;amp; \text{AB} &amp;amp; \text{BB} \\&#xA;\hline&#xA;\text{A is dominant and B is recessive} &amp;amp; M_{AA} &amp;amp; M_{AA} = M_{AB} &amp;amp; M_{BB} \\&#xA;\\&#xA;\\ &amp;amp; &amp;amp; M_{AA} &amp;gt; M_{AB} &amp;gt; M_{BB}\\&#xA;\text{Partial Dominance} &amp;amp; M_{AA} &amp;amp; \text{or} &amp;amp; M_{BB} &#xA;\\ &amp;amp; &amp;amp; M_{AA} &amp;lt; M_{AB} &amp;lt; M_{BB} \\&#xA;\\&#xA;\text{Codominance} &amp;amp; M_{AA} &amp;amp; M_{AB} = \frac{M_{AA} + M_{BB}}{2} &amp;amp; M_{BB} \\&#xA;\end{array}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because, in the codominance case $M_{AB}$ is necessarily between the values of $M_{AA}$ and $M_{BB}$ ($M_{AA} &amp;gt; M_{AB} &amp;gt; M_{BB}$ or $M_{AA} &amp;lt; M_{AB} &amp;lt; M_{BB}$), one can consider codominance as being a special case of partial dominance where neither $A$ or $B$ dominates because they both contribute as much to the determination of the tail length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Various definitions may exist for such concepts as well as for overdominance (also sometimes called heterozygous advantage) or stabilizing selection for examples. Those definitions differ in the sense that they sometimes apply to the value of the quantitative trait, to the fitness value (which is another quantitative trait) or to genetic polymorphism. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-07-04T12:40:13.837" LastActivityDate="2014-07-04T12:40:13.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19476" PostTypeId="1" AcceptedAnswerId="19477" CreationDate="2014-07-04T11:34:12.270" Score="0" ViewCount="457" Body="&lt;p&gt;since the title seems self explanatory;&#xA;It would be nice if anybody could provide a reference. I'm looking for a paper that I belive stated around 1.5 Mb but anything above will be cordialy welcomed.&#xA;thanks a lot&lt;/p&gt;&#xA;" OwnerUserId="8063" LastEditorUserId="8063" LastEditDate="2014-07-04T14:11:41.080" LastActivityDate="2014-07-04T14:11:41.080" Title="what is the biggest known functional distance between an enhancer and its target gene (TSS) in cis?" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;transcription-factor&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19477" PostTypeId="2" ParentId="19476" CreationDate="2014-07-04T12:01:47.440" Score="2" Body="&lt;p&gt;I haven't found 1.5 Mb, but 1 Megabase. This is the case for the shh gene in chicken, where the enhancer element is located 1 Mb upstream. The original article can be found here: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12837695&quot; rel=&quot;nofollow&quot;&gt;&quot;A long-range Shh enhancer regulates expression in the developing&#xA;limb and fin and is associated with preaxial polydactyly.&quot;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are two reviews which are also interesting in this context:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0012160610012315&quot; rel=&quot;nofollow&quot;&gt;When needles look like hay: How to find tissue-specific enhancers in&#xA;model organism genomes&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17403687&quot; rel=&quot;nofollow&quot;&gt;Remote control of gene expression.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-04T12:01:47.440" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19480" PostTypeId="2" ParentId="19466" CreationDate="2014-07-04T16:27:37.970" Score="0" Body="&lt;p&gt;Shorter answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The dominant/recessive paradigm that is taught in middle school and high school is not universally applicable.  It accurately describes only a small number of phenotypes, compared to all the genotype/phenotype interactions which an organism exhibits.  It was a useful place to start when it came to unraveling the relationship between genes and phenotypes, but it is very limited.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So trying to shoehorn all phenotypes into that paradigm is a serious mistake.  Just because all of your homework problems are solved using it doesn't mean that it's applicable to all real-life situations.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-07-04T16:27:37.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19482" PostTypeId="2" ParentId="19457" CreationDate="2014-07-04T17:21:38.390" Score="1" Body="&lt;p&gt;More like a comment:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It doesn't seem that such a database exists, but I think it's relatively easy to create a list of multicellular taxa and the rest should be considered unicellular. Since you use ncbi taxonomy, you can easily get higher-level parent for any species, so there is no need to define cellularity for individual species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The challenging groups would be different algal and fungal taxa, but there are some good reference books. You also have to decide, whether to introduce a separate category for colonial/coenobial/filamentous organisms.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-07-04T17:21:38.390" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19483" PostTypeId="2" ParentId="19436" CreationDate="2014-07-04T18:49:55.880" Score="1" Body="&lt;p&gt;As the previous answer said, there are some public HP1 ChIP-seq data from D. melanogaster if not from the DGRP, from modENCODE and maybe others. In the case of modENCODE, they've published not only the reads, but also their peak calls (mapping with Eland + calling with MACS).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;BEDTools ( &lt;a href=&quot;https://github.com/arq5x/bedtools2&quot; rel=&quot;nofollow&quot;&gt;https://github.com/arq5x/bedtools2&lt;/a&gt; )is a nice command line tool for manipulating intervals with genomic coordinates, and the bedtools closest command can calculate the distance to the closest feature. It would look something like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;bedtools closest -d -a genomic_features.gff3 -b peak_calls.gff3&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Where the &quot;genomic_features&quot; part would be any subset of genome annotation that you're interested in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've worked through a small example with modENCODE data, Flybase transcript annotation and BEDTools:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://martinsbioblogg.wordpress.com/2014/07/04/finding-the-distance-from-chip-signals-to-genes/&quot; rel=&quot;nofollow&quot;&gt;http://martinsbioblogg.wordpress.com/2014/07/04/finding-the-distance-from-chip-signals-to-genes/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cheers,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;m.&lt;/p&gt;&#xA;" OwnerUserId="8222" LastActivityDate="2014-07-04T18:49:55.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19484" PostTypeId="1" AcceptedAnswerId="20279" CreationDate="2014-07-04T19:09:48.377" Score="5" ViewCount="3644" Body="&lt;p&gt;Seems to me that these two sources (&lt;a href=&quot;https://www.youtube.com/watch?v=LVeR5JbiWls&quot; rel=&quot;nofollow&quot;&gt;M. Whitlock&lt;/a&gt;, &lt;a href=&quot;http://www.amazon.fr/Genetic-Load-Bruce-Wallace/dp/0133511979/ref=sr_1_1?ie=UTF8&amp;amp;qid=1404500945&amp;amp;sr=8-1&amp;amp;keywords=bruce%20wallace%20genetic%20load&quot; rel=&quot;nofollow&quot;&gt;B. Wallace&lt;/a&gt;) use different definitions of soft and hard selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;M. Whitlock: Soft selection occurs when the relative fitness of an individual is calculated relative to the fittest individual of the local patch. Hard selection occurs when the relative fitness of an individual is calculated relative to the fitness of the fittest individual in the whole metapopulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B. Wallace: Soft selection occurs when the relative fitness of an individual is calculated relative to the fittest individual in the population. Hard selection occurs when the relative fitness of an individual is calculated relative a hypothetical fitness. Therefore, extinction only occurs under hard selection but never (except eventually when all individuals have fitness of 0) in the soft selection case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there other definitions? What is the most common definition?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-08-07T09:35:31.443" LastActivityDate="2014-08-07T09:35:31.443" Title="Soft and Hard selection" Tags="&lt;evolution&gt;&lt;ecology&gt;&lt;natural-selection&gt;&lt;definitions&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19485" PostTypeId="1" CreationDate="2014-07-04T19:44:02.417" Score="2" ViewCount="499" Body="&lt;p&gt;I have found the information: `In the absence of lactose, the lac repressor binds to the operator sequence on DNA and bends the DNA by 40 degrees. This blocks access of T7 RNA polymerase to the promoter site and thus prevents leaky transcription of your gene before induction.' &#xA;I am confuse about one fact.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I add IPTG,  the lac repressor protein (from E.coli chromosome) can no longer bind the operator and native E. coli RNA polymerase begins transcribing, the T7 RNA polymerase gene engineered into its chromosome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if there is IPTG and lac repressor protein (from E.coli chromosome) can no longer bind the operator standing in front of the T7 RNA polymerase gene, why lac repressor protein still can bind to operator standing in front of the target gene from plasmid? &lt;/p&gt;&#xA;" OwnerUserId="6892" LastActivityDate="2014-07-05T17:58:11.520" Title="A question about IPTG induction" Tags="&lt;polymerase&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19486" PostTypeId="2" ParentId="7340" CreationDate="2014-07-04T20:05:52.570" Score="1" Body="&lt;p&gt;No, the &lt;em&gt;L&lt;/em&gt; axis in the &lt;a href=&quot;//en.wikipedia.org/wiki/HSL_and_HSV&quot; rel=&quot;nofollow&quot;&gt;HSL color space&lt;/a&gt; does not really correspond to &lt;a href=&quot;//en.wikipedia.org/wiki/Lightness_%28color%29&quot; rel=&quot;nofollow&quot;&gt;lightness&lt;/a&gt; as perceived by the human eye, except in the very crudest sense that, for given values of the &lt;em&gt;H&lt;/em&gt; and &lt;em&gt;S&lt;/em&gt; components, increasing &lt;em&gt;L&lt;/em&gt; produces an increase in the perceived lightness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;L&lt;/em&gt; component of the standard HSL color space is simply calculated as the average of the lowest and the highest RGB component of the color (in whichever &lt;a href=&quot;//en.wikipedia.org/wiki/RGB_color_space&quot; rel=&quot;nofollow&quot;&gt;RGB color space&lt;/a&gt; in being used): $$L = \frac{\min(R, G, B) + \max(R,G,B)}2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This definition alone should make it obvious that the &lt;em&gt;L&lt;/em&gt; value &lt;em&gt;cannot&lt;/em&gt; correspond to perceived lightness, since it completely ignores the middle one of the three RGB channels.  Thus, the color (&lt;em&gt;R&lt;/em&gt;=0, &lt;em&gt;G&lt;/em&gt;=0, &lt;em&gt;B&lt;/em&gt;=1), i.e. pure $\color{#0000ff}{\rm blue}$, has exactly the same &lt;em&gt;L&lt;/em&gt; value (0.5) as the color (&lt;em&gt;R&lt;/em&gt;=0, &lt;em&gt;G&lt;/em&gt;=1, &lt;em&gt;B&lt;/em&gt;=1), i.e. $\color{#00ffff}{\rm cyan}$, yet it's obvious at a glance that the latter color is visually much brighter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed, the HSL color space doesn't even &lt;em&gt;try&lt;/em&gt; to match the perceptual lightness of the colors; rather, the definition of the &lt;em&gt;L&lt;/em&gt; channel is chosen because it has the convenient feature that it maps black to &lt;em&gt;L&lt;/em&gt;=0, white to &lt;em&gt;L&lt;/em&gt;=1, and all the six maximally saturated pure RGB colors (red, yellow, green, cyan, blue and magenta), despite their wide perceptual lightness differences, to &lt;em&gt;L&lt;/em&gt;=0.5.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;A much better approximation to the perceived lightness of a color is the &lt;a href=&quot;//en.wikipedia.org/wiki/Luma_%28video%29&quot; rel=&quot;nofollow&quot;&gt;luma&lt;/a&gt; &lt;em&gt;Y&lt;/em&gt;', which is defined as a weighted average of the RGB channels.  The precise weights depend on the definition and the RGB color space used, but a common choice (from &lt;a href=&quot;//en.wikipedia.org/wiki/Rec._709&quot; rel=&quot;nofollow&quot;&gt;ITU-R Rec. 709&lt;/a&gt;) is: $$Y' = 0.2126\, R + 0.7152\, G + 0.0722\, B$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The weighs are chosen to account for the different perceived lightness of the different RGB primary colors.  A striking feature is the that the green component alone accounts for over 70% of the luma, nearly ten times as much as the blue component.  Yet a visual comparison of $\color{#0000ff}{\rm 100\%\ blue}$ with $\color{#00ff00}{\rm 100\%\ green}$ does clearly confirm that this choice of weights is justified: the pure green appears &lt;em&gt;much&lt;/em&gt; brighter than the blue, and almost as bright as the cyan (which is their sum) above.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;However, the definition of the luma still ignores the non-linearity of both the standard RGB color spaces (such as &lt;a href=&quot;//en.wikipedia.org/wiki/sRGB&quot; rel=&quot;nofollow&quot;&gt;sRGB&lt;/a&gt;) and the human eye.  While these two effects partly cancel out each other, allowing luma to be used as a reasonable approximation of perceptual lightness, for truly accurate results they need to be accounted for.  This involves several steps:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Convert the RGB color into a linear color space.  For sRGB, the following &lt;a href=&quot;//en.wikipedia.org/wiki/SRGB#The_reverse_transformation&quot; rel=&quot;nofollow&quot;&gt;formula&lt;/a&gt; may be used: $R_L = f(R), G_L = f(G), B_L = f(B)$, where: $$f(C) = \begin{cases}C / 12.92 &amp;amp; \text{if } 0 \le C \le 0.04045 \\ ((C + 0.055) / 1.055)^{2.4} &amp;amp; \text{if }  0.04045 &amp;lt; C \le 1 \end{cases}$$ (Here, $R$, $G$ and $B$ are the sRGB component values, and $R_L$, $G_L$ and $B_L$ the linear ones, both scaled to the range from 0.0 to 1.0.)  Alternatively, a very close approximation to the formula above is given by simple &lt;a href=&quot;http://en.wikipedia.org/wiki/Gamma_correction&quot; rel=&quot;nofollow&quot;&gt;gamma-expansion&lt;/a&gt; with $\gamma = 2.2$: $f(C) = C^{2.2}$.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Calculate the &lt;a href=&quot;//en.wikipedia.org/wiki/Luminance_%28relative%29&quot; rel=&quot;nofollow&quot;&gt;relative luminance&lt;/a&gt; as a weighted average of the linear RGB component values: $$Y = 0.2126\, R_L + 0.7152\, G_L + 0.0722\, B_L$$ (The weights are exactly the same as for the luma formula above, because that's where they come from; the luma calculation just blindly applies them to the gamma-compressed RGB values.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Convert the relative luminance value into an approximation of the percieved lightness, using something like the &lt;a href=&quot;//en.wikipedia.org/wiki/CIELAB&quot; rel=&quot;nofollow&quot;&gt;CIELAB&lt;/a&gt; formula: $\ell^* = 1.16\, g(Y) - 0.16$, where: $$g(Y) = \begin{cases} \tfrac13 \left(\tfrac{29}{6}\right)^2 Y + \tfrac{4}{29} &amp;amp; \text{if } 0 \le Y \le \left(\tfrac{6}{29}\right)^3\\ Y^{1/3} &amp;amp; \text{otherwise} \end{cases}$$ (Note: In the CIELAB standard, the $L^*$ value ranges from 0 to 100, but for the sake of consistency, in the formula above I chose to define $\ell^* = L^* / 100$, so that its range is also from 0 to 1.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="239" LastActivityDate="2014-07-04T20:05:52.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19487" PostTypeId="2" ParentId="19485" CreationDate="2014-07-04T20:50:27.047" Score="3" Body="&lt;p&gt;What makes you think that the lac repressor will still be bound at the target gene? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In strains with this type of regulatory configuration (usually with DE3 in the genotype) the idea is that IPTG induction turns on expression of T7 polymerase from a lac promoter on the chromosome, and then this T7 polymerase then transcribes the target gene on the plasmid. The presence of IPTG ensures that repressor will bind at neither site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Supplementary:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that I understand why you are confused now. Your picture of the way this works is based on the idea that the repressor is locked on to the operator until an inducer such as IPTG comes along. In fact there is an equilibrium between bound and unbound:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;repressor/operator &amp;lt;=&gt; repressor + operator&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and, in the brief periods when the repressor isn't bound, the E. coli RNA polymerase can bind and transcribe the operon. This is referred to as 'escape synthesis' and it is generally assumed that it is functionally relevant in ensuring that there are low levels of lac permease expression at all times so that lactose can be taken up. If this wasn't the case, how would the natural inducer (a derivative of lactose) ever be able to induce the lac operon?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In protein expression systems it is generally considered desirable to keep escape synthesis of the foreign protein to a minimum so that there is no selection acting on the gene to negate any deleterious effects of its expression. The use of T7 polymerase as an intermediate level of regulation helps to achieve this. Even if there is a low level of escape synthesis of T7 polymerase, the concentration of T7 polymerase will be so low in the uninduced state (compared to the endogenous RNA polymerase) that the amount of escape synthesis of the target protein due to T7 polymerase gaining productive access to the T7 promoter on the plasmid will be negligible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://sandwalk.blogspot.co.uk/2008/02/repression-of-lac-operon.html&quot; rel=&quot;nofollow&quot;&gt;Read more here.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-07-05T17:58:11.520" LastActivityDate="2014-07-05T17:58:11.520" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19488" PostTypeId="2" ParentId="17348" CreationDate="2014-07-04T21:07:08.710" Score="1" Body="&lt;h2&gt;Physiology&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My conjecture.&lt;/strong&gt; &#xA;The slightly elevated position causes greater venous return (work against gravity by smooth musculature and thoracic pump). &#xA;Why this is happening this way is partially based on my question &lt;a href=&quot;https://biology.stackexchange.com/questions/19464/fast-standing-and-the-hearts-insufficient-accommodation-of-the-increased-venous&quot;&gt;here&lt;/a&gt; about &lt;em&gt;Fast standing and the heart's insufficient accommodation of the increased venous return&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XaZdF.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where the venous return reacts first the change in the position from supine by shifting the VR1 to VR2. &#xA;The stroke volume increases initially to SV1 to SV2, while the end diastolic volume from EDV1 to EDV2. &#xA;The increased stroke volume cannot be maintained long time so the cardiac output shifts to the right from CO1 to CO2.&#xA;So the initial stroke volume SV1 is the same as SV3 (not in the picture). &#xA;However, the EDV has increased (EDV3 &gt;&gt; EDV1) which increases much the lymphatic drainage. &#xA;Lymphatic drainage is not dependent on the stroke volume. &#xA;Increased lymphatic drainage then again increases the circulation of lymph. &#xA;This then again supports the recovery from the upper respiratory infection where the fine regulation between&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the thoracic pump,&lt;/li&gt;&#xA;&lt;li&gt;respiratory pump, and &lt;/li&gt;&#xA;&lt;li&gt;smooth musculature&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;determine the final effect of the body position on the recovery times. &#xA;The size of the thoracic cavity puts some limitations, for instance.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Cardiology&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;In some cases, the upper respiratory infection can cause myocarditis. &#xA;This will decrease the functioning of the heart and cause possible &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;premature atrial contraction, and/or&lt;/li&gt;&#xA;&lt;li&gt;premature ventricular contraction.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Elevated position helps small arterioles of left ventricle supply preload. &#xA;Otherwise, &lt;a href=&quot;http://en.wikipedia.org/wiki/Ectopic_beat&quot; rel=&quot;nofollow noreferrer&quot;&gt;ectopic beat&lt;/a&gt; can be heard or also called &quot;epics beat&quot; which is sign of the two previous conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nurse is educated to listen to the patient and ask for possible jolts and flips in the chest. &#xA;Elevating position in such a case can help because of better supply for preload in the left ventricle.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Pathophysiology&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Upper respiratory infection is often acute respiratory infection (acute respiratory distress syndrome). &#xA;There is an increased permeability of the vessels. &#xA;The fluids and plasma proteins are going through alveoli. &#xA;Acute hyaline membranes are formed. &#xA;Cytokines play a big role in this process. &#xA;To maintain lymph retention, the result of increased venous return compensates. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These patients can breath normally in the sitting position. &#xA;There are also other reasons for the infection:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;overweight - the greater &lt;strong&gt;intra-abdominal pressure&lt;/strong&gt; $\to$ more liquid diffused into the lungs OR other organs are suppressed. &lt;/li&gt;&#xA;&lt;li&gt;Big chest suppresses lungs such that the architecture can change. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Pharmacology&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There are different drugs which effect is dependent on posture and position of the body. &#xA;Hypertension is a common disease which amount increases during ageing in population. &#xA;Let's take hypertensive drugs as a case study. &#xA;Peripherally acting sympathoplegic drugs are generally dependent on posture more than centrally acting ones. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In hypertension treatment, the peripheral acting sympatholegic drugs are used often in combination with diuretics. &#xA;Blood pressure can be under control when blood volume is 95% of normal, but much too high when blood volume is 105% of normal. &#xA;So this study should be considered with no hypertension and hypertension. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sources&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;For Pharmacology, Basic and Clinical Pharmacology, 11th edition, Katzung et all. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-12-26T09:33:29.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19489" PostTypeId="1" CreationDate="2014-07-04T21:40:31.993" Score="2" ViewCount="1533" Body="&lt;p&gt;What is the &lt;em&gt;pBR322 convention&lt;/em&gt;? For example in the description of the pET28a vector we can find information that the sequence is numbered by the pBR322 convention, so the T7 expression region is reversed on the circular map. &lt;/p&gt;&#xA;" OwnerUserId="6892" LastEditorUserId="1320" LastEditDate="2014-07-05T08:05:41.017" LastActivityDate="2014-08-06T04:47:05.577" Title="The pBR322 convention" Tags="&lt;plasmids&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19492" PostTypeId="1" CreationDate="2014-07-05T04:17:39.130" Score="5" ViewCount="2322" Body="&lt;p&gt;I have this  butterfly but I don't know its scientific name. I think that it's a common butterfly which can be seen everywhere (btw, I'm in Taiwan.) Thanks for your help :D&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FLssf.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8226" LastEditorUserId="3624" LastEditDate="2015-04-01T08:35:58.983" LastActivityDate="2015-04-01T08:35:58.983" Title="What is the scientific name of this butterfly?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19493" PostTypeId="2" ParentId="19489" CreationDate="2014-07-05T08:03:45.153" Score="1" Body="&lt;p&gt;pBR322 is a distant ancestor of pET28a. If you compare the two maps below you will see that they have the same &lt;em&gt;replicon&lt;/em&gt; labelled as &lt;em&gt;ori&lt;/em&gt; or pBR322_origin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The map of pBR322 is shown in the conventional orientation: the single EcoRI site is at coordinate 0/4359 and numbering proceeds in a clockwise direction through the BamHI site. The map of pET28a is presented with the pBR322-derived &lt;em&gt;ori&lt;/em&gt; element in the same orientation (note the labelling of a pBRrevBam_primer also). Because of the way that the pET vectors were built, this means that in the conventional depiction the expression region runs counter-clockwise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jabET.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HO8M6.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-07-05T08:03:45.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19494" PostTypeId="1" CreationDate="2014-07-05T12:38:04.727" Score="3" ViewCount="181" Body="&lt;p&gt;It sounds like some kind of crow but not really. Here is my recording: &lt;a href=&quot;https://www.youtube.com/watch?v=4TsKFUugot8&amp;amp;feature=youtu.be#t=06s&quot; rel=&quot;nofollow&quot;&gt;https://www.youtube.com/watch?v=4TsKFUugot8&amp;amp;feature=youtu.be#t=06s&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This bird always wakes me up at 04:00 and this started in late June. I live in a village in Hungary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I really need to know and don't know where to ask.&lt;/p&gt;&#xA;" OwnerUserId="8232" LastEditorUserId="8186" LastEditDate="2014-08-02T05:27:06.703" LastActivityDate="2014-08-17T04:41:29.670" Title="What bird makes this sound?" Tags="&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19495" PostTypeId="1" AcceptedAnswerId="19496" CreationDate="2014-07-05T15:27:33.013" Score="15" ViewCount="1327" Body="&lt;p&gt;How does a woodpecker go about smacking it's head into a tree without killing itself?&lt;/p&gt;&#xA;" OwnerUserId="8200" LastEditorUserId="338" LastEditDate="2014-07-06T05:25:24.867" LastActivityDate="2014-07-06T05:25:24.867" Title="How does a woodpecker not give itself concussions?" Tags="&lt;zoology&gt;&lt;ornithology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19496" PostTypeId="2" ParentId="19495" CreationDate="2014-07-05T16:08:40.773" Score="15" Body="&lt;p&gt;Various features of brain,skull and beak anatomy help to achieve protection.&lt;/p&gt;&#xA;&lt;p&gt;A paper was published in PLoSOne in 2011 on this very topic:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026490&quot; rel=&quot;noreferrer&quot;&gt;Why do woodpeckers resist head impact injury: a biomechanical investigation&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bbc.com/news/science-environment-15458633&quot; rel=&quot;noreferrer&quot;&gt;There is also a very readable summary on the BBC website.&lt;/a&gt; I advise that you read the whole article, but here is a quotation which lists the main findings:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The team's simulations showed that three factors were at work in sparing the birds injury.&lt;/p&gt;&#xA;&lt;p&gt;Firstly, the hyoid bone's looping structure around the whole skull was found to act as a &amp;quot;safety belt&amp;quot;, especially after the initial impact.&lt;/p&gt;&#xA;&lt;p&gt;The team also found that the upper and lower halves of the birds' beaks were uneven, and as force was transmitted from the tip of the beak into the bone, this asymmetry lowered the load that made it as far as the brain.&lt;/p&gt;&#xA;&lt;p&gt;Lastly, plate-like bones with a &amp;quot;spongy&amp;quot; structure at different points in the skull helped distribute the incoming force, thereby protecting the brain.&lt;/p&gt;&#xA;&lt;p&gt;The team stresses that it is the combination of the three, rather than any one feature, that keeps woodpeckers pecking without injury.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-07-05T17:01:05.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19497" PostTypeId="2" ParentId="19495" CreationDate="2014-07-05T16:15:46.367" Score="7" Body="&lt;p&gt;Gibson (2006) identified three characteristics that help woodpeckers avoid brain injury:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;their small size, which reduces the stress on the brain for a given acceleration&lt;/p&gt;&#xA;&lt;p&gt;the short duration of the impact, which increases the tolerable acceleration&lt;/p&gt;&#xA;&lt;p&gt;the orientation of the brain within the skull, which increases the area of contact between the brain and the skull.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Combined with &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026490&quot; rel=&quot;noreferrer&quot;&gt;Wang et al.'s findings&lt;/a&gt;, maybe that makes six features.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-7998.2006.00166.x/abstract&quot; rel=&quot;noreferrer&quot;&gt;Gibson, LJ. 2006. Woodpecker pecking: how woodpeckers avoid brain injury. Journal of Zoology 270: 462-465&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-07-05T16:15:46.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19500" PostTypeId="1" CreationDate="2014-07-05T16:49:23.817" Score="1" ViewCount="977" Body="&lt;p&gt;The plateau phase is maintained by influx of calcium and outflux of potassium in the second stage:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PdORj.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My conjecture&lt;/strong&gt; is that calcium transforms between two phases&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ionated phase (free calcium from i/c SR and e/c Ca-ATPase)&lt;/li&gt;&#xA;&lt;li&gt;non-ionated phase (bound to some proteins).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The initial form can be ionated. &#xA;The process of deionisation occurs only in all-or-nothing cases - I see no evidence that this process can be continuous in my data. &#xA;&lt;strong&gt;My another conjecture&lt;/strong&gt; why this deionisation can occur is because of the vortexes in the diastolic phase of ventricles (T wave; blood bouncing back to the tricuspid valve).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which sources can correspond to this non-ionated calcium more?&lt;/strong&gt; &#xA;My conjecture is e/c Ca more because longer travelling distance and entry involves accelerative movement. &#xA;Actually, this can differ depending on the situation at hand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The accelerative movement can also contribute more to ionisation process so the situation can be reverse in some cases. &#xA;&lt;strong&gt;How is Calcium released from Sarcoplasmic reticulum?&lt;/strong&gt;&#xA;Steadily or in accelerative motion or in a vortex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How are Calcium forms regulated during action potential of myocardial cell plateau phase?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Keywords: Local Ca2+ signaling in health and diseases.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-26T09:20:16.040" LastActivityDate="2019-10-22T17:45:35.060" Title="How is Calcium regulated in myocardic AP and plateau phase?" Tags="&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19501" PostTypeId="1" AcceptedAnswerId="19505" CreationDate="2014-07-05T23:16:22.460" Score="3" ViewCount="222" Body="&lt;p&gt;If I drink tea, then go to sleep for a while, when I wake up, will the effect of tea still be on me (the refreshing effect)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it depend on the duration of sleep?&lt;/p&gt;&#xA;" OwnerUserId="8240" LastEditorUserId="3952" LastEditDate="2014-07-05T23:40:36.600" LastActivityDate="2014-07-06T05:23:06.337" Title="Does tea have its effect if you have a sleep after drinking it?" Tags="&lt;human-biology&gt;&lt;pharmacology&gt;&lt;food&gt;&lt;sleep&gt;&lt;ethnobiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19502" PostTypeId="1" CreationDate="2014-07-06T00:08:47.110" Score="15" ViewCount="27969" Body="&lt;p&gt;&lt;strong&gt;Short:&lt;/strong&gt;&#xA;Thinking in particular of a Royal Python (US: Ball Python) such as some people keep as exotic companion animals, what sorts of &quot;emotions&quot; or &quot;feelings&quot; are they capable of?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long:&lt;/strong&gt; &lt;a href=&quot;http://simonsnakesite.tripod.com/snakebasics.html&quot;&gt;http://simonsnakesite.tripod.com/snakebasics.html&lt;/a&gt; says that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;scientific studies show that snakes just don't have the cerebral capacity for [emotions like joy, anger, and affection] but do have &quot;primitive&quot; feelings like aggression, fear, and pleasure&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Based on the parts of the human brain where we develop emotions, and on the more primitive brain in a snake, this makes sense, but beyond being able to tell whether it's feeling the primitives such as &quot;fear&quot; or &quot;safety&quot;, what &quot;emotions&quot; or &quot;feelings&quot; can we realistically ascribe to a snake?&lt;/p&gt;&#xA;" OwnerUserId="8109" LastEditorUserId="16651" LastEditDate="2015-12-18T02:21:53.130" LastActivityDate="2018-06-20T16:54:03.907" Title="What &quot;emotions&quot; can a snake feel?" Tags="&lt;brain&gt;&lt;behaviour&gt;&lt;reptile&gt;&lt;herpetology&gt;&lt;snake&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19503" PostTypeId="1" AcceptedAnswerId="19504" CreationDate="2014-07-06T00:24:15.343" Score="5" ViewCount="5123" Body="&lt;p&gt;I have found a few dozens of ants in my luggage after arriving back from holiday. Am I at the risk that they will form a colony in my home? Are those ants able to form colonies that are normally gathering food? Will any other kinds of ants be present in the luggage? What will happen to these ants after they start exploring my flat (which is distant from their original colony)?&lt;/p&gt;&#xA;" OwnerUserId="1413" LastActivityDate="2018-04-05T10:58:08.903" Title="Will ants arriving with travel luggage form a new colony?" Tags="&lt;ant&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19504" PostTypeId="2" ParentId="19503" CreationDate="2014-07-06T05:10:45.680" Score="6" Body="&lt;p&gt;An ant colony is started by a queen ant (&lt;a href=&quot;http://www.antnest.co.uk/colony.html&quot;&gt;reference&lt;/a&gt;). Worker ants are sterile, and cannot start a new colony (&lt;a href=&quot;http://researchnews.osu.edu/archive/harvant.htm&quot;&gt;reference&lt;/a&gt;). The ants in your luggage are worker ants (unless you have a colony in there :) ). The original queen ant never leaves her colony, but during a nuptial flight, new queen ants will land in (hopefully) good nesting sites.  (&lt;a href=&quot;http://en.wikipedia.org/wiki/Nuptial_flight&quot;&gt;reference&lt;/a&gt;) These ants can be told by their wings, which are non-existent in worker ants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The worker ants have an average life span of 45-60 days (&lt;a href=&quot;http://lingolex.com/ants.htm&quot;&gt;reference&lt;/a&gt;), so the ants in your luggage won't be around for very long. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also see:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If a worker ant gets separated from its colony, it's doomed. No other colony will take it in, and it can't start its own colony--only queens can do that. It might be able to live for a while, but generally not that long--a lost worker is generally more concerned with hunting for its colony than with feeding itself, and its energy reserves are fairly small (depending on the ant species--some have workers that are adapted to taking long foraging trips). A few ant species, however, have &quot;supercolonies,&quot; where neighboring colonies are established by queens directly related to one another. When queens are close relatives, their workers tend to have similar chemical profiles, meaning they can move from colony to colony without triggering the usual colony defenses against intruders. (Intruders are recognized by their chemical profile--their odor--and not by appearance, ID card, etc.) In such cases, workers routinely transfer between colonies, so a worker may end up working for its grandmother or, forgive me, its aunt. (&lt;a href=&quot;http://www.funtrivia.com/askft/Question118813.html&quot;&gt;From this page&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="338" LastActivityDate="2014-07-06T05:10:45.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19505" PostTypeId="2" ParentId="19501" CreationDate="2014-07-06T05:23:06.337" Score="1" Body="&lt;p&gt;Caffeine is the stimulant in tea. It has different effects on different people, but if you can sleep right after drinking it, it probably isn't strong enough to have long term 'refreshing effects', And yes, the duration of your sleep does matter. If you sleep for 12 hours, much more caffeine will filter out of your blood stream than after a 1 hour nap.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some info on how caffeine works, from &lt;a href=&quot;http://www.nature.com/neuro/journal/v8/n7/abs/nn1491.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Caffeine, a component of tea, coffee and cola, induces wakefulness. It binds to adenosine A1 and A2A receptors as an antagonist, but the receptor subtype mediating caffeine-induced wakefulness remains unclear. Here we report that caffeine at 5, 10 and 15 mg kg-1 increased wakefulness in both wild-type mice and A1 receptor knockout mice, but not in A2A receptor knockout mice. Thus, caffeine-induced wakefulness depends on adenosine A2A receptors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="338" LastActivityDate="2014-07-06T05:23:06.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19507" PostTypeId="1" CreationDate="2014-07-06T09:18:30.620" Score="1" ViewCount="193" Body="&lt;p&gt;After a long time of hard workout,not eating and nervousness makes your taste and scent of mouth very uncomfortable and bad why this happens and is there any way to prevent it? &lt;/p&gt;&#xA;" OwnerUserId="5700" LastActivityDate="2014-12-01T01:44:02.770" Title="Why the scent of mouth gets dirty after not eating for a long time?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19508" PostTypeId="1" AcceptedAnswerId="19511" CreationDate="2014-07-06T09:39:10.660" Score="12" ViewCount="3692" Body="&lt;p&gt;I have observed that frequently when people are hungry; they tend to get angry more easily on pointless issues. Does this mean that our fight or flight response is more active when a person is hungry? What is a possible reason for this? Is this phenomenon linked with our cell signaling pathways? If it is, then what would be the pathway that leads to the aggressive behavior?&#xA;&lt;p&gt;&#xA;To summarize the question: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;When a person is hungry and they get angry, is it due to a cell signaling pathway? If so, what pathway?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5729" LastEditorDisplayName="user24284" LastEditDate="2017-05-29T01:49:30.910" LastActivityDate="2017-05-29T01:49:30.910" Title="Why does Hunger lead to the aggressive behavior?" Tags="&lt;biochemistry&gt;&lt;ethology&gt;&lt;cell-signaling&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19509" PostTypeId="2" ParentId="19397" CreationDate="2014-07-06T15:17:24.353" Score="1" Body="&lt;p&gt;Could not fit in a comment…&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What kind of observations will you accept to be an observation? If we can demonstrate showing genetic data that two current species where actually only one some time in the past would it represent an observation to you? Or does it has to be a lab experiment (experimental evolution)? Experimental evolution with big animals take much time, I am afraid we probably have no evidence (not counter-evidence) of a mammal species that evolve to be phenotypically speaking as different than a fruit fly and a june bug (example coming from your comment). Would you accept considering microorganisms (I have no example in head though right now)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you noted yourself I think, it is difficult to know how different (phenotypically or genetically?) should two sister populations (populations who derived from a common ancestral population) be so that you would consider that one of these populations at least evolved into another &quot;kind&quot; (compare to the ancestral population). &lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-07-06T15:17:24.353" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19511" PostTypeId="2" ParentId="19508" CreationDate="2014-07-06T18:41:04.270" Score="8" Body="&lt;p&gt;Brain's main energy source is glucose. It uses about 20% of total glucose [1]. Brain hypoglycemia causes depressive-like behaviors in mice through adrenergic pathways [2].&lt;/p&gt;&#xA;&lt;p&gt;When it comes to humans, here is a study that claims low glucose leads to increased aggression in married couples (see &lt;a href=&quot;http://o.canada.com/health/hunger-in-the-form-of-low-blood-sugar-leads-to-greater-aggression-and-anger-in-married-couples-study-finds&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; too):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Self-control requires energy, part of which is provided by glucose. For 21 days, glucose levels were measured in 107 married couples. To measure aggressive impulses, each evening participants stuck between 0 and 51 pins into a voodoo doll that represented their spouse, depending how angry they were with their spouse. ... As expected, the lower the level of glucose in the blood, the greater number of pins participants stuck into the voodoo doll, and the higher intensity and longer duration of noise participants set for their spouse [3].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However, the conclusion is disputed:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Bushman et al.'s study does not demonstrate that fluctuations in blood glucose affect individuals' self-control abilities. As an important consequence, there is no reason to assume that giving couples a sugary “boost to their self-control energy” (p. 3) will reduce intimate partner violence. Because the glucose model of self-control lacks empirical foundation, it does not qualify as a framework for scientifically based intervention strategies [4].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;What is sure, is that hypoglycemia activates sympathetic nervous system:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;... the neurogenic symptoms of hypoglycemia are largely the result of sympathetic neural, rather than adrenomedullary, activation [5].&lt;/p&gt;&#xA;&lt;p&gt;Hypoglycemia increases plasma levels of both epinephrine and norepinephrine. These catechols are released primarily from the adrenal medulla. However, it is well documented that hypoglycemic increases muscle sympathetic nerve activity, and that both alpha and beta adrenergic activity increase [6].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;And this leads to behavioral changes (at least in animals):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Noradrenaline is involved in many different functions, which all are known to affect behaviour profoundly. ... Part of these effects may arise in indirect ways that are by no means specific to aggressive behaviour, however, they are functionally relevant to it. Other effects may affect brain mechanisms specifically involved in aggression. Hormonal catecholamines (adrenaline and noradrenaline) appear to be involved in metabolic preparations for the prospective fight; the sympathetic system ensures appropriate cardiovascular reaction, while the CNS noradrenergic system prepares the animal for the prospective fight. ... It appears that neurons bearing postsynaptic alpha2-adrenoceptors are responsible for the start and maintenance of aggression, while a situation-dependent fine-tuning is realised through neurons equipped with beta-adrenoceptors [7].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &amp;quot;Human brain,&amp;quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Human_brain&amp;amp;oldid=615456836&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Human_brain&amp;amp;oldid=615456836&lt;/a&gt; (accessed July 6, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Park MJ, Yoo SW, Choe BS, Dantzer R, Freund GG. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21820138&quot; rel=&quot;noreferrer&quot;&gt;Acute hypoglycemia causes depressive-like behaviors in mice.&lt;/a&gt; Metab. Clin. Exp. 2012 Feb;61(2):229-36. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.metabol.2011.06.013&quot; rel=&quot;noreferrer&quot;&gt;10.1016/j.metabol.2011.06.013&lt;/a&gt;. PubMed PMID: 21820138.&lt;/li&gt;&#xA;&lt;li&gt;Bushman BJ, Dewall CN, Pond RS, Hanus MD. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24733932&quot; rel=&quot;noreferrer&quot;&gt;Low glucose relates to greater aggression in married couples.&lt;/a&gt; Proc. Natl. Acad. Sci. U.S.A. 2014 Apr 29;111(17):6254-7. doi: &lt;a href=&quot;http://dx.doi.org/10.1073/pnas.1400619111&quot; rel=&quot;noreferrer&quot;&gt;10.1073/pnas.1400619111&lt;/a&gt;. PubMed PMID: 24733932.&lt;/li&gt;&#xA;&lt;li&gt;Lange F and Kurzban R (2014) Sugar levels relate to aggression in couples without supporting the glucose model of self-control. Front. Psychol. 5:572. doi: 10.3389/fpsyg.2014.00572&lt;/li&gt;&#xA;&lt;li&gt;DeRosa MA, Cryer PE. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14970007&quot; rel=&quot;noreferrer&quot;&gt;Hypoglycemia and the sympathoadrenal system: neurogenic symptoms are largely the result of sympathetic neural, rather than adrenomedullary, activation.&lt;/a&gt; Am. J. Physiol. Endocrinol. Metab. 2004 Jul;287(1):E32-41. doi: &lt;a href=&quot;http://dx.doi.org/10.1152/ajpendo.00539.2003&quot; rel=&quot;noreferrer&quot;&gt;10.1152/ajpendo.00539.2003&lt;/a&gt;. PubMed PMID: 14970007.&lt;/li&gt;&#xA;&lt;li&gt;Hoffman RP. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18220670&quot; rel=&quot;noreferrer&quot;&gt;Sympathetic mechanisms of hypoglycemic counterregulation.&lt;/a&gt; Curr Diabetes Rev. 2007 Aug;3(3):185-93. PubMed PMID: 18220670.&lt;/li&gt;&#xA;&lt;li&gt;Haller J, Makara GB, Kruk MR. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9491941&quot; rel=&quot;noreferrer&quot;&gt;Catecholaminergic involvement in the control of aggression: hormones, the peripheral sympathetic, and central noradrenergic systems.&lt;/a&gt; Neurosci Biobehav Rev. 1998;22(1):85-97. PubMed PMID: 9491941.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-07-09T19:57:01.377" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19513" PostTypeId="1" AcceptedAnswerId="19518" CreationDate="2014-07-06T21:03:41.650" Score="4" ViewCount="10201" Body="&lt;p&gt;A classic tip to revive wilted cut flowers is to plunge the stem into boiling water for some period of time, and then back into cold water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What process is occurring that causes the flower to be &quot;revived&quot;?&lt;/p&gt;&#xA;" OwnerUserId="8251" LastActivityDate="2014-07-07T11:27:03.387" Title="How does boiling water revive cut flowers?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19514" PostTypeId="1" AcceptedAnswerId="19520" CreationDate="2014-07-07T02:21:14.543" Score="4" ViewCount="1535" Body="&lt;p&gt;It is said that the stonefish (Synanceia) is able to stay out of the water for up to 24 hours. I wonder how they get oxygen from the air. Could someone explain this?&lt;/p&gt;&#xA;" OwnerUserId="8253" LastActivityDate="2014-07-07T12:44:34.610" Title="How does a stonefish get oxygen out of water?" Tags="&lt;ichthyology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19515" PostTypeId="1" AcceptedAnswerId="19889" CreationDate="2014-07-07T03:29:42.883" Score="5" ViewCount="796" Body="&lt;p&gt;A steroid, testosterone was injected in female body which led to development of secondary sexual characters but these characters were not developed over night (Response was very slow). What could be possible explanation of this phenomenon&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;a Steroid hormones produce a slow response because they do not have secondary messenger   &lt;/li&gt;&#xA;&lt;li&gt;Slow response is due to lack of cell membrane receptors and amplification enzymes&lt;/li&gt;&#xA;&lt;li&gt;Movement of this hormone is very slow in blood&lt;/li&gt;&#xA;&lt;li&gt;None of the above&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I think option 3 is correct because steroid hormones are hydrophobic in nature and cant be transported in the blood without the help of any carrier protein so this may be the reason but I am not sure about this.. &lt;/p&gt;&#xA;" OwnerUserId="5729" LastEditorUserId="69" LastEditDate="2014-07-08T18:27:41.380" LastActivityDate="2014-07-24T05:35:08.133" Title="Effect of testosterone hormone on cell signalling and behaviour?" Tags="&lt;biochemistry&gt;&lt;cell-signaling&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19517" PostTypeId="2" ParentId="19514" CreationDate="2014-07-07T10:15:27.980" Score="2" Body="&lt;p&gt;I have been trying to find an answer to this question, but until now, no one seems to have really analyzed why this is possible. The only hint I found comes from this paper:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.publish.csiro.au/paper/MF9610177.htm&quot; rel=&quot;nofollow&quot;&gt;A study of the distribution, habitat, behaviour, venom apparatus and&#xA;venom of the stonefish.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;They state:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At periods of low water, stone-fish are often left partially exposed&#xA;  by the retreating tide. At such times they may be surrounded only by a&#xA;  small quantity of water which fills the depression in which each lies&#xA;  and the main mass of water may be a considerable distance away. They&#xA;  can survive long periods (at least 24 hours) out of water providing&#xA;  their surroundings are kept moist.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Obviously the fish only needs minimal moisture to get enough oxygen. I would further speculate that the fish turns down its metabolism during this time to minimize the need for oxygen. This paper is widely cited as a source for this survival time, but there seems to be no follow up on it. What is widely analyzed is the toxin of the stonefish.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-07T10:15:27.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19518" PostTypeId="2" ParentId="19513" CreationDate="2014-07-07T11:27:03.387" Score="2" Body="&lt;p&gt;I could not find any scientific papers that have done research into this phenomenon but the general reason given for wilted flowers to being resuscitated is given as the hot water being absorbed faster and I quote&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Florists use warm water only for resuscitating wilted flowers, because&#xA;  warm water is absorbed quickly. For restoring wilted stems, hot water&#xA;  (110 degrees Fahrenheit) is recommended. For woody or badly wilted&#xA;  stems, very hot water (180 to 200 degrees) is better. Florists then&#xA;  move them into a refrigerator (&lt;a href=&quot;http://www.nytimes.com/2003/08/03/nyregion/cuttings-cold-water-plunge-perks-up-cut-flowers.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The reason for absorbtion faster is given as &lt;/p&gt;&#xA;&#xA;&lt;p&gt;luke warm water in a vase arrangement because warm water is “thinner” (has fewer air&#xA;bubbles) and moves up the stem faster than cold water (&lt;a href=&quot;http://www.ramseyadagency.com/how-to-booklets/read-booklets/cut-flowers/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) and Warm water molecules move faster than cold water molecules and so can be absorbed by flowers with greater ease (&lt;a href=&quot;http://www.bbg.org/gardening/article/cut-flower_care&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-07-07T11:27:03.387" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19519" PostTypeId="1" AcceptedAnswerId="19521" CreationDate="2014-07-07T12:27:31.413" Score="2" ViewCount="566" Body="&lt;p&gt;In my book are given several paired analogies with me being asked to give reason for them. I could solve all of them except this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;liver = thrifty house-keeper&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I mean, I do not understand why the liver is being called so. The functions of liver haven't been taught yet (so this is kind of out-of-course), but still, I thought I should ask it as the functions are not given anywhere in the entire book.&lt;/p&gt;&#xA;" OwnerUserId="8257" LastEditorUserId="6703" LastEditDate="2014-07-07T17:44:47.447" LastActivityDate="2014-07-07T17:44:47.447" Title="Biology Analogy" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;liver&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19520" PostTypeId="2" ParentId="19514" CreationDate="2014-07-07T12:34:16.487" Score="2" Body="&lt;p&gt;Two things to add the the answer from @Chris.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We are used to the idea that fish extract oxygen from water using gills. When such a fish is transferred into air we imagine that it can no longer breathe. However fish do in fact obtain a significant proportion of their oxygen through their skin. Furthermore, as long as the gills remain moist it should be possible to obtain some oxygen by direct diffusion from the air into the layer of water surrounding the gills.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Rombough PJ (1998) Partitioning of oxygen uptake between the gills and skin in fish larvae: a novel method for estimating cutaneous oxygen uptake. J Expt. Biol. 201: 1763 - 1769&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Adults of water-breathing fish typically obtain 10–20 % of their oxygen across the skin, but values as high as 30 % have been reported (Feder and Burggren, 1985).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The cited paper is: Feder, M.E. and Burggren WW (1985) Cutaneous gas exchange in vertebrates: design, patterns, control and implications. Biol. Rev. 60: 1-45. Table 1 of this paper presents measurements for the contribution of cutaneous respiration for a number of species including, for example, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Pleuronectes_platessa&quot; rel=&quot;nofollow&quot;&gt;European plaice (&lt;em&gt;Pleuronectes platessa&lt;/em&gt;)&lt;/a&gt; which apparently can obtain 27 % of its oxygen through its skin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are, of course many fish, which are designated as air-breathing e.g. the &lt;a href=&quot;http://en.wikipedia.org/wiki/Anguilla_vulgaris&quot; rel=&quot;nofollow&quot;&gt;European eel (&lt;em&gt;Anguilla vulgaris&lt;/em&gt;)&lt;/a&gt;. Table 2 of Feder &amp;amp; Burggren presents data acomparing the contribution of skin and gills for various air-breathing fish in water and in air. In the eel this goes from (skin/gills) 12%/88% in water to 33%/67% in air at 15 &amp;deg;C.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know if stone-fish are designated as 'air-breathing' but it is clear that as long as they are in a moist environment many fish can obtain significant amounts of oxygen from the surrounding air. @Chris suggests that the fish may &quot;turn down their metabolism&quot; under these circumstances. The very fact that the fish is no longer swimming presumably reduces oxygen requirement considerably.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-07-07T12:44:34.610" LastActivityDate="2014-07-07T12:44:34.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19521" PostTypeId="2" ParentId="19519" CreationDate="2014-07-07T13:16:33.057" Score="4" Body="&lt;p&gt;The liver does quite a lot of &quot;housekeeping&quot;. It is responsible for a lot of energy metabolism: &lt;a href=&quot;http://en.wikipedia.org/wiki/Gluconeogenesis&quot; rel=&quot;nofollow&quot;&gt;Gluconeogenesis&lt;/a&gt; (the synthesis of glucose), &lt;a href=&quot;http://en.wikipedia.org/wiki/Glycogenolysis&quot; rel=&quot;nofollow&quot;&gt;Glycogenolysis&lt;/a&gt; (the breakdown of glycogen into glucose), &lt;a href=&quot;http://en.wikipedia.org/wiki/Glycogenesis&quot; rel=&quot;nofollow&quot;&gt;Glycogenesis&lt;/a&gt; (the synthesis of glycogen from glucose).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important for protein degradation as well as for &lt;a href=&quot;http://en.wikipedia.org/wiki/Amino_acid_synthesis&quot; rel=&quot;nofollow&quot;&gt;amino acid synthesis&lt;/a&gt;, as well as in the lipid metabolism. This includes synthesis of cholesterols, lipoproteins and fatty acids. The liver produces a number of factors important for coagulation including prothrombin and a number of hormones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is very important for the breakdown of Bilirubin and insulin, and it detoxifies the body via the cytochrome P450 system. It is storing some substances as vitamin A, B12, D and K as well as iron and important for their regulation. For more details read the corresponding Wikipedia article on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Liver&quot; rel=&quot;nofollow&quot;&gt;liver&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So easy speaking does the liver a lot of maintenance in the human body which is important for a lot of different processes.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-07T13:16:33.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19522" PostTypeId="1" CreationDate="2014-07-07T14:38:05.693" Score="3" ViewCount="607" Body="&lt;p&gt;I'm working on a genome project and using an &lt;em&gt;in silico&lt;/em&gt; &lt;em&gt;k&lt;/em&gt;-mer analysis to estimate the size of our genome based on the available Illumina reads. The &lt;em&gt;k&lt;/em&gt;-mer based estimate is consistent across a wide range of &lt;em&gt;k&lt;/em&gt; values, but is substantially lower than the previous estimate based on flow cytometry (described in &lt;em&gt;Experimental procedures&lt;/em&gt; of &lt;a href=&quot;http://dx.doi.org/10.1111/j.0962-1075.2004.00514.x&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;). How accurate are estimations of genome size based on flow cytometry?&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="43" LastEditDate="2014-07-07T16:03:46.893" LastActivityDate="2014-07-07T16:03:46.893" Title="Accuracy of genome size estimation by flow cytometry" Tags="&lt;bioinformatics&gt;&lt;genomes&gt;&lt;flow-cytometry&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19523" PostTypeId="1" CreationDate="2014-07-07T19:44:06.243" Score="1" ViewCount="23" Body="&lt;p&gt;I did myocardial infarction experiments on mice and I am a newbie in this area. I need to isolate RNA and protein from the remote and the border zone. Where should I cut the heart so i can separate the infarct zone, border, and the remote zone? Can anybody help me with this?&lt;/p&gt;&#xA;" OwnerUserId="8259" LastActivityDate="2014-07-07T19:44:06.243" Title="border zone of the infarcted heart" Tags="&lt;molecular-biology&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19524" PostTypeId="1" CreationDate="2014-07-07T21:01:18.580" Score="2" ViewCount="86" Body="&lt;p&gt;There is strong evidence that chromosome 2 in humans is a fusion of two chimp chromosomes (i.e. common ancestor of chimps and humans) as explained at wikipedia &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosome_2_%28human%29&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is what are the odds of a similar event occuring at random in newborns?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read conflicting reports, some say these things happen in about 1 out of a 1000 live births, while others placed the odds at somewhere around 1 in 7 billion.&lt;/p&gt;&#xA;" OwnerUserId="6202" LastEditorUserId="6202" LastEditDate="2014-07-08T06:04:44.053" LastActivityDate="2014-07-08T06:04:44.053" Title="Odds of Fusion of Chromosome #2" Tags="&lt;evolution&gt;&lt;molecular-evolution&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19525" PostTypeId="1" AcceptedAnswerId="20275" CreationDate="2014-07-08T00:03:59.970" Score="4" ViewCount="4347" Body="&lt;p&gt;I recently attended an awake brain surgery  for deep brain stimulation and it seemed to me that only the skin surrounding the drilled hole got local anaesthesia. I know that the brain itself does not have nociceptors, but what about the skull? And how does this compare to other bones in the body? Would you feel a hole being drilled in your skull? Would you feel your leg being chopped off if the surrounding tissue was numbed? &lt;/p&gt;&#xA;" OwnerUserId="8260" LastActivityDate="2014-08-09T17:54:50.210" Title="Do skull bones have pain nerves (nociceptors)?" Tags="&lt;neuroscience&gt;&lt;bone-biology&gt;&lt;central-nervous-system&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19526" PostTypeId="1" CreationDate="2014-07-08T04:34:40.693" Score="2" ViewCount="74" Body="&lt;p&gt;I am not completely familiar with biology, but i had a genetics course in college along with practicals. Forgive me if there is something wrong with my question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a genetic disease which results in partially functioning or complete non functioning of genes resulting in little or no production of protein for eg Muscular dystrophy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so why can't we supply these protein from outside the way we do in the case of diabetes(insulin)?&lt;/p&gt;&#xA;" OwnerUserId="8261" LastEditorUserId="5762" LastEditDate="2014-07-08T05:10:56.260" LastActivityDate="2014-11-15T04:30:33.333" Title="regarding genetic disorders related to protein production" Tags="&lt;genetics&gt;&lt;pathology&gt;&lt;gene-expression&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19527" PostTypeId="2" ParentId="19526" CreationDate="2014-07-08T06:18:43.377" Score="2" Body="&lt;p&gt;There are many protein deficiency issues caused by genetic mutation for eg: Protein C whose deficiency causes abnormal blood clots. This protein is controlled by the PROC gene whose mutation causes Type I Protein C deficiency (&lt;a href=&quot;http://ghr.nlm.nih.gov/condition/protein-c-deficiency&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are treatments of replacing proteins like in the case of Protein C deficiency, protein C concentrates are used (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2721356/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). In the case of Alpha-1-antitrypsin (AAT) deficiency, augmentation is done with weekly intravenous infusion of the AAT protein (&lt;a href=&quot;http://copd.about.com/od/aatdeficiency/a/Treatment-Of-Alpha-1-Antitrysin-Aat-Deficiency.htm&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in many cases protein is actually supplied from outside the body and also many protein deficiency conditions can actually be controlled with balanced diets (&lt;a href=&quot;http://lifespa.com/protein-deficiency-the-hidden-signs/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) which unfortunately is not a solution for insulin deficiency. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-07-08T06:18:43.377" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19528" PostTypeId="2" ParentId="19146" CreationDate="2014-07-08T09:59:29.083" Score="2" Body="&lt;p&gt;Depends if your talking about interstitial fluid or lymph:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As per starling forces: the oncotic pressure of the late capillary plus hydrostatic pressure of interstitial space, would be higher than oncotic pressure of interstitium [though I dunno why since intertitial GAGs are very water hungry and they are responsible for the negative (hydrostatic?) pressures found in interstitium... Read lots of articles, still makes no sense to me] and hydrostatic pressure of the capillary... Thus there would be a net influx of interstitial fluid in the very ending part of the capillary, toward the venous side...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I say interstitial fluid, because it's not lymph yet since the interstitial fluid hasn't yet entered the adjacent lymph capillaries... if the interstitial fluid entered the lymph capillary then it would be stuck there, the mechanism of this one way flow is the junctions between the endothelial cells in these blind ended lymph capillary... These junctions which only opens up gaps between these endothelial cells when the interstitial pressure outside the lymph capillaries is higher than pressure inside the lymph capillaries... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lymph then goes forward through lymphatic vessels/nodes because external pressure (pulsing of adjacent artery, contraction of adjacent skeletal muscle, changes in thoracic pressuring during breathing, etc) and there is little back flow because of valves (just like venous valves which prevent back flow in the low pressure venous system)... Ultimately the lymph returns by either thoracic duct (in the angle between left subclavian and left jugular vein) or right lymphatic duct  (in the angle between right subclavian and right jugular vein)...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some sweet review articles from University of Bergen, Norway that go much more in depth on the physiology of interstitial fluid...&#xA;Here is one of their more recent review articles:&#xA;&lt;a href=&quot;http://m.physrev.physiology.org/content/92/3/1005&quot; rel=&quot;nofollow&quot;&gt;http://m.physrev.physiology.org/content/92/3/1005&lt;/a&gt; it's free&lt;/p&gt;&#xA;&#xA;&lt;p&gt;IN SUMMARY: the starling forces bring interstitial fluid into the blood (the &quot;peripheral part&quot; right after the capillary)... The thoracic and right lymphatic duct drain lymph into the blood (I'm assuming this does not apply by your definition of peripheral, since this venous blood is about to be drained into the right atrium and is destined for the lungs)...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. aqueous humor (in the eye), endolymph (cochlea aka inner ear) and CSF are also absorbed back into the blood... Also the brain has an interstitial fluid that is different from the CSF found in the subarachnoid spce of the meninges, i actually don't know how that drains... But anyway, the head is so special, I'm sure you weren't wondering about these specifics...&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2014-07-08T11:25:19.440" LastActivityDate="2014-07-08T11:25:19.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19529" PostTypeId="2" ParentId="19457" CreationDate="2014-07-08T12:18:10.690" Score="0" Body="&lt;p&gt;Recently i came across this text file which has Kingdom,Phylum etc.              &lt;a href=&quot;https://app.box.com/s/hsmvie7vgjdj1z3g0iuf&quot; rel=&quot;nofollow&quot;&gt;https://app.box.com/s/hsmvie7vgjdj1z3g0iuf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8135" LastActivityDate="2014-07-08T12:18:10.690" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19531" PostTypeId="1" CreationDate="2014-07-08T14:53:31.807" Score="1" ViewCount="54" Body="&lt;p&gt;Let's say I have two fragments of bacterial DNA (~50kb in length each) that overlap on the ends by roughly ~10kb; the overlap sequences are unknown. I would like to assemble these into longer fragments (in vitro) in some way, but the methods I've found so far rely on 24-40bp known overlaps (e.g., the isothermal assembly process in DG Gibson et al., Nature Communications 2009). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyone have any idea? I'm kind of new to this molecular biology stuff, so if this is an open problem, I apologize. I'm mainly just making sure I'm not overlooking something obvious. For all I know, there could be a standard protocol for this. Thanks in advance!&lt;/p&gt;&#xA;" OwnerUserId="6662" LastEditorUserId="6662" LastEditDate="2014-07-08T14:58:46.863" LastActivityDate="2014-07-08T14:58:46.863" Title="Assembling DNA fragments with ~10kb overlap in vitro" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;synthetic-biology&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19532" PostTypeId="1" CreationDate="2014-07-08T15:26:03.783" Score="3" ViewCount="120" Body="&lt;p&gt;Pretend that somehow in a laboratory two definitive ovums (finished 2nd miotic divisions) are&#xA;are fused together. Will they form a new species?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="5144" LastEditDate="2014-07-08T16:01:26.820" LastActivityDate="2014-07-08T16:44:58.597" Title="If two definitive ovums are fused will they form an organism?" Tags="&lt;embryology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19533" PostTypeId="1" AcceptedAnswerId="19719" CreationDate="2014-07-08T16:12:12.673" Score="3" ViewCount="316" Body="&lt;p&gt;Is there a website or other resource that catalogs all fossils ever found? Basically, is there a literal &quot;Fossil Record&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where do scientists gather their results from excavations? Are they just scattered in various peer-reviewed papers in science journals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm imagining something like manuscripts and master texts. You have some researchers who analyze manuscripts to produce the text of that manuscript in electronic form, for instance. Then, other researchers take these various readings and assemble a master text, taking into account the variations and attempting to recover the original work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By analogy, this would be like when a paleontologist at a dig site submits a paper about his/her findings to a science journal. Is there another group of scientists who look at all of these papers and compile a &quot;master text&quot; of the fossil record?&lt;/p&gt;&#xA;" OwnerUserId="866" LastEditorUserId="866" LastEditDate="2014-07-08T16:21:27.153" LastActivityDate="2014-07-16T16:49:52.210" Title="Master Catalog of all Fossils / Literal Fossil Record?" Tags="&lt;palaeontology&gt;&lt;research-tools&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19534" PostTypeId="2" ParentId="19532" CreationDate="2014-07-08T16:44:58.597" Score="4" Body="&lt;p&gt;No, it is not possible. The reason is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_imprinting&quot; rel=&quot;nofollow&quot;&gt;genetic imprinting&lt;/a&gt;, which takes place on the parental DNA in the egg and the sperm. Here small modifications are added to the DNA which marks them as silenced. So some genes are expressed from the mother (while the fathers copy is not expressed) and vice versa.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are even genetic diseases which are caused by imprinting. One example is the loss of a gene region on chromosome 15. Depending in which copy its lost, either the &lt;a href=&quot;http://en.wikipedia.org/wiki/Prader-Willi_syndrome&quot; rel=&quot;nofollow&quot;&gt;Prader-Willi Syndrome&lt;/a&gt; or the &lt;a href=&quot;http://en.wikipedia.org/wiki/Angelman_syndrome&quot; rel=&quot;nofollow&quot;&gt;Angelman Syndrome&lt;/a&gt; occur. PWS is inherited via the father, Angelman via the mother. Another interesting article on imprinting can be found &lt;a href=&quot;http://genetics.thetech.org/ask-a-geneticist/imprinting&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you combine two eggs, some genes, which are not imprinted in the father, will not be expressed in the developing embryo which will finally lead to death of it. However, researcher deleted the maternal imprinting in mice and mimicked the from the father and made off-springs from two mothers possible. This is something which is ethically very problematic in humans. The article can be found here: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v428/n6985/full/nature02402.html&quot; rel=&quot;nofollow&quot;&gt;Birth of parthenogenetic mice that can develop to adulthood&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-08T16:44:58.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19535" PostTypeId="1" CreationDate="2014-07-08T18:12:38.283" Score="1" ViewCount="433" Body="&lt;p&gt;Does it mean the position of the amino acid in the protein sequence, or something else?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, I came across the phrase &quot;S 368 phosphoryation&quot; where S is the modified residue and 368 is the modified residue position. What does it all mean?&lt;/p&gt;&#xA;" OwnerUserId="3474" LastEditorUserId="69" LastEditDate="2014-07-08T18:29:41.637" LastActivityDate="2014-07-08T18:36:19.053" Title="What does the term 'modified residue position' in phosphorylation mean?" Tags="&lt;proteins&gt;&lt;terminology&gt;&lt;amino-acids&gt;&lt;phosphorylation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19536" PostTypeId="2" ParentId="19535" CreationDate="2014-07-08T18:36:19.053" Score="3" Body="&lt;p&gt;You are correct, the &lt;code&gt;368&lt;/code&gt; stands for the position of the amino acid in the protein's sequence - this particular serine is the 368th residue in the protein counting from the amino-terminal end.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-07-08T18:36:19.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19537" PostTypeId="1" AcceptedAnswerId="19539" CreationDate="2014-07-08T18:43:15.450" Score="3" ViewCount="1414" Body="&lt;p&gt;Has anyone isolated plasmid DNA from frozen (at -20degrees) E. coli cell cultures (not pellets)? Has that worked and if so, with what yields? What would be the quality of the isolated plasmid DNA if run on a gel? Would most of it be degraded or intact?&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2014-07-08T19:34:51.807" Title="Efficiency of plasmid DNA isolation from frozen E. coli cell cultures" Tags="&lt;molecular-biology&gt;&lt;transformation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19538" PostTypeId="1" AcceptedAnswerId="19543" CreationDate="2014-07-08T19:03:44.830" Score="1" ViewCount="93" Body="&lt;p&gt;I was having a look at a &lt;a href=&quot;http://en.wikipedia.org/wiki/Rhizophora&quot; rel=&quot;nofollow noreferrer&quot;&gt;rhizophora&lt;/a&gt; plant (from the mangrove family), and I got curious about its inflorescence. I can't make out what kind of inflorescence it is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a photo of the inflorescence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kWzMx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know which kind of inflorescence it is?&lt;/p&gt;&#xA;" OwnerUserId="8101" LastEditorUserId="338" LastEditDate="2014-07-08T22:57:10.750" LastActivityDate="2014-07-08T22:57:10.750" Title="What is the name of this type of inflorescence?" Tags="&lt;botany&gt;&lt;reproduction&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19539" PostTypeId="2" ParentId="19537" CreationDate="2014-07-08T19:34:51.807" Score="4" Body="&lt;p&gt;I have done that and it works without any problems. We harvested the cultures at the optimal timepoint (density) and then froze them to do maxipreps later on. Therefore we simply thawed the culture, made sure it didn't got too warm (meaning we worked on ice) and then simply followed the maxiprep protocol. No problems with yield or quality of the plasmide. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I will do next time is to spin down the culture and take it up in max. 50 ml of medium before freezing. This way freezing will be faster as well as thawing. I have also done minipreps from stock cultures (glycerol stocks of plasmids in E.coli) which accidentally stayed out of the freezer for two days. Here the yields where not so great (but the density of the culture was also much lower), but the quality after standard miniprep was good and the plasmids worked both for subsequent cloning as well as for retransformation to make new stocks. &lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-08T19:34:51.807" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19540" PostTypeId="1" AcceptedAnswerId="19555" CreationDate="2014-07-08T19:51:11.987" Score="7" ViewCount="1885" Body="&lt;p&gt;does the order of genes within a chromosome matter? or is the main thing that the genes are there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so for example, our DNA is very similar to that of apes not only by the genes themselves but also by the arrangement of those genes in the chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;is the order of this arrangement significant? Or if it were shuffled around, then the functional impact would be more or less the same?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example, an &lt;a href=&quot;http://www.genome.gov/page.cfm?pageID=10005831&quot; rel=&quot;nofollow noreferrer&quot;&gt;international study&lt;/a&gt; in the mouse genome has revealed that virtually all mouse genes have direct counterparts in humans, i.e. humans and mice contain virtually the same set of genes. is the difference between humans and mice due primarily to the different order of the genes or to the slight differences in the genes themselves?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question was raised from a claim &lt;a href=&quot;https://biology.stackexchange.com/a/5568/6202&quot;&gt;here&lt;/a&gt; which seems to imply it does not matter.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The chances are infinitesimal that human chr 2 were to resemble those&#xA;  of other primates at random. This is what you say in science when you&#xA;  mean 'impossible'. One simply doesn't see a segment of DNA the size of&#xA;  Chr 2A and 2B being so similar for such a length when we look at rats,&#xA;  dogs, worms or any more distantly related living thing.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6202" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-07-09T16:29:05.267" Title="does order of genes in a chromosome matter?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19541" PostTypeId="2" ParentId="19540" CreationDate="2014-07-08T20:04:49.770" Score="4" Body="&lt;p&gt;Ye, the order matters. This can be seen in chromosomal translocations which can cause cancer.&#xA;A example for that would be the translocation of IRF4 which happens in a subtype of multiple myeloma. The translocation is permanently activating the transcription factor. See here for details: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21487109&quot; rel=&quot;nofollow noreferrer&quot;&gt;Translocations activating IRF4 identify a subtype of germinal&#xA;center-derived B-cell lymphoma affecting predominantly children and&#xA;young adults.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The main reason for this is the regulation of the genes - when the order is changed, the regulatory elements which are important for regulating the expression are missing. A lot of these regulatory elements are located many kB away from the gene and are still important for its activation or silencing.&#xA;This can look like the image below (image from &lt;a href=&quot;http://pbil.univ-lyon1.fr/members/sagot/htdocs/team/projects/chromo_net/purpose_chromo_net.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kOGzE.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the mouse question: On which chromosome a gene is located is not really important if you compare different species. The gene I worked on for a while is functionally equivalent between mouse and human (the human version works perfectly in mouse), but they are located on different chromosomes. It again comes down to different regulation and in some cases also a different amino acid sequence. Also mice (as other animals as well) have quite a number of genes which are unique for them and which make a difference between the two species. There are a few interesting papers on that topic:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000112&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lineage-Specific Biology Revealed by a Finished Genome Assembly of&#xA;the Mouse&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://hmg.oxfordjournals.org/content/12/7/701.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Comparison of the genomes of human and mouse lays the foundation of&#xA;genome zoology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-07-08T20:24:08.070" LastActivityDate="2014-07-08T20:24:08.070" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19542" PostTypeId="2" ParentId="9297" CreationDate="2014-07-08T22:37:32.253" Score="-1" Body="&lt;p&gt;To the answer above:  &quot;I am the being in the mirror&quot;, one has to ask themselves:  Is it so strange that a cat seeing it's own paw in front of it and recognizing it as it's his OWN, and not chasing it's own tail because it knows it's his and he's not a kitten anymore?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how much different is that when they come to understand, especially after you hold the cat several times in front of the mirror with you, making the association and he's no longer weirded out?  Many cats making this transition look in curiosity and awe and move on, never really caring that much about it -- much like kids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bring a cat into a bathroom with a mirrored wall behind the sinks, when he's dealing with something where the mirror is in his line of sight.  Walk in behind.  When the cat turns around to look at you to play instantly, instead of trying to play with the mirror -- it recognizes that it shows whats behind him.  I have observed this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a cat recognizing it's own tail out of it's &quot;perif&quot; is nothing special, neither is recognizing that it's him in the mirror.  He may not be cognitively advanced to think deeper than &quot;Yep, that's me, I have THIS look.  Oh, am I getting fat?&quot; -- they care less about that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good test would be to have a cat with whom you can put something on his head and he doesn't care -- unless it's something he HATES by its LOOK.  Once you've established that over and over 100%, and have been able to put it on him without him caring without him SEEING it -- put him in front of the mirror and see if he tries to take it off.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A red dot isn't going to do squat.  They don't give a shoot about things like that.  If you want to know whether they know IT'S THEM, put them in position where there's something they DON'T WANT on them -- and they try to get it off... where it's something they don't mind on them, they don't try to get it off after seeing themselves in the mirror.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not fool-proof, though.  They may not mind it on them because it's purely how it looks.  They can just walk away from the mirror and they don't have to worry about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But back to the original point:  I don't think it's a big deal that they can recognize that it's themselves.  To UTILIZE that for deeper thinking in making connections is another matter.&lt;/p&gt;&#xA;" OwnerUserId="8264" LastActivityDate="2014-07-08T22:37:32.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19543" PostTypeId="2" ParentId="19538" CreationDate="2014-07-08T22:50:26.907" Score="3" Body="&lt;p&gt;That is a woody &lt;a href=&quot;http://www.bcb.uwc.ac.za/ecotree/flowers/inflorescence2.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;compound umbel.&lt;/a&gt; A compound umbel is one with more than one set of &lt;a href=&quot;http://en.wikipedia.org/wiki/Pedicel_(botany)&quot; rel=&quot;nofollow noreferrer&quot;&gt;pedicels&lt;/a&gt; between the &lt;a href=&quot;http://en.wikipedia.org/wiki/Peduncle_(botany)&quot; rel=&quot;nofollow noreferrer&quot;&gt;peduncle&lt;/a&gt; and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Flower&quot; rel=&quot;nofollow noreferrer&quot;&gt;flower&lt;/a&gt;. &lt;a href=&quot;http://www.gutenberg.org/files/33757/33757-h/images/fig214.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hydrangeas also exhibit this type of inflorescence&lt;/a&gt;, although not necessarily woody.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the picture below, I've marked all the levels where the pedicels branch.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;End of peduncle, beginning of primary pedicels&lt;/li&gt;&#xA;&lt;li&gt;Beginning of secondary pedicels&lt;/li&gt;&#xA;&lt;li&gt;Beginning of tertiary pedicels&lt;/li&gt;&#xA;&lt;li&gt;Beginning of quaternary pedicels, which bear flowers&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/d1Rjw.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2014-07-08T22:50:26.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19544" PostTypeId="2" ParentId="19492" CreationDate="2014-07-08T23:19:18.647" Score="5" Body="&lt;p&gt;With the information given, I have to say I think it's a &lt;a href=&quot;http://en.wikipedia.org/wiki/Papilio_protenor&quot; rel=&quot;nofollow noreferrer&quot;&gt;Spangle, &lt;em&gt;Papilio protenor&lt;/em&gt;,&lt;/a&gt; of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Swallowtail_butterfly&quot; rel=&quot;nofollow noreferrer&quot;&gt;swallowtail family&lt;/a&gt;, probably a male.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also is listed on the &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_butterflies_of_Taiwan&quot; rel=&quot;nofollow noreferrer&quot;&gt;butterflies of Taiwan&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See pictures for comparison:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3fJqn.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/Yk0Ek.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;........................Male...............................................female............................................................................&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2014-07-08T23:19:18.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19545" PostTypeId="1" AcceptedAnswerId="20092" CreationDate="2014-07-08T23:50:37.917" Score="3" ViewCount="1266" Body="&lt;p&gt;What features make one plant able to withstand dry spells better than another with relatively similar structure? For instance, one of my &lt;a href=&quot;http://en.wikipedia.org/wiki/Rudbeckia&quot; rel=&quot;nofollow&quot;&gt;Rudbeckias&lt;/a&gt; is wilting from drought at the moment, and an &lt;a href=&quot;http://en.wikipedia.org/wiki/Oenothera&quot; rel=&quot;nofollow&quot;&gt;Oenothera&lt;/a&gt; next to it is not yet showing signs of dryness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or like &lt;a href=&quot;http://plants.usda.gov/core/profile?symbol=IMCA&quot; rel=&quot;nofollow&quot;&gt;jewelweed (Impatiens capensis)&lt;/a&gt;, which wilts even while the soil is damp, in full sun, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Ambrosia_artemisiifolia&quot; rel=&quot;nofollow&quot;&gt;ragweed (Ambrosia artemisiifolia)&lt;/a&gt;, which will grow in very dry locations without being phased.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it caused by a faster transpiration rate in some plants than in others?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2014-07-11T03:19:45.270" LastActivityDate="2014-10-09T15:14:20.790" Title="What is the difference between drought resistant non-succulent plants and plants that cannot be allowed to dry out?" Tags="&lt;botany&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19546" PostTypeId="1" AcceptedAnswerId="19549" CreationDate="2014-07-09T00:47:36.287" Score="2" ViewCount="2774" Body="&lt;p&gt;I would like to plant some home grown female mulberry trees in a circle, with a male plant in the center for pollination. How do I determine the gender of a tree seedling? I know it's possible, because I've seen mulberry trees labeled as 'male or 'female' at nurseries. Do I need special equipment?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen the related question: &lt;a href=&quot;https://biology.stackexchange.com/questions/14528/can-you-tell-the-sex-of-a-white-willow-when-its-not-flowering&quot;&gt;Can you tell the sex of a white willow when it's not flowering?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="22057" LastEditDate="2018-04-29T21:10:25.290" LastActivityDate="2018-04-29T21:10:25.290" Title="How can I determine the sex of a tree seedling?" Tags="&lt;botany&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19547" PostTypeId="1" CreationDate="2014-07-09T01:10:03.137" Score="2" ViewCount="186" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Q&lt;/em&gt;: Do species which have a closer common ancestor to humans tend to be more intelligent?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Our closest living relative, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Chimpanzee&quot; rel=&quot;nofollow&quot;&gt;chimpanzee&lt;/a&gt;, seems to be regarded as intelligent:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Chimpanzees make tools and use them to acquire foods and for social displays; they have sophisticated hunting strategies requiring cooperation, influence and rank; they are status conscious, manipulative and capable of deception; they can learn to use symbols and understand aspects of human language including some relational syntax, concepts of number and numerical sequence; and they are capable of spontaneous planning for a future state or event.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Does this hold in general?  And, if so, how strong is the correlation?&lt;/p&gt;&#xA;" OwnerUserId="8265" LastActivityDate="2016-01-01T14:37:18.057" Title="Do species which have a closer common ancestor to humans tend to be more intelligent?" Tags="&lt;evolution&gt;&lt;intelligence&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ClosedDate="2016-01-03T19:35:33.527" ContentLicense="CC BY-SA 3.0" />
  <row Id="19548" PostTypeId="1" AcceptedAnswerId="19551" CreationDate="2014-07-09T03:07:28.117" Score="4" ViewCount="2447" Body="&lt;p&gt;It seems like being nearsighted for much of your life due to elongated eyes would make it easier in general to focus on near objects rather than far since the lens would not have to change much. Since in old age we lose the ability to focus close images due to a hardening of the lens over time, wouldn't having eyes shaped more for near images be helpful in maintaining the ability to see close up, and thus nearsighted, or myopic people, would be less likely to develop farsightedness, or hyperopia, with age? It seems then that nearsightedness is more of an adaptation that occurs at a young age, so that these people can work up close for longer periods of time both in the the short term(studying) and long term(age). I'd love to hear if any research has been done on this subject, and any other input you have.&lt;/p&gt;&#xA;" OwnerUserId="8268" LastActivityDate="2015-11-18T05:09:48.197" Title="Does myopia tend to decrease the risk for later hyperopia?" Tags="&lt;eyes&gt;&lt;adaptation&gt;&lt;human-eye&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19549" PostTypeId="2" ParentId="19546" CreationDate="2014-07-09T05:12:49.720" Score="6" Body="&lt;p&gt;There is absolutely no way to tell to be honest because mulberry trees have the capability of changing sex (&lt;a href=&quot;http://www.twisted-tree.net/articles/the-mulberry-tree/&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;). From a paper titled &quot;&lt;a href=&quot;http://www.researchgate.net/publication/255059564_Diversification_of_mulberry_(Morus_indica_var._S36)_a_vegetatively_propagated_tree_species&quot; rel=&quot;noreferrer&quot;&gt;Diversification of mulberry (Morus indica var. S36), a vegetatively propagated tree species&lt;/a&gt;&quot;, I quote&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The sex expression of plants appears to be a function of hormonal&#xA;  control; there seems to be evidence that &lt;a href=&quot;http://en.wikipedia.org/wiki/Dioecy&quot; rel=&quot;noreferrer&quot;&gt;dioeciously&lt;/a&gt; plants (male and&#xA;  female reproductive organs on separate plants) are potentially&#xA;  bisexual and that a delicate internal hormonal balance results in one&#xA;  sex &quot;over-riding&quot; the other. A traumatic incident might, therefore,&#xA;  act by temporarily upsetting this balance, which is later restored in&#xA;  a way that leads to the opposite sexual character being manifested.&#xA;  Another pointer in this direction is the fact that a variety of&#xA;  artificially applied chemical substances has been shown to affect the&#xA;  sexual expression of a significant number of different plants. It is&#xA;  also reported that some chemicals known as the steroid hormones might&#xA;  be a major key to the sex expression lock. Thus, it is&#xA;  possible that to &quot;create&quot; a new sex in a plant by either a physical&#xA;  shock or a controlled chemical process&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They could also have male and female flowers (&lt;a href=&quot;http://en.wikipedia.org/wiki/Monoicous&quot; rel=&quot;noreferrer&quot;&gt;monoecious&lt;/a&gt;) on one plant with most of them being self pollinating (&lt;a href=&quot;http://www.mofga.org/Publications/MaineOrganicFarmerGardener/Summer2003/Mulberries/tabid/1487/Default.aspx&quot; rel=&quot;noreferrer&quot;&gt;references&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in effect, nurseries that are advertising these trees by sex are ignorant or quite plainly taking people for a ride. I would suggest that you plant your seeds and don't worry about it too much since they have the ability to self pollinate. If by bad luck, you find them all male/female or are not pollinating to your liking, go for a tree sex change after consulting an expert on the topic. Here is a basic guide to identifying between male and female trees/branches (&lt;a href=&quot;http://www.gardenguides.com/104541-tell-mulberry-tree-male-female.html&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6x08T.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;White mulberry male flowers (&lt;a href=&quot;http://tree-species.blogspot.in/2011/04/white-mulberry-spring-flowers.html&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HKh6L.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;red mulberry female flowers (&lt;a href=&quot;http://www.carolinanature.com/trees/moru.html&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-09T05:22:46.787" LastActivityDate="2014-07-09T05:22:46.787" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19551" PostTypeId="2" ParentId="19548" CreationDate="2014-07-09T06:22:13.403" Score="2" Body="&lt;p&gt;It is generally understood that we tend to become hyperopic as we age (&lt;a href=&quot;http://www.journalofvision.org/content/8/4/29.short&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). As to whether this aids in decreasing myopia is stated as marginal in papers. One paper titled &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12482270&quot; rel=&quot;nofollow&quot;&gt;Is there a hyperopic shift in myopic eyes during the presbyopic years?&lt;/a&gt;&quot; states that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;it was found that almost all hyperopic and &lt;a href=&quot;http://en.wikipedia.org/wiki/Emmetropia&quot; rel=&quot;nofollow&quot;&gt;emmetropic&lt;/a&gt; eyes showed an&#xA;  age-related hyperopic shift; but only a small proportion of myopic&#xA;  eyes shifted toward hyperopia, with others remaining relatively stable&#xA;  and still others increasing in myopia.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In a second study titled &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10892850&quot; rel=&quot;nofollow&quot;&gt;Age-Related Decreases in the Prevalence of Myopia: Longitudinal Change or Cohort Effect&lt;/a&gt;?&quot;, it was found that there is a decline in the prevalence of myopia in older adults. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some people in personal experiences have stated that their myopia has decreased (&lt;a href=&quot;http://ask.metafilter.com/76846/Myopia-reduction-with-age&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) while others found themselves wearing bifocals (&lt;a href=&quot;http://msgboard.snopes.com/cgi-bin/ultimatebb.cgi?ubb=get_topic;f=35;t=001797;p=1&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). In closing, I would say that this is something that your Ophthalmologist may be able to predict better but it is not a given that your myopia would decrease. It may or may not be so with many factors like your eye shape coming into play.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-11-15T08:40:05.900" LastActivityDate="2014-11-15T08:40:05.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19552" PostTypeId="2" ParentId="19547" CreationDate="2014-07-09T07:35:59.197" Score="7" Body="&lt;p&gt;Several issues here that make your question unanswerable:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Intelligence is not defined. How would you define it?&lt;/li&gt;&#xA;&lt;li&gt;What kind of relationship are you exactly looking for? Comparing average intelligence between groups or trying to fit a regression with intelligence on the Y-axis and relatedness to human on the X-axis? &lt;/li&gt;&#xA;&lt;li&gt;The general issue hidden behind methods of species comparison is &quot;How do you define a species?&quot;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;If you want to compare average intelligence between groups, meaning that you want to compare average intelligence of a group of closely related species of human to the average intelligence of all animals? Then the answer to your question will probably be &quot;Yes&quot; as primates seem in average to be more intelligent than the average animal and mammals tend to be in average more intelligent than the average animal. I'd expect too that vertebrates are probably on average more intelligent than the average animal. Let's not forget that some animals have no brain (e.g. Sponge).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But now if you want to fit a regression between intelligence and relatedness to human for all animals, you will probably have some trend (a regression with a significant slope (positive correlation)), but you will have many group of points that will not fit on your line. Many birds for example may be considered as much more intelligent than humans depending on your definition. Many invertebrates such as octopuses are very intelligent, too. If you allow for a broad definition of intelligence, then you may also consider the intelligence of social insects which may be surprising. Some aquatic mammals are very intelligent although other, more seemingly stupid mammals, are closer to humans than aquatic mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, keep in mind that intelligence is not easy to define, and depending on the definition, the answer will be different. Typically, if you use a very human-like definition of intelligence, you will probably find that intelligent species are more closely related to human. There is a correlation between intelligence and phylogeny (=tree of life), therefore yes, closely related species to humans may have some tendency to be fairly intelligent, but there are many other clades (groups of species on a phylogeny) that show some impressive intelligence, especially in insects, in mollusca, in  birds, the carnivora and the cetacea.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-07-09T15:47:00.533" LastActivityDate="2014-07-09T15:47:00.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19553" PostTypeId="1" CreationDate="2014-07-09T09:07:15.213" Score="2" ViewCount="930" Body="&lt;p&gt;What happens to blood pressure in cerebral edema; does systolic and diastolic rise equally? So the pulse actually slows down? Can't find anything about that, please help&lt;/p&gt;&#xA;" OwnerUserId="8270" LastActivityDate="2014-07-09T23:05:02.260" Title="cerebral edema and blood pressure, pulse" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19554" PostTypeId="1" CreationDate="2014-07-09T13:07:30.367" Score="2" ViewCount="173" Body="&lt;p&gt;There is strong evidence that chromosome 2 in humans is a fusion of two chromosomes of a common ancestor of chimps and humans as explained at wikipedia &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosome_2_%28human%29&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Was it necessary for the common ancestor with fused chromosome 2 to mate with another creature whose 2 chromosomes fused in a similar manner?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If yes, what would their offspring look like? would they also need to mate within themselves or could they mate with the chimp population?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;if possible, also, how in the world could a genetic disadvantage take over the population? doesn't this contradict natural selection?&lt;/p&gt;&#xA;" OwnerUserId="6202" LastEditorUserId="5144" LastEditDate="2014-07-09T15:54:05.887" LastActivityDate="2014-07-09T21:22:22.610" Title="How did the Chromosome #2 Fusion propagate?" Tags="&lt;evolution&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19555" PostTypeId="2" ParentId="19540" CreationDate="2014-07-09T16:29:05.267" Score="8" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;is the difference between humans and mice due primarily to the&#xA;  different order of the genes or to the slight differences in the genes&#xA;  themselves?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The latter.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This question was raised from a claim here which seems to imply it&#xA;  does not matter.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You are talking about two different things.  Gene expression is often controlled by nearby DNA sequences that don't code for protein.  Moving a gene away from the DNA that controls it can change its expression a lot, and have huge consequences on the organism.  But in many cases, you can move a whole gene, including its controlling sequences, to another place, and nothing much will happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;People were bringing up synteny as evidence of evolutionary relatedness, not as the cause for all primates looking similar.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-07-09T16:29:05.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19557" PostTypeId="1" AcceptedAnswerId="19562" CreationDate="2014-07-09T19:07:21.383" Score="2" ViewCount="171" Body="&lt;p&gt;Where can I find data regarding the times distinct cells take to synthesize distinct enzymes?&lt;/p&gt;&#xA;" OwnerUserId="561" LastEditorUserId="5762" LastEditDate="2014-07-09T19:46:08.933" LastActivityDate="2014-07-09T22:33:36.737" Title="How long does it take for a cell to synthesize an enzyme?" Tags="&lt;enzymes&gt;&lt;literature&gt;&lt;cell&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19559" PostTypeId="2" ParentId="19554" CreationDate="2014-07-09T21:22:22.610" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Was it necessary for the common ancestor with fused chromosome 2 to&#xA;  mate with another creature whose 2 chromosomes fused in a similar&#xA;  manner?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Of course not.  People with balanced translocations have kids with people with the wild-type chromosome arrangement all the time.  Such people have some fertility problems, due to problematic meiosis leading to more inviable gametes, but they can still reproduce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Someone already mentioned Robertsonian translocations to you in your previous question.  Didn't you look it up?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;would they also need to mate within themselves or could they mate with&#xA;  the chimp population?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What chimp population?  There were no modern chimps when the fusion happened.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look, you could ask a million questions here, and still learn nothing.  This board is helpful for people who have a good, accurate framework of the facts of biology, but who want specific holes in their knowledge base filled.  I don't think that's you.  I think you think you know the right answers to your questions, based not on science, but on other things, have imbibed or made up a whole slew of very wrong stuff about biology, and are asking questions here expecting people to confirm your wrong beliefs, trying to trick people in to confessing that mainstream biology is wrong, and you are right.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Picking at one bit or another of evolutionary biology is not going to help you.  You need to start by assuming that a lot of what you think you know about the scientific facts is wrong, and learn the real stuff.  It is not at all easy to get wrong information out of our brains, but until you do, this exercise isn't going to educate you much at all.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-07-09T21:22:22.610" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19560" PostTypeId="1" AcceptedAnswerId="19565" CreationDate="2014-07-09T22:07:33.577" Score="0" ViewCount="142" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Starting with a human population N = 2, is there any way the genetic variability seen today could have come about? I don't know that much about meiosis, but isn't there a very limited number of alleles that could be passed on by the parents? Without a population to start with, wouldn't the lineage eventually turn into clones of each other like the cheetahs are now?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are there any known mechanisms besides mutation that replenish the variability in alleles?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8276" LastEditorUserId="8276" LastEditDate="2014-07-13T18:57:17.440" LastActivityDate="2014-07-13T18:57:17.440" Title="What is the outcome of a human population starting with only 2 individuals?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;population-dynamics&gt;&lt;allele&gt;" AnswerCount="1" CommentCount="6" ClosedDate="2014-07-10T18:40:41.943" ContentLicense="CC BY-SA 3.0" />
  <row Id="19561" PostTypeId="1" CreationDate="2014-07-09T22:22:43.553" Score="2" ViewCount="51" Body="&lt;p&gt;Making the assumption:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Within 10 years, an adult will be able to genetically engineer (modify, enhance, clean, etc.) a child from their own DNA (and the DNA of a non-related partner).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;then would getting a vasectomy today preclude this?&lt;/p&gt;&#xA;" OwnerUserId="8277" LastActivityDate="2014-07-09T22:50:26.580" Title="Will a vasectomy prevent genetic engineering of a child?" Tags="&lt;human-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19562" PostTypeId="2" ParentId="19557" CreationDate="2014-07-09T22:33:36.737" Score="5" Body="&lt;p&gt;&lt;strong&gt;In human cells it takes about 20 s to make a 20,000 dalton enzyme.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that the cells concerned are already making mRNA for the enzyme, there will be two main factors:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) The time taken to synthesize the polypeptide&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) Any time taken to fold the protein&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(If the enzyme is secreted from the cell there will also be the time taken for the protein to traverse the secretory pathway - perhaps you want to include this time - if so it could be 10's of minutes.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here I will focus on (1). What is the rate of polypeptide elongation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For bacteria:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Young &amp;amp; Bremer (1976) Polypeptide-chain-elongation rate in Escherichia coli B/r as a function of growth rate Biochem. J. 160: 185-194&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They quote values of:&#xA;17 s&lt;sup&gt;-1&lt;/sup&gt; for fast-growing cells&#xA;and 12 s&lt;sup&gt;-1&lt;/sup&gt; for slower-growing cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For yeast:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bonven &amp;amp; Gullov (1979) Peptide chain elongation rate and ribosomal activity in Saccharomyces cerevisiae as a function of the growth rate. Mol. Gen. Genet. 170: 225-230&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;minimal glucose 9.3 s&lt;sup&gt;-1&lt;/sup&gt;&#xA;minimal acetate 5.5 s&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In human cells:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ramabhadran &amp;amp; Thach (1981) Translational elongation rate changes in encephalomyocarditis virus-infected and interferon-treated cells. J. Virol. 39: 573-583&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They measure a control value of 9.4 s&lt;sup&gt;-1&lt;/sup&gt; and quote (with citations) values of 9-10 s&lt;sup&gt;-1&lt;/sup&gt; in reticulocytes and CHO cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's use 9 s&lt;sup&gt;-1&lt;/sup&gt;, and assume 110 daltons per amino acid&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then e.g. a 20.000 dalton enzyme (= 182 amino acids) requires 20 seconds.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-07-09T22:33:36.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19563" PostTypeId="2" ParentId="19561" CreationDate="2014-07-09T22:50:26.580" Score="3" Body="&lt;p&gt;From the wording of your question the 'genetic engineering' that you are envisaging will involve sperm. So the question is really, does vasectomy affect sperm production?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer is that it does, but it doesn't abolish it. For example:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;McVicar et al. (2005) Effects of vasectomy on spermatogenesis and fertility outcome after testicular sperm extraction combined with ICSI. Human Reproduction 20: 2795-2800&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These authors found that sperm yield fell to about 35% &gt; 5 years post-vasectomy.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-07-09T22:50:26.580" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19564" PostTypeId="2" ParentId="19553" CreationDate="2014-07-09T23:05:02.260" Score="2" Body="&lt;p&gt;In cerebral oedema the observations (blood pressure, pulse, respiratory rate etc.) can be all over the place. They can depend on the cause e.g. infectious more likely to have raised pulse (tachycardia) with lower blood pressure (shock) but with the anxiety there might be raised blood pressure. Then with the vomiting, a symptom of cerebral oedema, this could lead to dehydration which leads to lower blood pressure or movement of fluid from the blood to the brain because it is oedematous could also drop the blood pressure. With the cerebral oedema affecting different structures, particularly the brain stem in coning (brain swells, pushes brain out through the big hole at the bottom where all the nerves come out particularly affecting respiratory rate) the respiratory rate could be low. It could also be high due to structures getting less oxygen causing the body to push the sympathetic nervous system to increase heart rate and respiratory rate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion, things can be completely over the place but usually blood pressure is low and there's reflex tachycardia for the reasons explained above. For these reasons, to diagnose cerebral oedema we usually use the characteristic symptoms of nausea, vomiting, faintness and other features in a patient we know is at risk because of the signs and symptoms of the original disease or cause of the cerebral oedema e.g. the cancer, trauma or infection. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-07-09T23:05:02.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19565" PostTypeId="2" ParentId="19560" CreationDate="2014-07-09T23:22:25.757" Score="1" Body="&lt;p&gt;Indeed natural selection decrease variability and therefore decrease information and mutation recreate this information. You can think of a bunch of pens of different colors. If you select &#xA;for the red pens you will decrease the variability in pen colors as the other colors will slowly disappear. If you allow for mutation to occur you will recreate blue and black and purple and yellow pens to occur again in your population of pens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is it an accurate statement that less variability means less total information?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, less variability means less information. Information is a concept that increases as predictability decreases. If no variability exist, you can predict at 100% what allele a given individual is carrying. You may want to have a look to shannon's theory of information &lt;a href=&quot;https://www.khanacademy.org/computing/computer-science/informationtheory&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; on Khan academy. Note: this has not much to do with biology but it has to the mathematical definition has to do with mathematics, probability and computer science.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are there any known mechanisms besides mutation that replenish the variability in alleles?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No, there is nothing else than mutations that creates new alleles. &quot;Mutation&quot; means any kind of structural change of DNA. So by definition any change in the DNA is due to mutations, therefore only mutations creates new alleles. Note: that some people may use the word mutation in a more narrow sense including some kind of DNA change such as indels but excluding chromosome rearrangement for example. I used here the word mutation in the broad sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Segregation and Recombination&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two other concepts may interest you though: Segregation (See &lt;a href=&quot;http://en.wikipedia.org/wiki/Mendelian_inheritance&quot; rel=&quot;nofollow&quot;&gt;Mendelian inheritance&lt;/a&gt;) and &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosomal_crossover&quot; rel=&quot;nofollow&quot;&gt;recombination&lt;/a&gt;(also called crossing over).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example if 2 individuals $AB$ (Allele $A$ on one chromosome and allele $B$ on the other chromosome) reproduce they can create the individuals $AA$, $AB$ or $BB$ thanks to segregation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two Genes set on chromosomes and if two genes are on the same chromosome, one might think that these two genes cannot segregate independently one from the other, they are linked! For example imagine an individual has the alleles $A_1$ and $B_1$ on two loci of one chromsome and alleles $A_2$ and $B_2$ on the two same loci but of the homologous chromosome. If this individual transmit the allele $A_2$ it must necessarily transmit the allele $B_2$ and can't transmit $B_1$ if recombination does not occur. But recombination does occur and allows for partially independent segregation of these two genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will find more information about these two concepts on wikipedia. I don't want to go too much into details but in short &lt;em&gt;these processes can in some conditions increase the &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenotype&quot; rel=&quot;nofollow&quot;&gt;phenotypic&lt;/a&gt; variance but in any case these phenomenon do not create new alleles. New alleles are created by mutations only.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can 2 individuals carry as much genetic information than today's world population?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No! As a very simple argument, two individuals can only have 4 different alleles. But we know several &lt;a href=&quot;http://en.wikipedia.org/wiki/Locus_%28genetics%29&quot; rel=&quot;nofollow&quot;&gt;loci&lt;/a&gt; (sing: locus, position on a chromosome) where there exist more than 4 different alleles. Therefore, mutations must have happened at some time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And only to enjoy some further arguments: if these two individuals had together 4 alleles at all loci, it would be extraordinary unlikely that their variation would have remained in today's population. Let's imagine two &lt;a href=&quot;http://en.wikipedia.org/wiki/Zygosity#Heterozygous&quot; rel=&quot;nofollow&quot;&gt;heterozygote&lt;/a&gt; (=who has two different alleles on their two chromosomes for a given locus) individuals are $AB$ and $CD$ that have two offsprings. The probability that their 4 alleles are present in the two offsprings is $1/4$. I don't when Adam and Eve were supposed to exist but it very sound like their variability would have not been maintained through times. This random process which diminish variability is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_drift&quot; rel=&quot;nofollow&quot;&gt;genetic drift&lt;/a&gt;. To be a bit more accurate, in a population that do not change in size, the expected loss of alleles due to genetic drift at each generation $1/2N$, where $N$ is the population size. So the bigger is the population size, the lower is the loss of alleles due to genetic drift. In the above example $N=2$ and therefore the expected loss is $1/4$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I don't know that much about meiosis, but isn't there a very limited number of alleles that could be passed on by the parents?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, as said above, one individual can only have two alleles at a given loci and can therefore not transmit more than two different alleles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Without a population to start with, wouldn't the lineage eventually turn into clones of each other[..]?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, because in absence of mutations (and in absence of different special types of selection such as overdominance) the variability is slowly lost due to the randomness of segregation. This process is called genetic drift.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-07-09T23:43:45.320" LastActivityDate="2014-07-09T23:43:45.320" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19567" PostTypeId="1" CreationDate="2014-07-10T00:41:56.293" Score="2" ViewCount="153" Body="&lt;p&gt;I know that blood cells can pass through the smallest of capillaries, but I was wondering is it possible for stem cells to pass through the smallest of capillaries?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, is it possible for a type of stem cell therapy where stem cells are injected into the vein in the arm for example and the stem cell would pass through into the tissue through a type of targeted therapy involving ultrasound or magnetic field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you very much ,&#xA;everyone&lt;/p&gt;&#xA;" OwnerUserId="8279" LastActivityDate="2014-07-28T11:30:20.677" Title="Stem cell that can pass through blood vessel" Tags="&lt;medicine&gt;&lt;stem-cells&gt;&lt;red-blood-cell&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19569" PostTypeId="2" ParentId="6937" CreationDate="2014-07-10T06:58:32.170" Score="11" Body="&lt;p&gt;it is impossible to know the exact number so here is my gross ballpark estimate of an upper bound -  i.e. the maximum number of organisms that could have lived on earth in the extreme best case scenario. in practice it is probably much less, but this is to get an idea of what kind of numbers we are dealing with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Volume_of_the_Earth#Volume&quot; rel=&quot;noreferrer&quot;&gt;earth's volume&lt;/a&gt; is about 1.08321 * 10^12 cubic kilometers =  1.08321 * 10^21 cubic meters&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The crust of the earth is 4-8km and the radius is about 6,353km &lt;a href=&quot;http://en.wikipedia.org/wiki/Crust_%28geology%29&quot; rel=&quot;noreferrer&quot;&gt;giving around 1%&lt;/a&gt; of the total volume available for life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, the volume available, i.e. the volume of the crust is about 1.1 x 10^19 Meters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An average-size bacterium such as the rod-shaped E-coli is about 2 micrometers long and 0.5 micrometers in diameter. Hence, the volume is roughly:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2*10^-6)*(0.5*10^-6)*(0.5*10^-6) = 0.5*10^-18 meters&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, if the entire volume of the crust of the earth were entirely filled with e-coli bacteria, there would be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1.1 x 10^19 meters)/(0.5*10^-18 meters) = 1.3*10^36 bacteria on the earth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria take time until they reproduce. If they reproduce faster than they grow, they will become reduced to zero size, so there must be a balance between growth and reproduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under ideal conditions the E-coli bacterium would divide every twenty minutes. &lt;a href=&quot;http://www.ugrad.math.ubc.ca/coursedoc/math100/notes/zoo/andromed.html&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say we have the maximum number of bacteria on earth dividing every twenty minutes. Somehow, they divide and then one dies so that the population is stable. (hypothetically)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The age of the earth is roughly 4.5 Billion years. Much of that time, it was not colonised, but just to give an upper bound let's assume it was colonized the whole time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are 525600 minutes in a year so this give&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4.5 ^ 10^9 * 5.3* 10^5 = 2.385 * 10^15 minutes&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dividing by twenty minutes gives 1.1925 * 10^14 total reproductions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, the number of organisms that ever lived if the entire volume of the crust of the earth were entirely filled with e-coli bacteria reproducing at the maximum of every 20 minutes would be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1.2*10^14) *  1.3*10^36 bacteria = &lt;strong&gt;1.56 * 10^50 bacteria&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is an highly exaggerated gross estimate of the maximum number of organisms that ever lived in the extreme best case scenario. In practice it is probably 5-15 orders of magnitude less than this but we get an idea of the kind of numbers we are dealing with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE: A more realistic number&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The number of bacteria currently on earth is about 5*10^30 forming a biomass which exceeds that of all plants and animals. &lt;a href=&quot;http://en.wikipedia.org/wiki/Bacteria&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC33863/&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt; cited by the previous wikipedia article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Most of the earth’s prokaryotes (bacteria) occur in the open ocean, in soil, and&#xA;  in oceanic and terrestrial subsurfaces, where the numbers of cells are&#xA;  1.2 × 10^29, 2.6 × 10^29, 3.5 × 10^30, and 0.25–2.5 × 10^30, respectively. The numbers of heterotrophic prokaryotes in the upper&#xA;  200 m of the open ocean, the ocean below 200 m, and soil are&#xA;  consistent with average turnover times of 6–25 days, 0.8 yr, and 2.5&#xA;  yr, respectively. Although subject to a great deal of uncertainty, the&#xA;  estimate for the average turnover time of prokaryotes in the&#xA;  subsurface is on the order of 1–2 × 10^3 yr. The cellular production&#xA;  rate for all prokaryotes on earth is estimated at 1.7 × 10^30 cells/yr&#xA;  and is highest in the open ocean.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hence we have about 1.7 x 10^30 New Cells/year&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Multiply this by the estimated 3.5 Billion years (3.5*10^9) when the earth was colonized and we get&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;5.95 * 10^39 Bacteria that ever lived.&lt;/strong&gt; of course there were other organisms, but as above even the biomass of bacteria exceeds that of&#xA;  all plants and animals combined so their effect on this number is&#xA;  negligible. Likewise, the life conditions were surely not ideal at all&#xA;  times, so this number may be lower still.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For some perspective, the estimated number of atoms comprising all of planet earth is about 1.33 * 10^50 according to this &lt;a href=&quot;http://education.jlab.org/qa/mathatom_05.html&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;ESTIMATE OF NUMBER OF MAMMALS THAT EVER EXISTED&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The upper bound for mammals is as follows.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The surface area of the land of the earth is 149 million square kilometers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let us consider if the entire land area of the earth was completely covered with mice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A mouse is typically 10cm from nose to base of tail and about 5 cm wide=0.1*.05=0.005 square meters. So we get 200 mice per square meter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, if the entire land area of the earth were covered with mice the world population of mice would be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;149*10^12 square meters * 200 mice per square meter = 1.788 * 10^15 mice&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mice typically produce a litter of 6-8 young and a female can have 5-10 litters per year. &lt;a href=&quot;http://en.wikipedia.org/wiki/House_mouse&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say we have this maximum population reproducing in a stable manner. i.e. for every new mouse, an old one dies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence the total number of new mice per year would be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1.8 * 10^15 * 8 young * 10 litters = 1.44*10^17 new mice per year.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mammals appeared around 200 million years ago (&lt;a href=&quot;http://en.wikipedia.org/wiki/Timeline_of_evolutionary_history_of_life&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;), so that makes&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1.44*10^17 new mice per year * 200 million years&lt;/p&gt;&#xA;&#xA;&lt;p&gt;= 2.88 * 10^25 total mice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practice mice need space and resources and compete with other mammals which take up space and which reproduce less frequently. Likewise, deserts and polar regions are less inhabitable, and sometimes there are periods of droughts, and they don't always reproduce at the maximum rate etc. so the total number is probably about around 4-10 orders of magnitude less than this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it is probably something &lt;strong&gt;like 10^20 total mammals ever existed&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6202" LastEditorUserId="6202" LastEditDate="2014-07-13T13:00:01.483" LastActivityDate="2014-07-13T13:00:01.483" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19572" PostTypeId="1" CreationDate="2014-07-10T10:17:24.643" Score="1" ViewCount="47" Body="&lt;p&gt;Why does phosphorylation activate an enzyme?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A common answer to this question is that the introduced phosphate group &quot;alters the structure&quot; of the enzyme.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can somebody point out a &lt;strong&gt;specific example&lt;/strong&gt; of such an alteration? I.e. like a &quot;before/after&quot; illustration?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is the whole mechanism of activation still largely uncharacterized?&lt;/p&gt;&#xA;" OwnerUserId="4971" LastActivityDate="2014-07-10T10:17:24.643" Title="Phosphorylation alters structure: Specific Example?" Tags="&lt;phosphorylation&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19575" PostTypeId="1" AcceptedAnswerId="19579" CreationDate="2014-07-10T13:52:10.530" Score="4" ViewCount="269" Body="&lt;p&gt;I'm studying a TCGA dataset trying to find correlations between gene expression and clinical data which might shed light on some pathways. One column of the clinical data provides a list of chemotherapy drugs the patient received and I'm pretty sure there's a wealth of possibility in this column but I don't know anything about how chemotherapy drugs work or what kinds of things it makes sense to classify about them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm making a spread sheet that will have the following columns: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Drug_Name      &#xA;Number_of_Patients_Received      &#xA;Mechanism      &#xA;Associated_Drugs      &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;But I don't know what else is important to know about these drugs. What would you think is important to know to help understand how these drugs might have played an interactive role with the pathways. Also, if you have any recommendations of online resources, I'll appreciate you mentioning them with a short explanation of what I might find there.&#xA;But my primary question is else should I look up about these drugs to help me understand their role/impact.&lt;/p&gt;&#xA;" OwnerUserId="8161" LastEditorUserId="14852" LastEditDate="2015-04-24T06:12:07.370" LastActivityDate="2015-05-28T14:23:32.237" Title="Classify chemotherapy drugs?" Tags="&lt;pharmacology&gt;&lt;cancer&gt;&lt;research-process&gt;&lt;tcga&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19576" PostTypeId="2" ParentId="17790" CreationDate="2014-07-10T16:02:12.087" Score="1" Body="&lt;p&gt;&lt;strong&gt;DIY Diffusion Experiment&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This procedure was done to see what happens qualitatively when semipermeable (dialysis) tubing containing a solution of  glucose and protein is immersed in a solution of glucose alone. Given that water would diffuse into the bag, the question to be answered was whether there would be an equilibrium increase of sugar concentration outside the bag.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Equipment:&lt;/strong&gt; one-inch dialysis tubing, bovine serum albumin (BSA), dextrose, an inexpensive commercial glucose meter, test strips for the meter.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;General procedure:&lt;/strong&gt;  A control dextrose solution was divided between a sac made of dialysis tubing and a drinking glass.  A small mass of powdered BSA was added to the sac. The sac was suspended in the sugar-only solution and the solution &lt;em&gt;outside the bag&lt;/em&gt; checked at 13 times during a 33-hour period. At about 8 hours protein was added to the bag since neither diffusion nor osmosis was being observed. After this the bag began to swell. Due to concern that BSA would affect the reading the measurements were compared with the control solution and not the inside of the bag$^1$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Results:&lt;/strong&gt; Results are given in the table below. Addition of protein is indicated by the arrow in the graph. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Discussion:&lt;/strong&gt; This procedure was suggested in this &lt;a href=&quot;https://chemistry.stackexchange.com/questions/14005/help-with-simple-diy-procedure-to-measure-diffusion&quot;&gt;answer&lt;/a&gt; at the Chemistry SE. The meter requires some practice to use. Protein was added to the bag in roughly 200mg increments until an influx of water occurred. &lt;em&gt;The solutions had probably reached equilibrium within a few hours of adding the extra protein but fluctuation in temperature made this difficult to determine.&lt;/em&gt; The gross trends correspond to air-conditioner use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Conclusion:&lt;/strong&gt; This procedure was done twice with similar results. The results are qualitative and suggest that sugar diffuses out through the membrane. This result is consistent with the &lt;a href=&quot;https://physics.stackexchange.com/questions/116255/a-simple-osmosis-problem&quot;&gt;answer at PhysicsSE&lt;/a&gt; and also this &lt;a href=&quot;http://www.mun.ca/biology/Osmosis_Diffusion/tutor2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;website&lt;/a&gt; (Figure 4.1) which indicates that diffusion and osmosis (diffusion of water) both occur. &lt;strong&gt;At equilibrium the concentration of sugar is slightly higher outside the bag.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Problems/issues&lt;/strong&gt; :  (1) The meter is very sensitive to temperature $^2.$ (2) Perhaps because the dextrose was incompletely dissolved the measurement of control solutions took about an hour to stabilize. That is why the measurements begin at 110 minutes. (3) The meter gave errors outside a range of 30-500 mg/dl and after checking the standard deviation for a few concentrations of dextrose a concentration of 90 mg/dl was chosen. (4) It was not assumed that the meter functioned properly in the presence of BSA. Except for the last measurements, the glucose was measured outside the bag only.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^1$ Four measurements were taken with the meter within 2 minutes of the last measurement to check variability of the meter. The numbers [mg/dl] were: 90, 94, 93, 89, $\mu = 91.5, \sigma = 2.38.$ At the last measurement the glucose concentration inside the bag was checked twice and the meter gave: 72, 80.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^2$ Concentration should remain the same after equilibrium [Fick equation] and should not be affected by temperature. Manufacture information for the meter omitted for this reason. &lt;em&gt;Caveat emptor.&lt;/em&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Table 1. Min.= minutes, contr. = control [mg/dl], dextr. = dextrose [mg/dl].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\begin{array}{c | c | c | c | c | c |c | c | c | c | c | c | c | c | } min. &amp;amp; 110 &amp;amp; 145 &amp;amp; 296 &amp;amp;  356 &amp;amp; 686 &amp;amp; 776 &amp;amp; 802 &amp;amp; 832 &amp;amp; 862 &amp;amp; 1352 &amp;amp; 1393 &amp;amp; 2053 &amp;amp; 2069 \\ \hline&#xA;dextr. &amp;amp; 90 &amp;amp;  80 &amp;amp; 88 &amp;amp; 83 &amp;amp; 90 &amp;amp; 91&amp;amp; 88 &amp;amp; 88 &amp;amp; 89 &amp;amp; 84 &amp;amp; 93 &amp;amp; 86 &amp;amp; 90 \\ \hline&#xA;contr.&amp;amp; 91 &amp;amp; 83 &amp;amp; 83 &amp;amp; 86 &amp;amp; 82 &amp;amp; 87 &amp;amp; 83 &amp;amp; 85 &amp;amp; 80 &amp;amp; 77 &amp;amp; 89 &amp;amp; 82 &amp;amp; 82   \\ \hline\end{array}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A graph (mg/dl v. minutes) was made from this table. The arrow indicates addition of protein to the bag. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dNNpQ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="-1" LastEditDate="2017-04-13T12:57:01.693" LastActivityDate="2014-07-18T13:16:35.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19579" PostTypeId="2" ParentId="19575" CreationDate="2014-07-10T16:33:03.060" Score="3" Body="&lt;p&gt;There's &lt;a href=&quot;http://www.pharmgkb.org/&quot; rel=&quot;nofollow&quot;&gt;this database&lt;/a&gt; of genetic/drug interactions, which I think is pretty much exactly what you're looking for. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably your best approach is to classify your drugs into a couple different categories of action. Some drugs will have to be in several categories at once(I'm lookin at you anthracyclines) Dose-dependent mutagens(cisplatin), growth-dependent mutagens(fluorouracil), topoisomerase inhibitors, tyrosine kinase inhibitors, microtubule inhibitors, retinoid signaling, immune adjuvants, and then 'misc'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alkylating agents and platinum-containing drugs like cisplatin directly damage DNA, while there are other drugs(methotrexate,fluorouracil) destroy or damage DNA by pretending to be nucleotides and breaking things that way. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anthracyclines bind into DNA strands damaging it, directly create free radicals, disable topoisomerase II, and displace histones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are the topoisomerase inhibitors which prevent cell growth by preventing DNA from being unwound for replication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a fairly diverse(chemically) class of 'mitotic inhibitors' that screw up microtubule formation or proper microtubule dissolution, any of which prevents mitosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sunitinib blocks tyrosine kinases, which are involved in blood vessel formation(and nerve formation and some other things). Other tyrosine kinase inhibitors are more specific to vascular endothelial growth factor(VEGF) receptors, but most tyrosine kinases target more or less specifically VEGFR and related receptors. Some are antibodies, some are just small molecules that bind TKRs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a few retinoid-related drugs most of which influence the vitamin A pathways, like tretinoin, bexarotene, etc. Dual use in skin creams.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Immunoadjuvants are designed to activate the immune system to aid in tumor cell destruction. Interferon-alpha, imidazoquinoline, et cetera.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the miscellaneous category:  Bortezomib, a short peptide that interferes with proper protein degradation. L-asparaginase slows all protein production by destroying asparagine, an amino acid. Some blood cancers respond to corticosteroids, and some ovarian/testicular cancers are treated with sex hormone inhibitors. Nearly any blood-borne poison works as a chemotherapy agent due to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Enhanced_permeability_and_retention_effect&quot; rel=&quot;nofollow&quot;&gt;EPR effect&lt;/a&gt;, so heavy metals or radioactive isotopes also are sometimes used. Arsenic trioxide, for instance, is just arsenic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also worth looking at the steroids that are given along with cancer treatment(dexamethasone) to mitigate side effects. As regulatory hormones, there's going to be a hefty impact on genetic regulation from regular steroid injections. If nothing else it's a confounding effect you'll need to control for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The preparations/solvents of chemotherapy agents can also be significant. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11527683&quot; rel=&quot;nofollow&quot;&gt;Cremophor&lt;/a&gt; was used to suspend some anticancer drugs, but &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21575719&quot; rel=&quot;nofollow&quot;&gt;recent developments&lt;/a&gt; imply that might be on its way out.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-07-10T16:33:03.060" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19580" PostTypeId="1" CreationDate="2014-07-10T18:34:38.067" Score="4" ViewCount="735" Body="&lt;p&gt;Columnar epithelial cells from the colonic mucosa are studied to identify abnormalities in cell signaling pathways. Abnormal epithelial cells from colonic adenocarcinoma are shown to have a mutation that blocks hydrolysis of GTP-bound active RAS. Normal columnar cells have active RAS protein that undergoes hydrolysis to the inactive GDP-bound form. Which of the following signaling pathways is most likely abnormally stimulated in the carcinoma cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a. Jak-Stat Pathway&lt;br&gt;&#xA;  b. MAP kinase pathway&lt;br&gt;&#xA;  c. p53&lt;br&gt;&#xA;  d. Both a &amp;amp; b&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think its MAP kinase pathway because RAS is part of MAP kinase pathway that ultimately leads to transcription and expression of genes but if GTP is not hydrolyzed then RAS will be constantly activated leading to continued gene expression that may lead to cancer but I am not completely sure about it because p53 is also a tumor suppressor gene. &lt;/p&gt;&#xA;" OwnerUserId="8284" LastEditorUserId="5144" LastEditDate="2014-07-11T12:13:32.687" LastActivityDate="2014-08-13T14:28:35.593" Title="which signalling pathway is involved in cancer?" Tags="&lt;biochemistry&gt;&lt;homework&gt;&lt;cancer&gt;&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19581" PostTypeId="1" AcceptedAnswerId="19583" CreationDate="2014-07-10T19:04:23.233" Score="2" ViewCount="197" Body="&lt;p&gt;Is there any research paper state the physical health pros and physical health cons for humans to be taller?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, shorter people seems to more likely to get involved in heart diseases and taller people to be more likely to be involved in cancer&lt;/p&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="5479" LastEditDate="2014-07-10T19:11:21.873" LastActivityDate="2014-07-11T05:42:46.600" Title="Is there any research paper state the pros and cons for human to be taller?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19582" PostTypeId="1" CreationDate="2014-07-10T19:12:32.207" Score="8" ViewCount="1858" Body="&lt;p&gt;I have captured wandering ant queen. I guess she was just fertilised and was looking for a place to start a hive.&#xA;I'd like to create my own ant hive in artificial environment.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I unfortunately only have a small clean chemical bottle (1.5 CM in radius) to keep her in. I was wondering how much space would she need to feel safe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm also not sure what should I feed her. Every morning, I have dropped few sugar crystals in the bottle. She shows much more individuality than an ant, because she has immediately started to collect them. It seems that she ate almost everything. I have also dropped few tiny drops of water in the bottle. Although it's hot and she ate the dry sugar she doesn't seem to drink it at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what does she need? (well, except of natural forest which I don't have in my room)&lt;/p&gt;&#xA;" OwnerUserId="6918" LastActivityDate="2014-07-21T06:14:26.723" Title="How should I feed and keep an ant queen?" Tags="&lt;metabolism&gt;&lt;experiment&gt;&lt;ant&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19583" PostTypeId="2" ParentId="19581" CreationDate="2014-07-10T19:48:00.833" Score="3" Body="&lt;p&gt;&lt;strong&gt;People with Shorter height may outlive Taller ones&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is a statistically established fact that they are more successful in terms of money, &#xA;as the study published &lt;em&gt;Journal of Applied Psychology, (Vol 89(3), Jun 2004, 428-441)&lt;/em&gt;.&#xA;But, still in the health, the counterpart succeed over the former.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;The Effect of Physical Height on Workplace Success and Income: Preliminary Test of a Theoretical Model.&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Author: Judge, Timothy A.; Cable, Daniel M.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;  &#xA;  &lt;p&gt;In this article, the authors propose a theoretical model of the&#xA;  relationship between physical height and career success. We then test&#xA;  several linkages in the model based on a meta-analysis of the&#xA;  literature, with results indicating that physical height is&#xA;  significantly related to measures of social esteem (p = .41), leader&#xA;  emergence (p = .24), and performance (p = .18). Height was somewhat&#xA;  more strongly related to success for men (p = .29) than for women (p =&#xA;  .21), although this difference was not significant. Finally, given&#xA;  that almost no research has examined the relationship between&#xA;  individuals' physical height and their incomes, we present four&#xA;  large-sample studies (total N = 8,590) showing that height is&#xA;  positively related to income (β = .26) after controlling for sex, age,&#xA;  and weight. Overall, this article presents the most comprehensive&#xA;  analysis of the relationship of height to workplace success to date,&#xA;  and the results suggest that tall individuals have advantages in&#xA;  several important aspects of their careers and organizational lives.&#xA;  (PsycINFO Database Record (c) 2012 APA, all rights reserved)&#xA;  Source: &lt;a href=&quot;http://psycnet.apa.org/journals/apl/89/3/428/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://psycnet.apa.org/journals/apl/89/3/428/&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Long back in 1975, the relationship between breast cancer and height had been nearly established.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;h2&gt;&lt;strong&gt;Breast Cancer Incidence and Nutritional Status with Particular Reference to Body Weight and Height&lt;/strong&gt;&lt;/h2&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Author&lt;/strong&gt;: F. de Waard&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;em&gt;Cancer Res 1975;35:3351-3356.&lt;/em&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Summary&lt;/strong&gt; The epidemiological literature on breast cancer is reviewed with particular emphasis on the possible etiological role of&#xA;  nutritional status as reflected by weight and height. The results of a&#xA;  prospective study and preliminary results of a population-based&#xA;  case-control study seem to indicate that body size or body mass rather&#xA;  than overweight (obesity) is a risk factor. A considerable proportion&#xA;  of the differences in incidence between the Netherlands and Japan can&#xA;  be explained by differences in body mass. The biological mechanisms&#xA;  mediating nutritional status and breast cancer are believed to be of&#xA;  an endocrinological- metabolic nature.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qV2Ny.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Primarily the investigators started with overweight problem but they have found a better correlation with height. They have concluded:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A further lead to biological mechanisms might be derived&#xA;  from the fact that several endocrine and metabolic functions&#xA;  (e.g., basal metabolic rate and cortisol production rate)&#xA;  seem to correlate better with body surface area than with&#xA;  body weight. The rationale for using surface area is often&#xA;  lacking except for the fact that it is estimated from both&#xA;  weight and height.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;h2&gt;Height and cancer risk are fairly clearly linked, with a 16 per cent higher relative risk for every extra 4 inches of height.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The answer may lies in the metabolic rate:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For one, taller people tend to weigh more than shorter people, even if&#xA;  their BMI isn’t any higher. For another, poor nutrition and stress can&#xA;  stunt height growth, and higher calorie diets have been associated&#xA;  with increased height. And that doesn’t even begin to take into&#xA;  account the psychosocial variables like increased income, education,&#xA;  and socioeconomic status.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;&lt;strong&gt;Other Diseases&lt;/strong&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;On the contrary, in a study examining cardiovascular disease risk and height in men found that men who were taller than 6′ 1″ (185 cm) had a 35% lower risk of having a heart attack than men who were shorter than 5′ 7″ (170 cm). Every inch a man gained in height resulted in a 2-3% decrease in heart attack risk.&#xA;In a study in among, Israeli civil servants, shows height was also associated with lower stroke risk. Taller people are more likely,around 76%,  to suffer from recurrent blood clots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;LINKS:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://blogs.discovermagazine.com/crux/2013/11/08/is-being-tall-hazardous-to-your-health/#.U79p3vmSzQJ&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://blogs.discovermagazine.com/crux/2013/11/08/is-being-tall-hazardous-to-your-health/#.U79p3vmSzQJ&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://scienceblog.cancerresearchuk.org/2011/07/21/height-and-cancer-risk-%E2%80%93-the-long-and-short-of-it/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://scienceblog.cancerresearchuk.org/2011/07/21/height-and-cancer-risk-%E2%80%93-the-long-and-short-of-it/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-07-11T05:42:46.600" LastActivityDate="2014-07-11T05:42:46.600" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19584" PostTypeId="2" ParentId="19582" CreationDate="2014-07-10T19:56:10.213" Score="7" Body="&lt;p&gt;First you need to identify your ant, for Czech Ants: &lt;a href=&quot;http://www.antweb.org/taxonomicPage.do?rank=species&amp;amp;project=czechants&amp;amp;images=true&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.antweb.org/taxonomicPage.do?rank=species&amp;amp;project=czechants&amp;amp;images=true&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;How should I feed and keep an ant queen?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Home for Pet Ant, Ant Farm:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are lots of things you can use, for example, a clean transparent glass or plastic jar, or a fish tank of a size which you will decide is best for the ants you're keeping in it. As long as the container provides enough space, and the addition of any air holes small enough to prevent the ants escaping (much easier said than done); and also so you can observe your ants going about their daily activities, then it should be fine! Worker ants like to forage, so your set up needs to allow for the ants to do a spot of hunting for their food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible to make your own type of &quot;Ant Farm&quot; by using lengths of wood or plastic which have 2 grooves cut into them, like the frame used in double glazing. As long as you can place the frame onto a sturdy base to prevent it from falling over; or you can use plaster and other materials such as aerated concrete blocks, better known as Ytong nests. Two panes of clear glass or plastic can be placed into the grooves and sealed. Use the silicone sealant that is used around baths or sold where you buy glass fish tanks, but do remember to let it set and dry out well, as this will allow any chemicals to disperse harmlessly into the air before you add any ants. Also make sure that you can safely access your ant home, so you can put food in etc. You can also check out this &lt;a href=&quot;https://www.youtube.com/watch?v=HQEar1JLR5E&quot; rel=&quot;nofollow noreferrer&quot;&gt;youtube video&lt;/a&gt; or &lt;a href=&quot;http://www.wikihow.com/Build-an-Ant-Farm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikihow&lt;/a&gt;.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/2rsx3.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;Always try to cover your ants when not observing them to exclude light, as for most of their lives ants live in underground nests or places well away from daylight. This does not mean that they won't tolerate light; but they prefer to be in total darkness if possible, and queens rarely come out from their nests in the wild.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Feed the ANT:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are using a  gel-filled ant farms, it  contains all the water and nutrients your ants need for survival. Make sure to keep your kit sealed so the gel does not dry out.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ISokl.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/M3voa.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In sand-filled ant farms, you need to add a few drops of water and small bits of food every few days. Ants also love a special treat of water with sugar dissolved in it, but this can’t take the place of fresh water for drinking. You can provide them with a bit of honey at times, and they will probably drink some of that. A small section of meal-worm can help provide her with a protein boost. Again, feeding them until the first workers arrive is not necessary as they do not forage during this period naturally.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/qudUP.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, Interesting Links:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://askabiologist.asu.edu/collecting-queen-ants&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://askabiologist.asu.edu/collecting-queen-ants&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://ant-farm-stores-review.toptenreviews.com/what-you-need-to-know-about-ant-farms.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://ant-farm-stores-review.toptenreviews.com/what-you-need-to-know-about-ant-farms.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;www.tarheelants.com/&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, try &quot;Ants can be pets&quot; group on Facebook.&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-07-21T06:14:26.723" LastActivityDate="2014-07-21T06:14:26.723" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19587" PostTypeId="1" CreationDate="2014-07-10T23:02:18.377" Score="4" ViewCount="1166" Body="&lt;p&gt;If one parent is nearsighted and the other is farsighted.&#xA;One parent developed nearsightedness later in life, while the other was born farsighted and they are both the first ones in their family to have any sort of eye problems.&#xA;Is there a possibility of their children having a perfect vision since both their conditions are the result of a recessive gene and can the probability of inheriting one over the other be assessed?&lt;/p&gt;&#xA;" OwnerUserId="8286" LastEditorUserId="69" LastEditDate="2014-07-14T12:57:19.430" LastActivityDate="2014-07-14T12:57:22.990" Title="Are common eye defects inherited?" Tags="&lt;eyes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19589" PostTypeId="2" ParentId="19545" CreationDate="2014-07-11T06:39:13.677" Score="-3" Body="&lt;p&gt;Plants in drier conditions usually have reduced surface area, thick waxy cuticle covering the epidermis, reduced number of stomata, and water storage tissues that presides in its roots and leaves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that even if the plants are similar, one of them might express more of one of the features shown above.&lt;/p&gt;&#xA;" OwnerUserId="8279" LastActivityDate="2014-07-11T06:39:13.677" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19590" PostTypeId="1" CreationDate="2014-07-11T06:54:10.017" Score="3" ViewCount="468" Body="&lt;p&gt;In &lt;a href=&quot;http://www.simonsfoundation.org/quanta/20140710-hints-of-lifes-start-found-in-a-giant-virus/#comment-142465&quot; rel=&quot;nofollow&quot;&gt;this piece&lt;/a&gt; about giant viruses and the origin of life, in the context of the move from RNA world to DNA world, virologist Valerian Dolja states:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In order to move from RNA to DNA, you need an enzyme called reverse transcriptase&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is this true though? Don't many DNA polymerases work with both, ssDNA and ssRNA templates, i.e. they function as reverse transcriptases although they're not &quot;true&quot; reverse transcriptases. So, in order to move from RNA to DNA, a reverse transcriptase was not a necessity like ribonucleotide reductase was for RNA to Uracil-DNA and thymidylate synthase was for Uracil-DNA to DNA?&lt;/p&gt;&#xA;" OwnerUserId="5784" LastEditorUserId="5784" LastEditDate="2014-07-11T11:00:07.373" LastActivityDate="2014-07-15T14:30:01.927" Title="The move from RNA to DNA and the necessity of reverse transcriptase" Tags="&lt;dna&gt;&lt;rna&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19591" PostTypeId="2" ParentId="19587" CreationDate="2014-07-11T07:37:04.880" Score="2" Body="&lt;p&gt;Both Nearsightedness and farsightedness are inheritable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://blog.23andme.com/23andme-research/citizen-scientists-look-into-nearsightedness/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Citizen Scientists Look into Nearsightedness&lt;/strong&gt;&lt;/a&gt;, 23andme blog:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nearsightedness, a condition in which far-away objects look blurry, is&#xA;  a problem of endemic proportions — approximately 30-40 percent of&#xA;  adults in the United States are nearsighted.  And, as computers and&#xA;  cellphones (which train our eyes to focus on short distances) play an&#xA;  ever-increasing role in our lives, we can only expect that this number&#xA;  will grow. One study in the United States highlights the rising rates&#xA;  of nearsightedness. These researchers found that in the early 1970’s,&#xA;  approximately 25 percent of Americans between the ages of 12 and 54&#xA;  were nearsighted, but thirty years later that number had skyrocketed&#xA;  to 42 percent. While it’s been clear that genetics play an important&#xA;  role in nearsightedness, until this month relatively little was known&#xA;  about which genes are involved. Two large studies on nearsightedness,&#xA;  however, have recently shed light on the subject. One of these studies&#xA;  was conducted by the 23andMe research team under the leadership of Amy&#xA;  Kiefer and Nick Eriksson. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Read more at&#xA;  &lt;a href=&quot;http://blog.23andme.com/23andme-research/citizen-scientists-look-into-nearsightedness/#ijOHfuvePBSFOm4A.99&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://blog.23andme.com/23andme-research/citizen-scientists-look-into-nearsightedness/#ijOHfuvePBSFOm4A.99&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which types of eye disease are inherited?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetic factors play a role in many kinds of eye disease, including those diseases that are the leading cause of blindness among infants, children and adults.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More than 60 percent of cases of blindness among infants are caused by inherited eye diseases such as congenital (present at birth) cataracts, congenital glaucoma, retinal degeneration, optic atrophy and eye malformations. Up to 40% of patients with certain types of strabismus (ocular misalignment) have a family history of the disease and efforts are currently under way to identify the responsible genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In adults, glaucoma and age-related macular degeneration are two of the leading causes of blindness, and both appear to be inherited in a large portion of cases. Researchers have mapped several genes for glaucoma and are starting to identify genes involved in macular degeneration. They also are making very significant progress in identifying the genes that cause retinitis pigmentosa, a degenerative disease of the retina that causes night blindness and gradual vision loss.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can common vision problems be inherited?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetics also play a role in vision problems that occur in otherwise healthy eyes. Genetic ophthalmologic researchers now have evidence that the most common vision problems among children and adults are genetically determined. The list includes strabismus (cross-eyes), amblyopia (lazy eye) and refraction errors such as myopia (nearsightedness), hyperopia (farsightedness) and astigmatism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can inherited eye diseases be corrected if an early diagnosis is made?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;YES&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://my.clevelandclinic.org/disorders/inherited_eye_disease/default.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://my.clevelandclinic.org/disorders/inherited_eye_disease/default.aspx&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058260/table/T1/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Table&lt;/a&gt; gives a better insight on Causes of Myopia:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/F6Af5.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-07-11T07:46:54.077" LastActivityDate="2014-07-11T07:46:54.077" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19592" PostTypeId="1" AcceptedAnswerId="19594" CreationDate="2014-07-11T08:16:35.400" Score="3" ViewCount="324" Body="&lt;p&gt;Proteins peptide bond is made by condensation process in which a molecule of water is released and according to this process it is not favorable in water systems than how peptide bond is formed by condensation in cytoplasm in the presence of water ?&lt;/p&gt;&#xA;" OwnerUserId="5729" LastActivityDate="2014-07-11T09:06:33.070" Title="Formation of peptide bond..?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19593" PostTypeId="1" AcceptedAnswerId="19602" CreationDate="2014-07-11T08:26:37.773" Score="1" ViewCount="721" Body="&lt;p&gt;why plants can only synthesize D-glucose why not L-glucose along with D glucose. I know it very well that plants have only enzymes which can synthesize D-glucose but Why not they have enzymes which can also manufacture L-glucose. So that we could have mixture of L and D glucose molecules? What is the significance of synthesis of only D-glucose by the plants ?&lt;/p&gt;&#xA;" OwnerUserId="5729" LastActivityDate="2014-07-24T20:03:01.760" Title="Significance of synthesis of D-glucose in plants..?" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19594" PostTypeId="2" ParentId="19592" CreationDate="2014-07-11T09:06:33.070" Score="4" Body="&lt;p&gt;The condensation is not done in water alone - the enzymatic function of the ribosome plays the essential part here. And in the active center of the ribosome where the formation of the peptide bond takes place, no water is present, only the growing peptide chain and the single amino acid (bound to the tRNA). See this schematic image from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Translation_%28biology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PITNS.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you make x-ray crystallography, this looks like this (from &lt;a href=&quot;http://www.esrf.eu/UsersAndScience/Publications/Highlights/2006/SB/SB04&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;). You can see that the tRNA with the unbound amino acid is actually inside the ribosome and protected from the outside:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PYjWS.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-11T09:06:33.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19595" PostTypeId="2" ParentId="19590" CreationDate="2014-07-11T09:17:41.220" Score="2" Body="&lt;p&gt;Yes, this is true. This flow of information is called the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Central_dogma&quot; rel=&quot;nofollow&quot;&gt;Central dogma of Molecular Biology&lt;/a&gt;&quot;. It basically describes the flow of information from DNA to RNA to proteins. Since a virus needs to amplify its genetic information before it can take over the infected cell and make only viral proteins and its genetic information, it has two possible options.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA viruses can use the cells replication and transcription machinery to make copies and express proteins. RNA viruses either have to use a reverse transcriptase to make DNA from its RNA genome to go on like the DNA viruses. Or they have to have a special, RNA-dependent (works only on RNA templates) RNA-polymerase (our RNA polymerase are all DNA-dependent and work only on DNA templates) to make more copies of their genome. Our DNA polymerases are dependent on DNA, the same is true for our RNA polymerases. So if the virus is not encoding (and actually bringing a few molecules with it in the virus) of the RT-polymerase or the special RNA-dependent RNA polymerase it will not be able to spread.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using ribonucleotide reductases would theoretically be possible, but it is not the way nature went. And since a cell contains huge amounts of RNA, I doubt this would be a feasible way, as the enzyme would reduce all RNA. And later on the new viruses also needs new (not reduced RNA) to be packaged into new viruses. This would also be problematic.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-07-11T10:00:59.970" LastActivityDate="2014-07-11T10:00:59.970" CommentCount="16" ContentLicense="CC BY-SA 3.0" />
  <row Id="19596" PostTypeId="1" CreationDate="2014-07-11T10:45:47.630" Score="3" ViewCount="59" Body="&lt;p&gt;I am new to the study of chromatin, and I am trying to understand what people mean when they write about chromatin states, chromatin interactions, and chromatin structures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the difference among these?&#xA;Is there someone available to explain them to me clearly?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are loops interactions or structures?&lt;/p&gt;&#xA;" OwnerUserId="885" LastActivityDate="2014-07-21T06:20:00.097" Title="In chromatin, what are the differences among states, interactions, and structures?" Tags="&lt;chromatin&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19599" PostTypeId="2" ParentId="17333" CreationDate="2014-07-11T12:00:16.557" Score="2" Body="&lt;p&gt;Just Download and Install: &lt;a href=&quot;http://www.ccp4.ac.uk/&quot; rel=&quot;nofollow&quot;&gt;CCP4: Software for Macromolecular Crystallography&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-11T12:00:16.557" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19600" PostTypeId="2" ParentId="16861" CreationDate="2014-07-11T14:56:34.503" Score="1" Body="&lt;p&gt;You might want to look at the Danish Data archive: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sa.dk/content/us/about_us/danish_data_archive&quot; rel=&quot;nofollow&quot;&gt;http://www.sa.dk/content/us/about_us/danish_data_archive&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have never used their data and I don't know what barriers there might be to accessing it, but the impression I got at a talk by Soren Brunak (&lt;a href=&quot;http://ctbr.hunter.cuny.edu/Brunak&quot; rel=&quot;nofollow&quot;&gt;http://ctbr.hunter.cuny.edu/Brunak&lt;/a&gt;), was that this was one of the most complete databases for studying relationships between people's DNA records and other health information that might be available about them.&lt;/p&gt;&#xA;" OwnerUserId="8161" LastActivityDate="2014-07-11T14:56:34.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19602" PostTypeId="2" ParentId="19593" CreationDate="2014-07-11T20:39:49.280" Score="1" Body="&lt;p&gt;Synthesis from chemicals in organisms is fundamentally different from laboratory synthesis of chemicals. In the latter, more than one chemical species or other unwanted byproducts are usually formed, whist living organisms use enzymes, that are often stereo-specific. This means that they usually can bind, in the case, produce, only one stereo-isomer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To produce both forms they would need double sets of enzymes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It makes sense for animals, bacteria, protozoa, etc. to digest whatever comes, so less specific enzyme, but since plants will only access the glucose they themselves formed use of a stereo-specific enzymatic pathway probably enables a more efficient metabolism.&lt;/p&gt;&#xA;" OwnerUserId="4036" LastActivityDate="2014-07-11T20:39:49.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19603" PostTypeId="1" AcceptedAnswerId="19622" CreationDate="2014-07-11T20:46:24.417" Score="2" ViewCount="649" Body="&lt;p&gt;I have seen the two terms &lt;code&gt;currency metabolite&lt;/code&gt; and &lt;code&gt;current metabolite&lt;/code&gt; used interchangeably. Is there a consensus on which is the right term?&lt;/p&gt;&#xA;" OwnerUserId="561" LastActivityDate="2014-07-12T18:06:23.120" Title="Currency metabolites vs. current metabolites: What's the right term?" Tags="&lt;metabolism&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19604" PostTypeId="1" AcceptedAnswerId="19613" CreationDate="2014-07-11T21:28:21.000" Score="5" ViewCount="4154" Body="&lt;p&gt;It seems impossible to have reptiles the size of dinosaurs, just because they are really big! Did they have different systems of maintaining body temperature or maybe they weren't the exact type of animals that we today call reptiles? &lt;/p&gt;&#xA;" OwnerUserId="8294" LastEditorUserId="5331" LastEditDate="2014-07-18T09:10:15.253" LastActivityDate="2014-07-18T09:10:15.253" Title="How big can cold-blooded animals get?" Tags="&lt;palaeontology&gt;&lt;herpetology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19606" PostTypeId="2" ParentId="19124" CreationDate="2014-07-12T01:13:38.423" Score="1" Body="&lt;p&gt;Up to a certain point, adding nitrogen to soil will increase plant growth. However, too much nitrogen will &quot;burn&quot; plants- stunting root growth and making the plant more susceptible to diseases. Unfortunately, I don't know at exactly what threshold nitrogen becomes &quot;too much&quot;- I suppose it would vary depending on the plants.&lt;/p&gt;&#xA;" OwnerUserId="8297" LastActivityDate="2014-07-12T01:13:38.423" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19608" PostTypeId="2" ParentId="8802" CreationDate="2014-07-12T03:20:37.273" Score="4" Body="&lt;p&gt;This &lt;a href=&quot;http://treechange.hubpages.com/hub/WEATHER-Natures-Forecasters-Insects-and-Spiders&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; claims that ants do sense approaching rain and modify their activities in preparation. The claim is not sourced. This &lt;a href=&quot;http://www.wikihow.com/Predict-the-Weather-Without-a-Forecast&quot; rel=&quot;nofollow&quot;&gt;weather&lt;/a&gt; site also speaks of ant mound-building before a rain but frankly places it in the &quot;some folks say&quot; category. The &lt;a href=&quot;http://www.antweb.org/antblog/ask-an-ant-expert/ant-behavior/2011/02/&quot; rel=&quot;nofollow&quot;&gt;AntBlog&lt;/a&gt; is associated with AntWeb, a large multi-university-affiliated database. The author of the linked blog states that ants can sense humidity with their antennae, which strikes me as a plausible means of anticipating rain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That ants might sense changes in barometric pressure is an intriguing idea but has not to my knowledge been demonstrated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A 2010 &lt;a href=&quot;http://jn.physiology.org/content/104/3/1249&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; in &lt;em&gt;Journal of Neurophysiology&lt;/em&gt; reports an almost unbelievable sensitivity to temperature in ant antennae, allowing them in principle to sense minute temperature changes ($0.005^o$C) over a wide range of temperatures and over 0.2 second time intervals (5Hz). This is said to assist them in orientation in their microenvironment but I think it goes a long way to accounting for an ability to detect looming weather fronts. Humans can sometimes 'smell' rain and we can detect gross temperature changes that almost always accompany rain, but to be able to detect humidity and micro-scale temperature changes would give the ants a real advantage in forecasting. After all, not all rainstorms are preceded by a dramatic drop in temperature but probably the majority are preceded by minute step-wise drops in temperature that evidently the ants can sense.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So while I think the building activity may be anecdotal (and probably true for some species) the ability to sense humidity changes and micro-scale temperature changes accounts for their ability to sense rain ahead of time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ants are very well-studied and it's hard to rule out that one has missed something. There are a few &quot;ask the expert&quot; questions on this topic online and no one seemed sure. &lt;/p&gt;&#xA;" OwnerUserId="1368" LastActivityDate="2014-07-12T03:20:37.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19610" PostTypeId="1" AcceptedAnswerId="19663" CreationDate="2014-07-12T04:54:12.847" Score="5" ViewCount="2358" Body="&lt;p&gt;In many compound and special inflorescences like &lt;a href=&quot;http://en.wikipedia.org/wiki/Spadix&quot; rel=&quot;nofollow noreferrer&quot;&gt;spadix&lt;/a&gt; and &lt;a href=&quot;http://wiki.answers.com/Q/What_is_hypanthodium&quot; rel=&quot;nofollow noreferrer&quot;&gt;hypanthodium&lt;/a&gt; there are sterile female flowers along with male and female fertile flowers and are often present in between male and female flowers, but what is their need in an inflorescence?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kb0dT.gif&quot; alt=&quot;enter image description here&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/vaAvj.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I know inflorescences are meant for perpetuation of a plant's race by pollination of female flowers by the male gametes [pollen grains which bears vegetative and reproductive cells].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know the infertile female flowers of the spadix inflorescence possess some surface area and this area would get some of the pollen grains which are coming in to the inflorescence, and eventually a sum of pollen grains might go in vain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the need of sterile female flowers when fertile ones are present in it?&lt;/p&gt;&#xA;" OwnerUserId="8101" LastEditorUserId="13148" LastEditDate="2015-02-08T17:59:32.043" LastActivityDate="2015-02-08T17:59:32.043" Title="Why are neutral [sterile] female flowers present in inflorescences when they are reproductively incompatible?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19612" PostTypeId="1" AcceptedAnswerId="19618" CreationDate="2014-07-12T08:13:13.863" Score="10" ViewCount="584" Body="&lt;p&gt;This plant was found growing in Germany. I have never seen it before, reverse Google image search did not help either. Can you help me identify what type of plant this is?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2YcJL.png&quot; alt=&quot;Full view&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/MrjTJ.jpg&quot; alt=&quot;Flower&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/GPiDX.jpg&quot; alt=&quot;Root&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks, looks like it is something like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://pflanzen-enzyklopaedie.eu/stauden/amerikanische-kermesbeere-phytolacca-americana/#more-4034&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://pflanzen-enzyklopaedie.eu/stauden/amerikanische-kermesbeere-phytolacca-americana/#more-4034&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Related question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://gardening.stackexchange.com/questions/2609/what-is-this-fast-growing-plant-with-blue-black-berries/2610#2610&quot;&gt;https://gardening.stackexchange.com/questions/2609/what-is-this-fast-growing-plant-with-blue-black-berries/2610#2610&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6137" LastEditorUserId="-1" LastEditDate="2017-04-13T12:42:26.137" LastActivityDate="2017-01-16T21:13:02.153" Title="What is the name of this plant?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19613" PostTypeId="2" ParentId="19604" CreationDate="2014-07-12T08:34:55.680" Score="7" Body="&lt;p&gt;Answer is quite simple as from @Alan Boyd link. They are cold blooded and thus, can go out for hunt in cold, they need to stay put till they get some prey. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, it mainly depend on the temperature of the outside, I found this interesting paper on relation of body sizes and latitude.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;h2&gt;Body sizes of poikilotherm vertebrates at different latitudes&lt;/h2&gt;&#xA;  &#xA;  &lt;p&gt;Maximum sizes of 12,503 species of poikilotherm vertebrates were&#xA;  analyzed for latitudinal trends, using published data from 75 faunal&#xA;  studies. A general trend appears which may be summarized by the rule&#xA;  &quot;among fish and amphibian faunas the proportion of species with large&#xA;  adult size tends to increase from the equator towards the poles&quot;. The&#xA;  rule holds for freshwater fish, deepsea fish, anurans, urodeles, and&#xA;  marine neritic fish arranged roughly in order of decreasing clarity of&#xA;  the trend). In general the rule applies not only within these groups&#xA;  of families but also within single families. In reptile groups, the&#xA;  rule holds weakly among snakes and not at all among lizards or&#xA;  non-marine turtles. Possible explanations include an association&#xA;  between small size and greater specialization in the tropics; the&#xA;  possibility in poikilo-therms of heat conservation or of some other&#xA;  physiological process related to surface/volume ratio; selection for&#xA;  larger size in regions subject to winter food shortages; and an&#xA;  association between large adult size and high reproductive potential&#xA;  in cold regions. Other suggestions can be advanced, but all are&#xA;  conjectural and few are subject to test. Global size - latitude trends&#xA;  should be looked for in other living groups.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;em&gt;Cite: Lindsey, C. C., 1966: Body sizes of poikilotherm vertebrates at&#xA;  different latitudes. Evolution: 456-465&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Now lets compare some of the largest cold blooded Animals:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Reptiles&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Amphibians&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Fishes (Pisces)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Reptiles:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The smaller size of Reptiles give them more agility to hunt andsave them predators but some times when they are top of food chain they can grow as giants.&#xA;Anacondas (Eunectes), gigantic snakes from South America, are undoubtedly the largest living snakes. &#xA;The largest species, the green anaconda (&lt;em&gt;E. murinus&lt;/em&gt;), likely only rarely exceeds 9 metres (30 feet) in length; nonetheless, &#xA;persistent but unsubstantiated reports have been made of anacondas that are 12 metres (40 feet) long. &#xA;The reticulated python (&lt;em&gt;P. reticulatus&lt;/em&gt;) of Southeast Asia and the East Indies has been recorded at 10.1 metres (33.3 feet).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Others:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;King Cobra(&lt;em&gt;Ophiophagus hannah&lt;/em&gt;) 5.5 meters (18 feet) &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Keeled rat snake (&lt;em&gt;Ptyas carinatus&lt;/em&gt;), at about 3.7 metres (12 feet). &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Nile crocodiles (&lt;em&gt;Crocodylus niloticus&lt;/em&gt;) 6 metres (20 feet) &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;American crocodile (&lt;em&gt;C.acutus&lt;/em&gt;) 4–5 metres (12–15 feet). &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Marine leatherback sea turtle (&lt;em&gt;D.coriacea&lt;/em&gt;) 2.7 metres (9 feet) &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Galápagos tortoise (&lt;em&gt;Geochelone nigra&lt;/em&gt;) 255 kg (560 pounds). &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Komodo dragon (&lt;em&gt;Varanus komodoensis&lt;/em&gt;) 3 metres (10 feet) &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Green iguana (&lt;em&gt;I. iguana&lt;/em&gt;) 2 metres (7 feet)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.wallshq.com/wp-content/uploads/main/2013_01/green_anaconda-wide.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Green Anaconda http://www.wallshq.com/wp-content/uploads/main/2013_01/green_anaconda-wide.jpg&lt;/a&gt;&#xA;Green Anaconda&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;&lt;img src=&quot;https://i.stack.imgur.com/CZqwM.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/h2&gt;&#xA;&#xA;&lt;h2&gt;Amphibians:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;According to Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The &lt;a href=&quot;https://i.stack.imgur.com/GElnx.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chinese giant salamander&lt;/a&gt; (&lt;em&gt;Andrias davidianus&lt;/em&gt;) is the largest&#xA;  salamander and largest amphibian in the world, reaching a length of&#xA;  180 cm (5.9 ft), although it rarely—if ever—reaches that size today&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Others:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;West African goliath frog, 30 cm (12 inches) 3.3 kg (7.3 pounds)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Caecilia thompsoni&lt;/em&gt; 1.5 metres (5 feet)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Axolotl(&lt;em&gt;Ambystoma mexicanum&lt;/em&gt;) 30 cm (12 in)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GElnx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chinese giant salamander&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dEXYi.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;African goliath frog&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PujvU.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Axolotl (Small 12 inch)&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Fish:&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;West Indian Ocean coelacanth, (Latimeria chalumnae), is 80 kg (176 lb), and they can reach up to 2 m (6.5 ft)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;African lungfish (Protopterus aethiopicus), 2 m (6.6 ft) and may weigh as much as 50 kg (110 lb)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Ray-finned bony fish (Actinopterygii)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Ocean sunfish (Mola mola) 4.3 m (14 ft) from fin-to-fin, 3.1 m (10 ft) in length&#xA;and weighed about 2,300 kg (5,100 lb)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;King of herrings or oarfish (Regalecus glesne) 6 m (20 ft)( The longest&#xA;known king of herrings, which was hit by a steamship, was measured as 13.7 m (45 ft) long) &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Bowfin (Amia calva)  109 centimetres (43 in) in length, and weigh 9.75 kilograms (21.5 lb).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;European conger (Conger conger) 3 m (10 ft) and a mass of 110 kg (240 lb)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Lancetfish (Alepisaurus ferox) 2.1 m (7 ft) long and can weigh up to 11 kg (24 lb)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Houndfish (Tylosurus crocodilus) 1.5 m (5 ft) and a weight of 6.35 kg (14.0 lb)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Giant Tigerfish (Hydrocynus goliath) 1.5 m (5 ft) and 50 kg (110 lb)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Golden Dorado (Salminus brasiliensis) 1 m (3.3 ft) in length and weigh 31.4 kg (69 lb)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Tambaqui (Colossoma macropomum) 1 m (3.3 ft) and 32.4 kg (71 lb)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Giant barb (Catlocarpio siamensis) 3 m (10 ft) and a weight of as much as 300 kg (660 lb)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Muskellunge (Esox masquinongy)  1.8 m (6.0 ft) and 45.4 kg (100 lb)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Atlantic tarpon (Megalops atlanticus) 161 kg (350 lb) and length is up to 2.5 m (8.2 ft).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The Atlantic cod (Gadus morhua) grows to 2 m (6.7 ft) long and 96 kg (212 lb)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;milkfish (Chanos chanos) 22.7 kg (50 lb) and 1.84 m (6.1 ft) long&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Electric eel (Electrophorus electricus) 2 m (6 ft 7 in) in length, and 20 kg (44 lb) &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Opah (Lampris guttatus) 2 m (6.6 ft) in length and weigh up to 270 kg (600 lb)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_largest_fish&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/List_of_largest_fish&lt;/a&gt;&#xA;Source: Britannica.com&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zTA8E.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;&lt;em&gt;Mola mola&lt;/em&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TgVR0.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Oarfish&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LSmFr.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;West Indian Ocean coelacanth&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2CO4o.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Bowfin&lt;/h2&gt;&#xA;&#xA;&lt;hr&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-07-18T07:06:43.663" LastActivityDate="2014-07-18T07:06:43.663" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19614" PostTypeId="1" AcceptedAnswerId="19621" CreationDate="2014-07-12T13:01:53.397" Score="8" ViewCount="2680" Body="&lt;p&gt;Im not sure how this would ever be tested but is there a limit to how much the brain can 'hold' before it reaches capacity ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess this could also be interpreted in terms of memory, as how well some one remember something before reaching capacity / forgetting 'old' memories to make way / space for new ones.&lt;/p&gt;&#xA;" OwnerUserId="3872" LastEditorUserId="3872" LastEditDate="2014-07-12T14:47:08.963" LastActivityDate="2014-07-13T02:47:59.843" Title="Is there any size limit to the amount of information a human (or other) brain can hold" Tags="&lt;brain&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19615" PostTypeId="2" ParentId="19508" CreationDate="2014-07-12T13:08:56.243" Score="2" Body="&lt;p&gt;&lt;em&gt;This is a short review about the issue and not complete.&#xA;This and the earlier answer are not proofs of the link between the two proceses.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To investigate this better, I think it would be much easier first to narrow the case to &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;testosterone and energy homeostasis (Embryology; or better formulated research case)&lt;/li&gt;&#xA;&lt;li&gt;catabolism and anger&lt;/li&gt;&#xA;&lt;li&gt;anger and aggressive behaviour.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Then, think about specific cases. &#xA;Think genes which are associated with aggressive behaviour and violence in catabolism (criminal studies). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Terms&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Satiety&lt;/li&gt;&#xA;&lt;li&gt;Appetite&lt;/li&gt;&#xA;&lt;li&gt;Hunger &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I was not sure in which specific area you are particularly interested. &#xA;At this stage, we cannot provide a proof between hunger and aggressive behaviour. &#xA;It depends so much on the individual (life style; genomics) what is the end result.&#xA;Here follows little general pieces of information:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some cases&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;InsR/FoxO1 Signaling Curtails Hypothalamic POMC Neuron Number&lt;/strong&gt; [1]: &lt;em&gt;it's possible that the hormonal and nutrient milieu contributes to alterations in POMC neuron development&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Early-Life Exposure to Testosterone Programs the Hypothalamic&#xA;Melanocortin System&lt;/strong&gt; [3].&lt;/li&gt;&#xA;&lt;li&gt;Study about testosterone and basal metabolic rate [2].&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Nuclei&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;hypothalamus lateral nucleus&lt;/li&gt;&#xA;&lt;li&gt;hypothalamus tuberal medial perifornical nucleus [4]&lt;/li&gt;&#xA;&lt;li&gt;hypothalamus arcuate nucleus (appetite and energy expenditure - POMC-CART; upregulative NPY AGRP)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Receptor&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;androgenic (NR3C4) (adipose tissue; more in visceral) (no link)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;where I found no receptor existing directly between those two events - appetite and testosterone secretion by comparing the NCBI gene databases between those two processes.&#xA;It is much more easier to show the thing first in the embryologic studies and then by using the gene found in bigger studies.&#xA;At the moment, more work is needed in these studies in Embryology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My initial clause is based on some of my notes in Embryology. &#xA;There are researches who are trying to show this link between studies in embryology. &#xA;The problem is at the moment in the development of hypothalamus and something else. &#xA;I will update this post when I remember about the situation better and when finding the right things from my notes.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sources&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271107/#!po=14.0625&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271107/#!po=14.0625&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402517/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402517/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060636/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060636/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;John E. Hall. Guyton and Hall Textbook of Medical Physiology. 12Th edition.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-07-12T13:08:56.243" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19618" PostTypeId="2" ParentId="19612" CreationDate="2014-07-12T14:35:05.673" Score="9" Body="&lt;p&gt;This looks like some species of &lt;em&gt;Phytolacca&lt;/em&gt; to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's possibly &lt;em&gt;Phytolacca americana&lt;/em&gt;, which is native to the US (in fact it's an enthusiastic 'volunteer' in my garden) but &lt;a href=&quot;http://books.google.com/books?id=5vd_ZE7UDV8C&amp;amp;lpg=PA1018&amp;amp;ots=tmnF-2RlZr&amp;amp;dq=european%20phytolacca&amp;amp;pg=PA43#v=onepage&amp;amp;q=phytolacca&amp;amp;f=false&quot;&gt;naturalized in Europe&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you still have any in the ground, once they ripen, the berries are intensely purple and &lt;a href=&quot;http://www.efloras.org/florataxon.aspx?flora_id=1&amp;amp;taxon_id=220010427&quot;&gt;can be used as dye (or even eaten?)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.efloras.org/florataxon.aspx?flora_id=1&amp;amp;taxon_id=220010427&quot;&gt;Mark A. Nienaber &amp;amp; John W. Thieret. Phytolaccaceae.  In: Flora of North America Editorial Committee, eds.  1993+.  Flora of North America North of Mexico. New York and Oxford. (link goes to entry of P. americana)&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2014-07-12T14:35:05.673" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19620" PostTypeId="2" ParentId="19580" CreationDate="2014-07-12T15:36:22.297" Score="5" Body="&lt;p&gt;The answer is b, as the mutation constantly activates the RAS protein. RAS is part of the MAP-Kinase pathway, constant signaling of it permanently activates this pathway and leads to changes in gene expression. See the image below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/d2Kms.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in more details, have a look at these papers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nrc/journal/v11/n11/full/nrc3106.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;RAS oncogenes: weaving a tumorigenic web&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://journal.frontiersin.org/Journal/10.3389/fgene.2011.00100/full&quot; rel=&quot;nofollow noreferrer&quot;&gt;RAS mutations and oncogenesis: not all RAS mutations are created&#xA;equally&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-08-13T14:28:35.593" LastActivityDate="2014-08-13T14:28:35.593" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19621" PostTypeId="2" ParentId="19614" CreationDate="2014-07-12T17:54:09.330" Score="7" Body="&lt;p&gt;Yes, there is a limit:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Despite the impressive complexity and processing power of the human brain, it is severely capacity limited [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Human brain has 78.82– 95.40 billion neurons [2] and about $3.6 \cdot 10^{14}$ synapses in the cortex [3]. We shouldn't worry about running out of space, because neurons connect with each other to exponentially increase brain capacity to about 2.5 million gigabytes as Paul Reber, professor of psychology at Northwestern University claims for Scientific American [4]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Each neuron forms about 1,000 connections to other neurons, amounting to more than a trillion connections. If each neuron could only help store a single memory, running out of space would be a problem. You might have only a few gigabytes of storage space, similar to the space in an iPod or a USB flash drive. Yet neurons combine so that each one helps with many memories at a time, exponentially increasing the brain’s memory storage capacity to something closer to around 2.5 petabytes (or a million gigabytes).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Marois R, Ivanoff J. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15925809&quot;&gt;Capacity limits of information processing in the brain.&lt;/a&gt; Trends Cogn. Sci. (Regul. Ed.). 2005 Jun;9(6):296-305. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.tics.2005.04.010&quot;&gt;10.1016/j.tics.2005.04.010&lt;/a&gt;. PubMed PMID: 15925809. Full text available on &lt;a href=&quot;http://www.psy.vanderbilt.edu/faculty/marois/Publications/Marois_Ivanoff-2005.pdf&quot;&gt;http://www.psy.vanderbilt.edu/faculty/marois/Publications/Marois_Ivanoff-2005.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Azevedo FA, Carvalho LR, Grinberg LT, Farfel JM, Ferretti RE, Leite RE, Jacob Filho W, Lent R, Herculano-Houzel S. Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled-up primate brain. J Comp Neurol. 2009 Apr 10 513(5):532-41. p.535 right column top sentence. Via Bionumbers &lt;a href=&quot;http://bionumbers.hms.harvard.edu//bionumber.aspx?id=106322&amp;amp;ver=4&quot;&gt;http://bionumbers.hms.harvard.edu//bionumber.aspx?id=106322&amp;amp;ver=4&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Roth G, Dicke U. Evolution of the brain and intelligence. Trends Cogn Sci. 2005 May9(5):250-7. p.253 right column 1st paragraph. Via Bionumbers &lt;a href=&quot;http://bionumbers.hms.harvard.edu//bionumber.aspx?id=106138&amp;amp;ver=2&quot;&gt;http://bionumbers.hms.harvard.edu//bionumber.aspx?id=106138&amp;amp;ver=2&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Paul Reber. &lt;em&gt;What Is the Memory Capacity of the Human Brain?&lt;/em&gt; Scientific American. Apr 2010. Available from &lt;a href=&quot;http://www.scientificamerican.com/article/what-is-the-memory-capacity/&quot;&gt;http://www.scientificamerican.com/article/what-is-the-memory-capacity/&lt;/a&gt;. Accessed 12.07.2014&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-07-12T17:54:09.330" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19622" PostTypeId="2" ParentId="19603" CreationDate="2014-07-12T18:06:23.120" Score="2" Body="&lt;p&gt;&lt;strong&gt;Currency&lt;/strong&gt; refers to anything that is used in any circumstances, as a medium of exchange [1]. That's why &lt;a href=&quot;http://en.wikipedia.org/wiki/Adenosine_triphosphate&quot; rel=&quot;nofollow&quot;&gt;ATP&lt;/a&gt; and NAD are considered as currency metabolites [2]. So currency metabolite can be used for any metabolite that has multiple uses in different reactions/pathways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Current&lt;/strong&gt; refers to something that is prevalent at the present time [3]. So current metabolite is used to refer a metabolite that is already available for a specific reaction/pathway and doesn't need to undergo supplementary transformations to fit for that specific reaction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same metabolite can be simultaneously a currency metabolite and a current metabolite for a specific situation.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Currency,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Currency&amp;amp;oldid=611672968&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Currency&amp;amp;oldid=611672968&lt;/a&gt; (accessed July 12, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Gerlee P, Lizana L, Sneppen K. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19808881&quot; rel=&quot;nofollow&quot;&gt;Pathway identification by network pruning in the metabolic network of Escherichia coli.&lt;/a&gt; Bioinformatics. 2009 Dec 15;25(24):3282-8. doi: &lt;a href=&quot;http://dx.doi.org/10.1093/bioinformatics/btp575&quot; rel=&quot;nofollow&quot;&gt;10.1093/bioinformatics/btp575&lt;/a&gt;. PubMed PMID: 19808881. &lt;/li&gt;&#xA;&lt;li&gt;The Free Dictionary by Farlex. &lt;a href=&quot;http://www.thefreedictionary.com/current&quot; rel=&quot;nofollow&quot;&gt;http://www.thefreedictionary.com/current&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-07-12T18:06:23.120" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19623" PostTypeId="2" ParentId="2050" CreationDate="2014-07-12T19:15:41.160" Score="3" Body="&lt;p&gt;The answer to this could be that there are &lt;strong&gt;many factors&lt;/strong&gt; contributing to the length of the life of tree species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Climate&lt;/strong&gt;: You can see that trees that have a reputation of becoming really old live in environments that have low moisture levels and much sunlight over the course of the year. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, you can see that the most long-lived trees in America are located in California, where the temperatures are relatively high, while moisture levels are low. If you have one without the other trees don't tend to live that long. Cold climates make growth&#xA;harder for each individual, yet hot and moist climates tend to help trees grow easier, but also die easier. Think of the amazon. It is one of the richest forests in the world, yet the growth of bacteria and high competition in the areas of the equator make life a lot harder for the longest living and slowest growing species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, the vast majority of the longest-living trees are located in California, or other regions of the same latitude!&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_oldest_trees&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/List_of_oldest_trees&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other species and the life around it/Its Ecosystem&lt;/strong&gt;: Individual trees tend to be less likely to be destroyed by a fire, as they are less likely to catch fire. At some instances, forest trees or dried-out grass can catch fire and pass it on to other individuals.&#xA;Microbes and bugs found in some parts of the world are known to their abilities to destroy trees!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Current size of the tree&lt;/strong&gt;: Larger trees are generally less likely to die of causes like drought or damage to their trunks, as they have greatly extensive nets of roots and thick trunks and thus are able to, even partly, recover these incidences. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a rockfall for example causes damage to one side of the tree, some of the brunches will probably die, but the rest of them, that have their own network to the roots, will probably survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that luck is involved and if the tree is lucky enough to avoid dying for a certain amount of time, regular fluctuations in the environment do not kill it as they would kill a younger, less robust tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Biology of tree species&lt;/strong&gt;: Debate is held as to whether tree cells have telomeres working the same way as they do in animals. Research published in 2001 suggests that telomeres don't work the same way, as plants developed without telomeres after six generations continue living and growing without problems. But even if they do use telomeres, they may use them in a different way. This is an area where research is still being conducted, though, and you may find controversies in the bibliography!&#xA;For example in the paper &quot;&lt;em&gt;Analysis of telomere length and telomerase activity in tree species of various life-spans, and with age in the bristlecone pine Pinus longaeva&quot;&#xA;Barry E. Flanary &amp;amp; Gunther Kletetschka&lt;/em&gt; which can be found in the rep&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;ved=0CCgQFjAB&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fpublication%2F7709949_Analysis_of_telomere_length_and_telomerase_activity_in_tree_species_of_various_life-spans_and_with_age_in_the_bristlecone_pine_Pinus_longaeva%2Ffile%2F9c96052bcf0a51be49.pdf&amp;amp;ei=zzrCU9OcMIjV0QXmt4CwCQ&amp;amp;usg=AFQjCNH7853fvZ8yneznSfIQQPsxtIDQag&amp;amp;sig2=-PELK5RCQlAGTvQODoyZ2A&amp;amp;bvm=bv.70810081,d.d2k&quot; rel=&quot;nofollow&quot;&gt;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;ved=0CCgQFjAB&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fpublication%2F7709949_Analysis_of_telomere_length_and_telomerase_activity_in_tree_species_of_various_life-spans_and_with_age_in_the_bristlecone_pine_Pinus_longaeva%2Ffile%2F9c96052bcf0a51be49.pdf&amp;amp;ei=zzrCU9OcMIjV0QXmt4CwCQ&amp;amp;usg=AFQjCNH7853fvZ8yneznSfIQQPsxtIDQag&amp;amp;sig2=-PELK5RCQlAGTvQODoyZ2A&amp;amp;bvm=bv.70810081,d.d2k&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;we can see that sometimes, short lived trees have longer telomeres than long lived ones!&#xA;(Look in the second paragraph of the section &quot;Results&quot;). This means that actually, nobody really knows!! It may be the telomeres, it may be something else, it may be a combination of factors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.madsci.org/posts/archives/2002-04/1019349924.Bt.r.html&quot; rel=&quot;nofollow&quot;&gt;http://www.madsci.org/posts/archives/2002-04/1019349924.Bt.r.html&lt;/a&gt;&#xA;(notice that this post has links to pages that are no longer available).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Distillation and the most important point&lt;/strong&gt;: The way that the tree is adapted to its environment determines its longevity in it. Planting an olive tree in the amazon is a great way of making sure it will not survive! Some trees are better at surviving in a certain climate (even if it is at your own garden) simply because they have evolved to live there. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That means that the trees probably don't have a defined lifetime in general, but the life expectancy is defined in each environment, depending on the circumstances!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that species we currently think of as short-lived can reach get really old: &#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11295506&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/11295506&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What some companies may have done is   try to combine characteristics of individuals through selective breeding - and yes, it works for trees as well!- to match the climate and terrain characteristics found in the certain country or region! Or they may have selected for resistance against the most common pests in your area!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope I answered you question adequately!&lt;/p&gt;&#xA;" OwnerUserId="8294" LastEditorUserId="8294" LastEditDate="2014-07-13T08:08:25.300" LastActivityDate="2014-07-13T08:08:25.300" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19624" PostTypeId="2" ParentId="14052" CreationDate="2014-07-12T19:29:32.880" Score="6" Body="&lt;p&gt;A mechanical stimulus can act on a tissue with elastic and viscoelastic properties in two ways [1, 2]:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;distort the cellular membrane which leads to opening of ion channels.&lt;/li&gt;&#xA;&lt;li&gt;create tension on the extracellular matrix or cytoskeleton, to which a ion channel is bound, thus leading to opening of the channel.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Stretch-activated ion channels opening leads to the formation of an action potential, if there is enough ionic flow to trigger depolarization [1, 3].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Stretch-activated ion channel,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Stretch-activated_ion_channel&amp;amp;oldid=606349902&quot;&gt;http://en.wikipedia.org/w/index.php?title=Stretch-activated_ion_channel&amp;amp;oldid=606349902&lt;/a&gt; (accessed July 12, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Grigg P. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2422151&quot;&gt;Biophysical studies of mechanoreceptors.&lt;/a&gt; J. Appl. Physiol. 1986 Apr;60(4):1107-15. PubMed PMID: 2422151. &lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Mechanotransduction,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Mechanotransduction&amp;amp;oldid=593605473&quot;&gt;http://en.wikipedia.org/w/index.php?title=Mechanotransduction&amp;amp;oldid=593605473&lt;/a&gt; (accessed July 12, 2014).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-07-29T13:02:51.360" LastActivityDate="2014-07-29T13:02:51.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19625" PostTypeId="2" ParentId="10519" CreationDate="2014-07-12T19:48:14.737" Score="4" Body="&lt;p&gt;Pathological potassium concentration promotes arrhythmia.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Increased extracellular potassium&lt;/strong&gt; inactivates &lt;span class=&quot;math-container&quot;&gt;$Na^+$&lt;/span&gt; channels and opens &lt;span class=&quot;math-container&quot;&gt;$K^+$&lt;/span&gt; channels, causing the cells to become refractory [1]:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Increased extracellular potassium levels result in depolarization of the membrane potentials of cells due to the increase in the equilibrium potential of potassium. This depolarization opens some voltage-gated sodium channels, but also increases the inactivation at the same time. Since depolarization due to concentration change is slow, it never generates an action potential by itself instead, it results in accommodation. Above a certain level of potassium the depolarization inactivates sodium channels, opens potassium channels, thus the cells become refractory. This leads to the impairment of neuromuscular, cardiac, and gastrointestinal organ systems. Of most concern is the impairment of cardiac conduction which can result in ventricular fibrillation or asystole.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Decreased extracellular potassium&lt;/strong&gt; leads to hyperpolarization [2]:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Lower potassium levels in the extracellular space will cause hyperpolarization of the resting membrane potential. As a result, a greater than normal stimulus is required for depolarization of the membrane in order to initiate an action potential.&lt;/p&gt;&#xA;&lt;p&gt;In the heart, hypokalemia causes hyperpolarization in the myocytes' resting membrane potential. The more negative membrane potentials in the atrium may cause arrhythmias because of more complete recovery from sodium-channel inactivation, making the triggering of an action potential less likely. In addition, the reduced extracellular potassium (paradoxically) inhibits the activity of the &lt;span class=&quot;math-container&quot;&gt;$I_{Kr}$&lt;/span&gt; potassium current and delays ventricular repolarization. This delayed repolarization may promote reentrant arrhythmias.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &amp;quot;Hyperkalemia,&amp;quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Hyperkalemia&amp;amp;oldid=612096441&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Hyperkalemia&amp;amp;oldid=612096441&lt;/a&gt; (accessed July 12, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &amp;quot;Hypokalemia,&amp;quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Hypokalemia&amp;amp;oldid=612818488&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Hypokalemia&amp;amp;oldid=612818488&lt;/a&gt; (accessed July 12, 2014).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-07-29T14:01:36.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19626" PostTypeId="1" CreationDate="2014-07-12T20:14:50.517" Score="11" ViewCount="1543" Body="&lt;p&gt;I just read the answer to &lt;a href=&quot;https://biology.stackexchange.com/questions/19614/is-there-any-size-limit-to-the-amount-of-information-a-human-or-other-brain-ca&quot;&gt;this question&lt;/a&gt;, and it got me thinking...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the human brain (or any other brain) has a finite amount of storage, what would happen once the brain has taken in its maximum amount of information?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is, or course, assuming that the individual can live long enough to acquire that much information. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would take a guess that just like how we forget things all the time, the new memories would &quot;override&quot; some older ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has there been any research or hypotheses on a brain's behavior once the its storage has maxed out?&lt;/p&gt;&#xA;" OwnerUserId="8304" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-07-15T00:43:41.583" Title="What happens once a brain is full?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;memory&gt;&lt;learning&gt;&lt;cognition&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19627" PostTypeId="2" ParentId="19626" CreationDate="2014-07-12T20:22:59.507" Score="8" Body="&lt;p&gt;Three possible mechanisms are mentioned in the first referenced article [1]:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Attentional blink&lt;/strong&gt; - the failure to detect a (visual) stimulus [2].&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Visual short-term memory&lt;/strong&gt; - non-permanent storage of visual information over an extended period of time [3].&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Psychological refractory period&lt;/strong&gt; - the period of time during which the response to a second stimulus is significantly slowed because a first stimulus is still being processed [4, 5].&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Marois R, Ivanoff J. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15925809&quot;&gt;Capacity limits of information processing in the brain.&lt;/a&gt; Trends Cogn. Sci. (Regul. Ed.). 2005 Jun;9(6):296-305. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.tics.2005.04.010&quot;&gt;10.1016/j.tics.2005.04.010&lt;/a&gt;. PubMed PMID: 15925809. Full text available on &lt;a href=&quot;http://www.psy.vanderbilt.edu/faculty/marois/Publications/Marois_Ivanoff-2005.pdf&quot;&gt;http://www.psy.vanderbilt.edu/faculty/marois/Publications/Marois_Ivanoff-2005.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Attentional blink,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Attentional_blink&amp;amp;oldid=615277943&quot;&gt;http://en.wikipedia.org/w/index.php?title=Attentional_blink&amp;amp;oldid=615277943&lt;/a&gt; (accessed July 12, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Visual short-term memory,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Visual_short-term_memory&amp;amp;oldid=508372290&quot;&gt;http://en.wikipedia.org/w/index.php?title=Visual_short-term_memory&amp;amp;oldid=508372290&lt;/a&gt; (accessed July 12, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Pashler H. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7972591&quot;&gt;Dual-task interference in simple tasks: data and theory.&lt;/a&gt; Psychol Bull. 1994 Sep;116(2):220-44. PubMed PMID: 7972591. &lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Psychological refractory period,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Psychological_refractory_period&amp;amp;oldid=603184270&quot;&gt;http://en.wikipedia.org/w/index.php?title=Psychological_refractory_period&amp;amp;oldid=603184270&lt;/a&gt; (accessed July 12, 2014).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-07-12T20:22:59.507" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19628" PostTypeId="2" ParentId="2050" CreationDate="2014-07-12T20:59:30.473" Score="3" Body="&lt;p&gt;Everything has a &lt;a href=&quot;http://www.thefreedictionary.com/lifespan&quot; rel=&quot;nofollow&quot;&gt;life span&lt;/a&gt;. When it comes to trees, there are significant variations between species (see &lt;a href=&quot;http://bigtree.cnre.vt.edu/TreeAge.htm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; some examples).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from the external factors, these variations seem to be related to telomeres length and telomerase activity [1]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The results from this study support the hypothesis that both increased telomere length and telomerase activity may directly/indirectly contribute to the increased life-span and longevity evident in long-lived pine trees (2000-5000 year life-spans) compared to medium-lived (400-500 year life-span) and short-lived (100-200 year life-span) pine trees, as well as in P. longaeva with age.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also, the lower metabolic rate of some trees increases life span [2]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... the extremely high longevity of trees may be explained by the lower metabolism displayed by the stems. These results clearly reflect different energy allocation and energy expenditure rate strategies between leaves and stems, which may result in different senescence rates (and life spans) in these organs. They also suggest that, in contrast to animals, the ROL (rate of living ) theory of aging may apply to woody plants at the organ level, thereby opening a promising new line of research to guide future studies on plant senescence.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Leaf longevity is also correlated to shoot growth [3]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These results suggest that leaf longevity is greater on shoots with low annual growth potential. Thus, a slow-growing tree at high elevation (low annual shoot growth potential) can have the same amount of foliage per shoot as a fast-growing tree at lower elevation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Flanary BE, Kletetschka G. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16034678&quot; rel=&quot;nofollow&quot;&gt;Analysis of telomere length and telomerase activity in tree species of various life-spans, and with age in the bristlecone pine Pinus longaeva.&lt;/a&gt; Biogerontology. 2005;6(2):101-11. doi: &lt;a href=&quot;http://dx.doi.org/10.1007/s10522-005-3484-4&quot; rel=&quot;nofollow&quot;&gt;10.1007/s10522-005-3484-4&lt;/a&gt;. PubMed PMID: 16034678. &lt;/li&gt;&#xA;&lt;li&gt;Issartel J, Coiffard C. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20963610&quot; rel=&quot;nofollow&quot;&gt;Extreme longevity in trees: live slow, die old?&lt;/a&gt; Oecologia. 2011 Jan;165(1):1-5. doi: &lt;a href=&quot;http://dx.doi.org/10.1007/s00442-010-1807-x&quot; rel=&quot;nofollow&quot;&gt;10.1007/s00442-010-1807-x&lt;/a&gt;. PubMed PMID: 20963610. &lt;/li&gt;&#xA;&lt;li&gt;Schoettle AW. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14972918&quot; rel=&quot;nofollow&quot;&gt;The interaction between leaf longevity and shoot growth and foliar biomass per shoot in Pinus contorta at two elevations.&lt;/a&gt; Tree Physiol. 1990 Dec;7(1_2_3_4):209-214. PubMed PMID: 14972918. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-07-12T20:59:30.473" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19629" PostTypeId="1" CreationDate="2014-07-12T21:21:31.897" Score="15" ViewCount="8840" Body="&lt;p&gt;Thanks for looking.&lt;/p&gt;&#xA;&lt;p&gt;First off, I am not a biologist, just a curious layman, so I apologize in advance if this isn't a &amp;quot;good&amp;quot; question.  Please don't downvote me into oblivion.&lt;/p&gt;&#xA;&lt;p&gt;I read today that the human brain has about 100 billion neurons and that got me wondering: is that number pretty standard for everyone or does someone like say,&#xA;Einstein, have many more neurons than this daft poster.&lt;/p&gt;&#xA;&lt;h1&gt;Question&lt;/h1&gt;&#xA;&lt;p&gt;Is there a correlation between total neuron count and intelligence, or does intelligence depend more on the way neurons are used--or some other factor like previous experience--rather than their total count?&lt;/p&gt;&#xA;&lt;h1&gt;Can this question be answered?&lt;/h1&gt;&#xA;&lt;p&gt;There are two very valid points-of-view posted as answers below, but it sounds like we simply don't have a solid answer to this question at this point in time, so I hesitate to select a &amp;quot;correct&amp;quot; answer.&lt;/p&gt;&#xA;" OwnerUserId="393" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-13T16:23:18.727" Title="Is there a correlation between total neurons and intelligence?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;neurotransmitter&gt;&lt;intelligence&gt;" AnswerCount="4" CommentCount="6" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19630" PostTypeId="2" ParentId="19629" CreationDate="2014-07-12T23:03:52.620" Score="6" Body="&lt;p&gt;There are an estimated 100 billion neurons within the human brain. In general a minor variation in the number of neurons should not effect individuals too much, however when there is a more significant loss, such as brain injury or in some forms of dementia cognitive abilities do decline. So in this sense yes the number of neurons does relate to intelligence. However this variation is not what accounts for general variation of intelligence in the population.&lt;/p&gt;&#xA;" OwnerUserId="8034" LastActivityDate="2014-07-12T23:03:52.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19631" PostTypeId="1" AcceptedAnswerId="19674" CreationDate="2014-07-13T00:24:23.103" Score="2" ViewCount="131" Body="&lt;p&gt;What is the risk, if any, associated with eating a 100th-generation mutated eggplant derived from a radioactive ancestor?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In another word, is that possible that organic toxin will be produced by the mutated plant and is it a good idea to plant it in America? These plant seems very beautiful to me! Ha Ha&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: The descendant eggplant is not radioactive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Motivation: There are many mutated eggplants around Japanese power plants.&lt;/p&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="5479" LastEditDate="2014-07-14T02:01:05.323" LastActivityDate="2014-07-14T20:32:39.543" Title="Is it dangerous to eat a mutated eggplant descended from a radioactive ancestor?" Tags="&lt;human-biology&gt;&lt;botany&gt;" AnswerCount="1" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="19632" PostTypeId="2" ParentId="9850" CreationDate="2014-07-13T02:17:21.680" Score="16" Body="&lt;p&gt;&lt;strong&gt;The Cicada&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A careful study of the noise-making apparatus of the cicada can be found in a 1994 paper by Young and Bennet-Clark.$^1$ The authors generated sounds at about 0-16 kHz at peaks on the order of 100 dB using cicadas in various stages of deconstruction.  The cicada uses a resonant organ-system called the &lt;em&gt;tymbal&lt;/em&gt; which buckles and unbuckles rapidly to produce sound. The buckling-in is caused by muscle contraction and is louder than the buckling-out (relaxation) phase. Air sacs (a feature of many other small noisemakers) serve to amplify the sound.  The tymbal itself, for the species in this paper, has a resonant frequency of about 4kHz (Young, page 1017). The song of the cicada as modified/amplified by air sacs and other structures, is often around 10kHz.$^{2}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Pure Tone vs. Diffuse Tone?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The vocalizations of large vertebrates are a complex superposition of waves that in the frequency spectrum are somewhat spread out. To the extent that a frog or a bird emits a pure tone, the energy will be confined to a narrow frequency range and this &lt;em&gt;may&lt;/em&gt; be a strategy for achieving greater amplitude. &lt;em&gt;Given comparable audio sensitivity&lt;/em&gt;, however, the intensity of pure tones will depend on amplitude (intensity), regardless of frequency.$^{3,4}$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other Small Loud Animals&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the songs of cicadas are intense, especially in concert, on an individual level there is competition from other species. According to a &lt;a href=&quot;http://gizmodo.com/5811368/animals-most-amazing-acoustic-feats/&quot;&gt;Gizmodo&lt;/a&gt; article quoting assorted scientists, the snapping shrimp produces a transient snap that is around 200 decibels, a level that &lt;a href=&quot;http://home.earthlink.net/~dnitzer/4HaasEaton/Decibel.html&quot;&gt;one site&lt;/a&gt; describes as &quot;deafening.&quot; For perspective, dolphins can emit short chirps of 220 dB but these are outside the range of human hearing. The lion emits a roar of 115 dB which is sustained and audible 5 miles away, according to the article. Elephants also are capable of 117 dB cries, as are howler monkeys.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both the shrimp and the cicada use non-vocal vibration to create their sounds. The shrimp uses a &quot;spring-loaded claw&quot; (the spring is muscle). The localized force of one part of the claw hitting the other generates a bubble (this is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Cavitation&quot;&gt;inertial cavitation&lt;/a&gt;). When the bubble collapses it generates a shock wave (noise) that stuns fish (prey).$^5$ The noise of frogs is produced as air passes from the lungs through the larynx, amplified by distended air sacs which resonate. Birds can produce up to 135dB (the Mollucan Cockatoo). They generally force air past (membranes and) a specialized organ called the &lt;em&gt;syrinx&lt;/em&gt; located at the bottom of the trachea (see the &lt;a href=&quot;http://en.wikipedia.org/wiki/Bird_vocalization&quot;&gt;Wikipedia&lt;/a&gt; note on bird vocalization).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Micronecta scholtzi,&lt;/em&gt; a 2mm-long aquatic insect, is &lt;em&gt;for its size&lt;/em&gt; the loudest known animal. It creates a sound of 99.2 dB intensity which (despite being largely lost in transition from water to air) is audible to humans ashore. According to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Micronecta_scholtzi&quot;&gt;Wikipedia note&lt;/a&gt; it creates this sound by &quot;stridulating a ridge on its penis across corrugations on its abdomen.&quot; The area involved is about 50$\mu m$ across. Details of the mechanism are poorly understood. The article's comparison of the sperm whale's 236 (underwater) dB song gives perspective, as a sperm whale can weigh 14 metric tons.      &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A Common Aspect of Sound Intensity: Cavity Resonance&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Descriptive studies of sound-creation by small animals (with the possible exception of the snapping shrimp) do not fully explain why a one-gram bug can make a bigger noise than a lion. Purely vocal methods of larger vertebrates produce sustained noise on the order of 100 dB but the non-vocal instruments of smaller creatures are capable of short bursts of amazing intensity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is difficult to generalize but because air sacs are part of many sound-making schemes, &lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/waves/cavity.html&quot;&gt;cavity resonance&lt;/a&gt; probably plays an important role. Like spring-mass systems or RLC circuits, cavities have resonant frequencies at which amplitude of a signal may be increased (the policeman's whistle is a familiar example). Another paper by Bennet-Clark and Young gives a sketch of a theory along these lines. At resonant frequencies the impedance of the instrument falls sharply and instead of being dissipated (generally as heat) the energy emerges as sound.$^6$  &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;$^1$ Bennet-Clark and Young, The Role of the Tymbal in Cicada Sound Production, J. of Experimental Biol. (1995) 198, 1001-1019.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^{2}$ The frequency of cicadas is variable, mostly on the order of 10kHz but occasionally very low (&amp;lt; 1kHz), mostly due to body size. See this &lt;a href=&quot;http://sci-s03.bacs.uq.edu.au/ins-info/Hab.htm&quot;&gt;article&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^3$ Sound--essentially a compression wave--diminishes with distance. So when the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sound_pressure&quot;&gt;Wiki article&lt;/a&gt; on noise levels compares noise levels it includes the distance from the object. For example, 100 db (comparable to the cicada) is the level of noise associated with a jack-hammer at 1 meter away.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^4$ Audible range for humans is roughly 15 Hz-16000 Hz. As mentioned below, the dolphin can emit very intense high-pitched sounds that we don't hear at all, so the analogy to EM waves (higher frequency = higher energy) doesn't help predict perception. See Pfaff and Stecker, Loudness and Frequency Content of Noise in the Animal House, &lt;em&gt;Lab. Animals&lt;/em&gt; (1976) 10, 111-117.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^5$ M. Versluis, B. Schmitz, A von der Heydt &amp;amp; D. Lohse (2000). &quot;How snapping shrimp snap: through cavitating bubbles&quot;. Science 289 (5487): 2114–2117.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^6$ Bennet-Clark and Young, Short Communication, The Scaling of Song Frequency in Cicadas, J. Exp. Biol. 191, 291-294 (1994). &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-07-19T14:41:16.517" LastActivityDate="2014-07-19T14:41:16.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19634" PostTypeId="2" ParentId="19626" CreationDate="2014-07-13T02:50:03.150" Score="9" Body="&lt;p&gt;It's very likely that memory is &quot;lossy&quot; and holographic, such that you can keep adding more information indefinitely, but retain it with less and less accuracy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Memory isn't a digital storage system with X gigabytes of capacity, and the inputs to memory aren't neat little packets. What we remember are a web of associations and patterns. Vastly oversimplified, we group similar memories together into a baseline, and remember the deviations from that. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you walk the same route to work every day, you take in a huge amount of information the first few days: stretches of residential buildings, cars parked on the street, portions of curb painted red, trash in the gutters. In successive days different cars will come and go, front yards will get overgrown and trimmed, etc, but these details get mixed in with what you saw the first few days into a blurrier and blurrier sort of average. Trillions of impressions from hundreds of days take up very little more capacity than the first day did, and still tell you what you need to know about the route. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine that there's a particular green car of common make and model, that was parked in front of a certain house about 3/4 of the time for the first hundred days you walked the route. Your memory reduces this to something like &quot;green car usually along here somewhere&quot;. If the green car stops parking there, you'll probably notice &quot;green car not there today&quot; because that's a contrast to the common case that you've memorized. But if a week goes by with no sightings of the green car, it's very hard to remember which day you last saw it, because you don't remember individual sightings. (I actually had this happen to me with &lt;em&gt;my own car&lt;/em&gt;; I discovered it stolen on a Wednesday and could not for the life of me recall whether I'd seen it on Monday or Tuesday even though I'd walked past the spot it should have been parked both days.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you remember more things, you remember them in less and less detail; you can't remember if you've been to New Orleans once or twice; you can't remember which memories were from your first trip to Las Vegas or your second, etc. So the brain never becomes full, it just becomes fuzzy.&lt;/p&gt;&#xA;" OwnerUserId="1302" LastEditorUserId="6330" LastEditDate="2014-07-14T23:26:40.717" LastActivityDate="2014-07-14T23:26:40.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19635" PostTypeId="1" CreationDate="2014-07-13T03:03:17.137" Score="1" ViewCount="45" Body="&lt;p&gt;I have a growing frustration with the lows 'new-age' parenting is reaching, along with asininity of so much of our public schools' (and summer camps') philosophies and policies in relation to our kids. Whatever the implications, this has continually lead me to the thought of&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;what the &lt;em&gt;natural precedent&lt;/em&gt; is for how primates (or other mammals) raise their young, collectively or otherwise -- how they're guided, rewarded, chastised, and conditioned.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;May someone please recommend a book that delves in to some of this? (Humans don't necessarily have to enter the picture, but something that does compare and contrast with the human condition would be a bonus.) (Preferably not a text book, but, by all means, please recommend those too.)&lt;/p&gt;&#xA;" OwnerUserId="8307" LastActivityDate="2014-08-09T05:49:53.003" Title="Book recommendation on mammal (or just primate) behaviour, especially in relation to child-rearing" Tags="&lt;ethology&gt;&lt;behaviour&gt;&lt;mammals&gt;&lt;book-recommendation&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19636" PostTypeId="1" AcceptedAnswerId="19641" CreationDate="2014-07-13T04:42:48.743" Score="2" ViewCount="144" Body="&lt;p&gt;Do all signalling pathways have something that can inhibit them? If the signal pathway is benefitial  and it is inhibited would the inhibitor be caused by a biological problem?  Are all inhibitors controlled by some subcellular  mechanism?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastActivityDate="2014-07-13T18:42:36.703" Title="Regarding signalling pathways" Tags="&lt;cell-biology&gt;&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19637" PostTypeId="1" AcceptedAnswerId="19638" CreationDate="2014-07-13T06:03:56.767" Score="3" ViewCount="55" Body="&lt;p&gt;If there is an apoptosis shut-off mechanism of any kind, one could call it a null-apoptosis mechanism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is possible, could there be a null-apoptosis inhibitor? Something that inhibits an apoptosis inhibitor?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastEditorUserId="57" LastEditDate="2014-07-13T19:35:22.990" LastActivityDate="2014-07-13T19:35:22.990" Title="Regarding apoptosis and inhibitors" Tags="&lt;cancer&gt;&lt;apoptosis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19638" PostTypeId="2" ParentId="19637" CreationDate="2014-07-13T09:28:11.737" Score="5" Body="&lt;p&gt;Apoptosis is very tightly controlled for obvious reasons. Setting it off without proper control would result in the uncontrolled loss of cells. Apoptosis is one of the major pathways which are either mutated or shut-off in cancers, preventing the body from eliminating malingnant cells. These two papers are interesting in this context:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2117903/&quot; rel=&quot;noreferrer&quot;&gt;Apoptosis: A Review of Programmed Cell Death&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nrc/journal/v5/n3/abs/nrc1560.html&quot; rel=&quot;noreferrer&quot;&gt;The role of apoptosis in cancer development and treatment response&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In this context it makes no sense to have a shut-off mechanism once the apoptosis cascade has started. It is only set off when there is a real reason (and is well controlled), so I don't think there a &quot;null-apoptosis&quot; mechanism. It would of course still be possible to artificially make substances, that inhibit parts of the activation cascade. But besides for apoptosis research I don't see any use for it. There is actually some research going on to find out how to activate apoptosis again in cancers.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-13T09:28:11.737" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19640" PostTypeId="1" AcceptedAnswerId="19696" CreationDate="2014-07-13T09:48:50.510" Score="8" ViewCount="459" Body="&lt;p&gt;The organ we have to provide us with current acceleration information is quite complicated. Because an ant queen didn't seem to notice when I picked up the bottle she was in, I have a suspicion that ants don't really care about acceleration and therefore can't tell where it's up and where it's down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I right? If not, how do they sense acceleration?&lt;/p&gt;&#xA;" OwnerUserId="6918" LastActivityDate="2014-07-15T15:52:05.050" Title="Do ants feel acceleration?" Tags="&lt;sensation&gt;&lt;ant&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19641" PostTypeId="2" ParentId="19636" CreationDate="2014-07-13T11:22:49.493" Score="2" Body="&lt;p&gt;There are some inhibitors in the cell, which have specific effects on &lt;a href=&quot;http://en.wikipedia.org/wiki/Signal_transduction&quot; rel=&quot;nofollow noreferrer&quot;&gt;signal transduction&lt;/a&gt;. These are mostly second messengers (like cAMP, cGMP, calcium ions,  inositol 1,4,5-trisphosphate and others), which are then able to diffuse relative fast to other proteins. There they can either amplify a signal or cause inhibiting processes to start which then terminate the activation of the signal transduction cascade.&#xA;The problem is that these inhibitors that they work unspecific in their inhibition and termination. Signal transduction is tightly controlled as they directly influence the expression of various genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lot of the proteins in these cascades are kinases which are activated upon phosphorylation and then carry on by phosphorylating the next step of the cascade. The activity is stopped by phosphatases which remove the phosphorylations from the kinases and thus inactivate them until the next signal is passed down the cascade. It works like in this figure (from &lt;a href=&quot;http://wiki.c2b2.columbia.edu/dream/index.php/The_Signalling-Cascade_Challenges._Description&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/htL4w.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specific inhibitors for single proteins in the signalling cascades are available as drugs against cancer. Since these signalling cascades regulate gene expression including cell cycle control, they are important targets for dysregulation in cancer. A numer of kinases in the MAP kinase pathway for example are mutated there and constantly active. The so called small molecule inhibitors bind to the protein and inhibit the kinase activity, preventing a permanent signal. See this article for more information: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nrc/journal/v9/n1/abs/nrc2559.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Targeting cancer with small molecule kinase inhibitors&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-07-13T18:42:36.703" LastActivityDate="2014-07-13T18:42:36.703" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19642" PostTypeId="1" AcceptedAnswerId="19643" CreationDate="2014-07-13T11:36:27.933" Score="8" ViewCount="17260" Body="&lt;p&gt;If we don't drink water for a long period of time(say,10 hours), as during fasting and then when we break our fast by drinking water why is it that our body starts sweating?&lt;/p&gt;&#xA;" OwnerUserId="3881" LastEditorUserId="3881" LastEditDate="2014-07-13T11:48:06.527" LastActivityDate="2014-07-13T11:53:45.750" Title="Perspiration after drinking water" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19643" PostTypeId="2" ParentId="19642" CreationDate="2014-07-13T11:53:45.750" Score="11" Body="&lt;p&gt;During the time when you are not drinking water you still loose some water to sweating and urine. Sweating is (especially in hot climates) an important function of the body to maintain the body temperature in desired range. If this water is not replaced, the body gets dehydrated. This induces a reaction which reduces the activity of the &quot;body thermostat&quot; to tolerate a higher body temperature without excessive sweating to maintain the fluid balance of the body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you start drinking again after this the dehydration period, the body starts sweating to regulate the body temperature again, since now the loss of water is not critical anymore for the body. For a detailed discussion (including further references) have a look at this publication: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762624/&quot;&gt;The effect of water temperature and voluntary drinking on the post&#xA;rehydration sweating&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-13T11:53:45.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19644" PostTypeId="2" ParentId="14794" CreationDate="2014-07-13T17:54:43.897" Score="20" Body="&lt;p&gt;I wouldn't say that a human is &quot;likely&quot; to get sick by drinking from a puddle, I'd say &quot;at some risk&quot;. It isn't &lt;em&gt;desperately&lt;/em&gt; dangerous, although don't take that as a recommendation. There are many infections you can get from water (bacterial, viral, amoebal, and I presume fungal). You don't want to risk them, but &lt;em&gt;probably&lt;/em&gt; won't actually encounter them in that puddle in your garden you see your dog drinking from. If the water is stagnant then the list of things in it that might hurt you is longer than if it's flowing. If you can avoid the mud, and anything that's been standing long enough to grow algae, fresh rainwater is a pretty good bet as these things go.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same is true of other species, but the risk per drink is lower, since they drink it more and develop resistance to more of the things on the list. Humans are no different. For example some areas tend to have Hepatitis A in the tap water. The local population is immune after they've been infected once, and most childhood infections cause no symptoms, so it's not a problem for the locals. But to an unvaccinated visitor, the water's not safe. Hep A normally won't kill you, but is still well worth avoiding since it will make you sick for several weeks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So basically, humans drink clean water because we can, not because we absolutely need to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lifespan of humans living &quot;in the wild&quot; (that is, populations prior to or independent of human agriculture) is pretty well agreed to be rather less than that of typical modern lifestyles. Water-borne disease is only one of many things responsible for that. The expected lifespan of a person used to purified water and so on, dropped into &quot;the wild&quot;, is even lower again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;clean-water&quot; problem in developing countries is primarily one of high population, relative to what the same area could possibly support in the absence of agriculture and other technology. The biggest risk of water-borne disease comes from contamination by human waste (although there are other sources, for example rats can contaminate water with Weil's disease). A small group of humans living in a large area doesn't have to worry about human contamination, they just drink upstream of where they defecate. This strategy doesn't help much once the population is dense enough that someone else is doing the same thing 20 metres away from you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And of course, human agriculture also supports a much higher rat population than would otherwise be present (they're omnivores too, so they'll eat pretty much any food humans do). I suspect most human disease can be blamed on agriculture one way or another: if not on the animals then on the close-quarters living. If the population of humans was closer to what it was in the palaeolithic (a few thousand or tens of thousands of people in Europe), and was used to drinking from natural sources, then the water would be mostly (not entirely) safe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it's not so much that humans need perfectly clean water, it's that &lt;strong&gt;humans have figured out how to live in populations so large that we tend to make all the nearby water particularly dirty&lt;/strong&gt;. Other species aren't completely unaffected by this, but they are &lt;em&gt;less&lt;/em&gt; affected because our waste is specifically contaminating the water with diseases that affect us.&lt;/p&gt;&#xA;" OwnerUserId="6132" LastEditorUserId="6132" LastEditDate="2015-06-12T18:58:01.480" LastActivityDate="2015-06-12T18:58:01.480" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19645" PostTypeId="2" ParentId="2250" CreationDate="2014-07-13T18:44:40.227" Score="14" Body="&lt;p&gt;In general, if you want to know &quot;exactly how much of X on an average is needed to be consumed to cause death&quot;, then the magic search term for Google is &quot;LD50&quot;, that is the dose that kills 50% of victims.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen the LD50 for water quoted as 90ml/kg for rats (that is, 90 ml per kg of body mass), for example on this &lt;a href=&quot;http://www.sciencelab.com/msds.php?msdsId=9927321&quot; rel=&quot;nofollow noreferrer&quot;&gt;safety data sheet&lt;/a&gt;. I presume that figure comes not from theorising about salt intake, but from giving measured quantities of distilled water to rats and counting how many die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's likely of the same order of magnitude for humans. Unlike many &quot;poisons&quot; it's not about subtleties of liver chemistry that will vary by species. What killed the rats was the swelling by osmosis of cells and tissues that they didn't want swelled.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a largeish human that dose is 7 litres, approx 14 pints, drunk at a sitting. Which is fairly unlikely in a school chemistry lesson. Besides, with effort you could drown in less than that!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The distilled water in your chemistry lab has a relatively much larger chance of killing you for some reason other than its inherent toxicity (although it's still fairly unlikely in absolute terms). For example if it's stored for a while there could be legionella in the tanks. Probably best not to drink it, just as it's best not to drink any water that may have been sitting around for weeks in an unsealed container.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Definitely don't drink other stuff from the labs that your friend tells you is poisonous, because some of it really is. In particular the one everybody thinks of (because, like the water, it's similar to something they know about): lab ethanol can have methanol as an impurity, and may well have had benzene intentionally added because that's an easy way to get the last 4.5% water out that otherwise cannot be removed by distillation. A mouthful of ethanol isn't normally lethal (although it might be illegal), whereas methanol and benzene are both &quot;properly&quot; toxic in the sense that a few grams will kill you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, I can confirm that in my school days I obtained the same experimental result you did.&lt;/p&gt;&#xA;" OwnerUserId="6132" LastEditorUserId="6132" LastEditDate="2017-04-21T09:22:11.317" LastActivityDate="2017-04-21T09:22:11.317" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19647" PostTypeId="1" CreationDate="2014-07-13T22:16:28.370" Score="3" ViewCount="165" Body="&lt;p&gt;I would like ensure that my reasoning is correct. Assuming that I know the aminoacids sequence of the protein of interest. I can't say anything about the structure looking only at the aminoacids sequence of this protein. But if I know this protein from another organism and the structure of this protein is known, then I can compare both of the sequences and conclude something, right? what I mean, is that there is no specific sequence corresponding to, for example, helix-two- turn-helix motif, and that I can take this sequence, check if my protein has it and say that there is helix-two- turn-helix motif or not. I can do this only by comparison to the protein which structure is already known, right? &lt;/p&gt;&#xA;" OwnerUserId="6892" LastEditorUserId="8179" LastEditDate="2014-07-16T16:22:04.300" LastActivityDate="2014-07-16T16:22:04.300" Title="How to recognize a conserved motifs of the protein" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19648" PostTypeId="1" AcceptedAnswerId="19682" CreationDate="2014-07-14T02:00:13.750" Score="1" ViewCount="533" Body="&lt;p&gt;Is it possible for a device to measure how much air we breathe in and out over the entire day and at what rate? I think if we have access to this data we can compare it across people.&lt;/p&gt;&#xA;" OwnerUserId="5860" LastActivityDate="2014-07-15T10:42:30.877" Title="How to know if your breathing is normal?" Tags="&lt;human-biology&gt;&lt;breathing&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19652" PostTypeId="1" AcceptedAnswerId="19654" CreationDate="2014-07-14T05:48:19.400" Score="1" ViewCount="126" Body="&lt;p&gt;I have to answer a question about a sub-task of my thesis: &lt;strong&gt;Can the bacteria &lt;em&gt;X&lt;/em&gt; produce the protein &lt;em&gt;Y&lt;/em&gt;?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I searched of course Google and BLAST. There is no data supporting that this specific bacteria ever produced this protein sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, my thesis supervisor wants me to go deeper&lt;sup&gt;[1]&lt;/sup&gt;, but I don't know how to do it &lt;em&gt;in silico&lt;/em&gt; in a way to offer a proper answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm thinking of doing with the data at hand is to create a DB on localhost with all the versions of the protein listed in BLAST (&lt;em&gt;I'm using ruby, not sure how can I fetch all this data in FASTA format yet, but I'll figure it out&lt;/em&gt;), and all the strains of the bacteria listed in BLAST and perform a &lt;a href=&quot;http://en.wikipedia.org/wiki/Approximate_string_matching&quot; rel=&quot;nofollow&quot;&gt;fuzzy string matching&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's like brute-forcing. After I have a possible score I can get the closest score of them all, study it a bit and then submit my answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any other way to attack this problem in order to submit a proper, at least partially polished answer?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NOTE: I don't have access to any lab, any &lt;em&gt;experiment&lt;/em&gt; must be performed in silico.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] My supervisor believes that IF this bacteria needed this protein it WOULD be able to to produce it at will without undergoing mutations. And since his level of dedication and knowledge revolving molecular biology is scary, it's kind of hard to believe that he is wrong.&lt;/p&gt;&#xA;" OwnerUserId="1856" LastEditorUserId="5331" LastEditDate="2014-07-14T10:20:04.510" LastActivityDate="2014-07-14T10:20:04.510" Title="To what extent is it possible to understand if a bacteria can produce a protein? (in silico only!)" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;proteins&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="19653" PostTypeId="1" AcceptedAnswerId="96315" CreationDate="2014-07-14T07:50:00.280" Score="5" ViewCount="782" Body="&lt;p&gt;I recently watched the video &lt;a href=&quot;https://www.youtube.com/watch?v=R3unPcJDbCc&quot;&gt;This Is Not Yellow&lt;/a&gt; explaining how red, green, and blue pixels can be used to create images of all other colors. Since yellow is created with red and green pixels, how is a person with red-green colorblindness (me, for instance) able to perceive yellow on a monitor?&lt;/p&gt;&#xA;" OwnerUserId="8318" LastActivityDate="2020-10-14T19:44:10.030" Title="How does someone with red-green colorblindness see yellow on a monitor/television?" Tags="&lt;neuroscience&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19654" PostTypeId="2" ParentId="19652" CreationDate="2014-07-14T09:27:31.903" Score="2" Body="&lt;p&gt;Your problem will finally boil down to searching your sequence in the Blast databases. Performing Blast seems to be probably the best way to find out if your bacteria has that specific protein expressed or not. If you could not find it in the nearest species using Blast, then try running PSI-BLAST, which would return you distant homologs, by which you can see if your protein is expressed in the other bacterial species. &lt;/p&gt;&#xA;" OwnerUserId="6455" LastActivityDate="2014-07-14T09:27:31.903" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19655" PostTypeId="2" ParentId="19338" CreationDate="2014-07-14T09:36:11.143" Score="-2" Body="&lt;p&gt;The e-value is required to have confidence in the hit, along with hit. Generally, an e-value of e-4 is preferred because, this cutoff is found to be sufficient enough by blast to confirm a hit as homolog. But, for a hit, an e-value greater than e-4 does not mean it is a homolog neither we can say it is not a homolog. We cannot surely infer anything from these hits. Therefore, researchers choose a value &#xA;" OwnerUserId="6455" LastActivityDate="2014-07-14T09:36:11.143" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19656" PostTypeId="1" AcceptedAnswerId="19659" CreationDate="2014-07-14T09:56:02.690" Score="7" ViewCount="1387" Body="&lt;p&gt;I'm aware that our earliest records of many major animal and plant phyla come from the Cambrian or Precambrian periods, and I'm also vaguely aware of some of the objections raised with general concept of phyla. With this in mind, I'm curious which of widely accepted biological phyla appeared most recently, and what evidence do we have of their relatively recent appearance? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm most interested in animals, but I'd also welcome any information about other organisms.&lt;/p&gt;&#xA;" OwnerUserId="6703" LastActivityDate="2014-07-14T15:43:22.277" Title="Which phylum appeared most recently" Tags="&lt;evolution&gt;&lt;taxonomy&gt;&lt;phylogenetics&gt;&lt;cladistics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19657" PostTypeId="2" ParentId="19656" CreationDate="2014-07-14T10:41:46.107" Score="4" Body="&lt;p&gt;As far as I know there is no phylum which appeared after the Cambrian. Every discussion beyond that is close to speculation, as the divergence estimates of different studies vary significantly. &#xA;You might want to look into one of the resources mentioned below:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.timetree.org/index.php&quot; rel=&quot;nofollow&quot;&gt;http://www.timetree.org/index.php&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.onezoom.org/&quot; rel=&quot;nofollow&quot;&gt;http://www.onezoom.org/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8015" LastActivityDate="2014-07-14T10:41:46.107" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19658" PostTypeId="1" AcceptedAnswerId="19662" CreationDate="2014-07-14T11:33:59.423" Score="6" ViewCount="205" Body="&lt;p&gt;I'm a computer scientist who is starting to dabble with biology. My eventual goal is to model different kinds of cells with a computer program. As of right now, I'm just trying to take some smaller steps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, I downloaded a complete human genome from &lt;a href=&quot;http://hgdownload.cse.ucsc.edu/downloads.html#human&quot; rel=&quot;noreferrer&quot;&gt;http://hgdownload.cse.ucsc.edu/downloads.html#human&lt;/a&gt;  There is a FASTA file for each chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, I wrote a java program which can convert FASTA DNA sequences into the appropriate amino acid chain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next, I made my program look for the &quot;start&quot; code (ATG) and &quot;stop&quot; codes (TAA, TAG, TGA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, now I have sequences of amino acids which might theoretically end up folding into proteins. But, before I start diving into protein folding, I wanted to try to verify that the steps I took so far were done correctly. I looked up some important human genes in an online database and found their amino acid sequences. I then searched through my program's data for those sequences and confirmed that they were there. However, the gene was in a different base-pair location than the database said that it should be in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This led me to some questions, which, so far I have been unable to answer and hopefully people here will be able to help shed some light.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;I know there are a lot of different publicly available genomes. Maybe the UCSC one that I downloaded is different from the one used by the gene database. How much does each genome vary from each other genome and in what ways do they vary?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In attempting to answer that first question, I was going to download a bunch of genomes from the 1000genomes website and do some comparisons, but I wasn't sure which files to download. Each of the files begins with either ERR or SRR and I'm not sure what that means. This is the folder I'm currently looking in &lt;a href=&quot;ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/HG00239/sequence_read/&quot; rel=&quot;noreferrer&quot;&gt;ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/HG00239/sequence_read/&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Lets say I'm trying to model a white blood cell. How do I know which parts of the genome get turned into proteins for that type of cell?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Sorry if anything I said doesn't make sense. As I said, my expertise lies in programming, not biology/genetics.&lt;/p&gt;&#xA;" OwnerUserId="8319" LastEditorUserId="1306" LastEditDate="2014-07-14T15:01:28.523" LastActivityDate="2014-07-14T17:29:02.727" Title="Turning publicly available genome data into proteins" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;proteins&gt;&lt;human-genome&gt;" AnswerCount="2" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19659" PostTypeId="2" ParentId="19656" CreationDate="2014-07-14T11:47:05.540" Score="5" Body="&lt;p&gt;In my view, we simply don't have good enough data to answer this question. The fossil evidence is too sparse prior to the Cambrian and the evidence that we do have suggests that the phyla were already too separated. Meanwhile, the depth of time and the different lifecycles and circumstances of the species involved mean that any &quot;genetic clocks&quot; we might use are likely to be too poor at keeping time and, indeed, different attempts have delivered different estimates of the time of divergence.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="2938" LastEditDate="2014-07-14T15:43:22.277" LastActivityDate="2014-07-14T15:43:22.277" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19661" PostTypeId="2" ParentId="19653" CreationDate="2014-07-14T13:28:49.303" Score="4" Body="&lt;p&gt;Normal people see color due to the bellow mentioned combination of red, green and blue:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/l99xj.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But due to genetic factors, The graph Distorts:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KNOdh.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now,If consider the normal &lt;a href=&quot;http://www.rapidtables.com/web/color/Yellow_Color.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Color code for yellow&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yellow = R(255) + G(255) + B(0)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or in other words&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Max. Red + Max. Green + no Blue = Yellow&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That means even if you can see a little of Red and Green, you can still a little deeper or lighter shade of yellow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So Summing it up in the images:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qzJT7.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Normal&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KBPaq.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Red ColorBlind&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6Sv7V.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Green ColorBlind&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QzpTp.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Blue ColorBlind&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.color-blindness.com/coblis-color-blindness-simulator/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Coblis — Color Blindness Simulator&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://wearecolorblind.com/article/a-quick-introduction-to-color-blindness/&quot; rel=&quot;nofollow noreferrer&quot;&gt;A quick introduction to colorblindness&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-07-17T04:55:38.680" LastActivityDate="2014-07-17T04:55:38.680" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19662" PostTypeId="2" ParentId="19658" CreationDate="2014-07-14T14:54:54.970" Score="11" Body="&lt;p&gt;No, your approach will not work, you are taking a very simplistic view of an extremely complex system. Some of the problems you are ignoring are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Genes (eukaryotic genes anyway) are &lt;a href=&quot;https://en.wikipedia.org/wiki/RNA_splicing&quot; rel=&quot;noreferrer&quot;&gt;spliced &lt;/a&gt;to produce mRNA, a process that removes &lt;a href=&quot;https://en.wikipedia.org/wiki/Intron&quot; rel=&quot;noreferrer&quot;&gt;introns&lt;/a&gt; and leaves only the &lt;a href=&quot;https://en.wikipedia.org/wiki/Exons&quot; rel=&quot;noreferrer&quot;&gt;exons&lt;/a&gt;. If you just translate the entire chromosome file you will get noise. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Splicing also changes the &lt;a href=&quot;https://en.wikipedia.org/wiki/Reading_frame&quot; rel=&quot;noreferrer&quot;&gt;frame&lt;/a&gt; a gene is read in, you don't mention frames at all in your question but you can't work with sequences unless you deal with them.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Many genes (most even, in some species) are &lt;a href=&quot;https://en.wikipedia.org/wiki/Alternative_splicing&quot; rel=&quot;noreferrer&quot;&gt;alternatively spliced&lt;/a&gt;. One gene can give rise to multiple protein sequences. Which one is produced at any one time can depend on a multitude of factors ranging from pure chance, through environmental conditions to the cell type where the gene is expressed.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Genes can be present on both strands of DNA and a gene on the + strand can overlap with a gene on the - strand. In some cases they can even overlap on the same strand (&lt;a href=&quot;https://en.wikipedia.org/wiki/Nested_gene&quot; rel=&quot;noreferrer&quot;&gt;nested genes&lt;/a&gt;). You need to check &lt;em&gt;both&lt;/em&gt; strands for coding sequences.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;You're assuming that all coding sequences start with ATG (most do, not all) and you seem to be assuming that an ATG always starts a coding sequence. A given gene can have dozens or hundreds of ATG codons, how can you know which one is used as a START codon? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The process of identifying the parts of the genome that get translated into protein is not trivial. It is the subject of countless PhD theses, mine for example. There are many programs (gene predictors) that are designed specifically to detect genes in genomic sequences. Having spent many years working with them I can assure you that they're not something you can just whip up one afternoon. They tend to involve very complex models of coding vs. non-coding sequences and are way more sophisticated than simply looking for START and STOP codons. Trying to write one without knowing a &lt;em&gt;lot&lt;/em&gt; more about biology than you seem to is just a waste of time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your specific questions are basically irrelevant because of the points mentioned above. Nevertheless, the answers are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;They vary but not much. For well annotated genomes like the human one, the differences will be negligible. That is not why you have strange results though as I explained above. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;All public FTP sites tend to have a README file that explains what the files provided are. You should read the relevant README from &lt;a href=&quot;ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/&quot; rel=&quot;noreferrer&quot;&gt;ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Answering that question will get you a Nobel prize. There simply is no way of predicting what genes will be activated in a particular cell. We're not even &lt;em&gt;close&lt;/em&gt; to that level of understanding of how a cell works but I can tell you that it will not depend on the sequence, you will never be able to predict whether a gene is active in a particular cell based on its DNA sequence. It will depend on various things including the gene's &lt;a href=&quot;https://en.wikipedia.org/wiki/DNA_methylation&quot; rel=&quot;noreferrer&quot;&gt;methylation&lt;/a&gt; state and is largely an emergent quality of the cell's complexity (think of various proteins interacting with one another, leading to the activation of a gene).  The best you can do is get a list of genes that are known to be active from the literature. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In summary, if you want to do something as complex as modelling a cell I suggest you first take the time and study some basic biology so you can understand the system you are trying to model a bit better. The cell is not only an extremely complex system that we don't fully understand yet, it is also not wholly deterministic and contains a lot of stochasticity that you seem to be ignoring completely. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-07-14T17:29:02.727" LastActivityDate="2014-07-14T17:29:02.727" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="19663" PostTypeId="2" ParentId="19610" CreationDate="2014-07-14T16:31:40.400" Score="5" Body="&lt;p&gt;Sterile flowers &lt;strong&gt;enrich pollination quality&lt;/strong&gt; by &lt;strong&gt;promoting pollen export and import&lt;/strong&gt;, while &lt;strong&gt;limiting the mating costs of geitonogamy&lt;/strong&gt; associated with large fertile displays.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;You are actually looking for this paper: Link: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523656/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523656/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sterile flowers increase pollinator attraction and promote female success in the Mediterranean herb &lt;em&gt;Leopoldia comosa&lt;/em&gt;&lt;/h2&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Key Results&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The presence of sterile flowers &lt;strong&gt;almost tripled pollinator attraction&lt;/strong&gt;,&#xA;  supplementing the &lt;strong&gt;positive effect of the number of fertile flowers on&#xA;  the number of bees approaching inflorescences&lt;/strong&gt;. Although attracted bees&#xA;  visited more flowers on larger inflorescences, the number visited did&#xA;  not additionally depend on the presence of sterile flowers. The&#xA;  presence of sterile flowers improved all aspects of plant performance,&#xA;  the magnitude of plant benefit being context dependent. During weather&#xA;  favourable to pollinators, the presence of sterile flowers increased&#xA;  pollen deposition on stigmas of young flowers, but this difference was&#xA;  not evident in older flowers, probably because of autonomous&#xA;  self-pollination in poorly visited flowers. Total pollen receipt per&#xA;  stigma decreased with increasing fertile display size. In the&#xA;  population with more pollinators, the presence of sterile flowers&#xA;  increased fruit number but not seed set or mass, whereas in the other&#xA;  population sterile flowers enhanced seeds per fruit, but not fruit&#xA;  production. These contrasts are consistent with dissimilar&#xA;  cross-pollination and autonomous self-pollination, coupled with the&#xA;  strong predispersal inbreeding depression exhibited by L. comosa&#xA;  populations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yURN0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-07-14T16:47:57.653" LastActivityDate="2014-07-14T16:47:57.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19664" PostTypeId="2" ParentId="19658" CreationDate="2014-07-14T16:33:46.603" Score="2" Body="&lt;p&gt;Why bother predicting proteins badly from DNA sequence when you could have just as well downloaded the manually curated human proteome?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to your questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Are you asking about human genomes or genomes in general? The vast majority of the variance in human genomes is in non-coding sequence. As to genomes in general, they vary in pretty much every imaginable way.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I think those files are quality filtered Illumina reads. SRA = Sequence Read Achieve. SRR = SRA RUN accession. ERA = EMBL SRA. ERR = ERA RUN accession.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;You should look into transcriptomics data. Predicting such stuff in silico is currently pretty much undoable.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5784" LastActivityDate="2014-07-14T16:33:46.603" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19665" PostTypeId="2" ParentId="1751" CreationDate="2014-07-14T17:49:47.803" Score="10" Body="&lt;p&gt;I found article in Nature:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nbt/journal/v19/n1/full/nbt0101_75.html&quot; rel=&quot;noreferrer&quot;&gt;A helper phage to improve single-chain antibody presentation in phage display&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Experimental protocol&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Standard cloning procedures, determination of colony-forming units and&#xA;plaque-forming units, and immunoblot after PAGE were carried out&#xA;according to Sambrook et al.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Construction of the packaging cell line.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;DH5alpha/pIII&#xA;[M13KO7DeltapIII]. The M13 pIII gene fused to promoter P/A1/04/03&#xA;(ref. 17) was inserted into the multiple cloning site of the&#xA;lambdaattP plasmid pLDR9 (ref. 18). The origin of replication and the&#xA;kanamycin resistance gene were cut out and the remaining&#xA;lambdaattP-pIII nonreplicative DNA was religated. Escherichia coli&#xA;DH5alpha containing plasmid pLDR8 (ref. 18) were transformed with the&#xA;lambdaattP-pIII nonreplicative DNA and plated on agar plates&#xA;containing 25 mug/ml ampicillin. After incubation overnight at 42°C,&#xA;the colonies obtained were replica-plated and ampicillin-resistant&#xA;clones were identified, named E. coli DH5alpha/pIII. They were&#xA;subsequently transformed with M13KO7DeltapIII, resulting in the&#xA;packaging cell line E. coli DH5alpha/pIII [M13KO7DeltapIII].&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Production of phage.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;To obtain M13KO7DeltapIII helper phage,&#xA;M13KO7DeltapIII DNA was electrotransfected into E. coli K802&#xA;containing pNDI (ref. 15). To obtain hyperphage, M13KO7DeltapIII DNA&#xA;was electrotransfected into E. coli DH5alpha/pIII. Phage were produced&#xA;by cultivation in the presence of 0.5 mM&#xA;isopropyl-beta-D-thiogalactoside (IPTG) at 30°C for 24 h with shaking&#xA;at 200 r.p.m. Escherichia coli Top10F' or E. coli Xl1blue carrying the&#xA;pSEXphOx(Yol) phagemid or a scFv library in pSEX81, respectively, were&#xA;infected with a helper phage preparation at a OD600 of 0.1 at a&#xA;multiplicity of infection of 20 as described.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Phage quantification by ELISA.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Dilution series of phage were coated in&#xA;100 mM NaHCO3, pH 8.6 in MaxiSorb ELISA plates (Life Technologies,&#xA;Karsruhe, Germany) for 16 h at 4°C. Blocking was done with 2% skim&#xA;milk powder in PBS (137 mM NaCl, 3 mM KCl, 8 mM Na2HPO4, 1 mM KH2PO4,&#xA;pH 7.3) for 2 h at room temperature. Phage were detected with the&#xA;monoclonal mouse antibody B62-FE2 (Progen, Heidelberg, Germany)&#xA;specifically binding an epitope on the pVIII major coat protein of the&#xA;M13 phage. M13KO7 phage of known colony-forming units were used for&#xA;standardization.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Immunoblot.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Approximately 1010 phage were applied per lane on a 10%&#xA;polyacrylamide gel. Blocking was done with 2% skim milk powder in PBS&#xA;for 2 h at room temperature. Immunostaining was done with the mouse&#xA;mAb anti-g3p (MoBiTec, Göttingen, Germany) recognizing the pIII coat&#xA;protein of M13KO7, visualized with 3,3', 5,5'-tetramethylbenzidene&#xA;(TMB) substrate (Promega, Madison, WI).&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Antigen-binding phage ELISA.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Dilution series of BSA-phOx antigen in&#xA;100 mM NaHCO3, pH 8.6, were coated in MaxiSorb ELISA plates (Life&#xA;Technologies) for 16 h at 4°C. After blocking of unspecific binding&#xA;with 2% skim milk powder in PBS for 2 h at room temperature, 2 times&#xA;109 single-chain phage diluted in 2% skim milk powder in PBS were&#xA;applied to each well for 1 h at room temperature. After washing six&#xA;times with 400 mul PBS per well, the bound phage were detected with&#xA;mAb B62-FE2 as described above.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Panning.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;A human scFv fragment library in pSEX81 with a calculated&#xA;maximal complexity of 2 times 107 was generated from peripheral&#xA;lymphocyte preparations as described21. Tetanus toxin obtained from&#xA;Virotech (Rüsselsheim, Germany) was coated to six ELISA wells (Life&#xA;Technologies) at a concentration of 0.1 mug/ml in 100 mM NaHCO3, pH&#xA;8.6, for 16 h at 4°C. The wells were blocked with 2% skim milk in PBS for 2 h at room temperature, after which 1011 phage of the library&#xA;were applied to each well and incubated at 4°C overnight. After five&#xA;washes with PBS/0.1% Tween and five with PBS, bound phage were eluted&#xA;with 1 mug/ml trypsin (Life Technologies) in PBS for 15 min at room&#xA;temperature. Eluted phage were used for the infection of 20 ml of E.&#xA;coli XL1blue at a OD600 of 0.4. Infected bacteria were grown on&#xA;Luria–Bertani agar plates containing glucose and ampicillin, scratched&#xA;from the plates, and used for the production of antibody phage for the&#xA;next round of panning as previously described.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sN7QR.gif&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-07-15T22:26:46.523" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19666" PostTypeId="2" ParentId="9850" CreationDate="2014-07-14T17:54:41.000" Score="2" Body="&lt;p&gt;intuitively, I would say that small creatures are not seen easily. therefore they need audible lighthouses to signal to others their location&lt;/p&gt;&#xA;&#xA;&lt;p&gt;big creatures don't usually have this need, though some do such as whales which can emit sounds heard hundreds of kilometers away&lt;/p&gt;&#xA;" OwnerUserId="6202" LastActivityDate="2014-07-14T17:54:41.000" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19667" PostTypeId="1" CreationDate="2014-07-14T18:15:20.143" Score="4" ViewCount="241" Body="&lt;p&gt;I am learning about the base excision repair mechanism. I understand generally how glycosylases work, but I am trying to understand this with much more detail. I found a paper where they write:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Monofunctional glycosylases catalyze the single-step displacement of damaged base via attack of an activated water molecule on c1' of the substrate.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am not sure what an activated water molecule is and how, for example, an aspartate residue is making a water molecule 'activated'. Furthermore, how is this activated water molecule hydrolyzing the N-glycosyl bond to remove the damaged base. Thank you for any help.&lt;/p&gt;&#xA;" OwnerUserId="6892" LastEditorUserId="6307" LastEditDate="2017-04-04T03:36:07.463" LastActivityDate="2017-04-04T03:36:07.463" Title="What is the mechanism of monofunctional glycosylases?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19668" PostTypeId="1" AcceptedAnswerId="19673" CreationDate="2014-07-14T18:19:00.863" Score="2" ViewCount="315" Body="&lt;p&gt;Take for example the human and the chimpanzee, they are &quot;closely related&quot; species since they are &quot;close&quot; to each other in a phylogenetic tree. However, this terminology seems pretty informal, what would be the formal way to specify that two or more species are &quot;closely related&quot;?&lt;/p&gt;&#xA;" OwnerUserId="8325" LastEditorUserId="3952" LastEditDate="2014-07-14T20:07:14.867" LastActivityDate="2014-07-14T21:05:48.627" Title="What is the formal terminology for two species that are &quot;close&quot; to each other in a phylogenetic tree?" Tags="&lt;terminology&gt;&lt;phylogenetics&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19669" PostTypeId="1" AcceptedAnswerId="19670" CreationDate="2014-07-14T18:34:04.600" Score="3" ViewCount="1197" Body="&lt;p&gt;Our lab uses old Gilson Pipetman pipettes. I've been using some for making mRNA by in vitro transcription and started running into RNAse issues. I'm trying to clean everything up, including the pipettes. I'm not sure these old pipettes can be autoclaved, at least not in one piece, I think I can take them apart and autoclave the parts that might touch the solutions. Is there some way to wash the pipettes out effectively and remove any RNAses?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I use boxes of RNAse free barrier tips, do all my work on new pieces of aluminum foil, use commercial RNAse free water, gloves, labcoat, facemask, etc. However yields from the in vitro transcription kit have been reduced, and yields from the tailing kit are even worse, sometimes losing 90% of the RNA. There's only so much I can do, our building is old and full of dust and the damn pipes above my work bench leak ( all the pipes leak, had 2 major pipe bursts in the last 6 months ). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll probably have to get new kits. Just have to prove to my advisor that the kits are contaminated.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-07-14T18:52:07.400" Title="Remove RNAse from pipettes?" Tags="&lt;rna&gt;&lt;transcription&gt;&lt;mrna&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19670" PostTypeId="2" ParentId="19669" CreationDate="2014-07-14T18:52:07.400" Score="2" Body="&lt;p&gt;According to the &lt;a href=&quot;http://www.gilson.com/Resources/LT801120_a_eng_030209%20BD.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gilson Pipettman User Guide&lt;/a&gt; you can autoclave the following parts: Tip ejector, Tip holder and the connecting nut (have a look into the PDF linked above if you are not sure about the parts). All other parts can not be autoclaved. Gilson says the following conditions can be used (page 17 in the user guide): Autoclave for 20 minutes at 121°C, 0.1 MPa.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, when you really have a DNAse contamination, you will not get rid of it with autoclaving, since RNAses are too stable. You can either try the various solutions on the market which made for killing RNAses or simply get a new set of pipettes used only for RNA work (on a different bench in a different lab with a completely different and fresh set of chemicals and plastic ware). And I would recommend filter tips for this work. They are more expensive but in the long run it will save money since you don't have to repeat experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding your leaking pipettes: The pipettes contain rubber rings and teflon seals in the inside which have to be replaced from time to time. The image below shows how (parts C and D), the ring can be purchased from Gilson. If you don't know how to do this work (and have no technician who does) you can also send in the pipettes for service. This costs a bit of money, but is ways better than to use unreliable, leaky pipettes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DGdMk.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And don't worry, Gilson pipettes are pretty good. I have used now more or less all brands on the market and I still prefer them. They only need some service from time to time.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-14T18:52:07.400" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19671" PostTypeId="1" CreationDate="2014-07-14T19:09:53.193" Score="3" ViewCount="641" Body="&lt;p&gt;Basically as far as i know cockroach consists of 10 terga and 9 sterna but what are the total number of pleura present in the cockroach.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pleura are situated between tergum and sternum of a body segment and help in the articulation of terga and sterna.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would that be in the case of the 10th abdominal segment in which sternum is absent ? Are pleura present there? If yes then what is their functions at that place?&lt;/p&gt;&#xA;" OwnerUserId="8101" LastEditorUserId="14826" LastEditDate="2015-03-29T19:10:31.403" LastActivityDate="2015-03-29T19:10:31.403" Title="Total number of pleura in the exoskeleton of cockroach" Tags="&lt;entomology&gt;&lt;anatomy&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19672" PostTypeId="2" ParentId="19668" CreationDate="2014-07-14T19:49:04.507" Score="2" Body="&lt;p&gt;As &lt;a href=&quot;http://en.wikipedia.org/wiki/Genus&quot; rel=&quot;nofollow&quot;&gt;genus&lt;/a&gt; comes above species I'd consider using this term for the species which are close genetically (&quot;these two species are from the same genus&quot;). Above genus comes family etc...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, the proximity or similarity of species could be probably &quot;measured&quot; by degree of &lt;a href=&quot;http://en.wikipedia.org/wiki/Biodiversity&quot; rel=&quot;nofollow&quot;&gt;biodiversity&lt;/a&gt;, and especially &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_diversity&quot; rel=&quot;nofollow&quot;&gt;genetic diversity&lt;/a&gt; considering two close species having low biodiversity and very different species as having higher biodiversity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thirdly, and I feel that this is the most strong term to use, you can &quot;express&quot; the genetic closeness of species as being &quot;genetically similar&quot;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Some monkeys and humans have 98% genetic similarity&quot; or &quot;are up to 98% genetically similar&quot; or &quot;... DNA similar&quot;... &lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2014-07-14T19:49:04.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19673" PostTypeId="2" ParentId="19668" CreationDate="2014-07-14T20:05:57.777" Score="3" Body="&lt;p&gt;Are you looking for something like &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sister_group&quot; rel=&quot;nofollow&quot;&gt;sister lineage&lt;/a&gt;&quot; (or &quot;sister taxon&quot; or &quot;sister group&quot;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This term may be more specific than what you're looking for, and to use it correctly you'd want to be a little careful – I guess in this case you might have to say something like: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;the lineage that includes chimpanzees and bonobos is sister to the&#xA;  lineage of which humans are the only extant species&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;or&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;the lineage that includes chimpanzees and bonobos and the lineage of&#xA;  which humans are the only extant species are sister lineages&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;both referring to &lt;a href=&quot;http://tolweb.org/Hominidae/16299&quot; rel=&quot;nofollow&quot;&gt;this phylogeny&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;It's also possible that explaining exactly what you mean by 'close', or what it entails, would be appropriate, be it Ilan's suggestion of % genetic similarity (or maybe genomic similarity?), # of nodes between your two taxa (again, this would have to be in reference to a specific phylogeny), or if you have a dated phylogeny you could refer to the time since divergence, as in &quot;coding DNA divergencies ...place the most recent common ancestor of humans and chimpanzees at between 5 and 6 million years ago.&quot;(&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12766228&quot; rel=&quot;nofollow&quot;&gt;Wildman et al 2003&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-07-14T21:05:48.627" LastActivityDate="2014-07-14T21:05:48.627" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19674" PostTypeId="2" ParentId="19631" CreationDate="2014-07-14T20:32:39.543" Score="1" Body="&lt;p&gt;While it's always possible that a mutated eggplant will produce a new toxin, this is very unlikely. I don't know how much higher the mutation rate is near Fukushima than in general but the difference can't be huge. Even if it's, say, 5 or 10 times higher than normal (I'm making up these numbers), the risk is still tiny. Actually, plant breeders sometimes use radiation to produce more variety to work with and we don't worry about that.&lt;/p&gt;&#xA;" OwnerUserId="5985" LastActivityDate="2014-07-14T20:32:39.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19675" PostTypeId="1" AcceptedAnswerId="19685" CreationDate="2014-07-15T00:40:47.227" Score="5" ViewCount="72" Body="&lt;p&gt;&lt;strong&gt;Illusion:&lt;/strong&gt; Lying down on a hard flat floor move arms up and down (as when doing a snow angel) while keeping them touching the floor. While repeating it a few times the floor begins to appear concave, with the deepest part where the arms as perpendicular to the rest of the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions:&lt;/strong&gt; What is the origin of this illusion? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My guess:&lt;/strong&gt; I think it might be related to the arms being harder to extend towards the back when they are perpendicular to the body than when they are at other angles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note:&lt;/strong&gt; The name above is only the way I like to call it. I found this illusion when I was a kid, but I am sure others might have noticed it as well.&lt;/p&gt;&#xA;" OwnerUserId="8327" LastEditorUserId="8327" LastEditDate="2014-07-15T02:05:59.343" LastActivityDate="2014-07-28T09:29:01.830" Title="Braquio-abduction illusion explanation and references" Tags="&lt;neuroscience&gt;&lt;perception&gt;&lt;bone-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19676" PostTypeId="1" CreationDate="2014-07-15T02:37:49.403" Score="4" ViewCount="69" Body="&lt;p&gt;I am working on success rate of DNA barcoding in identification of species using distance and tree based methods. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding distance based method, I have used Adhoc and species identifier and confirmed species identification using best closest match criteria (BCM). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please suggest program/software/method for tree based identification (using NJ, parsimony, bayes), exhibiting clustering (number of clusters formed for particular species) that will suggest singleton (=Ambigious) species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(For more details: Attached image)&#xA;(Please Note: It is not possible to do it manually as iam having &gt;4000 specimens)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Answers detailing methods or softwares appereciated! Thank you!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ikboE.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8328" LastEditorUserId="8328" LastEditDate="2014-07-15T06:10:53.900" LastActivityDate="2014-07-15T06:10:53.900" Title="DNA barcoding, querry regarding tree based (cluster) methods for species identification" Tags="&lt;phylogenetics&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19677" PostTypeId="1" AcceptedAnswerId="19678" CreationDate="2014-07-15T04:23:51.320" Score="3" ViewCount="310" Body="&lt;p&gt;Do ants understand which way is up or down? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could they differentiate between uphill and downhill?&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2018-09-14T07:05:55.247" Title="Do Ants have a sense of Direction?" Tags="&lt;physiology&gt;&lt;ant&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19678" PostTypeId="2" ParentId="19677" CreationDate="2014-07-15T04:23:51.320" Score="3" Body="&lt;p&gt;Actually No.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Amazingly there is this paper published on the motions on Ants which says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The isotropic distribution of average speed appears as a surprising&#xA;  result since it would be expected, for instance, that ants progressing&#xA;  uphill should be slower than when moving downhill. For instance, Seidl&#xA;  et al. found lower speeds on steeper inclines in desert ants moving&#xA;  uphill, but indicate that desert ants progressing downhill displayed&#xA;  high velocities [42]. &lt;strong&gt;This is in contrast with our finding with Lasius&#xA;  niger in the present set-up where the velocity showed no dependency to&#xA;  the walking direction, even for the steepest inclination.&lt;/strong&gt; However,&#xA;  Wohlgemuth et al. report, also in the desert ant, that speed was&#xA;  reduced in both their uphill and downhill channels (+540 ) compared to&#xA;  their flat channel, thereby excluding metabolic cost as a reliable&#xA;  means to gauge walked distance on various inclines [28]. In an attempt&#xA;  to determine the effects of inclination on the gross metabolic cost of&#xA;  locomotion in leaf-cutter ants, Holt &amp;amp; Askew report that ants&#xA;  travelled the fastest on a horizontal plane, and indeed moderated&#xA;  their speed with the inclination, both on the incline and the decline.&#xA;  They suggest that ants adapt their behavior so as to keep their&#xA;  metabolic rate constant despite changing mechanical demands.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0076531&quot; rel=&quot;nofollow&quot;&gt;How Do Ants Make Sense of Gravity? A Boltzmann Walker Analysis of Lasius niger Trajectories on Various Inclines&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-15T04:23:51.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19679" PostTypeId="1" AcceptedAnswerId="19680" CreationDate="2014-07-15T04:28:37.350" Score="2" ViewCount="182" Body="&lt;p&gt;How does an ant know about Earthquake is it because of an organ or due to other factors?&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-07-15T09:18:45.133" LastActivityDate="2014-07-15T09:18:45.133" Title="How Ants know about Earthquake?" Tags="&lt;physiology&gt;&lt;biophysics&gt;&lt;ant&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19680" PostTypeId="2" ParentId="19679" CreationDate="2014-07-15T04:28:37.350" Score="2" Body="&lt;p&gt;No, they may not sense Earthquake by an organ but due to other reasons. This may be any other physical factors which can be measured.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;&quot;...There is therefore&#xA;  little reason to believe that these ants react to earthquake&#xA;  precursors other, perhaps, than those that may affect colonies&#xA;  directly, by altering physical variables that can be directly measured&#xA;  by other means...&quot;&lt;/strong&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Fascinating though the behavior and physiology of ants may be, they cannot be employed as reliable predictors or even sensors of earthquakes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://jeb.biologists.org/content/208/16/3103.long&quot; rel=&quot;nofollow&quot;&gt;Shaken, not stirred: a serendipitous study of ants and earthquakes&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-07-15T09:17:27.727" LastActivityDate="2014-07-15T09:17:27.727" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19682" PostTypeId="2" ParentId="19648" CreationDate="2014-07-15T04:57:44.453" Score="3" Body="&lt;p&gt;What you are looking for is a spirometer. There are different types of spirometers serving different purposes like the Incentive spirometer and the peak flow meter. I would suggest that you go through the &lt;a href=&quot;http://en.wikipedia.org/wiki/Spirometer&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia page on it&lt;/a&gt; to get more info. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jnvac.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="8186" LastEditDate="2014-07-15T05:42:50.243" LastActivityDate="2014-07-15T05:42:50.243" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19683" PostTypeId="1" CreationDate="2014-07-15T07:25:05.853" Score="2" ViewCount="74" Body="&lt;p&gt;My nose is slightly bent. When I was born, I had an issue with breathing. My mom said that doctors had inserted a breathing tube in one of my nostrils. This tube may have caused the deformation. From childhood, I breathe through my mouth. Will there be an any problems in the future? Do I have to take any treatment? Please suggest.&lt;/p&gt;&#xA;" OwnerUserId="6878" LastEditorUserId="5762" LastEditDate="2014-07-15T09:05:41.720" LastActivityDate="2014-07-15T09:05:41.720" Title="Will breathing through mouth result in any disorders?" Tags="&lt;breathing&gt;&lt;health&gt;&lt;nose&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2014-07-15T11:29:11.777" ContentLicense="CC BY-SA 3.0" />
  <row Id="19684" PostTypeId="2" ParentId="19648" CreationDate="2014-07-15T10:42:30.877" Score="1" Body="&lt;p&gt;Another possibility is &lt;a href=&quot;http://www.serinth.gr/en/products/ergospirometers/portable-ergospirometers/cosmed-k4b2.html&quot; rel=&quot;nofollow&quot;&gt;K4 device&lt;/a&gt; and &lt;a href=&quot;http://www.cosmed.com/en/products/cardio-pulmonary-exercise-testing/k4-b2-mobile-cpet&quot; rel=&quot;nofollow&quot;&gt;K4 device&lt;/a&gt;. Beyond spirometry it can measure other variables such as: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Pulmonary Gas Exchange (VO2, VCO2)&lt;/li&gt;&#xA;&lt;li&gt;Breath by Breath Technology&lt;/li&gt;&#xA;&lt;li&gt;Telemetry Data Transmission up to 1000m&lt;/li&gt;&#xA;&lt;li&gt;Indirect Calorimetry&lt;/li&gt;&#xA;&lt;li&gt;Integrated GPS System&lt;/li&gt;&#xA;&lt;li&gt;Integrated Oxygen Saturation (SpO2)&lt;/li&gt;&#xA;&lt;li&gt;Integrated 12-lead Stress Testing ECG&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3494" LastActivityDate="2014-07-15T10:42:30.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19685" PostTypeId="2" ParentId="19675" CreationDate="2014-07-15T11:18:09.723" Score="4" Body="&lt;p&gt;It may be because, when we move our shoulders towards our the body, also know as abduction (Fig 1.) gives the central part of the body an elevation. when we rotate our arms more upwards (Adduction), the elevation will be lost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in other words, when we are making snow angels,  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Start Normal position (hands near thighs) = Back and shoulders on ground &lt;/li&gt;&#xA;&lt;li&gt;Middle position      (hands in middle)   = Back elevated and shoulders on ground &lt;/li&gt;&#xA;&lt;li&gt;Final Position        (hands upward) = Back and shoulders on ground again.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Due to this motion, it seems as if the ground become concave.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ltmCV.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=5YcNAPzDxDg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Anatomical Terms of Movement&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.dummies.com/how-to/content/articulating-the-importance-of-joints-in-anatomy.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Articulating the Importance of Joints in Anatomy&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-07-28T09:29:01.830" LastActivityDate="2014-07-28T09:29:01.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19687" PostTypeId="1" AcceptedAnswerId="19688" CreationDate="2014-07-15T11:47:26.370" Score="5" ViewCount="814" Body="&lt;p&gt;I've photographed this flower a few days ago in New York City:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ovp1z.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anybody know the name of it? (and how is the orange part called?)&lt;/p&gt;&#xA;" OwnerUserId="8014" LastActivityDate="2014-07-15T12:17:18.650" Title="What is the name of this flower with purple leaves and orange inner part in NYC?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19688" PostTypeId="2" ParentId="19687" CreationDate="2014-07-15T11:56:59.313" Score="8" Body="&lt;p&gt;&lt;a href=&quot;http://oglesbytc.com/catalog/patio-and-garden/echinacea/echinacea-prairie-splendor.html&quot;&gt;It's Echinacea.&lt;/a&gt; I've linked to one site but if you run an images search with Echinacea as the search term you'll see lots of examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Echinacea&quot;&gt;And here is the WP page.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Supplementary&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Echinacea are members of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Compositae&quot;&gt;Compositae&lt;/a&gt;. The flower (the &lt;strong&gt;head&lt;/strong&gt;) in your picture is actually made up of lots of individual smaller flowers (i.e. it is a &lt;em&gt;composite&lt;/em&gt; flower). The petals are formed by &lt;strong&gt;ray flowers&lt;/strong&gt;, and the central part, the &lt;em&gt;disc&lt;/em&gt; is made up of &lt;strong&gt;disc flowers&lt;/strong&gt;. More details at the WP page I have linked to for Compositae.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-07-15T12:17:18.650" LastActivityDate="2014-07-15T12:17:18.650" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19689" PostTypeId="1" AcceptedAnswerId="19690" CreationDate="2014-07-15T12:12:47.770" Score="4" ViewCount="304" Body="&lt;p&gt;Does anybody know the name of this bumblebee? (For categorization on Wikipedia Commons: &lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Flower-3.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt; and &lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Flower-7.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3YfGY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RrY52.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8014" LastEditorUserId="22057" LastEditDate="2019-06-25T19:38:38.087" LastActivityDate="2019-06-25T19:38:38.087" Title="What is the name of this yellow bumble bee that I photographed in New York City?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="19690" PostTypeId="2" ParentId="19689" CreationDate="2014-07-15T12:32:39.693" Score="5" Body="&lt;p&gt;It's a Brown-belted Bumble Bee (&lt;em&gt;Bombus griseocollis&lt;/em&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OYCSH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Details: &lt;a href=&quot;http://bugguide.net/node/view/3538&quot; rel=&quot;noreferrer&quot;&gt;http://bugguide.net/node/view/3538&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-15T12:32:39.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19691" PostTypeId="1" CreationDate="2014-07-15T12:34:54.507" Score="2" ViewCount="198" Body="&lt;p&gt;If this question is a little off topic for Biology, I'm sorry. I've recently read a lot about mesoporous silica nanoparticles as a promising drug delivery method. The huge range of customizability of the particles, coatings, contents, etc. can pretty much tailor them to be effective in delivering most drugs to most target locations in the body (or to specific cells). The research is not new, and all the articles hail the method as a very promising way to treat for example cancer. However, as far as I know, these methods are not widely used today. Why? Is there some catch that I don't see?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm no biology expert, but if this is so promising, and the research is at least a decade old, some companies would have produced this (they already produce the particles) in terms of drug delivery. So why not? Is it a case of null-findings not being published? Is it actually used and I'm blind?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your help!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;edit: for those interested, here is a &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/cm402592t&quot; rel=&quot;nofollow&quot;&gt;good review&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8333" LastEditorUserId="8333" LastEditDate="2014-07-15T13:09:35.257" LastActivityDate="2014-07-28T09:45:22.457" Title="Mesoporous silica particles as anti cancer drug delivery method" Tags="&lt;biochemistry&gt;&lt;pharmacology&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19692" PostTypeId="1" AcceptedAnswerId="31378" CreationDate="2014-07-15T13:56:06.810" Score="9" ViewCount="235" Body="&lt;p&gt;It is known from theoretician in the field of kin selection that kin selection (inclusive fitness theory) and group selection are actually two sides of the same coin. In other words, these two concepts are actually only one single process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Is group selection equivalent to kin selection for any evolutionary game or exclusively for the prisoner's dilemna?&lt;/li&gt;&#xA;&lt;li&gt;Can you please provide an intuitive explanation of why kin- and group-selection are the same thing?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-07-21T12:58:52.497" LastActivityDate="2016-04-07T19:31:22.160" Title="Intuitive explanation for Kin- and Group- selection" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;&lt;evolutionary-game-theory&gt;&lt;sociality&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19693" PostTypeId="2" ParentId="19590" CreationDate="2014-07-15T14:30:01.927" Score="2" Body="&lt;p&gt;I don't know if this is helpful in the context of moving from RNA to DNA world, but I do know that certain mutations to T7 RNA polymerase will allow that enzyme to use 2' deoxy nucleotides in addition to the normal ribonucleotides. These mutations were discovered by humans engineering the enzyme, but it's feasible that some transitional enzyme could have utilized both types of nucleotide. Then, those individuals with more DNA were favored because the DNA backbone is more stable than RNA backbone, eventually selecting for the modern DNA to RNA to Protein model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is an article: &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0168165613002940&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0168165613002940&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-07-15T14:30:01.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19694" PostTypeId="1" CreationDate="2014-07-15T14:51:52.067" Score="2" ViewCount="212" Body="&lt;p&gt;This morning I was looking round the garden and found this sticking out of a pit in patch of soil, next to the wall of the house (in a trough sort of thing). I came to the conclusion it must be part of an insects exoskeleton that was discarded or part of a pupae. Can anybody identify what this belongs to? My location is in the south-west (Wiltshire region) of Great Britain. I'm just interested in what exactly I've found!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6JxgW.jpg&quot; alt=&quot;Close up of markings&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/70jeX.jpg&quot; alt=&quot;Different angle&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/JYSe5.jpg&quot; alt=&quot;Size comparison to a 50p piece!&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6330" LastActivityDate="2014-07-15T17:16:18.097" Title="What is this discarded exoskeleton from?" Tags="&lt;species-identification&gt;&lt;invertebrates&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19696" PostTypeId="2" ParentId="19640" CreationDate="2014-07-15T15:52:05.050" Score="2" Body="&lt;p&gt;According to &lt;a href=&quot;http://books.google.fr/books?id=QRgynJASsi8C&amp;amp;pg=PA8&amp;amp;lpg=PA8&amp;amp;dq=%22vestibular+system%22+invertebrates&amp;amp;source=bl&amp;amp;ots=7qT3CmD4II&amp;amp;sig=VRtwd2e94A2UCFYL1DLMcih3u4c&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=T0zFU73OD8Ws0QXDuICoDw&amp;amp;ved=0CDsQ6AEwAw#v=onepage&amp;amp;q=%22vestibular%20system%22%20invertebrates&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Clinical Neurophysiology of the Vestibular System&#xA; By Robert William Baloh, Vicente Honrubia, page 8&lt;/a&gt;, the vestibular system (animals' &quot;accelerometer&quot;) is as old as 600 million years and is present in invertebrates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume (without a precise source) that this is especially important for flying insects (after all, accelerometers were engineered for flying machines in the first place!) and that the ant didn't respond because the acceleration to which you submitted it was not deemed harmful.&lt;/p&gt;&#xA;" OwnerUserId="6224" LastActivityDate="2014-07-15T15:52:05.050" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19697" PostTypeId="2" ParentId="9119" CreationDate="2014-07-15T16:13:01.950" Score="1" Body="&lt;p&gt;As far as we know, chromosomes tend to be equally distributed across normal gameteogenesis, following Mendel's second law of independent assortment. However some versions of DNA repair and chromosomal condensation can malfunction and result in more versions of one parents genes in a cell than another. Two phenomena which are exceptions to the equal parental ratio are &lt;strong&gt;Gene Conversion&lt;/strong&gt; and &lt;strong&gt;Chromosomal Fusions&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although a much smaller scale than chromosome segregation, &lt;a href=&quot;https://en.wikipedia.org/wiki/Gene_conversion&quot; rel=&quot;nofollow&quot;&gt;Gene Conversion&lt;/a&gt; is a case of unequal allele transmission. While repairing double strand breaks during meiosis, one parent's DNA may be used as the repair template instead of the original version. This phenomena distorts the 1:1 allele ratio on the scale of hundreds of base pairs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Robertson translocations are when two nonhomologous chromosomes fuse into one. Chromosomes which were once separate, segregate together into the same gamete. These cases can serve as exceptions to Mendel's second law of independent assortment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also several cases of transmission distortion, while these cases may not affect the segregation of chromosomes during meiosis, they do cause unequal fertilization. The &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0168952593900905&quot; rel=&quot;nofollow&quot;&gt;t-haplotype&lt;/a&gt; in male house mice, is passed on to up to 95% of offspring! The mechanism is still under investigation, but it appears that this gene when expressed in sperm, kills all other sperm without the &lt;em&gt;t&lt;/em&gt; gene. The Sd gene is a similar element in Drosophila. &#xA;A great book on selfish genetic elements and intragenomic conflict is Genes in Conflict by Burt and Trivers.&lt;/p&gt;&#xA;" OwnerUserId="6134" LastActivityDate="2014-07-15T16:13:01.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19698" PostTypeId="2" ParentId="19162" CreationDate="2014-07-15T17:08:57.757" Score="4" Body="&lt;p&gt;This may be what you are searching for:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dDlkk.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's actually a &lt;strong&gt;male purseweb spider&lt;/strong&gt; (Atypus affinis), the color fades to black, eventually.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.spiderzrule.com/purseweb2.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.spiderzrule.com/purseweb2.htm&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-15T17:08:57.757" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19699" PostTypeId="2" ParentId="19694" CreationDate="2014-07-15T17:16:18.097" Score="2" Body="&lt;p&gt;I can't be certain, but it is probably the pupal shell of a &lt;a href=&quot;http://en.wikipedia.org/wiki/Crane_fly&quot; rel=&quot;nofollow&quot;&gt;crane fly&lt;/a&gt; (daddy longlegs, &lt;em&gt;Tipula palidosa&lt;/em&gt;). &lt;a href=&quot;http://lastrefuge.co.uk/php/show-images-all-big.php?id=CHI0920&quot; rel=&quot;nofollow&quot;&gt;Here is an image to compare&lt;/a&gt;, and you can find lots more with a Google image search.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the UK at least, these are colloquially referred to as leatherjackets and if you find one in soil before the adult has emerged it will often twitch.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-07-15T17:16:18.097" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19700" PostTypeId="1" AcceptedAnswerId="19705" CreationDate="2014-07-15T18:14:31.837" Score="8" ViewCount="2308" Body="&lt;p&gt;I came through this pic while scrolling through facebook, and it was a bit strange to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I know apples have a corymbose type of inflorescence, in which a single pedicel ends in a single thalamus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And I am totally sure that the edible part, which is fleshy in the apple, is thalamus. How did this fruit came into existence? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want a biological answer for this query.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jEreA.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8101" LastEditorUserId="338" LastEditDate="2014-07-17T05:07:58.163" LastActivityDate="2014-07-18T04:46:37.857" Title="How did these apples grow together?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;fruit&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19701" PostTypeId="2" ParentId="17578" CreationDate="2014-07-15T18:29:27.780" Score="7" Body="&lt;p&gt;I think it's an &lt;em&gt;Vipera Aspis&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;from wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The dorsal markings vary strongly, but only rarely take the form of a&#xA;  clear zigzag, as in V. berus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hbHpe.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your Snake in Maximum RGB Color (Broken ZigZag)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RjvNT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Vipera Aspis&lt;/em&gt; from Google Image&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-15T18:29:27.780" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19703" PostTypeId="2" ParentId="19667" CreationDate="2014-07-15T18:42:52.847" Score="5" Body="&lt;p&gt;The article referred to in the question is &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/15102448&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fromme et al. (2004)&lt;/a&gt;. I was able to find several proposed mechanisms for the monofunctional uracil-DNA glycosylase but I'll discuss two that seem most relevant in the context of your question.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The first I'll mention was outline by &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/10805771&quot; rel=&quot;nofollow noreferrer&quot;&gt;Parikh et al. (2000)&lt;/a&gt; who studied recombinant human mitochondrial uracil-DNA glycosylase. They report a mechanism where the glycosidic bond cleavage is not induced by a nucleophilic attack by water but rather by valence electron rearrangement, induced by conformational changes of the substrate by the enzyme, leading to a resonance stabilized oxocarbenium intermediate. This figure shows an electron pushing representation as well as the various stabilizing effects produced by orbital overlaps which favours cleavage of the C-N bond:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6Jg8i.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Original caption: Structure-based reaction mechanism that resolves the apparent orthogonal paradox for electron transpositions by altering the substrate stereochemistry. (A) A simplified valence-bond representation of the glycosylic bond dissociation hides the paradox that the three electron pairs to be transposed are involved in orthogonal orbitals. (B) In the normal anti-conformation of deoxyuridine, the σ*-orbital involved in the anomeric effect and the π-orbital of the C2⩵O bond are orthogonal to one another, thus preventing orbital overlap. (C) Severe distortions of the deoxyribose and the glycosylic bond in the strained conformation of deoxyuridine enforced by the UDG active center align the pairs of atomic orbitals participating in each electron transposition, thereby electronically coupling the anomeric and σ-πArom effects to promote bond cleavage. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They also go on to say (emphasis added):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A water is tightly positioned 3.54 Å below the deoxyribose C1′ by four hydrogen bonds (Fig. 3B) but is &lt;strong&gt;likely a poor nucleophile&lt;/strong&gt;. Instead, the UDG–DNA substrate structure suggests this water is well positioned to become the 1′-α-OH &lt;strong&gt;after&lt;/strong&gt; dissociation of the incipient deoxyribose oxocarbenium ion from the uracil ring.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here is Fig. 3B from the article, where the water molecule is the red sphere at the bottom of the image coordinated by four hydrogen bonds:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ghTBi.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The next mechanism involves a nucleophilic attach by an activated water molecule and was outlined by &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/10508389&quot; rel=&quot;nofollow noreferrer&quot;&gt;Drohat et al. (1999)&lt;/a&gt; studying &lt;em&gt;Escherichia coli&lt;/em&gt; uracil-DNA glycosylase. Here is the first step of the mechanism:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/lzeu3.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;From the &lt;a href=&quot;http://en.wikipedia.org/wiki/Uracil-DNA_glycosylase&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia article on uracil-DNA glycosylase&lt;/a&gt; (accessed 15 Jul 2014)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/10508389&quot; rel=&quot;nofollow noreferrer&quot;&gt;Drohat et al. (1999)&lt;/a&gt; describe this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;UDG apparently follows a [...] mechanism by deprotonating the incoming water nucleophile using the completely conserved residue Asp64 as the general base. Site-directed mutagenesis studies of the human enzyme support the structural evidence that His187 and Asp64 act as a general acid and base, respectively, because conversion of these groups to leucine and asparagine resulted in 300- and 2500-fold losses in activity (11). However, structural and mutagenesis data alone cannot establish the catalytic roles and ionization states of active site groups; thus other complementary approaches must be utilized to establish a chemical mechanism. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To answer your question, the water molecule is considered activated because it is a better nucleophile due to proton abstraction by the aspartate residue side chain. Thus the electrons used in in the original O-H bond in water (which are polarized towards the electronegative oxygen) are free to attack the partial positive 1' carbon of the deoxyribose. Although it is a concerted mechanism, you could perhaps think of the nucleophile being the hydroxide anion, which is much stronger than water.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;So which mechanism is correct you might ask. Well, I don't know, but I refer you to a paragraph from &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/10805771&quot; rel=&quot;nofollow noreferrer&quot;&gt;Parikh et al. (2000)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Despite the importance of UDG and the many proposed mechanisms for its catalysis of glycosylic bond cleavage, the structural chemistry underlying efficient catalysis by UDG has remained elusive. Two groups, including our own, have proposed a traditional acid-base catalysis carried out by a cationic His-268 and an absolutely conserved Asp-145 (13, 26). Two proposals (27, 28) invoke only general base catalysis via the same catalytic aspartate and a neutral histidine. Another proposal (29), based on a computationally simulated uncleaved-substrate complex, predicts that Asp-145 is fully solvated in the substrate complex so that it cannot act as a general-base catalyst. These proposed mechanisms are inconsistent with each other and with the uncleaved-substrate crystal structure presented here. Moreover, they are problematic in that they rely entirely on functional group chemistry and thus do not adequately explain UDG's efficiency or the activity of mutants that alter evidently key functional groups (13, 27). UDG mutations that remove apparently key active site functional groups are actually faster enzymes than several wild-type DNA glycosylases (30). Thus, without knowledge of a substrate complex structure, the characterization of UDG mechanism is severely hindered. Here, we present the structures of UDG bound to both uncleaved-substrate analog at 1.8-Å resolution and cleaved-product DNA oligonucleotides at 2.0-Å resolution. These high-resolution cocrystal structures suggest how UDG applies part of the DNA-binding energy to glycosylic bond cleavage by conformationally altering its deoxyuridine substrate to take advantage of stereoelectronic and strain effects in what is then an apparently dissociative process. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/10508389&quot; rel=&quot;nofollow noreferrer&quot;&gt;Drohat AC, Jagadeesh J, Ferguson E, Stivers JT. 1999. Role of electrophilic and general base catalysis in the mechanism of Escherichia coli uracil DNA glycosylase. Biochemistry-US. 38(37):11866-11875.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/15102448&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fromme JC, Banerjee A, Verdine GL. 2004. DNA glycosylase recognition and catalysis. Curr Opin Struct Biol. 14(1):43-49.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/10805771&quot; rel=&quot;nofollow noreferrer&quot;&gt;Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA. 2000. Uracil-DNA glycosylase–DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. P Natl Acad Sci USA. 97(10):5083-5088.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2017-04-04T00:27:26.897" LastActivityDate="2017-04-04T00:27:26.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19705" PostTypeId="2" ParentId="19700" CreationDate="2014-07-15T18:56:19.540" Score="10" Body="&lt;p&gt;They are basically conjoined apples which share a common stalk. They are rare but do happen. Here is &lt;a href=&quot;http://www.dailymail.co.uk/news/article-2433619/Siamese-apples-Conjoined-fruit-discovered-lying-ground-mans-garden.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;an article&lt;/a&gt; of one discovered in a backyard. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/i4gxU.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;conjoined apple discovered in a store (&lt;a href=&quot;http://www.topix.com/album/detail/dittmer-mo/DRC833GMCVJKJMF3&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It apparently happens because of bad weather conditions, stress and insect damage. Fused fruits are also found in the case of cherries, watermelons, peaches etc.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Inadequate pollination because of heat and other adverse growing&#xA;  conditions causes that section of the fruit in which the seed did not&#xA;  develop to not grow and fill out. Also, the fruit primordium&#xA;  (embryonic growing point) can be damaged or altered by environmental&#xA;  factors and cause strange growth forms. Of course, Siamese twins or&#xA;  two fruit growing together is also rather common(&lt;a href=&quot;http://www.plantanswers.com/vegetable_shapes_gallery.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Read more about them on &lt;a href=&quot;http://www.weirdasianews.com/2010/07/27/freaky-conjoined-watermelon-weird-fruit-mutations/&quot; rel=&quot;nofollow noreferrer&quot;&gt;article 1&lt;/a&gt; and &lt;a href=&quot;http://www.gardeningknowhow.com/plant-problems/environmental/what-is-plant-buttoning.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;article 2&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorDisplayName="user1357" LastEditDate="2014-07-18T04:46:37.857" LastActivityDate="2014-07-18T04:46:37.857" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19706" PostTypeId="1" CreationDate="2014-07-15T19:34:17.443" Score="4" ViewCount="569" Body="&lt;p&gt;I want to make a DIY bracelet to measure my ECG. All I need is the interbeat interval. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can I design a bracelet on one arm only, with two electrodes slightly spaced from one another, and figure out the beat from the conduction timing differences down the arm?&lt;/p&gt;&#xA;" OwnerUserId="8335" LastActivityDate="2018-07-28T14:35:33.777" Title="Can you measure ECG from a single location?" Tags="&lt;human-biology&gt;&lt;cardiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19707" PostTypeId="1" AcceptedAnswerId="19739" CreationDate="2014-07-15T19:51:25.323" Score="4" ViewCount="5609" Body="&lt;p&gt;I'm looking for a surface, that will be impassable for ant's yet not poisonous or easily decaying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One idea is water - they really can't cross that. But water easily dries and is quite uncomfortable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there something their legs will find uncomfortable? Something spiky for example?&lt;/p&gt;&#xA;" OwnerUserId="6918" LastActivityDate="2018-08-01T02:44:33.037" Title="Is there a durable surface that ants can't pass?" Tags="&lt;ant&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19708" PostTypeId="1" AcceptedAnswerId="20402" CreationDate="2014-07-15T20:19:38.380" Score="6" ViewCount="1689" Body="&lt;p&gt;As steroid hormones can pass through the plasma membrane by simple diffusion because they are lipid derived hormones, it means that they are capable of passing through every cell of our body, BUT why are only specific cells responsive against steroid hormones?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, all of our body cells almost contains the genes for the development of secondary sexual characters but why do only specific cells show a response against these steroid hormones because the development of secondary sexual characters occur only in specific region of our body, that is, beard formation occur only in a specific region of the face, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;IN SUMMARY: When steroid hormones can pass through every cell of our body then why do they show only a localized response?&lt;/p&gt;&#xA;" OwnerUserId="5729" LastEditorUserId="355" LastEditDate="2014-07-16T04:04:36.920" LastActivityDate="2015-03-09T21:09:29.267" Title="Effect of steroid hormone on specific cells?" Tags="&lt;biochemistry&gt;&lt;endocrinology&gt;&lt;cell-signaling&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19709" PostTypeId="2" ParentId="19708" CreationDate="2014-07-15T20:55:30.907" Score="8" Body="&lt;p&gt;The quick answer is that only certain cell types express the required &lt;a href=&quot;http://en.wikipedia.org/wiki/Steroid_hormone_receptor&quot;&gt;steroid hormone receptors&lt;/a&gt; that are necessary to induce signaling and gene regulation when bound to their target steroid hormones, like estrogen, testosterone, cortisol, etc. If no receptor is present, the steroid doesn't effect any change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second part of the answer involves the particular signaling pathways induced by the ligation of certain receptors by certain classes of hormones. &lt;a href=&quot;http://en.wikipedia.org/wiki/Testosterone&quot;&gt;Testosterone&lt;/a&gt;, for example, has numerous effects across the body, from promoting the growth of hair to building muscle mass to effects on mental well-being. Testosterone and its primary metabolite 5α-dihydrotestosterone bind primarily to the cytoplasmic &lt;a href=&quot;http://en.wikipedia.org/wiki/Androgen_receptor&quot;&gt;androgen receptor&lt;/a&gt;, which then translocates to the nucleus, binds DNA at &lt;a href=&quot;http://en.wikipedia.org/wiki/Hormone_response_element&quot;&gt;hormone response elements&lt;/a&gt;, and alters the transcriptional activity of genes (either increasing or decreasing, depending on the gene and the cell type). Testosterone can also be metabolized to &lt;a href=&quot;http://en.wikipedia.org/wiki/Estradiol&quot;&gt;estradiol&lt;/a&gt; and bind &lt;a href=&quot;http://en.wikipedia.org/wiki/Estrogen_receptor&quot;&gt;estrogen receptors&lt;/a&gt;, which function similarly to the androgen receptor (although it can have DNA-independent effects as well).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, depending on the cell type, receptor expression levels, other DNA regulatory elements, the presence or absence of various testosterone-metabolizing enzymes, and other factors like age, gender, etc., a single steroid hormone can have a multitude of effects throughout the body.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-07-15T20:55:30.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19710" PostTypeId="2" ParentId="19707" CreationDate="2014-07-15T21:36:37.247" Score="6" Body="&lt;p&gt;I've found that ants do not walk through petroleum jelly. It is also convenient, as it isn't too messy, and can be whatever shape you want. I use it to keep ants from climbing into my hummingbird feeders. Make sure the area you treat is wider than the ant is long.&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2014-07-15T21:36:37.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19711" PostTypeId="1" AcceptedAnswerId="19712" CreationDate="2014-07-15T22:41:48.800" Score="2" ViewCount="286" Body="&lt;p&gt;I've heard that part of cognitive processing is information passing between left and right &lt;a href=&quot;http://en.wikipedia.org/wiki/Cerebral_hemisphere&quot; rel=&quot;nofollow&quot;&gt;cerebral hemispheres&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.taltalent.com/download/TL_the_right_brain_feels.pdf&quot; rel=&quot;nofollow&quot;&gt;This is what happens&lt;/a&gt; in the Cerebral Cortex which is divided into two hemispheres, &#xA;  left brain and right brain connected by a thick layer of nerve fibers called the corpus callosum. These nerve fibers allow messages to pass between the left and right brain &#xA;  hemispheres&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My question is &lt;strong&gt;When a thought 'crosses your mind', does it literally cross between left and right cerebral hemispheres?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Assumptions&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I'm making a big leap from 'electronic impulses of neurons' to 'thoughts'. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5417" LastActivityDate="2014-07-16T01:03:48.273" Title="When a thought 'crosses your mind', does it literally cross between left and right cerebral hemispheres?" Tags="&lt;brain&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19712" PostTypeId="2" ParentId="19711" CreationDate="2014-07-16T01:03:48.273" Score="4" Body="&lt;p&gt;Neuroscience doesn't really have a clear model for what a &quot;thought&quot; consists of exactly. Certain processes that are involved in thought have begun to be mapped--for example, this recent paper talks about a model for how the brain associates location in space with it's own mental map (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24462102&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/24462102&lt;/a&gt;, I'll try to find something related that's not behind a paywall...). This one doesn't address your particular problem though, they only measured activity on one side of the brain. So basically, &lt;strong&gt;it might be possible to partially answer your question for more specific brain processes, but different kinds of &quot;thoughts&quot; are processed in different ways.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And of course I am also conflating impulses crossing the corpus callosum with the thoughts themselves, but I don't think this is really accurate. The most popular models in the labs I'm familiar with suggest that a &quot;thought&quot; is composed of a bunch of neural activity taken together rather than the activities of a few neurons on their own. But that might ultimately just be arguing semantics.&lt;/p&gt;&#xA;" OwnerUserId="8336" LastActivityDate="2014-07-16T01:03:48.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19713" PostTypeId="2" ParentId="17757" CreationDate="2014-07-16T04:40:53.640" Score="2" Body="&lt;p&gt;It's look like Sac Spider (&lt;em&gt;Clubiona lutescens&lt;/em&gt;) to me.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VdzrC.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://ednieuw.home.xs4all.nl/Spiders/Clubionidae/Clubionidae.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://ednieuw.home.xs4all.nl/Spiders/Clubionidae/Clubionidae.htm&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-07-16T04:40:53.640" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19714" PostTypeId="2" ParentId="14169" CreationDate="2014-07-16T04:51:53.717" Score="4" Body="&lt;p&gt;It look like &lt;em&gt;Callobius severus&lt;/em&gt; to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/WcD2i.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/WcD2i.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="30140" LastEditDate="2017-05-01T04:11:19.603" LastActivityDate="2017-05-01T04:11:19.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19715" PostTypeId="2" ParentId="19647" CreationDate="2014-07-16T07:03:49.290" Score="1" Body="&lt;p&gt;It seems to me that you're asking about homology modelling. In that case, yes you need to compare your protein of interest to a protein (or proteins) of known structure. Homology modelling in a nutshell includes three (four?) steps: template identification/template alignment, modelling, quality assessment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You start with finding a template for your modelling. This is usually done by sequence alignment, for instance BLASTing. Preferably you use multiple sequence alignment which more sensitively aligns conserved regions. You then want a template with as high sequence identity as possible (above 50 % usually produces models with about 1 Å RMSE [&lt;a href=&quot;http://www.sciencemag.org/content/294/5540/93.full&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;] in main chain atoms. Avoid less than 30 % where modelling errors rapidly increase.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are then a number of different modelling strategies (&lt;a href=&quot;http://en.wikipedia.org/wiki/Homology_modeling#Model_generation&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;). But basically, they all aim to predict the structure of the conserved protein core as well as possible (which usually is what you're really interested in). Peripheral amino acids are more dynamic and more prone to evolution and are therefore more difficult to predict. Then, most importantly, you assess the quality of your model. This can be done by calculating violations of statistical potentials or physics based conformational energies (or using more advanced methods like &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242555/&quot; rel=&quot;nofollow&quot;&gt;multivariate regression methods&lt;/a&gt;). As in all modelling, this really is a most crucial step because prediction with a poor model is misleading and utterly useless.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you don't find any template you could resort to the exciting field of &lt;a href=&quot;http://en.wikipedia.org/wiki/De_novo_protein_structure_prediction&quot; rel=&quot;nofollow&quot;&gt;De novo protein structure prediction&lt;/a&gt;, where the aim is to predict the structure from the amino acid sequence alone. I am not very familiar with their methods, but de novo prediction is hard (!). I don't remember any exact numbers but the number of conformations in a normal sized protein is astronomically large, which leads to great algorithmic and computational challenges. Additionally, without any reference sequence the model assumptions are greater than those of homology modelling. Although, I have heard that the field has been making great progress the last few years.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Edit:&#xA;It struck me that you might be asking about protein fold recognition as well. There exists a large number of different tools and methods for recognizing and locating protein domains using the amino acid sequence as input. Many of them are available as web servers. For instance &lt;a href=&quot;http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index&quot; rel=&quot;nofollow&quot;&gt;phyre&lt;/a&gt; which uses the amino acid profile and predicted secondary structures to search structure libraries. Threading based methods like &lt;a href=&quot;http://zhanglab.ccmb.med.umich.edu/MUSTER/&quot; rel=&quot;nofollow&quot;&gt;MUSTER&lt;/a&gt;. A number based on &lt;a href=&quot;http://en.wikipedia.org/wiki/Hidden_Markov_model&quot; rel=&quot;nofollow&quot;&gt;Hidden Markov Models&lt;/a&gt; (HMMs) also exist. For instance &lt;a href=&quot;http://babel.ucmp.umu.se/fish/&quot; rel=&quot;nofollow&quot;&gt;FISH&lt;/a&gt; which uses structure anchored HMMs.&lt;/p&gt;&#xA;" OwnerUserId="8179" LastEditorUserId="8179" LastEditDate="2014-07-16T07:33:32.483" LastActivityDate="2014-07-16T07:33:32.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19717" PostTypeId="2" ParentId="17813" CreationDate="2014-07-16T09:31:18.920" Score="0" Body="&lt;p&gt;Three factors that influence the number of legs are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Sex : In some species of myriapoda, the females have been found to have more leg segments than males (&lt;a href=&quot;http://www.scielo.br/scielo.php?pid=S0031-10492013001300001&amp;amp;script=sci_arttext&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) eg: Himantarium gabrielis &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) age&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Growth is by adding segments and legs with successive molts&#xA;  (anamorphic), and myriapods continue to add additional segments and&#xA;  legs after they have reached sexual maturity (&lt;a href=&quot;http://www.newworldencyclopedia.org/entry/myriapoda&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;3) Working of a &quot;segmentation clock&quot; (set of genes) that periodically adds segments (&lt;a href=&quot;http://link.springer.com/article/10.1186%2F1741-7007-11-112&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-16T16:51:22.060" LastActivityDate="2014-07-16T16:51:22.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19718" PostTypeId="1" CreationDate="2014-07-16T15:49:03.103" Score="0" ViewCount="125" Body="&lt;p&gt;I'm writing a book, and a a portion of it involves a society of humanzees. Now, is there any &lt;em&gt;plausible&lt;/em&gt; way that a hybrid (such as a humanzee) could procreate either with one another, or with their father/mother species? I apologize for my lack of understanding of biology, any help would be much appreciated!&lt;/p&gt;&#xA;" OwnerUserId="8341" LastActivityDate="2014-07-16T17:38:58.473" Title="Is there any possible way that hybrids can mate?" Tags="&lt;zoology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19719" PostTypeId="2" ParentId="19533" CreationDate="2014-07-16T16:49:52.210" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://fossilworks.org/&quot; rel=&quot;nofollow&quot;&gt;fossilworks.org&lt;/a&gt; and &lt;a href=&quot;http://paleobiodb.org/#/&quot; rel=&quot;nofollow&quot;&gt;paleobiodb.org&lt;/a&gt; are reasonably good databases for fossil records. Paleobiodb has even got a map based view which is really convenient. Thank you.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-07-16T16:49:52.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19720" PostTypeId="1" CreationDate="2014-07-16T16:53:38.927" Score="0" ViewCount="942" Body="&lt;p&gt;According to biochemist Robert Shapiro, the &quot;primordial soup&quot; theory is as follows:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Early Earth had a chemically reducing atmosphere.&lt;/li&gt;&#xA;&lt;li&gt;This atmosphere, exposed to energy in various forms, produced simple organic compounds (&quot;monomers&quot;).&lt;/li&gt;&#xA;&lt;li&gt;These compounds accumulated in a &quot;soup&quot;, which may have been concentrated at various locations (shorelines, oceanic vents etc.).&lt;/li&gt;&#xA;&lt;li&gt;By further transformation, more complex organic polymers – and ultimately life – developed in the soup.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;From: &lt;a href=&quot;http://en.wikipedia.org/wiki/Primordial_soup&quot; rel=&quot;nofollow&quot;&gt;en.wikipedia.org/wiki/Primordial_soup&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't understand how in step four life forms out of nonliving organic polymers. Could you explain this process? Can it be reproduced in the lab?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Louis Pasteur already disproved &lt;a href=&quot;http://en.wikipedia.org/wiki/Spontaneous_generation&quot; rel=&quot;nofollow&quot;&gt;Spontaneous Generation&lt;/a&gt;: &lt;a href=&quot;http://en.wikipedia.org/wiki/Biogenesis&quot; rel=&quot;nofollow&quot;&gt;The law of biogenesis&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8343" LastEditorUserId="8343" LastEditDate="2014-07-20T06:35:24.150" LastActivityDate="2014-07-20T06:35:24.150" Title="How can you explain the origin of life out of nonliving matter (abiogenesis)?" Tags="&lt;cell-biology&gt;&lt;abiogenesis&gt;&lt;organic-chemistry&gt;" AnswerCount="2" CommentCount="2" ClosedDate="2014-07-17T07:56:48.507" ContentLicense="CC BY-SA 3.0" />
  <row Id="19721" PostTypeId="1" CreationDate="2014-07-16T17:08:16.257" Score="2" ViewCount="337" Body="&lt;p&gt;Lamellar bodies have been found to be secreted in lung cells many of their associated proteins have been identified. What is the current consensus or research on the function that these lamellar bodies play in lung? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Sourced answers, please)&lt;/p&gt;&#xA;" OwnerUserId="6027" LastActivityDate="2019-02-28T21:12:34.463" Title="What is the role of lamellar bodies in lung cells?" Tags="&lt;cell-biology&gt;&lt;respiration&gt;&lt;lungs&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19722" PostTypeId="2" ParentId="19706" CreationDate="2014-07-16T17:11:14.637" Score="2" Body="&lt;p&gt;I am afraid you cannot build the classic ECG using only 1 hand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably, you can measure HR - heart rate accordingly to pressure detection and similar sensors and from that you can &lt;em&gt;simulate&lt;/em&gt; ECG by picture. Simulate I mean you cannot build any reliably ECG curve on the monitor, but can show some waves after every heart beat.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2014-07-16T17:11:14.637" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19723" PostTypeId="2" ParentId="19720" CreationDate="2014-07-16T17:13:02.470" Score="4" Body="&lt;p&gt;Welcome to Biology.SE!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Your question has nothing to do with evolutionary biology&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolutionary Theory does not explain the origin of life just like the Theory of Gravity does not explain the diffraction of light! In other words, explaining the origin of life is not within the scope of evolutionary biology. You should edit your title. But still, your question is within the scope of Biology so that your question is totally on-topic. This question would probably also be on topic on Chemistry.SE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Some other posts may interest you&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may want to look at other posts on this site. &lt;a href=&quot;https://biology.stackexchange.com/questions/9921/why-cant-we-propose-a-solid-theory-regarding-origin-of-life&quot;&gt;This post&lt;/a&gt; for example explains what are our issues in order to select which of our hypotheses really explain the origin of life. &lt;a href=&quot;https://biology.stackexchange.com/questions/6861/has-any-large-scale-origin-of-life-simulation-experiment-been-done&quot;&gt;This post&lt;/a&gt;, &lt;a href=&quot;https://biology.stackexchange.com/questions/14175/why-did-abiogenesis-only-happen-once&quot;&gt;this one&lt;/a&gt; may eventually interest you as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Your question might be too broad. You may want to start with some introductory readings&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abiogenesis is not my field and I know very little about the origin of life. But at first sight, I am a bit afraid that your question is too broad and inaccurate and a good answer would ask for writing a lot. &lt;a href=&quot;https://biology.stackexchange.com/questions/115/good-source-that-explains-the-evolution-of-single-celled-organisms-from-scratch&quot;&gt;This post&lt;/a&gt; will give some good source of reading to further your knowledge. It may be good to start there and come back to this site with a more accurate question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope I could help you a bit.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-07-17T09:26:27.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19724" PostTypeId="2" ParentId="19718" CreationDate="2014-07-16T17:21:52.957" Score="2" Body="&lt;p&gt;This is a hypothetical scenario which I think could be compared in parallel to hybrids like a mule (offspring of a male donkey and a female horse) or a hinny (offspring of a male horse and a female donkey) or zebroids (&lt;a href=&quot;http://en.wikipedia.org/wiki/Zebroid&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). In the case of the fertility of mules on wikipedia it is stated that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A few female mules have produced offspring when mated with a purebred&#xA;  horse or donkey.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;with examples being given as &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Since 1527 there have been more than 60 documented cases of foals born&#xA;  to female mules around the world. There are reports that a mule in&#xA;  China produced a foal in 1984. In Morocco, in early 2002, a mare mule&#xA;  produced a rare foal. In 2007 a mule named Kate gave birth to a mule&#xA;  son in Colorado. Blood and hair samples were tested verifying that the&#xA;  mother was a mule and the colt was indeed her offspring (&lt;a href=&quot;http://en.wikipedia.org/wiki/Mule#Fertility&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the case of a hinny fertility is much more rare but there is a documented case on Wikipedia&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In China in 1981, a hinny mare proved fertile with a donkey stallion.&#xA;  When the Chinese hinny was bred to a donkey jack, she produced &quot;Dragon&#xA;  Foal,&quot; who resembled a donkey with mule-like features (&lt;a href=&quot;http://en.wikipedia.org/wiki/Hinny#Fertility.2C_sterility.2C_and_rarity&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Hybrid_%28biology%29&quot; rel=&quot;nofollow&quot;&gt;wikipedia page on hybrids&lt;/a&gt; will also be of interest in your research. In short, hybrids can procreate and give birth in rare cases. However, I wouldn't vouch on the survivability of the offsprings. Since your work is fictional, it is entirely left to your discretion on that topic. Btw, humazee or humzee makes a more intriguing name maybe. Good luck with the book.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-16T17:38:58.473" LastActivityDate="2014-07-16T17:38:58.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19725" PostTypeId="1" AcceptedAnswerId="20252" CreationDate="2014-07-16T17:24:03.027" Score="6" ViewCount="1057" Body="&lt;p&gt;In an animal cell, especially neuron and in particular its axon, while there is electrical resistance and capacitance mechanism in the cell, which play essential roles in the cable theory model of neuronal action potential transmission, is there a prominent self &lt;a href=&quot;http://en.wikipedia.org/wiki/Self_inductance&quot; rel=&quot;nofollow noreferrer&quot;&gt;inductance&lt;/a&gt; mechanism in the sense of electromagnetism?&lt;/p&gt;&#xA;" OwnerUserId="8344" LastEditorUserId="8344" LastEditDate="2018-10-31T07:14:41.977" LastActivityDate="2018-10-31T07:14:41.977" Title="Inductance in cell" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;cell-biology&gt;&lt;cell-membrane&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="19727" PostTypeId="2" ParentId="19718" CreationDate="2014-07-16T17:32:00.000" Score="1" Body="&lt;p&gt;Recent genetic analysis of human DNA shows &lt;a href=&quot;http://www.pnas.org/content/108/37/15129&quot; rel=&quot;nofollow&quot;&gt;neanderthal ancestry&lt;/a&gt;, so inter-species breeding to produce reproductively viable offspring (humanderthals?) appears to be possible - at least between species of the same genus. But with &lt;em&gt;Homo sapiens&lt;/em&gt; being the only extant species in the genus &lt;em&gt;Homo&lt;/em&gt; you'd be really stretching the boundaries of plausibility to have a human/ape or human/monkey hybrid.&lt;/p&gt;&#xA;" OwnerUserId="6810" LastActivityDate="2014-07-16T17:32:00.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19728" PostTypeId="1" CreationDate="2014-07-16T20:24:29.343" Score="5" ViewCount="128" Body="&lt;p&gt;Assume that there are two different signals occurring on the ECG - during depolarization and repolarization in the standard ECG. &#xA;I was advised not to use the standard ECG in measuring the exact electrical events during: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;stages 0-2&lt;/li&gt;&#xA;&lt;li&gt;3-4&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;We can get data about the electric activity of neurons in vivo in Fig. 1 where some data about the electric activity of neurons is present.&#xA;So my thought is that a similar technique could probably work with cardiomyocytes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fig. 1 Example of measurement for electric activity of neurons in vivo&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/LZdgw.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/LZdgws.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I estimate that there is about 18% uncertainty when using the standard ECG because of the peak in the stage 1 (Gibbs phenomenon) and those two complete different phases.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2016-10-17T22:38:43.303" LastActivityDate="2016-10-17T22:38:43.303" Title="How to measure Na/K channel activation at the membrane level?" Tags="&lt;biophysics&gt;&lt;electrophysiology&gt;&lt;action-potential&gt;&lt;electrocardiography&gt;&lt;signalling&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19730" PostTypeId="1" AcceptedAnswerId="19738" CreationDate="2014-07-16T22:26:57.150" Score="1" ViewCount="2802" Body="&lt;p&gt;I used Qiagen's RNeasy Mini Kit to isolate RNA from 5*10^5 C28/I2 (immortalized human chondrocytes). However, my yield is low (~25 ng/ul), but my 260/280 ratio is great (~2.3), and my 260/230 ratio is tragic (~0.06). I have already thrown the spin column away, but I would like to know 1) if I could raise my 260/230 ratio for the 40 ul of RNA I extracted, and 2) if I could precipitate the RNA out of solution so as to make a more concentrated solution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please let me know if further details are necessary. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2014-07-17T08:17:28.190" Title="RNeasy Mini Kit low 260/230 ratio -- can I purify this RNA for further use?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;lab-techniques&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19732" PostTypeId="2" ParentId="19720" CreationDate="2014-07-17T02:17:05.117" Score="0" Body="&lt;p&gt;Some might think that this is a chemistry question, and indeed most of the work is done in chemistry departments, but that isn't because its not biology.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as evolutionary theory, there is a well-established definition of life as self-replicating systems and very little else.  &lt;a href=&quot;http://www.stephenjaygould.org/library/dawkins_replicators.html&quot; rel=&quot;nofollow&quot;&gt;Richard Dawkins' theory of the Replicator&lt;/a&gt;  is not always completely accepted (the link is to Stephen Gould's essay, who was usually in the opposition to Dawkins until he passed away).  Nonetheless, its logic is hard to completely dismiss: Once and only once chemical systems can self replicate then evolution happens - selection, variation and replication.  Dawkins thought springs from the pretty justifiable position that DNA is the center of all inheritance and variation in living things.  I'm not going to get into the arguments for and against but suffice to say that the replicator model might not be entirely true, but its not entirely wrong.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as the fourth step you mention, there are theories which are very credible but its reasonable to say that we are short on details... they may not satisfy and they certainly have not duplicated step 4...  The most detailed and credible theory is the &lt;a href=&quot;https://en.wikipedia.org/wiki/RNA_world_hypothesis&quot; rel=&quot;nofollow&quot;&gt;RNA World Hypothesis&lt;/a&gt;.  At some stage, RNA polymers were able to self-replicate, pretty much by themselves it seems.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The evidence for RNA world is compelling but its more molecular archaeology than a series of coordinate events as we see it.  The ribosome and other RNA genes show that RNA could be fundamental genes.  In particular the ribosome consists of RNA whose structure are supported by protein, but RNA does all the chemical work.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider the odds.  The prebiotic soup may have existed for the better part of a billion years and covered all or a good part of Earth during much of that time.  As such, its exceedingly unlikely that we will be able to reproduce self replication of RNA in the lab.  Lucky and intelligent guesses may produce an environment that is just barely pre-biotic and produce a replicator, but even that seems quite unlikely.  Almost all this work tries to show that compounds and processes that come close to life are possible in pre-biotic Earth. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-07-17T02:17:05.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19733" PostTypeId="2" ParentId="19525" CreationDate="2014-07-17T02:20:14.030" Score="2" Body="&lt;p&gt;Yes, bones can be innervated. I say &quot;can be&quot; because although I'm not certain that ALL are, I know that most are. &quot;Innervation&quot; is your key word to learning more about the presence or absence of nerves reaching to any body part. Googling &quot;are bones innervated&quot; yields plentiful results, but the short answer is yes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you were to chop your leg off with surrounding tissue numbed, you would still feel it for this same reason. &lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2014-07-17T02:20:14.030" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19734" PostTypeId="2" ParentId="16845" CreationDate="2014-07-17T04:51:44.133" Score="1" Body="&lt;p&gt;I assume you mean &quot;why can't glutathione, NAC .. be added&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.lef.org/magazine/mag2010/jul2010_Deadly-FDA-Neglect_01.htm&quot; rel=&quot;nofollow&quot;&gt;lef.org&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There is one problem. The FDA prohibits combining existing drugs and&#xA;  dietary supplements unless a New Drug Application is filed, tens of&#xA;  millions of dollars of clinical studies are performed, and the FDA&#xA;  agrees to allow the combination to be sold. The whole process can cost&#xA;  upwards of $100 million and take a decade to complete.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's sad that would would be very likely an effective solution for the deaths and liver damage is not available or made more widely known.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Only about 10% of acetaminophen is metabolised through the glutathione conjugation pathway via NAQBI (the other 90% is direct sulfation and glucuronidation of acetaminophen). Many people take NAC supplements regularly (I used to).  While high does can have some side effects, a typical supplement level dose of a few hundred milligrams daily are well tolerated.&lt;/p&gt;&#xA;" OwnerUserId="8349" LastActivityDate="2014-07-17T04:51:44.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19735" PostTypeId="1" AcceptedAnswerId="19818" CreationDate="2014-07-17T05:51:10.837" Score="5" ViewCount="362" Body="&lt;p&gt;Why have higher-order animals lost the ability to regenerate body parts during evolution? Wouldn't it be better for survival? What is the evolutionary theory behind it?  &lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="5331" LastEditDate="2014-07-21T02:19:58.707" LastActivityDate="2014-07-21T05:28:40.563" Title="Lost Ability to Regenerate Body Parts during the Transition from Amphibians to Mammals" Tags="&lt;evolution&gt;&lt;healing&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="19736" PostTypeId="2" ParentId="19318" CreationDate="2014-07-17T07:08:02.143" Score="1" Body="&lt;p&gt;1) &lt;a href=&quot;http://en.wikipedia.org/wiki/Iwasaki&amp;#39;s_snail-eater&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pareas iwasakii&lt;/a&gt; has asymmetric mandibles.  A few more examples of asymmetric snakes (&lt;a href=&quot;http://snakesarelong.blogspot.in/2012/04/asymmetrical-snakes.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/65E8u.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pareas iwasakii skull &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Camels have an asymmetric penis (&lt;a href=&quot;https://science.naturalis.nl/en/research/character-evolution/left-right-asymmetry/&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) You could find quite a few in this article titled &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0960982209009269&quot; rel=&quot;nofollow noreferrer&quot;&gt;Animal asymmetry&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps. I am sure there are more but these are some I could find. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-07-17T07:08:02.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19737" PostTypeId="2" ParentId="19316" CreationDate="2014-07-17T07:51:01.447" Score="14" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_world_hypothesis&quot; rel=&quot;noreferrer&quot;&gt;RNA world hypothesis&lt;/a&gt; states that self-replicating RNA (that is, an autocatalytic RNA polymerase) was the first form or precursor of life. So, in that context, your question is basically asking how life originated. The obvious answer is that &lt;strong&gt;we don't know&lt;/strong&gt; (currently anyways), but I'm going to take this opportunity to describe a few really neat experiments which might give you some insight over a possibly contributing mechanism of how self-replicating molecules may have developed. I won't go over the &lt;a href=&quot;http://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment&quot; rel=&quot;noreferrer&quot;&gt;Miller-Urey &lt;/a&gt;or &lt;a href=&quot;http://en.wikipedia.org/wiki/Joan_Or%C3%B3#Origins_of_life&quot; rel=&quot;noreferrer&quot;&gt;Oró&lt;/a&gt; experiments, but let's assume that the early Earth contained organic molecules (especially nucleotides for our purposes). It's also important to keep in mind the immense time scales over which these processes occurred (the Earth is ~4.5 billion years old).&lt;/p&gt;&#xA;&lt;p&gt;Anyways, let's talk about in vitro evolution, also known as systematic evolution of ligands by exponential enrichment (SELEX). SELEX is a procedure whereby an initial library of random RNA sequences (flanked by known sequences to be used as primer sites) undergoes a selective process followed by amplification and mutation of the selected molecules. This is repeated several times. As an example, this process can be used to create aptamers, which are small RNA molecules which bind a specific ligand. A pool of random RNA is passed over a column containing the immobilized ligand. By chance, some RNA will have some amount of affinity to the ligand. Poorly bound RNA is washed off non-stringently and then slightly better bound RNA is eluted. This RNA is reverse transcribed and amplified by PCR. The PCR primers contain the T7 RNAP promoter which allows transcription of the cDNA to produce a new  RNA pool. Somewhere in this regeneration process, mutations are introduced so that the new pool contains randomly modified copies of the RNA which had some affinity. Through repeated steps of increasing stringency, an aptamer with high affinity can be developed.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Au8Dv.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;(Ellington, 1994); Outline of the SELEX process.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So how does this apply to the origin of the first RNA polymerase? It just so happens that Bartel and Szostak (1993) used in vitro selection to produce a ribozyme (a catalytic RNA molecule). This ribozyme was a ligase, that is it catalyzed the formation of a phosphodiester bond between two RNA molecules that are aligned on a template.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/u7bzP.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;(Bartel and Szostak, 1993); Methodology of the selection used to generate a ribozyme ligase.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;While the ribozyme created was not autocatalytic, the experiment had implications on the origin of self-replicating RNA and life in general, which were discussed in the paper:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The ribozymes that we have isolated from a pool of random sequences catalyze a chemical transformation similar to that catalyzed by polymerases. Their abundance in the random-sequence pool is therefore relevant to the hypothesis that life began with an RNA replicase that originated from prebiotically synthesized random-sequence RNA. We detected about 65 sequences (Fig. 8, pools 3 and 4) capable of carrying out a particular ligation reaction in a pool of more than &lt;span class=&quot;math-container&quot;&gt;$10^{15}$&lt;/span&gt; initial sequences, or a frequency of occurrence of one in about &lt;span class=&quot;math-container&quot;&gt;$2*10^{13}$&lt;/span&gt; sequences.&lt;/p&gt;&#xA;&lt;p&gt;[...]&lt;/p&gt;&#xA;&lt;p&gt;Presumably, sequences capable of acting as efficient template-directed RNA polymerases are more rare than this, and sequences capable of acting as an RNA replicase are even more rare. Evidently, catalysts of moderate activity could arise spontaneously from relatively small quantities of RNA (and perhaps related polynucleotides); however, a catalyst with the activity, accuracy, and dual functionality (enzyme and template) of an RNA replicase would be so rare that it could only arise spontaneously and in a single step from a truly enormous amount of RNA. The problem is compounded because two such sequences would be required for autocatalytic replication to begin, one to act as the polymerase and a second to act as the template. Therefore, an RNA replicase could only have arisen from primordial sequence pools that were not truly random. Joyce and Orgel anticipate this difficulty and propose that nonenzymatic, template-copying reactions may have had a dual role in generating primordial sequence pools that are more likely to give rise to a replicase (21). The initial pool may have been biased in favor of local secondary structure by a mechanism involving intermittent use of intramolecular sequence as the template. In addition, some sort of nonenzymatic catalysis was probably necessary for the initial copying of the replicase sequence to generate a molecule that could be used as a template, the copying of which by the replicase would generate more replicase molecules, thus initiating the autocatalytic explosion of life.&lt;/p&gt;&#xA;&lt;p&gt;[...]&lt;/p&gt;&#xA;&lt;p&gt;The ribozymes that we have selected provide a new starting point for the evolution or design of RNAs with RNA polymerase and replicase activity. A series of issues including sequence-independent primer-template binding, the use of mononucleotide triphosphates as substrates, fidelity, and product-template dissociation now need to be addressed before an RNA replicase activity, an activity that has probably been extinct for over 3 billion years, can be fully resuscitated.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Johnston et al. (2001) took this experiment even further: starting with a pool of slightly mutated ribozyme ligases developed in a previous SELEX experiment, they were able to generate a ribozyme polymerase. This polymerase was able to catalyze the addition of nucleotides to a growing oligonucleotide chain up to 14 bases long and based off of an RNA template. The polymerase was also quite accurate.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4pOyy.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;(Johnston et al., 2001); Excerpts from the in vitro evolution of a ribozyme polymerase.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However, the authors are skeptical of this being the sole mechanism behind the rise of an autocatalytic ribozyme:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;How could general polymerase activity have arisen on early Earth? If emergence of the first RNA replicase ribozyme coincided with the origin of life, it would have had to arise in a single step from prebiotically synthesized RNA, without the benefit of Darwinian evolution. Our shortest construct retaining activity was 165 nt, with about 90 nt involved in important Watson-Crick pairing and at least another 30 critical nucleotides (23). Ribozymes with the efficiency, accuracy, and other attributes of an RNA replicase might have to be even larger than this. However, current understanding of prebiotic chemistry argues against the emergence of meaningful amounts of RNA molecules even a tenth this length (1). This difficulty is anticipated by those who propose that life, and Darwinian evolution, began before RNA. Some speculate that in this &amp;quot;pre-RNA world,&amp;quot; life was based on an RNA-like polymer, yet to be identified, that possessed the catalytic and templating features of RNA but also a more plausible prebiotic synthesis (1). The pre-RNA life forms presumably later developed the ability to synthesize RNA, facilitating the emergence of an RNA replicase ribozyme, which in turn enabled the transition to the RNA world.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;There are other, similar experiments where people have made self-replicating ligases (Paul and Joyce, 2002) or a system of two, cross replicating ribozymes (Lincoln and Joyce, 2009). While the question still remains unanswered, perhaps from all of this you can get a sense of the plausibility.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Bartel DP, Szostak JW. 1993. Isolation of New Ribozymes from a Large Pool of Random Sequences. Science. 261(5127):1411-1418.&lt;/p&gt;&#xA;&lt;p&gt;Ellington AD. 1994. Aptamers achieve the desired recognition. Curr Biol. 4(5):427-429.&lt;/p&gt;&#xA;&lt;p&gt;Johnston WK, Unrau PJ, Lawrence MS, Glasner MR, Bartel DP. 2001. RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension. Science. 292(5520):1319-1325.&lt;/p&gt;&#xA;&lt;p&gt;Lincoln TA, Joyce GF. 2009. Self-Sustained Replication of an RNA Enzyme. Science. 323(5918):1229-1232.&lt;/p&gt;&#xA;&lt;p&gt;Paul N, Joyce GF. 2002. A self-replicating ligase ribozyme. P Natl Acad Sci USA. 99(20):12733-12740&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-07-21T06:53:29.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19738" PostTypeId="2" ParentId="19730" CreationDate="2014-07-17T08:17:28.190" Score="1" Body="&lt;p&gt;RNAeasy kit will not usually give phenolic contamination. Your poor 260/230 is perhaps because of low yield; check the absolute absorbance values. Low 260/230 (and low yield) also happens because of improper lysis. I would advise that you do the cell lysis using more effective methods. I would not advise another phenol-chloroform or alcohol precipitation step- you will lose your RNA. With what you have now, run a little bit on the gel to see the integrity. Also try heating the dissolved RNA at 65-70deg for 10-15min and measure OD again (use nanodrop or a similar device)&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-07-17T08:17:28.190" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19739" PostTypeId="2" ParentId="19707" CreationDate="2014-07-17T08:23:08.707" Score="4" Body="&lt;p&gt;Fluon is a substance that people use to make artificial ant nests. It is similar to teflon in property and fluon coated surfaces are too slippery for ants to cross. See &lt;a href=&quot;http://krungkuene.org/ameisen_page/fluon.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-07-17T08:23:08.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19740" PostTypeId="2" ParentId="14592" CreationDate="2014-07-17T09:35:33.533" Score="2" Body="&lt;p&gt;Some Differences are listed here&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EbbH6.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please consider reading these articles (&lt;a href=&quot;http://www.hort.uconn.edu/ipm/veg/htms/bltpot.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;article 1&lt;/a&gt;, &lt;a href=&quot;https://extension.umass.edu/vegetable/articles/recognizing-tomato-blights&quot; rel=&quot;nofollow noreferrer&quot;&gt;article 2&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-07-17T10:08:39.300" LastActivityDate="2014-07-17T10:08:39.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19741" PostTypeId="2" ParentId="14516" CreationDate="2014-07-17T10:54:07.420" Score="3" Body="&lt;p&gt;From a study titled &quot;&lt;a href=&quot;http://aem.asm.org/content/68/3/1211.full&quot; rel=&quot;nofollow&quot;&gt;Production of Penicillin by Fungi Growing on Food Products: Identification of a Complete Penicillin Gene Cluster in Penicillium griseofulvum and a Truncated Cluster in Penicillium verrucosum&lt;/a&gt;&quot;, moulds on food items were analyzed for fungi that could produce penicillin. The conclusion drawn was &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Among different fungal species belonging to the genus Penicillium that&#xA;  are currently used as starter cultures in the food industry or that&#xA;  are frequently isolated from cured meat products, only P. griseofulvum&#xA;  (in addition to the previously reported P. chrysogenum and P.&#xA;  nalgiovense) was found to produce penicillin and possess the three&#xA;  penicillin biosynthetic genes (pcbAB, pcbC, and penDE).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Even penicillin should be avoided as the paper states that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The presence of penicillin in food must be avoided, since it can lead&#xA;  to allergic reactions and the arising of penicillin resistance in&#xA;  human-pathogenic bacteria.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;During world war two, a strain of Penicillium chrysogenum was isolated from the mould growing on a cantaloupe (&lt;a href=&quot;http://botit.botany.wisc.edu/toms_fungi/nov2003.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) for the development of penicillin. This was after searching through many mould families developing on different food items so penicillin strains do develop but are rare.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem faced is that moulds cannot be differentiated from each other through sight nor is all penicillin moulds safe (&lt;a href=&quot;http://www.theguardian.com/lifeandstyle/2011/oct/26/food-mould-safe-or-toxic&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Whatever be the case, I hope that you didn't venture to try and eat that beetroot.  &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-07-17T10:54:07.420" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19742" PostTypeId="1" AcceptedAnswerId="19743" CreationDate="2014-07-17T11:06:55.307" Score="8" ViewCount="440" Body="&lt;p&gt;I am really passionate about theoretical and quantitative biology and I would like to build my future career around this topic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've just got my bachelor's degree in biology (ecology) but scince I've had only one math class through the years, my math skills are very poor, so I have problems in understanding even simpe models. My main interests are population dynamics, adaptive dynamics and game theoretical models of social conflicts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to improve my skills, but I have just no idea where/how to start. Could you give me some advice about textbooks or online resources?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have almost no knowledge in the field of math, I am interested in resources for complete beginners. And I would also appreciate any suggestions about skills/topics I should master if I am interested in these biological phenomena.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="8353" LastActivityDate="2014-07-17T13:06:23.753" Title="Start studying mathematical biology from basics" Tags="&lt;mathematical-models&gt;&lt;population-dynamics&gt;&lt;literature&gt;&lt;sociality&gt;&lt;computational-model&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19743" PostTypeId="2" ParentId="19742" CreationDate="2014-07-17T12:52:13.243" Score="9" Body="&lt;p&gt;There is one book that will perfectly suits your needs:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0691123446&quot; rel=&quot;noreferrer&quot;&gt;A biologist's guide to Mathematical Modeling in Ecology and Evolution&lt;/a&gt;, by Sally Otto&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is a very good book that is very easy to understand and in the meantime goes pretty far (It ends with the use of diffusion equation in Evolutionary Biology). I highly recommend it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It covers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;How to create a model&lt;/li&gt;&#xA;&lt;li&gt;Function approximation&lt;/li&gt;&#xA;&lt;li&gt;Find general solution with $n$ variables for discrete and continuous model&lt;/li&gt;&#xA;&lt;li&gt;Stability analysis&lt;/li&gt;&#xA;&lt;li&gt;Find equilibrium&lt;/li&gt;&#xA;&lt;li&gt;Analyzing cyclic behavior&lt;/li&gt;&#xA;&lt;li&gt;Gives very good introduction in linear algebra and probability theory&lt;/li&gt;&#xA;&lt;li&gt;Class structured population&lt;/li&gt;&#xA;&lt;li&gt;Stochastic modeling (birth-death processes and diffusion approximations)&lt;/li&gt;&#xA;&lt;li&gt;Transformations&lt;/li&gt;&#xA;&lt;li&gt;All examples are from the field of ecology and evolution and the author derives many of the most important equations in ecology and evolution.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Online ressources&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also I think that &lt;a href=&quot;https://www.khanacademy.org&quot; rel=&quot;noreferrer&quot;&gt;Khan Academy&lt;/a&gt; is a very good and easy source of information for improving your math skills but it takes quite a bit of time to go through all these lectures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a good and complete introduction to probability theory, I'd recommend &lt;a href=&quot;http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-041-probabilistic-systems-analysis-and-applied-probability-fall-2010/video-lectures/lecture-1-probability-models-and-axioms/&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; MIT Opencourseware but again, it takes time to go through all these videos.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For &lt;strong&gt;further recommendations in population genetics&lt;/strong&gt;, you should have a look to &lt;a href=&quot;https://biology.stackexchange.com/questions/16470/book-recommendation-on-population-evolutionary-genetics&quot;&gt;this post&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in theoretical biology, you may also want to learn about &lt;strong&gt;programming&lt;/strong&gt; (if you don't already know much about it). $R$ is used for data analysis purposes, $Mathematica$ or $Matlab$ for deal with mathematical modeling and $Python$, $Java$ or $C++$ for individual-based simulations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: A bit less than 2 years ago, I had the same interests than you and had to face the same issues than you.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-07-17T13:06:23.753" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="19744" PostTypeId="1" AcceptedAnswerId="19748" CreationDate="2014-07-17T12:54:35.723" Score="9" ViewCount="813" Body="&lt;p&gt;&lt;a href=&quot;https://cooking.stackexchange.com/a/45589/11251&quot;&gt;An answer on another SE site&lt;/a&gt; mentions that sugar &quot;at a certain level acts as a preservative&quot;. I've always been taught that microorganisms eat sugar and expel acids, that is why sugary food are damaging to teeth. &lt;strong&gt;How is it that sugar acts as a preservative, then?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Googling the question I've found &lt;a href=&quot;http://sciencefocus.com/qa/how-does-sugar-act-preservative&quot; rel=&quot;nofollow noreferrer&quot;&gt;conflicting&lt;/a&gt; &lt;a href=&quot;https://answers.yahoo.com/question/index?qid=20080423133918AAt7NvX&quot; rel=&quot;nofollow noreferrer&quot;&gt;answers&lt;/a&gt; though I don't credit the sources as being especially reputable. What is the real reason that sugar can act as a preservative?&lt;/p&gt;&#xA;" OwnerUserId="6967" LastEditorUserId="-1" LastEditDate="2017-04-13T12:33:29.980" LastActivityDate="2016-02-10T07:55:14.237" Title="Sugar as a defence against bacteria?" Tags="&lt;microbiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19746" PostTypeId="1" CreationDate="2014-07-17T15:44:59.713" Score="4" ViewCount="112" Body="&lt;p&gt;Why is it that &lt;a href=&quot;http://en.wikipedia.org/wiki/Honey&quot; rel=&quot;nofollow&quot;&gt;honey&lt;/a&gt; can last for decades and not spoil like other foods? Is there any chemical in honey which gives rise to this amazing feat?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="338" LastEditDate="2014-07-22T04:18:29.267" LastActivityDate="2014-07-22T04:18:29.267" Title="Why doesn't honey spoil quickly?" Tags="&lt;biochemistry&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2014-07-18T19:01:09.513" ContentLicense="CC BY-SA 3.0" />
  <row Id="19747" PostTypeId="2" ParentId="1805" CreationDate="2014-07-17T16:36:09.950" Score="2" Body="&lt;p&gt;Thanks for the searching and quoting Ilmari. According to some theories, and perhaps there is some research on stool to support these, we can aid our intestines for producing beneficial bacteria by eating PREbiotic foods which supposedly help create a good environment in the intestines for producing healthy bacteria on its own.  Some foods that are supposed to be prebiotic are onions, garlic, and fermented foods such as sauerkraut, kimchi, cortido, miso, kombacha, and sour cream, and also saturated fats such as butter and animal lard. Non-pasteurized full-fat yogurt is not only supposed to be PRObiotic but also PREbiotic as well.  That many priobiotic cultures do not appear to survive digestion perhaps our focus should be more on eating PREbiotic and not so much on consuming PRObiotic cultures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also foods that are could be harmful to the environment in the intestines.  These, according to theories, include refined sugar, soy, processed foods, and seed oils (the process of extracting oil from seeds and dry plant components is highly refined).  For some people, again according to theories, the harmful foods also include gluten and lactose from Holstein Friesian cattle (the most common dairy cow in the USA and I think Europe).&lt;/p&gt;&#xA;" OwnerUserId="8355" LastActivityDate="2014-07-17T16:36:09.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19748" PostTypeId="2" ParentId="19744" CreationDate="2014-07-17T21:23:08.810" Score="10" Body="&lt;p&gt;Sugar in high concentrations acts osmotic. This means that the water available in the cells is drawn towards the high concentration of a solutant (sugar), like in the image below (this is demonstrated with a plant cell, but the principle is the same for bacteria and other microorganisms):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZciJU.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since microorganisms can not survive without water, they are not able to grow or reproduce. This effectively safes food. The same mechanism works when salt is used to conserve meat or fish.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-17T21:23:08.810" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19749" PostTypeId="1" AcceptedAnswerId="20001" CreationDate="2014-07-17T22:44:00.773" Score="5" ViewCount="1278" Body="&lt;p&gt;I have some protein-ligand complexed that I have been docking with some other software and just want to use Autodock to evaluate those complexes. So, basically I just want to use it as a scoring function to take a look at the energy components - I don't want to re-dock the ligands into the protein binding sites. &#xA;From what I have found on the internet, I came up with this procedure, but I am not sure if this is the right approach, and also I get an error in the last step saying that &quot;atoms are outside the grid&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be nice if someone could take a look at it and tell me whether this make sense and if this is the right procedure (and maybe a suggestion for the error source)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1) Preparing the receptor&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;need to add hydrogens if not present&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;adds gasteiger charges to peptide&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;input&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;protein.pdb&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;output&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;protein.pdbqt&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;script:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;prepare_receptor4.py -r protein.pdb [options]&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2) Preparing the ligand&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;add hydrogens if not present &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;input:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ligand.pdb or ligand.mol2&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;output:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ligand.pdbqt&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;script&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;prepare_ligand4.py -l ligand.mol2 [options]&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;3) Generate grid parameter file&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;inputs&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ligand.pdbqt&lt;/li&gt;&#xA;&lt;li&gt;protein.pdbqt&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;output&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;protein.gpf&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;script:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;prepare_gpf4.py -l ligand.pdbqt -r protein.pdbqt [options]&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;4) AutoGrid: generate maps and grid data file&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;inputs:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;protein.pdbqt &lt;/li&gt;&#xA;&lt;li&gt;protein.gpf&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;outputs:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;protein.glg             Grid Log File&lt;/li&gt;&#xA;&lt;li&gt;protein.*.map         affinity maps for different atoms&lt;/li&gt;&#xA;&lt;li&gt;protein.maps.fld     Grid data file&lt;/li&gt;&#xA;&lt;li&gt;protein.d.map         desolvation map&lt;/li&gt;&#xA;&lt;li&gt;protein.e.map         electrostatic map&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;command:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;autogrid -p protein gpf&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;5) Generate docking parameter file&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;inputs&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ligand.pdbqt&lt;/li&gt;&#xA;&lt;li&gt;protein.pdbqt&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;output&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ligand_protein.dpf&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;script:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;prepare_dpf4.py -l ligand.pdbqt -r protein.pdbqt [options]&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;**&#xA;**&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;6) Prepare .dpf file and run autodock for re-scoring&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;**&#xA;**&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remove seach parameters and append the &quot;epdb&quot; keyword, so that an&#xA;examplary .dpf would look like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;autodock_parameter_version 4.2       # used by autodock to validate&#xA;parameter set &lt;/p&gt;&#xA;&#xA;&lt;p&gt;outlev 1                             # diagnostic output level &lt;/p&gt;&#xA;&#xA;&lt;p&gt;intelec                              # calculate internal&#xA;electrostatics &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ligand_types C HD N NA OA            # atoms types in ligand &lt;/p&gt;&#xA;&#xA;&lt;p&gt;fld rec.maps.fld                 # grid_data_file &lt;/p&gt;&#xA;&#xA;&lt;p&gt;map rec.C.map                    # atom-specific affinity map &lt;/p&gt;&#xA;&#xA;&lt;p&gt;map rec.HD.map                   # atom-specific affinity map &lt;/p&gt;&#xA;&#xA;&lt;p&gt;map rec.N.map                    # atom-specific affinity map &lt;/p&gt;&#xA;&#xA;&lt;p&gt;map rec.NA.map                   # atom-specific affinity map &lt;/p&gt;&#xA;&#xA;&lt;p&gt;map rec.OA.map                   # atom-specific affinity map &lt;/p&gt;&#xA;&#xA;&lt;p&gt;elecmap rec.e.map                # electrostatics map &lt;/p&gt;&#xA;&#xA;&lt;p&gt;desolvmap rec.d.map              # desolvation map &lt;/p&gt;&#xA;&#xA;&lt;p&gt;move lig.pdbqt                       # small molecule &lt;/p&gt;&#xA;&#xA;&lt;p&gt;about 17.6 22.2 32.6         # small molecule center &lt;/p&gt;&#xA;&#xA;&lt;p&gt;epdb                                   # small molecule to be&#xA;evaluated &lt;/p&gt;&#xA;&#xA;&lt;p&gt;**&#xA;**&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;inputs&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ligand_receptor.dpf&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;command:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;autodock -p ligand_protein.dpf&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Edit&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;I managed to use AutoDock Vina for re-scoring now, however, the output is not as detailed as the one that would be produced by AutoDock 4.2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, what I get is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Affinity: -2.06943 (kcal/mol)&#xA;Intermolecular contributions to the terms, before weighting:&lt;br&gt;&#xA;    gauss 1     : 51.97697&lt;br&gt;&#xA;    gauss 2     : 1133.84012&lt;br&gt;&#xA;    repulsion   : 7.41516&lt;br&gt;&#xA;    hydrophobic : 34.56441&lt;br&gt;&#xA;    Hydrogen    : 0.00000  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(what is also weird is that the &lt;code&gt;prepare_ligand4.py&lt;/code&gt; script to generate the .pdbqt file from the mol2 file removed the hydrogens)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In AutoDock4.2, the output would be, for example,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;epdb: USER Estimated Free Energy of Binding = -6.54 kcal/mol [=(1)+(2)+(3)-(4)]&lt;br&gt;&#xA;epdb: USER Estimated Inhibition Constant, Ki = 15.95 uM (micromolar) [Temperature = 298.15 K]&lt;br&gt;&#xA;epdb: USER&lt;br&gt;&#xA;epdb: USER (1) Final Intermolecular Energy = -7.14 kcal/mol&lt;br&gt;&#xA;epdb: USER vdW + Hbond + desolv Energy = -6.33 kcal/mol&#xA;epdb: USER Electrostatic Energy = -0.81 kcal/mol&lt;br&gt;&#xA;epdb: USER (2) Final Total Internal Energy = -0.20 kcal/mol&lt;br&gt;&#xA;epdb: USER (3) Torsional Free Energy = +0.60 kcal/mol&lt;br&gt;&#xA;epdb: USER (4) Unbound System's Energy [=(2)] = -0.20 kcal/mol  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyone knows if this might be available through VINA somehow?&lt;/p&gt;&#xA;" OwnerDisplayName="user6881" LastEditorDisplayName="user6881" LastEditDate="2014-07-18T22:42:01.240" LastActivityDate="2017-04-25T18:47:14.767" Title="How to use Autodock just for (re)scoring" Tags="&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19751" PostTypeId="2" ParentId="19749" CreationDate="2014-07-18T04:43:40.153" Score="4" Body="&lt;p&gt;You can use Autodock Vina. It provides an option to calculate local score only.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;displaying the individual contributions to the intermolecular score, before weighting (these are shown with &quot;--score_only&quot;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Autodock is better tool in speed and accuracy than Autodock itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For using it, you need :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Protein.pdbqt&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Ligand.pdbqt&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Config.txt (the confguration file):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;receptor = hsg1/rigid.pdbqt &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;ligand = ligand.pdbqt&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;center_x =  2 # Center of Grid points X&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;center_y =  6 # Center of Grid points Y &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;center_z = -7 # Center of Grid points Z&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;size_x = 25 # Number of Grid points in X direction&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;size_y = 25 # Number of Grid points in Y Direction&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;size_z = 25 # Number of Grid points in Z Direction&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Run your code as :&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;vina --score_only --config config.txt --log your_filename.log&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;for mmore information type:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;vina --help_advanced&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;source: &lt;a href=&quot;http://vina.scripps.edu/manual.html#faq&quot; rel=&quot;nofollow&quot;&gt;http://vina.scripps.edu/manual.html#faq&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;UPDATE:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Use:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;prepare_ligand4.py   -A 'hydrogens'&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;for Adding hydrogen&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For understanding the scoring of Vina:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041641&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading&lt;/strong&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-07-19T18:58:50.837" LastActivityDate="2014-07-19T18:58:50.837" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19752" PostTypeId="2" ParentId="19721" CreationDate="2014-07-18T05:11:15.227" Score="1" Body="&lt;p&gt;Well, The paper published in Nature 2003:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Despite two decades of progress in understanding the role of LGs and&#xA;their contents in epidermal barrier function, almost nothing is known&#xA;about the mechanisms responsible for the assembly of these unique&#xA;organelles.source: &lt;a href=&quot;http://www.nature.com/jid/journal/v120/n4/full/5601763a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.nature.com/jid/journal/v120/n4/full/5601763a.html&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Since then the word &amp;quot;Lamellar Granule&amp;quot; appeared only 5 more times in journals:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;1: Sando GN, Zhu H, Weis JM, Richman JT, Wertz PW, Madison KC.&#xA;&lt;strong&gt;Caveolin expression and localization in human keratinocytes suggest a&#xA;role in lamellar granule biogenesis.&lt;/strong&gt; J Invest Dermatol. 2003&#xA;Apr;120(4):531-41. PubMed PMID:&#xA;12648214.&lt;/p&gt;&#xA;&lt;p&gt;2: Akiyama M. &lt;strong&gt;The roles of ABCA12 in epidermal lipid barrier formation&#xA;and keratinocyte differentiation.&lt;/strong&gt; Biochim Biophys Acta. 2014&#xA;Mar;1841(3):435-40. doi:&#xA;10.1016/j.bbalip.2013.08.009. Epub 2013 Aug 15. Review. PubMed PMID: 23954554.&lt;/p&gt;&#xA;&lt;p&gt;3: Sakai K, Akiyama M, Sugiyama-Nakagiri Y, McMillan JR, Sawamura D,&#xA;Shimizu H. &lt;strong&gt;Localization of ABCA12 from Golgi apparatus to lamellar&#xA;granules in human upper epidermal keratinocytes.&lt;/strong&gt; Exp Dermatol. 2007&#xA;Nov;16(11):920-6. PubMed PMID:&#xA;17927575.&lt;/p&gt;&#xA;&lt;p&gt;4: Lee WS, Oh TH, Chun SH, Jeon SY, Lee EY, Lee S, Park WS, Hwang S.&#xA;&lt;strong&gt;Integral lipid in human hair follicle.&lt;/strong&gt; J Investig Dermatol Symp Proc.&#xA;2005 Dec;10(3):234-7. PubMed PMID: 16382672.&lt;/p&gt;&#xA;&lt;p&gt;5: Kelsell DP, Norgett EE, Unsworth H, Teh MT, Cullup T, Mein CA,&#xA;Dopping-Hepenstal PJ, Dale BA, Tadini G, Fleckman P, Stephens KG,&#xA;Sybert VP, Mallory SB, North BV, Witt DR, Sprecher E, Taylor AE,&#xA;Ilchyshyn A, Kennedy CT, Goodyear H, Moss C, Paige D, Harper JI, Young&#xA;BD, Leigh IM, Eady RA, O'Toole EA.  &lt;strong&gt;Mutations in ABCA12 underlie the&#xA;severe congenital skin disease harlequin ichthyosis.&lt;/strong&gt; Am J Hum Genet.&#xA;2005 May;76(5):794-803. Epub 2005 Mar 8. PubMed PMID: 15756637; PubMed&#xA;Central PMCID: PMC1199369.&lt;/p&gt;&#xA;&lt;p&gt;6: Ishida-Yamamoto A, Deraison C, Bonnart C, Bitoun E, Robinson R,&#xA;O'Brien TJ, Wakamatsu K, Ohtsubo S, Takahashi H, Hashimoto Y,&#xA;Dopping-Hepenstal PJ, McGrath JA, Iizuka H, Richard G, Hovnanian A.&#xA;&lt;strong&gt;LEKTI is localized in lamellar granules, separated from KLK5 and KLK7,&#xA;and is secreted in the extracellular spaces of the  superficial&#xA;stratum granulosum.&lt;/strong&gt; J Invest Dermatol. 2005 Feb;124(2):360-6. PubMed&#xA;PMID: 15675955.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;According to the last mentioned paper[6]:&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;LG(Lameller granule) constitute a specialized secretory system within the epidermis.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;LG are seen as isolated oval-shaped granules in post-embedding methods, whereas they appear as parts of beaded tubular structures in cryo-ultramicrotomy&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Result highlights the biological significance of LG in regulation of protease activities.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;LEKTI labels were aggregated and not evenly distributed throughout the LG system, indicating the heterogeneous nature of the LG  (Ishida-Yamamoto et al, 2004).&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Biologically active fragments derived from LEKTI are released extracellularly (Bitoun et al, 2003).&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;LEKTI labels were seen in the extracellular spaces in the superficial granular layers and the first cornified layer with release from the apical side of upper granular cells. Aggregates of LEKTI immunolabels were also closely associated with the TGN46-positive trans-Golgi network .&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Double labeling with antibodies to glucosylceramide, a well-known LG molecule, showed that each occupies a distinct domain of beaded tubular structure&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The ultrastructural localization of LEKTI was compared with that of KLK7. As reported previously (Sondell et al, 1995; Ishida-Yamamoto et al, 2004), KLK7 was localized in the LG system but was not co-localized with LEKTI within keratinocytes.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;This finding suggests that LEKTI is expressed and released earlier than its target proteases, which is consistent with a role in preventing premature proteolysis of extracellular matrix proteins or cell surface adhesion molecules, and in controlling the timing of desquamation.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;&lt;strong&gt;Source:&lt;/strong&gt; [6]. &lt;a href=&quot;http://www.nature.com/jid/journal/v124/n2/fig_tab/5602696f4.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.nature.com/jid/journal/v124/n2/fig_tab/5602696f4.html&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/ImJNv.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/ImJNv.gif&quot; alt=&quot;&quot; /&gt;&lt;/a&gt;&lt;br /&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://www.nature.com/jid/journal/v124/n2/images/5602696f4.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;nature.com&lt;/a&gt;)&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Caption:&lt;/strong&gt; Lympho-epithelial Kazal-type-related inhibitor (LEKTI) is&#xA;transported through the lamellar granule (LG) system. Post-embedding&#xA;immunoelectron microscopy using Lowicryl HM20 resin (A, D) and a&#xA;cryo-ultramicrotomy method (B, C, E). (A, B) LEKTI signals (black&#xA;arrows) are detected in the LG using polyclonal antibodies against&#xA;D8–D11 in (A) and D1–D6 in (B). Note that LG are seen as isolated&#xA;granules in the post-embedding method (A), but appear as beaded&#xA;tubular structures in the cryo-ultramicrotomy (B). Lamellar internal&#xA;structures are seen in both methods (white arrows). (C) LEKTI is&#xA;secreted from the apical side of upper granular cells (arrows). d,&#xA;desmosomes. Polyclonal antibody to D8–D11 and desmoglein 1 monoclonal&#xA;antibody were used and were labeled with 5 and 10 nm immunogold,&#xA;respectively. (D) LEKTI antibody to D8–D11 labels are closely&#xA;associated with those of the TGN46-positive trans-Golgi network. (E)&#xA;LEKTI (monoclonal antibody, 5 nm gold labels) and glucosylceramides&#xA;(GlcCer, 10 nm gold labels) are localized within the same continuous&#xA;beaded tubular structure of the LG system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-02-28T21:12:34.463" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="19753" PostTypeId="1" CreationDate="2014-07-18T05:29:22.223" Score="2" ViewCount="15115" Body="&lt;p&gt;Sometimes, when I bend over, areas of my skin like my back can suddenly itch quite intensely. Sometimes it may be another part of my body and the pattern seems to be a part of the skin organ that is not used to stretching quite that much in that spot, perhaps the skin not being so flexible there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realise that temperature, dryness, and a whole lot of other external and internal factors can come into play, but if my scenario is not too broad, and I'm pretty sure it's a universal trait in skin physiology, (and I don't have any skin allergies either), what is the basic science behind this phenomenon of skin stretching when it's not used to it, and you do it very suddenly?&lt;/p&gt;&#xA;" OwnerDisplayName="user3362" LastActivityDate="2014-07-18T05:29:22.223" Title="Why does skin sometimes suddenly itch when you stretch it?" Tags="&lt;physiology&gt;&lt;skin&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2014-08-08T04:59:42.843" ContentLicense="CC BY-SA 3.0" />
  <row Id="19754" PostTypeId="2" ParentId="19691" CreationDate="2014-07-18T08:16:51.973" Score="2" Body="&lt;p&gt;Though I totally agree with your views towards nanotechnology, There is always two sides of a coin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to this article &lt;a href=&quot;http://ethics.calpoly.edu/nanoethics/bad.html&quot; rel=&quot;nofollow&quot;&gt;THE BAD (of Nanotechnology)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Health:&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Nanoparticles have been shown to be absorbed in the livers of research&#xA;  animals and even cause brain damage in fish exposed to them after just&#xA;  48 hours.   If they can be taken up by cells, then they can enter our&#xA;  food chain through bacteria and pose a health threat like mercury in&#xA;  fish, pesticides in vegetables or hormones in meat.  The&#xA;  increasingly-popular carbon nanotube (20x stronger and lighter than&#xA;  steel) looks very much like an asbestos fiber – what happens if they&#xA;  get released into the air?  Being carbon-based, they wouldn’t set off&#xA;  the usual alarms in our bodies, making them difficult to detect.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Environmental:&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;If nanomaterials really are as strong as diamonds, how decomposable or&#xA;  persistent are they?  Will they litter our environment further or&#xA;  present another disposal problem like nuclear waste or space litter? &#xA;  In the distant future, will self-replicating nanobots – necessary to&#xA;  create the trillions of nanoassemblers needed to build any kind of&#xA;  product – run amok, spreading as quickly as a virus, in the infamous&#xA;  “&lt;strong&gt;gray goo&lt;/strong&gt;” scenario?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not only that Each country have a different point of view on the topic of nanotechnology in Health(or nano-medicine).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Regulation_of_nanotechnology&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Government Response on Nanotechnology:&lt;/strong&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;United Kingdom&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;In its seminal 2004 report &lt;strong&gt;Nanoscience and Nanotechnologies: Opportunities and Uncertainties, the United Kingdom's Royal Society&lt;/strong&gt; concluded that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many nanotechnologies pose no new risks to health and almost all the&#xA;  concerns relate to the potential impacts of deliberately manufactured&#xA;  nanoparticles and nanotubes that are free rather than fixed to or&#xA;  within a material. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They want to change the existing regulation to be modified on a precautionary basis because they expect that the toxicity of chemicals in the form of free nanoparticles cannot be predicted from their toxicity in a larger form.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;United States&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Rather than adopt a new nano-specific regulatory framework, FDA convenes an 'interest group' each quarter with representatives of FDA centers that have responsibility for assessment and regulation of different substances and products. This interest group ensures coordination and communication. A September 2009 FDA document called for identifying sources of nanomaterials, how they move in the environment, the problems they might cause for people, animals and plants, and how these problems could be avoided or mitigated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Berkeley, CA is currently the only city in the United States to regulate nanotechnology, which is still being opposed.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;European Union&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The European Union has formed a group to study the implications of nanotechnology called the Scientific Committee on Emerging and Newly Identified Health Risks which has published a list of risks associated with nanoparticles.&#xA;Consequently, manufacturers and importers of carbon products, including carbon nano-tubes will have to submit full health and safety data within a year or so in order to comply with REACH.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;According to REACH(from Page 22, 4.2 Pharmaceutical regulation, &lt;a href=&quot;http://www2.er.dtu.dk/publications/fulltext/2009/ENV2009-069.pdf&quot; rel=&quot;nofollow&quot;&gt;PhD Thesis of Steffen Foss Hansen, DTU&lt;/a&gt;):&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The application of engineered nanoparticles for medical use offers immense benefits &#xA;within areas like diagnosis, targeted drug delivery, and drug development and have been &#xA;marketed for more than 17 years (NanoRoad SME 2006, EGE 2007, Gaspar 2007).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well-described and understood medicinal products containing nanoparticles in the form &#xA;of liposomes, polymer protein conjugates, polymeric substances or suspensions have &#xA;been given Marketing Authorizations within the EU under the existing regulatory &#xA;framework e.g. Regulation 726/2004 on authorization and supervision of medicinal &#xA;products for human and veterinary use, Directive 2001/83/EC on medicinal products for &#xA;human use, Directive 93/42/EEC concerning medical devices, Directive 90/385/EEC &#xA;relating to active implantable medical devices, and Directive 98/79/EC on in vitro &#xA;diagnostic medical devices (EP &amp;amp; CEU 2004, Council of the European Communities &#xA;1990, 1993, 1998, 2001). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no specific mentioning of nanomedicine in the EU legislation on medicinal &#xA;products and devices, tissue engineering and other advanced therapies. None of these &#xA;regulations or directives was written with nanomedicinal applications in mind and &#xA;although their scope covers nanomedicine they have been accused for being general and &#xA;non-specific and fraught with concerns and difficulties when it comes to dealing with &#xA;drugs more complex than traditional ones (Editorial 2007, D'Silva and Van Calster &#xA;2008). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The use of nanoparticles in nanomedicine has not been subject to much regulatory &#xA;scrutiny since existing laws and regulatory instruments are believed also to cover &#xA;medical products based on nanotechnology. The extensive testing requirements prior to &#xA;marketing of medicine may also contribute to the notion that the potentially negative &#xA;effects will be discovered prior to marketing, that patients are adequately informed &#xA;about negative side-effects, and that benefits outweigh the risks or the adverse effects, &#xA;should such be found to occur (EGE 2007, N&amp;amp;ET Working Group 2007) . &lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-07-28T09:45:22.457" LastActivityDate="2014-07-28T09:45:22.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19755" PostTypeId="1" AcceptedAnswerId="19756" CreationDate="2014-07-18T08:35:30.757" Score="6" ViewCount="201" Body="&lt;p&gt;I was reading a paper, &lt;a href=&quot;http://www.pnas.org/content/109/8/E471.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.pnas.org/content/109/8/E471.short&lt;/a&gt;, where the authors claim that (e475)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Translation of the TfR (Transferrin Receptor) is regulated through sequences in the 3′ and 5′&#xA;  UTRs (untranslated regions) of its mRNA. To study the regulation of TfR levels independently&#xA;  of translational control, we measured the levels of TfR-EGFP expressed&#xA;  from a plasmid lacking the regulatory sequences present in the&#xA;  endogenous TfR mRNA (Fig. 6A).&#xA;  Endogenous and GFP-tagged expressed TfR levels were reduced equally in&#xA;  response to Rabenosyn-5 depletion, &lt;strong&gt;ruling out an effect of this&#xA;  protein on transcriptional or translational control of TfR expression&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I believe I understand that the effect can not be post-translational, since TfR-GFP has no region for translational regulation and so it cannot be regulated by any translationally active regulating factor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: Wouldn't the statement above, that Rabenosyn-5 has no effect on protein transcription, require a proof that mRNA levels are not affected by this protein?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8sAph.png&quot; alt=&quot;http://www.pnas.org/content/109/8/E471.figures-only&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fig. 6A, &lt;a href=&quot;http://www.pnas.org/content/109/8/E471.figures-only&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.pnas.org/content/109/8/E471.figures-only&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4971" LastActivityDate="2014-07-18T09:39:46.067" Title="How can I tell if regulation is at the transcriptional or translational level?" Tags="&lt;transcription&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19756" PostTypeId="2" ParentId="19755" CreationDate="2014-07-18T09:39:46.067" Score="6" Body="&lt;p&gt;From the Methods section:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Human TfR in plasmid cDNA was a gift from Tim McGraw (Weill-Cornell&#xA;  Medical College, New York, NY). Human TfR cDNA was subcloned in frame&#xA;  with EGFP in the Clontech pEGFP-N1 vector at the XhoI and BamHI&#xA;  restriction sites.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This TfR-GFP fusion protein does not have the endogenous TfR promoter. So it is not likely to be regulated by any TF that would directly regulate TfR transcription. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So they conclude that Rabenosyn-5 does not &lt;strong&gt;specifically&lt;/strong&gt; regulate TfR expression.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-07-18T09:39:46.067" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19758" PostTypeId="1" CreationDate="2014-07-18T14:36:35.670" Score="6" ViewCount="203" Body="&lt;p&gt;I have heard that fasting causes regeneration of memory cells(B- and T-lymphocytes) thereby improving immunity.Is this true? If yes, how?&lt;/p&gt;&#xA;" OwnerUserId="3881" LastActivityDate="2018-11-24T05:59:08.767" Title="Does fasting improves immunity?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19759" PostTypeId="2" ParentId="19758" CreationDate="2014-07-18T15:11:53.790" Score="8" Body="&lt;p&gt;Interestingly this effect seems to be true - there is one paper which claims that fasting for three days leads to the depletion of unused (and especially damaged) immune cells to save energy. When food is back at normal rates, the body starts to renew these cells which have been depleted before. This process also seems to enhance the self-renewal process of stem cells which start to replicate and further differentiate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This works like in the figure below (from the paper below):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yxR7H.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although this renews a part of the immune cells, I wouldn't say that this improves the immune system. I think that here mostly naive cells (which haven't) come in contact with an antigen are shut off. If you deplete memory cells (which had this contact) this would be counterproductive, since these cells are important for a fast immune response.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24905167&quot; rel=&quot;noreferrer&quot;&gt;Prolonged Fasting Reduces IGF-1/PKA to Promote&#xA;Hematopoietic-Stem-Cell-Based Regeneration and Reverse&#xA;Immunosuppression&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There is as well an article in Science Daily, which summarizes the original paper. It can be found &lt;a href=&quot;http://www.sciencedaily.com/releases/2014/06/140605141507.htm&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-07-18T15:39:06.370" LastActivityDate="2014-07-18T15:39:06.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19760" PostTypeId="1" AcceptedAnswerId="19769" CreationDate="2014-07-18T15:30:24.423" Score="2" ViewCount="792" Body="&lt;p&gt;The problem I've always had with evolution is the actual lack of variation between animals. More specifically, the lack of observable gradual change between species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take for example the hammerhead shark. It obviously has a strong connection with a normal shark, but where's the &quot;half-hammerhead&quot; shark? Where's the species that only has a SLIGHTLY wider head?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I really doubt that a single mutation on a normal shark resulted in a head shaped like that, it had to happen gradually. Right? As far as I understand, evolution works by random mutation in a child being somehow slightly beneficial to that animal so it get's to live longer and reproduce more, eventually resulting in it's genetic material in dominating the inferior ones before it. But if it was for whatever reason beneficial to have a slightly wider head, why don't all the sharks have slightly wider heads now? On the other hand, if it wasn't beneficial, how come the hammerhead still exists?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, I feel like some characteristics of a certain animal can't really have gradual benefits. There's a lizard that shoots blood out of it's eyes. The original ancestor certainly didn't, and I'm sure that if it's child only bled slightly from it's eyes it wouldn't really help if much in life. So for it to actually become beneficial, it seems to me that there had to be a ton of lizards that had a disadvantage of bleeding slightly. In fact, there had to be so many that they evolved even further in the same direction and kept doing that until they bled so much it's an actual benefit (sorry for this turning so gross). So why did the inbetweeners survive long enough to evolve even more, and why did they THEN die out?&lt;/p&gt;&#xA;" OwnerUserId="6340" LastActivityDate="2018-06-30T12:26:53.173" Title="Where are the evolutionary &quot;inbetweeners&quot;?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="3" CommentCount="8" ClosedDate="2014-07-18T20:12:03.567" ContentLicense="CC BY-SA 3.0" />
  <row Id="19761" PostTypeId="2" ParentId="19760" CreationDate="2014-07-18T16:38:58.360" Score="4" Body="&lt;p&gt;This sounds like a very basic question in evolutionary biology that often ask for a very long answer. But I think that you may get the answer you're looking for just if we ask you back how many inbetweeners would you expect to exist between the hammerhead shark and whatever is the closest currently living species of the hammerhead shark? If you had one more inbetweener would you still be surprised to not have more inbetweeners?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question might actually be &quot;Why are there species rather than individuals that show a long continuum of various traits?&quot;. If this is your question, then the answer would indeed need to be fairly long and explain about the process of speciation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might want to have a look at &lt;a href=&quot;https://biology.stackexchange.com/questions/48291/why-arent-there-any-transitional-animals-today&quot;&gt;this related post&lt;/a&gt; as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Studying a bit further the question of the hammerhead sharks, I discovered that there are actually 10 species of hammerhead sharks! You can find them &lt;a href=&quot;http://fr.wikipedia.org/wiki/Sphyrnidae&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; on the french wikipedia page&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let us know whether this comment/answer helped.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2017-01-30T17:19:08.533" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="19762" PostTypeId="1" AcceptedAnswerId="19764" CreationDate="2014-07-18T17:23:51.450" Score="32" ViewCount="4340" Body="&lt;p&gt;As I understand it, various animal traits have to evolve gradually, but what happens to the species that are &quot;neither here nor there&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To put it differently, if a species evolved from another, it did so because it's somehow better, right? So why are there examples of the original species not being extinct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What factors determine weather some species &quot;stick&quot;?&lt;/p&gt;&#xA;" OwnerUserId="6340" LastActivityDate="2019-04-02T01:18:53.357" Title="Why are there species instead of a continuum of various animals?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="6" CommentCount="7" FavoriteCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="19763" PostTypeId="2" ParentId="19762" CreationDate="2014-07-18T17:54:24.477" Score="10" Body="&lt;p&gt;Typically when both new and old species still exist it is because evolution pushed the new one into a different habitat or role.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a hypothetical example reef fish vs. deep water fish and their relative size.  Let's say deep water fish evolved into reef fish, but we still have deep water fish.  So there were deep water fish that were a little smaller than the rest of the deep water fish, and this gave them access to a new place to hide from sharks, shallow waters near reefs.  As time goes on this puts evolutionary pressure on the fish to shrink so as to better hide in the reef, those &quot;neither here nor there&quot; fish may have gotten some benefit from being near the reef but the smaller fish got even more benefit and eventually outcompeted the middle species.  Vice versa for the deep water fish vs this middle species. It was not as good in deep water so it was outcompeted there as well.  This continues until evolution has separated them into two new species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;edit:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What factors determine whether some species &quot;stick&quot;?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Evolution optimizes for the current environment, as long as that environment is stable and the species is a good fit for it then there is little pressure to change. If the environment changes then a species will adapt to it. Here environment is everything relevant to the species: predators, food availability, weather, everything that impacts their life.&lt;/p&gt;&#xA;" OwnerUserId="8360" LastEditorUserId="43480" LastEditDate="2019-03-27T23:28:01.143" LastActivityDate="2019-03-27T23:28:01.143" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="19764" PostTypeId="2" ParentId="19762" CreationDate="2014-07-18T17:59:22.473" Score="19" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why are there species rather than a long continuum?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Three important reasons I could think of are sex, non-uniform adaptive landscape and ancestry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure I'll answer your question so let me know if I miss your point or if I help!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;To start with, you might want to read &lt;a href=&quot;https://biology.stackexchange.com/questions/39664/how-could-humans-have-interbred-with-neanderthals-if-were-a-different-species/39669#39669&quot;&gt;this answer&lt;/a&gt; on the semantic difficulties behind the concept of species&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What factors determine whether some species &quot;stick&quot;?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Natural selection is nothing but differential fitness (fitness is a measure of both reproductive success and survival) among genotypes within a population. Individuals having greater fitness will leave more offsprings and therefore the genes of these individuals increase in frequency in the population. There are few generalities to be made about what &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenotype&quot; rel=&quot;nofollow noreferrer&quot;&gt;phenotypic&lt;/a&gt; traits are beneficial in a given population. For example, &quot;white fur&quot; is a very good trait for a polar bear but would highly deleterious for a mealworm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there is a thing called &lt;a href=&quot;https://biology.stackexchange.com/questions/10970/empirical-evidence-for-species-selection&quot;&gt;species selection&lt;/a&gt; wherein a given lineage at least, it is possible to identify specific traits that seem to either reduce the extinction rate or increase the speciation rate. This is, for example, the case for polyploidy in angiosperms (&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.genet.34.1.401&quot; rel=&quot;nofollow noreferrer&quot;&gt;Whitton and Otto, 2000&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;if a species evolved from another, it did so because it's somehow better, right?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you observe different extant species you cannot say that any of these species evolve from any other one you can today observe. The correct way of looking at two species is that they share a common ancestor in a given past. Therefore, looking at a cat and a &lt;a href=&quot;http://en.wikipedia.org/wiki/Eurasian_blue_tit&quot; rel=&quot;nofollow noreferrer&quot;&gt;blue tit&lt;/a&gt; you cannot say that one species evolved from the other one but you can only say that these two species share a common ancestor (just like any other pair of species) that was neither a cat nor a blue tit. The example is obvious because cats and blue tits are &quot;not so closely related&quot; (everything is relative) but the same logic holds for any pair of species.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why are there species rather than a long continuum?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sex&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The simplest and most obvious reason why there are species within which individuals are more similar compared to each than to individuals from other species is due to the definition (the most common definition because different definitions exist!) itself of a species. &lt;strong&gt;A species is a group of individuals that can interbreed&lt;/strong&gt;. See &lt;a href=&quot;https://biology.stackexchange.com/questions/39664/how-could-humans-have-interbred-with-neanderthals-if-were-a-different-species/39669#39669&quot;&gt;this&lt;/a&gt; for more info on the concept of species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take two originally different groups of individuals and allow them to interbreed. Their traits will mix up and you won't be able to tell two different groups apart. All individuals within the new mixed group are a mixture of the individuals from the two previous groups (under some circumstances this process has been sometimes called &quot;reverse speciation&quot;). If now you take one single group of individuals. You split them into two groups in the sense that you don't allow individuals from group 1 to mate with individuals from group 2. You will see that after some evolutionary time, the individuals of group 1 will tend to resemble much more to individuals of group 1 (its own group) than to individuals of group 2. If you wait long enough so that these two groups of individuals become different enough so that they can't interbreed any more because they diverged too much, then you have what is called a reproductive isolation and under the common definition of species, you can say that a &lt;a href=&quot;http://en.wikipedia.org/wiki/Speciation&quot; rel=&quot;nofollow noreferrer&quot;&gt;speciation&lt;/a&gt; (You may want to have a look to the wiki article for &quot;speciation&quot;) occurred and therefore you have two new species instead of one ancestral species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;why the two groups tend to diverge through times?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may wonder &quot;But why the two groups tend to diverge through times?&quot;. There are several processes that explain that divergence:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mutations&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Different mutations occur in the different groups (just by chance)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Natural selection&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The environment differs and the selection pressures differ selecting for different traits in the two species. Also, the accumulation of different mutations affects the selection pressure at other loci.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Genetic drift&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Shortly speaking genetic drift is due to random events. Different random events occur between the two populations. For more info about genetic drift, see &lt;a href=&quot;https://biology.stackexchange.com/questions/14543/why-is-the-strength-of-genetic-drift-inversely-proportional-to-the-population-si&quot;&gt;this post&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you are not very familiar with these concepts I recommend that you have a look at &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/home.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;Understanding Evolution (UC Berkeley)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Adaptive landscape&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note also that there are other reasons for explaining this pattern. One other reason is &quot;Because the adaptive landscape is not a flat function&quot;. What this means to the layman is that there are some combinations of traits that cannot really be beneficial.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Ancestry&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, individual phenotypes are not independent of each other and not only for ecological reasons but also because of shared ancestry. If you consider two families, you will easily accept no to see a continuum of phenotypes but two distinct groups (maybe in one family curly hair is common while in the other they all have straight hair).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="43480" LastEditDate="2019-03-27T23:29:50.717" LastActivityDate="2019-03-27T23:29:50.717" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="19765" PostTypeId="2" ParentId="19762" CreationDate="2014-07-18T18:00:08.213" Score="12" Body="&lt;p&gt;Nothing happens to them. Organisms exist.  They breed with other organisms who are genetically compatible.  We humans might try to categorize them according to certain traits, but our labels are just labels, biology isn't governed by them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Over time, we might see that a population used to have one trait, and its descendants no longer have it, they look different. Nothing earth shattering happened, no bright line was crossed, there was just a change in allele frequencies.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;if a species evolved from another, it did so because it's somehow&#xA;  better, right?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No.  This is just plain wrong on your part.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's just different.  Maybe it changed so that its traits better match the current environment, or maybe the change was random drift.  You can't easily categorize one species as &quot;better&quot; than another.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-07-18T18:00:08.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19766" PostTypeId="1" AcceptedAnswerId="19771" CreationDate="2014-07-18T18:01:56.593" Score="7" ViewCount="12750" Body="&lt;p&gt;Every tegmina of a cockroach has sclerites which are analogous to the bones of humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Every abdominal segment of cockroach consists of two lateral sclerite plates called pleura along with a dorsal terga and a ventral sterna. But what will be the case with the last body segment where 10th sternum is absent?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I mean will, there be any pleuron in the tenth segment because, following our textbook, pleura serve for articulation among sterna and terga and also spiracles are present in the first eight abdominal segments but the 10th sternum is absent in &lt;em&gt;Periplaneta americana&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually there is no evidence of the presence of any pleurons in the last segment in our text book.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, there are no abdominal spiracles in the 9th and 10th segments so there is no particular reason to say that pleura are present in the 9th and 10th segments as well. &lt;/p&gt;&#xA;" OwnerUserId="8101" LastEditorUserId="22956" LastEditDate="2017-05-23T09:49:48.507" LastActivityDate="2019-02-24T06:53:28.620" Title="How many abdominal sclerites would be there in a cockroach?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19767" PostTypeId="1" AcceptedAnswerId="31304" CreationDate="2014-07-18T19:05:10.337" Score="21" ViewCount="15162" Body="&lt;p&gt;With supercomputers doing calculation in petaflops ($10^{15}$ Calculations per Second), have we crossed the speed of Human Brain?&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2019-01-10T10:30:37.537" Title="Supercomputer Vs Human Brain" Tags="&lt;human-biology&gt;&lt;brain&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="19768" PostTypeId="2" ParentId="19767" CreationDate="2014-07-18T19:05:10.337" Score="21" Body="&lt;p&gt;I will just show the statistics of last attempt to mimic the brain process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In 2011 fastest computer in Japan was launched: &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;&lt;strong&gt;K computer OR SPARC64 VIIIfx 2.0GHz&lt;/strong&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Features:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Manufacturer:&lt;/strong&gt;    Fujitsu&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Cores:&lt;/strong&gt;   705,024&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Linpack Performance (Rmax)&lt;/strong&gt;   10,510 TFlop/s&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Theoretical Peak (Rpeak)&lt;/strong&gt; 11,280.4 TFlop/s&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Power:&lt;/strong&gt;   12,659.89 kW&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Memory:&lt;/strong&gt;  1,410,048 GB (16GB RAM per CPU)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Processor:&lt;/strong&gt;   SPARC64 VIIIfx 8C 2GHz (88,128 CPUs, 8-core each)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Operating System:&lt;/strong&gt;    Linux&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It's currently world's &lt;strong&gt;4th fastest supercomputer&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.top500.org/lists/2014/06/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Top 500 Supercoputers&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8zyjw.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image Source: &lt;a href=&quot;http://wondergressive.com/wp-content/uploads/2014/01/WG-k-computer.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://wondergressive.com/wp-content/uploads/2014/01/WG-k-computer.jpg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;h2&gt;An 83,000-Processor Supercomputer Can Only Match 1% of Your Brain&lt;/h2&gt;&#xA;  &#xA;  &lt;p&gt;...The most accurate simulation of the human brain to date has been&#xA;  carried out in a Japanese supercomputer, with a single second’s worth&#xA;  of activity from just one per cent of the complex organ taking one of&#xA;  the world’s most powerful supercomputers 40 minutes to calculate.&#xA;  Researchers used the K computer in Japan, currently the fourth most&#xA;  powerful in the world, to simulate human brain activity. &lt;strong&gt;The computer&#xA;  has 705,024 processor cores and 1.4 million GB of RAM, but still took&#xA;  40 minutes to crunch the data for just one second of brain activity&lt;/strong&gt;...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Source: &lt;a href=&quot;http://gizmodo.com/an-83-000-processor-supercomputer-only-matched-one-perc-1045026757&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://gizmodo.com/an-83-000-processor-supercomputer-only-matched-one-perc-1045026757&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;h2&gt;Human Brain:&lt;/h2&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;h2&gt;Do we have brain to spare?&lt;/h2&gt;&#xA;  &#xA;  &lt;p&gt;by David A. Drachman, MD&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Within the liter and a half of human brain, stereologic studies&#xA;  estimate that there are approximately &lt;strong&gt;20 billion neocortical neurons,&#xA;  with an average of 7,000 synaptic connections each&lt;/strong&gt;.1 The cerebral&#xA;  cortex has &lt;strong&gt;about 0.15 quadrillion synapses—or about a trillion&#xA;  synapses per cubic centimeter of cortex&lt;/strong&gt;. The white matter of the brain&#xA;  contains approximately &lt;strong&gt;150,000 to 180,000 km of myelinated nerve&#xA;  fibers at age 20&lt;/strong&gt;, connecting all these neuronal elements. Despite the&#xA;  monumental number of components in the brain, Szentagothai estimated&#xA;  that &lt;strong&gt;each neuron is able to contact any other neuron with no more than&#xA;  six interneuronal connections—“six degrees of separation.”&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZfGhY.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image Source: &lt;a href=&quot;http://www.nature.com/polopoly_fs/7.2933.1329907514!/image/far-to-go.jpg_gen/derivatives/fullsize/far-to-go.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.nature.com/polopoly_fs/7.2933.1329907514!/image/far-to-go.jpg_gen/derivatives/fullsize/far-to-go.jpg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Why Brain beats Supercomputer?&lt;/h2&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why is it so hard for computers to reproduce what your grey matter&#xA;  does as a matter of course? &lt;strong&gt;Volume&lt;/strong&gt;. The human brain consists of about&#xA;  200 billion nerve cells (neurons) that are linked together by&#xA;  trillions of connections called synapses. As the tiny electrical&#xA;  impulses shoot across each neuron, they have to travel through these&#xA;  synapses, each of which contains about 1000 different switches that&#xA;  route that electrical impulse. In total, one &lt;strong&gt;human brain could contain&#xA;  hundreds of trillions of these neural pathways&lt;/strong&gt;. It's like a Choose&#xA;  Your Own Adventure book that stretches from here to Jupiter.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-01-10T10:30:37.537" LastActivityDate="2019-01-10T10:30:37.537" CommentCount="7" ContentLicense="CC BY-SA 4.0" />
  <row Id="19769" PostTypeId="2" ParentId="19760" CreationDate="2014-07-18T19:05:41.977" Score="12" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;More specifically, the lack of observable gradual change between species.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Most significant phenotype differences occur over several thousand generations, which means several thousand years on up. While we certainly can create experiments where a &lt;a href=&quot;http://en.wikipedia.org/wiki/Blue_white_screen&quot; rel=&quot;nofollow noreferrer&quot;&gt;controlled form of evolution occurs within a very small time-frame&lt;/a&gt;, I'm going to assume that you're not interested in closed laboratory experiments given the nature of your question.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It obviously has a strong connection with a normal shark, but where's the &quot;half-hammerhead&quot; shark? Where's the species that only has a SLIGHTLY wider head?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The data below does answer you question, but in reverse. Hammerheads are much older than most of their relatives; so their cousins have actually grown smaller heads... but there are certainly intermediates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From Andrew Martin (1993 - mtDNA data) via Elasmo-research.org:&lt;br&gt;&#xA;*The circles represent the head-width vs. body-length ratio.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YZDwz.gif&quot; alt=&quot;Hammerhead taxa&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Martin's conclusion: &quot;...the hammer appeared rather suddenly and fully formed, and was later optimized along different lines to suit various selection pressures.&quot;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I really doubt that a single mutation on a normal shark resulted in a head shaped like that, it had to happen gradually. Right?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not necessarily. Single Nucleotide Polymorphisms (a.k.a. - &quot;SNPs&quot; - a change in one nucleotide) can have pretty wide-ranging effects. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The vast majority of humans, for instance, are lactose intolerant in adulthood. However, lactose tolerance &lt;a href=&quot;http://ghr.nlm.nih.gov/condition/lactose-intolerance&quot; rel=&quot;nofollow noreferrer&quot;&gt;evolved twice from two different SNPs&lt;/a&gt; in two different human populations: One European and one African. One gene. One regulatory mechanism change. Massive benefits (essentially opening up a whole new resource in adulthood).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Significant differences in phenotypes (the physical appearance of something) can require more gene mutations, or not. It depends on where the mutation is in the genome and what the gene does.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But if it was for whatever reason beneficial to have a slightly wider head, why don't all the sharks have slightly wider heads now?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The simple answer is because either there wasn't enough selective pressure that the rest of the shark phenotypes succumbed to that the hammerhead avoided, or that the hammerhead design doesn't give enough of an advantage to completely dominate the gene pool. An alternate, but more abstract answer, is that there simply hasn't been enough time for the hammerhead design to dominate the shark phenotype. Remember, evolution works by generations - not years. It would take unknown thousands of generations for a weakly-advantageous design to dominate an entire niche - if it ever would.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, it is worth it to point out that evolution doesn't &lt;em&gt;only&lt;/em&gt; select for advantageous mutations. Mutations that aren't very &lt;em&gt;detrimental&lt;/em&gt; can still exist within a population as long as the detriment doesn't prevent resource exploitation and offspring production. Think &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001775/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Huntington's Disease&lt;/a&gt; which severely restricts a person's survivability, but only after their mid-30's (in general) - plenty of time for the person to have sex and raise a kid into semi-adulthood. It is a genetic defect which sticks around &lt;em&gt;only&lt;/em&gt; because it allows humans to reproduce before it seriously affects them. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The original ancestor certainly didn't, and I'm sure that if it's child only bled slightly from it's eyes it wouldn't really help if much in life.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Maybe, maybe not. Maybe it shot something else before blood, and then a mutation caused it to shoot blood instead - but the overall effect (deterring predators) was the same so it doesn't really matter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You're correct that some traits might appear very awkward if they had evolved gradually, but the question then becomes: &lt;strong&gt;Did&lt;/strong&gt; they evolve gradually? Sometimes we simply do not know.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So why did the inbetweeners survive long enough to evolve even more, and why did they THEN die out?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Like I said above, just because a trait is detrimental doesn't necessarily mean it will be eliminated. As long as the being can survive long enough to reproduce successfully with the trait, the trait might not be eliminated for a very, very long time- if ever.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for in-betweeners dying out - it's difficult to think of it like that. You're talking bout LCAs (&quot;Last Common Ancestors&quot;) of extant (currently-living) species. While some LCAs just die out for some reason or another, it's more common that the LCA simply continued to evolve and become a genetic relative due to some sort of isolation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think of it like the in-betweeners coming to a fork in the road. Some choose right, some choose left. There isn't anybody left behind - merely two populations that are changing over time that were once one group until they don't really mate between each other anymore (or &lt;em&gt;can't&lt;/em&gt;). Heck, even Biologists have trouble deciding at what point a population is considered a different &quot;species&quot; because of discoveries in the last 50 years - so right now a firm answer like &quot;It takes 15% of the genome to change for a new species to emerge&quot; isn't possible as it doesn't really work like that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We'll get to it eventually, but for the time-being, it might be easier to say that everything currently living on Earth is an in-betweener of something else in the future. Everything in its current iteration will eventually die off, but not before something else emerges from our offspring which may or may not be significantly different from us due to however many genetic mutations our offspring have from us. It could be one that opens up a whole new realm of possibilities (like lactose tolerance) or an accumulation due to selective pressures (like Phoemelanin production and pale skin in humans [Redheads] to produce more Vitamin D3 at higher latitudes).&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2018-06-30T12:26:53.173" LastActivityDate="2018-06-30T12:26:53.173" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19770" PostTypeId="2" ParentId="19762" CreationDate="2014-07-18T19:07:49.787" Score="28" Body="&lt;p&gt;Mathematician/computer programmer's answer here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There &lt;em&gt;is&lt;/em&gt; a continuum of different animals — in fact it's pretty fair to say that every animal occupies a different place on this continuum. They're just not &lt;em&gt;uniformly distributed&lt;/em&gt; over the continuum; they're clustered around forms that are most likely to survive and reproduce, and the lowest-energy paths between them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is because evolution is basically a &lt;a href=&quot;http://en.wikipedia.org/wiki/Stochastic_optimization&quot;&gt;stochastic optimization&lt;/a&gt; algorithm, one that finds the &quot;best&quot; set of parameters for maximizing some function by randomly perturbing an initial set of input values. In fact, some of the best optimization algorithms today are based on ideas drawn directly from evolution and called &quot;evolutionary algorithms&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In mathematics, given enough time, these algorithms will all converge on one optimum solution and nothing else. Why isn't it like that in nature? Because in mathematics, the &quot;fitness function&quot; that we're optimizing for stays the same for a given problem for as long as the algorithm runs. It represents the specific problem we're trying to solve. In nature, there's no outside force imposing a fitness function; an organism's survival depends on millions of factors in its environment which change over time, many of which depend on the survival and properties of the &lt;em&gt;other&lt;/em&gt; organisms in its environment (competition, symbiosis, predator/prey relationships, etc.) This is a chaotic system so complex that it could easily go for billions of years without reaching a steady state, and even if it did, external changes (like the odd asteroid impact, to use an extreme example) would still come around to shake things up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another reason for the clustering is because a lot of the &quot;intermediate states&quot; in the genetic space have a fitness of zero — these are the states between species that can't interbreed, or that have sterile offspring. The categorization of &quot;species&quot; is based on this, and although it's not exact, it's still generally true that the more different two creatures are, the less likely they can have viable offspring. This makes evolution more likely to explore the spaces near already-successful organisms, and less likely to produce radical new things by hybridization.&lt;/p&gt;&#xA;" OwnerUserId="8361" LastEditorUserId="8361" LastEditDate="2014-07-18T19:32:47.757" LastActivityDate="2014-07-18T19:32:47.757" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="19771" PostTypeId="2" ParentId="19766" CreationDate="2014-07-18T19:35:59.877" Score="7" Body="&lt;h2&gt;Tergal plates:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There are ten tergal plates. The &lt;span class=&quot;math-container&quot;&gt;$8^{th}$&lt;/span&gt; tergum in the male and both &lt;span class=&quot;math-container&quot;&gt;$8^{th}$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$9^{th}$&lt;/span&gt; terga in the female are not visible  as they are overlapped by the &lt;span class=&quot;math-container&quot;&gt;$7^{th}$&lt;/span&gt; tergum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The &lt;span class=&quot;math-container&quot;&gt;$10^{th}$&lt;/span&gt; tergum extends beyond the posterior end of the body and has a deep groove in the middle of its free end.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Sternal plates:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Only nine sterna are present as the &lt;span class=&quot;math-container&quot;&gt;$10^{th}$&lt;/span&gt; sternum is absent.&#xA;In the male, nine sterna are visible whereas in the female, only seven sterna are visible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In females, the &lt;span class=&quot;math-container&quot;&gt;$7^{th}$&lt;/span&gt;, &lt;span class=&quot;math-container&quot;&gt;$8^{th}$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$9^{th}$&lt;/span&gt; sterna together forma brood pouch. The brood pouch has two parts: the anterior – genital chamber or gynatrium  and the posterior – gothecal chamber.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/RvH9a.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/RvH9a.gif&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;https://lanwebs.lander.edu/faculty/rsfox/invertebrates/images/blatt52L_x550_x_442x.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;lander.edu&lt;/a&gt;)&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/uJLDh.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/uJLDh.gif&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;https://lanwebs.lander.edu/faculty/rsfox/invertebrates/images/blatt48L_x550_x_349x.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;lander.edu&lt;/a&gt;)&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://www.biologydiscussion.com/wp-content/uploads/2014/01/clip_image00415.jpg&quot; alt=&quot;&quot;&gt;&#xA;&lt;img src=&quot;https://bugguide.net/images/cache/LKPK0K2KGKA01QT0PQB0GQC0EQZSVQRSXKHSWQZSGKDK4KUK4K1KLK10KKUKHKBKAQAKMKLSMK307K6K4QD0BQLSEQ.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.slideshare.net/prof_aarif/animal-types-cockroach&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.slideshare.net/prof_aarif/animal-types-cockroach&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://learnzoology.wordpress.com/category/periplaneta-americana/page/15/&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://learnzoology.wordpress.com/category/periplaneta-americana/page/15/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://zoologybaburao.in/pdfs/7.%20Unit%20VII.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://zoologybaburao.in/pdfs/7.%20Unit%20VII.pdf&lt;/a&gt; (Best)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.eskool.com/files/subject/ppt/103_11_07_04_01.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.eskool.com/files/subject/ppt/103_11_07_04_01.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sakshieducation.com/(S(clpea355rwddux55iuci1cer))/Inter(New)/Material/IstYearEM/Zoology/07_01_ARTHROPODA_COCKROACH_UPTO_LOCOMOTION.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.sakshieducation.com/(S(clpea355rwddux55iuci1cer))/Inter(New)/Material/IstYearEM/Zoology/07_01_ARTHROPODA_COCKROACH_UPTO_LOCOMOTION.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Update:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Youtube links for Cockroach dissection:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://youtube.com/watch?v=ZwvG69ICnps&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://youtube.com/watch?v=ZwvG69ICnps&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://youtube.com/watch?v=wF7ew2w24as&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://youtube.com/watch?v=wF7ew2w24as&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-02-24T06:53:28.620" LastActivityDate="2019-02-24T06:53:28.620" CommentCount="6" CommunityOwnedDate="2014-07-21T09:55:14.843" ContentLicense="CC BY-SA 4.0" />
  <row Id="19772" PostTypeId="2" ParentId="19760" CreationDate="2014-07-18T20:00:14.900" Score="-3" Body="&lt;p&gt;If an inbetweener offers a slight advantage to survival, and if the full-fledged trait even more so, then once the full-fledged population becomes sufficiently large, they will have the advantage and the inbetweeners will die out.&lt;/p&gt;&#xA;" OwnerUserId="8364" LastActivityDate="2014-07-18T20:00:14.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19774" PostTypeId="1" CreationDate="2014-07-19T02:00:31.353" Score="3" ViewCount="302" Body="&lt;p&gt;A question that appeared on my last exam was :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Which of the following has greater entropy A) An atom B) A&#xA;  macromolecule&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The question doesn't specify anything else(i.e. type/size of atom or macromolecule). The macromolecules we learned class were proteins, sugars, nucleic acids(DNA/RNA) or lipids. What is the correct answer and why(hypothetical calculation, if possible) ?&lt;/p&gt;&#xA;" OwnerUserId="8365" LastActivityDate="2014-07-20T02:45:49.390" Title="More entropy: Atom or Macromolecule?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;proteins&gt;" AnswerCount="3" CommentCount="8" ClosedDate="2014-07-20T03:23:25.687" ContentLicense="CC BY-SA 3.0" />
  <row Id="19775" PostTypeId="2" ParentId="9265" CreationDate="2014-07-19T02:26:16.020" Score="4" Body="&lt;p&gt;Animal Milk. The ideal environment for Kefir Grains is animal milk. Varieties include cow, goat, sheep, and other similar species. Kefir Grains thrive in animal milk due to the chemical makeup of the liquid. The lactose in animal milk provides the most efficient food source for the Kefir Grains and therefore the most efficient and effective culturing process. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternative Milks. While animal-based milks are the healthiest for the Kefir Grains, alternative types of “milk” (coconut, soy, rice, nut, etc.) can also be used under certain conditions. Generally speaking, Coconut Milk, Soy Milk, and Rice Milk can be cultured using Kefir Grains as long as a revitalization period is observed (see below). While some people report success culturing Kefir Grains in seed and nut milks (e.g. hemp milk, almond milk, etc.), these varieties tend to yield more inconsistent results.&#xA;Revitalization Period. When using a non-animal variety of milk, it is important to occasionally allow the Kefir Grains to revitalize in animal milk for 24 hours. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We recommend allowing the Kefir Grains a revitalization period at least once every few weeks and ideally more often. To revitalize the Kefir Grains, simply place the Kefir Grains in 1-2 cups of animal milk for 24 hours. Once the process is complete, the Kefir Grains can be returned to use with an alternative variety of milk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This may be technically why...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;''Kefiran produced by L. kefiranofaciens is a branched, water-soluble polysaccharide, containing equal amounts of D-glucose and D-galactose. The production of this polysaccharide is stimulated when L. kefiranofaciens grows in co-culture with S. cerevisiae (Cheirsilp et al., 2003).''&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Without galactose, one of the monosaccharides present in lactose (a disaccharide glucose-galactose), the structural protein that forms the grains can not be done. When taking apart from the grain, the microorganism complex don't behave the same way and are not able to ferment the substrate properly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm just starting and I will try with honey, which have a 10% galactose. Although not vegan, could work and try with other sources of galactose like beets... (Only they have little content but may be enough for a persistent growth and avoiding decay). Unless the lactose itself is needed in the process, it should work...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&#xA;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833126/&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833126/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8366" LastEditorUserId="-1" LastEditDate="2018-03-05T11:25:58.103" LastActivityDate="2018-03-05T11:25:58.103" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19776" PostTypeId="2" ParentId="19774" CreationDate="2014-07-19T03:53:17.943" Score="2" Body="&lt;p&gt;As this &lt;a href=&quot;http://www.chem.wisc.edu/deptfiles/genchem/netorial/modules/thermodynamics/entropy/entropy06.htm&quot; rel=&quot;nofollow&quot;&gt;table&lt;/a&gt; shows, the more complex a molecule is (in general) the more entropy it has.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Entropy is an absolute quantity which is zero at $0^o K.$ When an atom or molecule has no way to rotate (is 'frozen') there is only one state in which it can exist. An atom of a gas or a molecule of a diatomic gas at $25^oC$ is also somewhat constrained compared to a complex molecule like sugar at the same temperature and pressure. The carbons and hydrogens in sugar have more possible states in which to exist. So, for example, chlorine gas, $Cl_2 (g),$ has lower entropy than propane, $C_3H_8.$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trends for $S$ for various atoms and molecules generally reflect the idea that S is determined by molecular mass and restriction of motion. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A typical calculation.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to measure the entropy of a simple molecule you assume the entropy is 0 at $0^o K$ and measure &lt;em&gt;changes&lt;/em&gt; in entropy as the molecule is heated. In practice this might mean measuring the decrease in entropy of the surroundings as a substance heats up. By measuring the changes carefully up to a standard temperature (25$^oC)$ you get a number that is characteristic for each substance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The equation used in chemistry courses is usually given as &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\Delta S  = \frac{\Delta H}{T}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In English, the change in entropy equals the change in heat (per mass or per mole), usually at some phase change, divided by the temperature in degrees Kelvin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a simple example, if liquid benzene is converted to vapor at its boiling point $80.1^o C$ and the heat of vaporization for benzene is 394 J/g then for 50 g of liquid benzene ($C_6H_6$) the entropy change is  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\Delta S = \frac{(50 g)\cdot(394 J/g)}{(80.1+273.15)^oK} = 55.7 J/^oK$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chemists have created tables that measure entropy changes for states of various molecules. With the exception of very simple molecules predictions of entropy based on structure are difficult and the tables are empirically derived.  &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-07-19T14:40:16.257" LastActivityDate="2014-07-19T14:40:16.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19778" PostTypeId="2" ParentId="19774" CreationDate="2014-07-19T08:23:31.343" Score="4" Body="&lt;p&gt;Ahh entropy. The bane of many undergraduates. You won't need a lot of mathematical rigor needed to solve for absolute entropies in most biological fields so it's best to think of it abstractly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider the atom. What can it do? Well if you remember from chemistry class, it can bounce around a process we call translate, and the electrons can basically switch spins. For the most part, if you had a single atom alone in the universe, that's all it could do. Move around and have its electrons switch states. It's best to think of these as &quot;states&quot; of the atom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's see, the atom can move in the X direction and be in spin up. It can move in the x and y direction and be spin down...etc. But the point is, there is not a whole lot the single atom all by it's lonesome can do. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, if we start adding other atoms to the mix, say across chemical bonds, then they can start to do more. If two atoms are bonded, they can stretch and contract (vibrational states), they can rotate around each other, and they can do everything the atom can do as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, there a lot more &quot;things&quot; or &quot;states&quot; that the two atoms can be defined in at any one time. They can be rotating one direction, vibrating in one way, moving in another... etc etc...even this sentence seems to be getting more chaotic! And that is really all entropy is. Adding up more and more ways for matter to get into all these possible configurations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the answer to your question is the macromolecule. It has tons of atoms and bonds. An uncountable number of ways to rotate, translate and vibrate, and be struck with photons, and emit light, and do all kinds of chaotic &quot;stuff&quot; (you can count it actually, it's just really hard). &lt;/p&gt;&#xA;" OwnerUserId="3887" LastActivityDate="2014-07-19T08:23:31.343" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19779" PostTypeId="2" ParentId="19774" CreationDate="2014-07-19T09:39:13.943" Score="4" Body="&lt;p&gt;Entropy is a measure for the number of states accessible to a system. The more states available, the higher the entropy. &lt;br/&gt;&lt;br/&gt; If you think of an atom confined in a volume V, then, without further restrictions, the atom can be anywhere inside that volume, i.e. the number of states will be a function of the volume V. The bigger the volume, the bigger the entropy. Now, if you add another atom to that volume so that the two atoms form a gas, i.e. they do not bind, then these atoms can access states individually. The number of states for the system will be the number of states of atom1 times the number of states of atom2. Thus, in a gas, the number of states, and therefore the entropy, increases with the number of atoms. &lt;br/&gt;&lt;br/&gt;What happens now, if the two atoms bind together. They now can't access states individually, so the total number of states, and thus the entropy, will be smaller than that for a gas of the same atoms. But the two atoms can still access states similar to the one atom gas, plus they can do new things like rotating around each other. So the number of states of a molecule of two atoms will be bigger than the number of states of just one atom.&lt;br/&gt;&lt;br/&gt;Thus, if you compare the entropy of a single atom to the entropy of a molecule of N atoms, the entropy of the molecule will be larger. &lt;br/&gt; If you compare the entropy of a gas of N atoms to the entropy of a molecule build from these N atoms, the entropy of the gas will be larger. &lt;/p&gt;&#xA;" OwnerUserId="8373" LastEditorUserId="8373" LastEditDate="2014-07-20T02:45:49.390" LastActivityDate="2014-07-20T02:45:49.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19781" PostTypeId="1" CreationDate="2014-07-19T12:26:49.803" Score="6" ViewCount="353" Body="&lt;p&gt;I want to design a project for EEG signal processing. In my research I found the concept of &lt;a href=&quot;http://en.wikipedia.org/wiki/Steady_state_visually_evoked_potential&quot; rel=&quot;nofollow&quot;&gt;SSVEP&lt;/a&gt;. SSVEPs represent the electrical activity of the brain as measured via EEG, and are evoked by visual stimuli with low frequency applied to the eye. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is whether it is known how the electric activity of brain will change? And a second thing, does it mean that each frequency applied to the eye has a fixed reaction for the brain?&lt;/p&gt;&#xA;" OwnerUserId="8375" LastEditorUserId="9943" LastEditDate="2015-05-22T11:39:35.893" LastActivityDate="2015-05-22T11:39:35.893" Title="How does the frequency of a visual stimulus affect the steady-state visually evoked potential?" Tags="&lt;brain&gt;&lt;vision&gt;&lt;experimental-design&gt;&lt;electrophysiology&gt;&lt;electroencephalography&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19782" PostTypeId="1" CreationDate="2014-07-19T13:36:51.143" Score="1" ViewCount="286" Body="&lt;p&gt;Often for the DNA glycosylase enzyme assay we can see that the DNA glycosylase is incubated with oligonucleotide in 37C and then reaction is stopped by addition of formamide gel loading buffer (80% formamide/1 mM EDTA, pH 8.0y0.1% bromophenol blue/0.1% xylene cyanol). How the reaction is stopped by this buffer?&lt;/p&gt;&#xA;" OwnerUserId="4593" LastActivityDate="2014-07-20T19:59:52.777" Title="Question about the DNA glycosylase enzyme assay/formamide gel loading buffer" Tags="&lt;dna-damage&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19784" PostTypeId="1" AcceptedAnswerId="19785" CreationDate="2014-07-19T16:51:29.023" Score="4" ViewCount="1963" Body="&lt;p&gt;I live in the Pacific coast of South America. Seems to have two wings, like a wasp's. The &quot;tail&quot; is a bit bulky but is only connected to the rest of the body by a thin part. It's black overall. The antennae in the photo are downwards but they just spring normally to the front...&#xA; &lt;img src=&quot;https://i.stack.imgur.com/yg0ZI.jpg&quot; alt=&quot;the bug&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8321" LastEditorUserId="8186" LastEditDate="2014-07-19T16:58:51.187" LastActivityDate="2015-08-14T18:37:30.710" Title="What is this black insect (wasp-like?) South America?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19785" PostTypeId="2" ParentId="19784" CreationDate="2014-07-19T17:42:54.573" Score="6" Body="&lt;p&gt;Actually I took photoshop to help me find this little guy, &lt;a href=&quot;http://en.wikipedia.org/wiki/Evaniidae&quot;&gt;Ensign Wasp(Evaniidae)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://6legs2many.wordpress.com/tag/parasitoid-wasps/&quot;&gt;Google Images:&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://6legs2many.files.wordpress.com/2010/08/ensign-wasp-evaniidae-parasitoid.jpg&quot; alt=&quot;&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;My Photoshop research:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ynrL3.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/irad6.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-19T17:42:54.573" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19787" PostTypeId="1" AcceptedAnswerId="19797" CreationDate="2014-07-19T19:25:19.070" Score="1" ViewCount="315" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;It’s simple deductive logic to follow that for a species to survive it must provide it’s offspring with the best possible conditions to ensure it’s survival – either that or to reproduce in such quantity that it ensures survival. The obvious application of this for women is sharing parental investment with the best possible mate her own genetics allow her to attract and who can provide long term security for her and any potential offspring. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Thus women are biologically, psychologically and sociologically the filters of their own reproduction, where as &lt;strong&gt;men’s reproductive methodology is to scatter as much of his genetic material as humanly possible to the widest available quantity of sexually available females.&lt;/strong&gt; He of course has his own criteria for mating selection and determining the best genetic pairing for his reproduction. This is evidenced in our own hormonal biology; men possess between 12 and 17 times the amount of testosterone (the primary hormone in sexual arousal) women do and women produce substantially more estrogen (instrumental in sexual caution) and oxytocin (fostering feelings of security and nurturing) than men.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From a biological point of view, is the bold sentence correct? And is the quantity of hormonal differences the only explanation of this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Link to article: &lt;a href=&quot;http://therationalmale.com/2011/08/23/schedules-of-mating/&quot; rel=&quot;nofollow&quot;&gt;http://therationalmale.com/2011/08/23/schedules-of-mating/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8378" LastEditorUserId="8378" LastEditDate="2014-07-19T19:32:00.543" LastActivityDate="2014-07-20T10:12:21.217" Title="Schedules of mating for men" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;endocrinology&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19789" PostTypeId="1" AcceptedAnswerId="19802" CreationDate="2014-07-19T22:24:35.190" Score="3" ViewCount="2066" Body="&lt;p&gt;As I understand the ravages of sunlight upon the (human) eye; the cause of ocular damage and blindness is too much energy delivered to the cones and rods that ultimately make up our eyes; so the questions arise:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much light can a (human) rod take?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much light can a (human) cone take?&lt;/p&gt;&#xA;" OwnerUserId="1095" LastActivityDate="2014-07-21T19:12:14.763" Title="How much energy is required to blind someone?" Tags="&lt;human-biology&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19790" PostTypeId="2" ParentId="19782" CreationDate="2014-07-20T00:59:51.833" Score="1" Body="&lt;p&gt;&lt;em&gt;Escherichia coli&lt;/em&gt; endonuclease III (which I will now refer to as Nth), and the human homolog hNTH1, has both glycosylase and AP lyase activity. The section of the article you're referring is describing an assay of lyase activity. The assay tested both Nth and hNTH1 as well as HAP1, a human AP hydrolase that cleaves 5' to the AP site. Nth and hNTH1 were found by this assay to cleave 3' to the AP site. HAP1 is dependent on &lt;span class=&quot;math-container&quot;&gt;$Mg^{2+}$&lt;/span&gt; for catalytic activity. hNTH1 (and likely Nth, given the high conservation) are dependent on &lt;span class=&quot;math-container&quot;&gt;$Mg^{2+}$&lt;/span&gt; for substrate specificity (Eide et al., 2001). hNTH1 and Nth contain an &lt;span class=&quot;math-container&quot;&gt;$Fe-S$&lt;/span&gt; cluster that is involved in DNA binding (Thayer et al., 1995).&lt;/p&gt;&#xA;&lt;p&gt;Originally I thought that the reaction is stopped with EDTA. EDTA is a chelating agent; it binds and sequesters metal ions and prevents their use by enzymes. EDTA would prevent catalysis by HAP1 and DNA binding by Nth/hTNH1.&lt;/p&gt;&#xA;&lt;p&gt;However, Chris pointed out that the loading buffer contains 1 mM EDTA while the reaction buffer contains 5 mM &lt;span class=&quot;math-container&quot;&gt;$MgCl_2$&lt;/span&gt;. While the paper doesn't give the volumes of reaction and loading buffer mixed together, it is perhaps unlikely that EDTA chelation of &lt;span class=&quot;math-container&quot;&gt;$Mg^{2+}$&lt;/span&gt; is the sole mechanism for stopping the reaction. The high concentration of formamide (80%) in the loading buffer could then be responsible. Formamide is commonly used to denature nucleic acids and, at high concentrations, would likely have an effect on enzyme function.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Eide L, Luna L, Gustad EC, Henderson PT, Essigmann JM, Demple B, Seeberg E. 2001. Human Endonuclease III Acts Preferentially on DNA Damage Opposite Guanine Residues in DNA. Biochemistry-US. 40(22):6653–6659&lt;/p&gt;&#xA;&lt;p&gt;Thayer MM, Ahern H, Xing D, Cunningham RP, Tainer JA. 1995. Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure. EMBO J. 14(16):4108–4120.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-07-20T19:59:52.777" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="19791" PostTypeId="1" AcceptedAnswerId="19792" CreationDate="2014-07-20T02:47:26.077" Score="3" ViewCount="2547" Body="&lt;p&gt;Are any air plants &lt;a href=&quot;http://en.wikipedia.org/wiki/Tillandsia&quot; rel=&quot;nofollow&quot;&gt;(&lt;em&gt;Tillansia sp.&lt;/em&gt;)&lt;/a&gt; safe for humans to eat? I haven't been able to find whether or not there are. Pineapple is in the same family &lt;a href=&quot;http://en.wikipedia.org/wiki/Bromeliaceae&quot; rel=&quot;nofollow&quot;&gt;(Bromeliaceae)&lt;/a&gt;, but isn't an air plant.&lt;/p&gt;&#xA;" OwnerUserId="843" LastEditorUserId="843" LastEditDate="2014-07-22T19:17:54.810" LastActivityDate="2018-11-18T02:11:03.260" Title="Are there any air-plants with parts that are edible for humans?" Tags="&lt;botany&gt;&lt;food&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19792" PostTypeId="2" ParentId="19791" CreationDate="2014-07-20T03:18:02.767" Score="5" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Monstera_deliciosa&quot;&gt;&lt;em&gt;Monstera deliciosa&lt;/em&gt;&lt;/a&gt; seems to fit the bill. From Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This member of the arum &lt;a href=&quot;https://en.wikipedia.org/wiki/Family_(biology)&quot;&gt;family&lt;/a&gt; Araceae is an &lt;a href=&quot;https://en.wikipedia.org/wiki/Epiphyte&quot;&gt;epiphyte&lt;/a&gt; with &lt;a href=&quot;https://en.wikipedia.org/wiki/Aerial_roots&quot;&gt;aerial roots&lt;/a&gt;...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Wild seedlings grow towards the darkest area they can find until they find a tree trunk, then start to grow up towards the light, creeping up the tree.&lt;sup&gt;[6][dead reference link]&lt;/sup&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;h2&gt;Fruit&lt;/h2&gt;&#xA;  &#xA;  &lt;hr&gt;&#xA;  &#xA;  &lt;p&gt;The fruit of Monstera deliciosa is up to 25 cm long and 3–4 cm diameter, looking like a green ear of maize covered with hexagonal scales.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Fruits of plants of the Araceae (Arum family) often contain &lt;a href=&quot;https://en.wikipedia.org/wiki/Raphide&quot;&gt;Raphides&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Trichosclereid&quot;&gt;Trichosclereids&lt;/a&gt; – needle-like structures of calcium oxalate.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The fruit may be ripened by cutting it when the first scales begin to lift up and it begins to exude a pungent odor. It is wrapped in a paper bag and set aside until the scales begin popping off. The scales are then brushed off or fall away to reveal the edible flesh underneath. The flesh, which is similar to &lt;a href=&quot;https://en.wikipedia.org/wiki/Pineapple&quot;&gt;pineapple&lt;/a&gt; in texture, can be cut away from the core and eaten. It has a fruity taste similar to &lt;a href=&quot;https://en.wikipedia.org/wiki/Jackfruit&quot;&gt;jackfruit&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Pineapple&quot;&gt;pineapple&lt;/a&gt;. The unripe green fruits can irritate the throat and the latex of the leaves and vines can create rashes in the skin, because both contain potassium oxalate: that is the reason why the fruits have to be consumed when the scales lift up.&lt;sup&gt;[&lt;a href=&quot;http://www.reuna.unalmed.edu.co/temporales/memorias/especies/Vegetales/63_plantassilvestresalimenticias.htm&quot;&gt;9&lt;/a&gt;]&lt;/sup&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Plants grown indoors in temperate regions occasionally produce flowers and fruit.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In Mexico, a leaf or root infusion is drunk daily to relieve arthritis.&lt;sup&gt;[6][dead reference link]&lt;/sup&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In Martinique the root is used to make a remedy for snakebite.&lt;sup&gt;[6][dead reference link]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here's a picture of the fruit by &lt;a href=&quot;https://commons.wikimedia.org/wiki/User:B.navez&quot;&gt;Bruno Navez&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/File:Monstera_deliciosa_ripen_fruit_01.JPG&quot;&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/a/a7/Monstera_deliciosa_ripen_fruit_01.JPG&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Hylocereus_undatus&quot;&gt;Dragonfruit (Hylocereus undatus)&lt;/a&gt; is also &lt;a href=&quot;https://en.wikipedia.org/wiki/Hemiepiphytic&quot;&gt;hemiepiphytic&lt;/a&gt;. You may also be interested in &lt;a href=&quot;http://cactus-epiphytes.eu/z_page_les_fruits.htm&quot;&gt;this page about epiphytic cactus fruits&lt;/a&gt; and &lt;a href=&quot;https://groups.yahoo.com/neo/groups/epiphytes/conversations/topics/704&quot;&gt;this post on Yahoo! Groups&lt;/a&gt; where I found M. deliciosa. The author claims:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I have eaten the fruits off my &lt;a href=&quot;https://en.wikipedia.org/wiki/Acanthostachys_strobilacea&quot;&gt;Acanthostachys strobilacea&lt;/a&gt;, an epiphytic bromeliad, and they are reminiscent of the related terrestrial pineapple just slightly more acidic but still very palatable (to me at least). &lt;sup&gt;&lt;sub&gt;[Hyperlink added.]&lt;/sup&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5331" LastActivityDate="2014-07-20T03:18:02.767" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19793" PostTypeId="2" ParentId="15091" CreationDate="2014-07-20T03:30:18.583" Score="1" Body="&lt;p&gt;I just wanted to add, regarding CN VII.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CN VII receives stimulation via the facial nucleus from both the ipsilateral and the contralateral corticobulbar tracts. The upper muscles of facial expression (particularly around the eyes) receive stimulation from both the ipsilateral and the contralateral corticobulbar tracts. The lower portion of the face is innervated only from the contralateral corticobulbar tract. So in case of a stroke which wipes out an entire track (either left or right), there will be total loss of the lower muscles of facial expression, however there will be some sparing of the upper muscles because of the ipsilateral pathway redundancy.&lt;/p&gt;&#xA;" OwnerUserId="8381" LastActivityDate="2014-07-20T03:30:18.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19794" PostTypeId="1" CreationDate="2014-07-20T05:54:03.250" Score="2" ViewCount="1024" Body="&lt;p&gt;It's a lizard that has the ability to burst blood vessels in it's eyes and shoot blood as self defense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can this behavior be explained evolutionary? Wouldn't it mean that there had to be some intermediate evolutionary step where the lizard could bleed from it's eyes only slightly? How did that not cause it's extinction?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To generalize more, how does a specific trait evolve when it seems the intermediate traits are detrimental to survival?&lt;/p&gt;&#xA;" OwnerUserId="6340" LastEditorDisplayName="user1357" LastEditDate="2014-07-22T15:31:04.270" LastActivityDate="2017-03-23T17:42:34.643" Title="How did the horned lizard evolve?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19797" PostTypeId="2" ParentId="19787" CreationDate="2014-07-20T10:12:21.217" Score="3" Body="&lt;p&gt;Females are defined as the sex that produces that bigger gamete (ovule) while the males are those from the gender that produce the smaller gametes (spermatozoid). Because producing big gametes is costly, the number of females fix the reproductive limit in the population and in other words the variance in reproductive success in males is higher than in females. In the same logic, because females fix the reproductive limit in the population, males have to compete to access the females while the females are choosy. You may want to have a look at the wikipedia articles for &lt;a href=&quot;http://en.wikipedia.org/wiki/Bateman&amp;#39;s_principle&quot; rel=&quot;nofollow&quot;&gt;Bateman's principle&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Parental_investment&quot; rel=&quot;nofollow&quot;&gt;Parental Investment&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The conclusions of Bateman's principle holds in general but not systematically. In some species males produce huge amount of parental care and therefore, the females become choosy for example.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[..] men’s reproductive methodology is to scatter as much of his genetic material as humanly possible to the widest available quantity of sexually available females.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, in many cases but not everytime. Human are an example of the cases where this statement is wrong.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[..] for a species to survive it must provide it’s offspring with the best possible conditions to ensure it’s survival – either that or to reproduce in such quantity that it ensures survival.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It sounds a bit weird! The reason is that the sentence almost implies that individual's strategy evolved in order to increase the probability of survival of the species which is totally wrong. By the mechanisms of natural selection a population evolve in the direction so that each individual favors its number of offsprings which can be in some cases very detrimental to the species as a whole.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reading some bits of what I found no the webpage you linked i your question, it doesn't seem to me that the author is a good evolutionary biologist…but I haven't read much.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-07-20T10:12:21.217" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19799" PostTypeId="2" ParentId="19794" CreationDate="2014-07-20T11:50:33.577" Score="2" Body="&lt;p&gt;I'm speculating here, but it's likely that the taste of the blood has something to do with this. The blood of the horned lizard tastes foul to &lt;a href=&quot;http://en.wikipedia.org/wiki/Horned_lizard&quot; rel=&quot;nofollow&quot;&gt;feline and canine predators&lt;/a&gt;. Therefore, a small amount of blood leaking out of the eye might put predators off immediately after the first attack, if that attack was aimed at the head.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously, this is an advantage for the lizard, but since a large percentage of attacks to the head would result in debilitating injuries, there is a selective pressure to take this further so that the taste of the blood is &quot;communicated&quot; to the predator &lt;em&gt;before&lt;/em&gt; the initial attack. &lt;/p&gt;&#xA;" OwnerUserId="3631" LastActivityDate="2014-07-20T11:50:33.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19800" PostTypeId="2" ParentId="1640" CreationDate="2014-07-20T13:31:31.540" Score="1" Body="&lt;p&gt;I suspect the answer to this, is that in looking at agricultural fruits you are looking at plants that have been the subject of artificial selection, and the tree vs vine thing is a practical limit, but not the driving factor... for instance a jack fruit grows on tree and is watermelon sized... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think if you look at something like a pumpkin, you will likely see that pumpkins have 3 traits:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Indeterminate growth ... they will produce as many fruit as the season will let them.&lt;/li&gt;&#xA;&lt;li&gt;Individual fruit will try to complete growth and ripen before winter&lt;/li&gt;&#xA;&lt;li&gt;Vines with fewer fruit can devote more resources per fruit, and therefor larger fruit.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Even in apples; if all of the blooms go to fruit the apples will be smaller (commercially apples are thinned to make market acceptable sized fruit): &lt;a href=&quot;http://homeorchard.ucdavis.edu/8047.pdf&quot; rel=&quot;nofollow&quot;&gt;http://homeorchard.ucdavis.edu/8047.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I think the real issue is less tree vs vine, and more about growth patterns... it may be possible to have a watermelon sized apple, but the tree will have to be sturdy enough to support the fruit: so it isn't a non-issue, but support is a limiting factor.&lt;/p&gt;&#xA;" OwnerUserId="4054" LastActivityDate="2014-07-20T13:31:31.540" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19801" PostTypeId="2" ParentId="19794" CreationDate="2014-07-20T13:37:01.110" Score="2" Body="&lt;p&gt;There isn't always an intermediate step like &quot;oozing blood eyes&quot;, I suspect that this particular trait is pretty easily explained by having an area of weakness in a blood vessel that made the lizard bleed under high stress situations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;maybe in early version the lizard had to get some trauma or could intentionally hit its head on a rock or something... I don't know, but it doesn't really require any novel structure. &lt;/p&gt;&#xA;" OwnerUserId="4054" LastActivityDate="2014-07-20T13:37:01.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19802" PostTypeId="2" ParentId="19789" CreationDate="2014-07-20T15:39:31.193" Score="1" Body="&lt;p&gt;Light can affect retina in many ways [1]:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;photothermal mechanisms - exposure to intense flashes of less than 20 microseconds that cause a rise in temperature of at least 10 degrees Celsius [5];&lt;/li&gt;&#xA;&lt;li&gt;photomechanical mechanisms - exposure to flashes shorter than 5 nanoseconds [5];&lt;/li&gt;&#xA;&lt;li&gt;photochemical mechanisms - light is absorbed by a chromophore and leads to the formation of an electronically excited state of it, resulting in chemical transformations [5].&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The retina is more susceptible to light induced degeneration at lower wavelengths [2, 8]. The damage degree also depends on intensity and exposure duration. 12 hours a day of more than 500 lux light, more than three consecutive days can affect rat retina [3]. 2 hours  exposure to white light of 3000 lux has lead to apoptosis in rats retina [4].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sunlight irradiance is about 11 W/cm&lt;sup&gt;2&lt;/sup&gt; (ranges between 1.5 and 122 W/cm&lt;sup&gt;2&lt;/sup&gt;) and causes damage when exposure time is tens of minutes or even less [5].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Light induces apoptosis by different mechanisms:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Intense light triggers cell death in cones and rods by two distinct mechanisms: rapid, necrosis-like cell death occurs in cones; prolonged, apoptotic death is displayed by rods. However, the areas of cone and rod loss coincide, suggesting some interrelationship [6].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Cones and rods have different vulnerability [7].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Youssef PN, Sheibani N, Albert DM. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21178995&quot; rel=&quot;nofollow&quot;&gt;Retinal light toxicity.&lt;/a&gt; Eye (Lond). 2011 Jan;25(1):1-14. doi: &lt;a href=&quot;http://dx.doi.org/10.1038/eye.2010.149&quot; rel=&quot;nofollow&quot;&gt;10.1038/eye.2010.149&lt;/a&gt;. PubMed PMID: 21178995.&lt;/li&gt;&#xA;&lt;li&gt;Rozanowska, M. B. (2012), &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1751-1097.2012.01240.x/full&quot; rel=&quot;nofollow&quot;&gt;Light-Induced Damage to the Retina: Current Understanding of the Mechanisms and Unresolved Questions: A Symposium-in-Print.&lt;/a&gt; Photochemistry and Photobiology, 88: 1303–1308. doi: 10.1111/j.1751-1097.2012.01240.x &lt;/li&gt;&#xA;&lt;li&gt;Jin X, Wu L, Zheng H, Mishima S. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12579740&quot; rel=&quot;nofollow&quot;&gt;[Retinal light damage: I. The influences of light intensity and exposure duration at moderate and low intensities of cyclic light].&lt;/a&gt; Yan Ke Xue Bao. 1998 Dec;14(4):215-9. PubMed PMID: 12579740. &lt;/li&gt;&#xA;&lt;li&gt;Remé CE, Weller M, Szczyesny P, Munz K, Hafezi F, et al. Light-induced apoptosis in the rat retina in-vivo. In: Anderson RE, LaVail MM, Hollyfield JG, editors. Degenerative Diseases of the Retina. Plenum Press; New York: 1995. Via &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2831109/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2831109/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Malgorzata Rozanowska, Bartosz Rozanowski, Michael Boulton. LIGHT-INDUCED DAMAGE to the RETINA (2009). Available from &lt;a href=&quot;http://www.photobiology.info/Rozanowska.html&quot; rel=&quot;nofollow&quot;&gt;http://www.photobiology.info/Rozanowska.html&lt;/a&gt; (accessed 20.07.2014).&lt;/li&gt;&#xA;&lt;li&gt;Cortina MS, Gordon WC, Lukiw WJ, Bazan NG. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15180269&quot; rel=&quot;nofollow&quot;&gt;Light-induced photoreceptor damage triggers DNA repair: differential fate of rods and cones.&lt;/a&gt; Adv. Exp. Med. Biol. 2004;533:229-40. PubMed PMID: 15180269. &lt;/li&gt;&#xA;&lt;li&gt;Okano K, Maeda A, Chen Y, Chauhan V, Tang J, Palczewska G, Sakai T, Tsuneoka H, Palczewski K, Maeda T. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22220722&quot; rel=&quot;nofollow&quot;&gt;Retinal cone and rod photoreceptor cells exhibit differential susceptibility to light-induced damage.&lt;/a&gt; J. Neurochem. 2012 Apr;121(1):146-56. doi: &lt;a href=&quot;http://dx.doi.org/10.1111/j.1471-4159.2012.07647.x&quot; rel=&quot;nofollow&quot;&gt;10.1111/j.1471-4159.2012.07647.x&lt;/a&gt;. PubMed PMID: 22220722. &lt;/li&gt;&#xA;&lt;li&gt;Kuse Y, Ogawa K, Tsuruma K, Shimazawa M, Hara H. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24909301&quot; rel=&quot;nofollow&quot;&gt;Damage of photoreceptor-derived cells in culture induced by light emitting diode-derived blue light.&lt;/a&gt; Sci Rep. 2014 Jun 9;4:5223. doi: &lt;a href=&quot;http://dx.doi.org/10.1038/srep05223&quot; rel=&quot;nofollow&quot;&gt;10.1038/srep05223&lt;/a&gt;. PubMed PMID: 24909301. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-07-21T19:12:14.763" LastActivityDate="2014-07-21T19:12:14.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19803" PostTypeId="1" AcceptedAnswerId="19805" CreationDate="2014-07-20T16:02:38.417" Score="2" ViewCount="252" Body="&lt;p&gt;Note: Please tell me to re-post this in Cogsci or pets if this doesn't belong here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hello All,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know how dogs or other domesticated animals differentiate between normal chat and a command. Do they understand their master's language or body language? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If they understand the body language of the master alone, then how come they can do the same trick (in most of the cases) if some other person gives the same command?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And to what extent do they have this understanding, meaning how many words does a domesticated animal understand? &lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="1320" LastEditDate="2014-07-21T09:27:15.773" LastActivityDate="2014-07-21T09:27:15.773" Title="To what extent do domestic animals understand language?" Tags="&lt;zoology&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19804" PostTypeId="1" CreationDate="2014-07-20T16:04:54.190" Score="3" ViewCount="65" Body="&lt;p&gt;Say I take a blood sample from an adult, extract the white cells and apply to them the process described in &amp;lt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmedhealth/behindtheheadlines/news/2014-01-30-breakthrough-in-stem-cell-creation-using-acid-bath/&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;&gt;. Assuming this actually turns the adult white cells into stem cells, which I then transfer to a culture in order to grow an arbitrary quantity, how can I make sure in the end this culture is free of cancer stem cells? Is there a last step that can be applied which would eliminate any potential CSCs leaving only healthy cells in the culture?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="8384" LastActivityDate="2014-12-08T12:21:28.067" Title="How to make sure a stem cell culture is cancer free?" Tags="&lt;cancer&gt;&lt;stem-cells&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19805" PostTypeId="2" ParentId="19803" CreationDate="2014-07-20T16:20:55.653" Score="3" Body="&lt;p&gt;Yes, they can understand some words and even simple sentences.&lt;/p&gt;&#xA;&lt;p&gt;Here is what &lt;a href=&quot;http://www.animalplanet.com/pets/can-dogs-understand-what-we-say.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Animal Planet&lt;/a&gt; says:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Studies show that the average dog can understand about 165 different words, in some cases more if you make a point of training them. This includes the basic commands such as &amp;quot;sit,&amp;quot; &amp;quot;stay,&amp;quot; and &amp;quot;go,&amp;quot; as well as a range of other terms, assuming they're tangible words and not abstract ideas.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Here are some supporting studies:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Some domestic dogs learn to comprehend human words, although the nature and basis of this learning is unknown [1].&lt;/p&gt;&#xA;&lt;p&gt;A female mongrel dog, Sofia, was initially trained to respond to action (point and fetch) and object (ball, key, stick, bottle and bear) terms which were then presented as simultaneous, combinatorial requests (e.g. ball fetch, stick point). Sofia successfully responded to object-action requests presented as single sentences, and was able to flexibly generalize her performance across different contexts [2].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Tempelmann S, Kaminski J, Tomasello M (2014) &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0091014&quot; rel=&quot;nofollow noreferrer&quot;&gt;Do Domestic Dogs Learn Words Based on Humans’ Referential Behaviour?&lt;/a&gt; PLoS ONE 9(3): e91014. doi:10.1371/journal.pone.0091014&lt;/li&gt;&#xA;&lt;li&gt;Ramos D, Ades C (2012) &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0029689&quot; rel=&quot;nofollow noreferrer&quot;&gt;Two-Item Sentence Comprehension by a Dog (Canis familiaris).&lt;/a&gt; PLoS ONE 7(2): e29689. doi:10.1371/journal.pone.0029689&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-07-20T16:20:55.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19806" PostTypeId="1" CreationDate="2014-07-20T17:09:17.060" Score="8" ViewCount="548" Body="&lt;p&gt;Why do we have to get them from our diet, and if they aren't taken in our diet we will face disease? Then why we don't have the enzymes which are require for EFA synthesis?&lt;/p&gt;&#xA;" OwnerUserId="8301" LastEditorUserId="1320" LastEditDate="2017-07-31T21:38:10.703" LastActivityDate="2017-07-31T21:38:10.703" Title="Why are mammals unable to produce Essential Fatty Acids?" Tags="&lt;metabolism&gt;&lt;fat-metabolism&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19807" PostTypeId="1" CreationDate="2014-07-20T17:14:05.283" Score="5" ViewCount="1783" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/19582/6918&quot;&gt;I have captured an ant queen&lt;/a&gt; and now I'm trying to create an artificial ant nest.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have noticed that though she has dug a hole to hide in, she keeps the eggs out of it unless she feels that they are in danger.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tmS03.jpg&quot; alt=&quot;ant queen reaching for her eggs&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have two theories explaining why she does that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Ants naturally put eggs in sunlight to keep them warm. In her situation, they are not gonna be any warmer of course - the jar is whole about the same temperature.&lt;/li&gt;&#xA;&lt;li&gt;She is digging a nest and she needs some space. If this is true, where is all the dirt?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6918" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2019-01-18T17:06:00.970" Title="Why does ant queen keep the eggs out of her hive?" Tags="&lt;ethology&gt;&lt;ant&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19808" PostTypeId="2" ParentId="19807" CreationDate="2014-07-20T18:05:16.670" Score="1" Body="&lt;p&gt;According to various websites and literature I found, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Starting a new colony&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During the mating season, Queen Ant grows wings and mate with male (flying) ant. In most of the species the queen will fly away to a new place where, she will loose her wings and dig a tunnel. She may lay eggs inside or outside because of the humidity and temperature, mostly they wait till spring, so that the &lt;strong&gt;humidity is high as well as warm temperature&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For laying eggs she will dig a tunnel inside and close the gates. She won't eat or move and &lt;strong&gt;completely avoid light&lt;/strong&gt;, if the eggs are unhatched or some other problem occurs &lt;strong&gt;she will eats her own eggs&lt;/strong&gt;. After around 8-10 weeks eggs will pop and you will get new worker ant babies. They will form the hive and feed the queen ant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ev1be.jpg&quot; alt=&quot;&quot;&gt;    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More info: &lt;a href=&quot;http://antnest.co.uk/colony.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://antnest.co.uk/colony.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-01-18T17:06:00.970" LastActivityDate="2019-01-18T17:06:00.970" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="19809" PostTypeId="1" AcceptedAnswerId="19825" CreationDate="2014-07-20T19:11:02.643" Score="5" ViewCount="244" Body="&lt;p&gt;Cooperativity in gene expression is an important feature of many regulatory networks. Described using the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hill_equation_(biochemistry)&quot; rel=&quot;nofollow&quot;&gt;Hill function&lt;/a&gt;, the most common example is a transcription factor (TF) that when bound to its target regulatory site, increases the rate of binding of other transcription factors (usually through TF-TF dimerization).   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are numerous example of TF dimerization-based cooperativity in the literature. However, I am trying to find examples of positive transcriptional cooperativity that involve mechanisms &lt;em&gt;other than&lt;/em&gt; TF dimerization. In the dimer model, an unbound TF binds to its cognate promoter (containing multiple enhancers) with a certain affinity. With the first TF bound, another identical TF now has increased affinity for its target - binding to the enhancer and binding (dimerization) to the first TF. The expression profile is sigmoidal (near binary) and represents sharp on/off switching in activity.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although peer-reviewed articles experimentally or theoretically characterizing alternative mechanisms are preferred, I'm also interested in user hypotheses and discussions that are more speculative. Specifically, I'm interested in positive cooperativity that occurs without feedback from the regulated genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One potential mechanism could involve a DNA-binding TF consisting of a transcriptional activator domain and a chromatin remodeling or DNA methylation domain. When the TF binds it not only activates transcription but remodels local chromatin. If the remodeling increases affinity for the next TF, they act cooperatively (and positively). Perhaps something similar to this has already been described.    &lt;/p&gt;&#xA;" OwnerUserId="3061" LastEditorUserId="3061" LastEditDate="2014-07-20T23:00:28.390" LastActivityDate="2014-07-22T05:08:56.677" Title="What are some atypical examples of positive transcriptional cooperativity?" Tags="&lt;molecular-biology&gt;&lt;transcription&gt;&lt;gene-regulation&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19810" PostTypeId="1" AcceptedAnswerId="19813" CreationDate="2014-07-20T19:26:13.817" Score="5" ViewCount="327" Body="&lt;p&gt;The most well studied genetic oscillators in human genomes are involved in regulating the circadian clock (which operates on an approximately 24-hour cycle) and cell cycle activity (with single cycles usually lasting several hours to many days). Are there any known genetic oscillators in humans (or other mammals) that operate on shorter timescales? &lt;/p&gt;&#xA;" OwnerUserId="3061" LastEditorUserId="3061" LastEditDate="2014-07-20T20:51:37.980" LastActivityDate="2014-07-21T08:46:15.163" Title="High frequency human genetic oscillators?" Tags="&lt;molecular-biology&gt;&lt;circadian-rhythms&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19811" PostTypeId="1" AcceptedAnswerId="71876" CreationDate="2014-07-20T19:43:00.240" Score="2" ViewCount="1813" Body="&lt;p&gt;I have an ant queen in a jar. This is what she looks like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jTC29.jpg&quot; alt=&quot;black ant queen captured in jar&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because I'm planning to start an artificial ant nest, I'd like to learn something about that specific species of ant. This particular queen is very common in the Czech Republic, central Europe. It's also very common in cities.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Could you tell what kind of queen is that?&lt;/li&gt;&#xA;&lt;li&gt;Is there any image reference that would help me find out? Ideally with some location search possibility.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6918" LastActivityDate="2018-08-03T08:56:20.423" Title="Can I identify this black ant queen?" Tags="&lt;species-identification&gt;&lt;ant&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19813" PostTypeId="2" ParentId="19810" CreationDate="2014-07-20T20:07:10.827" Score="6" Body="&lt;p&gt;Here are some examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;electric oscillators:&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Neural_oscillation&quot; rel=&quot;nofollow&quot;&gt;neural activity&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;cardiac automatism (0.8 ... 1 Hz)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;mechanical oscillators (as a result of neural activity):&#xA;&lt;ul&gt;&#xA;&lt;li&gt;heart beats&lt;/li&gt;&#xA;&lt;li&gt;breathing (0.2 ... 0.3 Hz)&lt;/li&gt;&#xA;&lt;li&gt;intestinal peristaltic waves&lt;/li&gt;&#xA;&lt;li&gt;vocal chords activity (up to a few kHz)&lt;/li&gt;&#xA;&lt;li&gt;muscular spasm (pathological)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;chemical oscillators:&#xA;&lt;ul&gt;&#xA;&lt;li&gt;insulin variation in concordance with glucose intake&lt;/li&gt;&#xA;&lt;li&gt;endocrine oscillations&lt;/li&gt;&#xA;&lt;li&gt;menstruation&lt;/li&gt;&#xA;&lt;li&gt;feedback enabled metabolic pathways&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;See this Wikipedia page too: &lt;a href=&quot;http://en.wikipedia.org/wiki/Oscillation#Human&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Oscillation#Human&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When it comes to genetic oscillators, some of them follow circadian rhythm.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A typical proliferating human cell divides on average every 24 h. This division timing allows cells to synchronize with other physiological processes and with the environment. The circadian clock, which orchestrates daily rhythms, directly regulates the cell division cycle and is a major synchronizing factor [5].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Immune system:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In every single cell an oscillator goes ticking through a molecular clock operated by transcriptional/translational feedback loops driven by the rhythmic expression of circadian genes. This clock gene machinery steers daily oscillations in the regulation of immune cell activity, driving the periodicity in immune system function [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Glucose homeostasis:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The master circadian clock, localized in suprachiasmatic nucleus (SCN), regulates multiple metabolic pathways, while feeding behavior and metabolite availability can in turn regulate the circadian clock [2].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Retina:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... the retina itself possesses intrinsic circadian oscillations, exemplified by diurnal fluctuations in visual sensitivity, neurotransmitter levels, and outer segment turnover rates. Recently, it has been noted that both central and peripheral oscillators share a molecular clock consisting of an endogenous, circadian-driven, transcription-translation feedback loop that cycles with a periodicity of approximately 24 hours [3].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But there are others which don't.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Genetic oscillators are ubiquitous regulatory motifs in the molecular control circuits of living cells. Prominent examples include the cell cycle and cellular signaling [4].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The frequency is much lower in some human cells [6]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;&lt;pre&gt;&lt;code&gt;Cell Type      Process    Time&#xA;______________ __________ ______________________&#xA;fly embryo     mitosis    8 minutes&#xA;bacteria       mitosis    20 minutes&#xA;yeast          mitosis    2 hours&#xA;human skin     mitosis    20 - 24 hours&#xA;human sperm    meiosis    about 64 days&#xA;human liver    mitosis    1 year or more&#xA;human egg      meiosis    up to 40 years or more&#xA;human nerve    mitosis    never, once mature&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Vinciguerra M, Borghesan M, Pazienza V, Piepoli A, Palmieri O, Tarquini R, Tevy MF, De Cata A, Mazzoccoli G. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23489683&quot; rel=&quot;nofollow&quot;&gt;The transcriptional regulators, the immune system and the the circadian clock.&lt;/a&gt; J. Biol. Regul. Homeost. Agents. 2013;27(1):9-22. PubMed PMID: 23489683. &lt;/li&gt;&#xA;&lt;li&gt;Chrościcki P, Usarek M, Bryla J. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23799401&quot; rel=&quot;nofollow&quot;&gt;[The role of biological clock in glucose homeostasis].&lt;/a&gt; Postepy Hig Med Dosw (Online). 2013 Jun 20;67:569-83. doi: &lt;a href=&quot;http://dx.doi.org/10.5604/17322693.1053906&quot; rel=&quot;nofollow&quot;&gt;10.5604/17322693.1053906&lt;/a&gt;. PubMed PMID: 23799401. &lt;/li&gt;&#xA;&lt;li&gt;Ramsey DJ, Ramsey KM, Vavvas DG. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24010846&quot; rel=&quot;nofollow&quot;&gt;Genetic advances in ophthalmology: the role of melanopsin-expressing, intrinsically photosensitive retinal ganglion cells in the circadian organization of the visual system.&lt;/a&gt; Semin Ophthalmol. 2013 Sep 6;28(5-6):406-21. doi: &lt;a href=&quot;http://dx.doi.org/10.3109/08820538.2013.825294&quot; rel=&quot;nofollow&quot;&gt;10.3109/08820538.2013.825294&lt;/a&gt;. PubMed PMID: 24010846. &lt;/li&gt;&#xA;&lt;li&gt;Davit A. Potoyan and Peter G. Wolynes. &lt;a href=&quot;http://www.pnas.org/content/early/2014/01/23/1323433111.abstract&quot; rel=&quot;nofollow&quot;&gt;On the dephasing of genetic oscillators.&lt;/a&gt; PNAS 2014 ; published ahead of print January 27, 2014, doi:10.1073/pnas.1323433111&lt;/li&gt;&#xA;&lt;li&gt;Samuel Bernard and Hanspeter Herzel. &lt;a href=&quot;http://math.univ-lyon1.fr/homes-www/bernard/publi/bernard2006GenomeInfo.pdf&quot; rel=&quot;nofollow&quot;&gt;Why Do Cells Cycle with a 24 Hour Period?&lt;/a&gt; Genome Informatics 17(1): 72{79 (2006).&lt;/li&gt;&#xA;&lt;li&gt;wiseGEEK.org. &lt;a href=&quot;http://www.wisegeek.org/how-long-does-it-take-for-cells-to-divide.htm&quot; rel=&quot;nofollow&quot;&gt;How Long Does it Take for Cells to Divide?&lt;/a&gt; (accessed 21.07.2014)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-07-21T08:46:15.163" LastActivityDate="2014-07-21T08:46:15.163" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19814" PostTypeId="2" ParentId="3765" CreationDate="2014-07-20T21:40:18.713" Score="2" Body="&lt;p&gt;You've already mentioned &lt;strong&gt;rRNA&lt;/strong&gt;. An interesting review &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6976.1999.tb00399.x/full&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Tanner, 2006)&lt;/a&gt;, outlines some more:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Group I Introns&lt;/strong&gt; - self-splicing; &amp;quot;They are abundant in fungal and plant mitochondria...&amp;quot;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Group II Introns&lt;/strong&gt; - some have been shown to self-splice; &amp;quot;...they are found in fungal and plant mitochondria, in chloroplasts of plants ... and especially in the chloroplasts of the protist &lt;em&gt;Euglena gracilis&lt;/em&gt;.&amp;quot;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;RNase P&lt;/strong&gt; - involved in tRNA processing, found in mitochondria&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;None of these are strictly found in mitochondria or chloroplasts. However, the paper goes on to describe &lt;strong&gt;VS RNA ribozyme&lt;/strong&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The mitochondria of certain strains of &lt;em&gt;Neurospora&lt;/em&gt; contain the Varkud plasmid (a retroplasmid), which encodes a reverse transcriptase, and a small, unrelated, RNA (VS RNA). The VS RNA is transcribed from circular or multimeric VS plasmid DNA by a mitochondrial RNA polymerase, and the resulting transcripts are subsequently site-specifically cleaved and ligated to form circular, 881 nucleotides long, RNA monomers. These monomers are then reverse transcribed and made double stranded to form the mature VS plasmid.&lt;/p&gt;&#xA;&lt;p&gt;In vitro transcribed VS RNA precursors are cleaved and ligated by the RNA itself and this is presumed to occur in vivo as well. Of all the self-cleaving RNAs, the catalytic properties of VS RNA are the most poorly understood.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Tanner NK. 2006. Ribozymes: the characteristics and properties of catalytic RNAs. FEMS Microbiol Rev. 23(3):257-275.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-10-21T05:10:01.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19815" PostTypeId="2" ParentId="19809" CreationDate="2014-07-20T21:53:39.837" Score="2" Body="&lt;p&gt;Interesting question. I think I have two examples for you which might be interesting.&#xA;The first is the co-regulation of the microphthalmia-associated transcription factor (MITF) in pigmentation by SOX10 and PGC1a/b. See this paper:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23201126&quot; rel=&quot;nofollow&quot;&gt;PGC-1 coactivators regulate MITF and the tanning response.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The second is about the regulation of brown fat tissue by PGC1a and IRF4 which seem to interact in these cells. See this paper:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24995979&quot; rel=&quot;nofollow&quot;&gt;IRF4 Is a Key Thermogenic Transcriptional Partner of PGC-1α.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In both cases a transcription factor (SOX10 or IRF4) interacts with the co-activator PGC1 proteins to regulate gene expression. If the co-activator is missing, the expression is at least downregulated. These activations are not so atypical or rare but are occurring quite often. If you have problems in getting these articles, let me know.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-20T21:53:39.837" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19816" PostTypeId="1" CreationDate="2014-07-20T22:51:01.870" Score="3" ViewCount="1026" Body="&lt;p&gt;There are several often noted examples of convergent evolution (eyes, bat/bird wing evolution etc.)  How do we rule out horizontal gene transfer in these cases?  &lt;/p&gt;&#xA;" OwnerUserId="8388" LastActivityDate="2014-07-21T14:26:26.513" Title="Horizontal gene transfer versus convergent evolution" Tags="&lt;evolution&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19817" PostTypeId="1" CreationDate="2014-07-20T22:58:37.580" Score="6" ViewCount="7886" Body="&lt;p&gt;I couldn't find this question directly asked so I thought I would ask it&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;em&gt;Fundamentals of Biochemistry 3e&lt;/em&gt; (Voet et al), it has a small small little comment about pyrimidine synthesis:&#xA;(In a diagram showing UMP synthesis)&#xA;&quot;In the eukaryotic enzyme, which contains FMN and nonheme Fe, is located on the outer surface of the inner mitochondrial membrane where quinones supply its oxidizing power. The other five enzymes of pyrimidine biosynthesis are cytosolic in animal cells.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it seems for the most part pyrimidine synthesis occurs in the cytosol??&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the book talks about purine synthesis no mention is made of where this is actually happening in the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, if nucleotides are being made in the cytosol, I suspect there must be some kind of membrane protein that allows nucleotides to cross the nuclear and mitochondrial membranes... what are they??&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm a visual person, and knowing where and how these things are happening in the cell helps me understand it better than just following what's happening after each synthesis step.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="8389" LastActivityDate="2014-07-21T14:55:38.667" Title="Location of nucleotide synthesis and transport" Tags="&lt;nucleic-acids&gt;&lt;biosynthesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19818" PostTypeId="2" ParentId="19735" CreationDate="2014-07-21T00:31:26.850" Score="4" Body="&lt;p&gt;Regeneration of limbs in amphibians is an adaptation where new limbs are generated by dedifferentiated cells. This process is tightly linked to the embryonic program which, in most animal cells, is a difficult program to access once terminal differentiation has occurred (but it's possible, e.g. induced pluripotent stem cells). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of note, amphibians have a unique life cycle that includes metamorphosis. It is thought that organisms with more diverse stages in their development may have increased potential for regeneration. Mammals, after birth, do pass through multiple stages of development, but these stages are largely continuous. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the quick answer is: mammalian limbs are made up of terminally differentiated cells (and specialized stem cells) with high barriers of reprogramming. They're difficult to reprogram because there hasn't been strong selective pressure to do so. Limb regeneration might seem like a great adaptation, but it doesn't seem to be that important for the success of mammals. Additionally, selection for &quot;maintaining a full set of functional limbs&quot; could evolve many different ways. For example, primates may have evolved behaviors or reinforced anatomy that reduces their risk of injuring a limb. Also, larger animals are probably less likely to have limbs removed just given their size. And if they do, it may have little effect on their reproductive fitness. A legless amphibian probably finds few, if any, mates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org./content/110/43/17392.long&quot; rel=&quot;nofollow&quot;&gt;Yun Gates, and Brock. Regulation of p53 is critical for vertebrate limb regeneration, PNAS 2013&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3061" LastEditorUserId="3061" LastEditDate="2014-07-21T05:28:40.563" LastActivityDate="2014-07-21T05:28:40.563" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19819" PostTypeId="2" ParentId="19817" CreationDate="2014-07-21T02:34:35.443" Score="5" Body="&lt;p&gt;Correct, all but one step in pyrimidine synthesis occurs in the cytosol, and purine synthesis occurs in the cytosol only. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nucleotides freely diffuse through nuclear pores but are actively transported through mitochondrial membranes via embedded membrane transport proteins (i.e. ATP-ADP translocators, GTP transporters, and pyrimidine nucleotide transporters). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://themedicalbiochemistrypage.org/nucleotide-metabolism.php&quot; rel=&quot;nofollow&quot;&gt;http://themedicalbiochemistrypage.org/nucleotide-metabolism.php&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3061" LastEditorUserId="3061" LastEditDate="2014-07-21T14:55:38.667" LastActivityDate="2014-07-21T14:55:38.667" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19820" PostTypeId="2" ParentId="8327" CreationDate="2014-07-21T04:59:37.543" Score="2" Body="&lt;p&gt;In addition Alan Boyd's answer homocysteine interferes with Glutathione synthesis by reducing the catalytic efficiency of GCL (Glutamate–cysteine ligase), the enzyme which performs the rate-limiting step in GSH synthesis.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267299/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267299/&lt;/a&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Results of the present study are the first to suggest that the relatively high levels of homocysteine that accumulate during aging can interfere with de novo GSH synthesis. Although the precise nature of the underlying mechanism is at present unclear, our results demonstrate that physiological concentrations of free homocysteine can inhibit the efficiency of cysteine utilization by GCL in a competitive manner. Homocysteine has been shown to bind GCLc at the active site in vitro [25] as well as in vivo [35], forming γ-glutamylhomocysteine [36], which is then rapidly degraded enzymatically. An additional mechanism by which an age-related increase in free homocysteine can inhibit the catalytic efficiency of GCL in a competitive manner is described in [35]. It is possible that an aging-related increase in the competition between cysteine and homocysteine for the cysteine binding site of GCL might lead to a decrease in GC synthesis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Low glutathione means a reduced ability to detoxify and deal with oxidative stress and a more oxidised redox state which has many implications&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further reading:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Inhibition of glutathione synthesis in brain endothelial cells lengthens S-phase transit time in the cell cycle: Implications for proliferation in recovery from oxidative stress and endothelial cell damage&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S2213231713000244&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S2213231713000244&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glutathione reverses endothelial dysfunction and improves nitric oxide bioavailability&#xA;&lt;a href=&quot;http://content.onlinejacc.org/article.aspx?articleid=1125915&quot; rel=&quot;nofollow&quot;&gt;http://content.onlinejacc.org/article.aspx?articleid=1125915&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8349" LastActivityDate="2014-07-21T04:59:37.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19821" PostTypeId="2" ParentId="19816" CreationDate="2014-07-21T05:14:29.527" Score="1" Body="&lt;p&gt;Without any molecular evidence you could infer convergent evolution if the species being compared shared a common ancestor that lacked the trait in question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With genomic and developmental data you would measure the degree of similarity shared between the relative factors in each species. Little or no similarity indicates convergent evolution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Horizontal gene transfer is predominantly found in bacteria. Although there are examples of limited gene transfer in eukaryotes, the donor is almost always bacteria. And there are currently no known cases of multi-gene transmission of complex networks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is interesting to contemplate how a full network might be transmitted horizontally. Horizontal &lt;em&gt;Network&lt;/em&gt; Transfer would first require a mechanism for segregating the relevant genes from the rest of the genome. It would also require invasive machinery that allows the large amount of foreign genetic material to bypass the host's defense systems. Furthermore, integration of a foreign network is increasingly more difficult with the more genes you transmit due to positional and regulatory effects of the host genome. And on top of that, it is highly unlikely that a full complement of genes involved in a complex developmental process would function in any way resembling eye or wing development. These networks have been coevolving within massively complex genomic environments for hundreds of millions of years. Expressing a large network in a foreign cell would likely prove toxic.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A looser definition of HGT might include bioengineering, specifically stable transgene integration.    &lt;/p&gt;&#xA;" OwnerUserId="3061" LastEditorUserId="3061" LastEditDate="2014-07-21T14:26:26.513" LastActivityDate="2014-07-21T14:26:26.513" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19822" PostTypeId="1" AcceptedAnswerId="19823" CreationDate="2014-07-21T05:31:54.643" Score="5" ViewCount="405" Body="&lt;p&gt;I spotted this guy in Switzerland. It's clearly an &lt;a href=&quot;http://en.wikipedia.org/wiki/Opiliones&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Opilione&lt;/em&gt;&lt;/a&gt; (&lt;em&gt;Harvestman&lt;/em&gt;), but I really know nearly enough about this diverse group to be able to identify the species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ueVeF.jpg&quot; alt=&quot;Unidentified Opilione&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry, I didn't think to place any reference near it for scale. Can anyone tell me the species or at least the genus? (Bonus points if anyone can guess what it's feeding on)&lt;/p&gt;&#xA;" OwnerUserId="6703" LastActivityDate="2019-01-17T14:18:39.340" Title="Identify this Harvestman" Tags="&lt;zoology&gt;&lt;species-identification&gt;&lt;arachnology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19823" PostTypeId="2" ParentId="19822" CreationDate="2014-07-21T05:58:47.357" Score="2" Body="&lt;h2&gt;It is probably &lt;strong&gt;Daddy Longlegs (&lt;em&gt;Leiobunum vittatum&lt;/em&gt;)&lt;/strong&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8M9Du.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;this invert color image show the resemblance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uUfvI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &#xA;&lt;a href=&quot;http://www.insectidentification.org/insect-description.asp?identification=Eastern-Harvestman&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.insectidentification.org/insect-description.asp?identification=Eastern-Harvestman&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bugguide.net/node/view/840130&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://bugguide.net/node/view/840130&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Might be eating a cockroach:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KA6Ov.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;UPDATE:&lt;/h2&gt;&#xA;&#xA;&lt;h2&gt;OR&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;It might be &lt;em&gt;Mitopus morio&lt;/em&gt;(modern harvestman)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://www.abdn.ac.uk/rhynie/images/arthropods/harvestmen/harv6.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-01-17T14:18:39.340" LastActivityDate="2019-01-17T14:18:39.340" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="19824" PostTypeId="2" ParentId="19596" CreationDate="2014-07-21T06:20:00.097" Score="2" Body="&lt;p&gt;Chromatin state refers to the marks (i.e. methylated DNA, histone modifications, euchromatin v. heterochromatin) found at specific loci and is often referred to as open (readily bound by DNA binding proteins, like transcription factors) or closed (inaccessible to most factors). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chromatin interactions can include the binding of transcription factors and other DNA binding proteins, but is usually used to describe local and long distance functional contacts between two or more regions of chromatin. These interactions are generated actively through protein-dependent chromatin organization and passively via polymer physics and the nuclear environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chromatin structures can refer to the actual molecular shape and composition of the DNA or to the molecular modifications found at specific regions of chromatin (e.g. heterochromatin, DNA methylation). It can also refer to the ordered compaction of mitotic/meiotic chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chromatin loops are structures that may act in promoting regulatory interactions. Conversely, chromatin interactions may induce looping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nsmb/journal/v20/n3/full/nsmb.2474.html&quot; rel=&quot;nofollow&quot;&gt;Cavalli and Misteli, Functional Implications of Genome Topology, &lt;em&gt;Nature Structural and Molecular Biology&lt;/em&gt; 2013&lt;/a&gt;     &lt;/p&gt;&#xA;" OwnerUserId="3061" LastActivityDate="2014-07-21T06:20:00.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19825" PostTypeId="2" ParentId="19809" CreationDate="2014-07-21T08:15:47.020" Score="3" Body="&lt;p&gt;Positive co-operativity without feedback from the downstream genes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess Polycomb/Trithorax complexes will fit this criterion nicely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Polycomb group (PcG) represses Hox and other differentiation related genes (such as neurogenin) while Trithorax (TrxG) group promotes their expression. They are not like usual transcription factors that bind to promoters and recruit/exclude RNA-polymerase; they bind at regions called Polycomb Response Elements/Trithorax Response Elements and mediate epigenetic regulation of nearby genes by histone modifications (primarily methylation). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;PcG froms two main complexes PRC1 (Polycomb Repressive Complex-1) and PRC2. Different components of the complex have different molecular functions. For e.g SuZ has a Zinc finger domain and can bind to DNA/RNA, Ezh has histone methyltransferase activity etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.genet.38.072902.091907&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; is an old review but is still quite informative. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-07-22T05:08:56.677" LastActivityDate="2014-07-22T05:08:56.677" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19826" PostTypeId="2" ParentId="19811" CreationDate="2014-07-21T10:08:41.227" Score="2" Body="&lt;p&gt;As @skymnige said it is definitely &lt;strong&gt;Black garden ant (&lt;em&gt;Lasius niger&lt;/em&gt;)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/4/4c/Lasius_Niger_wingless_queen.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.257" LastActivityDate="2014-07-21T10:08:41.227" CommentCount="3" CommunityOwnedDate="2014-07-21T10:08:41.227" ContentLicense="CC BY-SA 3.0" />
  <row Id="19827" PostTypeId="1" AcceptedAnswerId="19831" CreationDate="2014-07-21T10:53:31.207" Score="8" ViewCount="35450" Body="&lt;p&gt;Can epistaxis or nosebleeds be a cause of death?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/o3wRX.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-01-14T12:03:48.540" LastActivityDate="2019-01-14T12:03:48.540" Title="Can nosebleeds cause death?" Tags="&lt;human-biology&gt;&lt;death&gt;&lt;nose&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="19829" PostTypeId="1" CreationDate="2014-07-21T11:23:44.447" Score="1" ViewCount="828" Body="&lt;p&gt;Does anyone have experience with the CRISPR/CAS9 platform performed on MEF? Or does anyone recall any relevant articles?&lt;/p&gt;&#xA;" OwnerUserId="8397" LastEditorUserId="49230" LastEditDate="2019-03-12T01:10:53.240" LastActivityDate="2019-03-12T01:10:53.240" Title="Has anyone used Crispr/Cas to induce a knock-in in MEF cells?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="19830" PostTypeId="2" ParentId="19827" CreationDate="2014-07-21T11:30:57.417" Score="6" Body="&lt;p&gt;Any injury, that results in external bleeding can lead to death, since it is a breach in the body's defenses and an entry point for pathogens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Explanation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you have nose bleeding the blood must be coming from somewhere. Usually from inside your body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That means there is a hole in your body which is big enough for blood to stream out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That in return also means that through the same hole things can get back inside your body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example any kind of virus or bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That does not mean every bleeding is potentially lethal. But depending on the environment the body is in the chance of infection is certainly greater with a lesion (hole in the circulatory system) than without it.&lt;/p&gt;&#xA;" OwnerUserId="6137" LastActivityDate="2014-07-21T11:30:57.417" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19831" PostTypeId="2" ParentId="19827" CreationDate="2014-07-21T11:42:45.460" Score="16" Body="&lt;p&gt;Yes, it can, but it is extremely rare.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... nosebleeds are rarely fatal, accounting for only 4 of the 2.4 million deaths in the U.S. in 1999 [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The main issue is that epistaxis can be a sign of potentially fatal diseases:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The instances in which nosebleed is potentially fatal are those in which there is a history of recent head injury, severe arteriosclerotic cardiovascular disease or an underlying vascular tumor in the nasal chambers. Fatal nasal bleeding has not been reported in children [2].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here are some causes which can lead to fatal complications if left untreated [3]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Leukaemia&lt;/li&gt;&#xA;  &lt;li&gt;Hypertension&lt;/li&gt;&#xA;  &lt;li&gt;Coagulation disorders&lt;/li&gt;&#xA;  &lt;li&gt;Hepatitis&lt;/li&gt;&#xA;  &lt;li&gt;Head injury&lt;/li&gt;&#xA;  &lt;li&gt;Myelodysplastic syndromes - Epistaxis&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Death by massive hemorrhage can occur when epistaxis is the result of a ruptured aneurysm [4, 5, 6]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An instance of fatal epistaxis is reported in a patient with an unsuspected aneurysm of the infraclinoid portion of the internal carotid artery. There was no known history of trauma. The aneurysm was subsequently detected on an old X-ray film. Epistaxis from an aneurysm at this site is nearly always preceded by significant head trauma and is associated with cranial nerve palsies, a syndrome with a high mortality. Epistaxis from rupture of a non-traumatic aneurysm is very rare [4].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Work Table I. Deaths from each cause by 5-year age groups, race and sex: US, 1999 Page 1922. U.S. Centers for Disease Control Published 2001-05-11. Via Wikipedia contributors, &quot;Nosebleed,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Nosebleed&amp;amp;oldid=617613780&quot;&gt;http://en.wikipedia.org/w/index.php?title=Nosebleed&amp;amp;oldid=617613780&lt;/a&gt; (accessed July 21, 2014).&lt;/li&gt;&#xA;&lt;li&gt;QUINN FB. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/13738727&quot;&gt;Fatal epistaxis.&lt;/a&gt; Calif Med. 1961 Feb;94:88-92. PubMed PMID: 13738727. &lt;/li&gt;&#xA;&lt;li&gt;Right Diagnosis (tm). Epistaxis Deaths. Available from &lt;a href=&quot;http://www.rightdiagnosis.com/symptoms/epistaxis/deaths.htm&quot;&gt;http://www.rightdiagnosis.com/symptoms/epistaxis/deaths.htm&lt;/a&gt; (accessed 21.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;HORNIBROOK, J. and RHODE, J. C. (1981), &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1445-2197.1981.tb05942.x/abstract&quot;&gt;FATAL EPISTAXIS FROM AN ANEURYSM OF THE INTRACRANIAL INTERNAL CAROTID ARTERY.&lt;/a&gt; Aust. N.Z. J. Surg., 51: 206–208. doi: 10.1111/j.1445-2197.1981.tb05942.x&lt;/li&gt;&#xA;&lt;li&gt;P. N. Pathak (1972). &lt;a href=&quot;http://journals.cambridge.org/action/displayAbstract?fromPage=online&amp;amp;aid=1141168&quot;&gt;Epistaxis - due to ruptured aneurysm of the internal carotid artery.&lt;/a&gt; The Journal of Laryngology &amp;amp; Otology, 86, pp 395-397. doi:10.1017/S0022215100075423. &lt;/li&gt;&#xA;&lt;li&gt;Urso-Baiarda F, Saravanappa N, Courteney-Harris R. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14988378&quot;&gt;An unusual cause of massive fatal epistaxis.&lt;/a&gt; Emerg Med J. 2004 Mar;21(2):266. PubMed PMID: 14988378. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-07-21T11:55:20.887" LastActivityDate="2014-07-21T11:55:20.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19832" PostTypeId="1" AcceptedAnswerId="19833" CreationDate="2014-07-21T13:01:53.757" Score="29" ViewCount="3764" Body="&lt;p&gt;More or less we humans are around 1.70 meters tall. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, would it be possible to scale us? that is, is it in principle possible having humans 1 cm tall, or 10 meters tall or is there some reason that makes our height somehow ideal?&lt;/p&gt;&#xA;" OwnerUserId="5966" LastEditorUserId="8186" LastEditDate="2014-07-21T13:07:38.287" LastActivityDate="2014-07-21T17:50:17.687" Title="Is humans' height ideal?" Tags="&lt;human-anatomy&gt;&lt;auxology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="19833" PostTypeId="2" ParentId="19832" CreationDate="2014-07-21T13:45:09.313" Score="39" Body="&lt;p&gt;Humans can, to some extent, be scaled: While most humans are two meters tall; the human body essentially works throughout the entire range from around a meter to around two and a half meters, although you tend to run into problems at the extremes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, outside of that range you run into the tyranny of the square-cube law:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you scale a creature (or, in fact, anything), it's mass increases proportionally to the cube of the scale, while its surface area increases proportionally to the square of the scale.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that as you scale humans down, their mass, and hence their ability to &lt;em&gt;generate&lt;/em&gt; heat would drop faster than their skin area, and hence their ability to &lt;em&gt;dissipate&lt;/em&gt; heat; meaning that if unaltered, smaller humans would rapidly run into problems of freezing to death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Small animals typically solve this through a number of methods: Higher metabolic rates, rounder bodies, and more fur. Small humans, i.e. babies also suffer under this, and solve it by having what is typically referred to as &quot;baby fat&quot;, a blubber that, among other things, aids thermoregulation.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, as the human body is scaled up, the opposite problem arises: The body becomes unable to dissipate heat quickly enough. Larger animals solve this problems with giant organs specifically suited to radiate heat, such as elephant ears; or through submersion in water, as seen is cetaceans and hippopotamuses; or simply through living in cold climates, such as the polar bear. (All of this is typically augmented by lower metabolic rates.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heat economy isn't the only problem with size, however:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Especially when scaling up, the strength of various structures in the body become problematic. Unusually (yet not even freakishly) tall humans generally have some manner of bone problems, and also often have problems with too small hearts, leading to low blood pressure, or too big ones, leading to heart failure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the change was gradual enough, with sufficient adaptation, this wouldn't &lt;em&gt;necessarily&lt;/em&gt; be a problem. After all, giraffes and elephants get on perfectly well; but a pump-valve heart such as we have cannot be scaled up indefinitely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With a continuous-flow heart, this limit could probably be stretched, but how that would even begin to work biologically I have no idea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further problems with very large humans include getting enough air flow through the lungs, the enormous chore it would be to stand up or sit down, and of course, just getting enough food to drive the enormous body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The long and short of it is: Anything less than about half a meter would probably leave us freezing to death; and anything more than two and a half meters is quite frankly a stretch (if you'll pardon the pun).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(There are people alive now that are more than two and a half meters tall, but they are not generally speaking in good health, although some do get on.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, all of this is predicated on the specific gravitational and atmospheric conditions on Earth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On another planet with a greater or lesser gravity, a different proportion of oxygen in the air, or just a denser atmosphere; many of these limits and limitations would be quite different indeed. (Which is why whales, living in such an alien world as the sea, can be an order of magnitude bigger than any animal that lives on land.)&lt;/p&gt;&#xA;" OwnerUserId="1095" LastEditorUserId="1095" LastEditDate="2014-07-21T17:50:17.687" LastActivityDate="2014-07-21T17:50:17.687" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19834" PostTypeId="2" ParentId="8535" CreationDate="2014-07-21T15:01:46.427" Score="4" Body="&lt;p&gt;As @WYSIWYG pointed, muscular atrophy is the main cause for height decrease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A spine injury leads to neural impairment and paresis / paralysis. This affects directly muscular trophism. It also limits physical activity, this being another favoring factor for muscular atrophy and overweight issues [1]. Association of bone degenerative processes (osteoporosis, osteopathy, osteolysis) is also a factor and it is dangerous because it promotes spinal cord injuries if vertebral height reduction amount is notable [2].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Focusing on muscular atrophy, here is how it can decrease height: by increasing vertebral column curvatures mostly on the upper region with articulating vertebrae. The vertebral column tends to gain a spring-like, spiral shape, associating accentuated cervical lordosis, accentuated thoracic  kyphosis and thoracic scoliosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FQ2Sc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;Image source: Scoliosis Treatment Alternatives. &lt;em&gt;&lt;a href=&quot;http://scoliosistreatmentalternatives.com/2012/05/chiropractic-for-scoliosis/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chiropractic for Scoliosis Treatment Review&lt;/a&gt;&lt;/em&gt; (2014). Accessed 21.07.2014 &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While reading the comments to the question I found something interesting:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;we know that the brain tells the body to grow, would a shock or something make the brain tell your body to shrink instead of growing?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, the brain (hypotalamus) initiates a neuroendocrine response that leads to growth hormone secretion. The secretion is about 700 micrograms/day in a young adolescent, while in a healthy adult it is about 400 micrograms/day [3]. The deficiency in an adult person leads to a tendency of fat mass increase and a relative decrease in muscle mass and, in many instances, decreased energy and quality of life [4]. The brain can't &quot;tell your body to shrink&quot;, but the lack of &quot;communication&quot; between the brain and organs leads to less to absolutely no use of that organ, thus inducing atrophy. The lack of both external and internal stimuli leads to atrophy (in general) [5].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Gupta N, White KT, Sandford PR. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16030513&quot; rel=&quot;nofollow noreferrer&quot;&gt;Body mass index in spinal cord injury -- a retrospective study.&lt;/a&gt; Spinal Cord. 2006 Feb;44(2):92-4. doi: &lt;a href=&quot;http://dx.doi.org/10.1038/sj.sc.3101790&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1038/sj.sc.3101790&lt;/a&gt;. PubMed PMID: 16030513.   &lt;/li&gt;&#xA;&lt;li&gt;Ji L, Dang XQ, Lan BS, Wang KZ, Huang YJ, Wen B, Duan HH, Ren F. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22945745&quot; rel=&quot;nofollow noreferrer&quot;&gt;Study on the safe range of shortening of the spinal cord in canine models.&lt;/a&gt; Spinal Cord. 2013 Feb;51(2):134-8. doi: &lt;a href=&quot;http://dx.doi.org/10.1038/sc.2012.99&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1038/sc.2012.99&lt;/a&gt;. PubMed PMID: 22945745. &lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Growth hormone,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Growth_hormone&amp;amp;oldid=616959802&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Growth_hormone&amp;amp;oldid=616959802&lt;/a&gt; (accessed July 21, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Molitch ME, Clemmons DR, Malozowski S, Merriam GR, Shalet SM, Vance ML, Stephens PA. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16636129&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evaluation and treatment of adult growth hormone deficiency: an Endocrine Society Clinical Practice Guideline.&lt;/a&gt; J. Clin. Endocrinol. Metab. 2006 May;91(5):1621-34. doi: &lt;a href=&quot;http://dx.doi.org/10.1210/jc.2005-2227&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1210/jc.2005-2227&lt;/a&gt;. PubMed PMID: 16636129. &lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Atrophy,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Atrophy&amp;amp;oldid=611770442&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Atrophy&amp;amp;oldid=611770442&lt;/a&gt; (accessed July 21, 2014).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-07-21T21:00:55.817" LastActivityDate="2014-07-21T21:00:55.817" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19836" PostTypeId="1" AcceptedAnswerId="19837" CreationDate="2014-07-21T16:21:49.547" Score="2" ViewCount="2218" Body="&lt;p&gt;I am trying to convert a MOL2 file (includes partial charges and hydrogen atoms) into a PDBQT file for re-scoring in AutoDock Vina. However, both approaches that I tried don't keep the hydrogen atoms from the MOL2 file (the PDBQT file doesn't contain hydrogen atoms).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The command I used for OpenBabel is &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;babel -i mol2 my.mol2 -o my.pdbqt&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;When I look at the documentation, they babel has a dedicated &quot;-d&quot; flag for removing hydrogens. So I assume that this shouldn't happen by default?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same thing happens if I use MGLTools&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;prepare_ligand4.py -l  my.mol2 &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Any ideas of what might be going on here?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your help!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;will append the MOL2 file if someone wants to try it:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;@&amp;lt;TRIPOS&amp;gt;MOLECULE&#xA;mymol2&#xA;   25    25     0     0     0&#xA;SMALL&#xA;USER_CHARGES&#xA;@&amp;lt;TRIPOS&amp;gt;ATOM&#xA;      1 C1         -1.0341   29.2934  -14.5590 C.ar      1 &amp;lt;0&amp;gt;       -0.1745 &#xA;      2 C2         -0.1917   29.9513  -13.6630 C.ar      1 &amp;lt;0&amp;gt;       -0.1483 &#xA;      3 C3         -2.3919   29.1585  -14.2689 C.ar      1 &amp;lt;0&amp;gt;       -0.1608 &#xA;      4 C4         -0.7068   30.4744  -12.4770 C.ar      1 &amp;lt;0&amp;gt;       -0.0956 &#xA;      5 C5         -2.9070   29.6816  -13.0828 C.ar      1 &amp;lt;0&amp;gt;       -0.1543 &#xA;      6 C6         -2.0573   30.3323  -12.2033 C.ar      1 &amp;lt;0&amp;gt;       -0.0209 &#xA;      7 C7         -5.0136   30.3602   -8.9792 C.2       1 &amp;lt;0&amp;gt;        0.9092 &#xA;      8 C8         -1.1556   29.8264   -9.1470 C.2       1 &amp;lt;0&amp;gt;        0.9071 &#xA;      9 C9         -2.6151   30.8987  -10.9189 C.3       1 &amp;lt;0&amp;gt;       -0.0262 &#xA;     10 C10        -3.5221   30.2951   -8.6255 C.3       1 &amp;lt;0&amp;gt;       -0.1568 &#xA;     11 C11        -2.5717   29.8912   -9.7583 C.3       1 &amp;lt;0&amp;gt;       -0.1554 &#xA;     12 O1         -5.7013   31.2223   -8.3667 O.co2     1 &amp;lt;0&amp;gt;       -0.8817 &#xA;     13 O2         -0.7003   30.9084   -8.6799 O.co2     1 &amp;lt;0&amp;gt;       -0.8929 &#xA;     14 O3         -5.3714   29.5329   -9.8669 O.co2     1 &amp;lt;0&amp;gt;       -0.8807 &#xA;     15 O4         -0.6188   28.6818   -9.1887 O.co2     1 &amp;lt;0&amp;gt;       -0.8571 &#xA;     16 H1         -0.6331   28.8861  -15.4824 H         1 &amp;lt;0&amp;gt;        0.0899 &#xA;     17 H2          0.8655   30.0564  -13.8891 H         1 &amp;lt;0&amp;gt;        0.1079 &#xA;     18 H3         -3.0478   28.6460  -14.9665 H         1 &amp;lt;0&amp;gt;        0.0917 &#xA;     19 H4         -0.0427   30.9855  -11.7849 H         1 &amp;lt;0&amp;gt;        0.2049 &#xA;     20 H5         -3.9661   29.5717  -12.8653 H         1 &amp;lt;0&amp;gt;        0.1145 &#xA;     21 H6         -2.0757   31.8190  -10.6595 H         1 &amp;lt;0&amp;gt;        0.0142 &#xA;     22 H7         -3.6485   31.2140  -11.1119 H         1 &amp;lt;0&amp;gt;        0.0547 &#xA;     23 H8         -3.4370   29.5769   -7.7988 H         1 &amp;lt;0&amp;gt;       -0.0109 &#xA;     24 H9         -3.2268   31.2722   -8.2199 H         1 &amp;lt;0&amp;gt;        0.0482 &#xA;     25 H10        -2.8394   28.8903  -10.1212 H         1 &amp;lt;0&amp;gt;        0.0739 &#xA;@&amp;lt;TRIPOS&amp;gt;BOND&#xA;    1     1     2 ar&#xA;    2     1     3 ar&#xA;    3     2     4 ar&#xA;    4     3     5 ar&#xA;    5     4     6 ar&#xA;    6     5     6 ar&#xA;    7     6     9 1&#xA;    8     7    10 1&#xA;    9     7    12 1&#xA;   10     7    14 2&#xA;   11     8    11 1&#xA;   12     8    13 1&#xA;   13     8    15 2&#xA;   14     9    11 1&#xA;   15    10    11 1&#xA;   16     1    16 1&#xA;   17     2    17 1&#xA;   18     3    18 1&#xA;   19     4    19 1&#xA;   20     5    20 1&#xA;   21     9    21 1&#xA;   22     9    22 1&#xA;   23    10    23 1&#xA;   24    10    24 1&#xA;   25    11    25 1&#xA;@&amp;lt;TRIPOS&amp;gt;SUBSTRUCTURE&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;h1&gt;EDIT:&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;The solution to the problem with &lt;code&gt;prepare_ligand4.py&lt;/code&gt; would be&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;prepare_ligand4.py -l  my.mol2  -U \&quot;&quot;&quot; -C&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;to keep the partial charges and hydrogen atoms (oddly, &lt;code&gt;-U &quot;&quot;&lt;/code&gt; didn't work for me: &lt;code&gt;prepare_ligand4.py: option -U requires argument&lt;/code&gt;)&lt;/p&gt;&#xA;" OwnerDisplayName="user6881" LastEditorDisplayName="user6881" LastEditDate="2014-07-21T18:22:05.433" LastActivityDate="2015-06-04T03:18:08.423" Title="MOL2 to PDBQT conversion via OpenBabel and MGLTools removes hydrogen atoms" Tags="&lt;bioinformatics&gt;&lt;pdb&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19837" PostTypeId="2" ParentId="19836" CreationDate="2014-07-21T16:25:46.903" Score="3" Body="&lt;p&gt;You saw my last &lt;a href=&quot;https://biology.stackexchange.com/questions/19749/how-to-use-autodock-just-for-rescoring&quot;&gt;answer of your question&lt;/a&gt;? you can do that easily, just use &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;prepare_ligand4.py -l  my.mol2 -A &quot;hydrogens&quot;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-07-21T16:25:46.903" CommentCount="15" ContentLicense="CC BY-SA 3.0" />
  <row Id="19838" PostTypeId="1" CreationDate="2014-07-21T17:58:54.243" Score="3" ViewCount="69" Body="&lt;p&gt;It is possible that life has invaded mars or the moon by way of probes rovers and other man made tech. How many years or generations of sequential and phenotypical diverge would be  necessary to establish the organism as astrobiology?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="3952" LastEditDate="2014-07-27T20:34:20.560" LastActivityDate="2014-07-27T20:34:20.560" Title="How much divergence would be needed for classifications as astrobiology?" Tags="&lt;terminology&gt;&lt;astrobiology&gt;&lt;classification&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19840" PostTypeId="1" AcceptedAnswerId="19902" CreationDate="2014-07-21T19:24:50.493" Score="3" ViewCount="2416" Body="&lt;p&gt;I have a microbiology question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When we put bacterial cells in sucrose solution with concentration higher than 0.5M we observe plasmolysis - the cytoplasmic membrane detaches from the cell wall due to water loss in order to balance the osmotic gradient. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If after that we put some lysozyme in the solution, the cells become spherical as they turn into spheroplasts, but they are still alive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we put lysozyme in a solution that contains bacterial cells, but no sucrose, they die. So my question is how does sucrose protect cells from lysis? &lt;/p&gt;&#xA;" OwnerUserId="3864" LastEditorUserId="3864" LastEditDate="2014-07-23T15:00:30.070" LastActivityDate="2014-07-23T16:47:29.663" Title="How does sucrose protect bacterial cells in lysozyme solutions?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19843" PostTypeId="1" AcceptedAnswerId="19844" CreationDate="2014-07-21T21:40:20.940" Score="3" ViewCount="1210" Body="&lt;p&gt;I've read that dogs can do move their ears independently, i.e., point one ear in the direction of a sound without having to point the other one at the same time. Is this a common trait with other canids, such as foxes? Can most eared mammals do this, with humans being an exception (except for a few exceptional humans)?&lt;/p&gt;&#xA;" OwnerUserId="8413" LastEditorUserId="5331" LastEditDate="2014-07-22T04:17:39.667" LastActivityDate="2014-07-22T04:17:39.667" Title="Can foxes move their ears independently?" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;hearing&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19844" PostTypeId="2" ParentId="19843" CreationDate="2014-07-22T00:46:49.320" Score="2" Body="&lt;p&gt;Yes, they can. Here are a couple pics I found of foxes moving their ears independently:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RdxYP.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HL1ZO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is something all canids can do &lt;a href=&quot;http://www.responsibledog.net/canine_senses.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;(1)&lt;/a&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0060113219&quot; rel=&quot;nofollow noreferrer&quot;&gt;(2)&lt;/a&gt; Btw, I can move my ears independantly. It's all in the finding the right muscles.&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2014-07-22T00:46:49.320" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19846" PostTypeId="2" ParentId="19794" CreationDate="2014-07-22T06:11:44.073" Score="4" Body="&lt;p&gt;The behavior can be explained evolutionarily just like any other trait. It came about either through adaptation, neutral evolution, or as a by-product of another adaptation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An intermediate step, like the one you suggested, is not required. But if it did occur, there's no reason to believe that such a trait would cause extinction. Bloody eyes, whether they squirt or not, could be beneficial in some species. We know that blood-squirting eyes appears to be a defensive trait. Take away the ability to squirt and the blood could provide defense in some other unexpected way, or it may have had nothing to do with defense at all. Maybe the blood was just a lubricant before, or maybe the blood somehow enhanced vision during a stressful event. Or maybe it was just there and didn't do anything; nothing good, but nothing bad. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's nothing special about this lizard. It does have a unique trait, but there's something novel in &lt;em&gt;every&lt;/em&gt; species. &lt;/p&gt;&#xA;" OwnerUserId="3061" LastActivityDate="2014-07-22T06:11:44.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19847" PostTypeId="2" ParentId="2076" CreationDate="2014-07-22T06:33:55.503" Score="0" Body="&lt;p&gt;A smell capsule with primary smells, concentrated non runny oils that can be heated up by a code sent to the capsule Then it will release the code, a built in fan will blow it to you from pc or phone, on a pc it could be renewed, maybe plugged in to a usb, Ive been thinking about this lately an have come to the conclusion that a smell Capsule would only need a collection of smells, if you type out banana there is a code behind the keys for the letter to appear, i think a smell program will be needed so that if some one sends you a coded image of a banana from there smell program the soon as you receive it and click on it the code will activate the same code in your program and you will smell the banana i have no idea how many primary smells there are or even if you can mix them but a collection of most common smells will do the job till the primary and mixing is masted,  I believe a pc is missing the smell capability and it will come along just as many other things have, it would be great to smell the ocean while watching ships or even while sailing one on a simulator, a heating of a oil scent will do the job fine, A thin wire sitting in each concentrated thick scented oil and all the different oils in separate compartments with there individual codes inside a complex capsule and a fan to blow out the heated one that the thin wire heated up     &lt;/p&gt;&#xA;" OwnerUserId="8421" LastEditorUserId="8421" LastEditDate="2014-07-22T08:40:50.363" LastActivityDate="2014-07-22T08:40:50.363" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19848" PostTypeId="1" AcceptedAnswerId="19849" CreationDate="2014-07-22T07:41:14.673" Score="0" ViewCount="13655" Body="&lt;p&gt;I know that ants have some sense of direction, but what is the physiology behind this sense?&lt;/p&gt;&#xA;" OwnerUserId="8292" LastEditorUserId="57" LastEditDate="2014-07-22T20:10:41.397" LastActivityDate="2014-07-22T20:10:41.397" Title="How do ants know where they are going without eyes?" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;ant&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ClosedDate="2014-07-22T22:51:11.180" ContentLicense="CC BY-SA 3.0" />
  <row Id="19849" PostTypeId="2" ParentId="19848" CreationDate="2014-07-22T08:00:43.077" Score="11" Body="&lt;p&gt;Well, first off, they have eyes, so there's that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, a lot of what ants wish to achieve can be done through a combination of a random walk and chemical trails.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When ants are exploring their surroundings, they are essentially wandering about without much in terms of a sense of purpose; laying down a chemical signature as they go.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When they find something interesting, like food, they use their own chemical trail to backtrack, laying down a new chemical trail indicating the nature of what they have discovered, making a kind of smell-road from the hill to the point of interest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any ants that subsequently come across this trail follow it, and subsequently join in transporting the food back to the hill.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An interesting implication of this behaviour is the antmill, wherein an ant will lose their trail, and revert to following a nearby ant. If the ant they follow are following &lt;strong&gt;them&lt;/strong&gt; to begin with, this can lead to a spiral of ants that can reach miles in diameter, consisting of confused ants walking until they die from exhaustion. &lt;/p&gt;&#xA;" OwnerUserId="1095" LastEditorUserId="1095" LastEditDate="2014-07-22T15:40:16.980" LastActivityDate="2014-07-22T15:40:16.980" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19850" PostTypeId="1" AcceptedAnswerId="19851" CreationDate="2014-07-22T08:02:15.937" Score="52" ViewCount="4018" Body="&lt;p&gt;What causes the noise when you crack a joint? Is joint cracking harmful? &lt;/p&gt;&#xA;" OwnerUserId="8424" LastEditorUserId="5331" LastEditDate="2014-07-22T09:11:59.930" LastActivityDate="2017-08-30T09:52:13.783" Title="Why does cracking a joint make noise?" Tags="&lt;bone-biology&gt;&lt;joints&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="19851" PostTypeId="2" ParentId="19850" CreationDate="2014-07-22T08:26:25.960" Score="46" Body="&lt;p&gt;The exact mechanism is unclear. Here are some possible causes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;rapid collapsing of cavities inside the joint [1];&lt;/li&gt;&#xA;&lt;li&gt;rapid ligament stretching [1];&lt;/li&gt;&#xA;&lt;li&gt;breaking of intra-articular adhesions [1];&lt;/li&gt;&#xA;&lt;li&gt;escaping gases from synovial fluid [2];&lt;/li&gt;&#xA;&lt;li&gt;movements of joints, tendons and ligaments [2];&lt;/li&gt;&#xA;&lt;li&gt;mechanic interaction between rough surfaces [2], mostly in pathological situations like arthritis (and it is called &lt;em&gt;crepitus&lt;/em&gt; [3]).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are no known bad effects of joint cracking [1, 4].&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There are no long term sequelae of these noises, and they do not lead to future problems. There is no basis for the admonition to not crack your knuckles because it can lead to arthritis. There are no supplements or exercises to prevent these noises [4].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And no good effects either:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Knuckle &quot;cracking&quot; has not been shown to be harmful or beneficial. More specifically, knuckle cracking does not cause arthritis [5].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Cracking joints,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Cracking_joints&amp;amp;oldid=617403659&quot;&gt;http://en.wikipedia.org/w/index.php?title=Cracking_joints&amp;amp;oldid=617403659&lt;/a&gt; (accessed July 22, 2014).&lt;/li&gt;&#xA;&lt;li&gt;The Library of Congress. Everyday Mysteries. &lt;em&gt;What causes the noise when you crack a joint?&lt;/em&gt; Available from &lt;a href=&quot;http://www.loc.gov/rr/scitech/mysteries/joint.html&quot;&gt;http://www.loc.gov/rr/scitech/mysteries/joint.html&lt;/a&gt; (accessed 22.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Crepitus,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Crepitus&amp;amp;oldid=615557134&quot;&gt;http://en.wikipedia.org/w/index.php?title=Crepitus&amp;amp;oldid=615557134&lt;/a&gt; (accessed July 22, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Johns Hopkins Sports Medicine Patient Guide to Joint Cracking &amp;amp; Popping. Available from &lt;a href=&quot;http://www.hopkinsortho.org/joint_cracking.html&quot;&gt;http://www.hopkinsortho.org/joint_cracking.html&lt;/a&gt; (accessed 22.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;WebMD, LLC. &lt;em&gt;Will Joint Cracking Cause Osteoarthritis?&lt;/em&gt; Available from &lt;a href=&quot;http://www.webmd.com/osteoarthritis/guide/joint-cracking-osteoarthritis&quot;&gt;http://www.webmd.com/osteoarthritis/guide/joint-cracking-osteoarthritis&lt;/a&gt; (accessed 22.07.2014)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-07-22T08:26:25.960" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19852" PostTypeId="1" AcceptedAnswerId="19853" CreationDate="2014-07-22T09:47:10.897" Score="1" ViewCount="353" Body="&lt;p&gt;I have a few questions in regards to attraction/stimulation in the immune system.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;What attracts leukocytes and antibodies to pathogens in the first place? &lt;/li&gt;&#xA;&lt;li&gt;What attracts CD4+ cells to professional antigen-presenting cells (APC)?&lt;/li&gt;&#xA;&lt;li&gt;What attracts CD8+ cells to cells with an antigen on a MHC-1 protein?&lt;/li&gt;&#xA;&lt;li&gt;What attracts macrophages to pathogens that have been tagged with antibodies?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Is it just a case of everything bumping into each other and if cells (and antibodies??) bump into chemokines and/or cytokines they will be stimulated (and not attracted) to stay around that area moving to an area of a greater concentration of chemokines and/or cytokines?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said point 1 can occur without chemokines and/or cytokines (in the case of antibodies, they could be taken/administered by the person).  While in case of point 3, (I may be wrong here) but chemokines and/or cytokines may not be present in the case of MHC-1?&lt;/p&gt;&#xA;" OwnerUserId="8426" LastActivityDate="2014-07-22T11:24:34.797" Title="What attracts cells to: pathogens, professional antigen-presenting cells, and cells with an antigen on its MHC-1 protein?" Tags="&lt;immunology&gt;&lt;antibody&gt;&lt;antibiotics&gt;&lt;antigen&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19853" PostTypeId="2" ParentId="19852" CreationDate="2014-07-22T10:20:00.133" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;What attracts leukocytes and antibodies to pathogens in the first&#xA;  place?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They just bump into them. If secreted antibody is already present in the blood then complement system can be activated. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What attracts CD4+ cells to professional antigen-presenting cells&#xA;  (APC)?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;APC release chemokines. All that is known is that this is a CC-type chemokine and signals via CCR4/CCR8 receptors. See &lt;a href=&quot;http://scholar.google.co.in/scholar?q=antigen+presenting+cells+chemotaxis+chemokine&amp;amp;hl=en&amp;amp;as_sdt=0&amp;amp;as_vis=1&amp;amp;oi=scholart&amp;amp;sa=X&amp;amp;ei=szfOU9aeFpajugS4vYLABg&amp;amp;ved=0CBkQgQMwAA&quot; rel=&quot;nofollow&quot;&gt;this list&lt;/a&gt; of articles (from Google Scholar). &lt;a href=&quot;http://jem.rupress.org/content/198/7/977.abstract&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; study reports a peptide called Chemrin that promotes chemotaxis via ChemR23 receptor.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What attracts CD8+ cells to cells with an antigen on a MHC-1 protein?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;CD8+/NK cells are activated by CD4+ cells before they kill their target. The MHC-1+antigenic peptide is just a mark for the cells that are to be attacked, as far as I understand.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What attracts macrophages to pathogens that have been tagged with&#xA;  antibodies?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Complement_system&quot; rel=&quot;nofollow&quot;&gt;Complement factors&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NOTE: Many of these concepts are old but still relevant. You should check out recent articles in this area for novel/atypical mechanisms.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-07-22T11:24:34.797" LastActivityDate="2014-07-22T11:24:34.797" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19856" PostTypeId="1" AcceptedAnswerId="34120" CreationDate="2014-07-22T11:48:04.347" Score="19" ViewCount="2208" Body="&lt;p&gt;I have been reading a fascinating paper: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848041/&quot;&gt;Valproate reopens critical-period learning of absolute pitch&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;18 individuals were given Sodium Valproate (VPA) for a fortnight during which they trained on a pitch-training game. Results suggest that VPA reopens the plasticity window that normally closes by adolescence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the paper seems to suggest that the exact mechanism of action is unknown.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Valproic acid is believed to have multiple pharmacological actions,&#xA;  including acute blockade of GABA transaminase to enhance inhibitory&#xA;  function in epileptic seizures and enduring effects on gene&#xA;  transcription as an histone deacetlyase (HDAC) inhibitor (Monti et&#xA;  al., 2009). Of relevance here is the epigenetic actions of this drug,&#xA;  as enhancing inhibition does not reactivate brain plasticity in&#xA;  adulthood (Fagiolini and Hensch, 2000), but reopening chromatin&#xA;  structure does (Putignano et al., 2007). While systemic drug&#xA;  application is a rather coarse treatment, the effects may differ&#xA;  dramatically by individual cell type (TK Hensch and P Carninci,&#xA;  unpublished observations). VPA treatment mimics Nogo receptor deletion&#xA;  to reopen plasticity for acoustic preference in mice (Yang et al.,&#xA;  2012), suggesting a common pathway through the regulation of&#xA;  myelin-related signaling which normally closes critical period&#xA;  plasticity (McGee et al., 2005). Future work will address the cellular&#xA;  actions of VPA treatment in the process of reactivating critical&#xA;  periods. Future MRI studies will also be needed to establish whether&#xA;  HDAC inhibition by VPA induces hyperconnectivity of myelinated,&#xA;  long-range connections concurrent with renewed AP ability (Loui et&#xA;  al., 2011).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So it is saying that the standard use of VPA is to increase GABA levels (which keeps firing rate down -- it is used as an antiepileptic), however it also acts as an HDAC inhibitor, which means it causes unwrapping of chromatin and consequently increased mRNA transcription, maybe even transcription of genes that would normally be entirely deactivated in an adult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my guess is that some protein is getting produced that messages neurons to generate new axon/dendrite growth and/or new synaptic connections.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone clarify how VPA might accomplish plasticity?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT (one month later): I have more detail, but I still can't quite make the connection. Here goes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neurites get wrapped by myelin/oligodendrocyte, which produces and exudes some of the chemical messagers {Nogo, OMgp, MAG}. The membrane surface of the neurite contains nogo 66 receptors (NgR-s) that get triggered by these messagers and inform the neuron to inhibit axon-growth. Somehow the 'HDAC inhibition' property of VPA is unwinding DNA enough to alter transcription rates of certain proteins, and one of these must be disabling the NgR.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But how is this happening?&lt;/p&gt;&#xA;" OwnerUserId="8435" LastEditorUserId="8435" LastEditDate="2014-08-23T16:46:26.223" LastActivityDate="2015-05-27T17:17:03.417" Title="How does Sodium Valproate cause neural plasticity" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;&lt;synapses&gt;&lt;neuroplasticity&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19859" PostTypeId="2" ParentId="8939" CreationDate="2014-07-22T13:24:35.867" Score="6" Body="&lt;p&gt;Wasps are &lt;strong&gt;extremely territorial creatures&lt;/strong&gt;. They also have &lt;strong&gt;great sight&lt;/strong&gt;. Wasp colonies will send out foragers and scouts to look for uninhabited areas with food in which they can build a nest. Because wasps are so fiercely territorial, a &lt;strong&gt;scout wasp will generally stay away from an area with another colony already in it&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of this fact fake wasps nest works!! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://docs.google.com/viewer?url=http%3A%2F%2Fwww.environmentalsociety.ca%2Fmain%2Fwp-content%2Fuploads%2F2011%2F05%2FFact-Sheet-Wasps.pdf&amp;amp;docid=903204c6cf64226baeac78b98d24690d&amp;amp;a=bi&amp;amp;pagenumber=1&amp;amp;w=800&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.environmentalsociety.ca/main/wp-content/uploads/2011/05/Fact-Sheet-Wasps.pdf&quot;&gt;http://www.environmentalsociety.ca/main/wp-content/uploads/2011/05/Fact-Sheet-Wasps.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-22T13:24:35.867" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19860" PostTypeId="2" ParentId="16436" CreationDate="2014-07-22T13:31:32.103" Score="4" Body="&lt;p&gt;Glucose and other ingested sugars have a natural affinity to bind to surface proteins on teeth (as well as many other proteins in tissues). This process is called glycosylation, and is expedited both by acidic environments (such as provided by the acidic soft drinks as indicated by The Last Word) or metabolism of adherent bacteria on the tooth surface (&lt;a href=&quot;http://www.jbc.org/content/early/2014/06/12/jbc.M114.565507&quot; rel=&quot;nofollow&quot;&gt;see one example&lt;/a&gt;). A discussion of oral cavity lubrication and how this influences tooth surfance glycosylation and biofilm formation has also &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0042600&quot; rel=&quot;nofollow&quot;&gt;been&lt;/a&gt; &lt;a href=&quot;http://www.biomedcentral.com/1471-2091/12/6&quot; rel=&quot;nofollow&quot;&gt;reported&lt;/a&gt;. The fuzzy feeling is a result of plaque formation. Plaques form as a byproduct of metabolism of bacteria on the tooth surfaces, that ingest and break down dietary sugars, and also secrete acids as a byproduct of this metabolism. The result, if left long enough, is plaque formation and eventually tooth decay. You can also notice this fuzzy feeling after a day or so of not brushing your teeth, as the bacteria have had a long time to metabolize the sugars ingested over that period to produce a plaque.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-07-22T13:31:32.103" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19861" PostTypeId="1" CreationDate="2014-07-22T15:09:11.203" Score="6" ViewCount="3101" Body="&lt;p&gt;I can lay down in a rested position with my mind at ease, but no matter how relaxed I am or for how long i do it, it seems I'll still need sleep eventually.  What's the difference - what is occurring during sleep that can't occur now matter how relaxed or rested you are?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if you know of any studies that have been done to try and mimic the benefits of sleep in a waking state - ie during some type of meditation or whatnot - I'd consider that relevant and interesting to know. &lt;/p&gt;&#xA;" OwnerUserId="6534" LastActivityDate="2014-07-24T05:25:20.307" Title="biologically speaking, what's the difference between sleeping and just resting?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19863" PostTypeId="1" CreationDate="2014-07-22T16:50:08.123" Score="2" ViewCount="326" Body="&lt;p&gt;Whether it's snacking on chips, munching on salad, or simply chewing gum, when I hear someone do it within an earshot, it drives me completely bonkers! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It doesn't matter if it's my girlfriend, my mom, someone sitting next to me at the office, or random stranger on the train, it bothers me just as much. The &quot;mouth open&quot; chewing type makes me want to get violent, and I often find myself in a blind rage. I also notice the slower, and more &quot;deliberate&quot; the chewing/munching is, the more I get tense and more it bothers me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes I feel like they are doing it on purpose, and completely fake, sort of like a commercial where they exaggerate the act of eating. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know more about &lt;a href=&quot;http://en.wikipedia.org/wiki/Misophonia&quot; rel=&quot;nofollow&quot;&gt;Misophonia&lt;/a&gt; or &quot;Hatred of Sound&quot;?&lt;/p&gt;&#xA;" OwnerUserId="8440" LastEditorUserId="8186" LastEditDate="2014-07-23T11:42:54.650" LastActivityDate="2014-07-24T14:23:31.300" Title="Why does chewing enrage me?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;hearing&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19864" PostTypeId="1" AcceptedAnswerId="24222" CreationDate="2014-07-22T17:07:43.147" Score="3" ViewCount="120" Body="&lt;p&gt;for a simulation I am developing I would like to know how the actin network in neurites is distributed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is actin confined to the periphery or is the whole neurite shaft containing actin with a rather constant density?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have any papers backing up the one or the other view don't hesitate to pass the link.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for answering.&lt;/p&gt;&#xA;" OwnerUserId="8196" LastActivityDate="2014-11-21T18:12:03.503" Title="Cross section of actin network in neurites" Tags="&lt;molecular-biology&gt;&lt;neuroscience&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19868" PostTypeId="2" ParentId="19850" CreationDate="2014-07-22T21:24:30.960" Score="15" Body="&lt;p&gt;Is joint-cracking harmful?  No.  Donald Unger was told by his mother that he'd get arthritis if he cracked his knuckles so he cracked his left knuckles every day for 60 years but never his right knuckles. He had no arthritis or any other problems in either hand and got a publication (D. L. Unger, &quot;Does knuckle cracking lead to arthritis of the fingers?&quot;, &lt;em&gt;Arthritis and Rheumatism&lt;/em&gt; 41(5):949&amp;ndash;950, 1998 &amp;ndash; &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/1529-0131(199805)41:5%3C949::AID-ART36%3E3.0.CO;2-3/abstract&quot;&gt;online version&lt;/a&gt; for those with appropriate access) and an &lt;a href=&quot;http://www.improbable.com/ig/ig-pastwinners.html#ig2009&quot;&gt;Ig Nobel Prize&lt;/a&gt; (2009) for his troubles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;OK, so one guy's knuckles prove nothing but who can resist the opportunity to cite an Ig Nobel winner?&lt;/p&gt;&#xA;" OwnerUserId="6928" LastActivityDate="2014-07-22T21:24:30.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19870" PostTypeId="1" AcceptedAnswerId="19911" CreationDate="2014-07-23T00:19:29.870" Score="4" ViewCount="71" Body="&lt;p&gt;I found a formula online which explained the reaction which occurred in the anode chamber of a microbial fuel cell but there was a typo&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\small NADH + Ferredoxin_{(ox)} (NADH-Ferredoxin\ Oxidoreductase) \longrightarrow NAD^+ + Ferredoxin_{(red)}\ \&#xA;Ferredoxin_{(red)} (Hydrogenase)\#61614;Ferredoxin_{(ox)} + 2H^+ + 2e^-$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I attempted to correct it but I'm not sure if I'm right could you check this and see if it's correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\small NADH-Ferredoxin\ Oxidoreductase \longrightarrow NAD^+ + Ferredoxin_{(red)}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\small Ferredoxin_{(red)} \longrightarrow Hydrogenase + Ferredoxin_{(ox)} + 2H^+ + 2e^-$&lt;/p&gt;&#xA;" OwnerUserId="6299" LastEditorUserId="3340" LastEditDate="2014-07-23T06:45:57.570" LastActivityDate="2014-07-23T18:12:39.363" Title="Microbial Fuel Cell Reaction" Tags="&lt;homework&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19872" PostTypeId="1" AcceptedAnswerId="19877" CreationDate="2014-07-23T02:45:13.683" Score="5" ViewCount="364" Body="&lt;p&gt;I'll use &lt;a href=&quot;http://en.wikipedia.org/wiki/Agaricus_bisporus&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Agaricus Bisporus&lt;/em&gt;&lt;/a&gt; as an example mushroom. If cultured in &lt;a href=&quot;http://www.neogen.com/Acumedia/pdf/ProdInfo/7149_PI.pdf&quot; rel=&quot;noreferrer&quot;&gt;potato dextrose yeast extract agar&lt;/a&gt;, will the resulting growth grow in a normal pattern? Will the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sporocarp_(fungi)&quot; rel=&quot;noreferrer&quot;&gt;sporocarps&lt;/a&gt; emerge from the surface (assuming there is one) properly? Will they develop inside the agar, or emerge an an angle?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Will the plant develop at a normal rate, and to normal proportions?&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2018-09-19T21:48:15.277" Title="How do mushrooms react to being grown in a microgravity environment?" Tags="&lt;mycology&gt;&lt;environment&gt;&lt;growth&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19873" PostTypeId="1" AcceptedAnswerId="19875" CreationDate="2014-07-23T02:51:32.997" Score="14" ViewCount="18611" Body="&lt;p&gt;Would I be able to genetically modify a plant at home? What equipment will be necessary? I think it might be a fun change from the 'norm' of regular hybridisation, to try some inter-family gene insertion, instead of staying within a genus. Are some plants easier to modify than others?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2014-11-12T16:38:58.190" LastActivityDate="2014-11-12T16:38:58.190" Title="Is it possible to genetically modify a plant at home?" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="5" CommentCount="6" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19874" PostTypeId="2" ParentId="19873" CreationDate="2014-07-23T04:24:41.290" Score="2" Body="&lt;p&gt;Yes, It is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An Indian Company IndieBB can help you get one.&#xA;&lt;a href=&quot;https://www.indiegogo.com/projects/indiebb-your-first-gmo&quot; rel=&quot;nofollow&quot;&gt;IndieBB: a DNA system designed to help you and your friends to explore genetic engineering and synthetic biology by making fluorescent bacteria at home.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-11-11T17:13:57.777" LastActivityDate="2014-11-11T17:13:57.777" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="19875" PostTypeId="2" ParentId="19873" CreationDate="2014-07-23T04:26:20.450" Score="9" Body="&lt;p&gt;Well, that depends on your home. ;) I think it is not an easy process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are &lt;strong&gt;two main methods&lt;/strong&gt; that are used to genetically modify plants:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Using the bacterium&lt;/strong&gt;, Agrobacterium tumifaciens, as a vector for the DNA. Agrobacterium has the ability to infect plants and insert DNA into a plant's genome. It causes crown gall tumours in natural infections. This method has mainly been used to modify broad leaved plants, such as sugar beet and oilseed rape, but is now also being applied to monocot species, such as maize and rice&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Particle bombardment&lt;/strong&gt; or biolistics where the DNA to be inserted is coated on minute gold particles and fired into plants cells. This approach is used for monocot plants such as maize and rice&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here I found simple step by step article, but lil bit old. may be there are new methods for this process.&#xA;&lt;a href=&quot;http://www.popsci.com/science/article/2011-01/life-cycle-genetically-modified-seed&quot;&gt;How To Genetically Modify a Seed, Step By Step&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8424" LastActivityDate="2014-07-23T04:26:20.450" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19876" PostTypeId="2" ParentId="16478" CreationDate="2014-07-23T08:11:08.357" Score="5" Body="&lt;p&gt;As most of the comment have pointed it out, It's &lt;strong&gt;nearly impossible&lt;/strong&gt; to find out. This is my try:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dr. L Alexander wrote in his paper, &lt;strong&gt;&lt;em&gt;Medical Science under Dictatorship&lt;/em&gt;&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hitler issued the first direct order for euthanasia in Germany on&#xA;  September 1, 1939, as his Panzers moved on the Blitzkrieg of Poland.&#xA;  Organizations with humanitarian-sounding names were immediately set up&#xA;  to execute &quot;health&quot; programs, again, under deceptively, euphemistic&#xA;  terms. For example, &lt;strong&gt;questionnaires collected by a &quot;Realm's Work&#xA;  Committee of Institutions for Cure and Care&quot; gathered and reported&#xA;  information on patients who had been ill five years or more and who&#xA;  were unable to work&lt;/strong&gt;. &lt;strong&gt;&quot;On the basis of name, race, marital status,&#xA;  nationality, next of kin, whether regularly visited and by whom, who&#xA;  bore financial responsibility, and so forth,&quot;&lt;/strong&gt; decisions were made at&#xA;  key universities about which &lt;strong&gt;patients should be killed&lt;/strong&gt; by&#xA;  psychiatrists who had themselves never seen the patients.Likewise, the&#xA;  &lt;strong&gt;&quot;Realm's Committee for Scientific Approach to Severe Illness Due to Heredity and Constitution&quot;&lt;/strong&gt; was exclusively devoted to the killing of&#xA;  children with congenital anomalies or chronic illnesses. In all,&#xA;  275,000 people were put to death in these killing centers before the&#xA;  Nazi Holocaust. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;h2&gt;&lt;img src=&quot;https://i.stack.imgur.com/4s6A0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/h2&gt;&#xA;&#xA;&lt;h2&gt;Law for the Prevention of Offspring with Hereditary Diseases (July 14, 1933)&lt;/h2&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Anyone suffering from a hereditary disease can be sterilized by a&#xA;  surgical operation if, according to the experience of medical science,&#xA;  there is a high probability that his offspring will suffer from&#xA;  serious physical or mental defects of a hereditary nature.    Anyone&#xA;  suffering from any of the following diseases is considered&#xA;  hereditarily diseased   under this law: &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;1. Congenital mental deficiency,&lt;/strong&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;2. Schizophrenia,&lt;/strong&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;3. Manic-depression,&lt;/strong&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;4. Hereditary epilepsy,&lt;/strong&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;5. Hereditary St. Vitus’ Dance (Huntington’s Chorea),&lt;/strong&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;6. Hereditary blindness,&lt;/strong&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;7. Hereditary deafness,&lt;/strong&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;8. Serious hereditary physical deformity.&lt;/strong&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Furthermore, anyone suffering from &lt;strong&gt;chronic alcoholism&lt;/strong&gt; can be sterilized.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If anyone is trying to get the statistical evidence that Eugenics have even remotely successful, have look at this table:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iqXam.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Current Top 50 death causes of Germany&lt;/strong&gt;. (Rate = &lt;span class=&quot;math-container&quot;&gt;$\frac{death}{1000}$&lt;/span&gt;)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;They have started various ways to brainwash people, one of them was movies.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;&lt;span class=&quot;math-container&quot;&gt;$\text{Ich klage an}$&lt;/span&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/ywoAQ.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/ywoAQ.jpg&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://www.filmportal.de/sites/default/files/imagecache/material_image/431CD4CC451D4EF786EFAF21772A266E_00104.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;filmportal.de&lt;/a&gt;)&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Plot: A woman suffering from multiple sclerosis pleads with doctors to kill her&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Current Scenario: Germany Rank &lt;span class=&quot;math-container&quot;&gt;$18^{th}$&lt;/span&gt; in the world in death due to Multiple sclerosis&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Alexander L. Medical science under dictatorship. N Engl J Med 1949;July 14. &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.life.org.nz/euthanasia/abouteuthanasia/history-euthanasia6&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.life.org.nz/euthanasia/abouteuthanasia/history-euthanasia6&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Table: &lt;a href=&quot;http://www.worldlifeexpectancy.com/country-health-profile/germany&quot; rel=&quot;nofollow noreferrer&quot;&gt;WHO, World Bank, UNESCO, CIA and individual country databases for global health and causes of death.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-02-27T16:01:11.423" LastActivityDate="2019-02-27T16:01:11.423" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="19877" PostTypeId="2" ParentId="19872" CreationDate="2014-07-23T08:46:34.007" Score="8" Body="&lt;p&gt;There were some experiments done in microgravity in longer space shuttle missions. The reports show that the fungi develop relatively normal but grow in random orientations instead of orientating upwards. See this images:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1hRjK.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The upper image shows fungi grown on earth which are subjected to normal gravity. The lower image shows fungi (actually only the fruiting bodies) which are grown during 7 day on the Spacelab D2 mission. The fungi obviously have a way of detecting gravity to let their fruiting body grow upwards. The image is from &lt;a href=&quot;http://www.mykoweb.com/articles/mycomorphology_2.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;, the article contains more information about this.&#xA;There is also a publication in this topic:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.davidmoore.org.uk/Assets/Printed_documents/my_reprints/1991_Moore_mushrooms_in_microgravityMycologist.pdf&quot; rel=&quot;noreferrer&quot;&gt;Mushrooms in microgravity - Mycology at the final frontier&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-23T08:46:34.007" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19879" PostTypeId="1" AcceptedAnswerId="19882" CreationDate="2014-07-23T09:59:16.630" Score="48" ViewCount="10078" Body="&lt;p&gt;Sometimes men wake up with an erection in the morning. Why does this happen?&lt;/p&gt;&#xA;" OwnerUserId="8424" LastEditorUserId="5563" LastEditDate="2015-05-10T17:45:10.497" LastActivityDate="2019-07-06T16:56:53.813" Title="What causes morning wood?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="19882" PostTypeId="2" ParentId="19879" CreationDate="2014-07-23T10:17:04.700" Score="54" Body="&lt;p&gt;&lt;strong&gt;Sometimes men wake up with an erection in the morning. Why does this happen?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Shortly speaking: &lt;a href=&quot;http://en.wikipedia.org/wiki/Rapid_eye_movement_sleep&quot; rel=&quot;nofollow noreferrer&quot;&gt;REM&lt;/a&gt; (Rapid Eye Movement) is one phase of sleep. During this phase, we dream and some of our &lt;a href=&quot;http://en.wikipedia.org/wiki/Neurotransmitter&quot; rel=&quot;nofollow noreferrer&quot;&gt;neurotransmitters&lt;/a&gt; are shut off. This include &lt;a href=&quot;http://en.wikipedia.org/wiki/Norepinephrine&quot; rel=&quot;nofollow noreferrer&quot;&gt;norepinephrine&lt;/a&gt;, which is involved in controlling erections. Norepinephrine prevents blood from entering the penis (preventing the &lt;a href=&quot;http://en.wikipedia.org/wiki/Erection&quot; rel=&quot;nofollow noreferrer&quot;&gt;erection&lt;/a&gt;). In absence of norepinephrine—during REM phase norepinephrine is absent—blood enters the penis, leading to an &lt;a href=&quot;http://en.wikipedia.org/wiki/Erection&quot; rel=&quot;nofollow noreferrer&quot;&gt;erection&lt;/a&gt;. This phenomenon is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Nocturnal_penile_tumescence&quot; rel=&quot;nofollow noreferrer&quot;&gt;nocturnal penile tumescence&lt;/a&gt;. Such erections typically occur 3 to 5 times a night. A related question concerning similar erections in women can be found &lt;a href=&quot;https://biology.stackexchange.com/questions/19915/what-get-women-instead-of-morning-wood&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;High pressure in the bladder may also lead to a &quot;reflex erection&quot;. This erection allows for preventing uncontrolled urination. The drawback is that when in the morning one has an erection and can't wait to pee it might get hard to accurately target the toilets!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=D1et5NgT6bQ&quot; rel=&quot;nofollow noreferrer&quot;&gt;This video&lt;/a&gt; is also a nice and easy source of information on the subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is it bad?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(&lt;em&gt;Reading my &quot;note&quot; below, you have edited your post to get rid of this question, thank you&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is perfectly healthy you don't have to worry about that. These erections are even thought of as contributing to penile health. At the opposite end of the spectrum, the absence of erections during the nights are an index of Erectile Dysfunction (E.D.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Be aware that medical questions are often considered off-topic on this site. Asking &quot;is it bad?&quot; turns your question into a medical one. Health-related questions (but not personal health) should be asked on &lt;a href=&quot;http://health.stackexchange.com&quot;&gt;health.SE&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4101" LastEditDate="2019-07-06T16:56:53.813" LastActivityDate="2019-07-06T16:56:53.813" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="19884" PostTypeId="2" ParentId="16234" CreationDate="2014-07-23T10:56:49.843" Score="2" Body="&lt;p&gt;There are two levels to take your question at.  The first is simpler but I'm not sure if it is what you are looking for:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you imagine the heart and all the blood vessels in your body as a closed plumbing system with no leaks (not entirely accurate) then when the heart contracts and squeezes the blood from the ventricles the total surface area the blood is pushing against has decreased - there is more blood in a smaller space.  This means that the pressure on the arteries from the blood has to increase when the heart contracts - in systole blood pressure is much higher than in diastole.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second level is a little more in depth:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cardiac output&lt;/strong&gt; (a measure of how much blood is being pumped around the body to the organs where it is needed) is defined as the product of &lt;strong&gt;stroke volume&lt;/strong&gt; and &lt;strong&gt;heart rate&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$CO = SV \times HR$$&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Heart rate is the number of times the heart beats per unit time&lt;/li&gt;&#xA;&lt;li&gt;Stroke volume is the amount of blood that is pumped out of the heart in one beat. It is this that is related to blood pressure.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The relation of stroke volume to blood pressure is defined by &lt;strong&gt;Starling's Law&lt;/strong&gt;.  This states that the more blood that is in the heart, the more its walls are stretched.  The more the walls are stretched, the harder the heart contracts in response.  This increases blood pressure as again more blood is displaced from the heart.&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2014-07-23T10:56:49.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19885" PostTypeId="1" CreationDate="2014-07-23T10:58:37.793" Score="4" ViewCount="1817" Body="&lt;p&gt;Today I had a slice of watermelon and when I reached the outer parts of the pulp I wondered why those are less sweet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whether or not the sugar occurs in crystalline form in watermelons is still an &lt;a href=&quot;https://biology.stackexchange.com/questions/8149/is-the-white-structure-on-the-break-of-bananas-or-watermelones-sugar&quot;&gt;open question&lt;/a&gt;, but a quick search on the internet did not yield acceptably thorough answers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The options I found are as follows (in descending order of personal preference):&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Watermelons &lt;a href=&quot;http://usatoday30.usatoday.com/news/science/wonderquest/2002-01-16-watermelon-seeds.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;ripen from the center&lt;/a&gt; outwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is the case, then watermelons wouldn't grow during the ripening, right? So they would need to achieve their final size before the ripening sets in. Or maybe it's the other way around: They ripen as they grow, and as such the center has the highest concentration of sugar.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;The sugar &lt;a href=&quot;https://answers.yahoo.com/question/index?qid=20080721230814AAQ22S0&quot; rel=&quot;nofollow noreferrer&quot;&gt;is needed&lt;/a&gt; by the new seedlings to grow. (Although I think this hypothesis has been disproven with apples.)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Has any of this been proven, has there been research done on this matter?&lt;/p&gt;&#xA;" OwnerUserId="5578" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2018-09-05T15:44:17.213" Title="Why are watermelons sweeter in the center?" Tags="&lt;botany&gt;&lt;fruit&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19886" PostTypeId="2" ParentId="19863" CreationDate="2014-07-23T12:15:51.963" Score="4" Body="&lt;h2&gt;Misophonia&lt;/h2&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Misophonia is a relatively unexplored chronic condition in which a&#xA;  person experiences autonomic arousal (analogous to an involuntary&#xA;  “fight-or-flight” response) to certain innocuous or repetitive sounds&#xA;  such as chewing, pen clicking, and lip smacking. Misophonics report&#xA;  anxiety, panic, and rage when exposed to trigger sounds, compromising&#xA;  their ability to complete everyday tasks and engage in healthy and&#xA;  normal social interactions.&lt;a href=&quot;https://i.stack.imgur.com/SbjWT.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;h2&gt;Physiology&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The auditory pathways may be functioning normally, but there is an abnormally strong reaction of the limbic (emotional system) and autonomic nervous system (body control system) to which the auditory system is intimately connected.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several definitions are listed for the disorder, including:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;“Abnormally strong negative reactions of the autonomic and limbic systems to specific sounds resulting from enhanced functional connections between the auditory and limbic systems for these sounds.  The auditory system works in a normal manner, without abnormally high activation.  At the behavioral level, sounds specific for a given patient evoke strong negative reactions.  This situation may cause general negative attitude to sound as well.  When fear is dominant emotion (patient is afraid of sound) phonophobia occurs (phobia – fear).  Phonophobia is a specific case of misophonia.”&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;“Selective sound sensitivity should be considered a type of misophonia, where soft sounds (typically eating and breathing sounds made by emotional attachment figures) are the focus, and the quality of those sounds causes annoyance and rage in the listener.” &lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;3&quot;&gt;&#xA;&lt;li&gt;&lt;p&gt;“Pre-puberty seems to be a very common age of onset for the majority of those with misophonia, with lifetime persistence for most cases, and there appears to be a genetic component.”&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;“Misophonia can be considered abnormally strong connections between the autonomic and limbic resulting from enhanced connections between the auditory and limbic systems.  These connections encompass both a high level of cortical level loop with involvement with cognition as well as subconscious connections, most probably involving the link between the medial geniculate body and the amygdale. The functions of these connections are governed by the principles of conditioned reflexes.”&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://lifewithmisophonia.files.wordpress.com/2012/02/limbic.gif&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://lifewithmisophonia.files.wordpress.com/2012/02/ear-anatomy.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SbjWT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;source:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/SbjWT.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691507/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Misophonia: physiological investigations and case descriptions&lt;/a&gt;&lt;br&gt;&#xA;[2] &lt;a href=&quot;http://www.misophonia-provider.com/What_is_Misophonia_4S_.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;MISOPHONIA 4S Provider Network USA&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Great Site: &lt;a href=&quot;http://lifewithmisophonia.wordpress.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://lifewithmisophonia.wordpress.com/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.273" LastActivityDate="2014-07-24T14:23:31.300" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19887" PostTypeId="1" AcceptedAnswerId="24726" CreationDate="2014-07-23T12:35:56.867" Score="3" ViewCount="348" Body="&lt;p&gt;Ants protect &lt;a href=&quot;http://en.wikipedia.org/wiki/Aphid&quot; rel=&quot;nofollow&quot;&gt;aphids&lt;/a&gt; from their predators (such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Ladybird&quot; rel=&quot;nofollow&quot;&gt;ladybirds&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Aphids and other hemipteran insects secrete a sweet liquid called honeydew, when they feed on plant sap. The sugars in honeydew are a high-energy food source, which many ant species collect. In some cases, the aphids secrete the honeydew in response to ants tapping them with their antennae. &lt;strong&gt;The ants in turn keep predators away from the aphids&lt;/strong&gt; and will move them from one feeding location to another. (source: &lt;a href=&quot;http://en.wikipedia.org/wiki/Ant&quot; rel=&quot;nofollow&quot;&gt;wiki: Ant&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Does a &lt;strong&gt;&lt;em&gt;presence of&lt;/strong&gt; a large amount of &lt;strong&gt;ants&lt;/em&gt;&lt;/strong&gt; on a plant in my garden (especially fruit trees, willow trees, flowers, vegetables) mean that the plant &lt;em&gt;has been &lt;strong&gt;infested by aphids&lt;/em&gt;&lt;/strong&gt;? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's &lt;em&gt;easier to spot the ants&lt;/em&gt; rather than the relatively smaller aphids so I am wondering if I may use this as a trigger for using an anti-aphid pesticide before the aphids start causing visible damage to the plants.&lt;/p&gt;&#xA;" OwnerUserId="8198" LastEditorUserId="8198" LastEditDate="2014-09-19T09:13:12.833" LastActivityDate="2014-12-09T13:21:07.720" Title="Does a presence of ants on a plant mean that the plant has been infested by aphids?" Tags="&lt;botany&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19888" PostTypeId="1" AcceptedAnswerId="19892" CreationDate="2014-07-23T13:21:43.263" Score="7" ViewCount="10063" Body="&lt;p&gt;I was asking myself this weird question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you get up or stand up too fast, sometimes, you see something like a dark veil, and you aren't able to see anything distinctly for 2 or 3 seconds, then it come back to normal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you know what causes this weird phenomenon (biologically speaking), or am i the only weird person feeling this sometimes?&lt;/p&gt;&#xA;" OwnerUserId="8331" LastActivityDate="2018-09-04T21:57:47.333" Title="Dark veil when getting up too fast" Tags="&lt;neuroscience&gt;&lt;eyes&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19889" PostTypeId="2" ParentId="19515" CreationDate="2014-07-23T13:23:41.853" Score="5" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Steroid hormones produce a slow response because they do not have secondary messenger&lt;/strong&gt;&lt;br&gt;&#xA;It's true that steroids don't have secondary messengers because they don't need them - they can go directly into a cells nucleus and affect transcription there.  This wouldn't slow down the response by much, however.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Slow response is due to lack of cell membrane receptors and amplification enzymes&lt;/strong&gt;&lt;br /&gt;&#xA;This is just the inverse of the first option, which again isn't really a cause of slowing down the response.  Steroids are amplified in that they act directly on DNA at the very first step of the synthesis pathways so don't need much amplification.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Movement of this hormone is very slow in blood&lt;/strong&gt;&#xA;&lt;br /&gt; Again I don't think there is much to this option, the difference in speed of distribution of steroid and peptide hormones is likely to be minimal&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This leaves us with:&lt;br /&gt;&#xA; 4. &lt;strong&gt;None of the above&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would personally have gone with this answer.  Steroids have a long time of action because they require the new transcription of genes that they activate.  This process takes time and consistent doses are needed to maintain the effect.&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2014-07-23T13:23:41.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19890" PostTypeId="2" ParentId="19861" CreationDate="2014-07-23T13:24:07.967" Score="2" Body="&lt;h2&gt;Difference between rest and sleep&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There are many factors which describe the difference between rest and sleep. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Rest&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Rest occurs with conscious breathing. This allows the autonomic nervous system (ANS) to rest. The autonomic nervous system belongs to the peripheral nervous system. ANS controls many organs and muscles in the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In most situations, people do not know about the workings of the ANS since it functions in an involuntary, reflexive manner. For instance, we hardly notice if blood vessels change size. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the same case when our heart beats faster. There are some people who can control some of the functions in the body and can know the heart rate or blood pressure. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sleep&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Sleep it is a natural state of rest for mind and body. It happens in cyclic pattern. This can be one of the reasons to describe the difference between rest and sleep. There are four stages of sleep. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the first stage of sleep, there is low-frequency, low-amplitude $\theta$ waves. This stage last several minutes before you enters into the next stage of sleep. In stage 2 of sleep, you brain moves into low frequency. In the third stage of sleep, you receive more high-amplitude $\delta$ waves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During stage 4, the delta waves account for more of your brain activity and then they return back to stage 1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Resting is more like being couch potatoes.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rest is important for health and sleep is a necessary factor. You need both for your physical and mental activity to create energy. When the energy level goes down and wastes increase, there is tiredness and body needs rest. When you take rest, energy is restored. All the waste in the body gets extinguished. Rest and sleep are dependent upon each individual’s ability to relax. If an individual is tensed, he cannot be in the state of rest. Rest is taken to counteract fatigue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.theatlantic.com/health/archive/2012/09/when-you-cant-sleep-how-good-is-lying-in-bed-with-your-eyes-closed/262484/&quot; rel=&quot;nofollow&quot;&gt;http://www.theatlantic.com/health/archive/2012/09/when-you-cant-sleep-how-good-is-lying-in-bed-with-your-eyes-closed/262484/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] &lt;a href=&quot;http://insomnia.ygoy.com/difference-between-rest-and-sleep/&quot; rel=&quot;nofollow&quot;&gt;http://insomnia.ygoy.com/difference-between-rest-and-sleep/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-23T13:24:07.967" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19891" PostTypeId="1" AcceptedAnswerId="19897" CreationDate="2014-07-23T13:25:35.050" Score="5" ViewCount="391" Body="&lt;p&gt;There are approximately 20k protein-coding genes found in the human genome. This number is presumably very small when considering all the genomes found in the diverse microbes associated with the human body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there an estimate for the total number of protein-coding genes found in human microbiome? &lt;/p&gt;&#xA;" OwnerUserId="3061" LastEditorUserId="8186" LastEditDate="2014-07-23T17:23:51.693" LastActivityDate="2014-07-23T17:23:51.693" Title="How many different protein coding genes are in the Human Biome?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;genomics&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19892" PostTypeId="2" ParentId="19888" CreationDate="2014-07-23T13:38:02.483" Score="14" Body="&lt;p&gt;It's caused by a sudden shift in the pressure needed to circulate blood to your brain which your body fails to respond to sufficiently quickly. This results in a sudden loss of blood pressure termed &lt;a href=&quot;http://en.wikipedia.org/wiki/Orthostatic_hypotension&quot;&gt;Orthostatic Hypotension&lt;/a&gt; which, in term, results in a transitory reduction in the blood supply necessary for brain function. You experience a momentary loss of vision for the same reason that you would if someone strangles you.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2014-07-23T13:38:02.483" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19894" PostTypeId="2" ParentId="19891" CreationDate="2014-07-23T13:49:08.477" Score="3" Body="&lt;h2&gt;Human Microbiome Project&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;According to Published data on HMP website:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The human microbiome consists of all the microorganisms that reside in or on the human body. &lt;/li&gt;&#xA;&lt;li&gt;They may cause illness but some are necessary for good health.&lt;/li&gt;&#xA;&lt;li&gt;There total count is 10 times more than Human cells.&lt;/li&gt;&#xA;&lt;li&gt;~800 genomes had been sequenced.&lt;/li&gt;&#xA;&lt;li&gt;~5000 Human sample had been used.&lt;/li&gt;&#xA;&lt;li&gt;Include 14 disease project samples.&lt;/li&gt;&#xA;&lt;li&gt;Total data stored on the DACC resource is 14 terabytes.&lt;/li&gt;&#xA;&lt;li&gt;Total protein(~8 million) coding genes found to be 360x of number of human genes&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_Microbiome_Project&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Human_Microbiome_Project&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] &lt;a href=&quot;http://commonfund.nih.gov/hmp/index&quot; rel=&quot;nofollow&quot;&gt;http://commonfund.nih.gov/hmp/index&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-07-23T16:21:41.170" LastActivityDate="2014-07-23T16:21:41.170" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="19896" PostTypeId="1" CreationDate="2014-07-23T15:06:22.930" Score="5" ViewCount="3104" Body="&lt;p&gt;Where can I find a list of enzyme cofactors and/or co-enzymes, ordered by how common they are?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, $O_2$, $H_2O$, $ATP$, $ADP$, $NAD$, should be ranked in the first places, because they participate in most reactions.&lt;/p&gt;&#xA;" OwnerUserId="561" LastEditorUserId="561" LastEditDate="2014-07-24T13:20:08.413" LastActivityDate="2016-07-04T14:56:43.983" Title="Where can I find a list of common enzyme cofactors and/or co-enzymes?" Tags="&lt;metabolism&gt;&lt;literature&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19897" PostTypeId="2" ParentId="19891" CreationDate="2014-07-23T15:11:45.907" Score="5" Body="&lt;p&gt;The Human Microbiome Project collected samples as shown in the image below from healthy volunteers:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FMnKs.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They give an estimate of about 8 Million genes in the human microbiome, which is about 360x the number of genes in the human genome. See &lt;a href=&quot;http://www.nih.gov/news/health/jun2012/nhgri-13.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for their press release with a lot of information. Additionally these two articles are as well interesting, if you want to dive deeper into the stuff:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v486/n7402/full/nature11209.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;A framework for human microbiome research&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Structure, function and diversity of the healthy human microbiome&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-23T15:11:45.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19898" PostTypeId="2" ParentId="19896" CreationDate="2014-07-23T15:28:19.023" Score="3" Body="&lt;h2&gt;Cofactor:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;coenzymes are organic molecules that are required by certain enzymes to carry out catalysis.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Database:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ebi.ac.uk/thornton-srv/databases/CoFactor/&quot; rel=&quot;nofollow noreferrer&quot;&gt;CoFactor - The organic enzyme cofactor database&lt;/a&gt; of EBI&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Examples:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Cz9bz.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-23T15:28:19.023" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19899" PostTypeId="2" ParentId="19896" CreationDate="2014-07-23T15:31:01.470" Score="4" Body="&lt;p&gt;Check &lt;a href=&quot;http://www.ebi.ac.uk/thornton-srv/databases/CoFactor/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; out. This resource lists organic cofactors and the associated enzymes. &#xA;See the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cofactor_%28biochemistry%29&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; page also.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many metals also serve as prosthetic groups in enzymes. They include- Magnesium, Manganese, Iron, Cobalt, Nickel, Copper, Zinc, Molybdenum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;FeS clusters are also an important part in many important enzymes in mitochondria and plastids. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-07-23T15:31:01.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19900" PostTypeId="1" AcceptedAnswerId="19901" CreationDate="2014-07-23T15:35:06.343" Score="4" ViewCount="768" Body="&lt;p&gt;I am stuck in trouble while pouring LB agar onto my petri dishes. I had to add kanamycin to my plates just before it started to solidify, out of forgetfulness, which I tried to mix using the tip. The plate was such a disaster! Is there a way to melt the agar in the plate and re-solidify it evenly.&lt;br&gt;&#xA;I use falcon sterile plastic petri dish.&lt;/p&gt;&#xA;" OwnerUserId="8142" LastActivityDate="2014-07-23T15:41:57.273" Title="Re-solidify disturbed agar plates" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19901" PostTypeId="2" ParentId="19900" CreationDate="2014-07-23T15:41:57.273" Score="4" Body="&lt;p&gt;Yes. It is quite simple actually. Do this inside a clean laminar hood:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Take a clean sterile scalpel blade or any other sterile long object. 1ml pipette tip would also do.&lt;/li&gt;&#xA;&lt;li&gt;Cut the agar on your plate. Scrape off cleanly.&lt;/li&gt;&#xA;&lt;li&gt;Put it in a sterile glass bottle.&lt;/li&gt;&#xA;&lt;li&gt;Heat in microwave&lt;/li&gt;&#xA;&lt;li&gt;Add kanamycin&lt;/li&gt;&#xA;&lt;li&gt;Pour back&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Another solution is to coat the agar surface with kanamycin just like spread plating. Check the appropriate concentrations.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-07-23T15:41:57.273" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19902" PostTypeId="2" ParentId="19840" CreationDate="2014-07-23T16:42:57.607" Score="2" Body="&lt;p&gt;This is an interesting question and as often, it has been noted by someone before. In this case it has been a researcher named Claes Weibull, who did his research in the 1950s. He noted (as you did) that sucrose has a protective function on the generation of protoplasts from Bacillus megaterium) with lysozyme. He published the following figure (from the first paper below):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JW2iX.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He did not really explain the phenomenon, but speculated about protective function of the sugar in solution when the bacterial cell wall is removed. This also works with PEG in solution (see the third paper below).&#xA;He published a number of papers on this (if you look him up in Pubmed, you will find more articles, but these seem most relevant):&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC317463/&quot; rel=&quot;nofollow noreferrer&quot;&gt;The isolation of protoplasts from Bacillus Megaterium by controlled treatment with lysozyme&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/13117796&quot; rel=&quot;nofollow noreferrer&quot;&gt;Characterization of the protoplasmic constituents of bacillus&#xA;megaterium.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/13262041&quot; rel=&quot;nofollow noreferrer&quot;&gt;Osmotic properties of protoplasts of Bacillus megaterium.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;It seems also possible to cultivate these protoplasts on agar plates and let them form &quot;normal shaped&quot; bacteria again:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC236197/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Morphological study of the reversion to bacillary form, of Bacillus&#xA;megaterium protoplasts.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-23T16:42:57.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19904" PostTypeId="1" AcceptedAnswerId="19905" CreationDate="2014-07-23T16:52:54.257" Score="6" ViewCount="2335" Body="&lt;p&gt;Why do we feel terribly cold on catching fever of any sort, however our body becomes hotter?&#xA;Why is it that a rise in temperature makes the sufferer feel colder? Also, sweating symbolises betterment of the conditions. Why?&#xA;{This question has been asked with reference to personal experiences}&lt;/p&gt;&#xA;" OwnerUserId="8216" LastActivityDate="2014-07-23T17:05:11.880" Title="Why do we feel cold on having fever?" Tags="&lt;human-biology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19905" PostTypeId="2" ParentId="19904" CreationDate="2014-07-23T17:05:11.880" Score="5" Body="&lt;p&gt;Body temperature results from a balance between the heat generated by our cells and the heat “lost” to the environment. Heat created by our cells comes from the energy used to keep us alive. Heat is lost through our skin and the air we breathe out. Human beings have an average temperature of 98.6 degrees Fahrenheit. The brain monitors body temperature and controls our bodies to keep our temperature within the normal range.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you get a fever when you’re sick, it’s because your brain has told your body to get hotter. It directs the body to make a number of changes to correct the imbalance. Those changes include increasing heat production within the body (by shivering, for example) and reducing heat loss to the environment. Heat loss is reduced by decreasing blood flow to the skin. &lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-23T17:05:11.880" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19907" PostTypeId="2" ParentId="19861" CreationDate="2014-07-23T17:24:28.317" Score="1" Body="&lt;p&gt;REST is not a deep sensation. We define various types of waves that are drawn using electroencephalogram.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;$\alpha$ waves: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Awake but resting position. &lt;/li&gt;&#xA;&lt;li&gt;Frequency: 8-13 Hz.&lt;/li&gt;&#xA;&lt;li&gt;They originate from occipital region&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;$\beta$ waves:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Alert wide awake person.&lt;/li&gt;&#xA;&lt;li&gt;They originate from frontal region.&lt;/li&gt;&#xA;&lt;li&gt;Frequency about 14-30 Hz.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;$\theta$ waves:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;They occur under stress and in case one is drowsy.&lt;/li&gt;&#xA;&lt;li&gt;Frequency about 4-7 Hz.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;$\delta$ waves:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;These originate when person is in deep sleep.&lt;/li&gt;&#xA;&lt;li&gt;Frequency about 1-3 Hz.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8088" LastEditorUserId="8186" LastEditDate="2014-07-24T05:25:20.307" LastActivityDate="2014-07-24T05:25:20.307" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19908" PostTypeId="1" AcceptedAnswerId="19943" CreationDate="2014-07-23T17:24:53.323" Score="10" ViewCount="202" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;General concept&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://digitalcommons.wayne.edu/humbiol/vol85/iss4/1/&quot; rel=&quot;noreferrer&quot;&gt;Cochran and Harpending (2013)&lt;/a&gt;, mothers transmits on average a number $x$ of new mutations to their offspring. This number $x$ is independent of the age of the Mother. Fathers, however transmit a number of new mutations to their offsprings that is very much dependent on the age of the father for developmental reasons. In short (and probably poorly stated due to my lack of knowledge in physiology), spermatogenesis is a continuous process that occurs during the lifetime of the individual while the creation of ovules occurs once and are then stocked.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Human example&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://digitalcommons.wayne.edu/humbiol/vol85/iss4/1/&quot; rel=&quot;noreferrer&quot;&gt;Kong et al.(2012)&lt;/a&gt;, in humans the mother transmit on average $15$ new mutations and the father transmit on average $25 + 2(g-20)\space\space$ new mutations, where $g$ is the age of the father. For example, a 30-year-old father transmits $25 + 2(30-20) = 45\space\space$ new mutations. (This approximation holds only for men older than 20 years).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question: How about plants?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Do you think that in plants too, male and female organs &lt;code&gt;(or individuals for (gyno/andro)diocious species and eventually sequential hermophroditic species)&lt;/code&gt; transmit a different number of new mutations for similar developmental reasons?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Do you think that in plants the number of new mutations is age-dependent in males but not in females alike in humans?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Do we have any estimate of the sex and age-specific number of new mutations transmitted in plants?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-01-29T22:06:46.310" LastActivityDate="2015-01-29T22:21:16.447" Title="Gender and age-specific mutation rate in plants" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;plant-physiology&gt;&lt;reproduction&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19910" PostTypeId="1" AcceptedAnswerId="19912" CreationDate="2014-07-23T17:53:34.863" Score="3" ViewCount="7185" Body="&lt;p&gt;Why do we have a running nose for quite some time after crying? It persists even after we stop crying. Why is it so? I have faced this always. Also, why does our nose redden on crying for long?&lt;/p&gt;&#xA;" OwnerUserId="8216" LastActivityDate="2014-07-23T18:05:50.890" Title="Why does crying lead to a running nose and reddened nose tip?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19911" PostTypeId="2" ParentId="19870" CreationDate="2014-07-23T18:03:04.647" Score="1" Body="&lt;h2&gt;Anode reaction,&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;$\small Glucose + 2NAD^+ (Embden-Meyerhof pathway) \leftrightharpoons 2 Pyruvate + 2NADH$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\small Pyruvate + Ferredoxin_{(ox)} (Pyruvate-ferredoxin Oxidoreductase) \leftrightharpoons Acetyl-CoA + CO_2 + Ferredoxin_{(red)}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\small NADH + Ferredoxin _{(ox)} (NADH-Ferredoxin Oxidoreductase) \leftrightharpoons NAD^+ + Ferredoxin_{(red)}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$Ferredoxin_{(red)} (Hydrogenase)\leftrightharpoons Ferredoxin_{(ox)} + 2H^+ + 2e^-$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[Last one: &lt;a href=&quot;http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase]&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase]&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Cathode reaction,&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;$4 H^+  + 4e^- + O_2 \leftrightharpoons H_2O$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$C_6H_{12}O_6 + 6O_2 \leftrightharpoons 6 CO_2 + 6 H_2O, DG° = - 2870 kj$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Full paper: &lt;a href=&quot;http://www.altenergymag.com/emagazine.php?issue_number=07.04.01&amp;amp;article=haldia&quot; rel=&quot;nofollow&quot;&gt;http://www.altenergymag.com/emagazine.php?issue_number=07.04.01&amp;amp;article=haldia&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-07-23T18:12:39.363" LastActivityDate="2014-07-23T18:12:39.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19912" PostTypeId="2" ParentId="19910" CreationDate="2014-07-23T18:05:50.890" Score="2" Body="&lt;p&gt;When you cry, you produce tears, which come out of your tear ducts. These are not only open to the eyes but also have a connection to your nose, see the image below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ufR73.gif&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A part of your tears runs through this connection and mixes with the mucus which is present in your nasal system making it thinner and allow it to flow more easily. If the tear flow is prolonged, the nose will produce more mucus and make your nose running for a longer time. The nose appears redder because the blood flow is increased. This is partly due to the production of more mucus and also because you repeatedly touch the nose when using a handkerchief.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-23T18:05:50.890" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19913" PostTypeId="1" AcceptedAnswerId="19914" CreationDate="2014-07-23T18:14:51.783" Score="4" ViewCount="768" Body="&lt;p&gt;My bio book refers to HEMOZOIN that is responsible for the shiver during malaria. How does hemozoin work to raise the body heat?&lt;/p&gt;&#xA;" OwnerUserId="8216" LastEditorUserId="8216" LastEditDate="2014-07-24T00:49:00.817" LastActivityDate="2014-07-24T05:01:03.870" Title="What does hemozoin do?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19914" PostTypeId="2" ParentId="19913" CreationDate="2014-07-23T18:54:11.410" Score="3" Body="&lt;p&gt;That is correct. When plasmodium infects red blood cells, it consumes the hemoglobin in the cell, leaving the heme behind, which they can not metabolize (heme is a heterocyclic porphyrine ring with an iron atom coordinated in the center). Since the heme (or $\alpha$-hematin) causes the production of reactive oxygen species and thus oxidative stress, it has to be removed from the cell. This is done by the conversion into the insoluble and inactive hemozoin (or $\beta$-hematin). This crystalizes in the cell and is not causing any harm to the parasite. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17111179&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the parasite finishes this development step, the cells burst and set their interior free into the blood stream. Among the substances released in this step are hemozoin and also glucose phosphate isomerase which stimulate macrophages to secrete cytokines and other factors which then cause the fever and the shivering observed in malaria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See here for more details: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15611273&quot; rel=&quot;nofollow&quot;&gt;Hemozoin Induces Macrophage Chemokine Expression through Oxidative&#xA;Stress-Dependent and -Independent Mechanisms&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24550911&quot; rel=&quot;nofollow&quot;&gt;Malarial pigment hemozoin and the innate inflammatory response.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23998019&quot; rel=&quot;nofollow&quot;&gt;Effect of malaria components on blood mononuclear cells involved in&#xA;immune response.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="3340" LastEditDate="2014-07-24T05:01:03.870" LastActivityDate="2014-07-24T05:01:03.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19915" PostTypeId="1" AcceptedAnswerId="19916" CreationDate="2014-07-23T18:57:02.857" Score="19" ViewCount="78796" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/19879/what-causes-morning-wood&quot;&gt;There was question&lt;/a&gt; about what causes &quot;morning wood.&quot; It was answered that the erection in the morning is caused by decline of norepinephrine during REM sleep. Which in part allows to prevent uncontrolled urination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: How does the decline in norepinephrine affect women? They obviously don't get erection.&lt;/p&gt;&#xA;" OwnerUserId="6930" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2016-05-14T15:26:57.163" Title="What is the female equivalent of the morning erection that some men experience?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19916" PostTypeId="2" ParentId="19915" CreationDate="2014-07-23T19:22:23.680" Score="24" Body="&lt;p&gt;Women have erections too! These erections are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Clitoral_erection&quot; rel=&quot;nofollow noreferrer&quot;&gt;clitoral erection&lt;/a&gt;. Clitoral erections are usually accompanied with &lt;a href=&quot;http://en.wikipedia.org/wiki/Vaginal_lubrication&quot; rel=&quot;nofollow noreferrer&quot;&gt;vaginal lubrification&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just like men (see &lt;a href=&quot;https://biology.stackexchange.com/questions/19879/what-causes-morning-wood&quot;&gt;here&lt;/a&gt;), the absence of norepinephrine during the &lt;a href=&quot;http://en.wikipedia.org/wiki/Rapid_eye_movement_sleep&quot; rel=&quot;nofollow noreferrer&quot;&gt;REM&lt;/a&gt; phase of the sleep causes erections. In women, this phenomenon is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Nocturnal_clitoral_tumescence&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nocturnal clitoral tumescence&lt;/a&gt; while it is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Nocturnal_penile_tumescence&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nocturnal penile tumescence&lt;/a&gt; in men. In women, not only the clitoris get engorged with blood but the vagina too.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2016-05-14T15:26:57.163" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19918" PostTypeId="1" AcceptedAnswerId="19923" CreationDate="2014-07-23T22:54:25.920" Score="11" ViewCount="6124" Body="&lt;p&gt;I'm writing a novel in which the main character's perception and thought processes are sped up considerably, in essence slowing down the world around him. To others, it seems like his reactions are far faster than normal. Of course, there's a fantasy explanation for this in the story, but it led me to wonder exactly what limits the speed of human perception and reasoning in the real world.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I know, the speed at which we perceive events appears to be a constant. What exactly determines that rate? Is it possible to change it? Is it possible that different people perceive things at different speeds?&lt;/p&gt;&#xA;" OwnerUserId="926" LastActivityDate="2019-02-26T00:32:37.690" Title="What limits the speed of human perception?" Tags="&lt;perception&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19921" PostTypeId="1" AcceptedAnswerId="20018" CreationDate="2014-07-24T02:03:58.727" Score="8" ViewCount="2648" Body="&lt;p&gt;I've noted that flies in my house have no problem landing on even perfectly clean mirrors. Why don't they fly straight into them? Can they sense that there is a surface there, even though they can't see it?&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2016-09-22T05:36:03.077" Title="How can flies sense mirrors?" Tags="&lt;entomology&gt;&lt;sensation&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="19922" PostTypeId="2" ParentId="19515" CreationDate="2014-07-24T05:35:08.133" Score="5" Body="&lt;p&gt;It may be important to consider the developmental stage of the &quot;female body&quot; as well. For instance, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19446073&quot; rel=&quot;noreferrer&quot;&gt;organizational vs. activational&lt;/a&gt; hypothesis--injecting testosterone during a critical period during development (it can be pre-natal, or during puberty) could produce permanent changes in secondary sexual characteristics and sex-specific behaviors; however, injecting testosterone after the organized system has &quot;crystallized&quot; (e.g. receptors are expressed in sex-specific regions, external genitalia is fully developed) may only induce temporary changes that may not be sex-specific.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for a &quot;female body&quot; to develop secondary sex characteristics with testosterone injections--if these characteristics are &quot;female&quot; secondary sex characteristics (e.g. increased subcutaneous fat deposition in breasts in humans), it is likely that the machinery has already been organized (e.g. more &quot;aromatase&quot; converts testosterone to estrogen, or the location/density of androgen receptors affects sensitivity, or there is less &lt;a href=&quot;http://en.wikipedia.org/wiki/Androgen-binding_protein&quot; rel=&quot;noreferrer&quot;&gt;androgen-binding protein&lt;/a&gt; to transport circulating testosterone), while if the secondary sex characteristics were &quot;male&quot; (e.g. laryngeal prominence) the testosterone injections happened during a critical development stage and/or were chronically administered (e.g. continuous administration, daily injections...). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phoenix et al (a review cited above) did a cool experiment that might interest you.&lt;/p&gt;&#xA;" OwnerUserId="8480" LastActivityDate="2014-07-24T05:35:08.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19923" PostTypeId="2" ParentId="19918" CreationDate="2014-07-24T08:28:45.630" Score="12" Body="&lt;h2&gt;&lt;strong&gt;Flicker Fusion Threshold:&lt;/strong&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The wikipedia definition:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;It is defined as the frequency at which an intermittent light stimulus appears to be completely steady to the average human observer.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Background&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;In 1824, &lt;strong&gt;Peter Mark Roget&lt;/strong&gt; (who also wrote the famous Thesaurus) first presented the concept of &quot;&lt;strong&gt;persistence of vision&lt;/strong&gt;&quot; to the Royal Society of London, as the ability of the retina to retain an image of an object for &lt;span class=&quot;math-container&quot;&gt;$\frac{1}{20}$&lt;/span&gt; to &lt;span class=&quot;math-container&quot;&gt;$\frac{1}{5}$&lt;/span&gt; second after its removal from the field of vision. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A second principle - the &lt;strong&gt;&lt;span class=&quot;math-container&quot;&gt;$\phi\ phenomenon$&lt;/span&gt; or stroboscopic effect&lt;/strong&gt; is closely related to flicker fusion. It was first studied by &lt;strong&gt;Max Wertheimer and Hugo Munsterberg&lt;/strong&gt; between 1912-16. Wertheimer and Munsterberg found that subjects can perceptually bridge the temporal gap between two consecutive displays, so that a series of static images appear as continuous movement. The discovery of flicker fusion became the perceptual basis for moving pictures, television, and all media based on stroboscopic presentation of stimuli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The minimal frequency at which flickering stimuli appear continuous is called the critical flicker frequency.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;&lt;strong&gt;Perceptual factors affecting the critical flicker fusion threshold&lt;/strong&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;This critical flicker fusion threshold depends on the stimulus’ &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Luminance (the Ferry-Porter law), &lt;/li&gt;&#xA;&lt;li&gt;Size (the Granit-Harper law), &lt;/li&gt;&#xA;&lt;li&gt;Color, &lt;/li&gt;&#xA;&lt;li&gt;Retinal eccentricity, &lt;/li&gt;&#xA;&lt;li&gt;Background Luminance, and other factors.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Biology Behind it:&lt;/h2&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Physiological evidence in humans and monkeys shows that flicker rates&#xA;  above the perceptual critical flicker frequency threshold can&#xA;  nevertheless generate cortical and subcortical visual responses.  Thus&#xA;  the temporal integration underlying flicker fusion does not occur at&#xA;  the level of the retina,  but must take place later in the visual&#xA;  hierarchy. Single-unit recordings in the primary visual cortex of&#xA;  primates suggests that,  for two brief-duration targets presented in&#xA;  close succession, the after-discharge to the first  target interferes&#xA;  with the onset-response to the second target (Macknik, 2006) (see&#xA;  Figure 5). The onset-response to the second flash is absent for&#xA;  inter-stimuli intervals of 30 msec or shorter (equivalent to 17 Hz&#xA;  periodic). If the flashes are separated by more than 30 ms, the&#xA;  after-discharge to the first flash and the onset-response to the&#xA;  second flash begin to recover (i.e. equivalent to &amp;lt;17 Hz flicker).&#xA;  These intervals roughly coincide with the critical flicker fusion&#xA;  threshold in humans for 100% contrast stimuli in the fovea .&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This suggests that perceptual flicker fusion may be due to the lack of&#xA;  robust transient responses to the flickering stimulus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://images.scholarpedia.org/w/images/thumb/8/8b/Flicker_fusion_fig5.png/360px-Flicker_fusion_fig5.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://images.scholarpedia.org/w/images/thumb/8/8b/Flicker_fusion_fig5.png/360px-Flicker_fusion_fig5.png&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Source:&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Bartley (1939). Some effects of intermittent photic stimulation. Journal of Experimental Psychology 25, 462-480.&lt;/li&gt;&#xA;&lt;li&gt;Bloch, A. M. (1885). Experience sur la vision. Comptes Rendus de Seances de la Societe de Biologie, Paris 37, 493-495.&lt;/li&gt;&#xA;&lt;li&gt;Brücke, E. (1864). Über den Nutzeffect intermittierender Netzhautreizungen. Sitzungsber k Akad Wissensch Math-naturw Cl, Wien 49, 128-153.&lt;/li&gt;&#xA;&lt;li&gt;Di Lollo, V., and Bischof, W. F. (1995). Inverse-intensity effect in duration of visible persistence. Psychol Bull 118, 223-237.&lt;/li&gt;&#xA;&lt;li&gt;Ferry, E. (1892). Persistence of vision. Amer J Sci 44, 192-207.&lt;/li&gt;&#xA;&lt;li&gt;Fukuda, T. (1979). Relation between flicker fusion threshold and retinal positions. Percept Mot Skills 49, 3-17.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.scholarpedia.org/article/User:Eugene_M._Izhikevich/Proposed/Flicker_fusion&quot; rel=&quot;nofollow noreferrer&quot;&gt;Flicker Fusion&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;What is the Different speeds of Visual Perception?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TDfBg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;First-order motion&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Experiment:&lt;/strong&gt; A moving sinusoidal grating with bright peaks and dark troughs is seen through a window. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Result:&lt;/strong&gt; Even when its velocity is so high that 30 of its bright peaks pass each location per second (30 Hz), observers still perceive its direction of&#xA;motion. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://1.bp.blogspot.com/_ydDJlxvKQlI/TCDIhHpmC4I/AAAAAAAAAEM/ULxcFAt1d1o/s1600/Sinusoid.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Depth from binocular disparity&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Experiment:&lt;/strong&gt; Two identical gratings, one in each eye, are viewed through identical windows. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Result:&lt;/strong&gt; One is spatially shifted relative to the other, introducing a binocular disparity that is perceived as depth. &#xA;Even when they move at a 30 Hz rate, the depth is still perceived. &#xA;If the input to depth mechanisms were blurred at a &gt;30 ms timescale, detecting the depth would be impossible at this rate.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Edges and texture boundaries&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Experiment:&lt;/strong&gt; Against a gray background, a field of white dots is adjacent to a field of black dots. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Result:&lt;/strong&gt; Both fields are set in rapid alternation between white and black, but out of phase – when&#xA;one is white, the other is black. The conspicuous boundary between them is perceived even at fast &#xA;rates of 30 Hz, whereas at faster rates the black and white are averaged by the brain into the same color as the background.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://ak.picdn.net/shutterstock/videos/3139525/preview/stock-footage-retro-geometric-dot-background-in-black-gray-and-white.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://ak.picdn.net/shutterstock/videos/3139525/preview/stock-footage-retro-geometric-dot-background-in-black-gray-and-white.jpg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Binding of color and orientation sharing a spatial location&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Experiment &amp;amp; Result: If a red, right-tilted patch is alternated with a green, left tilted patch, &#xA;it is easy to distinguish from the complementary pairing of red left alternating with green right, even at&#xA;fast 20 Hz rates.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Binding of form and color across space&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Alternating color-shape pairings can only be reported at rates below ~3 Hz.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/SgiNJ.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/SgiNJ.gif&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;source: &lt;a href=&quot;http://www.psych.usyd.edu.au/staff/colinc/HTML/dynamics.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.psych.usyd.edu.au/staff/colinc/HTML/dynamics.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Binding of global form with color&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Two specially constructed dot patterns that form distinct shapes alternate, with all the dots of one red and all the&#xA;dots of the other green. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At alternation rates faster than several a second it is very difficult to determine the shape color pairing even though the shapes and colors themselves&#xA;are easily identified.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Direction change and acceleration perception&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;A moving stimulus alternates between two speeds (acceleration) or two directions. When the alternation occurs&#xA;faster than several per second, these changes are unperceivable.&#xA;Its limit is 8-10 Hz.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Word perception&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Certain pairs of words (such as ‘jump’ and ‘pink’), when alternated in the same location, cannot be distinguished&#xA;from another matched pair at rapid rates as one perceives only the sum, which is the same for both pairs. &#xA;They can be distinguished only at rates slower than several items per second.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/EpmJs.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/EpmJs.gif&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.psych.usyd.edu.au/staff/alexh/research/words/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.psych.usyd.edu.au/staff/alexh/research/words/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Source:&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Holcombe AO (2009) Seeing slow and seeing fast: two limits on perception. Trends Cogn Sci 13:216 –221.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.psych.usyd.edu.au/staff/colinc/HTML/dynamics.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.psych.usyd.edu.au/staff/colinc/HTML/dynamics.htm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-02-26T00:32:37.690" LastActivityDate="2019-02-26T00:32:37.690" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="19924" PostTypeId="1" AcceptedAnswerId="19927" CreationDate="2014-07-24T08:35:25.370" Score="5" ViewCount="367" Body="&lt;p&gt;Is there any research done on the genetic variance for Music appreciation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, why is there no genetic variance for this trait?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vqVlD.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-01-19T22:35:58.673" LastActivityDate="2019-01-19T22:35:58.673" Title="Is there some genetic variance underlying music appreciation?" Tags="&lt;genetics&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="11" ContentLicense="CC BY-SA 4.0" />
  <row Id="19925" PostTypeId="2" ParentId="19918" CreationDate="2014-07-24T08:59:44.760" Score="3" Body="&lt;p&gt;The limitations are of several natures: cognitive once the signal has arrived in the brain, but also physical within the eye e.g. for vision.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For vision, the crucial bit is to transform changes of incoming light into an electrical signal. It is not completely elucidated. &lt;a href=&quot;http://www.sciencemag.org/content/338/6104/200.summary&quot; rel=&quot;nofollow&quot;&gt;Recent research&lt;/a&gt; shows e.g. that for some flies, there may be a mechanical intermediate stage: the light-sensing cells react by contracting, and this would modify the electric resistance of their membrane. I don't think it is known whether the human, who have less need for a fast response but want more detail of what they're looking at, have the same mechanism or not: maybe your hero has something of the fly that we don't have?&lt;/p&gt;&#xA;" OwnerUserId="6224" LastActivityDate="2014-07-24T08:59:44.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19926" PostTypeId="1" CreationDate="2014-07-24T10:01:37.547" Score="3" ViewCount="109" Body="&lt;p&gt;I got experimental data where hypersensitivity (i.e. tonic pain when touching ear canal) was recognised for about 100 minutes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not know which type of hypersensitivity is this one. &#xA;IgM can reach ear canal, I think (not sure) - it is just in the limit. &#xA;If IgM cannot reach ear canal, then the hypersensitivity must be caused by &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;humoral immune system&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which is responding slowly to the trigger. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is proposed that this cannot be &lt;strong&gt;contact dermatitis&lt;/strong&gt; because &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the reaction happened simultaneously in both ear canals &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;after irritating ear canals with plastic the subject is not allergic. &#xA;Irritation was also a selected signal which resulted in the dynamic cycle of bass music by Beats earphones. &#xA;It was studied the effect of the specific signal with bass music on the movement on the inner membrane on the subject with problem in maintaining the inner physiology of ear itself (also repeated cycle of ear infections during childhood). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can IgM reach ear canal?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hypersensitivity was simultaneous in both ear canals.&#xA;I did not know before that you can get hypersensitivity reaction in ear canals and also simultaneously. &#xA;I think hypersensitivity is not in normal condition. &#xA;There must be some etiological factors (probably neuronal) that can cause it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other organs which can have hypersensitivity too. &#xA;So I started to think what is the trigger of hypersensitivity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My conjecture is about Secreted substances of endothelium (EDRF, EDCF). &#xA;There are three types of substances secreted by the endothelium&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;NO&lt;/li&gt;&#xA;&lt;li&gt;Endothelium hyperpolarising factors&lt;/li&gt;&#xA;&lt;li&gt;Endothelins&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;NO is the most important one. &#xA;But what is its role in the hypersensitivity of ear canal is unknown to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the mechanism of hypersensitivity of our body and particularly in the ear canal?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-26T09:23:40.697" LastActivityDate="2014-12-26T09:23:40.697" Title="Hypersensitivity Simultaneously in Ear canals" Tags="&lt;physiology&gt;&lt;pathophysiology&gt;&lt;hypersensitivity&gt;&lt;endothelium&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19927" PostTypeId="2" ParentId="19924" CreationDate="2014-07-24T12:17:48.990" Score="5" Body="&lt;p&gt;In 2013, &#xA;&lt;strong&gt;Dr. Liisa Ukkola-Vuoti&lt;/strong&gt;, &lt;em&gt;University of Helsinki, Finland&lt;/em&gt;, done a detailed GWCNV(Genome-Wide Copy Number Variation) Analysis of certain group of people for musical creativity and aptitude.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Genome-Wide Copy Number Variation Analysis in Extended Families and Unrelated Individuals Characterized for Musical Aptitude and Creativity in Music&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;They did a Genome Wide Copy Number Variations (CNVs) in five extended&#xA;pedigrees and in 172 unrelated subjects characterized for musical&#xA;aptitude and creative functions in music&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Muscial Aptitude is taken as Sum of Scores of Auditory structuring ability, Seashores test for pitch and for time. Along with data on creativity in music was surveyed using a web-based questionnaire.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Several CNVRs containing genes that affect neurodevelopment, learning&#xA;and memory were detected.&lt;/strong&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A &lt;strong&gt;deletion at 5q31.1 covering the protocadherin-α gene cluster (Pcdha 1-9)&lt;/strong&gt; was found co-segregating with &lt;strong&gt;low music test scores (COMB)&lt;/strong&gt; in both sample sets. Pcdha is involved in neural migration, differentiation and synaptogenesis.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Creativity in music was found to co-segregate with a duplication covering &lt;strong&gt;glucose mutarotase gene (GALM) at 2p22&lt;/strong&gt;. GALM has influence on serotonin&#xA;release and membrane trafficking of the human serotonin transporter.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Genes related to serotonergic systems have been shown to associate not only with psychiatric disorders but also with creativity and music perception. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Both, Pcdha and GALM, are related to the serotonergic systems influencing cognitive and motor functions, important for music perception and practice. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A &lt;strong&gt;1.3 Mb duplication was identified in a subject with low COMB scores&lt;/strong&gt; in the &lt;strong&gt;region previously linked with absolute pitch (AP) at 8q24&lt;/strong&gt;. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;No differences in the CNV burden was detected among the high/low music test scores or creative/non-creative groups. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In summary, CNVs and genes found in this study are related to&#xA;  cognitive functions. Our result suggests new candidate genes for music&#xA;  perception related traits and supports the previous results from AP&#xA;  study.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;h2&gt;Source:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584088&quot; rel=&quot;nofollow&quot;&gt;Genome-Wide Copy Number Variation Analysis in Extended Families and Unrelated Individuals Characterized for Musical Aptitude and Creativity in Music&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2678260/&quot; rel=&quot;nofollow&quot;&gt;Musical Aptitude Is Associated with AVPR1A-Haplotypes&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-08-01T12:40:03.003" LastActivityDate="2014-08-01T12:40:03.003" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19928" PostTypeId="1" AcceptedAnswerId="19929" CreationDate="2014-07-24T13:53:42.487" Score="1" ViewCount="45" Body="&lt;p&gt;I'm trying to put together some documentation on the relation between the common (modern) horse and the okapi. I've found a tree that shows that connection but it has no references. I'm hoping that someone has documented this connection somehow.&lt;/p&gt;&#xA;" OwnerUserId="8183" LastActivityDate="2014-07-24T17:24:25.233" Title="Does documentation exist that shows the evolutionary connection between common horses and the okapi?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19929" PostTypeId="2" ParentId="19928" CreationDate="2014-07-24T14:05:32.227" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://tolweb.org/tree/&quot; rel=&quot;nofollow&quot;&gt;tolweb.org&lt;/a&gt; is your friend!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the okapi and the horse are not so closely related you will probably find several articles on the subject. Okapi belongs to the order of &lt;a href=&quot;http://fr.wikipedia.org/wiki/Artiodactyla&quot; rel=&quot;nofollow&quot;&gt;artiodactyla&lt;/a&gt; while the horse belongs to the order of &lt;a href=&quot;http://fr.wikipedia.org/wiki/Perissodactyla&quot; rel=&quot;nofollow&quot;&gt;perissodactyla&lt;/a&gt;. They are both mammals, eutheria, &lt;a href=&quot;http://fr.wikipedia.org/wiki/Ungulata&quot; rel=&quot;nofollow&quot;&gt;ungalata (superorder)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://tolweb.org/Eutheria/15997&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is the tree of the eutheria (within the mammals) from tolweb. You have approximatively 150 references. You can click on &lt;a href=&quot;http://tolweb.org/Perissodactyla/15980&quot; rel=&quot;nofollow&quot;&gt;perissodactyla&lt;/a&gt; and &lt;a href=&quot;http://tolweb.org/Artiodactyla/15976&quot; rel=&quot;nofollow&quot;&gt;artiodactyla&lt;/a&gt; and you will find 100 more references.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These two references may help you (I only read the titles)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9126561&quot; rel=&quot;nofollow&quot;&gt;Graur, D., M. Gouy, and L. Duret. 1997. Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata. Molecular Phylogenetics and Evolution 7:195-200&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8896369&quot; rel=&quot;nofollow&quot;&gt;Xu, X. F., A. Janke, and U. Arnason. 1996. The complete mitochondrial DNA sequence of the greater Indian rhinoceros, Rhinoceros unicornis, and the phylogenetic relationship among Carnivora, Perissodactyla, and Artiodactyla (plus Cetacea). Molecular Biology and Evolution 13:1167-1173&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-07-24T17:24:25.233" LastActivityDate="2014-07-24T17:24:25.233" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19930" PostTypeId="1" AcceptedAnswerId="19931" CreationDate="2014-07-24T16:16:30.977" Score="9" ViewCount="3020" Body="&lt;p&gt;I was just thinking about this, wouldn't it make more sense for a mango to have multiple seeds, as it would allow more seed propagation? &lt;/p&gt;&#xA;" OwnerUserId="8491" LastActivityDate="2017-03-27T20:02:26.557" Title="Why do Mangoes have a single large seed, and not multiple small ones?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19931" PostTypeId="2" ParentId="19930" CreationDate="2014-07-24T16:35:07.003" Score="12" Body="&lt;p&gt;It is an interesting question and it applies to other fruits with big seeds as the avocado as well. It is very likely that these fruits evolved to be spread by large animals (like big birds or large mamals) which existed for a relatively long time, but are extinct today. These animals swallowed whole fruits and excreted the seeds afterwards (most of these seeds are slighty laxative) together with dung to support the growth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionary_anachronism&quot;&gt;evolutionary anachronisms&lt;/a&gt;&quot; and there is a very interesting book about them, called &quot;The ghosts of evolution: nonsensical fruit, missing partners, and other ecological anachronisms.&quot; (which can be found as a PDF online)&#xA;Two interesting articles about this phenomenon can be found here:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.americanforests.org/magazine/article/trees-that-miss-the-mammoths/&quot;&gt;The Trees That Miss The Mammoths&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.thegreatstory.org/anachronistic_fruits/index.html&quot;&gt;Anachronistic Fruits and the Ghosts Who Haunt Them&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-07-24T16:42:09.573" LastActivityDate="2014-07-24T16:42:09.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19933" PostTypeId="2" ParentId="19593" CreationDate="2014-07-24T20:03:01.760" Score="1" Body="&lt;p&gt;D-Glucose and L-Glucose have similar names only because we humans decided that's how we should name sugars; they have as much in common as, for example, D-Glucose and D-Allose (one chiral bond is different).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in essence, organisms don't synthesize L-Glucose for the same reason they don't synthesize D-Allose: they have no use for it. Its similarity to Glucose is only coincidental, it is different enough that, biologically speaking, it's a totally different molecule.&lt;/p&gt;&#xA;" OwnerUserId="8095" LastActivityDate="2014-07-24T20:03:01.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19934" PostTypeId="1" CreationDate="2014-07-24T20:09:20.353" Score="1" ViewCount="284" Body="&lt;p&gt;I'm not entirely sure how normal this is, but since I was a child, I've been able to produce myself voluntarily a &quot;chill&quot; sensation that seems to start on my head and traverse the rest of my body, being least intense in the feet. Looking around the internet and forums, looks like other people but not everybody also describe this ability. However, unlike other people's reports, I don't see &quot;goose bumps&quot; on my skin, at least there aren't any visibly; it's just the sensation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anybody know if there are any relevant studies or knowledge out there about &quot;voluntary goose bumps&quot;? Is there even a proper name for that?&lt;/p&gt;&#xA;" OwnerUserId="8321" LastActivityDate="2014-11-18T23:59:14.630" Title="Any relevant knowledge/studies about voluntary goose bumps" Tags="&lt;human-biology&gt;&lt;skin&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ClosedDate="2014-12-06T10:25:41.433" ContentLicense="CC BY-SA 3.0" />
  <row Id="19935" PostTypeId="1" AcceptedAnswerId="19937" CreationDate="2014-07-24T20:35:18.953" Score="4" ViewCount="167" Body="&lt;p&gt;&lt;strong&gt;I'm curious to know if neurotransmitter degradation factors into drug tolerance and neural conduction and, if so, to what extent.&lt;/strong&gt; As I recall from textbooks I read as an undergrad, one mechanism of drug tolerance works by increasing the necessary thresh-hold at a synapse such that larger concentrations of neurotransmitter or more-frequent action potentials in the upstream axon were required to depolarize the membrane and propagate the signal. It seems to me that the same effect would occur if there were fewer available molecules of the required neurotransmitter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does over-stimulation of a neural pathway (through the use of a drug or other stimuli that up-regulates a given neurotransmitter) shorten the half-life of the neurotransmitters it uses? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could a diet which is poor for necessary precursor nutrients cause a person's neurotransmitter concentrations to drop and reduce signaling along specific neural pathways? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could lack of sleep or other physiological stressors have a similar effect? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not a neuroscientist so please correct (and forgive) me if I'm using any terms incorrectly or am flat-out wrong in any of my assumptions.&lt;/p&gt;&#xA;" OwnerUserId="8161" LastEditorUserId="8161" LastEditDate="2014-07-24T20:43:47.337" LastActivityDate="2014-07-25T01:02:26.287" Title="Can neurotransmitter depletion cause short-term drug tolerance?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19936" PostTypeId="2" ParentId="16863" CreationDate="2014-07-24T21:36:51.103" Score="1" Body="&lt;p&gt;Keegan's answer is good I gave it an up vote. I want to offer a valid alternative. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Psychology may induce redundant pathways which trigger approximate simultaneous firing of neurons near or in completely different parts of the brain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Emotionally intense memories can trigger emotions, basically hallucinations of the event, smells and touch based recollections. The pathways work in reverse as well actual sensory input triggering the memory. The more often you delve into your other memories the stronger your abilities to remember those events become it can be very vicious or pleasurable. &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-07-24T21:36:51.103" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19937" PostTypeId="2" ParentId="19935" CreationDate="2014-07-25T01:02:26.287" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;As I recall from textbooks I read as an undergrad, one mechanism of drug tolerance works by increasing the necessary thresh-hold at a synapse such that larger concentrations of neurotransmitter or more-frequent action potentials in the upstream axon were required to depolarize the membrane and propagate the signal.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes - usually through a reduced expression of receptors on the surface. Increasing the drug dosage merely increases the probability that one of the molecules will find the receptor. Chronic exposure of increasingly large doses can dramatically reduce receptor expression. In time, sans the drug, the receptor count will climb back up. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is why a common cause of chronic drug addicts who have just gone through rehab is overdose: After months in rehab or free of a drug they immediately go back to the amount of drug they were doing before rehab - with some severe side-effects at the least, death at the worst.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Does over-stimulation of a neural pathway (through the use of a drug or other stimuli that up-regulates a given neurotransmitter) shorten the half-life of the neurotransmitters it uses? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No. The half-life of a neurotransmitters is not a major concern; your body will construct them from stored resources if necessary, and healthy neurons have a significant store of neurotransmitters to prepare for multiple firings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A neuron can be artificially over-stimulated and the neurotransmitter pool emptied (or all the neurotransmitters is bound to its receptor) - but only for Ach receptors at &lt;strong&gt;neuromuscular&lt;/strong&gt; junctions. It hasn't been observed naturally, and not for other types of synapses. This does not result in the muscle no longer responding, but rather it will not respond any &lt;em&gt;faster&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Could a diet which is poor for necessary precursor nutrients cause a person's neurotransmitter concentrations to drop and reduce signaling along specific neural pathways?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, but by that point you're not in good shape, if not courting death. Neurotransmitters are either very common in the diet - like ions - or are constructed from very common constituents of a normal diet - like Glutamine, the most common amino acid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would not be a therapy to treat drug addiction.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Could lack of sleep or other physiological stressors have a similar effect? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You would die of lack of sleep first. Your body generally keeps a 30 day supply of absolutely essential vitamins and minerals, and will easily digest itself for precursors to construct neurotransmitters out of.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have not heard of any physical or mental stress which has reduced the amount of neurotransmitters released into the synapse beyond absolute starvation or artificial scarcity.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2014-07-25T01:02:26.287" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19938" PostTypeId="1" AcceptedAnswerId="28203" CreationDate="2014-07-25T03:11:39.843" Score="9" ViewCount="98" Body="&lt;p&gt;I use &lt;a href=&quot;http://msdssearch.dow.com/PublishedLiteratureDAS/dh_08e8/0901b803808e856e.pdf?filepath=turf/pdfs/noreg/010-60417.pdf&amp;amp;fromPage=GetDoc&quot; rel=&quot;nofollow noreferrer&quot;&gt;Clopyralid&lt;/a&gt; (3,6-dichloro-2-pyridinecarboxilic acid) to kill broad leaved weeds in lawns. From my understanding, it works by mimicking an auxin which affects plant growth. Naturally this pulls the chemical to the growing points (stems, roots) of the plant and disrupts the growth, killing the plant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vhGC2.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: Why doesn't this affect cool season lawn grasses (Winter rye, fescues, bluegrass)? It is also considered safe to use on some warm season grasses, but in my experience the results are not always good.&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2015-01-29T17:48:43.093" LastActivityDate="2015-01-31T22:48:25.033" Title="Why doesn't Clopyralid damage cool season lawn grasses?" Tags="&lt;botany&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19939" PostTypeId="1" AcceptedAnswerId="24221" CreationDate="2014-07-25T03:40:45.640" Score="6" ViewCount="362" Body="&lt;p&gt;I use &lt;a href=&quot;http://stonebrothers.com/shop/msma-6-plus-herbicide-5-gallons/&quot; rel=&quot;nofollow noreferrer&quot;&gt;MSMA&lt;/a&gt; (Monosodium methyl arsenate) to kill crabgrass in lawns. I am not certain of the mode of action. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kC29H.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this chemical work? How does it target the annual grassy weeds, without damaging the lawns much?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2015-01-28T03:25:05.247" LastActivityDate="2015-01-28T03:25:05.247" Title="How does MSMA kill crabgrass with only minimal damage to lawn grasses?" Tags="&lt;botany&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19940" PostTypeId="1" AcceptedAnswerId="28205" CreationDate="2014-07-25T03:54:48.520" Score="9" ViewCount="1609" Body="&lt;p&gt;I use &lt;a href=&quot;http://www.sedgehammer.com/sedgehammer-plus.html&quot; rel=&quot;noreferrer&quot;&gt;Halosulfuron-methyl&lt;/a&gt; to control yellow and purple nutsedge in lawns. This chemical acts by interfering with the acetolactate synthase enzyme, which quickly slows cell division, and growth at all points.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7F3LJ.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this work without also interfering with enzymes in the lawn grass?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2015-01-28T03:24:07.350" LastActivityDate="2018-08-15T02:10:04.213" Title="How does Halosulfuron-methyl kill nutsedge, while leaving lawn grass and most weeds undamaged?" Tags="&lt;botany&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19942" PostTypeId="1" AcceptedAnswerId="20031" CreationDate="2014-07-25T13:15:36.233" Score="5" ViewCount="845" Body="&lt;p&gt;The metabolic rate measures how much energy an organism &lt;strong&gt;expends&lt;/strong&gt; over a unit of time. Its breakdown for the human body in terms of its functions is well documented : so much for the heart, for the brain, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In West et al, 2002 I have found an estimate for the metabolic rate of a single cell. But how does this breakdown in terms of elementary functions in the cell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.g., how much of the energy made available from nutrients is used in the process of replicating genome, of expressing proteins, of trafficking...?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following Jeremy Kemball's link suggestions, I find in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7492307%2C7708012?dopt=Abstract&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; the fraction of ATP consumption for the following processes:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Protein synthesis    0.34&#xA;Na+/K+ ATPase        0.16&#xA;Ca2+ ATPase          0.17&#xA;RNA/DNA synthesis    0.25&#xA;Unidentified         0.09&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;(which adds up to 1.01 rather than 1 for spurious reasons). Their measurement is indirect, based on $O_2$ consumption for an assumed steady-state regeneration of ATP. I wonder how GTP-based processes are accounted for? Or are they negligible compared to ATP ones?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is for a specific cell type, rat thymocyte, is there a reason to expect that this will be hugely different for say a fibroblast? Also, they stimulate their thymocyte with concanavalin A. I understood they are not getting RNA/DNA consumption signal without Con-A, but didn't get why it would be so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, what would be in the remaining 9% ? One candidate for ATP consumption suggested by Jeremy Kemball is actin turnover, I guess it fits only in the &quot;unidentified&quot; line. Tubulin turnover is a GTP process, not sure about intermediate filaments (do they turnover?). All ATP-molecular motors (myosin, kinesin, dynein at least?) have to be there too.  What else?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am particularly interested in the total amount of ATP energy that goes to myosin.&lt;/p&gt;&#xA;" OwnerUserId="6224" LastEditorUserId="3340" LastEditDate="2015-06-04T11:44:51.573" LastActivityDate="2015-06-04T11:44:51.573" Title="Breakdown of energy expenditure at the level of a single cell" Tags="&lt;cell-biology&gt;&lt;metabolism&gt;&lt;bioenergetics&gt;&lt;cytoskeleton&gt;" AnswerCount="2" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="19943" PostTypeId="2" ParentId="19908" CreationDate="2014-07-25T13:50:31.823" Score="4" Body="&lt;p&gt;From &lt;a href=&quot;http://jxb.oxfordjournals.org/content/57/9/1847.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;Whittle and Johnston (2006)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Specifically, human epidemiological data and/or nucleotide substitution rates of selectively neutral DNA (which equals the mutation rate, Kimura, 1983; Miyata et al., 1987) have shown that more mutations occur in the male than in the female germ line for numerous animal taxa (e.g. humans, mice, chickens, and sheep) and in older rather than younger human males, patterns that each agree with the cell-division hypothesis (i.e. more DNA replications in males and in particular older males; Penrose, 1955; Risch et al., 1987; Becker et al., 1996; Moloney et al., 1996; Li, 1997; Green et al., 1999; Crow, 2000; Li et al., 2002; Makova and Li, 2002). Other data, however, have indicated that the mutation bias reported relative to gender and male age are not generally well correlated with the number of germ cell divisions and that other factors could explain these trends, such as methylation patterns, differential repair, metabolic rates, and preferential transmission of mutations to pro- geny from older males (Risch et al., 1987; Martin and Palumbi, 1993; Drost and Lee, 1995; Bromham et al., 1996; Hurst and Ellegren, 1998; Martin, 1999; Crow, 2000; Huttley et al., 2000; McVean, 2000; Sommer et al., 2001;Hebert et al., 2002; Hurst and Ellegren, 2002; Kumar and Subramanian, 2002; Li et al., 2002; Bartosch-Harlid et al., 2003).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;…so basically &lt;strong&gt;we don't really know&lt;/strong&gt; whether difference in gametogenesis between males and females lead to more sex and age-specific mutation rate!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, &lt;a href=&quot;http://jxb.oxfordjournals.org/content/57/9/1847.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;Whittle and Johnston (2006)&lt;/a&gt; in reviewing many articles also show that old seeds are more likely to carry chromosomal aberration and that old individuals are more likely because of the instability of their metabolism to transmit more mutations but that would be sex independent and would not result in different gametogenesis as I was expecting in asking this question. Also the kind of mutations that become more frequent with all parents are chromosomal abnormalities or important deletion but not so much substitutions (which was also what I was interested in when asking).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks @DevashishDas for finding &lt;a href=&quot;http://jxb.oxfordjournals.org/content/57/9/1847.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;. &lt;a href=&quot;http://web.udl.es/usuaris/e4650869/docencia/segoncicle/genclin98/recursos_classe_(pdf)/revisionsPDF/mut%26variat.pdf&quot; rel=&quot;nofollow&quot;&gt;This other one&lt;/a&gt; was interesting as well.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-01-29T22:21:16.447" LastActivityDate="2015-01-29T22:21:16.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19944" PostTypeId="2" ParentId="16863" CreationDate="2014-07-25T14:44:48.227" Score="4" Body="&lt;p&gt;Strictly stated, Hebb's rule applies only to existing synapses, and not to the formation of new synapses. (This answer applies to biological neurons, not to ANNs).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Synapse formation is a topic of active research. During development (and in fact continuously even during adulthood), many synapses are created and destroyed. It is not unreasonable to suspect that a similar form of rule is used to decide which synapses are removed and which should remain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Synaptic connections between neurons show a good deal of specificity -- for example, in the projection from the retina to the optic tectum, synaptic connections are made only with target neurons at an appropriate retinotopic location. This happens because growing axons follow molecular gradients.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within a cortical column, some possible connection pathways seem to be actively sought -- for example, axo-axonal cells connect specifically to the axon initial segments of target neurons. Neurons certainly have membrane molecules that could be used to identify target cell classes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there are probably a number of rules used to determine when a new synapse is made. However, I am not aware of a mechanism for a pre-synaptic neuron to detect how a putative post-synaptic parter is firing, without a synapse already being present. So it seems likely that some form of random process is involved to form new synapses with reasonable post-synaptic partners, after which some activity-dependent rule (like Hebb's) could be applied.&lt;/p&gt;&#xA;" OwnerUserId="8495" LastActivityDate="2014-07-25T14:44:48.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19945" PostTypeId="1" CreationDate="2014-07-25T15:41:29.483" Score="3" ViewCount="2942" Body="&lt;p&gt;I've read a couple people theorize that a cat playing with a mouse causes the mouse's body to be flushed with adrenaline before the final kill and that this adrenaline makes the meat more tender/easier to digest/more nutritious etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any evidence to support the idea that by playing with it's prey the cat is making it taste better or easier to eat?&lt;/p&gt;&#xA;" OwnerUserId="8496" LastEditorUserId="69" LastEditDate="2014-07-25T16:11:58.073" LastActivityDate="2014-07-27T10:06:36.373" Title="Why does a housecat (or other predator) play with it's food before killing and eating it? Does it make the food taste better?" Tags="&lt;ethology&gt;&lt;feline&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19946" PostTypeId="1" CreationDate="2014-07-25T17:18:06.210" Score="3" ViewCount="133" Body="&lt;p&gt;There are many studies on fine particles (PM2.5) and their fully negative effect on human health. There doesn't seem to have any positive aspect of inhaling particles, except very particular ones, but most often people smoke, and release all sort of unwanted and toxic PM2.5, same goes with for fuel combustion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At a huge dose, we die within minutes, like in a gas chamber, at small dose below this hazardous health risk level, is it still dangerous to us? If yes, why aren't we equipped to fight them, I guess this smoke concentration and pollution level is very recent on human evolution scale, but at the lowest layer of life, bacteria may develop to break and eat toxic particles, does it happen it our blood? Is it hard to explain to a non-biologist like me?&lt;/p&gt;&#xA;" OwnerUserId="4447" LastEditorUserId="4447" LastEditDate="2014-07-25T17:24:52.833" LastActivityDate="2014-07-27T05:50:07.117" Title="Why are particulate matter toxic to humans?" Tags="&lt;toxicology&gt;&lt;respiration&gt;&lt;breathing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19947" PostTypeId="1" CreationDate="2014-07-25T17:27:54.670" Score="2" ViewCount="47" Body="&lt;p&gt;I am looking for fast growing &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Leucaena_leucocephala&quot; rel=&quot;nofollow&quot;&gt;Leucaena leucocephala&lt;/a&gt;&lt;/em&gt; seeds. Now, I am cultivating &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Leucaena_leucocephala&quot; rel=&quot;nofollow&quot;&gt;Leucaena leucocephala&lt;/a&gt;&lt;/em&gt; which can grow 6 meters in a year. But I am looking for a genetically improved seed which can grow up to 10 Meters in a year.&lt;/p&gt;&#xA;" OwnerUserId="8497" LastEditorUserId="10456" LastEditDate="2015-03-29T18:33:30.733" LastActivityDate="2015-03-29T18:33:30.733" Title="Genetically improved *Leucaena leucocephala* seeds" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;growth&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19948" PostTypeId="1" AcceptedAnswerId="20007" CreationDate="2014-07-25T17:53:54.423" Score="5" ViewCount="255" Body="&lt;p&gt;I am currently growing up a specific strain of E.Coli with a knockout in 40mL of growth medium (LB) in a 250mL shaker flask... My ultimate goal is to scale up this process to a 1-5L large scale setup for the lab. But for now I'd like to quantitatively characterize this 250mL scale using Monod Kinetics so that the mathematical model can be used to build the aforementioned bio-reactor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Currently I am making two growth curves of the E.Coli in the current 250mL flask. One is OD vs. time and the other g.Dry mass vs. time. The idea of doing so is to ascertain the $\mu_g^{max}$ (maximum specific growth rate). However, I am stuck as to how to find the saturation constant (Ks). I am also stuck on how to measure the sugar concentration ([S]) at each time-point that I would measure the OD. The idea behind these two variables is to use the equation(s): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$D = \mu_g^{max} . \frac{[S]}{Ks + [S]}\\&#xA;D^{\ max} = \mu_g^{max} . \frac{[S^{\ max}]}{Ks + [S^{\ max}]}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I looking for the right variables and/or using the right equations?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks again for your help!&lt;/p&gt;&#xA;" OwnerUserId="8498" LastEditorUserId="3340" LastEditDate="2014-07-30T12:11:34.087" LastActivityDate="2014-07-30T12:11:34.087" Title="Scale up of Bacterial growth from 250mL to 1-5L?" Tags="&lt;biochemistry&gt;&lt;microbiology&gt;&lt;growth&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19949" PostTypeId="2" ParentId="14618" CreationDate="2014-07-25T18:16:47.103" Score="4" Body="&lt;p&gt;If there is a stimulus at E, there will be depolarization (membrane becomes relatively more positive). It is just that no action potentials are fired. Therefore, if a strong stimulus does arrive, it will depolarize the membrane to an extent depending on its strength. It will increase the height of the succeeding B phase or reduce the dip of the succeeding E phase. If it is strong enough, it might persist above the threshold till the refractory period is over, and then an action potential can be fired.&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3615" LastEditDate="2014-07-26T07:06:32.457" LastActivityDate="2014-07-26T07:06:32.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19951" PostTypeId="1" CreationDate="2014-07-25T19:05:49.927" Score="2" ViewCount="2503" Body="&lt;p&gt;Firstly I would like to apologise if this is not correct place to ask this question, as it can be seen more as chemistry and not biology question.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was looking around for data on psychedelic substance called &lt;code&gt;25i (25I-NBOMe)&lt;/code&gt; . It was fist synthesized in 2003 and is somewhat 'new'. I have found some data on overdoses and they are few, however I could not find any specific data on mortality to dose rate nor on LD50 (Dose where 50% of people would die). &lt;a href=&quot;http://en.wikipedia.org/wiki/25I-NBOMe&quot; rel=&quot;nofollow&quot;&gt;Wikipedia is quiet in this regard.&lt;/a&gt;&#xA;Judging by the dosage it being active in sub-milligram doses (600–1,200 µg) it should not be very lethal compared to most, should it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Where could I get data on LD50 for &lt;code&gt;25i (25I-NBOMe)&lt;/code&gt;?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="8129" LastActivityDate="2014-07-26T07:40:19.820" Title="What is LD50 for 25i (25I-NBOMe)?" Tags="&lt;pharmacology&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19952" PostTypeId="2" ParentId="17924" CreationDate="2014-07-25T19:29:32.650" Score="3" Body="&lt;p&gt;In cancer research, we never talk about &quot;curing&quot; cancer because, as others have pointed out, there is no way of being sure that all of the cancer has been eradicated. You may be interested to consider &quot;Recurrence&quot; statistics which describe the amount of time from when a cancer was treated to when it was detected to have returned.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are willing to do some statistics computations of your own, The Cancer Genome Atlas (&lt;a href=&quot;http://cancergenome.nih.gov/&quot; rel=&quot;nofollow&quot;&gt;http://cancergenome.nih.gov/&lt;/a&gt;) will let you download clinical datasets that include datasets like recurrence, &quot;Overall Survival&quot; (how long did the person live after being diagnosed with cancer), and others.&#xA;You can plug in either recurrence values or overall survival values and perform a Survival Analysis (&lt;a href=&quot;http://en.wikipedia.org/wiki/Survival_analysis&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Survival_analysis&lt;/a&gt;, &lt;a href=&quot;http://lifelines.readthedocs.org/en/latest/Survival%20Analysis%20intro.html&quot; rel=&quot;nofollow&quot;&gt;http://lifelines.readthedocs.org/en/latest/Survival%20Analysis%20intro.html&lt;/a&gt;) to see how long people tend to live cancer-free or live in general after their diagnosis depending on their cancer type (or other variable you feel like comparing). &lt;/p&gt;&#xA;" OwnerUserId="8161" LastActivityDate="2014-07-25T19:29:32.650" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19954" PostTypeId="1" CreationDate="2014-07-25T21:02:29.893" Score="0" ViewCount="41" Body="&lt;p&gt;I have a set of microRNA ages with corresponding labels suggesting which clade they first emerged from. For instance, for hsa-mir-1, let's say, it would have an age of Eutheria. I have several peaks in the distributions of my age. One idea I had was to check to see if these peaks correspond to periods of intense specialization. For instance, the Eutheria clade saw a vast diversification of species relative to other clades. I'd like to determine this from a more computational perspective rather than Googling each clade.&lt;/p&gt;&#xA;" OwnerUserId="8499" LastActivityDate="2014-07-27T05:55:37.147" Title="Periods of Heavy Speciation" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;microrna&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19955" PostTypeId="1" AcceptedAnswerId="19956" CreationDate="2014-07-25T22:00:18.537" Score="3" ViewCount="93" Body="&lt;p&gt;can human degrade the D-amino acid present in bacterial cell wall, I'm confused about it i have read somewhere that human can do so.If yes than why we need antibiotic to kill bacteria???If it is not so than why??&lt;/p&gt;&#xA;" OwnerUserId="8301" LastActivityDate="2014-07-25T22:58:06.147" Title="bacterial cell wall degradation in humans" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;enzymes&gt;&lt;amino-acids&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19956" PostTypeId="2" ParentId="19955" CreationDate="2014-07-25T22:58:06.147" Score="1" Body="&lt;p&gt;Humans have at least one enzyme which can break down D-amino acids, the &lt;a href=&quot;http://en.wikipedia.org/wiki/D-amino_acid_oxidase&quot; rel=&quot;nofollow noreferrer&quot;&gt;D-amino acid oxidase&lt;/a&gt; (DAAO). They are able to break down these amoino acids, interestingly D-serine seems to play a role as a neurotransmitter. For more information have a look at these papers:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17396222&quot; rel=&quot;nofollow noreferrer&quot;&gt;Physiological functions of D-amino acid oxidases: from yeast to&lt;br&gt;&#xA;humans.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17924443&quot; rel=&quot;nofollow noreferrer&quot;&gt;Human D-amino acid oxidase: an update and review.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0020711X9290322R&quot; rel=&quot;nofollow noreferrer&quot;&gt;d-Amino-Acid oxidase and its physiological function&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;We still need antibiotics, since only a small part of the bacterial cell wall is composed of D-amino acids. The cell wall is made of monomers from N-acetylglucosamine and N-acetylmuramic acid which are crosslinked by small peptides (these are short amino acids chains) to form the peptidoglycane polymer. A part of the amino acids in the crosslinking peptides are D-amino acids. I am not sure if the DAAO is able to attack these peptides in the polymer. Additionally most of the enzyme in the human body is present in liver and kidney, indicating that it breaks down D-amino acids that are transported there by the bloodstream. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iWjXm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-25T22:58:06.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19957" PostTypeId="1" AcceptedAnswerId="19960" CreationDate="2014-07-25T23:21:25.380" Score="3" ViewCount="460" Body="&lt;p&gt;According to wikipedia was Archaeopteryx rather glider than capable of active flight. As a hunting strategy it crawl up to a tree (or other high positioned place) and glide from it to a prey.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Most of the modern birds are capable of active flight. Does anybody know if a (purely) gliding species of bird exist in present?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="8500" LastActivityDate="2019-02-24T14:45:46.490" Title="Does a non-extinct gliding species of bird exist?" Tags="&lt;ornithology&gt;&lt;species&gt;&lt;flight&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19960" PostTypeId="2" ParentId="19957" CreationDate="2014-07-26T06:34:07.760" Score="6" Body="&lt;p&gt;There is a classification of birds called Soaring birds.&lt;/p&gt;&#xA;&lt;h2&gt;Soaring Birds&lt;/h2&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In definition, some land birds, such as vultures and certain hawks,&#xA;sustain flight for long periods without flapping their wings. They&#xA;take advantage of updrafts produced when the wind blows over hills and&#xA;mountain ridges or make use of rising columns of warm air called&#xA;&amp;quot;thermals.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;Vultures stay within thermals by flying slowly in tight circles. They&#xA;have short, broad wings and a low wing loading (ratio of bird weight&#xA;to wing area) that allows them to remain aloft and to be highly&#xA;maneuverable at slow speeds. [1]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;h2&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_soaring_birds&quot; rel=&quot;nofollow noreferrer&quot;&gt;List of soaring birds&lt;/a&gt;&lt;/h2&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Birds of Prey&lt;/strong&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Buzzards&lt;/li&gt;&#xA;&lt;li&gt;Condors&lt;/li&gt;&#xA;&lt;li&gt;Eagles&lt;/li&gt;&#xA;&lt;li&gt;Falcons&lt;/li&gt;&#xA;&lt;li&gt;Harriers&lt;/li&gt;&#xA;&lt;li&gt;Hawks&lt;/li&gt;&#xA;&lt;li&gt;Kites&lt;/li&gt;&#xA;&lt;li&gt;Osprey&lt;/li&gt;&#xA;&lt;li&gt;Secretary Bird&lt;/li&gt;&#xA;&lt;li&gt;Vultures&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Passerine&lt;/strong&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Chough&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Cranes&lt;/strong&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Sandhill&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Sea birds&lt;/strong&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Albatrosses&lt;/li&gt;&#xA;&lt;li&gt;Frigatebirds&lt;/li&gt;&#xA;&lt;li&gt;Gulls&lt;/li&gt;&#xA;&lt;li&gt;Herons&lt;/li&gt;&#xA;&lt;li&gt;Pelicans&lt;/li&gt;&#xA;&lt;li&gt;Petrels&lt;/li&gt;&#xA;&lt;li&gt;Shearwaters&lt;/li&gt;&#xA;&lt;li&gt;Storks&lt;/li&gt;&#xA;&lt;li&gt;Terns&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Extinct&lt;/strong&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Argentavis&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;h2&gt;Buzzard&lt;/h2&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://bucksbirdclub.co.uk/Images/AdeBuzzard-450.jpg&quot; alt=&quot;&quot; /&gt;&lt;/p&gt;&#xA;&lt;h2&gt;Chough&lt;/h2&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://2.bp.blogspot.com/_OFTHTAH9590/TABAroBVZ3I/AAAAAAAACe0/UT_frhfupC4/s1600/Chough+Pyrrhocorax+Pyrrhocorax1000.jpg&quot; alt=&quot;&quot; /&gt;&lt;/p&gt;&#xA;&lt;h2&gt;Sandhill&lt;/h2&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://fatfinch.files.wordpress.com/2008/10/sandhill_crane.jpg&quot; alt=&quot;&quot; /&gt;&lt;/p&gt;&#xA;&lt;h2&gt;Albatrosses&lt;/h2&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/gDlfj.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/gDlfj.jpg&quot; alt=&quot;&quot; /&gt;&lt;/a&gt;&lt;br /&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://www.scienceviews.com/animals/images/SIA2842.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;scienceviews.com&lt;/a&gt;)&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;h2&gt;Argentavis[Extinct]&lt;/h2&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/Fyad6.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/Fyad6.jpg&quot; alt=&quot;&quot; /&gt;&lt;/a&gt;&lt;br /&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://www.mnn.com/sites/default/files/styles/featured_blog/public/gall_argentavis2.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;mnn.com&lt;/a&gt;)&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;h2&gt;Update:&lt;/h2&gt;&#xA;&lt;h2&gt;Most similar morphology to Archaeopteryx is found in Hoatzin (&lt;em&gt;Opisthocomus hoazin&lt;/em&gt;) like claws as hands as they hold the branch when they are small.&lt;/h2&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/LgbJQ.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/LgbJQ.gif&quot; alt=&quot;&quot; /&gt;&lt;/a&gt;&lt;br /&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://watersgooberswiki.pbworks.com/f/1172371778/Q1_babyhoatz.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;pbworks.com&lt;/a&gt;)&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&lt;p&gt;[1] Soaring Birds by Paul R. Ehrlich, David S. Dobkin, and Darryl Wheye.&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-02-24T14:45:46.490" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="19961" PostTypeId="1" CreationDate="2014-07-26T07:22:32.337" Score="3" ViewCount="101" Body="&lt;p&gt;I just read news article about &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;banning caffeine in alcohol drinks and &lt;/li&gt;&#xA;&lt;li&gt;about that &lt;a href=&quot;http://www.newsweek.com/caffeine-dreams-energy-drinks-increase-urge-drink-alcohol-259616&quot; rel=&quot;nofollow noreferrer&quot;&gt;energy drinks increase the urge to drink alcohol&lt;/a&gt;. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Energy drinks cause sugar intoxication - answer about it &lt;a href=&quot;https://biology.stackexchange.com/a/2276/86&quot;&gt;here&lt;/a&gt; in the thread &lt;em&gt;Decreasing the alcohol proof and faster in hangover, why?&lt;/em&gt;. &#xA;Sugar dehydrates faster as well as causes a cascade of hormonal changes that are more immediately troubling than the alcohol. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to understand why energy drinks boosts you to drink more alcohol. &#xA;This suggests me that&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;malaise (caused by energy drinks) can be improved shortly by alcohol drinks&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;by some unknown mechanisms to me; and this can be the reason why people like to drink more alcohol after energy drinks.&#xA;I think that the mechanisms are related to some cascade which I do not know. &#xA;This mechanism can lead to improvement in the dehydration very shortly &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;by acting on the membranes of the cells &lt;/li&gt;&#xA;&lt;li&gt;or by stabilising the architecture of the endothelium i.e. stabilising the hormonal changes.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My conjecture&lt;/strong&gt; is that the alcohol can affect on the secretion of the substances from endothelium (EDRF, EDCF). &#xA;There are three types of substances secreted by the endothelium&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;NO&lt;/li&gt;&#xA;&lt;li&gt;Endothelium hyperpolarising factors&lt;/li&gt;&#xA;&lt;li&gt;Endothelins&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So sugar intoxication causes changes in the endothelium architecture which alcohol intoxication reverts shortly back which boosts people to drink more alcohol to recover from the malaise caused by the energy drinks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can non-carbonated energy drinks boost alcohol intoxication?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2018-06-06T12:47:43.797" Title="Can non-carbonated energy drinks boost alcohol intoxication?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;pathophysiology&gt;&lt;alcohol&gt;&lt;sugar&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19962" PostTypeId="2" ParentId="19951" CreationDate="2014-07-26T07:40:19.820" Score="1" Body="&lt;p&gt;Cimbi-5 or 25i (25I-NBOMe) is a class 2C psychedelic drug.(wiki site.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/e/e2/2C-I-NBOMe-skeletal.svg/792px-2C-I-NBOMe-skeletal.svg.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lethal dose or LD50 of &quot;Cimbi-5&quot; is &lt;strong&gt;still unknown&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though you can predict approximate the LD50 by &lt;a href=&quot;http://preadmet.bmdrc.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;structure computationally&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.360" LastActivityDate="2014-07-26T07:40:19.820" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19964" PostTypeId="1" CreationDate="2014-07-26T09:17:18.263" Score="3" ViewCount="122" Body="&lt;p&gt;Not all men who take Viagra experience any sexual side effects about 40% have no change of sexual abilities on the pill. However like many women the drug in such cases cause a &lt;a href=&quot;http://www.forbes.com/sites/alicegwalton/2013/12/10/viagra-might-help-ease-menstrual-pain/&quot; rel=&quot;nofollow&quot;&gt;strong pain reduction&lt;/a&gt; without any considerable side effects. Also in some cases is able to eliminate persistent nausea and increase oxygen flow through the lungs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could Viagra be used for cancer patients or others who need to manage pain?&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Update:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3107342/&quot; rel=&quot;nofollow&quot;&gt;Roles for Sildenafil(or Viagra) in Enhancing Drug Sensitivity in Cancer&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="8186" LastEditDate="2014-07-28T20:01:56.997" LastActivityDate="2014-07-28T20:01:56.997" Title="Viagra for pain management" Tags="&lt;human-biology&gt;&lt;pain&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19965" PostTypeId="1" AcceptedAnswerId="19966" CreationDate="2014-07-26T10:12:06.700" Score="9" ViewCount="116" Body="&lt;p&gt;I am working in bioinformatics(part of it in Drug Designing) for years, still if I have no idea about it. As it is too hard to prove (Pass all Clinical trials) and get FDA Approvals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, My question is there a drug available in market, which is actually designed computationally?  &lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-26T10:37:25.980" Title="Is there any completely Computation Drug ever launched in market?" Tags="&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19966" PostTypeId="2" ParentId="19965" CreationDate="2014-07-26T10:37:25.980" Score="7" Body="&lt;p&gt;Yes, there are a few. Mostly they are designed in combination with X-ray crystallography of the target which should be inhibited. Then molecules are designed which fit specifically into these targets.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The oldest example I could find is Dorzolamide which acts as a carbonic anhydrase inhibitor. See here: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8164249&quot;&gt;Application of the three-dimensional structures of protein target molecules in structure-based drug design.&lt;/a&gt;&quot;&#xA;Some more examples are names in the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Drug_design#Examples&quot;&gt;drug design&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While looking for an example, I found these articles, which also look interesting:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ingentaconnect.com/content/ben/cmc/2000/00000007/00000002/art00001&quot;&gt;Molecular Modeling and Computer Aided Drug Design. Examples of their&#xA;Applications in Medicinal Chemistry&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nrd/journal/v4/n8/abs/nrd1799.html&quot;&gt;Computer-based de novo design of drug-like molecules&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bib.oxfordjournals.org/content/10/5/579.short&quot;&gt;Recent advances in computer-aided drug design&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am also not sure, to what extent the modern small molecule inhibitors like Vemurafenib (PLX4032) and others are designed using computers. At least to some extent this should be true.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-26T10:37:25.980" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19967" PostTypeId="1" AcceptedAnswerId="19968" CreationDate="2014-07-26T11:43:42.160" Score="7" ViewCount="59878" Body="&lt;p&gt;Besides religious prohibition, there are several non-religious arguments against eating pork. A few of which are:  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Pigs and swine are so poisonous that you can hardly kill them with strychnine or other poisons.  &lt;/li&gt;&#xA;&lt;li&gt;Swine and pigs have over a dozen parasites within them, eg tapeworms, flukes, worms, and trichinae. There is no safe temperature at which pork can be cooked to ensure that they will be killed&lt;/li&gt;&#xA;&lt;li&gt;The swine carries about 30 diseases which can be easily passed to humans&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I would like to hear some scholarly verification regarding these points. Simple Yes-No-Yes will be enough, elaboration is welcome, though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank You&lt;/p&gt;&#xA;" OwnerUserId="5823" LastActivityDate="2014-11-18T17:10:28.163" Title="Is pork poisonous?" Tags="&lt;toxicology&gt;&lt;medicine&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19968" PostTypeId="2" ParentId="19967" CreationDate="2014-07-26T13:22:03.787" Score="27" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;Pigs and swine are so poisonous that you can hardly kill them with strychnine or other poisons.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This is a &lt;em&gt;non-sequitur&lt;/em&gt;. An animal being poisonous does not imply that it resists to poison, nor the reverse is true.&lt;/p&gt;&#xA;&lt;p&gt;In any case, to the extent of my knowledge pigs do not produce any specific poison. Obviously, if you could provide a more specific claim, this could be tested a bit more in depth.&lt;/p&gt;&#xA;&lt;p&gt;The second part, instead, is plain false. You can definitely kill a pig with strychnine.&lt;/p&gt;&#xA;&lt;p&gt;Both the &lt;a href=&quot;http://www.merckmanuals.com/vet/toxicology/strychnine_poisoning/overview_of_strychnine_poisoning.html&quot; rel=&quot;noreferrer&quot;&gt;Merk veterinary manual&lt;/a&gt; and &lt;a href=&quot;http://books.google.co.uk/books?id=IPOsWhQgNPkC&amp;amp;pg=PA977&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Diseases of swine, 9th edition&lt;/em&gt;&lt;/a&gt; report an oral lethal dose of 0.5-1 mg/kg.&lt;/p&gt;&#xA;&lt;p&gt;For comparison, &lt;a href=&quot;http://www.cdc.gov/niosh/idlh/57249.html&quot; rel=&quot;noreferrer&quot;&gt;the CDC&lt;/a&gt; reports a probable lethal oral dose of 1.5-2 mg/kg for humans.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Swine and pigs have over a dozen parasites within them, eg tapeworms, flukes, worms, and trichinae.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Sure, pigs do have parasites. &lt;a href=&quot;http://books.google.co.uk/books?id=IPOsWhQgNPkC&amp;amp;pg=PA904&quot; rel=&quot;noreferrer&quot;&gt;Chapter 55&lt;/a&gt; of &lt;em&gt;Diseases of swine&lt;/em&gt; is specifically on parasitic infections.&lt;/p&gt;&#xA;&lt;p&gt;Now, do ALL pigs have them? The answer is no, some parasites are more common than other, and the amount of parasites depends on the health status of the farm.&lt;/p&gt;&#xA;&lt;p&gt;For instance:&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Northern Europe&lt;/strong&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9650867&quot; rel=&quot;noreferrer&quot;&gt;Roepstorff et al. 1998&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In Denmark (DK), Finland (FIN), Iceland (I), Norway (N), and Sweden (S), 516 swine herds were randomly selected in 1986-1988. Individual faecal analyses (mean: 27.9 per herd) from eight age categories of swine showed that Ascaris suum, Oesophagostomum spp., Isospora suis, and Eimeria spp. were common, while Trichuris suis and Strongyloides ransomi-like eggs occurred sporadically. Large fatteners and gilts were most frequently infected with A. suum with maximum prevalences of 25-35% in DK, N and S, 13% in I and 5% in FIN. With the exception of the remarkably low A. suum prevalence rates in FIN, no clear national differences were observed. Oesophagostomum spp. were most prevalent in adult pigs in the southern regions (21-43% in DK and southern S), less common in the northern regions (4-17% adult pigs infected), and not recorded in I. I. suis was common in piglets in DK, I, and S (20-32%), while &amp;lt; 1% and 5% were infected in N and FIN, respectively. Eimeria spp. had the highest prevalences in adult pigs (max. 9%) without clear geographical differences. I. suis and Eimeria spp. were recorded for the first time in I, and I. suis for the first time in N.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;USA&lt;/strong&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10223350&quot; rel=&quot;noreferrer&quot;&gt;Gamble et al. 1999&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;To determine Trichinella infection in a selected group of farm raised pigs, 4078 pigs from 156 farms in New England and New Jersey, employing various management styles, were selected based on feed type (grain, regulated waste, non-regulated waste).&lt;br /&gt;&#xA;[...]&lt;br /&gt;&#xA;A total of 15 seropositive pigs on 10 farms were identified, representing a prevalence rate of 0.37% and a herd prevalence rate of 6.4%. A total of nine seropositive pigs and one suspect pig from six farms were tested by digestion; four pigs (representing three farms) harbored Trichinella larvae at densities of 0.003-0.021 larvae per gram (LPG) of tissue; no larvae were found in six pigs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;China&lt;/strong&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15710534&quot; rel=&quot;noreferrer&quot;&gt;Weng et al. 2005&lt;/a&gt;):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The prevalence of intestinal parasites was investigated in intensive pig farms in Guangdong Province, China between July 2000 and July 2002. Faecal samples from 3636 pigs (both sexes and five age groups) from 38 representative intensive pig farms employing different parasite control strategies were examined for the presence of helminth ova and protozoan oocysts, cysts and/or trophozoites using standard techniques. Of the 3636 pigs sampled, 209 (5.7%) were infected with Trichuris suis, 189 (5.2%) with Ascaris, 91 (2.5%) with Oesophagostomum spp., 905 (24.9%) with coccidia (Eimeria spp. and/or Isospora suis) and 1716 (47.2%) with Balantidium coli. &lt;strong&gt;These infected pigs were mainly from farms without a strategic anti-parasite treatment regime&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However, note that &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10831052&quot; rel=&quot;noreferrer&quot;&gt;Boes et al. 2000&lt;/a&gt; reports higher percentages.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The prevalence of helminths in pigs was investigated in five rural communities situated on the embankment of Dongting Lake in Zhiyang County, Hunan Province, People's Republic of China, in an area known to be endemic for Schistosoma japonicum. The helminth prevalences identified on the basis of faecal egg count analysis were: Oesophagostomum spp. (86.7%), Ascaris suum (36.7%), Metastrongylus spp. (25.8%), Strongyloides spp. (25.8%), Trichuris suis (15.8%), Globocephalus spp. (6.7%), Gnathostoma spp. (4.2%), Schistosoma japonicum (5.0%) and Fasciola spp. (1.3%).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Kenya&lt;/strong&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18509940&quot; rel=&quot;noreferrer&quot;&gt;Nganga et al. 2008&lt;/a&gt;):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;A total of 115 gastrointestinal tracts (GIT) from 61 growers and 54 adult pigs were examined between February 2005 and January 2006. Seventy eight (67.8%) had one or more helminth parasites, of which thirty six (31.3%) were mixed infection. Ten types of helminth parasites encountered in descending order of prevalence were, Oesophagostomum dentatum (39.1%), Trichuris suis (32.2%), Ascaris suum (28.7%), Oesophagostomum quadrispinulatum (14.8%), Trichostrongylus colubriformis (10.4%), Trichostrongylus axei (4.3%), Strongyloides ransomi (4.3%), Hyostrongylus rubidus (1.7%), Ascarops strongylina (1.7%) and Physocephalus sexalutus (0.9%).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;There is no safe temperature at which pork can be cooked to ensure that they will be killed&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;False. Proper cooking, as well as freezing (but see below) are effective in killing worms.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cdc.gov/parasites/trichinellosis/gen_info/faqs.html&quot; rel=&quot;noreferrer&quot;&gt;The CDC&lt;/a&gt; suggest:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The best way to prevent trichinellosis is to cook meat to safe temperatures. A food thermometer should be used to measure the internal temperature of cooked meat. Do not sample meat until it is cooked. USDA recommends the following for meat preparation.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;For Whole Cuts of Meat (excluding poultry and wild game)&lt;/strong&gt;&lt;br /&gt;&#xA;Cook to at least 145° F (63° C) as measured with a food thermometer placed in the thickest part of the meat, then allow the meat to rest for three minutes before carving or consuming.&lt;br /&gt;&#xA;&lt;strong&gt;For Ground Meat (excluding poultry and wild game)&lt;/strong&gt;&lt;br /&gt;&#xA;Cook to at least 160° F (71° C); ground meats do not require a rest time.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Also&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Curing (salting), drying, smoking, or microwaving meat alone does not consistently kill infective worms; homemade jerky and sausage were the cause of many cases of trichinellosis reported to CDC in recent years.&lt;br /&gt;&#xA;Freeze pork less than 6 inches thick for 20 days at 5°F (-15°C) to kill any worms.&lt;br /&gt;&#xA;Freezing wild game meats, unlike freezing pork products, may not effectively kill all worms because some worm species that infect wild game animals are freeze-resistant.&lt;br /&gt;&#xA;Clean meat grinders thoroughly after each use.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The swine carries about 30 diseases which can be easily passed to humans&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Again, sure pigs can carry diseases that can be passed to humans, but proper storing and cooking of meat is effective in getting rid of the great majority of bacteria.&lt;/p&gt;&#xA;&lt;p&gt;Finally in 2012 &lt;a href=&quot;http://www.hpa.org.uk/NewsCentre/NationalPressReleases/2012PressReleases/120613HPAissuesfoodsafetyreminder/&quot; rel=&quot;noreferrer&quot;&gt;Public health England&lt;/a&gt; reported food poisoning caused by red meat as accounting for 17% of all food poisoning incidents, with pork accounting for 3%. By comparison, poultry accounted for 29% of food poisoning events (although people eat more poultry than red meat).&lt;/p&gt;&#xA;&lt;p&gt;Similarly, the &lt;a href=&quot;http://www.cdc.gov/foodborneburden/attribution-1998-2008.html&quot; rel=&quot;noreferrer&quot;&gt;CDC report on the Attribution of Foodborn Illness&lt;/a&gt; (1998-2008) puts red meat accounting for 12%, pork as accounting for 5.4% and poultry 9.8%.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-07-26T13:22:03.787" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19969" PostTypeId="2" ParentId="19967" CreationDate="2014-07-26T15:31:57.667" Score="5" Body="&lt;p&gt;First: There is no biological reason to not eat pork. These bans (Jewish and Islamic) are based on religious rules, so this is more a cultural, not so much a biological answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reasoning that pork meat would deteriorate pretty fast in warm climates is true, but it is also true for all other sorts of meat (like cattle, goat or sheep). Besides cultural reasons (think of India, where cows are holy) there is another reason according to the antrologist Marvin Harris. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In his book &quot;The Sacred Crow and the Abominable Pigs&quot; (you can find a chapter on pigs &lt;a href=&quot;http://etnologija.etnoinfolab.org/dokumenti/82/2/2009/harris_1521.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and another interesting article on that topic &lt;a href=&quot;http://aurora.icaap.org/index.php/aurora/article/view/53/66&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) he says that feeding habits are important, too. While goats, cows and sheep can be fed a grass only diet, this is not possible for pigs. They need a grain-based diet (where they compete with the humans for the food) or at least rich woods to survive. As these were depleted by the humans in the middle east, pigs couldn't be held sustainable.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-11-18T17:10:28.163" LastActivityDate="2014-11-18T17:10:28.163" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19970" PostTypeId="1" CreationDate="2014-07-26T18:50:23.250" Score="1" ViewCount="47" Body="&lt;p&gt;Where are flies attracted most? Apart from food odours, of course. Why do they seem to be attracted by hot and humid places? Do they prefer shades or light? Why do they tend to get inside very easily?&lt;/p&gt;&#xA;" OwnerUserId="1620" LastActivityDate="2014-07-27T05:39:42.380" Title="Where do flies go?" Tags="&lt;zoology&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19971" PostTypeId="1" CreationDate="2014-07-26T21:33:16.823" Score="4" ViewCount="4840" Body="&lt;p&gt;I learned the citric acid cycle in biotechnology school and how cells work; about ADP and ATP and how the Cellular respiration (C6H12O6 + 6O2 -&gt; 6CO2+6H2O) works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested in understanding why exactly too much glucose is harmful, e.g. when having diabetes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens inside the cells so that the organs get damaged over time? Why can't the cells not simply &quot;ignore&quot; the needless glucose or convert it into energy?&lt;/p&gt;&#xA;" OwnerUserId="8504" LastActivityDate="2014-07-27T12:34:20.917" Title="Why is too much glucose harmful?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;glucose&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19972" PostTypeId="1" AcceptedAnswerId="39960" CreationDate="2014-07-26T21:43:34.000" Score="5" ViewCount="23367" Body="&lt;p&gt;As a child I watched tiny fiddler crabs living in conical shells, and many years later I find that people study fossil turritellids. So now I wonder: how old are shells, typically, that you see on beaches? Do they wear out after a year of sand abrasion? 100 years, a million? Is it known? &lt;/p&gt;&#xA;" OwnerUserId="8503" LastEditorUserId="9906" LastEditDate="2016-10-10T23:37:17.930" LastActivityDate="2018-05-02T18:12:01.873" Title="Age of shells on beach" Tags="&lt;marine-biology&gt;&lt;molluscs&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19973" PostTypeId="2" ParentId="19971" CreationDate="2014-07-26T22:08:36.087" Score="2" Body="&lt;p&gt;The glucose can react with proteins, damaging them.  This is called glycation.  Note that glucose is the preferred body fuel and has a 10 fold lower ability to cause glycation than fructose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Glycation&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Glycation&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8387" LastActivityDate="2014-07-26T22:08:36.087" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19974" PostTypeId="1" AcceptedAnswerId="20093" CreationDate="2014-07-26T22:28:42.617" Score="2" ViewCount="67" Body="&lt;p&gt;I have recently begun using &lt;a href=&quot;http://folding.stanford.edu/home/&quot; rel=&quot;nofollow&quot;&gt;Folding@Home&lt;/a&gt; and I am curious how people are prevented from cheating the system. It seems to me that unless the final result is easily verifiable users could submit bogus folds in order to quickly gain credits. Is it in fact the case that the final results of calculating a protein fold are easily verifiable?&lt;/p&gt;&#xA;" OwnerUserId="8505" LastActivityDate="2014-07-30T23:11:24.730" Title="Verifying Protein Folds" Tags="&lt;protein-folding&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19975" PostTypeId="1" AcceptedAnswerId="19976" CreationDate="2014-07-26T23:16:00.017" Score="-2" ViewCount="1259" Body="&lt;p&gt;I don't understand why, if a penis can be reconstructed from a clitoris for sex change, surgical penis enlargement is not possible.&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="1368" LastEditDate="2014-07-27T00:25:41.087" LastActivityDate="2017-09-22T18:50:16.607" Title="If penis reconstruction from a clitoris is possible why isn't penis enlargement possible?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="19976" PostTypeId="2" ParentId="19975" CreationDate="2014-07-27T01:14:25.807" Score="4" Body="&lt;p&gt;If you look at urological sites for female-to-male reconstructive surgery the procedures often involve significant skin/tissue grafts and/or prostheses. See, e.g. &lt;a href=&quot;http://www.savaperovic.com/ftm-srs-metoidioplasty-total-phalloplasty.htm&quot; rel=&quot;nofollow&quot;&gt;this interesting and somewhat graphic site.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Penis enlargement (see &lt;a href=&quot;http://www.marksolomonmd.com/cosmetic-surgery/penis-enlargement.cfm&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt;) for cosmetic purposes often entails less drastic measures, such as detaching the ligaments that keep part of the shaft inside the body or grafting (relatively small areas of) tissues to widen the penis. Weights are used to keep scar tissue from drawing the penis back into the body after surgery. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The seriousness of sex re-assignment surgery would seem to make it inappropriate&lt;br&gt;&#xA;for a patient who wants a cosmetic versus a morphological change. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a huge urological literature on these topics but I think the above give an indication of why the two situations might call for different sorts of surgery. &lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-07-27T01:33:11.047" LastActivityDate="2014-07-27T01:33:11.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19978" PostTypeId="2" ParentId="19971" CreationDate="2014-07-27T04:00:17.783" Score="1" Body="&lt;p&gt;Glucose transports from the blood into the cells via facilitated diffusion. This means that glucose goes from higher concentrations (in the blood) to lower concentration (in the cell). Therefore, if you have super high glucose concentrations in the blood, you will have a ton of glucose in the cells. Glucose will oxidize by itself, thus it will contribute a lot to the oxidative stress experienced by the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question of why they cannot &quot;ignore&quot; it, it is because it simply goes down its concentration gradient via facilitated diffusion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question of why they can't convert it to energy, well they can, but too much metabolism of glucose will also generate an excess of reactive oxygen species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion, high glucose in cells generates a lot of oxidative stress, which of course, is bad.&lt;/p&gt;&#xA;" OwnerUserId="6038" LastEditorUserId="1320" LastEditDate="2014-07-27T12:22:04.733" LastActivityDate="2014-07-27T12:22:04.733" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19979" PostTypeId="2" ParentId="19970" CreationDate="2014-07-27T05:39:42.380" Score="1" Body="&lt;p&gt;As far as getting inside, they are small, and they can get in through openings you don't notice, or just sneak in when you open the door. &lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-07-27T05:39:42.380" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19980" PostTypeId="1" AcceptedAnswerId="19984" CreationDate="2014-07-27T05:41:08.137" Score="0" ViewCount="77" Body="&lt;p&gt;When a molecule is being used in some biochemical process it has a certain 3-d structure. Is this maintained throughout it's usage or can one specific molecule change it's 3-d shape while it is being 'used' in the process. Can a specific molecule in all it's interactions in a cell say , take on 4 or 5 distinct 3-d shapes??&lt;/p&gt;&#xA;" OwnerUserId="6195" LastEditorUserId="6195" LastEditDate="2014-07-27T06:08:10.253" LastActivityDate="2014-07-27T06:08:10.253" Title="About molecules and their shape" Tags="&lt;biochemistry&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19981" PostTypeId="2" ParentId="19972" CreationDate="2014-07-27T05:49:48.473" Score="3" Body="&lt;p&gt;Ages of shell as a piece can be checked or counted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://njsurfriderdrafts.files.wordpress.com/2012/03/seashells1.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Procedure:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Examine the shell's ridges with a magnifying glass.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Tabulate the number of ridges. You can approximate by number of cell per unit length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Divide the total number of ridges by 365. Each day the little mollusk&#xA; earns a new ridge, thus total will give you its age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, that is age of one shell. If you are asking the age of all of them in a beach, my guess would be as old as the beach. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Read more : &lt;a href=&quot;http://www.ehow.com/how_6331956_tell-age-seashell.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ehow.com/how_6331956_tell-age-seashell.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.373" LastActivityDate="2016-06-18T09:59:53.290" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19982" PostTypeId="2" ParentId="19946" CreationDate="2014-07-27T05:50:07.117" Score="1" Body="&lt;p&gt;Particulates can accumulate in the aveolae in the lungs. This leads to inflammation and tissue damage and scarring. This reduces the available surface area for gas transfer. Low level exposure over long periods is harmful. Asbestos workers are well known to get sick, but miners can get black lung or silicosis from inhaling mining dust, and farmers can get lung disease from inhaling dirt that gets blown up as dust. This damage usually isn't seen until they are in their 50s or 60s.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-07-27T05:50:07.117" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19983" PostTypeId="2" ParentId="19954" CreationDate="2014-07-27T05:55:37.147" Score="1" Body="&lt;p&gt;My guess (as your question need heavy editing!!) would be &lt;a href=&quot;http://www.cs.mcgill.ca/~blanchem/mirdup/&quot; rel=&quot;nofollow&quot;&gt;MiRdup&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;MiRdup Goals:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;&lt;p&gt;Validation of pre-miRNAs predictions&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Prediction of mature miRNA   &lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;  &#xA;  &lt;p&gt;Abstract: MicroRNAs (miRNAs) are short RNA species derived from hairpin-forming miRNA precursors (pre-miRNA)&#xA;  and acting as key post-transcriptional regulators. Most computational&#xA;  tools labeled as miRNA predictors are in fact pre-miRNA predictors and&#xA;  provide no information about the putative miRNA location within the&#xA;  pre-miRNA. Sequence and structural features that determine the&#xA;  location of the miRNA, and the extent to which these properties vary&#xA;  from species to species, are poorly understood. We have developed&#xA;  miRdup, a computational predictor for the identification of the most&#xA;  likely miRNA location within a given pre-miRNA or the validation of a&#xA;  candidate miRNA. MiRdup is based on a random forest classifier trained&#xA;  with experimentally validated miRNAs from miRbase, with features that&#xA;  characterize the miRNA-miRNA* duplex&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-27T05:55:37.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19984" PostTypeId="2" ParentId="19980" CreationDate="2014-07-27T05:58:08.067" Score="3" Body="&lt;p&gt;All molecules have a 3D shape. This is referred to as it's conformation. Most molecules have certain degrees of flexibility. For example, single bonds usually allow free rotation, while double bonds don't. Cyclic structures have less freedom, but can still twist into several shapes. This can be important because some molecules bend into a certain conformation and then fit into protein binding sites they normally couldn't fit into. And it's not just small molecules, proteins, RNA, and DNA fold into specific shapes, and often must be unfolded, twisted, or bent in order to carry out their function. Protein dynamics is an active field of study. A great example is the ATP synthetase, which has a large rotating portion and acts a lot like a motor.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-07-27T05:58:08.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19985" PostTypeId="2" ParentId="19124" CreationDate="2014-07-27T06:06:25.920" Score="3" Body="&lt;p&gt;Too much nitrogen can run off during rain and collect in ponds, leading to eutriphication, find more here: &lt;a href=&quot;https://en.wikipedia.org/wiki/Eutrophication&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Eutrophication&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's probably also responsible for dead zones: &lt;a href=&quot;https://en.wikipedia.org/wiki/Dead_zone_%28ecology%29&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Dead_zone_%28ecology%29&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is an important question because we've more than doubled the amount of bioavailable nitrogen on Earth in the last 100 years simply because of the haber process and man made fertilizers. This amount of nitrogen has never been available before. &lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-07-27T06:06:25.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19986" PostTypeId="2" ParentId="17754" CreationDate="2014-07-27T06:23:22.307" Score="2" Body="&lt;p&gt;The discovery strengthens the bering strait land bridge hypothesis because if I remember right they did genetic analysis and her ancestors were almost certainly east asian. As for opposing migration models, they involve boats. Some evidence exists for polynesians reaching the west coast of south america, but probably in small numbers and not before humans walked in from the north. There is more information here: &lt;a href=&quot;https://en.wikipedia.org/wiki/Models_of_migration_to_the_New_World&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Models_of_migration_to_the_New_World&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-07-27T06:23:22.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19987" PostTypeId="2" ParentId="19838" CreationDate="2014-07-27T06:33:23.593" Score="2" Body="&lt;p&gt;I think if life was transferred to either body on a probe, it would not count as alien yet because it could not have had time to develop very far on its own, since all probes are recent evolution wise. These would be offshoots from earth life. Truly alien life would most likely use different biochemistry because it originated in a different planet, it would be a totally different tree of life. However, the presence of life on the moon or mars, even if just contaminating earth bacteria, would be incredibly important for astrobiologists, as it would provide direct evidence that life can survive in these harsh environments. Life on the moon would most likely be dormant bacteria, because there is no air or water or food. However, if bacteria could survive prolonged exposure to space and be revived upon entering a suitable environment, that would provide evidence for panspermia. Read this: &lt;a href=&quot;https://en.wikipedia.org/wiki/Surveyor_3&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Surveyor_3&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If panspermia is true, then those aliens might not be that unrelated after all. But until we find one, we can't make any conclusions.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-07-27T06:33:23.593" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19988" PostTypeId="2" ParentId="14081" CreationDate="2014-07-27T06:50:36.467" Score="1" Body="&lt;p&gt;I doubt it would be efficient. Your skin is a tight, water proof membrane designed to keep water and ions and other molecules inside while keeping the outside out. The molecules that are absorbed through the skin tend to be hydrophobic organic molecules. Ions, which any dissolved salt in water would become, do not easily pass through cellular membranes or your skin. If your skin is damaged, it may have tiny holes, which would allow ions into your blood. If the link provided in the comment can be trusted ( realrawfood.com... ), and I'm skeptical, the psoriasis could have caused the damaged needed to let ions in, but I AM HIGHLY SKEPTICAL OF THESE CLAIMS. There is nothing magical about the ions in seawater. You could dissolve the same salts in distilled water and fill a bath tub with it and achieve the same non-results.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-07-27T06:50:36.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19989" PostTypeId="2" ParentId="19945" CreationDate="2014-07-27T10:00:17.423" Score="5" Body="&lt;p&gt;Animal Planet is quoting researcher Dennis C. Turner who claims this is an instinct which is supposed to tire the prey:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cats, rather, wear down prey to avoid sustaining injuries. They're motivated by self-preservation, just like most other animals, and they know what could happen if they aren't careful. Mice and rats, for example, can deliver nasty bites that can cause injury or spread disease. Birds, for their part, are able to scratch and peck. So, what's a cat to do? Rather than playing with their prey for amusement, cats tire out their victims to the point where they're too worn down to fight back. And after that, the cats will feel better, and safer, about finishing them off, according to researcher Dennis C. Turner. So while it might look like a display of cruelty, a cat playing with its prey is just an (admittedly harsh) example of animal instinct in action [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Karen B. London (animal behaviorist) agrees:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Actually, the way that cats let go of and then recapture their prey is not a way for them to have fun, but rather a way for the cats to protect themselves from serious injury. Cats kill their prey by breaking the spinal cord with a strong bite to the neck. If a cat must let go of the animal in order to grab it on the neck, that cat is risking escape or retaliation by their prey [2].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Playing (not only with prey) also gives cats experience and improves their ability to make judgments [3].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Animal Planet. &lt;em&gt;Why do cats play with their prey?&lt;/em&gt; Available from &lt;a href=&quot;http://curiosity.discovery.com/question/why-cats-play-with-prey&quot; rel=&quot;noreferrer&quot;&gt;http://curiosity.discovery.com/question/why-cats-play-with-prey&lt;/a&gt; (accessed 27.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;Karen B. London, Ph.D.. &lt;em&gt;London Zoo: Why do cats play with their food?&lt;/em&gt; Available from &lt;a href=&quot;http://azdailysun.com/lifestyles/pets/london-zoo-why-do-cats-play-with-their-food/article_46a97775-232d-5e56-b0ea-dd1c8782b062.html&quot; rel=&quot;noreferrer&quot;&gt;http://azdailysun.com/lifestyles/pets/london-zoo-why-do-cats-play-with-their-food/article_46a97775-232d-5e56-b0ea-dd1c8782b062.html&lt;/a&gt; (acessed 27.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;Perfect Paws. &lt;em&gt;Predatory Behavior of Cats.&lt;/em&gt; Available from &lt;a href=&quot;http://www.perfectpaws.com/help3.html#.U9TLpON_tJk&quot; rel=&quot;noreferrer&quot;&gt;http://www.perfectpaws.com/help3.html#.U9TLpON_tJk&lt;/a&gt; (accessed 27.07.2014)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-07-27T10:06:36.373" LastActivityDate="2014-07-27T10:06:36.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19990" PostTypeId="1" AcceptedAnswerId="19991" CreationDate="2014-07-27T10:23:00.937" Score="6" ViewCount="645" Body="&lt;p&gt;I am a computer science student, focusing on machine learning applications. I have been always interested in biology but I lack any training in it. Now, I had an idea that I could introduce myself to biology more by buying a microscope, and doing some small (still serious, if possible) experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the problem one I am facing is what kind of microscope should I get? Preferred answer would outline what kind of research is possible to do with such and such microscope, and what is the typical price range for the system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there are any safety (e.g. does any of the UV leak from fluorescence microscopes?) or ethical concerns I would like to hear about them too. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="8509" LastActivityDate="2014-12-20T15:14:05.793" Title="What kind of microscope for ML/biological research?" Tags="&lt;microscopy&gt;&lt;fluorescent-microscopy&gt;&lt;safety&gt;&lt;research-tools&gt;" AnswerCount="4" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="19991" PostTypeId="2" ParentId="19990" CreationDate="2014-07-27T11:07:02.300" Score="6" Body="&lt;p&gt;This really depends on the application you have in mind. As with other precision instruments there is a huge range of qualities and applications. &#xA;If you just want brigth field illumination and look at relatively big things ( approx 100 microns) then you could find something decent for the price you mention if you buy used. &#xA;But if you want more complex imaging techniques like confocal microscopy or fluorescence microscopy to image smaler strutures and cell imaging then your budget is probably not enough. There you probably won't get a decent microscope for less than 2500 Euro. &#xA;I think you should figure out what you want to do with your instrument not just buy one and then get started.&lt;/p&gt;&#xA;" OwnerUserId="8494" LastActivityDate="2014-07-27T11:07:02.300" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="19992" PostTypeId="2" ParentId="19990" CreationDate="2014-07-27T11:52:37.127" Score="10" Body="&lt;p&gt;I agree with @Jeremias Brand's answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pretty much you will have to forget about fluorescence microscopy... you can probably find some dusty old one on eBay in your price range, but it probably won't be any good.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the good news is that seen that in your comment you mention &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a) plants, b) blood, c) liquids such as wine, d) food? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;transmitted light (white light) would be perfect for a start.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;eBay is surely a good place for finding used objectives at a cheap price. You may end up with a good collection of objectives for less than 100€.&#xA;That is surely tempting, and it may actually be OK as a start.&lt;br&gt;&#xA;However, I personally think that it is better to own a good lower magnification objective than a cheap high-magnification one, so be always be a bit wary about offers that look too good to be true (especially for new piece of equipment).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would strongly suggest getting a binocular microscope (so with two eyepieces), rather than a monocular one. Makes life much easier. &#xA;Also, be sure to have a camera attachment. While a camera may not be strictly necessary, especially at the beginning, it's better to have an attachment so that you can add one in the future, if you feel the need of taking pictures. Although many microscopes have specialized attachments for microscope cameras, you can get away with using your own normal camera, or even your cellphone, if you position it correctly (may need some DIY depending on the situation). &#xA;This &lt;a href=&quot;http://www.microbehunter.com/connecting-a-camera-to-a-microscope/&quot; rel=&quot;nofollow&quot;&gt;page&lt;/a&gt; has very detailed explanations on how to connect a camera to a microscope.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your samples, plants are a very good and easy thing to start observing. Onions are probably one of the best samples to start with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may also want to stain your samples. Probably the easiest thing to get is methylene blue, which should be a few euros for 20-30 ml. However, fountain pen ink &lt;a href=&quot;http://en.wikibooks.org/wiki/School_Science/Staining_onion_cells_without_methylene_blue&quot; rel=&quot;nofollow&quot;&gt;works as well&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whenever you use chemicals, remember to look for their safety data sheet (MSDS). Methylene blue is pretty safe to work with, provided you don't swallow it (doh...) and use gloves (standard latex gloves are OK). Be careful because it stains and can be a bit messy, which is true for pen ink as well!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Crystals are also pretty cool to watch under a microscope: take a coverslip, put on a drop of sugary or salty water and wait for it to dry!&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2014-10-07T17:47:07.470" LastActivityDate="2014-10-07T17:47:07.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19993" PostTypeId="2" ParentId="19971" CreationDate="2014-07-27T11:55:59.550" Score="1" Body="&lt;p&gt;Too much glucose leads to the formation of advanced glycated end products, which deposit in tissues like glomerulus and cause disease like diabetic nephropathy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also glucose is osmotically active, so when it starts appearing in urine (because of its high levels in blood), it leads to polyuria, following which the lost water is recovered from body tissues, leading to dehydration and increased thirst.&lt;/p&gt;&#xA;" OwnerUserId="8510" LastEditorUserId="1320" LastEditDate="2014-07-27T12:20:48.220" LastActivityDate="2014-07-27T12:20:48.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19994" PostTypeId="2" ParentId="19971" CreationDate="2014-07-27T12:34:20.917" Score="8" Body="&lt;h2&gt;High intracellular glucose.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Affects:&lt;/strong&gt; all cells that do not depend on insulin to take in glucose. Examples: neurons [1], kidney cells, retina cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Causes:&lt;/strong&gt; high extracellular glucose (in most cases hyperglycemia)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Effects:&lt;/strong&gt; promoting necrotic cell death through $H_2O_2$ (peroxide) formation, which may participate in the development of diabetic vasculopathies and associated disease [2].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;High extracellular glucose.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Affects:&lt;/strong&gt; extracellular matrix, cardiac muscle&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Causes:&lt;/strong&gt; lack of / low levels of insulin, &lt;a href=&quot;http://en.wikipedia.org/wiki/Insulin_resistance&quot;&gt;insulin resistance&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Effects:&lt;/strong&gt; enhances collagen production thus affecting kidney by thickening glomerular basal membrane [3, 4]. It promotes cardiomyocyte metabolic stress and altered glucose handling [5]. It is also a potential mechanism involved in cardiac glycogen accumulation [5].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Diabetes mellitus&lt;/strong&gt; involves:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;high extracellular glucose, leading to:&lt;/li&gt;&#xA;&lt;li&gt;high intracellular glucose in cells that do not depend on insulin to uptake glucose;&lt;/li&gt;&#xA;&lt;li&gt;low intracellular glucose in cells that depend on insulin (muscle and fat tissue).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;David R. Tomlinson and Natalie J. Gardiner. Glucose neurotoxicity (2008). Available from &lt;a href=&quot;http://didattica.uniroma2.it/assets/uploads/corsi/140868/Glucose_Neurotoxicity_-NATURE_Reviews-Neuro,_Jan_2008.pdf&quot;&gt;http://didattica.uniroma2.it/assets/uploads/corsi/140868/Glucose_Neurotoxicity_-NATURE_Reviews-Neuro,_Jan_2008.pdf&lt;/a&gt; (accessed 27.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;RnCeus.com. Glucose Homeostasis (2012). Available from &lt;a href=&quot;http://www.rnceus.com/dmeds/glucose.html&quot;&gt;http://www.rnceus.com/dmeds/glucose.html&lt;/a&gt; (accessed 27.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;Takeuchi A, Throckmorton DC, Brogden AP, Yoshizawa N, Rasmussen H, Kashgarian M. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7840239&quot;&gt;Periodic high extracellular glucose enhances production of collagens III and IV by mesangial cells.&lt;/a&gt; Am. J. Physiol. 1995 Jan;268(1 Pt 2):F13-9. PubMed PMID: 7840239. &lt;/li&gt;&#xA;&lt;li&gt;Ayo SH, Radnik RA, Garoni JA, Glass WF, Kreisberg JI. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2356864&quot;&gt;High glucose causes an increase in extracellular matrix proteins in cultured mesangial cells.&lt;/a&gt; Am. J. Pathol. 1990 Jun;136(6):1339-48. PubMed PMID: 2356864. &lt;/li&gt;&#xA;&lt;li&gt;Kimberley M. Mellor , Upasna Varma , David I. Stapleton , Lea M. D. Delbridge. &lt;a href=&quot;http://ajpheart.physiology.org/content/306/8/H1240&quot;&gt;&lt;em&gt;Cardiomyocyte glycophagy is regulated by insulin and exposure to high extracellular glucose.&lt;/em&gt;&lt;/a&gt; American Journal of Physiology - Heart and Circulatory PhysiologyPublished 15 April 2014Vol. 306no. H1240-H1245DOI: 10.1152/ajpheart.00059.2014&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-07-27T12:34:20.917" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19995" PostTypeId="2" ParentId="19990" CreationDate="2014-07-27T14:35:39.780" Score="9" Body="&lt;p&gt;With all respect I think the accepted answer underestimates the quality of current inexpensive instruments. What I have found comparing images on my recently acquired $400 scope to those produced by top-end Nikons is that it produces images which are aesthetically less appealing but nearly identical in detail. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mostly I have used it for fungi, which are well-suited for optical magnifications. To get the full benefit you need a PC to run the imaging software, so that expense must be factored in. Here is I think a pretty clear  image of &lt;em&gt;Aspergillus&lt;/em&gt; (tape mount) showing concave spores.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PXmDM.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I hit the Lotto I will get a $7000 scope but I am really amazed at what I can see with this very inexpensive scope (and there are several similar brands available). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example--&lt;a href=&quot;http://www.google.com/search?q=trichphyton%20images&amp;amp;client=safari&amp;amp;rls=en&amp;amp;tbm=isch&amp;amp;tbo=u&amp;amp;source=univ&amp;amp;sa=X&amp;amp;ei=xQfVU67QK5K3yASiu4H4BQ&amp;amp;ved=0CCAQsAQ&amp;amp;biw=1183&amp;amp;bih=727#facrc=_&amp;amp;imgdii=_&amp;amp;imgrc=XE_Kab2j9tbcUM%253A%3Bh9RnZxq4YOWb7M%3Bhttp%253A%252F%252Fwww.mycology.adelaide.edu.au%252Fimages%252Fajelloi1.jpg%3Bhttp%253A%252F%252Fwww.mycology.adelaide.edu.au%252Fvirtual%252F2011%252FID2-May11.html%3B400%3B277&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;here&lt;/strong&gt;&lt;/a&gt; is a high-end google image of &lt;em&gt;Trichophyton sp.&lt;/em&gt; showing the diagnostic macroconidium. Everything that is wrong and right with the inexpensive scope can be seen by comparing the photo below: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hXflW.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The color is a bit garish (the blue stain is intentional) and there is always a background color as opposed to a neutral field). But the detail is very good. I had borrowed a scope from a friend and did not hesitate to buy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The claim that one is restricted to objects of about 100$ \mu$ is incorrect. I bought a decent calibrating slide and here is a snippet of an image showing &lt;em&gt;Penicillium&lt;/em&gt; spores. The small divisions are 10 microns. I didn't bother to calibrate the slide but the order of magnification is amply supported by the sorts of structures I have seen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gY0O7.jpg&quot; alt=&quot;enter image description here&quot;&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, the clarity and aesthetic appeal of images captured with a $7000 scope cannot be achieved, nor can you do good phase-contrast or florescence. But the functionality is really pretty amazing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below is a group of very small Penicillium from potato dextrose agar. The spores are not much bigger than 1 micron in diameter. It's not a crisp image but conveys a good sense of what an intact structure looks like.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FJfV7.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.photomacrography.net/forum/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Amateurmicrography.net&lt;/a&gt; has some nice images that can give you an idea of what different scopes can do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: added an image 7/31/14.&lt;/p&gt;&#xA;" OwnerUserId="1368" LastEditorUserId="1368" LastEditDate="2014-12-20T15:14:05.793" LastActivityDate="2014-12-20T15:14:05.793" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="19996" PostTypeId="1" CreationDate="2014-07-27T14:52:53.287" Score="3" ViewCount="145" Body="&lt;p&gt;How are new staining protocols designed for microscopy? Is it manual work or does it rely on computer simulations?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Say for example I thought the H&amp;amp;E staining does not bring enough contrast. How would I go about producing The Superb H&amp;amp;E Staining Protocol (not necessarily using just hemalum and eosin Y)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking this from a mathematical point of view, the staining is some operator O applied on image I to produce enhanced image E. While clearly the operator O depends on the particular type of specimen, what I want to see, etc., there are surely some general principles guiding the search for finding an appropriate operator O? What are they?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the question is on hold, maybe I can try to put it even more clearly. How was the H&amp;amp;E staining invented? What was the process for its invention? I don't see why it would be unclear what I am asking. Dear biologists please take a more interdisciplinary approach.. If the question really is not answerable as such, please explain why. There's probably an answer in that.&lt;/p&gt;&#xA;" OwnerUserId="8511" LastEditorUserId="8511" LastEditDate="2014-07-28T20:00:49.317" LastActivityDate="2017-04-23T12:04:24.670" Title="How are new staining protocols designed for microscopy?" Tags="&lt;microscopy&gt;&lt;staining&gt;" AnswerCount="1" CommentCount="10" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="19997" PostTypeId="2" ParentId="10413" CreationDate="2014-07-27T18:49:09.763" Score="3" Body="&lt;p&gt;Osteocytes attach to each other by cytoplasmic extensions through gap junctions [1]. The connections between these cells are formed since they were osteoblasts and osteoid-osteocytes (type II preosteocyte) [1]. Osteoblasts have a greater volume than osteocytes and the lack of extracellular matrix favors their adhesion. As they begin to synthesize extracellular matrix, their volume is reduced and this matrix takes space between cells, but with respect to the existent intercellular junctions around which matrix forms canaliculi.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/File:Osteoblast_Organization.jpg#mediaviewer/File:Osteoblast_Organization.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/en/b/b1/Osteoblast_Organization.jpg&quot; alt=&quot;Osteoblast Organization.jpg&quot;&gt;&lt;/a&gt;&lt;br&gt;&quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/File:Osteoblast_Organization.jpg#mediaviewer/File:Osteoblast_Organization.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Osteoblast Organization&lt;/a&gt;&quot; by Physio Muse - I drew this figure in drawperfect, printed to .pdf, and converted to .jpg&#xA;Previously published: Not published in any form, including not used on any website. Via &lt;a href=&quot;//en.wikipedia.org/wiki/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;.&lt;/p&gt; &#xA;&#xA;&lt;p&gt;Osteoblasts are connected via gap junctions mediated by connexin43 protein [2]. Mature osteocytes attach to the bone matrix by integrins (alphavbeta3) [3].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Osteocyte,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Osteocyte&amp;amp;oldid=618657480&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Osteocyte&amp;amp;oldid=618657480&lt;/a&gt; (accessed July 27, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Civitelli R. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18424255&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cell-cell communication in the osteoblast/osteocyte lineage.&lt;/a&gt; Arch. Biochem. Biophys. 2008 May 15;473(2):188-92. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.abb.2008.04.005&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1016/j.abb.2008.04.005&lt;/a&gt;. PubMed PMID: 18424255. &lt;/li&gt;&#xA;&lt;li&gt;McNamara LM, Majeska RJ, Weinbaum S, Friedrich V, Schaffler MB. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19248169&quot; rel=&quot;nofollow noreferrer&quot;&gt;Attachment of osteocyte cell processes to the bone matrix.&lt;/a&gt; Anat Rec (Hoboken). 2009 Mar;292(3):355-63. doi: &lt;a href=&quot;http://dx.doi.org/10.1002/ar.20869&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1002/ar.20869&lt;/a&gt;. PubMed PMID: 19248169. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.387" LastActivityDate="2014-07-27T18:49:09.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19998" PostTypeId="1" AcceptedAnswerId="21289" CreationDate="2014-07-27T19:35:22.297" Score="5" ViewCount="4121" Body="&lt;p&gt;Which part of the brain is the first place (from top to bottom) where all 31 pairs of spinal nerves (on each side) meet? Or if they all start at one place - where is that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nominally, the beginning of the spinal cord is the medulla oblongata, but perhaps the spinal nerves or some sort of &quot;root&quot; of every nerve start at the Thalamus?&lt;/p&gt;&#xA;" OwnerUserId="8055" LastActivityDate="2017-07-27T15:59:56.993" Title="Where do the 31 spinal nerves start/meet?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;physiology&gt;&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="19999" PostTypeId="2" ParentId="14081" CreationDate="2014-07-27T20:50:22.227" Score="10" Body="&lt;p&gt;There is not very much transport of ions or water through the upper layer of the skin, mainly responsible for that is the stratum corneum (SC). Through this layer you will get only with small lipids and also substances which are able to penetrate the lipid layer of the cells like chloroform or DMSO. I think therefore that it is pretty unlikely that you can take up noteworthy amounts of ions (which would have to pass through the lipid layer of the cells which is highly hygrophobic) through the skin. Have a look at these publications:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0167273892903783&quot;&gt;Routes of ionic permeability through mammalian skin&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24392787&quot;&gt;Skin permeabilization for transdermal drug delivery: recent advances&#xA;and future prospects.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Interestingly this is different for other animals. The pacific hagfish is able to resorb organic nutients through his skin, see this &lt;a href=&quot;http://www.asknature.org/strategy/1f3507e596cbbc0ac8b4af4aa23d43aa#.U9VcGKMwJ8F&quot;&gt;article&lt;/a&gt; or this publication:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158932/&quot;&gt;Adaptations to in situ feeding: novel nutrient acquisition pathways&#xA;in an ancient vertebrate&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-27T20:50:22.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20000" PostTypeId="2" ParentId="19926" CreationDate="2014-07-27T20:52:20.057" Score="1" Body="&lt;p&gt;&lt;em&gt;This answer is based on embryological studies and is limited. &#xA;I will extend it later when understand better.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sensory areas&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;maculae acusticae - walls of utricle and saccule (this most probable area)&lt;/li&gt;&#xA;&lt;li&gt;cristae acusticae - change in body position&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Nerve &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;vestibular fibers of cranial nerve VIII (TODO each branchial arch has a nerve - how these differentiate between different arches?)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Embryonal Ganglion&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;statoacoustic (spinal) ganglion (19.5 C Fig)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Embryonal ganglion splits into two &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;cochlear portion&lt;/li&gt;&#xA;&lt;li&gt;vestibular portion&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which supply sensory cells of organ of Corti, and those of the saccule, utricle and semicircular canals, respectively&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Branchial Arches&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Each arch has a vessel, cartilage and nerve. &#xA;The task is to understand which part of embryonal ear is able to start hypersensitivity reaction. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Middle ear&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Tympanic Cavity and Auditory Tube&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;origin endoderm (1st pharyngeal pouch) - malleus and incus&lt;/li&gt;&#xA;&lt;li&gt;malleus - 2nd a.a.a.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Eardrum or Tympanic Membrane&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ectodermal epithelial lining at bottom of auditory meatus&lt;/li&gt;&#xA;&lt;li&gt;endodermal epithelial lining of the tympanic cavity&lt;/li&gt;&#xA;&lt;li&gt;intermediate layer of connective tissue (See Langmans' Fig 19.9B). TODO this part is superficially covered in Langmans. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Auricle&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;6 mesenchymal proliferations at dorsal ends of 1-2 a.a.a.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;TODO I must look again embryonal slides of ear to see where the nerves occur first and how they develop. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sources&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Langmans Medical Embryology, 12th ed, 2011&lt;/li&gt;&#xA;&lt;li&gt;My notes of Embryology classes, Spring 2014 (I did not have all my notes now so must study these things again after holiday)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-07-27T20:52:20.057" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20001" PostTypeId="2" ParentId="19749" CreationDate="2014-07-27T21:23:39.473" Score="2" Body="&lt;p&gt;Okay, I finally figured it out. Basically there are those following 6 steps:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Preparing a protein&lt;/li&gt;&#xA;&lt;li&gt;Preparing a ligand&lt;/li&gt;&#xA;&lt;li&gt;Generating a grid parameter file&lt;/li&gt;&#xA;&lt;li&gt;Generating maps and grid data files&lt;/li&gt;&#xA;&lt;li&gt;Generating a docking parameter file&lt;/li&gt;&#xA;&lt;li&gt;Running AutoDock&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Since the details are a little bit too lengthy for this post, I have written it up as a tutorial. A lot of people (like me) seemed to struggle to get it to work, so I thought this write-up could be a useful reference: &lt;a href=&quot;http://sebastianraschka.com/Articles/2014_autodock_energycomps.html&quot; rel=&quot;nofollow&quot;&gt;AutoDock4.2 re-scoring tutorial&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user6881" LastActivityDate="2014-07-27T21:23:39.473" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20002" PostTypeId="1" AcceptedAnswerId="20012" CreationDate="2014-07-28T01:33:23.987" Score="6" ViewCount="5557" Body="&lt;p&gt;Let's say I drink some Kefir Milk, what happens to the lactic acid in the Kefir Milk that has entered my digestive system?&lt;/p&gt;&#xA;" OwnerUserId="8513" LastActivityDate="2019-08-12T23:02:36.473" Title="What happens to lactic acid I eat?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;food&gt;&lt;digestive-system&gt;&lt;digestion&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20003" PostTypeId="2" ParentId="20002" CreationDate="2014-07-28T02:20:16.873" Score="5" Body="&lt;p&gt;Lactic acid has been found to act as a fuel for the muscles. Refer to:  &lt;a href=&quot;http://www.nytimes.com/2006/05/16/health/nutrition/16run.html?_r=0&quot;&gt;http://www.nytimes.com/2006/05/16/health/nutrition/16run.html?_r=0&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Most athletes consider lactic acid their enemy, and think that training helps eliminate the metabolic waste product from their muscles so the muscles will function longer and harder. But UC Berkeley physiologist George Brooks has found that training actually teaches muscle cells how to use lactic acid as a fuel to get more bang for the buck. With training, mitochondria grow, take in more lactate via a shuttle and burn it to generate more energy.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&quot;I gave rats radioactive lactic acid, and I found that they burned it faster than anything else I could give them,&quot; Dr. Brooks said.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You may also refer to &lt;a href=&quot;http://www.eatmoveimprove.com/2009/11/the-truth-about-lactic-acid/&quot;&gt;http://www.eatmoveimprove.com/2009/11/the-truth-about-lactic-acid/&lt;/a&gt; for details on lactic acid metabolism.&lt;/p&gt;&#xA;" OwnerUserId="8216" LastActivityDate="2014-07-28T02:20:16.873" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20004" PostTypeId="1" AcceptedAnswerId="28229" CreationDate="2014-07-28T02:35:00.200" Score="6" ViewCount="451" Body="&lt;p&gt;For controlling &lt;a href=&quot;http://en.wikipedia.org/wiki/Cynodon_dactylon&quot; rel=&quot;nofollow noreferrer&quot;&gt;bermudagrass, &lt;em&gt;Cynodon dactylon&lt;/em&gt;&lt;/a&gt;, a serious perennial grassy lawn weed in my area, I use the herbicide &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/B001D25Y0K&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fenoxaprop-P-ethyl&lt;/a&gt;. It kills the bermudagrass rather well, without damaging the cool season lawn grass in the least.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HXTC8.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe Fenoxaprop-P-ethyl acts by inhibiting the synthesis of fatty acids in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Meristem&quot; rel=&quot;nofollow noreferrer&quot;&gt;meristematic tissues&lt;/a&gt; of the weedy grasses (designed especially for bermudagrass).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this mode of action not affect the 'good' grasses (the fescues, bluegrasses, and ryegrasses popular in my area)?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2015-01-28T03:22:37.030" LastActivityDate="2015-02-01T12:21:41.587" Title="Why doesn't Fenoxaprop-P-ethyl damage cool season lawns?" Tags="&lt;botany&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20005" PostTypeId="1" AcceptedAnswerId="20010" CreationDate="2014-07-28T03:21:02.873" Score="3" ViewCount="263" Body="&lt;p&gt;In my area, the most common weeds that strongly resists &lt;a href=&quot;http://en.wikipedia.org/wiki/Glyphosate&quot; rel=&quot;nofollow noreferrer&quot;&gt;(N-(phosphonomethyl)glycine)&lt;/a&gt; (glyphosate) are the horseweed, or mare's tail, &lt;a href=&quot;http://en.wikipedia.org/wiki/Conyza_canadensis&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Conyza canadensis,&lt;/em&gt;&lt;/a&gt; and Canada thistle, &lt;a href=&quot;http://en.wikipedia.org/wiki/Cirsium_arvense&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Cirsium arvense&lt;/em&gt;&lt;/a&gt; There are several other weeds with similar resistance. I use the brand &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/B007XZ90QA&quot; rel=&quot;nofollow noreferrer&quot;&gt;Roundup&lt;/a&gt; on jobs where a complete kill is necessary. However, I sometimes have to go through again, with &lt;a href=&quot;http://www.bayercropscience.us/products/herbicides/liberty&quot; rel=&quot;nofollow noreferrer&quot;&gt;glufosinate&lt;/a&gt;, to control these weeds. I'd prefer not to, as the glufosinate lingers much longer in the soil.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/D6HOt.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glyphosate inhibits an enzyme used in the synthesis of the aromatic amino acids tryptophan, tyrosine,  and phenylalanine. It is taken in by the stomata in the leaves, and is moved throughout the plant to all the points of growth, acting fastest on those plants which are undergoing fastest growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't seem to find an article on how the weeds mentioned can tolerate this treatment. How do these weeds resist the glyphosate?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2015-01-28T03:21:25.180" LastActivityDate="2015-01-28T03:21:25.180" Title="How can a plant resist glyphosate (Roundup) herbicide?" Tags="&lt;botany&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20006" PostTypeId="1" AcceptedAnswerId="20138" CreationDate="2014-07-28T04:15:01.213" Score="6" ViewCount="10100" Body="&lt;p&gt;I sometimes use &lt;a href=&quot;http://www.ruralking.com/agristar-2-4-d-amine-1-gallon.html?utm_medium=cse&amp;amp;utm_source=google&amp;amp;CAWELAID=1624250989&amp;amp;CAGPSPN=pla&amp;amp;catargetid=520009190000031013&amp;amp;cadevice=c&amp;amp;gclid=CjwKEAjwxtKeBRDMzoeQmYn5uHcSJACGCF3Dhs22FITlehPhZgOacOeZU5_PbIz8W8iI4BOsuTyoPBoCeW7w_wcB&quot; rel=&quot;noreferrer&quot;&gt;2,4-Dichlorophenoxyacetic acid&lt;/a&gt; to control broadleaved weeds in lawns. It is selective, and quickly kills the dicot weeds, while other plants are unharmed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tGMsm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2,4-D is a synthetic auxin, a class of plant hormones. It is gets taken in through the stomata on the leaves, and is transported to the meristems of the plant. This causes uncontrolled, unsustainable growth, and the plant wilts, and dies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why doesn't this affect most monocotyledons?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2015-01-28T03:20:30.053" LastActivityDate="2019-11-28T17:12:06.470" Title="Why doesn't the herbicide 2,4-D damage lawn grass?" Tags="&lt;botany&gt;&lt;toxicology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20007" PostTypeId="2" ParentId="19948" CreationDate="2014-07-28T05:45:39.870" Score="3" Body="&lt;p&gt;Michaelis-Menten: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$V=V_{max}.\frac{[S]}{Ks+[S]}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lineweaver-Burk: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\frac{1}{V}=\frac{Ks}{V_{max}[S]}+\frac{1}{V_{max}}$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plot $\frac{1}{V}$ vs $\frac{1}{[S]}$; find the slope and intercept of this plot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending on what you consider as primary substrate (glucose??) measure the concentrations using appropriate assays. Glucose sensors (based on glucose oxidase) are available or you can do conventional biochemical assays (DNSA) for glucose and other reducing sugars. To find the growth rate, measure OD at different time-points and get the differences of OD in a time interval. A better method would be to make a scatter-plot of OD and time and fit a polynomial function. Get rate by taking the tangent of the curve at that time-point.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-07-28T07:49:10.837" LastActivityDate="2014-07-28T07:49:10.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20010" PostTypeId="2" ParentId="20005" CreationDate="2014-07-28T10:10:07.097" Score="3" Body="&lt;p&gt;I found &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080097/?report=classic&quot; rel=&quot;nofollow&quot;&gt;a paper investigating the mechanism of glyphosate resistance in &lt;em&gt;Conyza canadensis&lt;/em&gt;&lt;/a&gt;. They used &lt;sup&gt;31&lt;/sup&gt;P NMR to investigate the fate of the glyphosate &lt;em&gt;in vivo&lt;/em&gt;. What they found is that the resistant plants are able to transport glyphosate into the vacuole:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The following view of horseweed resistance to glyphosate emerges from&#xA;  the data presented herein. Glyphosate enters the cytoplasm of both R&#xA;  and S plant variants at the same rate. Within hours, however,&#xA;  glyphosate begins to occupy the vacuole in the R but not the S&#xA;  biotype. The identical pH values of R and S vacuoles speak against the&#xA;  possibility of a pH-driven process. This, coupled with the&#xA;  preferential movement of glyphosate from the cytosol to the vacuole in&#xA;  R tissue but not in S, suggests the presence of a transporter for&#xA;  glyphosate either specific to R or at a substantially greater&#xA;  concentration in R than in S tissue.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Another paper titled &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0176161712002945&quot; rel=&quot;nofollow&quot;&gt;&quot;Two non-target mechanisms are involved in glyphosate-resistant horseweed (Conyza canadensis L. Cronq.) biotypes&quot;&lt;/a&gt; found a different mechanism for glyphosate resistance in addition to the sequestration into the vacuole.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Glyphosate was metabolized faster in the R (C004) biotype than in the&#xA;  S biotype. The herbicide disappeared completely from the R (C004)&#xA;  biotype by conversion into glyoxylate, sarcosine and&#xA;  aminomethylphosphonic acid within 96 HAT.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The resistant plants seem to be able to metabolize glyphosate more effectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is of course not guarenteed that these are the only mechanisms for glyphosate resistance, there are likely more variations.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-07-28T10:10:07.097" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20011" PostTypeId="2" ParentId="9054" CreationDate="2014-07-28T10:43:40.080" Score="1" Body="&lt;p&gt;Yes, they can induce an acute attack.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Drugs metabolised by cytochrome P450 (CYP) such as analgesics may induce acute attacks in patients with hepatic porphyrias. In recent years, preclinical and clinical studies have suggested that cannabinoid pharmaceutical preparations may be potentially useful in the treatment of pain [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is even a clinical case about acute intermittent porphyria in a marijuana user:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mr. G is a 55 year old Caucasian male with a past medical history significant for acute intermittent porphyria (AIP), chronic back pain, renal insufficiency, hypertension, and nicotine dependence. The patient has presented to the hospital with multiple AIP exacerbations since diagnosed eleven year prior to the current case. [...] Urine drug screen was positive for cannabinoids, which he admitted to frequent marijuana use [2].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But an experimental study on mice failed to prove that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our findings indicate that CP-55,940 (a cannabinoid CB1 receptor agonist) and its metabolites do not behave as porphyrinogenic drugs and may potentially be safe for treating pain in patients with acute porphyrias [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Fontanellas A, Manzanares J, García-Bravo M, Buzaleh AM, Méndez M, Oliva JM, Batlle A, Palomo T, Enríquez de Salamanca R. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15896668&quot; rel=&quot;nofollow&quot;&gt;Effects of repeated administration with CP-55,940, a cannabinoid CB1 receptor agonist on the metabolism of the hepatic heme.&lt;/a&gt; Int. J. Biochem. Cell Biol. 2005 Aug;37(8):1620-5. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.biocel.2005.02.010&quot; rel=&quot;nofollow&quot;&gt;10.1016/j.biocel.2005.02.010&lt;/a&gt;. PubMed PMID: 15896668.&lt;/li&gt;&#xA;&lt;li&gt;Ware SK. Acute Intermittent Porphyria With Psychiatric Manifestations: A Case Report. Ment Health Clin. 2013;3(5):100. Available at: &lt;a href=&quot;http://cpnp.org/resource/mhc/2013/11/acute-intermittent-porphyria-psychiatric-manifestations-case-report&quot; rel=&quot;nofollow&quot;&gt;http://cpnp.org/resource/mhc/2013/11/acute-intermittent-porphyria-psychiatric-manifestations-case-report&lt;/a&gt;. Accessed July 27, 2014.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-07-28T10:43:40.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20012" PostTypeId="2" ParentId="20002" CreationDate="2014-07-28T11:15:21.830" Score="10" Body="&lt;p&gt;First, there are two different isomers of the lactic acid, the L(+)- and the D(-)-form. Both differ in the position of the OH-group in the molecule:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FdfH2.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both turn polarized light in different ways, the D(-) to the left and the L(+) to the right. The physiological form of lactic acid for the human body is the L(+) form, which is taken up in the gut and then metabolized by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Lactate_dehydrogenase&quot; rel=&quot;nofollow noreferrer&quot;&gt;L-Lactatdehydrogenase&lt;/a&gt; to form pyruvate and NADH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the D(-)-Lactate is has been thought the the D-Lactatedehydrogenase is only present in some lower animals and bacteria and that this lactate isoform is mostly excreted. This seems not to be true and there is some D-Lactatedehydrogenase in humans (and other mammals) as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See these publication for more information:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15987839&quot; rel=&quot;nofollow noreferrer&quot;&gt;D-lactate in human and ruminant metabolism.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-28T11:15:21.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20013" PostTypeId="2" ParentId="19567" CreationDate="2014-07-28T11:30:20.677" Score="2" Body="&lt;p&gt;Yes, stem cells can pass through blood vessels and capillaries (as @WYSIWYG points, these cells should be small enough to fit inside that capillary). The interesting thing is that they posses multiple mechanisms of transmigration. They are attracted by TNF-alpha activated endothelial cells [1] and can pass through by [1]:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;leukocyte-like diapedesis&lt;/li&gt;&#xA;&lt;li&gt;paracellular migration between endothelial cells&lt;/li&gt;&#xA;&lt;li&gt;transcellular, directly through individual endothelial cells&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I am thinking of some type of encapsulated stem cells where ultrasound, heat or magnetic fields from the MRI would break up the encapsulation releasing the stem cell at the targeted area.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;Note: I don't know if the following is plausible. It is just something I thought of and I consider it to be more effective than what you suggested.&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then what is the purpose of using stem cells that are capable of chemotactic movements and can go by themselves in targeted areas? The encapsulation you propose could be used to fit inside the cell a drug-containing capsule that would break upon external electromagnetic, ultrasonic (etc.) stimulation. This means that the capsule would also contain a substance capable of inducing cytoplasmic membrane lysis, so the drug could reach the interstitial space. Or the cell could be genetically engineered to secrete that drug, when available in cytoplasm, through exocytosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But why not get rid of that capsule? A cell could contain (for example) a cytostatic drug in its cytoplasm and also be fitted with membrane receptors for a specific tumoral marker. When it reaches the tumor, receptor stimulation should trigger exocytosis of drug.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Teo GS, Ankrum JA, Martinelli R, Boetto SE, Simms K, Sciuto TE, Dvorak AM, Karp JM, Carman CV. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22887987&quot; rel=&quot;nofollow&quot;&gt;Mesenchymal stem cells transmigrate between and directly through tumor necrosis factor-α-activated endothelial cells via both leukocyte-like and novel mechanisms.&lt;/a&gt; Stem Cells. 2012 Nov;30(11):2472-86. doi: &lt;a href=&quot;http://dx.doi.org/10.1002/stem.1198&quot; rel=&quot;nofollow&quot;&gt;10.1002/stem.1198&lt;/a&gt;. PubMed PMID: 22887987. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-07-28T11:30:20.677" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20014" PostTypeId="2" ParentId="14017" CreationDate="2014-07-28T13:00:08.213" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;if mother is O-&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That means:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;group O in ABO system: anti-A and anti-B antibodies&lt;/li&gt;&#xA;&lt;li&gt;group Rh- in Rh system: no D antigen and no ant-D antibodies unless previously senzitized&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;baby is any +ve blood group other than O+&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ABO system: A, B or both antigens present&lt;/li&gt;&#xA;&lt;li&gt;Rh system: D antigen present&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, the mother has anti-A and anti-B antibodies and her immune response will be directed towards the fetal RBCs containing A, B and D antigens. But, in theory, the immune system should also produce anti-D antibodies because of &lt;a href=&quot;http://en.wikipedia.org/wiki/Antigen-presenting_cell&quot; rel=&quot;nofollow&quot;&gt;antigen presenting cells&lt;/a&gt; which will expose D antigens to T lymphocytes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is known is that if the mother already has anti-D antibodies, no other are secreted from fetal D antigens. This is how passive immunization vaccines work:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This is done so that the fetal Rhesus D positive erythrocytes are destroyed before her immune system can discover them. This is passive immunity and the effect of the immunity will wear off after about 4 to 6 weeks (or longer depending on injected dose) as the anti-Rh antibodies gradually decline to zero in the maternal blood [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But the mechanism is not clearly understood:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The most fascinating aspect of the story scientifically is that we still do not have a complete, mechanistic understanding of how this therapy works. The original hypothesis that Rh-immune globulin functions by clearing fetal Rh(D)-positive red blood cells from the maternal circulation, thereby hiding this foreign antigen from the maternal immune system, is inconsistent with the fact that passive immunization with Rh-immune globulin guides the fetal red blood cells directly to antigen presenting cells, the same cells responsible for initiating an immune response to foreign antigens [2].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Rh disease,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Rh_disease&amp;amp;oldid=615938189&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Rh_disease&amp;amp;oldid=615938189&lt;/a&gt; (accessed July 28, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Eldad Hod. &lt;em&gt;A Treatment for RH Disease.&lt;/em&gt; Available from &lt;a href=&quot;http://pathology.columbia.edu/rh_disease.html&quot; rel=&quot;nofollow&quot;&gt;http://pathology.columbia.edu/rh_disease.html&lt;/a&gt; (accessed 28.07.2014)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-07-28T13:00:08.213" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20015" PostTypeId="1" AcceptedAnswerId="20016" CreationDate="2014-07-28T13:24:35.790" Score="8" ViewCount="982" Body="&lt;p&gt;I heard about Larger cats eating the cubs. Is it some kind of facultative cannibalism or they can eat there own kind like that? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the facultative cannibalism present in animal kingdom? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the genetic origin?&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2019-03-28T17:52:23.220" Title="Facultative Cannibalism?" Tags="&lt;zoology&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20016" PostTypeId="2" ParentId="20015" CreationDate="2014-07-28T13:54:08.690" Score="15" Body="&lt;p&gt;&lt;strong&gt;Lions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lions are a classic example of cannibalism. To understand why this occurs we have to understand their mating system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Males have a harem of females and males fight in order to access a harem (Note: females may also take part in the battle depending on which male they prefer). When a male takes over a new harem, he kills the young ones of the previous male if these young ones are still dependent on their mother. The reasons are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The mother is not fertile while she is taking care of a young baby while the male would appreciate that the female is ready to raise his own kids.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The mother needs to invest quite a lot of energy to feed/milk their young while the new male would prefer this energy to be invested in his own offspring.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In short, a male kills the young ones when he takes over a new harem because these young ones do not carry his genes and prevent this new male to optimally pass on his own genes as the offsprings of the previous male consume time and energy from the females of the harem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And well… once the offsprings are killed, it would be a shame to waste all this good and fresh meat. Better to eat them!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the cases of lions, cannibalism does not result from food shortage but from &quot;not wasting food&quot;. I think that the &quot;not wasting food&quot; hypothesis is the most explanation for cannibalism (I am not sure though). I guess that most often the &quot;not wasting food&quot; occurs after death due to competition as it is the case in lions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other Examples&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many cases of cannibalism in the animal kingdom. Chimpanzees eating other chimpanzees and bear eating other bears. In the &lt;a href=&quot;http://en.wikipedia.org/wiki/Tiger_salamander&quot; rel=&quot;nofollow noreferrer&quot;&gt;tiger salamander&lt;/a&gt;, there are cannibal morph and normal morphs. In this species cannibalism is very frequent as in nature one offspring over 5 is eaten through cannibalism (if I am not mistaken). Cannibalism is very common in &lt;a href=&quot;http://en.wikipedia.org/wiki/Prairie_dog&quot; rel=&quot;nofollow noreferrer&quot;&gt;prairie dogs&lt;/a&gt; as well (&lt;a href=&quot;http://www.sciencemag.org/content/230/4729/1037.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;). In Dragonflies cannibalism represents 95% of the total mortality (&lt;a href=&quot;http://artifex.org/~ecoreaders/lit/Polis1981.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sibling sharks eat each other in their mum's womb. &lt;a href=&quot;https://www.youtube.com/watch?v=ZrqgPjZ07Ts&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; is a video on the subject. This type of cannibalism is called siblicide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://en.wikipedia.org/wiki/Mantodea&quot; rel=&quot;nofollow noreferrer&quot;&gt;Praying mantis&lt;/a&gt; the female may eat her mate after copulation. This is referred to as &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sexual_cannibalism&quot; rel=&quot;nofollow noreferrer&quot;&gt;sexual cannibalism&lt;/a&gt;&lt;/em&gt;. The subject is slightly controversial, please have a look to the wiki article for more info.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In many species (including the dragonflies example above) the old individuals eat the young. This is referred to &lt;em&gt;size-structured cannibalism&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Filial_cannibalism&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fillial cannibalism&lt;/a&gt;&lt;/em&gt; is a type of cannibalism when the adults eat their own offsprings as it is the case in the prairie dogs example I cited above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a look to the Wikipedia links for filial cannibalism, sexual cannibalism and siblicide, they go further than my answer.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-28T17:52:23.220" LastActivityDate="2019-03-28T17:52:23.220" CommentCount="13" ContentLicense="CC BY-SA 4.0" />
  <row Id="20017" PostTypeId="2" ParentId="19990" CreationDate="2014-07-28T13:54:43.687" Score="2" Body="&lt;p&gt;Very popular microscopes for bio work these days are the inverted style, These allow you to view samples without preparing slides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Inverted_microscope&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Inverted_microscope&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biotechequipmentsales.com/equipment-for-sale/details/564/14/microscopes/nikon-eclipse-ts100&quot; rel=&quot;nofollow&quot;&gt;http://www.biotechequipmentsales.com/equipment-for-sale/details/564/14/microscopes/nikon-eclipse-ts100&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8518" LastActivityDate="2014-07-28T13:54:43.687" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20018" PostTypeId="2" ParentId="19921" CreationDate="2014-07-28T15:43:09.010" Score="4" Body="&lt;p&gt;It might be pretty straightforward. Common window/mirror glass is &lt;a href=&quot;http://www.pgo-online.com/intl/katalog/curves/whitefl_kurve.html&quot; rel=&quot;nofollow&quot;&gt;opaque to UV&lt;/a&gt;, so as far as the &lt;a href=&quot;http://jeb.biologists.org/content/49/3/669.full.pdf&quot; rel=&quot;nofollow&quot;&gt;fly is concerned&lt;/a&gt; mirrors are just translucent surfaces. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This of course leads to the question of why flies can't see window glass. Maybe the large amount of light passing through at visible frequencies makes it look like a tinted fog to the housefly? Maybe they're trying to fly through mirrors too, but land on their feet and just roll with it?&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-07-28T15:43:09.010" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20019" PostTypeId="1" AcceptedAnswerId="20022" CreationDate="2014-07-28T16:06:36.680" Score="4" ViewCount="978" Body="&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/lZrzJ.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/lZrzJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the picture above (Source: &lt;a href=&quot;http://ecx.images-amazon.com/images/I/71zKixilmEL._SL1500_.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Amazon.com&lt;/a&gt;, United Scientific MCT001 Hand Microtome) we can see a microtome. How is it operated?&lt;/p&gt;&#xA;" OwnerUserId="8511" LastEditorUserId="5144" LastEditDate="2017-04-24T15:23:52.867" LastActivityDate="2017-04-24T15:43:39.177" Title="How to operate a microtome?" Tags="&lt;microscopy&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20020" PostTypeId="1" AcceptedAnswerId="20023" CreationDate="2014-07-28T16:15:54.757" Score="2" ViewCount="89" Body="&lt;p&gt;I'm an amateur when it comes to genetics, I'm hoping to learn something from the corrections. I am taking epigenetics into account (kind of); all 3 entities are susceptible to external physical influences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kind regards,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Frank&lt;/p&gt;&#xA;" OwnerUserId="8521" LastActivityDate="2017-06-14T15:32:44.507" Title="What is wrong with this analogy: Individuals are to alleles what governments are to individuals" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20021" PostTypeId="1" CreationDate="2014-07-28T16:16:50.270" Score="4" ViewCount="2050" Body="&lt;p&gt;I know that there are many hermaphrodite animals and plants. But many of them seem to still exchange genes by mating with another member of their species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I now happened to read the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Beef_tapeworm&quot; rel=&quot;nofollow&quot;&gt;Beef tapeworm&lt;/a&gt;, and it turns out that there normally is one worm per host, and it self-fertilizes. Which makes some sense - if I were a large internal parasite, I wouldn't want to wait around for my host to pick up a second member of my species before I can reproduce. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But this means that there is no gene exchange when taenia reproduce. Does it mean that they are all clones of each other, barring spontaneous mutations? How does evolution function in taenia when they don't mate? How comes there are different taenia species if they can't evolutionary adapt to new environments by producing offspring with mixed-up genes? &lt;/p&gt;&#xA;" OwnerUserId="1578" LastEditorUserId="6422" LastEditDate="2014-08-03T19:09:49.773" LastActivityDate="2014-08-04T19:50:51.560" Title="How do taenia form a species?" Tags="&lt;reproduction&gt;&lt;phylogenetics&gt;&lt;parasitology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20022" PostTypeId="2" ParentId="20019" CreationDate="2014-07-28T16:35:49.353" Score="4" Body="&lt;p&gt;The imnstrument is shown here upside down. If it is turned around, it looks like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cwWXG.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The glass disc are placed around the middle tube. The operation principle can be seen in this image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/o88u7.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The specimen is placed in the tube in the middle and pushed out by turning the knob at the bottom. The minimal increment for this kind of microtome is 10 micrometers. The razor knife is used to cut the slices of the specimen.&#xA;An operation manual can be found &lt;a href=&quot;http://www.unitedsci.com/sites/www.unitedsci.com/files/activity-guides/MCT001.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-28T16:35:49.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20023" PostTypeId="2" ParentId="20020" CreationDate="2014-07-28T16:44:18.747" Score="0" Body="&lt;p&gt;Alleles are passed down (to individuals) and created by individuals (although not fully under their control). But individuals are not passed out or created by the governments (I suppose), although individuals are influenced by the governments and they can influence governments, whereas individuals can not necessarily influence the allele of the gene they already have unless you take epi-genetics into account. Also, the creation of an allele is not entirely influenced by individuals due to &lt;a href=&quot;http://www.nature.com/scitable/definition/principle-of-independent-assortment-law-of-independent-302&quot; rel=&quot;nofollow noreferrer&quot;&gt;independent assortment&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosomal_crossover&quot; rel=&quot;nofollow noreferrer&quot;&gt;chromosomal crossover&lt;/a&gt;, but individuals can more or less influence governments.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="107" LastEditDate="2017-06-14T15:32:44.507" LastActivityDate="2017-06-14T15:32:44.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20024" PostTypeId="1" AcceptedAnswerId="20035" CreationDate="2014-07-28T17:14:49.100" Score="6" ViewCount="7009" Body="&lt;p&gt;Everywhere I look describes how the 5 sacral vertebrae start fusing together during adolescence and are totally fused by the time you're 30 or so. But nobody seems to explain why this happens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems like it would be disadvantageous for women, since presumably having a fused sacrum makes giving birth more difficult- apparently post-partum fractures are not uncommon (&lt;a href=&quot;http://rheumatology.oxfordjournals.org/content/42/2/384.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://rheumatology.oxfordjournals.org/content/42/2/384.long&lt;/a&gt;). So why does it happen?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Matthew McTernan gave &lt;a href=&quot;https://biology.stackexchange.com/a/20035/8523&quot;&gt;a great answer&lt;/a&gt;, but I am greedy and would like to know more: Why does the sacrum only start fusing together in adolescence, and then finish in your late 20s - early 30s? Most major development ends in your early 20s. Does this have something to do with reproductive concerns? If so, why does it happen on the same timescale in men and women?&lt;/p&gt;&#xA;" OwnerUserId="8523" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-07-31T21:14:22.710" Title="Why does the sacrum fuse together?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20025" PostTypeId="2" ParentId="20021" CreationDate="2014-07-28T18:20:30.127" Score="2" Body="&lt;h2&gt;Extension of Question&lt;/h2&gt;&#xA;&#xA;&lt;h2&gt;Beef tapeworm or &lt;em&gt;Taenia saginata&lt;/em&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Beef tapeworm or &lt;em&gt;Taenia saginata&lt;/em&gt; shows both asexual and sexual reproduction. As you have mentioned if any other partner is not available then it will carry on asexual reproduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Scolex or the hook attahes to the host.&lt;/li&gt;&#xA;&lt;li&gt;Scolex reproduce asexually by budding. &lt;/li&gt;&#xA;&lt;li&gt;One tapeworm segment or proglottid takes around 10-12 weeks to mature. &lt;/li&gt;&#xA;&lt;li&gt;There can be 1000-2000 Proglottids in the worm body.&lt;/li&gt;&#xA;&lt;li&gt;Proglottids are Hermaphrodite when mature.&lt;/li&gt;&#xA;&lt;li&gt;Each of these proglottids will produce around 100s of eggs.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;That means,&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;A full grown tapeworm can produce from 1,000 to 2,000,000 eggs a day. They survive up to 20-25 years&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;Any mutation can be exponentially magnified in the generations as mostly the reproductions are sexual type(after the initial budding or occasional self sexual)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Update&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;According to wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because each proglottid contains the male and female reproductive&#xA;  structures, they can reproduce independently. Some biologists have&#xA;  suggested that each should be considered a single organism, and that&#xA;  the tapeworm is actually a colony of proglottids.[3]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;h2&gt;Source:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://en.wikipedia.org/wiki/Beef_tapeworm&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Beef_tapeworm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] &lt;a href=&quot;http://animaldiversity.ummz.umich.edu/accounts/Taenia_saginata/&quot; rel=&quot;nofollow&quot;&gt;http://animaldiversity.ummz.umich.edu/accounts/Taenia_saginata/&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[3] &lt;a href=&quot;http://en.wikipedia.org/wiki/Cestoda&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Cestoda&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-08-03T05:51:56.083" LastActivityDate="2014-08-03T05:51:56.083" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20026" PostTypeId="1" AcceptedAnswerId="20027" CreationDate="2014-07-28T19:21:46.463" Score="1" ViewCount="6148" Body="&lt;p&gt;I have been told that both are spread by pigs and cattle, respectively. I would like to know the complications caused by &lt;strong&gt;Taenia solium&lt;/strong&gt; and &lt;strong&gt;Taenia saginata&lt;/strong&gt;. Also elaborate how dangerous is one as compared to the other, as well as preventive measure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I googled , and found no &lt;em&gt;relative&lt;/em&gt; comparison between these two.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you. &lt;/p&gt;&#xA;" OwnerUserId="5823" LastEditorUserId="6422" LastEditDate="2014-07-28T19:48:25.033" LastActivityDate="2014-07-28T19:48:25.033" Title="Differentiating Taenia solium and Taenia saginata Infections" Tags="&lt;parasitology&gt;&lt;infection&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20027" PostTypeId="2" ParentId="20026" CreationDate="2014-07-28T19:36:17.713" Score="1" Body="&lt;p&gt;Taenia solium is more dangerous:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;T. saginata is relatively innocuous, since only the intestinal tapeworm phase occurs in man, whereas infection with T. solium has major health effects due to extraintestinal infection by the larval or cyst phase in the CNS [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The most feared complication of Taenia solium is &lt;a href=&quot;http://en.wikipedia.org/wiki/Cysticercosis&quot; rel=&quot;nofollow&quot;&gt;cysticercosis&lt;/a&gt;. Taenia saginata can lead in extreme cases to intestinal obstruction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Preventive measures:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;improved hygiene&lt;/li&gt;&#xA;&lt;li&gt;adequate thermal processing of meat [2]&lt;/li&gt;&#xA;&lt;li&gt;preventing contamination of animals (pigs and cattle) [3] &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Differential diagnosis:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;PCR [1, 4]&lt;/li&gt;&#xA;&lt;li&gt;Hematoxylin-Eosin Staining [1]&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Mayta H, Talley A, Gilman RH, Jimenez J, Verastegui M, Ruiz M, Garcia HH, Gonzalez AE. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10618076&quot; rel=&quot;nofollow&quot;&gt;Differentiating Taenia solium and Taenia saginata infections by simple hematoxylin-eosin staining and PCR-restriction enzyme analysis.&lt;/a&gt; J. Clin. Microbiol. 2000 Jan;38(1):133-7. PubMed PMID: 10618076. Cited text is from full text article available from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC86038/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC86038/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Taenia saginata,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Taenia_saginata&amp;amp;oldid=618599196&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Taenia_saginata&amp;amp;oldid=618599196&lt;/a&gt; (accessed July 28, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Taenia solium,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Taenia_solium&amp;amp;oldid=618599210&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Taenia_solium&amp;amp;oldid=618599210&lt;/a&gt; (accessed July 28, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Luis Miguel González, Estrella Montero, Leslie J. S. Harrison, R. Michael E. Parkhouse, and Teresa Garate. &lt;em&gt;&lt;a href=&quot;http://jcm.asm.org/content/38/2/737.long&quot; rel=&quot;nofollow&quot;&gt;Differential Diagnosis of Taenia saginata and Taenia solium Infection by PCR.&lt;/a&gt;&lt;/em&gt; J. Clin. Microbiol. February 2000 vol. 38 no. 2 737-744&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-07-28T19:46:00.010" LastActivityDate="2014-07-28T19:46:00.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20028" PostTypeId="1" CreationDate="2014-07-28T20:03:59.550" Score="4" ViewCount="4428" Body="&lt;p&gt;Does &lt;a href=&quot;http://en.wikipedia.org/wiki/Oxytocin&quot; rel=&quot;nofollow&quot;&gt;Oxytocin&lt;/a&gt; (or any other bonding hormone) increase more so for women than for men after sex? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Someone told me that it increases 4-fold for men and 12-fold for women (unconfirmed).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any observable or scientific relationship between sex, Oxytocin and the desire for a monogamous relationship with a sexual partner?&lt;/p&gt;&#xA;" OwnerUserId="8525" LastEditorUserId="5144" LastEditDate="2016-04-09T20:57:32.867" LastActivityDate="2016-04-09T20:57:32.867" Title="Do women experience more bonding hormones than men after sex?" Tags="&lt;physiology&gt;&lt;endocrinology&gt;&lt;sex&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20029" PostTypeId="2" ParentId="20028" CreationDate="2014-07-28T21:03:03.957" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Does Oxytocin increase more so for women than for men after sex?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Answer:&lt;/strong&gt; Yes, Oxytocin level shoot up for female after sexual. It is highest at orgasm, which is the main cause women could have multiple orgasm.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Someone told me that it increases 4-fold for men and 12-fold for women&#xA;  (unconfirmed).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Answer:&lt;/strong&gt; The level of oxytocin actually increase 5 times during sexual intercourse. Though some &lt;a href=&quot;http://www.smart-publications.com/articles/oxytocin-the-real-love-hormone&quot; rel=&quot;nofollow noreferrer&quot;&gt;online article&lt;/a&gt; claim the male and female level as much you said, but it is not confirmed in humans. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there any observable or scientific relationship between sex, Oxytocin and the desire for a monogomous relationship with a sexual partner?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Answer:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take a look at this experiment done on people to test Bonding:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bonding is an important part of human romantic relationships, and&#xA;  research has suggested OT as a possible mediator of this effect. A&#xA;  2005 study by $Grewen\ et\ al^{4}$. found that couples who reported a greater&#xA;  amount of partner support showed higher baseline OT plasma levels.&#xA;  These couples also showed higher levels at 4, 7, and 10 min following&#xA;  warm partner contact. For women, OT levels increased sharply 7 min&#xA;  following warm partner contact, regardless of partner support, while&#xA;  male levels remained unchanged. This study demonstrates a&#xA;  relationship between supportive romantic bonding and OT, and shows&#xA;  that warm contact has a greater physiological effect on women than on&#xA;  men.[1]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A very famous study done on rats confirm that Vassopressin and Oxytocin is actually the reason behind monogamous relationship.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Almost a decade ago, Thomas Insel, Director of the Center for&#xA;  Behavioral Neuroscience at Emory University, and colleagues at the&#xA;  National Institute of Mental Health and the University of Maryland&#xA;  implicated vasopressin and oxytocin in controlling the preference for&#xA;  particular partners in both male and female prairie voles. These&#xA;  investigators found that giving a male vasopressin causes it to stay&#xA;  with its mate, whereas blocking this hormone prevents a pair-bond from&#xA;  forming. The scientists saw similar effects in female prairie voles,&#xA;  with oxytocin determining the extent of pair-bonding. In contrast, the&#xA;  administration of these substances had no influence on social&#xA;  interactions in the promiscuous montane voles. Surprisingly,&#xA;  vasopressin and oxytocin are naturally found at similar levels in both&#xA;  prairie and montane voles.[5]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://www.americanscientist.org/Libraries/images/200332193024_307.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1]. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22107910&quot; rel=&quot;nofollow noreferrer&quot;&gt;The role of oxytocin in mating and pregnancy&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2]. &lt;a href=&quot;http://en.wikibooks.org/wiki/Relationships/Hormones#Oxytocin&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikibooks.org/wiki/Relationships/Hormones#Oxytocin&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[3]. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9949283&quot; rel=&quot;nofollow noreferrer&quot;&gt;The role of oxytocin in relation to female sexual arousal.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[4] Grewen, K.M., Girdler, S.S., Amico, J., Light, K.C., 2005. [Effects of partner support on resting oxytocin, cortisol, norepinephrine, and blood pressure before and after warm partner contact](Effects of partner support on resting oxytocin, cortisol, norepinephrine, and blood pressure before and after warm partner contact.). Psychosom. Med. 67, 531–538.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[5] &lt;a href=&quot;http://www.smart-publications.com/articles/oxytocin-the-real-love-hormone&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.smart-publications.com/articles/oxytocin-the-real-love-hormone&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.403" LastActivityDate="2014-07-28T21:03:03.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20030" PostTypeId="1" CreationDate="2014-07-28T21:09:25.237" Score="8" ViewCount="711" Body="&lt;p&gt;There are several sex determining systems in animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In mammals XY = male(except in rare cases where SRY crosses with genes on the X so that it is the reverse) and XX = female.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In  some birds it is just the opposite. That is XY(actually ZW) = fertile female and XX(actually ZZ) = fertile male.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In  some reptiles it is determined by temperature and has no genetic determination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In lots of insects there is XX = female and X0 = male. This is usually accompanied by males being haploid and females being diploid like it is in bees.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In some insects and reptiles there is also the ZW/ZZ system but they are not dependent on it. In other words ZZW in some insects and reptiles can give rise to either sex but there is no temperature determination either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why are there so many sex determining systems? Why did animals evolve to not all have the familiar XY system? It must be so confusing as to which species has which sex determining system when biologists are trying to determine the gender of an animal.&lt;/p&gt;&#xA;" OwnerUserId="5851" LastEditorUserId="5851" LastEditDate="2014-07-28T21:23:46.967" LastActivityDate="2016-09-29T16:45:56.057" Title="Why are there so many sex determining systems in animals" Tags="&lt;zoology&gt;&lt;sex&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20031" PostTypeId="2" ParentId="19942" CreationDate="2014-07-28T21:58:10.200" Score="6" Body="&lt;p&gt;I was musing on this and did some strange googling, and have some ballpark figures  for a bunch of different organisms. It's far from a complete answer but it's at least a start, and all this won't fit in a comment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA replication, I assumed, was a huge metabolic drain on the cell. Turns out that is far from the case. Many helicases are passive, requiring no ATP, and the amount of ATP-equivalent triphosphates to synthesize the entire genome is pretty small compared to the amount that gets used and recycled every day.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://bionumbers.hms.harvard.edu/search.aspx?task=searchbytrmorg&amp;amp;log=y&amp;amp;unt=y&amp;amp;trm=Body%20weight%20ATP/day&amp;amp;org=%25&quot;&gt;these guys&lt;/a&gt; humans go through their bodyweight in ATP every day, about 50% of which is actin turnover, and &lt;a href=&quot;http://bionumbers.hms.harvard.edu/bionumber.aspx?&amp;amp;id=110441&amp;amp;ver=7&amp;amp;trm=ATP/day&quot;&gt;30% is synthesis&lt;/a&gt; (60% or more in rapid bacteria). Proteins cost about &lt;a href=&quot;http://kirschner.med.harvard.edu/files/bionumbers/Estimated%20specific%20costs%20of%20component%20processes%20of%20protein%20turnover.pdf&quot;&gt;4-5 ATP&lt;/a&gt; per AA to break down and rebuild.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You're not going to get a really good general breakdown, I don't think, but in crop plants or E. coli there are &lt;a href=&quot;http://bionumbers.hms.harvard.edu/search.aspx?log=y&amp;amp;task=searchbytrmorg&amp;amp;trm=ATP&quot;&gt;number&lt;/a&gt;s for this, sort of. A lot of them are based on indirect measurements of protein uptake/turnover and ATP cost per AA or BP. They're fascinating but insane and often contradictory.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-07-28T21:58:10.200" CommentCount="2" CommunityOwnedDate="2014-07-28T21:58:10.200" ContentLicense="CC BY-SA 3.0" />
  <row Id="20033" PostTypeId="1" AcceptedAnswerId="20043" CreationDate="2014-07-28T22:37:41.740" Score="6" ViewCount="983" Body="&lt;p&gt;As you may know, some women claim that they have their period while they are pregnant. In the arab world they call it &quot;Deer pregnancy&quot;, since when the deer gets pregnant, it still gets its' monthly cycle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their doctors do confirm that. The appearance of such: The bleeding comes at the times when the period is expected, but is usually without pain, or smell, and lasts for less days. It is also of different color. But many women (and doctors) still call it a period.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Although we all know, a real period is impossible biologically).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How common is that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is, I think, different from implantation bleeding, since it mostly continues to three months and after that.&lt;/p&gt;&#xA;" OwnerUserId="8527" LastActivityDate="2014-07-29T07:55:21.360" Title="How common is it to be pregnant with periods?" Tags="&lt;cycle&gt;&lt;pregnancy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20034" PostTypeId="1" AcceptedAnswerId="20036" CreationDate="2014-07-28T22:42:59.097" Score="6" ViewCount="226478" Body="&lt;p&gt;&lt;strong&gt;Dry Humping&lt;/strong&gt;, is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;dry humping is the process of two people repeatedly moving up and down and back and forth on top of each other fully clothed( or missing various pieces, but the penis must not come in contact with the vagina with out some sort of fabric separating them ex: boxers,panties, or even sheets!!)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;We all know that the basic rule for impregnation is that the sperm must come in contact with the egg, and even be able to fertilize it. While sperm can get through clothes, semen (but this is yet been proven or disproved) gets stuck, thus the sperm dies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is your opinion about this? If two people are on top of each other, fully clothed, and the male comes to ejaculation, is there any chance that pregnancy can happen, in the &lt;strong&gt;realistic&lt;/strong&gt; and biological look at it (and not some probability or statistical way)? What advice should be given to teens on the matter?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am a computer scientist with no biology knowledge, and am very interested in getting the opinion of biologists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But since I know that the stackexchange community likes to see work done before asking questions, I did my own research (I am used to googling code and algorithms):&#xA;Very few research has been done on the subject. There is one shining research that  concluded, as I recall, that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If the underwear is &lt;strong&gt;completely saturated&lt;/strong&gt; with semen, and is in &lt;strong&gt;direct&lt;/strong&gt; contact with the woman's vagina, pregnancy is &lt;strong&gt;possible&lt;/strong&gt; statistically, but &lt;strong&gt;highly unlikely&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8527" LastEditorUserId="3553" LastEditDate="2016-02-23T07:37:28.900" LastActivityDate="2016-04-20T19:51:53.423" Title="Teens concerned about impregnation through clothes" Tags="&lt;sex&gt;&lt;pregnancy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20035" PostTypeId="2" ParentId="20024" CreationDate="2014-07-29T01:28:14.003" Score="4" Body="&lt;p&gt;It isn't just humans that have fused sacral vertebrae. Animals on the phylogenetic tree ranging from Squamata (lizards), to Aves (birds), to even Monotremata (egg-laying mammals) all have fused sacral vertebrae. The fused vertebrae can serve as a stronger, weight-baring structures for animals that do land locomotion, including humans. Any bones that have evolved to withstand extensive force will also be thick or fused together: and example is the fusion of the radius and ulna in frogs. This fusion of bones allows for the forearms to withstand the force of landing after a large leap. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photo references:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bird Sacrum: &lt;a href=&quot;http://www.discussfossils.com/forum/uploads/842/sacrum_2.jpg&quot; rel=&quot;nofollow&quot;&gt;http://www.discussfossils.com/forum/uploads/842/sacrum_2.jpg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Frog Radioulna: &lt;a href=&quot;http://classconnection.s3.amazonaws.com/573/flashcards/4420573/png/appendicular_skeleton-frog-142D89D722717E64724.png&quot; rel=&quot;nofollow&quot;&gt;http://classconnection.s3.amazonaws.com/573/flashcards/4420573/png/appendicular_skeleton-frog-142D89D722717E64724.png&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8530" LastActivityDate="2014-07-29T01:28:14.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20036" PostTypeId="2" ParentId="20034" CreationDate="2014-07-29T01:54:36.103" Score="14" Body="&lt;p&gt;If there has been an ejaculation by the male, and semen is present, there is a chance of getting pregnant. Period. Teens really need to know that.&lt;/p&gt;&#xA;&lt;p&gt;I think you may have your terms confused - semen is the overall fluid released during an ejaculation, sperm are the cells with tails that are produced in the testes and fertilize the egg. At any rate, according to the WHO, a normal sperm count is over 15 million per milliliter, with some counts much higher (&amp;gt;50e6/ml ), and an average between 20 and 40 million. The volume of the ejeculate tends to be anywhere from 1-6 ml. If you take a healthy young male at the peak of his reproductive capabilities, this equates to a very large number of sperm being released during a sexual encounter. All it takes is for one to reach an egg and fertilize it. Sperm are very very small, much smaller than the pore size of average fabric, so clothing will do very little to stop them. The female is likely sexually aroused during this activity as well, and produces additional fluids and lubricants that promote the survival and motility of sperm, among other things.&lt;/p&gt;&#xA;&lt;p&gt;So, it depends on many factors. If both parties are fully clothed (at least 4 layers of clothing between their respective reproductive organs) and there is a minumum of soaking through, the chances of pregnancy are correspondingly quite low. On the other hand, if only one partner is wearing just their underwear, it's essentially like there is no clothing present at all, and the relative chances go up significantly.&lt;/p&gt;&#xA;&lt;p&gt;Safe sex practices can't be emphasized enough to young people, as education and awareness is so much better than ignorance and myths. Even aside from pregnancy, if condoms are not utilized properly to contain all the semen there is the chance of sexually-transmitted diseases, ranging from herpes and gonorrhea to AIDS. None of these require penetration to be passed along, and one might argue that the additional presence of potentially irritating fabrics could open up raw areas or cuts and enhance their transmittal.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h2&gt;Take home message&lt;/h2&gt;&#xA;&lt;p&gt;Now, all this being said, the chances of impregnation through clothing without direct penetration of the penis into the vagina is quite low compared to &amp;quot;typical&amp;quot; unprotected fully-penetrating intercourse, especially depending on where the female is in her fertility cycle. According to &lt;a href=&quot;http://www.demographic-research.org/Volumes/Vol3/5/default.htm&quot; rel=&quot;noreferrer&quot;&gt;this study&lt;/a&gt;, a woman's most fertile day is two days before ovulation (as had been postulated before), and the chances of pregnancy on that day are about 25% (assuming penetrating intercourse). Overall, the chance of pregnancy throughout the month is about 5%.&lt;/p&gt;&#xA;&lt;p&gt;I don't have any hard numbers on the pregnancy chances when one or both partners have at least some clothing on, as obviously it will vary greatly depending on who is wearing what, the volume of ejaculate, contact time after ejaculation, etc. Just for fun, let's assume it's 100 times lower. That means the chances of impregnation two days pre-ovulation would be 0.25%, or 1 in 400. While rather low, this is still a non-zero chance.&lt;/p&gt;&#xA;&lt;p&gt;Condoms are about 98% effective if used properly during penetrative vaginal intercourse. Various other birth control methods such as contraceptive pills, intrauterine devices, implants and injections are quoted as being 99% effective on their own, although they do not protect against sexually transmitted diseases. I'm certainly not one for preaching abstinence, but done properly it should be 100% effective. Ultimately, it is up to both partners to decide what their risk tolerances are, together. It is much better to seriously talk about it beforehand than to be panicked and unsure afterwards.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;Hopefully this addresses your concerns, please leave comments if you have additional questions.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2016-02-22T18:53:53.670" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="20037" PostTypeId="2" ParentId="20030" CreationDate="2014-07-29T02:24:07.543" Score="7" Body="&lt;p&gt;Could not fit in a comment…&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't quite know how to answer. I think that the only answer one could give is &lt;code&gt;why not?&lt;/code&gt;. Various mechanisms may evolve under different life-history, different environment, different ecological strategy, different mutations occuring,..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In some species (including some amphibians) the evolution of sex determination system is highly dynamic and switch back and forth between one system and another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I highly recommend the book: &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0199657149&quot; rel=&quot;nofollow&quot;&gt;The Evolution of sex determination system (2014)&lt;/a&gt; that will give you a very good theoretical understanding of how sexual determination system evolve and make a complete review of empirical studies on the evolution and mechanisms of sex determination system. I think it is the only book existing on the subject.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2016-09-29T16:45:56.057" LastActivityDate="2016-09-29T16:45:56.057" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20038" PostTypeId="1" CreationDate="2014-07-29T02:37:17.660" Score="13" ViewCount="2112" Body="&lt;p&gt;It is often cited that humans share 99% (or 98%) of their DNA with chimpanzees.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand it is stated that siblings share only half of their genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What (if any) is the difference between DNA and genes; or, how can the above two claims be reconciled? (I am assuming of course that chimps and humans are more different from each other than two siblings are from each other.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I am asking this question as a layperson, who had a little biology in school but not much more.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;June 2015 Addendum:&lt;/strong&gt; Here is a nice &lt;a href=&quot;https://www.youtube.com/watch?v=IbY122CSC5w&quot; rel=&quot;nofollow&quot;&gt;YouTube video&lt;/a&gt; just released by MinuteEarth; I do not know how accurate this video is, but as a layperson I found it insightful.&lt;/p&gt;&#xA;" OwnerDisplayName="user4932" LastEditorDisplayName="user4932" LastEditDate="2015-06-25T12:37:42.457" LastActivityDate="2015-06-25T12:37:42.457" Title="&quot;Same&quot; DNA vs genes" Tags="&lt;genetics&gt;&lt;dna&gt;" AnswerCount="4" CommentCount="4" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20039" PostTypeId="2" ParentId="20038" CreationDate="2014-07-29T03:10:06.223" Score="11" Body="&lt;p&gt;The human genome is composed of roughly 3 billion DNA bases called &quot;nucleotides&quot;, typically represented as A, T, C, G.&lt;br&gt;&#xA;Genes are sequences of nucleotides that encode a protein; but they only comprise about 2% of the full genome. (&lt;a href=&quot;http://en.wikipedia.org/wiki/Human_genome&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Human_genome&lt;/a&gt;). Most components of cells are made of proteins.&#xA;The rest of the genome is made up of nucleotide sequences that: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;have regulatory functions in controlling when and to what degree genes are expressed to create the proteins they encode&lt;/li&gt;&#xA;&lt;li&gt;do not have any known function&lt;/li&gt;&#xA;&lt;li&gt;are likely remnants from certain viral infections we or our ancestors contracted&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The DNA that makes it into our genome is not necessarily there because we need it or because it confers some kind of reproductive advantage. A lot of our DNA is in our genome just because our ancestors had it and they happened to be reproductively successful. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So basically: humans and chimpanzees can share 99% of their DNA and have quite different genes because genes make up only a very small part of our genome.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, having similar nucleotide sequences in our genes does not guarantee that we will be similar because we still need to consider things like:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;how similar are the genes really?&lt;/em&gt; &#xA;  Some differences in a gene's sequence mean more than others&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;how similar are regulatory sequences affecting the gene?&lt;/em&gt;&#xA;  Having the same gene as another species is not the same as expressing it the same&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;how many copies of the gene are present?&lt;/em&gt; &#xA;  There's more than one way to take this into consideration&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For more information about comparing genes, refer to the other answers offered which go into greater detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a genetics learning resource that is pretty accessible to laypeople: &lt;a href=&quot;http://learn.genetics.utah.edu/content/basics/&quot; rel=&quot;nofollow&quot;&gt;http://learn.genetics.utah.edu/content/basics/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8161" LastEditorUserId="8161" LastEditDate="2014-07-29T15:41:55.617" LastActivityDate="2014-07-29T15:41:55.617" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20040" PostTypeId="2" ParentId="20028" CreationDate="2014-07-29T03:48:35.313" Score="1" Body="&lt;p&gt;I want to clear up something the other answer omit. It doesn't matter how much the comparative differences are between the oxy levels of men and women. This is because we are basically two entirely different subspecies concerning our &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Neuroscience_of_sex_differences&quot; rel=&quot;nofollow&quot;&gt;neurology&lt;/a&gt;. The effects of biochemistry on each system are going to be significantly different.&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-07-29T03:48:35.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20041" PostTypeId="2" ParentId="20038" CreationDate="2014-07-29T06:17:10.753" Score="6" Body="&lt;p&gt;When people say that siblings share half of their genes, they're talking about alleles, which are different versions of the same gene and generally differ slightly in nucleotide sequence. In essence, all humans share 100% of their genes (almost), but the number of shared alleles varies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;geneA, allele1: atgccc&lt;br&gt;&#xA;geneA, allele2: atgccg&lt;br&gt;&#xA;geneA, allele3: atgcac&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed, we share about 99% of our DNA and &lt;strong&gt;consequently&lt;/strong&gt; genes with chimps and bonobos. There are alleles of these genes that are unique to humans, unique to chimps and unique to bonobos. Of course, there are also many alleles that are shared between all three species. There are more shared alleles still between chimps and bonobos, since their most recent common ancestor lived after the most recent common ancestor of humans, chimps and bonobos. However, looking at the above example, you can nonetheless have a situation where Joe Sixpack and Charlie Chimp both have allele1 of geneA, whereas Joel Sixpack has allele2 of geneA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, the conclusion of Slavatron's answer is complete nonsense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Somebody made the same question &lt;a href=&quot;http://www.thenakedscientists.com/forum/index.php?topic=39643.0&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5784" LastEditorUserId="5784" LastEditDate="2014-07-29T09:36:01.233" LastActivityDate="2014-07-29T09:36:01.233" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20043" PostTypeId="2" ParentId="20033" CreationDate="2014-07-29T07:49:09.897" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;But many women (and doctors) still call it a period.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is not a period:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pregnant women can have some light irregular bleeding during pregnancy, but it should not be like a “normal” period. Some women can confuse this for their period because often it can come right around the time she was expecting her normal period. [...] It should not be enough bleeding to fill pads or tampons over a few days [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is quite common in the first trimester:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Vaginal bleeding during pregnancy can occur frequently in the first trimester of pregnancy and may not be a sign of problems. But bleeding that occurs in the second and third trimester of pregnancy can often be a sign of a possible complication [2].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It happens to about 25 % of pregnant women:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Up to 1 in 4 women have vaginal bleeding at some time during their pregnancy. Bleeding is more commonin the first 3 months (first trimester), especially with twins [3].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Repetitive bleeding is associated with preterm birth:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bleeding of multiple episodes, on multiple days, and with more total blood loss was associated with an approximate twofold increased risk of earlier preterm birth, PPROM (preterm premature rupture of the membranes), and preterm labor. In contrast, bleeding in the second trimester only, of a single episode, on a single day, and with less total blood loss was not associated with any category of preterm birth [4].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;American Pregnancy Association. &lt;em&gt;Am I Pregnant: FAQs On Early Pregnancy.&lt;/em&gt; Available from &lt;a href=&quot;http://americanpregnancy.org/gettingpregnant/pregnancyfaq.htm&quot; rel=&quot;noreferrer&quot;&gt;http://americanpregnancy.org/gettingpregnant/pregnancyfaq.htm&lt;/a&gt; (accessed 29.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;American Pregnancy Association. &lt;em&gt;Bleeding During Pregnancy.&lt;/em&gt; Available from &lt;a href=&quot;http://americanpregnancy.org/pregnancycomplications/bleedingduringpreg.html&quot; rel=&quot;noreferrer&quot;&gt;http://americanpregnancy.org/pregnancycomplications/bleedingduringpreg.html&lt;/a&gt; (accessed 29.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;U.S. National Library of Medicine. A.D.A.M. Medical Encyclopedia. &lt;em&gt;Vaginal bleeding in pregnancy.&lt;/em&gt; Available from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0003748/&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0003748/&lt;/a&gt; (accessed 29.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;Yang J, Hartmann KE, Savitz DA, Herring AH, Dole N, Olshan AF, Thorp JM. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15234932&quot; rel=&quot;noreferrer&quot;&gt;Vaginal bleeding during pregnancy and preterm birth.&lt;/a&gt; Am. J. Epidemiol. 2004 Jul 15;160(2):118-25. doi: &lt;a href=&quot;http://dx.doi.org/10.1093/aje/kwh180&quot; rel=&quot;noreferrer&quot;&gt;10.1093/aje/kwh180&lt;/a&gt;. PubMed PMID: 15234932. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-07-29T07:55:21.360" LastActivityDate="2014-07-29T07:55:21.360" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20044" PostTypeId="2" ParentId="19244" CreationDate="2014-07-29T10:29:05.417" Score="5" Body="&lt;p&gt;I will go with lesser water boatman(&lt;em&gt;Micronecta scholtzi&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;The loudest of everything as well as small.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Size:&lt;/strong&gt; 0.07-inch (2-millimeter)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Produces the highest sound by size ratio.&lt;/li&gt;&#xA;&lt;li&gt;It's sound is almost equivalent to pounding jackhammer at two feet distance.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0021089.g001&amp;amp;representation=PNG_L&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0021089.g001&amp;amp;representation=PNG_L&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source and Image Courtesy: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021089&quot; rel=&quot;nofollow noreferrer&quot;&gt;So Small, So Loud: Extremely High Sound Pressure Level from a Pygmy Aquatic Insect (Corixidae, Micronectinae)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Youtube: &lt;a href=&quot;https://www.youtube.com/watch?v=i7-hREXmMFM&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.youtube.com/watch?v=i7-hREXmMFM&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Update:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;If we consider voice, I will go with &lt;strong&gt;&lt;em&gt;Paedophryne amauensis&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Smallest frog an known vertebrate &lt;/li&gt;&#xA;&lt;li&gt;size: 7.7 mm (0.30 in)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Hl8Nd.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-01-22T10:57:19.147" LastActivityDate="2019-01-22T10:57:19.147" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="20045" PostTypeId="2" ParentId="16170" CreationDate="2014-07-29T11:15:47.813" Score="2" Body="&lt;p&gt;It could be Wood Mouse(Apodemus sylvaticus).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://ih0.redbubble.net/image.11495816.1176/flat,550x550,075,f.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Courtesy : &lt;a href=&quot;http://www.redbubble.com/people/neilborman/works/8511176-harvest-mouse-eating-corn&quot; rel=&quot;nofollow noreferrer&quot;&gt;redbubble.com&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.423" LastActivityDate="2014-07-29T11:15:47.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20046" PostTypeId="2" ParentId="13576" CreationDate="2014-07-29T12:02:36.537" Score="2" Body="&lt;p&gt;Here are some causes of bleeding during pregnancy:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;early pregnancy (first trimester):&#xA;&lt;ul&gt;&#xA;&lt;li&gt;implantation bleeding [1]&lt;/li&gt;&#xA;&lt;li&gt;infection [1]&lt;/li&gt;&#xA;&lt;li&gt;after intercourse [1]&lt;/li&gt;&#xA;&lt;li&gt;miscarriage [2]&lt;/li&gt;&#xA;&lt;li&gt;ectopic pregnancy [2]&lt;/li&gt;&#xA;&lt;li&gt;cervical changes [3]&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;second part of pregnancy:&#xA;&lt;ul&gt;&#xA;&lt;li&gt;abruptio placentae [1, 2]&lt;/li&gt;&#xA;&lt;li&gt;placenta previa [1, 2]&lt;/li&gt;&#xA;&lt;li&gt;miscarriage [2]&lt;/li&gt;&#xA;&lt;li&gt;vasa previa [2]&lt;/li&gt;&#xA;&lt;li&gt;preterm labour [1]&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;American Pregnancy Association. &lt;em&gt;Bleeding During Pregnancy.&lt;/em&gt; Available from &lt;a href=&quot;http://americanpregnancy.org/pregnancycomplications/bleedingduringpreg.html&quot; rel=&quot;nofollow&quot;&gt;http://americanpregnancy.org/pregnancycomplications/bleedingduringpreg.html&lt;/a&gt; (accessed 29.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;U.S. National Library of Medicine. A.D.A.M. Medical Encyclopedia. &lt;em&gt;Vaginal bleeding in pregnancy.&lt;/em&gt; Available from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0003748/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0003748/&lt;/a&gt; (accessed 29.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;WebMD, LLC. &lt;em&gt;Bleeding During Pregnancy.&lt;/em&gt; Available from &lt;a href=&quot;http://www.webmd.com/baby/guide/bleeding-during-pregnancy&quot; rel=&quot;nofollow&quot;&gt;http://www.webmd.com/baby/guide/bleeding-during-pregnancy&lt;/a&gt; (accessed 29.07.2014)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-07-29T12:12:19.403" LastActivityDate="2014-07-29T12:12:19.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20047" PostTypeId="2" ParentId="17109" CreationDate="2014-07-29T12:20:11.307" Score="3" Body="&lt;p&gt;Reason for Migrating Birds:&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Migrating for a Meal&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Food scarcity: If birds will stay and eat all the bees they find, there will be no bees to feed on for the next generation. So, they fly away to take advantage of these places where there is abundance of food. And when the insects or replenish they come back.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Migrating for Family&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Flocks of bird can be easy prey as they are small and are in a huge number. Also for the young ones who can't fly it is very dangerous. (Though they abandon the young one as soon they can fly)&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Migrating for better Climate:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Some of the species fly away to sustain the temperature and come back when it is suitable for them. So, Northern birds migrate to tropical places for the winter and come back to north for the summer to lay eggs.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;There are too many other theories for bird migration. It had been confirmed that migration is often due to genetics than any other reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further Reading: &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1949-8594.1908.tb01166.x/abstract&quot; rel=&quot;nofollow&quot;&gt;THEORIES OF BIRD MIGRATION&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://birding.about.com/od/birdbehavior/a/Why-Birds-Migrate.htm&quot; rel=&quot;nofollow&quot;&gt;http://birding.about.com/od/birdbehavior/a/Why-Birds-Migrate.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] &lt;a href=&quot;http://en.wikipedia.org/wiki/Bird_migration&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Bird_migration&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-29T12:20:11.307" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20048" PostTypeId="2" ParentId="19244" CreationDate="2014-07-29T12:32:12.457" Score="3" Body="&lt;p&gt;I'm putting my bets on the Pistol Shrimp (Alpheus heterochaelis)&#xA;They can be grow 3cm to 5cm Long which is incredibly small for the amount of db it can create.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their sound is a by-product of their large claw snapping shut and creating a cavitation bubble that creates a lot of pressure and then produces up to a recorded 218 Decibels.&#xA;This &quot;click&quot; or &quot;pop&quot; of the bubble only lasts less than 1 millisecond. It also produces around 5000k in heat from the popping of the bubble.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(According to the Daily Mail which I honestly may say is probably not the most trustworthy source of accurate information &lt;a href=&quot;http://www.dailymail.co.uk/sciencetech/article-1085398/Deadly-pistol-shrimp-stuns-prey-sound-loud-Concorde-UK-waters.html&quot; rel=&quot;nofollow&quot;&gt;http://www.dailymail.co.uk/sciencetech/article-1085398/Deadly-pistol-shrimp-stuns-prey-sound-loud-Concorde-UK-waters.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia Article : &lt;a href=&quot;http://en.wikipedia.org/wiki/Alpheidae&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Alpheidae&lt;/a&gt; )&lt;/p&gt;&#xA;" OwnerUserId="8536" LastEditorUserId="8536" LastEditDate="2014-07-29T12:44:07.093" LastActivityDate="2014-07-29T12:44:07.093" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20049" PostTypeId="2" ParentId="8964" CreationDate="2014-07-29T12:36:10.923" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I have been told the normal fibroblasts are very similar all over the body. Is this really true?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Strong evidence indicates that fibroblasts in different parts of the body are intrinsically different, and there may be differences between them even in a single region [3]. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They have morphological similarities, but they act differently (at least in cultures):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Examination of skin and lung fibroblasts derived from the same human fetuses revealed significant in vitro differences. Fetal lung cultures had faster cell replication rates, greater [$^3H$]thymidine incorporation into DNA, higher cell numbers at confluency, smaller cell volumes, decreased cellular RNA and protein contents and lengthened in vitro life spans when compared with fetal skin cultures. In addition, these cell cultures had different responses to the addition of hydrocortisone to culture media [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They hardly adapt to a different serum (&lt;em&gt;in vitro&lt;/em&gt;) [2]. Yet they have a great capacity to differentiate (&lt;em&gt;in vivo&lt;/em&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] fibroblasts also seem to be the most versatile of connective-tissue cells, displaying a remarkable capacity to differentiate into other members of the family. [...] “Mature” fibroblasts with a lesser capacity for transformation may, for example, exist side by side with “immature” fibroblasts (often called mesenchymal cells) that can develop into a variety of mature cell types [3].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;E.L. Schneider, Y. Mitsui, K.S. Au, S. Stuart Shorr. &lt;em&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0014482777800025&quot; rel=&quot;nofollow&quot;&gt;Tissue-specific differences in cultured human diploid fibroblasts.&lt;/a&gt;&lt;/em&gt; Experimental Cell Research. Volume 108, Issue 1, August 1977, Pages 1–6. DOI 10.1016/S0014-4827(77)80002-5&lt;/li&gt;&#xA;&lt;li&gt;Zamansky, GLEN B., et al. &lt;em&gt;&lt;a href=&quot;http://jcs.biologists.org/content/61/1/289.full.pdf&quot; rel=&quot;nofollow&quot;&gt;&quot;Adaptation of human diploid fibroblasts in vitro to serum from different sources.&quot;&lt;/a&gt;&lt;/em&gt; Journal of cell science 61.1 (1983): 289-297.&lt;/li&gt;&#xA;&lt;li&gt;Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. Fibroblasts and Their Transformations: The Connective-Tissue Cell Family. Available from: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26889/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK26889/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-07-29T12:36:10.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20050" PostTypeId="1" AcceptedAnswerId="20053" CreationDate="2014-07-29T12:38:02.663" Score="3" ViewCount="400" Body="&lt;p&gt;recently i came across a small dove who had its feathers tied by a rubber band so that it $would'nt$ fly. it looks some what like this &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Nen3v.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;i was stunned by seeing it as i have never seen a dove in brown colour. and after staring it for some time i noticed that it's feathers or hairs near the neck region were made into a cluster that makes it look like $spike$ $hair$ $style$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so in short what would be the scientific name of this dove ?? &lt;/p&gt;&#xA;" OwnerUserId="8101" LastActivityDate="2019-01-24T14:08:53.087" Title="what would be the scientific name of this variety of dove" Tags="&lt;nomenclature&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20051" PostTypeId="2" ParentId="6948" CreationDate="2014-07-29T12:56:58.203" Score="4" Body="&lt;p&gt;The exact mechanism is not known:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Modafinil has wake-promoting actions similar to sympathomimetic agents like amphetamine and methylphenidate, although the pharmacologic profile is not identical to that of sympathomimetic amines. [...] Modafinil-induced wakefulness can be attenuated by the α1-adrenergic receptor antagonist prazosin; however, Modafinil is inactive in other in vitro assay systems known to be responsive to α-adrenergic agonists, such as the rat vas deferens preparation. [...] Modafinil is not a direct- or indirect-acting dopamine receptor agonist. However, in vitro, Modafinil binds to the dopamine transporter and inhibits dopamine reuptake. This activity has been associated in vivo with increased extracellular dopamine levels in some brain regions of animals [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A 2010 study has concluded that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Recent evidence suggests that modafinil may block the dopamine transporter (DAT) and that the dopamine D1 receptor (D1R) may contribute to modafinil effects [2].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Another one confirms modafinil's dopaminergic activity:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These findings indicate that modafinil has a long duration of action, with alerting properties arising predominantly from dopaminergic activity [3].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It seems to be dependent on catecholaminergic signaling:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It binds competitively to the cell-membrane dopamine (DA) transporter and is dependent on catecholaminergic (dopaminergic and adrenergic) signaling for its wake-promoting effects. [...] Modafinil is an exceptionally weak, but apparently very selective, DA transporter inhibitor. [...] The conformational constraints on the interaction of modafinil with the DA transporter - and probably, as a consequence, its effects on trace amine receptor signaling in the catecholaminergic cell - are unique among catecholaminergic agents [4].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Drugs.com. Modafinil. Clinical Pharmacology. Available from &lt;a href=&quot;http://www.drugs.com/pro/modafinil.html&quot; rel=&quot;nofollow&quot;&gt;http://www.drugs.com/pro/modafinil.html&lt;/a&gt; (accessed 29.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;Young JW, Geyer MA. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20132929&quot; rel=&quot;nofollow&quot;&gt;Action of modafinil--increased motivation via the dopamine transporter inhibition and D1 receptors?&lt;/a&gt; Biol. Psychiatry. 2010 Apr 15;67(8):784-7. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.biopsych.2009.12.015&quot; rel=&quot;nofollow&quot;&gt;10.1016/j.biopsych.2009.12.015&lt;/a&gt;. PubMed PMID: 20132929. &lt;/li&gt;&#xA;&lt;li&gt;Turner C, Belyavin A, Nicholson A. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24306135&quot; rel=&quot;nofollow&quot;&gt;Duration of activity and mode of action of modafinil: Studies on sleep and wakefulness in humans.&lt;/a&gt; J. Psychopharmacol. (Oxford). 2013 Dec 3;28(7):643-654. doi: &lt;a href=&quot;http://dx.doi.org/10.1177/0269881113508173&quot; rel=&quot;nofollow&quot;&gt;10.1177/0269881113508173&lt;/a&gt;. PubMed PMID: 24306135. &lt;/li&gt;&#xA;&lt;li&gt;Wisor J. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24109471&quot; rel=&quot;nofollow&quot;&gt;Modafinil as a catecholaminergic agent: empirical evidence and unanswered questions.&lt;/a&gt; Front Neurol. 2013 Oct 7;4:139. doi: &lt;a href=&quot;http://dx.doi.org/10.3389/fneur.2013.00139&quot; rel=&quot;nofollow&quot;&gt;10.3389/fneur.2013.00139&lt;/a&gt;. PubMed PMID: 24109471. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-07-29T12:56:58.203" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20052" PostTypeId="1" CreationDate="2014-07-29T13:09:20.727" Score="6" ViewCount="268" Body="&lt;p&gt;Specifically I am looking at reopening of the critical period of plasticity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Modern neuroscience has started to unlock the secret of neuroplasticity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A common experimental setup is with mice. They have a critical period between days 20 and 32 when they learn binocular vision. And if you cover one eye during this period, they never learn to use it properly. Covering the eye even for extended periods outside of this window has no long term effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scientists can then test out various plasticity hypotheses. And they had indeed found several mechanisms that can restore binocular vision to adult mice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find a list towards the bottom of this paper: &lt;a href=&quot;http://www.hindawi.com/journals/np/2011/921680/&quot; rel=&quot;nofollow&quot;&gt;Autism -- A 'Critical Period' disorder?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;enzymatic degradation of PNNs&lt;/li&gt;&#xA;&lt;li&gt;SSRI&lt;/li&gt;&#xA;&lt;li&gt;HDAC inhibitors (which are suggested to knock out Nogo-66 receptor)&lt;/li&gt;&#xA;&lt;li&gt;AcetylCholineSterase inhibitors&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It is suggested that there is an underlying pattern of excitation/inhibition (E/I) balance that all of these 4 techniques perturb.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where can I read about this E/I balance in detail? The Wikipedia page on NeuroPlasticity (&lt;a href=&quot;http://en.wikipedia.org/wiki/Neuroplasticity&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) appears to be a dead-end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for an overview, rather than technical scientific papers that explore a particular aspect, already assuming familiarity with the big picture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How to get the big picture?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: T K Hensch seems to be a world leader in this research, and his papers answering my questions, for example &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24439367&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/24439367&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8435" LastEditorUserId="8435" LastEditDate="2014-07-30T14:46:32.277" LastActivityDate="2014-07-30T14:46:32.277" Title="What is the core mechanism behind neuroplasticity?" Tags="&lt;neuroscience&gt;&lt;neuroplasticity&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20053" PostTypeId="2" ParentId="20050" CreationDate="2014-07-29T13:11:06.087" Score="7" Body="&lt;p&gt;It's a rock pigeons (Columba livia).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nCbDZ.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;The Color coding of Pigeon&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There are three genes responsible for pigmentation in pigeons.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;– &lt;em&gt;Tyrp1&lt;/em&gt; gene produces a protein that helps make the pigment eumelanin.&#xA;  Pigeons with blue-black feathers have normal &lt;em&gt;Tyrp1&lt;/em&gt;. Ash-red and brown&#xA;  birds pigeons contain different mutations in the &lt;em&gt;Tyrp1&lt;/em&gt; gene, which&#xA;  leads to less or different pigmentation.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;– Mutations that affect the &lt;em&gt;Sox10&lt;/em&gt; gene override colors determined by&#xA;  various versions of the &lt;em&gt;Tyrp1&lt;/em&gt; gene. Regardless of whether the &lt;em&gt;Tyrp1&lt;/em&gt;&#xA;  version makes pigeons blue-black, ash-red or brown, mutations that&#xA;  regulate the &lt;em&gt;Sox10&lt;/em&gt; gene result in red pigeons.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;– Mutation of the &lt;em&gt;Slc45a2&lt;/em&gt; gene decreases the intensity of colors&#xA;  determined by &lt;em&gt;Tyrp1&lt;/em&gt;, &lt;em&gt;Sox10&lt;/em&gt; and their mutants. Depending on the version&#xA;  of the Tyrp1 gene – blue-black, ash-red, and brown − pigeons harboring&#xA;  the mutant Slc45a2 gene still display the same colors, but in&#xA;  watered-down or diluted versions, less intense than those with normal&#xA;  &lt;em&gt;Slc45a2&lt;/em&gt;. For example, a pigeon with both the ash-red version of &lt;em&gt;Tyrp1&lt;/em&gt;&#xA;  and the mutant &lt;em&gt;Slc45a2&lt;/em&gt; gene has ash-yellow feathers. Pigeons with&#xA;  &lt;em&gt;Sox10&lt;/em&gt; and &lt;em&gt;Slc45a2&lt;/em&gt; mutations are yellow, which is the dilute form of&#xA;  &lt;strong&gt;red.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://unews.utah.edu/news_releases/birds-of-a-different-color/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://unews.utah.edu/news_releases/birds-of-a-different-color/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: University of Utah &lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-01-24T14:08:53.087" LastActivityDate="2019-01-24T14:08:53.087" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="20054" PostTypeId="1" AcceptedAnswerId="20055" CreationDate="2014-07-29T13:19:03.480" Score="9" ViewCount="15425" Body="&lt;p&gt;I used to have many pigeons around the house. If by chance one of the chicks fell out of the nest, we used to put it back using gloves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually, if we would touch the chicks with our bare hands, however, the other pigeons would usually kill the chick. I want to know why they do that?  &lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="9943" LastEditDate="2015-06-17T13:58:30.830" LastActivityDate="2015-06-17T13:58:30.830" Title="Why do pigeons kill their chicks when touched by a human?" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20055" PostTypeId="2" ParentId="20054" CreationDate="2014-07-29T13:34:22.170" Score="9" Body="&lt;p&gt;This is a story I have been told as well when I was a kid. Usually this is related to the foreign smell that the humans leave on the chick. However, this seems to be an urban legend, as birds have not a great sense of &lt;a href=&quot;http://www.birdsandblooms.com/birding/birding-basics/can-birds-smell-taste/&quot;&gt;smell&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Snopes says about this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;However, Mother birds will not reject their babies because they smell&#xA;  human scent on them, nor will they refuse to set on eggs that have&#xA;  been handled by a person. Many birds have a limited sense of smell and&#xA;  cannot detect human scent, or if they can detect it, do not react to&#xA;  it.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What can happen is that the birds returning to their nest which find the nest disturbed compared to the situation when they left might cause them to temporarily or permanently abondon their nest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find this and more urban legends about birds &lt;a href=&quot;http://www.snopes.com/critters/wild/babybird.asp&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.placeforwildbirds.org/myths.html&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-07-29T18:21:52.890" LastActivityDate="2014-07-29T18:21:52.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20056" PostTypeId="2" ParentId="20038" CreationDate="2014-07-29T13:54:58.807" Score="5" Body="&lt;p&gt;This has nothing to do with the proportion of the genome that is coding as suggested in another answers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason the figures are so different is because they are measuring different things. The chimp-human figure is measuring &lt;em&gt;sequence similarity&lt;/em&gt; whilst the figure for kin are measuring &lt;em&gt;gene similarity by descent&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This gives two sources of difference in the two numbers: firstly, there is the distinction between sequence similarity and gene similarity. Let us suppose you have a 1000bp gene, which contains or does not contain a single nucleotide polymorphism. These two variants are different alleles so if you're considering gene similarity then you would say these are 100% different but if you're comparing sequence similarity then you would say that there is just a 1bp difference so these are 99.9% similar. This is how chimps can be both so similar to humans and so different - it is not a matter of how many base pairs are different but where those differences are. A single base pair change in a 1000 bp gene can have a dramatic effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, the figure for relatedness to your parents/siblings is talking about similarity &lt;em&gt;by descent&lt;/em&gt;. In fact, your actual gene similarity to your parents is likely to be substantially higher than 50% because your parents are likely to have &lt;em&gt;the same version of many genes&lt;/em&gt; so which parent you inherit the gene from makes no difference. Additionally, they will also be homozygous for a number of alleles so that you always inherit the same version of this gene from that parent and are thus more related to your siblings than a crude calculation of relatedness would suggest. The 50% figure comes from only considering two genes the same &lt;em&gt;if they come from the same source&lt;/em&gt;, i.e. similarity by descent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another, perhaps, better way of thinking of this would be: among those genes that exist in different forms in your parents you will share 50% of them with your parents and 50% of them with each of your siblings on average.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a bit of an aside: the figure for similarity between human and chimp DNA you've given is based on crude annealing. So if a highly similar piece of DNA occurs in both human and chimp DNA they will match up but this does not consider how the DNA is arranged within the genome so it actually misses a considerable amount of the variation between organisms.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="2938" LastEditDate="2014-07-30T08:02:20.333" LastActivityDate="2014-07-30T08:02:20.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20057" PostTypeId="2" ParentId="3815" CreationDate="2014-07-29T14:36:47.710" Score="2" Body="&lt;h2&gt;Condensin&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Condensin I:&lt;/strong&gt; present in &lt;em&gt;cytoplasm&lt;/em&gt; during interphase, has access to chromosomes after prophase. Contributes to condensed chromosome assembly during prometaphase and metaphase [1].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Condensin II:&lt;/strong&gt; present in &lt;em&gt;nucleus&lt;/em&gt; during interphase, involved in chromosome condensation. Contributes to condensed chromosome assembly during prometaphase and metaphase [1].&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Cohesin&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;It keeps sister chromatids connected with each other during metaphase and ensures that each sister chromatid segregates to opposite poles. &quot;It facilitates spindle attachment onto chromosomes. It facilitates DNA repair by recombination.&quot; [2]&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Condensin,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Condensin&amp;amp;oldid=606814199&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Condensin&amp;amp;oldid=606814199&lt;/a&gt; (accessed July 29, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Cohesin,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Cohesin&amp;amp;oldid=617481362&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Cohesin&amp;amp;oldid=617481362&lt;/a&gt; (accessed July 29, 2014).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-07-29T14:36:47.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20058" PostTypeId="2" ParentId="9277" CreationDate="2014-07-29T15:41:31.020" Score="2" Body="&lt;p&gt;Let's not confuse the type of power of a light emitting device with the type of light it produces.&lt;br /&gt;&#xA;&lt;sub&gt;This question is not about AC or DC current. It is about flicker frequency, light wavelength and their biological effects. &lt;/sub&gt;&lt;/p&gt;&#xA;&lt;h2&gt;Flicker frequency&lt;/h2&gt;&#xA;&lt;p&gt;The term &amp;quot;ache in the eye sockets&amp;quot; probably refers to &lt;a href=&quot;http://en.wikipedia.org/wiki/Asthenopia&quot; rel=&quot;nofollow noreferrer&quot;&gt;asthenopia&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Human eye cannot detect flicker with a frequeny above 75 Hz. But many computer displays have a refresh rate of 60 Hz [1]. Out of focus and  low refresh rate monitors are known to cause eye strain and asthenopia [2], favored by existing hypermetropia (and other vision issues).&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Visual discomfort has been related to 1) the presence of flicker; the possibility to regulate, 2) brightness, 3) height; and 4) inclination of monitor. Asthenopia has resulted statistically correlated to the presence of flicker and to the impossibility of regulating height and inclination of monitor for both sexes. The possibility to regulate monitor brightness has not determined a reduction of visual discomfort either in men or in women [3].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;h2&gt;Wavelength&lt;/h2&gt;&#xA;&lt;p&gt;Eye sensitivity is different (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Spectral_sensitivity&quot; rel=&quot;nofollow noreferrer&quot;&gt;spectral sensitivity&lt;/a&gt;):&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Cones_SMJ2_E.svg#mediaviewer/File:Cones_SMJ2_E.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/1/1e/Cones_SMJ2_E.svg/1200px-Cones_SMJ2_E.svg.png&quot; alt=&quot;Cones SMJ2 E.svg&quot;&gt;&lt;/a&gt;&lt;br&gt;&quot;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Cones_SMJ2_E.svg#mediaviewer/File:Cones_SMJ2_E.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cones SMJ2 E&lt;/a&gt;&quot; by Vanessaezekowitz at en.wikipedia / Later version uploaded by BenRG. - Based on Dicklyon's PNG version, itself based on data from Stockman, MacLeod &amp;amp; Johnson (1993) Journal of the Optical Society of America A, 10, 2491-2521d http://psy.ucsd.edu/~dmacleod/publications/61StockmanMacLeodJohnson1993.pdf (log E human cone response, via http://www.cvrl.org/database/text/cones/smj2.htm)&#xA;Transferred from en.wikipedia to Commons by &lt;a href=&quot;//commons.wikimedia.org/wiki/User:Richard001&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;User:Richard001&quot;&gt;User:Richard001&lt;/a&gt; using CommonsHelper.. Licensed under &lt;a href=&quot;http://creativecommons.org/licenses/by-sa/3.0&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Creative Commons Attribution-Share Alike 3.0-2.5-2.0-1.0&quot;&gt;CC BY-SA 3.0&lt;/a&gt; via &lt;a href=&quot;//commons.wikimedia.org/wiki/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikimedia Commons&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Light color and color contrast matter:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The study results showed that both visual acuity and the subjective visual fatigue were significantly affected by the color of light [4].&lt;/p&gt;&#xA;&lt;p&gt;Images with excessive energy at medium spatial frequencies (Fernandez and Wilkins, 2008 Perception 37 1098-1113), or that have high color contrast and little or no luminance contrast (Wilkins et al, 2008 Perception 37 Supplement, 144-145) appear uncomfortable or aversive and can induce headaches in hypersensitive observers. Such stimuli are uncharacteristic of natural images [...] [5].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Blue light can also reduce melatonin levels and affect sleep and mood (the studies don't have a strong conclusion though):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Melatonin concentrations after exposure to the blue-light goggle experimental condition were significantly reduced compared to the dark control and to the computer monitor only conditions. Although not statistically significant, the mean melatonin concentration after exposure to the computer monitor only was reduced slightly relative to the dark control condition [6].&lt;/p&gt;&#xA;&lt;p&gt;All light is not equal: blue wavelengths are the most potent portion of the visible electromagnetic spectrum for circadian regulation. [...] evening use of amber lenses to block blue light might affect sleep quality. Mood is also affected by light and sleep; [...] At the end of the study, the amber lens group experienced significant (p &amp;lt; .001) improvement in sleep quality relative to the control group and positive affect (p = .005). Mood also improved significantly relative to controls [7].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &amp;quot;Flicker fusion threshold,&amp;quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Flicker_fusion_threshold&amp;amp;oldid=615159751&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Flicker_fusion_threshold&amp;amp;oldid=615159751&lt;/a&gt; (accessed July 29, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &amp;quot;Asthenopia,&amp;quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Asthenopia&amp;amp;oldid=617227613&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Asthenopia&amp;amp;oldid=617227613&lt;/a&gt; (accessed July 29, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Rechichi C, Scullica L. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2081858&quot; rel=&quot;nofollow noreferrer&quot;&gt;[Asthenopia and monitor characteristics].&lt;/a&gt; J Fr Ophtalmol. 1991;13(8-9):456-60. PubMed PMID: 2081858.&lt;/li&gt;&#xA;&lt;li&gt;Lin CJ, Feng WY, Chao CJ, Tseng FY. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18413962&quot; rel=&quot;nofollow noreferrer&quot;&gt;Effects of VDT workstation lighting conditions on operator visual workload.&lt;/a&gt; Ind Health. 2008 Apr;46(2):105-11. PubMed PMID: 18413962.&lt;/li&gt;&#xA;&lt;li&gt;Juricevic I, Land L, Wilkins A, Webster MA. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20842966&quot; rel=&quot;nofollow noreferrer&quot;&gt;Visual discomfort and natural image statistics.&lt;/a&gt; Perception. 2010;39(7):884-99. PubMed PMID: 20842966.&lt;/li&gt;&#xA;&lt;li&gt;Figueiro MG, Wood B, Plitnick B, Rea MS. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21552190&quot; rel=&quot;nofollow noreferrer&quot;&gt;The impact of light from computer monitors on melatonin levels in college students.&lt;/a&gt; Neuro Endocrinol. Lett. 2011;32(2):158-63. PubMed PMID: 21552190.&lt;/li&gt;&#xA;&lt;li&gt;Burkhart K, Phelps JR. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20030543&quot; rel=&quot;nofollow noreferrer&quot;&gt;Amber lenses to block blue light and improve sleep: a randomized trial.&lt;/a&gt; Chronobiol. Int. 2009 Dec;26(8):1602-12. doi: &lt;a href=&quot;http://dx.doi.org/10.3109/07420520903523719&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.3109/07420520903523719&lt;/a&gt;. PubMed PMID: 20030543.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-08-02T11:05:07.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20059" PostTypeId="2" ParentId="17845" CreationDate="2014-07-29T15:56:44.923" Score="7" Body="&lt;p&gt;The major reason for this are differences in the preparation methods. &lt;a href=&quot;http://en.wikipedia.org/wiki/Attenuated_vaccine&quot;&gt;Live (attenuated) vaccines&lt;/a&gt; need permanent cooling, which makes their use in third world countries difficult. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Inactivated_vaccine&quot;&gt;Inactivated vaccines&lt;/a&gt; are inactivated either by heat, radiation of chemicals and are often freeze-dried after purification (removal of chemicals used for killing). In this condition, they have a very long shelf-life and need no cooling. Before use they are dissolved in water and then administered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is another problem with mixing these vaccines: Live vaccines can not be given to anybody, people which have a weakened immune system (because of an infection like HIV, chemotherapy or the adimistration of drugs, which downregulate the immune system after an organ transplantation) are not able to receive them. The attenuated pathogen which replicates usually only slowly would still be a possible danger for these people. So they can still be vaccinated with inactivated vaccines to provide at least some protection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information on this topic see the chapter on immunization in &quot;&lt;a href=&quot;http://pathmicro.med.sc.edu/ghaffar/immunization-ver2.htm&quot;&gt;Microbiology and Immunology online&lt;/a&gt;&quot; and this information from the &lt;a href=&quot;http://www.niaid.nih.gov/topics/vaccines/understanding/pages/typesvaccines.aspx&quot;&gt;National Institute of Health&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-29T15:56:44.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20060" PostTypeId="2" ParentId="16180" CreationDate="2014-07-29T16:21:47.573" Score="6" Body="&lt;p&gt;There is no problem to transform bacteria with more than one plasmid. The usual methods (either chemical competent cells or electroporation) are working fine, although electroporation might give you better results, as the cells take up more DNA. On the downside you have to make sure that your cells are prepared nicely, otherwise the electroporation cell will produce a short circuit (of course chemically competent cells can be problematic, too).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you will definitely need are two (or more) different selection markers. The easiest will probably be different antibiotics (something I used in the lab and which works nicely) or other like genes which provide essential substances for the cells. As long as the selection pressure on the cells is held up, both plasmids will stay in the cells, when you take away one of them, the corresponding plasmid will get lost within a few days.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the efficiency of co-transformations I haven't found any papers. There is however, some data available on factors which influence the effiency of single transformations and I don't see, why these shouldn't be applied for co-transformations as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, there is the size of the plasmid. The bigger the plasmid is, the lower gets the transformation efficiency. The figure from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2265755&quot; rel=&quot;nofollow noreferrer&quot;&gt;Inoue, 1990&lt;/a&gt; is pretty clear in this point:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VwCKY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for this reason I would use plasmids as small as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, the density at which the growing bacterial culture which is used to prepare the competent cells is harvested has a big influence on the transformation efficiency. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8052542&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tang and colleagues (1994)&lt;/a&gt; found out that growing the cells to a higher density than the classical OD$_{600}$ of 0.6 (which for example Inoue recommends in it paper cited above) is not a very good choice in terms of transformation efficiency. They found an OD$_{600}$ of about 0.94 working much better, see the corresponding figure:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JNWgK.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And finally the amount of competing DNA is a big factor. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6345791&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hanahan, 1983&lt;/a&gt; found out that the transformation efficiency gets lower, the more competing DNA is present:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/odlhu.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I would try to use as little of each DNA to work against this effect.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-07-29T20:25:54.867" LastActivityDate="2014-07-29T20:25:54.867" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20063" PostTypeId="1" CreationDate="2014-07-29T17:21:54.400" Score="4" ViewCount="463" Body="&lt;p&gt;I use ImageJ to do an analysis of a Westernblot Image. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If everything goes as wanted the workflow is fine. But if I do something wrong creating a lane there is no undo for a lane and also no way to remove all lanes that I can find. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do I get back to my original image or undo a lane creation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm using 1.49e on Mac OS&lt;/p&gt;&#xA;" OwnerUserId="8541" LastEditorUserId="8541" LastEditDate="2014-08-11T16:20:51.487" LastActivityDate="2014-08-11T16:20:51.487" Title="How to remove bad lanes in ImageJ Westernblot analysis" Tags="&lt;proteins&gt;&lt;western-blot&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20064" PostTypeId="2" ParentId="17351" CreationDate="2014-07-29T19:24:25.253" Score="2" Body="&lt;p&gt;Since posting, I did some more research using background refs from the intro (who knew?). The trick seems to be that when protons are pumped out, the cell regenerates them from water in order to maintain pH. So the solute concentration DOES increase inside the cell with more Na/H transport.&lt;/p&gt;&#xA;" OwnerUserId="6517" LastActivityDate="2014-07-29T19:24:25.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20065" PostTypeId="1" CreationDate="2014-07-29T19:28:25.677" Score="2" ViewCount="261" Body="&lt;p&gt;I'm working on a project where I'm going to analyze a large amount of transcriptome data. After assembling our RNA-Seq reads into contigs using Trinity, it looks like I'm going to have about 10GB of sequences in fasta format. Since these sequences are from several hundred tissue libraries but from a single species (chicken), I'm expecting there to be a lot of redundancy, so I'd like to cluster these sequences and just use a representative sequence from each cluster as I go forward with my analysis. I see there are quite a few tools that exist to do things like this, and I'm wondering which you all would recommend. I'll be running this on a Linux machine with 64 CPU cores and ~500GB of RAM.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I started looking at USEARCH, but it seems I'm going to run into some memory issues with the free 32-bit version and as much as I clicked around on their site I couldn't figure out how much the 64-bit version costs or how to buy it.&lt;/p&gt;&#xA;" OwnerUserId="1481" LastActivityDate="2014-07-31T03:43:51.633" Title="Recommended sequence clustering algorithm for transcriptome data" Tags="&lt;bioinformatics&gt;&lt;sequence-analysis&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20066" PostTypeId="2" ParentId="20065" CreationDate="2014-07-29T19:45:48.603" Score="3" Body="&lt;p&gt;It does sound like you have a lot of data.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would first try Robert Edgar's other newer tool UPARSE which is faster and can handle more data using the free 32-bit version.  I think you'll mainly be limited by machine memory though, right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Did you try CD-Hit?&lt;/p&gt;&#xA;" OwnerUserId="8544" LastActivityDate="2014-07-29T19:45:48.603" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20067" PostTypeId="1" AcceptedAnswerId="20071" CreationDate="2014-07-29T19:47:03.433" Score="5" ViewCount="473" Body="&lt;p&gt;Has the human species changed since first defined as homo sapiens sapiens?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm asking this question partly because I'm wondering how we might evolve next.&lt;/p&gt;&#xA;" OwnerUserId="8116" LastEditorUserId="27323" LastEditDate="2017-02-02T04:41:07.827" LastActivityDate="2017-04-25T18:05:04.203" Title="Is there evolution in humans since the first homo sapiens sapiens" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;human-evolution&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20069" PostTypeId="1" CreationDate="2014-07-29T23:24:48.663" Score="3" ViewCount="70" Body="&lt;p&gt;I would like to do some gene inheritance simulations, and I was wondering if there is an accepted model for what mating looks like in the general human population? I am not necessarily looking for the &lt;em&gt;exact&lt;/em&gt; graph of any population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, my current model has generations 1, 2, ..., n, n+1, ... where each individual in generation &lt;em&gt;i&lt;/em&gt; is the product of a mating between two individuals in generation &lt;em&gt;i&lt;/em&gt;-1. This is obviously over simplistic, and I was wondering if there are better models out there?&lt;/p&gt;&#xA;" OwnerUserId="8546" LastActivityDate="2015-12-14T21:51:00.693" Title="Is there a realistic &quot;family tree&quot; model for the human population?" Tags="&lt;human-genetics&gt;&lt;theoretical-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20070" PostTypeId="1" CreationDate="2014-07-30T02:04:05.483" Score="2" ViewCount="1253" Body="&lt;p&gt;Styes formed in the eyes are cured by dabbing at them with lukewarm water(I saw this being done many a times as a home remedy.) At times, common salt is added to the water before dabbing. My mother says, NaCl hastens the healing process; why is it so? What does salt do to cure the styes faster? Can salt be used for treating other eruptions anywhere else?&lt;/p&gt;&#xA;" OwnerUserId="8216" LastActivityDate="2014-07-30T02:04:05.483" Title="What does salt do to styes?" Tags="&lt;physiology&gt;&lt;eyes&gt;&lt;human-eye&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20071" PostTypeId="2" ParentId="20067" CreationDate="2014-07-30T02:24:39.957" Score="6" Body="&lt;p&gt;We continue to evolve all the time: &lt;a href=&quot;http://www.npr.org/2013/09/27/226837803/modern-humans-still-evolving-and-faster-than-ever&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.npr.org/2013/09/27/226837803/modern-humans-still-evolving-and-faster-than-ever&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For those who think the forces of natural selection no longer apply to modern humans, paleoanthropologist John Hawks would urge you to reconsider. In recent times — that's 10 to 20 thousand years, for a paleoanthropologist — Hawks says we've picked up genetic variations in skin color, and other traits that allow us to break down starch and digest cheese.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Homo sapiens sapiens is &lt;a href=&quot;http://en.wikipedia.org/wiki/Anatomically_modern_humans&quot; rel=&quot;nofollow noreferrer&quot;&gt;over 100,000 years old&lt;/a&gt; and we have changed in many ways since then, as noted in the above NPR article! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure we can say there is a &quot;first&quot; homo sapiens sapiens -- the change from one species to another is gradual.  You may know that mixing red and blue gives purple, but at what points do we officially have red, purple, or blue when mixing different levels of red and blue?&lt;/p&gt;&#xA;" OwnerUserId="8547" LastEditorUserId="8547" LastEditDate="2017-04-25T18:05:04.203" LastActivityDate="2017-04-25T18:05:04.203" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20072" PostTypeId="1" AcceptedAnswerId="20113" CreationDate="2014-07-30T03:09:56.050" Score="11" ViewCount="6012" Body="&lt;p&gt;Human body density is approximately 1 kg/l (same as fresh water) - which is not surprising (at first) given that we are 70% water, and &lt;em&gt;is&lt;/em&gt; surprising (on a second thought), given that the other 30% can be just about anything (from the air in the lungs to the relatively heavy bones).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How remarkable is that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider other mammalian species.&#xA;For each species, compute the average body density of an adult.&#xA;Thus, for each species we have the number - the mean body density.&#xA;How are these numbers distributed?&#xA;Mostly heavier than water? Lighter?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is unlikely that this kind of research has been done, so I would settle for something simpler: what are the densest/lightest mammals? (or, in general, vertebrae)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS. As you can guess, I am a mathematician, not a biologist :-)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PPS. Given abundance of water of Earth's surface (70%, same as above!), it makes a lot of sense to be as dense as water: not heavier (to avoid drowning), not lighter (to be able to dive for food), so natural selection should favor the density of 1.  Are there exceptions?&lt;/p&gt;&#xA;" OwnerUserId="4152" LastEditorUserId="4152" LastEditDate="2014-12-15T19:23:46.620" LastActivityDate="2016-12-18T21:27:21.373" Title="Mammal body density" Tags="&lt;mammals&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20073" PostTypeId="2" ParentId="20052" CreationDate="2014-07-30T04:04:05.110" Score="3" Body="&lt;p&gt;This is a good first source which suggests further references:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.scholarpedia.org/article/Balance_of_excitation_and_inhibition&quot; rel=&quot;nofollow&quot;&gt;http://www.scholarpedia.org/article/Balance_of_excitation_and_inhibition&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-07-30T04:04:05.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20074" PostTypeId="2" ParentId="19629" CreationDate="2014-07-30T04:06:48.223" Score="5" Body="&lt;p&gt;I know of no correlation between number of neurons in cortex and intelligence. This question is fraught with controversy because there has been very little work on it but much speculation. Some have suggested that the connectivity between neurons is what is important rather than the number which is logically possible but remains to be supported by definitive evidence.&lt;/p&gt;&#xA;" OwnerUserId="5694" LastActivityDate="2014-07-30T04:06:48.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20075" PostTypeId="1" CreationDate="2014-07-30T08:10:10.080" Score="5" ViewCount="613" Body="&lt;p&gt;Which algorithm or algorithms are considered the &lt;em&gt;standard&lt;/em&gt; or &lt;em&gt;state-of-the-art&lt;/em&gt; for &lt;a href=&quot;http://en.wikipedia.org/wiki/Multiple_sequence_alignment&quot;&gt;multiple sequence alignment&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How big is the need for better algorithms? How many sequences need to be alignment in a typical test? I am trying to understand how important problem this is in bioinformatics.&lt;/p&gt;&#xA;" OwnerUserId="8550" LastActivityDate="2016-04-18T11:04:40.000" Title="What is the state-of-the-art algorithm for multiple sequence alignment?" Tags="&lt;bioinformatics&gt;&lt;sequence-analysis&gt;&lt;sequence-alignment&gt;" AnswerCount="3" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="20076" PostTypeId="1" CreationDate="2014-07-30T08:26:09.820" Score="2" ViewCount="674" Body="&lt;p&gt;Are there any open and freely distributed standard datasets for testing new algorithms for &lt;a href=&quot;http://en.wikipedia.org/wiki/Multiple_sequence_alignment&quot; rel=&quot;nofollow&quot;&gt;multiple sequence alignment&lt;/a&gt;?&lt;/p&gt;&#xA;" OwnerUserId="8550" LastActivityDate="2017-03-17T02:11:43.883" Title="Standard datasets for testing new multiple sequence alignment algorithms?" Tags="&lt;sequence-analysis&gt;&lt;sequence-alignment&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20077" PostTypeId="1" AcceptedAnswerId="20079" CreationDate="2014-07-30T08:42:34.867" Score="2" ViewCount="1825" Body="&lt;p&gt;I've read it in a book and have heard people mention it, but I can't find any documentation about it. But the point being made is this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The human collarbone acts as a shock absorber for impact on the shoulder or stretched arm. If too much force is put on the shoulder (EG: during a fall), the collarbone is designed to break to prevent injury to the neck and/or head.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is this actually true and if so, can anybody point me to some documentation about it?&lt;/p&gt;&#xA;" OwnerUserId="8551" LastActivityDate="2014-07-30T10:45:22.550" Title="Is the human collarbone supposed to break?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20078" PostTypeId="1" AcceptedAnswerId="20142" CreationDate="2014-07-30T10:18:26.040" Score="7" ViewCount="2573" Body="&lt;p&gt;This is a quote from &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/ibi.12158/abstract&quot;&gt;Dey et al 2014&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hatching asynchrony is thought to be adaptive because...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What exactly does adaptive mean here? Does it mean hatching asynchrony has fitness benefits? Or does it mean hatching asynchrony is likely to be selected for?&lt;/p&gt;&#xA;" OwnerUserId="1216" LastActivityDate="2015-07-27T18:17:40.867" Title="What exactly does adaptive mean?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;ornithology&gt;&lt;adaptation&gt;&lt;reproductive-biology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20079" PostTypeId="2" ParentId="20077" CreationDate="2014-07-30T10:45:22.550" Score="4" Body="&lt;p&gt;This looks like a misinterpretation. Because collarbone is the only horizontal long bone of the human body [1], it is the first to fracture when falling on the shoulder.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its fracture can affect many structures:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The muscles involved in clavicle fractures include the deltoid, trapezius, subclavius, sternocleidomastoid, sternohyoid and pectoralis major muscles. The ligaments involved include the Conoid ligament and Trapezoid ligament [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is indeed a shock absorber, but for the upper torso (some way or another any bone can be considered a shock absorber):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The clavicle also serves as something of a &quot;shock-absorber&quot; for the upper torso. Physical contact from the side will be partially absorbed by the clavicle. Because of this function, the clavicle is a very commonly broken bone [2].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The fracture can lead to severe injuries:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Displaced or comminuted clavicle fractures are associated with complications such as subclavian vessels injury, hemopneumothorax, brachial plexus paresis [...] [3]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Clavicle fracture,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Clavicle_fracture&amp;amp;oldid=615723256&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Clavicle_fracture&amp;amp;oldid=615723256&lt;/a&gt; (accessed July 30, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Erich Rosenberger M.D. Anatomy And Physiology (2009). Available from &lt;a href=&quot;http://www.sciences360.com/index.php/anatomy-physiology-299-12859/&quot; rel=&quot;nofollow&quot;&gt;http://www.sciences360.com/index.php/anatomy-physiology-299-12859/&lt;/a&gt; (accessed 30.07.2014)&lt;/li&gt;&#xA;&lt;li&gt;George Mouzopoulos, Emmanuil Morakis, Michalis Stamatakos, Mathaios Tzurbakis. &lt;em&gt;Complications Associated With Clavicular Fracture.&lt;/em&gt; Orthopaedic Nursing, October 2009, Volume 28, Number 5, Pages 217 - 224 - See more at: &lt;a href=&quot;http://www.nursingcenter.com/lnc/cearticle?tid=938803#sthash.F09wonvJ.dpuf&quot; rel=&quot;nofollow&quot;&gt;http://www.nursingcenter.com/lnc/cearticle?tid=938803#sthash.F09wonvJ.dpuf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-07-30T10:45:22.550" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20080" PostTypeId="2" ParentId="20078" CreationDate="2014-07-30T10:53:10.020" Score="9" Body="&lt;p&gt;The question is probably more complicated than it seems because, if I am not wrong, the word adaptation here is understood at the group level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Definitions of adaptation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, there is not such thing as a single, standard definition of adaptation. But for most cases the accurate definition the author is using is not of much importance as all of the usual definitions totally fit in the sentence without changing the meaning of the concept they want to express. In you case however, the concept of adaptation seems to be a bit more complicated (and interesting) because it refers to a group-level adaptation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that most people does not really care about the exact definition they're using and this might yield to some confusion. It will probably be a bit hard to know exactly what the authors  (Dey et al.) of your article had in mind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Definition of Group-level adaptation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am here going to talk about how the term adaptation can be understood for a (social) group. This is important as I suspect the authors to use the term adaptation on a group phenotypic trait (emergent trait if you want).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Pareto optimality&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To my experience, the concept of group-level adaptation is defined in relation to the concept of &lt;a href=&quot;http://en.wikipedia.org/wiki/Pareto_efficiency&quot; rel=&quot;nofollow&quot;&gt;Pareto optimality&lt;/a&gt; which is a concept used in &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionary_game_theory&quot; rel=&quot;nofollow&quot;&gt;evolutionary game theory&lt;/a&gt;. Shortly speaking, in a system that is at Pareto optimality no individual can by any change of the trait under consideration increase its fitness without decreasing the fitness of another individual. In other words, a population that is at Pareto optimality has the greatest achievable population mean fitness. Therefore, it makes sense to consider a group to be (perfectly) adapted when it is at Pareto optimality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Nash equilibrium&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending on the underlying &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionary_game_theory&quot; rel=&quot;nofollow&quot;&gt;evolutionary game&lt;/a&gt;, the Pareto optimality may or may not be a &lt;a href=&quot;http://en.wikipedia.org/wiki/Nash_equilibrium&quot; rel=&quot;nofollow&quot;&gt;Nash equilibrium&lt;/a&gt;. Shortly speaking, a population is at Nash equilibrium if no individual can increase its fitness by changing the trait under consideration. Therefore, group-level adaptation can only be stable if the Nash equilibrium is Pareto optimal. An example of game where the Nash equilibrium is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Market_game&quot; rel=&quot;nofollow&quot;&gt;free-market game&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In your case&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At first sight, because asynchrony is a group level trait, it seems to me that the sentence &quot;Hatching asynchrony is thought to be adaptive [..]&quot; means that hatching asynchrony is thought to be at Pareto optimality. In other words, it means that hatching asynchrony is thought to be the state of the system where the mean fitness of the group is maximized, that is no individual can increase its fitness without decreasing the fitness of another individual by being synchronous.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-07-27T18:17:40.867" LastActivityDate="2015-07-27T18:17:40.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20082" PostTypeId="2" ParentId="20078" CreationDate="2014-07-30T11:07:14.377" Score="5" Body="&lt;p&gt;Your questions mean basically the same. Birdcare.com says: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The situation in which all the eggs in a clutch do not hatch at (more or less) the same time, as is more usual among birds, but have their hatching spread over several days. It is well seen in the various types of raptor, and is an adaptation to a type of food supply which may fluctuate. During seasons when food is short the later hatched young will probably starve as the earlier hatched young, being larger and stronger, deprive them of food, and so the size of the brood is reduced to a level in balance with the available food supply. In years of plenty all the young may be able to survive. In 'synchronous hatching' all the eggs hatch at more or less the same time.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;fitness benefit&lt;/em&gt; of hatching asynchrony on the species level is due to increased range of individual fitness among the young birds. The available resources do not need to be distributed equally among the offspring during unfavorable seasons such that fewer, but at least some of the hatchlings (the 'strongest') can survive. You see that this is the same as &lt;em&gt;beeing selected for&lt;/em&gt; because on average the number of agents passing their genes to the next generation is higher with asynchronous hatching than with synchronous hatching. Of course, the success of this strategy is strongly dependent on environmental factors. In very stable habitats it might turn out to be disadvantageous on the long run. &lt;/p&gt;&#xA;" OwnerUserId="8015" LastActivityDate="2014-07-30T11:07:14.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20083" PostTypeId="2" ParentId="20076" CreationDate="2014-07-30T11:45:04.527" Score="3" Body="&lt;p&gt;I would suggest you &lt;a href=&quot;http://www.ugr.es/~fortuno/pacalci.htm&quot; rel=&quot;nofollow&quot;&gt;PAcAlCI&lt;/a&gt; or &lt;strong&gt;Prediction of Accuracy in Alignments based on Computational Intelligence&lt;/strong&gt;, though the acronym in wierd the tool is good for testing new Sequence Alignments. They &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But before you start testing your algorithm, I suggest take a look at these papers:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://arxiv.org/pdf/1211.2160.pdf&quot; rel=&quot;nofollow&quot;&gt;Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence &#xA;Alignment&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] &lt;a href=&quot;http://nar.oxfordjournals.org/content/early/2010/07/17/nar.gkq625.full&quot; rel=&quot;nofollow&quot;&gt;Issues in bioinformatics benchmarking: the case study of multiple sequence alignment&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: I haven't tested or used the tool myself.&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-30T11:45:04.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20084" PostTypeId="1" AcceptedAnswerId="20100" CreationDate="2014-07-30T11:46:25.660" Score="4" ViewCount="725" Body="&lt;p&gt;I had to digest my insert containing plasmid and another vector into which my insert has to be ligated, each with BamHI and NotI.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Upon digestion, I ran the gel to check for results. The digestion seemed to be ok the first time with reasonably good bands. Since I needed more concentration I ran the gel with the same reaction setup (30microL) for the second time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well 1 - 100bp marker&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well 2 - Insert in a vector (820 ng/microL, 3microL)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well 3- Plasmid vector into which the insert has to be ligated (1000 ng/microL, 2microL)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The marker bands were faint while there were absolutely no bands in the other wells. What could be the reason for failure during the second run? I've performed the second time digestion in a span of 40 min after the first one.&lt;/p&gt;&#xA;" OwnerUserId="8142" LastEditorUserId="1320" LastEditDate="2014-07-30T12:50:21.723" LastActivityDate="2014-07-31T08:04:38.350" Title="No digested product bands, but markers are visible. What could be the reasons?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20085" PostTypeId="2" ParentId="20075" CreationDate="2014-07-30T12:14:40.050" Score="3" Body="&lt;p&gt;My Vote goes to &lt;strong&gt;Mafft(insi)&lt;/strong&gt; as it have ~86% accuracy and results in ~1.2 hour. Though fastest will be &lt;strong&gt;kalign&lt;/strong&gt; takes only ~3 minutes to finish with an accuracy of 74.3%. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For testing:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For each of the 218 reference alignments in the benchmark, we applied&#xA;  eight alignment programs, resulting in a total of 1744 automatically&#xA;  constructed MSAs. The overall quality of these automatic alignments&#xA;  was measured using the Column Score (CS) described in Methods.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UsThc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;FIGURE 1: &lt;strong&gt;Overall alignment performance for each of the MSA programs tested.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(A) Overall Accuracy &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(B) Total run time for constructing all alignments (a log10 scale is used for display purposes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;doi:10.1371/journal.pone.0018093.g003&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Compared Tools&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0018093.t001&amp;amp;representation=PNG_L&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0018093.t001&amp;amp;representation=PNG_L&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source and Photo Credits: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018093#pone-0018093-g003&quot; rel=&quot;nofollow noreferrer&quot;&gt;A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: This is from an old paper of 2011. If you want the new statistics you can always test on your own, by the process described in the source paper.&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-07-30T12:14:40.050" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20086" PostTypeId="1" AcceptedAnswerId="20101" CreationDate="2014-07-30T13:14:30.287" Score="3" ViewCount="170" Body="&lt;p&gt;Can you please give me some advice for a book in (evolutionary) &lt;a href=&quot;http://en.wikipedia.org/wiki/Conservation_genetics&quot; rel=&quot;nofollow&quot;&gt;conservation genetics&lt;/a&gt; that offers an in-depth review of the mathematical formulations used in this field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read the book &lt;a href=&quot;http://www.amazon.fr/Evolutionary-Conservation-Biology-R%C3%A9gis-Ferri%C3%A8re/dp/0521116082/ref=sr_1_3?ie=UTF8&amp;amp;qid=1406725200&amp;amp;sr=8-3&amp;amp;keywords=evolutionary%20conservation%20biology&quot; rel=&quot;nofollow&quot;&gt;Evolutionary Conservation Biology (Ferrière and Dieckmann, 2009)&lt;/a&gt; and I really liked it. I'm seeking for another book of the same kind that goes further on the part A (Theory of Extinction) and especially on the concern of the importance of population structure and the genetic load. I am also interested in &lt;a href=&quot;http://en.wiktionary.org/wiki/landscape_genetics&quot; rel=&quot;nofollow&quot;&gt;landscape genetics&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-07-31T10:03:32.040" LastActivityDate="2014-08-01T00:12:12.900" Title="Conservation Genetics - Book recommendations" Tags="&lt;evolution&gt;&lt;population-dynamics&gt;&lt;book-recommendation&gt;&lt;population-genetics&gt;&lt;conservation-biology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20088" PostTypeId="2" ParentId="8884" CreationDate="2014-07-30T18:19:48.243" Score="1" Body="&lt;p&gt;The best way to ensure you're getting an accurate skull, near as I can tell, is striking the &quot;model&quot; part of your question, and go straight for a &lt;em&gt;real&lt;/em&gt; skull.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A cursory search revealed, for instance, &lt;a href=&quot;http://www.skullsunlimited.com/o/82/natural-bone-human-skulls.htm&quot; rel=&quot;nofollow&quot;&gt;Skulls Unlimited International&lt;/a&gt;, &lt;a href=&quot;https://www.boneroom.com/welcome.aspx?c=1857&amp;amp;n=RealHumanSkulls&quot; rel=&quot;nofollow&quot;&gt;The Bone Room&lt;/a&gt;, and &lt;a href=&quot;http://theevolutionstore.com/store/real-human-skulls/&quot; rel=&quot;nofollow&quot;&gt;The Evolution Store&lt;/a&gt; although other providers probably exist as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A regulatory board for model skulls probably doesn't exist, given the apparent ease with which real skulls can be obtained and kept.&lt;/p&gt;&#xA;" OwnerUserId="1095" LastActivityDate="2014-07-30T18:19:48.243" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20089" PostTypeId="1" CreationDate="2014-07-30T19:33:32.627" Score="18" ViewCount="2866" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/B4UAu.jpg&quot; alt=&quot;side view&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We found this skull on a beach in southwestern Sweden, and are curious as to what kind of animal it was. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6GnIv.jpg&quot; alt=&quot;bottom view&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/b6e4s.jpg&quot; alt=&quot;frontal view&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8556" LastEditorUserId="16866" LastEditDate="2019-04-01T15:14:31.720" LastActivityDate="2019-09-09T09:50:25.023" Title="What kind of skull is this?" Tags="&lt;species-identification&gt;&lt;zoology&gt;&lt;ornithology&gt;&lt;bone&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20090" PostTypeId="2" ParentId="8648" CreationDate="2014-07-30T20:46:46.073" Score="4" Body="&lt;p&gt;The main reason seems to be a mechanism to save water and allow the excretion of higher concentrations of the ions. See the image (from &lt;a href=&quot;http://books.google.de/books?id=ZwydxKMbzz8C&amp;amp;lpg=PT34&amp;amp;ots=jFTj8JEL7d&amp;amp;dq=why%20do%20fish%20excrete%20divalent%20cations%20via%20kidney&amp;amp;hl=de&amp;amp;pg=PT35#v=onepage&amp;amp;q=why%20do%20fish%20excrete%20divalent%20cations%20via%20kidney&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rNTPT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The urine enters the glomeruli at a relatively low rate and with a low magnesium concentration. The paper cited below mentions a concentration of 1.5mM. First organic compounds as glucose are recovered actively, water follows the molecules passively. Then more ions as Ca$^{2+}$ enter in the proximal segment II. In the distal segment finally sodium and chloride are actively transported out while water passively leaves the segment. The divalent ions (magnesium, calcium) are left in high concentrations (the paper below says that the Mg concentration is now around 130mM). This helps concentrating these ions for excretion while loosing as little water as possible at the same time. Sodium and chloride are actively regulated in the gills.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a short overview, see the link at the image above, for a detailed view, have a look at the following publication: &quot;&lt;a href=&quot;http://ajprenal.physiology.org/content/ajprenal/286/5/F811.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kidneys sans glomeruli&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-30T20:46:46.073" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20091" PostTypeId="2" ParentId="20089" CreationDate="2014-07-30T21:14:26.867" Score="26" Body="&lt;p&gt;It's definitely a bird pelvis (&lt;a href=&quot;http://en.wikipedia.org/wiki/Synsacrum&quot;&gt;synsacrum&lt;/a&gt;). Based on the size (~30 cm), it came from a very large bird. Unfortunately, comparative images of bird pelves are rare on the internet. Some possibilities (large birds of Sweden possibly found on the coast):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Great northern loon&lt;/li&gt;&#xA;&lt;li&gt;Golden eagle&lt;/li&gt;&#xA;&lt;li&gt;Common crane&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;A loon skeleton (from &lt;a href=&quot;http://paolov.wordpress.com/2011/08/05/friday-mystery-object-107/&quot;&gt;http://paolov.wordpress.com/2011/08/05/friday-mystery-object-107/&lt;/a&gt;) shown below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BkOzJ.jpg&quot; alt=&quot;Loon skeleton&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2014-07-31T03:29:18.053" LastActivityDate="2014-07-31T03:29:18.053" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20092" PostTypeId="2" ParentId="19545" CreationDate="2014-07-30T22:41:45.137" Score="3" Body="&lt;p&gt;The difference may be related to how the plants fix carbon. While all plants convert CO₂ and H₂O to glucose and oxygen, there are at least three pathways that are used to do it. The C3 pathway is older and less efficient than the CAM and C4 pathways. Many drought tolerant plants use the CAM or C4 pathways because less water is needed. The C4 pathway is better than C3 in drier climates, hotter climates, and when CO₂ or nitrogen are limited. The hard part about this answer is that I'm not a botanist. Wikipedia lists some plants that use C4, CAM, and C3, but there is no comprehensive list, so I can't match up all the plants you mentioned in your question. In general, a higher percentage of monocots, especially grasses, use C4, but a wider diversity of dicots use C4. But you still can't draw conclusions about families of plants, because while corn and sorghum use C4, rice and barley use C3. Ragweed, a plant you say grows well in dry conditions, is a member of Asteraceae, which includes many plants that use C4. However, rudbeckias are also members of Asteraceae, but don't do as well in dry conditions. The C4 pathway has appeared and disappeared in several different plants, making any general claim hard to make. Here are some links that might help:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.en.wikipedia.org/wiki/C4_carbon_fixation&quot; rel=&quot;nofollow&quot;&gt;http://www.en.wikipedia.org/wiki/C4_carbon_fixation&lt;/a&gt;   &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.en.wikipedia.org/wiki/C3_carbon_fixation&quot; rel=&quot;nofollow&quot;&gt;http://www.en.wikipedia.org/wiki/C3_carbon_fixation&lt;/a&gt;   &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.en.wikipedia.org/wiki/Crassulacean_acid_metabolism&quot; rel=&quot;nofollow&quot;&gt;http://www.en.wikipedia.org/wiki/Crassulacean_acid_metabolism&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.brown.edu/Research/Edwards_Lab/reprints/sage_etal_2011jexb.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.brown.edu/Research/Edwards_Lab/reprints/sage_etal_2011jexb.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you know more about plants than me, that last link might be helpful, it's about the evolution of C4 pathway in plants and includes lists, but uses the formal species names I just don't recognize.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="3340" LastEditDate="2014-10-09T15:14:20.790" LastActivityDate="2014-10-09T15:14:20.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20093" PostTypeId="2" ParentId="19974" CreationDate="2014-07-30T23:11:24.730" Score="3" Body="&lt;p&gt;Besides duplication as verification there are numerous other computational methods to ensure that the result is valid. Proprietary software is used for folding at home so one can safely assume that they check &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Md5sum&quot; rel=&quot;nofollow&quot;&gt;hashes&lt;/a&gt; on processors and files regularly. If integrity is broken (by a crash, memory corruption or God forbid injection) the software client side and server side trashes the result. One can imagine that faulty hardware or other problems can result in a ban from the servers.&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-07-30T23:11:24.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20094" PostTypeId="1" CreationDate="2014-07-31T02:04:48.310" Score="1" ViewCount="113" Body="&lt;p&gt;Question I am trying to answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the popular film The Matrix, heat given off by humans is harvested as an energy source. I wondered, if this were possible, would humans be a good organism to choose? Would any other organism be better?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Question I want to ask:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many warm-blooded organisms produce heat by metabolism. Do different organisms produce different levels of heat for the same mass of input (food)? Is there any organism that directs energy flux into heat production more than any other organism?&lt;/p&gt;&#xA;" OwnerUserId="8559" LastEditorUserId="3340" LastEditDate="2014-08-01T06:02:02.900" LastActivityDate="2014-08-01T08:59:15.800" Title="What organism most efficiently converts a given quantity of mass into heat?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20095" PostTypeId="2" ParentId="20094" CreationDate="2014-07-31T03:08:21.187" Score="3" Body="&lt;p&gt;A small hardy warm blooded omnivore that is easily tamed.  I suggest rats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Small:  You don't want a lot of metabolic effort going into building bone and structure to support structure.&#xA;Hardy:  it needs to be survivable with little care.&#xA;Warm blooded:  You want to harvest energy from it.&#xA;Easily tamed:  The animal shouldn't try to escape its captivity.&lt;/p&gt;&#xA;" OwnerUserId="8387" LastActivityDate="2014-07-31T03:08:21.187" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20096" PostTypeId="2" ParentId="20065" CreationDate="2014-07-31T03:43:51.633" Score="2" Body="&lt;p&gt;Colin the only way to go is Edgar's software write him robert@drive5.com it's a thousand for a copy (in 2012) worth every penny. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CzGe5.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-07-31T03:43:51.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20097" PostTypeId="1" CreationDate="2014-07-31T06:15:20.653" Score="5" ViewCount="1508" Body="&lt;p&gt;In one of the comments in &lt;a href=&quot;https://biology.stackexchange.com/questions/20075/what-is-the-state-of-the-art-algorithm-for-multiple-sequence-alignment&quot;&gt;this question about multiple sequence alignment&lt;/a&gt;, it was stated&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;@5heikki: btw if you want a good bioinformatics problem, come up with an assembler that assembles any paired end illumina run optimally de novo without any input parameters.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What is a paired end illumina? How is optimally defined in this context? What are the usual input parameters?&lt;/p&gt;&#xA;" OwnerUserId="8561" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-07-31T07:39:06.340" Title="Why is assembling paired end illumina without any input parameters an important problem?" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;rna-sequencing&gt;&lt;sequence-assembly&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20098" PostTypeId="2" ParentId="20097" CreationDate="2014-07-31T06:36:52.463" Score="4" Body="&lt;p&gt;In Illumina sequencing, the DNA is (usually randomly) sheared into fragments. For paired end sequencing, fragments of a specific size range are selected and then sequenced &lt;strong&gt;from both sides&lt;/strong&gt;.&#xA;This results in two reads for each fragment. As read length is fixed, also the remaining &quot;middle part&quot; of the fragment is in a specific size range. In some cases there is no middle part, because the fragments have been chosen so small, that the reads overlap.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The information about the size of the fragment and/or the &quot;middle part&quot; as well as read length are some of the most important parameters you need for de novo assembly. Your could get away with not taking read size as a parameter, if you need it you can still run over all reads and check. But fragment size or insert size is important to place the reads, especially in scaffolding.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://thegenomefactory.blogspot.de/2013/08/paired-end-read-confusion-library.html&quot; rel=&quot;nofollow&quot;&gt;This blog entry&lt;/a&gt; also has some nice information about the often upcoming discussion what is meant by insert size (fragment size, the size of the middle part) and what can happen with overlapping reads and read-through.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is lots more to say about this. Illumina also provides some nice &lt;a href=&quot;https://www.youtube.com/watch?v=womKfikWlxM&quot; rel=&quot;nofollow&quot;&gt;videos&lt;/a&gt; available on youtube.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2014-07-31T06:36:52.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20099" PostTypeId="2" ParentId="20097" CreationDate="2014-07-31T06:43:49.133" Score="8" Body="&lt;p&gt;The Next-Gen sequencers cannot sequence a very long stretch of DNA with good reliability (~150 for the recent model- HiSeq2000; even less for older models such as GA (40), GA-II (70), GA-IIx (90)). For increasing the confidence in a certain hit, it was sequenced from both the ends. &#xA;For example, if you have selected 500bp DNA fragment, then after ligating adapters to both the ends, it is sequenced from both the direction up to 150bp. This would leave an unsequenced &quot;insert&quot; region of 200bp. (In the example image below, they have sequenced up to 40bp [case of old GA] )&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vhJwd.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;During assembly you stitch together the fragments of DNA to find out the larger DNA from where the fragments arise. In case of RNAseq, these arise from a transcript, and your assembly should give you the complete transcript (mRNA or ncRNA etc). There are two basic types of assembly: reference guided assembly and de-novo assembly. In the former you use a sequence such as the genome as a reference to assemble the transcripts. If such a reference is not available then you have to go for de-novo assembly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The assembly algorithms use several parameters and since these are computer algorithms and not some kind of magic, their output depends to an extent on the different parameters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case of paired end data there are some parameters that are important. Most important is the size of the insert. In case of a 500bp fragment, you'll end up with an unsequenced region of 200bp. This is not much of a problem with reference guided assembly because you can figure out the sequence of the insert based on where the sequenced region align to the reference. The average insert length is important to remove discordant reads (aligning too far apart in the reference). In case of de-novo assembly, the insert will remain unsequenced even if you know that the final transcript looks something like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;frag1-frag6-frag3-frag9-frag4&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to get the sequence of the assembly, you need to sequence the insert regions. This is not a problem if you at least know the order of fragments in the assembly. However you should know the insert size to get the assembly size correct and as skyminge said, in scaffolding. Obtaining this insert length is not that difficult (You need not provide it as a parameter. Most algorithms can calculate it automatically).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another parameter in de-novo assembly is k-mer length (the sequence reads are broken down into k-mers for better assembly). I cannot explain the algorithm of assembly here in detail. You can check the manuals/papers of common assembly algorithms like Velvet, SOAPdenovo, Euler [de novo]; cufflinks [reference based]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have mentioned transcriptome sequencing here but the principles are same for genome sequencing too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Back to your main question:&#xA;&lt;em&gt;Why is assembling paired end illumina without any input parameters an important problem?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because it is less effort; but tweaking may be difficult. I won't consider it as an important problem. There are other important algorithmic optimizations that are required with de-novo assembly.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-07-31T07:03:35.357" LastActivityDate="2014-07-31T07:03:35.357" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20100" PostTypeId="2" ParentId="20084" CreationDate="2014-07-31T08:04:38.350" Score="2" Body="&lt;p&gt;Usually there is no issue of mixing. One possible reason is degradation. But you say marker is faint (marker wont get degraded). Stain the gel with extra EtBr and see again. If you reused the gel then definitely stain it again because EtBr migrates towards the cathode.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It doesn't seem like degradation to me but to be cautious for the next time:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Use freshly autoclaved water. If you are not sure then filter using syringe and keep some 10ml for yourself&lt;/li&gt;&#xA;&lt;li&gt;Ensure that the plasticware are also autoclaved properly.&lt;/li&gt;&#xA;&lt;li&gt;Use endo&lt;sup&gt; -&lt;/sup&gt; plasmid extraction kits, if available&lt;/li&gt;&#xA;&lt;li&gt;Dissolve the plasmid in TE (only if conc is high and you need not put much in the reaction mix else EDTA interferes in the reactions. In that case use Tris-Cl pH-7.6 ).&lt;/li&gt;&#xA;&lt;li&gt;If you have to digest a lot of DNA then set up small reactions in many tubes.&lt;/li&gt;&#xA;&lt;li&gt;Do not incubate the reaction for a very long time (&gt;6h).&lt;/li&gt;&#xA;&lt;li&gt;Inactivate the enzyme by heating if you are not running the gel immediately.&lt;/li&gt;&#xA;&lt;li&gt;Ensure that the gel running buffers are not too old. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-07-31T08:04:38.350" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20101" PostTypeId="2" ParentId="20086" CreationDate="2014-07-31T11:48:19.777" Score="4" Body="&lt;p&gt;This book &quot;&lt;a href=&quot;http://www.cambridge.org/se/academic/subjects/life-sciences/ecology-and-conservation/primer-conservation-genetics&quot; rel=&quot;nofollow&quot;&gt;A primer of conservation genetics&lt;/a&gt;&quot; would suit quite well I think. In particular chapter five deals with &quot;Genetics and Extinction&quot; and is preceded by a lot of population genetics based theory. A beginner might also combine it with &quot;A primer of ecological genetics&quot; (Hartl &amp;amp; Conner) but you seem to have enough Pop gen knowledge to not need it!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The landscape genetics is perhaps a bit lacking from this book though. Maybe a better and more comprehensive solution, but slightly more advanced, is &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0470671459&quot; rel=&quot;nofollow&quot;&gt;this book&lt;/a&gt; which does feature some aspects of landscape genetics in chapter 15 along with good population genetics type coverage of extinction.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-07-31T11:48:19.777" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20103" PostTypeId="1" AcceptedAnswerId="20141" CreationDate="2014-07-31T14:35:21.403" Score="2" ViewCount="129" Body="&lt;p&gt;If Propionibacterium are obligate anaerobes (to wit, poisoned by oxygen), what makes 'Dairy' or classical propionibacteria (e.g. P. shermanii, P. jensenii, P. acidicpropionici, et al) viable in Fermentation starter cultures?&lt;/p&gt;&#xA;" OwnerUserId="8562" LastEditorUserId="8562" LastEditDate="2014-08-01T13:17:41.233" LastActivityDate="2014-08-01T21:13:32.020" Title="What makes certain obligate anaerobes viable in fermentation starter cultures?" Tags="&lt;physiology&gt;&lt;bacteriology&gt;&lt;food&gt;&lt;taxonomy&gt;&lt;microarray&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20104" PostTypeId="1" CreationDate="2014-07-31T15:27:50.010" Score="8" ViewCount="5525" Body="&lt;p&gt;I'm looking at a paper that uses several sequence logos to illustrate the consensus sequence of certain sites. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the most important of the sequence logos I'm interested in:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qGOKC.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The explanations I found about the exact meaning of this visualization were rather abstract and mathematical. I understand that the height of the letter stack is indicating in some way how strongly conserved that position is, but I have some difficulty judging the absolute values.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When are the positions considered to be significantly conserved? The paper where this data is from mentions the positions 5 and 6 as characteristic for the consensus sequence, which is not really obvious to me from this graph.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do I interpret the absolute value on the y-axis? What does it actually mean if position 16 has around 0.6 bits of information?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not so much interested in an exact mathematical treatment, but a general guide on how to read these graphs and how to interpret them in practice. &lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-08-02T15:47:51.813" Title="How do I read a sequence logo?" Tags="&lt;genetics&gt;&lt;visualization&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20105" PostTypeId="1" CreationDate="2014-07-31T16:42:51.870" Score="0" ViewCount="232" Body="&lt;p&gt;I'm trying to understand more about evolution theory.&#xA;(I am coming from a mathematical background)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What i understand till now is that the &quot;improvement&quot; of the dna is a purely random development and the Selection criteria if the improvement was not negative is by surviving.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The better the improvment was the higher the likelyhood of surviving is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What i don't understand is that the likelyhood that something useful comes from random changes in the dna is very low?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This reminds me of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Infinite_monkey_theorem&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Infinite_monkey_theorem&lt;/a&gt; it has surely a finite likelyhood but considering the complexity i still doesn't understand how for example wings of birds evolve. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider a pre-bird without wings, to get wings it has to have interstage with some useless pre-wings and then it has to learn how to flight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe someone can help me solve these mysteries :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other thing i am wondering is the smallest living element is the cell.&#xA;How did the first cell evolve?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you very much&lt;/p&gt;&#xA;" OwnerUserId="8566" LastActivityDate="2014-08-03T20:44:16.060" Title="Questions about the Evolution Theory" Tags="&lt;evolution&gt;&lt;development&gt;" AnswerCount="2" CommentCount="2" ClosedDate="2014-07-31T17:33:00.890" ContentLicense="CC BY-SA 3.0" />
  <row Id="20106" PostTypeId="2" ParentId="20105" CreationDate="2014-07-31T17:05:37.713" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;What i don't understand is that the likelyhood that something useful&#xA;  comes from random changes in the dna is very low?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, in that most changes are neutral, sure.  But EVERY organism on the planet has mutations.  It doesn't matter if the odds are low.  If you have billions of organisms in a square meter of soil, how likely do you think it is that not a &lt;strong&gt;single&lt;/strong&gt; mutation in a &lt;strong&gt;single&lt;/strong&gt; organism will be beneficial in that environment?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Consider a pre-bird without wings, to get wings it has to have&#xA;  interstage with some useless pre-wings and then it has to learn how to&#xA;  flight.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Ah, another Creationist who thinks that the universe can not possibly contain anything that s/he can not personally imagine.  There might be uses for intermediate structures that you just can't think off off the top of your head  (like gliding).  There might be intermediates paths that you just can't think of.  There might be other structures that worked in concert with the intermediates, and then faded away as things changes, much like you build an arch with a scaffold, and then remove the scaffold.  Just because you &lt;strong&gt;personally&lt;/strong&gt; can't imagine the possibility of a scaffold doesn't mean such things are literally impossible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have you even tried googling &quot;bird wing evolution&quot;?  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The other thing i am wondering is the smallest living element is the&#xA;  cell. How did the first cell evolve?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Come on.  That's a completely different question.  Surely someone who thinks they understand the problems of evolution better than professionals who have studied the data for years know that lipids spontaneously formed closed cells, right?  And knows that RNA can autocatlyze reactions, yes?&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-07-31T17:05:37.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20107" PostTypeId="2" ParentId="20105" CreationDate="2014-07-31T17:10:20.063" Score="3" Body="&lt;p&gt;Welcome to BiologyBeta.SE!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On stackExchange sites, an OP should always limit his/her post to one question and should make his/her question is not too broad. But before you split up your question I invite you to have a look to some other post that will give you some answers. For this reason your question will very likely get closed as too broad. But I am giving some indices below. Also your post is a bit poorly written. This also lead people to close posts. Please come back with better posts, show some efforts in seeking for some information and it will be my pleasure to help you!&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Origin of life&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are already a bunch of posts on the origin of life for example. Note that the origin of life is not a field that is part of evolutionary biology as evolutionary biology only explain the evolution of life and not its origin. As a mathematician you may prefer saying something like the domain of definition of evolutionary biology does not include the origin of life just like the shannon's theory of information says nothing about the euclidian geometry.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What i understand till now is that the &quot;improvement&quot; of the dna is a purely random development and the Selection criteria if the improvement was not negative is by surviving&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hum… that's sounds very weird. If I didn't know I would hardly recognize that you talk about evolution. You should have a look to some introduction to the field. Also, you should not confound the concepts of evolution, natural selection and mutations that I guess you confuse. A good, extremely simplistic view of evolution is that mutations occurs and create variance in the population. This traits are heritable. The variants that replicate the best increase in frequency in the population while the other variants will decrease in frequency up to the point to disappear. This is called natural selection.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Consider a pre-bird without wings, to get wings it has to have interstage with some useless pre-wings and then it has to learn how to flight&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You also seem to ask a question about how some traits may come to exist while what seem to be necessary intermediate would not be beneficial. This question has been answered probably a thousands of time as it is a common creationist argument.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Because your questions really sounds like creationist arguments I am a bit afraid that you are not trying to understand evolution but you wondering whether evolution does occur or not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note also that evolutionary biology is a very big field. You cannot expect to have a more or less good understanding of the whole science of evolutionary biology in less than a year. But if you are trying to just understand the very basic, sufficiently to persuade you that evolution does occur, then few weeks will probably be enough if you show some effort&#xA;Please don't forget the questions you may have. Seek by yourself for more knowledge and if you can't find something, then you're really welcome to come back to this site with an accurate question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a look to the definition of &lt;a href=&quot;http://en.wikipedia.org/wiki/Scientific_theory&quot; rel=&quot;nofollow&quot;&gt;scientific theory&lt;/a&gt;. Also, please read @Chris comment below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You misunderstand the meaning of &quot;direct observation&quot; that canadianer used. Observations we do in evolutionary biology are just as valid as those that has been made to confirm the theory of gravity. The only point concerns the easiness of understand these observations for non-literate in the field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, you are totally right. Just like the theory of gravity, the theory of evolution does not explain everything. It only applies to a subset of the phenomenons existing on earth. The theory of evolution is true, we know for a fact that evolution occurs but our theory is not global enough to explain things like the big bang or the surface tension and will never do so. The theory of evolution will never prove or disprove the existence of God as well (supposing you're concerned about that) because again it is not within its scope and will never be. However, the sociological impact of this theory tells much about the human behavior and our difficulties to accept something we know to be true if it contradicts some pre-establish believes even when these pre-established believes are not based on any logical developments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question has been closed because it is too broad. The issue also is that your questions concern much more than evolutionary biology and biology. It also concerns the very nature of science and this is a common reason why creationist missundestand evolution. They don't (only) missunderstand evolution but they missunderstand what science is.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-08-03T20:44:16.060" LastActivityDate="2014-08-03T20:44:16.060" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="20108" PostTypeId="1" CreationDate="2014-07-31T19:08:50.527" Score="2" ViewCount="101" Body="&lt;p&gt;I want to calculate the gene expression of an experiment with the Delta delta Ct method.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have these results from two runs of a real time PCR (one for the GOI(Gene of Interest) and one for the reference gene ($\beta$ actin) )&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Samples | GOI CT | reference gene CT |&#xA;&#xA;1         16.52         16.24&#xA;2         18.58         18.47&#xA;3         14.55         20.56&#xA;wt        23.06         24.17&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So to calculate the $2^{-\Delta\Delta CT}$ for my GOI I've done this :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1st - Normalize CTs of GOI to CTs of reference gene&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$ΔCT = CT_{sample's} -­ CT_{reference's}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This new table then occurs:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Samples | ΔCTs &#xA;&#xA;1         0.28        &#xA;2         0.11         &#xA;3        -6.01         &#xA;wt       ­-1.11 &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;After this i normalize these ΔCTs to a control sample. And here is where the question was born. On which criteria should i choose the control sample ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What i've done was to choose the sample with the bigest CT from the first table. And that was the sample No. 2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2nd - Normalizing all samples to the control sample&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\Delta\Delta CT = \Delta CT_{sample} -­ \Delta CT_{control}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and the final results are &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Samples | ΔΔCTs &#xA;&#xA;1         0.17        &#xA;2         0         &#xA;3        -­6.12         &#xA;wt       ­-3.08 &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Is that method correct ? If yes, let me write once more the question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On which criteria should i choose the control sample for the last normalization ? Should i choose the sample with the highest Ct or the lowest one ? And why ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope now be more clear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Question edited to be more clear.&lt;/p&gt;&#xA;" OwnerUserId="6032" LastEditorUserId="6032" LastEditDate="2014-08-03T10:44:56.040" LastActivityDate="2014-08-03T10:44:56.040" Title="Based on which criteria should i choose the control sample to calculate delta_delta_Ct" Tags="&lt;mathematical-models&gt;&lt;pcr&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20109" PostTypeId="1" AcceptedAnswerId="20112" CreationDate="2014-07-31T19:55:05.983" Score="3" ViewCount="23871" Body="&lt;p&gt;DNA is charged negative because of its phosphate backbone. Since charges need to be balanced (so that there are no charges building up somewhere), what is the positive charge which neutralizes this negative charge?&lt;/p&gt;&#xA;" OwnerUserId="8567" LastEditorUserId="5144" LastEditDate="2014-08-01T08:20:59.753" LastActivityDate="2017-10-08T05:50:26.730" Title="DNA is charged negative. Where is all the positive charge in my body?" Tags="&lt;cell-biology&gt;&lt;dna&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20110" PostTypeId="2" ParentId="17845" CreationDate="2014-07-31T20:05:57.557" Score="8" Body="&lt;p&gt;First let me point out that for the US, I'm not knowledgeable enough to speak for the rest of the world, you are correct.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;There are no approved live attenuated vaccines mixed with componet/subunit/inactivated vaccines.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Background:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Before we go into why that's true, let's work a little to show that's true.  The FDA publishes a &lt;a href=&quot;http://www.fda.gov/biologicsbloodvaccines/vaccines/approvedproducts/ucm093833.htm&quot; rel=&quot;noreferrer&quot;&gt;wonderful list&lt;/a&gt; of every approved vaccine for use in the US.  Of the 78 vaccines listed (and there is a lot of redundancy due to different manufacturers etc), only 16 are live attenuated (or about 20%).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another thing to notice is that we have vaccines to both &lt;a href=&quot;http://en.wikipedia.org/wiki/Virus&quot; rel=&quot;noreferrer&quot;&gt;viruses&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Bacteria&quot; rel=&quot;noreferrer&quot;&gt;bacteria&lt;/a&gt;.   Technically, some of the vaccines are to bacterial toxins, not bacteria themselves, but for the sake of simplicity, we're going to group all bacterial &lt;a href=&quot;http://www.vaccinesafety.edu/components.htm&quot; rel=&quot;noreferrer&quot;&gt;component, subunit, and inactivated vaccine preparations&lt;/a&gt; together in one group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First you will note that there is only one live attenuated vaccine for bacteria, &lt;a href=&quot;https://en.wikipedia.org/wiki/Mycobacterium_bovis&quot; rel=&quot;noreferrer&quot;&gt;Mycobacterium bovis&lt;/a&gt; (more on this exception later).  There are several reasons for this, but as a general rule, you don't want to put a foreign object capable of self replication inside a person.  Viruses cannot self replicate, they are &lt;a href=&quot;http://en.wikipedia.org/wiki/Obligate_parasite&quot; rel=&quot;noreferrer&quot;&gt;obligate parasites&lt;/a&gt; by definition, so they don't fall under this rule.  One could, however engineer bacteria that were sufficiently deficient in replication that this might not be an issue.  Another safety concern with live attenuated bacteria is &lt;a href=&quot;http://en.wikipedia.org/wiki/Sepsis&quot; rel=&quot;noreferrer&quot;&gt;sepsis&lt;/a&gt;.  Again by choosing a delivery route that doesn't involve injections, you might be able to mitigate this risk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also want to be clear that I think live attenuated bacterial/fungal (yeast mostly) vaccines can work more broadly, and are likely to be used in &lt;a href=&quot;http://dx.doi.org/10.1016/j.vaccine.2013.07.029&quot; rel=&quot;noreferrer&quot;&gt;innovative vaccine strategies&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main obstacle to a live attenuated bacteria vaccine is that the component and subunit vaccines &lt;strong&gt;work&lt;/strong&gt;.  Sometimes they work even better by only supply the part of an organism that is known to provide &lt;a href=&quot;http://en.wikipedia.org/wiki/Neutralizing_antibody#Broadly-neutralizing_antibodies&quot; rel=&quot;noreferrer&quot;&gt;broad neutralization&lt;/a&gt; (getting rid of) of the pathogen.  And if you know that you can provide protection with out the risk of putting the live organism in a person, why would you take that risk?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quite simply you don't.  Back to &lt;em&gt;M. bovis&lt;/em&gt;.  For the most part, humans are not vaccinated with &lt;em&gt;M. bovis&lt;/em&gt; (BCG) to prevent &lt;em&gt;M. Bovis&lt;/em&gt; infection (though &lt;a href=&quot;https://en.wikipedia.org/wiki/Zoonosis&quot; rel=&quot;noreferrer&quot;&gt;zoonotic&lt;/a&gt; infections can &lt;a href=&quot;http://whqlibdoc.who.int/hq/1996/WHO_EMC_ZOO_96.4.pdf&quot; rel=&quot;noreferrer&quot;&gt;occur&lt;/a&gt;).  Instead it is to prevent &lt;em&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis&quot; rel=&quot;noreferrer&quot;&gt;M. tuberculosis&lt;/a&gt;&lt;/em&gt; (MTB) infection.  &lt;a href=&quot;https://en.wikipedia.org/wiki/Attenuated_vaccine&quot; rel=&quot;noreferrer&quot;&gt;Attenuation&lt;/a&gt; of MTB is &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3544749/&quot; rel=&quot;noreferrer&quot;&gt;difficult&lt;/a&gt;, and &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC23125/&quot; rel=&quot;noreferrer&quot;&gt;not complete&lt;/a&gt;.  Indeed we don't have a subunit or component vaccine that has worked for MTB, and an inactivated MTB has &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3515764/&quot; rel=&quot;noreferrer&quot;&gt;more safety concerns&lt;/a&gt; than BCG.  Thus we choose a related organism, &lt;em&gt;M. Bovis&lt;/em&gt;, which naturally doesn't cause disease in humans (or rarely), but can provide some protection against TB.  Even the &lt;a href=&quot;http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM202934.pdf&quot; rel=&quot;noreferrer&quot;&gt;product insert&lt;/a&gt; admits that efficacy of the vaccine is in question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same pattern of necessity holds true for viral live attenuated vaccines.  They are used when you need a more &lt;a href=&quot;https://en.wikipedia.org/wiki/Immunogenicity&quot; rel=&quot;noreferrer&quot;&gt;immunogenic&lt;/a&gt; vaccine, and where we haven't been able to make safe and effective, inactivated, subunit, or &lt;a href=&quot;https://en.wikipedia.org/wiki/Virus-like_particle&quot; rel=&quot;noreferrer&quot;&gt;VLP&lt;/a&gt; vaccines.  Thus when you need a live attenuated vaccine, you really do need it to be alive for it work.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Answering the core question:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;As @MattDMo pointed out, the storage conditions are very different for live attenuated vaccines.  Not only that, but most of the &lt;a href=&quot;http://cellculturedish.com/2011/10/recombinant-albumin-enhances-stability-of-attenuated-vaccines/&quot; rel=&quot;noreferrer&quot;&gt;preservatives&lt;/a&gt; used in many inactivated vaccines cause &lt;a href=&quot;https://en.wikipedia.org/wiki/Titer&quot; rel=&quot;noreferrer&quot;&gt;titer&lt;/a&gt; loss (though there is &lt;a href=&quot;http://dx.doi.org/10.1016%2Fj.vaccine.2011.07.054&quot; rel=&quot;noreferrer&quot;&gt;work&lt;/a&gt; to find alternatives). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the theory that a picture is worth a thousand words, I did a little experiment just for this post (and also I was cleaning out an -80).  I took a high titer stock of measles virus that has a protein tag on one of the proteins so we can easily detect it (F is Flag tagged).  Then I spiked 3 different tubes of virus in ether &lt;a href=&quot;https://en.wikipedia.org/wiki/Phosphate_buffered_saline&quot; rel=&quot;noreferrer&quot;&gt;PBS&lt;/a&gt; (saline) or &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/002021.htm&quot; rel=&quot;noreferrer&quot;&gt;DTaP&lt;/a&gt; (an actual dose, just past expiration), and left them in the refrigerator (4oC) for 8h.  Note that &lt;a href=&quot;https://www.merckvaccines.com/Products/Mmr/Pages/storageandhandling&quot; rel=&quot;noreferrer&quot;&gt;Merk thinks&lt;/a&gt; you should toss the measles vaccine if you don't use it within 8/hours (also note their comment on preservatives).  Then I infected some cells that grow up measles, and harvested the cells in a total cell lysate.  Finally I ran equal amounts of total protein form each preparation on a gel for a &lt;a href=&quot;https://en.wikipedia.org/wiki/Western_blot&quot; rel=&quot;noreferrer&quot;&gt;western blot&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Y1J8S.png&quot; alt=&quot;Western of 3 measles replicates&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should notice the three pairs of bands, in each case the lighter band (indicating less protein) belongs to the DTaP group.  That is to say less measles F protein (something you want to make antibodies to) came from the samples that were put into the DTaP vaccine compared to PBS.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Another serious problem is &lt;a href=&quot;https://en.wikipedia.org/wiki/Cold_chain&quot; rel=&quot;noreferrer&quot;&gt;cold chain&lt;/a&gt;:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Again we need the virus to be &quot;alive&quot; when we give a person a vaccine.  This almost always means that we have to keep it frozen or at least refrigerated from the manufacturer, all the way up until moments before it goes into a person's arm.  There are &lt;a href=&quot;http://dx.doi.org/10.1016/j.biologicals.2014.05.007&quot; rel=&quot;noreferrer&quot;&gt;many good&lt;/a&gt; reviews on cold chain to be found.  Quite simply, inactivated and component vaccines do not have the thermo-stability requirements that live vaccines do.  It would be a waste of energy in most cases to chill all of the vaccines which could be left at room temperature, and it would remove one of their clear advantages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as the immunology is concerned, there is probably not a real limit on what the body can react to.  Indeed, as you point out, they are often administered at the same time in developed countries.  It is merely a question of how you can keep live-attenuated vaccines &quot;alive&quot; in the same preparation.  It is certainly possible that there is a solution to this, and vaccine stability is an active field of research.  Hopefully in 10-20 years we will be able to adjust this answer to say that such a vaccine has been made, and that it's safe enough for approval.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2014-07-31T20:13:33.483" LastActivityDate="2014-07-31T20:13:33.483" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20111" PostTypeId="2" ParentId="20109" CreationDate="2014-07-31T20:19:24.453" Score="3" Body="&lt;p&gt;Your cells have a high concentration of sodium ions that are positive. Other important cations are potassium and calcium. Additionally, many amino acids are positively charged at physiological pH. DNA is not the only source of negative charge in your body, other amino acids are negative, and most cell surfaces are negative as well. The interactions between charged species play an important role in many biochemical processes, but at the end of the day, and for the whole organism, the charges are all pretty much balanced out.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2014-07-31T22:01:29.453" LastActivityDate="2014-07-31T22:01:29.453" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20112" PostTypeId="2" ParentId="20109" CreationDate="2014-07-31T20:53:26.943" Score="12" Body="&lt;p&gt;DNA in the body is not available as a free molecule, it is organized around DNA binding proteins, mostly the &lt;a href=&quot;http://en.wikipedia.org/wiki/Histone_octamer&quot; rel=&quot;nofollow noreferrer&quot;&gt;histone octamers&lt;/a&gt;. These proteins carry positive charges (mostly from lysine side chains) which interact with the phosphate backbone of the DNA. It is like in the figure below, the charges play an important role in the tight packaging. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2313700&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HvhF1.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The charge (or the temporary neutralization at some points of the DNA) is also important for the regulation of the DNA. Acetylation neutralizes the histone tail and loosens the DNA-protein structure (see &lt;a href=&quot;http://genesdev.cshlp.org/content/12/5/599&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for more information).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Positively charged ions don't play a role in neutralizing the DNA charge in living cells (this is different for precipitations), as both are solubilized and split into ions. The concentration of positively charged ions like sodium and potassium are tightly controlled by the cells, as they are important for the function of transporters (for example the sodium-glucose transporters and others) or for keeping up membrane potentials. Moving the ions, which have to neutralize the DNA charge around would lead to a polarized nucleus.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-07-31T20:53:26.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20113" PostTypeId="2" ParentId="20072" CreationDate="2014-07-31T21:16:05.320" Score="11" Body="&lt;p&gt;Until someone has a better method to determine this, and I'm willing to go with idea of that this question is not answerable, I put forward the two likely forms of selection criteria:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which mammal has the highest percentage of keratin in it's body for the highest density, and which has the highest percentage of gas (over the day) for the lowest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also want point that measuring the density of mammals is tricky because we can change our &quot;volume.&quot;  Perhaps this doesn't seem like much for humans, but a small mammal with a large tongue stuck out could have an appreciable different density than one with the tongue in.  Same for retractable limbs (which are generically cool).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v197/n4863/abs/197179a0.html&quot; rel=&quot;noreferrer&quot;&gt;This article&lt;/a&gt; gives us an estimate for the density of keratin at &quot;1.283 g/c.c. for cow horn to 1.335 g/c.c. for echidna quill tip&quot; which putts it solidly more dense than water.  This means we're looking for a small heavily armored mammal, which leads me to suspect the &lt;a href=&quot;https://en.wikipedia.org/wiki/Pangolin&quot; rel=&quot;noreferrer&quot;&gt;pangolin&lt;/a&gt;.  I don't readily know it's density, and I would be fine with others taking the time to calculate it (I'm not interested in getting that specific).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have fewer ideas on which mammals are least dense.  Going by &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/277/1691/2193.full&quot; rel=&quot;noreferrer&quot;&gt;this article&lt;/a&gt; I would guess rodents have the least dense skeletons. In particular I was surprised by this graph:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iBl44.jpg&quot; alt=&quot;comparison of bird, bat, and rodent bone density&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But also don't know that means we should exclude something like a &lt;a href=&quot;https://en.wikipedia.org/wiki/Sperm_whale&quot; rel=&quot;noreferrer&quot;&gt;sperm whale&lt;/a&gt; which has a lot of fat (lower density than water) and has enough lung capacity to dive for hours in deep water.  But on the off chance that the skeletal density is the best bet, I'm going to guess the least dense animal is a rodent, and if I have to pick one species I'm going with the least massive, the &lt;a href=&quot;https://en.wikipedia.org/wiki/Shrew&quot; rel=&quot;noreferrer&quot;&gt;shrew&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Doubt any one has really researched the displacement of many of the animals that should be in the running for this, so I'm not convinced a more exact answer could be reached.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2014-08-01T14:03:50.953" LastActivityDate="2014-08-01T14:03:50.953" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20114" PostTypeId="1" CreationDate="2014-07-31T22:47:19.573" Score="4" ViewCount="117" Body="&lt;p&gt;I have two animal running trajectories. A regular one with repeated back and forth running between point A and B, like the one on top in the figure. The other one is very irregular, animal paused and turned around a lot in the middle. Is there any algorithm to measure the regularity of a trajectory, like repeated activity on the top? And compare the extend of regularity between the two trajectories? Thanks in advance.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/qmWSt.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6728" LastActivityDate="2014-08-05T08:46:27.777" Title="How to measure trajectory regularity?" Tags="&lt;neuroscience&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20115" PostTypeId="2" ParentId="20086" CreationDate="2014-08-01T00:12:12.900" Score="3" Body="&lt;p&gt;If you're interested in learning about the mathematics of population genetics, &lt;a href=&quot;http://onlinelibrary.wiley.com/book/10.1002/0470047356&quot; rel=&quot;nofollow&quot;&gt;Population Genetics and Microevolutionary Theory&lt;/a&gt; by Alan Templeton is an absolutely amazing resource.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you check out the index, here are entries under population structure:&#xA;assortative mating, admixture, linkage disequilibrium, coarse-grained spatial heterogeneity, gene flow, gene flow and population history, gene flow vs admixture, microevolution modeling, multiple inheritance modes, natural selection, adaptation, and fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heterozygosity and other mathematical descriptors are particularly relevant to conservation (the author has been involved in various conservation projects). Furthermore, there are various entries on viability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plus there's plenty of information in it about the effects of landscape on gene flow and other population structural features.&lt;/p&gt;&#xA;" OwnerUserId="8568" LastActivityDate="2014-08-01T00:12:12.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20116" PostTypeId="2" ParentId="16470" CreationDate="2014-08-01T00:20:10.023" Score="7" Body="&lt;p&gt;Not relatively short, but I'm going to repeat a recommendation I just made in another thread. &lt;a href=&quot;http://onlinelibrary.wiley.com/book/10.1002/0470047356&quot; rel=&quot;noreferrer&quot;&gt;Population Genetics and Microevolutionary Theory&lt;/a&gt; by Alan Templeton covers many of the topics listed above, and is heavy on the self-learning of various population structure statistics, with examples. It is an introductory textbook with for people with some statistical background (though it includes a statistical appendix as well). There is quite a bit of discussion of Bayesian inference and other modeling methods as well.&lt;/p&gt;&#xA;" OwnerUserId="8568" LastActivityDate="2014-08-01T00:20:10.023" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20117" PostTypeId="1" CreationDate="2014-08-01T00:23:28.983" Score="7" ViewCount="775" Body="&lt;p&gt;There are very goods in physics and mathematics (like Feynman lectures for exemple) that give an elementry but but broad view of their,therefore I'd like for help to find help to find a biology book that:&#xA;-Covers a variety of subject in an elementary fashion.&#xA;-Is written for the non-specialist.&lt;/p&gt;&#xA;" OwnerUserId="8569" LastActivityDate="2015-04-14T20:40:59.870" Title="Books for biology,popular but rigorous?" Tags="&lt;book-recommendation&gt;&lt;literature&gt;&lt;general-biology&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="2" ClosedDate="2014-08-06T09:48:04.000" ContentLicense="CC BY-SA 3.0" />
  <row Id="20118" PostTypeId="2" ParentId="20069" CreationDate="2014-08-01T00:45:01.180" Score="2" Body="&lt;p&gt;Well, there are some questions regarding what population. I don't have 50 rep, so I can't really ask for clarifications; populations range a lot, from your typical avoidance of inbreeding (laws against cousin marriage) to Tamils with their high rates of first cousin marriage (so high that they don't have any pedigree inbreeding depression due to selection, so it's not unhealthy).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mating in humans is often assortative for many traits including education, vocation, etc. When the Americas were settled (after aboriginal Americans were devastated by disease), skin color was a source of assortative mating. Arguably it still is. On the other hand, people tend to mate disassortatively for traits such as Major Histocompatibility Complex.&#xA;Furthermore, isolation in human populations tends to be by distance (though this is of course changing, leading to a lot of admixture in recent population history). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a result, what your population is will have a huge impact on your results; you'll need to calculate &lt;em&gt;f&lt;/em&gt; for any particular locus, and take a look at admixture. If &lt;em&gt;f&lt;/em&gt; is 0, then you have a random mating scenario (neither preference nor avoidance of inbreeding, and neither assortative nor disassortative mating).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TL;DR if you're doing a very simple analysis on dummy data, you can probably get away with assuming that mating is totally random. But if we're talking about actual populations, you'll need to run the models/calculations of &lt;em&gt;f&lt;/em&gt; and other population measures.&lt;/p&gt;&#xA;" OwnerUserId="8568" LastActivityDate="2014-08-01T00:45:01.180" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20119" PostTypeId="1" AcceptedAnswerId="20120" CreationDate="2014-08-01T00:53:13.087" Score="4" ViewCount="1405" Body="&lt;p&gt;The double bonds in naturally occurring fatty acids present in our body are in &lt;em&gt;cis&lt;/em&gt; configuration while the enzymes for beta oxidation can act on &lt;em&gt;trans&lt;/em&gt; double bond. Then what will be the significance of &lt;em&gt;cis&lt;/em&gt; double bond in naturally occurring fatty acids? Why the naturally occurring fatty acids don't have double bond in &lt;em&gt;trans&lt;/em&gt; configuration?&lt;/p&gt;&#xA;" OwnerUserId="8301" LastEditorUserId="948" LastEditDate="2014-08-01T16:20:19.253" LastActivityDate="2014-08-02T05:39:45.660" Title="naturally occuring fatty acids" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;fatty-acid-synthase&gt;&lt;fat-metabolism&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20120" PostTypeId="2" ParentId="20119" CreationDate="2014-08-01T03:27:02.510" Score="4" Body="&lt;p&gt;The diversity of fatty acids produced by an organism is limited by the diversity of enzymes which synthesize them. Unsaturated fatty acids contain carbon-carbon double bonds which do not isomerize. The capacity for humans to produce cis fatty acids is probably selected for because of their lower melting point which prevents arterial clogging. Cold blooded animals utilize cholesterol to increase membrane fluidity when their body temperature is low. &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-02T05:39:45.660" LastActivityDate="2014-08-02T05:39:45.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20121" PostTypeId="2" ParentId="20109" CreationDate="2014-08-01T03:51:41.940" Score="1" Body="&lt;p&gt;The negative charge in DNA is localized to individual oxygen atoms in DNA. This negative charge is balanced by positive ions in the body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of a magnet or molecules with a dipole, negative and positive magnetic field lines align to produce an overall magnetic field. DNA has many small dipole moments but none across the entire molecule. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of a neuron, an excess of negative charge inside the cell and positive charge outside the cell is maintained by the diffusion gradient of potassium and sodium across a membrane. An overall electric potential is not created with DNA.&lt;/p&gt;&#xA;" OwnerUserId="8570" LastActivityDate="2014-08-01T03:51:41.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20122" PostTypeId="2" ParentId="17773" CreationDate="2014-08-01T04:15:08.593" Score="0" Body="&lt;p&gt;Death is caused by a variety of factors, our ability to heal is among them. However, it is possible to die from causes other than a deficiency in healing ability. Most people in the world die from cardiovascular disease and cancer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The role of stem cells in the heart is an area of intense investigation. Vascular clogging is a more likely cause of cardiovascular failure than a disease of the heart muscle itself. In the case of clogged vessels, no biological mechanism exists to heal clogged arteries. Stem cells are irrelevant here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stem cells are most applicable to cancer in the immune system for the recognition of cancer cells. A decrease in actively dividing immune stem cells would correlate with an increased progression of cancer. This is exactly what happens with people undergoing chemotherapy. Chemotherapy kills actively dividing cells, including stem cells in the immune system. This is why they often suffer increased infections. It is rare to die from an infectious disease today. Decreased immune response from chemotherapy is a manageable side effect of treating cancer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you recreationally took chemotherapy drugs, this would inhibit the activity of stem cells. Your body would rapidly accumulate genetic mutations and systemic damage resulting in eventual death. This is why people coming in contact with individuals on chemotherapy should be careful not to touch any surface contaminated with the drugs. This especially applies to pregnant woman, where the danger is primarily with the fetus. In development, stem cells are vital in organ formation, not healing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In different circumstances, to different individuals, during different life stages, destroying or preserving stem cells may be therapeutic, or devastating. &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-01T04:48:36.427" LastActivityDate="2014-08-01T04:48:36.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20124" PostTypeId="2" ParentId="20117" CreationDate="2014-08-01T06:32:59.203" Score="5" Body="&lt;p&gt;Where I studied, every undergrad read &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0321558235&quot;&gt;Campbell Biology&lt;/a&gt;. You can start it as a non-specialist but you will not be one at the end..&lt;/p&gt;&#xA;" OwnerUserId="5784" LastActivityDate="2014-08-01T06:32:59.203" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20125" PostTypeId="1" AcceptedAnswerId="20132" CreationDate="2014-08-01T06:53:20.160" Score="5" ViewCount="5530" Body="&lt;p&gt;As I understand during anaerobic respiration, the electrons received from the decomposition of glucose are transferred to nicotinamide adenine dinucleotide and flavin adenine dinucleotide. As there is no oxygen the electrons are then transferred to something else, either Lactic Acid or Ethanol (in the case of yeast).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why do animals produce Lactic Acid and not Ethanol?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, (I know this is silly, but) what would happen if they did? &lt;/p&gt;&#xA;" OwnerUserId="6299" LastEditorUserId="1320" LastEditDate="2014-08-01T14:36:08.227" LastActivityDate="2018-10-25T23:49:41.140" Title="Why don't animals produce alcohol" Tags="&lt;anaerobic-respiration&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20126" PostTypeId="1" CreationDate="2014-08-01T07:57:08.507" Score="1" ViewCount="66" Body="&lt;p&gt;I am new in Bioinformatics and recently studying UCLUST algorithm by Robert Edgar(2010). It is a fast sequence searching and clustering algorithm. The algorithm is heuristic based. I studied that first, this algorithm finds unique common words(k-mers) between a query sequence and a target sequence.(one of the sequences from sequence database). If there are enough common k-mers between a target sequence and a database sequence then it is selected for the alignment in the next step, otherwise skipped. All such sequences having enough common k-mers are selected. Target sequences are compared in order of decreasing common k-mers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In next step, HSPs (High Scoring Segment Pairs) are identified. For this purpose, exact matching words between a query sequence and a target sequence (one of the sequences selected in the previous step) are found. I AM CONFUSED AT THIS POINT. Is it necessary that these matching words(between the query sequence and the target sequence) be at same positions ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kindly if some one explains with an example, will be very help full. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any guidance will highly be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="8572" LastActivityDate="2014-08-01T07:57:08.507" Title="How are HSPs identified in UCLUST" Tags="&lt;bioinformatics&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20127" PostTypeId="2" ParentId="19396" CreationDate="2014-08-01T08:23:00.350" Score="2" Body="&lt;p&gt;As everybody, I don't fully understand your question. Can you please add your definition of domestication?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would you consider domestication as soon as human can select for heritable traits? If yes, then the question may be split in two:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Do all animal populations have heritable traits?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes! But Depending on what kind of traits you want to consider no variance (yielding to no heritability) may exist in the population. For example, you'll have a hard time to select crocodiles to have fluffy hair as there is no variance in &quot;hair fluffiness&quot; in the population. Crocodiles have no hair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, some practical issues exist. For example, it might be hard to select for a given behavior if the animal is so small that we can hardly observe them during a sufficient amount of time to know whether or not the individual display this behavior. Typically, it might be hard to select for specific traits in a population of a species that live inside another species (endosymbionte, endoparasite).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Are humans able to breed any animal species?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No, we're not! Many species do not breed in captivity or do not even survive in captivity. This is due to our lack of knowledge of the ecology and social behavior of the species in question.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-08-01T08:23:00.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20128" PostTypeId="2" ParentId="20114" CreationDate="2014-08-01T09:36:17.607" Score="6" Body="&lt;p&gt;In the world of physics, you can distinguish between random motion (e.g. thermal Brownian walk) and directed motion (called ballistic: think of a cannon ball) by studying the &lt;a href=&quot;http://en.wikipedia.org/wiki/Mean_squared_displacement&quot; rel=&quot;nofollow noreferrer&quot;&gt;mean square displacement&lt;/a&gt; of the object: you'll be able to fit this displacement as a function of time by a linear law if it is random, and by a quadratic one if it is directed. Exponents in between will give you an indication of the degree of randomness. The advantage of this (even if it is not specialized for your case) is that there's a large body of work using this, including for living organisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note also that if your motion is as in the first case above, you'll have ballistic motion for times smaller than the travel time from left to right, and diffusive (random) for times larger than that. This has been used e.g. to analyse the run-and-tumble motion of bacteria who have a short-time ballistic motion and then after some time tumble to explore another randomly-chosen direction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example of this type of coexistence of two regimes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WzLee.jpg&quot; alt=&quot;http://ej.iop.org/images/0953-8984/25/41/415102/Full/cm476063f4_online.jpg&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the field of biophysics, much of this was initiated by &lt;a href=&quot;http://www.rowland.harvard.edu/labs/bacteria/index.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;Howard Berg and coworkers&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your first case, you'll have an initial ballistic regime and then something that plateaus (because you stay between A and B). The transition time-lag will be the travel time between A and B.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your second case, you'll be able to characterize the random walk: if the animal is aiming at going from A to B but randomly errs for short times, you'll have a short-time diffusive behaviour, and an intermediate time ballistic one. (And then again a plateau, as in the first case and for the same reasons). If the animal reaches B by mere chance, on the contrary, you'll have a diffusive regime only before this plateau.&lt;/p&gt;&#xA;" OwnerUserId="6224" LastEditorUserId="6224" LastEditDate="2014-08-05T08:46:27.777" LastActivityDate="2014-08-05T08:46:27.777" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20129" PostTypeId="1" AcceptedAnswerId="20210" CreationDate="2014-08-01T09:56:15.513" Score="8" ViewCount="12934" Body="&lt;p&gt;&lt;strong&gt;Very simple:&lt;/strong&gt; Why (and how) is regenerated skin different from original ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As we know we lose skin cells that becomes the dust in out homes and it always grows back to full thickness right ? So when I have a cut, I imagined it to heal provisionally with whatever possible and then after some time to replace itself with the normal skin that is coded in my chromosomes. So why doesn't it do that ? Scars remain and the color is always different from the neighbor parts.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Update:&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why we get scars?&lt;/li&gt;&#xA;&lt;li&gt;What about skin transplants ? &lt;/li&gt;&#xA;&lt;li&gt;Why doesn't skin actually grow/replace itself? &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Update 2:&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;(I've been thinking) Skin has lots of different layers, right ? So when an area is damaged does it regenerate all layers or just one for being simple and efficient (in &quot;hope&quot; the subject will take precautions not to damage this part of body again, so that regenerating everything back to 100% would be overkill) ?&lt;/li&gt;&#xA;&lt;li&gt;I'm not a scientist, I have only the basics from school, so I'll probably not understand most of the technical terms&lt;/li&gt;&#xA;&lt;li&gt;also I'm more interested about an explanation that goes towards the &quot;survival of the fittest&quot; rule, and not so much about the biochemical reactions in our bodies (because it was just some random mutation that turned out to be the better choice for us → why?)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8573" LastEditorUserId="8573" LastEditDate="2014-08-04T07:53:37.040" LastActivityDate="2014-08-04T14:45:14.263" Title="Why doesn't the human skin grow back exactly how it was before being damaged?" Tags="&lt;human-biology&gt;&lt;human-genetics&gt;&lt;skin&gt;" AnswerCount="2" CommentCount="10" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20130" PostTypeId="2" ParentId="20117" CreationDate="2014-08-01T10:06:16.793" Score="4" Body="&lt;p&gt;The &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0321558235&quot; rel=&quot;nofollow&quot;&gt;Campbell Biology&lt;/a&gt; is a good very introductory book to biology. It is popular book but a very standard text book. I am not aware of any popular and introductory book that are broad enough to encompass all of biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would suggest that you get the campbell and in parallel you can follow free online courseware. There are lots of them. Starting with &lt;a href=&quot;https://www.khanacademy.org/science/biology&quot; rel=&quot;nofollow&quot;&gt;KhanAcademy&lt;/a&gt; is maybe a good solution. It gives some introductory courses to a bunch of disciplines. ItunesU is also a good solution to search for further introductory courses given by the best universities such as Berkeley and the MIT typically.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-04-14T20:40:59.870" LastActivityDate="2015-04-14T20:40:59.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20131" PostTypeId="2" ParentId="20117" CreationDate="2014-08-01T10:06:43.087" Score="3" Body="&lt;p&gt;I would suggest something like &quot;The Selfish Gene&quot; by Richard Dawkins. It covers many examples or organisms and how their behaviour at a molecular level is ultimately selfish in order to ensure survival by passing their genes, which is perhaps the most important biological function of any living organism. However, as pointed in comments below, this book primarily concentrates on evolutionary biology and little else (at least in any noticeable depth) and puts forward many philosophical arguments regarding survival and passing your genes but doesn't talk about proteins or mRNA. &quot;The Extended Phenotype&quot; by Richard Dawkins again is an evolutionary biology book but it does talk about protein synthesis and the idea of phenotype and how genotype effects this and how the genotype of an organism can affect the environment!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Books by Richard Dawkins tends to give examples of whole organisms and in a sense the bigger picture to make his points about elementary concepts which allow life and its propagation and how it shapes the environment but doesn't go too much into details in order to keep the attention of the reader and keep it interesting to the lay audience. [for the lay audience] It is much easier to imagine a bird and its mating habits and how genes control this than knowing the molecular mechanism behind the signalling pathway responsible! However since the question is slightly subjective, my response tends to reflect a subjective response.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-01T10:34:41.040" LastActivityDate="2014-08-01T10:34:41.040" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20132" PostTypeId="2" ParentId="20125" CreationDate="2014-08-01T14:31:14.430" Score="7" Body="&lt;p&gt;Consider this from the point of view of integrating whole body metabolism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The body operates on a fuel economy built around glucose. Active muscle produces lactate (C3) which is exported to the liver through the bloodstream. Liver converts lactate to glucose (C6) which is then exported to the tissues. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What if muscle produced ethanol (C2)? Liver metabolises this to acetate. This could be converted to acetyl CoA and so on to fatty acids, but there is no way to achieve net synthesis of glucose from acetate. Muscle can of course use fatty acids, so you could conceive of an alternative system based upon this. It may be that this is less efficent from the point of view of energy useage - I haven't checked this because there is a more compelling argument against using ethanol.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2769631/&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;, lactate levels in the bloodstream can reach 15 - 25 mM during exercise. If muscle exported ethanol instead of lactate then blood alcohol content (BAC) would reach the same levels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The middle of that range, 20 mM ethanol, is equivalent to a BAC of 0.076% which is &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood_alcohol_content&quot; rel=&quot;nofollow&quot;&gt;just below the legal limit for driving&lt;/a&gt; in the USA and the UK, and above the legal limit in many European countries. This BAC is associated with effects upon reasoning, depth perception and peripheral vision. So, from an evolutionary position it really wouldn't make sense to have a metabolic system based around sending this much ethanol through the blood.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-08-01T16:06:45.337" LastActivityDate="2014-08-01T16:06:45.337" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20133" PostTypeId="2" ParentId="19380" CreationDate="2014-08-01T15:21:59.310" Score="2" Body="&lt;p&gt;As @WYSIWYG mentioned, I think HLA type is probably the best way to claim specificity.  Then the &lt;a href=&quot;https://en.wikipedia.org/wiki/Glycoprotein&quot; rel=&quot;nofollow&quot;&gt;glycoprotein&lt;/a&gt; (&lt;a href=&quot;https://en.wikipedia.org/wiki/Membrane_fusion_protein&quot; rel=&quot;nofollow&quot;&gt;fusion protein&lt;/a&gt; probably) on the virus fits only in an exact &lt;a href=&quot;https://en.wikipedia.org/wiki/MHC_class_II&quot; rel=&quot;nofollow&quot;&gt;MHC class II molecule&lt;/a&gt;.  If you want to hit some valid heavy science jargon, I recommend saying the virus was made with &lt;a href=&quot;https://en.wikipedia.org/wiki/Recombineering&quot; rel=&quot;nofollow&quot;&gt;recombineering&lt;/a&gt;, using a &lt;a href=&quot;https://en.wikipedia.org/wiki/Bacterial_artificial_chromosome&quot; rel=&quot;nofollow&quot;&gt;bacterial artificial chromosome&lt;/a&gt; (BAC), with a &lt;a href=&quot;https://en.wikipedia.org/wiki/Fluorescent_labelling&quot; rel=&quot;nofollow&quot;&gt;florescent marker&lt;/a&gt; to make the scientist's life easier (mush harder to work with viruses without nice markers).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a &lt;a href=&quot;http://dx.doi.org/10.1007/978-1-61779-876-4_3&quot; rel=&quot;nofollow&quot;&gt;methods paper&lt;/a&gt; that describes that exactly, and has the advantage of of a &lt;a href=&quot;http://download.springer.com/static/pdf/736/chp%253A10.1007%252F978-1-61779-876-4_3.pdf?auth66=1407078150_5ccead0e566871f7469d6a981b1e5c8d&amp;amp;ext=.pdf&quot; rel=&quot;nofollow&quot;&gt;free published protocol&lt;/a&gt; as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My problem with this method (using an HLA type to target) is that if you're targeting MHC Class II, it's going to be hard to kill the victim quickly.  Kill off all the cells would give a person AIDS, but not necessarily lead to a quick death.  Targeting MHC Class I could get around this, but then you're not targeting specific cells (could be nerves, could be skin cells), and the person would probably mount a pretty good immune response.  You'd probably have to hit the person with a pretty high dose to be sure you were infecting the cells you wanted to kill.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're willing to allow a two-step process, I think the more targeted approach would be to create an inducible latent virus.  Take one that commonly infects humans like &lt;a href=&quot;https://en.wikipedia.org/wiki/Human_cytomegalovirus&quot; rel=&quot;nofollow&quot;&gt;CMV&lt;/a&gt;, and modify it so that it was only induced out of latent infection by a specific trigger (tagged food for example).  Then further modify it so that it generates a highly toxic protein when it comes out of latency, like &lt;a href=&quot;https://en.wikipedia.org/wiki/Botulinum_toxin&quot; rel=&quot;nofollow&quot;&gt;botulinum&lt;/a&gt;, that will both kill the person very quickly and have the possible appearance of something natural.  If you use food is a trigger, then health workers would eventually figure out were all these people were eating and accuse them of food poising with botulism.  Whether that can help your character in the plot, I don't know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Back to the creation of the virus, I would still use the method above, though it's important to note that botulinum is a &lt;a href=&quot;https://en.wikipedia.org/wiki/Select_agent&quot; rel=&quot;nofollow&quot;&gt;select agent&lt;/a&gt;, and that proper &lt;a href=&quot;https://en.wikipedia.org/wiki/Biosafety_level&quot; rel=&quot;nofollow&quot;&gt;BSL&lt;/a&gt; would be a serious concern.  Have a hard time imagining it going down in someone's garage without them killing themselves.  But if the person known how/has materials for gene synthesis (many, many labs do), then acquisition is just a question of making the gene for the published botulinum sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It does occur to me that I might not should even post this based on it's ability to work...feel free to vote/comment to close if that is conciseness.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2014-08-01T15:21:59.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20134" PostTypeId="2" ParentId="19380" CreationDate="2014-08-01T15:38:28.170" Score="0" Body="&lt;p&gt;I would pick some virus that infects all people but then engineer it to not work properly on some specific host cells, e.g. some allele somehow preventing transcription of some key viral protein sort of like RNAi..&lt;/p&gt;&#xA;" OwnerUserId="5784" LastActivityDate="2014-08-01T15:38:28.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20136" PostTypeId="1" AcceptedAnswerId="20137" CreationDate="2014-08-01T16:51:59.983" Score="4" ViewCount="601" Body="&lt;p&gt;I've had a giant wasp hanging around outside my window the past few days, so I've resolved to learn more about it. I believe it is a male Cicada Killer, because it displays the following behavior:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;During the day, it is extremely localized in a region less than a square meter.&lt;/li&gt;&#xA;&lt;li&gt;It lands or hovers in the same grassy area all day, and occasionally chases off other wasps that come near it.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;First question: &lt;strong&gt;Am I correct that this is a male? The females should be off burrowing or catching Cicadas, right?&lt;/strong&gt; He is quite large (2 inches?), but I don't have a female for comparison in terms of morphology. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second question: &lt;strong&gt;Where does this guy go at night?&lt;/strong&gt; He leaves before sunset (~5 pm) and shows up again in the morning (~10 am).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Third: &lt;strong&gt;If he's around, I should be able to find some female burrows in the area as well, right?&lt;/strong&gt; Where should I look for these for confirmation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is admittedly a little vague since I am just trying to confirm I understand the behavior I am observing, but I've tried to isolate the specific questions I want answered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Finally got some pictures, only these two came out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bYnkv.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/sTp2C.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8576" LastEditorUserId="8576" LastEditDate="2014-08-01T21:00:21.703" LastActivityDate="2014-08-02T05:24:20.537" Title="Cicada Killer Behavior" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20137" PostTypeId="2" ParentId="20136" CreationDate="2014-08-01T17:03:57.413" Score="3" Body="&lt;p&gt;Yes, it's a male.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bugmugs.org/wordpress/wp-content/uploads/2012/08/cicada_killer_pair_00052.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://bugmugs.org/wordpress/wp-content/uploads/2012/08/cicada_killer_pair_00052.jpg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://bugmugs.org/2012/08/cicada-killer-pair/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://bugmugs.org/2012/08/cicada-killer-pair/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Update:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Wasps are in general very territorial. Even a paper bag can scare them as they take it as enemy hive. More on this: &lt;a href=&quot;https://biology.stackexchange.com/questions/8939/do-fake-wasp-nests-actually-fool-wasps&quot;&gt;Do fake wasp nests actually fool wasps?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Where does this guy go at night?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Wasps are known to be lazy(less active) at night. Probably they go to the nearby mud nest.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If he's around, I should be able to find some female burrows in the area as well, right?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;yes, there are chances of finding a female burrow near by, as they rarely fly away farther than the nest. Otherwise, there main food(cicada) is very heavy for them to carry to the nest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;follow this if you want to find it's borrow: &lt;a href=&quot;http://www.wikihow.com/Get-Rid-of-Ground-Digger-Wasps-(Cicada-Killers)-from-Your-Lawn&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.wikihow.com/Get-Rid-of-Ground-Digger-Wasps-(Cicada-Killers)-from-Your-Lawn&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-08-02T05:24:20.537" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20138" PostTypeId="2" ParentId="20006" CreationDate="2014-08-01T17:05:31.303" Score="7" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.purdue.edu/newsroom/research/2011/111122MurphyTransporter.html&quot; rel=&quot;noreferrer&quot;&gt;this link&lt;/a&gt; from Purdue, the seed of the answer is this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The herbicide is used to kill broadleaf weeds, which are dicots, while monocot grasses, such as sorghum and corn, are more resistant. That's because grasses inactivate 2,4-D inside the plant, while broadleaf dicots do not.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But on the other hand, &lt;a href=&quot;http://sourcedb.cas.cn/sourcedb_xtbg_cas/yw/ywlw/201312/P020131220579582246464.pdf&quot; rel=&quot;noreferrer&quot;&gt;Song 2014&lt;/a&gt; has this to say about 2,4-D:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;However, the underlying molecular mechanism of how auxinic herbicides selectively kill&#xA;  dicots and spare monocots is not&#xA;  understood yet (Grossmann 2000; Kelley&#xA;  and Riechers 2007; McSteen 2010). The mechanisms of auxin biosynthesis, transport,&#xA;  and signal transduction&#xA;  are conserved in monocots and dicots make this question more complex (McSteen 2010). Early research has&#xA;  proposed that the selectivity of auxinic herbicide is because of&#xA;  either limited translocation or rapid degradation&#xA;  of exogenous auxin, altered vascular anatomy, or altered perception of auxin in monocots (Monaco et al. 2002;&#xA;  Kelley and Riechers 2007). Auxin transport is influenced by plant vascular&#xA;  systems (Mattsson et al. 1999;&#xA;  Scarpella et al. 2006). The difference in vascular tissue structure between dicots&#xA;  and monocots may contribute&#xA;  to the selectivity of auxinic herbicides. In monocot&#xA;  stems, the vascular tissues (the phloem and xylem) are&#xA;  scattered in bundles, and lack a vascular&#xA;  cambium; in dicot stems, the vascular tissues are form&#xA;  ed in rings and&#xA;  possess a cambium. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So in other words, we don't know yet. It seems to be very strongly tied to auxin transport, but we do not have the full mechanism of action; since auxin is such an important plant hormone, and the pathway is therefore highly conserved (that is, the genes tend to be nearly identical on the parts of the sequence that affect the phenotype), the general conclusion is that the pathway itself is not affected, but an accessory pathway clears up auxin in levels excess of any normal amount in monocots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: Whoops, got the author's first/last names mixed up.&lt;/p&gt;&#xA;" OwnerUserId="8568" LastActivityDate="2014-08-01T17:05:31.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20140" PostTypeId="2" ParentId="7014" CreationDate="2014-08-01T20:27:42.117" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;There is a large population of birds that look like crows or ravens,&#xA;  yet fatter. They seem to be quite social and move around in large&#xA;  groups.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;First of all, this seems like a crow. Crows are very social birds, they live in flocks or murder.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Theory:&lt;/strong&gt; It may be a Mating Ritual?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No! The have a &lt;a href=&quot;https://www.youtube.com/watch?v=lNQ2Rs5BZ_g&quot; rel=&quot;nofollow&quot;&gt;very spectacular mating ritual!&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Theory&lt;/strong&gt;: It's Making a nest&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Obviously No! Crows nests are always way hidden at 18-60 feet above ground(mostly) in the tree trunk.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;&lt;strong&gt;My Theory&lt;/strong&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Crows are very curious birds. What you saw, might be a new play the young crows found. It's common that crows will do unusual thing when spectated by the elders and siblings.&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-08-01T20:27:42.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20141" PostTypeId="2" ParentId="20103" CreationDate="2014-08-01T21:13:32.020" Score="2" Body="&lt;p&gt;Here (mic.sgmjournals.org/content/127/1/121.full.pdf) is a link to a paper in which &lt;em&gt;P. shermanii&lt;/em&gt; is grown in flask culture. Although the conditions are clearly designed to achieve low oxygen concentrations in the culture (the flask is almost full and is only shaken occasionally), they also indicate that oxygen is not toxic for this organism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, this is from the WP page you linked to: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Obligate anaerobes are microorganisms that are killed by normal atmospheric concentrations of oxygen (21% O&lt;sub&gt;2&lt;/sub&gt;). Oxygen tolerance varies between species, some capable of surviving in up to 8% oxygen, others losing viability unless the oxygen concentration is less than 0.5%.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-08-01T21:13:32.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20142" PostTypeId="2" ParentId="20078" CreationDate="2014-08-01T22:02:29.293" Score="7" Body="&lt;p&gt;A trait is said to be adaptive when it causes fitness to increase. Fitness is generally understood as the (relative) contribution to future generations in terms of offspring or genes. The trait is selected for by the environment and hence increases fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/ibi.12158/abstract&quot; rel=&quot;nofollow&quot;&gt;the paper of Dey et al.&lt;/a&gt; this is the fitness of the parent birds. Hatching asynchrony causes size differences between chicks which may (1) &quot;facilitate brood reduction in unfavourable environmental conditions&quot;, (2) &quot;provide insurance against the failure of core offspring&quot; and (3) &quot;reduce competition among nestlings&quot;. Dey et al. also cite a reason why hatching asynchrony may be sustained in a population despite being maladaptive: initiating incubation before the clutch is completely laid is selected for and causes asynchronous hatching as a by-product. In this case, hatching asynchrony merely correlates with fitness, but does not cause fitness to increase and is thus not adaptive.&lt;/p&gt;&#xA;" OwnerUserId="8552" LastEditorUserId="8552" LastEditDate="2015-07-27T12:03:52.890" LastActivityDate="2015-07-27T12:03:52.890" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20143" PostTypeId="2" ParentId="20104" CreationDate="2014-08-02T02:05:52.673" Score="3" Body="&lt;p&gt;A very clear description is given in &lt;a href=&quot;https://en.wikipedia.org/wiki/Sequence_logo#Logo_creation&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The starting point is an alignment for the region under investigation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A. Basically, to get the height of the stack of letters for every position one has to calculate &lt;strong&gt;the degree of certainty about the residue&lt;/strong&gt; (= degree of conservation) at this position in the sequences belonging to this class. I'll explain what it means:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key parameter in this context is &lt;strong&gt;information&lt;/strong&gt;. 1 bit of information can be understood as the amount &quot;knowledge&quot; you get when receiving an answer to one yes/no question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say we have equal proportions of all four bases at a certain position in a set of DNA sequences. To &quot;guess&quot; a base at this position in some sequence we have to ask two binary questions. For example: &quot;is it Pyrimidine?&quot; If 'yes' we'd ask &quot;is it 'T'?&quot; Otherwise: &quot;is it G?&quot;. So, when the frequencies are equal we can get 2 bits of information from one observation of a base at this position in a sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the frequencies are distorted, we already have some ideas about the bases when coming to an individual observation. If we already know, say, that we have just G and A at this position with ratio of 1:1, we can just ask &quot;is it G?&quot;, so we get clearly 1 bit. When the ratios are not even (or when the number of alternative states is not 2&lt;sup&gt;n&lt;/sup&gt;), the analogy with the questions becomes much less clear and we have to resort to the very simple formula for &lt;a href=&quot;https://en.wikipedia.org/wiki/Entropy_%28Information_theory%29&quot; rel=&quot;nofollow&quot;&gt;Shannon entropy&lt;/a&gt;. Intuition and brief inspection of this formula would bring you the idea, that when the ratios of the residues are biased, we always have less information than for the case of equal frequencies (2 in the case of DNA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now to estimate the &quot;the degree of certainty&quot; we simply calculate the information based on the observed frequencies of different residues at this position and subtract it from the theoretical maximum (again: 2 in the case of DNA):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;certainty = maximal information possible - actual information&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;This value defines the height of a stack of letters at each position&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;maximum&lt;/strong&gt; value (2 bits) would be observed when we always have the same base, because &quot;actual information&quot; would be zero (there is no need to ask questions - we &quot;know&quot; the answer anycase). The &lt;strong&gt;minimum&lt;/strong&gt; (0 bits) is when we have no idea about the base. &lt;strong&gt;One bit&lt;/strong&gt; would be obtained if we had, say, just two equally frequent bases. And, for example, the value of 0.6 would be observed if you had, e.g. 68.5% of the time the same base A and in all other case C, G or T with equal frequencies of 10.5%.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B. As you probably already know: &lt;strong&gt;the proportions of all alternative bases are shown as relative heights of individual letters.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-08-02T15:47:51.813" LastActivityDate="2014-08-02T15:47:51.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20144" PostTypeId="2" ParentId="20038" CreationDate="2014-08-02T02:28:19.070" Score="-1" Body="&lt;p&gt;Here's a language metaphor. In a single language, words may be said or written across a spectrum of accents or spellings but have the same meaning. Likewise in a single species, genes (words) may exist in a spectrum of diversity (DNA sequence) but maintain the same meaning. So, when 2 species share &quot;most of their DNA&quot; they share most of the same genetic meaning (like 2 languages which share word origins). While siblings who share &quot;half their DNA&quot; share half sequence identity (same accent or spelling). &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-02T02:34:03.300" LastActivityDate="2014-08-02T02:34:03.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20145" PostTypeId="1" CreationDate="2014-08-02T02:34:01.267" Score="11" ViewCount="16190" Body="&lt;p&gt;It seems like when we observe animals in the wild, the occurrence of noticeable disease in adult individuals is much lower than in humans. Why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a number of reasons that this could happen, but I want to know which reasons contribute the most, or what other reasons I haven't thought of could be involved. So, here's my list of theories:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Animals that are prone to disease usually die when very young, while humans in developed countries are given vaccinations/medical attention and have a much greater chance to live to adulthood and advanced age. However, even taking this into consideration, it seems like human populations in third-world countries with little or no access to medicine are much, &lt;em&gt;much&lt;/em&gt; more riddled with disease than animal populations appear to be. (Or do they only look that way because that's what we see the most of in the news?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The animals that we see in documentaries are generally purposely selected for viewing as being healthy individuals or a mostly healthy group. This doesn't account for YouTube's many amateur safari videos and pictures, however, where it still seems like animals die much more from territorial disputes or preying than of disease. Safari-goers aren't likely to sit around filming diseased animals, but it still seems like animals 'in the background' and in herds appear to generally be very healthy when it'd be pretty easy to notice a somehow diseased or disabled person in an equivalently large group on the sidewalk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Most humans don't know what common wildlife diseases look or sound like, and at a distance they all appear healthy to us even if there is a roughly equivalent percentage of disease among adult animals as among adult humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3a) Animals are much better at concealing the symptoms of their common diseases than the average human, as a defense mechanism from predators. (I know that cats are particularly good at not showing that they're in pain, but I'm not sure how many other animals behave this way.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) While most modern humans go out of their way to do every possible thing they can to make sure an infant survives, animal parents purposely kill, abandon or even eat young that they can sense are diseased or disabled in some way. I saw an example of this on a youtube video where a lion cub was gored by a cape buffalo and its back legs were paralyzed. After numerous failed attempts to nudge the cub into standing or walking properly, the mother purposely killed the cub with a suffocating bite and ate it. &lt;em&gt;(Did/do humans practice this to any significant extent? I once read about a culture, can't remember which, that didn't consider an infant viable enough to even name until it was at least 3 months old. I also read that either the ancient Greeks or the Romans would bathe a newborn in wine, and if it survived, it was deemed strong enough to deserve a chance at life. I don't know how true either of these claims are, though. But that's kind of a different question, so consider it optional 'bonus points' to answer.)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5) Diseased and disabled animals are killed off by predators or rivals quickly enough that the populations we see are filled with healthy animals just because the infirm are constantly weeded out. This doesn't address animals that have few/no natural predators or rivals, such as in the case of areas that have so many deer with no natural predators that human hunters must cull them to keep them from reproducing out of control. Are these populations more prone to adulthood diseases than populations that have natural predators?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;6) At about seven billion, &lt;a href=&quot;http://www.npr.org/blogs/thetwo-way/2011/11/03/141946751/along-with-humans-who-else-is-in-the-7-billion-club&quot;&gt;humans are easily the most populous species that is the size of humans&lt;/a&gt;. Other animals with larger populations are much smaller than humans. Compared to other animals of our size or larger, we are intensely overcrowded, leading to lots of people coming in contact with lots of other people all the time, frequently on an international scale as thousands of planes and ships travel around the world on a daily basis. This only covers contagious diseases, though. Even the most isolated hermit could die from a genetic condition that he had since before he was born.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;7) Stress. Animals live what we would consider to be a very high-stress life, but they experience their stress in short, intense bursts. Humans, even (especially!) those who live in first-world countries with lots of information to learn and lots of things to do, often get to the point where they can't figure out where the 'off' switch for their stress is. Stress is a silent, gradual killer, and it's possible that minor genetic conditions that may have otherwise been fairly benign or unnoticed turn ugly as a person ages through a life where stress is constant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;8) Diet. It's no secret that there's a lot of heart disease and other diet-related issues in the modern world, but I don't know if that covers ancient humans, and there seems to have been plenty of disease to go around in the olden days even when people ate purely natural foods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't think of any other theories at the moment. One way I thought of to possibly help answer this question was to take into consideration domestic animals - how many diseases do veterinarians have to treat compared to how many diseases human doctors have to treat? This line of thought is rather tainted by the fact that domestic animals are often given vaccinations of their own, though, but it doesn't seem like they receive nearly as many as humans do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is my first time asking a question on stackexchange, so I hope I've given you plenty of meat to chew on with this post. I look forward to the replies!&lt;/p&gt;&#xA;" OwnerUserId="8578" LastActivityDate="2014-08-02T02:53:53.933" Title="Why do humans seem so much more prone to disease than animals?" Tags="&lt;human-biology&gt;&lt;zoology&gt;&lt;pathology&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2014-08-03T11:10:18.437" ContentLicense="CC BY-SA 3.0" />
  <row Id="20146" PostTypeId="2" ParentId="20145" CreationDate="2014-08-02T02:47:40.917" Score="5" Body="&lt;p&gt;Many examples of animals which have more difficulty maintaining their population size than humans exist. This is partially why some species go extinct. The Tasmanian Devil is at high risk for extinction from a genetic predisposition for cancer onset by infection. Your premise that humans are unhealthy is not sound. Humans are long lived, genetically diverse animals which reproduce exceptionally. We are among the most successful species. &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-02T02:53:53.933" LastActivityDate="2014-08-02T02:53:53.933" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20147" PostTypeId="2" ParentId="20129" CreationDate="2014-08-02T04:00:50.613" Score="4" Body="&lt;p&gt;You're confusing an emergent system with a determined system. Your cells have programming which emerges as the form you see. You are using determinism to decide what your form should be. Determinism gives one reaction for every action. Biology is emergent, not deterministic. The biological mechanisms which are responsible for healing exist in a different information space, with different evolutionary pressures from those which generated your form. The close approximation of scar tissue to undamaged flesh is an emergent property of these two instructions sharing the same physical location. There is no communication between the information which patterned your form and the information which heals your body. &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-02T20:50:00.023" LastActivityDate="2014-08-02T20:50:00.023" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20149" PostTypeId="2" ParentId="19942" CreationDate="2014-08-02T05:04:24.527" Score="1" Body="&lt;p&gt;A significant amount of heat generated by the cell does not come from the hydrolysis of an NTP. ATP is generated by a H+ gradient in the mitochondria, and this gradient is created by mechanisms which rely only in part by ATP.  Most of the energy stores in our bodies are not in the NTP pool. This is why CO₂ and urine are used to measure energy expenditure during physical exercise. On the scale of individual cells, it is a challenge to conceive a protocol which would account for all confounding variables. However, on the scale of a human, confounding variables in energy use are easily controlled. If you are interested in the energy expenditure of a single biological process, this would seem a better project rather than quantifying all processes simultaneously. &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="3340" LastEditDate="2014-10-09T15:00:54.867" LastActivityDate="2014-10-09T15:00:54.867" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20150" PostTypeId="2" ParentId="15293" CreationDate="2014-08-02T06:07:29.093" Score="1" Body="&lt;p&gt;I will strongly suggest you:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PredictSNP: It's the best tool for nsSNP detection as it compares and throw out result from all the tools available.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://loschmidt.chemi.muni.cz/predictsnp/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://loschmidt.chemi.muni.cz/predictsnp/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Paper: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894168/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894168/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tyuWs.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="338" LastEditDate="2014-08-02T21:13:14.153" LastActivityDate="2014-08-02T21:13:14.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20151" PostTypeId="1" AcceptedAnswerId="20153" CreationDate="2014-08-02T06:34:39.500" Score="1" ViewCount="346" Body="&lt;p&gt;In evolutionary terms, will the capsule cease to exist someday or will it improve ? Does it provide any boost to the organism in any way which harms us ? Can't we remove capsules or engineer E.coli without capsule ?&lt;/p&gt;&#xA;" OwnerUserId="8580" LastEditorUserId="1320" LastEditDate="2014-08-02T08:01:00.720" LastActivityDate="2014-08-02T08:01:00.720" Title="What is the specific use of a capsule in E.coli?" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20152" PostTypeId="2" ParentId="9597" CreationDate="2014-08-02T06:55:32.660" Score="1" Body="&lt;h2&gt;&lt;strong&gt;SNP Density&lt;/strong&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Human = ~1.18 SNPs per kbases&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Based on CgsSNP, the average numbers of SNPs per 10 kb was 8.33, 8.44,&#xA;  and 8.09 in the human genome, in intergenic regions, and in genic&#xA;  regions, respectively.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12909357&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution.&lt;/em&gt; by Zhao Z, Fu YX, Hewett-Emmett D, Boerwinkle E.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Drosophila melanogaster&lt;/em&gt; = ~0.02 SNP per kbases&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;FLYSNPdb provides high-resolution single nucleotide polymorphism (SNP)&#xA;  data of Drosophila melanogaster. The database currently contains 27&#xA;  367 polymorphisms, including &gt;3700 indels (insertions/deletions),&#xA;  covering all major chromsomes. These SNPs are clustered into 2238&#xA;  markers, which are evenly distributed with an average density of one&#xA;  marker every 50.3 kb or 6.6 genes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;source: &lt;a href=&quot;http://nar.oxfordjournals.org/content/37/suppl_1/D567.long&quot; rel=&quot;nofollow&quot;&gt;FLYSNPdb: a high-density SNP database of Drosophila melanogaster&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Mouse(&lt;em&gt;Mus musculus&lt;/em&gt;) = ~0.2 SNP per kbases&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.pnas.org/content/100/6/3380.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Genome-wide single-nucleotide polymorphism&#xA;analysis defines haplotype patterns in mouse&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-08-02T06:55:32.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20153" PostTypeId="2" ParentId="20151" CreationDate="2014-08-02T06:58:54.863" Score="1" Body="&lt;p&gt;According to wikipedia, the capsule contains tightly packed polysaccharides that preform several functions including keeping bacteriophages out, blocking recognition by macrophages, and holding water during dessication. Given the wide diversity of bacteria with capsules, it's probably been around for a long time, which implies it isn't going away any time soon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the capsule prevents the E. coli from being taken up by macrophages, then yes, it could allow the bacteria to harm us more effectively. This is one form of a virulence factor. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With proper conditions we probably could develop a bacteria with little to no capsule. We have developed L-form bacteria, which don't have peptidoglycan cell walls. It would seem to me that the cell wall is more important than the capsule, but L-form bacteria are very fragile. I don't know what advantage would be gained by producing capsule free bacteria. There would probably be more to gain from making bacteria with different capsules, perhaps carrying proteins that recognize certain substances and produce a signal, allowing the bacteria to be used as a biosensor, or to accumulate toxic compounds for bioremediation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;references: &lt;a href=&quot;http://en.wikipedia.org/wiki/Bacterial_capsule&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Bacterial_capsule&lt;/a&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/L-form_bacteria&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/L-form_bacteria&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-02T06:58:54.863" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20154" PostTypeId="2" ParentId="14531" CreationDate="2014-08-02T07:27:50.873" Score="2" Body="&lt;p&gt;The two amoxycillin formulations you mention pair the amoxycillin with a Beta lactamase inhibitor. This is because of the prevalence of resistance to beta lactam drugs including amoxycillin. If we were to invent a brand new never before seen beta lactam drug and started using it irresponsibly, there would probably be resistant bacteria within 5 years. The same beta lactam core structure that makes the drugs work against the peptidoglycan synthesis machinery make it susceptible to attack by beta lactamase. A new beta lactam could avoid the lactamase for a while, but the same evolutionary pressures that selected for resistant mutants against the other beta lactams would select for mutants resistant against the new one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same goes for the fluoroquinolines you mention. Their mechanism of action is different, they inhibit DNA synthesis by blocking topoisomerase II activity. But once a bacterial strain is selected for that has resistance against one member of a class of antibiotic it's relatively easy for it to acquire the mutations that confer resistance against other members of the class. Changing the structure of the drug enough so that cannot be defeated by the mechanism of resistance while retaining the drugs mechanism of action is probably impossible, or at least we haven't done it yet. Even vancomycin, one of our most powerful antibiotics, has some bacteria resistant to it.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-02T07:27:50.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20155" PostTypeId="2" ParentId="17941" CreationDate="2014-08-02T07:29:52.300" Score="2" Body="&lt;h2&gt;Getting SNP data from FTP Site of NCBI SNP:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;It's actually simple to download the data from the NCBI, if you follow the method given by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK44376/&quot; rel=&quot;nofollow noreferrer&quot;&gt;FAQ&lt;/a&gt;( as given by @WYSIWYG).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Step 1:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Goto organism FTP: &lt;a href=&quot;ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/&quot; rel=&quot;nofollow noreferrer&quot;&gt;ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tuixf.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Step 2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Open your required organism folder:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VW8Au.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;From here you can download any file you wanted. If you trying to study the whole organism please download any one of the whole folders(ASN.1, rs_fasta, XML(recommended)).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's not about the downloading it's about understanding the files which are provided. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;files types:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/XML&quot; rel=&quot;nofollow noreferrer&quot;&gt;XML files&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Abstract_Syntax_Notation_One&quot; rel=&quot;nofollow noreferrer&quot;&gt;ASN.1 or Abstract Syntax Notation One&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;rs_fasta&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;All of them contents almost the same data, just in different format. It's up to you how your script(preferably Python or Perl) works to get out the import information. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/sites/books/NBK56563/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Other way of Download from NCBI FTP&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can always use filezilla:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZE1dO.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Put Host as : &lt;a href=&quot;ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/&quot; rel=&quot;nofollow noreferrer&quot;&gt;ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;rest Username and Password, etc empty&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-08-02T07:29:52.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20156" PostTypeId="2" ParentId="16981" CreationDate="2014-08-02T07:34:49.177" Score="1" Body="&lt;p&gt;I think you're referring to radio frequency or microwave ablation. It works by heating the tissues up with electromagnetic radiation, just like you'd use to microwave food, but it's heating you instead. Healthy cells have better repair mechanisms and survive these treatments better. Cancer cells tend to have poor repair ability and can be killed more easily. I've heard of injecting metal nanoparticles which collect in the tumor due to the enhanced permeability and retention (EPR) effect. The nanoparticles respond to the microwaves much more powerfully than cells do and get hotter, burning the tumor from the inside out.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-02T07:34:49.177" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20157" PostTypeId="2" ParentId="8893" CreationDate="2014-08-02T08:15:22.000" Score="3" Body="&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/7/70/Common_clownfish_curves_dnsmpl.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's an example of &lt;a href=&quot;https://upload.wikimedia.org/wikipedia/commons/7/70/Common_clownfish_curves_dnsmpl.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;SYMBIOSIS&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clownfishes(&lt;em&gt;Amphiprion ocellaris&lt;/em&gt;) are never found without an anemone as they have this obligate association with them. Although they can survive without them, but studies show they are much more healthier with than without.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This association is more of a survival necessity. These anemones are actually toxic and the fish is resistance to it. If being attacked they will get inside these and the attacker might be stung with this actinotoxin.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The presence of an anemone is also essential to reproduction of the&#xA;  fishes: their eggs are laid beneath the oral disc overhang of the&#xA;  anemone, where they are tended by the male.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sea_anemone&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia on Sea anemone&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://jjgeisler.com/reeftank/anemones/ch5.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;INTERACTIONS BETWEEN FISH AND SEA ANEMONES&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.fordivers.com/en/fauna/especie/clownfish/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Clownfish and its mutualism relationship with anemones&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.460" LastActivityDate="2014-08-02T08:15:22.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20158" PostTypeId="2" ParentId="20117" CreationDate="2014-08-02T09:03:26.607" Score="3" Body="&lt;p&gt;Alongwith campbell ,look up some &quot;advanced&quot; books - like  Bruce Alberts molecular biology of The Cell , Lehninger, etc. It is not necessary to read everything in those books. Read whichever topics interest you the most. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also a very good site : ibiomagazine.org which has videos of some of the big shots of biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And remember, most important is to keep all your senses open always. There is so much biology going around. Observing and thinking about it can teach you things which 100 textbooks can't !&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-08-02T09:03:26.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20159" PostTypeId="2" ParentId="13455" CreationDate="2014-08-02T15:30:43.107" Score="3" Body="&lt;p&gt;Another factor involved is the effect that high salt concentrations have on the 3-D structure of proteins. At higher than &quot;normal&quot; concentrations of salt, many proteins will fold differently and no longer be in their &quot;active&quot; form. Since all biological reactions involve enzymes, which are protein, you can see why this unfolding might be problematic.&lt;/p&gt;&#xA;" OwnerUserId="8584" LastActivityDate="2014-08-02T15:30:43.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20162" PostTypeId="2" ParentId="11130" CreationDate="2014-08-02T17:28:41.773" Score="2" Body="&lt;p&gt;Second paper is an article in science Daily and have a pretty decent source from Texas A&amp;amp;M University. It's much better than the first as it is un-sourced post on yahoo answers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &#xA;&lt;a href=&quot;https://www.sciencedaily.com/releases/2008/05/080501125451.htm&quot; rel=&quot;nofollow&quot;&gt;&quot;Male Seahorses Are Nature's Mr. Mom, Researchers Say.&quot; ScienceDaily. ScienceDaily, 2 May 2008.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why male seahorses gets pregnant?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetic answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;May be because only $MHII\beta$ gene present in the male pouch which carries the babies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source and more on this topic:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117728/&quot; rel=&quot;nofollow&quot;&gt;The impact of sex-role reversal on the diversity of the major histocompatibility complex: Insights from the seahorse (Hippocampus abdominalis)&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-08-02T17:28:41.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20163" PostTypeId="1" CreationDate="2014-08-02T17:30:52.633" Score="3" ViewCount="5708" Body="&lt;p&gt;Given that most Americans seem to do fine using anti-perspirant, it got me wondering: is there an evolutionary purpose to underarm perspiration?  I can't imagine it acts to attract the opposite sex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is it just likely an unfortunate side effect of whole-body evaporative cooling via sweat?&lt;/p&gt;&#xA;" OwnerUserId="3292" LastActivityDate="2018-08-05T22:07:02.133" Title="Is there an evolutionary purpose to armpit perspiration?" Tags="&lt;evolution&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20164" PostTypeId="1" AcceptedAnswerId="20332" CreationDate="2014-08-02T17:58:15.153" Score="2" ViewCount="278" Body="&lt;p&gt;I at times have many goats grazing in our locality. Recently a few cows were seen too. I just offered one of the cows a few leaves from &lt;em&gt;Jasminum sambac&lt;/em&gt; plant growing in our garden. The cow smelled and left those leaves untouched. However on being given mango leaves, not a bit of it remained. The same situation did I observe with goats.I have the following questions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the difference between leaves of others and leaves of &lt;em&gt;Jasminum sambac&lt;/em&gt;?&#xA;Why do herbivores avoid consumption of these leaves?&#xA;Does it happen with other leaves too?&lt;/p&gt;&#xA;" OwnerUserId="8216" LastActivityDate="2019-03-10T03:19:59.740" Title="Leaves not liked by herbivores" Tags="&lt;zoology&gt;&lt;botany&gt;&lt;food&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="20165" PostTypeId="1" AcceptedAnswerId="20187" CreationDate="2014-08-02T18:27:03.273" Score="1" ViewCount="64" Body="&lt;p&gt;In the film &quot;The Perfect Human Diet&quot; at 32:36, a scientist points to animal remains and states &quot;we've got a scutella of reindeer there.&quot;  What is scutella in this context?  &lt;/p&gt;&#xA;" OwnerUserId="4358" LastActivityDate="2014-08-03T14:59:30.737" Title="What is a &quot;scutella of reindeer&quot;?" Tags="&lt;terminology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20166" PostTypeId="1" CreationDate="2014-08-02T19:11:03.517" Score="1" ViewCount="164" Body="&lt;p&gt;I would like to know whether the pCAMBIA1200 and pCAMBIA0380 be used for co-transformation of rice using Agrobacterium LBA4404.They probably have the same ori site so they belong to the same incompatibility group.So will they co-exist in one Agrobacterium strain and be transferred to the rice plant?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please let me know.&lt;/p&gt;&#xA;" OwnerUserId="8588" LastActivityDate="2014-08-03T16:26:17.833" Title="Is this pCAMBIA co-transformation possible?" Tags="&lt;botany&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20167" PostTypeId="2" ParentId="10806" CreationDate="2014-08-02T19:13:51.070" Score="1" Body="&lt;p&gt;As for how certain bacteria achieve their shapes, the cell wall plays an important role. Almost all bacteria have a cell wall made of a substance called peptidoglycan, a mesh of peptides and saccharides that provides rigidity and strength to the bacteria. This wall is produced through a complex series of steps that starts inside the cell, where the peptide and sugar units are attached to a lipid to make a compound called Lipid II. However, Lipid II must be flipped to the outer layer of the cell membrane to deliver the peptides and sugars to the growing cell wall. The proteins responsible for flipping the Lipid II are believed to be FtsW, RodA, and SpoVE. FtsW is considered the main enzyme for most cell growth. RodA is found in rod shaped bacteria and is considered necessary for cell elongation. SpoVE is used to build the thick cell walls of bacterial spores. By controlling how Lipid II is delivered to the growing cell wall, these proteins play a role in controlling cell shape.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2509435&quot; rel=&quot;nofollow&quot;&gt;Structural similarity among Escherichia coli FtsW and RodA proteins&#xA;and Bacillus subtilis SpoVE protein, which function in cell division,&#xA;cell elongation, and spore formation, respectively.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jbc.org/content/early/2014/04/07/jbc.M114.557371.abstract&quot; rel=&quot;nofollow&quot;&gt;Specificity of the transport of Lipid II by FtsW in Escherichia coli&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="5144" LastEditDate="2014-08-02T20:43:57.773" LastActivityDate="2014-08-02T20:43:57.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20168" PostTypeId="2" ParentId="7014" CreationDate="2014-08-02T19:23:46.703" Score="1" Body="&lt;p&gt;Crows have been known to use human actions in order to accomplish their own purposes: &lt;a href=&quot;http://www.pbs.org/lifeofbirds/brain/&quot; rel=&quot;nofollow&quot;&gt;read this story about them using cars and waiting for the lights to change at a crossroads&lt;/a&gt;. Then of course, the question is whether they have a specific purpose in your case with these sticks, or whether it's just... for the fun of it?&lt;/p&gt;&#xA;" OwnerUserId="6224" LastActivityDate="2014-08-02T19:23:46.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20169" PostTypeId="2" ParentId="20163" CreationDate="2014-08-02T20:42:01.173" Score="5" Body="&lt;p&gt;First: Not everything what happens in biology is necessarily directly selected for. Sweating is of course selected for, so our body can maintain its normal body temperature in hot climates. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a difference between sweat glands under our armpits and for example on the forearm. Under our armpits we have the so called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Apocrine_sweat_gland&quot; rel=&quot;noreferrer&quot;&gt;apocrine sweat glands&lt;/a&gt;&quot; while most of the rest of our body is covered with &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Eccrine_sweat_gland&quot; rel=&quot;noreferrer&quot;&gt;eccrine sweat glands&lt;/a&gt;&quot;. They are not only different in size, but produce different types of sweat. Eccrine sweat glands produce sweat, that is made mostly of water and salt, while the apocrine sweat glands sweat contains additionally lipids, proteins and also steroids. Decomposition of the sweat by bacteria which live on our skin produces the typical sweaty odor. The sweat glands also differ in their activation (see &lt;a href=&quot;https://www.inkling.com/read/dermatology-bolognia-jorizzo-schaffer-3rd/chapter-35/eccrine-apocrine-and-apoeccrine#c30b2757d0144c29a3d57d3c2bc26559&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; for more details), so can the apocrine glands be triggered by stress.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to this source (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18489347&quot; rel=&quot;noreferrer&quot;&gt;A short history of sweat gland biology&lt;/a&gt;&quot;) is roughly comparable, although the total numbers vary quite a lot between the single studies. Assuming that the amount of sweat is comparable, than another factor comes into play: The different evaporation from our arms and from under our armpits. The last form a kind of cavity where the sweat can not easily evaporate and will then stay. It might also play a role, that they can be activated by stress, which will happen in situations which are uncomfortable for us and make the situation worse.&#xA;A paper which also looks very interesting in this context (to which I unfortunately have no access) is: &quot;&lt;a href=&quot;http://link.springer.com/article/10.1007/BF01049065&quot; rel=&quot;noreferrer&quot;&gt;The evolution of sweat glands.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-02T20:42:01.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20170" PostTypeId="1" CreationDate="2014-08-02T21:08:32.190" Score="6" ViewCount="1493" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Holotropic&quot;&gt;Holotropic breathwork&lt;/a&gt; is a non-drug technique developed by Stanislav Grof used in psychotherapy. The therapy as a whole is usually called holotropic breathwork (at least by Grof himself) and will most probably rely on a range of effects. However, I am mainly concerned about the core technique, which leads to hallucination and a changed state of conciousness (i.e. being half concious and having a distorted perception of time).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As quick googling does not reveal any specific information of the technique, I will describe a demonstration of an amateur enactment of something which was stated to be based on the same principle as holotropic breathwork. (&lt;em&gt;I consider the respective people very irresponsible to have done this without trained assistance, it is probably very dangerous, do NOT try at home!&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A person squats curled near a wall and breaths as quickly and as heavily as possible for a few minutes. After that they quickly stand up in front of the wall and another person pushes them quickly in the chest and presses them strongly against the wall behind them. The pushed person collapses completely, their muscles relaxed, they even don't have the time to close eyes and you can see their eyeballs rolling around freely. They are in this state for about 15 seconds and then wake up reporting vivid hallucinations. Some of the people said that their perception e.g. of sources of light and surfaces were altered for another several hours.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what is the biological basis of this collapse and hallucinations? (It would be perhaps good to also comment on the possible risks.)&lt;/p&gt;&#xA;" OwnerUserId="8589" LastActivityDate="2017-03-01T05:13:33.347" Title="What is the biological principle of this &quot;holotropic breathwork&quot; technique?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;neurology&gt;&lt;breathing&gt;&lt;hallucinogens&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20171" PostTypeId="2" ParentId="20170" CreationDate="2014-08-02T21:28:06.253" Score="6" Body="&lt;p&gt;I think this is mostly caused by &lt;a href=&quot;http://en.wikipedia.org/wiki/Hyperventilation&quot; rel=&quot;nofollow&quot;&gt;hyperventilation&lt;/a&gt;. The excessive breathing disturbs the balance between CO$_{2}$ and oxygen in our lungs. This will cause &lt;a href=&quot;http://en.wikipedia.org/wiki/Respiratory_alkalosis&quot; rel=&quot;nofollow&quot;&gt;respiratory alkalosis&lt;/a&gt; (the blood pH, which is normally strictly regulated, gets higher), which can cause dizziness, headaches and fainting. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The shift in pH can also disturb the eclectrolyte balance, especially the concentration of the free dissolved calcium, as it binds to negatively charged plasma proteins (which release protons into the blood due to the higher pH). This can lead to craps and spasms.&#xA;I would be very careful not playing around here, as this can have some severe consequences.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2016-06-14T06:12:22.537" LastActivityDate="2016-06-14T06:12:22.537" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20172" PostTypeId="2" ParentId="20163" CreationDate="2014-08-02T21:31:03.407" Score="3" Body="&lt;p&gt;Armpit sweat does not have a strong intrinsic odor. What you smell is the waste of the microorganisms which colonize your armpits. It is a similar mechanism responsible for foot odor and bad breath. All external bodily surfaces have particular microbes which prefer different areas. This also includes the intestinal, oral and nasal regions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you charted these microbes on our body, their colonies would read like a map of microbial nations. Different lipids, sugars, proteins on individuals promote different types of microbes and different metabolic pathways giving individuals different scents. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our ability to perceive a wide range of microbial odors might have an evolutionary pressure given the importance of detecting microbes in spoiled food, etc. I hypothesize our ability to detect body odor is inherited from detecting microorganisms in general.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Surely as our olfactory sense has diminished over evolution, these microbial odors are being taken out of some ancient context.&lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-04T00:48:04.413" LastActivityDate="2014-08-04T00:48:04.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20173" PostTypeId="1" AcceptedAnswerId="35659" CreationDate="2014-08-02T21:48:14.473" Score="1" ViewCount="442" Body="&lt;p&gt;Are there any tree-dwelling mammals which might be found taking a living leech and eating it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(And do any hollow-dwelling birds of prey eat leeches?)&lt;/p&gt;&#xA;" OwnerUserId="8564" LastEditorUserId="24354" LastEditDate="2020-08-10T05:53:36.733" LastActivityDate="2020-08-10T05:53:36.733" Title="Are there any arboreal mammals which eat leeches?" Tags="&lt;zoology&gt;&lt;food&gt;&lt;mammals&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20174" PostTypeId="1" AcceptedAnswerId="20182" CreationDate="2014-08-02T22:40:46.257" Score="14" ViewCount="4343" Body="&lt;p&gt;Let's say I go to the gym and lift some weights an hour.  During this time my arms will grow due to the &quot;pump&quot; -- the extra blood rushing in to feed the muscles.  For example, I've measured about 2-3 centimeters increase just in the diameter of the upper arm (bicep+tricep).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But where did this blood come from?  Also, if my arms got bigger, since I'm the same weight that means some part of my body must have gotten smaller, right?&lt;/p&gt;&#xA;" OwnerUserId="8591" LastEditorUserId="86" LastEditDate="2014-08-03T09:00:06.317" LastActivityDate="2015-09-20T19:43:48.750" Title="Where does extra blood come from to fill your muscles during exercise?" Tags="&lt;physiology&gt;&lt;muscles&gt;&lt;blood-circulation&gt;&lt;congestion&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="20175" PostTypeId="2" ParentId="20170" CreationDate="2014-08-02T23:37:00.753" Score="2" Body="&lt;p&gt;Pressing on the chest changes the concentration of dissolved gasses in the blood stream. Your brain reacts due to excessive oxygen in the blood. This is oxygen toxicity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why the brain generates vivid imagery when unconscious is a big topic. There's a theory that correlates dreams with a lack of cognitive stimulation. This is called autostimulation and may function as pseudo-learning when external stimulation is low. For children it's thought this helps them learn when they can't communicate. We may dream less as we age because adults are highly stimulated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hypothesize dreaming while knocked unconscious has side effects which mimic dreaming. &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-02T23:44:28.487" LastActivityDate="2014-08-02T23:44:28.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20176" PostTypeId="1" AcceptedAnswerId="20200" CreationDate="2014-08-02T23:53:48.990" Score="6" ViewCount="486" Body="&lt;p&gt;There are many plants and animals named for the naturalist Charles Darwin, such as Darwin's Frog &lt;em&gt;(Rhinoderma darwinii)&lt;/em&gt;, but which were named by him? I'm finding it difficult to find such a list.&lt;/p&gt;&#xA;" OwnerUserId="8564" LastEditorUserId="3952" LastEditDate="2014-08-04T12:38:41.307" LastActivityDate="2014-08-05T21:58:01.790" Title="Which species were first described by Charles Darwin?" Tags="&lt;taxonomy&gt;&lt;nomenclature&gt;&lt;history&gt;&lt;species&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20177" PostTypeId="1" AcceptedAnswerId="20179" CreationDate="2014-08-03T01:36:53.903" Score="7" ViewCount="618" Body="&lt;p&gt;I barely know anything about biology and realize that this might be a stupid question, but I'll ask anyway! I know that species &quot;transform&quot; into other species through the process of evolution. Many species around today still co-exist with the species in which they evolved from, right? Actually, is it correct to say that all species coexist with some common ancestor? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, my question is; if the monkeys that we evolved from are still around today, then where are all the in-between species. Are there still early humans, like Neanderthal's or Hominids or what have you still roaming around some where?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If all early forms of humans are gone, is it because the more modern humans had a greater evolutionary advantage? But wouldn't these less modernized humans have those same advantages over the less evolved monkeys? &lt;/p&gt;&#xA;" OwnerUserId="8592" LastActivityDate="2014-08-05T08:02:13.540" Title="Extinction of species" Tags="&lt;evolution&gt;&lt;speciation&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20178" PostTypeId="2" ParentId="20174" CreationDate="2014-08-03T01:45:52.820" Score="2" Body="&lt;p&gt;If you stand up too quickly, you get a head rush. One way to counteract the symptoms of the head rush is to contract your leg muscles really intensely. This forces blood out of your legs and into the rest of your circulation, including your head. This is actually a tip my family doctor told me that I've always remembered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As mentioned in the links below working out a muscle group causes excess blood flow to these areas which could cause the blood vessels to dilate, causing the muscles in these areas to swell and appear larger. I now realize this has nothing to do with the head rush item I mentioned above, but still may be a useful piece of advice if you every get a head rush!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1479005/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1479005/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.livestrong.com/article/75670-swell-after-workout/&quot; rel=&quot;nofollow&quot;&gt;http://www.livestrong.com/article/75670-swell-after-workout/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8592" LastEditorUserId="8592" LastEditDate="2014-08-05T00:32:46.383" LastActivityDate="2014-08-05T00:32:46.383" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20179" PostTypeId="2" ParentId="20177" CreationDate="2014-08-03T02:03:05.127" Score="8" Body="&lt;p&gt;This is a common misconception about evolution, many skeptics ask something along the lines of &quot;If humans evolved from monkeys, why are there still monkeys?&quot; The answer is that evolution is not a linear process of one species becoming the next species becoming the next. Species branch off much more like a tree. At some point in the past the last common ancestor of humans and monkeys split into two directions, one that became the apes including humans, and one that became modern monkeys. Evolution did not stop for either branch, but only our branch became humans, after several more branchings. Sometimes species adapt and evolve without major changes in morphology, for example modern turtles look a lot like turtles from 100 million years ago, but this doesn't mean they haven't evolved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The intermediate species are often lost with time as environmental conditions and competition changes. For example, if one early human group found itself competing with a slightly more advanced human group with better tools, the more primitive group would have trouble getting enough food and eventually die off, leaving the more advanced group to pass its genes on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, if those more primitive humans were more suited to a particular niche, they could survive there. Lets say they could climb trees better ( assume REALLY primitive ancestors, barely out of the forest ), they might survive in the forested areas while the more advanced groups become dominant in the grasslands. Something like this is why our ancestors didn't totally displace monkeys, the monkeys were better suited for their forested ecosystem. If those same monkeys had to live on dry savannas we would have eaten them all long ago.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-03T02:03:05.127" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20180" PostTypeId="2" ParentId="11039" CreationDate="2014-08-03T02:43:03.533" Score="5" Body="&lt;p&gt;This entire post is taken from odd thinking:&#xA;&lt;a href=&quot;https://skeptics.stackexchange.com/questions/10309/do-japanese-people-have-a-lower-body-temperature-than-caucasians&quot;&gt;https://skeptics.stackexchange.com/questions/10309/do-japanese-people-have-a-lower-body-temperature-than-caucasians&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There may be a difference, depending on whether you are talking about internal or skin temperatures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This study compared 9 Japanese men to the results of a similar study done in Ohio with Caucasian men:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.springerlink.com/content/m111258v54503605/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Thermoregulatory responses to heat and exercise in Japanese and Caucasians&lt;/a&gt;&#xA;K. Ohara, N. Okuda and S. Takaba, International Journal of Biometeorology, Volume 19, Number 2 (1975), 99-107, DOI: 10.1007/BF01463865&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The subjects were made to walk on a treadmill for 2 hours, in carefully controlled conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There were a  number of differences in the amount and composition of their sweat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Internally, they maintained the same body temperature: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There were no differences in rectal temperature or heart rate, both at the period of equilibrium rectal temperature and at the end of the walk.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, there were differences in the skin temperature - perhaps not in the direction you were expecting:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mean skin temperature during the walk was significantly higher in Japanese than in Caucasians. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They concluded that: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the Japanese group was better heat acclimatized than Caucasians, though the two groups were considered to have been naturally heat exposed by season to the same extent.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;While this result is suggestive, I don't find it to be definitive, as the caucasians were tested at a different time in a different facility, making them a poor control. Also the sample sizes were small, in an area which may vary by age and other factors.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr/&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Joo-Young Lee, Hitoshi Wakabayashi, Titis Wijayanto, Nobuko Hashiguchi, Mohamed Saat and Yutaka Tochihara &lt;a href=&quot;http://www.springerlink.com/content/d578773105k772kt/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ethnic differences in thermoregulatory responses during resting, passive and active heating: application of Werner’s adaptation model&lt;/a&gt; European Journal of Applied Physiology, Volume 111, Number 12 (2011), 2895-2905, DOI: 10.1007/s00421-011-1912-5&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This study didn't involve Caucasians, but compared Malaysians (&quot;tropical natives&quot;) and Japanese males.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They put them under a number of different scenarios, such as soaking their feet in a warm bath, but also at resting.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The results saw that: tropical natives had a higher resting rectal temperature and lower hand and foot temperatures at rest [...]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="-1" LastEditorDisplayName="user1357" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2014-08-03T18:19:37.870" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20181" PostTypeId="2" ParentId="20174" CreationDate="2014-08-03T08:55:33.287" Score="7" Body="&lt;h2&gt;How does extra blood come from to fill your muscles during exercise?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Blood pumps (blood) and sucks (lymph). &#xA;There are many pumps in our body&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;thoracic pump&lt;/li&gt;&#xA;&lt;li&gt;smooth musculature&lt;/li&gt;&#xA;&lt;li&gt;respiratory pump&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which work together to provide the blood to the peripheral circulation. &#xA;These pumps provide us Pulse, Vasomotor tone and Respiratory waves which when act together can lead to local hyperemia or congestion; see my answer only about these waves &lt;a href=&quot;https://biology.stackexchange.com/a/19304/86&quot;&gt;here&lt;/a&gt; in the thread &lt;em&gt;What does irregular heartbeat mean in simple language&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By Starling law, anything that goes inside the heart goes out from there. &#xA;See this answer about &lt;a href=&quot;https://biology.stackexchange.com/a/19488/86&quot;&gt;elevated position on the venous return&lt;/a&gt; which is similar to the the exercise on the venous return. &#xA;Smooth musculature accommodates blood to the venous return. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Why your muscle gets bigger during exercise?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There are many reasons which can be explained by Frank-Starling principle and Fick's law. &#xA;They lead either to &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;hyperemia (increased local blood flow) or&lt;/li&gt;&#xA;&lt;li&gt;congestion&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;because of &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;protein intake before the exercise&lt;/li&gt;&#xA;&lt;li&gt;increased sympaticus (decreased parasympaticus; yes, sympathetic tone in digestive truct and some other systems is down-regulated) and blood flow through the muscle (see the above &lt;a href=&quot;https://biology.stackexchange.com/a/19488/86&quot;&gt;thread&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;unstretched muscle can have congestion during exercise which is felt as hard muscle, also long after the training&lt;/li&gt;&#xA;&lt;li&gt;too regular exercising without rest can also lead to congestion&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;in the spaces described in my earlier answers like &lt;a href=&quot;https://biology.stackexchange.com/a/16159/86&quot;&gt;here&lt;/a&gt; about &lt;em&gt;What can cause the swelling in high protein diet of Whey proteins&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0m6i2.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where explanations in my earlier answer. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Where does the extra blood come from to fill your muscles during exercise?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;From your body (See Cornelius' &lt;a href=&quot;https://biology.stackexchange.com/a/20182/86&quot;&gt;answer&lt;/a&gt; for specific locations)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;veins 50-60%&lt;/li&gt;&#xA;&lt;li&gt;spleen &lt;/li&gt;&#xA;&lt;li&gt;liver&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;under physiologic fine regulation where heart is the main pump (positive gradient) while its sucking effect (negative gradient; lymph) keeps homeostasis stable for exercising muscles to maintain hyperemia supported by rapid adaptive smooth musculature, vasomotor tone and respiratory pumps (three types of waves).  &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-08-05T07:57:05.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20182" PostTypeId="2" ParentId="20174" CreationDate="2014-08-03T09:37:56.763" Score="11" Body="&lt;p&gt;The blood comes from the body's reservoirs:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;spleen (mostly erythrocytes) [1]&lt;/li&gt;&#xA;&lt;li&gt;liver [2]&lt;/li&gt;&#xA;&lt;li&gt;veins (probably the most important blood resevoir as they contain 50-60 % of the volume) [3]&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In pathological situations, if hypovolemia occurs, blood can also come from:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;splachnic vascular bed [5]&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;But what attracts the blood into the muscle? The phenomenon is called active hyperemia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Active hyperemia is the &lt;em&gt;increase in organ blood flow (hyperemia) that is associated with increased metabolic activity of an organ or tissue.&lt;/em&gt; An example of active hyperemia is the increase in blood flow that accompanies muscle contraction, which is also called &lt;strong&gt;exercise or functional hyperemia&lt;/strong&gt; in skeletal muscle. Blood flow increases because the increased oxygen consumption of during muscle contraction stimulates the production of vasoactive substances that dilate the resistance vessels in the skeletal muscle [4].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;em&gt;&lt;a href=&quot;http://jap.physiology.org/content/92/5/2071&quot; rel=&quot;noreferrer&quot;&gt;The human spleen as an erythrocyte reservoir in diving-related interventions.&lt;/a&gt;&lt;/em&gt; Kurt Espersen, Hans Frandsen, Torben Lorentzen, Inge-Lis Kanstrup, Niels J. Christensen. Journal of Applied PhysiologyMay 2002,92(5)2071-2079;DOI: 10.1152/japplphysiol.00055.2001&lt;/li&gt;&#xA;&lt;li&gt;Lautt WW, Greenway CV. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/961879&quot; rel=&quot;noreferrer&quot;&gt;Hepatic venous compliance and role of liver as a blood reservoir.&lt;/a&gt; Am. J. Physiol. 1976 Aug;231(2):292-5. PubMed PMID: 961879. &lt;/li&gt;&#xA;&lt;li&gt;Michael J. Gregory, Ph.D. &lt;em&gt;&lt;a href=&quot;https://b51ab7d9e5e1e7063dcb70cee5c33cf7f4b7bad8.googledrive.com/host/0Bx6hk6AUBHxDc2d4TDJZTFIyMGs/files/Bio%20102/Bio%20102%20lectures/Circulatory%20System/circulat.htm&quot; rel=&quot;noreferrer&quot;&gt;The Circulatory System.&lt;/a&gt;&lt;/em&gt; Licensed under CC-BY-NC-SA-3.0&lt;/li&gt;&#xA;&lt;li&gt;Richard E. Klabunde, PhD. &lt;em&gt;Cardiovascular Physiology Concepts. Active Hyperemia.&lt;/em&gt; Available from &lt;a href=&quot;http://www.cvphysiology.com/Blood%20Flow/BF005.htm&quot; rel=&quot;noreferrer&quot;&gt;http://www.cvphysiology.com/Blood%20Flow/BF005.htm&lt;/a&gt; (accessed 03.08.2014)&lt;/li&gt;&#xA;&lt;li&gt;Blaber AP, Hinghofer-Szalkay H, Goswami N. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23305001&quot; rel=&quot;noreferrer&quot;&gt;Blood volume redistribution during hypovolemia.&lt;/a&gt; Aviat Space Environ Med. 2013 Jan;84(1):59-64. PubMed PMID: 23305001. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2015-09-20T19:43:48.750" LastActivityDate="2015-09-20T19:43:48.750" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20183" PostTypeId="2" ParentId="11039" CreationDate="2014-08-03T10:19:33.027" Score="8" Body="&lt;p&gt;Factors that can lower body temperature:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;low environment temperature&lt;/li&gt;&#xA;&lt;li&gt;low metabolic rate&lt;/li&gt;&#xA;&lt;li&gt;hypothyroidism&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I couldn't find any relevant study addressing the Japanese people situation, but:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There is significant variation in metabolic rate in humans, independent of differences in body size, body composition, age, and gender. Although it has been generally held that the normal human &quot;set-point&quot; body temperature is 37 degrees C, these interindividual variations in metabolic rate also suggest possible variations in body temperature [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And here's a factor that increases body temperature:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The present experiment investigated the effects of skin pressure by foundation garments (girdle and brassiere) on the circadian rhythms of core temperature and salivary melatonin. [...] The results suggest that skin pressure by clothing could markedly suppress the nocturnal elevation of salivary melatonin, resulting in an increase of rectal temperature [2].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Whether there are differences between Japanese and other people in metabolic rate and /or clothing behavior remains unclear. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Rising R, Keys A, Ravussin E, Bogardus C. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1415692&quot;&gt;Concomitant interindividual variation in body temperature and metabolic rate.&lt;/a&gt; Am. J. Physiol. 1992 Oct;263(4 Pt 1):E730-4. PubMed PMID: 1415692. &lt;/li&gt;&#xA;&lt;li&gt;Lee YA, Hyun KJ, Tokura H. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11128295&quot;&gt;The effects of skin pressure by clothing on circadian rhythms of core temperature and salivary melatonin.&lt;/a&gt; Chronobiol. Int. 2000 Nov;17(6):783-93. PubMed PMID: 11128295. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-08-03T10:19:33.027" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20184" PostTypeId="2" ParentId="20177" CreationDate="2014-08-03T11:47:07.697" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;If all early forms of humans are gone, is it because the more modern&#xA;  humans had a greater evolutionary advantage?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you take an environment where species dwell, three things could have happened:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The population got smaller and smaller, in a given environment, and then bam the last ones disappeared without producing any offspring. This is because population as a whole wasn't  reproducing as fast as they disappeared, for a variety of reasons. By disappeared I mean: went away to other environment or died out.&lt;/li&gt;&#xA;&lt;li&gt;In another environment, so much changes had spread through the population that at one time the new offspring was born with their genotype now &quot;too much&quot; different and thus incompatible. By &quot;too much&quot; I mean this: they could still mate with both partners from their population and with &quot;less changed&quot; neighboring populations, but they could only produce a &lt;strong&gt;fertile offspring&lt;/strong&gt; with former but &lt;strong&gt;not&lt;/strong&gt; with the latter. We nowadays refer to such situation as &quot;they became new species&quot;. From this point they obviously couldn't spread &quot;their&quot; genetic changes anymore to other environments via reproduction (spreading parts of genotypes). Their offspring would be infertile. They only could spread &quot;their&quot; genetic changes by sending whole groups of folks (complete genotypes) to other environment to try and cope there. And sometimes to kill others interfering, because, hey, that's what living creatures sometimes just do. &lt;/li&gt;&#xA;&lt;li&gt;The population lived without &quot;too much&quot; change in the genotype and still exists today in the given environment. Without &quot;too much&quot; change means they were unchanged or rather changed slow enough that at any given time they could leak their changes to other populated environments via reproduction (they kept being the same species as their neighbors).&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I have written about genetic &quot;changes&quot;. You call these &quot;advantages&quot; and even &quot;modernizations&quot;, but for the sake of argument it just doesn't matter (and only blurs the picture with the unnecessary concept of &quot;superiority&quot;). Advantages in one environment are disadvantages in another.&lt;/li&gt;&#xA;&lt;li&gt;I use &quot;environment&quot; here for simplicity, but a more proper term would be a &quot;habitat&quot;.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;We don't observe any early humans today. It seems that all their populations have met one of these two former fates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, you tend to overuse high-level abstract terms that distract you from thinking what have actually happened at low level. &quot;Evolution&quot; does not &quot;act&quot; on any &quot;scenario&quot;. This is just a bit too much of anthropomorphism.&lt;/p&gt;&#xA;" OwnerUserId="8593" LastEditorUserId="8593" LastEditDate="2014-08-03T11:58:36.047" LastActivityDate="2014-08-03T11:58:36.047" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20186" PostTypeId="2" ParentId="20176" CreationDate="2014-08-03T14:40:08.427" Score="9" Body="&lt;p&gt;I don't know if these are his earliest descriptions but Darwin did describe several species of Planaria, such as &lt;em&gt;Planaria vaginuloides&lt;/em&gt;, &lt;em&gt;P. oceania&lt;/em&gt;, plus a new genus, &lt;em&gt;Diplanaria&lt;/em&gt; in 1844.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://darwin-online.org.uk/content/frameset?itemID=F1669&amp;amp;viewtype=text&amp;amp;pageseq=1&quot;&gt;Darwin, C. R. 1844. Brief descriptions of several terrestrial planariæ, and of some remarkable marine species, with an account of their habits. Annals and Magazine of Natural History 14 (October): 241-251, 1 plate.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps his best known taxonomic work is on barnacles (Cirripedia). He described several species in his monograph first monograph on the group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://darwin-online.org.uk/content/frameset?itemID=F339.1&amp;amp;viewtype=text&amp;amp;pageseq=1&quot;&gt;Darwin, C. R. 1851 [=1852]. A monograph of the sub-class Cirripedia, with figures of all the species. The Lepadidæ; or, pedunculated cirripedes.. London: The Ray Society. Volume 1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first monograph was followed by three other monographs on living and fossil Cirripedia. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe that most of his writings after publication of &lt;em&gt;On the Origin of Species&lt;/em&gt; focused on expanding his evolutionary ideas rather than on descriptions of new species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read nearly all of Darwin's writings online at &lt;a href=&quot;http://darwin-online.org.uk&quot;&gt;http://darwin-online.org.uk&lt;/a&gt;. With careful searching you can find all (or nearly all) species descriptions.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-08-03T14:48:01.550" LastActivityDate="2014-08-03T14:48:01.550" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20187" PostTypeId="2" ParentId="20165" CreationDate="2014-08-03T14:59:30.737" Score="3" Body="&lt;p&gt;Scutella refers to shield or plate-like structure on animals (&lt;a href=&quot;http://dictionary.reference.com/browse/scutella?s=t&quot; rel=&quot;nofollow&quot;&gt;dictionary.com&lt;/a&gt;), such as the scutes of a turtle shell.  I have never seen reference to scutes or scutella or anything similar on any type of deer, including reindeer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have not seen the movie so I do not know the context of usage. My gut reaction is the person was trying to make something sound important or &quot;scientific&quot; when a much simpler (and perhaps more accurate) word would have sufficed.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-03T14:59:30.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20188" PostTypeId="2" ParentId="20177" CreationDate="2014-08-03T14:59:52.110" Score="2" Body="&lt;p&gt;I think other answers have explained natural selection, but I think it is also important to note that species boundaries are applied in retrospect. This sounds blindingly obvious, but when presented by skulls from two species, such as &lt;em&gt;Homo erectus&lt;/em&gt; and &lt;em&gt;Homo sapiens&lt;/em&gt;, many will then ask where the evidence is for the species that came between those two. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several reasons why you can't see all of these in-between forms: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;The fossil record is imperfect&lt;/strong&gt;. Although there are no longer any &quot;missing links&quot; in the fossil record for the evolution of humans from our most recent common ancestor with chimpanzees, not every change in skeleton shape has been preserved for us to look at.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Species boundaries are applied retrospectively&lt;/strong&gt;. This means that when we find a new set of bones that seem to be in-between two species, we give these bones a new species name, because they clearly don't belong to the other species we've already identified. The bones actually represent one of the &quot;in-between&quot; forms that people are asking about, but we can't just label it &quot;intermediate&quot; or &quot;missing link&quot;. It has to be categorised as a new species or sub-species.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;You're not technically looking for an &quot;intermediate&quot;&lt;/strong&gt;. It's not that chimpanzees are an &quot;intermediate&quot; between humans and some ancestral species. It's that humans and chimpanzees share a common ancestor. When you see a pictures of a neanderthal, they might superficially look like an intermediate between humans and chimpanzees, a sort of hybrid between the two, but that's not quite right. It's not that chimpanzees eventually became neanderthals, which eventually became modern humans. It's actually that humans and neanderthals &lt;em&gt;share a common ancestor&lt;/em&gt; and that ancestor is &lt;em&gt;no longer around&lt;/em&gt; for reasons given in other answers. Similarly, neanderthals and chimpanzees share a common ancestor that is now extinct. My point is that if you're looking for something like a &quot;crocatoo&quot; that's a hybrid between a crocodile and cockatoo, you won't find it. Yes, crocodiles and cockatoos share a common ancestor somewhere in their family trees, but there's no reason that it will look half like one species and half like the other! It might look nothing like either of them!&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;If you're looking for more information on evolution, I'd highly recommend &lt;a href=&quot;http://www.amazon.co.uk/The-Greatest-Show-Earth-Evolution/dp/B00CF665R4/ref=sr_1_2?ie=UTF8&amp;amp;qid=1407077784&amp;amp;sr=8-2&amp;amp;keywords=The+Greatest+Show+on+Earth%3A+The+Evidence+for+Evolution&quot; rel=&quot;nofollow&quot;&gt;&quot;The Greatest Show on Earth&quot; by Richard Dawkins&lt;/a&gt;. If you want citations for the points I make, you'll find all of it in there. It explains this stuff quite clearly, with ample evidence to back it up (assuming you can put up with his occasional rants about young earth creationists...)&lt;/p&gt;&#xA;" OwnerUserId="1017" LastEditorUserId="1017" LastEditDate="2014-08-03T15:43:43.687" LastActivityDate="2014-08-03T15:43:43.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20189" PostTypeId="2" ParentId="20163" CreationDate="2014-08-03T15:28:54.367" Score="6" Body="&lt;p&gt;There may be an evolutionary purpose to underarm perspiration, as alluded to in the &quot;hidden hint&quot; link of @DevashishDas, and also hinted at by the answer by @Chris. The apocrine sweat glands of our armpits produce steroids. One group of steroids secreted by the axillary apocrine glands are &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Pheromone#Axillary_steroids&quot;&gt;sex pheromones&lt;/a&gt;.  Although we may not consciously notice the chemical odors of sex pheromones, they do likely affect our behaviors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/260/1359/245.short&quot;&gt;Wedekind et al.&lt;/a&gt; showed that females showed distinct preferences for certain male odors. Women tended to prefer the odors of males that were genetically &lt;em&gt;different&lt;/em&gt; at the major histocompatibility complex (MHC) loci, a group of genes associated with our immune response system. Greater genetic variation of MHC genes generally translates to greater ability to combat disease.  Females that select males that are genetically different at the MHC would produce offspring with greater genetic variability at the complex, and therefore more likely to have greater resistance to disease or ability to fight disease. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These results suggest that the pheromones secreted in underarm perspiration is a sexually selected trait in humans. If so, underarm perspiration would have an evolutionary (fitness) advantage.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-03T15:28:54.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20190" PostTypeId="2" ParentId="20166" CreationDate="2014-08-03T16:26:17.833" Score="1" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uAbWq.png&quot; alt=&quot;pCAMBIA1200&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/efjj7.png&quot; alt=&quot;pCAMBIA0380&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rIJ5D.png&quot; alt=&quot;ori site description&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please check and tell me and how do I go about the co-transformation of rice using Agrobacterium starting from E.coli&lt;/p&gt;&#xA;" OwnerUserId="8596" LastActivityDate="2014-08-03T16:26:17.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20191" PostTypeId="1" AcceptedAnswerId="20192" CreationDate="2014-08-03T18:25:25.597" Score="6" ViewCount="12538" Body="&lt;p&gt;There appears to be a lot of material on the internet claiming that viruses can be only seen with electron microscopes, and not with light microscopes. To the contrary, for example &lt;a href=&quot;http://www.nature.com/nature/journal/v162/n4111/abs/162251a0.html&quot;&gt;this old paper published in Nature&lt;/a&gt; states that viruses &lt;em&gt;can be seen&lt;/em&gt; using phase-contrast (light) microscopy. Who's correct? What is the smallest thing I can see using a phase-contrast microscope?&lt;/p&gt;&#xA;" OwnerUserId="8597" LastActivityDate="2017-04-17T09:02:59.277" Title="Is it true that viruses cannot be seen with phase-contrast microscopy?" Tags="&lt;microscopy&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20192" PostTypeId="2" ParentId="20191" CreationDate="2014-08-03T18:40:56.750" Score="5" Body="&lt;p&gt;It is true for most viruses. They have a size of roughly 1/100 of bacteria (or smaller), so they are too small to be seen in light microscopy. According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Optical_microscope&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt; the maximum limit with light microscopy is around 1500x magnification (or making structures, which are at least around 200nm in size visible). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lot of viruses are smaller, for example the influenza A virus is around 80-120nm, the HIV virus around 120nm and the rhinovirus which causes the common cold around 30nm. They would only be visible in electon microscopy. The measles virus on the other hand has between 350 and 400nm and should be visible in light microscopy. However, since you are very close to the region where you reach the diffraction limit for visible light, it is usually not used very much.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-03T18:40:56.750" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20193" PostTypeId="2" ParentId="20177" CreationDate="2014-08-03T20:01:51.210" Score="-1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I know that species &quot;transform&quot; into other species through the process&#xA;  of evolution.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't think you are thinking about that right.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We have a population of organisms that are breeding together.  We humans label that a 'species'.  That population has descendants, and over time, the population changes, and when we humans think that the new population look sufficiently different from the old, we label them a new species.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many species around today still co-exist with the species in which&#xA;  they evolved from, right?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You might have founder situations, where a small sub population breaks off and inhabits a new environment, and changes a great deal more over time than the original population does, such that we continue to label the original population the same species, while we label the offshoot a different species.  But I think what happens more often is that the alleles that cause humans to label a population a distinct 'species' dwindle to nothing in the descendants, and then we say that the original species is extinct, replaced by the new one.  but that's a matter of labels: there is continuity in that the new 'species' is just the descendants of the older one.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Actually, is it correct to say that all species coexist with some&#xA;  common ancestor?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No.  Can you even name any examples where you think this is true?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;if the monkeys that we evolved from are still around today,&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What on earth makes you think that's remotely true?  For one thing we aren't descended from monkeys.  We are descended from primates that were more like apes, not monkeys.  There is no living population of primates that we would categorize as being the same species as that non-homo sapiens ancestor population.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Are there still early humans, like Neanderthal's or Hominids or what&#xA;  have you still roaming around some where?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm confused how you think an organism or a population existing in the 21st century could be &quot;early&quot;. All the hominids walking around today are members of homo sapiens sapiens. &lt;/p&gt;&#xA;" OwnerUserId="5148" LastEditorUserId="6" LastEditDate="2014-08-05T08:02:13.540" LastActivityDate="2014-08-05T08:02:13.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20194" PostTypeId="1" AcceptedAnswerId="20196" CreationDate="2014-08-03T20:48:11.240" Score="14" ViewCount="8766" Body="&lt;p&gt;When I was a kid, I was told not to ever touch a butterflies wing, as it would lose its ability to fly. This was because of some dust which was supposed to be in place on the wings and when disturbed it had the described consequences. I doubt at least the story about the dust, which sounds a bit too much like &quot;fairy dust&quot;, but am I right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What damage will be done by touching a butterfly?&lt;/p&gt;&#xA;" OwnerUserId="8598" LastEditorDisplayName="user31031" LastEditDate="2017-05-20T15:49:22.647" LastActivityDate="2017-05-20T15:49:22.647" Title="Can butterflies still fly after their wings are touched?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20195" PostTypeId="1" AcceptedAnswerId="20199" CreationDate="2014-08-03T21:13:10.227" Score="12" ViewCount="8394" Body="&lt;p&gt;My dad asked this question when I explained some circumstances surrounding &lt;em&gt;Homo sapiens&lt;/em&gt; survival against all odds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We know there is only one hominid species left in the world, &lt;em&gt;Homo sapiens&lt;/em&gt;. We also know that there are only 6 other species of great apes left: 2 species of chimpanzees, 2 species of gorillas, and 2 species of orangutans. These 7 species are the last remaining in the family Hominidae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All the other hominids besides &lt;em&gt;Homo sapiens&lt;/em&gt; died out tens of thousands of years ago, and we believe the reason our ancestors survived is because we were more &quot;adaptable&quot;, meaning we were not restricted to a single environment but could survive in many others. This is the reason we later spread out all over the world, and probably why we gained &quot;sapience&quot; and are able to contemplate these grim circumstances.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At one point, following the eruption of the Toba volcano 70,000 years ago, there were between 1,000 and 10,000 mating pairs of &lt;em&gt;Homo sapiens&lt;/em&gt; left, though there may have been other hominid species alive at the time. My dad asked, if the hominids faced such grueling environments and all but a few died, why did the great apes fare any better? Why are there 6 extant non-human Hominidae species left, but only 1 hominid species?&lt;/p&gt;&#xA;" OwnerUserId="8599" LastEditorUserId="8517" LastEditDate="2014-08-04T03:35:27.770" LastActivityDate="2016-09-11T17:35:07.807" Title="Why Did 6 Great Ape Species Survive But Only 1 Hominid Species?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20196" PostTypeId="2" ParentId="20194" CreationDate="2014-08-03T21:38:27.700" Score="19" Body="&lt;p&gt;Both the Forewing as well as the Hindwing of Butterflies are made of thin chitin structures which are pretty thin and sensitive. If you touch the wing with to much force, it may break.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then the upper side of the butterfly wing is covered with small scales - what you called the &quot;dust&quot;. This can be seen in this figure (from &lt;a href=&quot;http://animals.howstuffworks.com/insects/butterfly-wing-fragility1.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rFJtw.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and also in this electron microscopy image (from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Scale_%28Lepidopteran_anatomy%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/N3KFU.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The scales have a number of functions, they are responsible for the butterflies color and pattern (which are important for finding mating partners as well as for camouflage) and they also seem to play a role in insulation and thermo regulation (see &lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00379348?LI=true&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for more details).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The scales play also a role in making the wings stronger and help improving the flight characteristics. When flying upwards the get pressed to the wing and act aerodynamically, what the wings are in downward motion, they help stabilizing the flight. See here for more details: &quot;&lt;a href=&quot;http://dissertations.ub.rug.nl/faculties/science/2008/m.a.giraldo/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Butterfly wing scales : pigmentation and structural properties&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the scales get lost during flying and collecting nectar, so taken together, loss of a big number of them will influence the flight characteristics of a butterfly. However, I think it is much more likely that such a rude treatment will damage the wings, which is obviously more harmful. So light touches will not do harm, more severe will.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-03T21:38:27.700" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20197" PostTypeId="1" CreationDate="2014-08-03T23:44:42.637" Score="1" ViewCount="92" Body="&lt;p&gt;I want to download a comprehensive table of protein names from uniprot.org.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More precisely, I want to generate a tab-delimited table consisting of the &lt;code&gt;id&lt;/code&gt; (accession), &lt;code&gt;entry name&lt;/code&gt;, and &lt;code&gt;protein names&lt;/code&gt; &quot;columns&quot; from the UniProtKB database.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to get these three columns/fields for all 80M records in UniProtKB, and I don't want to specify all those Uniprot IDs through, e.g., a bazillion URL-encoded queries.  Also, I need to do this from a host that I can access only through a text interface, which basically rules out browser-based solutions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just spent a couple of hours going back-and-forth over the Uniprot site's docs, and I can find nothing useful.  The Perl example given &lt;a href=&quot;http://www.uniprot.org/faq/28#batch_retrieval_of_entries&quot; rel=&quot;nofollow&quot;&gt;there&lt;/a&gt;&lt;sup&gt;1&lt;/sup&gt; shows how to download &lt;em&gt;full records&lt;/em&gt;, but downloading every full record from UniProtKB would be too slow and onerous to be considered&lt;sup&gt;2&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know how to modify the Perl example (or any other way) to download only the three desired columns from UniProtKB?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;sup&gt;1&lt;/sup&gt; You need to click on the phrase &quot;Perl example&quot; to see the code.&lt;/sub&gt;&lt;br/&gt;&#xA;&lt;sub&gt;&lt;sup&gt;2&lt;/sup&gt; I downloaded a small test sample of 1000 full records, I found that the size of the information I actually want from those records is only 0.2% of the total.  IOW, downloading the full records would take up ~500x as long as downloading only the desired information.&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="3778" LastActivityDate="2014-08-04T06:05:41.390" Title="How to selectively download 3 fields from every record in UniProtKB?" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20198" PostTypeId="2" ParentId="13455" CreationDate="2014-08-04T02:49:18.783" Score="1" Body="&lt;p&gt;Salt draws water out of cells via the process of osmosis. Essentially, water moves across a cell membrane to try to equalize the salinity or concentration of salt on both sides of the membrane. If you add enough salt, too much water will be removed from a cell for it to stay alive or reproduce. Organisms that decay food and cause disease are killed by a high concentration of salt. A concentration of 20% salt will kill bacteria. Lower concentrations inhibit microbial growth, until you get down to the salinity of the cells, which may have the opposite and undesirable effect of providing ideal growing conditions! Salt can also be used when you are preserving a product via fermentation. The salt will inhibit the growth of moulds and yeasts. While some moulds and yeast are certainly needed during the fermentation process, by using small amounts of salt, it is possible to regulate and stabilise this process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is only possible to do this though if you are using salt that does not contain ‘free-flowing’ agents or iodine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Refer to :&lt;a href=&quot;https://suite.io/rachel-tsoumbakos/xpx288&quot; rel=&quot;nofollow&quot;&gt;https://suite.io/rachel-tsoumbakos/xpx288&lt;/a&gt; for details.&lt;/p&gt;&#xA;" OwnerUserId="8216" LastActivityDate="2014-08-04T02:49:18.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20199" PostTypeId="2" ParentId="20195" CreationDate="2014-08-04T02:54:43.250" Score="20" Body="&lt;p&gt;Determining why one species (or group of species survived) while others did not can be difficult to answer, but I can offer one possible explanation for the genus &lt;em&gt;Homo&lt;/em&gt;: competition. Competition between similar species is one possibility. Consider for example gorillas or chimps. The two species of gorillas occupy different habitats so they rarely compete with each other for resources (food, water, shelter, etc.). The two species of chimpanzees have non-overlapping ranges (or minimally so) so again they do not compete for resources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chimps and gorillas do overlap with each other for parts of their range and even potentially use the same resources, although no competition for resources has been observed (see &lt;a href=&quot;http://pin.primate.wisc.edu/factsheets/entry/gorilla&quot;&gt;this primate factsheet&lt;/a&gt; and McNeilage 2001). The same applies for the orangutans, which lives on two different southeast Asian islands.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genus &lt;em&gt;Homo&lt;/em&gt; is an entirely different story. As you may know, &lt;em&gt;Homo&lt;/em&gt; first evolved in east central Africa. The first species to leave Africa and disperse across Europe and Asia was &lt;em&gt;Homo erectus&lt;/em&gt;. This migration out of Africa happened as early as aout 1.8 million years ago. &lt;em&gt;Homo sapiens&lt;/em&gt; had not yet evolved. However, while &lt;em&gt;H. erectus&lt;/em&gt; was establishing itself across Europe and Asia, populations still in Africa continued to evolve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Modern &lt;em&gt;Homo sapiens&lt;/em&gt; evolved in central Africa perhaps about 250-200,000 years ago and dispersed out of Africa about 100,000 years ago. &lt;em&gt;Homo sapiens&lt;/em&gt; also dispersed across Europe and Asia. Both &lt;em&gt;H. erectus&lt;/em&gt; and &lt;em&gt;H. sapiens&lt;/em&gt; co-occurred across parts of their range. Some have argued (Stringer and Andrews, among others, I believe but I'll have to be at work before I can verify ths reference) that &lt;em&gt;H. sapiens&lt;/em&gt; outcompeted &lt;em&gt;H. erectus&lt;/em&gt;, leading to its eventual extinction by competition. They occurred together and used the same resources, so &lt;em&gt;H. sapiens&lt;/em&gt; could have caused the extinction of &lt;em&gt;H. erectus&lt;/em&gt;. This has been called the replacement hypothesis. The later evolving species (&lt;em&gt;H. sapiens&lt;/em&gt;) replaced the earlier evolving &lt;em&gt;H. erectus&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, &lt;a href=&quot;http://www.nature.com/nature/journal/v416/n6876/abs/416045a.html&quot;&gt;Templeton (2002)&lt;/a&gt; has argued that the two species interbred so the species became integrated rather replaced (if I am interpreting him correctly).  While I don't dispute the possibility of interbreeding, I am skeptical of Templeton's complete dismissal of replacement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Complicating the picture is &lt;em&gt;H. neanderthalensis&lt;/em&gt;. Genetic evidence published by &lt;a href=&quot;http://www.sciencemag.org/content/328/5979/710.full&quot;&gt;Green et al. (2010)&lt;/a&gt; suggests that Neanderthals diverged from &lt;em&gt;H. sapiens&lt;/em&gt; (in central Africa) between 800,000-500,000 years ago and also dispersed out of Africa.  They also provided evidence of interbreeding between &lt;em&gt;H. sapiens&lt;/em&gt; and &lt;em&gt;H. neanderthalensis&lt;/em&gt; in Europe.  Modern &lt;em&gt;H. sapiens&lt;/em&gt; may also have outcompeted &lt;em&gt;H. neanderthals&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of this was occurring during the Pleistocene ice age. Europe was experiencing repeated bouts of extensive glaciation. Thus, it is also possible that climate change caused or contributed to the extinction of &lt;em&gt;H. erectus&lt;/em&gt;, &lt;em&gt;H. neanderthalensis&lt;/em&gt;, or both.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, the processes that led to the extinction of other species of &lt;em&gt;Homo&lt;/em&gt; are complex and likey interactive. Competetion among species is, in my view, well within the realm of possibility but would be extremely difficult (if not impossible) to test. Climate change is also a very likely contributing factor. There are several other hypotheses but I have tried to hit the major highlights.  The debate is certainly not settled.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;McNeilage A. 2001. Diet and habitat use of two mountain gorilla groups in contrasting habitats in the Virungas. In: Robbins MM, Sicotte P, Stewart KJ, editors. Mountain gorillas: three decades of research at Karisoke. Cambridge (England): Cambridge University Press. p 265&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-08-07T23:06:51.237" LastActivityDate="2014-08-07T23:06:51.237" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20200" PostTypeId="2" ParentId="20176" CreationDate="2014-08-04T04:24:16.477" Score="7" Body="&lt;p&gt;I've discovered that searching for &lt;a href=&quot;http://eol.org/search?q=darwin&amp;amp;type%5B%5D=taxon_concept&quot; rel=&quot;nofollow&quot;&gt;Darwin on the Encyclopedia of Life&lt;/a&gt; (EOL) appears to prioritise in its search results those species named by Darwin rather than for him. The first page of results includes many barnacle species (as noted by 3cat). The first five species are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Amphibalanus amphitrite&lt;/em&gt; (Striped Barnacle)&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Megabalanus coccopoma&lt;/em&gt; (Titan Acorn Barnacle)&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Balanus glandula&lt;/em&gt; (Acorn Barnacle)&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Elminius modestus&lt;/em&gt; (New Zealand Barnacle)&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Balanus nubilus&lt;/em&gt; (Giant Barnacle)&lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are 370 results, but some of them are not species level (e.g. Chthamalidae), and some other entries are mixed in (e.g. &lt;a href=&quot;https://en.wikipedia.org/wiki/S.C.Darwin&quot; rel=&quot;nofollow&quot;&gt;S.C. Darwin&lt;/a&gt; and S.P.Darwin), and later results include, for example, &lt;em&gt;Nemoria darwiniata&lt;/em&gt;, so it's hard to quantify the results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I might try writing an SQL query for the downloaded &lt;a href=&quot;http://www.catalogueoflife.org/&quot; rel=&quot;nofollow&quot;&gt;Catalogue of Life&lt;/a&gt;, as its online interface doesn't seem to allow the relevant query.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The complete list: &lt;strong&gt;&lt;a href=&quot;http://eol.org/collections/12085&quot; rel=&quot;nofollow&quot;&gt;Species described by Charles Darwin (EOL)&lt;/a&gt;&lt;/strong&gt;, listing 81 species. (Pointed out in comments. Thanks 3Cat)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8564" LastEditorUserId="8564" LastEditDate="2014-08-05T21:58:01.790" LastActivityDate="2014-08-05T21:58:01.790" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20202" PostTypeId="2" ParentId="20197" CreationDate="2014-08-04T06:05:41.390" Score="2" Body="&lt;p&gt;Use BioMart. It retrieves UniProt information and you can select the features that you want. These files wont be that huge. So  you can download it in your PC and SFTP to wherever you are doing your analysis. A better way is to install BioMart in your workstation. See the BioMart &lt;a href=&quot;http://www.biomart.org/other/user-docs.pdf&quot; rel=&quot;nofollow&quot;&gt;documentation&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-08-04T06:05:41.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20203" PostTypeId="1" CreationDate="2014-08-04T08:33:23.573" Score="6" ViewCount="8854" Body="&lt;p&gt;I am in the process of Library preparation for Illumina MI-Seq using mtDNA. Using NEB Hotstart LongAmp Polymerase, I was able to obtain upto 10kb amplicons of mtDNA. However, when I switched to a different DNA sample, I am not noticing bands anymore in the gel. Strange thing is that, if I fragment these samples (Diagenode Bioruptor acoustic shearer) I get fragmented smears similar to the ones I expect from fragmenting a 10kb amplicon, even though these are stuck in the well. &#xA;Therefore, I dont know if a 10kb amplicon is stuck in the wells and is not migrating (given I see similar results for fragmentation for the samples that got stuck), or I am seeing in the wells what is genomic DNA and no amplification has occurred. Does the 260/230 value affect PCR amplification in any way? (I have a very high 260/230 value ~5 for the new DNA sample I am using) &lt;/p&gt;&#xA;" OwnerUserId="18932" LastActivityDate="2014-08-06T00:12:53.337" Title="Possible reasons for DNA getting stuck in well" Tags="&lt;dna&gt;&lt;pcr&gt;&lt;gel-electrophoresis&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20204" PostTypeId="1" CreationDate="2014-08-04T08:44:15.177" Score="2" ViewCount="425" Body="&lt;p&gt;Would I be correct in saying that the Bohr effect is ONLY related to the concentration of [H+] in the tissues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously the concentration of carbon-dioxide can contribute to this concentration by producing protons (through carbonic anhydrase) but it isn't directly involved in the effect?&lt;/p&gt;&#xA;" OwnerUserId="8605" LastActivityDate="2014-08-04T15:33:20.427" Title="Bohr effect in respiration" Tags="&lt;biochemistry&gt;&lt;respiration&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20205" PostTypeId="1" CreationDate="2014-08-04T09:10:49.887" Score="4" ViewCount="1143" Body="&lt;p&gt;My first impression of &lt;a href=&quot;http://www.youtube.com/watch?v=Za4uT1ob8qE&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=Za4uT1ob8qE&lt;/a&gt; is that the baboons were being altruistic and benevolent, but is this guess proven or affirmed by science? I sense there's more to this video. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;User dekar6279 comments:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;They didn't save the impala, they just defended their territory. Moreover, the baboons didn't eat the impala because surrely they were not hungry, animals don't kill if they don't have to eat or to defend something.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'd love to be enlightened by more videos. Some other  examples:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=77pK7D7A6I4&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=77pK7D7A6I4&lt;/a&gt;, &lt;a href=&quot;http://www.youtube.com/watch?v=nJzYhxpKYuM&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=nJzYhxpKYuM&lt;/a&gt;, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet the hippo appears to capitulate here: &lt;a href=&quot;http://www.youtube.com/watch?v=4LyVnzVVECA&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=4LyVnzVVECA&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4466" LastEditorUserId="3952" LastEditDate="2014-08-04T12:36:35.550" LastActivityDate="2014-08-05T20:09:23.823" Title="Animal altruism?" Tags="&lt;behaviour&gt;&lt;altruism&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20206" PostTypeId="2" ParentId="20203" CreationDate="2014-08-04T09:21:41.497" Score="5" Body="&lt;p&gt;There is one simple reason for that, your agarose gel is most likely too dense. Depending in the type of agarose, I would prepare a 0.5-0.6% gel at maximum. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tB3Yr.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.synbio.org.uk/gibson/page6/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Synbio&lt;/a&gt; gives this list for &quot;standard&quot; agarose, which fits pretty good with my experiences. If you use low melting agarose, this table looks a bit different, as the gel matrix is not a dense. The disadvantage is that the gel is much more prone to get damaged while handling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BdZnB.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-04T09:21:41.497" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="20207" PostTypeId="2" ParentId="20205" CreationDate="2014-08-04T10:10:04.000" Score="4" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;is this guess proven or affirmed by science?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It is a debated topic.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Such altruistic behaviors (toward non-kin) are extremely rare evolutionarily, with some theorists even proposing that they are uniquely human [1].&lt;/p&gt;&#xA;&lt;p&gt;Experimental evidence indicates that human altruism is a powerful force and is unique in the animal world. [...] Current gene-based evolutionary theories cannot explain important patterns of human altruism, pointing towards the importance of both theories of cultural evolution as well as gene-culture co-evolution [4].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Yet, similar behavior was observed in chimpanzees:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In addition, we demonstrate similar though less robust skills and motivations in three young chimpanzees [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Altruism has evolved under some conditions:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;We show that at least one of the four following conditions needs to be fulfilled: direct benefits to the focal individual performing a cooperative act; direct or indirect information allowing a better than random guess about whether a given individual will behave cooperatively in repeated reciprocal interactions; preferential interactions between related individuals; and genetic correlation between genes coding for altruism and phenotypic traits that can be identified. When one or more of these conditions are met, altruism or cooperation can evolve if the cost-to-benefit ratio of altruistic and cooperative acts is greater than a threshold value [2].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Altruism is related to kin selection:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In 1964, Hamilton formalized the idea of kin selection to explain the evolution of altruistic behaviours. Since then, numerous examples from a diverse array of taxa have shown that seemingly altruistic actions towards close relatives are a common phenomenon. Although many species use kin recognition to direct altruistic behaviours preferentially towards relatives, this important aspect of social biology is less well understood theoretically [3].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Warneken F, Tomasello M. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16513986&quot; rel=&quot;nofollow noreferrer&quot;&gt;Altruistic helping in human infants and young chimpanzees.&lt;/a&gt; Science. 2006 Mar 3;311(5765):1301-3. doi: &lt;a href=&quot;http://dx.doi.org/10.1126/science.1121448&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1126/science.1121448&lt;/a&gt;. PubMed PMID: 16513986.&lt;/li&gt;&#xA;&lt;li&gt;Lehmann L, Keller L. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16910958&quot; rel=&quot;nofollow noreferrer&quot;&gt;The evolution of cooperation and altruism--a general framework and a classification of models.&lt;/a&gt; J. Evol. Biol. 2006 Sep;19(5):1365-76. doi: &lt;a href=&quot;http://dx.doi.org/10.1111/j.1420-9101.2006.01119.x&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1111/j.1420-9101.2006.01119.x&lt;/a&gt;. PubMed PMID: 16910958.&lt;/li&gt;&#xA;&lt;li&gt;Agrawal AF. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11375095&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kin recognition and the evolution of altruism.&lt;/a&gt; Proc. Biol. Sci. 2001 May 22;268(1471):1099-104. doi: &lt;a href=&quot;http://dx.doi.org/10.1098/rspb.2001.1611&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1098/rspb.2001.1611&lt;/a&gt;. PubMed PMID: 11375095.&lt;/li&gt;&#xA;&lt;li&gt;Fehr E, Fischbacher U. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14574401&quot; rel=&quot;nofollow noreferrer&quot;&gt;The nature of human altruism.&lt;/a&gt; Nature. 2003 Oct 23;425(6960):785-91. doi: &lt;a href=&quot;http://dx.doi.org/10.1038/nature02043&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1038/nature02043&lt;/a&gt;. PubMed PMID: 14574401.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-08-04T10:10:04.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20208" PostTypeId="2" ParentId="20204" CreationDate="2014-08-04T11:37:07.260" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Would I be correct in saying that the Bohr effect is ONLY related to the concentration of [H+] in the tissues.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would say no. Because oxygen binding affinity is inversely related to &lt;strong&gt;both&lt;/strong&gt; [1]:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;high $[H^+]$ concentration &lt;strong&gt;and&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;$CO_2$ increase (which is can be a consequence of the first)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;$CO_2$ is involved in the Bohr effect:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The biological significance of the negative influence of the carbon dioxide pressure on the oxygen binding of blood is obviously very big. [...] During the bloods movement through the body the oxygen-pressure will decrease to a relatively low value, whereas at the same time the carbon dioxide-pressure rises. This will greatly support the oxygen release from the blood, resulting in an improved efficiency in oxygen usage [2].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Bohr effect,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Bohr_effect&amp;amp;oldid=618215597&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Bohr_effect&amp;amp;oldid=618215597&lt;/a&gt; (accessed August 4, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Chr. Bohr, K. Hasselbalch, and August Krogh. &lt;em&gt;Concerning a Biologically Important Relationship - The Influence of the Carbon Dioxide Content of Blood on its Oxygen Binding.&lt;/em&gt; Available from &lt;a href=&quot;http://www.udel.edu/chem/white/C342/Bohr%281904%29.html&quot; rel=&quot;nofollow&quot;&gt;http://www.udel.edu/chem/white/C342/Bohr%281904%29.html&lt;/a&gt; (accessed 04.08.2014)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-08-04T11:37:07.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20210" PostTypeId="2" ParentId="20129" CreationDate="2014-08-04T12:14:48.157" Score="5" Body="&lt;p&gt;Human skin is made up of three layers [1]:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Epidermis; it contains no blood vessels; it has 5 cellular layers (starting from surface):&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;stratum corneum&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;stratum lucidum&lt;/li&gt;&#xA;&lt;li&gt;stratum granulosum&lt;/li&gt;&#xA;&lt;li&gt;stratum spinosum&lt;/li&gt;&#xA;&lt;li&gt;stratum germinativum&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Dermis; it is separated from the above by the &lt;strong&gt;basal membrane&lt;/strong&gt;; made up of connective tissue (with blood vessels and nerve endings)&lt;/li&gt;&#xA;&lt;li&gt;Hypodermis - it is not even considered part of the skin&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Gray940.png#mediaviewer/File:Gray940.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/1/18/Gray940.png&quot; alt=&quot;Gray940.png&quot;&gt;&lt;/a&gt;&lt;br&gt;&quot;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Gray940.png#mediaviewer/File:Gray940.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gray940&lt;/a&gt;&quot;. Licensed under Public domain via &lt;a href=&quot;//commons.wikimedia.org/wiki/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikimedia Commons&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why (and how) is regenerated skin different from original ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why? Skin is a very important organ. It protects from pathogens, it maintains body temperature, it keeps body water [1], etc. How? That depends on what causes the regeneration. I've emphasized two terms in the above list.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Stratum corneum&lt;/em&gt; represents the &quot;skin cells that becomes the dust in our homes and it always grows back to full thickness&quot;. It is lost during a physiological process called desquamation [2]. The cells that are lost are non living corneocytes. Their only purpose is to from a protection barrier [3].&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Basement membrane&lt;/em&gt; holds the germinativum layer of the epidermis. Injuries that do not affect it are repaired by complete regeneration of all destroyed layers. However, if the injury destroys membrane continuity, the germinative cells on the edges will fail to &quot;reconnect&quot; with each other, thus the layers derived from them will follow the same rule. A process of fibrosis is triggered. The result of  extensive fibrosis is a scar, containing collagen secreted by the granulation tissue with dermal origins. Yet, the germinative layer tends to join back together [6], but probably the excess collagen production, without the limiting basement membrane, bulges into the epidermis and limits germinative layer extension. That's why keeping the edges of the tissue close to each other reduces excessive fibrosis and allows germinative layer regeneration, thus resulting in none to small, barely visible scars.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;How deep should an injury be in order not to affect basement membrane? No more than 0.06 to 0.08 mm [5].&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What about skin transplants ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Skin grafts contain at least a part of dermis [4], which will allow granulation tissue formation thus permitting revascularisation and making the graft stick. Otherwise it would fall off and/or be lost by necrosis.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Skin,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Skin&amp;amp;oldid=619454074&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Skin&amp;amp;oldid=619454074&lt;/a&gt; (accessed August 4, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Desquamation,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Desquamation&amp;amp;oldid=614028888&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Desquamation&amp;amp;oldid=614028888&lt;/a&gt; (accessed August 4, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Stratum corneum,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Stratum_corneum&amp;amp;oldid=615247326&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Stratum_corneum&amp;amp;oldid=615247326&lt;/a&gt; (accessed August 4, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Skin grafting,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Skin_grafting&amp;amp;oldid=603324006&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=Skin_grafting&amp;amp;oldid=603324006&lt;/a&gt; (accessed August 4, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Sandby-Møller J, Poulsen T, Wulf HC. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14690333&quot; rel=&quot;nofollow noreferrer&quot;&gt;Epidermal thickness at different body sites: relationship to age, gender, pigmentation, blood content, skin type and smoking habits.&lt;/a&gt; Acta Derm. Venereol. 2003;83(6):410-3. doi: &lt;a href=&quot;http://dx.doi.org/10.1080/00015550310015419&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1080/00015550310015419&lt;/a&gt;. PubMed PMID: 14690333. &lt;/li&gt;&#xA;&lt;li&gt;Dawn A. Tamarkin, Ph.D. &lt;em&gt;Repair of skin.&lt;/em&gt; 2011 STCC Foundation Press. Available from &lt;a href=&quot;http://faculty.stcc.edu/AandP/AP/AP1pages/Units1to4/skin/repairof.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://faculty.stcc.edu/AandP/AP/AP1pages/Units1to4/skin/repairof.htm&lt;/a&gt; (accessed 04.08.2014)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.477" LastActivityDate="2014-08-04T14:45:14.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20211" PostTypeId="1" AcceptedAnswerId="20246" CreationDate="2014-08-04T15:07:36.910" Score="3" ViewCount="7804" Body="&lt;p&gt;The pET plasmid is used for protein expression with T7 promotor in expression strains, such as &lt;em&gt;E.coli&lt;/em&gt; BL21(DE3)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It contains a lacI gene which codes for the lac repressor protein, a protein of interest under the control of a T7 promoter for T7 RNA polymerase and a lac operator which can block transcription, directly behind the promotor. The lac operon is another control of transcription of the protein of interest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, T7 polymerase is located in the genome as well under the control of the lac operon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When IPTG is added, the lac repressor is inactivated -&gt; T7 polymerase and therefore the protein of interest will be expressed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Lac I gene is already present in the genome of the expression strain used, why is it also cloned into the pET vectors?&lt;/p&gt;&#xA;" OwnerUserId="3042" LastActivityDate="2014-08-05T13:56:25.933" Title="Why does the pET- expression vector contain a LacI gene additionally to the one in the genome?" Tags="&lt;molecular-biology&gt;&lt;gene-expression&gt;&lt;lab-techniques&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20212" PostTypeId="2" ParentId="20063" CreationDate="2014-08-04T15:11:02.737" Score="7" Body="&lt;p&gt;ImageJ doesn't have a feature to remove individual lanes. But that shouldn't be a problem. All you have to do is &lt;strong&gt;draw the first lane correctly&lt;/strong&gt; (I'm referring to size). Then press &lt;kbd&gt;1&lt;/kbd&gt;. Now, while the selection is still... selected, click inside it, but not on the number (where the cursor becomes hand), and drag it where you want the next lane. And press &lt;kbd&gt;2&lt;/kbd&gt;. And so on. Draw all your lanes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, if you misplaced a lane, click the rectangle selection tool, then click on the lane number while the cursor is a hand. It will be selected. If you're having troubles with this, use the shortcuts &lt;kbd&gt;Ctrl+1&lt;/kbd&gt; and &lt;kbd&gt;Ctrl+2&lt;/kbd&gt; or the menu &lt;strong&gt;Analyze&lt;/strong&gt; - &lt;strong&gt;Gels&lt;/strong&gt; - &lt;strong&gt;Select Previous/Next Lane&lt;/strong&gt; to select between lanes. The cursor turns to normal. Click anywhere inside the lane and drag it on the right place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the first lane was bad and you want to remove all lanes, just go to &lt;strong&gt;Analyze&lt;/strong&gt;, &lt;strong&gt;Gels&lt;/strong&gt; and click on &lt;strong&gt;Reset&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-08-04T15:11:02.737" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20213" PostTypeId="2" ParentId="20204" CreationDate="2014-08-04T15:13:23.263" Score="1" Body="&lt;p&gt;In a strict sense, I think you are correct that [H$^+$] contributes &lt;em&gt;directly&lt;/em&gt; to the Bohr effect. A paper by &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022283680800222&quot; rel=&quot;nofollow&quot;&gt;Perutz et al. (1980)&lt;/a&gt; identified at least two amino acid residues in hemoglobin that account for the Bohr effect by interacting directly with H$^+$. CO$_2$ is not directly involved. Further, the Bohr effect (and the Root effect) are defined in terms of pH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You and @Cornelius are correct that CO$_2$ contributes to the Bohr effect but speaking strictly it is a contributor and not the proximal cause. CO$_2$ dissolved in water produces H$_2$CO$_3$ which dissociates to release H$^+$, decreasing pH. But, lactic acid (&lt;a href=&quot;http://www.biolbull.org/content/84/3/207.full.pdf&quot; rel=&quot;nofollow&quot;&gt;for example&lt;/a&gt;) can also contribute to the Bohr effect again through the release of H$^+$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While CO$_2$ and lactic acid contribute to the Bohr effect through the release of H$^+$, the H$^+$ is the actual cause through interaction with amino acids in the hemoglobin.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Perutz, M.F., et al. 1980. Identification of residues contributing&#xA;to the Bohr effect of human haemoglobin. J. Molecular Biology 138:&#xA;649-668.&lt;/li&gt;&#xA;&lt;li&gt;Root, R.W. and L. Irving. 1943. The effect of carbon dioxide and&#xA;lactic acid on the oxygen-combining power of whole and hemolyzed&#xA;blood of the marine fish &lt;em&gt;Tautoga onitis&lt;/em&gt; (Linn.). Biological&#xA;Bulletin 84: 207-212.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="6422" LastEditDate="2014-08-04T15:33:20.427" LastActivityDate="2014-08-04T15:33:20.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20215" PostTypeId="1" AcceptedAnswerId="20216" CreationDate="2014-08-04T16:17:49.037" Score="3" ViewCount="215" Body="&lt;p&gt;I've been looking at some sequenced exomes and found an interesting point mutation that causes a Proline-to-Leucine amino acid change in the protein. This seems like it could have a big impact on the protein's functionality but before I go any further I want to explore whether or not the variant is a sequencing artifact. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I looked at the coverage for this particular region of the genome and found that in some samples, the point mutation is seen in every single read covering the base in question while in others the point mutation is seen in approximately half of the reads. In all my samples, the base in question is covered by at least 15 separate reads but usually its more than 20. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My primary question is: &lt;strong&gt;how should I interpret the cases where the point mutation is seen in some but not all of the reads covering its location?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm also interested in any suggestions/advice on the more general topic of determining whether or not the mutation I've found is a sequencing artifact.&lt;/p&gt;&#xA;" OwnerUserId="8161" LastActivityDate="2014-08-05T05:16:35.953" Title="What if a Point Mutation is seen in only half the coverage for its location?" Tags="&lt;genomics&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20216" PostTypeId="2" ParentId="20215" CreationDate="2014-08-04T17:02:44.023" Score="8" Body="&lt;p&gt;I don't know, whether the organism you are working with is diploid, but suspect it's an animal (or even a mammal), so the most parsimonious explanation would be that you have &lt;a href=&quot;https://en.wikipedia.org/wiki/Zygosity#Homozygous&quot;&gt;homozygotes&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Zygosity#Heterozygous&quot;&gt;heterozygotes&lt;/a&gt; at this SNP-position.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-08-04T17:02:44.023" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20217" PostTypeId="1" AcceptedAnswerId="20219" CreationDate="2014-08-04T17:22:54.140" Score="1" ViewCount="1259" Body="&lt;p&gt;I saw this pic while crawling online and it was a bit different for me to predict which worm is this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/grEvP.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Source:&lt;/strong&gt; &lt;a href=&quot;http://www.seafishingtackle4u.com/softbaits/ragworms-latex-lures/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.seafishingtackle4u.com/softbaits/ragworms-latex-lures/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears somewhat different form other annelids as parapodia or setae are somewhat transparent and very attractive too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What worm is this?&lt;/p&gt;&#xA;" OwnerUserId="8101" LastEditorUserId="6422" LastEditDate="2014-08-04T17:25:45.350" LastActivityDate="2014-08-04T20:50:07.227" Title="What would be the scientific name of this worm" Tags="&lt;nomenclature&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20218" PostTypeId="2" ParentId="20217" CreationDate="2014-08-04T17:28:29.433" Score="2" Body="&lt;p&gt;If you would have read the text from the source of that image (which by the way you didn't mention, I did a Google Image search and edited your question to include it), you would have known that what is seen in the picture is not a living thing, it is a latex &lt;a href=&quot;http://en.wikipedia.org/wiki/Fishing_lure&quot; rel=&quot;nofollow&quot;&gt;fishing lure&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Product Description: Sandworm/Ragworm 8″ size, sure fire fish catching lures. Costing less than live worms, but lasting much longer, never be without worms again. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.seafishingtackle4u.com/softbaits/ragworms-latex-lures/&quot; rel=&quot;nofollow&quot;&gt;http://www.seafishingtackle4u.com/softbaits/ragworms-latex-lures/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-08-04T17:28:29.433" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20219" PostTypeId="2" ParentId="20217" CreationDate="2014-08-04T18:17:44.163" Score="1" Body="&lt;p&gt;As Cornelius correctly pointed out, it's not a living worm :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the question, what kind of worm they tried to imitate, I'd say, they had a &lt;a href=&quot;https://www.google.com/search?channel=fs&amp;amp;q=nereidae&amp;amp;tbm=isch&quot; rel=&quot;nofollow&quot;&gt;nereid&lt;/a&gt; (errant, i.e. wandering) in mind and were likely inspired by the segmentation of &lt;em&gt;&lt;a href=&quot;https://www.google.com/search?channel=fs&amp;amp;q=arenicola&amp;amp;tbm=isch&quot; rel=&quot;nofollow&quot;&gt;Arenicola&lt;/a&gt;&lt;/em&gt; (sedentary), which together created this appearance, unrealistic for an errant polychaete: with the body segments outnumbering parapodia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They also paid no attention to the head (a very important body part in polychaete systematics!), which seems to be absent. This feature could also be &quot;inherited&quot; from &lt;em&gt;Arenicola&lt;/em&gt;, the head end of which is not prominent and bears no appendages.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-08-04T20:50:07.227" LastActivityDate="2014-08-04T20:50:07.227" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20221" PostTypeId="1" CreationDate="2014-08-04T19:35:47.227" Score="2" ViewCount="381" Body="&lt;p&gt;I observerd myself and I can identify two different types of &quot;happines&quot;.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;First - called by me - After Pleasure :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Occurs AFTER (and last long) long activity that require from me engagement focus and effort  for example : &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;running 16KM&lt;/li&gt;&#xA;&lt;li&gt;learning for an hour things that I think are worthwhile&lt;/li&gt;&#xA;&lt;li&gt;reading book&lt;/li&gt;&#xA;&lt;li&gt;generally any mental or physical activity  &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Second - called by me - During Pleasure&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Occurs DURING (and last short time) activity that DON'T require any engagement, focus or effort, for example : &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;masturbation&lt;/li&gt;&#xA;&lt;li&gt;eating sweets&lt;/li&gt;&#xA;&lt;li&gt;eating tasty things in general&lt;/li&gt;&#xA;&lt;li&gt;having hot bathing time&lt;/li&gt;&#xA;&lt;li&gt;watching funny videos/TV&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I wonder is there any scientific distinction between those two states of my body and mind. And assuming that endorphins are the hormones are responsible for the &quot;oh-good&quot; state, are different kind of endorphins are released while taking this 2 different activities (like studying for 1hour and masturbation) ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for an answer in advance.&lt;/p&gt;&#xA;" OwnerUserId="8618" LastActivityDate="2014-08-04T19:35:47.227" Title="Is there a difference between endorphins that are released while physical activity and sex/masturbation?" Tags="&lt;human-biology&gt;&lt;theoretical-biology&gt;&lt;sex&gt;&lt;psychology&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20222" PostTypeId="2" ParentId="20021" CreationDate="2014-08-04T19:50:51.560" Score="3" Body="&lt;p&gt;This question has a related issue that should be addressed first: what is a species? To some extent, if you want to understand how speciation can occur, then you have to consider how you are going to define a species. There is no species concept that applies to all species, past or present. The most widely applied concept is the &lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/VA1BioSpeciesConcept.shtml&quot; rel=&quot;nofollow&quot;&gt;biological species concept&lt;/a&gt; (Mayr 1942), which applies (imperfectly) to sexually reproducing species. Of course, &lt;em&gt;Taenia&lt;/em&gt; does not always reproduce sexually. I think the discussion of species concepts is beyond this question but I encourage those that are interested to check out references [2-4] as well as a series of papers published in Systematic Zoology in the mid-70s. Here, I'll focus on genetic differentiation with a subtext of reproductive isolation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetic differences can accumulate between populations$^1$ of &lt;em&gt;Taenia&lt;/em&gt; in two different ways. The first is non-adaptive evolution via &lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/IIIDGeneticdrift.shtml&quot; rel=&quot;nofollow&quot;&gt;genetic drift&lt;/a&gt;. Drift is when allele frequencies change by random processes. For example, just by chance, tapeworms in a particular host may not live very long because the host was killed in a mudslide. Those tapeworms don't produce as many proglottids over their interrupted life so they don't leave as many copies of their alleles. Tapeworms in a host that lives a long time produces lots of proglottids and therefore produce many more copies of their alleles.  The key point here is that the process of genetic drift is random. Allele frequency changes in one population of &lt;em&gt;Taenia&lt;/em&gt; will be different from allele frequency changes in another population. Thus, over time, different populations of &lt;em&gt;Taenia&lt;/em&gt; can become genetically different solely by chance. It's called non-adaptive evolution because natural selection is not evolved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adaptive evolution by natural selection can still occur on individuals that are asexually reproducing. Genetic differences will accumulate in a population over time to due mutations. Some mutations may be beneficial, some may not. Selection can increase the frequency of beneficial mutations and decrease the frequency of very mutations. Note that non-lethal but harmful mutations can accumulate in asexually reproducing species (see &lt;a href=&quot;http://www.nature.com/nrg/journal/v6/n12/box/nrg1728_BX1.html&quot; rel=&quot;nofollow&quot;&gt;Muller's Ratchet&lt;/a&gt;) but I am assuming survivorship is decreased by harmful mutations for this example. If we assume that &lt;em&gt;Taenia&lt;/em&gt; in different populations are subject to different selective pressures, then genetic differences can accumulate, leading to speciation. Note that drift will also affect the allele frequencies of both beneficial and harmful alleles because drift is random.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That brings us to the &quot;mixed-up genes&quot;. I assume you mean the new genetic combinations that occur via sexual reproduction. Even if a host typically has only one individual of &lt;em&gt;Taenia&lt;/em&gt; (not always the case), I suspect the opportunities for sexual reproduction in a population of &lt;em&gt;Taenia&lt;/em&gt; are frequent, especially over evolutionary time. Consider places where tapeworm infestation of humans is high. Such places often have poor sanitary conditions so the opportunity for mixing of fecal material from different human hosts is high, and therefore the opportunity for mating among different individuals of &lt;em&gt;Taenia&lt;/em&gt; is also high. If you have many humans living in squalor over long periods of time, then you have conditions very favorable for sexual reproduction of &lt;em&gt;Taenia&lt;/em&gt;. Remember too that &lt;em&gt;Taenia&lt;/em&gt; produce lots of proglottids, each with the chance for reproduction. Each reproductive opportunity creates new genetic combinations potentially subject to natural selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The final point to consider is population size. If the population size of &lt;em&gt;Taenia&lt;/em&gt; is small (relatively few individuals) then genetic differences can accumulate fairly rapidly by genetic drift but the accumulation of beneficial mutations in the population will be low. If the population size is large then new mutations including beneficial ones can occur relatively often, increasing the rate of adaptive evolution among different populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Footnote&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;I'm assuming some sexual reproduction among individuals of the same population and individuals from different populations do not interbreed. Without sexual reproduction, we have to think about the individual as the species and that makes my head hurt.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Mayr, E. 1942. &lt;em&gt;Systematics and the origin of speceis from the&#xA;viewpoint of a zoologist.&lt;/em&gt; Columbia University Press, New York, USA.&lt;/li&gt;&#xA;&lt;li&gt;Howard, D.J. and S.H. Berlocher (eds.). 1998. &lt;em&gt;Endless forms:&#xA;Species and speciation.&lt;/em&gt; Oxford University Press, Oxford, England.&lt;/li&gt;&#xA;&lt;li&gt;Wheeler, Q.D. and Meier, R. (eds.). 2000. &lt;em&gt;Species concepts and&#xA;phylogenetic theory: A debate.&lt;/em&gt;  Columbia University Press, New&#xA;York, USA.&lt;/li&gt;&#xA;&lt;li&gt;Coyne, J.A. and H.A. Orr. 2004. &lt;em&gt;Speciation.&lt;/em&gt; Sinauer Associates,&#xA;Inc., Sunderland, Massachusetts, USA.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-04T19:50:51.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20223" PostTypeId="2" ParentId="10329" CreationDate="2014-08-04T19:55:56.983" Score="4" Body="&lt;p&gt;Electroencephalography has a good time resolution (milliseconds) but poor spatial resolution (several centimers). The usual estimated figure is that at least 50000 neurons need to fire simultaneously so that the activity can picked up by EEG.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer provided by @Jeremy Kemball is not very accurate. The reason why the spatial resolution of EEG is poor is that the signal from even a point-like source on the cortical surface spreads about to every sensor along the scalp due to the conductivity properties of the brain, CSF, skull, and scalp.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that in order to get that few centimeter accuracy I mentioned above, one must solve an inverse problem from sensors -&gt; cortex. Inverse problems are mathematically ill-posed, and have infinite number of solutions &lt;em&gt;unless&lt;/em&gt; some constraints to the solution are added.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll give a practical example. Say that a subject is presented some sounds. You record the EEG. Now, if you look at the sensor-level data, you can find brain activity related to the sounds from almost any sensor, from both sides of the brain (each ear projects to both hemispheres). If you want to know where the signal actually came from, you need to do the source localization using some inverse solver. Some commonly used are for example dSPM, sLORETA, or MNE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, I want to emphasize that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Brain regions deeper in the brain produce a 'blurred' signal that shows up on several electrodes at once.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;that this happens to &lt;em&gt;all&lt;/em&gt; activity recorded by EEG. Actually, EEG does not even pick subcortical activity too well.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there a more advanced method than electroencephalography for scaning brain activity in real time?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, that is called magnetoencephalography (MEG). MEG records the magnetic fields related to the electric activity. It reaches sub-centimeter localization accuracy, while still having millisecond time resolution. However, this is now strictly only for the cortical activity; MEG does not see subcortical activity almost at all. Google for Elekta Neuromag or CTF to see some MEG systems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you would be interested in studying some deep structure, like amygdala, your best choice is then fMRI, which has about ~2 second time-resolution and 1mm^3 spatial resolution.&lt;/p&gt;&#xA;" OwnerUserId="8620" LastEditorUserId="8620" LastEditDate="2014-08-04T20:30:40.440" LastActivityDate="2014-08-04T20:30:40.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20224" PostTypeId="1" CreationDate="2014-08-04T20:03:24.993" Score="6" ViewCount="1498" Body="&lt;p&gt;How is photosynthesis observed? &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Say I have plants A and B, and I want to find how fast they are able to turn carbon dioxide into oxygen. How would I experiment this?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Say I have one plant A, which has two kinds of leafs B and C. I hypothesize the B-leafs produce oxygen faster than the C-leafs. What kind of experiment could I set up to test this?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8620" LastActivityDate="2016-05-11T14:37:29.270" Title="How is photosynthesis observed?" Tags="&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20225" PostTypeId="1" AcceptedAnswerId="20231" CreationDate="2014-08-04T20:11:28.890" Score="7" ViewCount="201" Body="&lt;p&gt;Haven't looked into this to very long, but an initial search didn't return anything. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;HIV uses certain co-receptors to enter our cells. Could we flood the blood stream with specially designed proteins that mimic cell receptors, either locking the virus out of vulnerable cells, or even causing the virus to release its genetic material (pre-mature ejc. for viruses... :|), so it can't accidentally get away and infect a cell anyway? It seems like an obvious idea, so the fact that it may not already be happening must mean there are a host of challenges to it? Basically we design a protein that acts like a strait jacket, with tags that allow our body to recognize it as a 'friendly' body. T-cells use the same receptor though, so are there ways to identify a T-cell compared to a HIV virion?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously this wouldn't prevent some viruses managing to infect actual cells, but over time, if we can attack enough, say 2/3 of the virions, for each generation, we could seriously harm the population, and maybe keep it in check?&lt;/p&gt;&#xA;" OwnerUserId="8619" LastEditorUserId="1320" LastEditDate="2014-08-05T16:53:47.993" LastActivityDate="2017-08-02T15:37:37.663" Title="Can we attack viruses by attaching proteins and such to their shells?" Tags="&lt;dna&gt;&lt;microbiology&gt;&lt;rna&gt;&lt;virology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20226" PostTypeId="2" ParentId="17014" CreationDate="2014-08-04T20:51:03.230" Score="1" Body="&lt;p&gt;You might want to read about event related potentials (recorded by EEG) or event related fields (recorder by MEG). The idea is simple:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Pick some stimulus, e.g. a person touching the hand of a subject. Pick another stimulus, e.g. the subject seeing a person touching the hand of another subject. Record EEG/MEG.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Repeat each condition for at least few hundred times. Throw away bad data, and average the repetitions. You do the averaging because the signal-to-noise ratio is low in all non-invasive electrical measurements, and the signals are always riddled with movement, cardiac, and eye-blink artefacts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Compare the conditions in each sensor. Rest is statistics, though not very easy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually, the experiment above would be about &lt;a href=&quot;http://en.wikipedia.org/wiki/Mirror_neuron&quot; rel=&quot;nofollow&quot;&gt;mirror neurons&lt;/a&gt;, a relatively hot topic in neuroscience. (See e.g. recent issue from Nature)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The more general situation is that using pattern recognition/machine learning algorithms to study brain signals is already a standard thing to do. There are for example graduate/undergraduate programs in &lt;em&gt;computational neuroscience&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you would study some other signal (e.g. measure from a hand, leg), they are going to dull. Very dull. Mostly because then you have 1 time-series, instead of several hundreds of time-series to analyse.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For example I would want to know if applying hot/cold object to skin of both right and left limbs would cause the sensory neuron to send the same or similar signal (electrical impulse) to the spinal cord.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This you could too study with the event related fields/potentials.&lt;/p&gt;&#xA;" OwnerUserId="8620" LastEditorUserId="8620" LastEditDate="2014-08-04T20:57:11.260" LastActivityDate="2014-08-04T20:57:11.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20227" PostTypeId="2" ParentId="14221" CreationDate="2014-08-04T21:09:56.900" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I noticed that a strong background signal in the alpha-wave range was existent at ~10 Hz, but then after a while of doing other things and coming back to it the strong background signal at 10 Hz disappeared but a strong background signal at a smidgen over 8 Hz was present instead.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Alpha-waves (7-13 Hz) are related to a dozen of things. Here is an easy first experiment for you:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Sit still, stare at a wall, eyes open. Remove sources of noise such as TV, radio, etc.&lt;/li&gt;&#xA;&lt;li&gt;Repeat the same, but now hold your eyes closed.&lt;/li&gt;&#xA;&lt;li&gt;Record the signals in both conditions for about one minute.&lt;/li&gt;&#xA;&lt;li&gt;Compare the power spectrums between the two conditions: you will see a big difference in the alpha power, especially at the occipital electrodes.&lt;/li&gt;&#xA;&lt;li&gt;This is actually a standard test for &lt;em&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1388245707004002&quot; rel=&quot;nofollow&quot;&gt;resting-state&lt;/a&gt;&lt;/em&gt; analysis.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Back to the actual question: What you noticed is probably about drowsiness. When one gets sleepy, the alpha power starts to increase. You can try this by watching a boring movie.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Can alpha wave frequencies vary within a single subject over the course of a single day? If they can, by how much, and under what conditions?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, because of the varying cognitive load, thoughts, sleepiness, emotions, etc. The brain signals vary &lt;em&gt;a lot&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also notice that all sorts of artefacts (e.g. movement, cardiac, eye-blinks, biting of teeth) have a dramatic effect on the measured signal. If you blink your eyes it produces a signal that has 100x higher amplitude compared to the signal that comes from your brain. You cannot really say much what causes any differences in the EEG unless you would do research-level recordings with research-level equipment.&lt;/p&gt;&#xA;" OwnerUserId="8620" LastEditorUserId="8620" LastEditDate="2014-08-04T21:16:02.063" LastActivityDate="2014-08-04T21:16:02.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20228" PostTypeId="2" ParentId="20224" CreationDate="2014-08-04T21:15:54.253" Score="1" Body="&lt;p&gt;Not sure, this what you need, but &lt;a href=&quot;https://en.wikipedia.org/wiki/Photosynthesis_system&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; you can find a detailed description of how photosynthesis efficiency can be measured in the field, with a list of modern devices. In short, it's about measuring the uptake of CO&lt;sub&gt;2&lt;/sub&gt; and release of H&lt;sub&gt;2&lt;/sub&gt;O of individual leaves.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-08-04T21:15:54.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20229" PostTypeId="2" ParentId="2417" CreationDate="2014-08-04T21:21:03.710" Score="2" Body="&lt;p&gt;For DNA extraction, you would need only a few eggs. PCR would then give you all the copies of your target gene(s). A quick Google Scholar search on &lt;em&gt;Takifugu&lt;/em&gt; fecundity revealed a paper by &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1439-0426.2008.01071.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Yang and Chen (2008)&lt;/a&gt;. They found that &lt;em&gt;T. obscurus&lt;/em&gt; produced an average of 320.8 oocytes mg$^{-1}$ ovary wet weight. In comparison, &lt;em&gt;T. ocellatus&lt;/em&gt; produced 125.2 oocytes mg$^{-1}$ ovary wet weight. &lt;em&gt;Takifugu rupripes&lt;/em&gt; and other species are likely in a similar range, which is plenty of tissue for DNA. &lt;a href=&quot;http://ci.nii.ac.jp/naid/10016123524/&quot; rel=&quot;nofollow&quot;&gt;Kusakabe (1962)&lt;/a&gt; published on the fecundity of &lt;em&gt;T. rubripes&lt;/em&gt; but the paper is in Japanese and is not readily available to me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Beware:&lt;/strong&gt; &lt;em&gt;T. rubripes&lt;/em&gt; ovaries are &lt;a href=&quot;http://fishbase.org/summary/Takifugu-rubripes.html&quot; rel=&quot;nofollow&quot;&gt;highly toxic&lt;/a&gt;. Why not use other tissue instead?&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-04T21:21:03.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20230" PostTypeId="2" ParentId="3399" CreationDate="2014-08-04T21:54:36.683" Score="2" Body="&lt;p&gt;The answer provided by @MCM contains an important chunk of information (Bioluminescence!) but it does not answer the question entirely. First, let's correct a misunderstanding in the question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sunlight does penetrate beyond 200m in the ocean. The intensity is not enough for photosynthesis to occur (and thus no phytoplankton below 200m) but depths between 200-1000m can receive enough sunlight for vision. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The region between 200-1000m is called the mesopelagic. Because there is enough light for vision, many mesopelagic species have eyes to see. Because light is extremely dim (humans would not be able to see), mesopelagic species tend to have very large eyes to gather as much light as possible. Vision is very important to mesopelagic species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below 1000m, we reach the bathypelagic (and, continuing deeper, the abyssopelagic and hadopelagic). Here, light penetration is insufficient for vision. Below 1000m is pitch black. In the bathypelagic (and deeper), you tend to see a reduction of eye size and sometimes a complete loss of eyes. Bioluminescence is still present (although much more common in mesopelagic fishes) but much less important. The physiological cost of producing and maintaining eyes is energetically expensive, so most species that live below 1000m have very weak eyes, if they have them at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the eyes of bathypelagic (and deeper) species still serve their original function, I would say the eyes of deep-sea organisms are not &lt;a href=&quot;https://web.archive.org/web/20141207110708/https://jerrycoyne.uchicago.edu/excerpt.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;vestigial&lt;/a&gt;, in the sense of having completely lost their original function or serving a new function.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="9686" LastEditDate="2018-06-29T18:01:47.447" LastActivityDate="2018-06-29T18:01:47.447" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="20231" PostTypeId="2" ParentId="20225" CreationDate="2014-08-04T22:49:52.560" Score="6" Body="&lt;p&gt;Yes, that should be possible. And it is one of the ways antibodies work. It is already used as a treatment against &lt;a href=&quot;http://en.wikipedia.org/wiki/Rabies#Treatment&quot;&gt;rabies&lt;/a&gt;. There you get a dose of immunoglobulins directed against the rabies virus together with the vaccine. The immunoglobulins neutralize the virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same is possible when you vaccinate against the surface proteins which a virus uses to dock to a cell. With the resulting antibodies this docking is at least hindered if not completely prevented. And there are interesting results from the Ebola research which used a small molecule inhibitor to identify the protein which is important for cell binding of the virus. It is called NPC1, when the receptor on the virus surface is blocked, no docking can take place. This will be one of the approaches to make a therapeutic. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230319/&quot;&gt;here&lt;/a&gt; for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And it is of course possible to design more of the molecules - the problem is to find substances which do not interfere with body functions or which stimulate other pathways.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-04T22:49:52.560" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20232" PostTypeId="2" ParentId="6883" CreationDate="2014-08-04T23:37:25.397" Score="1" Body="&lt;p&gt;I just spoke with my histological colleague about your question. He said that you should be fine for gross examination but not for microscopy. Why? He says, &quot;When working with specimens, the higher resolution microscopy you try to achieve, the more 'potent' the fixative needs to be. A preservative will preserve what tissues are there. However, fixatives (like paraformaldehyde or glutaraldehyde) bind proteins together and, thus, are used to try to 'fix' a tissue posthumous in the manner that it was structured in life. For gross examination, a preserved specimen (without prior fixation) can act as a decent voucher for macroscopic evaluation of its internal organs; however, it will not suffice for any type of detailed histology at the light microscopy or electron microscopy level.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the short answer is that it depends on the type of work you need to accomplish.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-04T23:37:25.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20235" PostTypeId="1" CreationDate="2014-08-05T04:13:30.797" Score="1" ViewCount="64" Body="&lt;p&gt;Why DNA gyrase inhibitor, such as Nalidixic acid and Norfloxacin, do not stop gyrase from cutting DNA helix but only prevent them from decatenation replicating DNA?&lt;/p&gt;&#xA;" OwnerUserId="6728" LastActivityDate="2014-08-05T19:29:35.007" Title="Mechanism of DNA gyrase inhibitor" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20236" PostTypeId="2" ParentId="20215" CreationDate="2014-08-05T05:16:35.953" Score="0" Body="&lt;p&gt;Also I don't know what kind of genetic input your given but if there is variation in origin ie some saliva some cheek skin then there could be a tissue based difference in the genome.  &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-08-05T05:16:35.953" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20237" PostTypeId="2" ParentId="20203" CreationDate="2014-08-05T05:27:40.770" Score="2" Body="&lt;p&gt;After you check your gel it would behoove you to check primers, preparation, the quality of the XNA itself, then proper electrophoresis levels and other mechanical failures. I would think improper resistance of the electrophoresis wiring would cause your problem.&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-08-05T05:27:40.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20238" PostTypeId="1" AcceptedAnswerId="20239" CreationDate="2014-08-05T07:26:13.923" Score="0" ViewCount="75" Body="&lt;p&gt;Is there some chemical or chemicals or even special molecules that can be 'injected' into cancer cells that will turn any Apoptosis mechanisms 'back on'?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or maybe chemicals and/or molecules that might cause a certain gene or set of genes to switch to a configuration favorable to apoptosis? &lt;/p&gt;&#xA;" OwnerUserId="6195" LastEditorUserId="6422" LastEditDate="2014-08-05T07:56:20.387" LastActivityDate="2014-08-05T08:14:25.300" Title="Regarding apoptosis and turning it 'back on'" Tags="&lt;cancer&gt;&lt;apoptosis&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20239" PostTypeId="2" ParentId="20238" CreationDate="2014-08-05T08:14:25.300" Score="2" Body="&lt;p&gt;Yes, tons of things induce apoptosis. Here is a good list that you can get for research grade&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sigmaaldrich.com/life-science/cell-biology/cell-biology-products.html?TablePage=9560323&quot; rel=&quot;nofollow&quot;&gt;Sigma-Aldrich&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even your immune system can tell cells to &quot;commit suicide.&quot; Now the trick is, getting drugs, proteins, pathways, and your immune system to selectively target cancer cells. &lt;/p&gt;&#xA;" OwnerUserId="3887" LastActivityDate="2014-08-05T08:14:25.300" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20240" PostTypeId="2" ParentId="15899" CreationDate="2014-08-05T09:36:26.800" Score="0" Body="&lt;p&gt;Fungi cannot develop resistance that quickly. Potassium permanganate is only used to clean wounds. Therefore, the reimmerging of the fungus may be because it wasn't killed in the first place. I suggest antifungal cream should be used generously to kill the roots of the fungus in his hands/feet.&lt;/p&gt;&#xA;" OwnerUserId="8627" LastActivityDate="2014-08-05T09:36:26.800" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20241" PostTypeId="2" ParentId="16034" CreationDate="2014-08-05T12:28:34.047" Score="1" Body="&lt;p&gt;Sulfur is $3^{rd}$ most abundant mineral element in the body. Carnivores obtain it from Cysteine and Methionine in the animal protein which converted in to Glutathione.&lt;br&gt;&#xA;Excess of sulfur is stored into Glutathione or oxidised to sulfate by sulfite oxidase which is eventually eliminated by urine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/a/a9/Glutathion.svg/466px-Glutathion.svg.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1]: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2198910&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nimni ME, Han B, Cordoba F (2007). &quot;Are we getting enough sulfur in our diet?&quot;. Nutr Metab (Lond) 4 (1): 24. doi:10.1186/1743-7075-4-24&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2]: &lt;a href=&quot;http://en.wikipedia.org/wiki/Sulfur_metabolism&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia on Sulfur metabolism&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.500" LastActivityDate="2014-08-05T12:28:34.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20242" PostTypeId="2" ParentId="7178" CreationDate="2014-08-05T12:51:59.393" Score="1" Body="&lt;p&gt;Closest I reached:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DoLXN.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: Page 105, The Complete Recovery, By Anthea Hatfield &lt;a href=&quot;http://books.google.co.in/books?id=HlGwAAAAQBAJ&amp;amp;printsec=frontcover#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Google Book&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/b/b6/Pethidine3DanBS.gif&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.517" LastActivityDate="2014-08-12T10:20:33.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20243" PostTypeId="2" ParentId="7810" CreationDate="2014-08-05T13:28:12.577" Score="2" Body="&lt;p&gt;Working with hot phenolic solutions is rarely been done due to the dangers of this. Phenol needs to be handled in the fume hood anyway, at higher temperatures it gets even more volatile. So if you plan to do this, do it with extra care to avoid injury.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is one paper that describes this method for bacteria, but this should work for other samples as well: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18674572&quot; rel=&quot;nofollow&quot;&gt;Evaluation of isolation methods and RNA integrity for bacterial RNA quantitation&lt;/a&gt;&quot;. However, there is another method, which was developed for extracting RNA from plant material infected by bacteria which is also worth a try (although it might need some adaptation), which works without hot phenol: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071639/&quot; rel=&quot;nofollow&quot;&gt;&quot;An optimized method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7&quot;&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-05T13:28:12.577" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20245" PostTypeId="2" ParentId="13797" CreationDate="2014-08-05T13:46:39.493" Score="5" Body="&lt;p&gt;According to the link you provided, the phenomenon Haidinger's Brush seems to be associated with the &lt;a href=&quot;http://en.wikipedia.org/wiki/Macula_of_retina&quot;&gt;macula of the retina&lt;/a&gt;. The yellow color of the macula may explain the yellowness of Haidinger's Brush. This suggests to me that the brush may be an artifact of the structure of the eye, and others have claimed that Haidinger's brushes probably do not have any ecological significance (Greenwood et al. 2003). If the brushes do not have an ecological significance, then they are very unlikely to have any evolutionary significance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The brushes may be visible to other primates, such as Macaques (Snodderly et al. 1984), as they have a macula structure very similar to the human macula. This leads me to think the phenomenon would also be potentially visible to other primates such as chimps and gorillas. If so, then our nearest ancestor (forebearer) that could potentially see the brushes would be the common ancestor of humans and chimps. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a broader review of polarized vision and underlying evolutionary hypotheses, the paper you linked to by Cronin et al. (2003) is a good review. I also came across a book, &lt;em&gt;Polarized Light in Animal Vision. Polarization Patterns in Nature.&lt;/em&gt; by Gábor Horváth and Deszö Varjú and published by Springer. The front matter and table of contents are &lt;a href=&quot;https://arago.elte.hu/sites/default/files/PolBook-front-material.pdf&quot;&gt;available here&lt;/a&gt;.  It appears to be a very thorough review of polarization vision in animals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cronin, T.W. et al. 2003. Polarization vision and its role in biological signaling. Integrative and Comparative Biology 43: 549-558.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Greenwood, V.J., et al. 2003. Behaviorial investigation of polarisation sensitivity in the Japanese quail (&lt;em&gt;Coturnix coturnix japonica&lt;/em&gt;) and the European starling (&lt;em&gt;Sturnus vulgaris&lt;/em&gt;). Journal of Experimental Biology 206: 3201-3210.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Snodderly, D.M., J.D. Auron and F.C. Delori. 1984. The macular pigmnent. II. Spatial distribution in primate retinas. Investigative Ophthalmology and Visual Science 25: 674-685&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-05T13:46:39.493" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20246" PostTypeId="2" ParentId="20211" CreationDate="2014-08-05T13:56:25.933" Score="4" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.genetik.uni-bayreuth.de/download/page_34/teach_85/Publikationsdateien/Themen_Schumann/19_GlascockGene223-221.pdf&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;, a single &lt;em&gt;lacI&lt;/em&gt; gene copy gives rise to about 10 copies of lacI protein per cell, and we can conclude, therefore, that this is the amount required to keep a single &lt;em&gt;lac&lt;/em&gt; operon repressed.  The article also mentions the &lt;em&gt;lacI&lt;sup&gt;Q&lt;/sup&gt;&lt;/em&gt; mutation in the promoter of &lt;em&gt;lacI&lt;/em&gt; that results in a ten-fold increase in the level of lacI protein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a &lt;em&gt;lac&lt;/em&gt; expression construct is present at more than 100 copies per cell the result will be leaky repression, and this can result in selection for mutations in the gene of interest if it has deleterious effects on the host bacteria. The easiest way around this problem is to put a &lt;em&gt;lacI&lt;/em&gt; (or &lt;em&gt;lacI&lt;sup&gt;Q&lt;/sup&gt;&lt;/em&gt;) gene on the expression plasmid so that repressor levels are commensurate with the number of copies of the &lt;em&gt;lac&lt;/em&gt; operator, as in the pET vectors.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-08-05T13:56:25.933" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20247" PostTypeId="1" AcceptedAnswerId="20322" CreationDate="2014-08-05T16:15:23.807" Score="3" ViewCount="293" Body="&lt;p&gt;I live on the Gulf Coast, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Vibrio_vulnificus&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Vibrio vulnificus&lt;/em&gt;&lt;/a&gt; has recently made the &lt;a href=&quot;http://www.wtsp.com/story/news/health/2014/08/04/vibrio-vulnificus-flesh-eating-bacteria/13580615/&quot; rel=&quot;nofollow&quot;&gt;news&lt;/a&gt; due to an increase in the number of reported infections. Naturally, it has people around here worried. I live in an area that was affected by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Deepwater_Horizon_oil_spill&quot; rel=&quot;nofollow&quot;&gt;BP Deepwater Horizon oil spill&lt;/a&gt;, and many people are concerned that the oil or byproducts of the clean-up could be fueling the growth of this and other bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that bacterial species which are capable of metabolizing the components of crude oil exist, but are rare. I also know that &lt;em&gt;Vibrio vulnificus&lt;/em&gt; thrives in warm salt water, and since it is a &quot;flesh-eating&quot; bacteria that infects shellfish, it must be capable of &quot;eating&quot; organic material.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can think of several possibilities that might explain an increase in reported infections:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The amount of bacteria and the number of infections is actually the same, but reports have increased due to more awareness in the public and in the medical community.&lt;/li&gt;&#xA;&lt;li&gt;Warmer water temperatures in the Gulf in recent years have led to more bacterial growth.&lt;/li&gt;&#xA;&lt;li&gt;The bacteria is capable of metabolizing crude oil, its degradation products, or one of the other cleanup chemicals (&lt;a href=&quot;http://en.wikipedia.org/wiki/Corexit&quot; rel=&quot;nofollow&quot;&gt;Corexit&lt;/a&gt;, for example).&lt;/li&gt;&#xA;&lt;li&gt;The oil spill has compromised the immune systems of the organisms that are typically &lt;em&gt;V. vulnificus&lt;/em&gt; hosts, which has led to higher infection rates and therefore, more bacteria.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;There could of course be other explanations, but these are the ones I came up with off the top of my head. I imagine that if bacterial populations actually have increased, then any of these scenarios that are possible would likely contribute something.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in the short amount of research I have done, I haven't been able to find any concrete data that shows whether populations have increased at all, or whether they could be affected by the oil spill.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Are there any studies that show the population of &lt;em&gt;V. vulnificus&lt;/em&gt; over a time period covering the BP Horizon spill (this happened in April 2010, and oil products are still washing up on beaches in small amounts)&lt;/li&gt;&#xA;&lt;li&gt;Is it possible that it could be metabolizing oil or other chemicals related to the spill?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8628" LastEditorUserId="8628" LastEditDate="2014-08-05T16:27:09.367" LastActivityDate="2014-08-07T20:19:56.897" Title="Could the growth rates of Vibrio vulnificus be affected by an oil spill?" Tags="&lt;bacteriology&gt;&lt;infection&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20248" PostTypeId="1" AcceptedAnswerId="20391" CreationDate="2014-08-05T16:28:22.040" Score="3" ViewCount="1782" Body="&lt;p&gt;i basically don't know the procedure or sequence of steps involved in the formation of anthers but i have read it somewhere it is formed from the dedifferentiation of shoot apical meristem of the axillary bud through mitotic divisions&#xA;&lt;img src=&quot;https://i.stack.imgur.com/rjfB8.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so is it necessary that every theca of an anther of an angiosperm must contain two microsporangia, if yes then why are they two in number., can i get an account on the development of microsporangial lobes [here i am not asking about the process of development of pollen grains in them].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;i am asking how the microsporangial lobes itself are formed&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a diagrammatic answer would be highly appreciated&lt;/p&gt;&#xA;" OwnerUserId="8101" LastEditorUserId="8101" LastEditDate="2014-08-07T16:11:44.923" LastActivityDate="2014-08-10T23:55:29.997" Title="is it necessary that every theca of an angiospermic anther must contain two microsporangia" Tags="&lt;botany&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20249" PostTypeId="2" ParentId="17584" CreationDate="2014-08-05T17:20:12.153" Score="1" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;Is SS clearly different from Natural Selection (NS)?&#xA;Is SS nested within NS or are NS and SS two different and (anti- or not) parallel processes?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Darwin, in &lt;em&gt;The Descent of Man, and Selection in Relation to Sex&lt;/em&gt; defined sexual selection as a type of selection that &amp;quot;depends on the advantage which certain individuals have over other individuals of the same sex and species, in exclusive relation to reproduction.&amp;quot; Throughout, he distinguishes between natural and sexual selection. This suggests to me that Darwin thought of them as different processes.  A spot check of various evolutionary texts show the authors all using some variation of Darwin's definition.&lt;/p&gt;&#xA;&lt;p&gt;In my opinion, the two are are clearly different but not necessarily separate. Both NS and SS affect fitness, a major component of the evolutionary process.  I tend to think of SS as nested within NS. NS affects fitness indirectly. Beneficial traits increase survivorship.  The longer individuals survive, the more reproductive opportunities they will have and fitness will, on average, increase. But, survivorship does not guarantee reproduction. Thus, I think natural selection acts indirectly on reproductive success.&lt;/p&gt;&#xA;&lt;p&gt;SS operates directly on reproductive success because males selected by females will reproduce, increasing their fitness. Sex is, after all, a natural process. In my view, female choice is the &amp;quot;environment&amp;quot; of the male (as far as reproduction) so variation of male traits in the female choice &amp;quot;environment&amp;quot; differentially affects the fitness of the males. That is natural selection.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Is the evolutionary processes due to sexual conflict are SS processes?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Absolutely. Sexual selection ultimately arises because of a difference between genders of energy investment in gametes. Males produce lots of gametes and relatively little energetic cost. Females produce relatively few gametes with lots of energetic cost (think of tiny sperm vs large, yolk-filled eggs). It benefits males to mate with as many females as possible because, even if a mating produces no offspring, he lost very little of his energy investment. Females will be choosier because they can't afford to waste gametes. Thus, there is an inherent conflict of interest between males and females.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Are the evolutionary processes of sexually antagonist genes SS processes?&#xA;Sexually antagonist genes are those genes where one allele is favored in females while another allele is favored in males (my own definition)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Are these genes related exclusively to reproduction?  If so, then that would be consistent with the original concept of SS. However, sexually antagonistic genes are not necessarily the result of or a cause of SS.  For example, Rice (1992) argued that sexually antagonistic genes may explain the evolutionary reduction of recombination between primitive sex chromosomes.&lt;/p&gt;&#xA;&lt;p&gt;Rice, W.R. 1992. Sexually antagonistic genes: Experimental evidence. Science 256: 1436-1439.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Can SS be accurately defined or is there a continuum of kinds or processes from complete SS processes to complete NS processes?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I think SS is accurately defined, but whether is is a type of NS or not is (I think) open for debate. As I described above, I think of SS as a particular type of NS, one that operates directly on reproductive success rather than indirectly.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Below is a list of scenarios where you can answer by yes or no whether SS is involved in the evolution of some feature. In all of these scenarios, we'll consider cases where the males have to find a mate…&lt;/p&gt;&#xA;&lt;p&gt;The males need good ears to find the females before other males. Is SS involved in the adaptation of ears abilities?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Depends. Do males &lt;em&gt;and females&lt;/em&gt; also use their ears for other purposes, such as detecting prey or predators?  Is hearing ability much greater in males than in females? Darwin specifically &lt;a href=&quot;http://darwin-online.org.uk/content/frameset?itemID=F937.1&amp;amp;viewtype=text&amp;amp;pageseq=269&quot; rel=&quot;nofollow noreferrer&quot;&gt;addresses such a scenario&lt;/a&gt;. (Last sentence of page 256, first part of page 257.)&lt;/p&gt;&#xA;&lt;p&gt;I think these ideas play out for most of your scenarios. It depends on if the traits differ between the sexes (not specified in your scenarios) and the traits lead directly to increased male reproductive success. But I will address one more.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The males need good camouflage because when they fly to find a mate they may get eaten by a predator and die before reproducing. Here the difference is that the predators are attracted to the spot if they can sense many males. So the presence of the other males influence the probability of finding a mate of a given male. Is SS is involved in the adaptation to good flying abilities?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;In this case, I would say not SS. The camoflage is necessary for survival, not direct reproductive success. This is natural selection.  Increasing the probability of finding a mate is not the same as guaranteed reproduction.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-08-05T17:20:12.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20250" PostTypeId="2" ParentId="17585" CreationDate="2014-08-05T17:40:08.197" Score="1" Body="&lt;p&gt;In the linked paper, the authors discuss this as sex-based gene expression that evolved by sex-specific selection. The expression is not limited to one sex (which are sex-limited genes). Sex-biased genes are expressed by both sexes, but differently between sexes.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-05T17:40:08.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20251" PostTypeId="1" AcceptedAnswerId="20253" CreationDate="2014-08-05T18:02:01.093" Score="4" ViewCount="237" Body="&lt;p&gt;I know that adult ladybird beetles can secrete a fluid to keep predators from eating them. Can the larvae do that too? Or are these yellow droplets something else?&#xA;&lt;img src=&quot;https://i.stack.imgur.com/kZf8x.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8630" LastActivityDate="2020-10-21T14:45:13.693" Title="Is this ladybird larva secreting a protective fluid?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20252" PostTypeId="2" ParentId="19725" CreationDate="2014-08-05T18:34:46.147" Score="5" Body="&lt;p&gt;What one thinks, no matter how intuitive it may appear is not particularly relevant in science.  The inductance associated with a neural axon has been well documented since Cole (1966).  Its role in the propagation of neural signals is developed extensively in &lt;a href=&quot;http://neuronresearch.net/hearing/pdf/7Projection.pdf#page=39&quot; rel=&quot;noreferrer&quot;&gt;http://neuronresearch.net/hearing/pdf/7Projection.pdf#page=39&lt;/a&gt; .  The actual development begins earlier in Section 7.4 on page 322 of that document.&lt;br&gt;&#xA;Failure to consider the inductance associated with any alternating electrical signal passed along a coaxial cable leads to disaster.  The first undersea cable based on the ideas of William Thompson,Lord Kelvin, and described as an RC cable by Hermann (page 322 in the above document) was a technical and financial disaster.  Two years later, a more sophisticated RLC cable based on Maxwell's Equations for a coaxial structure was laid with great success.  No RC cable has ever been used in practice since that time.  For unknown reasons, the biological community keeps trying to ignore the inductance of the coaxial myelinated axon (leading to ridiculous modeling data).  This appears to be the result of introductory courses in electricity for non-engineers trying to avoid the necessary mathematics to understand electromagnetic signal propagation through space and along various types of cables and waveguides.&lt;/p&gt;&#xA;" OwnerUserId="8613" LastActivityDate="2014-08-05T18:34:46.147" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20253" PostTypeId="2" ParentId="20251" CreationDate="2014-08-05T18:46:33.650" Score="4" Body="&lt;p&gt;&lt;strong&gt;In larvae stage Ladybird beetles secretes yellow gooey alkaloids from its abdomen.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ladybird beetles oozes hemolymph(in other word its blood), which is toxic and very smelly, when threatened. It's a mixture of various alkaloids and repulse the predators. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good Job, There might be no picture more clearer than you provided&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ifb73.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;source:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1]: &lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF01240602&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ladybird defence alkaloids: Structural, chemotaxonomic and biosynthetic aspects (Col.: Coccinellidae), Désiré Daloze, Jean-Claude Braekman, Jacques M. Pasteels&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2]: &lt;a href=&quot;http://insects.about.com/od/beetles/a/10-facts-ladybugs.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;10 Fascinating Facts About Ladybugs&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-02-03T18:33:22.173" LastActivityDate="2019-02-03T18:33:22.173" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="20254" PostTypeId="2" ParentId="510" CreationDate="2014-08-05T19:27:37.823" Score="5" Body="&lt;p&gt;This question is related to the question: Why are some things transparent and others opaque? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Being able to see something requires that it is opaque and that sufficient light illuminates it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;UV and shorter wavelengths are not as prevalent as visible light on earth. The world would appear too dark to see if we used UV and shorter wavelengths. This is because our atmosphere absorbs most high energy light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Infrared and longer wavelengths of light pass through many objects which would make vision difficult. There's less light here reaching the earth and even less being refracted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think about how much our vision relies on indirect light. The frequencies at which most objects are opaque makes those frequencies useful for vision due to the accumulation of refracted light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why are many objects opaque in the visible spectrum of light? Longer wavelengths of light have less energy than the valence electrons on most matter. Shorter wavelengths have too much energy, they cause chemical reactions, in addition to not being very prevalent on the surface of the earth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Electrons are what absorb then remit light and have thresholds based on their chemistry for what they can absorb. No absorption = transparent. Too much energy and chemical reactions start to happen, which may be undesirable, or desirable in the synthesis of vitamin D by UV light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants extract energy for chemical reactions from wavelengths shorter than infrared, which is too weak to drive photosynthesis, and not as abundant as visible light. But also absorb wavelengths longer than ionizing frequencies, which are not very prevalent, and usually cause damage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Visible light is the spectrum of light which is prevalent enough on earth to see, but is not so energetic it would harm biological systems. The qualities for optimal light frequencies in sight and photosynthesis overlap because they have similar mechanisms for interacting with light. What is this mechanism? The chemistry of carbon based life.&lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-09T00:50:16.597" LastActivityDate="2014-08-09T00:50:16.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20255" PostTypeId="2" ParentId="20235" CreationDate="2014-08-05T19:29:35.007" Score="1" Body="&lt;p&gt;This might be a good article to read: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24497635&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/24497635&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Robert Kerns's lab has been doing a lot of work on fluoroquinolines, so look into his other work as an entry to the literature. And apparently X-ray crystals have been done for at least parts of this complex. There is some evidence for fluoroquinolines binding to DNA, then moving into the protein as it moves along the DNA. &lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-05T19:29:35.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20256" PostTypeId="2" ParentId="20205" CreationDate="2014-08-05T20:09:23.823" Score="0" Body="&lt;p&gt;I would argue that the behaviors you saw in these are not altruistic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Baboons will aggressively defend their territories against predators.  For example, watch this baboon chase a female lion.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=4ebd36p4zkw&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=4ebd36p4zkw&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The baboon eventually loses but only when the lion gets help. I'd say the baboons were just chasing away the cheetah and the hyenas as a matter of self defense. The antelope just got lucky.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same applies for the elephant. It doesn't really approach the buffalo and lion. The lion runs off soon after the elephant arrives in the area.  Elephants will also aggressively chase off predators likelions. The lions are right to be afraid. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=JDJV_nSqDDw&quot; rel=&quot;nofollow&quot;&gt;https://www.youtube.com/watch?v=JDJV_nSqDDw&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Same applies for the hippos. They can be aggressive towards crocodiles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=BTcMHB1Wubc&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=BTcMHB1Wubc&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the hippo &quot;saving&quot; the wildebeest, we always have to be careful about interpretation. Just because it looks like the hippo was trying to save the life of the wildebeest does not mean that it was the hippo was actually doing. For example, it may have simply been trying to remove the wildebeest from its territory. At times, the hippo puts its mouth around the wildebeest. Was it considering taking a bite? Was it trying to prod the wildebeest? Was it trying to play with the wildebeest? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's very difficult to demonstrate that any of the behaviors in the videos were displays of altruism.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-05T20:09:23.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20257" PostTypeId="2" ParentId="20203" CreationDate="2014-08-06T00:03:23.720" Score="1" Body="&lt;p&gt;First as you mentioned, which is I think the key thing, is that you need to clarify what DNA sample it is that you are observing in the gel. The best thing to do to ensure that you only have PCR generated DNA samples is that once your PCR is over, treat your DNA mixture with Dpn I enzyme, which cuts methylated DNA, which is essentially cellular DNA as they get methylated in cells and it should not effect you PCR generated DNA as it won't be methylated. Look at page 7 and page 12 of this document for further instructions on using Dpn I (&lt;a href=&quot;http://www.chem.agilent.com/library/usermanuals/Public/210518.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.chem.agilent.com/library/usermanuals/Public/210518.pdf&lt;/a&gt;). You can subsequently clean and isolate your PCR generated DNA using any kit such as QIAquick gel extraction kit (QAGEN) using essentially this protocol but you are not using any gels (&lt;a href=&quot;http://sites.bio.indiana.edu/~chenlab/protocol_files/agarose_gel_extraction.pdf&quot; rel=&quot;nofollow&quot;&gt;http://sites.bio.indiana.edu/~chenlab/protocol_files/agarose_gel_extraction.pdf&lt;/a&gt;). You can use other kits but this always worked for me! (please note that I'm not promoting any kits here!!) Now if you have any amplicons from your PCR then you should be able to nanodrop it (using the 260/230 ratio as your guide) and get a reasonable value for your amplicon concentration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now if at this stage you still have your PCR DNA as indicated by nanodrop and perhaps a test digest still gives the expected bands then the problem is with the running process and highly likely your gel which was the first thing I suspected to be the case. If not then you do not have any amplicons and you are simply trying to run your original DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although I have never worked with very large cellular DNA molecules before (I work with plasmids), however I was trained to run very large DNA (in agarose gel) on very low voltage such as 10-50 V overnight in a cold room since large cellular DNA doesn't tend to run very well in gels although that mostly applies to chromosomal DNA but 10kb is still quite large. I have run plasmid DNA of 12 kb in gels before at higher voltages but low voltage is best and it avoids tearing and shearing the DNA!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-06T00:12:53.337" LastActivityDate="2014-08-06T00:12:53.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20259" PostTypeId="1" AcceptedAnswerId="20270" CreationDate="2014-08-06T06:20:37.597" Score="1" ViewCount="1746" Body="&lt;p&gt;How does an embryo produce waste products even when its organ systems are not developed fully ? How does the placenta identify or differentiate waste materials from embryo ? Which organelle or specific cell acts as excretory organ ?&lt;/p&gt;&#xA;" OwnerUserId="8580" LastActivityDate="2014-08-06T12:29:37.963" Title="Waste generation by embryo" Tags="&lt;reproduction&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-08-06T18:53:09.363" ContentLicense="CC BY-SA 3.0" />
  <row Id="20263" PostTypeId="2" ParentId="7010" CreationDate="2014-08-06T08:39:14.750" Score="0" Body="&lt;p&gt;In addition to the above answers, the answer to your question also depends on your definition of immortality. There are a number of clonal organisms (the most famous of which is probably Pando, a quaking aspen &lt;a href=&quot;https://en.wikipedia.org/wiki/Pando_%28tree%29&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Pando_%28tree%29&lt;/a&gt; ) where there is a large area, sometimes multiple square miles, where individual shoots are sent above ground, giving anyone in the area the impression of a forest, but all of the trees are connected underground in one single large root system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such an organism could certainly be considered immortal, as its stems will constantly die off and be replaced by new organic material, enabling the network as a whole to live for tens of thousands of years (so far).&lt;/p&gt;&#xA;" OwnerUserId="8633" LastActivityDate="2014-08-06T08:39:14.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20264" PostTypeId="1" AcceptedAnswerId="20265" CreationDate="2014-08-06T08:49:51.693" Score="6" ViewCount="44749" Body="&lt;p&gt;According to my textbook, Davson-Danielli's model of a phospholipid bilayer sandwiched between two layers of globular protein was incorrect. The nonpolar protein portions would separate the polar portions of the phospholipids from water, causing the bilayer to dissolve. Meaning, the Davson-Danielli model is not only incorrect, but it is also impossible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand why the model is incorrect, but not why it is impossible. In my view, the nonpolar proteins would remain together in a micelle shape due to hydrophobic exclusion. Because of this, the phospholipid bilayer sandwiched on the inside would remain isolated from the water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why would a bilayer dissolve if the proteins were in contact with water and the phospholipids were isolated from the water? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that my confusion stems from many misunderstandings about the chemistry and structure of the cell membrane. In depth illustration of the error that my book mentioned would be most helpful.&lt;/p&gt;&#xA;" OwnerUserId="5179" LastEditorUserId="3553" LastEditDate="2016-06-10T07:03:46.930" LastActivityDate="2016-06-10T07:03:46.930" Title="Why was the Davson-Danielli model rejected?" Tags="&lt;cell-membrane&gt;&lt;history&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20265" PostTypeId="2" ParentId="20264" CreationDate="2014-08-06T09:24:17.620" Score="7" Body="&lt;p&gt;The original figure that Danielli and Davson proposed looks like this (from the &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jcp.1030050409/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;original publication&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZVnDo.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It shows the phospholipid bilayer of the membrane (which is correct) embedded between two layers of globular proteins. The hydrophobic tails of the lipids are orientated towards each other, while the hydrophilic heads are oriented to the outside.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although the membrane composition is correct (this was already published 1925 by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19868999&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gorter and Grendel&lt;/a&gt;), there are some problems with the proposed model:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Membranes are not identical. The differ in thickness and the ratio of&#xA;proteins:lipids.&lt;/li&gt;&#xA;&lt;li&gt;Membranes have distinct inside and outside layers (defined by the&#xA;membrane proteins which are present on the surface of the membrane)&lt;/li&gt;&#xA;&lt;li&gt;Other than predicted by the model, the membrane proteins do not have&#xA;a very good solubility in water - in fact they are amphiphatic,&#xA;meaning they have hydrophilic and hydrophobic regions. The&#xA;hydrophobic side is anchored inside the membrane.&lt;/li&gt;&#xA;&lt;li&gt;When the membrane proteins would cover the lipid bilayer, their&#xA;hydrophobic regions would be in contact with water, which&#xA;destabilizes this construct. Even if they would be oriented towards&#xA;the membrane, they would face towards the hydrophilic heads of the&#xA;phospholipids causing the same effect. Additionally the proteins&#xA;would also seperate the hydrophilic phospholipid heads from the&#xA;water. So there is no real stable solution in embedding the membrane&#xA;with proteins.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-06T09:24:17.620" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20266" PostTypeId="1" AcceptedAnswerId="20267" CreationDate="2014-08-06T10:45:48.283" Score="2" ViewCount="875" Body="&lt;p&gt;I understand that in PCR we're able to amplify only selected portions of the DNA... however despite reading it from multiple sources, I cannot figure out how this selection actually takes place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that by using proper primers, one each for coding and template strands, we can direct the DNA polymerases to specific sites to start with. I also understand that these primers make the replication proceed in opposite directions, towards each other. Like follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9N6Ug.png&quot; alt=&quot;My understanding of so far&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I wonder what makes the replication terminate when the polymerase reaches the primer at the other end? Because as far as I understand, replication should continue indefinitely until the physical end of the sample strand is reached... such that we may decide the starting points but never the ending points.&lt;/p&gt;&#xA;" OwnerUserId="8636" LastActivityDate="2014-08-06T16:12:17.843" Title="How are DNA segments selected in PCR?" Tags="&lt;molecular-biology&gt;&lt;pcr&gt;&lt;dna-replication&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20267" PostTypeId="2" ParentId="20266" CreationDate="2014-08-06T11:07:35.203" Score="7" Body="&lt;p&gt;Note: In your PCR program you always set extension time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Case:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Product length = 500bp&lt;/li&gt;&#xA;&lt;li&gt;PCR extension time = 50sec&lt;/li&gt;&#xA;&lt;li&gt;Assuming that polymerase adds 1000 nt/min&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Cycle 1:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Strand that binds FP: extends ~800nt to the right (as per the polymerization rate): 300 bp ahead of RP complementary site. This product is lets say &lt;code&gt;P1&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;Strand that binds RP: extends ~800nt to the left: 300bp ahead of FP complementary site. This is &lt;code&gt;P2&lt;/code&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vhjVq.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cycle 2: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The products of cycle-1 become templates for next round. &#xA;FP binds to &lt;code&gt;P2&lt;/code&gt; -300nt from its 3' end. Similarly RP binds to &lt;code&gt;P1&lt;/code&gt; -300nt from its 3' end.&#xA;The resultant products will be 500nt which give rise to a 500bp perfect dsDNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WYfGy.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some &lt;code&gt;P1&lt;/code&gt; and &lt;code&gt;P2&lt;/code&gt; will keep forming at a linear rate; since your template is low in amount compared to the amplified cycle1 and cycle-2 products, your expected PCR product will be much higher (which gets produced at an exponential rate).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-08-06T16:12:17.843" LastActivityDate="2014-08-06T16:12:17.843" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20268" PostTypeId="2" ParentId="20266" CreationDate="2014-08-06T11:21:47.617" Score="4" Body="&lt;p&gt;I'm not completely clear when you say &quot;what makes the replication terminate when the polymerase reaches the primer at the other end&quot; since when you perform a PCR you go through three phases. The denaturation, whereby the two DNA strands become single stranded, then the annealing, which is when primers attach to their appropriate matching site (but the original DNA template is still single stranded) and extension, which is when DNA polymerase use the primers to extend make the matching strand the primer is attached to (&lt;a href=&quot;http://en.wikipedia.org/wiki/Polymerase_chain_reaction&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Polymerase_chain_reaction&lt;/a&gt;). DNA polymerase continues to make the strand until it essentially either drops off or until the cycle is over and it is time for the cycle to repeat itself. The way you make sure to terminate a specific DNA replication at an appropriate length is to use the extension time as a control since as pointed in the above answer by @WYSIWYG the extension is largely assumed to be 1000 nt/min so if your product of interest is 500 bp, then you do 30-40 sec of extension in your PCR extension cycle program and if the product of interest is 1000 bp you do 60 sec of extension and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the training I received, it is usually not recommended to PCR DNA template which is very large such as an entire plasmid such as pUAST. The main issue even with high fidelity/proff-reading DNA polymerases is that you can get errors in replication if the strand is very long. what often happens is that you amplify a section of DNA if you want to check for the presence of something or if you need to use the amplified fragment then you design restriction sites at either end of your fragment by incorporating it in the primers itself then you go ahead with you digestion and fragment purification and then you sequence your fragment to make sure you do not have any errors although PCR has much much more applications.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-06T11:35:23.020" LastActivityDate="2014-08-06T11:35:23.020" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20269" PostTypeId="1" CreationDate="2014-08-06T11:26:25.217" Score="1" ViewCount="198" Body="&lt;p&gt;Where can I find some datasets of aligned nucleotide sequences? And what should I assume about the accuracy of the alignments there?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I would like to use such datasets for training the alignment model I am working on. In particular, to help me get an estimate on some parameters such as the frequency of single nt INDEL at some locations.)&lt;/p&gt;&#xA;" OwnerUserId="8060" LastEditorUserId="8060" LastEditDate="2014-08-08T20:39:52.807" LastActivityDate="2014-09-20T06:06:18.677" Title="Datasets of aligned nucleotide sequences" Tags="&lt;bioinformatics&gt;&lt;sequence-analysis&gt;&lt;sequence-alignment&gt;" AnswerCount="1" CommentCount="13" ClosedDate="2014-09-21T17:14:05.393" ContentLicense="CC BY-SA 3.0" />
  <row Id="20270" PostTypeId="2" ParentId="20259" CreationDate="2014-08-06T12:29:37.963" Score="2" Body="&lt;p&gt;Embryos still metabolize the nutrients delivered by the mother. The metabolism takes place in the cells, including in the developing organs. Metabolism produces waste products that must be removed. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Allantois&quot; rel=&quot;nofollow&quot;&gt;allantois&lt;/a&gt; is the structure that removes waste from the embryo. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure what you mean by the placenta identifying or differentiating waste materials from the embryo. The waste simply diffuses passively into the mother's blood from the embryo. The mother's excretory systems then handle it.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-06T12:29:37.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20271" PostTypeId="2" ParentId="17185" CreationDate="2014-08-06T13:25:57.257" Score="2" Body="&lt;p&gt;I don't know what background you have given the kids or what level, but here's something we do in a non-majors freshman level biology course that could easily be adjusted. First, to get them thinking about trees and relationships, give them a simple family genealogy (use only 1 parent for simplicity). I use my family tree going back to my grandmother. With cousins, aunts, and siblings, they begin to understand how to interpret family trees. You can substitute the family names with organism names to make it a basic phylogenetic tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We teach tree construction simply. We give students a list of six species (fake birds) with DNA sequences that are only 20 nucleotides long. Students have to calculate the number of base pair differences between each pair of sequences which, in our case, range from 2-10 nucleotides. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They then use the pairwise differences to construct their tree, with the understanding that fewer nucleotide differences between organisms means they are more closely related.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can do this type of activity over a couple of days (depending on time). Then, you can begin to show them trees that become gradually more complex. Because the kids will have constructed a tree and now &lt;em&gt;how&lt;/em&gt; it is constructed, they will have a much easier time interpreting larger trees.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-06T13:25:57.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20272" PostTypeId="2" ParentId="9832" CreationDate="2014-08-06T13:26:44.850" Score="1" Body="&lt;p&gt;Actaully there are quite a few animals which actually moves there lower eyelids:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Most of the birds&lt;/li&gt;&#xA;&lt;li&gt;Reptiles(Except Snake)&lt;/li&gt;&#xA;&lt;li&gt;Amphibians&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-08-06T13:26:44.850" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20273" PostTypeId="2" ParentId="17185" CreationDate="2014-08-06T13:31:53.600" Score="5" Body="&lt;p&gt;As per your requirements I will suggest:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.onezoom.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.onezoom.org/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4IXP7.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-01-31T02:09:18.910" LastActivityDate="2019-01-31T02:09:18.910" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="20274" PostTypeId="2" ParentId="9832" CreationDate="2014-08-06T13:45:51.240" Score="1" Body="&lt;p&gt;Nictitating membrane (inner eyelid) of sharks can cover sharks eye as it moves from the upper to the lower eye lid (&lt;a href=&quot;http://en.wikipedia.org/wiki/Nictitating_membrane&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Nictitating_membrane&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="6511" LastEditDate="2014-08-06T14:36:33.497" LastActivityDate="2014-08-06T14:36:33.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20275" PostTypeId="2" ParentId="19525" CreationDate="2014-08-06T13:57:13.537" Score="2" Body="&lt;p&gt;Thanks for your answer Alexandria,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you didn't seem entirely confident about the innervation in the skull bone, I ended up asking the neurosurgeon, and she indeed only anaesthetises the skin surrounding the drill hole and the subcutaneous tissue as the bone does not have nociceptive innervation in that area. &#xA;So you are right for the leg: if chopped off, you would still feel the pain from the nerves in the bone. In the case of deep brain stimulation however, the skull does not have nociceptive innervation in the area where the holes are drilled.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leaves the question of why there are some exceptions to bone innervation, but that's a problem for another day. &lt;/p&gt;&#xA;" OwnerUserId="8260" LastEditorUserId="8260" LastEditDate="2014-08-09T17:54:50.210" LastActivityDate="2014-08-09T17:54:50.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20276" PostTypeId="1" CreationDate="2014-08-06T14:09:51.097" Score="4" ViewCount="318" Body="&lt;p&gt;What is the relationship between &lt;strong&gt;mN&lt;/strong&gt; and &lt;strong&gt;mg&lt;/strong&gt; as the units involved to measure the changes in contraction?  A tool most widely used is an instrument called myograph. In these exoeriments, either units of &lt;strong&gt;mg&lt;/strong&gt; or &lt;strong&gt;mN&lt;/strong&gt; is used without any mention of why. Note that the first two examples use an experimental tool called a &lt;strong&gt;myograph&lt;/strong&gt; - used to measure the force produced by a muscle (in this case muscular blood vessels) when under contraction. Both examples mention tension. Wether these myograph experiments are completely different i'm unsure.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;This example shows force as 'mN' from &lt;a href=&quot;http://ajplung.physiology.org/content/293/4/L982&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper Fig 1A a&lt;/a&gt;.&lt;/strong&gt;&#xA;Those who are interested the caption is as follows&#xA;&lt;em&gt;&quot;Effects of Li+-PSS and NMDG-PSS in PGF2α-preconstricted pulmonary arteries. Intrapulmonary arteries (IPA) were first exposed to 80 mM K+, and endothelial function was assessed by relaxation of PGF2α contractions (10 μM) to acetylcholine (10 μM). Following a period of recovery, IPA were preconstricted to 10–15% 80K using PGF2α, and then physiological saline solution (PSS) was replaced by Li+-PSS in the continuing presence of the same concentration of PGF2α in endothelium-intact IPA&quot;&lt;/em&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/DNgCn.png&quot; alt=&quot;&quot;&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;This example shows units as 'g'. note that some examples from other papers also use units of mg essentiall x1000 similar to other unit conversions&lt;/strong&gt; from&#xA;&lt;a href=&quot;http://ajpcell.physiology.org/content/302/1/C307&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper Fig 1a&lt;/a&gt;.&#xA;The caption is pretty much the same as 1. Particularly thromboxane A2 (TXA2) is a pharmacological agent affecting a set of ion channels:&#xA;&lt;em&gt;&quot;Requirement of thromboxane A2 (TXA2) for hypoxic pulmonary vasoconstriction (HPV) in rat pulmonary arteries (PAs). A: hypoxia alone (3% PO2) did not &lt;strong&gt;induce contraction of PA (left)&lt;/strong&gt;. In the presence of 10 nM U46619, hypoxia &lt;strong&gt;induced a strong contraction&lt;/strong&gt; equivalent with the response to high K+ (80K, right)&quot;&lt;/em&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/HRz4S.png&quot; alt=&quot;&quot;&gt; &lt;/li&gt;&#xA;&lt;li&gt;For a third example &lt;a href=&quot;http://www.medsci.org/v10p0771.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;click here&lt;/a&gt;. It does interestingly state &lt;em&gt;&quot;The PA rings were stretched to a predetermined optimal passive tension of &lt;strong&gt;750 mg&lt;/strong&gt;&quot;&lt;/em&gt;. As such mg (or g) is an alternative representation of a unit of force as presumed. Figure 1 in this link again demonstrates mg as an y-axis unit of measurement under myograph experiment&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8637" LastEditorUserId="15950" LastEditDate="2019-01-25T10:19:53.293" LastActivityDate="2019-01-25T10:19:53.293" Title="Relationship between mN and mg in vessel contraction studies?" Tags="&lt;physiology&gt;&lt;blood-circulation&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="20277" PostTypeId="1" AcceptedAnswerId="20281" CreationDate="2014-08-06T14:28:28.167" Score="4" ViewCount="160" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In all &lt;a href=&quot;http://en.wikipedia.org/wiki/Eutheria&quot; rel=&quot;nofollow&quot;&gt;eutherian&lt;/a&gt; (mammals excluding the marsupials), the female (who is $XX$ for the pair of sexual chromosomes) inactivates one of her $X$. This is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Dosage_compensation&quot; rel=&quot;nofollow&quot;&gt;dosage compensation&lt;/a&gt;. This inactivation occurs at a given time during the development when randomly one $X$ is silenced. The daughters of this cell inherit the $X$-inactivation pattern epigenetically, which results in some part of a tissue having the maternal $X$ inactivated while others having the paternal $X$ inactivated (daughters of some other cell which silenced the paternal $X$). This process yield to the famous &lt;a href=&quot;http://en.wikipedia.org/wiki/Tortoiseshell_cat&quot; rel=&quot;nofollow&quot;&gt;turtoiseshell&lt;/a&gt; coat in female cats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;In short&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming X-inactivation occurred in the lineage of the oogonia/oocytes, when does the X-inactivation and X-reactivation occur in the lineage of the oocytes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;A bit developed&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are the X inactivated as well in primary oocytes? If not, is the $X$ inactivated in the secondary oocytes in a primary follicle? If not, did the diploid mother cells of the secondary oocytes have one $X$-inactivated? If yes, did all diploid mother cells of oocytes have the same $X$ inactivated (inactivation occurred relatively early in the development or is there an imprinting) or did the mother cells of oocytes differ in the $X$ they have inactivated (inactivation occurred relatively late in the development)&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-08-21T01:20:54.033" LastActivityDate="2014-08-21T01:20:54.033" Title="X-inactivation in ovaries" Tags="&lt;genetics&gt;&lt;chromosome&gt;&lt;epigenetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20278" PostTypeId="2" ParentId="19525" CreationDate="2014-08-06T14:53:36.140" Score="1" Body="&lt;p&gt;Sharp acute pain in response to acute physical breach comes mainly from the superficial periosteal innervation, and not much from internal bone innervation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am an orthopedic surgery internee. It's in our routine to drill ~3-5mm dia rods (steinmann pins) through bones of lower limb including femur, tibia and calcaneum. We too only inject anesthetic deeply into the skin, but that probably covers the perisoteal innervation too. At the end, when we doo the drilling, despite the great width of these aforementioned bones in comparision with the skull, patient seems calm while we transit through bone, and is only uneasy when the two skin ends are breached.&lt;/p&gt;&#xA;" OwnerUserId="8636" LastActivityDate="2014-08-06T14:53:36.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20279" PostTypeId="2" ParentId="19484" CreationDate="2014-08-06T15:19:24.403" Score="3" Body="&lt;p&gt;I think Wallace (1968) developed the ideas of hard and soft selection, as they relate to &lt;a href=&quot;http://www.blackwellpublishing.com/ridley/a-z/Genetic_load.asp&quot; rel=&quot;nofollow&quot;&gt;genetic load&lt;/a&gt;. He further explains the concept in Wallace (1975). As the idea was his, I'd go with Wallace's definition over Whitlock's.  I haven't had time to watch the Whitlock video to see if they are saying more or less the same thing overall.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider a hypothetical population of individuals, each with 1000 loci (I'm basing example and ideas on an example given by Ridley 2004, pgs. 162-167). Heterozygotes at each locus has the greatest fitness (&lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/misconcep_04&quot; rel=&quot;nofollow&quot;&gt;heterozygote advantage&lt;/a&gt;). Homozygotes at any locus will have reduced fitness. Therefore, the fitness of each genotype is given as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AA: $1-s_{AA}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aa: $1$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;aa: $1-s_{aa}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if every individual in the population at time zero was heterozygous at each locus, Mendelian inheritance ensures that no individuals will be heterozygous at &lt;em&gt;all&lt;/em&gt; loci after the second generation.  Assume that fitness reduction at each homozygous locus is just 1%. Given that well over half of the loci will be homozygous, fitness of those individuals will be reduced to 0. They will die before reproducing.  This is hard selection.  If hard selection of this magnitude occurred in a population, then extinction would occur. This is what Wallace (in your link) is saying.  This mortality due to the genetic load is &lt;em&gt;added&lt;/em&gt; to the normal background mortality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Soft selection compares the fitness of an individual to the genotype with the greatest fitness in the population, even if that genotype does not the theoretical optimum fitness. Soft selection &lt;em&gt;replaces&lt;/em&gt; some of the background mortality with selective mortality, so the population size is not decreased overall.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ridley, M. 2004. &lt;em&gt;Evolution.&lt;/em&gt; 3rd ed. Blackwell Publishing, Malden, Massachusetts, USA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wallace, B. 1968. Polymorphism, population size, and genetic load. pp. 87-108 in R.C. Lewontin, ed. Population biology and evolution. Syracuse University Press, Syracuse, New York, USA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wallace, B. 1975. Hard and soft selection revisited. Evolution 29: 465-473.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-06T15:19:24.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20280" PostTypeId="2" ParentId="19629" CreationDate="2014-08-06T15:19:57.107" Score="2" Body="&lt;p&gt;there is no question there is a rough correlation between neuron count and intelligence capability in a &lt;em&gt;general way&lt;/em&gt; from looking at the biological species &quot;spectrum&quot; &lt;em&gt;outside&lt;/em&gt; of humans. see wikipedia &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_animals_by_number_of_neurons&quot; rel=&quot;nofollow&quot;&gt;list of animals by number of neurons&lt;/a&gt;. eg in wide differences such as comparing insects vs primates etcetera. there is also a rough correlation of neuron count with body mass and total cell count in animals. however within a single species, small variations in neuron count probably do not have much effect on overall intelligence. also it is known that &lt;a href=&quot;http://en.wikipedia.org/wiki/Neanderthal&quot; rel=&quot;nofollow&quot;&gt;homo neanderthalensis&lt;/a&gt;, the ~30k yr precursor to [homo sapiens] had a larger brain cavity and therefore presumably more neurons but apparently less intellectual capacity than &lt;a href=&quot;http://en.wikipedia.org/wiki/Homo_sapiens&quot; rel=&quot;nofollow&quot;&gt;homo sapiens&lt;/a&gt;, possibly one factor in its extinction due to competitive evolutionary pressures. even various gorilla species have larger brain mass and conceivably correspondingly larger amounts of neurons (under a rough assumption that neuron density per mass would not vary strongly). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;it is also thought that brain size has been affected by evolutionary pressure wrt smaller skull size which has to comfortably fit through the birth canal as a constraint. another aspect to study is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Enteric_nervous_system&quot; rel=&quot;nofollow&quot;&gt;enteric nervous system&lt;/a&gt; in the human which has a large number of neurons but does not seem to exhibit a large measurable &quot;intelligence&quot; in the classic sense of guiding the animal behavior, but conceivably uses significant processing to manage gastrointestinal control.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;another aspect of the question to consider: &lt;a href=&quot;http://en.wikipedia.org/wiki/Programmed_cell_death#Role_in_the_development_of_the_nervous_system&quot; rel=&quot;nofollow&quot;&gt;programmed cell death in the developing nervous system&lt;/a&gt;. large numbers of neurons die during normal natal development in &quot;critical windows&quot; and this seems to show that biologically, total number of neurons is apparently not a key measure or controller of intelligence (otherwise evolutionary pressures would tend to decrease this). the nervous system appears to grow &quot;extra&quot; neurons more than &quot;necessary&quot; for smooth functioning of the human organism.&lt;/p&gt;&#xA;" OwnerUserId="5734" LastActivityDate="2014-08-06T15:19:57.107" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20281" PostTypeId="2" ParentId="20277" CreationDate="2014-08-06T16:47:50.287" Score="1" Body="&lt;p&gt;See these two papers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000860#abstract0&quot; rel=&quot;nofollow&quot;&gt;Early Loss of Xist RNA Expression and Inactive X Chromosome Associated Chromatin Modification in Developing Primordial Germ Cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.0030116&quot; rel=&quot;nofollow&quot;&gt;X Chromosome Reactivation Initiates in Nascent Primordial Germ Cells in Mice&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Basically it happens just before the meiosis. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-08-06T16:47:50.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20282" PostTypeId="1" AcceptedAnswerId="20283" CreationDate="2014-08-06T16:56:22.817" Score="3" ViewCount="657" Body="&lt;p&gt;Is it possible that a finger/thumb bone fracture is so superficial, that the doctor does not need to realign (re-set) the bone before applying the cast? Or does it &lt;em&gt;always&lt;/em&gt; require for even a finger/thumb broken bone to be put back in place before applying the cast?&lt;/p&gt;&#xA;" OwnerUserId="5362" LastEditorUserId="5144" LastEditDate="2014-08-06T17:50:29.437" LastActivityDate="2014-08-07T05:09:51.627" Title="Can a broken thumb/finger bone not require realignment of the bone?" Tags="&lt;bone-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20283" PostTypeId="2" ParentId="20282" CreationDate="2014-08-06T17:49:48.593" Score="2" Body="&lt;p&gt;Yes. You can figure that yourself if you look a bit at the types of fractures on Wikipedia, the &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Bone_fracture#Classification&quot; rel=&quot;nofollow&quot;&gt;Bone Fracture&lt;/a&gt;&lt;/em&gt; page:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Other considerations in fracture care are displacement (fracture gap) and angulation. If angulation or displacement is large, reduction (manipulation) of the bone may be required and, in adults, frequently requires surgical care.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;[...]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Other types of fracture are:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Complete fracture: A fracture in which bone fragments separate completely.&lt;/li&gt;&#xA;  &lt;li&gt;Incomplete fracture: A fracture in which the bone fragments are still partially joined. In such cases, there is a crack in the osseous tissue that does not completely traverse the width of the bone.&lt;/li&gt;&#xA;  &lt;li&gt;[...]&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Incomplete fractures and fractures with less or no displacement may heal correctly in some situations without needing realignment.&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-08-06T17:49:48.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20284" PostTypeId="1" CreationDate="2014-08-06T18:38:53.060" Score="1" ViewCount="389" Body="&lt;p&gt;I am looking for a freely distributed dataset of microscopic images. I am hoping to find a dataset that would feature histological images before and after staining (e.g. H&amp;amp;E or some other standard one, preferably). I have been searching through various databases, but I cannot find a proper set. I hope the sample size to be at least about 100. Suggestions?&lt;/p&gt;&#xA;" OwnerUserId="8640" LastActivityDate="2014-08-07T17:06:16.383" Title="Dataset of microscopic images before and after staining?" Tags="&lt;microscopy&gt;&lt;database&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20285" PostTypeId="1" AcceptedAnswerId="20289" CreationDate="2014-08-06T20:10:20.593" Score="1" ViewCount="75" Body="&lt;p&gt;What could cause a mammal to have and respond to a sense of touch with only isolated numbness but not feel pain?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="9943" LastEditDate="2016-03-10T20:55:09.933" LastActivityDate="2016-03-10T20:55:09.933" Title="What could cause no pain but sense of touch?" Tags="&lt;neuroscience&gt;&lt;touch&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20286" PostTypeId="1" AcceptedAnswerId="20288" CreationDate="2014-08-06T20:17:16.457" Score="1" ViewCount="28" Body="&lt;p&gt;I'll start by saying that I am no biologist. I am a math major trying to create a mathematical model for gonorrhea strain competition. My assignment is to create a model similar to a model that was already was already created, see page 9 of &lt;a href=&quot;http://mtbi.asu.edu/files/Evolution_of_within-host_Antibiotic_Resistance_in_Gonorrhea.pdf&quot; rel=&quot;nofollow&quot;&gt;Evolution of within-host Antibiotic Resistance in Gonorrhea&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wanted to try to incorporate the efflux pump into a mathematical model. Before I do that, I would first like to see whether efflux is gained through mutations. If it is, my model will be pointless since mutations are already covered in the original model from the research paper. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Feel free to add better tags. I thought mine was appropriate.&lt;/p&gt;&#xA;" OwnerUserId="8641" LastEditorUserId="1320" LastEditDate="2014-08-07T07:13:48.930" LastActivityDate="2014-08-07T07:14:03.283" Title="Are efflux pumps mutations or are they originally present in N. gonorrhoea?" Tags="&lt;bacteriology&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20288" PostTypeId="2" ParentId="20286" CreationDate="2014-08-06T22:27:24.463" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://en.m.wikipedia.org/wiki/Efflux_(microbiology)&quot; rel=&quot;nofollow&quot;&gt;Efflux pumps&lt;/a&gt; are common in bacteria, as well as eukaryotes. The mutations included in their model would not include efflux pumps. A mutation could potentially affect the efficiency of a pump in a strain but the mutations in their model are not creating the pumps.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="1320" LastEditDate="2014-08-07T07:14:03.283" LastActivityDate="2014-08-07T07:14:03.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20289" PostTypeId="2" ParentId="20285" CreationDate="2014-08-06T22:52:28.483" Score="1" Body="&lt;p&gt;I think &lt;a href=&quot;http://en.wikipedia.org/wiki/Congenital_insensitivity_to_pain_with_anhidrosis&quot; rel=&quot;nofollow&quot;&gt;Congenital insensitivity to pain with anhidrosis&lt;/a&gt; might be what you are looking for, it is the closest thing I can think of right now.&lt;/p&gt;&#xA;" OwnerUserId="8643" LastActivityDate="2014-08-06T22:52:28.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20291" PostTypeId="1" AcceptedAnswerId="20295" CreationDate="2014-08-06T23:12:26.773" Score="8" ViewCount="611" Body="&lt;p&gt;I understand that evolution occurred to form the current hominids from a common ancestor millions of years ago. As evolutionary processes take a long time, is there proof of evolution occurring with humans today?&lt;/p&gt;&#xA;" OwnerUserId="8644" LastEditorUserId="5144" LastEditDate="2014-08-07T09:02:12.787" LastActivityDate="2014-08-07T12:40:33.130" Title="Human Evolution in Modern Times" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20292" PostTypeId="2" ParentId="19629" CreationDate="2014-08-07T00:51:38.993" Score="5" Body="&lt;p&gt;Unlike a computer, the speed at which any brain can perform a computation is related to the number of synapses it goes through. This means fewer synapses in series correlate with decreased reaction time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of fewer neurons correlating with a decrease in reaction time is exemplified in sensory neurons. All sensory nerve cell bodies are all located in the dorsal ganglia of the spine. Only projections from single nerve cells here reach our tissues. Furthermore, it's only in ganglia, nuclei, and the cortex that we see additional nerve cells. This is because each nerve cell in series introduces latency. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Latency in our sensory and motor circuits is very important to survival. Our intelligence is limited by a pressure to have a desirable reaction time. Reaction time does correlate intelligence. This is why tests of the sort are timed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is another factor in intelligence relating to number of neurons: An increase in grey matter means an increase in white matter. There has been some speculation that humans have nearly reached the limit of our cognitive ability, as our ability to store white matter has been reached. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We seem to be occupying the intelligence Goldilocks zone where reaction time, energy consumption, white matter are all in near optimal balance. It's the balance of these things, the sophistication of the circuits themselves that determine intelligence, not neuron count.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.dailymail.co.uk/sciencetech/article-2020546/Full-brim-Scientists-claim-human-brain-capacity-tiring-smarter.html&quot; rel=&quot;nofollow&quot;&gt;Here's a news link about running out of room for white matter&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jneurosci.org/content/27/30/8122.full&quot; rel=&quot;nofollow&quot;&gt;Here's a study which correlates perception time with reaction time&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-07T17:48:08.977" LastActivityDate="2014-08-07T17:48:08.977" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20293" PostTypeId="2" ParentId="19396" CreationDate="2014-08-07T04:27:43.753" Score="10" Body="&lt;p&gt;As the previous answers clarify, all organisms have heritable traits that may be manipulated through selective breeding. It is the pragmatics that can be prohibitively challenging. From an (zoo)archaeological point of view, few animals have actually been domesticated, and only recently in our species' history. The dog is an unusual case, perhaps domesticated 14,000 years ago; most domesticated animals only show skeletal changes within the last 10,000 years. Cats, compared to livestock's total dependence on humans, are 'barely' domesticated--they got used to humans while camping out in Egyptian storehouses where all the mice were, perhaps around 4,000 years ago, but even today a fluffy house cat will revert to a feral state if abandoned. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many animals are behaviourally unsuitable for domestication. If an animal is dangerously aggressive, for example, they cannot be penned and isolated--so the many controlled generations it takes to reduce their baseline aggression cannot occur. Humans also tend to co-opt pre-existing social structures in a species, such as becoming the 'alpha' in a dog pack or the head 'ram' of a sheep herd. Species without a hierarchy or herd mentality are difficult to control and keep track of, and so do not lend themselves to human care. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You mentioned tigers in your question. Tigers have little to offer people (other than pelts), they're massive/aggressive, and they're jungle loners. You can't raise a herd of tigers; they'll kill each other and the survivor will kill you. That they're carnivores is also challenging, since a carnivore is much more expensive to feed than a bunch of grass-munching sheep. Altogether, there was never a situation in prehistory that would have turned tigers into giant house cats. House cats eat unwanted mice; tigers eat your cattle (and children). The occasional tiger 'pet' won't change that. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Domestication, outside of recent experiments (like the Russian foxes mentioned above), has always been a protracted, indirect process. People started interfering with animals that were already useful in some way(s). Dogs offer warmth, hunting aid, defence, transport, and (in a pinch) food. Alligators, tigers, and sharks are not useful enough to make the danger and cost of raising them worthwhile. Even if you did eventually produce a 'human-friendly' shark, there would still be a 'wild' population ready to eat you--and your complacent pet sharks, too!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a very readable explanation, try the chapter on domestication in Jared Diamond's (1997) &lt;em&gt;Guns, Germs, and Steel&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8646" LastActivityDate="2014-08-07T04:27:43.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20294" PostTypeId="2" ParentId="20282" CreationDate="2014-08-07T05:09:51.627" Score="1" Body="&lt;p&gt;Most finger fractures (including the thumb) and, for that matter, hand fractures will not need to be &quot;reset&quot; before applying a cast, as most fractures are simple and non-displaced. More serious fractures (displaced, involving an articular surface, and many comminuted fractures) will need manipulation and possibly pinning. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But to answer your question, the fracture need not be incomplete to be casted/immobilized without manipulation. It is not rare, but common.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-08-07T05:09:51.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20295" PostTypeId="2" ParentId="20291" CreationDate="2014-08-07T06:12:06.667" Score="9" Body="&lt;p&gt;Yes, there are examples. First: If you want to say, that humans and monkeys evolved, than it is better to say that they evolved from a common ancestor. This makes quite a difference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are looking for examples of human evolution then one of the most obvious traits under evolutionary selection is pigmentation. There is a clear correlation with lattitude (and this UV-index):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/czKjb.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AOmDt.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The changes in pigmentation occured - seen from a evolutionary perspective - pretty recent when humans moved out of africa and to other regions (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22923467&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;).&#xA;See these papers for more details:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0047248400904032&quot; rel=&quot;noreferrer&quot;&gt;The evolution of human skin coloration&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20445093&quot; rel=&quot;noreferrer&quot;&gt;Colloquium paper: human skin pigmentation as an adaptation to UV&#xA;radiation.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24112698&quot; rel=&quot;noreferrer&quot;&gt;Epidermal pigmentation in the human lineage is an adaptation to&#xA;ultraviolet radiation.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Other examples would be the tolerance for lactose (the sugar contained in the milk) in adults which arose during the last 5-10.000 years. Normally only babies can process these sugar which is contained in large amounts in the mothers milk. When they are weaned, usually the enzyme is not expressed anymore. However with the settling of the humans and the domestication of cattle this changed, so we can still drink milk and eat milk products without producing intestinal problems. See here for more details:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15114531&quot; rel=&quot;noreferrer&quot;&gt;Genetic signatures of strong recent positive selection at the lactase&#xA;gene.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15777735&quot; rel=&quot;noreferrer&quot;&gt;Adult-type hypolactasia and regulation of lactase expression.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;A third example would be the sickle-cell anemia, which happens due to a point mutation in the human hemoglobin protein. This causes an aggregation of the hemoglobin molecules in the red blood cells which then leads to a reduced elasticity (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22372205&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; for more details). It also leads to a protection against malaria (most likely by the reduction of the life span of the erythrocytes). The areas with high prevalence of the sickel cell anemia in africa correlate pretty nicely with the distribution of malaria.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.0020128&quot; rel=&quot;noreferrer&quot;&gt;An Immune Basis for Malaria Protection by the Sickle Cell Trait&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.mjhid.org/article/view/10928/html&quot; rel=&quot;noreferrer&quot;&gt;Sickle Cell Anaemia and Malaria&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you look further, you will find a number of different examples, where evolution is present after humans went through a genetic bottleneck (meaning the number of humans was drastically reduced).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-08-07T12:40:33.130" LastActivityDate="2014-08-07T12:40:33.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20296" PostTypeId="2" ParentId="19998" CreationDate="2014-08-07T06:50:51.427" Score="0" Body="&lt;p&gt;I am not sure whether I grasped the gist of your question appropriately, but let me provide some clarifications.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\text{Nerve}$ is simply a collection of axons. Therefore, all the spinal nerves are just bundles of assorted nerve axons.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the origin of nerve is slightly ambiguous as far as its meaning is considered. It can mean the &lt;strong&gt;physical origin&lt;/strong&gt;, the place where the particular branch of nerve starts off from a main trunk or some other nervous organ. It can also mean the location of the cell bodies the axons of which comprise the nerve, the &lt;strong&gt;functional origin&lt;/strong&gt;.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now coming back to the question, the &lt;em&gt;physical&lt;/em&gt; origin of the spinal nerves is not common. Each pair of spinal nerves originates from a specific segment of the spinal cord via two roots, the dorsal and the ventral. Therefore, each nerve originates separately and different spinal nerves cannot be traced back to a common physical origin. (The &lt;a href=&quot;http://en.wikipedia.org/wiki/Cauda_equina&quot; rel=&quot;nofollow&quot;&gt;cauda equina&lt;/a&gt;, is actually a collection of several spinal nerves which move dorsally and periodically gives of the nerves out of the vertebral column. Although the nerves comprising the Cauda Equina, second lumbar nerve onwards, appear to have a common origin, they actually originate from their own specific segment and then move caudally as a bundle to overcome the developmental constraint of spinal cord being shorter than the vertebral column, necessitating the caudal movement of nerves within the column to emerge at appropriate points)  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;functional&lt;/em&gt; origin is a bit more complicated. This is because each spinal nerve has a variety of nerve fibres. There are some sensory fibres with cell bodies in the dorsal root ganglion, there are motor fibres with their cell bodies in spinal cord, there are sympathetic fibres with cell bodies in the series of collateral or the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sympathetic_ganglion&quot; rel=&quot;nofollow&quot;&gt;sympathetic ganglia&lt;/a&gt;, connected to the spinal nerve via gray and white &lt;a href=&quot;http://en.wikipedia.org/wiki/Ramus_communicans&quot; rel=&quot;nofollow&quot;&gt;ramus communicans&lt;/a&gt;. There can also be cell bodies located directly in medulla which passes nerve fibres in cranial nerves as well as through its branches into the sympathetic ganglia and ultimately into the spinal nerves. Sacral nerves also contain parasympathetic nerve fibres functionally originating in the CNS. Thus, considering the functional origin, though each spinal nerve has a lot of origins, there is a slight convergence of origins for different nerves. The sympathetic ganglia and the spinal cord are two places where the origins of different spinal nerves may coincide or be structurally and functionally integrated.  But it must be kept in mind that this is a very limited convergence. There is an appreciable uniqueness to the functional origin of each spinal nerve and hence we cannot say that they &quot;meet&quot;.&lt;br&gt;&#xA;&lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/8/87/Spinal_nerve_CAT.svg&quot; rel=&quot;nofollow&quot;&gt;IMAGE&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3776" LastActivityDate="2014-08-07T06:50:51.427" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20298" PostTypeId="1" AcceptedAnswerId="20302" CreationDate="2014-08-07T10:24:17.940" Score="0" ViewCount="1361" Body="&lt;p&gt;My &lt;em&gt;very&lt;/em&gt; basic understanding is DNA gets transcribed into RNA by effectively replacing thymine with uracil, then RNA is translated to make proteins. Looking at it from an engineering perspective, it would appear that, while the RNA to protein translation is non-trivial, the DNA to RNA transcription process is rather redundant: As it's just a simple replacement, why not start with RNA in the first place? My assumption therefore is that there is something about the RNA molecule (e.g., too reactive, too unstable, etc.) that requires it to be put in &quot;cold storage&quot; as DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't have a background in genetics or biology, so could someone ELI5 why DNA is needed?&lt;/p&gt;&#xA;" OwnerUserId="8650" LastEditorUserId="8517" LastEditDate="2014-08-07T12:48:34.660" LastActivityDate="2014-08-07T12:59:26.737" Title="What is the purpose of DNA?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;rna&gt;" AnswerCount="3" CommentCount="0" ClosedDate="2014-08-07T20:32:50.513" ContentLicense="CC BY-SA 3.0" />
  <row Id="20299" PostTypeId="2" ParentId="20298" CreationDate="2014-08-07T10:29:55.757" Score="0" Body="&lt;p&gt;OK, I found this on &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA,_RNA_and_proteins:_The_three_essential_macromolecules_of_life#Why_DNA_is_best_for_encoding_genetic_information&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;. I probably should have checked there first!&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;DNA has three primary attributes that allow it to be far better than&#xA;  RNA at encoding genetic information. First, it is normally&#xA;  double-stranded, so that there are a minimum of two copies of the&#xA;  information encoding each gene in every cell. Second, DNA has a much&#xA;  greater stability against breakdown than does RNA, an attribute&#xA;  primarily associated with the absence of the 2'-hydroxyl group within&#xA;  every nucleotide of DNA. Third, highly sophisticated DNA surveillance&#xA;  and repair systems are present which monitor damage to the DNA and&#xA;  repair the sequence when necessary. Analogous systems have not evolved&#xA;  for repairing damaged RNA molecules.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8650" LastActivityDate="2014-08-07T10:29:55.757" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20301" PostTypeId="2" ParentId="20291" CreationDate="2014-08-07T12:39:58.867" Score="5" Body="&lt;p&gt;&lt;strong&gt;Lactase persistance is evidence of recent and ongoing natural selection in humans.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mammalian young produce lactase, an enzyme needed to break down the lactose sugar in the mother's milk. The young quit producing lactase after they are weaned because they no longer drink milk. Most humans (roughly 70%) also quit producing lactase when they are young. Without lactase, the adults can't break down the lactose sugars if they consume milk. The lactose builds up in the gut, which supports large populations of bacteria that cause gas and indigestion. This is &lt;a href=&quot;http://digestive.niddk.nih.gov/ddiseases/pubs/lactoseintolerance/&quot; rel=&quot;noreferrer&quot;&gt;lactose intolerance&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The remaining humans (about 30%) continue to produce lactase into adulthood. They can digest the lactose milk sugar so they do not suffer lactose intolerance. The persistence of the lactase enzyme in adults is associated with the human domestication of cattle.  A study by &lt;a href=&quot;http://www.micro.utexas.edu/courses/kalthoff/bio346/PDF/Readings/03Bersaglieri%20et%20al.%20(2004).pdf&quot; rel=&quot;noreferrer&quot;&gt;Todd Bersaglieri and colleagues&lt;/a&gt; (2004) showed that a mutation that allowed for continued lactase production spread rapidly by natural selection through populations in north European-derived people between 5000-10,000 years ago.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, a separate study by by &lt;a href=&quot;http://eebweb.arizona.edu/Faculty/Nachman/Archived%20Research%20Papers/Tishkoff_et_al_2007.pdf&quot; rel=&quot;noreferrer&quot;&gt;Sarah Tishkoff and her colleages&lt;/a&gt; (2007) identified a &lt;em&gt;different&lt;/em&gt; mutation that also allowed for continued lactase production spread quickly by natural selection through populations in east central Africa during the past 7000 years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Together these studies show how natural selection can act very quickly in humans. Two different mutations occurred in two different populations of humans. Both mutations, however, gave the same selective advantage of lactase persistance in developing agriculturally-based societies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bersaglieri, T. et al. 2004. Genetic signatures of strong recent positive selection at the lactase gene. American Journal of HUman Genetics 74: 1111-1120.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tishkoff et al. 2007. Convergent adaptation of human lactase persistance in Africa and Europe. Nature Genetics 39: 31-40.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-07T12:39:58.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20302" PostTypeId="2" ParentId="20298" CreationDate="2014-08-07T12:41:29.423" Score="3" Body="&lt;p&gt;Imagine you want to produce a widget. You have thousands of worker, but only one blueprint. Each worker needs the blueprint to build a widget (they're really forgetful and can't build from memory). So only one worker at a time can build your widgets.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you would do is to create copies of your blueprint and distribute them to your workers. That way multiple workers can produce the widget at the same time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA is the blueprint, and RNA is the copy. Your workers are the ribosomes that translate the RNA into proteins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is of course grossly simplified, and there are other reasons for the specific arrangement, but this is certainly one of the reasons why the intermediate RNA is used.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-08-07T12:41:29.423" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20303" PostTypeId="1" AcceptedAnswerId="21049" CreationDate="2014-08-07T12:59:20.720" Score="5" ViewCount="173" Body="&lt;p&gt;It is possible that strong (clearly visible) pattern of selection towards particular parameter is &lt;strong&gt;detectable only in environment with high variability&lt;/strong&gt; (&lt;em&gt;difference between used &lt;strong&gt;(red)&lt;/strong&gt; and non-used &lt;strong&gt;(grey)&lt;/strong&gt; space will be significant&lt;/em&gt;) whereas in sub-optimal environment used and non-used space do not differ due to low variability. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;And if this is possible, is there any relevant study which focuses on such issue?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/A3eCc.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;P.S. It seems to be very basic idea, however I could not find any relevant sources on this topic.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8500" LastActivityDate="2014-09-23T11:25:26.750" Title="Could habitat selection pattern be deformed in environment with low variability?" Tags="&lt;ecology&gt;&lt;environment&gt;&lt;selection&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20304" PostTypeId="2" ParentId="20298" CreationDate="2014-08-07T12:59:26.737" Score="1" Body="&lt;p&gt;RNA was almost certainly the first genetic molecule of inheritance. However, the single-stranded nature of RNA is not particularly stable and thus would not be reliable for the long-term storage of genetic information necessary for reproduction (and ultimately evolution).  The necessary stability is provided by DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question becomes, how did DNA evolve to replace RNA? This is an area of active research but &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK6360/&quot; rel=&quot;nofollow&quot;&gt;here is a nice summary&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-07T12:59:26.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20305" PostTypeId="1" CreationDate="2014-08-07T13:12:37.250" Score="5" ViewCount="866" Body="&lt;p&gt;Is dried grain considered dead or dormant botanically?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://hermeneutics.stackexchange.com/questions/12956/john-1224-does-the-grain-of-wheat-actually-die&quot;&gt;Related to a BH-SE questio&lt;/a&gt;n.&lt;/p&gt;&#xA;" OwnerUserId="8652" LastEditorUserId="-1" LastEditDate="2017-04-13T12:47:47.680" LastActivityDate="2019-03-14T14:58:40.367" Title="Is dried grain dead or dormant?" Tags="&lt;botany&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20306" PostTypeId="2" ParentId="15540" CreationDate="2014-08-07T13:43:54.960" Score="6" Body="&lt;p&gt;The urogenital system as a cohesive functional unit probably evolved very early in vertebrate history. Hagfishes and lampreys have separate systems for reproduction and excretion. More derived groups of fishes use kidney tubules and ducts for sperm delivery outside the body (Helfman et al. 2009). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The vertebrate nephron may be homologous to the invertebrate nephridia (&lt;a href=&quot;http://icb.oxfordjournals.org/content/34/4/542.short&quot;&gt;Ruppert 1994&lt;/a&gt;). The genetics underlying the development of vertebrate female reproductive organs shows many homologies with invertebrate reproductive organs (&lt;a href=&quot;http://www.nature.com/nrg/journal/v4/n12/full/nrg1225.html&quot;&gt;Kobayashi and Behringer 2003&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would hypothesize that the both the reproductive and extrectory systems of vertebrates show corresponding homologies to invertebrate organ systems (at least genetic and developmental homologies) but evolution of the urogenital organ system did not evolve until the early vertebrates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Helfman, G.S. et al. 2009. &lt;em&gt;The Diversity of Fishes. Biology, Evolution and Ecology.&lt;/em&gt; Wiley-Blackwell, Oxford, UK.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kobayashi, A. ad R.R. Behringer. 2003. Developmental genetics of the female reproductive tract in mammals. Nature Reviews Genetics 4: 969-980.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ruppert, E.E. 1994. Evolutionary origin of the vertebrate nephron. American Zoologist 34: 542-553.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-07T13:43:54.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20307" PostTypeId="2" ParentId="10605" CreationDate="2014-08-07T14:36:22.437" Score="3" Body="&lt;p&gt;It will depend on how quickly the salinity is raised and to what level.  Two studies (&lt;a href=&quot;ftp://mail.manomet.org/Water/For_DEP/Literature/Karraker_2007_roadsalt_greenfrog.pdf&quot; rel=&quot;nofollow&quot;&gt;Karraker 2007&lt;/a&gt;, &lt;a href=&quot;http://www.esajournals.org/doi/abs/10.1890/07-1644.1&quot; rel=&quot;nofollow&quot;&gt;Karraker et al. 2008&lt;/a&gt;) looked at the effects of road salt (used to reduce icing on roads in winter) in the spotted salamander, the wood frog (a small frog), and the green frog (a big frog). Their studies showed that survival decreased, especially for larval individuals, as salt concentration increased. Deformities in embryos and larvae increased with salt concentrations$^1$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another study (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/030096299290274T&quot; rel=&quot;nofollow&quot;&gt;Shpun et al. 1992&lt;/a&gt;) showed that a few species of frogs and toads that could tolerate high levels of blood plasma urea concentrations could also tolerate elevated levels of NaCl in their environment (but not all species that had high urea tolerance could tolerate high environmental salt concentrations.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There would naturally be an upper limit of salt tolerance in amphibians, especially if they are not able to retain or regain water at a rate they are losing it to the high salinity environment.  The studies suggest that higher salinities do decrease survivorship and increase deformities. While they may acclimate to the short term, I would question long term adaptation unless the rate of salinity increase is very gradual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Footnote&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;They made their salt solutions based on conductivity, measured as microsiemens. For lab experiments, they made salt solutions that varied from 5 µS (control) to 3000 µS. These translate to 1 mg/L to 945 mg/L Cl$^-$.  In the field, they measured salt concentrations that were more than 3000 µS.  &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Karraker, N.E. 2007. Are embryonic and larval green frogs (&lt;em&gt;Rana clamitans&lt;/em&gt;) insensitive to road deicing salt? Herpetological Conservation and Biology 2: 35-41.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Karraker, N.E. et al. (2008). Impacts of road deicing salt on the demography of vernal pool-breeding amphibians. Ecological Applications 18: 724-734.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-07T14:36:22.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20308" PostTypeId="1" AcceptedAnswerId="20316" CreationDate="2014-08-07T14:59:41.047" Score="2" ViewCount="663" Body="&lt;p&gt;According to my psychology textbook (Psychological Science: Modeling Scientific Literacy), high levels of epinephrine and low levels of cortisol are signs of stress. However, earlier in the textbook it is shown that the autonomic response of the human body releases norepinephrine and epinephrine, while the hypothalamic pituitary adrenal (HPA) axis pathway releases cortisol. So it seems to me that signs of stress would be high levels of both of these things. Is my textbook wrong or am I just understanding what stage of stress it's describing?&lt;/p&gt;&#xA;" OwnerUserId="5427" LastActivityDate="2014-08-07T18:23:34.783" Title="Why are high levels of epinephrine and low levels of cortisol signs of stress?" Tags="&lt;human-biology&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20309" PostTypeId="2" ParentId="20305" CreationDate="2014-08-07T15:26:07.193" Score="7" Body="&lt;p&gt;Dried grains are very mostly viable means they are in a dormant state until and unless suitable condition are provided. More dried it will be viable for longer.&lt;/p&gt;&#xA;&lt;p&gt;In fact there are seeds found in Siberia which are ~32,000 years and still viable.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/rIihP.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/rIihP.jpg&quot; alt=&quot;&quot; /&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Courtesy: &lt;a href=&quot;http://news.nationalgeographic.com/news/2012/02/120221-oldest-seeds-regenerated-plants-science/&quot; rel=&quot;noreferrer&quot;&gt;National Geographic&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Source:&#xA;&lt;a href=&quot;https://www.usaemergencysupply.com/information_center/packing_your_own_food_storage/seed_viability/introduction_to_seed_viability.htm#.U-OZHfmSzQI&quot; rel=&quot;noreferrer&quot;&gt;US Emergency Supply: Introduction to Seed Viability&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-03-14T14:58:40.367" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="20310" PostTypeId="1" CreationDate="2014-08-07T16:18:52.577" Score="2" ViewCount="1743" Body="&lt;p&gt;In some microscopic images, there is a bar scale at one of the corners or near a specific object. How are they added to the images? Does the slide have some markers, or are they digitally added? If so, how are they computed? I am planning to buy a microscope and wondering is there something I should look for. Thanks for any help!&lt;/p&gt;&#xA;" OwnerUserId="8653" LastActivityDate="2015-05-08T23:45:19.410" Title="Microscope scale bar" Tags="&lt;microscopy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20311" PostTypeId="2" ParentId="20310" CreationDate="2014-08-07T16:26:29.667" Score="1" Body="&lt;p&gt;It depends on the type of microscope you want to buy. Most microscopes come with a slide with precise measurement bars on them and you select the objective and if it is connected to some sort of camera and comes with a software then you can calibrate the scale bar for a particular objective using the software it comes with. Otherwise if you know the pixel per micron for each objective, then once you acquired your images, you can draw a scale bar using a software like Image-J. In terms of what microscope to buy and what to look for, it depends on the application so you need to clarify the question. I have answered a question similar to this here (&lt;a href=&quot;https://biology.stackexchange.com/questions/5470/what-to-look-for-when-buying-a-light-microscope/17313#17313&quot;&gt;What to look for when buying a light microscope?&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-08-07T16:56:37.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20312" PostTypeId="2" ParentId="20284" CreationDate="2014-08-07T16:39:12.243" Score="2" Body="&lt;p&gt;Virtual fly brain (&lt;a href=&quot;http://www.virtualflybrain.org/site/stacks/index.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.virtualflybrain.org/site/stacks/index.htm&lt;/a&gt;) is an excellent database of fly (&lt;em&gt;Drosophila&lt;/em&gt;) brain sections, which can be electronically processed/annotated/highlighted on the fly to show different areas of the fly brain as an overlay on top of the original images.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, you can use BrainTrap (&lt;a href=&quot;http://fruitfly.inf.ed.ac.uk/braintrap/&quot; rel=&quot;nofollow&quot;&gt;http://fruitfly.inf.ed.ac.uk/braintrap/&lt;/a&gt;) for the expression of proteins in the fly (&lt;em&gt;Drosophila&lt;/em&gt;) brain using brain sections. Another database which has silver stains of &lt;em&gt;Drosophila&lt;/em&gt; brain sections is the flybrain (&lt;a href=&quot;http://flybrain.neurobio.arizona.edu/Flybrain/html/atlas/&quot; rel=&quot;nofollow&quot;&gt;http://flybrain.neurobio.arizona.edu/Flybrain/html/atlas/&lt;/a&gt;) database. This database also contains 3D models of different fly brain structures and much more!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure there are many many similar databases, but these are the ones I knew of, which are widely used in the &lt;em&gt;Drosophila&lt;/em&gt; community.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-07T17:06:16.383" LastActivityDate="2014-08-07T17:06:16.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20314" PostTypeId="2" ParentId="14740" CreationDate="2014-08-07T17:43:35.687" Score="1" Body="&lt;p&gt;As pointed out by @kmm (&lt;a href=&quot;http://cancer.sanger.ac.uk/cancergenome/projects/cell_lines/&quot; rel=&quot;nofollow&quot;&gt;http://cancer.sanger.ac.uk/cancergenome/projects/cell_lines/&lt;/a&gt;) is an excellent database. Alternatively you can look at the broad institute page (&lt;a href=&quot;http://www.broadinstitute.org/software/cprg/?q=data-resource&quot; rel=&quot;nofollow&quot;&gt;http://www.broadinstitute.org/software/cprg/?q=data-resource&lt;/a&gt;) in the cancer cell line encyclopedia section, then go to the browse tab and select the cell line for a very comprehensive list of cell lines.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-08-07T17:43:35.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20315" PostTypeId="2" ParentId="775" CreationDate="2014-08-07T18:03:32.970" Score="2" Body="&lt;p&gt;I can make a rough analogy in terms of digital media storage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our memories exist as a relationship between our perceptions and our sensations. Computers store input readily. However, humans store memories perceptually. This means who we are and how we remember an event permanently changes our recollection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at the progression of lossy video codecs as resolution has increased you'll see the algorithms have changed. Each generation has become accustomed to seeing certain types of video artifacts: from film, to analog static, to vhs, to h.264. Think of the algorithms as individual modes of perception. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We have ancient basal circuits which allow visual and frontal cortex areas to collaborate in the formation of memories. It's not an objective process. We all have our own algorithms. &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-07T18:11:37.997" LastActivityDate="2014-08-07T18:11:37.997" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20316" PostTypeId="2" ParentId="20308" CreationDate="2014-08-07T18:23:34.783" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;So it seems to me that signs of stress would be high levels of both of these things.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes. Wikipedia claims [1] the same:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Stressors [...] activate the HPA axis, though via different pathways. [...] Stressors that are uncontrollable, threaten physical integrity, or involve trauma tend to have a high, flat diurnal profile of cortisol release (with lower-than-normal levels of cortisol in the morning and higher-than-normal levels in the evening) resulting in a high overall level of daily cortisol release. On the other hand, controllable stressors tend to produce higher-than-normal morning cortisol.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The same on a webpage of Society for Endocrinology [2]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In addition, in response to stress, extra cortisol is released to help the body to respond appropriately.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yet, there are conditions in which stress can lower cortisol levels. One of them is psoriazis [3]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] patients with persistently high levels of stressors seem to have a specific psychophysiological profile of lowered cortisol levels and may be particularly vulnerable to the influence of stressors on their psoriasis. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And some psychiatric disorders [4]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Several stress-associated neuropsychiatric disorders, notably posttraumatic stress disorder and chronic pain and fatigue syndromes, paradoxically exhibit somewhat low plasma levels of the stress hormone cortisol.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Hypothalamic–pituitary–adrenal axis,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Hypothalamic%E2%80%93pituitary%E2%80%93adrenal_axis&amp;amp;oldid=619115237&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Hypothalamic%E2%80%93pituitary%E2%80%93adrenal_axis&amp;amp;oldid=619115237&lt;/a&gt; (accessed August 7, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Society for Endocrinology. &lt;em&gt;Hormones. Cortisol&lt;/em&gt; (2013). Available from &lt;a href=&quot;http://www.yourhormones.info/hormones/cortisol.aspx&quot; rel=&quot;nofollow&quot;&gt;http://www.yourhormones.info/hormones/cortisol.aspx&lt;/a&gt; (accessed 07.08.2014)&lt;/li&gt;&#xA;&lt;li&gt;Evers AW, Verhoeven EW, Kraaimaat FW, de Jong EM, de Brouwer SJ, Schalkwijk J, Sweep FC, van de Kerkhof PC. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20716227&quot; rel=&quot;nofollow&quot;&gt;How stress gets under the skin: cortisol and stress reactivity in psoriasis.&lt;/a&gt; Br. J. Dermatol. 2010 Nov;163(5):986-91. doi: &lt;a href=&quot;http://dx.doi.org/10.1111/j.1365-2133.2010.09984.x&quot; rel=&quot;nofollow&quot;&gt;10.1111/j.1365-2133.2010.09984.x&lt;/a&gt;. PubMed PMID: 20716227. &lt;/li&gt;&#xA;&lt;li&gt;Yehuda R, Seckl J. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21971152&quot; rel=&quot;nofollow&quot;&gt;Minireview: Stress-related psychiatric disorders with low cortisol levels: a metabolic hypothesis.&lt;/a&gt; Endocrinology. 2011 Dec;152(12):4496-503. doi: &lt;a href=&quot;http://dx.doi.org/10.1210/en.2011-1218&quot; rel=&quot;nofollow&quot;&gt;10.1210/en.2011-1218&lt;/a&gt;. PubMed PMID: 21971152. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-08-07T18:23:34.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20318" PostTypeId="2" ParentId="15209" CreationDate="2014-08-07T18:36:19.820" Score="3" Body="&lt;p&gt;Actually the new data set will be,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;for k = 4 (&lt;a href=&quot;https://en.wikipedia.org/wiki/K-mer&quot; rel=&quot;nofollow noreferrer&quot;&gt;k-mer value&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CGTTCT -&gt; CGTT GTTC TTCT&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dEyr9.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874646/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874646/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-08-07T18:36:19.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20319" PostTypeId="2" ParentId="8319" CreationDate="2014-08-07T18:44:23.957" Score="2" Body="&lt;p&gt;Options:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;You can always &lt;a href=&quot;ftp://data.modencode.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;download the data&lt;/a&gt; (as @WYSIWYG has suggested in the comment). &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Transfer the data to &lt;a href=&quot;https://usegalaxy.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Galaxy&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Convert and export the selection of your choice.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/csXc2.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://modencode.oicr.on.ca/fgb2/gbrowse/fly/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://modencode.oicr.on.ca/fgb2/gbrowse/fly/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-08-07T18:44:23.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20320" PostTypeId="2" ParentId="14733" CreationDate="2014-08-07T19:03:27.110" Score="4" Body="&lt;p&gt;This is a very good question and it highlights a very frequent misconception about cell culture and it is using the passage numbers as an indication of how well a cell is behaving. Although this can be a good barometer but it is misleading. Passaging can stress the cells if performed very frequently, although again that depends on how fast the cells are dividing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should not think of passage (and cell culture in general) in terms of the procedure itself but in terms of population doubling (PD) which can be calculated using the formula provided here (&lt;a href=&quot;http://www.sciencellonline.com/site/techsupport.php&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencellonline.com/site/techsupport.php&lt;/a&gt;). I personally use [Log10(harvesting cell No/seeding cell No)/Log10(2)]. This should allow you to characterise your cellular behaviour between every passage and allows you to draw a cumulative PD graph. Once the cumulative PD versus time becomes non-linear, then you would know that the cells have changed behaviour and it might be best to use a fresh stock.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main advantage of this method is that you are not relying on guess work and deal with solid numbers and allows you to predict when you should expect to start a fresh batch for passage. Although passage numbers can do the same job if you assume per passage, the cells have done a certain PD but this is more of a guess work and you can not track how well your cells are doing at a given time point. For example one of the main problems with using a passage as a measure is that you can passage the cells at 98% confluence to a fresh flask and although that counts as a passage but it is pretty uninformative in terms of cell behaviour and gives you no solid numbers and you can do this many many times and although you would have done high number of passages but your cells would appear ok. Although such an exercise is pointless and will probably stress the cells but it is just to make the point that passage numbers are not necessarily a very informative and quantifiable measure of how well the cells are doing or behaving hence PD and cumulative PD should be used. Another advantage is that since you are dealing with actual cell numbers, if you changed your cell culture flask size from lets say T-75 to T-25, you don't have to be worried about changes to your frequency of passage or having to make further guess work on how that has effected your cell behaviour.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My main advice is that you should keep you frequency of passage the same at least in the beginning (although keep an eye on the cell density as you don't perhaps want to let cells to be too over-confluent or unconfluent when passaging, depending on your specific methodology and what has been established in your lab), but count your seeding and harvesting density (cell No) and calculate the PD and cumulative PD and draw a cumulative PD vs time graph and monitor the behaviour of cells. This should give you a good indication of you cellular behaviour under the conditions you are working with them since guidelines are just that, guides and they can never substitute experimental characterisation of your cells under your conditions and handling method!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-07T19:35:27.343" LastActivityDate="2014-08-07T19:35:27.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20321" PostTypeId="1" CreationDate="2014-08-07T19:06:35.893" Score="21" ViewCount="868" Body="&lt;p&gt;I would like solve some biological problems that would improve the state-of-the-art of biology or bioinformatics. In particular, I want to apply machine learning on light microscopic images. The equipment and experience I have are: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Bright-field, dark-field, and phase-contrast microscopy&lt;/li&gt;&#xA;&lt;li&gt;Modern laptop&lt;/li&gt;&#xA;&lt;li&gt;56-core super-computer with &gt;100 GB of memory (on request)&lt;/li&gt;&#xA;&lt;li&gt;Intricate knowledge of machine learning algorithms and signal processing&lt;/li&gt;&#xA;&lt;li&gt;PhD-level research skills&lt;/li&gt;&#xA;&lt;li&gt;Programming skills that would get me to work at Google&lt;/li&gt;&#xA;&lt;li&gt;Limited knowledge about biology, bioinformatics, and microscopy (yet)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I want to do some publishable research free from all academic hassle. I will do this solely on my own time, without hurry to publish, in an attempt to do something &lt;em&gt;good for the mankind&lt;/em&gt;. I can throw a few hundred dollars on the project every two months (or abour 1000 USD per year).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Much of the biological research published in &lt;em&gt;Science&lt;/em&gt;, &lt;em&gt;Nature&lt;/em&gt;, &lt;em&gt;PNAS&lt;/em&gt;, &lt;em&gt;Cell&lt;/em&gt;, etc. are so specialized that I find it difficult to detect important problems I could have a good chance of solving given my skill set. Thus, I am asking your help:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What kind of software you always wanted for light microscopic research, but did not know how to build?&lt;/li&gt;&#xA;&lt;li&gt;What are some important biological problems you would like to get solved? (For machine learning, problems with a binary decision task are particular well suited -- e.g. &quot;does this person have malaria or not&quot;?)&lt;/li&gt;&#xA;&lt;li&gt;What are some recent, high quality reviews on open problems in biology?&lt;/li&gt;&#xA;&lt;li&gt;Something else?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;While my question is a bit broad, I think this goes under the &quot;good intention&quot; (or whatever it is called) SE policy.&lt;/p&gt;&#xA;" OwnerUserId="8656" LastActivityDate="2014-09-20T10:53:56.807" Title="Machine learning for light microscopy -- problems to solve?" Tags="&lt;bioinformatics&gt;&lt;protocol&gt;&lt;microscopy&gt;&lt;software&gt;" AnswerCount="4" CommentCount="11" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20322" PostTypeId="2" ParentId="20247" CreationDate="2014-08-07T20:19:56.897" Score="1" Body="&lt;p&gt;I found these article, which show exponential increase in population of Vibrio in BP oil spill region (published in 2011 supported in 2013).&lt;span class=&quot;math-container&quot;&gt;$^{1,2}$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;There is evidence that Vibrio representatives can metabolize oil-derived compounds &lt;span class=&quot;math-container&quot;&gt;$^{3,4}$&lt;/span&gt;. There is a sizable amount, more than 31%, where found in the Deepwater Horizon Spill.&lt;span class=&quot;math-container&quot;&gt;$^5$&lt;/span&gt;. Though the reason is still to be proved &lt;span class=&quot;math-container&quot;&gt;$in\ vitro$&lt;/span&gt;, but studies shows they can persist in the presence of oil.&lt;span class=&quot;math-container&quot;&gt;$^6$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;h2&gt;Source:&lt;/h2&gt;&#xA;&lt;p&gt;[1]:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22109669&quot; rel=&quot;nofollow noreferrer&quot;&gt;High Numbers of Vibrio vulniﬁcus in Tar Balls Collected from Oiled Areas of the North-Central Gulf of Mexico Following the 2010 BP Deepwater Horizon Oil Spill&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;[2]:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920100/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Associations and dynamics of Vibrionaceae in the environment, from the genus to the population level&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;[3]: West 1984, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC241663/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Numerical taxonomy of phenanthrene-degrading bacteria isolated from the Chesapeake Bay.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;[4]: Moxley K., Schmidt S. (2010). Preliminary characterization of an estuarine, benzoate-utilizing Vibrio sp. isolated from Durban Harbour, South Africa. Curr. Res. Technol. Educ. Top. Appl. Microbiol. Microb. Biotechnol. 1249–1254&lt;/p&gt;&#xA;&lt;p&gt;[5]: &lt;a href=&quot;http://www.int-res.com/abstracts/ame/v63/n2/p101-109/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hamdan L. J., Fulmer P. A. (2011). Effects of COREXIT® EC9500A on bacteria from a beach oiled by the Deepwater Horizon spill. Aquat. Microb. Ecol. 63, 101 10.3354/ame01482&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;[6]: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23987095&quot; rel=&quot;nofollow noreferrer&quot;&gt;In situ and in vitro impacts of the Deepwater Horizon oil spill on Vibrio parahaemolyticus.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-08-07T20:19:56.897" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20323" PostTypeId="2" ParentId="20321" CreationDate="2014-08-07T20:39:14.180" Score="7" Body="&lt;p&gt;I know this question is going to close. But, if you want to work something you can work on: &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Cryo super-resolution fluorescence imaging&lt;/h2&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Highlights&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;CryoFM allows imaging of vitrified biological samples with fluorescence microscopy.&lt;/li&gt;&#xA;  &lt;li&gt;There are significant challenges to achieve high-resolution cryoFM imaging.&lt;/li&gt;&#xA;  &lt;li&gt;Fluorophore characteristics at low temperature offer additional advantages.&lt;/li&gt;&#xA;  &lt;li&gt;Cryo super-resolution fluorescence imaging will give dramatic resolution improvement.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1367593114000623&quot;&gt;Fluorescence cryo-microscopy: current challenges and prospects&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-08-07T20:39:14.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20325" PostTypeId="1" CreationDate="2014-08-07T21:17:57.760" Score="1" ViewCount="1295" Body="&lt;p&gt;I'm wondering if plasma glucose can be measured with a regular glucose meter and strips like &lt;a href=&quot;http://www.adwdiabetes.com/product/free-truebalance-meter-kit_1606.htm?source=GoogleBase&amp;amp;zmam=69792428&amp;amp;zmas=1&amp;amp;zmac=2&amp;amp;zmap=2129200312KIT&amp;amp;gclid=Cj0KEQjwx4yfBRCt2rrAs-P5vtkBEiQAOdFXbZicho2Iysf_AAL2oypo69bLltFs2rS1ETURpNfODNUaAs-e8P8HAQ&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;. I know these meters are normally used to measure whole blood glucose, but can they measure plasma glucose levels as well?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="8659" LastEditorUserId="16299" LastEditDate="2015-12-07T17:29:34.670" LastActivityDate="2015-12-07T17:29:34.670" Title="Can you measure plasma glucose with a regular glucose meter?" Tags="&lt;lab-techniques&gt;&lt;measurement&gt;&lt;glucose&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20326" PostTypeId="1" CreationDate="2014-08-07T21:39:25.657" Score="3" ViewCount="473" Body="&lt;p&gt;Many fruits are not homologous, originating from different parts of a plant. Yet they all have similar properties:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Ripe fruits all have yellow to dark red color&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;They all have a lot of water and sugars, even in dry climate where water is in shortage.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Besides sugars they usually have acids making them sour to sweet in taste&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I understand that these possibly developed as a contract between the plants and the animals in that the plant would provide beneficial fruit tissue so that the animal to swallow the seed so to propagate it for longer distances.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I wonder, why there are no fruits that would imitate the taste of meat, nuts, seeds,  foliage, grass, mushrooms, roots, milk and other food sources, common for the animals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why there are no salty fruits for instance or those rich in proteins rather than sugar and water, or having the smell of carrion?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="408" LastEditDate="2014-08-07T21:58:38.193" LastActivityDate="2014-08-08T13:34:51.953" Title="Convergent evolution of fruits" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;fruit&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20327" PostTypeId="2" ParentId="20326" CreationDate="2014-08-07T22:08:27.350" Score="0" Body="&lt;p&gt;How are you defining fruits? Because if you count any seed body of a flowering plant, you must include several items commonly described as vegetables, including pumpkins, zucchini, squash, cucumber, peppers, etc. And there are other colors of fruit, such as blue berries. These all serve similar functions for the plant, something eats the fruit, then deposits the seeds somewhere else.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you define a fruit by what the average person calls fruit, then you've biased the population because humans have selected for juicy sweet tasting fruits over thousands of years of breeding. Humans like large sweet tasting fruits, so they selected for those traits, driving most fruits to have those traits. Wild fruits probably have much more diversity, and there would much less distinction between fruit and vegetable.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2014-08-08T00:59:00.617" LastActivityDate="2014-08-08T00:59:00.617" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20329" PostTypeId="2" ParentId="16995" CreationDate="2014-08-08T05:34:06.743" Score="2" Body="&lt;p&gt;I am presuming this a Blue Green Algae(BGA) &lt;a href=&quot;http://publications.gc.ca/collections/collection_2011/agr/A125-8-2-2011-eng.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Identify your algae&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Growth rate for N1, N2 biomass at t1 and t2 time respectively, can be give as,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Growth rate:   &lt;span class=&quot;math-container&quot;&gt;$K'$&lt;/span&gt; = &lt;span class=&quot;math-container&quot;&gt;$\ln \frac{(N_2 / N_1)}{(t_2 - t_1)}$&lt;/span&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/KEmiq.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/KEmiq.gif&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://www.marine.csiro.au/microalgae/methods/support%20or%20original%20files/Growth2.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;csiro.au&lt;/a&gt;)&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, by this equation it is easy to calculate the doubling time of your algae. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KeDHP.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For BGA normal doubling time is 6-8 hours.&lt;span class=&quot;math-container&quot;&gt;$^2$&lt;/span&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.marine.csiro.au/microalgae/methods/Growth%20rate.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.marine.csiro.au/microalgae/methods/Growth%20rate.htm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://sites.google.com/site/biomonstaaar/algae&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://sites.google.com/site/biomonstaaar/algae&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-03-12T18:26:32.730" LastActivityDate="2019-03-12T18:26:32.730" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="20330" PostTypeId="2" ParentId="16330" CreationDate="2014-08-08T05:44:27.563" Score="1" Body="&lt;p&gt;I will Suggest:&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Selective Breeding in Aquaculture: An Introduction&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Authors: Trygve Gjedrem, Matthew Baranski&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ISBN: 978-90-481-2772-6 (Print) 978-90-481-2773-3 (Online)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://image.slidesharecdn.com/selectivebreedinginaquaculture-anintroductionreviews-methodsandtechnologiesinfishbiologyandfisheries-140725230642-phpapp01/95/selective-breeding-in-aquaculture-an-introduction-reviews-methods-and-technologies-in-fish-biology-and-fisheries-10-1-638.jpg?cb=1406347865&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://image.slidesharecdn.com/selectivebreedinginaquaculture-anintroductionreviews-methodsandtechnologiesinfishbiologyandfisheries-140725230642-phpapp01/95/selective-breeding-in-aquaculture-an-introduction-reviews-methods-and-technologies-in-fish-biology-and-fisheries-10-1-638.jpg?cb=1406347865&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-08-14T15:55:37.097" LastActivityDate="2014-08-14T15:55:37.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20331" PostTypeId="2" ParentId="17719" CreationDate="2014-08-08T05:57:55.373" Score="6" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;Is consumption of blood more &amp;quot;dangerous&amp;quot; compared to meat?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Actually yes, a simple high dose of blood is enough to kill. The cause is, though it is most important thing to live when flowing the vessel, it's highly toxic when consumed. There are high chances of getting haemochromatosis or &lt;a href=&quot;http://en.wikipedia.org/wiki/Iron_overload&quot; rel=&quot;nofollow noreferrer&quot;&gt;Iron overload&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Source and More on this:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.livescience.com/15899-drinking-blood-safe.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.livescience.com/15899-drinking-blood-safe.html&lt;/a&gt;&lt;/p&gt;&#xA;&lt;h2&gt;Composition of Blood&lt;/h2&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/Bsqp7.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/Bsqp7.gif&quot; alt=&quot;&quot; /&gt;&lt;/a&gt;&lt;br /&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://tech.snmjournals.org/content/35/2/55/F1.medium.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;snmjournals.org&lt;/a&gt;)&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-03-16T02:56:06.517" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="20332" PostTypeId="2" ParentId="20164" CreationDate="2014-08-08T06:11:53.250" Score="2" Body="&lt;p&gt;Cattles actually hate shrubs which are very tough to break and tasteless(for a cow). Some plants they won't touch are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Lantana urticoides&lt;/em&gt; (West Indian shrub verbena), &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Malvaviscus arboreus&lt;/em&gt; var.&lt;em&gt;drummondii&lt;/em&gt; (wax mallow)&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Rhus copallinum&lt;/em&gt; (winged sumac)&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Viburnum acerifolium&lt;/em&gt; (mapleleaf viburnum). &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Morella cerifera&lt;/em&gt; (wax myrtle)&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Ilex vomitoria&lt;/em&gt; (yaupon). &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.wildflower.org/expert/show.php?id=2108&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.wildflower.org/expert/show.php?id=2108&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://www.wildflower.org/image_archive/640x480/SAW/SAW_01939.JPG&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Lantana urticoides&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.wellgrowhorti.com/Pictures/Landscape%20Plants/Shrubs/Web%20Pictures1/M/Malvaviscus%20Arboreus.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.wellgrowhorti.com/Pictures/Landscape%20Plants/Shrubs/Web%20Pictures1/M/Malvaviscus%20Arboreus.jpg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Malvaviscus Arboreus&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.floridata.com/wallpaper/jpg/Rhus_copallinum_frt800.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.floridata.com/wallpaper/jpg/Rhus_copallinum_frt800.jpg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Rhus copallinum&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/cuxgu.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/cuxgu.jpg&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://www.naturallandscapesnursery.com/VibcassinoidesMound.JPG&quot; rel=&quot;nofollow noreferrer&quot;&gt;naturallandscapesnursery.com&lt;/a&gt;)&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Viburnum acerifolium&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://www.wildflower.org/image_archive/640x480/JAM6151/6151_IMG00748.JPG&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Morella cerifera&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://www.ncwildflower.org/images/plants/Ilex_vomitoria_berries.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Ilex vomitoria&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-03-10T03:19:59.740" LastActivityDate="2019-03-10T03:19:59.740" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="20333" PostTypeId="1" CreationDate="2014-08-08T06:25:10.117" Score="3" ViewCount="1789" Body="&lt;p&gt;What's the purpose for many mushrooms to have colorful caps? Is not it is in their interest to hide as well as possible? Or there are mushrooms that propagate by being eaten, like fruits?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why not all the mushrooms are poisonous?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="8186" LastEditDate="2014-08-08T07:20:25.453" LastActivityDate="2014-08-12T09:31:17.650" Title="What's the purpose of colorful mushrooms' caps?" Tags="&lt;evolution&gt;&lt;mycology&gt;&lt;mushroom&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20334" PostTypeId="2" ParentId="13795" CreationDate="2014-08-08T06:46:41.270" Score="1" Body="&lt;p&gt;It all depends on hunger. As in comment (@Remi.b), it has been mentioned, an animal won't throw if they are starving.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For example monkeys/apes only eat part of a fruit and then throw the rest.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Monkeys and apes can differentiate between good and bad part of the fruits. So, they eat what they can and if the color looks different (or however they differentiate them) they will throw the rest of them. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cats (big and small species) only eat some parts of their prey and then they abandon it.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Cats in general are very picky eaters. They actually have a very short digestive tract, so, they need something easy to breakdown into energy rather than complex processes of digestion. Their main food consist of meat, they leave the inner organs as such. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikibooks.org/wiki/Wikijunior:Big_Cats/Complete_Edition&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikibooks.org/wiki/Wikijunior:Big_Cats/Complete_Edition&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bigcatrescue.org/feed-cats/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://bigcatrescue.org/feed-cats/&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GNzh4.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/M1Iv6.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image Source:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://wordpress.as.edu.au/rspiers/2013/05/22/comparing-animals-digestive-systems/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://wordpress.as.edu.au/rspiers/2013/05/22/comparing-animals-digestive-systems/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://cats56971.wordpress.com/2012/10/30/eating-habits-of-a-african-lion/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://cats56971.wordpress.com/2012/10/30/eating-habits-of-a-african-lion/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-08-12T09:20:17.087" LastActivityDate="2014-08-12T09:20:17.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20336" PostTypeId="2" ParentId="20333" CreationDate="2014-08-08T07:20:09.480" Score="2" Body="&lt;p&gt;Mushroom is actually the reproductive organ of the actual fungal body beneath the surface. It have a high surface area to disperse or spread the spores.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the eating predators are low or dispersing is not an option, then it will need other organisms to attract to that they can be spread, so they are not toxic. Analogous to fruits, they uses different colors which are non-toxic to attract.$^1$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whereas brightly colored mushrooms are less toxic, whereas, most toxic ones are either brown or white.$^2$ &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Edible Mushrooms&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://img0.etsystatic.com/000/0/6267506/il_570xN.314617556.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Toxic Mushrooms:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://warosu.org/data/cgl/img/0067/18/1364138341944.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://baynature.org/articles/why-do-mushrooms-come-in-so-many-shapes-and-colors/&quot; rel=&quot;nofollow&quot;&gt;Why do mushrooms come in so many shapes and colors?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mushroom_poisoning&quot; rel=&quot;nofollow&quot;&gt;Mushroom poisoning&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Image Source:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.etsy.com/listing/93680839/antique-1900-edible-fungi-print&quot; rel=&quot;nofollow&quot;&gt;https://www.etsy.com/listing/93680839/antique-1900-edible-fungi-print&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-08-12T09:31:17.650" LastActivityDate="2014-08-12T09:31:17.650" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20337" PostTypeId="1" CreationDate="2014-07-31T14:00:03.847" Score="5" ViewCount="120" Body="&lt;p&gt;They are seen briefly in this video:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=nZoNdf6hlII&quot; rel=&quot;nofollow&quot;&gt;https://www.youtube.com/watch?v=nZoNdf6hlII&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The launch made international news, but there was no mention of the species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the entirety of &lt;a href=&quot;https://en.wikipedia.org/wiki/Iranian_Space_Agency#Animals_in_space&quot; rel=&quot;nofollow&quot;&gt;Wikipedia's description&lt;/a&gt; of the launch:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;On February 3, 2010, ISA launched a Kavoshgar-3 (Explorer-3) rocket with one rodent, &lt;strong&gt;two turtles&lt;/strong&gt;, and several worms into sub-orbital space and returned them to Earth alive. The rocket was enabled to transfer electronic data and live footage back to Earth. The Iranian Aerospace Organization (IAO) showed live video transmission of mini-environmental lab to enable further studies on the biological capsule. This was the first biological payload launched by Iran. Iran is the sixth country to send animals in space.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The Farsi language Wikipedia entry on &lt;a href=&quot;https://fa.wikipedia.org/wiki/%DA%A9%D8%A7%D9%88%D8%B4%DA%AF%D8%B1_%DB%B3&quot; rel=&quot;nofollow&quot;&gt;the launch&lt;/a&gt; (کاوشگر ۳) does not appear to contain any more information on the species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've tried searching &lt;a href=&quot;http://scholar.google.com/scholar?q=Kavoshgar-3%20turtle&quot; rel=&quot;nofollow&quot;&gt;Google Scholar&lt;/a&gt; for papers, but my search turned up nothing. I also tried &lt;a href=&quot;http://www.reddit.com/r/AskReddit/comments/axjwu/which_species_of_turtle_did_iran_fire_into_the/&quot; rel=&quot;nofollow&quot;&gt;asking Reddit&lt;/a&gt; on the day of the launch, also without results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bounty Note: I appreciate all answers, especially from herpetologists. However, the bounty will only be awarded only for a reliable, third-party, published source (i.e. &lt;a href=&quot;https://en.wikipedia.org/wiki/Wikipedia:SOURCES#Reliable_sources&quot; rel=&quot;nofollow&quot;&gt;acceptable&lt;/a&gt; for use on Wikipedia).&lt;/p&gt;&#xA;" OwnerUserId="8564" OwnerDisplayName="Qubei" LastEditorUserId="8564" LastEditDate="2014-08-08T09:38:27.000" LastActivityDate="2019-03-11T14:23:41.723" Title="Which turtle species was on board the Iranian Space Agency launch in 2010?" Tags="&lt;species-identification&gt;&lt;animal-models&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20338" PostTypeId="2" ParentId="20337" CreationDate="2014-08-08T08:13:50.293" Score="1" Body="&lt;p&gt;Sorry, too big for comment!&lt;/p&gt;&#xA;&lt;p&gt;It's actually hard to tell, as there is no official claim on this one.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HWv84.png&quot; alt=&quot;enter image description here&quot; /&gt;&#xA;Photo Link: &lt;a href=&quot;http://youtu.be/nZoNdf6hlII?t=17s&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://youtu.be/nZoNdf6hlII?t=17s&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Al I guess is, it can be:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Native breed of Iran like, Spur-Thighed Tortoise (&lt;em&gt;Testudo graeca&lt;/em&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://4.bp.blogspot.com/_ZsneujvMmRY/SHH-c9bFe_I/AAAAAAAAARg/eOZzcCTSzKw/s320/LakposhtMehmizdar-TestudoGraeca.jpg&quot; alt=&quot;&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;or something like this&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/5qf7c.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/5qf7c.jpg&quot; alt=&quot;&quot; /&gt;&lt;/a&gt;&lt;br /&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://www.deserttortoise.org/answeringquestions/images/tse4hr.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;deserttortoise.org&lt;/a&gt;)&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Trachemys scripta elegans&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-03-11T14:23:41.723" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="20339" PostTypeId="2" ParentId="15303" CreationDate="2014-08-08T09:32:11.560" Score="1" Body="&lt;p&gt;&lt;em&gt;This answer aims to list existing models and do meta-analysis about them. &#xA;This answer is a draft.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many models made based on the thrombus movement. &#xA;One of them is proposed by DevashishDas' answer but it seems to focus only on the first stage of hemostasis:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The model assumes thrombin is generated on the surface of activated&#xA;  platelets in the thrombus core and is transported through the fibrin&#xA;  network that surrounds the core both by advective flow of fluid&#xA;  permeating through the fibrin network and by diffusion through the&#xA;  fibrin gel.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and particularly the model keeps these values constant and simplifies&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To calibrate the model, we experimentally determined fibrin clot&#xA;  permeability and thrombin diffusion rates through a fibrin network.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;which I think should be dynamic (not constant) because of the three endothelium main factors listed below.&#xA;Endothelium is a dynamic structure controlling the fibrin clot. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681659/&quot; rel=&quot;nofollow&quot;&gt;Thrombus Hemodynamics Model&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681659/&quot; rel=&quot;nofollow&quot;&gt;Fibrin Networks Regulate Protein Transport during Thrombus Development&lt;/a&gt; by  diffusion-advection equation (Stokes, continuity, Brinkman equations)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which is about the first stage of hemostasis because of its simplification about fibrin clot permeability and thrombin diffusion rates. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Hemostasis&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There are three stages of hemostasis altogether which work parallel together:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;primary (formation of the platelet plug)&lt;/li&gt;&#xA;&lt;li&gt;secondary (formation of fibrin through the coagulation cascade)&lt;/li&gt;&#xA;&lt;li&gt;tertiary hemostasis (formation of plasmin for breakdown of the clot)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Primary hemostasis is the formation of the primary platelet plug. &#xA;It involves &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;platelets&lt;/li&gt;&#xA;&lt;li&gt;blood vessel wall&lt;/li&gt;&#xA;&lt;li&gt;von Willebrand factor&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Normal endothelium prevents hemostasis. &#xA;Injury of endothelium&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;involves vasoconstriction (local)&lt;/li&gt;&#xA;&lt;li&gt;enhances adherence of platelets to exposed platelet subendothelial surfaces&#xA;and activation of coagulation process&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The formation of primary platelet plug involves&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Platelet adhesion,&lt;/li&gt;&#xA;&lt;li&gt;Platelet activation, and &lt;/li&gt;&#xA;&lt;li&gt;Platelet aggregation.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Main steps in blood coagulation:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Formation of prothrombin activator complex (thrombokinase)&lt;/li&gt;&#xA;&lt;li&gt;Conversion of plasma protein prothrombin into thrombin&lt;/li&gt;&#xA;&lt;li&gt;Conversion of dissolved plasma fibrinogen into fibrin (makes filamen- tous skeleton of fibrin clot)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Clot retraction&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The platelets in the clot contain contractile proteins.&lt;/li&gt;&#xA;&lt;li&gt;They bring the edges of the wound together, which also reduces the chance of further bleeding - not vasoconstriction here!&lt;/li&gt;&#xA;&lt;li&gt;The contraction process also supports the wound healing process as it brings the ends of the wound together.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Clot retraction is the process of getting clot towards fibrinolysis process. Fibrinolysis is the process where a fibrin clot (product of coagulation) is broken down. Its main enzyme plasmin cuts the fibrin mesh at various places, leading to the production of circulating fragments that are cleared by other proteases or by the kidney and liver. Clot retraction and fibrinolysis are necessary to remove clot so wound healing can proceed.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Myogenic and metabolic autoregulation by endothelium&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Myogenic control involves the localized response of vascular smooth muscle to passive stretch - reflex contraction when stretched to decrease flow, reflex relax- ation when stretch is reduced to vasodilate and increase flow. This maintains a relatively constant flow locally when pressure fluctuates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Myogenic and metabolic Autoregulation is the automatic adjustment (local) of blood flow to each tissue in proportion to its needs (oxygen, nutrients, ...), and is controlled intrinsically by modifying the diameter of local arterioles. It involves localised response of vascular smooth muscle to passive stretch - reflex contraction when stretched to decrease flow, reflex relaxation when stretch is reduced to vasodilate and increase flow. This maintains a relatively constant flow locally when pressure fluctuates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are three types of substances secreted by the endothelium (1): &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;NO&lt;/li&gt;&#xA;&lt;li&gt;Endothelium hyperpolarising factors &lt;/li&gt;&#xA;&lt;li&gt;Endothelins.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;where I think the modelling should focus on these three factors. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sources&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;My discussion with a researcher in this field 7/2014&lt;/li&gt;&#xA;&lt;li&gt;My notes in three Physiology courses during years 2011-2014&lt;/li&gt;&#xA;&lt;li&gt;Costanzo, Physiology, book&lt;/li&gt;&#xA;&lt;li&gt;Guyton, Physiology, book&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-08-08T09:32:11.560" CommentCount="0" CommunityOwnedDate="2014-08-08T09:32:11.560" ContentLicense="CC BY-SA 3.0" />
  <row Id="20340" PostTypeId="1" AcceptedAnswerId="20341" CreationDate="2014-08-08T10:16:47.517" Score="4" ViewCount="7823" Body="&lt;p&gt;How long could a person of lets say 18 years be able to drink sea water without getting too much into trouble ? Or can a person drink it without noticing that it is a very bad idea ? I don't mean in just 1 drink session but like can one manage a day or two ? Can one drink it and go to sleep and be still &lt;em&gt;healthy&lt;/em&gt; (although very thirsty) in the morning ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;(this is just a hypothetical question, I'm not a scientist at all, I'm not sure what tags to use actually)&lt;/em&gt;&#xA;&lt;hr&gt;&#xA;Additional brainstorming:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;kidney failure&lt;/li&gt;&#xA;&lt;li&gt;any other organ failure&lt;/li&gt;&#xA;&lt;li&gt;dying of thirst&lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8573" LastEditorUserId="8573" LastEditDate="2014-08-08T10:29:10.267" LastActivityDate="2019-09-09T18:15:22.523" Title="For how long can a person drink sea water?" Tags="&lt;death&gt;&lt;kidney&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20341" PostTypeId="2" ParentId="20340" CreationDate="2014-08-08T10:57:07.220" Score="10" Body="&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/mU2dL.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/mU2dL.jpg&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://jcantou.free.fr/histoire_plongee/19770000_alain_bombard_protegeons_la_mer/19770000_alain_bombard_protegeons_la_mer.jpg&quot; rel=&quot;noreferrer&quot;&gt;free.fr&lt;/a&gt;)&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Alain_Bombard&quot; rel=&quot;noreferrer&quot;&gt;Alain Bombard&lt;/a&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;He is a french biologist who voluntarily tested how many days a man can survive drinking seawater and how?&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Biologist point of view&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Sea contains ~3.5% of salt&lt;span class=&quot;math-container&quot;&gt;$^1$&lt;/span&gt;. Our kidney separates the waste from water and excrete them in urine provided the salt content is less than ~2%.&lt;span class=&quot;math-container&quot;&gt;$^2$&lt;/span&gt;&#xA;So, it will take the water already present in the body. Causing excessive thirst and dehydration, eventually cause death.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Alain's Experiment&lt;/h2&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Just one spoon of seawater at 20 minute intervals, drinking very&#xA;  slowly and letting the saliva in your mouth reduce the saline in the&#xA;  water you have swallowed.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Though he survived 65 days (From and including: Sunday, 19 October 1952&#xA;to Tuesday, 23 December 1952, ~4,400km) of his journey and lost 25 kg of weight, this result is never successfully reproduced. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://oceanservice.noaa.gov/facts/whysalty.html&quot; rel=&quot;noreferrer&quot;&gt;http://oceanservice.noaa.gov/facts/whysalty.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://paradise.docastaway.com/drinking-sea-water&quot; rel=&quot;noreferrer&quot;&gt;http://paradise.docastaway.com/drinking-sea-water&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-03-18T20:19:24.090" LastActivityDate="2019-03-18T20:19:24.090" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="20343" PostTypeId="2" ParentId="20326" CreationDate="2014-08-08T13:28:07.583" Score="5" Body="&lt;p&gt;&lt;a href=&quot;https://www.uic.edu/labs/howe/pdfs/HoweARES82.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Howe and Smallwood (1982)&lt;/a&gt; provide a nice review of the many methods of seed dispersal that have evolved in plants. The review is broad but they do have a section on frugivory.  They highlight hypotheses developed by McKey, and Howe and Estabrook (see Howe and Smallwood for citations) that suggest plants may use one of two strategies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One strategy is the &quot;high investment model.&quot; Plants invest lots of resources to produce large seeds and nutrient rich fruits. THe hypothesis is that these types of fruits tend to attract relatively few but specialized frugivores that are will to invest the energy necessary to find these types of fruits and their associated nutritional reward. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second strategy is called the &quot;low investment model.&quot; In this model, plants invest little in individuals seeds and fruits but produce an abundance of them. The hypothesis is that these types of fruits will be eaten by as many different potential seed dispersers as possible. These tend to be very small or starchy although they can still be colored as you describe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other factors also come into play. For example, tropical fruits tend to have large seeds and nutrient rich pulp while temperate fruits tend to be smaller and offer less nutritional reward.  All of this is placed in the context of the community diversity of frugivores. The Howe and Smallwood paper was an interesting read.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A paper by &lt;a href=&quot;http://horizon.documentation.ird.fr/exl-doc/pleins_textes/pleins_textes_6/b_fdi_45-46/010006673.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gatier-Hion et al. (1985)&lt;/a&gt; looked at the characters of fruit choice and seed dispersal mechanisms by tropical forest vertebrates. The showed the relationships between fruit characteristics and the corresponding frugivores. They looked at 122 different fruit species and the frugivores that consumed them.  Their results showed that fruits tended to separate along one of three axes:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Heavy, indehiscent fruits with fibrous flesh and well protected&#xA;seeds vs light, dehiscent fruits with unprotected seeds. Many of&#xA;small fruits are red,&lt;/li&gt;&#xA;&lt;li&gt;Lots of seeds produced (typically the the large indehiscent) vs few&#xA;seeds produced, and&lt;/li&gt;&#xA;&lt;li&gt;Juicy and brightly colored fruits vs dry and dull-colored fruits.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Figure 2 from Gautier-Hion et al., shown here, shows the relationship between different frugivores and the fruit types.  Notice that small granivores, which are frugivores, don't eat large, juicy fruits. They consume lots of small green or brown grains that are easy to manipulate and produced in high quantities.  Squirrels are similar. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hOhsE.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, as you suspected, fruits and seeds have evolved in response to their frugivores but the fruits do not always have the traits you listed. I think, but do not know for certain, that the fruit traits you list are the result of selection being driving by the frugivores. The sugars provide lots of quick energy, which is necessary for active animals. The carbs probably provide a much greater nutritional reward than salts or proteins (which are present anyway). The colors may help the fruits to stand out against the green foliage (for organisms that are not red-green colorblind). These traits probably provide the greatest reward (lots of energy) with the lowest energy investment by the frugivore (easy to find). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Throughout, I've assumed natural conditions and not fruits modified by artificial selection for human consumption.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gautier-Hion, A., et al. 1985. Fruit characters as a basis of fruit choice and seed dispersal in a tropical forest vertebrate community. Oecologia 65: 324-337.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Howe, H.F. and J. Smallwood. 1982. Ecology of seed dispersal. Annual Reviews in Ecology and Systematics 13: 201-228.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-08-08T13:34:51.953" LastActivityDate="2014-08-08T13:34:51.953" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20344" PostTypeId="2" ParentId="15742" CreationDate="2014-08-08T15:33:41.153" Score="6" Body="&lt;p&gt;These equations describe how the haplotype frequencies will change over time due to a combination of recombination and natural selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before I proceed, I need to change your four $\delta X_i$ formulas above. &lt;a href=&quot;http://ib.berkeley.edu/labs/slatkin/popgenjclub/pdf/lewontin-kojima1960.pdf&quot;&gt;Lewontin and Kojima (1960)&lt;/a&gt; writes the equations as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\Delta X_i = \frac{X_i(w_i - \bar w) \pm Drw_{14}}{\bar w}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where the minus sign is used for $i = 1,4$ and the plus sign is used for $i=2,3$. (&lt;a href=&quot;http://www.tiem.utk.edu/%7Egavrila/583/C2.pdf&quot;&gt;See also this chapter by Sergey Gavrilets.&lt;/a&gt;) Decreasing the frequency of a haplotype through recombination will necessarily increase the frequency of a different haplotype (adjusted by selection).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$D$ is the measure of linkage disequilibrium. It ranges from $-0.25$ to $0.25$ and indicates how much the haplotype frequencies deviate from an expectation of no linkage ($D=0$, the loci are independent).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, assume no natural selection. That is, $w_i = 1$ and therefore ${\bar w} = 1$. When fitness is equal, the equations reduce down to &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\Delta X_i = \pm Dr$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some recombination will occur between the linked loci proportional to the distance between them. In a large randomly mating population with no selection, $D$ will eventually decay to zero.  The larger the value of $r$, the quicker that decay will occur. Eventually, the haplotype frequencies will appear as if they are not linked. (&lt;a href=&quot;http://www.blackwellpublishing.com/ridley/tutorials/Multi-locus_population_genetics12.asp&quot;&gt;See this figure.&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, assume that $A$ and $B$ are linked, with these four haplotype frequencies:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$A_1B_1 = 0.5$$&#xA;$$A_1B_2 = 0.38$$&#xA;$$A_2B_1 = 0.05$$&#xA;$$A_2B_2 = 0.07$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the absence of natural selection and assuming that $r=0.1$, then $\Delta X_i = \pm 0.0016$, again with plus or minus depending on the value of $i$. This is the rate the frequencies will change each generation.  As $r$ decreases, the rate of decay decreases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Differential fitness among the haplotypes will also affect the rate of decay. The fitness interactions among loci on the same chromosomes and between homologs can get rather complex depending heterozygote advantage, epistasis, etc. (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1210557/pdf/49.pdf&quot;&gt;Lewontin 1964&lt;/a&gt; for several fitness models). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The equation $w_i = X_1w_{i1} + X_2w_{i2} + X_3w_{i3} + X_4w_{i4}$ is the average fitness of the each haplotype in combination with all the other possible haplotypes. For example, for $w_1$, you're calculating the average fitness of four genotypes: $A_1B_1/A_1B_1$, $A_1B_1/A_1B_2$, $A_1B_1/A_2B_1$, and $A_1B_1/A_12B_2$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am uncertain why $w_{14}$ is used in the second term of the numerator. I thought it might be because that combination is heterozygous at both loci so recombination generates all four possible haplotypes. However, both Lewontin and Kojima (1960) and Lewontin (1964) use $w_{11}$. It may also be that a relative fitness component is necessary for comparison so the fitness of any one of the genotypes could be used there. I don't know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regrdless, as a simple example to illustrate the effects of selection, assume $r=0.1$, $\bar w = 0.5$, and $w_{14} = 1$ (heterozygote advantage, given maximum relative fitness). For $w_1 = 0.9$ then $\Delta X_1 = 0.397$. Selection strongly favors this haplotype in all genotypic combinations so it will increase in frequency.  For $w_1 = 0.3$ then $\Delta X_1 = -0.203$. The haplotype is selected against and decreases much more rapidly, relative to no selection at all.  The same idea would apply for the other haplotypes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lewontin, R.C. 1964. The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49: 49-67. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lewontin, R.C. and K.-I. Kojima. 1960. The evolutionary dynamics of complex polymorphisms. Evolution 14: 458-472. &lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-08T15:33:41.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20345" PostTypeId="1" AcceptedAnswerId="20346" CreationDate="2014-08-08T17:21:48.957" Score="6" ViewCount="431" Body="&lt;p&gt;I have photographed the following fly which is iridescent green in Pittsburgh, PA.&#xA;I guess it was about 0.5-1.5cm long.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you help me to identify it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Aobm3.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8014" LastEditorUserId="8014" LastEditDate="2014-08-08T21:40:49.727" LastActivityDate="2014-08-08T21:40:49.727" Title="What is the name if this glittery fly seen in Pittsburgh?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="20346" PostTypeId="2" ParentId="20345" CreationDate="2014-08-08T17:57:21.037" Score="7" Body="&lt;p&gt;Looks like a green bottle fly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Green_bottle_fly&quot;&gt;https://en.wikipedia.org/wiki/Green_bottle_fly&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Might be a Common Green bottle fly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Common_green_bottle_fly&quot;&gt;https://en.wikipedia.org/wiki/Common_green_bottle_fly&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-08T17:57:21.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20347" PostTypeId="1" CreationDate="2014-08-08T20:55:19.770" Score="2" ViewCount="316" Body="&lt;p&gt;how to determine/ find the longest poly-purine tract in any genome  and this needs to be on the E. coli genome . is it to figure out the polypurine tract and then figure out the longest chain ? or is it to splice the introns and exons away from the DNA ? since E. coli's genome is 4.6 million BP long, i need some help in breaking this down ?&lt;/p&gt;&#xA;" OwnerUserId="8666" LastActivityDate="2014-08-11T09:06:55.990" Title="determine longest poly-purine tract" Tags="&lt;molecular-biology&gt;" AnswerCount="4" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20348" PostTypeId="2" ParentId="20347" CreationDate="2014-08-08T22:09:08.460" Score="2" Body="&lt;p&gt;Why do you need to do this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is pretty simple with the right computer tools and some knowledge of how to use regular expressions, but the fact that you are daunted by a 4.6 Mbase file suggests to me you don't  have that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using an old copy of E.coli DH10B, and Lasergene's SeqBuilder, I found a stretch of 29 Cs and T's, so in the reverse stand, that would be a poly-purine.  I don't see a longer stretch in my fasta.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-08-08T22:09:08.460" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20349" PostTypeId="2" ParentId="20347" CreationDate="2014-08-08T22:21:19.373" Score="2" Body="&lt;p&gt;Since you said an internet sequence is good enough, I will propose a computer programming approach. The basic idea is to enter the sequence as a string of text and then have the program read the text, keeping track of the length of the current polypurine tract, and the longest encountered so far. When it's done, it reports the longest one. I'm not sure if you know any programming, so I'll attempt to write up an example in C++ and post it. There are probably other programs that can do this, but I don't know about them. &#xA;Here is the code:&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;main.cpp&lt;/h2&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;#include &amp;lt;fstream&amp;gt;&#xA;#include &amp;lt;iostream&amp;gt;&#xA;&#xA;// this program reads a DNA sequence from a text file and then looks for&#xA;// the longest polypurine sequence. Please make sure there isn't non DNA&#xA;// text in the text file. Please call your text file &quot;DNA.txt&quot; and place&#xA;// in the same folder as this program.&#xA;&#xA;std::string base_complement(std::string in){&#xA;    std::string return_me = &quot;&quot;;&#xA;    for(int i = 0; i &amp;lt; in.size(); i++){&#xA;        if(in.c_str()[i] == 'a' || in.c_str()[i] == 'a'){&#xA;            return_me += 'T';&#xA;        }&#xA;        if(in.c_str()[i] == 'g' || in.c_str()[i] == 'G'){&#xA;            return_me += 'C';&#xA;        }&#xA;        if(in.c_str()[i] == 't' || in.c_str()[i] == 'T'){&#xA;            return_me += 'A';&#xA;        }&#xA;        if(in.c_str()[i] == 'c' || in.c_str()[i] == 'C'){&#xA;            return_me += 'G';&#xA;        }&#xA;    }&#xA;    return return_me;&#xA;}&#xA;&#xA;int main(){&#xA;&#xA;    std::cout &amp;lt;&amp;lt; &quot;WELCOME TO POLYPURINE COUNTER&quot; &amp;lt;&amp;lt; std::endl;&#xA;    std::cout &amp;lt;&amp;lt; &quot;WRITTEN BY SAM CROWLEY, SAMUEL-CROWLEY@UIOWA.EDU&quot; &amp;lt;&amp;lt; std::endl;&#xA;    std::cout &amp;lt;&amp;lt; &quot;WILL READ THE DNA IN DNA.txt AND REPORT LONGEST PURINE STRETCH&quot; &amp;lt;&amp;lt; std::endl;&#xA;    std::cout &amp;lt;&amp;lt; std::endl;&#xA;    // open the file and read the contents into the string&#xA;    std::string DNA;    // this string will hold the entire DNA sequence&#xA;    std::string line;   // this will hold one line of the file at a time&#xA;    std::ifstream text_file(&quot;DNA.txt&quot;);&#xA;&#xA;    while(!text_file.eof()){        // read the file until we get to the end&#xA;        getline(text_file, line);   // get one line at a time in the line string&#xA;        DNA += line;                // add that line to the DNA string&#xA;    }&#xA;&#xA;    //std::cout &amp;lt;&amp;lt; DNA &amp;lt;&amp;lt; std::endl;  // output the DNA string just to check&#xA;&#xA;    int current_tract = 0;          // length of current tract&#xA;    int longest_tract = 0;          // length of longest tract so far&#xA;    // true = sense strand, false = opposite strand&#xA;    bool tract = (DNA.c_str()[0] == 'a' || DNA.c_str()[0] == 'g');&#xA;    char c = DNA.c_str()[0];&#xA;    std::string purine = &quot;&quot;;&#xA;    std::string pyrimidine = &quot;&quot;;&#xA;    std::string longest = &quot;&quot;;&#xA;    if(c == 'a' || c == 'g' || c == 'A' ||c == 'G'){&#xA;        purine += c;&#xA;    }else{&#xA;        pyrimidine += c;&#xA;    }&#xA;    for(int i = 1; i &amp;lt; DNA.size(); i++){    // iterate through the DNA string&#xA;        if(c == 'a' || c == 'g' || c == 'A' || c == 'G'){&#xA;            if(DNA.c_str()[i] == 'a' || DNA.c_str()[i] == 'g' || DNA.c_str()[i] == 'A' || DNA.c_str()[i] == 'G'){&#xA;                purine += DNA.c_str()[i];&#xA;            }else{&#xA;                std::cout &amp;lt;&amp;lt; purine &amp;lt;&amp;lt; std::endl;&#xA;                if(purine.size() &amp;gt; longest.size()){&#xA;                    longest = purine;&#xA;                }&#xA;                purine = &quot;&quot;;&#xA;                c = DNA.c_str()[i];&#xA;                pyrimidine += c;&#xA;            }&#xA;        }else{&#xA;           if(DNA.c_str()[i] == 't' || DNA.c_str()[i] == 'c' || DNA.c_str()[i] == 'T' || DNA.c_str()[i] == 'C'){&#xA;                pyrimidine += DNA.c_str()[i];&#xA;            }else{&#xA;                std::cout &amp;lt;&amp;lt; pyrimidine &amp;lt;&amp;lt; std::endl;&#xA;                if(pyrimidine.size() &amp;gt; longest.size()){&#xA;                    longest = pyrimidine;&#xA;                }&#xA;                pyrimidine = &quot;&quot;;&#xA;                c = DNA.c_str()[i];&#xA;                purine += c;&#xA;            }&#xA;        }&#xA;    }&#xA;    if(purine.size() &amp;gt; 0){&#xA;        std::cout &amp;lt;&amp;lt; purine &amp;lt;&amp;lt; std::endl;&#xA;        if(purine.size() &amp;gt; longest.size()){&#xA;            longest = purine;&#xA;        }&#xA;    }&#xA;    if(pyrimidine.size() &amp;gt; 0){&#xA;        std::cout &amp;lt;&amp;lt; pyrimidine &amp;lt;&amp;lt; std::endl;&#xA;        if(pyrimidine.size() &amp;gt; longest.size()){&#xA;            longest = pyrimidine;&#xA;            longest = base_complement(longest);&#xA;        }&#xA;    }&#xA;    longest_tract = longest.size();&#xA;    std::cout &amp;lt;&amp;lt; std::endl;&#xA;    std::cout &amp;lt;&amp;lt; &quot;LONGEST POLYPURINE STRETCH IS &quot; &amp;lt;&amp;lt; longest_tract &amp;lt;&amp;lt; &quot; BASES LONG.&quot; &amp;lt;&amp;lt; std::endl;&#xA;    std::cout &amp;lt;&amp;lt; &quot;LONGEST STRETCH IS &quot; &amp;lt;&amp;lt; longest &amp;lt;&amp;lt; std::endl;&#xA;}&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;If you're running linux put the file in a folder and use a terminal to go that folder, then run g++ main.cpp -o polypurine.exe Then run it with ./polypurine.exe &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The DNA sequence goes in a file called DNA.txt in the same folder. Make sure it only contains a, t, g, c, so remove any header data or other annotations. If it contains an X, N, or other symbol to represent ambiguous bases I don't know what will happen, but the results may not be accurate. I forget which is used for purines and which for pyrimidines, but if you tell me I can modify the code to make it work with some ambiguous bases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you use windows or mac this same code should work but compiling it into a working program will be different. I don't program on those machines so I don't know how to make this work on them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I ran a test on the cDNA for bee venom PLA2 and got a longest purine tract of 17 bases. I think I can post that DNA here:&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Bee Venom PLA2 cDNA&lt;/h2&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;If you use this program for publications or anything, let me know. I put it here so you can use it, but I'd at least like to know if it's used.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2014-08-09T05:42:56.953" LastActivityDate="2014-08-09T05:42:56.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20350" PostTypeId="1" AcceptedAnswerId="20351" CreationDate="2014-08-09T00:38:01.340" Score="2" ViewCount="917" Body="&lt;p&gt;After a day at the beach, my skin tans due to Melanin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I also observe the black hairs on my arm turn a blond colour. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is &lt;strong&gt;What is the chemical process involved in human hairs changing colour after sun exposure?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5417" LastActivityDate="2014-08-09T03:48:55.993" Title="What is the chemical process involved in human hairs changing colour after sun exposure?" Tags="&lt;skin&gt;&lt;hair&gt;&lt;light&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20351" PostTypeId="2" ParentId="20350" CreationDate="2014-08-09T01:42:55.043" Score="2" Body="&lt;p&gt;Melanin is the main compound responsible for the color in hair. It is &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanin&quot; rel=&quot;nofollow noreferrer&quot;&gt;synthesized&lt;/a&gt; from the amino acid tyrosine. The absorption of tyrosine is around 280nm, which is a shorter wavelength than humans can see. Tyrosine can not absorb or preferentially scatter visible light in order to appear colored. It appears colorless as it scatters visible light equivalently. After tyrosine is synthesized into melanin, a pigment is formed which can be seen. Melanin scatters and absorbs light preferentially, it appears non-white.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Q4usp.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The absorption of melanin is in the visible spectrum. This means it can absorb and scatter light in the visible spectrum differentially. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uwiqJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As your hair is exposed to sunlight, melanin begins to break down into lower molecular weight compounds which have their own absorbance spectra. The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2071942&quot; rel=&quot;nofollow noreferrer&quot;&gt;different forms of melanin&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671032/&quot; rel=&quot;nofollow noreferrer&quot;&gt;carotenoids&lt;/a&gt; in your hair can be oxidized by sunlight, giving hair a spectrum of possible colors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pigment in bleached hair has been oxidized into products absorbing light primarily outside the visible spectrum. White hair appears so because it lacks compounds which preferentially scatter and absorb light in the visible spectrum.&lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-09T03:48:55.993" LastActivityDate="2014-08-09T03:48:55.993" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20352" PostTypeId="2" ParentId="19918" CreationDate="2014-08-09T04:08:05.790" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.jneurosci.org/content/27/30/8122.full&quot; rel=&quot;nofollow&quot;&gt;Here's&lt;/a&gt; a paper on the link between perception and reaction time. The general theme in biology is that the greater number of neurons an animal has in series, the more latency that animal will have in that pathway. This can partially account for organisms which have tiny nervous systems and very quick reflexes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In our own body, we have reflex pathways which entirely circumvent our brain. These help us maintain our posture and remain upright. These are muscle spindles and spinal reflexes. They are among the quickest response mechanisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might want to look up synaptic pruning and synesthesia. These are two phenomena on opposite ends of the spectrum of synapse count. Synesthesia is an excess of sensory pathways in the brain and synaptic pruning is the natural deletion of pathways in the maturing brain.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of our movements are variations on muscle memories, mediated by the cerebellum. You can start your research on muscle memory &lt;a href=&quot;http://en.wikipedia.org/wiki/Muscle_memory&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. Developing muscle memory is a rigorous process, but is a fundamental learning tool for musicians and those in martial arts.&lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-09T04:26:22.813" LastActivityDate="2014-08-09T04:26:22.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20354" PostTypeId="2" ParentId="19635" CreationDate="2014-08-09T05:49:53.003" Score="1" Body="&lt;p&gt;Suggested Reads:&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Evolutionary Psychology&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;By Lance Workman, Will Reader&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Evolution of Human Behavior: Primate Models&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;edited by Warren G. Kinzey&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Social Behaviour of Children: A Cross Cultural Assessment&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;By Ralph E. S. Tanner&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-08-09T05:49:53.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20355" PostTypeId="2" ParentId="16993" CreationDate="2014-08-09T06:01:38.310" Score="2" Body="&lt;p&gt;Suggestions:&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Evolutionary Genetics : Concepts and Case Studies: Concepts and Case Studies&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Edited by Lexington Charles W. Fox Department of Entomology University of Kentucky, Faculty of Life Sciences University of Manchester Jason B. Wolf Lecturer&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;The mathematical theory of selection, recombination, and mutation&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;by R Bürger (as suggested by @rg255 in the comments)    &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;&lt;a href=&quot;http://sinauer.com/genetics-and-analysis-of-quantitative-traits.html&quot; rel=&quot;nofollow&quot;&gt;Lynch and Walsh's Genetics and Analysis of Quantitative Traits&lt;/a&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;(as suggested by @kmm in the comments)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: Do tell us if you found a better one.&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="1590" LastEditDate="2016-08-17T08:45:53.403" LastActivityDate="2016-08-17T08:45:53.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20356" PostTypeId="2" ParentId="7946" CreationDate="2014-08-09T06:07:14.647" Score="2" Body="&lt;p&gt;I would suggest:&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Koneman's Color Atlas and Textbook of Diagnostic Microbiology&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;by Elmer W. Konema&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-08-09T06:07:14.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20357" PostTypeId="2" ParentId="16540" CreationDate="2014-08-09T06:15:00.870" Score="2" Body="&lt;p&gt;I would suggest the course of Coursera.org:&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;&lt;a href=&quot;https://www.coursera.org/course/molevol&quot; rel=&quot;nofollow&quot;&gt;Computational Molecular Evolution&lt;/a&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;By Anders Gorm Pedersen&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Technical University of Denmark (DTU)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: Do tell us if you found a better book!&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-08-09T06:15:00.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20363" PostTypeId="1" CreationDate="2014-08-09T15:30:05.807" Score="1" ViewCount="69" Body="&lt;p&gt;I am trying to find the ET&lt;sub&gt;0&lt;/sub&gt; (Potential evapotranspiration) under the climate conditions of London (UK) and Coimbra (Portugal) for each month. From what I understand these data is available in the &lt;a href=&quot;http://www.fao.org/&quot; rel=&quot;nofollow&quot;&gt;FAO's website&lt;/a&gt; but I was struggling to find it. &lt;/p&gt;&#xA;" OwnerUserId="8680" LastActivityDate="2014-08-09T15:30:05.807" Title="Potential evapotranspiration constant for trees in the area of London" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;environment&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20364" PostTypeId="1" AcceptedAnswerId="20365" CreationDate="2014-08-09T16:21:21.103" Score="5" ViewCount="28368" Body="&lt;p&gt;Typically the microbial growth in liquid cultures is monitored by turbidity. Data is obtained with a spectrophotometer to measure optical density at 600nm. The slope of the bacterial kinetic curve in exponential phase is the growth rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I have seen two ways of calculate the growth rate:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Growth rate = Maximum slope value of the Kinetic curve&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;$Log_{10}$ transformation of the growth data and then calculate the slope.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I think the second one is right if you want to calculate the generation time:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;generation time = $\frac{ln(2)}{Growth rate}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the correct way to calculate the growth rate and then generation time?&lt;/p&gt;&#xA;" OwnerUserId="8675" LastEditorUserId="4747" LastEditDate="2014-08-09T19:18:39.367" LastActivityDate="2014-08-09T19:18:39.367" Title="Calculation of the bacterial growth rate from a spectrophotomer growth curve" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;mathematical-models&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20365" PostTypeId="2" ParentId="20364" CreationDate="2014-08-09T18:56:47.943" Score="7" Body="&lt;p&gt;This is a common experiment for microbiology courses and you can find instructions on the internet , here is an example from University of Wisconsin: &lt;a href=&quot;http://inst.bact.wisc.edu/inst/index.php?module=Book&amp;amp;func=displayarticle&amp;amp;art_id=114&quot;&gt;http://inst.bact.wisc.edu/inst/index.php?module=Book&amp;amp;func=displayarticle&amp;amp;art_id=114&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the general method is measure optical density at regular intervals and plot them on a semilog graph, which has the normal linear scale on the X axis for time, but a base 10 log scale on the Y axis for optical density. You can set this up in microsoft excel or libreoffice calc by right clicking the y axis and going to format axis, there should be a logarithmic scale option somewhere depending on the version. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After you have the data plotted, the exponential growth phase should appear as a line with positive slope. The logarithmic scale on the Y axis will automatically transform the exponential curve into a straight line. To determine growth rate in terms of generation per hour, you need to get the optical density at time 0, which is the beginning of the exponential phase, and time t, which is just some other time on the exponential phase. Use this equation to determine growth rate: $k =\frac{log(X_t) - log(X_0)}{0.301t}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you know the growth rate, you can determine the generation time with $t_{gen} = \frac{1}{k}$, which gives time for 1 generation in hours. To convert to minutes, just multiply by 60.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note, remember to blank your spectrophotometer with sterile media. Also, if the optical density goes over 2 it won't be as accurate, so dilute the aliquots to make the optical density go below 2. Remember to record the dilution factor so you can multiply the density by the dilution and get back to the &quot;original&quot; optical density for plotting.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-09T18:56:47.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20366" PostTypeId="2" ParentId="7772" CreationDate="2014-08-09T19:56:30.827" Score="7" Body="&lt;p&gt;The distribution of temperate hardwood forests, as well as deserts, tundras, savannahs, and other ecosystems, is determined primarily by average climate conditions, specifically average annual temperature and precipitation. You can see how biomes are related to climate in this figure, taken from Whittaker (1975):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zD14N.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Temperate forests tend to be between 2.5-17°C, and between 800-2500 mm precipation. These are not exact boundaries but reflect long-term climate conditions. As climate changes, so will the distribution of the biomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Temperature is important in many ways.  For example, most temperate trees go dormant during the winter. This requires metabolic preparation by the tree. If the weather turns cold too fast, then the trees may be be properly prepared. Alternatively, if the weather warms to quickly the trees may not be able to come out of dormancy properly. This technical report (&lt;a href=&quot;http://www.warnell.uga.edu/outreach/pubs/pdf/forestry/cold%20tolerance%20pub11-12.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Coder 2011&lt;/a&gt;) provides more detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The precise mechanism that restricts the distribution of any one species would require experimental determination. As it turns out, &lt;em&gt;Populus trichocarpa&lt;/em&gt; (black cottonwood), plus other &lt;em&gt;Populus&lt;/em&gt; and &lt;em&gt;Salix&lt;/em&gt; (all in the family Salicaceae) are quickly becoming model organisms for study. This should shed more light on specific distribution limitations, such as changes in soil nutrients, light intensity, or other environmental parameters. There are now regular symposia held on these model organisms. You can read an introduction to one symposium &lt;a href=&quot;http://treephys.oxfordjournals.org/content/31/12/1289.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;here (Tognetti et al. 2011)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note: One must be careful about the mapped distributions of popular trees like willows. Many species, including &lt;em&gt;Salix viminalis&lt;/em&gt;, have been introduced far outside their native range, including through out the eastern United States, as shown by the map you linked to. The native distribution of the species is the &lt;a href=&quot;http://openi.nlm.nih.gov/detailedresult.php?img=3276148_387f1&amp;amp;req=4&quot; rel=&quot;nofollow noreferrer&quot;&gt;Palearctic (Eurasia), shown here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coder, K.D. 2011. Trees &amp;amp; cold temperatures. Environmental Tolerance Series WSFNR11-12, Warnell School of Forestry and Natural Resources, University of Georgia, USA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tognetti, R. et al. 2011. Fifth international poplar symposium: Poplars and willows: From research to multipurpose trees for a bio-based society.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whittaker, R.H. 1975. &lt;em&gt;Communities and Ecosystems.&lt;/em&gt; MacMillan Publishing, New York, USA. &lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-08-10T21:26:36.020" LastActivityDate="2014-08-10T21:26:36.020" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20369" PostTypeId="1" AcceptedAnswerId="20370" CreationDate="2014-08-09T22:58:16.743" Score="3" ViewCount="282" Body="&lt;p&gt;I'm a physicist, so as a fellow scientist I want to apologize because this question will be entirely based on anecdotal inferences and I am well aware how irritating that can be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have an eidetic memory and I've never experienced any of the common forms of anterograde amnesia. No blackouts from rapid consumption of alcohol (and believe me, I've tried. That was the fun part. But not for kids; then it's not fun), not from extreme fatigue, head trauma, I even went in for surgery once and the anesthetist said at one point &quot;Well since you asked, the amnesiac should be setting in right about now&quot; and I vividly recall another couple minutes of conversation while we waited for the general anesthetic to knock me out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, naturally, I just assumed it must have been because of my eidetic memory. But I've always had an interest in neuroscience and now my curiosity has gotten the better of me. Surely the memory systems of all people are similar enough that amnesiacs and the like should work on everyone. So I ask, are eidetic memories (or perfect, or photographic, or other unusual forms) actually less susceptible to anterograde amnesia? Or perhaps have I just been the victim of probability; this is more a matter of luck not neuroscience?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please don't spare the gory details, neuroscience is cool (Neuroscientists are brainy guys. Sorry, I couldn't resist that pun). That said, I am physics, not biology; I'm probably under-specifying the question. Let me know if it's too broad and I'll try to focus.&lt;/p&gt;&#xA;" OwnerUserId="8682" LastActivityDate="2014-08-10T00:33:59.583" Title="Is an Eidetic Memory (or other unusual forms of memory) less susceptible to anterograde amnesia?" Tags="&lt;neuroscience&gt;&lt;memory&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20370" PostTypeId="2" ParentId="20369" CreationDate="2014-08-09T23:35:45.640" Score="2" Body="&lt;p&gt;This question is more of a medical question than one of the underlying mechanisms of biological function. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The formation of long term memories is related to long-term potentiation. There are multiple neurotransmitters involved in this process. Ethanol primarily affects NMDA receptors. Drugs used to specifically induce anterograde amnesia, like propofol, primarily affect other others, like GABAA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The process of memory formation relies on a variety of factors including the orchestration of multiple neurotransmitters. Anterograde amnesia can be induced by many factors and does not have a single known mechanism of action. It is not possible to conclude any single person will react identically to all inducers of anterograde amnesia. It is often the case that people have unique responses to drugs within a distribution of possible reactions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The individual nature of responding to drugs is why side effect lists are lengthy, and usually only a few out of this list are observed in any individual. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My hypothesis is, as a regular consumer of alcohol, your liver function is elevated and responsible for your high tolerance. The cytochrome p450 family of enzymes are responsible for much of the metabolism of drugs in the body.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Liver function tests are cheap and interesting, I find. You might have some blood work done at a local lab to check out those stats as well as your cholesterol, etc., if you have an interest in such things. &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-10T00:33:59.583" LastActivityDate="2014-08-10T00:33:59.583" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20371" PostTypeId="1" CreationDate="2014-08-10T00:03:12.783" Score="4" ViewCount="12531" Body="&lt;p&gt;Oxygenated blood is bright red and deoxygenated blood is dark red or brown.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you take oxygenated blood and leave it in the air it will turn dark red, then brown, then finally a bluish green from exposure to atmospheric oxygen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does it oxidize this far to get a copper oxide color to it after it has passed the phase where it is the same color as iron oxide? Why doesn't it stay at the iron oxide color?&lt;/p&gt;&#xA;" OwnerUserId="5851" LastActivityDate="2016-10-17T19:38:51.433" Title="why does blood when oxidized over time become bluish green?" Tags="&lt;hematology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20372" PostTypeId="2" ParentId="20347" CreationDate="2014-08-10T12:36:32.193" Score="4" Body="&lt;p&gt;Code Golf! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is my Python script, avoiding regex and not at all prettified.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;def gettract(strand):&#xA;    #if strand is 1 then replace C with T and split on T&#xA;    #else replace A with G and split on G&#xA;&#xA;    if strand==1:&#xA;        print 'top strand purine tracts:'&#xA;        aseq=seq.replace('C','T')&#xA;        tracts=aseq.split('T')&#xA;    elif strand==2:&#xA;        print 'top strand pyrimidine tracts:'&#xA;        aseq=seq.replace('A','G')&#xA;        tracts=aseq.split('G')      &#xA;    sortedtracts=sorted(tracts,key=len,reverse=True)&#xA;    for i in range(5):&#xA;        print len(sortedtracts[i]), sortedtracts[i]&#xA;&#xA;&#xA;&#xA;f=open('ec_dna.txt','r')&#xA;l=f.readlines()&#xA;print 'Sequence analysed is %s' % l[0][1:] #the header line&#xA;f.close()&#xA;seq=''.join([i.rstrip() for i in l[1:]])&#xA;print 'sequence length is %i' %len(seq)&#xA;print&#xA;gettract(1)&#xA;print&#xA;gettract(2)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;And here is the output:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sequence analysed is E. coli K-12 MG1655 U00096.2 (1 to 4639675 = 4639675 bp)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;sequence length is 4639675&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;top strand purine tracts:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;28 AGAGAGAAAAGAAGAAGAGAAAAGAAAA&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;22 GGGGGAGAAAGGGGGGAAAAGG&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;20 AAAGAGGAAAGGGGGGGGGG&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;20 GAAGAGGAAAAGAAAGAAGG&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;20 AAAAAAGAAGAGAAAAAAGA&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;top strand pyrimidine tracts:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;29 TTTTTCTCTTTCCCTTTTCCCTTCCCTCT&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;22 CCCTCCTCTTCTCTCCCTCCCC&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;21 TTCTCCTCCTTCTCTTTTCTT&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;21 TTTTTCTTCTCTCTTTTCCTC&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;21 CTCCCCTTTTCCCTTTTCTCC&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The longest purine tract is 29 bases long, and is on the bottom strand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This script doesn't handle the problem that the &lt;em&gt;E. coli&lt;/em&gt; genome is a circular molecule, so if the longest tract was split at the origin it would be missed - I leave that and obtaining the coordinates of the longest tract as an exercise.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-08-10T12:36:32.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20373" PostTypeId="2" ParentId="20371" CreationDate="2014-08-10T12:48:11.483" Score="4" Body="&lt;p&gt;Apparently there is a rare condition, &lt;a href=&quot;http://en.wikipedia.org/wiki/Sulfhemoglobin&quot; rel=&quot;nofollow&quot;&gt;sulfhemoglobinemia&lt;/a&gt; in which sulphide ions or H&lt;sub&gt;2&lt;/sub&gt;S combine with the haem group in haemoglobin, causing a greenish colour. This can be related to certain drugs being present in the blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://www.newscientist.com/article/dn12024-patient-shocks-surgeons-with-green-blood.html#.U-dpvVaHfEx&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for an example in which surgeons discovered dark green blood in their patient.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-08-10T12:48:11.483" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20375" PostTypeId="1" CreationDate="2014-08-10T14:13:35.543" Score="17" ViewCount="8827" Body="&lt;p&gt;When there is every thing same from their genes to their phenotype so then why they don't have same fingerprints? &lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="10401" LastEditDate="2015-12-25T00:23:24.500" LastActivityDate="2016-01-14T18:05:45.613" Title="Do identical twins have the same fingerprint?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;twins&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20376" PostTypeId="1" AcceptedAnswerId="20381" CreationDate="2014-08-10T15:01:25.223" Score="4" ViewCount="354" Body="&lt;p&gt;I was wondering whether there are hypotheses that take a different approach that is contrary to the heterotroph hypothesis. &#xA;The heterotroph hypothesis states that autotrophs evolved from heterotrophs because of the lack of food. &#xA;Is this issue still debated by scientists or is the heterotroph universally accepted? &lt;/p&gt;&#xA;" OwnerUserId="8644" LastActivityDate="2014-08-10T16:44:50.133" Title="Is the heterotroph hypothesis universally accepted?" Tags="&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20377" PostTypeId="2" ParentId="20375" CreationDate="2014-08-10T15:23:10.473" Score="17" Body="&lt;p&gt;Identical twins have, despite the name, neither identic fingerprints nor identic genetic fingerprints.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fingerprints: According to the papers listed below the fingerprints show higher similarities (the &quot;structure&quot; is the same), but they can be distinguished and are not the same.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0031320301002187&quot;&gt;On the similarity of identical twin fingerprints&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://biometrics.cse.msu.edu/Publications/Fingerprint&quot;&gt;Can identical twins be discriminated based on their fingerprints?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Genetic Fingerprint: Although identic (or monozygotic) twins share the same DNA, they are not the same and can still be distinguished with a DNA fingerprint, if enough regions are analyzed. The difference comes from small mutations (so called &quot;single nucleotide polymorphisms&quot;, one base mutations) which occur in each of us individually. The other difference comes from epigenetic modifications of our genome (basically adding methyl groups to our DNA) which are also not the same between identic twins (there is an interesting video on this on &lt;a href=&quot;https://www.youtube.com/watch?v=oqAbymytqdU&quot;&gt;Youtube&lt;/a&gt;). However, when using standard forensic kits it is usually not possible to discriminate between identical twins. Differences are detected with whole genome sequencing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a look at these publications:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.scientificamerican.com/article/identical-twins-genes-are-not-identical/&quot;&gt;Identical Twins' Genes Are Not Identical&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1872497313002275&quot;&gt;Finding the needle in the haystack: Differentiating “identical” twins&#xA;in paternity testing and forensics by ultra-deep next generation&#xA;sequencing&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12220446&quot;&gt;Epigenetic contributors to the discordance of monozygotic twins.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-10T15:23:10.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20378" PostTypeId="1" AcceptedAnswerId="20533" CreationDate="2014-08-10T16:16:32.247" Score="4" ViewCount="802" Body="&lt;p&gt;Is the any standard procedure or protocol followed for the identification of cause of new disease outbreak(or new pathogen)? Is it different for different countries?&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-08-15T05:42:27.933" LastActivityDate="2014-08-15T23:01:17.903" Title="Standard Process Identification of New Disease outbreak Causing Pathogen" Tags="&lt;human-biology&gt;&lt;species-identification&gt;&lt;pathology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20381" PostTypeId="2" ParentId="20376" CreationDate="2014-08-10T16:44:50.133" Score="4" Body="&lt;p&gt;I would say the the topic is still very much under debate. &lt;a href=&quot;http://mbe.oxfordjournals.org/content/23/6/1286.full&quot; rel=&quot;nofollow&quot;&gt;This paper by Ferry and House (2006)&lt;/a&gt; briefly review the heterotrophic vs chemoautotrophic hypotheses. They include citations from proponents of each hypothesis. Interestingly, Ferry and House propose an &quot;energy conservation&quot; hypothesis that attempts to merge ideas from the other two hypotheses.  Overall, much work remains to be accomplished in this field before we have a clear understanding of the origins of life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ferry, J.G. and C.H. House. 2006. The stepwise evolution of early life driven by energy conservation. Molecular Biology and Evolution 23: 1286-1292.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-10T16:44:50.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20382" PostTypeId="2" ParentId="8588" CreationDate="2014-08-10T17:18:04.880" Score="4" Body="&lt;p&gt;Insomnia most certainly occurs in other animals. One interesting example is the case of insomnia in &lt;em&gt;Drosophila melanogaster&lt;/em&gt;. In this &lt;a href=&quot;http://www.jneurosci.org/content/29/22/7148.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;study&lt;/a&gt; 3 day old male and female flies that demonstrated reduced sleep time were crossed together over 60 generations to create flies &lt;em&gt;insomnia-like&lt;/em&gt; (&lt;em&gt;ins-l&lt;/em&gt;) that sleep less than 60 minutes a day compared to 800 min a day in their control flies, which are generation 0 (Fig 1B). These (&lt;em&gt;ins-l&lt;/em&gt;) flies exhibited difficulty initiating sleep, maintaining sleep and showed cognitive impairment. They also had difficulty maintaining balance with elevated levels of triglycerides, cholesterol and fatty acids and although their core molecular clock remained intact, &lt;em&gt;ins-l&lt;/em&gt; flies lost their ability to sleep in constant dark. Using whole-genome transcriptome profiling using Affymetrix high density nucleotide microarrays, these flies are compared against the control flies and many genes were over-represented (changed in expression compared to control flies) which are involved in metabolism, neuronal activity, behaviour and sensory perception with changes in lipid metabolism and synaptic transmission being consistent with increased adiposity and learning defects in flies. In addition, these &lt;em&gt;ins-l&lt;/em&gt; flies were hyperactive and hyper responsive to environmental simulations and the over-representation of genes associated with sensory perception suggests that hyperarousal in insomnia may be attributed to increased activity in the sensory system and that these processes are under genetic control. Two genes in particular &lt;em&gt;Filamin-A&lt;/em&gt; (&lt;em&gt;Cheerio&lt;/em&gt;) and &lt;em&gt;Malic enzyme&lt;/em&gt; (&lt;em&gt;Men&lt;/em&gt;), which were found to be differentially regulated (changed in expression) in files are also modulated (changed) by sleep loss in humans, showing that the same processes are involved/get effected in humans and flies during insomnia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The research above clearly demonstrated the genetic regulation and effects of insomnia in other animals and shows that its not just a human dysfunction.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-08-10T17:18:04.880" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20383" PostTypeId="1" CreationDate="2014-08-10T17:56:06.313" Score="1" ViewCount="86" Body="&lt;p&gt;How is the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genbank/&quot; rel=&quot;nofollow&quot;&gt;GenBank&lt;/a&gt; used in typical biological research? According to the GenBank statistics, the database contains about 100 million sequences. I find it difficult to understand why is all that data needed. To make the question less broad, what are the most common use-cases? Check if someone already sequenced DNA of some plant or animal? &lt;/p&gt;&#xA;" OwnerUserId="8688" LastEditorUserId="8688" LastEditDate="2014-08-10T18:11:56.453" LastActivityDate="2014-08-10T23:10:06.970" Title="How is the GenBank used in typical biological research?" Tags="&lt;sequence-analysis&gt;&lt;sequence-alignment&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2014-08-11T11:39:54.433" ContentLicense="CC BY-SA 3.0" />
  <row Id="20384" PostTypeId="1" AcceptedAnswerId="20385" CreationDate="2014-08-10T19:59:55.613" Score="5" ViewCount="255" Body="&lt;p&gt;I have photographed the following plant in Pittsburgh, PA. It has many blooms and every bloom is very small (about 5mm diameter), purple on the outer and orange in the inner. You can see it here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/96RyJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the name of that plant?&lt;/p&gt;&#xA;" OwnerUserId="8014" LastActivityDate="2014-10-23T19:22:20.193" Title="What is the name of this plant with many purple blooms with orange inner parts?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20385" PostTypeId="2" ParentId="20384" CreationDate="2014-08-10T20:10:04.980" Score="7" Body="&lt;p&gt;This looks pretty much like &lt;a href=&quot;http://en.wikipedia.org/wiki/Buddleja_davidii&quot; rel=&quot;noreferrer&quot;&gt;Buddleja davidii&lt;/a&gt; to me. They are available in a range of different colors, see this image from the Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GoXhP.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-10T20:10:04.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20386" PostTypeId="1" AcceptedAnswerId="20408" CreationDate="2014-08-10T20:57:13.850" Score="7" ViewCount="229" Body="&lt;p&gt;I have just discovered that my kitchen sink pipe has been leaking for quite some time (possibly months) which has resulted in water and food deposits collecting in my cupboard.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I smeared some of the residue onto a slide and looked at it under my microscope. I could see a large number of &lt;strong&gt;translucent organisms&lt;/strong&gt; (visible at &lt;strong&gt;40x magnification&lt;/strong&gt;, they are &lt;strong&gt;roughly 100 µm in length&lt;/strong&gt;). They all appeared to be of the same species although they varied in size and developmental stage. The 'adults' are &lt;strong&gt;quite long and look similar to maggots; they scrunch their bodies into balls and then stretch out in order to propel themselves.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately I lack the equipment to take a photo of it but &lt;strong&gt;here's a rough sketch&lt;/strong&gt; of what it looks like moving to the right:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2iolP.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Don't take the features &lt;em&gt;too&lt;/em&gt; literally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone hazard a guess as to what it might be?&lt;/p&gt;&#xA;" OwnerUserId="8690" LastEditorUserId="8690" LastEditDate="2014-08-11T00:32:24.947" LastActivityDate="2019-03-17T16:20:38.997" Title="Organisms in food deposits" Tags="&lt;microbiology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20387" PostTypeId="1" CreationDate="2014-08-10T21:15:21.580" Score="4" ViewCount="45447" Body="&lt;p&gt;What is the purpose of CPH-4? Is it well represented in the movie Lucy?&lt;/p&gt;&#xA;" OwnerUserId="8691" LastEditorUserId="-1" LastEditDate="2015-03-09T04:16:20.990" LastActivityDate="2015-03-09T04:16:20.990" Title="Does CPH4 exists?" Tags="&lt;molecular-biology&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2014-08-12T09:17:41.377" ContentLicense="CC BY-SA 3.0" />
  <row Id="20389" PostTypeId="2" ParentId="10403" CreationDate="2014-08-10T22:48:24.453" Score="5" Body="&lt;p&gt;After looking around for a bit, I came across a few potential solutions however they are not a definitive answer to your question and requires testing under your experimental conditions to see which works best.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.researchgate.net/post/Why_do_some_cell_lines_grow_in_grape-like_aggregates&quot;&gt;page&lt;/a&gt; contained one excellent suggestion and that is to select for cells that do not clump during the passage, by pooling the cells in 15ml of media in a tube and letting the clumped cells to settle down by gravity for 5 minutes and afterwards taking the top 1ml and passaging it and after 20 passages using the exact same technique, you should be able to get single cell suspension. The main caveat is the heavy selection for non-clumped cells, which might harbour certain properties that might be undesirable for the procedure you are interested in so it might be nice to do some RNA expression profiling to observe the differences and perhaps even publish it! Amongst the suggestions on this &lt;a href=&quot;http://www.researchgate.net/post/Why_do_some_cell_lines_grow_in_grape-like_aggregates&quot;&gt;page&lt;/a&gt; included using different concentrations of Mn2+, Mg2+, and Ca2+ in your (custom?) media since cell adhesion is regulated by integrins, cadherins, and selections and in general, Mn2+ increases ligand affinity, Mg2+ promotes adhesion to cells, and Ca2+ decreases cell adhesion as referened &lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_adhesion_molecule&quot;&gt;here&lt;/a&gt;. You can also try heparin, as tested by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20589456&quot;&gt;this paper&lt;/a&gt; on CHO cells and it impotent to note that in the study, heparin did not reducing cell growth, antibody secretion, and antigen-binding activity although I'm unsure as to whether heparin would be classified as an anti-clumping agent and whether it interferes with the ability of the cells to get transfected but that can be simple tested by a GFP transfection and looking at the transfection efficiency of the heparin treated and control cells treated with whatever heparin is dissolved in.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-08-10T22:48:24.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20390" PostTypeId="2" ParentId="20383" CreationDate="2014-08-10T23:10:06.970" Score="2" Body="&lt;p&gt;Go to &lt;a href=&quot;http://scholar.google.com&quot; rel=&quot;nofollow&quot;&gt;Google Scholar&lt;/a&gt;. Enter &quot;Genbank&quot; into the search field and press return. Limit the results to 2013 and later (left side of the results).  Skip the few entries that say only &quot;GenBank.&quot; Browse through the pages and pages of search results to get a feel for the many ways that GenBank is used in scientific research. It's used from everything for phylogenetic analysis (relationships among organisms) to determining protein structure and so much more.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-10T23:10:06.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20391" PostTypeId="2" ParentId="20248" CreationDate="2014-08-10T23:55:29.997" Score="4" Body="&lt;p&gt;Is the necessary that stamens have two microsporangia per theca? No. Many species in &lt;em&gt;Cryptocarya&lt;/em&gt; group of Lauraceae have microsporangia that have fused such that they have only two microsporangia instead of the typical four (Rohwer et al. 2014). I interpret their description as saying that the microsporangia within a theca but it's not clearly stated as such.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within the Magnoliidae, one pollen sac of a theca is lost is some taxa &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8339.1989.tb01709.x/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Endress et al. 2008).&lt;/a&gt; Evolutionarily, the Hamamelidaceae have reduced the number of pollen sacs from two to one (&lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00936917&quot; rel=&quot;nofollow noreferrer&quot;&gt;Endress 1989&lt;/a&gt;). I could not find examples of plants with more than two microsporangia per theca.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do most plants have two pollen sacs per theca?  It's probably a result of the evolutionary history of plants in general because it is so common. Even those that have only a single pollen sac seems to start out developmentally with two.  It's probably due to the underlying genetics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genetics of floral development is complex but being slowly teased apart. The overall development of floral patterns is set by a group of developmental or regulatory$^1$ genes called MADS genes.  Collectively, the MADS genes (along with other regulatory genes) control the overall organization of the flower structure. For example, MADS genes determine the arrangement of floral whorls from sepals (outermost whorl) to petals to stamens to carpals (innermost whorl). Changes in use or timing of the MADS genes can contribute to different types of floral morphology, such as the loss of sepals or big, showy sepals but no petals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of these same MADS genes contribute to the formation of the stamen structure. The review by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC160355/pdf/051217.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Goldberg et al. (1993)&lt;/a&gt; gives a thorough but now dated review of the developmental genes that control anther development. The figure below (their figure 3) gives a nice overview of the stages that lead to development of the theca with two microsporangia and ultimately to the final stage of fertilization. Even more specific, &lt;a href=&quot;http://www.plantcell.org/content/3/8/749.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bowman et al. (1991)&lt;/a&gt; show that &lt;em&gt;AGAMOUS&lt;/em&gt; is one regulatory gene that is active during the development of the theca and microsporangia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/K4sLB.png&quot; alt=&quot;Figure 3 from Goldberg et al.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't speak in detail about how regulatory genes work in flowers (I know a bit more about regulatory genes in animal development, especially from an evolutionary developmental perspective). In animals, regulatory genes often work by concentration gradients, both by the concentration of the regulatory gene itself, by the concentration of other regulatory genes, and by the concentration of the regulated genes. This process helps to determine the anterior-posterior axis in animals with bilateral symmetry, as well as the left and right sides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect that floral regulatory genes work in a similar fashion.  Changes in regulatory expression can lead to bilaterally symmetric flowers (think of mint flowers, monkey flowers, etc. See &lt;a href=&quot;http://jbiol.com/content/8/10/90&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hileman and Cubas (2009&lt;/a&gt; for a good review.). I suspect it is some type of symmetric expression of regulatory genes that leads to the formation of two microsporangia per theca.  Mutations that cause changes in the expression patterns of other regulatory genes can cause the initial expression but subsequent loss of one of the microsporangia, as noted for the Lauraceae and the Hamamelidaceae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Footnote&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Broadly but simply, regulatory genes are genes such as transcription factors that regulate or control the expression of other genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bowman, J.L., et al. 1991. Expression of the Arabidopsis floral homeotic gene &lt;em&gt;AGAMOUS&lt;/em&gt; is restricted to specific cell types late in flower development. The Plant Cell 3: 749-758.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Endress, P.K. 1989. Aspects of evolutionary differentiation of the &lt;em&gt;Hamamelidaceae&lt;/em&gt; and the Lower &lt;em&gt;Hamamelididae&lt;/em&gt;. Plant Systematics and Evolution 162: 193-211.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Endress, P.K. and L.D. Hufford. 2008. The diversity of stamen structures and dehiscence patterns among Magnoliidae. Botanical Journal fo the Linnean Society 100: 45-85.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Goldberg, R.B., et al. 1993. Anther development: Basic principles and practical applications. The Plant Cell 5: 1217-1229.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hileman, L.C. and P. Cubas. 2009. An expanded evolutionary role for flower symmetry genes. Journal of Biology 8: 90.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rohwer, J.G., et al. 2014. A phylogenetic analysis of the &lt;em&gt;Cryptocarya&lt;/em&gt; group (Lauraceae), and relationships of &lt;em&gt;Dahlgrenodendron&lt;/em&gt;, &lt;em&gt;Sinopora&lt;/em&gt;, &lt;em&gt;Triadodaphne&lt;/em&gt;, and &lt;em&gt;Yasunia&lt;/em&gt;. Phytotaxa 158: 111-132.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-10T23:55:29.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20392" PostTypeId="1" CreationDate="2014-08-11T03:22:24.603" Score="5" ViewCount="534" Body="&lt;p&gt;It just seems arbitrary to me to say &quot;ok, now THIS is officially a human&quot; when you could look at its parents and find no noticeable differences. At no point in the line of my ancestral history is there ever a hard cutoff between one generation and the next. It's a gradual progression. So how can you possibly pick a certain point in time when humans &quot;first came around&quot;? What criteria is used to say what exactly differentiates humans from whatever our ancestors were before 200k years ago? Did we &quot;branch off&quot; from something else at this point?&lt;/p&gt;&#xA;" OwnerUserId="8693" LastActivityDate="2019-08-08T01:19:02.230" Title="If evolution is a gradual and continuous process, how can we say humans came about 200k years ago? What is so special about that point in time?" Tags="&lt;evolution&gt;&lt;phylogenetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20393" PostTypeId="1" AcceptedAnswerId="20395" CreationDate="2014-08-11T06:55:15.970" Score="4" ViewCount="2567" Body="&lt;p&gt;Out of 10 steps in glycolysis, only one reaction- Glyceraldehyde 3-phosphate (G3P) to 1,3-bisphosphoglycerate (PGP), uses NAD+ and thereby producing NADH. Furthermore, this very step is solely responsible for net gain of 2ATP in glycolysis since here phosphorylation occurs without the expenditure of ATP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is NAD+ used only in this step? Is it possible to predict by other information that this is the only step to require NAD+? Is it possible to make this reaction happen without the involvement of NAD(P)+? Is it possible to skip this step and directly produce 3-phosphoglycerate (Lets not worry even if we cannot produce ATP in this process). I am interested in this because, this step necessitates the ferementation for regeneration of NAD+ in anaerobic condition. E. &lt;em&gt;coli&lt;/em&gt; produced acetate as a side effect, as expected during anaerobic situations, but also rather unexpectedly during aerobic and high-growth rate situation (acetate-swtich, overflow problem). Production of acetate is unwanted in many industrial applications. &lt;/p&gt;&#xA;" OwnerUserId="1800" LastEditorUserId="1800" LastEditDate="2014-08-11T07:11:10.130" LastActivityDate="2014-08-11T07:37:10.530" Title="Consumption of NAD+ in glycolysis" Tags="&lt;molecular-biology&gt;&lt;microbiology&gt;&lt;metabolism&gt;&lt;ecoli&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20394" PostTypeId="2" ParentId="20347" CreationDate="2014-08-11T07:01:59.407" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Just search for /[AG/{30}]/ and if I didn't find it, I'd keep dropping the number until it hit - swbarnes2&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Code for swbarnes2's method (will work on Linux terminal, Mac Console and cygwin terminal)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Usually in a genome file a single fasta sequence will represent one chromosome. In E.coli there will be only one. You would need to pop the fasta header (first line) out when analyzing your sequence. (Assuming that you have done so).&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This code below will find all polypurine tracts of a given length in the genome. Basically you have to keep dropping the part from the sequence start to the match location and redo the regex search.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;cat ecoli_genome.fa | tr -d &quot;\n&quot; | awk '{for(i=30;i&amp;gt;=10;i--){&#xA;pp=&quot;[A|G]{&quot;i&quot;}&quot;&#xA;s=$0&#xA;while (match(s,pp)){&#xA;       print substr(s, RSTART, RLENGTH)&#xA;       s=substr(s, RSTART+RLENGTH)&#xA;    }&#xA; exit&#xA;}&#xA;}'&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Regex searches of type /pattern{N}/ may not work on all versions of awk. It does work in gawk &gt;=4.0 but doesn't work in mawk.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This will load the entire genome sequence in the RAM (this is not huge at all). If you have RAM limitations and the genome file is really huge then you can stream read letter by letter (but you can't do regex search in this case). Stream read and regex are two strong features of &lt;code&gt;awk&lt;/code&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-08-11T09:06:55.990" LastActivityDate="2014-08-11T09:06:55.990" CommentCount="0" CommunityOwnedDate="2014-08-11T07:07:28.750" ContentLicense="CC BY-SA 3.0" />
  <row Id="20395" PostTypeId="2" ParentId="20393" CreationDate="2014-08-11T07:37:10.530" Score="4" Body="&lt;p&gt;NAD+ is important in this step, since it is co-factor for the glyceraldehyde-3-phosphate dehydrogenase (G3PDH), which acts as a acceptor for the hydrogen atom from the C1 (see below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LMQcB.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at the reaction, the aldehyde from the C1 is oxidized to a carboxylic acid which in a second step is turned into a phosphoester. To do so, a cysteine from the active center of the G3PDH attacks the G3P and forms a hemiacetal. This is oxidized into a thioester, the hydride which is split off in this step is transfered to the NAD+ bound by the G3PDH. In the second step the thioester formed between the enzyme and the G3P is attacked by a molecule of inorganic phosphate to form 1,3-BPG. This step is only made possible by splitting the very energy rich thioester bond. So for this reaction to happen you need both steps, as the formation of an energy rich phosphate ester bond would otherwise not happen. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Glyceraldehyde_phosphate_dehydrogenase#Mechanism_of_catalysis&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To go directly from G3P to 3-PG you would need an enzyme which oxidizes the aldehyde group in the G3P. And then you need again an acceptor for the hydrogen which is split off here.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-11T07:37:10.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20396" PostTypeId="1" AcceptedAnswerId="20397" CreationDate="2014-08-11T08:13:01.433" Score="16" ViewCount="1240" Body="&lt;p&gt;Can somebody please identify this bird for me?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I spotted this in July 2012 while birding in &lt;a href=&quot;http://en.wikipedia.org/wiki/Ranganthittu_Bird_Sanctuary&quot;&gt;Ranganthittu Bird Sanctuary&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JLKNR.jpg&quot; alt=&quot;unknown bird&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8696" LastEditorUserId="6561" LastEditDate="2014-09-02T23:06:44.053" LastActivityDate="2018-04-12T15:33:41.127" Title="Can you identify this bird?" Tags="&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20397" PostTypeId="2" ParentId="20396" CreationDate="2014-08-11T08:47:19.443" Score="15" Body="&lt;p&gt;This is a Cattle Egret (&lt;a href=&quot;http://en.wikipedia.org/wiki/Bubulcus_ibis&quot;&gt;Bubulcus ibis&lt;/a&gt;), which is a heron in its breeding plumage. When not breeding, the bird is white. See the images for comparision:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ME9eW.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Breeding cattle egret with colored feathers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5tUiv.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nonbreeding cattle egret, completely white.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-08-11T09:11:06.143" LastActivityDate="2014-08-11T09:11:06.143" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20398" PostTypeId="1" AcceptedAnswerId="20404" CreationDate="2014-08-11T08:55:02.773" Score="2" ViewCount="173" Body="&lt;p&gt;As we know that tumor suppressor gene causes cancer only when both the alleles are recessive in nature.But in case of oncogenes if only one allele is dominant it can cause cancer.Why in case of oncogenes to become a cause of cancer both allele aren't recessive? &lt;/p&gt;&#xA;" OwnerUserId="8301" LastEditorUserId="3340" LastEditDate="2014-08-11T12:04:06.997" LastActivityDate="2014-08-11T12:04:06.997" Title="Why do oncogenes show genetic dominance?" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20400" PostTypeId="1" CreationDate="2014-08-11T09:41:05.997" Score="4" ViewCount="1602" Body="&lt;p&gt;I'm currently working on an underwater robot and was hoping to use the principle used by the nautilus for buoyancy control. So how do the &lt;a href=&quot;http://en.wikipedia.org/wiki/Chambered_nautilus&quot; rel=&quot;nofollow&quot;&gt;Chambered nautilus&lt;/a&gt; control its buoyancy?&lt;/p&gt;&#xA;" OwnerUserId="8697" LastEditorUserId="3624" LastEditDate="2014-11-05T08:51:22.357" LastActivityDate="2015-01-18T04:53:26.673" Title="What are the buoyancy control mechanisms of Chambered nautilus?" Tags="&lt;marine-biology&gt;&lt;bio-mechanics&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20402" PostTypeId="2" ParentId="19708" CreationDate="2014-08-11T10:07:06.657" Score="2" Body="&lt;p&gt;Unlike other types of hormones, steroid hormones do not have to bind to plasma membrane receptors. Instead, they can interact with intracellular receptors that are themselves transcription activators. Steroid hormones too hydrophobic to dissolve readily in the blood  travel on speciﬁc carrier proteins from their point of release to their target tissues. In the target tissue, the hormone passes through the plasma membrane by simple diffusion and binds to its speciﬁc receptor protein in the cytoplasm. The receptor-hormone complex then translocates into the nucleus where it acts by binding to highly speciﬁc DNA sequences called &lt;strong&gt;&lt;em&gt;hormone response elements (HREs)&lt;/em&gt;,&lt;/strong&gt; thereby altering gene expression. &#xA;Hormone binding triggers changes in the conformation of the receptor proteins so that they be- come capable of interacting with additional transcription factors. The bound hormone-receptor complex can either enhance or suppress the expression of adjacent genes. &#xA;The DNA sequences (HREs) to which hormone- receptor complexes bind are similar in length and arrangement, but differ in sequence, for the various steroid hormones. Each receptor has a consensus HRE sequence  to which the hormone-receptor complex binds well, with each consensus consisting of two six-nucleotide sequences, either contiguous or separated by three nucleotides, &#xA;The ability of a given hormone to act through the hormone-receptor complex to alter the expression of a speciﬁc gene depends on the exact sequence of the HRE, its position relative to the gene, and the number of HREs associated with the gene.&lt;/p&gt;&#xA;" OwnerUserId="8301" LastEditorUserId="-1" LastEditDate="2015-03-09T21:09:29.267" LastActivityDate="2015-03-09T21:09:29.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20403" PostTypeId="2" ParentId="20392" CreationDate="2014-08-11T11:15:57.550" Score="1" Body="&lt;p&gt;The 200,000 years are the age of the fossils that has been classified as the first modern human. It's not like a magic number and if an older fossil is discovered the age of the modern human will be changed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The modern human is an anatomical feat. You probably recall the look of the Neanderthals and the obvious differences between them and us, there is a whole list of anatomical feats that differ between them and us.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Somewhere between 200k and 500k years the clade Homini split up into a lot of different hominids. The others have gone extinct.&lt;/p&gt;&#xA;" OwnerUserId="8699" LastEditorUserId="8517" LastEditDate="2014-08-11T18:17:11.290" LastActivityDate="2014-08-11T18:17:11.290" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20404" PostTypeId="2" ParentId="20398" CreationDate="2014-08-11T11:54:48.547" Score="4" Body="&lt;p&gt;A tumor suppressor is an essential gene that regulates the cell cycle at different checkpoints. If one allele is lost due to a mutation then the function of that gene can be carried out by the other allele (There might be a less expression of that gene because of copy number reduction but it is not necessary in all cases- cases where there are feedback controls).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An oncogene is a gene that promotes cell division. Different kinds of mutations will have different kinds of effect.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mutation leading to loss/reduction of function: Nothing is likely to happen unless both alleles are affected.&lt;/li&gt;&#xA;&lt;li&gt;Mutation leading to hyperactivity: In this case one rogue allele will always remain active leading to uncontrolled growth stimulation. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, it is the second type of mutation that you are referring to as in the case of Ras.&#xA;Note that any mutation leading to formation of a toxic or hyperactive protein (rogue allele), will show genetic dominance. Also see the case of Huntington's disease.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-08-11T11:54:48.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20405" PostTypeId="1" CreationDate="2014-08-11T12:12:30.113" Score="2" ViewCount="162" Body="&lt;p&gt;What fraction of &quot;large animals&quot; are domesticated by humans, compared to those who are wild? I mean cows, pigs, sheep, horses, dogs, cats in relation to comparable wild animals. Different measurements to a similar effect would also be of interest. Possibly including even chicken and fisheries.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder if there are more &quot;large animals&quot; alive on Earth today than thousands of years ago when human agriculture was much smaller?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd also be interested in some measurement of how large a fraction of vegetable life on Earth consists of our agricultural cereals et cetera.&lt;/p&gt;&#xA;" OwnerUserId="8025" LastActivityDate="2014-08-11T12:12:30.113" Title="What fraction of biomass is cultivated by humans? Have we increased the number of large animals?" Tags="&lt;zoology&gt;&lt;agriculture&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20406" PostTypeId="2" ParentId="20400" CreationDate="2014-08-11T12:26:08.960" Score="5" Body="&lt;p&gt;The various species of nautilus use a combination of active transport of salts and passive diffusion of water for buoyancy (&lt;a href=&quot;http://journals.cambridge.org/action/displayAbstract?fromPage=online&amp;amp;aid=4365408&amp;amp;fileId=S0025315400033440&quot;&gt;Denton and Gilpin-Brown 1966&lt;/a&gt;, &lt;a href=&quot;http://www.jstor.org/stable/2400389&quot;&gt;Ward 1979&lt;/a&gt;, &lt;a href=&quot;http://www.nature.com/nature/journal/v286/n5768/abs/286055a0.html&quot;&gt;Greenwald et al. 1980&lt;/a&gt;). The chambers are filled with seawater. Salts from the seawater in the chambers is removed by a structure called the siphuncular epithelium. This process makes the chambered water hypotonic, meaning it has lower solute concentration relative to the animal. The hypotonic water then diffuses from the chambers into the blood, creating air pockets in the chambers. &lt;a href=&quot;http://link.springer.com/chapter/10.1007/978-90-481-3299-7_34&quot;&gt;Greenwald and Ward (2010)&lt;/a&gt; have a recent summary of what is known about nautilus buoyancy, if you want to know more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The diffusion of water in  is not a rapid process. The maximum ascent and descent rate of Nautilus from depths appears to be about 3.0 m m$^1$ &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016311&quot;&gt;(Dunstan et al. 2011)&lt;/a&gt;.  This does not seem like an efficient process or rate of depth change for an underwater robot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Denton, E.J. and J.B. Gilpin-Brown. 1966. On the buoyancy of the peraly nautilus. Journal of the Marine Biological Association of the United Kingdown 3: 726-759.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dunstan, A.J., et al. 2011. Vertical distribution and migration patterns of &lt;em&gt;Nautilus pompilius.&lt;/em&gt; PLoS ONE 6: e16311. doi:10.1371/journal.pone.0016311&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Greenwald, L., et al. 1980. Cameral liquid transport and buoyancy control in the chambered nautilus (&lt;em&gt;Nautilus macromphalus&lt;/em&gt;). Nature 286 55-56.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Greenwald, L. and P.D. Ward. 2010. Buoyancy in &lt;em&gt;NAutilus&lt;/em&gt;. Topics in Geobiology 6: 547-560.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ward, P.D. 1979. Cameral liquid in &lt;em&gt;Nautilus&lt;/em&gt; and ammontites. Paleobiology 5: 40-49.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-11T12:26:08.960" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20407" PostTypeId="2" ParentId="19429" CreationDate="2014-08-11T12:45:51.323" Score="1" Body="&lt;p&gt;those are phosphorylated because they are the present in &lt;strong&gt;consensus sequences&lt;/strong&gt; and enzyme are specific to phosphorylate the specific target that's why other are not phosphorylated and also because of the OH group of these amino acids&lt;/p&gt;&#xA;" OwnerUserId="8301" LastActivityDate="2014-08-11T12:45:51.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20408" PostTypeId="2" ParentId="20386" CreationDate="2014-08-11T13:20:33.850" Score="3" Body="&lt;p&gt;It seems like Euglena but I need more parameters than what you have provided.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/YHdNs.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/YHdNs.jpg&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://www.eastmarinedrive.com/contents/images/learn/biology/euglena3.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;eastmarinedrive.com&lt;/a&gt;)&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=ZHZZKwrYm4g&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.youtube.com/watch?v=ZHZZKwrYm4g&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;you can narrow it down by this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://goo.gl/XTEZ7S&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://goo.gl/XTEZ7S&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find them in commonly found microorganism in kitchen:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.colorado.edu/eeb/EEBprojects/FiererLab/Flores_etal_2012_kitchens.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.colorado.edu/eeb/EEBprojects/FiererLab/Flores_etal_2012_kitchens.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078866.t001/largerimage&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078866.t001/largerimage&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0078866&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0078866&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-03-17T16:20:38.997" LastActivityDate="2019-03-17T16:20:38.997" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="20411" PostTypeId="2" ParentId="16973" CreationDate="2014-08-11T19:20:07.853" Score="2" Body="&lt;p&gt;It depends on how different. Day length affects more than just how long the periods of light and dark are. Let's assume a very slow rotation, and a very long day, maybe 1 month light, 1 month dark. The light side would get much warmer while the dark side would get much cooler. At the border between light and dark sides, you'd expect to see powerful storms as the hot moist expanding air moved into the cooler side and had to lose moisture. Any life on a planet like this would have to adapt to surviving in both hotter and cooler temperatures. We can take this to an even worse extreme and look at a planet like uranus. Uranus's axis is tilted at 97.7 degrees, so even though it rotates, the day/night cycle is controlled by it's rotation around the sun. If the earth were tilted like this, then we would 6 months of light followed by 6 months of darkness. Life would either have to keep moving to stay in the moving temperate twilight zones or adapt to hibernate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we assumed a shorter day/night cycle, I think the changes would be less significant. Lets say we had a 4 hour day. ( There has to be a speed where things get thrown off the planet, but I don't think 4 hours per day is fast enough ) A 4 hour day would have 2 hours of light with 2 hours of dark. My guess is that circadian rhythms would be less important. Temperature changes from light to dark would be less significant than currently. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's an interesting thing to think about because the Earth's day is slowly getting longer as the moon exerts a tidal force on our planet, slowing our rotation and escaping further into space, but this change is so slow I doubt it will ever become a problem for humans.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-11T19:20:07.853" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20412" PostTypeId="1" AcceptedAnswerId="20417" CreationDate="2014-08-11T19:21:28.640" Score="7" ViewCount="12410" Body="&lt;p&gt;In my lab, human DNA is extracted from whole-blood samples. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't actually do the extractions and I am not familiar with the specific protocol but I understand that platelets and red blood cells do not have nuclei and therefore do not have DNA so I presume that isolating the sample's white blood cells is part of the procedure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also understand that different types of white blood cells have multi-lobed nuclei but I do not know how that affects the DNA which can be extracted from them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen a few papers, such as this one: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15113441&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/15113441&lt;/a&gt;, state that they extracted DNA from specific types of white blood cells; lymphocytes in this case. These papers to not focus on, or even address, immune function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why extract DNA from only one type of white blood cell?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do lymphocytes contain DNA that is more representative of the patient's genome than other types of white blood cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are certain types of white blood cells easier to isolate than others?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this just the standard DNA-from-blood extraction procedure or are there multiple options to choose between depending on your research goals? &lt;/p&gt;&#xA;" OwnerUserId="8161" LastActivityDate="2014-08-11T23:54:31.617" Title="Why extract DNA from certain white blood cells instead of whole blood?" Tags="&lt;genomics&gt;&lt;hematology&gt;&lt;protocol&gt;&lt;experimental-design&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20413" PostTypeId="1" CreationDate="2014-08-11T19:52:11.137" Score="1" ViewCount="30" Body="&lt;p&gt;I would like to study the freezing and melting of bacterial membranes and would like to use Differential Scanning Calorimetry (DSC) to obtain the glass transition temperature of the membrane. However, I am unsure where to find such protocols describing the process. Could someone please tell me how to use DSC for bacteria such as E. coli?&lt;/p&gt;&#xA;" OwnerUserId="8498" LastEditorUserId="5144" LastEditDate="2014-12-12T15:06:26.183" LastActivityDate="2014-12-12T15:06:26.183" Title="Differential Scanning Calorimetry for bacterial membranes" Tags="&lt;bacteriology&gt;&lt;cell-membrane&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20414" PostTypeId="1" CreationDate="2014-08-11T23:22:47.310" Score="4" ViewCount="73" Body="&lt;p&gt;Are there any famous biological processes that depend strongly on a chemical concentration reaching a particular value, like some sort of switch?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.g. if concentration of chemical x reaches concentration y at cell location z (membrane, organelle etc) then a particular biological process will occur?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="3338" LastActivityDate="2016-09-18T14:12:51.387" Title="Concentration dependent cellular processes" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;cell&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20416" PostTypeId="2" ParentId="20414" CreationDate="2014-08-11T23:31:28.280" Score="5" Body="&lt;p&gt;There are several, but I guess the most well known is the neuron action potential, where the concentrations of Na+, K+, and Cl- ions determine the membrane potential of the cell. When the potential reaches a certain level, it triggers the action potential. You can read about this in much more detail on wikipedia, &lt;a href=&quot;https://en.wikipedia.org/wiki/Action_potential&quot;&gt;https://en.wikipedia.org/wiki/Action_potential&lt;/a&gt; .&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But to be pedantic about it, almost every cellular process is concentration dependent.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-11T23:31:28.280" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20417" PostTypeId="2" ParentId="20412" CreationDate="2014-08-11T23:54:31.617" Score="4" Body="&lt;p&gt;There are several reasons why a lab might choose to get DNA from lymphocytes instead of whole blood. Generating genomic DNA from whole blood is not necessarily the best idea, as all the excess protein (mainly hemoglobin from RBCs) needs to be gotten rid of at some point. By narrowing down your input to just include cells that have DNA, you lessen the amount of protein you need to extract in comparison to the total amount of DNA present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Lymphocyte&quot; rel=&quot;nofollow&quot;&gt;Lymphocytes&lt;/a&gt; include &lt;a href=&quot;http://en.wikipedia.org/wiki/T_cell&quot; rel=&quot;nofollow&quot;&gt;T cells&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/B_cell&quot; rel=&quot;nofollow&quot;&gt;B cells&lt;/a&gt;, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Natural_killer_cell&quot; rel=&quot;nofollow&quot;&gt;NK cells&lt;/a&gt;, and are relatively easy to quickly purify, especially in a lab with the requisite experience and reagents/equipment. They are by no means the only type of white blood cells from which one could purify DNA - &lt;a href=&quot;http://en.wikipedia.org/wiki/PBMC&quot; rel=&quot;nofollow&quot;&gt;peripheral blood mononuclear cells (PBMCs)&lt;/a&gt; can also be used, for example. They contain lymphocytes as well as other cell types like &lt;a href=&quot;http://en.wikipedia.org/wiki/Monocyte&quot; rel=&quot;nofollow&quot;&gt;monocytes&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Macrophage&quot; rel=&quot;nofollow&quot;&gt;macrophages&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Dendritic_cell&quot; rel=&quot;nofollow&quot;&gt;dendritic cells&lt;/a&gt;, etc. (In my experience they are even more straightforward to purify from whole blood than just lymphocytes, as it is essentially a single-step protocol with a few washes afterwards.) The end result is the same, though - DNA from lymphs should be the same as DNA from PBMCs, granulocytes, or neutrophils.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any somatic nucleated cell in the body contains &lt;em&gt;&quot;representative&quot;&lt;/em&gt; DNA, as except for in a few specialized cell types like T and B cells that undergo genomic rearrangement to form the T- and B-cell receptors, respectively, all cells from an individual contain the same genomic DNA sequence. Blood is relatively easy to come by from patients and clinical study participants, which is why it is often the source of DNA for studies instead of, say, skin punches or mouth swabs.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-08-11T23:54:31.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20418" PostTypeId="1" AcceptedAnswerId="20419" CreationDate="2014-08-12T00:49:55.807" Score="3" ViewCount="197" Body="&lt;p&gt;I am wondering about one thing. I have read different accounts of this (prior to reading it on Wikipedia), so I am wondering.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are the two versions I have read:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;asparagus leads &lt;strong&gt;in a certain percentage of people&lt;/strong&gt; to a smell that has to do with a reaction of &lt;a href=&quot;https://en.wikipedia.org/wiki/Asparagusic_acid&quot; rel=&quot;nofollow&quot;&gt;asparagusic acid&lt;/a&gt;. That is: not every human body creates the reactions leading to the &quot;smelly&quot; thiol (sulphuric) compounds.&lt;/li&gt;&#xA;&lt;li&gt;asparagus leads to the processes of the aforementioned asparagusic acid in &lt;strong&gt;everybody&lt;/strong&gt; but only a part of the population is able to smell those compounds.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Which one is true? Or is perhaps some other version I haven't heard about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;btw: The Wikipedia article on &lt;a href=&quot;https://en.wikipedia.org/wiki/Asparagus#Effects_on_urine&quot; rel=&quot;nofollow&quot;&gt;asparagus&lt;/a&gt; references both versions, too. So I am hoping for a definite answer with references to the respective scientific papers/studies.&lt;/p&gt;&#xA;" OwnerUserId="3315" LastEditorUserId="3952" LastEditDate="2014-08-12T01:58:34.570" LastActivityDate="2014-08-12T01:58:34.570" Title="The smell from eating asparagus" Tags="&lt;human-biology&gt;&lt;metabolism&gt;&lt;food&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20419" PostTypeId="2" ParentId="20418" CreationDate="2014-08-12T01:08:13.540" Score="5" Body="&lt;p&gt;Apparently, both are true.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...Individual differences exist in both odorant production and&#xA;  odor perception. The biological basis for the inability to produce the metabolite in detectable quantities is unknown, but the inability to smell the odor is associated with a single nucleotide polymorphism (rs4481887) within a 50-gene cluster of olfactory receptors. &lt;em&gt;&lt;a href=&quot;http://chemse.oxfordjournals.org/content/early/2010/09/27/chemse.bjq081.full&quot;&gt;Pelchet et al. 2010&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;It's an open access paper (yay!), but to cut a long story short:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Pelchet et al. asked subjects to provide 'before-eating-asparagus'&#xA;and 'after-eating-asparagus' urine.&lt;/li&gt;&#xA;&lt;li&gt;The subjects then acted as&#xA;urine-smellers for their own and others samples, and were asked to&#xA;choose between two unlabeled flasks which contained the 'before'&#xA;urine and which contained the 'asparagus' urine.&lt;/li&gt;&#xA;&lt;li&gt;Most subjects produced 'asparagus' urine in which an odor was perceived&#xA;significantly more times than expected by chance, and&lt;/li&gt;&#xA;&lt;li&gt;Most subjects perceived 'asparagus' urine correctly significantly more times than&#xA;expected by chance, however&lt;/li&gt;&#xA;&lt;li&gt;~8% of subjects were non-producers, and&lt;/li&gt;&#xA;&lt;li&gt;~6% of subjects were non-smellers.&lt;/li&gt;&#xA;&lt;li&gt;Finally, looking at the actual amount of successes in perception: for&#xA;Caucasian subjects, one third of the variation in the amount of&#xA;correct odor perception was related to the A allele of rs4481887&#xA;(having AA or AG rather than GG). There was no connection between&#xA;this allele and production.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://chemse.oxfordjournals.org/content/early/2010/09/27/chemse.bjq081.full&quot;&gt;Pelchat, ML, C Bykowski, FF Duke, and DR Reed. 2010. Excretion and perception of a characteristic odor in urine after asparagus ingestion; A psychophysical and genetic study. &lt;em&gt;Chemical Senses&lt;/em&gt; doi:10.1093/chemse/bjq081&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-08-12T01:41:00.763" LastActivityDate="2014-08-12T01:41:00.763" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20420" PostTypeId="1" AcceptedAnswerId="20433" CreationDate="2014-08-12T01:43:26.133" Score="1" ViewCount="863" Body="&lt;p&gt;What are the main differences between lab-grown tissues and natural tissues from living animals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using a biologist's classic &quot;&lt;em&gt;structure (&lt;strong&gt;anatomy&lt;/strong&gt;) and function (&lt;strong&gt;physiology&lt;/strong&gt;)&lt;/em&gt;&quot; idea, I thought about the followings:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Structure:&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;It might be difficult to recreate the composition of different tissues / cells in living things precisely with artificial methods.&lt;/em&gt; This may lead to bad results when the tissue is used for tests of medicines and cosmetics.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Function:&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Cells might not function and produce as expected (or is harder to make them function) in artificial compositions, as cells need strictly regulated environments to function correctly.&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Also, I think using artificial tissues for drug tests helps researchers to avoid ethical issues which may arise if they use living animals instead. I think the cost is generally higher to make artificial tissues than to gather test animals; however I am not sure if this applies to every case - maybe some tissues are relatively cheap to grow in labs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are some other differences? The answer can be about the advantages and the disadvantages of making / using lab-grown tissues and using living animals as well.&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2014-08-12T14:14:46.433" Title="What are the main differences between lab-grown tissues and natural tissues from living animals?" Tags="&lt;tissue&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20421" PostTypeId="1" AcceptedAnswerId="20423" CreationDate="2014-08-12T04:43:47.430" Score="6" ViewCount="1348" Body="&lt;p&gt;To answer a question myself, recently I've read that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Years and years ago, a long umbilical cord enabled a woman to grasp her baby after birth and run away from predators&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Update:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$Question:$ How umbilical cord is evolved and what's the reason behind it's elongation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://arepitass.files.wordpress.com/2008/10/adam-200109-rua.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is at least one position that supports this claim:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So why 61 cm? Umbilical cords of whales, porpoises, goats and other&#xA;  mammals are rela- tively shorter than the human cord. Walker and Rye&#xA;  of Cambridge surmised in the British Medical Journal in 1960 that&#xA;  prehistoric humans evolved length for protection. Nature's purpose was&#xA;  to allow the mother to pick up the newborn without disturbing the&#xA;  placenta. The event of breast feeding would then separate the placenta&#xA;  - an event which could attract predators. Having the fetus in tow would allow escape for mother and child.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(title: Silent Risk, auth.:Jason H. Collins). Well, right now I feel confused a bit...&lt;/p&gt;&#xA;" OwnerUserId="8711" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.603" LastActivityDate="2015-05-27T17:48:28.640" Title="Evolution of umbilical cord and reason of its elongation" Tags="&lt;human-biology&gt;&lt;evolution&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="20422" PostTypeId="1" AcceptedAnswerId="39271" CreationDate="2014-08-12T05:23:11.490" Score="8" ViewCount="230" Body="&lt;p&gt;A &lt;a href=&quot;http://en.wikipedia.org/wiki/Cama_(animal)&quot;&gt;cama&lt;/a&gt; is a hybrid between a male &lt;a href=&quot;http://en.wikipedia.org/wiki/Dromedary&quot;&gt;dromedary&lt;/a&gt; camel and a female &lt;a href=&quot;http://en.wikipedia.org/wiki/Llama&quot;&gt;llama&lt;/a&gt;. The first cama was born on January 14, 1998, yet on the Wikipedia page it is said that a cama's life span is 30–40 years. How was that number determined? Is it simply the average between a camel's and a llama's life spans?&lt;/p&gt;&#xA;" OwnerUserId="630" LastEditorUserId="5144" LastEditDate="2014-12-12T15:08:12.683" LastActivityDate="2015-12-03T15:26:02.150" Title="How was the cama's life expectancy computed?" Tags="&lt;genetics&gt;&lt;zoology&gt;&lt;lifespan&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20423" PostTypeId="2" ParentId="20421" CreationDate="2014-08-12T06:19:24.567" Score="9" Body="&lt;p&gt;The woman running bit is obviously a myth but that is genius.. Other than that the length of the umbilical cord has been found to be highly variable depending on each individual. Characterizing it as just long would therefore not be right. According to Wikipedia, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The umbilical cord in a full term neonate is usually about 50&#xA;  centimeters (20 in) long and about 2 centimeters (0.75 in) in diameter&#xA;  (&lt;a href=&quot;http://en.wikipedia.org/wiki/Umbilical_cord&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Some complications during birth are &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A number of abnormalities can affect the umbilical cord. The cord may&#xA;  be too long or too short. It may connect improperly to the placenta or&#xA;  become knotted or compressed (&lt;a href=&quot;http://www.marchofdimes.com/pregnancy/umbilical-cord-abnormalities.aspx&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why does it become too long has been associated with these factors.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Long umbilical cords, defined as total length over 70 cm, have been&#xA;  significantly associated with:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Maternal factors:&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Systemic diseases. Delivery complications. Increased maternal age.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Fetal factors:&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Non-reassuring fetal status during labor. Respiratory distress. Vertex&#xA;  presentation Cord entanglement. Fetal anomalies. Male sex. Increased&#xA;  birth weight.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Placental features:&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Increased placental weight. Right-twisted cords. Hyper-coiled cords.&#xA;  True knots (&lt;a href=&quot;http://sonoworld.com/fetus/page.aspx?id=1149&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In conclusion, length of the umbilical cord has an average as mentioned before and being too long or short can lead to complications during birth. Regarding evolution of the cord, you could &lt;a href=&quot;https://in.answers.yahoo.com/question/index?qid=20081022201948AA7cVhN&quot;&gt;read this discussion&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-08-12T06:25:59.440" LastActivityDate="2014-08-12T06:25:59.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20425" PostTypeId="1" CreationDate="2014-08-12T07:28:18.527" Score="4" ViewCount="1482" Body="&lt;p&gt;I am trying to amplify ~10kb length fragments using NEB LongAmp Master Mix. I had been using one particular aliquot of DNA (template amount in each PCR reaction of 10ul being around 60ng) and getting amplification results as desired. However, when I switched to a different aliquot of similar concentration, I am not getting amplification all of a sudden. I tried a different DNA sample and different primers and got results. So the problem lies with either the template or the primers. I have tried increasing amount of template, increasing Mg&lt;sup&gt;2+&lt;/sup&gt; by 1mM in the final reaction etc. but to no avail. The DNA templates/100x primer stocks are stored at -20⁰C and the DNA had been phenol-chloroform extracted. What could possibly be wrong here ? &lt;/p&gt;&#xA;" OwnerUserId="18932" LastEditorUserId="3340" LastEditDate="2014-11-26T12:48:50.447" LastActivityDate="2018-06-28T19:58:34.547" Title="What are possible reasons for a DNA template not giving amplification?" Tags="&lt;pcr&gt;&lt;primer&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20427" PostTypeId="1" CreationDate="2014-08-12T10:48:20.757" Score="5" ViewCount="21450" Body="&lt;p&gt;In the human spine, what is the difference between intervertebral and vertebral foramina? Is it just a matter of perspective and do they refer to the same thing or are they different? &lt;/p&gt;&#xA;" OwnerUserId="8715" LastEditorUserId="5239" LastEditDate="2014-08-12T13:59:24.163" LastActivityDate="2019-07-17T12:31:36.353" Title="Difference between intervertebral and vertebral foramina" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;vertebrates&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20428" PostTypeId="2" ParentId="20427" CreationDate="2014-08-12T11:07:26.523" Score="5" Body="&lt;p&gt;They are actually different.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/eMeFg.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/eMeFg.jpg&quot; alt=&quot;&quot; /&gt;&lt;/a&gt;&lt;br /&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;https://www.emory.edu/ANATOMY/AnatomyManual/38.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;emory.edu&lt;/a&gt;)&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;INTERVERTEBRAL FORAMINA&lt;/strong&gt; is actually spaces between adjacent vertebrae which gives &lt;em&gt;passage for spinal nerves to exit&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Whereas, &lt;strong&gt;VERTEBRAL FORAMINA&lt;/strong&gt; forms &lt;em&gt;vertebral canal.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;h2&gt;Source:&lt;/h2&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.physiology.emory.edu/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Organization of the Nervous System: An introduction for students in the Human Anatomy Course&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-07-17T12:31:36.353" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="20429" PostTypeId="1" AcceptedAnswerId="20432" CreationDate="2014-08-12T12:47:14.170" Score="8" ViewCount="12965" Body="&lt;p&gt;I understand that oxygen is the acceptor of electrons and hydrogen ions during the electron transfer phosphorylation, the last step off the ATP-producing aerobic respiration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aren't there any other alternatives for this acceptor? Oxygen is already recognized to have several harmful effects to cells - wouldn't another molecule be a better choice?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does it even require an &quot;&lt;em&gt;acceptor&lt;/em&gt;&quot; to accept the electrons and hydrogen ions? What would happen if they were left alone?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I apologize if my question was due to my ignorance in basic chemistry or biology, but do please point it out and explain it to me. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="4254" LastEditorUserId="22057" LastEditDate="2017-04-13T16:20:23.610" LastActivityDate="2017-04-13T16:20:23.610" Title="Why is oxygen needed for the electron transfer phosphorylation?" Tags="&lt;biochemistry&gt;&lt;cellular-respiration&gt;&lt;energy-metabolism&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20431" PostTypeId="1" CreationDate="2014-08-12T12:56:03.653" Score="5" ViewCount="305" Body="&lt;p&gt;I have an ant nest in a jar. Whenever I want to observe them, I have to remove the cover and therefore put them in light - that scares them. They also can see shadow cast by myself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I often throw in some food when I'm uncovering the jar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was curious if ants will ever remember that I'm not dangerous and that light means food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, are there other things they can learn? Do they teach each other to hunt? Can queen learn things ants can not (queen has shown a lot of individuality compared to ants)?&lt;/p&gt;&#xA;" OwnerUserId="6918" LastActivityDate="2020-01-08T06:01:00.133" Title="Can ants learn things?" Tags="&lt;ant&gt;&lt;learning&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20432" PostTypeId="2" ParentId="20429" CreationDate="2014-08-12T13:28:05.650" Score="7" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Aren't there any other alternatives for this acceptor?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not that we're aware of. Every other alternative requires an anaerobic environment - which means small, and often less efficient.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Oxygen is already recognized to have several harmful effects to cells - wouldn't another molecule be a better choice?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;When we're talking about a molecule's fit there are many things to consider. Primarily its electronegativity, as that determines its stability, ability to accept and donate electrons, protons, and its ease of acquisition given plentiful amounts in the environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Molecular Oxygen is comparatively stable to a lot of di-atomic molecules, and comparatively reactive to others. It's in the butter zone for the act of being the terminal acceptor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's think about Fluoride: Almost all of it is bound up in rocks with other elements. It's not available everywhere. It might be an alright candidate if we could eat rocks, but it also replaces minerals in our bones and teeth. Yes, you're familiar with this - but too much leads to fluorosis - where too much of the calcium compound is replaced, and it ends up making the bones and teeth much &lt;strong&gt;weaker&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alright, let's think about Nitrogen - Very stable, pretty good electronegativity, abundant... but a little &lt;em&gt;too&lt;/em&gt; stable. Yup, it's a gas, it's everywhere, and we can't use a lick of it. It's so stable that it's basically inert. The only reason rhizomes and other beneficial bacteria can use it is because they're in a controlled environment away from oxygen with significantly different biochemical processes which produce much less energy (and probably wouldn't be able to support large multicellular organisms that are as active as we are). So, Nitrogen is out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carbon? Nope, as an ion it's dangerously reactive, and as anything else it's too stable. Plus, we're carbon-based! If we used carbon as the terminal acceptor then the proteins handling the electrons would have to be even more exotic and filled with other elements to prevent them accidentally gobbling up the electron and becoming useless.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sulfur? Not electronegative enough for human purposes, unfortunately. It wouldn't act as a terminal acceptor unless our bodies seriously oxidized it; and any oxidized molecules floating around would be &lt;em&gt;more&lt;/em&gt; dangerous than molecular oxygen floating around. Plus most sulfur is bound to minerals as well - not abundant unless you're in the ocean. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oxygen is both incredibly abundant and easy to perform the chemistry with. More reactive molecules are usually not abundant and tied up in the Earth's crust and could be &lt;em&gt;more dangerous&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Less reactive molecules tend to be so non-reactive that we can't do anything with them, and if we could force them into a state where they would be reactive they tend to be violently reactive or require very specific environments that we can't reproduce on a scale necessary to be as mobile as we are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oxygen is not perfect, but it's a good fit.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why does it even require an &quot;acceptor&quot; to accept the electrons and hydrogen ions? What would happen if they were left alone?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Same thing that would happen if you clogged a pipe or hose. Once all of the electron acceptors on the transport chain are full, movement stops. The electrons won't be magically absorbed by other parts of the proteins making up the chains, and while there might be errant reactions with other molecules, you'd be lucky to get a whole ATP molecule out in a day - assuming you could magically stay alive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In reality, &lt;a href=&quot;http://en.wikipedia.org/wiki/Cyanide#Toxicity&quot;&gt;Cyanide poisoning&lt;/a&gt; is precisely what you're asking, and will kill you very quickly.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2014-08-12T21:10:46.107" LastActivityDate="2014-08-12T21:10:46.107" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20433" PostTypeId="2" ParentId="20420" CreationDate="2014-08-12T14:14:46.433" Score="0" Body="&lt;p&gt;Immortalized cell lines are often cancerous, which has large effects on their gene expression profiles. They also adapt to cell culture conditions after several hundred passages in culture. I've cultured both HepG2 cells and primary mouse hepatocytes. The HepG2 are a hepatocellular carcinoma line and grow fine in culture, while the primary hepatocytes don't really grow in culture and only live for a few days after you extract them from a mouse. We were doing gene transfer assays with both sets of cells. The quickly dividing HepG2 cells were easy to transform using PEI, and while primary hepatocytes could be transformed with PEI, they worked better with calcium phosphate, probably because it was less toxic. I noticed that HepG2 cells were smaller than primary hepatocytes, and the primaries were far more fragile, we could run HepG2 through a peristaltic pump with no problems, but had to handle all the primary cells by hand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as cost goes, tissue culture is almost always cheaper. You can make a bottle of media for a few dollars worth of material and use it for several passages. The cost of running an incubator and biosafety cabinet are also minimal. So unless you're doing something unusual, cell culture is affordable. However, it's an incomplete model at best. Trying to create whole tissues in the lab counts as unusual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Doing work with animals is far more accurate than cell culture, but much more expensive. Our mice are cheap, but still cost about a dollar each, and about 20 cents a day for housing. A typical biodistribution experiment will use 3 mice per time point and 8 - 10 time points, so 24 to 30 mice assuming no mistakes during dosing. On top of that, doing animal work has a lot more bureaucracy involved, with animal use protocols and approvals and inspections.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question about whether to use animal models vs cell culture comes down to what you're trying to accomplish. If you're studying gene regulation or protein interactions, cell culture usually works better because it's more amenable to gene transfer and allows you to use techniques like fluorescent fusion proteins and bioconjugation. If you're studying drug metabolism and toxicity you should use whole animals because the interactions between metabolites and specific tissues are hard to reproduce in cell culture. In some far off future we may be able to totally replace animal models with cell culture or even computer models, but we're not even close.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-12T14:14:46.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20434" PostTypeId="1" CreationDate="2014-08-12T14:44:08.027" Score="1" ViewCount="374" Body="&lt;p&gt;They look like this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7uCMq.jpg&quot; alt=&quot;blue rubber butyl stoppers&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We have to do a lot of gas sampling and these are really difficult to assemble. I've been scouring the internet for advice but there are none. Do you have experience with these? Have you found a good way to put them on that doesn't destroy hands, hearts, and dreams?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;To clarify, the hard part is putting the blue stoppers in the tubes in the first place. Once they go thoroughly in, we can crimp them with our hand crimping tool. Since the time I posted this, I find a (little) better luck using a piece of cloth / putting the cap and the glass vial between a vice. With too much pressure, I actually broke a vial and glass shattered everywhere. The best way to put them in is with a twist, but that usually comes with an expense of bruised hands after extensive use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wish I had a camera on me, but they look somewhat like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dQw40.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8716" LastEditorUserId="8716" LastEditDate="2014-08-12T21:02:24.690" LastActivityDate="2014-08-12T21:02:24.690" Title="What is an effective method for putting on blue rubber butyl stoppers?" Tags="&lt;biochemistry&gt;&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20435" PostTypeId="2" ParentId="20434" CreationDate="2014-08-12T15:35:38.763" Score="2" Body="&lt;p&gt;From what I can tell from this machine (&lt;a href=&quot;https://www.youtube.com/watch?v=TwRtsAG5Oy4&quot; rel=&quot;nofollow&quot;&gt;https://www.youtube.com/watch?v=TwRtsAG5Oy4&lt;/a&gt;), the blue caps are put on the bottles first, then a loose version of the aluminium neck seals are put around the top of the capsule, which is then pressed in the machine to seal the lid hence if you use many gas sampling techniques, it might worth investing in purchasing a similar machine/technology to seal your samples, which would be the most efficient in the long run.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: as pointed by @user137 there are also hand crimping tools, which you can use, which are considerably cheaper, which as @user137 pointed out, can be found &lt;a href=&quot;http://vialcrimpers.com&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-12T18:07:45.847" LastActivityDate="2014-08-12T18:07:45.847" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20436" PostTypeId="2" ParentId="20429" CreationDate="2014-08-12T15:36:57.273" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Aren't there any other alternatives for this acceptor?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, there are multiple other acceptors used by anaerobic bacteria. Iron is probably the most common other acceptor used by a range of organisms in a range of environments but others are used as well, such as sulphur.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Aren't there any other alternatives for this acceptor? Oxygen is already recognized to have several harmful effects to cells - wouldn't another molecule be a better choice?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No, Oxygen is a very good acceptor. It's highly electronegative which makes the process highly efficient, and it's also abundant in the environment since its created by photosynthesis. This has two consequences: firstly, there's plenty around to use, making it a good choice (obviously) and, secondly, cells need to deal with the harmful effects of oxygen regardless of whether they're going to take advantage of it.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="2938" LastEditDate="2014-08-12T21:55:42.177" LastActivityDate="2014-08-12T21:55:42.177" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20437" PostTypeId="1" AcceptedAnswerId="20442" CreationDate="2014-08-12T16:28:29.480" Score="4" ViewCount="29705" Body="&lt;p&gt;recently i got into a debate with &lt;a href=&quot;https://hinduism.stackexchange.com/posts/comments/4386?noredirect=1&quot;&gt;this&lt;/a&gt; question on hinduism.se ,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;as the link given above shows, are sperms considered as living or non-living &lt;/p&gt;&#xA;&#xA;&lt;p&gt;as far as my knowledge is concerned, sperms undergo locomotion, senescence, more over the best thing to say they are living is they contain genome, i.e. haploid sets of chromosomes&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so in short are sperms living or non-living&lt;/p&gt;&#xA;" OwnerUserId="8101" LastEditorUserId="-1" LastEditDate="2017-04-13T12:51:17.687" LastActivityDate="2014-08-15T20:48:13.007" Title="are sperms considered living" Tags="&lt;life&gt;" AnswerCount="6" CommentCount="1" ClosedDate="2014-08-21T09:43:22.060" ContentLicense="CC BY-SA 3.0" />
  <row Id="20438" PostTypeId="2" ParentId="20437" CreationDate="2014-08-12T16:36:33.730" Score="-1" Body="&lt;p&gt;One requirement most biologists have to consider something living is the ability to reproduce. This is why viruses are generally not considered alive. They contain proteins and DNA or RNA, but require infecting a host cell and hijacking its replication machinery to reproduce itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fully differentiated sperm cells cannot divide and therefore can't reproduce. Their only role is delivering DNA cargo to an oocyte and creating an embryo. An individual sperm cell is just as alive as an individual neuron or muscle cell. These require nutrients and energy, carry out metabolism, perform functions, contain DNA, but a plate of neurons won't grow into a human.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-12T16:36:33.730" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="20441" PostTypeId="1" CreationDate="2014-08-12T19:30:20.923" Score="4" ViewCount="94" Body="&lt;p&gt;Recently the UK government suggested that all adults over the age of 50, without exception, would benefit from taking statins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have an elderly female relative who may, or may not have had a minor cardiac event (the diagnosis is still out) and low blood pressure. It has been suggested to them that they would benefit from statins and have asked me (a former biologist) to find out more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've had a look at the mechanisms of action, which seem clear. But the clinical data is somewhat confusing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems we can state with certainty that a small but significant number of users report relatively minor side effects, and a very tiny minority have serious ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In term of the benefits, however, the picture is much less clear. I have found a variety of statistics about how they reduce cardiac events but what this translates to in terms of length of life and quality of life is not stated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One &lt;a href=&quot;http://www.saga.co.uk/health/medicines/statins-case-against.aspx&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; I looked at suggested that on average, someone at high risk of heart disease taking statins for 30 years would only live an extra 9 months.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The author of that site has a book to sell, and may have an axe to grind. But there are several other articles out there - such as &lt;a href=&quot;http://www.drbriffa.com/2013/02/12/can-statins-extend-life-and-if-so-by-how-much/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;, and &lt;a href=&quot;http://www.zoeharcombe.com/2013/10/how-statin-drugs-really-lower-cholesterol-and-kill-you-one-cell-at-a-time/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; and &lt;a href=&quot;http://www.telegraph.co.uk/health/10717431/Why-Ive-ditched-statins-for-good.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; - which make worrying claims about statins being both more unsafe and less beneficial than clinical trials suggest. In particular there seems very limited evidence of any benefits to women.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am inclined to treat these as alarmist nonsense - they have that sense of hysteria about them. But given that the authors look legitimate, that clinical trials data do not appear to agree with one another (widely varying in the percentage of users reporting side effects, for example), and that this is a relative, I wanted to get a second opinion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So - can someone please crunch the numbers and tell me what the benefits of statin use are in terms of life years and quality of life? Is there any benefit for women with or without heart disease? And is there any basis to some of the alarmism around their use?&lt;/p&gt;&#xA;" OwnerUserId="5083" LastActivityDate="2014-09-15T13:49:18.203" Title="What are the benefits of statins in terms of prolonging life?" Tags="&lt;cardiology&gt;&lt;statistics&gt;&lt;medicine&gt;&lt;lipids&gt;&lt;fat-metabolism&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20442" PostTypeId="2" ParentId="20437" CreationDate="2014-08-12T19:46:05.303" Score="3" Body="&lt;p&gt;The question of what is living is nothing but a matter of definition. We can only tell you what are the standard definitions of what is a living thing but no absolute truth exist behind these definitions. Therefore, I am afraid that all discussions here will bring anything new to your ethic or religion related discussion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to argue that the @user137's answer is very misleading for two reasons. First, he based his discussion exclusively on the &quot;reproduction ability&quot; definition of life. Second because his definition of reproduction might be misleading as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reproduction is not only cell division obviously. Following this same definition one would not consider a human to be a living things but only to be a collection of living (and non-living) things. It is important to understand that a spermatozoid is just one phase of a life-cycle. This phase yield to the next phase. That's it. It seems weird to say that a kid is not alive just because he cannot reproduce. It seems weird to say that a grandmother is not alive because it cannot reproduce. You can say however that a kid is a living thing that cannot reproduce and at another moment of its life cycle it will be able to reproduce (assuming it will survive to this age). One should not think of spermatozoids as something totally detached from the human phase as we know it. These things just form a cycle and it seems to me miseleading to say that a part of this cycle is not alive. Saying such thing would yield someone to think that two living things create non-living things that by fusion will become alive. That seems weird. But again, it is nothing but a matter of definition. I cannot say that user137 is wrong, I cannot only say that his definition seem neither useful, intuitive nor common among biologists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may want to have a look to life-cycle and to understand what are the haplontic and diplontic phases with a bunch of wikipedia readings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other concepts such as the ability to synthesize its own components, having a boundary between interior and exterior and ability to response to environmental stimulis are often used in order to define what is a living thing and what is not.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-08-12T19:46:05.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20443" PostTypeId="1" CreationDate="2014-08-12T19:59:54.943" Score="5" ViewCount="6285" Body="&lt;p&gt;There are variabilities in the heart rate as well as strength of heartbeats. I want to know if one can predict which heartbeat will be strong or weak based on the corresponding EKG/ECG signal. I am interested in the displacement of brain due to the heartbeat, which probably correlates with the peak pressure, and total volume caused by the beat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is such a correlation, which part of EKG would be related? The interval between P and R? The amplitude of QRS?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human or primate information is preferred.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DkmYa.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;image from &lt;a href=&quot;http://en.wikipedia.org/wiki/Wiggers_Diagram&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2014-08-13T13:25:06.500" LastActivityDate="2014-08-18T10:43:50.590" Title="How does strength of a pulse related to EKG(ECG)?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;electrocardiography&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20444" PostTypeId="1" AcceptedAnswerId="20469" CreationDate="2014-08-12T21:14:12.593" Score="4" ViewCount="5655" Body="&lt;p&gt;We have a long protocol that we are optimizing that includes DpnI digestion of a PCR product (to remove any of the template DNA if it's methylated, and while we're not certain in the blind tests, likely relevant DNA will be methylated).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm wondering if we can extend the DpnI incubation/reaction time to 4-5 hours.  This will make concurrent steps in the screen easier to manage.  Has anyone extended DpnI digestions?  How &quot;leaky&quot; or nonspecific of a process can it be?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="1320" LastEditDate="2014-08-13T18:44:35.803" LastActivityDate="2017-03-31T14:00:40.217" Title="DpnI over-digestion" Tags="&lt;microbiology&gt;&lt;lab-techniques&gt;&lt;enzymes&gt;&lt;enzyme-kinetics&gt;&lt;dna-methylation&gt;" AnswerCount="3" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="20445" PostTypeId="2" ParentId="20305" CreationDate="2014-08-12T21:14:16.613" Score="0" Body="&lt;p&gt;I got to thinking that there must be a distinction between grain and the germ. The grain must die in order for the germ to come alive. I am confident that the germ will not grow so long as the grain is alive. It is through the process of its dying and acquiring moisture from the earth, that the grain converts to sugar which supports the germ and enables it to sprout. The germ is in the grain, but separate &amp;amp; distinct from the grain, like a baby in the womb is in the mother, but separate and distinct from her. With grain, the mother must die for the germination to occur. With humans not so. &lt;/p&gt;&#xA;" OwnerUserId="8652" LastActivityDate="2014-08-12T21:14:16.613" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20446" PostTypeId="2" ParentId="8115" CreationDate="2014-08-12T21:41:27.120" Score="2" Body="&lt;p&gt;I'm not a medical professional, so this isn't exhaustive or guaranteed 100% accurate: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can live a (*mostly) normal life without your:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;appendix&lt;/li&gt;&#xA;&lt;li&gt;tonsils&lt;/li&gt;&#xA;&lt;li&gt;spleen&lt;/li&gt;&#xA;&lt;li&gt;gallbladder&lt;/li&gt;&#xA;&lt;li&gt;pancreas&lt;/li&gt;&#xA;&lt;li&gt;portions of your liver (pieces can be removed and it will regenerate)&lt;/li&gt;&#xA;&lt;li&gt;portions of your small or large intestines&lt;/li&gt;&#xA;&lt;li&gt;both lungs (one is needed)&lt;/li&gt;&#xA;&lt;li&gt;both kidneys (one is needed)&lt;/li&gt;&#xA;&lt;li&gt;uterus&lt;/li&gt;&#xA;&lt;li&gt;testes&lt;/li&gt;&#xA;&lt;li&gt;ovaries&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;*there are some side effects such as lowered immune function or difficulty digesting fatty foods, but for the most part, you might not even notice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can live with some **detriment to your quality of life without:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;colon&lt;/li&gt;&#xA;&lt;li&gt;bladder&lt;/li&gt;&#xA;&lt;li&gt;up to half your brain&lt;/li&gt;&#xA;&lt;li&gt;stomach&lt;/li&gt;&#xA;&lt;li&gt;thyroid&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;** surgical interventions can replace the colon and bladder with pouches of intestine, drugs can regulate the loss of the thyroid. Losing half your brain messes up a lot, but it's survivable. &lt;/p&gt;&#xA;" OwnerUserId="8720" LastActivityDate="2014-08-12T21:41:27.120" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20447" PostTypeId="2" ParentId="20437" CreationDate="2014-08-12T21:55:56.450" Score="2" Body="&lt;p&gt;Sperm are unquestionably alive, according to all or most sensible definitions of life (They move around, they have goals, they eat things, they die). They are not, however, a human or animal life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vineet Menon has a shaky grasp of species definitions, and I'd like to correct some misunderstandings. Chromosome number is not that useful in distinguishing different species. There are a large number of genetic disorders that alter your chromosomal count without making you not a human being. (&lt;a href=&quot;http://en.wikipedia.org/wiki/Klinefelter_syndrome&quot; rel=&quot;nofollow&quot;&gt;Klinefelter&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Turner_syndrome&quot; rel=&quot;nofollow&quot;&gt;Turner&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Edwards_syndrome&quot; rel=&quot;nofollow&quot;&gt;Edward&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Down_syndrome&quot; rel=&quot;nofollow&quot;&gt;Down&lt;/a&gt;, etc.) It's also worth noting that all mosses are haploid except during the sporophyte stage of their life cycle, when they're diploid. I doubt Vineet Menon intends to categorically declare mosses 'not alive'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your blood is alive, and your feces is also thriving with bacteria. Some yogurt is alive, most cheese is alive. All fermented beverages are alive, or were once. Bread dough is alive. The argument you linked to is debating whether or not they are alive enough to qualify as a macroscopic living thing for ethical purposes, which is an entirely different question. A chicken definitely qualifies, single-celled algae like spirulina, mushrooms, and yeast do not. Eggs, fertilized or not, seem to be somewhere in the middle. It is a continuous spectrum with people and cats and chickens and things at one end, and viruses and tuberculosis and dirt at the other. Eggs and sperm and mushrooms I would put somewhere in the middle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So whether the answer to the question 'Are gametes alive?' is unquestionably yes;&#xA;The answer to the question of whether or not that makes them 'a life' is up to you.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-08-12T21:55:56.450" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20448" PostTypeId="1" AcceptedAnswerId="20454" CreationDate="2014-08-12T22:35:25.653" Score="6" ViewCount="234" Body="&lt;p&gt;This question is about &lt;a href=&quot;https://www.youtube.com/watch?v=bee6PWUgPo8&quot;&gt;this video&lt;/a&gt; I found on Youtube. I just want to know what is the mechanism which regulates the timing of motion of the parts of these molecular machines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that those big molecules moves using mechanical energy from ATP molecules and take advantage of the electric forces specially the hydrogen bonds, they also take advantage of the Brownian motion of water molecules around them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what is see, the green floating molecule triggers the whole process by attaching the purple one, then some electric equilibrium is disturbed so the {purple+green} molecule is attracted by the horizontal cyan molecule...etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the problem is: does the green molecule attaches to this group in a periodic timing ? or in other words does the &lt;a href=&quot;http://en.wikipedia.org/wiki/Okazaki_fragments&quot;&gt;Okazaki fragments&lt;/a&gt; have the same lenght evertytime ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance !&lt;/p&gt;&#xA;" OwnerUserId="8722" LastEditorUserId="8722" LastEditDate="2014-08-13T02:23:21.090" LastActivityDate="2014-08-13T16:49:48.130" Title="What regulates the timing of the motion of molecular machines during DNA Replication?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;proteins&gt;&lt;biophysics&gt;&lt;replication&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20449" PostTypeId="1" AcceptedAnswerId="20516" CreationDate="2014-08-12T23:11:11.930" Score="1" ViewCount="78" Body="&lt;p&gt;If a healthy human is at a certain muscle state and then experiences muscular atrophy solely due to disuse/lack of exercise, is it easier to gain that muscle back than if the human had never reached that certain muscle state. If so, is there a name for this effect. The reason I'm wondering is because it seems like muscle mass was definitely periodic in ancient times when food would become scarce during the winter, and that an increased ability to put back on muscle might have developed evolutionary-wise. I thought that this would fit best in biology, let me know if this isn't the case.&lt;/p&gt;&#xA;" OwnerUserId="8723" LastEditorUserId="8723" LastEditDate="2014-08-13T22:13:27.817" LastActivityDate="2014-08-15T08:40:18.637" Title="Periodic Muscular Growth in Humans" Tags="&lt;evolution&gt;&lt;anatomy&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20450" PostTypeId="1" CreationDate="2014-08-12T23:25:32.300" Score="2" ViewCount="61" Body="&lt;p&gt;Another question about &lt;a href=&quot;https://www.youtube.com/watch?v=9kOGOY7vthk&quot; rel=&quot;nofollow&quot;&gt;another Youtube video&lt;/a&gt;. At 0:50, the splicing process begins to remove the non-coding section of the DNA (intron), so the different parts of the spliceosome attach to the borders on the intron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, what is the code found in the borders of the intron which is recognized by the parts of the spliceosome, so they attach to it ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, in the transcription of the DNA, the process begins after the transcription factor &quot;TBP&quot; recognizes the code &quot;TATA&quot; in the DNA string, then attaches to it. This triggers a whole process described by &lt;a href=&quot;https://www.youtube.com/watch?v=5MfSYnItYvg&quot; rel=&quot;nofollow&quot;&gt;this video&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8722" LastActivityDate="2014-08-13T00:07:21.040" Title="What is the biding site code recognized by the parts of the spliceosome" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;proteins&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20451" PostTypeId="2" ParentId="20450" CreationDate="2014-08-13T00:07:21.040" Score="2" Body="&lt;p&gt;Did you try googling &quot;splice site recognition sequences&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, the first two letters of the intron must be GT, the next three are often ARG.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The last three letters of the acceptor site of the intron are virtually always YAG&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-08-13T00:07:21.040" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20452" PostTypeId="1" CreationDate="2014-08-13T03:15:14.783" Score="3" ViewCount="377" Body="&lt;p&gt;I have recently switched from electronics to computational biology. So having some hard time with my homeworks. Can someone guide me on this problem?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Consider 6 genes A,  B, C, D, E, F, G. Some recombination rates are&#xA;  given between these genes AB = 0.2, BC = 0.1, AC = 0.25, AD = 0.5, BD&#xA;  = 0.5, DE = .1, AE = 0.5 ,EF = 0.1 ,DF = 0.15.   &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;a) Find the number of linkage groups? b) Construct possible genetic&#xA;  map showing relative positions of these genes?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5669" LastActivityDate="2014-08-13T03:15:14.783" Title="A Genetic linkage problem" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;recombination&gt;&lt;genetic-linkage&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-08-13T09:02:36.860" ContentLicense="CC BY-SA 3.0" />
  <row Id="20453" PostTypeId="1" CreationDate="2014-08-13T03:41:15.640" Score="2" ViewCount="75" Body="&lt;p&gt;We have some bacterial genomes that were assembled using &lt;a href=&quot;http://bioinf.spbau.ru/spades&quot; rel=&quot;nofollow&quot;&gt;Spades&lt;/a&gt;, they were sequenced with and IonTorrent PGM.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many assemblers and they give different results. I was interested in a tool that can merge the results from different assemblers but there are not many. I found only 2 : &lt;a href=&quot;http://garm-meta-assem.sourceforge.net&quot; rel=&quot;nofollow&quot;&gt;GARM&lt;/a&gt; and &lt;a href=&quot;https://github.com/vice87/gam-ngs&quot; rel=&quot;nofollow&quot;&gt;GAM-NGS&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there other tools to do merges? Does this improves the genome seq quality?&lt;/p&gt;&#xA;" OwnerUserId="1004" LastActivityDate="2021-03-24T01:01:50.170" Title="Assembly reconciliation" Tags="&lt;genomics&gt;&lt;sequence-assembly&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20454" PostTypeId="2" ParentId="20448" CreationDate="2014-08-13T05:17:06.467" Score="5" Body="&lt;p&gt;That's a pretty neat video, I'll just give you some background information first. It's an illustration of the &quot;trombone model&quot; of DNA replication. The darker blue molecule is helicase, it unwinds the DNA and facilitates translocation (this is an ATP dependent process). The dark purple molecules are DNA polymerase, they catalyze DNA strand synthesis (an NTP dependent process) using an ssDNA template and 3'-OH primer (the primer:template junction). The green circular molecules are sliding clamps, they increase the processivity of DNA polymerase. The light purple molecule is the sliding clamp loader, unsurprisingly it loads the sliding clamp onto the DNA (ATP dependent). The light blue molecule is a flexible linker that connects everything together. The other green molecule (the one that contacts helicase) is primase, it synthesizes RNA primers (which contains the 3'-OH initially used by DNA polymerase). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Certainly intermolecular forces play a significant role in this (and every) biochemical process, but I'm not really sure what you're talking about when you're describing electric forces and Brownian motion.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Anyways, the answer to your question is no, Okazaki fragments do not have a fixed length. DNA synthesis, as mentioned above, occurs only by adding NTPs to a 3'-OH primer. Thus the length of Okazaki fragments is dependent on the spacing between primers on the lagging strand. This is dependent on &lt;strong&gt;when&lt;/strong&gt; primase binds which in turn is dependent on primase concentration as well as its binding affinity with DNA and other replication fork proteins (especially helicase). High concentration and/or high affinity leads to a higher binding frequency and therefore shorter Okazaki fragments. The opposite is true for low concentration and/or low affinity. Note that most (or all?) primases have some degree of sequence specificity which means that specific DNA motifs will increase binding affinity. For example, &lt;em&gt;Escherichia coli&lt;/em&gt; primase (DnaG) recognizes the trimer GTA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This process also requires some degree of coordination between leading and lagging strand synthesis. Primer synthesis and DNA polymerase recycling on the lagging strand is much slower than the continuous synthesis on the leading strand. It has been suggested that primase acts as a &quot;molecular brake&quot; by halting the replication fork during primer synthesis to prevent the leading strand polymerase from rapidly outpacing those on the lagging strand (Lee JB, Hite RK, Hamdan SM, Xie XS, Richardson CC, van Oijen AM. 2006. DNA primase actas as a molecular brake in DNA replication. Nature. 439(7076):621-624.).&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-08-13T16:49:48.130" LastActivityDate="2014-08-13T16:49:48.130" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20455" PostTypeId="2" ParentId="20437" CreationDate="2014-08-13T05:35:04.387" Score="2" Body="&lt;p&gt;Sperm, in my opinion can't truly be considered &quot;alive&quot;...but they are living. Bear with me before you skip my answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A cell can be considered a &quot;living&quot; thing since It has RNA/DNA, it imbibes nutrition, it grows and is destroyed, we cannot say however that it is alive. It has a specific set of instructions coded into the RNA which it follows till its death (which is also protein,and hence RNA, mediated). Alive is a term reserved for organisms and not single haploid somatic cells. On the other hand...sperms have spiral mitochondria hence they contain RNA.&#xA;In short..yes..they can be considered living&lt;/p&gt;&#xA;" OwnerUserId="8726" LastEditorUserId="8101" LastEditDate="2014-08-15T19:31:48.027" LastActivityDate="2014-08-15T19:31:48.027" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20456" PostTypeId="1" CreationDate="2014-08-13T05:45:19.507" Score="10" ViewCount="258" Body="&lt;p&gt;Some bacteriophages reproduce using the lytic cycle which ends with the destruction of the host bacterial cell. I was wondering if theoretically this could be used theraputically to treat bacterial diseases.&lt;/p&gt;&#xA;" OwnerUserId="8726" LastEditorUserId="1320" LastEditDate="2014-08-13T09:37:15.263" LastActivityDate="2014-08-13T09:38:50.093" Title="Can a bacteriophage be used to treat bacterial diseases?" Tags="&lt;cell-biology&gt;&lt;bacteriology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20457" PostTypeId="1" AcceptedAnswerId="20458" CreationDate="2014-08-13T05:59:49.263" Score="3" ViewCount="141" Body="&lt;p&gt;I am falling short of LB agar plates and I have a plate with less LB agar poured. I meant, the plate is not fully filled with the agar (it was the last plate I poured the medium into). Some part of plate is empty. Does this cause any contamination problems or moisture retention? Is it okay if I use this to streak a 5 cm line?&lt;/p&gt;&#xA;" OwnerUserId="8142" LastActivityDate="2014-08-13T06:17:31.260" Title="Can a plate with incompletely filled LB agar be used?" Tags="&lt;microbiology&gt;&lt;medium&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20458" PostTypeId="2" ParentId="20457" CreationDate="2014-08-13T06:17:31.260" Score="4" Body="&lt;p&gt;It won't be a problem other than that the surface would be uneven. Seal the plate with parafilm when not using to avoid moisture from accumulating inside. When you pour plates then swirl the plate gently so that the molten agar distributes evenly throughout the plate. The agar will be thin though, and you would have to streak gently so as not to cut the agar; you can add 0.5 % of normal agar-agar to make it a little dense. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or else use  smaller plates (2 inch) if you have them in your lab.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-08-13T06:17:31.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20460" PostTypeId="2" ParentId="20437" CreationDate="2014-08-13T06:43:23.230" Score="3" Body="&lt;p&gt;Damn.. this is getting into a huge debate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are different levels of life. What we mean by living when we say living is generally an &lt;strong&gt;Organism&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is highly debatable. If you say viruses are nonliving because they need a host then almost every hetertroph is nonliving because they need the support of autotrophs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An organ is living as long as it remains inside the body; similarly a cell in a multicellular organism can be considered alive only if it remains associated with the multicellular whole.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So is a single man alive?? Well he can eat, carry out metabolism, form a habitat but he cannot reproduce. Man as an organism is alive as he can sustain cell division and metabolism within himself but in that restricted zone human population is dying. He is living because he has the &lt;strong&gt;potential&lt;/strong&gt; to reproduce. It is same as a lone enzyme- it can carry out its metabolism but will one day degrade unless it is re-formed.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sperm on the other hand is just a vehicle- it doesn't have the potential to sustain itself; its sole aim is to deliver the potential to the egg so that life can be created.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To conclude- the question of what is &quot;life&quot; is purely philosophical. A more scientific question would be - &quot;What is a stable, self-sustaining and dynamic biological system&quot;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-08-14T08:11:10.767" LastActivityDate="2014-08-14T08:11:10.767" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20461" PostTypeId="2" ParentId="20456" CreationDate="2014-08-13T08:38:01.493" Score="10" Body="&lt;p&gt;Yes, this is possible and is researched as an alternative to antibiotics. It has been used experimentally before antibiotics became widely available. Research was abandoned when antibiotics became widely available. See for example &lt;a href=&quot;http://journals.lww.com/amjmedsci/Citation/1930/03000/THE_USE_OF_BACTERIOPHAGE_FILTRATES_IN_THE.5.aspx&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://archpedi.jamanetwork.com/article.aspx?articleid=1176117&quot;&gt;here&lt;/a&gt; for reports on this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Today bacteriophages are researched for the treatment of bacteria which have a lot of resistances against antibiotics like Mycobacterium tuberculosis, Enterococcus faecalis, Staphylococcus aureus, Acinetobacter baumannii and Pseudomonas aeruginosa. See the references for more details (the first article also contains a nice historic overview of the field):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://aac.asm.org/content/45/3/649.short&quot;&gt;Bacteriophage Therapy&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0924857907002038&quot;&gt;Bacteriophages: an appraisal of their role in the treatment of&#xA;bacterial infections&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1359644602024984&quot;&gt;New ways to treat bacterial infections&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2014-08-13T09:38:50.093" LastActivityDate="2014-08-13T09:38:50.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20462" PostTypeId="2" ParentId="15455" CreationDate="2014-08-13T12:11:39.363" Score="2" Body="&lt;p&gt;I think Spread will be best for this work.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;&lt;a href=&quot;https://www.kuleuven.be/aidslab/phylogeography/SPREAD.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;SPREAD: Spatial Phylogenetic Reconstruction of Evolutionary Dynamics&lt;/a&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://www.kuleuven.be/aidslab/phylogeography/tutorial/RacRABV_cont_vis.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Authors:&lt;/strong&gt; Filip Bielejec, Andrew Rambaut, Marc A. Suchard &amp;amp; Philippe Lemey&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Homepage:&lt;/strong&gt; &lt;a href=&quot;http://www.phylogeography.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.phylogeography.org&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;License:&lt;/strong&gt; LGPL&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.637" LastActivityDate="2014-08-13T12:11:39.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20464" PostTypeId="1" AcceptedAnswerId="20500" CreationDate="2014-08-13T12:44:15.163" Score="2" ViewCount="820" Body="&lt;p&gt;A girl pretended having a piece of food in her hand and pointed it to a Barbary Macaque in Gibraltar. As a response he made this facial expression to her. What does this mean?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VLdkB.jpg&quot; alt=&quot;GibraltarBarbaryMacaqueExpressions&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8729" LastEditorUserId="5144" LastEditDate="2014-08-14T15:52:21.773" LastActivityDate="2014-08-14T16:48:32.370" Title="What does this Barbary Macaque facial expression mean?" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;behaviour&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20465" PostTypeId="1" AcceptedAnswerId="20816" CreationDate="2014-08-13T14:02:27.977" Score="6" ViewCount="4842" Body="&lt;p&gt;I was watching sea birds eating fishes and wondered if fishes actually died from old age, or if they are all eaten before this can happen?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I reckon some big predator fishes must be able to live long enough to die from their age, but fishes who are lower in the food chain, do any of them actually reach an age old enough to die peacefully or are they all somewhat doomed to feed a bird or another fish?&lt;/p&gt;&#xA;" OwnerUserId="8732" LastEditorUserId="3952" LastEditDate="2014-08-26T19:27:55.093" LastActivityDate="2019-07-19T07:11:43.703" Title="In practice, do fishes die from old age?" Tags="&lt;senescence&gt;&lt;ichthyology&gt;&lt;life-history&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20466" PostTypeId="2" ParentId="11133" CreationDate="2014-08-13T14:42:31.413" Score="1" Body="&lt;p&gt;Here is a simple proof that the probability of fixation given an infinite time is indeed p (in a finite population, otherwise there will be no fixation):&#xA;Let's look at all 2N gametes in the population. Eventualy, according to the Wright-Fisher model, only one of them will be represented in the population. The probability for this gamete to be of an allele with initial frequency p is just p. Therefore the probability of fixation is p.&#xA;Simple.&lt;/p&gt;&#xA;" OwnerUserId="8734" LastActivityDate="2014-08-13T14:42:31.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20467" PostTypeId="1" CreationDate="2014-08-13T15:05:44.060" Score="5" ViewCount="723" Body="&lt;p&gt;How would having two nostrils be advantageous to your sense of smell or your ability to breath? I already hypothesized that either one of the nostrils could act as a back up for when another gets congested, but even then you can still breath through your mouth and at least for me I almost always have either both nostrils congested or neither at all.&lt;/p&gt;&#xA;" OwnerUserId="8733" LastActivityDate="2018-02-13T14:00:27.037" Title="What is the point of having evolved two nostrils?" Tags="&lt;human-biology&gt;&lt;evolution&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20469" PostTypeId="2" ParentId="20444" CreationDate="2014-08-13T16:28:01.890" Score="3" Body="&lt;p&gt;According to &lt;a href=&quot;http://stanxterm.aecom.yu.edu/wiki/data/Product_manuals_attach/quikchange2xl.pdf&quot; rel=&quot;nofollow&quot;&gt;this instruction&lt;/a&gt; it can be done for 1 hour but this is for large plasmids. I agree with Chris that it should not be of a problem. Alternatively you can setup your 37°C DpnI incubation step in a PCR machine and after however long that is recommended, you can set the PCR machine to cool to 4°C automatically, that way you can leave it there for as long as you want.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="5144" LastEditDate="2014-08-13T17:27:43.717" LastActivityDate="2014-08-13T17:27:43.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20470" PostTypeId="1" AcceptedAnswerId="20471" CreationDate="2014-08-13T17:42:08.793" Score="7" ViewCount="1070" Body="&lt;p&gt;Because DNA is soluble in water, is it possible to extract PCR product by dissolving excised gel containing the DNA band of desired length in water, mashing the gel piece with a pestle, centrifuging it and then pipetting out the supernatant ? &lt;/p&gt;&#xA;" OwnerUserId="18932" LastActivityDate="2018-06-06T10:43:51.143" Title="DNA extraction from agarose gel" Tags="&lt;dna&gt;&lt;gel-electrophoresis&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20471" PostTypeId="2" ParentId="20470" CreationDate="2014-08-13T17:53:39.383" Score="11" Body="&lt;p&gt;Yes, this is possible (and I have done it uncounted number of times) - the method is called &quot;Freeze and squeeze&quot;. What you basically do is to run the gel, cut out the band of interest (be careful with the UV light, it causes damage to your DNA and also sunburns, so wear appropriate shielding for your face), dissolve it in a buffer, then freeze it in liquid nitrogen (or the -70°C, doesn't matter) and centrifuge it at room temperature for 10 minutes. During this time the ice melts and the agarose pellets at the bottom. Take the supernatant, do a ethanol precipitation (with glycogen when you only have little DNA) and you have nice and clean DNA. No need for expensive kits and is done approximately in 2 hours.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find a very nice and detailed protocol here: &quot;&lt;a href=&quot;http://web.archive.org/web/20150906161340/http://personal.bgsu.edu/~gangz/Page099-103_Elution_of_DNA_from_Agarose_Gels.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Elution of DNA from Agarose Gels&lt;/a&gt;&quot; (The rest of the &lt;a href=&quot;http://web.archive.org/web/20151003090249/http://personal.bgsu.edu/%7Egangz/EFB601.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;handbook&lt;/a&gt; is also very useful).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2018-06-06T10:43:51.143" LastActivityDate="2018-06-06T10:43:51.143" CommentCount="15" ContentLicense="CC BY-SA 4.0" />
  <row Id="20472" PostTypeId="1" AcceptedAnswerId="20474" CreationDate="2014-08-13T19:20:53.120" Score="5" ViewCount="1131" Body="&lt;p&gt;I need the map of the pMON7124 plasmid. As this is not easy to find, I welcome any hints.&lt;/p&gt;&#xA;" OwnerUserId="416" LastEditorUserId="416" LastEditDate="2014-08-24T11:35:16.593" LastActivityDate="2014-08-24T11:35:16.593" Title="Where can I find the pMON7124 plasmid sequence?" Tags="&lt;sequence-analysis&gt;&lt;plasmids&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20473" PostTypeId="1" CreationDate="2014-08-13T19:25:42.343" Score="2" ViewCount="975" Body="&lt;p&gt;I am working with RNA-seq data from the Cancer Genome Atlas &lt;a href=&quot;http://cancergenome.nih.gov/&quot; rel=&quot;nofollow&quot;&gt;TCGA&lt;/a&gt; and I have been reading about how people have compared gene expression levels measured by RNA-seq. Many of the papers I have read talk about &quot;differential expression&quot; for comparing each gene's expression levels in the Experimental and Control conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In TCGA data, I typically have a patient cohort who have had the mRNA in their tumors sequenced just once so there is no Experimental-vs-Control dynamic. I am interested in finding which patients' tumors show gene-expression that is significantly higher than the rest of the cohort but I have not had any luck finding literature describing this kind of comparison. I'm thinking maybe I can apply existing differential expression techniques to my situation but that seems cumbersome and not-necessarily appropriate so thought I'd ask the community here if there's a better way of finding which members of a cohort are outliers for specific genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also: all of my RNA-seq data has already been RPKM normalized for me. I have been advised that using &lt;a href=&quot;http://www.biomedcentral.com/1471-2105/12/323&quot; rel=&quot;nofollow&quot;&gt;RSEM&lt;/a&gt; instead would be better for comparing gene expression across multiple samples but, for logistic reasons, I'm probably stuck with my RPKM-normalized expression levels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fundamentally, I'm looking for the best way to compare gene expression across samples to determine which samples have outlying high/low gene expression.&lt;/strong&gt; Intuitively, I figure I could just compute median z-scores for each gene's expression levels within my cohort and consider anyone with a |z-score| greater than 2 to be an &quot;outlier&quot; but I haven't found any literature to support this kind of approach either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any suggestions, papers, or advice will be greatly appreciated. &lt;/p&gt;&#xA;" OwnerUserId="8161" LastEditorUserId="14852" LastEditDate="2015-04-24T06:35:01.860" LastActivityDate="2016-01-05T18:26:23.997" Title="Using RNA-seq to compare gene expression across patients instead of between Control and Experimental conditions" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;gene-expression&gt;&lt;rna-sequencing&gt;&lt;tcga&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20474" PostTypeId="2" ParentId="20472" CreationDate="2014-08-13T20:01:41.000" Score="6" Body="&lt;p&gt;It seems that no good map of this plasmid is around. Life technology uses it in some of its bacterial strains, the quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;E. coli also contain the helper plasmid, pMON7124 (13.2 kb), which&#xA;  encodes the transposase and confers resistance to tetracycline. The&#xA;  helper plasmid provides the Tn7 transposition function in trans.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They link to the original publication, but the image quality in there is pretty bad:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GNOeZ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They give some information in the text, so I would recommend reading the paper (if you have no access, let me know, I can help here):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2850977&quot; rel=&quot;nofollow noreferrer&quot;&gt;A broad-host-range shuttle system for gene insertion into the&#xA;chromosomes of gram-negative bacteria.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If this is not enough, you could still try to get a better version from the author Gerard F. Berry (you can find his Monsanto email adress by googling for it).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-08-13T20:14:47.853" LastActivityDate="2014-08-13T20:14:47.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20476" PostTypeId="1" CreationDate="2014-08-14T01:36:14.523" Score="2" ViewCount="317" Body="&lt;p&gt;What can we consciously control in our bodies besides our muscles and brain (thought, memory, etc.)? Is the notion &lt;strong&gt;Bio Feedback&lt;/strong&gt; related to this matter?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt; I mean I can move my muscles at will but I can't order my liver to &quot;work&quot; since it's not managed consciously by the human mind. I heard about having some sort of control over temperature, heartbeat, sweating, etc. using techniques like breathing in martial arts or what they teach at the military to fool the lie detector. So my question is : &lt;em&gt;What CAN we control?&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="6363" LastEditorUserId="6363" LastEditDate="2014-08-14T14:29:02.180" LastActivityDate="2014-08-14T14:29:02.180" Title="Human body control?" Tags="&lt;human-biology&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ClosedDate="2014-08-14T08:46:07.127" ContentLicense="CC BY-SA 3.0" />
  <row Id="20479" PostTypeId="1" AcceptedAnswerId="20482" CreationDate="2014-08-14T06:05:30.983" Score="9" ViewCount="3794" Body="&lt;p&gt;This red spider has set up a web in my yard, in South Eastern, Texas, United States:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/gq8PQ.jpg&quot; alt=&quot;Spider 1&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/AspSb.jpg&quot; alt=&quot;Spider 2&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The spider itself is about an inch long (2.5 cm), and is predominantly red to brown in color, with red legs, and a very striking white line straight down the center of her back. The web is quite large&amp;mdash;at least 4 feet (1.2 m) in diameter. It seems to be nocturnal, as I haven't seen it during the day, yet I've walked into the web (or nearly walked into its web) twice at night. Unfortunately, due to lighting conditions I wasn't able to capture the color particularly well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've searched but haven't found a species that looks like this yet.&lt;/p&gt;&#xA;" OwnerUserId="6703" LastEditorUserId="22057" LastEditDate="2016-10-06T21:25:59.507" LastActivityDate="2017-03-09T21:34:15.723" Title="Spider identification" Tags="&lt;zoology&gt;&lt;species-identification&gt;&lt;arachnology&gt;&lt;invertebrates&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20480" PostTypeId="2" ParentId="20473" CreationDate="2014-08-14T06:13:43.653" Score="2" Body="&lt;p&gt;When you say RPKM do you mean crude RPKM or the estimates that you get using expectation maximization methods like cufflinks and eXpress?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is better if you get your RPKM or FPKM values from one of these programs because you can differentiate between transcript variants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have mostly used cufflinks and eXpress. Cufflinks package is better for multiple datasets. You can use cuffquant (which takes SAM/BAM) files to compute FPKM. Cuffquant will also need a reference &lt;code&gt;GTF&lt;/code&gt; file. Cuffquant gives a binary &lt;code&gt;.cxb&lt;/code&gt; file which you cannot read directly. Once you have generated the &lt;code&gt;.cxb&lt;/code&gt; files for all your cohort samples, then pass all these files to cuffnorm. It will normalize the data and give you FPKM values for each gene in each sample in the form of a huge table.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next point is which genes do you wish to compare. Do you want to compare known oncogenes which show consistent upregulation in all cancers? Actually there is a paper in which they have done this (I'll let you know the reference when I find it. Not able to recollect now).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can then see how many of these genes show consistent expression in your cohort. Basically you need to identify a set of genes before you go on to study which patient shows anomalous expression.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-08-14T15:47:02.117" LastActivityDate="2014-08-14T15:47:02.117" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20482" PostTypeId="2" ParentId="20479" CreationDate="2014-08-14T07:07:45.033" Score="12" Body="&lt;p&gt;After some more searching, I think stumbled across the answer. It appears to be an&amp;hellip;&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;&lt;em&gt;Eriophora ravilla&lt;/em&gt;:&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1uTYr.png&quot; alt=&quot;Eriophora ravilla&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/yND2h.png&quot; alt=&quot;Eriophora ravilla&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source &lt;a href=&quot;http://bugguide.net/node/view/236715&quot; rel=&quot;noreferrer&quot;&gt;BugGuide.net&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This species appears to have quite a diverse range of colors, and even thought I haven't found one that quite matches mine, the other similarities (the large abdomen, the stripe down the back, the four 'dimples', and the dark first leg segments) are enough to convince me. However, if anyone else can shed some light on this, I'd appreciate it.&lt;/p&gt;&#xA;" OwnerUserId="6703" LastActivityDate="2014-08-14T07:07:45.033" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20483" PostTypeId="2" ParentId="20414" CreationDate="2014-08-14T07:41:56.623" Score="1" Body="&lt;p&gt;What you are basically asking is if there are cellular processes that are thresholded (ultrasensitive). Yes; there are many examples and it would be difficult to list them all. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are different mechanisms by which such a switch like behaviour can be implemented. Positive feedback loops and co-operativity (in transcription factor binding or enzyme-ligand binding) are common mechanisms by which such switches can be implemented. Have a look at &lt;a href=&quot;https://en.wikipedia.org/wiki/Ultrasensitivity&quot; rel=&quot;nofollow noreferrer&quot;&gt;this wikipedia page&lt;/a&gt;. For more details you can refer to a book on enzyme kinetics and non-linear dynamics. If you search co-operativity and postitive feedback loops then you will find studies on specific examples. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But as &lt;a href=&quot;https://biology.stackexchange.com/a/20416/3340&quot;&gt;already pointed in the other answer&lt;/a&gt;, almost all cellular processes are concentration dependent. There are a very few examples where you can actually observe zero order kinetics. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2016-09-18T14:12:51.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20485" PostTypeId="2" ParentId="15012" CreationDate="2014-08-14T08:10:10.867" Score="3" Body="&lt;p&gt;The question is slightly unclear since it fails to clarify whether the GPL-1 receptor is endogenous or is over-expressed. Also does the GLP-1 belong the same species that Min-6 originates from or it belongs to a different species? Those are important points since if the receptor is endogenous then the main problem is sensitivity of the detection method, which can be difficult sometimes to detect an endogenous protein relative to an over-expressed one. Also if the GPL-1 belongs to a different species, which you are trying to over express in Min-6 it might not work since the cellular machinery might not support its production (tho unlikely) or its transport to the cell surface, which I have had this problem before. It could be that for the particular expression levels you have in those cells, if the GLP-1 is over expressed or if its non-endogenous, it causes toxicity and kills the cells that are expressing it hence why you do not see any GLP-1 expression (e.g due to excessive receptor activation). Also could you clarify what you mean by &quot;analogue for glp-1&quot;? does this mean it is not exactly GPL-1 or its a homologue or orthologue, which you are trying to detect using a GLP-1 specific antibody? that might again be a problem if the GLP-1 Ab you are using detects a region of the receptor, which is not conserved in its homologues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of solutions as pointed in the comments, the best way to go about this is to use a polyclonal Ab, which is raised against a large section of the peptide in question, allowing you a better chance of its detection. If that did not work, you might have to resort to GLP-1 mRNA detection using RT-PCR or qPCR, which you would need to design primers for based on you GPL-1 sequence which you can get help with &lt;a href=&quot;http://openwetware.org/wiki/Choosing_primers_for_qPCR&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-14T09:13:20.333" LastActivityDate="2014-08-14T09:13:20.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20486" PostTypeId="1" AcceptedAnswerId="20487" CreationDate="2014-08-14T09:01:46.200" Score="21" ViewCount="17857" Body="&lt;p&gt;Vomit comes from gastric acid, right? And in gastric acid there is HCl and HCl is corrosive (strong), how come when I vomit, it doesn't destroy things that it (as the vomit) hits (such as floor, table)?&lt;/p&gt;&#xA;" OwnerUserId="8651" LastEditorUserId="8751" LastEditDate="2014-08-14T17:55:08.080" LastActivityDate="2014-10-19T07:46:29.727" Title="Why isn't vomit corrosive?" Tags="&lt;human-biology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20487" PostTypeId="2" ParentId="20486" CreationDate="2014-08-14T09:16:28.580" Score="37" Body="&lt;p&gt;First of all, it is corrosive. People which are bulimic often get problems with their teeth getting damaged by the permanent exposure to the acidic stomach fluids. See the paper for more information:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://informahealthcare.com/doi/abs/10.1080/000163598423045&quot;&gt;Bulimia and tooth erosion&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Then it is a matter of concentration. According to Wikipedia, the concentration of the acid in the stomach is around 0.5% which is a pretty low concentration. Additionally the acid gets diluted when you eat or drink things. And last but not least not all things are very susceptible to a fast degradation by acids. Thing tend also not to disappear suddenly, if they come in contact with acids.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-14T09:16:28.580" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="20489" PostTypeId="1" AcceptedAnswerId="20493" CreationDate="2014-08-14T12:46:33.787" Score="17" ViewCount="11616" Body="&lt;p&gt;Is there any relationship between heartbeat rate and life span of an animal?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do they belong to a cause-and-effect relationship or are they both caused by some phenomenons or a common cause?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2019-04-07T23:52:45.433" Title="Is there any relationship between heartbeat rate and life span of an animal?" Tags="&lt;zoology&gt;&lt;cardiology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20491" PostTypeId="1" AcceptedAnswerId="20495" CreationDate="2014-08-14T13:05:36.633" Score="4" ViewCount="3657" Body="&lt;p&gt;Theoretically, mitochondria are said to be a separate organism that is concerned with its own life and its own processes. In fact, it even duplicates individually. I know a similar question is &lt;a href=&quot;https://biology.stackexchange.com/questions/14347/the-origin-of-mitochondria&quot;&gt;here&lt;/a&gt; but I have something else apart from that to ask.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Is the presence of their own DNA/RNA - like compound justify or prove that the mitochondria was once a separate living organism?&lt;/li&gt;&#xA;&lt;li&gt;If the mitochondria is indeed a separate living organism, then how is it controlled by the nucleus? Or is it not? Logic would suggest that since mRNA exists in the mitochondria separate from DNA in the nucleus, they have their own control over how they behave.&lt;/li&gt;&#xA;&lt;li&gt;Often, living organisms working together have to have some sort of payment system. For example, bacteria in the body provide Vitamin K and other breakdown vitamins, and in return the body gives it a suitable home to live in. Is there any such business occurring between the individual cell and the mitochondria? Does it keep some nutrients for itself? If not, what is its mode of nutrition? &lt;/li&gt;&#xA;&lt;li&gt;In effect, cells did exist before mitochondria joined the party. Is there any way to at least have a feasible hypothesis on why and how the cells bonded with the mitochondria or how the cells even existed in the first place without the presence of and organnelle that can break down food and convert it into energy?&lt;/li&gt;&#xA;&lt;li&gt;Why do mitochondria have their own membrane? And that too folded? Is that to increase the surface area available for the electron transport chain, or is it for simple compactness?&lt;/li&gt;&#xA;&lt;li&gt;Why does the mRNA in our bodies always exactly match the mRNA of our mothers and only our &lt;em&gt;mothers&lt;/em&gt;? Can any genetic mutation change this fact?&lt;/li&gt;&#xA;&lt;li&gt;Is it possible, that a mitochondrion can somehow escape the cell and start performing its life otherwise?&lt;/li&gt;&#xA;&lt;li&gt;mRNA would suggest that mitochondria make their own proteins / at least some basic amino acids. If there are any such proteins, are they utilized for the cell? Or are they used for cellular respiration? Or are they kept by the mitochondria for there own means?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I will appreciate all answers!,&#xA;SmallDeveloper (a.k.a SmallScientist :) )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT : Basically, I am asking 3 things:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Were mitochondria really separate organisms once?&lt;/li&gt;&#xA;&lt;li&gt;If so, how do they get their nutrition?&lt;/li&gt;&#xA;&lt;li&gt;How did cells exist before mitochondria came along? &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerDisplayName="user8269" LastEditorUserId="-1" LastEditorDisplayName="user8269" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2019-06-28T10:31:20.667" Title="Mitochondria - are they really separate organisms that once merged into eukaryotic cells?" Tags="&lt;cell-biology&gt;&lt;cellular-respiration&gt;&lt;mitochondria&gt;&lt;cell&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2019-06-28T16:52:45.327" ContentLicense="CC BY-SA 3.0" />
  <row Id="20493" PostTypeId="2" ParentId="20489" CreationDate="2014-08-14T13:21:46.400" Score="23" Body="&lt;p&gt;Interestingly there is a inverse negative correlation between heart rate and life span, meaning the faster your heart rate is, the shorter is your lifespan. See this figure (from the paper 2 cited below):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uLUcI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the authors plotted the approximately total heartbeats vs. the lifespan, the amount of total heartbeats was in a pretty narrow corridor:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sdp9c.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it seems that at least the hearts in mammals have a maximum number of strokes they could do. The obvious question what causes this phenomenon is not really answered.&#xA;Since the metabolism of small animals is (compared to their weight) higher and also their oxygen consumption is higher because of that, it is hypothesized that this causes more reactive oxygen species and related damage which subsequently leads to an earlier death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See the references for more details:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9316546&quot; rel=&quot;noreferrer&quot;&gt;Rest heart rate and life expectancy.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1568163708000524&quot; rel=&quot;noreferrer&quot;&gt;Heart rate, lifespan, and mortality risk&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pnas.org/content/85/8/2706.short&quot; rel=&quot;noreferrer&quot;&gt;Oxidative damage to DNA: relation to species metabolic rate and life&#xA;span&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-14T13:21:46.400" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="20494" PostTypeId="2" ParentId="8560" CreationDate="2014-08-14T13:29:30.977" Score="8" Body="&lt;p&gt;It reminds me of the smooth-barked Australian gum trees / eucalyptus, like a salmon gum, ghost gum, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although there are no squirrels in Australia :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This photo of a Salmon Gum is from &lt;a href=&quot;http://www.fpc.wa.gov.au/content_migration/plantations/species/arid/salmon_gum.aspx&quot; rel=&quot;noreferrer&quot;&gt;http://www.fpc.wa.gov.au/content_migration/plantations/species/arid/salmon_gum.aspx&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/r96zF.gif&quot; alt=&quot;Salmon Gum&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8745" LastActivityDate="2014-08-14T13:29:30.977" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20495" PostTypeId="2" ParentId="20491" CreationDate="2014-08-14T13:30:53.693" Score="5" Body="&lt;ol&gt;&#xA;&lt;li&gt;Yes. But it is incorrect to call mitochondria an organism now.&lt;/li&gt;&#xA;&lt;li&gt;Most of their genes were lost and are now encoded in the nuclear genome&lt;/li&gt;&#xA;&lt;li&gt;It gets most of its metabolites&lt;/li&gt;&#xA;&lt;li&gt;It is not known. See the &lt;a href=&quot;https://biology.stackexchange.com/questions/14347/the-origin-of-mitochondria&quot;&gt;other&lt;/a&gt; post for details.&lt;/li&gt;&#xA;&lt;li&gt;Why membrane: I guess you know that. Why folded: you guessed right.&lt;/li&gt;&#xA;&lt;li&gt;Only ovum donates mitochondria and other cytoplasmic factors. Sperm just provides the haploid genome.&lt;/li&gt;&#xA;&lt;li&gt;No&lt;/li&gt;&#xA;&lt;li&gt;Most of them are key respiratory enzymes&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-08-14T13:30:53.693" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20496" PostTypeId="2" ParentId="20467" CreationDate="2014-08-14T13:31:47.477" Score="5" Body="&lt;p&gt;There are two aspects to your question.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, organisms have some kind of symmetry. The field of evolutionary developmental biology has some theories on why our anatomy is the way that it is.  So, we have two eyes, two halves of our nose and two nostrils, one &quot;tube&quot; that becomes the path from our mouth to anus, etc. Our nostrils are just part of that symmetry. It may be evolutionary advantageous to keep two nostrils so that an animal can tell what direction a smell is coming from.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, we see that evolution has provided a path to having just one nostril.  Blowholes in toothed whales are just one nostril.  The other nostril does not have an opening to the outside of the whale.  It would be interesting to explore the split between baleen (two nostrils) and toothed whales (one nostril).  This evolutionary divergence may have been caused by differences in communication styles or the different blowholes may have caused a difference in communications &lt;a href=&quot;http://www.whoi.edu/science/B/people/kamaral/marinemammalacoustics.html&quot;&gt;http://www.whoi.edu/science/B/people/kamaral/marinemammalacoustics.html&lt;/a&gt; .&lt;/p&gt;&#xA;" OwnerUserId="8746" LastActivityDate="2014-08-14T13:31:47.477" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20497" PostTypeId="2" ParentId="17867" CreationDate="2014-08-14T15:34:58.087" Score="3" Body="&lt;p&gt;The main minerals in tap water are calcium and magnesium, which determine the hardness of water. The main minerals in mineral waters are calcium, magnesium, sodium, chloride, carbonate and sulfate. Tap water from different regions and various brands of mineral water can contain very different amounts of minerals, so it is impossible to make a general recommendation to drink more mineral water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mineral water high in calcium or magnesium can be a good source of calcium and magnesium for people who do not get enough calcium from foods. Foods are much better source of calcium and magnesium than water, though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Researchers from the World Health Organization (WHO) claim that water hardness (calcium and magnesium content) has no effects on health (positive or negative).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Foods high in calcium, beneficial and harmful effects of calcium and references to claims I made:&#xA;&lt;a href=&quot;http://www.nutrientsreview.com/minerals/calcium-ca.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nutrientsreview.com/minerals/calcium-ca.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Calcium concentration in bottled and mineral waters (US, Europe):&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2488164/table/Tab2/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2488164/table/Tab2/&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="4025" LastActivityDate="2014-08-14T15:34:58.087" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20499" PostTypeId="1" AcceptedAnswerId="20515" CreationDate="2014-08-14T15:45:19.813" Score="10" ViewCount="27045" Body="&lt;p&gt;Anal glands in all kinds of animals play a range of diverse functions - providing fat for preening feathers or waterproofing fur, generating distinct scent, even repelling predators.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;None of the resources I found about human anal glands ever mention their function. There's info or infections, location, treatment of problems related to them, but never a word about a role they might serve - if any. Are they vestigial organs without any role or do they have some evolutionary purpose?&lt;/p&gt;&#xA;" OwnerUserId="6512" LastEditorUserId="16651" LastEditDate="2015-12-25T01:28:38.563" LastActivityDate="2020-03-10T13:27:31.743" Title="Do human anal glands have any function?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;human-physiology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20500" PostTypeId="2" ParentId="20464" CreationDate="2014-08-14T15:51:33.487" Score="4" Body="&lt;p&gt;It looks like it is trying too threat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://www.frontiersin.org/files/Articles/894/fnbeh-03-050/image_n/fnbeh-03-050-g001.gif&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://journal.frontiersin.org/Journal/10.3389/neuro.08.050.2009/full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Individual differences in scanpaths correspond with serotonin transporter genotype and behavioral phenotype in rhesus monkeys (Macaca mulatta)&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.650" LastActivityDate="2014-08-14T15:51:33.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20502" PostTypeId="2" ParentId="20464" CreationDate="2014-08-14T16:48:32.370" Score="4" Body="&lt;p&gt;That is a threat face.  Barbary macaque threat faces often appear with a brow raise, lowered head, and an o-shaped mouth, sometimes with and sometimes without a vocalization.  Given the context you described it is not surprising the girl received a threat.  *Based on personal research experience&lt;/p&gt;&#xA;" OwnerUserId="8749" LastActivityDate="2014-08-14T16:48:32.370" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20503" PostTypeId="2" ParentId="20449" CreationDate="2014-08-14T16:55:20.613" Score="1" Body="&lt;p&gt;Disuse and lack of exercise are actually exceedingly new problems when considered on an evolutionary scale.  The bigger evolutionary pressure for the last few million years has been not starving to death, therefore not maintaining expensive muscle fibers unless they were absolutely necessary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't found any evidence of previous musculature effecting growth, but I'm going to look into it more (only some quick pubmed searches), and edit this answer.  If someone else knows more immediately, please feel free to answer.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2014-08-14T16:55:20.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20504" PostTypeId="2" ParentId="20467" CreationDate="2014-08-14T17:41:16.130" Score="3" Body="&lt;p&gt;We have two nostrils for the same reason we have 2 ears and 2 eyes. Having 2 nostrils means an odor molecule coming from one direction will have higher concentration in one nostril than the other, so we can determine what direction the smell is coming from, and allows us to find food or avoid predators more effectively. While humans no longer rely on smell very much, our distant ancestors and relatives did. Moles provide an excellent example and recent research displays their &quot;stereo smell&quot; ability, &lt;a href=&quot;http://news.nationalgeographic.com/news/2013/02/130205-moles-smell-stereo-animals-weird-science/&quot; rel=&quot;nofollow&quot;&gt;http://news.nationalgeographic.com/news/2013/02/130205-moles-smell-stereo-animals-weird-science/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And nostrils aren't the only example of smelling in directions, insects have 2 antenna, which are their scent organs. Moths can follow a pheromone trail using their antenna with great accuracy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why do humans still have two nostrils despite not needing to smell in stereo? There just hasn't been any evolutionary pressure to move towards 1 nostril. In fact, there would probably be pressure against it, because a human with 1 big hole in the middle of his face probably won't get a lot of dates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, not all cetaceans have a single blowhole. Gray whales have 2 nostrils, and sperm whales have a vestigial second nostril that doesn't reach the surface. &lt;a href=&quot;http://en.wikipedia.org/wiki/Blowhole_%28anatomy%29&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Blowhole_%28anatomy%29&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The position of the blowhole is interesting because it's on the top of the head, above the eyes. Rarely, other animals will be born with a disorder called cyclopia, where they have 1 eye in the middle of the face. They usually don't live very long at all, but their nose doesn't develop right either, if it develops at all it shows up above the eye, and is often a proboscis instead of a nose.&lt;a href=&quot;http://en.wikipedia.org/wiki/Cyclopia&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Cyclopia&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whales must have developed a way to keep the nose above the eyes while not messing anything else up.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2014-08-15T00:56:24.067" LastActivityDate="2014-08-15T00:56:24.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20506" PostTypeId="1" CreationDate="2014-08-14T18:30:32.877" Score="4" ViewCount="2416" Body="&lt;p&gt;Mikel Vsauce (Vsauce youtube channel) said in his video that it takes about 5 years for the body replace all of its atoms, while in asapscience youtube channel they are claiming that it takes 10 years. I am confused and I can't find anywhere the precise time it takes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=coGfGmOeLjE&amp;amp;index=37&amp;amp;list=UU6nSFpj9HTCZ5t-N3Rm3-HA&quot; rel=&quot;nofollow&quot;&gt;Mikel's video (minute 1:14)&lt;/a&gt; &#xA;&lt;a href=&quot;https://www.youtube.com/watch?v=6Ni5HOdGtzM&amp;amp;list=UUC552Sd-3nyi_tk2BudLUzA&quot; rel=&quot;nofollow&quot;&gt;AsapScience video (minute 1:07)&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8756" LastEditorUserId="1320" LastEditDate="2014-08-15T07:53:31.653" LastActivityDate="2017-08-03T09:08:20.003" Title="How much time does it take a human body to replace all of its atoms?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="20508" PostTypeId="2" ParentId="20378" CreationDate="2014-08-14T21:27:04.333" Score="6" Body="&lt;p&gt;I was first thinking of voting to close the question because it was too broad, but in reconsideration I think the answer of showing why it is too broad would constitute a proper answer in this case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, the term &lt;strong&gt;disease&lt;/strong&gt; is one of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Disease#Concepts&quot; rel=&quot;nofollow&quot;&gt;most general terms&lt;/a&gt; for a problem in medicine.  The only term that could be higher up is &quot;medical condition.&quot;  It could be an infectious disease, genetic disease, induced disease (think chemicals, tobacco, etc), or [insert organ here, ie heart] disease (which are not necessarily genetic).  There are attempts to distinguish between &quot;diseases&quot; and &quot;disorders,&quot; but the difference is not always clear.  The term &quot;disorder&quot; is growing in usage and scope because it is seen as having fewer negative connotations than disease (think disease of the mind vs. disorder of the mind).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus each field has it's own ways of identifying new diseases.  As a general trend new diseases are found now by identifying greater specificity within a previously general disease.  For example, a person could be said to have an &quot;adrenal cancer,&quot; but now we would want to know if they have an adrenocortical carcinoma.  In an infectious setting, we could think of all the particular pneumonia being specified out of &lt;a href=&quot;https://en.wikipedia.org/wiki/Diffuse_lung_disease&quot; rel=&quot;nofollow&quot;&gt;interstitial lung diseases&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diseases caused by external agents (&lt;a href=&quot;http://en.wikipedia.org/wiki/Pathogens&quot; rel=&quot;nofollow&quot;&gt;pathogens&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Toxins&quot; rel=&quot;nofollow&quot;&gt;toxins&lt;/a&gt;, etc) can sometimes be more uniquely novel, in that they can change into something unpredicted (new compound or virus made by man for example).  Perhaps you meant to ask if there were standard ways for identifying new viruses or microbes?&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2014-08-15T01:25:09.020" LastActivityDate="2014-08-15T01:25:09.020" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20509" PostTypeId="1" CreationDate="2014-08-15T00:20:02.967" Score="2" ViewCount="102" Body="&lt;p&gt;Consider a gamete in a typical human being. In the interest of being specific, let us say that we're talking about a typical ovum in a typical middle class woman living in a developed nation. What percentage, on the average, of the mutations in the genome of that ovum will have been caused by electromagnetic radiation?&lt;/p&gt;&#xA;" OwnerUserId="8761" LastEditorUserId="22057" LastEditDate="2016-03-22T23:06:48.057" LastActivityDate="2016-03-22T23:06:48.057" Title="Percentage of mutations caused by radiation?" Tags="&lt;mutations&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20510" PostTypeId="1" CreationDate="2014-08-15T03:12:51.670" Score="4" ViewCount="176" Body="&lt;p&gt;I read the book Genome by Matt Ridley for my AP biology course. I found it fascinating, although it seems another book must have been written on the topic since 1999. Anything you can recommend?&lt;/p&gt;&#xA;" OwnerUserId="8762" LastActivityDate="2014-08-15T03:12:51.670" Title="Is there a more updated version of the book &quot;Genome?&quot;" Tags="&lt;human-genome&gt;&lt;book-recommendation&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2015-05-28T23:30:58.983" ContentLicense="CC BY-SA 3.0" />
  <row Id="20511" PostTypeId="1" CreationDate="2014-08-15T06:03:57.897" Score="7" ViewCount="218" Body="&lt;p&gt;I have recently become fascinated with an awesome topic in biology and evolution that I feel is rarely covered in biology courses. That is, rates of meiotic recombination, or the the amount that an organism's genome is reshuffled before it is passed on to the next generation, varies across species! And no one really knows why.&#xA;A recent paper by &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/280/1771/20131945.short&quot; rel=&quot;noreferrer&quot;&gt;Segura et al&lt;/a&gt; which gathered average recombination rates for males across a dozen or so mammals and showed that there is a trend of increasing recombination rate with mammalian divergence.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Why is recombination increasing through mammalian evolution?&lt;/strong&gt; Is there any reason to believe that there is something special about placental mammals which would drive increased recombination?&lt;/p&gt;&#xA;&lt;p&gt;There are some catches to this study such as low sampling of marsupials and monotremes and low power for most of species wide recombination rates, ie the average recombination rate of cells in a single individual. But I can see how getting samples from multiple tigers would be difficult.&lt;/p&gt;&#xA;" OwnerUserId="6134" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-10-10T15:49:29.153" Title="Why are recombination rates increasing in mammals?" Tags="&lt;evolution&gt;&lt;mammals&gt;&lt;population-genetics&gt;&lt;recombination&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20512" PostTypeId="2" ParentId="7586" CreationDate="2014-08-15T06:38:06.243" Score="2" Body="&lt;p&gt;I found that E. coli exposed to predators such as amoeba changes completely from normal form to filaments (on agar) that look wound up like spaghetti but are not only longer but significantly wider. In this form the predator can't attack E. coli and it lives among the amoeba for extended periods. It does not look like a simple point mutation to me, which merely disables cell from cell dissociation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I have now two types of E.coli, opaque whitish looking filmaentous colonies and the normal more translucent colonies. In one case the filamentous form turned back to the normal form after repeated transfers on predator free plates. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the question here could be: which is the E. coli that lives in the real world out there in soil water and biofilms?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ralf Cord-Ruwisch Aug 2014&lt;/p&gt;&#xA;" OwnerUserId="8766" LastActivityDate="2014-08-15T06:38:06.243" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20513" PostTypeId="2" ParentId="20509" CreationDate="2014-08-15T07:26:47.500" Score="3" Body="&lt;p&gt;You might use the frequency of thymine-thymine dimers to extrapolate the rate of UV induced damage. &lt;a href=&quot;http://www.researchgate.net/publication/228590082_A_simple_and_efficient_method_for_the_quantitative_analysis_of_thymine_dimers_in_cyanobacteria_phytoplankton_and_macroalgae&quot; rel=&quot;nofollow&quot;&gt;This has been studied&lt;/a&gt; but I couldn't find a paper in human cell lines. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC204562/&quot; rel=&quot;nofollow&quot;&gt;It appears different cell lines&lt;/a&gt; have different susceptibilities to thymine-thymine dimers. The majority of DNA mutation in healthy people comes from endogenous sources, not radiation. Recombination during fertilization may also contribute significantly to changes in DNA sequence. &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_repair&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; nicely breaks down some of the different sources of mutation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Manifestations of mutations from endogenous sources is measurable as our bodies become genetically more chimeric with time. Regions of our bodies become deferentially susceptible to disease due in largest part to errors in DNA repair and replication, unrelated to electromagnetic insult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Damage due to UV radiation, like the creation of a thymine-thymine dimer, can be repaired readily by base excision and replacement. While DNA is dividing, it is cut many times to allow the molecule to unwind. Single strand breaks resulting from DNA damage have robust mechanisms for repair. For example, when a thymine-thymine dimer is excised or single strand break is otherwise introduced, enzymatic recognition makes identification of a template for repair possible. It is also very unlikely in a single strand break that another break will occur in the same location, decreasing the mutation effect of UV. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Double strand breaks and errors in DNA replication are intrinsically more permanent as a substituted base is chemically indistinguishable from any other of the same type. Much of the new genetic information introduced into any mammalian genome comes from endogenous sources, not the environment. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jbc.org/content/279/17/16895&quot; rel=&quot;nofollow&quot;&gt;Error rate of human DNA polymerase&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC307917/&quot; rel=&quot;nofollow&quot;&gt;Deamination is a major contributor to mutation rate&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-09-03T22:37:48.340" LastActivityDate="2014-09-03T22:37:48.340" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20514" PostTypeId="2" ParentId="20443" CreationDate="2014-08-15T08:29:48.143" Score="3" Body="&lt;p&gt;Higher QRS complexes particularly in the lateral leads would suggest hypertrophy of the left ventricle. This in turn would suggest a stronger pressure is in place, although it is not known whether this is because it is required (incompetent valves) or a physiological response to exercise (where the volume is likely to actually be bigger). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, if it really is just displacement of the brain you're interested in, why not use an EEG taken with an ECG and measure if there is a variation with each heartbeat. Then you can tease apart whether this is due to pressure or oxygenation or many other things. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise you could place something overlying the carotid which will loosely, but perhaps more accurately, reflect the pressure and one could potentially calculate the volume this way once enough other factors are known. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-08-15T08:29:48.143" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20515" PostTypeId="2" ParentId="20499" CreationDate="2014-08-15T08:34:15.393" Score="9" Body="&lt;p&gt;They are vital if not incredibly useful in many other mammals but not humans. People have tried to look for a role and seen that they activate in times of stress or anxiety. However this probably only serves to heighten both stress and anxiety as you now also don't smell that great either. There is no identifiable role in humans apart from causing a variety of disorders such as an abcess.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When physically examining a patient with a very painful condition, doing something that greatly provokes symptoms will often cause the anal glands to secrete. As a doctor, I interpret it as a clear warning that the patient is in distress, and that I need to exercise greater caution. I don't know of any science supporting this, but the function seems self-evident. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="57189" LastEditDate="2020-03-10T13:27:31.743" LastActivityDate="2020-03-10T13:27:31.743" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="20516" PostTypeId="2" ParentId="20449" CreationDate="2014-08-15T08:40:18.637" Score="1" Body="&lt;p&gt;Muscle memory specifically in the effects of hypertrophy. There is also muscle memory for skills which shares some factors but mostly differs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When muscle hypertrophies or &quot;gets bigger&quot; extra nuclei are recruited to make more sarcomeres or proteins involved in muscle action. Once these nuclei have been recruited and essentially activated once, they're much more easily activated again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Above is an answer based on my knowledge, but you can wait for Atl LED if you need references. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-08-15T08:40:18.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20517" PostTypeId="2" ParentId="20486" CreationDate="2014-08-15T08:49:06.090" Score="11" Body="&lt;p&gt;As Chris said it's a matter of a low concentration for a small amount of time. Most people clean up their vomit rather than leave it to sit. Most people who vomit also have recently eaten something which triggers the reflex but also dilutes the acid or may neutralise it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To further add to Chris' answer. Even heartburn or gastro-oesophageal reflux disease, is particularly corrosive. Damaging cells that line the oesophagus, it causes changes in the cells that make them pre-cancerous (Barret's oesophagus) and can lead to full blown cancer (carcinoma). This is because the cells change type to try to protect themselves. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even in the stomach a thick layer of mucus is required to prevent the stomach from eating itself. This is not only to protect the lining against its own acid, but the enzymes which are made are seriously dangerous and will digest our body if able, only work in acidic environments. To understand how dangerous they are, when the pancreas which makes these enzymes is blocked releasing these enzymes it can digest nearby structures such as major blood vessels and cause seriously dangerous bleeding. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-08-15T08:49:06.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20518" PostTypeId="1" AcceptedAnswerId="20530" CreationDate="2014-08-15T09:35:38.050" Score="5" ViewCount="426" Body="&lt;p&gt;I live in the Netherlands, and I am looking for an identification key for mushrooms. &#xA;Are there any keys you could share?&lt;/p&gt;&#xA;" OwnerUserId="8729" LastEditorUserId="3952" LastEditDate="2014-08-16T18:23:15.873" LastActivityDate="2014-08-16T18:23:15.873" Title="What is a good identification key for European mushrooms?" Tags="&lt;mycology&gt;&lt;literature&gt;&lt;mushroom&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20520" PostTypeId="1" CreationDate="2014-08-15T12:01:10.203" Score="5" ViewCount="323" Body="&lt;p&gt;Reading the following paragraph:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After staring at the red and blue shamrock, you saw a green and&#xA;  yellow afterimage. Opponent-process theory proposes that as you stared&#xA;  at the red and blue shamrock, you were using the red and blue portions&#xA;  of the opponent-process cells. After a period of 60 to 90 seconds of&#xA;  continuous staring, you expended these cells' capacity to fire action&#xA;  potentials. In a sense, you temporarily &quot;wore out&quot; the red and blue&#xA;  portions of these cells. Then you looked at a blank sheet of white&#xA;  paper. Under normal conditions, the while light would excite all of&#xA;  the opponent-process cells. Recall that white light contains all&#xA;  colors of light. But, given the exhausted state of your&#xA;  opponent-process cells, only parts of them were capable of firing&#xA;  action potentials. In this example, the green and yellow parts of the&#xA;  cells were ready to fire. The light reflected off of the white paper&#xA;  could excite only the yellow and green parts of the cells, so you saw&#xA;  a green and yellow shamrock. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(Ellen Pastorino &amp;amp; Susann Doyle-Portillo, What Is Psychology? Essentials, 2010)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I've been wondering:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can the negative afterimage appear only if there is light or is it possible in darkness? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words does the red color make the ganglion continue working even when there is no image and the afterimage appears green or is more light required in order for the afterimage to appear? &lt;/p&gt;&#xA;" OwnerUserId="8399" LastActivityDate="2014-10-24T13:12:49.327" Title="Can the negative afterimage appear only if there is light or is it possible in darkness?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;eyes&gt;&lt;vision&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20521" PostTypeId="1" AcceptedAnswerId="20535" CreationDate="2014-08-15T14:34:18.563" Score="4" ViewCount="1014" Body="&lt;p&gt;I want to know more about positive feedback in gene regulation and to know the similarity and differences between positive and negative feedbacks.&lt;/p&gt;&#xA;" OwnerUserId="8774" LastEditorUserId="3340" LastEditDate="2014-12-20T07:38:04.133" LastActivityDate="2014-12-20T07:38:04.133" Title="positive and negative feedback" Tags="&lt;cell-biology&gt;&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20522" PostTypeId="2" ParentId="20521" CreationDate="2014-08-15T15:19:54.160" Score="5" Body="&lt;p&gt;A feedback loop is a network structure in which the gene is able to regulate itself via a single path.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$A\rightarrow B\rightarrow C\rightarrow A$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interactions can be called positive or negative depending on their effect on the downstream gene. If a gene &lt;strong&gt;A&lt;/strong&gt; represses another gene &lt;strong&gt;B&lt;/strong&gt;, then it is a negative interaction; when it activates then the interaction is positive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you multiply the signs of all the interactions in the path from gene-&lt;strong&gt;A&lt;/strong&gt; back to itself you will get the sign of the loop. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So a positive FBL will result (in the above example) if :&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;A&lt;/strong&gt; activates (+) &lt;strong&gt;B&lt;/strong&gt;; &lt;strong&gt;B&lt;/strong&gt; activates (+) &lt;strong&gt;C&lt;/strong&gt;; &lt;strong&gt;C&lt;/strong&gt; activates (+) &lt;strong&gt;A&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;A&lt;/strong&gt; represses (-) &lt;strong&gt;B&lt;/strong&gt;; &lt;strong&gt;B&lt;/strong&gt; activates (+) &lt;strong&gt;C&lt;/strong&gt;; &lt;strong&gt;C&lt;/strong&gt; represses (-) &lt;strong&gt;A&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;A&lt;/strong&gt; activates (+) &lt;strong&gt;B&lt;/strong&gt;; &lt;strong&gt;B&lt;/strong&gt; represses (-) &lt;strong&gt;C&lt;/strong&gt;; &lt;strong&gt;C&lt;/strong&gt; represses (-) &lt;strong&gt;A&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;A&lt;/strong&gt; represses (-) &lt;strong&gt;B&lt;/strong&gt;; &lt;strong&gt;B&lt;/strong&gt; represses (-) &lt;strong&gt;C&lt;/strong&gt;; &lt;strong&gt;C&lt;/strong&gt; activates (+) &lt;strong&gt;A&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Any other combination of interaction will result in a negative feedback loop.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Differences are based on their properties. I'll mention two main unique properties of each.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;PFBL&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Switching circuits&lt;/li&gt;&#xA;&lt;li&gt;Hysteresis&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;NFBL&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Expression control (feedback control)&lt;/li&gt;&#xA;&lt;li&gt;Oscillations&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Similarity: well, nothing more that they both are called feedback loops and the topology is similar (just the nature of interaction is different).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-08-15T15:19:54.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20523" PostTypeId="1" CreationDate="2014-08-15T15:51:56.260" Score="7" ViewCount="208" Body="&lt;p&gt;Substances found in blood are present at microscopic scale and tend to be invisible to the unaided eye. Why is a whole vial of blood (at ml scale) is required to assess the presence and concentration of substances, given that the modern equipments and testing is becoming more and more sensitive and efficient?&lt;/p&gt;&#xA;" OwnerUserId="6035" LastEditorUserId="6511" LastEditDate="2014-08-15T16:27:40.730" LastActivityDate="2016-09-04T05:14:56.517" Title="Why ml scale blood retrieval is required to run a blood test?" Tags="&lt;human-biology&gt;&lt;hematology&gt;&lt;medicine&gt;" AnswerCount="3" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="20524" PostTypeId="2" ParentId="20506" CreationDate="2014-08-15T16:23:11.960" Score="1" Body="&lt;p&gt;No. Some structures in the body are ever present from birth to death. The first things which come to mind are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10416756&quot; rel=&quot;nofollow&quot;&gt;nerves&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Cornea&quot; rel=&quot;nofollow&quot;&gt;the eyes&lt;/a&gt;, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hair_cell&quot; rel=&quot;nofollow&quot;&gt;auditory hairs&lt;/a&gt; in the ears and the list goes on.....&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2014-08-15T23:16:40.080" LastActivityDate="2014-08-15T23:16:40.080" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="20525" PostTypeId="1" CreationDate="2014-08-15T16:39:15.320" Score="22" ViewCount="2828" Body="&lt;p&gt;I understand that high fructose corn syrup was found to have detrimental effects on peoples' health. Why is this so?&lt;/p&gt;&#xA;" OwnerUserId="8644" LastActivityDate="2015-04-29T00:51:24.200" Title="Why is high fructose corn syrup unhealthy?" Tags="&lt;physiology&gt;&lt;health&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20526" PostTypeId="2" ParentId="20525" CreationDate="2014-08-15T16:56:37.423" Score="21" Body="&lt;p&gt;Besides a lot of propaganda there is not much evidence that high fructose corn syrup (HFCS) is more dangerous than normal sugar. Lets have a look at the sugar in detail:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HFCS is produced from corn and is originally a glucose syrup. Since fructose is obviously much sweeter, the glucose is converted enzymatically into fructose (see &lt;a href=&quot;http://en.wikipedia.org/wiki/High_fructose_corn_syrup#Production&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for more details). Before the use in food production additional glucose is added to the syrup so that typical syrups contain 55% fructose and 42% glucose or 42% fructose and 53% glucose (the remaining % are water).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at saccharose (which is our ordinary sugar) then this is a disaccherid which is build from one molecule of glucose and one molecule of fructose. The enzyme &lt;a href=&quot;http://en.wikipedia.org/wiki/Sucrase&quot; rel=&quot;nofollow&quot;&gt;sucrase&lt;/a&gt; breaks this molecule up into one molecule of fructose and glucose each, so reaching a 50%:50% ratio between the sugars. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the ratios are more or less the same, it doesn't matter for the human body, where the sugar come from meaning that in this &lt;a href=&quot;http://en.wikipedia.org/wiki/High_fructose_corn_syrup#Health&quot; rel=&quot;nofollow&quot;&gt;context&lt;/a&gt; it is more too much sugar in the food than a problem with HFCS, as also this study suggests: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19064536&quot; rel=&quot;nofollow&quot;&gt;Straight talk about high-fructose corn syrup: what it is and what it&#xA;ain't.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Fructose itself is not without problems as this induces the production of fats in the liver, but again, it doesn't matter for the body, where this fructose comes from:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21067942&quot; rel=&quot;nofollow&quot;&gt;Fructose induced lipogenesis: from sugar to fat to insulin&#xA;resistance.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For further reading I can also recommend this article on Gizmodo: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://gizmodo.com/5891353/is-high-fructose-corn-syrup-really-bad-for-you&quot; rel=&quot;nofollow&quot;&gt;Is High Fructose Corn Syrup Really Bad for You?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-01-30T07:58:04.870" LastActivityDate="2015-01-30T07:58:04.870" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="20527" PostTypeId="2" ParentId="20523" CreationDate="2014-08-15T17:02:04.390" Score="10" Body="&lt;p&gt;It might be better to consider the sampling technology, economic and logistical issues with this question as well as the tech behind the tests. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, some tests still will want a few milliliters of blood - e.g. cell counts for specific cell types.  Then there is the need to create and stock many different kinds of sample collection devices and train the collection centers to use them effectively- the industry won't be wanting to completely retool whenever the volume requirement for the assays changes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mainly, since the expense of collecting and shipping a few milliliters of blood is pretty much identical to doing so with a few microliters of blood, what has happened is that the tubes are used to do multiple assays with excess included in case an assay has to be redone. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably all this blood currently collected is not necessary at all.   I expect that the cost of changing all the blood collection systems and protocols is not worth the cost of collecting the exact minimum amount of blood needed.  The benefit to the patient or the lab between collecting 3-5 ml of blood and collecting 50 microliters of blood to be shipped off for lab analysis is probably close to zero.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having more blood than you need does not hurt the lab either should they need to repeat the assay or when you need to use the sample for more than one different test. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-08-15T22:19:29.863" LastActivityDate="2014-08-15T22:19:29.863" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="20529" PostTypeId="2" ParentId="20467" CreationDate="2014-08-15T19:02:18.077" Score="1" Body="&lt;p&gt;I remember something from the anatomy lecture saying that one nostril picks up one, the other other kinds of molecules depending of the molecule's size and other attributes.&#xA;Meaning speed is important: if you breathe in through the nose right now, you'll probably feel the air coming in faster from one side than the other.&#xA;And still if i remember correctly this blocking of one side is achieved by blood vessels getting bigger.&#xA;The choice which one of the airways is blocked more comes from daily rhythms similar to sleep cycles.&lt;/p&gt;&#xA;" OwnerUserId="8779" LastActivityDate="2014-08-15T19:02:18.077" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20530" PostTypeId="2" ParentId="20518" CreationDate="2014-08-15T20:41:56.893" Score="5" Body="&lt;p&gt;There are various types of Mushroom identification Sites. you can take help from:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.mushroomexpert.com/major_groups.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mushroomexpert&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.rogersmushrooms.com/gallery/chooser.asp&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rogersmushrooms&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.mycokey.com/newMycoKeySite/MycoKeyIdentQuick.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;MycoKey 4.0&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rv4JJ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: MycoKey 4.0&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2014-08-15T20:41:56.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20531" PostTypeId="2" ParentId="20437" CreationDate="2014-08-15T20:48:13.007" Score="2" Body="&lt;p&gt;Your best chance of actually reaching an answer &lt;strong&gt;for yourself&lt;/strong&gt; (*) to this is by parallel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you consider independetly-living single-celled organisms alive? This includes bacteria, amoeba, bacteria, some parasites such as plasmodium (the malaria germ), and more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sperms are not quite independently-living single-celled organisms. They have many things in common with the ones mentioned above: they move, metabolise, communicate and sense, and most importantly they can cease to do all those things, i.e. they do what we commonly call, &quot;die&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main difference is, they don't reproduce themselves, they are the reproduction vessel for a larger organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is absolutely no objective way to decide whether that difference is sufficient to decide that all those single-celled creatures are alive and sperms aren't, it's a question of definition. You might even decide that you don't consider bacteria or anything that exists commonly as single cells &quot;alive&quot;, and thus this whole approach is pointless. In any case, it's not a biological question and thus should be discussed somewhere else.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(*) For yourself because there is no false or correct answer as long as nobody can get more than two people to agree on a definition of life.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2014-08-15T20:48:13.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20532" PostTypeId="2" ParentId="20525" CreationDate="2014-08-15T21:37:32.883" Score="11" Body="&lt;p&gt;The following study abstract of &lt;strong&gt;&quot;Consumption of high-fructose corn syrup in beverages may play a role in the epidemic of obesity&quot;&lt;/strong&gt; copied from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15051594&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/15051594&lt;/a&gt; seems to address your question.  I added a paragraph break; the second paragraph seems most relevant to me:&lt;p&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Obesity is a major epidemic, but its causes are still unclear. In this&#xA;  article, we investigate the relation between the intake of&#xA;  high-fructose corn syrup (HFCS) and the development of obesity. We&#xA;  analyzed food consumption patterns by using US Department of&#xA;  Agriculture food consumption tables from 1967 to 2000. The consumption&#xA;  of HFCS increased &gt; 1000% between 1970 and 1990, far exceeding the&#xA;  changes in intake of any other food or food group. HFCS now represents&#xA;   40% of caloric sweeteners added to foods and beverages and is the sole caloric sweetener in soft drinks in the United States. Our most&#xA;  conservative estimate of the consumption of HFCS indicates a daily&#xA;  average of 132 kcal for all Americans aged &gt; or = 2 y, and the top 20%&#xA;  of consumers of caloric sweeteners ingest 316 kcal from HFCS/d. &lt;p&gt;&#xA;  The increased use of HFCS in the United States mirrors the rapid&#xA;  increase in obesity. The digestion, absorption, and metabolism of&#xA;  fructose differ from those of glucose. Hepatic metabolism of fructose&#xA;  favors de novo lipogenesis. In addition, unlike glucose, fructose does&#xA;  not stimulate insulin secretion or enhance leptin production. Because&#xA;  insulin and leptin act as key afferent signals in the regulation of&#xA;  food intake and body weight, this suggests that dietary fructose may&#xA;  contribute to increased energy intake and weight gain. Furthermore,&#xA;  calorically sweetened beverages may enhance caloric overconsumption.&#xA;  Thus, the increase in consumption of HFCS has a temporal relation to&#xA;  the epidemic of obesity, and the overconsumption of HFCS in&#xA;  calorically sweetened beverages may play a role in the epidemic of&#xA;  obesity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8781" LastEditorUserId="5144" LastEditDate="2014-08-15T21:55:47.217" LastActivityDate="2014-08-15T21:55:47.217" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="20533" PostTypeId="2" ParentId="20378" CreationDate="2014-08-15T23:01:17.903" Score="5" Body="&lt;p&gt;Pathogen identification procedure is not necessarily standardised due to differences in resources available to each country but there are certainly several characterised and accepted approaches used to identify a disease causing pathogen. The predominant techniques used to identify pathogens relies upon conventional clinical microbiology-based approaches, which has been highlighted in the comments above. However these conventional techniques such as standard culture and susceptibility tests have many drawbacks such as time-consuption and lack of scalability in addition to lack of direct characterisation of virulence factors. Most pathogen (except prions) logically carry a unique DNA or RNA signatures that differentiate it from other organisms, which provides the basis for disease causing pathogen characterisation. According to this &lt;a href=&quot;http://www.premierbiosoft.com/tech_notes/pathogen-detection.html&quot;&gt;page&lt;/a&gt; there are two approaches used to detect a pathogen, once sampling has taken place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) qPCR based pathogen detection: allowing sensitive and real-time detection of genetic signatures, which is not currently matched by sensors such as immune-assay techniques (lagging in detection time, logistics and costing) and optical techniques (lacking specificity).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Microarray based pathogen detection: allowing combination of nucleic acid amplification (offered by PCR based techniques) combined with massive screening capability of microarray technology, resulting in high level of sensitivity, specificity, and throughput.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These techniques are obviously combined with powerful software technologies required to sieve through the data and allow for easing of experimental burden, minimising assay development as well as operational costs. Now clearly these techniques including sensors and conventional microbiology are used concurrently/synergistically to more efficiently identify a disease causing pathogen and strategies a treatment/preventative measure. This &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359816/&quot;&gt;review&lt;/a&gt; nicely illustrates the molecular basis for pathogen identification and discusses general considerations (in this case for fungus detection) such as DNA extraction methods, sampling preparations and strategies and goes on to highlight some other sequencing independent methods such as FISH and macroarray. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.nphl.org/documents/identificationofmicrobialpathogensusingnucleicacidsequencing.pdf&quot;&gt;paper&lt;/a&gt; writes about sequencing based strategies and using the BLAST (NCBI) tool and talks about identification of variant strains of known species, identification of non-cultivatable pathogens and more importantly related to this question, identification of new species using (rDNA) phylogenetic trees of bacterial 16S gene and the fungal 18S gene, commonly used for this type of analysis. This is done in order to determine the phylogenetic position of a the suspected new species compared to a closely known related species, which is useful when there is a &amp;lt;98% of the sequence similarity with known species. &lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-08-15T23:01:17.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20534" PostTypeId="1" CreationDate="2014-08-16T00:51:52.460" Score="1" ViewCount="356" Body="&lt;p&gt;I'm going to take a picture of a bacteria but I am unsure how large it is. What are the dimensions in angstrom of bacteria?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="3340" LastEditDate="2014-08-16T07:36:59.820" LastActivityDate="2014-08-16T07:36:59.820" Title="What are the dimensions in angstrom of bacteria?" Tags="&lt;bacteriology&gt;&lt;microscopy&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2014-08-17T06:42:07.627" ContentLicense="CC BY-SA 3.0" />
  <row Id="20535" PostTypeId="2" ParentId="20521" CreationDate="2014-08-16T01:35:21.770" Score="3" Body="&lt;p&gt;Positive and negative feedback are essential motifs that control transcriptional activity of genes. They may involve other genes, mRNA and/or proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A classical pattern of negative feedback is where transcription of a gene results in mRNA and translation of this mRNA in a protein that represses the expression of the gene again. Feedback loops may involve much larger structures, e.g. if a gene codes for a hormone that stimulates the release of another hormone in a remote organ and if that other hormone represses the expression of the first gene again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, negative feedback results in stable levels of certain products. Positive feedback leads to infinite growth (if not limited by a surrounding negative feedback loop or simply by lack of substrate).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is easy to identify positive and negative feedback by counting the positive and negative correlations within the loop. Feedback loops are defined as positive or regenerative loops if there is at least one positive correlator and the number of negative correlators is even. If the number of negative correlators is odd than the loop is negative or degenerative.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://biomedicalcybernetics.wikia.com/wiki/Feedback&quot; rel=&quot;nofollow&quot;&gt;http://biomedicalcybernetics.wikia.com/wiki/Feedback&lt;/a&gt; for a more detailed explanation.&lt;/p&gt;&#xA;" OwnerUserId="3865" LastActivityDate="2014-08-16T01:35:21.770" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20536" PostTypeId="2" ParentId="20534" CreationDate="2014-08-16T01:59:38.867" Score="4" Body="&lt;p&gt;According to Wikipedia: 3 um long with a diameter of 0.5 um. That equates to a length of 30 000 A and a diameter of 5 000 A. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.m.wikipedia.org/wiki/Helicobacter_pylori&quot; rel=&quot;nofollow&quot;&gt;http://en.m.wikipedia.org/wiki/Helicobacter_pylori&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-08-16T01:59:38.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20537" PostTypeId="1" CreationDate="2014-08-16T07:17:46.930" Score="12" ViewCount="23957" Body="&lt;p&gt;In transcription, there is no need for any primer. I guess the basic mechanism of DNA polymerase &amp;amp; RNA polymerase is the same. So why does replication have the need for a primer?&lt;/p&gt;&#xA;" OwnerUserId="8784" LastEditorUserId="806" LastEditDate="2014-08-19T17:51:47.940" LastActivityDate="2018-11-21T18:56:25.440" Title="Why does replication require primers while transcription does not?" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20538" PostTypeId="1" AcceptedAnswerId="20540" CreationDate="2014-08-16T09:20:13.053" Score="4" ViewCount="142" Body="&lt;p&gt;Let's suppose that I take a DrugA for ProblemA and then I got this ProblemB and started to take DrugB. Are there general rules I can look up to figure out whether I can take DrugA &amp;amp; DrugB simultaneously?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I mean drugs can cancel each other or vice versa increase effects of each other (in an extreme extend); or one of drugs has adverse effects that are bad for the other drug.&lt;/p&gt;&#xA;" OwnerUserId="3793" LastEditorUserId="3793" LastEditDate="2014-08-16T09:32:11.500" LastActivityDate="2020-06-04T09:42:01.300" Title="Compatibility drugs info" Tags="&lt;pharmacology&gt;" AnswerCount="2" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="20539" PostTypeId="2" ParentId="20537" CreationDate="2014-08-16T10:10:10.830" Score="6" Body="&lt;p&gt;I'm no expert at transcription but from what I can figure out &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21125481&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.lifetechnologies.com/uk/en/home/references/ambion-tech-support/probe-labeling-systems/general-articles/the-basics-in-vitro-transcription.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; transcription requires a promoter region acting as a template-directed mechanism for allowing transcription, which presumably bear a certain sequence recognised by the RNA polymerase and associated complexes. However DNA polymerase requires primers to guide it to the correct location on DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: In light of comments below, according to &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022283607003968&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_polymerase&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;, RNA polymerase is capable of &lt;em&gt;de novo&lt;/em&gt; synthesis meaning it is capable of initiating synthesis of RNA without primers and this is done by RNA polymerase binding to two nucleotides rather than nascent RNA polymer and a single nucleotide. Initiating nucleotide hold RNA polymerase rigidly in place, facilitating chemical attack on the incoming nucleotide. For bacteriophage T7 RNA polymerase, transcription begins with a marked preference for GTP at the + 1 and + 2 positions. DNA polymerase cannot add primers, and therefore, needs primase to add the primer &lt;em&gt;de novo&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-16T11:24:45.857" LastActivityDate="2014-08-16T11:24:45.857" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="20540" PostTypeId="2" ParentId="20538" CreationDate="2014-08-16T11:42:18.770" Score="4" Body="&lt;p&gt;I would like to start by suggesting you talk to whoever prescribed you the drug or your pharmacist. They should be most up to date with interactions and there are some interactions which may only affect you more seriously because of your medical history or current conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are some sites that you can check drug interactions in order of popularity: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://reference.medscape.com/drug-interactionchecker&quot; rel=&quot;nofollow&quot;&gt;Medscape&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.drugs.com/drug_interactions.php&quot; rel=&quot;nofollow&quot;&gt;Drugs.com&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.healthline.com/druginteractions&quot; rel=&quot;nofollow&quot;&gt;Healthline&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.webmd.com/interaction-checker/&quot; rel=&quot;nofollow&quot;&gt;WebMD&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.rxlist.com/drug-interaction-checker.htm&quot; rel=&quot;nofollow&quot;&gt;RxList&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-08-16T11:42:18.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20541" PostTypeId="1" AcceptedAnswerId="20636" CreationDate="2014-08-16T11:57:06.270" Score="9" ViewCount="9337" Body="&lt;p&gt;Fat people have a large amount of calories (energy) stored, but I have noticed all time when they do physical activities they get tired fast in comparison to fit people - why does this happen?  &lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="107" LastEditDate="2015-12-24T23:58:19.540" LastActivityDate="2015-12-24T23:58:19.540" Title="Why do obese people tire quickly?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20543" PostTypeId="1" CreationDate="2014-08-16T13:04:49.353" Score="14" ViewCount="695" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QY191.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone identify this bird: it looks like a zebra finch but they are not native to UK  are they? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photo taken from my garden in Shoreham, West Sussex on 16/8/2014.&lt;/p&gt;&#xA;" OwnerUserId="8788" LastEditorUserId="1320" LastEditDate="2014-08-19T07:56:34.070" LastActivityDate="2015-08-11T22:19:11.207" Title="Can anyone identify this bird?" Tags="&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20544" PostTypeId="2" ParentId="20541" CreationDate="2014-08-16T13:20:19.873" Score="2" Body="&lt;p&gt;Fat people have a large amount of body cells which need a large supply of oxygen from the blood.Heart beats at some constant rate and it has some upper limit to which it can supply blood. In fat people the same sized heart and same volume of blood needs to be circulated throughout the body and this becomes difficult during exercise or rather cells of the body of a fat person suffers from hypoxia faster than that of a thin person. thus he experiences fatigue faster.&lt;/p&gt;&#xA;" OwnerUserId="8789" LastActivityDate="2014-08-16T13:20:19.873" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20545" PostTypeId="2" ParentId="20543" CreationDate="2014-08-16T13:21:54.470" Score="17" Body="&lt;p&gt;This looks pretty much like a female zebra finch to me (the male have a more prominent feather pattern). See this picture:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cyqiu.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These birds are not native in Europe, this is correct. But it is always possible that birds escape captivity (or are released) and the live in countries where they originally not belong. I think this is the case with the zebra finch here. Since the birds are able to live in a pretty broad range of habitats, they can also survive in England.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to this &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_non-native_birds_of_Great_Britain&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt; page (thanks to @Orethrephes) zebra finches which escaped from captivity are quite common in Britain although they usually not survive for long.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-08-16T22:11:16.710" LastActivityDate="2014-08-16T22:11:16.710" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20546" PostTypeId="1" CreationDate="2014-08-16T15:21:25.120" Score="3" ViewCount="765" Body="&lt;p&gt;The brain purportedly produces very weak EM waves. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EEG is a method of measuring electrical brain activity, it has classifications for the types of brain wave it can detect: Theta, Alpha, Beta, Gamma etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these the weak EM waves the brain produces?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not what is the frequency range of the EM waves that the brain produces and does it vary depending on mental state?&lt;/p&gt;&#xA;" OwnerUserId="8790" LastActivityDate="2014-08-17T19:32:29.473" Title="EM Brainwaves VS Brain Wave (EEG)" Tags="&lt;brain&gt;&lt;neurology&gt;&lt;electroencephalography&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ClosedDate="2014-08-18T16:29:24.073" ContentLicense="CC BY-SA 3.0" />
  <row Id="20547" PostTypeId="2" ParentId="20538" CreationDate="2014-08-16T17:54:46.573" Score="1" Body="&lt;p&gt;Drugs.com provides good lists of side effects when combining drugs. Just type (drug) interactions into Google and it should come up. Then you can click on a given drug and see how dangerous the two are together/what they can cause. Of course, your doctor is always the best resource.&lt;/p&gt;&#xA;" OwnerUserId="8762" LastActivityDate="2014-08-16T17:54:46.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20549" PostTypeId="2" ParentId="20546" CreationDate="2014-08-16T20:23:43.073" Score="4" Body="&lt;p&gt;I assume with EM you refer to electromagnetic?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are right that the EEG (electroencephalogram) is a tiny signal. When about 50.000 neurons fire simultaneously, it possible to see a change in the measured signal. Typical EEG amplitudes are in the microvolt range.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, when the EEG is recorded, it is a function of time. You could for example collect data from 64 sensors, using a typical sampling frequency of 1000 Hz, and obtain 100000 samples from each sensor during a 100 second measurement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what are alpha, beta, gamma, etc? When the recorded EEG signals are transformed into the frequency-domain (using the discrete Fourier transform), the signals become represented as a function of frequency. The obtained frequency range is half of the sampling frequency (according to the sampling theorem). So, with $f_s = 1 $ kHz you may observe frequencies from $0$ to $500$ Hz. Now, to make it easier to discuss about specific parts of the frequency range, they have been given names: delta refers to frequencies from 0-4 Hz, alpha to frequencies 7-15 Hz etc. So, these are just arbitrary names for different frequency ranges. (And yes, some processes do occur in quite exact ranges.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what effects what the EEG spectra will look like? Just about everything. From a short segment of data, it is rather impossible to say anything. This is why many paradigms do averaging: for example, you are presented a sound 100 times, and the repetitions are averaged to cancel uncorrelated noise. Have a look at the so called oddball paradigm, for example. Single-trial and continuous recording are also done today, but they are more difficult to analyse.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Side note: since you asked about electromagnetic brain waves, have a look at magnetoencephalography too..)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For reference, see e.g. Luck (2005), An Introduction to the Event-related Potential Technique. Fourier transforms, sampling theorem, and signal averaging are well covered in Wikipedia.&lt;/p&gt;&#xA;" OwnerUserId="8787" LastEditorUserId="8787" LastEditDate="2014-08-16T21:03:01.317" LastActivityDate="2014-08-16T21:03:01.317" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20550" PostTypeId="2" ParentId="14148" CreationDate="2014-08-16T20:33:21.223" Score="4" Body="&lt;p&gt;The use of spikes is a mixture of their computational advantages and the limitations of the biological substrate in which they are implemented:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;They can travel long distances at high speeds because they can profit from the saltatory conduction which is much faster than diffusion and it can be maintained over long distances. A digital signal is less prone to noise which is also a reason why our computers operate digitally.&lt;/li&gt;&#xA;&lt;li&gt;Spikes can be modulated using chemical synapses which are a) directional b) can amplify the signal c) can modulate the signal d) can even inhibit the signal. Analog voltages have to be transmitted through electrical junctions that do not allow modulation.&lt;/li&gt;&#xA;&lt;li&gt;Frequency coding (signal lies in interspike interval) has a wider dynamic range than voltage coding. &lt;/li&gt;&#xA;&lt;li&gt;The spike generation can serve as non-linearity in the transfer function&lt;/li&gt;&#xA;&lt;li&gt;The spike can be used to code temporal signals more efficiently by reducing the redundancy (only signal change).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Btw. do not expect too much from the human brain project - it is a lot of talk and no results.&lt;/p&gt;&#xA;" OwnerUserId="8791" LastActivityDate="2014-08-16T20:33:21.223" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20551" PostTypeId="2" ParentId="20443" CreationDate="2014-08-16T20:41:32.343" Score="3" Body="&lt;p&gt;It is unclear from your question what exactly &quot;beat-to-beat variability&quot; means from a physiological perspective. It would help if you could provide more information on the application you are working on and what kind of sensors you have access to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you wanted to measure the force of the &lt;em&gt;arterial pulse&lt;/em&gt;, you would need to measure &lt;a href=&quot;http://en.wikipedia.org/wiki/Pulse_pressure&quot; rel=&quot;nofollow&quot;&gt;pulse pressure&lt;/a&gt; (which is the systolic blood pressure minus the diastolic blood pressure). However, these pressures do not only depend on the heart's action, but also on blood vessel compliance - which is influenced by ageaing, disease processes, and changes in the concentration of vasoactive substances in the blood. The EKG signal does not provide any of these latter parameters, and therefore it is highly unlikely that you would be able to estimate pulse pressure from an EKG. That being said, you could very easily measure pulse pressure with an arterial line, which would be the gold standard for such a task.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you wanted to measure the force of the &lt;em&gt;heartbeat&lt;/em&gt;, you could look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Ejection_fraction&quot; rel=&quot;nofollow&quot;&gt;ejection fraction&lt;/a&gt;, which is a measure of how much blood is ejected from the ventricle in one heartbeat. Again, this is not related purely to the electrical activity of the heart (contractility and heart rate), but also to extra-cardiac parameters (preload and afterload). The EKG, which only looks at the intrinsic electrical activity of the heart, does not provide information on these extra-cardiac factors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could settle and look purely at cardiac contractility, which measures how much force the heart generates during a heartbeat. Keep in mind that this does not reflect how &quot;well&quot; the heart is working - you could have very good contractility, but a poor ejection fraction for other reasons. This is also not necessarily related to how &quot;strongly&quot; a person will feel his/her heart beating. I'm aware of&#xA; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19616109&quot; rel=&quot;nofollow&quot;&gt;one paper&lt;/a&gt; on how to measure cardiac contractility from EKG tracings. &lt;/p&gt;&#xA;" OwnerUserId="8739" LastActivityDate="2014-08-16T20:41:32.343" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20552" PostTypeId="1" CreationDate="2014-08-16T21:25:13.990" Score="3" ViewCount="36" Body="&lt;p&gt;I've just received heterozygote C57BL mice from COMP and I need to start back-crossing them. I've read many colony management protocols, but couldn't understand if I need to use the same WT mouse for all ~10 generations of back-crossing or use a new one for each generation.&#xA;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="8793" LastEditorUserId="1320" LastEditDate="2014-08-19T07:51:42.250" LastActivityDate="2014-08-19T07:51:42.250" Title="Do I need to use the same WT C57BL individual for back-crossing or can I use a new one for each generation?" Tags="&lt;mice&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20553" PostTypeId="1" AcceptedAnswerId="20557" CreationDate="2014-08-16T21:42:04.980" Score="10" ViewCount="661" Body="&lt;p&gt;&lt;a href=&quot;https://imgur.com/36t0Nnd&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.imgur.com/36t0Nnd.jpg&quot; title=&quot;Hosted by imgur.com&quot; /&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was soft and covered in flies. My guess is fungi.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Location: South Florida. &lt;/p&gt;&#xA;" OwnerUserId="8139" LastEditorUserId="16866" LastEditDate="2016-03-21T06:32:10.387" LastActivityDate="2016-04-23T19:48:12.410" Title="Is this a plant or a fungus?" Tags="&lt;species-identification&gt;&lt;mycology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20554" PostTypeId="1" CreationDate="2014-08-16T21:42:30.997" Score="2" ViewCount="174" Body="&lt;p&gt;I am working on pectinase enzyme assay. I incubated 900 ul of substrate for 10 minutes in the water bath, followed by adding 2ml of DNSA reagent, then 100ul of enzyme extract added finally i read the absorbance @ 540 OD. However the values are high. How can I troubleshoot high enzyme blank values in Pectinase assay ?&lt;/p&gt;&#xA;" OwnerUserId="8794" LastActivityDate="2014-08-18T13:11:39.137" Title="Pectinase Enzyme Assay" Tags="&lt;proteins&gt;&lt;enzymes&gt;&lt;biotechnology&gt;&lt;enzyme-kinetics&gt;&lt;assay-development&gt;" AnswerCount="1" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="20555" PostTypeId="2" ParentId="9152" CreationDate="2014-08-16T22:02:17.733" Score="2" Body="&lt;p&gt;A possible solution is to use the &lt;a href=&quot;http://tools.lifetechnologies.com/content/sfs/manuals/cms_090740.pdf&quot; rel=&quot;nofollow&quot;&gt;DNA &lt;em&gt;ZAP&lt;/em&gt;&lt;/a&gt; solution, which I know many people used in adjacent labs and were happy with for cleaning their DNA free workbench. The product sheet states &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When 500 ng of template DNA is dried down in a PCR tube, it is rendered unamplifiable upon treatment with DNA &lt;em&gt;ZAP&lt;/em&gt; solutions. Additional experiments demonstrate that the DNA is degraded down to free nucleotides.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Please note that I'm not promoting any specific product here and you can purchase any similar product/technology for your particular application. Obviously &lt;strong&gt;the best recommendation is to use new plates for each reaction&lt;/strong&gt; but this/or a similar product can be an option too although the risk of DNA contamination in a PCR based reaction should be carefully balanced against simply using fresh plates considering the product itself is not free either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The product sheet provides instruction for cleaning/treating PCR tubes hence I assume you use the same protocol for plates if you have the plate centrifuges available in your lab. You can get rid of the solutions by tapping the plates on a tissue to get the liquid out of the wells.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-16T23:03:02.817" LastActivityDate="2014-08-16T23:03:02.817" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20556" PostTypeId="2" ParentId="16966" CreationDate="2014-08-17T01:57:06.110" Score="1" Body="&lt;p&gt;This may shed light on why the teenagers response to dopamine changes. &lt;a href=&quot;http://www.reuniting.info/science&quot; rel=&quot;nofollow&quot;&gt;Quote from reuniting website&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There's much still to learn, but it looks like a number of reward&#xA;  circuitry events occur after climax that have the potential to&#xA;  desensitize us for a time. First, androgen receptors decline after&#xA;  ejaculation, and take up to seven days to normalize. (That means the&#xA;  effects of testosterone on the reward circuitry are probably blunted&#xA;  for a while, quite possibly affecting outlook.) In addition, opioids&#xA;  released during copulation hang around for a while, apparently causing&#xA;  lingering declines in oxytocin, which hamper sexual responsiveness. As&#xA;  noted above, there is also likely a drop in responsiveness to a&#xA;  neurochemical vital to our sense of well-being: &lt;strong&gt;dopamine&lt;/strong&gt;. In effect,&#xA;  the brain has changed. &lt;strong&gt;It now requires more stimulation to get the&#xA;  same pleasure response as before, and sometimes no amount of&#xA;  stimulation will truly satisfy—until it recovers.&lt;/strong&gt; Anecdotal evidence&#xA;  suggests that such changes affect both sexes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The author further suggests that orgasm and ejaculation increase prolactin levels for up to 14 days, during which the brain is less responsive to pleasure and requires novel entertainment or partners to produce pleasure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the info on that site, it seems that the &lt;strong&gt;14 day dopamine-affecting cycle following orgasm continues for as long as a person is sexually active&lt;/strong&gt; (with orgasms). With this in mind, it appears that the adult response to dopamine release is the same as teenagers who are sexually active.&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2014-08-17T01:57:06.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20557" PostTypeId="2" ParentId="20553" CreationDate="2014-08-17T04:15:54.367" Score="11" Body="&lt;p&gt;Identified Species: &lt;em&gt;Clathrus ruber&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Scientific classification&lt;/strong&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Kingdom:  Fungi &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Division: Basidiomycota &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Class:    Agaricomycetes &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Order:    Phallales &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Family:   Phallaceae&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Genus:    Clathrus &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Species:  C. ruber&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/4/40/Clathrus_ruber_mature.jpg/800px-Clathrus_ruber_mature.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Clathrus_ruber&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Clathrus_ruber&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.663" LastActivityDate="2014-08-17T04:15:54.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20558" PostTypeId="2" ParentId="19494" CreationDate="2014-08-17T04:41:29.670" Score="2" Body="&lt;p&gt;It can't be confirmed but it sounds like a pelican.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/d/d4/Pelikan_Walvis_Bay.jpg/800px-Pelikan_Walvis_Bay.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.677" LastActivityDate="2014-08-17T04:41:29.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20559" PostTypeId="1" AcceptedAnswerId="20566" CreationDate="2014-08-17T06:09:19.497" Score="2" ViewCount="683" Body="&lt;p&gt;I have read somewhere that the plasma membrane has little cardiolipin but excess cholesterol whereas the inner mitochondrial membrane is rich in cardiolipin and has little cholesterol.I just wanted to know why there is this difference.&lt;/p&gt;&#xA;" OwnerUserId="8301" LastEditorUserId="1320" LastEditDate="2014-08-19T07:53:22.043" LastActivityDate="2014-08-19T14:05:01.673" Title="What is the functional significance of the difference in cardiolipin/cholesterol ratio in different membranes?" Tags="&lt;cell-biology&gt;&lt;cell-membrane&gt;&lt;cell-signaling&gt;&lt;membrane-transport&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20561" PostTypeId="1" AcceptedAnswerId="20565" CreationDate="2014-08-17T07:11:11.863" Score="3" ViewCount="67" Body="&lt;p&gt;I've been puzzled by the following though experiment for the past few days:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to make my own food from scratch, but I do not know where to start from.&#xA;I want to be 100% sure that what I eat will never contains something that can damage my body. For example: If you buy something from the local market you can not be 100% sure that it's safe to eat. (99.9 % maybe... but that's not 100%)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to ask you to tell me, how can I make a food that I can eat, or should I say - live on it, for the rest of my life, that's 100% safe, I can control every aspect of it's creation and has many combinations of taste because I love diversity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your time : )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&#xA;Because I realized my question is very broad and indeed is a little... too much scientific I want to close it. But before I do so, here's what I had in mind:&#xA;I wanted to take some chemical elements, put them in a jar, run some electricity, heat, whatever through it, filter it, do some additional processing and eat it.&#xA; I wanted to know if the stomach can take it, because I was going to eat food that's not hard to digest.&lt;/p&gt;&#xA;" OwnerUserId="8797" LastEditorUserId="8797" LastEditDate="2014-08-21T08:17:44.657" LastActivityDate="2014-08-21T08:17:44.657" Title="What are the minimal chemical requirements for a food which we all can eat?" Tags="&lt;organic-chemistry&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2014-08-18T13:54:49.280" ContentLicense="CC BY-SA 3.0" />
  <row Id="20563" PostTypeId="1" AcceptedAnswerId="20570" CreationDate="2014-08-17T09:23:02.330" Score="1" ViewCount="112" Body="&lt;p&gt;I am a physicist but I have always wanted to understand how my digestion takes place in as much detail as possible. I have no idea about books or reference on the subject of Gastro-intestinal and digestive physiology. Can you help me?&lt;/p&gt;&#xA;" OwnerUserId="1620" LastActivityDate="2014-08-17T22:34:59.303" Title="Gastro-intestinal physiology reference" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;gastroenterology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20564" PostTypeId="2" ParentId="2919" CreationDate="2014-08-17T10:26:57.273" Score="2" Body="&lt;p&gt;Ignoring the actual physiological mechanism(s) for why, consider that from a natural selection point of view, there probably isn't as much incentive for a body to heal itself of a condition that largely affects post-reproduction age individuals. While healing a broken bone would likely allow a young person to further reproduce, healing a heart ailment would have a disproportionately lower chance of doing so.&lt;/p&gt;&#xA;" OwnerUserId="8800" LastActivityDate="2014-08-17T10:26:57.273" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20565" PostTypeId="2" ParentId="20561" CreationDate="2014-08-17T14:21:51.143" Score="1" Body="&lt;p&gt;Considering the three basic biomolecules used by the body are carbohydrates, lipids, and proteins, you would need to consume these three molecules only. Now we can choose three substances.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Glucose, one of the most basic carbohydrates, is needed for ATP production, so that would be a food choice there.&lt;/li&gt;&#xA;&lt;li&gt;Any oil or butter will provide lipids.&lt;/li&gt;&#xA;&lt;li&gt;Protein comes from a variety of sources. Meat is typically though of as the best, but nuts are a pretty good source too.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Since nuts satisfy proteins and lipids, I'd say honey roasted peanuts are the most basic food you could live off of, if you replace pure glucose for the honey.&lt;/p&gt;&#xA;" OwnerUserId="8762" LastActivityDate="2014-08-17T14:21:51.143" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20566" PostTypeId="2" ParentId="20559" CreationDate="2014-08-17T16:57:08.013" Score="4" Body="&lt;p&gt;According to wikipedia, cardiolipin is found in two places, the inner mitochondrial membrane, and bacterial membranes. Given the endosymbiotic origin of mitochondria, it makes sense that they would retain some remnant of their bacterial ancestry. But more importantly, cardiolipin plays a role in the enzymatic functions of mitchondrial membranes. Cardiolipin forms a bicyclic resonance structure that allows it to trap a proton, which helps oxidative phosphorylation.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RJ0hN.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Because this structure also responds to pH and divalent cations, it can change it's conformation and aggregation behavior as cellular conditions change.&lt;/p&gt;&#xA;&lt;p&gt;Cardiolipin also plays a role in holding enzyme complex quaternary structures together. Mitochondrial Complex III requires 1 cardiolipin, Complex IV requires 2 cardiolipin, and Complex V binds 4 cardiolipins.&lt;/p&gt;&#xA;&lt;p&gt;Cardiolipin also plays a role in apoptosis, where it is oxidized and undergoes conformational changes that cause it to move from inner to outer mitochondrial membranes and generate pores that cytochrome C can escape through and trigger apoptosis.&lt;/p&gt;&#xA;&lt;p&gt;Cholesterol can be easily oxidized into oxysterols, which are thought to perform a variety of functions, but are not fully understood. If cholesterol levels in the mitochondria were high, I think it would be oxidized and cause trouble.&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Oxysterol&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Oxysterol&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-08-19T14:05:01.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20567" PostTypeId="2" ParentId="20546" CreationDate="2014-08-17T17:04:38.357" Score="2" Body="&lt;p&gt;It's important to clarify what an EEG machine measures. Electromagnetic waves are photons. An EEG does does not detect radiation. It detects magnetic fields by measuring an electrical current induced in the measuring device by the brain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Electricity is the movement of electrons. Electromagnetic waves are photons of light. Magnetism a force which fills space from energy and matter with electrical charge. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EEG machines detect magnetism induced by action potentials. Magnetism is not a wave. It's a field. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brain waves are an observation that action potentials may fire in a pattern which resembles a wave. There are also neurons which do not fire in wave like patterns. The wave here is an emergent property only. &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-17T19:32:29.473" LastActivityDate="2014-08-17T19:32:29.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20568" PostTypeId="2" ParentId="20525" CreationDate="2014-08-17T21:24:11.550" Score="6" Body="&lt;p&gt;Fructose has a special characteristic that other sugars do not have: &lt;strong&gt;its absorption in the human intestine is not regulated,&lt;/strong&gt; as opposed to glucose, for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The important implication is that all the fructose you consume will end inside your organism, either used immediately or stored as fat. Other sugars will only be partly assimilated, or will require more energy to assimilate. If you take the example of glucose again, a glucose molecule requires active transport (meaning consumes ATP, the most basic fuel of your organism) to transit across the intestinal wall. Fructose is absorbed &lt;em&gt;via&lt;/em&gt; free transport (&lt;em&gt;i.e.&lt;/em&gt; no ATP consumption).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This claim can be verified by opening any human physiology book, and while it is debatable whether fructose itself is deleterious, increasing the sugar amount in an already sugar-saturated environment clearly does not seem a good idea to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I (inf3rno) appended the answer with further details:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sucrose is split by digestive enzymes (sucrase, glycoside hydrolase) in the small intestine into fructose and glucose (1:1 ratio). By the high fructose corn syrup (HFCS hereafter) the fructose - glucose ratio is dependent on the HFCS type according to &lt;a href=&quot;http://en.wikipedia.org/wiki/High_fructose_corn_syrup&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;. For example HFCS90 has 90% fructose, while HFCS42 has only 42% fructose (the rest is glucose).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glucose is mainly transported by &lt;a href=&quot;http://en.wikipedia.org/wiki/Sodium-glucose_transport_proteins&quot; rel=&quot;nofollow&quot;&gt;SGLT1 (active transport, which involves ATP)&lt;/a&gt;, while fructose is mainly transported by &lt;a href=&quot;http://en.wikipedia.org/wiki/GLUT5&quot; rel=&quot;nofollow&quot;&gt;GLUT5 (passive transport, does not involve ATP)&lt;/a&gt; into enterocytes in the intestines. After that the cells transport these sugars with &lt;a href=&quot;http://en.wikipedia.org/wiki/GLUT2&quot; rel=&quot;nofollow&quot;&gt;GLUT2 (passive transport, not insulin dependent)&lt;/a&gt; into the blood. Fructose and glucose is transported to the liver (hepatocytes) from the blood, with GLUT2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the liver fructose is more dangerous than glucose, because it is transformed without any regulation. It uses the same pathways as glucose and mostly fatty acids are created from it, which increase the blood VLDL, LDL, FFA level and cause insulin resistance. The byproducts are urate and free radicals, which cause hyperuricaemia and oxidative stress. Hyperuricaemia cause decreased NO levels (by counteracting with eNOS and reacting with NO directly), which cause increased blood pressure due to vasoconstriction. Hyperuricaemia damages the liver and the kidney too. Too high urate levels enhance LDL oxidation as well, which cause atherosclerosis. The free radicals deplete the antioxidants of the body and probably cause cancer in long term.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;High dietary fructose intake: Sweet or bitter life? -&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158875/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158875/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;A causal role for uric acid in fructose-induced metabolic syndrome -&#xA;&lt;a href=&quot;http://ajprenal.physiology.org/content/290/3/F625&quot; rel=&quot;nofollow&quot;&gt;http://ajprenal.physiology.org/content/290/3/F625&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Gut microbial adaptation to dietary consumption of fructose,&#xA;artificial sweeteners and sugar alcohols: implications for&#xA;host–microbe interactions contributing to obesity -&#xA;&lt;a href=&quot;http://www.drperlmutter.com/wp-content/uploads/2014/04/Payne-et-al-2012-Obesity-reviews.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.drperlmutter.com/wp-content/uploads/2014/04/Payne-et-al-2012-Obesity-reviews.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Early Life Exposure to Fructose and Offspring Phenotype: Implications&#xA;for Long Term Metabolic Homeostasis -&#xA;&lt;a href=&quot;http://dx.doi.org/10.1155/2014/203474&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1155/2014/203474&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Dietary fructose, salt absorption and hypertension in metabolic&#xA;syndrome: towards a new paradigm -&#xA;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1748-1716.2010.02167.x/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1111/j.1748-1716.2010.02167.x/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Toward a Unifying Hypothesis of Metabolic Syndrome -&#xA;&lt;a href=&quot;http://pediatrics.aappublications.org/content/129/3/557.short&quot; rel=&quot;nofollow&quot;&gt;http://pediatrics.aappublications.org/content/129/3/557.short&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Uric acid transport and disease -&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877959/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877959/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;@Chris: So summed up I think this is enough proof that HFCS with higher fructose - glucose ratio, than sucrose have a higher health risk. &lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="3703" LastEditDate="2015-04-29T00:51:24.200" LastActivityDate="2015-04-29T00:51:24.200" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="20569" PostTypeId="2" ParentId="2919" CreationDate="2014-08-17T21:57:24.727" Score="3" Body="&lt;p&gt;Part of the answer is in fact extremely simple: &lt;strong&gt;coronary arteries (irrigating the heart muscle) are terminal vessels.&lt;/strong&gt; This means that when a coronary artery sustains damage, the area it was irrigating becomes biologically dead with a very limited potential for recovery. The affected area turns to fibrous tissue produced by cells with much lower oxygen requirements than cardiomyocytes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A fractured bone is not dead at all, in most cases. Put a fracture under a microscope, and you will see plenty of cells performing heavy duty. That is because the area, although damaged, still receives nutrients and at least some blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are special cases:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;bone that is terminally vascularized:&lt;/strong&gt; such bone regions will die when fractured, since they receive no more nutrients and oxygen. The classic example is fracture of the scaphoid bone in the wrist. Some types of fracture in this bone shear the nourishing artery, and the bone dies off instead of healing.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;slowly progressive ischemia due to atherosclerosis:&lt;/strong&gt; when a coronary artery progressively gets clogged instead of this being a sudden event, the cells inside the danger territory secrete messengers that will activate new vessel growth. This phenomenon is called &lt;strong&gt;collateralization&lt;/strong&gt;, and will allow a subset of the cells at risk to survive when the coronary artery gets completely clogged.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now about the stem cell issue: I seem to remember that stem cells do exist in the heart, but this is less pertinent in this case, since even stem cells need oxygen and nutrients to survive.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2014-08-18T10:06:16.707" LastActivityDate="2014-08-18T10:06:16.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20570" PostTypeId="2" ParentId="20563" CreationDate="2014-08-17T22:20:09.567" Score="6" Body="&lt;p&gt;If you have no medical background at all, you will need a general text that teaches more than just digestive physiology. That is because you need to understand the function of other systems that have an influence over the digestive system (for example, the peripheral nervous system).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are a few good general references to get you started:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/145570847X&quot;&gt;Physiology by Linda Costanzo&lt;/a&gt;, arguably the most synthetic. Extremely good, but I am unsure of its value for someone who has no medical background.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0073378305&quot;&gt;Vander's Human Physiology&lt;/a&gt;, arguably the simplest, used in first year of medical school.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1437717535&quot;&gt;Medical Physiology by  Walter F. Boron&lt;/a&gt;, arguably the most complex, I would not recommend it as a first try.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You can start by trying to read the digestive physiology chapters, and look up the knowledge you lack in other chapters.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2014-08-17T22:34:59.303" LastActivityDate="2014-08-17T22:34:59.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20571" PostTypeId="2" ParentId="14937" CreationDate="2014-08-17T22:37:38.957" Score="1" Body="&lt;p&gt;Having looked into this question, I came across &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21325655&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;, where they mixed biotin labelled EGFR-mutant-specific oligonucleotide and isolated the target using streptavidin beads followed by real-time TaqMan PCR allowing a 40 fold increase in detection sensitivity of the mutant allele, suggesting that biotin does not effect nucleotides in PCR based experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.lifetechnologies.com/uk/en/home/brands/product-brand/dynal/streptavidin-coupled-dynabeads/dynabeads-streptavidin.html&quot; rel=&quot;nofollow&quot;&gt;life technologies&lt;/a&gt; webpage claims that Streptavidin-Coupled Dynabeads M-270 can be used in a PCR reaction as stated below although certain streptavidin-coupled beads can have an effect on the PCR reaction. Hence I do not think biotin itself would be a problem for an amplification reaction.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;beads can be used directly in PCR, as they do not inhibit enzymatic reaction. Slight PCR-inhibition has been seen when 75–100 µg of Dynabeads® M-280 Streptavidin was used in 50 µL PCR reaction, and a concentration over 100 µg per 50 µL reaction seems to inhibit PCR completely. Dynabeads® M-270 Streptavidin do not show any inhibitory effect on PCR at these concentrations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In fact you can buy kits such as &lt;a href=&quot;http://www.epibio.com/applications/in-vitro-transcription-and-rna-amplification/in-vitro-transcription-kits/ampliscribe-t7-flash-biotin-rna-transcription-kit?details&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; where you can generate/incorporate biotin into your RNA of interest for any purpose. The use of biotin and its incorporation into nucleotides seems prevalent in the literature and there are even kits for this purpose hence you should be on the safe side with your biotin labelled RNA experiments. I think the biggest challenge in RNA work is to keep it from degradation, which as far as I know is achieved through maintenance at -80 oC.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-18T01:19:33.763" LastActivityDate="2014-08-18T01:19:33.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20572" PostTypeId="2" ParentId="2919" CreationDate="2014-08-17T23:22:38.203" Score="1" Body="&lt;p&gt;In simple terms, heart injury, most likely to be myocardial infarction (heart attack) involves death of the vascular heart tissue. Thus the word infarction. Death of a tissue just simply leads to the production of a fibrous scar. Therefore the heart muscle cannot repair that area of injury to 100% as before.&lt;/p&gt;&#xA;" OwnerUserId="8805" LastActivityDate="2014-08-17T23:22:38.203" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20573" PostTypeId="1" CreationDate="2014-08-18T00:01:09.017" Score="5" ViewCount="162" Body="&lt;p&gt;I want to know if qualitative experiments have been done growing chimpanzee neurons and human neurons in vitro and have any differences emerged, such as the amount of connections per neuron or anything else. &lt;/p&gt;&#xA;" OwnerUserId="1190" LastActivityDate="2014-09-18T22:58:00.830" Title="Do human neurons in a petri dish do different things from chimpanzee neurons" Tags="&lt;brain&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20574" PostTypeId="2" ParentId="14820" CreationDate="2014-08-18T01:16:09.123" Score="1" Body="&lt;p&gt;This &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2822713/&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; uses a similar technique to you by purifying total RNA, synthesis of double-stranded cDNA containing a T7 promoter sequence, cDNA purification, in vitro transcription in the presence of biotin-labeled ribonucleotides and this transcription is possible with T7 RNA polymerase since the cDNA contains the T7 promoter region, and finally fractionation of RNA. This then allows target biotin-labeled RNA for short (~ 25 nucleotides) oligonucleotide arrays. The T7 polymerase performs a linear amplification, and the in vitro RNA obtained reflects the abundance of each transcript in the initial RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence I assume you follow a similar protocol although I'm not sure why you do RT-qPCR on the fragmented RNA since that is unlikely to work if you are doing it using primers for specific regions as everything is fragmented. So I think you do a RT-qPCR before the fragmentation to test the expression levels of certain (known) genes (to see if you are getting the expected results) before you go ahead with fragmentation and look at the global RNA expression. If my assumptions are wrong, then it would be great if you added further details of your experimental protocols with the different steps and the exact orders of the steps followed and the results assessed and the experiments performed so that I can modify my response.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-08-18T01:16:09.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20576" PostTypeId="1" CreationDate="2014-08-18T05:18:30.727" Score="2" ViewCount="128" Body="&lt;p&gt;Very interesting examples to me are Trapezius or Latissimus - they both have places with more tendons than muscles. Taking into account that now they contract weaker and slower with all these tendons, what are the profits?&lt;/p&gt;&#xA;" OwnerUserId="3793" LastEditorUserId="630" LastEditDate="2019-05-29T06:53:54.950" LastActivityDate="2019-05-29T06:53:54.950" Title="Why some muscles have more tendons than others?" Tags="&lt;muscles&gt;&lt;tendons&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20577" PostTypeId="2" ParentId="9152" CreationDate="2014-08-18T05:59:52.783" Score="0" Body="&lt;p&gt;One of the claimed virtues of RT-PCR plates is their inability to bind DNA. (See for example the assortment at &lt;a href=&quot;http://www.fisher.co.uk/product/brand_listing.php/T/Thermo%20Scientific%20ABgene/PCR%20plate&quot; rel=&quot;nofollow&quot;&gt;http://www.fisher.co.uk/product/brand_listing.php/T/Thermo%20Scientific%20ABgene/PCR%20plate&lt;/a&gt; ). As such, all you need to do to remove the DNA (genomic, amplified, or primers) is to rinse them. This suggests that rinsing may also work for dNTP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other, many types of RT-PCR plates are made of polycarbonate, which is able to bind protein. I would be concerned about an uneven amount of polymerase sticking to the well. To go around that, you should re-use, in any PCR plate, only those wells that saw polymerase before.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have no idea whether other molecules bind to the wells, but presumably they fall on the DNA or protein paradigm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It will cost you only one plates and regents for as little as four reactions to test whether these plates are reusable. In the first run, measure two samples, A and B, for some transcript. Rinse the wells, and measure samples A and B again. If the transcript ratio A/B is the wildly different between first and second attempt, you know you can't reuse them. I would also be concerned if it will take many more cycles to reach the plateau stage at the second attempt. Passing these tests, you may be all set. Failing these tests, you may still be able to use the remaining wells. Let us know.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastEditorUserId="8809" LastEditDate="2014-08-18T13:09:02.927" LastActivityDate="2014-08-18T13:09:02.927" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20578" PostTypeId="2" ParentId="20554" CreationDate="2014-08-18T07:22:48.187" Score="1" Body="&lt;p&gt;So, your blank is everything but the enzyme? That is, substrate and DNSA with 100 uL water? If yes, measure, as negative controls, substrate alone and DNSA alone. If one of them is also highly absorbing light, it may be contaminated, and a new vial should be ordered. If both are highly absorbing, it may be the water you are using, or the spectrophotometer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, you may try to measure a time course. If blank's absorbance is increasing as time goes by, there is contamination, and reordering reagents may help you. If absorbance stays constant, you are not looking at an enzyme contamination, that is, the culprit is spoilt water, or broken spec, or even wrong protocol. (That is, reordering or repeating won't help.)&lt;/p&gt;&#xA;" OwnerUserId="8809" LastEditorUserId="8809" LastEditDate="2014-08-18T13:11:39.137" LastActivityDate="2014-08-18T13:11:39.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20579" PostTypeId="2" ParentId="20576" CreationDate="2014-08-18T10:21:00.167" Score="2" Body="&lt;p&gt;If you observe the general structure of the locomotor system, you will be able to roughly separate muscles in two main groups:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;the muscles used for static work and position maintenance.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;those exclusively used for manipulation of the external world.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You will also notice that most muscles with extensive tendinous attachments reside on the axial skeleton (&lt;em&gt;i.e&lt;/em&gt; the trunk). This is because they are used for maintenance of the upright position, and examples of those are: Trapezius, Latissmus dorsi, Rectus abdominis, and many more... Given their static nature, they contain a lot of slow muscle fibers, allowing them to keep working over extended periods of time without rest. However, this does not make them weak. If the postural muscles were to have a structure similar to more peripheral muscles, for example &lt;em&gt;biceps brachii&lt;/em&gt;, they would require an enormous number of different circular tendons extending in every direction to account for all the different body positions they act to maintain. To build a progressive example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;the &lt;strong&gt;biceps brachii&lt;/strong&gt; is a fusiform muscle including two main parts. It is designed to pull hard in a limited range of movement types (&lt;em&gt;i.e&lt;/em&gt; arm flexion). For that, it has evolved a small number of strong tendon attachments.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the &lt;strong&gt;serratus anterior&lt;/strong&gt; was designed for a more extensive panel of moves. It therefore possesses several main bodies of muscles extending in different directions, with their own tendon attachment on the ribs.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the &lt;strong&gt;trapezius&lt;/strong&gt; muscle has been designed to allow the head to keep its upright position (among other functions), and therefore is used as a positional link to guarantee the positional relation between head and shoulders. Its a static muscle and must be able to pull efficiently in a wide range of different directions, so its tendinous apparatus is extensive.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are also special cases. If you take the &lt;strong&gt;digastric muscle&lt;/strong&gt; of the neck for example, the tendons are used as attachments, but also as a kind of hinge to redirect the directional strength of the muscle.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2014-08-18T11:46:12.603" LastActivityDate="2014-08-18T11:46:12.603" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20580" PostTypeId="1" CreationDate="2014-08-18T10:37:34.603" Score="3" ViewCount="127" Body="&lt;p&gt;VPA is a known HDAC inhibitor. But I cannot find what class it is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What class is it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And is there any method of finding an answer better than floundering with Google?&lt;/p&gt;&#xA;" OwnerUserId="8435" LastEditorUserId="9829" LastEditDate="2015-05-19T20:38:16.473" LastActivityDate="2015-05-19T20:38:16.473" Title="What class of histone deacetylase (HDAC) inhibitor is sodium valproate (VPA)?" Tags="&lt;histone-deacetylase&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20582" PostTypeId="2" ParentId="11335" CreationDate="2014-08-18T10:43:45.060" Score="1" Body="&lt;p&gt;Possible Species: &lt;strong&gt;California Fungi&lt;/strong&gt; - &lt;em&gt;Gymnopilus luteofolius&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uf6Db.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mykoweb.com/CAF/species/Gymnopilus_luteofolius.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.mykoweb.com/CAF/species/Gymnopilus_luteofolius.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://mushroomobserver.org/174362?q=28kZM&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://mushroomobserver.org/174362?q=28kZM&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/u81eK.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="15950" LastEditDate="2019-02-05T15:38:59.147" LastActivityDate="2019-02-05T15:38:59.147" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="20583" PostTypeId="2" ParentId="20443" CreationDate="2014-08-18T10:43:50.590" Score="1" Body="&lt;p&gt;If you want a likely predictor candidate for the pulse wave amplitude (which seems to be what you are looking for), you will need to take into account some factors:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;is the heart normal or pathologic?&lt;/li&gt;&#xA;&lt;li&gt;are the vessels normal or pathologic?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now from your question, I assume that you want your model to represent a sane vascular system. In this case, the best predictor of a strong heart beat would most likely be the &lt;strong&gt;area under the curve&lt;/strong&gt; (AUC) of the QRS complex. However, you seem interested exclusively  in the arterial pulse wave of the great circulation. If that is the case, Maybe it would be better to reduce your sampling to the &lt;strong&gt;QR waves AUC&lt;/strong&gt; in an attempt to restrict your signal to the left ventricle contraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, you are trying to predict the &lt;strong&gt;beat-to-beat cardiac output from ECG&lt;/strong&gt;. Some have already investigated that sort of thing. You could try looking at &lt;a href=&quot;http://www.google.ch/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CDEQFjAA&amp;amp;url=http%3A%2F%2Fwww.nihonkohden.de%2Fuploads%2Fmedia%2FesCCO_Info_Vol.1_01.pdf&amp;amp;ei=0dfxU6iuGejQ4QSmvIGYAw&amp;amp;usg=AFQjCNHRezqcbg2GvT8cX-547r_XGZKTRg&amp;amp;sig2=rMdx-sCr1VSHt_ga5JpDag&amp;amp;bvm=bv.73231344,d.bGE&quot; rel=&quot;nofollow&quot;&gt;this device&lt;/a&gt; for a start, and then look up the list of supporting reference for additional information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;good luck!&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-08-18T10:43:50.590" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20585" PostTypeId="1" AcceptedAnswerId="20691" CreationDate="2014-08-18T13:25:20.823" Score="3" ViewCount="546" Body="&lt;p&gt;Does a woman's G-spot actually exist? Are there any research studies?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Links:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/G-spot&quot; rel=&quot;nofollow&quot;&gt;G-spot (Gräfenberg spot)&lt;/a&gt; at Wikipedia&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.dailymail.co.uk/health/article-2134752/Yes-does-exist-U-S-gynaecologist-says-G-spot-very-small.html&quot; rel=&quot;nofollow&quot;&gt;U.S. gynaecologist says he has found the G-spot&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1195" LastEditorUserId="1195" LastEditDate="2014-08-22T08:22:23.083" LastActivityDate="2014-08-22T10:10:12.017" Title="Does a woman's G-spot actually exist?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ClosedDate="2014-08-23T04:13:05.123" ContentLicense="CC BY-SA 3.0" />
  <row Id="20586" PostTypeId="2" ParentId="20541" CreationDate="2014-08-18T14:52:24.920" Score="2" Body="&lt;p&gt;Firstly we must acknowledge there is a difference between being thin and being fit. An unfit thin person will also tire more quickly than a fit person, performance is not always directly related to weight. This is due to the &quot;use it or lose it&quot; nature of fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to the factors mentioned by Deepanjali Dwivedi it is often the case that overweight people are less active and so build up less of the muscle required for the particular task at hand. For example/comparison if you had to use one arm to lift a heavy bag it would be significantly harder than if you were to use both your arms and the muscles in that arm would fatigue more quickly. &lt;/p&gt;&#xA;" OwnerUserId="8811" LastActivityDate="2014-08-18T14:52:24.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20587" PostTypeId="1" AcceptedAnswerId="20638" CreationDate="2014-08-18T15:28:51.133" Score="1" ViewCount="146" Body="&lt;p&gt;Do snail shells increase the number of rounds with snail age?&lt;/p&gt;&#xA;" OwnerUserId="408" LastActivityDate="2014-08-20T10:59:34.527" Title="Do snail shells increase the number of rounds with age?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20588" PostTypeId="1" CreationDate="2014-08-18T15:48:27.583" Score="3" ViewCount="1803" Body="&lt;p&gt;I understand that the blue spectrum is emitted when Hoechst 33342 binds to nuclear DNA. But what exactly is the red spectrum telling us? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read that the red spectrum can be indicative of apoptosis, cellular complexity, or a proxy for cytoplasmic content. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What exactly is the red spectrum indicative of in terms of the cellular context?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;edit**&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry for not getting back to this question sooner. I found the answer in this paper:&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0022175995002146#&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/0022175995002146#&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently condensed chromatin during apoptosis causes hoechst to shift to a red spectrum.&lt;/p&gt;&#xA;" OwnerUserId="90" LastEditorUserId="90" LastEditDate="2014-08-20T17:58:09.953" LastActivityDate="2014-08-20T17:58:09.953" Title="Hoechst red and blue spectra - what does the red emission tell us?" Tags="&lt;staining&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20589" PostTypeId="1" AcceptedAnswerId="20591" CreationDate="2014-08-18T15:55:32.413" Score="10" ViewCount="169" Body="&lt;p&gt;Super simple question, but I can't find the answer on the Internet (and I'm in a foreign country so the library is not English.) As the title says, what is the smallest scale at which blood vessels, nerves, lymphatic vessels, bronchi, renal structures, etc.. are deterministic (same for most of the population)? For example, I'd imagine capillaries are pretty much random, while (most?) people have an aorta, so where does the pattern break? Is there a scale at which an animal's body is probably similar to their siblings but dissimilar to a complete stranger? Or is it just a statistical distribution thing (the smaller you go the more standard deviation you get)?&lt;/p&gt;&#xA;" OwnerUserId="8812" LastEditorUserId="1320" LastEditDate="2014-08-19T07:43:24.143" LastActivityDate="2014-08-19T17:31:52.587" Title="What is the smallest scale at which blood vessels, nerves and other structures are deterministic?" Tags="&lt;zoology&gt;&lt;mathematical-models&gt;&lt;development&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20591" PostTypeId="2" ParentId="20589" CreationDate="2014-08-18T16:56:13.170" Score="4" Body="&lt;p&gt;Indeed a very good question. I'm afraid it might remain without a proper anatomy-based answer, but my intuition would tend towards agreeing with &quot;the smaller you get, the more deviation you'll find&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or rather, I would expect the same principle as in conservation of genetic patterns to apply here: the more central a tissue structure is to survival, i.e. the more downstream systems depend on it, the more likely it will grow in conserved patterns.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an excellent example, the largest blood vessels including the aorta and its first- and second-degree branches are identical in branch number, approximate relative branch size and approximate branching location across probably all living humans (given that babies born with malformations on this scale would probably not survive without drastic surgery). Similarly, the largest-level nerves and nuclei are identical across the species. These are central systems that provide core functionality for survival.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, teeth are quite important, but the odd tooth missing or additional doesn't harm terribly as no downstream systems depend on them. Indeed, it isn't uncommon for humans to be missing a permanent tooth and keep their primary (baby) tooth in that spot for decades; similarly, missing 8th teeth or additional 9th teeth also occur.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2014-08-19T08:52:59.100" LastActivityDate="2014-08-19T08:52:59.100" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20593" PostTypeId="1" AcceptedAnswerId="20595" CreationDate="2014-08-18T18:04:32.813" Score="4" ViewCount="157" Body="&lt;p&gt;This one is too basic question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just came across $Ihh^{-/-}\ $ mouse. Is that means this mouse devoid of that gene Ihh. What is this sign called and are there other such representations?&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="1320" LastEditDate="2014-08-19T07:40:19.223" LastActivityDate="2014-08-19T07:40:19.223" Title="What is an Ihh-/- mouse?" Tags="&lt;lab-techniques&gt;&lt;animal-models&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20594" PostTypeId="2" ParentId="20593" CreationDate="2014-08-18T18:41:18.860" Score="4" Body="&lt;p&gt;The &lt;em&gt;IHH&lt;/em&gt; gene encodes the &lt;a href=&quot;http://en.m.wikipedia.org/wiki/IHH_(protein)&quot; rel=&quot;nofollow&quot;&gt;Indian hedgehog homolog protein&lt;/a&gt;, a member of the family of hedgehog proteins that  regulates bone formation. The &lt;em&gt;ihh&lt;sup&gt;-/-&lt;/sup&gt;&lt;/em&gt; notation represents an animal which is homozygous for a null mutation in the gene (i.e. the animal has no functional &lt;em&gt;IHH&lt;/em&gt; gene).&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-08-18T18:41:18.860" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20595" PostTypeId="2" ParentId="20593" CreationDate="2014-08-18T19:26:17.217" Score="3" Body="&lt;p&gt;These are allele notations or nomenclatures and they refer to a gene, and what changes a particular gene has undergone, if any. In this case, the -/- refers to the fact that the &lt;em&gt;Ihh&lt;/em&gt; gene is homozygous for a null mutation as correctly stated by @Alan Boyd. This &lt;a href=&quot;http://www.informatics.jax.org/mgihome/nomen/allmut_quickhelp.shtml&quot; rel=&quot;nofollow&quot;&gt;page&lt;/a&gt; has further examples of allele nomenclatures. This &lt;a href=&quot;http://www.informatics.jax.org/mgihome/nomen/gene.shtml#navsma&quot; rel=&quot;nofollow&quot;&gt;page&lt;/a&gt;, which can be reached from the previous link provides comprehensive guidelines for nomenclature of genes, genetic markers, alleles, and mutations in mouse and rat. Please note that (if you look at the examples &lt;a href=&quot;http://flystocks.bio.indiana.edu/Fly_Work/nomenclature.htm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) a nomenclature can be different in different species for example in the fly field, you tend not to use the -/- sign to denote a null mutation and instead it can be a name or a number for example &lt;em&gt;Rab5(1)&lt;/em&gt;. The only reason this is called allele 1 is that it shows the most severe phenotype, which is embryonic lethality. You can read &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12743108&quot; rel=&quot;nofollow&quot;&gt;this paper here&lt;/a&gt; for some of the &lt;em&gt;Rab5&lt;/em&gt; alleles produced in &lt;em&gt;Drosophila&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-18T21:14:49.420" LastActivityDate="2014-08-18T21:14:49.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20596" PostTypeId="2" ParentId="14909" CreationDate="2014-08-18T20:39:47.547" Score="3" Body="&lt;p&gt;The main question can be answered in a very dumb way: because the lower part of the body also needs blood... and this configuration is the surest way of doing that because of reasons given below (among many others, I am sure).&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;If you want an anatomical reason, well the most pertinent one would be that embryologically, &lt;strong&gt;the heart and vascular system are derived from a single straight tube&lt;/strong&gt;, that then begins contracting and folding over itself to form the heart chambers, the aorta, and the pulmonary trunk.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If you want a physiological explanation, the aorta curves slowly because it is a point of the circulatory system where pressure is high. Apart from the fact that &lt;strong&gt;sharp kinks would cause a massive and useless loss of kinetic energy&lt;/strong&gt; on blood flow from shear stress over the aortic walls (and therefore more heart workload), the induced &lt;strong&gt;shear stress would also damage the aortic walls&lt;/strong&gt; much more quickly than in the actual configuration.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The third reason is just theory on my part, but it seems the vascular system is designed by priorities: you could imagine a system with two aortas. One for the upper body going up, and a second going down. However, such a configuration makes it mechanically impossible to balance perfusion to the organs, and especially ensure brain perfusion. For example, how would the body compensate if the upper aorta got clogged while the other stayed wide open? The single aorta configuration allows the heart to adapt to such mechanical perturbation &lt;em&gt;scenarii&lt;/em&gt; using, for example, left ventricular hypertrophy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However to add to some elements of your question:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the reason of the aortic coiling has certainly very little to do with elasticity and the vessel compression chamber principle.&lt;/li&gt;&#xA;&lt;li&gt;Higher elasticity means the aorta is &lt;strong&gt;less&lt;/strong&gt; stiff, not more.&lt;/li&gt;&#xA;&lt;li&gt;When the aorta gets stiff (elasticity decreases) as it is often the case with age and calcification of the aortic walls, it is correct that the heart will need to work more, that systolic pressure will get higher, and diastolic pressure lower. This gives the classical clinical symptom of &lt;strong&gt;&quot;cannonball&quot;&lt;/strong&gt; or &lt;strong&gt;&quot;gunshot&quot;&lt;/strong&gt; &lt;strong&gt;pulse&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2014-08-18T21:03:58.113" LastActivityDate="2014-08-18T21:03:58.113" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20597" PostTypeId="2" ParentId="15214" CreationDate="2014-08-18T20:56:06.913" Score="2" Body="&lt;p&gt;While correct, @AndroidPenguin 's answer is only part of the explanation. By far the main reason of the pressure difference is that the peripheral circulatory system has two main compartments:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;a &lt;strong&gt;resistive&lt;/strong&gt; compartment, represented by arterioles&lt;/li&gt;&#xA;&lt;li&gt;a &lt;strong&gt;capacitance&lt;/strong&gt; compartment, represented by capillaries&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The reason for the abrupt pressure fall from arterioles onward is precisely that &lt;strong&gt;this is the main function of the arterioles&lt;/strong&gt;: they contract and dilate to adjust capillary pressure. Since a good part of capillary function depends on exchanges along oncotic pressure gradients, hydrostatic pressure cannot be allowed to stay too high in the capillary compartment. So in conclusion, @AndroidPenguin gave you the physical reason, but mine is the physiological reason.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-08-18T20:56:06.913" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20598" PostTypeId="2" ParentId="14900" CreationDate="2014-08-18T21:02:44.070" Score="2" Body="&lt;p&gt;The aorta is a compression chamber because it is an important drive for diastolic perfusion. To keep the blood flowing constantly, and not only during systole (as would be the case with a rigid aorta), the &lt;strong&gt;high elasticity of the aortic walls allows it to dilate as a consequence of the high systolic pressure&lt;/strong&gt;. This &lt;strong&gt;allows the aorta to accumulate blood&lt;/strong&gt; in its proximal part, which is then &lt;strong&gt;propelled by the passive elastic contraction of the aorta during diastole&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-08-18T21:02:44.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20599" PostTypeId="2" ParentId="20589" CreationDate="2014-08-18T21:15:05.977" Score="2" Body="&lt;p&gt;The answer is... basically none. The variability is high, and can also happen in the macroscopic range. If you want a quick-and-dirty idea of the fraction of the population presenting a certain variability in humans, I would suggest a good anatomy atlas or manual. A good resource would be &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0443066841&quot; rel=&quot;nofollow&quot;&gt;Gray's Anatomy&lt;/a&gt; (the book, not the soap ;-).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from that, @Armatus is in my opinion correct in assuming that variability is inversely proportional to scale. However I would like to point out that even the largest blood vessels can derive from the classical structure in many ways, and are certainly not identical among all living humans.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-08-18T21:15:05.977" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20600" PostTypeId="1" CreationDate="2014-08-18T21:36:56.767" Score="0" ViewCount="312" Body="&lt;p&gt;To my knowledge, the pineal gland is responsible for the release of dimethyltryptamine (DMT) upon death.  Would it be possible to force the pineal gland to release this DMT while still living?&lt;/p&gt;&#xA;" OwnerUserId="8818" LastEditorUserId="1320" LastEditDate="2014-08-18T22:29:36.130" LastActivityDate="2014-08-18T22:29:36.130" Title="Would it be possible to force the pineal gland to release dimethyltryptamine on command?" Tags="&lt;brain&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20601" PostTypeId="2" ParentId="20600" CreationDate="2014-08-18T21:53:49.940" Score="2" Body="&lt;p&gt;According to this &lt;a href=&quot;http://en.wikipedia.org/wiki/Pineal_gland&quot; rel=&quot;nofollow&quot;&gt;page&lt;/a&gt; the release of DMT upon death is speculative and its presence has so far been confirmed in rodents brain and human melanoma cell line &lt;a href=&quot;http://en.wikipedia.org/wiki/Dimethyltryptamine&quot; rel=&quot;nofollow&quot;&gt;SK-Mel-147&lt;/a&gt;. DMT is also produced in humans; however, its production and purpose in the brain has yet to be proven or understood (&lt;a href=&quot;http://en.wikipedia.org/wiki/Dimethyltryptamine&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Dimethyltryptamine&lt;/a&gt;). Hence from what I have gathered on the matter DMT has not yet been proven to get secreted from human pineal gland and its command based secretion is yet to be discovered.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-08-18T21:53:49.940" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20602" PostTypeId="1" AcceptedAnswerId="39872" CreationDate="2014-08-18T23:52:27.407" Score="7" ViewCount="13551" Body="&lt;p&gt;I've been told that flies take off backwards, but I haven't really been able to prove it to myself. The closest I've gotten was noticing that they fly into window glass back-first, with their heads pointing up. Is that how they take off?&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2015-10-23T07:29:03.470" Title="Do flies actually take off backwards?" Tags="&lt;entomology&gt;&lt;flight&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20603" PostTypeId="2" ParentId="3807" CreationDate="2014-08-18T23:59:23.697" Score="-1" Body="&lt;p&gt;It's for control, coordination and balance. From a mathematical point of view, parallel lines won't intersect and thus line A won't affect line B unless they intersect and thus would hardly influence the other unless and an external force is applied to any of the lines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is also why corpus callosum connects the left and the right side of the brain.&lt;/p&gt;&#xA;" OwnerUserId="8819" LastActivityDate="2014-08-18T23:59:23.697" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20604" PostTypeId="2" ParentId="20602" CreationDate="2014-08-19T00:47:44.617" Score="9" Body="&lt;p&gt;From this &lt;a href=&quot;https://www.youtube.com/watch?v=1w_JGihdvc0&quot;&gt;video&lt;/a&gt; demonstration in caltech, you can clearly see that &lt;em&gt;Drosophila&lt;/em&gt; can fly forwards as well as backwards using high fps video image capture and it even does unexpected behaviours in times of perceived danger/threat.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-08-19T00:47:44.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20605" PostTypeId="2" ParentId="20589" CreationDate="2014-08-19T01:16:14.323" Score="1" Body="&lt;p&gt;Biology is not deterministic. Traits like this have variable expressivity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A phenotype with 100% expression in a population with an allele is said to have complete penetrance. There is no gene which could specify a single blood vessel pattern that could have complete penetrance. Variable expressivity means the same genes yield a spectrum of forms of the same phenotype. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/scitable/topicpage/phenotype-variability-penetrance-and-expressivity-573&quot; rel=&quot;nofollow&quot;&gt;A description of phenotype variability, penetrance and expressivity&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-19T17:31:52.587" LastActivityDate="2014-08-19T17:31:52.587" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20610" PostTypeId="1" CreationDate="2014-08-19T04:06:22.750" Score="3" ViewCount="901" Body="&lt;p&gt;I know bees make honey from nectar, and I know they drink the juice of fallen fruit, but do they actually make honey from fruit, or do they only eat from it for themselves?&lt;/p&gt;&#xA;" OwnerUserId="8821" LastActivityDate="2015-07-13T19:34:49.227" Title="Do bees make honey from fallen fruit?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20612" PostTypeId="1" CreationDate="2014-08-19T07:06:08.640" Score="2" ViewCount="373" Body="&lt;p&gt;I am interested in performing nucleotide sequence pattern-mining (regular expressions) which is 12 characters (sequences) in length from a dataset. Is that possible to script using MATLAB?&lt;/p&gt;&#xA;" OwnerUserId="8824" LastEditorUserId="6511" LastEditDate="2014-08-19T10:59:53.963" LastActivityDate="2014-08-19T17:31:42.663" Title="How do I perform recurring pattern mining or regular expressions of nucleotide sequences?" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20613" PostTypeId="2" ParentId="20580" CreationDate="2014-08-19T08:02:54.160" Score="2" Body="&lt;p&gt;This is explained at &lt;a href=&quot;http://en.wikipedia.org/wiki/Histone_deacetylase_inhibitor#HDAC_classification&quot; rel=&quot;nofollow noreferrer&quot;&gt;the WP page for HDAC&lt;/a&gt;. There are five classes:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;hydroxamic acids (or hydroxamates), such as trichostatin A&lt;/p&gt;&#xA;&lt;p&gt;cyclic tetrapeptides (such as trapoxin B), and the depsipeptides&lt;/p&gt;&#xA;&lt;p&gt;benzamides&lt;/p&gt;&#xA;&lt;p&gt;electrophilic ketones&lt;/p&gt;&#xA;&lt;p&gt;the aliphatic acid compounds such as phenylbutyrate and valproic acid&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;and valproate is in the final class, aliphatic acids.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-08-19T08:02:54.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20614" PostTypeId="1" CreationDate="2014-08-19T08:38:51.703" Score="3" ViewCount="156" Body="&lt;p&gt;An idle question - if a glass if filled from the tap and consumed immediately, it contains some dissolved oxygen from the physical process of moving through the pipes &amp;amp; tap. If left out (unrefridgerated) and then consumed later the bubbles are gone and there is presumably less dissolved gases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm wondering whether this might have the effect of changing the relative levels of oxygen available to microbiota in the gut, and hence have some effect on the human host?&lt;/p&gt;&#xA;" OwnerUserId="8825" LastEditorUserId="10401" LastEditDate="2015-12-25T00:24:02.503" LastActivityDate="2015-12-26T14:42:21.657" Title="Is there a difference between drinking water straight from the tap compared to leaving it to sit?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20615" PostTypeId="2" ParentId="13486" CreationDate="2014-08-19T09:04:05.383" Score="-1" Body="&lt;p&gt;Its true that T-test are used when your dependent variable is Numeric and Chi-Square test is used when you are analysis categrical variable. But how about this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You have a categorical response (0,1) to a campaign. 1 who bought the product and 0 who did not. If you sum up the responses in your Test group and Control group and devide them by thier respective population size, lets say you get something like this - .23% response rate in Test Group and .01% response rate in Control Group. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can't you use T-Test to see if these reponse rates are different? If yes, then let me remind that these variables were categorical (0,1) but we still used them as numeric. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All I want to say is that if we are comparing response rates or percentages, then T-Tests can be used irrespective if the dependent variable is character or numeric. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sachin &lt;/p&gt;&#xA;" OwnerUserId="8826" LastActivityDate="2014-08-19T09:04:05.383" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20616" PostTypeId="1" CreationDate="2014-08-19T10:34:11.420" Score="1" ViewCount="165" Body="&lt;p&gt;Are there known evolutionary reasons why mammals contain 2 of some organs (such as lungs and kidneys) and only 1 of some (such as liver)?&lt;/p&gt;&#xA;" OwnerUserId="8644" LastEditorUserId="8644" LastEditDate="2015-01-01T20:45:22.973" LastActivityDate="2015-01-01T20:45:22.973" Title="Duplicity Vs. Singularity of Mammals Organs" Tags="&lt;evolution&gt;&lt;physiology&gt;&lt;liver&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ClosedDate="2014-08-19T15:32:49.903" ContentLicense="CC BY-SA 3.0" />
  <row Id="20617" PostTypeId="2" ParentId="20612" CreationDate="2014-08-19T11:09:01.093" Score="1" Body="&lt;p&gt;I'm no expert in MATLAB but I know that it is possible to do regular expressions in MATLAB with the general rules explained &lt;a href=&quot;http://www.mathworks.co.uk/help/matlab/matlab_prog/regular-expressions.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. However there are alternative approaches and softwares you could use to achieve this with softwares that are freely available and quite powerful in performing such functions. Although I'm aware that perl and python are the programs of choice for regular expression analysis; however I would urge you to consider the &lt;a href=&quot;http://www.r-project.org&quot; rel=&quot;nofollow&quot;&gt;R&lt;/a&gt; language. R allows you to construct your mining results in a format of a table, which each column containing the data you are interested! there are many packages in R that allows you to process many data types. I would say R is worth the investment to learn for any future data analysis. I use the &lt;a href=&quot;http://www.rstudio.com&quot; rel=&quot;nofollow&quot;&gt;RStudio&lt;/a&gt; to interact with the R language software.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best place to get help for MATLAB or R is the &lt;a href=&quot;http://stackoverflow.com&quot;&gt;http://stackoverflow.com&lt;/a&gt; which you can sign on with you current account. In fact I have asked a few questions there on regular expressions and the community is very helpful however ensure that you show your attempt at the problem and where you are stuck in order to get a constructive responses!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-08-19T11:09:01.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20618" PostTypeId="2" ParentId="20614" CreationDate="2014-08-19T12:26:18.680" Score="3" Body="&lt;p&gt;If you are speaking especially of the stomach, it actually makes no difference because the extremely low pH of the stomach allows very few bacterial organisms to survive. Often, &lt;a href=&quot;http://en.wikipedia.org/wiki/Helicobacter_pylori&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Helicobacter pylori&lt;/em&gt;&lt;/a&gt; can however be present. Whether dissolved oxygen makes a difference to it is, to my knowledge, unknown. However, pure water does not stay long inside the stomach and passes almost immediately through to the intestines in most cases, so I doubt it would make that big a difference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, it seems you are actually referring to the intestines in your question. Well, in fact the &lt;strong&gt;bacteria that inhabit the gut are almost exclusively limited to the colon and to a limited extent to the distal part of the ileum&lt;/strong&gt; (small intestine). The stomach and almost all the length of the small intestine are sterile. &lt;strong&gt;Water absorption takes place in the jejunum&lt;/strong&gt; (proximal part of the small intestine), which is a sterile region proximal to the locations colonized by bacteria. &lt;strong&gt;In conclusion, the oxygen content of tap water will not influence the bacterial flora simply because it does not come into contact with those bacteria.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW, the major difference between tap water that you leave sitting and the one that just came out of the tap is the chlorine concentration (decreases with time). Of course this will favor microorganism development, since it is precisely one of the reasons why we put chlorine in the water in the first place...&lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2014-08-20T00:49:07.850" LastActivityDate="2014-08-20T00:49:07.850" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="20619" PostTypeId="2" ParentId="20616" CreationDate="2014-08-19T13:54:22.820" Score="2" Body="&lt;p&gt;It's just how we evolved. At some point in the past, a distant ancestor of ours had two lungs, two kidneys, one liver etc.( maybe then there was a pretty good reason for this). We evolved following that pattern and now we ourselves have two lungs, two kidneys, one liver etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Snakes, for example, have just one functional lung because their elongated form doesn't cope well with having two full-grown lungs. Humans on the other hand have a body shape that works very well with two lungs, so we didn't have to sacrifice one lung.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other examples of different organ distribution, like the octopus which has 3 hearts. Usually the more different the internal symmetry, the more distant the common ancestor.&lt;/p&gt;&#xA;" OwnerUserId="8814" LastEditorUserId="57" LastEditDate="2014-08-21T05:26:02.807" LastActivityDate="2014-08-21T05:26:02.807" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20621" PostTypeId="2" ParentId="20612" CreationDate="2014-08-19T17:27:27.243" Score="1" Body="&lt;p&gt;With awk it is as simple as this (Assuming that the sequences are in fasta format and the sequences are not interrupted by line breaks): &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;awk -v p=&amp;lt;some_patttern&amp;gt; '/&amp;gt;/{name=$0} !/&amp;gt;/{&#xA;    s=$0&#xA;while (match(s,p)){&#xA;       print name,substr(s, RSTART, RLENGTH)&#xA;       s=substr(s, RSTART+RLENGTH)&#xA;    }&#xA;&#xA;}' fastafile.fa&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This script will print all matches for a pattern in a given set of sequences.I cannot explain how this script works in this forum; Stackoverflow would be more suitable for that.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-08-19T17:27:27.243" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20623" PostTypeId="1" AcceptedAnswerId="20624" CreationDate="2014-08-19T17:56:04.030" Score="4" ViewCount="5289" Body="&lt;p&gt;E. coli has a generation time of about 20 min, and a single CFU will generate a colony a few millimeters in diameter after 16 hours of incubation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this the upper limit? How much faster can bacteria grow? How much faster can colonies grow?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2019-01-08T10:31:22.040" Title="What is the fastest growing bacterium?" Tags="&lt;bacteriology&gt;&lt;growth&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20624" PostTypeId="2" ParentId="20623" CreationDate="2014-08-19T18:14:06.297" Score="3" Body="&lt;p&gt;The article and published work &lt;a href=&quot;http://newsoffice.mit.edu/2013/how-quickly-can-a-bacterium-grow-0827&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://scitation.aip.org/content/aip/journal/jcp/139/12/10.1063/1.4818538&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; respectively, reveals that &lt;em&gt;E. coli&lt;/em&gt; replication is close to thermodynamic limits of efficiency having modelled this process using mathematical equations. However an interesting article and published work &lt;a href=&quot;http://www.iaglr.org/jglr/release/37/37_1_203-206.php&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0380133010002510&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, respectively reports a bacteria (homologous to &lt;em&gt;Thermobrachium celere&lt;/em&gt; and &lt;em&gt;Caloramator indicus&lt;/em&gt;, which are closely related) with doubling times as short as 10 minutes have been discovered in areas of hot water emissions in Lake Tanganyika.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Small chimneys emitting hot water at temperatures of 66 to 103 degrees Celsius (150 to 217 degrees Fahrenheit) have been discovered at the shallow lake bottom of Lake Tanganyika, East Africa. In a study searching for thermophilic sulfate reducing bacteria in this extreme environment, a spore-forming bacterium was discovered that grew with a doubling time as short as 10 minutes. In theory, a single cell of this bacterium in this environment can multiply to 500 million in less than 5 hours under optimal conditions (60 degrees Celcius).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;EDIT: If the question is exclusively about &lt;em&gt;E. coli&lt;/em&gt; and it takes into account laboratory conditions then I also came across this references &lt;a href=&quot;http://www.pnnl.gov/science/highlights/highlight.asp?id=879&quot; rel=&quot;nofollow&quot;&gt;page&lt;/a&gt; claiming tha &lt;em&gt;E. coli&lt;/em&gt; doubling time is between 4-20 minutes. Based on this &lt;a href=&quot;http://msb.embopress.org/content/6/1/390.long&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; the page reports that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Internationally renowned researcher Bernhard Palsson and other researchers from the University of California San Diego led a team of scientists from PNNL, the University of Heidelberg, and the German Cancer Research Center to study how &lt;em&gt;E. coli&lt;/em&gt; bacteria changed and evolved from one environment to another in a laboratory setting. The team then compared proteomics, genomic, and metabolic data from the study with a computational model for bacterial growth.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The page then goes on to say&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Using high-performance liquid chromatography coupled to mass spectrometry, the team gathered data on how the bacteria changed their protein profile as they grew and reproduced in different mediums. The scientists found that the data and model were correlated to a surprising degree (more than 98% in some cases), validating the model's ability to predict the growth of &lt;em&gt;E. coli&lt;/em&gt; bacteria under specific conditions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This confirms the comments above that the growth rate of &lt;em&gt;E. coli&lt;/em&gt; depends on the specific conditions in which it is in and furthermore its growth rate under specific conditions can be predicted based on the devised model.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-19T22:56:14.993" LastActivityDate="2014-08-19T22:56:14.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20625" PostTypeId="2" ParentId="20541" CreationDate="2014-08-19T18:38:02.490" Score="1" Body="&lt;p&gt;The most popular method of getting fat in the first place involves exerting yourself as little as possible. This leads to the muscles and metabolism failing to become conditioned for strenuous activity, ie. remaining very untrained.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, a person who became fat in this manner is mentally and physically unprepared for intense activity, for the simple reason that they have seldom done it before and their body did not become adapted to it. It is not surprising that they are very bad at it compared to people of moderate fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus the correlation between being fat and lacking endurance is not due to causality from the former towards the latter, but due to another factor causing both (also known as a confound). An added factor is that you over-simplify by focusing on calories: In the real world, the sort of diet and lifestyle that results in excessive weight also drastically impairs cardiovascular health, which then in turn impairs performance. However, this goes back to the question of being trained vs. untrained for strenuous activity, since exercise also influences cardiovascular health.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, fat is a good thermal insulator and most likely interferes with performance by making it difficult to evacuate heat. I don't think this effect is significant compared to the above reasoning, evidenced by the fact that even in extremely cold weather, a naked fat man will not suddenly become an effective athlete.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A further caveat is that an athlete who became very fit to begin with, could subsequently amass a large amount of fat without losing much muscle. This often does not impair performance all that much (and is a common practice in some bodybuilding circles).&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-08-19T18:43:32.440" LastActivityDate="2014-08-19T18:43:32.440" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20626" PostTypeId="1" AcceptedAnswerId="20627" CreationDate="2014-08-19T19:46:31.230" Score="8" ViewCount="1719" Body="&lt;p&gt;I would like to know the steps the body takes to heal a broken bone and what happens if it cannot heal properly.  I am not looking for advice or explanations on resting and not doing activity, I am genuinely interested in understanding the outcome if activity is not stopped&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the scenario:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A rock climber develops a pain in the lower part of their middle finger.  The pain is not so bad so the climber continues to climb for four weeks, but the pain has not gone away.  The climber decides to go to the doctor fearing they have an A2 Pulley tear.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To their surprise the Doctors tests show no A2 pulley tear but rather a minor stress fracture of the Proximal Phalanx.  The doctor says stop climbing, however the climber has several trips planned and does not experience any pain while climbing nor a loss of strength or power while climbing.  The only time pain is felt is when the lower part of the middle finger is squeezed.  Because of this the climber decides to continue climbing as they just love it so much.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question:  What will happen to a stress fracture in the finger if adequate rest is not given?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand the first thing the body does is try to stabilize the break and then starts to repair.  What happens if it is continually used and not given the chance to properly heal?  Will the climber just have a sore spot on their finger for the rest of their life or will it progressively get worse and worse? &lt;/p&gt;&#xA;" OwnerUserId="8828" LastEditorUserId="1320" LastEditDate="2014-08-20T11:54:21.763" LastActivityDate="2014-08-20T11:54:21.763" Title="What happens to bones that do not heal?" Tags="&lt;human-anatomy&gt;&lt;bone-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20627" PostTypeId="2" ParentId="20626" CreationDate="2014-08-19T21:42:40.837" Score="9" Body="&lt;p&gt;Fracture healing occurrs in several steps:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;haemorrhage:&lt;/strong&gt; blood and surrounding cells fill the space created by the fracture.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;fibrous callus:&lt;/strong&gt; chondrocytes colonize the fracture space, with neovascularization.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;bony callus:&lt;/strong&gt; osteocytes colonize the fracture space and rearrange in &lt;strong&gt;woven bone&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;remodelling:&lt;/strong&gt; in long bones, woven bone is remodelled into &lt;strong&gt;lamellar bone&lt;/strong&gt; and creates a new &lt;strong&gt;haversian system&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;If the fracture is not immobilized enough (not enough rest), several things can happen that are mutually exclusive:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;normal healing:&lt;/strong&gt; luckily, the bone is not too much mobilized and is able to heal normally&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;fracture displacement:&lt;/strong&gt; the bone heals, but in an incorrect alignment. This gets partially corrected over time, but the correction mechanism is limited, especially in adults.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;pseudarthrosis:&lt;/strong&gt; the worst case. instead of normal healing, cartilage grows to protect the bony extremities that are mobilized and prevents further healing. This causes pain, and will require surgery in most cases.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2014-08-19T21:48:48.540" LastActivityDate="2014-08-19T21:48:48.540" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20628" PostTypeId="2" ParentId="20573" CreationDate="2014-08-19T22:41:50.937" Score="1" Body="&lt;p&gt;I have came across several studies indicating large similarities between chimpanzee and humans. A study by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690614/?report=classic&quot; rel=&quot;nofollow&quot;&gt;Bianchi et al., 2013&lt;/a&gt; used immunohistochemistry, electron microscopy, and Golgi staining to characterise synaptic density and dendritic morphology of pyramidal neurons in primary somatosensory (area 3b), primary motor (area 4), prestriate visual (area 18), and prefrontal (area 10) cortices of developing chimpanzees (Pan troglodytes). They found that synaptogenesis occurs synchronously across cortical areas, with a peak of synapse density during the juvenile period (3–5 y). Moreover, similar to findings in humans, dendrites of prefrontal pyramidal neurons developed later than sensorimotor areas. These results suggest that evolutionary changes to neocortical development promoting greater neuronal plasticity early in postnatal life preceded the divergence of the human and chimpanzee lineages. This study however does note that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Despite sharing these neurodevelopmental similarities, it is important to note that cognitive ontogeny in chimpanzees differs from humans in several respects. Behavioral studies suggest that the different social and environmental contexts in which humans and chimpanzee develop may have also been important in the evolution of human-specific socio-cognitive abilities. For example, whereas young chimpanzees do not fully wean until 4–5 y of age and remain closely attached to their mothers during the early years of development, human infants often interact with multiple caregivers and engage in joint attention.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In another study by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22875862&quot; rel=&quot;nofollow&quot;&gt;Bianchi et al.,&lt;/a&gt; also published in 2013 regional variation in the morphology of pyramidal neurons in the cerebral cortex of great apes, humans' closest living relatives were investigated. The study used the rapid Golgi stain to quantify the dendritic structure of layer III pyramidal neurons in 4 areas of the chimpanzee cerebral cortex: Primary somatosensory (area 3b), primary motor (area 4), prestriate visual (area 18), and prefrontal (area 10) cortex. The study showed that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Consistent with previous studies in humans and macaque monkeys, pyramidal neurons in the prefrontal cortex of chimpanzees exhibit greater dendritic complexity than those in other cortical regions, suggesting that prefrontal cortical evolution in primates is characterized by increased potential for integrative connectivity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Compared with chimpanzees, the pyramidal neurons of humans had significantly longer and more branched dendritic arbors in all cortical regions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These studies show that despite significant morphological and developmental similarities between human and chimpanzee neurons, there are still notable observable differences.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-08-19T22:41:50.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20629" PostTypeId="1" CreationDate="2014-08-20T00:47:24.207" Score="4" ViewCount="1272" Body="&lt;p&gt;It is said by people opposed to Evolution, that the fossil record contradicts and disproves it. They say all the animals suddenly appeared, exploded everywhere, were fully formed, had no transitions, no gradualism, no change, and no sign of an evolutionary trend by which they could have emerged from an earlier type.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They then use these quotes to back this up from Evolutionists themselves:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;All the larger groups of animals, e.g. fishes, amphibians, reptiles, mammals seem to have appeared suddenly on the earth, spreading themselves, so to speak, in an explosive manner in their various shapes and forms. Nowhere is one able to observe or prove the transition of one species into another, variation only being possible within the species themselves&quot; Evolutionist, Max Westenhofer as quoted in Dewar's More Difficulties, p. 94&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The evidence of Geology today is that species seem to come into existence suddenly and in full perfection, remain substantially unchanged during the terms of their existence, and pass away in full perfection. Other species take their place, apparently by substitution, not by transmutation&quot; Geologist, Joseph Le Conte&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology (study of fossils). In any local area, a species does not arise gradually by the steady transformation of its ancestors, it appears all at once and fully formed.&quot; -- Dr. Stephen J. Gould, Prof of Geology and Paleontology, Harvard University. Mentioned in one of his regular columns in Natural History Magazine (1977) and also in The Panda's Thumb, 1980, p. 181-182&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;different species usually appear and disappear from the record without showing the transitions that Darwin postulated -- we are now about 120 years after Darwin and the knowledge of the fossil record has been greatly expanded. We now have a quarter of a million fossil species but the situation hasn't changed much -- We have fewer examples of evolutionary transitions than we had in Darwins' time&quot; Dr. David Raup, a paleontologist at the Field Museum of Natural History in Chicago. Field Museum Natural History Bulletin 50:22- 29&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Evolution requires intermediate forms between species and paleontology does not provide them&quot; Dr. David B. Kitts, Paleontologist&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The known fossil record fails to document a single example of phyletic evolution accomplishing a major morphologic transition&quot; Evolutionist, Dr. Steven M. Stanley&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The record certainly did not reveal gradual transformations of structure in the course of time. On the contrary, it showed that species generally remained constant throughout their history. New types or classes seemed to appear fully formed, with no sign of an evolutionary trend by which they could have emerged from an earlier type.&quot; Bowler, 'Evolution: The History of an Idea', 1984, p. 187&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;We are still in the dark about the origin of most major groups of organisms. They appear in the fossil record as Athena did from the head of Zeus -- full-blown and raring to go, in contradiction to Darwin's depiction of evolution as resulting from the gradual accumulation of countless infinitesimally minute variations, which, in turn, demands that the fossil record preserve an unbroken chain of transitional forms.&quot; Jeffrey H. Schwartz, Sudden Origins: Fossils, Genes, and the Emergence of Species (New York: John Wiley &amp;amp; Sons, 1999)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this true? If not, why not? Does the fossil record prove or disprove Evolution?&lt;/p&gt;&#xA;" OwnerUserId="6157" LastActivityDate="2014-08-20T01:52:25.250" Title="Does the fossil record disprove Evolution?" Tags="&lt;evolution&gt;&lt;palaeontology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ClosedDate="2014-08-20T08:50:34.127" ContentLicense="CC BY-SA 3.0" />
  <row Id="20630" PostTypeId="2" ParentId="20629" CreationDate="2014-08-20T01:52:25.250" Score="3" Body="&lt;p&gt;Fossil records are fossil records. The people who use them to attempt to prove or disprove evolution use them to represent their causes in different ways, gleaning sometimes completely contradictory facts from the same bodies of information, sometimes even the same samples.&#xA;It is my personal belief that evolution isn't ever entirely phyletic, I like to imagine that once in a while a pup would be born or an egg would crack open and there'd be a malformed creature in there the likes of which the world has never seen, if only because its deformity has made it more adaptable or stronger to its environment, not the opposite which is usually the case with birth defects. And then yes this prototype would survive and find a mate and have offspring with its varied genes dominating, some same, some different, and begin the phyletic process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But that's not the answer to your question. Your question isn't really answerable. Fossil records only prove that a creature once lived at that time period, and its bone structure and posture can reveal certain things to any observer, but they dont prove or disprove anything. A great deal of the works you quote speak on the topic with great finality, yet they are decades old. &lt;/p&gt;&#xA;" OwnerUserId="8831" LastActivityDate="2014-08-20T01:52:25.250" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20631" PostTypeId="1" AcceptedAnswerId="20692" CreationDate="2014-08-20T02:17:21.147" Score="13" ViewCount="530" Body="&lt;p&gt;Having recently pulled an &quot;all-nighter&quot; while trying to fix a fatal bug in our release code, I started thinking of any health risks that I might have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the adverse effects of staying up for staying up for 42 hours, considering I took no caffeine or other stimulants, as well as no depressants such as alcohol?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Upon googling I found a lack of facts, what would be good is a list of effects and rough times that they start happening.  And any significant problems I would face, but moreover I would like to know what causes them?  Unfortunately I only studied Biology until GCSE (UK - SAT/TAKS Alternative) and might need some simplified explanations or links to help understand more complex tasks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not even sure if this question is grammatically correct, and my brain power has slowly dwindled, should I be worried?  I have read &lt;a href=&quot;https://biology.stackexchange.com/questions/3817/why-does-non-continuous-sleep-makes-you-feel-tired&quot;&gt;this&lt;/a&gt; and understand it to a vague extend.&lt;/p&gt;&#xA;" OwnerUserId="8832" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2017-08-07T17:46:01.930" Title="What are the effects of sleep deprivation?" Tags="&lt;sleep&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="20632" PostTypeId="1" CreationDate="2014-08-20T03:30:05.050" Score="5" ViewCount="4422" Body="&lt;p&gt;How does &lt;em&gt;E. coli&lt;/em&gt; uptake oxygen? Most of the literature I found is concerned with response to oxygen level supplied in the medium, as opposed to how much is actually transported inside. Can they shut down the oxygen uptake if required? For example, to avoid damaging effects of &lt;em&gt;reactive oxygen species&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There exist bacteria which die in presence of oxygen (strict anaerobe), while some use oxygen when available but also can survive in absence of it (facultative anaerobes, like &lt;em&gt;E. coli&lt;/em&gt;). Are there bacteria which cannot consume oxygen for metabolism, but when exposed to oxygen they don't die, rather simply discard the oxygen and carry out fermentation? In a sense, they are strict anaerobe (their mode of metabolism is anaerobic), but they can still survive in presence of oxygen in environment.&lt;/p&gt;&#xA;" OwnerUserId="1800" LastEditorUserId="1320" LastEditDate="2014-08-20T13:36:25.373" LastActivityDate="2014-10-10T06:54:48.790" Title="What is the mechanism of oxygen uptake in E. coli?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;metabolism&gt;&lt;ecoli&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20633" PostTypeId="1" AcceptedAnswerId="20650" CreationDate="2014-08-20T04:39:06.627" Score="2" ViewCount="88" Body="&lt;p&gt;I read a lot of articles on the internet about how dog see the the world. But I can't find the source of these study. I want to know how did scientist setup the experiment to find out animal vision. I don't know which keyword should I use to search for the information on the internet. Can anybody please send me some research paper about the problem?&lt;/p&gt;&#xA;" OwnerUserId="8834" LastEditorUserId="1320" LastEditDate="2014-08-20T13:32:09.513" LastActivityDate="2014-08-20T22:21:32.837" Title="Where I can find information about the study of animal vision?" Tags="&lt;zoology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20634" PostTypeId="2" ParentId="20632" CreationDate="2014-08-20T05:11:28.530" Score="3" Body="&lt;p&gt;The plasma membrane is quite permeable to oxygen and thus oxygen enters the cell simply by diffusion. Reactive oxygen species can be reduced enzymatically in aerobic organisms. Obligate anaerobes lack or don't produce sufficient quantities of these enzymes. An organism that doesn't use oxygen for metabolism but is also not relatively harmed by it can be classified as aerotolerant.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vEhZK.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Image from: &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Anaerobic_organism&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.m.wikipedia.org/wiki/Anaerobic_organism&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Original Caption: Aerobic and anaerobic bacteria can be identified by growing them in test tubes of thioglycollate broth:&#xA;1: Obligate aerobes need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen concentration is highest.&#xA;2: Obligate anaerobes are poisoned by oxygen, so they gather at the bottom of the tube where the oxygen concentration is lowest.&#xA;3: Facultative anaerobes can grow with or without oxygen because they can metabolise energy aerobically or anaerobically. They gather mostly at the top because aerobic respiration generates more ATP than either fermentation or anaerobic respiration.&#xA;4: Microaerophiles need oxygen because they cannot ferment or respire anaerobically. However, they are poisoned by high concentrations of oxygen. They gather in the upper part of the test tube but not the very top.&#xA;5: Aerotolerant organisms do not require oxygen as they metabolise energy anaerobically. Unlike obligate anaerobes however, they are not poisoned by oxygen. They can be found evenly spread throughout the test tube.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-08-20T05:11:28.530" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20635" PostTypeId="1" CreationDate="2014-08-20T05:50:35.220" Score="3" ViewCount="58" Body="&lt;p&gt;Epitope mapping means identifying the binding site of antibodies on the target antigen. This means that the site to be identified is part of the antigen and not antibody, am I right?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="8835" LastEditDate="2014-08-21T08:13:59.820" LastActivityDate="2014-08-21T08:13:59.820" Title="What does the term 'epitope mapping' mean?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;bioinformatics&gt;&lt;immunology&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2014-08-20T11:50:55.857" ContentLicense="CC BY-SA 3.0" />
  <row Id="20636" PostTypeId="2" ParentId="20541" CreationDate="2014-08-20T10:42:14.837" Score="11" Body="&lt;p&gt;Fatigue on exercise is proportional to unmet demand for oxygen and glucose (sugar/fuel).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In people who are &quot;fat&quot;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;They typically do less exercise. Therefore their cardiovascular system is not conditioned with the heart being able to cope with increased exercise i.e. it is unable to beat more efficiently and instead must beat A LOT more faster to cope consuming more oxygen and glucose. Even at rest, they will typically have a higher resting rate. They also have less efficient muscles (i.e. the muscles themselves can't breakdown energy as well, use it as well and the body isn't as great at picking the right set of muscles)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The fat itself can compress vessels carrying blood. This pressure increases blood pressure. This is worsened by a typical high diet of salt and again by typical lack of exercise. Higher blood pressure means the heart has to beat harder and faster to pump blood around the body&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;They weigh more so each movement requires A LOT more energy. Their resting metabolic rate is higher than a thinner person as is any exercise they do. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;On exercise they do not lose heat fast enough. This impairs the breakdown of glucose and also more energy is required to lose the excess heat&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;They may be subclinically diabetic. Their body may have lots of glucose floating around in the blood but they can't use it because their muscles can't absorb it.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;They have far increased rates of build up of fatty plaques on the blood vessel walls. This narrows the vessels and only multiplies with all the other problems&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Then there's lots of other more minor but very important reasons like psychological (reduced capacity to brave through fatigue), reduced sleep meaning a higher baseline of tiredness (in the extreme side caused by obstructive sleep apnoea), increased rates of smoking (which does millions of things to reduce exercise capacity)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-08-20T10:42:14.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20638" PostTypeId="2" ParentId="20587" CreationDate="2014-08-20T10:59:34.527" Score="1" Body="&lt;p&gt;Yes. Once secreted the shell cannot increase in size, so that the growth of the body is accompanied by continuous growth of the shell, i.e. by the gradual increase in the number of the whorls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This also means that the topmost whorls are the oldest and the aperture marks the front of the new shell.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-08-20T10:59:34.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20639" PostTypeId="1" CreationDate="2014-08-20T11:03:01.170" Score="1" ViewCount="40" Body="&lt;p&gt;I came across three terms in an article on pseudocopulation. However I don't quite understand what it means. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) solitary and haplodiploid&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) social and haplodiploid&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) diploid&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are mentioned in reference to pollinator mating systems in orchids. Could anyone please explain the above mentioned terms?&lt;/p&gt;&#xA;" OwnerUserId="6390" LastEditorUserId="3952" LastEditDate="2014-08-22T01:20:25.393" LastActivityDate="2014-11-20T03:08:08.357" Title="Pollinator mating system in orchids" Tags="&lt;botany&gt;&lt;entomology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20640" PostTypeId="2" ParentId="20633" CreationDate="2014-08-20T12:02:10.037" Score="3" Body="&lt;p&gt;Color vision was shown to be dichromatic (sensitivity to two color peaks) by &lt;a href=&quot;http://www.researchgate.net/profile/Jay_Neitz/publication/20669235_Color_vision_in_the_dog/links/02e7e523a1355b4a00000000&quot; rel=&quot;nofollow&quot;&gt;Neitz et al. (1989)&lt;/a&gt;. For a broader review of color vision of mammals, see &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-185X.1993.tb00738.x/abstract;jsessionid=734488C8E1224B4B3DAECF73D5C68A85.f04t02?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;Jacobs (1993)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Jacobs, G.H. 1993. The distribution and nature of colour vision among the mammals. Biological Reviews 68: 413-471.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neitz, J. et al. 1989. Color vision in the dog. Visual Neuroscience 3: 119-125.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-20T12:02:10.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20641" PostTypeId="2" ParentId="20639" CreationDate="2014-08-20T12:33:19.013" Score="1" Body="&lt;p&gt;As 3cat already stated, the terms actually refer to the pollinators. While &lt;em&gt;solitary&lt;/em&gt; and &lt;em&gt;social&lt;/em&gt; describe the behavioural traits (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Solitary_bee#Solitary_and_communal_bees&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; wikipedia article), &lt;em&gt;diploid&lt;/em&gt; and &lt;em&gt;haplodiploid&lt;/em&gt; give information about the chromosome number of the pollinators (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Diploidy#Diploid&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Haplodiploid&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The descriptions in the article depict different combinations of both characteristics.&lt;/p&gt;&#xA;" OwnerUserId="8015" LastActivityDate="2014-08-20T12:33:19.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20644" PostTypeId="2" ParentId="20632" CreationDate="2014-08-20T16:40:31.200" Score="4" Body="&lt;p&gt;This question got me thinking about what are the metabolic enzymes that take oxygen up in &lt;em&gt;E.coli&lt;/em&gt;. I searched the &lt;a href=&quot;http://biocyc.org/overviewsWeb/celOv.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;metacyc database&lt;/a&gt; for reactions that consume molecular oxygen and there are only 3 that take in oxygen and one that produces oxygen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All three consumers of oxygen in &lt;em&gt;E.coli&lt;/em&gt; are the oxidation of ubiquinone by at two sites in cytochrome-&lt;em&gt;bcl&lt;/em&gt; or by cytochrome-&lt;em&gt;bo&lt;/em&gt;.  All of these export protons to create the gradient that drives ATP formation by F₀F₁ ATPase in the periplasm (the region between &lt;em&gt;E.coli&lt;/em&gt; 's inner and outer membrane). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QpbOE.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the production side, superoxide dismutase reduces superoxide to oxygen to control oxidation damage.  Apparently the innards of &lt;em&gt;E.coli&lt;/em&gt; are somewhat oxygen tolerant.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3340" LastEditDate="2014-10-10T06:16:08.663" LastActivityDate="2014-10-10T06:16:08.663" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20645" PostTypeId="2" ParentId="20537" CreationDate="2014-08-20T18:19:52.360" Score="2" Body="&lt;p&gt;The primer is an universal recruiter, for all DNA polymerases, bringing them to the DNA template. You must have both strands in place for a DNA polymerase to stop by. Moreover, the catalytic activity of all the polymerases requires a preexistent 3' end on the growing strand. You must have a 3' free end near a template, for a DNA polymerase to act. (A far longer description of the chemistry is at &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK22374/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK22374/&lt;/a&gt; .) In contrast, RNA polymerases, including primase, are recruited to the template by DNA-binding proteins, such as ori-binding proteins, transcription factors etc., meaning there is no need for primers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It may make some functional sense too. Once a cell decides to replicates, its ori-binding proteins are synthesized and/or activated. They bind the DNA template, and bring in the primase. Only after the primase does its job, DNA polymerase can take over. The cell needs stringent regulation only at the level of the ori-binding protein, because DNA polymerases are so strongly dependent on the preceding steps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we think in evolutionary terms, and we accept the RNA world hypothesis, the RNA polymerases (or at least their ancestors) should have evolved earlier than the DNA polymerases. In these conditions, the earliest DNA polymerase came in a world where double stranded RNA already existed, meaning it had access to a primed template. There was no immediate need for a primer-independent DNA polymerase, and no urgent need afterwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All these are speculations. There seems to be a primer-independent DNA polymerase in a thermophile bacterium (DOI: 10.1021/bi0489614). Its existence may be interpreted in two opposite ways: ancient mechanism, or recent evolution, forced by the special conditions where these bacteria live. The former will deny almost everything I wrote. &quot;Why?&quot; questions in biology are always tricky.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastActivityDate="2014-08-20T18:19:52.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20647" PostTypeId="1" CreationDate="2014-08-20T20:55:30.133" Score="3" ViewCount="119" Body="&lt;p&gt;I am reading Avi Chaudhuri's &lt;a href=&quot;http://ukcatalogue.oup.com/product/9780195433753.do&quot; rel=&quot;nofollow&quot; title=&quot;Fundamentals of Sensory Perception&quot;&gt;Fundamentals of Sensory Perception&lt;/a&gt; and wondering if the information given about the somatosensory system could tell us anything about the way it evolved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems (at least naively) reasonable to assume that nerves became larger and more myelinated as time went on. The types of somatosensory nerve fibre are (in order from least to most myelinated):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C &amp;lt; A-delta &amp;lt; A-beta &amp;lt; A-alpha&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This gives an ordering on receptors of:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;warm receptors &amp;lt; cold receptors &amp;lt; nociceptors &amp;lt; tactile mechanoreceptors &amp;lt; proprioceptors&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is then: was this the order in which these receptors evolved? If not, can myelination still give us useful information about the evolutionary history of the nervous system?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. Meta question: is this question better suited for the Bio or Cog Sci stack exchange? I asked it here since it seemed to be more about evolution than neurons.&lt;/p&gt;&#xA;" OwnerUserId="8523" LastActivityDate="2014-11-29T00:14:05.687" Title="What can myelination tell you about the evolution of sensory receptors?" Tags="&lt;evolution&gt;&lt;neuroscience&gt;&lt;sensation&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20648" PostTypeId="1" AcceptedAnswerId="20658" CreationDate="2014-08-20T21:00:01.633" Score="2" ViewCount="165" Body="&lt;p&gt;I'm wondering about the effects of different durations and intensities of pain on the body. So the two can be compared, let's say that the cause of pain is the same in both cases, but in one the duration is shorter although the pain is more severe, and vice versa. Also, by effects, I mean biological but also psychological (which is probably more interesting), but the latter might be out of the scope of this site, so forgive me if it is.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the sake of a (rather grim) example, if someone is exposed to a painful stimulus such as a mid-voltage shock for a long duration, and if someone else is exposed to a much higher voltage shock for a much shorter duration of time, which would produce worse effects on the body's normal functioning? (Somewhat morbidly, I should say to assume that they both live and do not die on the spot.) Since the answer very well might depend on the type of harmful stimulus, I'll give another example of a burn. If one is repeatedly subjected to a first-degree burn for a while and another is subjected to a third-degree burn only once, which is worse?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Upon pondering the question, it seems that the psychological effects would be more interesting since they should be roughly the same regardless of the type of stimulus, but biologically the effects obviously differ.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your time, and any responses or thoughts on this would be greatly appreciated.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt; Obviously most experiments to test this would be subjective and unethical, especially in the case of psychological effects, so just an opinion from someone more knowledgeable in biology is more than fine.&lt;/p&gt;&#xA;" OwnerUserId="8840" LastActivityDate="2014-08-21T14:25:22.890" Title="Is severe but short-term pain worse than moderate but prolonged pain for the body?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;pain&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20650" PostTypeId="2" ParentId="20633" CreationDate="2014-08-20T22:09:21.077" Score="2" Body="&lt;p&gt;While their work was in the cat rather than the dog, your starting point should be the work of Hubel and Wiesel.  They are the indisputable pioneers for vision research in general.  They won the Nobel Prize in 1981 for Physiology and Medicine.&lt;/p&gt;&#xA;&lt;p&gt;See their Wikipedia entries (&lt;a href=&quot;http://en.wikipedia.org/wiki/David_H._Hubel&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hubel&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Torsten_Wiesel&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wiesel&lt;/a&gt;), the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359523/pdf/jphysiol01247-0121.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;original 1962 paper&lt;/a&gt;, their &lt;a href=&quot;http://hubel.med.harvard.edu/&quot; rel=&quot;nofollow noreferrer&quot;&gt;popular press book&lt;/a&gt;, the &lt;a href=&quot;http://www.nobelprize.org/nobel_prizes/medicine/laureates/1981/presentation-speech.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nobel Prize speech&lt;/a&gt; about their work and Roger Sperry's, and Wurtz's review (cited below).&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Hubel, D.H. and Wiesel, T.N. (1962). Receptive fields, binocular interaction and functional architecture in the cat's visual cortex, &lt;em&gt;The Journal of Physiology, 160&lt;/em&gt;(1), 106-154.&lt;/p&gt;&#xA;&lt;p&gt;Wurtz, R.H. (2009). Recounting the impact of Hubel and Wiesel. &lt;em&gt;The Journal of Physiology, 587&lt;/em&gt;, 2817-2823. &lt;a href=&quot;http://dx.doi.org/10.1113/jphysiol.2009.170209&quot; rel=&quot;nofollow noreferrer&quot;&gt;DOI&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="57" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-08-20T22:21:32.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20651" PostTypeId="1" CreationDate="2014-08-21T02:36:34.567" Score="2" ViewCount="57" Body="&lt;p&gt;I'm curious how people measure &lt;strong&gt;&lt;em&gt;quantitatively&lt;/em&gt;&lt;/strong&gt; photosynthetic rate in labs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen many qualitative examples with direct observations of bubbles forming in water due to photosynthetic output of aquatic plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ways I have come up with are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;to measure the CO&lt;sub&gt;2&lt;/sub&gt; intake.&lt;/li&gt;&#xA;&lt;li&gt;to measure the O&lt;sub&gt;2&lt;/sub&gt; output.&lt;/li&gt;&#xA;&lt;li&gt;to measure the amount of sugar produced.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The 3rd option seems most trivial, but I don't know how to measure the amount of CO&lt;sub&gt;2&lt;/sub&gt; present in a container. With a reaction? Or with a measuring machine of some sort? What about O&lt;sub&gt;2&lt;/sub&gt;?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastEditorUserId="3340" LastEditDate="2014-11-26T12:26:57.663" LastActivityDate="2014-11-26T15:00:40.523" Title="How can oxygen production during photosynthesis be measured?" Tags="&lt;photosynthesis&gt;&lt;experimental-design&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2014-11-27T02:06:46.137" ContentLicense="CC BY-SA 3.0" />
  <row Id="20652" PostTypeId="1" AcceptedAnswerId="20654" CreationDate="2014-08-21T05:33:55.590" Score="4" ViewCount="2342" Body="&lt;p&gt;What is a protective epitope? An epitope is basically a part of antigen. So does it mean that when the epitope combines with an antibody, it helps in the functioning of the antibody instead of going against it?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="948" LastEditDate="2014-08-22T00:27:16.787" LastActivityDate="2017-07-22T09:35:55.953" Title="What is a protective epitope?" Tags="&lt;molecular-biology&gt;&lt;immunology&gt;&lt;antibody&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20653" PostTypeId="1" AcceptedAnswerId="20655" CreationDate="2014-08-21T08:54:10.513" Score="4" ViewCount="115" Body="&lt;p&gt;In general, for dioecious species, a large portion of the genome passed from parents to offspring of both sexes - in mammals the X-chromosomes and autosomes are passed from a mother to both daughters and sons, and autosomes from the father to both sons and daughters. Only the small amount of genes present in the Y-chromosome and mitochondria are inherited solely within one sex. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any species (not just mammals) where most, or even all, of the genome is inherited in a sex-specific trajectory? What is the most sex-limited genome known to researchers?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="3340" LastEditDate="2014-08-21T09:45:19.793" LastActivityDate="2014-12-10T05:51:02.977" Title="sex limited genome transmission" Tags="&lt;genetics&gt;&lt;sex&gt;&lt;genomes&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20654" PostTypeId="2" ParentId="20652" CreationDate="2014-08-21T09:30:07.483" Score="6" Body="&lt;p&gt;Lets define the nomenclature first: An &lt;a href=&quot;http://en.wikipedia.org/wiki/Antigen&quot; rel=&quot;noreferrer&quot;&gt;antigen&lt;/a&gt; is a large structure (protein, virus, bacteria and so an) which is recognized by the immune system as foreign. The word antigen derives from the abbreviation ANTIbody GENerator. Exposure of our immune system to an antigen results in an immune response and the generation of many antibodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An &lt;a href=&quot;http://en.wikipedia.org/wiki/Epitope&quot; rel=&quot;noreferrer&quot;&gt;epitope&lt;/a&gt; is a small part of an antigen - typically these are small structural elements or small peptides (8-11 amino acids in length) which are recognized by the binding site of an antibody. See the picture below (from &lt;a href=&quot;http://de.wikipedia.org/wiki/Epitop&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4J23O.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here the antigen is the albumin protein. On the surface you can see 8 different epitopes which lead to the generation of 8 highly specific antibodies against the epitopes (antikörper is the german word for antibody). Every antibodies is highly specific for its epitope and will recognize no other epitope and helps raising an immune response against it. What happens after an antibody bound to its epitope can be read &lt;a href=&quot;http://en.wikipedia.org/wiki/Antibody#Function&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antibodies directed against a protective epitope are directed against (highly) conserved structures of the antigen. For example the recognize a highly conserved structure of a virus which means that even when this virus mutates (like influenza does) it will still recognize the conserved epitope and give protection against this virus (or better: antigen).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-08-21T11:42:40.303" LastActivityDate="2014-08-21T11:42:40.303" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="20655" PostTypeId="2" ParentId="20653" CreationDate="2014-08-21T09:42:31.800" Score="2" Body="&lt;p&gt;In birds and reptiles females are the heterogametic sex with allosome configuration &lt;code&gt;ZW&lt;/code&gt;. However it has been &lt;a href=&quot;http://www.newscientist.com/blogs/shortsharpscience/2010/11/boa-constrictors-born-by-virgi.html&quot; rel=&quot;nofollow&quot;&gt;reported&lt;/a&gt; that a homogametic &lt;code&gt;WW&lt;/code&gt; female boa was born by parthenogenesis. So it means that although W is shorter than Z, it can still support life. So I guess that &lt;code&gt;ZW&lt;/code&gt; system in general exchanges more sex-limited genetic material than &lt;code&gt;XY&lt;/code&gt; system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Platypus has 5 pairs of sex chromosomes. See &lt;a href=&quot;http://www.nature.com/nature/journal/v432/n7019/full/nature03021.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. This can qualify as the top case of sex-limited transmission. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-08-21T09:42:31.800" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20656" PostTypeId="1" CreationDate="2014-08-21T11:39:05.327" Score="10" ViewCount="3149" Body="&lt;p&gt;What are the atmospheric requirements for large dinosaurs? and are the atmospheric constituents for supporting large dinosaurs any different from the atmosphere today?&lt;/p&gt;&#xA;" OwnerUserId="8845" LastEditorUserId="1320" LastEditDate="2014-08-21T15:51:33.877" LastActivityDate="2018-07-14T16:34:12.547" Title="What are the atmospheric requirements for large dinosaurs?" Tags="&lt;evolution&gt;&lt;anatomy&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20657" PostTypeId="1" AcceptedAnswerId="20664" CreationDate="2014-08-21T13:34:35.190" Score="49" ViewCount="27197" Body="&lt;p&gt;Some people say that it's awful that humans eat animals.  They feel that it's barbaric, because you're killing life and then on top of that, you're eating it, and that you should eat vegetation instead.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But isn't vegetation life too?  Personally, I see no difference between animals and veg as all life has cells, dna etc&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is, is it possible for humans to live healthy long lives without eating any type of life, i.e no animals, no plants, no cells (dead or alive) etc? If it is possible, how would it be done?&lt;/p&gt;&#xA;" OwnerUserId="668" LastEditorUserId="668" LastEditDate="2014-08-22T15:47:23.280" LastActivityDate="2014-09-10T13:04:21.067" Title="Can humans survive without consuming life?" Tags="&lt;food&gt;&lt;nutrition&gt;&lt;life&gt;&lt;diet&gt;" AnswerCount="11" CommentCount="18" FavoriteCount="19" ClosedDate="2014-08-29T06:53:41.340" ContentLicense="CC BY-SA 3.0" />
  <row Id="20658" PostTypeId="2" ParentId="20648" CreationDate="2014-08-21T14:25:22.890" Score="1" Body="&lt;p&gt;The biological part of the answer to your question depends on the thing causing the pain. Burning for example, a large burn can be very life threatening biologically but small burns are not as harmful comparatively. But the psychological harm they would cause is phenomenal. This is because large burns open up the body to infections, dehydration and a lot of other harm. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's take stabbing as another cause of pain. One stab in a less dangerous place missing all important structures may be not that harmful but may be painful. However multiple small stabs into important structures like arteries or spinal cord could be horribly destructive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then let's look at headaches or nerve pain. Here it is only the pain and usually there isn't any destructive or harmful process. Most individuals would take one really, really bad headache followed by never having a headache then chronic daily &quot;tension&quot; headaches. &#xA;Psychologically though usually the chronic daily pain is the worst. Particularly as without adequate pain management from the start, it is less responsive to painkillers (analgesia). It frequently adds to depression if it does not cause it itself and can lead to suicide. Also painkillers themselves may cause chronic pain which does not help. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, acute severe pain suggests something is seriously wrong and needs to be dealt with immediately biologically as there is likely a damaging process underlying it. However if this event is survived, it may be linked with high disability from any biological process that underpinned the pain. Chronic daily pain suggests a long continuing process. The cause of this may be life threatening, such as cancers, but is usually less dangerous at least compared to acute severe pain biologically. However the psychological aspects of this pain are seriously important as they can be particularly detrimental. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-08-21T14:25:22.890" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20659" PostTypeId="2" ParentId="20657" CreationDate="2014-08-21T14:51:05.873" Score="36" Body="&lt;p&gt;Living organisms can be divided into hetrotrophs and autotrophs. Autotrophs like plants and algae are able to produce complex &lt;em&gt;organic&lt;/em&gt; compounds from relatively simple &lt;em&gt;inorganic&lt;/em&gt; components. They are satisfied with sunlight, water and other abiotic stuff and do not need to consume &quot;life&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We -- along with all other animals -- are not autotrophs, but heterotrophs. This means that we cannot produce organic compounds by ourselves but need to 'reuse' the ones that are produced by autotrophic organisms. That's why no human will ever be able to live without consuming other life.&lt;/p&gt;&#xA;" OwnerUserId="8015" LastEditorUserId="1320" LastEditDate="2014-08-21T18:43:38.570" LastActivityDate="2014-08-21T18:43:38.570" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="20660" PostTypeId="2" ParentId="20657" CreationDate="2014-08-21T16:04:06.407" Score="4" Body="&lt;p&gt;It may be feasible to live without consuming anything that was alive, but it would be incredible difficult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, all humans need to consume glucose to survive. Glucose is the only food source used by cells in the brain. Plants are the easiest source of food source for glucose. If we can't get glucose from plants, then we would need to synthesize it without the aid of enzymes or any sort of organism. A quick google search does not yield any hits for how this synthesis could be performed. Probably because it is so easy to get a plant to make the sugars for us.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now think about all the amino acids, vitamins, fats, and minerals that we would also need to synthesize or extract without any organism intervention.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You have gone from the good intention of not harming another organism to the creation of a whole chemical industry dedicated to the production of nutrients for people.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think about this as well. When you poop, a lot of the poop is actually dead bacteria that was living in your gut. &lt;/p&gt;&#xA;" OwnerUserId="8849" LastActivityDate="2014-08-21T16:04:06.407" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="20661" PostTypeId="2" ParentId="20657" CreationDate="2014-08-21T16:29:54.627" Score="9" Body="&lt;p&gt;Depends on how you define &quot;life&quot;? Is unfertilized chicken eggs alive?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about cow milk? Well there are bacteria in it. What if you get rid of that bacteria? Then some people would not be able to utilize lactose...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also as &lt;code&gt;Bez&lt;/code&gt; mentioned rice grains are quiescent, meaning they are in a dormant state and not really &quot;alive&quot; but again depends on how you define &quot;life&quot;. Even top biologist have trouble defining &quot;life&quot; and there exist many competing definitions of &quot;life&quot;. All of them have their advantages and disadvantages, but there is no universal definition of life on which all biologists would agree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you consider everything above as &quot;life&quot; then it is not really possible for humans to survive without consuming other life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If only we could sustain chloroplasts in our epidermis layer we would be able to synthesize sugars for ourselves. But then we would become little green men...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it is much better to respect your meat. Whenever you eat meat just be conscious that something had to die to produce that meat. Be grateful for that lost life and realize that part of it will live in you.&lt;/p&gt;&#xA;" OwnerUserId="8850" LastEditorUserId="8850" LastEditDate="2014-08-21T16:44:08.597" LastActivityDate="2014-08-21T16:44:08.597" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20662" PostTypeId="2" ParentId="20653" CreationDate="2014-08-21T16:43:19.650" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there any species (not just mammals) where most, or even all, of the genome is inherited in a sex-specific trajectory?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here are a bunch of cases and specific examples that may interest you&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;There is a species of ants where both genders evolve to be able to reproduce by parthenogenesis (which means that males might be call females as well). In this species, the two genders mate together to create workers that do not reproduce! Therefore, when you look at the phylogenetic tree you can see that males and females are on two totally separate branches as there is reproductive isolation between the sexes in terms of fertile offspring. There is an article by L. Keller on the subject.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In the amazon molly, there are no males. But it is interesting because females need sperm to start the development of their ovules although they don't even use the genetic material of the sperm. Therefore, the amazon mollies need to find mates in sister species. In consequence, they imitate the females of the other species. There is a recent article from Hanna Kokko that investigate with a mathematical model how such system may be able (not cause the extinction of the amazon molly or of the sister species).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Sex-specific segregation distorter. Nasonia sp. may be an interesting case study&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Haplo-diploidy. In ants for example, sons receive genetic material from their mother only. They are haploid.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;if the rate of sexual reproduction is different from 1 then, females are responsible for more than half of the inherited genes in the next generation.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I apologize for the lack of references $\ddot \smile$&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-12-10T05:51:02.977" LastActivityDate="2014-12-10T05:51:02.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20663" PostTypeId="1" CreationDate="2014-08-21T16:51:15.877" Score="6" ViewCount="1124" Body="&lt;p&gt;I imagine this could be used as a universal Identifier.&lt;/p&gt;&#xA;" OwnerUserId="8483" LastActivityDate="2014-08-21T22:03:31.280" Title="Is there a known minimal stretch of DNA that can distinguish any two people in the world?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;dna-sequencing&gt;&lt;genomics&gt;&lt;human-genome&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20664" PostTypeId="2" ParentId="20657" CreationDate="2014-08-21T18:05:13.063" Score="53" Body="&lt;p&gt;The answer to your question is &lt;strong&gt;yes&lt;/strong&gt; it is certainly possible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At one time it was thought that there was something special about &quot;organic&quot; chemicals which meant that they could not be artificially synthesised out of fundamental elements. In 1828 Frederick Wöhler synthesised urea (CO(NH&lt;sub&gt;2&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;) which is often taken as the first demonstration that the organic v inorganic distinction was not a sound one (for more on this see the &lt;a href=&quot;https://en.wikipedia.org/wiki/W%C3%B6hler_synthesis&quot;&gt;Wikipedia article on Wöhler synthesis&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as we know all essential human nutrients can be synthesised from inorganic ingredients, even complex molecules such as Vitamin B&lt;sub&gt;12&lt;/sub&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other contributors have pointed out that organic pathways for synthesising our food have evolved over long periods to be very efficient - at least in the conditions prevailing on Earth. You haven't ruled out copying biochemical pathways using chemicals that are entirely of inorganic origin. Anyone trying to do this seriously could create glucose (for example) by artificially creating enzymes (perhaps via artificial DNA) to do the job. The thing is that we already have self-replicating and repairing machines to do that already (plants).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There might be circumstances when we needed to use artificial synthesis. I can think of two science-fiction stories that deal with this question, the first of which goes into some detail:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/The_Moon_Is_Hell!&quot;&gt;The Moon is Hell&lt;/a&gt; by John W. Campbell, in which astronauts are stranded on the moon and forced to make food from what they find there.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Technical_Error&quot;&gt;Technical Error&lt;/a&gt; by Arthur C. Clarke, in which a man is accidentally rotated through the fourth dimension. His employers contemplate the difficulty caused by the &quot;handedness&quot; of many biological molecules meaning they would have to artificially synthesise many of his foods.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It may be that a future expedition to Mars (say) might have to think about these things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A little searching fails to come up with standard inorganic syntheses of glucose and similar substances. The reason for this is almost certainly because it is so easy to use organic inputs. Glucose is easily made by the hydrolysis of starch. Starch is very common and cheap. Even l-glucose is usually made out of organically derived precursors (or sometimes even using d-glucose).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE: sources etc&lt;/strong&gt;&#xA;One problematic question is: where do you get your input for making nutrients? As others have pointed out, exactly where to draw the line is difficult. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This problem starts in defining what is alive in the first place. Do you count viruses (which can go down to a few thousand base pairs of RNA) or satellite viruses (STobRV has only 359 base pairs) or prions? In a sense these are &quot;just&quot; very large molecules. But then really simple bacteria are not many orders of magnitude more complex. As an aside most systems of ethics that do not permit eating meat do not make an alive/non-alive distinction, choosing some other aspect such as sentience, though Jainism comes close to doing so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second problem is, if we reject living things as sources of food, how far removed from those living things are we allowed to get? You say no cells in any state including &quot;dead&quot;. That would exclude (say) fruit even though most fruits are expressly created by plants in order to be eaten (and in some cases must be eaten) - something that vegans, jains, fruitarians and others would be happy with eating. If we could use dead material things would be much easier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But would you also include hydrocarbons (coal, oil, gas) which were once living organisms? If you do, then you are in difficulty because terrestrial carbon is recycled through the biosphere. All CO2 was (to a close approximation) once a part of a living thing. If you take that position then of course you are going to have to go off-planet to find your source chemicals and your problem becomes very much harder.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was assuming that you were restricting yourself to consuming cells that retain some of their cell structure but had not completely degraded. If that is where you draw the line then there are ample sources of raw materials on earth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetic modification is much more science fiction though not entirely impossible. Some nutrients could be made by humans without much difficulty. Our inability to manufacture vitamin C is down to one missing enzyme (L-gulono-gamma-lactone oxidase) which is present in most vertebrates (I think of mammals only guinea pigs, humans and some bats are unable to synthesise it). You could certainly imagine some very careful genetic modification changing humans so they no longer need to consume vitamin C.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But photosynthesis would be much harder. Chloroplasts (which do the job in most plants) are really a very primitive form of life living in plant cells which may independently reproduce  (and for that reason might be excluded by you - they aren't &quot;cells&quot; but they have membranes). They could easily end up in conflict with our mitochondria (since intracellular conflict between organelles is possible) and you would need to do enormous amounts of work to make human cells co-operate with them properly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More in keeping with your theme would be adding photosynthetic systems directly to human cells along with a suite of enzymes to manufacture all the things we cannot. That is of course in principle scientifically possible (since plants do it) but much harder than it looks. Living systems are very complicated and small changes can have unexpected consequences. Even very minor genetic modifications are problematic. The human autotroph is likely to be some way off.&lt;/p&gt;&#xA;" OwnerUserId="8853" LastEditorUserId="-1" LastEditDate="2014-08-25T22:40:48.623" LastActivityDate="2014-08-25T22:40:48.623" CommentCount="16" ContentLicense="CC BY-SA 3.0" />
  <row Id="20665" PostTypeId="1" CreationDate="2014-08-21T18:09:34.053" Score="13" ViewCount="695" Body="&lt;p&gt;I've read that CRISPR/Cas9 is currently being implemented and tested for its ability to edit genomes in live cells, and that it is supplanting other genome editing tools in labs, such as TALENs and Zinc finger nucleases.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that there may be a few metrics used for analyzing any genome editing system.  One is the efficiency, which could be measured perhaps in edits per time or edits per molecule.  Another metric might be error-rate.  What is the probability that a genome is altered in something other than the intended way?  Another metric might be the length of the genome that may be edited at once.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've also read that CRISPR/Cas9 evolved in bacteria.  When did CRISPR/Cas9 evolve in the history of life on earth? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If CRISPR/Cas9 evolved in bacteria, and before other evolutionary advances, including some of those that may have enabled certain multiceullar forms of life, I have to wonder if other systems like CRISPR/Cas9 but superior to it in some metric evolved as well.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does recombination in sexual reproduction work?  Might it involve biomolecular machinery like that of CRISPR/Cas9?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does the adaptive immune system work?  How does VDJ recombination work?  Does it involve an advanced (relative to CRISPR/Cas9) genome editing system?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How might one estimate the probability that a system superior to CRISPR/Cas9 exists already?&lt;/p&gt;&#xA;" OwnerUserId="160" LastEditorUserId="160" LastEditDate="2014-08-26T19:16:35.693" LastActivityDate="2019-08-13T12:17:01.893" Title="When did CRISPR/Cas9 evolve and what is the likelihood that a superior system for live cell genome editing has already evolved on earth since then?" Tags="&lt;evolution&gt;&lt;molecular-biology&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20666" PostTypeId="2" ParentId="20663" CreationDate="2014-08-21T18:26:06.783" Score="4" Body="&lt;p&gt;When designing PCR primers we typically use a minimum length of 20 bases, because the probability of a sequence of N bases appearing by random is $\frac{1}{4^N}$, and $\frac{1}{4^{20}}$ is about 9x$10^{-13}$, or about 1 in a trillion. Since the human genome is a little over 3 billion bases long, a 20 base sequence should appear only once. However, most of an individual's DNA isn't random, it's inherited from their parents, and they got their's from their parents, etc. Long story short, there isn't a lot of unique DNA in any given person. The uniqueness is only visible on the large scale, you have half of your DNA from your father, and half from your mother. So would any of your siblings, but the specific DNA they got from each parent would be different from yours.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think we can calculate the odds of getting a specific set of chromosomes from a parent. If there are 23 pairs of chromosomes, then the probability of getting any given set should be $\frac{1}{2^{23}}$, since we have 2 parents, the odds of getting your specific set of DNA is $(\frac{1}{2^{23}})^2$, which is about 1 in 70 trillion. So the odds of you having a non-identical twin that has the same DNA as you is very low. But any given 20 base sequence should have a 50% probability of appearing in you and the sibling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if we look at 2 20 base sequences of DNA in you and your sibling, and each had a 50% chance of appearing, then the probability of both sequences appearing in the both of you is 25%. If we add a third, it goes to 12.5%, and so on. If there are 7 billion humans on earth, we need a probability of less than 1 in 7 billion, and $2^{33}$ is about 8.6 billion, so if you looked at 33 different sites on the genome it should be able to differentiate you from every human on the planet&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, did I do the math right? I'm not a mathmagician and I could have made a mistake in my probability calculations. I have also assumed that the spontaneous mutation rate and crossing over rates are low enough to ignore, but both would serve to make your DNA a little more unique.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2014-08-21T20:31:55.233" LastActivityDate="2014-08-21T20:31:55.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20667" PostTypeId="2" ParentId="20653" CreationDate="2014-08-21T18:57:23.930" Score="1" Body="&lt;p&gt;The new mexico whiptail reproduces purely through parthenogenesis. The species itself originates as a hybrid of two other species of whiptail, but the hybridization can't make fertile males. The females can reproduce through parthenogenesis so that's how the species continues to exist. So 100% of the genome is passed mother to daughter for many generations, very few new mexico whiptails are made through a fresh hybridization of the parental species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cnemidophorus_neomexicanus&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Cnemidophorus_neomexicanus&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-21T18:57:23.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20668" PostTypeId="1" CreationDate="2014-08-21T19:20:07.343" Score="5" ViewCount="838" Body="&lt;p&gt;I've noticed different functions in different R libraries have different ways of assessing significance for Blomberg's K. For instance, picante's phylosignal looks at a distribution of PIC variance values from shuffled trait values to assess significance; when phytool's phylosig calculates a null distribution of Blomberg K values for shuffled traits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the interpretative difference between the two and when should one approach be used over another? And what does it mean if the observed Blomberg's K is greater than 1 (traits less similar than expected under Brownian Motion model of evolution), but significantly greater (or less) than the null distribution of Blomberg's K-values?&lt;/p&gt;&#xA;" OwnerUserId="8856" LastActivityDate="2014-08-23T22:46:33.400" Title="Null distribution of Blomberg's K" Tags="&lt;ecology&gt;&lt;phylogenetics&gt;&lt;community-ecology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20669" PostTypeId="1" CreationDate="2014-08-21T19:25:45.407" Score="5" ViewCount="1409" Body="&lt;p&gt;Gram negative bacteria perform oxidative phosphorylation in their periplasmic regions, between the inner and outer membrane where a proton gradient is maintained and used by the ATP synthase to make ATP.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gram positive bacteria do not have a second membrane, but only a porous polysaccharide capsule.  Oxidative phosphorylation then would on try to pump protons to the outside of the bacterium and it could diffuse out into the surrounding environment.  Does this cause gram positive bacteria to operate less efficiency?  does it make them more vulnerable to a basic pH in their environment? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XABEf.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-08-22T01:07:22.873" Title="Is oxidative phosphorylation less efficient in gram positive bacteria?" Tags="&lt;respiration&gt;&lt;phosphorylation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20670" PostTypeId="2" ParentId="20657" CreationDate="2014-08-21T19:51:52.763" Score="2" Body="&lt;p&gt;It is entirely possible to live without consuming life using only current technology.  In fact, there is a company called &lt;a href=&quot;http://www.soylent.me/&quot; rel=&quot;nofollow&quot;&gt;Soylent&lt;/a&gt; which has developed a food substituent designed to replace all eating, entirely.  The philosophy of that company is that &amp;ndash; food is just a collection of chemicals for the body to process, and that as long as the body gets all of the necessary chemicals, it will survive fine. That is exactly what soylent aims to do &amp;ndash; the powdered mix they produced has all the chemicals necessary for human life. &lt;/p&gt;&#xA;" OwnerUserId="8859" LastEditorUserId="6928" LastEditDate="2014-08-23T11:48:28.937" LastActivityDate="2014-08-23T11:48:28.937" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20671" PostTypeId="2" ParentId="20657" CreationDate="2014-08-21T20:41:03.000" Score="7" Body="&lt;p&gt;Question: Is it possible for humans to live healthy long lives without eating any type of life, i.e no animals, no plants?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, according to a &lt;a href=&quot;http://www.biology-online.org/dictionary/Living_thing&quot; rel=&quot;nofollow&quot;&gt;definition of a living organism&lt;/a&gt;(biology-online), milk is not live, because it does not have an ability to reproduce itself, among other...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My claim: If you consider milk and honey non-live (no DNA), then, yes, humans can survive for some time by consuming only these, and water. An example are infants, who can live exclusively on human breast milk and water for more than 1 year.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is &lt;a href=&quot;http://nutritiondata.self.com/facts/dairy-and-egg-products/95/2&quot; rel=&quot;nofollow&quot;&gt;human milk composition&lt;/a&gt; (Nutritiondata), from which you can see it contains all &lt;a href=&quot;http://www.nutrientsreview.com/glossary/essential-nutrients&quot; rel=&quot;nofollow&quot;&gt;essential nutrients&lt;/a&gt; (Nutrientsreview) (essential amino acids, fatty acids, vitamins and probably all essential minerals - not all essential minerals are listed in Nutritiondata milk composition, though).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But to actually prove that humans can or cannot &quot;live healthy long lives&quot; by consuming only milk and honey, one would need to do a human trial...and I'm not aware of any.&lt;/p&gt;&#xA;" OwnerUserId="4025" LastEditorUserId="4025" LastEditDate="2014-08-22T11:15:41.170" LastActivityDate="2014-08-22T11:15:41.170" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20672" PostTypeId="2" ParentId="20657" CreationDate="2014-08-21T21:54:23.103" Score="14" Body="&lt;p&gt;Your question is phrased somewhat ambiguously as to whether you're asking about the theoretical possibility, the feasibility, or the practical ability in everyday life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1) Theoretically, yes.&lt;/strong&gt; It is chemically possible to produce all substances that humans need to survive without the use of living organisms in the process. In the end, biological systems use chemical processes, so at the very least it would be possible to isolate the biological (enzymatic) machinery and use it without the live organism around it. The latter is within current biotechnological capabilities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2) Feasibly, no.&lt;/strong&gt; Going through the hassle of making all those substances in that way would probably be less efficient than simply using the biological (live) systems that already exist and are very efficient at it - in particular, plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;3) Practically, no.&lt;/strong&gt; Using only currently commercially available products (i.e. things you could buy right now), you will probably not be able to source a full human diet without relying on some live organism at some point in its production exactly because of number (2) above.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2014-08-21T21:54:23.103" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20673" PostTypeId="2" ParentId="20663" CreationDate="2014-08-21T22:03:31.280" Score="5" Body="&lt;p&gt;Here is what the data says. UK government must have had some scientific evidence when it settled on a 10 variable-length sections of genome for their database, SGM+. In one such variable sections, some people have 10 repeats of CTTT, others have 11, others have 12 etc. The largest of those fragments, at its maximum length, are about 350 base pairs. The US government uses 13 such variable-length sequences for its CIA database, called CODIS. On both sides of the Atlantic, roughly 3-4 thousand base pairs were judged to be enough, with some safety margin, by the most advanced geneticists in the world, working on public money.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The catch is that these variable length sequences are disjoint, so you end up requiring far more than 4,000 bp. If you need these markers on the same DNA strand (chromosome), you should space them by 50 centimorgans, at which distance they recombine independently. But according to &lt;a href=&quot;http://www.sciencemag.org/site/feature/data/genomes/265-5181-2094.pdf&quot; rel=&quot;noreferrer&quot;&gt;http://www.sciencemag.org/site/feature/data/genomes/265-5181-2094.pdf&lt;/a&gt; , the longest chromosome only has 350-400 centimorgan. It means you cannot get 10 independent DNA sequences on a human chromosome, be it the longest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I predict there is no such continuous DNA stretch, that would tell apart any two non-twins. Since it is much better to use multiple chromosomes in DNA fingerprinting, I doubt you will find more relevant experimental data.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastActivityDate="2014-08-21T22:03:31.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20674" PostTypeId="1" AcceptedAnswerId="20693" CreationDate="2014-08-21T22:33:59.460" Score="1" ViewCount="243" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19336412&quot; rel=&quot;nofollow&quot;&gt;NCBI&lt;/a&gt;, type I REases have a specific target sequence but randomly make cuts at sites far from the target sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does the restriction enzyme travel from the target sequence to the distant site of restriction, and what is the point of having a target sequence if the cuts are random and far away from the target sequence?&lt;/p&gt;&#xA;" OwnerUserId="5179" LastEditorUserId="1320" LastEditDate="2014-08-22T11:59:08.327" LastActivityDate="2014-08-22T11:59:08.327" Title="How do Type I restriction enzymes work?" Tags="&lt;restriction-enzymes&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20675" PostTypeId="1" AcceptedAnswerId="20676" CreationDate="2014-08-21T23:40:49.527" Score="4" ViewCount="635" Body="&lt;p&gt;I have photographed the following plant in our garden in Pittsburgh, PA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you know the name of the plant?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pySUH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KDVLs.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kdjjz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9hdLk.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8014" LastActivityDate="2014-08-22T00:02:30.177" Title="What is the name of this big plant with a purple trunk and green to purple berries?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ClosedDate="2014-08-22T22:10:17.727" ContentLicense="CC BY-SA 3.0" />
  <row Id="20676" PostTypeId="2" ParentId="20675" CreationDate="2014-08-22T00:02:30.177" Score="3" Body="&lt;p&gt;The plant looks like &lt;a href=&quot;http://extension.umass.edu/landscape/weeds/phytolacca-americana&quot; rel=&quot;nofollow&quot;&gt;Pokeweed (&lt;em&gt;Phytolacca americana&lt;/em&gt;)&lt;/a&gt; to me, a common &quot;weed&quot; in the U.S.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-22T00:02:30.177" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20677" PostTypeId="2" ParentId="20656" CreationDate="2014-08-22T00:19:18.683" Score="8" Body="&lt;p&gt;Oxygen levels have changed greatly throughout Earths's history starting with very little atmospheric oxygen and gradually increasing as photosynthetic activity appeared until all the oxygen sinks such as minerals had been filled, then taking off, reaching as high as 35% of the atmosphere during the carboniferous period &lt;a href=&quot;https://en.wikipedia.org/wiki/Geological_history_of_oxygen&quot; rel=&quot;nofollow noreferrer&quot;&gt;3&lt;/a&gt;. The reasons behind this sudden increase in O₂ has to do with the development of bark covered wooden plants, a feature made possible by the molecule lignin, which strengthens the trunks of trees and makes tall plants possible. However, lignin was hard for microbes to digest, and the dead trees built up, never returning their carbon to the atmosphere as CO₂. So the oxygen they had made while alive stayed in the air &lt;a href=&quot;https://en.wikipedia.org/wiki/Lignin&quot; rel=&quot;nofollow noreferrer&quot;&gt;4&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KbciR.png&quot; alt=&quot;Graph of O2 in atmosphere over time&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The plot shows the upper (red) and lower (green) estimates for O₂ concentration over time. The data for this plot was taken from a review of analysis of sulfur, carbon, iron, and manganese deposits &lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/361/1470/903.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;. If you're interested in how isotopic analysis can give information about atmospheric oxygen, read that paper, it's detailed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That spike in the plot is the carboniferous. This period in history is interesting because of the appearance of large invertebrates, such as 3 foot wide dragonflies and 6 foot long centipedes &lt;a href=&quot;https://en.wikipedia.org/wiki/Carboniferous&quot; rel=&quot;nofollow noreferrer&quot;&gt;5&lt;/a&gt;. Since these animals move oxygen through a series of tubes called trachea, where air just moves through by diffusion, it was speculated that the higher concentration of oxygen allowed this growth. Recent research indicates that insects can force air through their trachea, and that competition between predators and prey could have explained most of the size &lt;a href=&quot;https://en.wikipedia.org/wiki/Protodonata&quot; rel=&quot;nofollow noreferrer&quot;&gt;6&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how does this affect dinosaurs? The carboniferous period was about 350-300 million years ago, which corresponds with the spike on the graph. Dinosaurs appeared in the Triassic, which was about 250-200 million years ago, but oxygen levels were at 16% of the atmosphere at the time &lt;a href=&quot;https://en.wikipedia.org/wiki/Triassic&quot; rel=&quot;nofollow noreferrer&quot;&gt;7&lt;/a&gt; ( current O₂ levels are about 20% ) If we move into the Jurassic, about 200-150 million years ago, oxygen levels rise to about 26% &lt;a href=&quot;https://en.wikipedia.org/wiki/Jurassic&quot; rel=&quot;nofollow noreferrer&quot;&gt;8&lt;/a&gt;. In the Cretaceous, about 150-65 million years ago, O₂ was at about 30% &lt;a href=&quot;https://en.wikipedia.org/wiki/Cretaceous&quot; rel=&quot;nofollow noreferrer&quot;&gt;9&lt;/a&gt;. The O₂ percentages are taken from the infoboxes on the right side of the wikipedia articles, which in turn take the number from a plot very similar to the plot I posted here, despite being in German &lt;a href=&quot;https://en.wikipedia.org/wiki/File:Sauerstoffgehalt-1000mj.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;10&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I compiled lists of heaviest and lightest dinosaurs by going through the wikipedia article on dinosaur size &lt;a href=&quot;https://en.wikipedia.org/wiki/Dinosaur_size&quot; rel=&quot;nofollow noreferrer&quot;&gt;11&lt;/a&gt; and going to the article on each dinosaur and checking if it was Triassic, Jurassic, or Cretaceous.&#xA;If we look at the heaviest dinosaurs, most of them appeared during the Cretaceous:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Heaviest Dinosaurs          &#xA;Theropods                           Metric Tons     Period&#xA;Spinosaurus aegyptiacus             7-20.9          Cretaceous&#xA;Carcharodontosaurus saharicus       6.1-15.1        Cretaceous&#xA;Giganotosaurus carolinii            6.1-13.8        Cretaceous&#xA;Tyrannosaurus rex                   6-9.5           Cretaceous&#xA;Oxalaia quilombensis                5-7             Cretaceous&#xA;Acrocanthosaurus atokensis          5.6-6.2         Cretaceous&#xA;Tyrannotitan chubutensis            4.9-5.6         Cretaceous&#xA;Suchomimus tenerensis               2.7-5.2         Cretaceous&#xA;Therizinosaurus cheloniformis       5               Cretaceous&#xA;Tarbosaurus bataar                  4-5             Cretaceous&#xA;&#xA;Sauropods                           Metric Tons     Period&#xA;Amphicoelias fragillimus            122.4           Jurassic&#xA;Argentinosaurus huinculensis        60-90           Cretaceous&#xA;Antarctosaurus giganteus            69-80           Cretaceous&#xA;Mamenchisaurus sinocanadorum        75              Jurassic&#xA;Sauroposeidon proteles              40-60           Cretaceous&#xA;Paralititan stromeri                59              Cretaceous&#xA;Brachiosaurus altithorax            28.7-56.3       Jurassic&#xA;Puertasaurus reuili                 50              Cretaceous&#xA;Ruyangosaurus giganteus             50              Cretaceous&#xA;Alamosaurus sanjuanensis            50-60           Cretaceous&#xA;Futalognkosaurus dukei              38.1-50+        Cretaceous&#xA;Turiasaurus riodevensis             40-50.9         Jurassic/Cretaceous&#xA;Camarasaurus supremus               47              Jurassic&#xA;Diplodocus hallorum                 30-42.5         Jurassic&#xA;Supersaurus vivianae                32-40.2         Jurassic&#xA;Elaltitan lilloi                    42.9            Cretaceous&#xA;Tehuelchesaurus benitezii           41.3            Jurassic&#xA;Apatosaurus louisae                 18-41.3         Jurassic&#xA;&#xA;Ornithopods                         Metric Tons     Period&#xA;Shantungosaurus giganteus           9.9-22.5        Cretaceous&#xA;Iguanodon seeleyi                   15              Cretaceous&#xA;Saurolophus angustirostris          6.6-9           Cretaceous&#xA;Iguanodon bernissartensis           8.3-8.6         Cretaceous&#xA;Edmontosaurus annectens             3.2-7.6         Cretaceous&#xA;Brachylophosaurus canadensis        4.5-7           Cretaceous&#xA;Saurolophus osborni                 6.6             Cretaceous&#xA;Lanzhousaurus magnidens             6               Cretaceous&#xA;Parasaurolophus walkeri             3-5.1           Cretaceous&#xA;Charonosaurus  jiayinensis          5               Cretaceous&#xA;Barsboldia sicinskii                5               Cretaceous&#xA;&#xA;Ceratopsians                        Metric Tons     Period&#xA;Triceratops horridus                5-14            Cretaceous&#xA;Triceratops prorsus                 6.5-11          Cretaceous&#xA;Titanoceratops ouranos              6.5-11          Cretaceous&#xA;Eotriceratops xerinsularis          10              Cretaceous&#xA;Pentaceratops sternbergii           3-4.8           Cretaceous&#xA;Pachyrhinosaurus canadensis         3-4.4           Cretaceous&#xA;Styracosaurus albertensis           4.2             Cretaceous&#xA;Agujaceratops mariscalensis         2.6             Cretaceous&#xA;Centrosaurus apertus                1.1-2.5         Cretaceous&#xA;Coronosaurus brinkmani              2               Cretaceous&#xA;Rubeosaurus ovatus                  2               Cretaceous&#xA;Achelousaurus horneri               2               Cretaceous&#xA;Pachyrhinosaurus lakustai           2               Cretaceous&#xA;Chasmosaurus belli                  2               Cretaceous&#xA;&#xA;Thyreophorans                       Metric Tons     Period&#xA;Dacentrurus armatus                 5-7.4           Jurassic&#xA;Ankylosaurus magniventris           1.7-6           Cretaceous&#xA;Stegosaurus stenops                 2.6-5.3         Jurassic&#xA;Cedarpelta bilbeyhallorum           5               Cretaceous&#xA;Hesperosaurus mjosi                 3.5-5           Jurassic&#xA;Tuojiangosaurus multispinus         4.8             Jurassic&#xA;Wuerhosaurus homheni                4               Cretaceous&#xA;Niobrarasaurus coleii               4               Cretaceous&#xA;Stegosaurus ungulatus               3.5             Jurassic&#xA;Gobisaurus domoculus                3.5             Cretaceous&#xA;Nodosaurus textilis                 3.5             Cretaceous&#xA;Palaeoscincus costatus              3.5             Cretaceous&#xA;Sauropelta edwardsi                 3               Cretaceous&#xA;Edmontonia rugosidens               3               Cretaceous&#xA;Edmontonia schlessmani              3               Cretaceous&#xA;Edmontonia longiceps                2.3-3           Cretaceous&#xA;Tuojiangosaurus multispinus         2.8             Jurassic&#xA;Euoplocephalus tutus                2-2.7           Cretaceous&#xA;Jiangjunosaurus junggarensis        2.5             Jurassic&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This isn't exactly a fair way to do it, but I didn't want to calculate average dinosaur mass over time. I know that some groups, such as the ceratopsians didn't appear until the late Jurassic, skewing the results, and I didn't make any attempt to differentiate between late or early periods. However I also noticed that many of the smallest dinosaurs appeared in the Cretaceous as well. Pay attention to the units, even the smallest sauropods are measured in metric tons.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Lightest Dinosaurs&#xA;Theropods                           kg              Period&#xA;Parvicursor remotus                 0.137           Cretaceous&#xA;Epidexipteryx hui                   .164-.391       Jurassic&#xA;Compsognathus longipes              0.26            Jurassic&#xA;Ceratonykus oculatus                0.3             Cretaceous&#xA;Juravenator starki                  0.34-0.41       Jurassic&#xA;Ligabueino andesi                   0.35            Cretaceous&#xA;Microraptor zhaoianus               0.4             Cretaceous&#xA;Sinosauropteryx prima               0.55-0.99       Cretaceous&#xA;Rahonavis ostromi                   0.58            Cretaceous&#xA;Mahakala omnogovae                  0.76-0.79       Cretaceous&#xA;Xiaotingia zhengi                   0.79            Jurassic&#xA;Mei long                            0.85            Cretaceous&#xA;Microraptor gui                     0.95-1.50       Cretaceous&#xA;&#xA;Sauropods                           Metric Tons     Period&#xA;Pleurocoelus nanus                  0.5             Cretaceous&#xA;Magyarosaurus dacus                 0.75            Cretaceous&#xA;Europasaurus holgeri                0.8-1           Jurassic&#xA;Bonatitan reigi                     1               Cretaceous&#xA;Lapparentosaurus madagascariensis   1.4             Jurassic&#xA;Lessemsaurus sauropoides            1.8             Triassic&#xA;Lirainosaurus astibiae              1.8-4           Cretaceous&#xA;Shunosaurus lii                     2.2-6.7         Jurassic&#xA;Ampelosaurus atacis                 2.5             Cretaceous&#xA;Amargasaurus cazaui                 2.6-3.8         Cretaceous&#xA;Hypselosaurus priscus               2.7-8           Cretaceous&#xA;Euhelopus zdanskyi                  3.4             Cretaceous&#xA;Neuquensaurus australis             3.5-6.1         Cretaceous&#xA;Rinconsaurus caudamirus             4.1             Cretaceous&#xA;Atacamatitan chilensis              4.3             Cretaceous&#xA;Dicraeosaurus hansemanni            4.4-5           Jurassic&#xA;&#xA;Ornithopods                         kg              Period&#xA;Gasparinisaura cincosaltensis       1-13            Cretaceous&#xA;Yueosaurus tiantaiensis             3.9             Cretaceous&#xA;Fulgurotherium australe             6               Cretaceous&#xA;Notohypsilophodon comodorensis      6               Jurassic&#xA;Yandusaurus hongheensis             6.6-7.5         Jurassic&#xA;Hypsilophodon foxii                 7-21            Cretaceous&#xA;Thescelosaurus sp.                  7.9-86          Cretaceous&#xA;Valdosaurus canaliculatus           10              Cretaceous&#xA;Haya griva                          11              Cretaceous&#xA;Agilisaurus louderbacki             12              Jurassic&#xA;Drinker nisti                       20              Jurassic&#xA;Changchunsaurus parvus              20              Cretaceous&#xA;Qantassaurus intrepidus             20              Cretaceous&#xA;Zephyrosaurus schaffi               20              Cretaceous&#xA;Oryctodromeus cubicularis           20              Cretaceous&#xA;Orodromeus makelai                  20              Cretaceous&#xA;&#xA;Ceratopsians                              kg        Period&#xA;Liaoceratops yanzigouensis                2         Cretaceous&#xA;Yamaceratops dorngobiensis                2         Cretaceous&#xA;Psittacosaurus sinensis                   4.1       Cretaceous&#xA;Psittacosaurus lujiatunensis              5         Jurassic&#xA;Yinlong downsi                            5.5       Cretaceous&#xA;Micropachycephalosaurus hongtuyanensis    5.9       Jurassic&#xA;Chaoyangsaurus youngi                     6         Jurassic&#xA;Xuanhuaceratops niei                      6         Jurassic&#xA;Bagaceratops rozhdestvenskyi              7         Cretaceous&#xA;Psittacosaurus meileyingensis             8         Cretaceous&#xA;Psittacosaurus neimongoliensis            8-8.4     Cretaceous&#xA;Archaeoceratops oshimai                   10        Cretaceous&#xA;Psittacosaurus mongoliensis               12.1-20   Cretaceous&#xA;Psittacosaurus sibiricus                  15        Cretaceous&#xA;&#xA;Thyreophorans                       kg              Period&#xA;Scutellosaurus lawleri              3               Jurassic&#xA;Emausaurus ernsti                   50              Jurassic&#xA;Scelidosaurus harrisonii            64.5-270        Jurassic&#xA;Animantarx ramaljonesi              300             Cretaceous&#xA;Struthiosaurus transylvanicus       300             Cretaceous&#xA;Struthiosaurus austriacus           300             Cretaceous&#xA;Gargoyleosaurus parkpinorum         300             Jurassic&#xA;Mymoorapelta maysi                  300             Jurassic&#xA;Minmi paravertebra                  300             Cretaceous&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So what does this mean for the relationship between oxygen levels and dinosaur size? Higher oxygen levels in the Jurassic and Cretaceous probably allowed for larger animals to exist, however as time went on Dinosaurs became more diverse in general, including size. Many of them evolved to become smaller, despite being allowed to become larger by higher levels of oxygen. We should also note that even though oxygen levels were still lower than they were during the carboniferous, the animals were much larger, most likely due to their more efficient oxygen transport systems (lungs, 3(4?) chambered hearts, sealed circulatory systems, hemoglobin).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we think about what could drive species to become larger, competition for food and protection from predators comes to mind. Sauropods that could reach the leaves in taller trees had distinct advantages over those who could not. Prey animals stood a better chance at fighting off predators if they were bigger. Likewise, predators could kill larger prey if they became larger too. Oxygen didn't drive them to become larger, it simply allowed them to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To actually answer the question, could the modern atmosphere support animals as large as dinosaurs? It probably could. The heaviest living animal today is the blue whale, at an average mass of 110 metric tons, is heavier than all but 1 of the sauropods on the list I compiled. The heaviest land animal living today is the African Elephant, with average mass of 4.9 metric tons and as high as 10 metric tons, would be a respectable competitor with many of the dinosaur groups I listed &lt;a href=&quot;https://en.wikipedia.org/wiki/Largest_organisms&quot; rel=&quot;nofollow noreferrer&quot;&gt;12&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another interesting question is not how oxygen affected the size of organisms, but how it affects it their metabolism. Cold blooded animals don't need as much oxygen because they don't spend as much energy. Warm blooded animals must constantly expend energy to maintain body heat, and this requires greater consumption of oxygen. Obviously being large and warm blooded would force you to need even greater levels of oxygen than 1 or the other. It may be that the advantages of being warm blooded outweighed the advantages of large size, but I don't want to dig into that question right now.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="3340" LastEditDate="2014-10-09T16:54:20.680" LastActivityDate="2014-10-09T16:54:20.680" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20678" PostTypeId="1" AcceptedAnswerId="20680" CreationDate="2014-08-22T00:27:32.957" Score="6" ViewCount="387" Body="&lt;p&gt;During a pit stop on the road from North Carolina to New York (somewhere in Delaware) I found the following (dead) insect in the car park:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QLlZM.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see from the quarter next to it (25 mm diameter) it is rather large - maybe six centimeters, including the &quot;horns&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What was it?&lt;/p&gt;&#xA;" OwnerUserId="8668" LastEditorUserId="8668" LastEditDate="2014-08-22T00:30:00.907" LastActivityDate="2014-08-22T00:55:59.293" Title="What is this beetle?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20679" PostTypeId="1" CreationDate="2014-08-22T00:28:20.780" Score="4" ViewCount="326" Body="&lt;p&gt;I live in the midwestern United States.  I cycle to work, sometimes on heavily wooded roads, and I can't help but notice that in most places within the surrounding deciduous forests Pine and evergreen trees don't seem to be doing so well - the few that exist don't look too happy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In some places, however, there are majestic stands of pines - often completely free of the &quot;seasonal&quot; variety of trees.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is this?  What allows the slow growing pines to out-compete the other arboreal denizens of the forest?  And generally in such particular areas?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks, this is killin' me... &lt;/p&gt;&#xA;" OwnerUserId="8866" LastEditorUserId="16866" LastEditDate="2018-11-01T01:08:19.137" LastActivityDate="2019-02-17T04:27:00.587" Title="Why do pine stands exist?" Tags="&lt;botany&gt;&lt;ecology&gt;&lt;trees&gt;&lt;community-ecology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="20680" PostTypeId="2" ParentId="20678" CreationDate="2014-08-22T00:49:57.367" Score="7" Body="&lt;p&gt;Looks like it must be a male &lt;em&gt;Dynastes tityus&lt;/em&gt; (Linnaeus, 1763).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are photos for comparison, and a full description with maps and some interesting notes on habitat and behavior, on the University of Nebraska State Museum &lt;a href=&quot;http://museum.unl.edu/research/entomology/Guide/Scarabaeoidea/Scarabaeidae/Dynastinae/Dynastinae-Tribes/Dynastini/Dynastes/D-tityus/Dtityus.html&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Generic Guide to New World Scarab Beetles&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-08-22T00:55:59.293" LastActivityDate="2014-08-22T00:55:59.293" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20681" PostTypeId="2" ParentId="20669" CreationDate="2014-08-22T01:07:22.873" Score="5" Body="&lt;p&gt;A similar question was already answered at &lt;a href=&quot;https://biology.stackexchange.com/questions/16258/how-do-gram-bacteria-use-a-proton-gradient-for-f-type-atpase&quot;&gt;How do Gram + bacteria use a proton gradient for F-type ATPase?&lt;/a&gt; . In those answers, there is a general belief that Gram negative bacteria do not have much control over their intermembrane space pH, because their outer membranes have many porins, such as OmpC, which allows free passage both ways for protons and other molecules smaller than 600 daltons. If that is true, there is not much of a difference between Gram positive and Gram negative ability to control pH just outside the inner membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a long review at DOI: 10.1016/j.bbamem.2005.09.010 . The first two examples of pH sensitivity are E. coli (divides more slowly when pH goes from 7 to 8.7) and B. subtilis (divides more slowly when pH goes from 7 to 8.5). The first is Gram-negative, the second is Gram-positive. B. subtilis undergoes growth arrested at pH 9, suggesting it might be more sensitive, but again, the difference is just subtle.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastActivityDate="2014-08-22T01:07:22.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20682" PostTypeId="1" CreationDate="2014-08-22T01:21:39.440" Score="4" ViewCount="641" Body="&lt;p&gt;I'm considering the idea of drinking water that I &lt;a href=&quot;https://en.wikipedia.org/wiki/Condensation_trap&quot; rel=&quot;nofollow&quot;&gt;trap from what is transpired by trees&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, is this water a fairly (or maybe even extraordinarily) pure form of H₂O, a remarkably pure by-product of the respiration / evapotranspiration processes - so does the process give off a fairly distilled form of water into the atmosphere - or is there actually a fairly measurable amount of trace elements that also are transpired in that water through the leaves?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A second complication which would be good to clarify, is that even if minerals / other chemicals are excreted along with the H₂O, would condensing that water in a water trap still only collect the pure H₂O anyway?&lt;/p&gt;&#xA;" OwnerDisplayName="user3362" LastActivityDate="2015-06-28T03:29:37.507" Title="Is the water transpired by plants pure H₂O, or does it contain trace minerals?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20683" PostTypeId="1" AcceptedAnswerId="20713" CreationDate="2014-08-22T02:47:54.093" Score="7" ViewCount="2148" Body="&lt;p&gt;I was watching a &lt;a href=&quot;https://www.youtube.com/user/crashcourse&quot; rel=&quot;noreferrer&quot;&gt;Crash Course on Biology&lt;/a&gt; YouTube video by Hank Green: &lt;a href=&quot;https://www.youtube.com/watch?v=WVrlHH14q3o&quot; rel=&quot;noreferrer&quot;&gt;Great Glands - Your Endocrine System&lt;/a&gt;.  Hank humorously describes a sex determination experiment by &lt;a href=&quot;http://en.wikipedia.org/wiki/Alfred_Jost&quot; rel=&quot;noreferrer&quot;&gt;Alfred Jost&lt;/a&gt; as follows (beginning at time 9.17 in the video):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;So, he, ah, very carefully... very, very carefully (and this is a little disturbing) removed bunny embryos from their mother, and then, also very carefully, removed the part that would become the ovaries or the testes from the bunny embryos.  And then, also very carefully, he put the embryos back in the momma rabbit.&lt;/p&gt;&#xA;&lt;p&gt;What Jost found, after the bunnies were born, was that the ones that he performed the surgery on turned out to be girls.  So, in the absence of gonads, and therefore hormones that specifically instructed the development of testes and the growth of a pee-pee and a deep bunny voice, he discovered that the default setting for mammalian embryos is &amp;quot;make it female&amp;quot;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Q&lt;/strong&gt;: How did Alfred Jost actually perform this experiment?&lt;/p&gt;&#xA;&lt;p&gt;Essentially I'm after a less superficial description of how Jost implemented this experiment in practice.&lt;/p&gt;&#xA;&lt;p&gt;I did a bit of Googling; what I found was consistent with Hank's description, but still omits a description of &lt;em&gt;how&lt;/em&gt; Jost excised rabbit embryo gonads (instead just asserting that he did it).&lt;/p&gt;&#xA;" OwnerUserId="5611" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2017-03-31T06:50:35.100" Title="Alfred Jost's rabbit experiment: how did he actually do it?" Tags="&lt;human-genetics&gt;&lt;lab-techniques&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20684" PostTypeId="2" ParentId="20657" CreationDate="2014-08-22T02:55:11.593" Score="20" Body="&lt;p&gt;Even on a purely synthetic diet, your body would still use living cells as an energy source. Our bodies contain more bacterial cells than human, mostly contained in our gut. These microbes process any nutrients we ingest and when they die, we absorb their cellular components as nutrition. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lining of the gut is the most rapidly dividing population of cells in the body. Unlike skin cells, when these die, our intestines recycle much of this as nutrition. Throughout the rest of our bodies, when a cell dies, its components are recycled: red and white blood cells, mucosal membranes, invading microbes, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you kiss, engage in intercourse, there's also an exchange of living cells which die in the process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abstaining from organic food, human contact will not stop the fundamental processes of autophagy, apoptosis, digestion, cell turnover of both our own and microbial cells. &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-24T06:59:44.633" LastActivityDate="2014-08-24T06:59:44.633" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20687" PostTypeId="2" ParentId="17361" CreationDate="2014-08-22T04:16:25.573" Score="0" Body="&lt;p&gt;I don't think any of the answers here are quite right, so I'll give a try:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(A) The resting membrane potential of -70 mV would not change with either GABA or glutamate treatments.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer here is:  &quot;It depends&quot;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For glutamate, if the neuron only had NMDA receptors that were not &quot;open&quot; at -70 mV, there would be no change in resting membrane potential. If there were at least some AMPA receptors, though, the membrane potential would change to more positive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For GABA, if the cell has only GABAa receptors, then the resting membrane potential wouldn't change, because the reversal potential for GABAa is right there at -70 mV.  But if the cell had at least some GABAb receptors, their reversal potential is around -100 mV, and so would cause a change in the resting membrane potential to something more negative than -70 mV.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(B) The membrane potential would be even more negative than resting phase with GABA treatment.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, if GABAa receptors only, then no, it would be no more negative and would in fact stay the same at -70 mV.  If there are GABAb receptors, then yes, the resting membrane potential would be even more negative.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(C) The membrane potential would be positive when the neuron was exposed to glutamate.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe--it depends on whether the neuron is allowed to have an action potential. Glutamate receptors generally reverse around 0 mV.  0 mV is neither positive nor negative. If there were no action potential in this neuron, we should therefore not say the membrane would be &quot;positive&quot; (though this is splitting hairs, I suppose). However it could be said to be &quot;more positive than -70 mV&quot;. However, if the cell were allowed to have an action potential, then yes, the membrane potential would shoot up to about +20 mV, so could be said to be positive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(D) The membrane potential would be more negative than resting potential after glutamate treatment.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No. Again, glutamate receptors' reversal potential is about 0 mV, so it would only move the membrane potential to more positive values, close to or right at 0 mV.&lt;/p&gt;&#xA;" OwnerUserId="587" LastEditorUserId="587" LastEditDate="2014-08-22T04:28:42.627" LastActivityDate="2014-08-22T04:28:42.627" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20688" PostTypeId="2" ParentId="20657" CreationDate="2014-08-22T08:13:06.943" Score="4" Body="&lt;p&gt;Well, technically if you are eating something from a plant or animal without killing that plant or animal, then technically you would not be &quot;consuming life&quot; as nothing as been killed. Fruits, for example, can be removed from the tree without harming it and in fact are meant to be removed as that is how the tree reproduces. Ditto with berries, melons, squash, cucumbers, peppers, beans, seeds, nuts, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for animal products I think only milk and honey would qualify as technically an egg is a future animal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes, I would say that it is completely possible to live a healthy life without once killing another living thing.&lt;/p&gt;&#xA;" OwnerUserId="8879" LastActivityDate="2014-08-22T08:13:06.943" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20689" PostTypeId="2" ParentId="16899" CreationDate="2014-08-22T09:29:49.770" Score="4" Body="&lt;p&gt;You can try the R package &lt;a href=&quot;http://cran.r-project.org/web/packages/dendextend/&quot; rel=&quot;nofollow&quot;&gt;dendextend&lt;/a&gt;. The function &lt;code&gt;tanglegram&lt;/code&gt; can do the trick.  Several associated functions are also available for getting plots with minimum entanglements such as &lt;code&gt;untangle_step_rotate_2side&lt;/code&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8884" LastActivityDate="2014-08-22T09:29:49.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20690" PostTypeId="2" ParentId="20679" CreationDate="2014-08-22T09:45:22.373" Score="2" Body="&lt;p&gt;In nature, species compete for resources like water, light, nutrients, etc. and need to find 'their place' in this struggle. According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Ecological_niche&quot; rel=&quot;nofollow noreferrer&quot;&gt;niche theory&lt;/a&gt;, every species occupies a certain spot in the multidimensional niche space (the dimensions describe the number of environmental factors) where it performs better than any other species. If there would not be such a place, the species is doomed to extinction in free nature.&#xA;Let's look at the pine (Kiefer) and the beech (Buche), a common european deciduous tree:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Fk8zO.jpg&quot; alt=&quot;competition between pine (=Kiefer) and beech (=Buche)&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You see that the beech outcompetes the pine under intermediately moist conditions, although these conditions are theoretically best suited for the pine  (physiological optimum). However, the pine can outcompte the beech at the extremes of the gradient (ecological optimum). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now imagine many environmental factors and many species. Under the predominant conditions in the midwest USA, deciduous tree species are favored over confifers because they are the better competitors. If conditions change towards the more extreme (very dry/moist, harsh climate,...), the pine gains the upper hand and forms large stands.&lt;/p&gt;&#xA;" OwnerUserId="8015" LastEditorUserId="19468" LastEditDate="2018-10-31T18:59:14.787" LastActivityDate="2018-10-31T18:59:14.787" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="20691" PostTypeId="2" ParentId="20585" CreationDate="2014-08-22T10:10:12.017" Score="3" Body="&lt;p&gt;The existence of the G-spot remains highly debated among researchers.  Two recent publications (&lt;a href=&quot;http://www.ajog.org/article/S0002-9378(01)15335-4/abstract&quot; rel=&quot;nofollow&quot;&gt;Hines 2001,&lt;/a&gt; &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1743-6109.2011.02623.x/abstract;jsessionid=9A8FFD67816AD8F62367685771328013.f02t02&quot; rel=&quot;nofollow&quot;&gt;Kilchevsky et al. 2012&lt;/a&gt;) review studies of the so-called G-spot and conclude the evidence is too inconsistent to claim its definite existence.  &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1743-6109.2009.01231.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Foldes and Buisson (2009)&lt;/a&gt; argue that the G-spot is actually just a clitoris that is richly  innervated. This would be consistent with the reported variability of G-spot presence or absence due to natural variation in innervation among women. (This last statement is my hypothesis offered without citation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As noted by @Armatus in the comments, a few minutes following some of the Wikipedia links to the scientific journals (not the BBC, CNN, pop news sites, etc.) would give you lots of information about the G-spot. Still, I thought you question was worth typing up a brief answer for the sake of completeness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Foldès, P. and O. Buisson. 2009. The clitoral complex: a dynamic sonographic study. The Journal of Sexual Medicine 6: 1223–31.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hines T. 2001. The G-Spot: A modern gynecologic myth. American Journal of Obstetrics and Gynecology 185: 359–62.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kilchevsky, A, et al. 2012. Is the Female G-Spot Truly a Distinct Anatomic Entity? Journal of Sexual Medicine. 719-726.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-22T10:10:12.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20692" PostTypeId="2" ParentId="20631" CreationDate="2014-08-22T10:31:48.693" Score="11" Body="&lt;p&gt;&lt;strong&gt;24 Hour Mark&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The consequences of sleep deprivation at 24 hours is comparable to the cognitive impairment of someone with a blood-alcohol content of 0.10 percent, according to a 2010 study in the International Journal of Occupational Medicine and Environmental Health.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;36 Hours&lt;/strong&gt;      &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now your health begins to be at risk. High levels of inflammatory markers are in the bloodstream, said Cralle, which can eventually lead to cardiovascular disease and high blood pressure. Additionally, hormones are affected — your emotions can be all over the place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;48 Hours&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After two days of no sleep, the body begins compensating by shutting down for microsleeps, episodes that last from half a second to half a minute and are usually followed by a period of disorientation. “The person experiencing a microsleep falls asleep regardless of the activity they are engaged in,” she said. Microsleeps are similar to blackouts, and a person experiencing them is not consciously aware that they're occurring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;72 Hours&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Expect significant deficits in concentration, motivation, perception, and other higher mental processes after many sleepless hours, Cralle said. “Even simple conversations can be a chore,” noted Kelley. This is when the mind is ripe for hallucinations. Kelley recalled a time he was on guard duty and repeatedly saw someone standing with a rifle in the woods, ready to sneak into camp. Upon closer inspection, he determined he was actually looking at a branch and shadows.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch/?v=pwNMvUXTgDY&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sleep: Why We Need It and What Happens Without It - SciShow&lt;/a&gt; from &lt;a href=&quot;https://biology.stackexchange.com/users/8733/humza-zaidi&quot;&gt;Humza Zaidi's&lt;/a&gt; &lt;a href=&quot;https://biology.stackexchange.com/questions/20631/what-are-the-effects-of-sleep-deprivation#comment32511_20631&quot;&gt;comment&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8832" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2017-02-08T00:49:33.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20693" PostTypeId="2" ParentId="20674" CreationDate="2014-08-22T11:42:23.533" Score="3" Body="&lt;p&gt;To answer your last question first: as long as a restriction enzyme recognises a specific sequence then goes on to cut the DNA it really doesn't matter where the cut takes place, as long as the invading DNA is destroyed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;https://en.wikipedia.org/wiki/Restriction_enzyme&quot; rel=&quot;nofollow&quot;&gt;WP page on restriction enzymes&lt;/a&gt; provides a useful summary of the various classes of restriction enzyme, and led me to a review about Type I enzymes &lt;a href=&quot;http://mmbr.asm.org/content/64/2/412.long&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unlike the familiar Type II enzymes, Type I enzymes require ATP, which they use to power their movement along the DNA, once they have been activated by binding their recognition sequence. The HsdR subunit of the enzyme (R, M and S subunits) contains sequence motifs which mark it out as being related to DNA helicases, which, of course, are able to translocate along a duplex and unwind the duplex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One particularly striking demonstration of the DNA translocation ability of EcoK1 (a Type I enzyme) is described in &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Davies &lt;em&gt;et al.&lt;/em&gt; (1999) The DNA translocation and ATPase activities of restriction-deficient mutants of EcoKI. J. Molec. Biol. &lt;strong&gt;292&lt;/strong&gt;: 787-796 doi:10.1006/jmbi.1999.3081&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The experiments are based upon the mechanism by which phage T7 injects DNA into &lt;em&gt;E. coli&lt;/em&gt; cells.  The phage ejects about 850 bp of the 40 kb genome into the host; the entry of the bulk of the DNA is coupled to transcription, first by host  RNA polymerase, and subsequently by the phage-specific RNA polymerase, once the corresponding gene has entered the cell. If the drug rifampin is used to block transcription then the whole process stalls. This block is overcome if the initial leader of 850 bp is engineered to contain a recognition sequence for EcoK1 whereupon the restriction enzyme is able to translocate the entire genome into the cell at 100 - 200 bp per second. Mutations in the helicase motifs of the HsdR subunit abolish this activity.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-08-22T11:42:23.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20694" PostTypeId="1" CreationDate="2014-08-22T12:06:59.993" Score="2" ViewCount="301" Body="&lt;p&gt;I am interested to know the process of development of puberty. During puberty, when boys/girls reache 12-14 (puberty) years of their age, their hypothalamus releases gonadotropin releasing hormone (GnRH) and then this hormone in turn affects the pituitary gland which releases FSH and LH. FSH/LH hormones promote male/female features. For e.g. girls start their first menstruation cycle and males start to produce sperm; their voices become smooth and intense respectively. So all these phenomena are dependent on GnRH.My question is that if those hormones are produced due to the effect of GnRH then how is GnRH production itself regulated. In other words how does our body &quot;know&quot; that we are in the age of puberty and it should secrete GnRH?        &lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="3340" LastEditDate="2014-08-22T13:15:23.250" LastActivityDate="2014-09-21T16:23:56.860" Title="What triggers the release of gonadotrophin-releasing hormone with the onset of puberty?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20695" PostTypeId="2" ParentId="9537" CreationDate="2014-08-22T12:52:35.607" Score="1" Body="&lt;p&gt;There are no reports for it yet. I don't think just because they show overall homology, they would exhibit crosstalk. Just see the alignment of the DNA binding domains of these proteins first ~70 residues from N-terminal. Moreover their DBDs belong to different PFAM families.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly with the promoter sequences.&#xA;As reported in iGEM website:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Mnt promoter: &lt;code&gt;tagatctcctatagtgagtcgtattaattt&lt;/code&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;cI promoter: &lt;code&gt;gtgttgactattttacctctggcggtgata&lt;/code&gt;    &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;They are quite different.&#xA;Moreover, if iGEM has a reported standard part such as a bistable system component: Mnt/cI promoter (&lt;a href=&quot;http://parts.igem.org/wiki/index.php?title=Part%3aBBa_K228003&quot; rel=&quot;nofollow&quot;&gt;BBa_K228003&lt;/a&gt;) then it would have been pretty much standardized. iGEM parts are usually reliable.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-08-22T12:52:35.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20696" PostTypeId="1" CreationDate="2014-08-22T13:23:57.593" Score="2" ViewCount="522" Body="&lt;p&gt;I have got an estimate of sperm head volume from internet.Like consider it as a disk of order 4-5µm. Now I wanted to find the DNA density in the sperm head. How to find that? &lt;/p&gt;&#xA;" OwnerUserId="5669" LastEditorUserId="3340" LastEditDate="2014-10-10T07:22:53.377" LastActivityDate="2014-10-10T07:22:53.377" Title="How to estimate the DNA density in human sperm head?" Tags="&lt;cell-biology&gt;&lt;homework&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2014-10-10T14:14:42.737" ContentLicense="CC BY-SA 3.0" />
  <row Id="20697" PostTypeId="1" AcceptedAnswerId="20698" CreationDate="2014-08-22T14:02:34.787" Score="2" ViewCount="576" Body="&lt;p&gt;I was wondering why establishment of cDNA library required the step of reverse transcription (i.e. turning the sequence into DNA) why not directly using the extracted RNA for sequencing and converting the U to T base? Why bother to have one more step? super super confusing&lt;/p&gt;&#xA;" OwnerUserId="8889" LastActivityDate="2014-08-22T14:12:57.243" Title="Regarding the difference between cDNA library and RNA sequencing (Biochem. technique)" Tags="&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20698" PostTypeId="2" ParentId="20697" CreationDate="2014-08-22T14:12:57.243" Score="1" Body="&lt;p&gt;The construction of a cDNA library involves making a DNA 'copy' of the mRNA because the aim is to synthesise a large set of recombinant plasmid molecules, each containing a different cDNA and each propagated in E. coli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heyday of cDNA library construction predates the invention of PCR. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key difference between the two approaches that you are comparing is that one (cDNA library) involves creation of a physical representation of the expressed genome whereas the other is an informational representation.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-08-22T14:12:57.243" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20699" PostTypeId="2" ParentId="20696" CreationDate="2014-08-22T14:20:21.910" Score="4" Body="&lt;p&gt;Find, or calculate, a value for the volume of the sperm head.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Find a value for the size of the human genome (haploid or diploid?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Convert the genome size, which will probably in Giga basepairs, into mass (I suggest picograms).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Divide mass by volume to get a density, pg &amp;mu;m&lt;sup&gt;-3&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Refinement - does the sperm nucleus take up all of the head volume? Do you need to factor this in?&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-08-22T14:20:21.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20701" PostTypeId="1" AcceptedAnswerId="20741" CreationDate="2014-08-22T14:32:24.583" Score="4" ViewCount="224" Body="&lt;p&gt;I was wondering can multiple HIV virus infecting same T cell ?&#xA;Coz in flu virus they have SA to cleave of those sialic acid residue preventing re-infection of the same cell by other viruses to maximize the amount of cell get infected.&#xA;I was wondering is there any mechanism found in HIV virus like what found in flu virus to prevent re-infection of an already HIV-infected T cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(little bit more about HIV virus that is irrelevant to the question, coz i was told that there is some HIV possible to hide in our body, but then i don't understand what it is the meaning of this hiding? Q1:Is the &quot;hiding&quot; refer to the genome of HIV that integrated into T cell. some of these infected T cells circulating in the blood Q2: will some of them reside in lymph node? Q3: and what make these infected B cell proliferate so to keep these B cell with the hiv genome long existing? will the virus transform these T cells into self proliferating? but will that be like cancer cell uncontrollably proliferating or well controlled?) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you everybody &lt;/p&gt;&#xA;" OwnerUserId="8889" LastEditorUserId="8889" LastEditDate="2014-08-22T14:49:52.930" LastActivityDate="2015-10-22T19:28:01.930" Title="multiple HIV infection in same T cell" Tags="&lt;immunology&gt;&lt;virology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20702" PostTypeId="1" AcceptedAnswerId="20729" CreationDate="2014-08-22T15:11:18.797" Score="6" ViewCount="1169" Body="&lt;p&gt;I saw this foto &lt;a href=&quot;http://www.reddit.com/r/mildlyinteresting/comments/2e7vw2/a_friend_found_a_pink_grasshopper_while_working/&quot; rel=&quot;nofollow noreferrer&quot;&gt;on Reddit&lt;/a&gt; recently:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ZWcwj.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this possible? How can a grasshopper become like this? Is this just natural genetic mutation?&lt;/p&gt;&#xA;" OwnerUserId="1224" LastActivityDate="2014-09-02T07:03:49.507" Title="(How) can a pink grasshopper exist?" Tags="&lt;genetics&gt;&lt;entomology&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20703" PostTypeId="1" CreationDate="2014-08-22T15:30:57.903" Score="4" ViewCount="28418" Body="&lt;p&gt;Breathing rate and heart rate are directly connected. This is because the heart is connected to the lungs via the pulmonary artery.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I first thought that breathing rate would be half of the heart rate since half of the heart cycle occurs in the lungs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I know that is not true with a normal 12 BPM(breaths per minute) breathing rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what is the ratio of breathing rate to heart rate?&lt;/p&gt;&#xA;" OwnerUserId="5851" LastActivityDate="2019-04-30T09:53:48.970" Title="What is the ratio of breathing rate to heart rate?" Tags="&lt;cardiology&gt;&lt;pulmonology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20704" PostTypeId="5" CreationDate="2014-08-22T15:39:07.433" Score="0" Body="&lt;p&gt;Pulmonology is a branch of medicine concerned with the anatomy, physiology, and pathology of the lungs and . Questions related to breathing rate, respiratory disease, and other questions related to the respiratory system should have this tag.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.acponline.org/patients_families/about_internal_medicine/subspecialties/pulmonology/&quot; rel=&quot;nofollow&quot;&gt;http://www.acponline.org/patients_families/about_internal_medicine/subspecialties/pulmonology/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5851" LastEditorUserId="107" LastEditDate="2014-08-22T21:48:41.110" LastActivityDate="2014-08-22T21:48:41.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20705" PostTypeId="4" CreationDate="2014-08-22T15:39:07.433" Score="0" Body="The study of the respiratory system and diseases of it, especially the lungs" OwnerUserId="5851" LastEditorUserId="5851" LastEditDate="2014-08-22T22:09:50.897" LastActivityDate="2014-08-22T22:09:50.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20706" PostTypeId="1" AcceptedAnswerId="20708" CreationDate="2014-08-22T15:40:49.887" Score="2" ViewCount="158" Body="&lt;p&gt;Although I am admittedly not anywhere near an expert on any topic, I still have a hard time understanding how Black Death and Bubonic plague are one in the same. Since plague still exists, with news stories about it every once in a while, and especially in places like India, why doesn't it spread with anywhere near the rate it did during the Middle Ages?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously global society in general is much more sanitary than it was then, people also tend not to live in close quarters with animals today as they did then, however in places like rural India and China this lifestyle still takes place and plague still exists, so why aren't there large out breaks of plague in these areas if it indeed is Black Death?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible that Black Death has been miscategorised due to various historical circumstances and scholarly errors? &lt;/p&gt;&#xA;" OwnerUserId="8891" LastEditorUserId="8891" LastEditDate="2014-08-22T15:47:29.053" LastActivityDate="2014-08-23T00:26:39.060" Title="Why isn't Bubonic Plague as virulent as it once was?" Tags="&lt;bacteriology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20707" PostTypeId="2" ParentId="20694" CreationDate="2014-08-22T15:52:25.107" Score="1" Body="&lt;p&gt;GnRH-secreting neurons are not fully independent. To date, their most studied regulators are kisspeptin-secreting neurons. During childhood, kisspeptin-secreting neurons are off, due to GABAergic higher level structures and to lack of free leptin. So both brain and body fat have a word on it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Caveat: most of the evidence is circumstantial (for example, higher circulating kisspeptin in naturally occurring precocious puberty) and I am oversimplifying, so the picture is more complex and will become even more so.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastActivityDate="2014-08-22T15:52:25.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20708" PostTypeId="2" ParentId="20706" CreationDate="2014-08-22T16:06:52.130" Score="4" Body="&lt;p&gt;The identification of the Black Death with plague is now fairly well-established - see &lt;a href=&quot;http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1001134&quot; rel=&quot;nofollow&quot;&gt;this paper (open access)&lt;/a&gt; in which PCR and protein detection were used to detect the presence of &lt;em&gt;Yersina pestis&lt;/em&gt; in human skeletons from plague-related mass graves across Europe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Outbreaks of plague do occur in rural environments, see this &lt;a href=&quot;http://www.who.int/csr/don/archive/disease/plague/en/&quot; rel=&quot;nofollow&quot;&gt;WHO page&lt;/a&gt; for some details. The WHO plays a role in responding to these outbreaks, as long as they are notified by the relevant countries. Plague infections respond well to antibiotic treatment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There has also been a &lt;a href=&quot;http://www.vice.com/read/the-hot-zone-0000414-v21n8&quot; rel=&quot;nofollow&quot;&gt;recent outbreak in Madagascar&lt;/a&gt;. According to the epidemiologists we are still in the midst of the 3rd plague pandemic, which started in China in the mid 19th century.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-08-22T16:06:52.130" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20709" PostTypeId="1" AcceptedAnswerId="20715" CreationDate="2014-08-22T16:08:01.010" Score="12" ViewCount="2966" Body="&lt;p&gt;A vast majority of humans get at least some grey hair as they age. As far as I know this applies to both genders and all races. Presumably this means that at least some grey haired humans have noticeable reproductive advantage, or maybe they had it in the recent past.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Theoretically, because this feature is so prevalent, there must be a strong evolutionary pressure to keep it. Am I right? If so, what is it?&lt;/p&gt;&#xA;" OwnerUserId="8894" LastEditorUserId="1590" LastEditDate="2014-10-10T10:28:30.670" LastActivityDate="2018-11-10T10:49:25.593" Title="Why has grey hair evolved?" Tags="&lt;genetics&gt;&lt;human-genetics&gt;&lt;natural-selection&gt;" AnswerCount="5" CommentCount="7" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20711" PostTypeId="2" ParentId="20682" CreationDate="2014-08-22T16:51:57.557" Score="1" Body="&lt;p&gt;It will depend a bit on the specimen of tree / plant that is doing the transpiration. Minerals will typically stay behind during evaporation, but volatile compounds (think the minty smell of Eucalyptus) would evaporate at the same time as the water, and might condense (in some concentration) at the same time as well; this will depend a bit on the temperature of the leaf, the relative humidity of the air (lower will favor evaporation - higher means there is a lot of moisture already in the air, and you don't necessarily know where it came from) and the temperature of the surface used for condensation (lower condensation temperature will trap things besides water).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note - this is more a physicist's answer than a biologist's... betraying my background here.&lt;/p&gt;&#xA;" OwnerUserId="8668" LastActivityDate="2014-08-22T16:51:57.557" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20712" PostTypeId="2" ParentId="20703" CreationDate="2014-08-22T19:42:14.283" Score="5" Body="&lt;p&gt;&quot;This is because the heart is connected to the lungs via the pulmonary artery.&quot; It's not like heart rate or breathing rate are regulated by pulmonary arteries. The relation is more sophisticated than that. For example heart rate is controlled by nerves and hormones, and neither comes straight from the lung. But fast breathing leads to changes in blood oxygen and pH, which are picked up by sensors such as the carotid body, which informs the medulla, which then talks to the sinoatrial node. There is also more direct influence, because ample breathing increases pressure in the thorax.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But at each step, there are many other factors interfering, meaning the correlation between the two gets ever looser. There isn't really a &quot;normal&quot; ratio of heart rate to respiration rate. There is a healthy heart rate and a healthy respiratory rate, but they are both wide intervals (60-100 and 12-20, respectively). Dividing one by the other, you get a very wide interval, from 60 beats per minute / 20 breaths per minute = &lt;strong&gt;3&lt;/strong&gt;, to 100 beats per minute / 12 breaths per minute = &lt;strong&gt;8&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps in practice the most common values for beats per breath are in a narrower interval. But &quot;normal&quot; values are defined in relationship to abnormal conditions, and there is no disease in which a change in this ratio is a cardinal feature. It makes little sense for clinicians to define a normal range for beats per breath, and therefore it makes little sense for epidemiologists to estimate most common values.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastEditorUserId="8809" LastEditDate="2014-08-23T04:10:27.393" LastActivityDate="2014-08-23T04:10:27.393" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="20713" PostTypeId="2" ParentId="20683" CreationDate="2014-08-22T21:11:03.813" Score="5" Body="&lt;p&gt;Check out Fig. 7 in the document at &lt;a href=&quot;http://ipubli-inserm.inist.fr/bitstream/handle/10608/4343/MS_1991_3_263.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://ipubli-inserm.inist.fr/bitstream/handle/10608/4343/MS_1991_3_263.pdf&lt;/a&gt; . The caption says: &quot;Castration of a 23 day fetus. [Mother's] womb is open, the rear end of the fetus is pulled out, a flank incision is performed, and the testicle, located on the mesonephros, is exposed, then cut. After bilateral testicular removal, the fetus is re-placed in the womb. [..] For ease of explanation, an older fetus is in fact shown.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iDYeR.png&quot; alt=&quot;Figure 7 from the linked document&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8809" LastEditorUserId="5611" LastEditDate="2014-08-23T01:25:16.563" LastActivityDate="2014-08-23T01:25:16.563" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20715" PostTypeId="2" ParentId="20709" CreationDate="2014-08-22T21:52:38.657" Score="10" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Presumably this means that at least some grey haired humans have&#xA;  noticeable reproductive advantage, or maybe they had it in the recent&#xA;  past.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No it doesn't.  Natural selection is not that strong, it doesn't optimize every single possible physical trait towards maximum reproducing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And as others have mentioned, having lots of grey hair usually happens after reproduction is over.  Historically, lots of women did a lot of reproducing before they had any grey hair.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-08-22T21:52:38.657" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20717" PostTypeId="2" ParentId="20706" CreationDate="2014-08-23T00:26:39.060" Score="3" Body="&lt;p&gt;An addition to the Alan's answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;some sort of selection for more resistant genotypes inevitably did take place and left &lt;a href=&quot;http://www.pnas.org/content/early/2014/01/30/1317723111&quot; rel=&quot;nofollow&quot;&gt;distinct footprints in the human populations&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-08-23T00:26:39.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20719" PostTypeId="2" ParentId="20657" CreationDate="2014-08-23T01:45:46.087" Score="6" Body="&lt;p&gt;No.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible but extraordinarily impractical to &lt;em&gt;nourish yourself&lt;/em&gt; without killing animals, plants or even bacteria, as many have explained in detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, your immune system constantly kills pathogens that infect your body. What's worse, the macrophages literally catch and eat these bacteria alive, so you are very much &quot;consuming&quot; them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could live in a bubble, but even then there are bacteria in your gut. In your gut, they are not attacked by your immune system, but they can sometimes get through the gut lining into the body, where they &lt;em&gt;are&lt;/em&gt; attacked. They could also escape from you anus into the environment, and then end up elsewhere in your body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if you had a magic force field keeping the gut flora inside the space of your intestinal lumen, they could still mutate and &lt;em&gt;become&lt;/em&gt; immunogenic, then get consumed by your macrophages. Anyhow, collectively, &lt;a href=&quot;http://discovermagazine.com/galleries/zen-photo/m/microbiome&quot;&gt;your gut flora has more cells than your body&lt;/a&gt;, so is it really fair to say &quot;you&quot; did not consume any life when this symbiotic bacterial mass living inside you (more like &lt;em&gt;you&lt;/em&gt; are the parasite living &lt;em&gt;outside it&lt;/em&gt;) consumes some of its own cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But let's say you get rid of your gut flora, too. It's a hell of a life, and you wouldn't wish it on your enemy, but it solves that problem. Now only human cells are present inside your bubble. What happens when eventually your cells mutate and you get cancer? There are natural killer cells that will try to consume the cancer. So you have still consumed life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say you made yourself immune to cancer. That's impossible, but let's say you made your DNA polymerase so high fidelity that it takes millions of years for even a single mutation to occur (this is also almost impossible). Your body still has to kill cells through apoptosis as part of maintaining its own function. Again, to conserve resources, these cells are literally &lt;em&gt;swallowed&lt;/em&gt;. It's debatable whether an apoptotic cell is alive, but it is &lt;em&gt;made&lt;/em&gt; to die by influence of other cells, so this is very analogous to killing a chicken and eating it. In principle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer is no, but your question becomes meaningless if you define &quot;life&quot; scientifically. It is only possible to live without consuming life if &quot;life&quot; means &lt;em&gt;only plantae, metazoa and fungi&lt;/em&gt;. But that is not what it means, because at least &lt;a href=&quot;https://en.wikipedia.org/wiki/Ahimsa_in_Jainism#Important_constituents&quot;&gt;some Eastern religions&lt;/a&gt; &lt;em&gt;do&lt;/em&gt; consider eating microbes to be &quot;consuming life&quot;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Lame, boring answer&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The Universe has a finite reserve of (dis)entropy. When that runs out, no more life can exist, because all life must increase entropy. Even on Earth, by simply being alive you are taking up space that could be used by other organisms. To be alive you require some form of energy; even if this energy is solar, you would still be using up energy that could have been used by a plant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By simply existing, you are irreversibly destroying vital resources necessary for other life. Thanks to you, at least some life somewhere will be left without resources and starve. Therefore you cannot exist without harming life.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-08-23T01:45:46.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20720" PostTypeId="1" AcceptedAnswerId="20723" CreationDate="2014-08-23T05:59:51.157" Score="2" ViewCount="862" Body="&lt;p&gt;There is some literature which shows that all start codons code for methionine. However, in the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG1&quot; rel=&quot;nofollow&quot;&gt;standard genetic code&lt;/a&gt;, the alternative start codons clearly code for leucine. Does that mean these codons will code for leucine when they are encountered during translation (after start codon has been initialised and translated).&lt;/p&gt;&#xA;" OwnerDisplayName="user6417" LastEditorUserId="1320" LastEditDate="2014-08-23T07:58:19.653" LastActivityDate="2014-08-23T15:56:16.163" Title="Do alternative start codons code for methionine after transcription?" Tags="&lt;translation&gt;&lt;genetic-code&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20721" PostTypeId="2" ParentId="20709" CreationDate="2014-08-23T06:57:18.193" Score="2" Body="&lt;p&gt;I do not think there is a reproductive advantage in gray hair - it's the other way around: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Normal colored hair has a reproductive advantage.&#xA;But it also has a cost in terms of substances needed to build it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I make the assumption here that grey hair - which is often also more sparse - has a lower cost in terms of material. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think we are investing the cost for the part of the live that is exposed to direct evolutionary reproductive pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Later, we do not longer invest the cost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That makes sense if we assume that hair becoming gray is a process of degradation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not supported by an investment, but by the absence of an investment, following from absence of evolutionary pressure.&lt;/p&gt;&#xA;" OwnerUserId="6194" LastActivityDate="2014-08-23T06:57:18.193" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20722" PostTypeId="1" AcceptedAnswerId="20726" CreationDate="2014-08-23T07:44:34.313" Score="3" ViewCount="151" Body="&lt;p&gt;What are the botanical differences between the species S. parva and S. senegambica? Please highlight the main ones.&#xA;I have 2 groups of plants. One with label &quot;Sansevieria dooneri&quot; (a synonym of S. parva) and one with label &quot;Sansevieria senegambica&quot; and sadly both groups look awfully the same at first sight.&lt;/p&gt;&#xA;" OwnerUserId="8907" LastActivityDate="2014-08-23T13:51:39.263" Title="Sansevieria species specification needed" Tags="&lt;botany&gt;&lt;species&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20723" PostTypeId="2" ParentId="20720" CreationDate="2014-08-23T08:02:16.250" Score="3" Body="&lt;p&gt;I commented that this was a duplicate, but reading the question more carefully you seem to be asking something slightly different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the context of a 'start' these codons will be recognised by fMet-tRNA and a formyl-methionine will be inserted as the first amino acid. Subsequent occurrences of the same codon within the open reading frame will be translated normally (e.g. GUG &gt; valine).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The use of GTG as an initiation codon in the &lt;em&gt;E. coli&lt;/em&gt; &lt;em&gt;lacI&lt;/em&gt; gene&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this paper&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Frottini et al. (2006) The Proteomics of N-terminal Methionine Cleavage. Molec. &amp;amp; Cell. Proteomics 5: 2336-2349&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;the authors report assays of &lt;em&gt;E. coli&lt;/em&gt; methionine aminopeptidase with model peptides showing that when Lys is the 2nd residue, Met removal is very inefficient. They also show that when Pro is the 3rd residue, Met removal is very inefficient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This explains the fact that when the lacI repressor protein was sequenced:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Beyreuther et al. (1973) The amino-acid sequence of lac repressor. PNAS 70: 3576-3580&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;it was found to have a Met residue at its N terminus (sequence Met-Lys-Pro-).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, when the &lt;em&gt;lacI&lt;/em&gt; gene was sequenced:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Farabaugh (1978) Sequence of the &lt;em&gt;lacI&lt;/em&gt; gene. Nature 274: 765-769&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;the corresponding DNA sequence was GTG AAA CCA, demonstrating that the N-terminal residue is encoded by a GTG(Val) codon. LacI residue Val23 is encoded by a GTG codon, demonstrating the normal use of that codon in the body of the mRNA.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-08-23T15:56:16.163" LastActivityDate="2014-08-23T15:56:16.163" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20724" PostTypeId="1" AcceptedAnswerId="20727" CreationDate="2014-08-23T09:22:55.647" Score="4" ViewCount="1463" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8D5vr.jpg&quot; alt=&quot;Effect of CatB or CatL or both on VSV-EGP infectivity&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This graph appeared in a practice test for the MCAT. I am trying to interpret it, but it confuses me a bit. On the x-axis we have some introduced genes, and on the y-axis we have % of cells infected. What I don't get is what the top part represents. How do the &quot;Culture cell genotypes&quot; relate to the rest of the graph. I would also like to know what -/- and +/+ mean. By the way, information in the passage lists CatB and CatL as mammalian proteases, and their inhibitors reduce the infectivity of viruses with the EGP glycoprotein (found in Ebola virus).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are some questions based on the graph:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Based on the passage, does optimal VSV-EGP infection in vitro require CatB, CatL, or both?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Based on the passage, is CatL expression sufficient for VSV-EGP infection of the mouse cell lines presented in Figure 1?&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="4478" LastActivityDate="2019-02-15T02:26:01.197" Title="How do I interpret this graph regarding introduced genes and virus-infected cells?" Tags="&lt;genetics&gt;&lt;virus&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20726" PostTypeId="2" ParentId="20722" CreationDate="2014-08-23T13:51:39.263" Score="1" Body="&lt;p&gt;You could use &lt;a href=&quot;http://www.biodiversitylibrary.org/page/11492757#page/201/mode/1up&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; key to the genus. The differences between both species should become obvious when tracing back the decision tree. It seems that they can be distinguished mainly by the leaf size/shape of adult plants.&lt;/p&gt;&#xA;" OwnerUserId="8015" LastActivityDate="2014-08-23T13:51:39.263" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20727" PostTypeId="2" ParentId="20724" CreationDate="2014-08-23T14:56:33.217" Score="7" Body="&lt;p&gt;Plus and minus describe what is happening in a specific locus in the genome. When a + sign is shown, the locus contains the natural, fully working gene (wild type). When a - is shown, it means that by natural mutation or lab manipulation, cells lack that natural gene, or make a negligible amount of it, or make a broken variant etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These cells are diplod, meaning they have two homologous chromosomes. If +/+ is shown, both chromosomes carry, in that locus, a working gene. If -/- is shown, both copies are not working. If a cell is CatL -/-, both its natural copies of CatL are missing or defective, and the cell is unable to make the corresponding protein. The manipulation through which a naturally occurring +/+ is turned into a defective -/- is called a knock out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The top part of your chart shows what is happening in the nucleus, on the chromosomes, at the actual places where normal cells store their CatL genes. You don't give much detail, but the bottom of the chart appears to show some manipulation away from the normal locus. There are ways to introduce more copies, to stick them into the nucleus, or even in chromosomes etc, but the main point about introducing DNA is that often it will not work as well as the natural thing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Optimal infection means something close to the first column, about 25%. By skimming through the chart we are definitely seeing good infection in column 3. Also by comparison with the low levels, we could call acceptable the infection in column 8. The other columns are all clear failures to infect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second column is the simplest to interpret: knock out CatB alone, and the infection is gone. Thus, &lt;strong&gt;CatB is required&lt;/strong&gt; for infection. The third column reinforces the same point: restore CatB and infection is back to normal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sixth column shows cells where CatL and CatB were knocked out, but then CatB was reintroduced. We know from column 3 that knocking out and restoring CatB should keep infectivity, but in column 6 infection is gone. The only difference between columns 3 and 6 is the knockout of CatL, and its consequence is lack of infection. Thus, CatL is also &lt;strong&gt;required&lt;/strong&gt; for infection. You may say &lt;strong&gt;both CatL and CatB are required&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other columns are control conditions which show that the experiment was well designed and yielded expected results, rather than gibberish. For example, column 5 show that if you knock out both, infection is gone. It would have been very concerning if it weren't gone. Etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your second question is really one of logic: is CatL sufficient? We established that CatB is required, and so there is little CatL could do to supplant its absence. Therefore, logically, &lt;strong&gt;CatL should not be sufficient&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But we have a better proof, from the experiments. In column 4, those cells have their natural (endogenous) CatL, topped by some more CatL. But they are still not infected, beause they lack CatB. So CatL, even in larger-than-life amounts, cannot compensate the absence of CatB. &lt;strong&gt;CatL is not sufficient&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastEditorUserId="8809" LastEditDate="2014-08-23T16:04:38.617" LastActivityDate="2014-08-23T16:04:38.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20728" PostTypeId="1" CreationDate="2014-08-23T16:30:09.820" Score="1" ViewCount="184" Body="&lt;p&gt;Many medications are intended only for the brain, but are taken orally. Hence &amp;lt;10% finds its intended target, while the remaining &gt;90% is at best wasted, and at worst causes unwanted side-effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Valproate is a classic example; it is medicated as an antiepileptic, but only a small fraction crosses the brain blood barrier to make it into the brain. Because of this, a large dose is required, and unwanted side-effects are common.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, certain (small molecule?) drugs (e.g. Ibuprofen) can be applied transdermally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a drug intended for brain tissue that allows transdermal application, is there any sense in applying on the (preferably shaved) scalp?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this a known mechanism of administration? If so, does it have a name?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any way of correctly scaling the dosage? For example, if experiment shows that 50% of substance X taken transdermally reaches the bloodstream, if it is administered to the scalp is there any way of figuring out how much ends up in the brain and how much ends up in the rest of the body?&#xA;Since this is a tricky and obscure question, may I also ask this: how to go about finding an answer to this? Where else can I ask?&lt;/p&gt;&#xA;" OwnerUserId="8435" LastEditorUserId="8435" LastEditDate="2014-08-23T18:52:40.220" LastActivityDate="2014-08-23T19:05:25.693" Title="Applying drugs to brain via scalp (transdermal)" Tags="&lt;pharmacology&gt;&lt;medicine&gt;&lt;transdermal&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20729" PostTypeId="2" ParentId="20702" CreationDate="2014-08-23T16:41:40.543" Score="7" Body="&lt;p&gt;Pink individuals of the katydid species &lt;em&gt;Amblycorypha oblongifolia&lt;/em&gt; are a relatively uncommon but natural phenomenon with a long history of research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It looks from popular press accounts (&lt;a href=&quot;http://www.sciencefriday.com/blogs/01/02/2013/pink-katydids.html?audience=2&amp;amp;series=17&quot; rel=&quot;noreferrer&quot;&gt;Science Friday&lt;/a&gt;, &lt;a href=&quot;http://blogs.scientificamerican.com/running-ponies/2013/08/13/in-north-american-katydids-green-isnt-the-dominant-colour-pink-is/&quot; rel=&quot;noreferrer&quot;&gt;Scientific American&lt;/a&gt;) that the pink coloration may be caused by a dominant allele, and is only rare because of a high selection pressure against pink individuals (i.e. they're much less good at hiding among leaves, and are eaten before they can reproduce).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HQvtb.jpg&quot; alt=&quot;Photo by Richard Whitby, via flickr.com/blueboat2 (cc-by-sa 2.0)&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photo by Richard Whitby, via flickr.com/blueboat2 (cc-by-sa 2.0)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-08-23T16:54:23.350" LastActivityDate="2014-08-23T16:54:23.350" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20730" PostTypeId="2" ParentId="20728" CreationDate="2014-08-23T19:05:25.693" Score="4" Body="&lt;p&gt;The short answer is no, it will take forever for a drug to pass through skull bones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The usual reason to apply drugs on skin is if you want them to act right there, on the skin. Acne creams fit here. You need less drugs, you get where it is needed sooner, and you have fewer off-target effects, when compared to taking them by mouth. The brain is not &quot;right there&quot;, so this scenario does not apply.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second reason is convenience. Some drugs cannot by taken by mouth, because they would be degraded by the stomach or guts. In most cases, the drug has to be given through painful, expensive injections. But if such a drug does pass through skin (usually when it is a fat-loving small molecule), you may get away with applying it on skin. Testosterone is one such drug. However, it usually doesn't matter whether the skin you are applying on is close of far from the target organ. The drug will be taken from the skin by blood, get to the heart through veins, and then spread to the whole body, eventually reaching the target. There is no reason to shave your head, since it will go through the same detour before reaching the desired destination.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastActivityDate="2014-08-23T19:05:25.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20731" PostTypeId="1" AcceptedAnswerId="20732" CreationDate="2014-08-23T19:45:45.193" Score="28" ViewCount="2661" Body="&lt;p&gt;It is well known that the European colonists brought many infectious diseases to the Americas, and that these had a deadly effect on the native populations, because they had no immunity to them. Were there any local infectious diseases to which the colonists were not immune? I’ve never heard of such. I’m not aware that the colonists suffered any epidemics, or that they brought any new and unusual diseases back to Europe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why not? Is this merely an accident of history, that there were no infectious diseases in the Americas which did not already exist in Eurasia? Or is there some explanation?&lt;/p&gt;&#xA;" OwnerUserId="975" LastEditorUserId="4747" LastEditDate="2014-08-23T20:24:35.773" LastActivityDate="2016-10-09T02:32:59.757" Title="Why was disease transfer to the Americas one-way?" Tags="&lt;human-biology&gt;&lt;infection&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="20732" PostTypeId="2" ParentId="20731" CreationDate="2014-08-23T20:04:03.047" Score="24" Body="&lt;p&gt;In &quot;Guns, Germs, and Steel&quot; Jared Diamond includes quite a bit on this topic. His conclusion is that Europeans, and old world humans in general were much more exposed to their farm animals, often living in the same buildings. This allowed a much greater number of diseases to jump from animal to human, forcing us to development immunity against these pathogens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The native americans never domesticated as many animals, and weren't exposed to as many pathogens. As a result the foreign pathogens could freely move through their populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why did it only go one way? A lot more Europeans came to American than vice-versa, so there just wasn't as much opportunity for American pathogens to move to Europe. Additionally, the Europeans brought a lot of animals here, including cattle, horses, and pigs. These would have carried pathogens as well, again, very few American animals were taken to Europe.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-23T20:04:03.047" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20733" PostTypeId="2" ParentId="20731" CreationDate="2014-08-23T20:25:35.933" Score="19" Body="&lt;p&gt;There is at least one important exception - it is generally thought that &lt;a href=&quot;http://en.m.wikipedia.org/wiki/History_of_syphilis&quot;&gt;syphilis&lt;/a&gt; came to Europe from the Americas.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-08-23T20:25:35.933" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="20734" PostTypeId="2" ParentId="5383" CreationDate="2014-08-23T21:32:45.257" Score="1" Body="&lt;p&gt;I realize this question is about yeast, but I'm afraid that people may try to expand the answer to all systems, and beta galactosidase is not good for all systems, particularly for animal studies. I've seen too many gene therapy papers try to get away with using it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beta galactosidase is not a good reporter gene for in vivo gene delivery studies. There is too much endogenous activity in most tissues to distinguish the exogenous activity. When doing non viral gene delivery, the amount of DNA expressed is often so low that you cannot overwhelm the endogenous activity and therefore cannot conclusively say the enzyme activity you detected is from your new DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Luciferase is far superior for in vivo work. First, there is no endogenous luciferase activity in most animals ( you're out of luck if you're doing work on fireflies ) so you can be sure that any luciferase activity you detect is real. Luciferase activity can be determined noninvasively though bioluminescent imaging, allowing for repeated measurements on the same animal. Beta glucosidase can require killing the animal, dissecting the tissues, preparing microscope slides, and then analysis, so doing a time course study will require using many more animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only advantage I can see beta glucosidase having over luciferase is if you want to see what percentage or precisely what type of cells are expressing the reporter gene. However, I think GFP or another fluorescent protein would be more appropriate because of the endogenous activity issue I described earlier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, my answer applies for animal use. If you're just growing yeast on a plate, the beta galactosidase is probably the cheaper way to go. We did some 384 and 1536 well plate assays on primary hepatocytes with luciferase, and the luciferase reagent was about $250 for 10mL. You might also consider fluorescent proteins for screening. I've made bactieral colonies with RFP that were visibly red, so no need for UV, but even if you need UV light to see the fluorescence, a standard UV transluminator for viewing gels will be good enough, and no extra reagents to add.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-23T21:32:45.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20735" PostTypeId="2" ParentId="20668" CreationDate="2014-08-23T22:46:33.400" Score="2" Body="&lt;p&gt;The methods should be equivalent, given the same data. Using &lt;code&gt;phylosignal&lt;/code&gt;'s demo:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;library(&quot;picante&quot;)&#xA;library(&quot;phytools&quot;)&#xA;&#xA;set.seed(5)&#xA;randtree &amp;lt;- rcoal(20)&#xA;randtraits &amp;lt;- rTraitCont(randtree)&#xA;&#xA;phylosignal(randtraits[randtree$tip.label],randtree)&#xA;&#xA;phylosig(randtree, randtraits[randtree$tip.label], method=&quot;K&quot;,test=TRUE)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;phylosignal&lt;/code&gt; returns:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;         K PIC.variance.obs PIC.variance.rnd.mean PIC.variance.P PIC.variance.Z&#xA;1 1.430635          0.01147             0.4631411          0.001      -2.662701&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and &lt;code&gt;phylosig&lt;/code&gt;:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;$K&#xA;[1] 1.430635&#xA;&#xA;$P&#xA;[1] 0.001&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Both give K = 1.430635 and an identical P-value. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematically, it shouldn't matter if you shuffle the trait values or generate a null distribution of K. To get a null distribution for K, you have to shuffle something, and the tip values are probably being shuffled. You could check the code to be sure. An analogy is that, when doing a randomization for an ANOVA-like test, you can either shuffle the observed values or the group membership. Either way will give the same answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for interpretation, Brownian motion is the simplest model for trait evolution, implying no direction, optima, rate changes, etc. K = 1 when the observed variation equals the expected variation. If K is greater than 1 then neighboring tips tend to resemble each other more than you would expect, suggesting a deviation from Brownian motion. &lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2014-08-23T22:46:33.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20736" PostTypeId="1" CreationDate="2014-08-24T02:56:04.860" Score="2" ViewCount="50" Body="&lt;p&gt;I am a computer scientist with no biological background and working on analyzing lab  results of patients with Acute myeloid leukemia. They have been tagged with following subtypes of AML:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;AML with No maturation&lt;/li&gt;&#xA;&lt;li&gt;AML with granulocytic differentiation&lt;/li&gt;&#xA;&lt;li&gt;AML with monocytic  differentitaion.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I know there are two classifications for AML subtypes: FAB(M0-M7) and WHO. I think these patients have been classified using FAB, but their corresponding subtypes' names do not match in any of the names associated with M0-M7:  &lt;a href=&quot;http://www.cancer.org/cancer/leukemia-acutemyeloidaml/detailedguide/leukemia-acute-myeloid-myelogenous-classified&quot; rel=&quot;nofollow&quot;&gt;http://www.cancer.org/cancer/leukemia-acutemyeloidaml/detailedguide/leukemia-acute-myeloid-myelogenous-classified&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I checked a lot of literature but still not sure about the class of the last two tags in FAB classification. Could someone please help me with that?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;AML with No maturation&quot;  is M1?&lt;/li&gt;&#xA;&lt;li&gt;&quot;AML with granulocytic differentiation&quot; is M2 (or M4, M5) ?&lt;/li&gt;&#xA;&lt;li&gt;&quot;AML with monocytic  differentiation&quot; is M4 or M5 or both ?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8919" LastEditorUserId="107" LastEditDate="2014-08-24T04:41:22.793" LastActivityDate="2014-08-24T04:41:22.793" Title="Subtypes of Acute myeloid leukemia" Tags="&lt;immunology&gt;&lt;pathology&gt;&lt;cancer&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20737" PostTypeId="2" ParentId="20702" CreationDate="2014-08-24T04:50:30.467" Score="0" Body="&lt;p&gt;In response to Oreotrephes answer I see fit to point that the selective pressure against an insect being pink and a manual being pink is quite different but could also be the same.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take our species for example: the first humans were dark skinned thought to be as a genetic advantage to our then dark forrest and tree land environment. As we evolved into a plethora of colors each equally evolved but separately specialised (to the same basic tasks) under the pressure of different environments some of us became lighter skinned and lost some of our protection from the sun. Pinkness in caucasians is common but its a genetic disadvantage due to the introduction of an extremely greater probability of Melanoma. Those with darker skin sometimes can develop Melanoma but its rare. It is thought we evolved light skin as a way of knowing we needed greater amounts of D3 in diet due to low UV environments. The same also with blue eyes the eye equivalent of whiteness (melatonin depletion).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If its evolution was simular to ours then I would suspect that your little pink insect needed a key vitamin in its diet but thats just a guess. &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2014-09-02T07:03:49.507" LastActivityDate="2014-09-02T07:03:49.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20739" PostTypeId="1" CreationDate="2014-08-24T11:08:26.360" Score="2" ViewCount="613" Body="&lt;p&gt;I have got one assignment to calculate the approximate sum total of all cells in the human body. How to tackle this problem? I know that the current statistics is $10^{13}$ cells. I wanted some hints.&lt;/p&gt;&#xA;" OwnerUserId="5669" LastActivityDate="2014-08-24T16:15:17.683" Title="How to measure the total number of cells in an average human body?" Tags="&lt;cell-biology&gt;&lt;homework&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20740" PostTypeId="2" ParentId="20739" CreationDate="2014-08-24T16:15:17.683" Score="2" Body="&lt;p&gt;This is a classic &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Fermi_estimate&quot; rel=&quot;nofollow&quot;&gt;Fermi estimation problem&lt;/a&gt;. The usual approach is to estimate the volume of a body, estimate the volume of a cell, and divide one by the other, remembering of course to have both volumes in the same units. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My quick attempt gave 10&lt;sup&gt;13&lt;/sup&gt; to the nearest order of magnitude.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-08-24T16:15:17.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20741" PostTypeId="2" ParentId="20701" CreationDate="2014-08-24T16:19:21.437" Score="7" Body="&lt;p&gt;Yes, HIV does attempt to prevent multiple infection of the same cell. Once a T cell or other cells are infected, HIV downregulates the CD4 receptor which it uses to gain entry. Because of this, there are less receptors so another HIV is less likely to infect that cell. Meanwhile, the infection itself upregulates CD4 receptors on other cells which means the downregulation is even more effective. There are other mechanisms but this is a major one.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hiding means it is somewhere where we don't know where it is and it isn't that active. When HIV is active it is destructive but also the cell is aware it is there. The cell can then try to alert other cells that it is infected. If HIV isn't active but instead hiding, it can stay where it is without really being detected. Even the drugs we use usually only affect HIV whilst it is replicating. So again if it's in a cell that's long lasting and the HIV is not replicating then it is essentially hiding. Such a cell includes macrophages and memory cells when we are just talking about the immune system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Will HIV reside in the lymph node? Well yes, this is an exciting place for it. There's loads of exposed CD4 receptors and lot's of it's favourite T cells about. An infected cell will transmit HIV to other cells when they are signalling to each other. Even worse is when a dendritic cell is infected. Instead of instructing the immune system how to detect HIV infected cells, it is infecting them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;HIV is an infection. As soon as the body detects it, it goes into overdrive trying to eradicate it. This means there are more cells for HIV to infect. More foreign material means the immune system is even further stimulated to make even more cells. However it doesn't want CD8 cells to proliferate too much nor too many HIV specific cells so driving too much proliferation is a bad idea. What HIV does do is make lots and lots of useless copies of itself. HIV particles that are so badly made they aren't functional. The body tries to fight these and makes more cells to combat these but there's no point because they aren't the problem. But this immune diversion and a larger target number of cells is exactly what HIV wants. Proliferation of HIV specific cells, particular CD8, is associated with delayed disease progression or control.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually the cancers caused by HIV are because of other viruses running unchecked. Kaposi's sarcoma or lymphomas for example. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2014-08-24T16:19:21.437" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20742" PostTypeId="1" CreationDate="2014-08-24T17:26:37.797" Score="3" ViewCount="204" Body="&lt;p&gt;How much are phase-contrast and dark-field microscopy used in biological research today? It seems these were invented a long time ago, so I am thinking would it be a good idea to learn these techniques. (I will start an undergraduate program in biology next spring.. but I am still mostly interest how much the researchers use these technologies: if little, I should use my time better)&lt;/p&gt;&#xA;" OwnerUserId="8930" LastActivityDate="2014-08-25T04:13:18.627" Title="How much are phase-contrast and dark-field microscopy used in biological research?" Tags="&lt;microscopy&gt;" AnswerCount="2" CommentCount="1" ClosedDate="2014-08-26T04:29:28.727" ContentLicense="CC BY-SA 3.0" />
  <row Id="20743" PostTypeId="1" CreationDate="2014-08-24T18:30:27.443" Score="0" ViewCount="647" Body="&lt;p&gt;How much does a typical biologist know about signal processing, machine learning, and (theoretical) computer science?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coming from a neuroscience background where knowing about algorithms and computer science is a must, it seems to me that in biology there is much less cross disciplinary work. Though, yes, there are bioinformatics (but you only do sequence alignment and clustering?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, given a typical PhD student in biology, how much does he/she need to know about programming, signal processing, etc?&lt;/p&gt;&#xA;" OwnerUserId="8930" LastActivityDate="2014-08-24T21:44:52.893" Title="How much does a typical biologist know about signal processing, machine learning, and (theoretical) computer science?" Tags="&lt;bioinformatics&gt;" AnswerCount="5" CommentCount="1" ClosedDate="2014-08-24T21:48:07.520" ContentLicense="CC BY-SA 3.0" />
  <row Id="20745" PostTypeId="1" CreationDate="2014-08-24T18:52:56.737" Score="1" ViewCount="57" Body="&lt;p&gt;Some bacteria are known to communicate using bioluminescence (quorum sensing). Do we observe the same phenomena in any macroscopic species?&lt;/p&gt;&#xA;" OwnerUserId="8934" LastActivityDate="2014-08-25T11:37:08.987" Title="Does bioluminescence communcation occur on macroscopic level?" Tags="&lt;bioluminescence&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20746" PostTypeId="2" ParentId="20743" CreationDate="2014-08-24T19:39:07.773" Score="3" Body="&lt;p&gt;I don't know what a &quot;typical&quot; biologist is, but I'd guess they don't know much about computers, because the population in general is computer illiterate. In my department, we do have a lab that does a lot of computational work on proteins. And of course bioinformatics relies on computers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can see where programming would come in handy for an ecologist, and maybe hardware and electronics too. Lets say you want to track animals in the woods. Traditionally, you'd give them a radio collar, then you'd have to triangulate their position in the woods, and at the end of the day all you'd have is location data. You could use something like a Raspberry Pi or Arduino to create a device that has GPS, a camera, and cell phone antenna, which could record much more information about the animal's location and activity and send it back you without as much effort.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In our modern computerized age, knowing some programming is always a plus, no matter what field you're in. Finding ways to apply that skill aren't always easy. I know both Java and C++, but I've really only written a few programs that I've used in research, 1 to calculate number of possible peptides given a size and some amino acids that won't change, and one to calculate how much DNA to use in ligation reactions.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-24T19:39:07.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20747" PostTypeId="2" ParentId="20743" CreationDate="2014-08-24T20:09:23.777" Score="1" Body="&lt;p&gt;I agree that a &quot;typical&quot; biologist (if such thing really exists) is generally not skilled in CS nor, very scaringly, in statistics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My experience is that most biologists think of these things as burdens that do not really interest them and only get to do some basic statistics (most biologists would sort of know what a t-test or an ANOVA is, although they most probably won't master the statistical theory behind it) before writing a paper, so that they can put the little stars on their graphs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if you go into fields like neuroscience (which I count as biology, I am not sure why you seem to imply it is not) then you start meeting people who know quite a bit of CS. Generally you either have these hybrid mathematician/statistician/programmer/math-y guy/biologist or you have biologists working together with more CS people.&lt;br&gt;&#xA;In my last lab, for instance, we used to have a physicist and a programmer to help out with biological data analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, if you're into imaging, then there may be a lot of programming needed  for 3D reconstruction, image segmentation, particle tracking, etc. etc. Although there is some fairly impressive off-the-shelf software out there for the most common tasks, as soon as you want something a bit more specific you're better off programming it yourself, or finding a collaboration with some computer scientists. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would say that as a biologist it is important to understand these things, but not necessarily to be able to actually perform them, as you can rely on CS specialists/bioinformaticians to do that for you. However, it is very important for the biologist to understand what the bioinformatician does, and vice versa, as communication is obviously of great importance in these situations.&lt;/p&gt;&#xA;" OwnerUserId="115" LastEditorUserId="115" LastEditDate="2014-08-24T20:17:44.143" LastActivityDate="2014-08-24T20:17:44.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20748" PostTypeId="2" ParentId="20742" CreationDate="2014-08-24T20:44:42.293" Score="1" Body="&lt;p&gt;If you're planning on doing any kind of cell biology work (and if you're going into biology, it is almost certain you will at some point), learning how to use a microscope is a must. You will use a scope frequently when growing cells to analyze their morphology, count them, look for signs of contamination, visualize differentiation, etc. Microscopes are also used when performing &lt;a href=&quot;http://en.wikipedia.org/wiki/Immunofluorescence&quot; rel=&quot;nofollow&quot;&gt;immunofluorescence&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Immunohistochemistry&quot; rel=&quot;nofollow&quot;&gt;immunohistochemistry&lt;/a&gt; staining protocols. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, even though the instruments and some of the techniques have been around for quite a while, they are still very relevant today.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-08-24T20:44:42.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20749" PostTypeId="2" ParentId="20743" CreationDate="2014-08-24T20:46:27.063" Score="1" Body="&lt;p&gt;Without addressing the &quot;typical biologist&quot; aspect of your answer, I have some computer science background but mostly programming and little &quot;theoretical.&quot;  In my initial Ph.D. program in the late '80s and early '90s, I took several programming classes in Pascal and C.  I wrote a fairly involved dBase program for a systematic research fish collection.  I haven't messed with these for a number of years but I've retained enough knowledge to write programs in R and dabble in Python. I've used these for various professional reasons, from research to teaching. I teach very basic R in my biogeography class so my students even get some exposure. I'm teaching myself Postgresql as time permits. I use LaTeX regularly, which isn't always programming but its draws from a similar mindset. Plus, I can read the LaTeX code when I want to learn how something works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a colleague in my department who is very fluent in SAS programming but I don't know what other programming skills he might have. Yet another colleague took lots of computer science courses during his Ph.D. program. And yet another colleague, now departed to the administrative dark side, was very proficient in Perl and probably a few other scripting languages.  On the other hand, many of my colleagues use word processing and spreadsheet programs and that's about it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scientists are no different from other people. They go where their natural interests take them. For some of us &quot;typical&quot; biologists, that includes computers.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-24T20:46:27.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20750" PostTypeId="2" ParentId="20743" CreationDate="2014-08-24T20:57:16.973" Score="0" Body="&lt;p&gt;As much as they need to know, but rarely more. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would say that the 'typical' biology undergrad is not so much of a tech freak and thus has not so much knowledge about programming and computer science in general. One might speculate that young people that feel attracted to these things tend to study math or physics rather than biology. Machine learning just isn't such a fundamental part of basic biology as it is to other scientific disciplines. This is by no means a as there are lots of other things to learn and understand before you can even apply computer-based solutions to biological problems. Many biologists will hardly need any programming skills ever.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, as a PhD student you will need programming skills at least to some degree, let it be some R to do statistical analyses or some Python to automate workflows. And of course you will find really skilled programmers among biologists as well. As an ecologist, the first thing that comes to my mind are complex ecological models mostly written in C++.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To summarize, the pressure to be familiar with concepts of CS increases with the academical degree, and so does the proportion of proficient biologists.&lt;/p&gt;&#xA;" OwnerUserId="8015" LastActivityDate="2014-08-24T20:57:16.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20751" PostTypeId="2" ParentId="20745" CreationDate="2014-08-24T21:09:23.853" Score="1" Body="&lt;p&gt;Almost certainly. In the deep-sea, some species of laternfishes (Myctophidae) show sexual dimorphism in their light organs. Males have large light organs. The females are much smaller. &lt;a href=&quot;http://www.amnh.org/explore/news-blogs/research-posts/bioluminescent-fish-flashing-patterns-might-facilitate-mating&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a brief summary, based on an interview with Dr. John Sparks at the American Museum of Natural History. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sparks is discussing his recent publication with colleagues (&lt;a href=&quot;http://download.springer.com/static/pdf/790/art%253A10.1007%252Fs00227-014-2406-x.pdf?auth66=1409087089_a7e5af4ebd301445752aa35e03da4cc2&amp;amp;ext=.pdf&quot; rel=&quot;nofollow&quot;&gt;Davis et al. 2014&lt;/a&gt;) that suggests that bioluminescent communication may actually facilitate speciation in some deep-sea fishes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are probably more instances of communication using bioluminscence in deep-sea organims but, to my knowledge, the Davis et al. paper provides the best evidence so far.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Davis, M.P. et al. 2014. Species-specific bioluminescence facilitates speciation in the deep sea. Marine Biology 161: 1139-1148. (open access)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;On land, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC299859/&quot; rel=&quot;nofollow&quot;&gt;Stoltz et al. 2003&lt;/a&gt; has demonstrated that positive selection has acted on bioluminescent color in Jamaican click beetles. The male beetles use the flashing to attract females for mating. Some males emit yellow light while males in a separated area have orange light.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Stoltz, U. et al. 2003. Darwinian natural selection for orange bioluminescent color in a Jamaican click beetle. Proceedings of the National Academy of Sciences USA 100: 14955-14959.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-08-24T21:18:43.080" LastActivityDate="2014-08-24T21:18:43.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20752" PostTypeId="2" ParentId="20743" CreationDate="2014-08-24T21:35:04.707" Score="2" Body="&lt;p&gt;First I want to say that studying the dynamic of enzymatic reactions, studying the movement of the arm, studying the structure of the DNA, Using mathematical modeling (and individual-based simulation) in population genetics, studying the turnover of soil nutrients, and others, ... require cross-disciplinary. Cross.disciplinary knowledge in biology is not restricted to the intersection between computer science and Biology.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Then I guess/hope that if I give you an overview of my knowledge in computer science and how I acquired it, it may help you (in addition to other answers) to estimate the level in computer science of an average biologist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;From my Bachelor and Master&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During my Bachelor and Master degrees I have learned about statistics (and statistics applied to genetic data) and learned to program in R for data analysis purposes. I have been involved in a project during my Master where I had to use Approximate Bayesian Computation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Self-learning&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have learned by myself the basis of theoretical computer science (NP-hard, genetic algorithm, running time function (the Big O notation), …) but I still know very little. I also learned Python (and a bit of Java) and Object-oriented programming. I also learned HTML and CSS in order to construct my website. All I know about information theory and signal processing comes from a bunch of Khan academy lectures on the subject that I watched.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-08-24T21:44:52.893" LastActivityDate="2014-08-24T21:44:52.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20753" PostTypeId="2" ParentId="20742" CreationDate="2014-08-25T02:59:41.277" Score="2" Body="&lt;p&gt;I use phase contrast very often, as it is only a matter of switching a lens group from bright field. Instead of spending hours with staining, or, worse, immunostaining, I get the big picture (cell diameter) in a few seconds. I can even go back to the same cells next day. Switching to dark-field is also a matter of turning a dial or pushing a switch.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you already use brightfield, there is not much to learn about them in terms of actually useful physics, or sample preparation. The things you could learn - say, that colors are altered in darkfield - will rarely be needed in practice. These methods are the sort of things you don't really need to know in depth unless your experiments require them. Even then, practice and elbow grease would be more helpful than advanced optics. Remember that in most cases, the scientific hypothesis is more important than the tools you can use to solve it.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastEditorUserId="8809" LastEditDate="2014-08-25T04:13:18.627" LastActivityDate="2014-08-25T04:13:18.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20754" PostTypeId="1" AcceptedAnswerId="21587" CreationDate="2014-08-25T04:45:11.033" Score="2" ViewCount="636" Body="&lt;p&gt;In relation to microbiology and the naming of the various areas of the plant as it relates to microbial inhabitance, I am confused as to the difference between the terms &lt;strong&gt;endorhiza&lt;/strong&gt; and &lt;strong&gt;rhizosphere&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://books.google.com.au/books?id=pQyRyIdm7O0C&amp;amp;pg=PA131&amp;amp;lpg=PA131&amp;amp;dq=Phyllosphere%20%22stems%22&amp;amp;source=bl&amp;amp;ots=VAvyV0LpP1&amp;amp;sig=GKHLjD6vRhMmZ-Wkt7hi9t17C8M&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=Mbj6U_CyCI2LuATo3oKIBw&amp;amp;ved=0CDkQ6AEwBQ#v=onepage&amp;amp;q=rhizosphere%20%22roots%22&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; case I see rhizosphere referred simply to as the 'roots', but in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21947430&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; case I also see endorhiza explained simply as 'roots' also.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9115091&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;this&lt;/em&gt;&lt;/a&gt; case, I see a further explanation for endorhiza (which does make sense etymologically): 'internal root tissues'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this mean &lt;em&gt;endorhiza&lt;/em&gt; is be a sub-term for the area inside the roots, and the larger area of the rhizome in general represented by &lt;em&gt;rhizosphere&lt;/em&gt;, and that is the difference?&lt;/p&gt;&#xA;" OwnerDisplayName="user3362" LastEditorUserId="16866" LastEditDate="2020-04-15T13:00:33.637" LastActivityDate="2020-04-15T13:00:33.637" Title="Rhizosphere vs. Endorhiza?" Tags="&lt;botany&gt;&lt;microbiology&gt;&lt;terminology&gt;&lt;etymology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20756" PostTypeId="1" CreationDate="2014-08-25T05:46:06.890" Score="1" ViewCount="205" Body="&lt;p&gt;in case it isn't obvious i'll begin by stating that i'm a layman, trying to understand something about this subject from reading books. the books i've looked at so far give murky and confusing accounts of meiosis (example: a schaum's outline refers to chromosomes that are &quot;identical, but not the same&quot;), and they always seem to duck the questions i most want answered. what i'm reaching for right now is a coherent, schematic understanding of meiosis. i'm aware that the real world is messier than that, but there clearly is a simple schema that accounts for the most typical cases of meiosis in an approximative fashion. in particular, there must be some way of deriving the approximate correctness of mendelian independent assortment of alleles from the molecular process of recombination. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;here's what i think i can make out so far: if two chromosomes x1...xn and y1...yn get paired together then some number of interstices (spaces between successive loci) get picked and each chromosome gets broken at each interstice. after crossover each of the two resulting chromosomes have x-segments alternating with y-segments. for example if only one interstice is picked, and it's between the k-th and (k+1)-th loci, then the chromosomes that are there after crossover are x[1]...x[k] y[k+1]...y[n] and y[1]...y[k] x[k+1]...x[n]. it also seems clear that all interstices are equally likely to get picked. have i got at least this much right? and if so, how many interstices get picked? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;also, if anyone knows a book that might suit my needs i would obviously be glad to hear about it. thanks if you can help&lt;/p&gt;&#xA;&#xA;&lt;p&gt;peace&#xA;stm&lt;/p&gt;&#xA;" OwnerUserId="8945" LastActivityDate="2014-08-25T22:41:25.350" Title="what is the modern, molecular explanation of independent assortment of alleles?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20757" PostTypeId="1" CreationDate="2014-08-25T07:36:14.387" Score="4" ViewCount="437" Body="&lt;p&gt;i recently developed a b-actin-ab-incubated PVDF-WB-Membrane with the Thermo Scientific Pierce ECL Kit. According to the manufacterers orders i mixed Reagent 1 and Reagent 2 1:1. But unfortunately i got kind of &quot;unbalanced&quot; bands (on the right side of the picture). Then someone gave me the tip to try to mix the reagents 2:1. For this substrate i got the result on the left side which actually looks much better. &#xA;Has anyone of you had the same experience and can anyone explain to me why this is so?&#xA;Is it &quot;legal&quot; to do so, or does it alter somehow the results of my experiment?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yours,&#xA;p1ssn3lk3 &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UzIYj.gif&quot; alt=&quot;WB with b-Actin-AB, developed with Thermo Scientific Pierce ECL&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8701" LastActivityDate="2015-02-11T13:30:27.920" Title="Western Blot: Fischer ECL substrate 2:1 instead of 1:1?" Tags="&lt;molecular-biology&gt;&lt;western-blot&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20758" PostTypeId="2" ParentId="20754" CreationDate="2014-08-25T08:15:18.767" Score="0" Body="&lt;p&gt;The rhizosphere is the &lt;em&gt;narrow region of soil that is directly influenced by root secretions and associated soil microorganisms&lt;/em&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/Rhizosphere#cite_note-2&quot; rel=&quot;nofollow&quot;&gt;(wiki)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And endorrhiza (also termed Endomycorrhiza, AMS or AM) is a special case of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Mycorrhiza&quot; rel=&quot;nofollow&quot;&gt;mycorrhiza&lt;/a&gt;, a mutualistic relationship between fungi and plant roots, where the fungus cells are stored within the root and not on its surface. &lt;/p&gt;&#xA;" OwnerUserId="8015" LastActivityDate="2014-08-25T08:15:18.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20759" PostTypeId="1" AcceptedAnswerId="20764" CreationDate="2014-08-25T08:40:12.297" Score="12" ViewCount="576" Body="&lt;p&gt;I often read that people believe that human vision has an inherent frames-per-second rate (FPS) that causes stroboscopic effects - such as seeing the spokes of a rotating wheel apparently rotating at a different speed or appearing stationary when moving.&lt;/p&gt;&#xA;&lt;p&gt;For example: in a Physics.SE answer to &lt;a href=&quot;https://physics.stackexchange.com/a/132121/12613&quot;&gt;Can a “superhuman” move so fast that an average person cannot see them?&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The human eye-brain visual refresh rate has an &amp;quot;effective frame rate&amp;quot; of around 30fps.&lt;/p&gt;&#xA;&lt;p&gt;Have you never watched the rims of the wheel in a car next to yours? I can clearly recall many times watching as the wheels sped up how it appears to stand still then move backwards.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This surprises me as I would expect there is no synchronisation of neuron firing in the retina, that neuron firing rates would vary widely depending on light levels and that the brain has no need to process the continuous signals in fixed cycles or in cycles whose length is invariant.&lt;/p&gt;&#xA;&lt;p&gt;I believe this question, or a good answer to it, would differ from &lt;a href=&quot;https://biology.stackexchange.com/q/10694&quot;&gt;What is the equivalent of shutter-speed in Human eye?&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Is human vision in any way subject to a fixed frame rate of 30 FPS?&lt;/p&gt;&#xA;" OwnerUserId="1642" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-04-30T08:43:19.557" Title="Is mammalian vision processed as a sequence of frames?" Tags="&lt;brain&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20760" PostTypeId="2" ParentId="20757" CreationDate="2014-08-25T10:01:16.353" Score="2" Body="&lt;p&gt;Well usually in an ECL kit, one of the reagents is the substrate and the other one is hydrogen peroxide, which activates the substrate for breakdown using the HRP on your secondary antibody (Ab) so I genuinely doubt what you are seeing is the result of ratio difference. In order to make that conclusion you need to run your samples twice (on two separate membranes) and do a 1:1 and 2:1 ECL and if you observed such a difference then you are on firmer grounds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect what has happened in the above experiment is that you have done a 1:1 (with 1Ab and 2Ab not distributed equally on the membrane) then after perhaps not a very thorough wash, you have done another 1Ab and 2Ab incubation using the a 2:1 mix. I suspect what has happened is that in your 1:1 the left hand side has not received the Ab mixtures very well and when you did the 2:1 since the right hand still Ab attached to it (if you didn't strip the membrane) so the left hand side was &quot;forced&quot; to get the Abs hence again the Ab mixture and ECL not equally bound. It is obvious since one image is opposite the other so its the Ab incubation step that has gone wrong. Otherwise if you have done the second ECL incubation mixture straight after the first and didn't do a wash step, the same can result if the membrane did not receive the initial ECL mixture equally since you can get a blocking effect by the old ECL mixture and perhaps what has happened is that the H2O2 or the substrate was present in excess in the second incubation step hence amplifying the signal in the sections of the membrane that did not receive the ECL mixture very well in the first place, relative to the rest of the membrane, which still has ECL liquid on it from the last experiment (again if you haven't washed the membrane well as ECL can be active for up to 24 hours in some kits but after a few hours the activity usually reduces but can still be observed)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you need to do is after ECL, wash the membrane with TBST for a few minutes followed by TBS, leave the membrane in the sun to dry so that the Ab slowly denature (although that doesn't always happen specially with high affinity Abs such as anti-tubulin and actin). After at least 24 hours, strip the membrane from Ab and redo the Ab incubation. The best thing to do is to do all the incubation steps in a sealed bag then make sure the membrane receives the ECL mixture equally and do the visualisation. I would say however since the membrane is unequally &quot;contaminated&quot; with the Abs then the best thing to do is to redo the experimental run and re-run the gel. Its a pain but you need to get to the button of this! &lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-25T10:23:07.997" LastActivityDate="2014-08-25T10:23:07.997" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20761" PostTypeId="2" ParentId="20757" CreationDate="2014-08-25T10:45:08.547" Score="1" Body="&lt;p&gt;Try rinsing the blot in TBS or PBS before treating. Shake it try and place on level dry surface. When I pour the a chemo reagent on there I just pour enough so the surface tension keeps the fluid on the paper not allowing it to run off. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other possibilities I see could be in your transfer. The temp could not be uniform in the buffer&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-08-25T10:45:08.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20762" PostTypeId="1" CreationDate="2014-08-25T11:22:37.020" Score="1" ViewCount="58" Body="&lt;p&gt;I have stumbled upon the following past exam question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;4 decapeptides A, B, C, D, made only of glycine residues, have&#xA;  different conformations, and the phi and psi angles of individual&#xA;  peptides are indicated on the Ramachandran plot (unfortunately I&#xA;  cannot provide a specific plot). Order these peptides by decreasing&#xA;  length.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;How should I solve this, what information useful in solving this problem can I deduce from the Ramachandran plot?&lt;/p&gt;&#xA;" OwnerUserId="3751" LastActivityDate="2014-08-25T21:51:09.517" Title="Deduce length order of 4 decapeptides based on the Ramachandran plot" Tags="&lt;proteins&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20763" PostTypeId="2" ParentId="20745" CreationDate="2014-08-25T11:37:08.987" Score="0" Body="&lt;p&gt;Some species of fireflies (Lampyridae, Coleoptera) synchronize their light patterns during the mating procedure. &lt;a href=&quot;http://www.nps.gov/grsm/naturescience/fireflies.htm&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8015" LastActivityDate="2014-08-25T11:37:08.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20764" PostTypeId="2" ParentId="20759" CreationDate="2014-08-25T11:55:35.027" Score="12" Body="&lt;p&gt;Short answer: no, there is no fixed frame rate or frame-based processing in mammalian vision.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photons arriving at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Photoreceptor_cell&quot;&gt;photoreceptors&lt;/a&gt; at the back of the human retina interact with photo-sensitive pigments called &lt;em&gt;opsins&lt;/em&gt;, and modulate their release of the neurotransmitter &lt;em&gt;glutamate&lt;/em&gt; . The level of glutamate released from a photoreceptor then changes the membrane potential of the other neurons in the retina connected to the photoreceptor (&lt;em&gt;bipolar cells&lt;/em&gt;, for instance). Signals are processed within the retina, then passed through &lt;em&gt;retinal ganglion cells&lt;/em&gt; (RGCs), along the optic nerve, through sub-cortical structures and in to visual cortex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This process occurs continuously, but all of the elements along the way have intrinsic time constants and other temporal constraints (number of photons required for opsin activation; recovery rate of the opsins in the photoreceptors; membrane time constants and refractory periods of neurons; synaptic delays; etc.). Persistence of vision (the effect underlying the perception of a movie as a continuous stream rather than a series of distinct frames) probably relies on the conjunction of many of these time constants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Concretely, a flashed visual stimulus produces a response in (primate) visual cortex after around 30–50 ms (&lt;a href=&quot;http://maunsell.med.harvard.edu/Downloads/publications/92bMaunsell.pdf&quot;&gt;Maunsell and Gibson 1992&lt;/a&gt;). You can recognise and subsequently recall a lot of detail from a sequence of images flashed at around 100–150 ms per image [citation needed]. These are still not hard and fast definitions of the &quot;speed&quot; of vision.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since we only learnt to produce movies as sequences of distinct frames, it's tempting to guesstimate the speed of human vision in those terms. Biology, as always, is more complicated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as the &quot;spinning rims&quot; issue goes, there are many aspects of cortical and subcortical activity that tend towards oscillatory activity. In a system with an intrinsic frequency (for example, the neurons in the thalamocortical loop between LGN and primary visual cortex), providing an oscillatory stimulus can synchronise the system to the stimulus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many of the intrinsic time-constants I described above could result in a tendency to oscillate at some intrinsic frequency, and then be subject to phase locking due to a periodic stimulus close to that frequency.&lt;/p&gt;&#xA;" OwnerUserId="8495" LastEditorUserId="8495" LastEditDate="2014-08-25T12:02:46.627" LastActivityDate="2014-08-25T12:02:46.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20765" PostTypeId="1" AcceptedAnswerId="20771" CreationDate="2014-08-25T12:23:15.467" Score="1" ViewCount="555" Body="&lt;p&gt;There are many online calculators for measuring walking/running/bicycling calories burn rate. They differ in input parameters like some might need my weight as well as height and some don't. Almost none take into account duration of the exercise (and this is crucial in my opinion).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question here is: Where are these formulas (used in these calculators) coming from? Any scientific studies perhaps? Are they reliable?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also I would like to know what is the most accurate method available for measuring the burn rate (I'm only interested in the scientific part, not going to do this myself).&lt;/p&gt;&#xA;" OwnerUserId="8950" LastEditorUserId="3340" LastEditDate="2015-06-04T11:44:27.727" LastActivityDate="2015-06-04T11:44:27.727" Title="Calories burn rate calculation — scientific studies" Tags="&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20766" PostTypeId="2" ParentId="17568" CreationDate="2014-08-25T12:31:04.290" Score="3" Body="&lt;p&gt;Ok, let's talk about mammalian neocortex rather than about the entire central nervous system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The vast majority of synapses within the cortex are formed between neurons within the same cortical area (&lt;a href=&quot;http://dx.doi.org/10.1523/JNEUROSCI.1400-04.2004&quot; rel=&quot;nofollow&quot;&gt;Binzegger et al 2004&lt;/a&gt;). Although most of these synapses will not be self-connections (from a single neuron back to itself), they are &lt;em&gt;recurrent&lt;/em&gt; in the sense that there is a high degree of interconnectivity within a cortical area. In visual cortex, connections within the superficial layers of cortex (layer 2/3 &amp;lt;-&gt; layer 2/3) make up around &lt;strong&gt;70% of all&lt;/strong&gt; excitatory synapses in visual cortex!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In contrast, the &quot;feed-forward&quot; pathway into visual cortex makes up &lt;strong&gt;less than 1%&lt;/strong&gt; of the excitatory synapses in visual cortex (&lt;a href=&quot;http://dx.doi.org/10.1002/cne.22133&quot; rel=&quot;nofollow&quot;&gt;Costa &amp;amp; Martin 2011&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you change your scope to look only at inter-cortical-regional projections, then there is comparatively less recurrence (i.e. strong bi-directional connections between two cortical areas), although it still exists. Connections between cortical areas seem to be correlated with physical distance across the cortex (&lt;a href=&quot;http://dx.doi.org/10.1177/1073858404268478&quot; rel=&quot;nofollow&quot;&gt;Vezoli et al. 2004&lt;/a&gt;). Connections between adjacent areas (V1 and V2, for example) are strong in both directions, and appear to project to similar cortical laminae in both directions. In contrast, projections over longer distances are comparatively weaker, and target different cortical laminae in either direction.&lt;/p&gt;&#xA;" OwnerUserId="8495" LastActivityDate="2014-08-25T12:31:04.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20767" PostTypeId="2" ParentId="8580" CreationDate="2014-08-25T12:40:13.697" Score="1" Body="&lt;p&gt;We don't know yet in detail how different cortical areas are wired up, so it's difficult to say to what extent the wiring differs. But the overall structure of different cortical areas is remarkably similar, in terms of the layers of cortex and their cellular components.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Certainly the structure of the input is very different between cortical areas, and cortex seems to take great care during development how that input is structured.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We don't know why cortex is parcellated the way it is. But connections &lt;em&gt;within&lt;/em&gt; cortical areas devoted to a single &quot;function&quot; are much more prevalent than connections &lt;em&gt;between&lt;/em&gt; cortical areas. This suggests two things: many connections are required between neurons processing similar information, which implies that those neurons should be close together, because wire is expensive in the brain (i.e. requires resources and takes up a &lt;em&gt;lot&lt;/em&gt; of space); alternatively, maybe the information is easier to process if it's kept physically separated.&lt;/p&gt;&#xA;" OwnerUserId="8495" LastActivityDate="2014-08-25T12:40:13.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20768" PostTypeId="2" ParentId="20520" CreationDate="2014-08-25T12:49:02.893" Score="1" Body="&lt;p&gt;Glutamate release from photoreceptors is &lt;em&gt;inhibited&lt;/em&gt; by incident photons (&lt;a href=&quot;http://en.wikipedia.org/wiki/Photoreceptor&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;). During photobleaching, assume that the effect of an incident photon drops to zero. The implication then is that if all light is removed subsequent to selective photobleaching, there will be no difference in activation between bleached photoreceptors and unbleached photoreceptors. This observation suggests that no afterimage will be visible in darkness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But there might be rebound effects or other effects of light adaptation that will result in a perceivable afterimage in darkness. Certainly there are hallucinatory visual patterns than can be generated cortically, suggesting that a cortical afterimage could be generated in darkness.&lt;/p&gt;&#xA;" OwnerUserId="8495" LastActivityDate="2014-08-25T12:49:02.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20770" PostTypeId="1" CreationDate="2014-08-25T13:54:25.657" Score="4" ViewCount="353" Body="&lt;p&gt;Sexual dimorphism is very common and (normally) requires the evolution of sex-specific genetic variation/regulation so the genetic correlation between the sexes can be &amp;lt;1. Is there consensus as to how this type of variation predominantly spreads? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can see it could evolve by drift and selection and I expect it is predominantly via selection (sexually antagonistic selection for different optimal genotypes)- We typically associate sex differences in traits with sex differences in selection (ecological, sexual selection...).&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-08-25T13:59:43.973" LastActivityDate="2014-08-26T10:21:20.840" Title="Main mechanism of the evolution of sexual dimorphism" Tags="&lt;evolution&gt;&lt;sexual-dimorphism&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20771" PostTypeId="2" ParentId="20765" CreationDate="2014-08-25T14:44:38.163" Score="1" Body="&lt;p&gt;Disclaimer: Not my field but I'm doing my best.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We often measure the calories consumed indirectly by measuring the quantity of oxygen consumed. As we have a reserve of &lt;a href=&quot;http://en.wikipedia.org/wiki/Adenosine_triphosphate&quot; rel=&quot;nofollow&quot;&gt;ATP&lt;/a&gt;(ATP is a molecule, a stock of ATP is some kind of battery of our body) in our body, at very short term the oxygen consumption is not necessarily perfectly correlated with energy use but at a longer term it works perfectly fine. Seek for further information on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Citric_acid_cycle&quot; rel=&quot;nofollow&quot;&gt;Citric Acid Cycle&lt;/a&gt; to understand why the oxygen consumption is directly related to the energy created (which is itself at a long enough term directly related to energy use). If I am not mistaken a bunch of seconds should probably be a long enough term (time to consume all ATP at the start of an important effort) but I would appreciate if someone could give a reference for that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For small animals we often put the animal in a chamber and calculate the energy consumption by measuring the volume of CO2 that they expire. For this purpose we have to measure the volume of CO2 at the entrance and at the exit (of the chamber) to measure the difference. For humans, we often put a mask on the face of the &quot;cobaye&quot;. We allow him to breath normally without doing any effort for a while and then we ask him to run/bike/whatever on a home trainer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know much about such studies but it is important to 1) know the variance in energy consumption in the population for a typical exercice 2) understand that lab condition probably differ in various ways from person-to-person real life condition (no wind, no dust, stress of the experimentator, discomfort of the mask, ...).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I have no idea concerning the variance in the population I cannot tell how representative are the summary values that we can find on many popular websites but I would tend to think that given the experimentation, these numbers has probably been fairly accurately measured. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-08-25T14:44:38.163" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20772" PostTypeId="2" ParentId="20762" CreationDate="2014-08-25T15:24:06.063" Score="1" Body="&lt;p&gt;When &amp;phi; = &amp;psi; = 180&amp;deg; the peptide is in the fully extended conformation i.e. it is the 'longest' it can be. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it isn't possible to deduce a length order based on this information then I guess you will have to do some geometry to calculate the sums of the distances between the &amp;alpha; C atoms using the known values for all of the bond angles - sounds laborious to me!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bmb.uga.edu/wampler/tutorial/prot2.html&quot; rel=&quot;nofollow&quot;&gt;This site&lt;/a&gt; tabulates values of &amp;phi;/&amp;psi; for typical structures (helix, sheet, turn) so it may be possible to decide if some of peptides are adopting these.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-08-25T15:50:47.377" LastActivityDate="2014-08-25T15:50:47.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20773" PostTypeId="2" ParentId="20759" CreationDate="2014-08-25T15:30:46.363" Score="3" Body="&lt;p&gt;While in human made cameras light sensor and any image processor are separate devices, in the living eye the first steps of image analysis begin in retina already as light sensing cells are part of the nervous system. The optic nerve carries pre-processed information and not the encoded original image to the brain. This pre-processed information is not segmented into frames.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;image processing system&quot; of the human vision would generalize a presented sequence of frames into logical continuous movement, even if the frame rate is as low as &lt;a href=&quot;https://www.quora.com/Whats-the-least-amount-of-frames-per-second-I-can-get-away-with-that-still-shows-fluid-movement-when-creating-homemade-Youtube-quality-animation&quot; rel=&quot;nofollow noreferrer&quot;&gt;few FPS only&lt;/a&gt;. This does not mean the eye cannot see that is going on. Frame rates as high as 120 FPS are required to reach the inertia limits so that the &lt;a href=&quot;https://en.wikipedia.org/wiki/Flicker_(screen)&quot; rel=&quot;nofollow noreferrer&quot;&gt;flickering&lt;/a&gt; really cannot be seen.&lt;/p&gt;&#xA;" OwnerUserId="5924" LastEditorUserId="5924" LastEditDate="2019-04-30T08:43:19.557" LastActivityDate="2019-04-30T08:43:19.557" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="20774" PostTypeId="1" AcceptedAnswerId="20776" CreationDate="2014-08-25T15:33:46.840" Score="3" ViewCount="241" Body="&lt;p&gt;I'm looking for a general (and easy, this is going to be for an undergrad class) protocol to isolate and culture primary cells from fruit flies.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-08-26T11:17:57.467" Title="Looking for protocol to produce a drosophila primary cell line" Tags="&lt;cell-culture&gt;&lt;drosophila&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20776" PostTypeId="2" ParentId="20774" CreationDate="2014-08-25T18:13:44.380" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4625067&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; is the original 1972 paper describing the isolation of the S2 cells from &lt;em&gt;Drosophila&lt;/em&gt;. However it would be best if you specify what application you are planning to pursue with the cells, which would make it easier to suggest which ones to isolate. I have personally isolated garland cells, which are visible with the naked eye and highly suitable for endocytic assays. It takes a few minutes to isolate them and all you need are two grade 5 or grade 4 sharp tweezers and 2nd or 3rd instar  &lt;em&gt;Drosophila&lt;/em&gt; larvae and a dish and some PBS to submerge the larvae in. You don't even need to pin them! If you are interested I can edit this response and write their isolation technique as I can't find a good technique online.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have not personally isolated S2 cells although I have extensively worked with S2 and S2R+ cell lines (which are embryonic). Garland cells are excellent to work with for endocytic assays using Dextran (fluorescent dye used for bulk endocytosis assays) and Dynasore [dynamin inhibitor] (and infact they were used to characterise &lt;em&gt;Drosophila&lt;/em&gt; dynamin homologue, shibire, &lt;a href=&quot;http://jcb.rupress.org/content/97/2/499.full.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2808544&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and its temperature sensitive behaviour in Shi[ts] mutants and shi role in endocytosis) as an example shown &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24816559&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; in fig 6 using S2 cells. I have never cultured the garland primary cells so I do not know their PD and how they behave in Schneider+FBS (since I only isolated them and performed andocytic assays with them while they were in schneiders) and I don't think anyone has (but have a look) so it would be a great protocol to stablish and publish in a methods paper. I'm more than happy to share the isolation technique with you, tried looking on jove or youtube for a video but failed to find one, and let you know what to look for if you wish. Just as a cautionary note, garland cells are multi-nucleated (i have seen up to 4) so it might not divide very well or at all so just bear that in mind.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-26T11:17:57.467" LastActivityDate="2014-08-26T11:17:57.467" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20777" PostTypeId="2" ParentId="8580" CreationDate="2014-08-25T19:00:59.477" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;The brain is separated into different regions, and different regions perform different tasks&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not really. This kind of claims stem from the early brain research, where every area was thought to specialize in one particular task. Sure, some categorization is possible (e.g. where the visual input is &lt;em&gt;mostly&lt;/em&gt; processed). However, your question is basically an argument that is false.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just look for example the temporal lobes and compare how the sulcal and gyral areas differ with respect to information processing.&lt;/p&gt;&#xA;" OwnerUserId="8954" LastActivityDate="2014-08-25T19:00:59.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20778" PostTypeId="2" ParentId="20756" CreationDate="2014-08-25T19:38:07.247" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;some number of interstices (spaces between successive loci) get picked&#xA;  and each chromosome gets broken at each interstice.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That number is usually around 1.  It's not common to have a lot more than that per chromosome.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It also seems clear that all interstices are equally likely to get&#xA;  picked.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No, there certainly are &quot;hot spots&quot; that are more likely to be cross-over junctions than other sequences.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-08-25T19:38:07.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20779" PostTypeId="2" ParentId="20762" CreationDate="2014-08-25T21:36:43.330" Score="1" Body="&lt;p&gt;The Ramachandran plot describes secondary structure. If you see a lot of beta sheets in your plot you will have a more compact molecule than one which is wholly alpha helix. Gly can be almost anywhere in any quadrant. Look for residues with secondary structure to determine tertiary structure. &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-25T21:51:09.517" LastActivityDate="2014-08-25T21:51:09.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20780" PostTypeId="1" CreationDate="2014-08-25T22:27:53.950" Score="0" ViewCount="49" Body="&lt;p&gt;Which poses the greater threat to ecology Global Ocean Acidification or Warming?&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="4747" LastEditDate="2014-08-25T22:52:41.667" LastActivityDate="2014-08-25T22:58:46.267" Title="Global Acidification or Warming" Tags="&lt;global-warming&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-08-26T05:50:09.820" ContentLicense="CC BY-SA 3.0" />
  <row Id="20781" PostTypeId="2" ParentId="20756" CreationDate="2014-08-25T22:41:25.350" Score="2" Body="&lt;p&gt;Parts of your general idea are correct, others need some refinement. To skip ahead to the conclusion: I'm going to recommend that you read up about linkage disequilibrium. Everything else is background information that will hopefully help you understand why linkage disequilibrium is what I think you're looking for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background: Meiosis Basics&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, in the bare principle, meiosis is quite simple. Let's consider meiosis in a human cell, i.e. the division of a primary spermatocyte (the only other example is division of primary oocytes). That's this one we're talking about: &lt;a href=&quot;http://en.wikipedia.org/wiki/File:Figure_28_01_04.jpg&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/File:Figure_28_01_04.jpg&lt;/a&gt; In simple terms, the ready-to-develop primary spermatocyte contains 46 chromosomes, two (2n) each of chromosomes 1-22, an X and a Y chromosome. Two chromosomes of the same type (e.g. &quot;chromosome 4&quot;) are called homologues. Homologues contain different versions (= alleles) of the same genes. During Meiosis I, homologues align in pairs, recombine, and then separate into two new cells (which are now 1n). The following Meiosis II is basically a mitosis, meaning that the two (identical apart from previous recombinations) chromatids of the chromosomes are separated and packaged into separate cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Recombination and Interstices&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During the alignment of homologues in Meiosis I, the attraction between the two chromosomes depends on their homology - i.e. similarities in DNA sequences that end up being close to each other in this setting. This attraction is on the molecular level, so the tightly-condensed neighbouring DNA double-helices actually physically stick to each other because the polarities/charges across relatively large stretches of the molecules complement each other. I don't think how this exactly works is well understood yet, but what is clear is that homologues attract each other at this point because they contain mostly the same DNA sequence, apart from small differences (which make the different alleles).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How exactly recombination occurs at this point isn't entirely clear either on the molecular level (&lt;a href=&quot;http://en.wikipedia.org/wiki/Homologous_recombination#In_eukaryotes&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Homologous_recombination#In_eukaryotes&lt;/a&gt;). Just to get an idea of how it could work: while the two chromosomes are aligned, it's not difficult for them to actually tangle up and break, leaving the repair machinery with the potential to fuse the wrong chromosome ends together. The breaking and exchange might also be a programmed process with dedicated cell machinery (quite probably so I think personally).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, &lt;strong&gt;not all locations are equally likely to recombine&lt;/strong&gt;. It depends on levels of homology (i.e. &quot;stickiness&quot;) between individual stretches of DNA and other unknown factors. Just in the same way, the number of break points in each chromosome isn't pre-determined.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Mendelian Inheritance&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, the concept of loci is arbitrary and has no molecular basis. A locus is simply &quot;a place on a chromosome&quot; and could refer to an individual base(-pair) or a whole stretch of DNA. The concept is however useful when talking about inheritance, as it illustrates the principle of &lt;em&gt;linkage&lt;/em&gt;, or rather &lt;strong&gt;linkage disequlibrium&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I am aware, it comes from a time before we began thinking in chromosomes. One could study whether there was linkage between two traits (or more generally loci), i.e. a higher-than-random chance to inherit the two together. We now know that linkage simply means that the two loci are on the same chromosome (for example, chromosome 6). Thus, if no linkage exists, the chance to inherit both loci together is no larger than expected by random Mendelian inheritance (which makes sense as there is no molecular mechanism that makes offspring e.g. more likely than 50/50 to inherit chromosome 6 and 19 together from the same parent). If linkage exists , the loci are on the same chromosome, and any case where the two are &lt;em&gt;not&lt;/em&gt; inherited together must be caused by recombination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea of linkage disequlibrium is that loci that are close to each other on a chromosome are more likely to remain together (and be inherited together) than far-apart loci. This is obviously due to the increased chance of a recombination event occurring between them with increased distance. This actually seems to be what you are looking for as a pointer for where to go next, so I recommend using your preferred internet search engine to learn more about that :)&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2014-08-25T22:41:25.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20782" PostTypeId="2" ParentId="20780" CreationDate="2014-08-25T22:58:46.267" Score="2" Body="&lt;p&gt;The issues of global ocean acidification and global warming are two symptoms of the same disease, too much carbon in the atmosphere. And they have 1 solution, put less carbon into the atmosphere. It doesn't really matter which aspect is the more harmful one, you can't treat one without treating the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If reducing carbon output were simple, we would have done it by now. However, it will most likely require radical changes to our energy infrastructure, with moves away from coal, oil, and natural gas and towards solar, wind, and nuclear power. It will probably require changes to our agricultural practices, and you should really watch &lt;a href=&quot;https://www.youtube.com/watch?v=vpTHi7O66pI&quot; rel=&quot;nofollow&quot;&gt;Allan Savory's TED Talk&lt;/a&gt; for how those changes should be implemented. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;People are very slow to change their habits, and short term profit is a powerful motivator against change, but I believe these we can and must solve these problems if humanity is to continue to thrive on Earth.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-25T22:58:46.267" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="20783" PostTypeId="1" CreationDate="2014-08-26T00:30:26.663" Score="1" ViewCount="2252" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HwTjo.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would happen (in reality or theoretically) if the entire right side of a human's body was removed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could they live (aside from all the probable infections and such)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would guess that humans can live without part of the liver or brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The left brain controls the right side of the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do you think (or know) will happen?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you very much in advance!&lt;/p&gt;&#xA;" OwnerUserId="8730" LastEditorUserId="6289" LastEditDate="2016-05-07T06:54:31.867" LastActivityDate="2016-05-07T06:54:31.867" Title="What would happen if a person had the right side of their body totally removed (including the brain)?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ClosedDate="2014-08-26T10:43:05.970" ContentLicense="CC BY-SA 3.0" />
  <row Id="20784" PostTypeId="2" ParentId="20783" CreationDate="2014-08-26T02:04:49.040" Score="5" Body="&lt;p&gt;They would die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's imagine that we perfectly cut a person down the middle. That would mean cutting the spinal cord in half, probably damaging the tissue so much that the remaining half wouldn't work well. The liver would be gone. The intestines and bladder would just be open. The heart would have to be adjusted to the left. The surgery would probably cause so much blood loss that they wouldn't even survive to die of other organ failure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And you already alluded to the mismatch between what side of the brain controls what side of the body, so if you kept the pseudocorpse &quot;alive&quot; on an IV, heart lung machine, and hemodialysis, they'd probably still be paralyzed.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-26T02:04:49.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20786" PostTypeId="2" ParentId="20783" CreationDate="2014-08-26T02:37:15.007" Score="4" Body="&lt;p&gt;We humans are not perfectly symmetrical. Some organs exist only on one side of the body which are critical for life.That said you can however live without half your brain (if you call that state living) and some other organs also have distributed function over thier surface. &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2014-08-27T06:32:39.750" LastActivityDate="2014-08-27T06:32:39.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20787" PostTypeId="1" CreationDate="2014-08-26T02:57:11.040" Score="3" ViewCount="1464" Body="&lt;p&gt;I have a few issues with this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;An enzyme assay is performed and the kinetic data graphed. The y-intercept of a Lineweaver-Burk plot is 0.6 min/ΔA. The substrate being assayed has a molar absorbance coefficient (ε) of 4500 L/mol.cm.&#xA;What is the V max of the enzyme in mmol/L.min?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My working:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vmax = 1 / 0.6min/ΔA = &lt;strong&gt;1.66ΔA/min&lt;/strong&gt; (the units switch back I believe?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And then 1.66ΔA/min / 4.5L/mmol.cm to get &lt;strong&gt;0.37 mmol/L.min?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="8605" LastActivityDate="2014-08-26T04:28:33.063" Title="Enzyme Assay, absorbance change to concentration change" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20790" PostTypeId="1" CreationDate="2014-08-26T04:08:55.200" Score="2" ViewCount="87" Body="&lt;p&gt;I am trying to clone a rice gene under a different endogenous rice promoter.I will be cloning the CDS of the rice gene.So I wanted to know what is the minimum or maximum distance I should put between the rice and the promoter so that I can get good expression levels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Should I check the expression of the construct in E.coli before transforming it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What should steps should I follow before finally transforming the construct into rice?&lt;/p&gt;&#xA;" OwnerUserId="8617" LastActivityDate="2014-08-26T04:08:55.200" Title="What should be the distance between plant promoter and gene?" Tags="&lt;botany&gt;&lt;cloning&gt;&lt;biotechnology&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20791" PostTypeId="2" ParentId="20787" CreationDate="2014-08-26T04:28:33.063" Score="1" Body="&lt;p&gt;see &lt;a href=&quot;https://biology.stackexchange.com/questions/19948/scale-up-of-bacterial-growth-from-250ml-to-1-5l/20007#20007&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;y-intercept = $\frac{1}{V_{max}}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To convert absorbance to concentration, plot the standard curve and get the linear relationship between the two quantities. Make sure that the line that you fit (for standard curve) passes through origin. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-08-26T04:28:33.063" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20796" PostTypeId="2" ParentId="20682" CreationDate="2014-08-26T06:23:09.207" Score="0" Body="&lt;p&gt;The minerals will stay behind. They are too heavy to be transported via the vacuoles of MOST, and most must be stressed when dealing with plants, plants during transpiration. Though the water-soluble compounds- including the volatile compounds mentioned like terpenes and even flavonoids will and can exit during transpiration. Terpenes are not bad for humans, the term volatile refers only to the reactivity, not whether or not it is bad.&lt;/p&gt;&#xA;" OwnerUserId="8960" LastActivityDate="2014-08-26T06:23:09.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20797" PostTypeId="1" AcceptedAnswerId="20798" CreationDate="2014-08-26T06:42:01.510" Score="3" ViewCount="346" Body="&lt;p&gt;Long Range PCR using NEB Master Mix - Hot Start Taq was working fine for me (amplicon sizes of ~10kb) but stopped working all of a sudden. Is it possible that many freeze-thaw cycles on the DNA template introduces nicks into the DNA strand that hamper the polymerase activity ? In certain cases, I am getting no amplification and in some I am getting very weak amplification. Because the integrity of the DNA should be intact over the entire length in case of long range PCR, am I right in thinking nicks in DNA will be especially detrimental if we are trying to amplify large fragments ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concentration of the DNA templates I used was 90-140ng/ul in a 10ul PCR reaction, DNA eluted in TE buffer after a magnetic bead method of DNA extraction. &lt;/p&gt;&#xA;" OwnerUserId="18932" LastActivityDate="2014-08-26T07:15:59.810" Title="How do nicks in the DNA strand affect the success of Long Range PCR?" Tags="&lt;dna&gt;&lt;pcr&gt;&lt;dna-damage&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20798" PostTypeId="2" ParentId="20797" CreationDate="2014-08-26T07:15:59.810" Score="2" Body="&lt;p&gt;It is not unlikely that nicking is causing trouble. The question is if repeated freezing and thawing is causing the problem, there is an article which has been published in B.R.L. Focus in 1983 which disputes this effect. You can find the PDF with the article &lt;a href=&quot;https://tools.lifetechnologies.com/Content/Focus/Focus%20Volume%205%20Issue%202.PDF&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, the article itself starts on page 10 in the PDF. On the other hand there is this paper (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20810770&quot; rel=&quot;nofollow&quot;&gt;Impact of long-term storage on stability of standard DNA for nucleic acid-based methods.&lt;/a&gt;&quot;), which shows that sstorage conditions do have an effect on the effciency of qPCR standards. Whatever causes nicking, it is a problem in (long) PCR. The following quote is from &lt;a href=&quot;http://www.sigmaaldrich.com/technical-documents/protocols/biology/amplification-of-dna-with-red-dye.html#sthash.qyOjBVNh.dpuf&quot; rel=&quot;nofollow&quot;&gt;Sigma&lt;/a&gt; in their long PCR enzyme mix:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Template High quality and adequate length of the template are&#xA;  essential for reliable amplification of larger fragments. Extreme care&#xA;  must be taken in the preparation and handling of the DNA target for&#xA;  long PCR. Nicked or damaged DNA can serve as a potential priming site&#xA;  resulting in high background. Avoid freezing, or, alternatively,&#xA;  freeze only once to minimize damage. The condition of the target DNA&#xA;  is critical. Depurination during cycling is minimized by use of&#xA;  buffers with a pH greater than 9.0 at 25 °C.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This paper (&quot;&lt;a href=&quot;http://nar.oxfordjournals.org/content/24/24/5026.long&quot; rel=&quot;nofollow&quot;&gt;Effect of Highly Fragmented DNA on PCR&lt;/a&gt;&quot;) shows that induced nicks affect the efficiency of PCR (although they do a much shorter amplification than you). So to overcome this problem I would make small aliquots of fresh DNA preps and then see, if this helps.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-26T07:15:59.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20799" PostTypeId="1" CreationDate="2014-08-26T09:09:06.007" Score="2" ViewCount="69" Body="&lt;p&gt;I am writing a project proposal and I have to talk about this problem: &lt;strong&gt;how to identify the genes that distal enhancers pair&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am really new to this topic and I don't know what it is all about. I have been searching the literature but I did not find anything useful. Can someone explain to me what it is all about?&#xA;Maybe suggest some papers to me.&lt;/p&gt;&#xA;" OwnerUserId="885" LastEditorUserId="3340" LastEditDate="2014-08-26T10:17:33.063" LastActivityDate="2014-08-26T10:17:33.063" Title="How to identify the genes that distal enhancers pair?" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20800" PostTypeId="2" ParentId="20799" CreationDate="2014-08-26T09:25:17.287" Score="2" Body="&lt;p&gt;Check this technique called Chromosome Conformation Capture (3C). Its variants exist such as 4C, Hi-C etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, the principle of this technique is based on the physical interaction between the enhancer and promoter that is bridged by a transcriptional modulator(protein). &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The chromatin is crosslinked&lt;/li&gt;&#xA;&lt;li&gt;DNA is sheared&lt;/li&gt;&#xA;&lt;li&gt;The protein is pulled down (Optional)&lt;/li&gt;&#xA;&lt;li&gt;The fragments of the promoter and enhancer are ligated together and then sequencing/qRTPCR is done. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Sequencing (low throughput- sanger) can be used to identify enhancers of a given promoter. qRTPCR can be used to quantify the strength of the association.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I just said is not a high throughput technique. Hi-C is high throughput variant of 3C. See the protocol &lt;a href=&quot;http://www.jove.com/video/1869/hi-c-a-method-to-study-the-three-dimensional-architecture-of-genomes&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-08-26T09:52:35.380" LastActivityDate="2014-08-26T09:52:35.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20801" PostTypeId="2" ParentId="20770" CreationDate="2014-08-26T10:13:28.463" Score="2" Body="&lt;p&gt;Sexual dimorphism evolves, as you suspect, via natural selection, specifically sexual selection (which I view as a form of natural selection).  &lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/IIIDGeneticdrift.shtml&quot; rel=&quot;nofollow&quot;&gt;Genetic drift&lt;/a&gt;, by definition, is random. Random changes of allele frequencies are extremely unlikely to lead to the consistent evolution of phenotypic differences between males and females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/IIIE3Sexualselection.shtml&quot; rel=&quot;nofollow&quot;&gt;Sexual selection&lt;/a&gt; on the other hand can lead to rapid evolution of secondary sexual characteristics (sexual dimorphism). If you consider natural selection in the broad sense, an organism's traits affect survivorship but do not guarantee reproduction. Individuals that live longer have an increased &lt;em&gt;chance&lt;/em&gt; of reproducing more frequently but this does not mean the organism actually &lt;em&gt;will&lt;/em&gt; reproduce more often than any other individual. In contrast, sexual selection acts directly on mating success. If a female chooses a male based on his secondary sexual characters, then that male will mate. His fitness (offspring produced) will be increased relative to males that are not chosen and do not mate. This can lead to &lt;a href=&quot;http://www.pnas.org/content/78/6/3721.full.pdf&quot; rel=&quot;nofollow&quot;&gt;runaway sexual selection&lt;/a&gt; for male traits and even &lt;a href=&quot;http://www.nature.com/nature/journal/v403/n6772/full/403886a0.html&quot; rel=&quot;nofollow&quot;&gt;speciation&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are correct that sexual selection results from &lt;a href=&quot;http://www.cell.com/current-biology/pdf/S0960-9822(05)00753-0.pdf&quot; rel=&quot;nofollow&quot;&gt;sexual conflict&lt;/a&gt;. Such conflict can arise because females invest considerable energy into relatively few eggs. Thus, it benefits her to be selective for her mates. If she chooses poorly, her fitness can be decreased quite a bit. On the other hand, males can produce copious quantities of sperm rapidly and with little energy cost. If a male wastes sperm on a genetically-poor female, his fitness is not really reduced. He can quickly mate with other females at little cost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any evolutionary text. They cover the basics of sexual selection in some detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gavrilets, S. 2000. Rapid evolution of reproductive barriers driven by sexual conflict. Nature 403: 886-889.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hosken, D.J. and P. Stockley. 2005. Sexual conflict. Current Biology 15: R535-R536.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lande, R. 1981. Models of speciation by sexual selection on polygenic traits. Proceeedings of the National Academy of Sciences USA 78: 3721-3725.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-08-26T10:21:20.840" LastActivityDate="2014-08-26T10:21:20.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20803" PostTypeId="2" ParentId="20657" CreationDate="2014-08-26T11:45:58.523" Score="2" Body="&lt;p&gt;Honey is produced from nectar that does not contain any living cells and carefull beekeeper should be able to take at least some from the hive without killing any bees. However bees themselves will also consume pollen that is alive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also may be possible to feed on fruits; while cells there are still alive, they are about to die soon without any prospects of future surviving. If you really do not want to harm the plant in any way, take the seed from the fruit and plant it somewhere. Fruits are for seed propagation only and the plant should really not have any pretensions to you afterwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dead leaves in the autumn may contain the needed materials; unfortunately they are not edible directly and would need some pre-processing technology.&lt;/p&gt;&#xA;" OwnerUserId="5924" LastEditorUserId="5924" LastEditDate="2014-09-10T13:04:21.067" LastActivityDate="2014-09-10T13:04:21.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20805" PostTypeId="1" AcceptedAnswerId="20806" CreationDate="2014-08-26T12:06:53.147" Score="3" ViewCount="117" Body="&lt;p&gt;I've stumbled upon a table comparing the sensitivities of different detection methods in NMR spectroscopy: &quot;Direct&quot;, &quot;DEPT&quot; and &quot;Inverse&quot;, where &quot;Inverse&quot; seems to be the most sensitive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iHbiI.png&quot; alt=&quot;Sensitivity of Detection Methods in NMR Spectroscopy&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What exactly are those different methods are and how do they differ?&lt;/p&gt;&#xA;" OwnerUserId="8964" LastEditorUserId="6307" LastEditDate="2017-04-02T20:17:41.263" LastActivityDate="2017-04-02T20:17:41.263" Title="NMR spectroscopy detection methods for proteins" Tags="&lt;biophysics&gt;&lt;protein-structure&gt;&lt;methods&gt;&lt;spectroscopy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20806" PostTypeId="2" ParentId="20805" CreationDate="2014-08-26T13:14:10.640" Score="5" Body="&lt;p&gt;In most cases when you perform NMR experiments on proteins you detect the signal on the protons. Even if you're looking at other nuclei, in the end you transfer the magnetization to a proton and detect that signal. This is simply the most sensitive method due to the high gyromagnetic ratio of &lt;sup&gt;1&lt;/sup&gt;H, and this is the method that is labeled &quot;inverse&quot; in your figure. This is pretty much the default way to measure heteronuclear spectra.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Direct detection means that you directly observe the less sensitive nucleus like &lt;sup&gt;13&lt;/sup&gt;C. This has certain advantages especially for large proteins where you often have to deuterate the protons to be able to measure anything useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DEPT is a type of experiment where magnetization is transferred from the directly attached protons to the heteronucleus. This increases the sensitivity and allows to distinguish CH and CH&lt;sub&gt;3&lt;/sub&gt; groups from CH&lt;sub&gt;2&lt;/sub&gt; groups&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="3340" LastEditDate="2014-10-31T12:35:13.983" LastActivityDate="2014-10-31T12:35:13.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20807" PostTypeId="1" CreationDate="2014-08-26T13:22:39.143" Score="1" ViewCount="38" Body="&lt;p&gt;Can we have the technology to recreate the informations (like images, sounds etc.)[as in the form of signals in our mind] from human mind to human understandable format? In short, can we read human mind?&lt;/p&gt;&#xA;" OwnerUserId="8902" LastActivityDate="2014-08-26T13:22:39.143" Title="Is it possible to convert nerve signals or electrical pulses into a readable format?" Tags="&lt;neuroscience&gt;" AnswerCount="0" CommentCount="14" FavoriteCount="1" ClosedDate="2014-08-26T22:55:27.890" ContentLicense="CC BY-SA 3.0" />
  <row Id="20808" PostTypeId="1" AcceptedAnswerId="20825" CreationDate="2014-08-26T14:13:40.110" Score="3" ViewCount="75" Body="&lt;p&gt;I am involved in a synthetic biology project where I have to do modelling with ODEs. The biological process I want to model is the chelation of Cd&lt;sup&gt;2+&lt;/sup&gt; with phytochelatins, to know how much can be chelated. I know the basics of ODEs and I already did other modelling tasks, but I never studied anything related to chelation (I am a computer scientist) so any hint about how these kind of biochemical reactions are modelled would be helpful to get started.&lt;/p&gt;&#xA;" OwnerUserId="8966" LastEditorUserId="8979" LastEditDate="2014-08-27T05:37:27.950" LastActivityDate="2014-08-30T20:21:57.467" Title="Modelling how much cadmium a cell will be able to chelate with phytochelatins" Tags="&lt;bioinformatics&gt;&lt;mathematical-models&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20809" PostTypeId="1" AcceptedAnswerId="20810" CreationDate="2014-08-26T14:35:11.540" Score="3" ViewCount="1536" Body="&lt;p&gt;While reading a 19th century text of new species description, I'm confused by some Latin phrases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The case here is: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Corp. long. 8 poll., caud. 9 poll.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I guess 'corp.' and 'long.' are abbreviations of some Latin terms, and the whole meaning of the combination of these two words is probably &quot;body length&quot;. But I still can't figure out what &quot;caud.&quot; and &quot;poll.&quot; (the number seems like is in inch though) are stand for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The species described is a rodent species. Full text could be found &lt;a href=&quot;http://biodiversitylibrary.org/page/28500480&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; (p.185).&lt;/p&gt;&#xA;" OwnerUserId="8965" LastActivityDate="2014-08-26T15:51:04.807" Title="19th century Latin species description" Tags="&lt;taxonomy&gt;&lt;history&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20810" PostTypeId="2" ParentId="20809" CreationDate="2014-08-26T14:46:52.257" Score="8" Body="&lt;p&gt;&quot;Caud.&quot; refers to the tail (lat: cauda) and, judging from the description, &quot;poll.&quot; seems to be another word for inch. So the translation should be something like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Body length: 8 inches, tail length: 9 inches.&lt;/p&gt;&#xA;" OwnerUserId="8015" LastActivityDate="2014-08-26T14:46:52.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20812" PostTypeId="2" ParentId="20809" CreationDate="2014-08-26T15:51:04.807" Score="12" Body="&lt;p&gt;The &lt;em&gt;pollex&lt;/em&gt; was a &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Ancient_Roman_units_of_measurement#Length&quot;&gt;Roman length measurement&lt;/a&gt;, approximately equivalent to an inch. The &lt;em&gt;pollex&lt;/em&gt; was also known as the &lt;em&gt;uncia&lt;/em&gt;, which is where the word &quot;inch&quot; comes from. There were 12 &lt;em&gt;unciae&lt;/em&gt; in a &lt;em&gt;pes&lt;/em&gt; ...&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-08-26T15:51:04.807" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20813" PostTypeId="2" ParentId="20465" CreationDate="2014-08-26T16:36:21.960" Score="1" Body="&lt;p&gt;Fish do not die from old age, nor do any other animals. Rather, the older the animal gets the weaker it becomes which means that it is an easier target for predators or can easily succumb to disease.&lt;/p&gt;&#xA;" OwnerUserId="8733" LastActivityDate="2014-08-26T16:36:21.960" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20816" PostTypeId="2" ParentId="20465" CreationDate="2014-08-26T19:27:39.267" Score="6" Body="&lt;p&gt;Yes, at least some fishes have intrinsic lifespans and deaths that are related to their own life-history and not to external forces such as predation or disease.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fishes show three types of senescence. Lampreys, eels and pacific&#xA;  salmon exhibit rapid senescence and sudden death at first spawning.&#xA;  The guppy, red panchax, medaka, platyfish, Indian murrel and many&#xA;  other teleosts undergo gradual senescence, as observed in most of the&#xA;  vertebrates. A number of fishes (e.g. sturgeons, paddlefish, female&#xA;  plaice, flatfish, rockfish) show indeterminate growth, the occurrence&#xA;  of senescence in them is supposed to be very slow or negligible.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7926851&quot; rel=&quot;nofollow&quot;&gt;Patnaik BK, N Mahapatro, and BS Jena. 1994. 'Ageing in fishes' &lt;em&gt;Gerontology&lt;/em&gt; &lt;strong&gt;40&lt;/strong&gt;:113-32&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2014-08-26T21:54:09.897" LastActivityDate="2014-08-26T21:54:09.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20817" PostTypeId="1" CreationDate="2014-08-26T21:13:30.140" Score="1" ViewCount="1498" Body="&lt;p&gt;Does E. coli survive at any pH level? If I was to incubate it in agar of different pH, would it still form a bacterial lawn as it's called?&lt;/p&gt;&#xA;" OwnerDisplayName="user8970" LastEditorUserId="107" LastEditDate="2014-08-27T00:28:22.613" LastActivityDate="2014-08-27T10:58:52.920" Title="Does E. coli survive at any pH level?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20818" PostTypeId="1" CreationDate="2014-08-26T21:39:38.513" Score="2" ViewCount="191" Body="&lt;p&gt;Dear fellow biochemists,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I need some advice on Western Blotting, more specifically the use of certain protease inhibitors with the RIPA cell lysis buffer and protease inhibitor cocktail. A Millipore technical representative recommended my using &quot;539134 | Protease Inhibitor Cocktail Set III, EDTA-Free - Calbiochem&quot; as a good general protease inhibitor cocktail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have another protease inhibitor cocktail which includes: AEBSF, bestatin, E-64, and pepstatin A (E.coli protease inhibitor cocktail) but it does not include the aprotinin or the leupeptin inhibitors. Is there a risk of proteolysis in a mammalian cell lysate without these latter 2 inhibitors? The specific cell types which we are using are: HUVEC (human umbilical vein endothelial cells) and HT-29 adenocarcinoma cell line.&lt;/p&gt;&#xA;" OwnerUserId="8974" LastEditorUserId="948" LastEditDate="2014-08-26T22:00:00.263" LastActivityDate="2014-08-26T23:14:59.090" Title="can a bacterial protease inhibitor cocktail be used for Western Blotting involving HUVEC cells and HT-29 adenocarcinoma cells?" Tags="&lt;proteins&gt;&lt;protocol&gt;&lt;western-blot&gt;&lt;enzyme-kinetics&gt;&lt;protein-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20819" PostTypeId="2" ParentId="20817" CreationDate="2014-08-26T21:48:18.980" Score="1" Body="&lt;p&gt;I assume you are asking if &lt;em&gt;E. coli&lt;/em&gt; can survive extreme pH conditions and according to &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056796&quot; rel=&quot;nofollow&quot;&gt;this study&lt;/a&gt; &lt;em&gt;E. coli&lt;/em&gt; K-12 W3110 survives at pH 1.2 – pH 2.0 under low oxygen. This study cultured different strans overnight and exposed to pH 2.0 for 2 hours before diluting 1:80,000 and 1:400,000, under anoxic and aerated conditions. Dilutions where then plated allowing colonies to grow up overnight at 37 oC so this study measured survival as far as I can tell. &lt;em&gt;E. coli&lt;/em&gt; can demonstrate robustness and &lt;em&gt;E. coli&lt;/em&gt; survives and grows 'accustomed' at pH 7-8 based on the paper &lt;a href=&quot;http://www.scribd.com/doc/11337868/Optimal-Conditions-for-the-Growth-of-E-Coli&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. However it would be great if you clarified your agar pH and the &lt;em&gt;E. coli&lt;/em&gt; genetic background you are interested in if you have a specific question about its particular limits (growth or survival).&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-08-27T10:58:52.920" LastActivityDate="2014-08-27T10:58:52.920" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20820" PostTypeId="2" ParentId="20818" CreationDate="2014-08-26T21:56:57.630" Score="2" Body="&lt;p&gt;In general, leupeptin (a cysteine, threonin and serine protease) and aprotinin (sometimes called Trasylol; trypsin inhibitor) are included in most mammalian cell lysate buffers. Whether you need them is really up to your protein of interest: if you know how it gets degraded in vitro, then you should be fine with inhibition of just those proteases. If instead you want to preserve as much protein as possible, then you should add them. Should you not use them, then yes, those proteases will degrade some of the cell proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The good news is that you can buy aprotinin and leupeptin individually and supplement them to the necessary concentrations for a working lysis buffer.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorDisplayName="user560" LastEditDate="2014-08-26T23:14:59.090" LastActivityDate="2014-08-26T23:14:59.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20822" PostTypeId="1" AcceptedAnswerId="20830" CreationDate="2014-08-27T01:19:58.463" Score="1" ViewCount="2117" Body="&lt;p&gt;Can standard viruses infect bacteria?  I'm not speaking of bacteriophage but typical RNA and DNA virus such as influenza and Ebola.&lt;/p&gt;&#xA;" OwnerUserId="8969" LastEditorUserId="5144" LastEditDate="2014-08-28T08:08:57.100" LastActivityDate="2014-08-28T08:12:52.783" Title="Can viruses that normally infect eukaryotic cells also infect bacteria?" Tags="&lt;bacteriology&gt;&lt;virus&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20823" PostTypeId="2" ParentId="14143" CreationDate="2014-08-27T01:35:32.557" Score="4" Body="&lt;p&gt;The dog was probably freaked out by the weird costume.  Humans do it all the time (I've been seeing Halloween decorations for sale since early August, which is terrifying) but we generally comprehend what's going on.  Dogs may not fully understand the idea of a costume, much as a human infant might be scared by masks or beards (or the sudden removal thereof).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S016815919601129X#&quot; rel=&quot;nofollow&quot;&gt;this 1997 article titled &lt;em&gt;Canine fears and phobias; a regime for treatment without recourse to drugs&lt;/em&gt;&lt;/a&gt; is kind of a fun read and has some interesting tidbits about, go figure, canine fears and phobias.  One thing it discusses is the importance of the primary associations brought on by sight, smell, and hearing.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;However with a fear of hot air balloons the dog will &lt;em&gt;hear&lt;/em&gt; the propane burner and &lt;em&gt;see&lt;/em&gt; the balloon but a primary (coming from the balloon), olfactory cue will be missing. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Missing out on that is enough to freak 'em out.  &lt;a href=&quot;http://psycnet.apa.org/journals/cep/6/3/141/&quot; rel=&quot;nofollow&quot;&gt;This research article from the 1950s&lt;/a&gt; is a little more exact/thorough and has what you want.  It's worth reading in more detail if this topic interests you, but the part that answers you is here (emphasis added):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Some at least of the test objects could not have been discriminated by smell, as with the bronze deer, or the mechanical turtle, and in the course of the work it was frequently clear that &lt;strong&gt;visual cues were affective before olfactory ones&lt;/strong&gt; could have been. &lt;strong&gt;Vision also can dominate olfaction&lt;/strong&gt;: fear of a modelled human head was observed although the model was completely wet with dog urine.*&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Likely what happened was the dog saw a weird/scary/new person and, were upset that their vision and smell didn't match up, and continued being freaked out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(*The urine experiment comes from &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1439-0310.1949.tb01462.x/abstract&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article out of 1944 Germany, in what is now known as &lt;em&gt;Ethology&lt;/em&gt;, in case you feel like reading German.)&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="9686" LastEditDate="2016-05-19T21:43:05.713" LastActivityDate="2016-05-19T21:43:05.713" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20824" PostTypeId="1" AcceptedAnswerId="20832" CreationDate="2014-08-27T02:21:29.840" Score="9" ViewCount="1202" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/N24Sl.jpg&quot; alt=&quot;unidentified creature&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since it has six legs, I believe it's some sort of insect, but I could be wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I spotted it in my Central Texas backyard (Austin area). It was very slow and not at all skittish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For size reference, it's standing on a 2x4. It was a good 3-5 inches long, not counting antennae.&lt;/p&gt;&#xA;" OwnerUserId="8980" LastActivityDate="2014-08-28T00:12:28.677" Title="What is this creature?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20825" PostTypeId="2" ParentId="20808" CreationDate="2014-08-27T02:24:55.020" Score="1" Body="&lt;p&gt;One of the best ways that I have found for modeling reaction pathways is to set up a boolean network for that specific pathway. The boolean will give you an idea of the possible different states in that pathway (dependencies) and while not really necessary I find it helps orient you to the system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The next step once you have yourself oriented is to set up Michaelis-Menten equations which you can then use to run you ODEs. Here is a great primer on how to set up these equations: &lt;a href=&quot;http://depts.washington.edu/wmatkins/kinetics/michaelis-menten.html&quot; rel=&quot;nofollow&quot;&gt;http://depts.washington.edu/wmatkins/kinetics/michaelis-menten.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The subsequent modules provided in that link are also helpful in explaining how to set-up quadratic velocity equations and do different sequential models. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I'm sure you know this but, it bears saying: these are all steady-state kinetics. If you are looking for a more accurate model of what is occurring in that reaction you are going to have to set-up stochastic models of your system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully, that answers you question. Good luck!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found a paper that seems to relavent to the process you are trying to model. It goes into a bit more detail than I think you are looking for but the basics seems sound. &lt;a href=&quot;http://www.fitorem.unah.edu.cu/Materiales%20did%C3%A1cticos%20cursos%20PG/Curso%20Biorremediaci%C3%B3n/Literatura%20especializada/Bibliografia%20Ecuador/Estres%20Cd%20Modelo%20en%20plantas.pdf&quot; rel=&quot;nofollow&quot;&gt;Mendoza-Cozatl and Moreno-Sanchez, 2006&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8979" LastEditorUserId="1320" LastEditDate="2014-08-30T20:21:57.467" LastActivityDate="2014-08-30T20:21:57.467" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20826" PostTypeId="1" CreationDate="2014-08-27T02:40:35.070" Score="7" ViewCount="1811" Body="&lt;p&gt;I know this may be silly, but I am confused to what a membrane potential actually is. I understand that at resting membrane potential is -70- -80 mV. But what does that exactly mean and how does this all tie into diffusion potentials and equilibrium potentials.&lt;/p&gt;&#xA;" OwnerUserId="8981" LastEditorUserId="3553" LastEditDate="2016-06-10T08:05:34.027" LastActivityDate="2020-12-08T11:01:36.833" Title="What is a membrane potential?" Tags="&lt;biochemistry&gt;&lt;cell-membrane&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20827" PostTypeId="2" ParentId="20826" CreationDate="2014-08-27T05:08:44.940" Score="7" Body="&lt;p&gt;The existence of membrane potential is just that: as long as they are alive, cells try to keep their cytosol different from the outside soup, mainly by expelling sodium ions. There is a longer story, with cells pumping other ions in or out, or leaking ions due to the imbalance, but &lt;strong&gt;resting membrane potential&lt;/strong&gt; really revolves around sodium. There is an imbalance in sodium across the membrane, and that makes sodium naturally try to balance out, by trying to leak back in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am sure you have heard about the famous sodium/potassium ATPase. It expels sodium ions, while letting in fewer positive ions. It is just the most studied way the cells are going about making sure their innards poorer in cations, that is, negatively charged when compared to their environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All these pumps are ATP-dependent, and you would know ATP is the main energy store. So as long as cells live and make ATP, they can maintain this difference between their innards and the environment. Once they die, ATP is gone, pumps stop, and there is no sodium disequilibrium - no membrane potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Diffusion potential&lt;/strong&gt; is an artificial concept that we use in order to make sense of the membrane. We imagine a membrane that opposes sodium movement alone, and we calculate how hard will it be (how much energy must be spent) to keep the asymmetry of low sodium inside - higher sodium outside, were a hole punched in the semipermeable membrane. Luckily, we can use some physics and maths, and figure that this energy is dependent of the ratio of sodium concentrations ([Na]in divided by [Na]out). For typical cells, there are 150 mM Na outside and 15 mM Na inside a cell; physics tells us it will take 62 milli-electronvolts to hold a Na ion out once some hole is found.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you don't provide those 62 meV and you don't close the doors for leaking, sodium ions will fly in. And that is indeed what happens in depolarization, when sodium gets a chance to move.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These electronvolts are a unit of energy, or work. We can think of a few ways of performing this work on a Na ion that tries to leak in: heat the cell until ions stop caring about direction of movement, hold the outside Na in some tight  chemical structure etc. But the simplest way is to apply an electric field. If you add to the concentration imbalance a 62 mV electrical difference in electrical potential, you stopped the flow of sodium either way. Get a bit less than 62 mV, and the Na ions will carry on their old ways and try to no avail to leak into the cell. Get a bit above 62 mV, and the flow of sodium will be force in the opposite way. Stay on 62 mV and you achieve &lt;strong&gt;equilibrium potential&lt;/strong&gt;: neither direction will have the upper hand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The picture is way more complex once you factor in the other ions, but the facts are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;resting and action potentials are voltages one can measure across membranes, quite often during cells' lives &lt;/li&gt;&#xA;&lt;li&gt;diffusion potentials are part of an abstract model&lt;/li&gt;&#xA;&lt;li&gt;equilibrium potential is something one could impose on a cell - not something that you'd find in natural frequently, yet not plain fiction.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8809" LastEditorUserId="8809" LastEditDate="2016-07-08T16:23:09.653" LastActivityDate="2016-07-08T16:23:09.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20830" PostTypeId="2" ParentId="20822" CreationDate="2014-08-27T06:10:51.783" Score="4" Body="&lt;p&gt;I'm not so sure about my answer. But I think &quot;bacteriophage&quot; is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Polyphyly&quot; rel=&quot;nofollow&quot;&gt;polyphyletic&lt;/a&gt; name of which was defined by the ability of infecting bacteria, but not defined by the genetic, evolutionary, or morphological relationships. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that if a species (or a taxon in a higher taxonomic level) of virus is infectious to bacteria, it will be classified as a member of the bacteriophage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0923250803000676&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a review article about the phage classification.&lt;/p&gt;&#xA;" OwnerUserId="8965" LastEditorUserId="8965" LastEditDate="2014-08-28T07:58:39.390" LastActivityDate="2014-08-28T07:58:39.390" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20832" PostTypeId="2" ParentId="20824" CreationDate="2014-08-27T09:02:08.607" Score="12" Body="&lt;p&gt;Walkingsticks, like that in your photo, belong to the insect order Phasmida (also sometimes called Phasmatodea). The species in your photo belongs to the family Pseudophasmatidae. Texas has &lt;a href=&quot;http://www.texasento.net/sticks.htm&quot;&gt;two species documented&lt;/a&gt; for this family. One is &lt;a href=&quot;http://phasmida.speciesfile.org/Common/basic/Taxa.aspx?TaxonNameID=1199469&quot;&gt;&lt;em&gt;Anisomorpha ferruginea&lt;/em&gt;&lt;/a&gt;, commonly called the dark walkingstick or northern two-striped walkingstick.  The other species is &lt;a href=&quot;http://phasmida.speciesfile.org/Common/basic/Taxa.aspx?TaxonNameID=1199463&quot;&gt;&lt;em&gt;Anisomorpha buprestoides&lt;/em&gt;&lt;/a&gt;, commonly called Florida stick insect or two-striped walkingstick.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to W.S. Blatchley's &lt;em&gt;Orthoptera of Northeastern America&lt;/em&gt; (1920), &lt;a href=&quot;http://books.google.com/books?id=KcvwAAAAMAAJ&amp;amp;pg=PA780&amp;amp;lpg=PA780&amp;amp;dq=anisomorpha+buprestoides+vs+ferruginea&amp;amp;source=bl&amp;amp;ots=HhRc1bDOqD&amp;amp;sig=zX63hhHOqcKnY3MolnowBkvGDZI&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=Xpz9U9jnL9S98QGFp4CwCA&amp;amp;ved=0CEgQ6AEwDg#v=onepage&amp;amp;q=anisomorpha%20buprestoides%20vs%20ferruginea&amp;amp;f=false&quot;&gt;pg. 145&lt;/a&gt;, &lt;em&gt;A. ferruginea&lt;/em&gt; has narrow stripes and is a bit shorter than &lt;em&gt;A. buprestoides&lt;/em&gt;, which has broad stripes. Based on the appearance of the stripes in your photo, I'd say you have &lt;em&gt;A. buprestroides.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-08-27T10:31:20.603" LastActivityDate="2014-08-27T10:31:20.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20833" PostTypeId="2" ParentId="3327" CreationDate="2014-08-27T10:32:27.413" Score="13" Body="&lt;p&gt;&lt;a href=&quot;http://informahealthcare.com/doi/abs/10.3109/03014460.2013.807878&quot;&gt;Bianconi et al. 2013&lt;/a&gt; give an estimated lower bound of 3.72 × 10^13 (which, by the way, is approximately the geometric mean of 10^13 and 10^14).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, from the table in their Supplemental Information (where estimates for about fifty different types of cells are added up), it is clear that the vast majority of these are the erythrocytes, also known as red blood cells: estimated at 2.63 × 10^13. While the second largest class are the glial cells (from the nervous system), estimated at 0.30 × 10^13. Three other classes (endothelial cells {vessels}, dermal fibroblasts {skin}, and platelets {blood}) add up to another 0.58 × 10^13. These, in total, is about 3.5 × 10^13, and we can stop there, because the uncertainty in all these estimates swamps all the other cell type populations, which are much smaller.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that if we only consider the 5 most abundant cell types in the body, we already get a very good estimate. Is it likely that we have missed a cell type of which there are a trillion cells in the body? It's not impossible, but unlikely, because it would be hard to miss all these cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe there is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Long_tail&quot;&gt;long tail&lt;/a&gt; (i.e. a large number of minor cell types, each with a small, but significant population) that wasn't considered? Together, these could add up to a significant adjustment to the above figure. I don't know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This estimate is for a typical human person: 30 year old young adult, 70 kg, 1.72 m tall and with a surface area of 1.85 m^2. For this person, the figure is given with roughly a +-20% uncertainty.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given all the above, it's probably safe to say &quot;30 to 50 trillion&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(This obviously doesn't take into account any of the bacteria mentioned above.)&lt;/p&gt;&#xA;" OwnerUserId="6598" LastActivityDate="2014-08-27T10:32:27.413" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20835" PostTypeId="1" AcceptedAnswerId="20839" CreationDate="2014-08-27T12:12:15.870" Score="3" ViewCount="7507" Body="&lt;p&gt;As far as I know, osmosis occurs in Eukaryotic cells, and I'm wondering if it could take place in prokaryotic cells too.&lt;/p&gt;&#xA;" OwnerUserId="6114" LastActivityDate="2014-08-28T07:52:08.747" Title="Does osmosis take place in prokaryotic cells?" Tags="&lt;osmosis&gt;&lt;prokaryotes&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20837" PostTypeId="2" ParentId="3834" CreationDate="2014-08-27T13:02:38.840" Score="14" Body="&lt;p&gt;Most mammalian males have nipples. The duck-billed platypus does not have nipples but you begin to see development of nipples in marsupials (&lt;a href=&quot;http://www.cabdirect.org/abstracts/20043175290.html;jsessionid=708CD968A3EA792683AF92AE0D2AE6C1&quot; rel=&quot;noreferrer&quot;&gt;Park and Lindberg 2004&lt;/a&gt;) like the opossum and kangaroo.  Development of a complete nipple begins in the eutherian (placental) mammals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mammary glands develop early in the embryo along a pair of ridges called the mammary ridge, mammary lines, or milk line (shown in an adult human in the figure below, taken from Wikipedia). The nipples form along this line. In humans, this happens during the &lt;a href=&quot;https://www.glowm.com/resources/glowm/cd/pages/v5/v5c030.html&quot; rel=&quot;noreferrer&quot;&gt;fifth week&lt;/a&gt; of development. Within a few days, nipples begin to form. The number of nipples pairs that form is characteristic of the species (e.g., 1 pair in humans to 9 pairs in pigs). The development of nipples occurs &lt;em&gt;before&lt;/em&gt; sexual differentiation begins which, in humans, is during the sixth week of development. That's why both males and females have nipples. This same order of develop occurs in other mammals, revealing our common ancestry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/x9wRf.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, because the process is under genetic control, mistakes can happen. Occasionally, humans (and other mammals) can develop extra nipples, the so-called supernumerary nipple(s). The most common places that humans develop one or more supernumerary nipples are identified by the circles in the figure above. The actor Mark Wahlberg is not shy about showing his.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3WflX.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a general overview of mammary gland development, Dr. Jacqueline Veltmaat has a &lt;a href=&quot;http://www.veltmaatlab.net/research.html&quot; rel=&quot;noreferrer&quot;&gt;nice web page&lt;/a&gt; that highlights her research in this area. For those interested in the more technical genetic aspects of mammary gland development, a paper by &lt;a href=&quot;http://dev.biologists.org/content/135/6/995.full&quot; rel=&quot;noreferrer&quot;&gt;Watson and Khaled&lt;/a&gt; (2007) reviews the genetic processes that regulate development of the mammary gland in mammals, based on the mouse model system. The article covers all stages of mammary gland development, from the embryo through puberty to pregnancy. Their &lt;a href=&quot;http://dev.biologists.org/content/135/6/995/F1.expansion.html&quot; rel=&quot;noreferrer&quot;&gt;Figure 1&lt;/a&gt; shows one row of embryonic mammary buds (labeled MB1 - MB5) in the embryonic mouse. In the case of the mouse, all of the mammary buds will develop into fully functioning mammary glands.  Another paper by &lt;a href=&quot;http://www.nature.com/nrg/journal/v8/n12/full/nrg2227.html&quot; rel=&quot;noreferrer&quot;&gt;Robinson (2007)&lt;/a&gt; discusses the signalling pathways during development of the mammary glands. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Park, C.S. and G.L. Lindberg. 2004. The mammary gland and lactation. pp. 720-741 in &lt;em&gt;Dukes' Physiology of Domestic Animals&lt;/em&gt;, W.O. Reece, ed.  (Publisher not identified.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Robinson, G.W. 2007. Cooperation of signalling pathways in embryonic mammary gland development.  Nature Reviews Genetics 8: 963-972.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Watson, C.J. and W.T. Khaled. 2008. Mammary development in the embryo and adult: a journey of morphogenesis and commitment. Development 135: 995-1003.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-27T13:02:38.840" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20839" PostTypeId="2" ParentId="20835" CreationDate="2014-08-27T14:01:05.100" Score="3" Body="&lt;p&gt;Osmosis works across every cell membrane along a concentration gradient as its a physico-chemical principle. Water can cross the membrane (or cell wall), while the substance dissolved in it (for example salts) can not. Because eukaryotic cells only have a cell membrane, they will burst eventually, while bacteria (and also plant cells) have a more rigid cell wall, which will mostly prevent bursting. However the influx (or outflux) of water creates a pressure which is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Turgor_pressure&quot; rel=&quot;nofollow noreferrer&quot;&gt;turgor pressure&lt;/a&gt;. How this works is shown below (figure from &lt;a href=&quot;http://dc276.4shared.com/doc/qiQSx7RZ/preview.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;), bacterial cells and plant cells work pretty much the same way:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rSfP9.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-08-27T15:33:58.760" LastActivityDate="2014-08-27T15:33:58.760" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20840" PostTypeId="1" CreationDate="2014-08-27T14:35:15.197" Score="8" ViewCount="132" Body="&lt;p&gt;I've asked this before in stack overflow's cognitive science community, and someone recommended me to ask here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've found a couple of studies using microdialysis on insects, but didn't found any in &lt;em&gt;Drosophila&lt;/em&gt;. I've found that the membrane diameter are from 240um, and it seems that &lt;em&gt;Drosophila melanogaster&lt;/em&gt; brain must be between 200-300um , but I was wondering if the lack of studies of perfused drugs in &lt;em&gt;Drosophila&lt;/em&gt; is due to this technical constraint, or is just I'm searching wrongly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;--&#xA;Edit: I specified the original target, &lt;em&gt;Drosophila melanogaster&lt;/em&gt;, since there are bigger parients like Hawaian &lt;em&gt;D. heteroneura&lt;/em&gt; and &lt;em&gt;D. cyrtoloma&lt;/em&gt;. that could be subject to MD with current probes.&lt;/p&gt;&#xA;" OwnerUserId="8992" LastEditorUserId="8992" LastEditDate="2014-08-27T19:24:25.660" LastActivityDate="2016-09-16T01:10:27.417" Title="Can microdialysis be made in Drosophila melanogaster?" Tags="&lt;lab-techniques&gt;&lt;drosophila&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20841" PostTypeId="2" ParentId="15497" CreationDate="2014-08-27T16:00:54.633" Score="4" Body="&lt;p&gt;&quot;&lt;em&gt;Monosomy for the X chromosome in humans creates a genetic Achilles' heel for nature to deal with.&lt;/em&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article I quoted&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1287212/&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;&lt;/sup&gt; tackles this issue.  It's from the turn of the century, though, so quite old in sequencing/genetic terms, but the science is still sound as far as I can tell.  Here's the money quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hence, the X chromosome appears to have a lower gene density and should yield fewer deleterious mutations per megabase of DNA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In short, &lt;strong&gt;yes&lt;/strong&gt;, you're correct.  There appears to be less overall information on the X-chromosome, deleterious or not, and selection is faster; the X chromosome is just flat-out less diverse.  &lt;a href=&quot;http://www.biomedcentral.com/1471-2148/11/156&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; goes into quite a bit more but says essentially the same thing: &quot;&lt;em&gt;On one hand, the greater effectiveness of selection on males due to the hemizygous expression of the X, which may be further reinforced by sexual selection, is expected to lower the mutation load for females at shared loci.&lt;/em&gt;&quot;  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1188000/&quot; rel=&quot;nofollow&quot;&gt;Here is a more recent article&lt;/a&gt; stating the same: &quot;&lt;em&gt;This finding&lt;/em&gt; [X-chromosomes with lower linkage disequalibrium] &lt;em&gt;is consistent with more rapid selection against deleterious mutations when the X is monosomic in males, and to a lesser extent, under random inactivation (Lyonization) in females.&lt;/em&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, &lt;a href=&quot;http://blogs.discovermagazine.com/gnxp/2011/07/why-the-human-x-chromosome-is-less-diverse/&quot; rel=&quot;nofollow&quot;&gt;here is a piece&lt;/a&gt; written a few years back by a colleague of mine that goes into depth on the subject.  The second half deals with population differences (also fascinating), but the first part has a lot of good detail on what you want.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2014-08-27T16:00:54.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20842" PostTypeId="2" ParentId="10746" CreationDate="2014-08-27T21:06:05.353" Score="0" Body="&lt;p&gt;I'm not a scientist, so this is my best guess:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since humans are an uncommon exception among mammals for lacking snouts, we should find the benefits of a snout by looking at other ways that humans are unique among animals, enabling us to not have snouts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the answer is the opposable thumb; animals need snouts because it does for them what thumbs do for humans. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For most animals, their mouths are all they have to manipulate their environments — it's what they use to lift, carry, or break objects, as well as hunt and fight. Humans have thumbs, as well the ability to use tools, to do all these things. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A snout provides more surface area for biting or carrying, better dexterity to grasp between bones, rocks or other obstacles, a larger mandible for powerful jaw muscles to attach to. It also places the mouth in front the eyes rather than below them, which should make it easier for an animal to see what it's about to pick up with its mouth. I think that all these things would suggest that an animal with a shorter snout is at a disadvantage.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another explanation for snouts that I've seen is that hairy animals cool off through their mouths rather than through their skin, and a snout gives them a larger mouth and more surface area to do so. &lt;/p&gt;&#xA;" OwnerUserId="8998" LastEditorUserId="8998" LastEditDate="2014-08-27T21:18:38.297" LastActivityDate="2014-08-27T21:18:38.297" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20843" PostTypeId="2" ParentId="10746" CreationDate="2014-08-27T21:18:58.990" Score="0" Body="&lt;p&gt;Long snouts may have an advantage in long noses. A longer nostril could give more room for olfactory neurons and allow for a more sensitive sense of smell. Animals would rely on smell to find prey or avoid predators, so better smell would give better advantage. The only predators I can think of off the top of my head that would have short snouts would be big cats, but lions and tigers have more prominent snouts than house cats.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-08-27T21:18:58.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20844" PostTypeId="1" AcceptedAnswerId="20877" CreationDate="2014-08-27T21:28:21.250" Score="3" ViewCount="834" Body="&lt;p&gt;I would like to get myself up to speed with what is currently known to science about yeast transformation. Specifically, transformation of plasmids and linear DNA fragments. I am particularly interested in practical aspects, such as:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What is salmon sperm for? What if I don't use it? What if I use more?&lt;/li&gt;&#xA;&lt;li&gt;What is the relationship between number of cells, amount of transforming DNA, and transformation efficiency?&lt;/li&gt;&#xA;&lt;li&gt;How does choice of electroporation cuvette gap size affect efficiency?&lt;/li&gt;&#xA;&lt;li&gt;What can I do to get more colonies after transforming my yeast?&lt;/li&gt;&#xA;&lt;li&gt;What steps can I skip to make the transformation quicker if I am doing an easy transformation?&lt;/li&gt;&#xA;&lt;li&gt;How do different genetic backgrounds and media affect efficiency? Are there any common ones that reduce efficiency substantially? Are there any uncommon ones that increase it substantially?&lt;/li&gt;&#xA;&lt;li&gt;What is the effect of post-transformation &quot;recovery&quot; time (eg. culture 12 h without selection and then plate on selective medium)?&lt;/li&gt;&#xA;&lt;li&gt;Is making spheroplasts worth it?&lt;/li&gt;&#xA;&lt;li&gt;Does the same transformation protocol work for different species (S. cerevisiae, S. pombe, C. albicans, etc.)?&lt;/li&gt;&#xA;&lt;li&gt;Is there a coherent theoretical framework for understanding what actually happens when yeast are transformed, as opposed to &quot;you mix some chemicals with DNA and throw cells in, abra kadabra, transformants come out&quot;? The sort of theory I'm asking about would be useful in predicting conditions for better efficiency.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;I am not expecting you to comprehensively answer these questions in your answer.&lt;/em&gt;&lt;/strong&gt; This would make for a very long answer, and each of these could be a question here in its own right.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead, &lt;strong&gt;&lt;em&gt;I want the answer to name reference materials&lt;/em&gt;&lt;/strong&gt; which can be studied to learn more about the points above. For example, recent reviews or textbooks by established experts in the fields would be quite useful.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-08-29T21:21:12.633" Title="What is the best current understanding of how yeast transformation works?" Tags="&lt;yeast&gt;&lt;transformation&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20845" PostTypeId="1" CreationDate="2014-08-27T22:08:20.377" Score="1" ViewCount="104" Body="&lt;p&gt;I have some EEG recordings of $1$ minutes, with $500$ samples per seconds and $63$ channels. For each recordings, this effectively yields a $30,000\times 63$ matrix $M$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do I extract isopotential maps from the data?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My first try was to simply take each row $m_i\in M_{i,j}$ such that $m$ has length $63$ and plot them with respect to the $x,y$ coordinates given by the location of each of the $63$ channels... However, I seem to get bad plots...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also tried to bandpass the data first. For alpha waves, my Mathematica code looks like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;BANDPASSALPHA[x_] := &#xA; BandpassFilter[x, {8 Pi, 13 Pi}, SampleRate -&amp;gt; 500]&#xA;bpalpha = Map[BANDPASSALPHA, dataz];&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I bandpassed the columns of the matrix $M$. That is the signal $x$ that is used in BANDPASSALPHA[x] is one of the columns of $c_j\in M_{i,j}$ and are of length $30,000$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Wikiepdia: &lt;a href=&quot;http://en.wikipedia.org/wiki/Isopotential_map&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Isopotential_map&lt;/a&gt;, the spatial derivative needs to be computed first...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know how isopotential maps from EEG recordings?&lt;/p&gt;&#xA;" OwnerUserId="8999" LastActivityDate="2014-08-27T22:08:20.377" Title="How are isopotential maps computed from EEG channel data" Tags="&lt;electroencephalography&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20854" PostTypeId="2" ParentId="20826" CreationDate="2014-08-28T06:57:51.817" Score="5" Body="&lt;p&gt;To understand what a membrane potential is, you should understand the units for -80mv. The negative sign is relative to the observer, yourelf, to the inside of a cell. From your perspective, the inside has an excess of negative ions. On the outside of the cell, there is an excess of positive ions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unlike electricity, where charge separation is quantified by electrons, action potential is quantified by ions. Ions are matter, like Na+, K+, Cl-. When electricity flows through a wire, electrons are flowing from excess negative charge to a deficiency of negative charge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a cell establishes an action potential, it moves Na+ outside the cell, which moves the potential from 0mv, negative. The number -80mv, or whatever potential that may be observed, is the point at which a net flow of positive ions are not leaving the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Na+ is actively pumped outside a cell, using energy. K+ is passively driven into the cell by simple diffusion to neutralize the charge imbalance. Opposing the outward flow of Na+ and inward flow of K+ is their diffusion gradients. Ions flow from a high concentration to low concentration. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At -80mv, the Na+ concentration is high outside the cell. Intracellular Na+ is being pumped out to counteract any leaking back in. The K+ concentration is high inside the cell from its passive diffusion to cancel the electrical potential. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The physics of why K+ does not neutralize the -80mv is in its concentration gradient. K+ is being pulled outside the cell by this gradient and driven inwards by an electrical potential. The net electrical potential across the cell membrane is -80mv for a given cell's capacity to maintain the concentration of its intracellular ions. &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-28T07:09:59.960" LastActivityDate="2014-08-28T07:09:59.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20856" PostTypeId="2" ParentId="20822" CreationDate="2014-08-28T07:32:31.540" Score="2" Body="&lt;p&gt;The word infect is an encapsulation of several activities: transcription, translation, viral entry, budding, lysis, etc. When you ask if a eukaryotic virus (influenza, ebola) can infect a prokarytoic cell (bacteria) you are asking if these viruses can do the same activities. The answer is no. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Translation is mediated by ribosomes, which are different in&#xA;prokaryotes/eukaryotes. &lt;/li&gt;&#xA;&lt;li&gt;Transcription is mediated by viral RNA polymerase which may be contained in viral nucleic acid. This is possible, but useless without translation of the mRNA.&lt;/li&gt;&#xA;&lt;li&gt;Viral entry is mediated by cell surface features and would be incompatible for eukaryotic viral entry into prokaytoic cells, and the reverse.&lt;/li&gt;&#xA;&lt;li&gt;Viral budding is mediated by viral proteins inserted into the cell membrane. This is prohibited since a eukaryotic virus is unable to enter a prokaryotic cell/translate its proteins. &lt;/li&gt;&#xA;&lt;li&gt;Lysis is mediated by excessive buildup of viral particles inside a cell. This is also prohibited by an incompatibility of eukaryotic/prokaryotic cell surface, translation machinery. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-28T08:12:52.783" LastActivityDate="2014-08-28T08:12:52.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20857" PostTypeId="2" ParentId="20835" CreationDate="2014-08-28T07:52:08.747" Score="1" Body="&lt;p&gt;The force driving osmosis exists in any system with an imbalance of solute molecules across a semipermeable membrane. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think of a concentration gradient as an electrical potential, where high concentration is negative charge and low concentration is positive charge. In the case of electricity, its the magnetic force which causes the interactions leading to charge equilibrium. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In osmosis, there is no communication between solute molecules by an 'osmotic force'. Osmosis is a result of entropy. In chemistry, a separation of solute concentrations is called a chemical potential. As entropy increases in the system, this chemical potential is decreased, either endo or exothermically. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a chart showing the change in heat for the dissolution of substances. Negative numbers mean a system loses heat (enthalpy) and is exothermic. Cold packs use ammonium nitrate, which absorb heat as they are dissolved in water. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The processes of osmosis, entropy are fundamental to our universe, not to a specific domain of life. &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Enthalpy change of solution for some selected compounds&#xA;hydrochloric acid   -74.84&#xA;ammonium nitrate    +25.69&#xA;ammonia             -30.50&#xA;potassium hydroxide -57.61&#xA;caesium hydroxide   -71.55&#xA;sodium chloride     +3.87&#xA;potassium chlorate  +41.38&#xA;acetic acid         -1.51&#xA;sodium hydroxide    -44.51&#xA;Change in enthalpy ΔHo in kJ/mol in water at 25°C[1]&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="8570" LastActivityDate="2014-08-28T07:52:08.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20858" PostTypeId="1" AcceptedAnswerId="20859" CreationDate="2014-08-28T09:52:17.143" Score="5" ViewCount="1220" Body="&lt;p&gt;I'm a masters student attempting to conduct a parentage analysis on a population of fish for my thesis. My advisor and post-docs haven't been very helpful, so I need some help! I have dinucleotide microsatellite markers that I've run on a set of individuals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm using GeneMapper 4.0 to score the alleles of said markers but something isn't making sense. My alleles are shifted to where they are not evenly distributed in their sizes. For example, at a given locus for one individual I have one allele peak at 152 while the other allele peak is at 161 (It's an obvious heterozygote). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &quot;shift&quot; doesn't make sense considering my markers are dinucleotide and should be spaced 2 bp apart, right? So either 152 is actually 151/153 or 161 is actually 162/160. How can I score these and resolve this issue while keeping consistency for my analysis later? I see this shift everywhere and I've already ruled out contamination and I'm positive these peaks are real. Any pop gen people out there that have a clue what to do?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been stuck on this for weeks, no amount of web searching/paper reading helped.&#xA;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="9005" LastActivityDate="2014-08-28T10:11:00.123" Title="Microsatellite shifts (peak calling) GeneMapper! Thesis help!" Tags="&lt;genetics&gt;&lt;population-genetics&gt;&lt;allele&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20859" PostTypeId="2" ParentId="20858" CreationDate="2014-08-28T10:11:00.123" Score="5" Body="&lt;p&gt;Your markers are probably fine, especially because you keep seeing the same allele in multiple individuals. Dinucleotide repeats do not always copy perfectly. More likely, remember that the primers you use to amplify your microsatellites bind outside of the actual repeat region. You could have an insertion/deletion in the region between the primers and the repeat region, changing your allele sizes from to even to odd (or vice versa).&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-28T10:11:00.123" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20862" PostTypeId="1" CreationDate="2014-08-28T14:40:53.667" Score="2" ViewCount="64" Body="&lt;p&gt;We are doing a genome-wide analysis of methylation via bisulfite sequencing for an insect species. Previous experimental techniques have suggested the presence of methylation in this organism, including an AFLP analysis using methylation-sensitive restriction enzymes and a differential expression analysis using a methylation inhibitor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our bisulfite sequencing data, however, is giving us essentially no evidence of methylation. If this finding is true, it will be a pretty big deal. But before we go down that path, we want to make sure we've counted out all sources of technical error.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;First, we wondered if the bisulfite treatment failed, but quickly determined that this would not explain the result. If the C --&gt; T conversion had failed at an extremely high rate, you would expect to see methylation all over the place. That's the opposite of what we're seeing, which is essentially no methylation.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Second, we wondered if there was some kind of &quot;overexposure&quot; issue in the bisulfite treatment that caused even methylated Cs to convert to Ts. We found a paper describing this phenomenon&lt;sup&gt;&lt;a href=&quot;http://dx.doi.org/10.1093/nar/gkn691&quot; rel=&quot;nofollow&quot;&gt;[1]&lt;/a&gt;&lt;/sup&gt;, but reports we can find suggest this happens at a low (&amp;lt;10%) rate, which cannot explain our data.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Third, we wondered if perhaps there was an issue with the reads mapping to the genome, we got at least 70% mapping efficiency for each BS-seq sample, so that can't be it either.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Are there any other sources of technical error we should consider and check for before believing this result?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1093/nar/gkn691&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Genereux DP, Johnson WC, Burden AF, Stöger R, Laird CD&lt;/strong&gt; (2008) Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequencies. &lt;em&gt;Nucleic Acids Research&lt;/em&gt;, &lt;strong&gt;36&lt;/strong&gt;(22):e150, doi:10.1093/nar/gkn691.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="43" LastActivityDate="2014-08-30T03:11:24.757" Title="Genome-wide methylation analysis: sources of technical error?" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;&lt;dna-methylation&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20863" PostTypeId="1" CreationDate="2014-08-28T18:40:46.390" Score="2" ViewCount="4617" Body="&lt;p&gt;I understand that alcohol and phenytoin are two examples of drugs that follow zero-order kinetics. Why do these two particular drugs follow zero-order kinetics as opposed to first-order kinetics? &lt;/p&gt;&#xA;" OwnerUserId="8977" LastEditorUserId="1320" LastEditDate="2014-08-28T18:49:30.497" LastActivityDate="2018-11-16T18:29:59.437" Title="Pharmacokinetics: why do certain drugs follow zero-order kinetics?" Tags="&lt;pharmacology&gt;&lt;pharmacokinetics&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20864" PostTypeId="1" AcceptedAnswerId="20865" CreationDate="2014-08-28T20:18:09.777" Score="3" ViewCount="301" Body="&lt;p&gt;I work with a lot of mice. I don't do any behavioral analysis, I just inject DNA or RNA and do imaging assays. However, I have noticed some effect of isolation on mouse behavior. Normally, the mice are housed in our university's animal facility with no more than 5 mice to a cage. Sometimes, 1 mouse will be put in a cage by itself. When I go to get these lone mice from their cages, they seem more skittish, harder to grab, and more likely to bite me than mice kept in groups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, our Office of Animal Resources, which is responsible for getting in the mouse shipments and putting them into cages, has recently changed how our mice are caged, with a group of 4 mice being normal, any leftover mice are put into cages with other mice, making a 5 mouse cage. This means I haven't seen a single mouse in a cage for a while. So I might not be the only one to have noticed an effect of isolation on the animal's health.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have heard of studies on monkeys by B.F. Skinner, where he induced very severe depression and other psychological issues by isolating them, so I suspect similar studies have been attempted on mice using far more quantitative methods than I've been able to do.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="1320" LastEditDate="2014-08-30T19:59:14.803" LastActivityDate="2014-08-30T19:59:14.803" Title="Does isolation have any effect upon mouse behavior?" Tags="&lt;psychology&gt;&lt;animal-models&gt;&lt;mouse&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20865" PostTypeId="2" ParentId="20864" CreationDate="2014-08-28T20:58:05.857" Score="4" Body="&lt;p&gt;Yeah, it's &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19447287&quot; rel=&quot;nofollow&quot;&gt;not good&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Social isolation (SI) rearing in rodents causes a &lt;strong&gt;variety of behavioral changes&lt;/strong&gt;, including &lt;strong&gt;hyperlocomotion, anxiety, impulsivity, aggression, and learning and memory deficits&lt;/strong&gt;. These behavioral abnormalities in rodents may be related to the symptoms in patients with neuropsychiatric disorders, such as attention-deficit hyperactivity disorder, obsessive-compulsive disorder, autism, schizophrenia and depression...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our findings suggest that [social isolation]-induced behavioral abnormality is a &lt;strong&gt;psychobehavioral complex relevant to various clinical symptoms observed in neuropsychiatric disorders, including ADHD, schizophrenia and depression&lt;/strong&gt;, and that SI-reared mice are a useful animal model to study the pathophysiology/pathogenesis of these diseases.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There's &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117867/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In contrast, long-term social isolation is a model to study the behavioral and neurochemical consequences of depriving rodents of social interaction. Many of the symptoms caused by long-term isolation &lt;strong&gt;resemble those seen in depression and anxiety disorders&lt;/strong&gt;. Furthermore, long-term isolation of male mice is known to induce &lt;strong&gt;offensive and aggressive behavior, such as attacks.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1924499&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These data suggest that long-term isolation may induce &lt;strong&gt;functional changes&lt;/strong&gt; in the sensitivity of alpha 2 receptor in the noradrenergic system...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776895/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the present study, we found that social isolation &lt;strong&gt;elevated the anxiety levels&lt;/strong&gt; of mice...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Emphasis all my own.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's a lot more meat in those studies, and especially the paper they cite in their introductions.  Some of them, as well as &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0024320508000751&quot; rel=&quot;nofollow&quot;&gt;others&lt;/a&gt; also explore the effect of isolation in addition to other substances.  It can absolutely affect your studies, in particular behavioral or expression-based studies.  Your mouse house is good to change their practices.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastActivityDate="2014-08-28T20:58:05.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20868" PostTypeId="1" CreationDate="2014-08-29T09:45:28.753" Score="1" ViewCount="63" Body="&lt;p&gt;It was &lt;a href=&quot;http://www.jstor.org/stable/2408385&quot; rel=&quot;nofollow&quot;&gt;theorised in 1984&lt;/a&gt; that sexually antagonistic genetic (SA) variation should more easily evolve on the X-chromosome. This is partly because female beneficial/male deleterious mutations face less powerful selection against them; the X is in females twice as often as in males so mutations will persist up to the point where male cost is &amp;lt;2x the females gain. Furthermore, male beneficial/female deleterious recessive mutations (&lt;em&gt;p&lt;/em&gt;) will always be expressed in males and, when rare, only very occasionally in females; if the frequency of &lt;em&gt;p&lt;/em&gt; 0.1 then 1 in 10 males will express that trait and only 1 in 100 of the females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is therefore expected that the X-chromosome should become a hotspot for SA variation in comparison to the autosomes. A result would be increased persistence of genetic variation on the X- within sexually antagonistic loci. However, &lt;strong&gt;how would a sexually concordant (male &amp;amp; female beneficial, or male &amp;amp; female deleterious) fare in the X- compared to the autosomes?&lt;/strong&gt; Just eyeballing it, it feels like the X- should be better able to select on recessive mutations because they are always expressed in males; removing deleterious and spreading beneficial mutations more rapidly. &lt;strong&gt;Should there then be less genetic variation on the X- than autosomes?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-08-29T09:45:28.753" Title="Evolution of sexually concordant genetic variation on the X-chromosome" Tags="&lt;evolution&gt;&lt;chromosome&gt;&lt;sexual-selection&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20869" PostTypeId="1" AcceptedAnswerId="20870" CreationDate="2014-08-29T15:11:37.533" Score="6" ViewCount="404" Body="&lt;p&gt;While reading about the predator satiation hypothesis of the periodical cicadas' 13/17 year life cycles, I started wondering about its premise. By the way, I understand the math behind the prime number life cycle. 13 and 17, being prime numbers are only divisible by themselves and 1, and thus have as few divisors as possible. But my question is about the premise of why a predator would even want to synchronize its life cycle with a divisor of the prey's life cycle in the first place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the predator has a set life cycle, but its individuals are evenly distributed in regards to their development within that life cycle at any given time (for example there could be roughly even amounts of mature and immature predators at any given time), then what difference does the life cycle make? Here I am assuming that eating cicadas is most beneficial to a specific developmental stage of the predators, which is the only reason I can think of why there would be an advantage to this synchronization. By the way, is this even a correct assumption in regards to this hypothesis?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be clear, my main question is why life cycle synchronizations between predator and prey matter when/if predators aren't all undergoing the same stages of their life cycles simultaneously.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;edit&lt;/strong&gt;: To be even more clear, I am asking what the benefits are to the predator to synchronize its life cycle with the prey (the cicadas, in my example).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My reference&lt;/strong&gt;: Wikipedia says the following: *It was hypothesized that the emergence period of large prime numbers (13 and 17 years) was a predator avoidance strategy adopted to eliminate the possibility of potential predators receiving periodic population boosts by synchronizing their own generations to divisors of the cicada emergence period.&#xA;&lt;strong&gt;Goles, E.; Schulz, O.; Markus, M. (2001). &quot;Prime number selection of cycles in a predator-prey model&quot;. Complexity 6 (4): 33–38. doi:10.1002/cplx.1040.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have interpreted &quot;synchronizing their own generations to divisors...&quot; to mean synchronizing the length of the life cycle. I am happy to hear of another interpretation.&lt;/p&gt;&#xA;" OwnerUserId="9016" LastEditorUserId="3624" LastEditDate="2015-02-06T12:27:54.280" LastActivityDate="2015-02-06T12:27:54.280" Title="Premise of life cycle synchronization between predator and prey" Tags="&lt;ecology&gt;&lt;population-dynamics&gt;&lt;predation&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20870" PostTypeId="2" ParentId="20869" CreationDate="2014-08-29T16:39:15.463" Score="4" Body="&lt;p&gt;&lt;strong&gt;New Answer,&lt;/strong&gt; based on first comment by user2686410 and subsequent edits to the question.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I have interpreted &quot;synchronizing their own generations to divisors...&quot; to mean synchronizing the length of the life cycle. I am happy to hear of another interpretation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;First, the overall goal of &lt;a href=&quot;http://www.web-frog.com/pics/GoSM01.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Goles et al. (2001)&lt;/a&gt; does not seem to test hypotheses related to the evolution of life cycles in the cicadas &lt;em&gt;per se&lt;/em&gt;. It seems their overall goal instead may have been to explore the generation of prime numbers from numerical theory, using biologically-based models. For example, from the abstract they state,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The model marks an encounter of two seemingly unrelated disciplines: biology and number theory. A restriction to the latter, provides an evolutionary generator of arbitrarily large prime numbers.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and at the end of the discussion they write,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Although there are traditional methods for prime number detection (see e.g., Ref. 23) that are faster than the methods presented here, it is remarkable that the generation of prime numbers can be performed using a biological model.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To more directly address your question and if I understand their models, Goles et al. (2001) do seem to allow the the life cycles of both predators and prey to co-evolve yet this is not always clear. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We compare now a prey mutating to a cycle Y' with the resident prey (cycle length Y ) at &lt;em&gt;constant&lt;/em&gt; X. Analogously, we compare mutant cycles X' with resident cycles X at &lt;em&gt;constant&lt;/em&gt; Y (Goles et al. 2001, pg. 34; emphasis added).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here, they seem to be saying that the life cycle of one (predator or prey) can change while other other remains constant (prey or predator). The life cycles don't coevolve.  Subsequent formulas and statements imply an interactive effect between the predator &lt;em&gt;and&lt;/em&gt; prey life cycles. (Honestly, their writing is somewhat opague to me and they do not define all of their mathematical terms, making it difficult to follow the logic of their models.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regardless, the results of their initial models, shown in the figure below, shows the prey converging on a 17 year life cycle while the predators converge on a 4 year cycle. Somewhat more complex models tended to converge on 13 and 17 year cycles, although other primes like 11, 19 and 23, had similar probabilities of evolving.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mGnxc.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Goles et al. (2001) admit at the outset of their paper that there is no evidence for predators with periodical cycles that align with the life cycles of cicadas. This would be consistent with general ecological observations. Most predators consume multiple prey items. Highly specialized predators would be more vulnerable to extinction if their prey source went extinct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another numerical model, developed by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690011/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tanaka et al. (2009)&lt;/a&gt; explicitly to explore life cycle evolution of cicadas, does not include predator life cycles at all. Their results still converge on 13 and 17 year life cycles although they restricted the possible range of life cycles to between 10 and 20 years. Thus, it does not appear to be necessary for predators to evolve a life cycle that coincides with prey life cycles for the predator satiation hypothesis to work. Of course, this is consistent with the real world observations that cicadas do not appear to have predators with concommitant life cycles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Original answer, lightly edited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strike&gt;In the case of the cicadas, they are the prey, not the predators. They are not synchronizing their life cycles with the predators (if I am interpreting your entire question correctly).&lt;/strike&gt; The argument is that cicadas have evolved synchronized life cycles to maximize survivorship.  By having a large number of individuals emerge within a very short period of time, the very high density means most individuals will live long enough to reproduce because the predators (birds, small rodents, etc.) will be satiated (see &lt;a href=&quot;http://hydrodictyon.eeb.uconn.edu/projects/cicada/resources/reprints/Williams%26Simon_1995.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Williams and Simon 1995&lt;/a&gt; for a review and pointers to early literature). Some predators of cicadas will be always present so the cicadas are not synchronizing to any specific predator.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.web-frog.com/pics/GoSM01.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Goles et al. (2001)&lt;/a&gt; used numerical models to argue that such life cycles will tend to converge on prime numbers. (As discussed in the update above) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690011/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tanaka et al. (2009)&lt;/a&gt; recently argued, again using numerical models, that the prime number-based life cycles of cicadas evolved as a result of the &lt;a href=&quot;http://www.nature.com/scitable/knowledge/library/allee-effects-19699394&quot; rel=&quot;nofollow noreferrer&quot;&gt;Allee effect&lt;/a&gt;. The Allee effect basically states that there is a positive association between the fitness of individuals in the population and the population size or density. Below a certain size, a population is unable to sustain itself and is vulnerable to extinction. Tanaka et al. argue that the Allee effect results in prime-based life cycles under varying environmental parameters. They further argue that maintenance of alternate life cycles minimize hybridization between groups with different life cycle timings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What seems to really remain to understand the evolution of cicada life cycles is to unravel the genetic mechanisms involved with timing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Goles, E. et al. 2001. Prime number selection of cycles in a predator-prey model. Complexity 6: 33-38.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tanaka, Y. et al. 2009. Allee effect in the selection for prime-number cycles in periodical cicadas. Proceedings of the National Academy of Sciences USA 106: 8975-8979.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Williams, K.S. and C. Simon. 1995. The ecology, behavior, and evolution of periodical cicadas. Annual Reviews of Entomology 40: 269-295.&lt;br /&gt;&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-08-29T21:16:10.593" LastActivityDate="2014-08-29T21:16:10.593" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20871" PostTypeId="1" CreationDate="2014-08-29T18:22:18.097" Score="3" ViewCount="2134" Body="&lt;p&gt;What do you call it when a bacterium dies? Cellular death is apoptosis, necrosis, and bacterial is ...? I don't simply want to write in a paper that it - well dies!&lt;/p&gt;&#xA;" OwnerDisplayName="user8970" LastEditorUserId="1320" LastEditDate="2014-08-30T20:04:08.530" LastActivityDate="2014-08-30T20:04:08.530" Title="Is there a specific word for bacterial death?" Tags="&lt;bacteriology&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20872" PostTypeId="2" ParentId="20869" CreationDate="2014-08-29T19:14:02.060" Score="1" Body="&lt;p&gt;Mike Taylor's answer is well-researched and inspired the following thought experiment that might help you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine a predator of the cicada which takes several years to reach maturity(say, five). The population of this predator is distributed evenly across all the different stages of its life cycle, at least at first. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One year there is a cicada eruption and all the members of this predator species are incredibly well-fed for a month or two. If the effects of this prey glut aren't perfectly evenly spread across all ages of the predator species, there will be a fitness advantage to one age group or another. Maybe the young ones grow faster, or the old ones spend more time looking for mates instead of eating. It doesn't matter which(it can even be both) as long as it's not even across all members of the predator species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now examine the next generation, five years down the line. The effects of the prey glut are felt here too (more parents-&gt; more children, bigger parents-&gt;stronger children, etc etc). If the cicada cycle is five years, or even ten, every predator generation(or every other generation) that coincides with the cicada eruption gets a fitness/population bump. After many iterations, the age group of predators that matures or spawns or whatever in time to get the maximal benefit from the cicada eruption dominates. Instead of evenly distributed age ranges, you get a big group of predator species that are synced up to benefit optimally from the cicada eruptions, which is bad news for the cicadas.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thing that regulates the predator life cycle length is the time to sexual maturity, or the generation time. If this is a factor of the cicada hibernation time, cycles develop and the cicadas are in trouble. If the cicadas use a large prime number, the number of cicada generations between matching predator generations is very large. (a five year predator cycle and 17 year cicada cycle only overlap once every 85 years.) For every predator generation that benefits optimally from the cycle, 17 of them have to live without the benefit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally speaking taking a long time to reach sexual maturity is bad news for a predator species(all other things being equal), so no species to my knowledge has evolved to sync up its generations with the cicadas. &lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="4109" LastEditDate="2014-09-23T10:23:12.873" LastActivityDate="2014-09-23T10:23:12.873" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20875" PostTypeId="2" ParentId="20871" CreationDate="2014-08-29T21:08:11.100" Score="1" Body="&lt;p&gt;Death is appropriate. Using this word to describe both unicellular and multicellular organisms places them in the same hierarchy. This hierarchy is the domain of life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both prokaryotes and eukaryotes have unicellular and multicellular species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you choose another word for death I would suggest not using it exclusively for bacteria. If a reader finds the idea of bacterial death esoteric, they may be inspired to dig deeper into the subject. Encouraging an informed reader would seem to be an effective device in a paper for communicating scientific information. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could qualify the word 'death' to be more precise. Senescence is the natural process of deterioration of life with age.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Google has a great tool for tracking word popularity. &lt;a href=&quot;https://books.google.com/ngrams/graph?year_start=1800&amp;amp;year_end=2008&amp;amp;corpus=15&amp;amp;smoothing=7&amp;amp;case_insensitive=on&amp;amp;content=senescence&amp;amp;direct_url=t4%3B%2Csenescence%3B%2Cc0%3B%2Cs0%3B%3Bsenescence%3B%2Cc0%3B%3BSenescence%3B%2Cc0%3B%3BSENESCENCE%3B%2Cc0&quot; rel=&quot;nofollow&quot;&gt;Here's a Google graph&lt;/a&gt; for 'senescence'. &lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-30T01:28:57.837" LastActivityDate="2014-08-30T01:28:57.837" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20876" PostTypeId="1" AcceptedAnswerId="20879" CreationDate="2014-08-29T21:19:56.187" Score="0" ViewCount="6052" Body="&lt;p&gt;Is it true that using scratched Teflon-coated pans contain carcinogens, and if so, can they be consumed through the food cooked in them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.g.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.dailymail.co.uk/health/article-61407/The-deadly-toxins-non-stick-frying-pans.html&quot; rel=&quot;nofollow&quot;&gt;The deadly toxins from non-stick frying pans&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1195" LastEditorUserId="1195" LastEditDate="2014-09-03T08:47:11.550" LastActivityDate="2014-09-03T08:47:11.550" Title="Does scratched Teflon coated frying pans contain carcinogens which can cause cancer?" Tags="&lt;cancer&gt;&lt;toxicology&gt;&lt;liver&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ClosedDate="2014-08-30T09:16:16.257" ContentLicense="CC BY-SA 3.0" />
  <row Id="20877" PostTypeId="2" ParentId="20844" CreationDate="2014-08-29T21:21:12.633" Score="4" Body="&lt;p&gt;I have never worked much with yeast, but I can still give some answers:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Salmon sperm is used as a the so called &quot;carrier DNA&quot;. It is thought to bind to the yeast cell wall and thus prevents that the DNA which shall be transformed does so. This raises the transformation efficiency. See here for more details: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12073338&quot; rel=&quot;nofollow&quot;&gt;Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method.&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Effect of the recovery time: In this time you typically give the cells the chance to recover from the relative rude treatment and to express the resistance gene (when used) before moving them to a selective medium. This raises the efficiency of the transformation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Spheroblasts: As far as I remember they are terribly fragile and painful to handle. However, when you succeed making them, you have cells which take up high quantitaties of DNA which makes them pretty efficient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think these reviews are definitely worth looking at (they also contain a lot more references):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://eeb.lu.lv/ftp/grozs/MolekularasBiologijas/Genetiskais%20eksperiments/Publikacijas/Fjodorovs%20Aleksejs/01304rv02_10885a.pdf&quot; rel=&quot;nofollow&quot;&gt;Genetic Transformation of Yeast&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056089/&quot; rel=&quot;nofollow&quot;&gt;Transformation of Saccharomyces cerevisiae and other fungi - Methods&#xA;and possible underlying mechanism&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://2008.igem.org/wiki/images/2/27/JHU_0708_paper_ForeignGeneExpression.pdf&quot; rel=&quot;nofollow&quot;&gt;Foreign gene expression in yeast: a review&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you have a chance to get hands on a copy of &quot;&lt;a href=&quot;http://www.cshlpress.com/default.tpl?cart=140934485820372490&amp;amp;fromlink=T&amp;amp;linkaction=full&amp;amp;linksortby=oop_title&amp;amp;--eqSKUdatarq=526&quot; rel=&quot;nofollow&quot;&gt;Methods in Yeast Genetics: A Cold Spring Harbor Laboratory Course Manual&lt;/a&gt;&quot;, I think this will be very helpful.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-08-29T21:21:12.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20878" PostTypeId="2" ParentId="11026" CreationDate="2014-08-29T23:48:52.663" Score="4" Body="&lt;p&gt;Well, the answer which explains the difference between calcium and potassium is quite simple. Do we agree that charge separation (between the two sides of the membrane) is the thing which creates the potential? meaning, if the charge concentrations at the two sides were the same, then the membrane potential was zero. right?&#xA;So here is the thing. You have much more Ca outside the cell than inside and you have much more potassium inside than outside. So now, if you add Ca outside, you increase the difference between the two sides (the separation of Calcium ions) so that Ca will be in a greater state of unrest, the system will be less stable and the potential will be higher. On the other hand, when you add K outside, you narrow the gap between its two concentrations on the two sides (decrease its gradient), so now it'll experience less tension, less unrest, hence contribute less potential to the membrane. &#xA;Remember that in our cells, the ion pumps are the ones which serve as the battery that keeps the potential fixed. When do you think the pumps will have to work harder and to do more work (voltage times charge is work), when you add more K outside, or when it's the Ca which is being added? &lt;/p&gt;&#xA;" OwnerUserId="9021" LastActivityDate="2014-08-29T23:48:52.663" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20879" PostTypeId="2" ParentId="20876" CreationDate="2014-08-30T00:14:11.600" Score="5" Body="&lt;p&gt;Teflon is a polymer of perfluorooctanoic acid (PFOA) and related compounds.  PFOA is thought to be a carcinogen.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think there's an urban legend that if you really heat teflon up or burn it (it doesn't burn as flouroxides are not stable in air) that you might get some of the constituent chemicals out into the air.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once the flourocarbons are polymerized into fibers and surface coated a metal pan, they are chemically inert and &lt;a href=&quot;http://www.webmd.com/cancer/features/teflon-pans&quot; rel=&quot;nofollow&quot;&gt;aren't carcinogenic&lt;/a&gt;.  Teflon can be made to burn and some noxious fumes produced, but they are not especially carcinogenic.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even after all this, &lt;a href=&quot;http://www.jstor.org/discover/10.2307/27822994?uid=3739560&amp;amp;uid=2&amp;amp;uid=4&amp;amp;uid=3739256&amp;amp;sid=21104635781623&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; reviewed PFOA exposure and points out that most people in industrialized countries have some PFOA in their blood and this does not seem to be related to a strong incidence of cancer as the level of exposure is so low. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Flouro-carbon compounds are terribly inert - thats why teflon is so tough.  If PFOA is dangerous, then Teflon is &gt; 10 million times less dangerous.  If PFOA is dangerous, crossing the street is many more times dangerous.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.washingtonpost.com/wp-dyn/content/article/2006/01/25/AR2006012502041.html&quot; rel=&quot;nofollow&quot;&gt;Even PFOA will be eliminated from Teflon production, supposedly next year&lt;/a&gt; (2015). &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-09-01T14:48:23.210" LastActivityDate="2014-09-01T14:48:23.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20882" PostTypeId="2" ParentId="20876" CreationDate="2014-08-30T02:47:10.900" Score="1" Body="&lt;p&gt;The question and link imply that if cooking with Teflon generates carcinogens that carcinogens then always lead to cancer. This is not always true. In some cases exposure to carcinogens may signal protective pathways. Oncogenesis and exposure to both genotoxic and non-genotoxic carcinogens are not always positively correlated. Cooking with Teflon influences how you cook, and it's how you cook that has the greatest effect on the levels of carcinogens in food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cooked food contains carcinogens in the form of reactive oxygen species. This is related more to the heat its cooked at than the type of cookware used. Carcinogen exposure in the heating of biological material is an interesting subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carcinogens can be classified in 2 categories &lt;a href=&quot;http://www.nature.com/srep/2013/131003/srep02783/full/srep02783.html&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Genotoxic carcinogens (Reactive Oxygen Species/ROS)&lt;/li&gt;&#xA;&lt;li&gt;Non-genotoxic carcinogens (PFOA is thought to be here)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Genotoxic carcinogens facilitate the formation of cancer through alterations in a cell's DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Non-genotoxic '...carcinogens have no direct interaction with DNA; they are believed to cause tumors by disrupting cellular structures and by changing the rate of either cell proliferation or of processes that increase the risk of genetic error. (1)'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The molecular mechanism most often thought of for cancer formation is genotoxic oncogenesis, damage to DNA. Here, genotoxic oncogenesis often involves a reactive oxygen species (ROS). ROS may generate free radicals which, when reacting with other molecules, generate more free radicals. Another example of a reaction involving free radicals is a fire. Human cells contain genes for antioxidant enzymes, like glutathione and superoxide dismutase, which catalytically converts the free radical superoxide into hydrogen peroxide. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The abundance of ROS in our cells has 2 components:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Production of ROS&lt;/li&gt;&#xA;&lt;li&gt;Depletion of ROS by upregulation of antioxidant enzymes&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Intracellular levels of ROS positively regulate levels of antioxidant enzymes like glutathione and superoxide dismutase &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12441363&quot; rel=&quot;nofollow&quot;&gt;(2).&lt;/a&gt; This means that more oxidative stress leades to more protection from ROS by antioxidant enzymes. This is why exercise, while increasing ROS levels, actually protects against them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ROS are also produced during the cooking of food, especially meat &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16386858&quot; rel=&quot;nofollow&quot;&gt;(3)&lt;/a&gt;. This applies to any type of cookware, any method of heating of any food: protein, carbohydrates, fats. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;'For example, it only takes a few hours at 70C to have the same extent of autoxidation which at room temperature requires months &lt;a href=&quot;http://books.google.com/books?id=zJloknx0L6kC&amp;amp;pg=PA64&amp;amp;lpg=PA64&amp;amp;dq=temperature%20at%20which%20free%20radicals%20are%20formed%20in%20food&amp;amp;source=bl&amp;amp;ots=CBSOw0zZdj&amp;amp;sig=xObTBgYpErh4YTQ4CgMlHYQ9TeQ&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=lTUBVP6wA8zHgwS8xIGABQ&amp;amp;ved=0CEEQ6AEwBA#v=onepage&amp;amp;q=temperature%20at%20which%20free%20radicals%20are%20formed%20in%20food&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;(4)&lt;/a&gt;'&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Intracellular ROS are unavoidable. They are produced by normal metabolism, exercise, cosmic radiation, during the consumption of food. Balancing this are endogenous antioxidant enzymes. The antioxidant power of glutatione exceeds any known nutritional supplement &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2129149/&quot; rel=&quot;nofollow&quot;&gt;(5)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exercise is an extremely effective upregulator of antioxidant enzymes, eclipsing any antioxidant supplement or change in cookware. Regular physical activity will most likely be the best prevention one can take against ROS induced genotoxic oncogenesis.&lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-08-31T06:23:35.813" LastActivityDate="2014-08-31T06:23:35.813" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20888" PostTypeId="2" ParentId="20871" CreationDate="2014-08-30T04:36:19.213" Score="-3" Body="&lt;p&gt;The word &lt;em&gt;bacteriocidal&lt;/em&gt; is commonly used when describing agents that kill them, as opposed to agents that slow their growth which are said to be  &lt;em&gt;bacteriostatic&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8969" LastEditorUserId="1320" LastEditDate="2014-08-30T20:02:17.953" LastActivityDate="2014-08-30T20:02:17.953" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20889" PostTypeId="1" AcceptedAnswerId="20922" CreationDate="2014-08-30T04:58:39.413" Score="3" ViewCount="856" Body="&lt;p&gt;By my own experience, &lt;a href=&quot;http://en.wikipedia.org/wiki/Louse&quot; rel=&quot;nofollow&quot;&gt;lice&lt;/a&gt; seems to be &lt;a href=&quot;http://en.wikipedia.org/wiki/Head_lice_infestation&quot; rel=&quot;nofollow&quot;&gt;prevalent&lt;/a&gt; in the hair of human children, but not in adults. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is &lt;strong&gt;Why are human children more likely to get lice than adults?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Assumptions:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Can be referred to lice/louse/nits&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5417" LastEditorUserId="1320" LastEditDate="2014-08-30T20:17:34.637" LastActivityDate="2014-09-01T07:09:44.920" Title="Why are human children more likely to get lice (nits) than adults?" Tags="&lt;human-biology&gt;&lt;parasitology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20890" PostTypeId="2" ParentId="2602" CreationDate="2014-08-30T06:36:42.733" Score="15" Body="&lt;p&gt;This is an excellent question, I have been training people to culture cells for about 12 years and students have a hard time grasping this and appreciating the importance etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What cells are usually experiencing during pipetting is analogous to a crowd of people trying to fit through the doorway of a building. Shearing during pipetting  is certainly a legitimate concern in cell culture. You will notice its negative effect on viability most explicitly when pipetting cells in freezing&#xA; medium (containing DMSO) following a thaw. Until their DMSO concentration drops their membranes are weaker &amp;amp; more fluid. That's why you pipette the frozen cells drop-wise to the fresh medium, to be especially gentle at this point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prokaryotic cells such as the above mentioned TOP10 cells are treated with Calcium chloride and glycerol which has essentially the same effect on their walls and membranes. Hence pipetting should be delicately performed after thawing these cells as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With that being said, if you compare the sensitivity of prokaryotic and eukaryotic cells to shearing, eukaryotic cells are profoundly more sensitive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For individuals using competent bacteria for sub-cloning and other routine uses, killing a small percentage of of your cells is not that important. However if you are using the transformation to generate cDNA libraries it's very important that you have a titer sufficiently representing the transcriptome the library is composed of. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In these instances using a more premium competent cell, adhering to correct temperatures and minimizing pipetting is essential. This is why many are taught to swirl the DNA the with the competent cells, rather than the harsher alternative: pipetting up-and-down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The four most important factors that contribute to cellular shearing are, and in order form most to least contributory:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Diameter of the bore in the pipette tip, the smaller the more shearing. &lt;/li&gt;&#xA;&lt;li&gt;Speed at which the suspension is passing through the opening of the tip. The faster the more damaging.  &lt;/li&gt;&#xA;&lt;li&gt;Size and rigidity of the cell. Larger cells are more prone to damage.  Cells with a murein wall are less prone to damage.  &lt;/li&gt;&#xA;&lt;li&gt;Concentration of cells. Cultures that are more concentrated are more prone to damage.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Because the make up if the cell itself is so influential on the amount of damage, and because of the enormous variety of cells; designing a representative experiment to assess damage would be very difficult and  laborious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally,  the variety of tips and seriologicals is also enormous. However if one were to attempt to assess this it could be done:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Choose a representative variety of cell lines, choose a representative variety of pipettes. One would probably want to use a robotic pipette to be able to  evaluate incrementally assigned speeds and pressures. Look at different culture concentrations,  phases of the growth curve, time between pipetting and analysis, distance between the exiting fluid and the culture etc, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think a very successful analysis method would be using propidium iodide and FACS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After your experiment which will cost a lot of time and $, I think you will find common sense rules: keep pipetting to a minimum and use wider tips whenever possible.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-10-21T13:34:07.887" LastActivityDate="2014-10-21T13:34:07.887" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20891" PostTypeId="2" ParentId="3445" CreationDate="2014-08-30T06:47:56.790" Score="4" Body="&lt;p&gt;Some things to consider. If you spinning too fast and too long, that is going to pack the pellet more. You can spin longer at a slower speed and you will notice your pellet is not as tightly packed. I always do 2000 rpm, 20 minutes, 4C if I'm doing a midi or maxi sized prep and harvesting bacteria in a 50ml conical.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I'm doing a miniprep I will take the 1.5 micro centrifuge tube (with pellet and buffer p1) and scrape the bottom of the tube 1 or 2 times across all the holes in the rack. This vibrates the tube good loosening and breaking up the pellet. You can consistently perform this step across many samples, this does a good job of re suspending the bugs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have noticed that cultures that are overgrown, contaminated, or grown in incorrectly formulated lysogeny broth, will give the pellet some weird characteristic including color and the pellet 'texture.' &lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-09-02T01:32:44.307" LastActivityDate="2014-09-02T01:32:44.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20896" PostTypeId="2" ParentId="20871" CreationDate="2014-08-30T13:42:03.443" Score="1" Body="&lt;p&gt;Apoptosis and necrosis are only two ways by which eukaryote death is achieved. Certainly there are other ways. Say, if a tissue or organism burns, death is achieved before any nuclear changes, cell swelling or shrinking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Same thing goes with bacteria. Death is the generic term. If you have more details, you can be more specific. In laboratories, cells die by &lt;strong&gt;lysis&lt;/strong&gt; induced by the human experimenters, either by fancy P1 buffer or by the less sophisticated bleach. &lt;strong&gt;Sporulating&lt;/strong&gt; bacteria autolyse the mother cells in the process of spore release. Overcrowded bacteria may decide to relieve some the pressure by having some individuals commit controlled suicide, called &lt;strong&gt;autolysis&lt;/strong&gt;. For example, lytA is an autolysin stimulated by crowding in the pneumococci. The couple ccdA-ccdB sitting on the E coli plasmid F help ensure that daughter cells that did not inherit any plasmid copies commit &lt;strong&gt;programmed suicide&lt;/strong&gt;. Details about these and some other described mechanisms of death in bacteria are to be found in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99002/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99002/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if you are looking at some bacteria dying, and you have no evidence about the molecular mechanisms, &lt;strong&gt;death&lt;/strong&gt; is good enough.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastEditorUserId="8809" LastEditDate="2014-08-30T15:38:27.050" LastActivityDate="2014-08-30T15:38:27.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20897" PostTypeId="2" ParentId="20889" CreationDate="2014-08-30T16:32:35.720" Score="0" Body="&lt;p&gt;Lice prefer clean hair, so in addition to closer contact among children, adults seem to use more hair product (gel, hair spray, etc.) than children in preparation for their day. Lice have difficulty moving through hair strands that are stuck together with product, so this may also contribute to the prevalence in children.&lt;/p&gt;&#xA;" OwnerUserId="9018" LastActivityDate="2014-08-30T16:32:35.720" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20898" PostTypeId="1" AcceptedAnswerId="20900" CreationDate="2014-08-30T17:14:54.100" Score="4" ViewCount="1736" Body="&lt;p&gt;In preparing agar plates with NGM, and also liquid cultures for growing c elegans, how essential is the addition of cholesterol and heavy metals? I have prepared both. I can't notice any obvious difference and I hate having to add all these supplements.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm using yeast extract and peptone as the primary components of the base. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isn't this just supposed to be a moist semi-soft substrate for them to crawl around, their nutrients come from the bacteria they eat.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="1320" LastEditDate="2014-08-30T20:15:38.177" LastActivityDate="2014-08-30T20:15:38.177" Title="Is it essential to add cholesterol to agar or liquid culture for C. elegans?" Tags="&lt;growth-media&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20899" PostTypeId="2" ParentId="10746" CreationDate="2014-08-30T17:55:59.570" Score="3" Body="&lt;p&gt;When asking why a particular group of organisms, such as mammals, has a particular feature, such as a long snout, you must be careful about the hypothesized reasons.  While the other answers here propose various adaptive reasons, they do not actually explain the presence of the long snout in the majority of mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead, you have to look at the evolutionary history of mammals and vertebrates. Modern mammals have long snouts because they inherited the trait from their earliest mammalian ancestors, such as &lt;em&gt;Morganocodon&lt;/em&gt;. In turn &lt;em&gt;Morganucodon&lt;/em&gt; and other early mammals had long snouts inherited from their synapsid (&quot;reptilian&quot;) ancestors like the sphenacodontid (see the first phylogenetic tree below). Why did the synapsids have long snouts, then?  Because the earliest tetrapods like &lt;em&gt;Ichthyostega&lt;/em&gt; had snouts. Before that, the lobe-finned fishes like &lt;em&gt;Eustenopteron&lt;/em&gt; and &lt;em&gt;Panderichthys&lt;/em&gt; had the elongated snouts (see the second phylogenetic tree below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AYOoq.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3MykK.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, the mammalian snouts were modified through natural selection to take on various shapes and sizes (or become greatly reduced) for various (presumably) adaptive reasons, as suggested by the other answers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An analogous question is why do all mammals have four appendages (arms and legs)? They inherited the four appendages from their common tetrapod ancestor, which in turn inherited the appendages from their ancestral lobe-finned fishes. The appendages are later modified by natural selection. That same reasoning applies to this question about mammalian snouts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When using phylogenetic trees to study the adaptive changes of particular traits (such as snouts), a researcher can first use comparative techniques like phylogenetically independent contrasts to tease out the effects of inheritance due to common ancestry. See for example &lt;a href=&quot;http://www.jstor.org/discover/10.2307/2461605?uid=3739256&amp;amp;uid=2&amp;amp;uid=4&amp;amp;sid=21104573023027&quot; rel=&quot;nofollow noreferrer&quot;&gt;Felsenstein, J. (1985)&lt;/a&gt; and the many, many papers that cite this one.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125: 1-15.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Credits&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Fishapod_evolution.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eusthenopteron&lt;/em&gt; to &lt;em&gt;Pederpes&lt;/em&gt; phylogeny&lt;/a&gt; modified from Maija Karala, Wikimedia Commons (CC-BY-SA-3.0).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Palaeohatteria_DB.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;sphenacodontid&lt;/a&gt; by dmitrchel, Wikimedia Commons (public domain).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Morganucodon.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Morganucodon&lt;/em&gt;&lt;/a&gt; by Michael B.H., Wikimedia Commons (CC-BY-SA-3.0).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Ichthyostega_BW_2.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Ichthyostega&lt;/em&gt;&lt;/a&gt; by ArthurWeasley, Wikimedia Commons (CC-BY-2.5)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Tiktaalik_BW.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Tiktaalik&lt;/em&gt;&lt;/a&gt; by Nobu Tamura, Wikimedia Commons (CC-BY-2.5).&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-08-30T18:27:21.143" LastActivityDate="2014-08-30T18:27:21.143" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20900" PostTypeId="2" ParentId="20898" CreationDate="2014-08-30T20:13:45.103" Score="7" Body="&lt;p&gt;&lt;em&gt;C. elegans&lt;/em&gt; &lt;a href=&quot;http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0020345&quot;&gt;needs cholesterol, but can't make it&lt;/a&gt;. Since bacteria don't make cholesterol either, the food bacteria aren't a source. As explained in the linked paper,  lack of cholesterol affects normal development.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-08-30T20:13:45.103" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20901" PostTypeId="1" CreationDate="2014-08-30T20:20:38.900" Score="1" ViewCount="510" Body="&lt;p&gt;Why is the enteral route seem by far the most common way to administer a drug to the body?&lt;/p&gt;&#xA;" OwnerUserId="8977" LastEditorUserId="3632" LastEditDate="2014-08-31T11:48:45.997" LastActivityDate="2014-09-02T18:36:59.883" Title="Pharmacology: Drug Administration" Tags="&lt;pharmacology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20902" PostTypeId="2" ParentId="20901" CreationDate="2014-08-31T01:20:08.357" Score="0" Body="&lt;p&gt;Pill, tablet and time release are great enteral treatments because of their ability to control dosage by the patient at home. Compared with an IV and oil/sublinguals they are less effective at due to the greater risk of causing toxic damage to the liver and kidneys but there is little chance of overdose by reason of mechanical failure. That is the reason that viagra and metformin are first lines of defense; followed by insulin and alprostadil if they so fail. You do not infect yourself typically with a pill but with an injection its possible for a needle to be dirty. Likewise also there is the ever fear of an air bubble.&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2014-08-31T04:55:01.733" LastActivityDate="2014-08-31T04:55:01.733" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="20903" PostTypeId="2" ParentId="2602" CreationDate="2014-08-31T03:07:45.007" Score="3" Body="&lt;p&gt;This question would be better served in the physics se or chemistry. I don't think we have a generic engineering where fluid dynamics could be described in a different method than physics but if we did it should also be answered there.&lt;/p&gt;&#xA;&lt;p&gt;Indeed the osmotic or liquid pressure in and of itself would cause changes possibly damages to the cell. Then other eexothermic and endothermic reactions to the chemicals due to force of impact like a chem or friction burn.&lt;/p&gt;&#xA;&lt;p&gt;I'm sure the other requirements of conservation of energy which I half-hazardly ignored.&lt;/p&gt;&#xA;&lt;p&gt;I found this interesting paper which focuses on the shear stress in general.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17492777&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pipetting causes shear stress and elevation of phosphorylated stress-activated protein kinase/jun kinase in preimplantation embryos.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Xie Y1, Wang F, Puscheck EE, Rappolee DA.&lt;/p&gt;&#xA;&lt;p&gt;Shear stress at 1.2 dynes/cm(2) induces stress-activated protein kinase/jun kinase phosphorylation that precedes and causes apoptosis in embryos (Xie et al., 2006b, Biol Reprod). Pipetting embryos is necessary for many protocols, from in vitro fertilization to collecting embryos prior to analyzing gene expression by microarrays. We sought to determine if pipetting upregulates phosphorylated MAPK8/9 (formerly known as stress-activated protein kinase/jun kinase/SAPK/JNK1, 2). We found that phosphorylated MAPK8/9, a marker of MAPK8/9 activation, is upregulated in a dose-dependent manner by pipetting. Whereas embryos with the zona pellucida removed were more sensitive to stress-induced lethality mediated by 1.2 dynes/cm(2) shear force, phosphorylated MAPK8/9 was induced at lower numbers of pipet triturations in hatched embryos at E4.5. E4.5 embryos were more sensitive to induction of MAPK8/9 than unhatched embryos at E2.5 or E3.5. E3.5 embryos also showed a pipetting dose-dependent induction of FOS protein (formerly known as c-fos), a marker of shear stress in many cell types. Phosphorylated MAPK8/9 measured in ex vivo embryos from E1.5 to E4.5 were expressed at low levels. Embryos that had been pipetted sufficiently to induce phosphorylated MAPK8/9 and FOS had the same number of cells as untreated embryos 24 hr later. This suggests that rapid phosphorylation of MAPK8/9 due to transient shear stress does not mediate long-term negative biological outcomes. But, it is possible that techniques requiring multiple handling events would induce MAPK8/9 and cause biological outcomes or that other biological outcomes are affected by low amounts of transient shear stress. This study suggests that embryo handling prior to experimental measurement of signal transduction phosphoproteins, proteins and mRNA should be performed with care. Indeed, it is likely that shear stress may cause rapid transient changes in hundreds of proteins and mRNA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="-1" LastEditorDisplayName="user1357" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-01T23:25:29.860" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20905" PostTypeId="1" CreationDate="2014-08-31T05:05:43.437" Score="0" ViewCount="200" Body="&lt;p&gt;I read an article on howstuffworks.com and they mentioned how we have found soft tissue in dinosaurs. According to the article even Mummies and Mammoths have no soft tissue left. Is there any evidence that soft tissue can remain intact this long even under perfect conditions? and if not what are some hypotheses that could explain it?&lt;/p&gt;&#xA;" OwnerUserId="8845" LastActivityDate="2014-08-31T12:54:55.773" Title="Is there any evidence that soft tissue can be preserved for 65m+ years and if not what hypotheses exist to explain it?" Tags="&lt;evolution&gt;&lt;tissue&gt;&lt;decay&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20906" PostTypeId="1" AcceptedAnswerId="20910" CreationDate="2014-08-31T07:23:49.710" Score="8" ViewCount="9529" Body="&lt;p&gt;I recently had ants find and then swarm to a food container that I put down on a desk. I'm curious as to whether an ant would have needed to get lucky (i.e., discovering the food after crawling up the desk) or ants have the ability to sense food from a distance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm skeptical of believing that ants simply scout around until finding food; I'll use this case as an example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;My room has had no food or drink in it for weeks, so the area wouldn't be a &quot;hotspot&quot; for ants to be interested in.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I put the mostly empty food container down on my clean desk and turned my lamp off to work on the computer. No more than 2 hours later did I turn my light back on to discover a trail of ants swarming to the container I put down. It happened pretty quickly.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The desk is high, standing on four thin legs. I find it difficult to believe that an ant would crawl up the desk as often as a 2 hour time frame to scout for food, for the message to be passed to the colony so quickly. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I've been curious about this scenario for a long time. So my question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can ants sense food from a long distance?&lt;/strong&gt; If so, how does it work? If not, how is the phenomena (ants locating food quickly in unlikely places) explained?&lt;/p&gt;&#xA;" OwnerUserId="19073" LastEditorUserId="16866" LastEditDate="2017-04-03T17:33:37.447" LastActivityDate="2017-04-03T17:33:37.447" Title="Can ants sense food from a long distance?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;food&gt;&lt;sensation&gt;&lt;ant&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20907" PostTypeId="1" AcceptedAnswerId="20909" CreationDate="2014-08-31T09:37:51.053" Score="5" ViewCount="497" Body="&lt;p&gt;This tree is recently photographed in Quito, Ecuador. It grows everywhere. I'm new to South American flora, so I'd like to know what the species it is?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VwuSd.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6647" LastEditorUserId="1320" LastEditDate="2014-09-02T08:58:37.227" LastActivityDate="2014-09-02T08:58:37.227" Title="Species identification, tree from Ecuador" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20909" PostTypeId="2" ParentId="20907" CreationDate="2014-08-31T11:22:09.917" Score="6" Body="&lt;p&gt;Your plant appears to be &lt;a href=&quot;http://images.google.com/#q=Chionanthus+pubescens&quot;&gt;&lt;em&gt;Chionanthus pubescens&lt;/em&gt;&lt;/a&gt;, the pink fringe tree, which is native to Ecuador and Peru. The genus has a &lt;a href=&quot;http://www.theplantlist.org/tpl1.1/search?q=Chionanthus&quot;&gt;number of species&lt;/a&gt;. It belongs to the family &lt;a href=&quot;http://www.theplantlist.org/1.1/browse/A/Oleaceae/&quot;&gt;Oleaceae&lt;/a&gt;, which includes well known plants like jasmine, forsythia, ash trees and olives. I could not find much biological information on the pink fringe tree but &lt;a href=&quot;http://www.theplantlist.org/tpl1.1/record/kew-367509&quot;&gt;plantlist.org&lt;/a&gt; contains a number of links to various databases that may be helpful if you want to dig deeper. &lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-31T11:22:09.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20910" PostTypeId="2" ParentId="20906" CreationDate="2014-08-31T11:38:45.077" Score="10" Body="&lt;p&gt;Ants follow odor cues in the wind.  A study by &lt;a href=&quot;http://jeb.biologists.org/content/203/5/857.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;Wolf and Wehner (2000)&lt;/a&gt; manipulated ant antennae and wind direction to show that ants followed odor plumes on the wind. A more recent study by &lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822(14)00254-1&quot; rel=&quot;noreferrer&quot;&gt;Buehlmann et al. (2014)&lt;/a&gt; showed that desert ants of the genus &lt;em&gt;Cataglyphis&lt;/em&gt; cued in on linoleic acid, a so-called necromone (death scent) released by dying insects. Here's a &lt;a href=&quot;http://theweek.com/article/index/259714/how-ants-use-death-signals-to-scavenge-for-food&quot; rel=&quot;noreferrer&quot;&gt;popular article&lt;/a&gt; that summarizes the latter study.  Chances are good the ants are followed the odor plumes coming from your mostly empty food container.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Buelhman, C. et al. 2014. Desert ants locate food by combining high sensitivitty to food odors with extensive crosswind runs. Current Biology 24: 960-964.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wolf, H. and R. Wehner. 2000. Pinpointing food sources: Olfactory and anemotactic orientation in desert ants, &lt;em&gt;Cataglyphis fortis&lt;/em&gt;.  Journal of Experimental Biology 203: 857-868. &lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-08-31T11:47:49.920" LastActivityDate="2014-08-31T11:47:49.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20911" PostTypeId="2" ParentId="20905" CreationDate="2014-08-31T12:54:55.773" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1685849/#!po=18.5714&quot; rel=&quot;nofollow noreferrer&quot;&gt;Schweitzer et al. (2007)&lt;/a&gt; studied soft tissue preservation in a number of specimens, including an 800-1000 year old moas, 300,000 year old mammoth and mastodon, and 65 million year old *T. rex. and &lt;em&gt;Triceratops&lt;/em&gt;. The oldest specimen was a 78 million year old &lt;em&gt;Brachylophosaurus&lt;/em&gt;. Their goal was to try to find common environmental conditions that favor soft tissues preservation in fossils. As of this study, they have not been able to identify a single common environmental factor that seems to favor soft tissue preservation. They did note, however, that the specimens from which they could extract soft tissue (with varying success) were from fluvial sandstone environments, meaning sandy rivers. They (so far) could not extract soft tissue from terrestrial mudstone or marine environments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that Schweitzer et al. &lt;em&gt;did&lt;/em&gt; successfully extract soft tissue from the mastodon. The conditions required for mummification are probably not conducive to soft tissue preservation.  Here is a &lt;a href=&quot;http://scienceblogs.com/pharyngula/2008/07/30/tyrannosaur-morsels/&quot; rel=&quot;nofollow noreferrer&quot;&gt;good blog article&lt;/a&gt; on one of Schweitzer's previous studies of soft tissue preservation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The importance of extracting soft tissue from fossils cannot be overstated. Based on Schweitzer's work, her and her colleagues &lt;a href=&quot;http://www.sciencemag.org/content/320/5875/499&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Organ et al. 2008)&lt;/a&gt; were able to develop a phylogeny that incorporated both mastodon and &lt;em&gt;T. rex&lt;/em&gt;. The used the amino acid sequence from collagen, a protein that is abundant in soft tissue. She and her colleagues repeated the analysis &lt;a href=&quot;http://www.sciencemag.org/content/324/5927/626.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Schweitzer et al. 2009)&lt;/a&gt; and included &lt;em&gt;Brachylophosaurus&lt;/em&gt;, a hadrosaur. As predicted by morphological and other evidence, the mastodon was most closely related to modern elephants and the two dinosaurs were most closely related to modern birds and alligators.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the phylogenetic tree derived from Schweitzer's 2009 study. &lt;em&gt;Mammut&lt;/em&gt; is the mastodon. &lt;em&gt;Brachylophosaurus&lt;/em&gt; and &lt;em&gt;T. rex&lt;/em&gt; are the two dinosaurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mU9m8.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Organ, C.L. et al. 2008. Molecular phylogenetics of mastodon and &lt;em&gt;Tyrannosaurus rex&lt;/em&gt;. Science 320: 499.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Schweitzer, M.H. et al. 2007. Soft tissue and cellular preservation in vertebrate skeletal elements from the Cretaceous to the present. Proceedings of the Biological Society of London B: 274: 183-197.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Schweitzer, M.H. et al. 2009. Biomolecular characterization and protein sequences of the Campanian hadrosaur, &lt;em&gt;B. canadensis&lt;/em&gt;. Science 324: 626-631.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-08-31T12:54:55.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20912" PostTypeId="1" AcceptedAnswerId="20913" CreationDate="2014-08-31T13:55:23.460" Score="15" ViewCount="4053" Body="&lt;p&gt;Throughout high school, I remember learning about Darwin's theory of evolution as if it were near-fact. But something always seemed wrong about the ideas presented.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Survival of the fittest&lt;/li&gt;&#xA;&lt;li&gt;Random mutation&lt;/li&gt;&#xA;&lt;li&gt;Natural Selection&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;All of these things seem to account for some margin of evolutionary progress, but I always remained skeptical that the extremely complex features of life could have formed from these methods alone, even after hundreds of millions of years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's what I notice:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any time a species has needed the development of a specific feature to survive, it has developed that feature, and that feature precisely.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I'm going to use this example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Turtles on an island where shrubbery grew higher up developed longer necks, to reach the leaves.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I imagine that turtle looking up at that food, and sub-consciously wishing to get to it, constantly straining, for its entire lifetime. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;It seems plausible to me that we (advanced life) could have a biological mechanism to &quot;write&quot; needed alterations into either our own DNA or our reproductive DNA over time, triggering the very specific evolutionary developments necessary to our survival without relying on random mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is this possible?&lt;/strong&gt; Does any similar mechanism exist that we know of? &lt;em&gt;If not, how can so many specific (advanced) evolutionary leaps be otherwise explained?&lt;/em&gt;&lt;br&gt;&lt;/p&gt;&#xA;" OwnerUserId="19073" LastEditorUserId="49230" LastEditDate="2019-03-29T18:01:57.973" LastActivityDate="2019-03-29T20:54:25.927" Title="Is there a biological mechanism for evolution encoded into our DNA?" Tags="&lt;evolution&gt;&lt;dna&gt;&lt;natural-selection&gt;" AnswerCount="8" CommentCount="7" FavoriteCount="7" ContentLicense="CC BY-SA 4.0" />
  <row Id="20913" PostTypeId="2" ParentId="20912" CreationDate="2014-08-31T16:57:48.073" Score="42" Body="&lt;p&gt;This entire answer will be long, so read the short part first, then read the rest if you (or anyone else) is curious. Citations are included in the long section. I can include additional citations in the short section if needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long Story Short&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question touches on some common misconceptions about how the evolutionary process. Organisms don't &quot;want&quot; to evolve traits. Traits evolve through the biological processes of random mutation and natural selection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Organisms do not &quot;want&quot; to evolve traits.  (Well, OK, I'd love to evolve an extra pair of hands but that is not possible.) Natural selection works by modifying existing traits. Your turtle can stare all she wants at food out of reach but she will not evolve a longer neck. Instead, natural variation exists among neck lengths of the turtles because of variation of the genes that determine features related to overall boxy size. Those individuals with longer necks may be able to get a bit more food, live a little longer, and reproduce a little more. They will pass along their genes to their offspring, so perhaps more of their offspring will also have longer necks. Over many generations, the turtles may have somewhat longer necks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A common misconception is that the traits of organisms are precisely adapted for a specific need. They are not, for a few reasons. First, natural selection occurs relative to the current environment. Adaptations that work well in one environment may not be so useful in another environment. Environments are rarely stable over evolutionary time so traits are subject to constant change. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next, as mentioned above, natural selection can only work on what traits are present. While an extra set of arms would be handy, I am a tetrapod. My four appendages, along with the appendages of all other tetrapods, trace back to our common ancestor. The appendages of all tetrapods are modifications of that ancestral trait. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, organisms haven't &quot;sampled&quot; the entire realm of possible mutations and combinations of mutations. In other words, a certain mutation or set of mutations might actually be able to adaptively improve a particular trait in the current environment but, if the mutations never occur, then the improvement can never happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We only need to look at ourselves to realize how imperfectly adapted we are. We get bad backs and knees because our bodies weren't designed to walk upright. We evolved from quadrupedal organisms. This has happened so recently that changes in the structure of our knees and backs haven't yet evolved (and may never).  Search the internet for the &quot;blind spot&quot; eye test. We have a mass of blood vessels in &lt;em&gt;front&lt;/em&gt; of the retina of our eyes, which reduces our visual accuity. We often have to have teeth pulled from our jaws because the flattening of our face (relative to our australopithicine ancestors) has shorted our jaws. We don't have as much room for our teeth but we have not evolved a reduced number of teeth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for human technology being able to make direct changes to our DNA to improve our adaptability, I would say no. While I do not have the ability to see into the future, the complexity of our genome, and more specifically how genes are regulated, suggests to me this would be a very daunting if not impossible task.  See the long answer below for more on regulatory genes but the gist is that a small set of regulatory genes control most of the other genes (including other regulatory genes). The interactions are extremely complex and we have a detailed understanding of very few of these interactions.  I speculate that affecting one such gene in a &quot;positive&quot; way is very likely to have many unintended negative consequences. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below are some simple math and other ideas to show you how mutations can lead to the many adaptive traits that you see among the diversity of life on earth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long Story&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;how can so many specific (advanced) evolutionary leaps be otherwise explained?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Mutations occur at random throughout the genome. Most mutations will be neutral. That is, they are neither bad or good from an evolutionary viewpoint. The mutations are neutral because the genome for most organisms is non-functional. Mutations that occur in the functional regions of DNA (i.e., protein-encoding and related regions) are more likely to be detrimental (bad) because the mutation may negatively affect the function of the protein or even the ability to produce the protein.  However, some mutations are beneficial. The mutation may actually enhance the functionality of the protein or even produce new proteins.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A couple of factors have to be considered regarding mutations.  The mutation &lt;em&gt;rate&lt;/em&gt; is very low.  For example, &lt;a href=&quot;http://www.pnas.org/content/99/2/803.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kumar and Subramanian (2002)&lt;/a&gt; compared the DNA sequences of 5669 protein-encoding genes from 326 species of mammals.  Their results suggested that the average mutation rate among mammals is 2.2 x 10&lt;span class=&quot;math-container&quot;&gt;$^{-9}$&lt;/span&gt; per base pair (bp) per year.  This means that, on average, a point mutation has changed each DNA nucleotide position in the mammalian genome slightly more than twice (2.2 times) every billion (10&lt;span class=&quot;math-container&quot;&gt;$^9$&lt;/span&gt;) years. That's a lot of time!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this same rate occurs in every individual in the population, so you have to consider the population sizes of the organisms. So, let's do a simple exercise. Consider a species like the &lt;a href=&quot;http://www.hhmi.org/biointeractive/making-fittest-natural-selection-and-adaptation&quot; rel=&quot;nofollow noreferrer&quot;&gt;rock pocket mouse&lt;/a&gt; or another small mammal that has a very short generation time. For this simple example, let's assume the generation time is one year. That means that the mutation rate of 2.2 x 10&lt;span class=&quot;math-container&quot;&gt;$^{-9}$&lt;/span&gt; per bp per year would then correspond to 2.2 x 10&lt;span class=&quot;math-container&quot;&gt;$^{-9}$&lt;/span&gt; mutations per bp per generation. Generation time is important because new mutations are inherited only through reproduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume the average mammalian diploid genome is about 6 billion (6 x 10&lt;span class=&quot;math-container&quot;&gt;$^9$&lt;/span&gt;) nucleotides in size. The number of heritable mutations that occur in a single offspring is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$(6 \times 10^9) \times (2.2 \times 10^{-9}) = 13.2.$$&lt;/span&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next, assume that about 2.5% of the mammalian genome is composed of functional, transcribed sequences that may affect the phenotype (the traits of the organism). That means that, of all the mutations that occur in every offspring every generation, about 2.5% could potentially affect the phenotype.  That is,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$13.2 \times 0.025 = 0.33.$$&lt;/span&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still a small number.  But, now we have to account for population size. Small mammals, like mice and voles, generally have large population sizes.  Assume that the population of rock pocket mice contains 100,000 reproducing individuals. If so, then&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$0.33 \times 100,000 = 33,000,$$&lt;/span&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;which is the number of new heritable mutations that could occur in the population. Most of these mutations will be detrimental and removed from the population by natural selection but, if even a small fraction of these new mutations are beneficial, then natural selection can cause these beneficial mutations to increase rapidly in frequency in the population during future generations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In humans, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461236/pdf/10978293.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nachman and Crowell (2000)&lt;/a&gt; estimated that the average mutation rate was 2.5 x 10&lt;span class=&quot;math-container&quot;&gt;$^{-8}$&lt;/span&gt; mutations per bp per generation (not year), by comparing the genomes of humans and chimps. If we assume the same genome size and effective human population size of 500,000 individuals, then applying the same math suggests that 1,875,000 new mutations that potentially affect phenotype occur in the human population every generation. Again, only some of these will be beneficial but that is still the possibility of a number of new beneficial mutations. In evolutionary terms, a mouse or human generation is the blink of an eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How long would it take for a beneficial mutation to spread through a population? That depends on two things. How beneficial is the mutation (called the strength of selection, &lt;em&gt;s&lt;/em&gt;) and the population size? To estimate how long it would take for a beneficial mutation to spread through a population, we can use the formula,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$t = \frac{2}{s}\mathrm{ln}(2N_e),$$&lt;/span&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where &lt;span class=&quot;math-container&quot;&gt;$t$&lt;/span&gt; is time in generations, &lt;span class=&quot;math-container&quot;&gt;$s$&lt;/span&gt; is the strength of selection, and &lt;span class=&quot;math-container&quot;&gt;$N_e$&lt;/span&gt; is the effective population size (number of reproducing individuals). For the strength of selection, let's assume &lt;span class=&quot;math-container&quot;&gt;$s=0.01$&lt;/span&gt;, which is weak but positive natural selection. Going back to our rock pocket mice with &lt;span class=&quot;math-container&quot;&gt;$N_e = 100,000$&lt;/span&gt;, then the beneficial mutation would be spread throughout the population in only 2441 generations (remember, we're talking evolutionary time so 2000 years is nothing). If &lt;span class=&quot;math-container&quot;&gt;$N_e = 10,000$&lt;/span&gt;, the mutation spreads in only 1981 generations.  If we increase the strength of selection t 0.2, then the times are 122 and 99 years for population sizes of 100,000 and 10,000 years, respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These &quot;back of the napkin&quot; calculations show just how quickly even weakly beneficial mutations can appear and spread throughout a population. Yet, this doesn't include other types of mutations like gene duplications that can also allow new proteins to evolve. For example, human ability to see red colors is due to a simple gene duplication &lt;a href=&quot;http://cichlid.umd.edu/cichlidlabs/kc/Teaching/Visionpdfs/Nathans1986.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Nathans et al. 1996&lt;/a&gt; and references therein). This duplication also explains the common form of red-green colorblindness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Whew!&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's yet more to our mutational story. Consider humans and chimps, which are nearly identical from a genetic standpoint (between 96-99% depending on how you calculate it) yet they appear very different.  If humans and chimps diverged from their common ancestor within the past five million years, how could they differ so much? This question was initially posted by [King and Wilson (1975)]. They argued that mutations to structural proteins (like those that compose bones and muscles) would not be enough to explain the phenotype differences between humans and chimps. The proposed that &lt;a href=&quot;http://www.nature.com/scitable/topic/gene-expression-and-regulation-15&quot; rel=&quot;nofollow noreferrer&quot;&gt;regulatory genes&lt;/a&gt; are the key to understanding the big differences. Regulatory genes are those that control other genes, by turning them on or off and other important functions. Changes to the regulatory genes can cause fairly rapid changes to the phenotype.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This understanding has led to the broad (and fascinating) field of &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evodevo_01&quot; rel=&quot;nofollow noreferrer&quot;&gt;evolutionary developmental biology&lt;/a&gt;. This field focuses on how mutations in regulatory genes associated with development (from embryo to adult) have had a long-term evolutionary impact. The field is rich with examples, but one cool one is associated with duck feet and bat wings. Let's begin with the embryo. Most vertebrate embryos have membranes between the digits (fingers and toes) during an early stage of development. For most vertebrates, the membranes are lost later in development. The small flaps of skin you have between your fingers are the remnants of your embryonic membranes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A set of regulatory genes called BMPs (and a couple of others) are responsible for causing the loss of the membrane in vertebrates. However, through different sets of mutations, the BMPs are not able to function in duck feet and bat hands. Thus, they both end up with membranes between their digits (&lt;a href=&quot;http://www.pnas.org/content/103/41/15103.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;Weatherbee et al. 2006&lt;/a&gt;).  Thus, two different mutations block the same set of developmental genes, leading to novel adaptations in two very different types of vertebrates. One final example is the evolution of bird feathers from scales. As you may know, birds are evolved from dinosaurs. It turns out that bird feathers and alligator scales (alligators are birds closest &lt;em&gt;living&lt;/em&gt; relative) use the same regulatory genes to develop. The genes are BMP2 and SHH (sonic hedgehog for fans of the old computer game) (&lt;a href=&quot;http://prumlab.yale.edu/sites/default/files/harris_etal_2002.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Harris et al. 2002&lt;/a&gt;). Other regulatory genes underlie the different types of feathers, like downy feathers and flight feathers (Harris et al. 2002).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Harris, M.P. et al. 2002. &lt;em&gt;Shh-Bmp2&lt;/em&gt; Signaling module and the evolutionary origin and diversification of feathers. Journal of Experimental Biology 294: 160-178.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;King, M.-C. and A.C. Wilson. 1975. Evolution at two levels in humans and chimpanzees. Science 188: 107-116.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kumar, S. and S. Subramanian. 2002. Mutation rates in mammalian genomes. Proceedings of the National Academy of Sciences USA 99: 803-808.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nachman, M.W. and S.L. Crowell. 2000. Estimate fo the mutation rate per nucleotide in humans. Genetics 156: 297-304.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Weatherbee, S.D. et al. 2006. Interdigital webbing retention in bat wings illustrates genetic changes underlying amniote limb diversification. Proceedings of the National Academy of Sciences USA 103: 15103-15107,&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="49230" LastEditDate="2019-03-29T20:54:25.927" LastActivityDate="2019-03-29T20:54:25.927" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="20914" PostTypeId="2" ParentId="20912" CreationDate="2014-08-31T17:04:44.160" Score="12" Body="&lt;p&gt;&lt;strong&gt;About your question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This kind of very basic question has the drawback to need a very long answer. In consequence, your question might get some close vote. I'll do my best to help but you might want to look at some source of information as an introduction to evolutionary biology. A book eventually or Khan academy maybe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Darwin's evolution theory&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The expression &quot;Darwinian evolution theory&quot; easily yield to misunderstanding because Darwin was probably the most important scientist (and one of the first if not the first) to develop evolution theory but not the only one. Evolution theory is not anymore Darwin's evolution theory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is Natural Selection? Lewontin Recipe&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You list:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;- Survival of the fittest&#xA;- Random mutation&#xA;- Natural Selection&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;It is a list of different concepts that might be present in evolutionary biology but its nothing like a recipe for evolution to occur. This list I think already shows some point you misunderstood about evolution. The Lewontin recipe is a good way in order to understand what is natural selection and when it occurs. The Lewontin recipe says that natural selection occurs whenever:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Individuals in a population vary in terms of a given trait&lt;/li&gt;&#xA;&lt;li&gt;This trait has some (additive) heritability. &lt;a href=&quot;https://biology.stackexchange.com/questions/16576/can-i-force-evolution-in-a-group-of-cells-by-removing-all-the-smaller-cells/16578#16578&quot;&gt;Here&lt;/a&gt; is one of the several posts that explain the concept of heritability. It might be slightly a post that is a bit advanced for you though but shortly speaking it means that offspring are more similar to their parents more than they are to other non-kin individuals in the population.&lt;/li&gt;&#xA;&lt;li&gt;The fitness varies (not necessarily linearly) as the trait varies.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Simple example:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;In a population, there are blue pens and red pens&lt;/li&gt;&#xA;&lt;li&gt;Reproduction is asexual and blue pens create other blue pens while red pens create other red pens.&lt;/li&gt;&#xA;&lt;li&gt;blue pens make more offspring than red pens.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In such a situation, natural selection occurs yielding the frequency of the blue pens to increase in the population while the frequency of red pens will decrease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is evolution?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution is not only natural selection. It is for example very important to consider random events. One of them is &lt;em&gt;mutation&lt;/em&gt;, another is &lt;em&gt;genetic drift&lt;/em&gt; (I am not trying to list every parameter that influence evolution but only to give you a sense of why natural selection is different than evolution with a goal of explaining why a trait that is needed do not necessarily appear). Both mutations and genetic drift explain why a species will not necessarily be perfectly adapted to its environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Mutations&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the broad sense mutation is any change in the DNA sequence. Some changes are more likely to happen than other but in any case, the likeliness of these changes to happen is not dependent on the consequence they will have on the phenotype (shortly speaking, a phenotype is how an individual looks like) and on the reproductive success. So mutations occur randomly and the specific mutation that would be needed in the population may not occur. Therefore saying, if a trait is needed (in the sense of &quot;if a trait would be beneficial&quot;), then a mutation will occur to make this trait existing is totally wrong. You may be surprised by the level of adaptation of life but this does not mean that what they needed was created with the purpose to help these individuals surviving but it only means that random mutations occur, most of them are deleterious (decrease the reproductive success) while few of them are beneficial (increase the reproductive success) and those that are beneficial are more likely to rise in frequency in the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Genetic drift&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the change in frequency of mutations would depend exclusively on natural selection, then I would not have said before that a beneficial mutation is more likely to raise in frequency but I would have said that a beneficial mutation will raise in frequency. An intuitive explanation of what is genetic drift can be found on &lt;a href=&quot;https://biology.stackexchange.com/questions/14543/why-is-the-strength-of-genetic-drift-inversely-proportional-to-the-population-si/14545#14545&quot;&gt;this post&lt;/a&gt;. It will also allow you to understand why a small population undergo a more random change in frequency of their genes that are big population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, when you say that you noticed that &lt;code&gt;Any time a species has needed the development of a specific feature to survive, it has developed that feature, and that feature precisely&lt;/code&gt; is wrong. You only noticed that species has some level of adaptiveness if I can say so. It is very hard to imagine what new mutation would be beneficial of a given individual in a population but there are in reality many mutations that are beneficial that has never occurred or that has disappeared because of genetic drift. Also, as it is implied in the Lewtontin recipe different individuals have different traits yielding to different reproductive success. If you do not consider mutations that have never occurred but only to sites in the genome that are polymorphic (where different variants exist in the population), then it is worth knowing that any single individual carries quite a lot of deleterious variants. These deleterious mutations explain many genetic diseases. No, we are not perfect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;About your question again&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps a bit. But I would need days in order to explain further what evolution is. It is a bit field in biology. Your question is a bit too broad and as I said at the beginning you should seek some information by yourself and come back to this site with a question that can be more quickly answered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-29T14:18:58.990" LastActivityDate="2019-03-29T14:18:58.990" CommentCount="8" ContentLicense="CC BY-SA 4.0" />
  <row Id="20915" PostTypeId="1" AcceptedAnswerId="20926" CreationDate="2014-08-31T17:11:07.140" Score="6" ViewCount="3902" Body="&lt;p&gt;For most animals, the whole bottom of their face sticks out and they have a snout with a mouth and nose at the end.  But humans have a flat face and just a nose that sticks out.  We used to have the whole face sticking out, but our jaws got smaller and smaller.  Because our noses still needed space to do their job, they had to stay sticking out.  People who come from very cold areas have bigger noses than people from where it is hot, so they can warm the air up more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why has our nose evolved with the nostrils facing down? Is it because we were water animals, and that would help with water coming in?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="8129" LastEditorUserId="8517" LastEditDate="2014-09-01T20:24:29.577" LastActivityDate="2018-10-17T08:00:54.247" Title="Why has our nose evolved with the nostrils facing down?" Tags="&lt;evolution&gt;&lt;human-anatomy&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20916" PostTypeId="2" ParentId="20912" CreationDate="2014-08-31T17:31:14.213" Score="7" Body="&lt;p&gt;Short answer version:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It seems plausible to me that we (advanced life) could have a&#xA;  biological mechanism to &quot;write&quot; needed alterations into either our own&#xA;  DNA or our reproductive DNA over time, triggering the very specific&#xA;  evolutionary developments necessary to our survival without relying on&#xA;  random mutation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No, it's not.  Despite what your feelings tell you, despite what you wish the case might be, there is no evidence in molecular biology to suggest that such a mechanism exists, there is no evidence that such a mechanism is required to explain the different phenotypes we see.  &lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-08-31T17:31:14.213" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20918" PostTypeId="2" ParentId="20912" CreationDate="2014-08-31T21:47:25.613" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;blockquote&gt;&#xA;    &lt;p&gt;&lt;strong&gt;Any time a species has needed the development of a specific feature to survive, it has developed that feature, and that feature precisely.&lt;/strong&gt;&lt;/p&gt;&#xA;  &lt;/blockquote&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;This statement is clearly false. The dinosaurs didn't develop what they needed, did they?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It turned out that on this occasion, the mammals happened to be best adapted to the conditions at the time, just as the fish had managed to get the upper hand over the large arthropods and the ammonites previously. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In hindsight many of nature's solutions seem wonderfully elegant, but they were arrived at by luck under intense pressure to survive.&lt;/strong&gt; The fact that our eye is designed with blood vessels on the front of the optical surface instead of the back is an example of a design that could have been done better if thought out from scratch. There are many vestigial features from previous generations which persist, even though they are no longer needed. Notice that flatfish hatch with eyes on opposite sides of their head and one eye then migrates to be on the same side as the other, and whale embryos that have teeth which have disappeared by the time they are born, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Natural selection is a combination of lucky mutations which happen to fit in with the prevailing conditions.&lt;/strong&gt; It's a tough world out there. Even the plants are strangling each other, as can be seen on this video: &lt;a href=&quot;https://www.youtube.com/watch?v=aNjR4rVA8to&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.youtube.com/watch?v=aNjR4rVA8to&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The turtle didn't have much time to stare longingly at the leaves he couldn't reach.&lt;/strong&gt; Some other turtle with a slightly longer neck came and ate them. And he got bigger and stronger and fought with the first turtle so he got to mate with all the females. And so the next generation of turtles had longer necks than the last. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;It's easy to forget, with our comfortable lives, what a struggle nature is. The reason for this is that humans as a species have developed the most devastating weapon of all: cooperation.&lt;/strong&gt; Compared to most other organisms, we treat other individuals of the same species pretty well (most of the time) &lt;em&gt;and&lt;/em&gt; we actually &lt;strong&gt;teach&lt;/strong&gt; each other how to do things. While some other species cooperate among individuals, humans have taken this to a whole new level. As a result, we have been able to eradicate many species which pose a threat to us and bring many other species which are useful to us under control. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;If you want to know why this didn`t happen before:&lt;/strong&gt; humans evolved from an ape-like creature that, due to changes in its environment, came down out of the trees and started walking on the ground. This creature then had its hands free to use tools, and by sheer chance this combination of factors made a bigger brain advantageous, so this creature (which was already social, like apes but unlike octopi, one of the few other creatures blessed with the ability to perform complex manipulations) became even more intelligent and began to educate its offspring in how to control its environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;There is nothing in biology which enables the mutation of genes to be directed. Finally, human technology has developed to the point where it may be possible to modify genes directly.&lt;/strong&gt; However, there are significant ethical issues regarding the use of this technology. The termination of an &quot;imperfect&quot; human is frowned upon because it is considered that all members of the species should be given the best chance to survive. Besides, &lt;strong&gt;it is not at all clear if there is really ever such thing as a &quot;defective&quot; gene.&lt;/strong&gt; For example carriers of the gene responsible for sickle cell anaemia have increased resistance to malaria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, &lt;strong&gt;long before humans were able to manipulate genes directly, they were able to produce massive changes in the phenotype of dogs in a remarkably small number of generations.&lt;/strong&gt; There is a breed of dog adapted to every possible use. An unfortunate consequence is that &lt;strong&gt;the gene pool in each breed is rather small, leading to breed-specific illnesses.&lt;/strong&gt; If these breeds were left alone it would take many generations for mutations to allow their genotypes to diversify again. And who knows what the final animal would look like?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;blockquote&gt;&#xA;    &lt;p&gt;&lt;strong&gt;It seems plausible to me that we (advanced life) could have a biological mechanism to &quot;write&quot; needed alterations into either our own DNA or our reproductive DNA over time, triggering the very specific evolutionary developments necessary to our survival without relying on random mutation.&lt;/strong&gt;&lt;/p&gt;&#xA;  &lt;/blockquote&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;There is no evidence for such a mechanism, and it is very unclear how a mutation could be proved beneficial without being tested in the environment. What there is, is a way of mixing and matching genes, so that the best ones can propagate throughout the population.&lt;/strong&gt; Unicellular organisms do this by a variety of means. &lt;strong&gt;For multicellular organisms the way of doing is sexual reproduction.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The cost of this is enormous.&lt;/strong&gt; Look at a flowering plant. That flower has evolved exclusively to enable pollination, typically by insects. In some cases, virtually all the plant's energy goes into making that flower and relatively little into making the actual seeds. Plants do have a particular problem exchanging genes because they do not move about. Stationary animals, such as the barnacle, also have similar problems. The barnacle solves this by having a &quot;penis&quot; several times longer than its body length so that it can copulate with its neighbour without moving from its spot. In humans, fully half the population is male and therefore unable to bear offspring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Asexual reproduction is far more efficient at producing offspring but does not enable the interchange of genes. The offspring are clones of their parent and therefore have the same genetic strengths and weaknesses.&lt;/strong&gt; Asexual reproduction does exist, even in some animals, but exclusively asexual reproduction would preclude the spread of beneficial mutations. &lt;strong&gt;That's why organisms invest so much energy in sex.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aphids are a good example of an animal that reproduces both sexually and asexually. At the boom times of the year, aphids reproduce asexually and are actually born as already pregnant females! When the availability of food slows down, they switch to the slower, sexual reproduction system with males and females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In many animals, males must demonstrate their good health in order to be able to mate with the females (who are choosy, because they have to take the cost of bearing the young.) In many large herbivorous mammals, this is done by males fighting. Male birds often display their health by elaborate plumage, the classic example being the peacock. It is debatable whether such a conspicuous waste of resources is really beneficial to the species, but the females have evolved to select males in this way. In some fish, there is only one male in a group, and when something happens to him, the biggest healthiest female actually changes sex to become a male.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So, if an organism were able to program its own genes, why invest so much energy in sexual reproduction?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="9036" LastEditorUserId="43480" LastEditDate="2019-03-29T17:07:02.933" LastActivityDate="2019-03-29T17:07:02.933" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="20919" PostTypeId="1" AcceptedAnswerId="20920" CreationDate="2014-08-31T22:47:39.840" Score="0" ViewCount="37596" Body="&lt;p&gt;These are extremely simple questions — basic biology — but I would like to make sure that the way I have answered is at the very least correct. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Hydrogen bonds are very weak, so how is it possible that they are so important in the properties of water? &lt;em&gt;Hydrogen bonds in water provide many characteristic benefits to water: cohesion (holding water molecules together), high specific heat (absorbing heat when breaking, releasing heat when forming; minimizing temperature change), high heat of vaporization (several hydrogen bonds must be broken in order to evaporate water), lower density of ice (molecules in ice are spaced farther apart), and solubility (polar molecules are attracted to ions and polar compounds, making them soluble in water).&lt;/em&gt;  &lt;/li&gt;&#xA;&lt;li&gt;Why do we feel cooler immediately after we go swimming than we do after we have fully dried off? &lt;em&gt;We feel cooler immediately after we go swimming than we do after we have dried off because it takes a lot of heat to evaporate water; however, once we dry off we remove much of the water from our skin, and the water is evaporated much more quickly.&lt;/em&gt; &lt;/li&gt;&#xA;&lt;li&gt;If water were non-polar, would our temperature heat up less quickly or more quickly if we went outside on a hot day? Why? More quickly. &lt;em&gt;Because hydrogen bonds within water slow down the movement of molecules and allow for water to have a very high specific heat.&lt;/em&gt; &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9038" LastActivityDate="2014-09-01T01:19:10.343" Title="What is the importance of hydrogen bonds in water? and other questions:" Tags="&lt;homework&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-09-01T04:38:58.090" ContentLicense="CC BY-SA 3.0" />
  <row Id="20920" PostTypeId="2" ParentId="20919" CreationDate="2014-09-01T01:19:10.343" Score="1" Body="&lt;ol&gt;&#xA;&lt;li&gt;You are saying what hydrogen bonds are doing, not why are they able of such achievements, despite being so weak. Their strength is in numbers. At room temperature, fully one fifth of the water molecules are engaged in four bonds with other water molecules, while the remainder forms two such bonds. (More detail at &lt;a href=&quot;http://www1.lsbu.ac.uk/water/hbond.html&quot; rel=&quot;nofollow&quot;&gt;http://www1.lsbu.ac.uk/water/hbond.html&lt;/a&gt; ). In contrast, hydrogen sulfide forms essentially no hydrogen bonds with other hydrogen sulfide molecules, despite significant similarity between oxygen and sulfide. The difference in size between oxygen and sulfur makes the former much more electronegative. I could go on with other hydrogen compounds, but the fact that answers your first question is: each water molecule is involved in a series of bonds with other water molecules, on an unequaled scale.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Also, hydrogen bonds are stronger, pickier about distance and angle than the alternatives available to other molecules (dipole-dipole, van der Waals etc.) So even if they seem feeble, and even if the alternatives were as plentiful as hydrogen bonds, the latter would still be more capable of tying up molecules.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The effect of water drying (which comes after swimming, but also after sweating, bathing, or cleaning oneself with a hot oshibori) is caused by water evaporation. Each state transition, including that from liquid water to air-borne vapors, is a heat-consuming phenomenon. When skin dries, the heat to turn water into vapors has to come from somewhere. In perspiration's case, it is one's body.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Note that cooling down while water evaporates is not only something we feel, but a physical reality, occurring even in innate systems. For example, Amazon forests and Sahara are similarly close to the Equator, but the former is cooler than the latter, in part because heat it receives is in part used up to evaporate water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your answer was good.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Again, you are right. Were water non-polar, it would have lower latent heat, or, in lay terms, it would evaporate without much heat consumption. Were sweat made of a non-polar liquid, it will fail to consume heat when evaporating, leaving one to warm up sooner / faster.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8809" LastActivityDate="2014-09-01T01:19:10.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20921" PostTypeId="1" AcceptedAnswerId="20939" CreationDate="2014-09-01T05:41:44.790" Score="3" ViewCount="671" Body="&lt;p&gt;What is the meaning of propensity score of amino acid? How is it calculated? &lt;br/&gt;(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)&lt;/p&gt;&#xA;" OwnerUserId="8835" LastActivityDate="2014-09-02T01:34:56.553" Title="Propensity Score for amino acid" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20922" PostTypeId="2" ParentId="20889" CreationDate="2014-09-01T07:09:44.920" Score="2" Body="&lt;p&gt;Children generally don't care about their hair as much as adults do. So unless parents insist, they don't care for their hair as much (&lt;a href=&quot;http://www.boston.com/lifestyle/family/articles/2010/05/24/why_do_kids_get_lice_so_much_more_often_than_adults/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Kids generally get lice because they are in close contact with each other during play-dates, slumber parties, and sports activities. They are also prone to exchange hair brushes and other personal items more often than adults (&lt;a href=&quot;http://www.parents.com/toddlers-preschoolers/health/other-issues/lice-facts/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An interesting difference I came across between articles is that one article says that its&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;theoretically possible to get infested if your hair makes contact with&#xA;  items such as hats, combs, or brushes (&lt;a href=&quot;http://www.babycenter.com/0_head-lice-101-what-lice-look-like-how-they-behave-and-how-ki_10892.bc&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Another article insists that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;You’re extremely unlikely to get head lice by sharing hats, combs or&#xA;  pillows – a louse’s lifespan is very short once it’s removed from your&#xA;  head (&lt;a href=&quot;http://www.bupa.co.uk/individuals/health-information/directory/h/head-lice&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Between the two, I believe that it is extremely likely that lice would spread if you use a infected hairbrush immediately after it was used by someone harboring the parasite since the time span is short. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-09-01T07:09:44.920" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20923" PostTypeId="2" ParentId="9343" CreationDate="2014-09-01T09:02:19.413" Score="2" Body="&lt;p&gt;Teflon® is a brand name for a man-made chemical known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Polytetrafluoroethylene&quot; rel=&quot;nofollow&quot;&gt;polytetrafluoroethylene&lt;/a&gt; (PTFE) and it has been used since 1940s (discovered by &lt;a href=&quot;http://en.wikipedia.org/wiki/DuPont&quot; rel=&quot;nofollow&quot;&gt;DuPont Co.&lt;/a&gt;). &lt;a href=&quot;http://en.wikipedia.org/wiki/Perfluorooctanoic_acid&quot; rel=&quot;nofollow&quot;&gt;Perfluorooctanoic acid&lt;/a&gt; (PFOA, also known as C8) is another man-made chemical and it is used in the process of making Teflon and similar chemicals (known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Fluorotelomer&quot; rel=&quot;nofollow&quot;&gt;fluorotelomers&lt;/a&gt;), although it is burned off during the process and is not present in significant amounts in the final products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Teflon itself is not suspected of causing cancer&lt;/strong&gt;, but PFOA has the potential to be more of a health concern because it can stay in the environment and in the human body for long periods of time. Studies have found that PFOA is present at very low levels in just about everyone's blood in the US and it can be found at low levels in some foods, drinking water, and in household dust. It can be higher in areas due to contamination. People can be exposed to PFOA from fabrics, ski wax or carpeting which has been treated to be stain resistant. However non-stick cookware is not a significant source of exposure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Studies in laboratory animals have found that PFOA exposure increases the risk of certain tumors of the liver, testicles, mammary glands, and the pancreas in these animals. Overall, well-conducted animal studies do a good job predicting that cause cancer in humans exposures. But for PFOA, there are clear differences in the way the body of laboratory animals and humans handle this chemical. Because of these differences, it is clear that the process chemical to cause cancer in animals also occur in humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human studies have shown that people with workplace exposure to PFOS have a higher risk of cancer of the bladder and kidneys.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several national and international agencies studying various substances in the environment, to determine if they cause cancer (carcinogens, substances that cause cancer and help cancer grow). However, at this time, these agencies do not formally assessed whether PFOA can cause cancer. The US Environmental Protection Agency (&lt;strong&gt;EPA&lt;/strong&gt;), an electronic database that contains information on human health effects from exposure to various substances in the environment, &lt;strong&gt;has not officially classified PFOA as to its carcinogenicity&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other than the possible risk of fumes from overheating the pan, there are no known risks to humans using Teflon-coated cookware.&lt;/strong&gt; When PFOA is used to make Teflon, does not occur (or not present in very small amounts) in a Teflon-coated products. Because the way by which people may be exposed to PFOS are not known, it is not clear what steps to take for people to reduce exposure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Currently, EPA states:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Consumer products made with fluoropolymers and fluorinated telomers,&#xA;  such as Teflon and other trademark products, are not PFOA. PFOA is&#xA;  used as a processing aid in the manufacture of fluoropolymers and can&#xA;  be also be produced by the breakdown of some fluorinated telomers. The&#xA;  information that EPA has available does not indicate that the routine&#xA;  use of consumer products poses a concern. At present, the EPA does not&#xA;  recommend any steps for consumers to take to reduce exposures to&#xA;  PFOA.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.cancer.org/cancer/cancercauses/othercarcinogens/athome/teflon-and-perfluorooctanoic-acid--pfoa&quot; rel=&quot;nofollow&quot;&gt;Teflon and Perfluorooctanoic Acid (PFOA)&lt;/a&gt; at Cancer.org&lt;/p&gt;&#xA;" OwnerUserId="1195" LastActivityDate="2014-09-01T09:02:19.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20924" PostTypeId="1" CreationDate="2014-09-01T10:11:05.730" Score="4" ViewCount="344" Body="&lt;p&gt;Chromosomes are grouped as sex chromosomes or autosomes, with the X, Y, Z and W all falling in to the former category. The Z and X are present both in the homogametic and heterogametic sexes, and the Y and W only in the heterogametic sex. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a collective name for the chromosomes in such groupings (X/Z &amp;amp; Y/W)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to talk about Z- and X- (and analagous) chromosomes in general. Rather than having to write &quot;The X-chromosome, and analagous chromosomes such as the Z-, are present in both sexes....&quot; I'd like to say &quot;The &lt;em&gt;blank&lt;/em&gt; chromosomes are present in both sexes....&quot;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-09-02T14:13:33.153" Title="Collective name for the X- and Z-chromosomes" Tags="&lt;genetics&gt;&lt;terminology&gt;&lt;chromosome&gt;" AnswerCount="4" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20925" PostTypeId="1" AcceptedAnswerId="20927" CreationDate="2014-09-01T10:13:29.013" Score="3" ViewCount="3991" Body="&lt;p&gt;I'm just curious as there was a bit controversy around this topic. It is possible for person with AIDS be negative for HIV antibodies?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As of 1989, the CDC reported that 5% of all U.S. AIDS patients who had been tested for HIV to that time were HIV-negative. No figures have been reported by the CDC since 1989.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, how it's possible?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cdc.gov/Mmwr/preview/mmwrhtml/00017329.htm&quot; rel=&quot;nofollow&quot;&gt;Unexplained CD4+ T-Lymphocyte Depletion in Persons Without Evident HIV Infection -- United States&lt;/a&gt; at Centers for Disease Control and Prevention&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1195" LastEditorUserId="1195" LastEditDate="2014-09-01T10:31:46.640" LastActivityDate="2016-12-26T03:20:52.940" Title="It is possible for person with AIDS be negative for HIV antibodies?" Tags="&lt;virus&gt;&lt;antibody&gt;&lt;hiv&gt;&lt;aids&gt;" AnswerCount="2" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="20926" PostTypeId="2" ParentId="20915" CreationDate="2014-09-01T12:19:22.763" Score="5" Body="&lt;p&gt;I have not been able to find any studies that look specifically at the genetic mechanism for nose development. I certainly do not know but I'll offer up two hypotheses. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My first hypothesis is that the elongated nose is a remnant of the elongated lower face of our ancestral species, as you note in your answer. Take a look at &lt;a href=&quot;http://www.youtube.com/watch?v=wFY_KPFS3LA&quot; rel=&quot;noreferrer&quot;&gt;this brief YouTube video&lt;/a&gt; (1:17 long, the part relevant to this answer begins at 33 seconds) of a time-lapse composite showing the develop of the human face. Our face develops as two separate halves that meet together in the middle. That's what creates the &lt;a href=&quot;http://en.wikipedia.org/wiki/Philtrum&quot; rel=&quot;noreferrer&quot;&gt;philtrum under our nose&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Watch the especially carefully from the 54 second mark to 1 minute mark. Note that our nostrils are pointing directly forward and the overall region looks somewhat like a pig snout. The mouth is vertical aligned with the front of the nose. The overall face is much more rectangular and the eyes are on the sides of the face.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, the face begins to become rounder and flatten. The eyes move to the front of the face and the recesses our our eye sockets recede. The lower face below the nose recedes, becoming flatter. The only part that does not recede is the nose area. The flattening of the lower face may actually cause the nostrils to turn downward.  Our nose does not develop outward from a flat face but instead is left behind as the rest of the face flattens.  This would be my initial thought as the &lt;em&gt;primary&lt;/em&gt; reason for the shape of the nose and direction of the nostrils.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My second hypothesis (and honestly independent of the comment by @Remib) is related to our sense of smell and taste. Although our ability to detect flavors is a complex process, the primary sense involved is smell (&lt;a href=&quot;http://www.cajal.csic.es/actividades2011/smell-images.pdf&quot; rel=&quot;noreferrer&quot;&gt;Shepherd 2006&lt;/a&gt;). Therefore, downward-pointing nostrils are located directly above the mouth so we get a good smell of the food just before it enters the mouth, perhaps enhancing our flavor-sensing ability.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Shephered, G.M. 2006. Smell images and the flavour system in the human brain. &lt;a href=&quot;http://www.nature.com/nature/journal/v444/n7117/abs/nature05405.html&quot; rel=&quot;noreferrer&quot;&gt;Nature 444: 316-321&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Note that these two hypotheses are not mutually exclusive. The downward pointing nostrils may be a remnant of our facial development but provides an (adaptive?) advantage for flavour perception.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-09-01T12:19:22.763" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20927" PostTypeId="2" ParentId="20925" CreationDate="2014-09-01T12:28:00.587" Score="11" Body="&lt;p&gt;Usually an antibody test against HIV is positive three month after the infection. Before this time a test can only be done with molecular biology methods as PCR. However, it is possible, that patients which have definitely been tested in an early phase using molecular biology methods and which afterwards receive a antiretroviral therapy (ART) that these patients do not develop high serum levels of antibodies, as the virus titer in the blood is not high enough for a sufficient reaction and thus stay undetected by the tests. This has been improved, so that the kits are supposed to have a higher sensitivity now. See these papers for more details:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16447118&quot;&gt;Seroreversion in subjects receiving antiretroviral therapy during&#xA;acute/early HIV infection.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16831088&quot;&gt;The effects of early antiretroviral therapy and its discontinuation&#xA;on the HIV-specific antibody response.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I haven't found any papers on the decline of HIV-antibodies in AIDS (which is the late stage of the disease), but if they do, this is probably due to the effects of the infection on the immune system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Low counts in CD4 positive T cells (which are usually associated with an HIV infection) can also occur with other diseases. See these papers (especially the first, as this is a review which contains a lot of further references):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23930241&quot;&gt;Idiopathic CD4 Lymphocytopenia: Spectrum of opportunistic infections,&#xA;malignancies, and autoimmune diseases.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9844052&quot;&gt;Decreased CD4 and increased CD8 counts with T cell activation is&#xA;associated with chronic helminth infection.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7909464&quot;&gt;Acquired immunodeficiency without evidence of HIV infection: national&#xA;retrospective survey.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-01T12:28:00.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20928" PostTypeId="2" ParentId="20924" CreationDate="2014-09-01T13:01:19.003" Score="3" Body="&lt;p&gt;I think you can safely use the terms &lt;strong&gt;heterogametic&lt;/strong&gt; (Y/W) and &lt;strong&gt;homogametic&lt;/strong&gt; (X/Z) chromosomes, meaning that a heterogametic chromosome is the chromosome which makes one of the sexes heterogametic (i.e. defines the difference between the two types of gametes of the respective sex).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These terms applied to chomosomes &lt;a href=&quot;http://scholar.google.com/scholar?q=%22heterogametic%20chromosome%22&quot; rel=&quot;nofollow&quot;&gt;do have some usage&lt;/a&gt; in the literature, e.g. in &lt;a href=&quot;http://mbe.oxfordjournals.org/content/29/6/1645.full&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-09-01T13:01:19.003" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20929" PostTypeId="2" ParentId="20924" CreationDate="2014-09-01T13:15:02.977" Score="0" Body="&lt;p&gt;Regarding the meio/majo or micro/macro suggestion, I do not think it is the way to go for the following reasons:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Micro and macro-chromosomes are terms already used in species such as chicken whose genomes combine very small and big chromosomes&lt;/li&gt;&#xA;&lt;li&gt;Although this is more the exception than the rule, bear in mind that sometimes the Y chromosome is bigger than the X chromosome (e.g. in &lt;a href=&quot;http://www.ibp.cz/cs/oddeleni/vyvojova-genetika-rostlin/vyzkum/&quot; rel=&quot;nofollow&quot;&gt;S. latifolia&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;As for the initial question, I do not know of a term the X/Z - Y/W groups. What comes to my mind is the term sex-restricted sex chromosome for the Y/W (as it is normally present only in one sex) although it does not seem to be widely used according to Google.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could also oppose them as recombining vs non recombining sex chromosome which would hold true for most heteromorphic sex chromosomes (if we do not take PAR into consideration). It might be confusing as some persons would think you speak about the pair and not the individual chromosome. However, &lt;a href=&quot;http://scholar.google.es/scholar?hl=en&amp;amp;q=%22non-recombining%20sex%20chromosome%22&amp;amp;btnG=&amp;amp;as_sdt=1%2C5&amp;amp;as_sdtp=&quot; rel=&quot;nofollow&quot;&gt;it seems to be used&lt;/a&gt; in the literature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I checked one of my manuscript on the topic and we used X/Z when needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: first sentence clarified.&lt;/p&gt;&#xA;" OwnerUserId="605" LastEditorUserId="605" LastEditDate="2014-09-02T11:40:37.933" LastActivityDate="2014-09-02T11:40:37.933" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20930" PostTypeId="1" AcceptedAnswerId="20932" CreationDate="2014-09-01T13:37:55.473" Score="1" ViewCount="205" Body="&lt;p&gt;There are typically hundreds of retroviruses found in &lt;em&gt;healthy&lt;/em&gt; human beings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are retroviruses then cytotoxic? (In other words, are they able to kill or damage other cells).&lt;/p&gt;&#xA;" OwnerUserId="1195" LastEditorUserId="3632" LastEditDate="2014-09-01T15:09:26.127" LastActivityDate="2014-09-01T18:11:01.400" Title="Are retroviruses cytotoxic?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;retrovirus&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="20931" PostTypeId="2" ParentId="5577" CreationDate="2014-09-01T13:38:13.870" Score="4" Body="&lt;p&gt;These are different things. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nitrogen Narcosis or more commonly Gas Narcosis is the narcotic effect of gasses like Oxygen and Nitrogen under pressure. The effects are most prominent under 30m and commercial/technical dives doing dives to 40/50m on air tend to experience the effects most. (Narcosis is managed by adding an inert gas - in most gases Helium - to air to form a mixture referred to as Trimix (Helium/Oxygen/Nitrogen) this then produces an effect as if the diver is diving to a shallower depth and is referred to as Equivalent Narcotic Depth, in some cases Heliox (Helium &amp;amp; Oxygen) was also used)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;High Pressure Nervous Syndrome is an interesting aspect of deep diving and used to be called Helium Jitters/Tremors as the accepted standard was that it was caused by breathing Helium mixtures under 150m. Some people hold this to be true and others claim that it has nothing to do with Helium but rather the pressure disrupting the flow of electric signals thru the nervous system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is interesting is that they found that if you used Trimix (Helium/Nitrogen/Oxygen) rather than Heliox (Helium/Oxygen) the onset happened later or not as severe. And the slower your descent is the slower the onset of the symptoms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Some Docs to Read:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.divingmedicine.info/Ch%2018%20SM10c.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Narcosis&lt;/a&gt; - Relatively simple document on Narcosis&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.scuba-doc.com/narked.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Narcosis&lt;/a&gt; - &quot;Narcosis is not unique to nitrogen; however, it can occur with many of the so-called “noble” or inert gases, with the exception of helium. Add to this the fact that other inert gases each have their own brand of narcotic effects at depth, and you have a complicated picture for technical and commercial divers. One of these rare gases, argon, for example, has about twice the narcotic potency of nitrogen, but helium has very weak narcotic properties and is less soluble than nitrogen in body tissues.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.divingmedicine.info/Ch%2019%20SM10c.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;HPNS&lt;/a&gt; - Relatively Simple doc on HPNS&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://archive.rubicon-foundation.org/xmlui/bitstream/handle/123456789/9056/Bennett_2004_3.pdf?sequence=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;HPNS&lt;/a&gt; - Very technical discussion on gasses, from a HPNS and Narcosis view point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bennett, P.B. 1982b. The high pressure nervous syndrome in man. In: The Physiology and Medicine of Diving and Compressed Air Work. (P.B. Bennett and D.H. Elliot, eds), Balliere-Tindall, London. pp. 262-296.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bennett, P.B. 1990. Inert gas narcosis and HPNS. In: Diving Medicine, Second Edition (A.A. Bove and J.C. Davis, eds.).W.B. Saunders Company, Philadelphia. pp. 69-81.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bennett, P.B, R. Coggin, and J. Roby. 1981. Control of HPNS in humans during rapid compression with trimix to 650 m (2132 ft). Undersea Biomed. Res., 8(2): 85-100.&lt;/p&gt;&#xA;" OwnerUserId="9047" LastEditorUserId="9047" LastEditDate="2017-03-30T20:28:45.527" LastActivityDate="2017-03-30T20:28:45.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20932" PostTypeId="2" ParentId="20930" CreationDate="2014-09-01T15:09:05.700" Score="8" Body="&lt;p&gt;As you point out human beings (and other organisms) have hundreds of retroviruses and many can be seen in the human genome, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK7934/&quot;&gt;some of which appear to be the remains of deactivated viruses, others which may be active&lt;/a&gt;.   Most retroviruses are not pathogenic - they don't cause disease.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is because many retroviruses replicate slowly, budding and secreting from the cell surface in small numbers &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK19458/&quot;&gt;without killing their host cell&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several disease-causing retroviruses.  Human T-cell Leukemia Virus (HTLV) can cause T-cells to replicate in an uncontrolled fashion, resulting in leukemia.  This is not a necessary result for HTLV to replicate, but it is a result of viral infection as viral replication tweaks the cell machinery to replicate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While it's not clear exactly how, Human Immunodeficiency Virus (HIV) kills its hosts cells.  Unfortunately HIV's hosts are CD4 immune cells.  The fact that sporadic replication of HIV can cause all host immune cells to die entirely makes HIV a pathogen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disease is usually thought of as a lack of adaptation of a pathogen and host: viruses do better if they do not kill their host.  Both these cases are possibly not the future for either virus: either could adapt to reproduce without causing a disease. Or they might have already , having spun off some strains into the pool of quiet retroviruses medical science does not concern itself with. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="1320" LastEditDate="2014-09-01T18:11:01.400" LastActivityDate="2014-09-01T18:11:01.400" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20933" PostTypeId="2" ParentId="20912" CreationDate="2014-09-01T16:54:22.830" Score="3" Body="&lt;p&gt;The answer provided by Mike Taylor is just perfect and complete. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I'd like to add some thoughts of my own in a more colloquial style:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Survival of the fittest is not always true. There is also &quot;survival of the luckiest&quot; (e.g. the fittest is showing off in the beach with the other turtles and is struck by lightning). &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Reproduction is not that simple and many times the female mates with several mates (apart from the fittest one) and a paternal test should be procured. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Mutation changes are not always gradual (i.e. the turtles might develop a long neck in just one generation).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Mutations don't always lead to a phenotype change. Sometimes, depending of the environment, the phenotype change doesn't occur. For example, the turtles might only grow a long neck if the live in a sunny island.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Not all mutations are beneficial and not all beneficial mutations have an impact on survival (e.g. many actors/actresses are not very tall although they reproduce successfully).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In my opinion there are many shades of grays in between the ideas behind evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The features of the &quot;fittest&quot; are sometimes lost by random reasons as the listed above, and the features of the &quot;less fitted&quot; are sometimes transmitted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And finally, sometimes, an organism develops (or is developing) a mechanism to alter the genes directly (e.g. human beings). Where would that lead? Does evolution mean something anymore?&lt;/p&gt;&#xA;" OwnerUserId="9049" LastActivityDate="2014-09-01T16:54:22.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20934" PostTypeId="1" CreationDate="2014-09-01T17:50:09.437" Score="11" ViewCount="1604" Body="&lt;p&gt;I understand that the human body when performing Fatty Acid Synthesis can synthesize only until C16 (palmitate). However the ER has desaturases and elongases. I know that desaturases are used to add double bonds, but do humans have elongases to add even more Carbons to a double bond? If so, then this would mean that the human body can synthesize fats longer than C16? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lets take a hypothetical case and say that humans have both desaturases and elongases. Would it be feasible to add double bonds to palmitate via desaturases, then add more carbons to the chain via elongases and then add more double bonds via desaturases? This way, the resulting fatty acid will have an increased length and more unsaturated character (i.e. more double bonds than the prescribed 4 that humans can add at positions 4, 5, 6, and 9)?&lt;/p&gt;&#xA;" OwnerUserId="9050" LastEditorUserId="16299" LastEditDate="2015-11-26T19:03:47.017" LastActivityDate="2017-01-24T15:52:23.553" Title="Synthesis of Fatty Acids Longer than 16 Carbons" Tags="&lt;biochemistry&gt;&lt;lipids&gt;&lt;fat-metabolism&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20935" PostTypeId="1" CreationDate="2014-09-01T22:38:42.980" Score="1" ViewCount="93" Body="&lt;p&gt;My Masters program is focused on formal methods such as SAT solving and constraint programming. I am interested in applying such techniques to problems in sequence alignment and sequence analysis, areas that have been dominated by statistical methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So can you give me examples of some research problems suitable to be approached as constraints satisfaction problems?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: By constraint programming I also include more flexible paradigms like &lt;a href=&quot;http://en.wikipedia.org/wiki/Weighted_constraint_satisfaction_problem&quot; rel=&quot;nofollow&quot;&gt;weighted constraint programming&lt;/a&gt;, where a solution may violate some of the constraints.&lt;/p&gt;&#xA;" OwnerUserId="8060" LastActivityDate="2014-12-01T13:53:54.667" Title="Applying Constraint Programming to sequence alignment/analysis" Tags="&lt;bioinformatics&gt;&lt;sequence-analysis&gt;&lt;sequence-alignment&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20936" PostTypeId="2" ParentId="20912" CreationDate="2014-09-01T23:07:35.470" Score="1" Body="&lt;p&gt;To add to the previous answers that treat specifically of the biological Darwinism, there is also &lt;strong&gt;Universal Darwinism&lt;/strong&gt; which postulates that evolution is a natural phenomenon that appears when a set of conditions and constraints are present. And indeed, it has successfully been applied to a number of fields (see below the quote), which seems to imply that evolution is not a property of the evolving individuals (as you implied) but &lt;strong&gt;a property of the system&lt;/strong&gt; where the individuals evolve (as long as the individuals satisfy a few special properties, namely variation and heredity, see below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the definition from Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At the most fundamental level, Charles Darwin's theory of evolution states that organisms evolve and adapt to their environment by an iterative process. This process can be conceived as an evolutionary algorithm that searches the space of possible forms (the fitness landscape) for the ones that are best adapted. The process has three components:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;variation of a given form or template. This is usually (but not necessarily) considered to be blind or random, and happens typically by mutation or recombination.&lt;/li&gt;&#xA;  &lt;li&gt;selection of the fittest variants, i.e. those that are best suited to survive and reproduce in their given environment. The unfit variants are eliminated.&lt;/li&gt;&#xA;  &lt;li&gt;heredity or retention, meaning that the features of the fit variants are retained and passed on, e.g. in offspring.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;  &#xA;  &lt;p&gt;After those fit variants are retained, they can again undergo variation, either directly or in their offspring, starting a new round of the iteration. The overall mechanism is similar to the problem-solving procedures of trial-and-error or generate-and-test: evolution can be seen as searching for the best solution for the problem of how to survive and reproduce by generating new trials, testing how well they perform, eliminating the failures, and retaining the successes.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The generalization made in &quot;universal&quot; Darwinism is to replace &quot;organism&quot; by any recognizable pattern, phenomenon, or system. The first requirement is that the pattern can &quot;survive&quot; (maintain, be retained) long enough or &quot;reproduce&quot; (replicate, be copied) sufficiently frequently so as not to disappear immediately. This is the heredity component: the information in the pattern must be retained or passed on. The second requirement is that during survival and reproduction variation (small changes in the pattern) can occur. The final requirement is that there is a selective &quot;preference&quot; so that certain variants tend to survive or reproduce &quot;better&quot; than others. If these conditions are met, then, by the logic of natural selection, the pattern will evolve towards more adapted forms.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Examples of patterns that have been postulated to undergo variation and selection, and thus adaptation, are genes, ideas (memes), neurons and their connections, words, computer programs, firms, antibodies, institutions, quantum states and even whole universes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also, you may be interested in some terminology associated with this theory, for example for John Maynard Smith an individual that can evolve in an evolvable system is called a &lt;em&gt;Unit of evolution&lt;/em&gt; [1]. This shows how much abstract and generalizable evolution can be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1]: Fernando C, Vasas V, Szathmáry E, Husbands P (2011) Evolvable Neuronal Paths: A Novel Basis for Information and Search in the Brain. PLoS ONE 6(8): e23534. doi: 10.1371/journal.pone.0023534&lt;/p&gt;&#xA;" OwnerUserId="9054" LastEditorUserId="49230" LastEditDate="2019-03-29T18:02:58.537" LastActivityDate="2019-03-29T18:02:58.537" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="20937" PostTypeId="1" AcceptedAnswerId="21047" CreationDate="2014-09-01T23:14:03.967" Score="4" ViewCount="81" Body="&lt;p&gt;How many Type II restrictions enzymes are currently available (commercially) for purchase as of the date of this posting (September 1, 2014)&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-09-05T10:49:47.653" Title="How many Type II restrictions enzymes are currently available (commercially)" Tags="&lt;restriction-enzymes&gt;" AnswerCount="3" CommentCount="6" ClosedDate="2014-09-05T18:42:16.743" ContentLicense="CC BY-SA 3.0" />
  <row Id="20938" PostTypeId="1" AcceptedAnswerId="20986" CreationDate="2014-09-02T01:05:19.307" Score="2" ViewCount="363" Body="&lt;p&gt;I was looking at &lt;a href=&quot;http://www.nature.com/nbt/journal/v26/n3/full/nbt0308-274.html&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; which talks about the miscalculations in the BLOSUM matrices and how the &quot;wrong&quot; BLOSUM62 matrix performs better than the corrected version. I was trying to find the corrected version they talk about to experiment with, but &lt;a href=&quot;http://web.mit.edu/bamel/blosum/&quot; rel=&quot;nofollow&quot;&gt;the link they list in the paper&lt;/a&gt; appears dead.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know where I can find the corrected matrix that the authors talk about?  (preferably a version listing frequencies rather than scores)&lt;/p&gt;&#xA;" OwnerUserId="8060" LastActivityDate="2014-09-03T19:01:59.663" Title="Where to find the corrected BLOSUM matrices?" Tags="&lt;bioinformatics&gt;&lt;sequence-alignment&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20939" PostTypeId="2" ParentId="20921" CreationDate="2014-09-02T01:15:55.587" Score="3" Body="&lt;p&gt;As a simplified response:&#xA;Propensity score is used to predict protein secondary structure. It is derived from looking at the aa residue of the accessible surface of the protein and also the interface which enables interactions between other proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The equation is as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Propensity= [probability of the residue in the interface / probability of the residue on the surface]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;prob of the residue in the interface = [number of amino acids in the interface / total number of amino acids of any type of interface] &lt;/p&gt;&#xA;&#xA;&lt;p&gt;and,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;prob of the residue on the surface =  [number of surface amino acids / total number of surface amino acids]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check out this PLOS paper for an example. PLoS One. 2014; 9(5): e97158. &lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-09-02T01:34:56.553" LastActivityDate="2014-09-02T01:34:56.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20940" PostTypeId="2" ParentId="20937" CreationDate="2014-09-02T01:29:03.177" Score="4" Body="&lt;p&gt;The &lt;a href=&quot;http://www.biocompare.com/Cloning-and-Expression/6525-Restriction-Enzymes/&quot; rel=&quot;nofollow&quot;&gt;Restriction Enzymes&lt;/a&gt; section at &lt;a href=&quot;http://www.biocompare.com&quot; rel=&quot;nofollow&quot;&gt;Biocompare&lt;/a&gt; is likely not comprehensive, but short of contacting every single molecular biology company and merging all their inventories into a master list, it's probably the best you can do on short notice. They currently list &lt;strong&gt;289 uniquely-named enzymes&lt;/strong&gt;, but I'm not enough of an expert to say how many are similar in activity/recognition sequence, or whether they might also be known by other names not currently listed. For your purposes, however, it'd probably be enough to tell your students that there are on the order of 300 common commercially-available enzymes. Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-09-02T01:29:03.177" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20941" PostTypeId="2" ParentId="20924" CreationDate="2014-09-02T07:20:18.800" Score="1" Body="&lt;p&gt;I just tried a search of major and minor sex chromosomes and found &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299550/&quot; rel=&quot;nofollow&quot;&gt;a paper here by Judith Mank&lt;/a&gt; who refers to the X and Z as the Major Sex Chromosomes and Y and W as the Minor Sex Chromosomes. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I will therefore refer to the W and Y as minor sex chromosomes, and&#xA;  will use the term major sex chromosomes in reference to the X and Z.&#xA;  These terms are based on abundance and do not refer in any way to size&#xA;  (discussed below) or relative effect. In fact, the effect of the minor&#xA;  sex chromosomes is, in many ways, anything but minor.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think I will go with this naming as the hetero-/homogametic chromosomes distinction could become confusing in the context I am using it (Talking about expression of the X/Z in the homogametic and heterogametic sex). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further I think it is wrong because, while &quot;heterogametic chromosome&quot; would be somewhat suitable for Y/W chromosomes, to call the X and Z the homogametic chromosome is wrong because the X/Z can be present in both a homogametic sense (in females/males respectively) and a heterogametic sense (paired with a Y or W).&#xA;Calling the X/Z the homogametic chromosome implies that it is only present in homogametic sexes no less than &quot;minor sex chromosome&quot; might imply a minor role for the Y.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another suggestion could be to call the Y/W chromosomes the sex-limited chromosomes, but then the question of what to call the X/Z remains... non-limited? shared? sex-unlimited?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or recombining and non-recombining sex chromosomes.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-09-02T11:47:09.453" LastActivityDate="2014-09-02T11:47:09.453" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="20942" PostTypeId="1" CreationDate="2014-09-02T08:16:40.890" Score="3" ViewCount="926" Body="&lt;p&gt;In histology we know that epithelium tissue isn't vascularized so it takes the nutrition from Lamina propia (CT) via diffusion and in other hand we know all epithilial cells have tight junction which inhibits the flow of substance so how can it diffuse nutrients between themselves because of the tight junction how can they distribute nutrients, same way in capillaries which are endothelium  how interstitial fluid passes throw endothelial cells because of thier tight junction?  &lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="8570" LastEditDate="2014-09-03T21:43:18.867" LastActivityDate="2014-09-03T21:47:29.363" Title="How do tight junctions in stratified squamous epithelia affect nutrient supply?" Tags="&lt;histology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20943" PostTypeId="1" CreationDate="2014-09-02T08:17:50.447" Score="1" ViewCount="516" Body="&lt;p&gt;I am working on an enzyme assay for a fungal pectinase.I assayed the enzyme in different buffers from pH 1-12.5 However,the enzyme has good activities starting from pH1-10.5.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to have enzyme activity over such a broad range of pH?&lt;/p&gt;&#xA;" OwnerUserId="8794" LastEditorUserId="1320" LastEditDate="2014-09-02T12:37:06.113" LastActivityDate="2014-09-02T12:37:06.113" Title="What is the expected effect of pH on the activity of a fungal pectinase?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;microbiology&gt;&lt;enzymes&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20944" PostTypeId="2" ParentId="20943" CreationDate="2014-09-02T08:38:59.423" Score="2" Body="&lt;p&gt;I actually doubt that the pectinase has such a broad pH range in which it works optimally. Searching the web I found two figures which support my doubts:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nAPbr.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sszn3.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first is from an article (&quot;&lt;a href=&quot;http://scielo.sld.cu/scielo.php?pid=S1027-28522013000200003&amp;amp;script=sci_arttext&quot; rel=&quot;nofollow noreferrer&quot;&gt;Immobilization of pectinase by adsorption on an alginate-coated chitin support&lt;/a&gt;&quot;) which compares the activity of native and immobilized pectinase under different conditions. The second is from the &lt;a href=&quot;http://www.biovet.com/rus/pdfs/Pectinase.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;datasheet&lt;/a&gt; of a company which sells the enzyme. Both show an activity over 50% roughly between pH 3.5 and 5.5 but not at higher or lower pH values.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-02T08:38:59.423" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20945" PostTypeId="1" AcceptedAnswerId="20950" CreationDate="2014-09-02T08:42:18.720" Score="1" ViewCount="65" Body="&lt;p&gt;What does localization of B-Cell mean?? &lt;br/&gt;&quot;Localization of B and T cell in allergens may not coincide&quot;. What does this statement mean? &lt;br/&gt;&lt;br/&gt;(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)&lt;/p&gt;&#xA;" OwnerUserId="8835" LastActivityDate="2020-05-15T07:27:51.153" Title="Localization of B and T cell" Tags="&lt;molecular-biology&gt;&lt;immunology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20946" PostTypeId="1" CreationDate="2014-09-02T10:07:00.707" Score="7" ViewCount="4717" Body="&lt;p&gt;I heard that the footprints of Neil Armstrong are still there, so I was wondering if someone were to die there, would they remain preserved, too? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not how long would it take for them to decay?&lt;/p&gt;&#xA;" OwnerUserId="8845" LastEditorUserId="57" LastEditDate="2014-09-02T19:08:07.910" LastActivityDate="2019-11-10T15:57:02.057" Title="If someone were to die on the moon, would their body decay?" Tags="&lt;microbiology&gt;&lt;speculative&gt;&lt;decay&gt;" AnswerCount="3" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="20947" PostTypeId="2" ParentId="20906" CreationDate="2014-09-02T10:55:24.007" Score="5" Body="&lt;p&gt;I'd also like to point out that ants leave a &lt;a href=&quot;http://dnr.wi.gov/wnrmag/html/stories/1999/jun99/ants.htm&quot; rel=&quot;noreferrer&quot;&gt;trail which they patrol&lt;/a&gt; so the food need not be detected from a far only by a single worker patrolling near a region. Once found they have various means to &lt;a href=&quot;http://readingpack.com/article/?i=8805a716ba380606ad0fc6c77ef86488c32552d1&quot; rel=&quot;noreferrer&quot;&gt;initiate a swarm&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-09-02T10:55:24.007" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="20948" PostTypeId="2" ParentId="20937" CreationDate="2014-09-02T11:01:13.173" Score="0" Body="&lt;p&gt;Because of the &lt;a href=&quot;http://www.particlesciences.com/news/technical-briefs/2009/protein-structure.html&quot; rel=&quot;nofollow&quot;&gt;extreme complexity&lt;/a&gt; and &lt;strong&gt;quite easy synthesis and customization&lt;/strong&gt; of proteins this question is unanswerable. That is to say there is such a great number of potential enzymes from any set domain or with the functionality there of that no one is able to fathom the depth even when restricted to current availability.&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorDisplayName="user1357" LastEditDate="2014-09-03T16:22:42.150" LastActivityDate="2014-09-03T16:22:42.150" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20949" PostTypeId="2" ParentId="20935" CreationDate="2014-09-02T11:23:38.407" Score="1" Body="&lt;p&gt;First read how &lt;a href=&quot;http://en.wikipedia.org/wiki/Sequence_alignment#Global_and_local_alignments&quot; rel=&quot;nofollow&quot;&gt;local and global alignment&lt;/a&gt; differ from each other. Then decide an objective function, i.e. how to measure the similarity between two sequences? Maybe use Hamming distance? Or Levenshtein distance? After this the optimization part probably comes out quite naturally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Be sure to check the existing softwares. Easy things have been tried out already. (And by the way, for some reason biologists call &lt;em&gt;n-grams&lt;/em&gt; as &lt;em&gt;k-mers&lt;/em&gt;.)&lt;/p&gt;&#xA;" OwnerUserId="9059" LastEditorUserId="9059" LastEditDate="2014-09-02T12:53:23.370" LastActivityDate="2014-09-02T12:53:23.370" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20950" PostTypeId="2" ParentId="20945" CreationDate="2014-09-02T13:52:33.560" Score="3" Body="&lt;p&gt;I think the reason you are having trouble discerning the statement is because it doesn't really make much sense, nor is it in my opinion sufficiently explained in the paper. The sentences preceding the it give a little explanation as to what the author may be getting at:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So far, 1500 allergenic structures have been identified. Online allergen databases and allergy prediction tools are being used to find cross-reactivity between known allergens. Localization of B and T cells in the allergen may not coincide.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;During an exaggerated immune response (allergy) the lymphocytes (B and T) will localize (travel or accumulate at) to the site of the antigen (allergen). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I could guess I would say the author is stating that data has shown that no immune response is taking place (data generated by assessing the accumulation of lymphocytes near the allergen), despite the fact that these online allergen predictors say that an immune response should be generated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The statement in my opinion moves to discredit these online allergen predictors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did look over some of the rest of the manuscript, and found two other ambiguities within. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The author does cite another paper in your sentence that may shed more light on this:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686541/?report=reader&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686541/?report=reader&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An overview of it provided little clarity however.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I fear that only  a crystal ball or this question addressed to the senior author may answer your question with complete certainty:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dr. Rajat Kumar De &#xA;Professor &#xA;Machine Intelligence Unit &#xA;Indian Statistical Institute &#xA;203 Barrackpore Trunk Road, Kolkata 700108, India. &lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-09-02T23:25:28.273" LastActivityDate="2014-09-02T23:25:28.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20951" PostTypeId="2" ParentId="20924" CreationDate="2014-09-02T14:13:33.153" Score="0" Body="&lt;p&gt;Based on answers and discussion so far and my own searches, I think there is &lt;em&gt;no&lt;/em&gt; widely understood and used term for grouping the X/Z and W/Y chromosomes. You could coin your own term or pluck one from obscurity in the literature, however, I think you would probably be better off not doing so and simply writing X/Z and W/Y wherever you need to refer to the grouping.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2014-09-02T14:13:33.153" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20952" PostTypeId="1" CreationDate="2014-09-02T16:59:09.057" Score="5" ViewCount="935" Body="&lt;p&gt;I am not a biologist, but I am fascinated by evolution.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was watching the news this morning and, as so often is the case, there was a news story about a corrupt politician who was accepting bribes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This started me thinking about how greed can become such a strong factor in one's life that it cancels out empathy for your fellow human beings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I was wondering--is greed an evolved trait?  Maybe some result of an evolutionary pressure to hoard food for example?&lt;/p&gt;&#xA;" OwnerUserId="393" LastEditorUserId="5144" LastEditDate="2015-03-27T08:59:12.780" LastActivityDate="2015-03-27T08:59:12.780" Title="Is greed an evolved trait?" Tags="&lt;evolution&gt;&lt;behaviour&gt;&lt;collective-behaviour&gt;&lt;altruism&gt;&lt;sociobiology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20953" PostTypeId="1" AcceptedAnswerId="20979" CreationDate="2014-09-02T17:00:04.653" Score="2" ViewCount="317" Body="&lt;p&gt;To specify, I mean plain corn-on-the-cob, not anything processed like corn flakes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since one of the main important functions of corn is that it's not digestible, and therefore helps with digestion by loosening feces, would that make it just as beneficial as chopping up and eating a plastic bag?&lt;/p&gt;&#xA;" OwnerUserId="464" LastActivityDate="2014-09-03T14:43:13.323" Title="Is plastic just as good for you as corn?" Tags="&lt;food&gt;&lt;digestion&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20954" PostTypeId="2" ParentId="20863" CreationDate="2014-09-02T17:01:20.953" Score="3" Body="&lt;p&gt;Basically &lt;strong&gt;any compound in concentrations sufficient to saturate its metabolization machinery will show zero-order pharmacokinetics&lt;/strong&gt;. This reflects the fact that metabolization is taking place at full speed while facing a comparatively enormous amount of substrate (just as @WYSIWYG pointed out). This effect can also be shown &lt;em&gt;in vitro&lt;/em&gt; with pure substrate/enzyme solutions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the above is a rather simplistic model, valid only in specific situations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the time in humans, zero-order kinetics stem from the fact that liver enzymes are saturated. However, for most drugs the &lt;strong&gt;redistribution phase&lt;/strong&gt; is much more important than metabolization/elimination in defining the duration of effect. A good example of that would be sodium thiopental. As a single iv bolus dose, it will induce loss of consciousness for a short time due to redistribution. However, continued infusion will allow blood and tissue concentrations to equilibrate, and then the metabolization/elimination rate will become much more prominent in defining the duration of effect. And as sodium thiopental happens to have zero-order metabolization kinetics &lt;strong&gt;in continued infusion&lt;/strong&gt;, it will take you a loooooooooong time to wake up! This is why in human pharmacology, we use &lt;strong&gt;context sensitive half-life&lt;/strong&gt; to better represent drug kinetics.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2014-09-02T18:17:07.397" LastActivityDate="2014-09-02T18:17:07.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20955" PostTypeId="1" AcceptedAnswerId="20960" CreationDate="2014-09-02T17:53:06.543" Score="3" ViewCount="592" Body="&lt;p&gt;I was reading the textbook &lt;a href=&quot;http://www.math.duke.edu/~rtd/Gbook/PM4DNA_0317.pdf&quot; rel=&quot;nofollow&quot;&gt;Probability Models for DNA Sequence Evolution&lt;/a&gt; by &lt;code&gt;Durrett&lt;/code&gt;. In chapter 1, he discusses the Wright Fisher model and the coalescent theory which I am interested in. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;He defines heterozygosity as the probability that two copies of an allele are the same. In theorem 1.3, he derives the expected value of heterozygousity, but what he seems to derive is the expected value of the probability that two allelles have a common ancestor. This does not seem to be the same as heterozygosity to me. Am I missing something here? &lt;/p&gt;&#xA;" OwnerUserId="6353" LastEditorUserId="8517" LastEditDate="2014-09-02T19:44:56.950" LastActivityDate="2014-09-02T21:09:45.557" Title="Heterozygosity and the Wright-Fisher model" Tags="&lt;bioinformatics&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20956" PostTypeId="2" ParentId="20901" CreationDate="2014-09-02T17:57:27.157" Score="2" Body="&lt;p&gt;Let's review drug administration routes, and see for yourself:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;transdermal/ionophoric:&lt;/strong&gt; expensive, unreliable release concentrations (which makes it expensive because of the extensive research needed for controlled release), noticeable to others (&quot;why do you have that skin patch, mom?&quot; Er...)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Sublingual:&lt;/strong&gt; quite similar to oral route, however absence of first pass hepatic metabolism can result in completely different blood concentrations between the two routes. Impairs speech. Could cause mouth irritation (quite disabling). Requires patient compliance.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;intravenous:&lt;/strong&gt; quite unpractical in outpatient settings. Invasive measure.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;intramuscular/intradermal:&lt;/strong&gt; hurts. As all things using a needle. Usable, but impractical in the outpatient setting. Can lead to skin lesions (insulin injection in diabetes, for example)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;rectal:&lt;/strong&gt; culturally unacceptable to some, unreliable release.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;vaginal:&lt;/strong&gt; similar to rectal, but only for women obviously&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;spinal/epidural:&lt;/strong&gt; very invasive, only in inpatient settings.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;topical:&lt;/strong&gt; usually only acts locally, can cause discomfort (eyes)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;oral/enteral:&lt;/strong&gt; well known pharmacokinetics, mostly invisible to others, practical in the outpatient setting, requires limited patient compliance, well known excipients. Of course there can be secondary effects, but that is the case for all administration routes. Most common side effects are abdominal discomfort and nausea, but no one can see you in the water closet. Plus people are used to see pills as medication, something which might not be the case for other routes, depending on the cultural background of the patient.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This answer is of course somewhat subjective, however the importance of the patient's perception and his/her view of what the administration route implies socially cannot be overemphasized.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2014-09-02T18:36:59.883" LastActivityDate="2014-09-02T18:36:59.883" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20957" PostTypeId="2" ParentId="20946" CreationDate="2014-09-02T18:13:29.913" Score="5" Body="&lt;p&gt;Decay is a process where the body is digested by bacteria, fungi and other living things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The moon has no known biological processes and while &lt;a href=&quot;http://www.popsci.com/technology/article/2010-08/bacteria-survive-553-day-exposure-exterior-iss&quot; rel=&quot;noreferrer&quot;&gt;its possible for some microorganisms to survive in space&lt;/a&gt;, I think its generally understood that the lunar surface would not support life in a significant way, especially if the body is in vacuum. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other processes would definitely take place. Mummification can result from the body dehydrating and direct exposure to solar radiation will also break down the corpse, but it will mostly leave the body intact. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-09-02T18:13:29.913" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20958" PostTypeId="2" ParentId="20946" CreationDate="2014-09-02T20:01:14.837" Score="6" Body="&lt;p&gt;I am assuming &lt;em&gt;in spacesuit&lt;/em&gt; here, on the face (lit side) of the moon. Bodily degradation involves much more than external fungi and bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cells that receive no oxygen or nutrients die. We talk of such tissue death as &lt;em&gt;dry gangrene&lt;/em&gt; when it affects extremities, such as fingers, feet, etc. However, we also recognize gangrenous bowel, etc. which results in tissue necrosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such necrotic cell death is the consequence of acute disruption of cellular metabolism, leading to ATP depletion, ion dysregulation, mitochondrial and cellular swelling, activation of degradative enzymes, plasma membrane failure and cell lysis &lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lysis is messy and wet. Combined with the fluids in our bodies, what one would end up with is a mushy, smelly degraded body, not a preserved body. For a while, anaerobic bowel bacteria would flourish (which smell terrible). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Add to this the extremes of temperature (253° F in the sun and -243° F in the dark.) The suit would have lost it's heating and cooling mechanisms, so the body would alternately spend 14 days in the heat and 14 days in the freezing cold depending exactly where it was (lets say the equator of the moon.) These freeze/bake cycles would further contribute to degradation through ice crystal formation and thawing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eventually, because there was no new substrate, degradation would come to a halt, but I'm not sure at what stage this would be. I assume, though, there would be a vast difference between a mummified body (done by dehydration) and a body left to degrade in a spacesuit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] The mitochondrial permeability transition in cell death: a common mechanism in necrosis, apoptosis and autophagy, John J. Lemasters et. al, Biochimica et Biophysica Acta 1366 (1998) 177-196&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-09-02T20:01:14.837" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20960" PostTypeId="2" ParentId="20955" CreationDate="2014-09-02T21:09:45.557" Score="1" Body="&lt;p&gt;The following borrows from Gillespie, J.H., 1998. &lt;em&gt;Population Genetics: A Concise Guide.&lt;/em&gt; The Johns Hopkins University Press. It is a good concise guide, and reduces to some extent the mathematics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Theorem 1.3 is used to show the decay of heterozygosity in a population due to genetic drift.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider alleles in a population.  Two alleles drawn at random can differ by state, meaning they have two different DNA sequences. In other words, they are different alleles. Or the randomly drawn can have the same state, meaning they are the same allele. For alleles that are identical by state, they could differ by origin, meaning they are the same allele from two different chromosomes. The two alleles in a homozygous individual differ by &lt;em&gt;origin&lt;/em&gt; (sampled from maternal and paternal homologs) but are identical by &lt;em&gt;state&lt;/em&gt;.  Or, two identical alleles could differ by descent, meaning they are the same because they trace ultimately back to a common ancestor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To calculate heterozygosity, you can first account for homozygosity, the frequencies of alleles that are identical by state. First consider two alleles identical by origin.  If you draw two alleles identical by origin when t=1, the probability that the two alleles are copies of same original allele (from the same chromosome) is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{1}{2N}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;because there was only a single copy of that allele on that one chromosome in the population prior to the round of mating, so it is 1 out of the 2N alleles at time point 0 ($t=0$).  The probability that two alleles identical by state are &lt;em&gt;not&lt;/em&gt; identical by origin then is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$1-\frac{1}{2N}.$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, total homozygosity ($G'$) in the population (identical by state) after one round of random mating is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$G' = \frac{1}{2N} + (1-\frac{1}{2N})G,$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $G$ is the homozygosity prior to the round of mating.  Of course, anything not homozygous is heterozygous. So, heterozyosity ($H$) is simply,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$H=1-G.$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By substituting the formula for $G$ into the above equation, the equation for $H$ becomes,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$H' = 1-G' = (1-\frac{1}{2N})H$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $H$ is the heterozygosity prior to the round of mating.  This formula represents the change in heterozygosity after one round of random mating.  This can now be expanded for several rounds of random mating. For example, the change from $t=0$ to $t=1$ is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$H_1 = (1-\frac{1}{2N})H_0.$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The change from $t=1$ to $t=2$ is,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$H_2 = (1-\frac{1}{2N})H_1$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, the change in heterozygosity from $t=0$ to $t=2$ is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$H_2 = (1-\frac{1}{2N})^2H_0.$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can be expanded to any time $t$ with the equation,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$H_t = (1-\frac{1}{2N})^tH_0,$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;which you will recognize as Durrett's Theorem 1.3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, in the Wright-Fisher model, two alleles that have a common ancestor are by definition identical by state and so cannot contribute to heterozygosity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps. I was a bit rushed and have not explained this often (mostly to myself in my mind) so if I can clarify something, please let me know.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-09-02T21:09:45.557" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20961" PostTypeId="1" CreationDate="2014-09-02T22:04:41.077" Score="2" ViewCount="1624" Body="&lt;p&gt;I frequently ran into an issue where the bands of my ladder become skewed. What causes this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's an example: 0.7% agarose gel, 100V, 60 minutes. Same problem occurs with 1%. I loaded 10 ul of a 20 ul PCR reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rSCcy.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, the problem is not smiling per se. The lanes themselves are fairly vertical and straight. Just the bands themselves appear warped. What could cause this issue?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-09-02T23:47:03.643" Title="What causes skewed ladder bands on an agarose gel?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;gel-electrophoresis&gt;&lt;experiment&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="20962" PostTypeId="2" ParentId="20961" CreationDate="2014-09-02T23:47:03.643" Score="1" Body="&lt;p&gt;If the ladder is on an edge of the gel, it may be a process of different density as a result of how the gel cooled (or was poured too slowly). I've loaded more DNA loaded in a gel and it doesn't cause this kind of warping for me. It may be the buffer of the ladder is different from that used to make the gel. Your bands don't look particularly sharp, so I would suspect that the running voltage is too high and causing the surface of the gel to heat up and therefore &quot;smearing&quot; the bands. Try running the voltage at 75 V  for a proportionately longer time to see if this solves your problem.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-09-02T23:47:03.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20963" PostTypeId="2" ParentId="15386" CreationDate="2014-09-03T00:09:58.707" Score="2" Body="&lt;p&gt;@Chris's suggestion is very possible, high salt characteristically shows this towards the end of the gel. But there are additional suspects. This looks like it's just an agarose gel, Correct? I've seen a few things cause this including the gel not being level, the gel shifting during during it's run the percentage of agarose not being uniform and the temperature jacking up towards the end. If you do it again keep an eye on your amperage during the second hour or so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But first, try doing a quick PCR cleanup on a column (be sure to get one that will not loose your smaller fragments) or alternatively a phenol extraction followed by an ETOH precipitation will purify your reaction; and the force will be with you. &lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-09-03T00:09:58.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20964" PostTypeId="1" AcceptedAnswerId="20967" CreationDate="2014-09-03T00:46:20.783" Score="3" ViewCount="544" Body="&lt;p&gt;How long does it take for a wild hard clam (&lt;em&gt;Mercenaria mercenaria&lt;/em&gt;) to reach an age where they are reproductive? How does fecundity depend on age and size? I've looked at several hard clam life cycles and none of them have this information. They tend to agree that hard clams are long lived and take multiple years to reach a size suitable for harvest. While I am more interested in wild hard clam, please do also share information on farmed hard clam if you have it?&lt;/p&gt;&#xA;" OwnerUserId="6893" LastActivityDate="2014-09-03T02:02:58.717" Title="How long does it take for a hard clam (Mercenaria mercenaria) to reach sexual maturity?" Tags="&lt;ecology&gt;&lt;marine-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20965" PostTypeId="1" AcceptedAnswerId="20969" CreationDate="2014-09-03T01:19:46.293" Score="8" ViewCount="2131" Body="&lt;p&gt;There are several species of herbivores that have a very visible white hindquarters: several kinds of deer, rabbits, antelopes, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the white fur serve a functional purpose, or is it purely random?  Is it defensive enabling them to escape predators, or is it for intraspecies communication?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples photos to clarify: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/Icgl0.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/Icgl0.jpg&quot; alt=&quot;Rabbit&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://i1.treknature.com/photos/17630/roe_deer.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;deer&lt;/a&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notice that otherwise relatively well camouflaged animals have visible white fur.&lt;/p&gt;&#xA;" OwnerUserId="9068" LastEditorUserId="16651" LastEditDate="2015-12-25T00:22:10.357" LastActivityDate="2015-12-25T00:22:10.357" Title="Why do rabbits often have white hindquarters?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;mammals&gt;&lt;adaptation&gt;&lt;morphology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20966" PostTypeId="2" ParentId="20965" CreationDate="2014-09-03T01:53:28.000" Score="1" Body="&lt;p&gt;It is unknown the reason why vertebrates hair in general varies in pigmentation. In the case of humans our genetic evolution for light and dark hair grew out of an adaptation to our environment. Camo is a key to other mammals so other species have predatory relationships that they must adapt to as well as environment. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Coloration is a diagnostic tool for identifying mammals, but inquiry into its function has lain dormant for almost a century. Recently, the topic has been revived and modern phylogenetic methods have been applied to large data sets, allowing researchers to assess, for the first time, the relative importance of three classic hypotheses for the function of coloration in mammals: concealment, communication, and regulation of physiological processes. Camouflage appears to be the single most important evolutionary force in explaining overall coloration in mammals, whereas patches of colored fur are used for intraspecific signaling. Sexual selection is associated with flamboyant ornamentation in a minority of primates and other restricted mammalian taxa, but to a far lesser extent than in birds. Interspecific signaling among mammals includes aposematic coloration, exaggeration of signals to deter pursuit, and lures for misdirecting predatory attack. Physiological causes of coloration, including melanism, are evident but poorly researched. The relative importance of evolutionary forces responsible for external coloration varies greatly between vertebrate taxa, but the reasons for this variation are not yet understood.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;-&lt;a href=&quot;http://bioscience.oxfordjournals.org/content/55/2/125.short&quot; rel=&quot;nofollow&quot;&gt;The Adaptive Significance of Coloration in Mammals&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-09-03T01:53:28.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20967" PostTypeId="2" ParentId="20964" CreationDate="2014-09-03T02:02:58.717" Score="2" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.nwrc.usgs.gov/wdb/pub/species_profiles/82_11-075.pdf&quot; rel=&quot;nofollow&quot;&gt;Ebersole 1987&lt;/a&gt;, &lt;em&gt;Mercenaria mercenaria&lt;/em&gt; reaches sexual maturity at two years of age although some individuals can reach maturity at 1 year of age under certain growing conditions.  The mean size of individuals reaching sexual maturity is 33 mm with males somewhat smaller than females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ebersole cited a few studies that estimated fecundity of &lt;em&gt;M. mercenaria&lt;/em&gt;. The results were highly variable. Individuals of about 60 mm in size released between 2 million and 6 million eggs.  Other estimates were as high as 25 million eggs.  Ebersole also cited a paper by Bricelj and Malouf (1980) where they found a general association of increasing fecundity with increasing clam size.  I don't have access to that paper but a book called &lt;a href=&quot;http://books.google.com/books?id=T9kTLfYGe2oC&amp;amp;printsec=frontcover&amp;amp;dq=The+Great+South+BAy&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=v3EGVMGCMcjIgwSjt4GQBw&amp;amp;ved=0CB4Q6AEwAA#v=onepage&amp;amp;q=The%20Great%20South%20BAy&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;The Great South Bay&lt;/em&gt;&lt;/a&gt; edited by Schubel et al. 1991 discussed the results of Bricelj and Malouf. Scroll to page 45 of the Google Books preview.  They show the mean fecundity and size as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Seed (&amp;lt;48mm): 1.6 million eggs / individual&#xA;Little Necks (48-70mm): 2.9 million&#xA;Cherrystones (70-79mm): 5.9 million&#xA;Chowders (&gt;79mm): 6.3 million&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the figure on page 45 of Schubel et al., and taken from the Bricelj and Malout (1980) paper, shows a lot of variability in fecundity at different size classes.  Hopefully, the citations in the Ebersole paper will point you to other useful studies. If you don't have ready access to the book, your local library may be able to get it for you on loan.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bricelj, V.M. and R.E. Malout. 1980. Aspects of reproduction of hard clams (&lt;em&gt;Mercenaria mercenaria&lt;/em&gt;) in Great South Bay, New York. Proceedings of the National Shellfish Association 70: 216-229.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ebersole, 1987. Species profiles: Life histories and environmental requirements of coastal fishes and invertebrates (South Atlantic). Hard clams. US Fish and Wildlife Service Biological Report 82 (11.75).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Schubel, J.R. et al. (editors) 1991. &lt;em&gt;The Great South Bay&lt;/em&gt;.  State University of New York Press, Albany, New York, USA.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-09-03T02:02:58.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20968" PostTypeId="2" ParentId="20938" CreationDate="2014-09-03T02:52:45.190" Score="0" Body="&lt;p&gt;Your question made it difficult to understand what you are looking for so I hope these two links will provide you with the desired data. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://phdtree.org/pdf/18073099-blosum62-miscalculations-improve-search-performance/&quot; rel=&quot;nofollow&quot;&gt;0. A source link to the paper in question&lt;/a&gt; and its &lt;a href=&quot;http://web.mit.edu/bamel/blosum/styczynski2007supp.pdf&quot; rel=&quot;nofollow&quot;&gt;supplementary file&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blosum/blosum.tar.Z&quot; rel=&quot;nofollow&quot;&gt;1. What blast is currently using.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0098983#pone-0098983-g006&quot; rel=&quot;nofollow&quot;&gt;2. What the math calls for.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-09-03T02:52:45.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20969" PostTypeId="2" ParentId="20965" CreationDate="2014-09-03T04:24:58.877" Score="9" Body="&lt;p&gt;Apparently the most noticeable research on this subject of a rabbit's white behind has been done by &lt;a href=&quot;http://www.uni-goettingen.de/en/265280.html&quot;&gt;Dr Dirk Semmann&lt;/a&gt; of the University of Goettingen. He proposes that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;these spots actually confuse predators because of their very&#xA;  noticeable nature. By focusing on the bright spot, the would-be&#xA;  predator ignores the larger body of the animal. Then, when the rabbit&#xA;  executes a sharp turn, the spot disappears and the predator has to&#xA;  readjust to focus on the camouflaged coat, losing vital seconds&#xA;  (&lt;a href=&quot;http://blogs.nature.com/news/2013/08/why-rabbits-have-white-tails.html&quot;&gt;reference 1&lt;/a&gt;, &lt;a href=&quot;http://www.dailymail.co.uk/sciencetech/article-2386779/How-rabbits-tail-save-life-Bright-white-tufts-evolved-distract-confuse-predators.html&quot;&gt;reference 2&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It could be the same reason for the white behind of a deer. As to why deer flag their tails, there is a paper on the subject which lists 4 possible reasons for the behaviour. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Flash behaviour&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Alarm Signal&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Cohesive signal&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) Detection signal&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More can be read about it in &lt;a href=&quot;http://www.jstor.org/discover/10.2307/2460873?uid=3737496&amp;amp;uid=2&amp;amp;uid=4&amp;amp;sid=21104116028641&quot;&gt;this paper&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-09-03T04:24:58.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20970" PostTypeId="1" CreationDate="2014-09-03T05:29:26.193" Score="2" ViewCount="127" Body="&lt;p&gt;I hear different sources claiming different things, bbc said they did, wikipedia says it hasn't which is it?&lt;/p&gt;&#xA;" OwnerUserId="8845" LastEditorUserId="1320" LastEditDate="2014-09-03T18:09:32.493" LastActivityDate="2014-09-03T18:09:32.493" Title="Has it been confirmed yet that the DNA found in dinosaurs was really DNA?" Tags="&lt;dna&gt;&lt;palaeontology&gt;&lt;decay&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20971" PostTypeId="1" AcceptedAnswerId="20973" CreationDate="2014-09-03T06:50:55.103" Score="4" ViewCount="530" Body="&lt;p&gt;Can someone please explain me the concept of Immunodominant peptide in simple language?? I did read the wiki article but did not understand it clearly. Please help!&#xA;&lt;br&gt;&lt;br&gt;(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)&lt;/p&gt;&#xA;" OwnerUserId="8835" LastActivityDate="2015-11-23T18:40:21.593" Title="Immunodominant Peptide" Tags="&lt;molecular-biology&gt;&lt;immunology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20972" PostTypeId="2" ParentId="20970" CreationDate="2014-09-03T06:53:24.723" Score="2" Body="&lt;p&gt;Apparently it wasn't. According to Wikipedia, A study that reported Dinosaur DNA was, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;mitochondrial cytochrome b sequences that had apparently been&#xA;  extracted from dinosaur bones dating to over 80 million years ago&#xA;  (&lt;a href=&quot;http://www.sciencemag.org/content/266/5188/1229&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, contamination was found in the reported study (&lt;a href=&quot;http://www.hedgeslab.org/pubs/69.pdf&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Don't expect too much because this is a close to impossible task (&lt;a href=&quot;http://dinosaurs.about.com/od/dinosaurcontroversies/a/Can-We-Clone-A-Dinosaur.htm&quot; rel=&quot;nofollow&quot;&gt;reference 1&lt;/a&gt;). Most researchers pinned their hopes on DNA surviving trapped in amber resin but even that is not possible (&lt;a href=&quot;http://www.telegraph.co.uk/science/dinosaurs/10303795/Jurassic-Park-ruled-out-dinosaur-DNA-could-not-survive-in-amber.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If interested in cloning a dinosaur, quickly go through &lt;a href=&quot;http://www.unmuseum.org/dnadino.htm&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; (or not). &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-09-03T06:53:24.723" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20973" PostTypeId="2" ParentId="20971" CreationDate="2014-09-03T07:24:12.990" Score="4" Body="&lt;p&gt;If you have an antigen (something foreign for the immune system, for example a virus or bacteria) this consists of many different epitopes (immunogenic regions), as shown in the figure below (from the German Wikipedia, Antikörper means antibodies). The antigens are taken up by special cells of the immune system and processed to get small peptides:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vHdWz.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To produce highly specific antibodies, the body has to undergo a specific immune reaction against these peptides. In the beginning of this reaction antibodies usually have a rather low affinity (bind only weak) against their antigen. This is changed by the so called affinity maturation in which the antibodies are mutated to make a variety of different new antibodies. These are then again &quot;checked&quot; against the antigen and the ones with a higher affinity are positively selected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So antibodies with a strong binding to their antigen are favoured against such which have a less strong binding which can lead the selection of only a few antibodies, even if a complex antigen which has many immunogenic peptides is used. This is positive in the way that these antibodies are very effective in directing an immune response against the virus/bacteria but can be critical if the pathogen has a high mutation rate as this leads to a pathogen which does not have this antigen anymore.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-03T07:24:12.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20974" PostTypeId="1" CreationDate="2014-09-03T07:40:04.690" Score="2" ViewCount="82" Body="&lt;p&gt;I am thinking if paternal or maternal genetic line is the risk factor. &#xA;Mitochondrial DNA is coming from maternal line. &#xA;I do not know the pathogenesis of epilepsy so well that I could answer my question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is epilepsy more heritable from the maternal side?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="1590" LastEditDate="2014-09-03T08:08:41.943" LastActivityDate="2014-09-04T07:51:55.070" Title="Is epilepsy more heritable from maternal side?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20976" PostTypeId="2" ParentId="15955" CreationDate="2014-09-03T08:59:31.100" Score="0" Body="&lt;p&gt;The CFG do not use consistent nomenclature for their glycan structures in the excel files they provide. It is human readable but not machine readable. So you'll have to curate their list first. I have bash scripts that do this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We convert glycan array structures into CFG symbols &#xA;&lt;a href=&quot;http://glycam.org/Pre-builtLibraries.jsp&quot; rel=&quot;nofollow&quot;&gt;http://glycam.org/Pre-builtLibraries.jsp&lt;/a&gt;&#xA;You want to click on the cfglibs and maybe give it a few secs to load. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are still interested in doing this send in an email to glycam@gmail.com explaining what you would like and include my name &quot;Oliver&quot;. &lt;/p&gt;&#xA;" OwnerUserId="9073" LastActivityDate="2014-09-03T08:59:31.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20978" PostTypeId="1" CreationDate="2014-09-03T13:31:27.643" Score="3" ViewCount="1517" Body="&lt;p&gt;Sometimes, you remember a vivid picture of a dream that you saw. What is the role of your eye in this experience? Please provide me with the answer that is as simple as possible since I am in Class 10(Grade 10).&lt;/p&gt;&#xA;" OwnerUserId="9076" LastEditorUserId="3624" LastEditDate="2014-09-04T18:59:28.187" LastActivityDate="2018-03-18T05:34:03.633" Title="Do the eyes play any role in producing the visual experiences you have during dreaming?" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;dreaming&gt;&lt;human-eye&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20979" PostTypeId="2" ParentId="20953" CreationDate="2014-09-03T14:43:13.323" Score="6" Body="&lt;p&gt;The part of the corn kernel that is visible in human feces is the outer coat of bran called the pericarp (&lt;a href=&quot;http://www.geochembio.com/IMG/corn-kernel-anatomy.png&quot;&gt;see this image&lt;/a&gt;). This is a common structure in &lt;a href=&quot;http://en.wikipedia.org/wiki/Bran&quot;&gt;cereal grains like corn and wheat&lt;/a&gt;.  However, the bulk of the corn kernal is &lt;a href=&quot;http://en.wikipedia.org/wiki/Endosperm&quot;&gt;starchy endosperm&lt;/a&gt;, which is readily digestible by humans and provides &lt;a href=&quot;http://www.fns.usda.gov/sites/default/files/HHFS_CORN_FRESH_900210Dec2012.pdf&quot;&gt;carbohydrates and vitamins A and C&lt;/a&gt;.  The non-digestible (by humans) pericarp does help to keep &lt;a href=&quot;http://www.livestrong.com/article/477602-why-does-the-human-body-not-digest-corn/&quot;&gt;fecal material soft&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plastic bags do not provide those same benefits. Studies on human consumption of plastic bags are lacking, for obvious reasons.  However, marine organisms like sea turtles unfortunately consume large amounts of plastic debris (&lt;a href=&quot;http://www.docbrownscience.com/uploads/4/8/7/2/4872895/plastic_pollution_1.pdf&quot;&gt;Derraik 2002&lt;/a&gt;). &lt;a href=&quot;http://www.seaturtle.org/PDF/BugoniL_2001_MarPollutBull.pdf&quot;&gt;Bugoni et al. (2001)&lt;/a&gt; found that plastic debris caused mortality for 13% of the green turtles in their study. A review of 408 leatherback sea turtle autopsy records by &lt;a href=&quot;https://dspace.lib.uoguelph.ca/xmlui/bitstream/handle/10214/2014/Leatherback_plastic.pdf?sequence=4&quot;&gt;Mrosovsky et al. (2009)&lt;/a&gt; found plastic inside 34% of turtles. The mortality in the sea turtles may be due to the accumulation of plastics in the gut which can &lt;a href=&quot;http://water.epa.gov/type/oceb/marinedebris/md_impacts.cfm&quot;&gt;block movement of food, alter feeding behaviors, and prevent absorbtion of nutrients&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If humans were to consume chopped up plastic bags, the evidence suggests that instead of receiving the same benefits as we do from whole kernal corn we are much more likely to be harmed. Eat your corn, recycle your plastic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bugoni, L. et al., 2001. Marine debris and human impacts on sea turtles in southern Brazil. Marine Pollution Bulletin 42: 1330-1334.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Derraik, J.G.B. 2002. The pollution of the marine environment by plastic debris: A review. Marine Pollution Bulletin 44: 842-852.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mrosovsky, N. et al. 2009. Leatherback turtles: The menance of plastic. Marine Pollution Bulletin 58: 287-289.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-09-03T14:43:13.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20980" PostTypeId="1" CreationDate="2014-09-03T16:07:02.707" Score="1" ViewCount="1590" Body="&lt;p&gt;Is chromosomal crossover considered a mutation? Would this be a large-scale mutation?&lt;/p&gt;&#xA;" OwnerUserId="9077" LastEditorUserId="8570" LastEditDate="2014-09-03T23:43:01.313" LastActivityDate="2014-09-03T23:43:01.313" Title="Does chromosomal crossover result in a mutation?" Tags="&lt;chromosome&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20981" PostTypeId="2" ParentId="20980" CreationDate="2014-09-03T16:17:09.710" Score="0" Body="&lt;p&gt;Yes. And it is especially considered a large-scale mutation when compared to point mutations which effect single bases.&lt;/p&gt;&#xA;" OwnerUserId="584" LastActivityDate="2014-09-03T16:17:09.710" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="20982" PostTypeId="2" ParentId="20978" CreationDate="2014-09-03T16:19:31.647" Score="2" Body="&lt;p&gt;Your eye doesn't play a part in your dream aside from giving you the basic images which your brain later used to form the dream. The visual image in your dream comes from your brain itself.&lt;/p&gt;&#xA;" OwnerUserId="584" LastActivityDate="2014-09-03T16:19:31.647" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20983" PostTypeId="1" AcceptedAnswerId="21019" CreationDate="2014-09-03T16:27:27.037" Score="4" ViewCount="422" Body="&lt;p&gt;These insects lived inside the wood of my bed in little round holes. They bite, lеаving very itchy red marks. And when crushed stink really bad. In the picture the lines are notebook lines for size comparison.&#xA;   I live in Eastern Europe, so I don't think they are fire ants, if they are ants at all.&#xA;Any suggestions would be appreciated!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/e8qtY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7VlKp.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gSP3f.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9078" LastEditorUserId="9078" LastEditDate="2014-09-04T17:12:20.833" LastActivityDate="2020-01-11T18:33:08.510" Title="Identification of this insect" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="20985" PostTypeId="1" CreationDate="2014-09-03T16:43:00.623" Score="11" ViewCount="2234" Body="&lt;p&gt;I often find the fungus below growing on my (ostensibly) sterile plates in the 4⁰C room. Presumably it takes a few days to reach this size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The colony looks puffy and dimpled in the middle, like a chocolate cake. The colony is actually black, but looks grey because of what I assume are hyphae and/or spores on top.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It looks like if I disturb the colony physically spores will be released (I haven't tried this because I don't want to contaminate the whole lab with aggressive spores). I notice that the center of the mass curves upward over time, and after a few more days of growth this colony will probably tear itself apart, leaving a gaping hole in the middle (based observation of similar contaminants on other plates, not pictured).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect this is a very common lab contaminant. It grew to this size in less than 2 weeks, and was at 4C the entire time. I noticed many plates in the same batch/sleeve were contaminated, but each plate had only one colony, so it somehow spreads from plate to plate but not within the plate. What is it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3ablT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If anyone has any suggestions for simple but informative, classical microbiological techniques that would help identification (common stains, inexpensive selective media) I would be happy to try them - although it would be hard to justify very involved experiments since this doesn't pertain to my main research (in other words, if this was bacteria, sequencing the 16S would probably be out but a Gram stain is fine - this is very likely not bacteria, but I don't know the equivalents of those methods for fungi). Since identifying species is not really my strong suit, I'd appreciate if you link to a protocol when suggesting methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update:&lt;/strong&gt; I have found 4 more plates, all LB-Ampicillin, with what I suspect to be the same contaminant. With regard to Alan Boyd's comments, the colony morphology seems to be uniform in several aspects. It is not necessarily flower-shaped as I have claimed, but on the other hand, it never has a halo of satellites (dots) around it either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photos of the plates:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://i.imgur.com/KzwUFU6.jpg&quot; rel=&quot;noreferrer&quot;&gt;View from the top (agar side close to the benchtop)&lt;/a&gt; - shows round colony morphology and various stages of growth. Bottom left colony shows small dimple as the mass begins to swell. Top right shows cracks (actually tears) appearing as the mass is distorted by growth. Note that there is never two colonies on the same plate. The plates all came from the same sleeve in a cold room storage.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://i.imgur.com/5qpoNYM.jpg&quot; rel=&quot;noreferrer&quot;&gt;View of same colonies from the bottom&lt;/a&gt; - note star-shaped inward creases which form as the colonies grow and distort the surface.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="540" LastEditorUserId="3340" LastEditDate="2014-11-21T16:18:12.713" LastActivityDate="2015-02-25T02:53:00.063" Title="What is this fuzzy, black fungus that grew on my plates in the 4⁰C room?" Tags="&lt;microbiology&gt;&lt;species-identification&gt;&lt;mycology&gt;" AnswerCount="0" CommentCount="12" FavoriteCount="1" ClosedDate="2015-02-26T09:37:28.310" ContentLicense="CC BY-SA 3.0" />
  <row Id="20986" PostTypeId="2" ParentId="20938" CreationDate="2014-09-03T19:01:59.663" Score="4" Body="&lt;p&gt;Okay, I emailed Dr. Mark Styczynsk (one of the authors) to ask about a link to the matrix. Here are the links he gave me:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://web.mit.edu/bamel/blosum/revised_blosum.c&quot; rel=&quot;nofollow&quot;&gt;http://web.mit.edu/bamel/blosum/revised_blosum.c&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://web.mit.edu/bamel/blosum/original_blosum.c&quot; rel=&quot;nofollow&quot;&gt;http://web.mit.edu/bamel/blosum/original_blosum.c&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://web.mit.edu/bamel/blosum/RBLOSUM64&quot; rel=&quot;nofollow&quot;&gt;http://web.mit.edu/bamel/blosum/RBLOSUM64&lt;/a&gt; (isentropic with BLOSUM62)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://web.mit.edu/bamel/blosum/RBLOSUM62&quot; rel=&quot;nofollow&quot;&gt;http://web.mit.edu/bamel/blosum/RBLOSUM62&lt;/a&gt; (not isentropic, but it's 62)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first link is to the c code to generate the corrected BLOSUM. According to Mark, just replacing the original c file in &lt;a href=&quot;ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blosum/blosum.tar.Z&quot; rel=&quot;nofollow&quot;&gt;the original BLOSUM tarball&lt;/a&gt; with the revised c file can generate the corrected matrix for any of the BLOSUMs (30, 50, 92). Haven't yet tried that myself.&lt;/p&gt;&#xA;" OwnerUserId="8060" LastActivityDate="2014-09-03T19:01:59.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20987" PostTypeId="2" ParentId="20983" CreationDate="2014-09-03T20:19:49.997" Score="2" Body="&lt;p&gt;I can't tell you the species but it appears to be a termite. The &lt;a href=&quot;http://australianmuseum.net.au/What-are-the-differences-between-ants-and-termites&quot; rel=&quot;nofollow noreferrer&quot;&gt;Australian Museum&lt;/a&gt; explains some of the differences between termites and ants. Termites have straight antennae. Ants have bent antennae with a distinct elbow.  Your insect has straight antennae without an elbow. Termites have a broad waist. Ants have a very narrow waist. Your insect appears to have a broader waist. You also find more at &lt;a href=&quot;https://flrec.ifas.ufl.edu/media/flrecifasufledu/pdfs/pestants/DifferenceBetweenAntAndTermite.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;The University of Florida&lt;/a&gt;. I'm not an entomologist and I do not live in Eastern Europe so consider my answer with a degree of caution.  If you have a pest control company nearby, you can take the specimen to them for verification, in case it is a termite species capable of home damage.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="55929" LastEditDate="2020-01-11T18:33:08.510" LastActivityDate="2020-01-11T18:33:08.510" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="20989" PostTypeId="1" AcceptedAnswerId="29962" CreationDate="2014-09-03T21:33:17.077" Score="0" ViewCount="2325" Body="&lt;p&gt;I hate having to run MOPS PFA agarose gels with DEPC and everything just to verify my RNA integrity. I came across an &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22222980&quot; rel=&quot;nofollow&quot;&gt;alternative protocol&lt;/a&gt; that uses ordinary household bleach in the gel to inhibit RNases and was wondering if anyone here has tried it and what the success was like? Or any helpful insight is welcomed also.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;here's a protocol I put together based on what was done in that paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a 50ml gel&#xA;IN a RNase-free 250ml Erlenmeyer flask&#xA;Mix:&#xA;5 mls of 10x TAE that I gave you&#xA;42.5mls ultra purified water&#xA;0.5g of the agarose I gave you&#xA;2.5mls of household bleach (6% sodium hypochlorite, use clorox)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incubate 5-10 minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Microwave for the minim amount of time on the lowest heat setting that’s needed to completely solubilize the agarose, you don’t want evaporation adjusting your solutions volume&#xA;Check your volume with a sterile 50ml serological pipette, if you have lost more than 5% volume I would redo, using less heat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Add 3µl 10mg/ml ethidium bromide, swirl to mix.&#xA;Pour in casting frame, allow to cool, submerge in 1xTAE&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Combine 1µg of your total RNA, 2µg RNase free 6x loading dye and q.s to 12µl in RNAse feree water, you can use the water from the qiagen kit for this.&#xA;Run at 100V, about 30 min, get  good scanned image of it and use Photoshop to assess the band intensity. The 28S should be twice the brightness  of the 18S in a sample with little to no fragmentation.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="3340" LastEditDate="2015-02-26T13:28:15.850" LastActivityDate="2017-01-26T12:33:20.253" Title="Alternative protocol for evaluating RNA integrity, using a bleach gel" Tags="&lt;rna&gt;&lt;gel-electrophoresis&gt;" AnswerCount="2" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="20990" PostTypeId="2" ParentId="20942" CreationDate="2014-09-03T21:47:29.363" Score="2" Body="&lt;p&gt;Tight junctions function to occlude the baso-apical flow of small molecules. However, tight junctions &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22671602&quot; rel=&quot;nofollow noreferrer&quot;&gt;do not always completely seal a cell's lateral surface&lt;/a&gt;. In addition to regulating diffusion, tight junctions &lt;a href=&quot;http://books.google.com/books?id=3AgPBAAAQBAJ&amp;amp;pg=PA389&amp;amp;lpg=PA389&amp;amp;dq=transcytosis%20in%20stratified%20squamous%20epithelium&amp;amp;source=bl&amp;amp;ots=IJwsx01AmL&amp;amp;sig=aqt6fbpthJISUP05vO9SmD44--4&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=04cHVNfCD8WwggS4k4C4CQ&amp;amp;ved=0CEMQ6AEwBA#v=onepage&amp;amp;q=transcytosis%20in%20stratified%20squamous%20epithelium&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;promote cell polarity&lt;/a&gt;. Establishment of polarity and prevention of water loss are the major roles of tight junctions in stratified squamous epithelia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In simple epithelia, transcytosis allows the flow of molecules through a cell with tight junctions. However, stratified squamous cells do not use transcytosis for nutrient supply. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the stratum granulosum, skin cells &lt;a href=&quot;http://en.wikipedia.org/wiki/Stratum_granulosum&quot; rel=&quot;nofollow noreferrer&quot;&gt;lose their nuclei&lt;/a&gt; and become non-viable. In the stratum lucidum, an oily layer is produced by exocytosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is the loss of nuclei, organells, production of an oily layer at the stratum granulosum and lucidum that contributes most to the death of skin cells, not the limits of nutrient diffusion. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/k7JW7.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8570" LastActivityDate="2014-09-03T21:47:29.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20991" PostTypeId="2" ParentId="20980" CreationDate="2014-09-03T22:01:07.367" Score="1" Body="&lt;p&gt;There are many different ways a DNA sequence can change. Labeling a change as a mutation implies that there was a biological process in which DNA was damaged then not properly repaired. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Crossing over during the formation of gametes does not result in a mutation.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Crossing over during repair of a double stranded DNA break &lt;strong&gt;does&lt;/strong&gt; result in a mutation.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8570" LastActivityDate="2014-09-03T22:01:07.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="20992" PostTypeId="1" AcceptedAnswerId="20993" CreationDate="2014-09-03T23:16:46.223" Score="5" ViewCount="3254" Body="&lt;p&gt;From what I understand, your body needs certain amounts of vitamins and minerals to maintain health. Why can't we just take enough pills to obtain these vitamins and minerals?&lt;/p&gt;&#xA;" OwnerUserId="6035" LastEditorUserId="6035" LastEditDate="2014-09-03T23:45:23.040" LastActivityDate="2017-01-30T14:45:00.397" Title="Why can't you just take a vitamin? Why you need a healthy diet on top of that?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;nutrition&gt;&lt;vitamins&gt;&lt;minerals&gt;" AnswerCount="5" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20993" PostTypeId="2" ParentId="20992" CreationDate="2014-09-03T23:32:27.147" Score="-1" Body="&lt;p&gt;This is more of a biochemistry question and to be honest its a little bit out of my league because I have not had the necessary grad classes to explain nutrition but indeed I will try.&lt;/p&gt;&#xA;&lt;p&gt;Unknown metabolite cofactors and things like ionization, oxidation and state of matter are the reason that straight up vitamins are rejected by the body and cause really expensive urine and a difficult time otherwise excreting.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are the loosely bound organic cofactors, often called coenzymes.&lt;/p&gt;&#xA;&lt;p&gt;Each class of group-transfer reaction is carried out by a particular cofactor, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. An example of this are the dehydrogenases that use nicotinamide adenine dinucleotide (NAD+) as a cofactor. Here, hundreds of separate types of enzymes remove electrons from their substrates and reduce NAD+ to NADH. This reduced cofactor is then a substrate for any of the reductases in the cell that require electrons to reduce their substrates.&lt;/p&gt;&#xA;&lt;p&gt;Therefore, these cofactors are continuously recycled as part of metabolism. As an example, the total quantity of ATP in the human body is about 0.1 mole. This ATP is constantly being broken down into ADP, and then converted back into ATP. Thus, at any given time, the total amount of ATP + ADP remains fairly constant. The energy used by human cells requires the hydrolysis of 100 to 150 moles of ATP daily, which is around 50 to 75 kg. In typical situations, humans use up their body weight of ATP over the course of the day. This means that each ATP molecule is recycled 1000 to 1500 times daily.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;-&lt;a href=&quot;http://en.wikipedia.org/wiki/Cofactor_(biochemistry)#Cofactors_as_metabolic_intermediates&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;If you did not like that explanation of cofactors maybe you will this:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Whole foods offer three main benefits over dietary supplements:&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Greater nutrition&lt;/strong&gt;. Whole foods are complex, containing a variety of the micronutrients your body needs — not just one. An orange, for example, provides vitamin C plus some beta carotene, calcium and other nutrients. A vitamin C supplement lacks these other micronutrients.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Essential fiber&lt;/strong&gt;. Whole foods, such as whole grains, fruits, vegetables and legumes, provide dietary fiber. Most high-fiber foods are also packed with other essential nutrients. Fiber, as part of a healthy diet, can help prevent certain diseases, such as type 2 diabetes and heart disease, and it can also help manage constipation.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Protective substances&lt;/strong&gt;. Whole foods contain other substances important for good health. Fruits and vegetables, for example, contain naturally occurring substances called phytochemicals, which may help protect you against cancer, heart disease, diabetes and high blood pressure. Many are also good sources of antioxidants — substances that slow down oxidation, a natural process that leads to cell and tissue damage.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;-&lt;a href=&quot;http://www.mayoclinic.org/healthy-living/nutrition-and-healthy-eating/in-depth/supplements/art-20044894&quot; rel=&quot;nofollow noreferrer&quot;&gt;The great Mayo Clinic&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-03T23:32:27.147" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="20994" PostTypeId="1" AcceptedAnswerId="21018" CreationDate="2014-09-03T23:41:12.787" Score="3" ViewCount="233" Body="&lt;p&gt;What is this vinca like vine? Is it poisonous? 62521 USA Illinois &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sVdTH.jpg&quot; alt=&quot;&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/REgWY.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastEditorUserId="3952" LastEditDate="2014-09-04T11:38:13.257" LastActivityDate="2015-01-06T23:02:28.800" Title="What is this vinca like vine?" Tags="&lt;botany&gt;&lt;species-identification&gt;&lt;toxicology&gt;&lt;ethnobiology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20995" PostTypeId="1" AcceptedAnswerId="21103" CreationDate="2014-09-04T00:12:34.340" Score="3" ViewCount="347" Body="&lt;p&gt;We can't rely on pills to provide us our nutrients because we don't absorb the nutrients from the pills as effectively. Presumably this is because pills are &lt;a href=&quot;https://biology.stackexchange.com/questions/20992/why-cant-you-just-take-a-vitamin-why-you-need-a-healthy-diet-on-top-of-that&quot;&gt;lacking components&lt;/a&gt; that are required for certain reactions to take place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why can't we just create a pill that does have all the necessary components?&lt;/p&gt;&#xA;" OwnerUserId="6035" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-09-07T22:26:22.650" Title="Why do we absorb vitamins better from whole foods than from pills?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20998" PostTypeId="1" CreationDate="2014-09-04T02:15:55.593" Score="8" ViewCount="1385" Body="&lt;p&gt;I don't know if this question has an answer at this time, but I would like to know if there is some biological reason why the current Ebola outbreak is so much more complicated and widespread than in the past. Traditionally it has been initially very virulent and has then has rapidly waned. I hope what I am saying is accurate, and if so why dont we see the same pattern now ? &lt;/p&gt;&#xA;" OwnerUserId="9084" LastEditorUserId="5144" LastEditDate="2014-09-04T06:33:11.543" LastActivityDate="2014-09-04T12:11:20.193" Title="Why is the current Ebola outbreak different from previous outbreaks?" Tags="&lt;pathology&gt;&lt;virology&gt;&lt;epidemiology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="20999" PostTypeId="1" AcceptedAnswerId="21001" CreationDate="2014-09-04T02:31:25.700" Score="0" ViewCount="150" Body="&lt;p&gt;This question arises from the explanation of what the resting potential of a cell membrane is. In the Goldman formula, there is no interaction between different ion types. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If diffusion is caused by random movement of ions and collisions, then how is it that the K+ ions do not seem affected by the very high concentration of Na+ ions outside of the membrane? Shouldn't there be an effect due to the fact that outside, the ion concentration overall is higher than inside? How come they are all independent?&lt;/p&gt;&#xA;" OwnerUserId="8260" LastActivityDate="2014-09-04T21:52:31.770" Title="How is it that ionic diffusion is independent of other ions?" Tags="&lt;cell-biology&gt;&lt;cell-membrane&gt;&lt;electrophysiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21001" PostTypeId="2" ParentId="20999" CreationDate="2014-09-04T04:13:28.380" Score="1" Body="&lt;p&gt;Most importantly, the whole Goldman-Hodgkin-Katz model is, well, a model. It is a way we would like to find and explain phenomena, given pen and paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Often, scientists build models in order to explain data in hand, but even then, they will have to add something from their imagination. For example, early astronomers saw planets moving differently from stars, and came up with the idea that, you know, planets do not circle the earth, but maybe around some points in space, which in turn circle the earth. That didn't work well, so they created the heliocentric model, where planets and the Earth circled the sun. That was still perfectible, and Newton suggested the planets do not move on circles, but on ellipses. Each generation of astronomers had almost the same data in hand, but chose to make some assumptions in their models.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same goes with the lack of interaction between potassium and sodium ions: it is a theoretical assumption. As models go, the GHK model is quite good, because it fits experimental findings better than any other model. Its assumptions have a great chance of being true, of reflecting the physical world. I guess you really asked what are the physical facts that underlie the assumption of ion independence. The fact is, you are looking for explanations for a fact that may be or may not be - so any response you will receive is, to a degree, speculation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My thought is that the number of water molecules (55 molar) that may collide with an ion is far greater than the number of cations (up to a few hundred nanomolar, about 100 million rarer). Perhaps the number of ion-ion collisions is negligible. There is one bottleneck, in the actual channels, but there different species do not meet, because each has its own channels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another, more factual, is that the model is imperfect, and independence is more of a wish than a complete truth. Quoting from &lt;a href=&quot;http://books.google.com/books?id=SmJoSwnwSh0C&amp;amp;lpg=PA353&amp;amp;ots=3fvI19Sk5Q&amp;amp;dq=ghk%20ion%20independence%20fails&amp;amp;pg=PA353#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;http://books.google.com/books?id=SmJoSwnwSh0C&amp;amp;lpg=PA353&amp;amp;ots=3fvI19Sk5Q&amp;amp;dq=ghk%20ion%20independence%20fails&amp;amp;pg=PA353#v=onepage&amp;amp;q&amp;amp;f=false&lt;/a&gt; : &quot;The rich literature on how ion channels fail to obey the independence principle is reviewed in Chapter 14 of Hille (1991), and some specific models will be studied in the following chapter.&quot;&lt;/p&gt;&#xA;" OwnerUserId="8809" LastActivityDate="2014-09-04T04:13:28.380" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21002" PostTypeId="2" ParentId="15648" CreationDate="2014-09-04T04:18:38.920" Score="2" Body="&lt;p&gt;Virus induced gene silencing (VIGS) is definitely an option. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ease of using VIGS depends on a lot of factors. Current VIGS vectors have limited host ranges. Depending on the species of plant that you are working with, there may or may not be suitable, pre-made VIGS vectors available and published techniques for using them. Many of the VIGS vectors that are available may be limited in terms of which tissues they can infect. Working with the vectors themselves requires that you have some way to propagate them and some way of getting them into your target plants (for example Biolistics, Agrobacterium or direct application of infectious virus). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been a number of VIGS vectors developed over the years, capable of infecting a diversity of plant species. Modified Tobacco mosaic virus (TMV) and Tobacco rattle virus (TRV) are two common VIGS vectors used for silencing in a variety of plants. TRV in particular is known to have a very wide host range. If your species doesn't fall within or even near the documented host range of available vectors it may be worth just trying a few different ones. Or, you could always isolate a virus specific to your target plant and build you're own. What fun!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The length of time that silencing will last is difficult to predict. In my experience, it will typically last a few weeks. But this may vary depending on a number of host factors and the VIGS vector used.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One potential alternative would be to just use Agrobacterium. It could be combined with a recombinase system to satisfy your condition of transience. To build such a system you could insert you're silencing construct into a binary vector. By including an inducible recombinase sequence adjacent to your silencing construct sequence and by flanking both of these with the recombinases recognition sequences, you would be able to remove inserted DNA at some point down the road after transforming the plant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, depending on which species and variety of plant you're working on, this could require some trial and error as there may not be published techniques for Agro mediated transformation of you're target plant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While Agro mediated transformation may not quite be what you're looking for in terms of transient silencing, it may be sufficient for a proof of concept.&lt;/p&gt;&#xA;" OwnerUserId="9079" LastActivityDate="2014-09-04T04:18:38.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21005" PostTypeId="2" ParentId="20998" CreationDate="2014-09-04T07:10:51.860" Score="12" Body="&lt;p&gt;This is too long for a comment, so I put this in here: The main reasons are sociological. From the data I have read so far, this outbreak (actually these are two independent outbreaks, one in West-Africa and another one -not connected- in the Democratic Republic of Congo) is not exceptionally deadly in terms of Ebola. The death rate is about 60% which is extremely high compared to other diseases, but Ebola had reached up to 90%...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the main differences are that this outbreak struck in a much more populated area which has a very poor health care system (if you can call it like this at all). Then it happened in a border region, I recall reports about a traditional funeral of a Ebola victim which infected visitors, some of them crossed the border afterwards. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then it was completely underestimated in the beginning, because a lot of cases stayed unknown. This led to a wider spreading as people who got sick infected relatives and medical personnel subsequently. And although the reaction has been powered up a lot since then, it is still not adequate to contain the outbreak. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Former outbreaks happened in rural areas which where easier to contain with a smaller number of personal, which is not possible this time. If you want to read further about this, I recommend the blog of &lt;a href=&quot;http://scienceblogs.com/aetiology/&quot;&gt;Tara C. Smith&lt;/a&gt; which has been doing research about Ebola for some time and also worked in crisis response teams.&#xA;Especially interesting are these two:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://scienceblogs.com/aetiology/2014/08/07/a-historical-perspective-on-ebola-response-and-prevention/&quot;&gt;A historical perspective on Ebola response and prevention&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://scienceblogs.com/aetiology/2014/08/06/addressing-more-ebola-myths/&quot;&gt;Addressing more Ebola myths&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorDisplayName="user1357" LastEditDate="2014-09-04T08:35:58.633" LastActivityDate="2014-09-04T08:35:58.633" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21007" PostTypeId="2" ParentId="20998" CreationDate="2014-09-04T07:44:39.297" Score="11" Body="&lt;p&gt;For some background, it is essential to know that Ebola is actually a group (genus) of ebolaviruses, each with different fatality rates. There are five known species of Ebola, and four are known to cause disease humans (&lt;a href=&quot;http://www.who.int/mediacentre/factsheets/fs103/en/&quot;&gt;WHO: Ebola virus disease&lt;/a&gt;; &lt;a href=&quot;http://en.wikipedia.org/wiki/Ebolavirus&quot;&gt;wikipedia&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The known species of Ebola includes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Zaire ebolavirus (or just ebolavirus)&lt;/li&gt;&#xA;&lt;li&gt;Sudan ebolavirus&lt;/li&gt;&#xA;&lt;li&gt;Bundibugyo ebolavirus&lt;/li&gt;&#xA;&lt;li&gt;Tai ebolavirus (only one known human case)&lt;/li&gt;&#xA;&lt;li&gt;Reston ebolavirus (can infect but does not seem to cause disease in humans)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Zaire ebolavirus is the deadliest strain (with Sudan second), and also the one that is causing the current outbreak. A table of all known ebola outbreaks can be found in the WHO report (&lt;a href=&quot;http://www.who.int/mediacentre/factsheets/fs103/en/&quot;&gt;WHO: Ebola virus disease&lt;/a&gt;), which shows that the historical fatality of the Zaire strain has been between 44% and above 90%. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From my limited understanding, when dealing with ebola it is essential for infected individuals to be identified early so that they can get intensive care (most importantly intravenous fluids because of dehydration), but also to prevent further spread. This is probably what has failed during this outbreak, but another problem is also that the size of the outbreak has put tremendous strain on an already weak healthcare system. These outbreaks have also occurred in well populated areas in countries with very weak governments, that also lacked experience in dealing with ebola (both in the administration and among the population). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In many former outbreaks, the initial death rate is very high since early victims are found at late stages of the disease, but when the outbreak is more controlled the death rate drops due to supporting care of infected individuals. I don't know to what extent this has been the case during the current west african outbreak. However, the overall fatality rate of the current outbreak is 52% (tabulated Aug. 28 2014), with 44% in Sierra Leone and 66% in Guinnea (&lt;a href=&quot;http://www.who.int/csr/don/2014_08_28_ebola/en/&quot;&gt;WHO: Ebola virus disease update - west Africa&lt;/a&gt;), and this lies well within the normal fatality rate of the Zaire ebolavirus.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-09-04T12:11:20.193" LastActivityDate="2014-09-04T12:11:20.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21008" PostTypeId="1" AcceptedAnswerId="21015" CreationDate="2014-09-04T07:46:35.510" Score="1" ViewCount="115" Body="&lt;p&gt;I'm just trying to find out whether the male side-blotched lizard is the hetero- or homogametic sex in side-blotched lizards (&lt;em&gt;Uta stansburiana&lt;/em&gt;) - some reptiles are ZW system (female heterogamete) and some are XY (male heterogamete).&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-09-04T09:56:45.030" Title="Which sex is homogametic in side-blotched lizards?" Tags="&lt;chromosome&gt;&lt;reptile&gt;&lt;sex-chromosome&gt;&lt;gamete&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21009" PostTypeId="2" ParentId="20974" CreationDate="2014-09-04T07:51:55.070" Score="3" Body="&lt;p&gt;Epilepsy is a neurological disorder characterized by hypersynchronous discharge of neurons .i.e abnormal electrical activity in the brain. Epileptic seizures caused primarily due to i) inhibition of inhibitory neurotransmitter systems such GABA neurotransmitters or ii) Enhancement of excitatory neurotransmitter systems such as nAchR. These conditions arise due to head injury, trauma and genetic factors. But there is no evidence as of now regarding Mitochondrial DNA taking part in inhibitory and excitatory systems. so, epileptic seizures are not specific in inheriting from any side (Maternal or paternal side) as far as pathophysiology of epilepsy is concerned.&lt;/p&gt;&#xA;" OwnerUserId="9089" LastActivityDate="2014-09-04T07:51:55.070" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21011" PostTypeId="1" AcceptedAnswerId="21014" CreationDate="2014-09-04T09:03:45.103" Score="8" ViewCount="553" Body="&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/jav.00367/abstract?campaign=woletoc&quot;&gt;This paper&lt;/a&gt; concludes that birds can adaptively modulate brood sex ratios. How do birds modulate brood sex ratios? Are they somehow able to influence the sex of their young? Or once young are born, do they provision one sex with more food so that the other sex does not survive?&lt;/p&gt;&#xA;" OwnerUserId="1216" LastEditorUserId="1216" LastEditDate="2014-09-04T09:39:27.740" LastActivityDate="2014-09-04T11:34:43.333" Title="How do birds influence brood sex ratios?" Tags="&lt;ornithology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21012" PostTypeId="1" AcceptedAnswerId="21024" CreationDate="2014-09-04T09:21:49.093" Score="1" ViewCount="4340" Body="&lt;p&gt;How can a placenta turn hostile to the mother or fetus ?&#xA;What are the abnormalities found during placental delivery ?&lt;/p&gt;&#xA;" OwnerUserId="8580" LastActivityDate="2014-09-04T16:20:53.227" Title="Negative role of Placenta" Tags="&lt;physiology&gt;&lt;reproduction&gt;&lt;embryology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21013" PostTypeId="2" ParentId="21012" CreationDate="2014-09-04T09:31:10.180" Score="0" Body="&lt;p&gt;An abnormal placenta position can lead to increased risk of heavy bleeding during placental delivery which further complicates the process by needing blood transfusion drugs. Anterior placental attachment is associated with increased risk of pregnancy induced hypertension , gestational diabetes mellitus due to dysfunction of lactogen hormone secreted by placenta, placental abruption, intra uterine retarded growth or fetal death.Rh factor incompatibility is a complication during the second delivery. Also, placenta encapsulation(conversion of placenta into capsules) has side effects on mother's health like pelvic girdle pain, constipation or diarrhea , PMS like emotional outbursts. &#xA;Placenta is an intimate connection between the fetus and mother but locational abnormalities can make placenta hostile to both fetus and mother. Also, the Rh factor incompatibility stays a major factor in being harmful.&lt;/p&gt;&#xA;" OwnerUserId="8580" LastActivityDate="2014-09-04T09:31:10.180" CommentCount="2" CommunityOwnedDate="2014-09-04T09:31:10.180" ContentLicense="CC BY-SA 3.0" />
  <row Id="21014" PostTypeId="2" ParentId="21011" CreationDate="2014-09-04T09:36:45.000" Score="8" Body="&lt;p&gt;On a more general level it is possible for parents to influence sex-ratio of broods in a number of ways, and there are other reasons why a brood might have a sex ratio distortion. The paper I've been reading this morning is about side-blotched lizards doing just this. I'll give a quick basic answer just from the top of my head and hopefully someone can give some specific examples in birds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Bias in gamete production&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming XY chromosome systems where the males are heterogametic (XY, females XX) the male can influence the brood sex ratio by producing more or less Y-bearing sperm. Sperm carrying an X-chromosome will always produce daughters and sperm carrying a Y- will always produce sons. The opposite would be true for ZZ/ZW where female gamete type determines the sex, they could only produce Z eggs, therefore only having sons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Female cryptic sperm choice&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A fairly modern idea is that females can selectively fertilise eggs with sperm based on the DNA they carry, this could include whether the sperm is Y- or X-bearing. This idea is thought to explain how females produce daughters from small sires and sons from large sires in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15009280&quot; rel=&quot;nofollow&quot;&gt;the paper I mentioned at the start.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Meiotic drive and sex ratio distorters&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Meiotic drive elements may be responsible for sex-ratio distortion in broods. Just like the biased sperm production this can alter the sex-ratio at the gamete level. Genetic effects mean that fewer offspring of one sex than the other are produced. &lt;a href=&quot;http://www.pnas.org/content/98/23/13183&quot; rel=&quot;nofollow&quot;&gt;Here is one example where suppressors of the distorter have evolved in the autosomes&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Direct selection by the parents&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the paper you mention above, and with most studies, it is possible that the parents are selecting which offspring to raise after they hatch (or as an egg - it may be possible to determine sex at that point) and if females are more costly to raise and conditions are poor, they may kill/neglect the female offspring early on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Within brood competition&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If one sex is stronger as a chick it possible that the broods could become sex biased in certain conditions which consistently favour one over the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Consequence of environmental strain&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly to the last two points, if conditions are poor it may be harder for one sex to reach maturity than the other which would result in sex-bias. This is the conclusion the authors in your paper seem to come to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Environmental effects&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As with some reptiles, environment can determine the sex of the offspring. For example, &lt;a href=&quot;http://en.wikipedia.org/wiki/Temperature-dependent_sex_determination&quot; rel=&quot;nofollow&quot;&gt;incubation temperature in turtles has a considerable effect on offspring sex ratio&lt;/a&gt;. Given how close birds and reptiles are in evolutionary time, and the importance of active incubation in birds, I don't see that it's impossible for the parent to vary some kind of environmental factor in order to bias sex-ratio.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;There are certainly more potential mechanisms and some of these ideas are fairly new in evolutionary biology research so there are many unanswered questions. I hope I will have time to find some bird specific examples later.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-09-04T11:34:43.333" LastActivityDate="2014-09-04T11:34:43.333" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21015" PostTypeId="2" ParentId="21008" CreationDate="2014-09-04T09:56:45.030" Score="1" Body="&lt;p&gt;Lizards of the genus &lt;em&gt;Uta&lt;/em&gt; are apparently male heterogametic (XY) (&lt;a href=&quot;http://www.karger.com/Article/Abstract/130018&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pennock et al. 1969)&lt;/a&gt;. The XY system seems to be the most common mode of sex determination in iguanid lizards (&lt;a href=&quot;http://aerg.canberra.edu.au/library/sex_general/1983_Kasahara_etal.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kasahara et al. 1983&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Kasahara, Y et al. 1983. Chromosome mechanisms of sex determination, G- and C-band patterns and nucleolus organizer regions in &lt;em&gt;Tropidurus torquatus&lt;/em&gt; (Sauria, Iguanidae).  Genetica 60: 151-156.&lt;/p&gt;&#xA;&lt;p&gt;Pennock, L.A. et al. 1969. Minute Y chromosome in the lizard genus &lt;em&gt;Uta&lt;/em&gt; (Family Iguanidae). Cytogenetics and Genome Research 8: 9-19.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-04T09:56:45.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21016" PostTypeId="1" CreationDate="2014-09-04T10:26:16.473" Score="2" ViewCount="515" Body="&lt;p&gt;What is the formal name for animals with full digestive tracts, by which I mean a mouth and an anus, and what is the classification for animals that have a single hole for exchanging food and waste?&lt;/p&gt;&#xA;" OwnerUserId="9092" LastActivityDate="2014-09-04T13:39:37.993" Title="What is the classification for animals with full tube digestive tracts?" Tags="&lt;classification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21018" PostTypeId="2" ParentId="20994" CreationDate="2014-09-04T11:37:46.623" Score="5" Body="&lt;p&gt;Wintercreeper, &lt;em&gt;Euonymus fortunei&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that you're just over in Illinois, here's the &lt;a href=&quot;http://tinyurl.com/nkmetp5&quot; rel=&quot;noreferrer&quot;&gt;page from our Plant Finder database&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In regards to your second question, this &lt;a href=&quot;http://climbers.lsa.umich.edu/wp-content/uploads/2013/07/EuonfortCELAFINAL.pdf&quot; rel=&quot;noreferrer&quot;&gt;factsheet from UMich&lt;/a&gt; mentions (and gives citations) for its use as a medicine. Given that, I'd avoid eating it if I were you, but there's not mention of it being especially toxic.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2014-09-04T11:37:46.623" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21019" PostTypeId="2" ParentId="20983" CreationDate="2014-09-04T12:27:01.680" Score="5" Body="&lt;p&gt;This looks like an ant, but I cannot say which species. Their small size, colour, bite and being found indoors made me think of &lt;a href=&quot;http://en.wikipedia.org/wiki/Pharaoh_ant&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pharaoh ants (&lt;em&gt;Monomorium pharaonis&lt;/em&gt;)&lt;/a&gt;, but I haven't heard that they smell bad. &lt;a href=&quot;http://mypestprevention.com/2011/09/ghost/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ghost ants (&lt;em&gt;Tapinoma melanocephalum&lt;/em&gt;&lt;/a&gt;) are rather similar and have a foul smell when crushed, and have been found indoors in Europe. They usually have a dark head/thorax and lighter abdomen though. They can also be separated from Pharaoh ants by having a one segmented &lt;a href=&quot;http://en.wikipedia.org/wiki/Petiole_%28insect_anatomy%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;petiole&lt;/a&gt; (the Pharaoh ant has two). A closely related species to the Ghost ant is &lt;a href=&quot;http://en.wikipedia.org/wiki/Tapinoma_sessile&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Tapinoma sessile&lt;/em&gt;&lt;/a&gt;, which also smells but has a uniform colour (usually darker than your specimen though, see picture at &lt;a href=&quot;http://bugguide.net/node/view/87301/bgimage&quot; rel=&quot;nofollow noreferrer&quot;&gt;bugguide.net&lt;/a&gt;). The petiole not being clearly seen in your specimen points towards the two latter species, or other species with a short/hidden petiole (see hidden petiole at &lt;a href=&quot;http://antkey.org/glossary-terms/petiole-hidden-gaster&quot; rel=&quot;nofollow noreferrer&quot;&gt;antkey.org&lt;/a&gt;). However, these are only a couple of suggestions, and there are probably many other possible species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Termites have larger mandibles (jaws) relative to their size, and no distinct narrow division between thorax and abdomen (your specimen does). Your animal also has eyes (termites don't) and I think you can spot a long first antenna segment, which ants have (hard to see in the picture though). &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="46609" LastEditDate="2020-01-05T03:39:00.303" LastActivityDate="2020-01-05T03:39:00.303" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="21021" PostTypeId="1" AcceptedAnswerId="21046" CreationDate="2014-09-04T13:28:05.050" Score="15" ViewCount="872" Body="&lt;p&gt;According to simple models of selection the genetic variance in a population should be reduced by selection. (Fisher's fundamental theorem states that the rate at which a population can evolve is limited by its variance). If we select the next generation from one population we will only ever capture as much, and probably only a subset of, the variation that exists in a the first generation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Did Darwin ever discuss this loss of variation? What did he conclude?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(For now lets ignore the potential roles of sexual antagonism, pleiotropy and such)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A little clarification on my question:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Darwin saw variation in phenotypes, and variation in fitness dependent on phenotype - an effect he called selection. He also saw that this variation was heritable (but did not know how). This is the basic concept of evolution, and is mathematically speaking, the breeders equation: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$r = h^2 s$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He also would have realized that life must therefore have started out as a simple unit, and new variance in traits (and whole new traits) must have arisen over time, i.e. that some kind of changes (mutations) were going on in the heritable information (genes). However, what I'm asking is, &lt;strong&gt;did he realize that selection would act to reduce the variation in a population?&lt;/strong&gt; This would reduce the rate at which evolution can occur over time (Fisher's fundamental theorem - assuming no influx of variance or potential for pleiotropy to maintain variation). &lt;strong&gt;Or was it Fisher that first formally discussed the concept of lost phenotypic/genetic variance?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="3624" LastEditDate="2018-10-15T12:31:42.927" LastActivityDate="2018-10-15T12:31:42.927" Title="Did Darwin ever reach the conclusion that selection will remove variation?" Tags="&lt;evolution&gt;&lt;population-genetics&gt;&lt;natural-selection&gt;&lt;history&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21022" PostTypeId="2" ParentId="21016" CreationDate="2014-09-04T13:39:37.993" Score="1" Body="&lt;p&gt;Animals with a single hole do not form a monophyletic group: metazoa &gt; eumetazoa &gt;bilateria almost all have separate mouth and anus (except notably flatworms which is one reason it does not form a monophyletic group).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As species are not grouped in monophyletic groups by what they don't have (eg. invertebrates do not form a monophyletic group while vertebrates do) there is no particular group. Eumetazoa before the bilateria have a single mouth-anus.&lt;/p&gt;&#xA;" OwnerUserId="6182" LastActivityDate="2014-09-04T13:39:37.993" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21023" PostTypeId="1" AcceptedAnswerId="21025" CreationDate="2014-09-04T15:53:58.007" Score="6" ViewCount="1968" Body="&lt;p&gt;Current evidence indicates that fruit bats are a reservoir host for Ebola. Has any research established what is different about their cell biology or immune system that reduces virulence for them? &#xA;Failing research on this particular system, do you have an example in another system of how virulence is reduced in the reservoir host? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm teaching a cell biology class, so actual examples of modified proteins or enzymes or inflammatory molecules in the reservoir is preferred.&lt;/p&gt;&#xA;" OwnerUserId="6517" LastEditorUserId="2949" LastEditDate="2014-10-24T18:58:04.963" LastActivityDate="2014-10-24T18:58:04.963" Title="What about a bat's immune system protects them from Ebola?" Tags="&lt;virus&gt;&lt;ebola&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21024" PostTypeId="2" ParentId="21012" CreationDate="2014-09-04T16:14:00.620" Score="2" Body="&lt;p&gt;The placenta does not turn &quot;hostile&quot; to the mother or fetus. Placentation abnormalities can result in harmful situations, but these are a secondary result.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Structural anomalies of placentation:&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;&lt;em&gt;placenta accreta/percreta:&lt;/em&gt;&lt;/strong&gt; means that the placenta took hold not only in the uterine mucosa, which is the normal state, but through it up to the myometrium (muscle layer, in &lt;em&gt;placenta accreta&lt;/em&gt;), or even up to the serosa (outermost uterine layer, in &lt;em&gt;placenta percreta&lt;/em&gt;). These anomalies will convey a much higher chance of massive haemorrage at delivery, and therefore are dangerous to the mother.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;&lt;em&gt;placenta praevia:&lt;/em&gt;&lt;/strong&gt; placental insertion covers the entrance to the uterine cervical canal, partially or totally. Therefore, the way of the fetus for natural delivery is blocked, and the placenta will tear during labor, causing massive haemorrage.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;marginal implantation of placental vessels:&lt;/strong&gt; vessels linking the placenta to the fetus (the umbilical cord) are implanted on the periphery of the placenta. This causes structural fragility, and a greater risk of bleeding for both the mother and fetus.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;retroplacental hematoma:&lt;/strong&gt; in such cases, the placenta partially or totally loses its hold on the mucosa, and blood fills the space left behind. This is an immediate threat to both the fetus and mother because of the potential for massive haemorrhage and interruption of oxygen delivery to the fetus.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Deleterious side effects of pregnancy:&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;preeclampsia/eclampsia:&lt;/strong&gt; misunderstood biological syndrome that causes the classical signs of arterial hypertension, peripheral edema, hepatic cytolysis, and thrombocytopenia in the mother. Eclampsia is all that plus added seizures (in which case maternal mortality is high). This is not due to placentation abnormalities, even if it is true that delivery is the only cure, and can justify a premature artificially induced delivery in extreme cases.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;fetal/maternal rhesus factor incompatibility:&lt;/strong&gt; During labor and delivery, a small amount of fetal blood will come into contact with the mother's organism. If the mother is Rh neg, and the baby Rh pos, the mother can develop antibodies against the rhesus factor. This can cause haemolysis in the newborn, and in grave cases, kernicterus (toxicity of degraded red blood cell metabolites to the baby). While this may threaten the baby to be born, problems are much more common for subsequent Rh pos pregnancies. We check for antibody presence in the mother with the &lt;strong&gt;Kleihauer test&lt;/strong&gt; and give preventive injections of rhesus antibodies to Rh neg mother with a Rh pos pregnancy to decrease the chance that the mother develops her own antibodies.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Other special cases:&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;molar pregnancy/choriocarcinoma:&lt;/strong&gt; A structural genetic accident happening on fecundation that can cause the embryo to behave as a type of cancer.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;ingesting placental extracts:&lt;/strong&gt; this is mentioned is another answer here. This has nothing to do with the placenta, but the deleterious secondary effects are due to direct toxicity of the hormones contained in those extracts ingested in an inadapted situation. This is not to say that one should take them while pregnant, because hormonal deregulation would also be toxic in a normal pregnancy.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2014-09-04T16:20:53.227" LastActivityDate="2014-09-04T16:20:53.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21025" PostTypeId="2" ParentId="21023" CreationDate="2014-09-04T16:22:50.950" Score="10" Body="&lt;p&gt;The main reason for this is that fruit bats are most likely (I don't think there has been a direct proof for Ebola so far) the reservoir host for this disease. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Natural_reservoir&quot;&gt;reservoir host&lt;/a&gt; is adapted to the disease and can harbour it for an indefinite time (with recurring infections) without showing signs of an infection or being affected by it. Although it is not getting sick, the reservoir host can pass the disease to other animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is very little known about the immune system of bats, but they seem to be different, so they are not affected by diseases which cause havoc in humans. The following papers go into some details and they are interesting to read:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://cmr.asm.org/content/19/3/531.full&quot;&gt;Bats: Important Reservoir Hosts of Emerging Viruses&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23265969&quot;&gt;Bats and their virome: an important source of emerging viruses&#xA;capable of infecting humans.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;These papers give an interesting view of the bats immune system. The first article is a short explanation of the most important findings of the second. It looks into differences between species and analyse how the bats immune system may have evolved. Really interesting.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://blogs.mcgill.ca/osscontributors/2013/02/19/of-bats-flight-and-immunity-to-viruses/&quot;&gt;Of bats, flight and immunity to viruses&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23258410&quot;&gt;Comparative analysis of bat genomes provides insight into the&lt;br&gt;&#xA;evolution of flight and immunity.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1863-2378.2012.01528.x/abstract&quot;&gt;Antiviral Immune Responses of Bats: A Review&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-09-04T18:29:20.477" LastActivityDate="2014-09-04T18:29:20.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21026" PostTypeId="1" CreationDate="2014-09-04T17:13:01.437" Score="2" ViewCount="57" Body="&lt;p&gt;Besides oxidizing fatty acids to form prostglandins, leukotrienes, and epoxides, what other roles do cyclooxygenase, lipoxygenase, and epoxygenase have in signal transduction?&lt;/p&gt;&#xA;" OwnerUserId="8977" LastActivityDate="2014-12-05T01:17:56.373" Title="What roles do cyclooxygenase, lipoxygenase, and epoxygenase have in signal transduction?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2014-12-09T04:13:50.737" ContentLicense="CC BY-SA 3.0" />
  <row Id="21027" PostTypeId="2" ParentId="2946" CreationDate="2014-09-04T17:40:44.233" Score="4" Body="&lt;p&gt;Yes, in all clinical situations where you need pure vasoconstriction without heart rate acceleration (mostly valid for iv administration route).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The classical example would be in the operative setting. If the patient is in a hypotensive state due to hypnotic drugs, opiates, etc. and has atherosclerosis, you will prefer a drug that will reverse the hypotension without an increase in heart rate, &lt;em&gt;i.e&lt;/em&gt; phenylephrine. The reason is that an increase in heart rate will shorten the duration of diastole, which will therefore shorten the time interval where the coronary arteries are perfused. Moreover, an increase in heart rate also means an increase in heart oxygen consumption. The end result will be an imbalance between oxygen input and requirement, &lt;em&gt;i.e&lt;/em&gt; ischemia and potential heart infarction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conversely, if you have a patient with aortic valve insufficiency (regurgitation), you will prefer ephedrine (or any drug with beta 1 activity), because you will be aiming at shortening the available time for regurgitation to occur.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-09-04T17:40:44.233" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21028" PostTypeId="1" AcceptedAnswerId="21061" CreationDate="2014-09-04T19:55:01.997" Score="7" ViewCount="1025" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concept of mutational variance can be found in many articles including &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2012.01649.x/abstract&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt; for example. The mutational variance of a trait number $i$ can be found in the M-matrix in position $m_{ii}$ (in the diagonal). Elements of the off-diagonal represent mutation covariance. For example element at position $m_{ij}$ of the M-maitrx is the mutational covariance between traits $i$ and $j$. More info about the M (and G) matrix can be found &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17439608&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does &quot;Mutational Variance&quot; mean? What does it mean for a population to have a high or a low mutational variance?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does &quot;mutational variance&quot; refers to:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Average effect of new mutations on fitness (mutational effect) (parameter $s$)&lt;/li&gt;&#xA;&lt;li&gt;Variance in the effect of new mutations on fitness (variance in $s$)&lt;/li&gt;&#xA;&lt;li&gt;Average effect of new mutations on phenotype&lt;/li&gt;&#xA;&lt;li&gt;Variance in the effect of new mutations on phenotype&lt;/li&gt;&#xA;&lt;li&gt;The increase in genetic variance ($V_G$) due to a new mutation&lt;/li&gt;&#xA;&lt;li&gt;The increase in additive genetic variance ($V_A$) due to a new mutation&lt;/li&gt;&#xA;&lt;li&gt;Genetic variance in the population at mutation-selection-drift equilibrium.&lt;/li&gt;&#xA;&lt;li&gt;Is it a concept that is opposed to genetic canalization?&lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-09-08T01:37:32.210" LastActivityDate="2014-09-08T01:37:32.210" Title="What does &quot;Mutational Variance&quot; mean?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;population-dynamics&gt;&lt;population-genetics&gt;&lt;definitions&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21029" PostTypeId="1" AcceptedAnswerId="21030" CreationDate="2014-09-04T20:59:41.747" Score="3" ViewCount="625" Body="&lt;p&gt;My homework wants me to plot all crystal structures determined per year, but when I search on PDB for all structures, many of the articles say &quot;crystal structure,&quot; but some say &quot;solution structure&quot; or even &quot;complex structure.&quot; Are all of these considered to be subsets of &quot;crystal structure&quot;?&lt;/p&gt;&#xA;" OwnerUserId="6128" LastActivityDate="2014-09-05T06:05:01.537" Title="Is there a difference between any of these terms for proteins: &quot;crystal structure,&quot; &quot;NMR structure,&quot; &quot;solution structure,&quot; and &quot;complex structure&quot;?" Tags="&lt;proteins&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21030" PostTypeId="2" ParentId="21029" CreationDate="2014-09-04T21:23:19.967" Score="4" Body="&lt;p&gt;Depending on who you talk to (typically laymen and scientists who are not structural biochemists), the term &lt;em&gt;&quot;crystal structure&quot;&lt;/em&gt; is frequently taken to mean &lt;em&gt;&quot;some determination of molecular structure, whether by actual crystallography or some other means&quot;&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, a graduate student is talking to her adviser, an immunologist, about the structure-function relationship between a certain viral &lt;a href=&quot;http://en.wikipedia.org/wiki/Capsid&quot; rel=&quot;nofollow&quot;&gt;capsid&lt;/a&gt; protein and the peptide antigens they are using to create families of antibodies to the virus. The adviser consistently refers to the recently-published &quot;crystal structure&quot; of the protein, even though the actual study was performed using a combination of NMR spectra obtained from solution, electron microscopy, and quantum mechanical computational chemistry modeling techniques, and no crystals were actually studied.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, you probably want to talk to your teacher/professor and clarify what s/he is looking for. Most likely, if you're in some sort of undergrad or first-year graduate class, they're just looking for &quot;structural determination&quot; in general, but they may specifically be looking for those models that were generated using actual crystals, so asking is always best.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I should note that there are significant methodological and computational differences when determining structure via X-ray crystallography, various types of NMR, electron microscopy (with or without crystals as the target), so-called &quot;complex&quot; determinations, etc. Find a structural biologist to learn much, much more.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-09-04T21:23:19.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21031" PostTypeId="2" ParentId="21029" CreationDate="2014-09-04T21:32:01.990" Score="3" Body="&lt;p&gt;I agree with what MattDMo has said, but just to emphasise - a 'solution' or 'NMR' structure is not a crystal structure. ('Complex structure' probably means structure of a complex. e.g between a protein and a ligand.) To be a crystal structure the structure should be determined using X-ray crystallography.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the &lt;a href=&quot;http://www.rcsb.org/pdb/search/advSearch.do&quot; rel=&quot;nofollow&quot;&gt;Protein Data Bank home page&lt;/a&gt; choose &lt;em&gt;Advanced Search&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then use the pull-down menu &lt;em&gt;Choose a Query Type:&lt;/em&gt; to select &lt;em&gt;Experimental Method&lt;/em&gt;. This will automatically populate with the &lt;strong&gt;X-RAY&lt;/strong&gt; option which is what you want - have a look at the other options.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can then use &lt;em&gt;Add Search Criteria&lt;/em&gt;  to append a new field where you can select a date range.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-09-05T06:05:01.537" LastActivityDate="2014-09-05T06:05:01.537" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21032" PostTypeId="2" ParentId="20999" CreationDate="2014-09-04T21:52:31.770" Score="0" Body="&lt;p&gt;Maybe I'm missing something here (and it's not my area of expertise) but...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the &lt;a href=&quot;http://en.wikipedia.org/wiki/GHK_flux_equation&quot; rel=&quot;nofollow&quot;&gt;GHK formula&lt;/a&gt; includes the parameter &lt;em&gt;V&lt;sub&gt;m&lt;/sub&gt;&lt;/em&gt; which is the transmembrane potential. This parameter is determined by the intracellular and extracellular concentrations of all ions. A high external concentration of Na&lt;sup&gt;+&lt;/sup&gt; will therefore influence the net movement of K&lt;sup&gt;+&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the assumptions of the GHK equation is that the ions do not directly interact.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-09-04T21:52:31.770" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21033" PostTypeId="1" CreationDate="2014-09-04T21:54:39.427" Score="3" ViewCount="564" Body="&lt;p&gt;I can understand how if you are not circulating enough (warm) blood, by not moving much while in a cold environment, your extremities &lt;em&gt;themselves&lt;/em&gt; lose heat, and become cold - but I don't understand how they (the hands, feet, and head) can make the &lt;em&gt;rest&lt;/em&gt; of your body lose heat too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;'Drawing the heat out of your body' (as people have termed it to me) doesn't make sense itself - what is the actual mechanism(s) behind the (exposed, relatively uncirculated) extremities, 'drawing' heat out of the body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it that it merely draws the &lt;em&gt;need&lt;/em&gt; to heat those (poorly insulated, circulated) extremities from the existing distribution of heating the other parts of your body, thus lowering how warm those other parts are?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, how does &lt;em&gt;that&lt;/em&gt; happen? In the case above, where you're not moving the body to circulate warm blood to the hands (or using other warming stimuli like friction), how would 'heat transfer' to the hands occur then? Or does it just indeed slowly 'lose heat' and get colder and colder (which would then lead me back to my question, how would that explain the rest of your body becoming colder as a result of the extremities becoming colder)?&lt;/p&gt;&#xA;" OwnerDisplayName="user3362" LastActivityDate="2014-09-04T22:10:40.050" Title="What's the mechanism behind 'losing heat through your extremities'?" Tags="&lt;physiology&gt;&lt;heat&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21034" PostTypeId="2" ParentId="21033" CreationDate="2014-09-04T22:10:40.050" Score="3" Body="&lt;p&gt;Your extremities lose heat at a faster rate than the rest of your body because they have higher surface area per unit volume. Heat exchange happens at surfaces, so if you have more surface, you transfer heat more quickly. Imagine you have a sphere of water with 1L volume, and a long cylinder of water, also 1L, lets say 1cm wide, the sphere will hold heat longer because it has less surface area per unit volume.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does losing heat through extremities cool the rest of your body? Because of your blood. As blood runs through your core, it takes heat from surrounding tissues. The blood carries that heat to the extremities, where cooler tissues pull it away from the blood. It's kind of like how the coolant in your car takes heat from the engine block to the radiator.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When it is very cold, your body will reduce blood flow to the extremities to save heat, making your fingers vulnerable to frostbite. However, it cannot stop bloodflow, those tissues still need oxygen, so you still lose some heat.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-09-04T22:10:40.050" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21035" PostTypeId="2" ParentId="21021" CreationDate="2014-09-04T22:38:40.357" Score="1" Body="&lt;p&gt;I think Darwin just stuck to the empirical observation that variation exists.  Without knowing about genetics and mutations, he didn't know the mechanism that generates variation, and he knew that he was lacking that, but he knew variation was being generated.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-09-04T22:38:40.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21037" PostTypeId="2" ParentId="14230" CreationDate="2014-09-04T23:36:42.633" Score="3" Body="&lt;p&gt;Answers in comments are correct. The tail effect of hypnotic drugs combined to opiates given for pain relief will make you feel really tired just after surgery.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if you are referring to a more long-term effect, such as feeling tired for several days after surgery, then several factors combine:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;psychological stress&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;physical deconditioning:&lt;/strong&gt; inpatients usually do not move much. And even a few days of immobility will have a huge impact on your physical abilities. That is why in modern medicine, every effort is made to make the patient move as quickly as possible. Intensive physical therapy, readaptation therapy, and fast-track pathways are a result of this effort.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;physical stress:&lt;/strong&gt; undergoing surgery &lt;strong&gt;is&lt;/strong&gt; a physical effort. Your body needs to accommodate for large shifts in volemia, positive pressure ventilation, reaction to pain (which still takes place during anesthesia), etc. The physical abilities of the patient are evaluated by the anesthesiologist for that reason, using MET effort units (often measured in number of flights of stairs you can climb without stopping). People with angina pectoris or diagnosed atherosclerosis can also be submitted to an ergometric test (cycling) or stress echocardiography/scintigraphy to evaluate if their heart can tolerate the physical stress of surgery.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2014-09-05T02:54:00.547" LastActivityDate="2014-09-05T02:54:00.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21039" PostTypeId="1" CreationDate="2014-09-04T23:59:55.210" Score="3" ViewCount="622" Body="&lt;p&gt;This is not a duplicate of all the other 260/280 ratio questions, I already know that DNA is supposed to be 1.8 and RNA is supposed to be 2.0. However, this might be more appropriate for chemistry, and will move it if I have to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question has to do with the Poly A tails on mRNA. I've been doing in vitro transcription and tailing for a while now and have noticed that the untailed RNA has a 260/280 of about 2.0, like you'd expect, but successful tailing results in ratios from 2.15 to 2.45, with higher ratios correlating to better band shifts on agarose gels, implying a longer tail. I suspect the reason for this is because the adenine has a much higher 260/280 than the other bases, so if you add a lot of adenines to the 3' end of the RNA you add much more 260 absorbance than 280 absorbance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After seeing this I tried to come up with a mathematical method to estimate tail length based on 260/280, since gels are annoying, while I can get the ratio directly from the nanodrop.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I started by using the 260/280 for each nucleotide, A: 4.50, G: 1.15, C: 1.51, U: 4.00, T: 1.47 source here: &lt;a href=&quot;http://www.bio.davidson.edu/projects/gcat/protocols/NanoDrop_tip.pdf&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;. I then took the sequence for the Luciferase gene I'm using for mRNA and counted the nucleotides, 449 A, 566 C, 470 G, 374 U. I tried to get the weighted average of the 260/280 for my RNA. &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;A: 449 x 4.50 = 2020.50&#xA;C: 566 x 1.51 =  854.60&#xA;G: 470 x 1.15 =  540.50&#xA;U: 374 x 4.00 = 1496.00&#xA;Sum:            4911.60&#xA;&#xA;Nucleotides: 449 + 566 + 470 + 374 = 1859&#xA;Sum / Nucleotides : 4911.60 / 1859 = 2.64&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;2.64 is clearly not 2.0. Even accounting for the potential effect of pH and ionic strength on RNA 260/280 ( acidic solutions have lower ratios ) I can't explain why the calculated ratio is so high. Even if we assumed an RNA with 25% of each base, the weighted average is still (1.15 + 4.50 + 1.51 + 4.00)/4 = 2.79, even higher than for my real sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Doing the same calculation for DNA, (1.15 + 4.50 + 1.51 + 1.47)/4 = 2.16.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why don't my calculated ratios for RNA and DNA 260/280 match the &quot;ideal&quot; ratios of 2.0 and 1.8?&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-09-04T23:59:55.210" Title="Origin of the 260/280 ratio?" Tags="&lt;rna&gt;&lt;lab-techniques&gt;&lt;dna-isolation&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21040" PostTypeId="2" ParentId="20952" CreationDate="2014-09-05T00:37:13.250" Score="10" Body="&lt;p&gt;The whole point about your question is to define what is an &quot;evolved trait&quot;? &lt;strong&gt;The concept of &quot;evolved trait&quot; does not exist in evolutionary biology&lt;/strong&gt;. Here are various definitions I can think of that could apply to the expression &quot;evolved traits&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Heritable Traits&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Does evolved traits mean heritable traits?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A trait may be heritable or not. See for example my answer to this post to understand what heritable mean. You may want to understand the difference between the narrow and broad sense of heritability. Greed is probably heritable as several studies showed that many personality traits are heritable. &lt;a href=&quot;https://biology.stackexchange.com/questions/16589/list-of-heritability-estimates-in-humans&quot;&gt;This post&lt;/a&gt; will maybe give you more info.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;--&gt; Greed is probably a heritable trait&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Traits that evolve&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Does evolved traits mean traits that can evolve?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any (existing) biological trait evolves. Not necessarily because they are selected for or against, neither even for genetic reasons, but traits change through times. Culture changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;--&gt; Yes, greediness can evolve&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Traits that are adaptations&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Does evolved traits mean traits that are adaptations?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concept of adaptation is not always easy to define and its definition may vary from authors to authors. Simply speaking, an adaptation might be defined as a trait that is now fixed in the population (meaning that all individuals in the population carry this trait) but when it was not fixed yet it was beneficial. Such definitions would not fit the concept of greediness if we assume there is some genetic variance for greediness. But while I am not aware of any study on the subject, a level of greediness very probably influence the fitness  (=~ reproductive success) of its carrier. If someone is extremely greedy, he might not find a mate and may fail to reproduce. On the other side, someone that is extremely generous may give everything it has up to its life and would definitely fail to reproduce. Therefore, it seems at first though that there is what we call stabilizing selection on the level of greediness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;--&gt; It depends on the meaning of adaptation. But yes, it seems intuitive that greediness is a trait that undergoes (stabilizing) selection.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Social traits&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Greediness is the kind of trait that are particularly interesting because it influences not only the fitness of its carrier but also the fitness of other individuals in the population. We say that it is a social trait and the field that study such traits is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Social_evolution&quot; rel=&quot;nofollow noreferrer&quot;&gt;social evolution&lt;/a&gt;. You'll need to get in touch with Hamilton's rule (&lt;a href=&quot;http://en.wikipedia.org/wiki/Kin_selection&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kin selection&lt;/a&gt;) and &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionary_game_theory&quot; rel=&quot;nofollow noreferrer&quot;&gt;evolutionary game theory&lt;/a&gt; to understand more about the evolution of social traits. &lt;a href=&quot;https://biology.stackexchange.com/questions/10742/what-if-rb-c-in-hamiltons-rule/10770&quot;&gt;This post&lt;/a&gt; may eventually help you.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-01-08T13:22:53.263" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21041" PostTypeId="2" ParentId="16792" CreationDate="2014-09-05T00:44:47.363" Score="3" Body="&lt;p&gt;You cannot change the oxygen concentration of inhaled air in the absence of an external source of oxygen. However, you can use your lungs at their maximum capacity doing this:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;breathe deeply:&lt;/strong&gt; =increase tidal volume. Your muscles will inflate your lungs as much as they are able to, inflating parts of the lungs that were not fully inflated (atelectases) in the process. This also allows you to inhale a volume much greater than your physiologic dead space (volume of inhalation that does not participate in gas exchanges)&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;breathe to high enough frequency:&lt;/strong&gt; the faster you will want to expel $CO_2$ and replace it with room air, the higher frequency you will need to adopt.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Frequency and tidal volume are the two components of &lt;strong&gt;minute ventilation&lt;/strong&gt; (= (frequency/minute) X tidal volume), which is the physiologic value you are working to increase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Position:&lt;/strong&gt; The upright position is best suited, since the weight of the lung tissue pulling downwards will facilitate inflation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;WARNING: using those techniques unsupervised can cause acute respiratory alkalosis, which is unhealthy and puts you in immediate danger.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="11841" LastEditDate="2015-01-21T23:50:34.970" LastActivityDate="2015-01-21T23:50:34.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21042" PostTypeId="2" ParentId="14273" CreationDate="2014-09-05T00:54:10.753" Score="1" Body="&lt;p&gt;The below structure circled in green clearly is part of the stomach antrum. The location is correct, and the mucosal folds are characteristic. Kerckring valves of the small intestine and semilunar folds of the colon both look different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2rqIU.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-09-05T00:54:10.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21043" PostTypeId="2" ParentId="7964" CreationDate="2014-09-05T01:33:14.753" Score="1" Body="&lt;p&gt;The process of urine concentration in mammals occurs due to the interaction of the loop of Henle and its nearby collecting tubule. When someone is dehydrated, the kidney will aim to a maximal water reabsorption.&#xA;To concentrate urine, a &lt;strong&gt;maximal&lt;/strong&gt; amount of ions will be reabsorbed. This is to maximalize the concentration gradient for water. However, the main driving force for water reabsorption is the &lt;strong&gt;urea&lt;/strong&gt; concentration gradient (created by the loop of Henle). Then aquaporins will allow water to flow from the collecting tubule to the nearby medulla because of the presence of the neighboring loop of Henle. &lt;strong&gt;It is this proximity between the loop of Henle and the collecting tubule that allows such a high efficiency for water reabsorption.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Concentrating urine is not about leaving more ions in the water, it is about reabsorbing a maximal amount of water.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-09-05T01:33:14.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21044" PostTypeId="2" ParentId="7112" CreationDate="2014-09-05T02:04:48.903" Score="0" Body="&lt;p&gt;@Michael Kunh &lt;strong&gt;Carbonic anhydrase&lt;/strong&gt; is used in the human body to tip the balance of the reaction  $H_2CO_3\rightleftharpoons H^++HCO_3^-$ to the right side, and is an important player in acidobasic homeostasis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer the question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$HCO_3^-$ is excreted through the kidneys. This represents the metabolic compensation to respiratory alkalosis that appears in altitude.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To summarize:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;ascension leaves us in with a &lt;strong&gt;lower partial pressure of oxygen&lt;/strong&gt;. This will &lt;strong&gt;stimulate the peripheral chemoreceptors&lt;/strong&gt; of the carotid bodies and aortic arch to increase ventilation (hypoxic ventilatory response). In consequence, an &lt;strong&gt;acute respiratory alkalosis&lt;/strong&gt; develops.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;renal adaptation begins after more or less 8 hours, and reestablishes homeostasis after 24-48h. To do that, the kidney will excrete $HCO_3^-$, which will tend to acidify blood (metabolic acidosis to counterbalance respiratory alcalosis). To accelerate this phase, one could take some &lt;strong&gt;acetazolamide&lt;/strong&gt;, a diuretic drug that causes $HCO_3^-$ excretion.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-09-05T02:04:48.903" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21045" PostTypeId="2" ParentId="14876" CreationDate="2014-09-05T02:09:43.540" Score="0" Body="&lt;p&gt;The radius of a blood vessel is entirely defined by only two parameters:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1.blood pressure&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2.compliance of the vessel walls&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, active contraction can decrease the vessel radius. Physically, this is a decrease in compliance, so the above relation always remains true.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-09-05T02:09:43.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21046" PostTypeId="2" ParentId="21021" CreationDate="2014-09-05T09:09:08.893" Score="9" Body="&lt;p&gt;After reading your question, I had a vague memory that this subject was indirectly touched upon in &quot;&lt;em&gt;On the Origin of Species&lt;/em&gt;&quot;, so I did some text searches (in &lt;a href=&quot;http://www2.hn.psu.edu/faculty/jmanis/darwin/originspecies.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; pdf version I found online). From what I can see, Darwin never used the technical term 'variance' (I don't know how old this use of the word is), but 'variability' is often used, both with regard to accumulated variation but also meaning variation between individuals within a population. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All-in-all, I could not find clear support for the idea that selection will decrease the amount of variation. However, there are number of passages where the subject of variation vs selection comes up (often indirectly), but, to me, these just as often (most often?) indicate that Darwin saw no risk that selection would reduce variation as the opposite. Here are the most interesting passages I could find (searching for combinations of 'variab*', 'selection', 'decrease' etc), with page references referring to the pdf version and a short comment below each quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A large number of individuals,&#xA;  by giving a better chance for the appearance within&#xA;  any given period of profitable variations, will compensate &#xA;  for a lesser amount of variability in each individual, &#xA;  and is, I believe, an extremely important&#xA;  element of success.&#xA;  (p. 44)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is clearly discussing amounts of variation within species, where large numbers can compensate for a smaller amounts of standing variability, by increasing the chance of advantageous mutations.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nothing can be effected, unless favourable variations&#xA;  occur, and variation itself is apparently always a very&#xA;  slow process. The process will often be greatly retarded &#xA;  by free intercrossing. Many will exclaim that&#xA;  these several causes are amply sufficient wholly to&#xA;  stop the action of natural selection. I do not believe&#xA;  so. On the other hand, I do believe that natural selection &#xA;  will always act very slowly, often only at long&#xA;  intervals of time, and generally on only a very few&#xA;  of the inhabitants of the same region at the same time.&#xA;  (p. 103)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not directly related to selection vs variation, but deals with the rate of evolution vs amount of variation.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But what here more&#xA;  especially concerns us is, that in our domestic animals &#xA;  those points, which at the present time are undergoing &#xA;  rapid change by continued selection, are&#xA;  also eminently liable to variation. Look at the breeds&#xA;  of the pigeon; see what a prodigious amount of difference &#xA;  there is in the beak of the different tumblers,&#xA;  in the beak and wattle of the different carriers, in the&#xA;  carriage and tail of our fantails, &amp;amp;c., these being the&#xA;  points now mainly attended to by English fanciers.&#xA;  Even in the sub-breeds, as in the short-faced tumbler, &#xA;  it is notoriously difficult to breed them nearly&#xA;  to perfection, and frequently individuals are born&#xA;  which depart widely from the standard. There may&#xA;  be truly said to be a constant struggle going on between, &#xA;  on the one hand, the tendency to reversion to&#xA;  a less modified state, as well as an innate tendency&#xA;  to further variability of all kinds, and, on the other&#xA;  hand, the power of steady selection to keep the breed&#xA;  true. In the long run selection gains the day, and we&#xA;  do not expect to fail so far as to breed a bird as coarse&#xA;  as a common tumbler from a good short-faced strain.&#xA;  But as long as selection is rapidly going on, there&#xA;  may always be expected to be much variability in&#xA;  the structure undergoing modification.&#xA;  (p. 141)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is maybe the most interesting passage, which to me indicates that he saw little risk that selection could/would limit variability (see especially beginning and end).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For forms existing in larger&#xA;  numbers will always have a better chance, within&#xA;  any given period, of presenting further favourable&#xA;  variations for natural selection to seize on, than will&#xA;  the rarer forms which exist in lesser numbers. Hence,&#xA;  the more common forms, in the race for life, will tend&#xA;  to beat and supplant the less common forms, for&#xA;  these will be more slowly modified and improved.&#xA;  (P. 162)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also on limitations for variation that selection can act on, and the value of large populations.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... firstly, because new varieties are&#xA;  very slowly formed, for variation is a very slow process, &#xA;  and natural selection can do nothing until&#xA;  favourable variations chance to occur, and until a&#xA;  place in the natural polity of the country can be better &#xA;  filled by some modification of some one or more&#xA;  of its inhabitants. And such new places will depend&#xA;  on slow changes of climate, or on the occasional immigration &#xA;  of new inhabitants, and, probably, in a still&#xA;  more important degree, on some of the old inhabitants &#xA;  becoming slowly modified, with the new forms&#xA;  thus produced and the old ones acting and reacting&#xA;  on each other.&#xA;  (p. 163)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;On the limiting nature of variation, but does not connect selection to decreased variation.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It cannot be asserted that organic beings&#xA;  in a state of nature are subject to no variation; it cannot &#xA;  be proved that the amount of variation in the&#xA;  course of long ages is a limited quantity; no clear&#xA;  distinction has been, or can be, drawn between spe-&#xA;  cies and well-marked varieties.&#xA;  (p. 425)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;On variation over the long run.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are the most interesting sections I found on the subject from my (quick and limited) searches. I hope you find them useful. However, this is only based on the first edition of &quot;&lt;em&gt;On the Origin of Species&lt;/em&gt;&quot;, and it is possible that it is is modified in later editions or that he touches upon this in his other writings. However, when looking at these particular passages in the sixth edition, I cannot see a major change in his thinking.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-12-19T17:54:44.057" LastActivityDate="2014-12-19T17:54:44.057" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21047" PostTypeId="2" ParentId="20937" CreationDate="2014-09-05T10:49:47.653" Score="2" Body="&lt;p&gt;A quick look in &lt;a href=&quot;http://rebase.neb.com/&quot; rel=&quot;nofollow&quot;&gt;REBASE&lt;/a&gt; finds 15999 type II restriction enzymes of which 616 are listed as having suppliers. Obviously some of these will share recognition and cut sites.&lt;/p&gt;&#xA;" OwnerUserId="4117" LastActivityDate="2014-09-05T10:49:47.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21048" PostTypeId="2" ParentId="19464" CreationDate="2014-09-05T12:40:05.993" Score="1" Body="&lt;p&gt;Raoul's gives sensible comments:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ventricle overloading not sensible&lt;/li&gt;&#xA;&lt;li&gt;retrosternal pain $\to$ myocardial ischemia&lt;/li&gt;&#xA;&lt;li&gt;other cause reminding retrosternal pain such as celiac disease:&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Posterior 1/3 of the septum is supplied by the following artery where any ischemia can weaken the isovolumetric contraction (TODO this has to be discussed much more carefully):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ischemia coronariaea posterioris created by problem in &lt;em&gt;ramus interventricularis posterior arteriae coronariae dextrae&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-05T21:39:01.437" LastActivityDate="2014-12-05T21:39:01.437" CommentCount="0" CommunityOwnedDate="2014-09-05T12:40:05.993" ContentLicense="CC BY-SA 3.0" />
  <row Id="21049" PostTypeId="2" ParentId="20303" CreationDate="2014-09-05T13:22:00.583" Score="3" Body="&lt;p&gt;If I understand your question correctly, I've seen this idea in many papers, sometimes stated clearly and sometimes in more implicit terms. After a quick look I found a paper which should be relevant as a starting point for you: &lt;a href=&quot;http://www.esajournals.org/doi/abs/10.1890/06-1672.1&quot; rel=&quot;nofollow&quot;&gt;Mayor et al. 2007. Spectrum of selection: new approaches to detecting the scale-dependent response to habitat. Ecology 88(7)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my mind, there are two questions here. First, to what extent will low population size in sub-optimal environments (leading to a smaller sample to work with) lead to more uncertain inferences of preferred habitat/substrate; basically saying that noise might swamp signal in sub-optimal environments. Second, to detect selection for a particular habitat/substrate, you must sample a wide enough range of environments so that you capture both preferred and unpreferred habitats and transitions between them. In the paper I linked to this issue is touched upon in the discussion:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Second, evidence of habitat selection depends on the scale of analysis. To understand scale dependence, investigations must encompass a spatial scope sufficiently wide to uncover scale domains of selection and the thresholds or transitions between them. In both cases, spatial scale is the empowering principle, and scaling continua are the means of application.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I've seen similar ideas as this show up in papers on habitat choice in birds living in agricultural landscapes as well, where some species are often found in rather poor environments (because these environments are common). Looking at habitat preferences only in these environments might then give a misleading view, since individual choices are constrained. Also relevant, even if not mentioned in your question, is the concept of &lt;em&gt;maladaptive habitat selection&lt;/em&gt; (sometimes called &lt;a href=&quot;http://en.wikipedia.org/wiki/Ecological_trap&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;ecological traps&lt;/em&gt;&lt;/a&gt;), where you can have situations where species use environmental cues that used to indicate high fitness habitats, but might now result in maladaptive choices, see e.g. &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs10336-007-0226-1&quot; rel=&quot;nofollow&quot; title=&quot;Pärt et al. 2007. Empirical evidence for ecological traps: a two-step model focusing on individual decisions.  Journal of Ornithology 148(2)&quot;&gt;Pärt el al. (2007)&lt;/a&gt;. However, in this case you will still have a clear preference/selection (as in your high variability environment), the problem being that the organism is selecting suboptimal habitats from a fitness perspective.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-09-23T11:25:26.750" LastActivityDate="2014-09-23T11:25:26.750" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21050" PostTypeId="1" CreationDate="2014-09-05T15:58:52.813" Score="4" ViewCount="83" Body="&lt;p&gt;What non-SDS buffer can I use to isolate protein from mammalian cells? The protein is intended for testing electron transport chain complexes. &lt;/p&gt;&#xA;" OwnerUserId="8994" LastActivityDate="2014-09-05T17:19:55.823" Title="Protein Isolation from mammalian cells" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21051" PostTypeId="2" ParentId="21050" CreationDate="2014-09-05T17:19:55.823" Score="5" Body="&lt;p&gt;Short answer - you will need to use a nonionic detergent. These will dissolve lipid membranes but leave most protein complexes intact, and many proteins in active form.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However &lt;a href=&quot;http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=14572924&quot;&gt;there are many of these available&lt;/a&gt; and finding the right one for a particular job is a black art.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The usual approach is to start off with something widely-used and not too expensive like Triton X-100. Detergents with glycoside head groups are also widely-used but tend towards the expensive.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-09-05T17:19:55.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21053" PostTypeId="1" AcceptedAnswerId="21055" CreationDate="2014-09-05T20:32:59.773" Score="2" ViewCount="101" Body="&lt;p&gt;While reading my Molecular Bio textbook, I came across a sentence that stated that NMR cannot be used on large RNA molecules to determine their structure. Why is this? Is it because RNA is single stranded?&lt;/p&gt;&#xA;" OwnerUserId="9002" LastActivityDate="2014-09-05T20:51:31.223" Title="Why can't NMR be used on large RNA molecules?" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21055" PostTypeId="2" ParentId="21053" CreationDate="2014-09-05T20:51:31.223" Score="3" Body="&lt;p&gt;RNA usually has pretty complex structures. What causes the problem with NMR however is that large RNAs, such as mRNAs, don't have 1 structure, they have a population of possible secondary structures, and even if small parts of the RNA always have the same local structure, the overall molecule will occupy a variety of forms. The NMR will see a population of structures and won't be able to get good signal. DNA and RNA seem like tempting targets for NMR because the phosphorus in the backbone is NMR active, potentially allowing for backbone structure determination, but this only works on short pieces of RNA that adopts a single conformation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately I don't have sources to cite, only a couple semesters of NMR courses and a year of in vitro transcription of mRNA.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-09-05T20:51:31.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21057" PostTypeId="2" ParentId="21026" CreationDate="2014-09-05T23:21:04.663" Score="2" Body="&lt;p&gt;I just took a quick look.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These classes of enzymes are important to a family of lipid based molecules which perform intra and intercellular signalling with a lot of medical importance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Epoxygenase&quot; rel=&quot;nofollow&quot;&gt;Epoxygenases can create epoxides of arachidonic acid&lt;/a&gt;,  which can modulate cell proliferation.  Arachidonic acid is a well known second messenger in many tissues in the cell, so these enzymes clearly would affect many signalling pathways. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cyclooxygenases (COX) enzymes are such &lt;a href=&quot;http://en.wikipedia.org/wiki/Cyclooxygenase&quot; rel=&quot;nofollow&quot;&gt;important mediators of inflammation signalling that they are the primary targets of aspirin and other Non steroidal anti-inflammatory drugs&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lipoxygenases oxygenate compounds such as prostaglandins which are downstream from aranchidonic acid (as does COX).&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-09-05T23:21:04.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21058" PostTypeId="1" AcceptedAnswerId="24673" CreationDate="2014-09-05T23:23:09.077" Score="10" ViewCount="1021" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Importance of the additive genetic variance&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As stated &lt;a href=&quot;https://biology.stackexchange.com/questions/14957/fishers-fundamental-theorem-of-natural-selection&quot;&gt;here&lt;/a&gt;, the fundamental theorem of Natural Selection (NS) by Fisher says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The rate of increase in the mean fitness of any organism at any time ascribable to NS acting through changes in gene frequencies is exactly equal to its genetic variance in fitness at that time.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;NS reduces the additive genetic variance&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, NS reduces additive genetic variance (discussion about the origin of this knowledge can be found &lt;a href=&quot;https://biology.stackexchange.com/questions/21021/did-darwin-ever-reach-the-conclusion-that-selection-will-remove-variation&quot;&gt;here&lt;/a&gt;). The genetic variance of a population for multiple traits is best described by the G-matrix (&lt;a href=&quot;https://biology.stackexchange.com/questions/10894/what-is-needed-for-a-g-matrix&quot;&gt;here&lt;/a&gt; is a post on the subject).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;What is a G-matrix&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A G-matrix is a matrix where additive genetic variance of trait $i$ can be found at position $m_{ii}$. In other words, the diagonal contains the additive genetic variance for all traits. The other positions $m_{ij}$, where $i≠j$ contains the additive genetic covariance between the traits $i$ and $j$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can one model how the G-matrix changes over time because of selection (assuming no mutation)?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2016-08-17T08:49:06.987" Title="How does Natural Selection shape Genetic Variation?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;population-dynamics&gt;&lt;theoretical-biology&gt;&lt;quantitative-genetics&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21061" PostTypeId="2" ParentId="21028" CreationDate="2014-09-05T23:57:23.587" Score="1" Body="&lt;p&gt;In &lt;a href=&quot;http://global.oup.com/academic/product/phenotypic-integration-9780195160437;jsessionid=0FCBD8AF74A8E07DD8250E14F740E73B?cc=ch&amp;amp;lang=en&amp;amp;&quot; rel=&quot;nofollow&quot;&gt;Pigliucci (2004)&lt;/a&gt; (repeated in &lt;a href=&quot;http://www.annualreviews.org/doi/pdf/10.1146/annurev.ecolsys.37.091305.110224&quot; rel=&quot;nofollow&quot;&gt;Hansen (2006)&lt;/a&gt;) the mutational variance is defined as being the new additive genetic variance entering in the population each generation due to mutations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In consequence the mutational variance is not define at the level of the mutation in the sense that we do not care about how many mutations yield to this new genetic variance. So none of the suggestions of possible answers in the OP's question is correct.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-09-08T01:37:06.813" LastActivityDate="2014-09-08T01:37:06.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21062" PostTypeId="1" AcceptedAnswerId="21063" CreationDate="2014-09-06T00:25:21.330" Score="3" ViewCount="1348" Body="&lt;p&gt;Sometimes at night when I'm inside with a light on, I can hear (I'm sure) moths fly into the window, and it's so loud I can sometimes hear it over the TV from the other side of the room.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since they're so small, how do they hit the window hard enough to cause such a big noise and not die?&lt;/p&gt;&#xA;" OwnerUserId="9106" LastActivityDate="2015-01-25T22:54:32.387" Title="Why do moths not die when they fly into a window?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21063" PostTypeId="2" ParentId="21062" CreationDate="2014-09-06T01:02:59.060" Score="4" Body="&lt;p&gt;Simply because their body mass is small. It's the same as if an ant falls off from the roof of a building. It will suffer no harm because the speed of its fall will be very slow, but try the same yourself and you will surely die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More scientifically, it's a question of kinetic energy: $E_{kinetic}=\frac{1}{2}\times mv^2$&#xA;You can see from this formula that if mass is small, then kinetic energy will also be small.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second reason is that although insects are small in size, the materials they are made of are extremely resistant comparatively to their size. Therefore, the bug will survive when it meets the window pane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An interesting corollary is that the common saying &quot;if an ant was the size of a human, it could carry a locomotive, because it can carry many times its weight&quot; is totally wrong. If an ant the size of a man tried that, it would break its back just like you and me, because material resistance is not proportional to size.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2015-01-25T22:54:32.387" LastActivityDate="2015-01-25T22:54:32.387" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21067" PostTypeId="1" AcceptedAnswerId="21074" CreationDate="2014-09-06T05:33:57.953" Score="1" ViewCount="51" Body="&lt;p&gt;In a microarray, which one is called a target and which one is the probe? the one that is added later , is that the probe or the one present in the slots of the microarray, that is the probe?&lt;br&gt;&#xA;(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if the question seems to silly, forgive me)&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="8835" LastEditDate="2014-09-06T06:07:06.963" LastActivityDate="2014-09-06T17:59:45.753" Title="Microarray probe and target" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;bioinformatics&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21069" PostTypeId="1" AcceptedAnswerId="21096" CreationDate="2014-09-06T05:52:52.270" Score="2" ViewCount="89" Body="&lt;p&gt;Can someone please tell me what is Degenerate alignment analysis? Could not find a good article on the internet that could help me understand what it means?&lt;br&gt;&lt;br&gt;&#xA;(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="8835" LastEditDate="2014-09-06T06:07:25.643" LastActivityDate="2014-09-07T14:06:59.227" Title="Degenerate Alignment Analysis" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;bioinformatics&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21070" PostTypeId="1" AcceptedAnswerId="21105" CreationDate="2014-09-06T06:23:06.580" Score="2" ViewCount="6095" Body="&lt;p&gt;Complementarity determining regions (CDRs) are part of the variable domains in immunoglobulins (antibodies) and T cell receptors, generated by B-cells and T-cells respectively, where these molecules bind to their specific antigen. (source: WIKI, with a minor change)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now does this mean that this CDR is the paratope? As it has the same functionality as paratope, to bind to epitope of the antigen. So is CDR a type of paratope?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="416" LastEditDate="2015-11-01T11:41:07.753" LastActivityDate="2015-11-01T18:29:47.373" Title="Complementarity Determining Regions (CDRs)" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;immunology&gt;&lt;antibody&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21071" PostTypeId="1" CreationDate="2014-09-06T07:32:01.293" Score="3" ViewCount="391" Body="&lt;p&gt;I came across the following sentence while reading the paper: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nanchen, Annik, et al. &quot;Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose limitation in Escherichia coli.&quot; Journal of bacteriology 190.7 (2008): 2323-2330.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These in vivo flux data are qualitatively corroborated by in vitro&#xA;  enzyme activities in the Crp and Cya mutants, which exhibited&#xA;  significantly reduced activity of the key glyoxylate shunt key enzyme isocitrate lyase ...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My understanding of &lt;em&gt;in vitro&lt;/em&gt; experiments is: those performed in artificial set up , possibly only with part of the cell, where the complete cell is not potentially alive. For, example we can test the inhibition activity of a particular enzyme by a metabolite. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the paper cited, experiments from which flux are derived (chemostat) are considered &lt;em&gt;in vivo&lt;/em&gt;. What would it mean to say the enzyme activity was tested &lt;em&gt;in vitro&lt;/em&gt; on the mutant? When we say the response of the a single gene knock out mutant, the cell should be intact except for lacing one gene, which would mean that the response is &lt;em&gt;in vivo&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please help me if I am misunderstanding some thing.&lt;/p&gt;&#xA;" OwnerUserId="1800" LastActivityDate="2014-09-07T16:19:51.840" Title="What does it mean to perform in vitro experiments with mutant bacteria?" Tags="&lt;microbiology&gt;&lt;enzymes&gt;&lt;experimental-design&gt;&lt;ecoli&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21072" PostTypeId="2" ParentId="21071" CreationDate="2014-09-06T09:00:40.800" Score="1" Body="&lt;p&gt;It is possible to conduct an in vitro experiment with cell extracts. Meaning that you break up the cells and put their pieces into a reaction glass and do your experiment. It is assumed that the cell molecules (enzyme, sugar or cofactors) will still carry out their functions even though the cell is no more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, you used the mutant to produce the enzymes you need (minus the knock-outed one) to set up the desired reaction requirements. Once the products are there, you don't need the producers alive or intact any more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check the method part in your paper and see whether it is so.&lt;/p&gt;&#xA;" OwnerUserId="3762" LastActivityDate="2014-09-06T09:00:40.800" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21074" PostTypeId="2" ParentId="21067" CreationDate="2014-09-06T12:53:51.033" Score="1" Body="&lt;p&gt;In an RNA microarray, a hybridization event between a probe and target sequence would indicate a presence of the transcript within the sample. The probes are oligonucleotide sequences found on the microarray chip. The target sequences are representative of the entire transcriptome. The targets are found within your biological sample and have gone through many rounds of amplification in addition to labeling with fluorescent dyes. The fluorescently labeled target when bound to the probe can then be detected using a scanning laser. &lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-09-06T17:59:45.753" LastActivityDate="2014-09-06T17:59:45.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21075" PostTypeId="1" CreationDate="2014-09-06T15:57:59.337" Score="4" ViewCount="16561" Body="&lt;p&gt;Why would ethanol show up in a blood test if a person had not been drinking alcohol in many years. What are other reasons for showing ethanol?&lt;/p&gt;&#xA;" OwnerUserId="9110" LastEditorUserId="107" LastEditDate="2014-09-10T18:13:23.087" LastActivityDate="2016-02-19T06:04:11.867" Title="Why does a blood test show ethanol when no alcohol was consumed?" Tags="&lt;physiology&gt;&lt;pathology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21076" PostTypeId="1" CreationDate="2014-09-06T16:37:11.400" Score="2" ViewCount="14974" Body="&lt;p&gt;At first I thought it may be related to physics.  You know, in one half of the day, the gravity changes, and the scale shows a different weight than the other.  Then at night, gravity intensifies, and you become slightly heavier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I'm a bit skeptical about that. Is that true?  That it's somehow related to gravitational fields? &lt;/p&gt;&#xA;" OwnerUserId="9111" LastEditorUserId="6422" LastEditDate="2014-09-06T16:48:58.520" LastActivityDate="2016-01-24T03:23:18.430" Title="Why do we weigh less in the morning?" Tags="&lt;metabolism&gt;&lt;circadian-rhythms&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21077" PostTypeId="2" ParentId="21075" CreationDate="2014-09-06T16:43:54.203" Score="4" Body="&lt;p&gt;There are some situations when ethanol-like compounds can be present in the blood stream:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] exposure to hand sanitizers, after shave lotions, perfumes, medications, hygiene products, cosmetics, foods [...]  Uncontrolled diabetes mellitus can cause false positive alcohol tests. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Source:&lt;/em&gt;&lt;/strong&gt; Dr. Kokil Mathur. Answer on: &lt;em&gt;&lt;a href=&quot;http://www.medhelp.org/posts/Undiagnosed-Symptoms/False-Positives-for-blood-alcohol-content/show/1437256&quot; rel=&quot;nofollow&quot;&gt;False-Positives for blood alcohol content.&lt;/a&gt;&lt;/em&gt; Available from MedHelp forums.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other causes as pointed on &lt;a href=&quot;http://www.ehow.com/info_8345134_causes-false-positive-alcohol-test.html&quot; rel=&quot;nofollow&quot;&gt;eHow.com&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;low calorie diets&lt;/li&gt;&#xA;&lt;li&gt;gasoline, paints, lacquers&lt;/li&gt;&#xA;&lt;li&gt;lower hematocrit values&lt;/li&gt;&#xA;&lt;li&gt;diabetes mellitus&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-09-06T16:43:54.203" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21078" PostTypeId="2" ParentId="21076" CreationDate="2014-09-06T17:03:14.627" Score="5" Body="&lt;p&gt;There is indeed a slight weight variation during the day. About 2 - 4 lbs (approx. 1 - 2 kg) [1, 2].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some causes are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;water loss &lt;em&gt;through respiration, perspiration or urination&lt;/em&gt; [1].&lt;/li&gt;&#xA;&lt;li&gt;the relative long period without eating and drinking [2].&lt;/li&gt;&#xA;&lt;li&gt;metabolic processing of food and drinks during sleep.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Cindy Banyai. &lt;a href=&quot;http://www.livestrong.com/article/483853-how-much-can-weight-fluctuate-from-morning-to-night/&quot;&gt;http://www.livestrong.com/article/483853-how-much-can-weight-fluctuate-from-morning-to-night/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.weightlossforall.com/weighing-less-morning.htm&quot;&gt;http://www.weightlossforall.com/weighing-less-morning.htm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-09-06T17:03:14.627" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21079" PostTypeId="1" AcceptedAnswerId="21091" CreationDate="2014-09-06T17:32:47.957" Score="2" ViewCount="309" Body="&lt;p&gt;I wonder why bacteria and fungi cannot develop resistance and mutate agains essential oils?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, some fungi get killed by oregano oil.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Being not a biologist, I hope my question is not so stupid..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="9112" LastEditorUserId="1320" LastEditDate="2014-09-07T08:42:40.590" LastActivityDate="2014-09-07T08:42:40.590" Title="Why is it that bacteria and fungi cannot develop resistance against essential oils?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21080" PostTypeId="1" AcceptedAnswerId="21087" CreationDate="2014-09-06T19:15:36.630" Score="2" ViewCount="9603" Body="&lt;p&gt;I am writing the section about history of DNA sequencing in the introduction chapter and after reading quite a few research papers, I am still confused about them. Here I compile some questions to make sure that I understand it correctly.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Is second generation sequencing the same as next generation sequencing?&lt;/li&gt;&#xA;&lt;li&gt;Is Sanger sequencing the first generation?&lt;/li&gt;&#xA;&lt;li&gt;As of today, is there any commercial 3rd generation sequencing technology in use (or is it still in development)?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;If there is any paper reference that could explain all of the above then it would be really great.&lt;/p&gt;&#xA;" OwnerUserId="8612" LastEditorUserId="540" LastEditDate="2014-09-07T01:44:52.340" LastActivityDate="2014-09-08T16:33:22.513" Title="What is the difference between second and third generation sequencing" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21081" PostTypeId="1" AcceptedAnswerId="21083" CreationDate="2014-09-06T19:29:37.070" Score="1" ViewCount="11539" Body="&lt;p&gt;On another SE site, there was a comment that told me something  about biology that I already know:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;A man left murdered in the fields would soon have a flock of crows mobbing his fragrant corpse.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I don't quite understand why. Is it the &quot;death&quot; part,the fact that someone was injured/bleeding or just the fact the he was immobilized,that would attract the crows?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is suppose you tied up someone and left him on the field. Would that attract the crows?&#xA;Suppose this person fell down, was bleeding, and immobile, but not seriously injured? Or is it the death part?&lt;/p&gt;&#xA;" OwnerUserId="9113" LastEditorUserId="1320" LastEditDate="2014-09-07T08:17:37.647" LastActivityDate="2014-09-07T08:17:37.647" Title="What would cause crows to be attracted to a human body?" Tags="&lt;death&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21082" PostTypeId="1" AcceptedAnswerId="21088" CreationDate="2014-09-06T20:09:33.860" Score="2" ViewCount="1135" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RARDM.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hi guys, looking at your average neuron, it is very difficult for me to imagine how this could be translated into a core-conductor model&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oNTnz.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the neuron above, where would be the intracellular space and where would be the extracellular space? Also, where is this membrane we are talking about?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastActivityDate="2014-09-07T02:35:55.887" Title="How does core-conductor model correspond to an actual neuron?" Tags="&lt;cell&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21083" PostTypeId="2" ParentId="21081" CreationDate="2014-09-06T21:23:04.560" Score="3" Body="&lt;p&gt;I think the key is &lt;em&gt;&quot;his fragrant corpse.&quot;&lt;/em&gt; When an animal dies and begins to rot, a number of quite smelly chemicals are given off, including &lt;a href=&quot;http://en.wikipedia.org/wiki/Putrescine&quot; rel=&quot;nofollow&quot;&gt;putrescine&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Cadaverine&quot; rel=&quot;nofollow&quot;&gt;cadaverine&lt;/a&gt;. Crows and other carrion birds like vultures are probably very sensitive to these compounds, rather like sharks are to the smell of blood.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-09-06T21:23:04.560" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21085" PostTypeId="2" ParentId="21081" CreationDate="2014-09-06T23:20:41.427" Score="2" Body="&lt;p&gt;Carrion birds, such as crows and vultures, eat dead animals. As a whole, it's possible that they detect carrion by the smell or visually.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Crows specifically are omnivorous and predatory in addition to being carrion scavengers. I suspect that they will try to eat anything that doesn't fight back, especially if they are hungry enough and there is exposed flesh. I don't know if crows prefer dead meat or fresh meat, but they certainly eat both.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Suppose you tied up someone and left him on the field. Would that attract the crows?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The crows would probably be attracted because they are curious and want to check out the new, unfamiliar object. They would certainly be able to tell that you are alive by body temperature and sounds of breathing or heartbeats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think they will be hesitant to eat you because live humans are unfamiliar to them. They will probably find other carrion nearby and eat that instead. If you stayed unconscious for several days, the crows would get used to you, lose their fear, and eventually one would go for a taste. Once the first gets a bite or two, and you fail to retaliate, I think the others will quickly join in.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Suppose this person fell down, was bleeding, and immobile, but not seriously injured? Or is it the death part?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The fact that they can see and smell the meat, and don't have to bother piercing the skin, would make you more attractive to the crows (supposedly, they like to go for things like eyeballs even on live prey).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, even if immobile, a conscious human could struggle (shake their head, yell, roll around) which would startle the crows and keep them at bay for a time. If you can't actually interfere with them pecking you, I'm sure they would eventually get over their fear and attack you. If you can physically swat or shake off the crows, they'd just wait for you to get tired or die, which probably won't take too long given the injuries.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In conclusion,&lt;/strong&gt; I don't think it's impossible for crows to eat bits of a live human, whether conscious or not. However, for various reasons, it would probably take a few days for them to actually get around to it. If you are not dead by this point, larger animals would show up and attack you, and crows would end up picking at the scraps.&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-09-06T23:30:12.643" LastActivityDate="2014-09-06T23:30:12.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21086" PostTypeId="2" ParentId="21076" CreationDate="2014-09-06T23:21:12.220" Score="0" Body="&lt;p&gt;There is only one way to gain weight, consume things. Thus after any period of time not consuming anything (i.e. sleeping) we must necessarily weigh &amp;lt;= what we weighted at the start of that time period. Add in respiration, and that becomes a strict inequality!&lt;/p&gt;&#xA;" OwnerUserId="9115" LastActivityDate="2014-09-06T23:21:12.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21087" PostTypeId="2" ParentId="21080" CreationDate="2014-09-07T00:08:14.270" Score="7" Body="&lt;p&gt;I'm assuming you mean DNA sequencing (excluding things like RNA-seq).&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Is Sanger sequencing the first generation?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19997069&quot; rel=&quot;nofollow&quot;&gt;Metzker 2010&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The automated Sanger method is considered as a &quot;first-generation&quot; technology&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Some of the technology that was in development when this review was written is no longer in development, but this is still an excellent review and a great place to start.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Is second generation sequencing the same as next generation sequencing?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Also from Metzker 2010:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;and newer methods are referred to as next-generation sequencing (NGS).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The &quot;newer methods&quot; in the review are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Emulsion PCR based like Roche/454&lt;/li&gt;&#xA;&lt;li&gt;Solid phase amplification like Illumina/Solexa&lt;/li&gt;&#xA;&lt;li&gt;Single molecule like Helicos BioSciences and Pacific Biosciences&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;As of today, is there any commercial 3rd generation sequencing technology in use (or is it still in development)?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The development of single molecule methods (third item in the above list) has historically taken longer than the other two, so &lt;a href=&quot;http://genomena.com/technology-how-we-look-at-dna/third-generation-genome-sequencing/&quot; rel=&quot;nofollow&quot;&gt;sometimes&lt;/a&gt; they are &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0958166914000202&quot; rel=&quot;nofollow&quot;&gt;referred to&lt;/a&gt; as third generation. However, note how Metzker above considers them all &quot;next-gen&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A recent &lt;a href=&quot;http://hmg.oxfordjournals.org/content/19/R2/R227.short&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; from PacBio itself makes the distinction of halting:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Second-generation sequencing (SGS): Sequencing of an ensemble of DNA molecules with wash-and-scan techniques. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Third-generation sequencing (TGS): Sequencing single DNA molecules without the need to halt between read steps (whether enzymatic or otherwise). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Ultimately, I think the &quot;generations&quot; are more useful to make the &quot;Sanger vs. Not Sanger&quot; distinction. Sanger sequencing is very different than next-gen in terms of what kind of experiment you can do and what sort of data you obtain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Past that, the number of a generation is more of a marketing term. For instance, at the bottom of the PacBio paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Conflict of Interest statement. All authors are employees of Pacific Biosciences and own stock in the company.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In practice, PacBio competes with second generation platforms. It is in their interest to say their technology is on &quot;another level&quot; compared to what's available on the market, but in practice, this is debatable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyhow, to answer your question:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;There is a technology in use and commercially available which has been referred to as third gen (PacBio)&lt;/li&gt;&#xA;&lt;li&gt;There was a technology in development that falls under most definitions of third gen (Helicos), which went bankrupt in 2012&lt;/li&gt;&#xA;&lt;li&gt;There is a technology in development (ON MinION) that is single-molecule based and was introduced after PacBio, so if PacBio is third generations, so is MinION (although the MinION is apparently very different from PacBio)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-09-08T16:33:22.513" LastActivityDate="2014-09-08T16:33:22.513" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="21088" PostTypeId="2" ParentId="21082" CreationDate="2014-09-07T01:26:19.640" Score="2" Body="&lt;p&gt;What may be confusing is that the myelin is wrapped around the membrane of the axon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The easiest way to see this is in cross-section:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tvFNP.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://commons.wikimedia.org/w/index.php?title=User:Ralph_Walterberg&amp;amp;action=edit&amp;amp;redlink=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The axon is indicated by #1 in the diagram and the myelin sheath is #4&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The intracellular space (as represented by the horizontal resistors in the case of your model of the axon) is the fluid, replete with ions, that is contained within the membrane of the axons.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the nodes of Ranvier, there is a break in the myelin sheath, exposing the underlying membrane of the axon.  In membrane in those gaps of the sheath, there are sodium channels (voltage gated) and potassium channels that facilitate the influx and efflux of ions that &quot;refresh&quot; the action potential as it travels down the axon.  The extracellular space is simply the milieu of fluid in the space between the axon and any adjoining cells.  For the purposes of analyzing the currents of the neuron, the sodium and potassium ions (and the conductances of the channels) are all that you really need to be concerned with. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is confusing about your diagram is that it represents the conductance -- the inverse of the resistance of the channels -- of the channels (inwards and outwards) as a single vertical resistor in between the horizontal resistors of the intracellular membrane. This oversimplification is handy when doing the cable theory-type analysis, but it betrays the actual physiology of the neuron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a model standpoint, I'm breaking all the rules here, but you can think of things like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ytfjz.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where one &quot;rung&quot; of your resistor ladder has $r_m$ broken out into the 2 components and drawn differently.&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="57" LastEditDate="2014-09-07T02:35:55.887" LastActivityDate="2014-09-07T02:35:55.887" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21089" PostTypeId="1" CreationDate="2014-09-07T01:42:41.930" Score="1" ViewCount="141" Body="&lt;p&gt;This year, &lt;a href=&quot;https://www.nanoporetech.com/&quot; rel=&quot;nofollow&quot;&gt;Oxford Nanopore MinION&lt;/a&gt; has been shipped to some researchers for testing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The advantage of a table-top sequencer for diagnostics and personalized medicine is obvious. Similarly, research &quot;in the field&quot; and forensic science could be aided greatly by this device. My question is about the applications in the research lab.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does MinION do that a well-equipped lab with access to Sanger and next-gen sequencing cannot already do?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How well does the MinION work? How powerful is it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What important scientific discoveries are being made using the MinION?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the website of Oxford Nanopore has a list of publications, the most recent one is from 2013. This is before the early access program began - I am particularly interested in developments since February 2014.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-09-07T01:42:41.930" Title="What good is the MinION?" Tags="&lt;dna-sequencing&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21091" PostTypeId="2" ParentId="21079" CreationDate="2014-09-07T08:41:33.017" Score="3" Body="&lt;p&gt;Here are my thoughts on this, taking your example, oregano oil.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The active anti-microbial ingredient in this essential oil is &lt;a href=&quot;http://en.wikipedia.org/wiki/Carvacrol&quot; rel=&quot;nofollow&quot;&gt;carvacrol&lt;/a&gt;. The WP article states that it probably acts by disruption of the membrane.&#xA; There appear to be no examples of carvacrol resistance, as suggested by your question. In mammals the compound is detoxified in the liver via esterification to increase solubilty, thus promoting excretion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that we can create a situation with a strong selective pressure for the development of resistance in a microbe, what would that resistance look like? If the carvacrol does indeed disrupt the membrane, then it is probably useless to develop intracellular degradation - what is needed is the secretion of an enzyme that is able to inactivate the compound, analogous to the &amp;beta;-lactamases that inactivate antibiotics like penicillin (which also has an extracellular mode of activity).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, unlike &amp;beta;-lactams, carvacrol is insoluble in water. This suggests to me that most of the time, in the natural environment, free-living bacteria will not experience significant levels of the compound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary - it may be difficult to evolve a system for the degradation of a lipophilic compound, and because it is lipophilic it may be that it is rarely a problem for bacteria unless they are being subjected to laboratory tests for antimicrobial activity.  &lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-09-07T08:41:33.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21092" PostTypeId="2" ParentId="21076" CreationDate="2014-09-07T08:58:32.400" Score="6" Body="&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/channel/UCHnyfMqiRRG1u-2MsSQLbXA&quot; rel=&quot;nofollow&quot;&gt;Veritasium&lt;/a&gt; created &lt;a href=&quot;https://www.youtube.com/watch?v=lL2e0rWvjKI&quot; rel=&quot;nofollow&quot;&gt;an excellent video just on this topic&lt;/a&gt;, which I would recommend watching, but will summarize here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A common misconception is that we lose weight when we digest food or burn calories. Keep in mind that that broken down food and those calories&lt;code&gt;*&lt;/code&gt; aren't &quot;going anywhere&quot;, so technically you shouldn't loose any mass (unless you get rid of the molecules by going to the restroom).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in the &quot;informal&quot; tests done by Derek Muller, &lt;strong&gt;he lost about 250 grams each night&lt;/strong&gt;. Since during the night you sweat (which evaporates or gets absorbed into the sheets and blankets), he estimated that about &lt;strong&gt;150 grams was lost through perspiration and breathing out water vapor&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The more surprising loss of mass, was 0.012 grams of carbon lost with each breath when breathing in oxygen, and then breathing out carbon dioxide. Although this seems like a tiny loss, assuming you breathe in and out about 7,680 times each night, that tiny mass loss adds up to almost &lt;strong&gt;100 grams of weight loss through breathing alone&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess health magazines should start running articles like &lt;em&gt;&quot;Top way to lose more weight? Researchers say breathe more!&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&#xA;" OwnerUserId="6166" LastEditorUserId="20846" LastEditDate="2016-01-24T03:23:18.430" LastActivityDate="2016-01-24T03:23:18.430" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21093" PostTypeId="1" AcceptedAnswerId="21098" CreationDate="2014-09-07T09:40:36.637" Score="2" ViewCount="5754" Body="&lt;p&gt;Just curious, does there exist a medical condition in which a patient is advised not to or simply cannot cut their (head) hair?&lt;/p&gt;&#xA;" OwnerUserId="3141" LastActivityDate="2019-08-21T05:08:56.750" Title="Is there a medical condition in which you can't cut your hair?" Tags="&lt;hair&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21094" PostTypeId="1" CreationDate="2014-09-07T11:42:46.123" Score="5" ViewCount="89" Body="&lt;p&gt;I have seen peer-reviewed papers mentioning the daily changes in gut microbiota composition according to dietary changes. See for example this paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://genomebiology.com/2014/15/7/R89&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://genomebiology.com/2014/15/7/R89&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is related to this one:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/1999/relationship-between-our-microbiome-and-personalized-nutrition/2000#2000&quot;&gt;Relationship between our microbiome and personalized nutrition&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If, according to these recently published scientific results, it takes a day to change the gut microbiota to adjust to the dietary change, and the presence of certain microbes makes food assimilation more effective,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this mean that alternating a protein-rich meat and dairy diet with a carbs-rich diet every day would make our microbiota switch daily and not have time to increase calorie uptake?&lt;/p&gt;&#xA;" OwnerUserId="658" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2020-10-20T22:02:35.253" Title="Can you change your gut microbiota by changing your diet? Would that affect calorie uptake?" Tags="&lt;microbiology&gt;&lt;metabolism&gt;&lt;diet&gt;&lt;microbiome&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21095" PostTypeId="2" ParentId="21071" CreationDate="2014-09-07T13:26:48.953" Score="2" Body="&lt;p&gt;&lt;strong&gt;Answer clarified&lt;/strong&gt; based on comment by @DurgaDatta&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What would it mean to say the enzyme activity was tested in vitro on the mutant? When we say the response of the a single gene knock out mutant, the cell should be intact except for lacing one gene, which would mean that the response is in vivo.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The knockouts were performed inside the &lt;em&gt;E. coli&lt;/em&gt; cells and, as you noted, the flux measurements were in vivo (in the cell) inside of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemostat&quot; rel=&quot;nofollow&quot;&gt;chemostat culture&lt;/a&gt;. They identified two mutants, Crp and Cya, that yielded much higher biomass. On page 2326, the authors write, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the Cya (encoding adenylate cyclase) and Crp mutants that lack the cAMP-CRP complex, in vivo glyoxylate shunt activity was essentially abolished....&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am not familiar with these genes but the implication is that the wild type regulators have the cAMP-CRP complex. Because this complex is missing from the mutants, the enzymes no longer function the same. However, it would be possible that some type of interaction of the mutants with other enzymes caused the observed result in vivo. They therefore verified the result by extracting the Crp and Cya mutant enzymes from the cells and assaying their enzyme activity in isolation from the other enzymes (in vitro). The technique is explained in the answer by @dgg32.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your comment to that answer, you ask.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;what difference does it make whether the enzyme was taken from wild-type or the mutant one, since it is the same enzyme?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is the same enzyme in name but not in function. The mutant enzyme lacks the cAMP-CRP complex so it cannot perform the same function as the wild type. In vitro, they first showed that mutant enzyme activity was altered relative to the wild type.  They then added the wild type enzyme to the in vitro test and restored normal wild type activities:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To verify that the observed changes were not due to polar effects of the still present marker gene or secondary-site mutations, we complemented the Crp mutant with the plasmid-based Crp gene and cultivated the complemented mutant under the same chemostat conditions. In vitro enzyme activities demonstrated that both the isocitrate lyase and isocitrate dehydrogenase activities were restored to the wild-type level&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, this was performed inside the chemostat cultures but only with the enzymes, not the living &lt;em&gt;E. coli&lt;/em&gt; cells.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-09-07T16:19:51.840" LastActivityDate="2014-09-07T16:19:51.840" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21096" PostTypeId="2" ParentId="21069" CreationDate="2014-09-07T14:06:59.227" Score="2" Body="&lt;p&gt;First, degeneracy in a basic sense refers to redundancy of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_code#RNA_codon_table&quot; rel=&quot;nofollow&quot;&gt;codons in the genetic code&lt;/a&gt;.  For example, the amino acid proline is coded for by one of four codons: CCA, CCC, CCG and CCU. The third codon position (the third letter in each group of three) is called four-fold degenerate because it can change without affecting the coding for proline. Phenylalanine is two-fold degenerate because it is coded for by UUC and UUU.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this does not account for the alignment part of your question. Without more specific information (such as a reference you saw), I can't be certain of your intent but this paper by &lt;a href=&quot;http://genome.cshlp.org/content/18/4/571.full&quot; rel=&quot;nofollow&quot;&gt;Morin et al. (2008)&lt;/a&gt; may be helpful. They had a series of small RNA sequences (each about 24 nucleotides long). They wanted to identify DNA sequences in the genome of Lodgepole pine  (&lt;em&gt;Pinus contorta&lt;/em&gt;) and rice (&lt;em&gt;Oryiza sativa&lt;/em&gt;). To accomplish this goal, they used degeneracy alignment. Here's the relevant section from their methods:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;altered to allow searches against genomic sequence. Alignments were kept if they were no shorter than L − 3, where L is the query sequence length. No more than a total of three mismatches or insertions/deletions were allowed within the aligned region.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Their approach was to find genomic sequences that correspond to the small RNAs. They allowed for some degeneracy, either in the genome or the RNA. The sequences could differ in length by no than three nucleotides or mismatches (an A in the query sequence but a C in the target sequence instead of a T; I'm assuming the query is RNA and the target is the genomic DNA). Their degeneracy alignment allowed for a small amount of freedom in identifying potential matches of conserved RNA clusters (high similarity) in the genomes of distantly related plant species. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Morin, R.D. et al. 2008. Comparative analysis of the small RNA transcriptomes of &lt;em&gt;Pinus contorta&lt;/em&gt; and &lt;em&gt;Oryza sativa&lt;/em&gt;. Genome Research 18: 571-584. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-09-07T14:06:59.227" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21097" PostTypeId="2" ParentId="21093" CreationDate="2014-09-07T15:41:21.927" Score="2" Body="&lt;p&gt;Alopecia and balding, these individual experience hair loss, thus nothing to cut &lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-09-07T15:41:21.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21098" PostTypeId="2" ParentId="21093" CreationDate="2014-09-07T18:12:29.290" Score="2" Body="&lt;p&gt;An phobia or OCD released to appearance might lead someone to face dire situations when their hair is cut even death if the fear leads to a heart attack.&lt;/p&gt;&#xA;" OwnerDisplayName="user1357" LastActivityDate="2014-09-07T18:12:29.290" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21100" PostTypeId="1" AcceptedAnswerId="21958" CreationDate="2014-09-07T20:34:48.950" Score="0" ViewCount="273" Body="&lt;p&gt;Please see the following picture:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5DyZn.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my book, the author claims that these chromosomes are in metaphase (a metaphase stopped by cholchicin).&#xA;I don't understand why they don't have two chromatids...A chromosome looks, by everything I've learned, like TWO chromatids (&lt;a href=&quot;http://i60.photobucket.com/albums/h1/GameMaster57/Chromosomestructure.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://i60.photobucket.com/albums/h1/GameMaster57/Chromosomestructure.jpg&lt;/a&gt;) and should be together in metaphase. These chromosomes only look like chromatids to me (1 of 2 pairs).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have they been separated?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am also asked to specify which chromosomes are from the father and which are from the mother. How would I go by doing that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2014-10-08T14:47:38.290" Title="Chromatids in metaphase?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;chromosome&gt;&lt;human-genome&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21101" PostTypeId="2" ParentId="21100" CreationDate="2014-09-07T21:40:50.317" Score="0" Body="&lt;p&gt;There are two important terms to note:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sister chromatids&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Homologous  chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sister chromatids are visible during most phases of mitosis, but not rest of cell cycle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;colchasine is an inhibitor of micro tubules so it prevents the chromosomes from 'lining&lt;strong&gt;strong text&lt;/strong&gt; up&quot; during metaphase hence it arrests  at metaphase and the chromosomes are scattered all&#xA;Over the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The spindle also helps withpairing up sister chromatids (for each homolog) so that each new daughter cell gets a complete genome. Since the spindle is not intact the chromatids are not localized. &lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-10-08T14:47:38.290" LastActivityDate="2014-10-08T14:47:38.290" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21102" PostTypeId="1" AcceptedAnswerId="21106" CreationDate="2014-09-07T22:14:24.423" Score="5" ViewCount="9494" Body="&lt;p&gt;Could you explain to me, what is the meaning of &quot;&lt;em&gt;Effective population size ($N_e$)&lt;/em&gt;&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would appreciate an example as well.&lt;/p&gt;&#xA;" OwnerUserId="9128" LastEditorUserId="8986" LastEditDate="2014-09-08T10:52:39.507" LastActivityDate="2014-09-08T10:52:39.507" Title="Definition of &quot;Effective population size&quot;" Tags="&lt;population-genetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21103" PostTypeId="2" ParentId="20995" CreationDate="2014-09-07T22:26:22.650" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Why can't we just create a pill that does have all the necessary components?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm assuming you mean micronutrients (vitamins &amp;amp; minerals). A day's worth of macronutrients (energy and building-block providing chemicals - proteins, fats, sugars) are already very abundant and dense - a pill containing a day's worth would be the size of an egg. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise, we do. There are vitamin/mineral pills which have a very high absorbancy rate (usually those chelated or chemically bonded to various amino acids &lt;strong&gt;[words ending in -nate on the label]&lt;/strong&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The big problem is that while the vitamins and minerals may satisfy your bare biochemical needs, that is &lt;em&gt;all&lt;/em&gt; they do. They will not satisfy a hunger instinct (proteins and fats do that), and there are untold millions of compounds in the untold thousands of plants and products humans can pick up from the market. These compounds usually do not do much, but some are beneficial to our health.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So while multivitamins exist which provide you with a very efficient method of absorbing most of your vitamins and minerals, it's always recommended to get them directly from food since food will provide macronutrients (thus satisfying your hunger), the micronutrients you're curious about, &lt;em&gt;and&lt;/em&gt; &lt;strong&gt;many&lt;/strong&gt; potential beneficial compounds which are &lt;em&gt;not&lt;/em&gt; necessary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are still interested, &lt;a href=&quot;http://www.soylent.me/&quot; rel=&quot;nofollow&quot;&gt;Soylent Shakes&lt;/a&gt; are an attempt to provide all the micro- and macronutrients the body needs in an easier-to-consume form without all the messy cooking or multivitamin pills. Keep in mind the long-term effects of sticking to such a diet are more or less unknown, but it's as close as we can likely get to an &quot;all-in-one&quot; meal.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2014-09-07T22:26:22.650" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21104" PostTypeId="2" ParentId="21102" CreationDate="2014-09-07T22:42:12.197" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer:&lt;/strong&gt; The effective population size of a population is the corresponding population size of a idealized (fisherian) population that would function in the same way with respect to genetic drift and inbreeding as the focal population under interest.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Long answer, below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Definitions:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Heterogenity&lt;/em&gt;: &lt;br&gt;the probability that two randomly sampled alleles in the population are identical (&lt;a href=&quot;http://en.wikipedia.org/wiki/Identity_by_descent&quot; rel=&quot;nofollow noreferrer&quot;&gt;identical by descent&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Census Population Size:&lt;/em&gt; &lt;br&gt;The census population size ($N$) is the number of individuals in the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fisherian population&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A fisherian population is an idealized population of size $N$, where all individuals mate at random, there is no selection, there is no population structure, there is no mutation and generations are non-overlapping. There probably are no perfectly fisherian populations in nature!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_drift&quot; rel=&quot;nofollow noreferrer&quot;&gt;Genetic drift&lt;/a&gt; causes a decrease in heterogeneity. As the genetic drift is a function of the population size (see &lt;a href=&quot;https://biology.stackexchange.com/questions/14543/why-is-the-strength-of-genetic-drift-inversely-proportional-to-the-population-si&quot;&gt;this post&lt;/a&gt;) this decrease of heterogeneity is a function of the population size. The heterogeneity at time $t$ is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ H_t = H_{0}\left( 1-\frac{1}{2N} \right)^t$$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $H_0$ is the heterogeneity at $t=0$. You can verify by yourself that as $t$ increase , $H_t$ decreases. Also, as $N$ decreases, $H_t$ decreases. In other words, the longer you observe, the more heterogeneity gets lost and the smaller is the population, the higher is the loss of heterogeneity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Effective Population Size&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let &lt;code&gt;Pop_A&lt;/code&gt; be a real population. The effective population size ($Ne$) of &lt;code&gt;Pop_A&lt;/code&gt; is the size of an idealized fisherian population that would have the same loss of heterogeneity than &lt;code&gt;Pop_A&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read the above sentence twice to make sure you understand it. It basically is the definition of the concept of effective population size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words: Let $N$ be the population size of &lt;code&gt;Pop_A&lt;/code&gt;. If &lt;code&gt;Pop_A&lt;/code&gt; is a perfect fisherian population, then its loss of heterozygosity through time is given by:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ H_t = H_{0}\left( 1-\frac{1}{2N} \right)^t$$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If &lt;code&gt;Pop_A&lt;/code&gt; is not a perfect fisherian population, then it's decrease in heterozygosity is greater than the one given by the above formula. The decrease in heterozygosity of &lt;code&gt;Pop_A&lt;/code&gt; corresponds to the decrease of heterozygosity of an idealize fisherian population of a different size. This size is called the effective population size $Ne$. So, we can rewrite the loss of heterogosity through time of &lt;code&gt;Pop_A&lt;/code&gt; as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ H_t = H_{0}\left( 1-\frac{1}{2Ne} \right)^t$$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Note $N$ has been replaced by $Ne$)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $Ne$ is the effective population size of &lt;code&gt;Pop_A&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually $Ne &amp;lt; N$, meaning that a real population undergoes more genetic drift than does a fisherian population of the same census size. There are many reasons that may yield a real population to have a higher drift than it would be expected with the same census size but respecting the assumptions of the fisherian population. Below I discuss three reasons:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Examples&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Unequal sex-ratio&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think as a first example of a population where the sex-ratio is extremely biased to the point of having one male for 99 females. In such population, half of the alleles of a given locus at the next generation will come directly from the father. In such situations, the genetic drift is much higher than what would be expected from a fisherian population of size 100. Therefore $Ne&amp;lt;N=100$. To calculate $Ne$ when the sex-ratio in unequal you can use this formula:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$Ne=\frac{4N_mN_f}{N_m+N_f}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $N_m$ and $N_f$ are the census populatino size of males and females respectively. You can verify that when $N_f = N_m$, then $N_f + N_m = N = Ne$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Variation in population size through time&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your population size varies throughout a given time (a year for example) and that at time $t=3$ (a given period of the year) the census population size is given by $N_i$, then the effective population size is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$Ne = \frac{1}{\frac{1}{t}\sum_{i=1}^t\frac{1}{N_i}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is particularly relevant for insects for example which population size varies a lot between seasons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Selection&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think now of a population where there is a great variance in fitness (there is selection). In such population, maybe all offspring will be produced by only a tenth of the current population. As a result the effective population is ten times smaller than the census population size.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;You can probably find all these informations from wikipedia: &lt;a href=&quot;http://en.wikipedia.org/wiki/Effective_population_size&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Effective_population_size&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me know if the concept of the effective population makes more sense to you now.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-09-08T09:58:17.160" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21105" PostTypeId="2" ParentId="21070" CreationDate="2014-09-07T23:27:50.577" Score="4" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Paratope&quot; rel=&quot;nofollow noreferrer&quot;&gt;paratope&lt;/a&gt; is the part of an antibody that binds the &lt;a href=&quot;http://en.wikipedia.org/wiki/Epitope&quot; rel=&quot;nofollow noreferrer&quot;&gt;epitope&lt;/a&gt; on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Antigen&quot; rel=&quot;nofollow noreferrer&quot;&gt;antigen&lt;/a&gt;. The CDRs (heavy chain CDRs shown below) are part of the structure of the variable domain, and contain the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hypervariable_region#Antibodies&quot; rel=&quot;nofollow noreferrer&quot;&gt;hypervariable regions&lt;/a&gt; that bind to the epitope. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9Efjw.png&quot; alt=&quot;heavy chain CDRs&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Complementarity_determining_regions.PNG&quot; rel=&quot;nofollow noreferrer&quot;&gt;From Wikimedia&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The actual paratope is within the hypervariable regions, which are within the CDRs - the paratope is not necessarily made up of the entire CDR region, and in fact may only be composed of amino acids contained within one or two of the three CDRs on each antibody chain (heavy and light).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're in the market for a good introductory immunology text, I highly recommend &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0815342438&quot; rel=&quot;nofollow noreferrer&quot;&gt;Janeway's &lt;em&gt;Immunobiology&lt;/em&gt;&lt;/a&gt;. An earlier version is also available on the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10757/&quot; rel=&quot;nofollow noreferrer&quot;&gt;NCBI Bookshelf&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2015-11-01T18:29:47.373" LastActivityDate="2015-11-01T18:29:47.373" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21106" PostTypeId="2" ParentId="21102" CreationDate="2014-09-07T23:29:44.867" Score="5" Body="&lt;p&gt;I'll add an informal answer to complement @Remi.b's excellent answer. In a very simple sense, you can think of the effective population size as the number of reproducing (breeding) individuals in a population. Nature Education has a very good (and free) Scitable article on &lt;a href=&quot;http://www.nature.com/scitable/topicpage/genetic-drift-and-effective-population-size-772523&quot;&gt;Genetic Drift and Effective Population Size&lt;/a&gt;. The article makes four points, which I've annotated below.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The population has an equal number of males and females. All&#xA;individuals are able to reproduce.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Populations of many species contain individuals that have not yet reached sexual maturity, have passed an age of reproductive capability, or might have a genetic condition that prevents reproduction.  All of these individuals count towards the census population size (actual number of individuals present) but not count towards effective population size because they can't reproduce.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;All individuals in the population are equally likely to reproduce. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Mating is random.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Not all indivduals (assuming individuals that meet assumption #1 above) are equally likely to reproduce. For example, the process of &lt;a href=&quot;http://www.nature.com/scitable/knowledge/library/sexual-selection-13255240&quot;&gt;sexual selection&lt;/a&gt; means that some individuals are much more likely to reproduce than other individuals. Sexual selection is not random, and lowers effective population size. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The number of breeding individuals is constant from one generation to&#xA;the next.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Population sizes for some species can fluctuate over many generations. For example, freshwater mussels have declined rapidly in population size due to habitat loss and other factors. Nearly 72% of the species in the United State and Canada are endangered, threatened or of conservation concern (&lt;a href=&quot;http://fishwild.vt.edu/mussel/PDFfiles/Conservation_status.pdf&quot;&gt;Williams et al. 1993&lt;/a&gt;). The population sizes for the majority of mussels species are but a fraction of what they once were. This is the case for many endangered species. This too lowers effective population size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a simple mathematical treatment to highlight points 1-3. Consider a population of zebras. Zebras like the Plains Zebra (&lt;em&gt;Equus quagga&lt;/em&gt;) form harems where one male mates with several females. He prevents other males from mating with the females in his harem. Let's make the following assumptions: 1) the population has 250 males and 250 females, all capable of breeding and 2) each male that is able to form a harem gets five females. If so, then only 50 males will actually get to reproduce. The census size is 500 individuals but the effective population size, as shown in Remi.b's answer, is calculate by&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$N_e = \frac{4N_m N_f}{N_m+N_F}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where, $N_e$ is the effective population size, $N_m$ is the number of breeding males and $N_f$ is the number of breeding females. Given assumptions 1 and 2 above, $N_m$ is 50 and $N_f$ is 250 (50 males $\times$ 5 females each). Therefore,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$N_e = \frac{4\times 50 \times 250}{50 + 250} = 166.67$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clearly, the effective population size is much smaller than the census population size.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-09-07T23:54:33.240" LastActivityDate="2014-09-07T23:54:33.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21107" PostTypeId="1" AcceptedAnswerId="42730" CreationDate="2014-09-08T00:07:09.147" Score="11" ViewCount="5911" Body="&lt;p&gt;My friend and I were having a discussion over how &quot;efficient&quot; human digestion is. If a human ate a 1000 calorie hamburger, how many of those calories (how much energy) does the body process into usable energy (i.e. fat or other stores). I've heard things like &quot;it's better to workout on an empty stomach because you will burn fat instead of energy from the food you just ate&quot; - so from this I presume that storing energy as fat is less efficient than using the energy from digestion immediately (though in all honesty I'm not sure if that even makes sense.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to summarize: how many calories of food does your body turn into usable calories via digestions? Percentages would be nice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bonus question: If the body does not process at 100%, does the FDA take this into account when labeling food products on their calorie content? If my Basal Metabolic Rate is 1800 calories a day, do I need to eat more than that since my body won't process all of the calories into usable energy?&lt;/p&gt;&#xA;" OwnerUserId="9130" LastEditorUserId="3340" LastEditDate="2015-06-04T11:43:54.497" LastActivityDate="2016-01-27T23:46:03.130" Title="How efficient is the human body at metabolizing food?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;metabolism&gt;&lt;biophysics&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21108" PostTypeId="1" AcceptedAnswerId="21263" CreationDate="2014-09-08T02:03:45.447" Score="3" ViewCount="87" Body="&lt;p&gt;Do river sharks of the genus &lt;em&gt;Glyphis&lt;/em&gt; have reduced or absent rectal glands for salt removal?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rectal gland of marine sharks removes excess salts to maintain osmotic balance (&lt;a href=&quot;http://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1047&amp;amp;context=ichthynicar&quot; rel=&quot;nofollow&quot;&gt;Oguri 1964&lt;/a&gt;).  In freshwater stingrays (&lt;em&gt;Potamotrygon&lt;/em&gt; spp.), the rectal glands are greatly reduced in size  (&lt;a href=&quot;http://www.biolbull.org/content/154/3/508.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Thorson et al. 1978&lt;/a&gt;) but are apparently functionless (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0305049171901866&quot; rel=&quot;nofollow&quot;&gt;Goldstein and Forster 1971&lt;/a&gt;). This is not surprising because freshwater rays do not experience the regular influx of salt water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been unable to determine whether such degeneracy or loss has been observed for the river sharks of Australia (genus &lt;em&gt;Glyphis&lt;/em&gt;). &lt;a href=&quot;https://www.nerpmarine.edu.au/system/files/Mellin_EffectivenessofBiologicalSurrjournal.pone_.0020141.pdf&quot; rel=&quot;nofollow&quot;&gt;Pillans et al. (2009)&lt;/a&gt; suggest that osmoregulation is probably similar to bull shark, which would not be surprising because they are in the same family. However, bull sharks that live in salt water but regularly enter fresh water have rectal glands that are normal size (Oguri 1964). River sharks are obligate freshwater species and thus have no need to maintain a large rectal gland for the same reason as the freshwater rays.  From an evolutionary perspective, I would predict reduction or loss of the rectal gland. &lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-09-13T00:27:13.227" Title="Do river sharks (genus Glyphis) have reduced rectal glands for salt removal?" Tags="&lt;ichthyology&gt;&lt;homeostasis&gt;&lt;osmoregulation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21109" PostTypeId="1" CreationDate="2014-09-08T02:36:10.413" Score="1" ViewCount="60" Body="&lt;p&gt;I recently came across an article indicating that the half life of DNA in the most ideal situations is 521 years (&lt;a href=&quot;http://www.nature.com/news/dna-has-a-521-year-half-life-1.11555&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/news/dna-has-a-521-year-half-life-1.11555&lt;/a&gt;). However, since human's DNA is 99.9% identical (and 98% identical to chimps), I can't quite understand how DNA evidence is often used in old samples. There has been DNA extracted from 100,000 year old Neanderthals, and DNA evidence has been used in cases over 50 years old. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, with a 521 year half life, after only  0.75 years, there would only be 99.9% of the DNA left. Surely if 99.9% of a human's DNA is identical after only this short amount of time wouldn't it be impossible to distinguish any sample from any other? After 50 years only 93% would remain the same, meaning it would be much less similar to a human than just any chimp I would think.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And the 100,000 year old Neanderthal would only have 1.6*10^-57 % of the original sample left. How is there possibly any sort of useful information left?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All in all, how can DNA be distinguished from other samples when they are all so similar and the half life is so low?&lt;/p&gt;&#xA;" OwnerDisplayName="user2836596" LastEditorUserId="5144" LastEditDate="2014-09-08T06:32:38.103" LastActivityDate="2014-09-08T10:13:10.660" Title="DNA Fingerprint" Tags="&lt;radiation&gt;&lt;measurement&gt;&lt;history&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21110" PostTypeId="1" CreationDate="2014-09-08T06:30:13.630" Score="2" ViewCount="144" Body="&lt;p&gt;Does intelligence play a vital role in the evolution of an organism? In other words does an expansion of learning capacity, increase the odds of evolution for the particular biological entity? &lt;/p&gt;&#xA;" OwnerUserId="5709" LastEditorUserId="5709" LastEditDate="2016-12-01T10:41:01.977" LastActivityDate="2016-12-01T10:41:01.977" Title="Conscious evolution" Tags="&lt;evolution&gt;" AnswerCount="3" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21111" PostTypeId="1" AcceptedAnswerId="21114" CreationDate="2014-09-08T08:01:51.637" Score="135" ViewCount="16527" Body="&lt;p&gt;I know that the cells of mammals at least stop dividing when they are old, and then die a programmed cell death. Then other cells have to replace them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But in a bacterial colony, each cell replicates for itself. Obviously, if a division of a bacterial cell of generation N were to produce two new cells of generation N+1, and all bacteria died of old age at generation M, there would be no bacteria left around. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how is it regulated in bacteria? Are their divisions simply unlimited? Does a cell never die and just divide forever? &lt;/p&gt;&#xA;" OwnerUserId="1578" LastEditorUserId="3952" LastEditDate="2014-09-09T21:39:00.913" LastActivityDate="2014-09-09T21:39:00.913" Title="Do bacteria die of old age?" Tags="&lt;bacteriology&gt;&lt;reproduction&gt;&lt;senescence&gt;&lt;life-history&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="34" ContentLicense="CC BY-SA 3.0" />
  <row Id="21112" PostTypeId="1" AcceptedAnswerId="21115" CreationDate="2014-09-08T08:03:37.740" Score="3" ViewCount="453" Body="&lt;p&gt;What is meant by drug tolerance?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question is in my biology textbook for IGCSE and I have no idea what drug tolerance is. It would be very helpful if someone could clarify. Thank you.&lt;/p&gt;&#xA;" OwnerUserId="9045" LastActivityDate="2014-09-08T10:24:05.867" Title="What is meant by drug tolerance?" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21113" PostTypeId="1" AcceptedAnswerId="21117" CreationDate="2014-09-08T08:03:47.290" Score="7" ViewCount="2660" Body="&lt;p&gt;I was looking at the GC content percentages of few organisms. I also know calculating the GC content percentage. But, what I want to know is, what information would we get., let us suppose if human genome has 40% of GC in the genome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it help us compare the number of genes between different species, for example, a bacteria has less GC content than human, so does it mean Human produce more genes than bacteria?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or Is it that the 40% of the genome,has coding regions in them and more genes are found in those regions? What is the number &quot;40%&quot; actually indicate us?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please help me understanding the concept. Would be thankful your answers and suggested reading.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: My question is what does knowing percentage of GC content help us knowing? If the GC content is 40%, does it correlate to number of genes in the genome?&#xA;Regards,&#xA;Prakki Rama.&lt;/p&gt;&#xA;" OwnerUserId="6455" LastEditorUserId="6455" LastEditDate="2014-09-08T08:31:27.023" LastActivityDate="2017-06-05T10:51:52.327" Title="Importance of knowing GC Content of an organism" Tags="&lt;molecular-biology&gt;&lt;genomes&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21114" PostTypeId="2" ParentId="21111" CreationDate="2014-09-08T08:18:21.053" Score="123" Body="&lt;p&gt;This is a interesting question and for a long time it was thought that they do not age. In the meantime there are some new papers which say that bacteria do indeed age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aging can be defined as the accumulation of non-genetic damages (for example oxidative damage to proteins) over time. If too much of these damages are accumulated, the cell will eventually die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For bacteria there seems to be an interesting way around this. The second paper cited below found that bacteria do not divide symmetrically into two daughter cells, but seem to split into one cell which receives more damage and one which receives less. The latter one can be called rejuvenated and seems to make sure that the bacteria can seemingly divide forever. Using this strategy limits the non-genetic damage to relatively few cells (if you consider the doubling mechanism) which could eventually die to save the others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a look at the following publications which go into detail (the first is a summary of the second but worth reading):&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedaily.com/releases/2011/10/111027150207.htm&quot;&gt;Do bacteria age? Biologists discover the answer follows simple&lt;br&gt;&#xA;economics&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822%2811%2901020-7&quot;&gt;Temporal Dynamics of Bacterial Aging and Rejuvenation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15685293?dopt=Abstract&quot;&gt;Aging and death in an organism that reproduces by morphologically&#xA;symmetric division.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="-1" LastEditDate="2014-09-08T22:08:28.373" LastActivityDate="2014-09-08T22:08:28.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21115" PostTypeId="2" ParentId="21112" CreationDate="2014-09-08T08:47:35.023" Score="2" Body="&lt;p&gt;It basically means, that the body gets used to certain drugs and that you need to raise the dose to reach an effect. This is for example true for a number of anesthetics or pain medications as morphine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Permanent application leads to a down-regulation of the drug receptor (for morphin this is the mu-opiod receptor) and the activation of counteracting signaltransduction pathways. To still get an activation you will need a higher drug concentration.&#xA;For more details have a look at these articles: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9864069&quot; rel=&quot;nofollow&quot;&gt;Opiate tolerance and dependence: receptors, G-proteins, and&#xA;antiopiates&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1038/bjp.2008.100/full&quot; rel=&quot;nofollow&quot;&gt;Cellular neuroadaptations to chronic opioids: tolerance, withdrawal&#xA;and addiction&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-09-08T10:24:05.867" LastActivityDate="2014-09-08T10:24:05.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21116" PostTypeId="1" CreationDate="2014-09-08T08:54:51.470" Score="5" ViewCount="146" Body="&lt;p&gt;Living in southern Germany, I often visit nearby forests and pastures.&lt;br&gt;&#xA;From early spring to autumn, I frequently see lots of dorbeetles on my wanderings. An estimated amount of 50% of those bugs seem to be somewhat handicapped or crippled. All of them share the same symptoms:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;They stretch their legs away from their body, moving them in a&#xA;swimming-like manner, which causes them to be unable to get over the&#xA;smallest rocks or plants. It looks very clumsy, almost drunk. Often they draw back one of their rear-end legs, getting caught in parts of plants.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Many of them are lying on their backs, struggling to get back on&#xA;their feet. When I turn them around, they will start walking in the&#xA;fashion I described above, falling over again almost instantly&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Like already pointed out, not all of the dorbeetles behave like this. I see lots of bugs that seem to be perfectly fine, too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What can possibly cause this?&lt;/p&gt;&#xA;" OwnerUserId="9133" LastEditorUserId="1320" LastEditDate="2014-09-08T13:36:03.933" LastActivityDate="2014-09-08T13:36:03.933" Title="Why do I see so many handicapped dorbeetles?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21117" PostTypeId="2" ParentId="21113" CreationDate="2014-09-08T09:02:28.960" Score="5" Body="&lt;p&gt;Interesting question. The GC-content seems to evolve over time and it also seems that the GC-content of coding regions is higher than for the surrounding non-coding regions (see reference 1). If there is a specific function for this higher GC-content or not is (if I understand this right) debated among the groups which do research in this field. Have a look at the references (and probably also their references) to decide on this:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18371205&quot; rel=&quot;noreferrer&quot;&gt;Both selective and neutral processes drive GC content evolution in&#xA;the human genome.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12082137&quot; rel=&quot;noreferrer&quot;&gt;Integrating genomics, bioinformatics, and classical genetics to&#xA;study the effects of recombination on genome evolution.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://mbe.oxfordjournals.org/content/21/6/984.short&quot; rel=&quot;noreferrer&quot;&gt;Recombination Drives the Evolution of GC-Content in the Human Genome&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.genetics.org/content/159/2/907.long&quot; rel=&quot;noreferrer&quot;&gt;GC-Content Evolution in Mammalian Genomes: The Biased Gene&#xA;Conversion Hypothesis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909565/&quot; rel=&quot;noreferrer&quot;&gt;Contrasting GC-content dynamics across 33 mammalian genomes:&#xA;Relationship with life-history traits and chromosome sizes&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-08T09:02:28.960" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21119" PostTypeId="2" ParentId="21109" CreationDate="2014-09-08T10:13:10.660" Score="2" Body="&lt;p&gt;The original article cited in your reference is &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/279/1748/4724.full&quot; rel=&quot;nofollow&quot;&gt;available here for free&lt;/a&gt;. After a quick skim, I saw that their study was based on fossils of a single species (Moas) all taken within a 5 km radius. Thus, it's possible the fossils were preserved under relatively similar conditions, despite different preservation ages. So, it's not yet clear how their results would compare to other species and varying preservation conditions (which they address to some extent).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regardless, DNA does degrade in fossils yet scientists have been able to recover very high quality sequences from fossils, such as &lt;a href=&quot;http://www.eva.mpg.de/neandertal/index.html&quot; rel=&quot;nofollow&quot;&gt;Neanderthals&lt;/a&gt;.  This is because the samples contain many &lt;em&gt;copies&lt;/em&gt; of the DNA. If bonds in one copy of the DNA break in several places it is very unlikely that another copy will break in the exact places.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a number of different techniques but in essence scientists simply amplify and sequence a very large number of the DNA fragments. Each fragment is relatively short compared to the total amount of DNA but the large number of fragments ensures (within reason) that the entire genome is covered.  Complex computer algorithms are used to align the different fragments with each other.  You can read about the techniques used in one of the major Neanderthal genome studies by &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867408007733&quot; rel=&quot;nofollow&quot;&gt;Green et al. (2008)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-09-08T10:13:10.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21120" PostTypeId="1" AcceptedAnswerId="21186" CreationDate="2014-09-08T10:27:40.963" Score="2" ViewCount="8688" Body="&lt;p&gt;What is the specific function of a satellite in a chromosome ? How are sat-chromosomes different from others ? On molecular basis, what are the functional advantages of it ?&lt;/p&gt;&#xA;" OwnerUserId="8580" LastActivityDate="2014-09-10T16:51:52.037" Title="what is the function of satellite in a chromosome?" Tags="&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21121" PostTypeId="2" ParentId="21110" CreationDate="2014-09-08T11:33:19.783" Score="0" Body="&lt;p&gt;Seems safe to assume that intelligence CAN influence fitness, depending on the selection pressures. As Hav0k mentioned, this won't necessarily be favorable, i.e. lead to more progeny. In the case of modern humans, even if a person got more mating opportunities by being, or just appearing to be very intelligent in some areas, it might not do much to affect the population if he/she chose to have fewer or no offspring. To the extent that intelligence was valued in a population, it could of course become very influential. Whether or not (potential) intelligence is something quantifiable that is vertically transferred is another discussion I guess.&lt;/p&gt;&#xA;" OwnerUserId="9137" LastEditorUserId="9137" LastEditDate="2014-09-08T11:39:11.803" LastActivityDate="2014-09-08T11:39:11.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21123" PostTypeId="2" ParentId="21116" CreationDate="2014-09-08T12:47:59.053" Score="3" Body="&lt;p&gt;I do not know for certain but one possibility is an internal parasite. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A number of parasites have been documented to alter the behavior of the hosts to suit the life cycle needs of the parasite.  For example, &lt;em&gt;Toxoplasma&lt;/em&gt; is a parasite use rats and cats as hosts. &lt;em&gt;Toxoplasma&lt;/em&gt; alters the behavior of the rats so that they no longer respond to the smell of a cat. That makes the rats much more likely to be captured by the cats, which transfers the parasite to the cat from the rat &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1690701/&quot; rel=&quot;nofollow&quot;&gt;(Berdoy et al. 2000)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=XuKjBIBBAL8&quot; rel=&quot;nofollow&quot;&gt;This YouTube video&lt;/a&gt; shows how a fungal parasite of ants alters the ant behavior to help the fungus reproduce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My favorite example, which I use in my introductory biology course, is &lt;a href=&quot;http://bio390parasitology.blogspot.com/2012/02/euhalplorchis-californiensis_07.html&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Euhaplorchis californiensis&lt;/em&gt;&lt;/a&gt;, a parasitic fluke. The parasite lives in marshy habitats, such as &lt;a href=&quot;http://carpinteria.ucnrs.org&quot; rel=&quot;nofollow&quot;&gt;Carpinteria Marsh&lt;/a&gt; in California, USA. This parasite uses wading birds (herons and egrets), a snail and a fish as it's host.  The adult lives in the gut of the wading birds. Eggs from the adults pass out with the bird feces. Horn snails consume the fecal material and the eggs.  The eggs hatch inside the snail. The larvae actually castrate the snails so that the snails cannot reproduce. Instead, the snails only feed, which provides nutrients for the parasite larvae. The larvae then leave the snail and swim into the marsh, where they are consumed by the California killifish (&lt;em&gt;Fundulus parvipinnis&lt;/em&gt;). The parasite works its way from the gut of the fish to the brain, where it releases chemicals that alter the behavior of the killifish. Normally, if a killifish sees a wading bird, it would dive deep. Instead, the parasitized fishes no longer dive. They remain near the surface and swim eratically. This behavior makes it much easier for the wading bird to see and catch the killifish. The parasite is transfered back to the wading bird, and its life cycle begins again. Details of this fascinating life cycle can be found in (&lt;a href=&quot;http://parasitology.msi.ucsb.edu/pubs/Shaw%20et%20al.%202010%20JP.pdf&quot; rel=&quot;nofollow&quot;&gt;Shaw et al. 2010&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, it is possible that the behavior of the dorbeetles is being influenced by an internal parasite. These &lt;a href=&quot;http://www.newforestexplorersguide.co.uk/wildlife/other-notable-insects/dung-beetles.html&quot; rel=&quot;nofollow&quot;&gt;dung beetles&lt;/a&gt; may consume a parasite when they ingest dung from a certain species. The parasite could alter the behavior of the beetle making them more vulnerable to a particular predator, thereby continuing the next step of the parasite's life cycle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your description of the beetle behavior would fit this hypothesis but I stress that I do not know this. I raise the idea as one possibility among many.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good not technical book on parasites is &lt;a href=&quot;http://carlzimmer.com/books/parasiterex/index.html&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Parasite Rex&lt;/em&gt;&lt;/a&gt; by &lt;a href=&quot;http://carlzimmer.com&quot; rel=&quot;nofollow&quot;&gt;Carl Zimmer&lt;/a&gt;. It covers the biology of parasites, the many ways that parasites can affect their hosts, and the creative scientific minds that uncover the complex life histories of many parasites. (I have no connection to the author or the book.)  The book covers the above examples and more in some detail.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-09-08T12:47:59.053" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21124" PostTypeId="2" ParentId="21110" CreationDate="2014-09-08T13:17:51.883" Score="3" Body="&lt;p&gt;&lt;strong&gt;First Comment&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The questions in the OP's post (and his/her comments below the post) are very poorly phrased and let the reader think that the OP has few knowledge about evolution (no offense). This is a reason why I don't directly address my below answer in the terms of the question as it seems that the OP uses a unusual definition of the term &quot;evolution&quot;. @Chris comment (&quot;No, it doesn't. Evolution is a statistical process which is not influenced by any means of intelligence&quot;) probably sums up what the OP needed to read but I can't stand but giving a more complete answer about why is intelligence just a random trait and in the meantime arguing in a far-fetched text that intelligence still has actually some funny properties as it may yield to social help (social help does not necessarily needs intelligence) and eugenics programs (that might be argued that it doesn't need intelligence as well).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Summary of the answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Intelligence (as many other traits) influences fitness&lt;/li&gt;&#xA;&lt;li&gt;Intelligence (as many other traits) influence the environment that individuals are facing influencing then future evolution&lt;/li&gt;&#xA;&lt;li&gt;Evolution is not dependent on the will of the individuals in the population.&lt;/li&gt;&#xA;&lt;li&gt;Indirectly, intelligence may be of some particular interest as it yields to knowledge about physiology and evolution allowing Eugenic program and medicine which both influence future evolution.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Fitness&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intelligence influence fitness (=reproductive success). So yes it plays a role in evolution just like any other trait that influence fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Environment&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intelligence evolves and by its presence it will change future evolution as it changes the environment the individual faces. For example, if a bird is intelligent enough to bottle milk bottle, it might over the long term (and assuming that humans are not inventing some solutions to prevent birds from opening their bottles) evolve longer beak to seek for milk from the bottle. Also Intelligence shape culture (set of traditions). Theoretically, all traits does the exact same thing, so again there is nothing so exceptional about intelligence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a subset of the impact of intelligence on the environment the individual experience: Intelligence allow culture which changes through time and it is some kind of evolution called memetics. Again, culture changes the environment the individual faces and if culture changes often because of high intelligence, then the environment may change quickly as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;General basic comment on evolution&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is very important to not think that intelligence will allow a population to &quot;better evolve&quot;. Being intelligent does not yield to higher probability of adaptable evolution. It is not because you know what issue you're facing that you'll be consciously able to evolve to that. For adaptation to occur you have to select individuals that are more fit in the population. If individuals in the population know who are fit doesn't mean that those fit individuals will be more selected than otherwise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Social help and eugenic programs&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to the previous paragraph I must point to some potential, indirect impacts of intelligence on the evolution of a population. A population of intelligent individuals may as a group decide on which individuals will reproduce. This is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Eugenics&quot; rel=&quot;nofollow&quot;&gt;eugenics&lt;/a&gt; and this is the kind of process by which intelligence influence future evolution in a particularly interesting and unique way. For example, we may decide that all people that carry a non-expressed disease gene are not allowed to reproduce in order to suppress this gene from the population. In the same order of idea the population learn how to treat people that have a given genetic disease, the selection against the gene variants (alleles) causing the disease will decrease, increasing then the frequency of the disease in the population. Therefore, some medical actions (and other kind of social help) cause less adaptable evolution while some eugenic program cause more adaptable evolution. &lt;em&gt;I am not talking about ethics here and am not saying we SHOULD stop treating people with genetic disease&lt;/em&gt;. Note that other things like the evolution of trait architecture will yield to different ability to undergoes adaptive evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Interpreting my answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important for a starter in evolutionary theory to make sure to learn more about evolution before trying to interpret further this answer in an incorrect way. I want to avoid that someone with few knowledge in evolution starts to think that intelligence is some kind of magical trait or that evolution is a process answering to the conscious needs individuals may have. For the moment keep in mind that evolution has no foresight and is not the result of the will of the individuals in the population (except for eugenic program). Behind this answer there are (maybe hidden) slightly advanced topics such as the strength of selection, mutation-selection-drift equilibrium, the genetic load, trait architecture and evolvability.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-09-08T23:05:57.593" LastActivityDate="2014-09-08T23:05:57.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21126" PostTypeId="1" AcceptedAnswerId="21155" CreationDate="2014-09-08T14:23:35.173" Score="3" ViewCount="386" Body="&lt;p&gt;What is Serological Analysis of cDNA expression library?&lt;br&gt;&lt;br&gt; I went through this article:&lt;br&gt;&lt;a href=&quot;http://cancerimmunity.org/serex/introduction/&quot; rel=&quot;nofollow&quot;&gt;http://cancerimmunity.org/serex/introduction/&lt;/a&gt;&lt;br&gt; but could not really make out. Can someone please explain this to me in a simpler manner?&lt;br&gt;&lt;br&gt;(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)&lt;/p&gt;&#xA;" OwnerUserId="8835" LastActivityDate="2014-09-09T08:33:30.550" Title="SEREX serological analysis of cDNA expression library" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;bioinformatics&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21129" PostTypeId="1" CreationDate="2014-09-08T16:12:13.893" Score="3" ViewCount="282" Body="&lt;p&gt;During assaying an enzyme at high temperature, the substrate (Pectin) is degraded by the high temperature rather than by enzyme, so, how can I minimize degradation of the substrate by the temperature? &lt;/p&gt;&#xA;" OwnerUserId="8794" LastActivityDate="2015-06-30T16:28:44.610" Title="Enzyme Assay - pectinase" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;enzymes&gt;&lt;biotechnology&gt;&lt;enzyme-kinetics&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21130" PostTypeId="1" CreationDate="2014-09-08T16:50:50.000" Score="3" ViewCount="1106" Body="&lt;p&gt;Can someone help me identify this bird (sorry only had the iphone)? It looks like a grackle, but the bill is much longer than any I have seen. The bill looks like a Le Conte's thrasher, but it was all black. It looked pretty ratty because he was molting. It was definitely black, and in an area with lots of grackles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pictures don't do it justice, it was a really long bill. The pictures were taken in Phoenix, Arizona, US on Greenway bike path near Thomas Rd on 7 Sept 2014.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PcIMA.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The picture is not that clear, but it definitely was not something that the bird was holding in his beak. That was my first thought when I saw him, but I watched him awhile, it was very clearly his beak that was long and decurved. Sure wish I had my real camera at the time.&lt;/p&gt;&#xA;" OwnerUserId="9143" LastEditorUserId="69" LastEditDate="2014-09-10T10:23:57.233" LastActivityDate="2016-04-29T06:52:34.240" Title="Is this a grackle with an unusually long decurved bill (Phoenix AZ, USA)" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21132" PostTypeId="1" CreationDate="2014-09-08T18:11:38.897" Score="2" ViewCount="109" Body="&lt;p&gt;I recently purchased a small cactus plant from my local store for about $5.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been giving the cactus lots of sunlight and a good watering every week.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've noticed that since I bought it, the other cactii at the store have sprouted long and deadly looking spikes of at least 2 inches in length. My cactus has extra little clones growing out of it but its spikes are stunted and disappointing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why won't my cactus grow spikes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My cactus is of this variety:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.friendsschoolplantsale.com/sites/default/files/images/colors/a-flat-cactus2-ns.jpg?1364265449&quot; rel=&quot;nofollow&quot;&gt;http://www.friendsschoolplantsale.com/sites/default/files/images/colors/a-flat-cactus2-ns.jpg?1364265449&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9147" LastActivityDate="2014-09-08T18:11:38.897" Title="Why Hasn't my Cactus Grown Deadly Spines?" Tags="&lt;botany&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2015-01-29T20:54:36.747" ContentLicense="CC BY-SA 3.0" />
  <row Id="21133" PostTypeId="1" CreationDate="2014-09-08T18:17:40.587" Score="3" ViewCount="1400" Body="&lt;p&gt;I found this spider hanging from a web off the side of my house (in Buffalo, NY). It's probably 3-4in total length. Any thoughts on what kind of spider this is? And if it's dangerous?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7gBRg.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9148" LastActivityDate="2014-09-08T20:52:00.433" Title="What kind of spider is this? And is it dangerous? (photo)" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21135" PostTypeId="2" ParentId="21133" CreationDate="2014-09-08T18:46:22.990" Score="2" Body="&lt;p&gt;I would think this is a European garden spider (or cross spider). See &lt;a href=&quot;http://en.wikipedia.org/wiki/European_garden_spider&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://naturemappingfoundation.org/natmap/facts/cross_spider_712.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&#xA;It can bite humans but it is not dangerous for them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1H2hK.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-09-08T20:08:11.730" LastActivityDate="2014-09-08T20:08:11.730" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21136" PostTypeId="2" ParentId="1581" CreationDate="2014-09-08T19:15:59.477" Score="2" Body="&lt;p&gt;I've thought about this many times but enjoyed theorizing on possibilities vs researching evolutionary theory.  I like these thoughts above- def agree to certain extent- but it seems to me that:&#xA;    If &lt;em&gt;almost&lt;/em&gt; all &quot;fishes&quot; utilize side to side motion/morphology, it seems that this is certainly more efficient, and would be adopted, over many millions of yrs...at least in some examples...by marine mammals; HOWEVER, there's one difference and physiological necessity that I believe actually may make the horizontal fluke/tail advantageous. This would make the vertebrae idea just a shaping mechanism in such evolution- instead of a restricting agent.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to breath -in order to do so efficiently- surfacing is necessary, thus vertical thrust is of the utmost importance.  Esp, since other air-breathing marine species (evolved from land animals...) that have NOT evolved a solid fluke (whether by lack of evolutionary time, or prior morphological diffferences...) in most cases have a more flexible propulsion system to achieve efficiency via improved or altered maneuverability. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Certain pinnipeds- as discussed in article above- have less solid structures, thus improved flexibility/mobility and in my mind- going hand-in-hand with creating sufficient breathing efficiency.  Then, in non-mammal instances, penguins are a solid example- as the use of &quot;forelimb&quot; (wings) create both the flexibility/mobility to achieve said necessities, but also... effectively acting quite similarly (in the vertical thrust department) to the horizontal fluke----in the process of surfacing to breath, porpoise, or reach land.&lt;/p&gt;&#xA;" OwnerUserId="9152" LastActivityDate="2014-09-08T19:15:59.477" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21137" PostTypeId="1" CreationDate="2014-09-08T19:32:01.053" Score="8" ViewCount="1912" Body="&lt;p&gt;I have not been able to locate any research that indicates whether a single axon of a neuron or nerve cell can conduct multiple simultaneous (i.e. spatially separate) action potentials. I am aware that in many neurons refractory periods would preclude this possibility, however in some cases delays along axons are large enough. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this the case? Can you point me to any citations supporting your answer?&lt;/p&gt;&#xA;" OwnerUserId="9151" LastEditorUserId="9943" LastEditDate="2014-12-18T01:14:37.550" LastActivityDate="2014-12-18T01:14:37.550" Title="Can a single axon propagate multiple simultaneous action potentials?" Tags="&lt;neuroscience&gt;&lt;biophysics&gt;&lt;action-potential&gt;&lt;neurophysiology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21138" PostTypeId="1" AcceptedAnswerId="21154" CreationDate="2014-09-08T20:07:07.757" Score="4" ViewCount="122" Body="&lt;p&gt;I am the kind of biologist who doesn't know much about molecular genetics and about the dynamic of biochemical reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question concerns the influence of temperature on the dynamic of molecular genetic processes. Typically, I'd like to know how (quantitatively speaking, looking for the &lt;a href=&quot;http://en.wikipedia.org/wiki/Q10_(temperature_coefficient)&quot; rel=&quot;nofollow noreferrer&quot;&gt;$Q_{10}$&lt;/a&gt; for example) the following parameters get modified with temperature.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;rate of transcription&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;UPDATE&lt;/strong&gt; See &lt;a href=&quot;https://biology.stackexchange.com/questions/21198/how-is-the-rate-of-transcription-influenced-by-temperature&quot;&gt;How is the rate of transcription influenced by temperature?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;protein binding to a DNA-binding-motif&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;UPDATE&lt;/strong&gt; see &lt;a href=&quot;https://biology.stackexchange.com/questions/21189/influence-of-temperature-on-protein-binding-and-decay-rates&quot;&gt;influence of temperature on protein binding and decay rates&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;rate of protein decay&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;UPDATE&lt;/strong&gt; see &lt;a href=&quot;https://biology.stackexchange.com/questions/21189/influence-of-temperature-on-protein-binding-and-decay-rates&quot;&gt;influence of temperature on protein binding and decay rates&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;rate of mRNA decay&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;UPDATE&lt;/strong&gt; answered by @Chris below&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why do I ask this question?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to know what kind of default parameters values I should enter for modeling purposes in evolutionary biology. While our scope is large we decided we would consider parameters values that are observed in yeast.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-09-10T22:55:39.033" Title="Influence of temperature on transcription, protein binding and decay rates" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;proteins&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21139" PostTypeId="2" ParentId="21133" CreationDate="2014-09-08T20:52:00.433" Score="1" Body="&lt;p&gt;Looks like a variety of the very common and diverse group of &quot;garden&quot; and/or &quot;orb weaver&quot; group(s).  They really pop up everywhere during the spring/summer but die off w cold weather (in southeastern US).  Like mentioned, they'll bite but not poisonous...  They're the guys whose webs you're constantly being freaked out by when u hit it face-first---but then never see the spider, or at least aren't bitten normally.&lt;br&gt;&#xA;The ones you gotta watch for around here don't make webs that you'll typically see, and either leave their webs often and/or remain in cracks/crevices (e.g.) brown recluse or black widow...).&lt;/p&gt;&#xA;" OwnerUserId="9153" LastActivityDate="2014-09-08T20:52:00.433" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21140" PostTypeId="2" ParentId="21110" CreationDate="2014-09-08T21:04:23.007" Score="0" Body="&lt;p&gt;Intelligence can have an impact on selection, but keep in mind that flexible intelligence (like the kind humans possess) is a high-cost/high-reward kind of adaptation.  Brains &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1834002/&quot; rel=&quot;nofollow&quot;&gt;consume a lot of energy&lt;/a&gt;, so the resulting intelligent behavior needs to 'pay for itself' (in terms of survivability and ability to reliably gather the necessary food) if it's going to create a competitive advantage.&lt;/p&gt;&#xA;" OwnerUserId="9155" LastActivityDate="2014-09-08T21:04:23.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21141" PostTypeId="1" AcceptedAnswerId="21248" CreationDate="2014-09-08T21:21:52.430" Score="3" ViewCount="163" Body="&lt;p&gt;I am looking for examples of different functions that are good fit to how signals are computed in order to respond to the environment. Let's make my question more copmrehensible with an example...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;One example&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been told (I haven't found an article yet) that in plants, in order to know if it is overshadowed by a big tree, the plant computes that ratio of two signals (UV intensity over Infrared intensity or something similar) so that it can decide whether or not it should grow bigger leaves or other attributes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This plant radiation example would be an example of a species that computes the function $\frac{S_1}{S_2}$ (where $S_1$ and $S_2$ are two types of signals) in order to take decisions about their response to the environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can you please give me examples (&lt;em&gt;examples with a diversity different functions, with different numbers of different signals&lt;/em&gt;) of organism using environmental signals to adaptively respond to their environment?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, can you give me examples of the adaptive response to the environment is giving by the following functions of 2 signals:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Continuous traits:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;$f(S_1, S_2)= S_1 + S_2$&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Produce a trait value at $K_1 + K_2\cdot \left(S_1 + S_2\right)$&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;$f(S_1, S_2)= \frac{S_1}{S_2}$&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Produce a trait value at $K_1 + K_2\cdot \frac{S_1}{S_2}$&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;$f(S_1, S_2)= S_1^2 \cdot S_2$&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Produce a trait value at $K_1 + K_2\cdot \left(S_1^2 \cdot S_2\right)$&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;$f(S_1, S_2)= funA(S_1, S_2)$&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Produce a trait value at $K_1 + K_2\cdot S_1$ iff $S_1$ is detected.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;$f(S_1, S_2)= funB(S_1, S_2)$&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Produce a trait value at $K_1 + K_2\cdot S_1$ iff $S_1 &amp;lt; S_2$.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Boolean traits:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;$f(S_1, S_2)= OR(S_1, S_2)$&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Iff signal 1 or signal 2 is detected, produce the trait&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;$f(S_1, S_2)= AND(S_1, S_2)$&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Iff signal 1 and signal 2 are detected, produce the trait&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;$f(S_1, S_2)= FunA(S_1, S_2)$&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Iff $S_1$ &amp;lt; $S_2$, produce the trait&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;, where &lt;code&gt;iff&lt;/code&gt; means &lt;code&gt;if and only if&lt;/code&gt; and $K_1$ and $K_2$ are constant values.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What I am NOT asking&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am NOT interested in the accurate description of the signal transduction (Description of the kinase cascade and names of the genes and transcriptions factors). I am interested in having examples of mathematical functions that are computed by the cell in order to take decision about which phenotype to produce (plasticity).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-09-14T00:56:30.567" LastActivityDate="2014-09-14T00:56:30.567" Title="Integration of several environmental signals" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;theoretical-biology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21142" PostTypeId="1" CreationDate="2014-09-08T21:36:14.833" Score="2" ViewCount="2385" Body="&lt;p&gt;To what extent does the 260/230 value affect the efficiency of PCR reactions ? Do the constituents leading to a low 260/230 value (EDTA, guanidine salts and oligosaccharides) inhibit PCR ? I have been getting pretty low values of 260/230 (0.5-1.0) for DNA extracted using Charge Switch Protocol using Magnetic beads and the PCR has been failing. Also, is there any reason why I might be getting low 260/230 values in Charge Switch method ? (I was getting good values using Phenol-Chloroform extraction method)&lt;/p&gt;&#xA;" OwnerUserId="18932" LastActivityDate="2014-09-09T01:47:10.957" Title="Effect of 260/230 values on PCR" Tags="&lt;pcr&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21144" PostTypeId="2" ParentId="21142" CreationDate="2014-09-09T01:34:26.623" Score="2" Body="&lt;p&gt;EDTA carbohydrates, phenol all have absorbance near 230 nm.  TRIzol reagent is a phenolic solution which absorbs in the UV both at 230 nm and ~270 nm &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Guanidine HCL used for most DNA isolations will absorb at ~230 nm also&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All these things will seriously inhibit your pcr, (and lower your ratio) especially the denaturing agents like guanadine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All these DNA kits are different spins of a pretty similar process. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have a good steady centrifuge stick to the phenol &amp;amp; ethanol. Be certain you are drying your pellet well, but don't over dry it. I'll hear my pellet at 37 for 3-4 min to get rid of ethanol. Ethanol no good in pcr. If you hate doing ethanol precipitation (which I do) cause of invisible pellets, add a high grade bit of glycogen to your aqueous phase before the precipitation. This will make your pellet visible and is completely inert.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your cleanup isn't the problem do an annealing  and Mg gradient and up your primer quantity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;May want to give me more info like the individual absorbance, pcr conditions, template size etc&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Traditionally bead purifications gives really good purity, reason I use it for microarrays. But it's expensive and not necessary for pcr. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Charge switch is just changing the charge of the bead by changing the ph.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-09-09T01:47:10.957" LastActivityDate="2014-09-09T01:47:10.957" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="21145" PostTypeId="1" CreationDate="2014-09-09T02:03:01.717" Score="1" ViewCount="370" Body="&lt;p&gt;Coming from computer science with an interest in genetic programming (a process emulating evolution) I'm curious about whether the rate of mutation is homogeneous across the whole genome, or if some parts of the genome differ in the rate of mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example we could imagine, without going to into details that could invalidate the example, that parts of the genome associated with the immune system could have a relatively higher mutation rate, because this would allow for a quicker adaptation to quickly evolving pathogens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any empirical support for that different part of a genome of some species have different mutation rates, that would give us empirical support for the possibility that some species under evolution have the ability to adjust (by NS itself or even epigenetics) the mutation rate of specific parts of the genome?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Clarification&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm only interested in the mutations happening in the scope of the lifetime of a individual organism, I'm not interested in whether the mutations persisted under NS are equally distributed over the genome.&lt;/p&gt;&#xA;" OwnerUserId="9124" LastEditorUserId="9124" LastEditDate="2014-09-09T13:53:31.743" LastActivityDate="2014-09-09T13:53:31.743" Title="Is the mutation rate in organisms in general consistent over the genome?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21146" PostTypeId="1" AcceptedAnswerId="21152" CreationDate="2014-09-09T02:08:20.773" Score="4" ViewCount="147" Body="&lt;p&gt;Most amino acids can be encoded by more than one codon. For example, &lt;code&gt;Serine&lt;/code&gt; can be encoded by any one of &lt;code&gt;{UCU, UCC, UCA, UCG, AGU, AGC}&lt;/code&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is in two parts: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) what are the relative frequencies of those codons? This question can be equivalently phrased in probabilistic terms: What is the probability that a given amino acid was encoded by particular codon?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Is this probability dependent on the context (the neighboring codons/amino acids)?&lt;/p&gt;&#xA;" OwnerUserId="8060" LastEditorUserId="8060" LastEditDate="2014-09-09T02:24:01.707" LastActivityDate="2014-09-10T17:00:05.253" Title="where to find the relative frequency distribution of synonymous codons" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21148" PostTypeId="2" ParentId="21145" CreationDate="2014-09-09T02:51:38.573" Score="1" Body="&lt;p&gt;Well, for start, there are &quot;mutational hot spots&quot;, regions that are more prone to mutation than others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for immune system genes, first of all, lung cells and heart cells and retina cells don't need to mutate those genes, because they don't use them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But you are right that in immune cells there is a lot of DNA futzing in the sequences for the heavy and light chains, in order to generate diversity in T and B-cell receptors.  Those receptor sequences are built in a mix-and match fashion, like building an outfit from a closet with a few pairs of pants and a few shirts.  Add in some messiness in cutting out the specific sequences, and you have a fair bit of diversity in receptor sequences possible from a single genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Later, once a B-cell or T-cell meets a matching antigen, the cell multiplies, and each descendant cell is subject to somatic hypermutation, in the hopes that one of the tweaked sequences will better match the antigen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But none of that is going to be very evolutionary relevant, since only mutations in gametes or gamete stem cells are passed on to the next generation.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-09-09T02:51:38.573" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21152" PostTypeId="2" ParentId="21146" CreationDate="2014-09-09T06:34:32.607" Score="5" Body="&lt;p&gt;The phenomenon of using different codons with different probabilities is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Codon_usage_bias&quot;&gt;codon usage bias&lt;/a&gt;. How the different codons are used is sometimes pretty different between species and requires some care. This is especially true when you want to overexpress sequences in bacteria to produce protein, which may need codon optimization to ensure an optimal codon usage (otherwise rare tRNAs can slow down the translation process). There is a database (based on the NCBI Genbank) which gives you the codon probabilities for different species:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.kazusa.or.jp/codon/&quot;&gt;Codon Usage Database&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Additionally, these papers might be interesting:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11719972&quot;&gt;Synonymous codon usage in bacteria.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;An evaluation of measures of synonymous codon usage bias.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Regarding your second question, I don't think (and I haven't found any evidence either) that the codon usage is dependent on the neighbours.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-09T06:34:32.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21153" PostTypeId="1" CreationDate="2014-09-09T06:47:08.607" Score="3" ViewCount="6717" Body="&lt;p&gt;I have always wondered if the lens in our eyes have any sort of magnification by default. And if yes, if we're actually seeing everything around us bigger/smaller than what they actually are!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has any research been done on this?&lt;/p&gt;&#xA;" OwnerUserId="9163" LastActivityDate="2014-09-09T12:05:38.233" Title="Does human eye lens have a magnification of its own?" Tags="&lt;eyes&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21154" PostTypeId="2" ParentId="21138" CreationDate="2014-09-09T08:13:36.920" Score="4" Body="&lt;p&gt;This sounds straightforward when thinking about it but finding hard evidence is not really easy. As this is too long for a comment, I have to put it in as an answer. Just a few thoughts: All enzymatic reactions are of course temperature dependent and usually have a temperature optimum at the specific living temperatures. For yeast this is around 27°C, for thermophiles this is much higher. For transcription an number of other factors including accessibility of the chromatin and the availability of cofactors play an important role besides the higher activity of one enzyme. This paper might be interesting for you: &quot;&lt;a href=&quot;http://genomebiology.com/2014/15/3/R45&quot; rel=&quot;nofollow&quot;&gt;Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA binding should be a statistical process between association and dissociation at a given binding site. At higher temperatures the turn-over at the binding site should be higher (because there is more energy available to promote dissociation). T&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.biophys.32.110601.141800&quot; rel=&quot;nofollow&quot;&gt;The thermodynamics of DNA structural motifs&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11509389&quot; rel=&quot;nofollow&quot;&gt;Thermodynamics of specific and nonspecific DNA binding by two&#xA;DNA-binding domains conjugated to fluorescent probes.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-09T08:13:36.920" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21155" PostTypeId="2" ParentId="21126" CreationDate="2014-09-09T08:33:30.550" Score="2" Body="&lt;p&gt;With this method you want to identify proteins on cancer cells which are immunogenic so you can use them to boost an immune response against the cancer cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To do so, you extract the complete mRNA from a cancer. These mRNAs represent all the genes which this cancers expresses (which then also contains the immunogenic proteins). These mRNAs are cloned into bacteriophages (viruses that only infect bacteria) and are then used to infect bacteria. During this infection the virus expresses the protein which has been cloned into his sequence and which originates from the cancer cell. The infection of the bacteria leads to the formation of plaques (wholes) in the bacteria which grow on the surface of a culture plate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You then use the serum of cancer patients on these expressed proteins to see, if there are antibodies which can recognize these cancer antigens (and could be used to detect and mark them). If there are proteins which only react to the sera of cancer patients but not to controls (to exclude) unspecific reactions, then these proteins are identified and can be used to generate antibodies against this specific cancer type. It works like in the figure below (from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21339995&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; paper):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Q9rA3.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-09T08:33:30.550" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21156" PostTypeId="2" ParentId="21137" CreationDate="2014-09-09T09:52:44.720" Score="2" Body="&lt;p&gt;I don't see why not, once the sodium and potassium channels along the axon have returned to their resting state. But I am not aware of a hard citation. I would suggest looking in the recent optogenetic literature, where researchers are exciting axons and axonal terminals using channelrhodopsin. People have most likely quantified action potentials for varying illumination durations and intensities, and you might be able to judge by the maximum firing rate how feasible multiple simultaneous spikes would be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, it's most likely possible to trigger an antidromic spike while the neuron is firing an orthodromic spike. Not quite what you asked, but close.&lt;/p&gt;&#xA;" OwnerUserId="8495" LastActivityDate="2014-09-09T09:52:44.720" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21157" PostTypeId="1" AcceptedAnswerId="21161" CreationDate="2014-09-09T11:50:57.867" Score="6" ViewCount="2252" Body="&lt;p&gt;Do female chest size have anything to do with muscle?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know many female athlete and their average breast size is much bigger than normal female that does not tend to play sports. Do this have any relation to chest muscle?? If so can you explain how it does.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance&lt;/p&gt;&#xA;" OwnerUserId="9166" LastEditorUserId="5144" LastEditDate="2014-09-09T18:03:58.470" LastActivityDate="2014-09-10T00:21:27.007" Title="Chest muscle and female breast size" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21158" PostTypeId="2" ParentId="21153" CreationDate="2014-09-09T12:05:38.233" Score="5" Body="&lt;p&gt;The magnification by the lens of the eye is well understood.  &lt;a href=&quot;http://www2.ensc.sfu.ca/~glennc/e894/e894l5i.pdf&quot; rel=&quot;noreferrer&quot;&gt;This document&lt;/a&gt;, written by &lt;a href=&quot;http://www2.ensc.sfu.ca/~glennc/&quot; rel=&quot;noreferrer&quot;&gt;Dr. Glenn Chapman&lt;/a&gt; at Simon Frasier University in British Columbia, Canada, lays out some of the technical details.  The image below is taken from that document. I modified it slightly by enlarging the $s$ and $s'$ variables because they are important for this answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qFQlD.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a simple lens like that in our eyes, magnification, $m$, is calculated as &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$m= \frac{s'}{s}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $s'$ is the distance between the lens and the retina at the back of the eye, and $s$ is the distance between the object and the lens. For the human eye, the distance $s'$ is about 24 mm, or just a bit under 1 inch.  For an object to have exactly 1:1 size ratio (no magnification or reduction), it would have to be exactly that same distance from the lens. That is, the object would have to be about 24 mm in front of our eye. The problem is that, unless you are &lt;a href=&quot;http://www.aoa.org/patients-and-public/eye-and-vision-problems/glossary-of-eye-and-vision-conditions/myopia?sso=y&quot; rel=&quot;noreferrer&quot;&gt;myopic (nearsighted)&lt;/a&gt;, you cannot focus on objects closer than about 25 cm (about 10 inches)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most objects are much farther away from the lens than 24 mm. That means $s$ is a much larger value than $s'$, making $m$ a fraction less than 1. A value less than 1 means that our lens is not magnifying the object but instead is reducing or demagnifying the object. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a simple experiment, hold your finger upright in front of your eyes at arms length.  Bring your finger closer and closer until you feel your eye lashes. Your finger looks smallest when it is farthest away from your eye. As you bring it closer ($s$ is getting smaller) your finger appears larger and larger. When your finger gets to about 24 mm, then $m=1$. When your finger touches your eye lashes, the distance is less than 24 mm, and the finger is magnified to larger than actual size ($s &amp;gt; s'$ and $m &amp;gt; 1$). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This also explains why distant objects appear smaller than closer objects. If you see a stop sign at 500 m and a stop sign at 100 m, the closer sign looks larger than the more distant sign.  But which is the actual size? Neither, because the lens changes the apparent size. The way to see the actual size is to stand with your eye about 24 mm away from the sign. Then, magnification will be exactly 1:1 and you'll know the true size of the sign. You just won't be able to focus on it.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-09-09T12:05:38.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21159" PostTypeId="1" AcceptedAnswerId="21163" CreationDate="2014-09-09T12:06:11.470" Score="65" ViewCount="9125" Body="&lt;p&gt;I was thinking yesterday about insects (as there was a spider in the house, and I couldn't help but think of anything else, even though they aren't insects), and I started to wonder if ants sleep? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After thinking about it for a while I decided that they might sleep, but then what would be the purpose of sleeping for them? My limited understanding of the need of sleep is that it is used for the brain to compartmentalise the events of the day and allow memories to be formed. But ants don't really have to think about much during the day, given that they act more as a collective than an individual. Or in the case of other insects, they have simpler more instinctive brains which rely on taxis, reflexes and kineses. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, do ants and other insects sleep (or do they have a different type of sleep to us) and what would the purpose of it be for them?&lt;/p&gt;&#xA;" OwnerUserId="6330" LastActivityDate="2015-12-17T10:54:57.710" Title="Do ants or other insects sleep, and if so why?" Tags="&lt;entomology&gt;&lt;sleep&gt;&lt;behaviour&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="21" ContentLicense="CC BY-SA 3.0" />
  <row Id="21160" PostTypeId="2" ParentId="21159" CreationDate="2014-09-09T12:29:12.057" Score="37" Body="&lt;p&gt;The short answer is apparently yes.  Studies on sleep in insects date back to papers published by Phil and Nellie Rau in &lt;a href=&quot;http://chla.library.cornell.edu/cgi/t/text/pageviewer-idx?c=chla;cc=chla;rgn=full%20text;idno=5077679_4177_003;didno=5077679_4177_003;view=image;seq=0003;node=5077679_4177_003%3A3.1&quot;&gt;1916&lt;/a&gt; and &lt;a href=&quot;http://chla.library.cornell.edu/cgi/t/text/pageviewer-idx?c=chla;cc=chla;rgn=full%20text;idno=5077679_4199_004;didno=5077679_4199_004;view=image;seq=0128;node=5077679_4199_004%3A4.18&quot;&gt;1938&lt;/a&gt;. &lt;a href=&quot;http://learnmem.cshlp.org/content/16/11/698.full.html&quot;&gt;Hussaini et al. (2003)&lt;/a&gt; showed that sleep does affect memory formation in honey bees. They showed that retention of &lt;a href=&quot;http://www.springerreference.com/docs/html/chapterdbid/319711.html&quot;&gt;extinction learning&lt;/a&gt; is significantly reduced in bees that were sleep-deprived.  More about sleep in honeybees can be found in this paper by &lt;a href=&quot;http://www.researchgate.net/publication/255718730_4._Eban-Rothschild_A._D._Bloch_G._(2012)_Circadian_Rhythms_and_Sleep_in_Honey_Bees_chapter_1.3._p._31-46_in__Honeybee_Neurobiology_and_Behavior/file/50463520692ec8d481.pdf&quot;&gt;Eban-Rothschild and Block (2012)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did not find anything on sleeping in ants after a brief Google Scholar search but ants and bees are both hymenopterans, so it's reasonable to hypothesize that many of the effects of sleep (and sleep deprivation) found in bees could also apply to ants. The Eban-Rothschild and Block paper linked above has some comparisons of circadian rhythms between ants and bees before discussing sleep as a function of circadian rhythms.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-09-09T12:29:12.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21161" PostTypeId="2" ParentId="21157" CreationDate="2014-09-09T12:47:11.557" Score="10" Body="&lt;p&gt;The female breast is composed primarily of &lt;a href=&quot;http://ww5.komen.org/BreastCancer/TheBreast.html&quot;&gt;fat and connective tissue&lt;/a&gt; plus lobules and ducts for milk production and delivery.  The pectoralis muscles form a thin layer beneath the breast, as seen in the figure in the link. An athletic female can enlarge the size of the pectoralis muscle and the laterals muscles, just as male athletes can enlarge their &quot;pecs&quot; and &quot;lats&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exercise burns fat so athletic women often &lt;a href=&quot;http://www.livestrong.com/article/390722-can-exercise-reduce-breast-size/&quot;&gt;experience reduction in breast size&lt;/a&gt;. Of course, other factors such as diet and genetics also influence the effects of exercise on fat burning.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, athletic females with enlarged lateralis muscles and pectoralis muscles may have a larger overall bust size but the cup size of their breasts might actually be reduced.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-09-10T00:21:27.007" LastActivityDate="2014-09-10T00:21:27.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21162" PostTypeId="2" ParentId="21145" CreationDate="2014-09-09T13:02:32.640" Score="1" Body="&lt;p&gt;If by &quot;consistent&quot; you mean homogenous, the answer is no. Regions conserved among individuals (and/or species) tend to accumulate less mutations (specially avoiding deleterious mutations). Even within a gene sequence, there are conserved regions which accumulate low number of changes, whereas non-conserved regions accumulate many mutations.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastActivityDate="2014-09-09T13:02:32.640" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21163" PostTypeId="2" ParentId="21159" CreationDate="2014-09-09T13:35:44.537" Score="61" Body="&lt;p&gt;A quick search on Web of Science yields &quot;Polyphasic Wake/Sleep Episodes in the Fire Ant, Solenopsis Invicta&quot; (&lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs10905-009-9173-4&quot;&gt;Cassill et al., 2009&lt;/a&gt;, @Mike Taylor found an accessable copy &lt;a href=&quot;http://www.dormivigilia.com/wp-content/uploads/2009/04/sleep-in-ants.pdf&quot;&gt;here&lt;/a&gt;) as one of the first hits. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main points from the abstract:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Yes, ants sleep.&lt;/li&gt;&#xA;&lt;li&gt;indicators of deep sleep: &#xA;&lt;ul&gt;&#xA;&lt;li&gt;ants are non-responsive to contact by other ants and antennae are folded&lt;/li&gt;&#xA;&lt;li&gt;rapid antennal movement (RAM sleep)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Queens have about 92 sleep episodes per day, each 6 minutes long.&lt;/li&gt;&#xA;&lt;li&gt;Queens synchronize their wake/sleep cycles.&lt;/li&gt;&#xA;&lt;li&gt;Workers have about 253 sleep episodes per day, each 1.1 minutes long.&lt;/li&gt;&#xA;&lt;li&gt;&quot;Activity episodes were unaffected by light/dark periods.&quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you study the paper you might find more information in its introduction or in the references regarding why ants sleep, although there doesn't seem to be scientific consens. The abstract only says that the shorter total sleeping time of the workers is likely related to them being disposable.&lt;/p&gt;&#xA;" OwnerUserId="9167" LastEditorUserId="9167" LastEditDate="2014-09-09T13:44:01.803" LastActivityDate="2014-09-09T13:44:01.803" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21165" PostTypeId="2" ParentId="21146" CreationDate="2014-09-09T13:52:56.537" Score="3" Body="&lt;p&gt;The codon usage biases are species-dependant, so you may have to measure it for the genome or set of genes you are interested in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This bias is at least in some cases correlated to the genome composition in terms of A, T, G and C (see figure 3 of this &lt;a href=&quot;http://dx.doi.org/10.1093/molbev/msu105&quot; rel=&quot;nofollow&quot;&gt;paper about cyanobacteria&lt;/a&gt;). So in a sense, it is indeed dependent on the context if you include nucleotide composition in what you call &quot;context&quot;.&lt;/p&gt;&#xA;" OwnerUserId="1486" LastActivityDate="2014-09-09T13:52:56.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21169" PostTypeId="1" CreationDate="2014-09-09T22:51:59.050" Score="3" ViewCount="1177" Body="&lt;p&gt;I read that X-inactivation doesn't tend to happen in males, but then when someone is XXY, they are a male because of the Y. However these individuals tend to live. So does that mean that X-inactivation happens in males or else these individuals would die?&lt;/p&gt;&#xA;" OwnerUserId="9050" LastEditorUserId="-1" LastEditDate="2014-10-30T20:45:42.837" LastActivityDate="2014-10-30T20:45:42.837" Title="XXY (Klinefelter's) &amp; Trisomy 21 &amp; X-inactivation" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21170" PostTypeId="2" ParentId="21169" CreationDate="2014-09-10T02:41:01.620" Score="7" Body="&lt;p&gt;X-inactivation does occur in XXY individuals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In phenotypically normal XX females, one X chromosome is inactivated.  Which one of the two X chromosomes is inactivated in any given cell &lt;a href=&quot;http://www.nature.com/scitable/topicpage/x-chromosome-x-inactivation-323&quot;&gt;is random&lt;/a&gt;. Therefore, about one half of the cells should have the maternal X active and the other half should have the paternal X active.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;XXY individuals show a wide range of clinical symptoms and intellectual ability.  &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/1096-8628(20010101)98:1%3C25::AID-AJMG1015%3E3.0.CO;2-X/abstract&quot;&gt;Iitsuka et al. (2000)&lt;/a&gt; suggested that this variation may be explained by a bias in X-inactivation.   They found that about 31% (5 of 16) individuals (either XXY or XXYY) shows a very strong bias of X inactivation, which they defined as at least 80% of the cells inactivating one particular X chromosome. Two individuals has biased inactivation of the paternal X and the other three had biased inactivation of one of the maternal X chromosomes. The sample size is rather small (not surprising) but X inactivation is occuring.  &lt;a href=&quot;http://47xxy.com/Hermes/Samango%20Sprouse.pdf&quot;&gt;Samango-Sprouse (2001)&lt;/a&gt; argues that incomplete inactivation of one X chromosome may also explain some of the more severe clinical mental disorders.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For &lt;a href=&quot;http://www.nature.com/scitable/topicpage/trisomy-21-causes-down-syndrome-318&quot;&gt;Trisomy 21 (Down's Syndrome)&lt;/a&gt;, the individual as three copies of chromosome 21, so X inactivation is not an issue. However, scientists are studying whether &lt;a href=&quot;http://phenomena.nationalgeographic.com/2013/07/17/how-to-shut-down-the-extra-chromosome-in-downs-syndrome/&quot;&gt;Xist can shut down the third copy of chromosome 21&lt;/a&gt;.  The Xist gene is transcribed to produce a large molecule of RNA. That RNA is what usually causes X inactivation.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848249/&quot;&gt;Jiang et al. (2013)&lt;/a&gt; were able to show that Xist can coat one of the chromosome 21 copies, performing essentially the same inactivation function that it does for the X chromosome. So far, though, this work has been entirely in the lab (in vitro).&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-09-10T02:41:01.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21172" PostTypeId="2" ParentId="21130" CreationDate="2014-09-10T05:58:41.733" Score="4" Body="&lt;p&gt;It could be a crow, a blackbird or a raven for all we know because deformed bills on birds has been a matter of debate (&lt;a href=&quot;http://www.rrbo.org/conservation-science/research/bird-banding/bill-deformities/&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;) and there is a group on flickr (&lt;a href=&quot;https://www.flickr.com/groups/badbills/&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;) where you can post such pictures. I have actually noticed few pictures of birds with beaks that resemble the one in your photo. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/D4tNm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;A crow with a deformed bill (&lt;a href=&quot;https://www.flickr.com/photos/25348030@N07/9470671637/in/pool-badbills&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-09-10T05:58:41.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21173" PostTypeId="1" CreationDate="2014-09-10T09:30:50.780" Score="5" ViewCount="9007" Body="&lt;p&gt;I'm slightly confused as to the difference between thylakoids and lamellae. My understanding was that thylakoids are 'discs' that are stacked into grana and there is a membrane between the grana called the integranal lamellae. However in my text book it says that 'the inner membrane is folded into lamellae, which are stacked up like piles of pennies. Each stack of lamallae is called a granum.' This sounds to me like the description of thylakoids.&#xA;It later says 'grana are stacks of flattened membrane compartments, called thylakoids'...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could someone clarify this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance :)&lt;/p&gt;&#xA;" OwnerUserId="6136" LastEditorUserId="3624" LastEditDate="2014-09-10T18:35:53.037" LastActivityDate="2018-05-08T21:03:07.573" Title="Difference between thylakoids and lamellae in a chloroplast?" Tags="&lt;botany&gt;&lt;plant-anatomy&gt;&lt;chloroplasts&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21174" PostTypeId="2" ParentId="14919" CreationDate="2014-09-10T09:40:50.703" Score="18" Body="&lt;p&gt;The pigmentation of hairs is achieved by the follicular melanocytes (specialized pigment cells) at the base of the hair shaft. These cells produce the pigment which is subsequently transported into the cells which produce the hair and integrated into the hair matrix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides genetic reasons, there are two major ways of losing this pigmentation. First, as a part of the normal &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_hair_growth&quot; rel=&quot;noreferrer&quot;&gt;hair cycle&lt;/a&gt;, the hair grows for a while until it falls out and the hair follicle regresses. In this process the cells in the hair follicle die, including those which made the hair as well as of the melanocytes. In this step of the hair cycle the hair follicle changes its morphology. When a new hair cycle starts, the pigment cells in the hair follicle are replenished from a stem cell population called melanocyte stem cells. These cells are located in the hair bulge (marked in red in the figure below). The cells then start to proliferate to multiply their number. A few of these cells stay stem cells (to be able to repopulate the pigment cells after the next hair cycle.) Others differentiate into melanocytes which subsequently migrate towards the bottom of the hair bulb (shown in green in the figure). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5tFDA.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Over time, the number of stem cells gets lower, and at some point there are none left. This leads to a situation where the pigment cells are not replenished at the beginning of a new hair cycle and the hair stays unpigmented. As this is a continuous process, the pigmentation gets weaker before it is completely lost. As far as this process is understood to date, this depigmentation is irreversible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two very interesting papers about this topic:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S009286740500293X&quot; rel=&quot;noreferrer&quot;&gt;Melanocyte Stem Cell Maintenance and Hair Graying&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23018363&quot; rel=&quot;noreferrer&quot;&gt;Melanocyte stem cells: biology and current aspects.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The other reason for losing pigmentation (temporarily or permanent) is the generation of so called &quot;reactive oxygen species&quot; (Hydrogenperoxide) in the cells of the hair follicle, which then destroy the pigment. This is basically the same reaction which is used to bleach hairs, but in this instance from inside. This reaction can have numerous causes, among them are vitiligo and stress. The reason for the build-up of the hydrogenperoxides is that enzymes, which usually break them down before they can cause harm are either mutated or downregulated. If the level of these enzymes (the catalases) goes back to normal, pigmentation is also getting back to normal. This has been tested experimentally with people who suffer from the pigmentation disease vitiligo.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929555/&quot; rel=&quot;noreferrer&quot;&gt;Oxidative Stress in Ageing of Hair&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.fasebj.org/content/early/2013/04/29/fj.12-226779.abstract&quot; rel=&quot;noreferrer&quot;&gt;Basic evidence for epidermal H2O2/ONOO−-mediated oxidation/nitration&#xA;in segmental vitiligo is supported by repigmentation of skin and&#xA;eyelashes after reduction of epidermal H2O2 with topical&#xA;NB-UVB-activated pseudocatalase PC-KUS&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2019-03-22T07:54:38.140" LastActivityDate="2019-03-22T07:54:38.140" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="21175" PostTypeId="2" ParentId="14919" CreationDate="2014-09-10T10:09:16.703" Score="8" Body="&lt;p&gt;A search of the Internet shows many anecdotal cases of people reporting their grey or white hair returning to their normal color.  Interestingly, many of these ancedotal cases begin by stating that their hair had turned grey or white at a young age (early 20s) before returning to it's natural color.  Finding a scientific explanation does not seem as easy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dr. Robert Graves &lt;a href=&quot;http://www.nejm.org/doi/pdf/10.1056/NEJM184709010370503&quot;&gt;reported in 1847&lt;/a&gt; a case of a military field officer that had contracted dysentery, fever and other diseases. Prior to his illinesses, the officer's hair had turned white. After a few years of receiving treatment for his illiness, his hair had returned to its natural color.  This is consistent with a study by &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2710.1992.tb01307.x/abstract&quot;&gt;Bublin and Thompson (1992)&lt;/a&gt; which found that various drugs can cause sudden hair color changes. (The abstract does not say whether this includes a change from white to natural color.) &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2133.2002.04591.x/abstract&quot;&gt;Schaffrali et al. 2002)&lt;/a&gt; noted two people that had a disease called &lt;a href=&quot;http://www.porphyriafoundation.com/about-porphyria/types-of-porphyria/PCT&quot;&gt;porphyria cutanea tarda&lt;/a&gt; regained their hair color.  Therefore, stress from disease or drugs may cause hair color changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://ebm.sagepub.com/content/70/1/79.short&quot;&gt;Flesch (1949)&lt;/a&gt; found that the fur of black rats could be turned white when fed a diet deficient in copper. Restoring copper to the diet turned the fur color back to its normal color. &lt;a href=&quot;http://jn.nutrition.org/content/87/1/69.full.pdf&quot;&gt;Arthur (1965)&lt;/a&gt; found that excess molybdenum in the diet of guinea pigs can inhibit copper,  causing their hair to turn white. These results suggest that diet can also play a role in color loss and gain in mammals.  &lt;a href=&quot;http://archderm.jamanetwork.com/article.aspx?articleid=547429&quot;&gt;Vitamin B12 deficiency&lt;/a&gt; may also have affect hair color.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These studies show that regaining hair pigmentation has many possible causes. Of course, I have no way of knowing whether any of these apply to you, nor am I qualified to make such judgements. But, hopefully, some of this information will help you to understand some of the possible reasons for hair color change in humans.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-09-10T10:09:16.703" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21176" PostTypeId="1" CreationDate="2014-09-10T10:24:39.980" Score="0" ViewCount="189" Body="&lt;p&gt;I have protein sequences from STRING database:&#xA;The amino acid sequence files are like this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;4932.Q0010 (Saccharomyces cerevisiae)&#xA;  MYYIMFLYNMLLIIILIFYSIVGVPIIIFNNNYYWDPDIFLFIIYYFIKFIIIFNLYLYYMINYIVYTPSGSPPGRGTYI&#xA;  LLYNMLYSYNMFIDYVMKFITCVTYMYLMFWLLSPTPSPYYVSEVPVS&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I want the corresponding nucleotide sequence for the same protein ID.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;4932.Q0010&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I tried emboss &lt;a href=&quot;http://www.ebi.ac.uk/Tools/st/emboss_backtranseq/&quot; rel=&quot;nofollow&quot;&gt;http://www.ebi.ac.uk/Tools/st/emboss_backtranseq/&lt;/a&gt;&#xA;But emboss is based on codon usage and backtranslate and it doesn't give me the original nucleotide sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then I tried DDBJ &lt;a href=&quot;http://getentry.ddbj.nig.ac.jp/top-e.html&quot; rel=&quot;nofollow&quot;&gt;http://getentry.ddbj.nig.ac.jp/top-e.html&lt;/a&gt;&#xA;But DDBJ gives only amino acid sequences for corresponding Uniprot ID.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do i get the original nucleotide sequence for the STRING protein sequences using STRING id or UniProt ID?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help in this regard is highly appreciated.&lt;/p&gt;&#xA;" OwnerUserId="8135" LastActivityDate="2014-09-11T14:57:09.157" Title="Nucleotide sequence for STRING protein sequence" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21177" PostTypeId="1" AcceptedAnswerId="21180" CreationDate="2014-09-10T11:21:12.117" Score="11" ViewCount="1452" Body="&lt;p&gt;I was just reading the sleep threads, and I wondered, why is the body so constructed so that sleep is necessary? (Is it just a design error?) But then, how do things come to be awake at all? How did this happen? Yes, I can see the advantages, but how did it happen? What is &quot;awake&quot;? Are single-cell animals awake? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question I want to ask is, how did things progress from just sitting around ingesting and growing, like plants, to being something more? Is it more? What do &quot;wakers&quot; have that the rest don't?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry, I'm not a biologist, this may be a foolish question, or in the wrong place.&lt;/p&gt;&#xA;" OwnerUserId="9183" LastActivityDate="2018-06-08T15:22:53.983" Title="Why sleep? No, actually, why wake?" Tags="&lt;sleep&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21178" PostTypeId="2" ParentId="21176" CreationDate="2014-09-10T11:37:20.717" Score="2" Body="&lt;p&gt;Google is not a bad resource for such a question.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case I find that the Yeast Genome site has a button which returns the nucleotide sequence. You can select the genomic sequence for the locus or the coding (CDS) sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=Q0010&quot; rel=&quot;nofollow&quot;&gt;http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=Q0010&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They also give a link to NCBI at the bottom of the page.  I think the reason you were having such a hard time is that UniProt extracted the protein sequence from the mitochondrial genome record.  Like many genome ORF predictions, Q0010 does not seem to have a distinct nucleotide record assigned yet.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Summary: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general  you can do a web search for the uniprot id to start.  In many cases, like this one you will find that the nucleotide seq is only a chromosomal sequence record.   Biodatabases are a bit of a maze - there are scores of them out there, you may find that someone has clipped the nucleotide sequence of the gene out, which is helpful if there are introns!&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-09-11T14:57:09.157" LastActivityDate="2014-09-11T14:57:09.157" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21179" PostTypeId="2" ParentId="21177" CreationDate="2014-09-10T12:41:54.340" Score="-2" Body="&lt;p&gt;All organisms (except viruses?) need some kind of nutrition to survive and reproductive activities for the species to survive. As humans don't do these while asleep in a first approximation I would consider those life phases as sleep when these do not happen. In this sense clostridium bacteria could be considered asleep when in their endospore states, a sunflower seed could also be considered asleep as it is inactive.&lt;/p&gt;&#xA;" OwnerUserId="1413" LastActivityDate="2014-09-10T12:41:54.340" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="21180" PostTypeId="2" ParentId="21177" CreationDate="2014-09-10T12:46:10.100" Score="17" Body="&lt;p&gt;Based on various comments, I've expanded this answer. Though long, I cannot cover the depth of the topic of sleep but I tried to address the issues asked in the original question while broadly highlighting various aspects about sleep research. I welcome any suggestions for improvement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is sleep?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To know what it means to be awake, you must know what it means to be in a state of sleep. These are two alternative states for animals that sleep. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finding a concise scientific definition of sleep is difficult, probably because sleep is a very complex process. For example, &lt;a href=&quot;http://www.researchgate.net/publication/40834254_The_memory_function_of_sleep/file/d912f5032417709272.pdf&quot; rel=&quot;noreferrer&quot;&gt;Diekelmann and Born (2010)&lt;/a&gt; state that,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sleep has been identified as a state that optimizes the consolidation of newly acquired information in memory...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and later&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sleep is characterized by the cyclic occurrence of rapid eye movement (REM) sleep and non-REM sleep, which includes slow wave sleep (SWS, stages 3 and 4) and lighter sleep stages 1 and 2....&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Most attempts to explain what sleep is include the four stages of sleep along with REM (rapid eye movement sleep). The stages are nicely explained by this National Institutes of Heath website on &lt;a href=&quot;http://www.ninds.nih.gov/disorders/brain_basics/understanding_sleep.htm&quot; rel=&quot;noreferrer&quot;&gt;Brain Basics: Understanding Sleep&lt;/a&gt;. Each stage of sleep can be identified by specific types of brain waves, shown below (image from &lt;a href=&quot;http://bama.ua.edu/~sprentic/large101%20outline-sleep.htm&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/M3eNt.jpg&quot; alt=&quot;Comparison of brain wave activity in the states Awake, Drowsy, Stage 1 sleep, Stage 2 sleep, Slow-wave sleep (stage 3 and stage 4 sleep), and REM sleep&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notice that the first wave pattern is characteristic of being awake.  The wave patterns change as an individual becomes drowsy and then falls asleep. While asleep, the brain cycles through the different stages, each with its characteristic brain waves.  Associated with these stages are changes in metabolic activity and physical capabilities. For example, the &lt;a href=&quot;http://www.ninds.nih.gov/disorders/brain_basics/understanding_sleep.htm&quot; rel=&quot;noreferrer&quot;&gt;Brain Basics&lt;/a&gt; site notes that we become less responsive to external stimuli and metabolic activity slows. During REM, breathing becomes rapid and we can't move the muscles in our arms or legs. Similar states are found in other invertebrate and vertebrate organisms, which suggests that these are common indicators of sleep or a sleep-like state. Some examples of these states are given in the citations and links below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Defining &quot;awake&quot; seems just as difficult as defining &quot;asleep&quot; but once again neural activity seems to be key indicator. As shown in the figure above, being awake has characteristic wave patterns in the brain that are distinct from the wave patterns associated with sleep. In addition, none of the physiological/physical states associated with sleep stages are present when you are awake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In both cases, asleep and awake, the indicators seem to be based on characteristic neurological activities in the brain or, in the case of some invertebrtes, the organized nervous system.  This interpretation is important when considering whether organisms without any type of nervous system is capable of sleep or the alternate state: awake.  More on this at the end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why sleep?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Science magazine, in the 125th anniversary issue, made a list of 125 big questions that remain to be answered by scientists. One of those questions was &quot;Why do we sleep?&quot; The role of sleep remains elusive but many ideas have been put forth about the role of and the evolution of sleep. The leading idea seems to be memory consolidation. This article by &lt;a href=&quot;http://www.eeb.ucla.edu/Faculty/Kavanau/OriginEvolutionSleep.pdf&quot; rel=&quot;noreferrer&quot;&gt;Kavanau (1997)&lt;/a&gt; reviews ideas about the function of sleep and why it evolved.  He suggests that sleep and memory evolved as as ways to improve or maintain effective connections among the nerve cells in the brain. Some circuits are used frequently, such as those used to process sensory information like vision. Other circuits are used less frequency, such as circuits that can be used to store memories. Sleep may allow those infrequently used circuits to be activated and used without causing conflict with the circuits used during &quot;restful waking.&quot; In other words, sleep may allow the lesser used circuits to be exercised, which can help to consolidate memories. So, at least one function of sleep may be to help maintain efficiency in how information is moved around the brain by maintaining the brain circuitry.  See also this review by &lt;a href=&quot;http://www.nature.com/nature/journal/v437/n7063/full/nature04285.html&quot; rel=&quot;noreferrer&quot;&gt;Siegel (2005)&lt;/a&gt; and the previously mentioned article by Diekelmann and Born (2010).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.nature.com/scitable/blog/scibytes/got_sleep&quot; rel=&quot;noreferrer&quot;&gt;Scitable article&lt;/a&gt; has a nice overview of the importance of sleep for humans, as does the &lt;a href=&quot;http://www.ninds.nih.gov/disorders/brain_basics/understanding_sleep.htm&quot; rel=&quot;noreferrer&quot;&gt;Brain Basics&lt;/a&gt; site. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What organisms sleep or have sleep-like activity?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sleep has been well-studied in vertebrates, from fishes &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1644087/pdf/procrsmed00350-0073a.pdf&quot; rel=&quot;noreferrer&quot;&gt;(Marshall 1972)&lt;/a&gt; to mammals &lt;a href=&quot;http://www.mb.mahidol.ac.th/neuroscience/intranet/2011/Allan%20Hobson_The%20Neurobiology%20of%20Sleep.pdf&quot; rel=&quot;noreferrer&quot;&gt;(Pace-Schott and Hobson 2002)&lt;/a&gt;. However, not all vertebrates necessarily sleep &lt;a href=&quot;http://www.eeb.ucla.edu/Faculty/Kavanau/VertebratesNeverSleep.pdf&quot; rel=&quot;noreferrer&quot;&gt;(Kavanau 1998)&lt;/a&gt;. For example, continuously swimming fishes like some sharks and blind cave fishes may not sleep. These are just three references of &lt;em&gt;many&lt;/em&gt; about sleep in vertebrates. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sleep and sleep-like activity has not been as well studied in inertebrates. As noted in &lt;a href=&quot;https://biology.stackexchange.com/q/21159/8517&quot;&gt;this thread&lt;/a&gt;, there is evidence for sleep in at least some insects. Cephalopods like octopuses show signs of sleep &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1053810006001504&quot; rel=&quot;noreferrer&quot;&gt;(Mather 2008)&lt;/a&gt;. &lt;em&gt;Caenorhabditis elegans&lt;/em&gt;, a nematode worm and model biological system, shows sleep-like states tht are similar to mammals and fruit flies &lt;a href=&quot;http://www.its.caltech.edu/~bi250c/papers/Raizen%20et%20al%202008.pdf&quot; rel=&quot;noreferrer&quot;&gt;(Raizen et al. 2008)&lt;/a&gt;. The most basal organism that shows evidence of sleep-like patterns is a jellyfish called &lt;em&gt;Chironex fleckeri&lt;/em&gt; &lt;a href=&quot;http://homepage.psy.utexas.edu/HomePage/Class/Psy355D/jellyfish.pdf&quot; rel=&quot;noreferrer&quot;&gt;(Kavanau 2006)&lt;/a&gt;. Cnidarians like jellyfishes are the basal (most &quot;simple&quot;) group of organisms with an organized nervous system. Interestingly, &lt;em&gt;C. fleckeri&lt;/em&gt; process a lot of visual information obtained through their 24 eyes. Twelve of the eyes are simple, light-receiving structures but 8 of the eyes are camera-like, meaning they have a lens.  Kavanau (2006) argued that sleep (up to 15 hours) in this jellyfish allows time for its simple nervous system to process the visual information obtained while it is awake. The presence of sleep-like activity in jellyfish and nematode worms suggest that sleep is an evolutionarily ancient phenomenon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Sleep_(non-human)&quot; rel=&quot;noreferrer&quot;&gt;sleep in non-humans&lt;/a&gt; overviews evidence for sleep in vertebrates and invertebrates. It's not clear whether androids sleep or &lt;a href=&quot;http://en.wikipedia.org/wiki/Do_Androids_Dream_of_Electric_Sheep%3F&quot; rel=&quot;noreferrer&quot;&gt;what they dream about&lt;/a&gt; if they do sleep.$^1$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do single-celled organisms sleep?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is (to me) a tricky question. Sleep is associated with specific types of neural activity in the brain or nervous system. In addition, sleep-like neural activity has been found in diversity of organisms with some type of nervous system, and seems evolutionarily old. I therefore think that any organism that has some form of organized neural center (brain, brain-like organ or centralized nervous system) has the potential to show some type of sleep-like patterns. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In contrast, organisms lacking any type organized nervous system would not be capable of sleep, at least as currently defined. If they do not sleep, then they also cannot be awake because being &quot;awake&quot; seems to be recognized as neural activity not typical of sleep.  Therefore, it seems to me that single celled organisms like bacteria and paramecium are neither sleeping nor awake.  Plants are neither sleeping nor awake. They are metabolically active but they are neither asleep nor awake because they do not have any type of neural activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not a sleep researcher (but sometimes I am a sleepy one) nor am I a neurophysiologist. I just walked through my train of thought. I welcome contrary views along with the supporting science.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature Cited&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diekelmann, S. and J. Born. 2006. The memory function of sleep. Nature Reviews Neuroscience 11: 114-126.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kavanau, J.L. 1997. Origin and evolution of sleep: Roles of vision and endothermy. Brain Research Bulletin 42: 245-264.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kavanau, J.L. 1998. Vertebrates that never sleep: Implications for sleep's basic function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kavanau, J.L. 2006. Is sleep's 'supreme mystery' unraveling? An evolutionary analysis of sleep encounters no mystery; nr does life's earliest sleep, recently discovered in jellyfish. Medical Hypotheses 66: 3-9.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Marshall, N.B. 1972. Sleep in fishes. Proceedings of the Royal Society of Medicine (abstract).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mather, J.A. 2008. Cephalopod consciousness: Behavioral evidence. Consciousness and cognition 17: 37-48.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pace-Schott, E.F. and J.A. Hobson. 2002. The neurobiology of sleep: Genetics, cellular physiology and subcortical networks. Nature Reviews Neuroscience 3: 591-605.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Raizen, D.M. et al. 2008. Lethargus is a &lt;em&gt;Caenorhabditis elegans&lt;/em&gt; sleep-like state. Nature 451: 561-572.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Siegel, J.M. 2005. Clues to the functions of mammalian sleep. Nature 437: 1264-1271.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Footnote&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;I could not resist.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="-1" LastEditDate="2018-06-08T15:22:53.983" LastActivityDate="2018-06-08T15:22:53.983" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="21181" PostTypeId="1" AcceptedAnswerId="21184" CreationDate="2014-09-10T14:31:30.697" Score="12" ViewCount="6668" Body="&lt;p&gt;What happens if one actually does go about eating the beads in those &quot;do-not-eat&quot; packets?&lt;/p&gt;&#xA;" OwnerUserId="9179" LastEditorUserId="1320" LastEditDate="2014-09-10T14:43:02.400" LastActivityDate="2016-04-04T00:29:37.740" Title="What would happen if one eats silica gel?" Tags="&lt;human-biology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21182" PostTypeId="2" ParentId="21181" CreationDate="2014-09-10T14:42:43.017" Score="3" Body="&lt;p&gt;I don't think it would harm you: apparently silica gel is a widely-used food additive. &lt;a href=&quot;http://en.wikipedia.org/wiki/Silica_gel#Food_additive&quot; rel=&quot;nofollow noreferrer&quot;&gt;According to Wikipedia:&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Silica gel, also referred to as silica aerogel or hydrated silica, has FDA GRAS (generally recognized as safe) status, meaning it can be added to food products without needing approval. Silica is allowed to be added to food in the US at up to 2% as permitted under 21 CFR 172.480. In the EU it can be in up to 5% concentrations.&lt;/p&gt;&#xA;&lt;p&gt;Listed uses include: anticaking agent, defoaming agent, stabilizer, adsorbent, carrier, conditioning agent, chillproofing agent, filter aid, emulsifying agent, viscosity control agent, and anti-settling agent.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However, obviously, you shouldn't plan on eating lots of it.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-10T14:42:43.017" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21183" PostTypeId="1" CreationDate="2014-09-10T15:16:16.450" Score="5" ViewCount="390" Body="&lt;p&gt;Which protocol of DNA extraction from plant oil-containing seeds take fast and good result in purity that can use in RT-PCR(Real Time polymerase chain reaction)?&lt;/p&gt;&#xA;" OwnerUserId="9101" LastEditorUserId="9101" LastEditDate="2014-09-10T15:35:27.493" LastActivityDate="2015-01-14T09:44:50.653" Title="DNA extraction from oil-containing seeds" Tags="&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21184" PostTypeId="2" ParentId="21181" CreationDate="2014-09-10T15:42:16.293" Score="17" Body="&lt;p&gt;Usually, nothing happens if you eat silica gel. In fact, you eat it all the time. Silica is added to improve flow in powdered foods. It occurs naturally in water, where it may help confer resistance against developing senility. Silica is just another name for silicon dioxide, the main component of sand.&#xA;Mayby you think if silica is harmless to eat, why do the packets carry the warning? The answer is that some silica contains toxic additives. For example, silica gel beads may contain toxic and potentially carcinogenic cobalt(II) chloride, which is added as a moisture indicator. You can recognize silica containing cobalt chloride because it will be colored blue (dry) or pink (hydrated). Another common moisture indicator is methyl violet, which is orange (dry) or green (hydrated). Methyl violet is a mutagen and mitotic poison. While you can expect most silica you encounter will be non-toxic, ingestion of a colored product warrants a call to Poison Control.&lt;/p&gt;&#xA;" OwnerUserId="9101" LastActivityDate="2014-09-10T15:42:16.293" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21185" PostTypeId="1" CreationDate="2014-09-10T16:14:56.697" Score="5" ViewCount="111" Body="&lt;p&gt;Khavari et al. recently demonstrated that a significant fraction of  one of the major forms of skin cancer (cutaneous squamous cell carcinomas) are associated with a mutated KNSTRN gene (a protein associated with the kinetochore). They identify a specific region of the gene as being a hotspot for UV induced mutation and suggest that these mutations may be an early event in the development of this type of skin cancer.(1)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abstract from their nature paper (paywalled):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Here we report the discovery of recurrent mutations concentrated at an ultraviolet signature hotspot in KNSTRN, which encodes a kinetochore protein, in 19% of cutaneous squamous cell carcinomas (SCCs). Cancer-associated KNSTRN mutations, most notably those encoding p.Ser24Phe, disrupt chromatid cohesion in normal cells, occur in SCC precursors, correlate with increased aneuploidy in primary tumors and enhance tumorigenesis in vivo. These findings suggest a role for KNSTRN mutagenesis in SCC development.(2)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My question:&#xA;Scientists could theoretically alter the nucleotide sequence of the KNSTRN gene to remove the mutation hotspot, potentially lowering the incidence of this type of skin cancer. But are there any downsides to doing so? Are there any cases where a UV mutatable hotspot has shown to have some useful function in a cell or organism?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.sciencedaily.com/releases/2014/09/140907181722.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedaily.com/releases/2014/09/140907181722.htm&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3091.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3091.html&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9079" LastEditorUserId="9079" LastEditDate="2014-09-16T02:02:19.903" LastActivityDate="2014-09-16T06:38:07.247" Title="Are there known downsides to removing UV mutation hotspots to prevent some skin cancers (Genetic sunblock)?" Tags="&lt;cell-biology&gt;&lt;molecular-genetics&gt;&lt;cancer&gt;&lt;mutations&gt;&lt;synthetic-biology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21186" PostTypeId="2" ParentId="21120" CreationDate="2014-09-10T16:51:52.037" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;There are at least 2 SAT chromosomes in each diploid nucleus. They&#xA;  play a vital role in the formation of the nucleolus after cell&#xA;  division is completed.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In humans, chromosomes number 13, 14, 15, 21 and 22 are examples of&#xA;  SAT chromosomes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;cuted from &lt;a href=&quot;http://en.wikipedia.org/wiki/Satellite_chromosome&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Satellite_chromosome&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9101" LastActivityDate="2014-09-10T16:51:52.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21188" PostTypeId="1" AcceptedAnswerId="21192" CreationDate="2014-09-10T17:13:51.787" Score="2" ViewCount="89" Body="&lt;p&gt;&lt;a href=&quot;http://genomebiology.com/2014/15/3/R45&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; gives measurement of transcription rate  and the unit they're using is microarray per hour.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, at 27°C the average expression of their genes is 236.1 microarray per hour (page 4). What does this unit mean? Given that each DNA spot in a microarray contain 1 picomole of DNA (&lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_microarray&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;), does it mean that the gene is transcribed into 1 picomole of RNA (or of nucleotides?) per hour? Or does it mean that 236.1 RNA are created every hours?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="5144" LastEditDate="2014-09-10T17:28:49.397" LastActivityDate="2014-09-10T19:36:45.767" Title="Transcription rate expressed in microarray per hour" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;dna-sequencing&gt;&lt;transcription&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21189" PostTypeId="1" AcceptedAnswerId="21236" CreationDate="2014-09-10T17:33:16.093" Score="1" ViewCount="170" Body="&lt;p&gt;For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on the dynamic of biochemical reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, my question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How does temperature influences rate of protein binding to a DNA-binding motif?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I am NOT looking for..&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not looking for a theoretical explanation of how temperature influences this process (I have basic understanding of the importance of the activation energy as displayed on a Maxwell-Boltzman distribution and of the michaelis-menten equation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I am looking for..&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for a function (eventually expressing the michaelis-menten constant as a function of the temperature) that I can plug in my algorithms to incorporate the influence of various temperatures on the process I want to simulate. I want to simulate the average gene network from an average standard eukaryote. For other purpose, I chose parameter values coming from the yeast. A index such as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Q10_(temperature_coefficient)&quot; rel=&quot;nofollow noreferrer&quot;&gt;$Q_{10}$&lt;/a&gt; would be very useful as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Similar already-answered question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A similar question (influence of temperature on transcription rate) has been asked and answered (by @rhill45) &lt;a href=&quot;https://biology.stackexchange.com/questions/21258/how-does-temperature-influences-rate-of-protein-decay&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-09-13T02:56:25.033" Title="Influence of temperature on protein binding and decay rates" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;proteins&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21192" PostTypeId="2" ParentId="21188" CreationDate="2014-09-10T18:01:55.513" Score="2" Body="&lt;p&gt;The units here are relative units of intensity.  There may be about a picomole of probes on a microarray spot, but the units of intensity are not scaled to the precise concentration of DNA on the spot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many variables which make exact measurements of intensity difficult to translate into the number of RNA bound to a spot.  The main one is nonspecific or non-target binding.  The oligomer on the array surface is typically between 25 and 50 bases long - it isn't the entire length of the RNA being tested by a given spot.  Another RNA may have some or most of the same sequence as a probe, or some labelled RNA will tend to get associated with some spots.  Usually factors such as the position of the spot on the array surface, the GC composition of the probe and variations in the batch of RNA preparation will also cause the intensity to vary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still, even with all this, with the same prep conditions and with an identical set of arrays, its valid to look at the intensity over time.  In this paper, the investigators took array measurements at different time points and at two different temperatures after 4-Thiouracil  is added to the cells, which allows one to follow RNA produced by transcription at a given time.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the units are arbitrary but still proportional to the mRNA found in the cells, a difference experiment like this is valid, even if the absolute concentration of any given RNA is still a bit of a mystery. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-09-10T19:36:45.767" LastActivityDate="2014-09-10T19:36:45.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21193" PostTypeId="2" ParentId="21075" CreationDate="2014-09-10T18:11:44.010" Score="0" Body="&lt;p&gt;Convincing answer was given &#xA;In Syrups or injections Drugs to dissolve the active ingredients use different types of alcohol use or alcohol is also used in some Toothpaste that maybe cause +alcohol test&lt;/p&gt;&#xA;" OwnerUserId="9101" LastActivityDate="2014-09-10T18:11:44.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21194" PostTypeId="1" AcceptedAnswerId="21211" CreationDate="2014-09-10T18:41:13.990" Score="4" ViewCount="390" Body="&lt;p&gt;When chasing away wasps or bees there is a danger of them stinging us in self-defense.&#xA;Can a similar danger arise when chasing away a mosquito which is otherwise not hungry? I understand that mosquitoes bite to feed (by sucking blood), but do they use their bites in self-defense against large targets, like humans? Mosquito bites can be somewhat painful or at least uncomfortable, and can carry dangerous diseases, making them theoretically viable as a self-defense weapon.&lt;/p&gt;&#xA;" OwnerUserId="3798" LastEditorUserId="24354" LastEditDate="2020-08-06T12:22:01.643" LastActivityDate="2020-08-06T12:22:01.643" Title="Can mosquitos bite in self-defense?" Tags="&lt;entomology&gt;&lt;behaviour&gt;&lt;mosquitoes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21195" PostTypeId="2" ParentId="21185" CreationDate="2014-09-10T18:45:35.400" Score="2" Body="&lt;p&gt;This is actually a bad idea for severeal reasons: First it is not a good idea to tamper with genes, especially not with ones which are involved in the regulation of mitosis and the correct segregation of sister chromatids. Remember that a one amino acid exchange because of a C to T transition causes the problems with SCC? Into what do you want to change the sequence anyway?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then this is not the only mutation linked to SCC - mutations in TP53 and CDKN2A are more important here. And even if you manage to change the sequences here which are the causative reason for SCC there are other mutations that will then occur. Simply by chance. It is probably a good idea to target the mutant KNSTRN protein with a treatment as this is already done for other proteins (although these are usually enzymes), but changing it will most likely not only not work but cause other problems as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another problem (even when you use a synonymous codon which does not lead to an amino acid exchange) is that you can disrupt genetic regulatory regions. Not all of these regions are located in the promoters of genes, quite a number of them are found inside of genes. Here even a single nucleotide exchange can prevent a transcription factor from binding to its recognition site. A prominent example for the is the HERC2/OCA2 polymorphism where a single nucleotide polymorphism in HERC2 alters a transcription factor binding site and thus alters the expression of OCA2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The solution here is pretty easy: Avoid prolonged exposure to UV light whenever possible. &lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-09-16T06:38:07.247" LastActivityDate="2014-09-16T06:38:07.247" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21197" PostTypeId="1" AcceptedAnswerId="34629" CreationDate="2014-09-10T22:22:03.783" Score="6" ViewCount="200" Body="&lt;p&gt;I've noticed for the past few weeks that near a small fire ant nest near my house there will be a new concentrated &quot;large&quot; pile of dead fire ants every few days. I went and checked out the pile and noticed that one ant in the pile was very slowly moving so I moved it in front of a nearby ant to see if it would take it back to the pile. The ant immediately picked up the slowly moving ant and took it back to the nest, passing right through the dead pile I might add. I'm curious what would invoke this type of behavior among the ants. I'm also curious if fire ants dispose of all of their dead this way. &lt;/p&gt;&#xA;" OwnerUserId="6382" LastActivityDate="2015-05-28T07:21:34.073" Title="Fire Ant Behavior" Tags="&lt;entomology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21198" PostTypeId="1" AcceptedAnswerId="21224" CreationDate="2014-09-10T22:51:55.207" Score="1" ViewCount="681" Body="&lt;p&gt;&lt;strong&gt;How is the rate of transcription influenced by temperature?&lt;/strong&gt; More precisely, I am looking for an article who quantitatively measured the rate of transcription of an &quot;average gene&quot; and show how this rate is influenced by temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On &lt;a href=&quot;https://biology.stackexchange.com/questions/21138/influence-of-temperature-on-transcription-protein-binding-and-decay-rates&quot;&gt;this question&lt;/a&gt; @Chris found &lt;a href=&quot;http://genomebiology.com/2014/15/3/R45&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt; where such measurement were performed but they were using some arbitrary unit (as it as been pointed out by @shigeta &lt;a href=&quot;https://biology.stackexchange.com/questions/21188/transcription-rate-expressed-in-microarray-per-hour&quot;&gt;here&lt;/a&gt;) that cannot be related to any comprehensive unit such as &quot;mole of amino acid per hours&quot; or something like that.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-09-11T19:40:58.347" Title="How is the rate of transcription influenced by temperature?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;transcription&gt;&lt;organic-chemistry&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21199" PostTypeId="2" ParentId="14077" CreationDate="2014-09-11T01:04:38.010" Score="3" Body="&lt;p&gt;Did you ever get an answer to your question? I know this may be too late now, but I was noseying around and spotted it, so I'll take a stab nonetheless. I could be wrong, but I suspect what you're seeing here may be an extracellular representation of an action potential (and/or it could be a filtering artefact, see below). From the video on the spikerbox website, it looks like you place the electrodes (nails?) into the animal and hope to get close to axons and see spiking activity. Correct me if I'm wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a brief reading of the literature it would appear, under optimal conditions, the waveform of the extracellular action potential (EAP) is dependent on the cell type and location of the electrode along the neuron (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16467426&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; paper illustrates this nicely). As you move away from the soma and down the axon/dendrites, you tend to see this more prominent initial spike, as you see in your recordings. This is due to the ionic conductances and timings of channel openings. So that's one possible explanation...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oaoRE.png&quot; alt=&quot;Extracellular spike with filters&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the other: the signal is filtered in some way. I notice in your figure your signal is very smooth without any noise and your EAP very long (assuming your x axis is seconds), which suggests to me your acquisition rate is quite low and/or being filtered. I've attached an image of an EAP I acquired (from a cell soma) a while back (with an acquisition rate of 10Khz, i.e. I 'sampled' the signal 10000 times per second to get the trace). They're all the same EAP on the same scale with different types of filters applied. The original signal is the one on the left; note all that baseline noise. The middle one is a low pass filter of 2KHz (gets rid of signals higher than that). The right hand one is a 750 - 1000 Hz band pass filter. This type of filter does funky things to signals if used incorrectly (such as in this example!). It basically only allows signals within a given region and gets rid of signals outside of it. What you end up with is the signal on the right, which looks suspiciously like yours!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I'd hazard a guess and say it's a problem due to how the system collects and filters data. BUT, there could be a biological basis for it too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there is one thing that does confuse me, and that is the polarity of your waveform. I would normally expect the prominent point of your EAP to be pointing downward. I have two suggestions as to what may be the cause of this: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;You're actually measuring currents here; the units for your Y-axis would help answer that one.&lt;/li&gt;&#xA;&lt;li&gt;Some grounding issue.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9195" LastActivityDate="2014-09-11T01:04:38.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21200" PostTypeId="1" AcceptedAnswerId="21202" CreationDate="2014-09-11T01:35:57.390" Score="13" ViewCount="12348" Body="&lt;p&gt;When we humans look around, we pan smoothly from one side to the other. Birds on the other hand seem to point their head in one direction for a while, then abruptly point their head in another direction and stay in the new position for a while. Then they continue with the abrupt movement. Why is that?&lt;/p&gt;&#xA;" OwnerUserId="9196" LastActivityDate="2019-11-09T17:47:36.767" Title="Why do birds move their heads abruptly?" Tags="&lt;ornithology&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21202" PostTypeId="2" ParentId="21200" CreationDate="2014-09-11T05:26:41.030" Score="14" Body="&lt;p&gt;Most species of birds have 2 foveas, the &lt;strong&gt;temporal fovea&lt;/strong&gt; and the &lt;strong&gt;central fovea&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;temporal fovea, which is like ours in the sense that it looks straight&#xA;  ahead and offers binocular vision (i.e. the temporal foveas of both&#xA;  eyes point in the same direction). But birds also have a central&#xA;  fovea, which points sideways and is, obviously, monocular (i.e., the&#xA;  central foveas of both eyes look in opposite directions).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So the bird has a choice of which fovea it wants to look through. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It can look straight ahead with its temporal foveas, to the left with&#xA;  the central fovea of its left eye, or to the right with the central&#xA;  fovea of its right eye. And this is not a hypothetical possibility:&#xA;  Birds actually do switch between foveas all the time! This is why they&#xA;  tend to swing their heads erratically in turns of about 90° (&lt;a href=&quot;http://www.cogsci.nl/blog/bird-brains-and-fish-eyes/165-a-bit-about-birds-looking-sideways&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-09-11T09:58:13.283" LastActivityDate="2014-09-11T09:58:13.283" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21205" PostTypeId="2" ParentId="21185" CreationDate="2014-09-11T08:46:09.247" Score="3" Body="&lt;p&gt;Short-wave UV light (UVB and UVC) causes transition mutations at dipyrmidine sequences (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15748635&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref.&lt;/a&gt;). In the work presented on &lt;em&gt;KNSTRN&lt;/em&gt; quoted by the OP the authors report that 19 from a panel of 100 squamous cell carcinomas (SCC) contained a mutation in &lt;em&gt;KNSTRN&lt;/em&gt; (and furthermore three of these contained no other mutation across the six genes that were analysed (Fig. 1b)). Normalising for ORF length this makes it the 3rd most recurrent mutated gene. It would seem therefore that it a fairly important mutagenic target. In a broadened set of SCCs they found a total of 29 KSTRN mutations, and of these 13 were Ser24Phe (TCC&amp;gt;TTC) mutations, which they refer to as a 'hotspot'.&lt;/p&gt;&#xA;&lt;p&gt;Accepting the arguments in the answer from @Chris it is still interesting to consider how one might remove such a hotspot. The normal amino acid at this position is a serine. Here is the human codon useage for ser, obtained from &lt;a href=&quot;http://www.genscript.com/cgi-bin/tools/codon_freq_table&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;TCT 14.6%&lt;/p&gt;&#xA;&lt;p&gt;TCC 22.0%&lt;/p&gt;&#xA;&lt;p&gt;TCA 15.0%&lt;/p&gt;&#xA;&lt;p&gt;TCG  6.0%&lt;/p&gt;&#xA;&lt;p&gt;AGT 11.9%&lt;/p&gt;&#xA;&lt;p&gt;AGC 19.4%&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It would seem therefore that it would be theoretically possible to edit the Ser24 codon from the UV-sensitive TCC to AGC, essentially eliminating this 'hotspot'.&lt;/p&gt;&#xA;&lt;p&gt;This, of course, doesn't answer the question - are there downsides to this? I already selected a synonymous codon with a similar frequency of useage so that shouldn't be a problem. However &lt;a href=&quot;http://jmg.bmj.com/content/40/10/e115.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;here is an example&lt;/a&gt; of a synonymous codon substitution which has an effect upon splicing of the &lt;em&gt;LMNA&lt;/em&gt; gene resulting in muscular dystrophy, and the paper cites several other examples of this. (I haven't actually checked to see where the Ser24 codon lies in relation the exon-intron boundaries in the &lt;em&gt;KNSTRN&lt;/em&gt; gene.) No doubt there are other mechanisms by which my proposed edit could have unwanted effects. It would have to be tested carefully, and so we come back around to a cost-benefit analysis - would it be worth developing this editing idea (even if it were feasible as a therapy) given that there are clearly many paths to SCC not involving this specific mutation.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-11T08:46:09.247" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21206" PostTypeId="2" ParentId="2839" CreationDate="2014-09-11T09:09:15.100" Score="2" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;If the meal you eat is hot, you will get some heat and if your body will consider it as excessive heat, it will try to get rid of some by making you sweat.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Drinking water and sweating after a meal may be coincidentally related and probably caused by hot meal rather than water. A side note: When you are dehydrated, you sweat less and when well hydrated you can sweat &quot;normally,&quot; but drinking water by itself does not stimulate sweating. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Some people with &quot;reactive hypoglycemia&quot; can sweat and get anxious after meals. In this case, after a meal, food passes through the stomach rapidly to the small intestine, where glucose from the food is quickly absorbed and raises blood glucose level considerably. This triggers excessive insulin release that allows quick uptake of glucose by the cells resulting in drop of blood glucose under the normal level (hypoglycemia). This triggers the release of adrenaline, which breaks down some glycogen from the liver to produce glucose. Adrenaline also triggers sweating. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Certain underlying neurological conditions (not necessary diseases), such as increased tonus of the vagal nerve (that supplies the gut) can make you sweet more in certain circumstances.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A meal can be a &quot;stress&quot; (psychological or physical) which can trigger the release of adrenaline, which makes you sweat (just like in anxiety from any cause).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Sources:&#xA;Diaphoresis (excessive sweating) &lt;a href=&quot;http://www.ehealthstar.com/diaphoresis.php&quot; rel=&quot;nofollow&quot;&gt;Ehealthstar.com&lt;/a&gt;&#xA;Reactive hypoglycemia &lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/diabetes/expert-answers/reactive-hypoglycemia/faq-20057778&quot; rel=&quot;nofollow&quot;&gt;Mayo Clinic&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4025" LastEditorUserId="4025" LastEditDate="2014-09-11T09:43:42.960" LastActivityDate="2014-09-11T09:43:42.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21207" PostTypeId="1" AcceptedAnswerId="21208" CreationDate="2014-09-11T09:18:38.330" Score="21" ViewCount="26211" Body="&lt;p&gt;So when we swim, we can make water not enter through our nose and mouth, simply by holding our breath. However, the mouth and the nose aren't the only cavities. What about the anus and the genitals? They obviously can't &quot;hold breath&quot;, so how do they stop water from entering?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought the reason is gravity, but then, people would be killed when diving because your butt is facing up, against the gravity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another explanation might be that the internal pressure is higher than the external one, but I fail to recall any organ that creates the pressure..&lt;/p&gt;&#xA;" OwnerUserId="8651" LastEditorUserId="5762" LastEditDate="2014-09-12T06:31:44.900" LastActivityDate="2014-09-12T06:31:44.900" Title="Why doesn't water enter my body through my anus or genitals when swimming?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21208" PostTypeId="2" ParentId="21207" CreationDate="2014-09-11T09:32:37.383" Score="44" Body="&lt;p&gt;For the same reason that when you urinate or use the toilet, you have to exert pressure and urine or faeces just does not simply leak out when you stand up. The urethra seals shut when the &lt;a href=&quot;http://en.wikipedia.org/wiki/Urethral_sphincter&quot;&gt;urethral sphincter muscle&lt;/a&gt;s relax. Similarly &lt;a href=&quot;http://en.wikipedia.org/wiki/Sphincter_ani_externus_muscle&quot;&gt;Sphincter ani externus muscle&lt;/a&gt; seals shut in the anal canal when there is no antagonistic force. So water can't just simply enter our body in such huge quantities that we die. It is possible to get more water through your anus with some pressure which is what happens when you get an enema.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-09-11T09:48:52.047" LastActivityDate="2014-09-11T09:48:52.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21210" PostTypeId="1" CreationDate="2014-09-11T11:36:04.973" Score="2" ViewCount="60" Body="&lt;p&gt;After being in the sun, how much 'rest' is required before you can expose yourself again?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;e.g. from &lt;a href=&quot;https://en.wikipedia.org/wiki/Sunburn&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sunburn can occur in less than 15 minutes&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So if you were in a place where sunburn would occur after &lt;strong&gt;15 minutes&lt;/strong&gt; and you stayed in the sun for &lt;strong&gt;10 minutes&lt;/strong&gt; you shouldn't get sunburn. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How long would you then have to stay out of the sun before you could go into the sun again for 10 minutes without getting sunburn?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm pretty sure that 1 minute wouldn't be enough, but 24 hours would be fine, is there any logic as to where between those two figures it actually is?&lt;/p&gt;&#xA;" OwnerUserId="9206" LastActivityDate="2014-09-11T11:36:04.973" Title="How much time is required between repeated exposures to sun to prevent sunburn" Tags="&lt;skin&gt;&lt;uv&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2014-09-11T22:34:08.030" ContentLicense="CC BY-SA 3.0" />
  <row Id="21211" PostTypeId="2" ParentId="21194" CreationDate="2014-09-11T12:54:36.550" Score="8" Body="&lt;p&gt;Probably not. An immediate defense against predators requires an immediate response. The sting of Hymenoptera like the wasps and bees has an immediately painful reaction.  In addition, in the eusocial (colony-forming) species, multiple individuals typically contribute to defense of their nest. One sting may not deter a predator or invader but dozens or hundreds of stings would create an immediate deterrent.  See for example this paper by [Breed et al. (2004)] on the defense behavior of honey bees.  Animal bites that are immediately painful, such as an ant bite or dog bite create an immediate response in the organism being bitten. &lt;a href=&quot;http://www.researchgate.net/publication/226156061_Thorns_as_induced_defenses_experimental_evidence/file/72e7e51d9c86e60ddb.pdf&quot;&gt;Spines and thorns&lt;/a&gt; on plants deter organisms from biting the plant. Odors released by &lt;a href=&quot;http://en.wikipedia.org/wiki/Skunk&quot;&gt;skunks&lt;/a&gt; and &lt;a href=&quot;http://www.jstor.org/stable/25002664&quot;&gt;some insect&lt;/a&gt; provide an immediate response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bite of blood-sucking mosquitoes does not provide an immediate deterrent. (Not all mosquitoes suck blood.) This paper by &lt;a href=&quot;http://olivermbarham.com/omb_images/NCSU/research/IOP_published_9-8-2008.pdf&quot;&gt;Ramasubramanian et al. (2008)&lt;/a&gt; provides a detailed explanation of how a mosquito penetrates the skin.  The paper is related to microneedle design but they are using the mosquito as a comparison for &lt;em&gt;painless&lt;/em&gt; needle design. Go to page 3 to get a description of the mosquito anatomy and piercing behavior. Comparison of painless microneedle design to the mosquito's proboscis is instructive.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The proboscis is the set of modified mouth parts the mosquito uses to penetrate the skin and suck the blood.  The study states that microneedles that penetrate human skin less than 1.5mm is usually painless or effectively so. These needles have a very small diameter, only about 40-100 micrometers in diameter, similar to the width of a human hair. The mosquito's proboscis is about 1.5-2.0 mm long. The diameter of the various structures used to cut through the skin and suck the blood are all less than 40 micrometers in diameter. Thus, the size of the mosquito's proboscis is so small that it does not cause immediate pain, or the pain is so little that it is an annoyance at best. In addition, the proboscis is weak enough that the moquito may have to probe the skin several times before a spot suitable for penetration can be found. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, only the females of blood-sucking mosquitoes feed on blood and have the penetrating mouth parts. Males do not. They feed &lt;a href=&quot;http://www.inrs.illinois.edu/expo/pdf-files/mosquito-facts.pdf&quot;&gt;entirely on nectar and water.&lt;/a&gt; Males would thus not be capable of such defense.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastActivityDate="2014-09-11T12:54:36.550" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21212" PostTypeId="1" AcceptedAnswerId="21213" CreationDate="2014-09-11T13:06:33.253" Score="9" ViewCount="53727" Body="&lt;p&gt;In most popular medical dramas, when a patient has a cardiac arrest and &quot;flatlines&quot; the doctors many times use a defibrillator to &quot;shock the heart back into rhythm'. I know that actually, the proper protocol is CPR and epinephrine (if possible), and that you should shock rhythms such as ventricular fibrillation. But why doesn't shocking the heart in asystole help?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If anyone could please explain, that'd be great.&lt;/p&gt;&#xA;" OwnerUserId="8840" LastEditorUserId="10456" LastEditDate="2015-12-08T11:38:31.020" LastActivityDate="2020-04-11T11:18:58.283" Title="Why is defibrillation in asystole (&quot;flat line&quot;) useless?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;ventricles&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21213" PostTypeId="2" ParentId="21212" CreationDate="2014-09-11T13:21:17.113" Score="16" Body="&lt;p&gt;In layman's terms: an Asystole is not affected by the electric shocks of a defibrillator. A defibrillator is used when the heart goes in fibrillations because it actually CAUSES an asystole. The idea is that you basically reset the heart to a blank state so you can start normal CPR procedure to help the heart go back to a normal rythm. That's why you see them applying CPR between shocks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;sources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://emedicine.medscape.com/article/757257-treatment&quot;&gt;http://emedicine.medscape.com/article/757257-treatment&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Defibrillation#In_popular_culture&quot;&gt;http://en.wikipedia.org/wiki/Defibrillation#In_popular_culture&lt;/a&gt; (citation needed)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://calsprogram.org/manual/volume3/section12/CV/08-CV7AsystoleTreatment13.html&quot;&gt;http://calsprogram.org/manual/volume3/section12/CV/08-CV7AsystoleTreatment13.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9208" LastEditorUserId="9208" LastEditDate="2014-09-11T14:08:02.887" LastActivityDate="2014-09-11T14:08:02.887" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21215" PostTypeId="1" CreationDate="2014-09-11T13:50:55.630" Score="3" ViewCount="417" Body="&lt;p&gt;The TL;DR version&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a fast way to determine what the cell environment of a particular cell (E.g RBC) is? (in terms of solute/ionic concentration)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I'm not sure if the question belongs here, but hear me out. I was doing revision and I kept coming across the line &quot;put the cell in a solution which has the same solute/ionic concentration to prevent the cell from bursting or shrinking&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I get that concept, basically it's sort of replicating the internal environment of the cell with the buffer/solution so that the cell feels &quot;at home.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then my question is, how does one go about finding out how much exactly for each cell? I would think different cells have different internal environments and I don't believe that scientists actually just have stock solutions of buffers ranging from 0.00001M to 100M and trying every single solution until they find the perfect concentration.&lt;/p&gt;&#xA;" OwnerUserId="9179" LastActivityDate="2014-10-12T02:43:55.250" Title="How does one determine intracellular concentration?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21216" PostTypeId="1" AcceptedAnswerId="21220" CreationDate="2014-09-11T14:21:18.433" Score="295" ViewCount="279507" Body="&lt;p&gt;I was just sitting with my hand next to my nose and I realized that air was only coming out of the right nostril. Why is that? I would think I would use both, it seems much more efficient. Have I always only been breathing out of my right nostril?&lt;/p&gt;&#xA;" OwnerUserId="9212" LastEditorUserId="9225" LastEditDate="2014-09-11T23:17:53.370" LastActivityDate="2020-09-03T07:18:03.490" Title="Why do I only breathe out of one nostril?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;nose&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="87" ContentLicense="CC BY-SA 3.0" />
  <row Id="21217" PostTypeId="1" AcceptedAnswerId="21247" CreationDate="2014-09-11T15:25:04.053" Score="5" ViewCount="272" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Developmental_noise&quot;&gt;Developmental noise&lt;/a&gt; is a concept that correspond to the amount of possible phenotypic variance of a given genotype in a given environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intrinsic noise (aka &lt;a href=&quot;http://en.wikipedia.org/wiki/Cellular_noise&quot;&gt;Cellular noise&lt;/a&gt;) is a component of developmental noise and it refers to phenotypic variations caused by the stochasticity of biochemical processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the other component(s) of developmental noise?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-09-11T17:45:39.193" LastActivityDate="2016-04-25T18:14:16.310" Title="Components of the concept of Developmental Noise?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;physiology&gt;&lt;natural-selection&gt;&lt;development&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21218" PostTypeId="2" ParentId="21215" CreationDate="2014-09-11T15:28:14.200" Score="1" Body="&lt;p&gt;In fact the line that you quote doesn't mean that the solution is formulated to be identical to the cytosol. All that it means is that the solution should be buffered to physiological pH (typically slightly alkaline); should contain a relatively high concentration of sodium ions and a low concentration of potassium ions; and should be isotonic (i.e have the same osmolarity as the cytosol) to avoid osmotic effects such as plasmolysis (shrinkage due to loss of water) or osmotic lysis (bursting due to uptake of water).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many such solutions, but a commonly used simple one is &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphate_buffered_saline&quot; rel=&quot;nofollow&quot;&gt;phosphate buffered saline&lt;/a&gt;. Another is &lt;a href=&quot;http://en.wikipedia.org/wiki/Ringer%27s_solution&quot; rel=&quot;nofollow&quot;&gt;Ringer's solution&lt;/a&gt;. If the aim is to keep the cells metabolically active these are often supplemented with glucose or lactate, depending upon the cell type.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Addendum in response to comment from OP&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Ringer%27s_solution&quot; rel=&quot;nofollow&quot;&gt;the WP entry for Ringer's solution&lt;/a&gt;, Sydney Ringer determined the requirement for Na, K and Ca salts in a specific proportion when carrying out experiments with perfused frog hearts. This was in the late 19th century. A  Google search &lt;em&gt;measurement of intracellular ion concentrations&lt;/em&gt; reveals current methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://physrev.physiology.org/content/physrev/61/2/296.full.pdf&quot; rel=&quot;nofollow&quot;&gt;This review&lt;/a&gt; starts off with a discussion of early measurements of intracellular pH (see page 298). Basically these all consisted of making cell lysates, with various attempts to prevent post-lytic changes. If you do a Google search &lt;em&gt;determination of intracellular pH&lt;/em&gt; you will find lots of current methods. &lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-09-11T15:59:05.227" LastActivityDate="2014-09-11T15:59:05.227" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21219" PostTypeId="2" ParentId="21216" CreationDate="2014-09-11T17:49:52.610" Score="144" Body="&lt;p&gt;This is a natural phenomenon called the nasal cycle. It is discussed in this paper by &lt;a href=&quot;http://www.ijpp.com/IJPP%20archives/1994_38_2/133-137.pdf&quot; rel=&quot;noreferrer&quot;&gt;Telles et al. (1994)&lt;/a&gt;, among many others. The nostrils are used on an alternating cycle of about 2-3 hours, controlled by the &lt;a href=&quot;http://www.ndrf.org/ans.html&quot; rel=&quot;noreferrer&quot;&gt;autonomic nervous system&lt;/a&gt;. If you notice alternating congestion, that also seems to be coupled to the nasal cycle (Hasegawa and Kern &lt;a href=&quot;http://europepmc.org/abstract/MED/609283&quot; rel=&quot;noreferrer&quot;&gt;1977&lt;/a&gt;, &lt;a href=&quot;http://europepmc.org/abstract/MED/635366&quot; rel=&quot;noreferrer&quot;&gt;1978&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;p&gt;Normally, the direct cause is blockage caused by alternating engorgement of erectile tissues on each side of the nose.&#xA;&lt;a href=&quot;https://i.stack.imgur.com/ZdwsE.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZdwsE.jpg&quot; alt=&quot;Anatomy of the nose showing the erectile tissues&quot; /&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Below, I explain that the nasal cycle may be an artifact of the way the autonomous system works in humans (and some other organisms) or it may provide a first barrier against invasion of infective organisms via the nose. The full answer requires some background information.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Wikipedia and the nasal cycle&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;The Wikipedia article on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nasal_cycle&quot; rel=&quot;noreferrer&quot;&gt;nasal cycle&lt;/a&gt;, nicely paraphrased in the answer by George Daccache, offers hints but not real answers.  For example, the Wiki section called &lt;a href=&quot;http://en.wikipedia.org/wiki/Nasal_cycle#Research_on_the_effects&quot; rel=&quot;noreferrer&quot;&gt;Research on the effects&lt;/a&gt; states,&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In 1994, breathing through alternate nostrils showed effects on brain hemisphere symmetry on EEG topography.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;suggesting that perhaps natural nasal cycling relates somehow to communication or coordination between the two brain hemispheres. However, the cited study &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7876041&quot; rel=&quot;noreferrer&quot;&gt;(Stancak and Kuna 1994)&lt;/a&gt; is based on forced alternate nostril breathing (FANB). The Wiki section then states,&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;D.S. Shannahoff-Khalsa published in 2007 on the effect of this cycle and manipulation through forced nostril breathing on one side on the endogenous ultradian rhythms of the autonomic and central nervous system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;All this sentence ultimately says is that a 2007 paper looked at the effects of FANB on &lt;a href=&quot;http://www.cnsspectrums.com/aspx/articledetail.aspx?articleid=1163&quot; rel=&quot;noreferrer&quot;&gt;ultradian rhythms&lt;/a&gt;. The Wiki section doesn't actually include results from the study so it provides no useful information.&lt;span class=&quot;math-container&quot;&gt;$^1$&lt;/span&gt; I will try to explain with more depth.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;What is Forced Air Nostril Breathing?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Forced Air Nostril Breathing (FANB) requires a person to close one nostril, breath in, close the second nostril and open the first nostril, and breath out. The person repeats this process several times in a 10-15 minute period. In fact, FANB is a yoga technique called &lt;a href=&quot;http://www.artofliving.org/us-en/yoga/breathing-techniques/alternate-nostril-breathing-nadi-shodhan&quot; rel=&quot;noreferrer&quot;&gt;Nadi Shodhan Pranayama&lt;/a&gt;. The Telles et al. paper mentioned above used FANB, as has nearly every study on the effects of the nasal cycle.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;None of these studies actually explain the natural nasal cycle.&lt;/em&gt;  FANB is not natural. It changes natural breathing rhythms and requires the person to focus on the physical movements of the fingers to close the alternating nostrils. FANB occurs for a 10-15 minute period of time and is finished. This is not the same as the 2-3 hour natural nasal cycle. In my opinion, any conclusions drawn from studies using FANB apply only to FANB but not to the natural nasal cycle.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Then why does the nasal cycle occur?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;The nasal cycle is a natural ultradian cycle (see &lt;a href=&quot;http://www.cnsspectrums.com/aspx/articledetail.aspx?articleid=1163&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://sequencewiz.org/wp-content/uploads/2014/08/Lateralized-rhythms-of-the-central-and-autonomic-nervous-systems.-D.-Shannahoff-Khalsa.pdf&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;. Not only is it present in humans, but the nasal cycle has also been observed in rats, rabbits, domestic pigs, cats and dogs (see references in &lt;a href=&quot;http://erj.ersjournals.com/content/9/2/371.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;Eccles 1996&lt;/a&gt;]). Thus, the nasal cycle may at least be a feature of mammals but it may be a feature of other bilateral animals that use nostrils for respiration. In addition, the nasal cycle may be an artifact of the evolution of bilateral symmetry in animals, and how the autonomic nervous system operates between the two sides.&lt;/p&gt;&#xA;&lt;p&gt;The autonomic nervous system controls the nasal cycle. The autonomic nervous system has two divisions, the sympathetic nervous system and the parasympathetic nervous system. Interestingly, these two divisions show a lateralized ultradian rhythm &lt;a href=&quot;http://www.cnsspectrums.com/aspx/articledetail.aspx?articleid=1163&quot; rel=&quot;noreferrer&quot;&gt;(Shannahoff-Khalsa 2007)&lt;/a&gt;.  This means that the parasympathetic nervous system dominates one side of the body and the sympathetic nervous system dominates the other side of the body. The two systems later switch dominate sides. This dominance switching back and forth between the parasympathetic and sympathetic happens with a regular rhythmic cycle every few hours. As it happens, this switching between sides correlates very well with the nasal cycle &lt;a href=&quot;http://sequencewiz.org/wp-content/uploads/2014/08/Lateralized-rhythms-of-the-central-and-autonomic-nervous-systems.-D.-Shannahoff-Khalsa.pdf&quot; rel=&quot;noreferrer&quot;&gt;(Shannahoff-Khalsa 1991)&lt;/a&gt;.  When the parasympathetic-sympathetic systems switch sides, so do the nostrils. This is also associated with a switch in EEG activity between the two brain hemispheres &lt;a href=&quot;http://europepmc.org/abstract/MED/6874437&quot; rel=&quot;noreferrer&quot;&gt;(Werntz et al. 1983)&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Therefore, the nasal cycle may not have a specific function, adaptive or otherwise. Instead, it could result from dominance of the parasympathetic system. Whichever side is dominated by the parasympathetic system will have the primary nostril in use for respiration. However, others have argued that the nasal cycle does provide a function. For example, &lt;a href=&quot;http://erj.ersjournals.com/content/9/2/371.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;Eccles (1996)&lt;/a&gt; argued that the nasal cycle may function as a respiratory defense mechanism. They found that the rate of cycling increases when nasal infection is present in the nose. They argue that the congestion-decongestion helps generate &amp;quot;plasma exudate&amp;quot; (nasal fluids derived from blood plasma) which may help remove bacteria and viruses.&lt;/p&gt;&#xA;&lt;p&gt;The nasal cycle is an interesting phenomenon but whether it evolved as an adaptation (such as a mechanism proposed by Eccles et al. (1996) or is simply an artifact of the operation of the autonomic nervous system may never be known for sure.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Footnote&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;One of many reasons why you should always interpret Wikipedia entries very cautiously, even skeptically.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;&lt;strong&gt;Citations&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Eccles, R. 1996. A role for the nasal cycle in respiratory defense. European Respiratory Journal 9: 371-376.&lt;/p&gt;&#xA;&lt;p&gt;Hasegawa, M. and E.B. Kern. 1977. The human nasal cycle. Mayo Clinic Proceedings 52: 28-34.&lt;/p&gt;&#xA;&lt;p&gt;Hasegawa, M. and E.B. Kern. 1978. Variations in nasal resistance in man: a rhinomanometric study of the nasal cycle in 50 human subjects. Rhinology 16: 19-29.&lt;/p&gt;&#xA;&lt;p&gt;Stancak, A. and M. Kuna. 1994. EEG changes during forced alternate nostril breathing. International Journal of Psychophysiology 16: 75-79.&lt;/p&gt;&#xA;&lt;p&gt;Telles, S. et al. 1994. Breathing through a particular nostril can alter metabolism and autonomic activities.&lt;/p&gt;&#xA;&lt;p&gt;Werntz, D.A. et al. 1983. Alternating cerebral hemispheric activity and the lateralization of autonomic nervous function. Human Neurobiology 2: 39-43.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="33365" LastEditDate="2020-09-03T07:18:03.490" LastActivityDate="2020-09-03T07:18:03.490" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="21220" PostTypeId="2" ParentId="21216" CreationDate="2014-09-11T18:03:47.877" Score="249" Body="&lt;p&gt;Apparently you're not the first person to notice this; in 1895, a German nose specialist called Richard Kayser found that we have tissue called erectile tissue in our noses (yes, it is very similar to the tissue found in a penis). This tissue swells in one nostril and shrinks in the other, creating an open airway via only one nostril. What's more, he found that this is indeed a 'nasal cycle', changing every 2.5 hours or so. Of course, the other nostril isn't completely blocked, just mostly. If you try, you can feel a very light push of air out of the blocked nostril.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is controlled by the autonomic nervous system. You can change which nostril is closed and which is open by laying on one side to open the opposite one.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, some researchers think that this is the reason we often switch the sides we lay on during sleep rather regularly, as it is more comfortable to sleep on the side with the blocked nostril downwards.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to why we don't breathe through both nostrils simultaneously, I couldn't find anything that explains it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources:&lt;br&gt;&#xA;&lt;a href=&quot;http://www.todayifoundout.com/index.php/2010/03/about-85-of-people-only-breathe-out-of-one-nostril-at-a-time/&quot;&gt;About 85% of People Only Breathe Out of One Nostril at a Time&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Nasal_cycle&quot;&gt;Nasal cycle&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8840" LastEditorUserId="-1" LastEditDate="2014-09-14T21:52:36.523" LastActivityDate="2014-09-14T21:52:36.523" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21222" PostTypeId="1" CreationDate="2014-09-11T18:55:46.503" Score="3" ViewCount="172" Body="&lt;p&gt;Lead is known to be bad for your health for a long time, but I can't find a explanation why is it so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In school they teach that heavy metals are poisonous, and they are trapped inside our bodies. I can just assume that the liver can't process those elements. But I still don't understand why this happens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And finally why is lead different from, let's say, gold that is also a very dense metal, but is safe.&lt;/p&gt;&#xA;" OwnerUserId="9222" LastEditorUserId="1320" LastEditDate="2014-09-11T20:45:06.680" LastActivityDate="2018-04-04T03:26:33.317" Title="Why is lead dangerous?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ClosedDate="2014-09-12T02:46:08.133" ContentLicense="CC BY-SA 3.0" />
  <row Id="21223" PostTypeId="1" AcceptedAnswerId="21237" CreationDate="2014-09-11T19:02:47.690" Score="3" ViewCount="80" Body="&lt;p&gt;Is there any simulation protocol or paper which can simulate the dynamics of drug entry and  interaction with the target protein?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://news.slac.stanford.edu/sites/default/files/images/image/oak-ridge.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="8186" LastEditDate="2014-09-12T04:54:56.580" LastActivityDate="2014-09-13T01:18:24.530" Title="Simulating Drug Entry in Protein and binding?" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;book-recommendation&gt;&lt;computational-model&gt;&lt;pharmacodynamics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21224" PostTypeId="2" ParentId="21198" CreationDate="2014-09-11T19:34:45.280" Score="2" Body="&lt;p&gt;If your looking at transcription then your talking about RNA POLYMERASE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And there are many variants. Here's a good Nature paper that discusses temperature and RNA Pol&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/ncomms/journal/v1/n6/full/ncomms1076.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/ncomms/journal/v1/n6/full/ncomms1076.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And another:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/m/pubmed/12729734/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/m/pubmed/12729734/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I couldn't get full access to this JBC paper but I think the answer would be clearly in here, prob worth a look&lt;/p&gt;&#xA;&#xA;&lt;p&gt;M. Chamberlin and J. Ring. Characterization of T7-specific ribonucleic acid polymerase. 1. General properties of the enzymatic reaction and the template specificity of the enzyme. J Biol Chem. 248: 2235-44 (1973)&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-09-11T19:40:58.347" LastActivityDate="2014-09-11T19:40:58.347" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21226" PostTypeId="2" ParentId="21222" CreationDate="2014-09-11T19:52:17.613" Score="4" Body="&lt;p&gt;Lead acts as a poison in a variety ways relative to what tissue it is exposed to. For example, lead is able to pass through the blood-brain barrier where it can act act as Calcium homolog to interfere with neurotransmitter release. In the blood, Lead inhibits porphobilogen synthase, an enzyme required for heme synthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lead's toxicity mechanisms include: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Its ability bind sulfhydryl groups, common to many enzymes &lt;/li&gt;&#xA;&lt;li&gt;Its ability displace metals in enzyme complexes&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Its ability to act as a Calcium homolog&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/TuAvR.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/TuAvR.png&quot; alt=&quot;Periodic Table&quot;&gt;&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Lead's valence electron configuration is $\require{mhchem} \ce{[Xe] 4f^14 5d^10 6s^2 6p^2}$; which means it has two electrons in its valence shell. This pair of valence electrons contribute's to Lead's ability to act as a Calcium analog and to Lead's tendency to form compounds in which it has an oxidation state of +2. Many such compounds dissolve in lightly acidic solutions. This has created lead exposure hazards when acidic tap water was pumped through lead pipes and when fruit juices have been served from ceramic vessels with lead-containing glazes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Lead_poisoning&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lead Poisoning&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Lead&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lead&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8161" LastEditorUserId="31230" LastEditDate="2018-04-04T03:26:33.317" LastActivityDate="2018-04-04T03:26:33.317" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21227" PostTypeId="2" ParentId="21216" CreationDate="2014-09-11T20:23:29.790" Score="39" Body="&lt;p&gt;As others have said, this phenomena is called the nasal cycle, a process controlled by the autonomic nervous system that alternants congestion between your nostrils. Mentalfloss of all places has an article about this that explains:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...it makes our sense of smell more complete. Different scent&#xA;  molecules degrade at different rates, and our scent receptors pick up&#xA;  on them accordingly. Some smells are easier to detect and process in a&#xA;  fast-moving airstream like the decongested nostril, while others are&#xA;  better detected in the slower airstream of the congested nostril.&#xA;  Nasal cycling also seems to keep the nose maintained for its function&#xA;  as an air filter and humidifier. The alternating congestion gives the&#xA;  mucous and cilia (the tiny hairs up in your nose) in each nostril a&#xA;  well-deserved break from the onslaught of air and prevents the insides&#xA;  of your nostrils from drying out, cracking and bleeding.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;link: &lt;a href=&quot;http://mentalfloss.com/article/30363/why-does-your-nose-get-stuffy-one-nostril-time&quot;&gt;http://mentalfloss.com/article/30363/why-does-your-nose-get-stuffy-one-nostril-time&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9221" LastActivityDate="2014-09-11T20:23:29.790" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21229" PostTypeId="1" CreationDate="2014-09-12T00:52:40.577" Score="3" ViewCount="286" Body="&lt;p&gt;Biologically, how prevalent is hair loss on a nuclear submarine? How can prolonged exposure to radiation levels typically present on a nuclear sub affect a person, say over a year or even more?&lt;/p&gt;&#xA;" OwnerUserId="9232" LastEditorUserId="9829" LastEditDate="2015-01-07T20:41:44.557" LastActivityDate="2015-01-07T20:41:44.557" Title="Hair loss in a nuclear submarine?" Tags="&lt;radiation&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2014-12-25T20:17:57.357" ContentLicense="CC BY-SA 3.0" />
  <row Id="21231" PostTypeId="1" CreationDate="2014-09-12T01:52:30.153" Score="0" ViewCount="33" Body="&lt;p&gt;I have 10 molecules in VMD main screen and I was wondering if there is a script command to change what molecule is the &lt;code&gt;top&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, molecule &lt;code&gt;ID 9&lt;/code&gt; is the top. But I want to change the &lt;code&gt;top&lt;/code&gt; to 1, without using mouse.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="9236" LastActivityDate="2014-09-12T01:52:30.153" Title="VMD set molecule as top using script" Tags="&lt;proteins&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21232" PostTypeId="2" ParentId="21229" CreationDate="2014-09-12T04:47:29.280" Score="1" Body="&lt;p&gt;If the question is related to exposure to radiation in a &lt;strong&gt;Nuclear&lt;/strong&gt; submarine then the answer is valid for radiation exposure irrespective of the place. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you are aware there are many effects of radiation. Some of them are.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Nausea and vomiting&lt;/li&gt;&#xA;  &lt;li&gt;Diarrhea&lt;/li&gt;&#xA;  &lt;li&gt;Skin burns (skin reddening)&lt;/li&gt;&#xA;  &lt;li&gt;Weakness&lt;/li&gt;&#xA;  &lt;li&gt;Lethargy and fatigue&lt;/li&gt;&#xA;  &lt;li&gt;Loss of appetite (anorexia)&lt;/li&gt;&#xA;  &lt;li&gt;Fainting&lt;/li&gt;&#xA;  &lt;li&gt;Dehydration&lt;/li&gt;&#xA;  &lt;li&gt;Inflammation of tissues (swelling, redness or tenderness)&lt;/li&gt;&#xA;  &lt;li&gt;Hemorrhages under the skin&lt;/li&gt;&#xA;  &lt;li&gt;Bleeding from your nose, gums or mouth&lt;/li&gt;&#xA;  &lt;li&gt;Anemia &lt;/li&gt;&#xA;  &lt;li&gt;Hair loss (usually from just the scalp)&lt;/li&gt;&#xA;  &lt;li&gt;Decrease in platelets (&lt;a href=&quot;http://www.naturalnews.com/032087_radiation_sickness_symptoms.html#&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;)&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Of course there is no safe quantity of radiation that has been quantified (&lt;a href=&quot;http://yosemite.epa.gov/R10/CLEANUP.NSF/webpage/how+does+radiation+affect+human+health?OpenDocument&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) and there are personal anecdotes by submarine officers about first hand problems they faced due to radiation (&lt;a href=&quot;http://aquilinefocus.blogspot.in/2006/09/three-submarine-radiation-stories.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). However, since this is a career you chose, you can be happy that the amount of radiation that you would be exposed to has decreased over the years (&lt;a href=&quot;http://nnsa.energy.gov/sites/default/files/nnsa/02-12-multiplefiles/NT-11-2%20FINAL.pdf&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Since you are interested in the biological aspect of what happens in your body due to radiation, I quote&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When cells -- and what lies within them -- get exposed to radiation,&#xA;  components of DNA and critical proteins within the cell get all jazzed&#xA;  up (ionized), meaning that the electrons with our atoms get kicked&#xA;  out, causing the DNA strands to break and the proteins to cramp up&#xA;  (denature).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Ionizing Radiation:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Leads to the production of free radicals&lt;/li&gt;&#xA;  &lt;li&gt;Breaks critical chemical bonds&lt;/li&gt;&#xA;  &lt;li&gt;Leads to changes in cellular structure within irradiated cells&lt;/li&gt;&#xA;  &lt;li&gt;Damages vital molecules, such as DNA, RNA, and other regulatory&#xA;  proteins&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;  &#xA;  &lt;p&gt;Because our cells are mostly water, this ionizing radiation breaking&#xA;  H$_2$0 down is harmful to free radicals (H$^+$ and OH$^-$). While cells are&#xA;  damaged by free radicals all the time, they normally repair&#xA;  themselves, keeping the body healthy. However, high doses of radiation&#xA;  can damage the cell's ability to repair itself, and then all hell&#xA;  breaks loose.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This shakes things up all over the body.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Let's do a head-to-toe walk-through to investigate how high doses of&#xA;  radiation can damage the human body.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;BRAIN:&lt;/strong&gt; Nerve cells (neurons) and brain blood vessels can die, leading to seizures.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;EYES:&lt;/strong&gt; Radiation exposure increases the risk of cataracts.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;THYROID:&lt;/strong&gt; When a nuclear reactor malfunctions, radioactive iodine (I-131) can be released into the atmosphere (this is one of the&#xA;  particles that hangs out in a &quot;radioactive plume&quot;). The thyroid is&#xA;  very sensitive to the effects of I-131 (in fact, I-131's affinity for&#xA;  the thyroid is used therapeutically to specifically attract radiation&#xA;  to the thyroid in order to treat thyroid cancer and overactive&#xA;  thyroid). When a healthy thyroid is exposed to I-131, it can lead to&#xA;  decreased thyroid function and, over time, thyroid cancer.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;LUNGS:&lt;/strong&gt; When you breathe in invisible nuclear fallout particles, it can lead to lung cancer down the road.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;HEART:&lt;/strong&gt; High doses of radiation can damage the cells in the blood vessels that feed the heart, reducing cardiac function.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;GI TRACT:&lt;/strong&gt; Sensitive cells in the intestinal lining can be damaged, leading to nausea, bloody vomiting, and bloody diarrhea.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;REPRODUCTIVE ORGANS:&lt;/strong&gt; Rapidly dividing cells (eggs and sperm) in the ovaries and testes can die, leading to sterility.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;SKIN:&lt;/strong&gt; Rapidly dividing skin cells can be damaged, leading to skin lesions and burn.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;LYMPHATIC SYSTEM:&lt;/strong&gt; Rapidly dividing lymphatic cells die and damaged bone marrow may have trouble replenishing these immune-boosting cells,&#xA;  increasing the risk of infection (&lt;a href=&quot;http://www.psychologytoday.com/blog/owning-pink/201103/radiation-101-how-does-nuclear-radiation-affect-the-body&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Many jobs have occupational diseases connected with it so I would say don't worry about it too much, enjoy your job and keep your fingers off the firing mechanism. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="3340" LastEditDate="2014-12-25T12:04:26.167" LastActivityDate="2014-12-25T12:04:26.167" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21233" PostTypeId="1" AcceptedAnswerId="21239" CreationDate="2014-09-12T04:58:18.400" Score="3" ViewCount="648" Body="&lt;p&gt;Apologies for the confusing question; I did not know how to better ask it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was doing a search on wikipedia when I found this statement. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia's entry on hair states; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The hair that is visible is the hair shaft, which exhibits no&#xA;  biochemical activity and is considered &quot;dead&quot;.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;With that being said, why does one use shampoo? Is it because of the scalp that requires nourishment and cleaning because skin is not of a &quot;dead&quot; nature? Or is it to maintain the silkiness and smoothness of hair? Because it seems really redundant to take care of and maintain something which is already &quot;dead&quot;.&lt;/p&gt;&#xA;" OwnerUserId="9179" LastActivityDate="2021-01-19T02:25:44.893" Title="What is the use of shampoo; is it for the hair or for the scalp?" Tags="&lt;human-biology&gt;&lt;hair&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21235" PostTypeId="1" CreationDate="2014-09-12T06:43:37.170" Score="1" ViewCount="1069" Body="&lt;p&gt;Anyone know of a good source which explains this?  Or is this still an open question?  This wikipedia article describes some molecular biology behind morphine tolerance, but it sounds like its newer research, and isn't fully understood. &lt;a href=&quot;http://en.wikipedia.org/wiki/Drug_tolerance&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Drug_tolerance&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would have thought that something like this would be very well understood.&lt;/p&gt;&#xA;" OwnerUserId="9240" LastActivityDate="2014-09-12T10:31:47.237" Title="What are the molecular mechanisms behind tachyphylaxis (downregulation of receptors in response to an agonist?)" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21236" PostTypeId="2" ParentId="21189" CreationDate="2014-09-12T07:30:26.703" Score="2" Body="&lt;p&gt;Let's do your second one first, you want to find the rate of binding:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes you are right you need to calculate for km&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think I found the paper that ties temp into the reaction rate:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;statistical approach called response surface methodology (RSM) is used for the prediction of the kinetic constants of glucose oxidase (GOx) as a function of reaction temperature and pH. Lineweaver–Burk transformation of the Michaelis–Menten equation was utilized as the integral part of the RSM algorithm. The effects of variables, namely reciprocal of substrate concentration (0.033–0.5 mM−1), reaction temperature (14.9–40.1 °C) and reaction pH (pH 4.4–8.5) on the reciprocal of initial reaction rate were evaluated and a second order polynomial model was fitted by a central composite circumscribed design (CCCD).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biochemical Engineering Journal&#xA;August 2005, Vol.25(1):55–62, doi:10.1016/j.bej.2005.04.001&#xA;A new approach for determination of enzyme kinetic constants using response surface methodology&#xA;İsmail Hakkı Boyacı&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the decay&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm still working on the first I'm suggesting to check this out but need sleep I can read it tomorrow&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.eastcoastbio.com/productcart/pc/stability_testing.asp&quot; rel=&quot;nofollow&quot;&gt;http://www.eastcoastbio.com/productcart/pc/stability_testing.asp&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-09-12T07:30:26.703" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21237" PostTypeId="2" ParentId="21223" CreationDate="2014-09-12T07:39:53.103" Score="4" Body="&lt;p&gt;This is a tough topic, have a look at the following references and see, if they can help you:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22155026&quot; rel=&quot;nofollow&quot;&gt;Structural modelling and dynamics of proteins for insights into drug&#xA;interactions.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.febsletters.org/article/S0014-5793%2811%2900529-1/abstract?cc=y&quot; rel=&quot;nofollow&quot;&gt;Ligand entry pathways in the ligand binding domain of PPARγ receptor&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pnas.org/content/108/32/13118.long&quot; rel=&quot;nofollow&quot;&gt;Pathway and mechanism of drug binding to G-protein-coupled receptors&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.hindawi.com/journals/bmri/2013/390920/&quot; rel=&quot;nofollow&quot;&gt;Molecular Dynamic Simulation and Inhibitor Prediction of Cysteine&#xA;Synthase Structured Model as a Potential Drug Target for&#xA;Trichomoniasis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-12T07:39:53.103" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21238" PostTypeId="2" ParentId="21235" CreationDate="2014-09-12T10:31:47.237" Score="1" Body="&lt;p&gt;There are many mechanisms of receptor down-regulation, including internalisation and degradation e.g for the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12648464?dopt=Abstract&amp;amp;holding=f1000,f1000m,isrctn&quot; rel=&quot;nofollow&quot;&gt;epidermal growth factor receptor&lt;/a&gt; and uncoupling via post-translational modifcation e.g. for &lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.neuro.27.070203.144206?url_ver=Z39.88-2003&amp;amp;rfr_id=ori:rid:crossref.org&amp;amp;rfr_dat=cr_pub%3dpubmed&quot; rel=&quot;nofollow&quot;&gt;G protein-coupled receptors&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of opioid receptors there is emerging evidence that down-regulation is achieved, at least in part, by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23085997&quot; rel=&quot;nofollow&quot;&gt;post-transcriptional regulation by a microRNA.&lt;/a&gt; Presumably this could also accompanied by inactivation of existing receptors, but if the adaptation/desenitisation is long-term then normal receptor turnover may be sufficient.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-09-12T10:31:47.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21239" PostTypeId="2" ParentId="21233" CreationDate="2014-09-12T11:14:09.043" Score="7" Body="&lt;p&gt;We shampoo our hair because of sebum. In humans, sebaceous glands are most numerous on the face and scalp, with (on the scalp at least) several glands plus a hair follicle making up a pilosebaceous unit.&lt;/p&gt;&#xA;&lt;p&gt;Each gland secretes sebum, initially a colorless and odorless fatty substance (plus dead cells) that spreads from the scalp outward over the hair, but that breaks down by bacteria producing strong odors.&lt;/p&gt;&#xA;&lt;p&gt;Look at a person who has not washed their hair in a week and it will be easy to understand why we wash the &amp;quot;dead&amp;quot; stuff on our heads. It looks oily and it eventually smells bad as well.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="13405" LastEditDate="2021-01-19T02:25:44.893" LastActivityDate="2021-01-19T02:25:44.893" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="21240" PostTypeId="2" ParentId="21212" CreationDate="2014-09-12T11:30:50.757" Score="11" Body="&lt;p&gt;The heart has nerve cells which are supposed to fire synchronously. This is what allows the heart to pump effectively. Fibrillation is when nerve cells (or the cardiac cells themselves, which have some &quot;pacemaker&quot; activity) are firing asynchronously, which means blood isn't getting pumped. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The shock causes all of the units to fire at once (which isn't exactly asystole), in the hopes that when electrical activity resumes (after giving a shock, we wait and look at the monitor to see if there is a regular heart beat, we do not start CPR unless there is not), it will do so in an orderly, synchronous manner. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In asystole (flat line), there is no longer any effective electrical activity of the heart. There is basically no disorganized electrical activity to try to reset with a shock.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is why it makes no sense to shock someone in asystole. On television, people in flatline are shocked into a stable sinus rhythm. That just doesn't happen in real life. Neither does a deep breath and fluttering open of eyelids, as often shown on television when someone arrests and resuscitation is successful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://emedicine.medscape.com/article/757257-overview&quot;&gt;Asystole&lt;/a&gt; @ Medscape.com&lt;br&gt;&#xA;&lt;a href=&quot;http://emedicine.medscape.com/article/757257-treatment&quot;&gt;Treatment of Asystole&lt;/a&gt; @ Medscape.com &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-09-12T12:05:06.427" LastActivityDate="2014-09-12T12:05:06.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21241" PostTypeId="1" AcceptedAnswerId="23468" CreationDate="2014-09-12T11:50:24.717" Score="1" ViewCount="5277" Body="&lt;p&gt;There are &lt;a href=&quot;http://happyhomemaker88.com/2009/05/02/recipe-for-homemade-citrus-enzyme-a-natural-cheap-effective-all-purpose-cleaner/&quot; rel=&quot;nofollow&quot;&gt;many recipes which call for using fruit peel fermentation process&lt;/a&gt; to make a concentrated enzyme cleaner solution, some variations call to add bakers yeast. So the question arises that does this recipe really have those &lt;a href=&quot;http://www.cleanlink.com/casestudieswhitepapers/details/Green-Cleaning-Understanding-Bioenzymatic-Cleaners--24615&quot; rel=&quot;nofollow&quot;&gt;cleaning  enzymes&lt;/a&gt; and how are they generated?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://littlehouseinthesuburbs.com/2013/07/7-things-you-should-know-before-making-citrus-enzyme-cleaner.html&quot; rel=&quot;nofollow&quot;&gt;This says&lt;/a&gt; that it may not have the cleaning enzymes, but maybe some other cleaning agents like vinegar or alcohol.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ecowalkthetalk.com/blog/2011/03/04/responses-how-effective-are-garbage-enzymes/&quot; rel=&quot;nofollow&quot;&gt;A discussion from two independent researchers on this topic give contrasting positions&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover if fruits  like Pineapple and papaya are used does it make the solution more potent?&lt;/p&gt;&#xA;" OwnerUserId="9253" LastEditorUserId="9253" LastEditDate="2014-10-30T11:52:14.023" LastActivityDate="2014-10-30T13:08:39.463" Title="Does &quot;Garbage Enzyme cleaner&quot; contain cleaning enzymes?" Tags="&lt;cell-biology&gt;&lt;microbiology&gt;&lt;enzymes&gt;&lt;fermentation&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21243" PostTypeId="1" AcceptedAnswerId="21306" CreationDate="2014-09-12T12:07:26.210" Score="5" ViewCount="2540" Body="&lt;p&gt;Which buffer is best for DNA Electrophoresis and which is best for Protein to be have a sharp bond?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering a higher electrical conductivity compared to TAE &amp;amp; TBE and the generation of less heat. If anyone has a particular formulation (add other materials to improve quality) which is obtained as a result of practical experience. I would be grateful if you send me that.&lt;/p&gt;&#xA;" OwnerUserId="9101" LastEditorUserId="5144" LastEditDate="2014-09-14T11:36:47.443" LastActivityDate="2014-09-15T12:48:43.117" Title="Appropriate Buffer for electerophoresis of DNA &amp; Protein TBE or TAE?" Tags="&lt;biochemistry&gt;&lt;gel-electrophoresis&gt;&lt;protocol&gt;&lt;biotechnology&gt;&lt;dna-isolation&gt;" AnswerCount="4" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21244" PostTypeId="1" AcceptedAnswerId="26408" CreationDate="2014-09-12T12:31:01.173" Score="8" ViewCount="279" Body="&lt;p&gt;There are some species of animals that give birth to more than one pup at a time. In these species, are the fertilized eggs all from one or a limited group of meiosis processes, or are they from different ones?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To illustrate the idea, take for example a case where some animal ends up with seven offspring in a litter. Do the original eggs come from different meiosis events?&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Meiosis   Meiosis   Meiosis   Meiosis   Meiosis   Meiosis   Meiosis&#xA;   |         |         |         |         |         |         |&#xA;   V         V         V         V         V         V         V&#xA;   1         2         3         4         5         6         7&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Or from a smaller set of events?&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;  Meiosis     Meiosis&#xA; / |  | \     |  |  |&#xA;V  V  V  V    V  V  V&#xA;1  2  3  4    5  6  7&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I am aware that, at least in mammals, that egg cells are actually produced long before they are used, and pooled for later use:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Meiosis  Meiosis  Meiosis&#xA;   \\\\    ||||    ////&#xA;    VVVV   VVVV   VVVV&#xA;    =====Egg Pool======&#xA;    |  |  |  |  |  |  |&#xA;    V  V  V  V  V  V  V&#xA;    1  2  3  4  5  6  7&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I do not have any idea how this would work for other types of life though, like birds, reptiles, or fish. How does it work for those sorts of life?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am mainly interested in this to understand how the mother's chromosomes are represented in the offspring. Are all of her chromosomes guaranteed to be represented in at least one offspring?&lt;/p&gt;&#xA;" OwnerUserId="9252" LastActivityDate="2015-04-19T17:10:49.770" Title="Do the eggs for larger litters come from the same meiosis events, or different ones?" Tags="&lt;genetics&gt;&lt;reproduction&gt;&lt;chromosome&gt;&lt;meiosis&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21245" PostTypeId="2" ParentId="21243" CreationDate="2014-09-12T14:20:57.600" Score="4" Body="&lt;p&gt;I have had good experience using a lithium boric acid buffer from &lt;a href=&quot;http://fasterbettermedia.com/&quot; rel=&quot;nofollow&quot;&gt;Faster Better Media&lt;/a&gt;. I use it for RNA gels, but it's advertised for DNA gels. I don't think it can do protein, but I've never tried it. I'm not an electrician, but higher conductivity may be the opposite of what you want. The lithium boric acid buffer claims to have less conductivity than a tris based buffer, allowing you turn the voltage up much higher while producing less heat. The higher voltage pushes the DNA down the gel faster, and keeps the bands sharper. My RNA gels take 30 minutes to run, used to take 3 hours. Of course, those slow gels used a MOPS based buffer and formaldehyde to denature the RNA.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2014-09-12T14:26:11.797" LastActivityDate="2014-09-12T14:26:11.797" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21247" PostTypeId="2" ParentId="21217" CreationDate="2014-09-12T16:38:57.070" Score="3" Body="&lt;p&gt;There are two good papers on this that I like a lot: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1360161/&quot; rel=&quot;nofollow&quot;&gt;Noise in Gene Expression: Origins, Consequences, and Control&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21414483&quot; rel=&quot;nofollow&quot;&gt;Cellular decision making and biological noise: from microbes to mammals.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think they can tell you better than I can, but the major other source of noise is &lt;strong&gt;extrinsic noise&lt;/strong&gt;. Extrinsic noise typically is taken to means two things (both of which are related): &#xA;1. Physical noise from the environment that affects biological processes (thermodynamic fluctuations, for example)&#xA;2. Intercellular heterogeneity caused by, for example, unequal division. This is also related to cells not being &quot;well mixed&quot; - essentially, molecules found inside of cells are not evenly distributed throughout it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There may be other kinds of noise, but I think extrinsic is really the main one you should think about. &lt;/p&gt;&#xA;" OwnerUserId="3804" LastEditorUserId="5144" LastEditDate="2014-09-12T18:43:55.560" LastActivityDate="2014-09-12T18:43:55.560" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21248" PostTypeId="2" ParentId="21141" CreationDate="2014-09-12T16:47:21.967" Score="3" Body="&lt;p&gt;What you are looking for sounds like the mechanism for a &lt;strong&gt;fold-change detector&lt;/strong&gt;. I would recommend looking at these two papers: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896310/&quot; rel=&quot;nofollow&quot;&gt;The incoherent feedforward loop can provide fold-change detection in gene regulation&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an example of this working in a real system, I recommend looking at the NFkB pathway, as recently detailed by Suzanne Gaudet:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1097276514000872&quot; rel=&quot;nofollow&quot;&gt;Fold Change of Nuclear NF-κB Determines TNF-Induced Transcription in Single Cells&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are a few others that I found just by searching for &quot;Fold change detection&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057455&quot; rel=&quot;nofollow&quot;&gt;Comparing Apples and Oranges: Fold-Change Detection of Multiple Simultaneous Inputs&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/107/36/15995.full&quot; rel=&quot;nofollow&quot;&gt;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057455&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://journals.aps.org/pre/abstract/10.1103/PhysRevE.89.022712&quot; rel=&quot;nofollow&quot;&gt;Efficient fold-change detection based on protein-protein interactions&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure by looking at the referenced papers in the above you can find more examples as well. &lt;/p&gt;&#xA;" OwnerUserId="3804" LastEditorUserId="5144" LastEditDate="2014-09-12T18:47:20.213" LastActivityDate="2014-09-12T18:47:20.213" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21249" PostTypeId="1" CreationDate="2014-09-12T18:13:38.063" Score="1" ViewCount="621" Body="&lt;p&gt;Which part of brain is responsible for advance or unseen imagination&#xA;For example:ones brain can make a situation in mind which is impossible to happen ...which part of brain is hyper active?&lt;/p&gt;&#xA;" OwnerUserId="9259" LastActivityDate="2014-09-14T12:21:04.227" Title="brain activity responsible for imagination" Tags="&lt;physiology&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21251" PostTypeId="1" AcceptedAnswerId="21253" CreationDate="2014-09-12T19:14:36.713" Score="3" ViewCount="642" Body="&lt;p&gt;I am learning about DNA cloning for the first time. What I understand is that, in order to clone DNA, we break-up the original gene into shreds. Then try to piece it back together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why exactly do we do this? Instead wouldn't it be better to clone one base at a time? Basically in pseudo code:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;old_dna_strand = 'ACTCATGCGAGCGTCAGTAGTACGTACTG'&#xA;new_dna = &quot;&quot;&#xA;for base in old_dna_strand:&#xA;    new_dna+=base&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;That looks a lot more easier and a lot less prone to errors. Why do we have weird methods such as shotgun?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance. Let me know if i should clarify or update anything in this question.&lt;/p&gt;&#xA;" OwnerUserId="9264" LastActivityDate="2014-09-12T20:31:24.587" Title="Why do we use DNA sequencing methods such as shotgun?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21252" PostTypeId="1" CreationDate="2014-09-12T19:15:28.890" Score="6" ViewCount="5147" Body="&lt;p&gt;One design for underwater human inhabited environments is to have equal pressure between the surrounding water and the submerged habitat, thus allowing a section of the floor to be open to the water and removing the necessity for strong plating to protect it.  This requires the air pressure within the environment to be greater than atmospheric pressure so that it can withstand the pressure of both the atmosphere and the pressure from the overlying water.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how much pressure can the human body survive in without need for special suits and breathing apparatuses (as this would place a limit on how deep you could build such an environment without special accommodation)?     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: So far i've found an article about a man trapped in a sunken boat who survived for days in an air pocket trapped in the bathroom 100 feet down.  He couldn't resurface without the use of a diving bell and gradual decompression; but this case provides a lower bound for how high the highest pressure can be.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Calculations:  14.7 psi (atm pressure) + 1200 inches*0.037 psi/in^3 = 60 psi for the underwater pocket (roughly 4 times atmospheric pressure).&#xA;&lt;a href=&quot;http://news.nationalgeographic.com/news/2013/12/131204-nigerian-air-bubble-survival-shipwreck-viral-video-science/&quot; rel=&quot;noreferrer&quot;&gt;http://news.nationalgeographic.com/news/2013/12/131204-nigerian-air-bubble-survival-shipwreck-viral-video-science/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9052" LastEditorUserId="9052" LastEditDate="2014-09-12T19:45:32.077" LastActivityDate="2018-12-10T05:08:41.663" Title="Highest Pressure Human Body Can Survive In?" Tags="&lt;human-biology&gt;&lt;respiration&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21253" PostTypeId="2" ParentId="21251" CreationDate="2014-09-12T19:31:52.627" Score="3" Body="&lt;p&gt;This is a technique from the &quot;old time&quot; of genome sequencing. The underlying method for sequencing is the Sanger chain termination method which can have read lenghts between 100 and 1000 basepairs (depending on the instruments used). This means you have to break down longer DNA molecules, clone and subsequently sequence them. There are two methods possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Primer_walking&quot; rel=&quot;nofollow&quot;&gt;chromosome (or primer) walking&lt;/a&gt; and starts with sequencing the first piece. The next piece of DNA (which is  and then uses a specific primer from the end of the sequence. The next (contigous) piece of the sequence is then sequenced using a primer which is complementary to the end of the first sequence read and so on. This technique doesn't require much assembling, but you need a lot of primers and it is relatively slow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To overcome this problem the shotgun sequencing method was developed. Here the DNA is broken into different pieces (not all broken at the same place), cloned and sequenced with primers specific for the vector used for cloning. The leads to overlapping sequences which then have to be assembled into one sequence on the computer. This method allows the parallelization of the sequencing (you can prepare a lot of sequencing reactions at the same time and run them) which makes the process much faster and also avoids the need for sequence specific primers. The problems are to sequence repetitive sequences, as overlaps are not as clear here. To resolve this problems a first draft is made and then critical regions are resequenced using other techniques as primer walking. Have a look at the Wikipedia page about &lt;a href=&quot;http://en.wikipedia.org/wiki/Shotgun_sequencing&quot; rel=&quot;nofollow&quot;&gt;shotgun sequencing&lt;/a&gt; if you want to read more details.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-09-12T20:31:24.587" LastActivityDate="2014-09-12T20:31:24.587" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21254" PostTypeId="1" AcceptedAnswerId="21255" CreationDate="2014-09-12T20:07:36.797" Score="2" ViewCount="1105" Body="&lt;p&gt;This is a very very basic question. I've looked at methods such as chromosome sequencing and shotgun sequencing. Wikipedia says that:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, with methods such as shotgun, we already have the original DNA. If we have access to the original DNA itself, don't we ALREADY know the sequence of nucleotides?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why exactly do we need to 're-build' the DNA with methods such as shotgun and chromosome walking, when we already have the original DNA available? If we have the original DNA, don't we already have the original sequence of nucleotides? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It makes me think that these techniques for 'DNA sequencing' is sort-of pointless. But, obviously I am misunderstanding something.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance, any simple pointers would be great.&lt;/p&gt;&#xA;" OwnerUserId="9264" LastEditorUserId="9264" LastEditDate="2014-09-12T20:14:04.893" LastActivityDate="2014-09-12T20:36:21.180" Title="What is the point of DNA sequencing?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21255" PostTypeId="2" ParentId="21254" CreationDate="2014-09-12T20:36:21.180" Score="4" Body="&lt;p&gt;No, you don't. Having the DNA in your hand means that you have access to a macromolecule, not more. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think of the DNA as a book (or a library). From holding the book in your hands, you don't know what the content is. You have to actively read the book to get this information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sequencing a piece of DNA is basically the same. Your readout is the sequence of the bases which is essential to understand (or do research on it) a certain piece of DNA. With this knowledge you can see where genes start and end, define introns and exons (for eukaroytes) and so on.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-12T20:36:21.180" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21256" PostTypeId="1" CreationDate="2014-09-12T20:46:56.140" Score="4" ViewCount="4214" Body="&lt;p&gt;After reading &lt;a href=&quot;https://biology.stackexchange.com/questions/21216/why-do-i-only-breathe-out-of-one-nostril&quot; title=&quot;why do I only breathe out of one nostril&quot;&gt;the question why do I only breathe out of one nostril&lt;/a&gt; I realized that breathing out of both isn't common. I have always breathed out of both, and when I get a stuffy nose, or a runny nose, it's on both sides. If only one side is stuffed, I'll just lay on my side a bit to even it out until I can breathe out of both again. I've always though that was totally normal! What does it mean that my autonomous nervous system is not alternating my breathing?&lt;/p&gt;&#xA;" OwnerUserId="9265" LastActivityDate="2014-09-14T05:00:34.697" Title="Why do I breathe out of BOTH nostrils?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;human-anatomy&gt;&lt;nose&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21258" PostTypeId="1" AcceptedAnswerId="24218" CreationDate="2014-09-12T22:24:30.937" Score="4" ViewCount="1695" Body="&lt;p&gt;For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on biochemical reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, my question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How does temperature influence the rate of protein degradation?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Reducing the scope of my question&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question might be too broad in the sense that there might have too much variance in how different proteins respond to temperature in order to draw in general tendency. If this is so, someone willing to answer may reduce the question to transcription factor, to &lt;a href=&quot;http://en.wikipedia.org/wiki/General_transcription_factor&quot; rel=&quot;nofollow noreferrer&quot;&gt;General Transcription Factor (GTF)&lt;/a&gt; or even to &lt;a href=&quot;http://en.wikipedia.org/wiki/Transcription_factor_II_A&quot; rel=&quot;nofollow noreferrer&quot;&gt;TFIIA&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I am NOT looking for..&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not looking for a theoretical explanation of how temperature influences this process (I have basic understanding of the importance of the activation energy as displayed on a Maxwell-Boltzman distribution and of the Michaelis-Menten equation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I am looking for..&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for a function that I can plug in my algorithms to incorporate the influence of various temperatures on the process I want to simulate. I want to simulate the average gene network from an average standard eukaryote. For other purpose, I chose parameter values coming from the yeast. A index such as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Q10_(temperature_coefficient)&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Q&lt;sub&gt;10&lt;/sub&gt;&lt;/strong&gt;&lt;/a&gt; would be very useful as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Similar already-answered question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similar questions have been asked and answered &lt;a href=&quot;https://biology.stackexchange.com/questions/21198/how-is-the-rate-of-transcription-influenced-by-temperature/21224#21224&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;https://biology.stackexchange.com/questions/21189/influence-of-temperature-on-protein-binding-and-decay-rates&quot;&gt;here&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-06-30T06:47:34.507" Title="How does temperature influence the rate of protein degradation?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;proteins&gt;&lt;mathematical-models&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21259" PostTypeId="1" CreationDate="2014-09-12T22:26:40.207" Score="2" ViewCount="470" Body="&lt;p&gt;Why is gastric lavage considered to be helpful only if a patient comes to a hospital within 1 hour of a toxic ingestion? How severe would the effects be if a patient came to the hospital after the recommended 1 hour time frame?&lt;/p&gt;&#xA;" OwnerUserId="8977" LastActivityDate="2014-09-13T15:03:50.900" Title="Why is gastric lavage considered to be helpful only if a patient comes to a hospital within 1 hour of a toxic ingestion?" Tags="&lt;toxicology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21260" PostTypeId="2" ParentId="21259" CreationDate="2014-09-12T22:40:57.067" Score="4" Body="&lt;p&gt;Gastric lavage only washes out (&quot;lavages&quot;) the stomach (&quot;gastrium&quot;). &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17074022&quot;&gt;Gastric emptying time&lt;/a&gt; is generally ~60-120 min, probably on the lower end of that for ingested liquids. After that amount of time, most of the toxic substance will be beyond the level of the pyloric sphincter (i.e. in the duodenum) and not accessible to lavage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second question is not possible to answer without some information about what specific toxic ingestion you are interested in knowing about.&lt;/p&gt;&#xA;" OwnerUserId="9268" LastActivityDate="2014-09-12T22:40:57.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21261" PostTypeId="2" ParentId="21249" CreationDate="2014-09-12T22:51:18.753" Score="1" Body="&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;: Added two studies to better show how different types of imagination tasks use different parts of the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagination is a complex process that can use many regions of the brain. Insights into how our brain imagines have been gained through a number of studies. There is not an &quot;imagination&quot; area of the brain. Instead, different areas, and often several at a time, may be used depending on the type of imagination. I'll highlight a few examples here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://cercor.oxfordjournals.org/content/17/5/1139.long&quot; rel=&quot;nofollow&quot;&gt;Ogino et al. (2007)&lt;/a&gt; asked 10 male participants to imagine feeling pain while watching pictures suggesting either pain or fear. Both pain and fear tended to activate an area of the brain called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Anterior_cingulate_cortex&quot; rel=&quot;nofollow&quot;&gt;anterior cingulate cortex (ACC)&lt;/a&gt;, which helps to regulate blood pressure and heart rate among other basic nervous functions. Imagining pain activated not only the ACC but also another four areas of the brain were especially active. In comparison, fear tended to activate the ACC and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hypothalamus&quot; rel=&quot;nofollow&quot;&gt;hypothalamus&lt;/a&gt;, which regulates the &quot;flight or fight&quot; response. Both sides of the brain were activated at the same time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bernardbaars.pbworks.com/f/Locked+in+volitional+brain+NI2007.pdf&quot; rel=&quot;nofollow&quot;&gt;Boly et al. (2007)&lt;/a&gt; studied 12 brain-injured patients who where not capable of communicating. They were not in a coma. They were asked to imaging tasks involving spatial skills or motor skills. The two most common areas of the brain that were activated were the &lt;a href=&quot;http://en.wikipedia.org/wiki/Supplementary_motor_area&quot; rel=&quot;nofollow&quot;&gt;supplementary motor area&lt;/a&gt;, which helps to control movement, and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Premotor_cortex&quot; rel=&quot;nofollow&quot;&gt;dorsal premotor cortex&lt;/a&gt;, which may contribute to movement and spatial coordination. (Wikipedia information so interpret cautiously.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A detailed study was recently provided in a study by &lt;a href=&quot;http://www.pnas.org/content/110/40/16277&quot; rel=&quot;nofollow&quot;&gt;Schlegel et al. 2013&lt;/a&gt;. (An alternate version is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791746/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;; both versions are open access.) Summaries of their work written for the general public can be found in &lt;a href=&quot;http://www.popsci.com/science/article/2013-09/how-imagination-works&quot; rel=&quot;nofollow&quot;&gt;Popular Science&lt;/a&gt; and &lt;a href=&quot;http://www.sciencedaily.com/releases/2013/09/130916162003.htm&quot; rel=&quot;nofollow&quot;&gt;Science Daily&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The scientists identified what they called the &quot;mental workspace&quot; which is not a particular region of the brain but instead is several different regions of the brain (from both sides of the brain) interacting together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The researchers asked the study participants (9 males and 6 females) to select from a set of abstract shapes to assemble a particular target shape.  The target shape (the one the participants had to create) was a 2x2 grid. Each abstract shape that to be selected would fit one of the grids. So, four abstract shapes had to be selected to assemble the target shape. They also tested the reverse: Given a target shape, could the participants identify the four abstract shapes needed to make the target shape.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During the task, the researchers used &lt;a href=&quot;http://fmri.ucsd.edu/Research/whatisfmri.html&quot; rel=&quot;nofollow&quot;&gt;functional magnetic resonance imaging (fMRI)&lt;/a&gt; to monitor brain activity. After the analysis of the fMRI results, they identified 11 distinct regions of the brain were active during the task.  In nearly all cases, the regions were active in both sides of the brain. However, I noticed that one region, the medial frontal cortex, only appeared to be active in the left side of the brain. This region was identified as one important component of the mental workspace for certain tasks.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The researchers concluded that four of the 11 regions were most important. You can see the regions of the brain in any four of the links above (and the abstract shapes in all but the Science Daily article). They argue that the interaction among the four major and seven minor regions contribute to our process of imagination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each of the three studies I highlighted requires the participants to perform different types of imgination tasks. Each type of task showed that different regions of the brain were used. Each type of task also required that several areas of the brain were used simultaneously during the imagination process. Together, these results show that no single part of the brain is used for imagination. Instead, many different areas are used, depending on what the person is imagining.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Citations&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Boly, M. et al. 2007. When thoughts become action: An fMRI paradigm to study volitional brain activity in non-communicative brain injured patients. NeuroImage 36: 979-992.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ogino, Y. et al. 207. Inner experience of pain: Imagination of pain while viewing images showing painful events forms subjective pain representation in human brain. Cerebral Cortex 17: 1139-1146.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Schlegel et al. 2013.  Network structure and dynamics of the mental workspace.  Proceedings of the National Academy of Sciences USA 110: 16277-16282.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-09-14T12:21:04.227" LastActivityDate="2014-09-14T12:21:04.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21262" PostTypeId="1" AcceptedAnswerId="21281" CreationDate="2014-09-12T23:12:54.377" Score="4" ViewCount="177" Body="&lt;p&gt;All right, I was reading article on nutrition, that focussed on content analysis of pastry-like food product for kids. I have to say that I am not sure this article would pass the imaginary smell test, although it didn't raise any serious red flags, except one.&#xA;Among other things, this article said that oxidation means inflammation. It said this in connection with use of rapeseed oil in said product, saying rapeseed oil is less saturated and therefore more likely to oxidize. It then implied, that when this oxidation takes place in the human body, it leads to inflammation.&#xA;Now I am no biology, medicine, or nutrition specialist, but if something is still stuck in my head from high school biology, it is that inflammation is the physical manifestation of our immune system fighting off infection, no? Apart of some autoimmune reactions, I don't see how ingesting rapeseed oil could cause inflammation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is this: is it really possible to safely say: &quot;oxidation = inflammation&quot;? Or is it total nonsense? Or is there some theory that could support such claim and how reliable is this theory? Isn't it just one of those hypothesis disguised as theories?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Said article is in Czech, otherwise I would link it for you.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;EDIT: &lt;a href=&quot;http://www.vyvazenezdravi.cz/pitevni-protokol-bebe-brumik-30g-kraft-foods-cr-sro&quot; rel=&quot;nofollow&quot;&gt;Article link here&lt;/a&gt;, you can try it with Google translate :)&lt;/p&gt;&#xA;" OwnerUserId="9269" LastEditorUserId="9269" LastEditDate="2014-09-13T00:03:34.503" LastActivityDate="2014-09-13T18:24:01.427" Title="Oxidation means inflamation?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;metabolism&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21263" PostTypeId="2" ParentId="21108" CreationDate="2014-09-12T23:48:20.713" Score="3" Body="&lt;p&gt;I contacted Richard Pillans, the primary author of the article linked to in the question. He told me that he did not know whether the rectal gland was reduced. Researchers are hesitant to capture and dissect the freshwater sharks because of their &lt;a href=&quot;http://www.iucnredlist.org/details/39379/0&quot; rel=&quot;nofollow&quot;&gt;endangered status&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;He did tell me that they have gathered much more data on the movement of the sharks since the 2009 paper was published.  Apparently, river shark is a bit misleading (my words, not Dr. Pillans). &lt;em&gt;Glyphis&lt;/em&gt; does occur in freshwater (no salt) but tends to be found in the middle range of &lt;a href=&quot;http://www.princeton.edu/~achaney/tmve/wiki100k/docs/Brackish_water.html&quot; rel=&quot;nofollow&quot;&gt;brackish water&lt;/a&gt;. Brackish water is considered to be anything that is not purely freshwater nor purely salt water, with typical values between 0.5 and 30 parts per thousand (ppt). Freshwater is 0 ppt and open ocean salt water is 35 ppt, the equivalent of 35 grams of salt in one liter of water. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If &lt;em&gt;Glyphis&lt;/em&gt; is found primarily in the mid-range of brackish water, then I would expect the rectal gland not show signs of reduction. &lt;a href=&quot;http://www.researchgate.net/profile/Craig_Franklin3/publication/8398895_Plasma_osmolyte_concentrations_and_rectal_gland_mass_of_bull_sharks_Carcharhinus_leucas_captured_along_a_salinity_gradient/links/0deec5167b82cbc4d9000000&quot; rel=&quot;nofollow&quot;&gt;Pillans and Franklin (2004)&lt;/a&gt; showed that rectal gland mass of brackish water bullsharks (&lt;em&gt;Carcharhinus leucas&lt;/em&gt;) in Australia did not differ significantly from either freshwater or saltwater individuals.  So, pending further evidence, I would conclude that &lt;em&gt;Glyphis&lt;/em&gt;, which in the same family as bull sharks, probably does not show rectal gland reduction.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pillans, R.D. and C.E. Franklin, 2004.  Plasma osmolyte concentrations and rectal gland mass of bull sharks &lt;em&gt;Carcharhinus leucas&lt;/em&gt;, captured along a salinity gradient.  Comparative Biochemistry and Physiology, Part A 138: 363-371.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-09-13T00:27:13.227" LastActivityDate="2014-09-13T00:27:13.227" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21265" PostTypeId="2" ParentId="21223" CreationDate="2014-09-13T01:18:24.530" Score="3" Body="&lt;p&gt;Absolutely, the two I've had the most success are working with a radiolabeled and a fluorescently labeled version of the drug. Many drugs autofluoresce as well and this can be easily tracked. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When it's labeled as mentioned above microscopy or a luminometer, spectrophomoter or a scintillation counter can evaluate fractions or whole cells, or purified binding substrates.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-09-13T01:18:24.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21267" PostTypeId="2" ParentId="21259" CreationDate="2014-09-13T08:56:25.520" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Gastric emptying, which used to be well-accepted and seems intuitively&#xA;  beneficial, should not be routinely done. It does not clearly reduce&#xA;  overall morbidity or mortality and has risks. Gastric emptying is&#xA;  considered if it can be done within 1 h of a life-threatening&#xA;  ingestion. However, many poisonings manifest too late, and whether a&#xA;  poisoning is life threatening is not always clear. Thus, gastric&#xA;  emptying is seldom indicated and, if a caustic substance has been&#xA;  ingested, is contraindicated (see &lt;a href=&quot;http://www.merckmanuals.com/professional/injuries_poisoning/poisoning/caustic_ingestion.html&quot; rel=&quot;nofollow&quot;&gt;Caustic Ingestion&lt;/a&gt;). &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;If gastric emptying is used, gastric lavage is the preferred method.&#xA;  Gastric lavage may cause complications such as epistaxis, aspiration,&#xA;  or, rarely, oropharyngeal or esophageal injury. Syrup of ipecac has&#xA;  unpredictable effects, often causes prolonged vomiting, and may not&#xA;  remove substantial amounts of poison from the stomach. Syrup of ipecac&#xA;  may be warranted if the ingested agent is highly toxic and transport&#xA;  time to the emergency department is unusually long, but this is&#xA;  uncommon in the US.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;ref:&lt;a href=&quot;http://www.merckmanuals.com/professional/injuries_poisoning/poisoning/general_principles_of_poisoning.html#v1118455&quot; rel=&quot;nofollow&quot;&gt;http://www.merckmanuals.com/professional/injuries_poisoning/poisoning/general_principles_of_poisoning.html#v1118455&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9101" LastEditorUserId="9101" LastEditDate="2014-09-13T15:03:50.900" LastActivityDate="2014-09-13T15:03:50.900" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21268" PostTypeId="1" AcceptedAnswerId="21270" CreationDate="2014-09-13T10:36:05.840" Score="6" ViewCount="3484" Body="&lt;p&gt;I spotted this dove in a park. It was foraging among Rock Doves, Seagulls, Ibises and a few others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears similar to Pied Rock Doves, but I am not certain if this is correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KVf6l.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any idea what the name of this dove is?&lt;/p&gt;&#xA;" OwnerUserId="8177" LastActivityDate="2014-09-13T19:36:11.470" Title="Name of This Black and White Dove" Tags="&lt;species-identification&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21269" PostTypeId="1" AcceptedAnswerId="21285" CreationDate="2014-09-13T11:36:07.880" Score="9" ViewCount="1675" Body="&lt;p&gt;I got this plant sprouting in my window box this spring. Starting from a single seed, it has grown into an impressive array of branching climbing vines, reaching 6 feet tall. The stem turned red as it matured. The most awesome feature of this plant is that &lt;strong&gt;the stem is covered in micro hooks that cling to everything&lt;/strong&gt;. I've seen it cling to a paint on a metal gutter pipe I can think of these hooks as velcro or gecko feet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can someone help me identify this plant?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;climbing vine&lt;/li&gt;&#xA;&lt;li&gt;stem is covered in tiny hooks that are very clingy&lt;/li&gt;&#xA;&lt;li&gt;grows to 6 feet tall&lt;/li&gt;&#xA;&lt;li&gt;stem turns to red as it matures&lt;/li&gt;&#xA;&lt;li&gt;segmented leaves&lt;/li&gt;&#xA;&lt;li&gt;leaves grow to palm size&lt;/li&gt;&#xA;&lt;li&gt;new leaves sprout from stem where old leaves were connected&lt;/li&gt;&#xA; - &#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/D3Ic1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2018-07-12T01:15:20.857" Title="Help identify this awesome climbing plant with velcro like stem" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21270" PostTypeId="2" ParentId="21268" CreationDate="2014-09-13T11:52:22.867" Score="8" Body="&lt;p&gt;It's a pied version of the Rock Pigeon (&lt;em&gt;Columbia livia&lt;/em&gt;), aka Rock Dove. According to the &lt;a href=&quot;http://www.allaboutbirds.org/guide/rock_pigeon/lifehistory&quot; rel=&quot;nofollow&quot;&gt;Cornell Lab of Ornithology&lt;/a&gt;, the pied variety of Rock Pigeon is one of any color that has splotches of white on the body. I think that fits your bird very well. It's not a different species, but just one of several color varieties of Rock Pigeon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are not familiar with Cornell's site and enjoy birds, their All About Birds site is very nice.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-09-13T19:36:11.470" LastActivityDate="2014-09-13T19:36:11.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21271" PostTypeId="1" CreationDate="2014-09-13T11:58:19.743" Score="8" ViewCount="2073" Body="&lt;p&gt;When researching water quality standards, I found that a minimum and maximum was set for water hardness. Several sources also state that water can in fact be too hard. The question is how does hard water harm marine life? I understand that it is required to reduce the toxicity of Hydrogen ions and other trace metals, but cannot find anything concerning the effect of water that is too hard.&lt;/p&gt;&#xA;" OwnerUserId="9276" LastActivityDate="2018-02-04T19:33:42.473" Title="Effect of extremely hard water on marine life?" Tags="&lt;marine-biology&gt;&lt;aquatic-biology&gt;&lt;calcium&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21272" PostTypeId="1" AcceptedAnswerId="21275" CreationDate="2014-09-13T14:13:08.593" Score="12" ViewCount="1844" Body="&lt;p&gt;In &lt;a href=&quot;https://aviation.stackexchange.com/a/8554/1467&quot;&gt;this answer&lt;/a&gt; on aviation.SE a comparison is made between the shapes of airplanes wings and the shapes of birds wings. It concludes with the following remark:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After all, no bird has winglets. Not a single one.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In addition to be a disputable assertion (the wing tips such as the eagle's could be considered akin to a &quot;winglet&quot; of the fanned type) this has stricken me as based on a quite wrong assumption of how evolution works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried to make my point in the comments only to reach this point:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So you consider evolved wings as not mature. The winglet modification is just waiting to happen? Nature never tried it, in &gt;100 million years of biological flight? Could be, yes. But is extremely unlikely. That settles it for me.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Am I correct in identifying this in a wrong interpretation of the evolutionary process?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I understand the evolutionary process, the current bird wings are not necessarily perfect, are simply the version that so far has given the best advantage. The lack of &quot;winglets&quot; in birds cannot then be explained simply by assuming that they do not improve the wing, but it could also be that there has never been an evolutionary pressure to evolve them or that since birds flap their wings they would be detrimental instead of beneficial or whatever other reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is my understanding of the evolutionary process correct? if not, where am I at fault?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;As a small addendum, another user cited the &quot;Spandrels&quot; in comparison to the above debate, could someone explain what could have been the meaning of the comparison?&lt;/p&gt;&#xA;" OwnerUserId="9247" LastEditorUserId="-1" LastEditDate="2017-04-13T12:59:54.113" LastActivityDate="2014-10-17T16:16:35.663" Title="The evolutionary process in bird wings, especially with regard to winglets" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;ornithology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21273" PostTypeId="2" ParentId="21272" CreationDate="2014-09-13T15:04:55.840" Score="9" Body="&lt;p&gt;There are two possibilites with evolutionary processes: The development either never went into this direction or it brought no advantages. Besides this two possibilities the claims from the other forum are wrong. Birds (not all of them though) do have winglet-like structures. If you look at big birds, you can see feathers on the end of the wings looking like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1pug4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Tgwct.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These feather fulfill exactly the same purpose here. Some more information can be found &lt;a href=&quot;http://jeb.biologists.org/content/180/1/285&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; and also in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Alula&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-09-13T18:23:30.547" LastActivityDate="2014-09-13T18:23:30.547" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21275" PostTypeId="2" ParentId="21272" CreationDate="2014-09-13T15:53:44.430" Score="16" Body="&lt;p&gt;I looked up winglets so I had context for this answer. I'm interpreting winglets as the &lt;a href=&quot;http://www.airspacemag.com/flight-today/how-things-work-winglets-2468375/?no-ist&quot; rel=&quot;noreferrer&quot;&gt;vertical tips at the end of airplane wings&lt;/a&gt;. If so, then you are correct. The spread primary feathers of soaring birds like eagles function as winglets &lt;a href=&quot;http://jeb.biologists.org/content/180/1/285.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;(Tucker 1993&lt;/a&gt;). Airbus has a &lt;a href=&quot;http://www.airbus.com/innovation/eco-efficiency/design/biomimicry/&quot; rel=&quot;noreferrer&quot;&gt;biomimicry web page&lt;/a&gt; devoted to some of the biological designs, including winglets, they incorporated into their airplane designs. Some studies suggest airplant winglets do increase efficiency (e.g., &lt;a href=&quot;http://www.waset.org/publications/5593&quot; rel=&quot;noreferrer&quot;&gt;Hossain et al. 2011&lt;/a&gt;), but there is still &lt;a href=&quot;https://aviation.stackexchange.com/a/8557&quot;&gt;some debate&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;From the &lt;a href=&quot;https://aviation.stackexchange.com/a/8554&quot;&gt;aviation.se answer&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Look at birds: They use two different wingtip designs. I guess we will both agree that those designs are mature after millions of years of evolution. And still there are two distinct wing tip shapes: One is the &amp;quot;fingered&amp;quot; wingtip with large, spread-out feathers, and one is the pointed tip you find from seagulls to albatrosses. Why is there not one, mature design?&lt;/p&gt;&#xA;&lt;p&gt;This has to do with the environment they are used in. Seabirds fly in an unobstructed environment with steady winds and need to stay aloft for longer duration. All other birds have to cope with trees obstructing a straight flight path and gusts from hills, or those trees. They need to maneuver quickly and cope with gusty winds. This is helped by a reduced span and the possibility to fold the outer wing in or fan it out in an instance. Hence the fingered wingtip.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Although bird wings do tend to match his descriptions, he is not correct that these correspond entirely to ocean-going birds vs all other birds. Many inland birds have pointed wings, including &lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/1/11/Barn_Swallow_(Hirundo_rustica)_(13).JPG&quot; rel=&quot;noreferrer&quot;&gt;swallows&lt;/a&gt;, &lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/7/71/Chordeiles_minorEJN31CB.jpg&quot; rel=&quot;noreferrer&quot;&gt;nightjars&lt;/a&gt;, &lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/9/93/Tachymarptis_melba_-Barcelona,_Spain_-flying-8.jpg&quot; rel=&quot;noreferrer&quot;&gt;swifts&lt;/a&gt;, and &lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/6/61/Falco_peregrinus_-Morro_Rock,_Morro_Bay,_California,_USA_-flying-8.jpg&quot; rel=&quot;noreferrer&quot;&gt;falcons&lt;/a&gt;.  Some seagoing birds have winglets, such as &lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/7/79/Brown_pelican_-_natures_pics.jpg&quot; rel=&quot;noreferrer&quot;&gt;pelicans&lt;/a&gt; and &lt;a href=&quot;https://c2.staticflickr.com/4/3172/2903748194_1c9f3aa8e8_z.jpg?zz=1&quot; rel=&quot;noreferrer&quot;&gt;cormorants&lt;/a&gt;.  While wing type is shaped by natural selection in a given environment, it also reflects the evolutionary history of the birds.&lt;/p&gt;&#xA;&lt;p&gt;There is not &amp;quot;one, mature design&amp;quot; because wings many different shapes and sizeshave evolved under varying selective pressures. For example, the long pointed wings of ocean-going albatrosses are excellent for gliding with little energy expenditure but they are lousy for taking flight or for landing. Other wings are shorter and broader, providing greater maneuverability in the woods. In this sense, there is no perfect wing. Each has evolved for different evolutionary reasons.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;The main question&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;From the aviation.SE thread:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;the fact that no random mutation has produced a winglet* in birds is in no way a demonstration that airplanes do not benefit from them, there is no logical relationship. [*even though the &amp;quot;fanned&amp;quot; design you refer, such as the eagle's, can be considered a form of optimum winglet] –  Federico&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;followed by this response:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;So you consider evolved wings as not mature. The winglet modification is just waiting to happen? Nature never tried it, in &amp;gt;100 million years of biological flight? Could be, yes. But is extremely unlikely. That settles it for me...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Federico is correct. The basic wing type was set long ago as birds evolved from &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evograms_06&quot; rel=&quot;noreferrer&quot;&gt;non-avian dinosaurs&lt;/a&gt;. Comparisons of modern bird wings with fossils suggest that the basic structure of bird wings has not changed very much since then. The current structure may be the best that has evolved by natural selection so far but that does not mean the wing cannot be improved further. As you noted, mutations could occur in existing genes that lead to further improvements of the structure and function of the wings. If those mutations never occur, then the improvements won't occur. This is one constraint of the evolutionary process &lt;a href=&quot;http://press.princeton.edu/chapters/s3_10100.pdf&quot; rel=&quot;noreferrer&quot;&gt;(Hoffman 2014)&lt;/a&gt;. Natural selection can only work with existing traits, using existing genes and genetic variation.&lt;/p&gt;&#xA;&lt;p&gt;Another consideration is that wings for powered flight have evolved independently at least four times (birds, bats, insects, pterosaurs). Each time, a different type of wing evolved. Is one better than another? Bat wings have aerodynamic properties very different from birds but function very well for bats &lt;a href=&quot;http://mysite.verizon.net/res77pzy/sitebuildercontent/sitebuilderfiles/hjs_bb_09.pdf&quot; rel=&quot;noreferrer&quot;&gt;(Hedenstrom et al. 2009)&lt;/a&gt;. Along the lines of your argument above, each wing type perhaps is (or was for pterosaurs) optimum given the environmental circumstances and evolutionary constraints. That doesn't mean they could not be improved.  If a wing evolves again in some organismal group in the distant evolutionary future, odds are very good that the structure will be different from those that have evolved so far. Perhaps that wing will be even more efficient than current wings.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Spandrels&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Another user cited the &amp;quot;Spandrels&amp;quot; in comparison to the above debate, could someone explain what could have been the meaning of the comparison?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The use of &amp;quot;spandrels&amp;quot; in evolutionary biology stems back to a well-known paper by Stephen Jay Gould and Richard C. Lewontin called &amp;quot;The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptionist programme&amp;quot;, published in 1979 &lt;a href=&quot;http://www.sci.uidaho.edu/biol483/articles/Gould%20and%20Lewontin%201979.pdf&quot; rel=&quot;noreferrer&quot;&gt;(Gould and Lewontin 1979)&lt;/a&gt;. A &lt;a href=&quot;http://en.wikipedia.org/wiki/Spandrel&quot; rel=&quot;noreferrer&quot;&gt;spandrel&lt;/a&gt; is the space that forms between two adjacent arches or between an arch and a rectangular shape.  The spandrel emerges as a result of putting two arches next to each other and filling the space. It &lt;em&gt;results&lt;/em&gt; from the joining of two arches. It was not specifically &lt;em&gt;designed&lt;/em&gt; as part of the arch. Gould and Lewontin claim that evolutionary biologists are too quick to assign adaptive value to every trait on an organism, and argue that not every trait results directly from adaptation. Instead, they say, the trait may be a &amp;quot;spandrel&amp;quot; that emerged as a by-product of other traits. The &amp;quot;spandrel trait&amp;quot; has no adaptive value in and of itself.&lt;/p&gt;&#xA;&lt;p&gt;The use of spandrels in the comments of the aviation discussion is not clear to me. Clearly, the person intended the evolutionary meaning, mentioning the paper by name. But I cannot tell at all the person's intent.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Edits:&lt;/strong&gt; Incorporated comments by @Federico and @Andrew - thanks. I corrected horrendous typos and attempted to add clarity.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Citations&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Hedenstrom, A. et al. 2009. Bird or bat: comparing airframe design and flight performance. Bioinspiration &amp;amp; Biomimetics 4 015001. &lt;a href=&quot;http://dx.doi.org/10.1088/1748-3182/4/1/015001&quot; rel=&quot;noreferrer&quot;&gt;doi:10.1088/1748-3182/4/1/015001&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Hoffmann, A.A. 2014. Evolutionary limits and constraints. Pp. 247-252. In: The Princeton Guide to Evolution, Princeton University Press, USA.&lt;/p&gt;&#xA;&lt;p&gt;Hossain et al. 2011. Drag analysis of an aircraft wing model with and without bird feather like winglet. International Journal of Mechanical, Aerospace, Industrial and Mechatronics Engineering 5: 30-35.&lt;/p&gt;&#xA;&lt;p&gt;Tucker, V.A. 1993. Gliding birds: Reducion of induced drag by wing tip slots between the primary feathers. Journal of Experimental Biology 180: 285-310.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-13T21:20:34.630" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21276" PostTypeId="1" AcceptedAnswerId="21277" CreationDate="2014-09-13T15:53:46.783" Score="4" ViewCount="1432" Body="&lt;p&gt;I remember being told as a child that dogs stick their tongue out to stay cool, because they can't sweat like us. This made sense to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But only a couple of days ago I suddenly thought: What about all the other animals?! I mean, I don't see a cat or a horse putting their tongues out, and yet I don't see them sweating either. How do they lose heat? How do different kinds of animals lose heat? &lt;/p&gt;&#xA;" OwnerUserId="9279" LastActivityDate="2014-09-13T16:57:27.927" Title="How do animals lose heat?" Tags="&lt;zoology&gt;&lt;heat&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21277" PostTypeId="2" ParentId="21276" CreationDate="2014-09-13T16:13:53.797" Score="3" Body="&lt;p&gt;There are a number of ways, which are briefly &lt;a href=&quot;http://www.biosciweb.net/animal/pdf/thermo.pdf&quot; rel=&quot;nofollow&quot;&gt;summarized here&lt;/a&gt;. I also recommend reading this nice &lt;a href=&quot;http://www.nature.com/scitable/knowledge/library/homeostatic-processes-for-thermoregulation-23592046&quot; rel=&quot;nofollow&quot;&gt;Scitable article&lt;/a&gt; on thermoregulation. It is not too technical. &lt;a href=&quot;http://activerain.trulia.com/image_store/uploads/5/0/0/8/1/ar131157178218005.jpg&quot; rel=&quot;nofollow&quot;&gt;Felines do pant&lt;/a&gt; when they get hot. &lt;a href=&quot;http://www.horsesaddleshop.com/signs-of-bad-saddle-fit.html#.VBRrTlbLx94&quot; rel=&quot;nofollow&quot;&gt;Horses do sweat&lt;/a&gt;. Jackrabbits can enlarge the &lt;a href=&quot;http://bio1152.nicerweb.com/Locked/media/ch40/40_01Jackrabbit-L.jpg&quot; rel=&quot;nofollow&quot;&gt;blood vessels in their large ears&lt;/a&gt; to eliminate excess heat. Bird use a process called &lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/thumb/5/5d/BFAL_SOTE_shade.JPG/800px-BFAL_SOTE_shade.JPG&quot; rel=&quot;nofollow&quot;&gt;gular flapping&lt;/a&gt;, which is similar to panting of dogs and cats.  Animals can move into shaded areas.  The possible mechanisms are many.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="4108" LastEditDate="2014-09-13T16:57:27.927" LastActivityDate="2014-09-13T16:57:27.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21278" PostTypeId="1" CreationDate="2014-09-13T17:22:22.280" Score="8" ViewCount="1153" Body="&lt;p&gt;I recently watched a presentation on RNA-seq that covered some of the choices one can make along the way, and I didn't fully understand one of the choices in particular.  Near the beginning of the process, you can choose a fragmentation method (e.g. RNA: nebulization, hydrolysis; cDNA: sonication, Dnase I treatment). Each fragmentation method is biased in its own way, and the goals of the study may influence the choice of method.&lt;/p&gt;&#xA;&lt;p&gt;I didn't fully understand the reasons for the characteristic biases (&lt;strong&gt;how do they happen?&lt;/strong&gt;), and when to choose one method versus the other (&lt;strong&gt;which methods work best for which goals?&lt;/strong&gt;).  Put another way, what are the mechanistic explanations for the characteristic biases that result from each method, and what is the significance as far as downstream processing and associated challenges?&lt;/p&gt;&#xA;&lt;h3&gt;Edit:&lt;/h3&gt;&#xA;&lt;p&gt;The heart of this question is about fully understanding the particular choice of when and how to fragment.  The reason I have not accepted an answer, yet, is that the answers provided so far address the mechanism part of the question, but not the ultimate reasons for choosing one versus the other.&lt;/p&gt;&#xA;" OwnerUserId="5888" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-21T22:51:27.733" Title="RNA-Seq library construction challenges: the biases of RNA fragmentation vs cDNA fragmentation" Tags="&lt;bioinformatics&gt;&lt;rna-sequencing&gt;&lt;sequence-analysis&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21279" PostTypeId="2" ParentId="14336" CreationDate="2014-09-13T18:01:50.960" Score="6" Body="&lt;p&gt;There are two pieces to this question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;a) How does bone resorption (movement of Ca/Phos out of bone into the blood) result in net improvement in bone structure?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bones are constantly remodeling, primarily in response to mechanical stressors. Although you clearly already realize this, I will make it explicit: osteoblasts are the cells that create new bone; osteoclasts break down (&lt;em&gt;resorb&lt;/em&gt;) bone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quoting &lt;em&gt;Harrison’s Internal Medicine&lt;/em&gt;&lt;sup&gt;1&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Radioisotope studies indicate that as much as 18% of the total skeletal calcium is deposited and removed each year. Thus, bone is an active metabolizing tissue.…The cycle of bone resorption and formation is a highly orchestrated process carried out by the basic multicellular unit, which is composed of a group of osteoclasts and osteoblasts &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Bone mineral density (BMD) can not be equated with bone &lt;em&gt;quality&lt;/em&gt;. (This is the difference between osteoporosis – deficient bone density – and rickets – poor bone architecture.) Thus, vitamin D’s stimulation of both osteoblast and osteoclast activity is beneficial to bone structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;b) How does vitamin D lead to overall increased bone density?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to the effects above, you mentioned that vitamin D increases serum calcium by several mechanisms. This is true. Both this increased serum calcium as well as the direct effects of Vitamin D on the parathyroid gland suppress PTH production.* As PTH has powerful actions to increase bone resorption by mobilizing calcium and phosphorus to move from the bone into the blood, the suppression on its excretion applied both directly and indirectly by Vitamin D results in a net increase in bone density.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, both by its effects on bone &lt;em&gt;quality&lt;/em&gt; and &lt;em&gt;quantity&lt;/em&gt;, vitamin D is a net boon for the bones. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;*Parathyroid hormone, a.k.a. parathormone. There &lt;em&gt;is&lt;/em&gt; a paradox here, because drugs such as &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/druginfo/meds/a603018.html&quot; rel=&quot;nofollow&quot;&gt;teriparatide&lt;/a&gt; (a.k.a. Forteo, recombinant PTH) are &lt;strong&gt;anabolic&lt;/strong&gt; for bone and are used to treat osteoporosis. Although the mechanism is unresolved, intermittent administration (as in the case of drug treatment) &lt;em&gt;increases&lt;/em&gt; BMD while chronic sustained elevations &lt;em&gt;decrease&lt;/em&gt; BMD.&lt;sup&gt;2&lt;/sup&gt; &#xA;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&#xA;References&#xA;&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&#xA;1. Bringhurst F, Demay M.B., Krane S.M., Kronenberg H.M. (2012). Chapter 352. Bone and Mineral Metabolism in Health and Disease. In Longo D.L., Fauci A.S., Kasper D.L., Hauser S.L., Jameson J, Loscalzo J (Eds), Harrison's Principles of Internal Medicine, 18e.&#xA;&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&#xA;2. Rosen CJ. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=12839095&quot; rel=&quot;nofollow&quot;&gt;The cellular and clinical parameters of anabolic therapy for osteoporosis&lt;/a&gt;. Crit Rev Eukaryot Gene Expr. 2003;13(1):25.&#xA;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2015-05-18T23:29:39.663" LastActivityDate="2015-05-18T23:29:39.663" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21280" PostTypeId="2" ParentId="21278" CreationDate="2014-09-13T18:07:08.760" Score="4" Body="&lt;p&gt;Good question, a lot of this is still being figured out. Here's what's known so far:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fragmentation methods based on restriction enzymes aren't random. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reverse-transcription performed with poly dT-oligomers, which bind to the 3' poly-A tails, is strongly biased towards 3’ end of transcripts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reverse-transcription with random hexamers results in an under-representation of 3’ ends. This is from the reduced number of priming positions at which the reverse transcriptase enzyme can start cDNA synthesis. &lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-09-14T02:05:30.417" LastActivityDate="2014-09-14T02:05:30.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21281" PostTypeId="2" ParentId="21262" CreationDate="2014-09-13T18:24:01.427" Score="4" Body="&lt;p&gt;Oxidation does &lt;strong&gt;not&lt;/strong&gt; mean inflammation. But oxidation can be a cause of inflammation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oxidation processes are part of normal cell metabolism (mostly in mithocondria). They lead to reactive oxygen species ($O_2^-$, $H_2O_2$ and $OH-$) which can trigger inflammation via activation of some transcription factors:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;NF-κB, AP-1, p53, HIF-1α, PPAR-γ, β-catenin/Wnt, and Nrf2 [1]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The metabolic processes also produce some  antioxidants to inactivate those reactive oxygen species. But the excess of oxidants leads to oxidative stress which seem to be linked with inflammation and even to cancer [1].&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;rapeseed oil is less saturated and therefore more likely to oxidize&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Being &quot;less saturated&quot; I guess it would be better, as studies have found that saturated fatty acid promote inflammation [2], while unsaturated fats decrease the production of inflammatory cytokines and reactive oxygen species [3].&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So my question is this: is it really possible to safely say: &quot;oxidation = inflammation&quot;?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;NO.&lt;/strong&gt; By definition, oxidation is a &lt;strong&gt;chemical reaction&lt;/strong&gt; in which a molecule, atom or ion loses electrons [4]. On the other hand, inflammation is a very complex process, a &lt;strong&gt;biological response&lt;/strong&gt; to harmful stimuli and requires cellular interaction [5].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Reuter S, Gupta SC, Chaturvedi MM, Aggarwal BB. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20840865&quot; rel=&quot;nofollow&quot;&gt;Oxidative stress, inflammation, and cancer: how are they linked?&lt;/a&gt; Free Radic. Biol. Med. 2010 Dec 1;49(11):1603-16. doi: &lt;a href=&quot;http://dx.doi.org/10.1016/j.freeradbiomed.2010.09.006&quot; rel=&quot;nofollow&quot;&gt;10.1016/j.freeradbiomed.2010.09.006&lt;/a&gt;. PubMed PMID: 20840865. &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;&lt;a href=&quot;http://atvb.ahajournals.org/content/30/4/692.full&quot; rel=&quot;nofollow&quot;&gt;Saturated Fatty Acids and Inflammation: Who Pays the Toll?&lt;/a&gt;&lt;/em&gt;&#xA;Alan Chait and Francis Kim&#xA;&lt;strong&gt;Arterioscler Thromb Vasc Biol.&lt;/strong&gt; 2010;30:692-693, doi:10.1161/ATVBAHA.110.203984&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Supplement: n–3 Fatty Acids: Recommendations for Therapeutics and Prevention:&lt;/strong&gt;&#xA;Philip C Calder&#xA;&lt;em&gt;&lt;a href=&quot;http://ajcn.nutrition.org/content/83/6/S1505.full&quot; rel=&quot;nofollow&quot;&gt;n−3 Polyunsaturated fatty acids, inflammation, and inflammatory diseases&lt;/a&gt;&lt;/em&gt;&#xA;Am J Clin Nutr June 2006 83: 6 S1505-1519S&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Redox,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Redox&amp;amp;oldid=621442954&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Redox&amp;amp;oldid=621442954&lt;/a&gt; (accessed September 13, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Inflammation,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Inflammation&amp;amp;oldid=625272396&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Inflammation&amp;amp;oldid=625272396&lt;/a&gt; (accessed September 13, 2014).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-09-13T18:24:01.427" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21282" PostTypeId="2" ParentId="21278" CreationDate="2014-09-13T18:35:27.930" Score="3" Body="&lt;p&gt;messenger RNA has a poli A tail at its 5´ end. thus when the poly-dT hybridize the mRNA in the reverse transcription the cDNA will carry this poly-dT at its 3`end. Thus, as reverse transcription will always start at the 3´ and of the mRNA its is more likely that this region is better rev. transcribed. Bigger the mRNA is bigger will be this concern.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About the bias related to RNA fragmentation I don't know, I can make the guess that both ends are more lost due to the fragmentation itself&lt;/p&gt;&#xA;&#xA;&lt;p&gt;watch this video from life technologies&#xA;&lt;a href=&quot;http://www.youtube.com/watch?v=0MJIbrS4fbQ&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=0MJIbrS4fbQ&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="3657" LastEditDate="2014-09-16T10:39:32.350" LastActivityDate="2014-09-16T10:39:32.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21283" PostTypeId="2" ParentId="21268" CreationDate="2014-09-13T18:46:15.580" Score="3" Body="&lt;p&gt;Also called Piebald (Pied for short as mentioned above.) It's a pretty common mutation among different animals. Dogs, deer, and snakes such as the ball python exhibit this trait. So yeah, your bird is still a rock dove.&lt;/p&gt;&#xA;" OwnerUserId="9017" LastActivityDate="2014-09-13T18:46:15.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21284" PostTypeId="2" ParentId="21272" CreationDate="2014-09-13T19:02:51.110" Score="11" Body="&lt;p&gt;The logical assertion &quot;winglets have not happened in a long time, therefore they are not advantageous&quot; is incorrect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible for an advantageous trait not to evolve even when advantageous, if there is no &quot;path&quot; to it. The trait only occurs gradually, in small incremental steps. If intermediary steps are harmful, the trait will not occur, even if the end result would be beneficial.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(now, this does not say anything specific about winglets, just about the general argument)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;One famous example of an &quot;imperfection&quot; that keeps existing despite a better solution being available can be seen here: &lt;a href=&quot;https://www.youtube.com/watch?v=cO1a1Ek-HD0&quot; rel=&quot;nofollow&quot;&gt;https://www.youtube.com/watch?v=cO1a1Ek-HD0&lt;/a&gt; (beware, video features dissection of a giraffe)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a nerve that connects the brain to the larinx. In fish, this nerve is somewhat short, but in the giraffe, it is enormous. The interesting thing is: the points this nerve connects are very near, even on the giraffe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happened was the the nerve passes below an artery. For fish, this is irrelevant. But, as larger mammals evolved, the nerve had to gradually grow to a bigger path. Evolution could not do the &quot;reengeneering&quot; to have a smaller nerve, because there was no immediately advantageous way to do it.&lt;/p&gt;&#xA;" OwnerUserId="1167" LastEditorUserId="1167" LastEditDate="2014-10-17T16:16:35.663" LastActivityDate="2014-10-17T16:16:35.663" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21285" PostTypeId="2" ParentId="21269" CreationDate="2014-09-13T19:54:15.580" Score="7" Body="&lt;p&gt;I think this might be Japanese hops. Well, what I have in my yard is Japanese hops.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ShIoh.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;As I said, it's horrible.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/posts/21285/edit&quot;&gt;Description and Biology&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Plant: herbaceous annual, twining, shallow-rooted vine that can climb to heights of ten or more feet with the help of rough-textured stems covered with short, sharp, downward pointing prickles that can be very irritating to the skin.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Leaves: leaves are rough-textured, paired, simple, palmate (like a hand) with typically 5-7 lobes; leaf margins are toothed.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Flowers, fruits and seeds: flowering occurs in July and August; male and female flowers are borne on separate plants; male flowers are very small, greenish yellow and occur in branched panicles; female flowers are in pale green, plump, drooping, cone-like structures with overlapping scales that become ‘hops’; hop scales and the seeds are covered with yellow glands; seeds are about 1/8 in. in diameter, roundish with a blunt tip, and light brown with darker specks; seeds mature through September.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Spreads: by seed which begins to germinate in early spring, but new plants may continue to emerge as the season progresses if sunlight and moisture are available; seeds are dispersed by animals (including people), machinery and floodwaters.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Look-alikes: native common hop (Humulus lupulus) looks very much like Japanese hop but it is usually 3-lobed or unlobed; native bur cucumber (Sicyos angulatus) lacks prickles, has tendrils, and the leaves have much less pronounced lobes.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Prevention and Control: &lt;strong&gt;Do not purchase, plant or transplant this species.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-13T22:32:37.287" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21286" PostTypeId="1" AcceptedAnswerId="21287" CreationDate="2014-09-13T20:11:43.630" Score="6" ViewCount="502" Body="&lt;p&gt;A major concern of conservationists  in south Florida is the population of native Pumas, the Florida Panther. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Until recently, it was thought that the Pumas were a genetically distinct subspecies, but some genetic studies have shown that they may not be, and so their subspecies status is disputed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the population of Pumas in Florida is genetically distinct from other populations in North America, is there any precedent for using a distinct subspecies to bolster populations of an endangered subspecies? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the population of Pumas in Florida is not genetically distinct from other populations in North America, would there be any behavioral issues (hunting, etc.) in animals brought from other biomes to south Florida, either as adults or offspring of transplanted adults?&lt;/p&gt;&#xA;" OwnerUserId="9284" LastActivityDate="2014-09-17T21:08:16.757" Title="Cross-integration of puma subspecies populations" Tags="&lt;zoology&gt;&lt;adaptation&gt;&lt;species&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21287" PostTypeId="2" ParentId="21286" CreationDate="2014-09-13T23:57:12.200" Score="6" Body="&lt;p&gt;The study you are referring to is probably a study by &lt;a href=&quot;http://jhered.oxfordjournals.org/content/91/3/186.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Culver et al. (2000)&lt;/a&gt;. They performed a genetic analysis of 315 individuals of the American Puma (&lt;em&gt;Puma concolor&lt;/em&gt;), also known as the cougar. Their thorough analysis (especially for the late 1990s) showed that the Florida panther and the western North American pumas were the same subspecies, &lt;em&gt;Puma concolor couguar&lt;/em&gt; (note the proper spelling of the subpecies). All individuals north of Nicaragua are this subspecies. From Nicaragua south into South America, they recognized five additional subspecies of American Puma.  The distribution of the subspecies, as well as the sample locations, are shown in the figure below, taken from Culver et al. (2000).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zIRaj.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notice in the figure above that the American Puma used to occupy most of North America but now is restricted to the the region west of the Rocky Mountains, except for the isolated Florida population. Because the genetics of the Florida Panther and the western American Puma are effectively the same, individuals from the western US can be introduced into southern Florida. This idea was first proposed (to my knowledge) by &lt;a href=&quot;http://parkinson.cos.ucf.edu/Courses/PCB5556C/pdf/Hedrick_panther.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hedrick (1995)&lt;/a&gt; as a conservation measure by introducing genetic variation and reduce the effects of inbreeding. In that same year, eight female pumas were transferred to Florida from Texas, which had the population of panthers closest to Florida. Introducing pumas from outside of Florida has pros and cons, reviewed by &lt;a href=&quot;http://www.gwu.edu/~clade/bisc%20207/pimm_geneticrescue.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pimm et al. (2005)&lt;/a&gt;, from both a short-term conservation perspective as well as long-term evolutionary perspectives.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several years after the Texas pumas were introduced, &lt;a href=&quot;http://www.wec.ufl.edu/faculty/olim/johnson_etal_panther_genetics_science_sept2010.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Johnson et al. (2010)&lt;/a&gt; performed a genetic analysis of the Florida population. They showed that the Texas females were indeed reproducing in Florida. The release of Texas panthers did introduce more genetic variation into the Florida population and reduce the effects of inbreeding. The net effect was that more Florida panthers were surviving. The downside is that habitat loss continues and the &lt;a href=&quot;https://biology.stackexchange.com/questions/21102/definition-of-effective-population-size&quot;&gt;effective population size&lt;/a&gt; is still very small. That means that inbreeding is still very much an issue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The studies to date have focused on genetic integration and overall recovery due to the introduction of genetic variation but I did not find any studies that reported any behavioral changes since the 1995 introduction. Given that it was only 8 females, I would not expect any significantly different behaviors to be introduced into the Florida population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Introducing more genetic variation from Texas (and perhaps populations farther west) may be helpful but ultimately preservation of habitat and improving ability of individuals to move among available &lt;a href=&quot;http://www.floridapanthernet.org/index.php/handbook/threats/habitat_fragmentation1/#.VBTLLFbLx94&quot; rel=&quot;nofollow noreferrer&quot;&gt;habitat fragments via corridors&lt;/a&gt; is necessary to protect the species long term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Citations&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Culver, M. et al. 2000. Genetic ancestry of the American Puma (&lt;em&gt;Puma concolor&lt;/em&gt;). Journal of Heredity 91: 186-197. (&lt;a href=&quot;http://jhered.oxfordjournals.org/content/91/3/186.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;open access&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hedrick, P.W. 1995. Gene flow and genetic restoration: The Florida panther as a case study. Journal of Conservation Biology 9: 996-1007.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Johnson, W.E. et al. 2010. Genetic restoration of the Florida Panther. Science 329: 1641-1645.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pimm, S.L. et al. 2005. The genetic rescue of the Florida panther. Animal Conservatation 9: 115-122. This issue of Animal Conservation has a few articles dedicated to the Florida Panther.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-09-17T21:08:16.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21288" PostTypeId="2" ParentId="2051" CreationDate="2014-09-14T01:47:57.397" Score="1" Body="&lt;p&gt;In a coupled reaction energy required by 1 process is supplied by another process. For example: glucose + phosphate becomes glucose.6.phosphate. This is an endergonic reaction and the energy is supplied to this reaction by another reaction which has to be exergonic reaction i.e. ATP which can become ADP+energy. &lt;/p&gt;&#xA;" OwnerUserId="9287" LastEditorUserId="6511" LastEditDate="2014-09-14T09:49:34.060" LastActivityDate="2014-09-14T09:49:34.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21289" PostTypeId="2" ParentId="19998" CreationDate="2014-09-14T02:02:55.403" Score="5" Body="&lt;p&gt;They don’t meet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Some framework:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Spinal nerves contain motor, sensory, and autonomic fibers. Each of these have different pathways.  &lt;/li&gt;&#xA;&lt;li&gt;Spinal nerves don’t go to the brain. Rather, they synapse in the spinal cord with other neurons which in turn go to the brain (sometimes requiring one more synapse).&lt;/li&gt;&#xA;&lt;li&gt;In the case of motor neurons, we talk about &lt;em&gt;upper&lt;/em&gt; and &lt;em&gt;lower&lt;/em&gt; motor neurons. In the sensory system, we talk about &lt;em&gt;first order&lt;/em&gt; and &lt;em&gt;second order&lt;/em&gt; neurons. Explanation below. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Regarding sensory (afferent) neurons:&lt;/strong&gt;   &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Touch and limb position sense are mediated by the dorsal column-medial lemniscus system. The &lt;em&gt;first order&lt;/em&gt; (primary sensory) neurons from the spinal nerves, synapse on a &lt;em&gt;second order&lt;/em&gt; neuron in the dorsal column in the medulla. There it decussates (i.e. courses to the contralateral side) and ascends via the medial lemniscus to the thalamus. There it synapses with a third neuron that courses via the internal capsule to the primary somatic sensory cortex.&lt;/li&gt;&#xA;&lt;li&gt;Pain, itch, and temperature sense are mediated by the anterolateral system. These &lt;em&gt;first order&lt;/em&gt; (primary sensory) neurons synapse at the spinal level they enter. The &lt;em&gt;second order neuron&lt;/em&gt; decussates at that level and courses rostrally via the anterolateral column, ending up in the thalamus. There it synapses with a third neuron that courses via the internal capsule to the primary somatic sensory cortex.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Conclusion: It takes three neurons (inclusive) to get from the spinal nerve to the primary sensory cortex in the postcentral gyrus of the parietal lobe. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Regarding motor (efferent) neurons:&lt;/strong&gt;   &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Limb muscles are innervated by circuits beginning in the primary motor cortex. These &lt;em&gt;upper motor neurons&lt;/em&gt; descend to the medulla, decussate here, and continue caudally via the lateral corticospinal tract. At the level of the spinal nerve, they synapse with neurons in the lateral ventral horn. These are the &lt;em&gt;lower motor neurons&lt;/em&gt; that become the spinal nerve.&lt;/li&gt;&#xA;&lt;li&gt;Axial/girdle muscles are innervated by circuits that also begin in the primary motor cortex. These &lt;em&gt;upper motor neurons&lt;/em&gt; synapse in the midbrain, descend, and decussate at the appropriate spinal level. They synapse there with the &lt;em&gt;lower motor neurons&lt;/em&gt; that exit the spinal cord and end up in the muscles.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Conclusion: It takes two neurons (inclusive) to get from the primary motor cortex in the pre-central gyrus of the frontal lobe to a spinal nerve. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the cortex, these circuits also don’t all come together. They are actually quite diffusely organized across the sensory and motor cortices. Here is a representation of the sensory cortex.* It is a schematic of the post-central gyrus with pictures to indicate where the signals from various body parts end up. The motor cortex is similar. (&lt;a href=&quot;https://www.google.com/?gfe_rd=ssl&amp;amp;ei=gmwWVPSbMMSc8Aazp4G4DQ#q=homunculus&amp;amp;spell=1)&quot; rel=&quot;nofollow noreferrer&quot;&gt;Google &lt;em&gt;homunculus&lt;/em&gt; if interested.&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YMs7P.jpg&quot; alt=&quot;sensory&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition the pathways described for cognitive perception and control, there are others that help with sub-conscious control of movement (e.g. those involving the cerebellum and basal ganglia), sub-cortical perception of pain signals (e.g. amygdala), and even spinal reflex arcs that never reach the brain. Not all circuits that begin or end in the spinal nerves are destined for or originate from the cortex&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is already considerably over-simplified, and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Autonomic_nervous_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;autonomic system&lt;/a&gt; is more complex yet and is not confined to spinal nerves, so I won’t detail it. These signals originate in and feed back to an entirely different area of the brain (mostly hypothalamus). Similar to the motor and sensory systems, at least one synapse is required to connect the brain to the peripheral nerve.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conclusion: they don’t meet. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&#xA;Reference:&#xA;&lt;/sup&gt;&#xA;&lt;sup&gt;&#xA;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/007138183X&quot; rel=&quot;nofollow noreferrer&quot;&gt;Martin, John. &lt;em&gt;Neuroanatomy: Text and Atlas.&lt;/em&gt; McGraw-Hill Medical; 3 edition (March 27, 2003)&lt;/a&gt;&#xA;&lt;/sup&gt;&lt;br&gt;&#xA;&lt;sup&gt;&#xA;*The source of this image is: &lt;a href=&quot;http://www.mindtrippingshow.com/mind-trip-of-the-week-17-how-do-we-feel-the-world&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.mindtrippingshow.com/mind-trip-of-the-week-17-how-do-we-feel-the-world&lt;/a&gt;&#xA;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-09-16T03:04:16.203" LastActivityDate="2014-09-16T03:04:16.203" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21290" PostTypeId="2" ParentId="21256" CreationDate="2014-09-14T05:00:34.697" Score="1" Body="&lt;p&gt;The odds are that you're noticing the equality of patent nostrils in the middle of a changeover, when both are equally patent. Also, the shape of your nose may be permitting the congested side to still be fairly patent. Your nose is doing what it's supposed to be doing (and everybody suffers bilateral congestion during colds, allergies, etc.) If it were not, you would be plagued by dry, painful and bleeding nares (um... are you?) &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-09-14T05:00:34.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21291" PostTypeId="1" AcceptedAnswerId="21292" CreationDate="2014-09-14T11:30:29.787" Score="4" ViewCount="341" Body="&lt;p&gt;I came across an old saying (I would even call it a myth) that vitamins are concentrated under (or close under) the peel of apples or potatoes and&#xA;other fruit. This implies that they are more healthier when not pealed. My question is: Is this true? And does it make sense to concentrate important&#xA;substances there, where they might get lost when the peel is damaged?&lt;/p&gt;&#xA;" OwnerUserId="8598" LastActivityDate="2014-09-14T12:16:14.430" Title="Vitamins located closely under the peel?" Tags="&lt;fruit&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21292" PostTypeId="2" ParentId="21291" CreationDate="2014-09-14T12:16:14.430" Score="3" Body="&lt;p&gt;There are some vitamins in the peel of some fruits/vegetables. The color of many fruits and vegetables is the result of high &lt;a href=&quot;http://en.wikipedia.org/wiki/Carotene&quot; rel=&quot;nofollow&quot;&gt;carotene&lt;/a&gt; concentration in the peel. $\beta$-carotene is converted by the human body into retinal, which is a form of vitamin A [1].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example is vitamin C. Guava and citrus category fruits contain high amounts of ascorbic acid in their peel and orange's peel contains greater amounts of vitamin C than its juice [2].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also other compounds in fruits peel like B vitamins and minerals [2].&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This implies that they are more healthier when not pealed.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In most situations, yes. The peel can absorb insecticide sprays and can also contain high amounts of fibers which can cause indigestion [2]. The peel can contain allergens [3].&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;And does it make sense to concentrate important substances there, where they might get lost when the peel is damaged?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes. For example carotene plays a role in photosynthesis [1]. Fibers improve mechanical properties of the peel, thus protecting the fruit.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Carotene,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Carotene&amp;amp;oldid=625015773&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Carotene&amp;amp;oldid=625015773&lt;/a&gt; (accessed September 14, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Umesh Rudrappa, www.nutrition-and-you.com. &lt;em&gt;&lt;a href=&quot;http://www.nutrition-and-you.com/fruit-peel.html&quot; rel=&quot;nofollow&quot;&gt;Fruit peel nutrition facts&lt;/a&gt;&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Peel (fruit),&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Peel_(fruit)&amp;amp;oldid=624708837&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Peel_(fruit)&amp;amp;oldid=624708837&lt;/a&gt; (accessed September 14, 2014).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-09-14T12:16:14.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21295" PostTypeId="1" AcceptedAnswerId="21299" CreationDate="2014-09-14T14:06:15.447" Score="5" ViewCount="1978" Body="&lt;p&gt;I have noticed that during summer, beautiful spider colonies grow wherever a strong light is:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/h57Xo.jpg&quot; alt=&quot;spider colony on a bridge lamp&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm wonder whether spiders evolved to seek naturally lighted areas where they build nests (before artificial lights) or if they always had the ability to seek places full of juicy insects - and in cities this ability just leads them to lights.&lt;/p&gt;&#xA;" OwnerUserId="6918" LastEditorUserId="8517" LastEditDate="2014-09-15T01:35:56.353" LastActivityDate="2018-02-24T23:21:40.580" Title="Did spiders respond to light for building webs before artificial light was invented?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21296" PostTypeId="2" ParentId="9154" CreationDate="2014-09-14T14:32:13.007" Score="0" Body="&lt;p&gt;This is because the Group A or Group B recipient's plasma contain soluble A or soluble B (antigen not bound to red cell surface). These free antigens will bind to the antibodies from the donors and prevent it to react on the red cell surface antigen A or B. The other thing is usually universal O should be low titer Anti-A or Anti-B.&lt;/p&gt;&#xA;" OwnerUserId="9292" LastActivityDate="2014-09-14T14:32:13.007" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21298" PostTypeId="2" ParentId="9154" CreationDate="2014-09-14T14:39:45.940" Score="0" Body="&lt;p&gt;If red blood cells have no A or B antigen on its surface it means it O blood group.it is said Universal donor bcz no antigen antibody reaction take place the reason is that it has no antigen for any antibody&lt;/p&gt;&#xA;" OwnerUserId="9259" LastActivityDate="2014-09-14T14:39:45.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21299" PostTypeId="2" ParentId="21295" CreationDate="2014-09-14T14:46:14.793" Score="10" Body="&lt;p&gt;&lt;strong&gt;New Answer&lt;/strong&gt;, following discussion in comments below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Spiders are capable of choosing habitats based on the specific requirements of the species (reviewed by &lt;a href=&quot;http://books.google.com/books?hl=en&amp;amp;lr=&amp;amp;id=rc6Vz-cWickC&amp;amp;oi=fnd&amp;amp;pg=PA23&quot;&gt;Riechert and Gillepsie 1986&lt;/a&gt;). Spiders move within and among suitable habitat for a number of reasons, including damage to existing webs, and life history changes that require new habitat types. They point out that spiders are probably choosing the proper habitat based on various cues from the habitat. How the spiders respond to the cues would have been shaped by natural selection. The specific cues used will vary among the different species of spiders but may include wind speed and direction, thermal regime (which affects dehydation foraging time), odor cues, density of competing spiders, and more. The many options are reviewed by &lt;a href=&quot;http://books.google.com/books?hl=en&amp;amp;lr=&amp;amp;id=rc6Vz-cWickC&amp;amp;oi=fnd&amp;amp;pg=PA23&quot;&gt;Riechert and Gillepsie&lt;/a&gt;, which is freely available and not too filled with technical jargon.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many species of spiders do select their habitat based on prey availability. &lt;a href=&quot;http://www.americanarachnology.org/JoA_free/JoA_v15_n1/JoA_v15_p81.pdf&quot;&gt;Gillespie (1987)&lt;/a&gt;  lists a number of references. She also studied the long-jawed orb weaving spider, which lives along streams and rivers.  She found that this spider tends to build nests in open areas near water, which prevented dehydration, but the exact site chosen was determined by prey availability. &lt;a href=&quot;http://www.jstor.org/discover/10.2307/2424265?uid=3739256&amp;amp;uid=2&amp;amp;uid=4&amp;amp;sid=21104627557887&quot;&gt;Enders (1973)&lt;/a&gt; studied a different orb-weaving species. He found that the juveniles were most often in densely vegetation areas but that the adults were in more open areas at the edges of woods. He suggested that web site selection of adults is driven by light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/s002650050590&quot;&gt;Heiling (1999)&lt;/a&gt; performed an interesting study on a nocturnal orb-web spider. The spider lives near the water so it will sometimes build its orb webs on the bridges crossing the water. She found that more spiders build their webs near the lights on one particular bridge compared to unlit parts of the bridge that were otherwise built the same. She found that there was more insect activity around the lighted area (no surprise there) and that the spiders that built near the lights caught more of those insects compared to the spiders that built away from the lights.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps the most interesting result is when she studied the behavior of these spiders in the lab. Spiders that were born and raised in the lab preferentially went to the artificial light source. These had never before been exposed to the artificial lights. She argued that the light-seeking ability of the orb-web spiders she studied is genetic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These studies suggest that light may have functioned as a visual cue for web location long before humans lit up the night sky with house and street lights, at least for spiders that build webs in open areas. Spiders may identify open areas by light cues (lighter vs darker), perhaps along with other cues such as air movement and humidity. Lighter areas would presumably be more open and thus favorable to large numbers of flying insects. Natural selection would favor spiders that responded to light for web construction. Artificial lights may present a very strong visual cue that attracts spiders, as well as insects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, other cues such as olfactory cues (mentioned by Riechert and Gillepsie 1986) may attract spiders. If insect prey are found in high abundance in open areas or near artificial lights, then you would expect higher concentrations of chemical odors emitted by the insects, thus drawing more spiders.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clearly, more studies similar to that of Heiling (1999) but across a broader range of web-building spiders are necessary to determine whether many web-building spiders are responding to light and if the response is genetically determined. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Citations&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Enders, F. 1973. Selection of habitat by the spider &lt;em&gt;Argiope aurantia&lt;/em&gt; Lucas (Araneidae). American Midland Naturalist 90: 47-55.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gillepsie, R.G. 1987. The mechanism of habitat selection in the long-jawed orb-weaving spider &lt;em&gt;Tetragnatha elongata&lt;/em&gt; (Araneae, Tetragnathidae). Journal of Arachnology 15: 81-90. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heiling, A.M. 1999. Why do noctural orb-web spiders (Araneidae) search for light? Behavioral and Ecological Sociobiology 46: 43-49.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Riechert, S.E. and R.G. Gillespie. 1986. Habitat choice and utilization in web-building spiders. In: Spiders: Webs, Behavior, and Evolution (W.A. Shear, ed). Stanford University Press, California, USA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Legacy answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Spiders evolved long before street lights were invented. The oldest known spider fossil dates back to between 374-380 million years ago &lt;a href=&quot;http://www.researchgate.net/profile/Jonathan_Coddington/publication/234150610_Systematics_and_Evolution_of_Spiders_%28Araneae%29/links/00463520a3ecd86c9d000000&quot;&gt;(Coddington and Levi 1991&lt;/a&gt;.  Street lighting of any type only goes back &lt;a href=&quot;http://www.isglighting.com/files/History%20of%20Street%20Lights%20in%20the%20United%20States%20Of%20America.pdf&quot;&gt;a few centuries&lt;/a&gt;. So, spiders were spinning webs long &lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/IIE2cHumanevop2.shtml&quot;&gt;before humans evolved&lt;/a&gt;, and before we humans began lighting our streets and homes at night.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The spiders are simply taking advantage of the situation. The lights draw insects, the food for the spiders. Webs constructed near light sources may catch more insects than webs constructed away from lights.  Could this affect the current or future evolution of spiders? Perhaps. The spiders that build webs near the lights may get more food, which allows them to obtain more energy, and potentially produce more offspring. This would increase their &lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/IIIE2Fitness.shtml&quot;&gt;fitness&lt;/a&gt; relative to spiders that do not build webs near lights, which could lead to evolutionary change occurring over the next several thousands of years. However, it may be that so many insects flying around the web end up damaging the web much more often than the spiders away from the lights, so the spiders near the light expend much more energy maintaining the web and removing insects they don't eat.  This is one extremely hypothetical example (of many; see comments) to illustrate the point. We can't actually predict what evolutionary changes might occur, or even if they will occur. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the hypotheses stated in the comments below could be tested to determine whether natural selection is possibly occurring on spider species that build near lights, or if the observation is simply observation bias as noted by @Oreotrephes. &lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-09-15T01:39:54.583" LastActivityDate="2014-09-15T01:39:54.583" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="21304" PostTypeId="1" AcceptedAnswerId="21305" CreationDate="2014-09-14T23:05:10.653" Score="2" ViewCount="164" Body="&lt;p&gt;In order to properly complete male reproductive development:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;A. primordial germ cells must begin Meiosis I in utero.&#xA;B. Sertoli cells must produce testosterone.&#xA;C. Dihydrotestosterone must masculinize Wolffian duct derivatives&#xA;D. the paramesonephric ducts must degenerate&#xA;E. the metanephros must form the genital epithelium&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;My attempt:  I think the answer is C because testosterone turns into DHT which then masculinzing the wolffian duct.  Other people I am studying with claim the answer is D (which is true) except that I dont think the loss of the paramesonephric duct is needed to complete male repro development. &lt;/p&gt;&#xA;" OwnerUserId="558" LastActivityDate="2014-09-15T01:54:18.503" Title="Which process is needed to complete male reproductive development?" Tags="&lt;homework&gt;&lt;reproduction&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21305" PostTypeId="2" ParentId="21304" CreationDate="2014-09-15T01:54:18.503" Score="3" Body="&lt;p&gt;&lt;strong&gt;Regarding option C&lt;/strong&gt;:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although it is correct that testosterone is converted into DHT, it is the former, not the latter, which is responsible for differentiation of the mesonephric (a.k.a. Wolffian) ducts:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Between 8 and 12 weeks, the initial secretion of testosterone stimulates mesonephric ducts to transform into a system of organs—the epididymis, vas deferens, and seminal vesicle—that connect the testes with the urethra.* &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;DHT (dihydrotestosterone) is produced in the Leydig cells by the 5α-Reductase enzyme. It is required for induction of the external male genitalia (urethra, penis, and scrotum) and prostate from the embryonic ureteral groove, and for testicular descent into scrotum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Regarding option D:&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sertoli cells secrete Anti Müllerian Hormone (AMH), which causes degeneration of the müllerian (a.k.a. paramesonephric) ducts between weeks 8 and 10.  It is normal to speak about &lt;em&gt;degeneration&lt;/em&gt; of the müllerian ducts as a defining aspect of male embryology, and thus I believe answer &lt;strong&gt;D&lt;/strong&gt; is correct. Your point is taken, however:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nevertheless, small müllerian duct remnants can be detected in the adult male, including a small cap of tissue associated with the testis, called the appendix testis, and an expansion of the prostatic urethra, called the prostatic utricle.*&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&#xA;*Larsen's Human Embryology , Fourth Edition. &lt;em&gt;Chapter 15: Development of the Urogenital System&lt;/em&gt;. pp 479-541. &#xA;Copyright © 2009 by Churchill Livingstone, an imprint of Elsevier Inc. &#xA;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastActivityDate="2014-09-15T01:54:18.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21306" PostTypeId="2" ParentId="21243" CreationDate="2014-09-15T05:40:05.517" Score="4" Body="&lt;p&gt;The question which buffer for DNA is better is quite old. Both have their pros and cons and I list a few of them:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;TBE is a better conductor and is thus less prone for overheating the&#xA;gel&lt;/li&gt;&#xA;&lt;li&gt;Borate is a powerful enzyme inhibitor, so if you want to apply&#xA;enzymatic steps downstream, TAE is the better choice&lt;/li&gt;&#xA;&lt;li&gt;TAE gives a better resolution for large fragments&lt;/li&gt;&#xA;&lt;li&gt;TBE has a higher resolution for fragments &amp;lt;2kb so it is better here&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Both buffers appeared in the 70s when the electrophoresis of nucleic acids was developed (in fact it was derived from protein electrophoresis)&#xA;and haven't been changed or optimized much since then, although there is a number of disadvantages:&#xA;First EDTA is not really necessary for DNA electrophoresis (it is for RNA, which is also the most likely reason it is still in there). Then&#xA;Tris is not the best buffering substance here. Besides being relative expensive it creates a temperature-current feedback loop,&#xA;meaning the higher the current gets, the higher the temperature will be. This leads to a higher gel temperature with all the&#xA;negative effects of it. For more details on this, have a look into reference 1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There has been some research on this matter and there are some suggestions available for better running buffers (details are in references 2 and 3).&#xA;In short these are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;10mM sodium boric acid (Na2B4O7/Borax): separation of DNA fragments&#xA;from 100bp-5kbp&lt;/li&gt;&#xA;&lt;li&gt;5mM lithium acetate (LiOOCCH3): separation of fragments longer than 3&#xA;kbp&lt;/li&gt;&#xA;&lt;li&gt;1mM lithium boric acid (Li2B4O7): separation of small DNA fragments&#xA;and ssDNA&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The borate in this buffers is still problematic in terms of a possible enzymatic inhibition, but this can be overcome with a simple ethanol&#xA;precipitation of the DNA (which of course also applies for use of TBE buffer).&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cc.ahs.chula.ac.th/Molmed/DNA%20electro%27s%20conductive%20media.pdf&quot; rel=&quot;nofollow&quot;&gt;History and principles of conductive media for standard DNA&#xA;electrophoresis.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.biotechniques.com/multimedia/archive/00036/BTN_A_04362BM02_O_36180a.pdf&quot; rel=&quot;nofollow&quot;&gt;Sodium boric acid: a Tris-free, cooler conductive medium for DNA&#xA;electrophoresis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.biotechniques.com/multimedia/archive/00037/BTN_A_04374ST04_O_37093a.pdf&quot; rel=&quot;nofollow&quot;&gt;Ultra-fast high-resolution agarose electrophoresis of DNA and RNA&#xA;using low-molarity conductive media&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-15T05:40:05.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21307" PostTypeId="2" ParentId="21243" CreationDate="2014-09-15T05:57:54.400" Score="4" Body="&lt;p&gt;Grossly, it does not matter what buffer you use. It is the pH that matters. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For DNA electrophoresis EDTA is added in order to chelate divalent cations that serve as cofactors for nucleases. Tris is the base of the buffer and is used to set pH. Along with Tris one can use Boric acid, Acetic acid or phosphoric acid for adjusting the pH. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The buffering range can be obtained by the Henderson-Hasselbalch equation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The choice of buffers depends on pH range, ease of preparation/storage and fine resolving properties and runtime properties such as heating etc (also mentioned by others). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;MOPS is another buffering agent. I am not very sure why MOPS is used instead of Tris for RNA gels; perhaps the latter forms adducts with formaldehyde  by Mannich's reaction whereas MOPS cannot undergo that reaction. MOPS is also a Zwitter-ionic species and maintains neutral pH. RNA should not be kept in alkaline pH. At acidic pH, RNA will become neutral and will not move. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For protein electrophoresis things are a little different. Glycine-Chloride buffer is used because it allows stacking. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-09-15T06:25:09.180" LastActivityDate="2014-09-15T06:25:09.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21310" PostTypeId="2" ParentId="21243" CreationDate="2014-09-15T12:48:43.117" Score="4" Body="&lt;p&gt;There are already many great answers to your question, however I thought I put my comments in form of an answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The standard for DNA agarose gel is TAE and for the protein, it depends on the size of the protein and the gel type used! Some times MOPS works best and sometimes Tris-acetate works best. It really depends on the gel used and also the protein and its size. You just have to experiment with them and see which works best for you! &lt;a href=&quot;http://tools.lifetechnologies.com/Content/SFS/ProductNotes/F_050711_NuPage-TS-TL-MKT-HL.pdf&quot; rel=&quot;nofollow&quot;&gt;This document&lt;/a&gt; by Invitrogen might be of help. To prevent apparatus over heating, put them in a cold room. I can give you my TAE components if you wish!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TAE is the standard DNA agarose gel buffer according to Sambrook et al., 1989 and is used by practically every scientist that I know of for running agarose gels for DNA. Please look at &lt;a href=&quot;http://www.lifetechnologies.com/uk/en/home/life-science/protein-expression-and-analysis/protein-gel-electrophoresis/protein-gels/novex-nupage-sds-page-gels/nupage-sds-page-bis-tris-gel.html&quot; rel=&quot;nofollow&quot;&gt;figure 2&lt;/a&gt; for the best gel to use for your protein of interest, which has been shown in form of a table.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-09-15T12:48:43.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21311" PostTypeId="2" ParentId="21107" CreationDate="2014-09-15T13:28:15.680" Score="3" Body="&lt;p&gt;I suspect that what you are actually looking for is the following:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;- 1 gram of fat = 9 kcal&#xA;- 1 gram of protein = 4 kcal&#xA;- 1 gram of sugar = 4 kcal&#xA;- 1 gram of alcohol = 7 kcal&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Those are general and inexact values. They're just often used to give a rough idea of the amount of energy we get from different types of food.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2014-09-15T19:38:22.010" LastActivityDate="2014-09-15T19:38:22.010" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21312" PostTypeId="2" ParentId="20441" CreationDate="2014-09-15T13:49:18.203" Score="4" Body="&lt;p&gt;I suspect I won't be crunching as much numbers as you'd want me to, however here are some basic points:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Statins have shown a clear ability to improve the blood llipid profile.&lt;/li&gt;&#xA;&lt;li&gt;Their use in primary/secondary prevention for cardiac events is justified by the belief that less blood lipid will leave less lipids to clog the arteries with. This is an old paradigm, and it is debated, even if we nowadays indeed give statins to all (potential) cardiac patients. There is evidence for a positive effect of those drugs, but it is not undisputable.&lt;/li&gt;&#xA;&lt;li&gt;An enormous amount of money is made from statins, and the pharma pushes very hard for their use.&lt;/li&gt;&#xA;&lt;li&gt;They do have undesirable effects, but those appear mostly early, so patients are usually well monitored for them and they mostly pose no real threat.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;On the subject of women: women before menopause are protected from cardiac events by their hormone profile, and would therefore likely benefit very little from statins at that time. After menopause, women present the same cardiac risk as men do. I do not know if studies have shown a difference in outcome for statins in postmenopausal women. If you want to know more, I advise you to go searching for it on &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed&quot; rel=&quot;nofollow&quot;&gt;Pubmed&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DISCLAIMER: The above does not represent professional medical advice, and is subject to debate.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-09-15T13:49:18.203" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21313" PostTypeId="1" CreationDate="2014-09-15T13:57:29.610" Score="3" ViewCount="198" Body="&lt;p&gt;Why do babies of any mammal tend to play ? From humans to small dog pups, cubs of a lion, baby bears, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*I am not sure if the tag I chose is correct or not. Please correct me if I'm wrong.&lt;/p&gt;&#xA;" OwnerUserId="9314" LastEditorUserId="1320" LastEditDate="2014-09-15T14:33:35.603" LastActivityDate="2014-09-15T19:38:56.770" Title="Why do baby mammals tend to play?" Tags="&lt;evolution&gt;&lt;behaviour&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2015-02-26T14:19:26.417" ContentLicense="CC BY-SA 3.0" />
  <row Id="21314" PostTypeId="1" AcceptedAnswerId="21315" CreationDate="2014-09-15T14:24:37.360" Score="2" ViewCount="114" Body="&lt;p&gt;Recently, kinesiology tape has become popular, especially in CrossFit. I have also noted its' use in the NFL, and I want to say Tennis as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What beneficial effects does this tape offer our bodies (muscles, joints)?  Is there any definitive proof of its' benefits? Can there be negative effects? I don't foresee any, but if it does &lt;em&gt;something&lt;/em&gt; to your body, I could see a &lt;em&gt;possibility&lt;/em&gt; of prolonged use causing some kind of alternate effects.&lt;/p&gt;&#xA;" OwnerUserId="9315" LastEditorUserId="9315" LastEditDate="2014-09-15T14:41:51.073" LastActivityDate="2014-09-26T08:11:18.890" Title="Kinesiology Tape Benefits" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;muscles&gt;&lt;healing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21315" PostTypeId="2" ParentId="21314" CreationDate="2014-09-15T14:37:38.040" Score="2" Body="&lt;p&gt;This is in the discussion for quite a while. I have found no scientific studies which back the claims of kinesio tape. A review article (from which the quote below is taken) found no clinically important results which support the claims of the tape. The results about range-of-motion were inconsistant and it is not clear if the changes found were beneficial or not. They state:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;KT had some substantial effects on muscle activity, but it was unclear&#xA;  whether these changes were beneficial or harmful. In conclusion, there&#xA;  was little quality evidence to support the use of KT over other types&#xA;  of elastic taping in the management or prevention of sports injuries.&#xA;  KT may have a small beneficial role in improving strength, range of&#xA;  motion in certain injured cohorts and force sense error compared with&#xA;  other tapes, but further studies are needed to confirm these findings.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The study can be found here (links to the PDF):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://performance.nd.edu/assets/114735/kt_review_article.pdf&quot; rel=&quot;nofollow&quot;&gt;Kinesio Taping in Treatment and Prevention of Sports Injuries&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Other (also critical) studies are these:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23306413&quot; rel=&quot;nofollow&quot;&gt;A systematic review of the effectiveness of kinesio taping for&#xA;musculoskeletal injury.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23088702&quot; rel=&quot;nofollow&quot;&gt;The clinical effects of Kinesio® Tex taping: A systematic review.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The problem with these studies is that they are obviously not rigorous enough to make clear statements if KT is beneficial or not. Or (and this is also very possible) that the effect which is claimed to be there does not exist. Besides this, a placebo effect exists very well, since there is an intervention and also something present on the athlete. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is now a new study avalaible which is blinded and placebo-controlled. This study finds no benefits for Kinesio Tape above a placebo. The study can be found &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25150913&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, there is also a summary available &lt;a href=&quot;http://edzardernst.com/2014/09/kinesiology-tape-another-theatrical-placebo/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-09-26T08:11:18.890" LastActivityDate="2014-09-26T08:11:18.890" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21316" PostTypeId="1" AcceptedAnswerId="21317" CreationDate="2014-09-15T15:59:32.953" Score="3" ViewCount="220" Body="&lt;p&gt;Does anyone know what is the maximal concentration of oxygen that can be tolerated by the parasite &lt;em&gt;Giardia intestinalis&lt;/em&gt;? &lt;/p&gt;&#xA;" OwnerUserId="9317" LastEditorUserId="948" LastEditDate="2014-09-15T18:15:46.783" LastActivityDate="2014-09-15T18:31:44.193" Title="Question about microaerophilic parasite tolerance for oxygen" Tags="&lt;parasitism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21317" PostTypeId="2" ParentId="21316" CreationDate="2014-09-15T16:45:02.407" Score="3" Body="&lt;p&gt;&lt;strong&gt;Short answer: 50-60 &amp;micro;M O&lt;sub&gt;2&lt;/sub&gt; is ok; 80 &amp;micro;M is toxic.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Giardia_lamblia&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Giardia lamblia&lt;/em&gt;&lt;/a&gt; (aka &lt;em&gt;intestinalis&lt;/em&gt;) is a microaerophilic intestinal parasite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Lloyd et al. (2000) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11101669&quot; rel=&quot;nofollow&quot;&gt;The microaerophilic flagellate Giardia intestinalis: oxygen and its reaction products collapse membrane potential and cause cytotoxicity.&lt;/a&gt; Microbiology 146: 3109 - 3118&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Giardia colonises the upper intestine, and the oxygen concentration there has been measured at 60 &amp;micro;M. At oxygen concentrations up to 50 &amp;micro;M the organism can scavenge oxygen; above 80 &amp;micro;M oxygen inhibits the oxygen-scavenging process. In this paper the authors used 10% air (equivalent to 25 &amp;micro;M oxygen) to characterise  oxygen toxicity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The source of oxygen sensitivity was investigated by:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Li and Wang (2006) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16359329&quot; rel=&quot;nofollow&quot;&gt;A likely molecular basis of the susceptibility of Giardia lamblia towards oxygen&lt;/a&gt; Molecular Microbiology 59: 202 - 211&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These authors propose that the enzyme DT-diaphorase, previously suggested as a component of the oxygen detoxification system promotes the formation of reactive oxygen species which lead to death. Thus they found that overproduction increased sensitivity to oxygen, whereas a knock-down decreased sensitivity. This work does not, however, use controlled microaerophilic conditions.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1320" LastEditDate="2014-09-15T18:31:44.193" LastActivityDate="2014-09-15T18:31:44.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21318" PostTypeId="1" CreationDate="2014-09-15T16:58:12.693" Score="2" ViewCount="1516" Body="&lt;p&gt;&lt;em&gt;Based on what we learned on condensation reactions, how many water molecules will be generated when single nucleotides are used to make this RNA: 5’-UUAACCGUCAG-3’&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I had an online biology quiz with this question, and I thought it would be one molecule for each nucleotide, for 11 total. The answer I have been given is 10. I feel like I am missing something obvious.&lt;/p&gt;&#xA;" OwnerUserId="9318" LastActivityDate="2014-09-15T17:23:39.290" Title="How many water molecules will be generated when single nucleotides are used to make this RNA: 5’-UUAACCGUCAG-3’?" Tags="&lt;rna&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21319" PostTypeId="2" ParentId="21318" CreationDate="2014-09-15T17:23:39.290" Score="6" Body="&lt;p&gt;It's one for every phosphodiester bond formed. 11 nucleotides, but only 10 bonds needed to join them into an oligonucleotide:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;1  2  3  4  5  6  7  8  9  10 11&#xA;N--N--N--N--N--N--N--N--N--N--N&#xA; 1  2  3  4  5  6  7  8  9  10&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-09-15T17:23:39.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21320" PostTypeId="1" CreationDate="2014-09-15T17:35:07.160" Score="1" ViewCount="111" Body="&lt;p&gt;Can we Manufacture bio molecules say e.g. the simplest Sugar, C12,H22,O11 the way we do with any other mechanical component. So, we know all about the Structure and arrangement of Atoms in Sugar - so do the design send the commands to the manufacturing machine which will use C,H and O elements and put them in them specified order !&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it's not doable today, what's the reason? - &#xA;1. Our lack of understanding of the Structure of Sugar atoms  or&lt;br&gt;&#xA;2. The specialized method which will put nascent atoms into the configuration of Sugar. Are people anywhere in the world trying to work this way? Please give references.&lt;/p&gt;&#xA;" OwnerUserId="9320" LastActivityDate="2014-09-16T14:00:13.587" Title="Manufacturing of Bio Molecules" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="5" ClosedDate="2014-09-16T21:44:05.173" ContentLicense="CC BY-SA 3.0" />
  <row Id="21321" PostTypeId="2" ParentId="21320" CreationDate="2014-09-15T18:12:07.577" Score="4" Body="&lt;p&gt;There are literally millions of biomolecules.  Some of them we know the structures and chemical properties of others we know nothing about.   I'm going to focus on sugars.  It would be too broad a question probably even to list all biomolecules, much less describe how their chemical synthesis would be performed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The good news is that industrial manufacturing of biomolecules is done for thousands of compounds and even available.  Certainly chemical synthesis of sugars is possible and even available but is very expensive and often produces side products compared to fermentation processes or extraction from plants say.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sugars, for instance &lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/thumb/c/c6/Alpha-D-Glucopyranose.svg/200px-Alpha-D-Glucopyranose.svg.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;glucose&lt;/a&gt; are very similar, but if you look at this structure you will see that the four OH (alcohol) groups could point up or down.  Any manufacture of glucose would have to get each one of these bonds exactly right.  This is D-glucose, which is commonly available as extracted with water from sugar beets and sugar cane.  I can buy 10 pounds of it at the store for less than $10.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JuoJT.png&quot; alt=&quot;glucose&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Compare with L-glucose, which is synthesized by a chemist.  Its available (though not really recommended for human consumption because its got impurities and doesn't necessarily pass FDA definitions of purity to be a food) at the cost of &lt;a href=&quot;http://www.sigmaaldrich.com/catalog/product/sigma/g5500?lang=en&amp;amp;region=US&quot; rel=&quot;nofollow noreferrer&quot;&gt;$87 per gram&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the answer is probably best put like this: who would pay \$87,000 for a bag of sugar when they could pay $10?  Cases where one would have to pay a company to produce a biomolecule, its going to cost...&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-09-15T18:12:07.577" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21322" PostTypeId="1" AcceptedAnswerId="21325" CreationDate="2014-09-15T19:37:44.190" Score="2" ViewCount="54" Body="&lt;p&gt;I came across an article about flavodiiron proteins that are responsible for reducing ${\rm O}_2$ to ${\rm H}_2{\rm O}$ thereby protecting the anaerobic prokaryotes and some eukaryotes from oxidative stress. However, I am confused about the structure of that protein and its relation to heme proteins. Is this a heme protein?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article I am reading is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=The%20O2-scavenging%20Flavodiiron%20Protein%20in%20the%20Human%20Parasite%20Giardia%20intestinalis&quot; rel=&quot;nofollow&quot;&gt;Di Matteo &lt;em&gt;et al.&lt;/em&gt;, The O2-scavenging flavodiiron protein in the human parasite Giardia intestinalis. J Biol Chem. 2008 Feb 15;283(7):4061-8. Epub 2007 Dec 12.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9317" LastActivityDate="2014-09-15T20:38:29.167" Title="Question about flavodiiron protein" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21324" PostTypeId="2" ParentId="21322" CreationDate="2014-09-15T19:48:53.310" Score="2" Body="&lt;p&gt;No, &lt;a href=&quot;http://en.wikipedia.org/wiki/Heme&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hemes&lt;/a&gt; are not proteins. They are porphyrins (large organic molecules) which are composed of four pyrrolic groups linked together. In the middle the coordinate the iron atom which is responsible for the activity. The combination of heme and iron is called a &lt;a href=&quot;http://en.wikipedia.org/wiki/Cofactor_%28biochemistry%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;prosthetic group&lt;/a&gt; or co-factor. They are bound by the protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UJ1PB.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image shows the Heme B from the Wikipedia.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-15T19:48:53.310" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21325" PostTypeId="2" ParentId="21322" CreationDate="2014-09-15T20:38:29.167" Score="2" Body="&lt;p&gt;No flavodiiron proteins are not haem proteins. See &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ja5022443&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for a simple depiction. Basically there is a flavin, and there are two iron atoms which go through a FeII/FeIII cycle during catalytic activity. These iron atoms are not held in  haem, but rather via carboxylate ligands.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-09-15T20:38:29.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21326" PostTypeId="1" CreationDate="2014-09-15T20:54:00.580" Score="4" ViewCount="789" Body="&lt;p&gt;I need to draw a map of the core metabolism of E.coli. Associated with each reaction in the map I have a number that indicates the flux through this reaction. I want the map to reflect these fluxes through the color of each reaction in the map.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried using tools like Mathematica and Cytoscape, but it is very hard to get a nice layout of the metabolic network. I have seen maps of E.coli metabolism which look very nice on paper. What I need is a map like these, but where I can define the colors of the reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, see the image below for an example. Forget about the yellow bounding boxes delimiting compartments. I can spare those.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/vAGU2.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="561" LastEditorUserId="3624" LastEditDate="2014-11-21T15:44:52.263" LastActivityDate="2018-12-18T18:27:51.503" Title="Plotting metabolic networks?" Tags="&lt;bioinformatics&gt;&lt;metabolism&gt;&lt;ecoli&gt;&lt;visualization&gt;" AnswerCount="3" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="21327" PostTypeId="1" AcceptedAnswerId="21333" CreationDate="2014-09-15T21:01:13.700" Score="5" ViewCount="194" Body="&lt;p&gt;I'm doing an archive binge of a paper comic &quot;The Kiekeboes&quot;. One of the characters is an elderly woman currently at the doctor, and she says the has the following illnesses:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Erythema Exsudativum Multiforme;&lt;/li&gt;&#xA;&lt;li&gt;Necrobiosis Lipoïdica;&lt;/li&gt;&#xA;&lt;li&gt;Phlegmasia Alba Dolens;&lt;/li&gt;&#xA;&lt;li&gt;and Metropathia Haemorrhagica.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;now, I googled these, and these are apparently real diseases (which actually makes sense, since she said she found them in her medical dictionary), namely 3 skin diseases and 1 menstruation problem. However, I find it hard to believe an elderly woman could have 3 different skin diseases and a menstrual disorder at the same time, especially since she already stopped menstruating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible for a patient to have all 4 of these illnesses at the same time? Or do the causes interfere with each other too much for that? I don't want to know how to cure it, I just wonder how much they're talking out of their anuses.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Image I just took with my camera:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9umZZ.jpg&quot; alt=&quot;Phone camera photo of the situation above&quot;&gt;&#xA;Kiekeboe 21: the Piri-Piri Pills, Page 17, strip 30. Author: Merho. Publisher: J.Hoste NV (currently part of Standaard Uitgeverij). Picture taken by Nate Kerkhofs on 16 september 2014.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is in Dutch, but the names of the illenesses are clearly readable (since they're Latin anyway).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The doctor asks &quot;what are you here for, madame? a cold, reumathism, headache?&quot; right before this. The woman answers &quot;no, doctor, I'm struggling with ... and also ... not to mention ... and a really annoying .... The doctor then replies &quot;but madame, where did you get all those illnesses?&quot; the woman replies &quot;in my medical encyclopaedia!&quot;.&lt;/p&gt;&#xA;" OwnerUserId="9208" LastEditorUserId="9208" LastEditDate="2014-09-16T16:36:14.737" LastActivityDate="2019-01-09T13:50:48.397" Title="Could this Francobelgian comic book woman really have these 4 diseases at the same time?" Tags="&lt;medicine&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21328" PostTypeId="1" CreationDate="2014-09-15T21:30:51.363" Score="3" ViewCount="81" Body="&lt;p&gt;If someone is taking treatment for a psychiatric disorder (e.g. diazepine), then would traces of the metabolized drug be detectable in their sweat or saliva? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any links to resources regarding this, or any help is greatly appreciated!&lt;/p&gt;&#xA;" OwnerUserId="9327" LastEditorUserId="16299" LastEditDate="2015-12-31T20:20:44.133" LastActivityDate="2015-12-31T20:20:44.133" Title="How are drug metabolism and detection related?" Tags="&lt;pharmacology&gt;&lt;pharmacokinetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21329" PostTypeId="1" AcceptedAnswerId="21334" CreationDate="2014-09-15T21:32:11.010" Score="7" ViewCount="4028" Body="&lt;p&gt;What's the longest functional transcript known?  I'm wondering about RNA length post splicing, so not including introns.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3340" LastEditDate="2014-09-16T05:40:43.177" LastActivityDate="2017-11-01T13:00:12.427" Title="What's the longest transcript known?" Tags="&lt;rna&gt;&lt;genomics&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21330" PostTypeId="2" ParentId="16911" CreationDate="2014-09-15T21:42:41.843" Score="13" Body="&lt;p&gt;As far as I am aware, cockroaches don't burst from being sprayed with soapy water (&lt;strong&gt;water + some liquid dish detergent&lt;/strong&gt;). We previously had many cockroaches in our apartment (some came back after a year of nothing!), and we regularly sprayed the cockroaches with soapy water plus some vineger (more as a disinfectant/cleaner) and they never burst. We've killed at least 30 using this method.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Having said that&lt;/strong&gt;, what you likely witnessed was the &lt;strong&gt;egg sacs&lt;/strong&gt; dislodging from the back of the female cockroach. As you didn't mention what species of cockroach you were dealing with, I am assuming you had German cockroaches as they seem to be the most common type in non-tropical/hot areas.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to a number of biology &lt;a href=&quot;http://ento.psu.edu/extension/factsheets/german-cockroaches&quot;&gt;sites&lt;/a&gt;, German cockroaches are particularly difficult to control and eradicate is because they carry their egg sacs with them until they are ready to hatch. At which point they drop the sac.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are able to catch a few that seem especially big, you will notice that they have a sac at their back.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you don't have German cockroaches, I have not idea why they would burst...&lt;/p&gt;&#xA;" OwnerUserId="9326" LastEditorUserId="9326" LastEditDate="2014-10-06T23:50:00.307" LastActivityDate="2014-10-06T23:50:00.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21331" PostTypeId="2" ParentId="21329" CreationDate="2014-09-15T22:02:49.510" Score="6" Body="&lt;p&gt;I think a good candidate is the human &lt;a href=&quot;http://en.wikipedia.org/wiki/Titin&quot;&gt;titin&lt;/a&gt; gene. The gene itself has 363 exons, depending on the isoform it has between 27.000 and 34.000 residues. This makes up a processed mRNA length of up to 100kb for the full length isoform. See either the Wikipedia article or the one linked below for more details: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://circres.ahajournals.org/content/89/11/1065.full.pdf&quot;&gt;The complete gene sequence of titin, expression of an unusual&#xA;approximately 700-kDa titin isoform, and its interaction with&#xA;obscurin identify a novel Z-line to I-band linking system&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you are looking for the longest primary transcript, then the human &lt;a href=&quot;http://en.wikipedia.org/wiki/Dystrophin&quot;&gt;dystrophin&lt;/a&gt; gene should be your favorite. It has a length of about 2.4 Megabases for the primary transcript, the processed transcript has only a length of about 14kb. It takes about 16 hours to transcribe and co-transcriptionally splice the sequence. See here for more details:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7719347&quot;&gt;The human dystrophin gene requires 16 hours to be transcribed and is&#xA;cotranscriptionally spliced.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-15T22:02:49.510" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21332" PostTypeId="2" ParentId="21328" CreationDate="2014-09-16T00:37:29.097" Score="5" Body="&lt;p&gt;Short answer: Yes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Diazepine&lt;/em&gt; is a ring-structure that forms the basis for the class of drugs called &lt;a href=&quot;http://en.wikipedia.org/wiki/Benzodiazepine&quot; rel=&quot;nofollow&quot;&gt;benzodiazepines&lt;/a&gt;. This class includes long acting and short acting agents. If you're actually talking about &lt;a href=&quot;http://en.wikipedia.org/wiki/Diazepam&quot; rel=&quot;nofollow&quot;&gt;diazepam&lt;/a&gt;, it's one of the long acting agents, which means the half-life of the metabolite in your body (and it's detection) is &lt;em&gt;long&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The National Highway Traffic Safety Administration has good reasons to want to collect samples of various drugs non-invasively, and, indeed, they're headed toward &lt;a href=&quot;http://www.nhtsa.gov/people/injury/research/stateofknwlegedrugs/stateofknwlegedrugs/pages/3Detection.html&quot; rel=&quot;nofollow&quot;&gt;saliva&lt;/a&gt; for screening. A neat little item called a Drugwipe can pick up traces of diazepam from not only saliva and sweat, but from surfaces people have touched.*&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The real kicker, though, is &lt;em&gt;hair&lt;/em&gt;, from any part of your body. Drug use(including diazepam) can be  detected in hair for &lt;em&gt;months&lt;/em&gt; after (even single) use, and many employers are now going for hair sample testing to screen for drug use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Saliva and Sweat Testing With &lt;a href=&quot;http://link.springer.com/chapter/10.1007%2F978-1-59259-951-6_10&quot; rel=&quot;nofollow&quot;&gt;Drugwipe®&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-09-16T01:48:13.983" LastActivityDate="2014-09-16T01:48:13.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21333" PostTypeId="2" ParentId="21327" CreationDate="2014-09-16T01:26:56.240" Score="4" Body="&lt;p&gt;Erythema multiforme (minor) can and does occur in a lot of people; while it is usually self-limited, it can recur, especially when the trigger is an unsuspected food.&lt;sup&gt;[1]&lt;/sup&gt; How common is it? It is very common.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Necrobiosis Lipoidica is not uncommon in diabetics, less common but still found in non-diabetics. It can occur at any age, including the eighth decade. It also shows a sex predilection, being 3 times more common in women than in men.&lt;sup&gt;[2]&lt;/sup&gt; How common is it? It is not rare.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phlegmasia Alba and Cerulea Dolens&lt;sup&gt;[3]&lt;/sup&gt; is serious and associated with deep vein thrombosis, which is an acute event. It is not uncommon, but it's not chronic. (More than 600,000 cases of venous thromboembolism are estimated to occur each year in the United States, all of which can lead to Phlegmasia Alba and Cerulea Dolens. How common is it? Luckily, not very. If the author is referring to garden-variety thrombophlebitis, though, that's a chronic problem, and not uncommon in the elderly. Thrombophlebitis is chronic and common enough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not going to address Metropathia Haemorrhagica, because, as you have noted, it's found in menstruating women.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diseases generally don't really &lt;em&gt;interfere&lt;/em&gt; with each other; some diseases can't co-exist (you can't have hyperthyroidism and hypothyroidism at the same time, for example, or have an active pituitary gland tumor and empty sella syndrome at the same time), but diseases don't &lt;em&gt;interfere&lt;/em&gt; with each other exactly. Some diseases have common underlying foundations, so can occur co-morbidly, for example collagen vascular diseases can manifest with skin, joint, and lung findings, which might not be &lt;em&gt;diagnosed&lt;/em&gt; as several manifestations of one disorder if it's not obvious. A better example might be diabetes, where similar underlying pathologies cause, say, heart disease, skin disease, eye-problems and kidney disease together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whatever, the likelihood of a little old lady having all four of your diseases are nil. The first three all the time (assuming not garden variety thrombophlebitis) - nil. Once, not impossible once, but not chronically. Of the first two - not far fetched. The first - common as dirt (comes and goes, though.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helped. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://emedicine.medscape.com/article/1122915-overview&quot; rel=&quot;nofollow&quot;&gt;Erythema Multiforme&lt;/a&gt; on Medscape&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://emedicine.medscape.com/article/1103467-overview#a0101&quot; rel=&quot;nofollow&quot;&gt;Necrobiosis Lipoidica&lt;/a&gt; on Medscape&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://emedicine.medscape.com/article/461809-overview#a01121&quot; rel=&quot;nofollow&quot;&gt;Phlegmasia Alba and Cerulea Dolens&lt;/a&gt; on Medscape&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-09-16T16:45:43.523" LastActivityDate="2014-09-16T16:45:43.523" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21334" PostTypeId="2" ParentId="21329" CreationDate="2014-09-16T04:50:23.443" Score="9" Body="&lt;p&gt;Top 10 long processed transcripts in humans (with multiple isoforms), from gencode 19 annotations:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Transcript    Length(bases)&#xA;------------------------&#xA;TTN-018        108861     &amp;lt;-- Titin&#xA;TTN-019        103988      &#xA;TTN-002        101206     &#xA;KCNQ1OT1-001    91666&#xA;TTN-201         82413&#xA;TTN-202         82212&#xA;TTN-003         81838&#xA;MUC16-001       43732&#xA;TSIX-001        37026&#xA;MCC-009         29616&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Ignoring isoforms (only longest isoforms shown)&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Transcript    Length(bases)&#xA;------------------------&#xA;TTN-018         108861&#xA;KCNQ1OT1-001     91666&#xA;MUC16-001        43732&#xA;TSIX-001         37026&#xA;MCC-009          29616&#xA;TRAPPC9-015      29514&#xA;SYNE1-001        27602&#xA;GRIN2B-001       27204&#xA;OBSCN-011        26811&#xA;NEB-204          26020&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Titin clearly is the longest transcript&lt;/strong&gt; in humans&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However this is the list of longest &lt;strong&gt;genes&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Gene           Length(Kb)&#xA;-------------------------&#xA;CNTNAP2        2304.64&#xA;LSAMP          2186.93&#xA;DLG2           2169.35&#xA;DMD            2092.29&#xA;PTPRD          2084.57&#xA;MACROD2        2057.83&#xA;CSMD1          2056.87&#xA;EYS            1987.24&#xA;LRP1B          1900.28&#xA;PCDH15         1806.76&#xA;CTNNA3         1783.65&#xA;ROBO2          1740.82&#xA;RBFOX1         1691.87&#xA;NRXN3          1619.64&#xA;DAB1           1548.83&#xA;RP11-420N3.2   1536.21&#xA;PDE4D          1513.42&#xA;FHIT           1502.09&#xA;AGBL4          1491.06&#xA;CCSER1         1474.33&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Top 5 in Zebrafish (Zv9.75); longest isoforms:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ttna-203             93727   &amp;lt;-- Titin&#xA;ttnb-202             82632&#xA;si:dkey-16p6.1-001   67263&#xA;syne2b-201           31867&#xA;si:dkey-30j22.1-001  29269&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Top 5 in Drosophila (FlyBase r6.02); longest isoforms:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;dp-RQ           71300   &amp;lt;-- Dumpy&#xA;sls-RP          56448   &amp;lt;-- Titin&#xA;Muc14A-RA       48719&#xA;Msp300-RG       43105&#xA;Ank2-RU         42107&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Top 5 in C.elegans (WormBase WS220); longest isoforms:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;W06H8.8g        55623   &amp;lt;-- Titin&#xA;K07E12.1a.2     39257   &amp;lt;-- dig-1&#xA;ZK973.6         25608&#xA;C09D1.1b        24198&#xA;C41A3.1         23457&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Top 5 in Arabidopsis (TAIR 10.23):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;AT1G67120.1     16272   &amp;lt;-- Midasin homolog&#xA;AT3G02260.1     15451   &amp;lt;-- Calossin-like protein&#xA;AT5G28263.1     15194&#xA;AT1G43060.1     14622&#xA;AT5G30269.1     14590&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Top 5 in yeast (SGD):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;YLR106C         14733   &amp;lt;-- Midasin&#xA;Q0045           12884   &amp;lt;-- Subunit I of cytochrome c oxidase&#xA;YKR054C         12279&#xA;YHR099W         11235&#xA;YDR457W          9807&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-08-03T08:05:37.677" LastActivityDate="2016-08-03T08:05:37.677" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21337" PostTypeId="1" AcceptedAnswerId="30724" CreationDate="2014-09-16T05:30:26.573" Score="7" ViewCount="611" Body="&lt;p&gt;What is an MHC restricted peptide? &lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I got this definition from wikipaedia, but cannot exactly extract what the phrase MHC restricted peptide means.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;MHC-restricted antigen recognition, or MHC restriction, refers to the fact that a given T cell will recognize a peptide antigen only when it is bound to a host body's own MHC molecule. Normally, as T cells are stimulated only in the presence of self-MHC molecules, antigen is recognized only as peptides bound to self-MHC molecules.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful.&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="12909" LastEditDate="2015-03-30T16:21:57.850" LastActivityDate="2015-03-30T16:24:45.130" Title="MHC restricted peptide" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21338" PostTypeId="2" ParentId="20992" CreationDate="2014-09-16T07:26:15.583" Score="5" Body="&lt;p&gt;I think the piece of missing information here is the distinction between &lt;a href=&quot;http://fnic.nal.usda.gov/food-composition/macronutrients&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;i&gt;macro&lt;/i&gt;nutrients&lt;/a&gt; and &lt;a href=&quot;http://www.who.int/nutrition/topics/micronutrients/en/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;i&gt;micro&lt;/i&gt;nutrients.&lt;/a&gt; The info from Mayo clinic quoted in the &lt;a href=&quot;https://biology.stackexchange.com/a/20993/9268&quot;&gt;another answer&lt;/a&gt; addresses some reasons why whole foods might be better than pills for obtaining micronutrients (i.e. vitamins and minerals).  While this may be true, most of it remains to be conclusively demonstrated (arguably). However, one clear reason “why….you need a healthy diet on top of that” is (unarguably) to obtain the fat, protein, and carbohydrates that your body uses to create energy. Unlike the minerals that act as cofactors, these macronutrients are the substrate. They are broken down to create the ATP that keeps everything running and they are built up to create the very structure of the body. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The energy that is consumed in the form of food or drinks can either be stored in the body in the form of fat (the major energy store), glycogen (short-term energy/carbohydrate reserves), or protein. . . to be used by the body to fuel energy-requiring events. *&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These are called &lt;i&gt;macro&lt;/i&gt;nutrients because they are required in gram quantities &amp;mdash; hundreds or even thousands of times more massive than the requirements for most &lt;i&gt;micro&lt;/i&gt;nutrients. As such, they don’t fit in a pill. As tragic as it is, we must keep eating.  &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;*Gibney, M. J., &amp;amp; Nutrition Society. (2009). &lt;em&gt;Introduction to Human Nutrition.&lt;/em&gt; Chichester, West Sussex, U.K.: Wiley-Blackwell.&#xA;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-07-06T16:47:22.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21342" PostTypeId="1" CreationDate="2014-09-16T10:50:28.177" Score="3" ViewCount="54" Body="&lt;p&gt;Sexually antagonistic genetic variation, in a simple model, will persist if the benefit to one sex is (near) equal to the cost in the other, otherwise the polymorphism will be selected out of the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[Rice's theory][1] suggests that sexually antagonistic genetic variance should be over-represented on the X-chromosome, because males are hemizygous (thus express male beneficial alleles more often than females) and females have the X-chromosome 2/3rds of the time (thus female benefit does not need to equal male cost for persistence). This model expands the range of conditions under which SA variation can persist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[Fry argues here][2] that unequal dominance means the conditions under which sexually antagonistic variation can be maintained in the autosomes. Because of dominance the mean population fitness is increased under conditions of polymorphism (cost of a new allele to one sex &amp;lt; the benefit to the other). This model also expands the range of conditions under which SA variation can persist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think Fry concludes that the X-chromosome should therefore be expected to, not only not be a hotspot, but to be a coldspot (a dearth of SA variation on the X). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Conceptually, why does the hypothesis of unequal dominance make the autosomes more permissive to genetic variation than the X-chromosome?&lt;/strong&gt; (Therefore making the X- a coldspot for SA variation). This is what his abstract says, it seems to suggest that...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;..such polymorphisms are expected to be more common on the&#xA;  X-chromosome... here I show that there are plausible assumptions under&#xA;  which the reverse is expected to be true.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-09-19T09:31:54.847" LastActivityDate="2014-09-19T09:31:54.847" Title="Does unequal dominance mean the X-chromosome should be a coldspot for antagonistic variation?" Tags="&lt;theoretical-biology&gt;&lt;sexual-selection&gt;&lt;sex-chromosome&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21343" PostTypeId="1" AcceptedAnswerId="21401" CreationDate="2014-09-16T10:59:16.123" Score="6" ViewCount="9205" Body="&lt;p&gt;What is MHC haplotype? I did check out the wiki article, but did not understand.&#xA;&lt;br&gt;&lt;br&gt;&#xA;(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="948" LastEditDate="2014-09-16T15:42:57.193" LastActivityDate="2014-09-17T13:26:28.873" Title="What is MHC haplotype?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;immunology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21344" PostTypeId="1" AcceptedAnswerId="21351" CreationDate="2014-09-16T11:10:07.300" Score="3" ViewCount="5647" Body="&lt;p&gt;Is the difference only in its structure? Like conformational epitope has 3D structure while sequential has a linear structure?&lt;br&gt;&lt;br&gt;(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="8835" LastEditDate="2014-09-16T11:15:15.403" LastActivityDate="2017-06-15T06:16:46.450" Title="Difference between sequential and conformational epitope" Tags="&lt;human-biology&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;bioinformatics&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21345" PostTypeId="1" AcceptedAnswerId="21348" CreationDate="2014-09-16T11:16:38.250" Score="0" ViewCount="52" Body="&lt;p&gt;What is affinity isolated peptides??&lt;br&gt;&lt;br&gt;(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="948" LastEditDate="2014-09-16T15:38:22.740" LastActivityDate="2014-09-16T15:38:22.740" Title="Affinity isolated peptide" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21346" PostTypeId="1" AcceptedAnswerId="21377" CreationDate="2014-09-16T12:41:36.277" Score="5" ViewCount="1862" Body="&lt;p&gt;In a &lt;a href=&quot;https://biology.stackexchange.com/questions/21272/&quot;&gt;former question&lt;/a&gt;, as a side question, I asked a clarification about the &quot;Spandrels&quot; paper. Being not a biologist, it was the first time I encoutered it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Subsequently I tried to collect some information, because I read that the paper is debated and deemed &quot;wrong&quot; by at least a part of the community.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite my efforts I have not fully grasped what the issue is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;is the incorrect reference to the architectural element? (i.e., the paper is wrong because it uses a not fully agreeable comparison)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;are some (or all) the claims in it wrong? if yes, are there any suggested reading to understand why?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I ask specifically because the &lt;a href=&quot;https://aviation.stackexchange.com/questions/8544/is-wingtip-design-mature/8554#comment15289_8554&quot;&gt;first reference&lt;/a&gt; I encountered points to Dawkins, and I would like to understand if this paper is a mere pawn in the big &quot;gradualists versus punctuationists&quot; debate or if it has merits on his own.&lt;/p&gt;&#xA;" OwnerUserId="9247" LastEditorUserId="-1" LastEditDate="2017-04-13T12:59:54.113" LastActivityDate="2014-09-17T09:43:59.063" Title="What is the &quot;Spandrels&quot; debate about?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21347" PostTypeId="1" CreationDate="2014-09-16T12:47:02.207" Score="6" ViewCount="2428" Body="&lt;p&gt;I was discussing with a colleague whether speaking would require more energy than communicating via instant message (GTalk, etc..). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is possible, then I'm particularly interested in whether certain sounds may consume more energy that others, and consequently could one language be more efficient than another.&lt;/p&gt;&#xA;" OwnerUserId="9332" LastEditorUserId="107" LastEditDate="2014-09-17T12:33:58.037" LastActivityDate="2017-03-14T23:55:08.683" Title="Is it possible to calculate the energy required to speak a word?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21348" PostTypeId="2" ParentId="21345" CreationDate="2014-09-16T12:50:10.720" Score="1" Body="&lt;p&gt;A peptide or protein can be purified by affinity chromatography. The principle is that the peptide has some substrate to which it will bind, retarding its progress through the column compared to the rest of the peptide population. A couple of typical examples are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Using a His6 tag put on recombinant molecules, IIRC it binds to Ni2+ trapped in the chromatographic resin and is eluted with a chelator like EDTA. &lt;/li&gt;&#xA;&lt;li&gt;Immunoaffinity chromatography, where you have a population of antibodies on the chromatographic resin which are specific to the protein that you want to purify (or alternatively having the immunogen bound to the resin so that you can purify the antibodies against it)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Mighty Wikipedia has a link about affinity chromatography &lt;a href=&quot;http://en.wikipedia.org/wiki/Affinity_chromatography&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6810" LastEditorUserId="1320" LastEditDate="2014-09-16T13:10:41.343" LastActivityDate="2014-09-16T13:10:41.343" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21350" PostTypeId="1" CreationDate="2014-09-16T13:22:43.827" Score="1" ViewCount="48" Body="&lt;p&gt;Like the title explains I am looking for a way to exclusively label microtubule minus end &lt;strong&gt;in vivo&lt;/strong&gt;. Looking through the literature I could not find any techniques yet. Do you have an idea?&lt;/p&gt;&#xA;" OwnerUserId="8196" LastEditorUserId="3340" LastEditDate="2014-12-06T06:03:18.440" LastActivityDate="2015-01-05T06:54:25.437" Title="Exclusive microtubule minus-end labeling" Tags="&lt;proteins&gt;&lt;fluorescent-microscopy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21351" PostTypeId="2" ParentId="21344" CreationDate="2014-09-16T13:29:38.587" Score="2" Body="&lt;p&gt;Yes, the difference is &quot;only&quot; in the 3D structure. This makes some differences when proteins change their shape; antibodies which recognize conformational epitopes are usually not well suited for lab work, as proteins are often denatured here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The different epitopes are also called &lt;a href=&quot;http://en.wikipedia.org/wiki/Linear_epitope&quot; rel=&quot;nofollow noreferrer&quot;&gt;linear epitopes&lt;/a&gt; (for the sequential) and &lt;a href=&quot;http://en.wikipedia.org/wiki/Conformational_epitope&quot; rel=&quot;nofollow noreferrer&quot;&gt;discontinous epitope&lt;/a&gt; (for the conformational). Schematically this look like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cLIfV.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="6307" LastEditDate="2017-06-15T06:16:46.450" LastActivityDate="2017-06-15T06:16:46.450" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21352" PostTypeId="2" ParentId="21320" CreationDate="2014-09-16T14:00:13.587" Score="0" Body="&lt;p&gt;In short, no, molecules aren't synthesised that way. This is because the common atoms that in biomolecules (C, O, H, N, P) don't occur as individual atoms in nature and it would be extremely difficult (and unnecessary) to keep them in a single-atom state ready for assembly into a molecule in some way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, chemists &lt;em&gt;are&lt;/em&gt; able to synthesise almost any kind of biomolecule desired by performing different routine reactions in a targeted fashion. The efficiency of production and the purity of the product obtained can vary extremely, but in principle any biomolecule up to a reasonable size could be synthesised chemically that way - as long as the desired product is itself chemically stable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While theoretically, the repertoire of reactions you can do that way might be limited, there is no machine that does them routinely according to a program you put in, because there are too many variables that need to be adjusted depending on the current aim of synthesis and much more flexibility is needed than such a machine could provide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm waiting for a reply from my chemistry friend on a few examples of those reactions.&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2014-09-16T14:00:13.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21353" PostTypeId="2" ParentId="21347" CreationDate="2014-09-16T14:08:41.400" Score="3" Body="&lt;p&gt;For animals to check the amount of energy used for a certain behavior you can use a RESPIROMETER. It basically calculates the oxygen consumption.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your case you could calculate for writing a sentence vs speaking the same sentence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding your second question:&#xA;At least in birds more than the type of sound (the frequency modulation) what matters for energy consumption is the amplitude --&gt; how loud is your sound.&lt;/p&gt;&#xA;" OwnerUserId="9333" LastActivityDate="2014-09-16T14:08:41.400" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21354" PostTypeId="2" ParentId="21343" CreationDate="2014-09-16T14:44:14.713" Score="5" Body="&lt;p&gt;As stated in wiki&#xA;&quot;The major histocompatibility complex (MHC) is a set of cell surface molecules encoded by a large gene family in all vertebrates which controls a major part of the immune system. MHC molecules mediate interactions of leukocytes, also called white blood cells (WBCs), which are immune cells, with other leukocytes or with body cells. MHC determines compatibility of donors for organ transplant as well as one's susceptibility to an autoimmune disease via crossreacting immunization. In humans, MHC is also called human leukocyte antigen (HLA).&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, MHC control immune system and it work based on principle lock and key. MHC has specific cell surface that can bind to foreign materials that have compatible binding site and recognise it as pathogen or harmful compound.&lt;/p&gt;&#xA;" OwnerUserId="9334" LastActivityDate="2014-09-16T14:44:14.713" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21355" PostTypeId="2" ParentId="17599" CreationDate="2014-09-16T14:57:45.133" Score="6" Body="&lt;p&gt;The first 2 are correct.&#xA;The third one is actually a hooded crow. The different color of the wing depends on the generation of feathers. Feathers of different generations (changed during different time) are abraded (used) in a different way. The wing feathers of this guy are older than the rest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cheers and good luck birding :)&lt;/p&gt;&#xA;" OwnerUserId="9333" LastActivityDate="2014-09-16T14:57:45.133" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21356" PostTypeId="2" ParentId="21347" CreationDate="2014-09-16T15:05:12.257" Score="1" Body="&lt;p&gt;It could be theoratically possible if you fitted a glucose sensor to a person's body and asked that person to do nothing other than talk, for say a period of 1 minute. Then, when he/she talks, the amount of glucose metabolized during that time period could be measured, and subsequently, the no. of calories required for speech. Of course, the amount of calories required for breathing and even doing nothing (sitting, which consumes 75 calories of energy per hour) must be deducted. &lt;/p&gt;&#xA;" OwnerUserId="9336" LastEditorUserId="9336" LastEditDate="2014-09-16T19:06:15.440" LastActivityDate="2014-09-16T19:06:15.440" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21357" PostTypeId="1" AcceptedAnswerId="21359" CreationDate="2014-09-16T15:15:53.210" Score="-4" ViewCount="31483" Body="&lt;p&gt;There are many stories that blood contains the life-force energy and specifically menstrual (period) blood has always been a feature of many rituals and some ancient Sumerian tablets mentioned that menstrual blood was the 'gold of the gods'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it is true that the menstrual blood is highly oxygenated, the purest of all blood and it carries the decoded DNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Or what differences are known to modern science between regular blood, a woman's period blood and virgin's period blood?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1195" LastEditorUserId="3340" LastEditDate="2014-09-16T16:48:47.890" LastActivityDate="2016-11-09T16:26:00.610" Title="What is the difference between regular blood, a woman's and a virgin's menstrual blood?" Tags="&lt;hematology&gt;&lt;red-blood-cell&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21358" PostTypeId="1" AcceptedAnswerId="21378" CreationDate="2014-09-16T16:03:06.207" Score="3" ViewCount="2351" Body="&lt;p&gt;I was looking for a term which describes a bipolar disorder of lesser severity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know from experience from someone I know well, what a very severe case of the bipolar disorder looks like, when an otherwise very intelligent and very sane person can become completely unstable in both directions, and requires medication to basically survive it. &#xA;I'm searching for a term which has indeed the symptoms of the bipolar disorder, but is not as severe as to require medication to basically survive the mood swings. I'm not talking about being just sad for something or craving attention. I'm talking about the very real symptoms of mania, followed by depression, just not as severe to be fatally dangerous without medical intervention. A severity which I would describe of being able to cope with by learning about it and a good degree of self-control, exercise, and good eating habits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought the term was clinical versus non-clinical depression, but a search of the Internet made me doubt it. They talked about it as if the clinical was a case where there is a &quot;disorder of the brain&quot; and the non-clinical was &quot;just sad because of a sad event&quot;, so either were those forums wrong (I guess so, because of their apparent unprofessional writing style, and they never seemed to know about bipolar, they thought manic depression was just about being very very sad), or there is another term which best answers my question.&lt;/p&gt;&#xA;" OwnerUserId="3798" LastEditorUserId="9268" LastEditDate="2014-09-17T09:42:00.657" LastActivityDate="2016-04-11T13:23:58.827" Title="What is the difference between clinical and non-clinical depression, and is there a term for different severity of the bipolar disorder?" Tags="&lt;neuroscience&gt;&lt;pathology&gt;&lt;terminology&gt;&lt;psychology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21359" PostTypeId="2" ParentId="21357" CreationDate="2014-09-16T16:18:19.403" Score="12" Body="&lt;p&gt;The &quot;purest of all blood&quot; is fresh out of the bone marrow, i.e. in your circulatory system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Menstrual blood is a combination of blood, some mucous, and dead endometrial tissue. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The endometrium consists of a single layer of columnar epithelium resting on the stroma, a layer of connective tissue that varies in thickness according to hormonal influences. Simple tubular uterine glands reach from the endometrial surface through to the base of the stroma, which also carries a rich blood supply of spiral arteries... Proliferation is induced by estrogen (follicular phase of menstrual cycle), and later changes in this layer are engendered by progesterone from the corpus luteum (luteal phase). It is adapted to provide an optimum environment for the implantation and growth of the embryo. In the absence of progesterone, the arteries supplying blood to the functional layer constrict, so that cells in that layer become ischaemic and die, leading to menstruation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, menstrual &quot;blood&quot; is a combination of sloughed off stromal and glandular tissue, broken down vascular cells and blood, and, no, it is not highly oxygenated (it's kind of darker than normal blood. It doesn't carry any &quot;decoded DNA&quot;. It's basically a waste product at this point, dead, dying and no longer functional tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Virgin's flow is just as dead as non-virgin's flow. Cultures obtained at hysterectomy indicate that the endometrial cavity is normally sterile. The major difference between a virgin and a non-virgin is that the possibility of infection of endometrial tissue exists in non-virgins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course myths will arise around menstrual flow. After all, when it was alive, it was the medium for implantation of a blastocyst. But they are just myths.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Endometrium#Histology&quot;&gt;Endometrium Histology&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.glowm.com/section_view/heading/Infections%20as%20a%20Cause%20of%20Infertility/item/327&quot;&gt;Infections as a Cause of Infertility&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-09-16T16:18:19.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21361" PostTypeId="1" CreationDate="2014-09-16T16:25:21.000" Score="2" ViewCount="211" Body="&lt;p&gt;How closely related (from the evolutional point of view) are parasites &lt;em&gt;Giardia intestinalis&lt;/em&gt; and &lt;em&gt;Trichomonas vaginalis&lt;/em&gt;? &lt;em&gt;Giardia&lt;/em&gt; genome is about 12 Mb and its major cellular proceses are rather simple. The genome of &lt;em&gt;Trichomonas&lt;/em&gt; is approximately 160 Mb. What about its cellular processes, is it also a 'minimalist'? &lt;/p&gt;&#xA;" OwnerUserId="9317" LastEditorUserId="1195" LastEditDate="2014-09-17T14:41:04.360" LastActivityDate="2014-09-17T14:41:04.360" Title="How closely related are two parasites Giardia intestinalis and Trichomonas vaginalis?" Tags="&lt;evolution&gt;&lt;phylogenetics&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21362" PostTypeId="1" CreationDate="2014-09-16T16:37:20.693" Score="3" ViewCount="303" Body="&lt;p&gt;We recently learned in genetics class that exons always cap the ends of nascent RNA. I have been trying to figure out the reason why introns can't instead be found on the ends instead of exons. The end introns would still have their 5' and 3' splice sites, and assuming the splicing machinery functions correctly, these introns would be removed. The only thing I could imagine occurring is inappropriate nucleophilic attack of the end 3' hydroxy group at the end 5' phosphate leading to a single circular RNA. However, in a normal situation where exons are at the ends, if introns in an RNA are  all removed simultaneously than it is possible that the free 3' hydroxy group of say intron 2 could attack the 5' end of another intron leading to inappropriate cleavage of the intervening exon so having exons at the ends does not solve that problem. I don't think my explanation is correct, any ideas?&lt;/p&gt;&#xA;" OwnerUserId="9344" LastEditorUserId="3340" LastEditDate="2014-09-17T04:13:40.847" LastActivityDate="2014-09-17T04:13:40.847" Title="Why aren't introns found on the ends of pre-RNA?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;splicing&gt;" AnswerCount="2" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21363" PostTypeId="2" ParentId="21361" CreationDate="2014-09-16T17:16:31.563" Score="2" Body="&lt;p&gt;Basically, &lt;a href=&quot;http://tolweb.org/Fornicata/121182&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Giarda&lt;/em&gt;&lt;/a&gt; is a an &lt;em&gt;Excavates&lt;/em&gt; while &lt;em&gt;Trichomonas&lt;/em&gt; is a &lt;a href=&quot;http://tolweb.org/Cercozoa/121187&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Cercozoa&lt;/em&gt;&lt;/a&gt; meaning a &lt;em&gt;Rhizaria&lt;/em&gt; (&lt;em&gt;Chromealveolates&lt;/em&gt; in the broad sense as noticed by @har-wradim in the comments (now deleted) because Cercozoa are neither &lt;em&gt;Chromista&lt;/em&gt; nor &lt;em&gt;alveolata&lt;/em&gt;). Because the very basis of the tree of eukaryotes is still unresolved (&lt;a href=&quot;http://tolweb.org/Eukaryotes/3&quot; rel=&quot;nofollow&quot;&gt;eukaryotes&lt;/a&gt;), the most recent common ancestor of these two species is just an old eukaryote! In other words, these two species are not more closely related than are related a cat and a chestnut tree!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The links yield to Tolweb.org which shows you the phylogenetic tree and allows you to explore the relationships between organisms. Have a look to eukaryote tree especially to see the positions of the &lt;em&gt;Rhizaria&lt;/em&gt; and &lt;em&gt;Cercozoa&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-09-17T12:57:02.277" LastActivityDate="2014-09-17T12:57:02.277" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21364" PostTypeId="1" CreationDate="2014-09-16T18:34:54.853" Score="2" ViewCount="711" Body="&lt;p&gt;I am considering to buy the Zeiss Primo star microscope. There are two variants: one with so called &quot;Full Köhler&quot; illumination and one with &quot;Fixed-Köhler&quot; illumination. Are there any drawbacks to having it fixed? When I would not want to have Köhler illumination?&lt;/p&gt;&#xA;" OwnerUserId="9347" LastActivityDate="2017-04-17T08:43:40.197" Title="Are there any drawbacks to having a fixed-Köhler microscope?" Tags="&lt;microscopy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21365" PostTypeId="2" ParentId="21362" CreationDate="2014-09-16T18:41:51.477" Score="1" Body="&lt;p&gt;RNA splicing begins with assembly of helper proteins at the intron/exon borders. These splicing factors act as beacons to guide small nuclear ribo proteins to form a splicing machine, called the spliceosome. These animation is showing this happening in real time.&#xA;see&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://education-portal.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.html#lesson&quot; rel=&quot;nofollow&quot;&gt;http://education-portal.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.html#lesson&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=FVuAwBGw_pQ&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=FVuAwBGw_pQ&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sumanasinc.com/webcontent/animations/content/mRNAsplicing.html&quot; rel=&quot;nofollow&quot;&gt;http://www.sumanasinc.com/webcontent/animations/content/mRNAsplicing.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9101" LastActivityDate="2014-09-16T18:41:51.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21368" PostTypeId="2" ParentId="16404" CreationDate="2014-09-16T19:14:41.163" Score="1" Body="&lt;p&gt;Whether a reaction is reversible or irreversible, in the presence or absence of an enzyme, is not related to activation energy. An enzyme lowers activation energy in both directions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A reaction is reversible or irreversible depending on the conditions in which this reaction occurs. If there's a sustained high concentration of substrates, most of the reaction flux goes from substrates to products, and the reaction is practically irreversible. The same happens the other way. Note that whether the concentrations are high enough or not depends on the kinetic constants involved.&lt;/p&gt;&#xA;" OwnerUserId="561" LastActivityDate="2014-09-16T19:14:41.163" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21369" PostTypeId="1" CreationDate="2014-09-16T21:06:44.017" Score="1" ViewCount="54" Body="&lt;p&gt;Linkage disequilibrium D equals&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$D=x_{11}−p1⋅q1$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Haplotype        Frequency&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$A_{1}B_{1}          = x_{11}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$A_{1}B_{2}          = x_{12}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$A_{2}B_{1}          = x_{21}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$A_{2}B_{2}          = x_{22}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Allele    Frequency&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$A_{1}=p_{1}=    x_{11}+x_{12}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$A_{2}       = p_{2}=x_{21}+x_{22}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$B_{1}       = q_{1}=x_{11}+x_{21}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$B_{2}       = q_{2}=x_{12}+x_{22}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Shouldn't: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) $D = x_{11}-p_{1}q_{1}$ or $x_{11} = p_{1}q_{1}+D $&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) $**D=  x_{12}-p_{1}q_{2}$ or $x_{12} = p_{1}q_{2}+D**$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) $**D=  x_{21}-p_{2}q_{1}$ or $x_{21} = p_{2}q_{1}+D**$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) $D=  x_{22}-p_{2}q_{2}$ or $x_{22} = p_{2}q_{2}+D$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do all the papers show: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) $x_{11}=p_{1}q_{1}+D$  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) $**x_{12}=p_{1}q_{2}-D**$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) $**x_{21}=p_{2}q_{1}-D**$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) $x_{22}=p_{2}q_{2}+D$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ex: &lt;a href=&quot;http://en.wikipedia.org/wiki/Linkage_disequilibrium&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Linkage_disequilibrium&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;why for the relationship between the haplotype frequencies and allele frequencies and D is there a difference in sign. In other words by the formula shouldn't it always be +D rather than -D? &lt;/p&gt;&#xA;" OwnerUserId="9349" LastEditorUserId="9349" LastEditDate="2017-01-19T21:16:26.033" LastActivityDate="2017-01-19T21:16:26.033" Title="Linkage disequilibrium D sign" Tags="&lt;molecular-genetics&gt;&lt;genetic-linkage&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21370" PostTypeId="1" CreationDate="2014-09-16T22:13:35.550" Score="3" ViewCount="51" Body="&lt;p&gt;Are the introns present in a nascent rna molecule removed simultaneously or are they removed in some sort of sequential fashion or is removal completely random?&lt;/p&gt;&#xA;" OwnerUserId="9344" LastActivityDate="2020-09-20T20:37:03.073" Title="Is intron removal coordinated?" Tags="&lt;exons&gt;&lt;introns&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21373" PostTypeId="2" ParentId="785" CreationDate="2014-09-17T00:54:00.227" Score="0" Body="&lt;p&gt;While aerobic organisms during respiration use oxygen as a terminal electron acceptor, anaerobic organisms use other electron acceptors. These inorganic compounds have a lower reduction potential than oxygen, meaning that respiration is less efficient in these organisms and leads to slower growth rates than aerobes. Many facultative anaerobes can use either oxygen or alternative terminal electron acceptors for respiration depending on the environmental conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most respiring anaerobes are heterotrophs, although some do live autotrophically. All of the processes described below are dissimilative, meaning that they are used during energy production and not to provide nutrients for the cell (assimilative). Assimilative pathways for many forms of anaerobic respiration are also known:&lt;a href=&quot;http://en.m.wikipedia.org/wiki/Sulfur_oxidizing_bacteria&quot; rel=&quot;nofollow&quot;&gt;http://en.m.wikipedia.org/wiki/Sulfur_oxidizing_bacteria&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="146" LastActivityDate="2014-09-17T00:54:00.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21375" PostTypeId="1" AcceptedAnswerId="21383" CreationDate="2014-09-17T02:10:59.623" Score="2" ViewCount="511" Body="&lt;p&gt;Could you tell me the steps to find and download a gene sequence from GeneBank?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would appreciate your help.&lt;/p&gt;&#xA;" OwnerUserId="9128" LastEditorUserId="1320" LastEditDate="2014-09-17T06:17:06.160" LastActivityDate="2014-09-17T07:36:33.150" Title="How can I download a gene sequence from GenBank (NCBI)?" Tags="&lt;bioinformatics&gt;&lt;molecular-genetics&gt;&lt;genomics&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-09-17T10:17:29.393" ContentLicense="CC BY-SA 3.0" />
  <row Id="21376" PostTypeId="1" AcceptedAnswerId="21388" CreationDate="2014-09-17T02:35:09.200" Score="6" ViewCount="1435" Body="&lt;p&gt;I am really curious if hair actually tuns white/gray from default color, or does it have a defect as it is made and grows out of your head a different color? &lt;/p&gt;&#xA;" OwnerUserId="9356" LastEditorUserId="5144" LastEditDate="2014-09-17T08:56:06.460" LastActivityDate="2014-09-17T09:10:37.407" Title="Does gray/white hair turn gray/white from a normal hair? or does a gray/white hair actually grow gray/white originally?" Tags="&lt;pigmentation&gt;&lt;hair&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21377" PostTypeId="2" ParentId="21346" CreationDate="2014-09-17T02:46:05.000" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short version&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper has nothing to do with &lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/VIIA1bPunctuated.shtml&quot; rel=&quot;nofollow&quot;&gt;punctuated equilibrum vs. gradualism&lt;/a&gt; (see &lt;a href=&quot;http://www.pbs.org/wgbh/evolution/library/03/5/l_035_01.html&quot; rel=&quot;nofollow&quot;&gt;also here&lt;/a&gt;), which was published a few years earlier. This debate is &lt;em&gt;much&lt;/em&gt; different (but equally important, I think).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors of the Spandrels paper criticized evolutionary biologists of taking a very narrow view of the evolutionary process. They claiming (wrongly) that evolutionary biologists believed that &lt;em&gt;every&lt;/em&gt; single trait on an organism was an adaptation that resulted from natural selection. The trait would not be present unless it was an adaptation. The authors claimed (rightly) that traits could not be considered independently. Instead, the traits had to be considered in light of the evolutionary history and developmental biology of the organism. To your specific questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The architectural metaphor was wrong. Does it make their entire argument wrong? No. They did not understand architecture. That does not mean they did not understand evolutionary biology.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are some of their claims wrong? I think yes and no, but the full answer requires more nuance than can really be given here so read the long answer below if interested. I don't know of a single reference that supports/rebuts the Spandrels paper but consider &lt;a href=&quot;http://jerrycoyne.uchicago.edu&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Why Evolution is True&lt;/em&gt;&lt;/a&gt; by Jerry Coyne, &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Greatest_Show_on_Earth:_The_Evidence_for_Evolution&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;The Greatest Show in Earth&lt;/em&gt;&lt;/a&gt; by Richard Dawkins, and &lt;a href=&quot;http://seanbcarroll.com/endless-forms-most-beautiful/&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Endless Forms Most Beautiful&lt;/em&gt;&lt;/a&gt; by Sean Carroll. None of these address directly the charges lodged by the Spandrels paper but they do show how evolutionary biology is integrative of many ideas instead of isolating each trait without considering the biology of the entire organism. (I have no commerical interest in any of these books. I simply support the ideas presented.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long version from my perspective.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In 1979, &lt;a href=&quot;http://www.stephenjaygould.org&quot; rel=&quot;nofollow&quot;&gt;Stephen J. Gould&lt;/a&gt; and Richard C. Lewontin (hereafter, G&amp;amp;L) published a paper, &quot;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/205/1161/581.short&quot; rel=&quot;nofollow&quot;&gt;The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme&lt;/a&gt;&quot;, in the Proceedings of the Royal Society of London, Series B.  The title of the paper mixes two metaphors. The first is the character Dr. Pangloss from &lt;a href=&quot;http://www.literature.org/authors/voltaire/candide/index.html&quot; rel=&quot;nofollow&quot;&gt;Voltaire's &quot;Candide&lt;/a&gt;.&quot; Dr. Pangloss is a bit of an optimist, who &lt;a href=&quot;http://www.literature.org/authors/voltaire/candide/chapter-01.html&quot; rel=&quot;nofollow&quot;&gt;says&lt;/a&gt;,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is demonstrable ... that things cannot be otherwise than as they are; for as all things have been created for some end, they must necessarily be created for the best end. Observe, for instance, the nose is formed for spectacles, therefore we wear spectacles. The legs are visibly designed for stockings, accordingly we wear stockings. ... [A]nd they, who assert that everything is right, do not express themselves correctly; they should say that everything is best.&quot; - Dr. Pangloss&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Dr. Pangloss is saying that everything has a purpose, and each thing is designed specifically for that purpose. G&amp;amp;L extend this metaphor to evolutionary biologists.  G&amp;amp;L claim that evolutionary biologists (at least to the time of their publication) tended to make claims similar to Dr. Pangloss: every trait that could be found on an organism results from natural selection and adaptation.  G&amp;amp;L write,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An adaptationist programme has dominated evolutionary thought in England and the United States during the past forty years. It is based on faith in the power of natural selection as an optimizing agent. It proceeds by breaking an organism into unitary &quot;traits&quot; and proposing an adaptive story for each considered separately. - G&amp;amp;L&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hence, the Panglossian paradigm. Every trait has an adaptive purpose and is necessarily the &quot;best&quot; that it can be. G&amp;amp;L then argue that evolutionary biologists of the time failed to consider the entire organism when assigning adaptive value to each trait separately.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We criticize this approach and attempt to reassert a competing notion ... that organisms must be analyzed as integrated wholes, with &lt;em&gt;bauplane&lt;/em&gt; so constrained by phyletic heritage, pathways of development, and general architecture that the constraints themselves become more interesting and more important in delimiting pathways of change than the selective force that may mediate change when it occurs. - G&amp;amp;L&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;G&amp;amp;L are saying that the many organismal traits are functions of evolutionary history, developmental pathways, and other structural contraints.  G&amp;amp;L argue that most evolutionary biologists of the time did not consider the entire organism when ascribing adaptive value to any one trait. In G&amp;amp;L Panglossian metaphoric terms, evolutionary biologists had decided that the adaptive value of the nose was to support glasses, but they had failed to consider that the nose may have evolved for other reasons (e.g., smell) and that the supportive value of the nose was an evolutionar by-product instead of an evolutionary cause. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This brings us to the second metaphor, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Spandrel&quot; rel=&quot;nofollow&quot;&gt;architectural spandrels&lt;/a&gt;. Spandrels are &lt;a href=&quot;http://youthvoices.net/sites/default/files/image/2713/jan/the_spandrels_of_san_marco_and_the_panglossian_paradigm.jpg&quot; rel=&quot;nofollow&quot;&gt;triangular spaces&lt;/a&gt; that form when two arches meet, or when an arch meets a rectangle.  According to G&amp;amp;L, spandrels are a necessary by-product of the architectural joining of the two shapes. The spandrel itself serves no purpose. In evolutionary terms, spandrels have no adaptive significance that resulted from natural selection. Instead, they are an evolutionary by-product that resulted from selection on other traits (arches and rectangles).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the architectural metaphor &lt;a href=&quot;http://web.archive.org/web/20020118023602/http://www.americanscientist.org/articles/96articles/Mark-full.html&quot; rel=&quot;nofollow&quot;&gt;apparently fails&lt;/a&gt;, their primary argument does not change.  Traits cannot be considered individually. Traits of an organisms must be evaluated as one part of the entire organism, together with it's developmental biology and its evolutionary history. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are two examples to represent their argument, written for a general audience. The first example is based on the human hand.  Our hand has five fingers. Each finger except the thumb has three bones (called phalanges), which you can see easily when you curl your finger. The thumb has only two phalanges. What is the adaptive value of having four fingers with three bones each, and a thumb with two bones? You might say that such a structure imparts excellent manual dexterity, from grasping to manipulating objects. But, would we not have that same dexterity if we had four fingers, or six? Why does the thumb have only two bones and not three? How could that be adaptive? These specific traits may not be the direct result of natural selection.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The structure of our hand is explained by our evolutionary history. Our primate ancestors had five fingers. So did our earliest mammalian ancestors, as did our earliest reptilian ancestors. However, some of the earliest amphibian ancestors, such as &lt;a href=&quot;http://tolweb.org/Acanthostega_gunnari/15016&quot; rel=&quot;nofollow&quot;&gt;Acanthostega&lt;/a&gt;, had more than five digits (toes, fingers). Somewhere in early amphibian evolutionary history, our ancestral lineage converged on five digits, and most descendant vertebrates retain that five digit pattern. Even those vertebrates today without five digits usually display five digits during development, such as the &lt;a href=&quot;http://scienceblogs.com/tetrapodzoology/2009/06/19/limusaurus-is-awesome/&quot; rel=&quot;nofollow&quot;&gt;ostrich&lt;/a&gt; (scroll down to image of blue-stained bones). If we assigned an adaptive purpose to the  human hand independently of its evolutionary history, we might very well be wrong.  Science doesn't like wrong. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think about the five toes of your foot. Each toe has three bones except for the big toe, which has two bones. Manual dexterity? No. Evolutionary history? Yes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second example is the groove in your upper lip below your nose. This groove is called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Philtrum&quot; rel=&quot;nofollow&quot;&gt;philtrum&lt;/a&gt;. Can you think of an adaptive function for the philtrum? You might think that it helps to direct odors towards our nostrils, or hypothesize some other adaptive purpose. However, it appears that the philtrum is a by-product of the &lt;a href=&quot;https://www.youtube.com/watch?v=wFY_KPFS3LA&quot; rel=&quot;nofollow&quot;&gt;development of our embryonic face&lt;/a&gt; (YouTube video). The trait of our philtrum may not have adaptive significance. It is a by-product our face formation when the two sides meet in the middle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;G&amp;amp;L's publication produced quite an uproar. It's easy to find criticisms of the paper. Some have &lt;a href=&quot;http://web.archive.org/web/20020118023602/http://www.americanscientist.org/articles/96articles/Mark-full.html&quot; rel=&quot;nofollow&quot;&gt;criticized the architectural metaphor&lt;/a&gt;. A bad metaphor does not necessarily make a bad scientific argument. Others have criticized the scientific rigor of their arugments. This &lt;a href=&quot;http://oikosjournal.wordpress.com/2011/08/26/why-the-spandrels-of-san-marco-isnt-a-good-paper/&quot; rel=&quot;nofollow&quot;&gt;blog entry&lt;/a&gt;, associated with the respected ecology journal &lt;em&gt;Oikos&lt;/em&gt;, dislikes the paper and identifies several problems. The Oikos blog also links to several other sites that either support or dislike the G&amp;amp;L article. Most evolutionary biologists disliked the claim that they did not see the &quot;whole organism.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rightfully so, I think. I do not know of one evolutionary biologist (myself included) that has ever considered a particular trait without considering the broader evolutionary history of an organism. Indeed, considerable effort is spent by evolutionary biologists to determine how the evolutionary history of an organism influences its trait. The same applies for evolutionary developmental biology and other biological processes. For example, &lt;a href=&quot;http://www.pnas.org/content/90/9/4087.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Martin et al. (1993)&lt;/a&gt; related evolutionary rate to body size, metabolic rate, and generation time of various animals, a very integrative (not isolating) approach.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be fair, I think the G&amp;amp;L paper needs to be considered in the context of its time. Remember that i was published in 1979. Reread the first G&amp;amp;L quote above. They say, &quot;during the past forty years.&quot;  The G&amp;amp;L paper was published in 1979. Forty years before this paper was published was during the &lt;a href=&quot;http://evolution.berkeley.edu/evosite/history/modsynth.shtml&quot; rel=&quot;nofollow&quot;&gt;&quot;modern evolutionary synthesis.&quot;&lt;/a&gt; Without going into details (ask another question on Biology.SE!) the modern evolutionary synthesis provided the genetic mechanism (and so much more) that explaiend how Darwin's concept of natural selection could actually work. Once the relationship between &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/history_13&quot; rel=&quot;nofollow&quot;&gt;Mendelian genetic inheritance&lt;/a&gt; and natural selection was proposed, many evolutionary biologists tested this connection. It is not surprising to me that G&amp;amp;L perceived this strong &quot;bias&quot; towards a selectionist (Panglossian) paradigm because many biologists of the time were trying to understand how Mendelian genetics contributed to natural selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the time of the modern synthesis, the structure of DNA was not yet known.  The structure was finally realized by &lt;a href=&quot;http://www.nature.com/scitable/topicpage/discovery-of-dna-structure-and-function-watson-397&quot; rel=&quot;nofollow&quot;&gt;Watson and Crick (and Franklin!)&lt;/a&gt; in 1953, only 26 years before G&amp;amp;L's paper. Today we think nothing about the DNA structure but molecular genetics has advanced so much since G&amp;amp;L's publication that we have a &lt;em&gt;much&lt;/em&gt; greater understanding of evolution and natural selection at the genetic level. Today, you can't study the evolution of a trait without considering its underlying genetic architecture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my opinion, one of the most, and perhaps &lt;em&gt;the&lt;/em&gt; most, important development in the field of evolutionary biology is the field of evolutionary developmental biology (evo-devo). This field did not really mature as a discipline until about 2000, when the Proceedings of the National Academy of Sciences in the US devoted an &lt;a href=&quot;http://www.pnas.org/content/97/9/4424.full&quot; rel=&quot;nofollow&quot;&gt;entire issue&lt;/a&gt; to the topic. Developmental biology was a discpline that G&amp;amp;L had argued was important to consider. I'd bet that even they had no idea how important the evo-devo discipline would become to understanding evolutionary change. Still, recognition of the relationship between evolution and development was recognized as long ago as the mid-1800s by &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/history_15&quot; rel=&quot;nofollow&quot;&gt;Ernst Haeckel&lt;/a&gt;. Evolutionary biologists were not necessarily considering traits in isolation from evolutionary history or developmental biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the end, G&amp;amp;L used broad brush strokes to paint evolutionary biologists into a small canvas, claiming that biologists had a narrow evolutionary viewpoint. The evolutionary biologists responded (then and now) that their perspective was wide, even when focused on a particular trait. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The G&amp;amp;L paper continues to prompt considerable debate, which I think is the value of their paper. Every young graduate student should be required to read the paper. Even jaded scientists need a refreshing jolt to an established way of thinking. Our thought processes will alway benefit when we are reminded that evolutionary biology is a broad discipline that must embrace many other disciplines to arrive at a full understanding of the history of life on Earth.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-09-17T09:43:59.063" LastActivityDate="2014-09-17T09:43:59.063" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21378" PostTypeId="2" ParentId="21358" CreationDate="2014-09-17T03:57:38.050" Score="5" Body="&lt;p&gt;I think the main question here is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there a term…which describes a bipolar disorder of lesser severity[?]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes. There are a couple ways to think about this, but you’re clearly accustomed to differentiating the &lt;em&gt;manic&lt;/em&gt; and &lt;em&gt;depressive&lt;/em&gt; phases of bipolar disorder, so I’ll start with that. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is &lt;strong&gt;mania&lt;/strong&gt; (excerpted from DSM 5*):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A. A distinct period of abnormally and persistently elevated, expansive, or irritable mood and abnormally and persistently increased goal-directed activity or energy, lasting &lt;strong&gt;at least 1 week&lt;/strong&gt; and present most of the day, nearly every day...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;B. During the period of mood disturbance and increased energy or activity, three (or more) of the following symptoms (four if the mood is only irritable) are present to a significant degree and represent a noticeable change from usual behavior: &lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Inflated self-esteem or grandiosity.&lt;/li&gt;&#xA;  &lt;li&gt;Decreased need for sleep &lt;/li&gt;&#xA;  &lt;li&gt;More talkative than usual or pressure to keep talking.&lt;/li&gt;&#xA;  &lt;li&gt;Flight of ideas or subjective experience that thoughts are racing.&lt;/li&gt;&#xA;  &lt;li&gt;Distractibility &lt;/li&gt;&#xA;  &lt;li&gt;Increase in goal-directed activity &lt;/li&gt;&#xA;  &lt;li&gt;Excessive involvement in activities that have a high potential for painful consequences &lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;  &#xA;  &lt;p&gt;C. The mood disturbance is &lt;strong&gt;sufficiently severe to cause marked impairment&lt;/strong&gt; in social or occupational functioning....&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And there is &lt;strong&gt;hypomania&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A. A distinct period of abnormally and persistently elevated, expansive, or irritable mood and abnormally and persistently increased activity or energy, lasting &lt;strong&gt;at least 4 consecutive days&lt;/strong&gt; and present most of the day, nearly every day. ….&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;B. [This criteria is the same as for mania.]&lt;br&gt;&#xA;  ....&lt;br&gt;&#xA;  E. The episode is &lt;strong&gt;not severe enough to cause marked impairment&lt;/strong&gt; in social or occupational functioning or to necessitate hospitalization.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I have bolded the main differences between the two definitions. You can see that &lt;strong&gt;hypomania&lt;/strong&gt; is the term for the less severe form of the manic phase of bipolar depression. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neither mania nor hypomania is likely to occur in the absence of depressive symptoms, however. Thus, there are two basic phenotypes of bipolar disorder (summarized from DSM 5*):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Bipolar I disorder&lt;/strong&gt;: Patient experiences mania; depressive periods may not qualify as Major Depressive Disorder. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Bipolar II disorder&lt;/strong&gt;: Major Depressive episodes are required; manic phase may be hypomanic. (This is classically considered a less severe syndrome, but this notion has been challenged in recent years.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And finally, one more term for you:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cyclothymic disorder&lt;/strong&gt;: patient experiences both hypomanic and depressive periods without ever fulfilling the criteria for an episode of mania, hypomania, or major depression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Your other question you seem to already know the answer to, but since it's in the title.....  &lt;strong&gt;Nonclinical depression&lt;/strong&gt; refers to something on the spectrum of normal (i.e. not pathological), such as situational mood disturbance. A related concept, &lt;strong&gt;subclinical depression&lt;/strong&gt; is a loose term to describe depressive symptoms that don't meet criteria for Major Depressive Disorder..)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;*American Psychiatric Association. (2013). &lt;em&gt;Diagnostic and statistical manual of mental disorders&lt;/em&gt; (5th ed.). Arlington, VA: American Psychiatric Publishing.&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-09-17T19:23:52.237" LastActivityDate="2014-09-17T19:23:52.237" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21379" PostTypeId="2" ParentId="21362" CreationDate="2014-09-17T04:12:50.323" Score="2" Body="&lt;p&gt;RNA splicing refers to a certain kind of RNA processing mechanism which leads to the excision and exclusion of some regions of the primary transcript. You should note that this is not the only method by which such a thing can happen; Endo-ribonucleases can clip the ends of the transcript and this happens in the case of tRNA-processing. But as &quot;splicing&quot; happens it is essential that the excised region be in the interior of the transcript. See the figure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/olwXP.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-09-17T04:12:50.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21380" PostTypeId="1" AcceptedAnswerId="21398" CreationDate="2014-09-17T07:07:40.573" Score="1" ViewCount="41" Body="&lt;p&gt;And six for &lt;a href=&quot;http://www.catalogueoflife.org/col/search/all/key/Haliclona%20digitata/match/1&quot; rel=&quot;nofollow&quot;&gt;Haliclona digitata&lt;/a&gt;, and five for &lt;a href=&quot;http://www.catalogueoflife.org/col/search/all/key/Ichneumon%20varius/match/1&quot; rel=&quot;nofollow&quot;&gt;Ichneumon varius&lt;/a&gt;. A couple of the duplicate entries are synonyms for other species, which is understandable, but most are the &quot;accepted name&quot;. Shouldn't there just be one &lt;a href=&quot;http://www.catalogueoflife.org/col/search/all/key/Pimpinella%20dioica/match/1&quot; rel=&quot;nofollow&quot;&gt;Pimpinella dioica&lt;/a&gt;? By my count there are 3068 species with two or more &quot;accepted name&quot; entries in the 2014 database. Where do these duplicate entries originate? Do they serve a purpose or are they errors?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably a question for catalogueoflife.org forums, but they don't seem to have any discussion area, so seeing if anyone here can answer.&lt;/p&gt;&#xA;" OwnerUserId="8564" LastActivityDate="2014-09-17T20:41:25.870" Title="Why are there seven entries for Pimpinella dioica in the Catalogue of Life?" Tags="&lt;taxonomy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21381" PostTypeId="1" AcceptedAnswerId="21387" CreationDate="2014-09-17T07:27:30.713" Score="3" ViewCount="33" Body="&lt;p&gt;My professor says that some drugs cannot be used with grapefruit. &#xA;I am trying to search a list of cytochromes and their effect to block members in the cytochrome family. Some in Cyt P450.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the main meta-analysis of fruits in blocking cytochrome family?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-09-17T08:51:57.770" Title="Meta-analysis of fruits in blocking Cytochrome family" Tags="&lt;biochemistry&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21382" PostTypeId="1" AcceptedAnswerId="21470" CreationDate="2014-09-17T07:28:50.963" Score="-1" ViewCount="91" Body="&lt;p&gt;Could not find a single article regarding this. What is hTAP? Tap is Transfer associated protein, that I know, but what is hTAP??&lt;br&gt;&lt;br&gt;(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)&lt;/p&gt;&#xA;" OwnerUserId="8835" LastActivityDate="2014-09-19T12:51:53.267" Title="What is hTAP?? Please help" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;bioinformatics&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2015-03-12T13:33:04.143" ContentLicense="CC BY-SA 3.0" />
  <row Id="21383" PostTypeId="2" ParentId="21375" CreationDate="2014-09-17T07:36:33.150" Score="4" Body="&lt;p&gt;Go to the &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/&quot; rel=&quot;nofollow&quot;&gt;NCBI website&lt;/a&gt;, fill the search field with relevant information in the upper part of page, select &quot;nucleotide&quot; from the drop-down menu just to the left of the search field and click search. You will get a list of items, by clicking &quot;FASTA&quot; link below any of them will bring you the corresponding sequence. &#xA;Depending on your interest, you can choose other databases from that menu, and some of them are interlinked. For example you can do the search by selecting &quot;gene&quot; instead of &quot;nucleotide&quot; and when displaying a selected gene info, you can see the links that lead to nucleotide database for getting the sequence.&lt;/p&gt;&#xA;" OwnerUserId="1458" LastActivityDate="2014-09-17T07:36:33.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21384" PostTypeId="1" AcceptedAnswerId="21540" CreationDate="2014-09-17T07:41:35.920" Score="2" ViewCount="87" Body="&lt;p&gt;Databases like STRING have so many predicted as well as experimental interactions data for many organisms.However there is a bias in the data which they have?.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;a)The first is gene co-occurrence  which is more like a circular argument.&lt;/p&gt;&#xA;&lt;p&gt;b)And the second one is that all interactions that are predicted computationally are tested for experimental interactions.This leads to a bias in the interaction data available for organisms in STRING.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;How do we overcome this data bias while using STRING interaction data for analysis purpose?&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;a)Avoiding evidence channels of gene co-occurrence is one way.Is there any other way other than this?&lt;/p&gt;&#xA;&lt;p&gt;b)How to statistically say that the bias is not governing the data or any way to test statistical significance of the data bias?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8135" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-22T11:41:21.493" Title="Data Bias in protein-protein interactions data" Tags="&lt;bioinformatics&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21386" PostTypeId="1" CreationDate="2014-09-17T08:50:52.980" Score="1" ViewCount="53" Body="&lt;p&gt;Can anyone advise me a literature supporting the claim that &lt;em&gt;Encephalitozoon cuniculi&lt;/em&gt; is an aerobic organism? I have seen papers saying otherwise, but also I was told that this is not quite true.&lt;/p&gt;&#xA;" OwnerUserId="9317" LastActivityDate="2014-09-17T08:50:52.980" Title="Encephalitozoon cuniculi" Tags="&lt;parasitology&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21387" PostTypeId="2" ParentId="21381" CreationDate="2014-09-17T08:51:57.770" Score="4" Body="&lt;p&gt;While I haven't found a list which is restricted to fruits, I found this page: &lt;a href=&quot;http://medicine.iupui.edu/clinpharm/ddis/main-table/&quot; rel=&quot;nofollow&quot;&gt;P450 Drug interaction table&lt;/a&gt;. They list quite a number of substances which inhibit different isoforms of the P450 protein and also give the original references.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.pharmacologyweekly.com/content/pages/medications-herbs-cytochrome-p450-cyp-enzyme-inhibitors&quot; rel=&quot;nofollow&quot;&gt;list&lt;/a&gt; gives a large number of herbals which inhibit different P450 isoenzymes. The disadvantage is that they do not give further references so if you want to have a closer look you will probably have to spend some time with Pubmed.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-17T08:51:57.770" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21388" PostTypeId="2" ParentId="21376" CreationDate="2014-09-17T09:10:37.407" Score="7" Body="&lt;p&gt;It can actually be for both reasons and it more or less depends on the age what happens. The pigment of the hair is produced by pigment cells (the melanocytes) in the hair bulge and is then integrated into the growing hair (image from &lt;a href=&quot;http://www.stembook.org/node/581&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Zngix.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pigment melanin produced by these cells can be destroyed by reactive oxigen species which then leads to grey hair which can still be pigmented at the tip. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other possibility is connected to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hair_follicle#Hair-follicle_cycling&quot; rel=&quot;nofollow noreferrer&quot;&gt;hair cycle&lt;/a&gt;. After growing for a while the growth stops, the hair falls out and the hair follicle goes into a resting state. In this phase the pigment cells die. When the hair follicle starts a new hair cycle, the pigment cell population in the hair bulb is renewed from the melanocyte stem cells in the hair bulge. Over time the number of the melanocyte stem cells gets lower until there are none left eventually. At this point new hairs will grow without pigment and be grey/white.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two interesting publications about this topic:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929555/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Oxidative Stress in Ageing of Hair&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S009286740500293X&quot; rel=&quot;nofollow noreferrer&quot;&gt;Melanocyte Stem Cell Maintenance and Hair Graying&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-17T09:10:37.407" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21390" PostTypeId="1" AcceptedAnswerId="21403" CreationDate="2014-09-17T09:22:10.770" Score="3" ViewCount="81" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19922443&quot; rel=&quot;nofollow noreferrer&quot;&gt;This paper uses two equations&lt;/a&gt; to explain the different conditions under which sexually antagonistic genetic variance is maintained in a population, while allowing for unequal dominance, for autosomally linked loci:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$h_f / 1-h_m + h_fs_f   &amp;lt;$ $ $ $   s_m/s_f   &amp;lt;  1-h_f/h_m(1-s_f)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And X-chromosome linked (X-linked) loci:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$2 h_f / 1+h_f s_f &amp;lt; $ $ $ $ s_m/s_f &amp;lt; $ $ $ $2(1-h_f)/1-h_f s_f$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $s_m$ and $s_f$ are the selection coffecients against the less fit homozygote (or hemizygote) in males and females respectively where the most fit genotype has a relative fitness of 1. Similarly $h_m$ and $h_f$ represent the dominance of the less fit allele in males and females, and $h_m$ is not applicable in the X-linked equation because there is no dominance (due to hemizygosity it can only be homozygote).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I'm having a little trouble understanding how $s$ and $h$ are defined here.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For $s$, is it the fitness of the deleterious homozygote or the difference in relative fitness between the two homozygotes? Such that either $s$ = the relative fitness of the homozygote, or, $s$ = 1 - relative fitness of deleterious homozygote, where one represents the fitness of the fittest homozygote thus giving the fitness differential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For $h$, is the dominance defined as the fitness difference between the less-fit homozygote and the heterozygote, or the most-fit homozygote and the heterozygote? Or is it the deviation from the average fitness of the two homozygotes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Going from the graph (see below for values of fitnesses), what are the values of $s_m$, $s_f$, $h_m$, and $h_f$ where the dashed line is Females and solid line is Males. I see possible values of either $s_m$ = 0.2 or 0.8 (fittest genotype - fitness of weakest), likewise $s_f$ is either 0.3 or 0.7, $h_m$ is either 0.1 (deviation from most-fit genotype), 0.7 (deviation from least-fit) , or 0.3 (deviation from average) and $h_f$ is either 0.3, 0.4, or 0.05. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AmLgz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The values here are, as fitnesses for genotypes A1A1, A1A2, and A2A2, for males, 1.0, 0.9, 0.2, and for females 0.3, 0.7, 1.0.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-09-17T10:18:33.953" LastActivityDate="2014-09-18T13:05:45.277" Title="Defining dominance and selection in these formulae" Tags="&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;sex-chromosome&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21392" PostTypeId="2" ParentId="21380" CreationDate="2014-09-17T11:12:44.700" Score="2" Body="&lt;p&gt;This is because &lt;a href=&quot;http://www.catalogueoflife.org&quot; rel=&quot;nofollow&quot;&gt;Catalogue of life&lt;/a&gt; is a database created and maintained via consulting other, taxonomically narrower databases. This leads to propagation of the original inaccuracies and introduction of new ones during the process of data transfer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of &lt;em&gt;Pimpinella dioica&lt;/em&gt;, for example, the information was imported from the &lt;a href=&quot;http://rbg-web2.rbge.org.uk/URC/frames.html?http://rbg-web2.rbge.org.uk/URC/dbases/dbaseshomepage.html&quot; rel=&quot;nofollow&quot;&gt;World Umbellifer Database&lt;/a&gt;. If you search there for &quot;Pimpinella dioica&quot; you get a list of names, &lt;a href=&quot;http://rbg-web2.rbge.org.uk/cgi-bin/nph-readfile.pl/dataset=/parent=umbindex/filename=umbnomen?12845076%7Cretq=genus_xref%3DPimpinella%26taxon_name_xref%3Ddioica%26species_xref%3D%7Cfirstval=1%7Clino=3%7Cnocount=%7Cdataonly=%7CSID=2328.1410951950&quot; rel=&quot;nofollow&quot;&gt;only one&lt;/a&gt; of which is explicitly labeled as synonym (by Linné, the same one as in CoL). CoL interpreted this situation as if others were accepted as valid, BUT this was not the case: all other records are marked as &quot;provisional&quot; and most of them actually contain information about probable synonymy in &lt;a href=&quot;http://rbg-web2.rbge.org.uk/cgi-bin/nph-readfile.pl/dataset=/parent=umbindex/filename=umbnomen?9609908%7Cretq=genus_xref%3DPimpinella%26taxon_name_xref%3Ddioica%26species_xref%3D%7Cfirstval=1%7Clino=4%7Cnocount=%7Cdataonly=%7CSID=2984.1410950863&quot; rel=&quot;nofollow&quot;&gt;&quot;Comments&quot;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, in the description of World Umbellifer Database the one can learn, that the database guarantees accuracy principally for generic names only.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-09-17T20:19:06.283" LastActivityDate="2014-09-17T20:19:06.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21393" PostTypeId="1" CreationDate="2014-09-17T11:14:54.673" Score="2" ViewCount="93" Body="&lt;p&gt;I'm currently working on a toy robot for a student project. Part of this robot is the fact that it will be moving around quite fast. As such hitting the child can and most likely will happen. As such we are obviously worried about safety. So what type of forces can a child safely withstand? The robot will most likely not be very tall (45 cm) and be shaped like the top half of a sphere, as such most collisions will happen with the shins or the feet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do hope this is in the correct  stack exchange and that this isn't supposed to go into a different stack exchange.&lt;/p&gt;&#xA;" OwnerUserId="9364" LastEditorUserId="9364" LastEditDate="2014-09-18T10:27:11.563" LastActivityDate="2014-09-18T10:27:11.563" Title="force required to do damage to child's leg/feet in collision" Tags="&lt;human-biology&gt;&lt;bio-mechanics&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-09-18T10:59:22.983" ContentLicense="CC BY-SA 3.0" />
  <row Id="21394" PostTypeId="1" AcceptedAnswerId="36906" CreationDate="2014-09-17T11:17:38.900" Score="9" ViewCount="2141" Body="&lt;p&gt;I know the sodium-potassium pump pumps out 3 Na&lt;sup&gt;+&lt;/sup&gt; ions and pumps in 2 K&lt;sup&gt;+&lt;/sup&gt; ions per reaction so the negative charge in the axon increases. However, once the voltage (difference of charge inside and outside of the neuron) gets down to -70 mV, this stops going further below. Why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that this is because of other transport proteins and the presence of anions and cations in the axon, but what are those proteins and ions precisely? There are always negatively charged proteins inside a cell, including a neuron, so I assume there must be a strong force which keeps the voltage from going down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, is the opening and closing of an ion channel triggered by the voltage of the neuron or the concentration of the ion?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastEditorUserId="9943" LastEditDate="2016-03-11T20:48:26.510" LastActivityDate="2016-03-11T20:48:26.510" Title="What keeps the resting potential of neurons constant at -70 mV?" Tags="&lt;neuroscience&gt;&lt;biophysics&gt;&lt;electrophysiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21395" PostTypeId="1" CreationDate="2014-09-17T11:24:20.900" Score="1" ViewCount="95" Body="&lt;p&gt;&lt;em&gt;Cryptosporidium muris&lt;/em&gt; infects mostly rodents and it is usually found in gastric gladns. &lt;em&gt;Cryptosporidium parvum&lt;/em&gt; infects humans and certain animals and it is found in the terminal ileum and colon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also &lt;em&gt;Cryptosporidium hominis&lt;/em&gt; that infects only humans. My question is &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;where exactly in the human gastrointestinal tract it resides?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9317" LastActivityDate="2020-09-20T20:41:25.857" Title="Question about *Cryptosporidium hominis*" Tags="&lt;parasitology&gt;&lt;parasitism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21396" PostTypeId="1" AcceptedAnswerId="21399" CreationDate="2014-09-17T12:13:57.143" Score="15" ViewCount="16780" Body="&lt;p&gt;How long does a mosquito take to land on a host, start its bite, end its bite and then fly off?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And what about different species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am most interested in human hosts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References to web sites or books would be appreciated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I cannot find this even after extensive trawling of Google.&lt;/p&gt;&#xA;" OwnerUserId="9366" LastEditorUserId="9366" LastEditDate="2014-09-17T12:34:25.537" LastActivityDate="2017-08-06T01:20:49.810" Title="How long does a mosquito take to land on a host, bite, and fly off?" Tags="&lt;entomology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21397" PostTypeId="2" ParentId="837" CreationDate="2014-09-17T12:29:58.910" Score="2" Body="&lt;p&gt;&quot;There are antibiotics which contain carbohydrates, such as Gentamycin and Streptomycin (the aminoglycosides). These must be the antibiotics that could account for this phenomenon.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My conjecture that the carbohydrate moities contained within aminoglycosides account for the high energy is incorrect. Aminoglycosides are NEVER metabolized by the body, they are excreted out into the urine UNCHANGED. See here: &lt;a href=&quot;http://www.ebmedicine.net/topics.php?paction=showTopicSeg&amp;amp;topic_id=43&amp;amp;seg_id=839&quot; rel=&quot;nofollow&quot;&gt;http://www.ebmedicine.net/topics.php?paction=showTopicSeg&amp;amp;topic_id=43&amp;amp;seg_id=839&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And even if it were possible to metabolize the carbohydrate molecules within them, the energy released would be far less than the energy consumed to break their linkages in the first place, thus placing a negative energy balance on the body, and thus, not providing the burst of energy that is apparently observed after taking antibiotics. &lt;/p&gt;&#xA;" OwnerUserId="9336" LastActivityDate="2014-09-17T12:29:58.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21398" PostTypeId="2" ParentId="21380" CreationDate="2014-09-17T12:42:42.267" Score="3" Body="&lt;p&gt;While any large database may have errors that can lead to multiple entries (sensu har-wradim's answer), I think most of the multiple entries detail the taxonomic history associated with that species. Your link to the sponge &lt;a href=&quot;http://www.catalogueoflife.org/col/search/all/key/Haliclona%20digitata/match/1&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Haliclona digitata&lt;/em&gt;&lt;/a&gt; provides a clear example. First, dismiss the &lt;em&gt;H. digitata&lt;/em&gt; (Schmidt, 1862) entry. As clearly stated, it is a synonym for a different species of sponge, &lt;em&gt;Tedania anhelans&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The remaining entries are all links to various &lt;a href=&quot;http://www.iapt-taxon.org/nomen/main.php?page=art53&quot; rel=&quot;nofollow&quot;&gt;homonyms&lt;/a&gt; of &lt;em&gt;H. digitata&lt;/em&gt;. Skimming through the World Porifera Database entries (via the &quot;Online resource&quot; links), provides the necessary information. Lendenfeld's use of &lt;em&gt;Chalinorhaphis&lt;/em&gt; is the original description. It is the senior homonym, meaning the specific epithet (&lt;em&gt;digitata&lt;/em&gt;) has precedence over junior names. The junior names include &lt;em&gt;Adocia digitata&lt;/em&gt; (Baer) and &lt;em&gt;Gellius digitatus&lt;/em&gt; (Koltun). It was probably Tanita &amp;amp; Hoshino that transfered &lt;em&gt;digitata&lt;/em&gt; to the genus &lt;em&gt;Haliclona&lt;/em&gt; but I cannot verify this without seeing the article. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The taxonomic history can also be tracked for &lt;em&gt;Ichneumon varius&lt;/em&gt;, but the linked databases don't hvae as much detail as the Porifera database for &lt;em&gt;H. digitata&lt;/em&gt;. Still, it suggests that the description by Pontoppidan in 1763 is the senior homonym, and the subsequent uses by Cuvier, Gmelin and Muller are junior homonyms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is also what I think har-wradim is alluding to for &lt;em&gt;Pimpinella dioica&lt;/em&gt;. Unfortunately, the Umbellifer database seems to have little detail in this regard.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Catalogue of Life provides a convenient mechanims to begin a thorough search for the taxonomic history of a species. &lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-09-17T20:41:25.870" LastActivityDate="2014-09-17T20:41:25.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21399" PostTypeId="2" ParentId="21396" CreationDate="2014-09-17T12:47:09.620" Score="14" Body="&lt;p&gt;That's an interesting question and not easy to answer. I haven't found data for humans but from experiments with mice. They analysed how the mosquito actually bites, probes for the blood vessels (not all bites are successful) and finally sucks bloods. In their research  they observed feeding times between 150 and 329 seconds, depending on the size of the blood vessel. The mean feeding time was 240 seconds. It also depends on the age of the mosquito, older mosquitos suck longer. To this comes the time for probing (mean time 142 seconds) and the time before the mosquito starts probing after it landed (mean time 6.5 seconds). This totals to about 389 seconds (or roughly 6.5 minutes) total time after landing. This data can be found in table 1 of reference 2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is pretty interesting, they also show videos of the mosquito probing the skin for a blood vessel. You can find a pretty nice summary in the first reference and the original paper in the second:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://phenomena.nationalgeographic.com/2013/08/06/heres-what-happens-inside-you-when-a-mosquito-bites/&quot;&gt;Here’s What Happens Inside You When a Mosquito Bites&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0050464&quot;&gt;Visualizing Non Infectious and Infectious Anopheles gambiae Blood&#xA;Feedings in Naive and Saliva-Immunized Mice.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-09-17T20:51:00.807" LastActivityDate="2014-09-17T20:51:00.807" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21400" PostTypeId="1" AcceptedAnswerId="30128" CreationDate="2014-09-17T12:54:20.890" Score="6" ViewCount="423" Body="&lt;p&gt;There is the following bulletin published for the History of Chemistry Vol. 32: 105-118 in 2007:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.scs.illinois.edu/~mainzv/HIST/awards/OPA%20Papers/2009-Deichmann.pdf&quot;&gt;“MOLECULAR” VERSUS “COLLOIDAL”: CONTROVERSIES IN BIOLOGY AND BIOCHEMISTRY, 1900–1940*&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;written by PhD habilitation research professor &lt;a href=&quot;https://de.wikipedia.org/wiki/Ute_Deichmann&quot;&gt;Ute Deichmann&lt;/a&gt; at the Leo Baeck Institute (&lt;a href=&quot;https://en.wikipedia.org/wiki/Leo_Baeck_Institute&quot;&gt;LBI&lt;/a&gt;) in London and leader of the History of the Biological and Chemical Sciences Research Group at the Instritute for Genetics, University of Cologne.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, the question is: What is Colloidal biology, what are the basic differences between molecular biology and does it have any background in modern scientific community?&lt;/p&gt;&#xA;" OwnerUserId="1195" LastActivityDate="2015-03-04T11:02:20.570" Title="What is Colloidal biology and does it have any scientific background?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21401" PostTypeId="2" ParentId="21343" CreationDate="2014-09-17T13:19:14.437" Score="7" Body="&lt;p&gt;A haplotype is commonly defined as &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...a group of genes within an organism that was inherited together from a single parent. -- &lt;a href=&quot;http://www.nature.com/scitable/definition/haplotype-haplotypes-142&quot;&gt;Nature Scitable&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This definition of haplotype applies whether it is just a few genes or all of the genes on an entire chromosome$^1$. In the case of the major histocompatibility complex, it is a group of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK27156/&quot;&gt;more than 200 genes on chromosome 6&lt;/a&gt; (Janeway et al. 2001). The set of alleles$^1$ inherited together from one parent form the MHC haplotype. Thus, one offspring will inherit two different MHC haplotypes, one from each parent. The different haplotypes with so many genes helps keep genetic variation in the overall complex, which improves the immune response ability of the organism.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term is derived from &lt;a href=&quot;http://www.nature.com/scitable/definition/haploid-309&quot;&gt;haploid&lt;/a&gt;, which means half of the normal set of chromosomes. Humans for example are &lt;a href=&quot;http://www.nature.com/scitable/definition/diploid-310&quot;&gt;diploid&lt;/a&gt;, meaning it has two copies of each chromosome, one inherited from the mother (maternal) and one inherited from the father (paternal). So, when you inherit just one half of the crhomosome pair, you are inheriting a haplotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For general reference, it's important to note that haplotype was not always used to reference a group of two or more genes inherited together. It was commonly used to as a term to represent a sequence of nucleotides together on the same chromosome, even if only part of a single gene. For example, &lt;a href=&quot;http://www.pnas.org/content/92/9/3731.full.pdf&quot;&gt;Bowen et al. (1995)&lt;/a&gt; used mitochondrial haplotypes to study the migration of loggerhead turtles across the Pacific Ocean. They used 350 nucleotides of the &lt;a href=&quot;http://www.geneticorigins.org/mito/mitoframeset.htm&quot;&gt;mitochondrial control region&lt;/a&gt;. The control region is over 1000 nucleotides in size but Bowen and colleagues only used 350 nucleotides from part of the control region.  This use was very common in the 1990s and early 2000s before it became easier and less expensive to sequence entire genomes, or at least many genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Citaton&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bowen, B.W. et al. 1995. Trans-Pacific migrations of the loggerhead turtle (*Caretta caretta) demonstrated with mitochondrial DNA markers. Proceedings of the National Academy of Sciences USA 92: 3731-3734.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Janeway, Jr., C.A. et al. 2001. &lt;em&gt;Immunobiology&lt;/em&gt;, 5th edition. Garland Science, New York.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Footnote&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;More accurately, it would be the set of alleles at each gene locus (gene location) inherited together. The same genes are inherited from either parent, but the alleles (variations of the gene) may be different between the two parents.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-09-17T13:26:28.873" LastActivityDate="2014-09-17T13:26:28.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21402" PostTypeId="1" CreationDate="2014-09-17T14:23:49.657" Score="1" ViewCount="283" Body="&lt;p&gt;According to the recent research about &lt;a href=&quot;http://arxiv.org/abs/1104.3113v2&quot; rel=&quot;nofollow&quot;&gt;Electromagnetic Signals from Bacterial DNA&lt;/a&gt; (A. Widom, J. Swain, Y. N. Srivastava, S. Sivasubramanian) it seems there is a possibility of a &quot;wireless&quot; version of intercellular communication which was found in bacterial communities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper's abstract reports:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Chemical reactions can be induced at a distance due to the propagation&#xA;  of electromagnetic signals during intermediate chemical stages.&#xA;  Although is is well known at optical frequencies, e.g. photosynthetic&#xA;  reactions, electromagnetic signals hold true for muck lower&#xA;  frequencies. In E. coli bacteria such electromagnetic signals can be&#xA;  generated by electric transitions between energy levels describing&#xA;  electrons moving around DNA loops.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The authors further note:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There has been considerable interest in bacterial communities wherein&#xA;  a bacterium is connected to neighboring bacteria by means of narrow&#xA;  nanowires[5-7]. It is believed that the purpose of the nanowires is to&#xA;  allow for intercellular electronic communications. More advanced on&#xA;  the evolutionary scale are the more modern bacterial communities which&#xA;  are wireless. The electromagnetic signals sent from a bacterium to&#xA;  neighboring bacteria can be due to relatively low frequency electron&#xA;  level transitions within DNA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Conclusions says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Although biochemical reactions are often described in terms of&#xA;  molecular contacts, electromagnetic signals can often be employed to&#xA;  allow chemical reaction control at a distance.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The wireless broadcasts can in principle be of both the AM and FM&#xA;  variety due to the magnetic flux periodicity in electron energy&#xA;  spectra in bacterial DNA orbital motions. AM signals can arise from&#xA;  the Bohr transition frequencies between different electronic energy&#xA;  orbitals about the DNA loops.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Wired article &lt;a href=&quot;http://www.wired.com/2011/04/bacterial-radio/&quot; rel=&quot;nofollow&quot;&gt;Bacteria on the Radio: DNA Could Act as Antenna&lt;/a&gt; comments:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Theoretical physicists have proposed an explanation for how bacteria&#xA;  might transmit electromagnetic signals: Chromosomes could act like&#xA;  antennae, with electrons traveling gene circuits to produce&#xA;  species-specific wavelengths.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In Widom’s arXiv paper, he and other physicists calculate that as&#xA;  electrons flowed through loops of DNA in E. coli and Mycoplasma pirum,&#xA;  the species tested by Montagnier, they should generate wavelengths&#xA;  similar to what was recorded.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;“Different species have different lengths of DNA” in their&#xA;  chromosomes, he said. “These lengths probably determine frequency.”&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;“This could be a wireless version,” said Widom. “Bacteria that set up&#xA;  nanowires are, on an evolutionary scale, fairly old. It’s occurred to&#xA;  me that more modern bacteria may use wireless.”&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It seems that the concept of electromagnetic signal transmission in bacteria is not new and such an idea originates with Nobel Laureate virologist &lt;a href=&quot;https://en.wikipedia.org/wiki/Luc_Montagnier&quot; rel=&quot;nofollow&quot;&gt;Luc Montagnier&lt;/a&gt; (2009), who detected electromagnetic signals after wrapping inductor coils around flasks of water, hooked up to an amplifier, which contained E. coli and Mycoplasma pirum. The frequency of the signals measured was about 1kHz.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That kind of communication could also explain the phenomenon of &lt;a href=&quot;https://en.wikipedia.org/wiki/Quorum_sensing&quot; rel=&quot;nofollow&quot;&gt;quorum sensing&lt;/a&gt; mechanism, where bacteria communicate with one another to establish the population density of micro-organisms of their own kind within their proximal environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Based on above, the question is, is there any possibility that the diseases can be transmitted wirelessly? Are there any further research around this topic?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1195" LastActivityDate="2014-09-17T14:23:49.657" Title="Can diseases be transmitted wirelessly?" Tags="&lt;biochemistry&gt;&lt;bacteriology&gt;&lt;pathology&gt;&lt;chemical-communication&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ClosedDate="2014-09-18T23:34:29.660" ContentLicense="CC BY-SA 3.0" />
  <row Id="21403" PostTypeId="2" ParentId="21390" CreationDate="2014-09-17T14:55:04.513" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654548/&quot; rel=&quot;nofollow&quot;&gt;Fry (2010)&lt;/a&gt; borrowed his variables from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1213615/pdf/171.pdf&quot; rel=&quot;nofollow&quot;&gt;Kidwell et al. (1977)&lt;/a&gt;.  Kidwell defines the fitness of each genotype as,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_{m1}$, $w_{f1}$ = male and female fitness of the A$_1$A$_1$ genotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_{m2}$, $w_{f2}$ = male and female fitness of the A$_1$A$_2$ genotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_{m3}$, $w_{f3}$ = male and female fitness of the A$_2$A$_2$ genotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kidwell then establishes the following parameters for each fitness variable for opposing additive selection,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_{m1} = w_{f3} = 1$,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_{m2} = 1-.5s_m$,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_{f2} = 1-.5s_f$,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_{m3} = 1-s_m$, and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_{f1} = 1-s_f$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$s_m = 1-w_{m3}$, and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$s_f = 1-w_{f1}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$s_m$ and $s_f$ are the relative fitness differences &lt;em&gt;between&lt;/em&gt; the two homozygous genotypes of each gender. The heterozygotes are assumed to have half of that differential. This is what Fry refers to on page 2 (page 1511 of the publication):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In Kidwell et al.’s notation ... the most fit genotype in a given sex has a relative fitness of 1, and $s_m$ and $s_f$ are the selection coefficients against the less-fit homozygote (or hemizygote) in males and females, respectively.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For opposing selection with arbitrary dominance, Kidwell parameterizes the heterozygous fitness components as&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_{m2} = 1-h_ms_m$, and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_{f2} = 1-h_fs_f$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notice that $h$ is modifying the fitness difference $s$ in the heterozygotes. This is due to incomplete dominance of one allele over the other. If both alleles in a heterozygote contribute equally to the phenotype, then $h = 0.5$, and you have the additive fitness described above ($w = 1-.5s$).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If one allele is incompletely dominant over the other, the selective difference $s$ will be modified by some amount, $h$. If A$_1$ is only slightly dominant over A$_2$, (say, $h=0.6$), the effect on $w$ won't be much different than if $h=0.5$. Both alleles will affect fitness but the more dominant allele will have a slightly greater affect on fitness than the other allele. If one allele is much more dominant, then $h$ becomes larger and the more dominant allele contributes more to the overall fitness than the other allele.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, if $h=1$ then one allele is completely dominant so the other allele will not contribute at all to fitness. When $h=1$, the equations reduce to $w = 1 - s$ (for the respective genders), remembering that $h$ is based on the dominance of the allele with maximum fitness in the &lt;em&gt;other&lt;/em&gt; gender. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider a female. Her maximum fitness is the A$_2$A$_2$ genotype.  If A$_1$ is completely dominant over A$_2$, then a heterozygous female would have fitness equal to the A$_1$A$_1$ genotype which, for females is defined as $w = 1-s_f$. On the other hand, if A$_1$ is not completely dominant over A$_2$, then the heterozygote will have some reduction in fitness but not as much as for complete dominance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your final question about your figure, given the following values for A$_1$A$_1$, A$_1$A$_2$, and $_2$A$_2$, respectively:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_m = 1, 0.9, 0.2$, and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_f = 0.3, 0.7, 1$, then&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$s_m = 1 - 0.2 = 0.8$, and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$s_f = 1 - 0.7 = 0.7$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the heterozygosity effect ($h$), given that&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w = 1 - hs$, then&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$h = \frac{1-w}{s}$, therefore&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$h_{m2} = \frac{1 - 0.9}{0.8} = 0.125$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A$_1$ is nearly completely dominant over A$_2$ in males, so the presence of A$_2$ is the male is not reducing his fitness by very much. For females,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$h_{f2} = \frac{1-0.7}{0.7} = 0.429$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The presence of the dominant A$_1$ allele in females has stronger heterozygous effect so her fitness is reduced more, compared to heterozygous males. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Citations&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fry, J.D. 2010. The genomic location of sexually antagonistic variation: some cautionary comments. Evolution 64: 1510-1516.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kidwell, J.F. et al. 1977. Regions of stable equilibria for models of differential selection in the two sexes under random mating. Genetics 85: 171-183. &lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-09-18T13:05:45.277" LastActivityDate="2014-09-18T13:05:45.277" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21404" PostTypeId="1" AcceptedAnswerId="21417" CreationDate="2014-09-17T15:14:07.317" Score="5" ViewCount="2263" Body="&lt;p&gt;I want to do a text mining study using full-text versions of articles I find on PubMed. My intended search protocol will be roughly as follows:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Search PubMed using a gene name (and any alternate names) as the query, all matching papers are subjected to Step 2&lt;/strong&gt;; my understanding is that this will return articles that mention the gene in their abstract&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Search full-text for any and all matches from a list of keywords; assign each paper a score based on the number of matching keywords&lt;/strong&gt;; any papers that match have to be read by a human but the most relevant papers will have a higher score and get read first&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The two-step search needs to be repeated many times with different genes in Step1 so an automated approach is probably worth the time it will take to develop.&#xA;I know enough about programming that I could write a script to do Step2 if I had the paper as a plain-text document (I program in Perl but I also know a little Python) but I have no idea how I could automate the process of searching for papers, downloading them, converting them to plain-text documents that my program could work on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I considered posting this in StackOverflow but have opted for this site because I have not ruled out the possibility that this can be done without doing my programming.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE: I have found one &lt;a href=&quot;http://www.ebscohost.com/biomedical-libraries/medline-with-full-text&quot; rel=&quot;nofollow&quot;&gt;tool&lt;/a&gt; that might be very useful for exactly this problem. Unfortunately, I am not in a position to ask for a free trial so I cannot evaluate it. Even if it is an appropriate tool, I will most likely not be able to use it for my study. &lt;/p&gt;&#xA;" OwnerUserId="8161" LastEditorUserId="3952" LastEditDate="2015-04-20T20:03:35.110" LastActivityDate="2015-04-20T20:03:35.110" Title="How can I text-mine full-text articles from PubMed?" Tags="&lt;bioinformatics&gt;&lt;literature&gt;" AnswerCount="2" CommentCount="8" ClosedDate="2015-04-21T08:53:48.497" ContentLicense="CC BY-SA 3.0" />
  <row Id="21405" PostTypeId="1" AcceptedAnswerId="21406" CreationDate="2014-09-17T15:15:17.687" Score="2" ViewCount="367" Body="&lt;p&gt;I have to make 100mL of 400mM NaOH. How do I go about calculating what I need to prepare this?&lt;/p&gt;&#xA;" OwnerUserId="8991" LastActivityDate="2014-09-17T18:09:32.230" Title="How do I prepare a solution? (Calculation)" Tags="&lt;ph&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-09-17T17:58:31.017" ContentLicense="CC BY-SA 3.0" />
  <row Id="21406" PostTypeId="2" ParentId="21405" CreationDate="2014-09-17T15:30:30.783" Score="4" Body="&lt;p&gt;This is relatively easy. First: Look up the molecular weight of &lt;a href=&quot;http://en.wikipedia.org/wiki/Sodium_hydroxide&quot; rel=&quot;nofollow&quot;&gt;sodium hydroxide&lt;/a&gt;: Wikipedia gives a molar weight of 39.997 grams/mole (lets round this to 40 g/mole thats easier to calculate and the error in this is marginal).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when you dissolve 40 g of it in 1 l of water, you have a 1000 mM (or 1 M) solution. Since you only want to have a 400 mM solution, you need to multiply the final concentration with the molar weight to get the amount of NaOH for one litre: &#xA;40 g/mole * 0.4 mole/l = 16 g of NaOH per litre. Since you only need 100 ml, you only need 1/10th of the NaOH (1.6 g).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to prepare 100 ml of a 400 mM NaOH solution you dissolve 1.6 g of NaOH in 80ml of water and fill up to 100ml in a appropriate messuring cylinder.&lt;/p&gt;&#xA;" OwnerUserId="8598" LastEditorUserId="1320" LastEditDate="2014-09-17T18:09:32.230" LastActivityDate="2014-09-17T18:09:32.230" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21407" PostTypeId="1" AcceptedAnswerId="21409" CreationDate="2014-09-17T15:32:44.943" Score="3" ViewCount="1472" Body="&lt;p&gt;During the process of plasmid purification and quantification, which step is the most critical to the success of the process?&lt;/p&gt;&#xA;" OwnerUserId="8991" LastActivityDate="2018-04-24T04:23:01.390" Title="What is the most critical step of plasmid purification?" Tags="&lt;plasmids&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21408" PostTypeId="1" AcceptedAnswerId="21418" CreationDate="2014-09-17T15:35:18.740" Score="1" ViewCount="79" Body="&lt;p&gt;In PDB file, SEQRES represent the aminoacids but some pdb file present the &quot;GLC&quot; and some other.&#xA;for example&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;SEQRES   1 A   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC          &#xA;SEQRES   2 A   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC          &#xA;SEQRES   1 B   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC          &#xA;SEQRES   2 B   26  GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC GLC       &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;In that PDB ID: 1C58&lt;br&gt;&#xA;What are this and What are represent the SEQRES?&lt;/p&gt;&#xA;" OwnerUserId="9132" LastEditorUserId="9132" LastEditDate="2018-05-31T09:02:05.550" LastActivityDate="2018-05-31T09:02:05.550" Title="PDB file SEQRES have different data?" Tags="&lt;bioinformatics&gt;&lt;pdb&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="21409" PostTypeId="2" ParentId="21407" CreationDate="2014-09-17T15:52:04.610" Score="4" Body="&lt;p&gt;There are a few critical steps (which sounds horrible if written together, but the method per se is robust and usually without problems):&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Resuspension of the pellet: Make sure it is really resuspended and not floating around as a big blob. If it is not resuspended properly your yields will go down dramatically.&lt;/li&gt;&#xA;&lt;li&gt;NaOH/SDS-Lysis: Don't lyse for too long as you may end up with low quality DNA. This denatures the plasmid and makes it often useless for subsequent enzymatic reactions.&lt;/li&gt;&#xA;&lt;li&gt;Mixing: Don't mix too harsh once you lyse the cells, otherwise you may break up genomic DNA of the bacteria which subsequently stays in solution and is not precipitated during neutralization.&lt;/li&gt;&#xA;&lt;li&gt;Neutralization: Make sure you mix good here (by inverting the tubes 4-6 times) but not too harsh. It is critical to neutralize the whole lysate, otherwise proteins may stay in solution.&lt;/li&gt;&#xA;&lt;li&gt;Drying: Overdrying of pellets can cause problems when you try to dissolve them again.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="4747" LastEditDate="2014-09-17T16:01:40.893" LastActivityDate="2014-09-17T16:01:40.893" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21410" PostTypeId="1" AcceptedAnswerId="23679" CreationDate="2014-09-17T15:57:01.840" Score="5" ViewCount="821" Body="&lt;p&gt;How much time is needed for the fermentation to acetic acid production cycle, and the conversion of apple vinegar in a sealed container incubated at 37 °C? &#xA;Should be in the fully closed?&#xA;What is right yeast?&#xA;I do it with powder, grated apple in a plastic soda bottle and I add a few peas and a slice of bread. I am waiting for make that. &#xA;If you have a better idea on what to do to get a good apple cider vinegar produce in my own house.&lt;/p&gt;&#xA;" OwnerUserId="9101" LastEditorUserId="5144" LastEditDate="2014-11-03T22:16:33.860" LastActivityDate="2014-11-03T22:42:11.227" Title="Fermentation to acetic acid" Tags="&lt;biochemistry&gt;&lt;microbiology&gt;&lt;food&gt;&lt;cellular-respiration&gt;&lt;fermentation&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21411" PostTypeId="2" ParentId="21404" CreationDate="2014-09-17T16:34:22.377" Score="3" Body="&lt;p&gt;I think it's possible with &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK179288/&quot; rel=&quot;nofollow&quot;&gt;Entrez Direct&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You'd start with something like:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;esearch -db pubmed -query &quot;atp6&quot;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;And then pipe that to maybe &lt;code&gt;efetch -format&lt;/code&gt; ?? and then continue with gnu coreutils. It might be that only abstracts are available as text, in this case, you'd have to extract e.g. pubmed ids and then come up with a way to batch fetch those somehow..&lt;/p&gt;&#xA;" OwnerUserId="5784" LastEditorUserId="5784" LastEditDate="2014-09-18T06:51:43.590" LastActivityDate="2014-09-18T06:51:43.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21412" PostTypeId="1" CreationDate="2014-09-17T16:45:31.473" Score="1" ViewCount="828" Body="&lt;p&gt;I am having trouble understanding what is the source of band &quot;2&quot; in the following gel-electrophoresis:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ghyPg.jpg&quot; alt=&quot;Gel&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this experiment, we took an E.coli transformant colony and ran its nucleic acids in the gel, after adding a restriction enzyme which cuts the recombinant plasmid molecule into two corresponding bands (&quot;3&quot; and &quot;5&quot; [&quot;5&quot; is very weak in the scanned version, but is well seen in the &quot;hard copy&quot; )  . I know the first line (&quot;1&quot;) corresponds to possible genomic DNA we took from untransformed bacteria, and that the fourth line (&quot;4&quot;) corresponds to a plasmid molecule without an insert. 6 is also well understood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is- &#xA;What is the source of band &quot;2&quot; which contains more base pairs than any of the parts of the plasmid and its insert , and in particular more base pairs than the insert? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;WIll someone please help me understand this ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance&lt;/p&gt;&#xA;" OwnerUserId="9375" LastActivityDate="2014-09-17T16:45:31.473" Title="An unknown band appearing in my gel electrophoresis" Tags="&lt;genetics&gt;&lt;gel-electrophoresis&gt;" AnswerCount="0" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="21414" PostTypeId="1" CreationDate="2014-09-17T17:36:09.073" Score="2" ViewCount="25" Body="&lt;p&gt;I have 16 gene sequences that I am interested in their detection in clinical samples. I already measured their RNA levels by using RT-qPCR technique and their benefit has already been proven to help in diagnosis of clinical cases. Now I want to take this gene expression profiling into another level of automation. The first thing came to my mind is the microrray chips. I don't have much experience in micrarrary, I want to have a custom chip containing these 16 genes in question. These are 13 target human genes and 3 reference genes (housekeeping genes) for normalization. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;br&gt;&#xA;- is it possible to have this custom chip?&lt;br&gt;&#xA;- How can I get such a custom microarray chip?&lt;br&gt;&#xA;- What is needed to automate this process at a production level?&lt;/p&gt;&#xA;" OwnerUserId="3320" LastActivityDate="2014-09-17T17:36:09.073" Title="How to automate this custom gene expression microarray chip?" Tags="&lt;gene-expression&gt;&lt;mrna&gt;&lt;microarray&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21415" PostTypeId="1" AcceptedAnswerId="21416" CreationDate="2014-09-17T17:46:52.360" Score="16" ViewCount="2957" Body="&lt;p&gt;Forgive me if this is a silly question. I can't understand the basics. Why doesn't the cell membrane just break apart? What's keeping the layers in the phospholipid bilayer together? I know that the membrane is embedded with proteins and lipids, but I still can't wrap my head around the &quot;why&quot;. Are the hydrophobic interactions in the middle &quot;stronger&quot; than the hydrophilic interactions on the outside? What's keeping the individual phosphate heads together instead of, say, one of them just drifting away due to a nearby water molecule?&lt;/p&gt;&#xA;" OwnerUserId="4557" LastEditorUserId="19099" LastEditDate="2016-06-11T10:00:26.347" LastActivityDate="2017-09-20T16:09:53.910" Title="Why doesn't the cell membrane just...break apart?" Tags="&lt;biophysics&gt;&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21416" PostTypeId="2" ParentId="21415" CreationDate="2014-09-17T18:03:15.017" Score="17" Body="&lt;p&gt;The membrane bilayer is held together by hydrophobic forces. This is an entropy driven process. When a greasy or hydrophobic molecule is suspended in water, the water molecules form an organized &quot;cage&quot; around the hydrophobic molecule. When two hydrophobic molecules come into contact, they force the water between them out. This increases the entropy because the freed waters don't need to be organized into the cage. Lipid bilayers have many many many hydrophobic lipids that squeeze out a lot of water and greatly increase entropy. The polar phosphates allow the water to interact with the surface of the membrane, without a polar head group the lipids would form a spherical blob instead of a membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Read &lt;a href=&quot;http://en.wikipedia.org/wiki/Entropic_force#Hydrophobic_force&quot;&gt;this section on wikipedia&lt;/a&gt; for more.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-09-17T18:03:15.017" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21417" PostTypeId="2" ParentId="21404" CreationDate="2014-09-17T18:03:21.977" Score="6" Body="&lt;p&gt;Below is a Python script that might help you to get started  (apologies if it fails the Pythonic test - it works!). It uses the Entrez part of the &lt;a href=&quot;http://biopython.org/wiki/Main_Page&quot;&gt;Biopython library&lt;/a&gt;. The script sets up a query, in this case &lt;em&gt;yeast AND Saccharomyces&lt;/em&gt; against the pmc database. Also note that this script uses the 2 step process that NCBI likes you to use - the first part of the fetchByQuery function gets a set of results then the second part uses those results to actually obtain the data. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The output is an xml file which you get to parse with your favourite tools. In your case you will need to get out the text sections and do your token analysis. If you use Python for that I recommend the &lt;a href=&quot;http://www.nltk.org&quot;&gt;Natural Language Toolkit (NLTK)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your case you could just set up search terms as a Python list and loop through writing each dataset to a file named from the search term.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;from Bio import Entrez&#xA;&#xA;import urllib &#xA;import urllib2&#xA;import sys&#xA;&#xA;def fetchByQuery(query,days):&#xA;    Entrez.email = &quot;xxx&quot; # you must give NCBI an email address&#xA;    searchHandle=Entrez.esearch(db=&quot;pmc&quot;, reldate=days, term=query, usehistory=&quot;y&quot;)&#xA;    searchResults=Entrez.read(searchHandle)&#xA;    searchHandle.close()&#xA;    webEnv=searchResults[&quot;WebEnv&quot;]&#xA;    queryKey=searchResults[&quot;QueryKey&quot;]&#xA;    batchSize=10&#xA;    try:&#xA;        fetchHandle = Entrez.efetch(db=&quot;pmc&quot;, retmax=100, retmode=&quot;xml&quot;, webenv=webEnv, query_key=queryKey)&#xA;        data=fetchHandle.read()&#xA;        fetchHandle.close()&#xA;        return data&#xA;    except:&#xA;        return None&#xA;&#xA;days=100 #looking for papers in the last 100 days&#xA;termList=[&quot;yeast&quot;,&quot;Saccharomyces&quot;] &#xA;&#xA;query=&quot; AND &quot;.join(termList)&#xA;xml_data=fetchByQuery(query,days)&#xA;if xml_data==None: &#xA;    print 80*&quot;*&quot;+&quot;\n&quot;&#xA;    print &quot;This search returned no hits&quot;&#xA;&#xA;else:&#xA;    f=open(&quot;pmcXml.txt&quot; ,&quot;w&quot;)&#xA;    f.write(xml_data)&#xA;    f.close()&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-09-17T18:03:21.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21418" PostTypeId="2" ParentId="21408" CreationDate="2014-09-17T18:25:21.133" Score="3" Body="&lt;p&gt;The pdb file that you mention is entitled:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;V-Amylose at atomic resolution: X-ray structure of a cycloamylose with 26 glucose residues (cyclomaltohexaicosaose).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, it isn't a protein at all, it is a circular oligosaccharide consisting of 26 glucose (GLC) residues. I imagine that the usual fields in the pdb file have been fudged to accommodate this.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-09-17T18:25:21.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21419" PostTypeId="1" CreationDate="2014-09-17T19:00:51.490" Score="2" ViewCount="63" Body="&lt;p&gt;If an organism with multiple nuclei, such as the slime mold Physarum polycephalum, was to be exposed to a mutagen, such as 5-bromouracil, what would be the effect (besides death)? Especially if multiple nuclei were effected differently by the exposure.&lt;/p&gt;&#xA;" OwnerUserId="9378" LastActivityDate="2014-09-17T19:00:51.490" Title="Question about mutation of multiple nuclei?" Tags="&lt;molecular-genetics&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21420" PostTypeId="1" CreationDate="2014-09-17T19:45:32.683" Score="8" ViewCount="237" Body="&lt;p&gt;I've been looking for help topics about methanol in metabolism. Specifically, I wish to know what is a common dietary component that generates methanol following metabolism and comment on its toxicity?  I cannot seem to find any relevant data and i'm seeking to know if anyone here has any experience and knowledge of this.&lt;/p&gt;&#xA;" OwnerUserId="9001" LastEditorUserId="16299" LastEditDate="2015-12-31T20:20:54.800" LastActivityDate="2016-03-05T22:15:16.463" Title="Is there a metabolic pathway that generates methanol?" Tags="&lt;molecular-biology&gt;&lt;metabolism&gt;&lt;toxicology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21421" PostTypeId="1" CreationDate="2014-09-17T19:54:28.153" Score="1" ViewCount="61" Body="&lt;p&gt;So I posted another question with respects to methanol and aspartame in metabolism with respects to toxicity.  So another question I have is &quot;Why is aspartame used as a dietary component to generate methanol following metabolism?&quot;  This is a topic of discussion in my thermonuclear pharmaceuticals class at my institution, and more or less it's also part of an active assignment that we're expected to cover for a weekly discussion which is no graded; otherwise I wouldn't seek free advice on this.  As much as I read in my book it does not go into detail and I am curious if anyone out there has any advice on this or perhaps you could point me towards relevant articles?&lt;/p&gt;&#xA;" OwnerUserId="9001" LastActivityDate="2014-09-17T21:45:34.150" Title="aspartame in relation to generating methanol" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21422" PostTypeId="1" AcceptedAnswerId="21436" CreationDate="2014-09-17T20:52:31.603" Score="5" ViewCount="669" Body="&lt;p&gt;I recently came across an &lt;a href=&quot;http://www.nytimes.com/2012/02/21/science/tipsy-fruit-flies-on-a-mission-to-kill-parasites.html?_r=0&quot;&gt;article saying that fruit flies use alcohol to deter parasites&lt;/a&gt;. The researcher was quoted as saying there have not been any studies on the effect of human alcohol consumption on parasites. Is there any research being done on this? Another related question I have is whether the fruit flies can tolerate higher alcohol concentrations than mammals/humans.&lt;/p&gt;&#xA;" OwnerUserId="37" LastActivityDate="2014-09-18T09:11:47.213" Title="Effect of alcohol on parasites" Tags="&lt;parasitology&gt;&lt;alcohol&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21423" PostTypeId="2" ParentId="21421" CreationDate="2014-09-17T21:45:34.150" Score="1" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AuwAK.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aspartame is the methyl ester of the aspartic acid phenylalanine dipeptide. Esters are very easily hydrolyzed by esterase enzymes in the body. This will create an acid and an alcohol. In this case the alcohol is methanol, because it was generated from the methyl group. I'm not familiar with why thermonuclear pharmaceuticals would be concerned with aspartame, generally thermoncuclear refers to nuclear fusion, and even radioactive drugs don't undergo fusion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, some people are afraid that aspartame is toxic because the methanol it generates is toxic. This fear is unrealistic because the amount of methanol it takes to cause blindness is about 10mL, and the smallest amount needed to kill someone is about 30mL &lt;a href=&quot;http://en.wikipedia.org/wiki/Methanol#Toxicity&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;. To generate this much pure methanol from aspartame would require you to eat an impossible amount of aspartame.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-09-17T21:45:34.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21424" PostTypeId="1" CreationDate="2014-09-18T00:03:43.887" Score="1" ViewCount="39" Body="&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How (quantitatively speaking) does temperature influences rate of turnover of transcription factors?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which protein?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I am not looking for any accurate number I am talking about an &quot;average&quot; transcription factor. I leave to you the choice of answering this question with some very accurate example (Transcription factor GTF II A for example) or with some broad observation on how temperature influences protein turnover.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The organism I'd like to model is a typical unicellular eukaryote such as a yeast for example that lives at &quot;standard&quot; range of temperature (between 5°C and 35°C roughly speaking).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, I am not interested in considering a transcription factor that is directly involved in some response to a change in environmental temperature. I am interested in transcription factors which are involved in developmental pathways that have nothing to do with reaction of the body to temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for a referenced answer $\ddot \smile$&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-09-18T00:03:43.887" Title="How does Temperature influences the rate of protein turnover?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;proteins&gt;&lt;molecular-genetics&gt;&lt;transcription&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-12-02T14:22:57.300" ContentLicense="CC BY-SA 3.0" />
  <row Id="21425" PostTypeId="1" AcceptedAnswerId="21426" CreationDate="2014-09-18T02:42:51.113" Score="8" ViewCount="27134" Body="&lt;p&gt;I often hear or read this statement:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;It's not a human, it's a fetus.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In other words, some think a fetus is non-human until a certain point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And another similar statement:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The fetus isn't alive until 26 weeks of gestation.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So some think the fetus is not actually &quot;alive&quot; until a certain point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does biology have to say about these two statements?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I encounter these statements often in discussions about abortion, but that issue, and other similar philosophical issues, are outside this question. &lt;strong&gt;I'm wondering strictly from a scientific/biological standpoint: are these statements true?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the fetus in a human mother non-human until a certain point?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the fetus not classify as &quot;alive&quot; until a certain point?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The people I encountered truly believed these statements (3 of the 4 in mind also claimed science was on their side), so it's not as if the question has no merit. I assumed that in the realm of science and biology, there must be a convincing and sure answer.&lt;/p&gt;&#xA;" OwnerUserId="9385" LastEditorUserId="72" LastEditDate="2014-09-18T22:15:45.923" LastActivityDate="2015-05-01T19:11:53.870" Title="Do biological facts determine when a human fetus is considered alive and human?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="19" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21426" PostTypeId="2" ParentId="21425" CreationDate="2014-09-18T03:31:19.273" Score="15" Body="&lt;p&gt;&lt;a href=&quot;http://www.merriam-webster.com/medical/life&quot;&gt;&lt;em&gt;Life&lt;/em&gt;&lt;/a&gt; is generally distinguished from non-life by &lt;a href=&quot;http://en.wikipedia.org/wiki/Metabolism&quot;&gt;metabolism&lt;/a&gt; and growth. As such, &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/002398.htm&quot;&gt;a fetus is alive&lt;/a&gt;. The reference to &quot;not...until 26 weeks gestation&quot; that you've heard likely refers to &lt;a href=&quot;http://www.merriam-webster.com/dictionary/viable&quot;&gt;&lt;em&gt;viability&lt;/em&gt;&lt;/a&gt;.* With the most aggressive medical care, &lt;a href=&quot;http://en.wikipedia.org/wiki/Viability_(fetal)&quot;&gt;this is the approximate age&lt;/a&gt; when a fetus may be able to survive outside the womb. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term &lt;a href=&quot;http://en.wiktionary.org/wiki/viable&quot;&gt;&lt;em&gt;human&lt;/em&gt;&lt;/a&gt; from a biologic perspective is a species label.** Given that a fetus is genetically indistinguishable (in broad strokes) from a post-natal human, I think it would be hard to argue that it is anything other than human.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Summary: Yes, a human fetus is both &lt;em&gt;alive&lt;/em&gt; and &lt;em&gt;human&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;*Note that this use of the word &lt;em&gt;viable&lt;/em&gt; is standard but deviates somewhat from &lt;a href=&quot;http://en.wiktionary.org/wiki/viable&quot;&gt;the etymology of the word&lt;/a&gt;.&lt;br&gt;&#xA;**I'm ignoring here other ancient species (&lt;em&gt;homo-&lt;/em&gt;) which may be considered &lt;em&gt;human&lt;/em&gt; but are irrelevant to the question. &#xA;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-09-18T09:25:23.800" LastActivityDate="2014-09-18T09:25:23.800" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="21427" PostTypeId="1" CreationDate="2014-09-18T03:54:37.650" Score="7" ViewCount="302" Body="&lt;p&gt;The immune system has a great role in our body. When foreign particles&#xA;enter our body, the immune system can recognize and start&#xA;defense mechanisms such as the complement system and others. But when sperm enters&#xA;into the female organism, why does her immune system not recognize this?&#xA;In that time which kind of mechanism is active in the woman's body?&lt;/p&gt;&#xA;" OwnerUserId="9132" LastEditorUserId="9132" LastEditDate="2017-06-15T08:57:49.803" LastActivityDate="2017-06-15T08:57:49.803" Title="Why can't the immune system start at the mating time?" Tags="&lt;human-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21428" PostTypeId="1" CreationDate="2014-09-18T04:50:28.097" Score="0" ViewCount="171" Body="&lt;p&gt;Most people with a strong interest in biology will have heard of Kanzi the Bonobo, the ape that has the wherewithal to collect fuel for a campfire and play pac-man.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But is it conceivable to influence the course of their evolution so that it becomes more likely they gain the intelligence to support a civilization in the distant future?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's face it: it's easy to imagine that Bonobos are looking &lt;a href=&quot;http://io9.com/5794988/are-humans-more-like-chimps-or-bonobos-the-correct-answer-is-changing&quot; rel=&quot;nofollow&quot;&gt;superficially like early human ancestors&lt;/a&gt;.  They have been forced to become more peaceable and social because they are polyamourous (which is why the &lt;a href=&quot;http://www.thedailysteak.com/content/secrets-phallus-why-penis-shaped&quot; rel=&quot;nofollow&quot;&gt;human phallus&lt;/a&gt; is shaped the way it is).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we are willing to genetically modify them, we would have to do so so heavily the depend on the genetic modifications, or they might just get bred out again - &lt;a href=&quot;http://www.huffingtonpost.com/2013/05/22/people-getting-dumber-human-intelligence-victoria-era_n_3293846.html&quot; rel=&quot;nofollow&quot;&gt;intelligence may be delicate&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion, is it conceivable to &quot;enlighten&quot; some groups of primates and send them into the wild, in the hopes they (much) later evolve intelligence?  Their existence would serve as an &quot;insurance policy&quot; on intelligent life in the not unlikely event we destroy ourselves.&lt;/p&gt;&#xA;" OwnerUserId="8866" LastActivityDate="2014-09-18T08:12:23.853" Title="Can we influence evolution by teaching primates to control fire? Should we?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-01-05T13:58:53.683" ContentLicense="CC BY-SA 3.0" />
  <row Id="21429" PostTypeId="2" ParentId="21425" CreationDate="2014-09-18T06:15:57.507" Score="9" Body="&lt;p&gt;The fetus is certainly &quot;alive&quot; from the very beginning, since conception. The second comment hence does not make sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding whether it is &quot;human&quot; or not, that would depend on the definition of &quot;human&quot;. It seems to be more a philosophical than biological question. From the biology point of view it all goes down to this, a fetus in a human womb is a &quot;human fetus&quot;, certainly not a &quot;mouse fetus&quot;. Fetus only indicates a time period in the development of a mammal (before being born). Another question is whether the fetus has attributes of grown up humans, like the ability to talk. But then, a newborn does not have many of those attributes yet it is considered a human.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastActivityDate="2014-09-18T06:15:57.507" CommentCount="16" ContentLicense="CC BY-SA 3.0" />
  <row Id="21430" PostTypeId="2" ParentId="19873" CreationDate="2014-09-18T06:19:39.803" Score="4" Body="&lt;p&gt;Yes it is. The easiest plant to transform would be Arabidopsis, which can be transformed by agrobacterium using the floral dip method. The process would be as follows:&#xA;1. Design a gene sequence you wish to insert into the plant&#xA;2. Synthesize (or otherwise acquire the DNA)&#xA;3. Insert the DNA into your agrobacterium, at home you would use a cold snap transformation process described here: &lt;a href=&quot;https://www.youtube.com/watch?v=PvkfIECvyqs&quot; rel=&quot;nofollow&quot;&gt;https://www.youtube.com/watch?v=PvkfIECvyqs&lt;/a&gt; This can be done at home using a dry ice bath.&#xA;4. Then use the floral dip method to insert the dna into the plant. This involves growing a plant to just the right age when it is flowering and dipping the Arabidopsis flowers into a solution of the agrobacterium.&#xA;5. Then grow the flowers to seed and grow the seeds on a suitable select able marker (which you designed into your DNA plasmid).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The specific experimental conditions needed to do all this are too long for this answer, but you can look them up online as all the procedures are standard.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants which result from this process would not be legal to release into the wild due to USDA regulations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Engineering other plants, depending on the species, can be more complex but could possibly also done at home. There are even designs online for an open source gene gun if you didn't want to use agrobacterium.&lt;/p&gt;&#xA;" OwnerUserId="9381" LastActivityDate="2014-09-18T06:19:39.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21431" PostTypeId="1" CreationDate="2014-09-18T06:38:20.040" Score="5" ViewCount="123" Body="&lt;p&gt;I heard and read telomere 'health' or 'length' ( if that's right ) has alot to do with cell 'health'. If telomere 'abilities' are 'restored' to a 'healthier' status then the cell it is in functions as though it were 'younger'.  I was wondering since cancer cells grow without limit and 'older' cells or unstable cells grow with less ferver do cancer cells have functioning telomeres within them and would they somehow be alot more 'robust' then telomeres in normal cells? If this is true could telomeres from cancer cells somehow revitalize the telomeres in normal cells? &lt;/p&gt;&#xA;" OwnerUserId="6195" LastActivityDate="2014-12-17T19:44:27.860" Title="Regarding cellular self-destruction" Tags="&lt;cell-biology&gt;&lt;cancer&gt;&lt;telomere&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21432" PostTypeId="2" ParentId="20321" CreationDate="2014-09-18T07:06:27.690" Score="2" Body="&lt;p&gt;You might be interested in reading the article &quot;Machine learning in cell biology – teaching computers to recognize phenotypes&quot; (&lt;a href=&quot;http://jcs.biologists.org/content/126/24/5529.long&quot; rel=&quot;nofollow&quot;&gt;http://jcs.biologists.org/content/126/24/5529.long&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="9389" LastActivityDate="2014-09-18T07:06:27.690" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21433" PostTypeId="2" ParentId="21427" CreationDate="2014-09-18T07:43:35.503" Score="5" Body="&lt;p&gt;These questions are not completely easy to answer, since the immune reaction in this area is not completely understood. There are two different mechanisms  which play a role here: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Semen is immunogenic and can cause the generation of specific antibodies against it in men and women. The main question here is if the presence of semen in the females reproductive tract is the consequence of a suppressed immune reaction or because it is not recognized. There are indications for both possibilities but I think the first is a bit stronger. The mucus from the vagina is immunosuppressive as well as the seminal fluid, which contains prostaglandins which have the same effect. Have a look at this article for some more background: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://molehr.oxfordjournals.org/content/4/4/309.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;Sperm survival in the female reproductive tract: presence of&#xA;immunosuppression or absence of recognition?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For the situation in the uterus between mother and fetus the situation is better understood. This is the so called &lt;a href=&quot;http://en.wikipedia.org/wiki/Immune_privilege&quot; rel=&quot;noreferrer&quot;&gt;immune privilege&lt;/a&gt; of some tissues (among them are the uterus, testes and the eye) where immune reactions are suppressed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The placenta forms an immunologic barrier which seperates mother and fetus. This is done by secreting immunomodulary substances and also by the subpression of some T cell subpopulations. For more details see &lt;a href=&quot;http://en.wikipedia.org/wiki/Immune_tolerance_in_pregnancy&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;. This is a highly developed system to protect the developing fetus (which is foreign) from the mothers immune system.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-18T07:43:35.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21434" PostTypeId="2" ParentId="20321" CreationDate="2014-09-18T07:47:45.820" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;RE:&lt;/strong&gt; What kind of software you always wanted for light microscopic&#xA;  research, but did not know how to build?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I research fruit flies and in this field (and many other insect ecology model systems like beetles, moths, butterflies) we use a lot of visually scored data, e.g. body size, wing size, wing morphology, eye colours, bristle numbers, genital morphology, sex comb morphology... the list is huge! One program used is &lt;a href=&quot;https://www.youtube.com/watch?v=Nq-OIGKzdLk&quot; rel=&quot;nofollow noreferrer&quot;&gt;WingMachine&lt;/a&gt; - though the &lt;a href=&quot;http://bio.fsu.edu/~dhoule/Welcome2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;link to the software seems to be broken&lt;/a&gt; - which can measure morphology aspects of a fly wing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something I'd like to be able to do is put a vial of food under a scope and have it quickly count the number of eggs on the surface of the food. &lt;a href=&quot;https://biology.stackexchange.com/questions/7927/software-for-counting-fly-eggs&quot;&gt;I asked a question about it a while back&lt;/a&gt;.. This would be very useful, many labs have to count eggs (to make the number of eggs constant in each vial, variation here can have serious effects on the adult fly so control is important in ecology studies) and it is a slow, difficult and highly inaccurate, particularly variable between people. If there was some way of putting the vial under the scope, hitting a button and getting an approximation of the number it would be great!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A colleague counts dead beetles at the moment, I'm sure he'd appreciate a similar kind of program where he could image and have the software count automatically. I think both of these problems would be easy to solve with very similar software. Making software that is easy to &quot;teach&quot; how to recognize individuals is the key.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A slightly more complex bit of machine learning might be getting it to count different phenotypes in one image. Fitness assays in flies often use a wild type fly with dark bodied (ebony) competitors, the body of the wild type is comparatively more yellow. The fitness of the focal wild type fly is then the number of wild type offspring among the total (the dark body phenotype is recessive, therefore when the focal wild type mates with an ebony it produces wild type flies, if two ebonies mate we get a dark body offspring). Here the machine would have to be able to tell the difference and count both.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I'll attach a proper picture from under the scope later, the picture in my previous question was taken with a digital camera, not via a scope but it gives an idea of what it looks like.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-09-18T07:55:00.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21435" PostTypeId="2" ParentId="21428" CreationDate="2014-09-18T08:12:23.853" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is it conceivable to influence the course of their evolution so that it becomes more likely they gain the intelligence to support a civilization in the distant future?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No, I don't think so, based on what is known about evolution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your idea is in keeping with the opening of Kubrick's &lt;em&gt;2001: A Space Odessey&lt;/em&gt;, where the monolith inspires one of the primates to see a femur as a weapon. He picks it up, hits an opponent with it, and the idea catches on within his group; the implication is that this inspired male's (female's?) group goes on to domination and are the progenitors of the human race.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In real life, that's not how intelligence is passed on. You can teach a gifted bonobo how to build a fire, but if he's not into roasted meat, or really cold, or trying to scare away predators (or if he doesn't realize that's what fire is good for), all you have is one bonobo who can start fires. It doesn't influence his genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To actually influence evolution of bonobos, I imagine it would look like this: You capture 4/5ths of all the bonobos in the world (leave the 1/5 for genetic pool variation). You test them for basics of quick-wittedness. Kill all the bonobos that fall below a certain threshold, and release. Repeat several generations later. Keep doing so for 50 cycles. What you will have are a race of quick-witted bonobos - &lt;em&gt;maybe&lt;/em&gt;. Because if the quick-wittedness you selected for doesn't provide them with a survival advantage, it (and they) will die out. What if the smarter bonobos all want to be alphas, and all that fun cuddling and sex-as-peacekeeping were to disappear? They might not survive the bonobo-chimpanzee wars, because they won't live in large, peaceful, cooperative groups any more. Maybe you can teach the bonobos to plant crops, assuring a food source. Will they irrigate, too? What would this decrease in roaming mean for pygmies who hunt bonobos for food?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My point is, we can't control evolution very much unless we also control the total environment they live in. That's one way we have been able to have such an impact on a rather extraordinary species: dogs. But in the end, a dog, whether it's a sheep-herding or rat-catching or boar-hunting or bull-baiting or duck-fetching breed, is still only a dog. Invaluable helpers, but after all that selective breeding, they're just dogs. The &lt;a href=&quot;http://www.popsci.com/science/article/2013-07/i-met-worlds-smartest-dog&quot; rel=&quot;nofollow&quot;&gt;smartest dog in the world&lt;/a&gt; still likes to play fetch more than anything in the world. Even eating, if she's anything like my two Border Collies.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-09-18T08:12:23.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21436" PostTypeId="2" ParentId="21422" CreationDate="2014-09-18T08:27:53.793" Score="3" Body="&lt;p&gt;Drosophila is seen as a highly alcohol tolerant species which is mainly dependent on the environment it lives in. So are flies, which are captured in the cellar of a wine yard more tolerant to alcohol than flies which are captured outside (see first reference).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The environment in which the flies grow up and live does not influence the activity of the alcohol dehydrogenase enzyme but seems to influence the expression (amount) of it. The more alcohol is present, the higher the expression is (see reference 2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't seen explicit data on the comparison between humans/mammals and drosophila, but since drosophila is seen as a good model organism to study alcoholism, I would think it is not too different. (see reference 3).&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1213135/&quot; rel=&quot;nofollow&quot;&gt;Micro-differentiation in a Natural Population of DROSOPHILA&lt;br&gt;&#xA;MELANOGASTER to Alcohol in the Environment&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.dgrc.kit.ac.jp/~jdd/class/070302/07030222.pdf&quot; rel=&quot;nofollow&quot;&gt;Alcohol tolerance, ADH activity, and ecological niche of Drosophila&#xA;species&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://ac.els-cdn.com/S089662730000101X/1-s2.0-S089662730000101X-main.pdf?_tid=cb33fd56-3f0a-11e4-9a20-00000aacb35d&amp;amp;acdnat=1411027812_71d2565b3e3a9001f111a3d575407b62&quot; rel=&quot;nofollow&quot;&gt;Functional Ethanol Tolerance in Drosophila&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="9179" LastEditDate="2014-09-18T09:11:47.213" LastActivityDate="2014-09-18T09:11:47.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21437" PostTypeId="1" AcceptedAnswerId="21438" CreationDate="2014-09-18T08:58:08.680" Score="2" ViewCount="33" Body="&lt;p&gt;&lt;a href=&quot;http://www.sdsc.edu/pb/edu/pharm201/11/c35.pdf&quot; rel=&quot;nofollow&quot;&gt;B-CELL EPITOPE PREDICTION&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding this article:   &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&quot;Such a molecule can be synthesized or, in case of a protein, its&#xA;gene can be cloned into an expression vector.&quot;----- is a particular&#xA;line in this article. What does expression vector mean here??&lt;/li&gt;&#xA;&lt;li&gt;&quot;antipeptide antibodies&quot;---- what are these?&lt;/li&gt;&#xA;&lt;li&gt;&quot;immunogenic peptides&quot;----these are basically epitopes, am I right??&lt;br&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="5144" LastEditDate="2014-09-18T09:06:25.000" LastActivityDate="2014-09-18T09:11:25.973" Title="epitope prediction/ mapping" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21438" PostTypeId="2" ParentId="21437" CreationDate="2014-09-18T09:11:25.973" Score="3" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;An &lt;a href=&quot;http://en.wikipedia.org/wiki/Expression_vector&quot; rel=&quot;nofollow&quot;&gt;expression vector&lt;/a&gt; is a (usually circular) piece of DNA which is able to replicate inside a (bacterial) cell independently of the genome. Vectors can be transferred between bacteria and can express proteins from their own DNA sequence. They are used to express proteins inside of bacterial cells which can subsequently be purified. In this case the sequence for an immunogenic peptide is cloned into a vector and expressed in bacteria.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;These are antibodies which are directed against a certain peptide. This is one technique of generating these antibodies. Making a (synthetic) peptide and then immunize animals against it. Then you can purify the antibodies from the serum of the animal.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Yes. You make short peptides of 8-12 amino acids (which is the length that the antibodies binds to) and use them for immunization.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-18T09:11:25.973" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21439" PostTypeId="1" AcceptedAnswerId="21442" CreationDate="2014-09-18T11:58:40.373" Score="7" ViewCount="3790" Body="&lt;p&gt;Exocytotic vesicles take away membrane proteins and glycocalyx on the cell's plasma membrane surface. When those vesicles are released into the interstitial fluid and wherever else, where do they go?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do they stick to the vesicle everywhere? Or do they get removed from the vesicle? If the vesicle fuses into another cell, do those proteins and carbohydrate attachments stick to the new cell?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2014-09-18T13:00:30.383" Title="Where do lost membrane proteins go after exocytosis?" Tags="&lt;proteins&gt;&lt;cell-biology&gt;&lt;carbohydrates&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21440" PostTypeId="1" CreationDate="2014-09-18T12:00:34.683" Score="13" ViewCount="38431" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/15220/rate-of-cell-division-in-humans&quot;&gt;This question&lt;/a&gt; suggests that we have, on average, 50-70 billion cell divisions per day. I just read that cancer cells divide more often and are therefore more prone to radiation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering, for a specific type of cancer, how fast cancer do cells divide (approximately) compared to normal cells. Does the ratio of cancer mitosis rate to the normal cell mitosis rate varies a lot?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I checked &lt;a href=&quot;http://bionumbers.hms.harvard.edu/search.aspx?log=y&amp;amp;task=searchbytrmorg&amp;amp;trm=cancer%20mitosis%20rate&quot; rel=&quot;nofollow noreferrer&quot;&gt;bio-numbers&lt;/a&gt; but there's not much data there. &lt;/p&gt;&#xA;" OwnerUserId="6228" LastEditorUserId="19099" LastEditDate="2017-06-29T07:35:33.983" LastActivityDate="2019-05-24T01:36:52.223" Title="How fast do cancer cells divide (compared to normal cells)?" Tags="&lt;cell-biology&gt;&lt;cancer&gt;&lt;mitosis&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21442" PostTypeId="2" ParentId="21439" CreationDate="2014-09-18T13:00:30.383" Score="5" Body="&lt;p&gt;In the process of exocytosis materials which are about to be released are transported in small vesicles to the plasma membrane. The plasma membrane fuses with these vesicles and this sets the substances free on the outside of the cell. See the figure (from &lt;a href=&quot;http://legacy.owensboro.kctcs.edu/gcaplan/bio/notes/BIO%20Notes%20D%20Cell%20Membranes.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;img src=&quot;https://i.stack.imgur.com/39bA6.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other possibility for transport vesicles is that they arrive at their target cell and either fuse with the membrane and release the transported substance into the cell or that they are taken up in another vesicle which is then targeted towards the endosome/lysosome. See the figure (from &lt;a href=&quot;http://jonlieffmd.com/blog/vesicles-transport-information&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oVAIF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It doesn't matter which way is chosen, the membrane of the vesicle is recycled either by integration into another membrane of by going through the lysosome.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-18T13:00:30.383" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21445" PostTypeId="1" CreationDate="2014-09-18T13:24:14.053" Score="0" ViewCount="44" Body="&lt;p&gt;Suppose an organism has 8 chromosomes.  When the female and male organisms mate,  how many chromosomes will the mother contribute to the offspring? Why?&lt;/p&gt;&#xA;" OwnerUserId="9396" LastActivityDate="2014-09-18T14:05:53.093" Title="Meiosis I or II" Tags="&lt;reproduction&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2014-09-18T14:45:47.250" ContentLicense="CC BY-SA 3.0" />
  <row Id="21446" PostTypeId="1" CreationDate="2014-09-18T13:56:46.227" Score="1" ViewCount="465" Body="&lt;p&gt;The book by Dr Harvey Karp (MD) &lt;em&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0553381466&quot; rel=&quot;nofollow&quot;&gt;The Happiest Baby on the Block&lt;/a&gt;&lt;/em&gt; proposes that the duration of human gestation has evolved as a tradeoff between cranial size and development of the infant.  He hypothesizes that from an overall developmental perspective human babies are all premature and would benefit from additional time in their mother's womb; however, because humans have such big brains, and therefore our babies have big brains, the infant needs to be born earlier than would be developmentally ideal so that it doesn't get stuck in the birth canal.  The result is babies that have big brains but are highly vulnerable and dependent on their parents until their development progresses further.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I discussed this with some students in class as an example of the use of ideas from human evolutionary ecology and life history theory in the popular press, but with the disclaimer that I had no idea if any of Karp's ideas are backed up by any evolutionary or anthropological data.  Could anyone point me towards literature that support or contradicts Karp's claims?  For example, are human infants more dependent than those of other primates?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[The upshot of Karp's theories are that the best way to have a &quot;happy&quot; newborn is to mimic conditions that it would experience in the womb, such as swaddling.  Works for my child!]&lt;/p&gt;&#xA;" OwnerUserId="1361" LastActivityDate="2014-09-18T18:32:27.280" Title="Evolutionary support for parenting book &quot;The happiest baby on the block&quot;" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;human-anatomy&gt;&lt;life-history&gt;&lt;anthropology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21447" PostTypeId="2" ParentId="21445" CreationDate="2014-09-18T14:05:53.093" Score="1" Body="&lt;p&gt;Both the male and the female would give half of the total number of chromosomes for their species (assuming both cells are normal). So if the organism has a total of 8 chromosomes, the mother and father would each give 4. &lt;/p&gt;&#xA;" OwnerUserId="9378" LastActivityDate="2014-09-18T14:05:53.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21448" PostTypeId="1" CreationDate="2014-09-18T14:19:14.393" Score="1" ViewCount="84" Body="&lt;p&gt;I have tried to make cDNA libraries from FFPE tumor blocks (highly degraded RNA) using the 3' end RNA seq protocol provided by West lab. Here is the link for the same.&#xA;&lt;a href=&quot;http://med.stanford.edu/labs/vanderijn-west/Protocols.html&quot; rel=&quot;nofollow&quot;&gt;http://med.stanford.edu/labs/vanderijn-west/Protocols.html&lt;/a&gt;&#xA;After PCR enrichment, a gel purification step follows. My trouble was, the fragments always gave rise to a smear rather than a band between 200-300 bp. Can anyone provide any suggestions as to why this may be happening?&#xA;Thank You&lt;/p&gt;&#xA;" OwnerUserId="9397" LastActivityDate="2014-09-18T21:26:46.437" Title="3 end RNA seq library construction" Tags="&lt;rna-sequencing&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21451" PostTypeId="2" ParentId="21446" CreationDate="2014-09-18T18:32:27.280" Score="1" Body="&lt;p&gt;How many more weeks in utero does Karp think would be ideal? I don't know Karp at all, but a quick search indicates he's known for soothing babies by swaddling. Great. My mother swaddled all her infants many decades ago.&lt;/p&gt;&#xA;&lt;p&gt;If he is comparing human neonates to  primate neonates, he's correct. Baby primates are born pretty much knowing how to cling onto the mother with four extremities, necessary because primates are quadripedal, and need their arms to walk as well, meaning baby needs to hold on, aided by opposable toes. (Chimps and gorillas do support the baby with one hand longer, though.&lt;/p&gt;&#xA;&lt;p&gt;But what evolutionary advantage would it serve for our infants to come out grasping? humans are bipedal, meaning we have arms that can be used to carry an infant. If we need our arms, we have the intelligence to fashion slings or carriers.&#xA;The same goes for any ability: sight, motor skills, etc. They don't need to be born with these skills, because they are cared for.&lt;/p&gt;&#xA;&lt;p&gt;Antelopes drop a newborn which is up in minutes and able to see and run. Cats drop a newborn which can wiggle, crawl some, is blind and as helpless as a human.&lt;/p&gt;&#xA;&lt;p&gt;Babies, through evolution, are able to live outside the womb (assuming no complications) without extraordinary maternal assistance from about 36 weeks on. A look at growth charts show steep rises in both cranial size and weight gain.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fZ5gQ.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;But you can see that a baby's head at the 10%ile takes at least six weeks to catch up to a baby the size of one born at 90%ile. Why doesn't that baby just gestate for 6 more weeks?&lt;/p&gt;&#xA;&lt;p&gt;There is much more than head size going on here. There is the placental size, the amount of amniotic fluid, the possibility of meconium aspiration, etc.&lt;/p&gt;&#xA;&lt;p&gt;Stillbirths are twice as common at 42 weeks and 4 times as common at 43 weeks.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Approximately 20% of postterm (41 weeks gestation) fetuses have fetal postmaturity syndrome, with chronic intrauterine growth restriction from uteroplacental insufficiency. These pregnancies are at increased risk of umbilical cord compression from oligohydramnios, [low Apgar scores], intrauterine passage of meconium, and short-term neonatal complications (such as hypoglycemia, seizures, and respiratory insufficiency). ...[T]he 4-fold decrease in the incidence of the meconium aspiration syndrome in the United States from 1990-1998 has been attributed primarily to a reduction in the postterm delivery rate [(induced delivery at 41.5 weeks)]. Postterm pregnancy is also an independent risk factor for neonatal encephalopathy and for death in the first year of life.[17, 18]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Maternal complications and death also increase with post-term deliveries.&lt;/p&gt;&#xA;&lt;p&gt;Are term babies actually evolutionary preemies? I haven't read Dr. Karp's book or heard his reasoning, but it seems superficial to me. Medically, from an infant and maternal standpoint, a 38 week delivery is ideal. Over hundreds of thousands of years, the female uterus and pelvis, and the fetal placenta and amniotic fluid found the most favorable time for delivery into a &lt;em&gt;human environment&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;p&gt;If we gestated for two years, like elephants, yes, our babies would be more capable at birth, but we aren't elephants, and mothers and babies would die.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://emedicine.medscape.com/article/261369-overview&quot; rel=&quot;nofollow noreferrer&quot;&gt;Postterm Pregnancy&lt;/a&gt; (Medscape)&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Elephant#Birthing_and_calves&quot; rel=&quot;nofollow noreferrer&quot;&gt;Elephant birthing and calves&lt;/a&gt; (Wikipedia)&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-18T18:32:27.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21452" PostTypeId="2" ParentId="16837" CreationDate="2014-09-18T20:53:42.517" Score="1" Body="&lt;p&gt;From what I can understand, TOPflash is a luciferase reporter plasmid that contains two sets of 3 copies of the wild-type TCF binding regions. If the canonical Wnt signaling is activated, beta-catenin will translocate to the nucleus to associate with TCF/LEF transcription factors to activate transcription of Wnt target genes. Since this is a luciferase plasmid, you should see an increase in relative luciferase activity when substrate is added. If Wnt signaling is inhibited, you will see loss of luciferase expression. The FOPflash is used as a negative control because the TCF binding regions upstream of the luciferase gene is mutated so even if beta-catenin translocates to the nucleus to activate TCF-mediated transcription, you should not see any luciferase activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="9399" LastActivityDate="2014-09-18T20:53:42.517" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21453" PostTypeId="1" AcceptedAnswerId="21473" CreationDate="2014-09-18T20:59:36.917" Score="8" ViewCount="3010" Body="&lt;p&gt;Fisher's geometric model is still today one of the most important and fundamental model in evolutionary biology but it seems to me that most student in evolutionary biology don't really understand it (and I am one of these students). Such standard models are often found on wikipedia but in this case the wikipedia article (&lt;a href=&quot;http://en.wikipedia.org/wiki/Fisher&amp;#39;s_geometric_model&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) offers nothing more than a simple analogy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.nature.com/nrg/journal/v6/n2/abs/nrg1523.html&quot; rel=&quot;nofollow&quot;&gt;Orr 2005&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fisher's geometric model shows that the probability $P_a(x)$ that a random mutation of a given phenotypic size, $r$, is favorable is $1-\Phi(x)$, where $\Phi$ is the cumulative distribution function of a standard normal random variable is a standardized mutational size, $x=r\frac{\sqrt{n}}{2z}$, where $n$ is the number of characters and $z$ the distance to the optimum.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can you please explain what the Fisher's geometric model and the math behind it (how are these functions calculated)?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-09-22T02:39:56.870" LastActivityDate="2014-09-24T10:29:26.593" Title="Fisher's Geometric Model for Dummies" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;&lt;population-dynamics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21454" PostTypeId="1" AcceptedAnswerId="21469" CreationDate="2014-09-18T21:32:35.757" Score="4" ViewCount="564" Body="&lt;p&gt;Problem&#xA;A transmembrane protein has 1000 aa. The 5th aa is found on the external side of the cell membrane. It interacts with the aqueous environment outside the cell. Amino acid 90 is inside the membrane bilayer. Aa 100-600 are intracellular, and 200-400 make a tight ball with minimal exposure to the aqueous cytoplasm. Amino acid 979 is found on the extracellular side of the protein where it forms a weak ionic bond with Cl-.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a. Can you draw the protein and mark positions of all mentioned aa in it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b. What are the properties of these amino acids?&#xA;￼￼￼￼￼&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I dont necessarily want/need the exact answers to these questions, rather i would like some guidance in what principles i would need to understand and conceptualize to attack this problem. Thanks all !&lt;/p&gt;&#xA;" OwnerUserId="8059" LastActivityDate="2014-09-19T11:40:15.240" Title="Transmembrane Protein Problem" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;experiment&gt;" AnswerCount="2" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="21455" PostTypeId="2" ParentId="21454" CreationDate="2014-09-18T22:30:39.110" Score="2" Body="&lt;p&gt;Membrane proteins are usually drawn as topological digrams with two parallel horizontal lines representing the membrane.  lines as 'extracellular' and below the lines as 'intracellular' for instance, but that is not what is being asked for here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its not clear to me that the number of transmembrane spans are fully described, nor are the boundaries of the transmembane spans.  I think what is being asked for could be a domain diagram of the amino acid chain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Draw a line on graph paper representing the peptide and use a scale to label each point described. For regions draw a box around the peptide line to describe a domain, and label it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think its hard to talk about amino acid properties other than hydrophilic/hydrophobic.  hope this helps?&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-09-18T22:30:39.110" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21456" PostTypeId="1" CreationDate="2014-09-19T04:41:43.277" Score="0" ViewCount="106" Body="&lt;p&gt;If an animal is fertile does it follow that both its parents of the same species (not necessarily the same species of the offspring)? Was it Mayer who said a fertile male and fertile female of two different species, if they 'reproduce' and the offspring survives it won't be fertile. Reproductive isolation I think this is called. So if an animal is fertile then both its parents should be of the same species, right?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastEditorUserId="1320" LastEditDate="2014-09-19T05:48:22.103" LastActivityDate="2014-09-19T05:48:22.103" Title="Regarding inherited fertility in animals" Tags="&lt;evolution&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21457" PostTypeId="2" ParentId="21456" CreationDate="2014-09-19T05:16:43.690" Score="1" Body="&lt;p&gt;No it isn't necessary that the parents should be of the same species. Mules (male donkey X female horse) have been found to be fertile (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3378453?dopt=Abstract&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). The wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Hybrid_(biology)&quot; rel=&quot;nofollow&quot;&gt;hybrids&lt;/a&gt; lists many inter-species hybrids that are fertile including &lt;a href=&quot;http://en.wikipedia.org/wiki/Beefalo&quot; rel=&quot;nofollow&quot;&gt;Beefalo&lt;/a&gt; (Domestic male cattle X american bison). There are also many canine hybrids which are fertile. &lt;a href=&quot;http://en.wikipedia.org/wiki/Wholphin&quot; rel=&quot;nofollow&quot;&gt;Wholphins&lt;/a&gt; have been found to be fertile.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A wholphin or wolphin is an extremely rare hybrid born from a mating&#xA;  of a female bottlenose dolphin (Tursiops truncatus) with a male false&#xA;  killer whale (Pseudorca crassidens).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So in short, for a hybrid offspring to be fertile, it doesn't necessarily need to be of the same species. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-09-19T05:16:43.690" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21458" PostTypeId="1" CreationDate="2014-09-19T06:37:20.813" Score="3" ViewCount="228" Body="&lt;p&gt;I was reading up about Biotechnology and the use of insects, and came across an interesting article about Insect Cell culture Techniques that specifically talked about the usage of the Baculovirus. If I understand correctly does this virus help express certain genes when inserted into a cell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry if I am way off or did not use proper terminology, I am a high school IB Biology student who still has a a lot to learn&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="9402" LastActivityDate="2014-09-19T07:46:00.060" Title="What is the Baculovirus and how does it help in research?" Tags="&lt;entomology&gt;&lt;virus&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21460" PostTypeId="1" CreationDate="2014-09-19T07:02:17.840" Score="3" ViewCount="78" Body="&lt;p&gt;I'm currently helping develop a rhythm game, and as part of the scoring system, I'd like to make scores and ranks based more on accurate pattern recognition rather than hitting notes very exactly on time as is the case for many games of this variety.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In many cases, the margin of error for the best judgment in rhythm games is so small that it seems to be a matter of chance more than skill that a certain judgment is counted between &quot;excellent&quot; and &quot;good&quot; (for example, one game has the margin as small as &amp;pm;0.011 s).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, some people are better at hitting notes accurately than others either naturally or through practice, but I would like to find some actual research into what the base neurological limitations to rhythmic precision are and to what degree practice can actually improve it.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;As a baseline benchmark for the best judgment, I was thinking of looking for some research into how accurately people can follow the tick of a metronome - for example, by measuring the average deviation of somebody tapping a button to a regular beat after about 100 beats or so when they've gotten used to it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A Google search didn't return anything useful, probably because the search terms draw up so much other, irrelevant content. Is there any prior research on this subject? If so, where can I find it? If not, how could I conduct such an experiment myself?&lt;/p&gt;&#xA;" OwnerUserId="1899" LastActivityDate="2014-11-30T20:04:49.213" Title="Is there any research on how accurately people can follow a beat?" Tags="&lt;neuroscience&gt;&lt;literature&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21461" PostTypeId="1" CreationDate="2014-09-19T07:32:18.367" Score="14" ViewCount="17529" Body="&lt;p&gt;Every time before eating a corn, I count its lines. I would always find 12 or 14 rows of seeds, but never 13.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any biological/scientific reason behind this?&lt;/p&gt;&#xA;" OwnerUserId="8337" LastEditorUserId="107" LastEditDate="2015-09-09T16:05:38.183" LastActivityDate="2016-01-02T23:14:15.637" Title="Why can't a corn cob have 13 rows of seeds?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21462" PostTypeId="2" ParentId="21458" CreationDate="2014-09-19T07:46:00.060" Score="2" Body="&lt;p&gt;Baculoviruses are a a class of viruses which infect only a pretty small number of insects (or their cells in cell culture). To do so, the virus has to infect a cell, take it over to produce the own proteins and DNA to make new virus particles and finally set these new particles free. This is basically what is shown in the image below (from &lt;a href=&quot;http://www.microbiologybytes.com/virology/kalmakoff/baculo/baculo.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vDiOu.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the proteins encoded by the viral genome, not all are essential, meaning removing them will not do harm to the virus or its function. And this is used in Biotech to produce proteins of choice. One of the non-essential proteins is replaced by the sequence of the protein you want to have produced by the cells. You then take insect cells in cell culture (these are single insect cells which live in a big vessel full of culture medium), infect these cells with the modified virus and eventually harvest the protein from the culture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The advantage of Baculoviruses is that they only infect the insect cells on which they are specialized so they are a safe way of producing proteins for pharmaceutic applications. If you want to read some more about this, start &lt;a href=&quot;http://www.microbiologybytes.com/virology/kalmakoff/baculo/baculo.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-19T07:46:00.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21464" PostTypeId="1" AcceptedAnswerId="21471" CreationDate="2014-09-19T09:08:34.117" Score="3" ViewCount="318" Body="&lt;p&gt;Note: this is not a question about history, but about &lt;em&gt;human digestive system over time&lt;/em&gt; :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know a lot of colleagues who traveled for business trips to India. &lt;strong&gt;All&lt;/strong&gt; of them caught  terrible diarrhea there, in spite of keeping all the rules related to use of reboiled or canned water only, eating only peeled fruits, not eating the street food etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My question is&lt;/strong&gt;: how did the millions (or hundred thousands, &lt;a href=&quot;https://history.stackexchange.com/q/15298/6812&quot;&gt;I am not sure with the amount&lt;/a&gt;) of Britons survived in India during the time of the &lt;a href=&quot;http://en.wikipedia.org/wiki/British_Raj&quot; rel=&quot;nofollow noreferrer&quot;&gt;British Raj&lt;/a&gt; 1858-1947?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Did they have to keep the same safety dietary rules as the contemporary Westerners all the time? (I cannot see this as technically possible...)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Were our intestinal flora and fauna different one hundred years ago?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Was the hygiene level and quality of water much lower in Europe then so coming to India was not such a biological shock? (Well, I would believe this in the 1800s but not in the 1900s...)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or did just some of them die and the rest got accustomed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am aware that there is an initial shock for your body when travelling to a very different area generally. However, the Indians (and other Asians) can easily drink the tap water in most of the EU countries and eat the street food, which is not valid vice-versa. So there &lt;em&gt;must&lt;/em&gt; be some difference.&lt;/p&gt;&#xA;" OwnerUserId="8198" LastEditorUserId="-1" LastEditDate="2017-04-13T12:47:54.283" LastActivityDate="2014-09-19T18:02:35.630" Title="Did the Britons 100 years ago have different intestinal flora and fauna?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;digestive-system&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21465" PostTypeId="1" AcceptedAnswerId="21468" CreationDate="2014-09-19T09:18:07.547" Score="5" ViewCount="5060" Body="&lt;p&gt;There is only hydrogen bond different. &#xA;Cortisol is synthesized by our body, while cortisone is given to the patient. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why you cannot give cortisol directly to the patient?&#xA;I think the reason is metabolism that cortisol will break (probably in liver) and not be useful. &#xA;Or expansive to produce. &#xA;Cortisone however can be given.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the physiological difference between cortisone and cortisol?&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="5144" LastEditDate="2014-12-28T22:08:49.673" LastActivityDate="2014-12-28T22:09:23.693" Title="What is the physiological difference between cortisone and cortisol?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21466" PostTypeId="1" AcceptedAnswerId="21474" CreationDate="2014-09-19T10:06:33.990" Score="2" ViewCount="132" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The recent technology is peptide–MHC microarray or artificial antigen-presenting chip.&#xA;  In this technique, recombinant peptide–MHC complexes and co-stimulatory molecules are immobilized on a surface, and population of T cells is incubated with the microarray. The T cell spots act as artificial antigen-presenting cells containing a defined MHC-restricted peptides. The advantage of using peptide–MHC is that it can map MHC-restricted T cell epitope.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These few lines are from Chapter 3 of &lt;a href=&quot;http://www.springer.com/biomed/immunology/book/978-1-4939-1114-1&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Immunoinformatics&lt;/em&gt;, De, Rajat K., Tomar, Namrata (Eds.)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is recombinant peptide MHC? What is MHC restricted peptide? How did the advantage get derived?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="8835" LastEditDate="2014-09-21T04:29:08.637" LastActivityDate="2017-12-14T08:15:25.777" Title="peptide MHC microarray" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;bioinformatics&gt;&lt;immunology&gt;" AnswerCount="2" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="21467" PostTypeId="1" AcceptedAnswerId="27667" CreationDate="2014-09-19T10:12:13.303" Score="0" ViewCount="66" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;One can measure two or more signals simultaneously determined by a single feature, i.e.,&#xA;  epitope in immunomic microarray DNA microarrays measure one response value for each gene per sample; that is, mRNA concentration produced by the gene but a single epitope&#xA;  can generate different response values corresponding to different epitopes in peptide–MHC chips. In case of B cell epitope, it can be recognized by different isotypes of immunoglobulins, so here, one can measure both intensity and quality of antibody response.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These few lines are from the book: &#xA;&lt;a href=&quot;http://www.springer.com/biomed/immunology/book/978-1-4939-1114-1&quot; rel=&quot;nofollow&quot;&gt;http://www.springer.com/biomed/immunology/book/978-1-4939-1114-1&lt;/a&gt;&#xA;Chapter 3&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does measure of one response value for each gene per sample mean?&lt;br&gt;&#xA;Different response value means??&lt;br&gt;&#xA;how is intensity and quality both are being measured??&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="948" LastEditDate="2014-09-19T14:49:10.460" LastActivityDate="2015-01-15T05:54:21.560" Title="Immunomic Microarray" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21468" PostTypeId="2" ParentId="21465" CreationDate="2014-09-19T11:14:02.423" Score="5" Body="&lt;p&gt;Cortisol is directly given to the patient - it is then called &lt;a href=&quot;http://en.wikipedia.org/wiki/Cortisol#Pharmacology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hydrocortisone&lt;/a&gt;. I don't know why this is done but probably to avoid confusion because both names are too similar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The difference between both forms is one hydrogen atom at the C11 position of the molecule in Cortisol (or Hydrocortison) (image from &lt;a href=&quot;http://www.kon.org/urc/v9/liebman.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LxIv8.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise is Cortisol (or Hydrocortisone) the active version, while &lt;a href=&quot;http://en.wikipedia.org/wiki/Cortisone&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cortisone&lt;/a&gt; isn't very active in the human body.&#xA;Both forms can &lt;a href=&quot;http://en.wikipedia.org/wiki/11-Beta_hydroxysteroid_dehydrogenase&quot; rel=&quot;nofollow noreferrer&quot;&gt;enzymatically&lt;/a&gt; turned into the other form (from active to inactive and vice versa). Since Cortisone needs to be activated in the liver, it can only be used for oral uptake. Most of the uses which are colloquially called Cortisone in fact contain Hydrocortisone.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-12-28T22:09:23.693" LastActivityDate="2014-12-28T22:09:23.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21469" PostTypeId="2" ParentId="21454" CreationDate="2014-09-19T11:40:15.240" Score="3" Body="&lt;p&gt;I made a quick sketch on the basis of the information you gave (this is not to scale):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3T6gO.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aminoacid 5 (aa5) of the protein is on the outside, aa90 is inside the membrane. What we don't know here where the transmembrane part starts (directly with aa6 or later) and how it is organised (I indicated this as a transmembrane helix, but this can of course be different). Then we know that the border between the transmembrane part and the cytosolic part is somewhere between aa90 and aa100, that aa100 to aa200 seems to be some connecting part. The aa200 to aa400 is a globular domain which shields hydrophobic amino acids from the cytosol, so this part has to contain a high percentage of hydrophobic amino acids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The part from 400 to 600 is again cytosolic but with no further information about the structure. After aa600 starts a second transmembrane part of the protein, but here we don't know how long it is. The maximum possibility would be until aa977, since we know the aa978 is outside of the membrane.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-19T11:40:15.240" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21470" PostTypeId="2" ParentId="21382" CreationDate="2014-09-19T12:51:53.267" Score="2" Body="&lt;p&gt;hTAP refers to human TAP protein (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10454577&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). And how do you know that TAP refers to Transfer Associated Protein? I believe it stands for Transporter Associated with Antigen Processing (&lt;a href=&quot;http://en.wikipedia.org/wiki/Transporter_associated_with_antigen_processing&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Your facts are wrong which is why your question couldn't be answered.  &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-09-19T12:51:53.267" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21471" PostTypeId="2" ParentId="21464" CreationDate="2014-09-19T13:20:47.917" Score="2" Body="&lt;p&gt;Who said they did not have the same problems? I'm sure they did and I'm sure most of them had horrible diarrhea. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A quick google search brought up &lt;a href=&quot;http://books.google.fr/books?id=Coaj-geZZVEC&amp;amp;pg=PA252&amp;amp;lpg=PA252&amp;amp;dq=%22british%20colonization%22%20india%20diarrhea&amp;amp;source=bl&amp;amp;ots=CrAm21DpZy&amp;amp;sig=HtXd_zHFqh4cLu0GZd2uGBqUUVs&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=JCwcVIOwJYHaOoHsgcAP&amp;amp;redir_esc=y#v=onepage&amp;amp;q=%22british%20colonization%22%20india%20diarrhea&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Man and Microbes&lt;/em&gt;: Disease and Plagues in History and Modern Times, by Arno Karlen&lt;/a&gt; which states that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In 1817, when the first cholera pandemic began [...]. In Calcutta and Jessore, cholera killed 5,000 British soldiers within weeks&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, those who survived would get used to it eventually. Cholera is much more serious than simple dysentery of course but its main symptom is also diarrhea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The locals of wherever you happen to be are used to the pathogens that are common in the drinking water. If I am not from a place and drink water with new pathogens, I will be sick. I will also, however, eventually get over it and my body will be used to them. Depending on the details, either because I have developed an immunity or because I have developed the necessary intestinal fauna to deal with it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So while the intestinal fauna may indeed have changed over time, this has absolutely nothing to do with what you're asking. First because your assumption is wrong (the British were subjected to the same health issues as modern Europeans visiting Asia) and second because people adapt. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-09-19T18:02:35.630" LastActivityDate="2014-09-19T18:02:35.630" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21472" PostTypeId="1" AcceptedAnswerId="21478" CreationDate="2014-09-19T14:30:57.007" Score="1" ViewCount="121" Body="&lt;p&gt;Sequencing projects sequence one strand and call that the + strand and then extrapolate the sequence of the - strand. This means that sometimes the genomic sequence that you download from a database might be the complement of the actual sequence you are looking for.ORF tools like exonerate and genewise takes this into account and thereby look for six possible reading frames.Do sequence similarity tools like blastn take this into account and do pairwise alignment for complement of the actual sequence also?&lt;/p&gt;&#xA;" OwnerUserId="8135" LastEditorUserId="8135" LastEditDate="2014-09-20T08:28:07.987" LastActivityDate="2014-09-20T08:28:07.987" Title="BLASTn vs ORF tools" Tags="&lt;bioinformatics&gt;&lt;blast&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21473" PostTypeId="2" ParentId="21453" CreationDate="2014-09-19T14:43:52.717" Score="5" Body="&lt;p&gt;Fishers Geometric Model (&lt;strong&gt;FGM&lt;/strong&gt;) is a theoretical prediction about the adaptation process in traits. There are a number of things to establish before attempting comprehend FGM. Firstly, shifts in an adaptive landscape, in natural scenarios, are generally quite small. Because populations have been evolving for such a long time and the small shifts in adaptive peaks it means that most populations should be near or on a local fitness optimum within the relevant landscape. The adaptive landscape comes from S. Wright, discussed in the Orr paper, where he spoke of a field of possible gene combinations&quot; each with a fitness value, some combinations are fitter than others. Adaptive peaks represent the fittest combinations of all traits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can picture all of this using a single trait:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/esnOW.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here there is a local optimum (which is also global, Fisher assumed that adaptive landscapes are less rugged than Sewall Wright and had only one optimum) for the trait. The population starts at point A (the red ball), just off the adaptive peak for the initial fitness distribution (blue trace). Then selection alters (red trace), initiating a new bout of adaptation, making the population (green ball) further from the optimum. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1fNPq.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From here lets imagine this is two seperate populations, the green population (A) wants to move along the red line to the highest point, the red population (B) along the blue line also for its own optimum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a mutation which has a very small effect arises then there is 50% probability in both populations that it will improve fitness (assuming no neutral mutation) because it will either be recessive or deleterious. This value is shown in box 2 figure 1 of the Orr paper. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7JD1j.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now if a large effect mutation was to arise in then there is less chance of it being beneficial for population B than for population A, this is because B is closer to its phenotypic optimum so a large effect mutation is likely to &quot;overshoot&quot; the optimum. (The black line illustrates where either population would end up after a large effect mutation in the direction of the adaptive peak). You can see this mutation would put population A very close to its peak (the red line) and population B would have a reduced fitness. This is summed up nicely in the opening to the Orr paper.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Precise adaptation is possible only if organisms can come to fit their environments by many minute adjustments&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XdIyh.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, descriptively, this is why we see a reduced probability of large effect beneficial mutations as we approach an optimum; we expect most bouts of adaptation to be due to small shifts in adaptive landscape and populations to start bouts near to the former adaptive peak.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The FGM expands this out beyond one trait (or, as Kauffman and Gillespie did, the sequence - with the latter seemingly being more successful than the former). As shown in figure 1 of the Orr paper,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eUi0l.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a highly multidimensional space, with one dimension per trait, therefore more complex organisms by definition will have more complex spaces. The centre of this sphere is the phenotypic optimum, and each layer represents and adaptive movement, or substitution of the wild type as in the Maynard-Smith adaptive walks system. The red line shows the movement made by the population through this sphere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And now for some math. (Refer to box two in the Orr paper). $P_a (\chi)$ is the probability that a mutation (of effect size $r$) is favourable. Thinking about what I discuss above, that is, $P_a (\chi)$ is the probability that a mutation will increase fitness, which must therefore be a product of the landscape complexity (the number of characters affecting the fitness), the distance from the population to the optimum, and the size of the effect. $\chi$ is the standardized mutation size, which accounts for the distance to optima, as $z$, the number of characters affecting fitness as $n$, and the effect size $r$. This means that $\chi$ = $r \sqrt{n} /2z$: therefore an increase in the distance to the phenotypic optimum ($z$) reduces the value of $\chi$ (thus increasing the probability that a mutation has a beneficial effect), whereas increases in $r$ or $n$ will decrease the probability that the mutation is beneficial (i.e. large effect mutations and high complexity). In the context of the above example, both populations have an $n$ of 1, and the values of $z$ vary - this means population A can tolerate a larger value of $r$, or in other words, population A is more able to make adaptive substitutions because it is further from peak fitness, thus more tolerant to large effects, than population B.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Difference between $r$ and $\chi$: $r$ is the raw value of effect size of a mutation, whereas $\chi$ is the standardized effect size. Assuming equal effect sizes the relative effect of mutations will depend on the number of traits affecting fitness (see the diagrams below), thus we have to correct for this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does complexity affect the probability of beneficial mutations? Look at the following diagram. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xtT15.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each point represents a possible combination of traits when we have three traits affecting fitness, each with two possible incarnations (A or a [most fit and least fit respectively]). The outer green ring has one possible occupying combination (aaa) which is the least fit - it's the furthest from the optimal combination, the red point. On the green ring the probablity of increasing fitness with a mutation is 3/3 (because there are 3 possible mutations all of which increase fitness). &lt;em&gt;Note, assume all changes are equal effect.&lt;/em&gt; If we change one trait to the A version we can have 3 possible outcomes (Aaa, aAa, aaA) which occupy the yellow ring. From the yellow ring a further single mutation has four possible outcomes, of which 3 can increase fitness so the probability of improving fitness with a mutation is reduced (3/4). In the blue ring there is a 1/4 probability of increasing fitness. Jumping to the red point, where all traits are A, every possible mutation will reduce fitness (0/3).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1Grs9.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bearing this in mind, lets change n (the number of traits affecting fitness) from 3 to 4. The least fit starts in the red ring (aaaa), from here there is a 4/4 probability of increased fitness via mutation. From the green ring there is a 6/7 probability. From the yellow ring there is a 4/8 probability of increasing fitness, and from the blue a 1/7 chance. Compare this to when n=3, from the blue ring there was a 1/4 chance, when n=4 it is 1/7 - there are more possible combinations and still only one fittest combination&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Put another way;&lt;/strong&gt; if we consider it in terms of single point mutations in a sequence, a mutation which affects 1 trait affecting fitness (n=1) then the probability it will increase fitness is drawn from the distribution of probable fitness effects. If the point mutation affects 5 traits then the effect is drawn from the distribution 5 times, and because we assume most mutations are deleterious and beneficial ones are relatively constrained to being small, there is a greater probability of reducing fitness when n&gt;1.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-09-24T10:29:26.593" LastActivityDate="2014-09-24T10:29:26.593" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21474" PostTypeId="2" ParentId="21466" CreationDate="2014-09-19T14:59:56.670" Score="7" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0000065&quot;&gt;this&lt;/a&gt; paper (Yoav Soen et al. PLoS Biology 2003), peptide:MHC microarrays are a type of cellular microarray (a microarray designed to identify cell types; &lt;a href=&quot;http://en.wikipedia.org/wiki/Cellular_microarray&quot;&gt;Wikipedia&lt;/a&gt;). These microarrays have attached a MHC molecule bound to a peptide, which allows them to work as artificial antigen presenting cells (APCs) that activate specific subpopulations of T cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another recent paper is &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0011355#pone.0011355-Soen1&quot;&gt;here&lt;/a&gt; where they specifically use the word recombinant peptide:MHC.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The expression &lt;em&gt;MHC restricted&lt;/em&gt; refers to the positive selection (in the thymus) of T cells that recognize MHC molecules of the host but not other self-antigens (&lt;a href=&quot;http://en.wikipedia.org/wiki/Major_histocompatibility_complex#T_lymphocyte_recognition_restrictions&quot;&gt;Wikipedia&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="9099" LastEditorUserId="9099" LastEditDate="2014-09-22T06:25:38.203" LastActivityDate="2014-09-22T06:25:38.203" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21475" PostTypeId="1" CreationDate="2014-09-19T15:00:38.487" Score="7" ViewCount="3950" Body="&lt;p&gt;I want to study biology. I have zero previous knowledge of biology but I know Physics, Chemistry and Maths. From which book should I start? I have heard about &lt;em&gt;Campbell Biology&lt;/em&gt;, but it is very costly in India(more than my 1 month's earning). So please suggest books that:   &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strike&gt; Are cheap OR &lt;/strike&gt; could be found on internet &lt;/li&gt;&#xA;&lt;li&gt;Require no previous knowledge of biology  &lt;/li&gt;&#xA;&lt;li&gt;Contain no technical mistakes&lt;/li&gt;&#xA;&lt;li&gt;Adequately explain the topics which they deal with&lt;/li&gt;&#xA;&lt;li&gt;and also mention some history of the topics   &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not looking for online videos. I want books; my internet is slow and there are some other problems. You can also tell costly books--Perhaps I could find them in the library or could print it somehow. If Campbell Biology book is available online then please give me the download link.   &lt;/p&gt;&#xA;" OwnerUserId="8337" LastEditorUserId="8337" LastEditDate="2014-09-20T06:47:10.803" LastActivityDate="2018-07-16T23:04:19.263" Title="Books for beginners" Tags="&lt;book-recommendation&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="3" ClosedDate="2014-09-22T14:51:49.557" ContentLicense="CC BY-SA 3.0" />
  <row Id="21476" PostTypeId="2" ParentId="21475" CreationDate="2014-09-19T15:21:03.933" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.flipkart.com/biological-science-english-3rd/p/itmczzceuzhgweqv?q=Biological+Science+%28English%29+3rd+Edition&amp;amp;as=on&amp;amp;as-show=on&amp;amp;otracker=start&amp;amp;as-pos=p_1&amp;amp;pid=9780521684170&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/x7eDi.jpg&quot; alt=&quot;Biological sciences&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a low price edition available in India on flipkart.com, it covers all topics extensively. It costs around ₹ 570.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.flipkart.com/biological-science-english-3rd/p/itmczzceuzhgweqv?q=Biological+Science+%28English%29+3rd+Edition&amp;amp;as=on&amp;amp;as-show=on&amp;amp;otracker=start&amp;amp;as-pos=p_1&amp;amp;pid=9780521684170&quot; rel=&quot;nofollow noreferrer&quot;&gt;Biological Science (English) 3rd Edition by Taylor&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8135" LastEditorUserId="8337" LastEditDate="2014-09-19T15:49:30.473" LastActivityDate="2014-09-19T15:49:30.473" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21477" PostTypeId="2" ParentId="21475" CreationDate="2014-09-19T16:46:58.387" Score="6" Body="&lt;p&gt;As @metacompactness said in the comments, the campbell (9th edition) is available and free in pdf online (&lt;a href=&quot;http://m-learning.zju.edu.cn/G2S/eWebEditor/uploadfile/20120925133308427.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;). This book is a classic that most undergraduate students know quite well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Online resources&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some very good online resources to get an introduction to biology. I think that online resources might have the drawback that they may miss the big picture that a whole book can give you and it may be complicated to really understand in what order you should look at the videos particularly if you jump from one website to another. Otherwise, it is often quicker to learn from someone speaking in a video than from reading a book. I learned lots in various field thanks to free online courses. I appreciate a lot reading books but I think that free online resource is the best option for you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I did my undergrad in biology, I never really needed this kind of resource but generally speaking I find Khan Academy to be very good for introducing students to new fields of knowledge. And there is a whole biology section on &lt;a href=&quot;https://www.khanacademy.org/science/biology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Khan Academy&lt;/a&gt;. The &lt;a href=&quot;http://ocw.mit.edu/courses/biology/&quot; rel=&quot;nofollow noreferrer&quot;&gt;MIT courseware&lt;/a&gt; is also a very good free resource. &lt;a href=&quot;http://education-portal.com/academy/course/introduction-to-biology.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Education portail&lt;/a&gt; might be a good starting point as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you google &quot;free introductory course biology&quot; you will find many other resources.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=gM95HHI4gLk&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; is a ted talk by Salman Khan (from Khan Academy) for the fun.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2018-07-16T23:04:19.263" LastActivityDate="2018-07-16T23:04:19.263" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="21478" PostTypeId="2" ParentId="21472" CreationDate="2014-09-19T16:51:52.483" Score="1" Body="&lt;p&gt;It depends on the flavor of BLAST you are using. Some do, some don't. Specifically, the classic BLAST flavors are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;blastp&lt;/strong&gt; : &#xA;compares an amino acid query sequence against a protein sequence database&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;blastn&lt;/strong&gt; :&#xA;compares a nucleotide query sequence against a nucleotide sequence database&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;blastx&lt;/strong&gt; :&#xA;compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;tblastn&lt;/strong&gt; : &#xA;compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands).&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;tblastx&lt;/strong&gt; : &#xA;compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. (Due to the nature of tblastx, gapped alignments are not available with this option)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Of these, &lt;code&gt;tblastn&lt;/code&gt;, &lt;code&gt;tblastx&lt;/code&gt; and &lt;code&gt;blastx&lt;/code&gt; all check the 6 possible reading frames (both strands). This only makes sense for protein searches since that's the only case where the reading frame is relevant. The simple blastn does not deal with reading frames but it does deal with hits against the reverse strand. The matching strand is highlighted in the output and the numbers in the HSP reflect that. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, these are the first and last lines of one of the hits when blasting the reverse complement of the human tP53 gene against the human sequences of the &lt;code&gt;nr&lt;/code&gt; database:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Range 1: 1 to 2591GenBankGraphics Next Match Previous Match&#xA;Alignment statistics for match #1 Score Expect  Identities  Gaps    Strand&#xA;4673 bits(5182)     0.0     2591/2591(100%)     0/2591(0%)  Plus/Minus&#xA;&#xA;Query  1     CACCCCTCAGACACACAGGTGGCAGCAAAGTTTTATTGTAAAATAAGAGATCGATATAAA  60&#xA;             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||&#xA;Sbjct  2591  CACCCCTCAGACACACAGGTGGCAGCAAAGTTTTATTGTAAAATAAGAGATCGATATAAA  2532&#xA;&#xA;&#xA;[...]&#xA;&#xA;Query  2521  AGACTTTTGAGAAGCTCAAAACTTTTAGCGCCAGTCTTGAGCACATGGGAGGGGAAAACC  2580&#xA;             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||&#xA;Sbjct  71    AGACTTTTGAGAAGCTCAAAACTTTTAGCGCCAGTCTTGAGCACATGGGAGGGGAAAACC  12&#xA;&#xA;Query  2581  CCAATCCCATC  2591&#xA;             |||||||||||&#xA;Sbjct  11    CCAATCCCATC  1&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Note that 1) the strands are given as &quot;Plus/Minus&quot; which means that the query sequence is aligned against the - strand of the target and 2) that the coordinates of the subject sequence start from the end (2591) and go to the beginning (1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes, even simple tools like untranslated BLAST take the two strands into account.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-09-19T16:51:52.483" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21480" PostTypeId="1" AcceptedAnswerId="21491" CreationDate="2014-09-19T19:37:44.950" Score="1" ViewCount="57" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vti3Z.jpg&quot; alt=&quot;ATPase in question&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In respects to this certain ATPase transporter. What do i look for in respects to determining what specific kind it is out of:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;F-ATPases&lt;/li&gt;&#xA;&lt;li&gt;V-ATPases&lt;/li&gt;&#xA;&lt;li&gt;A-ATPases&lt;/li&gt;&#xA;&lt;li&gt;P-ATPases&lt;/li&gt;&#xA;&lt;li&gt;E-ATPases&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Im assuming that analyzation of the gradients dealt with will guide me to the answer. With that logic, i can assume that this is an F-ATPase since i know this membrane protein can synthesize ATP using a H+ gradient, and work in the reverse to create a H+ gradient using the energy gained from the hydrolysis of ATP.( I see 2H+ cations being expelled) Is this a correct method in differentiating ATPases ?&lt;/p&gt;&#xA;" OwnerUserId="8059" LastActivityDate="2014-09-20T06:32:58.323" Title="Determining and Differentiating specific ATPases" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;intracellular-transport&gt;&lt;membrane-transport&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21481" PostTypeId="1" AcceptedAnswerId="21482" CreationDate="2014-09-19T20:50:21.133" Score="5" ViewCount="328" Body="&lt;p&gt;As of 2014-09-14 at least 5347 cases of ebola have been identitied. Some estimates are much higher. While experts are sounding the alarm to try to get sufficient resources to contain the outbreak, some people are also speaking very hopefully about containment to roughly the current affected area. &lt;a href=&quot;http://www.washingtonpost.com/news/to-your-health/wp/2014/09/19/ebola-in-the-u-s-dont-bet-on-it/&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; puts the risk of the outbreak reaching the United States as low as 3%. I'm not an expert in the field, but it seems like there are almost countless ways in which an increased number of cases increases the risk of further exponential growth. It's encouraging to hear that in countries with better healthcare, death rates would likely be much lower, but at this point, isn't it inevitable that the outbreak will run its course as a global pandemic?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, which of these possibilities is just my imagination, or likely so improbable that we don't need to worry about it?&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Scared carriers not yet showing symptoms sneak or force their way across boarders to unaffected regions.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Objects, food, or water touched by the infected go unnoticed until they end up leaving the containment zone.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If it can jump from bats or monkeys, thousands of infected humans increase points of contact to create vectors into other species, perhaps one that will travel unnoticed far beyond the containment zone.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;After months of the same security precautions day in and day out, airport checkpoints, and other points of entry become lazy, and let infected through.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;With numbers as high as they are, and possibly higher than we even know, is this really containable at all?&lt;/p&gt;&#xA;" OwnerUserId="5018" LastEditorUserId="2949" LastEditDate="2014-10-24T18:46:39.080" LastActivityDate="2014-10-26T07:07:01.137" Title="How is it possible to even hope for an ebola epidemic of this current size to remain contained to a relatively small part of Africa?" Tags="&lt;epidemiology&gt;&lt;ebola&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21482" PostTypeId="2" ParentId="21481" CreationDate="2014-09-19T21:08:00.973" Score="5" Body="&lt;p&gt;This is too long for a comment, so my thoughts about this here. The CDC Director said a few days ago after a visit in Africa &quot;&lt;a href=&quot;http://www.wired.com/2014/09/cdc-director-ebola/&quot;&gt;The window of opportunity is closing&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;This can happen. However, you are not getting contagious unless you show symptoms. This is different in other diseases like chicken pox or measles where you spread the virus before showing symptoms. So there has to be a lot of awareness. Also doctors need to be very careful with patients showing these symptoms. This is most likely one of the main reasons for the wide spreading of the disease.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Same problem as in 1. Theoretically this is easy to prevent, but in a situation of chaos this can cause problems. But since infected people which show symptoms will not handle large amounts of food, this is most likely less of a problem.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Every crossing of a species-barrier is a rare event. Double-crossings are even less likely. So I don't think this is a problem. Besides this, we already have to independent Ebola outbreaks which has never happened before. One is the one in West-Africa, the other one is happening in the Democratic Republic of Congo. Both are independent cross-overs.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;This can cause problems. The advantage of the first world is that we have functional health care systems. They allow better care for the persons and also better isolation of contact persons. I think it is unlikely that it would spread widely. The perspective will be different, if the virus makes the jump into the densely populated regions in South-East Asia. There a lot of people live closely together, this can cause real problems. Fortunately for us the virus is not highly contagious. To infect yourself you need unprotected contact to the body fluids (blood, stool, feces, sweat etc.) of infected persons.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-19T21:08:00.973" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21483" PostTypeId="2" ParentId="19934" CreationDate="2014-09-19T23:25:11.230" Score="-1" Body="&lt;p&gt;Recent studies prove that this involuntary phenomenon must be untrue. Obviously this is false, in order for research like this to take place people need to spend money. It would be interesting if we could create a crowd sourcing account maybe on kick starter to find ways to bring money into the research. I wish I had more information for you, I've been able to do it as long as. When you go to the dentist, just curious, you don't happen to have two bones underneath your tongue that is an anomaly as well? I've been trying to think of correlations for years. I can get the medical terms, if you like. Find me on Facebook Chris Azzy&lt;/p&gt;&#xA;" OwnerUserId="9406" LastActivityDate="2014-09-19T23:25:11.230" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21484" PostTypeId="2" ParentId="21460" CreationDate="2014-09-20T00:14:52.373" Score="2" Body="&lt;p&gt;You might begin your search with the characteristics of Parkinson's disease. This degenerative disorder is precipitated by the death of neurons in the substantia niagra. This brain structure is composed of multiple neurological nuclei. Its function is to connect cortical regions and nuclei together, most significantly with the basal ganglia. The difference between nuclei and cortical brain circuits is important to your question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The symptoms of Parkinson's are directly correlated with the function of nuclei in central nervous system: the integration of information. It's the integration of conscious thought, muscle memory, sensory-motor pathways that makes voluntary movement possible. Disruption of this network in Parkinson's degrades one's ability to voluntarily execute a movement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cerebellum also controls voluntary movement. As a cortical structure, it is involved more with the formation and maintenance of muscle memory than information integration. Damage here results in the loss of fine motor control as opposed to gross motor control in Parkinson's. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This problem has a sensory and motor component. It might be difficult to tackle your problem as a whole. Perhaps breaking it down into smaller pieces would shed some light on what you're looking for. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are 2 articles I found relating motor control with the cerebellum and substantia niagra. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566602/&quot; rel=&quot;nofollow&quot;&gt;Relating cerebellar damage with learning sequence information&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704838/&quot; rel=&quot;nofollow&quot;&gt;Relating the substantia niagra with interval timing&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8570" LastEditorUserId="8570" LastEditDate="2014-09-20T04:52:49.580" LastActivityDate="2014-09-20T04:52:49.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21485" PostTypeId="2" ParentId="21440" CreationDate="2014-09-20T00:38:24.010" Score="4" Body="&lt;p&gt;Different cancers divide at different rates. One way to qualitatively visualize this is observe hair loss in patients who are undergoing chemotherapy. Commonly, a drug like cisplatin will be administered which will cross-link DNA, inhibiting cell division by activating apoptosis. Tissues which are killed most readily by cisplatin are those which are dividing most rapidly: intestines, head hair, red and white blood cells, tumors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite the loss of hair on the head, many patients do not lose slower growing hair on their arms, eyebrows, eyelashes, etc. Likewise, though cell death in the intestinal lining may be dramatic on cisplatin, the skin may not show lesions as it is a more slowly dividing population of cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rate of cell division correlates with the rate of cell death while taking the chemotheraputic drug cisplatin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may make a rough visual survey of the cells in the body which divide so rapidly that they die, and divide so slowly that they largely survive chemotherapy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rate of cell division of head hair and other body hair spans the rate of cell division over which cisplatin effectively acts on tumor cells.  &lt;/p&gt;&#xA;" OwnerUserId="8570" LastActivityDate="2014-09-20T00:38:24.010" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21486" PostTypeId="2" ParentId="21475" CreationDate="2014-09-20T00:51:19.817" Score="1" Body="&lt;p&gt;A great place to start is Khan academy. It is free and very easy to understand.&#xA;&lt;p&gt;&#xA;Also, another thing you could try would be Bob Jones Biology (books A&amp;amp;B). I don't know how much those cost in India. But, they explain things in great detail starting at the bottom and working upward. I  will let you know that they have a strong Christian influence which some people would disagree with. However, if you can look past that, they are excellent, well-written books!&lt;/p&gt;&#xA;" OwnerUserId="6289" LastActivityDate="2014-09-20T00:51:19.817" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21489" PostTypeId="2" ParentId="20269" CreationDate="2014-09-20T06:06:18.677" Score="2" Body="&lt;p&gt;You can find 46-way multiz alignment from &lt;a href=&quot;http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&amp;amp;position=chr21:33031597-33041570&amp;amp;hgsid=389402211_SFYtjw2KmAIALH2TNU4GijR6BRXA&quot; rel=&quot;nofollow&quot;&gt;UCSC genome browser&lt;/a&gt;, it is down on comparative genomics part and labelled as &quot;cons 46-way&quot;, which is a genome alignment of 46 vertebrate species. You can use data on their genome browser on the site, or get download information &lt;a href=&quot;http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in pair-wise alignments, I don't know of any pair-wise alignment database, but in fact you don't need one. You can search for nucleotide sequences from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nucleotide/&quot; rel=&quot;nofollow&quot;&gt;NCBI nucleotide database&lt;/a&gt; and align them using &lt;a href=&quot;https://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;sqi=2&amp;amp;ved=0CCYQFjAB&amp;amp;url=https%3A%2F%2Fblast.ncbi.nlm.nih.gov%2FBlast.cgi%3FPAGE_TYPE%3DBlastSearch%26BLAST_SPEC%3Dblast2seq%26LINK_LOC%3Dalign2seq&amp;amp;ei=WhYdVPnyEeq_ygO-poLoCg&amp;amp;usg=AFQjCNHW6Z7VY8iAUn0taVKiKq4rmn9xlw&amp;amp;bvm=bv.75775273,d.bGQ&quot; rel=&quot;nofollow&quot;&gt;BLAST on their website&lt;/a&gt;. BLAST is maybe the most common tool for pair-wise alignments and also for database alignment searches, where a single query sequence is searched for matches throughout a database of sequences. If you want to do a large number of alignments, you can download BLAST to your computer to do them faster. &lt;/p&gt;&#xA;" OwnerUserId="1458" LastActivityDate="2014-09-20T06:06:18.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21490" PostTypeId="1" CreationDate="2014-09-20T06:30:23.400" Score="3" ViewCount="300" Body="&lt;p&gt;Please help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know how to isolate the different cells (astrocytes, other glial cells, neurons and synaptosomes) from brain tissue using a Ficoll-based separation but how do I determine the purity of the fractions that I have isolated if I cannot use immunological techniques, FACS or SEM analysis.&lt;/p&gt;&#xA;" OwnerUserId="9409" LastEditorUserId="1320" LastEditDate="2014-09-20T15:38:50.830" LastActivityDate="2014-09-21T05:27:19.267" Title="How can I determine the purity of cells isolated from rat brains if I cannot use FACS, Immunohistochemistry or SEM anaysis?" Tags="&lt;biochemistry&gt;&lt;neuroscience&gt;&lt;brain&gt;&lt;cell-sorting&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21491" PostTypeId="2" ParentId="21480" CreationDate="2014-09-20T06:32:58.323" Score="1" Body="&lt;p&gt;First of all, I think you need to research the subunit structures of the various ATPase classes in the list because I am pretty sure that several of them are not as complex as this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although this superficially looks like the F-ATPase responsible for synthesising ATP by using the proton gradient generated by the electron chain, there is a clue in that diagram that this may actually be a V-ATPase. The V-ATPases use ATP hydrolysis to move protons from the cytoplasm into the lumen of acidic organelles like lysosomes. The diagram in the question depicts a process like that (ATP is being hydrolysed). Now, you &lt;em&gt;can&lt;/em&gt; drive the F ATPase in reverse to achieve this situation, so that isn't definitive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The labelling of the two compartments is also consistent with the idea that it is a V-ATPase since 'lumen' isn't a word that is usually used in the context of the mitochondrion (it would normally be 'matrix').&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I would suggest that you find out if the subunit labelling is like that used in F-ATPase or V-ATPase (or both). A Google image search will help you to find cartoons of ATPases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My guess, before doing the suggested research, is that this is a V-ATPAse.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-09-20T06:32:58.323" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21492" PostTypeId="2" ParentId="21490" CreationDate="2014-09-20T06:50:04.127" Score="2" Body="&lt;p&gt;You can do qPCR for certain markers from the extract. GFAP for astrocytes, Tuj1 for neurons, Myelin for oligodendrocytes etc and calculate their percentages to have an estimate of the relative populations. If you are quite used to microscopy and studying these cells then you can identify the different populations of cells with normal light microscopy as well; this is not quantitative and is susceptible to bias.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-09-21T05:27:19.267" LastActivityDate="2014-09-21T05:27:19.267" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21493" PostTypeId="1" AcceptedAnswerId="21494" CreationDate="2014-09-20T08:09:58.923" Score="7" ViewCount="23792" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Yb7z1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conjunctivitis or 'pink eye'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a few questions on conjunctivitis. When I was suffering from conjunctivitis, my doctor advised me to wear sunglasses so that no one else gets infected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder how it happens that if someone looks into an infected eye, then there is a chance for that person to also get infected. &lt;strong&gt;Specifically, why does this apparently happen only when we see an infected eye?&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another question I have is &lt;strong&gt;why does our eye get watery when we see the eyes of an infected person?&lt;/strong&gt;. &lt;/p&gt;&#xA;" OwnerUserId="5643" LastEditorUserId="5762" LastEditDate="2014-09-20T08:43:36.447" LastActivityDate="2018-06-22T20:02:19.787" Title="How the conjunctivitis virus spread just by seeing a person's eye who is infected" Tags="&lt;virus&gt;&lt;infection&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21494" PostTypeId="2" ParentId="21493" CreationDate="2014-09-20T10:02:13.767" Score="17" Body="&lt;p&gt;You can't catch conjunctivitis by looking at someone, but you can spread it around by touching your eye and touching something else, which then can pass the virus to someone else (viral conjunctivitis can be highly contagious). There are no hard facts, but one estimate is that people touch their faces an average of 3.6 times per hour, more if your eyes are itchy. Wearing sunglasses can not only help the possibly increased sensitivity of eyes with conjunctivitis, but they may also cut down on the number of times you touch your eye (thus spreading the virus).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no evidence to support that our eye get watery when we see the eyes of an infected person. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cdc.gov/conjunctivitis/clinical.html&quot;&gt;Conjunctivitis (Pink Eye) - CDC&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.livescience.com/25086-stop-touching-yourself-flu-researchers-say.html&quot;&gt;Stop Touching Yourself, Flu Researchers Say&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-09-20T10:02:13.767" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21495" PostTypeId="2" ParentId="21461" CreationDate="2014-09-20T10:15:22.667" Score="30" Body="&lt;p&gt;Most varieties of corn bred for modern use have between 8-20 rows of kernels &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23377180&quot; rel=&quot;noreferrer&quot;&gt;(Bommert et al. 2013.&lt;/a&gt;. Nearly all varieties have an even number of kernel rows.  This is due to the early development of the ear.  Ears of corn are developed from pistillate flowers on the ear &lt;a href=&quot;http://jxb.oxfordjournals.org/content/58/5/909.full&quot; rel=&quot;noreferrer&quot;&gt;(Bortiri and Hake 2007)&lt;/a&gt;. Pistillate flowers are the female flowers, so they will bear seeds. The seeds are the individual kernals.&lt;/p&gt;&#xA;&lt;p&gt;Long before the ear of corn has the kernels, it has several rows of flowers. The flowers develop on the ear in long rows. Early in development of the ear, the individual rows of flowers double, forming rows of double flowers, as shown in the simple diagram from Bortiri and Hake (2007). Both male flowers (left) and female flowers (right) have this two-row structure.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ALe5s.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;You can see the doubled pattern forming in this scanning electron micrograph of the very early development of the ears, also from Bortiri and Hake (2007). Notice the tip of the ear still has the single rows but the rows begin to double a little farther away from the tip. You can usually see this even on mature ears of corn.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QdmFm.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;You can see remnants of this arrangement if you look carefully at a cross section of an ear of corn. I've drawn arrows to show the connections where the flowers once connected together. If you look carefully at the ear of corn, you can identify the rows. The doubled rows have the kernels exactly opposite of each other. Each doubled row is staggered slightly from the neighboring rows. I've drawn lines to highlight each doubled row.  These two photos are from the &lt;a href=&quot;http://extension.entm.purdue.edu/pestcrop/2010/issue17/&quot; rel=&quot;noreferrer&quot;&gt;agriculture extension office&lt;/a&gt; at Purdue University.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/t67UF.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QMqre.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The development of corn flowers and all other flowers follows what is called the ABC model of floral development &lt;a href=&quot;http://ww2.biol.sc.edu/%7Ekrizeklab/0905NRG.pdf&quot; rel=&quot;noreferrer&quot;&gt;(Krizek and Fletcher 2005)&lt;/a&gt;. The model has been greatly expanded since molecular genetics has increased our understanding of flower development. Many genes are involved, and the genes are used in different ways by different species of plants. The pattern of gene usage is similar in most grasses, which explains the double-flower arrangement of corn. Most grasses have the double-flower arrangement, and corn is a type of grass.&lt;/p&gt;&#xA;&lt;p&gt;Some highly inbred variety of corn can produce odd numbers of kernel rows, as shown in figure below, taken from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23377180&quot; rel=&quot;noreferrer&quot;&gt;Bommert et al. (2013)&lt;/a&gt;. KRN is kernel row number.  RIL is recombinant inbred lines, which means different varieties that have been inbred for particular traits. Thirteen is possible, as are other odd row numbers. An odd number of rows is unusual, however.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9g6aw.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Citations&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Bomblies, K. et al. 2003. Duplicate FLORICAULA/LEAFY homologs zfl1 and zfl2 control inflorescence architecture and flower patterning in maize. Development 130: 2385-2395.&lt;/p&gt;&#xA;&lt;p&gt;Bommert, P. et al. 2013. Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nature Genetics 45: 334-337.&lt;/p&gt;&#xA;&lt;p&gt;Bortiri, E. and S. Hake. 2007. Flowering and determinacy in maize. Journal of Experimental Botany 58: 909-916.&lt;/p&gt;&#xA;&lt;p&gt;Krizek, B.A. and J.C. Fletcher. 2005. Molecular mechanisms of flower development: An armchair guide. Nature Reviews Genetics 6: 688-698.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-20T12:20:01.163" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21496" PostTypeId="2" ParentId="20321" CreationDate="2014-09-20T10:40:09.583" Score="2" Body="&lt;p&gt;One of my colleagues does lots of histological work, staining and identifying tissue at the microscopic level. Software that could be helpful to that discipline might be the ability to distinguish among the different types of tissues present, and perhaps calculate the &quot;area&quot; occupied by each tissue type as well as empty space. This would not be unlike a GIS type problem, but I don't know if it fits well with a Yes/No binary decision framework. I don't know if it could be trained to learn to identify specific types of tissue, but perhaps it could recognize each distinct area of a cross section as different from other such areas.  Here are a few cross sections to show you what I mean:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Colon:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sv8Cg.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;a href=&quot;http://histologyatlas.wisc.edu/slides/397/original&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Smooth muscle:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vXNuZ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;a href=&quot;http://wahoo.nsm.umass.edu/histology/content/smooth-muscle-0s&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Seminiferous tubules from testes:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Eg0Qh.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;a href=&quot;http://legacy.owensboro.kctcs.edu/gcaplan/anat2/histology/histo%20b%20male%20reproductive.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notice the different tissue types in each cross section, plus the white space. Each tissue type has different light transmission patterns, which may allow a computer to learn to distinguish among the different tissue types.&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-09-20T10:53:56.807" LastActivityDate="2014-09-20T10:53:56.807" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21497" PostTypeId="1" CreationDate="2014-09-20T16:48:16.020" Score="2" ViewCount="747" Body="&lt;p&gt;In a project we're doing (in python), we want to create a distance matrix for a phylogenetic tree with multiple, different length sequences. However, what we've seen so far (AlignIO in biopython, etc.) requires the sequences' length to be equal. Is there any pythonic way to get the matrix with sequences of different length? Or any other indirect way that would get us to the same result?&lt;/p&gt;&#xA;" OwnerUserId="9412" LastEditorUserId="9412" LastEditDate="2014-09-20T16:51:06.577" LastActivityDate="2015-01-01T12:18:12.453" Title="Distance matrix with different length sequences" Tags="&lt;bioinformatics&gt;&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21499" PostTypeId="2" ParentId="19873" CreationDate="2014-09-20T17:50:54.340" Score="3" Body="&lt;p&gt;genetic modification can be done with mutations. A mutation is a permanent change in the sequence of DNA. In order to obtain an observable effect, mutations must occur in gene exons, or regulatory elements. Changes in the non-coding regions of DNA (introns and junk DNA) generally do not affect function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations can be caused by:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;external (exogenous) factors, such as chemicals and radiation &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;or&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;endogenous (native) factors&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Mutations can be advantageous and lead to an evolutionary advantage of a certain genotype..this will be a solution for your plant modification..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A mutagen is a physical or chemical agent that changes the genetic material, usually DNA, of an organism and thus increases the frequency of mutations above the natural background level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;chemical mutagens:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Bromine &lt;/li&gt;&#xA;&lt;li&gt;Sodium azide&lt;/li&gt;&#xA;&lt;li&gt;Psoralen&lt;/li&gt;&#xA;&lt;li&gt;Benzene&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;long term treatment plant with mutagens caused mutations some might be advantage&#xA;then select advantage ..&#xA; As many mutations cause cancer, mutagens are therefore also likely to be carcinogens!&lt;/p&gt;&#xA;" OwnerUserId="9414" LastEditorUserId="231" LastEditDate="2014-09-20T18:53:22.373" LastActivityDate="2014-09-20T18:53:22.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21500" PostTypeId="1" CreationDate="2014-09-20T17:56:02.990" Score="4" ViewCount="2241" Body="&lt;p&gt;I've lately seen a lot of instances where a leaf is dangling from a piece of web coming down off a tree. What purpose/s does this serve for the spider? Is it some sort of mechanism for the spider to determine the wind / disturbances in that region?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen a &lt;a href=&quot;http://calamvalecreek.awardspace.com/web-leaf.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;suggestion&lt;/a&gt; that it's to help act as a plumb during web construction to keep part of it tight, but do we actually know for sure?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a national geographic image showing what I mean:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Mhqag.jpg&quot; alt=&quot;enter image description here&quot;&gt; &#xA;&lt;a href=&quot;http://ngm.nationalgeographic.com/ngm/photo-contest/2012/entries/177963/view/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://ngm.nationalgeographic.com/ngm/photo-contest/2012/entries/177963/view/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9415" LastEditorUserId="9415" LastEditDate="2014-09-20T18:26:39.747" LastActivityDate="2018-06-01T09:26:01.237" Title="Why do spiders have a leaf at the bottom of a piece of web?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21501" PostTypeId="1" CreationDate="2014-09-20T19:38:14.373" Score="6" ViewCount="1104" Body="&lt;p&gt;I learned how the CO$_2$ cycle works in several biology classes, high school, elementary school, geology, and physics. Then today there was an &lt;a href=&quot;http://www.nytimes.com/2014/09/20/opinion/to-save-the-planet-dont-plant-trees.html&quot; rel=&quot;noreferrer&quot;&gt;article published in the NY Times&lt;/a&gt; claiming:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...it is a myth that photosynthesis controls the amount of oxygen in the atmosphere. Even if all photosynthesis on the planet were shut down, the atmosphere's oxygen content would change by less than 1 percent.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm really confused. If the earth naturally has 20% oxygen in the absence of photosynthisis, why did it spike durring &lt;a href=&quot;http://en.wikipedia.org/wiki/Great_Oxygenation_Event&quot; rel=&quot;noreferrer&quot;&gt;Great Oxygenation Event&lt;/a&gt;? I reread that several times. There's no citation; no further context that can explain this. If this were coming from the climate change denier camp, I'd just shrug it off, but the credentials would say otherwise. It's in the NY Times and &lt;a href=&quot;http://environment.yale.edu/profile/nadine-unger/&quot; rel=&quot;noreferrer&quot;&gt;Nadine Unger&lt;/a&gt; is an atmospheric chemist at Yale.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My guess is that this is simply a misleading paragraph with a grain of truth. The question is, where is that grain? How long would the atmospheric oxygen content remain at within 1% of the current level if we turned off photosynthesis?&lt;/p&gt;&#xA;" OwnerUserId="810" LastEditorUserId="1320" LastEditDate="2014-09-20T21:33:29.483" LastActivityDate="2014-09-21T01:17:05.190" Title="Would oxygen levels be stable without photosynthesis?" Tags="&lt;ecology&gt;&lt;climate-change&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21502" PostTypeId="2" ParentId="8946" CreationDate="2014-09-21T00:25:20.610" Score="0" Body="&lt;p&gt;This is more likely snails eggs.  If it is in a wet or very humid area, and the eggs seem to be immersed in a matrix of a clear substance, that help retain water.  Insects do not lay their eggs in substances like that, since there are more resistant to desiccation.&lt;/p&gt;&#xA;" OwnerUserId="9422" LastActivityDate="2014-09-21T00:25:20.610" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21503" PostTypeId="2" ParentId="9176" CreationDate="2014-09-21T00:54:43.190" Score="0" Body="&lt;p&gt;Maybe this is a late answer, but the difference between an assasing bug (Reduviidae) and a squash bug (or leaf-footed bug, Coreidae) is the structure of the beak.  Reduviidae, being predaceous, have relative short, bended beaks, made of three segments and do not go beyond the first pair of legs.  Coreidae, herbivores, have a long beak made of four segments.  This can be see it clearly in the third and fifth picture, it is a Coreidae.&lt;/p&gt;&#xA;" OwnerUserId="9422" LastActivityDate="2014-09-21T00:54:43.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21504" PostTypeId="2" ParentId="21501" CreationDate="2014-09-21T01:17:05.190" Score="6" Body="&lt;p&gt;The answer to your question is in the first graph of the Wikipedia article you linked to: &lt;a href=&quot;http://en.wikipedia.org/wiki/Great_Oxygenation_Event&quot;&gt;Great Oxygenation Event&lt;/a&gt;. In that graph, where time is measures in billions of years, you see that O&lt;sub&gt;2&lt;/sub&gt;, as it was produced, was absorbed in oceans, seabed rock, land surfaces, and finally, about .85 billion years ago, &lt;em&gt;O&lt;sub&gt;2&lt;/sub&gt; sinks filled&lt;/em&gt; and the gas accumulated in the atmosphere.&lt;sup&gt;[1]&lt;/sup&gt; The spike you speak of was probably due to &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the evolution of the large vascular land plants that brought about increased O&lt;sub&gt;2&lt;/sub&gt; production and increased O&lt;sub&gt;2&lt;/sub&gt; levels due to the enhanced global burial of microbially resistant, lignin-rich organic matter during the Permo–Carboniferous (Berner 2004).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;More simply put, there hadn't been equilibrium established yet between the amount of oxygen being produced, the stabilization of the ocean layers and the 'burial of excess carbon' in the deepest ocean layers. Most of the O&lt;sub&gt;2&lt;/sub&gt; on earth was produced many millions of years ago; it is a myth that the O&lt;sub&gt;2&lt;/sub&gt; we breathe today is the same O&lt;sub&gt;2&lt;/sub&gt; made by, say, ocean phytoplankton yesterday.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nadene Unger states in the &lt;a href=&quot;http://www.nytimes.com/2014/09/20/opinion/to-save-the-planet-dont-plant-trees.html?_r=0&quot;&gt;NYT article&lt;/a&gt; that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[I]t is a myth that photosynthesis controls the amount of oxygen in the atmosphere. Even if all photosynthesis on the planet were shut down, the atmosphere’s oxygen content would change by less than 1 percent.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is because there are tremendous &lt;em&gt;oxygen sinks&lt;/em&gt; that store oxygen gas, such as the surface layers of the ocean. As O&lt;sub&gt;2&lt;/sub&gt; is used, the ocean would give up free O&lt;sub&gt;2&lt;/sub&gt;. Because of these sinks, some estimate that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;if photosynthesis were to cease, atmospheric oxygen would be depleted in 5000 years due to respiration, weathering, and combustion.&lt;sup&gt;[2]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;while others state that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If photosynthesis were for some reason to stop, oxidation of the entire organic carbon reservoir would consume less than 1% of O&lt;sub&gt;2&lt;/sub&gt; presently in the atmosphere and there would be no further O&lt;sub&gt;2&lt;/sub&gt; loss (since there would be no organic carbon left to be oxidized). Conversely, if respiration and decay were to stop, conversion of all atmospheric CO&lt;sub&gt;2&lt;/sub&gt; to O&lt;sub&gt;2&lt;/sub&gt; by photosynthesis would increase O&lt;sub&gt;2&lt;/sub&gt; levels by only 0.2%.&lt;sup&gt;[3]&lt;/sup&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is very hard to get a comprehensive answer of what would happen exactly. Do we assume all vegetation/phytoplankton suddenly disappears, or does it die (thus increasing to the carbon drain on O&lt;sub&gt;2&lt;/sub&gt;)? Do we assume quick quick death of animals based on lack of vegetation/plankton, etc. as food, or would it be slower? As I said, a comprehensive answer is difficult to find. In any case, the atmospheric O&lt;sub&gt;2&lt;/sub&gt; would not fluctuate wildly in any immediate fashion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/361/1470/903.full.pdf&quot;&gt;The oxygenation of the atmosphere and oceans&lt;/a&gt; Heinrich D Holland, Phil. Trans. R. Soc., 29 June 2006&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://paos.colorado.edu/~fasullo/pjw_class/oxygencycle6.html&quot;&gt;The Global Oxygen Cycle&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://acmg.seas.harvard.edu/people/faculty/djj/book/bookchap6.html&quot;&gt;Introduction to Atmospheric Chemistry&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-09-21T01:17:05.190" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21506" PostTypeId="1" CreationDate="2014-09-21T03:06:38.813" Score="2" ViewCount="144" Body="&lt;p&gt;I was at Sprouts health store and saw a lot of vitamins/herbs that claimed to be &quot;Study Aids&quot; etc, so if there is any basis to it, where exactly does it hold truth? And are these supplements safe?&lt;/p&gt;&#xA;" OwnerUserId="9402" LastActivityDate="2014-09-22T01:00:29.790" Title="Vitamins that could help &quot;make us smarter&quot;?" Tags="&lt;vitamins&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-09-22T09:19:38.053" ContentLicense="CC BY-SA 3.0" />
  <row Id="21507" PostTypeId="1" AcceptedAnswerId="21510" CreationDate="2014-09-21T05:24:19.747" Score="39" ViewCount="45202" Body="&lt;p&gt;We all suffer from common cold, and that, frequently. Why have we not developed immunity against it till now? By immunity I mean immunity as a species.&lt;/p&gt;&#xA;" OwnerUserId="9186" LastEditorUserId="3971" LastEditDate="2014-10-01T18:59:00.723" LastActivityDate="2018-01-07T17:05:32.067" Title="Why don't we develop immunity against common cold?" Tags="&lt;immunology&gt;&lt;virology&gt;&lt;virus&gt;&lt;infection&gt;&lt;immunity&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="21509" PostTypeId="1" AcceptedAnswerId="21543" CreationDate="2014-09-21T10:12:41.687" Score="3" ViewCount="76" Body="&lt;p&gt;I was reading about reaction-diffusion processes, morphogenesis concept by Alan Turing and works of Murray in describing pattern formation on animals etc. But one question which came to my mind was even if we describe these processes in mathematical and physical contexts, are there any application areas awaiting for the results?&lt;/p&gt;&#xA;" OwnerUserId="5669" LastActivityDate="2014-09-22T14:19:09.540" Title="What are the application areas of Pattern formation studies specific to biology?" Tags="&lt;mathematical-models&gt;&lt;development&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-09-22T15:54:25.880" ContentLicense="CC BY-SA 3.0" />
  <row Id="21510" PostTypeId="2" ParentId="21507" CreationDate="2014-09-21T11:26:55.957" Score="37" Body="&lt;p&gt;Long lasting immunity is obtained by means of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Adaptive_immune_system&quot;&gt;adaptive immune system&lt;/a&gt;, and mainly involves the development of antibodies that identify specific parts (&lt;a href=&quot;http://en.wikipedia.org/wiki/Epitope&quot;&gt;epitopes&lt;/a&gt;) of the pathogen's proteins. Common cold is typically caused by a type of virus called &lt;a href=&quot;http://en.wikipedia.org/wiki/Common_cold&quot;&gt;rhinovirus&lt;/a&gt;. Viruses have very high mutation rates, which alter the sequence of the virus proteins, modifying their antigenic properties. This consequently alters the ability of antibodies to recognize a particular antigen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, we &lt;em&gt;do&lt;/em&gt; develop long lasting immunity against the virus that causes us a cold today, but the virus that causes us a cold a few months later is somewhat different, and the adaptive immune system has to start from scratch.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastActivityDate="2014-09-21T11:26:55.957" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21511" PostTypeId="1" AcceptedAnswerId="21521" CreationDate="2014-09-21T14:49:36.570" Score="20" ViewCount="25960" Body="&lt;p&gt;Isopropyl alcohol (2-propanol) can be used as disinfectant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For increasing concentration of it in water, the effect as disinfectant increases, and then decreases again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Typical concentrations for use as disinfectant seem to be 60-75% isopropyl alcohol in water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Isopropyl_alcohol#Medical&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia: Isopropyl alcohol - Medical&lt;/a&gt; mentions membrane pores of bacteria that will not open without water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That does not feel like the full explanation to me; I expect there are bacteria with membrane pores of diverse kind.&#xA;Does 100% isopropyl alcohol not disinfect at all - or just more slowly? What abour the effect on other pathogens?&lt;/p&gt;&#xA;" OwnerUserId="6194" LastEditorUserId="6194" LastEditDate="2017-02-22T11:39:10.220" LastActivityDate="2018-04-17T17:20:27.673" Title="How does isopropyl alcohol disinfect less in higher concentration?" Tags="&lt;bacteriology&gt;&lt;alcohol&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21513" PostTypeId="1" CreationDate="2014-09-21T15:39:06.710" Score="7" ViewCount="651" Body="&lt;p&gt;Various mammals seem to get away with &lt;strong&gt;eating parts of carcasses&lt;/strong&gt; that we would prefer to &lt;strong&gt;not even touch&lt;/strong&gt;, and that we assume will make us sick.&lt;br&gt;&#xA;Because of that, I assume botulinum toxin is more dangerous to humans than many animals.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is that right so far - can they &lt;strong&gt;handle more&lt;/strong&gt; of some toxins compared to us?&lt;br&gt;&#xA;Or are they &lt;strong&gt;better in avoiding&lt;/strong&gt; harmful substances based on more suited olfactory sense?&lt;br&gt;&#xA;Or are we just &lt;strong&gt;more afraid&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming the differences exist - what is the cause for it?&lt;br&gt;&#xA;Are there plausible explanations in terms of evolutionary pressure?&lt;/p&gt;&#xA;" OwnerUserId="6194" LastEditorUserId="107" LastEditDate="2014-09-21T17:40:25.180" LastActivityDate="2014-09-23T10:38:31.240" Title="Why does botulinum toxin seem to be more dangerous to humans than to other mammals?" Tags="&lt;evolution&gt;&lt;bacteriology&gt;&lt;mammals&gt;&lt;medicine&gt;&lt;bacterial-toxins&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21515" PostTypeId="2" ParentId="21506" CreationDate="2014-09-21T18:48:24.713" Score="4" Body="&lt;p&gt;&lt;strong&gt;Are there vitamins that make us smarter?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vitamins are micronutrients required in small quantities for normal human metabolism. Extra high (&lt;a href=&quot;http://www.merriam-webster.com/medical/supraphysiological&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;supra-physiological&lt;/em&gt;&lt;/a&gt;) doses do not generally result in improved performance. Of course, if one is deficient in certain vitamins (e.g. Vit B-1 deficiency causing Wernicke-Korsakoff encephalopathy), taking a vitamin can restore normal function. However, with adequate access to a normal diet, you are unlikely to be deficient. Commonly cited exceptions include:  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;strict vegans (Vit B12)&lt;/li&gt;&#xA;&lt;li&gt;alcoholics (thiamine (B1), folate)&lt;/li&gt;&#xA;&lt;li&gt;cultures highly dependent on maize as a staple (niacin (B3))&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In people with a normal diet, &lt;a href=&quot;http://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/24490265&quot; rel=&quot;nofollow&quot;&gt;taking additional vitamin supplements is usually not helpful&lt;/a&gt;.* (An exception may be Vitamin D depending on whom you talk to, but this is unrelated to cognitive performance.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been scattered studies showing some benefit of various plant extracts and other “natural” substances. Studies such as &lt;a href=&quot;http://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/11498727&quot; rel=&quot;nofollow&quot;&gt;this one about Bacopa monniera&lt;/a&gt; do demonstrate benefit. However, many such studies are of limited value due to sponsorship by the makers of supplements and publication in journals with questionable quality of peer review. &lt;a href=&quot;http://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/14624946&quot; rel=&quot;nofollow&quot;&gt;This meta-analysis&lt;/a&gt; reviewing the effects of phosphatidylserine, phosphatidylcholine, citicoline, piracetam, vinpocetine, acetyl-L-carnitine, and antioxidants reached a more guarded conclusion:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;for most of the &quot;brain-specific&quot; nutrients we review, some mildly suggestive effects have been found in preliminary controlled studies &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Note that most of the substances discussed thus far are not &lt;a href=&quot;http://en.wikipedia.org/wiki/Vitamin&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;vitamins&lt;/em&gt;&lt;/a&gt; but rather amino acids, more complex plant extracts, or &amp;mdash; in the case of caffeine &amp;mdash; a synthetic crystalline xanthine alkaloid. These sorts of things are commonly included in supplements found at health stores. As for vitamins specifically, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17474991&quot; rel=&quot;nofollow&quot;&gt;this large randomized controlled trial&lt;/a&gt; found no effect of multivitamin and mineral supplementation on cognitive function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What component of Cognitive Supplements are active?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer is usually caffeine. Caffeine is cheap, widely available, and markedly improves short-term cognitive and physical performance. By &lt;a href=&quot;http://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/25175970&quot; rel=&quot;nofollow&quot;&gt;modulating adenosine activity&lt;/a&gt; in the central nervous system, it &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25057583&quot; rel=&quot;nofollow&quot;&gt;improves alertness&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20394312&quot; rel=&quot;nofollow&quot;&gt;prevents impairment in neuro-plasticity&lt;/a&gt; associated with sleep deprivation, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22101644&quot; rel=&quot;nofollow&quot;&gt;potentiates synaptic transmission&lt;/a&gt; in animal models, and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23625556&quot; rel=&quot;nofollow&quot;&gt;may slow neurodegeneration&lt;/a&gt; in certain disease states. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23206286&quot; rel=&quot;nofollow&quot;&gt;This review article&lt;/a&gt; looked at ”enhancement supplements” containing taurine, guaraná, ginseng, glucuronolactone, B-vitamins, and other compounds  as well as caffeine and concluded:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;there is an overwhelming lack of evidence to substantiate claims that components of [energy supplement drinks], other than caffeine, contribute to the enhancement of physical or cognitive performance.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To your question,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Are these supplements safe?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You should look at the ingredients. If it is caffeine, the answer is: &lt;a href=&quot;http://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/20492310&quot; rel=&quot;nofollow&quot;&gt;usually&lt;/a&gt;. However, it is not recommended for those with insomnia, anxiety, palpitations, or who are underweight. As for other components of these, you need to read the label and do your research. As mentioned in the footnote, vitamins themselves are not without the possibility of harm at supra-physiological doses. For other components the danger is likely uncertain and under-researched. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;*For those interested in the vitriol around this subject, check out &lt;a href=&quot;http://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/24490268&quot; rel=&quot;nofollow&quot;&gt;this series&lt;/a&gt; of editorials that followed the paper linked above. Quoting the first of these:&lt;br&gt;&#xA;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;sub&gt; In conclusion, β-carotene, vitamin E, and possibly high doses of vitamin A supplements are harmful. Other antioxidants, folic acid and B vitamins, and multivitamin and mineral supplements are ineffective for preventing mortality or morbidity due to major chronic diseases. Although available evidence does not rule out small benefits or harms or large benefits or harms in a small subgroup of the population, we believe that the case is closed— supplementing the diet of well-nourished adults with (most) mineral or vitamin supplements has no clear benefit and might even be harmful. These vitamins should not be used for chronic disease prevention. Enough is enough. &lt;/sub&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-09-22T01:00:29.790" LastActivityDate="2014-09-22T01:00:29.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21516" PostTypeId="1" AcceptedAnswerId="21551" CreationDate="2014-09-21T19:01:26.083" Score="11" ViewCount="1538" Body="&lt;p&gt;I picked an apple from the ground, it was wet with dew and a woodlouse was stuck to it, with its back against the apple. When it got loose, it started flexing its &quot;tail&quot; like this for a while. Why?&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/qJTZm.gif&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8630" LastActivityDate="2014-09-22T20:15:46.290" Title="What is this woodlouse doing?" Tags="&lt;zoology&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21517" PostTypeId="1" CreationDate="2014-09-21T19:55:10.320" Score="2" ViewCount="105" Body="&lt;p&gt;Genetics textbooks (and some internet searching) yield abundant examples of Hfr strains conjugating with F- cells, but these sources are surprisingly silent regarding the results of an Hfr encountering another Hfr strain. Will conjugation occur in both directions, or will it not occur at all? Similarly, can F+ cells conjugate with other F+ cells?&lt;/p&gt;&#xA;" OwnerUserId="1906" LastActivityDate="2014-09-21T19:55:10.320" Title="Can two Hfr strains of E. coli conjugate?" Tags="&lt;genetics&gt;&lt;bacteriology&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21518" PostTypeId="1" AcceptedAnswerId="41903" CreationDate="2014-09-21T19:55:14.353" Score="2" ViewCount="688" Body="&lt;p&gt;At mutation-drift balance, the increased heterozygosity brought by new mutations is exactly equal to the loss of heterozygosity due to genetic drift. At equilibrium, the expected heterozygosity for a given locus is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\hat h = \frac{4Nu}{1+4Nu}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The expected heterozygosity is only the first moment of the whole distribution of locus specific heterozygosity. &lt;strong&gt;What is the (among loci) variance in heterozygosity?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2016-04-29T12:26:38.680" Title="Mutation-drift equilibrium and among loci variance in heterozygosity" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21519" PostTypeId="2" ParentId="21511" CreationDate="2014-09-21T20:05:38.457" Score="10" Body="&lt;p&gt;So this is a good question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;70% is optimal for most cell types, especially those with a cell wall like prokaryotes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia is a little off here. The reason you add water is to make the solution hypotonic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The alcohol disrupts the hydrophobic forces holding the phospholipids of the membrane while dehydrating any peptidogylcan of the wall enough to cause it to become less fluid/more brittle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now that you have essentially made the protection of the cell like brittle glass, the hypotonicity causes the cell to swell and now easily burst.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria aren't going to last long in 100% either. They fix instead, which although irreversible takes a little longer to occur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also a little more economical and less wasteful to use 70% if it's just as, if not a little more, effective&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="9429" LastEditDate="2014-09-21T22:42:08.523" LastActivityDate="2014-09-21T22:42:08.523" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21520" PostTypeId="1" AcceptedAnswerId="28157" CreationDate="2014-09-21T20:51:26.527" Score="5" ViewCount="5647" Body="&lt;p&gt;The popular potted plant, Pothos aureus (or Epipremnum aureum) is happy to grow in a jar, with only water, for years. How is this possible when other plants need at least Nitrogen, Phosphorus and Potassium?&lt;/p&gt;&#xA;" OwnerUserId="9427" LastActivityDate="2016-05-10T04:53:41.100" Title="How does Pothos grow in only water?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21521" PostTypeId="2" ParentId="21511" CreationDate="2014-09-21T20:51:36.937" Score="17" Body="&lt;p&gt;The main reason why alcohols (isopropanol and ethanol mostly) can be used as disinfectants is that they denature (bacterial) proteins. This is also the reason why they work on such a broad spectrum of microorganisms (bacteria, fungi, viruses), but not on spores, as these are better protected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The higher the concentration of the alcohol is, the faster this denaturation is happening. And this can cause problems: When you denature the proteins of the bacterial cell wall, they will form some kind of protective layer around some of the cells which allows their survival. Diluting the alcohols makes the disinfection happening slower and thus gives the alcohols more time to get into the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information about concentrations and also for a ton of references, have a look into the CDC's disinfection guidelines in the subchapter on &lt;a href=&quot;http://www.cdc.gov/hicpac/Disinfection_Sterilization/6_0disinfection.html#a1&quot;&gt;alcohols&lt;/a&gt;.&#xA;More details can be found in this review: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://cmr.asm.org/content/12/1/147.full&quot;&gt;Antiseptics and Disinfectants: Activity, Action, and Resistance&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="6928" LastEditDate="2014-09-22T02:37:48.607" LastActivityDate="2014-09-22T02:37:48.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21522" PostTypeId="1" AcceptedAnswerId="21697" CreationDate="2014-09-21T22:03:51.210" Score="4" ViewCount="56" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Robustness_(evolution)&quot; rel=&quot;nofollow&quot;&gt;robustness&lt;/a&gt; of a genotype is the ability of this genotype to resist (always produce the same phenotype) to various parameters such as mutations and environment. The ability of a genotype to resist to mutations is called mutational robustness while the ability of a genotype to resist to varying environmental variables is called environmental robustness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there a correlation between environmental and mutational robustness?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words the above question is: is there a among-species/populations/genotype correlation between mutational robustness and environmental robustness? i.e., Knowing that species $A$ has high mutational robustness, is species $A$ more or less likely than a randomly picked species $B$ to have a high environmental robustness? Or are the concepts of environmental and mutational robustness completely different and involve completely different genes and genetic architecture? Both theoretical and empirical studies that offer insights to this question are welcome.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-09-25T01:08:30.793" LastActivityDate="2014-11-22T20:35:38.330" Title="Is there an association between environmental and mutational robustness?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;&lt;genomics&gt;&lt;population-dynamics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21523" PostTypeId="1" AcceptedAnswerId="21526" CreationDate="2014-09-21T23:40:30.917" Score="34" ViewCount="20345" Body="&lt;p&gt;If you are in pitch black and you close your eyes, you sometimes can see strange shapes of various colors. A lot of the time these shapes and colors change as you observe them. This phenomenon still occurs if you are not in complete darkness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering what this is that you are `seeing'? Is this phenomenon classified as seeing, as how can we be looking at something if our eyes are closed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are not seeing these shapes and colors, then what you observe is pure darkness. What is this pure darkness that you are seeing? Since you are seeing it, is something stimulating the vision parts of your brain? Is it the back of your eyelid?&lt;/p&gt;&#xA;" OwnerUserId="8592" LastEditorUserId="8592" LastEditDate="2014-09-22T14:48:41.767" LastActivityDate="2017-12-09T11:49:46.303" Title="What do you see when your eyes are closed?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;vision&gt;&lt;human-eye&gt;&lt;visualization&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="21525" PostTypeId="2" ParentId="13595" CreationDate="2014-09-22T00:20:03.663" Score="18" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;How did multicellularity evolved?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;It is an ongoing field of research - Some insights about the origin of multicellularity&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a big ongoing field of research. To start with an example, there was relatively recently (2012) an important article by &lt;a href=&quot;http://www.zoology.ubc.ca/veg/RatcliffEtAl2012.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ratcliff et al.&lt;/a&gt; that shows that yeast can quickly evolve multicellularity under selection on the speed they sink to lower water layers. This article is one among many others and is far from being able to explain everything we would like to understand about the evolution of multicellularity. Typically, I think that this yeast species had a multicellular ancestor and we might think that this species would already have fixed alleles (=variants of genes that is fixed meaning that the whole population is carrying this variant today) in the population predisposing this species to easily (re-)evolve multicellularity. Also, they may have kept some standing additive genetic variance in their genome from their past and they would therefore very quickly respond to selection as they don't need de novo mutations. (Sorry if this last sentence was slightly technical).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the first traits that we usually refer to when talking about the evolution of multicellularity is the presence of sticky proteins allowing individual cells to paste to each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Some insights about the evolution from simple multicellular to more complex multicellular&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, we could talk about more complex multicellular and argue how do these simple multicellular evolve into some more complex organisms. A common argument is that multicellular can have specialized cells are very could at doing what they're doing as they are specialized. Also, some level of complexity is thought to have raised due to the fact that multicellular organisms tend to have smaller population size than unicellular (see &lt;a href=&quot;http://www.sciencemag.org/content/302/5649/1401.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lynch and Conery, 2003&lt;/a&gt;). It is important not to confuse evolution of complexity with the evolution of multicellularity although these two notions are somehow related.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What do you mean by multicellularity?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The evolution of multicellularity can be discussed in the context where sister cells form an organism together or when unrelated cells (among the same species or even cells from different species) come together to form an organism. Also, the multicellularity can be discussed at a different level depending on how we want to define multicellularity. Is a stack of cells reproducing individually, working for their own benefit a multicellular? Do we need a division of labor? Do we need a division between germline (reproductive caste) and soma line (non-reproductive case)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How many times did multicellularity evolve independently?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some people consider that there are multicellular bacteria (biofilms) but we will avoid discussions that are based on limit-case definitions. Let's talk about eukaryotes. Most Eukaryotes are unicellular and multicellularity evolved many times independently in eukaryotes. To my knowledge, complex multicellularity however evolved only (only?) 6 times independently in eukaryotes.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Metazoa (animals)&lt;/li&gt;&#xA;&lt;li&gt;Ascomyceta (fungi)&lt;/li&gt;&#xA;&lt;li&gt;Basidiomyceta (fungi)&lt;/li&gt;&#xA;&lt;li&gt;Viridiplantae (green plants)&lt;/li&gt;&#xA;&lt;li&gt;Florideophyceae (red algae)&lt;/li&gt;&#xA;&lt;li&gt;Laminariales (brown algae)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Model organisms and interesting cases to study multicellularity&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a bunch of specific clades that are particularly interested in studying multicellularity because they present transition states. For example &lt;a href=&quot;http://en.wikipedia.org/wiki/Volvox&quot; rel=&quot;nofollow noreferrer&quot;&gt;Volvox&lt;/a&gt; is a chlorophyte genus and the species in this clade present different stages of multicellularity; Some species are exclusively multicellular, some form small groups, some create big colonies, some have some division of labor and some even have separation between the germline and the soma (Some castes don't reproduce). (&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/early/2011/12/05/rspb.2011.1999.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref1&lt;/a&gt;, &lt;a href=&quot;http://icb.oxfordjournals.org/content/43/2/247&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref2&lt;/a&gt;, &lt;a href=&quot;http://mbe.oxfordjournals.org/content/23/8/1460&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref3&lt;/a&gt;, &lt;a href=&quot;http://www.sciencemag.org/content/329/5988/128.1.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref4&lt;/a&gt;, &lt;a href=&quot;http://www.sciencemag.org/content/329/5988/223.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref5&lt;/a&gt;, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1369526610001585&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref6&lt;/a&gt;). Yeasts are also a good model organism for studying the evolution of multicellularity. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-28T01:01:14.010" LastActivityDate="2019-03-28T01:01:14.010" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="21526" PostTypeId="2" ParentId="21523" CreationDate="2014-09-22T01:25:38.813" Score="38" Body="&lt;p&gt;This is called a &lt;a href=&quot;http://medical-dictionary.thefreedictionary.com/Phosphenes&quot;&gt;phosphene&lt;/a&gt; &amp;mdash; the experience of perceiving light in the visual cortex without light actually entering the eye. This commonly happens due to stimulation of the retinal ganglion cells by something else. The most frequent source in normal individuals is pressure to the retina (e.g. rubbing a closed eye.) It is also possible for phosphenes to occur due to neuronal stimulation at the cortical level. Most people have had the experience of “seeing stars” when you stand up too quickly. This happens because &lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/orthostatic-hypotension/basics/definition/con-20031255&quot;&gt;orthostatic hypotension&lt;/a&gt; results in transiently decreased cerebral perfusion; it is the metabolic shift in oxygenation and/or glucose delivery to cortical neurons that causes the perception of light. Something similar occurs with brief rises in intracranial pressure that occurs with sneezing or coughing.* &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24618215&quot;&gt;Magnetic stimuli&lt;/a&gt; can also induce this phenomenon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phosphenes can also be pathologic (i.e. disease-associated). Migraine headache sufferers may experience a visual “aura” prior to a headache, which is a type of phosphene, likely mediated at the cortical level. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19076647&quot;&gt;There is some evidence&lt;/a&gt; to suggest that preventing the phosphene may also reduce headache frequency. Other conditions associated with phosphenes include &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7062073&quot;&gt;abnormalities of the optic nerve&lt;/a&gt;** and retina &amp;mdash; just as stimulation of a peripheral somatic sensory nerve might cause a pain signal to arrive in the brain in the absence of true tactile stimulation, disorders of the optic nerve can generate disorganized signals that the brain perceives as light.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;*Increased intracranial pressure leads to decreased perfusion due to the differential between peripheral and cerebral pressures.&#xA;&lt;/sub&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;**If you read nothing else linked to this question, take a look at that paper (free in PMC). It describes optic neuropathy associated with auditory-evoked phosphenes. The patients perceived &lt;em&gt;sound&lt;/em&gt; as &lt;em&gt;light&lt;/em&gt;!&#xA;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-09-22T07:37:33.440" LastActivityDate="2014-09-22T07:37:33.440" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21527" PostTypeId="1" AcceptedAnswerId="21534" CreationDate="2014-09-22T04:38:38.697" Score="19" ViewCount="7779" Body="&lt;p&gt;In most biomes on earth, and certainly in the most densely-populated, the best camouflage color or pattern for an animal would be a variant of green, so as to blend in with the leaves and grasses of the surrounding environment.  Whether predator or prey, the art of not being seen is hugely important in the natural world, and yet to the best of my knowledge there isn't a single mammal on the planet with fur that is even partially green.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a reason for that?  It seems like animals have evolved some pretty crazy color patterns to break up their silhouette or blend into the background, but why haven't any mammals taken the obvious route of &quot;look like leaves&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it really THAT not-easy being green?&lt;/p&gt;&#xA;" OwnerUserId="5917" LastActivityDate="2015-12-13T03:35:26.713" Title="Why is green fur not a thing?" Tags="&lt;evolution&gt;&lt;adaptation&gt;&lt;antipredator-adaptation&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21529" PostTypeId="2" ParentId="10694" CreationDate="2014-09-22T05:26:43.440" Score="4" Body="&lt;p&gt;The light receptor of the eye is a protein called &lt;a href=&quot;https://en.wikipedia.org/wiki/Rhodopsin&quot; rel=&quot;nofollow&quot;&gt;Rhodopsin&lt;/a&gt;.  To me the equivalent of shutter speed for the eye is the (de)&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12742390&quot; rel=&quot;nofollow&quot;&gt;sensitization of rhodopsin by phosphorylation&lt;/a&gt;.  The brighter the light, the more sites on rhodopsin are phosphorylated, diminishing the intensity of the signal coming from the photo receptor via the transducin G protein that conveys the visual signal onward.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This process takes a few seconds, but then its possible to see when stepping into sunlight or in a darkened room.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is more like a volume knob than a shutter speed since the same signal comes out at the same rate of each light sensor, but it has a similar effect - it modulates the intensity of the image. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-09-22T05:26:43.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21530" PostTypeId="1" CreationDate="2014-09-22T06:37:36.270" Score="3" ViewCount="100" Body="&lt;p&gt;Scenario: I'm about to fall asleep with the T.V. on. Having completely forgotten that it was, no longer even &lt;em&gt;hearing&lt;/em&gt; it, just before falling asleep I turn over with a 'fresh' ear and it's blaring. If I roll back over it will be noticeable, but quiet again. Waking hours my ears are fine, no worries. Is this some weird sleep induced brain shut-down going on?&lt;/p&gt;&#xA;" OwnerUserId="8559" LastActivityDate="2014-09-22T06:37:36.270" Title="TV's so loud when I turn over" Tags="&lt;brain&gt;&lt;sleep&gt;&lt;hearing&gt;&lt;human-ear&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21532" PostTypeId="1" AcceptedAnswerId="21693" CreationDate="2014-09-22T07:40:26.740" Score="5" ViewCount="152" Body="&lt;p&gt;Winter Moth (&lt;em&gt;Operophtera brumata&lt;/em&gt;) is a small brachypterous (females have stunned wings - unable to fly) moth which places eggs on thick branches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know which abiotic and biotic factors may play a role in selection of place for oviposition. Taking into account that &lt;strong&gt;level of humidity is probably the same on whole tree&lt;/strong&gt; (and probably whole forest) and the branches are so thick that they are not distinguishionable from surrounding environment (and &lt;strong&gt;there is no accumulated heat to identify their orientation&lt;/strong&gt; (south, north etc.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What other factors may play a role?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="9435" LastEditorUserId="9435" LastEditDate="2014-09-22T09:04:30.767" LastActivityDate="2014-09-27T15:07:40.617" Title="Which factors may affect a choice of an oviposition place in nocturnal moths?" Tags="&lt;entomology&gt;&lt;ecology&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21533" PostTypeId="1" AcceptedAnswerId="21536" CreationDate="2014-09-22T08:01:07.327" Score="24" ViewCount="21028" Body="&lt;p&gt;If I were to count my father, my grandfather, my great-grandfather, and so on up till, say chimps, or the most common ancestor, or whatever that suits the more accurate answer, how many humans would there have been in my direct lineage?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And would it be almost the same for every human being currently living?&lt;/p&gt;&#xA;" OwnerUserId="3141" LastEditorUserId="3624" LastEditDate="2014-09-22T08:59:49.797" LastActivityDate="2019-04-29T02:01:38.217" Title="How many humans have been in my lineage? Is it almost the same for every human currently living?" Tags="&lt;evolution&gt;&lt;population-dynamics&gt;" AnswerCount="4" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21534" PostTypeId="2" ParentId="21527" CreationDate="2014-09-22T08:35:25.090" Score="17" Body="&lt;p&gt;The technical answer is: Because the coloration of skin and hair is done by the two forms of melanin: Eumelanin, which is dark brown to black and Pheomelanin which is yellow to red. This enables colors from white (not pigmentation) to black (dense eumelanin pigmentation) and also colors in between by different ratios of the two pigments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The evolutionary answer is that it obviously made no evolutionary advantage to have other colors. If you look closer at this, you will see that most habitats are not green or only for a part of the year. If you think about african plains, these are mostly brown, something like artic landscapes are only green for a very short timeframe in the summer, for the rest of the year these are white to brown. And even tropical rainforests are mostly dark to brown on the ground. They would clearly stick out of the environment with green colored hair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For all these different habitats the animals living there have adapted their hair color. It is not uncommon for artic animals to change their hair color with the course of the year, dark to brown in the summer and white in the winter (artic foxes and snow hare) for example. Animals which live in deserts will have a paler color than those which live in dark colored mountain areas. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this article for more information: &quot;&lt;a href=&quot;http://bioscience.oxfordjournals.org/content/55/2/125.full&quot;&gt;The Adaptive Significance of Coloration in Mammals&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also interesting in this context is this article which looks at the reason for zebra stripes: &quot;&lt;a href=&quot;http://www.nature.com/ncomms/2014/140401/ncomms4535/abs/ncomms4535.html&quot;&gt;The function of zebra stripes&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-09-22T08:43:46.143" LastActivityDate="2014-09-22T08:43:46.143" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21535" PostTypeId="1" AcceptedAnswerId="21601" CreationDate="2014-09-22T08:50:44.260" Score="2" ViewCount="235" Body="&lt;p&gt;I've been facing this lately, where I will wake up in the middle of the night after sleeping for perhaps 2-3 hours and be wide awake, but when I go back to sleep, I wake up more tired than before.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone shed some light on this?&lt;/p&gt;&#xA;" OwnerUserId="9179" LastActivityDate="2014-10-25T23:09:46.280" Title="Is the quality of sleep dependent on sleep duration?" Tags="&lt;human-biology&gt;&lt;sleep&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21536" PostTypeId="2" ParentId="21533" CreationDate="2014-09-22T08:51:01.810" Score="26" Body="&lt;p&gt;A quick back-of-the-envelope answer to the number of generations that have passed since the estimated human-chimp split would be to divide the the split, approximately 7 million years ago (&lt;a href=&quot;http://www.pnas.org/content/109/39/15716&quot; rel=&quot;noreferrer&quot; title=&quot;Langergraber et al. 2012. Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. PNAS 109(39)&quot;&gt;Langergraber et al. 2012&lt;/a&gt;), by the human generation time. The human generation time can be tricky to estimate, but 20 years is often used. However, the average number is likely to be higher. Research has shown that the great apes (chimps, gorilla, orangutan) have generation times comparatble to humans, in the range of 18-29 years (&lt;a href=&quot;http://www.pnas.org/content/109/39/15716&quot; rel=&quot;noreferrer&quot; title=&quot;Langergraber et al. 2012. Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. PNAS 109(39)&quot;&gt;Langergraber et al. 2012&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using 7 million years and 20 years yields an estimated &lt;strong&gt;350000 ancestral generations&lt;/strong&gt; for each living human. A more conservative estimate, using an average generation time of 28, would result in 250000 generations. However, some have argued that the human-chimp split is closer to 13 million years old, which would mean that approximately 650000 generations have passed (using a generation time of 20 years). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact number of ancestral generations for each human will naturally differ a bit, and some populations might have higher or lower numbers on average due to chance events or historical reasons (colonizations patterns etc). However, due to the law of large numbers my guess would be that discrepancies are likely to have averaged out. In any case, the current estimates of the human-chimp split and average historical generation times are so uncertain, so that they will swamp any other effects when trying to calculate the number of ancestoral generations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this is only answering the number of ancestral generations. The &lt;strong&gt;number of ancestors in your full pedigree&lt;/strong&gt; is something completely different. Since every ancestor has 2 parents, the number of ancestors will grow exponentially. Theoretically, the full pedigree of ancestors can be calculated using:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$N_\text{ancestors} = \sum_{i=1}^t 2^i \hspace{1em} \text{or} \hspace{1em} 2^{t+1}-2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where t is the number of generations. However, this will yield an unreasonably large number of ancestors (~$2.3*10^{105}$ over just 350 generations), since it assumes that all of your ancestors are unrelated. Basically, you run into something called &lt;a href=&quot;http://en.wikipedia.org/wiki/Pedigree_collapse&quot; rel=&quot;noreferrer&quot;&gt;pedigree collapse&lt;/a&gt;, which means that your pedigree will have many overlaps (due to inbreeding, overlapping generations etc), so all of your ancestors cannot be seen as unrelated. In practice, this means that the number of ancestors in successive generations will stop doubling for each generation you go back, and will eventually start shrinking, which will drastically reduce the number of unique ancestors. For more on this, see answers to the question &lt;a href=&quot;https://biology.stackexchange.com/questions/16147/initial-population-when-i-count-backwards/16160#16160&quot;&gt;Initial population when i count backwards?&lt;/a&gt;. That question is basically asking about the same issue, but less specifically. There might be studies that have tried to calculate the average number of ancestors to living humans, but I haven't seen any. Therefore, I cannot say anything more specific about the average number of unique ancestors for a living human individual.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-09-22T12:03:38.043" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21537" PostTypeId="1" AcceptedAnswerId="21546" CreationDate="2014-09-22T09:47:08.320" Score="6" ViewCount="187" Body="&lt;p&gt;In a reaction like &lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/8/82/Disulfide-bond.png&quot;&gt;disulphide bond formation&lt;/a&gt; protons and electrons are released. These particles are presumably damaging in high levels. What systems are in place to prevent a build up of electrons and protons? &lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="1320" LastEditDate="2014-09-22T12:26:31.473" LastActivityDate="2014-09-22T15:23:51.043" Title="Where do the electrons and protons formed from biological reactions go?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21538" PostTypeId="2" ParentId="21533" CreationDate="2014-09-22T10:45:51.283" Score="4" Body="&lt;p&gt;Everyone on earth shares a single most common recent ancestor around 3500 years ago (&lt;a href=&quot;http://www.nature.com/nature/journal/v431/n7008/abs/nature02842.html&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;), and given the vast depth of time between this ancestor and the human/chimp split it seems reasonable to assume that the number of ancestors derived via this route vastly outweighs all other ancestors so it makes sense to conclude that the difference in number of ancestors between people is a small proportion of the total number.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for estimating how large that number is, I'm really not sure how you'd do it.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="2938" LastEditDate="2014-09-22T12:31:45.827" LastActivityDate="2014-09-22T12:31:45.827" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="21539" PostTypeId="1" CreationDate="2014-09-22T11:36:09.267" Score="1" ViewCount="237" Body="&lt;p&gt;My shin splints are clearly tied to running. Though the pain level doesn't seem to correlate  to my running intensity. So what is it about running that causes shin splints?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My real hope is that if I understand the cause clearly enough I can adjust to fix them.&lt;/p&gt;&#xA;" OwnerUserId="9438" LastActivityDate="2014-09-23T07:13:30.533" Title="What Causes Shin Splints?" Tags="&lt;muscles&gt;&lt;bone-biology&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-09-23T10:20:12.637" ContentLicense="CC BY-SA 3.0" />
  <row Id="21540" PostTypeId="2" ParentId="21384" CreationDate="2014-09-22T11:41:21.493" Score="4" Body="&lt;p&gt;I'm one of the STRING maintainers, so I hope I can clear things up a bit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Gene co-occurrence:&lt;/strong&gt; genomic context methods are very useful for bacterial genomes, but not so much for eukaryotes. However, they are actually the most unbiased data we have, since there's no human influence (beyond selecting species for sequencing).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Benchmarking:&lt;/strong&gt; Interactions predicted from text-mining etc. are benchmarked against the KEGG database. However, this doesn't necessarily lead to biases, as this benchmarking is basically a calibration step.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Actual biases:&lt;/strong&gt; For eukaryotes, most interaction data comes from the experimental, database and text-mining channel. All of these are biased in various ways: e.g. there are study biases (disease genes will get more attention) and technical biases (some proteins are hard to work with) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As we don't know the actual set of protein-protein interactions, we can probably not test for biases in the data.&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2014-09-22T11:41:21.493" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21541" PostTypeId="1" CreationDate="2014-09-22T12:05:54.833" Score="4" ViewCount="233" Body="&lt;p&gt;Million of years ago there lived dinosaurs up to 36 m high. About 10,000 years ago lived &lt;em&gt;Machairodontinae&lt;/em&gt; -compared to cats today they were huge. About 400,000 years ago lived &lt;em&gt;Mammuthus trogontherii&lt;/em&gt;: it reached over 4 m at the shoulder. And these are just some examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Todays biggest living creatures look small compared to previous. So my question is, why are all creatures getting smaller? Why doesn't evolution generate any big creatures with size comparable to the dinosaurs?&lt;/p&gt;&#xA;" OwnerUserId="9439" LastEditorUserId="1320" LastEditDate="2014-09-22T16:18:37.570" LastActivityDate="2014-12-14T13:34:15.820" Title="What governs the size of animal bodies?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21542" PostTypeId="1" AcceptedAnswerId="21547" CreationDate="2014-09-22T12:27:04.040" Score="0" ViewCount="791" Body="&lt;p&gt;Name the things associated with Antonie Van Leeuwenhoek - (6 pictures are given for help and four of them are associated with these clues)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a)Leeuwenhoek was the first to describe these and hence called the &quot;Father of Microbiology&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b)He found many of these (rotifers) in the rainwater collected in ditches and canals&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c)Leeuwenhoek was the first to describe plant vessels in this cross section of an ash tree&lt;/p&gt;&#xA;&#xA;&lt;p&gt;d)Leeuwenhoek used this to observe microorganisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wxOuG.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KICis.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/b7CXY.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/u8wiA.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cqJAJ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3M4ZI.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9440" LastEditorUserId="3340" LastEditDate="2014-09-22T12:53:16.740" LastActivityDate="2014-09-29T15:07:35.097" Title="Answer the questions in one word with help of clues and images given" Tags="&lt;microbiology&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ClosedDate="2014-09-22T15:53:24.360" ContentLicense="CC BY-SA 3.0" />
  <row Id="21543" PostTypeId="2" ParentId="21509" CreationDate="2014-09-22T14:19:09.540" Score="2" Body="&lt;p&gt;Ok, I'm not quite sure if we are at the repairing an organ phase, but here are a few interesting examples: &#xA;1. Philip Maini at Oxford has used pattern formation to give insight into jaguar patterning: &lt;a href=&quot;https://people.maths.ox.ac.uk/maini/PKM%20publications/212.pdf&quot; rel=&quot;nofollow&quot;&gt;Paper&lt;/a&gt;. He also has a book chapter &lt;a href=&quot;https://people.maths.ox.ac.uk/maini/PKM%20publications/119.pdf&quot; rel=&quot;nofollow&quot;&gt;Pattern formation and wound healing&lt;/a&gt; that could of of interest, although I'm not sure if this is a direct application as much as a heuristic understanding of how wound healing happens. &lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;&lt;p&gt;From the biomedical side, Michael Levin at Tufts is doing amazing work in regenerative medicine, and a lot of what he does is inspired by pattern formation as well, although I am not sure if it explicitly uses the theory - &lt;a href=&quot;http://ase.tufts.edu/biology/labs/levin/publications/&quot; rel=&quot;nofollow&quot;&gt;his papers&lt;/a&gt;. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v434/n7037/abs/nature03461.html&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; is one of my favorite from Ron Weiss - engineered pattern formation. Will most likely have important biomedical applications some day, although not currently. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3804" LastActivityDate="2014-09-22T14:19:09.540" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21544" PostTypeId="2" ParentId="21541" CreationDate="2014-09-22T14:44:01.453" Score="2" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;I agree with other commenters that we are not necessarily living in a time of small body masses. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://arxiv.org/pdf/0808.4014.pdf&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a paper on a body mass distribution. It's quite mathematical, but the first author (Aaron Clauset) is good. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;For individual body masses, you can look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Kleiber&amp;#39;s_law&quot; rel=&quot;nofollow&quot;&gt;Kleiber's law&lt;/a&gt; - this says that body mass and metabolism are related by a power law. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3804" LastActivityDate="2014-09-22T14:44:01.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21546" PostTypeId="2" ParentId="21537" CreationDate="2014-09-22T15:23:51.043" Score="6" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iDTBW.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've reproduced the diagram that you linked to. It shows the oxidation of a pair of thiols to create a disulphide. What is missing from this scheme is the accompanying oxidising agent. So for example this could be carried out without catalysis in a reaction with molecular oxygen, in which case hydrogen peroxide would be formed. So the electrons and protons have ended up on the oxygen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a biological system this oxidation would usually be carried out by an enzyme, in which case the oxidising agent would probably be &lt;a href=&quot;http://en.wikipedia.org/wiki/Flavin_adenine_dinucleotide&quot; rel=&quot;nofollow noreferrer&quot;&gt;FAD (flavin adenine dinucleotide)&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide&quot; rel=&quot;nofollow noreferrer&quot;&gt;NAD&lt;sup&gt;+&lt;/sup&gt;(nicotinamide adenine dinucleotide)&lt;/a&gt;. These are by far the most commonly used redox cofactors. In a typical eukaryotic cell these would end up either (a) being reduced either by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Electron_transport_chain&quot; rel=&quot;nofollow noreferrer&quot;&gt;mitochondrial electron transport chain&lt;/a&gt; (in which case the ultimate electron acceptor would again be oxygen); or (b) when they were used as a reducing agent in a metabolic reaction.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-09-22T15:23:51.043" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21547" PostTypeId="2" ParentId="21542" CreationDate="2014-09-22T15:35:48.933" Score="1" Body="&lt;p&gt;Since you have apparently tried to answer the question here is my interpretation. I list the six pictures (numbered from top to bottom) and link four of them to an answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1 - yeast cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2 -  ash tree section (c)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3 - rotifer (b)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4 - muscle fibre??&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5 - bacteria? (a)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;6 - Leeuwenhoek's microscope (d)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the WP page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Antonie_van_Leeuwenhoek&quot; rel=&quot;nofollow&quot;&gt;van Leeuwenhoek&lt;/a&gt; he did describe the banded pattern in muscle, but there is no mention of yeast (although he would have had no trouble seeing these cells if he could see bacteria). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a very odd question.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastEditorUserId="1590" LastEditDate="2014-09-29T15:07:35.097" LastActivityDate="2014-09-29T15:07:35.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21548" PostTypeId="2" ParentId="21527" CreationDate="2014-09-22T15:59:36.277" Score="9" Body="&lt;p&gt;Just to add a different dimension to the answer from @Chris. Not all animal colouration is produced by melanin. A whole range of bright colours in insects, birds and reptiles comes under the heading of &lt;a href=&quot;http://en.wikipedia.org/wiki/Structural_coloration&quot;&gt;structural colouration&lt;/a&gt;, which basically involves having a repeating structure at the microscopic level to interact with light. This is the basis for macaw colours, peacock feathers, and some butterfly wing colours.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also occurs in mammals - see for example the &lt;a href=&quot;http://en.wikipedia.org/wiki/Mandrill&quot;&gt;mandrill&lt;/a&gt;. In this case the coloured patches are bare skin containing ordered collagen fibres to create the effect, (&lt;a href=&quot;http://jeb.biologists.org/content/207/12/2157.full&quot;&gt;science here&lt;/a&gt;). I have no idea if collagen could be structured to produce a green colour. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, an anecdote: a number of years ago a polar bear in the San Diego zoo was seen to develop green patches. Upon investigation this was found to be due to damaged hair shafts in areas where the animal rubbed against surfaces in its enclosure. In the polar bear the hair shafts are hollow, for insulation, and the damaged hairs were being colonised by algae. So you could imagine a green mammal could evolve by using this effect.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-09-22T15:59:36.277" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21549" PostTypeId="2" ParentId="21513" CreationDate="2014-09-22T19:24:22.630" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Because of that, I assume botulinum toxin is more dangerous to humans than many animals.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Couldn't find too many examples but, there are some things to consider (according to [1]):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;there are seven distinct types of toxin with &lt;strong&gt;variable&lt;/strong&gt; action among animals &lt;/li&gt;&#xA;&lt;li&gt;different dose / effect intensity ratio between toxin types&lt;/li&gt;&#xA;&lt;li&gt;toxins A, B, E and F cause disease in humans&lt;/li&gt;&#xA;&lt;li&gt;toxin C and D are more common to birds, cattle, horses&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And here are some numbers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;cattle median lethal dose: 0.388 ng /kg [2] of C type toxin&lt;/li&gt;&#xA;&lt;li&gt;mouse median lethal dose ( 12.88 times more than cattle): 5 ng/kg [2] of C type toxin&lt;/li&gt;&#xA;&lt;li&gt;human median lethal dose: 1 ng/kg [1] of A type toxin&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;When it comes to carcasses toxicity, there are some papers to consider:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Smith GR, Turner A. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3297745&quot;&gt;Factors affecting the toxicity of rotting carcasses containing Clostridium botulinum type C.&lt;/a&gt; Epidemiol. Infect. 1987 Jun;98(3):345-51. PubMed PMID: 3297745. - Persistent toxicity at 20 and 37 degrees Celsius even for a long time. No toxicity at 16 degrees Celsius&lt;/li&gt;&#xA;&lt;li&gt;Smith GR, Turner A, Till D. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3288491&quot;&gt;Factors affecting the toxicity of rotting carcasses containing Clostridium botulinum type E.&lt;/a&gt; Epidemiol. Infect. 1988 Jun;100(3):399-405. PubMed PMID: 3288491. - Maximal toxicity at 30 degrees Celsius that is lost in time.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;are they better in avoiding harmful substances based on more suited olfactory sense?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not if we are talking about nonproteolytic B, E and F type bacteria. Indeed, Clostridium botulinum, proteolytic type A, B and F types produce odor [3].&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Or are we just more afraid?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't see how fear could (significantly) influence pharmacodynamics and pharmacokinetics of the toxin.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;CIDRAP - Center for Infectious Disease Research and Policy. &lt;em&gt;Botulism.&lt;/em&gt; Available from &lt;a href=&quot;http://www.cidrap.umn.edu/infectious-disease-topics/botulism&quot;&gt;http://www.cidrap.umn.edu/infectious-disease-topics/botulism&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Moeller RB, Puschner B, Walker RL, Rocke T, Galey FD, Cullor JS, Ardans AA. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14667014&quot;&gt;Determination of the median toxic dose of type C botulinum toxin in lactating dairy cows.&lt;/a&gt; J. Vet. Diagn. Invest. 2003 Nov;15(6):523-6. PubMed PMID: 14667014. &lt;/li&gt;&#xA;&lt;li&gt;P. Kendall. &lt;em&gt;Botulism.&lt;/em&gt; Colorado State University Extension. Available from &lt;a href=&quot;http://www.ext.colostate.edu/pubs/foodnut/09305.html&quot;&gt;http://www.ext.colostate.edu/pubs/foodnut/09305.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-09-22T19:24:22.630" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21550" PostTypeId="2" ParentId="13595" CreationDate="2014-09-22T19:27:10.283" Score="4" Body="&lt;p&gt;&lt;em&gt;Disclaimer: Not my field of research, and not a field where I know the litterature well. See it as a complement to the other answers.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;A distinct advantage of multicellularity is specialized functions of different cells. This can allow for higher efficiency of e.g. metabolic processes, and also that redundant functions can be removed from some cell lines, since they can be handled by other cells. Therefore, the constituent parts can become simpler, while the resulting organism becomes more complex at the same time. Mathematical modelling of cellular systems have shown how this type of division of labour can evolve from unicellular lines (&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/early/2011/12/05/rspb.2011.1999.full&quot; rel=&quot;nofollow&quot; title=&quot;Ispolatov et al. 2011. Division of labour and the evolution of multicellularity.  Proc. R. Soc. B. doi:10.1098/rspb.2011.1999&quot;&gt;Ispolatov et al. 2011&lt;/a&gt;), through the steps of aggregation and differentiation from preexisting functions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An interesting intermediate step that can provide some clues to how multicellularity can evolve, is in cyanobacteria, where some unicellular species can show partial specialization e.g. when part of cellular biofilms. A phylogenetic study of cyanobacteria has also shown that they have reversed from multicellularity to unicellularity at least five times, and most extant cyanobacteria seem to descend from multicellular ancestors (&lt;a href=&quot;http://www.biomedcentral.com/1471-2148/8/238&quot; rel=&quot;nofollow&quot; title=&quot;Schirrmeister et al. 2011. The origin of multicellularity in cyanobacteria. BMC Evolutionary Biology 11:45&quot;&gt;Schirrmeister et al. 2011&lt;/a&gt;). This means that the evolution of multicellularity is not a one-way process, but seems to be a much more complex process.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-09-23T16:53:47.377" LastActivityDate="2014-09-23T16:53:47.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21551" PostTypeId="2" ParentId="21516" CreationDate="2014-09-22T20:15:46.290" Score="11" Body="&lt;p&gt;It was moistening its respiratory and osmoregulatory organs:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Woodlice as all other terrestrial arthropods face the major challenge of preserving water balance. In their case the two systems that immediately suffer from desiccation are osmoregulation itself and respiration. In woodlice these two functions are carried out mostly by the pleopods: modified leaf-like appendages on the ventral side of the hind body part (&quot;tail&quot;) (see &lt;a href=&quot;http://watchingtheworldwakeup.blogspot.de/2010/06/patio-spider-part-1-prey-revisited.html&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://lanwebs.lander.edu/faculty/rsfox/invertebrates/armadillidium.html&quot;&gt;here&lt;/a&gt; some annotated photos and drawings of ventral side of woodlice).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To maintain these structures in moist state woodlice have a number of adaptations, one of them being the ability to &quot;pick up water from external sources via uropodal dipping, with the water moving upwards by capillarity&quot; (see &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/030096299390235V&quot;&gt;here&lt;/a&gt;). Uropods are the tiny rod-like appendages on the tip of the &quot;tail&quot;, and dipping of the uropods is exactly what you were observing.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-09-22T20:15:46.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21552" PostTypeId="2" ParentId="21539" CreationDate="2014-09-22T20:18:36.537" Score="3" Body="&lt;p&gt;By shin splints you probably mean the pain on the inner front side of the lower 2/3 parts of the shins? This is called medial tibial stress syndrome (MTSS).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Causes, mechanism, prevention and treatment of shin splints are still poorly understood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I managed to find, custom-made cushion insoles are the only proven prevention that can help in some cases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What has not been proven to help (I'm not saying it does not help, only it has not been firmly proven):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;various types of shoes (supinator/pronator)&lt;/li&gt;&#xA;&lt;li&gt;taping&lt;/li&gt;&#xA;&lt;li&gt;stretching/strengthening exercises&lt;/li&gt;&#xA;&lt;li&gt;various running techniques (pose-tech, chi-running, barefoot...)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Possible causes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;running downhill or on an uneven terrain with heel striking and forefoot slapping&lt;/li&gt;&#xA;&lt;li&gt;sudden increase in running intensity, mileage or frequency&lt;/li&gt;&#xA;&lt;li&gt;a way of running with moving the hips (left , right) forward&lt;/li&gt;&#xA;&lt;li&gt;(my experience): running in a forced, conflicting way, like you feel you should not run and you still go...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Possible mechanism: vibration stress in the shinbone (tibia) and the pulling force of the muscles and tendons attached to it and possible local inflammation of then periosteum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do not try to run through the pain. The pain will go away but on the long-term, shin splints may worsen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: Shin Splints (MTSS) (&lt;a href=&quot;http://www.ehealthstar.com/conditions/shin-splints&quot; rel=&quot;nofollow&quot;&gt;Ehealthstar&lt;/a&gt;)  &lt;/p&gt;&#xA;" OwnerUserId="4025" LastEditorUserId="4025" LastEditDate="2014-09-23T07:13:30.533" LastActivityDate="2014-09-23T07:13:30.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21553" PostTypeId="1" CreationDate="2014-09-22T22:23:00.527" Score="5" ViewCount="74" Body="&lt;p&gt;Binding of adrenaline (epinephrine) to the β-Adrenergic receptor leads to formation of cAMP (via G protein activation), activation of protein kinase A and subsequently to the expression of specific genes related to glucose metabolism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How long does it take (in units of time) until translation of the first protein related to the adrenalin binding event is completed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I can accept a reasonable guess at the time scale (+/- factor of ten). Also, it can be also any another kind of ligand/receptor system.&lt;/p&gt;&#xA;" OwnerUserId="4971" LastEditorUserId="3340" LastEditDate="2014-11-14T08:28:21.133" LastActivityDate="2014-11-14T08:38:43.117" Title="What's the duration between the binding of adrenaline to β-AR and the first translated protein?" Tags="&lt;cell-signaling&gt;&lt;translation&gt;&lt;protein-expression&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21554" PostTypeId="2" ParentId="13595" CreationDate="2014-09-22T23:04:02.970" Score="4" Body="&lt;p&gt;I STRONGLY encourage to read work from the lab of Nicole King - she studies Choanoflagellates, which are the &quot;out-group&quot; for animals - they are, in some sense, the most animal-like single-celled organism that exists. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chaonos are also amazing because they go through a single to multicellular transition &lt;em&gt;in there own life cycle&lt;/em&gt;, so they provide an amazing opportunity to understand when it is more beneficial to be single-celled vs. multi-celled. Currently, one of the working hypotheses of the group is that one of the main drivers of the push towards multicellularity may have just been simple fluid dynamics: the flows around a spherical multicellular &quot;rosette&quot; of chaonos bring more food to them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in the evolutionary transition to multicellularity you must read work from the &lt;a href=&quot;http://kinglab.berkeley.edu/&quot; rel=&quot;nofollow noreferrer&quot;&gt;King Group&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3804" LastEditorUserId="16866" LastEditDate="2019-03-28T01:48:50.927" LastActivityDate="2019-03-28T01:48:50.927" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="21555" PostTypeId="1" CreationDate="2014-09-22T23:09:39.280" Score="3" ViewCount="230" Body="&lt;p&gt;I learned in my food microbiology class that Streptococcus thermophilus and Lactobacillus bulgaricus precipitate the curd of swiss cheese. However, I was wondering what type of mechanisms do these bacteria use in order to accomplish this process. &lt;/p&gt;&#xA;" OwnerUserId="8977" LastActivityDate="2015-02-22T19:33:51.733" Title="How do Streptococcus thermophilus and Lactobacillus bulgaricus precipitate the curd of swiss cheese?" Tags="&lt;microbiology&gt;&lt;food&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21556" PostTypeId="2" ParentId="21527" CreationDate="2014-09-23T00:08:08.657" Score="6" Body="&lt;p&gt;A dimension not explored by the other (excellent) answers has to do with color perception under trees. Leaves are green while on the tree, which tends to make mostly green light available to the understory. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Viewed under green light, a green-furred animal would appear bright green, roughly the same as a white creature viewed under green light. A red or brown creature would appear grey-brown or black, and reflect much less light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Orangutans apparently do this for camouflage, according to this book I haven't read:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Russon, Anne E.  2000.  Orangutans:  wizards of the rain forest.  Firefly Books, Buffalo, New York, USA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;which I was told about by &lt;a href=&quot;http://bioweb.uwlax.edu/bio203/s2008/ahrens_just/interesting%20facts.htm&quot; rel=&quot;noreferrer&quot;&gt;these guys&lt;/a&gt;. It's not the first place I've heard this factoid, but it does make first-pass sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a difference between looking the same as a background of green leaves under sunlight and looking the same as a background of tree trunks or leaf litter under a greenish light.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-09-23T00:08:08.657" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21557" PostTypeId="2" ParentId="21541" CreationDate="2014-09-23T02:00:10.467" Score="2" Body="&lt;p&gt;There are lots of parameters that influence body size. Here is a non-exhaustive list:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;visibility to predators&lt;/li&gt;&#xA;&lt;li&gt;ability to hunt bigger preys or to manipulate smaller preys&lt;/li&gt;&#xA;&lt;li&gt;running faster&lt;/li&gt;&#xA;&lt;li&gt;be more impressive&lt;/li&gt;&#xA;&lt;li&gt;fighting ability&lt;/li&gt;&#xA;&lt;li&gt;energy consumption for maintaining a body&lt;/li&gt;&#xA;&lt;li&gt;Quantity/quality of food to be found&lt;/li&gt;&#xA;&lt;li&gt;homothermy (heat loss)&lt;/li&gt;&#xA;&lt;li&gt;sustaining its own weight&lt;/li&gt;&#xA;&lt;li&gt;Rooms for the organs&lt;/li&gt;&#xA;&lt;li&gt;Attractiveness to the other sex&lt;/li&gt;&#xA;&lt;li&gt;being more able to move freely (in viscous environment (water))&lt;/li&gt;&#xA;&lt;li&gt;mechansisms for bringing nutrients and air to the tissues&lt;/li&gt;&#xA;&lt;li&gt;density of the body (water)&lt;/li&gt;&#xA;&lt;li&gt;excretion of wastes&lt;/li&gt;&#xA;&lt;li&gt;moving in small habitats&lt;/li&gt;&#xA;&lt;li&gt;Hiding in small areas&lt;/li&gt;&#xA;&lt;li&gt;bearing big and complex structures&lt;/li&gt;&#xA;&lt;li&gt;Parental care&lt;/li&gt;&#xA;&lt;li&gt;flying better&lt;/li&gt;&#xA;&lt;li&gt;artificial selection&lt;/li&gt;&#xA;&lt;li&gt;etc..&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Saying that today's species are smaller than previous species is maybe over generalize. For example, the largest species that is thought to have ever lived is currently extant, it is the blue whale (it can weight more than 200 tons). The tyrannosaurus is roughly the same weight that the african elephant (7 tons). However it is true that insects were typically bigger before than they are today. It is also true the the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sauropoda&quot; rel=&quot;nofollow&quot;&gt;sauropoda&lt;/a&gt; are particularly impressive as some of them were 3 or 4 times taller than a giraffe and weight around 100 tons. [Bruhathkayosaurus](The &lt;a href=&quot;http://en.wikipedia.org/wiki/Bruhathkayosaurus&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Bruhathkayosaurus&lt;/a&gt;), the largest land animal that ever lived may have had a weight comparable to the blue whale!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A common argument to account for the big size of dinosaurs and especially of insects during  the triassic is the oxygen concentration in the atmosphere (&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/early/2010/03/04/rspb.2010.0001.full&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;). It is particularly relevant for insects as they have no hemoglobin, meaning that the oxygen has to be dissolved into their body liquid (mostly water) to be brought to the cells. From Henry's law, the concentration of a gas such as oxygen in a liquid is a function of the concentration of this gas in the atmosphere. Therefore, the highest is the oxygen concentration, the easiest it is to bring oxygen to all the cells of a big body and therefore the lowest is the cost of having a big body.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3340" LastEditDate="2014-12-14T13:34:15.820" LastActivityDate="2014-12-14T13:34:15.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21558" PostTypeId="1" CreationDate="2014-09-23T03:45:57.990" Score="3" ViewCount="2950" Body="&lt;p&gt;How many times can a human get chicken pox?&#xA;For example: I got chicken pox, and recovered. If I was infected with HIV, and I am exposed to chicken pox again, can it infect me second time?, According to what I've heard, chicken pox comes only one time, because of the immune system of humans. But if I am infected with HIV and so definitely have immune system damage, will chicken pox come a second time, or will the immune system still protect the body from chicken pox?&lt;/p&gt;&#xA;" OwnerUserId="9447" LastEditorUserId="338" LastEditDate="2014-09-23T03:56:24.530" LastActivityDate="2014-09-23T06:46:52.090" Title="How many times can a human get chicken pox?" Tags="&lt;pathology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21562" PostTypeId="2" ParentId="21558" CreationDate="2014-09-23T06:46:52.090" Score="4" Body="&lt;p&gt;Usually you get &lt;a href=&quot;http://www.cdc.gov/vaccines/pubs/pinkbook/varicella.html&quot; rel=&quot;nofollow&quot;&gt;chicken pox&lt;/a&gt; only once in your life, the recurring form are usually shingles.  But: It can happen (also in people which are not immunocompromized). I know two persons which got chicken pox twice and which are otherwise normal in regards of their immune system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Persons with an HIV infection are more at risk here. They can develop both forms and depending on how much their immune system is already affected by the HIV infection can develop severe forms of the infection. It might be necessary to treat them with antiviral drugs. So it is clearly recommended to ask a MD about this. See &lt;a href=&quot;http://hivinsite.ucsf.edu/insite?page=kb-00&amp;amp;doc=kb-05-03-01&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for more details.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-23T06:46:52.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21563" PostTypeId="1" CreationDate="2014-09-23T08:26:12.780" Score="4" ViewCount="140" Body="&lt;p&gt;I have recently seen images of big areas covered in spider webs:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;After flood in Australia&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://news.nationalgeographic.com/news/2012/03/pictures/120307-spiderwebs-australia-floods-wagga-wagga-world-science/#/spider-webs-australia-floods-bush_49725_600x450.jpg&quot; rel=&quot;nofollow&quot;&gt;http://news.nationalgeographic.com/news/2012/03/pictures/120307-spiderwebs-australia-floods-wagga-wagga-world-science/#/spider-webs-australia-floods-bush_49725_600x450.jpg&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.dailymail.co.uk/news/article-2111390/Australia-floods-Spiders-cover-fields-cobwebs-flee-rising-water.html&quot; rel=&quot;nofollow&quot;&gt;http://www.dailymail.co.uk/news/article-2111390/Australia-floods-Spiders-cover-fields-cobwebs-flee-rising-water.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.hoax-slayer.com/spider-fields-australian-floods.shtml&quot; rel=&quot;nofollow&quot;&gt;http://www.hoax-slayer.com/spider-fields-australian-floods.shtml&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.theatlantic.com/infocus/2012/03/spiders-flee-australian-flood/100265/&quot; rel=&quot;nofollow&quot;&gt;http://www.theatlantic.com/infocus/2012/03/spiders-flee-australian-flood/100265/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://io9.com/5891091/massive-spiderwebs-engulf-australian-town-as-arachnids-escape-floods&quot; rel=&quot;nofollow&quot;&gt;http://io9.com/5891091/massive-spiderwebs-engulf-australian-town-as-arachnids-escape-floods&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I would like to read about this on wikipedia. So I am looking for a name of this phenomenon. Do you know how it is called?&lt;/p&gt;&#xA;" OwnerUserId="8014" LastEditorUserId="8014" LastEditDate="2015-09-08T11:29:27.180" LastActivityDate="2015-09-08T11:29:27.180" Title="Does this &quot;fleeing spiders leaving fields of webs&quot; phenomenon have a name?" Tags="&lt;arachnology&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21564" PostTypeId="1" AcceptedAnswerId="21576" CreationDate="2014-09-23T09:19:37.050" Score="4" ViewCount="2225" Body="&lt;p&gt;I am currently working on SDS-PAGE technique having 20% acrylamide concentration for hydrolyzed BSA protein. Here I attached a gel photo for trypsin hydrolyzed BSA. I don't know , is it a good result and how do I interpreted this result?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lVe7i.jpg&quot; alt=&quot;20% sds page&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8423" LastEditorUserId="6" LastEditDate="2014-09-24T06:08:09.740" LastActivityDate="2014-09-24T06:08:09.740" Title="Troubleshooting SDS-PAGE of trypsin-treated BSA" Tags="&lt;gel-electrophoresis&gt;&lt;sds-page&gt;" AnswerCount="1" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="21567" PostTypeId="2" ParentId="21513" CreationDate="2014-09-23T10:38:31.240" Score="3" Body="&lt;p&gt;You seem to not understand how botulism works. It is impossible for vultures (or anybody else) to get botulism from a carcass. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, you have &lt;strong&gt;spores&lt;/strong&gt;. They are ubiquitous in nature, and you have probably eaten lots of them. They are especially common on vegetables growing around/in dirt, like garlic. The spores are &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;indestructible when using common cooking methods &lt;/li&gt;&#xA;&lt;li&gt;dormant under normal food storage conditions &lt;/li&gt;&#xA;&lt;li&gt;not dangerous to humans above 1 year of age. They remain dormant in the human body and get excreted without causing anything. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Then, you have &lt;strong&gt;botulinum bacteria colonies&lt;/strong&gt;. To get a colony going, you need to take some spores and cut off the oxygen supply. For example, storing raw garlic in oil provides both a possible contamination route and a perfect growth environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bacteria themselves are &#xA;  - easy to kill off with heat &#xA;  - not prone to establishing a colony in your body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem with the bacteria: Once there has been a colony, it starts producing the toxin. This toxin is very poisonous even in minute amounts, and stays around to harm you even after you have killed the bacteria which produced it (e.g. with acid). It is not especially heat stable, certainly not as stable as the spores. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the way you get botulism is: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Start out with food contaminated by the spores (meat is rarely such food, vegetables are more common. Of course, cross contamination in your kitchen is possible.) &lt;/li&gt;&#xA;&lt;li&gt;Cut off all oxygen supply for some time. A colony forms. &lt;/li&gt;&#xA;&lt;li&gt;Sterilizing the food by placing it in boiling water for some time doesn't matter, the spores will survive it easily. (This is why industrial food is canned at much higher temperatures, and safe home canning recipes are quite acidic). &lt;/li&gt;&#xA;&lt;li&gt;eat the food after it has been stored with the colony inside. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, vultures don't have any special resistance to botulism toxin, they just don't come in contact with it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a side note, there are quite a few other pathogens which are common in meat, and vultures are probably more resistant to them than humans. But it is normal for bacteria to be able to only make one species, or a small range of species sick. Just ask the poor medical researchers trying to heal human disease in mouse models - there are huge differences. &lt;/p&gt;&#xA;" OwnerUserId="1578" LastActivityDate="2014-09-23T10:38:31.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21568" PostTypeId="1" CreationDate="2014-09-23T12:24:56.427" Score="2" ViewCount="63" Body="&lt;p&gt;I have genotype data from few chicken population and I want to (need to) upload them somewhere online with free access. I have searched the web but I haven't found any place for non-human genotype data! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have an idea where I can upload it, which is publicly available and user friendly?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;bests&lt;/p&gt;&#xA;" OwnerUserId="9453" LastEditorUserId="3340" LastEditDate="2014-12-03T12:29:46.367" LastActivityDate="2014-12-03T12:29:46.367" Title="Where can I upload non-human Genotype data?" Tags="&lt;genetics&gt;&lt;genomics&gt;&lt;snp&gt;&lt;chickens&gt;&lt;data&gt;" AnswerCount="0" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21569" PostTypeId="1" CreationDate="2014-09-23T13:27:40.327" Score="3" ViewCount="29" Body="&lt;p&gt;I'm studying neuro-anatomy right now and I was surprised to learn that there are only three neurons along the Dorsal Column Medial Lemniscal Pathway (DMLP) which relays mechanical sensations from the limbs to the brain. Is this the same across all mammals? Is there an evolutionary motivation behind having exactly three neurons, instead of 4 or 2?&lt;/p&gt;&#xA;" OwnerUserId="5427" LastActivityDate="2014-09-23T13:27:40.327" Title="Evolutionary motivation behind number of neurons in DCMMP" Tags="&lt;evolution&gt;&lt;neuroanatomy&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21570" PostTypeId="1" CreationDate="2014-09-23T16:46:54.350" Score="6" ViewCount="3875" Body="&lt;p&gt;Will every wave length of UV work for killing bacteria? So will UV A, UV B and UV C all work? Or will only the shortest of the three, UV C, work? Also, will the average UV lamp help against bacterial growth (if it is shone on an object for 3-5 minutes for example)? What about a longer period: a bacterial colony in a petri dish under an average household UV lamp for a day? Would the growth be reduced noticeably? Or would the change be too small to notice when using the average UV lamp? Does the type of UV also matter for this (A/B/C)?&lt;/p&gt;&#xA;" OwnerUserId="9455" LastActivityDate="2016-12-09T01:41:17.137" Title="Does every wave length of UV kill bacteria?" Tags="&lt;bacteriology&gt;&lt;uv&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21571" PostTypeId="1" AcceptedAnswerId="21575" CreationDate="2014-09-23T16:49:28.423" Score="4" ViewCount="368" Body="&lt;p&gt;In &lt;a href=&quot;http://www.zoology.ubc.ca/edg/pdfs/Stathos_2014.pdf&quot; rel=&quot;nofollow&quot;&gt;Stathos and Fishman (2014)&lt;/a&gt;, the authors refer to the concept of structural underdominance. The first time they mention it is in the first paragraph of the second page (left column) and the term is followed by some kind of definition in parenthesis. It is written:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Furthermore, artifical doubling of chromosomes in sterile plant hybrids can sometimes restore normal meiosis and fertility (Stebbins 1950), a pattern diagnostic of structural underdominance (heterozygote inferiority).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In addition to how they use the term &quot;Structural underdominance&quot; in this paper, the above definition is confusing to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is structural underdominance a specific type of underdominance (heterozygote disadvantage)? Is it the evolutionary process by which a population is lead to diminish the average underdominance along their loci? Is it a predisposition of the genetic architecture to display underdominance when a chromosomal rearrangement occurs? In short the question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the definition of &quot;structural underdominance&quot;?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-09-23T21:19:17.520" Title="Definition of &quot;structural underdominance&quot;?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;terminology&gt;&lt;chromosome&gt;&lt;speciation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21574" PostTypeId="2" ParentId="21570" CreationDate="2014-09-23T18:57:03.250" Score="6" Body="&lt;p&gt;The CDC's &lt;a href=&quot;http://www.cdc.gov/hicpac/Disinfection_Sterilization/10_0MiscAgents.html#2&quot;&gt;disinfection guidelines&lt;/a&gt; lists UV radiation between 328 and 210nm as effective for disinfection, with a maximum of bactericidal activity occurring between 240-280nm. At this wavelength DNA damage (Thymine dimers) is induced with a high rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Due to practical reasons UV light is mostly used to disinfect water, if used in rooms there is some effectiveness against microorganisms in the air and some on surfaces, but on one hand the effectiveness is reduced  by square with the distance from the UV source and on the other hand you need completely empty surfaces where nothing casts shadows. The other problems are plastic materials which may get damaged by repeated UV exposure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a look at this reference (only available via Google Books): &quot;&lt;a href=&quot;http://books.google.de/books?id=3f-kPJ17_TYC&amp;amp;pg=PA31&amp;amp;lpg=PA31&amp;amp;dq=Russell%20AND.%20Ultraviolet%20radiation.&amp;amp;source=bl&amp;amp;ots=KmAkHB7KJ0&amp;amp;sig=BQ_eD64D2hVCMqOm1pCB0BzZvkc&amp;amp;hl=de&amp;amp;sa=X&amp;amp;ei=OsAhVKC4MqWGywO81oDwAg&amp;amp;ved=0CFoQ6AEwBQ#v=onepage&amp;amp;q&amp;amp;f=false&quot;&gt;Principles and practices of disinfection, preservation and sterilization.&lt;/a&gt;&quot; and this &lt;a href=&quot;http://books.google.de/books?id=BGET7CkL8_cC&amp;amp;lpg=PA303&amp;amp;ots=6UT132t746&amp;amp;dq=Russell%20AND.%20Ultraviolet%20radiation.&amp;amp;hl=de&amp;amp;pg=PA302#v=onepage&amp;amp;q&amp;amp;f=false&quot;&gt;subchapter&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-23T18:57:03.250" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="21575" PostTypeId="2" ParentId="21571" CreationDate="2014-09-23T20:39:11.227" Score="3" Body="&lt;p&gt;I understand &lt;em&gt;heterozygote inferiority&lt;/em&gt; (also &lt;em&gt;underdominance&lt;/em&gt; or &lt;em&gt;heterozygote disadvantage&lt;/em&gt;) as the opposite of &lt;em&gt;heterozygote advantage&lt;/em&gt;, that is, lower fitness of the heterozygous genotype than either homozygote (as reference, see &lt;a href=&quot;http://books.google.se/books?id=bKBugGixXa4C&amp;amp;pg=PA119#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot; title=&quot;Hedrick. 2009. Genetics Of Populations. Jones &amp;amp; Bartlett Learning&quot;&gt;Hedrick, 2009&lt;/a&gt;, p. 119). I haven't seen the term &lt;em&gt;structural underdominance&lt;/em&gt; before. However, heterozygote disadvantage can sometimes be seen in species/subspecies hybrids and also chromosomal heterozygotes (see &lt;a href=&quot;http://books.google.se/books?id=bKBugGixXa4C&amp;amp;pg=PA140#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot; title=&quot;Hedrick. 2009. Genetics Of Populations. Jones &amp;amp; Bartlett Learning&quot;&gt;Hedrick, 2009&lt;/a&gt;, p 140), and this might be what the term &lt;em&gt;structural underdominance&lt;/em&gt; is describing (structural as in chromosomal). This can then lead to unbalanced gametes with low viability, which means low fitness compared to homozygotes. The quote you have included also talks about plant hybrids, which makes this explanation likely, and it also makes sense since they mention artifical doubling as a solution. If I have understood the process correctly, chromosomal doubling should lead to better pairing of chromosomes and lower risk of unbalanced chromosome translocations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also note that Hedrick labels &lt;em&gt;heterozygote disadvantage&lt;/em&gt; as an unstable equilibrium (p. 140ff), but I haven't looked more closely at the dynamics behind this.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-09-23T21:19:17.520" LastActivityDate="2014-09-23T21:19:17.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21576" PostTypeId="2" ParentId="21564" CreationDate="2014-09-23T22:48:53.357" Score="3" Body="&lt;p&gt;I'm going to treat this as a partial homework question but provide some guidance as to how you can potentially address your question and have solid theory to back it up. &lt;a href=&quot;http://en.wikipedia.org/wiki/Chymotrypsin&quot; rel=&quot;nofollow&quot;&gt;Chymotrypsin&lt;/a&gt; preferentially cleaves peptide amide bonds where the carboxyl side of the amide bond (the P1 position) is a large hydrophobic amino acid (tyrosine, tryptophan, and phenylalanine). So one solution which is often used by experimental biologists (such as myself) performing mass spectrometry (MS) is to put their protein sequence (in this case BSA) in an algorithm such as &lt;a href=&quot;http://web.expasy.org/peptide_cutter/&quot; rel=&quot;nofollow&quot;&gt;PeptideCutter&lt;/a&gt; (from ExPASy), which performs a theoretical digest of the protein sequence having chosen the desired enzyme or combination of enzymes) and see what peptide fragments are expected to be produced and work out their length/molecular weight and compare that to your experimental data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having had an initial look, I noticed that your protein marker/ladder is missing, which is quite important in figuring out the peptide sizes produced! Also what is 1-8 lanes? are they different concentration of enzymes? if so then it looks ok to me since the higher the enzyme concentration from left to right, the higher the amount of digest products you have. If the peptide sizes obtained are not the ones expected then perhaps increase or decrease the digestion time since you could have a problem due to either incomplete digest or unspecific digestion, depending. I guess since BSA MW is ~ 66kDa your gel concentration is appropriate since you have a problem with the 15% gel as the products are too small and too abundant to resolve.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-09-23T23:51:29.937" LastActivityDate="2014-09-23T23:51:29.937" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21578" PostTypeId="1" AcceptedAnswerId="21583" CreationDate="2014-09-23T23:25:47.820" Score="21" ViewCount="32645" Body="&lt;p&gt;If I understand evolutionary biology correctly, mammals first evolved on land as small, rodent-like creatures, in a time when reptiles were dominant on land. Eventually, they diversified into the species we know today. Some of these species, however, are aquatic - whales and dolphins readily spring to mind. Why did the ancestors of whales and dolphins leave the land to go to the oceans? How did they evolve from their original form to their superficially ichthyoid appearance today?&lt;/p&gt;&#xA;" OwnerUserId="9458" LastActivityDate="2015-03-18T15:30:44.197" Title="How and why did mammals go back to the oceans?" Tags="&lt;evolution&gt;&lt;mammals&gt;&lt;marine-biology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21579" PostTypeId="1" CreationDate="2014-09-24T00:09:40.327" Score="2" ViewCount="474" Body="&lt;p&gt;Ok, this may be just wild nonsense and I have to warn that my knowledge on the subject is limited.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was reading about how in some countries people choose to have children later in life. After that this question came to my mind?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If human couples chose to have children later in life, lets say 40s 50s - disregarding keeping an younger self gamete preserved - wouldn't this result in the people less resistant to the effect of aging being unable to reproduce,  creating a more longevous generation? thus enabling future generations to reproduce even later lenghtening the average lifespan of humans?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ps: After reading this sounded a little too eugenic, by no means I'm trying to make this an legitimate theory or suggest an experiment, it's just a doubt - maybe good for some science fiction story...&lt;/p&gt;&#xA;" OwnerUserId="9459" LastActivityDate="2014-09-25T13:36:45.670" Title="Do couples having children later in life act as an evolutionary mechanism?" Tags="&lt;evolution&gt;&lt;senescence&gt;" AnswerCount="2" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21580" PostTypeId="1" AcceptedAnswerId="21614" CreationDate="2014-09-24T02:18:18.777" Score="4" ViewCount="46" Body="&lt;p&gt;Would wild type N2 be best or Dyp-11? I know they're different, but I just want to observe the worms to see life stages, movement, etc. Dyp-11 seems like it would be easy to see but N2 is the wild type so I need help making an appropriate decision.&lt;/p&gt;&#xA;" OwnerUserId="8991" LastActivityDate="2014-09-24T20:48:11.230" Title="Which C. elegans would be appropriate for general study?" Tags="&lt;reproduction&gt;&lt;growth&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21581" PostTypeId="2" ParentId="16700" CreationDate="2014-09-24T03:00:04.300" Score="2" Body="&lt;p&gt;In our labs we just use something like palmolive or bleach followed by a 95% EtOH rinse and finally rinsing with DI water.&lt;/p&gt;&#xA;" OwnerUserId="8991" LastActivityDate="2014-09-24T03:00:04.300" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21582" PostTypeId="2" ParentId="21535" CreationDate="2014-09-24T03:04:53.310" Score="0" Body="&lt;p&gt;From experience I cannot say quality is dependent on duration. For example, you can take a 30 minute power nap and feel much more refreshed than sleeping 8 hours. It may have something to do with dehydration and hunger during the long periods of sleep that disrupt our REM sleeping, our deep-sleep. &lt;/p&gt;&#xA;" OwnerUserId="8991" LastActivityDate="2014-09-24T03:04:53.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21583" PostTypeId="2" ParentId="21578" CreationDate="2014-09-24T03:30:52.140" Score="36" Body="&lt;p&gt;I'll focus on whales and dolphins (cetaceans) as you mention them by name and they are representative for other marine mammals such as seals or manatees. The evolution of cetaceans was one of the fascinating evolutionary mysteries. Clearly, they were mammals, but which mammals were their closest relatives? Clues to solve this mystery began to appear in the 1980s and 1990s.&lt;/p&gt;&#xA;&lt;p&gt;During the 1980s and into the 1990s, paleontologists discovered several fossils that were clearly land-based mammals but shared many skeletal features with cetaceans. These fossils, including &lt;em&gt;Pakicetus&lt;/em&gt; [(Gingerich et al. 1983)] and &lt;em&gt;Rodhocetus&lt;/em&gt; &lt;a href=&quot;http://deepblue.lib.umich.edu/bitstream/handle/2027.42/62571/368844a0.pdf?sequence=1&quot; rel=&quot;noreferrer&quot;&gt;(Gingerich et al. 1994)&lt;/a&gt;, shared skeletal features that are unique to whales and to the &lt;a href=&quot;http://www.ucmp.berkeley.edu/mammal/artio/artiodactyla.html&quot; rel=&quot;noreferrer&quot;&gt;Artiodactyla&lt;/a&gt;, commonly known as the even-toed mammals. Artiodactyls includes deer, sheep, pigs, bison, and hippopotamuses. Artiodactyls and the fossil whales share a unique skeletal feature of the ankle called an astrogalus, shown in the picture below. The astragalus is a &amp;quot;double pulley&amp;quot; structure that contributes to the ankle joint. This picture is taken from an excellent summary of whale evolution, provided by the &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evograms_03&quot; rel=&quot;noreferrer&quot;&gt;Understanding Evolution&lt;/a&gt; site hosted by University of California at Berkeley. The astragalus is not present in other mammals.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2dvlm.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The fossil whales and modern cetaceans also share unique features of the skull around the area of the ear, called a tympanic bulla. Although all mammals have bullae (plural of bulla), the bullae of cetaceans and the whale fossils is unique compared to other mammals. For more on the bulla, see this &lt;a href=&quot;http://www.talkorigins.org/features/whales/&quot; rel=&quot;noreferrer&quot;&gt;Talk Origins page&lt;/a&gt;. More on fossil whales can be found at the &lt;a href=&quot;http://www.ucmp.berkeley.edu/mammal/cetacea/cetacean.html&quot; rel=&quot;noreferrer&quot;&gt;Berkeley Comparative Museum of Paleontology&lt;/a&gt;. The many fossils that have been found are &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/lines_03&quot; rel=&quot;noreferrer&quot;&gt;transitional forms&lt;/a&gt; that link artiodactyls and modern cetaceans.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TovuG.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&#xA;&lt;a href=&quot;http://scienceblogs.com/retrospectacle/2007/02/07/what-does-a-whales-ear-look-li/&quot; rel=&quot;noreferrer&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Around the same time as the fossil discoveries, genetic analysis added additional evidence supporting a relationship between the artiodactyls and cetaceans &lt;a href=&quot;http://www.researchgate.net/publication/30018105_Revised_phylogeny_of_whales_suggested_by_mitochondrial_ribosomal_DNA_sequences/file/79e41509811cc6ad26.pdf&quot; rel=&quot;noreferrer&quot;&gt;(Milinkovitch et al. 1993)&lt;/a&gt;. Although early genetic analytical techniques were not as robust as they are today, many genetic studies have since supported and refined the conclusions of Milinkovitch et al. Current evidence shows that the closest &lt;em&gt;living&lt;/em&gt; relative of cetaceans are the hippos (see, for example &lt;a href=&quot;http://www.researchgate.net/publication/7665216_A_complete_phylogeny_of_the_whales_dolphins_and_even-toed_hoofed_mammals_(Cetartiodactyla)/file/3deec521e33865a8e0.pdf&quot; rel=&quot;noreferrer&quot;&gt;Price et al. 2005&lt;/a&gt; and &lt;a href=&quot;http://www.researchgate.net/publication/5262443_The_phylogeny_of_Cetartiodactyla_the_importance_of_dense_taxon_sampling_missing_data_and_the_remarkable_promise_of_cytochrome_b_to_provide_reliable_species-level_phylogenies/file/60b7d518fb5d130590.pdf&quot; rel=&quot;noreferrer&quot;&gt;Agnarsson and May-Collado 2008&lt;/a&gt;). The relationships are shown below in this figure from the Agnarsson and May-Collado paper. The dark lines are the artiodactyls and cetaceans, formally called the Cetartiodactyla.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qOk2R.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The question remains: why? The most likely explanation is that cetaceans evolved to exploit an unfilled &lt;a href=&quot;http://www.learner.org/courses/envsci/unit/text.php?unit=4&amp;amp;secNum=7&quot; rel=&quot;noreferrer&quot;&gt;ecological niche&lt;/a&gt; or adapted to new niches that formed as a result of plate tectonics or other types of environmental changes that occurred &lt;a href=&quot;http://www.scotese.com/newpage9.htm&quot; rel=&quot;noreferrer&quot;&gt;50-55 million years ago&lt;/a&gt;. The niche describes all of the living and non-living resources needed by an organism to survive. Although land-based mammals were increasing in diversity, few or none were present in the oceans. The basic hypothesis is that the early whale-like artiodactyls, like &lt;em&gt;Indohyus&lt;/em&gt; and &lt;em&gt;Pakicetus&lt;/em&gt; were land-based (terrestrial) mammals that spent most of their time near the water's edge. Over time, they adapted to the niches in the ocean. Fossils like &lt;em&gt;Ambulcetus&lt;/em&gt; and &lt;em&gt;Rodhocetus&lt;/em&gt; showed clear &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evograms_03&quot; rel=&quot;noreferrer&quot;&gt;evidence of swimming ability&lt;/a&gt;, with flattened tails and the enlarged rear feet. In addition, the nostrils shifted from the front of the face to the top of the head, which we recognize as the blowhole.&lt;/p&gt;&#xA;&lt;p&gt;The shift to the aquatic habitat allowed these species to exploit resources that were not available to land-based mammals, thereby reducing &lt;a href=&quot;http://www.nature.com/scitable/knowledge/library/species-interactions-and-competition-102131429&quot; rel=&quot;noreferrer&quot;&gt;competition&lt;/a&gt; for the resources. Reduced competition allows more individuals to survive and reproduce.&lt;/p&gt;&#xA;&lt;p&gt;Similar scenarios are very likely for other marine mammals, such as seals or manatees. They evolved to take advantage of ecological niches that were not filled by other organisms. This basic concept, evolving to fill available niches, is a common outcome of the evolutionary process.&lt;/p&gt;&#xA;&lt;p&gt;The of adaptation of cetaceans and other mammals to the oceans may be similar to that of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hippopotamus&quot; rel=&quot;noreferrer&quot;&gt;hippopotamus&lt;/a&gt;. Hippos spend most of their time in the water, and they show many adaptations that allow them to live in the aquatic environment.  The eyes and nostrils of the hippo are high on the head, which allows them to remain almost entirely submerged but still see and smell, as shown below.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pAWv9.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&#xA;(Hippo photo by &lt;a href=&quot;http://www.flickr.com/photos/johanneslundberg/&quot; rel=&quot;noreferrer&quot;&gt;Johannes Lunberg&lt;/a&gt;, Flickr Creative Commons.)&lt;/p&gt;&#xA;&lt;p&gt;Hippos feed underwaters, they are heavy enough to walk on the bottom of the river, and the mate and give birth underwater. The young can suckle underwater. Clearly, hippos seem to be another mammal that is &amp;quot;returning to water.&amp;quot; Similar types of processes must have occurred in cetaceans for them to adapt to the marine habitat.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Citations&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Agnarsson, I. and L.J. May-Collado. 2008. The phylogeny of Cetartiodactyla: The importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies. Molecular Phylogenetics and Evolution 48: 964-985.&lt;/p&gt;&#xA;&lt;p&gt;Gingerich, P.D. et al. 1983. Origin of whales in epicontinental remnant seas: New evidence from the early Eocene of Pakistan. Science 220: 403-406.&lt;/p&gt;&#xA;&lt;p&gt;Gingerich, P.D. et al. 1994. New whale from the Eocene of Pakistan and the origin of cetacean swimming. Nature 368: 844-847.&lt;/p&gt;&#xA;&lt;p&gt;Milinkovitch, M.C. et al. 1993. Revised phylogeny of whales suggested by mitochondrial ribosomal DNA sequences. Nature 361: 346-348.&lt;/p&gt;&#xA;&lt;p&gt;Price, S.A. 2005. A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla). Biological Reviews 80: 445-473.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-24T12:56:54.443" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="21586" PostTypeId="2" ParentId="21578" CreationDate="2014-09-24T08:44:34.533" Score="8" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;How did they evolve from their original form to their superficially ichthyoid appearance today?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is an example of &lt;a href=&quot;http://en.wikipedia.org/wiki/Convergent_evolution&quot;&gt;&lt;em&gt;convergent evolution&lt;/em&gt;&lt;/a&gt;. Fish appear as they do (streamlined body shape, wide tail, fins, etc.) since these are adaptations to the underwater environment they're living and evolving in. These features are only &quot;ichthyoid&quot; or &quot;fishy&quot; because the fish 'got there first'. Instead, we can think of such features as &quot;ocean-favourable&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reptiles evolved on land, and hence have a generally different appearance from fish, but those which went back into the oceans to become the ichthyosaurs adapted again to live in that environment. Since they faced similar problems as fish (drag from the water, the need to maneuver in 3D, etc.), natural selection would favour the same &quot;ocean-favourable&quot; features as the fish (but not exclusively; for example, turtles have a rather different appearance, which is &quot;ocean-favourable&quot; but not as &quot;fishy&quot;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When mammals ventured into the oceans, they also faced these same problems and the same selection pressures, so they also gained a more &quot;ocean-favourable&quot; appearance.&lt;/p&gt;&#xA;" OwnerUserId="9463" LastEditorUserId="3624" LastEditDate="2014-09-24T09:18:14.937" LastActivityDate="2014-09-24T09:18:14.937" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21587" PostTypeId="2" ParentId="20754" CreationDate="2014-09-24T10:41:35.620" Score="2" Body="&lt;p&gt;Healthy plant growth depends on a microbial community that lives around and inside the roots of plants &lt;a href=&quot;http://link.springer.com/article/10.1007/s11627-001-0122-y&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Bais et al. 2001)&lt;/a&gt;. Roots secrete from the roots a number of chemical compounds that influences the microbial community around but outside of the roots. The microbial community can include bacteria, fungi, and single-celled parasites, as well as larger organisms like insect larvae and even roots from other plants. Some chemicals attract certain organisms while other chemicals repel organisms. This community of organisms around the roots is called the rhizosphere &lt;a href=&quot;http://www.plantphysiol.org/content/132/1/44.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Walker et al. 2003)&lt;/a&gt;. The paper by Walker (open access) describes some of the many types of &lt;a href=&quot;http://en.wikipedia.org/wiki/Symbiosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;symbiotic relationships&lt;/a&gt; that occur in the rhizosphere.&lt;/p&gt;&#xA;&lt;p&gt;Endorhiza refers to the internal environment of the root system. The endorhiza contains another microbial community of bacteria and fungi &lt;a href=&quot;http://worldcocoafoundation.org/wp-content/files_mf/backman2008.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Backman and Sikora 2008)&lt;/a&gt;. The organisms of this endorhizal community are collectively called endophytes. Like the rhizosphere, the organisms in the endorhiza are important symbiotic species that benefit the health of the plant.&lt;/p&gt;&#xA;&lt;p&gt;Similar communities have been identified for other regions of the plant, such as the phyllosphere, the organisms that live on the leaves, stems and other plant parts above the ground &lt;a href=&quot;http://worldcocoafoundation.org/wp-content/files_mf/backman2008.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Backman and Sikora 2008)&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Citations&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Backman, P.A. and R.A. Sikora. 2008. Endophytes: An emerging tool for biological control. Biological Control 46: 1-3.&lt;/p&gt;&#xA;&lt;p&gt;Bais, H.P. et al. 2001. Root specific metabolism: The biology and biochemistry of underground organs. In Vitro Cellular &amp;amp; Developmental Biology - Plant 37: 730-741.&lt;/p&gt;&#xA;&lt;p&gt;Walker, T.S. et al. 2003. Root exudation and rhizosphere biology. Plant Physiology 132: 44-51.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-24T10:41:35.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21589" PostTypeId="1" AcceptedAnswerId="21590" CreationDate="2014-09-24T12:41:00.100" Score="2" ViewCount="876" Body="&lt;p&gt;As far as I know the glucose gets processed from carbs and fats and as a result carbon dioxide, water and &quot;energy&quot; are released. The carbon dioxide and water are expelled by the body, and then energy is used by the muscles. But how exactly is it used? What happens to this &quot;energy&quot; and what is it exactly?&lt;/p&gt;&#xA;" OwnerUserId="9469" LastEditorUserId="3340" LastEditDate="2015-06-04T11:43:33.053" LastActivityDate="2015-06-04T11:43:33.053" Title="How does the human body use energy?" Tags="&lt;metabolism&gt;&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21590" PostTypeId="2" ParentId="21589" CreationDate="2014-09-24T13:04:42.530" Score="2" Body="&lt;p&gt;You can break down the energy expenditure of the human body in terms of the different organs which use it up: this is done in this biochemistry book for instance, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK22436/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK22436/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also look at the detailed expenditure of each cell: although the amounts will vary according to cell type (neuron vs. muscle cell, say!), the &quot;budget items&quot; are the same. See this thread: &lt;a href=&quot;https://biology.stackexchange.com/questions/19942/breakdown-of-energy-expenditure-at-the-level-of-a-single-cell&quot;&gt;Breakdown of energy expenditure at the level of a single cell&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6224" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-09-24T13:04:42.530" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21591" PostTypeId="2" ParentId="21579" CreationDate="2014-09-24T13:10:41.863" Score="2" Body="&lt;p&gt;Many factors have to be considered.  First, although more women are delaying pregnancy until after the age of 35, the overall percentage of women doing so remains very small, as shown by this figure from this &lt;a href=&quot;http://parenting.blogs.nytimes.com/2012/06/20/pregnancy-rates-rise-for-women-over-40/?_php=true&amp;amp;_type=blogs&amp;amp;_r=0&quot; rel=&quot;nofollow noreferrer&quot;&gt;New York Times article&lt;/a&gt;. Only about 9% of pregnancies in the United States (for 2008) were in women over the age of 35. Most pregnancies still occur in younger women. I suspect this is especially true when considered globally.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WsoaP.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Getting pregnant later in life is more difficult, is more likely to result in miscarriage, and is more likely to result in some types of birth defects. The issues are discussed by the &lt;a href=&quot;http://www.mayoclinic.org/healthy-living/getting-pregnant/in-depth/pregnancy/art-20045756&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mayo Clinic&lt;/a&gt;, &lt;a href=&quot;http://www.webmd.com/baby/news/20140203/babies-born-to-moms-over-35-may-have-lower-risk-for-certain-birth-defects&quot; rel=&quot;nofollow noreferrer&quot;&gt;WebMD&lt;/a&gt;, and summarized by &lt;a href=&quot;http://www.parenting.com/article/pregnancy-at-20-30-40&quot; rel=&quot;nofollow noreferrer&quot;&gt;Parenting Magazine&lt;/a&gt;. On average, individuals with birth defects are themselves less likely to reproduce &lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJM199904083401401&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Skjaerven 1999)&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;For natural selection to favor a particular trait (such as later pregnancy), the individuals with the trait must have higher relative &lt;a href=&quot;http://www.nature.com/scitable/nated/article?action=showContentInPopup&amp;amp;ontologyPK=83&quot; rel=&quot;nofollow noreferrer&quot;&gt;fitness&lt;/a&gt;, meaning they produce more offspring on average compared to other individuals. However, relatively few women have late-age pregnancies, more of the offspring are likely to have birth defects, and those offspring are themselves less likely to reproduce. In other words, on average, late-age pregnancies would have reduced fitness compared to individuals that get pregnant at earlier ages.&lt;/p&gt;&#xA;&lt;p&gt;Most importantly, though, the decision to wait until later in life is a conscious choice, not a genetic trait. Natural selection can only work on genetic variation associated with particular traits. If the choice for delayed pregnancy has no genetic basis, then it is invisible to natural selection, and so cannot evolve.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Citation&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Skjaerven, R. et al. 1999. A population-based study of survival and childbearing among female subjects with birth defects and the risk of recurrence in their children. The New England Journal of Medicine 340: 1057-1062.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-24T13:10:41.863" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21592" PostTypeId="1" CreationDate="2014-09-24T13:34:52.923" Score="4" ViewCount="209" Body="&lt;p&gt;I realize all of the disadvantages, but I am wondering if the food industry can actually benefit from the formation of biofilms.&lt;/p&gt;&#xA;" OwnerUserId="8991" LastActivityDate="2015-01-05T20:50:59.513" Title="Is there any way the food industry can benefit from biofilms?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;food&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21594" PostTypeId="1" AcceptedAnswerId="21596" CreationDate="2014-09-24T14:09:04.000" Score="3" ViewCount="624" Body="&lt;p&gt;We hear talk of different body types, and that it is more difficult for certain people to lose weight than others. On the other hand, when my physician recommends that I lose weight, they say that it is really just as simple as &quot;calories in, calories out&quot;. How can we reconcile these two?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps the &quot;calories out&quot; portion is different for different people? I.e. some people burn more calories than others do, doing the same activities, but their hunger level does not compensate for this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apologies if this is off-topic&lt;/p&gt;&#xA;" OwnerUserId="5350" LastActivityDate="2015-02-20T23:09:22.567" Title="What does it mean to have different &quot;metabolism&quot;?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21595" PostTypeId="1" CreationDate="2014-09-24T14:21:08.913" Score="2" ViewCount="96" Body="&lt;p&gt;If we look into how energy is produced by the humans, it always involves some kind of periodicity: fuel combustion rotates engines, water rotates turbines, nuclear chain reactions heat up water, which rotates turbines, dynamo machines, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So that means that with a few exceptions humans produce most energy (electricity) using rotation or some kind of cyclical rotative movement (as it proved to be the most efficient way of doing that).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now what if we look at the human body? It is producing the energy from the food that we consume, converting carbs and proteins into glucose, which is then broken down into carbon dioxide, water and ATP. This ATP is then used in chemical reactions that are needed to contract the muscles or to send impulses within the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is: Does anybody know – are those chemical reactions also cyclical in their nature? And if not, what's the common dynamical property (pattern) that can be observed in them all, if any?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you and sorry for the long intro, but I thought it's important you know where I come from.&lt;/p&gt;&#xA;" OwnerUserId="9469" LastEditorUserId="3340" LastEditDate="2015-06-04T11:43:11.367" LastActivityDate="2015-06-04T11:43:11.367" Title="Is body energy production and consumption cyclical?" Tags="&lt;metabolism&gt;&lt;bioenergetics&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21596" PostTypeId="2" ParentId="21594" CreationDate="2014-09-24T15:43:26.187" Score="3" Body="&lt;p&gt;There are differences in metabolism, and the &quot;calories in&quot; part is the one which differs more than the &quot;calories out&quot; part. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;People do lose different amount of calories for the same action, but for mostly mechanical reasons. If a 50 kg person walks up a mountain at 3 km/h, and a 100 kg person walks up the same mountain at the same speed, the 100 kg person will expend more energy, because they did more work. And then there are slight differences in how we do our movement - some people's gait is more efficient than others', and uses less energy. But this is not really interesting for the explanation of having it easy/hard to lose weight. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The point is that the amount of food we intake is determined by our hunger, and our hunger is determined by hormones. Then, the amount of fat we store is also determined by hormones. If your body &quot;thinks&quot; you should be putting on weight, and you go on a calorie-reduced diet, it won't just start complementing the missing energy from the fat stored in your adipose tissue. Rather, it will continue diverting some of your food intake to make more fat storage, all the while rationing the energy available for other activities: making you feel tired so you don't move much, shutting down some luxurious, energy-hungry processes in the brain, mostly the ones associated with higher mental functioning, and making you feel hungry and cold so you will be more motivated to seek out food and eat. The hormones which regulate these processes are many, most of them are poorly understood, some are probably not yet discovered (orexin, one of the main hunger regulating compounds, was only discovered sometime in the last 5 years I think), and we really don't have a complete picture of everything that is involved. It is a complex mesh of finely balanced homeostatic systems which interact with each other and the environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The people who say that it is as simple as &quot;calories in, calories out&quot; are right. They are right in the sense that, if you just observe a human being and measure their energy household, you will be able to document the amounts of energy consumed, expended and stored, and the energy consumed will equal the energy consumed plus the energy stored. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But to derive from this that we are talking about a passive overflow system and, if we reduce intake, storage is also reduced, is a big leap of faith and has been proven wrong again and again. Living systems are actively reacting to any influences from outside, by mechanisms much more intricate than simple mechanic rules. Mechanics tells us that if I push you, you will fall over; experience tells us that if I push you, you will brace yourself so you don't fall over, and then try to stop me from pushing you by using words, force, or whatever else you have at your disposal. Our physiological systems are the same way. They like the situation they have chosen to be in as much as you like standing upright. If somebody comes from outside and tries to forcibly change their status quo, they do whatever they can to 1) resist and retain the status quo, and 2) stop the outside force if possible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the difference in metabolism: the hormone systems of different people are differently &quot;tuned&quot;. For example, eating pure glucose causes insulin production to spike, and excess insulin causes glucose to be removed from the bloodstream, plus a handful of other effects. But the size of the insulin spike is different in different people. Also, the extent to which cells react to elevated insulin is different. When the reaction becomes dangerously weak at even high insulin levels, we say that it's a pathological variation, and call it &quot;metabolic syndrome&quot;. If goes really towards zero, it's called diabetes type two. And this is an example about just one of the hormones connected to metabolism and the distribution and use of energy in the body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a simpler level, there is no difference in metabolism where physical energy calculation is concerned. Expending one molecule of ATP will let the same number of Na+ ions to move the same distance along a nerve dendrite, across humans. But this level is not really interesting when it comes to gaining or losing weight. &lt;/p&gt;&#xA;" OwnerUserId="9471" LastActivityDate="2014-09-24T15:43:26.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21597" PostTypeId="1" AcceptedAnswerId="21608" CreationDate="2014-09-24T15:49:08.053" Score="3" ViewCount="1756" Body="&lt;p&gt;Does anybody recognize this picture and can tell me what organ it came from? &#xA;&lt;img src=&quot;https://i.stack.imgur.com/SRCvi.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9471" LastActivityDate="2014-09-25T16:09:14.577" Title="What is this tissue?" Tags="&lt;histology&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21600" PostTypeId="1" AcceptedAnswerId="21611" CreationDate="2014-09-24T16:48:16.740" Score="8" ViewCount="3441" Body="&lt;p&gt;Given that the appendix does not seem to be used by the human body, what is the biological reason that it is potentially lethal when this organ bursts?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, what would cause the 'burst'?&lt;/p&gt;&#xA;" OwnerDisplayName="user9474" LastEditorUserId="9268" LastEditDate="2014-09-25T07:21:14.620" LastActivityDate="2014-09-27T12:26:27.937" Title="What is the biological reason for a burst appendix being potentially lethal?" Tags="&lt;medicine&gt;&lt;pathophysiology&gt;&lt;gastroenterology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21601" PostTypeId="2" ParentId="21535" CreationDate="2014-09-24T17:00:53.883" Score="1" Body="&lt;p&gt;Sleep duration certainly affects the quality of sleep, but it is nowhere near a simple correlation. It is just one of many factors, and these factors don't work in isolation. Statistically speaking, it's a multivariate model - and one which includes a differential equation, because the way sleep duration affects your sleep today depends on the sleep quality (and also the sleep duration) from yesterday. For example, if you go several day with too little sleep, but keeping firm going-to-bed and waking-up times, the ratio of your sleep phases changes significantly, giving you much more deep sleep. This is what compression therapy is based on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And beyond that, the way you feel upon waking is also dependent on sleep quality in very complicated ways, and other factors (for example the synchronisation of the time at which you woke with your circadian cycle) play a much larger role than the sleep quality you got. Also, there are some unexpected effects, where getting too little sleep making you feel good - it's a kind of lightheaded, giddy state, somewhat comparable to having had a small glass of champagne. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes, there is a dependence, but you cannot expect that having had lots of sleep will make you feel good in the morning. &lt;/p&gt;&#xA;" OwnerUserId="9471" LastActivityDate="2014-09-24T17:00:53.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21602" PostTypeId="2" ParentId="21600" CreationDate="2014-09-24T17:08:27.700" Score="5" Body="&lt;p&gt;The appendix doesn't burst by itself. It just lives there quietly, not causing problems. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if it gets infected, it gets full of bacteria, their waste (frequently toxic), and whatever liquids your body exuded into it to fight the infection. It is also connected to your digestive tract, which contains half-digested food. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the appendix swells due to the infection, the pressure can build up enough that it bursts - unlike, say, the bladder, which also can be infected, and also has a baglike shape, but it also has a way to get emptied, which reduces the pressure. It is like having a boil filled with pus, you know how the skin on them gets thin and can burst. But this boil is inside of you, not on the outside. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And once it's burst, all this pus goes into your bloodstream, full of bacteria and toxins. If this is not treated, you get sepsis and die. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the biological &lt;em&gt;mechanism&lt;/em&gt; for dying from burst appendix.If by &lt;em&gt;reason&lt;/em&gt; you are asking why we have  a useless organ which can kill us - &lt;strike&gt; nobody knows for sure, but our best guess is that evolution just hasn't gotten around to get rid of it. It served a function once, and has been getting smaller and smaller since then, but the genes which cause it to appear haven't yet been bred out of humanity. &lt;/strike&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As pointed out in the comment, it is not a useless organ (turns out my biology teacher in highschool was wrong). It has a function, and just like any other organ, it is useful while healthy and can kill you if it gets a disease. &lt;/p&gt;&#xA;" OwnerUserId="9471" LastEditorUserId="9471" LastEditDate="2014-09-25T08:12:01.873" LastActivityDate="2014-09-25T08:12:01.873" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21603" PostTypeId="1" AcceptedAnswerId="21604" CreationDate="2014-09-24T17:36:22.510" Score="3" ViewCount="2520" Body="&lt;p&gt;It is well known that stress isn't good for psoriasis , yet why do we treat the illness with Cortisone, a compound very similar to cortisol (and &quot;has a similar name, genesis, and function&quot;, according to wikipedia) whilst cortisol is released in the body in stress situations?&lt;/p&gt;&#xA;" OwnerDisplayName="user4436" LastEditorUserId="3624" LastEditDate="2014-09-25T09:13:49.163" LastActivityDate="2014-09-25T09:13:49.163" Title="Why is Psoriasis treated with Cortisone, when stress (which releases Cortisol) is known to aggravate the condition?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21604" PostTypeId="2" ParentId="21603" CreationDate="2014-09-24T17:49:17.583" Score="4" Body="&lt;p&gt;For treatment reasons cortisol is named Hydrocortisone (probably to avoid problems with the similar names) and this is often only referenced to as cortisone (although this is not correct). Cortisol (Hydrocortisone) is the active form, while cortison is not. See &lt;a href=&quot;https://biology.stackexchange.com/questions/21465/what-is-the-physiological-difference-between-cortisone-and-cortisol&quot;&gt;here&lt;/a&gt; for some more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cortisol#Immune_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;Glucocorticoids&lt;/a&gt; (like Cortisol or Prednisolone) suppress acute inflammation and also have immuno modulative (downregulate) or suppressive function. Since the immune system causes the problems in Psoriasis it is downregulated to control the outcome of the disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First it sounds counterintuitive to use Glucocorticoids for the treatment of psoriasis as this hormone is released during stress (in this case to mobilize energy resources). However, there is a study which looked precisely at the cortisol levels in psoriasis patients and also recorded their stress levels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What they found was interesting: First they could correlate the peaks in the stress levels with a psoriasis attack about four weeks later. Then they found that the Cortisol levels of the patients where significantly lower in stres situations than for healthy control persons. Additionally they found that patients which had permenant high stress levels also showed significantly lower permanent Cortisol levels. So here the stress seems to negatively influence the cortisol levels which then prepares the way for psoriasis attacks. Using high levels of topically administered Cortisol seems to reverse this effect.&#xA;You can find the study here: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.filedropper.com/showdownload.php/evers2010&quot; rel=&quot;nofollow noreferrer&quot;&gt;How stress gets under the skin: cortisol and stress reactivity in&#xA;psoriasis.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-09-24T18:35:43.443" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21605" PostTypeId="1" CreationDate="2014-09-24T17:53:39.377" Score="6" ViewCount="40" Body="&lt;p&gt;I want to clone ~100 different coding sequences from human or mouse into an expression vector to analyze phenotypes in tissue culture. I can do all of the steps, but I'm not sure what I should use as the template for my reactions. Ideally, I would purchase a pool of full length cDNAs from a bunch of organs, and amplify from that. Less ideally, I can generate cDNAs myself, from multiple organs and pool them. Does anyone have suggestions on a template source?&lt;/p&gt;&#xA;" OwnerUserId="3619" LastActivityDate="2014-11-12T12:11:20.617" Title="Need to make a library of mammalian coding sequences" Tags="&lt;pcr&gt;&lt;protein-expression&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21606" PostTypeId="2" ParentId="21597" CreationDate="2014-09-24T18:43:32.220" Score="5" Body="&lt;p&gt;I'm not really sure, but it seems like a cross section of intestinal villi / intestinal glands from the large intestine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are some images:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Jubal Harshaw. &lt;a href=&quot;http://www.shutterstock.com/pic-20628100/stock-photo-large-intestine-villi-cross-sectioned-showing-goblet-cells-x-cs.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Large intestine villi cross sectioned showing goblet cells_100X_CS0187&lt;/a&gt; on ShutterStock&lt;/li&gt;&#xA;&lt;li&gt;Jubal Harshaw. &lt;a href=&quot;http://www.shutterstock.com/pic-20628109/stock-photo-large-intestine-villi-shown-in-both-longitudinal-section-and-cross-section.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Large intestine villi shown in both longitudinal section and cross section&lt;/a&gt; on ShutterStock&lt;/li&gt;&#xA;&lt;li&gt;Garry DeLong. &lt;a href=&quot;http://www.gettyimages.com/detail/photo/light-micrograph-of-large-intestine-villi-high-res-stock-photography/121820877&quot; rel=&quot;nofollow noreferrer&quot;&gt;Light micrograph of large intestine villi in cross section, showing goblet cells (Magnification x400)&lt;/a&gt; on Getty Images&lt;/li&gt;&#xA;&lt;li&gt;Hill, M.A. (2014) Embryology Gastrointestinal Tract - Colon Histology. Retrieved September 24, 2014, from &lt;a href=&quot;https://php.med.unsw.edu.au/embryology/index.php?title=Gastrointestinal_Tract_-_Colon_Histology&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://php.med.unsw.edu.au/embryology/index.php?title=Gastrointestinal_Tract_-_Colon_Histology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And this is one image from the last link:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Crypts of Lieberkühn - (intestinal gland, intestinal crypt) [...] Transverse&#xA;  &lt;img src=&quot;https://i.stack.imgur.com/kVLZ6.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-09-25T14:09:23.277" LastActivityDate="2014-09-25T14:09:23.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21608" PostTypeId="2" ParentId="21597" CreationDate="2014-09-24T19:05:55.490" Score="4" Body="&lt;p&gt;&lt;strong&gt;Update 3:&lt;/strong&gt; Credit should go to @Cornelius and @DMSever for initially identifying the tissue correctly. I incorporated D M Sever's answer into mine (Update 2,below) because his answer is being down voted for brevity, but he is a recognized authority in the field. I'll remove his answer from mine if his answer ends up being retained.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I showed this question to my histological colleague. He suggested that the tissue is most likely a submucosal gland from either the duodenum (Brunner's glands) or the esophagus. My colleague also said that your image is quite similar to submucosal glands in the large intestine but the presence of smooth muscle surrounding the glands eliminates the large intestine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update 1:&lt;/strong&gt; My histological colleague forwarded your question to one of &lt;em&gt;his&lt;/em&gt; histological colleagues. He too said Brunner's gland.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update 2:&lt;/strong&gt; My histological colleague forwarded your question to his &lt;em&gt;most trusted&lt;/em&gt; histological colleague. He said colon, specifically the transverse sections through &lt;a href=&quot;http://medcell.med.yale.edu/histology/gi_tract_lab/crypts_of_lieberkuhn.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;Crypts of Lieberkuhn&lt;/a&gt;. He then signed on as @DMSever and posted a brief but authoritative answer. He's a veteran of histological affairs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a photo of Brunner's glands in the duodenum, taken from &lt;a href=&quot;http://achmad-zaifullah.blogspot.com/2011/04/lower-gastrointestinal-tract.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QPStT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a photo of the esophageal submucosal glands, taken from &lt;a href=&quot;http://www.vetmed.vt.edu/education/curriculum/vm8304/lab_companion/histo-path/vm8054/labs/Lab18/EXAMPLES/Exesoph3.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Nspda.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="8517" LastEditDate="2014-09-25T14:15:44.417" LastActivityDate="2014-09-25T14:15:44.417" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21610" PostTypeId="1" CreationDate="2014-09-24T20:09:10.277" Score="0" ViewCount="67" Body="&lt;p&gt;So I am taking a new class at my institution called Theoretic Nuclear Thermochemical Pharmacology, (I know big name, it's an elective from a real pioneering fronteirsman in our department :P) and I am curious about the metabolism of gabapentin and how this might relate to thermochemistry?  I am curious how this drug metabolizes in the liver and how it neurochemically alters the brain such that it reduces mania in patients that are bipolar and may also have mood disorders.  Any kind of relevant literature would be appreciated, something to guide me in the right direction.  I mean I understand liver metabolism and what it does but its relation to mania and how it's thermochemical still boggles me.  &lt;/p&gt;&#xA;" OwnerUserId="9001" LastActivityDate="2014-09-24T20:09:10.277" Title="Thermochemistry of gabapentin" Tags="&lt;pharmacology&gt;&lt;pharmacodynamics&gt;&lt;pharmacokinetics&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21611" PostTypeId="2" ParentId="21600" CreationDate="2014-09-24T20:13:18.070" Score="16" Body="&lt;p&gt;&lt;strong&gt;Necessary conditions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order for the process culminating in appendiceal rupture to begin, there must first be proximal obstruction of the lumen (the inside cavity of the appendix) that prevents normal communication with the bowel.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Obstruction is most commonly caused by a fecalith, which results from accumulation and inspissation of fecal matter around vegetable fibers.&#xA;  The bowel wall inside the (now closed) appendix continues to secrete muscous, and bacteria continue to multiply, producing the distention that is often perceived as nausea, vomiting, and poorly localized abdominal pain.&lt;sup&gt;1&lt;/sup&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The process leading to rupture&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the pressure in the appendix increases, venous pressure is exceeded. This means blood can no longer exit the venules of the appendix normally. In the presence of ongoing arterial flow, this leads to vascular engorgement, worsening the distention and increasing pressure further. The inflammatory process spreads from the lumen (inside) of the appendix to the serosa (outside) and then to the parietal peritoneum (lining of the abdominal cavity). This last step is what causes the characteristic shift in pain from poorly localized visceral pain to focal right lower quadrant pain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As distention worsens, arterial pressure is eventually exceeded, and the most poorly vascularized areas of the appendix (generally just beyond the point of obstruction on the antimesenteric border) infarct first. Dead tissue has very little structural integrity, and once infarction happens perforation is likely to follow quickly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why this is (sometimes) lethal&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several possible mechanisms, more than one of which is probably operative in most cases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The three I have listed below all converge on the same final common pathway: In the absence of adequate systemic blood pressure (shock), the heart is not able to pump normally and will eventually deteriorate into a non-perfusing rhythm (a.k.a death).&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Bacteria in the peritoneal cavity&lt;/strong&gt;:&#xA;As in bowel perforation of any cause (e.g. perforated peptic ulcer, perforated diverticulum, traumatic perforation), bacteria in the peritoneal cavity (the “free space” outside the bowel within the abdomen) triggers an intense inflammatory reaction and fluid sequestration. Fluid pulled from the circulation into the peritoneal space causes hypotension and (hypovolemic) shock.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Infarcted bowel&lt;/strong&gt;: Dead tissue connected to the body is never a good situation. Intracellular contents are released into the bloodstream – electrolyte release can cause hyperkalemia and other electrolyte imbalances; reactive oxygen species can lead to hypotension and (distributive) shock.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Sepsis&lt;/strong&gt;: Bacteria (generally gram negative rods from among normal gut flora – most commonly Escherichia coli or Bacteroides fragilis)&#xA;may enter the bloodstream due to compromised vessels during the process of infarction and rupture. Lipopolysaccharides in the cell wall of gram-negative bacterial organisms lead to activation of monocytes and macrophages. This results in increased levels of interleukin-1 and tumor necrosis factor and eventually of IL-6 and IL-8. These cause widespread endothelial injury leading to &lt;a href=&quot;http://en.wikipedia.org/wiki/Diffuse_alveolar_damage&quot; rel=&quot;nofollow&quot;&gt;diffuse alveolar damage&lt;/a&gt; in the lungs and activation of the coagulation system leading to &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000573.htm&quot; rel=&quot;nofollow&quot;&gt;disseminated intravascular coagulation&lt;/a&gt;. These cytokines also lead to systemic vasodilation and (distributive, septic) shock.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&#xA;References&#xA;&lt;/sup&gt;&lt;br&gt;&#xA;&lt;sup&gt;&#xA;1. Silen W. Chapter 300. &lt;em&gt;Acute Appendicitis and Peritonitis&lt;/em&gt;. In: Longo DL, Fauci AS, Kasper DL, Hauser SL, Jameson J, Loscalzo J. eds. Harrison's Principles of Internal Medicine, 18e. New York, NY: McGraw-Hill; 2012.&#xA;&lt;/sup&gt;&#xA;&lt;sup&gt;&lt;br&gt;&#xA;2. Kemp WL, Burns DK, Brown TG. Chapter 8. &lt;em&gt;Hemodynamics.&lt;/em&gt; Pathology: The Big Picture. New York, NY: McGraw-Hill; 2008.&#xA;&lt;/sup&gt;&lt;br&gt;&#xA;&lt;sup&gt;&#xA;3. Charles Brunicardi, F. &lt;em&gt;Acute Appendicitis.&lt;/em&gt; Schwartz's Manual of Surgery; 2006.&#xA;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-09-27T12:26:27.937" LastActivityDate="2014-09-27T12:26:27.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21612" PostTypeId="2" ParentId="21597" CreationDate="2014-09-24T20:26:46.293" Score="1" Body="&lt;p&gt;It is from the Colon - transverse sections through crypts of Lieberkuhn seen there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For references see:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.elsevier-etextbooks.com/product/wheater&quot; rel=&quot;nofollow&quot;&gt;Wheater's Functional Histology&lt;/a&gt; p. 283 Fig. 14.29e&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://embryology.med.unsw.edu.au/embryology/index.php?title=Gastrointestinal_Tract_-_Colon_Histology&quot; rel=&quot;nofollow&quot;&gt;UNSW Embryology&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9478" LastEditorUserId="3624" LastEditDate="2014-09-25T16:09:14.577" LastActivityDate="2014-09-25T16:09:14.577" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21613" PostTypeId="1" CreationDate="2014-09-24T20:39:10.807" Score="3" ViewCount="75" Body="&lt;p&gt;if willing to recolonize earth desert , let's say sahara or any dehydrated and sterile land, without intensive human intervention, what would be the first plants / algae / fungi /bacteria to grow ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;what could be the strategy to slowly bring back biodiversity and trigger new water cycles ?&lt;/p&gt;&#xA;" OwnerUserId="6546" LastEditorUserId="6546" LastEditDate="2014-09-25T10:57:29.183" LastActivityDate="2014-09-25T12:07:30.827" Title="recolonize earth desert with plants : which plants first?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;adaptation&gt;&lt;climate-change&gt;&lt;agriculture&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21614" PostTypeId="2" ParentId="21580" CreationDate="2014-09-24T20:48:11.230" Score="3" Body="&lt;p&gt;I suspect that that dpy-11-mutants (that's what you likely meant) are not very representative neither from the morphological nor from the behavioral points of view, because they have anomalies in body shape (dumpy appearance) and male tail morphology (see in &lt;a href=&quot;http://www.wormbase.org/species/c_elegans/gene/WBGene00001073?from=http://www.wormbase.org/db/gene/gene?name=dpy-11#0-9e-3&quot; rel=&quot;nofollow&quot;&gt;WormBase&lt;/a&gt; and in &lt;a href=&quot;http://dev.biologists.org/content/129/5/1185.full.html&quot; rel=&quot;nofollow&quot;&gt;Ko and Chow&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a general purpose the wild-type should be best.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-09-24T20:48:11.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21615" PostTypeId="1" AcceptedAnswerId="21616" CreationDate="2014-09-24T22:01:55.583" Score="1" ViewCount="637" Body="&lt;p&gt;I have a question regarding how organism replicate them self to create an other organism,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We know that in animal reign, we need a male and female that will generate a new being.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;what I want to know is if there is a micro organism that can create another one without a partner of the same kind? and in that case how this organism can do that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;hope my question was clear!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks! &lt;/p&gt;&#xA;" OwnerUserId="9483" LastActivityDate="2014-09-24T23:55:12.130" Title="Can Mono-Cell or other organism self-replicate?" Tags="&lt;cell-biology&gt;&lt;replication&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21616" PostTypeId="2" ParentId="21615" CreationDate="2014-09-24T23:55:12.130" Score="1" Body="&lt;p&gt;The short answer is &lt;em&gt;yes&lt;/em&gt;, there are single-celled organisms that can reproduce without another &quot;partner&quot;. Probably the most famous example is that of bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you're talking about is known as &lt;em&gt;asexual reproduction&lt;/em&gt;. In bacteria, the process is known as &lt;em&gt;binary fission&lt;/em&gt;, where one bacterium (known as the &lt;em&gt;parent cell&lt;/em&gt;) divides into two organisms (known as &lt;em&gt;daughter cells&lt;/em&gt;). These two cells will be genetically identical (barring any mutations) to the parent cell, because there has been no combination (for lack of a better term) of DNA, as there is in sexual reproduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The process works the same way it does in cells in multicellular organisms, such as humans: DNA &quot;unwinds&quot; (again due to lack of a better term) in the center of the cell, complementary bases are added to each of the now-separate strands (adenine with thymine, guanine with cytosine), the other parts of the cell are duplicated, and, gradually, the bacterium splits in two. The process can be very quick, compared to the nine months humans spend in the womb.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Asexual reproduction is not unique to single-celled organisms, though. While it is prevalent (and easy) in bacteria, some multicellular organisms reproduce asexually. Some plants are capable or this via &lt;em&gt;self-pollination&lt;/em&gt;, and there have been some reports (albeit rather dubious) of certain &quot;common&quot; animals reproducing asexually.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are advantages and disadvantages to asexual reproduction. One advantage is obvious: no mate necessary. As long as an organism has enough energy and nutrients to reproduce, it can. Also, the process is quick, and easy. There are some disadvantages, though. The big one is that there is no recombination from multiple DNA sources - that is, the resulting organism will have exactly (again, barring mutations) the same genes as its parent - for better or for worse. If an asexually-reproducing organism has a defect that still allows it to reproduce, chances are, its offspring will have that defect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some sources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://plato.acadiau.ca/courses/biol/Microbiology/Replication.htm&quot; rel=&quot;nofollow&quot;&gt;http://plato.acadiau.ca/courses/biol/Microbiology/Replication.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.yourarticlelibrary.com/biology/asexual-reproduction-in-animals-characteristics-occurrence-and-types/11727/&quot; rel=&quot;nofollow&quot;&gt;http://www.yourarticlelibrary.com/biology/asexual-reproduction-in-animals-characteristics-occurrence-and-types/11727/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mpipks-dresden.mpg.de/~mbsffe09/talks/Krug.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.mpipks-dresden.mpg.de/~mbsffe09/talks/Krug.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.britannica.com/EBchecked/topic/498542/reproduction&quot; rel=&quot;nofollow&quot;&gt;http://www.britannica.com/EBchecked/topic/498542/reproduction&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9458" LastActivityDate="2014-09-24T23:55:12.130" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21620" PostTypeId="1" AcceptedAnswerId="21626" CreationDate="2014-09-25T02:03:33.647" Score="2" ViewCount="2530" Body="&lt;p&gt;I know that one way is to use the reagent sticks and the refractometer, but this is inaccurate. Is protein distinguishable when using a microscope? Is it time sensitive(i.e. have to test it right away)?&lt;/p&gt;&#xA;" OwnerUserId="6682" LastActivityDate="2014-09-26T08:45:57.290" Title="What are the ways to test for protein in the canine urine?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21622" PostTypeId="2" ParentId="10176" CreationDate="2014-09-25T02:49:02.540" Score="4" Body="&lt;p&gt;Eating many small meals or eating large meals is irrelevant. The only thing that matters is getting the right amount of calories needed for your body to function properly.&#xA;Fat accumulation does not happen if you do not go over your daily calorie limit.&#xA;After a big meal your food is not only stored as fat but as a polysaccharide form of glucose called glycogen that is stored in the liver and or muscles for later use.&#xA;Therefore, there is no better way to eat, it depends on what size you like your meals to be as long as you stay within your calorie range.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://www.choosemyplate.gov&quot; rel=&quot;nofollow&quot;&gt;http://www.choosemyplate.gov&lt;/a&gt; for more information.&lt;/p&gt;&#xA;" OwnerUserId="9490" LastActivityDate="2014-09-25T02:49:02.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21623" PostTypeId="1" CreationDate="2014-09-25T03:03:53.600" Score="1" ViewCount="64" Body="&lt;p&gt;I was wondering how some animals (bulls, elephants etc.) become so large by only eating grass or plant based material and why some humans can build large amounts of muscle and mass without a proper diet. &#xA;1. How do both get their essential amino acids in order to build muscle and mass?&#xA;2. Can hormones independently build muscle and mass regardless of the food or amount of calories ingested?&lt;/p&gt;&#xA;" OwnerUserId="9490" LastActivityDate="2014-09-25T03:03:53.600" Title="Hormones and body mass" Tags="&lt;food&gt;&lt;endocrinology&gt;&lt;nutrition&gt;&lt;muscles&gt;&lt;amino-acids&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21624" PostTypeId="1" CreationDate="2014-09-25T03:05:56.683" Score="1" ViewCount="54" Body="&lt;p&gt;I am wondering if it is theoretically possible to create &quot;artificial sperm&quot; via cell culture adaptation. That is at very high level, can you replace the genes of one sperm cell with those of another sperm cell and still have a functioning cell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An area of application would be male infertility due to &quot;weak sperm&quot;. Here you would take a &quot;strong swimmers&quot; from a donor, replace the genes with those from infertile male, and used the cultured adaption in fertilization. &lt;/p&gt;&#xA;" OwnerUserId="9491" LastActivityDate="2014-09-25T03:05:56.683" Title="Creating Sperm via cell culture adaptation" Tags="&lt;cell-culture&gt;&lt;reproductive-biology&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21625" PostTypeId="1" CreationDate="2014-09-25T03:46:10.923" Score="2" ViewCount="111" Body="&lt;p&gt;I am not a biologist, so sorry to anybody for misinformation in this post.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I understand correctly, dogs evolved the ability to show emotions through various sounds and tail-wagging in order to better communicate with their symbiotic partners, humans. Is it possible that recently, dog breeding has disassociated this with the communication of emotions due to the fact that humans like dogs which are more naturally happy? Considering that they have been tamed, and therefore their actions wouldn't be a good indicator, it seems plausible to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please correct me on misinformation.&lt;/p&gt;&#xA;" OwnerUserId="9492" LastActivityDate="2014-09-25T03:46:10.923" Title="How likely is it that through dog breeding, tail-wagging has been disassociated with happiness?" Tags="&lt;evolution&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21626" PostTypeId="2" ParentId="21620" CreationDate="2014-09-25T06:24:31.093" Score="3" Body="&lt;p&gt;After some research, I could primarily find two tests for testing the protein content in dog urine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) The Urinalysis dipstick test (&lt;a href=&quot;http://www.peteducation.com/article.cfm?c=2%202116&amp;amp;aid=3136&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;) which has a chance of giving false positive results (&lt;a href=&quot;http://www.merckmanuals.com/vet/clinical_pathology_and_procedures/diagnostic_procedures_for_the_private_practice_laboratory/urinalysis.html#v4702088&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;). &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20113233&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here is the link&lt;/a&gt; to a lab test done using the dipstick method and the results that the researchers got. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/h8h4W.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A sample Dipstick (&lt;a href=&quot;http://www.pet-informed-veterinary-advice-online.com/kennel-cough.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The second test would be the benzethonium chloride test (&lt;a href=&quot;https://ahdc.vet.cornell.edu/sects/clinpath/test/urine/protein.cfm&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This test precipitates the protein and increases the turbidity of the&#xA;  sample. The turbidity is proportional to the protein concentration.&#xA;  This technique is very sensitive and can yield accurate results in&#xA;  samples with very low protein concentrations (&amp;lt; 20 mg/dL).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A lab study done using this procedure to precipitate protein (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6821941&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The urine sample is best read within 30 minutes of collection&#xA;  otherwise certain factors (like crystals, bacteria and cells) may&#xA;  alter their composition (dissolve or multiply) over time. If you&#xA;  collect a urine sample at home, please drop it off at your veterinary&#xA;  clinic as soon as possible (&lt;a href=&quot;http://www.huffingtonpost.com/donna-solomon-dvm/pet-urine_b_3693280.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Reasons for excess protein if present in the urine of your pet is listed in &lt;a href=&quot;http://www.petmd.com/dog/conditions/urinary/c_multi_proteinuria&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-09-26T08:45:57.290" LastActivityDate="2014-09-26T08:45:57.290" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21628" PostTypeId="1" AcceptedAnswerId="21639" CreationDate="2014-09-25T10:25:36.430" Score="6" ViewCount="15077" Body="&lt;p&gt;I have tried to calculate the relatedness for haplodiploid organisms, but cannot understand the calculations behind full sister and full brother.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ldMRV.png&quot; alt=&quot;Haplodiploidy r taken from wikipedia&quot; /&gt;&#xA;(taken from &lt;a href=&quot;http://en.wikipedia.org/wiki/Haplodiploidy#Relatedness_ratios_in_haplodiploidy&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia: haplodiploidy&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;I have managed to solve the other cases. Since female will have ZZ:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;female will share 1/2 of her genes with daughter&lt;/p&gt;&#xA;&lt;p&gt;female will share 1/2 of her genes with son&lt;/p&gt;&#xA;&lt;p&gt;female will share 1/2 of her genes with mother&lt;/p&gt;&#xA;&lt;p&gt;female will share 1/2 of her genes with father&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Since male will have only Z:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;male will share 1 (100%) of his genes with his daughter&lt;/p&gt;&#xA;&lt;p&gt;male won't share anything with his son (unfertilized eggs leads to male in haplodiploidy system)&lt;/p&gt;&#xA;&lt;p&gt;male will share 1(100%) of his genes with his mother&lt;/p&gt;&#xA;&lt;p&gt;male won't share anything with his father (unfertilized eggs leads to male in haplodiploidy system)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Even though I figured out how others work, I wasn't able to calculate r for fullsister fullbrother? How can it be 3/4,1/4,1/2,1/2?&lt;/p&gt;&#xA;" OwnerUserId="9494" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-08T20:36:10.203" Title="How to calculate relatedness in haplodiploid organisms (mainly full sisters and full brothers)?" Tags="&lt;genetics&gt;&lt;altruism&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21629" PostTypeId="1" AcceptedAnswerId="21666" CreationDate="2014-09-25T10:45:54.123" Score="2" ViewCount="265" Body="&lt;p&gt;I came across the &lt;a href=&quot;http://en.wikipedia.org/wiki/Spinning_Dancer&quot; rel=&quot;nofollow noreferrer&quot;&gt;spinning dancer&lt;/a&gt; as part of the brain test to determine left brain vs right brain dominance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZmQYC.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I saw the dancer is turning clockwise. The other people around me saw it turning clockwise for the first time, but soon they got confused and said they saw it turning it in both direction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know the tips of how to see it anti clockwise, but no matter what I do I always see it clockwise. I have shown it to a number of people and all of them could see it spinning in both direction after looking at it for longer time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am the only person who has never see the dancer turning in both direction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is does this has anything to do with my eyesight? I have very limited(almost blind) eyesight in my left eyes. This is from birth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does my visual impairment has anything to do with this or does this mean anything else?&lt;/p&gt;&#xA;" OwnerUserId="9495" LastActivityDate="2014-09-26T05:53:50.133" Title="Does Spinning dancer has anything to do with your eyesight" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;vision&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21630" PostTypeId="2" ParentId="21613" CreationDate="2014-09-25T10:49:47.580" Score="0" Body="&lt;p&gt;i suppose a strategy would be :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-find among xerophyte plant ( &lt;a href=&quot;http://en.wikipedia.org/wiki/Xerophyte&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Xerophyte&lt;/a&gt; ).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-selecting plants that needs the less water, grow fast and expand on surface, and produce the maximum biomass.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-the soil produced by the pioneer plants would allow other plants to grow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-these last plants would be selected for their better ability to condensate water and cool the atmosphere down and humidify it, and for producing more biomass that would allow a third pool of plants to grow &lt;/p&gt;&#xA;" OwnerUserId="6546" LastActivityDate="2014-09-25T10:49:47.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21631" PostTypeId="1" CreationDate="2014-09-25T10:56:20.247" Score="2" ViewCount="232" Body="&lt;p&gt;In an effort to select for the most suitable plants to possibly colonise desert and stop its expansion, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;what would be the xerophyte plants that grow the faster and expand on surface, while using the less water and produce a maximum of biomass?&lt;/p&gt;&#xA;" OwnerUserId="6546" LastActivityDate="2014-11-24T11:34:40.700" Title="Among xerophyte plants, which one grow faster and consume water the least?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;adaptation&gt;&lt;agriculture&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2014-12-06T21:21:31.877" ContentLicense="CC BY-SA 3.0" />
  <row Id="21632" PostTypeId="1" AcceptedAnswerId="21984" CreationDate="2014-09-25T11:11:47.527" Score="7" ViewCount="1903" Body="&lt;p&gt;I've noticed some pain killers working great for me, while others have no effect.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Works for me&lt;/h3&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Aspirin&quot; rel=&quot;nofollow&quot;&gt;Aspirin&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;APC &lt;sup&gt;&amp;dagger;&lt;/sup&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Naproxen&quot; rel=&quot;nofollow&quot;&gt;Naproxen&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h3&gt;Doesn't work for me&lt;/h3&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Paracetamol&quot; rel=&quot;nofollow&quot;&gt;Paracetamol&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Diclofenac&quot; rel=&quot;nofollow&quot;&gt;Diclofenac&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Tramadol&quot; rel=&quot;nofollow&quot;&gt;Tramadol&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I doubt there is much of a placebo effect at work, since most of these either did or did not work when I first took them, without having expectations either way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whenever I have a head ache, I take an APC. I suspect it's actually the aspirin in there that does the job, since when I take &lt;em&gt;just&lt;/em&gt; paracetamol, it doesn't do squat. As a kid I got children's aspirin, which worked.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I once had a severe back ache. I was prescribed diclofenac (a heavier variant than the over the counter one), which didn't work. I was then prescribed tramadol &amp;mdash; same results. I then tried naproxen, which worked rightaway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why do some pain killers work while others don't?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there an underlying mechanism, that explains why some of these work while others don't? Does that predict if pain killers that I haven't used yet will work?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please note that I'm &lt;strong&gt;not&lt;/strong&gt; looking for medical advice on which pain killers to take; I'm just curious about how my body interacts with the various ones.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&amp;dagger;: the one consisting of aspirin, &lt;em&gt;paracetamol&lt;/em&gt;, and caffeine, &lt;strong&gt;not&lt;/strong&gt; the one containing &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenacetin#Uses&quot; rel=&quot;nofollow&quot;&gt;phenaticin&lt;/a&gt;. Think &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Excedrin&quot; rel=&quot;nofollow&quot;&gt;Excedrin&lt;/a&gt;&lt;/em&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="6800" LastEditorUserId="6800" LastEditDate="2015-07-25T06:06:43.920" LastActivityDate="2015-07-25T06:06:43.920" Title="Why do different pain killers have different effects on people?" Tags="&lt;pharmacology&gt;&lt;pharmacodynamics&gt;&lt;pharmacokinetics&gt;&lt;analgesia&gt;&lt;treatment&gt;" AnswerCount="2" CommentCount="11" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21636" PostTypeId="1" AcceptedAnswerId="21655" CreationDate="2014-09-25T11:34:03.060" Score="9" ViewCount="2008" Body="&lt;p&gt;This image appears on the cover of Peter Gabriel's album New Blood.  It appears to be a photograph of some microscopic biological cell.  But it doesn't look like a blood cell to me.   What kind of cell is it? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4iDWB.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9496" LastActivityDate="2014-09-25T18:29:05.657" Title="What is this microscopic image from Peter Gabriel's New Blood album cover?" Tags="&lt;microbiology&gt;&lt;hematology&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21637" PostTypeId="1" CreationDate="2014-09-25T11:45:30.627" Score="4" ViewCount="434" Body="&lt;p&gt;is there any evidences of these differences during development stages prior to hormone driven sexual differentiation? mice studies ?&lt;/p&gt;&#xA;" OwnerUserId="6546" LastActivityDate="2014-09-25T13:07:49.870" Title="Are there anatomical differences between male and female mammal brains before action of hormones?" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;development&gt;&lt;sexual-dimorphism&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21638" PostTypeId="2" ParentId="21628" CreationDate="2014-09-25T11:46:54.317" Score="7" Body="&lt;p&gt;It is useful to think in terms of the proportion of genetic material that an individual gets from each parent and the amount of this genetic material that will be shared with another individual (on average), and then sum this together i.e. as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$ relatedness = prop_{mother} * shared_{mother} + prop_{father} * shared_{father} $ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A female will share 50% of the genetic material from the mother's side and 100% if the material from the father's side with her full sisters: $0.5*0.5 + 0.5*1 = 0.75$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A female will share 50% of the genetic material from the mother's side and 0% if the material from the father's side with her brother: $0.5*0.5 + 0.5*0 = 0.25$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A male will share 50% of the genetic material from the mother's side with his sister (and doesn't get any from the father's side).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A male will share 50% of the genetic material from the mother's side with his brother (and doesn't get any from the father's side).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remember also that this only holds if the female has only mated once.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-09-25T14:30:23.773" LastActivityDate="2014-09-25T14:30:23.773" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="21639" PostTypeId="2" ParentId="21628" CreationDate="2014-09-25T11:55:46.203" Score="3" Body="&lt;p&gt;This is a relative thing in haplodiploidy system.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;r = Mother's side + father's side(in this case)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;D--Daughter&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;S--Son&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;F-Father&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;M-Mother&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;You can get the below things from the question image itself.(All that you need to do is to read male and female appropriately as son,father,mother,daughter based on the context.So simple!)&#xA;  &lt;img src=&quot;https://i.stack.imgur.com/70Yt9.png&quot; alt=&quot;question image&quot;&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;1.r&lt;sub&gt;MD&lt;/sub&gt;=1/2&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;2.r&lt;sub&gt;MS&lt;/sub&gt;=1/2&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;3.r&lt;sub&gt;DM&lt;/sub&gt;=1/2&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;4.r&lt;sub&gt;DF&lt;/sub&gt;=1/2&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;5.r&lt;sub&gt;FD&lt;/sub&gt;=1&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;6.r&lt;sub&gt;FS&lt;/sub&gt;=0&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;7.r&lt;sub&gt;SM&lt;/sub&gt;=1&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;8.r&lt;sub&gt;SF&lt;/sub&gt;=0&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;case 1:&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;r&lt;sub&gt;DD&lt;/sub&gt;=(r&lt;sub&gt;DM&lt;/sub&gt;*r&lt;sub&gt;MD&lt;/sub&gt;) + (r&lt;sub&gt;DF&lt;/sub&gt;*r&lt;sub&gt;FD&lt;/sub&gt;)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;r&lt;sub&gt;DD&lt;/sub&gt;=(1/2*1/2)+(1/2*1)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;r&lt;sub&gt;DD&lt;/sub&gt;=&lt;strong&gt;3/4&lt;/strong&gt;&#xA;  &lt;img src=&quot;https://i.stack.imgur.com/NiFWO.jpg&quot; alt=&quot;female full sister&quot;&gt;&#xA;  &lt;strong&gt;case 2:&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;r&lt;sub&gt;DS&lt;/sub&gt;=(r&lt;sub&gt;DM&lt;/sub&gt;*r&lt;sub&gt;MS&lt;/sub&gt;) + (r&lt;sub&gt;SF&lt;/sub&gt;*r&lt;sub&gt;FD&lt;/sub&gt;)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;r&lt;sub&gt;DS&lt;/sub&gt;=(1/2*1/2)+0*1&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;r&lt;sub&gt;DS&lt;/sub&gt;=&lt;strong&gt;1/4&lt;/strong&gt;&#xA;  &lt;img src=&quot;https://i.stack.imgur.com/VbZCw.jpg&quot; alt=&quot;female full brother&quot;&gt;&#xA;  &lt;strong&gt;case 3:&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;r&lt;sub&gt;SD&lt;/sub&gt;=(r&lt;sub&gt;SM&lt;/sub&gt;*r&lt;sub&gt;MD&lt;/sub&gt;) + (r&lt;sub&gt;DF&lt;/sub&gt;*r&lt;sub&gt;FS&lt;/sub&gt;)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;r&lt;sub&gt;SD&lt;/sub&gt;=(1*1/2)+(1/2*0)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;r&lt;sub&gt;SD&lt;/sub&gt;=&lt;strong&gt;1/2&lt;/strong&gt;&#xA;  &lt;img src=&quot;https://i.stack.imgur.com/DjLZX.jpg&quot; alt=&quot;male full sister&quot;&gt;&#xA;  &lt;strong&gt;case 4:&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;r&lt;sub&gt;SS&lt;/sub&gt;=(r&lt;sub&gt;SM&lt;/sub&gt;*r&lt;sub&gt;MS&lt;/sub&gt;) + (r&lt;sub&gt;SF&lt;/sub&gt;*r&lt;sub&gt;FS&lt;/sub&gt;)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;r&lt;sub&gt;SS&lt;/sub&gt;=(1*1/2)+(0*0)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;r&lt;sub&gt;SS&lt;/sub&gt;=&lt;strong&gt;1/2&lt;/strong&gt;&#xA;  &lt;img src=&quot;https://i.stack.imgur.com/eATSf.jpg&quot; alt=&quot;male full brother&quot;&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8135" LastEditorUserId="8135" LastEditDate="2014-09-25T14:27:12.597" LastActivityDate="2014-09-25T14:27:12.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21641" PostTypeId="2" ParentId="21613" CreationDate="2014-09-25T12:07:30.827" Score="2" Body="&lt;p&gt;This is a big idea that's gaining momentum in many people's minds across the world.  This is a brief and probably inadequate survey and hopefully other answers / comments will fill out a better picture. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the plans to reclaim arid regions are not completely hands off.  It seems that the current thinking is that if we waited for microbes and lichen to reclaim arid soil, it would take too long.  Most of them focus on trees.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trees are fantastic because they &lt;a href=&quot;http://www.sciencedaily.com/releases/2013/07/130731093456.htm&quot; rel=&quot;nofollow&quot;&gt;can grow in climates that have minimal water once they are established&lt;/a&gt;.  They can claim moisture from the air, remove pollution from the air, reduce the ground temperature, sequester carbon, prevent erosion, and make the environment more accommodating to other plants.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some estimates are that to curb the expansion of deserts worldwide, &lt;a href=&quot;http://www.psmag.com/environment/seeing-drylands-trees-42998/&quot; rel=&quot;nofollow&quot;&gt;30 billion trees should be planted every year for the next decade&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The tree one plants varies depending on the place and application, but the selection of the plant is more than just a climatic choice.  Trees are grown in nurseries when their needs for water are most intensive, and then need to be cared for until they are established enough to survive on their own.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.greenbeltmovement.org/what-we-do/tree-planting-for-watersheds/income-generating-activities&quot; rel=&quot;nofollow&quot;&gt;Green Belt project&lt;/a&gt; was the focus of the 2004 Nobel Peace Prize.  Its success in rolling back desertification was because of its understanding of the causes of desertification in many cases as a social effect.*  People harvest the trees, graze the land dry, burn grassland etc.  Green Belt created networks of local people and incentivized them to grow trees, selecting trees which had agricultural and economic value so that they would help the local economy.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.newyorker.com/magazine/2011/12/19/the-great-oasis&quot; rel=&quot;nofollow&quot;&gt;Great Green Wall project&lt;/a&gt; is a successor to this idea.  Attempting to contain the Sahara desert's spread across the continent of Africa.   Their plan is to have a different organization in each country, including automation of sorts to collect water from the air and rain for more continuous support of young trees. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ted.com/talks/allan_savory_how_to_green_the_world_s_deserts_and_reverse_climate_change&quot; rel=&quot;nofollow&quot;&gt;there are arguments that ultimately the animal ecosystem needs to be involved&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-09-25T12:07:30.827" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21643" PostTypeId="2" ParentId="21637" CreationDate="2014-09-25T12:13:16.030" Score="3" Body="&lt;p&gt;Yes. &lt;a href=&quot;http://ts-si.org/files/SexuallyDimorphicGeneExpressionPrecedesGonadalDifferentiation.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dewing et al. (20030&lt;/a&gt; found that gene expression in mouse brains differs between male and female mice about 10.5 days after the mice had sex. This occurs before hormonal contributions to brain development. They identified about 35 genes that were appeared to show preferential expression in the female brain and another 16 that appeared to be show preferential expression in the male brain. Most of the genes identified were transcriptional regulators, signaling molecules, or involved with cellular differentiation. Of these 51, three were verified as showing female bias, and two of these were located on the X chromosome. Four genes were verified showing male bias, and two of these were located on the Y chromosome.&lt;/p&gt;&#xA;&lt;p&gt;Similar results were found by &lt;a href=&quot;http://hmg.oxfordjournals.org/content/11/12/1409.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;Xu et al. (2002)&lt;/a&gt;. They identified several of the same genes as Dewing et al., plus others that were linked to the sex chromosomes. They identified a total of six genes on the X chromosome that showed strong female expression bias during brain development. At least three of the genes were homologous between the X and Y chromosomes but showed different expression patterns between male and female brains at different stages of development.&lt;/p&gt;&#xA;&lt;p&gt;The differences in genetic expression may cause some microscopic anatomical differences during brain development that is not explained by hormones &lt;a href=&quot;http://books.google.com/books?id=zx3GngnlbVcC&amp;amp;pg=PA245#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Bocklandt and Vilain 2007)&lt;/a&gt;. They reviewed several studies that found differences in neuron growth, and density of vasopressin fibers in the lateral septum were more likely to be due to genetic expression than to hormonal expression. Bocklandt and Vilain did not identify the specific ages of the mice that showed these apparently gene-regulated differences but it is reasonable to speculate that these differences begin to appear in association with the differential gene expression.  Bocklandt and Vilain did not identify macroscopic differences between male and female brains prior to hormonal expression.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Citations&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Bockland, S. and E. Vilain. 2007. Sex differences in brain and behavior: Hormones versus genes. pgs 245-266. In: &lt;em&gt;Genetics of sexual differentiation and sexually dimorphic behaviors&lt;/em&gt; (D. Yamamoto, ed.). Academic Press.&lt;/p&gt;&#xA;&lt;p&gt;Dewing, P. et al. 2003. Sexually dimorphic gene expression in mouse brain precedes gonadal differentiation. Molecular Brain Research 118: 82-90.&lt;/p&gt;&#xA;&lt;p&gt;Xu, J. et al. 2002. Sex differences in sex chromosome gene expression in mouse brain. Human Molecular Genetics 11: 1409-1419.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8517" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-09-25T13:07:49.870" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21645" PostTypeId="1" CreationDate="2014-09-25T13:13:08.387" Score="1" ViewCount="85" Body="&lt;p&gt;I am involved in a modelling task of a biological process described as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;--&#xA;&quot;Objective: to model behavior of a sender receiver type system&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The process goes as follows&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Pre-signal [PS] is in media&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Pre-signal diffuses into bacteria&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Pre-signal binds to activator as a co-activator&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Co-activator activator complex binds to DNA and starts transcription of enzyme mRNA&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Enzyme mRNA is transcribed then translated into enzyme&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Enzyme begins converting Pre-signal to signal [S]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Signal diffuses out of the cell into media&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Signal diffuses into receiver cell from media&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Signal binds to repressor inducing activation of reporter gene&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Questions for model:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What concentrations of signal will be required to get a response from receiver cell?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;--&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions are: what kind of mathematical/computational model or simulation tool is more suitable for this task? is it neccesary to model every step, or can some of these be ignored? I know the basics of ODEs, so I wonder if these are enough or something else would be required. Any other advice about how to go through the modelling is welcome.&lt;/p&gt;&#xA;" OwnerUserId="8966" LastEditorUserId="3340" LastEditDate="2014-12-02T12:34:09.113" LastActivityDate="2014-12-02T12:35:08.077" Title="Modeling intracellular interactions between sender and receiver bacteria" Tags="&lt;bioinformatics&gt;&lt;mathematical-models&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21646" PostTypeId="2" ParentId="21579" CreationDate="2014-09-25T13:29:18.863" Score="2" Body="&lt;p&gt;You will appreciate reading &lt;a href=&quot;https://biology.stackexchange.com/questions/17077/why-does-evolution-not-make-our-life-longer/17078&quot;&gt;this post&lt;/a&gt; and have a look to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_ageing&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia article&lt;/a&gt; on the evolution of aging. I make below a quick summary and apply it to your question but I think it is worth looking at the other post on aging.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In short: Theory of aging&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine a deleterious (=negative) allele (=variant of a gene) that is expressed throughout the lifetime. This allele (by definition of a deleterious allele) will decrease the reproductive success of the carrier. Now consider another allele who is expressed only late in life, maybe after the first reproduction but before the second reproduction. This allele will decrease the reproductive success of the carrier but by a lower magnitude that did the allele that was acting throughout the lifetime so that it is more likely for this second allele to rise in frequency in the population to the point of becoming fixed (=reaching a frequency of 100%). In other words, natural selection is less strong on alleles acting late in life.  i.e. deleterious alleles acting late in life are more likely to get fixed resulting in the expression of many disease late in life. In the worst case, we can talk about alleles that are expressed after the time of the last reproduction. These alleles are not at all selected against (I make abstraction of kin selection here). Therefore, we should not be able to live long after the age of reproduction. non-reproductive grandmothers is kind of an exception and is explained by kin selection but I don't want to go into these details. Also, today's medicine explain why we live so long even after the last reproduction. For example articulation related disease that we experience at older age is often caused by this kind of alleles that are expressed only late in life. You can also consider alleles that are beneficial early in life but detrimental at the end of the life. THeir probability of fixation is even greater and these alleles have already been observed in nature. For more info about the evolution of aging, have a look to &lt;a href=&quot;https://biology.stackexchange.com/questions/17077/why-does-evolution-not-make-our-life-longer/17078&quot;&gt;this post&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What happen if human decide to delay their reproduction age&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what happen if suddenly all humans decide to reproduce later. Well, this will increase the selection against alleles that are expressed late in life and in the long run this will increase human lifespan (or at least it will increase the time during which humans are healthy). So yes, your hypothesis is right. However, as a sidenote, medicine may mess things up in the story!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is it plausible that humans will start delaying their reproduction age?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For consideration of whether it is likely that the human population decide to delay their reproduction age, see @MikeTaylor's answer.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-09-25T13:36:45.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21648" PostTypeId="2" ParentId="21636" CreationDate="2014-09-25T17:05:08.750" Score="7" Body="&lt;p&gt;This looks like a macrophage to me, which is a white blood cell. Try Googling &quot;macrophage sem&quot; to see similar images (SEM  = scanning electron microscopy/micrograph).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The clue is the nature of the cell surface - those ruffles reflect the macrophage's role in engulfing foreign material. Indeed it is possible that some of the particles on the surface are bacteria which have been opsonised and are bound by the macrophage cell surface.&lt;/p&gt;&#xA;" OwnerUserId="1320" LastActivityDate="2014-09-25T17:05:08.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21649" PostTypeId="1" CreationDate="2014-09-25T17:43:54.210" Score="5" ViewCount="430" Body="&lt;p&gt;According to &lt;a href=&quot;https://www.youtube.com/watch?v=DHgR8jlNW60&quot; rel=&quot;nofollow&quot;&gt;this video&lt;/a&gt; (sorry for the poor reference but it represents my level of understanding in physiology), muscle grow as a consequence of repairing micro-lesions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How are these micro-lesions sensed in order to activate protein synthesis? What are the key molecules that trigger myosin synthesis and muscle growth?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4113" LastEditorUserId="4113" LastEditDate="2014-09-30T16:09:05.517" LastActivityDate="2014-11-29T17:17:23.023" Title="Mechanism of Muscle Growth" Tags="&lt;cell-biology&gt;&lt;physiology&gt;&lt;proteins&gt;&lt;transcription&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21650" PostTypeId="1" AcceptedAnswerId="21767" CreationDate="2014-09-25T17:52:58.153" Score="4" ViewCount="234" Body="&lt;p&gt;The length of a bone is caused by growth of hyaline cartilage which is then replaced by bone tissue. How do cells know whether they should grow the hyaline cartilage? What are the key molecules that trigger the synthesis of hyaline cartilage?&lt;/p&gt;&#xA;" OwnerUserId="4113" LastEditorUserId="630" LastEditDate="2019-06-25T19:20:01.243" LastActivityDate="2019-06-25T19:20:01.243" Title="Mechanisms of bone growth" Tags="&lt;cell-biology&gt;&lt;physiology&gt;&lt;growth&gt;&lt;histology&gt;&lt;bone-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21651" PostTypeId="1" AcceptedAnswerId="21654" CreationDate="2014-09-25T17:59:15.090" Score="5" ViewCount="611" Body="&lt;p&gt;When a cure has been found for a virus, can it be called such anymore?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Virus implies it's something you've contracted that you just have to live with until (hopefully) your body can overwhelm and destroy it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But say someone found a cure for the Common Cold tomorrow, would we still call it the cold virus or would it just be known as the &quot;cold infection&quot; or something to that effect?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is &quot;Virus&quot; just a nomenclature we've adopted for a bug that has no cure, or is it used to describe a certain type of organism?&lt;/p&gt;&#xA;" OwnerUserId="9503" LastActivityDate="2014-09-25T23:02:31.947" Title="What do you call a virus when it's cured?" Tags="&lt;microbiology&gt;&lt;virus&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21652" PostTypeId="2" ParentId="21636" CreationDate="2014-09-25T18:12:12.500" Score="6" Body="&lt;p&gt;In addition to Alan Boyd's answer of a &lt;a href=&quot;http://en.wikipedia.org/wiki/Macrophage&quot;&gt;macrophage&lt;/a&gt;, it could also be a &lt;a href=&quot;http://en.wikipedia.org/wiki/T_cell&quot;&gt;T cell&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/B_cell&quot;&gt;B cell&lt;/a&gt;. Try doing an image search for &lt;a href=&quot;https://www.google.com/search?site=imghp&amp;amp;tbm=isch&amp;amp;q=lymphocyte+SEM&quot;&gt;lymphocyte SEM&lt;/a&gt; and browsing through the different cell types. While the traditional image of T and B cells has been of a smooth round blast cell, they actually have numerous projections, folds, etc. to aid in forming the &lt;a href=&quot;http://en.wikipedia.org/wiki/Immunological_synapse&quot;&gt;immunological synapse&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-09-25T18:12:12.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21654" PostTypeId="2" ParentId="21651" CreationDate="2014-09-25T18:22:24.320" Score="7" Body="&lt;p&gt;Lets start with the definition of a virus (from the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Virus&quot; rel=&quot;nofollow noreferrer&quot;&gt;viruses&lt;/a&gt;): &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A virus is a small infectious agent that replicates only inside the&#xA;  living cells of other organisms. Viruses can infect all types of life&#xA;  forms, from animals and plants to bacteria and archaea.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So basically speaking you have a piece of genetic information (DNA or RNA) which encodes proteins which are important for the function of the virus and a hull (not always, but mostly). These invade a cell type, take over the cell (litarally, after an infection the cell will mostly only make viral proteins and DNA/RNA). Finally new viruses are built inside the cell and released to infect more cells. In principle this works like in the figure below (from &lt;a href=&quot;http://www.intechopen.com/books/lipid-metabolism/lipid-involvement-in-viral-infections-present-and-future-perspectives-for-the-design-of-antiviral-st&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XjvB3.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two possibilities for cures: The first one are vaccinations. Here you either use dead or attenuated viruses (or parts of viruses) to train the immune system. When this has happened, the immune system &quot;knows&quot; this specific agent and can rise a fast and highly specific immune answer against it, before the virus can replicate in high numbers and infect a lot of cells. This happened for example for the small pox virus which could be eradicated from the human population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other would be drugs which either target a virus (or some of it functions) specifically or prevent them from spreading. The immune system usually does the final cleanup here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both methods only work for people which either take the drug or are vaccinated, so they have no influence on the virus in people which are not protected. For further information have a look on the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Virus&quot; rel=&quot;nofollow noreferrer&quot;&gt;Viruses&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-25T18:22:24.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21655" PostTypeId="2" ParentId="21636" CreationDate="2014-09-25T18:29:05.657" Score="15" Body="&lt;p&gt;This is an embryonic stem cell on the tip of a needle photographed on a scanning electron microscope (SEM). The image was taken by Steve Gschmeissner, see here for the &lt;a href=&quot;http://www.sciencephoto.com/media/214491/view&quot;&gt;original&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-25T18:29:05.657" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21656" PostTypeId="2" ParentId="21649" CreationDate="2014-09-25T18:47:55.000" Score="2" Body="&lt;p&gt;During exercise muscles are put under stress which eventually causes micro tears in the muscle fibres.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These micro tears put pressure on the nerve endings which causes the pain. &#xA;The body will then repair the tears during rest and recovery using proteins and sufficient fuel. The muscle will then become slightly bigger and stronger.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Energy systems used to repair these lesions are the following&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are three different types of energy systems:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Phosphocreatine&lt;/li&gt;&#xA;&lt;li&gt;Lactic Acid&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;-Aerobic&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1.Phosphocreatine Energy System&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The ATP-PC system lasts for 8-10 seconds.&#xA;During the ATP-PC system a phosphate breaks off of the ATP to form ADP and a lot of energy.&#xA;ADP will then bind with another free phosphate to form ATP.&#xA;The ATP-PC system is an anaerobic energy system as it dose not use oxygen. &lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;Lactic Acid Energy System&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Glucose is broken down sustain performance for a longer amount of time than the ATP-PC system.However this system does not use oxygen so is not suited for events over 90 seconds.&#xA;When the ATP-PC system starts to fade the process of anaerobic glycolysis begins.&#xA;Glycogen is stored in the liver and is broken down without the presence of oxygen.&#xA;This produces lactic acid which limits energy production.&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;3&quot;&gt;&#xA;&lt;li&gt;Aerobic Energy system&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The aerobic energy system is constantly being used in your body to supply the muscles with energy.&#xA;In sport the aerobic energy system is used for events that last anything over 90 seconds.&#xA;The aerobic system can be used constantly but only if there is a constant supply of glycogen and fatty acids.&#xA;The aerobic system uses oxygen, glucose and fatty acids to yield large amounts of ATP.&#xA;The system takes place within the mitochondria and produces two bi-products, carbon dioxide and water.&lt;/p&gt;&#xA;" OwnerUserId="8059" LastActivityDate="2014-09-25T18:47:55.000" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21657" PostTypeId="1" AcceptedAnswerId="28150" CreationDate="2014-09-25T19:54:47.363" Score="6" ViewCount="281" Body="&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02507.x/abstract&quot;&gt;Franklin (2009)&lt;/a&gt; describes how plants use the ratio of the red wavelength (660-670nm) over the far-red wavelength (725-735nm) (R:FR) in order to avoid shading.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: &lt;strong&gt;which receptor is stimulated by the red and which receptor is stimulated by the far-red?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In his paragraph on Phytochromes (3rd page, right column), K. Franklin seems to say that PhyB is responsible for measuring this ratio but I am not sure.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2015-02-04T12:59:10.110" Title="Receptors for red and far-red light in plants: Shade avoidance" Tags="&lt;molecular-biology&gt;&lt;botany&gt;&lt;perception&gt;&lt;receptor&gt;&lt;light&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21658" PostTypeId="1" AcceptedAnswerId="21670" CreationDate="2014-09-25T20:19:36.320" Score="4" ViewCount="8222" Body="&lt;p&gt;Is this another name for the active site of an enzyme? What does the structure of the catalytic domain of an enzyme look like?&lt;/p&gt;&#xA;" OwnerUserId="3751" LastActivityDate="2014-09-26T06:49:57.357" Title="What is a catalytic domain of an enzyme?" Tags="&lt;proteins&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21661" PostTypeId="1" CreationDate="2014-09-25T23:05:07.353" Score="3" ViewCount="754" Body="&lt;p&gt;My TA mentioned these three mutations of C. elegans since we started working with the worms but seems to skip over what the differences are...&lt;/p&gt;&#xA;" OwnerUserId="8991" LastActivityDate="2014-09-26T01:10:17.677" Title="What is the difference between a DPY-10, DPY-11, and DPY-13?" Tags="&lt;genetics&gt;&lt;mutations&gt;&lt;animal-models&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21662" PostTypeId="2" ParentId="21661" CreationDate="2014-09-26T01:10:17.677" Score="2" Body="&lt;p&gt;Dpy is a class of genes. Usually they're written in lowercase when referring to a mutant allele. The name Dpy itself stands for dumpy and comes from the morphological change that occurs when one or more of the genes are mutated: the worms appear short and fat, or dumpy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another big class is Unc. Mutations in those genes cause uncoordinated movement. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a description of the genes, see &lt;a href=&quot;http://www.wormbase.org&quot; rel=&quot;nofollow&quot;&gt;http://www.wormbase.org&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-09-26T01:10:17.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21665" PostTypeId="1" CreationDate="2014-09-26T05:38:12.147" Score="1" ViewCount="76" Body="&lt;p&gt;What is the meaning of this poor sequencing result? What is the problem?&#xA;Can anyone guide me, please. Thank you.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/shy7b.png&quot; alt=&quot;poor sequencing result 1&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ywGWB.png&quot; alt=&quot;poor sequencing result 2&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9462" LastActivityDate="2014-09-26T05:38:12.147" Title="What is the meaning of this poor sequencing result?" Tags="&lt;dna-sequencing&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21666" PostTypeId="2" ParentId="21629" CreationDate="2014-09-26T05:45:59.217" Score="2" Body="&lt;p&gt;For a bit of background, this test was devised by Nobuyuki Kayahara and it was originally thought that it shows the dominance of one part of the brain to the other. This was later on discarded as a misconception (&lt;a href=&quot;http://theness.com/neurologicablog/index.php/left-brain-right-brain-and-the-spinning-girl/&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;). It is now widely believed that the clockwise - counter-clockwise rotation is a phenomenon called Bistable perception (&lt;a href=&quot;http://greengabbro.net/2007/10/20/the-spinning-dancer-and-the-brain/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference 1&lt;/a&gt; and &lt;a href=&quot;http://www.jneurosci.org/content/22/14/6195.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference 2&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Multistable perceptual phenomena are a form of perceptual phenomena in&#xA;  which there are unpredictable sequences of spontaneous subjective&#xA;  changes. While usually associated with visual perception, such&#xA;  phenomena can be found for auditory and olfactory percepts. Famous&#xA;  examples include the Necker cube, structure from motion, monocular&#xA;  rivalry and binocular rivalry, but many more visually ambiguous&#xA;  patterns are known. Since most of these images lead to an alternation&#xA;  between two mutually exclusive perceptual states, they are sometimes&#xA;  also referred to as bistable perception(&lt;a href=&quot;http://en.wikipedia.org/wiki/Multistable_perception&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference 1&lt;/a&gt; and&#xA;  &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0959438803000990&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference 2&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No, the fact that you can only see her turn clockwise has not got anything to with your vision (for the record, I have never been able to see the girl go counter- clockwise myself).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sometimes, a person will stare at an image and it will never reverse.&#xA;  Dr. Toppino advises staring at one part of the image, such as the&#xA;  foot, and most of the time it will eventually flip. In people who&#xA;  can’t see the reversal, it may be that one underlying neural structure&#xA;  is more dominant, but once someone finally manages to see the flip, it&#xA;  will start to happen more often (&lt;a href=&quot;http://well.blogs.nytimes.com/2008/04/28/the-truth-about-the-spinning-dancer/?_php=true&amp;amp;_type=blogs&amp;amp;_r=0&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/M80uO.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This image would help you watch her rotate counter-clockwise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hmbXp.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here she is spinning clockwise.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-09-26T05:53:50.133" LastActivityDate="2014-09-26T05:53:50.133" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21667" PostTypeId="1" CreationDate="2014-09-26T06:05:05.993" Score="0" ViewCount="35" Body="&lt;p&gt;I have installed the genomatix software which is a jar file the name is InstallChipInspector21.jar.But now I really don;t know how do I start it ,can any one suggest me a method??&lt;/p&gt;&#xA;" OwnerUserId="5164" LastActivityDate="2014-09-26T06:10:35.300" Title="genomatix software linux install" Tags="&lt;sequence-analysis&gt;&lt;microarray&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-09-26T17:38:51.460" ContentLicense="CC BY-SA 3.0" />
  <row Id="21668" PostTypeId="2" ParentId="21667" CreationDate="2014-09-26T06:10:35.300" Score="1" Body="&lt;p&gt;I don't know what else to say as an answer but &lt;a href=&quot;https://www.genomatix.de/download/software/ChipInspector_Manual_V2.pdf&quot; rel=&quot;nofollow&quot;&gt;here is a link&lt;/a&gt; to the user manual. If you are looking for more specific usage instructions, I would suggest that you try &lt;a href=&quot;https://www.biostars.org/&quot; rel=&quot;nofollow&quot;&gt;Biostars&lt;/a&gt; though I can't guarantee that you receive an answer.&lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-09-26T06:10:35.300" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21669" PostTypeId="1" CreationDate="2014-09-26T06:28:03.893" Score="7" ViewCount="892" Body="&lt;p&gt;Why is it advised to take bath in warm water when we are sick?I know that as homeotherms we need to generate metabolic heat to adapt to the environment temperature.But what is the mechanism by which it makes people feel better(except those who are allergic to it)?&lt;/p&gt;&#xA;" OwnerUserId="9494" LastEditorUserId="9494" LastEditDate="2014-09-27T18:11:03.697" LastActivityDate="2017-12-01T02:23:54.463" Title="Warm water bath" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-09-26T22:06:08.227" ContentLicense="CC BY-SA 3.0" />
  <row Id="21670" PostTypeId="2" ParentId="21658" CreationDate="2014-09-26T06:49:57.357" Score="5" Body="&lt;p&gt;Both parts overlap. Proteins are a chain of linked amino acids. This chain can be grouped into functional units which are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Protein_domain&quot; rel=&quot;nofollow noreferrer&quot;&gt;protein domains&lt;/a&gt;. Usually all parts of a domain are closely located in the protein and they form functional domains in the 3D structure of the protein. Proteins usually contain more than one domain (these are manifold but for example can be dimerization, activation or binding domains).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The catalytic domain is the part of the protein chain which contains the region where the catalyzed chemical reaction takes place. The 3D structure of the catalytic domain forms the active site, so the enzyme requires proper folding to be active. If you denature the enzyme, the catalytic domain will still be present (as this is a function of the protein sequence) but the active site will be gone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As there are really many enzymes for all kinds of reactions it is hard to define a general form for the active site. A motif which is present in a lot of enzymes is the the form of a catalytic pocket or groove to which only the correct substrate of the enzyme has access. Additionally the binding of the substrate to the enzyme often induces a conformational change in the protein which closes this pocket. When the reaction is finished and the substrate is not bound anymore by the enzyme, the conformation changes again and releases the products of the reaction. See the image for a schematically drawing of this principle (image from &lt;a href=&quot;http://chemwiki.ucdavis.edu/Wikitexts/Sacramento_City_College/SCC%3A_Chem_309/Chapters/16%3A_Proteins_and_Enzymes/16.6%3A_Enzymatic_Catalysis&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9yZEk.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-26T06:49:57.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21671" PostTypeId="2" ParentId="21669" CreationDate="2014-09-26T06:52:12.340" Score="7" Body="&lt;p&gt;1) A hot bath, or soak in hot water raises our body temperature. Several benefits of this rise include:  Improved blood circulation, Improved lymph circulation, increased metabolism and calmer nervous system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) During this increased temperature your body releases endogenous opioid peptides, which are primarily endorphins.That’s why you might feel like a new person after a hot bath!(&lt;a href=&quot;http://tubyoga.com/benefits-of-a-hot-bath-why-it-feels-so-good/&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It apparently also takes your feeling of loneliness away (&lt;a href=&quot;http://www.dailymail.co.uk/sciencetech/article-2007555/How-soaking-warm-bath-stop-feeling-lonely.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2017-12-01T02:23:54.463" LastActivityDate="2017-12-01T02:23:54.463" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21672" PostTypeId="1" AcceptedAnswerId="21673" CreationDate="2014-09-26T08:54:13.987" Score="3" ViewCount="1328" Body="&lt;p&gt;Most Google Images results for &quot;eye anatomy&quot; are pictures of eyes that don't have the hyaloid canal while some do (&lt;a href=&quot;https://www.google.com/search?site=&amp;amp;tbm=isch&amp;amp;source=hp&amp;amp;biw=1680&amp;amp;bih=949&amp;amp;q=eye+anatomy&amp;amp;oq=eye+anatomy&amp;amp;gs_l=img.3..0l10.22.1421.0.2147.11.7.0.4.4.0.304.574.5j3-1.6.0....0...1ac.1.54.img..1.10.590.SB42fKc_bxg&quot; rel=&quot;nofollow&quot;&gt;proof&lt;/a&gt;). Do humans have it, after all, or not? :)&lt;/p&gt;&#xA;" OwnerUserId="9512" LastEditorUserId="9512" LastEditDate="2014-09-26T17:54:37.727" LastActivityDate="2014-09-26T17:54:37.727" Title="Do humans have the hyaloid canal, after all?" Tags="&lt;human-biology&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21673" PostTypeId="2" ParentId="21672" CreationDate="2014-09-26T09:04:46.173" Score="3" Body="&lt;p&gt;Yes, humans do have the hyaloid canal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LIqCr.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Schematic diagram of the human eye (&lt;a href=&quot;http://en.wikipedia.org/wiki/Hyaloid_canal&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For function and other information, please refer to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1465472/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this journal article&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-09-26T09:04:46.173" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21675" PostTypeId="1" AcceptedAnswerId="21685" CreationDate="2014-09-26T12:02:08.263" Score="2" ViewCount="966" Body="&lt;p&gt;A eukaryotic animal cell is a complicated piece of biological machinery.  Some major structures inside of the cell (see the image below) include: the nucleus, mitochondria, Golgi vesicles, and various tubular structures.  Why then is the single-celled, unfertilized chicken egg so homogeneous when it is cooked (or before)?  The only major structure I can recognize is the cell nucleus.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uGAtQ.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;*Image Credit: &quot;Animal cell structure en&quot; by LadyofHats (Mariana Ruiz) - Own work using Adobe Illustrator. Image renamed from Image:Animal cell structure.svg. Licensed under Public domain via Wikimedia Commons - &lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Animal_cell_structure_en.svg#mediaviewer/File:Animal_cell_structure_en.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://commons.wikimedia.org/wiki/File:Animal_cell_structure_en.svg#mediaviewer/File:Animal_cell_structure_en.svg&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6098" LastEditorUserId="3624" LastEditDate="2014-09-26T19:14:00.560" LastActivityDate="2015-05-18T11:29:35.697" Title="Why are hard boiled eggs so homogeneous?" Tags="&lt;cell-biology&gt;&lt;cell&gt;&lt;eggs&gt;&lt;reproductive-biology&gt;&lt;chickens&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="21676" PostTypeId="1" AcceptedAnswerId="41432" CreationDate="2014-09-26T12:16:29.270" Score="9" ViewCount="473" Body="&lt;p&gt;I found this larva in Sweden in July. It was about 15 mm long. It reminded me of &lt;em&gt;Orgyia antiqua&lt;/em&gt; that I've seen before, but smaller and with a somewhat different colouration.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/B9Ijx.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dxz87.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8630" LastActivityDate="2015-12-11T19:55:05.190" Title="Some sort of Lymantriidae caterpillar?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21677" PostTypeId="1" CreationDate="2014-09-26T13:20:17.570" Score="1" ViewCount="157" Body="&lt;p&gt;Sometimes, when people are concerned about radiation, it is not because it is precisely quantified how dangerous it is, but because we don't know how dangerous it is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How well understood are the long-term effects of nuclear radiation, for example on cancer? (As opposed to short-term effects such as acute radiation sickness, which is easy to quantify)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume this can be researched from an epidemiological approach (Wikipedia mentions an epidemiological study on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Atomic_bombings_of_Hiroshima_and_Nagasaki#Post-attack_casualties&quot; rel=&quot;nofollow&quot;&gt;atomic bombing of Hiroshima and Nagasaki&lt;/a&gt;, for example), and also from an experimental approach.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, is the effects of radiation easy to understand, or difficult? My assumption is that something physical, like radioactivity, would be easier to understand than the effects of more complicated things, like complicated organic chemicals or obesity.&lt;/p&gt;&#xA;" OwnerUserId="576" LastActivityDate="2014-09-26T15:06:34.287" Title="How well understood are the long-term effects of nuclear radiation?" Tags="&lt;radiation&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21678" PostTypeId="2" ParentId="757" CreationDate="2014-09-26T13:50:35.357" Score="0" Body="&lt;p&gt;With all due respect, a few of these answers, although good examples of selection at work, were voted too high given the specific question asked: “documented examples of by evolutionary leaps being made, over the course of just a few generations?”&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes we’re better being honest and identifying something as an ‘unknown’ or ‘yet to be observed’ than to list (and have people up-vote) poor examples.  &lt;strong&gt;We do evolution a dis-service when we promote poor examples as answers to questions like these.&lt;/strong&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To expound:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cricket losing the ability to sing (communicate) examples does demonstrate mutation and natural selection at work, but really only shows the REDUCTION of a capability.  It’s not a good example of evolutionary leaps.  It only happens to be beneficial in one SPECIFIC context.  This would be analogous to tanks on a battle-field which communicate via radio, vulnerable to radio-frequency tracking missiles.  Any tank with a broken radio would not be vulnerable to these missiles.  Although technically ‘beneficial’ in this context, it’s an example of a loss of capability, not a gain of capability.  We need to promote examples of mutations that PRODUCE capabilities.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lactase persistence example likewise is an example of mutation and natural selection, but not a good example of a GAIN in functionality (as some have pointed out in the comments).  It’s technically the loss of the normal switching-off mechanism of lactase production following weaning.  So once again, a loss, that happens to have a beneficial side-effect.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding punctuated equilibrium, I’m not surprised that was mentioned but was surprised that it got some votes.  It’s a hypothetical explanation for why we see gaps in the fossils, but not conclusive ‘evidence’, or in the case of the question asked not “documented examples”.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again: We do evolution a dis-service when we promote poor examples as answers to questions like these.  Let’s focus on quality, not quantity when it comes to presenting evidence for evolution.&lt;/p&gt;&#xA;" OwnerUserId="9501" LastEditorUserId="9501" LastEditDate="2014-09-26T14:34:23.707" LastActivityDate="2014-09-26T14:34:23.707" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21679" PostTypeId="1" CreationDate="2014-09-26T14:37:33.623" Score="5" ViewCount="197" Body="&lt;p&gt;&lt;strong&gt;How often do &lt;a href=&quot;https://en.wikipedia.org/wiki/Chromosomal_rearrangement&quot; rel=&quot;nofollow noreferrer&quot;&gt;chromosomal rearrangements&lt;/a&gt; occur?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I am interested about these kind of chromosomal rearrangements that are passed on to the descendants, i.e. germ line chromosomal rearrangements. The value I am looking for is similar to the mutation rate but only take into account major mutations such as chromosomal rearrangements.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Supposing there might have some important variance in this rate among species, then I am interested in eukaryotes and particularly in plants. If needed, the answer can be split into the different types of chromosomal rearrangements (robertsonian translocation, other translocations, inversions, ...)&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="6307" LastEditDate="2017-08-18T19:23:56.693" LastActivityDate="2020-12-28T22:43:09.627" Title="At what rate do chromosomal rearrangements occur?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;mutations&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21680" PostTypeId="2" ParentId="21677" CreationDate="2014-09-26T15:06:34.287" Score="2" Body="&lt;p&gt;The three major nuclear incidents I can think of are the Japanese atomic bomb attacks, the Chernobyl disaster, and Fukushima disaster. Of course other nuclear incidents have occurred, but usually give much higher doses to far fewer people.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many studies have been done on the survivors from the atomic bomb attacks, and increased rates of cancer have been the strongest conclusion. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19454804&quot; rel=&quot;nofollow noreferrer&quot;&gt;This review article&lt;/a&gt; looks at those studies for both cancer and non-cancer effects. Leukemia is the most well known cancer to be caused by radiation, and excess leukemia was discovered in bomb survivors within 5 years of the attacks. Rates of most solid tumors had increased by 10 years after the attacks. However &quot;Even 55 years after the&#xA;bombings over 40% of the Life Span Study cohort remain alive&quot;, indicating that the amount of radiation most people were exposed to wasn't enough to kill them. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12852470&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here is another article on atomic bomb survivors.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Chernobyl accident was a very different type of exposure, but many people were exposed to radioactive materials. Immediately after the disaster, the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Liquidator_%28Chernobyl%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;liquidators&lt;/a&gt;&quot; received high doses of radiation while cleaning up the site and building the containment structures, but very few have &lt;a href=&quot;http://en.wikipedia.org/wiki/Deaths_due_to_the_Chernobyl_disaster&quot; rel=&quot;nofollow noreferrer&quot;&gt;died&lt;/a&gt; from radiation exposure. While the environment around the power plant did suffer in the years after the accident, after the humans moved away the environment has greatly improved. &lt;a href=&quot;http://en.wikipedia.org/wiki/File:Belarus_radioactivity_and_thyroid_cancer.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;Thyroid cancer rates increased&lt;/a&gt; due to Iodine-131 exposure, especially among those exposed as children, but rates were still low.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/DEhMu.png&quot; alt=&quot;enter image description here&quot;&gt; Yellow = adults Blue = Adolescents Red = Children.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is too soon to draw many conclusions about the Fukushima accident, but some studies (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25251702&quot; rel=&quot;nofollow noreferrer&quot;&gt;7&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24361922&quot; rel=&quot;nofollow noreferrer&quot;&gt;8&lt;/a&gt;) have tried to predict the number of cancer cases that will be caused by it. In general the rates are expected to be low, with far fewer deaths than were caused by the earthquake and tsunami that caused the accident.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few instances exposed small numbers of people to very high doses, and are interesting from a radiation safety veiwpoint. The infamous &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Demon_core&quot; rel=&quot;nofollow noreferrer&quot;&gt;Demon Core&lt;/a&gt;&quot; killed 2 scientists in separate accidents while handling the core. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Goi%C3%A2nia_accident&quot; rel=&quot;nofollow noreferrer&quot;&gt;Goiania incident&lt;/a&gt; involved men breaking into an old hospital and stealing a radiation source without realizing what it was. They broke the source open and passed the radioactive material around because it looked cool, resulting in several deaths due to acute radiation sickness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While radiation can be dangerous, with proper precautions we can avoid accidents and disasters. Remember that Chernobyl was a poorly designed Soviet reactor, and that Fukushima was a 50 year old plant that needed both a magnitude 9 earthquake and a 30 foot wave to disable it. Modern nuclear plants can be built safely and provide clean electricity for many decades, and if they are breeder reactors can recycle the used fuel to reduce both the amount and half-life of the material, making storage easier.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-09-26T15:06:34.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21682" PostTypeId="1" CreationDate="2014-09-26T16:14:31.743" Score="6" ViewCount="7190" Body="&lt;p&gt;Ok, this is a bit of a tangent question, but it came up yesterday and I didn't know the answer: &#xA;How are arms and legs defined physiologically? For example, we say humans have two arms and two legs, while cats have four legs, and some monkeys (appear) to have four arms (although I guess they could be legs too). It's really unclear to me how we make these distinctions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the physiological definition of both &quot;arm&quot; and &quot;leg&quot;? How are they different?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="3804" LastEditorUserId="231" LastEditDate="2018-11-14T20:31:51.067" LastActivityDate="2018-11-14T20:31:51.067" Title="How are arms different than legs?" Tags="&lt;physiology&gt;&lt;human-anatomy&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21683" PostTypeId="1" AcceptedAnswerId="21686" CreationDate="2014-09-26T17:31:49.587" Score="2" ViewCount="993" Body="&lt;p&gt;I am trying to use &lt;code&gt;bowtie2&lt;/code&gt; to analyze my data in FASTA format, but it seems that this version can't read properly my data. My command line is as follows:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;bowtie2 -x $REFERENCE -f $TARGET -S $TARGET.sam&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The version 2 of bowtie complains with the following:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Warning: skipping read 'ORIGINAL: GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT' because length (0) &amp;lt;= # seed mismatches (0)&#xA;Warning: skipping read 'ORIGINAL: GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT' because it was &amp;lt; 2 characters long&#xA;Warning: skipping read 'ORIGINAL: GGCTATCTTGAAGCCAATGAGTTGTTAACTGGCAAG' because length (0) &amp;lt;= # seed mismatches (0)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Note that &lt;code&gt;bowtie&lt;/code&gt; (version 1) is pleased by my FASTA! Here's a snippet and what &lt;code&gt;bowtie&lt;/code&gt; says:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt;ORIGINAL: GCTACGGAATAAAACCAGGAACAACAGACCCAGCAC&#xA;GCTACGGAATAAAACCAGGAACAACAGACCCAGCAC&#xA;&amp;gt;ORIGINAL: ATTAACAACAAAGGGTAAAAGGCATCATGGCTTCAG&#xA;ATTAACAACAAAGGGTAAAAGGCATCATGGCTTCAG&#xA;&amp;gt;ORIGINAL: GCAGAAAATGGGAGTGAAAATCTCCGATGAGCAGCT&#xA;AATGGGAGTGAAAATCTCCGATGAGCAGC&#xA;&#xA;# reads processed: 471409&#xA;# reads with at least one reported alignment: 464583 (98.55%)&#xA;# reads that failed to align: 6826 (1.45%)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Now I'm at loss. Can anyone see what I'm doing wrong here? Can I trust anyway &lt;code&gt;bowtie2&lt;/code&gt; when it finishes and outputs how many sequences are aligned?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="9522" LastEditorUserId="9522" LastEditDate="2014-09-26T17:52:16.750" LastActivityDate="2014-09-26T18:59:18.143" Title="Bowtie: cannot read fasta file?" Tags="&lt;bioinformatics&gt;&lt;sequence-alignment&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21684" PostTypeId="1" CreationDate="2014-09-26T17:57:36.173" Score="1" ViewCount="25" Body="&lt;p&gt;I'm studying the somatic sensation pathways in neuro-anatomy and I was wondering what was the experimental procedure for identifying the number and location of the synapses in these pathways? Additionally, how were they known to not branch anywhere? Did they use dyes or green fluorescent protein? These are the only visualization techniques I know.&lt;/p&gt;&#xA;" OwnerUserId="5427" LastEditorUserId="948" LastEditDate="2014-09-26T18:22:52.587" LastActivityDate="2014-09-26T18:22:52.587" Title="How were the synaptic areas identified in the somatic sensation pathways?" Tags="&lt;human-anatomy&gt;&lt;experimental-design&gt;&lt;neuroanatomy&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21685" PostTypeId="2" ParentId="21675" CreationDate="2014-09-26T18:58:56.283" Score="5" Body="&lt;p&gt;&lt;em&gt;Disclaimer: This is my understanding of the egg anatomy as a general biologist. There is most certainly better references and sources out there to explain this (please add better references if you know of any).&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;If I understand you correctly, your question is why we do not see cell organelles in a cracked or boiled egg. If so, your question seems to stem from a misunderstanding of what the egg white and egg yolk represents. A chicken egg is not simply an enlarged cell, and the egg yolk is not the cell nucleus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When an oocyte matures in the chicken ovary, it stores yolk inside the cell and therefore enlarges. The yolk is therefore part of the oocyte cytoplasm. However, as it enlarges, the yolk is separated from the germinal disc, which holds all the other cell organelles (including the nucleus). The germinal disc is seen as a small white area on the egg yolk. Eventually, when the oocyte has accumulated enought yolk, it disattaches from the ovary (ovulation) and goes into the hens oviduct. This process is happening continuously, and oocytes of different stages of maturation are present on the ovary, which can be seen in this image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uJrdV.jpg&quot; alt=&quot;chicken reproductive tract, from chickscope.beckman.uiuc.edu/explore/embryology/day05/ovary.html&quot;&gt;&lt;br&gt;&#xA;(image from &lt;a href=&quot;http://chickscope.beckman.uiuc.edu/explore/embryology/day05/ovary.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Chickscope: Formation of the Egg&lt;/em&gt;. University of Illinios&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the oocyte passes through the oviduct it builds up layers of egg white (albumen) and other supporting structures. The shell is formed last in the shell gland, which is located at the end of the oviduct. Therefore, the egg white and the shell is formed externally of the oocyte and the egg yolk. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the reason why we do not see more structures in a boiled egg is that the majority of the egg is yolk and egg white, which are both structures to store energy ment for a growing embryo (mainly protein and fat). It should also be noted that oocytes in most (all?) animals contain yolk granules, but the storage of yolk is most extreme in birds (see &lt;a href=&quot;http://faculty.clintoncc.suny.edu/faculty/michael.gregory/files/bio%20102/Bio%20102%20lectures/animal%20development/animal.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;this webpage on animal development&lt;/a&gt; from State university of New York for a short comparison).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It should also be noted that an egg that is fertilized will naturally contain more than one cell, since the embryo will have started growing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://chickscope.beckman.uiuc.edu/explore/embryology/day05/ovary.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Chickscope: Formation of the Egg&lt;/em&gt;. University of Illinios (webpage)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://chickscope.beckman.uiuc.edu/explore/embryology/day01/the_yolk.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Chickscope: The yolk&lt;/em&gt;. University of Illinios (webpage)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Chapter &quot;Eggs&quot; in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26842/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Johnson et al. 2002. Molecular Biology of the Cell. 4th ed. Garland Science, New York&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Egg_%28food%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia: Egg&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://faculty.clintoncc.suny.edu/faculty/michael.gregory/files/bio%20102/Bio%20102%20lectures/animal%20development/animal.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Animal development&lt;/em&gt;. State university of New York (webpage&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-05-18T11:29:35.697" LastActivityDate="2015-05-18T11:29:35.697" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21686" PostTypeId="2" ParentId="21683" CreationDate="2014-09-26T18:59:18.143" Score="7" Body="&lt;p&gt;Since I apparently don't have enough reputation to comment, I'll post this as an answer and let someone move it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, try to ensure that the order of the arguments are correct. You should be typing &lt;code&gt;bowtie2 -f -x $TARGET -U $TARGET -S $TARGET.sam&lt;/code&gt;, since bowtie2 (as with many other programs) can be a bit picky about the argument order.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, it's usually advisable for the example input to include lines that are causing the problem (since it's apparently not complaining about the lines you posted, we can only assume that it's aligning them).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thirdly, you'll typically only get those warnings if they're true. For example, if you were to &lt;code&gt;grep -A 1 -w GACACTGTTCATGCTGGTGTCGCTGTCGGGCATTAT $target&lt;/code&gt; then my guess is that you'd find it to have no remaining sequence. Presumably these are the result of you trimming adapters or something like that, so just have your trimmer discard really short results (they won't align meaningfully anyway).&lt;/p&gt;&#xA;" OwnerUserId="9523" LastActivityDate="2014-09-26T18:59:18.143" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21687" PostTypeId="1" CreationDate="2014-09-26T19:08:20.070" Score="-2" ViewCount="1815" Body="&lt;p&gt;How safe are cobalt-chromium and nickel-chromium alloys used in dental implants (porcelain fused metal)? IARC groups nickel and cobalt metals in group 2B and chromium in group 3 (hexavalent chromium is group 1!). But what is the likelihood of these metals leaching from implants and affecting the body? Aren't some of these metals already used for kitchenware (stainless steel vessels for instance contain chromium) and in industrial containers used for food processing? Is the risk much higher when these metals (not their more toxic compounds/salts though) are present in mouth when compared to their being used for food storage or cooking?&lt;/p&gt;&#xA;" OwnerUserId="9524" LastActivityDate="2018-01-20T19:14:50.053" Title="Safety of cobalt-chromium and nickel-chromium dental implants" Tags="&lt;human-biology&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2018-01-22T20:38:47.083" ContentLicense="CC BY-SA 3.0" />
  <row Id="21691" PostTypeId="1" AcceptedAnswerId="21692" CreationDate="2014-09-27T02:56:38.567" Score="2" ViewCount="218" Body="&lt;p&gt;If cancer cells have telomeres are they different than the telomeres in non-cancerous cells? Would cancer cell telomeres be somehow 'set-up' to function almost indefinitely; in other words are 'they' very 'robust' or 'durable'? If these cancer cell telomeres are 'durable could their functioning cause any apoptosis mechanisms to 'shut down'?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastActivityDate="2014-11-09T14:13:06.183" Title="Regarding cancer cells and telomeres" Tags="&lt;cell-biology&gt;&lt;cancer&gt;&lt;telomere&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21692" PostTypeId="2" ParentId="21691" CreationDate="2014-09-27T06:06:45.643" Score="4" Body="&lt;p&gt;In a normal cell, during each replication the telomere is shortened slightly due to the &lt;a href=&quot;http://www.madsci.org/posts/archives/1999-01/915659165.Cb.r.html&quot; rel=&quot;nofollow&quot;&gt;end replication problem&lt;/a&gt;, as you probably know. As mutations occur and a normal cell begins to exhibit cancerous characteristics, it needs a way to stop the self-destruction which happens when the telomeres become too short. In fact it is the cancer cells themselves which 'short-circuit' the shortening process and cause the telomeres to stay long enough.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;90% of tumors do this by activating &lt;em&gt;telomerase&lt;/em&gt;, an enzyme complex which elongates telomeres and keeps them from getting too short, so that the cell is effectively immortal from this sort of destruction. Usually telomerase is not active in most cells, except for stem, germ, and hair follicle cells, but cancer cells use this to their advantage and activate it to stay immortal. The other 10% or so employ a method called ALT, or Alternative Telomere Lengthening, a not yet thoroughly understood process which involves the recombination of tandem repeats between sister chromatids.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.news-medical.net/health/Telomeres-and-Cancer.aspx&quot; rel=&quot;nofollow&quot;&gt;This page&lt;/a&gt; explains how cancer cells bypass the telomere shortening process well, and also provides a series of further reading on telomeres and telomere shortening.&lt;/p&gt;&#xA;" OwnerUserId="8840" LastActivityDate="2014-09-27T06:06:45.643" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21693" PostTypeId="2" ParentId="21532" CreationDate="2014-09-27T11:23:53.920" Score="1" Body="&lt;p&gt;The winter moth's preferred host plants are mainly deciduous trees, oak being the main food plant and also many fruit trees, birch and hazel. Females generally deposit eggs in bark crevices, under bark scales, bark snags and under lichen along tree trunks of host species. Eggs are initially small and green but gradually change colour to orange and then red before hatching (&lt;a href=&quot;http://extension.umass.edu/fruitadvisor/news/winter-moth-operophtera-brumata&quot; rel=&quot;nofollow&quot;&gt;reference 1&lt;/a&gt; and &lt;a href=&quot;http://www.goert.ca/documents/Operophtera-brumata.pdf&quot; rel=&quot;nofollow&quot;&gt;reference 2&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though the oak is preferred, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There does not seem to be much discrimination in selection of host&#xA;  plant or oviposition site by the female (&lt;a href=&quot;http://www.jstor.org/discover/10.2307/4564?uid=3737496&amp;amp;uid=2&amp;amp;uid=4&amp;amp;sid=21104231472941&quot; rel=&quot;nofollow&quot;&gt;Wint 1983&lt;/a&gt;), as the choice of&#xA;  larval food plant depends on the female's pupation site and the&#xA;  direction she takes on emerging, as she just climbs up the nearest&#xA;  tree. So it might be fair to say that the larvae contribute more to&#xA;  host plant choice than the adults, as the larvae can balloon if the&#xA;  host plant is unsuitable. However there is the possibility that year&#xA;  after year each generation of females will climb up the same tree as&#xA;  their mother, and oaks (one of the most common host plants) can be&#xA;  hundreds of years old, so there could have been hundreds of&#xA;  generations of winter moth on the same tree (&lt;a href=&quot;http://www.bumblebee.org/HomeworkAnswers/Essay3.htm&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So that in effect means, that the thickness of branches or being indistinguishable should not be a factor. Regarding abiotic and biotic condition, the main abiotic conditions are precipitation, temperature and photoperiod. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An increase in temperature leads to more activity and a faster metabolism (&lt;a href=&quot;http://www.ibles.pl/documents/13012/495762/jaworski13-4-7-e.pdf&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) Since leaf buds open faster, there is a chance for eggs to be laid faster according because the larva needs to burrow into the buds before the leaf opens (bud-burst) Hatching is temperature dependant but I do not think that it effects the number of eggs much. Biotic factors like the presence of parasitic predators reduce population but does not seem to reduce the number of eggs.. (&lt;a href=&quot;http://irs.ub.rug.nl/dbi/5062c89611062&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;)  &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2014-09-27T15:07:40.617" LastActivityDate="2014-09-27T15:07:40.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21695" PostTypeId="1" CreationDate="2014-09-27T13:11:40.117" Score="0" ViewCount="153" Body="&lt;p&gt;I have seen on a &lt;a href=&quot;http://youtu.be/5Tg_3OVizrA?t=2m15s&quot; rel=&quot;nofollow&quot;&gt;youtube video&lt;/a&gt; that the female body produces antigenes and antibodies when she is pregnant with a boy. But this behaviour is not produced when she is pregnant with a girl. These means that the more antigenes she produces, the more femminin the next child will be. More antigenes are produced when she is pregnant with a boy.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Is this correct? if yes, then why does the female body produce antibodies and antigenes when the fetus is a boy and not a girl?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What other pregnancy actions or behaviours are gender based?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8097" LastEditorUserId="8097" LastEditDate="2014-09-27T19:24:56.127" LastActivityDate="2014-09-27T19:24:56.127" Title="Does a pregnant female body treat the fetus based on gender?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;pregnancy&gt;" AnswerCount="0" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21696" PostTypeId="1" AcceptedAnswerId="21703" CreationDate="2014-09-27T13:34:50.493" Score="9" ViewCount="711" Body="&lt;p&gt;Recently I was reading about myopia and I understood a few basic facts about it:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Its initial cause is a constant spasm in the ciliary muscle.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;To do less work, the eyeball elongates a tiny bit.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;During adolescence, because of the growth of the body, the eyeball elongates accordingly even more (i.e. the myopia is progressing).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I don't really understand the exact mechanism responsible for the transition from 1 to 2. Is the ciliary muscle capable of elongating the eyeball on its own, or is there some other relationship to another part of the eye?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's weird how myopia is so common these days and I wasn't able to find the precise mechanism behind it.&lt;/p&gt;&#xA;" OwnerUserId="9512" LastEditorUserId="9268" LastEditDate="2014-09-27T18:48:37.267" LastActivityDate="2014-09-28T21:26:08.673" Title="How does myopia develop, exactly?" Tags="&lt;vision&gt;&lt;pathophysiology&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21697" PostTypeId="2" ParentId="21522" CreationDate="2014-09-27T14:38:12.730" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.37.091305.110224?journalCode=ecolsys&quot; rel=&quot;nofollow&quot;&gt;Hansen (2006)&lt;/a&gt; says (middle of page 140):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A link between genetic and environmental robustness is plausible, because genetic en environmental disturbances may often affect the same functional pathways in the organism, and ny increase in the robustness of a pathway leads to both genetic and environmental canalization. Evidence for a correlation between environmental and genetic robustness has been fund in studies of RNA folding (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11069142&quot; rel=&quot;nofollow&quot;&gt;Ancel &amp;amp; Fontana 2000&lt;/a&gt;), in the effects of heat-shock proteins (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1420-9101.1995.8050539.x/full&quot; rel=&quot;nofollow&quot;&gt;Stearns et al. 1995&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;He also cites &lt;a href=&quot;http://www.nature.com/nature/journal/v438/n7065/abs/nature04114.html&quot; rel=&quot;nofollow&quot;&gt;Rifkin et al. (2005)&lt;/a&gt; who also showed evidence for this correlation. Finally Hansen cites &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2005.tb01799.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Dworkin (2005)&lt;/a&gt; who did not find this link.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hansen does not cite any theoretical paper and does not offer clear arguments of why this link exist but it is the best I could find&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-11-22T20:35:38.330" LastActivityDate="2014-11-22T20:35:38.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21699" PostTypeId="1" AcceptedAnswerId="21706" CreationDate="2014-09-27T15:34:28.010" Score="4" ViewCount="1457" Body="&lt;p&gt;If you picked two people in the world at random, sequenced each of their entire genome, and compared their DNA, what would the expected percentage match be?&lt;/p&gt;&#xA;" OwnerUserId="9531" LastEditorUserId="9531" LastEditDate="2014-09-27T15:39:49.487" LastActivityDate="2014-09-27T22:13:44.713" Title="What percentage of DNA do people share?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21703" PostTypeId="2" ParentId="21696" CreationDate="2014-09-27T18:39:12.840" Score="9" Body="&lt;p&gt;&lt;strong&gt;What is myopia?&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Myopia, a.k.a. near-sightedness, is a refractory error. Refraction is the process by which the optical system focuses images of objects on the retina, which are then transmitted to the visual cortex of the brain to be interpreted as vision. The major components of refraction are the cornea, lens, and axial eye length (distance from the front to the back of the eye). The problem in myopia is that images are focused anterior to the retina, like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IQ307.gif&quot; alt=&quot;myopia&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Causes of myopia&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You ask&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I don't really understand the exact mechanism responsible for the transition from 1 [ciliary muscle spasm] to 2 [elongation of the eye].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Swelling or spasm of the ciliary body (the circumferential tissue inside the eye composed of the ciliary muscle and ciliary processes) can be seen after trauma or in inflammatory conditions. Contraction of the ciliary muscles causes decreased tension in the suspensory ligaments that connect the ciliary body to the lens. The results in the lens becoming more rounded and/or moving anteriorly. Both processes also bring the focal point more anterior, i.e. further in front of the retina, resulting in a configuration as in the picture above. You could call this &quot;elongation of the eye&quot; if you wanted. &lt;a href=&quot;http://blausen.com/?Topic=8723&quot; rel=&quot;noreferrer&quot;&gt;This 25 second video&lt;/a&gt; explains the process succinctly with pretty pictures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although interesting to think on, this is not the most common cause of myopia. Myopia is an extremely common condition, occurring in ~25% of the US population. Myopia can be classified as axial or refractive.   &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Axial myopia&lt;/strong&gt;: The refracting power of the eye is normal but the length of the eye is too long.   &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Refractive myopia&lt;/strong&gt;: The length of the eye is normal, but the lens refracts too much for a given axial length. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Both axial and refractive myopia are usually caused by failure of &lt;a href=&quot;http://en.wikipedia.org/wiki/Emmetropia&quot; rel=&quot;noreferrer&quot;&gt;emmetropization&lt;/a&gt;, the process by which a normal eye has coordinated growth of its refractive components. This process takes place mostly during the childhood and adolescent years, which is why myopia most commonly develops during that time. There are certain disease conditions that increase lens power (e.g. osmotic effects in diabetes) or axial length (e.g. posterior staphyloma) that may also cause myopia at other points in life, but these are less common.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;References:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;/sub&gt;&#xA;&lt;sub&gt;&#xA;1. Neil J. Friedman and Peter K. Kaiser. &lt;em&gt;Essentials of Ophthalmology&lt;/em&gt;. © 2007, Elsevier Inc. &#xA;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&#xA;2. Albert, Daniel M., MD MS.Albert &amp;amp; Jakobiec's &lt;em&gt;Principles &amp;amp; Practice of Ophthalmology&lt;/em&gt;, Third Edition. © 2000, 1994 by W.B Saunders Company, © 2008, Elsevier Inc.&#xA;&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;Image from:&lt;br&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Myopia&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Myopia&lt;/a&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-09-28T21:26:08.673" LastActivityDate="2014-09-28T21:26:08.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21704" PostTypeId="1" CreationDate="2014-09-27T18:42:21.263" Score="0" ViewCount="1240" Body="&lt;p&gt;When you use a mirror to look at something, you can position it at an angle arbitrary to your face and still look at an object far away. My question is, for degraded eyesight, how come the picture is still degraded in the mirror? Is it because of an imperfect mirror? Is it theoretically possible to have a mirror that when looked at an angle with perfect scattering to give you better vision than without the mirror, just looking regularly with degraded vision? I am just wondering, it seems like a photonic process, but i don't know enough about the eyes to turn them into any sort of functional system&lt;/p&gt;&#xA;" OwnerUserId="9534" LastActivityDate="2014-09-30T04:42:35.320" Title="How come degraded eyesight still holds with a mirror?" Tags="&lt;eyes&gt;" AnswerCount="2" CommentCount="3" ClosedDate="2014-09-30T10:04:07.340" ContentLicense="CC BY-SA 3.0" />
  <row Id="21705" PostTypeId="2" ParentId="20665" CreationDate="2014-09-27T18:51:29.687" Score="5" Body="&lt;p&gt;Lots of interesting questions! Let me try to address a few of them as I don't think I am qualified to answer them all but hopefully I can get this thread started. I am a graduate student in the biophysical chemistry field and have been following a little bit of the Crispr Cas9 craze in the last couple of years. So I am not an expert on Cas9 by any means but I do find it interesting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many speculate that as long as their have been cellular life, viruses or some obligate parasites have existed as well. This stems from the idea that viruses perhaps are not &quot;non-self&quot; but rather are parts of the host that happen to become inanimate particles that escape the cell and then find another suitable host. Some viruses have co-evolved with the host, perhaps to prevent other viruses from invading its &quot;home/birth mother&quot;. Again, much of this paragraph is just speculation, but it is likely that CRISPR systems, or an adaptive immune systems like it have existed as long as viruses/obligate parasites have. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Error rates, you can look at some of the papers that have come out recently but the idea is that there are a lot of error rates, especially if the RNA is constitutively transcribed from a plasmid. Some people have suggested delivering, not the plasmids for the guide RNAs and the Cas9 protein, but instead, the Cas9 protein complexed to the RNA itself. Other ways to control the amount you deliver to a cell include delivering the RNA for the Cas9 protein so it is eventually degraded. This avoids the complication of delivering DNA which can be transcribed multiple times potentially flooding your cell with cas9 protein or guide RNAs, increasing the likelihood of off target effects. Or you can have the cas9 protein and the guide RNA plasmids under inducible promoters, so you only get expression say if you introduce a small molecule to your cultured organism and limit the amount you deliver of it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to if there are other systems &quot;superior&quot; to it, and by superior you mean more efficient, and has less off targeting effects? Sure those things may very well exist, since we haven't sequenced the entire planet yet! All joking aside, maybe start looking around at research groups that do adaptive immunity in prokaryotes, you might find some interesting ideas...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;VDJ is a very cool system that I know only a little about but this review might be worth checking out:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Mechanism and Control of V(D)J Recombination versus ClassSwitch Recombination: Similarities and Differences&quot;, which can be found &lt;a href=&quot;http://web.archive.org/web/20120109190037/http://www.idi.harvard.edu/uploads/investigators/Dudley_Adv_Immunol_05.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also recombination in meiotic versus mitotic replication is covered in this review: &quot;Meiotic versus Mitotic Recombination: Two Different Routes for Double-Strand Break Repair&quot;, which is available &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090628/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to answer your question, I will have to defer to someone else!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question to you is what is &quot;advanced&quot;? Life as we understand it has been evolving for about 3-4 billion years. &quot;Advanced&quot; suggests that one organism has evolved better or faster. I don't know if I would call anything more advanced per se, but maybe more complicated and more capable of rapidly adapting to new environmental pressures? Bacteria have us trumped if there were rapid changes to the environment, global warming, asteroids careening into the planet etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Estimating this probability requires knowing how large the entire sequence space of the Earth is, some have estimated 5-50 million eukaryotic species but depends on what metric you would use to define a new species. It is unknown for prokaryotes. My guess is that you have 100's of millions of different organisms that are capable of having some type of adaptive immune system that may be inherently different from CRISPR/Cas9 system but still use some similar elements, like nucleic acid complementation, as a mode of defending against obligate parasites. Then the questions are how many of those organisms have we sequenced and how many proteins do we have any idea how they function based on sequence similarities to other proteins? Or if we have directly characterized their 3D structure based on Cryogenic Transmission Electron Microscopy (Cryo EM), NMR or X-ray crystallography. So, I imagine we have just hit the tip of the iceberg in finding natural enzymes that can function as gene editing and gene locating tools. Plus, we may start designing our own enzymes like what Professor David Baker at UW works on. Huge ocean to go exploring, bring a molecular fishing pole :-)&lt;/p&gt;&#xA;" OwnerUserId="9535" LastEditorUserId="5144" LastEditDate="2019-08-13T12:17:01.893" LastActivityDate="2019-08-13T12:17:01.893" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="21706" PostTypeId="2" ParentId="21699" CreationDate="2014-09-27T22:13:44.713" Score="2" Body="&lt;p&gt;Based on fine scale mapping of human genome structural variation, which is expanded on &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_genetic_variation&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, according to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2424287/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; study, the amount of genome structural (nucleotide diversity) ranges from 0.1% to 0.4% (look under section &quot;Fine-scale map of human genome structural variation&quot;). Hence humans have an up to 99.9% nucleotide similarity. And according to &lt;a href=&quot;http://www.nature.com/ng/journal/v36/n11s/full/ng1435.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; study the average proportion of nucleotide differences between a randomly chosen pair of humans (i.e., average nucleotide diversity, or pi) is consistently estimated to lie between 1 in 1000 and 1 in 1500.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-09-27T22:13:44.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21708" PostTypeId="2" ParentId="21704" CreationDate="2014-09-27T22:44:39.897" Score="1" Body="&lt;p&gt;It's been too long since physics to have a good answer, but I know that if you look at an object in a flat mirror, the light coming off the mirror would be identical to light coming a real object in the same position. The angles of the light rays are the same. Therefore, no matter how close the mirror is to your face, your eyes treat the image as if it's coming from 10 feet away, or however far the object in the mirror is away from the mirror. Bent mirrors will change this, that's why you get the &quot;OBJECTS IN MIRROR ARE CLOSER THAN THEY APPEAR&quot; warning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I made a diagram to to try and explain it better.&lt;img src=&quot;https://i.stack.imgur.com/pdZyn.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The eye is looking at a mirror, the light from the arrow on the left of the mirror reflects off the mirror and toward the eye. The eye sees an image that appears as if it were behind the mirror, on the right.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-09-27T22:44:39.897" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21709" PostTypeId="2" ParentId="15444" CreationDate="2014-09-27T23:11:46.167" Score="3" Body="&lt;p&gt;As discussed in the comments, there are theoretical and practical problems with arriving at such data. There have been controlled experiments using canines, but you have specifically stated your interest in humans. I offer a summary of a few observational studies that may be helpful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=8472565&quot; rel=&quot;nofollow&quot;&gt;this study&lt;/a&gt;, 117 patients in intensive care units (who are likely to have the most abnormal blood gas parameters among the living) were monitored with continuous optode-based blood gas analysis system. Of the 1,341 measurements, the ranges were:&lt;sup&gt;1,2&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;pH: 7.14 to 7.64&lt;/li&gt;&#xA;&lt;li&gt;PaCO2: 19 torr  - 98 torr&lt;/li&gt;&#xA;&lt;li&gt;PaO2: 38 torr – 413 torr&lt;sup&gt;3&lt;/sup&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=8143467&quot; rel=&quot;nofollow&quot;&gt;Another study&lt;/a&gt; included a total of 487 samples were obtained in ICU patients with severe respiratory failure and found the following ranges:  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;pH 7.23 – 7.55&lt;/li&gt;&#xA;&lt;li&gt;PaCO2: 19 torr – 83 torr&lt;/li&gt;&#xA;&lt;li&gt;PaO2 30 torr – 522 torr&lt;sup&gt;3&lt;/sup&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;These are reasonable ranges for pseudo-stable ICU patients. &#xA;Contrast that with &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1114160/&quot; rel=&quot;nofollow&quot;&gt;normal ranges&lt;/a&gt; (+/- 2 standard deviations):  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;pH: 7.35 – 7.45&lt;/li&gt;&#xA;&lt;li&gt;PaCO2: 35 torr – 45 torr&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;On the other hand, you’re interested in the most extreme recorded values, which are likely going to occur during cardiac arrest. According to &lt;a href=&quot;http://emj.bmj.com/content/27/10/800.long&quot; rel=&quot;nofollow&quot;&gt;this case report and literature review&lt;/a&gt;, the lowest published arterial pH of an adult who survived cardiac arrest with neurologic recovery is 6.33. The caveat here is that this was a near-drowning victim, and the associated hypothermia provides neurologic protection. The authors go on to report several others including their own patient with pH in the range of 6.5 - 6.6 with neurologic recovery in the absence of hypothermia.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;Notes&#xA;&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;1. Bicarbonate measurements on whole blood are calculated rather than measured and so not included in such studies. The more accurate test for this measurement is serum chemistry. The bounds are usually defined by the assay. It’s possible for a living human to have HCO3 less than assay (5 mmol/L in most labs by serum chemistry) or greater than assay (~50 mmol/L by most labs).&#xA;&lt;/sub&gt;    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;2. All data provided are arterial. Venous blood gases are of little clinical utility except as a cop-out for obtaining an arterial blood gas.&#xA;&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;3. These upper values are intubated patients breathing 100% FiO2. (The lower values are those about to be intubated breathing 100% FiO2....) The theoretical maximum PaO2 on room air is derived from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Alveolar_gas_equation&quot; rel=&quot;nofollow&quot;&gt;alveolar gas equation&lt;/a&gt;, ~100 torr.&#xA;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-09-27T23:27:14.590" LastActivityDate="2014-09-27T23:27:14.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21710" PostTypeId="1" CreationDate="2014-09-28T00:07:47.490" Score="2" ViewCount="4135" Body="&lt;p&gt;I'm studying for my intro to microbiology test and I have a question asking why a culture of yeast responsible for producing alcohol would be growing, but not producing alcohol?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The multiple choice answers are:&#xA;a) the maltose is toxic&#xA;b) O2 is in the medium&#xA;c) Not enough protein is available in the agar&#xA;d) The temperature is too low&#xA;e) The temperature is too high&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: There is not much more context that what I gave here. The question simply asks me to assume the position of a scientist at a wine production company, and then asks the question I posed above - nothing too specific.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it is (b) because the presence of O2 would cause the yeast to respire aerobically, but I can't eliminate (d) and (e)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I figure it probably isn't (a) because a toxic chemical would inhibit the growth of the yeast. I don't believe protein is relevant so I don't think it is (c).&lt;/p&gt;&#xA;" OwnerUserId="9539" LastEditorUserId="9539" LastEditDate="2014-09-28T01:02:57.450" LastActivityDate="2017-03-24T01:22:26.193" Title="Why would yeast grow but not produce alcohol?" Tags="&lt;microbiology&gt;&lt;yeast&gt;&lt;fermentation&gt;&lt;anaerobic-respiration&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21711" PostTypeId="2" ParentId="21710" CreationDate="2014-09-28T01:12:08.763" Score="1" Body="&lt;p&gt;You're right, the answer is b since the presence of oxygen would lead to aerobic respiration and not fermentation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If maltose was toxic, the yeast wouldn't grow. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Proteins are required for growth, but the yeast is growing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any temperature that is extreme enough to prevent fermentation would also prevent other cellular processes and the yeast wouldn't grow. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-09-28T01:12:08.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21713" PostTypeId="1" AcceptedAnswerId="21714" CreationDate="2014-09-28T04:55:20.387" Score="1" ViewCount="1106" Body="&lt;p&gt;When there is 'excessive' cell growth 'ordered' by the human body in some specific part of the body that is not part of the usual repairing mechanisms, does this cause extra telomere 'shortening' or damage even though a lot of cell growth and repair is 'required'. If a lot of cell growth is 'activated' with problematic telomeres does this cause telomerase to be formed which then might shut down the apoptosis mechanisms and keep the cell 'going' indefinately. Note; I read some acid reflux problem causes parts of the throat to scar or be damaged causing excessive cellular repairs on those parts of the throat where tumors have later developed. When someone gets sunburned on the shoulders say, and this damages the skin there, then does every future time the persons shoulders get in the sun ,do those same areas get further damage causing excessive growth and repair of skin cells on the shoulder. With a lot of excessive repair tumors might develop. SO could excessive cell growth (that might be caused by many different factors ) help to cause cancer??&lt;/p&gt;&#xA;" OwnerUserId="6195" LastActivityDate="2014-09-28T06:46:16.853" Title="About excessive cellular growth" Tags="&lt;cell-biology&gt;&lt;cancer&gt;&lt;telomere&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21714" PostTypeId="2" ParentId="21713" CreationDate="2014-09-28T06:46:16.853" Score="0" Body="&lt;p&gt;Long story short: Absolutely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Short story long:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While your intuition that growing a lot of cells can increase the risk of damage that might cause cancer is spot on, your specifics are a little off. It's not the telomeres themselves that are the problem, but broad spectrum DNA damage and transcriptional changes. The condition of the telomeres doesn't directly affect the likelihood of a cell growth becoming more cancer-like. A cell with perfect telomeres fresh from a telomerase-expressing stem cell and cell with shortened telomeres have an equal chance of becoming cancerous. Cell populations with longer telomeres have 'more time' or more chances to develop mutations and cell expression damage, however. You're more likely to get in a car crash if you go to the store across town  than the neighborhood convenience store, even though it's not intrinsically more dangerous per mile driven. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sunburn example can be a little misleading. It's not cell regrowth that's the key carcinogenic factor, but instead the direct DNA damage UV radiation can cause. In a particularly bad sunburn your skin cells may be killed or commit suicide(apoptosis) because of the DNA damage they've sustained. If the cells are damaged but do not die, they're likely to recover. Over time and repeated sun exposure, the skin cells that are most resistant to orders from the body to stop growing or die stick around and may grow and divide. Freckles are when this happens to a population of skin cells that ignore orders about how much brown pigment to be, but still listen to the orders that instruct them on how to be skin. When they stop listening to the skin orders, they officially become precancerous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The acid reflux example is excellent. There are populations of stem cells throughout the adult body that produce skin cells and hair follicles and blood cells and all the other kinds of cells that are more or less expendable. Generally speaking these stem cells don't have do very much work replenishing esophagus cells, so when they are taxed by something killing off the esophagus lining regularly, they can 'break down' and lose control of their own replication. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems like you're both pretty interested in cellular mechanisms of cancer and a little shaky on current theories of cancer formation(there are a few), so if there's a section of this answer that needs to be more detailed or followup questions please let me know.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-09-28T06:46:16.853" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21715" PostTypeId="1" AcceptedAnswerId="21727" CreationDate="2014-09-28T06:49:25.693" Score="35" ViewCount="3900" Body="&lt;p&gt;When I watch wilderness specials for more than a few minutes, I notice a familiar pattern: predators are depicted as being alerted by the scent of blood. Wounded animals seem to make the best prey and predators seem to have a heightened awareness for the smell of blood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would seem that it would then be a disadvantage to evolutionary survival for female organisms to menstruate. How do females of a species not attract predators to the signal of menstrual blood? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do female organisms in the wild actually menstruate? If so, is there a difference in the composition of menses that does not alert predators? How would this not at the very least give predators an idea of the general vicinity of the female?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If wild animals excrete their menses, do they have ways in which they are able to mask the evidence of its release or are they somehow internalizing the tissue so that they are not released?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If female organisms in the wild do menstruate, then why is this not a survival disadvantage?&lt;/p&gt;&#xA;" OwnerUserId="5917" LastEditorUserId="16651" LastEditDate="2015-12-11T05:19:27.263" LastActivityDate="2017-03-30T22:04:35.103" Title="Why is menstruation in wild animals not a disadvantage to organismal survival?" Tags="&lt;evolution&gt;&lt;reproductive-biology&gt;&lt;antipredator-adaptation&gt;&lt;predation&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21717" PostTypeId="1" CreationDate="2014-09-28T09:59:08.200" Score="3" ViewCount="2429" Body="&lt;p&gt;Quite often, I have heard the remark that children become hyperactive when high amounts of sugar are consumed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But common websites suggest that sugar is a sedative, and the hyperactivity in children is more likely caused by 'artificial dyes and preservatives'. (&lt;a href=&quot;http://curezone.com/forums/am.asp?i=1444631&quot; rel=&quot;nofollow&quot;&gt;http://curezone.com/forums/am.asp?i=1444631&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, is Sugar a stimulant (for adults and children) or is it a sedative? Is there any conclusive research to validate this theory?&lt;/p&gt;&#xA;" OwnerUserId="9272" LastEditorUserId="9272" LastEditDate="2014-09-29T05:53:29.563" LastActivityDate="2018-04-20T09:23:41.483" Title="Is Sugar a stimulatant or a weak sedative?" Tags="&lt;diet&gt;&lt;sugar&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21718" PostTypeId="2" ParentId="16306" CreationDate="2014-09-28T10:49:24.663" Score="3" Body="&lt;p&gt;This is a part answer (as this is outside of my field), but the article &lt;a href=&quot;http://benthamopen.com/tocsj/articles/V002/1TOCSJ.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Self Regulation of the Heart: Natural Frequency and Damping of the &#xA;Heart Contractions &lt;/a&gt; (Bahramali et al. 2009) imply that 'normal' frequencies may not be possible to precisely define, due to:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;ECG frequency analysis is complicated by the fact that ECG signals are non-stationary, that is, their activity &#xA;  patterns change slowly or intermittently as a result of variations in a number of physiological and physical influences. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The article extensively reviews the general frequency analysis, divided into P, Q, R, S and T components.  However, they define 'optimal conditions' (i.e. 'normal and healthy) as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;optimal conditions of the heart contraction as those under&#xA;  which the dynamics of contraction shows the best&#xA;  agreement with underdamped harmonic oscillation&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;An example of this is visualised in the diagram below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/o9Y7M.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;this example is provided on the University of Pennsylvania tutorial site &lt;a href=&quot;http://cal.vet.upenn.edu/projects/lgcardiac/ecg_tutorial/heartrate.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;ECG Tutorial&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the article &lt;a href=&quot;http://research.ijcaonline.org/ccsn/number2/ccsn011.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Comparison of Power Spectral Density (PSD) of Normal &#xA;and Abnormal ECGs&lt;/a&gt; (Das and Chakraborty, 2011), note comprisons for the QRS component, as&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;QRS complexes are chosen because &#xA;  it shows distinct differences for different heart diseases&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In other words, distinguishing healthy from not-so-healthy.&lt;/p&gt;&#xA;" OwnerDisplayName="user9474" LastEditorDisplayName="user9474" LastEditDate="2014-09-28T11:13:29.840" LastActivityDate="2014-09-28T11:13:29.840" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21719" PostTypeId="1" AcceptedAnswerId="23139" CreationDate="2014-09-28T14:07:13.377" Score="1" ViewCount="307" Body="&lt;p&gt;I have a quick question: Are triglycerides essentially what we call &quot;fats&quot;?&#xA;I've tried reading up on it but there seems to be some conflicting information.&#xA;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="6576" LastEditDate="2014-09-28T16:05:52.437" LastActivityDate="2014-10-20T17:41:39.330" Title="Are triglycerides fat?" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21720" PostTypeId="2" ParentId="21715" CreationDate="2014-09-28T15:44:31.200" Score="10" Body="&lt;p&gt;It is a very nice question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Menstruation_(mammal)&quot;&gt;wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Though there is some disagreement in definitions between sources, menstruation is generally considered to be limited to primates. Overt menstruation (where there is bleeding from the uterus through the vagina) is found primarily in humans and close evolutionary relatives such as chimpanzees. It is common in simians including Old World monkeys and apes and New World monkey, but variably expressed in prosimians, being completely lacking in strepsirrhine primates and possibly weakly present in tarsiers. Outside the primates it is known only in bats and the elephant shrew.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This other &lt;a href=&quot;http://en.wikipedia.org/wiki/Menstruation#Evolution&quot;&gt;wiki article&lt;/a&gt; says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many have questioned the evolution of overt menstruation in humans and related species, speculating on what advantage there could be to losing blood associated with dismantling the endometrium rather than absorbing it, as most mammals do. Humans do, in fact, reabsorb about two-thirds of the endometrium each cycle. Strassmann asserts that overt menstruation occurs not because it is beneficial in itself. Rather, the fetal development of these species requires a more developed endometrium, one which is too thick to reabsorb completely. Strassman correlates species that have overt menstruation to those that have a large uterus relative to the adult female body size&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I just cite two wiki articles but it is probably worth going through some more reading in order to give a more complete overview of the selection pressure underlying the evolution of menstruation in mammals and especially in primates. In the first paragraph above, wiki cites 5 articles. From the title of one of those, it seems that menstruation is also a defense against pathogens transported in sperm. I hope someone will give a better answer than mine.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-09-28T16:17:50.653" LastActivityDate="2014-09-28T16:17:50.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21722" PostTypeId="2" ParentId="2790" CreationDate="2014-09-28T16:16:11.483" Score="0" Body="&lt;p&gt;I think that it started like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First stage:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chemicals like Na, Cl, O₂, O₃, CO₂, CO, HCN,  and H₂SO₄ react to form small molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second Stage:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next those small molecules react to form macromolecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Third Stage:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA, being the most stable was first to replicate. A membrane eventually enveloped this and formed the nucleus&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fourth Stage:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Via Endosymbiosis it envelops mitochondria in an outer membrane&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fifth Stage: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cell starts forming membrane and protein for all of its organelles. It is now a eukaryotic cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the DNA world Hypothesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because DNA can be single, double, triple, or quadruple stranded in organisms(That would be ssDNA, dsDNA, tsDNA, and qsDNA respectively) it can do much more than just code for proteins or rRNA or tRNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the single stranded state it can act like an enzyme forming deoxyribozymes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the triple and quadruple stranded states it can act inhibitory without needing another protein or methyl group.&lt;/p&gt;&#xA;" OwnerUserId="5851" LastEditorUserId="3340" LastEditDate="2014-10-09T16:51:25.803" LastActivityDate="2014-10-09T16:51:25.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21723" PostTypeId="2" ParentId="2790" CreationDate="2014-09-28T18:02:35.423" Score="2" Body="&lt;p&gt;If you are interested in this question, I highly recommend you look at the work of &lt;a href=&quot;http://molbio.mgh.harvard.edu/szostakweb/&quot; rel=&quot;nofollow&quot;&gt;Jack Szostak&lt;/a&gt; -  Nobel Prize winner at Harvard who is currently doing some of the best work in this area. His work is grounded in good experiments that point to how abiogenesis &lt;em&gt;could&lt;/em&gt;&#xA; have happened. &lt;/p&gt;&#xA;" OwnerUserId="3804" LastActivityDate="2014-09-28T18:02:35.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21724" PostTypeId="1" AcceptedAnswerId="21743" CreationDate="2014-09-28T18:22:48.030" Score="1" ViewCount="896" Body="&lt;p&gt;My professor tells us that carbohydrate is an important part of phospholipid, but phospholipid is composed of Choline, Phosphate, Glycerol and two Fattyacid, and I don't think even one of them is carbohydrate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's wrong with my statements?&lt;/p&gt;&#xA;" OwnerUserId="3179" LastActivityDate="2014-09-29T17:54:26.627" Title="Is carbohydrate an important part of phospholipid?" Tags="&lt;cell&gt;" AnswerCount="2" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="21725" PostTypeId="2" ParentId="7375" CreationDate="2014-09-28T18:34:14.107" Score="1" Body="&lt;p&gt;I would say theoretically yes, if you know lots of other information, but practically no, because of all the unknowns.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://mbe.oxfordjournals.org/content/17/8/1232.full&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; cysteine content and therefore sulfur content of proteins vary depending on what kind of organism your organic material is coming from. Animals have more, bacteria tend to have less.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sulfur content as a fraction of protein content in a given animal or plant is constant or nearly constant across the entire animal/plant. If a sample's protein content is 50:50 corn protein:sheep protein it's possible to estimate the sulfur content of the protein fraction from the sulfur contents of the sources of the protein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition the sulfur content can be affected by fermentation and sulfur/sulfate-reducing bacteria, many but not all of which are anaerobes. So figures for whatever the source of the feedstock is (as far as cysteine content) can be affected by whatever happens to it afterwards. Chicken waste with a high sulfur content allowed to ferment may give off fairly large amounts of hydrogen sulfide, lowing the sulfur content without necessarily affecting the bulk protein content. The reverse might also happen, where protein is digested and sulfur is released as sulfates but kept in the mixture. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if you know for certain the sources of all of the protein(and that no further biological activity has changed them), the unknown amount of organic acids is going to throw off your sulfur estimates if there are sulfur-containing organic acids in the N-free fraction.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-09-28T18:34:14.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21726" PostTypeId="2" ParentId="21717" CreationDate="2014-09-28T19:01:57.977" Score="3" Body="&lt;p&gt;The idea that 'dyes and preservatives' cause hyperactivity dates back to &lt;a href=&quot;http://www.feingold.org/Research/PDFstudies/Feingold76.pdf&quot; rel=&quot;nofollow&quot;&gt;this '76 paper&lt;/a&gt; by one Dr. Feingold. Despite being &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/353681&quot; rel=&quot;nofollow&quot;&gt;disproved neatly&lt;/a&gt; in 1978, it's still around.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as sugar goes, I recommend &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8747098&quot; rel=&quot;nofollow&quot;&gt;this review paper&lt;/a&gt; covers both the arguments for and against sugar causing hyperactivity, as well as 12 double-blind placebo controlled studies showing sugar has no effect on children's actual behavior.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-09-28T19:01:57.977" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21727" PostTypeId="2" ParentId="21715" CreationDate="2014-09-28T21:06:12.660" Score="31" Body="&lt;p&gt;Thanks to &lt;a href=&quot;https://biology.stackexchange.com/a/21720/9268&quot;&gt;the other answer&lt;/a&gt; for pointing me in the right direction with some references. It seems that two biologists in the early 1990s had a back-and-forth over this topic in &lt;em&gt;The Quarterly Review of Biology.&lt;/em&gt;&lt;sup&gt;1,2&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A statement of the problem:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The function of menstruation is a central enigma of mammalian, and especially primate, reproductive physiology. Each cycle the uterus builds a glandular epithelium with a high secretory capacity and an elaborate microvasculature, only to reabsorb or void it with the menses if implantation does not oc-cur. Why does the endometrium not maintain a steady state of readiness for implantation by the blastocyst? What is the selective advantage of cyclical regeneration and regression?&lt;sup&gt;1&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;One hypothesis&lt;/strong&gt;&lt;sup&gt;2&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In  1993, Margie Profet hypothesized that menstruation is primarily advantageous as a defense against pathogens transported by sperm. During mammalian insemination, she stated, bacteria from the male and female genitalia cling to sperm tails and are transported to the uterus. Menstruation, triggered by the abrupt constriction (causing necrosis of endometrial lining) followed by dilation (causing shedding of said necrotic tissue), forces loose not only the endometrial lining but sperm-borne pathogens contained therein. In addition to shedding the uterine tissue harboring these bacteria, menstruation delivers immune cells to the uterine cavity, triggered by the mechanical pressure exerted via the shedding of endometrial lining.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this 50 page (!) article, Profet also points out that other mammals with covert menstruation take advantage of some of these same benefits, as the immunological stimulation includes phagocytosis of pathogens by cells that may be expelled in cervical/vaginal mucous. Further, proestrous  bleeding (i.e. that preceding ovulation, 180 degrees off from the human cycle), which occurs in some mammals (domestic dog, coyote, etc), seems to serve a similar function.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If not eliminated prior to estrus, these tenacious pathogens might otherwise attach to incoming sperm during estrus and ascend the oviducts. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As to why humans and other primates are subject to overt bleeding in contrast to other mammals, she lays out a theoretical argument that selection pressure to menstruate should increase with decreasing per-cycle “fecundability” (the probability of pregnancy) because copulation not followed by bleeding risks infection. In contrast to, e.g., mice (98% fecundability), humans have some of the lowest fecundability rates, primarily due to “concealed” ovulation which de-couples copulation and ovulation. (Contrast this to most mammals whose females have a defined estrous period during which they are receptive to male sexual advances; the data for the existence of such a period in humans are controversial, and sexual behavior is driven primarily by “higher” social, environmental, and cognitive cues.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A different view&lt;/strong&gt;&lt;sup&gt;1&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In response/objection to this paper, Beverly Strassman in the same journal published an article outlining an alternative hypothesis about the potential adaptive value of menstruation. She proposed a hypothesis based on energy conservation: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[T]he uterine endometrium is shed/resorbed whenever implantation fails because cyclical regression and renewal is energetically less costly than maintaining the endometrium in the metabolically active state required for implantation. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Her research determined that, in its regressed state (i.e. s/p endometrial shedding), oxygen consumption in the endometrial tissue is markedly declined, nearly sevenfold. Although this would seem to be a trivial component of whole-body metabolism, she argues otherwise:  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Metabolic rate is at least 7% lower, on average, during the follicular phase than during the luteal phase in women, which signifies an estimated energy savings of 53 MJ over four cycles, or nearly six days worth of food. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Her argument shares with Profer’s the implication that mammals with lower fecundability are more likely to menstruate. In those with high probability of pregnancy at every cycle, the energetic benefits of ridding the body of the need to support endometrial lining (relevant only in the absence of pregnancy), are decreased. Her hypothesis also predicts the larger volume of menstrual shedding in humans and chimps in contrast to other mammals related to the increased uterine size relative to the female body (a ratio that is largely determined by the especially large head of the human fetus).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Conclusion&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As noted in the comments, only primates have overt menstrual bleeding. The adaptive benefits have been variously explained, and it is probable that there is more than one operative explanatory model. Whatever the small decrement in survivalship incurred by the intermittent and uncontrolled depositing of blood in the wild, it is apparently outweighed in these species by the processes described above.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&#xA;&lt;strong&gt;References and Notes&lt;/strong&gt;&#xA;&lt;/sup&gt;&#xA;&lt;sup&gt;&lt;br&gt;&#xA;&lt;strong&gt;1&lt;/strong&gt;. Strassmann, Beverly I.  &lt;em&gt;The Evolution of Endometrial Cycles and Menstruation&lt;/em&gt; The Quarterly Review of Biology, June 1996; Vol. 71, No. 2 pp 181-220.&#xA;&lt;/sup&gt;&#xA;&lt;sup&gt;&lt;br&gt;&#xA;&lt;strong&gt;2&lt;/strong&gt;. Profet, Margie. &lt;em&gt;Menstruation as a Defense Against Pathogens Transported by Sperm&lt;/em&gt;. The Quarterly Review of Biology, Sept 1993; Vol. 68, No. 3  pp. 335-386.&#xA;&lt;/sup&gt;&#xA;&lt;sup&gt;&lt;br&gt;&#xA;&lt;strong&gt;Note&lt;/strong&gt;: Your comparison to urine and feces is an interesting one. Perhaps a vaginal sphincter would be a good idea…..were it not for men and babies….&#xA;&lt;/sup&gt;  &lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2017-03-30T22:04:35.103" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21728" PostTypeId="1" AcceptedAnswerId="21731" CreationDate="2014-09-28T23:30:43.383" Score="3" ViewCount="415" Body="&lt;p&gt;The concepts of robustness and canalization are fashionable today in the biology literature. However, I am not sure of their definitions and I am not sure either that all authors actually use the same definition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am therefore asking here for a the &lt;strong&gt;definitions of these terms or for a short review of the common definitions of robustness and canalization&lt;/strong&gt;. How do different authors define these words? I am particularly interested in...&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The differences between robustness and canalization (canalization seems to apply more in developmental biology than robustness who seems to be a more general concepts)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;At what level do these concepts apply? To populations, to genotypes, to both, ..?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How does the concept of adaptation link to these definitions.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How does the concept of plasticity fits in opposition of the concepts of robustness and canalization?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-11-06T20:27:24.837" LastActivityDate="2015-04-12T22:11:13.010" Title="Definitions of robustness and canalization" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;natural-selection&gt;&lt;adaptation&gt;&lt;definitions&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21729" PostTypeId="1" CreationDate="2014-09-29T00:09:14.307" Score="1" ViewCount="217" Body="&lt;p&gt;A microbiologist has discovered what she thinks are two new types of algae. The first cell &#xA;(Organism 1) appears cubic and is approximately 1.5 μm long, 1.5 μm wide and 1.5 μm deep. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second (Organism 2) is rectangular and 2 μm wide by 5 μm long by 2μm deep.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a.  What is the surface area/volume ratio of each organism?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b.  Which organism will find it more difficult to interact with surrounding environment (receive nutrients, excrete metabolites etc.)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c.  How will this organism cope with the reduced capacity to interact with environment?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;In respects to question A.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;V of Rectangular organism= (V = L x W x D)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Surface Area= (L x W) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Im assuming these simple rules still apply to organisms concerning minuscule measurements. &lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;&lt;p&gt;Im assuming for question B., that the molecule with the smaller dimensions will have the most difficult time interacting with its environment, due to the fact that it has a smaller perimeter with less channels &amp;amp; ports. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I am completely lost for problem C.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Any insight Would be awesome. Thanks all !&lt;/p&gt;&#xA;" OwnerUserId="8059" LastActivityDate="2014-10-29T04:57:47.630" Title="Bacterial Cell Problem" Tags="&lt;cell-biology&gt;&lt;differentiation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21730" PostTypeId="1" AcceptedAnswerId="34878" CreationDate="2014-09-29T02:47:42.457" Score="9" ViewCount="2230" Body="&lt;p&gt;In the picture below, which I obviously do not own: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GFIir.gif&quot; alt=&quot;Image of Animal Phylogeny&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;it depicts two different phylogenic trees, one which is based on molecular comparisons and another one which is based on body-plan grades. My question is which is more common or accepted in the current Biology world?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image reference: &lt;a href=&quot;http://www.zo.utexas.edu/faculty/sjasper/images/32.12.gif&quot; rel=&quot;noreferrer&quot;&gt;http://www.zo.utexas.edu/faculty/sjasper/images/32.12.gif&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9547" LastActivityDate="2015-07-08T19:58:41.137" Title="Regarding the kingdom Animalia, which phylogenic tree is more common: Molecular Comparisons or Body-Plan Grades" Tags="&lt;zoology&gt;&lt;taxonomy&gt;&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21731" PostTypeId="2" ParentId="21728" CreationDate="2014-09-29T04:09:44.387" Score="3" Body="&lt;p&gt;As canalization is defined in your question (also in wikipedia) it means robustness. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Semantically it is possible to differentiate the two. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Robustness of a system refers to its sensitivity to perturbations. In other words small differences in parameters would not affect the steady state of the system (parameter changes in a physically plausible range would not lead to bifurcations).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By system I mean a set of entities connected to each other in a defined fashion. For example an ecosystem in which different species are connected to each other by interactions of the food chain. At steady state a system configuration (for instance- 10 foxes, 100 rabbits, 10000 grasses, 1000 honeybees etc) remains constant over time (that, however, doesn't mean it is static). Or in case of development a system may be the body defined by a set of certain phenotypes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Canalization/channelization refers to mechanisms that make the system follow a certain trajectory. So if you see it mathematically canalization keeps the trajectory dictated by a  given set of eigenvectors. In case of development you may call mechanisms such as dosage compensation, functional compensation by isoforms, parallel metabolic flux channels etc as canalizing mechanisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in contemporary usage we can call a system robust (a property of a system) whereas we should address mechanisms that help to preserve trajectories as canalizations. The final aim of canalization is to render robustness to the system but it is not the only mechanism that is responsible for robustness (for e.g. the steady state may just be independent of certain parameters).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Robustness is a property of the system and is dependent on how the different entities of the system are coupled and what their interaction parameters are (rates etc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;You should note that these are parlances that are adopted by different groups in the scientific community and may perhaps mean the same thing- this is merely my attempt to remove redundancy of terms by the means of semantics.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, plasticity is a different concept altogether. Plasticity is in a way opposite to robustness. This means that the qualitative nature of the system can change if certain parameters are tweaked. However, the system should still maintain its stability. In a stable system mild perturbations from steady state will result in system going back to that steady state - like a ball in a well. However, a system may inherently allow for multiple steady states (like switches), and depending on certain parameters the system can be in either of the states (but if pushed too far then the system can go to another stable steady state). This is called multistability. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;NOTE: some people also use the term plastic to mean &quot;responsive&quot;. The above definition may not be exhaustive or the most perfect.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-09-29T12:32:04.270" LastActivityDate="2014-09-29T12:32:04.270" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21732" PostTypeId="2" ParentId="21729" CreationDate="2014-09-29T04:19:35.590" Score="1" Body="&lt;p&gt;B. Higher surface to volume ratio allows better interface with environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C. To increase surface area the cell can form processes such as microvilli. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-09-29T04:19:35.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21733" PostTypeId="2" ParentId="21724" CreationDate="2014-09-29T08:17:51.463" Score="3" Body="&lt;p&gt;There's nothing wrong in your statements! &#xA;Maybe your professor was talking about &lt;em&gt;glycolipids&lt;/em&gt;, that are lipids (also &lt;em&gt;phospholipids&lt;/em&gt;) with a carbohydrate attached; they can be found on the outer surface of all eukaryotic cell membranes. They are important because they work as a recognition site for specific chemicals or for antibodies.&lt;/p&gt;&#xA;" OwnerUserId="3645" LastActivityDate="2014-09-29T08:17:51.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21735" PostTypeId="1" AcceptedAnswerId="21741" CreationDate="2014-09-29T11:59:46.540" Score="3" ViewCount="623" Body="&lt;p&gt;I wonder what are typical bone mass values for adult males and females? And do they change significantly with workout and diet?&lt;/p&gt;&#xA;" OwnerUserId="1458" LastActivityDate="2014-09-29T17:15:37.460" Title="What are typical values for bone mass in humans?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21736" PostTypeId="1" CreationDate="2014-09-29T14:43:20.383" Score="2" ViewCount="172" Body="&lt;p&gt;I'm doing research into the Hodgkin-Huxley Model from an electronics/mathematics perspective and I'm looking to find actual numerical results from experiments on squid axons. I want to compare the results of the experiments to the curves produced by modelling the equations in MATLAB.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My problem is, that while there are an abundance of resources discussing the equations and methodology of the experiments, I am having great difficulty finding tabulated experimental data (not just numbers generated from modelling the equations).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I am coming from outside the field of biology I would like to know are there sources of quality numerical data for these types of experiments? In particular I am looking for the data for Potassium Conductance vs Time, here is the plot from the 5th paper in their series of publications that earned them a Nobel prize:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1392413/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hodgkin AL, Huxley AF. A quantitative description of membrane current and its application to conduction and excitation in nerve. The Journal of Physiology. 1952;117(4):500–544&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AQvjW.png&quot; alt=&quot;Potassium Conductance vs Time&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9553" LastActivityDate="2014-09-29T14:43:20.383" Title="Biology Experiment Data (Hodgkin-Huxley)" Tags="&lt;physiology&gt;&lt;neuroscience&gt;&lt;bioinformatics&gt;&lt;neuroanatomy&gt;&lt;electrophysiology&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21738" PostTypeId="1" AcceptedAnswerId="21739" CreationDate="2014-09-29T15:24:55.913" Score="1" ViewCount="3090" Body="&lt;p&gt;I recently read a report that stated &quot;We found 430 &lt;strong&gt;fixed substitutions&lt;/strong&gt; […], with an additional 34 &lt;strong&gt;single nucleotide polymorphisms&lt;/strong&gt; (SNPs) fixed within individual patients.&quot; What is the difference between both terms?&lt;/p&gt;&#xA;" OwnerUserId="89" LastEditorUserId="89" LastEditDate="2014-09-29T16:25:18.140" LastActivityDate="2016-01-28T12:13:37.397" Title="What is the difference between a fixed substitution and a single nucleotide polymorphism (SNP)?" Tags="&lt;genetics&gt;&lt;snp&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21739" PostTypeId="2" ParentId="21738" CreationDate="2014-09-29T15:36:27.590" Score="3" Body="&lt;p&gt;If you look into a certain population, you will find mutations (for example SNPs) in some ratio with the wild-type allele. When a mutation reaches &lt;a href=&quot;http://en.wikipedia.org/wiki/Fixation_%28population_genetics%29&quot; rel=&quot;nofollow&quot;&gt;fixation&lt;/a&gt;, it will be the only allele, reaching 100% penetrance in this population. See &lt;a href=&quot;http://jaguar.biologie.hu-berlin.de/~wolfram/pages/seminar_theoretische_biologie_2007/ausarbeitungen/zackay.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for more information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the context given I would interpret it in the way that a total of 464 SNPs were found, 430 of these were in fixation (so can only be discovered when comparing them to another population) and 34 SNPs which haven't reached fixation and thus cannot be found in all members of the population.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-29T15:36:27.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21741" PostTypeId="2" ParentId="21735" CreationDate="2014-09-29T17:15:37.460" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I wonder what are typical bone mass values for adult males and females?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This seems hard to find. The only value I could find is on Bionumbers at it says that vertebrates compact bones have a mean density of 2 mg/cm$^3$ [1]. However in medical practice two scores are used to indicate the ratio between tested bone density and ideal bone density [2, 3] and absolute values are uncommon.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;And do they change significantly with workout and diet?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Bone mass is mainly influenced by genetic factors. Only up to 25 % may be influenced by environmental factors such as diet and exercise [4].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Among the medical conditions that influence bone mass, osteoporosis is the most frequent especially in women. Other conditions are: hyperparathyroidism, glucocorticoid therapy, other bone abnormalities and fractures [2].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Brian Cotterell, Fracture and Life, Imperial College Press, 2010 p.77 bottom paragraph via &lt;a href=&quot;http://bionumbers.hms.harvard.edu//bionumber.aspx?id=108642&amp;amp;ver=2&quot; rel=&quot;nofollow&quot;&gt;http://bionumbers.hms.harvard.edu//bionumber.aspx?id=108642&amp;amp;ver=2&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Bone density. (2014, September 15). In Wikipedia, The Free Encyclopedia. Retrieved 17:08, September 29, 2014, from &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Bone_density&amp;amp;oldid=625737182&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Bone_density&amp;amp;oldid=625737182&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.niams.nih.gov/Health_Info/Bone/Bone_Health/bone_mass_measure.asp&quot; rel=&quot;nofollow&quot;&gt;http://www.niams.nih.gov/Health_Info/Bone/Bone_Health/bone_mass_measure.asp&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.niams.nih.gov/Health_Info/Bone/Osteoporosis/bone_mass.asp&quot; rel=&quot;nofollow&quot;&gt;http://www.niams.nih.gov/Health_Info/Bone/Osteoporosis/bone_mass.asp&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-09-29T17:15:37.460" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21742" PostTypeId="1" CreationDate="2014-09-29T17:29:09.143" Score="9" ViewCount="970" Body="&lt;p&gt;The bat's ability for echolocation is amazing (so are other the abilities of other animals). I was wondering how all of it came to be.&lt;/p&gt;&#xA;" OwnerUserId="9448" LastActivityDate="2016-02-15T05:36:32.773" Title="What is the evolutionary explanation for bat's echolocation" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="2" ClosedDate="2014-09-30T16:10:59.733" ContentLicense="CC BY-SA 3.0" />
  <row Id="21743" PostTypeId="2" ParentId="21724" CreationDate="2014-09-29T17:54:26.627" Score="5" Body="&lt;p&gt;Your thinking is correct based on typical carbohydrates, but glycerol, the backbone of the phospholipid, is a 3-carbon carbohydrate that is usually derived from glucose.  It is not a sugar, but it does fall into the general class of polyols (aka sugar alcohols) that are a type of carbohydrate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A carbohydrate definitely is an important structural part of the phospholipid, but your instructor probably should have been more clear in describing why that is the case; I can definitely understand your confusion here.&lt;/p&gt;&#xA;" OwnerUserId="9476" LastActivityDate="2014-09-29T17:54:26.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21744" PostTypeId="1" CreationDate="2014-09-29T17:54:40.803" Score="9" ViewCount="27406" Body="&lt;p&gt;Losing a little blood is okay. If your a normal healthy person, and got into an accident, how do they know if you need a transfusion or if you'll be okay? This is hypothetical. &lt;/p&gt;&#xA;" OwnerUserId="9448" LastActivityDate="2017-07-10T11:12:23.880" Title="What percent of your blood can you lose before you need a transfusion" Tags="&lt;hematology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21745" PostTypeId="2" ParentId="21744" CreationDate="2014-09-29T18:01:21.127" Score="8" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;What percent of your blood can you lose before you need a transfusion&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Bleeding#Classification&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;: starting with Class III (more than 30 % of circulating volume loss), hemorrhage requires transfusion.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;&lt;strong&gt;Class I Hemorrhage&lt;/strong&gt; involves up to 15% of blood volume. There is typically no change in vital signs and fluid resuscitation is not usually necessary.&lt;/li&gt;&#xA;  &lt;li&gt;&lt;strong&gt;Class II Hemorrhage&lt;/strong&gt; involves 15-30% of total blood volume. [...] Volume resuscitation with crystalloids (Saline solution or Lactated Ringer's solution) is all that is typically required. Blood transfusion is not typically required.&lt;/li&gt;&#xA;  &lt;li&gt;&lt;strong&gt;Class III Hemorrhage&lt;/strong&gt; involves loss of 30-40% of circulating blood volume. [...] Fluid resuscitation with crystalloid and blood transfusion are usually necessary.&lt;/li&gt;&#xA;  &lt;li&gt;&lt;strong&gt;Class IV Hemorrhage&lt;/strong&gt; involves loss of &gt;40% of circulating blood volume. The limit of the body's compensation is reached and aggressive resuscitation is required to prevent death.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Of course this applies to a healthy person. If suffering from anemia or other blood conditions, smaller amounts of bleeding may require transfusion. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;how do they know if you need a transfusion or if you'll be okay?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In most situations it is hard to estimate how much blood was lost. So in medical practice some indicators are used. These include (according to &lt;a href=&quot;http://www.psbc.org/indications/redcells.htm&quot; rel=&quot;nofollow&quot;&gt;Puget Sound Blood Center&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;hemoglobin / hematocrit ratio and/or values lesser than 7 / 21 &lt;/li&gt;&#xA;&lt;li&gt;small hemoglobin correlated with clinical signs (symptomatic anemia)&lt;/li&gt;&#xA;&lt;li&gt;low O$_2$ saturation&lt;/li&gt;&#xA;&lt;li&gt;acute blood loss of more than 30 % (when it can be observed)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-10-02T10:47:25.083" LastActivityDate="2014-10-02T10:47:25.083" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21746" PostTypeId="2" ParentId="21742" CreationDate="2014-09-29T18:33:04.647" Score="10" Body="&lt;p&gt;The main reason for bats to &quot;develop&quot; their echolocation system was the avalability of an almost empty niche: Hunting insects at night. Birds are not able to hunt without light and here is where the bats come in. They are able to hunt at night and also to live and orientate in environments where they are protected over the day: Caves. Bats at night are also protected from predatory birds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is are a few interesting sources if you want to dive deeper into the stuff:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3760/mfhfuj9l_pdf.htm&quot;&gt;The evolution of flight and echolocation in bats: another leap in&#xA;the dark&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.mapoflife.org/topics/topic_574_Echolocation-in-bats/&quot;&gt;Echolocation in bats&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.mnf.uni-greifswald.de/fileadmin/Zoologisches_Museum/Hildebrandt/Dokumente/neuweiler03.pdf&quot;&gt;Evolutionary aspects of bat echolocation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-09-29T18:33:04.647" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21747" PostTypeId="2" ParentId="21742" CreationDate="2014-09-29T19:42:17.003" Score="5" Body="&lt;p&gt;Remember, evolution says things don't initially develop &quot;for a reason&quot; -- they develop at random, non-harmful mutations are kept in the gene pool, and eventually a selection event occurs (opportunity to exploit another food source or avoid a hazard) which selects for the mutation in some subset of the population. Over the kind of timescales evolution works on, that's enough to take something that is harmless, turn it into something that is just barely useful (though not necessarily for what it's now used for, eg feathers), and then continue to randomly vary it so it works better or differently or whatever.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Echolocation by itself isn't so remarkable -- we generally can tell about what size room we're in by listening to the echos around us. It's &lt;em&gt;focused&lt;/em&gt; echolocation that was a breakthrough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Late addition: In fact, it is possible for humans to learn to echolocate well enough to get an accurate picture of their surroundings. Some blind individuals have demonstrated this under MRI imaging of their brains. It's not common, but this may be because not enough respect has been given to the technique -- just as ASL was not respected until deaf linguists were able to explain why it was so much better than the alternatives.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So maybe what's special about bats is not the ability, but their reliance upon it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.m.wikipedia.org/wiki/Human_echolocation&quot; rel=&quot;nofollow&quot;&gt;https://en.m.wikipedia.org/wiki/Human_echolocation&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5947" LastEditorUserId="5947" LastEditDate="2016-02-15T05:36:32.773" LastActivityDate="2016-02-15T05:36:32.773" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21748" PostTypeId="1" CreationDate="2014-09-29T21:51:59.183" Score="0" ViewCount="148" Body="&lt;p&gt;I found several online articles discussing sugar withdrawal symptoms that people experience after cutting back on large sugar intake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://healthyeating.sfgate.com/refined-sugar-withdrawal-symptoms-9911.html&quot; rel=&quot;nofollow&quot;&gt;http://healthyeating.sfgate.com/refined-sugar-withdrawal-symptoms-9911.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.growyouthful.com/remedy/sugar-addiction-recovery.php&quot; rel=&quot;nofollow&quot;&gt;http://www.growyouthful.com/remedy/sugar-addiction-recovery.php&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One question that came to mind, was the following: If one experiences a sugar withdrawal, what happens if they apply sugar to the tongue, but do not digest it? Does that trick the brain into stopping the sugar withdrawal, or is it far more complicated than that?&lt;/p&gt;&#xA;" OwnerUserId="9107" LastActivityDate="2014-09-30T06:31:44.010" Title="Does applying sugar to the tongue taste buds releave sugar withdrawal symptoms?" Tags="&lt;sugar&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21749" PostTypeId="2" ParentId="21744" CreationDate="2014-09-29T22:07:22.953" Score="11" Body="&lt;p&gt;Typically transfusions are indicated for hemoglobin &amp;lt; 7 g/dL (for adults normally: 12-15 grams per deciliter &lt;sup&gt;[1]&lt;/sup&gt;) or &amp;lt; 8-10 g/dL if there is cardiac disease where diminished oxygen carrying capacity cannot be compensated by increased cardiac output. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer above is &lt;em&gt;theoretical&lt;/em&gt; because there is no accurate way to measure blood loss in the clinical setting - it's usually a mess. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most useful parameter to assess intravascular volume in the immediate term is blood pressure. Again, the actual number is variable but a 30% drop from baseline in the acute setting is bad. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another less acute indicator of hypovolemia is urine output (normal is .5-1 ml/kg body weight/hr, dropping below ~35 ml/hr therefore is an indicator of hypovolemia.)&lt;sup&gt;[2]&lt;/sup&gt; Hypovolemia is often corrected with sterile saline fluid and adding packed red blood cells only as needed to keep hemoglobin in the above required range, unless someone is actively bleeding (trauma, bleeding ulcer, etc.) in which case &quot;whole blood&quot; (or packed red blood cells, fresh-frozen plasma and platelets) is given.&lt;sup&gt;[3]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://www.mdconsult.com/books/page.do?eid=4-u1.0-B978-1-4377-0974-2..00008-7--s0025&amp;amp;isbn=978-1-4377-0974-2&amp;amp;type=bookPage&amp;amp;from=content&amp;amp;uniqId=465528433-2&quot; rel=&quot;nofollow&quot;&gt;McPherson: Henry's Clinical Diagnosis and Management by Laboratory Methods, 22nd ed.&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://www.ccmtutorials.com/renal/pathphys/page_04.htm&quot; rel=&quot;nofollow&quot;&gt;Oliguria &amp;amp;  Volume Depletion&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=4&amp;amp;ved=0CDAQFjAD&amp;amp;url=http%3A%2F%2Fwww.springer.com%2Fcda%2Fcontent%2Fdocument%2Fcda_downloaddocument%2F9781441959225-c1.pdf%3FSGWID%3D0-0-45-924742-p173951577&amp;amp;ei=TPEpVO6nDtGvyAT1x4KgDA&amp;amp;usg=AFQjCNFALLbAJ0vI3RHvY_kaquLnh_fiVg&amp;amp;sig2=s3Ss7uqD3MIjJyi8xs8Isw&amp;amp;bvm=bv.76247554,d.aWw&quot; rel=&quot;nofollow&quot;&gt;Fluid Resuscitation and Volume Assessment&lt;/a&gt;&lt;/sub&gt; &lt;/p&gt;&#xA;" OwnerUserId="9560" LastEditorUserId="-1" LastEditDate="2014-09-30T10:06:59.977" LastActivityDate="2014-09-30T10:06:59.977" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21750" PostTypeId="1" AcceptedAnswerId="21751" CreationDate="2014-09-29T22:20:51.987" Score="4" ViewCount="249" Body="&lt;p&gt;I am am physical scientist working in biology, and have recently started doing experiments. I would like a manual akin to &quot;Numerical Recipes&quot;, but for the lab: straight forward, easy instructions on how to do the (100) most basic biology experiments - PCR, cloning, etc. I realize that a lot of these depend on kits, and specific equipment, but it seems like there still should be something that would give you the outline of how to do these experiments. Does anyone know of a resource like this? &lt;/p&gt;&#xA;" OwnerUserId="3804" LastActivityDate="2014-09-29T23:23:04.923" Title="Short, concise, practical manual for doing experimental biology" Tags="&lt;lab-techniques&gt;&lt;book-recommendation&gt;&lt;experiment&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21751" PostTypeId="2" ParentId="21750" CreationDate="2014-09-29T22:51:07.313" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://www.molecularcloning.com/&quot; rel=&quot;noreferrer&quot;&gt;Molecular Cloning&lt;/a&gt; is updated and in its 4th edition.  Every lab used to have it.  Its comprehensive, but really no book could be complete. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-09-29T22:51:07.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21752" PostTypeId="2" ParentId="21750" CreationDate="2014-09-29T23:23:04.923" Score="4" Body="&lt;p&gt;Along with @shigeta's &lt;a href=&quot;https://biology.stackexchange.com/a/21751/948&quot;&gt;answer&lt;/a&gt;, I'd highly recommend Springer/Humana Press's series &lt;a href=&quot;http://link.springer.com/search?facet-series=%227651%22&amp;amp;facet-content-type=%22Book%22&quot; rel=&quot;nofollow noreferrer&quot;&gt;Methods in Molecular Biology&lt;/a&gt;, which started out as just a single collection of protocols (as I recall...) and is now a series of 1208 books, published between 1984 and 2015. There are a ton of protocols available online at places like &lt;a href=&quot;http://www.springerprotocols.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Springer Protocols&lt;/a&gt; and &lt;a href=&quot;http://cshprotocols.cshlp.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cold Spring Harbor Protocols&lt;/a&gt;, as well as at many locations across the 'net, with varying degrees of accuracy, reproducibility, and clarity. As you mentioned, you can do just about every molbio assay with a kit nowadays, and the manufacturer's websites (like &lt;a href=&quot;http://www.qiagen.com/resources/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Qiagen's&lt;/a&gt;) are often great resources, and frequently (but not always) include some scientific background as well, if you want to go back to the literature. There are also sites (some independent, some sponsored) that cater to specialized areas of research. For example, I work in immunology, and the &lt;a href=&quot;http://www.humanimmunologyportal.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Human Immunology Portal&lt;/a&gt; is a pretty good resource for basic and advanced protocols and assays.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, there are quite a number of digital resources available, which I actually prefer because there is a greater chance that they are kept up-to-date, and will have new technological advances much more quickly than they are likely to show up in a revised edition of a book. Best of all, most of the online resources are free, and if you have academic access through your institution, you may be able to access some of the pay sites as well, such as the archives area from Cold Spring Harbor.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-09-29T23:23:04.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21753" PostTypeId="1" AcceptedAnswerId="21758" CreationDate="2014-09-29T23:48:21.967" Score="2" ViewCount="33" Body="&lt;p&gt;I'm sending the blood samples to a lab and this takes some time until the actual testing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some information on the tests.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TLI : &lt;a href=&quot;http://www.vcahospitals.com/main/pet-health-information/article/animal-health/trypsin-like-immunoreactivity/405&quot; rel=&quot;nofollow&quot;&gt;http://www.vcahospitals.com/main/pet-health-information/article/animal-health/trypsin-like-immunoreactivity/405&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CPLI : &lt;a href=&quot;https://www.vetstream.com/canis/Content/Lab_test/lab00522&quot; rel=&quot;nofollow&quot;&gt;https://www.vetstream.com/canis/Content/Lab_test/lab00522&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6682" LastActivityDate="2014-09-30T06:14:42.300" Title="Are the cpli and ctli tests time senstive(i.e. is it needed to test right away in order to get accurate results)?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21755" PostTypeId="1" CreationDate="2014-09-30T03:02:29.793" Score="6" ViewCount="320" Body="&lt;p&gt;Quite a lot of Latin binomials from different genera contain the same species name. For example, there are a number that reflect the physical properties of the species (Tables have the latin name, a translation, and the number of European species according to the &lt;a href=&quot;http://eunis.eea.europa.eu/&quot; rel=&quot;nofollow noreferrer&quot;&gt;European Nature Information System&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;nigr[a|o|um]    black        545&#xA;minim[us|a]     small        325&#xA;alb[us|um|a]    white        264&#xA;maxim[us|a]     big          166&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and some which reflect the way in which they become apparent to us humans&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;vulgar[is|e]    common       691&#xA;sativa          cultivated   70&#xA;domesticus      domesticated 19&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;as well as reduplication for particularly salient/familiar species (e.g. Gallus gallus, Mephitis mephitis)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I'm wondering why there are so many &lt;code&gt;elegans&lt;/code&gt; (471 European species on the database). It's particularly widespread, but meaning &quot;elegant&quot; or &quot;refined&quot;, it's a rather nondescript name to give. &lt;em&gt;Maybe&lt;/em&gt; someone might describe a species like this if they were &lt;em&gt;really&lt;/em&gt; running thin on defining characteristics, but if this is the reason, why would the name occur so often?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I'm fairly sure I'm missing something important about how species get named. What is/was the reason for naming so many species &quot;&lt;em&gt;elegans&lt;/em&gt;&quot;? Does it have perhaps have something to do with type species?&lt;/p&gt;&#xA;" OwnerUserId="180" LastEditorUserId="16866" LastEditDate="2017-04-26T19:45:05.697" LastActivityDate="2017-04-26T19:45:05.697" Title="What is the context in which a species gets the name &quot;elegans&quot;" Tags="&lt;nomenclature&gt;&lt;etymology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21756" PostTypeId="1" AcceptedAnswerId="21778" CreationDate="2014-09-30T03:39:21.850" Score="6" ViewCount="550" Body="&lt;p&gt;I need help identifying this bird.  (Some sort of heron?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was seen in Wuhan, Hubei, China, in September.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is very common there.  It can also swim like a duck, but I've only seen it do this once (it's not something they commonly do).  I can supply more photos upon request.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are two different individuals:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/f8oyv.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZeonQ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8194" LastActivityDate="2014-10-31T18:19:55.860" Title="What bird species is this? (Heron-like waterfowl from China)" Tags="&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21757" PostTypeId="2" ParentId="21704" CreationDate="2014-09-30T04:42:35.320" Score="0" Body="&lt;p&gt;Degraded eyesight can mean two basic processes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1)  Degradation of the imaging optics in your eye that focus light onto the retina such that light is not focused correctly, or&#xA;2)  Damage to the retina itself so that light is focused, but signals to your brain are not generated in response to light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What these two processes have in common is that they are problems with your eyes ability to process and interpret light.  Placing a mirror close to your eye (but outside of it) does not directly compensate for either of these problems because, other than transforming the coordinate system, it doesn't actually do anything to the light or to your eye.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Possibly what you are thinking of by &quot;degraded&quot; eye sight is simply being near or far sighted, which is the specific case where your vision still works normally, but your eye does not under some conditions (nearby for farsighted, etc) due to a loss of accommodation (the physical flexing the lens of your eye that adjusts its focusing).  In this case, a curved mirror can be chosen that operates just like eye glasses.&lt;/p&gt;&#xA;" OwnerUserId="9561" LastActivityDate="2014-09-30T04:42:35.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21758" PostTypeId="2" ParentId="21753" CreationDate="2014-09-30T06:14:42.300" Score="2" Body="&lt;p&gt;From doing a bit of research, I quote&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The various analytes have different stability in serum. &lt;strong&gt;Serum TLI and&#xA;  PLI are stable for up to 2 weeks at room temperature.&lt;/strong&gt; However, serum&#xA;  folate shows limited stability at room temperature. Therefore, serum&#xA;  samples for folate analysis should be kept at 4ºC for not longer than&#xA;  48 hours, but freezing is preferred. Furthermore, folate is light&#xA;  sensitive and samples should be stored in the dark or wrapped in foil (&lt;a href=&quot;http://vetmed.tamu.edu/gilab/service/faq&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, it should be fine if the tests are conducted in two weeks. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-09-30T06:14:42.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21759" PostTypeId="2" ParentId="21748" CreationDate="2014-09-30T06:31:44.010" Score="1" Body="&lt;p&gt;Theoretically if you could somehow activate the G-protein-coupled receptors (GPCRs) corresponding to sweet stimuli without absorption of the sugar into the bloodstream than it may be possible to &quot;trick&quot; the brain. (See this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21481196&quot; rel=&quot;nofollow noreferrer&quot;&gt;review&lt;/a&gt; to learn more about how taste signaling works). However, the process of absorbing sugars into the blood stream begins in the mouth (see this &lt;a href=&quot;https://biology.stackexchange.com/questions/7019/what-nutrients-can-humans-absorb-in-the-mouth&quot;&gt;question&lt;/a&gt;), so testing your idea would be nearly impossible. &lt;/p&gt;&#xA;" OwnerUserId="9562" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-09-30T06:31:44.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21760" PostTypeId="2" ParentId="21756" CreationDate="2014-09-30T07:55:00.140" Score="3" Body="&lt;p&gt;I'd go with juvenile striated heron. I ruled out others such as the &lt;a href=&quot;http://www.pbase.com/tombac/image/134271698&quot; rel=&quot;nofollow&quot;&gt;chinese pond heron&lt;/a&gt; because of the spotted wing plumage and slightly different shape of the patch around the eye. The &lt;a href=&quot;http://www.google.se/imgres?imgurl=&amp;amp;imgrefurl=http%3A%2F%2Fwww.birdinginformation.com%2Fbirds%2Fherons-bitterns-egrets%2Fblack-crowned-night-heron%2F&amp;amp;h=0&amp;amp;w=0&amp;amp;tbnid=5G3V-IauqM4e9M&amp;amp;zoom=1&amp;amp;tbnh=188&amp;amp;tbnw=268&amp;amp;docid=z9MbczxKVoi_YM&amp;amp;tbm=isch&amp;amp;ei=nGAqVNKJL6uiygObtILYCQ&amp;amp;ved=0CAQQsCUoAA&quot; rel=&quot;nofollow&quot;&gt;night heron&lt;/a&gt; seems to have a more red eye than the &lt;a href=&quot;http://www.gobirding.eu/Photos/StriatedHeron.php&quot; rel=&quot;nofollow&quot;&gt;striated heron&lt;/a&gt; and appears to have a stubbier beak.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.arkive.org/striated-heron/butorides-striata/&quot; rel=&quot;nofollow&quot;&gt;Arkive&lt;/a&gt; is a good place to see a lot of pictures of birds, &lt;a href=&quot;http://carolinabirds.org/INDEX/WLD_indx_A.htm&quot; rel=&quot;nofollow&quot;&gt;this is a good birding site&lt;/a&gt;, and otherwise I use generic google searching (e.g. start with &quot;herons china&quot; or &quot;herons asia&quot;) - this at least helps narrow down the search quite substantially and is considerably cheaper than having a library of the worlds bird books!&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-09-30T07:55:00.140" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21763" PostTypeId="1" CreationDate="2014-09-30T13:03:44.127" Score="5" ViewCount="38413" Body="&lt;p&gt;Which term is used to calculate water potential? Does osmotic potential mean the same as solute potential?&lt;/p&gt;&#xA;" OwnerUserId="9569" LastEditorUserId="6" LastEditDate="2014-10-01T09:56:47.753" LastActivityDate="2020-06-18T12:40:06.030" Title="What is the difference between osmotic potential and osmotic pressure?" Tags="&lt;membrane-transport&gt;&lt;osmosis&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21766" PostTypeId="1" AcceptedAnswerId="21768" CreationDate="2014-09-30T15:16:59.727" Score="6" ViewCount="4704" Body="&lt;p&gt;Last year I got a moderately-deep cut on my finger, and it left a scar. Six months later, the scar is still there. On the other hand, I've had lots of other cuts on my fingers, though none have left scars. Why is this? Is scarring related to the severity of the cut, or something else?&lt;/p&gt;&#xA;" OwnerUserId="9458" LastActivityDate="2014-09-30T19:26:18.793" Title="Why do some cuts leave scars, while others do not?" Tags="&lt;skin&gt;&lt;injury&gt;&lt;healing&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21767" PostTypeId="2" ParentId="21650" CreationDate="2014-09-30T15:57:19.283" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;How do cells know whether they should grow the hyaline cartilage?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Both growth factors and cytokines are involved but the trigger mechanism is unclear [1].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bones grow in length at the level of epiphyseal plate where chondrocytes produce hyaline cartilage which by addition of calcium and phosphorus ions turns into hard bone [2].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is believed that the growth process is under the regulation of local mediators like cytokines and growth factors:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In recent years, a large number of cytokines have been discovered and their molecular structures and biological activities described. A surprisingly large number of cytokines have been shown to affect skeletal tissues, at least experimentally, making this a complex topic, but one which is furthering knowledge of how the cellular events of bone growth may be so precisely regulated [3].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Ossification. (2014, July 3). In Wikipedia, The Free Encyclopedia. Retrieved 15:47, September 30, 2014, from &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Ossification&amp;amp;oldid=615387908&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Ossification&amp;amp;oldid=615387908&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.personal.psu.edu/staff/m/b/mbt102/bisci4online/bone/bone5.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.personal.psu.edu/staff/m/b/mbt102/bisci4online/bone/bone5.htm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;J.S. Price, B.O. Oyajobi and R.G.G. Russell. The cell biology of bone growth. Available from &lt;a href=&quot;http://archive.unu.edu/unupress/food2/UID06E/UID06E0U.HTM&quot; rel=&quot;nofollow&quot;&gt;http://archive.unu.edu/unupress/food2/UID06E/UID06E0U.HTM&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-09-30T15:57:19.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21768" PostTypeId="2" ParentId="21766" CreationDate="2014-09-30T19:12:12.773" Score="6" Body="&lt;p&gt;This depends on a number of factors. Here are the first two that come to mind:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Is the cut deep enough to reach the dermis (this is the layer below the epidermis) where scar tissue will form?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) What is your general state of health, and was there an infection at the site of the cut, which would have altered the normal healing process. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, not all cuts are created equal, especially if some are deeper than others and become infected. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This article studied scratch depth&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17440346&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/17440346&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9571" LastEditorUserId="9571" LastEditDate="2014-09-30T19:26:18.793" LastActivityDate="2014-09-30T19:26:18.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21770" PostTypeId="2" ParentId="21755" CreationDate="2014-09-30T20:41:00.897" Score="5" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Since &quot;meaningfulness&quot; &lt;a href=&quot;http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp?nfv=true&amp;amp;article=11&quot; rel=&quot;nofollow&quot;&gt;is not listed&lt;/a&gt; among the requirements for new names, any author is free in his choice of name derivation. [There are nevertheless some natural restrictions, such that new names are to be treated as Latin irrespective of the etymology and should follow Latin grammar (with botanical nomenclature being &lt;a href=&quot;http://www.iapt-taxon.org/nomen/main.php?page=art60&quot; rel=&quot;nofollow&quot;&gt;much more meticulous&lt;/a&gt; in this respect).]&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There are indeed some cases when the name of the species &lt;a href=&quot;http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp?nfv=true&amp;amp;article=68&quot; rel=&quot;nofollow&quot;&gt;may be meaningful&lt;/a&gt; for the purpose of the choice of type species (the &quot;typicus/a/um&quot; names and tautonomous names like &quot;Glis glis&quot;), but &quot;elegans&quot; doesn't belong here.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So, the high frequency of &quot;elegans&quot; has nothing to do with typification and reflects nothing else than the will of authors to reflect their emotions. One recurrent cause of &quot;elegans&quot;-names among paleontologists, for example, is good preservation of the respective fossil material. [By the way, there are even more emotionally loaded (but less frequent) names like &quot;mirabilis/e&quot; or &quot;enigmatica/us/um&quot;.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since providing etymologies for names alongside formal descriptions of new species at a certain moment became an official &lt;a href=&quot;http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp?nfv=true&amp;amp;article=25&quot; rel=&quot;nofollow&quot;&gt;recommendation&lt;/a&gt;, you can make your own collection of causes people provide to justify their choice of &quot;elegans&quot; as species names.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;: I've just found this &lt;a href=&quot;http://books.google.de/books?id=CyHwAAAAMAAJ&amp;amp;pg=PA97&quot; rel=&quot;nofollow&quot;&gt;revelation&lt;/a&gt;: (Oxytomoides elegans, fossil bivalve) &quot;Etymology. Elegans, Latin for choice or select, referring to what we regard as esthetically pleasing appearance of the species&quot;. &lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-09-30T22:58:34.947" LastActivityDate="2014-09-30T22:58:34.947" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21771" PostTypeId="1" AcceptedAnswerId="21773" CreationDate="2014-09-30T21:01:01.780" Score="1" ViewCount="1760" Body="&lt;p&gt;I want to know if it would be possible for a surgeon to &quot;shut off&quot; a person's senses without causing paralysis of any kind. The person would have to maintain their ability to speak and move, but not be able to hear their own voice or sense the physical world around them at all. &lt;/p&gt;&#xA;" OwnerUserId="9572" LastActivityDate="2014-10-01T00:16:23.323" Title="Can you disconnect sensation from the brain without destroying muscle functions?" Tags="&lt;physiology&gt;&lt;neuroscience&gt;&lt;neuroanatomy&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21772" PostTypeId="1" AcceptedAnswerId="21776" CreationDate="2014-09-30T23:32:58.287" Score="60" ViewCount="52025" Body="&lt;p&gt;Arthropods have 6 or more limbs and arthropods with 6 limbs appear to move faster than arthropods with 8 limbs so I wonder whether this might have something to do with fast and efficient locomotion. But, this is just a guess. I wonder what the official explanation is, if it exists.&lt;/p&gt;&#xA;" OwnerUserId="9573" LastActivityDate="2019-03-26T15:13:38.757" Title="Why don't mammals have more than 4 limbs?" Tags="&lt;evolution&gt;&lt;mammals&gt;" AnswerCount="5" CommentCount="7" FavoriteCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="21773" PostTypeId="2" ParentId="21771" CreationDate="2014-10-01T00:11:24.830" Score="4" Body="&lt;p&gt;Even if it were possible to selectively destroy sensory (afferent) nerves alone, the individual would not be able to walk/move normally immediately afterwards, because there would be no environmental stimuli with which to orient one's actions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two of the senses people often overlook are &lt;em&gt;balance&lt;/em&gt; (or spatial orientation) and &lt;em&gt;proprioception&lt;/em&gt; (where the body parts are with respect to each other and the physical world). (Some people lump the two; it's easier to think of them independently, because they really do quite different things.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Proprioception (and closely associated &lt;em&gt;kinesthetics&lt;/em&gt;) is possible because of nerve signals from skin, tendons, muscles, and joints. This gives us the senses of limb position and movement, the sense of tension or force, the sense of effort, the sense of &lt;em&gt;gravity&lt;/em&gt;.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Patients (lacking proprioceptive feedback) made large directional and amplitude errors when performing a reaching task without visual feedback....The errors were associated with differences in velocity and acceleration for movements in different directions.&lt;sup&gt;[2]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Basically, without proprioception, you could not touch your little finger to your thumb without visual input, let alone actually perform more complex voluntary movements successfully.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The vestibular system exists through input from three semicircular canals located in the inner ear on each side. The canals are oriented at (basically) 90° angles to each other so that we can maintain our balance no matter which position our head is in. These are also connected to one's ocular reflexes. Together they're called the vestibolo-occular system, which functions as a reflex (VOR).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Three sensory systems, vestibular, visual, and somatosensory/proprioceptive, serve our sense of balance. Each of these systems provides unique sensory information to the brain where it is integrated (often in complex ways) to produce a final motor output to muscle groups for maintaining gaze, head and body posture, and controlling static and dynamic balance.&lt;sup&gt;[3]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Without these systems, we would be completely unable to get or stay in a standing position. We certainly could not walk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, long story short, the answer is no. Not only is it surgically impossible, but if it were, you would not have a coordinated, working body left. Eventually even speech would be affected (as proprioceptors on the mouth are involved in speaking).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://physrev.physiology.org/content/81/2/539?ijkey=4bef0a50592685f7746c89010deaddafa6a6dcf2&amp;amp;keytype2=tf_ipsecsha&quot; rel=&quot;nofollow&quot;&gt;Proprioception From a Spinocerebellar Perspective&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://jn.physiology.org/content/73/1/347?ijkey=08270d1ce45ec1cc6faf7b799071b85dc25e0ae6&amp;amp;keytype2=tf_ipsecsha&quot; rel=&quot;nofollow&quot;&gt;mpairments of reaching movements in patients without proprioception. I. Spatial errors&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2975108/&quot; rel=&quot;nofollow&quot;&gt;Anatomical and Physiological Considerations in Vestibular Dysfunction and Compensation&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-10-01T00:11:24.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21774" PostTypeId="2" ParentId="21771" CreationDate="2014-10-01T00:16:23.323" Score="0" Body="&lt;p&gt;The nerves for sensation do travel intimately close to motor nerves outsides the spinal cord. In these locations only disease processes can preferentially target a particular class of nerves. Diabetic neuropathy is a common condition causing this kind of peripheral nerve injury resulting in sensory loss. In the spinal cord, afferent (incoming) and efferent (outgoing) conduction pathways are segregated into bundles so a traumatic event can cause a selective deficit of sensation or movement of a region. Further up the chain (brain) entire functions are segregated so it is possible to create not only deficits of physical regions but of specific complex motor functions or sensory processes. Interestingly most of our senses are handled by cranial nerves that are not in the spinal cord. These nerves are generally purely sensory.&lt;/p&gt;&#xA;" OwnerUserId="9560" LastActivityDate="2014-10-01T00:16:23.323" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21775" PostTypeId="1" AcceptedAnswerId="23866" CreationDate="2014-10-01T00:44:13.097" Score="2" ViewCount="763" Body="&lt;p&gt;I've been trying to find a comprehensive explanation concerning the nature of the 'delay' in neurons' delayed rectifier potassium channels. As it's written in my intro to neuroscience textbook, these channels are voltage gated and become activated when the typical neuronal membrane reaches an electrical potential of approx. -40mV. While the channel is activated at this point, it only opens up after a delayed period of approx 1ms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm mostly trying to clarify that this isn't an confusion in wording and that delayed rectifiers aren't actually activated when the inner membrane reaches a charge of approx +40mV which would be correlated (at least in textbook examples) with the '1ms delay', but caused by the actually typical charge observed at approx 1 ms of delay during an action potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks so much. Let me know if I can clarify something. I know this wasn't necessarily so well asked&lt;/p&gt;&#xA;" OwnerUserId="9574" LastActivityDate="2014-11-10T12:40:01.137" Title="What is the mechanism responsible for the 'delay' in delayed rectifier potassium channels?" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;&lt;cell-membrane&gt;&lt;action-potential&gt;&lt;membrane-transport&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21776" PostTypeId="2" ParentId="21772" CreationDate="2014-10-01T00:58:16.140" Score="84" Body="&lt;p&gt;&lt;strong&gt;Number of legs in terrestrial vertebrates&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not only do mammals have four legs but actually all terrestrial vertebrates (which include mammals) have four legs. There are slight exceptions though as some lineages have lost their legs. Typically snakes have no legs anymore. &lt;a href=&quot;http://www.nature.com/nature/journal/v440/n7087/abs/nature04413.html&quot; rel=&quot;noreferrer&quot;&gt;Apesteguia and Zaher (2006)&lt;/a&gt; discuss the evolution of snakes legs reduction and report a fossil of snakes with a robust sacrum. &lt;a href=&quot;http://en.wikipedia.org/wiki/Cetacea&quot; rel=&quot;noreferrer&quot;&gt;Cetaecea (whales and friends)&lt;/a&gt; have lost their hind legs but we can still spot them on the skeleton. See for example the orca (killer whale, easily recognizable to its teeth) on the picture below. Pay attention to the small bones below its vertebral column at the level on the left side of the picture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also want to draw attention to the importance of the definition of legs. I guess that we would call something a pair of legs if it is constructed using a similar developmental pathway than current existing legs. If we are using some broader definition, then a &lt;a href=&quot;http://en.wikipedia.org/wiki/Prehensile_tail&quot; rel=&quot;noreferrer&quot;&gt;prehensile tail&lt;/a&gt; as found in some new world monkeys, for example, could be considered as a leg (but only a single leg, not a pair of legs obviously). A list of animals having a prehensile tail can be found &lt;a href=&quot;http://en.wikipedia.org/wiki/Prehensile_tail#Animals_with_fully_prehensile_tails&quot; rel=&quot;noreferrer&quot;&gt;here (Wikipedia)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Did you say Natural Selection?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think (might be wrong) that you have too selectionist a view of evolution. What I mean is that you are wondering why mammals have four legs and you're looking for an explanation of the kind &quot;because mammal have this kind of need of locomotion and for this purpose four is the most optimal number of legs&quot;. Consider the following sentence: &quot;If there is a need, natural selection will find a way!&quot;. This sentence is wrong! Evolution is not that easy. This false view of evolution is sometimes referred to as panselectionist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reality is that it is not easy to evolve such a developmental pathway as drastic as having an extra pair of legs that are well integrated into the body of the carrier of this new trait. Such an individual would need a brain, a nerve code, a heart and some other features that are adapted to have extra legs. Also, assuming such a thing came to existence it is rather complicated to imagine how it could be selected for. To go slightly further, you have to realize that there are many stochastic processes in evolution (including mutation and random variation in reproductive success) and an organism is a piece of complex machinery and is not necessarily easily transformable to some other form that would be more efficient (have higher reproductive success). Often going from one form to another may involve a &quot;valley crossing&quot; meaning that if several mutations are needed, intermediate forms may have low reproductive success and therefore a high amount of genetic drift (stochasticity in reproductive success) to cross such valley of low reproductive success. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Shifting_balance_theory&quot; rel=&quot;noreferrer&quot;&gt;shifting balance theory&lt;/a&gt;. Finally, even if there is selection for another trait, it may take time for the mean trait in the population to shift especially if there is only little genetic variance. A complete discussion on why the sentence &quot;If there is a need, natural selection will find a way!&quot; is wrong would fill up a whole book.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/royprsb/205/1161/581.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;Gould (1979)&lt;/a&gt; is a classic article on the subject and is very easy to read even for a layperson. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why 4 legs?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Terrestrial vertebrates have four legs because they evolved from a fish ancestor that had four members that were not too far from actual legs (members that could &quot;easily&quot; evolve into legs). This is what we call a &lt;a href=&quot;https://en.wikipedia.org/wiki/Computational_phylogenetics#Phylogenetic_signal&quot; rel=&quot;noreferrer&quot;&gt;phylogenetic signal&lt;/a&gt;. The explanation is as simple and basic as that. You can have a look at the diversity of terrestrial vertebrates &lt;a href=&quot;http://tolweb.org/Terrestrial_Vertebrates/14952&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; (click on the branches).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Number of legs in invertebrates&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Arthropoda (Spiders (and other chelicerata), insects (and other hexapods), crustaceans (crabs, shrimps…) and Myriapoda (millipedes) and Trilobite as well)) evolved from a common ancestor who had a highly segmented body. From this ancestor, many groups have fused some segments. In these taxa, each pair of legs is attached to a particular segment (I don't think the segments are still visible in spiders today). In insects, for example, all 6 legs are attached to the thorax but to 3 different segments of the thorax, the pro- meso and meta-thorax (see below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note, it is interesting to know that the wings in insects did not evolve from the legs (as it is the case in birds and bats). There are two competing hypotheses for the origin of insect wings. Wings either developed from gills or from sclerite (chitine plate, the hard part of the insect). When insect first wings, they actually evolved three pairs of wings (one on each segment of the thorax). At least one pair has then been lost in all modern species. In the diptera, a second pair of wings have been lost and are replaced by halteres, particularly easy to spot in craneflies (see below picture). In millipedes, the link between segmentation and legs is even more obvious (see picture below). You can have a look at the diversity of Arthropoda &lt;a href=&quot;http://tolweb.org/Arthropoda/2469&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; (click on the branches).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Pictures&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/22Zb4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1NRYn.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/M6dC2.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Qcemi.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update 1&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Asking how likely it is for a given population to evolve a given trait is extremely hard to answer. There are two main issues: 1) a definition of the question issue and 2) a knowledge issue. When asking for a probability one always needs to state the a priori knowledge. If everything is known a priori, then there is nothing stochastic (outside quantum physics). So to answer the question one has to decide what we take for granted and what we don't. The second issue is a knowledge issue. We are far from having enough knowledge in protein biophysics (and many other fields)  to answer that question. There are so many parameters to take into account. I would expect that creating a third pair of legs would need major changes and therefore one mutation will never be enough in order to develop a third pair of legs. But, no I cannot cite you any reference for this, I am just guessing! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following the wings example in insects. Insects have had three pairs of wings. While some mutation(s) prevented the expression of the third (the first actually) pair many of the genetic information for this third pair remain in the genotype of insects as they still use it for the two other pairs. Taking advantage of that, &lt;a href=&quot;http://en.wikipedia.org/wiki/Treehopper&quot; rel=&quot;noreferrer&quot;&gt;Membracidae (treehoppers)&lt;/a&gt; developed some features using a similar biochemical pathway than the one used to develop wings. Those structures are used as protection or &lt;a href=&quot;http://en.wikipedia.org/wiki/Batesian_mimicry&quot; rel=&quot;noreferrer&quot;&gt;batesian mimicry&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update 2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's imagine that an extremely unlikely series of mutations occur that create some rodent with 6-legs. Let's imagine this rodent with six legs has a larger heart in order to pump blood to these extra legs and it has a brain that is adapted to using six legs and some changes in its nerve cord so that it can control its 3rd pair of legs. Will this rodent have higher reproductive success than other individuals in the population? Well… let's imagine that with its six legs, it can run faster or whatever and has a very high fitness. How would the offspring of a six-leg mother (or father) and a four-leg father (or mother) look like? Will it be able to reproduce? See the issue is that it is hard for such trait to come to existence because 1) it needs many steps (mutations) and 2) it is hard to imagine how it could be selected for. For those reasons, there exist no vertebrates with 6 fully functional legs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well, let's assume it does and in consequence, after 200 generations or so, the whole population is only made of 6-legged individuals. Maybe the species got extinct then and no fossil record has ever been found. This is possible. It is not because something has existed that we necessarily find something in the fossil record.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-26T15:13:38.757" LastActivityDate="2019-03-26T15:13:38.757" CommentCount="12" ContentLicense="CC BY-SA 4.0" />
  <row Id="21778" PostTypeId="2" ParentId="21756" CreationDate="2014-10-01T03:27:45.490" Score="1" Body="&lt;p&gt;Based on some external advice, I believe it might be a juvenile night heron (&lt;em&gt;Nycticorax nycticorax&lt;/em&gt;), the only remaining question being why I didn't see any adults.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.google.com/search?tbm=isch&amp;amp;q=Nycticorax+nycticorax+juvenile&quot; rel=&quot;nofollow&quot;&gt;Link to Google Image search results&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update:&lt;/strong&gt; I went back to the same location today and saw some adult night herons, which convinced me that these were juveniles of the same species.&lt;/p&gt;&#xA;" OwnerUserId="8194" LastEditorUserId="8194" LastEditDate="2014-10-01T12:24:56.710" LastActivityDate="2014-10-01T12:24:56.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21779" PostTypeId="1" CreationDate="2014-10-01T04:58:37.897" Score="-1" ViewCount="96" Body="&lt;p&gt;In the movie the Matrix Agent Smith said something like, 'all animals strive to find a natural 'equilibrium' with there environment ,... a harmonious existence with their ecosystem', ( forgive misquoting). Is this true that each animal 'does' a lot of activity whether by instinct or an ad-hoc form of 'simple' planning to 'cooperate' with it's environment ,or exist 'harmoniously with it?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastEditorUserId="6195" LastEditDate="2014-10-02T02:40:09.307" LastActivityDate="2021-01-19T21:40:37.507" Title="About animal ecology and one view of this in science fiction" Tags="&lt;ecology&gt;&lt;environment&gt;" AnswerCount="3" CommentCount="0" ClosedDate="2021-01-29T20:53:12.870" ContentLicense="CC BY-SA 3.0" />
  <row Id="21781" PostTypeId="2" ParentId="2382" CreationDate="2014-10-01T05:33:26.213" Score="3" Body="&lt;p&gt;Anti-oxidants affect human metabolism by altering the redox states of the cell and redox-regulated functions and signaling mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following quotes are from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3267846/&quot; rel=&quot;nofollow&quot;&gt;The Redox Stress Hypothesis of Aging&lt;/a&gt; (Free Radic Biol Med. Feb 2012)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;More recently, in a major conceptual shift, ROS have been found to be&#xA;  physiologically vital for signal transduction, gene regulation, and&#xA;  redox regulation, among others, implying that their complete&#xA;  elimination would be harmful. An alternative notion, advocated here,&#xA;  termed the &quot;redox stress hypothesis,&quot; proposes that aging-associated&#xA;  functional losses are primarily caused by a progressive pro-oxidizing&#xA;  shift in the redox state of the cells, which leads to the&#xA;  overoxidation of redox-sensitive protein thiols and the consequent&#xA;  disruption of the redox-regulated signaling mechanisms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Many proteins contain cysteine residues which can undergo reversible modifications such as S-nitrosylation and S-glutationylation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The redox state affects the oxidation levels of these redox-sensitive protein thiols and the consequent disruption in protein activity and the redox-regulated signaling mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under normal conditions the usual types of oxidation modifications of these protein thiols are reversible, and is a way to protect the thiol in transient periods of oxidative stress.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the redox state shifts to a more oxidised point then more irreversiable protein thiol modifications occurs, i.e. damages the protein.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As shown in Figure 6, prolonged exposure of sulfenic acid, formed at&#xA;  the active or regulatory sites, to H2O2, sequentially leads to the&#xA;  formation of sulfinic- (−SO2H) and sulfonic-acids (−SO3H), which are&#xA;  deemed to be largely irreversible reactions. In addition, protein&#xA;  disulfides may undergo over-oxidation, leading to the formation of&#xA;  thiosulfenate and thiosulfonate, which are also believed to be&#xA;  relatively irreversible reactions. The level of oxidation of protein&#xA;  cysteinyl thiolates depends upon the strength (concentration) and the&#xA;  duration of exposure to H2O2.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Protein activity and enzyme catalytic efficiency which affects metabolism, such as sirtuins, are affected by the these thiol redox modifications.&#xA;(eg &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20385619&quot; rel=&quot;nofollow&quot;&gt;SIRT1 is a redox-sensitive deacetylase that is post-translationally modified by oxidants and carbonyl stress&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24451382&quot; rel=&quot;nofollow&quot;&gt;A redox-resistant sirtuin-1 mutant protects against hepatic metabolic and oxidant stress.&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The primary arbiter of redox state is glutathione, i.e. the GSH/GSSG couple. The effect of anti-oxidants appears to vary depending on whether it affects the redox state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The antioxidant activities of SOD and catalase neutralize the ROS species, O2− and H2O2, without having a direct impact on glutathione redox state.  However this frees up glutathione from having to neutralize the ROS species, which it can do so with the glutathione peroxidase enzyme.&lt;/p&gt;&#xA;" OwnerUserId="8349" LastEditorUserId="8349" LastEditDate="2014-10-01T07:59:53.683" LastActivityDate="2014-10-01T07:59:53.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21782" PostTypeId="2" ParentId="21772" CreationDate="2014-10-01T06:20:13.980" Score="16" Body="&lt;p&gt;I think I might interpret your question as asking, not just why don't mammals have more than four limbs, but why arthropods have more variety.  Insects have six, but others have eight, ten, or more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Partly there are just many more species of arthropods.  80% of animal species are some sort of arthropod, and some lineages of arthropods are distantly related to each other because arthropods as a group have existed since the Cambrian period.  With so many more species, it's no surprise that they've managed to tack on some extra variety.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although it might seem that insects and spiders are more closely related than, say, humans and fish, the reverse is actually true.  In fact, insects split off from other arthropods at approximately the same time that fish were diversifying into the three main lineages that would eventually become cartilaginous fish (sharks &amp;amp; rays), ray-finned (&quot;regular&quot;) fish, and lobe-finned fish (coelacanths and lungfish).  All of these things happened at approximately the same time, geologically speaking, at around 400 million years ago.  Some ancient lungfish crawled up onto land a short while after, giving rise to land animals.  So in light of this, it's not really surprising that arthropods would have so much diversity in body plan - you don't look much like a leafy sea dragon (I hope).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But perhaps another way of looking at it is in the difficulty involved in adapting the body plans of these different types of animals.  Arthropods have segmented bodies.  In some arthropods, especially the myriapoda (centipedes, millipedes and so on), there's a pretty straightforward arrangement of one segment to one pair of legs (excluding the head).  Vertebrates have a segmented body plan too, but our segments aren't quite so well-separated.  In vertebrates, a &quot;segment&quot; is approximately equal to one vertebra.  So since vertebrates aren't in the habit of attaching a pair of legs to each vertebra, it's harder to grow more legs.  Instead, vertebrates have internal skeletons, with the familiar hips and shoulders in land animals.  Vertebrates do have good luck adapting the internal structure when they need to.  Most use the traditional four-leg layout, but humans, birds, whales, and snakes have all made pretty significant changes to it.  But internally, it's still the familiar hips and shoulders - even snakes still have the necessary bones.  Given another few hundred million years, they might disappear entirely, but it seems like the basic bone structure is tough to change.  Who knows, in a hundred million years, the far future descendants of snakes might end up with legs again, and grow six or eight instead of four!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, overall, I'd say that the two main reasons are that the arthropod body plan is just a little more flexible due to its higher degree of modularity, and that different kinds of arthropods are actually more distantly related than you might expect.&lt;/p&gt;&#xA;" OwnerUserId="9575" LastActivityDate="2014-10-01T06:20:13.980" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21786" PostTypeId="1" CreationDate="2014-10-01T09:01:58.323" Score="4" ViewCount="26828" Body="&lt;p&gt;Is it common to forget a 4 or 5 numeric code which has been used extensively for months and well remembered?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's an article on the &lt;a href=&quot;http://www.theguardian.com/commentisfree/2007/aug/20/money.comment&quot; rel=&quot;nofollow&quot;&gt;guardian&lt;/a&gt; describing this phenomenon and by the number of comments it seems quite common yet no scientific aspect trying to solve the mistery.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it some common phenomenon of the brain? Some erasing of irrelevant numeric things happening during sleep?&lt;/p&gt;&#xA;" OwnerUserId="9580" LastEditorUserId="1590" LastEditDate="2014-10-01T13:16:19.437" LastActivityDate="2018-02-21T20:49:53.700" Title="Why do we suddenly forget things, like PIN or phone numbers, that we've known for years?" Tags="&lt;brain&gt;&lt;memory&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21787" PostTypeId="2" ParentId="21763" CreationDate="2014-10-01T09:27:42.577" Score="4" Body="&lt;p&gt;Osmotic pressure: pressure applied by a solution to prevent the inward flow of water across a semi-permeable membrane. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Osmotic potential: the potential of water molecules to move from a hypotonic solution to a hypertonic solution across a semi-permeable membrane. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Osmotic pressure can be calculated using the following formula:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$Π = iMRT$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where&#xA;$Π$ is the osmotic pressure in atm&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$i$ = van 't Hoff factor of the solute.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$M$ = molar concentration in mol/L&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$R$ = universal gas constant = 0.08206 L·atm/mol·K&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$T$ = absolute temperature in K&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following &lt;a href=&quot;http://chemistry.about.com/od/workedchemistryproblems/a/Osmotic-Pressure-Calculation-Example.htm&quot; rel=&quot;nofollow&quot;&gt;page&lt;/a&gt; has a worked out example. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your question on solute potential vs osmotic potential, the answer is that they are indeed the same. You can compare the formula for $\Psi_{\pi}$ on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Water_potential&quot; rel=&quot;nofollow&quot;&gt;wikipedia page&lt;/a&gt; and the page of this &lt;a href=&quot;http://en.wikipedia.org/wiki/Water_potential&quot; rel=&quot;nofollow&quot;&gt;pearson textbook&lt;/a&gt;. These formulas are the same:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\Psi_{\pi} = -Π =-iMRT$  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there's a simple relationship between osmotic pressure and osmotic potential. &lt;/p&gt;&#xA;" OwnerUserId="9573" LastActivityDate="2014-10-01T09:27:42.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21788" PostTypeId="2" ParentId="21786" CreationDate="2014-10-01T12:00:12.173" Score="2" Body="&lt;p&gt;Forgetfulness is a common phenomenon that tends to increase with age. It usually affects short term memories but it can affect long term ones too. Here are some possible causes which I quote from &lt;a href=&quot;http://www.healthline.com/symptom/memory-loss&quot; rel=&quot;nofollow&quot;&gt;Healthline&lt;/a&gt; (the full list available at that link):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;sleep deprivation&lt;/li&gt;&#xA;  &lt;li&gt;use of alcohol or drugs and some prescription medications&lt;/li&gt;&#xA;  &lt;li&gt;lack of oxygen to the brain&lt;/li&gt;&#xA;  &lt;li&gt;migraine&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It can happen at any age and it is normal if (quoting Deane Alban, &lt;a href=&quot;http://bebrainfit.com/lifestyle/drains/memory-loss-normal-serious/&quot; rel=&quot;nofollow&quot;&gt;Memory Loss: When It’s Normal and When It’s Serious&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Are you overworked and stressed out? Are you eating poorly? Are you on a low-fat diet or skipping meals to lose weight?  Do you struggle with insomnia? Do you drink too much?&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;If you answer “yes” to any of these questions, it’s likely you are losing your memory because your lifestyle is catching up with you. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You mention loss during sleep in your question. Sleep affects memories (see &lt;a href=&quot;http://www.webmd.com/sleep-disorders/sleep-deprivation-effects-on-memory&quot; rel=&quot;nofollow&quot;&gt;WebMD&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Sleep_and_memory&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;deprivation of sleep leads to memory loss&lt;/li&gt;&#xA;&lt;li&gt;during sleep brain selects &lt;em&gt;relevant&lt;/em&gt; information gathered during the day and turns it into memories&lt;/li&gt;&#xA;&lt;li&gt;certain stages of sleep improve memories&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-10-01T12:00:12.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21789" PostTypeId="1" AcceptedAnswerId="21796" CreationDate="2014-10-01T12:35:04.597" Score="9" ViewCount="1186" Body="&lt;p&gt;It is fairly common for a woman to have one breast larger than the other.  I have also heard that, for a breastfeeding mother it is common for one of the breasts to yield a creamier milk whilst the other is more watery and has less nutritional value.&lt;/p&gt;&#xA;&lt;p&gt;Is there any correlation between the larger of the two breasts and the one which yields the fattier milk?&lt;/p&gt;&#xA;" OwnerUserId="1203" LastEditorUserId="5144" LastEditDate="2020-08-06T19:41:02.760" LastActivityDate="2020-08-06T19:41:02.760" Title="Does a bigger breast give creamier milk?" Tags="&lt;human-biology&gt;&lt;milk&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="21790" PostTypeId="1" AcceptedAnswerId="21801" CreationDate="2014-10-01T12:45:10.643" Score="9" ViewCount="27294" Body="&lt;p&gt;If the brain sends a signal to move what's the time it takes the signal to travel via neurons to motor neurons in hands, arms and legs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How fast do those signals travel?&lt;/p&gt;&#xA;" OwnerUserId="152" LastEditorUserId="1590" LastEditDate="2014-10-01T13:15:12.937" LastActivityDate="2017-12-20T19:15:39.910" Title="How long does a signal from the brain take to reach the limbs?" Tags="&lt;neuroscience&gt;&lt;movement&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21792" PostTypeId="2" ParentId="21790" CreationDate="2014-10-01T13:55:44.920" Score="1" Body="&lt;p&gt;It is generally not a one-way process. The lag also depends on which frequencies you look at (the brain and limbs kind of speak using several channels at the same time). Near 10 Hz the lag is few dozen milliseconds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look for articles about EMG and EEG (or MEG) coupling for more precise info. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Use the paper &lt;a href=&quot;http://homes.mpimf-heidelberg.mpg.de/~mhelmsta/pdf/2002%2520MEG%2520muscle%2520Review.pdf&quot; rel=&quot;nofollow&quot;&gt;http://homes.mpimf-heidelberg.mpg.de/~mhelmsta/pdf/2002%2520MEG%2520muscle%2520Review.pdf&lt;/a&gt; as a starting point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS. There is no neurons in limbs&lt;/p&gt;&#xA;" OwnerUserId="9585" LastEditorUserId="9585" LastEditDate="2014-10-01T17:59:29.330" LastActivityDate="2014-10-01T17:59:29.330" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21793" PostTypeId="2" ParentId="21772" CreationDate="2014-10-01T13:59:46.490" Score="10" Body="&lt;p&gt;The answer by Remi.B is excellent, I'll just attempt an explanation by way of gene networks:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In genetics we see new genes &quot;linking&quot; to the older genome by regulation pathways and by being &quot;fit&quot; only in the context of the existing genome. This has the effect of making the older genes indispensable. Change them and you rupture the whole mesh. If you want to increase the number of limbs, you'd have to take that up with the HOX genes, that control the basic body plan. These are awfully ancient, originating in the common ancestor of flies and humans [1]. So as a rule of thumb, these genes will also be awfully hard to mutate without ruining everything. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another line of reasoning is that the HOX genes not only appeared early in evolution, but they are also expressed early in the development of the embryo. When anything that goes on in development depends on what has preceded it, mutations in HOX genes has a bigger chance of ruining something than mutations that are only expressed late in development. &#xA;I'm going out on a ledge here, but consider that the color of hair, skin and eyes of a human baby are often not fully expressed until months after its birth and consider also the range of harmless variations in these colors. &#xA;These superficial colors don't affect anything else, so the corresponding genes are free to mutate into a great variety. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://www.nature.com/nrg/journal/v2/n1/box/nrg0101_033a_BX1.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nrg/journal/v2/n1/box/nrg0101_033a_BX1.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9583" LastEditorUserId="9583" LastEditDate="2016-05-09T09:01:50.600" LastActivityDate="2016-05-09T09:01:50.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21794" PostTypeId="1" CreationDate="2014-10-01T14:30:35.677" Score="1" ViewCount="120" Body="&lt;p&gt;5,6-dihydrouracil can be formed from cytosine after exposure of DNA to ionizing radiation under anoxic conditions &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8524238&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[&lt;strong&gt;Ref&lt;/strong&gt;]&lt;/sup&gt;&lt;/a&gt;. What are other ways by which 5,6-dihydrouracil is formed in DNA? What about 5,6-dihydroxyuracil? &lt;/p&gt;&#xA;" OwnerUserId="9587" LastEditorUserId="3340" LastEditDate="2014-12-14T13:38:00.117" LastActivityDate="2014-12-15T16:29:32.760" Title="5,6-dihydrouracil and 5,6-dihydroxyuracil - how they arise in DNA?" Tags="&lt;biochemistry&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21795" PostTypeId="1" CreationDate="2014-10-01T14:49:33.367" Score="3" ViewCount="1417" Body="&lt;p&gt;Which types of blood vessels can regenerate in humans/mammals?&#xA;From what I understand, arteries and arterioles can be created later in life, while this is not necessarily the case with veins. However I don't understand why damaged blood vessels in an eye recover, while this is not the case for other body parts. Also, I don't understand how angiogenic agents work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The types of blood vessels I've been thinking about include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Arteries&lt;/li&gt;&#xA;&lt;li&gt;Arterioles&lt;/li&gt;&#xA;&lt;li&gt;Capillaries&lt;/li&gt;&#xA;&lt;li&gt;Venules&lt;/li&gt;&#xA;&lt;li&gt;Veins&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Also, does the capability vary in different organs (e.g. blood vessels in a hand vs blood vessels in an eye)?&lt;/p&gt;&#xA;" OwnerUserId="9588" LastEditorUserId="3624" LastEditDate="2014-10-02T09:09:38.637" LastActivityDate="2019-09-26T16:11:48.553" Title="Which types of blood vessels can regenerate in humans/mammals?" Tags="&lt;human-biology&gt;&lt;blood-circulation&gt;&lt;physiology&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21796" PostTypeId="2" ParentId="21789" CreationDate="2014-10-01T16:22:55.490" Score="14" Body="&lt;p&gt;Because &lt;em&gt;mammary glands&lt;/em&gt; define us (mammals), the genetics of the ability to make milk has been of interest.&lt;sup&gt;[1]&lt;/sup&gt; Because we consume milk, we have a dairy industry. Because the industry places a monetary value to certain milk constituents, the genetics of milk component production has been a viable area of study&lt;sup&gt;[2]&lt;/sup&gt;. Since you are talking of cream production, we'll stick to that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The effect of nutrition and the environment (e.g. temperature) on milk fat production has long been known, and the ability to selectively breed for higher fat content has been exercised for decades if not longer&lt;sup&gt;[3][4]&lt;/sup&gt;, But the molecular genetics of milk fat production is only recently starting to be understood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mammals with the highest fat content are those in cold environments where an insulating layer of fat is required, such as gray seal milk (53.2% fat), whale milk (34.8%), and polar bear (31%). Humans and cows have approximately the same milk fat percentage (~4.5% fat).&lt;sup&gt;[5]&lt;/sup&gt;  The gene most studied to date is the &lt;em&gt;DTAG1 allele&lt;/em&gt;&lt;sup&gt;[6]&lt;/sup&gt; on chromosome 14.&lt;sup&gt;[7]&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is very clear that &lt;em&gt;genetically&lt;/em&gt; milkfat production is under the governance of part of chromosome 14.&lt;sup&gt;[7]&lt;/sup&gt;&lt;sup&gt;[8]&lt;/sup&gt; Since this chromosome is identical in both breasts, genetically one breast cannot make milk with a higher fat content than the other. Environmental and nutritional factors affect both breasts equally, so those can be ruled out as a source of fat percentage differences. The only factors left that can be variables are 1) fat content of one breast over the other, and 2) demand from one breast over the other. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In cows, more frequent milking increased milk production but decreased fat percentage; in the end, the effect on fat in milk was the least influenced by frequency of milking (significance questionable).&lt;sup&gt;[9]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Triglycerides in milk are synthesized in the smooth endoplasmic reticulum of the mammary &lt;em&gt;alveolar cell&lt;/em&gt; from precursor fatty acids and glycerol (obtained from blood nutrients), and while other cell types are involved in milk let down, etc., there is no known function of interstitial adipocytes (fat cells).&lt;sup&gt;[10]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That was the long answer. The short answer is: &lt;em&gt;no&lt;/em&gt;&lt;sup&gt;[11].&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://jbiol.com/content/8/4/37&quot; rel=&quot;nofollow noreferrer&quot;&gt;The origin and evolution of lactation&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://extension.psu.edu/animals/dairy/nutrition/nutrition-and-feeding/diet-formulation-and-evaluation/milk-components-understanding-the-causes-and-importance-of-milk-fat-and-protein-variation-in-your-dairy-herd&quot; rel=&quot;nofollow noreferrer&quot;&gt;Milk Components: Understanding the Causes and Importance of Milk Fat and Protein Variation in Your Dairy Herd&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12778586&quot; rel=&quot;nofollow noreferrer&quot;&gt;A review of nutritional and physiological factors affecting goat milk lipid synthesis and lipolysis&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[4] &lt;a href=&quot;http://www.ilri.org/InfoServ/Webpub/fulldocs/ilca_manual4/Factors.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Factors affecting milk composition&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[5] &lt;a href=&quot;http://healthyeating.sfgate.com/highest-percentage-fat-milk-animal-10855.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Highest Percentage of Fat in the Milk of an Animal&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[6] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1470998/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evidence for multiple alleles at the DGAT1 locus better explains a quantitative trait locus with major effect on milk fat content in cattle.&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[7] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459411/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Identification of novel single nucleotide polymorphisms in the DGAT1 gene of buffaloes by PCR-SSCP&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[8] &lt;a href=&quot;http://www.genomenewsnetwork.org/articles/03_02/bovine_genomics.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;Scientists pinpoint gene linked to fat in cow’s milk &lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[9] &lt;a href=&quot;http://www.journalofdairyscience.org/article/S0022-0302%2811%2900565-0/pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Covariance among milking frequency, milk yield, and milk&#xA;composition from automatically milked cows&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[10] &lt;a href=&quot;http://mammary.nih.gov/reviews/lactation/Neville001/&quot; rel=&quot;nofollow noreferrer&quot;&gt;MILK SECRETION: AN OVERVIEW&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[11] &lt;a href=&quot;https://biology.stackexchange.com/questions/21789/does-a-bigger-breast-give-creamier-milk/21796#21796&quot;&gt;Does a bigger breast give creamier milk?&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-10-01T17:54:02.330" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="21797" PostTypeId="2" ParentId="15764" CreationDate="2014-10-01T16:23:57.307" Score="1" Body="&lt;p&gt;I and II depend on the type of electrical signal applied to the axon. for III, most receptors can perceive other sense as well, so for example striking a vision receptor may produce the perception of light (even in complete darkness) - my guess is the you would feel pain, even if you could isolate the destructive signal away from nearby pain receptors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;search &quot;action potential&quot; in duckduckgo.com, it will get you going.&lt;/p&gt;&#xA;" OwnerUserId="9592" LastActivityDate="2014-10-01T16:23:57.307" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21798" PostTypeId="1" CreationDate="2014-10-01T17:44:05.687" Score="9" ViewCount="6432" Body="&lt;p&gt;I'm trying to figure out how I can download a file that represents the complete human DNA sequence. I don't care too much about the format – I'm able to write C++ code to parse it. FASTA seems like a simple format though. What I haven't figured out yet is where I can find a complete file – I have found what appear to be subsets of genes or other sequences or single chromosomes but aren't there 46 chromosomes to include or are some of those duplicates (i.e. 22 chromosomes + 2 sex chromosomes)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On this page, I have found this list of files under &quot;Human &gt; Genome assembly: GRCh38&quot; but it appears to be broken up by chromosome or something? If so, would I merge these? My goal is to display all the letters via projector onto a wall and I want to be able to point at it and tell someone, that's all the DNA for a human (not a subset). Also, to double check, it is a &quot;genome assembly&quot; I want right? By the way, I don't care about allele variants right now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please consider in your response that I am not familiar with much of the lingo, thank you.&lt;/p&gt;&#xA;" OwnerUserId="9594" LastActivityDate="2014-10-03T18:27:00.217" Title="How can I find a complete human genome file" Tags="&lt;dna-sequencing&gt;" AnswerCount="5" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21799" PostTypeId="2" ParentId="21798" CreationDate="2014-10-01T18:06:34.763" Score="11" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/guide/howto/dwn-genome/&quot;&gt;The National Centre for Biotechnology Information&lt;/a&gt; has a link to a genomes FTP site - on that page, there is a file labelled &lt;a href=&quot;ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/&quot;&gt;.../genomes/H_sapiens&lt;/a&gt; (this a direct link to that directory).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are numerous files therein.  From the &lt;a href=&quot;ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/README&quot;&gt;README&lt;/a&gt; file:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sequence data include chromosomes, contigs, RNAs, and proteins &#xA;  generated through the NCBI Reference Sequence and NCBI Genome &#xA;  Annotation projects. Map data presented in the Map Viewer resource are&#xA;  also provided here.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerDisplayName="user9474" LastActivityDate="2014-10-01T18:06:34.763" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21800" PostTypeId="2" ParentId="21779" CreationDate="2014-10-01T18:18:23.430" Score="2" Body="&lt;p&gt;There is a purely philosophical issue behind your question. What does trying mean? Does trying doing A means that an individual is aware of how to achieve A and will behave so to achieve it? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The likely correct answer (it really depends on you definition) is &quot;No&quot; (with some eventual exception among those that have high cognitive abilities such as humans). No, animals don't try to create a nice ecosystem. Animals (just like any living things) just evolve in response to their environment and this ends up creating ecosystems. The ecosystemic balance is just the result of the non-cooperative actions of the different species at play in the ecosystem. For example, animals reject nitrogen not in order to help plants to grow but only because nitrogen is a waste and is toxic for them. You may want to make you understand how evolution works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For those who have a good enough knowledge in evolutionary biology, I have to admit that the above answer might be slightly wrong if we consider some special kinds of selection such as kin selection, species selection or even ecosystem selection. I think the answer to the question remains &quot;no&quot; given the &quot;conscious&quot; side of the definition of trying that the OP was probably using.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cooperation is easy to explain, real altruism is more complicated. Real altruism is when one individual makes an action that benefits to the others lifespan reproductive success but decreases the lifetime reproductive success of the one producing the action.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within population real altruism can be explained by kin selection. see &lt;a href=&quot;https://biology.stackexchange.com/questions/10742/what-if-rb-c-in-hamiltons-rule&quot;&gt;this post&lt;/a&gt; for more info.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Between species real altruism is much more complicated to explain. It would need to use concepts such as species selection. But does between species real altruism even exist (beside some behaviour from species with high cognitive abilities)? I don't think so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you are interested in is inter/species cooperation. Very often the individual that offers something to the other also directly gain something. For example, the animal excrete nitrogen because it is toxic and the plant take advantage of this. But sometimes an individual (actor) pay a cost for producing something to the benefit of the other individual (recipient). In return, the actor will receive something back from the recipient. For example, in the lichen, the algae offers energy while the fungi offers shelter. If one stops the other will die and both will lose. There are known cases also where individual A stops offering goods t individual B if individual B stops offering goods to individual A. This kind of traits are best studies with the tools of game theory.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-10-02T03:46:15.137" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21801" PostTypeId="2" ParentId="21790" CreationDate="2014-10-01T18:32:50.840" Score="6" Body="&lt;p&gt;Speed of transmission is going to vary depending on the neuron fiber subtype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, the biggest gains will be seen with cross-sectional area (feel free to ask why on physics.stackexchange.com) and neurons with myelin sheathes (fat wrappings which affect saltatory conduction rates).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You're specifically asking about Efferent neuron transmission rates, but here's a general idea:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WijjW.gif&quot; alt=&quot;From medscape.com&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Keep in mind that the entire circuit (from pre-motor cortex to muscle spindles) will involve several different types. In-general, your central nervous system (brain, brain-stem, spinal chord) are A-alpha, and if I recall correctly - the somatic nervous system (the voluntarily-activated neurons throughout the rest of your body in the PNS [peripheral nervous system]) are A-delta. If I'm wrong, somebody please correct me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On average non-voluntary reflexes (which is actually information going to the CNS, being processed, and then going out to the motor neurons) take about 0.3 seconds. However, the average human can blink in about 0.1 seconds, which is probably a better measure.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2014-10-01T18:32:50.840" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21802" PostTypeId="2" ParentId="21507" CreationDate="2014-10-01T18:38:19.073" Score="24" Body="&lt;p&gt;First, I want to note that ddiez has a good answer, but I thought this was good question to have a more expanded answer on immunology and pathogenesis.  &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;The First thing we need to establish what is a &lt;a href=&quot;https://en.wikipedia.org/wiki/Common_cold&quot; rel=&quot;noreferrer&quot;&gt;&quot;cold&quot;&lt;/a&gt;.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The most common cold is &lt;a href=&quot;https://en.wikipedia.org/wiki/Rhinovirus&quot; rel=&quot;noreferrer&quot;&gt;rhinovirus (HRV)&lt;/a&gt;, but the second place holder is a little harder to define.  For example, &lt;a href=&quot;https://en.wikipedia.org/wiki/Human_respiratory_syncytial_virus&quot; rel=&quot;noreferrer&quot;&gt;respiratory syncytial virus (RSV)&lt;/a&gt; has been shown to be nearly ubiquitous by &lt;a href=&quot;http://archpedi.jamanetwork.com/article.aspx?articleid=512921&quot; rel=&quot;noreferrer&quot;&gt;age two&lt;/a&gt;.  I actually disagree with the Wiki article on the common cold which puts &lt;a href=&quot;https://en.wikipedia.org/wiki/Human_coronavirus&quot; rel=&quot;noreferrer&quot;&gt;coronaviruses&lt;/a&gt; (plural, which is not clear in the article) in second place.  For example, if you take look at &lt;a href=&quot;http://www.choa.org/Menus/Documents/Flu/Virometer.pdf&quot; rel=&quot;noreferrer&quot;&gt;sessional reports from hospitals&lt;/a&gt;, you can find that RSV and influenza are the more common.  Now this does select for those who were sick enough to seek hospital treatment, but if you look at a recent more &lt;a href=&quot;http://www.hindawi.com/journals/jrm/2014/469393/&quot; rel=&quot;noreferrer&quot;&gt;in-depth study&lt;/a&gt; conducted through health clinics, you will again find coronavirus in much lower showing:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Qebl7.jpg&quot; alt=&quot;Table of PCR results seeking viral RNA from nasopharyngeal samples&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[Editorial note, if someone wants to take the time to MathJax that table in, please go ahead.  It seemed too large to insert the table as text. &lt;a href=&quot;http://www.hindawi.com/journals/jrm/2014/469393/tab1/&quot; rel=&quot;noreferrer&quot;&gt;Here’s the original&lt;/a&gt;.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, a cold is an infection from any of the above viruses, with a common cold likely being HRV or RSV.  But how the body reacts to each of those is different.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Secondly, how do we mount an immune response to a cold?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There are two different kinds of immune responses in humans: &lt;a href=&quot;https://en.wikipedia.org/wiki/Innate_immune_system&quot; rel=&quot;noreferrer&quot;&gt;innate&lt;/a&gt; or &lt;a href=&quot;https://en.wikipedia.org/wiki/Adaptive_immune_system&quot; rel=&quot;noreferrer&quot;&gt;adaptive&lt;/a&gt;. (to not get to technical, you can come up with responses outside of these).  Both responses are excitingly complex, and needed to fight a cold.  The innate immune system is designed to handle the initial reactions to the pathogens, but often the adaptive immune system is what &quot;clears&quot; (viral clearance being the removal of the infection) the infection totally.  In a novel infection, the adaptive immune system takes a &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/25210145&quot; rel=&quot;noreferrer&quot;&gt;few days to ramp up&lt;/a&gt;, which is why a cold can last for a few days to two weeks. This is when you get &lt;a href=&quot;https://en.wikipedia.org/wiki/B_cell&quot; rel=&quot;noreferrer&quot;&gt;B-cells&lt;/a&gt; producing enough antibody to clear the infection.  Then the next time you are infected by something of the same &lt;a href=&quot;https://en.wikipedia.org/wiki/Serotype&quot; rel=&quot;noreferrer&quot;&gt;serotype&lt;/a&gt; you will have a reservoir of cells already primed to make an immune response, and it will happen quicker.  At least that is what the human body is trying to do.  Viruses are trying to &quot;evade&quot; the immune system and proliferate (acknowledging of course that is a personification of viruses, and that they are not &quot;trying&quot; to do anything). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key word in the adaptive response is &quot;novel.&quot;  If the pathogen is different enough, that is the &lt;a href=&quot;https://en.wikipedia.org/wiki/Epitope&quot; rel=&quot;noreferrer&quot;&gt;epitopes&lt;/a&gt; are different enough, then the immune system won't recognize it.  This is the principal strategy used by HRV.  Depending on who you ask there are between 96-120 serotypes of HRV, so using a number of about 100 seems reasonable (120 is a much more recent number and the increase has largely correlated with better diagnostic tools).  There don't seem to be additional stereotypes developing/mutating quickly (though conceivably they could), so as opposed to being infected by a mutated version of the cold you had last year, you're getting a different strain/serotype that was already in circulation.  Thus if you got a different HRV infection once a year, you have about 100 years of rihno viruses colds (when you actually get that old you have senescence problems in the immune system).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RSV is a different story.  You don't mount a &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/24362689&quot; rel=&quot;noreferrer&quot;&gt;lasting immune response&lt;/a&gt; to the virus in the first place:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YDsiG.png&quot; alt=&quot;Humoral Response to Acute Viral Infection in Humans&quot;&gt; (Table 10.6.  &lt;em&gt;Fields Virology&lt;/em&gt;; 6th Edition.  LWW 2013)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, I know a researcher who would infect his lab members with the exact same strain of RSV every 6 months for years (before people would stop such a thing...).  Why RSV doesn't elicit lasting immunity--and in fact notably shorter immunity--is the subject of current research.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see in Table 10.6, &lt;a href=&quot;https://en.wikipedia.org/wiki/Mucosal_immune_system&quot; rel=&quot;noreferrer&quot;&gt;mucsal responses&lt;/a&gt; are generally not as long lasting as systemic infections.  This can make sense from a macro view—the mucus successfully prevented the pathogen from spreading to the rest of the tissues in the body, so it's not as critical to respond to.  On a more specific level we know that more &lt;a href=&quot;https://en.wikipedia.org/wiki/Immunoglobulin_A&quot; rel=&quot;noreferrer&quot;&gt;IgA&lt;/a&gt; is produced and the &lt;a href=&quot;https://en.wikipedia.org/wiki/Cytokine&quot; rel=&quot;noreferrer&quot;&gt;cytokines&lt;/a&gt; can be &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.0300-9475.2004.01382.x/abstract;jsessionid=18A0FB4ACC19FF265B744A1B04734309.f03t02&quot; rel=&quot;noreferrer&quot;&gt;different&lt;/a&gt;.  But RSV seems specifically reduced. One leading idea is that two of the proteins produced by the virus, NS1 and NS2, cause an immune response to not be properly mounted.  In other words, the virus is making materials that deliberately interfere with adaptive immune response.  &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/25249281&quot; rel=&quot;noreferrer&quot;&gt;An interesting paper&lt;/a&gt; that just came out addresses this idea for a possible vaccine candidate.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="39366" LastEditDate="2018-01-07T17:05:32.067" LastActivityDate="2018-01-07T17:05:32.067" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21803" PostTypeId="1" CreationDate="2014-10-01T18:44:15.993" Score="1" ViewCount="30" Body="&lt;p&gt;According to my neuro-anatomy class, both the Corsticospinal Tract (CST) and the Rubrospinal Tract (RuST) control upper limb movement. What the evolutionary reasoning behind this redundancy and the fact that the RuST is much more important in non-human primates when compared to humans?&lt;/p&gt;&#xA;" OwnerUserId="5427" LastEditorUserId="5427" LastEditDate="2014-10-02T16:26:49.400" LastActivityDate="2014-10-02T16:26:49.400" Title="Evolutionary reasoning behind redundancy of CST and RuST" Tags="&lt;evolution&gt;&lt;neuroanatomy&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21804" PostTypeId="2" ParentId="21779" CreationDate="2014-10-01T19:10:20.573" Score="2" Body="&lt;p&gt;The answer to the question as stated is, certainly: No. Neither on a conscious level, nor at the level of instinct does an animal have the goal of keeping the ecological balance of its environment intact. Quite the opposite: it is constantly trying to overturn that balance, attempting to change the system and bring it to a new situation, one in which it (the animal) and its children have a higher survival and procreation chance than the current one. Whether the new situation will be stable (= a balance) or not is not a criterion, and cannot be predicted by any animal acting on the environment (including the humans). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To use an example: As the news outlets have been warning us in recent years, if all bees were to die, our whole ecosystem could collapse. Yet no bee is pollinating flowers because it somehow feels that this will prevent the collapse of the current ecosystem. It gathers pollen because its swarm is hungry. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also nothing &quot;natural&quot; about the equilibrium our ecosystem is in, at least not in the sense implying that &quot;this is how it should be, and everything else is so bad that it goes against the very laws of nature&quot;. It is just one random equilibrium of many possible states of our planet, some including an ecosystem in equilibrium, others including self-destruction of the ecosystem. All of these states are equally natural, and the planet has passed through several of them before establishing the current one (which isn't about to stay here forever either). &lt;/p&gt;&#xA;" OwnerUserId="1578" LastActivityDate="2014-10-01T19:10:20.573" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21805" PostTypeId="2" ParentId="21798" CreationDate="2014-10-01T21:48:18.403" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;but aren't there 46 chromosomes to include or are some of those&#xA;  duplicates&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;First of all, while each person has 2 copies of each chromosome, those copies are 99% identical.  So it would be a waste to repeat the whole thing twice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, the technology is such that it's not easy to generate, say, the whole sequence of a chromosome that came from their mother.  You either get sanger traces which show the two sequences superimposed on each other, or very short reads that are not mixed, but you can't tell which parent generated which fragment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in general, a reference genome will just have one consensus letter at every position, even though that's not biologically realistic.  It doesn't much matter what the reference is, as long as everyone knows that it's just a reference.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;My goal is to display all the letters via projector onto a wall and I&#xA;  want to be able to point at it and tell someone, that's all the DNA&#xA;  for a human (not a subset).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Can you really display 3 billion characters like that?&lt;/p&gt;&#xA;" OwnerUserId="5148" LastEditorUserId="5144" LastEditDate="2014-10-01T21:50:00.363" LastActivityDate="2014-10-01T21:50:00.363" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21806" PostTypeId="1" AcceptedAnswerId="21811" CreationDate="2014-10-01T21:56:27.043" Score="2" ViewCount="999" Body="&lt;p&gt;I am using ImageJ to analyze Western Blots. I have scanned films in as grayscale images because this is how we did it in my old lab. People in my current lab are not satisfied with that explanation and think I should consider using color images. I've been searching for protocols but they all seem to address how to use the program once you have some films scanned. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone help me figure out what considerations go into choosing &lt;strong&gt;how&lt;/strong&gt; I scan my films?&lt;/p&gt;&#xA;" OwnerUserId="8161" LastActivityDate="2014-10-02T04:43:13.477" Title="Can I use grayscale images when working with ImageJ?" Tags="&lt;proteins&gt;&lt;protocol&gt;&lt;western-blot&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21807" PostTypeId="2" ParentId="21798" CreationDate="2014-10-01T23:20:56.017" Score="3" Body="&lt;p&gt;If I understand your question correctly, you want a single file, i.e. a single string, which represents the sequence of an entire human genome.  However, there is no such thing.  The human genome is stored in 46 different strings (chromosome), and these strings have &lt;em&gt;no natural order&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The numbers used to refer to the genomes are based on their order when arranged by size.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All operations on the genome (such as copying it before mitosis) happen in parallel, with proteins operating on each chromosome individually.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to represent an entire human genome &quot;honestly&quot;, I would say your best bet is to put 46 separate strings on the projector, perhaps running parallel to one another like the code in the Matrix.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to display one big long string, any sequence of concatenation is as (in)correct as any other, so just open the files in alphabetical order and concatenate them all.&lt;/p&gt;&#xA;" OwnerUserId="9599" LastActivityDate="2014-10-01T23:20:56.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21808" PostTypeId="2" ParentId="21798" CreationDate="2014-10-01T23:47:43.790" Score="9" Body="&lt;p&gt;Non-biologist here stepping in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;@swbarnes2 has a good point pinning the fact that (approx) 3Giga nucleotides to display &quot;on a wall&quot; (as you state) even with a good projector is gonna be a hard task.&#xA;You'll need several projectors and a hell of a big wall.&#xA;(say you take the smallest readable police setting you'll have each letter take a space of 4*6 pixels which for the whole will bring you to ~[227k x 342k] pixels so around 35k HD-projectors)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which led me to think of why you would want to do such a thing.&#xA;The most plausible of which is : it is for some sort of artistic/cultural intent.&#xA;In such case, rather than showing letters (ATGC) I recommend to encode it in binary (00,01,10,11) and make this value code for a colored pixel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That will leave you with a square matrix of around 57k pixels edge (which remains humongous) of shaded in 4 tones black to white dots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to go even farther, trichromia stands to the rescue, don't make pixels code for just one nucleotide each.&#xA;Make them code for one &quot;pseudo-codon&quot; (triplet) each.&#xA;First nucleotide defining the red shade,&#xA;Second nucleotide defining the green shade,&#xA;last nucleotide defining the blue shade.&#xA;(plain and simple Additive color RGB stuff).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-EDIT-&#xA;Knowing that the notion of codon is invalid and that any nucleotide (except the leading and trailing 2 of each chromosome) could be part of three distinct codon (depending on wether they are in an intron, exon or even alternatively spliced) we see that this grouping by 3 is not THAT right.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In such case why not take even more liberties ?&#xA;Group your nucletides by 12 (3 groups of 4) giving you more depths in the color shades.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-END OF EDITED SECTION-&lt;/p&gt;&#xA;&#xA;&lt;p&gt;you'll get a much nicer and significantly smaller matrix of [30k x 30k] (which is still gonna take you a big wall and a few HD-projectors ~150 but at this point you can compress the output with several methods and get merged pixels, yet 150 is far less than 35000).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know I don't bring actual solutions to the asked question (but I really think @Omen did it pretty well) but I sensed that there maybe here some insight worth handing (at the risk of making a fool of myself)&lt;/p&gt;&#xA;" OwnerUserId="9600" LastEditorUserId="9600" LastEditDate="2014-10-03T18:27:00.217" LastActivityDate="2014-10-03T18:27:00.217" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21809" PostTypeId="2" ParentId="3481" CreationDate="2014-10-02T01:04:11.553" Score="0" Body="&lt;p&gt;If your cats/dogs had a choice they would prefer a diet rich in raw meat because that is what they will eat if they lived in nature. Dry feed is not their preference, I tried this by giving my dog raw chicken and beef and he went absolutely crazy for it. He was also more active and alert. &#xA;For humans, switching diet is necessary in order to receive all vital nutrients and keep the gut bacteria active and guessing by introducing new foods. &lt;/p&gt;&#xA;" OwnerUserId="9490" LastActivityDate="2014-10-02T01:04:11.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21810" PostTypeId="2" ParentId="19507" CreationDate="2014-10-02T01:29:14.267" Score="1" Body="&lt;p&gt;This is caused by a build up of ketone bodies in your blood which lowers the pH of your body and can cause bad breath. Ketone bodies are a response of your body breaking down fatty acids for energy instead of glucose when in a low food intake (fasting) state. This is also true for morning breath since your body has been in a fasting state.&#xA;The way to prevent this is to eat the proper amount of calories needed for your body to function normally.&lt;/p&gt;&#xA;" OwnerUserId="9490" LastActivityDate="2014-10-02T01:29:14.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21811" PostTypeId="2" ParentId="21806" CreationDate="2014-10-02T04:33:50.643" Score="3" Body="&lt;p&gt;There is no evidence that one is better than the other, most likely because it differs from case to case. Neither you, nor your critics, are right. There is a tiny bit of science in a paper on digitizing blots, generalizing from blots of a specific protein (PMID: 19517440), and they use grayscale for no given reason. Come to think, that is the best paper in the field of immunoblot quantification., and it still lacks evidence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Immunoblot is semiquantitative, meaning it may sort and order bands (and protein amounts), but it fails often at estimating differences and ratios, and may even fail to see differences. Just try your best to find a difference, in the knowledge that if there is no difference in protein amounts, any fiddling with contrast won't create a difference in bands quantitation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is almost no difference between color and black-and-white digitized images of an immunoblot. The parts of the blot that are black will still appear in the computer as White = 0, even though a tri-color image file will detail it to Red = 0, Green = 0, Blue = 0. The parts that are nearly black will still be very close to zero.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only thing that changes a lot between RGB and color is the background.  The background may change, for example, from White = 200, to Red = 190, Green = 190, Blue = 220. There is one consequence of such switching between values for background. (These changes may be induced by switching between grayscale and RGB, but also by altering exposure time etc.) When you use a method where the background gets too close to the blots, the &quot;amplitude&quot; of the blots, the height of the peaks in ImageJ, will be reduced. This loss of contrast should wash out some of the differences between blot bands and lessen support for differences between bands (i.e., for the alternative hypothesis), making you miss a genuine protein difference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, if your blot bands are different enough so that your percent increase / decrease is huge, and your p value is small, you are all set, regardless of the method you chose. Ask your critics to explain your observed differences other than by differences in protein. But if your quantification fails the p test, I think it will be a honest effort, to change the color from grayscale to RGB, or the other way around, just in case your first choice had been the one that dampens contrast. &lt;/p&gt;&#xA;" OwnerUserId="8809" LastEditorUserId="8809" LastEditDate="2014-10-02T04:43:13.477" LastActivityDate="2014-10-02T04:43:13.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21812" PostTypeId="1" CreationDate="2014-10-02T05:20:05.570" Score="9" ViewCount="2232" Body="&lt;p&gt;In a vacuum, there is a one-to-one correspondence between light frequency ($\nu$) and wavelength ($\lambda$), ie. $\lambda=c/\nu$. But in a refractive medium, $\lambda=v/\nu$, so while the frequency may remain constant, the wavelength may not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen that in biology, wavelength is mostly used. But, I recall reading that human vision is sensitive to frequency. So, is human vision sensitive to wavelength or frequency?&lt;/p&gt;&#xA;" OwnerUserId="3810" LastEditorUserId="3340" LastEditDate="2014-12-03T19:07:04.337" LastActivityDate="2016-09-15T12:59:32.353" Title="Is human vision sensitive to frequency or wavelength?" Tags="&lt;vision&gt;&lt;biophysics&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21813" PostTypeId="2" ParentId="21812" CreationDate="2014-10-02T06:07:53.250" Score="2" Body="&lt;p&gt;In the context of human vision, wavelength and frequency are not mutually exclusive, but given by the first equation you pointed out in the question. That is, whenever the range of human vision is given they are not assuming that wavelength and frequency can change independently.  &lt;/p&gt;&#xA;" OwnerUserId="9562" LastActivityDate="2014-10-02T06:07:53.250" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21814" PostTypeId="2" ParentId="13693" CreationDate="2014-10-02T06:31:28.523" Score="0" Body="&lt;p&gt;This &lt;a href=&quot;http://www.sciencedaily.com/releases/2014/10/141001184414.htm&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; claims to be a new level of evidence for group selection.  Its a little early to tell at this point whether the critics will be moved.  They have &lt;a href=&quot;http://www.nature.com/nature/journal/v466/n7310/full/nature09205.html&quot; rel=&quot;nofollow&quot;&gt;not been in the past&lt;/a&gt;!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;sorry if this is a bit short - its late, but i'll try to come back and do more later..&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-10-02T06:31:28.523" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21815" PostTypeId="2" ParentId="21812" CreationDate="2014-10-02T06:43:21.407" Score="4" Body="&lt;p&gt;Wavelength-frequency relation is $\lambda=\frac{c}{\nu}$ or $\nu\cdot \lambda=c$ in vacuum. In some refractive media you can substitute $c$ with speed of light at corresponding medium, essentially nothing changes. Speed determines the product of wavelength and frequency, not their ratio, as you suggested. Hence at different speeds frequency and wavelength will both decrease or increase, there is no reason to think that one of them stays constant and the other one changes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you still want to make a distinction and describe physical property of light with one of them, frequency $\nu$ would be more relevant as matter/light (photon/electron) interactions work as described by the formula $E=h\cdot \nu$&lt;/p&gt;&#xA;" OwnerUserId="1458" LastActivityDate="2014-10-02T06:43:21.407" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21816" PostTypeId="2" ParentId="21812" CreationDate="2014-10-02T09:02:29.480" Score="10" Body="&lt;p&gt;It is not the wavelength or frequency that determines light absorption- it is the energy of the photon that matters. The energy of incident light should match the excitation energy of the chromophore. The medium itself can also affect light absorption by electronically interacting with the chromophore. Frequency is proportional to the energy (given by the relationship $E=h\nu$); while wavelength and velocity change in different media, frequency and energy remain constant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The chromophore in the opsins (retinal) absorb energy to become active and you can say that they detect the frequency. However, sufficient number of opsins have to become active for the retinal cells to transmit the signal. So the overall light flux is also important. An interesting thing to note is that activation of the opsins hyperpolarizes the photoreceptor cell and reduces its tendency to fire.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wavelength plays a role in diffraction and therefore diffraction is less in a medium with higher refractive index. Wavelength also determines scattering. So, while the opsins actually detect frequency, the wavelength can slightly affect the overall &quot;vision&quot; because of scattering/diffraction effects.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-09-15T12:59:32.353" LastActivityDate="2016-09-15T12:59:32.353" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21817" PostTypeId="2" ParentId="21798" CreationDate="2014-10-02T10:07:16.220" Score="3" Body="&lt;p&gt;If you want to merge all the sequences as a single sequence then download the sequence of all the chromosomes and then concatenate them. Simple command for that if you use linux: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;grep -v &quot;&amp;gt;&quot; chromosome*.fa &amp;gt; entire_genome.txt&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now it makes sense to separate the genome chromosome-wise because there is no physical connection between one chromosome and the other. Moreover there are many orders by which you can concatenate the chromosomes together which will give you &lt;code&gt;23!&lt;/code&gt; number of genome sequences. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now you should note that all of this can give you serious errors if you are trying to do study genomic context of any gene. So better go chromosome wise. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I have interpreted you wrong and what you meant is to have all the chromosome fasta sequences in a single file, yet not merge the sequences then it is a pretty straightforward command.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;cat chromosome*.fa &amp;gt; genome.fa&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, what you download is a reference sequence. You have to find variants etc for your data by controlling your alignment parameters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And I really don't understand why you want to project it on the wall. There are easier and better ways of analyzing the genome.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-10-02T10:07:16.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21818" PostTypeId="1" AcceptedAnswerId="21836" CreationDate="2014-10-02T11:54:15.020" Score="1" ViewCount="8542" Body="&lt;p&gt;Is that possible that ovulation happens in the time of actual menstrual haemorrhage in human females - let say in a case that woman has 21 day cycle and her menstrual period is 7 days? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If yes, does it means that in this particular case the woman has lower chances to conceive?&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="9268" LastEditDate="2014-10-03T05:21:28.787" LastActivityDate="2019-12-12T12:53:43.667" Title="Can ovulation and menstruation occur simultaneously?" Tags="&lt;reproduction&gt;&lt;endocrinology&gt;&lt;pregnancy&gt;&lt;ovulation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21819" PostTypeId="1" CreationDate="2014-10-02T12:30:52.803" Score="1" ViewCount="26" Body="&lt;p&gt;What is Sequence based method for prediction of continuous B cell epitope? What is the algorithm/procedure of this method? Can someone please explain this to me in simple language?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="948" LastEditDate="2014-10-02T15:03:30.490" LastActivityDate="2014-10-02T15:03:30.490" Title="Sequence based method for prediction of continuous B cell epitope" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;immunology&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21820" PostTypeId="1" CreationDate="2014-10-02T13:15:31.217" Score="3" ViewCount="80" Body="&lt;p&gt;I know that there are flipases and flopases that facilitate this sort of thing, but I'm curious about other possible influences. Can the Donnan effect be reversed so that phospholipids follow ions? For example, calcium efflux from cells causes it to be more energetically favorable for phosphatidylserine (slightly more negative, and thus slightly more likely to follow a positive charge) to be ejected from inner to outer leaflet.&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorDisplayName="user38945" LastEditDate="2018-05-05T12:33:25.243" LastActivityDate="2018-05-05T12:33:25.243" Title="Can the Donnan effect be reversed so phospholipids follow ions?" Tags="&lt;cell-membrane&gt;&lt;membrane-transport&gt;&lt;membrane&gt;" AnswerCount="0" CommentCount="6" ClosedDate="2016-06-20T06:47:00.580" ContentLicense="CC BY-SA 4.0" />
  <row Id="21821" PostTypeId="1" AcceptedAnswerId="23516" CreationDate="2014-10-02T13:19:01.780" Score="0" ViewCount="55" Body="&lt;p&gt;What is epitope annotted protein?? &lt;br&gt; The book from which I got this term is : &lt;br&gt;&lt;a href=&quot;http://www.springer.com/biomed/immunology/book/978-1-4939-1114-1&quot; rel=&quot;nofollow&quot;&gt;http://www.springer.com/biomed/immunology/book/978-1-4939-1114-1&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="948" LastEditDate="2014-10-02T15:01:57.783" LastActivityDate="2014-10-27T16:38:02.710" Title="Epitope annotated protein" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21822" PostTypeId="2" ParentId="21772" CreationDate="2014-10-02T13:33:41.100" Score="9" Body="&lt;p&gt;Here is a more morphologic, less genetic answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Sansom 2013, the 2 sets of paired appandages (shoulder and pelvic) was set in stone when agnathans transitioned into gnathostomes (ie. when the first vertebrate organisms began to evolve jaws, an anatomic change that allows for classification of different stages of history found in the fossil record). They found variations where an agnathan had a paired set of anal fins (sort of the 3rd set of paired appendage, since anal fins are typically unpaired).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, moving forward millions of years, the &lt;em&gt;Sarcopterygii&lt;/em&gt; (lobe fin fish) evolved into the tetrapods (4 limbed land vertebrate including amphibians, reptiles, birds, and mammals), this pattern (2 sets of paired limbs) became immutable, though much less fundamental variation throughout the phylogenesis of the various tetrapods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sansom RS,Gabbott SE, Purnell MA. 2013 Unusual anal fin in a Devonian jawless vertebrate reveals complex origins of paired appendages. Biol Lett 9: 20130002.&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2016-07-13T20:17:29.603" LastActivityDate="2016-07-13T20:17:29.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21824" PostTypeId="1" AcceptedAnswerId="21862" CreationDate="2014-10-02T14:45:29.280" Score="3" ViewCount="97" Body="&lt;p&gt;In angiosperm, &lt;strong&gt;in which layer of the meristem does a new mitotic mutation occurring has chance to be found in a pollen grain or in an ovule?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also welcome some insights about non-angiosperm plants.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-10-17T14:26:06.093" LastActivityDate="2014-10-17T14:26:06.093" Title="Somatic Mutations in meristem tissue in plants" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;plant-physiology&gt;&lt;mutations&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21825" PostTypeId="1" AcceptedAnswerId="21840" CreationDate="2014-10-02T15:02:40.033" Score="21" ViewCount="59752" Body="&lt;p&gt;Many cells in the human body can divide and reproduce, making healing possible. Neurons, however, cannot reproduce, which makes diseases affecting the brain particularly crippling. Why can't neurons divide - that is, what makes them different from &quot;normal&quot; cells? Are there any ways to artificially stimulate neuron cell division?&lt;/p&gt;&#xA;" OwnerUserId="9458" LastActivityDate="2017-06-29T14:17:04.560" Title="Why can't neurons undergo cell division?" Tags="&lt;neuroscience&gt;&lt;cell-division&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21826" PostTypeId="2" ParentId="21825" CreationDate="2014-10-02T15:16:08.493" Score="12" Body="&lt;p&gt;&lt;strong&gt;Morphological point of view&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neurons cannot divide because they lack &lt;a href=&quot;http://en.wikipedia.org/wiki/Centriole&quot;&gt;centrioles&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because centrioles function in cell division, the fact that neurons lack these organelles is consistent with the amitotic nature of the cell [1].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Functional point of view&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;New cells in the nervous system wouldn't do any good. The whole nervous system is based on interneuronal connections, so adding an extra neuron would mess up these connections and alter both the functionality and the &quot;stored&quot; information.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Each nerve cell has a specific place in our nervous system. Its job is all about taking a signal from one specific place to another one. Adding new nerve cells would mess up these very specific connections in a very complex system [2].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;SEER Training. NERVE TISSUE. Available from &lt;a href=&quot;http://training.seer.cancer.gov/anatomy/nervous/tissue.html&quot;&gt;http://training.seer.cancer.gov/anatomy/nervous/tissue.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;UCSB Science Line. Available from &lt;a href=&quot;http://scienceline.ucsb.edu/getkey.php?key=1710&quot;&gt;http://scienceline.ucsb.edu/getkey.php?key=1710&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-10-02T15:24:18.843" LastActivityDate="2014-10-02T15:24:18.843" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21827" PostTypeId="1" CreationDate="2014-10-02T15:25:41.800" Score="13" ViewCount="2869" Body="&lt;p&gt;Scenario: In a boat in the middle of the sea, no freshwater or food stores, no desalination equipment, no rain, but you can catch fish and eat it raw. Can you get enough water this way to survive, let's say for 14 days? (Enough clothes to protect against cold, shade available)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2, 000 g of raw Pacific cod contains 1,650 mL water, 350 g protein, 2,200 mg sodium (source: &lt;a href=&quot;http://ndb.nal.usda.gov/ndb/foods/show/4710?fg=&amp;amp;man=&amp;amp;lfacet=&amp;amp;count=&amp;amp;max=25&amp;amp;qlookup=fish&amp;amp;offset=0&amp;amp;sort=&amp;amp;format=Abridged&amp;amp;reportfmt=other&amp;amp;rptfrm=&amp;amp;ndbno=&amp;amp;nutrient1=&amp;amp;nutrient2=&amp;amp;nutrient3=&amp;amp;subset=&amp;amp;totCount=&amp;amp;measureby=&amp;amp;_action_show=Apply%20Changes&amp;amp;Qv=1&amp;amp;Q8971=71&quot; rel=&quot;noreferrer&quot;&gt;usda.gov&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By my calculation, you would need to excrete 2,800 mL of urine to excrete urea from protein metabolism (8 mL urine per 1 g protein; source: &lt;a href=&quot;http://www.nap.edu/openbook.php?record_id=10925&amp;amp;page=135&quot; rel=&quot;noreferrer&quot;&gt;nap.edu&lt;/a&gt;), so after eating fish you would be in the negative water balance for more than 1,150 mL solely from urea. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions are &lt;em&gt;strictly about fish as a water source&lt;/em&gt;, not about other water sources or survival time:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Does protein really expel so much urine that makes fish an inappropriate source of water? &lt;/li&gt;&#xA;&lt;li&gt;Any other appropriate source of water from fish, apart from eyeballs? Can you somehow squeeze the water from fish?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="4025" LastEditorUserId="4025" LastEditDate="2014-10-03T07:34:59.727" LastActivityDate="2014-10-03T07:34:59.727" Title="Can you get enough water by eating only fish?" Tags="&lt;proteins&gt;&lt;ichthyology&gt;&lt;dehydration&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21829" PostTypeId="1" CreationDate="2014-10-02T18:29:00.700" Score="5" ViewCount="2062" Body="&lt;p&gt;It is autumn out there. Green, brown, red, yellow, and mixed-colored leaves drop from the trees to the ground. What determines the colors of the leaves?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Plant_senescence&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; tells me&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Leaf senescence is the cause of autumn leaf color in deciduous trees.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Ok. What does the color code? If a leaf is red, why is it red and not yellow or brown or green or mixed-colored?&lt;/p&gt;&#xA;" OwnerUserId="9617" LastEditorUserId="3952" LastEditDate="2015-05-24T16:16:23.627" LastActivityDate="2015-05-24T16:16:23.627" Title="What determines the autumn leaf color?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;senescence&gt;&lt;life-history&gt;&lt;phenology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21830" PostTypeId="2" ParentId="21829" CreationDate="2014-10-02T18:45:08.940" Score="3" Body="&lt;h2&gt;What&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There are two theories according to &lt;a href=&quot;http://www.yale.edu/edex/new_haven_trees/Tree-colors-final.html&quot; rel=&quot;nofollow&quot;&gt;Jennifer Wells, Leaf Color Change&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Competition theory&lt;/em&gt;&lt;/strong&gt; - states that nutrients are redistributed to important parts of the plant. &lt;strong&gt;Lack of nutrients&lt;/strong&gt; in the leaves will decrease the chlorophyll synthesis thus the leaves change their color. The redistribution does not happen equally that's why some leaves are multicolored (see &lt;a href=&quot;http://blogs.cornell.edu/bioee1610/2011/09/30/do-you-fall-for-leaves/&quot; rel=&quot;nofollow&quot;&gt;Ecology and the Environment at Cornell Blogs&lt;/a&gt;).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Mutual enhancement&lt;/em&gt;&lt;/strong&gt; - states that specific hormones (&lt;strong&gt;senescence factors&lt;/strong&gt;) work in conjunction and cause the color change.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;All these happen under the influence of light - the absorbed dose of light is modulated by internal factors. The result is a reversed balance between carotenoids and chlorophyll (increase in carotenoids).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These carotenoids (fat-soluble) turn the leaf into orange and yellow depending on their concentration. There are also anthocyanins (water-soluble) which are responsible for red coloration.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Why&lt;/h2&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Chlorophyll and its derivatives, if not carefully processed by organized biochemical pathways in green cells, can be toxic when illuminated.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;According to: &lt;a href=&quot;http://www.sidthomas.net/pdf/paperpdfs/128.pdf&quot; rel=&quot;nofollow&quot;&gt;Howard Sidney Thomas, Leaf senescence and autumn leaf coloration&lt;/a&gt;. Check also Figure 3 from this link (on the last page).&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-10-02T19:31:32.043" LastActivityDate="2014-10-02T19:31:32.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21831" PostTypeId="2" ParentId="21829" CreationDate="2014-10-02T19:09:56.617" Score="7" Body="&lt;p&gt;There is no color code for the leafs - the color results from biochemical reactions. Basically there are three colors: Green, yellow and red.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Green color is caused by the chlorophyll inside the chloroplasts,&#xA;when the leafs are active in photosynthesis.&lt;/li&gt;&#xA;&lt;li&gt;Yellow color is caused by &lt;a href=&quot;http://en.wikipedia.org/wiki/Autumn_leaf_color#Carotenoids&quot;&gt;Carotenoids&lt;/a&gt;, which are present in the&#xA;leafs all the time, but are masked by the chlorophyll. The&#xA;carotenoids become visible when the amount of chlorophyll in the&#xA;leafs is reduced, which usually happens in the fall.&lt;/li&gt;&#xA;&lt;li&gt;The red color is caused by &lt;a href=&quot;http://en.wikipedia.org/wiki/Autumn_leaf_color#Anthocyanins&quot;&gt;Anthocyanins&lt;/a&gt;, which are usually not&#xA;present in the leafs. They are made during the late summer and can&#xA;also mix up with the carotenoids (color mix) to get intermediate&#xA;colors.&lt;/li&gt;&#xA;&lt;li&gt;Brown color is caused by the cell wall of dry leafs which have no&#xA;other color.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For further reading these articles are interesting:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.biology.upatras.gr/attachments/article/650/Archetti%20et%20al%20Trends%20in%20Ecology%20and%20Evolution.pdf&quot;&gt;Unravelling the evolution of autumn colours: an interdisciplinary&#xA;approach.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.usna.usda.gov/PhotoGallery/FallFoliage/ScienceFallColor.html&quot;&gt;The Science of Color in Autumn Leaves&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;There is also the hypothesis around, that the bright colors are a warning sign to insects, this is called the co-evolution theory of autumn colors. The color should warn the insects that the tree has a high level of defense and thus reduce its parasitory load. You can read more about this hypothesis here: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15306345&quot;&gt;The coevolution theory of autumn colours.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20495371&quot;&gt;The shared and separate roles of aposematic (warning) coloration and&#xA;the co-evolution hypothesis in defending autumn leaves.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-02T19:09:56.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21833" PostTypeId="1" AcceptedAnswerId="21834" CreationDate="2014-10-02T19:31:29.110" Score="17" ViewCount="2721" Body="&lt;p&gt;Any ideas? I didn't know any other way to explain it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I live in Indiana, USA if that helps. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Someone said it might be a &quot;stink bug&quot; but I'm not sure and not willing to find out!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/1lpea.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/1lpea.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9619" LastEditorUserId="16866" LastEditDate="2019-06-24T19:57:30.240" LastActivityDate="2019-06-24T19:57:30.240" Title="Horned Mohawk looking insect. What is it?" Tags="&lt;species-identification&gt;&lt;zoology&gt;&lt;entomology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21834" PostTypeId="2" ParentId="21833" CreationDate="2014-10-02T20:09:15.677" Score="21" Body="&lt;p&gt;Its definitely a True bug (Hemiptera), and based on its distinct pronotum and small head I'm guessing its a &lt;a href=&quot;http://entnemdept.ufl.edu/creatures/trees/wheel_bug.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wheel bug (&lt;em&gt;Arilus cristatus&lt;/em&gt;)&lt;/a&gt;. It is a common species that is also found in Indiana.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are aggresive predators and are part of the family &lt;a href=&quot;http://en.wikipedia.org/wiki/Reduviidae&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reduviidae&lt;/a&gt; also known as Assassin bugs. Assassin bugs have a painful bite, and they inject a toxin when they stab their victim (so humans should watch out). This is not a part of the world I know well though, and there might be similar closely related species that I've missed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Links:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bugguide.net/node/view/454&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bug guide&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.gbif.org/species/2008593&quot; rel=&quot;nofollow noreferrer&quot;&gt;Records in GBIF&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://entnemdept.ufl.edu/creatures/trees/wheel_bug.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Univerity of Florida: Entomology &amp;amp; Nematology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Some pictures:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TX0X0.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uTb0J.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="15950" LastEditDate="2019-02-08T10:58:17.883" LastActivityDate="2019-02-08T10:58:17.883" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="21836" PostTypeId="2" ParentId="21818" CreationDate="2014-10-03T00:30:13.270" Score="3" Body="&lt;p&gt;Ovulation and menstruation don’t happen in normally cycling women at the same time. A basic outline of the hormonal cycle that triggers these events will make this clear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Proliferative (a.k.a follicular*) phase&lt;/strong&gt;&lt;br&gt;&#xA;Beginning after menses (when the endometrium is thinned), the hypothalamus produces GnRH which stimulates the anterior pituitary to produce LH and FSH. These in turn stimulate ovarian follicles to develop. A dominant follicle produces estradiol which causes the endometrium to thicken (proliferate).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At a certain level of estrogen (actually estrogen/progesterone ratio), the feedback on the hypothalamus flips from a negative to a positive feedback loop. Thus, there is a GnRH followed by a LH surge. The latter triggers ovulation. Note that at this time the endometrium is stable due to relatively high estrogen levels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Secretory (a.k.a. luteal*) phase&lt;/strong&gt;&lt;br&gt;&#xA;After ovulation, the high levels of LH trigger formation of a corpus luteum from the tissues left behind after ovulation. The corpus luteum makes progesterone. This hormone triggers a change in the endometrium from a proliferative to a secretory state. Progesterone also provides negative feedback to the hypothalamus and anterior pituitary, maintaining low levels of GnRH, LH, and FSH, so no new dominant follicles develop at this time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If pregnancy does not occur, the corpus luteum will eventually (10-12 days) degenerate and stop producing progesterone. It is this abrupt drop in progesterone that triggers the sloughing of the endometrial lining. You can see these hormone shifts in an illustration like this: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eoHt2.png&quot; alt=&quot;menstrual hormones&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The decline of the corpus luteum is correlated with a decline in serum levels of ovarian hormones including progesterone, estradiol, and inhibin A. Release from negative feedback provided by these hormones at the level of the hypothalamus and pituitary permits FSH to rise, and the cycle begins again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should now be able to see that: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Around the time of ovulation, the uterine lining is not fully developed and is stable due to the hormonal milieu. Menstruation does not occur.&lt;/li&gt;&#xA;&lt;li&gt;Around the time of menstruation, FSH and LH are suppressed in a way that is not conducive to ovulation. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In theory, yes, of course there would be a lower chance of initiating a viable pregnancy (&lt;em&gt;implantation&lt;/em&gt; rather than &lt;em&gt;conception&lt;/em&gt; is the most obvious problem) were the endometrial lining to be unstable at the time of ovulation. The problem of &lt;a href=&quot;http://www.sart.org/uploadedFiles/ASRM_Content/News_and_Publications/Practice_Guidelines/Committee_Opinions/Luteal%20phase%20deficiency2012noprint.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;luteal phase deficiency&lt;/a&gt; is along these lines. In this condition, the corpus luteum does not produce adequate progesterone during the luteal phase to develop the endometrial lining in such a way as to support a healthy pregnancy. However, ovulation and menstruation are still time-separated events for the reasons outlined above. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Note that the first term is with respect to the endometrium; the second is with respect to the ovary.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Abbreviations:&lt;br&gt;&#xA;&lt;sub&gt;&#xA;GnRH - Gonadotropin Releasing Hormone; LH - Luteinizing Hormone; FSH - Follicule Stimulating Hormone&#xA;&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;References&lt;br&gt;&#xA;&lt;sub&gt;&#xA;1. &lt;a href=&quot;http://cnx.org/content/col11496/1.6/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Anatomy &amp;amp; Physiology, Connexions Web site&lt;/a&gt;. Illustration is also from here.&#xA;&lt;/sub&gt;&#xA;&lt;sub&gt;&lt;br&gt;&#xA;2. Jerome Strauss, Robert Barbieri. &lt;em&gt;Yen &amp;amp; Jaffe's Reproductive Endocrinology.&lt;/em&gt; September,  2013. Saunders.&#xA;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-10-03T06:33:13.557" LastActivityDate="2014-10-03T06:33:13.557" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21837" PostTypeId="1" AcceptedAnswerId="21839" CreationDate="2014-10-03T01:11:41.290" Score="4" ViewCount="384" Body="&lt;p&gt;There's been a lot of talk lately about the man who recently came down with ebola in Dallas, Texas. While I live elsewhere, I keep hearing quotes from CDC and state officials that ebola is not contagious &lt;em&gt;until a person shows symptoms&lt;/em&gt;. This is generally used in the context of &quot;Don't worry too much; we have the situation under control.&quot; Is this true in all cases? Why?&lt;/p&gt;&#xA;" OwnerUserId="9458" LastEditorUserId="2949" LastEditDate="2014-10-24T18:46:25.803" LastActivityDate="2014-10-26T04:58:02.013" Title="Is ebola non-contagious until symptoms appear? Why?" Tags="&lt;pathology&gt;&lt;ebola&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21838" PostTypeId="2" ParentId="21827" CreationDate="2014-10-03T01:32:11.460" Score="11" Body="&lt;p&gt;If you have a man in a box scenario where you only look at numbers, the answer is, no, he won't last 14 days.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The difficulty with this question for me is that the body doesn't always behave the way it's supposed to. The 3-3-3 rule (3 minutes without air, 3 days without water, three weeks without food) and the &quot;100 hour rule&quot; (4.166 days) aren't absolutes.&lt;sup&gt;[2]&lt;/sup&gt; Some people die in hours, some 10 days. The variables are too great.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Guinness World Records puts the record for survival without water at 18 days&lt;sup&gt;[3]&lt;/sup&gt; by an 18 year old male forgotten in a cell by the police. But he was in a cool basement, and licked the walls which had a small amount of moisture on them. Had he been sweating or 2 decades older, he probably wouldn't have lasted as long.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Water requirement under extreme circumstances varies. How much clothes is your male wearing? Does he have shade? Where in the ocean is he? How inactive can he be? Can he oil his skin with fish oil? But mostly, does he have a &lt;em&gt;still suit&lt;/em&gt; (j/k)? These things all matter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eating protein without water isn't wise. Carbs are better, but your guy doesn't have them. The better thing for your guy, who can certainly live for 14 days without food, is to suck the water out of the fish, and what he can't suck out, wring out at the end. If he has access to the whole fish, the eyeballs and the spine also have water in them.* The body has all kinds of homeostatic mechanisms to preserve fluids, including continuous secretion of ADH (Anti-Diuretic Hormone), osmoreceptors and baroreceptors to regulate fluid volume and how much water is lost from the kidneys.&lt;sup&gt;[4]&lt;/sup&gt; He'll suffer terribly; fluid will be sucked out of his joints and cells and his blood urea nitrogen will go up and his kidneys will be damaged, he'll hallucinate, he'll need hospitalization, but might he live? If he is young, healthy and hydrated going in, and other factors (a tarp for shade, etc.) mitigate his water loss, I think the answer is yes, he might.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*&lt;sub&gt;In 1953, a French physician and sea survival expert, Alain Bombard, set sail in a Zodiac inflatable dinghy with the only food and water officially sealed to discourage himself from using it. He started immediately with drinking small amounts of seawater, and would suck water from fish, and, if he had any fresh rain water, would eat raw fish. He sailed from Minorca to Barbados, eating supplied food and water only once. His rival survivalist, another physician, Hannes Lindemann, contested Bombard's claims, but did well at sea as well.&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[1] &lt;a href=&quot;http://books.google.com/books?id=Lqz-4XU5m28C&amp;amp;pg=PA52&amp;amp;lpg=PA52&amp;amp;dq=the+100+hour+rule+for+survival+without+water&amp;amp;source=bl&amp;amp;ots=j89K-vVgVI&amp;amp;sig=F0DwxG3wjormIqQjic7Docqsv8U&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=-uUtVKnOE8LgsAT98ILQBw&amp;amp;ved=0CCAQ6AEwAA#v=onepage&amp;amp;q=the%20100%20hour%20rule%20for%20survival%20without%20water&amp;amp;f=false&quot; rel=&quot;noreferrer&quot;&gt;The Biology of Human Survival : Life and Death in Extreme Environments&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://www.thevisualmd.com/searchimg/?idu=1033609084&quot; rel=&quot;noreferrer&quot;&gt;Dehydration&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://en.wikipedia.org/wiki/Andreas_Mihavecz&quot; rel=&quot;noreferrer&quot;&gt;Andreas Mihavecz&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[4] &lt;a href=&quot;http://www.anaesthesiamcq.com/FluidBook/fl5_6.php&quot; rel=&quot;noreferrer&quot;&gt;Fluid Physiology, Ch. 5, 6&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-10-03T01:32:11.460" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21839" PostTypeId="2" ParentId="21837" CreationDate="2014-10-03T02:36:41.027" Score="5" Body="&lt;p&gt;First, confirmation from the &lt;a href=&quot;http://www.who.int/mediacentre/factsheets/fs103/en/&quot;&gt;World Health Organisation&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The incubation period, that is, the time interval from infection with the virus to onset of symptoms is 2 to 21 days. Humans are not infectious until they develop symptoms. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;People remain infectious as long as their blood and body fluids, including semen and breast milk, contain the virus. Men who have recovered from the disease can still transmit the virus through their semen for up to 7 weeks after recovery from illness.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They also state that deceased people may still transmit the virus via body fluids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to why the patients become infectious only when symptoms show, there are several related ideas.  For example, from the &lt;a href=&quot;http://www.cdc.gov/vhf/ebola/hcp/clinician-information-us-healthcare-settings.html&quot;&gt;CDC&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ebola virus enters the patient through mucous membranes, breaks in the skin, or parenterally and infects many cell types, including monocytes, macrophages, dendritic cells, endothelial cells, fibroblasts, hepatocytes, adrenal cortical cells and epithelial cells. The incubation period may be related to the infection route (i.e., 6 days for injection versus 10 days for contact). Ebola virus migrates from the initial infection site to regional lymph nodes and subsequently to the liver, spleen and adrenal gland. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.askdrray.com/ebola-virus-an-emerging-killer-infection/&quot;&gt;Dr. Ray Schilling&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ebola virus disease has an incubation time of 8 to 10 days where the person may complain of some tiredness, but is not sick yet. &lt;strong&gt;This is the time when the Ebola virus multiplies. It  paralyzes the immune system and distributes itself through the organ system.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From there, the symptoms and effects of Ebola are fast, according to the article &quot;Ebola Virus Pathogenesis: Implications for Vaccines and Therapies&quot; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC224575/&quot;&gt;Sullivan et al. 2003&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ebola virus replicates at an unusually high rate that overwhelms the protein synthesis apparatus of infected cells and host immune defenses&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerDisplayName="user9474" LastEditorUserId="3624" LastEditDate="2014-10-03T07:02:50.460" LastActivityDate="2014-10-03T07:02:50.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21840" PostTypeId="2" ParentId="21825" CreationDate="2014-10-03T03:21:05.277" Score="11" Body="&lt;p&gt;Neurons do not divide due to the reasons mentioned in Cornelius's answer. However, some new neurons can be generated in adults (Ref: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10920/&quot;&gt;Neuroscience, 2nd edition&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generation of new neurons in adults was first demonstrated in birds, where labeled DNA precursors could be found in differentiated neurons. Experiments in mammals and humans demonstrated later that new neurons are created in the central nervous system (CNS) in adults, although it seems to be restricted to some particular regions: granule cell layer of the olfactory bulb and dentate gyrus of the hippocampus. These new neurons seem to be local circuit neurons and interneurons (i.e. no long distance neurons).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How are the new neurons produced if neurons cannot divide? They come from neural stem cells (&lt;a href=&quot;http://en.wikipedia.org/wiki/Neural_stem_cell&quot;&gt;NSCs&lt;/a&gt;) that were preserved in the sub-ventricular zone during development. NSCs are presumed to play a part in brain plasticity in the adult brain. However, they have therapeutic potential. Check the brief information in &lt;a href=&quot;http://en.wikipedia.org/wiki/Neural_stem_cell#Potential_clinical_applications&quot;&gt;wikipedia&lt;/a&gt;), or &lt;a href=&quot;http://www.nature.com/nrn/journal/v7/n1/full/nrn1829.html&quot;&gt;this perspective in Nature neuroscience&lt;/a&gt; that may contain further details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Neuroscience, 2nd edition. Purves D, Augustine GJ, Fitzpatrick D, et al., editors.&#xA;Sunderland (MA): &lt;a href=&quot;http://www.sinauer.com&quot;&gt;Sinauer Associates&lt;/a&gt;; 2001.&lt;/li&gt;&#xA;&lt;li&gt;Gene therapy: can neural stem cells deliver?  Müller FJ, Snyder EY,&#xA;Loring JF. Nat Rev Neurosci. 2006 Jan;7(1):75-84. Review. Erratum in:&#xA;Nat Rev Neurosci. 2006 Feb;7(2):167. PMID:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16371952&quot;&gt;16371952&lt;/a&gt; [PubMed -&#xA;indexed for MEDLINE]&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9099" LastEditorUserId="9099" LastEditDate="2014-10-03T04:31:15.630" LastActivityDate="2014-10-03T04:31:15.630" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21841" PostTypeId="1" CreationDate="2014-10-03T06:47:09.907" Score="2" ViewCount="281" Body="&lt;p&gt;When I download CNV SNP array data for ovarian cancer from TCGA data portal, I see some very small numbers like -5, -6 in the &quot;Segment_Mean&quot; column of the segmentation data files. I am very new to genetics, and I don't understand how that much deletion can occur in the gene. We have 2 copies of each gene in our normal cells, and my intuition tells that the minimum loss for a gene in a cell can be -2 (both copies of that gene are lost). So, could someone please explain shortly how this -5, -6 copy number losses are computed?&lt;/p&gt;&#xA;" OwnerUserId="5054" LastEditorUserId="14852" LastEditDate="2015-04-24T04:08:23.940" LastActivityDate="2015-04-24T04:08:23.940" Title="How TCGA CNV values are calculated?" Tags="&lt;genetics&gt;&lt;tcga&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21842" PostTypeId="1" CreationDate="2014-10-03T09:16:22.577" Score="2" ViewCount="733" Body="&lt;p&gt;You and me are different at DNA level. My eye color gene is different from yours. So, my DNA is different from yours. How can a scientist identify a certain gene in a chromosome (and its function) if chromosomes are different? How can we talk about &quot;the&quot; human DNA when nobody share the same (except twins)? Please, this is a practical question about how scientists identify genes, not a philosophic one (a question that bother me every time I read about discoveries in genetic)&lt;/p&gt;&#xA;" OwnerUserId="9631" LastActivityDate="2014-10-03T10:18:02.220" Title="How to identify genes?" Tags="&lt;genetics&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21843" PostTypeId="2" ParentId="21842" CreationDate="2014-10-03T10:18:02.220" Score="4" Body="&lt;p&gt;First of all: We are not very different on the genetic level - the identity is somewhere around 99.6 to 99.9%. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2424287/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for details. If this wouldn't be like this, things like blood transfusions or organ transplants wouldn't work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To identify genes there are different routes. &quot;In the old days&quot; (meaning before the possibility of massive high throughput sequencing or DNA microarrays), genes were usually discovered when they were connected to a disease which had a noticable phenotype. Researchers then tried to find out which protein or pathway was affected and from there went backwards to identify the genetic region. This way of discovery was relatively slow. An example for this kind of identification is the identification of the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8343963&quot; rel=&quot;nofollow&quot;&gt;Mitf&lt;/a&gt; gene which is important for the development of pigmentation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you sequence DNA (doesn't matter here if these are complete genomes or only parts of it) you can identify genes based on homology with already known genes. You can also predict the presence of genes in a certain sequence based on regulatory sequences in the region before the gene (the promoter). These sequences are known and also highly conserved, so this gives a good estimate. Predicted genes usually need to be verified experimentally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is done today are the so called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Genome-wide_association_study&quot; rel=&quot;nofollow&quot;&gt;genome wide association studies&lt;/a&gt;&quot;. Here you take a big cohort of people which all share one phenotype (for example blue eye color). Then you take a second group of people which do not show this phenotype and analyse their genomes (usually by sequencing or SNP genotyping). Then you compare the two groups to find the differences. Ideally you can then more or less directly identify a causative mutation which is responsible for the phenotypic difference between the two study groups. This usually needs also to be verified further.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-03T10:18:02.220" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21844" PostTypeId="1" CreationDate="2014-10-03T12:38:44.820" Score="3" ViewCount="392" Body="&lt;p&gt;I know that galactose can be found in sugar beets and some gums so I thought plants could synthesize galactose but in my book the answer to the question &quot;Which of these can be synthesized with photosynthesis in plants&quot; was only fructose and glucose. Is that correct?&lt;/p&gt;&#xA;" OwnerUserId="9633" LastActivityDate="2014-10-03T12:38:44.820" Title="Can Galactose be synthesized with photosynthesis?" Tags="&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21845" PostTypeId="1" CreationDate="2014-10-03T13:37:17.030" Score="1" ViewCount="47" Body="&lt;p&gt;What are the options for programmatic fast searching of 100-1000 short reads to a public server and obtain list of nearby genes where the reads map?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Input: ~100-1000 short reads&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Output: GFF list of genes it maps to or nearby genes&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genome UCSC is restrictive to the number of searches and AFAICS it won't allow programmatic use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any ideas? I've asked this question to another forum without much luck:&#xA;&lt;a href=&quot;https://www.biostars.org/p/114124/&quot; rel=&quot;nofollow&quot;&gt;https://www.biostars.org/p/114124/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2014-10-04T06:36:22.800" Title="programmatic fast search of 100-1000 short reads to a public server and obtain list of nearby genes" Tags="&lt;dna&gt;&lt;database&gt;&lt;blast&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21846" PostTypeId="1" CreationDate="2014-10-03T18:15:03.110" Score="2" ViewCount="909" Body="&lt;p&gt;I was in my biology class, learning the history of spontaneous generation and how this idea was discarded. I told my teacher that is the same as evolution but in a different timeline. I Argue that evolution does not explain how life formed, but complemented by abiogenesis. Ultimately it is almost the same thing. Therefore it could not rule out spontaneous generation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I got an F. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My appreciation is so wrong?&lt;/p&gt;&#xA;" OwnerUserId="9373" LastEditorUserId="9373" LastEditDate="2014-10-03T18:20:07.947" LastActivityDate="2014-10-03T21:21:07.433" Title="are the spontaneous generation and evolution the same idea but in a different time scale?" Tags="&lt;evolution&gt;&lt;homework&gt;&lt;abiogenesis&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21847" PostTypeId="1" CreationDate="2014-10-03T18:37:50.833" Score="6" ViewCount="23051" Body="&lt;p&gt;What happens when you mix different blood types that are not compatible? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, if a patient has type A blood and receives type B blood, or v.v.? &lt;/p&gt;&#xA;" OwnerUserId="9636" LastActivityDate="2016-12-10T23:13:09.623" Title="What happens when you mix type A with type B blood (and v.v)" Tags="&lt;hematology&gt;&lt;blood-circulation&gt;&lt;red-blood-cell&gt;&lt;antigen&gt;&lt;transfusion&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21848" PostTypeId="2" ParentId="21846" CreationDate="2014-10-03T18:40:29.980" Score="2" Body="&lt;p&gt;You are right in the sense the evolutionary biology doesn't try to explain the origin of life as it is not within its scope. Other fields of biology investigate the question of origin of life (abiogenesis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, there is a very important difference between spontaneous generation and evolution. Life originated at some point and the through repetitive speciation events, created the whole diversity of species existing on earth. You could say that what really happens is that there was one spontaneous creation of life (although there is more a continuum from non-living to living things than a sudden switch from non-living to living) out of non-living things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main fallacy of spontaneous generation is that under the spontaneous-generation-conceptualization of life, every species are made de novo and independently which is definitely not the case as in reality species speciate (split in two) causing the existence of to two new species. There are tons of fallacies hidden behind the spontaneous generation conception of life, one of which relates to the concept of species and another one is the origin of within population variation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in short spontaneous generation is definitely something different from a single abiogenesis and evolution and the hypothesis of spontaneous generation has been ruled out a long time ago already.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I am not so much aware of the grading philosophy in your school but your argumentation was wrong and probably the F was worth. Next time, you will probably want to discuss your opinions with your teacher before the test to make sure you agree.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-10-03T18:40:29.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21850" PostTypeId="2" ParentId="21847" CreationDate="2014-10-03T19:04:22.783" Score="5" Body="&lt;p&gt;The blood type of people is determined by proteins which are anchored into the surface of the red blood cells. Cells can either express the A, B, A and B or no marker, resulting in the blood groups A, B, AB and 0. People which have a certain blood type (for example A) have antibodies against the other blood type (in this case B). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This will lead to the attachment of antibodies against the subtype which you don't have (so B for people with A and vice versa) on the transfused blood cells and their lysis. Depending on the amount of blood transfused, this can also lead to a very serious immune reaction. This works like in the figure below (from &lt;a href=&quot;http://learn.genetics.utah.edu/content/inheritance/blood/&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4kFOs.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To avoid this reaction a sample of the blood, which is about to be transfused is mixed with blood from the patient before the transfusion takes place. This looks like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information look here: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Acute_hemolytic_transfusion_reaction&quot; rel=&quot;noreferrer&quot;&gt;Acute hemolytic transfusion reaction&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/001303.htm&quot; rel=&quot;noreferrer&quot;&gt;Transfusion reaction - hemolytic&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://learn.genetics.utah.edu/content/inheritance/blood/&quot; rel=&quot;noreferrer&quot;&gt;Genes and Blood Type&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pathology.med.umich.edu/bloodbank/manual/bbch_7/&quot; rel=&quot;noreferrer&quot;&gt;Adverse reactions to transfusion&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-03T19:04:22.783" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21852" PostTypeId="2" ParentId="21846" CreationDate="2014-10-03T21:21:07.433" Score="1" Body="&lt;p&gt;Evolution is about descent with modification.  Spontaneous generation doesn't have that.  It's about &lt;strong&gt;modern&lt;/strong&gt; organisms emerging from raw molecules.  If flies spontaneously appeared from rotting cow meat, why would they have DNA that made them look like they were evolutionarily related to other insects?&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-10-03T21:21:07.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21853" PostTypeId="1" CreationDate="2014-10-04T00:04:20.863" Score="3" ViewCount="977" Body="&lt;p&gt;How do we know we are made of stardust? As our cells divide, are our atoms repurposed from existing materials or spontaneously generated? Do we consume materials after we are born that contain elements that were in stars? This I would understand. Or, as our cells are initially dividing after conception, but before birth, are we already repurposing existing materials to grow?&lt;/p&gt;&#xA;" OwnerUserId="9640" LastActivityDate="2014-10-07T02:59:46.893" Title="Stardust or the elements in our bodies" Tags="&lt;cell-biology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21854" PostTypeId="1" AcceptedAnswerId="21859" CreationDate="2014-10-04T02:28:48.043" Score="2" ViewCount="48" Body="&lt;p&gt;I know that dynein arms and microtubules are involved in the contraction of certain parts of the flagella to produce a wave motion, but I don't understand they are related to the 9+2 structure of the basal body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do flagella work in prokaryotes and eukaryotes?&lt;/p&gt;&#xA;" OwnerUserId="5179" LastActivityDate="2014-10-04T05:29:11.727" Title="Mechanisms of Flagella" Tags="&lt;cell&gt;&lt;movement&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21855" PostTypeId="2" ParentId="20912" CreationDate="2014-10-04T02:48:47.327" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;I imagine that turtle looking up at that food, and sub-consciously&#xA;  wishing to get to it, constantly straining, for its entire lifetime.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;It seems plausible to me that we (advanced life) could have a&#xA;  biological mechanism to &quot;write&quot; needed alterations into either our own&#xA;  DNA or our reproductive DNA over time, triggering the very specific&#xA;  evolutionary developments necessary to our survival without relying on&#xA;  random mutation.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That is a pre-Darwin idea of evolution called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Inheritance_of_acquired_characteristics&quot; rel=&quot;nofollow noreferrer&quot;&gt;inheritance of acquired characteristics&lt;/a&gt;&quot; or Lamarckism after it's creator French natural philosopher Jean-Baptiste Lamarck. Lamarck postulated that given the use of tissues altered those tissues e.g. lifting weights makes muscles bigger, then an organisms descendants would benefit if everything the parent's tissues &quot;learned&quot; could be passed on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are actually epigenetic factors in cells that selectively turn genes on or off or otherwise modify their use generation to generation. But this is not evolution because the genes are always there, ready to be used if needed and no new information is ever created. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The flaws in Lamarckism are that, even if the mechanism existed to transmit acquired characteristics, how would it know what characteristics led to what outcome? How could it distinguish positive changes from negative ones? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most fatally, how could an organism evolve a system that was not related to an existing behavior? For the turtle to stretch its neck, it must desire to eat the leaves and exert effort to do so. How did it acquire the behavior of desiring to eat the leave in the first place? Going forward, if the plants it does eat goes away, how would it ever find another food source? It wouldn't desire to eat inedible plants so it would never exert itself to do so and would never pass that exertion on to it's young.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hiccup in your understanding of Darwinism is that you've got it backwards. Species don't find solutions and evolve. It's not something species do. It's something that &lt;strong&gt;&lt;em&gt;happens&lt;/em&gt;&lt;/strong&gt; to species, a force from the outside. It's not analogous to humans setting down to consciously solve a problem. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Darwin was originally going to use the analogy of &quot;wedging&quot; instead of &quot;natural selection.&quot; He wanted to emphasize that it was the environment squeezing in on species that formed them. (Today we think of wedges largely for their splitting power but in but in Darwin's day, if you wanted to compress something you used a wedge hammered in from the side. It was a common tool that performed the same jobs as jacks and hydraulics do today.) But he went with the anthropomorphic analogy of nature being an animal breeder selecting for traits for reproductive success and a lot of misunderstandings followed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution is not random. Only variations themselves are random. The selection of them is not. It's like shooting dice. The fall of the dice is random but only certain values of dice are winning number and are &quot;selected.&quot; The same mutation might show up in every generation for millions of years but produce no change until the environment changes to make the mutation useful. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Species have no existence independent from their environment. The environment squeezes them into a specific form, one that best satisfies the demands of the Second Law of thermodynamics. If the environment doesn't change, then the organism won't either. From that perspective, adaptation is about as amazing as a rock rolling downhill. (That would look pretty fantastic if you didn't know about gravity.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine you had never seen clay and never seen molding. Your walk along a stream bank lined with clay. Walking one way you pass a blank stretch of clay. After you pass, a leaf falls into the claw and creates a near perfect imprint before being blown away. When you return past that spot, it looks like the clay has somehow altered itself, against all probability, into an exact mirror duplicate of a leaf. How you might wonder, could the clay possibly know how to exactly duplicate the shape of a leaf?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the clay did nothing. The clay did not alter to fit the leaf, the force of the falling leaf altered the clay. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Likewise, species do not evolve themselves, they are evolved by external forces. Species seem to miraculous fit their ecological niches but, just like the clay, did nothing to shape themselves to the niche. Just as the clay will be passively shaped by the pressure of molding, species have no choice but to assume the forms they do. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's not survival of the &lt;em&gt;fittist&lt;/em&gt; but survival of the &lt;strong&gt;&lt;em&gt;fitted&lt;/em&gt;&lt;/strong&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="9612" LastEditorUserId="43480" LastEditDate="2019-03-29T17:10:20.557" LastActivityDate="2019-03-29T17:10:20.557" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="21856" PostTypeId="2" ParentId="21853" CreationDate="2014-10-04T03:32:01.830" Score="8" Body="&lt;p&gt;The saying that you are referring to is from Carl Sagan, when he stated that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;We are a way for the universe to know itself. Some part of our being knows this is where we came from. We long to return. And we can, because the cosmos is also within us. We're made of star stuff,&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.livescience.com/32828-humans-really-made-stars.html&quot;&gt;Quote source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In answer to your question, yes, we are 'repurposing' the elements that make us up, as are all living and non-living matter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chris Impey, professor of astronomy at the University of Arizona is quoted in the article &lt;a href=&quot;http://www.livescience.com/32828-humans-really-made-stars.html&quot;&gt;Are We Really All Made of Stars?&lt;/a&gt; (Melina, 2010) as stating:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the fact that the carbon, nitrogen and oxygen atoms in our bodies, as well as atoms of all other heavy elements, were created in previous generations of stars over 4.5 billion years ago. Because humans and every other animal as well as most of the matter on Earth contain these elements, we are literally made of star stuff&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The elements that make up the cells etc in humans and any life forms, as with the materials that make up the Earth itself were ultimately formed by &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleosynthesis&quot;&gt;nucleosynthesis&lt;/a&gt; processes (mostly fusion and neutron capture) in stars, explained in the webpage &lt;a href=&quot;http://www2.glos.ac.uk/gdn/origins/earth/ch2_4.htm&quot;&gt;Origin of the Chemical Elements&lt;/a&gt; as being:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the early Universe consisted almost entirely of the element hydrogen, with a small amount of helium present too. Hydrogen, therefore, is thought to be the starting material from which all other elements have been built. This is consistent with the very high abundance of hydrogen in the solar abundance profile. The process may be thought of as a series of fusion reactions which weld together simple atomic nuclei to build increasing complex atomic nuclei.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerDisplayName="user9474" LastActivityDate="2014-10-04T03:32:01.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21857" PostTypeId="2" ParentId="9085" CreationDate="2014-10-04T04:30:01.537" Score="4" Body="&lt;p&gt;The problem with Intelligent Design is that it doesn't appreciate that the forces that shape species (and individual organism) have to be constant and ongoing or the species disappears. The past matters little, it's what happens right here, right now that keeps species in any particular form. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biological system are not static structures like a building. You put energy into a building when you move and shape it material during construction. Immediately though, the energy in the structure begins to flow out into the ambient environment, causing the building to loose it's structure and decay. Eventually it will fall to dust. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biological systems are dynamic, not static. A living organism is like a whirlpool.  A whirlpool is a complex ordered structure that dissipates energy caused by friction between streams moving at different velocities next to each other.  It is never composed of the same molecules of water from moment to moment and once water has passed through the whirlpool it never returns. The whirlpool is the structure, not the transitory water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Changing the rate of flow, depth of the water, temperature etc changes the exact structure of the whirlpool instantly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biological systems are non-material structures like whirlpools. Matter and energy constantly flows into and out of bodies. We stop stop breathing, we die. Your body, even scars and bones are continuously begin torn down and regenerated. The average half life of atoms in your body is seven years. Even atoms that do remain in the body are moved from molecule to molecule and from tissue to tissue. Only the pattern remains semi-constant. Species and individuals organisms are the structures, not the transitory matter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Changing the flow of matter and energy into an organism, changes it's structure instantly. Changing the flow over long periods, changes entire species.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I show a picture of a whirlpool in water but crop it so you can't see whether it's occurring in a natural stream or a flow tank in a lab, how could tell whether the whirlpool was artificial or not?  You couldn't, because there is no structural difference between an artificial whirlpool and natural whirlpool. They look the same because the same forces and laws create them and do so continuously&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same is true of life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can't look at living things and determine whether they are natural or artificial because just like a whirlpool, it is the flow of matter and energy through life, at any particular moment, that defines it's structure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if some intelligence, divine or material, did alter or even start life, it would have to fit into the material environment exactly like one that arose naturally. It would be indistinguishable from a natural one because the same forces would give it shape and maintain it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the best argument against intelligent design is that we don't need to evoke it explain how life exist now, moment to moment. If natural forces continuously create and maintain life continuously today, then they had to be able to do so yesterday and the day before, all the back. &lt;/p&gt;&#xA;" OwnerUserId="9612" LastActivityDate="2014-10-04T04:30:01.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21858" PostTypeId="1" AcceptedAnswerId="23672" CreationDate="2014-10-04T05:26:14.867" Score="3" ViewCount="7241" Body="&lt;p&gt;&lt;strong&gt;Plus lens therapy&lt;/strong&gt; is the theory that most myopia is environmentally triggered and that conventional corrective minus lenses increase nearsightedness over time. Thus the hypothesis that applying &lt;em&gt;plus&lt;/em&gt; lenses for nearsightedness will invert the environmental pressures and halt or reverse existing myopia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;What is the scientific majority and minority opinion on plus lens therapy?&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4788" LastActivityDate="2014-12-06T00:36:30.997" Title="What is the scientific opinion on plus lens therapy?" Tags="&lt;human-eye&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21859" PostTypeId="2" ParentId="21854" CreationDate="2014-10-04T05:29:11.727" Score="2" Body="&lt;p&gt;Flagella in prokaryotets is very different from that of eukaryotes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main structural protein in a prokaryotic flagellum is flagellin. The flagellar motion is caused by a molecular motor similar to Mitochondrial ATP-synthase; molecular motion generated by the chemiosmotic energy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eukaryotic flagella or cilia are made of microtubules with dynein attached on to them and cause the movement by the energy generated by ATP hydrolysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See the &lt;a href=&quot;http://en.wikipedia.org/wiki/Flagellum&quot; rel=&quot;nofollow&quot;&gt;wikipedia article&lt;/a&gt;. It is clear enough.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-10-04T05:29:11.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21860" PostTypeId="2" ParentId="21845" CreationDate="2014-10-04T06:12:18.007" Score="2" Body="&lt;p&gt;This can be done offline and wont require too much of computational resource.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you will need:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A fast short read aligner such as STAR or even bowtie (STAR is faster)&lt;/li&gt;&#xA;&lt;li&gt;Genome sequence (you will have to build index for the genome for your aligner)&lt;/li&gt;&#xA;&lt;li&gt;A GTF annotations file (get it from GENCODE or any other standard genome repository for your organism of interest)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Before you align remove redundant reads. Keep their counts if necessary.&#xA;Align the reads using any of these aligners and obtain the alignment co-ordinates. The default output is SAM format for STAR and a tabular format for bowtie (bowtie also gives SAM). &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Column-3 of SAM shows the name of the reference sequence&#xA;where alignment happened (chromosome)&lt;/li&gt;&#xA;&lt;li&gt;Column-4 is sequence start&lt;/li&gt;&#xA;&lt;li&gt;Column-10 is read sequence. Add the length of this to column 4 value to get stop site.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;The columns are tab separated&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now define a window that you define as proximal/nearby (lets say 500nt). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now all you have to do is find genes that lie $\pm500nt$ from your start/stop sites. In your reference GTF parse for the lines that have the feature &quot;&lt;strong&gt;gene&lt;/strong&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am giving an example using awk. You can use any programming language you are comfortable with. Check the &lt;a href=&quot;http://asia.ensembl.org/info/website/upload/gff.html&quot; rel=&quot;nofollow&quot;&gt;GTF format&lt;/a&gt; also.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that you made a file (reads.txt) from your SAM output in this format:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Chromosome &amp;lt;tab&amp;gt; Orientation (+/-) &amp;lt;tab&amp;gt; Start &amp;lt;tab&amp;gt; Stop&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I am giving an example awk script:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;example.awk&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;#!/bin/gawk&#xA;&#xA;BEGIN{FS=OFS=&quot;\t&quot;}&#xA;&#xA;NR==FNR{&#xA;    a[$1 FS $2][$3 FS $4] # store the co-ordinate information from your reads file&#xA;    next&#xA;}&#xA;&#xA;$3==&quot;gene&quot; &amp;amp;&amp;amp; ($4 FS $7) in a{ # quick parse for reference chromosome and orientation&#xA;&#xA;    i=$4 FS $7&#xA;    for(j in a[i]){&#xA;        split(j,jj,FS) &#xA;        if(jj[1]&amp;gt;=$4 &amp;amp;&amp;amp; jj[2]&amp;lt;=$5)&#xA;            print $0&quot;;contained&quot;&#xA;&#xA;        else if($4&amp;lt;=jj[2]+500 || $5&amp;gt;=jj[1]-500)&#xA;            print $0&quot;;partial overlap/proximal&quot;&#xA;        }&#xA;}&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;call it like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;awk -f example.awk reads.txt annotations.gtf&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;NOTE&lt;/strong&gt;: In the above script I have not considered antisense proximity. If you want to allow that then don't parse for orientation. Also gawk version &amp;lt; 4.0 doesn't allow multidimensional arrays. So install gawk&gt;=4.0&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The output is by default a GTF because you are printing selected lines of the reference GTF. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-10-04T06:36:22.800" LastActivityDate="2014-10-04T06:36:22.800" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21861" PostTypeId="2" ParentId="21853" CreationDate="2014-10-04T06:30:05.200" Score="3" Body="&lt;p&gt;Unless you are inside a star or a fusion reactor- Matter is neither created nor destroyed. However, fission of unstable isotopes is fairly common on earth's surface.&#xA;You may accumulate one of such isotopes but usually the ones that are generally absorbed in our bodies such as C-14 have very long decay times (more than your lifetime). So for all practical purposes you are created from the atoms of existing matter and these keep getting recycled from the environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the composition of different stars is different and statement like &quot;&lt;em&gt;Do we consume materials after we are born that contain elements that were in stars&lt;/em&gt;&quot;, is too farfetched. Many millions of years have passed since earth came out of a star and lot of nuclear reactions have happened in this time. So the composition is of course different. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-10-06T04:14:38.457" LastActivityDate="2014-10-06T04:14:38.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21862" PostTypeId="2" ParentId="21824" CreationDate="2014-10-04T07:12:57.653" Score="2" Body="&lt;p&gt;You can see the wikipedia article on meristem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The apical meristem differentiates into floral meristem that gives rise to flowers.&#xA;From this the cells specifically expressing &lt;em&gt;APETALA3 (AP3), PISTILLATA (PI), AGAMOUS (AG) and SEPALLATA (SEP)&lt;/em&gt; would give rise to the stamen &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0168952507002715&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[ref]&lt;/sup&gt;&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;CRC gene is essential for female development and plants lacking this will not produce pistils. So cells expressing this gene will give rise to female parts&lt;a href=&quot;http://www.plantphysiol.org/content/150/4/1764.full&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[ref]&lt;/sup&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nonetheless mutation happening at any stage of the development of floral meristem can be transmitted to the pollens/ovules if the mutated cells stochastically give rise to that lineage. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-10-04T07:12:57.653" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21863" PostTypeId="1" AcceptedAnswerId="24377" CreationDate="2014-10-04T07:13:12.473" Score="1" ViewCount="259" Body="&lt;p&gt;Technology has evolved so much as to clone animals. But, what about human cloning?&#xA;Is it really possible to create humans in lab? Or is it that technology has not advanced to that level..?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why cant it be attempted..? &lt;/p&gt;&#xA;" OwnerUserId="9642" LastEditorUserId="3340" LastEditDate="2014-12-05T18:30:03.473" LastActivityDate="2014-12-05T18:30:03.473" Title="Possibility of Human cloning" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;human-genetics&gt;&lt;cloning&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21864" PostTypeId="1" AcceptedAnswerId="42117" CreationDate="2014-10-04T10:56:33.827" Score="10" ViewCount="7410" Body="&lt;p&gt;I have a large wooden cutting board which is used in my kitchen mainly for preparing egg pasta. The wood type is &lt;em&gt;Populus&lt;/em&gt; (poplar or aspen or cottonwood).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main ingredients used with the cutting board are: flour (mainly soft wheat flour), hens' eggs, white sugar, butter, and baking powder.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After the food preparation, the cutting board is cleaned by scraping away the ingredients remains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The board has some cracks and some small unknown insects are living inside the cracks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The board has also a lot of holes due to woodboring beetles but I think the woodworms operated long time ago and they no longer live in the cutting board.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The unknown insect has an approximate length of 1 mm (along the direction of their movements) and a width of 0.3 mm. The unknown insects do not have wings, they just walk. I am not able to see how many pairs of legs they have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The color of the insect is pale brown.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cutting board was free from these unknown insects some months ago but then they appeared.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;What insects are they?&lt;/li&gt;&#xA;&lt;li&gt;Are these insects poisonous to humans?&lt;/li&gt;&#xA;&lt;li&gt;How can I get rid of them?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The unknown insects could be &lt;em&gt;Acarus siro&lt;/em&gt;, I will try to get a picture of the insects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update 2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a picture. The bottom part of the image is a one Euro coin, the top part of the image is a caliper (each bright area is one mm tick).&#xA;&lt;img src=&quot;https://i.stack.imgur.com/9d0M2.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some more pictures:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Q22Fg.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hAhBi.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ShJFV.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9643" LastEditorUserId="16866" LastEditDate="2018-11-10T16:34:08.170" LastActivityDate="2019-02-09T05:08:38.093" Title="Questions about insects eating flour and living in the cracks of a wooden cutting boards" Tags="&lt;species-identification&gt;&lt;zoology&gt;&lt;entomology&gt;&lt;food&gt;&lt;pest-control&gt;" AnswerCount="1" CommentCount="13" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21865" PostTypeId="1" CreationDate="2014-10-04T11:58:40.987" Score="22" ViewCount="418" Body="&lt;p&gt;Hiccups (&lt;a href=&quot;http://www.memidex.com/singultus&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;singultus&lt;/em&gt;&lt;/a&gt;) are caused by involuntary spasm of the intercostal muscles and diaphragm, producing a sudden inspiration with associated glottic closure. It seems the neurobiology of the reflex has been relatively well worked out (nicely summarized in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=22891647&quot; rel=&quot;noreferrer&quot;&gt;this review&lt;/a&gt;):&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Afferent limb: the vagus, phrenic, and cervical sympathetic chain&lt;/li&gt;&#xA;&lt;li&gt;Central mediators: the hypothalamus, medullary reticular formation, and brainstem respiratory centers&lt;/li&gt;&#xA;&lt;li&gt;Efferent limb:  primarily mediated by the phrenic nerve but also including the intercostals, and secondarily the recurrent laryngeal nerve to cause glottic closure&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;To my knowledge, hiccups are always cyclical, with a period of between 1 and 30 seconds. According to the afore cited article, this interval is relatively constant it a given individual. The cycling stops after some time; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=25055206&quot; rel=&quot;noreferrer&quot;&gt;efferent vagal tone can suppress it&lt;/a&gt;, or it stops spontaneously. My question is:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What is the mechanism responsible for this periodicity?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;&lt;em&gt;Something&lt;/em&gt; must be triggering that afferent limb every 1 - 30s, but I can’t think of a normal physiologic process that triggers the firing of one or more nerves with such periodicity and then stops abruptly.&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-10-06T00:57:40.903" Title="What is the mechanism responsible for the periodicity of hiccups?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21866" PostTypeId="1" AcceptedAnswerId="21892" CreationDate="2014-10-04T13:48:34.267" Score="4" ViewCount="130" Body="&lt;p&gt;I am actually a computational biologist, pardon me if my question description is a bit off-note, my curiosity is driving me on&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A bit of background and context:&lt;/strong&gt;&#xA;In bacteria, a regulatory protein termed CsrA binds certain structures in the UTR regions of genes and prevents their translation. These structures are short hairpin-like and all have AGGA nucleotides in the exposed part. There are sRNAs that isolate the protein from its targets, a common feature of these sRNAs is that they have several repetitive hairpins that more or less display AGGA nucleotides in the exposed part. So basically, the sRNAs mimic the structures on the targets of the proteins and that makes them potent competitors for protein binding against the genes actually targeted by the protein. By relying on this mimickry the sRNAs bind CsrA, isolate it from its targets and remove its suppression on gene translation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My question:&lt;/strong&gt; Are there any other examples that illustrate similar mechanisms of analogy/mimickry of sRNAs to bind protein?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What I tried&lt;/strong&gt;&#xA;I've skimmed through a lot of literature to identify other similar systems in bacteria where sRNAs have conserved repetitive structures but to no avail. I hope someone with deeper experience directs me to such examples in any living organism, preferably bacteria but I am open to suggestion.&#xA;I found CRISPRs but these are  DNA based, I have come across few other cis-acting sRNAs which target mRNAs and aren't protein-binding. So could it be the case that sRNA mimickers aren't very pervasive in bacteria after all ?!&lt;/p&gt;&#xA;" OwnerUserId="9647" LastEditorUserId="3340" LastEditDate="2014-10-06T11:16:41.450" LastActivityDate="2014-10-06T11:16:41.450" Title="protein-binding sRNAs" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;protein-binding&gt;&lt;protein-interaction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21867" PostTypeId="1" AcceptedAnswerId="24783" CreationDate="2014-10-04T15:55:34.073" Score="2" ViewCount="3960" Body="&lt;p&gt;Can someone tell me the fundamental reason why K+ has low concentration outside of the cell and more inside of the cell?&lt;/p&gt;&#xA;" OwnerUserId="9648" LastActivityDate="2014-12-11T15:26:14.837" Title="Why does K+ have more concentration inside of the cell compared to outside of the cell? Why is Na+ and Cl- the opposite?" Tags="&lt;cell-membrane&gt;" AnswerCount="2" CommentCount="5" ClosedDate="2014-12-11T18:28:09.000" ContentLicense="CC BY-SA 3.0" />
  <row Id="21868" PostTypeId="1" AcceptedAnswerId="34347" CreationDate="2014-10-04T18:09:47.253" Score="2" ViewCount="535" Body="&lt;p&gt;I am trying to get standard ECG by using PhysioNet's &lt;a href=&quot;http://physionet.org/cgi-bin/atm/ATM&quot; rel=&quot;nofollow noreferrer&quot;&gt;ATM&lt;/a&gt; with parameters&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Wjozi.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;but I get&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AB9yx.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It should be something like&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4aFMc.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can you get complete standard 12-lead ECG out of Physionet database?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2015-05-18T22:17:30.330" Title="To get Standard ECG from PhysioNet?" Tags="&lt;cardiology&gt;&lt;electrocardiography&gt;&lt;research-tools&gt;&lt;research-process&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21869" PostTypeId="2" ParentId="21868" CreationDate="2014-10-04T19:01:15.347" Score="4" Body="&lt;p&gt;I don't think that all leads are available.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I looked at the &lt;strong&gt;Signals&lt;/strong&gt; combobox for different databases. This combobox seems to be the list of all available leads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, take a look at &lt;strong&gt;iafdb&lt;/strong&gt; (Intracardiac Atrial Fibrillation Database). It will plot you an ECG containing leads II, V1 and aVF and some other leads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example is the EEG database &lt;strong&gt;eegmmidb&lt;/strong&gt; (EEG Motor Movement/Image Dataset) which contains many leads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look also at the &lt;strong&gt;mimic2wdb/39&lt;/strong&gt; (MIMIC II waveform database, version 3 part 9) which contains 4 ECG leads and some other parameters like breath rate.&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-10-04T19:01:15.347" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21870" PostTypeId="2" ParentId="21868" CreationDate="2014-10-04T19:13:06.777" Score="3" Body="&lt;p&gt;As another answer suggested, it's a matter of choosing a database that has all of the leads. The St Petersburg INCART 12-lead Arrhythmia Database (incartdb) contains all 12 signals. &lt;a href=&quot;http://physionet.org/physiobank/database/incartdb/&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is the directory. The tracings are available by selecting it from the drop-down menu on the page you linked.&lt;/p&gt;&#xA;" OwnerUserId="9268" LastActivityDate="2014-10-04T19:13:06.777" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21871" PostTypeId="1" CreationDate="2014-10-04T15:54:04.617" Score="0" ViewCount="104" Body="&lt;p&gt;It's one of those names which are often said not to exist, like philtrum.&lt;/p&gt;&#xA;" OwnerDisplayName="Michael" LastEditorUserId="6561" LastEditDate="2015-10-12T23:11:06.047" LastActivityDate="2015-10-12T23:11:06.047" Title="Can anyone remind me of the name for the inter-scapular space on the back?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21872" PostTypeId="2" ParentId="21871" CreationDate="2014-10-04T18:25:58.657" Score="3" Body="&lt;p&gt;&quot;Inter-scapular space&quot; is defined as the space between the scapulae.  It was most likely created by doctors who had no name for the space.  Yet another expansion of the English language by those who have need of a word or phrase to describe something that has no word or phrase already.  I found no other definition.&lt;/p&gt;&#xA;" OwnerDisplayName="Carl N Graves" LastActivityDate="2014-10-04T18:25:58.657" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21875" PostTypeId="1" CreationDate="2014-10-04T22:42:39.147" Score="6" ViewCount="150" Body="&lt;p&gt;I am a 15 year old that enjoys looking at the micro world. The only issue that I have is that I can't find a good online source that will help me classify the name of the micro organism that I'm looking at. Does anyone know a place that will help me do this? Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="9653" LastEditorUserId="3553" LastEditDate="2016-03-25T02:05:48.213" LastActivityDate="2016-03-25T02:05:48.213" Title="What is a good source that will help me classify protists?" Tags="&lt;microbiology&gt;&lt;database&gt;&lt;microscopy&gt;&lt;classification&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21876" PostTypeId="1" CreationDate="2014-10-04T22:53:58.250" Score="3" ViewCount="1090" Body="&lt;p&gt;To clarify, I'm not asking about the common properties of living organisms, such as reproducing and having a metabolism, etc. What I'm curious about is, what is the difference between organic molecules and actual living beings?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, if a person's heart stops beating, they are technically dead, but all the chemical compounds and molecules are still there.. I guess another approach to this question would be &quot;If we bring together all the atoms of a living being in the same exact arrangement, would that new thing be alive?&quot;&lt;/p&gt;&#xA;" OwnerUserId="9633" LastActivityDate="2014-10-04T22:53:58.250" Title="What makes living beings alive?" Tags="&lt;life&gt;" AnswerCount="0" CommentCount="5" ClosedDate="2014-10-08T15:51:10.897" ContentLicense="CC BY-SA 3.0" />
  <row Id="21877" PostTypeId="1" AcceptedAnswerId="21879" CreationDate="2014-10-05T01:57:51.787" Score="2" ViewCount="52521" Body="&lt;p&gt;How are they similar and how are they different?&lt;/p&gt;&#xA;" OwnerUserId="9648" LastActivityDate="2014-10-05T05:23:42.360" Title="Whats the difference between voltage gated and ligand gated neurons?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-10-05T10:07:02.100" ContentLicense="CC BY-SA 3.0" />
  <row Id="21878" PostTypeId="1" CreationDate="2014-10-05T04:10:26.443" Score="2" ViewCount="829" Body="&lt;p&gt;My idea to calculate this is: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Define up to what age will do the calculation. (for instance 60)&lt;/li&gt;&#xA;&lt;li&gt;Determine how many cells born and died up to that point in life. (by type of cell)&lt;/li&gt;&#xA;&lt;li&gt;Determine how many proteins are synthesized in the cells life. (by type of cell) &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Points 2 and 3 are not constant throughout the life of the human body. To calculate this data I need a function. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After obtaining all the data: complete calculations of addition and multiplication. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is not about mathematics, but about useful data to make these calculations. Another approach would be welcome too.&lt;/p&gt;&#xA;" OwnerUserId="9373" LastEditorUserId="3340" LastEditDate="2014-10-06T04:40:51.943" LastActivityDate="2014-10-06T04:40:51.943" Title="How many proteins are synthesized in human body throughout life?" Tags="&lt;human-biology&gt;&lt;homework&gt;&lt;development&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21879" PostTypeId="2" ParentId="21877" CreationDate="2014-10-05T05:23:42.360" Score="2" Body="&lt;p&gt;There is no such thing as voltage gated or ligand gated NEURONS. I believe what you are refering to are what is known as voltage gated and ligand gated ion CHANNELS. Each neuron has both types of channels in their cell membrane. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Voltage gated ion channels open in response to voltage (i.e. when the cell gets depolarized) where as ligand gated channels open in response to a ligand (some chemical signal) binding to them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both types of channels are critical for proper activation of the post synaptic neuron. The pre synaptic neuron releases neurotransmitters into the synaptic cleft, these neurotransmitters then bind to the ligand gated channels, thus activating them. The ligand gated channels open up and allow the influx of sodium, which depolarizes the cell. This depolarization activates nearby voltage gated ion channels, which open up and let in even more sodium. Voltage gated sodium channels open up one region at a time, the previous region providing enough depolarization to activate the next regions voltage gated channels. This effectively allows the action potential to propagate through the cell.&lt;/p&gt;&#xA;" OwnerUserId="6038" LastActivityDate="2014-10-05T05:23:42.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21881" PostTypeId="1" CreationDate="2014-10-05T09:42:22.800" Score="12" ViewCount="3582" Body="&lt;p&gt;For example you have a cell or already a bunch of cells. Those cell(s) divide and after several week you have a grown organism, for example a human with limbs, several different organs etc. &#xA;However, how do cells know where up, down, left, right etc. is?&#xA;I know left and right can be defined clearly in physics, for example by the Wu experiment verifying parity violation really occur. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However how do cells define those directions? What are the mechanisms for them to grow into a certain direction and tell other cells to attain a certain property?&lt;/p&gt;&#xA;" OwnerUserId="9370" LastEditorUserId="9370" LastEditDate="2016-09-19T17:27:03.193" LastActivityDate="2016-09-19T17:27:03.193" Title="How does an embryo know where to grow limbs etc" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;development&gt;&lt;embryology&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21882" PostTypeId="1" AcceptedAnswerId="21883" CreationDate="2014-10-05T09:46:04.280" Score="4" ViewCount="217" Body="&lt;p&gt;&lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi&quot; rel=&quot;nofollow&quot;&gt;http://blast.ncbi.nlm.nih.gov/Blast.cgi&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this website, when I want to apply the psi-blast algorithm on a sequence, under the section of algorithm parameters , what does PSI-BLAST threshold mean? The question mark says it means that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Set the statistical significance threshold to include a sequence in the model used by PSI-BLAST to create the PSSM on the next iteration.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Another parameter is there called pseudocount. Did not understand that too. Could not understand what this means, someone please explain in simple language.&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="9099" LastEditDate="2014-10-05T10:50:06.303" LastActivityDate="2014-12-04T12:05:55.710" Title="PSI-BLAST website algorithm parameters" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21883" PostTypeId="2" ParentId="21882" CreationDate="2014-10-05T10:28:31.817" Score="3" Body="&lt;p&gt;PSI-BLAST is an iterative algorithm. Each cycle it uses a model (the position-specific scoring matrix, or &lt;a href=&quot;http://en.wikipedia.org/wiki/Position_weight_matrix&quot; rel=&quot;nofollow&quot;&gt;PSSM&lt;/a&gt;) to search for sequences matching the model, next updates the model with the sequences found, and then runs the search again with the updated model. That P-value controls which of the sequences found in each iteration should be included in the new model (i.e. only include those sequences satisfying the P-value).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the &lt;em&gt;pseudocounts&lt;/em&gt;, this is a value to be added to each column in the PSSM. The reason is to avoid zero count entries, which may give problems later. But as the help suggests:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pseduocount parameter. If zero is specified, then the parameter is automatically determined through a minimum length description principle (PMID 19088134). A value of 30 is suggested in order to obtain the approximate behavior before the minimum length principle was implemented.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is probably OK to leave the default option unless you have some reason to change it.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastEditorUserId="9099" LastEditDate="2014-10-05T10:38:36.830" LastActivityDate="2014-10-05T10:38:36.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21884" PostTypeId="1" CreationDate="2014-10-05T13:27:53.177" Score="4" ViewCount="793" Body="&lt;p&gt;Plant-&lt;strong&gt;A&lt;/strong&gt; has on average &lt;strong&gt;N&lt;/strong&gt; chloroplasts per cell. Plant-&lt;strong&gt;B&lt;/strong&gt; has on average &lt;strong&gt;M&lt;/strong&gt; chloroplasts per cell. If &lt;strong&gt;N &gt; M&lt;/strong&gt;, is plant-&lt;strong&gt;A&lt;/strong&gt; more efficient in turning carbon dioxide into oxygen? Also, is it possible to see chloroplasts with a standard bright-field microscope?&lt;/p&gt;&#xA;" OwnerUserId="9658" LastEditorUserId="3340" LastEditDate="2014-10-06T05:27:26.080" LastActivityDate="2017-01-18T09:13:59.120" Title="Is chloroplasts per cell indicative of the photosynthetic power of a plant?" Tags="&lt;plant-physiology&gt;&lt;photosynthesis&gt;&lt;chloroplasts&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21885" PostTypeId="1" AcceptedAnswerId="21899" CreationDate="2014-10-05T17:23:51.747" Score="4" ViewCount="176" Body="&lt;p&gt;Other than olfactory senses do sharks use some kind of sense that uses electromagnetic waves? Is this similar to an electric eel? I saw a book with the cover statement 'Sharks never get cancer'. IS this possible or just 'quackery' ? Could being constantly 'bathed' in some kind of electromagnetic field cause pre-cancer cells ( that are already unstable) to be 'disrupted'?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastActivityDate="2015-04-29T19:15:17.210" Title="About sharks and how they find fish" Tags="&lt;cancer&gt;&lt;ichthyology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21886" PostTypeId="1" AcceptedAnswerId="21887" CreationDate="2014-10-05T19:11:46.533" Score="8" ViewCount="2990" Body="&lt;p&gt;The wikipedia page on Hela cells refers to George Gey being able &quot;to isolate one specific cell, multiply it, and start a cell line.&quot; Later it says, &quot;In 1955 HeLa cells were the first human cells successfully cloned.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the difference between multiplying the cells and cloning them? How is multiplying not cloning?&lt;/p&gt;&#xA;" OwnerUserId="5160" LastActivityDate="2014-10-05T19:23:35.970" Title="What's the difference between growing cells in culture and cloning them?" Tags="&lt;cell-biology&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21887" PostTypeId="2" ParentId="21886" CreationDate="2014-10-05T19:23:35.970" Score="9" Body="&lt;p&gt;Clones are genetically identical daughter cells from one parent cell. So when you start you culture from one cell, all new cells are clones of this cell. &#xA;The first three cells (red, green and blue) undergo clonal expansion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/aE4Jf.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you multiply cells in cell culture you usually start with thousands of cells, as this can be seen in the second part of the figure. These cells are not genetically identical, as they individually collect mutations. So the daughter cells of each &quot;starter cell&quot; (a lot of them) in the mixture are technically clones, but the whole culture is not seen as clones. See also the &lt;a href=&quot;http://en.wikipedia.org/wiki/Clone_%28cell_biology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt; on this topic.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-05T19:23:35.970" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21889" PostTypeId="2" ParentId="21881" CreationDate="2014-10-06T00:31:19.483" Score="12" Body="&lt;p&gt;You may want to look into &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionary_developmental_biology&quot;&gt;&lt;strong&gt;&quot;Evolutionary - Developmental Biology&quot;&lt;/strong&gt;&lt;/a&gt;, which deals with how an embryo develops into a grown organism.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Thus, by combinatorial specifying the identity of particular body&#xA;  regions, &lt;strong&gt;Hox genes determine where limbs and other body segments will&#xA;  grow&lt;/strong&gt; in a developing embryo or larva. A paragon of a toolbox gene is&#xA;  Pax6/eyeless, which controls eye formation in all animals. It has been&#xA;  found to produce eyes in mice and Drosophila, even if mouse&#xA;  Pax6/eyeless was expressed in Drosophila.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In short, there's a sequence of gene activations that progressively map body into different regions. At first, there are just 3 regions (head, body, tail), then these get broken down into more and more finely defined sections. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can think of these sections as GPS coordinates for the body. A gene combination at a certain point means that a limb will grow there. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can look into &quot;Sonic Hedgehog&quot; gene, which allowed scientists to produce fuzzy growth on a fruit fly head. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most interesting thing is that &lt;strong&gt;every living creature is mapped/built using the same toolbox of genes&lt;/strong&gt;. The genes that define where a fruit fly wing is also define where a human arm is.&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="577" LastEditDate="2014-10-06T00:38:49.300" LastActivityDate="2014-10-06T00:38:49.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21890" PostTypeId="2" ParentId="21865" CreationDate="2014-10-06T00:57:40.903" Score="6" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Van_der_Pol_oscillator&quot; rel=&quot;nofollow noreferrer&quot;&gt;Check out Van Der Pol (chaotic) oscillator&lt;/a&gt;. It can be used to model heart rhythms. If a stimulus is applied to the oscillator, it will return to the curved envelope discussed in the article.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if &quot;pushed just right&quot;, the oscillator's current state will be pushed towards the very center of the loop, and it will stop oscillating. This is the mechanism by which a sudden blow to the chest can stop the heart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reading up on hiccups, their &quot;almost regular&quot; interval sounds similar to a chaotic oscillator. The abrupt stop may represent pushing the oscillator towards the middle of the limit cycle, from which it cannot recover, effectively stopping hiccups&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8ZO9q.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2014-10-06T00:57:40.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21891" PostTypeId="2" ParentId="21884" CreationDate="2014-10-06T04:36:41.920" Score="4" Body="&lt;p&gt;You can say that but chloroplasts do not have uniform morphology across different species. Moreover some organisms such as red algae have chloroplasts of different origin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Real indicator would be lets say number of chloroplast ATP synthases and/or light harvesting photosystems; these can be perhaps indirectly approximated by the total surface area of the thylakoids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But for all practical purposes and comparison between not so distant species &lt;strong&gt;density&lt;/strong&gt; of chloroplasts is a decent enough approximate for photosynthetic power. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;About &lt;em&gt;turning carbon dioxide to oxygen&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should note that the source of oxygen is not CO&lt;sub&gt;2&lt;/sub&gt;. Oxygen comes from photolysis of water; this is the initial step in the electron transport chain (ETC) in chloroplasts. The ETC results in production of ATP and NADPH; the latter is used in the Calvin-Benson cycle to fix CO&lt;sub&gt;2&lt;/sub&gt; to sugar. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So photosynthesis and carbon fixation, though associated in chloroplasts are basically different biochemical processes. Theoretically as long as NADPH is provided a plant should be able to fix CO&lt;sub&gt;2&lt;/sub&gt; &lt;em&gt;[this is just my guess]&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is difficult to observe internal structure of chloroplasts with normal bright-field microscope but you can count them easily at 40x magnification. See &lt;a href=&quot;http://www.photomacrography.net/forum/viewtopic.php?t=16211&amp;amp;view=next&amp;amp;sid=bfe494b246809113759a31a5a0bb32f7&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-10-06T05:31:38.520" LastActivityDate="2014-10-06T05:31:38.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21892" PostTypeId="2" ParentId="21866" CreationDate="2014-10-06T05:23:11.400" Score="2" Body="&lt;p&gt;The sRNA mediated regulation in bacteria operates via diverse mechanisms. This case of sRNA competing with a mRNA for a protein is a passive kind of regulation. This might be good for finetuning but may not be very efficient. It is much better to actively regulate a mRNA by direct binding. Also, it will work only if the concerned protein is in limiting concentrations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't come across any examples of what you are interested in. There may be one similar situation in case of a eukaryotic system. miRNAs can be titrated away by long RNAs that bear multiple binding sites for that miRNA, thus making the miRNAs unavailable for binding to the target mRNA. These long RNAs are called ceRNA (competing endogenous RNA) or miRNA-sponges (this term is mostly used if the RNA is exogenous). However this is not really a protein-RNA interaction even though RISC complex contains proteins. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-10-06T05:23:11.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21893" PostTypeId="2" ParentId="16367" CreationDate="2014-10-06T06:42:18.607" Score="3" Body="&lt;p&gt;Bioinformatics journals can deal perfectly with this type of papers. If you target a journal like &lt;a href=&quot;http://bioinformatics.oxfordjournals.org&quot; rel=&quot;nofollow&quot;&gt;Bioinformatics&lt;/a&gt;, then you can be as technical as you want (and you probably should). Biologists that read those journals will most likely understand the terminology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even traditional experimental biology journals, like &lt;a href=&quot;http://nar.oxfordjournals.org&quot; rel=&quot;nofollow&quot;&gt;Nucleic Acids Research&lt;/a&gt;, now include a section for Computational Biology that can be a perfect target for a paper on DNA motif analysis. If you submit to such a journal, however, you have to consider the target audience may be more broad than the typical Bioinformatics journal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you aim for Biologists to understand the concepts, you have to accept that there will be Biologists with very variable degrees of understanding of Bioinformatics. For example, as mentioned in some of the comments, some Biologists may understand what Hidden Markov Models are, others, however, may have never heard the term before. I would suggest that if you target a Biology centered journal, try to explain things in &lt;em&gt;very&lt;/em&gt; simple terms, connecting the concepts to real life examples. You can use those explanations as introduction to more detailed descriptions. Depending on the journal, you may want to put the technical details, including formulas, in supplementary material. Keeping the technical details out of the main manuscript will make it accessible to general readership, yet having the details in supplementary material will give rigor to your paper and allow anyone interested in your research to check the details.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastActivityDate="2014-10-06T06:42:18.607" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21895" PostTypeId="2" ParentId="21884" CreationDate="2014-10-06T07:39:11.057" Score="3" Body="&lt;p&gt;As @wysiwig already pointed out the different morphology of chloroplasts is something that is hard to come by. This influences the amount of chlorophyll in these organelles which is the key for photosynthesis. So it is very difficult (to impossible) to compare chloroplasts of different plants as they differ pretty much. There is one paper from 1929 which goes into detail here: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323716/&quot; rel=&quot;nofollow&quot;&gt;The relation between maximum rate of photosynthesis and concentration&#xA;of chlorophyll.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;However, there is a paper which studies the photosynthesis rate in connection to the number of chloroplasts when manganese ions are a limiting factor. Manganese is part of the active center of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Photosynthetic_reaction_centre#Photosystem_II&quot; rel=&quot;nofollow&quot;&gt;Photosystem II&lt;/a&gt; in the photosynthesis. So without maganese, photosynthesis is not possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article finds the number of chloroplasts in cells approximately reduced to the half compared with leafs without maganese-deficiency. Testing the photosynthesis capacity of these leafs, they find that the photosynthetic activity in the manganese-deficient leaves is reduced by about 40%, which fits nicely to the reduction in chloroplast number. They do not find other significant changes in the biochemistry of the photosynthesis in these plants, so is the ratio between chlorophyll a and b not affected, and also the ability to transfer electrons is not affected. The findings are presented in this paper:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3767/dihsro95_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Reduction in chloroplast number accounts for the decrease in the&#xA;photosynthetic capacity of Mn-deficient pecan leaves&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-06T07:39:11.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21896" PostTypeId="1" AcceptedAnswerId="21898" CreationDate="2014-10-06T07:59:14.677" Score="9" ViewCount="364" Body="&lt;p&gt;Typically, how many RNA-binding proteins can simultaneously bind to a single mRNA?&#xA;Or said differently, how many &quot;binding sites&quot; does an mRNA have?&#xA;What order of magnitude?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested in RNA granules like stress granules or P-bodies. They contain, inter alia, mRNA and RNA-binding proteins. I am not a biologist and I didn't come across this information so far in the related literature.&lt;/p&gt;&#xA;" OwnerUserId="9662" LastEditorUserId="3340" LastEditDate="2014-10-07T04:28:11.573" LastActivityDate="2016-09-16T06:30:58.230" Title="How many RNA-binding proteins can simultaneously bind on a single mRNA?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;rna&gt;&lt;mrna&gt;&lt;protein-binding&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21898" PostTypeId="2" ParentId="21896" CreationDate="2014-10-06T10:48:24.173" Score="11" Body="&lt;p&gt;See this &lt;a href=&quot;http://dx.doi.org/10.1186/gb-2014-15-1-r3&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper&lt;/a&gt;. They have studied RBP-protected sites in the entire human transcriptome by RNA-protein crosslinking followed by RNAse digestion and sequencing: PIPseq. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://genomebiology.com/2014/15/1/R3/figure/F1?highres=y&quot; rel=&quot;nofollow noreferrer&quot;&gt;Figure 1&lt;/a&gt; of the paper shows distribution of protein protected sites in RNAs. They also correlate it with different regions of mRNA and its expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They show number of protein protected sites (PPS) per transcript but that is not a proper metric in my opinion. The number should be normalized with transcript length so that you get density of protected sites. From &lt;a href=&quot;http://genomebiology.com/2014/15/1/R3/figure/F4&quot; rel=&quot;nofollow noreferrer&quot;&gt;figure 4&lt;/a&gt; (see below) you can roughly estimate that average PPS density is close to 0.6 which means that 60% of any RNA is expected to be protein bound. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/ZKXTV.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Figure 4&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Other points to be noted:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Highly translated mRNAs will have multiple ribosomes on their CDS and&#xA;are likely to be more protected.&lt;/li&gt;&#xA;&lt;li&gt;Sequestered RNAs in stress granules will also have high density of PPS&lt;/li&gt;&#xA;&lt;li&gt;Footprint of different RBPs will be different. So number of proteins that can bind to a mRNA will differ between different RBPs.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Further reading:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1186/gb4153&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://dx.doi.org/10.1186/gb4153&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.cell.2012.04.031&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://dx.doi.org/10.1016/j.cell.2012.04.031&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.molcel.2012.05.021&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://dx.doi.org/10.1016/j.molcel.2012.05.021&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-09-16T06:30:58.230" LastActivityDate="2016-09-16T06:30:58.230" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21899" PostTypeId="2" ParentId="21885" CreationDate="2014-10-06T11:11:59.113" Score="7" Body="&lt;p&gt;Sharks sense their prey with the normal senses, they see, hear and smell them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They have a remarkable sensitive sense of smelling, which enables them to sense highly diluted traces of prey. They can also use their smelling to determine the direction where a certain smell comes from. This is achieved by the timing in which the senses arrive in different parts of the sharks nose. See references 1 and 2 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While sharks have eyes which are similar to that of vertebrates, they have an additional reflective tissue called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Tapetum_lucidum&quot;&gt;tapetum lucidum&lt;/a&gt;&quot; behind their retina, which reflects the light back and therefore raises the sensitivity of the eye. It seems that a lot of shark species are either colorblind (because they only have rod cells but no cones) or they had only one kind of cone cells which allows them only to see one color. For sharks it is obviously more important to detect objects than to see colors. See references 3 and 4 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sense of hearing of sharks is also highly sensitive and is able to detect sounds from far away. See also references 5 and 6 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most interesting sense of sharks is their electrosensory organ. This is also called &lt;a href=&quot;http://en.wikipedia.org/wiki/Ampullae_of_Lorenzini&quot;&gt;Ampullae of Lorenzini&lt;/a&gt; which is a number of sensory cells along the head and which are able to detect the weak electric fields that exist around living animals. This sense only works on a very short distance. See references 7 and 8 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally sharks have the so-called &lt;a href=&quot;http://en.wikipedia.org/wiki/Lateral_line&quot;&gt;lateral lines&lt;/a&gt; (which are present in most fish), which is an organ which detects movements and vibrations in the water around the shark. See the &lt;a href=&quot;http://en.wikipedia.org/wiki/Lateral_line&quot;&gt;Wikipedia&lt;/a&gt; page for more information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And for the sake of completeness (already quite nicely answered by @Susan in the comments), sharks do get cancer. All cures which are made from shark and claim to be able to treat cancer are pseudoscientific nonsense. This also endangers many shark species as they get radically overfished. See references 9 and 10 for more details.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://elasmo-research.org/education/white_shark/smell.htm&quot;&gt;Smell and Taste&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://shell.cas.usf.edu/motta/Gardiner%20and%20Atema%202010.pdf&quot;&gt;The Function of Bilateral Odor Arrival Time Differences in Olfactory&#xA;Orientation of Sharks&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://reefwatch.files.wordpress.com/2011/01/mspstudy_colorvisioninsharks.pdf&quot;&gt;Microspectrophotometric evidence for cone monochromacy in sharks.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://elasmo-research.org/education/white_shark/vision.htm&quot;&gt;Vision and a Carpet of Light&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.elasmo-research.org/education/white_shark/hearing.htm&quot;&gt;Hearing and Vibration Detection&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3767/zkgpwkro_pdf.htm&quot;&gt;Functional anatomy of the auditory system in sharks and rays&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://faculty.bennington.edu/~sherman/the%20ocean%20project/shark%27s%20electric%20sense.pdf&quot;&gt;The Shark's Electric Sense&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Electroreception&quot;&gt;Electroreception&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://blogs.scientificamerican.com/science-sushi/2011/09/01/mythbusting-101-sharks-will-cure-cancer/&quot;&gt;Mythbusting 101: Sharks will cure cancer&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15574750&quot;&gt;Shark cartilage, cancer and the growing threat of pseudoscience.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-06T11:11:59.113" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21900" PostTypeId="1" CreationDate="2014-10-06T12:10:46.597" Score="0" ViewCount="65" Body="&lt;p&gt;What does the dissolving of pectin have to do with the colour of a fruit?&lt;/p&gt;&#xA;" OwnerUserId="5709" LastActivityDate="2014-10-06T12:14:28.163" Title="Fruit colour related to the dissolving of pectin" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21901" PostTypeId="2" ParentId="21900" CreationDate="2014-10-06T12:14:28.163" Score="3" Body="&lt;p&gt;During ripening, pectinases are produced which break down pectin and render it soluble. Color change is also associated with fruit ripening. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence the correlation. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-10-06T12:14:28.163" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21906" PostTypeId="1" AcceptedAnswerId="21907" CreationDate="2014-10-06T20:18:37.953" Score="1" ViewCount="626" Body="&lt;p&gt;A bunch of stuff in the human nervous system decussates. Optical information inputs from the eyes cross over in the optical chiasm. Multiple sensory and motor pathways cross-over before ascending the spinal chord or within the brain stem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the current hypotheses being explored for justifying this anatomical phenomena?&lt;/p&gt;&#xA;" OwnerUserId="5427" LastActivityDate="2014-10-07T00:17:08.197" Title="What's the evolutionary reason behind decussation?" Tags="&lt;evolution&gt;&lt;human-anatomy&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21907" PostTypeId="2" ParentId="21906" CreationDate="2014-10-06T20:56:39.780" Score="2" Body="&lt;p&gt;I don't think it is a clever thing to group all types of &lt;a href=&quot;http://en.wikipedia.org/wiki/Decussation&quot; rel=&quot;nofollow noreferrer&quot;&gt;decussation&lt;/a&gt; and look for a general explanations. I would tend to think that different decussation have different explanations. It is like asking what are the hypothesis to explain evolution of body size. There is no general answer to that but only a list of case specific impact of different factors on body size (see &lt;a href=&quot;https://biology.stackexchange.com/questions/13745/body-size-what-are-the-evolutionary-trade-offs&quot;&gt;this post&lt;/a&gt;). Consider the two case-studies 1) &amp;quot;why does left brain controls the right part of the body&amp;quot; and 2) &amp;quot;Torsion in gastropoda&amp;quot; as examples of how different explanation applies to different decussation.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;why does left brain controls the right part of the body?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;See &lt;a href=&quot;https://biology.stackexchange.com/questions/3807/why-do-the-two-hemispheres-of-the-brain-control-the-opposite-sides-of-the-body/&quot;&gt;@shigeta's answer to this post&lt;/a&gt;. It is very interesting.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Torsion in Gastropoda&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Torsion in Gastropoda is an interesting case. In this lineage individuals undergo some torsion during their development. &lt;a href=&quot;http://en.wikipedia.org/wiki/Gastropoda&quot; rel=&quot;nofollow noreferrer&quot;&gt;This&lt;/a&gt; wikipedia articles say:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Snails are distinguished by an anatomical process known as torsion, where the visceral mass of the animal rotates 180° to one side during development, such that the anus is situated more or less above the head. This process is unrelated to the coiling of the shell, which is a separate phenomenon. Torsion is present in all gastropods, but the opisthobranch gastropods are secondarily detorted to various degrees.[13][14]&lt;/p&gt;&#xA;&lt;p&gt;Torsion occurs in two mechanistic stages. The first is muscular and the second is mutagenetic. The effects of torsion are primarily physiological - the organism develops an asymmetrical nature with the majority of growth occurring on the left side. This leads to the loss of right-paired appendages (e.g., ctenidia (comb-like respiratory apparatus), gonads, nephridia, etc.). Furthermore, the anus becomes redirected to the same space as the head. This is speculated to have some evolutionary function, as prior to torsion, when retracting into the shell, first the posterior end would get pulled in, and then the anterior. Now, the front can be retracted more easily, perhaps suggesting a defensive purpose.&lt;/p&gt;&#xA;&lt;p&gt;However, this &amp;quot;rotation hypothesis&amp;quot; is being challenged by the &amp;quot;asymmetry hypothesis&amp;quot; in which the gastropod mantle cavity originated from one side only of a bilateral set of mantle cavities.[15]&lt;/p&gt;&#xA;&lt;p&gt;Gastropods typically have a well-defined head with two or four sensory tentacles with eyes, and a ventral foot, which gives them their name (Greek gaster, stomach, and poda, feet). The foremost division of the foot is called the propodium. Its function is to push away sediment as the snail crawls. The larval shell of a gastropod is called a protoconch.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;You can find more information &lt;a href=&quot;http://en.wikipedia.org/wiki/Torsion_(gastropod)&quot; rel=&quot;nofollow noreferrer&quot;&gt;there&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-10-07T00:17:08.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21908" PostTypeId="1" CreationDate="2014-10-06T21:40:50.923" Score="1" ViewCount="67" Body="&lt;p&gt;Is there a Variant Caller comparable algorithmically and in performance to GATK Haplotype Caller but Open Source Compliant (non-restrictive use)?&lt;/p&gt;&#xA;" OwnerUserId="658" LastActivityDate="2014-10-06T21:40:50.923" Title="Open Source Variant Caller comparable to GATK Haplotype Caller?" Tags="&lt;mutations&gt;&lt;software&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21909" PostTypeId="1" AcceptedAnswerId="21913" CreationDate="2014-10-06T22:03:50.787" Score="10" ViewCount="1763" Body="&lt;p&gt;Let's assume I am wearing a labcoat for two reasons:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Prevent the various bacteria, proteins, skin cells and substances on my clothes and my skin from contaminating my experiments.&lt;/li&gt;&#xA;&lt;li&gt;Prevent various dangerous things from the experiment getting on me, and ruining my clothes or endangering my health (eg. toxic chemicals, pathogenic bacteria, ecotropic virus, etc)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;A labcoat is an imperfect, but valuable barrier against such hazards. Perhaps a droplet of some &lt;em&gt;Nasty Substance™&lt;/em&gt; ends up flying towards my arm, but instead of getting on my exposed skin, hits my labcoat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, what happens when I take off my labcoat? My gloves, which have just been in contact with lots of &lt;em&gt;Nasty Substance™&lt;/em&gt;, go through the sleeves of the coat, possibly smearing the substance all over the inside of the fabric. When I put on the coat again the next day, now my skin is in contact with these smears.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could remove my gloves before taking off the labcoat, to avoid this smearing. But this time, I have to touch the labcoat with my bare hands as I remove it. Remember the &lt;em&gt;Nasty Substance™&lt;/em&gt; that was stopped when it splattered on the outside of the fabric instead of my skin? What if I know end up touching that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that for truly dangerous conditions, there is specialized equipment and detailed procedure. Even at BSL2+, traditionally disposable labcoats are required, rendering the issue somewhat irrelevant. So let's assume the highest level below that, BSL2, as the context for answers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In short,&lt;/strong&gt; what is the correct way of putting on and taking off gloves and non-disposable labcoat when working in BSL2 conditions?&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-10-07T03:58:27.733" LastActivityDate="2014-10-07T03:58:27.733" Title="How do I put on a labcoat?" Tags="&lt;lab-techniques&gt;&lt;safety&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21910" PostTypeId="1" CreationDate="2014-10-06T22:14:56.997" Score="10" ViewCount="11194" Body="&lt;p&gt;A common precaution for preparing EtBr-agarose gels is to add EtBr only after the gel solution has cooled somewhat, because EtBr is a dangerous mutagen. Supposedly, adding it to a hot liquid allows EtBr vapors to get into the air and everyone's lungs, where it can act as a carcinogen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to this are commonly seen special procedures for handling EtBr vials and gels (fresh nitrile gloves, avoid contaminating other work areas, special waste disposal rules).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there's also some saying that EtBr isn't all that mutagenic and all this care is over the top.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the reality? Just how dangerous is EtBr, especially in amounts used at a typical biological lab? How long does the danger persist? Are even trace amounts hazardous (for instance, touching a &quot;clean&quot; pipette without changing gloves after working with EtBr)?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2015-08-09T12:14:09.937" Title="Just how dangerous is ethidium bromide?" Tags="&lt;biochemistry&gt;&lt;safety&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21911" PostTypeId="1" CreationDate="2014-10-06T22:32:07.003" Score="1" ViewCount="564" Body="&lt;p&gt;I was reading in my pharmacology textbook about fluorouracil, and my book mentioned that fluorouracil is an antimetabolite whose function is to inhibit pyrimidine synthesis. However, I was curious to know how exactly does fluorouracil accomplish this. Is this drug involved in a specific mechanism that enables it to prevent pyrimidine synthesis? If so, how?&lt;/p&gt;&#xA;" OwnerUserId="8977" LastActivityDate="2014-10-06T23:46:15.507" Title="How does fluorouracil inhibit pyrimidine synthesis?" Tags="&lt;biochemistry&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21912" PostTypeId="2" ParentId="21911" CreationDate="2014-10-06T23:46:15.507" Score="4" Body="&lt;p&gt;Your cells produce thymidine by converting uridine using an enzyme called &lt;a href=&quot;http://en.wikipedia.org/wiki/Thymidylate_synthase&quot; rel=&quot;nofollow noreferrer&quot;&gt;Thymidylate Synthase&lt;/a&gt;. 5-Fluorouracil irreversibly inhibits this enzyme.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the structure of 5-Fluorouracil: &lt;img src=&quot;https://i.stack.imgur.com/ujtiP.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the mechanism the enzyme uses to make thymidine:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/9X1jz.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It looks like the enzyme forms a bond to the uridine ring through a sulfur. 5-Fluorouracil probably inhibits the reaction at the next step because fluorine is much more electronegative than the proton it replaced. This makes it harder for the electrons on the double bond in step 2 to attack the folate. Might also inhibit step 3 because the fluorine won't want to give up its electrons to reform the double bond. Because 5-fluorouracil is stuck to the enzyme's active site, the enzyme can't perform its given duty of converting uridine to thymidine. Because you can't use uridine in your DNA, your cells don't have enough thymidine to copy the DNA and replication is slowed. If thymidine supplies are low enough, cells might die.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-10-06T23:46:15.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21913" PostTypeId="2" ParentId="21909" CreationDate="2014-10-06T23:47:32.330" Score="9" Body="&lt;p&gt;Wear two sets of gloves.  First, use nitrile gloves, not latex for this. 4mm or thicker is a specification I would recommend to avoid tearing.  Latex will bind too well to itself and tear easily with increased friction etc (same logic behind not using two condoms).  Also, use a coat with an elastic cuff on the sleeve.&#xA;So here's the breakdown&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Put on first set of gloves&lt;/li&gt;&#xA;&lt;li&gt;Put on coat over gloves.  Decon if needed for application.&lt;/li&gt;&#xA;&lt;li&gt;Put on second set of gloves.&lt;/li&gt;&#xA;&lt;li&gt;Science&lt;/li&gt;&#xA;&lt;li&gt;Take off second set of gloves.&lt;/li&gt;&#xA;&lt;li&gt;Decon as needed for your health&lt;/li&gt;&#xA;&lt;li&gt;Take off coat&lt;/li&gt;&#xA;&lt;li&gt;Take off first set of gloves&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I can find sources for this, but I've been doing ABSL2 and BSL3 for a while, and they always go through this in safety training.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: My internal nagging to site got the better of me, so some examples that recommend double gloving:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://oehs.vcu.edu/chemical/labsafe/perchloricacid.pdf&quot;&gt;http://oehs.vcu.edu/chemical/labsafe/perchloricacid.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://extranet.fhcrc.org/EN/sections/ehs/hamm/chap3/section6.html&quot;&gt;https://extranet.fhcrc.org/EN/sections/ehs/hamm/chap3/section6.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://orsp.umich.edu/policies/um/committees/BRRC/ADDITIONAL_PRACTICES_revised_8_7_14.pdf&quot;&gt;http://orsp.umich.edu/policies/um/committees/BRRC/ADDITIONAL_PRACTICES_revised_8_7_14.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://ehs.columbia.edu/carcmutguide.html&quot;&gt;http://ehs.columbia.edu/carcmutguide.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could go on, but I think you get the idea.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2014-10-07T00:30:57.120" LastActivityDate="2014-10-07T00:30:57.120" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21915" PostTypeId="1" CreationDate="2014-10-07T01:36:05.990" Score="4" ViewCount="1296" Body="&lt;p&gt;mutation-selection-drift equilibrium is one of the most important concept of population genetics. I could easily find the calculations for mutation-secltion equilibrium and for mutation-drift equilibrium but not for mutation-selection-drift equilibrium.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;mutation-selection equilibrium&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At mutation-selection equilibrium the expected frequency $p$ of a given allele is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$p ≈ \frac{\mu}{s\cdot h}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $\mu$ is the mutation rate, $s$ is the selection coefficient and $h$ is the coefficient of dominance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;mutation-drift equilibrium&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At mutation-drift equilibrium the expected frequency $p$ of a given allele is &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$p ≈ \frac{1}{4N\mu+1} $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $N$ is the population size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the allelic frequency at mutation-selection-drift equilibrium?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-01-16T01:24:59.960" LastActivityDate="2015-01-16T01:24:59.960" Title="Mutation-Selection-Drift Equilibrium" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21916" PostTypeId="2" ParentId="21910" CreationDate="2014-10-07T02:34:36.327" Score="5" Body="&lt;p&gt;Inspired by Jason Patterson's comment, I looked up &quot;ethidium bromide cattle&quot; and found &lt;a href=&quot;http://bitesizebio.com/95/ethidium-bromide-a-reality-check/&quot; rel=&quot;noreferrer&quot;&gt;a blog post&lt;/a&gt; about ethidium bromide toxicity. Apparently ethidium is routinely used to treat sleeping sickness in african cattle at 1mg/kg without ill effects. All data concerning ethidium toxicity comes from in vitro tests that may not apply to in vivo use. You should still wear gloves, but don't freak out over it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The blog post had some references, but most are dead links now. &lt;a href=&quot;http://rrresearch.fieldofscience.com/2006/10/heresy-about-ethidium-bromide.html&quot; rel=&quot;noreferrer&quot;&gt;Here is the only working link left&lt;/a&gt;. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21080764&quot; rel=&quot;noreferrer&quot;&gt;Here's a review article on dye therapy for parasites&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-10-07T02:34:36.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21917" PostTypeId="2" ParentId="21853" CreationDate="2014-10-07T02:59:46.893" Score="1" Body="&lt;p&gt;It might be helpful to think about where elements in general come from. Here is a plot of relative elemental abundance.&lt;img src=&quot;https://i.stack.imgur.com/RRZMe.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the Y axis is logarithmic, so H and He are much much much more common than anything else. You'll notice that Li, Be, and B are rare, and C, N, and O are fairly common, and are the main components in biological chemistry. Fe is relatively abundant, and after Fe elemental abundance falls off. The explanation for the abundances comes from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleosynthesis#The_major_types_of_nucleosynthesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;processes involved in nucleosynthesis&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Big bang nucleosynthesis was the generation of hydrogen and helium within the first 3 minutes of the universe as the quark-gluon plasma cooled and formed the protons and neutrons. As the universe expanded and cooled, it lost the energy needed to keep making atoms within 20 minutes, so only very small amounts of Li, Be, and B could be made.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stellar nucleosynthesis is the creation of &quot;heavy&quot; elements by nuclear fusion in stars. This is how we get C through Fe. As the stars age and use up their fuel, they generate elements up to Fe because energy can be released from fusion of atoms up to iron, past iron fusion takes more energy than can be released.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Elements heavier than Fe must be created through supernova explosions. This is the only natural way to get enough energy to jam the nuclei together. This only works well for elements up to uranium, where nuclei become unstable and decay at relatively fast rates. These unstable elements are produced in nuclear reactors and particle accelerators. Note that supernova explosions don't just make heavier elements, they are also responsible for blasting the elements made in stars into space where they can form new stars and planets. This is where the matter that makes us comes from, hence the stardust.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another method for generating light atoms is cosmic spallation, where a cosmic ray hits an atom and blows some protons and neutrons out of the nucleus. This material becomes light atoms, such as Li, Be, and B.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a periodic table that shows where each element comes from.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Xzmei.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-10-07T02:59:46.893" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21918" PostTypeId="1" CreationDate="2014-10-07T03:08:39.273" Score="2" ViewCount="358" Body="&lt;p&gt;I am a Biology novice so I apologize in advance if I state anything incorrectly....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, are the DNA codon mappings arbitrary? I understand that the DNA code is made up of codons which each consist of 3 base pairs. There can be 64 codons which map to 20 amino acids (some are duplicated and others act as stop codons). So was there a reason why one particular codon mapped to one particular amino acid - or is the mapping completely arbitrary?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="9669" LastEditorUserId="3340" LastEditDate="2014-10-07T08:33:09.900" LastActivityDate="2018-06-21T13:00:27.130" Title="Are the DNA codon mappings arbitrary?" Tags="&lt;dna&gt;&lt;molecular-genetics&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21919" PostTypeId="2" ParentId="21847" CreationDate="2014-10-07T03:26:18.937" Score="1" Body="&lt;p&gt;What determines blood types is the type of antigens found on the surface of the blood. A blood cells have A antigens on their surface, B has B antigens, AB has both, and O has no antigens. What is an antigen?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;an antigen (Ag), or antibody generator, is any substance which provokes an adaptive immune response. An antigen is a molecule that also induces an immune response in the body.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now, not only is the blood important here but also the plasma. The plasma contains antibodies. Antibodies are (according to wikipedia)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a large Y-shape protein produced by plasma cells that is used by the immune system to identify and neutralize foreign objects such as bacteria and viruses. The antibody recognizes a unique part of the foreign target, called an antigen.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Members of the A group have B antibodies in their plasma, members of the B group have A antibodies in their plasma, AB has neither, and O has both.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now taking this all into account and to answer your question, if B blood is given to a patient of type A, the antigens on the surface of the A blood cells would react as if the incoming B blood cells are foreign, harmful substances. To from the book &quot;Blood Groups and Red Cell Antigens&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2265/&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If incompatible blood is given in a transfusion, the donor cells are treated as if they were foreign invaders, and the patient's immune system attacks them accordingly.&#xA;  Not only is the blood transfusion rendered useless, but a potentially massive activation of the immune system and clotting system can cause shock, kidney failure, circulatory collapse, and death.”&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The same would result if A blood is given to a B blood type patient, the B blood cells would initiate an immune response to the A blood cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To further expand on your question, this is why O is the universal donor. There are no antigens on its surface that will illicit an immune response from other blood groups. It also has both A and B antibodies in its plasma. Similarly, AB is the universal recipient. It has both antigens on its surface meaning that neither A nor B antigens will illicit an immune response from other blood groups.&lt;/p&gt;&#xA;" OwnerUserId="9002" LastActivityDate="2014-10-07T03:26:18.937" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21920" PostTypeId="2" ParentId="21918" CreationDate="2014-10-07T04:59:44.580" Score="3" Body="&lt;p&gt;There is no reason for why a certain codon came to represent a certain amino acid. But some reason is attributed to similarity of degenerate codons. Usually the degenerate codons only differ in their last (third) nucleotide. The corresponding first anticodon in tRNA usually bears a modified nucleotide such as inosine which can (promiscuously) pair with A, C and U. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see the wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Wobble_base_pair&quot; rel=&quot;nofollow&quot;&gt;wobble base-pairing&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-10-07T04:59:44.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21921" PostTypeId="2" ParentId="21910" CreationDate="2014-10-07T07:50:34.687" Score="9" Body="&lt;p&gt;I usually find the treatment of Ethidium bromide in the lab widely exaggerates the true dangers of this chemical.&#xA;It is not really toxic (the LD&lt;sub&gt;50&lt;/sub&gt; is 1.5 g/kg bodyweight, as a comparision NaCl has a LD&lt;sub&gt;50&lt;/sub&gt; of 3 g/kg). It has also only been shown to exhibit mutagenic potential to bacteria after it had been treated with liver extracts. This means that some of the metabolized products of EtBr in the liver are mutagenic, but EtBr itself not. See reference 1 for details here. It is also not classified as a cancerogenic substance by the regulation bodies (for example see the National Toxicology Program of the US on &lt;a href=&quot;http://ntp.niehs.nih.gov/testing/status/agents/ts-m940107.html&quot; rel=&quot;nofollow&quot;&gt;Ethidium bromide&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As already mentioned, it is used to cure Trypanosoma infections in cattle (reference 2). Here up to 1 mg/kg bodyweight are given, with no signs of toxic or other adverse effects. The typical concentration used in the lab to prepare gels is 1 μg/ml. It works as a drug by interfering with the mitochondrial DNA (changing it to the Z-form, which is not available for replication). See reference 3 for details. Ethidium bromide also acts as a Topoisomerase I inhibitor as other chemotherapeutic drugs. See reference 4 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, EtBr is negatively charged and cannot enter cells or the nucleus, since cannot pass the membranes. I would wear gloves and also apply the usual safety rules when working with gloves (do not touch anything you don't need to touch, especially things like door knobs, keyboards or phones as you might spread contamination) dispose your gloves when not needed anymore and you should be fine.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1061098&quot; rel=&quot;nofollow&quot;&gt;Detection of carcinogens as mutagens in the Salmonella/microsome&#xA;test: assay of 300 chemicals.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3768/2z2m5lz9_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Comparison of isometamidium chloride and homidium bromide as&#xA;prophylactic drugs for trypanosomiasis in cattle at Nguruman, Kenya.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://libgen.org/scimag/get.php?doi=10.1016/j.mrfmmm.2005.12.003&quot; rel=&quot;nofollow&quot;&gt;A low dose of ethidium bromide leads to an increase of total&#xA;mitochondrial DNA while higher concentrations induce the mtDNA 4997&#xA;deletion in a human neuronal cell line.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://nar.oxfordjournals.org/content/39/3/1014&quot; rel=&quot;nofollow&quot;&gt;The geometry of DNA supercoils modulates the DNA cleavage activity&#xA;of human topoisomerase I&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-08-09T12:14:09.937" LastActivityDate="2015-08-09T12:14:09.937" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21926" PostTypeId="1" AcceptedAnswerId="21936" CreationDate="2014-10-07T12:11:43.303" Score="4" ViewCount="2171" Body="&lt;p&gt;For a human, when diving underwater, everything is blurry because of the water's different refractive index compared to that of air, which we are accustomed to. How do animals, like turtles, seals or penguins, handle that difference when changing the medium? Are they nearly blind at surface and can focus underwater or the other way around? Can they adapt to different refractive indexes on the fly? How?&lt;/p&gt;&#xA;" OwnerUserId="9672" LastEditorUserId="9099" LastEditDate="2014-10-07T12:36:54.980" LastActivityDate="2018-11-16T11:43:50.220" Title="How do animals handle light refraction in different media?" Tags="&lt;physiology&gt;&lt;zoology&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21927" PostTypeId="2" ParentId="21918" CreationDate="2014-10-07T15:18:59.513" Score="2" Body="&lt;p&gt;Evidence suggests that the correspondence between DNA codons and amino acids (i.e. the genetic code ) is not random. A good place to start with this interesting topic is the Wikipedia article about the &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_code&quot; rel=&quot;nofollow&quot;&gt;genetic code&lt;/a&gt;, in particular, about its &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_code#Origin&quot; rel=&quot;nofollow&quot;&gt;origin&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many hypotheses on the evolutionary origins of the genetic code have been proposed. Four themes run through the many hypotheses about the evolution of the genetic code:&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here I summarize the four themes (adapted from wikipedia).&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Chemical principles governing specific RNA interaction with amino acids.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Biosynthetic expansion. The standard modern genetic code grew from a simpler earlier code through a process of &quot;biosynthetic expansion&quot;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Natural selection has led to codon assignments of the genetic code that minimize the effects of mutations.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Information channels: Information-theoretic approaches models suggest that the genetic code originated as a result of the interplay of the three conflicting evolutionary forces: the needs for diverse amino-acids, for error-tolerance and for minimal cost of resources.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Other models combine some of these hypothesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Selected references:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9732450&quot; rel=&quot;nofollow&quot;&gt;The genetic code is one in a million&lt;/a&gt;. Freeland SJ, Hurst LD. J Mol Evol. 1998 Sep;47(3):238-48.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10366854&quot; rel=&quot;nofollow&quot;&gt;Selection, history and chemistry: the three faces of the genetic code&lt;/a&gt;. Knight RD, Freeland SJ, Landweber LF. Trends Biochem Sci. 1999 Jun;24(6):241-7. Review.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9099" LastActivityDate="2014-10-07T15:18:59.513" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21930" PostTypeId="1" CreationDate="2014-10-07T15:49:56.413" Score="5" ViewCount="2740" Body="&lt;p&gt;Can anyone tell me why proteinase K doesn't degrade itself?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If possible please provide me the source.&lt;/p&gt;&#xA;" OwnerUserId="9676" LastEditorUserId="9099" LastEditDate="2014-10-07T16:30:44.560" LastActivityDate="2014-10-07T20:45:59.980" Title="Why proteinase K doesn't degrade itself?" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21931" PostTypeId="1" AcceptedAnswerId="21933" CreationDate="2014-10-07T15:54:34.967" Score="4" ViewCount="437" Body="&lt;p&gt;The protein isoforms I am interested in comparing appear as distinct bands on the gel I have already run. I have an Excel sheet with optical density measurements I obtained using ImageJ; it looks something like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Lane    Iso1       Iso2       GAPDH&#xA;1       149.06     194.646    893.08&#xA;2       832.654    494.473    148.335&#xA;3       49.998     490.539    147.361&#xA;4       29.347     208.53     120.652&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;For the other proteins I've analyzed so far, I've been computing fold-change relative to my loading control, GAPDH, with the following equation:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Fold-Change = Log2(Protein/GAPDH)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I'm not sure how best to compare my isoforms to each other and considering the following two equations:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;1. Fold-Change = Log2[(Iso2/GAPDH)/(Iso1/GAPDH)]&#xA;&#xA;2. Fold-Change = Log2(Iso2/Iso1)/GAPDH&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I've already computed both of these values for all my samples, graphed them and found that the resulting graphs look pretty different. &lt;strong&gt;Which of the two equations do you think is a better way to compare the relative quantities of these proteins?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternative equations are also welcome.&lt;/p&gt;&#xA;" OwnerUserId="8161" LastActivityDate="2015-11-03T10:23:19.613" Title="What equation to compare protein isoforms in a Western Blot?" Tags="&lt;proteins&gt;&lt;statistics&gt;&lt;western-blot&gt;&lt;data&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="21932" PostTypeId="2" ParentId="21930" CreationDate="2014-10-07T16:41:06.263" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://tools.lifetechnologies.com/content/sfs/manuals/proteinasek_solution_man.pdf&quot; rel=&quot;nofollow&quot;&gt;According to invitrogen&lt;/a&gt; proteinase K does undergo autolysis, but that some leftover fragments still have protease activity. The solution should be stored at -20C, this low temperature is probably the best way to prevent autolysis. If you're using the enzyme to digest protein at 37C, you'll just have to deal with losing the proteinase k during the reaction and make sure you add enough to destroy the target protein before the proteinase is depleted.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-10-07T16:41:06.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21933" PostTypeId="2" ParentId="21931" CreationDate="2014-10-07T17:53:30.380" Score="3" Body="&lt;p&gt;In my opinion you should use this formula:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ \frac{\text{log}_2(\text{Iso}_1/\text{Iso}_2)}{\text{log}_2(\text{GAPDH})} $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This will normalize the relative fold differences between the isoforms with the loading control- GAPDH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since both numerator and denominator are log transformed they are in comparable domains unlike the formula-2 that you mention in your question. This is just a modified formula-2.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-11-03T10:23:19.613" LastActivityDate="2015-11-03T10:23:19.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21934" PostTypeId="1" CreationDate="2014-10-07T19:00:31.900" Score="6" ViewCount="1303" Body="&lt;p&gt;&lt;strong&gt;Backstory:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My girlfriend reacts heavily to chocolate and drinks containing stellar anise, in a way that seems comparable to psychedelic drugs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After consuming it, it takes approximately five minutes for the reaction to become apparent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Observed Effects:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Due to the heavy reaction, she tends to avoid these foods, however, we could observe the following effects:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Heavy giggling, occasional outbursts of loud laughter;&lt;/li&gt;&#xA;&lt;li&gt;Much less frequent: Crying (just kind of starts from the giggling and subsequently fades back into giggling);&lt;/li&gt;&#xA;&lt;li&gt;Minor hallucinations (Sparkling hair, glowing faces);&lt;/li&gt;&#xA;&lt;li&gt;Loss of motor skills, especially balance;&lt;/li&gt;&#xA;&lt;li&gt;Feeling time pass much faster (to her, a 15 minute episode felt like 1-2 minutes, an hour like 5-10 minutes);&lt;/li&gt;&#xA;&lt;li&gt;Some memory loss (probably related to the time perception?);&lt;/li&gt;&#xA;&lt;li&gt;Unfocused mind;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Her speech remains clear and articulate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Observations are anecdotal, as I only observed two episodes, and we realized what happened only after the first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Googling Results:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently, around 1-3% of humans react in some way. However I couldn't find any detailed explanations of the hows and whys, nor any actual research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am very curious about this. Is it dangerous? Are there any related effects (genetic disorders, maybe?). &lt;strong&gt;All explanations, and hints how to google better, are welcome.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="9677" LastEditorUserId="9677" LastEditDate="2015-06-10T19:59:40.037" LastActivityDate="2015-06-10T19:59:40.037" Title="What are the psychedelic effects of (star) anise and how many people are affected?" Tags="&lt;pharmacology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21935" PostTypeId="1" CreationDate="2014-10-07T19:39:35.083" Score="1" ViewCount="546" Body="&lt;p&gt;With water, boiling will kill harmful pathogens. Does this also hold true for milk ? If it does not, what in the milk will continue to cause gatrointestinal distress ? Shouldn't boiling kill the harmful bacteria ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd rather not get into a discussion whether animal milk should be consumed by humans. I am asking about a typical person who is not lactose intolerant and does not have any milk allergies.&lt;/p&gt;&#xA;" OwnerUserId="5090" LastActivityDate="2014-10-07T19:39:35.083" Title="Does drinking spoiled milk that has been boiled upset the GI tract?" Tags="&lt;pathology&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21936" PostTypeId="2" ParentId="21926" CreationDate="2014-10-07T20:29:51.723" Score="5" Body="&lt;p&gt;It is more complicated than this, but... I don't think it has as much to do with the refractive index of water but rather the shape of our corneas and the loss of this shape advantage under water, for if the eyes are protected by goggles, one can see quite clearly underwater (much the same as a camera can, as the shape of it's lenses are not affected). Any change in the shape of the cornea changes the way light passes through the eye, and results in a change in vision. The following is from Ch. 9 Optics of the eyes of marine animals, from &lt;a href=&quot;http://books.google.com/books?hl=en&amp;amp;lr=&amp;amp;id=nyc9AAAAIAAJ&amp;amp;oi=fnd&amp;amp;pg=PA149&amp;amp;dq=corneal+shape+differences+and+vision+in+terrestrial+and+aquatic+animals&amp;amp;ots=QqqBkWe7Bi&amp;amp;sig=UK47BbHOtOCS-k4MNUAu-PTHZDw#v=onepage&amp;amp;q=corneal%20shape%20differences%20and%20vision%20in%20terrestrial%20and%20aquatic%20animals&amp;amp;f=false&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Light and Life in the Sea&lt;/em&gt;&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MQEhv.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is different for penguins (and turtles): the surface of their eyes, the cornea, is not as much vaulted as for humans (it's much flatter), and the lens is much rounder (meaning the shape can change more than our relatively flat lenses can), so the difference between air and water is not so big and the light isn't refracted too strongly. Also, the ciliary muscles (not to be confused with the pupillary muscles) holding the eye's lens (behind the pupil) are stronger, increasing their accommodation, so a penguin has a sharp sight in the water. Or as stated in &lt;a href=&quot;http://link.springer.com/chapter/10.1007/978-1-4684-3363-0_19&quot; rel=&quot;noreferrer&quot;&gt;A Survey of Vertebrate Strategies for Vision in Air and Water&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Whereas the cornea is usually the major refractive element of the terrestrial eye, it is of little or no refractive consequence to an aquatic vertebrate.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;See the difference in these four vertebrae groups (the first is man, the second is fish, the third is whales (similar to penguins) and the fourth is sirenians - manatees and dugongs)&lt;sup&gt;&lt;a href=&quot;https://i.stack.imgur.com/MQEhv.png&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt;&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/o9ekH.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.pinguins.info/Engels/BioKop_eng.html&amp;lt;/sub&amp;gt;&quot; rel=&quot;noreferrer&quot;&gt;Penguins.info&lt;/a&gt;&lt;br&gt;&#xA;[&lt;a href=&quot;https://i.stack.imgur.com/MQEhv.png&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt;] &lt;a href=&quot;http://books.google.com/books?hl=en&amp;amp;lr=&amp;amp;id=dt0dhi5qB4YC&amp;amp;oi=fnd&amp;amp;pg=PA121&amp;amp;dq=corneal+shape+differences+and+vision+in+terrestrial+and+aquatic+animals&amp;amp;ots=pRarq6OpXz&amp;amp;sig=TBMZ8vU7U7pnZ-2gF-H6AeEfveo#v=onepage&amp;amp;q=corneal%20shape%20differences%20and%20vision%20in%20terrestrial%20and%20aquatic%20animals&amp;amp;f=false&quot; rel=&quot;noreferrer&quot;&gt;Comparative anatomy and physiology of vision in aquatic tetrapods&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-10-07T20:29:51.723" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21937" PostTypeId="2" ParentId="21930" CreationDate="2014-10-07T20:45:59.980" Score="4" Body="&lt;p&gt;Proteinase K is sensitive for autolysis. The enzyme is stabilized by the presence of calcium ions (which bind to the protein). Absence of calcium promotes autolysis of the enzyme and also reduces the half life of the enzyme activity. The most likely reason why most researchers never notice an substancial effect of autolysis is that this takes around 48h to get noticed, while the most proteinase K digest take only a few hours. For details read the following paper:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1988.tb14301.x/full&quot; rel=&quot;nofollow&quot;&gt;The enzymatic activity of proteinase K is controlled by calcium&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-07T20:45:59.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21939" PostTypeId="1" AcceptedAnswerId="21998" CreationDate="2014-10-07T21:14:12.633" Score="6" ViewCount="2150" Body="&lt;p&gt;As far as I know, in developed countries protection suits used by people who treat patients with Ebola are disposed of after a shift.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a rather ambitious costume last year, I still have a &lt;a href=&quot;http://en.wikipedia.org/wiki/Dangerous_goods&quot; rel=&quot;nofollow&quot;&gt;hazmat&lt;/a&gt; suit like &lt;a href=&quot;http://ecx.images-amazon.com/images/I/41XevZr2oXL.jpg&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt; and &lt;a href=&quot;http://www.conney.com/wcsstore/Conney/images/fullsize/z75345.gif&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; full-face gas mask.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More out of curiosity than out of real concern, I was wondering whether it would be possible to use this equipment in a potential outbreak of the virus. My greatest concern would be reusing the suit, as it might not be safe after the first use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a way to disinfect the suit and mask with publicly available chemicals? For example, I could imagine a friend spraying me with a solution of chlorine. Would that be feasible and make wearing the suit reduce the risk of an infection?&lt;/p&gt;&#xA;" OwnerUserId="9678" LastEditorUserId="8198" LastEditDate="2014-10-16T19:17:18.297" LastActivityDate="2014-10-16T19:17:18.297" Title="Ebola: cleaning of protective suit" Tags="&lt;virus&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21941" PostTypeId="1" AcceptedAnswerId="21962" CreationDate="2014-10-07T23:57:32.907" Score="5" ViewCount="2833" Body="&lt;p&gt;I have run an in vitro transcription reaction and produced some RNA of a single species and definite size. I would like to visualize it to check if the reaction worked.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can I do this on an agarose gel? Is it sufficient to simply make a 1% TAE-agarose gel with EtBR that you would use for routine DNA electrophoresis, and run this? Is it necessary to take special measures against possible RNAses in the gel or the running buffer?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-10-09T07:30:54.483" Title="How do you visualize RNA on a gel?" Tags="&lt;rna&gt;&lt;lab-techniques&gt;&lt;gel-electrophoresis&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21942" PostTypeId="2" ParentId="21941" CreationDate="2014-10-07T23:57:32.907" Score="2" Body="&lt;p&gt;RNA is amenable to folding, which produces secondary structure and alters its mobility (compare to supercoiled DNA). Therefore, if you don't denature your RNA appropriately, even a single species will produce a smear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A common strategy is to incorporate denaturing chemicals such as formaldehyde into the procedure. See this &lt;a href=&quot;http://www.lifetechnologies.com/us/en/home/references/protocols/nucleic-acid-purification-and-analysis/rna-protocol/agarose-gel-electrophoresis-of-rna.html&quot; rel=&quot;nofollow&quot;&gt;Life Technologies&lt;/a&gt; protocol.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently, you can also just make a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3699176/&quot; rel=&quot;nofollow&quot;&gt;standard DNA gel with some added bleach&lt;/a&gt;. I haven't used this technique, but they have some samle results.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-10-07T23:57:32.907" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21948" PostTypeId="1" CreationDate="2014-10-08T03:52:32.073" Score="2" ViewCount="234" Body="&lt;p&gt;We know that an action potential is produced by an active cell membrane when the stimulus reaches a certain threshold. When it does, an action potential fires, and when it doesn't, nothing happens. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are dozens of videos online painstakingly illustrating this point, using examples going from plumbing to pebbles falling down a paper towel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But this is such a simple idea. There doesn't need to be analogies. When I push a button, something moves, when I don't push it, nothing moves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what is the fundamental principle behind this? What biochemical device causes this all or nothing phenomena?&lt;/p&gt;&#xA;" OwnerUserId="9648" LastEditorUserId="86" LastEditDate="2014-10-08T10:51:51.333" LastActivityDate="2014-10-08T17:27:16.020" Title="All or nothing phenomena" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21952" PostTypeId="1" AcceptedAnswerId="21957" CreationDate="2014-10-08T10:38:50.863" Score="3" ViewCount="3137" Body="&lt;p&gt;I am reading up on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nervous_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;nervous system&lt;/a&gt; using wikipedia and trying to interpret one infographic on &lt;a href=&quot;http://en.wikipedia.org/wiki/Nervous_system#mediaviewer/File:Nervous_system_organization_en.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;this page&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/laIw3.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;I've always thought of the human nervous system as a singular network of neurons. This diagram however makes a distinction between 'Motor neurons' and 'Sensory neurons'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can the sensory neuron network and the motor neuron network be considered seperate networks?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indirectly they will definitely be interconnected (because of impulse-response relations), but physically, are they connected or disconnected?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or are there more?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is very well possible that I am missing some knowledge to make this question make sense.&lt;/p&gt;&#xA;" OwnerUserId="5453" LastEditorUserId="9099" LastEditDate="2014-10-08T11:43:33.790" LastActivityDate="2014-10-08T13:16:38.690" Title="Can the sensory neuron network and the motor neuron network be considered separate networks?" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21953" PostTypeId="2" ParentId="21948" CreationDate="2014-10-08T10:49:31.790" Score="2" Body="&lt;p&gt;The fundamental principle behind this is a &quot;sensor&quot; or the &lt;strong&gt;excitation-contraction coupling&lt;/strong&gt;, regardless where you are. &#xA;Let's consider the striated muscle and the cardiac muscle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The function of excitation-contraction coupling in skeletal muscle is as &lt;strong&gt;voltage sensor&lt;/strong&gt; to tell the SR, &quot;We have got an action potential; release Ca2+ for contraction&quot;.&#xA;This is a contrast to a heart muscle which works like a Ca2+ channel (i.e. Ca2+ is flowing in cardiac muscle continuously). &#xA;Similarly, xcitation-contraction coupling in cardiac muscle translates the action potential into the production of tension. &#xA;There are individual steps in this process of cardiac muscle:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;ol&gt;&#xA;&lt;li&gt;The cardiac action potential is initiated in the myocardial cell membrane, and the depolarization spreads to the interior of the cell via the T tubules. &#xA;Recall that a unique feature of the cardiac action potential is its plateau (phase 2), which results from an increase in Ca and an inward Ca2+ current in which Ca2+ flows through L-type Ca2+ channels (dihydropyridine receptors) from extracellular fluid (ECF) to intracellular fluid (ICF).&lt;/li&gt;&#xA;&lt;/ol&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;Entry of Ca2+ into the myocardial cell produces an increase in intracellular Ca2+ concentration. &#xA;This increase in intracellular Ca2+ concentration is not sufficient alone to initiate contraction, but it triggers the release of more Ca2+ from stores in the sarcoplasmic reticulum through Ca2+ release channels (ryanodine receptors). &#xA;This process is called Ca2+- induced Ca2+ release, and the Ca2+ that enters during the plateau of the action potential is called the trigger Ca2+. &#xA;Two factors determine how much Ca2+ is released from the sarcoplasmic reticulum in this step: the amount of Ca2+ previously stored and the size of the inward Ca2+ current during the plateau of the action potential.&lt;/li&gt;&#xA;&lt;/ol&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;ol start=&quot;3&quot;&gt;&#xA;&lt;li&gt;and 4. Ca2+ release from the sarcoplasmic reticulum causes the intracellular Ca2+ concentration to increase even further. &#xA;Ca2+ now binds to troponin C, tropomyosin is moved out of the way, and the interaction of actin and myosin can occur. &#xA;Actin and myosin bind, cross-bridges form and then break, the thin and thick filaments move past each other, and tension is produced. &#xA;Cross-bridge cycling continues as long as intracellular Ca2+ concentration is high enough to occupy the Ca2+-binding sites on troponin C.&lt;/li&gt;&#xA;&lt;/ol&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;ol start=&quot;5&quot;&gt;&#xA;&lt;li&gt;A critically important concept is that the magnitude of the tension developed by myocardial cells is proportional to the intracellular Ca2+ concentration. &#xA;Therefore, it is reasonable that hormones, neurotransmitters, and drugs that alter the inward Ca2+ current during the action potential plateau or that alter sarcoplasmic reticulum Ca2+ stores would be expected to change the amount of tension produced by myocardial cells.&lt;/li&gt;&#xA;&lt;/ol&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I like this figure about the topic in summarising stimuli in the smooth muscle:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/X18Ap.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In heart&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sZYQY.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the gastrointestinal tract, we have then again special cells, &lt;strong&gt;Cajal cells&lt;/strong&gt;, that work as &quot;pacemakers&quot; of the GI tract. &#xA;Myenteric Interstitial cells of Cajal [ICC-MY] serve as a pacemaker which creates the bioelectrical slow wave potential that leads to contraction of the smooth muscle.&#xA;This activity differs along the length of the system&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;3 per minute in the stomach &lt;/li&gt;&#xA;&lt;li&gt;11-12 per minute in the duodenum &lt;/li&gt;&#xA;&lt;li&gt;9-10 per minute in the ileum &lt;/li&gt;&#xA;&lt;li&gt;3-4 per minute in the colon&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You can see them as to work analogously through the &quot;all-or-none&quot; principle.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sources&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Costanzo, Physiology&lt;/li&gt;&#xA;&lt;li&gt;Pocock, Physiology&lt;/li&gt;&#xA;&lt;li&gt;My notes during during years 2011-2014 (in three Physiology courses and research)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-10-08T17:27:16.020" LastActivityDate="2014-10-08T17:27:16.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21954" PostTypeId="1" CreationDate="2014-10-08T11:23:24.557" Score="1" ViewCount="26" Body="&lt;p&gt;Does the graminaceous plants have passive uptake of Fe(II) via a passive Fe(II)-transporter enzyme? Or it it only dicots and non-graminaceous plants that have the Fe(II)-transporter enzyme? Also, can Fe(III)-reductase reduce Fe-EDDHA (&lt;em&gt;Ethylenediamine-N,N'-bis(2-hydroxyphenylacetic acid)&lt;/em&gt;) and Fe-DPTA (&lt;em&gt;diethylene triamine pentaacetic acid&lt;/em&gt;) without the cost of energy?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Best regards,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathias&lt;/p&gt;&#xA;" OwnerUserId="8699" LastEditorUserId="3340" LastEditDate="2015-01-14T08:45:46.417" LastActivityDate="2016-05-09T17:40:34.847" Title="Fe(II) and Fe(III) transport from rhizosphere across plasma membrane" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21955" PostTypeId="1" AcceptedAnswerId="21956" CreationDate="2014-10-08T11:31:10.143" Score="6" ViewCount="3792" Body="&lt;p&gt;Knowing that today iodine comes either from fish products or (artificially) enriched table salt, how did people who lived far from the sea survive before (especially during the the Middle Ages)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit 1: nowadays we could find some iodine in cow milk, cheese and eggs but those sources are artificial &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(Increased iodine content in food due to greater use in: food&#xA;  processing, animal rations, antimicrobial agents...)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.milkquality.ie/documents/BOBrien.pdf&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit 2&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A small amount of iodine enters the atmosphere and, through rain,&#xA;  enters ground water and soil near the sea &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.merckmanuals.com/home/disorders_of_nutrition/minerals/iodine_deficiency_and_toxicity.html&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Summarized of the comments: thanks to  ddiez this question has been partially answered. But as vsz pointed out the the mystery remains: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;areas with iodine deficiency didn't get completely depopulated during the Middle Ages &#xA;  seems to suggest that it does not affect all people that severely. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So the question remains: could humans survive and reproduce without any iodine source?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit 3: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;“If all women in the UK took iodine supplements while pregnant, IQ&#xA;  would rise by 1.2 points per child” but some says &quot;Some observational studies suggest supplements could even lower IQ, perhaps because excess iodine might harm the thyroid gland.&quot; (Newscientist, August 2015)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5603" LastEditorUserId="5603" LastEditDate="2015-08-17T04:08:10.153" LastActivityDate="2015-08-17T04:08:10.153" Title="iodine: how did they manage without it in old ages? (People who were living far from the sea)" Tags="&lt;metabolism&gt;&lt;health&gt;&lt;minerals&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21956" PostTypeId="2" ParentId="21955" CreationDate="2014-10-08T12:02:27.937" Score="5" Body="&lt;p&gt;Iodine is naturally found in sea water and soil but it is not evenly distributed, with many areas in the world with low levels of iodine. Iodine accumulates &lt;em&gt;naturally&lt;/em&gt; in fish, and plants growing in iodine-rich soil. Mammals that eat these plants get iodine from them, which then accumulates in the milk, making dairy and its products (e.g. cheese) another &lt;em&gt;natural&lt;/em&gt; source of iodine. &lt;a href=&quot;http://www.thyroid.org/iodine-deficiency/#table1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Table 1&lt;/a&gt; from the &lt;a href=&quot;http://www.thyroid.org/iodine-deficiency&quot; rel=&quot;nofollow noreferrer&quot;&gt;Iodine deficiency&lt;/a&gt; section at the &lt;a href=&quot;http://www.thyroid.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;American Thyroid Association&lt;/a&gt; web page contains a brief list of iodine-rich food.&lt;/p&gt;&#xA;&lt;p&gt;Quoting the web site:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;What are the sources of iodine?&lt;/p&gt;&#xA;&lt;p&gt;Iodine is present naturally in soil and seawater. The availability of iodine in foods differs in various regions of the world. Individuals in the United States can maintain adequate iodine in their diet by using iodized table salt (unless they have to restrict the amount of salt in their diet), by eating foods high in iodine, particularly dairy products, seafood, meat, some breads, and eggs, and by taking a multivitamin containing iodine (see below). However, the amount of iodine in foods is not listed on food packaging in the U.S., and it can be difficult to identify sources of iodine in foods.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;As mentioned, the amount of iodine in some food depends on how much iodine is present in the water or soil. For example, in the &lt;a href=&quot;http://www.iccidd.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;International Council for the Control of Iodine Deficiency Disorders (ICCIDD)&lt;/a&gt; there is some mention about the natural &lt;a href=&quot;http://www.iccidd.org/p142000267.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;sources of iodine&lt;/a&gt; and its limitations:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Most of the iodine we consume comes from what we eat and drink. Seafood is usually a good source because the ocean contains considerable iodine. Freshwater fish reflect the iodine content of the water where they swim, which may be deficient. Other foods vary tremendously in iodine content, depending on their source and what may have been added. Plants grown in iodine-deficient soil do not have much iodine, nor do meat or other products from animals fed on iodine-deficient plants. Because the breast concentrates iodine, dairy products are usually a good source, but only if the cows get enough iodine.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Iodine_deficiency&quot; rel=&quot;nofollow noreferrer&quot;&gt;Iodine deficiency&lt;/a&gt; causes &lt;a href=&quot;http://www.iccidd.org/p142000268.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;important health problems&lt;/a&gt;. Iodine is necessary to produce &lt;a href=&quot;http://en.wikipedia.org/wiki/Thyroid_hormone&quot; rel=&quot;nofollow noreferrer&quot;&gt;thyroid hormones&lt;/a&gt;. Lack of thyroid hormones causes &lt;a href=&quot;http://en.wikipedia.org/wiki/Hypothyroidism&quot; rel=&quot;nofollow noreferrer&quot;&gt;hypothyroidism&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Cretinism&quot; rel=&quot;nofollow noreferrer&quot;&gt;cretinism&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Goitre&quot; rel=&quot;nofollow noreferrer&quot;&gt;goiter&lt;/a&gt;. However, iodine deficiency is not mortal &lt;em&gt;per se&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Conclusion&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;As a consequence, in the Middle Ages iodine deficiency was not an issue in places where water and/or soil was rich in iodine. In other places they would suffer of iodine deficiency, leading to a higher impact of the related diseases.&lt;/p&gt;&#xA;&lt;p&gt;Nowadays, iodine is added artificially to food in order to prevent iodine deficiency. This practice has diminished the impact of iodine deficiency-related diseases. However, iodine deficiency is still an important issue today, as reported by the &lt;a href=&quot;http://www.who.int&quot; rel=&quot;nofollow noreferrer&quot;&gt;World Health Organization&lt;/a&gt; in its map describing the &lt;a href=&quot;http://www.who.int/vmnis/iodine/status/summary/severity_color.pdf?ua=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Degree of Public Health Significance of Iodine Nutrition&lt;/a&gt;. As shown in the map, in many places in the world there is still risk of severe iodine deficiency.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/klJqU.png&quot; alt=&quot;WHO - Degree of Public Health Significance of Iodine Nutrition&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Sources:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Iodine_deficiency&quot; rel=&quot;nofollow noreferrer&quot;&gt;Iodine deficiency - Wikipedia&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.thyroid.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;American Thyroid Association&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.who.int&quot; rel=&quot;nofollow noreferrer&quot;&gt;World Health Organization&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.iccidd.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;International Council for the Control of Iodine Deficiency Disorders (ICCIDD)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9099" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-10-09T16:15:24.247" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="21957" PostTypeId="2" ParentId="21952" CreationDate="2014-10-08T12:58:42.473" Score="4" Body="&lt;p&gt;The sensory and motor pathways can indeed be considered separately both in concept and physically. Of course the nervous systems &lt;em&gt;is&lt;/em&gt; a single network of neurons, but that doesn't stop it from having separate components.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One can indeed often simplify neural pathways as &quot;IN (sensory) ===&gt; (black box with decision-making magic) ===&gt; OUT (motor)&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reflexes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reflex arcs are a great way of demonstrating this separation because they do not involve the more complicated integration of the brain. Let's take the knee-bend (patellar) reflex as an example: &lt;a href=&quot;https://en.wikipedia.org/wiki/Patellar_reflex&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Patellar_reflex&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3RwyP.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The diagram is correct in concept but let me add the anatomical detail to illustrate how sensory and motor pathways are separate, yet connected: When the reflex is triggered, the signal travels up from the sensory neuron ends located under the knee cap (these are dendrites) to the sensory neuron's body in the spinal chord. The sensory cell relays the signal via its axon, which then synapses with a motor neuron's body also in the spinal chord. The motor neuron then sends a motor impulse via its axon back down to the leg, where it triggers muscle contraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Physically, in this case there will be a separation also in nerves (at least if I may trust Wikipedia for now), where the sensory reflex neurons' dendrites travel from the leg to the spinal chord through an afferent nerve and the motor neurons' axons travel in the reverse direction through an efferent nerve. The only physical and conceptual connection between the sensory pathway and the motor pathway is the synapse between the sensory and the motor neurons in the spinal chord.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More complex sensorimotor pathways might include interneurons or integration with various circuits in the brain, but it is usually possible to define discreet separate parts of the pathway, one sensory and one motor, with the only connection being those interneurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sensory and motor separation in the CNS&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The central nervous system (CNS, which includes the brain and the spinal chord) is actually surprisingly organised in this regard, with quite strict separation of motor and sensory pathway components. For example, the cortex of the brain has distinct regions which contain sensory neurons for evaluation of various types of peripheral skin sensation. Separate from these are regions which contain motor neurons for movement of skeletal (voluntary-control) muscle. The interaction of these is of course more complex given that it involves skin sensation and conscious decision making in regards to movement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8IaMh.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Likewise, the spinal chord is structured into sensory and motor regions. In summary, the spinal chord consists of: 1) cell bodies (motor, sensory, inter; grey in the picture), 2) ascending axons (blue), 3) descending axons (red). Similar to nerves, axons going up or down the spinal chord are bundled into &quot;tracts&quot;. Sensory axons are never bundled with motor axons, making it possible to create a map of the spinal chord in cross-section.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The tracts' names might be a bit confusing at first, but on second look are actually pretty self-explanatory. They usually contain where the axons come from and where they are going in order to synapse with other neurons. E.g. the spinocerebellar tract is formed of axons coming from the spine and going to the cerebellum. Given that the cerebellum is near the brain and the spine is further down, this is obviously an ascending tract - and ascending tracts are always sensory (because sensory information never needs to be carried downwards due to the brain being at the top).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4HZru.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Where it gets blurry&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sensory/motor separation isn't always as clear as I've described above. In fact, nerves (bundles of axons anywhere in the body outside of the CNS) will usually contain both sensory and motor pipelines. In particular, the cranial nerves (12 of the most important nerves) all include sensory and motor components for the respective part of the body that they manage. E.g. the facial nerve contains both the sensory connections for parts of the tongue and the motor connections that control facial muscles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another more complex example is pain sensation, where interneurons in the spinal chord can feed back onto sensory neurons and inhibit their signals, or axons can inhibit those packed in the same nerve bundle simply due to electrical effects.&lt;/p&gt;&#xA;" OwnerUserId="806" LastEditorUserId="806" LastEditDate="2014-10-08T13:16:38.690" LastActivityDate="2014-10-08T13:16:38.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21958" PostTypeId="2" ParentId="21100" CreationDate="2014-10-08T14:30:07.283" Score="1" Body="&lt;p&gt;The chromosomes in your picture do have sister chromatids, they are just very close together. A chromosome needs to pass through replication before it can compact into the typical metaphase chromosome shape depicted above. When I prepare metaphase chromosomes, I usually see a mixture of chromosome sets where the chromatids are close together (like above) and clearly separated. I think this is related to the time each metaphase has spent in the colcemid block-the longer the cell has been blocked at metaphase for, the longer the enzymes that work to separate the two chromatids have acted on it. Also chromosomes keep getting more and more compacted during the colcemid block-if you leave them for too long, they become a lot smaller.  This paper has very cool pictures showing the links between the sister chromatids:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18461479&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/18461479&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9684" LastActivityDate="2014-10-08T14:30:07.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21961" PostTypeId="1" AcceptedAnswerId="21976" CreationDate="2014-10-08T15:40:53.110" Score="8" ViewCount="1607" Body="&lt;p&gt;I hesitated to ask this question because it seems so obvious and intuitive. However, I am not able to explain this tendency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to me that small organisms make faster movements than big organisms. I don't mean that they are able to travel at higher speed (the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cheetah&quot;&gt;cheetah&lt;/a&gt; is a big animal and is the fastest terrestrial species) but I mean that their movement are fast, quick and their members undergo high acceleration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Examples&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would guess for example that the legs of a &lt;a href=&quot;http://en.wikipedia.org/wiki/Tiger_beetle&quot;&gt;tiger beetle&lt;/a&gt; (clade of fast sprinter beetles) (see &lt;a href=&quot;https://www.youtube.com/watch?v=VIYX82t30zo&quot;&gt;movie&lt;/a&gt;) undergo much higher acceleration than the legs of a &lt;a href=&quot;http://en.wikipedia.org/wiki/Cheetah&quot;&gt;cheetah&lt;/a&gt; (fastest terrestrial organism on earth) (see &lt;a href=&quot;https://www.youtube.com/watch?v=iarsmqA3dck&quot;&gt;movie&lt;/a&gt;). To avoid taking the extreme, I would think that the legs of a Drosophila (see &lt;a href=&quot;https://www.youtube.com/watch?v=h8_vsv20rZc&quot;&gt;movie&lt;/a&gt;) undergo higher acceleration than the legs of a dog (see &lt;a href=&quot;https://www.youtube.com/watch?v=hWJ8NjKw8cU&quot;&gt;movie&lt;/a&gt;). The organism that is able to create the fastest acceleration is the mantis shrimp. &lt;a href=&quot;http://en.wikipedia.org/wiki/Mantis_shrimp&quot;&gt;Wikipedia&lt;/a&gt; says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Both types (smashers and spearers) strike by rapidly unfolding and swinging their raptorial claws at the prey, and are capable of inflicting serious damage on victims significantly greater in size than themselves. In smashers, these two weapons are employed with blinding quickness, with an acceleration of 10,400 g (102,000 m/s2 or 335,000 ft/s2) and speeds of 23 m/s from a standing start. Because they strike so rapidly, they generate cavitation bubbles between the appendage and the striking surface. The collapse of these cavitation bubbles produces measurable forces on their prey in addition to the instantaneous forces of 1,500 newtons that are caused by the impact of the appendage against the striking surface, which means that the prey is hit twice by a single strike; first by the claw and then by the collapsing cavitation bubbles that immediately follow. Even if the initial strike misses the prey, the resulting shock wave can be enough to stun or kill the prey.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Finally, note that &lt;a href=&quot;http://www.pnas.org/content/100/15/8748.full&quot;&gt;Gabel and Berg (2003)&lt;/a&gt; show that the flagella can rotates up to 270 Hz.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Am I right to think that small organisms tend to make faster movements than big organisms?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If yes: Why do small creatures make faster movements?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Does it has to do with time for chemical diffusion?&lt;/li&gt;&#xA;&lt;li&gt;Does it has to do with mechanics? ($F=ma$... But muscles are smaller as well).&lt;/li&gt;&#xA;&lt;li&gt;Does it has to do with the resistence of biological tissues?&lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-10-08T18:21:48.990" LastActivityDate="2014-10-08T19:38:23.080" Title="Why do small organisms make faster movements than big organisms?" Tags="&lt;physiology&gt;&lt;zoology&gt;&lt;entomology&gt;&lt;anatomy&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21962" PostTypeId="2" ParentId="21941" CreationDate="2014-10-08T15:47:15.583" Score="6" Body="&lt;p&gt;You have two possibilities: When you only need a quick check if your RNA is ok and you indeed only get one band, you can try a &quot;quick and dirty&quot; method. Heat the sample for 5 minutes at 65°C and then immediately cool it down in an icebath and keep it there until loading. By doing so, you melt up the secondary structure of the RNA and keep it in this state. You will most likely then see only one band.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this doesn't work or if you want to use a RNA size marker, there is no way around denaturating gel electrophoresis. Here you denature your sample in the loading buffer and then run a denaturating gel in which prevents the secondary structures. There is a good paper about this:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3769/aiwh9lys_pdf.htm&quot;&gt;Denaturing RNA electrophoresis in TAE agarose gels&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The classical method using formaldehyde (which is more dangerous in handling) is described in the following paper and also in the &quot;Molecular Cloning: A Laboratory Manual&quot; book by Maniatis and colleagues: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3769/9t6tbzgc_pdf.htm&quot;&gt;RNA molecular weight determinations by gel electrophoresis under&#xA;denaturing conditions, a critical reexamination&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-08T15:47:15.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21964" PostTypeId="1" AcceptedAnswerId="23076" CreationDate="2014-10-08T17:11:04.173" Score="0" ViewCount="80" Body="&lt;p&gt;Please have a look at this close up light microscopic image of a thyroid gland:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OOXNl.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I'm guessing the cubic epithelial cells surrounding this big red pulp are the secreting cells...? If so, is the red pulp a blood vessel that they are secreting into?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I misunderstanding?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2014-10-13T11:38:49.937" Title="Help me understand how the thyroid secretes" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21973" PostTypeId="1" CreationDate="2014-10-08T18:20:04.457" Score="26" ViewCount="4269" Body="&lt;p&gt;Our bodies can repair quite a number of injuries very well. However, it takes time. For larger wounds, complete recovery can last many weeks. Why is this time so long, what is the most important limiting factor? The speed of cell division? I thought cell division was faster, and if necessary, cells could also be transported in the blood stream. Thrombocytes, as far as I know, are transported to the location of the emergency by the blood, and are not produced locally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the pure physics and chemistry allowed, for example, a 2x faster healing rate, wouldn't there be any evolutionary pressure for it?&lt;/p&gt;&#xA;" OwnerUserId="3798" LastEditorUserId="1590" LastEditDate="2014-10-08T18:20:21.757" LastActivityDate="2018-01-14T18:50:07.230" Title="What limits our healing speed?" Tags="&lt;healing&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="21974" PostTypeId="2" ParentId="21973" CreationDate="2014-10-08T19:21:29.513" Score="19" Body="&lt;p&gt;The process of wound healing is pretty complicated and is much more than only cell division. The woundhealing process starts almost immediately in the moment of the injury and depending on the injury can take quite a long time. Have a look at the figure below (from the second reference), which shows the phases:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/I76A1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically this can roughly be diveded into four phases:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Hemostasis/Coagulation:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;vascular constriction (blood vessel contraction)&lt;/li&gt;&#xA;&lt;li&gt;platelet aggregation, degranulation, and fibrinformation (formation of a thrombus and closure of the wound)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Inflammation:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;neutrophil infiltration&lt;/li&gt;&#xA;&lt;li&gt;monocyte infiltration and differentiation into different kinds of macrophages&lt;/li&gt;&#xA;&lt;li&gt;lymphocyte infiltration&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Proliferation:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;re-epithelialization&lt;/li&gt;&#xA;&lt;li&gt;angiogenesis (formation of new blood vessels)&lt;/li&gt;&#xA;&lt;li&gt;collagen synthesis (formation of new connective tissue)&lt;/li&gt;&#xA;&lt;li&gt;formation of the extracellular matrix&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Remodeling:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;collagen remodeling&lt;/li&gt;&#xA;&lt;li&gt;vascular maturation and regression&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This process takes some time and can be prolonged when a wound is infected.  So I don't think there is much room to speed this up, as you need to go through all these phases. This process is also the result of extensive evolutionary processes; otherwise, such complex cooperation between different cells is not possible. For more details on the process itself, have a look at the references.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20139336&quot; rel=&quot;noreferrer&quot;&gt;Factors affecting wound healing.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19668939&quot; rel=&quot;noreferrer&quot;&gt;Cellular aspects of wound healing.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="9704" LastEditDate="2014-10-10T00:45:27.937" LastActivityDate="2014-10-10T00:45:27.937" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="21975" PostTypeId="2" ParentId="21961" CreationDate="2014-10-08T19:28:05.480" Score="4" Body="&lt;p&gt;An increase in linear dimension by $x$ causes an increase of $x^3$ in volume and mass.  The force that a muscle can generate roughly scales with the cross-sectional area of the muscle, an increase of $x^2$ for a muscle scaled by a factor of $x$.     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that larger animals need proportionally larger muscles (by a factor of $\sqrt {x}$) to achieve the force required to generate any given acceleration.  This becomes impractical fairly quickly, so we just make do with less acceleration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you consider a 1 cm ant scaled to human size with no other modifications (a 200-fold increase), it would be 8,000,000 times more massive but its muscles would only be 40,000 times stronger.  It may have started out about 50 times stronger than a human, mass-for-mass, but at human scale, it's only 1/4th as strong; it would barely be able to move at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other biomechanical factors that can influence speed that favor smaller creatures as well.  One example is the ability of mantis shrimp to store amounts of mechanical energy that are quite large on their scale in the curvature of their exoskeleton (like storing energy in a car's leaf spring.)  Similar energy storage on a human scale is just not practical.&lt;/p&gt;&#xA;" OwnerUserId="9476" LastActivityDate="2014-10-08T19:28:05.480" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21976" PostTypeId="2" ParentId="21961" CreationDate="2014-10-08T19:38:23.080" Score="5" Body="&lt;p&gt;It's a general phenomenon that the time scale correlates with the size scale of complex systems. &#xA;Energy consumption is the main concern dealing with the speed for biological organizations.&#xA;In the absolute sense, a turtle has a higher speed than a small bug. But based on their sizes, the bug seems much quicker and faster. So we need to normalize the speed with the size scale which we can temporarily call 'fastness&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the relationship between the fastness and the mass:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tOAGN.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where u is speed of the organism, M is mass, alpha is a constant which we assume that the metabolic energy is related to the body mass of the organism with a power law.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The final equation says that if alpha &gt; 1.67 then the larger would be faster. But our observation tells us that the smaller the faster. Therefore, we know alpha &amp;lt; 1.67. &#xA;In fact &lt;a href=&quot;http://en.wikipedia.org/wiki/Kleiber&amp;#39;s_law&quot; rel=&quot;noreferrer&quot;&gt;Kleiber's law&lt;/a&gt; tells us that the alpha is about 0.75. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can check some numbers related to some animals &lt;a href=&quot;http://www.speedofanimals.com/&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9687" LastActivityDate="2014-10-08T19:38:23.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21977" PostTypeId="2" ParentId="21973" CreationDate="2014-10-08T19:39:52.273" Score="16" Body="&lt;p&gt;The time needed for a wound to heal is related to the type of tissue injured and the amount of tissue that needs to be 'reconstructed.' Cell division rates are also a factor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Healing is a complex process that involves multiple stages.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The body has to limit the damage that can result from an injury. So, first it tries to stop the bleeding and then a local inflammatory process is triggered. This inflammation will:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;stop pathogens from entering the systemic circulation&lt;/li&gt;&#xA;&lt;li&gt;'clean' the injured tissue by removing dead cells&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In order to recreate the tissue, there is the need for blood which will deliver nutrients and other factors. So, fibroblasts and endothelial cells migrate in the wounded area and form temporary tissue and new blood vessels; the new tissue is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Granulation_tissue&quot; rel=&quot;noreferrer&quot;&gt;granulation tissue&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The granulation tissue allows for the formation of definitive tissue. This is the remodelling phase. Depending on the wound, the tissue that grows can either be the same as the original one or be fibrous scar tissue.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Looking at the time required by each of these steps:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;should be the fastest as it relies on blood cells and factors that are already present in blood. Also, the wound itself will stimulate the local production of some cells/factors involved (inflammatory factors, vasodilator, vasoconstrictor factors.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;and 3. depend on the duration of cell-division processes, extracellular matrix formation, and vascularization. Cell division time can be slowed down by a lack of required nutrients and/or substances.  While the granulation tissue forms in almost constant time no matter the injury, the final tissue depends on what type it will be. One simple example is bone tissue versus skin.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References &amp;amp; Links:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Wound_healing&quot; rel=&quot;noreferrer&quot;&gt;Wound healing on Wikipedia&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;John Miller: &lt;a href=&quot;http://physioworks.com.au/treatments-1/what-are-the-phases-of-a-soft-tissue-injury&quot; rel=&quot;noreferrer&quot;&gt;http://physioworks.com.au/treatments-1/what-are-the-phases-of-a-soft-tissue-injury&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="9704" LastEditDate="2014-10-10T00:44:57.617" LastActivityDate="2014-10-10T00:44:57.617" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21978" PostTypeId="1" AcceptedAnswerId="21989" CreationDate="2014-10-08T21:17:25.337" Score="2" ViewCount="3372" Body="&lt;p&gt;What causes our epiphyseal plates close up in our late teens or early twenties?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize that one's genetics plays the main role in this. I assume there is a gene that controls the epiphyseal plates in our long bones. I guess there would be genes dedicated to every single epiphyseal plate found in our body too. So to rephrase the question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does the gene for our epiphyseal plates turn off in our lates teens or early twenties?&lt;/p&gt;&#xA;" OwnerUserId="5491" LastActivityDate="2014-10-09T07:26:48.957" Title="Why do our epiphyseal plates close up in our late teens or early twenties?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;gene-expression&gt;&lt;bone-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21979" PostTypeId="2" ParentId="21973" CreationDate="2014-10-08T21:43:22.043" Score="6" Body="&lt;p&gt;I claim that one great limitation in our understanding of the healing process is that biologists have &lt;strong&gt;no understanding of the progression of disease or infection&lt;/strong&gt;, that not enough time may be given for the body to recover, and that doctors might &lt;strong&gt;not understand how to help their patients recover from disease or infection&lt;/strong&gt;. &#xA;Each patient is different, and personalised recovering plan is often important.&#xA;So, too few resources — e. g.:  the time of a doctor and/or a nurse — are offered to patients, so doctors have little time to build their understanding of the disease or injury with which their patients are dealing. &#xA;It is the patient who makes himself or herself able to recover.&#xA;But, without understanding, the recovery process is not optimal.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Healing from upper respiratory infection:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I will give one example in LOR Medicine. &#xA;Upper respiratory infections are one of the most common infections and most expensive diseases in society. &#xA;One reason is that people do not understand:   &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;how to recover from disease&lt;/li&gt;&#xA;&lt;li&gt;how long the common cold or flu lasts (doctors underestimate the time that it will take for their patients to heal very often.)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In nursing school, they teach students how to, among other things:  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;prevent reinfection&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/a/19488/86&quot;&gt;prevent acute hyaline membrane formation by elevated sleeping position&lt;/a&gt; (in LOR, for instance.)  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There is no way to measure what the correct course of treatment is for any given patient during the course of, for example, an upper respiratory infection. &#xA;Nurses ask the patient when he or she feels their best and adjusts treatment accordingly. &#xA;So, good communication is essential in nursing. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Wound healing:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Chris and Cornelius cover some of the basic cellular processes of wound healing.&#xA;However, some big steps are still missing in regards to healing.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;The primary healing of wounds is aided by:&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;adequate wound-edge coaptation&lt;/li&gt;&#xA;&lt;li&gt;healing without complications&lt;/li&gt;&#xA;&lt;li&gt;minimal scar tissue&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;through the cellular processes of wound healing described by Cornelius and Chris.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Secondary healing of wounds is characterized by:&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;wound tissue left exposed (open)&lt;/li&gt;&#xA;&lt;li&gt;defect filled with granulation tissue&lt;/li&gt;&#xA;&lt;li&gt;surface covering the epithelium&lt;/li&gt;&#xA;&lt;li&gt;less functionality&lt;/li&gt;&#xA;&lt;li&gt;possible thermal and mechanical injuries&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Embryological and biochemical aspects of tissue healing&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I cover here some growth factors.&#xA;If they are not present, then their absence will surely be a limitation to the healing process.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;TGF - transforming growth factor&lt;/li&gt;&#xA;&lt;li&gt;MDGF - macrophage-derived growth factor&lt;/li&gt;&#xA;&lt;li&gt;HB-ECG - heparin-binding epidermal growth factor&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Here are some other factors:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;bFGF - basic fibroblast growth factor&lt;/li&gt;&#xA;&lt;li&gt;KAF - keratinocyte-derived growth factor&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Special cytokines for inflammation may later come into play.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sources&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Human skin wounds: a major and snowballing threat to public health and the economy. Sen C.K., Gordillo G.M., Roy S., Kirsner R., Lambert L., Hunt T.K., Gottrup F., Gurtner G.C., Longaker M/T. Wound Repair Regen. 2009 NovDec;17(6):763-71.&lt;/li&gt;&#xA;&lt;li&gt;My notes during 4 years of nursing&lt;/li&gt;&#xA;&lt;li&gt;My notes during classes of Surgery&lt;/li&gt;&#xA;&lt;li&gt;My notes of Embryology and Surgery about the growth factors&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-10-10T00:45:19.103" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="21980" PostTypeId="1" AcceptedAnswerId="21983" CreationDate="2014-10-08T22:01:40.127" Score="0" ViewCount="654" Body="&lt;p&gt;How does cells use the DNA inside them? I am looking on DNA as a strip of tape of &lt;a href=&quot;http://en.wikipedia.org/wiki/Turing_machine&quot; rel=&quot;nofollow&quot;&gt;Turing machine&lt;/a&gt;, but with machines its easy. I can read the tape and calculate the behavior of that machine. With cells its different we don't really understand the language of DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So instead of trying to understand the language I was wandering if there are any particular behaviors of cells that we can associate to different &quot;outputs&quot; of the DNA tape.&lt;/p&gt;&#xA;" OwnerUserId="9688" LastActivityDate="2014-10-08T23:57:39.443" Title="If DNA is the input, what is the output?" Tags="&lt;dna&gt;&lt;cell&gt;" AnswerCount="2" CommentCount="8" ClosedDate="2014-10-09T09:02:07.310" ContentLicense="CC BY-SA 3.0" />
  <row Id="21981" PostTypeId="2" ParentId="21980" CreationDate="2014-10-08T22:43:03.670" Score="2" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology&quot; rel=&quot;nofollow&quot;&gt;central dogma of molecular biology&lt;/a&gt; states that DNA encodes the information for building proteins, the information is copied to messenger RNA through &lt;a href=&quot;http://en.wikipedia.org/wiki/Transcription_%28genetics%29&quot; rel=&quot;nofollow&quot;&gt;transcription&lt;/a&gt;, and messenger RNA is used to build proteins through &lt;a href=&quot;http://en.wikipedia.org/wiki/Translation_%28biology%29&quot; rel=&quot;nofollow&quot;&gt;translation&lt;/a&gt;. DNA is also copied through &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_replication&quot; rel=&quot;nofollow&quot;&gt;replication&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So while it's true that DNA contains the information needed to build a living organism, I don't think it can described as &quot;turing tape&quot; If I understand &lt;a href=&quot;http://en.wikipedia.org/wiki/Turing_machine&quot; rel=&quot;nofollow&quot;&gt;turing machines&lt;/a&gt; correctly, you have a string of 1s or 0s, and a machine reads this string. Based on rules provided by an instruction set the machine can set positions on the tape to 1 or 0. The analogy with DNA fails because DNA does not have a separate instruction set and cannot be written to. DNA produces RNA and DNA with the help of many many proteins and other molecules, all tightly regulated to coordinate replication of the genome and to produce the right amounts of RNA and protein at the right times. DNA can mutate when replication makes an error, but this is accidental, not comparable to turing machines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're interested in how DNA might be used like a computer, there are several articles on &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=dna%20computing&quot; rel=&quot;nofollow&quot;&gt;DNA Computing&lt;/a&gt;, though you'll have to sort through those papers because many look like they just used a computer to analyze DNA.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2014-10-08T23:01:34.447" LastActivityDate="2014-10-08T23:01:34.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21982" PostTypeId="1" CreationDate="2014-10-08T23:47:49.637" Score="3" ViewCount="724" Body="&lt;p&gt;Carl Jung has long ago proposed a rather controversial notion of &lt;em&gt;collective unconsciousness&lt;/em&gt;&lt;a href=&quot;http://www.britannica.com/EBchecked/topic/125572/collective-unconscious&quot; rel=&quot;nofollow&quot;&gt; [1&lt;/a&gt;, &lt;a href=&quot;http://www.thefreedictionary.com/collective+unconscious&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Collective_unconscious&quot; rel=&quot;nofollow&quot;&gt;3],&#xA;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a form of the unconscious (that part of the mind containing memories&#xA;  and impulses of which the individual is not aware) common to mankind&#xA;  as a whole and originating in the inherited structure of the brain. It&#xA;  is distinct from the personal unconscious, which arises from the&#xA;  experience of the individual.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;While the complete original formulation of the idea may be interpreted as unfalsifiable and hence unscientific, suppose that we try to redefine it to some more modest idea, e.g. a set of inheritable subconscious memories, impulses and reactions present in populations/groups, with some expected degree of variation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, it has been shown that memories reside in specific brain cells&lt;a href=&quot;http://newsoffice.mit.edu/2012/conjuring-memories-artificially-0322&quot; rel=&quot;nofollow&quot;&gt; [4]&lt;/a&gt;. What is also known is the direct impact of environment (which - as far as I understand it - also includes our thoughts, feelings and expectations) on gene expression and epigenetic inheritance. In the light of these insights, could the notion of collective unconsciousness be revitalized and interpreted in some non-trivial way that could be used to better understand the way we dream, feel, identify with characters in stories etc.?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, do new discoveries in neurobiology, evolutionary biology and epigenetics shed any new light on Jung's writings (e.g. timescale for such structures to adapt between generations etc.) and perhaps confirm some of his ideas? If not, could experiments be performed that would provide some new insights? Or is the idea so trivial at its core that basic evolution is enough to explain it in its entirety?&lt;/p&gt;&#xA;" OwnerUserId="3583" LastEditorUserId="3583" LastEditDate="2014-10-16T17:29:37.810" LastActivityDate="2014-10-16T17:29:37.810" Title="Does the Jungian notion of collective unconsciousness have any legitimacy in the light of modern neurobiology and epigenetics?" Tags="&lt;evolution&gt;&lt;neuroscience&gt;&lt;brain&gt;&lt;epigenetics&gt;&lt;psychology&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="21983" PostTypeId="2" ParentId="21980" CreationDate="2014-10-08T23:57:39.443" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;but with machines its easy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's not that easy...the Turing machine can't interpret the tape without knowing something about what the 1s and 0's mean.  A complied C++ program is gibberish if read through a Perl interpreter.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA isn't as abstract as that, anyway.  A DNA molecule interacts with other molecules based on its shape, which the sequence of letters defines.  There are thousands of molecules in a cell which the DNA strand can interact with, and those molecules are affected by other molecules.  Think about it...for the most part, all the DNA in your cells is the same, but obviously the cells in your liver are doing different things than the cells in your skin.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;With cells its different we don't really understand the language of&#xA;  DNA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That's not the problem.  We just don't understand ALL the relevant interactions, because there are so many of them.  There is not one thing reading through the string of DNA once.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I was wandering if there are any particular behaviors of cells that we&#xA;  can associate to different &quot;outputs&quot; of the DNA tape.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The outputs would be proteins, but you can't just look at the DNA sequence and know what proteins will be made when and in what quantities, not without having &lt;strong&gt;empirically&lt;/strong&gt; learned a lot about those proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look, there are lots of people who know a lot about computers and a lot about biology.  If thinking about DNA as a simple string of information was fruitful, people would be doing that.  We don't, because biology is more complicated than that.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-10-08T23:57:39.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21984" PostTypeId="2" ParentId="21632" CreationDate="2014-10-09T02:10:42.190" Score="2" Body="&lt;p&gt;I don't know of any interesting mechanism that is specific to pain killers, so I will instead answer for drugs in general.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Drug action is a complex process consisting of many steps. Let's take a simple example: A systemic direct inhibitor of a kinase. This drug would need to*:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Be absorbed into your bloodstream&lt;/li&gt;&#xA;&lt;li&gt;Remain in your bloodstream for sufficient time&lt;/li&gt;&#xA;&lt;li&gt;Be absorbed into the tissue&lt;/li&gt;&#xA;&lt;li&gt;Be able to bind the target protein&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;1 can fail due to interaction with other concurrently taken drugs or food, or simply genetic factors affecting the particular functioning of the gut mucosa. 2 can fail because the kidneys are too good at eliminating it, or the liver is metabolizing it too agressively (both also subject to modulation by other drugs, foods and genetic factors). 3 can fail because the transports in the cells aren't working as rapidly, or represent an allele less likely to take in the drug, or are modulated by other drugs/foods. The tissue can also have efflux pumps or enzymes that break down the drug. 4 can fail because the drug was designed for a specific allele of that kinase, but you happen to have a different allele, which has a slightly different structure that is no longer targeted by this drug.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then you have a host of physiological variables, and addiction/tolerance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently the most common genetic reason by far for variable drug sensitivity is the specific set of &lt;a href=&quot;http://ghr.nlm.nih.gov/geneFamily/cyp&quot; rel=&quot;nofollow&quot;&gt;CYP genes&lt;/a&gt; you have. CYP enzymes are abundant in the liver and chemically process various molecules (including drugs).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides this, an interesting set of specific examples used to be available from 23andme. I'm not sure if they still provide this after the FDA ban on health information.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Clopidogrel sensitivity - CYP2C19 variation&lt;/li&gt;&#xA;&lt;li&gt;Proton Pump Inhibitor (stomach acid reduction) - CYP2C19 variation&lt;/li&gt;&#xA;&lt;li&gt;Abacavir (HIV drug) - HLA-B*5701 &lt;a href=&quot;https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism&quot; rel=&quot;nofollow&quot;&gt;SNP&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Acetaldehyde (alcohol flush) - ALDH2 mutation&lt;/li&gt;&#xA;&lt;li&gt;5-fluorouracil (chemotherapy) - DPYD mutation&lt;/li&gt;&#xA;&lt;li&gt;PEG-IFN-alpha/RBV combination (Hepatitis C medicine) - IL28B SNP&lt;/li&gt;&#xA;&lt;li&gt;Phenytoin (epilepsy drug) - CYP2C9 variants&lt;/li&gt;&#xA;&lt;li&gt;Choline esters (class of muscle relaxants) - BCHE (CE degrader) variants&lt;/li&gt;&#xA;&lt;li&gt;Sulfonylurea (used for type 2 diabetes) - CYP2C9 variants&lt;/li&gt;&#xA;&lt;li&gt;Thiopurine (immune suppressant) -  TPMT (enzyme that degrades thiopurine) variation&lt;/li&gt;&#xA;&lt;li&gt;Warfarin (anticoagulant) - CYP2C9 variants&lt;/li&gt;&#xA;&lt;li&gt;Caffeine - CYP1A2 SNP&lt;/li&gt;&#xA;&lt;li&gt;Metformin (diabetes drug) - SNP rs11212617, near the ATM gene&lt;/li&gt;&#xA;&lt;li&gt;Antidepressant - SNPs in ABCB1 affect likelihood of sexual dysfunction (common side effect)&lt;/li&gt;&#xA;&lt;li&gt;Beta-Blocker (heart disease) - Mutations in ADRB1 which is normally blocked by the drug&lt;/li&gt;&#xA;&lt;li&gt;Floxacillin (drug for staphylococcal infections) - SNPs in the &lt;a href=&quot;https://en.wikipedia.org/wiki/Major_histocompatibility_complex&quot; rel=&quot;nofollow&quot;&gt;MHC region&lt;/a&gt; affect liver toxicity of this drug&lt;/li&gt;&#xA;&lt;li&gt;Heroin - OPRM1 receptor (target of heroin) SNPs affect efficacy&lt;/li&gt;&#xA;&lt;li&gt;Lumiracoxib (used to treat pain and symptoms of osteoarthritis) - SNPs in the MHC region affect liver toxicity&lt;/li&gt;&#xA;&lt;li&gt;Naltrexone (alcohol and narcotic addiction drug) - SNPs in OPRM1 affect how much it can reduce pleasurable feeling from narcotics&lt;/li&gt;&#xA;&lt;li&gt;Statins (cardiovascular disease) - SNPs in &lt;a href=&quot;https://en.wikipedia.org/wiki/COQ2&quot; rel=&quot;nofollow&quot;&gt;COQ2&lt;/a&gt; (mitochondrial component) affect risk of myopathy&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;As you can see, our friends the CYP family enzymes come up frequently, and some are even repeat offenders like CYP2C9. Besides that, there is a fair number of cases where variation in the specific target of the drug are relevant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that this list is not comprehensive: Many drugs have not been studied in sufficient detail, and some may have complicated mechanisms instead of just &quot;bind and inhibit protein X&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have omitted many details and links to literature, I am sure you can easily find them by searching on Google Scholar with the keywords I already gave. Let me know if that doesn't work, though.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;*: Note that these aren't necessarily required for all drugs. For example, some drugs can be applied directly to the skin and hence do not need to pass through blood.&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-10-11T18:46:35.630" LastActivityDate="2014-10-11T18:46:35.630" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="21986" PostTypeId="1" AcceptedAnswerId="21992" CreationDate="2014-10-09T02:41:58.667" Score="4" ViewCount="8559" Body="&lt;p&gt;I'm trying to think about how two neurons communicate, typically shown in pictures as an electric pulse traveling along a long, thin connective tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Is this depiction somewhat accurate, and if so, what happens if both neurons fire at the same time on that connection?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps the connections are one-way, or they can facilitate pulses going in opposite directions at the same time, or perhaps it's something different all-together. It'd be interesting to have this explained, at least vaguely. &lt;/p&gt;&#xA;" OwnerUserId="19073" LastEditorUserId="19073" LastEditDate="2014-10-09T02:53:49.970" LastActivityDate="2019-10-01T01:40:38.127" Title="Are neural connections one-way?" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;&lt;neurotransmitter&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21989" PostTypeId="2" ParentId="21978" CreationDate="2014-10-09T07:26:48.957" Score="3" Body="&lt;p&gt;During Endochondral ossification  chondrocytes in the plate are rapidly dividing, newer daughter cells stack facing the epiphysis while the older cells are pushed towards the diaphysis. As the older chondrocytes degenerate, osteoblasts ossify the remains to form new bone. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In puberty increasing levels of estrogen, in both females and males, leads to increased apoptosis of chondrocytes in the epiphyseal plate. Depletion of chondrocytes due to apoptosis leads to less ossification and growth slows down and later stops when the entire cartilage have become replaced by bone, leaving only a thin epiphyseal scar which later disappears. Once the adult stage is reached, maximum height is reached.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question addresses the genetics of this process however it is more so regulated by the endocrine system. There has not been a single gene assigned to growth plates, or its regulation, and I find it unlikely that there ever will be. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rather, endochondrial ossification takes place because of hundreds of genes interacting with each other. If you start to look at genes involved in apoptosis and the estrogen receptor pathway, you will begin to appreciate more the complexity behind the physiology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a hunch you were looking for a gene, that with age just shuts off, or turns on. Recent evidence has show this does in fact happen as methylation may be a candidate mechanism of mediating not only environmental, but also genetic effects on age-related phenotypes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002629&quot; rel=&quot;nofollow&quot;&gt;http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002629&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-10-09T07:26:48.957" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21992" PostTypeId="2" ParentId="21986" CreationDate="2014-10-09T09:29:24.420" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Are neural connections one-way?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes. Action potentials travel only from dendrites towards axon.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;typically shown in pictures as an electric pulse traveling along a long, thin connective tissue.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What &lt;a href=&quot;http://en.wikipedia.org/wiki/Connective_tissue&quot; rel=&quot;nofollow noreferrer&quot;&gt;connective tissue&lt;/a&gt;? That thin &quot;wire&quot; which carries the action potential is a part of the neural cell body called axon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending on what the axon connects to, there are 6 types of synapses:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Blausen_0843_SynapseTypes.png#mediaviewer/File:Blausen_0843_SynapseTypes.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/3/33/Blausen_0843_SynapseTypes.png/1200px-Blausen_0843_SynapseTypes.png&quot; alt=&quot;Blausen 0843 SynapseTypes.png&quot;&gt;&lt;/a&gt;&lt;br&gt;&quot;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Blausen_0843_SynapseTypes.png#mediaviewer/File:Blausen_0843_SynapseTypes.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;Blausen 0843 SynapseTypes&lt;/a&gt;&quot; by &lt;a href=&quot;//commons.wikimedia.org/wiki/User:BruceBlaus&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;User:BruceBlaus&quot;&gt;BruceBlaus&lt;/a&gt;. When using this image in external sources it can be cited as:&#xA;Blausen.com staff. &quot;Blausen gallery 2014&quot;. Wikiversity Journal of Medicine. DOI:10.15347/wjm/2014.010. ISSN 20018762. - Own work. Licensed under &lt;a href=&quot;http://creativecommons.org/licenses/by/3.0&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Creative Commons Attribution 3.0&quot;&gt;CC BY 3.0&lt;/a&gt; via &lt;a href=&quot;//commons.wikimedia.org/wiki/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikimedia Commons&lt;/a&gt;.&lt;/p&gt; &#xA;&#xA;&lt;p&gt;A synapse is the connection between &lt;strong&gt;two&lt;/strong&gt; structures: the axon of a neuron which &quot;outputs&quot; a signal (chemical or electrical) and the other structure (&quot;input&quot;) that can be:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;a dendrite or any other specific receptor from a cell&lt;/li&gt;&#xA;&lt;li&gt;a neural body (can receive both electrical and chemical stimuli) &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;what happens if both neurons fire at the same time on that connection?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the situation of an axoaxonic synapse (example 2 and even 5 and 6 from the above illustration), the presynaptic neuron can have inhibitory action (nicely explained on &lt;a href=&quot;http://michaeldmann.net/mann13.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;michaeldmann.net&lt;/a&gt; at Presynaptic inhibition) from where I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Activity at the axoaxonic synapse partially hypopolarizes the terminal so that, when an action potential comes down the [...] afferent fiber into that terminal, its amplitude is reduced. Because the amount of transmitter substance released by a bouton is proportional to the amplitude of the action potential in it, less transmitter substance is released, resulting in a smaller EPSP and less excitation of the postsynaptic cell [...]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Links:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Synapse&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Synapse&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.getbodysmart.com/ap/nervoussystem/neurophysiology/synapses/introduction/synaptic_contacts/tutorial.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.getbodysmart.com/ap/nervoussystem/neurophysiology/synapses/introduction/synaptic_contacts/tutorial.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://michaeldmann.net/mann13.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://michaeldmann.net/mann13.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.690" LastActivityDate="2014-10-09T10:07:43.090" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21993" PostTypeId="1" CreationDate="2014-10-09T09:42:04.163" Score="25" ViewCount="2020" Body="&lt;p&gt;I've set up some dummy data in R which makes 40 genetically related lines, they are all siblings within a line so are genetically related by a factor of ½ thus additive genetic variance should be twice the variance explained by line. For the lines there are 200 individuals being measured, for three characters/traits. The first trait has low phenotypic variance, the second has high environmental variance, and the third has high genetic variance.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;rm(list=ls())&#xA;re = 200 # replicate individuals per line&#xA;li = 40  # lines&#xA;&#xA;# setup&#xA;set.seed(5)&#xA;data = data.frame(rep(1:li, each = re))&#xA;colnames(data)=&quot;Line&quot;&#xA;library(nlme)&#xA;library(lme4)&#xA;par(mfrow=c(1,3))&#xA;&#xA;# trait 1: little variance (Va or Ve)&#xA;data$Trait = rnorm(li*re,10,1)&#xA;boxplot(data$Trait~data$Line, ylim=c(0,20), main = expression(&quot;Low V&quot;[A]*&quot;&amp;amp; Low V&quot;[E]))&#xA;var1 = var(data$Trait); mean1 = mean(data$Trait); m1 = lmer(data$Trait ~ (1|data$Line))&#xA;&#xA;# trait 2: high enivronmental variance, little Va&#xA;data$Trait = rnorm(li*re,10,1); data$Trait = data$Trait + rnorm(re*li,0,3)&#xA;boxplot(data$Trait~data$Line, ylim=c(0,20),main = expression(&quot;Low V&quot;[A]*&quot;&amp;amp; High V&quot;[E]))&#xA;var2 = var(data$Trait); mean2 = mean(data$Trait); m2 = lmer(data$Trait ~ (1|data$Line))&#xA;&#xA;# trait 3: high additive genetic variance, little Ve&#xA;data$Trait = rnorm(li*re,10,1); data$Trait = data$Trait+rep(rnorm(li,0,3),each=re)&#xA;boxplot(data$Trait~data$Line, ylim=c(0,20), main = expression(&quot;High V&quot;[A]*&quot;&amp;amp; Low V&quot;[E]))&#xA;var3 = var(data$Trait); mean3 = mean(data$Trait); m3 = lmer(data$Trait ~ (1|data$Line))&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Plots of the three traits,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GnAOd.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then to estimate additive variance ($V_A$) I extract the line variance ($V_L$) from the lmer model and double it,&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;# line variances (variance in additive effect of each haploid genome)&#xA;m1_line = unlist(VarCorr(m1))[[1]]; &#xA;m2_line = unlist(VarCorr(m2))[[1]]; &#xA;m3_line = unlist(VarCorr(m3))[[1]]&#xA;&#xA;# additive variance (double the line variance because it is a hemiclone)&#xA;m1_add = 2*m1_line; &#xA;m2_add = 2*m2_line; &#xA;m3_add = 2*m3_line&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Residual variances should be (assuming perfect experimental design, no measurement error etc.) the estimate of environmental variance ($V_E$) and phenotypic variance ($V_P$) should be the sum of $V_L$ and $V_E$,&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;# residual variance&#xA;m1_res = attr(VarCorr(m1), &quot;sc&quot;)^2&#xA;m2_res = attr(VarCorr(m2), &quot;sc&quot;)^2&#xA;m3_res = attr(VarCorr(m3), &quot;sc&quot;)^2&#xA;&#xA;# phenotypic variance&#xA;m1_phe = m1_line + m1_res&#xA;m2_phe = m2_line + m2_res&#xA;m3_phe = m3_line + m3_res&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Heritability is additive variance divided by the phenotypic variance&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$h^2 = V_A / V_P$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I think it is correct in this case to use line variance rather than additive variance (if someone could explain in an answer that would be useful), so I've done,&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;# heritability (line/ (line+ residual))&#xA;m1_h2 = m1_line/ m1_phe&#xA;m2_h2 = m2_line/ m2_phe&#xA;m3_h2 = m3_line/ m3_phe&#xA;m1_h2; m2_h2; m3_h2&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My question(s):&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it appropriate to use the &lt;code&gt;lmer&lt;/code&gt; function in R to extract variance components in this manner?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have I calculated $V_A$, $V_E$, $V_P$, $h^2$ correctly? I think $V_A$ and $V_E$ are correct, $V_P$ could perhaps be the sum of $V_A$ and $V_E$ rather than $V_L$, and subsequently $h^2$ may be $V_A/V_P$.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-02-28T22:25:59.750" LastActivityDate="2020-09-19T04:07:35.783" Title="Additive genetic variance components from LMER in R" Tags="&lt;bioinformatics&gt;&lt;biostatistics&gt;&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="21994" PostTypeId="2" ParentId="21986" CreationDate="2014-10-09T12:22:19.470" Score="1" Body="&lt;p&gt;First of all, let me clear up a small confusion: a connective tissue is a histological term and isn't relevant to this question :) Check &lt;a href=&quot;https://en.wikipedia.org/wiki/Connective_tissue&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Connective_tissue&lt;/a&gt; on that&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That already suggests that the depiction you describe isn't accurate. I would hope that you have seen something like this, which shows a neuron's structure in a very simplified version:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/di59L.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Summarised and simplified, various kinds of impulses (chemical, mechanical or electrical for example) are received at the dendrites, where they generate electrical potential changes. These spread by diffusion across the cell body. At the axon hillock, the point where the axon starts, all of these changes collect and sum up to a net change. If this crosses a certain threshold, the axon hillock generates a so-called action potential, i.e. an electrical impulse. This impulse then travels down the axon until it reaches the terminals. Terminals attach to other neurons (or e.g. muscle cells) via synapses. When an action potential reaches a terminal, the impulse will be carried across the synapse and cause a specific effect on the next cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, there is a clear single-direction signal transfer here: Input -&gt; Cell body -&gt; Axon -&gt; Output. The cell that receives the output can't &quot;fire back&quot; in any way because it receives that signal as an input itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A diagram of a pathway including several neurons might thus look like this (neurons are drawn as yellow cell bodies and arrows to indicate where their axons reach):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4sOKl.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Taken from Hubel, D: Eye, Brain and Vision, &lt;a href=&quot;http://hubel.med.harvard.edu/book/b6.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://hubel.med.harvard.edu/book/b6.htm&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This does get a bit more complicated when you consider &lt;em&gt;nerves&lt;/em&gt; rather than individual neurons. Nerves are bundles of several axons and contain no cell bodies. This means that in effect, nerves are a lot like electrical cables, and like cables it is actually possible to force electrical current running either way along the cable, or to override a signal running in one direction by sending a signal in the opposite direction. This is relevant for example in pain perception where some theories suggest that pain signals might actually be interrupted on their way up a nerve by direct inhibition on the axon bundle (caused by other neurons), see the first diagram here under 8.2: &lt;a href=&quot;http://neuroscience.uth.tmc.edu/s2/chapter08.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://neuroscience.uth.tmc.edu/s2/chapter08.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="806" LastActivityDate="2014-10-09T12:22:19.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21996" PostTypeId="1" CreationDate="2014-10-09T15:09:22.417" Score="2" ViewCount="387" Body="&lt;p&gt;If I shone a UVC lamp (11W) on something (say for example a plastic phone case) for an hour, would that kill off a noticeable amount of bacteria? That is, if I were to go over the case with a cotton swab before the hour and swipe the cotton swab over a petri dish with nutrients and if I were to do the same after the hour with a different cotton swab and a different petri dish. Do you think that after a week there would be a noticeable difference in bacterial growth between the dishes? I think it should, since some filters for ponds work the same way, but I'm not sure, since in my case, the light needs to penetrate about 10 inches of air first and the environment isn't as closed off. What are your ideas on this?&lt;/p&gt;&#xA;" OwnerUserId="9455" LastEditorUserId="86" LastEditDate="2014-10-10T19:42:40.433" LastActivityDate="2014-11-09T20:33:46.860" Title="Will an 11W UVC lamp kill bacteria?" Tags="&lt;bacteriology&gt;&lt;uv&gt;&lt;surgery&gt;&lt;sterilisation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21997" PostTypeId="1" AcceptedAnswerId="22024" CreationDate="2014-10-09T16:09:21.287" Score="2" ViewCount="200" Body="&lt;p&gt;I am looking for a book that covers the following topics in ethology:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Behaviour&lt;/strong&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Sensory filtering, reponsive-ness, sign stimuli, learning and memory, instinct, habituation, conditioning, imprinting. &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Role of hormones in drive&lt;/strong&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;role of pheromones in alarm spreading; crypsis, predator detection, predator tactics, social hierarchies in primates, social organization in insects. &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Navigation and Biological Rythms&lt;/strong&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Orientation, navigation, homing, biological rhythms, biological clock, tidal, seasonal and circadian rhythms.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Methodology&lt;/strong&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Methods for studying animal behaviour including sexual conflict, selfishness, kinship and altruism.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Do you have any suggestions?&lt;/p&gt;&#xA;" OwnerUserId="9674" LastEditorUserId="4108" LastEditDate="2014-10-09T21:59:42.787" LastActivityDate="2014-10-10T15:28:01.693" Title="Book-recommendation: Ethology" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;behaviour&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="21998" PostTypeId="2" ParentId="21939" CreationDate="2014-10-09T16:25:56.457" Score="6" Body="&lt;p&gt;Notice: the only &lt;a href=&quot;https://en.wikipedia.org/wiki/Select_agent&quot; rel=&quot;nofollow noreferrer&quot;&gt;select agent&lt;/a&gt; I've worked with is &lt;a href=&quot;http://en.wikipedia.org/wiki/Vesicular_stomatitis_virus&quot; rel=&quot;nofollow noreferrer&quot;&gt;VSV&lt;/a&gt; which was a &lt;a href=&quot;https://en.wikipedia.org/wiki/Select_agent#Animal_Agents&quot; rel=&quot;nofollow noreferrer&quot;&gt;USDA select pathogen&lt;/a&gt; (not as big of a concern for humans).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;TLDR:  It would provide some protection, but I would be most worried about a false sense of security.  It would unlikely be up to rated &lt;a href=&quot;https://www.osha.gov/pls/oshaweb/owadisp.show_document?p_table=STANDARDS&amp;amp;p_id=9766&quot; rel=&quot;nofollow noreferrer&quot;&gt;standards&lt;/a&gt;, but it would likely be better than a t-shirt.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;First let's start with &lt;a href=&quot;https://en.wikipedia.org/wiki/Ebolavirus&quot; rel=&quot;nofollow noreferrer&quot;&gt;ebolaviruses&lt;/a&gt;.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Ebola, like HIV and many other viruses, doesn't do well &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/9988181&quot; rel=&quot;nofollow noreferrer&quot;&gt;outside a host&lt;/a&gt;.  This might be because the protein structures &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/24074577&quot; rel=&quot;nofollow noreferrer&quot;&gt;beneficial in the host&lt;/a&gt; are not the same as needed for stability in &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/22369502&quot; rel=&quot;nofollow noreferrer&quot;&gt;exposed air&lt;/a&gt; and &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/21858822&quot; rel=&quot;nofollow noreferrer&quot;&gt;room temperature&lt;/a&gt;.  A counter example of a very stable virus would be something like &lt;a href=&quot;https://en.wikipedia.org/wiki/Rhinovirus&quot; rel=&quot;nofollow noreferrer&quot;&gt;human rhino virus (HRV)&lt;/a&gt;.  If HRV was compared to be like a rock, ebola would be over cooked spaghetti.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Certainly the virus has to maintain some stability in the environment, otherwise it wouldn't succeed evolutionary.  As I'm sure you've heard on the news, ebola is spread by contact with &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/25059478&quot; rel=&quot;nofollow noreferrer&quot;&gt;contaminated fluid&lt;/a&gt;s.  I would like to point out a &lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMp1410741&quot; rel=&quot;nofollow noreferrer&quot;&gt;wonderful info-graphic&lt;/a&gt; that was made for public consumption, especially the image on viral life cycle:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8cxav.jpg&quot; alt=&quot;Infographic on ebolaviruses life cycle&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that you're not going splunking in bat inhabited caves in West Africa, it's safe to assume that what we are worried about is human to human transmission through infectious fluids.  Ebola actual isn't that stable &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/?term=SLA-1%200401%20and%20identification%20of%20influenza%20A%20H1N1%20virus&quot; rel=&quot;nofollow noreferrer&quot;&gt;in water&lt;/a&gt;, so just soaking a &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/12875924&quot; rel=&quot;nofollow noreferrer&quot;&gt;surface in water and a little oil&lt;/a&gt; might help you out (if you don't have bleach handy).  I want to be clear that I'm not recommending this, in reality you should just avoid contaminated objects.  I think that we have clearly established that what we're really concerned about is infectious bodily fluid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leads me to the &lt;a href=&quot;http://dx.doi.org/10.1016/S0140-6736(14)61343-X&quot; rel=&quot;nofollow noreferrer&quot;&gt;wonderful note&lt;/a&gt; by &lt;a href=&quot;http://www.hem.waw.pl/?idp=10&amp;amp;cmd=15&quot; rel=&quot;nofollow noreferrer&quot;&gt;Jose Martin-Moreno&lt;/a&gt; titled &quot;Is respiratory protection appropriate in the Ebola response?&quot;  I don't think I can express the problem better than he can, so hopefully I will be allowed a substantial quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This transmission [of ebola] occurs via close family contact or in&#xA;  health-care settings, particularly when placing orotracheal intubation&#xA;  or when caring for a patient who is vomiting or bleeding. Ebola is&#xA;  rarely transmitted via an airborne route. Although these routes of&#xA;  transmission are well known, most agencies, including governmental&#xA;  agencies responsible for repatriating western patients, apply&#xA;  infection-control measures appropriate for airborne diseases.&#xA;  Excessive precautions could offer reassurance to those responding to&#xA;  Ebola, yet complete respiratory protection is expensive,&#xA;  uncomfortable, and unaffordable for countries that are the most&#xA;  affected. Worse, such an approach suggests that the only defence is&#xA;  individual protective equipment, which is inaccessible to the general&#xA;  population. Moreover, the image of workers with spectacular protective&#xA;  clothing might contribute to the panic in some communities. If this&#xA;  leads people to flee affected areas it could increase the spread of&#xA;  infection.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;With that said, all your full face gas mask is going to help with is prevention of fluids from hitting your head.  You could probably take the actual filters out to breath more easily (I find breathing in them a giant pain).  And as @Chris pointed out, they are easily clogged which could necessitate the need to take off the whole mask (which might be doing some good) to prevent suffocation.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Moving to &lt;a href=&quot;https://en.wikipedia.org/wiki/Dangerous_goods&quot; rel=&quot;nofollow noreferrer&quot;&gt;hazmat&lt;/a&gt; suit.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;It's actually good news that you don't need the air containment of the suit, as that's the hardest element to maintain.  To state the obvious, the main purpose of the suit is to prevent your body from coming in contact with infectious fluids (in this case).  To do that you don't need to be in &lt;a href=&quot;https://en.wikipedia.org/wiki/Positive_pressure_personnel_suit&quot; rel=&quot;nofollow noreferrer&quot;&gt;positive pressure personnel suit (PPPE)&lt;/a&gt;, or follow &lt;a href=&quot;http://www.cdc.gov/biosafety/publications/bmbl5/BMBL5_sect_IV.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;BSL4 considerations&lt;/a&gt;.  The respiratory concerns from in an BSL4 environment come from other select agents, and the personal working in such a facility are going to be doing very different activities from what you should be doing as person trying to avoid an outbreak (they could be purposefully growing up purified high-titer virus stocks and running around with pointy things as an example).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here I'm going to run into citation problems because no one (that I could find) has tested the kind of scenario I'm about to discuss, so it should be seen as informed conjecture.  Assuming yous suit is actually an analog of a &lt;a href=&quot;http://www.dupont.com/products-and-services/personal-protective-equipment/chemical-protective-garments/brands/tychem.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tychem&lt;/a&gt; QC suit, it's probably not a rated OSHA unit (A-D), but that doesn't necessarily matter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On it's first use it would likely be sufficient to protect against incidental exposure.  Let's assume for the sake of argument that you didn't run into any Ebola when you used it as a costume, and don't the next time you put it on.  At this point decontamination (decon) isn't the concern, failure of the material is.  In other words, are you sure you don't have any holes, tears or cracks in the material?  I think this is going to be the real limiting factor in the life of the suit.  Using good old fashioned duct tape will be give you a few more uses, but the suits are just not designed to last through prolonged use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now let's assume the worst and that you get substantial blood splatter on you (while wearing your suit) from an ebola patient.  And not a little that could easily be wiped of with a spray bottle of 10% bleach and a paper towel (how most decon could be done).  Instead let's assume you're standing next to someone who suffers a traumatic injury on top of having &lt;a href=&quot;https://en.wikipedia.org/wiki/Ebola_virus_disease&quot; rel=&quot;nofollow noreferrer&quot;&gt;ebola virus disease (EVD)&lt;/a&gt;.  I'm imagining something like a point-blank shotgun wound or, given the probability of this scenario, a falling grand piano. In this case, you're going to want to decontaminate the suit before you take it off, which is the same thing professionals are going to do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're friends with your local fire department, and you live in an area with a large enough population to have a HAZMAT team, you can probably get them to at least give you a run through of how it's done in ideal conditions.  &lt;a href=&quot;http://www.youtube.com/watch?v=ZuYDqh3gsk4&quot; rel=&quot;nofollow noreferrer&quot;&gt;YouTube videos&lt;/a&gt; are also not hard to find, just search &lt;a href=&quot;http://jestc.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;JESTC&lt;/a&gt; and decontamination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Presumably you would have a hard time going through several rinse and wash steps, but you would want emulate this as much as possible.  With ebola, you would be fine to decontaminate with a 10% bleach solution (or if you use bargain/cheap bleach 15%).  The trick is that you would want to do it a few times, and with a friend (also hopefully in a suit).  Thus if you got two generic soap sprayers, filled one with 10% bleach, and the other with water, and then alternated spraying your partner with bleach and water, wiping down as you went, you should be able to decon the suit pretty well.  If possible you're going to want to collect all the run off an rinsate.  Again professionals tend to use actual kiddie pools for this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But just the act of using so much bleach on the suit is going to weaken the fabric, again leading to the principle problem of failure of the fabric. Thus I would be worried that such a suit would provide a false sense of security, leading one to go into dangerous infectious environments when one shouldn't.  Just avoiding and going away from contaminated individuals is going to be the best solution, regardless of a suit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I considered going into why I think it's highly unlikely that any of the ebolaviruses would evolve to be airborne, but I consider that outside the scope of the question.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2014-10-16T15:39:39.750" LastActivityDate="2014-10-16T15:39:39.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="21999" PostTypeId="1" AcceptedAnswerId="22007" CreationDate="2014-10-09T17:20:38.763" Score="1" ViewCount="230" Body="&lt;p&gt;I am curious what the first plants are thought to have been like, what they may have evolved from, and how much earlier (or later) than animals they are thought to have moved to land, if they even started in water like animal-life?&lt;/p&gt;&#xA;" OwnerUserId="9700" LastActivityDate="2014-10-12T20:00:07.787" Title="Evolution, What would the first plants have been like?" Tags="&lt;evolution&gt;&lt;botany&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="22000" PostTypeId="1" CreationDate="2014-10-09T17:26:03.740" Score="2" ViewCount="65" Body="&lt;p&gt;I was wondering my girlfriend and I used the same perfume for a while and we sprayed the same place. And after a day her skin still smells nice while mine smells normal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Will different types of perfume hold longer on different skin types? &lt;/p&gt;&#xA;" OwnerUserId="8116" LastEditorUserId="3340" LastEditDate="2014-12-06T05:26:18.860" LastActivityDate="2014-12-06T05:26:18.860" Title="Why does some skin hold perfume longer than others" Tags="&lt;skin&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22001" PostTypeId="2" ParentId="11230" CreationDate="2014-10-09T17:32:35.830" Score="0" Body="&lt;p&gt;I have not posted or read much on this forum before but thought I would throw in my two cents.  Perhaps a more accurate and comprehensive term is &quot;reproductive selection&quot;.  This would include &quot;sexual selection (eg qualities making an individual more attractive to the opposite sex) and &quot;survival selection&quot; - to the extent that survival allows one to produce more offspring.  (Dead organisms don't tend to reproduce).  Reproductive selection would correctly exclude fitness traits promoting post-reproductive survival that did not contribute to the reproductive success of progeny, eg a longer lifespan spent away from mates or offspring.  Reproductive selection would apply to a range of replicative mechanisms,  spanning sexual, asexual, mitotic and even possible early-stage RNA-strand replication.  It would also include both natural and artificial selection.  Finally, it has the advantage of being a more intuitive term that IMHO gets more at the core principle driving this aspect of evolution (as opposed to genetic drift, etc).  Not sure if this term is in common usage.  As a clinical physician I am not very familiar with the literature on evolution.&lt;/p&gt;&#xA;" OwnerUserId="9701" LastActivityDate="2014-10-09T17:32:35.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22002" PostTypeId="1" CreationDate="2014-10-09T18:38:12.080" Score="3" ViewCount="7066" Body="&lt;p&gt;I have heard that this is an effective replacement for patients who have a dysfunctional larynx, partly due to cancer.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am curious to know the inner working of this device and why such a robotic voice comes out?&lt;br&gt;&#xA;What is the basic principle of this device. Does it simply captures vibrations and converts it to sound? Just like how a mic does?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="9702" LastEditorUserId="3340" LastEditDate="2014-10-09T19:02:33.553" LastActivityDate="2014-10-09T19:37:12.327" Title="How does electrolarynx work?" Tags="&lt;human-biology&gt;&lt;homework&gt;&lt;cancer&gt;&lt;biomedical-technology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22003" PostTypeId="1" AcceptedAnswerId="22010" CreationDate="2014-10-09T19:00:48.733" Score="9" ViewCount="279" Body="&lt;p&gt;Can anyone identify this caterpillar we found on a cauliflower? This was the only photo we could get of it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Location : Ceres, Fife, Scotland&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pUdBB.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9703" LastEditorUserId="3624" LastEditDate="2016-04-02T06:43:51.093" LastActivityDate="2016-04-02T06:43:51.093" Title="Can anyone identify this caterpillar?" Tags="&lt;species-identification&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="22004" PostTypeId="2" ParentId="22002" CreationDate="2014-10-09T19:37:12.327" Score="1" Body="&lt;p&gt;Your vocal chords vibrate to produce a tone, but your mouth shapes that tone into the sounds that make up voice. If your vocal chords fail or are removed, the electrolarynx can be used to vibrate the throat for you, but your mouth still needs to shape that sound into words. Because the electrolarynx produces a mechanical buzzing vibration, you get mechanical buzzing words. This is similar to how the talkbox works with electric guitars, the guitar sound is piped through a tube into the musicians mouth, they have to shape that sound into words with their mouth. Go listen to Peter Frampton for a good example.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-10-09T19:37:12.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22005" PostTypeId="1" AcceptedAnswerId="22018" CreationDate="2014-10-09T21:04:06.140" Score="2" ViewCount="312" Body="&lt;p&gt;I've stumbled upon the article &quot;Telmisartan Treatment of Refractory Proteinuria in a Dog.&quot;* What is refractory proteinuria?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&#xA;*Bugbee AC1, Coleman AE, Wang A, Woolcock AD, Brown SA. J Vet Intern Med. 2014 Sep 30. doi: 10.1111/jvim.12471. [Epub ahead of print]&#xA;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="6682" LastEditorUserId="9268" LastEditDate="2014-10-10T10:34:06.623" LastActivityDate="2014-10-10T10:34:06.623" Title="What is refractory proteinuria?" Tags="&lt;terminology&gt;&lt;kidney&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22006" PostTypeId="1" AcceptedAnswerId="22019" CreationDate="2014-10-09T21:16:47.910" Score="0" ViewCount="19" Body="&lt;p&gt;Searching on &lt;a href=&quot;http://www.ncbi.nlm.nih.gov&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov&lt;/a&gt; I could only find the article titled as &quot;Telmisartan Treatment of Refractory Proteinuria in a Dog&quot;.&lt;/p&gt;&#xA;" OwnerUserId="6682" LastEditorUserId="9268" LastEditDate="2014-10-10T11:01:43.533" LastActivityDate="2014-10-10T12:35:41.883" Title="What studies are there showing the effectiveness of any substance on canine hypertension?" Tags="&lt;pharmacology&gt;&lt;blood-pressure&gt;&lt;dogs&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22007" PostTypeId="2" ParentId="21999" CreationDate="2014-10-09T22:17:35.073" Score="4" Body="&lt;p&gt;You can have a look to the most basal branches and you may get a pretty good idea of what those early plants looked like. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What we call plants is what we call &lt;em&gt;plantae&lt;/em&gt; or &lt;em&gt;Archaeplastida&lt;/em&gt; in Latin. This clade contains the red algae and the green algae. Within the green algae are the land plants. In the land plants are the embryophyta which contain all what you think of when talking about plants. Below are a bunch of pictures so that you can get an idea of what the basal branches look like.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(Basal Plantae) Red algae&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dQO7Y.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/YRFcr.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(Basal Green Algae) Green Algae&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MJN9v.gif&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/QkSGD.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(Basal embryophyta) Green Algae &gt; Embryophyta &gt; Hornworts&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QxKEy.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(Basal embryophyta) Green Algae &gt; Embryophyta &gt; Mosses&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ziHku.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can explore the tree of life by yourself by going on &lt;a href=&quot;http://tolweb.org/tree/&quot; rel=&quot;nofollow noreferrer&quot;&gt;tolweb.org&lt;/a&gt;. You can try to find the apple tree, the ladybug of the human by clicking on the links. It is fun and it is good to learn a bit how the tree of life looks like.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-10-12T20:00:07.787" LastActivityDate="2014-10-12T20:00:07.787" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="22008" PostTypeId="1" CreationDate="2014-10-09T22:32:02.400" Score="0" ViewCount="121" Body="&lt;p&gt;What is the simplest biological organism from which a DNA sample has been or could be obtained?  Could the resulting DNA be processed and examined in such a way that the resulting information would give biologists a rudimentary understanding of life's minimal requirements?  &lt;/p&gt;&#xA;" OwnerUserId="9704" LastEditorUserId="12909" LastEditDate="2015-04-20T00:00:29.683" LastActivityDate="2015-04-20T00:00:29.683" Title="Simplest Biological Organism?" Tags="&lt;evolution&gt;&lt;dna&gt;&lt;dna-sequencing&gt;&lt;genomes&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ClosedDate="2014-10-10T14:14:27.010" ContentLicense="CC BY-SA 3.0" />
  <row Id="22009" PostTypeId="2" ParentId="22008" CreationDate="2014-10-09T22:40:14.557" Score="1" Body="&lt;p&gt;Could not fit in a comment...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/1382/which-organism-has-the-smallest-genome-length&quot;&gt;This post&lt;/a&gt; (and the excellent answer from Richard Smith-Unna) lists the species that have the smallest genome that we are aware of in different clades.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes we can/could sequence these tiny genomes and try to understand what each sequence does. I think that to understand the minimum requirements for life you will mostly be interested in theoretical cytology and synthetic biology than in sequencing simple genomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the basic requirement really depends on how you define life. Is a virus alive although it has no metabolism? Would a self-replicating RNA be a living thing? Because we were able to artificially synthesize self-replicating RNA. While the subject is interesting, the main issue is a purely philosophical one: How do you define life?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-10-09T22:40:14.557" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="22010" PostTypeId="2" ParentId="22003" CreationDate="2014-10-09T22:45:45.020" Score="3" Body="&lt;p&gt;It might be an &lt;a href=&quot;http://urbanfarmsista.com/imported-cabbageworm/&quot; rel=&quot;nofollow noreferrer&quot;&gt;imported cabbageworm&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bJ0bH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or a &lt;a href=&quot;http://www.ukbutterflies.co.uk/species.php?species=napi#Larva&quot; rel=&quot;nofollow noreferrer&quot;&gt;green-veined white&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WbaxJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both exist where you are, and the former is more common than the latter. I can't tell them apart, but consulting the pages might help.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-10-09T22:45:45.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22011" PostTypeId="1" AcceptedAnswerId="22012" CreationDate="2014-10-10T00:00:18.377" Score="4" ViewCount="4715" Body="&lt;p&gt;If every neuron has only one Axon but can can have thousands of (or let's say, even just ten) incoming Axon connections via its dendrites, where are the extra connections coming from?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/W74XG.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to me that since neurons dont act as initiators (that is, decide to initiate signals) but rather act more as repeaters (that is, sending incoming signals forward to the neuron that their axon is connect to), then for every neuron, there must be at least one neuron whose axon is connected to it, and at least one neuron that its axon connects to (because without those two things, the neuron does basically nothing, right?), but since each neuron can only have one axon, I'm confused about where all of these extra axons are coming from. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on that understanding: 1 billion neurons means exactly 1 billion axons and one billion required inputs (axon -&gt; dendrite connections), eliminating the possibility of any one neuron having more than one dendrite connection, since there can only be one billion axons to connect to those dendrites (and each neuron would require at least one input to function, right?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But regardless, I've been hearing people talk about neurons having thousands of connections. &lt;em&gt;And based on my understood model, the brain would have to be just one long linear chain of neurons, which makes no sense at all.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So clearly I've got something wrong in my understanding of neural structure. What is it?&lt;/p&gt;&#xA;" OwnerUserId="19073" LastEditorUserId="19073" LastEditDate="2014-10-10T03:09:27.557" LastActivityDate="2018-04-10T23:52:54.127" Title="Neurons with thousands of connections: where are the extra connections coming from?" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="22012" PostTypeId="2" ParentId="22011" CreationDate="2014-10-10T04:07:56.073" Score="7" Body="&lt;p&gt;As you say, a neuron can have thousands of inputs via its thousands of dendrites.  Each of those dendrites can have a synaptic connection to the (axonic) output of a different neuron.  So the neuron can take inputs from thousands of different neurons, not just from one other neuron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the other end of the neuron, the output of the axon can form synaptic connections with many distinct neurons; that's what the branching at the end of the axon is for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, it's misleading to say neurons don't &quot;decide to initiate signals&quot;.  Neurons in the brain do &quot;decide&quot; when to initiate an output.  The decision is a complicated function of the arrival of pulses at dendrites from different neurons.  Only some combinations of incoming pulses will cause the neuron to fire a pulse on its output axon while other combinations will not.  The specific combinations can change over time; this forms the basis of learning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So a brain neuron is in the middle of a very complicated network of synaptic connections from many neurons to many other neurons.&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2014-10-10T04:07:56.073" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="22014" PostTypeId="2" ParentId="20632" CreationDate="2014-10-10T06:54:48.790" Score="0" Body="&lt;p&gt;I am adding a supplement/concluding remarks to the existing answers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some points to be considered:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Electron transport chain can work without oxygen and can use other chemical species as electron acceptors.&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;E.coli&lt;/em&gt; is capable of aerobic respiration, anaerobic (anoxic) respiration and fermentation (substrate level phosphorylation).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How does E. coli uptake oxygen?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Short answer as already mentioned by canadianer: Passive diffusion&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Can they shut down the oxygen uptake if required?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Oxygen is the primary electron acceptor and &lt;em&gt;E.coli&lt;/em&gt; would prefer oxygen to other electron acceptors. Only in the absence of oxygen is the FNR regulon switched on. Other bacteria can show negative aerotaxis i.e. running away from oxygen (they obviously have to be motile) &lt;sup&gt;[&lt;a href=&quot;http://www-04.all-portland.net/bsr/017/0335/0170335.pdf&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;]&lt;/sup&gt;. This paper also comments that positive and negative aerotaxis happens via a common mechanism- sensitivity of proton motive force to O₂. However, ROS has no role to play in it. It is most likely that at high oxygen levels &lt;em&gt;E.coli&lt;/em&gt; will try to jack up anti-oxidant response. To conclude- they cannot regulate oxygen &lt;strong&gt;uptake&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aerotolerant anaerobes: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11207604&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Clostridium perfringens&lt;/em&gt;&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16549683&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Clostridium intestinale&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-10-10T06:54:48.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22015" PostTypeId="2" ParentId="21137" CreationDate="2014-10-10T07:21:02.783" Score="3" Body="&lt;p&gt;When you say multiple simultaneous action potentials I assume that the stimuli for all of them are temporally overlapping. In such case a neuron can integrate the different stimuli and launch an action potential. Of the multiple stimuli some can be excitatory while others can be inhibitory. The net response would be an integration of all the signals &lt;sup&gt;[&lt;a href=&quot;http://www.els.net/WileyCDA/ElsArticle/refId-a0000208.html&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;]&lt;/sup&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if there is a gap in the stimuli then the cell may not react as it would be in its refractory period (which results until the ions levels are back to their original state and the membrane potential is restored). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There can be long delays, which depends on various factors such as ion deficiency, ATP deficiency (ATP is needed by Na&lt;sup&gt;+&lt;/sup&gt;/K&lt;sup&gt;+&lt;/sup&gt; ATPase) or neuropathological conditions. In case of nervous signaling over many neurons then synapses can suffer from &lt;a href=&quot;http://en.wikipedia.org/wiki/Synaptic_fatigue&quot; rel=&quot;nofollow&quot;&gt;synaptic fatigue&lt;/a&gt;, which results because of depletion of neurotransmitters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maximum AP propagation speed/Nerve conduction velocity = ~120m/s (Can't find original source. From &lt;a href=&quot;http://en.wikipedia.org/wiki/Nerve_conduction_velocity&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Longest myelinated axon (sciatic nerve in humans) = ~ 1m&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Time required to reach synapse = ~8ms&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Time required for repolarization = ~5µs&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So multiple action potentials (~160), are possible (lets call it situation-X). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The squid giant axon is ~500µm. I believe it is also non-myelinated. In this case if NCV is less than 100m/s then situation-X can happen. NCV can go as low as 0.5m/s (again the reference is wikipedia as I cannot find the original source).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having said that, situation-X can also cause synaptic fatigue if the firing rate (AP frequency) goes beyond a certain value. This value would depend on how much neurotransmitter is released per AP, how much is in storage and the uptake rate. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-17T11:30:33.177" LastActivityDate="2014-12-17T11:30:33.177" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="22016" PostTypeId="2" ParentId="22005" CreationDate="2014-10-10T07:30:45.900" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Proteinuria&quot; rel=&quot;nofollow&quot;&gt;Proteinuria&lt;/a&gt; is the presence of proteins in urine. &lt;a href=&quot;http://www.merriam-webster.com/dictionary/refractory&quot; rel=&quot;nofollow&quot;&gt;Refractory&lt;/a&gt; means &quot;persistent&quot; or &quot;stubborn&quot;, but in medical terms it means &lt;a href=&quot;http://medical-dictionary.thefreedictionary.com/refractory&quot; rel=&quot;nofollow&quot;&gt;resistant to treatment or cure&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastActivityDate="2014-10-10T07:30:45.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22017" PostTypeId="2" ParentId="20709" CreationDate="2014-10-10T10:26:15.803" Score="4" Body="&lt;p&gt;Grey hair is one of many age related traits. Other traits showing a positive correlation with age include Parkinson's, cancer, and Alzheimer's. There are two key theories as to why age-related disease &amp;amp; decline occurs. But the key message is just because something evolves, it doesn't mean it's advantageous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all is mutation accumulation (MA) theory. This theory basically suggests that as we age there is less likelihood that selection can remove the alleles that cause genetically determined aging. If we consider something like cancer, which is clearly deleterious it becomes clearer, though grey hair may be deleterious (reduces fitness) it is at least less obvious. If a cancer has early onset, affects people aged 10, then it is highly unlikely to spread through a population because those carrying the allele are unlikely to reproduce. If a cancer has late onset, causing cancer at 60 years old, then there is a much lesser chance it will affect reproductive success - most 60 year olds don't have more children in the future. In the case of MA the effect of selection is weak if a trait reduces survival post-reproduction. The same could be true of grey hair, even if it is costly it's arrival late in life is not that surprising.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other theory is antagonistic pleiotropy (AP) which suggests that genes which improve fitness might reduce survival. For example, the genes that cause cancer at age 60 might also make you better at attracting mates, fertilising, and raising offspring. In this case it would be beneficial to carry the cancer gene (from an evolutionary perspective). I think there is some evidence (but can't find it right now) that grey hair is associated with higher fitness, in that case it could be that grey hair has evolved directly because of sexual selection (people might prefer silver haired partners) or because of AP - grey haired people are better at other fitness related things because of pleiotropy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to answer your question: direct selection is not necessarily the reason that grey hair has evolved, it could be because of mutation accumulation or pleiotropic gains associated with the genes affecting grey hair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read more about &lt;a href=&quot;https://biology.stackexchange.com/questions/17077/why-does-evolution-not-make-our-life-longer/17091#17091&quot;&gt;these theories of aging in this answer and for references.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-10-10T10:26:15.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22018" PostTypeId="2" ParentId="22005" CreationDate="2014-10-10T10:30:16.170" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25270397&quot; rel=&quot;nofollow&quot;&gt;The article itself&lt;/a&gt;&lt;sup&gt;1&lt;/sup&gt;  defines what the authors mean by both &lt;em&gt;proteinuria&lt;/em&gt; and &lt;em&gt;refractory&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...progressive proteinuria, with [urine protein-to-creatinine] values ranging from 0.6 at initial evaluation to 5.16 at highest (reference interval, &amp;lt;0.2), despite medical intervention with increasing doses of benazepril HCl (0.5-1.02 mg/kg PO q12h) and control of systemic hypertension.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background note&lt;/strong&gt;&lt;br&gt;&#xA;Proteinuria is normally quantified as a ratio of urinary protein to urinary creatinine to account for the wide fluctuations in urine concentration according to hydration status. Normally, in humans and (apparently) in dogs, there is little to no detectable protein in the urine. In certain disease conditions (most commonly: hypertension and diabetes), proteinuria tends to increase with poorly controlled blood pressure/glycemia. Proteinuria&lt;sup&gt;2&lt;/sup&gt; may represent &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15210602&quot; rel=&quot;nofollow&quot;&gt;a novel risk factor for coronary disease&lt;/a&gt; in humans. Angiotensin converting enzyme inhibitors (ACEI, e.g. benazepril) and angiotensin receptor blockers (ARB, e.g. telmisartan) are &lt;a href=&quot;http://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/12661873&quot; rel=&quot;nofollow&quot;&gt;commonly used to mitigate proteinuria&lt;/a&gt; (citing a dog article this time - this benefit is widely accepted in humans).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The point of this article&lt;/strong&gt; seems to be that an ARB was superior to an ACEI to decrease proteinuria in this dog.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&#xA;1. Sorry, I was able to access it through a library but free text is not available without such access to my knowledge. If it is, OP please post it!&#xA;&lt;/sup&gt;&lt;br&gt;&#xA;&lt;sup&gt;&#xA;2. Also sometimes measured (as in the cited article) as albuminuria - ratio of albumin to creatinine - rather than total protein. There are subtle differences is these approaches, but they are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24614247&quot; rel=&quot;nofollow&quot;&gt;highly correlated&lt;/a&gt;.&#xA;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastActivityDate="2014-10-10T10:30:16.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22019" PostTypeId="2" ParentId="22006" CreationDate="2014-10-10T10:59:05.407" Score="1" Body="&lt;p&gt;Check out &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=17552466&quot; rel=&quot;nofollow&quot;&gt;this consensus statement&lt;/a&gt; (PMID 17552466):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;J Vet Intern Med. 2007 May-Jun;21(3):542-58.&lt;br&gt;&#xA;&lt;strong&gt;Guidelines for the identification, evaluation, and management of systemic hypertension in dogs and cats.&lt;/strong&gt;&lt;br&gt;&#xA;Brown S1, Atkins C, Bagley R, Carr A, Cowgill L, Davidson M, Egner B, Elliott J, Henik R, Labato M, Littman M, Polzin D, Ross L, Snyder P, Stepien R; American College of Veterinary Internal Medicine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It includes 185 references, at least a dozen of which are related to your question. Also, if you look to the right of the article on PubMed, there are links to other relevant articles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;FYI: I located this article using search string  &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;(canine hypertension) NOT pulmonary Filters: Review&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;There are quite a few others. (Canine pulmonary hypertension is apparently a popular research topic, so I found it useful to exclude those.)&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-10-10T12:35:41.883" LastActivityDate="2014-10-10T12:35:41.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22020" PostTypeId="1" AcceptedAnswerId="23579" CreationDate="2014-10-10T12:50:48.113" Score="4" ViewCount="834" Body="&lt;p&gt;When stimulating a group of neurons with an electrode, let's say we put it in a region that contains axons, what is the mechanism by which the axons are stimulated? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been told electrodes (usually silver or gold) must be coated with ions, usually chloride, to allow the passing of the stimulus. So I'm not sure if the stimulus is based on changing the extracellular concentration of ions by injecting chloride, therefore changing the membrane potential with a depolarization (elevating the potential, possibly generating an action potential). Let's call this idea A.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other idea, B, that seems possible would be having the ions in the extracellular fluid conduct the current to the nearby axons, thus changing the potential but not the intra or extracellular concentration of ions. &lt;/p&gt;&#xA;" OwnerUserId="9707" LastEditorUserId="9707" LastEditDate="2014-10-10T13:32:15.750" LastActivityDate="2014-10-30T10:31:00.820" Title="Mechanisms of extracellular stimulation of neurons" Tags="&lt;neuroscience&gt;&lt;electrophysiology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="22021" PostTypeId="1" CreationDate="2014-10-10T12:52:10.263" Score="1" ViewCount="65" Body="&lt;p&gt;There was a suspected case of Ebola in France, which was later dismissed, since the suspect lastly came into contact with a potentially contaminated person more than 21 days before, which is the maximum of Ebola's incubation period.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, more generally speaking, how does one determine the period of incubation ? How do we know the day a person was contaminated ?&lt;/p&gt;&#xA;" OwnerUserId="6624" LastActivityDate="2014-10-10T12:52:10.263" Title="How do we determine a disease's incubation period?" Tags="&lt;pathology&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="22022" PostTypeId="1" CreationDate="2014-10-10T12:52:14.677" Score="1" ViewCount="704" Body="&lt;p&gt;I have a follow-up question about an in-lecture question (this is not a homework question). As you can see I have already answered the question and the question is closed to further submissions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/A7Yv9.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, this is my reasoning. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The male has the genotype Gg and BB. Fur color is incompletely dominant so to have black fur this implies the male has the genotype BB not Bb (which would likely be gray). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The female has genotype Gg and Bb because as the question states, the female is doubly heterozygotic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two have a FEMALE offspring - this is critical. This means that the male &quot;donates&quot; a copy of his X chromosome to the offspring. Now if the question had asked about a male offspring, then that would mean the male had donated a copy of his Y chromosome instead, and the male would have no &quot;say&quot; in the male progeny's eye color. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the probability of green eyes between a cross of Gg with Gg is 3/4. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The probability of black fur between a cross of BB and Bb is 1/2 given that there is incomplete dominance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the probability of both events occurring simultaneously is 3/4 * 1/2 = 3/8 = 0.375. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this correct? Or should I account for the &quot;female&quot; offspring part and half the answer? &lt;/p&gt;&#xA;" OwnerUserId="6759" LastEditorUserId="6759" LastEditDate="2014-10-10T13:00:06.407" LastActivityDate="2014-10-10T19:37:53.873" Title="Incomplete Dominance and Probability" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22023" PostTypeId="2" ParentId="22022" CreationDate="2014-10-10T15:13:53.640" Score="2" Body="&lt;p&gt;The male has a phenotype XGY BB, and the female, XGXg Bb. Thus the probability is 0.25.&lt;/p&gt;&#xA;" OwnerUserId="4821" LastActivityDate="2014-10-10T15:13:53.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22024" PostTypeId="2" ParentId="21997" CreationDate="2014-10-10T15:28:01.693" Score="1" Body="&lt;p&gt;I can suggest three books, none of them cover all those aspects, though:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) The Foundations of Ethology, Konrad Lorenz. The best introduction I know for the field of ethology. Lorenz is called by some &quot;the father of ethology&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Sociobiology: The New Synthesis, Edward Wilson. The deepest study of animal societies I know of.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Evolutionary Ecology, Eric Pianka. If my memory is right, it says something about the Navigation and Biological Rythms part.&lt;/p&gt;&#xA;" OwnerUserId="4821" LastActivityDate="2014-10-10T15:28:01.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22025" PostTypeId="2" ParentId="20511" CreationDate="2014-10-10T15:36:54.753" Score="3" Body="&lt;p&gt;If rates of meiotic recombination DIDN'T vary across species - THIS would require an explanation! After all, evolution creates diversity, not homogeneity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can only wonder that more recombination would allow for a faster diversification. The more DNA you shuffle, the more distinct each individual offspring may be (though I'm not 100% sure). The recombination rate has an energetic price, so not all animals recombine so much their DNA like later mammals. I.e. they needed a selective pressure to justify paying that price.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps it was useful for a group rapidly occupying the &quot;vague niches&quot; left by dinosaurs? This make sense, since the primary mammalian irradiation occured in the beginning of the Cenozoic era, right after the Cretaceous mass extinction that killed most big animals, including the biggest dinosaurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately I have no references on the subject, it is just what makes sense to me, given evolutionary logic.&lt;/p&gt;&#xA;" OwnerUserId="4821" LastEditorUserId="4821" LastEditDate="2014-10-10T15:49:29.153" LastActivityDate="2014-10-10T15:49:29.153" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="22026" PostTypeId="1" CreationDate="2014-10-10T18:31:03.457" Score="11" ViewCount="2636" Body="&lt;p&gt;My lab stores biological material (tissue, cells, plasma, serum) in a -130 C, liquid nitrogen freezer. The cryotubes that we use to store a samples are labelled by hand which frequently creates legibility problems. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its my understanding we can't print out stickers to use as labels because they will degrade in the cold. The solution of putting barcodes on the tubes has been suggested but its undesirable because in addition to the cost and logistic complications; we would have to choose between thawing and refreezing all of our samples to transfer them to new tubes OR live with the nightmare of having both labeling systems in use at the same time; one which humans can read and one which humans cannot. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ideal situation would be a small, portable machine that can physically label the tubes for us. I'm envisioning:&#xA; - an adjustable clamp to hold the tube in place; ideally with sensors that would infer the shape, size, and position of the area that can be labelled.&#xA; - a very-fine tipped pen attached to a motor that would mimic a printer's line-by-line printing action; this would have to take into account the shape and size of the area that can be labelled&#xA;- rollers in the clamp to adjust the available space for labeling&#xA; - a screen/keyboard interface that would display how the label will appear&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anything like this exist? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you have any other suggestions about how to deal with the problem of legible hand-writing on cryotubes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please advise if there is a more-appropriate SE site to post this question&lt;/p&gt;&#xA;" OwnerUserId="8161" LastActivityDate="2020-01-08T00:32:22.517" Title="How can I label cryotubes in a way that eliminates the problem of legible hand-writing?" Tags="&lt;lab-techniques&gt;&lt;protocol&gt;&lt;biomedical-technology&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="22027" PostTypeId="1" AcceptedAnswerId="23300" CreationDate="2014-10-10T19:23:21.627" Score="5" ViewCount="806" Body="&lt;p&gt;I am trying to computationally simulate a population based on the Wright-Fisher model I would like to get to the classic result of the neutral theory of molecular evolution that the rate of neutral substitution equals the rate of mutation. However, the results of my simulations never show that. I will briefly explain my simulation process and how I calculate the mutation and substitution rates. Please let me know if there is something wrong in my procedure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a non-structured haploid population that grows in discrete time steps. I start with a population of N individuals in an environment with carrying capacity K. I use a K-allele model of mutation. At each generation, every individual will reproduce n offsprings and it will immediately die afterwards. A u fraction of offsprings will be chosen randomly to have a single mutation in each generation (u is mutation rate per gene per generation). At each generation, I record how many mutations have occurred and how many mutations have reached fixation in the population (reached frequency of more than 99% of individuals). Thus, mutation rate and substitution rate per generation is calculated as the number of mutations and number of substitutions divided by population size, respectively. With this set up, even with hundreds of repetitions, the rate of fixation will never be as big as mutation rate u.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where do you think is the problem?&#xA;I have struggled with this a lot and I appreciate any help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&#xA;My code is written in Python. This my pseudo-code:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Parameters: population size, genome_size, mutation_rate, generation_number, fixation_threshold.&#xA;&#xA;'''&#xA;Population_size: Here it is 1500&#xA;Genome_size: the number of loci that can be mutated. Each locus can be mutated to any of ACTG. Here 10^4&#xA;Mutation_rate: number of mutations per genome per generation. Here 0.05&#xA;Generation_number: The number of generations that the population grows. Here 1000&#xA;Fixation_threshold: The fraction of individuals having an allele in the population so that the allele is considered fixed. Here 0.99&#xA;'''&#xA;&#xA;The initial population is created. All individuals are the same without any mutations&#xA;A vector to hold the number of mutations and a vector to hold the number of fixations is created&#xA;&#xA;For each generation:&#xA;    I determine how many individuals in each generation should be mutated. Here 8.&#xA;    I randomly choose  (uniform with replacement) the individuals to be mutated &#xA;    For each individual in the population:&#xA;        It will produce an offspring. The offspring inherits the genome of its parent, i.e. the mutations of the parent.&#xA;        If the individual is among the ones to be mutated, the offspring will receive a mutation that is randomly picked.&#xA;            The mutation can be a back mutation&#xA;        The individual will die&#xA;    I record the number of mutations that occurred (it will always be 8 in this case)&#xA;    I record any mutation that has a frequency in the population of more than 0.99 of individuals. This is the number of fixations&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I run this code for at least 100 times. I expect that the average number of fixations to be equal to the average number of mutations in each generation, or they converge over generations. Because the neutral theory of Evolution by Kimura predicts that for neutral sites in the genome, substitution rate is equal to the mutation rate.&lt;/p&gt;&#xA;" OwnerUserId="9711" LastEditorUserId="9711" LastEditDate="2014-10-13T10:45:12.480" LastActivityDate="2014-10-19T15:37:38.660" Title="Simulating substitution rate of neutral mutations" Tags="&lt;evolution&gt;&lt;population-genetics&gt;" AnswerCount="2" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="22028" PostTypeId="2" ParentId="21996" CreationDate="2014-10-10T19:30:51.927" Score="1" Body="&lt;p&gt;Some physical methods of sterilisation are in hospitals&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Steam autoclaving&lt;/li&gt;&#xA;&lt;li&gt;Dry heat – thermostat&lt;/li&gt;&#xA;&lt;li&gt;White light / UV light sterilization &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;where continuous UV light has poor penetration. &#xA;UV radiation heat is absorbed by proteins and nucleic acid. &#xA;All micro-organisms contain tehm. &#xA;They inactivate the DNA. &#xA;There will be electronic and photochemical reactions by&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;photolysis&lt;/li&gt;&#xA;&lt;li&gt;loss of colony-forming ability&lt;/li&gt;&#xA;&lt;li&gt;enzyme inactivation&lt;/li&gt;&#xA;&lt;li&gt;destruction of nucleic acid. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If I shone a UVC lamp (11W) on something (say for example a plastic&#xA;  phone case) for an hour, would that kill off a noticeable amount of&#xA;  bacteria?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Direct answer: &lt;strong&gt;Not all bacteria, but some&lt;/strong&gt;. &#xA;UV light has poor penetration so it will not expose all bacteria. &#xA;Most prevalent bacteria there&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;streptococci, &lt;/li&gt;&#xA;&lt;li&gt;staphylococci and &lt;/li&gt;&#xA;&lt;li&gt;some others. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I estimate that the majority of the bacteria will remain because the light cannot reach each corner of the object. &#xA;In clinics, many hours and high temperatures are used to kill bacteria. &#xA;UV light is not efficient there. &#xA;I think the problem is that you cannot reach each corner of the object. &#xA;The high temperature and disinfectants can then again reach the clinical instruments throughly. &#xA;Manual work is however still needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can then take examples of bacteria. &#xA;Search their corresponding temperature ranges. &#xA;The survival can also be dependent on the nature of the light of the bulb. &#xA;Each bacteria has an individual structure. &#xA;We can manipulate the environment to make bacteria more vulnerable to the heating i.e. to change the structure of the bacteria. &#xA;We can increase the duration of the heat exposure to make kill of the bacteria more effective. &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-10-10T19:46:58.940" LastActivityDate="2014-10-10T19:46:58.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22029" PostTypeId="2" ParentId="22022" CreationDate="2014-10-10T19:37:53.873" Score="2" Body="&lt;p&gt;Eye color is sex-linked. So a green-eyed male has genotype G- (only one X chromosome) for eye color and BB for fur color. The female has genotype GgBb. For the offspring to be female, 1/2 probability, to have green eyes 1/1 probability (G is dominant and it will receive the G from the father), and for gray fur 1/2 (1/2 chance it will receive b from the mother). So 1/2 * 1/1 * 1/2 = 1/4 &lt;/p&gt;&#xA;" OwnerUserId="9711" LastActivityDate="2014-10-10T19:37:53.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22030" PostTypeId="1" AcceptedAnswerId="22035" CreationDate="2014-10-10T20:14:01.220" Score="12" ViewCount="5403" Body="&lt;p&gt;These critters were flying around the neighborhood on an autumn evening in Seattle, WA, USA. Their most notable feature was the small amount fuzz on them. They were quite slow in their flight compared to similar-sized fruit flies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any ideas?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are two close-ups:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0eBBr.jpg&quot; alt=&quot;closeup&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/OIRqK.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One one for size comparison:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OQqNJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9713" LastActivityDate="2020-10-05T20:07:05.277" Title="Identification of small fuzzy flying insect (pic)" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="22031" PostTypeId="2" ParentId="22027" CreationDate="2014-10-10T20:36:42.090" Score="2" Body="&lt;p&gt;&lt;strong&gt;I don't fully understand how your model works&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't fully understand how you model your population. Is it a standard $oop$ (object-oriented programming) where you simulate each individual? Or is it a simulation where you already use some mathematical model? You could eventually copy-paste your code. it is probably not very long, right? What language did you use? Do you have only one locus? Do you simulate several positions within these locus? Do you allow for back mutations?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that you allow the population size to change over time and I don't quite understand how your parameter $K$ does limit the growth rate though. You should write down some equations about that. In any case, change in population size will modify the probability of mutation fixation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Here is probably some important modifications to do on your code&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is a bit hard to comment on your simulations without actually seeing some equations or seeing the code but I really think that you'll need two important modifications in your code.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;fix population size $N$. &lt;/li&gt;&#xA;&lt;li&gt;To simulate reproduction, randomly choose (uniform distribution) individuals (with replacement) from the population. The chosen individuals form the new generation. For example:&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In &lt;strong&gt;R&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;new_pop = sample(old_pop, N, replace=T)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;or directly&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;pop = sample(pop, N, replace=T)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;In &lt;strong&gt;Python&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;from random import randrange&#xA;new_pop = []&#xA;for i in xrange(N):&#xA;    new_pop.append(old_pop[randrange(N)])&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;When you get your results, don't forget that you're talking about a stochastic process and you may want to run enough simulation or enough independent loci in order to be able to compare with the predictions from mathematical models.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-10-11T05:01:16.767" LastActivityDate="2014-10-11T05:01:16.767" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="22033" PostTypeId="2" ParentId="22026" CreationDate="2014-10-10T20:59:35.080" Score="4" Body="&lt;p&gt;What I find works is to scotch tape the labels to the tubes, they hold up fine in our -70C freezer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I did was go into excel 2010, go to View tab, click on Page Layout on the left side, not normal view! Then, go to home tab, select all the cells on the page. Go to the right side of the home tab, hit Format, then Row Height. This lets you set height in real units, I typically enter &quot;10mm&quot;. Do the same for Column Width, I like 20mm. Now reselect the page of cells because changing the cell size will push some off the page. Right click the cells and format them to center the text horizontally and vertically. Now you can type your label text into the cells. I suggest font size 8 or smaller so you can fit it all in the cell. To make cutting the labels easier, put borders on all sides of all cells. Just print it out, cut them apart and tape them on your tubes. Sorry microsoft makes it so hard to set the size of a cell in real units.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just to see if I could, I tried to create a QR code and make it small enough to fit on the 10x20mm label. But my phone can't read it once I print it out at that size. With a better camera and a good printer you could probably make it work. I don't know enough about alternative bar code systems to try anything else.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2014-10-10T21:25:44.277" LastActivityDate="2014-10-10T21:25:44.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22035" PostTypeId="2" ParentId="22030" CreationDate="2014-10-10T22:01:42.700" Score="8" Body="&lt;p&gt;To me, it looks like a male &lt;a href=&quot;https://en.wikipedia.org/wiki/Aphid&quot; rel=&quot;noreferrer&quot;&gt;Aphid&lt;/a&gt; (males are winged, and have four wings) from the genus Eriosoma (wooly aphids). The white feathery substance is a wax secretion.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a look at &lt;a href=&quot;http://bugguide.net/node/view/7465/bgimage&quot; rel=&quot;noreferrer&quot;&gt;Bugguide: Eriosoma&lt;/a&gt;, &lt;a href=&quot;http://influentialpoints.com/Gallery/Eriosoma_aphids.htm&quot; rel=&quot;noreferrer&quot;&gt;InfluencialPoints: Eriosoma&lt;/a&gt; and &lt;a href=&quot;http://www.extension.umn.edu/garden/insects/find/woolly-aphids-on-trees-and-shrubs/&quot; rel=&quot;noreferrer&quot;&gt;this page&lt;/a&gt; from the Uni of Minnesota for some more info.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A picture of a species from the genus:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/98dbd.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2014-10-10T22:01:42.700" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="22036" PostTypeId="1" CreationDate="2014-10-11T02:59:11.817" Score="3" ViewCount="278" Body="&lt;p&gt;Does having a central axon and dendrites result in any advantage compared to if the neuron was symmetrical? &lt;/p&gt;&#xA;" OwnerUserId="9717" LastActivityDate="2014-10-12T02:44:53.130" Title="What is the advantage to neurons being asymmetrical?" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22038" PostTypeId="1" CreationDate="2014-10-11T05:03:17.347" Score="4" ViewCount="142" Body="&lt;p&gt;I know chitosan will decrease the absorption of fat. However unsaturated fatty acid, such as DHA, is beneficial. Does chitosan effect the absorption of unsaturated fatty acid?&lt;/p&gt;&#xA;" OwnerUserId="9719" LastEditorUserId="5144" LastEditDate="2014-10-11T06:42:17.863" LastActivityDate="2014-10-11T19:42:41.340" Title="Can chitosan affect the absorption of unsaturated fatty acid?" Tags="&lt;metabolism&gt;&lt;lipids&gt;&lt;health&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22039" PostTypeId="1" AcceptedAnswerId="22040" CreationDate="2014-10-11T06:43:58.043" Score="6" ViewCount="14773" Body="&lt;p&gt;I was told in a physiology lecture that alcohol inhibits gluconeogenesis because 'NADH produced from ethanol catabolism leads to product inhibition'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But is NADH not a reactant coenzyme of gluconeogenesis? It would make more sense if NADH inhibits glycolysis by product inhibition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what is wrong here? Or is it because of some other reason why alcohol inhibits gluconeogenesis and leads to hypoglycemia?&lt;/p&gt;&#xA;" OwnerUserId="3814" LastEditorUserId="1320" LastEditDate="2017-05-28T12:07:20.117" LastActivityDate="2017-05-28T12:18:57.413" Title="Does NADH inhibit gluconeogenesis?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="22040" PostTypeId="2" ParentId="22039" CreationDate="2014-10-11T07:06:31.057" Score="7" Body="&lt;p&gt;Yes, this is the effect of metabolizing ethanol and also the reason why excess ethanol can lead to hypoglycemia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ethanol is oxidized by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Alcohol_dehydrogenase&quot; rel=&quot;nofollow noreferrer&quot;&gt;alcohol dehydrogenase&lt;/a&gt; to acetaldehyde. This reaction consumes one molecule of NAD&lt;sup&gt;+&lt;/sup&gt; per molecule ethanol oxidized: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Ethanol + NAD+ &amp;lt;=&amp;gt; Acetaldehyde + NADH + H+&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Acetaldehyde is oxidized by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Acetaldehyde_dehydrogenase&quot; rel=&quot;nofollow noreferrer&quot;&gt;acetaldehyde dehydrogenase&lt;/a&gt; in a second reaction in the mitochondria to Acetyl-CoA, which produces another molecule of NADH:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Acetaldehyde + NAD+  + CoA &amp;lt;=&amp;gt; Acetyl-CoA + NADH + H+&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;If you now take a look at gluconeogenesis, there is one critical step which needs NAD&lt;sup&gt;+&lt;/sup&gt;: the oxidation of lactate to pyruvate by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Lactate_dehydrogenase&quot; rel=&quot;nofollow noreferrer&quot;&gt;lactate dehydogenase&lt;/a&gt; which then cannot be processed into oxalacetate, phosphoenolpyruvate and so on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wxagg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adding excess NADH shifts the reaction equilibrium completely to the side of lactate and also leads to the production of additional lactate, leading to hypoglycemia and lactic acidosis. Excess NADH from the ethanol oxidation inhibits the oxidation of fatty acids in the liver - this process also generates NADH for the production of ATP. NADH signals this process that enough energy is available in the cell. And finally excess NADH also inhibits the &lt;a href=&quot;http://en.wikipedia.org/wiki/Malate_dehydrogenase&quot; rel=&quot;nofollow noreferrer&quot;&gt;malate dehydrogenase&lt;/a&gt; reducing the amount of oxalacetate for gluconeogenesis further.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1320" LastEditDate="2017-05-28T12:18:57.413" LastActivityDate="2017-05-28T12:18:57.413" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="22042" PostTypeId="2" ParentId="22026" CreationDate="2014-10-11T08:37:53.263" Score="8" Body="&lt;p&gt;This is indeed a problematic point. I have been using machine printed labels for a while now (sometimes with some extra scotch tape around it to prevent it from falling) off, which worked pretty nicely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there is a printer available on the market (though I haven't tested it yet) which claims that they can print on any tube. This printer is called &lt;a href=&quot;http://tubewriter.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tubewriter&lt;/a&gt;, which is probably also worth a look. The backside is the price, &lt;a href=&quot;http://www.fishersci.com/ecomm/servlet/fsproductdetail_10652_13801915__-1_0&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fisher Scientific&lt;/a&gt; lists them around 40.000$, which will make them unavailable for most labs, except for cell banks etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/t2MmL.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/TZgaD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="3340" LastEditDate="2014-10-27T09:05:24.727" LastActivityDate="2014-10-27T09:05:24.727" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="22043" PostTypeId="1" CreationDate="2014-10-11T10:28:18.117" Score="8" ViewCount="798" Body="&lt;p&gt;The title is the question. If additional specificity is needed I will add clarification here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any multicellular forms of life which exist without requiring the consumption (destruction) of other forms of life in some manner? Thus purely on inorganic material.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do understand that the definition of life is a semantic distinction, so for this discussion I will assume the one Wikipedia provides:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Life is a characteristic distinguishing physical entities having signaling and self-sustaining processes from those that do not, either because such functions have ceased (death), or because they lack such functions and are classified as inanimate. Biology is a science concerned with the study of life.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am open to considering alternative suggestions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="9722" LastActivityDate="2019-03-27T01:03:31.877" Title="Are there any multicellular forms of life which exist without consuming other forms of life in some manner?" Tags="&lt;evolution&gt;&lt;biochemistry&gt;&lt;cell-biology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="22045" PostTypeId="1" CreationDate="2014-10-11T16:06:41.247" Score="3" ViewCount="1092" Body="&lt;p&gt;I've read that CT scan causes radiation equivalent to few hundreds of ordinary X ray scan. It sound scary at the first look of it but I wonder is it the amount considered significant? Can dosage equal to the 1 CT scan significantly increase chance of developing cancer or other adverse effects?&lt;/p&gt;&#xA;" OwnerUserId="9725" LastActivityDate="2014-10-12T07:05:44.897" Title="Can radiation equilevant to 1 CT (computer tomography) scan causes significant changes in human body?" Tags="&lt;cancer&gt;&lt;radiation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22046" PostTypeId="2" ParentId="22043" CreationDate="2014-10-11T16:08:11.920" Score="23" Body="&lt;p&gt;Yes, plants for example!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Autotrophs vs. heterotrophs&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants are &lt;a href=&quot;http://en.wikipedia.org/wiki/Autotroph&quot; rel=&quot;nofollow noreferrer&quot;&gt;autotrophs&lt;/a&gt; while animals and fungi are &lt;a href=&quot;http://en.wikipedia.org/wiki/Heterotroph&quot; rel=&quot;nofollow noreferrer&quot;&gt;heterotrophs&lt;/a&gt;. Have a look at the Wikipedia articles. In short, autotrophs organisms are organisms that synthesize their own compounds from &lt;em&gt;inorganic&lt;/em&gt; compounds. Heterotrophs organisms are organisms that synthesize their own compounds from &lt;em&gt;organic&lt;/em&gt; compounds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, any multicellular plants are multicellular organisms that &quot;exist without consuming other forms of life&quot; (with the exceptions of carnivorous plants).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Consuming nonliving organic matter&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, many life forms feed on organic matter but only on non-living organic matter. Such life forms do not kill to feed. It is the case of all &lt;a href=&quot;https://en.wikipedia.org/wiki/Detritivore&quot; rel=&quot;nofollow noreferrer&quot;&gt;detritivores&lt;/a&gt; (such as earthworms) and &lt;a href=&quot;https://en.wikipedia.org/wiki/Decomposer&quot; rel=&quot;nofollow noreferrer&quot;&gt;decomposer&lt;/a&gt; such as fungi.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Competition vs predation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As @TechZen said, not consuming other organisms doesn't mean that the existence of an individual of this species is not causing the death of another individual (competition and parasitism that does not involve consuming the other individual).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-26T22:06:11.623" LastActivityDate="2019-03-26T22:06:11.623" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="22047" PostTypeId="2" ParentId="22045" CreationDate="2014-10-11T16:32:57.993" Score="2" Body="&lt;p&gt;As a rule of thumb you can say that a CT scan exposes you to a higher dose than a X-ray examination, due to the different techniques. For &lt;a href=&quot;http://en.wikipedia.org/wiki/X-ray_computed_tomography&quot; rel=&quot;nofollow noreferrer&quot;&gt;CT scans&lt;/a&gt; a number of single 2D photos is processed into the 3D models. However, the dose strongly depends on what body part is examined. See a part of this table (the complete table can be found in reference 1):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pVYU7.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The additional risk for most examinations is low to very low and since we don't get x-rayed on a daily basis this is a risk which can be tolerated. Besides this, there are other exposures to radiation which also accumulate, but where people usually don't hink about it. These are for example smoking and flights at great altitudes. See the answer from @anongoodnurse for some more details on this.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.radiologyinfo.org/en/safety/?pg=sfty_xray&quot; rel=&quot;nofollow noreferrer&quot;&gt;Radiation Dose in X-Ray and CT Exams&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.icrp.org/publication.asp?id=ICRP%20Publication%20103&quot; rel=&quot;nofollow noreferrer&quot;&gt;The 2007 Recommendations of the International Commission on&#xA;Radiological Protection&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.aapm.org/publicgeneral/CTDoseResponse.asp&quot; rel=&quot;nofollow noreferrer&quot;&gt;AAPM Response in Regards to CT Radiation Dose and its Effects&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-10-12T07:05:44.897" LastActivityDate="2014-10-12T07:05:44.897" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="22049" PostTypeId="2" ParentId="21632" CreationDate="2014-10-11T19:34:34.777" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;: different people have different amount of active receptors. &#xA;In treatment, combination scores of Pharmacodynamics and Pharmacokinetics determine the final effect of the drug. &#xA;Receptors determine many effects of the drug in many pathways. &#xA;Different people also sense pains differently (Psychology). &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;&lt;strong&gt;Review answer&lt;/strong&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The purpose of treatment is to relieve pain and maintain function. &#xA;Your question is biased. &#xA;You cannot only concentrate on painkilling in maintaining health. &#xA;These both are the reasons for the complains of the patient, not only the pain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, in rheumatoid arthritis, response to therapy can be quantitated using many measures including American College of Rheumatology system values ACR20, ACR50 and ACR70, which denotes the percentage of patients showing an improvement of 20%, 50% or 70% in a global assessment of signs (maintaining function) and symptoms (pains).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each patient has own health, different from one another. &#xA;Our body adapts to the environment and individual conditions of the body to maintain homeostasis. &#xA;Receptors adapt for instance. &#xA;They can be active or inactive - in short-run and long-run - again depending on the conditions at hand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Painkillers i.e. analgesics have different properties:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;anti-inflammatory effect - acute and chronic conditions (inflammation is the major mechanism under many pathologies) e.g. &lt;strong&gt;nonsteiroidal anti-inflammatory drugs&lt;/strong&gt; (NSAIDs, please, see &lt;a href=&quot;https://biology.stackexchange.com/a/23217/86&quot;&gt;this answer&lt;/a&gt; about the particular mechanisms and how different people have different effects from NSAID painkillers) and &lt;strong&gt;glucocorticoids&lt;/strong&gt; (most) &lt;/li&gt;&#xA;&lt;li&gt;symptoms relieving specific drugs e.g. &lt;strong&gt;disease-modifying antirheumatic drugs&lt;/strong&gt; (DMARDs)&lt;/li&gt;&#xA;&lt;li&gt;anti-platelet effect - e.g. the older you get, the more platelets stick together.&lt;/li&gt;&#xA;&lt;li&gt;anti-pyretic effect&lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which all can be toxic. &#xA;Note that many drugs alone or/and as combination can work as painkillers i.e. pain relievers. &#xA;Aspirin for instance has both anti-inflammatory and anti-platelet properties. &#xA;However, it is rarely anymore used as anti-inflammatory. &#xA;The anti-platelet property is dependent on the exact dosage of the administration. &#xA;Aspirin's mechanism of action is to inhibit platelet COX which antiplatelet effect lasts 8-10 days (life of the platelet). &#xA;In other tissues, synthesis of new COX replaces the inactivated enzyme so that ordinary doses have a duration of 6-12 hours. &#xA;Please, review any Pharmacology -textbook for more info about aspirin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each these drug has own &lt;strong&gt;Pharmacodynamics&lt;/strong&gt; and &lt;strong&gt;Pharmacokinetics&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Pharmacodynamics answers to the question &lt;strong&gt;What drug does to the body?&lt;/strong&gt; It stimulates some receptors, activates some pathways, ...&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Pharmacokinetics&lt;/strong&gt; - &lt;strong&gt;What does body do to the drug?&lt;/strong&gt; It metabolises it (enzymes, receptors). It distributes it. It excretes it (kidneys, feaces).  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In treatment, you consider what is the target organ. &#xA;You need to think what is causing the dysfunction and the pain. &#xA;You try to restore the function and relieve pain. &#xA;The component of drug needs to reach the target tissue e.g. your pancreas' beta cells do no produce insulin so your blood glucose is high. &#xA;Complications of this are polyuria and eventually exodus if untreated. &#xA;Insulin is injected into the fatty tissue. &#xA;We do not have long-term acting insulin administered orally - our metabolism start to break the drug so it does not have wanted treatment. &#xA;If insulin administered to the muscle, the time of action is too times less, again because muscle is metabolising the insulin i.e. a chain of peptides (protein).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No all symptoms and diseases have painkillers. &#xA;For instance, prehemorrhoid and some types of itching related to  posthemorrhoids. &#xA;However, for both, there are some special salvas for proplylaxis but they are not complete.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, you can start to read something in SuperBest's answer about host's physiological variables and addiction/tolerance which alters the mechanisms (receptors) of pathways in Pharmacodynamics and Pharmacokinetics.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sources&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Basic and Clinical Pharmacology, 11th edition, 2009, Bertram Katzung.&lt;/li&gt;&#xA;&lt;li&gt;My notes in Pharmacology classes during 2014.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-10-16T18:55:06.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="22050" PostTypeId="2" ParentId="22038" CreationDate="2014-10-11T19:42:41.340" Score="2" Body="&lt;p&gt;It seems that there is no difference in the effects of chitosan on the uptake of saturated and unsaturated fatty acids. The study cited below (which has been done on guinea pigs) fed the animals a diet which contained different digestion-resistant fibers (maltodextrin, cellulose and chitosan) and also fats. Then the fatty acid content of the feces was measured afterwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Only for the group which got additional feeding of chitosan showed a significant increase in the excreted fatty acids. This was true for the saturated (lauric, myristic and palmitic acid) but also for the unsaturated fatty acids (Oleic, linoleic and α-linolenic acid). This effect is specific for fatty acids, The uptake of neutral sterols and bile acids was not affected in any of the experimental groups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second paper suggests that chitosan forms an emulsion with fatty acids under the acidic conditions of the stomach. This emulsion is stable and later excreted with the feces.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3772/g3xe54ik_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Selective in vivo effect of chitosan on fatty acid, neutral sterol&#xA;and bile acid excretion: a longitudinal study.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16306685&quot; rel=&quot;nofollow&quot;&gt;Interaction between chitosan and oil under stomach and duodenal&lt;br&gt;&#xA;digestive chemical conditions.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-11T19:42:41.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23048" PostTypeId="1" CreationDate="2014-10-11T20:09:10.527" Score="1" ViewCount="64" Body="&lt;p&gt;I want to express GFP in rice as a method for differentiating transgenic from non transgenic rice seeds. I want to know if I can visualize them using a hand held UV lamp as the GFP I will be using has a excitation maxima at 395nm. If yes, how is to be done? Do I just flash the UV lamp on the seeds in the dark room and I can see the GFP expressing seeds glowing green?&lt;/p&gt;&#xA;" OwnerUserId="8617" LastEditorUserId="9099" LastEditDate="2014-10-12T07:06:40.313" LastActivityDate="2014-10-12T07:06:40.313" Title="Visualizing GFP in transgenic rice seeds?" Tags="&lt;botany&gt;&lt;biotechnology&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23050" PostTypeId="1" CreationDate="2014-10-11T22:43:39.180" Score="1" ViewCount="2433" Body="&lt;p&gt;After seeing &lt;a href=&quot;https://biology.stackexchange.com/questions/22043/are-there-any-multicellular-forms-of-life-which-exist-without-consuming-other-fo&quot;&gt;this question&lt;/a&gt; I remembered that in secondary school we watched a documentary stating something along the lines of &lt;em&gt;&quot;all organisms derive their energy directly or indirectly from the sun. *pause* Well, except a couple of organisms in the deep sea cultures that get their energy from small undersea volcanoes&quot;&lt;/em&gt; . Now, after doing a lot of searching I was able to find the 'giant tube worm', however that still indirectly relies on energy from the sun as well as it relies on free Oxygen being available that in the end comes from photosynthesis (if my understanding is correct). So my question is two fold, am I correct in my understanding of the giant tube worm and if so, are there any organisms that function in a way that does not require any energy source beyond geothermal energy?&lt;/p&gt;&#xA;" OwnerUserId="8039" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-09-18T17:51:00.863" Title="Organisms using thermal energy as their sole energy source" Tags="&lt;photosynthesis&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23051" PostTypeId="2" ParentId="23050" CreationDate="2014-10-11T23:36:46.257" Score="2" Body="&lt;p&gt;I had to re-read your last sentence a few times to make sure I understood it correctly, but I think that now I do, and I can answer your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you're talking about are &lt;a href=&quot;http://en.wikipedia.org/wiki/Thermophile&quot; rel=&quot;nofollow&quot;&gt;thermophiles&lt;/a&gt;. They're small organisms that &lt;em&gt;love&lt;/em&gt; hot conditions - up to nearly 250 degrees Fahrenheit. They can be found places with a lot of hot water, such as hot springs - and, yes, ocean vents. Many use sulfur as a fuel during &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemosynthesis&quot; rel=&quot;nofollow&quot;&gt;chemosynthesis&lt;/a&gt;, oxidizing it to make sulfuric acid. They take the energy from the heat source to do this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all thermophiles use chemosynthesis. Those in hot springs may get a lot of sunlight, and they can use &lt;a href=&quot;http://en.wikipedia.org/wiki/Photosynthesis&quot; rel=&quot;nofollow&quot;&gt;photosynthesis&lt;/a&gt;. However, those in the deep sea cannot undergo photosynthesis, and are forced to use the energy from the vents to undergo chemosynthesis. In fact, entire ecosystems can be built off them!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thermophiles may even have been some of the first organisms on Earth. Around the time that life is thought to have first formed, Earth wasn't a very hospitable place. As Ashwini Kumar Lal &lt;a href=&quot;http://arxiv.org/vc/arxiv/papers/0907/0907.3552v1.pdf&quot; rel=&quot;nofollow&quot;&gt;writes&lt;/a&gt; of the first forms of life,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many of them are evolutionary relics called “archaea”, believed to be among the first homesteaders on the Earth 3.8 billion years ago. They are presumably&#xA;  the first version of life on our planet when its atmosphere was devoid of oxygen, and comprised largely of ammonia, methane, water vapour and carbon dioxide. They are microorganisms similar to bacteria in size and simplicity of structure, but continue as an ancient group intermediate between bacteria and eukaryotes. Heat – loving microbes, or “thermophiles”, are among the best studied of the extremophiles that can reproduce or grow readily in temperatures exceeding 45º C, and some of them, referred to as “hyperthermophiles”, are capable of thriving even thrive in temperatures as high as 110º C – more than boiling water temperature.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;While we do not know (and may never know) the truth of this hypothesis, it is certainly plausible, given the locations where some extremophiles have been found.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1: &lt;a href=&quot;http://serc.carleton.edu/microbelife/extreme/extremeheat/index.html&quot; rel=&quot;nofollow&quot;&gt;Microbial Life in Extremely Hot Environments&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2: &lt;a href=&quot;http://en.academic.ru/dic.nsf/enwiki/18641&quot; rel=&quot;nofollow&quot;&gt;http://en.academic.ru/dic.nsf/enwiki/18641&lt;/a&gt; (link no longer works, for some reason)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3: &lt;a href=&quot;http://arxiv.org/vc/arxiv/papers/0907/0907.3552v1.pdf&quot; rel=&quot;nofollow&quot;&gt;Origin of Life&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: While I list several Wikipedia articles throughout the answer, I did not use them for the information in this answer. I think they're a good starting point to lead you to &lt;em&gt;other&lt;/em&gt; sources, though.&lt;/p&gt;&#xA;" OwnerUserId="9458" LastEditorUserId="9458" LastEditDate="2015-09-12T23:07:14.987" LastActivityDate="2015-09-12T23:07:14.987" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="23052" PostTypeId="2" ParentId="22045" CreationDate="2014-10-12T01:03:43.783" Score="2" Body="&lt;p&gt;Xrays are not scans. They are one shot (or a series of a few). Say that a chest Xray (two views) doses you with .1 mSv of radiation. The dose from a standard chest CT is 7 mSv.&lt;sup&gt;[1]&lt;/sup&gt; That is 70 times what a chest film gives you, not a few hundred (though that might seem like quibbling). The TL;DR answer is: no one knows for sure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Radiation (especially in fetuses -children) increases the likelihood of cancer. Our information comes mostly from atomic bomb survivors, people exposed at Chernobyl, people treated with high doses of radiation for cancer and other conditions, and people exposed to high levels of background radiation, e.g. uranium miners. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can one CT scan increase your chance of developing cancer? Yes, but how &lt;em&gt;significant&lt;/em&gt; that is remains debatable. It depends on a lot of unmeasurable things: genetics, your age, your ability to repair the damage, which area of the body is being dosed, whether there are other carcinogens at work (e.g. viruses or co-carcinogens), etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following are commonly found numbers (which does not mean they're accurate). Given 10,000 people, about 2000 will die of non-radiation related cancers. If you expose those 10,000 people to 10 mSv of radiation, you can expect 5-6 additional cancer deaths in that 10,000 (or .5% increase). &lt;sup&gt;[2]&lt;/sup&gt; However, if you expose someone to 10 mSv twice, with two months in between, the risk does not double. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The average dose of radiation per year from background sources is 1.5-3.5 mSv/yr.&lt;sup&gt;[3]&lt;/sup&gt; &lt;sup&gt;[4]&lt;/sup&gt; Because of our ability to repair damaged DNA over time, it's generally estimated that, from natural background radiation, the risk of developing cancer from background radiation is about 1% of our total cancer risk.&lt;sup&gt;[5]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, let's say that your average CT scan is going to give you 7 mSv of exposure (that's a high estimate). What is your chance of getting a &lt;em&gt;lethal cancer&lt;/em&gt; from that? The answer is: no one knows.&lt;sup&gt;[6]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Relative risk has be calculated by some. The following all give you a (estimated) 1 in a million chance of dying from that event&lt;sup&gt;[7]&lt;/sup&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Smoking 1.4 cigarettes (lung cancer)  &lt;/li&gt;&#xA;  &lt;li&gt;Eating 40 tablespoons of peanut butter&lt;/li&gt;&#xA;  &lt;li&gt;Spending 2 days in New York City (air pollution)  &lt;/li&gt;&#xA;  &lt;li&gt;Driving 40 miles in a car (accident)  &lt;/li&gt;&#xA;  &lt;li&gt;Flying 2500 miles in a jet (accident)  &lt;/li&gt;&#xA;  &lt;li&gt;Canoeing for 6 minutes  &lt;/li&gt;&#xA;  &lt;li&gt;Receiving 10 mrem (.1 mSv) of radiation (cancer) &lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, you can estimate that (maybe) the risk of dying from a 7 mSv CT scan is about equivalent to driving 2800 miles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The point of all this is, no one knows your exact risk of developing a lethal or r&lt;em&gt;elatively non-lethal&lt;/em&gt; cancer (yes, that does exist) from an imaging study. Most ethical Radiologists will tell you there is no known safe radiation exposure, and that one should avoid unnecessary radiation exposure. While some imaging studies &lt;strong&gt;are&lt;/strong&gt; unnecessary, some of them are not, and the risk of avoiding the study greatly outweighs the risk of undergoing it. What you can do to protect yourself:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;ask if an MRI will give the doctor the same information (no radiation, but 2-3x the cost, longer wait)  &lt;/li&gt;&#xA;  &lt;li&gt;ask the doctor if the test is absolutely necessary (a lot of tests are ordered to &lt;em&gt;cover one's ass&lt;/em&gt;)  &lt;/li&gt;&#xA;  &lt;li&gt;ask if there is another way to obtain the same information (e.g. colonoscopy instead of barium study)  &lt;/li&gt;&#xA;  &lt;li&gt;get your study from the newest scanners available (radiation can be reduced up to 60% between generations of CT scanners)&lt;/li&gt;&#xA;  &lt;li&gt;reduce conflict of interest: any CT scan ordered &lt;em&gt;in house&lt;/em&gt; (or by a doctor that owns a share in the imaging facility) should be questioned (but not necessarily refused.)&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://www.xrayrisk.com/calculator/calculator-normal-studies.php?id=17&quot; rel=&quot;nofollow&quot;&gt;XrayRisk.com&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://www.epa.gov/radiation/understand/health_effects.html#est_health_effects&quot; rel=&quot;nofollow&quot;&gt;USEPA Radiation and Health&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://www.world-nuclear.org/info/Safety-and-Security/Radiation-and-Health/Radiation-and-Life/&quot; rel=&quot;nofollow&quot;&gt;Radiation and Life&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[4] Higher accumulated doses of radiation might produce a cancer which would only be observed several - up to twenty - years after the radiation exposure. This delay makes it impossible to say with any certainty which of many possible agents were the cause of a particular cancer. In western countries, about a quarter of people die from cancers, with smoking, dietary factors, genetic factors and strong sunlight being among the main causes. Radiation is a weak carcinogen, but undue exposure could certainly increase health risks.&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[5] &lt;a href=&quot;http://www.maricopa.gov/emerg_mgt/pvngs_radiation.aspx&quot; rel=&quot;nofollow&quot;&gt;American Nuclear Society&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[6] &lt;a href=&quot;https://radiology.ucsf.edu/patient-care/patient-safety/radiation-safety/risks-of-radiation&quot; rel=&quot;nofollow&quot;&gt;Risks of Radiation&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[7] &lt;a href=&quot;http://www.physics.isu.edu/radinf/risk.htm&quot; rel=&quot;nofollow&quot;&gt;Radiation and Risk&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-10-12T05:42:14.163" LastActivityDate="2014-10-12T05:42:14.163" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23053" PostTypeId="2" ParentId="22026" CreationDate="2014-10-12T02:33:40.613" Score="2" Body="&lt;p&gt;I hate this problem but I hate even more when I pull up a cryo vial that some one wrote on with a dry erase marker.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Get printable &lt;a href=&quot;http://www.usascientific.com/Tough-Tags-1.28x0.5-white.aspx&quot; rel=&quot;nofollow&quot;&gt;tough tags&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two options after that, print on them with your laser printer. Can do many at a time.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;You can take a step further and overlay the tag with some 3m single sided tape (scotch tape is gonna brittle up from the N&lt;sub&gt;2&lt;/sub&gt;.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Write on it with a fisher brand solvent free marker. This is the only &lt;a href=&quot;http://www.fishersci.com/ecomm/servlet/fsproductdetail?storeId=10652&amp;amp;productId=631386&amp;amp;catalogId=29104&amp;amp;matchedCatNo=133796%7C%7C133795%7C%7C133797%7C%7C133794&amp;amp;fromSearch=1&amp;amp;searchKey=plastic%7C%7Cfisher%20scientific%7C%7CFisher%7C%7Cmarkers%7C%7Cfisherbrand%7C%7Cplastics%7C%7Cfishers%7C%7CMarker&amp;amp;highlightProductsItemsFlag=Y&amp;amp;endecaSearchQuery=%23store%3DScientific%23nav%3D0%23rpp%3D25%23offSet%3D0%23keyWord%3DFisher%2BMarker%2Bplastics%23searchType%3DPROD%23SWKeyList%3D%5B%5D&amp;amp;xrefPartType=From&amp;amp;savings=0.0&amp;amp;xrefEvent=1413080960848_1&amp;amp;searchType=PROD&amp;amp;hasPromo=0&quot; rel=&quot;nofollow&quot;&gt;marker&lt;/a&gt; alcohol will not take off!!! &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I would love to find the ink in this market and be able to put it in my printer for the tough tags.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I like these types of questions on here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are elaborate systems out there like Chris's answer and they are of course preferable. But expensive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I didn't think to use the QR codes for as mentioned by 1st answer, I may try this.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="3340" LastEditDate="2014-10-27T09:08:12.393" LastActivityDate="2014-10-27T09:08:12.393" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23055" PostTypeId="2" ParentId="21215" CreationDate="2014-10-12T02:43:55.250" Score="1" Body="&lt;p&gt;Patch clamping &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultracentrifugation to get soluble fractions. If you get enough of it and u have validated its purity you could runs conductivity probe into your fraction&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-10-12T02:43:55.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23056" PostTypeId="2" ParentId="22036" CreationDate="2014-10-12T02:44:53.130" Score="3" Body="&lt;p&gt;Asymmetry to essential to neuronal function, particularly in the peripheral nervous system. This is because the dendrites of a neuron receive synaptic potentials, which are graded and decay with distance. Dendrites are typically short such that a synaptic potential is still above threshold by the time it reaches the axon hillock (sometimes called trigger zone), so that a subsequent action potential can fire. Axons need to be long (some are up to a meter long, in the leg) to transmit signals long distances in the body. To make a neuron symmetrical, one of these qualities would have to be compromised and neuronal function would suffer as a result.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: Principles of Neural Science, 5th ed (2012), Kandel et al. Chapters 1-6. &lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2014-10-12T02:44:53.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23057" PostTypeId="2" ParentId="22043" CreationDate="2014-10-12T06:10:45.353" Score="4" Body="&lt;p&gt;There are multicellular organisms which do not actively eat other organisms, however, there are no organisms who do not kill other organisms, period. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trees and other vertical plants evolved in the first place in a competition for sunlight. For plants, being in the shade is like smother or starving a human since they literally use sunlight to create and create food and oxygen. Plants carry out complex chemical war against a wide range of other life forms from microbes to other similar plants. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants don't eat other organisms, save indirectly, but they do kill. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All multicellular organisms have an immune system that wages and unrelenting slaughter against microbes which in turn are constantly assaulting multicellular organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, every individual organism and probably all strains and species, displace other individuals, strains or species just by existing. No energy is wasted in the biosphere. If something is living in one place or niche and then dies, the energy it was living on becomes available for something else. Conversely, while it lives it prevents other organisms from evolving to fill the niche, or as an individual moving into the physical niche. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just by our very existence, we kill. &lt;/p&gt;&#xA;" OwnerUserId="9612" LastEditorUserId="43480" LastEditDate="2019-03-27T01:03:31.877" LastActivityDate="2019-03-27T01:03:31.877" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="23058" PostTypeId="2" ParentId="9739" CreationDate="2014-10-12T06:37:46.923" Score="2" Body="&lt;p&gt;You can't predict the evolution of anything because evolution is driven solely by the environment. It is the environment that squeezes species into to specific forms. We have has a much say in our shape and form as a whirlpool does and for the same reasons, both humans and whirlpools result form powerful outside forces. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to have shot at even making a credible guess about future evolution, you'd have to know what the environment around humans will be over the next 100,000 years at a minimum. About all you can say is the likelihood of this or that modification, based on existing physiology. The more that has to change to evolve a new structure, the less likely it will, even given strong selection pressure. We won't evolve wings or eyes in the back of head but we could get taller, shorter, hairier, larger brained, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea that evolution is the result of some innate guiding or shaping natural force arose shortly after Darwin advanced the theory of transmutation of the species by natural selection. The scientific community got on board with whole transmutation of one species into another, but they view natural selection as to happenstance and taking to long to be the primary mechanism. Instead they came to believe that some force was driving organisms to become more complex, in a particular pattern, over relatively short periods of time 1,000 of years. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is why, we call the concept &quot;evolution&quot; in the first place. It was not a word Darwin used or liked because it had existed since the 16th century. Literally, it meant &quot;to unroll&quot; like a scroll and implied a preset motion or sequence. Seeds were said to &quot;evolve&quot; into plants. Sailors and soldiers practicing repetitive drills, practiced their &quot;evolutions&quot;. The word meant the unfolding of predetermined pattern, the exact opposite of natural selection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, this erroneous mechanism would dominate evolutionary theory for 80 years until the development of synthetic theory in 1947. But by then, the idea of evolution being predetermined, fixed, with &quot;levels&quot;, &quot;stages&quot;, &quot;higher&quot;, &quot;lower&quot; and generally progress, had been fixed in the public mind. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you still see a lot of nonsense about the &quot;next stage of human evolution&quot; when under natural selection such a concept is simple gibberish. We will be what ever the environment shapes us to be. &lt;/p&gt;&#xA;" OwnerUserId="9612" LastActivityDate="2014-10-12T06:37:46.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23059" PostTypeId="1" CreationDate="2014-10-12T10:50:43.023" Score="4" ViewCount="1154" Body="&lt;p&gt;I would like to see some examples of proteins with PDB ID so that I can download and see them in &lt;a href=&quot;http://www.ks.uiuc.edu/Research/vmd/&quot; rel=&quot;nofollow&quot;&gt;VMD&lt;/a&gt; software. I need some proteins with alpha helix only and proteins with beta sheets alone.&lt;/p&gt;&#xA;" OwnerUserId="5669" LastEditorUserId="5669" LastEditDate="2014-10-12T15:05:45.600" LastActivityDate="2014-10-13T23:45:35.070" Title="Proteins with alpha helices alone and beta sheets alone?" Tags="&lt;proteins&gt;&lt;pdb&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23062" PostTypeId="1" AcceptedAnswerId="31106" CreationDate="2014-10-12T11:57:05.893" Score="5" ViewCount="205" Body="&lt;p&gt;I'm a freshman med student and I've noticed that on all the feet (and hands) of deceased people that I've worked with, the bottom of the feet always turns red and also the inside of the palm? Why is this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-04-07T03:05:56.680" Title="Formaldehyde turns plantar region of feet red?" Tags="&lt;biochemistry&gt;&lt;medicine&gt;&lt;decay&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23063" PostTypeId="1" AcceptedAnswerId="23064" CreationDate="2014-10-12T13:01:39.857" Score="1" ViewCount="129" Body="&lt;p&gt;At my med school we have human samples (body parts, organs, etc.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are soaked in some sort of solution for long term storage. I'm quite sure that it's not formaldehyde as that would be really toxic and we're allowed to pick them up from the tubs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What sort of solution could this be?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2014-10-12T13:36:16.523" Title="Preservation of human tissue" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23064" PostTypeId="2" ParentId="23063" CreationDate="2014-10-12T13:36:16.523" Score="3" Body="&lt;p&gt;Embalming solutions for cadaver study differ from institution to institution (and are reportedly somewhat different from embalming for funerals, but I'm not sure of those details). Typically embalming solutions for cadavers meant to be stored indefinitely consist mostly of water with lesser but roughly equal amounts alcohol (usually methanol), gylcerin, phenol, and a smaller percentage of formalin/formaldehyde to prevent mold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.einstein.yu.edu/administration/environmental-health-safety/training/anatomy-students.aspx&quot; rel=&quot;nofollow&quot;&gt;A document from Albert Einstein College of Medicine&lt;/a&gt; lists:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Methanol: 11.1%&lt;/li&gt;&#xA;&lt;li&gt;Glycerin: 11.1%&lt;/li&gt;&#xA;&lt;li&gt;Phenol: 9.3%&lt;/li&gt;&#xA;&lt;li&gt;Formaldehyde: 1.9%&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you want to know what your institution uses, you should just ask, and they should be willing and able to tell you.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2014-10-12T13:36:16.523" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23066" PostTypeId="2" ParentId="23059" CreationDate="2014-10-12T14:38:14.743" Score="5" Body="&lt;p&gt;You may consider taking a look at the &lt;a href=&quot;http://scop.mrc-lmb.cam.ac.uk/scop/index.html&quot; rel=&quot;noreferrer&quot;&gt;SCOP&lt;/a&gt; structural classification of proteins to check &lt;a href=&quot;http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.c.html&quot; rel=&quot;noreferrer&quot;&gt;all beta proteins&lt;/a&gt; and &lt;a href=&quot;http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.b.html&quot; rel=&quot;noreferrer&quot;&gt;all alpha proteins&lt;/a&gt;. As per specific examples and though not belonging to the SCOP classes mentioned above, &lt;a href=&quot;http://en.wikipedia.org/wiki/Porin_(protein)&quot; rel=&quot;noreferrer&quot;&gt;Porin&lt;/a&gt; for a beta protein (PDB:&lt;a href=&quot;http://www.rcsb.org/pdb/explore/explore.do?structureId=1A0S&quot; rel=&quot;noreferrer&quot;&gt;1A0S&lt;/a&gt;), and &lt;a href=&quot;http://en.wikipedia.org/wiki/Rhodopsin&quot; rel=&quot;noreferrer&quot;&gt;Rhodopsin&lt;/a&gt; for an alpha protein (PDB:&lt;a href=&quot;http://www.rcsb.org/pdb/explore/explore.do?structureId=1f88&quot; rel=&quot;noreferrer&quot;&gt;1F88&lt;/a&gt;) are two nice structures to look at.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastActivityDate="2014-10-12T14:38:14.743" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23068" PostTypeId="1" CreationDate="2014-10-12T16:35:09.443" Score="2" ViewCount="1211" Body="&lt;p&gt;If an element, ion or molecule is found in a cell is it possible to tell which method of transport was used? for example if a hydrogen or sodium ion was found in the cell could you tell if it got there by diffusion, or facilitated diffusion, or endocytosis, pinocytosis etc? If not could you at least narrow down the number of transport methods it could have used?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm very interested in which substances are let throught the cell membrane and by which method.&lt;/p&gt;&#xA;" OwnerUserId="9735" LastEditorUserId="9735" LastEditDate="2014-10-12T17:04:14.103" LastActivityDate="2014-10-12T21:53:09.933" Title="Active &amp; passive transport question" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;cell&gt;&lt;membrane-transport&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23069" PostTypeId="1" AcceptedAnswerId="23071" CreationDate="2014-10-12T18:47:37.473" Score="1" ViewCount="24882" Body="&lt;p&gt;Here is a question form my test.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If you could measure the pH of the interior of thylakoids and the&#xA;  surrounding stroma during active photosynthesis what would be the&#xA;  relative pH of each?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The answer is C.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the stroma would have a higher pH&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I understand that proton gradient is from stroma to thylakoid space, but that does not mean stroma would have less protons than thylakoid space, if stroma would have a higher pH, then the proton will never flow from stroma to thylakoid space, right?&lt;/p&gt;&#xA;" OwnerUserId="3179" LastEditorUserId="5144" LastEditDate="2014-10-12T21:24:41.493" LastActivityDate="2018-05-10T12:33:56.857" Title="Why would the stroma have a higher pH during photosynthesis?" Tags="&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23071" PostTypeId="2" ParentId="23069" CreationDate="2014-10-12T20:02:05.300" Score="4" Body="&lt;p&gt;Energy from an electron transport chain is used to actively transport protons from the stroma to the thylakoid lumen. Thus the lumen has a relatively higher proton concentration and therefore a lower pH than the stroma.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Higher [H&lt;sup&gt;+&lt;/sup&gt;] means lower pH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lower [H&lt;sup&gt;+&lt;/sup&gt;] means higher pH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Keep in mind that the flow of actively transported protons from the stroma to the lumen is against their concentration gradient. There wouldn't be a net flow of protons this way without active transport.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="22057" LastEditDate="2018-05-10T12:33:56.857" LastActivityDate="2018-05-10T12:33:56.857" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="23072" PostTypeId="2" ParentId="23068" CreationDate="2014-10-12T21:53:09.933" Score="1" Body="&lt;p&gt;Welcome to BioSE! As @Chris mentioned, transported atoms and molecules don't typically retain a record of their past history, so just by looking at a molecule in the cell you can't in general tell how it arrived in the cell (an exception might be proteins that have some chemical modification on them that allows them to be imported via a specific mechanism, such as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Mannose_6-phosphate&quot; rel=&quot;nofollow&quot;&gt;mannose-6-phosphate enzyme re-uptake system&lt;/a&gt;). In order to infer if a molecule typically enters a cell by a particular method, you will have to do several different types of experiments. I'll list a few off of the top of my head. &lt;em&gt;Note to other SE contributors:&lt;/em&gt; since this is not my area of expertise, I'm not sure how feasible some of these experiments are, or how they are typically done, so please edit my answer to be more accurate!&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Diffusion&lt;/strong&gt; If you want to know if something &lt;em&gt;can&lt;/em&gt; diffuse across a membrane, then the easiest way would be to try it &lt;em&gt;in vitro.&lt;/em&gt; One way I can imagine doing this is to use a phospholipid bilayer to separate two compartments: one with your molecule of interest, one without. By measuring the concentration of your molecule that transfers from one compartment to the other, you can see if your molecule can diffuse across a lipid bilayer. Note that this will only tell you if diffusion is &lt;em&gt;possible&lt;/em&gt; for your molecule. It may be that cells have ways to actively prevent your molecule from diffusing across your membranes, which you wouldn't be able to know from this assay.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Endocytosis or pinocytosis&lt;/strong&gt; One way to assess if your molecule is taken up by endocytosis or pinocytosis would be to knock out (genetically or with an inhibitory drug) these processes in your cell and see if your molecule of interest still ends up in the cell. Depending on the context of the molecule you're interested in, you might be able to simply place cells in solution with your molecule of interest and measure the concentration of the molecule outside the cells over time. You could compare how much of your molecule is lost from solution when cells can't endocytose and compare to when they can; if your molecule stays around when cells endocytose, you have some indication that process is necessary. Note that there would have to be a lot of other controls for this experiment as well: e.g. ensuring the effect you observe is specifically caused by endocytosis being inhibited. Since endocytosis and pinocytosis form vesicle intermediates containing your particle of interest, one check to see if endocytosis might be reasonable is to see if you can see vesicles containing your molecule of interest in the cell. Of course, this requires a method for being able to visualize your molecule of interest (maybe it's fluorescent, or can be modified with a fluorescent marker? Or maybe there is a fluorescent protein that binds your molecule and can change color on binding? These things all exist, they just depend on your particular molecule and context).&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Transport channels:&lt;/strong&gt; In a similar vein, how does the uptake of your molecule change when you inhibit or remove from the cell a particular type of channel? You could measure this in a similar way as the bullet point above.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Active vs passive transport:&lt;/strong&gt; If you wanted to see if uptake of your molecule requires active transport, you could try inhibiting ATP synthesis with a drug and see if transport of your molecule decreases over time. Note that this is in general not good for the cell (really!), so you might also have to have some more controls for this, maybe showing that transport of a molecule known to travel by passive transport is not affected on the timescale you're looking at, for example.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This list is by no means exhaustive, but I hope it gives you a sense of the type of experiments and ways of thinking you might be able to use to figure this out. Some general thoughts:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;This tends to be case-by-case.&lt;/strong&gt; While the type of experiments you might do to determine the mode of transport for different molecules are similar, the controls you will have to do to shore up your conclusions will really depend on the system involved, what type of effect a molecule has on your cells, whether your cell imports &lt;em&gt;and&lt;/em&gt; exports this molecule, under what circumstances you might expect the cell to take up this molecule (so you have a way to trigger the cells to take up this molecule for your experiment). I don't know of a completely generic method for resolving this type of question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Being able to measure abundance of your molecule is important.&lt;/strong&gt; All of the experiments above rely on being able to measure the concentration of your molecule, either outside of the cell, or inside of the cell. This is often easiest if you can modify your molecule to be visualizable in a microscope or spectrophotometer, but however you do it, you need a good, reliable, robust assay in order to make strong conclusions with this assay. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Controls are &lt;em&gt;really&lt;/em&gt; important.&lt;/strong&gt; Thinking up all the different alternative possibilities and trying to come up with ways to rule them out is the heart of experimental science. Fortunately, it also happens to often be rewarding and thought-provoking! I certainly had fun thinking about this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Best of luck!&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2014-10-12T21:53:09.933" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23073" PostTypeId="1" CreationDate="2014-10-12T21:57:53.897" Score="3" ViewCount="110" Body="&lt;p&gt;Sewall Wright in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1076930/&quot; rel=&quot;nofollow&quot;&gt;this article (1937)&lt;/a&gt; at the end of page 313 gives the equation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\Delta q = (s+tq)q(1-q) \space\space\space\space\space\space\space\space\space(1)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This equation is an approximation who holds only when $t$ and $s$ are small. $q$ is the frequency of allele &lt;code&gt;A&lt;/code&gt;. $s$ and $t$ define the fitness of the three possible genotypes &lt;code&gt;AA&lt;/code&gt;, &lt;code&gt;AB&lt;/code&gt; and &lt;code&gt;BB&lt;/code&gt;. I am not sure which genotype has fitness equal to 1 and I don't how $t$ and $s$ define the genotype fitnesses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's assume for example that the genotype &lt;code&gt;BB&lt;/code&gt; has fitness of 1. Then, the fitness of the genotypes &lt;code&gt;AB&lt;/code&gt; and &lt;code&gt;AA&lt;/code&gt; might be given by $1-t$ and $1-s$ respectively or $1-s$ and $1-t$ respectively or eventually by $1-t$ and $1-(s+t)$ (or variants) or even $s$ and $t$ (and opposite) or $st$ and $s$ (and variants). The genotypes fitness might as well be given by $1-st$ and $1-s$ but it would not be make much sense given the assumptions used for the approximation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: do you know &lt;strong&gt;how is the fitness of the three genotypes defined in equation (1)?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-10-17T12:33:55.037" LastActivityDate="2014-10-17T12:33:55.037" Title="Understanding the meaning of $s$ and $t$ in a population genetics equation" Tags="&lt;evolution&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23074" PostTypeId="1" AcceptedAnswerId="27905" CreationDate="2014-10-13T00:33:37.463" Score="26" ViewCount="1593" Body="&lt;p&gt;I just saw a recent &lt;a href=&quot;https://physics.stackexchange.com/questions/141030/does-liquid-immersion-protect-against-g-forces&quot;&gt;Physics question&lt;/a&gt; that mentioned &lt;a href=&quot;http://en.wikipedia.org/wiki/Liquid_breathing&quot; rel=&quot;nofollow noreferrer&quot;&gt;liquid breathing&lt;/a&gt; (which I had never heard of before) and I started to wonder about its long-term effects. Let's imagine a person underwent liquid breathing for some wacky reason - see the Wikipedia page for some starters - for a long time, maybe a month. What would begin to happen to them? Would any effects be reversible?&lt;/p&gt;&#xA;" OwnerUserId="9458" LastEditorUserId="-1" LastEditDate="2017-04-13T12:40:13.457" LastActivityDate="2021-01-12T10:39:18.220" Title="What are the side-effects of long-term liquid breathing?" Tags="&lt;human-anatomy&gt;&lt;respiration&gt;&lt;health&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23076" PostTypeId="2" ParentId="21964" CreationDate="2014-10-13T11:38:49.937" Score="2" Body="&lt;p&gt;That &quot;red pulp&quot; spaces you're referring are not blood vessels but, in fact, thyroid follicles that selectively absorb iodine from the blood for production of thyroid hormones and storage of thyroglobuline. So, they act as a reservoir of the materials used by the thyroid's epithelial cells, also called follicular cells, to produce thyroid hormones (T3 and T4).&lt;/p&gt;&#xA;" OwnerUserId="6543" LastActivityDate="2014-10-13T11:38:49.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23077" PostTypeId="1" CreationDate="2014-10-13T14:59:17.973" Score="2" ViewCount="62" Body="&lt;p&gt;I am up for all scientifically sound speculations, and sources are highly welcome. I've looked into this quite a bit myself via &lt;a href=&quot;http://scholar.google.com/scholar?q=last+universal+common+ancestor&amp;amp;btnG=&amp;amp;hl=en&amp;amp;as_sdt=0%2C39&quot; rel=&quot;nofollow&quot;&gt;scholar.google&lt;/a&gt;, the wiki article, and &lt;a href=&quot;http://www.reddit.com/r/askscience/comments/2j3x8m/what_evidence_do_we_have_that_a_last_universal&quot; rel=&quot;nofollow&quot;&gt;/r/askscience&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm really looking for more speculation about physical details of the organism, its environment, and its immediate ancestors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;e.g. How did they (referring to the LUCA and some immediate ancestors) acquire nutrients? What forms of mobility were available to them? How long was it until photosynthesizing organisms emerged?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;mods: If this is too open-ended or too speculative, please let me know where I can redirect this question.&lt;/p&gt;&#xA;" OwnerUserId="9743" LastActivityDate="2014-10-13T14:59:17.973" Title="What do we know about the cellular structure, processes, environment, and immediate ancestors of the last universal common ancestor (LUCA)?" Tags="&lt;evolution&gt;&lt;cell-biology&gt;&lt;microbiology&gt;&lt;archaea&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ClosedDate="2014-12-02T19:49:12.980" ContentLicense="CC BY-SA 3.0" />
  <row Id="23078" PostTypeId="1" CreationDate="2014-10-13T15:52:48.910" Score="4" ViewCount="112" Body="&lt;p&gt;The multivariate breeders equation (MBE) by Lande predicts the change in a trait $\Delta \bar z$ (response) as &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\Delta \bar z = G \beta$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $G$ is a genetic variance-covariance matrix and $\beta$ is a vector of the selection coefficients. What are the limitations on the number of traits the MBE can tolerate? Is there a theoretical limit on the number of traits $G$ and $\beta$ could contain? Or does the calculation lose power with increasing complexity? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Theoretically as an example, could I take the expression of 10000 genes, compare them to fitness to to make a 10000 row $\beta$ vector, and generate a 10000 * 10000 G-matrix from estimates of male and female gene expression in some lines, and then put them through the MBE?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2015-08-13T01:34:40.107" Title="How many traits can a multivariate breeders equation handle?" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23079" PostTypeId="1" CreationDate="2014-10-13T18:36:58.703" Score="2" ViewCount="667" Body="&lt;p&gt;As our society and it's functioning is closely related to the ones of animals, one question arises: Do animals in nature have social status as humans? People often display it publicly, by buying nice cars, searching for women and partners and so on, accumulating wealth and so on. Does similar things happens in nature? How our behavior is similar to animals? &lt;/p&gt;&#xA;" OwnerUserId="9744" LastActivityDate="2014-10-13T18:36:58.703" Title="Do animals have social status as humans in our society?" Tags="&lt;human-biology&gt;&lt;behaviour&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23080" PostTypeId="1" AcceptedAnswerId="23476" CreationDate="2014-10-13T21:05:31.890" Score="2" ViewCount="793" Body="&lt;p&gt;I read two contradictory arguments which both seem logical to me, related to the &lt;em&gt;tree pruning&lt;/em&gt; and &lt;em&gt;hedge trimming&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;You should prune/cut trees only &lt;strong&gt;outside&lt;/strong&gt; the &lt;a href=&quot;http://en.wikipedia.org/wiki/Growing_season&quot; rel=&quot;nofollow&quot;&gt;growing season&lt;/a&gt;, when the tree is &quot;sleeping&quot;. In some countries there is even a law forbidding to cut/prune trees within the growing season!&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;You should trim the hedges only &lt;strong&gt;within&lt;/strong&gt; the growing seasons, when the tree is &lt;em&gt;not&lt;/em&gt; sleeping and thus able to heal the cuts.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Which of these two arguments is true and how are they supported by the plant biology?&lt;/p&gt;&#xA;" OwnerUserId="8198" LastEditorUserId="8198" LastEditDate="2014-10-16T18:42:55.177" LastActivityDate="2014-10-26T00:22:50.410" Title="The biology behind tree pruning and hedge trimming" Tags="&lt;botany&gt;&lt;dendrology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23081" PostTypeId="5" CreationDate="2014-10-13T21:07:46.693" Score="0" Body="&lt;p&gt;Dendrology or xylology is the study of wooded plants (trees, shrubs, and lianas) and the anatomy of wood (Wood anatomy or Xylotomy). It includes direct study of wood structure, as well as deciphering different informations from wood, like studying plant classification and evolution, identification of a wooden object or plant (including forensic study), study of fossil woods, ecological-significance of different anomalous secondary growths, deciphering environmental data in growth ring or any other type growth-records in wood (dendrochronology), economic use of woods, wood disease in living plants, wood deterioration after harvesting, etc.&lt;/p&gt;&#xA;" OwnerUserId="25568" LastEditorUserId="25568" LastEditDate="2016-09-08T18:52:33.183" LastActivityDate="2016-09-08T18:52:33.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23082" PostTypeId="4" CreationDate="2014-10-13T21:07:46.693" Score="0" Body="Dendrology or xylology is the study of wooded plants (trees, shrubs, and lianas) and the anatomy of wood (Wood anatomy or Xylotomy). Includes dendrochronology, i.e. deciphering environmental data in growth ring or any other type growth-records in wood ." OwnerUserId="8198" LastEditorUserId="25568" LastEditDate="2016-09-08T18:52:42.947" LastActivityDate="2016-09-08T18:52:42.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23083" PostTypeId="1" CreationDate="2014-10-13T21:10:33.093" Score="1" ViewCount="835" Body="&lt;p&gt;I am studying evolutionary biology, and been presented with this graph:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Qofm7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am having some difficulties understand its meaning. For a start, why is time measured as a fraction of the population size? Also, what does it mean by allele frequency? Does it mean the frequency of a single allele? But if the first caption it referred to 'frequencies'... Any help? :)&lt;/p&gt;&#xA;" OwnerUserId="9747" LastEditorUserId="3624" LastEditDate="2014-11-24T11:43:30.263" LastActivityDate="2014-11-24T23:32:50.677" Title="Interpretation of graph from evolutionary biology" Tags="&lt;evolution&gt;&lt;homework&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23084" PostTypeId="1" AcceptedAnswerId="23088" CreationDate="2014-10-13T21:16:29.340" Score="4" ViewCount="553" Body="&lt;p&gt;I've been reading this paper entitled &lt;a href=&quot;http://www.nature.com/nature/journal/v503/n7475/full/nature12644.html&quot; rel=&quot;nofollow&quot;&gt;&quot;A high-resolution map of the three-dimensional chromatin interactome in human cells&quot;&lt;/a&gt;, about interactome in 3D chromatin.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We next applied the above algorithm to the &lt;strong&gt;518,032 anchor regions in&#xA;  the human genome&lt;/strong&gt;, with each containing one or a few HindIII&#xA;  restriction fragments (fragments shorter than 2 kilobases (kb) are&#xA;  merged) (Fig. 2a), and uncovered a total of 1,116,312 chromatin&#xA;  interactions with a false discovery rate (FDR) of 0.1&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Simple questions: &lt;strong&gt;what are these anchor regions in the human genome?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How could I group them into types/categories?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="885" LastActivityDate="2016-10-01T18:29:53.793" Title="What are &quot;anchor regions&quot; in the human genome?" Tags="&lt;chromatin&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23085" PostTypeId="1" CreationDate="2014-10-13T21:34:19.170" Score="0" ViewCount="1105" Body="&lt;p&gt;My professor said that light reactions and dark reactions happen at the thylakoid. He did not choose the answer that &quot;both reactions happen at chloroplast&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isn't the thylakoid a part of the chloroplast?&lt;/p&gt;&#xA;" OwnerUserId="3179" LastEditorUserId="6307" LastEditDate="2014-10-14T07:52:00.993" LastActivityDate="2014-10-14T07:52:00.993" Title="Do the light and dark reactions happen at the thylakoid?" Tags="&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23086" PostTypeId="1" AcceptedAnswerId="23094" CreationDate="2014-10-13T21:54:48.810" Score="1" ViewCount="9929" Body="&lt;p&gt;I was popped this questions today, &quot;what is a glycerinated muscle fiber, and what is required for its contraction,&quot; and had little idea. I'm assuming the question is &quot;what's required for its contraction as compared to normal muscle tissue?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's a limited amount of information out there about this. It appears that it is a type of &lt;em&gt;in vitro&lt;/em&gt; system requiring special preparation of typical muscle tissue. I was wondering if anyone here had a little more information. Is this something that's just used in teaching lab exercises?&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2017-10-23T01:59:28.243" Title="What is meant by a muscle fiber being glycerinated?" Tags="&lt;muscles&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23087" PostTypeId="1" AcceptedAnswerId="23090" CreationDate="2014-10-13T22:04:07.687" Score="0" ViewCount="141" Body="&lt;p&gt;So we know that there is a first gene therapy drug in the market out there called Alipogene tiparvovec to address  lipoprotein lipase deficiency (LPLD) at a genetic level. Does this genetic drug target all cell types (except germline) that expresses the LPL gene in the human body or simply the parenchymal cells that process fat? I have not been able to find information specific to Glybera. &lt;/p&gt;&#xA;" OwnerUserId="9748" LastEditorUserId="9748" LastEditDate="2014-10-13T22:24:54.870" LastActivityDate="2014-10-13T22:25:18.367" Title="Cell targets of Glybera" Tags="&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;human-genetics&gt;&lt;biotechnology&gt;&lt;lipids&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23088" PostTypeId="2" ParentId="23084" CreationDate="2014-10-13T22:04:13.587" Score="2" Body="&lt;p&gt;Good question. Anchor regions are regions that connect to the nuclear matrix. More specifically, in eukaryotic organisms, chromatin is anchored to the nuclear matrix by short DNA sequences of about 100-2,000 bp called matrix attachment regions or MAR. To answer the second part of your question, there are many categories (and opinions about those categories) of anchor regions. The most comprehensive way of categorizing these regions however I believe is by whether they are constitutively (always) or transiently (sometimes) bound to the nuclear structure.   &lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-10-13T22:04:13.587" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23090" PostTypeId="2" ParentId="23087" CreationDate="2014-10-13T22:25:18.367" Score="0" Body="&lt;p&gt;Glybera doesn't target all cells, and doesn't target fat processing cells. Glybera is adeno-associated virus 1, which normally infects skeletal muscles. Glybera is delivered by intramuscular injection, so the virus easily infects the muscle tissue. The infected muscle cells produce a variant of lipoprotein lipase that has better activity than normal LPL and secrete it into the bloodstream. Once in the blood LPL can interact with chylomicrons and make them smaller.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22691709&quot; rel=&quot;nofollow&quot;&gt;Here is a paper about viral gene therapy&lt;/a&gt; for LPL deficiency, specifically about glybera, but I don't think it's open access.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-10-13T22:25:18.367" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23091" PostTypeId="2" ParentId="23059" CreationDate="2014-10-13T23:45:35.070" Score="2" Body="&lt;p&gt;You can find examples by using the &quot;drilldown&quot; function at the RCSB PDB homepage:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Click on the number 103921 at the top of the page at &lt;a href=&quot;http://www.rcsb.org&quot; rel=&quot;nofollow&quot;&gt;http://www.rcsb.org&lt;/a&gt; then find the &quot;SCOP Classification&quot; section and then e.g. select &quot;All alpha proteins&quot;.&lt;/p&gt;&#xA;" OwnerUserId="3150" LastActivityDate="2014-10-13T23:45:35.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23092" PostTypeId="1" CreationDate="2014-10-14T01:23:51.183" Score="4" ViewCount="389" Body="&lt;p&gt;Captured this under my stereo microscope. Much more beautiful than appearing on my camera sensor.&#xA;Can someone help me identify it and explore more?&#xA;Also is it having a compound eye ?&lt;/p&gt;&#xA;&lt;p&gt;Location: New Delhi.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sRpBa.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/MQnr9.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bNBCx.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vMA60.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="1110" LastEditorUserId="16866" LastEditDate="2021-05-13T04:14:04.067" LastActivityDate="2021-05-13T04:39:56.133" Title="What is the scientific and common name of this bug?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="23093" PostTypeId="2" ParentId="23085" CreationDate="2014-10-14T04:27:00.597" Score="1" Body="&lt;p&gt;The light dependent reactions involve an electron transport chain with enzymes embedded in the thylakoid membrane. NADPH and ATP are generated in the stroma and water is oxidized in the thylakoid lumen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure if it's correct to say that the light independent reactions occur &quot;at the thylakoid&quot; since, in plants, they could really occur anywhere in the stroma (not necessarily &quot;at&quot; the thylakoid, and certainly not within it). It's possible that the enzymes involved in the light independent reactions are somehow localised at the the stromal side of the thylakoid membrane for efficient use of substrates, but I have no idea if that is actually the case and I don't have time to review any literature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In plants, all of these processes occur in the chloroplast. However, photosynthetic bacteria don't have chloroplasts so you can't categorically say that the photosynthetic reactions occur only within chloroplasts. Cyanobacteria do have thylakoids where the light dependent reactions occur.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-10-14T06:03:02.577" LastActivityDate="2014-10-14T06:03:02.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23094" PostTypeId="2" ParentId="23086" CreationDate="2014-10-14T04:34:40.207" Score="3" Body="&lt;p&gt;From: &lt;a href=&quot;http://www.acad.carleton.edu/curricular/BIOL/classes/bio126/Documents/Lab_5.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.acad.carleton.edu/curricular/BIOL/classes/bio126/Documents/Lab_5.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Glycerination disrupts the membranes of the muscle cells, ruptures mitochondria, and leaches out soluble constituents such as ATP and inorganic ions. However, glycerinated muscle retains the organized structural array of myosin thick filaments and actin thin filaments, actin-associated proteins like troponin and tropomyosin which regulate contraction, and the functional capacity for contraction.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would expect that because the sample has lost ATP and inorganic ions, you would need to supply ATP (the source of energy), $Mg^{2+}$ (which is necessary for ATP hydrolysis) and $Ca^{2+}$ (to induce the contraction). &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-10-14T04:34:40.207" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23095" PostTypeId="1" CreationDate="2014-10-14T09:31:25.360" Score="2" ViewCount="426" Body="&lt;p&gt;I'm curios to know how many times neurons send signals in one second when the brain is highly active (Highly active meaning during difficult problem solving, or any task that might bring the brain to it's higher volume of activity).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;When the mind is highly active, roughly how many neurons become excited in one second?&lt;/strong&gt; The question might also be posed as: &quot;How many action potentials might &quot;occur&quot; in the brain over the course of one second during any form of complex mental process?&quot;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Answers accurate to whatever accuracy we're currently capable of would suit my interests.&lt;/p&gt;&#xA;" OwnerUserId="19073" LastEditorUserId="19073" LastEditDate="2014-10-15T05:24:30.173" LastActivityDate="2014-10-15T05:24:30.173" Title="When the mind is highly active, roughly how many neurons become excited in one second?" Tags="&lt;brain&gt;&lt;synapses&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="23096" PostTypeId="1" CreationDate="2014-10-14T12:30:27.840" Score="1" ViewCount="80" Body="&lt;p&gt;In coma, there is the medullary depression (stage of agony). &#xA;Spontaneous respiration and circulation cease i.e. vasomotor center. &#xA;There is no full circulatory and respiratory support.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume you could stimulate and coordinate fully the autonomic nervous system of the heart. &#xA;You know exactly which pacemaker cells and pathways are blocked in the particular coma patient. &#xA;I have in mind Schumacher's case - where you have head injury. &#xA;I think you should consider, in his case, the pressure of the head also if you can restore circulation and respiration artificially. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some neurologists say that it is practically very difficult to wake a person if he has been in coma for six months. &#xA;I would like to understand this.&#xA;I think it is because of atrophy of muscles and probably something with atherosclerotic changes. &#xA;However, I am still interested in your opinion about the theoretical situation - if you can restore heart and respiration centre, can the recovery start?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the limitations of restoring the function of the body by restoring the circulation and respiration i.e. vasomotor centers after long stay in coma?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-10-14T12:30:27.840" Title="Recovering Coma patient with theoretical full knowledge of heart function" Tags="&lt;cardiology&gt;&lt;neurology&gt;&lt;pathophysiology&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23098" PostTypeId="1" AcceptedAnswerId="23099" CreationDate="2014-10-14T14:44:19.267" Score="7" ViewCount="598" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The effective population size ($N_e$) is a central concept of evolutionary biology and is influenced by several parameters. For example: sex ratio bias affects $N_e$ $\left(N_e = \frac{4N_mN_f}{N_m+N_f}\right)$ and varying population size over time influences $N_e$ $\left(N_e = \frac{n}{\sum_{i=1}^n\frac{1}{N_i}}\right)$. &lt;a href=&quot;https://biology.stackexchange.com/questions/15746/effective-population-size-and-overlapping-generations&quot;&gt;There&lt;/a&gt; is a post on how overlapping generations influences population size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Selection also influences the effective population size. Intuitively, I'd expect that the higher is the fitness variance, the lower is the effective population size as fewer individuals contribute to the next generation. &lt;strong&gt;Am I right? How (what is the mathematical formulation) does fitness variance influences the effective population size?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-09-08T16:58:21.613" Title="Effects of selection on effective population size" Tags="&lt;evolution&gt;&lt;ecology&gt;&lt;natural-selection&gt;&lt;theoretical-biology&gt;&lt;population-dynamics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23099" PostTypeId="2" ParentId="23098" CreationDate="2014-10-14T16:21:03.190" Score="3" Body="&lt;p&gt;From &lt;a href=&quot;http://www.sinauer.com/a-primer-of-ecological-genetics.html&quot; rel=&quot;nofollow&quot;&gt;Conner and Hartl's &lt;em&gt;A primer of ecological genetics&lt;/em&gt;&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Any variance in reproductive success among individuals greater than&#xA;  random expectations, a commonplace concurrence in natural populations,&#xA;  reduces effective population size.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So yes, selection does reduce the effective population size and for the reason you suggest - it removes some individuals from the mating pool/ reduces their contribution to the next generation. Mathematically it can be derived as&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$N_e \approx \frac{ 8N_a}{V_m + V_f + 4 }$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $V_m$ and $V_f$ are sex-specific variances of offspring production (males are often more variable in reproductive success than females). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They give an example of selection affecting $N_e$, in a population of deer 33 males had four times the variance ($V_m$ = 41.9) in reproductive success of 35 females where variance was $V_f$ = 9.1. Thus effective population size was&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$N_e \approx \frac{ 8 * (33 + 35)}{41.9 + 9.1 + 4 } = 9.9$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The notation $N_a$ is the &lt;em&gt;actual&lt;/em&gt; number of individuals in the population. This can be seen in the calculation of effective population size when the number of males and females are not equal&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$N_e = \frac{4 N_m N_f}{N_m + N_f} = \frac{4 N_m N_f}{N_a}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example is a population of 80 males and 80 females compared to a population of 70 males and 90 females. Both populations have equal sizes but effective population size is reduced by unequal sex ratios&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$N_e = \frac{4 * 80 * 80}{160} = 160 \neq \frac{4 * 70 * 90}{160} = 157.5$ &lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-10-15T08:28:56.110" LastActivityDate="2014-10-15T08:28:56.110" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="23100" PostTypeId="1" AcceptedAnswerId="23104" CreationDate="2014-10-14T16:23:51.907" Score="2" ViewCount="1754" Body="&lt;p&gt;Is the result of meiosis ONLY the sex gametes (male and female) which later meet to form a somatic cell?&#xA;Sometimes I feel as if my book is hinting towards meiosis is the process where sperm cells meet oocytes?? I'm a bit confused.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2014-10-15T07:30:37.813" Title="What is the result of meiosis?" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;chromosome&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23101" PostTypeId="2" ParentId="20992" CreationDate="2014-10-14T16:41:12.897" Score="1" Body="&lt;p&gt;&lt;em&gt;The Question:&lt;/em&gt; Why can't we just take enough pills to obtain these vitamins and minerals?&lt;/p&gt;&#xA;&lt;h3&gt;We don't know enough about nutrition.&lt;/h3&gt;&#xA;&lt;p&gt;There are about &lt;a href=&quot;http://www.nutrientsreview.com/glossary/essential-nutrients&quot; rel=&quot;nofollow noreferrer&quot;&gt;45 essential nutrients&lt;/a&gt;, which you need to consume to be healthy and live. You can get all of them from food without thinking about them. I'm not sure if currently there are a lot of supplements on the market that contain all essential nutrients. Also, we may currently still not know which all nutrients are essential, so we may miss some when designing multivitamin/mineral pills.&lt;/p&gt;&#xA;&lt;h3&gt;Food is easier!&lt;/h3&gt;&#xA;&lt;p&gt;A healthy adult who regularly consumes both plant and animal foods in reasonable variety and amount does not really need any vitamin/mineral supplements. And you need to eat foods to get calories. Yes, you could make supplements to substitute calorific content; imagine some sort of carbohydrate powder. But why complicate this when food is readily available, much cheaper, and easier?&lt;/p&gt;&#xA;" OwnerUserId="4025" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-07-06T17:19:08.913" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23103" PostTypeId="1" AcceptedAnswerId="23119" CreationDate="2014-10-14T18:32:45.163" Score="1" ViewCount="297" Body="&lt;p&gt;I've been studying immunology on my own lately and I would like to know if the macrophages and the other components of the innate immune system are capable of identifying all foreign antigens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I understand the innate immune system is responsible for activating the adaptive immune response that will produce antibodies. So the innate immune system should be able to identify new antigens, antigens that the body has never seen before.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If that's the case, how does it work? Does everything &quot;alive&quot;, from virus to bacteria, present the same molecular pattern that is responsible for triggering an innate immune response? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="9750" LastActivityDate="2014-10-15T05:28:14.847" Title="Is the innate immune system capable of identifying all foreign antigens?" Tags="&lt;human-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23104" PostTypeId="2" ParentId="23100" CreationDate="2014-10-14T18:46:31.983" Score="4" Body="&lt;p&gt;In principle, &lt;a href=&quot;http://en.wikipedia.org/wiki/Meiosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Meiosis&lt;/a&gt; is only the process in which the haploid egg or sperm are generated. Have a look at this figure, which shows Meiosis I and II (from the Wikipedia):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HNhXl.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During Meiosis I homologous recombination between homologous chromosomes can happen, the chromosomes are then distributed normally among the daughter cells. In Meiosis II the cells split again and here the sister chromatids are divided and the haploid gametes form. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the oocytes the process is in principle the same, but the cells get arrested in the so-called diplotene stage of Meiosis I (picture from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK9901/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EJOxz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the diplotene stage the chromatin is decondensated and transcriptionally active, this helps maintaining a correct chromosome structure, as the diplotene stage can last up to 50 years. When the cell receives the hormonal signal to enter the fallopian tube, Meiosis I is finished. The resulting cells are not divided symmetrical, building one big oocyte and one polar body containing the second set of chromosomes. Most vertebrate cells are arrested in this stage again until they are fertilized. Then another asymmetrical division is done, leading to a haploid cell with two polar bodies. This oocyte is then fertilized.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This process can happen almost at the same time in a lot of vertebrate species, including humans. This is probably what was meant by your textbook.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For further reading I can recommend: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK9901/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Meiosis and Fertilization&lt;/a&gt; from the NIH bookshelf.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-10-15T07:30:37.813" LastActivityDate="2014-10-15T07:30:37.813" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23107" PostTypeId="1" CreationDate="2014-10-14T21:10:48.987" Score="3" ViewCount="394" Body="&lt;p&gt;Would testes be produced? If SRY is functional, can it produce other proteins that can direct the production of testes, which may or may not be sterile?&lt;/p&gt;&#xA;" OwnerUserId="4863" LastActivityDate="2014-10-15T07:27:24.650" Title="What would happen if there were no SOX9 in an XY human?" Tags="&lt;development&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23108" PostTypeId="2" ParentId="15746" CreationDate="2014-10-14T22:21:33.077" Score="1" Body="&lt;p&gt;There are many different ways to do this, depending on what assumptions you make on e.g. stable age structure, distribution of offspring, haploidy/diploidy, population growth etc. As you probably know, there are also two main approaches to effective population sizes, namely ones based on:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;the rate of inbreeding ($N_{e,i}$)&lt;/li&gt;&#xA;&lt;li&gt;the increase in variance of allele frequencies ($N_{e,v}$), and they can sometimes differ a bit from each other.   &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;An early attemp to calculate effective population size with overlapping generations comes from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1212678/&quot; rel=&quot;nofollow&quot; title=&quot;Felsenstein. 1971. Inbreeding and Variance Effective Numbers in Populations with Overlapping Generations. Genetics 68(4): 581–597. &quot;&gt;Felsenstein (1971)&lt;/a&gt;, which is based on life table information. This paper includes several derivations, both on inbreeding $N_e$ and variance $N_e$. As an example, the formula of inbreeding $N_e$ for a diploid population is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$N_e = \frac{N_1T}{1 + \sum_i^\inf l_i s_id_i v_{i+1}^2}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here, $T$ is the generation time, $l_i$ is the survival up to age i, $s_i$ is the survival from age i, $d_i$ is the probability of death at the end of age i (i.e. 1-$s_i$), and $v_{i+1}$ is the reproductive value of individuals in stage i+1. However, this is assuming a constant population size and a stable age distribution, so some rather restrictive assumptions. The paper also includes models for haploid populations, and I haven't gone through it carefully.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A couple of more recent papers that calculate $N_e$ for overlapping generations are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1450432/&quot; rel=&quot;nofollow&quot; title=&quot;Engen et al. 2005. Effective Size of a Fluctuating Age-Structured Population. Genetics 170(2): 941–954.&quot;&gt;Engen et al. (2005)&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17683430&quot; rel=&quot;nofollow&quot; title=&quot;Engen et al. 2007. Effective size of fluctuating populations with two sexes and overlapping generations. Evolution 61(8):1873-1885&quot;&gt;Engen et al. (2007)&lt;/a&gt;. These papers use diffusion approximations to derive several formulas for $N_e$ under different assumptions, for age-structured density independent populations. One model for a haploid population in a fluctuating environment is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\begin{align} &#xA;N_e &amp;amp; = \frac{N}{\sigma_d^2T} \text{, with} \\&#xA;\sigma_d^2 &amp;amp; \approx \sum_{i=0}^k \frac{\lambda^{-2}}{u_i} \left[\left(\frac{\delta\lambda}{\delta b_i}\right)^2\sigma_i^2 + \left(\frac{\delta\lambda}{\delta s_i}\right)^2 s_i(1-s_i) + 2\left(\frac{\delta\lambda}{\delta b_i}\right)\left(\frac{\delta\lambda}{\delta s_i}\right) c_i \right] &#xA;\end{align}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $T$ is the generation time and $\sigma_d^2$ is the demographic variance. In the lower equation, $\lambda$ is the deterministic growth rate (dominant eigenvalue), $u_i$ is the proportion of the population in stage i (a component of the stable age distribution), $b_i$ is the expected number of offspring with variance $\sigma_i^2$, $s_i$ is the survival rate of stage i (with binomial variance), and $c_i$ is the covariance between reproduction and survival. You really need to dive into these papers to fully understand how these equations are derived and how the variables are defined (will take up far to much space here). However, at its core, it is using a diffusion approximation on an allele at a selectively neutral locus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many other papers out there deriving effective population sizes, under different assumptions and restrictions, but the ones cited above should be a good starting point, and by looking at citations to and from these you should get a decent overview of the topic. Many textbooks also cover ways to calculate effective population sizes with overlapping generations, e.g. &lt;a href=&quot;http://books.google.se/books/about/Genetics_of_Populations.html?id=pBq69Luwf7UC&amp;amp;redir_esc=y&quot; rel=&quot;nofollow&quot; title=&quot;Hedrick. 2011. Genetics Of Populations. Jones &amp;amp; Bartlett Learning&quot;&gt;Hedrick (2011)&lt;/a&gt; and &lt;a href=&quot;http://evolution.gs.washington.edu/pgbook/pgbook.html&quot; rel=&quot;nofollow&quot; title=&quot;Felsenstein. 2013. Theoretical Evolutionary Genetics&quot;&gt;Felsenstein (2013, free pdf)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-01-12T12:18:18.100" LastActivityDate="2015-01-12T12:18:18.100" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23109" PostTypeId="1" CreationDate="2014-10-14T22:46:47.587" Score="0" ViewCount="174" Body="&lt;p&gt;I'm in my third week of university, and a large number of people I know, including myself, still have &quot;fresher's flu&quot;, which is probably just a cold and a cough. My lectures are constantly punctuated by the sound of violent coughing. What I don't understand is: how do colds ever go away, given these conditions? Surely by the time you've gotten rid of your cold you've passed it onto someone sitting near you in a lecture, who could then spread it back to you directly or indirectly later? Why don't we have an infinite recursion of colds, coughs and other minor infections throughout the year?&lt;/p&gt;&#xA;" OwnerUserId="8642" LastActivityDate="2014-10-15T16:17:36.913" Title="How do colds and flu not infinitely recur?" Tags="&lt;pathology&gt;&lt;infection&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23110" PostTypeId="1" AcceptedAnswerId="23142" CreationDate="2014-10-14T23:20:01.493" Score="7" ViewCount="86571" Body="&lt;p&gt;I have heard that offspring can't grow taller than either of their parents but I've also heard that sometimes some gene activation can skip generations. Is it possible for a child to grow taller than their tallest parent?&lt;/p&gt;&#xA;" OwnerUserId="5491" LastEditorUserId="3624" LastEditDate="2015-08-12T13:02:02.593" LastActivityDate="2016-02-20T20:57:43.913" Title="Is it possible for a child to grow taller than their tallest parent?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;human-genetics&gt;" AnswerCount="3" CommentCount="7" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23111" PostTypeId="2" ParentId="23110" CreationDate="2014-10-15T00:38:39.183" Score="1" Body="&lt;p&gt;Yes it is quite possible, recall nature vs nurture. I myself am slightly taller than both of my parents by about a head. As long as you have sufficient nutrition it should be quite possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And what you said about gene activation skipping generations is quite true- it can indeed happen, and if the gene responsible for height is not expressed in the parents but is in their offspring then it will also be more likely for the child to grow taller than their parent. &lt;/p&gt;&#xA;" OwnerUserId="9730" LastEditorUserId="9730" LastEditDate="2014-10-15T00:48:14.943" LastActivityDate="2014-10-15T00:48:14.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23115" PostTypeId="1" AcceptedAnswerId="23118" CreationDate="2014-10-15T04:15:17.883" Score="1" ViewCount="749" Body="&lt;p&gt;I read the following statement in &lt;a href=&quot;http://www.ibtimes.com.au/top-10-factors-why-hiv-vaccine-or-cure-very-difficult-medical-researchers-create-1314253&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Vaccines are designed to protect against invaders that are encountered&#xA;  rarely - not all the time&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is it true? If yes, why?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="9750" LastEditorUserId="87" LastEditDate="2015-05-29T04:18:45.977" LastActivityDate="2015-05-29T04:18:45.977" Title="True or False: Vaccines are designed to protect against invaders that are encountered rarely, not all the time" Tags="&lt;immunology&gt;&lt;vaccination&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23117" PostTypeId="2" ParentId="23107" CreationDate="2014-10-15T04:59:41.030" Score="1" Body="&lt;p&gt;Quoting the abstract of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16467253&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper verbatim:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sox9 is an Sry-box-containing gene that encodes a transcriptional&#xA;  activator. During mouse gonadogenesis, Sox9 is detected in the male&#xA;  gonad at 11.5 days postcoitus (dpc). At 12.5 dpc, testicular cords&#xA;  form, morphologically distinguishing the male gonad from the ovary.&#xA;  From this stage onwards, Sox9 expression is restricted to the Sertoli&#xA;  cell lineage and persists in the adult. Humans with heterozygous&#xA;  mutations in SOX9 develop a skeletal syndrome known as campomelic&#xA;  dysplasia. Furthermore, most XY SOX9 heterozygotes show variable&#xA;  male-to-female sex reversal, implicating SOX9 in testis development.&#xA;  Sox9 heterozygous knockout mice die at birth with a syndrome similar&#xA;  to that of human campomelic dysplasia. In contrast to humans, XY&#xA;  Sox9+/- mice form normal appearing testes. Germ-line knockout of Sox9&#xA;  using a conditional null allele provides a tool for generating Sox9-/-&#xA;  mice by simple genetic crosses. However, Sox9-/- mice die soon after&#xA;  11.5 dpc because of cardiovascular defects. In vitro culture of the urogenital ridges of XY Sox9-/- results in gonads lacking testicular&#xA;  cords and Sertoli cell marker expression, but with the expression of&#xA;  ovarian-specific markers. Therefore, Sox9 is essential for diverting&#xA;  an intrinsically ovarian program of organogenesis toward testis&#xA;  formation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.informatics.jax.org/marker/MGI:98371&quot; rel=&quot;nofollow&quot;&gt;MGI page&lt;/a&gt; on Sox9:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Null mutant heterozygotes and conditional knockout mutants display&#xA;  perinatal lethality with cleft palate, hypoplasia and distortion of&#xA;  numerous cartilage-derived skeletal structures, and premature&#xA;  mineralization in many bones. Specific conditional knockout mutations&#xA;  are sex-reversed.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-10-15T04:59:41.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23118" PostTypeId="2" ParentId="23115" CreationDate="2014-10-15T05:10:37.137" Score="5" Body="&lt;p&gt;Not true. Vaccines were initially made for the highly contagious diseases that used to cause epidemics (which obviously means they were not &lt;em&gt;rare&lt;/em&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The efficacy of a vaccine depends on multiple factors which includes adaptability of the pathogen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;all-the-time&lt;/em&gt; encountered pathogen that the article is talking about is HIV; the reason for why no effective vaccine exists for it is because it has high mutation rate.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-10-15T05:18:55.443" LastActivityDate="2014-10-15T05:18:55.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23119" PostTypeId="2" ParentId="23103" CreationDate="2014-10-15T05:19:59.660" Score="2" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;TL;DR the huge block of text:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The innate immune system only recognizes certain antigens, called PAMPs.&lt;/li&gt;&#xA;&lt;li&gt;The activate immune system &lt;em&gt;usually&lt;/em&gt; requires the immune system, but it can get around this in some cases.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;You're on the right track.&lt;/p&gt;&#xA;&lt;h2&gt;Pathogen-associated molecular patterns (PAMPs)&lt;/h2&gt;&#xA;&lt;p&gt;Innate immune cells such as macrophages and denritic cells (DCs) only recognize certain pathogen-associated molecular patterns (PAMPs), and this occurs primarily through membrane-bound receptors called Toll-Like Receptors (TLRs). Diversity of PAMPs is extremely limited compared to the extraordinary diversity in recognition by the active immune system. However, they include many molecules and classes of molecules that are essential for certain pathogens, such as flagellin, lipopolysaccharide, and viral double-stranded RNA.&lt;/p&gt;&#xA;&lt;p&gt;To answer some of your question right away, the immune system can't adapt, but it can recognize antigens that the body hasn't seen before, because the set of antigens it can recognize (the PAMPs) are dictated by the genes associated with Toll-Like Receptors and other &amp;quot;Pattern-Recognition Receptors&amp;quot;.&lt;/p&gt;&#xA;&lt;h2&gt;Exception 1: T cell anergy&lt;/h2&gt;&#xA;&lt;p&gt;The major link between the innate and active immune systems that you mentioned is through the presentation of antigens to T helper cells in lymph nodes by DCs: DCs present antigens (digested parts of pathogens) to T helper cells through a process called antigen cross-presentation.&lt;/p&gt;&#xA;&lt;p&gt;When this happens, the T helper cell is activated through a series of chemical exchanges between the DC and the T helper cell, with two that are important to mention here: 1) the T cell recognizes the antigen–MHC class II complex on the DC (called T cell stimulation), and 2) the T cell receives a signal (called co-stimulation). The first signal only requires cross-presentation and recognition by a T cell. But for the DC to release the co-stimulatory signal, Toll-Like Receptors (TLRs) on its surface need to have recognized a PAMP.&lt;/p&gt;&#xA;&lt;p&gt;With these interactions (plus some more), the T cell will begin proliferating. However, immunology is very nuanced; you can probably find exceptions to every sentence I just wrote (I see a lot even while writing this). It turns out that a T cell can still be activated even without co-stimulation if its own stimulation is strong enough. This occurs through a process called T cell anergy. Activation of an anergic T cell—that is, one that was activated but did not receive a co-stimulation signal—has to do with the autocrine and paracrine nature of a signal called IL-2, which T cells normally produce only small amounts of but produce much more when fully stimulated.&lt;/p&gt;&#xA;&lt;h2&gt;Exception 2: B cells T-independent activation&lt;/h2&gt;&#xA;&lt;p&gt;But T cells are only half of the active immune system. It turns out that B cell activation follows similar rules, though not through DCs. B cell activation usually occurs with help from activated T helper cells (only one that recognizes the antigen the B cell is specific for). However, B cells can become activated without T cell help in two situations: an antigen binds to the B cell receptor and to a TLR, or 2) the B cell receptors become saturated with highly repetitive epitopes. Situation #2 technically occurs without help of the innate immune system.&lt;/p&gt;&#xA;&lt;p&gt;So you're mostly correct that the active immune system requires innate immune system help, except that there are these two exceptions. And since immunology has so many exceptions, there are likely to be more.&lt;/p&gt;&#xA;" OwnerUserId="9652" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-10-15T05:28:14.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23120" PostTypeId="2" ParentId="23115" CreationDate="2014-10-15T05:20:28.270" Score="4" Body="&lt;p&gt;The source article had several major errors in it. I wouldn't trust any of it.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Vaccines are designed to protect against invaders that are encountered rarely - not all the time.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is one of the major errors. There is a vaccine for chicken pox now - an infection which affected approximately 4,000,000 cases per year in the US before the vaccine. That is a very high number of children.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The overall HPV prevalence was 26.8% among US females aged 14 to 59 years before the vaccine. (This vaccine refutes two major errors in the paper.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Measles, mumps, German Measles, Influenza, Haemophilus influenzae, and Pneumoccocal pneumonia were all common before vaccines for them were developed. Those are just the ones I can think of off the top of my head.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Factors that influence the ability to make a vaccine against a pathogen include the mechanism of pathogenicity, the ability to render the vaccine less harmful than the wild-type illness (such as polio), the ability to mass produce easily, reliably, etc. &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-10-15T05:20:28.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23121" PostTypeId="1" AcceptedAnswerId="23145" CreationDate="2014-10-15T05:21:09.503" Score="2" ViewCount="545" Body="&lt;p&gt;Is protein kinase-A located in the cytosol/cytoplasm of cells or in the plasma membrane?  Also, is it considered a receptor molecule since it is dependent on cAMP?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any and all help is appreciated. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="9762" LastEditorUserId="5144" LastEditDate="2014-10-15T16:07:10.017" LastActivityDate="2014-10-16T11:49:10.053" Title="Localization of Protein Kinase-A" Tags="&lt;cell-biology&gt;&lt;cell-signaling&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23122" PostTypeId="1" AcceptedAnswerId="23124" CreationDate="2014-10-15T05:24:38.593" Score="1" ViewCount="263" Body="&lt;p&gt;I've asked a lab colleague the same question. She said, it would loosen the bacterial cells in the LB medium and plasmids would come out. Is that true? and why?&lt;/p&gt;&#xA;" OwnerUserId="8142" LastActivityDate="2016-04-16T04:55:26.717" Title="Does adding antibiotic after 5-10 mins of innoculation affect the protein yield or growth?" Tags="&lt;molecular-biology&gt;&lt;microbiology&gt;&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23123" PostTypeId="2" ParentId="23121" CreationDate="2014-10-15T05:41:12.793" Score="1" Body="&lt;p&gt;It is present throughout the cytosol but can also be anchored to plasma membrane and mitochondria via indirect interactions. Can also be translocated to the nucleus. (See &lt;a href=&quot;http://www.uniprot.org/uniprot/P17612#section_comments&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not called a receptor for cAMP (though the mechanism is homologous). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-10-15T05:41:12.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23124" PostTypeId="2" ParentId="23122" CreationDate="2014-10-15T05:54:00.683" Score="1" Body="&lt;p&gt;That is not true. If you had forgotten to add the antibiotic before inoculation then you can add it before the bacteria starts growing. Make sure you add it when the bacteria is still in &lt;strong&gt;lag phase&lt;/strong&gt;. If you add it later then it won't be effective as some non-resistant (non-transformed) bacteria would have already expanded their population. Ampicillin and kanamycin are best effective when the bacteria are growing. Even though these antibiotics are considered bacteriocidal, you would end up having unnecessary biomass in your culture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So 5min delay for &lt;em&gt;E.coli&lt;/em&gt; is not an issue. (I think this happens to all of us: forgetting to add antibiotic). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-04-16T04:55:26.717" LastActivityDate="2016-04-16T04:55:26.717" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23128" PostTypeId="2" ParentId="23107" CreationDate="2014-10-15T07:27:24.650" Score="1" Body="&lt;p&gt;SOX9 is indeed the factor which is important for the developent of the sexual organs and not only for men, but also for women. Expression of SOX9 regulates the expression of the anti-Müllerian Hormone, which inhibits the formation of the female reproduction system. See reference 1 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations in or around (in regulatory regions) of the SOX9 gene lead to severe developmental changes and to the genetic disorder &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Campomelic_dysplasia&quot; rel=&quot;nofollow&quot;&gt;Campomelic dysplasia&lt;/a&gt;&quot;. The disorder leads to changes in the bones and also in the sex determination, it is often lethal in the neonatal period due to respiratory problems. Have a look into reference 2 for more details. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In mice, the complete loss of SOX9 is embryonical lethal, have a look at reference 3 for details. Although there are no data available for humans (for obvious ethical reasons) I assume that the effect is the same. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Development of testis starts by the activation of SOX9 by the testis determination factor. SOX9 in turn activates a number of other transcription factors (have a look into references 4 and 5 for details) which finally lead to the development of the testis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations in SOX9 in men (with XY chromosomes) also lead to the reversal of the sex, meaning these individuals will develop female reproduction organs (see reference 4). It has also been shown that female mice will develop testis when SOX9 is induced in these animals (see reference 6). You can also have a look into the &lt;a href=&quot;http://omim.org/entry/608160&quot; rel=&quot;nofollow&quot;&gt;OMIM&lt;/a&gt; database for an extensive review.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9774680&quot; rel=&quot;nofollow&quot;&gt;Direct interaction of SRY-related protein SOX9 and steroidogenic&#xA;factor 1 regulates transcription of the human anti-Müllerian hormone&#xA;gene.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7666392&quot; rel=&quot;nofollow&quot;&gt;A clinical and genetic study of campomelic dysplasia.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3776/43w245vh_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Sex determination: a tale of two Sox genes&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19429785&quot; rel=&quot;nofollow&quot;&gt;The PGD2 pathway, independently of FGF9, amplifies SOX9 activity in&#xA;Sertoli cells during male sexual differentiation.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16700629&quot; rel=&quot;nofollow&quot;&gt;Fgf9 and Wnt4 act as antagonistic signals to regulate mammalian sex&#xA;determination.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3776/w7lpgloc_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Sox9 induces testis development in XX transgenic mice&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-15T07:27:24.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23131" PostTypeId="2" ParentId="4971" CreationDate="2014-10-15T10:12:21.423" Score="1" Body="&lt;p&gt;LUCA was the LAST universal ancestor not the first.  Naturally it competed with other extinct species.   My reseach suggests that LUCA was resulted from the fusion of 2 genomes.  The evidence for this is that on reconstructing the amino acid sequences for LUCA enzymes we find some contain no cystine but do contain tryptophan or the opposite. &lt;/p&gt;&#xA;" OwnerUserId="9770" LastActivityDate="2014-10-15T10:12:21.423" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23132" PostTypeId="1" CreationDate="2014-10-15T10:17:30.600" Score="1" ViewCount="105" Body="&lt;p&gt;This question does not assume that &lt;em&gt;we are meant to be carnivores&lt;/em&gt; in the first place; In fact I have no idea to which category we belong to anyway! There are several posts online indicating that classifying humans as carnivores and pointing to our canine teeth as evidence might be fallacious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, the fact that Hippos, the largest canine teeth of any land mammal, are herbivores indicates there are exceptions to this view. A couple of other animals like the Gorilla are also herbivores with big and sharp canines. I have also read about the lack of cellulace production in humans as a counterargument to the above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To what category would we fit in to? What evidence is required to support this idea? Do scientists agree upon a common theory?&lt;/p&gt;&#xA;" OwnerUserId="9769" LastActivityDate="2014-10-15T10:17:30.600" Title="Is Canine teeth enough evidence to prove that one is a Carnivore?" Tags="&lt;human-biology&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23133" PostTypeId="1" AcceptedAnswerId="23138" CreationDate="2014-10-15T12:16:28.620" Score="0" ViewCount="1813" Body="&lt;p&gt;On Wikipedia article about &lt;a href=&quot;https://en.wikipedia.org/wiki/Urine_specific_gravity&quot; rel=&quot;nofollow&quot;&gt;Urine specific gravity&lt;/a&gt; we can read:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A specific gravity greater than 1.035 is consistent with &lt;strong&gt;frank dehydration&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What is &lt;em&gt;frank dehydration&lt;/em&gt;? How it is different than regular dehydration?&lt;/p&gt;&#xA;" OwnerUserId="1195" LastEditorUserId="5144" LastEditDate="2014-10-15T12:18:56.963" LastActivityDate="2014-10-15T13:51:33.263" Title="What is frank dehydration?" Tags="&lt;terminology&gt;&lt;dehydration&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23135" PostTypeId="1" AcceptedAnswerId="30889" CreationDate="2014-10-15T13:12:35.987" Score="7" ViewCount="491" Body="&lt;p&gt;Sexual reproduction can be feasible with anisogamy (gametes of different sizes i.e. genders) or isogamy (gametes of same size i.e. mating types) or with undifferentiated gametes (i.e. true random mating; although I have to confess that I am not aware of such example).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;De novo evolution of sexual reproduction happened several times independently. &lt;strong&gt;What seem to be the most ancestral states of gamete differentiation (isogamy or anisogamy)?&lt;/strong&gt;. Does it differ between lineages?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3624" LastEditDate="2016-01-21T16:13:46.823" LastActivityDate="2016-01-21T16:13:46.823" Title="What is most ancestral: isogamy or anisogamy?" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;natural-selection&gt;&lt;sex&gt;&lt;sexual-reproduction&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23136" PostTypeId="1" CreationDate="2014-10-15T13:18:14.010" Score="2" ViewCount="127" Body="&lt;p&gt;Most (maybe all?) species that reproduce sexually have either genders (anisogamy) or mating types (isogamy). There exist today many different type of sexual determination system. There is a whole complicated continuum from species where the gender is exclusively determined genetically (genetic determination system, GSD) to those where the gender is determined by the environment (environment determination system, ESD).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Knowing that genders (and mating types) evolved several independently, &lt;strong&gt;what seem to be the ancestral states of sex determination system?&lt;/strong&gt; Where the first sexually reproducing lineages GSD or ESD? Does it differ between lineages? &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-10-17T12:58:07.693" LastActivityDate="2014-10-17T12:58:07.693" Title="Ancestral states of sex determination system" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;natural-selection&gt;&lt;sex&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23137" PostTypeId="2" ParentId="23092" CreationDate="2014-10-15T13:36:08.873" Score="2" Body="&lt;p&gt;It belongs to &lt;a href=&quot;http://en.wikipedia.org/wiki/Pentatomidae&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pentatomidae&lt;/a&gt; family. More on the Wiki page&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://www.britishbugs.org.uk/heteroptera/Pentatomidae/Pentatomidae_images/forest_bug_1.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.707" LastActivityDate="2014-10-15T13:36:08.873" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23138" PostTypeId="2" ParentId="23133" CreationDate="2014-10-15T13:51:33.263" Score="4" Body="&lt;p&gt;&quot;Frank dehydration&quot; is not really a regular medical term. You can suspect this by using Google search with &quot;frank dehydration&quot; in quotes and &lt;a href=&quot;https://www.google.com/search?num=100&amp;amp;newwindow=1&amp;amp;site=&amp;amp;source=hp&amp;amp;q=site%3Agov%20%22frank%20dehydration%22&amp;amp;oq=site%3Agov%20%22frank%20dehydration%22&amp;amp;gs_l=hp.12...1209.14004.0.19437.28.28.0.0.0.0.409.3387.1j20j4-1.22.0....0...1c.1.55.hp..21.7.1035.TGsbGVv3Mmg&quot; rel=&quot;nofollow&quot;&gt;site:gov&lt;/a&gt; (only 3 websites showing up) and &lt;a href=&quot;https://www.google.com/search?num=100&amp;amp;newwindow=1&amp;amp;q=site%3Aedu%20%22frank%20dehydration%22&amp;amp;oq=site%3Aedu%20%22frank%20dehydration%22&amp;amp;gs_l=serp.3...52488.53656.0.53985.6.6.0.0.0.0.23.68.6.6.0....0...1c.1.55.serp..6.0.0.cu6zFhhPgHY&quot; rel=&quot;nofollow&quot;&gt;site:edu&lt;/a&gt; (2 websites) operators.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term &quot;frank dehydration&quot; as an informal term can refer to &quot;obvious,&quot; &quot;actual,&quot; &quot;test-confirmed&quot; dehydration as opposed to feeling dehydrated or thirsty. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tests to confirm dehydration include a combination of the body exam (dry mouth, prolonged skin turgor, decreased body weight), urine tests (dark urine, increased urine specific gravity, decreased urination frequency and 24-hour urine volume) and blood tests (increased sodium levels - hypernatremia).&lt;/p&gt;&#xA;" OwnerUserId="4025" LastActivityDate="2014-10-15T13:51:33.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23139" PostTypeId="2" ParentId="21719" CreationDate="2014-10-15T14:23:30.503" Score="3" Body="&lt;p&gt;Fats include free fatty acids and their compounds with glycerol: mono-, di- and triglycerides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a cooking context, fats refer to solid fats, and oils to fats that are liquid at room temperature. Most of them contain triglycerides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fats belong to a broader group--lipids--, which are substances that are usually not soluble in water and usually soluble in certain organic solvents, such as ether or acetone. Besides fats, lipids include sterols (cholesterol, plant sterols), waxes, lipid-soluble vitamins (A, D, E, K) and steroid hormones (aldosterone, corticosterone, etc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples of complex lipids are phospholipids, glycolipids and lipoproteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fats and lipids are often used as synonyms. However, you usually say dietary fats and blood lipids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/lipids.htm&quot; rel=&quot;nofollow&quot;&gt;http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/lipids.htm&lt;/a&gt;&#xA;&lt;a href=&quot;http://biology.about.com/od/molecularbiology/ss/lipids.htm&quot; rel=&quot;nofollow&quot;&gt;http://biology.about.com/od/molecularbiology/ss/lipids.htm&lt;/a&gt;  &lt;/p&gt;&#xA;" OwnerUserId="4025" LastEditorUserId="4025" LastEditDate="2014-10-20T16:26:02.590" LastActivityDate="2014-10-20T16:26:02.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23140" PostTypeId="1" AcceptedAnswerId="23302" CreationDate="2014-10-15T14:46:01.210" Score="1" ViewCount="545" Body="&lt;p&gt;&lt;strong&gt;Are there multicellular isogamous species?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Seeking through the examples of &lt;a href=&quot;http://en.wikipedia.org/wiki/Isogamy&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; I would tend to think that there are no multicellular isogamous species.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-10-19T17:22:04.190" LastActivityDate="2014-10-19T17:35:44.090" Title="Are there multicellular isogamous species?" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;natural-selection&gt;&lt;sex&gt;&lt;gamete&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23141" PostTypeId="1" CreationDate="2014-10-15T14:53:40.177" Score="3" ViewCount="61" Body="&lt;p&gt;I have question about Gibson assembly. I have done it several times and it always worked okay for us, but now I want to assemble together a fragment which has sequence like this: 5'CTTTTTCTTCGTCGAAAAAGGCAATAAAAATTTTTATCACGTTTCTT3'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you think a AA and TT repetitions will cause any problems? We usually used 30 bp of homology at both sides of sequence. Should I use more in this case? What are your experiences regarding this AT repetitive sequences?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks, &#xA;Martin Kavšček&lt;/p&gt;&#xA;" OwnerUserId="4860" LastActivityDate="2014-10-15T14:53:40.177" Title="Gibson assembly - primer design with A and T rich regions" Tags="&lt;dna&gt;&lt;molecular-genetics&gt;&lt;cloning&gt;&lt;plasmids&gt;&lt;sequence-assembly&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23142" PostTypeId="2" ParentId="23110" CreationDate="2014-10-15T15:08:49.003" Score="12" Body="&lt;p&gt;&lt;strong&gt;People can grow taller than their parents.&lt;/strong&gt; Anecdotally: I'm 185 cm, my parents are 155 cm and 178 cm. &lt;a href=&quot;http://en.wikipedia.org/wiki/Joakim_Noah&quot;&gt;Joakim Noah&lt;/a&gt;, an NBA basketball player is 211 cm, his &lt;a href=&quot;http://en.wikipedia.org/wiki/Yannick_Noah&quot;&gt;dad was 193 cm&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/C%C3%A9cilia_Rodhe&quot;&gt;mother was 175 cm&lt;/a&gt;... how?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetics and environment play a role in determining height. First of all, a more nutritious environment during development can lead to increased height, &lt;a href=&quot;http://www.scientificamerican.com/article/why-are-we-getting-taller/&quot;&gt;this is one reason why more recent generations appear to be taller.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Height is also an example of a &lt;a href=&quot;http://en.wikipedia.org/wiki/Quantitative_genetics&quot;&gt;quantitative trait&lt;/a&gt; - this means many genes (or loci [singular is locus], locations in the DNA) affect the phenotype (the physical measurable result i.e. a persons height). It is infact how the vast majority of traits are determined. At each locus that affects height there may be polymorphism (when more than one allele, or variant of that gene, exists).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Example:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose height entirely is determined by 2 &lt;a href=&quot;http://en.wikipedia.org/wiki/Additive_genetic_effects&quot;&gt;additive&lt;/a&gt; loci, $A$ and $B$, and no environmental effect occurs, and there is &lt;a href=&quot;http://en.wikipedia.org/wiki/Ploidy&quot;&gt;diploidy&lt;/a&gt; (two of each locus, one from each parent, determines height in a person). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each locus has two alleles denoted by $A_1$, $A_2$, $B_1 $ and $B_2$. Each copy of alleles $A_1$ and $B_1$ add 40 cm to a persons height, $A_2$ and $B_2$ add 50 cm to a persons height. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now a man who is $A_1 A_1, B_1 B_2$ (remember, humans are diploid) and a woman who is $A_2 A_1, B_1 B_1$ have children. Both parents are 170 cm tall. The theoretical limits for the population would be 160 cm and 200 cm. The children will inherit one copy of $A_1$ from the father and $B_1$ from the mother, but they could inherit either $B_1$ or $B_2$ from the father and either $A_1$ or $A_2$ from the mother. If a child inherited both of the taller alleles then they would be taller than the parents ($A_1 A_2, B_1 B_2$ = 180 cm). Likewise some offspring could be shorter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course the reality is much more complex; height is determined by many more than 2 loci, by the environment, and gene * environment interactions. This principle was a hugely important because it meant that reproduction did not necessarily remove variation from the gene pool (a fundamental problem with early evolutionary theory was the thought of &quot;blending&quot; - when offspring are the average of their parents)&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-10-15T15:15:04.850" LastActivityDate="2014-10-15T15:15:04.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23143" PostTypeId="1" AcceptedAnswerId="23180" CreationDate="2014-10-15T15:14:39.377" Score="1" ViewCount="173" Body="&lt;p&gt;I’ve been intrigued by gene duplication and want to learn more about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I’ve read the following from &lt;a href=&quot;http://www.biology-online.org/articles/comparative_genomics_using_fugu/background.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;several studies suggest that the proportion of duplicated genes&#xA;  retained in vertebrate genomes is much higher than is predicted by&#xA;  this model [4-6]. This has led to the suggestion of an alternative&#xA;  model whereby complementary degenerative mutations in independent&#xA;  subfunctions of each gene copy permits their preservation in the&#xA;  genome, as both copies of the gene are now required to recapitulate&#xA;  the full range of functions present in the single ancestral gene. This&#xA;  was formalized in the Duplication-Degeneration-Complementation (DDC)&#xA;  model [7] in a process referred to as subfunctionalization.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Can someone explain this?  What is meant by “both copies of the gene are now required to recapitulate the full range of functions present in the single ancestral gene”?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you suggest any other good articles on gene duplication?&lt;/p&gt;&#xA;" OwnerUserId="9772" LastEditorUserId="9099" LastEditDate="2014-10-15T17:20:51.717" LastActivityDate="2014-10-16T01:14:22.877" Title="Gene duplication and subfunctionalization" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23144" PostTypeId="2" ParentId="23109" CreationDate="2014-10-15T15:47:23.743" Score="1" Body="&lt;h1&gt;Short answer:&lt;/h1&gt;&#xA;&lt;p&gt;Because your immune system adapts to the virus causing the flu or the common cold and, thus, you become immune to it.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h1&gt;Longer answer:&lt;/h1&gt;&#xA;&lt;p&gt;When B cells first encounter an antigen (usually a protein on the surface of a pathogen), the antigen attaches to a receptor, stimulating the B cells. Some B cells change into memory cells, which remember that specific antigen, and others change into plasma cells. Plasma cells produce antibodies that are specific to the antigen that stimulated their production.&lt;/p&gt;&#xA;&lt;p&gt;After the first encounter with an antigen, production of enough of the specific antibody takes several days. Thus, the primary immune response is slow and that's the reason you experience the symptoms of the disease.&lt;/p&gt;&#xA;&lt;p&gt;But thereafter, whenever B cells encounter the antigen again, memory B cells very rapidly recognize the antigen, multiply, change into plasma cells, and produce antibodies. This response is quick and very effective.&lt;/p&gt;&#xA;&lt;p&gt;This means that, theoretically, you shouldn't be able to become sick twice by the same virus.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;However,&lt;/strong&gt;&#xA;virus are very prone to mutations. If these mutations occur in the genes that code for antibody-binding sites, the antibodies produced by B Cells become less effective. This is called Antigenic drift and the reason you might catch the Flu every year &lt;strong&gt;(because, with enough time, the virus antigens become different enough to &amp;quot;fool&amp;quot; your immune system)&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;Also, there are a few explanations why the flu has a seasonal pattern, with a peak usually at winter. One of the theories postulates that in cold weather, people tend to stay indoor, favoring virus transmission.&lt;/p&gt;&#xA;&lt;p&gt;Recently, an interesting article was published that found that:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;transmission of influenza B viruses is enhanced at colder&#xA;temperatures, providing an explanation for the seasonality of&#xA;influenza epidemics in temperate climates&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://jvi.asm.org/content/86/8/4279.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6543" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-10-15T16:17:36.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23145" PostTypeId="2" ParentId="23121" CreationDate="2014-10-15T16:06:21.743" Score="3" Body="&lt;p&gt;The localization of the protein kinase A (PKA) cannot be explicitly answered, since the localization depends on the activation state of the protein. Lets have a look at the protein itself first, as this is important for the activation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Protein_kinase_A&quot; rel=&quot;nofollow noreferrer&quot;&gt;PKA&lt;/a&gt; consists of four subunits, two catalytic subunits and two regulatory subunits. See the image from the Wikipedia article on PKA:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SnurS.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each regulatory subunit R is binding two cyclic AMP (cAMP) molecules and dissociates then from the protein complex. This sets the catalytic subunits free, which can then transfer phosphate groups from ATP to serine or threonine residues of target proteins. Among the target proteins is also the Phosphodiesterase (PDE) which gets activated by phosphorylation from PKA. Activated PDE hydrolyzes cAMP into AMP which reduces the amount of free cAMP which is necessary for PKA activation. PKA is also inactivated by phosphorylation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the cell you will find PKA almost everywhere. The traditional belief is that the protein is activated in the cytosol and enters the nucleus where it phosphorylates targets like CREB which then subsequently binds the the CRE sequence in gene promoters and activates this genes. Reference 1 shows that PKA is also activated in the nucleus, meaning that also the inactive form is present there. Reference 2 gives a nice summary of the article.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The regulatory subunit of inactive form of PKA binds to a special class of proteins: The &lt;a href=&quot;http://en.wikipedia.org/wiki/AKAP&quot; rel=&quot;nofollow noreferrer&quot;&gt;A-kinase anchor proteins&lt;/a&gt; (AKAP). These are membrane bound and allow the association of PKA to membranes, although the protein itself is not directly binding to the membrane. The AKAP family is rather big (at least 50 family members are known today), which probably allows the localization of PKA at different membranes. Have a look at references 3-5 for details on the localization and the anchoring.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22366721&quot; rel=&quot;nofollow noreferrer&quot;&gt;Regulation of nuclear PKA revealed by spatiotemporal manipulation of&#xA;cyclic AMP.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.news-medical.net/news/20120627/Protein-kinase-A-activated-in-the-nucleus-as-well-as-the-cytoplasm.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;Protein kinase A activated in the nucleus as well as the cytoplasm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://faculty.washington.edu/scottjdw/pdfs/smith_tibs_2006_p316.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;The where's and when's of kinase anchoring&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3776/uojdeup6_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Localization of A-kinase through anchoring proteins.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3776/h7tznfvj_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;The biological functions of A-kinase anchor proteins&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="8598" LastEditDate="2014-10-16T11:49:10.053" LastActivityDate="2014-10-16T11:49:10.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23150" PostTypeId="1" CreationDate="2014-10-15T17:46:33.323" Score="3" ViewCount="1372" Body="&lt;p&gt;Connections between neurons are said (by Wikipedia) to be strengthened as part of learning - can they also be weakened (below the original level)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand the concept of the connections strengthening. After reading the article &lt;a href=&quot;http://nautil.us/issue/12/feedback/ants-swarm-like-brains-think&quot; rel=&quot;nofollow&quot;&gt;Ants Swarm Like Brains Think&lt;/a&gt;, my understanding is that positive feedback (I forget the words that I should use for positive vs negative action potentials) should strengthen the connection, and negative feedback should weaken it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested to know whether neural connections can weaken below their original connection strength.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm curious about this so as to grasp the way that the human brain (or even simply the ant brain) learns good and bad. If I'm not completely wrong about what I'm asking, then I think I get it pretty well: The things that are good (like finding food) trigger positive feedback among the associated neuron groups, and the things that are bad (like pain or danger) trigger negative feedback in the associated neurons, and that's basically how brains learn good from bad. &lt;/p&gt;&#xA;" OwnerUserId="19073" LastEditorUserId="9943" LastEditDate="2015-07-01T14:21:45.653" LastActivityDate="2015-11-03T16:45:50.433" Title="Can connections between neurons be weakened?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23151" PostTypeId="2" ParentId="21682" CreationDate="2014-10-15T17:48:40.050" Score="3" Body="&lt;p&gt;I think that's more of a matter of linguistics rather than any scientific/physiological reason. For instance, in Portuguese, you wouldn't call legs to a cat or a dog's limbs. You would say they have 4 &quot;patas&quot; (roughly translated as &quot;paws&quot;). And calling them legs, in Portuguese at least, would be weird.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When veterinary doctors refer to animal limbs, they usually use anterior and posterior limbs. In fact, &lt;strong&gt;anatomically speaking&lt;/strong&gt;, anterior limbs in cats and dogs (and probably in other animals too) have more in common with human arms (upper limbs) that with their own posterior limbs.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Also, as rg255 commented, maybe the reason behind the colloquial nomenclature is quite simple... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To (miss)quote Nancy Sinatra: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These &quot;legs&quot; are made for walking&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;And that's just what they'll do&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6543" LastEditorUserId="1590" LastEditDate="2016-08-17T08:49:42.687" LastActivityDate="2016-08-17T08:49:42.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23152" PostTypeId="1" AcceptedAnswerId="23164" CreationDate="2014-10-15T17:58:23.350" Score="10" ViewCount="3822" Body="&lt;p&gt;The article &lt;a href=&quot;http://nautil.us/issue/12/feedback/ants-swarm-like-brains-think&quot;&gt;Ants Swarm Like Brains Think&lt;/a&gt; really helped me to understand the way that neurons which are pretty dumb on their own (like ants) can work together to create a pretty genius system (a brain or an ant-hive). The idea is that both the neurons and the ants function majorly via positive and negative feedback, which is really neat to understand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However as shown in that article, sometimes groups of ants get caught in something called a feedback loop. They can repeat the same action over and over because the positive feedback is just being relayed from ant to ant to ant in a circle, and the ants can do something unhealthy such as walk in a circle for days. I don't know any examples of negative feedback loops but they would presumably also be unhealthy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As noted in the comments, this is an analogy, but not without a good reason: The brain does work via positive and negative feedback. And that does create the potential for feedback loops.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I'm curious about what biological features in neurons help to avoid these feedback loops in our brains. &lt;strong&gt;How does the brain avoid feedback loops?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="19073" LastEditorUserId="19073" LastEditDate="2014-10-15T19:15:38.213" LastActivityDate="2018-08-31T09:21:35.977" Title="How does the brain avoid feedback loops?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="10" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23153" PostTypeId="1" CreationDate="2014-10-15T18:01:21.413" Score="2" ViewCount="843" Body="&lt;p&gt;I know that epiphyseal growth plates seal up once people become young adults and that it is currently impossible to restore them to actively produce new bone growth but, is it theoretically possible via genetic or epigenetic means to reactivate them to produce new bone?&lt;/p&gt;&#xA;" OwnerUserId="5491" LastActivityDate="2014-10-15T18:01:21.413" Title="Can sealed epiphyseal growth plates theoretically be restored via epigenetic or genetic methods?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;human-genetics&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23154" PostTypeId="1" AcceptedAnswerId="23158" CreationDate="2014-10-15T18:16:32.450" Score="6" ViewCount="262" Body="&lt;p&gt;That's something that's been bugging me for a while...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our gastrointestinal tract produces proteases that degrade proteins. Prions are proteins. Shouldn't they be broken by proteases?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, how can a prion pass the gastrointestinal barrier? Shouldn't the intestine be able to absorb aminoacids only (instead of full proteins)?&lt;/p&gt;&#xA;" OwnerUserId="9777" LastEditorUserId="6543" LastEditDate="2014-10-15T18:27:56.353" LastActivityDate="2014-10-16T10:25:22.890" Title="How can ingesting a prion &quot;infect&quot; someone?" Tags="&lt;human-biology&gt;&lt;prion&gt;&lt;human-physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23155" PostTypeId="1" AcceptedAnswerId="23161" CreationDate="2014-10-15T18:23:12.823" Score="2" ViewCount="415" Body="&lt;p&gt;I noticed that coconut oil has ~96% saturated fat, and I was under the assumption that saturated fats = bad for health.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is it that coconut oil is healthier to alternatives with much less saturated fat?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="107" LastEditDate="2014-10-15T19:16:51.340" LastActivityDate="2014-10-15T19:16:51.340" Title="Why is coconut oil healthier when it has so much saturated fat?" Tags="&lt;biochemistry&gt;&lt;food&gt;&lt;diet&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23156" PostTypeId="2" ParentId="801" CreationDate="2014-10-15T18:31:40.900" Score="2" Body="&lt;p&gt;Just to clear out some things:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As stateted above, NADH is produced in catabolic reactions and is later used in the electron transport chain to obtain energy by converting NADH back to NAD+.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NADPH is primarily produced in the oxidative part of the pentose phosphate pathway. NADPH is used in &#xA;a) anabolic syntheses to produce cholesterol, fatty acids, transmittor substances and nucleotides.&#xA;b) detoxifying processes as an antioxidant. NADPH is for example an essential part of CYP450 in the liver and rereduces gluthatione (one of the most potent antioxidants in nature) in order to make it active once again.&lt;/p&gt;&#xA;" OwnerUserId="9778" LastActivityDate="2014-10-15T18:31:40.900" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23157" PostTypeId="2" ParentId="23150" CreationDate="2014-10-15T18:33:39.077" Score="2" Body="&lt;p&gt;neural connections can be weaken below their original connection strength. from neuroscience, new memories mean new neural connections, and the new neural connections require repeated activation. neurons that fire together, wire together, so it neurons or groups of neurons donot fire together often enough, new connections do not form. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;i am not sure the relationship with ants, i think the neural connections is strength by frequently practice. &lt;/p&gt;&#xA;" OwnerUserId="8972" LastActivityDate="2014-10-15T18:33:39.077" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23158" PostTypeId="2" ParentId="23154" CreationDate="2014-10-15T18:36:31.683" Score="7" Body="&lt;p&gt;Prions are misfolded proteins with abnormal tertiary or quaternary structures. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24338008&quot; rel=&quot;noreferrer&quot;&gt;That grants them resistance (to some extent, at least) to proteases (1)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also researchers believe that &lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJM199609193351218&quot; rel=&quot;noreferrer&quot;&gt;prions are able to replicate (2)&lt;/a&gt;, by changing the structure of other proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the gastrointestinal barrier, that isn't exactly true. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3060169&quot; rel=&quot;noreferrer&quot;&gt;It has been shown that small quantities of intact proteins do cross the gastrointestinal tract in animals and adult humans (3)&lt;/a&gt;, and that this is a physiologically normal process required for antigen sampling by subepithelial immune tissue in the gut&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;So, the resistance to the proteases and the ability to replicate in certain conditions might explain the odds of a prion crossing the gastrointestinal tract and infecting an individual.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24338008&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/24338008&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJM199609193351218&quot; rel=&quot;noreferrer&quot;&gt;http://www.nejm.org/doi/full/10.1056/NEJM199609193351218&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3060169&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/3060169&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6543" LastEditorUserId="6543" LastEditDate="2014-10-16T10:25:22.890" LastActivityDate="2014-10-16T10:25:22.890" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23159" PostTypeId="1" AcceptedAnswerId="23171" CreationDate="2014-10-15T18:46:06.360" Score="2" ViewCount="54" Body="&lt;p&gt;I'm interested in understanding how isolated different parts of the brain are from each-other. I'm trying to understand the way that different sections of the brain work together. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More specifically, I'm interested in whether or not the different sections are all intertwined together into a wild mass, or work in a more isolated way:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do different specialized areas of the brain have specific, consolidated connection areas where they exchange information&lt;/strong&gt; (sort of like they do their job and pass on the necessary information to the other modules)&lt;strong&gt;?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or do they instead mesh very thoroughly, connecting freely to other parts of the brain sort of like tangled string, with no obvious points of consolidated interaction?&lt;/p&gt;&#xA;" OwnerUserId="19073" LastEditorUserId="19073" LastEditDate="2014-10-15T18:55:36.740" LastActivityDate="2014-10-16T08:09:40.370" Title="How isolated are different areas of the brain?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23160" PostTypeId="1" AcceptedAnswerId="23167" CreationDate="2014-10-15T19:03:06.917" Score="1" ViewCount="128" Body="&lt;p&gt;I understand that each half of the human brain handles different parts of our thinking. Left brain, right brain, that whole topic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But in pictures, the brain is always depicted as having symmetrical structure. I'm curious about that. I realize that it might be silly to expect such a complex tool to be &lt;em&gt;truly&lt;/em&gt; symmetrical, so my question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is the brain &lt;em&gt;functionally&lt;/em&gt; symmetrical or not?&lt;/strong&gt; By functionally, I'm referring to whether the specialized groups within the brain all exists on both sides or rather each side contains different components.&lt;/p&gt;&#xA;" OwnerUserId="19073" LastActivityDate="2014-10-15T20:24:47.240" Title="Is the brain functionally symmetrical?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23161" PostTypeId="2" ParentId="23155" CreationDate="2014-10-15T19:03:30.133" Score="5" Body="&lt;p&gt;coconut oil is composed mainly of medium-chain triglycerides, 1)it is smaller than other long-chain triglycerides so that it can be digested easily, 2)the digestion of coconut oil does not involve in the Pancreatic digestive enzyme system, 3) liver prefer use medium-chain triglycerides as the fuel sources 4) medium-chain triglycerides will convert to monoglyceride and medium-chain fatty acid which have strong antibacterial &lt;/p&gt;&#xA;" OwnerUserId="8972" LastActivityDate="2014-10-15T19:03:30.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23162" PostTypeId="1" AcceptedAnswerId="23177" CreationDate="2014-10-15T19:32:46.427" Score="2" ViewCount="492" Body="&lt;p&gt;I've read somewhere that inverted microscope also allows phase contrast microscopy. Is that true? Do all inverted microscope have this ability? Do they have any other functions? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="6214" LastActivityDate="2014-11-15T01:15:27.483" Title="Can inverted microscope also be phase contrast microscope?" Tags="&lt;microscopy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23163" PostTypeId="1" CreationDate="2014-10-15T19:55:53.463" Score="4" ViewCount="143" Body="&lt;p&gt;So i'm looking into the ebola crisis and it seems the death toll is really getting crazy.  I understand that it's a cytomegalovirus and that it basically overwhelms the immune system due to it's size and virulence but why is it so bad now?  What has changed about it?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The folks at the Dallas hospital were said to have 'broken protocol' but to me it seems the virus may be more infectious this time around.  Has it changed?  Mutated?  &lt;/p&gt;&#xA;" OwnerUserId="9001" LastActivityDate="2014-10-15T23:06:03.540" Title="Why is the ebola virus so intense now?" Tags="&lt;biochemistry&gt;&lt;microbiology&gt;&lt;pathology&gt;&lt;virus&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23164" PostTypeId="2" ParentId="23152" CreationDate="2014-10-15T20:03:08.803" Score="11" Body="&lt;p&gt;Normally, after an excitatory neuron fires, it becomes more resistant to firing again for a period of time (refractory period). This is due to electrical changes within the excitatory neuron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After depolarazing and reaching an action potential(firing), the neuron enters the refractory period, in which its charge will go back to normal (resting potential). This refractory period can be divided in two phases: &lt;em&gt;Absolute&lt;/em&gt; and &lt;em&gt;relative&lt;/em&gt;. During the &lt;strong&gt;Absolute refractory period, the neuron cannot be discharged again&lt;/strong&gt;, since the sodium channels are inactive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's the relative refractory phase, however, that is more relevant to your question. During this period, the neuron enters a hyperpolarization states, meaning that it's resistant to firing again, unless it receives a greater stimulus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So, basically, after firing and for a while, a neuron requires greater stimulus to be fired again. This works as a Feedback control, since even if you overstimulate a neuron it can fire only so often.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Inhibitory and excitatory neurons (and inhibitory and excitatory neurotransmitters) also play a role in the feedback control. Inhibitory neurons reduce the likelihood of a postsynaptic neuron to fire while excitatory neurons do the opposite.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;However, sometimes these mechanism fail. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, in Epilepsy, the resistance of excitatory neurons to fire during the refractory period is decreased. A group of neurons begin firing in an abnormal, excessive, and synchronized manner, resulting in a wave of depolarization known as a &lt;em&gt;paroxysmal depolarizing shift&lt;/em&gt;, causing seizures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Parkinson disease, decreased dopamine causes increased inhibitory output (excess negative feedback) of the motor circuit, which leads to hypokinesia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In contrast, excess dopamine and dopaminergic neuron activity seem to be related with Schizophrenia.&lt;/p&gt;&#xA;" OwnerUserId="6543" LastEditorUserId="6543" LastEditDate="2018-08-31T09:21:35.977" LastActivityDate="2018-08-31T09:21:35.977" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="23165" PostTypeId="1" AcceptedAnswerId="23169" CreationDate="2014-10-15T20:20:43.540" Score="3" ViewCount="245" Body="&lt;p&gt;What insect is this on these photos?&#xA;Found in Russia in the living room.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/f6L6o.jpg&quot; alt=&quot;Unknown insect&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/oWJxP.jpg&quot; alt=&quot;Unknown insect&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3280" LastEditorUserId="3280" LastEditDate="2014-10-16T19:58:39.780" LastActivityDate="2014-10-16T19:58:39.780" Title="What insect is this on the photos?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23166" PostTypeId="2" ParentId="19246" CreationDate="2014-10-15T20:21:42.343" Score="0" Body="&lt;p&gt;Well, there are antiviral drugs that inhibit virus development. However, they are drugs, not cells but they can be quite effective in controlling diseases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are also quite available to the public and perhaps you (or someone close) have used them. For instance, Zovirax (acyclovir) is used in lip herpes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, HIV therapy is used effectively to increase the life expectancy of AIDS patients.  &lt;/p&gt;&#xA;" OwnerUserId="6543" LastActivityDate="2014-10-15T20:21:42.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23167" PostTypeId="2" ParentId="23160" CreationDate="2014-10-15T20:24:47.240" Score="3" Body="&lt;p&gt;No. For instance, Broca's area exists only in the frontal lobe of one hemisphere, usually the left. (it's responsible for speech, btw)&lt;/p&gt;&#xA;" OwnerUserId="6543" LastActivityDate="2014-10-15T20:24:47.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23169" PostTypeId="2" ParentId="23165" CreationDate="2014-10-15T20:48:51.500" Score="3" Body="&lt;p&gt;I think I found it. It can be Lacewings:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Chrysopidae&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Chrysopidae&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3280" LastActivityDate="2014-10-15T20:48:51.500" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23170" PostTypeId="1" CreationDate="2014-10-15T20:55:35.140" Score="5" ViewCount="323" Body="&lt;p&gt;I'm often surprised by the human ability to correctly identify other individuals despite significant modifications due to ageing, hairstyle, injury, etc. But, sometimes the addition of a beard and a hat can radically increase the identification error.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder whether all facial regions are equally important when we try to recognise human faces? Do we focus more on some regions than others? I doubt that this is the case, but I'm not certain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far I've read through the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) &lt;a href=&quot;http://en.wikipedia.org/wiki/Face_perception&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Face_perception&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998394/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998394/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far I haven't found an answer so I decided to try Biology.StackExchange.&lt;/p&gt;&#xA;" OwnerUserId="9573" LastEditorUserId="16866" LastEditDate="2019-02-09T04:24:34.530" LastActivityDate="2019-02-09T04:24:34.530" Title="Are some facial features more important than others in human facial recognition?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="23171" PostTypeId="2" ParentId="23159" CreationDate="2014-10-15T21:26:09.010" Score="2" Body="&lt;p&gt;Well, to answer your question, both your hypothesis are true, at least &lt;strong&gt;partially&lt;/strong&gt; true.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The brain has several known specialized connections called neural pathways that connect specific areas of the brain and are responsible for determined functions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, when you move your leg, the stimulus starts at the motor cortex and travels through the pyramidal tract to your leg and then back.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, one can argue that the stimulus didn't start at the motor cortex. Why? you thought about moving, then made the decision and only then perform the real action of moving your leg.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And here's a more complex (and maybe humorous) example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;You see a dog running ferociously at you. &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;The stimulus travels through your visual pathway to your visual cortex.&lt;/em&gt; &lt;/li&gt;&#xA;&lt;li&gt;The image of a dog forms in your brain. &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;It then travels to your Hippocampus.&lt;/em&gt; &lt;/li&gt;&#xA;&lt;li&gt;You realise that's a dog and also remember a traumatic childhood experience with a dog.&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;The stimulus travels to your amigdala&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;li&gt;You feel fear&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;The stimulus activates the sympathetic system.&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;You're now prepared to fight or flight&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;The frontal lobe is activated&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;You decide to kick the dog&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;The stimulus goes from your motor cortex to your cerebellum&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;Your cerebellum &quot;remembers&quot; the karate classes you had as a kid&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;The stimulus goes to your leg&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;You kick the poor dog. He runs.&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Nucleus accumbens is activated&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;You feel good with yourself&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, in short, &lt;strong&gt;the brain has pathways that connect specific areas of the brain but, in a sense, all parts of the brain are connected either directly or indirectly&lt;/strong&gt;. Like the saying &quot;all roads lead to rome!&quot; &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;DISCLAIMER: I do not endorse animal cruelty.&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="6543" LastEditorUserId="6543" LastEditDate="2014-10-16T08:09:40.370" LastActivityDate="2014-10-16T08:09:40.370" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23173" PostTypeId="2" ParentId="9276" CreationDate="2014-10-15T22:53:49.123" Score="1" Body="&lt;p&gt;Why cells differentiate or specialize is an ephemeral question. I'll make an attempt to answer--the more specialized cells an organism has, the better equipped that organism is to function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a given organism, differentiation after n divisions or after t time during development is due to changes that are both intrinsic (genetic) or extrinsic (environmental). For two examples of how intrinsic and extrinsic determinants interact are: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19433085&quot; rel=&quot;nofollow&quot;&gt;&quot;Unfolding a chordate developmental program, one cell at a time: invariant cell lineages, short-range inductions and evolutionary plasticity in ascidians.&quot;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://goo.gl/4DWPf7&quot; rel=&quot;nofollow&quot;&gt;&quot;Cell Patterning&quot;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a cell changes after n divisions at t time, it may be due to its local cellular environment, or in the case of some animals, hormonal regulation that each cell may respond to differently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As such, why do cell differentiate? Because in organisms, which are large collections of cells, survival is wholly dependent on the segregation of cellular function.&lt;/p&gt;&#xA;" OwnerUserId="9782" LastEditorUserId="9782" LastEditDate="2014-10-15T23:49:00.680" LastActivityDate="2014-10-15T23:49:00.680" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23174" PostTypeId="2" ParentId="23163" CreationDate="2014-10-15T23:06:03.540" Score="2" Body="&lt;p&gt;The answer here lies in epidemiology and the pathogenic nature of the virus. Humans infected with Ebola have a range of recovery rates of 5-75%, meaning that most of those infected will not survive infection. Given the combination of preparedness factors at first recognizing a true outbreak in Ebola and viral load which had already been spread by the point healthcare workers have organized an efficient response, it is not surprising that some outbreaks are worse than others. I think attempting to correlate the virulence to the type, size with the extent of the viral spread is not pertinent, but rather, as you mentioned breaking &quot;protocol&quot; can have more deleterious effect than simply explaining it by a mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is not to say that this strain of Ebola is not different from those detected in other outbreaks--in fact it is likely to be quite different and accumulated several mutations.&lt;/p&gt;&#xA;" OwnerUserId="9782" LastActivityDate="2014-10-15T23:06:03.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23177" PostTypeId="2" ParentId="23162" CreationDate="2014-10-16T00:30:09.760" Score="3" Body="&lt;p&gt;Definitely true, an inverted microscope is one where the optics are positioned below the specimen, and the light source above, providing an optimal situation for looking at a live culture. The Phase rings that shift the light come soon after the light source. For phase, the orientation doesn't matter, just the order:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Upright microscope&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Orientation&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(top)eye---&gt;objective---&gt;specimen---&gt;phase---&gt;light source&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;order&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;eye--&gt;Phase compatible objective--&gt;specimen--&gt;phase disk--&gt;light source&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Inverted microscope&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Orientation&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(top)light source---&gt;phase---&gt;specimen----&gt;Objective---&gt;eye&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;order&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;eye--&gt;phase compatible objective--&gt;specimen--&gt;phase disk--&gt;light source&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all microscopes have phase no, they are an important and expensive addition to a microscope. Adding phase not only required the phase disk but also a phase compatible objective.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-10-16T00:30:09.760" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23180" PostTypeId="2" ParentId="23143" CreationDate="2014-10-16T01:14:22.877" Score="1" Body="&lt;p&gt;Suppose a gene performs two distinct functions 1 and 2, both of which are essential. We'll call this gene A, for ancestral gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A duplication copies A to another locus. Now there are two genes, A and B, that perform the same two functions. At this point, if either A or B is deleted, the organism is fine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Over evolutionary time, A and B undergo genetic drift to become A' and B', respectively. Let's say that B' loses function 1, and that A' loses function 2. This isn't a problem for the organism since A' still performs function 1, and B' still performs function 2. In other words, the two genes complement each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, now A' can't be deleted without losing function 1, and, similarly, B' can't be deleted without losing function 2. The result is that both genes are fixed in the genome by evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that now, after hundreds of millions of years of relevant evolution and genetic drift, we many duplications like A' and B'. The key to this is that through genetic drift with no selective pressure, it's very easy to lose function but extremely difficult to gain it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your second question, I'll look for a paper on gene duplications that I think would be the most helpful, but there are many.&lt;/p&gt;&#xA;" OwnerUserId="9652" LastActivityDate="2014-10-16T01:14:22.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23181" PostTypeId="2" ParentId="2711" CreationDate="2014-10-16T01:38:34.537" Score="1" Body="&lt;p&gt;I don't know any true &lt;em&gt;disease&lt;/em&gt; associations, but since this question still has no answers, I'll offer one...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One class of associations you might be missing is difference in drug response. Patients with HLA-B*5701 are known to be hypersensitive to abacavir. Genetic screens are available to screen for this allele, and this information is used clinically.&lt;/p&gt;&#xA;" OwnerUserId="9652" LastActivityDate="2014-10-16T01:38:34.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23182" PostTypeId="1" CreationDate="2014-10-16T01:43:20.430" Score="1" ViewCount="5065" Body="&lt;p&gt;My teacher told me that drinking water that is room temperature is better for you then drinking cold water, but she did not tell me why that is. I want to know because I often drink cold water (with ice), because I can't stand water that is room temperature or warm. &lt;/p&gt;&#xA;" OwnerUserId="9787" LastActivityDate="2014-11-23T12:54:03.663" Title="Why is it better to drink room temperature water instead of cold water?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ClosedDate="2014-11-24T04:54:26.900" ContentLicense="CC BY-SA 3.0" />
  <row Id="23183" PostTypeId="2" ParentId="2711" CreationDate="2014-10-16T01:46:57.633" Score="0" Body="&lt;p&gt;Bone marrow transplant for leukemia and multiple myeloma. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Uses extensive HLA typing like you said are you looking for additional diseases?&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-10-16T01:46:57.633" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23186" PostTypeId="1" AcceptedAnswerId="23205" CreationDate="2014-10-16T02:07:27.213" Score="6" ViewCount="104" Body="&lt;p&gt;What about tuberculosis makes it difficult to produce a safe vaccine that is effective at producing an immunogenic response in &gt;99% of individuals against all strains of the bacteria?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am aware of the BCG vaccine which has a variable efficacy depending on how it is measured and am aware of the 4 current vaccine candidates (MVA85A, rBCG30, 72F fusion protein, and ESAT6-Ag85b fusion protein). I am curious about the very specific question of aspects of the bacteria that make the TB vaccine difficult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many, many thanks.&lt;/p&gt;&#xA;" OwnerUserId="666" LastActivityDate="2014-10-16T11:22:05.177" Title="What (if anything) about tuberculosis makes producing a highly effective vaccine difficult?" Tags="&lt;infection&gt;&lt;tuberculosis&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23189" PostTypeId="1" AcceptedAnswerId="27928" CreationDate="2014-10-16T02:27:54.160" Score="4" ViewCount="998" Body="&lt;p&gt;I read the following on &lt;a href=&quot;http://en.wikipedia.org/wiki/Advanced_glycation_end-product&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There is, however, no agent known that can break down the most common&#xA;  AGE, glucosepane, which appears 10 to 1,000 times more common in human&#xA;  tissue than any other cross-linking AGE.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(AGEs are related to oxidative stress, aging and chronic diseases.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering maybe the article is out of date, and there is a glucosepane cross-link breaker available. Do you know anything of that, or a current research which aims to find that?&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-16T03:04:53.207" LastActivityDate="2019-06-03T03:47:32.377" Title="Is there a known glucosepane cross-link breaker?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;physiology&gt;&lt;pharmacology&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23192" PostTypeId="2" ParentId="2711" CreationDate="2014-10-16T03:54:24.403" Score="0" Body="&lt;p&gt;Actually it can help by curing specific types of cancer e.g. &lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMoa1103849&quot; rel=&quot;nofollow&quot;&gt;Chimeric Antigen Receptor–Modified T Cells in Chronic Lymphoid Leukemia&lt;/a&gt;. But ofc. it does not help in every case. You can live without B-cells, but you cannot live without liver...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes it can be used by designing a therapy for a disease, if that's the question.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-16T03:54:24.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23194" PostTypeId="1" AcceptedAnswerId="23196" CreationDate="2014-10-16T04:23:21.690" Score="6" ViewCount="308" Body="&lt;p&gt;Why do scientists (pretty consistently) call it &lt;em&gt;&lt;a href=&quot;http://www.who.int/mediacentre/factsheets/fs103/en/&quot; rel=&quot;nofollow&quot;&gt;Ebola virus disease&lt;/a&gt;&lt;/em&gt;, rather than just &lt;em&gt;Ebola&lt;/em&gt;, or &lt;em&gt;Ebola disease&lt;/em&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many other diseases are caused by viruses, but they don't seem to have this detail of terminology.  Nor do you hear the analogous terminology for bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.who.int/mediacentre/factsheets/fs367/en/&quot; rel=&quot;nofollow&quot;&gt;Rubella&lt;/a&gt; is caused by the rubella virus.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.who.int/mediacentre/factsheets/fs211/en/&quot; rel=&quot;nofollow&quot;&gt;Influenza&lt;/a&gt; is caused by various influenza viruses (genus names Influenzavirus A/B/C).&lt;/li&gt;&#xA;&lt;li&gt;Some strains of &lt;a href=&quot;http://www.who.int/mediacentre/factsheets/fs125/en/&quot; rel=&quot;nofollow&quot;&gt;E. coli&lt;/a&gt; (pathogenic E. coli) cause disease, but you never hear E. coli bacteria disease.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="320" LastEditorUserId="1590" LastEditDate="2015-06-02T14:46:28.780" LastActivityDate="2015-06-02T14:46:28.780" Title="Why is it called &quot;Ebola virus disease&quot;, not just &quot;Ebola&quot; or &quot;Ebola disease&quot;?" Tags="&lt;virology&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23196" PostTypeId="2" ParentId="23194" CreationDate="2014-10-16T07:26:00.607" Score="14" Body="&lt;p&gt;This is now how new viral diseases are being named, &lt;em&gt;possibly&lt;/em&gt; because one can have/carry a virus without having a disease (e.g. HIV, herpes simplex, etc.). It is not as uncommon as you think.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A bit of googling will turn up reputable sites which discuss the epidemiology of Hantavirus disease, Hendra Virus Disease, Powassan Virus Disease, Lake Victoria Marburgvirus disease, Lujo virus disease, Ross River virus disease, Nipah virus disease, respiratory syncytial virus disease, Kunjin virus disease, Chikungunya Virus Disease, Heartland virus disease, St. Louis encephalitis virus disease, West Nile virus disease, Eastern equine encephalitis virus disease, Western equine encephalitis virus disease, and California serogroup virus disease (includes infections with the following viruses: La Crosse, Jamestown Canyon, snowshoe hare, trivittatus, Keystone, and California encephalitis viruses) and others, but I'm stopping here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria cause diseases, but many already had/have names: Typhus (Rickettsia typhi or Rickettsia prowazekii), Rocky Mountain Spotted Fever (Rickettsia rickettsii), Diptheria (Corynebacterium diphtheriae), Lyme disease (at least three species of bacteria belonging to the genus Borrelia), Pertussis/Whooping Cough (Bordetella pertussis), Tetanus (Clostridium tetani), etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, I have started to see scholarly articles for Clostridium Difficile Disease, which was an entirely new name for what we used to call Antibiotic-Associated Diarrhea. So maybe there will be a shift in that direction as well; time will tell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How diseases are named is another whole thing.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-10-16T07:26:00.607" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23197" PostTypeId="1" AcceptedAnswerId="23198" CreationDate="2014-10-16T09:10:36.813" Score="1" ViewCount="8219" Body="&lt;p&gt;Consider a plant like Aloe Vera that grows up in a toxic environment where the concentration of pesticides, and materials like lead, mercury, cadmium, arsenic etc is very high(e.g. Marshland dumping yard ). Would that mean that the extract from these plants would contain all these toxic elements.  &lt;/p&gt;&#xA;" OwnerUserId="9791" LastActivityDate="2020-05-17T18:47:15.687" Title="Do plants absorb toxins from the soil?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23198" PostTypeId="2" ParentId="23197" CreationDate="2014-10-16T09:21:44.133" Score="3" Body="&lt;p&gt;Not &quot;all of them&quot;. But yes, plants suck up water from the soil, with everything dissolved in this water - nutrients, heavy metals, poisons. And also they breathe air, and absorb stuff via this route. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There probably are some toxins which will not enter the plant, because their molecules are too large and/or fragile. For example, should a plant root come in contact with snake venom, I cannot imagine that any venom will end up stored in the plant leaves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants also have their own metabolism, so they will change/deactivate some toxins. I've seen claims that some plants &quot;purify&quot; formaldehyde, although I don't trust the sources enough to be sure of that.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the smaller the poison molecule, and the less similar to stuff which is usually digested in nature, the more likely that it will enter the plant and stick around instead of being broken down. The heavy metals you mentioned are prime candidates. If they are present in the groundwater - or also lead from air pollution, before we banned leaded gasoline - they end up in plants, including food plants. And mushrooms are even more at risk. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Growing food near waste dumps is a known problem in farming, and sometimes makes the news, for example here: &#xA;&lt;a href=&quot;http://bigstory.ap.org/article/mafia-toxic-waste-dumping-poisons-italy-farmlands&quot; rel=&quot;nofollow&quot;&gt;http://bigstory.ap.org/article/mafia-toxic-waste-dumping-poisons-italy-farmlands&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="1578" LastActivityDate="2014-10-16T09:21:44.133" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23199" PostTypeId="2" ParentId="19246" CreationDate="2014-10-16T09:32:19.217" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;But is there something like an anti-virus? A single celled entity that&#xA;  does the opposite: spreads around 'kills' other viruses and/or cures&#xA;  diseases. Has anybody discovered something like it or is there any&#xA;  research group working on synthesizing one?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Actually there is, it is called immune system. :-)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the cells in your body have &lt;a href=&quot;http://en.wikipedia.org/wiki/Proteasome&quot; rel=&quot;noreferrer&quot;&gt;proteasomes&lt;/a&gt;, which can degrade proteins from the inside of the cell. The cells randomly choose sample proteins (possibly viral or cancer proteins) which are degraded by a proteasome into small 8-10 amino-acid length peptides. After that the cell chooses some of these peptides and send them to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Endoplasmic_reticulum&quot; rel=&quot;noreferrer&quot;&gt;endoplasmatic reticulum&lt;/a&gt; in where each of them meet with an &lt;a href=&quot;http://en.wikipedia.org/wiki/MHC_class_I&quot; rel=&quot;noreferrer&quot;&gt;MHC1 molecule (major histocompability complex)&lt;/a&gt; and binds to it. After that the cell sends the MHC1-sample complex to its surface. So every cell with nucleus has a lot of MHC1-randomProteinSample on its surface. These samples are checked an immune cell type called &lt;a href=&quot;http://en.wikipedia.org/wiki/Cytotoxic_T_cell&quot; rel=&quot;noreferrer&quot;&gt;cytotoxic T-cells&lt;/a&gt;. These immune cells attach to the MHC1 of other cells using their &lt;a href=&quot;http://en.wikipedia.org/wiki/T-cell_receptor&quot; rel=&quot;noreferrer&quot;&gt;TCR (T-cell receptor)&lt;/a&gt; and their &lt;a href=&quot;http://en.wikipedia.org/wiki/CD8&quot; rel=&quot;noreferrer&quot;&gt;CD8 coreceptor&lt;/a&gt;. The TCR has a part which consist of a random amino-acid sequence. Thanks to this random part it can recognize a very specific pattern of the small peptides which are bound to MHC1. So every cytotoxic T-cell is different and each of them can recognize a very specific pattern with its T-cell receptors. When a T-cell has a pattern match for the first time it waits for verification signal. It gets that signal on its &lt;a href=&quot;http://en.wikipedia.org/wiki/CD28&quot; rel=&quot;noreferrer&quot;&gt;CD28 receptor&lt;/a&gt;. The signal &lt;a href=&quot;http://en.wikipedia.org/wiki/B7_%28protein%29&quot; rel=&quot;noreferrer&quot;&gt;B7-protein&lt;/a&gt; is provided by a professional &lt;a href=&quot;http://en.wikipedia.org/wiki/Antigen-presenting_cell#Professional_APCs&quot; rel=&quot;noreferrer&quot;&gt;APC (antigen-presenting cell)&lt;/a&gt; which is infected by the virus or which phagocytized the virus, processed it, and now expresses it on MHC1 and &lt;a href=&quot;http://en.wikipedia.org/wiki/MHC_class_II&quot; rel=&quot;noreferrer&quot;&gt;MHC2&lt;/a&gt; (MHC2 is similar to MHC1, but it can be found only on professional APCs). By virus infected APC the MHC1 can be enough to activate the cytotoxic T-cell. By not-infected APC the cytotoxic T-cell requires further help for activation. This help can be provided by a &lt;a href=&quot;http://en.wikipedia.org/wiki/T_helper_cell&quot; rel=&quot;noreferrer&quot;&gt;helper T-cell&lt;/a&gt;, which attaches to the MHC2 receptor and after the verification it sends the necessary &lt;a href=&quot;http://en.wikipedia.org/wiki/Cytokine&quot; rel=&quot;noreferrer&quot;&gt;cytokines&lt;/a&gt; to activate the cytotoxic T-cell. After the activation the cytotoxic T-cell can destroy every cell on which it finds an MHC1 with matching protein sample, and it can proliferate, so make many copies of itself. This whole process (activating the &lt;a href=&quot;http://en.wikipedia.org/wiki/Adaptive_immune_system&quot; rel=&quot;noreferrer&quot;&gt;adaptive immune system&lt;/a&gt;) takes appr. 3-4 days. Until that the &lt;a href=&quot;http://en.wikipedia.org/wiki/Innate_immune_system&quot; rel=&quot;noreferrer&quot;&gt;innate immune system&lt;/a&gt; holds the infection. The innate immune system is not so specific as the adaptive immune system, but it contains most of the APCs, so these two systems work together in order to defeat the infection. By the next infection there will be already active &lt;a href=&quot;http://en.wikipedia.org/wiki/Memory_T_cell&quot; rel=&quot;noreferrer&quot;&gt;memory T-cells&lt;/a&gt; available, so the whole process will be much faster... This is shortly how a human immune response works by viral infections. &lt;em&gt;Note that I left out the B-cell response against viral surface polysaccharides to stay short and simple. ;-)))&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Synthetic drugs usually have a single active ingredient or just a few of them, so you cannot do an universal cure for viral infections because every virus is different. There are a few treatments already available (&lt;a href=&quot;http://www.retrovirology.com/content/10/S1/P72&quot; rel=&quot;noreferrer&quot;&gt;viral interference&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Maraviroc&quot; rel=&quot;noreferrer&quot;&gt;receptor antagonists&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Antiviral_drug&quot; rel=&quot;noreferrer&quot;&gt;viral enzyme inhibitors&lt;/a&gt;, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0140673610603571&quot; rel=&quot;noreferrer&quot;&gt;RNA interference&lt;/a&gt;, etc...), but the most important thing is prevention due to &lt;a href=&quot;http://en.wikipedia.org/wiki/Vaccination&quot; rel=&quot;noreferrer&quot;&gt;vaccination&lt;/a&gt; (create memory T-cells by an infection with attenuated virus strains or by fooling the immune system with viral proteins, polysaccharides and some chemicals which kill a few cells). Probably in the distant future there will be &lt;a href=&quot;http://en.wikipedia.org/wiki/Nanorobotics&quot; rel=&quot;noreferrer&quot;&gt;nanobots&lt;/a&gt; which will be programmed to cure any type of viral infections and cancer, but with current technology that seems like a miracle...&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-16T09:32:19.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23200" PostTypeId="1" AcceptedAnswerId="23202" CreationDate="2014-10-16T10:23:36.310" Score="0" ViewCount="121" Body="&lt;p&gt;So I am trying to write a code in C++ about the cardiac excitation threshold. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that this excitation threshold is the shortest stimulus2 value at which it can conduct an action potential (known as the effective refractory period) at that stimulus1 value. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is: In my code should I have: apply_stimulus1 for basic_cycle_length = 1000 and while you are applying this stimulus1 apply and a stimulus2 and print out the shortest value of s2 where I can have a potential? -&gt; the way I am thinking this is apllying both stimulus simultaneously. If we say .... this is stimulus 1 and this is ,,,, stimulus2 at the end I will have ;;;;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or should I say when you finish applying that stimulus1 apply a stimulu2 and give me the shortest time where I get action potential? But here I will have stimulu1 .... || (meaning ends applying stimulus1) ,,,, apply stimulus2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this how I am thinking it correct or I just got lost in my own thoughts and it is easier than I make it look?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My &lt;strong&gt;question&lt;/strong&gt; is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do I get the cardiac excitation threshold using stimulus1 and stimulus2 and how can I incorporate the theory in my C++ code.&lt;/p&gt;&#xA;" OwnerUserId="9794" LastEditorUserId="9794" LastEditDate="2014-10-16T11:44:45.057" LastActivityDate="2014-10-16T11:44:45.057" Title="Cardiac Excitation Threshold - in C++ modelling" Tags="&lt;bioinformatics&gt;&lt;cardiology&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="6" ClosedDate="2014-10-16T11:53:15.033" ContentLicense="CC BY-SA 3.0" />
  <row Id="23201" PostTypeId="1" AcceptedAnswerId="23204" CreationDate="2014-10-16T10:28:58.923" Score="2" ViewCount="176" Body="&lt;p&gt;Why can't we smell our own bad breath. Is there any way we can do that?&lt;/p&gt;&#xA;" OwnerUserId="9791" LastActivityDate="2014-10-16T11:21:38.697" Title="Why can't we smell our own bad breath?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-10-16T14:14:00.227" ContentLicense="CC BY-SA 3.0" />
  <row Id="23202" PostTypeId="2" ParentId="23200" CreationDate="2014-10-16T10:36:10.377" Score="0" Body="&lt;p&gt;You wouldn't normally apply the stimuli simultaneously. The idea is to apply stimulus1, which has a given amplitude and duration, and follow that with stimulus2, which also has a given amplitude and duration, after a variable lag. You'll then see that the effective refractory period is dependent on the amplitude of stimulus2 (at least until you hit the absolute refractory period).&lt;/p&gt;&#xA;" OwnerUserId="9523" LastActivityDate="2014-10-16T10:36:10.377" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23204" PostTypeId="2" ParentId="23201" CreationDate="2014-10-16T11:21:38.697" Score="2" Body="&lt;p&gt;What you might be experiencing is olfactory fatigue, the temporary, normal inability to distinguish a particular odor after a prolonged exposure to it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a form of neural adaptation, a change over time in the responsiveness of the sensory system to a constant stimulus. This adaptative mechanism might prevent the overloading of the nervous system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, some people (maybe most of them?) are able to smell their own breath. At least, I know I do. I can't point you to any statistics, but it might be an interesting research project, figuring out how many people can smell their own breath.&lt;/p&gt;&#xA;" OwnerUserId="6543" LastActivityDate="2014-10-16T11:21:38.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23205" PostTypeId="2" ParentId="23186" CreationDate="2014-10-16T11:22:05.177" Score="4" Body="&lt;p&gt;Thats an interesting and complex question. First, Mycobacteria tuberculosis is present for a long time in the human population and evolved to evade our immune system. One of the keys are glycolipids and sugars which are part of the bacterial cell wall. These either help suppressing an immune response or help the bacteria to enter host cells in which they can stay without being identified by the immune system. See references 1-3 for details on this topic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then most tuberculosis infections are hold of by the immune system, mostly they come up, when the carriers immune system is compromised. M. tuberculosis can successfully hide inside macrophages and multiply there and start an infection from this hiding place. See references 4 and 5 for more details here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the main problems with the development of new vaccines is that this takes quite a long time from successful experiments in the lab to the availability of a usable vaccine. Tuberculosis has been neglected here for decades. Then the market for such a vaccine wasn't deemed lucrative enough from the pharma companies, as this is mostly important for poor and developing countries. For use there, the vaccine needs to be cheap and easy to administer. Additionally humans are the main host for M.tuberculosis which makes chossing appropriate animal models for research and testing not an easy task.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The development of novel vaccine candidates follow different routes. First, there are live vaccinations, which mainly consist of modified strains of the BCG vaccine strain. Then there are vaccines in the development which are supposed to support the immune answer by BCG and finally, there are vaccines which are independent of BCG and are mostly composed from proteins of the outer bacterial cell wall. For an overview about this field, I can recommend the review articles 6 and 7, if you want to go deeper in the field, also the references 8-10.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://iai.asm.org/content/77/10/4574.full&quot; rel=&quot;nofollow&quot;&gt;Mycobacterium tuberculosis Cell Wall Glycolipids Directly Inhibit&#xA;CD4+ T-Cell Activation by Interfering with Proximal T-Cell-Receptor&#xA;Signaling&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22880012&quot; rel=&quot;nofollow&quot;&gt;Divergent Effects of Mycobacterial Cell Wall Glycolipids on&#xA;Maturation and Function of Human Monocyte-Derived Dendritic Cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://ac.els-cdn.com/S0966842X98013018/1-s2.0-S0966842X98013018-main.pdf?_tid=06531716-5520-11e4-8e2c-00000aab0f6b&amp;amp;acdnat=1413455856_eef5bac024d3f6ab671c91a859c6cbed&quot; rel=&quot;nofollow&quot;&gt;Interactions between Mycobacterium tuberculosis and host cells: are&#xA;mycobacterial sugars the key?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3777/rfv5wsfq_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Annulling a dangerous liaison: vaccination strategies against AIDS&#xA;and tuberculosis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://jid.oxfordjournals.org/content/191/1/65.full&quot; rel=&quot;nofollow&quot;&gt;Macrophages Play a Dual Role during Pulmonary Tuberculosis in Mice&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1002607&quot; rel=&quot;nofollow&quot;&gt;Vaccines against Tuberculosis: Where Are We and Where Do We Need to&#xA;Go?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.biomedcentral.com/1471-2334/14/S1/S2&quot; rel=&quot;nofollow&quot;&gt;Vaccine against tuberculosis: what’s new&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://genmico.unizar.es/PDF/MartinOp2006.pdf&quot; rel=&quot;nofollow&quot;&gt;Tuberculosis vaccines: past, present and future.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3777/ifggnqzo_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Childhood tuberculosis: old and new vaccines.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jidc.org/index.php/journal/article/download/23492994/837&quot; rel=&quot;nofollow&quot;&gt;Exploiting the mycobacterial cell wall to design improved vaccines&#xA;against tuberculosis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-16T11:22:05.177" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23207" PostTypeId="1" AcceptedAnswerId="23211" CreationDate="2014-10-16T13:43:06.620" Score="3" ViewCount="14676" Body="&lt;p&gt;I can not find some useful sources unfortunately.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please tell me about some important characteristics of DH5 alpha.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What makes DH5 alpha suitable for the gene cloning?&lt;/p&gt;&#xA;" OwnerUserId="9797" LastEditorUserId="5144" LastEditDate="2014-10-17T13:33:48.423" LastActivityDate="2014-11-12T20:37:44.653" Title="What are some of the general characteristics of the DH5 alpha strain?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23208" PostTypeId="1" AcceptedAnswerId="23513" CreationDate="2014-10-16T14:33:27.827" Score="29" ViewCount="13406" Body="&lt;p&gt;I was reading &lt;a href=&quot;http://xkcd.com/1434/&quot;&gt;a comic&lt;/a&gt; from XKCD which inspired me to ask this question: &quot;well, where do they go when it rains?&quot; I know that when it rains you usually don't see any birds flying through the sky.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I imagine they normally hide in trees or under other kinds of cover. But for migratory birds, I don't think it is possible to hiding under cover until the rain passes. There might not be any cover (trekking across seas) or it might stay rainy for a very long time (and therefore cold...).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I did some research, but the answers are conflicting. Some people say they do stay in trees, others say they AVOID trees (because trees can snap in a storm, plus if there's lightning then sitting in a tree will net fried birds). Then there's people saying that birds have a waterproof coating... but that's a bit contradictory with me not seeing birds when it rains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So where do birds go when it rains?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume that different bird species and groups of birds will behave in different ways. I am interested in the case of migratory birds because they are likely to encounter different climates and have perhaps devised strategies to be safe. I would appreciate any well-referenced examples.&lt;/p&gt;&#xA;" OwnerUserId="9798" LastEditorUserId="9798" LastEditDate="2014-10-21T11:46:05.820" LastActivityDate="2017-08-24T09:13:52.280" Title="Where do migratory birds go when it rains?" Tags="&lt;ethology&gt;&lt;ornithology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="23209" PostTypeId="1" AcceptedAnswerId="23686" CreationDate="2014-10-16T14:48:20.420" Score="14" ViewCount="908" Body="&lt;p&gt;It's the age old question, why can't we tickle ourselves? If you rub your fingers along your skin, sure there's sensation but you don't break down into a laughing fit (at least I don't :P), if someone else does it to you, you're rolling around on the ground begging them to stop tickling you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is it that other people can tickle us but we can't tickle ourselves by touch? (I'm aware that if you use a feather or foreign object on yourself you can be tickled by it so that doesn't count.)&lt;/p&gt;&#xA;" OwnerUserId="9503" LastActivityDate="2018-06-05T01:49:20.750" Title="Why can you not tickle yourself?" Tags="&lt;human-biology&gt;&lt;sensation&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23211" PostTypeId="2" ParentId="23207" CreationDate="2014-10-16T15:06:46.163" Score="3" Body="&lt;p&gt;There are two possible sources: One is the article from the Bethesda Research Laboratories (reference 1), which names a few, the other is the book &quot;DNA cloning: A practical approach&quot; (see reference 2)., which sits here in my bookshelf.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taking both together, the DH5 alpha strain is derived from the DH5 strain with the introduction of a few additional features. The naming DH are the initials of Douglas Hanahan which developed the strain. The strain is easy to transform with high efficency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The new features of DH5 alpha are the recA and the endA1 mutations: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The endA1 mutation inactivates an intracellular endonuclease that&#xA;degrades plasmid DNA.&lt;/li&gt;&#xA;&lt;li&gt;The recA mutation eliminates homologous recombination. This reduces the chance for deletions and plasmid multimerization.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The DH5 strain also has the following features:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The hsdR17 mutation eliminates the restriction endonuclease of the&#xA;EcoKI restriction-modification system, so DNA lacking the EcoKI&#xA;methylation will not be degraded. DNA prepared from hsdR strains that&#xA;are wt for hsdM will be methylated and can be used to transform wt E.&#xA;coli K-12 strains.&lt;/li&gt;&#xA;&lt;li&gt;Δ(lacZ)M15 is the alpha acceptor allele needed for blue-white&#xA;screening with many lacZ based vectors.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Of special interest are the references 3 and 4, which gives you all the details you want to know.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://ebookbrowsee.net/focus-volume-8-issue-2-pdf-d420447162&quot; rel=&quot;nofollow&quot;&gt;Bethesda Research Laboratories. 1986. BRL pUC host: E. coli DH5α&#xA;competent cells. Focus 8(2):9.&lt;/a&gt; The article is on page 13 in this paper.&lt;/li&gt;&#xA;&lt;li&gt;DNA Cloning: A Practical Approach. Glover, D. M. (ed.), 1985, Vol. 1, p. 109, IRL Press, McLean, Virginia&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bitesizebio.com/10292/choosing-a-competent-ecoli-strain/&quot; rel=&quot;nofollow&quot;&gt;Choosing a Competent E.coli Strain&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://openwetware.org/wiki/E._coli_genotypes&quot; rel=&quot;nofollow&quot;&gt;E. coli genotypes&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-11-12T20:37:44.653" LastActivityDate="2014-11-12T20:37:44.653" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23212" PostTypeId="1" CreationDate="2014-10-16T15:11:14.210" Score="3" ViewCount="48" Body="&lt;p&gt;I've heard from several sources that the predominant form of alternative splicing (at least in mammals) is exon skipping. However, my personal evidence is only anecdotal: I've heard it and read it, but have not seen references to literature. Is there a seminal paper or set of papers establishing this finding that I can cite?&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2014-10-17T04:39:00.187" Title="Exon skipping in mammals" Tags="&lt;molecular-genetics&gt;&lt;genomics&gt;&lt;splicing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23214" PostTypeId="2" ParentId="23208" CreationDate="2014-10-16T16:36:04.357" Score="0" Body="&lt;p&gt;Birds can easily cover enough distance flying that they can avoid short showers entirely by not sitting right below clouds, unless they have an actual reason to stick around. Birds move around a lot more than we do.&lt;/p&gt;&#xA;" OwnerUserId="9801" LastActivityDate="2014-10-16T16:36:04.357" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23215" PostTypeId="1" AcceptedAnswerId="23219" CreationDate="2014-10-16T18:01:35.623" Score="1" ViewCount="286" Body="&lt;p&gt;I have 4 question (not homework)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What happens to the cells membrane potential if:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) Na+ outside rises by 40mM&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) K+ inside rises by 10mM&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c) K+ outside rises by 10mM&lt;/p&gt;&#xA;&#xA;&lt;p&gt;d) A- (impermeable ion) inside rises by 100mM&lt;/p&gt;&#xA;&#xA;&lt;p&gt;e) Na+ outside decline by 50mM&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So my answers are:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a – hyperpolarisering (more negative)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b – Depolarisering (more positive)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;c – Hyperpolarisering&lt;/p&gt;&#xA;&#xA;&lt;p&gt;d – Depolarisering&lt;/p&gt;&#xA;&#xA;&lt;p&gt;e - Depolarisering&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Membrane potential is the DIFFERENCE in electrical potential inside and outside the cell. When we say a cell has a resting potential of -60mV we mean that the cell has 60mV LESS than the extracellular space.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when I am asked what happens if all of a sudden, the extracellular space increases in mV (first question) then I can say that the difference is now GREATER than 60 mV, it is now in fact 100 mV, as the extracellular space has increased by 40 mV, then plussing the already established 60 mV.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this the correct way to think about these problems?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="3340" LastEditDate="2014-10-17T04:31:46.707" LastActivityDate="2014-10-17T04:31:46.707" Title="Understanding intra and extracelullar concentrations (membrane potential)" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;homework&gt;&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23217" PostTypeId="2" ParentId="2922" CreationDate="2014-10-16T18:48:15.180" Score="2" Body="&lt;p&gt;&lt;em&gt;This is a draft.&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;How do the pharmacodynamics of the NSAIDs differ - -?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Merck's manual ch. 36 to start little bit at an introductory level:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The anti-inflammatory activity of the NSAIDs is mediated chiefly&#xA;  through inhibition of biosynthesis of prostaglandins (Figure 36–2). &#xA;  Various NSAIDs have additional possible mechanisms of action,&#xA;  including inhibition of chemotaxis, down-regulation of interleukin-1&#xA;  production, decreased production of free radicals and superoxide,&#xA;  and interference with calcium-mediated intracellular events.  Aspirin&#xA;  irreversibly acetylates and blocks platelet cyclooxygenase, while most&#xA;  non-COX-selective NSAIDs are reversible inhibitors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and see the coming answer below. &#xA;These questions should be answered together. &#xA;To split them can be confusing.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Is there any difference in the degree to which these drugs manipulate/inhibit the enzymes (I assume their affinities for COX-1 and COX-2 are at least somewhat different)?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Please, see ch 1.03.3 in &lt;em&gt;Comprehensive Natural Products II: Chemistry and Biology: 10 Volume Set&lt;/em&gt;: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/niANK.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and their conclusions about the structure&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5wzhZ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and please, see the whole chapter of the book, since its about the topic - and I think good one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;em&gt;Katzung et al.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Selectivity for COX-1 versus COX-2 is variable and incomplete for&#xA;  the older NSAIDs, but many selective COX-2 inhibitors have been&#xA;  synthesized. The selective COX-2 inhibitors do not affect platelet&#xA;  function at their usual doses.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;On the other hand, selective COX-2 inhibitors may increase the&#xA;  incidence of edema and hypertension.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;To varying degrees, all newer NSAIDs are analgesic, anti-inflammatory, and antipyretic, and all (except the COX-2- selective&#xA;  agents and the nonacetylated salicylates) inhibit platelet&#xA;  aggregation. NSAIDs are all gastric irritants and can be associated&#xA;  with gastrointestinal ulcers and bleeds as well, although as a group&#xA;  the newer agents tend to cause less gas- trointestinal irritation than&#xA;  aspirin.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In short, there must be differences to which these drugs manipulate/inhibit the enzymes.&#xA;Please, see&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Selinsky BS, Gupta K, Sharkey CT, Loll PJ. Structural analysis of&#xA;NSAID binding by prostaglandin H2 synthase: time-dependent and time&#xA;independent inhibitors elicit identical enzyme conformations. Biochemistry 40, 5172–5180 (2001).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Defining the COX Inhibitor Selectivity of NSAIDs: Implications for Understanding Toxicity. Expert Rev Clin Pharmacol. 2010;3(6):769-776&lt;/em&gt;. And see the chapter &lt;em&gt;Expert Commentary&lt;/em&gt; which locates at the end of the publication there:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Not withstanding the caveats on the merit of IC50 values, in vitro&#xA;  analyses of COX-1 and COX-2 selectivity of NSAIDs has driven the&#xA;  concept that inhibition of COX-1 explains the predominant reduction in&#xA;  synthesis of mucosal protective PGs and hence gastrointestinal&#xA;  toxicity of NSAIDs relative to COX-2 inhibition, which plays a role in&#xA;  ulcer healin&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Merck's manual chapter 36&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The discovery of two cyclooxygenase isoforms (COX-1 and COX-2) led to&#xA;  the concept that the constitutive COX-1 isoform tends to be&#xA;  homeostatic in function, while COX-2 is induced during inflammation&#xA;  and tends to facilitate the inflammatory response. On this basis,&#xA;  highly selective COX-2 inhibitors have been developed and marketed on&#xA;  the assumption that such selective inhibitors would be safer than&#xA;  nonselective COX-1 inhibitors but without loss of efficacy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Inflammatory processes are expressed by both COX-1 and COX-2 differently. &#xA;This means that a change in the cell membrane expresses lysosomal enzymes differently:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The cell damage associated with inflammation acts on cell membranes to&#xA;  cause leukocytes to release lysosomal enzymes; arachidonic acid is&#xA;  then liberated from precursor compounds, and various eicosanoids are&#xA;  synthesized.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also, the cyclooxygenase (COX) pathway of arachidonate metabolism produces prostaglandins, which have a variety of effects on blood vessels, on nerve endings, and on cells involved in inflammation. (See Merck, ch. 18)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I like the Figure 36.2 in Merck's manual. &#xA;To better answer your question, one could label the arrows there with relevant enzymes in each processes and compare those between COX-1 and COX-2 and relate to corresponding publications (only few existing!). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adrenaline and other compounds activate the cyclooxygenase pathway, COX-1 pathway for instance, and the conversion of arachidonate to PGs and TXs. [2, p. 67] &#xA;The classic law of mass action allows to describe the reversible binding:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;\begin{equation}&#xA;    [Protein] + [L] \rightleftharpoons^{k_{1}}_{k_{-1}} [Protein-L]&#xA;\end{equation}&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $L$ is ligand, Protein-L the protein-ligand complex, $k_1$ the rate constant of the forward reaction, while $K_{-1}$ the rate constant of the reverse reaction. &#xA;This fine regulation differs between COX-1 and COX-2 at enzymatic level regulated by &lt;strong&gt;cytokines&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;COX-1 becomes only little activated in inflammation, in comparison to COX-2. &#xA;COX-2 is present in macrophages (chronic inflammation! - cytokines), fibroblasts, endothelial cells, synovial fluids, and chondriocytes.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;[A]re there “resistant” COX phenotypes?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I have not heard about this that there would not be. &#xA;There are so many components in PGHSs which can develop resistances.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;[A]re there any known phenotypes of COX-1 and COX-2 enzymes that are present in the general population that affect the ability of these drugs to act?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Please, see for the phenotypes of COX-1 &lt;a href=&quot;http://www.yeastgenome.org/locus/S000007260/phenotype&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;, while about COX-2 much less has been research, see &lt;a href=&quot;http://www.yeastgenome.org/locus/S000007281/phenotype&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; - no known phenotypes, see &lt;a href=&quot;http://www.bioinformatics.org/textknowledge/all.php?term=PGHS-2&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt;.&#xA;Please, note also that COX has at least two isoforms: COX-1 (PGHS-1) and COX-2 (PGHS-2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;COX-1 phenotypes&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;176805, &lt;a href=&quot;http://www.bioinformatics.org/textknowledge/all.php?term=PGHS1&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Is there any evidence as to whether the the NSAIDs collect in certain areas of the body in a compartmental fashion?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;No.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each disease has its own characteristics. &#xA;&lt;a href=&quot;https://uqu.edu.sa/files2/tiny_mce/plugins/filemanager/files/4250110/NSAIDs&amp;amp;tt%20Gout.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gout&lt;/a&gt;, for instance, has swelling of syvovial joints and usage of NSAIDs with COX-2.&#xA;My professor of abdominal surgery answered to this question directly - &lt;em&gt;impossible to answer generally&lt;/em&gt; which I agree with her. (17.10.2014) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the OP has in mind some antibiotics which concentrate in some parts of the body (such as 1st generation quinolones concentrating in the renal tubules and bladder, thus exerting local antibacterial effect). &#xA;There is no similar effect with NSAIDs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead, NSAIDs have local and systemic effects, not because they are concentrating in some parts of the body, but because they have several mechanisms itself. &#xA;Please, see this thread about &lt;a href=&quot;http://www.researchgate.net/post/Effect_of_NSAIDS_on_stomach&quot; rel=&quot;nofollow noreferrer&quot;&gt;Effect of NSAIDS on stomach&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Are there differences in fat solubility, etc., between the different drugs?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Fat burner - of course, there are differences in fat solubility between different NSAIDs. &#xA;Please, see this publication &lt;em&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs10953-011-9709-z&quot; rel=&quot;nofollow noreferrer&quot;&gt;Solubility of Nonsteroidal Anti-inflammatory Drugs (NSAIDs) in Aqueous Solutions of Non-ionic Surfactants&lt;/a&gt;&lt;/em&gt;. &#xA;I will update this part next week more. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Other sources&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Basic and Clinical Pharmacology, 11th edition, 2009, Bertram Katzung.&lt;/li&gt;&#xA;&lt;li&gt;My notes during Biochemistry classes in Tartu 2011-2013&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-10-18T11:10:21.293" LastActivityDate="2014-10-18T11:10:21.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23219" PostTypeId="2" ParentId="23215" CreationDate="2014-10-16T19:21:54.243" Score="3" Body="&lt;p&gt;Afaik you can describe the potentials between the two sides of the cell membrane using the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nernst_equation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nernst-equation&lt;/a&gt;. Yepp wikipedia writes the same &lt;a href=&quot;http://en.wikipedia.org/wiki/Membrane_potential&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Membrane potential is a very important thing, because human cells require stable internal concentrations of Na+, K+, Ca2+, etc... in order to work properly. These concentration can depend on species, for example plants cells work completely different than animal cells, they have higher Na+ than K+ in their cytoplasm. So every human cell has to maintain a membrane potential if they don't want to die. It requires a lot of ATP (energy) to do so... Human cells typically maintain this potential against the blood plasma. Cytoplasm has around 120mM K+ and 15mM Na+, while the blood plasma has about 5mM K+ and 140mM Na+. You can count the membrane potential from these concentrations using the Nernst equation (a &lt;a href=&quot;https://www.youtube.com/watch?v=t7Gr_tmShm4&quot; rel=&quot;nofollow noreferrer&quot;&gt;short presentation about how&lt;/a&gt;). I don't remember the exact mV value, does not matter. So human cells are working hardly on keeping the Na+ outside and K+ inside, and they can possibly die because of membrane potential changes (e.g. when they require too much energy to maintain the internal concentrations and/or osmolarity).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Excitable cells, e.g. nerve cells or muscle cells are very special because they can change their membrane potential rapidly by sending out K+, Ca+ or sending in Na+. This can create small electric discharges, which can be used to send electric signals or contract muscles, etc... Different cells have different discharge diagrams, e.g. axons have something like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3SqhP.gif&quot; alt=&quot;axon electric discharge diagram&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Figure 1 - axon electric discharge diagram - &lt;a href=&quot;http://mcat-review.org/specialized-eukaryotic-cells-tissues.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and muscles have something like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bJFKl.jpg&quot; alt=&quot;muscle discharge diagrams&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Figure 2 - muscle electric discharge diagrams - &lt;a href=&quot;http://cnx.org/contents/14fb4ad7-39a1-4eee-ab6e-3ef2482e3e22@7.1:127/Anatomy_&amp;amp;_Physiology&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Summa summarum it can depend on the cell type what happens, but basicly you can count the new potential using the Nernst equation by the concentration changes you mentioned...&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-16T19:28:05.027" LastActivityDate="2014-10-16T19:28:05.027" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23221" PostTypeId="1" AcceptedAnswerId="23225" CreationDate="2014-10-16T20:30:13.067" Score="6" ViewCount="1210" Body="&lt;p&gt;I understand that membrane potential is the difference of the extracellular and intracellular ionic charges, due to their concentrations. We say that the extracellular space has a charge of 0 and then take the membrane potential with respect to the extracellular space. The intracellular space is normally around -60mV due to more negative charges being in the cell than the extracellular space.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is how I understand membrane potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this understanding, it is hard for me to see why I can't get this right:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We work with a regular cell with potassium 120mM inside and 4.5mM outside.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Say that we increase the intracellular concentration of potassium by 10 mM, a +1 valence ion which contributes to POSITIVE membrane potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I envision is that as we put more positive ions in the cell, the cell is now more positive in regard to the extracellular matrix. However the Nernst equation states that the membrane potential actually gets MORE NEGATIVE!!&#xA;&lt;a href=&quot;http://www.physiologyweb.com/calculators/nernst_potential_calculator.html&quot;&gt;http://www.physiologyweb.com/calculators/nernst_potential_calculator.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is it that I am misunderstanding? Thank you.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2014-10-18T13:21:31.533" Title="Problems understanding membrane potential" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;biophysics&gt;&lt;cell-membrane&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23225" PostTypeId="2" ParentId="23221" CreationDate="2014-10-17T03:00:29.213" Score="9" Body="&lt;p&gt;I think this question has more to do with &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemical_kinetics&quot;&gt;kinetics&lt;/a&gt; / &lt;a href=&quot;http://en.wikipedia.org/wiki/Transport_phenomena&quot;&gt;transport phenomenons&lt;/a&gt; than biology, but that's okay, everything is connected especially my computer to the internet. ;-)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The basic idea behind &lt;a href=&quot;http://en.wikipedia.org/wiki/Transport_phenomena&quot;&gt;transport phenomenons&lt;/a&gt; is that there will always be a &lt;a href=&quot;http://en.wikipedia.org/wiki/Flux&quot;&gt;flux&lt;/a&gt; of &lt;a href=&quot;http://en.wikipedia.org/wiki/Intensive_and_extensive_properties&quot;&gt;quantitative properties&lt;/a&gt; (e.g. charges, particle number, entropy, volume, etc...) where the &lt;a href=&quot;http://en.wikipedia.org/wiki/Intensive_and_extensive_properties&quot;&gt;qualitative properties&lt;/a&gt; like (electrical potential, chemical potential, temperature, pressure, etc...) have a &lt;a href=&quot;http://en.wikipedia.org/wiki/Gradient&quot;&gt;gradient&lt;/a&gt; in space (note that kinetics of chemical reactions can be described similarly without the space gradient part).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case we are talking about &lt;a href=&quot;http://en.wikipedia.org/wiki/Electrochemical_potential&quot;&gt;electrochemical potential&lt;/a&gt; gradient and &lt;a href=&quot;http://en.wikipedia.org/wiki/Ion&quot;&gt;ion&lt;/a&gt; flux. It is very important to recognize that the electrochemical potential is not the same as the electric potential. It has a chemical component, so the result will depend on both charge and concentration gradients. By a single ion channel system (e.g. Na⁺ channel only) you can count the potential of each side of the membrane using the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nernst_equation&quot;&gt;Nernst equation&lt;/a&gt;, by a system with multiple ion channels it is more complicated, so in that case you have to use the &lt;a href=&quot;http://en.wikipedia.org/wiki/Goldman_equation&quot;&gt;Goldman equation&lt;/a&gt;. So at the end you can say something like one side has a potential of &lt;strong&gt;&lt;em&gt;x[mV]&lt;/em&gt;&lt;/strong&gt; and the other side has a potential of &lt;strong&gt;&lt;em&gt;y[mV]&lt;/em&gt;&lt;/strong&gt; and so the difference is:  &lt;strong&gt;&lt;em&gt;d[mV] = x[mV] - y[mV]&lt;/em&gt;&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sign of &lt;strong&gt;&lt;em&gt;d&lt;/em&gt;&lt;/strong&gt; depends on &lt;strong&gt;&lt;em&gt;x&lt;/em&gt;&lt;/strong&gt; or &lt;strong&gt;&lt;em&gt;y&lt;/em&gt;&lt;/strong&gt; has a greater value. By single ion channel systems this expresses an &lt;strong&gt;&lt;em&gt;x → y&lt;/em&gt;&lt;/strong&gt; direction so by positive &lt;strong&gt;d&lt;/strong&gt; the cation flow direction is &lt;strong&gt;&lt;em&gt;x → y&lt;/em&gt;&lt;/strong&gt; and by negative &lt;strong&gt;&lt;em&gt;d&lt;/em&gt;&lt;/strong&gt; it is &lt;strong&gt;&lt;em&gt;y → x&lt;/em&gt;&lt;/strong&gt;. By anion flow it is the opposite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By cells we use the &lt;strong&gt;&lt;em&gt;out → in&lt;/em&gt;&lt;/strong&gt; direction by counting the membrane potential. We can count the potentials using the &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Nernst equation:&#xA;$$E_m = \frac{RT}{zF} \times ln \left(\frac{c_{out}}{c_{in}}\right)$$ or the &lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Goldman equation: &#xA;$$E_m = \frac{RT}{F} \times ln \left(\frac{p_{K^+}.[K^+]_{out} + p_{Na^+}.[Na^+]_{out} + p_{Cl^-}.[Cl^-]_{in}} {p_{K^+}.[K^+]_{in} + p_{Na^+}.[Na^+]_{in} + p_{Cl^-}.[Cl^-]_{out}}\right)$$&#xA;where  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;$Em$ is the membrane potential&lt;/li&gt;&#xA;&lt;li&gt;$z$ is the ion charge&lt;/li&gt;&#xA;&lt;li&gt;$[X]$ is the ion concentration&lt;/li&gt;&#xA;&lt;li&gt;$p_X$ is the relative membrane permeability for the actual ion&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and so on...&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So for example by an average human cell in blood plasma, assuming that the inside of the membrane has a small negative charge&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the &lt;strong&gt;&lt;em&gt;Na⁺&lt;/em&gt;&lt;/strong&gt; has a positive effect (positive charge, high &lt;strong&gt;&lt;em&gt;out → in&lt;/em&gt;&lt;/strong&gt; concentration gradient, low &lt;strong&gt;&lt;em&gt;out → in&lt;/em&gt;&lt;/strong&gt; charge gradient),&lt;/li&gt;&#xA;&lt;li&gt;the &lt;strong&gt;&lt;em&gt;K⁺&lt;/em&gt;&lt;/strong&gt; has a negative effect (positive charge, high &lt;strong&gt;&lt;em&gt;in → out&lt;/em&gt;&lt;/strong&gt; concentration gradient, low &lt;strong&gt;&lt;em&gt;out → in&lt;/em&gt;&lt;/strong&gt; charge gradient),&lt;/li&gt;&#xA;&lt;li&gt;the &lt;strong&gt;&lt;em&gt;Cl¯&lt;/em&gt;&lt;/strong&gt; has a negative effect (negative charge, high &lt;strong&gt;&lt;em&gt;out → in&lt;/em&gt;&lt;/strong&gt; concentration gradient, low &lt;strong&gt;&lt;em&gt;in → out&lt;/em&gt;&lt;/strong&gt; charge gradient)&lt;/li&gt;&#xA;&lt;li&gt;the &lt;strong&gt;&lt;em&gt;Mg⁺⁺&lt;/em&gt;&lt;/strong&gt; has a small positive effect (positive charge, low &lt;strong&gt;&lt;em&gt;out → in&lt;/em&gt;&lt;/strong&gt; concentration gradient, low &lt;strong&gt;&lt;em&gt;out → in&lt;/em&gt;&lt;/strong&gt; charge gradient)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;on the membrane potential. It is hard to find an ion in this case which flow is charge gradient dominated instead of concentration gradient...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I understand that membrane potential is the difference of the&#xA;  extracellular and intracellular ionic charges, due to their&#xA;  concentrations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The (sign and) value of the membrane potential is not determined by the charge gradient because the concentration gradients usually have a much bigger effect on it. The cells maintain these concentration gradients by using up energy.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We work with a regular cell with potassium 120mM inside and 4.5mM&#xA;  outside.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Say that we increase the intracellular concentration of potassium by&#xA;  10 mM, a +1 valence ion which contributes to POSITIVE membrane&#xA;  potential.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In your case &lt;strong&gt;&lt;em&gt;K⁺&lt;/em&gt;&lt;/strong&gt; has a negative effect on the membrane potential, because of the high concentration gradient with reverse direction. So decreasing the concentration gradient will increase the membrane potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to learn more about how to count membrane potentials, you should read &lt;a href=&quot;http://www.physiologyweb.com/lecture_notes/resting_membrane_potential/resting_membrane_potential_nernst_equilibrium_potential.html&quot;&gt;this&lt;/a&gt; and its &lt;a href=&quot;http://www.physiologyweb.com/lecture_notes/resting_membrane_potential/resting_membrane_potential_in_real_cells_multiple_ions_contribute_to_the_membrane_potential.html&quot;&gt;next section&lt;/a&gt; instead of wikipedia...&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-18T13:21:31.533" LastActivityDate="2014-10-18T13:21:31.533" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="23226" PostTypeId="2" ParentId="23212" CreationDate="2014-10-17T04:39:00.187" Score="2" Body="&lt;p&gt;You can see &lt;a href=&quot;http://www.nature.com/nrg/journal/v11/n5/full/nrg2776.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; review. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There are several different types of alternative splicing (AS) events,&#xA;  which can be classified into four main subgroups. The first type is&#xA;  exon skipping, in which a type of exon known as a cassette exon is&#xA;  spliced out of the transcript together with its flanking introns (see&#xA;  the figure, part a). Exon skipping accounts for nearly 40% of AS&#xA;  events in higher eukaryotes &lt;sup&gt;[17, 111]&lt;/sup&gt; but is extremely rare in lower&#xA;  eukaryotes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-10-17T04:39:00.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23230" PostTypeId="1" AcceptedAnswerId="23231" CreationDate="2014-10-17T06:07:42.237" Score="2" ViewCount="162" Body="&lt;p&gt;I need to have a book which covers following topics two may also be fine:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(a) Structure and role of carbohydrates, fats, fatty acids and cholesterol, proteins and amino-acids, nucleic acids. Bioenergetics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) Glycolysis and the Krebs cycle, oxidation and reduction, oxidative phosphorylation, energy conservation and release, ATP cycle, cyclic AMP – its structure and role.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(c) Hormone classification (steroid and peptide hormones), biosynthesis and functions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(d) Enzymes: types and mechanisms of action.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(e) Vitamins and co-enzymes&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(f) Immunoglobulin and immunity.&lt;/p&gt;&#xA;" OwnerUserId="9674" LastEditorUserId="22057" LastEditDate="2019-02-05T16:38:55.003" LastActivityDate="2019-02-05T16:38:55.003" Title="Book-recommendation: Biochemistry" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="23231" PostTypeId="2" ParentId="23230" CreationDate="2014-10-17T07:14:16.423" Score="2" Body="&lt;p&gt;Lehninger Principles of Biochemistry by Nelson and Cox is quite popular and covers everything you listed in great detail except for immunology. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't really have a recommendation for an immunology book; I think pretty well any of them will cover immunoglobulins (they're pretty integral). My university uses Kuby Immunology by Kindt et al. Molecular Biology of the Cell by Alberts et al. has a couple chapters (some 115 pages) on the subject. As a bonus, it's an amazing reference for cell biology (which you'll need, at least someday, if you're pursuing biochemistry). &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-10-17T07:25:34.000" LastActivityDate="2014-10-17T07:25:34.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23234" PostTypeId="2" ParentId="23221" CreationDate="2014-10-17T10:02:50.667" Score="7" Body="&lt;p&gt;I think &lt;a href=&quot;https://biology.stackexchange.com/users/3703/inf3rno&quot;&gt;inf3rno&lt;/a&gt;'s answer is very complete, so I will just be adding some notes that might help OP understanding what's happening.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Say that we increase the intracellular concentration of potassium by&#xA;  10 mM, a +1 valence ion which contributes to POSITIVE membrane&#xA;  potential.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Let's say we do that, in an &lt;em&gt;in vitro&lt;/em&gt; cell model, using a syringe with &lt;strong&gt;only K⁺ ions&lt;/strong&gt;. What would happen? &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What I envision is that as we put more positive ions in the cell, the&#xA;  cell is now more positive in regard to the extracellular matrix.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And that is true, at least instantly. However, due to the differences in concentration gradients, the K⁺ would quickly flow out until electrochemical balance was restored. This would lead to an increase in K⁺ concentration outside our cell model so, in the end, the net charge would decrease inside the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you can think of the Nernst equation as a mathematical model to the cell in equilibrium. &lt;/p&gt;&#xA;" OwnerUserId="6543" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-10-17T11:07:41.920" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23235" PostTypeId="1" AcceptedAnswerId="23251" CreationDate="2014-10-17T10:09:08.297" Score="0" ViewCount="34858" Body="&lt;p&gt;I started to to think the pathophysiology of elevating legs high next to the wall too often and when you are tired. &#xA;I think possible manifestations&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;some damage to valves of the veins (&lt;strong&gt;No!&lt;/strong&gt;)&lt;/li&gt;&#xA;&lt;li&gt;because of collateral circulation, rhombus, heart damage, ... (&lt;strong&gt;No!&lt;/strong&gt; Only in pathological situation but cannot be considered here. I think here that the risk of thrombus leaving legs is higher when you elevate your legs.)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Other side is when you should do this. &#xA;To do regularly like every evening - may not be the right way to go. &#xA;If you are tired and you do this, the vasomotor tonus is already lower so smooth muscles can less help to keep the blood so much more stress to the valves. &#xA;Cardiac output is also less because of tiredness so lymphatic drainage is less. &#xA;Elevating legs will move more lymph and blood to the middle of the body. &#xA;So less lymph and blood can be moved back to legs when you tired. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the risks of elevating legs for too long time in Short time and Long time?&lt;/strong&gt; &#xA;Is there any advantage in elevating legs like increasing blood circulation of our body? &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;In what manner would elevating legs harm valves?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There should be no damage to valves because the direction of the blood circulation does not change. &#xA;Blood is only going from legs to heart. &#xA;I think the vasoconstriction of smooth muscles occurs first in the legs. &#xA;This returns some blood to the legs. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;How is lymph made - -?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Lymph is made in lymph nodes. &#xA;After leaving the node, it is rich in lymphocytes. &#xA;After leaving digestive system, it is rich in triglycerides so called chyle. &#xA;I think after leaving legs it is also rich in triglycerides. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;[W]hat is the danger of lymph leaving the legs?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I think the effective lymph (that one used in legs) is coming from the lymph nodes of the legs. &#xA;Some lymph can be made in lymph nodes of legs so no danger of lymph leaving legs. &#xA;However, some may come from the region of coxa. &#xA;&lt;strong&gt;How long distance can lymph travel as effective unit of immune system?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If all lymph nodes are working, there is no danger of lymph leaving the legs, I think. &#xA;If there are problems with lymph nodes of legs, then there may occur some constitutional symptoms of legs - but not sure about how fast. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Does the heart get tired like your head does, or like muscles after exercise?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;No.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="9268" LastEditDate="2014-10-25T14:58:21.777" LastActivityDate="2015-07-24T00:46:58.497" Title="What are the risks of elevating the legs too regularly and when tired?" Tags="&lt;physiology&gt;&lt;blood-circulation&gt;&lt;pathophysiology&gt;&lt;veins&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23236" PostTypeId="1" AcceptedAnswerId="23237" CreationDate="2014-10-17T10:41:26.993" Score="3" ViewCount="30762" Body="&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=27TxKoFU2Nw&quot; rel=&quot;nofollow&quot;&gt;https://www.youtube.com/watch?v=27TxKoFU2Nw&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the above video it shows that during DNA replication, the lagging strand require RNA primase to add 3' -OH group for further addition of nucleotides. However, it hasn't been shown that the above strand ( leading strand) require it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides, RNA is needed to initiate the polymerization because it has the 3'-OH.&#xA;But when I look at the structure of deoxynucleotide, it also has the 3'-OH but it does not have the 2'-OH. So why DNA cannot initiate the polymerization? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your answer!&lt;/p&gt;&#xA;" OwnerUserId="9811" LastActivityDate="2014-10-17T11:01:21.037" Title="Does DNA replication in 5' to 3' (leading strand) need RNA primase?" Tags="&lt;dna&gt;&lt;replication&gt;&lt;primer&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23237" PostTypeId="2" ParentId="23236" CreationDate="2014-10-17T11:01:21.037" Score="3" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_polymerase&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA polymerase&lt;/a&gt; also needs a RNA primer on the leading strand to be able to start polymerization. Afterwards this is not needed anymore, since the &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_replication&quot; rel=&quot;nofollow noreferrer&quot;&gt;replication&lt;/a&gt; goes on without a break. On the lagging strand polymerization replication can only work between the replication fork and the next region of double-stranded DNA. See the figure (from &lt;a href=&quot;http://biology.tutorvista.com/cell/dna-replication.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TeaqU.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for the need for RNA primers is located in the function of the enzymes. While the DNA polymerase can only work on a double stranded template (add nucleotides to the 3'OH-end of the strand) the &lt;a href=&quot;http://en.wikipedia.org/wiki/Primase&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA Primase&lt;/a&gt; (actually an RNA polymerase) can work on single stranded targets and thus add the RNA primer there.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-17T11:01:21.037" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23238" PostTypeId="1" CreationDate="2014-10-17T11:32:57.027" Score="2" ViewCount="317" Body="&lt;p&gt;After looking through the available Stack Exchange sites, this one seems to come closest to the appropriate place to ask...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Popular opinion, including my own, is that banning flights to and from the Ebola-ridden portion of Africa would protect us overall. I understand it would increase pressure on that region, making it more chaotic and less conducive to tracking people, so that eventually it could &quot;explode uncontrollably&quot; out of that region in a year or whatever time frame. Sanjay Gupta explains this briefly in &lt;a href=&quot;http://news.yahoo.com/daily-show-jon-stewart-ebola-video-153138326.html&quot; rel=&quot;nofollow&quot;&gt;Jon Stewart's (at points hysterical) report&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The disadvantage of &lt;em&gt;allowing&lt;/em&gt; free travel to and from these regions, as I see it, is that the disease spreads much much faster, and to many many more disparate locations. This is because of the variety of places where each passenger comes from. And also the flight crew and plane itself, which affects all future passengers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd appreciate more educated opinions. I'm far from it, regarding these issues, as are many Americans.&lt;/p&gt;&#xA;" OwnerUserId="9812" LastEditorUserId="9812" LastEditDate="2014-10-17T13:28:58.263" LastActivityDate="2014-11-16T22:31:58.660" Title="What are the disadvantages of forbidding flights to and from the African Ebola region?" Tags="&lt;human-biology&gt;&lt;virology&gt;&lt;epidemiology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23239" PostTypeId="1" CreationDate="2014-10-17T12:48:03.297" Score="6" ViewCount="1959" Body="&lt;p&gt;There are many information about viral hepatitis. But it is interesting for me, can bacteria cause the hepatitis too?&lt;/p&gt;&#xA;" OwnerUserId="9815" LastEditorUserId="3340" LastEditDate="2014-10-20T06:25:01.133" LastActivityDate="2017-05-10T01:22:21.347" Title="Can Hepatitis be caused by Bacteria?" Tags="&lt;human-biology&gt;&lt;bacteriology&gt;&lt;hepatitis&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23240" PostTypeId="1" CreationDate="2014-10-17T12:49:18.727" Score="4" ViewCount="232" Body="&lt;p&gt;&lt;strong&gt;How many cells are there in the apical meristematic tissue?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at this picture...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rj2qBm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, I would tend to think that there are few hundreds cells in the meristem tissue. But I guess this is a picture of a root tip and the answer will be much different if we look at big branches and big trunks of roots. Also, the answer will probably differ between monocots and eudicots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Roughly speaking, how many cells are there in different apical&lt;/strong&gt; meristematic tissues (root, branches, trunk, different species)?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="12898" LastEditDate="2015-04-18T05:24:22.807" LastActivityDate="2020-08-14T12:07:08.553" Title="How many cells are there in the apical meristematic tissue?" Tags="&lt;cell-biology&gt;&lt;physiology&gt;&lt;botany&gt;&lt;plant-physiology&gt;&lt;histology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23241" PostTypeId="1" AcceptedAnswerId="23242" CreationDate="2014-10-17T13:28:39.587" Score="12" ViewCount="2166" Body="&lt;p&gt;I'm sure there will be variation depending on what the contaminated item or surface is made of - linens, I could imagine, would remain dangerous for longer than a door-knob. But if the items are not decontaminated in some way, how long can the virus survive outside a host?&lt;/p&gt;&#xA;" OwnerUserId="9817" LastEditorUserId="2949" LastEditDate="2014-10-24T18:29:13.157" LastActivityDate="2014-10-26T05:03:23.287" Title="How long does the Ebola virus remain infectious on contaminated items or surfaces?" Tags="&lt;virus&gt;&lt;virology&gt;&lt;infection&gt;&lt;epidemiology&gt;&lt;ebola&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23242" PostTypeId="2" ParentId="23241" CreationDate="2014-10-17T13:59:27.480" Score="12" Body="&lt;p&gt;This really depends on the environment, one study (listed below as reference 1) found that the Ebola virus can survive under ideal conditions on flat surfaces in the dark for up to six days - see the figure from the same publication. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0dLLL.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the virus is quite sensitive to UV radiation (see reference 2 for all the details) and most viral particles are likely to get inactivated within relatively short time. It might still be possible to get positive tests for Ebola from really sensitive PCR-based tests, but these are most likely not infectious anymore. The CDC lists common bleach (or any other routinely used disinfected) as a good way to get rid of Ebola viruses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/s00705-010-0791-0/fulltext.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Persistence in darkness of virulent alphaviruses, Ebola virus, and&#xA;Lassa virus deposited on solid surfaces&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/s00705-010-0847-1/fulltext.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sensitivity to ultraviolet radiation of Lassa, vaccinia, and Ebola&#xA;viruses dried on surfaces&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-17T13:59:27.480" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23243" PostTypeId="1" AcceptedAnswerId="23255" CreationDate="2014-10-17T14:16:22.950" Score="2" ViewCount="1030" Body="&lt;p&gt;Replication has an error rate of less than 1 in 100 million. DNA polymerase forms H-bond with the H-bond acceptor atoms in the minor groove. &amp;lt;-- enhance fidelity here?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Binding of the triphosphate group to the active site of DNA polymerase triggers a conformational change. Changing a conserved Tyr residue increases the error rate by 40 fold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't quite understand the above two statements. Can anyone explain in detail to me? Thanks!&lt;/p&gt;&#xA;" OwnerUserId="9811" LastEditorUserId="3340" LastEditDate="2014-10-20T06:21:39.837" LastActivityDate="2019-10-06T14:38:14.513" Title="How does high-fidelity of DNA replication depend on the formation of hydrogen bonds?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;genomics&gt;&lt;replication&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23246" PostTypeId="1" AcceptedAnswerId="23795" CreationDate="2014-10-17T16:18:13.933" Score="5" ViewCount="6350" Body="&lt;p&gt;I was wondering how protein denaturation works.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Are there covalent bonds, such as disulfide bridges involved, or is it based purely on non-covalent bonds such as hydrogen bonds? Why is denaturation irreversible in most cases if only non-covalent bonds are involved?&lt;/li&gt;&#xA;&lt;li&gt;Is it possible to denature protein by rapid changes in electromagnetic field or pressure? (The articles I have read so far mention only stress factors like sudden pH, osmolarity, temperature changes...)&lt;/li&gt;&#xA;&lt;li&gt;How can I protect a protein against denaturation? e.g. in PCR we use a heat resistant DNA polymerase, so certain amino acid sequences might protect against heat denaturation, but I need reassurance about this.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-17T16:47:11.523" LastActivityDate="2014-11-07T08:15:01.567" Title="How does protein denaturation work?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23247" PostTypeId="2" ParentId="23246" CreationDate="2014-10-17T17:41:34.827" Score="5" Body="&lt;p&gt;Really the question how does protein folding work?  But let me answer your questions...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Very few proteins have disulfide bonds &lt;a href=&quot;https://en.wikipedia.org/wiki/Disulfide_bond#Occurrence_in_proteins&quot; rel=&quot;nofollow&quot;&gt;(usually secreted proteins)&lt;/a&gt; or really any covalent bond stabilizing the amino acid chain beyond the bonds that make up the polypeptide itself.  Denaturation is only reversible in relatively few cases in fact.  A few proteins, usually very small ones can be nursed back into a native folded state from an unfolded one, and then only a percentage of the sample will reattain the folded state.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Sure.  In fact pressure changes the hydrogen bonded structure of the water and also therefore the thermodynamics of protein structure and has been used to study protein folding. Generally the electomagnetic field does not affect the state of the protein fold.  I cite the fact that many many proteins have been studied via nuclear magnetic resonance, in which the proteins have been inserted into some of the most powerful magnets that can fit into a reasonably sized room.   That is not to say that the protein &lt;em&gt;function&lt;/em&gt; might not be affected by such a field.  I'm sure by the time the field is large enough to ionize water or the peptide change you would see something... so you can always push things too the breaking point.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Many proteins from thermophilic organisms are more resistant to denaturation and companies actually engineer proteins to be resistant to all sorts of outrageous conditions and still be folded and functional.  Laundry detergent is full of crystallized enzymes that will sit happily in detergent for a long time.  I don't even know if these products have a shelf life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall proteins are vulnerable to denaturation for a good reason- the cell degrades them when it doesn't need their function and can recycle them for their component amino acids. If they were all this robust the cell would starve to death quickly.  If there is a biological role to a protein that is denatured and then refolds itself it is only for extremely rare situations.  Proteins for the most part don't fall apart once they are folded and if they do, they are done. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some possible exceptions: some antibiotic peptides which fold into pores that kill their targets and the amyloid plaque which takes on a different fold when in the brain which is associated with - but may not cause - Alzheimer's.  &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-10-18T04:41:06.460" LastActivityDate="2014-10-18T04:41:06.460" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="23248" PostTypeId="1" CreationDate="2014-10-17T20:23:59.233" Score="2" ViewCount="258" Body="&lt;p&gt;Gynodioecy is when a population features individuals that produce both male and female gametes and individuals that produce just female gametes. Androdioecy is when a population features individuals that produce both male and female gametes and individuals that produce just male gametes. The former is &quot;not uncommon&quot; and the latter is &quot;virtually unknown.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencemag.org/content/251/4997/1030.abstract&quot; rel=&quot;nofollow&quot;&gt;Charlesworth&lt;/a&gt; 1991 states that this is common because cosexual populations would normally evolve a male sterile mutation first, causing gynodioecy, and then female sterility mutation(s) will build up leading to dioecy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why should it be so much more common for male sterility mutations to evolve first?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I think the answer lies within articles cited in the above paper, Charlesworth &amp;amp; Charlesworth &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/205/1161/513.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;1979 Proc R Soc B&lt;/a&gt;, and &lt;a href=&quot;http://www.jstor.org/stable/2409184&quot; rel=&quot;nofollow&quot;&gt;1987 Evolution&lt;/a&gt; which I'll try to read this weekend, if it is I'll post a self-answer but in the mean time...).&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-10-17T20:37:28.700" LastActivityDate="2014-10-17T20:37:28.700" Title="Why is gynodioecy common and androdioecy rare?" Tags="&lt;sex&gt;&lt;sex-chromosome&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23249" PostTypeId="2" ParentId="23243" CreationDate="2014-10-17T20:47:35.487" Score="2" Body="&lt;p&gt;High-fidelity DNA polymerases have several safeguards to protect against both making and propagating mistakes while copying DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such enzymes have a significant binding preference for the correct versus the incorrect nucleoside triphosphate during polymerization. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If an incorrect nucleotide does bind in the polymerase active site, incorporation is slowed due to the sub-optimal architecture of the active site complex. This lag time increases the opportunity for the incorrect nucleotide to dissociate before polymerase progression, thereby allowing the process to start again, with a correct nucleoside triphosphate (1,2). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If an incorrect nucleotide is inserted, proofreading DNA polymerases have an extra line of defense &lt;img src=&quot;https://i.stack.imgur.com/XjbTw.jpg&quot; alt=&quot;dna mismatch&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The perturbation caused by the mispaired bases is detected, and the polymerase moves the 3´ end of the growing DNA chain into a proofreading 3´→5´ exonuclease domain. There, the incorrect nucleotide is removed by the 3´→5´ exonuclease activity, whereupon the chain is moved back into the polymerase domain, where polymerization can continue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From: New England biolabs:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.neb.com/tools-and-resources/feature-articles/polymerase-fidelity-what-is-it-and-what-does-it-mean-for-your-pcr&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.neb.com/tools-and-resources/feature-articles/polymerase-fidelity-what-is-it-and-what-does-it-mean-for-your-pcr&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-10-17T20:47:35.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23250" PostTypeId="2" ParentId="23246" CreationDate="2014-10-17T20:47:58.080" Score="4" Body="&lt;p&gt;Are you taking in an &lt;em&gt;in vitro&lt;/em&gt; context for preventing protein denaturation after protein isolation from for example &lt;em&gt;E. coli&lt;/em&gt; or are you more worried about proteins in the context of the whole cell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm no expert in the protein folding/conformation studies but from laboratory based prospective if you want to achieve denaturation for experimental purposes, you treat your samples with SDS and high heat (~ 100 oC for 10 min) to eliminate H-bonds and to get rid of disulphide bonds, you use a reducing agent such as beta-ME or DTT, which is commonly found in molecules such as Ab or cell surface receptors such as &lt;a href=&quot;http://www.jbc.org/content/273/18/11150.full&quot; rel=&quot;nofollow&quot;&gt;EGFR&lt;/a&gt; so obviously for western-blot experiments which you need your disulphide bridges to be preserved you do not use reducing agents but you still heat your samples and treat with SDS to get rid of the hydrogen bonds and linearalise your protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0023643896901188&quot; rel=&quot;nofollow&quot;&gt;this study&lt;/a&gt;, which used BSA and β-lactoglobulin, denaturation caused by high pressure is similar to that caused by the cleavage of hydrogen bonds with urea or guanidine hydrochloride so, yes, rapid changes in environmental conditions can have denaturing effects similar to chemical based agents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are trying to prevent protein denaturation in a whole cell, then you need to treat them with cryo-preservation media containing usually 10% DMSO such as &lt;a href=&quot;http://www.sigmaaldrich.com/catalog/product/sigma/c2874?lang=en&amp;amp;region=GB&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;. If you are working just with proteins alone, the best method is to work with your samples freshly prepared (lysed etc) and when isolating your proteins for future used, snap freeze them in liquid nitrogen and store at -80 oC. If your proteins are attached to beads such as GST-tagged proteins, then store your beads in a buffer congaing glycerol and put at -20 oC. I use 50% glycerol (v/v) and it works well for me! If however this response does not answer your particular question or concern, please edit and elaborate on what exactly you are worried about in your line of work and I shall modify my response accordingly. Hope this helped in some way!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-10-17T20:56:41.920" LastActivityDate="2014-10-17T20:56:41.920" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23251" PostTypeId="2" ParentId="23235" CreationDate="2014-10-17T21:19:57.530" Score="6" Body="&lt;p&gt;To answer your questions, one needs to address certain issues one at a time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Veins do have valves, but they function to hold blood from settling in the legs. When you flex muscles, the blood flows towards the heart. Valve failure occurs when people stand (especially if they stand relatively still) for long periods of time every day over many years, dilating veins. You can see this on the surface of the legs as varicose veins. One way to treat varicose veins is with &lt;em&gt;elevation&lt;/em&gt;. So, elevation does not harm vein valves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lymph is made at the arterial end of capillaries and is part of the interstitial fluid of tissues. It bathes cells, and returns to the circulation via the lymphatic system (which also has one-way valves), goes through lymph nodes, and returns to the blood via connections with the subclavian veins. The treatment for too much lymph in the lower extremities (also known as edema) is to &lt;em&gt;elevate the legs&lt;/em&gt;. So, elevation does not harm the lymphatics system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heart was made to pump all day, every day, for many, many years. It doesn't get &quot;tired&quot; during a tiring day, and doesn't need to rest like we do. But it can get weak and pump inefficiently if injured (e.g. myocarditis, myocardial infarct), or if it pumps against high arterial pressure (hypertension).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As long as you have healthy arteries to the legs, I can't see how your legs can suffer by elevation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main effect that I can think of is on baroreceptors. The increased volume of blood in your upper body will cause an increased stroke volume from the heart, sensed by baroreceptors, and may cause smooth muscle dilation of the vascular system. In the short term, that means you will experience more pronounced orthostatic hypotension on standing (you will be dizzier). The long-term effect from elevation for a couple of hours a day are basically nil.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since you asked about these parameters only, I won't elucidate on other possible effects.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-10-17T21:19:57.530" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23252" PostTypeId="2" ParentId="23238" CreationDate="2014-10-17T21:43:44.120" Score="1" Body="&lt;p&gt;I think the disadvantages are mostly economical in that region and so they has nothing to do with epidemiology. Possibly a long term effect can be, that the economy of the region turns from bad to worse, which can affect the healthcare too, but that's just speculation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The advantages are obvious, ebola is quarantined at some level, so these measures prevent or at least slow down its spread around the world.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-17T21:43:44.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23253" PostTypeId="1" AcceptedAnswerId="23279" CreationDate="2014-10-17T21:50:06.707" Score="6" ViewCount="7980" Body="&lt;p&gt;I have ran out of trypsin and need to passage my cells (immortalized chondrocytes, C28/I2) today or tomorrow. I have been out of town and forgot to order more trypsin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering if there are any alternative, &quot;homemade&quot; ways to detach cells. Googling this results in a lot of commercially available detachment solutions. I may or may not have a cell scraper available, but I have never tried it. I have hyaluronidase and I was thinking that might work. &lt;/p&gt;&#xA;" OwnerUserId="1917" LastActivityDate="2014-10-19T11:39:44.393" Title="Alternatives to trypsin for cell detachment?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;lab-techniques&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="23254" PostTypeId="1" CreationDate="2014-10-17T22:17:01.490" Score="4" ViewCount="873" Body="&lt;p&gt;Specifically, I'd like to look at changes in HA (hyaluronic acid) production. Most often you only see people staining the cell surface or removing cells from culture for fixation and then imaging. Does anyone know how to analyze the ECM (extracellular matrix) and proteoglycans that surround a cell if you're looking to see if a condition may be changing the way a cell remodels it's ECM? Is it even possible with some fluorescent tags?&lt;/p&gt;&#xA;" OwnerUserId="3232" LastEditorUserId="9829" LastEditDate="2014-10-18T04:14:30.613" LastActivityDate="2014-12-02T19:34:43.747" Title="How to visualize the ECM?" Tags="&lt;cell-biology&gt;&lt;microscopy&gt;&lt;cell-membrane&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23255" PostTypeId="2" ParentId="23243" CreationDate="2014-10-18T01:19:24.000" Score="3" Body="&lt;p&gt;DNA polymerase must catalyse the addition of 4 different nucleotides to the growing strand. This means that it cannot directly determine which base to incorporate at a specific point (how would it 'know' which base to incorporate and how it would it change its specificity for different bases). This means that the specificity for which base pair to incorporate is dependent on the template DNA strand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Correct Watson-Crick base pairing (that is, hydrogen bonding) between the template strand and the nucleotide to be incorporated triggers the closing of the finger domain of DNAP around the primer-template junction and positions the latter in the optimal position for catalysis (with the $\ce{\alpha-PO_4}$ of the incoming nucleotide near the $\ce{3'-OH}$ of the primer for a nucleophilic attack catalysed by two $\ce{Mg^{2+}}$ ions). This is where the conserved tyrosine residue you mentioned comes into play. An incorrectly paired nucleotide will not trigger this conformational change and will not be positioned optimally, thus catalysis is less likely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, the DNA polymerase makes contacts with the minor groove of the primer-template junction through hydrogen bonds. This interaction is not base-specific (all Watson-Crick base pairs have he same pattern of hydrogen-bond acceptors in the minor groove) but only occurs when the correct nucleotide is incorporated, thus stabilising the complex. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, discrimination between ribonucleotides and deoxyribonucleotides is done by steric exclusion of the $\ce{2'-OH}$ by amino acid residues in the binding pocket.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These factors can be thought of as kinetic proofreading as they simply slow down the reaction rate and provide time for an incorrectly paired nucleotide to dissociate. However, they can still be incorporated and many DNA polymerases have a $\ce{3'-&amp;gt;5'}$ proofreading exonuclease that can remove incorrectly paired nucleotides. This proofreading is again mediated by interactions between the DNAP and the primer-template junction (ie hydrogen bonding with the minor groove). A weakened interaction due to an incorrectly paired base reduces the affinity between DNA and the catalytic site and increases the affinity between DNA and the proofreading site (because it has a preference for cleaving ssDNA from the 3' end).&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-10-18T01:19:24.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23258" PostTypeId="1" CreationDate="2014-10-18T02:50:28.423" Score="0" ViewCount="104" Body="&lt;p&gt;Congenital &lt;a href=&quot;http://en.wikipedia.org/wiki/Nystagmus&quot; rel=&quot;nofollow&quot;&gt;Nystagmus&lt;/a&gt; is an eye focusing disorder. It happens in manuals. Wikipedia lists several treatments on its page. Are any of those FDA approved for human use of that disease. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;drugs found to be effective against nystagmus in some patients include memantine, levetiracetam, 3,4-diaminopyridine, 4-aminopyridine, and acetazolamide.&#xA;  -&lt;a href=&quot;http://en.wikipedia.org/wiki/Nystagmus&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9828" LastEditorUserId="9828" LastEditDate="2014-10-18T05:53:21.673" LastActivityDate="2014-10-18T05:53:21.673" Title="Nystagmus drug FDA approval?" Tags="&lt;human-eye&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23259" PostTypeId="1" AcceptedAnswerId="23263" CreationDate="2014-10-18T04:00:59.780" Score="0" ViewCount="72" Body="&lt;p&gt;Poachers are only after the ivory horns right? I read this story from the New York Times ( I think) of saving a Rhinocerous by some Park Rangers and a Vet. ( forgive spelling) ; they tranquilized the Rhino and took its horn off so it wouldn't be killed. I know Rhinos need their horns so maybe a hard plastic 'prosthesis' could be put in its place. Maybe the 'prosthesis' could be colored yellow or have some markings on it so any poacher would know it's fake. Of course this could all be done for the elephant too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could this be a feasible way to save Elephants or Rhinos??&lt;/p&gt;&#xA;" OwnerUserId="6195" LastEditorUserId="3624" LastEditDate="2014-10-19T08:33:59.010" LastActivityDate="2014-10-19T08:33:59.010" Title="About the plight of Elephants and efforts to conserve them?" Tags="&lt;zoology&gt;&lt;mammals&gt;&lt;conservation-biology&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2014-10-18T09:35:59.400" ContentLicense="CC BY-SA 3.0" />
  <row Id="23260" PostTypeId="2" ParentId="3888" CreationDate="2014-10-18T04:16:20.767" Score="1" Body="&lt;p&gt;First of all there is no solanine in green tomato, there wasn't, and there never will be.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Steroidal glycoalkaloids (SGAs) extracted from tomato leaves and&#xA;  berries (Lycopersicon esculentum Mill.) were separated and identified&#xA;  using optimized reversed-phase liquid chromatography with electrospray&#xA;  ionization (ESI) and ion trap mass spectrometry (ITMS). The ESI source&#xA;  polarity and chromatographic conditions were evaluated. The ESI&#xA;  spectra contain valuable information, which includes the mass of SGAs,&#xA;  the mass of the aglycones, and several characteristic fragment ions.&#xA;  Cleavage at the interglycosidic bonds proximal to the aglycones is the&#xA;  most prominent process in the ESI process. A protonated molecule,&#xA;  [M+H]+, accompanied by a mixed adduct ion, [M+H+Na]2+, was observed&#xA;  for α-tomatine (i.e., m/z 1034.7 and 528.9) and dehydrotomatine (i.e.,&#xA;  m/z 1032.6 and 527.9) in positive ion mode spectra. The structures of&#xA;  these tomato glycoalkaloids were confirmed using tandem mass&#xA;  spectrometry. The identification of a new α-tomatine isomer&#xA;  glycoalkaloid, named filotomatine (MW 1033), which shares a common&#xA;  tetrasaccharide structure (i.e., lycotretraose) with α-tomatine and&#xA;  dehydrotomatine, and soladulcidine as an aglycone, is described for&#xA;  the first time. It occurs in significant amounts in the extracts of&#xA;  wild tomato foliage. Multistage mass spectrometry both of the&#xA;  protonated molecules and of the doubly charged ions was used for&#xA;  detailed structural elucidation of SGAs. Key fragmentations and&#xA;  regularities in fragmentation pathways are described and the&#xA;  fragmentation mechanisms involved are proposed.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2005 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/rcm.2176/abstract?systemMessage=Wiley%20Online%20Library%20will%20be%20disrupted%20on%20the%2018th%20October%20from%2010%3A00%20BST%20%2805%3A00%20EDT%29%20for%20essential%20maintenance%20for%20approximately%20two%20hours%20as%20we%20make%20upgrades%20to%20improve%20our%20services%20to%20you&amp;amp;userIsAuthenticated=false&amp;amp;deniedAccessCustomisedMessage=&quot; rel=&quot;nofollow&quot;&gt;Analysis of tomato glycoalkaloids by liquid chromatography coupled with electrospray ionization tandem mass spectrometry&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Your bitter nightshade really has solanine content:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Alkaloids are well known for their antimicrobial activity. Though all&#xA;  natural alkaloids come from plants, not all plants produce alkaloids.&#xA;  Plants of the Solanaceae family are known for their high alkaloid&#xA;  content. Alkaloids are found in all plant parts like roots, stems,&#xA;  leaves, flowers, fruits and seeds. In the present study, those plant&#xA;  parts of Solanum dulcamara were selected which have been reported to&#xA;  produce a high content of a specific alkaloid: solanine (from unripe&#xA;  fruits), solasodine (from flowers) and β-solamarine (from roots).&#xA;  These alkaloids were extracted from various parts of S. dulcamara by&#xA;  well-established methods and were screened for their antibacterial&#xA;  activity. Human pathogenic bacteria, viz., Enterobacter aerogenes,&#xA;  Escherichia coli, Staphylococcus aureus, were selected for the study.&#xA;  All three alkaloids inhibited the growth of E. coli and S. aureus.&#xA;  However, no significant activity was observed against E. aerogenes.&#xA;  Minimum inhibitory concentration and minimum bactericidal&#xA;  concentration were also evaluated.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://www.tandfonline.com/doi/abs/10.1080/14786410802267692#.VEHfhxaWdqQ&quot; rel=&quot;nofollow&quot;&gt;Biological activity of alkaloids from Solanum dulcamara L.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The glycoalkaloid content usually decrease by ripening, so that the animals can eat them safely and deliver the seeds. At least that's my observation. So there is a good chance that the ripe fruits are edible...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If they are not, it is hard to get rid of the solanine. Solanine is heat stable it decomposes over 200°C (about 240-260°C afaik) and it is not (poorly) water soluble. So cooking in hot water does not help.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Reduction in concentration of α-chaconine (CHA) and α-solanine (SOL),&#xA;  toxic glycoalkaloids in potatoes, during cooking by 3 procedures was&#xA;  investigated. Raw or cooked potato samples (2 g) were extracted twice&#xA;  with 5% acetic acid solution. The extract was purified on Sep-Pak C18&#xA;  and CHA and SOL contents were determined by HPLC. Recoveries of CHA&#xA;  and SOL from raw potatoes were 96.5 and 98.2%, respectively, vs. 96.2&#xA;  and 96.7% from cooked potatoes. &gt;93.9% of CHA and 95.9% of SOL&#xA;  remained in potatoes after boiling. Contents of both were reduced by&#xA;  15% on microwave treatment. On deep-frying alkaloid contents varied&#xA;  according to temperature. At 157°C, both alkaloids were unaffected; at&#xA;  170°, potatoes showed a large variation in residual alkaloids. At&#xA;  210°, alkaloids were partially decomposed; after 10 min heating, 64.9%&#xA;  of CHA and 59.7% of SOL remained. It is suggested that the critical&#xA;  temperature for decomposition of both alkaloids in potatoes may be&#xA;  around 170°. Results confirmed the relatively high stability of CHA&#xA;  and SOL in potatoes under normal home cooking conditions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1990 - &lt;a href=&quot;http://www.cabdirect.org/abstracts/19920754606.html;jsessionid=907C291A43003744E417CC3E0DF80AA4&quot; rel=&quot;nofollow&quot;&gt;Effect of cooking on contents of α-chaconine and α-solanine in potatoes.&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Deep frying over 200 °C might help, because it degrades the glycoalkaloids and probably moves them from the fruits to the oil, but be aware that this is an old article... Teflon will burn over 270°C afaik, and you should check the smoke point of the oil, because most of them have in a range of 150°C to 250°C. I guess there are other methods which I don't know of, but I think you don't want to eat that pie... ;-)&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-18T04:16:20.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23261" PostTypeId="1" CreationDate="2014-10-18T05:07:04.307" Score="1" ViewCount="121" Body="&lt;p&gt;Benign tumors can grow to dangerous size yet are they capable of metastisizing ; if not what stops this? Also with a benign tumor if you call its cells 'near' its edges its tumor 'cell wall' I was wondering if the cells in its Tumor Cell Wall still have apoptosis mechanisms in them that function?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastActivityDate="2014-10-18T05:07:04.307" Title="Regarding benign tumors and what 'stops' them" Tags="&lt;cancer&gt;&lt;apoptosis&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23262" PostTypeId="2" ParentId="21466" CreationDate="2014-10-18T05:35:19.653" Score="2" Body="&lt;p&gt;This is an important topic in immunology, especially for vaccine development.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MHC or HLA is a molecule expressed by some cells of the immune system which acts like a &quot;catcher's mitt&quot; and &quot;presents&quot; short snippets of protein to other immune cells. Other molecules act alongside MHC to provide co-signals which promote or suppress immune attack against the peptides that MHC presents. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, it's a protein that holds out chunks of other proteins in order to educate the rest of the immune system. Here's the catch: different people have different genes for MHC which do a better or worse job of presenting certain peptides. This is one reason why different people can respond to different vaccines or different pathogens or cancers: they have different MHCs which may or may not present peptides from the relevant targets. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, one big challenge in medicine right now is to develop good models for which peptides are best to include in a vaccine. The right answer depends on the genetics of the vaccine target (ebola, a tumor, e. coli etc) and also on the genetics of the person being vaccinated (does this person's MHC gene properly present this vaccine?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to datafy this, people sometimes make arrays which allow us to quantify which peptides bind to which MHC genes in high throughput. Then we can use that data to learn which factors are most important for P:MHC binding. &quot;MHC restricted&quot; means that we are talking about a specific genetic subtype of these molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps. &#xA;Bion Alex Howard&lt;/p&gt;&#xA;" OwnerUserId="9831" LastActivityDate="2014-10-18T05:35:19.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23263" PostTypeId="2" ParentId="23259" CreationDate="2014-10-18T06:25:24.247" Score="1" Body="&lt;p&gt;Dehorning of rhinos has been tried with limited success. Poachers have killed dehorned rhinos anyway, either out of spite or to avoid tracking worthless prey in the future. There is the problem of anesthesia (always a risk) and the fact that rhino horns are usually not destroyed but saved in the event of decriminalization. But at least horn grows back.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering the strength of horn and ivory, and the force applied in their use, plastic would not be of much use to them (especially elephants with long tusks).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;They are used for digging for water, salt, and roots; debarking or marking trees; and for moving trees and branches when clearing a path. When fighting, they are used to attack and defend, and to protect the trunk. - Wikipedia&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To detusk elephants would be akin to declawing a lion, though much more dangerous and painful. Though this &lt;em&gt;might&lt;/em&gt; help prevent poaching, the future of these animals lies in prevention.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-10-18T06:25:24.247" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="23264" PostTypeId="1" AcceptedAnswerId="23265" CreationDate="2014-10-18T09:38:29.657" Score="4" ViewCount="206" Body="&lt;p&gt;Are there organisms that have incorporated (manmade) plastic into their lives in any way? Either in their diet, or as a part of their body?&lt;/p&gt;&#xA;" OwnerUserId="3141" LastEditorUserId="3141" LastEditDate="2014-10-18T11:39:25.277" LastActivityDate="2015-10-01T04:06:07.297" Title="Are there organisms that have incorporated plastic into their lives?" Tags="&lt;ecology&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23265" PostTypeId="2" ParentId="23264" CreationDate="2014-10-18T12:45:55.217" Score="6" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Biodegradable waste is a type of waste which can be broken down, in a&#xA;  reasonable amount of time, into its base compounds by micro-organisms&#xA;  and other living things, regardless of what those compounds may be.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;from wikipedia&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So yes, there are microbes which are capable of biodegradating manmade plastic. It depends on plastic types.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you meant creating new pathways to biodegradate non-biodegradable plastics, then I don't think so. My opinion that by some of those plastics there are theoretical barriers (e.g. energy barriers or toxic byproducts), and by some of them evolution might create a pathway in time (I don't think in our lifetime, but nothing is impossible).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are microbes which build plastics to store energy. They are just polymers like starch or cellulose (sugar polymers), with different building stones... Afaik the first biodegradable plastics came from here, but so they were very expensive. Nowadays we don't need microbes in the polymerization process, e.g. we can create polylactic-acid without the presence of microbes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;edit:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found an interesting article in the topic. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Now, for the first time, researchers have found detailed evidence that&#xA;  bacteria in an animal’s gut can safely biodegrade plastic and&#xA;  potentially help reduce the environmental impact of plastic in&#xA;  landfill and elsewhere. The animal in question? The humble mealworm –&#xA;  which turns out to be not so humble after all.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Researchers led by Stanford University in US and Beihang University in&#xA;  China found that the mealworm – the larval form of the darkling beetle&#xA;  – can safely subsist on a diet of Styrofoam and other kinds of&#xA;  polystyrene, with bacteria in the worm’s gut biodegrading the plastic&#xA;  as part of its digestive process. The findings are significant because&#xA;  it was previously thought that these substances were non-biodegradable&#xA;  – meaning they ended up in landfill (or worse, our oceans, where&#xA;  they’d accumulate for decades).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencealert.com/scientists-find-worms-can-safely-eat-the-plastic-in-our-garbage?perpetual=yes&amp;amp;limitstart=1&quot; rel=&quot;nofollow&quot;&gt;ScienceAlert - Scientists find worms can safely eat the plastic in our garbage&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2015-10-01T04:06:07.297" LastActivityDate="2015-10-01T04:06:07.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23266" PostTypeId="1" AcceptedAnswerId="23269" CreationDate="2014-10-18T13:56:37.537" Score="2" ViewCount="4195" Body="&lt;p&gt;When a reflex arc occurs the signal from the receptor passes straight to the motor neuron instead of being passed onto the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a rather simplistic explanation, I was hoping to make it more detailed. How does the body know when a threshold, heat for example, has been crossed and what mechanism is able to activate the reflex? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also where does this occur, in the receptor or the spine?&lt;/p&gt;&#xA;" OwnerUserId="9834" LastEditorUserId="9268" LastEditDate="2014-10-18T15:53:16.700" LastActivityDate="2014-10-20T06:45:35.240" Title="What is the mechanism of reflex arcs?" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;&lt;reflexes&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23267" PostTypeId="1" AcceptedAnswerId="23268" CreationDate="2014-10-18T14:36:03.227" Score="1" ViewCount="124" Body="&lt;p&gt;I'm studying the motor pathways of the brain and I'm a bit confused about how the lateral corticospinal tract descends.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;code&gt;Neuroanatomy: Text and Atlas&lt;/code&gt; by Martin, J. H., 4th edition, right before Figure 10-4:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Some of these [terminating] axons descend ipsilaterally; many descend&#xA;  contra-laterally and re-cross midline within the gray matter in lamina 10.&#xA;  The function of these ipsilateral axons is not well understood.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I understand that the axons cross over at the Pyramidal decussation, but this paragraph is really confusing me. What descent is being referenced here? Is it descending in the spinal chord? Alternatively, is the paragraph implying that some axons don't decussate in the pyramidal decussation?&lt;/p&gt;&#xA;" OwnerUserId="5427" LastEditorUserId="57" LastEditDate="2014-10-19T01:13:06.500" LastActivityDate="2014-10-19T21:03:14.083" Title="Lateral corticospinal tract and termination" Tags="&lt;neuroanatomy&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23268" PostTypeId="2" ParentId="23267" CreationDate="2014-10-18T14:57:20.627" Score="1" Body="&lt;p&gt;The answer ends up being on the next page when discussing the ventral corticospinal tract.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many ventral corticospinal tract axons have branches that decussate in&#xA;  the spinal cord, similar to the re-crossed lateral coticospinal tract&#xA;  axons described earlier.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In other words, some axons of the lateral corticospinal tract ignore the pyramidal decussation, join the anterior corticospinal tract (which then synapses bilaterally later at the spinal commissure).&lt;/p&gt;&#xA;" OwnerUserId="5427" LastEditorUserId="5427" LastEditDate="2014-10-19T21:03:14.083" LastActivityDate="2014-10-19T21:03:14.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23269" PostTypeId="2" ParentId="23266" CreationDate="2014-10-18T15:45:13.433" Score="2" Body="&lt;p&gt;&lt;strong&gt;Withdrawal reflex&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You asked specifically about the withdrawal reflex and the receptors that trigger this. The initiation of the reflex arc is determined at the level of the nociceptors (pain-transducing receptors) in the epidermis. For the most part, these are part of “free” (not encapsulated) nerve endings of sensory fibers. These fibers course within spinal nerves whose cell bodies are located in the dorsal root ganglia adjacent to the spinal cord. There are two types of nociceptive endings:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;mechanical: with parent fibers Aδ&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;transduce severe mechanical deformation   &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;polymodal: with parent C-fiber units&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;transduce heat, cold, irritant signals&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This picture shows free nerve endings in the epidermis. The boxed portion of the big picture is expanded in the bottom right.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/08K7V.png&quot; alt=&quot;free nerve endings&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The withdrawal reflex initiated by these receptors is mediated by a polysnaptic (multiple neurons) arc. The sensory neuron synapses with interneurons in the spinal cord.&lt;sup&gt;1&lt;/sup&gt; Some of these use glutamatergic connections to activate appropriate muscle groups mediating withdrawal. Others inhibit the reciprocal muscle groups (&lt;em&gt;reciprocal inhibition&lt;/em&gt;) to allow this movement to be unimpeded. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a cartoon diagram showing the spinal components of the reflex arc in a cross-sectional level of the spinal cord. Notice the interneuron between the sensory and motor neurons (although it's not labeled as such here):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZnAn6.png&quot; alt=&quot;reflex arc&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Stretch reflex&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to provide a broader picture of the basic principles involved in spinal reflexes, it's helpful to also mention the stretch reflex. This is perhaps the quintessential reflex arc because it is monosynaptic, exemplified by the patellar tendon reflex. The stretch reflex is fast, with a latency (stimulus–response interval) of about 15–25 ms (contrast the polysynaptic withdrawal reflex with &lt;a href=&quot;http://f1000research.com/articles/2-158/v1&quot; rel=&quot;nofollow noreferrer&quot;&gt;latency ~70-100 ms&lt;/a&gt;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The stretch is initiated at the Golgi tendon organs. These are found at the junction between muscle and tendon. The (Ib) nerve fiber splays out and intertwines with tendon fiber bundles. The  nerve endings are activated by the tension of muscle contraction (either passive (as when the patellar tendon is tapped), or active (as during voluntary movement). The afferent sensory neurons directly excite homonymous motor neurons  (i.e. motor neurons supplying the same muscles), and inhibit (via interposed “Ia internuncials”) the antagonist muscles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have limited the discussion here to the withdrawal reflex you asked about and another basic spinal reflex arc as an illustration of principle. There are many other, mostly more complex reflex arcs that are beyond the scope of this answer, but I highly recommend checking out a neuroanatomy or neurophysiology textbook such as the one I've listed below if you'd like more information.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&#xA;&lt;strong&gt;Note&lt;/strong&gt;&#xA;&lt;/sup&gt;&#xA;&lt;sup&gt;&lt;br&gt;&#xA;1. Although the discussion here is limited to the anatomy of the reflex arc, there are additional synapses within the spinal cord that connect with ascending circuits, as described in the section about afferent neurons of spinal nerves &lt;a href=&quot;https://biology.stackexchange.com/a/21289/9268&quot;&gt;in another answer&lt;/a&gt;. Some of these tracts end up at the cortex and are the basis for conscious perception. However, note that this process is multisynaptic and takes longer. The beauty of the spinal reflex arc is that it does not require information to travel all the way up to the brain and back down, which would slow down the response considerably. Practically, this means that you will pull your hand away from a hot stove before you have conscious sensory awareness of the burn.&#xA;&lt;/sup&gt;&#xA;&lt;br/&gt;&lt;br&gt;&#xA;&lt;sup&gt;&#xA;&lt;strong&gt;Reference&lt;/strong&gt;&#xA;&lt;/sup&gt;&lt;br&gt;&#xA;&lt;sup&gt;&#xA;Apart from linked article and images with sources below, all information is summarized from:&#xA;&lt;/sup&gt;&lt;br&gt;&#xA;&lt;sup&gt;&#xA;MJ Turlough FitzGerald,  Gregory Gruener, Estomih Mtui. &lt;em&gt;Clinical Neuroanatomy &amp;amp; Neuroscience&lt;/em&gt; © 2012, Elsevier Limited. &#xA;&lt;/sup&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;br&gt;&#xA;Image 1 from: &lt;a href=&quot;http://en.wikipedia.org/wiki/Free_nerve_ending&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Free_nerve_ending&lt;/a&gt;&#xA;&lt;/sup&gt;&lt;br&gt;&#xA;&lt;sup&gt;&#xA;Image 2 from: &lt;a href=&quot;http://www.tutorvista.com/content/biology/biology-iv/nervous-coordination/natural-reflex.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.tutorvista.com/content/biology/biology-iv/nervous-coordination/natural-reflex.php&lt;/a&gt;&#xA;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-10-20T06:45:35.240" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23270" PostTypeId="1" AcceptedAnswerId="23272" CreationDate="2014-10-18T16:23:44.437" Score="0" ViewCount="4848" Body="&lt;p&gt;Can you refer me to a good source containing the genus and species name of different breeds of dogs?&lt;/p&gt;&#xA;" OwnerUserId="5823" LastEditorUserId="6511" LastEditDate="2014-10-18T17:07:09.307" LastActivityDate="2019-07-25T08:46:59.030" Title="What are the genus and species name of different breeds of dog?" Tags="&lt;nomenclature&gt;&lt;species&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23271" PostTypeId="2" ParentId="23270" CreationDate="2014-10-18T16:33:07.873" Score="8" Body="&lt;p&gt;All breeds of dogs are members of the same (sub) species: &lt;em&gt;Canis lupus familiaris&lt;/em&gt;. &quot;Breeds&quot; of dogs are not scientific designations but are collections of traits recognized as unique by different breeding organizations. As such, certain breeds are recognized as unique in some organizations do not exist in others (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Dog_breed#Classification&quot;&gt;here&lt;/a&gt; for examples).&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2014-10-18T16:33:07.873" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23272" PostTypeId="2" ParentId="23270" CreationDate="2014-10-18T16:36:31.847" Score="9" Body="&lt;p&gt;All the different breeds of dogs - from Irish setters to greyhounds - are all part of the same species, &lt;em&gt;canis lupus familiaris&lt;/em&gt;. The common, domesticated dog is actually a &lt;em&gt;subspecies&lt;/em&gt; of the grey wolf. The different breeds do have different genetic characteristics (just as humans have, say, different eye or hair colors), but they're a all one and the same. The different names for different breeds are not like the scientific classifications of organisms via domain, kingdom, etc. They're just our choices.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.vetinfo.com/scientific-name-for-dogs.html&quot;&gt;http://www.vetinfo.com/scientific-name-for-dogs.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Dog_breed#Description&quot;&gt;https://en.wikipedia.org/wiki/Dog_breed#Description&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Subspecies_of_Canis_lupus&quot;&gt;https://en.wikipedia.org/wiki/Subspecies_of_Canis_lupus&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.choosing-a-dog-made-easy.com/dog-types.html&quot;&gt;http://www.choosing-a-dog-made-easy.com/dog-types.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="9458" LastEditorUserId="9458" LastEditDate="2014-10-18T17:21:18.520" LastActivityDate="2014-10-18T17:21:18.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23273" PostTypeId="1" AcceptedAnswerId="23278" CreationDate="2014-10-18T16:40:42.980" Score="29" ViewCount="7224" Body="&lt;p&gt;From what I know, the main function of red blood cells (RBCs) is hemoglobin transport. So, why do we need cells packed with hemoglobin: why can't it travel freely in the bloodstream? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My own thoughts were: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Having hemoglobin packed into cells means it can be released where it's most needed. For example, when we are exercising, our muscles need more oxygen, so more erythrocytes release their oxygen in the muscle tissue. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The diameter of a capillary is much bigger than a single protein molecule's diameter, but comparable to a cell's diameter. So, when cells are traveling through a capillary, all of them are close to its walls. However, when free molecules are traveling through it, some of them are close to the walls, while the others are in the &quot;middle&quot;. I figured, those in the &quot;middle&quot; can't exchange oxygen with the surrounding tissues. So, red blood cells make gas exchange more effective.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you think any of this makes sense? Why in reality do RBCs exist? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any insight or book recommendations would be very appreciated:) &lt;/p&gt;&#xA;" OwnerUserId="9835" LastEditorUserId="3624" LastEditDate="2018-04-06T07:37:34.163" LastActivityDate="2018-04-06T07:37:34.163" Title="Why do we need red blood cells?" Tags="&lt;cell-biology&gt;&lt;human-anatomy&gt;&lt;hematology&gt;&lt;red-blood-cell&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="23274" PostTypeId="1" CreationDate="2014-10-18T17:30:52.480" Score="1" ViewCount="58" Body="&lt;p&gt;Like the title says, I am looking for a good introductory text to histology. It would ideally cover &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;sample preparation&lt;/li&gt;&#xA;&lt;li&gt;microscopy&lt;/li&gt;&#xA;&lt;li&gt;staining, and&lt;/li&gt;&#xA;&lt;li&gt;several example experiments&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Suggestions?&lt;/p&gt;&#xA;" OwnerUserId="9836" LastActivityDate="2014-10-18T17:30:52.480" Title="A good introductory book to histology?" Tags="&lt;book-recommendation&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23275" PostTypeId="2" ParentId="23273" CreationDate="2014-10-18T17:36:27.347" Score="6" Body="&lt;p&gt;This is a well worded question. There are more reasons than the following but the most apparent is hemoglobin production and its transport. The erythrocyte is a cell whose structure is optimal for its function-the production and transport of hemoglobin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It lacks a nucleus and organelles so that it can devote almost 100% of its energy to hemoglobin production. It has this  bi-concave disk shape to increase its surface area thus increasing the exposure of hemoglobin to oxygen and CO2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a small and flexible cell allowing them to easily maneuver the capillaries (where they work). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because it's anuclear it has a short lifespan but they are rapidly produced and regulated by erythropoietin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order for tissues to receive oxygen and rid themselves of carbon dioxide there needs to be an orderly transfer and movement of hemoglobin from the tissues to the lungs and back-and-forth. Without this cycling of hemoglobin on the erythrocyte the protein would move more in the body through diffusive means. This would not promote the required segregation of oxyhemoglobin in the tissues and carbaminohemaglobin in the lungs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check out any edition of Anatomy and Physiology by Marieb. All editions have an entire chapter related to the subject&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-10-18T17:36:27.347" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="23276" PostTypeId="1" CreationDate="2014-10-18T20:17:24.907" Score="2" ViewCount="75" Body="&lt;p&gt;I have progressive myopia. I grew up with perfectly normal eyes but slowly started getting myopic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thing is, my brain knows (or &lt;em&gt;should&lt;/em&gt; know) what the world looks like -- it knows that far away objects do not suddenly blur. So when the input from the retina changes, why doesn't the brain correct it in perception?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm assuming here that this should work by the same principles as size and colour constancy. In both cases the input from the retina is different but the brain doesn't perceive it as an actual change in size or colour.&lt;/p&gt;&#xA;" OwnerUserId="9838" LastActivityDate="2014-12-06T11:47:04.897" Title="Like size and colour constancy, why does the brain not maintain focus constancy?" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23277" PostTypeId="1" CreationDate="2014-10-18T20:21:06.323" Score="1" ViewCount="566" Body="&lt;p&gt;These antibiotics include&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;amoxicillin + acidum clavulanicum (beta-lactam, inhibit cell wall synthesis, broad specturm, 3rd gen aminopenicillin) / last part preventing the resistance&lt;/li&gt;&#xA;&lt;li&gt;ceftriaxone (3rd gen cephalosporine, inhibit cell wall synthesis, broad spectrum)&lt;/li&gt;&#xA;&lt;li&gt;clarithromycin (macrolide, inhibit protein synthesis by binding to ribosomal subunit S50)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;used regularly for cyclic middle ear infections for years during the childhood - ages 2-10 for a patient with untreated celiac disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking what kind of immunosuppression can this lead to. &#xA;I think it mostly conquered by suppression of adaptive immune system. &#xA;Little lowered innate immunity lowered too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am especially interested in the antigen-presenting cells (mostly dendritic cells) and their function in an immunosuppressed patients of the antibiotics. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There may be other factors which I have not mentioned related to this kind of immunosuppression. &#xA;Feel, free to propose. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can dendritic cells work in an immunosuppressed patients?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can assume any combination of cases for the three antibiotics: 8 possible cases. &#xA;For instance, &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;(1) and (2) high antibiotic resistance, and only susceptible to (3)&lt;/li&gt;&#xA;&lt;li&gt;High antibiotic resistance to (1)-(3)&lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Possible cases which reminds&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;this immunosuppression can remind this one: &lt;em&gt;immune reconstitution syndrome&lt;/em&gt; like in HIV but milder&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-10-19T10:29:56.053" LastActivityDate="2014-10-19T10:29:56.053" Title="Which immunosuppression caused by long-term usage of these antibiotics in untreated celiac disease?" Tags="&lt;immunology&gt;&lt;pharmacology&gt;&lt;immunosuppression&gt;&lt;antibiotic-resistance&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23278" PostTypeId="2" ParentId="23273" CreationDate="2014-10-18T21:03:41.147" Score="19" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Hemoglobin molecules used to manufacture these products are not&#xA;  contained by a red cell membrane, and when released into the&#xA;  vasculature, these molecules rapidly scavenge nitric oxide.This can&#xA;  result in systemic vasoconstriction, decreased blood flow, increased&#xA;  release of proinflammatory mediators and potent vasoconstrictors, and&#xA;  a loss of platelet inactivation,17- 20 creating conditions that may&#xA;  lead to vascular thrombosis of the heart or other organs. This&#xA;  mechanism has recently been shown in preclinical models to be&#xA;  responsible for injury during hemolytic states, in which hemoglobin is&#xA;  also released into the circulation.21&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Unlike naturally occurring hemoglobin, manufactured cell-free&#xA;  hemoglobin-based blood substitutes (HBBSs) can be chemically altered&#xA;  to theoretically minimize such toxicities. It has been postulated that&#xA;  cross-linking, polymerization, or pegylation of hemoglobin will create&#xA;  larger, more stable HBBS molecules, preventing extravasation and&#xA;  thereby leading to a reduction in toxicities related to nitric oxide&#xA;  scavenging. At least 1 manufacturer has also chemically increased the&#xA;  affinity of its HBBS for oxygen (lower P50, the partial pressure of&#xA;  oxygen required for 50% hemoglobin saturation) to decrease arteriole&#xA;  oxygen transfer and thereby potentially eliminate untoward&#xA;  cardiovascular effects.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://jama.jamanetwork.com/article.aspx?articleid=181940&amp;amp;quizId=2349&amp;amp;atab=7&quot; rel=&quot;noreferrer&quot;&gt;Cell-Free Hemoglobin-Based Blood Substitutes and Risk of Myocardial Infarction and Death&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So cell free hemoglobin is toxic. As you can see this toxicity can be reduced in other ways too, so it seems like there is an evolutionary pressure in the direction of having blood cells, maybe it is simpler this way. To answer the other question, I think there can be free HGB in the blood when blood cells fall apart because of an infection e.g. malaria, etc...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hemolysis in falciparum malaria results in NO quenching by cell-free&#xA;  hemoglobin, and may exacerbate endothelial dysfunction, adhesion&#xA;  receptor expression and impaired tissue perfusion. Treatments that&#xA;  increase NO bioavailability may have potential as adjunctive therapies&#xA;  in SM&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://jid.oxfordjournals.org/content/200/10/1522.full&quot; rel=&quot;noreferrer&quot;&gt;Relationship of Cell-Free Hemoglobin to Impaired Endothelial Nitric Oxide Bioavailability and Perfusion in Severe Falciparum Malaria&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Btw. I agree with rhill45, I think too that it is easier to regulate O2 and CO2 exchange if you have a specialized cell type, so it might have regulation purposes. It can have recycling purposes either, because it is hard to distinguish between old (damaged) and new HGB when they are in a cell-free form. This problem probably can be solved by destroying only glycosylated hemoglobin, but I guess it is much easier to filter out the old RBCs in the spleen...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the process of maturation, a basophilic pronormoblast is converted&#xA;  from a cell with a large nucleus and a volume of 900 fL to an&#xA;  enucleated disc with a volume of 95 fL. By the reticulocyte stage, the&#xA;  cell has extruded its nucleus, but is still capable of producing&#xA;  hemoglobin.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;according to wikipedia (without citation).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Other sources claim the same, with the extension that this period lasts only for a short time, because the cell soon loses its mRNA and so it stops producing HGB. So according to these articles RBCs create the HGBs in the early stages of their life. (I did not find a real scientific article about this, but I can accept this theory.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Chris this toxicity is just a protection mechanism, so I dug deeper.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bacterial virulence is greatly enhanced by freely available iron, such&#xA;  as that in fully-saturated transferrin or free haemoglobin. Following&#xA;  trauma a fall in tissue Eh and pH due to ischaemia, plus the reducing&#xA;  powers of bacteria, can make iron in transferrin freely available and&#xA;  abolish the bactericidal properties of tissue fluids with disastrous&#xA;  results for the host. Hyperbaric oxygen is a possible therapeutic&#xA;  measure that could restore normal bactericidal systems in infected&#xA;  tissues by raising the Eh and pH.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1016/j.femsim.2004.11.010/full&quot; rel=&quot;noreferrer&quot;&gt;Iron and infection: the heart of the matter&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Iron lies at the center of a battle for nutritional resource between&#xA;  higher organisms and their microbial pathogens. The iron status of the&#xA;  human host affects the pathogenicity of numerous infections including&#xA;  malaria, HIV-1, and tuberculosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.sciencemag.org/content/338/6108/768.short&quot; rel=&quot;noreferrer&quot;&gt;Hepcidin and the Iron-Infection Axis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So RBCs protect the iron against microbial pathogens, that's their key role. I think every other related problem, like O2 release regulation, free HGB toxicity, HGB recycling, etc... can be solved with free HGB as well, so most probably iron protection is the evolutionary pressure to store HGB in blood cells instead of letting it be in the blood in a cell free form. It's funny that every single book gets this wrong, and they claim that carrying oxygen is the most important role of this cell type, while they aren't mention anything about iron protection... :-)&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-19T22:38:03.903" LastActivityDate="2014-10-19T22:38:03.903" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="23279" PostTypeId="2" ParentId="23253" CreationDate="2014-10-18T21:15:30.503" Score="6" Body="&lt;p&gt;Lets make this a proper answer: There are a few possibilities to detach adherent cells without Trypsin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;PBS/EDTA:&lt;/strong&gt; Integrins and Cadherins play an important role in the adhesion and also in maintaining cell-cell contacts. These function of these proteins depends on Calcium&lt;sup&gt;2+&lt;/sup&gt; ions, so EDTA will chelate them and make them unavailable. First remove the culture media, rinse the cells with warm PBS to get rid of most ions and then incubate them for 5 min (the time needs to be optimized for each cells line) in PBS with 10mM EDTA in it. The cells either detach themself, can be washed of the surface with a pipette or can be gently knocked off the surface (this works only in tightly closing flasks). Centrifuge the cells shortly to pellet them and get rid of the PBS/EDTA and take them up in fresh medium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Wash cells of the surface:&lt;/strong&gt; Some cell lines are so loosely attached (which makes working with them pretty hard), that they can simply be washed off the surface. To do so, use the pipetboy to get some medium and then pump it out again against the cell layer. You can see the cells disappearing from the surface and the medium (or the PBS) get more cloudy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Knock off cells:&lt;/strong&gt; To do so, you take the flask with medium in one hand and knock it gently 4 or 5 times against the palm of the other hand. The cells should come off then and can be centrifuged down to separate from the medium. Alternatively you could replace the medium first and then knock them off. This method is not recommended for very sensitive cell lines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides these methods, there are a number of commercial products available which claim to be better than the classical Trypsin/EDTA method and to be less harmful for the cells. Since I haven't tested them, I cannot say anything about them. In my experience Trypsin and the methods described above work perfectly.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-18T21:15:30.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23280" PostTypeId="1" AcceptedAnswerId="23284" CreationDate="2014-10-18T23:07:54.337" Score="3" ViewCount="152" Body="&lt;p&gt;When I was young, I was told never to put a fluorescent light in a hen house because it continuously turns on and off. Extra lighting is used, as far as I know, to 'extend' a chicken's day. Human eyes don't have the refresh frequency to notice that, but there are animals who have a frame-rate of up to 200 Hz (so they actually see the lights turn off and back on again). I was told chickens are among those animals and that they'd stop laying eggs when continuously exposed to interrupted lighting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, my neighbour has fluorescent lighting in his hen house. So either the above is bogus, or I have my facts mixed up. So, how (if at all) are chickens affected by light?&lt;/p&gt;&#xA;" OwnerUserId="9842" LastActivityDate="2014-10-19T01:57:30.943" Title="How are chickens affected by light?" Tags="&lt;zoology&gt;&lt;ornithology&gt;&lt;light&gt;&lt;chickens&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23281" PostTypeId="2" ParentId="20486" CreationDate="2014-10-18T23:17:42.703" Score="4" Body="&lt;p&gt;Chris is right, I just want to extend his answer a little bit more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The presence of corrosion and the corrosion speed highly depends on the concentration of the acid, which is very low (0.5% according to Chris) in this case (considering that ccHCl is about 35-40%). According to wikipedia the vapour pressure of water is about 2645 kPa while the vapour pressure of HCl is about 4352 kPa on 22°C. The atmospheric pressure is about 1000 kPa, so one part of the (few) HCl will evaporate before the water does, which makes, the concentration even lower. So I highly doubt that it can cause any damage to a regular floor or metal/wood table in an open environment.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;so, the Hollywood &quot;acid spill = instant shaft&quot; is completely false? – &#xA;  Jan Dvorak&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is possible to do that with much more concentrated acid. E.g. a bottle of hot concentrated sulfuric acid can cause very serious damage to people in a short time...&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-18T23:17:42.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23282" PostTypeId="2" ParentId="2498" CreationDate="2014-10-19T01:30:27.560" Score="1" Body="&lt;p&gt;I agree with Armatus, however I feel his answer incomplete.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sodium (along with chlorine) is the most important ion in the blood if we are talking about osmolarity and water transport. Water wants to move to the high osmolarity places so its transport is mainly controlled by the transport of sodium through selective sodium channels. This is not just about blood osmolarity, e.g. the absorption of water from the guts, the filtration of blood in the kidney, the sweating, etc... all major water transport in the body is mediated by sodium transport. So sodium is essential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your friends are right about too much sodium can harm you. Just try out something: eat something salty, and wait a few minutes. You will be thirsty, because sodium concentration increased your blood osmolarity, and so your body released hormones to restore osmolarity, and these hormones make you thirsty. After you drunk water, your blood pressure becomes higher until the kidney get rid of the extra sodium. High blood pressure is bad to your heart. This is just one way too much sodium can harm you...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your friends probably meant that if you don't have a lot of training and so you don't sweat a lot, you don't need crystalline salt in your food, because your food already contains enough sodium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is an interesting question why do we love extra salt despite the fact that our food contains enough of sodium. I don't know the answer of that. It certainly makes foods tastier, but I cannot find or find out anything about why this is evolutionary good. I think it is something similar to narcotics or sugar, it has a (small) hedonic value, despite that it isn't necessary good...&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-19T12:38:10.483" LastActivityDate="2014-10-19T12:38:10.483" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23283" PostTypeId="1" AcceptedAnswerId="23290" CreationDate="2014-10-19T01:42:18.503" Score="4" ViewCount="5971" Body="&lt;p&gt;I was reading about non-homologous end joining (NHEJ) in my molecular biology of the gene textbook but the explanation provided in the text was rather vague to me, and I was not able to understand it completely. I understood that NHEJ can be used as a repair mechanism when double-strand breaks in DNA occur. The two broken ends are then joined together. What I didn't understand is how this is done. The two broken ends won't always have complementary bases so, won't this lead to mismatched bases? How is this problem fixed? I really need a detailed explanation of how NHEJ occurs please.&lt;/p&gt;&#xA;" OwnerUserId="9002" LastEditorUserId="6307" LastEditDate="2014-10-19T08:36:32.587" LastActivityDate="2014-10-19T09:14:33.107" Title="How does non-homologous end joining (NHEJ) work?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;dna-damage&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23284" PostTypeId="2" ParentId="23280" CreationDate="2014-10-19T01:57:30.943" Score="3" Body="&lt;p&gt;It seems like they are not affected by fluorescent light frequency. I did not find anything about their visual sampling rate. &lt;a href=&quot;http://link.springer.com/article/10.1007/BF00196905&quot; rel=&quot;nofollow&quot;&gt;Their hearing is between 0-200Hz with an average of 86Hz&lt;/a&gt; so I guess the visual sampling rate is under this, but that's just a guess.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We conclude that at the illumination levels used in this experiment,&#xA;  the hens did not perceive the flicker of low-frequency light or they&#xA;  perceived it but did not find it aversive. Low-frequency fluorescent&#xA;  light does not appear to adversely affect the welfare of hens.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;1996 - &lt;a href=&quot;http://pubs.aic.ca/doi/abs/10.4141/cjas96-027&quot; rel=&quot;nofollow&quot;&gt;Laying hens do not have a preference for high-frequency versus low-frequency compact fluorescent light sources&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It concludes that there is no evidence that fluorescent or high&#xA;  pressure sodium lighting, irrespective of intensity or spectral&#xA;  distribution, has any consistent detrimental effect on growth, food&#xA;  utilization, reproductive performance, mortality, behaviour or live&#xA;  bird quality in either domestic fowl or turkeys, nor in the egg&#xA;  production of geese.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;1998 - &lt;a href=&quot;http://journals.cambridge.org/action/displayAbstract?fromPage=online&amp;amp;aid=621444&amp;amp;fileId=S004393399800004X&quot; rel=&quot;nofollow&quot;&gt;Responses of domestic poultry to various light sources&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A monochromatic (LED) light can be more beneficial according to this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A significant reduction in egg production was observed in all 880nm&#xA;  groups; no differences in egg production and quality were found in the&#xA;  other groups. Feed consumption was significantly lower by 7% in all&#xA;  0.01 W/m2 groups. We suggest that an important reduction in rearing costs of laying hens may be obtained by using this system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;1998 - &lt;a href=&quot;http://ps.oxfordjournals.org/content/77/11/1695.short&quot; rel=&quot;nofollow&quot;&gt;New monochromatic light source for laying hens&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-19T01:57:30.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23285" PostTypeId="1" AcceptedAnswerId="23286" CreationDate="2014-10-19T02:40:16.153" Score="2" ViewCount="8981" Body="&lt;p&gt;I'm researching about the basal lamina in lung tissue and I'm not sure if the basal membrane is the same.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the difference between them?&lt;/p&gt;&#xA;" OwnerUserId="5680" LastActivityDate="2014-10-21T04:17:05.273" Title="What is the difference between the basal membrane and the basal lamina?" Tags="&lt;physiology&gt;&lt;blood-circulation&gt;&lt;tissue&gt;&lt;endothelium&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23286" PostTypeId="2" ParentId="23285" CreationDate="2014-10-19T04:04:43.580" Score="4" Body="&lt;p&gt;The basal lamina is a specialised type of extracellular matrix. It is found on the basal side of all epithelial tissue but can also surround other cell types like myocytes and adipocytes. It is also called the basement membrane, although it is not the traditional plasma membrane that we have come to know and love. Rather, it is composed of proteins (often glycosylated) and polysaccharides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The basal membrane is the actual plasma membrane on the basal side of an epithelial cell (adjacent to the basal lamina/basement membrane).&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-10-21T04:17:05.273" LastActivityDate="2014-10-21T04:17:05.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23287" PostTypeId="2" ParentId="23283" CreationDate="2014-10-19T07:42:47.117" Score="3" Body="&lt;p&gt;NHEJ is indeed error prone. It is called &quot;non-homologous&quot; because it does not use a &quot;homologous&quot; template from another sequence-matching piece of DNA to guide the repair. Homologous repairs avoid causing mutations because the similar string of DNA  acts as a template so that the cell knows what letters to put into the gap. When there's no template, there's no way for the repair machinery to know what specific letters to use...hence the mutations in NHEJ.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, this NHEJ phenomenon is used to drive the current state-of-the-art in genetic engineering: CRISPR/Cas9 RNA-guided endonucleases. If you cause a double-strand DNA break near the beginning of the protein-coding sequence of a gene, this break will be repaired with NHEJ, causing an &quot;indel&quot; (insertion or deletion) mutation to occur. Inserting or deleting letters into the coding sequence of a gene will cause a &quot;frame shift&quot; where the 3-letter codons which tell the cell which amino acids to use get all jumbled up because the normal 3-3-3-3-3-3-3 pattern is disturbed. In this way, we can turn off genes that we want to target: just cause a frameshift in that gene with CRISPR.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we want to INSERT something using genome editing, we need &quot;homology directed repair&quot; -- we'll give the CRISPR alongside another string of nucleotides which matches the strings that flank the place we are cutting, with a new sequence in the middle. So when CRISPR makes the cut, our homologous template will stick to the sides of the cut and the center piece will provide the cell with a blueprint for the insertion or edit we want to make.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, you'll see as you think about it that the &quot;homology&quot; which is missing from NHEJ is the strand used as a repair template, and by manipulating these natural DNA repair processes which may or may not use homologous templates, we have a possible method to turn on, turn off, edit or insert genes. This means NHEJ isn't just a biological process anymore: it is an engineering technique.&lt;/p&gt;&#xA;" OwnerUserId="9831" LastActivityDate="2014-10-19T07:42:47.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23289" PostTypeId="2" ParentId="23277" CreationDate="2014-10-19T07:50:09.300" Score="1" Body="&lt;p&gt;One possibility is that these antibiotics could disrupt your normal gut bacteria. Given that your gut has the surface area of a tennis court and is typically coated with symbiotic microbes, antimicrobial therapies could dramatically change the population dynamics of your gut ecosystem. One might imagine that the immune system of the gut is in homeostasis with these gut microbes, and if they all die off all at once because you're taking some sort of 'cillin, your immune system might suffer for lack of stimulation. Fewer immune cytokines released by your intestinal immune cells into your blood =&gt; systemic reduction in immune function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other possibilities could include: the drug just randomly fits into a bad spot on some important immune protein; the drug targets bacterial-related genes in the mitochondrial genome and disrupts the metabolism of the immune cells; the drug disrupts your ability to absorb nutrients required for immune function...the list of potential mechanisms is undoubtedly long.&lt;/p&gt;&#xA;" OwnerUserId="9831" LastEditorUserId="9831" LastEditDate="2014-10-19T07:55:18.797" LastActivityDate="2014-10-19T07:55:18.797" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23290" PostTypeId="2" ParentId="23283" CreationDate="2014-10-19T09:14:33.107" Score="6" Body="&lt;p&gt;Non-homologous end joining indeed induces errors in the affected sequence. But you have to keep in mind, that NHEJ is an emergency repair mechanism which involves a &quot;repair or die&quot; chance. If the chromosomal break is not repaired it is not unlikely that the cell will get into apoptosis, or, even worse, develops into a cancer cell. Introducing small errors is a relatively small price compared to this, although this can still disrupt genes or regulatory sequences. For the mechanism have a look onto the figure (from the first reference):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2k7NY.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For further reading have a look onto the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Non-homologous_end_joining&quot; rel=&quot;noreferrer&quot;&gt;NHEJ&lt;/a&gt; and/or the following references:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17999957&quot; rel=&quot;noreferrer&quot;&gt;The mechanism of human nonhomologous DNA end joining.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20192759&quot; rel=&quot;noreferrer&quot;&gt;The mechanism of double-strand DNA break repair by the nonhomologous&#xA;DNA end-joining pathway.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-19T09:14:33.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23293" PostTypeId="2" ParentId="14370" CreationDate="2014-10-19T11:28:29.803" Score="3" Body="&lt;p&gt;This addition to the protocol worked out and good RNA quality was obtained:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Homogenization&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Homogenized the embryos, suspended (and frozen) in trizol by passing through 2ml insulin syringes. (About 10 times).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Washing&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Washed 2 times with 500µl 80% Ethanol&lt;/li&gt;&#xA;&lt;li&gt;Washed 3 times with 500µl 70% Ethanol&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Dechorionation was dispensable and Proteinase-K treatment was too harsh on early stage embryos. So I did not dechorionate this time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the number of washes can be reduced (1×80% and 2×70%) but this is what I stuck to (out of superstition :P)&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-12-12T05:45:37.927" LastActivityDate="2016-12-12T05:45:37.927" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23294" PostTypeId="2" ParentId="23253" CreationDate="2014-10-19T11:39:44.393" Score="2" Body="&lt;p&gt;Addition to what Chris already said:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Papain&lt;/strong&gt; can be used for cells sensitive to trypsin (neurons etc)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Collagenase&lt;/strong&gt;  can be used for certain cells where trypsin is ineffective (Accutase is a commercially available enzyme mix(?) which has collagenase activity)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Hyaluronidase&lt;/strong&gt; - I don't know where it is specifically preferred but it is used.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Pronase&lt;/strong&gt; and &lt;strong&gt;Proteinase K&lt;/strong&gt; - Can be used to disrupt tough tissues. I have used them mostly to dechorionate zebrafish embryos. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/General_Information/2/biofiles_issue2.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; documentation by Sigma-Aldrich on cell disruption enzymes.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-10-19T11:39:44.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23295" PostTypeId="1" CreationDate="2014-10-19T11:44:44.777" Score="3" ViewCount="9256" Body="&lt;p&gt;Neuronal tissues can be excited by electrical stimulation. Two commonly encountered characteristics for electrically stimulating nerve cells is the threshold and the rheobase. My question is what the difference is between rheobase and threshold? In the definitions I've read it's described as almost the same thing. The &lt;strong&gt;threshold&lt;/strong&gt;, or minimal stimulus, is defined as &quot;the electrical stimulus whose strength (or voltage) is sufficient to excite the tissue. &lt;strong&gt;Rheobase&lt;/strong&gt; is defined as &quot;the minimum strength (voltage) of stimulus which  can  excite  the  tissue&quot;. What is the difference?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="9943" LastEditDate="2016-02-20T21:48:39.947" LastActivityDate="2016-02-20T21:48:39.947" Title="What is the difference between rheobase and threshold?" Tags="&lt;neurophysiology&gt;&lt;biophysics&gt;&lt;electrophysiology&gt;&lt;signal-processing&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23297" PostTypeId="1" AcceptedAnswerId="23298" CreationDate="2014-10-19T13:36:34.483" Score="9" ViewCount="725" Body="&lt;p&gt;I found this dude hanging out in my sink, but he didn't fly away when I put a dish in the sink. Turned out it was dead. The front part looks exactly like a housefly. But, I've never seen the back end (abdomen) look like this. Any ideas?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/R2wIj.jpg&quot; width=&quot;250&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/hqyuh.jpg&quot; width=&quot;250&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/7fBTw.jpg&quot; height=&quot;250&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9847" LastEditorUserId="3624" LastEditDate="2015-06-03T08:59:15.083" LastActivityDate="2015-06-03T08:59:15.083" Title="What kind of fly is this?" Tags="&lt;entomology&gt;&lt;species-identification&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23298" PostTypeId="2" ParentId="23297" CreationDate="2014-10-19T15:10:32.097" Score="19" Body="&lt;p&gt;This is probably a fly killed by the fungi &lt;a href=&quot;http://en.wikipedia.org/wiki/Entomophthora_muscae&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Entomophthora muscae&lt;/em&gt;&lt;/a&gt; (or closely related) or maybe a &lt;a href=&quot;http://en.wikipedia.org/wiki/Cordyceps&quot; rel=&quot;noreferrer&quot;&gt;Cordyceps fungus&lt;/a&gt;. These kinds of fungi mainly attacks insects, and you sometimes see attacks as white, swollen abdomens in flies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iUq2u.jpg&quot; alt=&quot;picture from Bugguide.net&quot;&gt;&lt;br&gt;&#xA;(Picture of common infection, from bugguide.net)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These fungi are also known to change the behaviour of infected individuals, so that they e.g. climb up tall plants to die (sometimes called &quot;zombie-insects&quot;), to allow for better dispersal and transmission of the fungal spores. Lots of information about the behavioural modifications of hosts by fungi can be found in &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.ento.51.110104.150941&quot; rel=&quot;noreferrer&quot; title=&quot;BIZARRE INTERACTIONS AND ENDGAMES: Entomopathogenic Fungi and Their Arthropod Hosts&amp;quot;. Annual Review of Entomology&quot;&gt;Roy et al. (2006)&lt;/a&gt;, but they can involve both climbing to exposed locations and special mechanisms for host attachement at death: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In many cases the final interactions, or endgames, between a host and pathogen involve complex behavioral modifications such as the infected insect seeking an elevated position where wind currents can effectively disseminate conidia. Elevation seeking by insects at late stages of infection is a common phenomenon that was recognized by early insect pathologists who noted that diseased lepidopteran larvae, such as Lymantria monacha (the nun moth), infected with baculoviruses migrated to the tops of trees where they died (94). This host-altered behavior was named “Wipfelkrankheit” or “Wipfelsucht” (meaning tree top disease in German) for viral diseases (41) and “summit disease” for fungal diseases (24, 57, 106).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Some fungi do not produce rhizoids, but the host is held in situ by host structures alone, namely the legs or mouthparts (mandibles or stylets). The pose of the dead insect is generally characteristic of the pathogen species involved. For instance, E. grylli-infected grasshoppers (Figure 3a) and E. scatophagae–infected yellow dung flies (Figure 3b) seek elevated positions on grasses or other vegetation and cling tightly (death grip) with their legs (96). Tipulids infected with fungal species from the genera Eryniopsis and Entomophaga also attach to grasses with their long legs, often overhanging water (Figures 5b,c).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you do google image searches on &lt;a href=&quot;https://www.google.se/search?q=Entomophthora+fly+abdomen&amp;amp;client=firefox-a&amp;amp;hs=BuZ&amp;amp;rls=org.mozilla:sv-SE:official&amp;amp;channel=sb&amp;amp;source=lnms&amp;amp;tbm=isch&amp;amp;sa=X&amp;amp;ei=d91DVMKxGou9ygPop4KwCw&amp;amp;ved=0CAgQ_AUoAQ&amp;amp;biw=1600&amp;amp;bih=773&quot; rel=&quot;noreferrer&quot;&gt;&quot;&lt;em&gt;Entomophthora fly abdomen&lt;/em&gt;&quot;&lt;/a&gt; or &lt;a href=&quot;https://encrypted.google.com/search?q=fly+Cordyceps+abdomen&amp;amp;biw=1600&amp;amp;bih=773&amp;amp;source=lnms&amp;amp;tbm=isch&amp;amp;sa=X&amp;amp;ei=pNNDVNieIsL8ywPIroKAAQ&amp;amp;ved=0CAYQ_AUoAQ#tbm=isch&amp;amp;q=fly+Cordyceps&quot; rel=&quot;noreferrer&quot;&gt;&quot;&lt;em&gt;fly Cordyceps&lt;/em&gt;&quot;&lt;/a&gt; you can see some examples of infections. I don't know about the fly species, but &lt;em&gt;Musca domestica&lt;/em&gt; is probably likely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For some more examples and information on &lt;em&gt;Entomophthora muscae&lt;/em&gt; and related fungi see:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Roy et al. 2006. &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.ento.51.110104.150941&quot; rel=&quot;noreferrer&quot; title=&quot;BIZARRE INTERACTIONS AND ENDGAMES: Entomopathogenic Fungi and Their Arthropod Hosts&amp;quot;. Annual Review of Entomology&quot;&gt;&lt;em&gt;Bizzare Interactions and Endgames: Entomopathogenic Fungi and Their Arthropod Hosts&lt;/em&gt;&lt;/a&gt;. Annual Review of Entomology 51(1) (&lt;a href=&quot;http://www1.bio.ku.dk/forskning/oe/cse/gml_sider/media/roy2006.pdf&quot; rel=&quot;noreferrer&quot;&gt;pdf&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.biocontrol.entomology.cornell.edu/pathogens/entomophagamuscae.php&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Biological Control: Entomophthora muscae&lt;/em&gt;&lt;/a&gt;, webpage from Cornell Uni.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Harmon. 2012. &lt;a href=&quot;http://www.nature.com/news/fungus-that-controls-zombie-ants-has-own-fungal-stalker-1.11787&quot; rel=&quot;noreferrer&quot; title=&quot;Harmon. 2012. Fungus that controls zombie-ants has own fungal stalker. Nature&quot;&gt;&lt;em&gt;Fungus that controls zombie-ants has own fungal stalker&lt;/em&gt;&lt;/a&gt;. Nature  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://kdshives.com/2014/01/07/mind-controlling-fungus-turns-insects-into-zombies/&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Mind-controlling fungus turns insects into zombies&lt;/em&gt;&lt;/a&gt; (blog post)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-06-03T08:30:27.063" LastActivityDate="2015-06-03T08:30:27.063" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23299" PostTypeId="1" AcceptedAnswerId="23328" CreationDate="2014-10-19T15:20:27.617" Score="1" ViewCount="351" Body="&lt;p&gt;I have the pdb file of H-ras protein &lt;a href=&quot;http://rcsb.org/pdb/explore/explore.do?structureId=5P21&quot; rel=&quot;nofollow&quot;&gt;5P21.pdb&lt;/a&gt;. I am supposed to compare the output of &lt;a href=&quot;http://www.cmbi.ru.nl/dssp.html&quot; rel=&quot;nofollow&quot;&gt;DSSP&lt;/a&gt; and &lt;a href=&quot;http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py&quot; rel=&quot;nofollow&quot;&gt;STRIDE&lt;/a&gt; files after feeding this pdb file to respective servers. My question is how to make a quick comparison between these two results?&lt;/p&gt;&#xA;" OwnerUserId="5669" LastEditorUserId="3340" LastEditDate="2014-10-20T06:18:57.007" LastActivityDate="2014-10-20T21:00:28.983" Title="How can I compare the STRIDE and DSSP output files of a particular pdb file?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;pdb&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23300" PostTypeId="2" ParentId="22027" CreationDate="2014-10-19T15:37:38.660" Score="2" Body="&lt;p&gt;This just got too big for a comment and I think might actually qualify as an answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you give me a source for what you're reading? According to &lt;a href=&quot;http://www.nature.com/scitable/topicpage/neutral-theory-the-null-hypothesis-of-molecular-839&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;, which matches the definitions you are using, K=(Nu)/N=u where K is the substitution rate, u is the mutation rate in the population, Nu is the individual mutation rate, and N is the population size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I went back to Kimura's original paper in Nature in 1968 and he derives that u(p), the substitution rate in the population, is (almost exactly) the same as the mutation rate in an individual(p). But this follows from a different paper(prolific guy) where he shows that the fixation probability for a given allele is roughly 1/N, where N is the population size. Your individual mutation rate in your model is not u, but Nu.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are confusing the mutation/substitution rate in the population, which is used for molecular clocks and other things, and the individual mutation rate. If the molecular mutation rate, is say, 1/20 (as you assume in your model) then you are expecting a fixation rate per mutation of 1, essentially. If the substitution rate is going to be the same as the molecular mutation rate, every single mutation must reach fixation. If the same locus mutates twice in the same generation(quite possible with enough individuals), then both must somehow reach fixation, even though the first to reach fixation will necessarily destroy the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope that helps you sort out why Nu will never equal K, and helps the results of your model make sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(sidebar: Nu isn't the raw molecular mutation rate but the individual mutation rate, which is actually higher because while growing to adulthood the average human gamete is involved in about 50 cell divisions, which leads to a few more mutations per person.)&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-10-19T15:37:38.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23301" PostTypeId="1" AcceptedAnswerId="23322" CreationDate="2014-10-19T16:31:58.760" Score="2" ViewCount="270" Body="&lt;p&gt;I've found multiple sources claiming that damage or impairment as a result of alcohol to the vermis of the cerebellum results in speech impairment. I find this a bit surprising, since the only areas I know that are used for speech production are Broca's area. Additionally, I don't know of any way that the vermis influences this area or any other facial nerve that may need co-ordination to produce speech.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why does damage/impairment of the vermis result in dysarthria?&lt;/p&gt;&#xA;" OwnerUserId="5427" LastEditorUserId="57" LastEditDate="2014-10-19T20:52:51.277" LastActivityDate="2014-10-20T18:54:58.300" Title="Why is the vermis of the cerebellum associated with speech?" Tags="&lt;human-anatomy&gt;&lt;neuroanatomy&gt;&lt;anatomy&gt;&lt;language&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23302" PostTypeId="2" ParentId="23140" CreationDate="2014-10-19T17:35:44.090" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Our knowledge about the sexual transmission of mitochondria and&#xA;  plastids (hereafter organelles) in isogamous eukaryotes comes mostly&#xA;  from studies of the yeast Saccharomyces cerevisiae and the green alga&#xA;  Chlamydomonas reinhardtii which are both unicellular species. To&#xA;  investigate organelle inheritance in a multicellular organism with&#xA;  morphological isogamy, we studied the filamentous brown alga&#xA;  Ectocarpus siliculosus, in which each gamete contributes one plastid&#xA;  and at least one mitochondrion to the zygote. ...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2004 - &lt;a href=&quot;http://www.tandfonline.com/doi/abs/10.1080/09670260410001683241#.VEP16RaWdqQ&quot; rel=&quot;nofollow&quot;&gt;Inheritance of organelles in artificial hybrids of the isogamous multicellular chromist alga Ectocarpus siliculosus (Phaeophyceae)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So it is possible, but it seems like very rare.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-19T17:35:44.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23304" PostTypeId="2" ParentId="23273" CreationDate="2014-10-19T21:00:42.730" Score="2" Body="&lt;p&gt;This is not an answer to the question, but tangent comments that might be useful for how you look at the problem (and too long for a comment). First, for a question like this it is useful to look at other solutions to the same problem. For instance, the second most common molecule for oxygen transport is &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemocyanin&quot; rel=&quot;nofollow&quot;&gt;Hemocyanin&lt;/a&gt;, and this is not bound to cells but is directly suspended in hemolymph (arthropod/mollusc &quot;blood&quot;). So specialized cell types for oxygen transport is not a necessity for effecient oxygen transport in rather advanced organsism. So your question; &quot;&lt;em&gt;why do we need cells packed with hemoglobin: why can't it travel freely in the bloodstream?&lt;/em&gt;&quot;, while being true for humans and other vertebrates, is not true for oxygen transport in all &quot;complex&quot; animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, while there seems to be good reasons for why hemoglobin is bound in RBC, you should at least entertain the idea that the cause of RBC-bound hemoglobin in vertebrates is an evolutionary contingency (i.e. a random historical event). Evolution is always constrained by previous evolutionary history, and the reason that all vertebrates (+ a number of other organsisms) share RBC-bound hemoglobin may simply be that they share a common ancestor. This does not mean that it lacks advantages, but it also means that it might be misleading to search for &lt;strong&gt;the&lt;/strong&gt; reason for RBC-bound hemoglobin in a particular species. For some background on evolutionary contingencies and many useful references in the intro, as well as an interesting experiment to test for contingencies, you can have a look at &lt;a href=&quot;http://www.pnas.org/content/105/23/7899.full&quot; rel=&quot;nofollow&quot; title=&quot;Blount et al. 2008. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. PNAS&quot;&gt;Blount et al. (2008)&lt;/a&gt; (part of Lenski's &lt;a href=&quot;http://myxo.css.msu.edu/ecoli/&quot; rel=&quot;nofollow&quot;&gt;Long-term Experimental Evolution project&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-10-19T21:27:52.307" LastActivityDate="2014-10-19T21:27:52.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23305" PostTypeId="1" AcceptedAnswerId="23306" CreationDate="2014-10-19T22:29:19.797" Score="4" ViewCount="243" Body="&lt;p&gt;I found a critter on my bathroom towel. It's really tiny. Maybe 2 milimetres? I placed it on an envelope for the photograph.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone identify what it is?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/51A8X.png&quot; alt=&quot;A critter I found on my bathroom towel.&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9855" LastEditorUserId="57" LastEditDate="2014-10-19T23:17:24.673" LastActivityDate="2014-10-19T23:17:24.673" Title="What is the name of the critter depicted in the attached image?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23306" PostTypeId="2" ParentId="23305" CreationDate="2014-10-19T23:07:40.420" Score="5" Body="&lt;p&gt;That is the larva of a &lt;a href=&quot;http://en.wikipedia.org/wiki/Varied_carpet_beetle&quot; rel=&quot;nofollow noreferrer&quot;&gt;carpet beetle&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Larvae feed on natural fibers and can damage carpets, furniture, clothing and insect collections.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/P0vkI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&quot;Anthrenus verbasci - larva side (aka)&quot; by André Karwath aka Aka on Wikimedia&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Related question: &lt;a href=&quot;https://biology.stackexchange.com/questions/7626/what-kind-of-caterpillar-is-this&quot;&gt;What kind of caterpillar is this?&lt;/a&gt;, though I think that the larva photographed in that example is either of a different species or at a different time period within the larval stage.&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-10-19T23:15:28.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23312" PostTypeId="1" AcceptedAnswerId="27514" CreationDate="2014-10-20T13:28:56.427" Score="9" ViewCount="645" Body="&lt;p&gt;Transcriptional regulation is generally modeled as a Hill's function (similar to Michaelis-Menten Kinetics):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{dm_X}{dt}=\alpha _{m_X}.\frac{R}{K+R} -\beta _{m_X}.m_X$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where $m_X$ is the mRNA for some gene-$X$, $R$ is a Regulator $\alpha$ and $\beta$ are formation and degradation rate constants respectively. This equation denotes a saturation kinetics; increasing activator wont cause indefinite increase in transcription. Sounds logical because all promoter sites will be occupied at some point. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case of a repression the equation looks like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{dm_X}{dt}=\alpha _{m_X}.\frac{K}{K+R} -\beta _{m_X}.m_X$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to model &lt;strong&gt;repression of translation&lt;/strong&gt; using a &lt;strong&gt;similar equation&lt;/strong&gt;. However, the issue is that even though a single mRNA can be saturated by a regulator, increasing mRNA will require more regulators. So effectively the regulator available for a single mRNA molecule will be total regulator &lt;strong&gt;÷&lt;/strong&gt; total mRNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is that whether in such a case the following equation is logical:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{dX}{dt}=\alpha _{X}.m_X.\frac{K}{K+R/m_X} -\beta _{X}.X$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where $X$ is the protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which means we are taking into consideration the effective concentration of a regulator per mRNA. In other words the Hill's constant $K'$ should scale with mRNA concentration. ($K'=K\times m_X$)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Assumptions&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Well mixed system&lt;/li&gt;&#xA;&lt;li&gt;System at thermodynamic limit&lt;/li&gt;&#xA;&lt;li&gt;Amino-acid pool infinite&lt;/li&gt;&#xA;&lt;li&gt;Ribosomes infinite&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-01-02T12:08:39.337" LastActivityDate="2015-01-09T22:25:51.053" Title="Hill's function for translational regulation" Tags="&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="14" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23314" PostTypeId="1" CreationDate="2014-10-20T13:48:20.333" Score="6" ViewCount="887" Body="&lt;p&gt;As an instrumentation engineer, I have designed temperature control systems&#xA;capable of measuring and controlling temperature with a precision of 0.001K over a&#xA;wide temperature range.  I have always wondered how the human body maintains its&#xA;temperature within a fraction of a degree; specifically, where and how is the &#xA;temperature measurement done?&lt;/p&gt;&#xA;" OwnerUserId="9860" LastActivityDate="2015-12-02T04:56:40.733" Title="Which organs in the body are responsible for measuring temperature?" Tags="&lt;physiology&gt;&lt;temperature&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23315" PostTypeId="1" AcceptedAnswerId="23317" CreationDate="2014-10-20T15:42:41.833" Score="2" ViewCount="218" Body="&lt;p&gt;Epithelial with the ability to transport NaCl is bathed in an isotonic salt solution with these values (in mM): 136 Na, 6 K, 140 Cl.&#xA;The intracellular concentrations are: 45 Na, 100 K, 13 Cl.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cell's resting potential is -63 mV and the temperature is 37 Celcius.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Which ions will passively diffuse over the membrane?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;My attempt:&lt;/em&gt; I calculate the nernst potential of each ion and taking the first ion (Na) as an example I get that it's equilibrium is at 29 mV. So as there are more of these cations outside the cell and the membrane potential is negative, the ions will want to &quot;reach&quot; 29 mV by flowing INSIDE the cell (to increase the membrane potential). I think they will do this by diffusing into the cell? I'm not sure if I am attacking the problem correctly or if it's rather lunging at my abilities in transporters. The NaK transporter is active transport so maybe the do not diffuse at all?? However there are Na channels that can open...Which is passive diffusion..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Calculate the cation permeability Pna/Pk&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have no idea how to do this. I still need more constants in the Goldman equation (Pcl for example) before I could isolate even one of these.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2014-10-20T17:35:43.430" Title="Help me understand my membrane potential assignment" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23316" PostTypeId="1" AcceptedAnswerId="23318" CreationDate="2014-10-20T16:06:07.350" Score="3" ViewCount="1134" Body="&lt;p&gt;I have read in biology text-books that one of the most important constraints on the size of an insect happens to be the importance of the surface-volume ratio. It simply states that &#xA;if we assume constant oxygen levels and increase the size of an insect there would be a point where the insect's exoskeleton would no longer be able to support its weight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some textbooks go on to say that this is why we don't have insects the size of elephants. But, if this is true...is there a least upper-bound on the maximal body mass of an insect?&lt;/p&gt;&#xA;" OwnerUserId="9573" LastActivityDate="2014-10-21T05:00:14.537" Title="Is there a maximum size for an insect?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23317" PostTypeId="2" ParentId="23315" CreationDate="2014-10-20T16:24:24.520" Score="3" Body="&lt;p&gt;If there is passive transport for each ion, then every ion will diffuse over the membrane until the concentrations will be the same, and the membrane potential will be zero. So there is active transport in the cell, which maintains the resting potential which is -63mV.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So with the current concentrations the membrane potential will differ from this -63mV, and so the cell will change the ion levels to change the current potential to be equal to the resting potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think you should try to simply summarize the Nernst potentials. It won't be so accurate as the Goldman equation, but you don't have the relative permeabilities of this cell type, so the questioner probably does not wait the Goldman equation from you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would solve it this way:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Em = RT/zF * ln(out/in)&#xA;&#xA;R = 8,314 J/molK&#xA;T = 37 + 273 = 310K&#xA;F = 96485 J/molV&#xA;&#xA;RT/F = 26,712mV&#xA;&#xA;ENa = 26,712mV*ln(136/45) = +29,543mV&#xA;EK = 26,712mV*ln(6/100) = -75,152mV&#xA;ECl = -26,712mV*ln(140/13) = -63,486mV&#xA;Em = ENa + EK + ECl = -109,95mV&#xA;&#xA;Emr = -63mV&#xA;Emr - Em = -63mV + 110mV = +47mV&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So we have to increase the membrane potential. Decreasing intracellular K+, Cl- concentration and increasing intracellular Na+ concentration can do that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Concentrations: extracellular 136 Na, 6 K, 140 Cl, intracellular 45 Na, 100 K, 13 Cl. So possible passive transports are increase Na+, decrease K+, increase Cl-.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conclusion the passive transports will be increasing Na+, decreasing K+ the active transport will be decreasing Cl-.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Note that I haven't used these terms for 5 years, so if you can consult with somebody else about this, then ask him/her whether this is correct.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-20T17:35:43.430" LastActivityDate="2014-10-20T17:35:43.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23318" PostTypeId="2" ParentId="23316" CreationDate="2014-10-20T16:36:12.727" Score="4" Body="&lt;p&gt;I assume there must be a maximum size for insects, and I atmospheric oxygen probably has something to do with it. Insects do not breath like vertebrates, they have a series of tubes call &lt;a href=&quot;https://en.wikipedia.org/wiki/Trachea#Invertebrates&quot; rel=&quot;nofollow&quot;&gt;trachea&lt;/a&gt; that run through their bodies and open to the surface at spiracles. Air passes through these tubes and oxygen and CO&lt;sub&gt;2&lt;/sub&gt; passively diffuse through the tissues. Insects can force air through the trachea to increase the diffusion rate, but they just aren't as efficient as vertebrates with lungs and hemoglobin to carry oxygen around the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the &lt;a href=&quot;https://en.wikipedia.org/wiki/Carboniferous&quot; rel=&quot;nofollow&quot;&gt;past&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Geological_history_of_oxygen&quot; rel=&quot;nofollow&quot;&gt;oxygen levels were much higher&lt;/a&gt;. Higher amounts of oxygen could allow for larger invertebrates, and there were &lt;a href=&quot;https://en.wikipedia.org/wiki/Arthropleura&quot; rel=&quot;nofollow&quot;&gt;6 foot long millipedes&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Meganisoptera&quot; rel=&quot;nofollow&quot;&gt;giant dragonflies&lt;/a&gt;. Their size probably was not entirely caused by the extra oxygen, this was before they faced competition from vertebrates, so increased competition probably had more to do with their size reduction than loss of oxygen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know what the maximum size for an insect is at modern oxygen levels, but you'd have to eliminate the other selective pressures such as competition and limits on food before an insect could reach that size.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="3340" LastEditDate="2014-10-21T05:00:14.537" LastActivityDate="2014-10-21T05:00:14.537" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23319" PostTypeId="2" ParentId="21719" CreationDate="2014-10-20T17:41:39.330" Score="0" Body="&lt;p&gt;As far as I know fats are solid lipids while oils are liquid lipids in (I guess) room temperature. So saturated triglycerides are usually fats, and unsaturated triglycerides are usually oils.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is because saturated and trans-unsaturated fatty acid chains are linear while cis-unsaturated fatty acid chains are curly (non-linear). Forces between linear chains are stronger that's why they are solid after a length.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-20T17:41:39.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23320" PostTypeId="1" AcceptedAnswerId="23323" CreationDate="2014-10-20T18:41:54.747" Score="4" ViewCount="2296" Body="&lt;p&gt;I have to do a research about the enzymes in the human body and the things that affect them. I know that the body temperature affects the activity of enzyemes but I'd like to know if the outer temperature of the air affects them, too?&#xA;When the temperature goes to 47°C or more we get tired and exhausted. Is this because the activity of enzymes decrease or is something else?!&lt;/p&gt;&#xA;" OwnerUserId="9861" LastEditorUserId="9861" LastEditDate="2014-10-20T19:00:48.727" LastActivityDate="2014-10-20T19:30:53.350" Title="Is the activity of enzymes in the human body affected by the outer temperature?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;enzymes&gt;&lt;temperature&gt;&lt;systems-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23322" PostTypeId="2" ParentId="23301" CreationDate="2014-10-20T18:54:58.300" Score="1" Body="&lt;p&gt;Although speech production is in generally executed in the cerebral domain, the dysarthria resulting from damage of the vermous is a symptom of the resulting general muscle weakness. So yes, you get slurred speech because your muscles are weak, but the weak muscles certainly aren't ever isolated to speech production.&lt;/p&gt;&#xA;" OwnerUserId="5427" LastActivityDate="2014-10-20T18:54:58.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23323" PostTypeId="2" ParentId="23320" CreationDate="2014-10-20T19:30:53.350" Score="2" Body="&lt;p&gt;Enzymes usualy have a relative narrow temperature optimum, for those of our body this is usually around 37°C. It is around 37,2°C in the morning and goes slightly up to 37,7°C in the evening (see reference 1 for details). The temparature optimum for most enzymes looks somewhat like displayed in the figure (from &lt;a href=&quot;http://bitesizebio.com/120/why-do-enzymes-have-optimal-temperatures/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;, interesting to read):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Skdxp.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Enzymes are relatively tolerant to lower temperatures (although their reaction rate is much lower), but generally they work. If you go too high with the temperature, the activity will soon be reduced to zero, as the enzymes are denaturated and are not able to catalyze any reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The human body does quite a lot to control its temperature and to keep it within a pretty small limit. It does either excessive sweating (when it's hot) or shivering (when it's cold) to maintain its temperature within or at least near the optimum. For further details on the themorgulation have a look on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Thermoregulation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt; article on this topic or reference 2 and 3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although our enzymes work at slightly lower reaction rates when the body temperature is higher (think of fever), this is not a major issue. Slightly higher temperatures can thus be tolerated, although you don't feel very nice. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The effect of to hot temperatures is different, though. It is mostly due to not consuming enough water, so that the body has not the possibility to control its temperature via sweating. This condition will ultmatively lead to a heatstroke, see &lt;a href=&quot;http://en.wikipedia.org/wiki/Heat_stroke&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for more details. Before you reach the temperature in which your enzymes reaction rate will go down drastically, you have long collapsed.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.google.de/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;ved=0CCEQFjAA&amp;amp;url=http%3A%2F%2Fwww.id.uzh.ch%2Fcl%2Fdl%2Fsw%2Fstatmath%2Fspss%2Fspsskurs2%2Faufgaben%2Ffieber%2Fa_critical_appraisal_journal.pdf&amp;amp;ei=JVtFVMqzNOLNygOjpoLADA&amp;amp;usg=AFQjCNFhXoF8hNMtYlD3RvLw6swQenZ5Gg&amp;amp;bvm=bv.77880786,d.bGQ&amp;amp;cad=rja&quot; rel=&quot;nofollow noreferrer&quot;&gt;A critical appraisal of 98.6 degrees F, the upper limit of the&#xA;normal body temperature, and other legacies of Carl Reinhold August&#xA;Wunderlich.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12744548&quot; rel=&quot;nofollow noreferrer&quot;&gt;Skin blood flow in adult human thermoregulation: how it works, when&#xA;it does not, and why.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://ajpregu.physiology.org/content/292/1/R37&quot; rel=&quot;nofollow noreferrer&quot;&gt;Thermoregulation: some concepts have changed. Functional&#xA;architecture of the thermoregulatory system&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-20T19:30:53.350" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23324" PostTypeId="1" AcceptedAnswerId="23325" CreationDate="2014-10-20T19:35:44.690" Score="5" ViewCount="969" Body="&lt;p&gt;While doing some research on cosmetic surgery, I discovered that there are several ways of doing breast enhancements, one of which was using body fat. While I haven't researched this method, I assume they transfer the patients body fat from one part of the body to another. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would the body use this transferred fat for as energy, or would it ignore it as it wasn't stored there in the first place? Does the body differentiate fat cells stored in different parts of the body?&lt;/p&gt;&#xA;" OwnerUserId="9862" LastEditorUserId="3340" LastEditDate="2015-06-04T11:42:18.477" LastActivityDate="2015-06-19T03:05:30.743" Title="Burning fat transferred from one part of the body to another" Tags="&lt;metabolism&gt;&lt;bioenergetics&gt;&lt;fat-metabolism&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23325" PostTypeId="2" ParentId="23324" CreationDate="2014-10-20T19:46:07.487" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Would the body use this transferred fat for as energy, or would it&#xA;  ignore it as it wasn't stored there in the first place?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It would use it as energy source, there is no such thing as &quot;ignored tissue&quot;. Fatty acid mobilization is regulated by epinephrine and insulin. These are hormones which are ofc. carried by blood, so every white adipose (fat) tissue is affected by them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DCKuM.png&quot; alt=&quot;fatty acid mobilization&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Figure 1 - FFA and glycerol mobilization - &lt;a href=&quot;http://themedicalbiochemistrypage.org/fatty-acid-oxidation.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2003 - &lt;a href=&quot;http://kines.umich.edu/sites/webservices.itcs.umich.edu.drupal.kinesprod/files/resource_files/HorowitzTEMrev.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fatty acid mobilization from adipose&#xA;tissue during exercise&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Does the body differentiate fat cells stored in different parts of the body?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is obvious, just check breasts and butts of girls. ;-) (Those are subcutaneous fat depos. They size is probably regulated by estrogen.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other things involved here, we can talk about subcutaneous (fat below the skin), intramuscular (fat in the muscles) and visceral (abdominal fat) white adipose tissue (there are white, brown and beige adipose tissues). The visceral fat is associated with metabolic diseases, obesity etc... &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;1995 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/j.1550-8528.1995.tb00462.x/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pathophysiology and Pathogenesis of Visceral Fat Obesity&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2012 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1038/oby.2011.401/full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lower Thigh Subcutaneous and Higher Visceral Abdominal Adipose Tissue Content Both Contribute to Insulin Resistance&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://www.cell.com/trends/endocrinology-metabolism/abstract/S1043-2760%2813%2900168-9&quot; rel=&quot;nofollow noreferrer&quot;&gt;Genomic and epigenomic regulation of adipose tissue inflammation in obesity&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The regulation of body fat distribution and amount is complicated and regulated differently by subcutaneous, intramuscular and visceral fat. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The total transmissible variance ranged from about 40 percent for the&#xA;  amount of subcutaneous fat to 60 percent for the pattern of&#xA;  subcutaneous fat distribution. Biological inheritance accounted for&#xA;  only 5 percent of the variance for subcutaneous fat and the body mass&#xA;  index, but 20 to 30 percent for the percentage of body fat, fat mass,&#xA;  fat-free mass, and fat distribution. These data suggest that the&#xA;  amount of internal fat is influenced by heredity more than the amount&#xA;  of subcutaneous fat. Furthermore, we consistently found that&#xA;  nongenetic influences are quite important in determining the amount&#xA;  and distribution of body fat in the population.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1988 - &lt;a href=&quot;http://europepmc.org/abstract/MED/3391737&quot; rel=&quot;nofollow noreferrer&quot;&gt;Inheritance of the amount and distribution of human body fat&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These data suggest that adiponectin concentrations are determined by&#xA;  intra-abdominal fat mass, with additional independent effects of age&#xA;  and sex. Adiponectin could link intra-abdominal fat with insulin&#xA;  resistance and an atherogenic lipoprotein profile.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2003 - &lt;a href=&quot;http://link.springer.com/article/10.1007/s00125-003-1074-z&quot; rel=&quot;nofollow noreferrer&quot;&gt;Relationship of adiponectin to body fat distribution, insulin sensitivity and plasma lipoproteins: evidence for independent roles of age and sex&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The FFA storage pathway, which had remained undetected in&#xA;  postabsorptive humans until recently, can have considerable,&#xA;  long-term, and sex-specific effects on body fat distribution. It can&#xA;  also offer a way of protecting the body from excessive circulating FFA&#xA;  in obesity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://diabetes.diabetesjournals.org/content/60/8/2032.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Storage of Circulating Free Fatty Acid in Adipose Tissue of Postabsorptive Humans&#xA;Quantitative Measures and Implications for Body Fat Distribution&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Different colors (white, brows, beige) and orgin (subcutaneous, intramuscular, visceral) originate from different progenitor cells.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These results reveal a major ontogenetic difference between visceral&#xA;  and subcutaneous WAT, and pinpoint the lateral plate mesoderm as a&#xA;  major source of visceral WAT. They also support the notion that&#xA;  visceral WAT progenitors are heterogeneous, and suggest that&#xA;  mesothelium is a source of adipocytes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.nature.com/ncb/journal/v16/n4/full/ncb2922.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Visceral and subcutaneous fat have different origins and evidence supports a mesothelial source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Brown and white adipocytes have been shown to derive from different&#xA;  progenitors. In this study we sought to clarify the molecular&#xA;  differences between human brown and white adipocyte progenitors cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0303720714002159&quot; rel=&quot;nofollow noreferrer&quot;&gt;Comparative gene array analysis of progenitor cells from human paired deep neck and subcutaneous adipose tissue&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The regulation of fat distribution is under research, and not fully understood yet. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fat distribution differs in men and women, but in both sexes, a&#xA;  predominantly gluteal-femoral compared with abdominal (central) fat&#xA;  distribution is associated with lower metabolic risk. Differences in&#xA;  cellular characteristics and metabolic functions of these depots have&#xA;  been described, but the molecular mechanisms involved are not&#xA;  understood.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://press.endocrine.org/doi/abs/10.1210/jc.2012-2953&quot; rel=&quot;nofollow noreferrer&quot;&gt;Distinct Developmental Signatures of Human Abdominal and Gluteal Subcutaneous Adipose Tissue Depots&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-21T19:43:31.397" LastActivityDate="2014-10-21T19:43:31.397" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23328" PostTypeId="2" ParentId="23299" CreationDate="2014-10-20T21:00:28.983" Score="1" Body="&lt;p&gt;Here a solution that does not require you to upload the files to the servers: You can graphically visualize DSSP and Stride at the Sequence Page at RCSB PDB:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=5P21&amp;amp;bionumber=1&quot; rel=&quot;nofollow&quot;&gt;http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=5P21&amp;amp;bionumber=1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;add annotation&quot; -&gt; Stride and look at the graphical comparison between DSSP and Stride.&lt;/p&gt;&#xA;" OwnerUserId="3150" LastActivityDate="2014-10-20T21:00:28.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23330" PostTypeId="1" CreationDate="2014-10-21T04:01:33.677" Score="1" ViewCount="4850" Body="&lt;p&gt;The kidney is composed of tissues, and those tissues are made up of numerous cells - so how do these cells excrete their wastes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, are there any wastes in the venous blood (renal vein), what makes the renal artery and vein different? - what substances do they each carry? &lt;/p&gt;&#xA;" OwnerUserId="9870" LastEditorUserId="9870" LastEditDate="2014-10-22T01:50:29.147" LastActivityDate="2014-10-31T12:33:39.380" Title="How do kidney cells excrete their own wastes?" Tags="&lt;kidney&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23331" PostTypeId="1" CreationDate="2014-10-21T04:40:06.103" Score="2" ViewCount="1221" Body="&lt;p&gt;What would be the resultant by-products of a completely decomposed dead skin cell?&#xA;What would be the size of each of the by-products of a decomposed dead skin cell? How long would it take for a dead skin cell to begin to decompose? &#xA;I am curious because anything below the 10 micron range can enter the alveoli of the lungs and cause emphysema. I have had eczema since early childhood, and therefore have breathed in more dead skin cells and by-products of dead skin cells than those without eczema, principally during sleep. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The epidermis, the outermost layer of the skin, sheds corneocytes. Corneocytes are 30-50 micrometers in diameter. &lt;a href=&quot;http://www.nanoscience.de/richter.old/corn.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nanoscience.de/richter.old/corn.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user9871" LastEditorDisplayName="user9871" LastEditDate="2014-10-21T04:58:18.973" LastActivityDate="2014-10-21T04:58:18.973" Title="Dead skin cell decomposition" Tags="&lt;skin&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23334" PostTypeId="1" AcceptedAnswerId="23603" CreationDate="2014-10-21T06:37:41.457" Score="8" ViewCount="1628" Body="&lt;p&gt;I've ridden a virtual roller coaster on an Oculus Rift. I felt tension as I went up to the top, but more interestingly I actually felt my stomach drop when I went down the steep drop on the other side. Why can I feel this, when no forces are actually being applied to my stomach?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A bonus question: If you took someone that had never ridden a roller coaster, or even been exposed to rapid acceleration, and had them try a virtual one - would they feel the same stomach lurch as I did?&lt;/p&gt;&#xA;" OwnerUserId="9874" LastActivityDate="2014-10-31T01:00:14.353" Title="Why do I feel funny in my tummy when riding a virtual roller coaster?" Tags="&lt;physiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23338" PostTypeId="1" AcceptedAnswerId="23358" CreationDate="2014-10-21T08:45:06.577" Score="0" ViewCount="168" Body="&lt;p&gt;I am interested in synthetic biology, but not a scientist, and would like some advice on where to look for an online forum on synthetic biology and creating fictional species and animals or if someone could suggest the best website to set such a forum up on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The current research into synthetic biology with biobricks and all the complicated discussion of biochemistry and genetics is too advanced for myself and not what I am interested in. I have fictional ideas of how to create new organisms and symbiotic organisms that are designed and grown for humans to wear and utilise and would like to bounce ideas off other people who may be in to the same area - the potential application of synthetic biology in the far future.&#xA;Thank you for any suggestions.&lt;/p&gt;&#xA;" OwnerUserId="342" LastActivityDate="2018-07-03T07:31:17.023" Title="Forum on synthetic biology and hypothetical biology?" Tags="&lt;synthetic-biology&gt;&lt;speculative&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2018-07-08T21:00:21.390" ContentLicense="CC BY-SA 3.0" />
  <row Id="23339" PostTypeId="1" AcceptedAnswerId="23346" CreationDate="2014-10-21T09:28:18.133" Score="0" ViewCount="68" Body="&lt;p&gt;There are many web puzzle to identify, but does it really have any scientific proof?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;something like - &lt;a href=&quot;http://braintest.sommer-sommer.com/en/&quot; rel=&quot;nofollow&quot;&gt;http://braintest.sommer-sommer.com/en/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;any logic behind it?&lt;/p&gt;&#xA;" OwnerUserId="9877" LastEditorUserId="9877" LastEditDate="2014-10-21T11:54:26.947" LastActivityDate="2014-10-21T19:05:33.677" Title="Is there any research paper which identifies left and right brained behavior?" Tags="&lt;human-biology&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23340" PostTypeId="1" CreationDate="2014-10-21T13:57:08.647" Score="1" ViewCount="57" Body="&lt;p&gt;What is the predominant purpose of &lt;em&gt;Alkaline Phosphatase&lt;/em&gt; in skeletal muscle fibers and liver cells. I know that it is a hydrolase enzyme that speeds up the degredation of proteins, lipids, starch and other biomolecules. But what does it does it &lt;strong&gt;specifically&lt;/strong&gt; do in muscle and liver cells. And why is it in higher concentration in the liver ? Is it because of the livers purpose as an organ (cleanse and detoxification) ? Therefore pino/or endocytosis occur in higher rates ? I appreciate anyone with any intelligent insight. &lt;/p&gt;&#xA;" OwnerUserId="8059" LastActivityDate="2014-10-21T13:57:08.647" Title="Alkaline Phosphatase" Tags="&lt;cell-biology&gt;&lt;microbiology&gt;&lt;enzymes&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23341" PostTypeId="1" AcceptedAnswerId="23344" CreationDate="2014-10-21T15:56:23.283" Score="15" ViewCount="3096" Body="&lt;p&gt;Are there any birds whose legs fold the same way human legs do, in a knee, instead of an elbow which is what all the birds I know have?&lt;/p&gt;&#xA;" OwnerUserId="3228" LastEditorUserId="1590" LastEditDate="2016-01-07T11:37:19.627" LastActivityDate="2016-02-26T16:06:49.923" Title="Are there birds with knees instead of elbows?" Tags="&lt;ornithology&gt;&lt;joints&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23342" PostTypeId="1" CreationDate="2014-10-21T15:58:25.720" Score="1" ViewCount="373" Body="&lt;p&gt;I work in a microbiology lab where we do a lot of cloning. I have always used restriction endonucleases to cleave the DNA to have sticky ends and not blunt ends. I currently am working on a project that suggests using a blunt end restriction enzyme, such as EvoRV, and then to perform a T-tailing of the plasmid, pl4440. My question is why do I not treat my pcr'd insert with a restriction digest just like I would the plasmid as the protocol suggests? How do I know the insert has ends that are able to ligate into the plasmid if I don't design the restriction sites into the primers? &lt;/p&gt;&#xA;" OwnerUserId="9061" LastActivityDate="2015-01-01T18:20:26.390" Title="Molecular Cloning- Blunt end restriction endonucleases" Tags="&lt;microbiology&gt;&lt;cloning&gt;&lt;restriction-enzymes&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="23343" PostTypeId="2" ParentId="23330" CreationDate="2014-10-21T16:03:44.593" Score="-2" Body="&lt;p&gt;The kidneys keep the composition, or makeup, of the blood stable, which lets the body function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each kidney is made up of about a million filtering units called nephrons. The nephron includes a filter, called the glomerulus, and a tubule.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nephrons work through a two-step process. The glomerulus lets fluid and waste products pass through it; however, it prevents blood cells and large molecules, mostly proteins, from passing. The filtered fluid then passes through the tubule, which sends needed minerals back to the bloodstream and removes wastes.&lt;/p&gt;&#xA;" OwnerUserId="9881" LastEditorUserId="9881" LastEditDate="2014-10-21T23:41:05.153" LastActivityDate="2014-10-21T23:41:05.153" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23344" PostTypeId="2" ParentId="23341" CreationDate="2014-10-21T16:04:02.080" Score="26" Body="&lt;p&gt;The joint you are thinking of is not a &lt;a href=&quot;http://en.wikipedia.org/wiki/Knee&quot; rel=&quot;nofollow noreferrer&quot;&gt;knee&lt;/a&gt;, nor is it an &lt;a href=&quot;http://en.wikipedia.org/wiki/Elbow&quot; rel=&quot;nofollow noreferrer&quot;&gt;elbow&lt;/a&gt;, instead it is an &lt;a href=&quot;http://en.wikipedia.org/wiki/Ankle&quot; rel=&quot;nofollow noreferrer&quot;&gt;ankle&lt;/a&gt; which is bending the same way as us humans. You can see from the below diagram that the knee - the joint between the femur and tibia - is just further up the leg normally hidden by feathers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Birds have a comparatively elongated metatarsus which gives the impression that the knee bends backwards more like an elbow, but it's just the ankle. (&lt;a href=&quot;http://en.wikibooks.org/wiki/Anatomy_and_Physiology_of_Animals/The_Skeleton&quot; rel=&quot;nofollow noreferrer&quot;&gt;Image from here&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/e/e6/Anatomy_and_physiology_of_animals_Birds_skeleton.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also liked this diagram from a &lt;a href=&quot;http://skeletaldrawing.blogspot.se/2011/09/um-hey-scientific-american-bird-knees.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;blogpost&lt;/a&gt; on a similar theme...&#xA;&lt;img src=&quot;https://i.stack.imgur.com/uzS1m.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To follow up there appears to be no animals whose ankles bend the &quot;wrong&quot; way. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.answers.com/Q/Which_animal_has_backward_knees&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.answers.com/Q/Which_animal_has_backward_knees&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://qi.com/infocloud/knees&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://qi.com/infocloud/knees&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ehow.com/info_12317202_birds-knees-backwards.html#page=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ehow.com/info_12317202_birds-knees-backwards.html#page=1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though these are far from conclusive resources. I'd guess the way knee is defined (it means something to humans but not to nature (a bit like the species being a concept which has weak biological bounds)) has something to do with that &lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.720" LastActivityDate="2016-02-26T16:06:49.923" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23346" PostTypeId="2" ParentId="23339" CreationDate="2014-10-21T18:58:15.373" Score="3" Body="&lt;p&gt;In general I'd say &quot;left and right brained behaviour&quot; is total nonsense. I guess the origin of this kind of claim is a bad press release or something.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's start with something simple. Say hearing. When you hear a sound to your left ear, it is projected strongly to the contra-lateral side (right hemisphere), and weakly to the ipsi-lateral (left hemisphere) of your brain. So the brain response to a sound presented to the left ear is &lt;em&gt;lateralized&lt;/em&gt;. Typically, this means that the other hemisphere is &quot;more&quot; responsible for processing the input. Similar thing happens for the other senses too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what is interesting about lateralized brain responses? Well, it would be very interesting to know for example are memories lateralized. It would tell something about the system: is it a kind of distributed system, where parts of a memory are scattered here and there, according to some logic, or is a single memory stored on a small area (and maybe only on the other side of the brain), etc. The distributed hypothesis seems more plausible according to recent research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's talk about handedness next. Are you right handed? Or left handed? Or ... something between? Actually, even something like handedness is not a binary thing. It is more like a value on a range from 0 (&quot;very left handed&quot;) to 100 (&quot;very right handed&quot;). This is taken into account in decent research, where ~1 hr per participant is used to assess that value (if it is relevant to the study).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So we have now talked about lateralization. How about the &quot;left and right brained behaviour&quot; then? In the URL you have provided it is implied that certain behavioural attributes are somehow related to lateralization. Lateralization of what? All the attributes, e.g. &quot;being rational&quot; depend on so many things: seeing, hearing, thinking, retrieving memories, ... that saying such a thing is not plausible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, many brain processes are lateralized. That is the word to look up for for more information. But a thing like &quot;behaviour&quot; is too complex to be put to one hemisphere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference: Accumulated wisdom from being a research assistant in a neuroscience project. (so you should trust pubmed.org more than me).&lt;/p&gt;&#xA;" OwnerUserId="9883" LastEditorUserId="9883" LastEditDate="2014-10-21T19:05:33.677" LastActivityDate="2014-10-21T19:05:33.677" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23347" PostTypeId="2" ParentId="23334" CreationDate="2014-10-21T19:16:35.520" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;If you took someone that had never ridden a roller coaster, or even been exposed to rapid acceleration, and had them try a virtual one - would they feel the same stomach lurch as I did?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Probably not. A congenitally blind person, who can distinguish between a globe and a cube by her touch, is not able to tell which one is which (without touching) when given sight. For details see the article &quot;The newly sighted fail to match seen with felt&quot; from Nature: &lt;a href=&quot;http://www.nature.com/neuro/journal/v14/n5/abs/nn.2795.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/neuro/journal/v14/n5/abs/nn.2795.html&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9883" LastActivityDate="2014-10-21T19:16:35.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23348" PostTypeId="1" CreationDate="2014-10-20T02:16:40.970" Score="6" ViewCount="130" Body="&lt;p&gt;There are National Preserves in the National Parks where some human activities are permitted. But can it make sense to create &quot;exclusion zones&quot; so no human would be permitted in a certain area, not even scientists or researchers just so Grizzlies and Wolves can have a whole world to themselves ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know we won't be able to find out how those species are doing, but would there be any benefit ? Has any country ever tried that ?&lt;/p&gt;&#xA;" OwnerUserId="9889" OwnerDisplayName="fahadash" LastEditorUserId="461" LastEditDate="2014-10-22T02:22:16.453" LastActivityDate="2014-10-22T02:22:16.453" Title="Can &quot;human exclusion zones&quot; in national parks for preserving Wolves and Grizzlies be a good idea?" Tags="&lt;ecology&gt;&lt;population-dynamics&gt;&lt;conservation-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23349" PostTypeId="2" ParentId="23348" CreationDate="2014-10-20T02:40:16.240" Score="3" Body="&lt;p&gt;I think it is a neat idea that should be discussed.&#xA;Not just for wolves or large predators but for all wildlife situations&#xA;There should be small habitats for all wildlife to refuge scattered around. Of course national parks, reserves and refuges are there for this purpose, but humans have become far too abundant on this planet to coexist anymore, and maybe we need to take it a step further? Again, it's something that should be discussed and awareness made of the issue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And by far the best reason for this if nothing else is to have a scientific &quot;control&quot; spot for environmental research. It is important to have a control in all experiments, and to have a human exclusion zone helps create that control. If we had that, maybe someone could actually prove how much humans really are screwing up the planet, or maybe someone will prove they aren't :D&lt;/p&gt;&#xA;" OwnerDisplayName="Man" LastActivityDate="2014-10-20T02:47:01.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23350" PostTypeId="1" CreationDate="2014-10-21T23:43:19.330" Score="2" ViewCount="52" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Largest_prehistoric_animals&quot; rel=&quot;nofollow&quot;&gt;The largest dinosaurs and pterosaurs seem to have been much larger than the largest animal terrestrial/avian species since&lt;/a&gt;. Was the Mesozoic somehow more hospitable to large animal species than today's world? Have subsequent evolutionary innovations shifted the balance towards smaller species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly &lt;a href=&quot;http://animals.howstuffworks.com/animal-facts/question687.htm&quot; rel=&quot;nofollow&quot;&gt;the still-existing blue whale seems to be the largest animal ever&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4697" LastActivityDate="2014-10-21T23:43:19.330" Title="Why are the largest land/air animals today smaller than in the Mesozoic?" Tags="&lt;palaeontology&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2018-07-16T18:37:12.540" ContentLicense="CC BY-SA 3.0" />
  <row Id="23352" PostTypeId="1" CreationDate="2014-10-22T00:34:34.603" Score="1" ViewCount="16" Body="&lt;p&gt;When antioxidant molecules stabilize free radicals, they themselves become unstable and reactive but to a lesser degree. How reactive are these reduced antioxidant molecules? And what substance stabilizes reduced antioxidants?&lt;/p&gt;&#xA;" OwnerUserId="9490" LastActivityDate="2014-10-22T00:34:34.603" Title="How reactive are reduced antioxidant molecules?" Tags="&lt;metabolism&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23353" PostTypeId="1" AcceptedAnswerId="23356" CreationDate="2014-10-22T01:09:03.780" Score="7" ViewCount="562" Body="&lt;p&gt;I'm looking for clarification on the answer to this question. It's in my biochemistry class but I figured this is more Biology than Chemistry, so I'm asking it here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One of the more effective treatments for HIV-positive individuals has been for them to take &#xA;  protease inhibitor cocktails. Certain proteases are required for the virus to mature and these inhibitors prevent them from functioning. A cocktail of inhibits means that numerous inhibitors are used at once. Why would a cocktail be more effective than a single inhibitor?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My answer to this is that there could be more than one mutation of the virus, and with each mutation a variation in specific protease. So, the protease cocktail would defend against a wider range of the mutated virus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this correct? Is there an answer that might involve describing epitopes?&lt;/p&gt;&#xA;" OwnerUserId="9550" LastEditorUserId="9099" LastEditDate="2014-10-22T04:51:18.373" LastActivityDate="2014-10-22T04:51:18.373" Title="HIV and effectiveness of inhibitor cocktail over single inhibitor" Tags="&lt;biochemistry&gt;&lt;homework&gt;&lt;immunology&gt;&lt;hiv&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23354" PostTypeId="2" ParentId="23330" CreationDate="2014-10-22T01:50:58.937" Score="1" Body="&lt;p&gt;I checked my anatomy notes and online figures about the kidney. There is no mention about dedicated arteries for feeding kidney cells. So it does not work the same way as the heart does, where there is a dedicated coronary artery. The kidneys use the same blood vessels for filtering and for nutrition/waste transport purposes too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wt1ol.jpg&quot; alt=&quot;kidney&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 1 - kidney anatomy - &lt;a href=&quot;http://www.interactive-biology.com/3254/the-anatomy-of-the-kidney/&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7yLyI.jpg&quot; alt=&quot;nephron&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 2 - nephron anatomy - &lt;a href=&quot;http://osmoregulation-apbio3.wikispaces.com/Kidney&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The urea is created from NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt; and HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; in the liver (mostly) and the kidney because of blood pH regulation purposes. It neutralizes the HCO3- created by the lungs from CO&lt;sub&gt;2&lt;/sub&gt; and OH&lt;sup&gt;-&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The urea cycle (also known as the Ornithine cycle) is a cycle of&#xA;  biochemical reactions occurring in many animals that produces urea&#xA;  ((NH&lt;sub&gt;2&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;CO) from ammonia (NH&lt;sub&gt;3&lt;/sub&gt;). This cycle was the first metabolic&#xA;  cycle discovered (Hans Krebs and Kurt Henseleit, 1932), five years&#xA;  before the discovery of the TCA cycle. In mammals, the urea cycle&#xA;  takes place primarily in the liver, and to a lesser extent in the&#xA;  kidney.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In chemical terms, urea synthesis is an irreversible, energy driven&#xA;  neutralization of the strong base HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; by the weak acid NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;, and the&#xA;  average daily excretion of 30 g of urea is equivalent to the disposal&#xA;  of about 1 mol of HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; per day. Thus, a major function of hepatic&#xA;  urea synthesis is to effect this neutralization, without which the&#xA;  body would otherwise be confronted by a major load of alkali.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Urea is excreted by the kidney, and is normally present in plasma and&#xA;  body fluids at a concentration of 3.0–6.5 mmol/L.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Urea_cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia - Ornithine cycle&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.gastrohep.com/ebooks/rodes.asp&quot; rel=&quot;nofollow noreferrer&quot;&gt;Textbook of Hepatology&lt;/a&gt; - &lt;a href=&quot;http://www.gastrohep.com/ebooks/rodes/Rodes_2_3_7.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ammonia, urea production and pH regulation - Dieter Häussinger&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1984 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0968000484902937&quot; rel=&quot;nofollow noreferrer&quot;&gt;The role of ureagenesis in pH homeostasis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The kidney reabsorbs urea in order to concentrate the urine:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ASPc1.jpg&quot; alt=&quot;nephron transports&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 3 - nephron with material transports - urea resorption at the end of the urine creation process - &lt;a href=&quot;http://www.tutorvista.com/content/biology/biology-iv/excretion/formation-composition-urine.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;About 40% of the urea filtered is normally found in the final&#xA;  urine, since there is more reabsorption than secretion along the&#xA;  nephron.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Renal_urea_handling&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia - Renal urea handling&lt;/a&gt;:&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2007 - &lt;a href=&quot;http://jasn.asnjournals.org/content/18/3/670.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Critical Role of Urea in the Urine-Concentrating Mechanism&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The kidney secretes the urea to the urine, but it absorbs more by the reabsorption than it secreted.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The kidney freely filters urea at the glomerulus, and then it both&#xA;  reabsorbs and secretes it. Because the tubules reabsorb more urea than&#xA;  they secrete, the amount of urea excreted in the urine is less than&#xA;  the quantity filtered. In the example shown in Figure 36-1A (i.e.,&#xA;  average urine flow), the kidneys excrete ∼40% of the filtered urea.&#xA;  The primary sites for urea reabsorption are the proximal tubule and&#xA;  the medullary collecting duct, whereas the primary sites for secretion&#xA;  are the thin limbs of the loop of Henle.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.inkling.com/read/medical-physiology-boron-boulpaep-2nd/chapter-36/urea&quot; rel=&quot;nofollow noreferrer&quot;&gt;Medical Physiology by Walter F. Boron and Emile L.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So if we are talking about urea, then it is secreted to the urine. If we are talking about other waste products, then e.g. CO&lt;sub&gt;2&lt;/sub&gt; is certainly handled by the veins.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3340" LastEditDate="2014-10-31T12:33:39.380" LastActivityDate="2014-10-31T12:33:39.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23355" PostTypeId="2" ParentId="3064" CreationDate="2014-10-22T02:56:33.257" Score="3" Body="&lt;p&gt;Sequences that don't appear in a genome are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Nullomers&quot; rel=&quot;nofollow&quot;&gt;&quot;nullomers&quot;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That article claims that there are &lt;strong&gt;no 10bp sequences&lt;/strong&gt; that don't appear in the human genome, and &lt;strong&gt;80 11bp sequences&lt;/strong&gt; that don't, citing &lt;a href=&quot;http://psb.stanford.edu/psb-online/proceedings/psb07/hampikian.pdf&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9888" LastActivityDate="2014-10-22T02:56:33.257" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23356" PostTypeId="2" ParentId="23353" CreationDate="2014-10-22T03:31:15.667" Score="6" Body="&lt;p&gt;Your answer is correct. &lt;a href=&quot;http://en.wikipedia.org/wiki/Subtypes_of_HIV&quot; rel=&quot;nofollow noreferrer&quot;&gt;HIV-1&lt;/a&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/HIV-1_protease&quot; rel=&quot;nofollow noreferrer&quot;&gt;encodes&lt;/a&gt; a single homodimeric aspartic &lt;a href=&quot;http://en.wikipedia.org/wiki/Protease&quot; rel=&quot;nofollow noreferrer&quot;&gt;protease&lt;/a&gt;, with each monomer containing the classic &lt;a href=&quot;http://en.wikipedia.org/wiki/Aspartate_protease&quot; rel=&quot;nofollow noreferrer&quot;&gt;Asp-Thr-Gly&lt;/a&gt; motif, and the dimer's active site being formed with the two monomeric active sites creating a cleft where the proteolysis takes place. In it, water acts as a nucleophile in conjunction with the aspartic acid residue to hydrolyze the peptide bond in the protein's target. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/0/00/Aspartyl_protease_mechanism.png/800px-Aspartyl_protease_mechanism.png&quot; alt=&quot;Aspartyl protease mechanism of action&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Aspartyl_protease_mechanism.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;WikiMedia: Aspartyl protease mechanism.png&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A number of HIV-1 proteins are synthesized as polyproteins, and protease is required to cleave them in the appropriate spot(s) so they can assume their mature forms. This is a very big deal, because without these cleavage events HIV-1 cannot complete its replication cycle, and so becomes non-infectious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/5/51/HIV-replication-cycle.svg/700px-HIV-replication-cycle.svg.png&quot; alt=&quot;HIV replication cycle&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:HIV-replication-cycle.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;WikiMedia: HIV-replication-cycle.svg&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Protease inhibitors act by &quot;sticking&quot; in the binding cleft, obscuring the aspartate and preventing binding of the target proteins. However, these small-molecule inhibitors are very specific to HIV-1 and the amino acid residues that compose the binding cleft, otherwise they could potentially inhibit one or more of the many aspartyl proteases our body makes naturally. While it is not very likely that a destructive mutation in the Asp-Thr-Gly motif would result in a replication-competent virus, other more conservative mutations may occur in the binding cleft that still allow the target to bind and be cleaved. However, depending on the exact protease inhibitor being used, a single mutation, even if it's conservative, may still be enough to dramatically decrease the inhibitor's binding efficiency and allow protease to maintain some or all of its functional capacity. This is why cocktails of inhibitors are used: they each depend on different amino acids for their binding, so if mutations arise at some point that do affect the activity of one inhibitor, others may still be unaffected. Evolutionarily-speaking, the inhibitors put a tremendous selection pressure on the virus, which combined with HIV-1's naturally &quot;sloppy&quot; replication process, leads to mutants appearing in relatively short periods of time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two kinds of &lt;a href=&quot;http://en.wikipedia.org/wiki/Epitope&quot; rel=&quot;nofollow noreferrer&quot;&gt;epitopes&lt;/a&gt; in the adaptive immune system: those recognized by &lt;a href=&quot;http://en.wikipedia.org/wiki/Antibody&quot; rel=&quot;nofollow noreferrer&quot;&gt;antibodies&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/B_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;B cells&lt;/a&gt;, and those recognized by &lt;a href=&quot;http://en.wikipedia.org/wiki/T_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;T cells&lt;/a&gt; when presented in the context of &lt;a href=&quot;http://en.wikipedia.org/wiki/Major_histocompatibility_complex&quot; rel=&quot;nofollow noreferrer&quot;&gt;MHC&lt;/a&gt;. Antibody epitopes are generally found on the surface of a pathogen or a pathogen-infected cell (when speaking in the context of infectious diseases), as proteins or other compounds capable of raising an immune response that are only located completely inside of the pathogen or infected cell are not available for binding. T cell epitopes, on the other hand, are linear peptide fragments (and sometimes other molecules, like glycolipids) generated by &lt;a href=&quot;http://en.wikipedia.org/wiki/Major_histocompatibility_complex#Antigen_processing_and_presentation&quot; rel=&quot;nofollow noreferrer&quot;&gt;internal processing&lt;/a&gt; in the antigen-presenting cell, and are usually pretty representative of the complete contents of the cell, native and foreign. Native epitopes generally don't produce immune responses - when they do, autoimmunity occurs. Foreign epitopes are recognized by circulating T cells, and help prime an immune response against the infected cells. (As a side note, since HIV-1 infects a subset of T cells, it is a way for them to escape immune detection). Mutations in the protease protein may affect some of the epitopes it produces, but those mutations are just as likely to increase visibility to the immune system as decrease it, so overall there's no net gain or loss.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.733" LastActivityDate="2014-10-22T03:31:15.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23357" PostTypeId="2" ParentId="16626" CreationDate="2014-10-22T04:01:03.447" Score="4" Body="&lt;p&gt;As I have already mentioned in my &lt;a href=&quot;https://biology.stackexchange.com/a/23354/3703&quot;&gt;other post&lt;/a&gt;, the most important role of urea synthesis by humans is blood pH regulation and urine concentration, so it is not just about excreting a waste product. I don't think human body is very special in this case, so I think most of the urea excreting mammals use urea for the same purposes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The urea is created from NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt; and HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; in the liver (mostly) and the kidney because of blood pH regulation purposes. It neutralizes the HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; created by the lungs from CO&lt;sub&gt;2&lt;/sub&gt; and OH&lt;sup&gt; -&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The urea cycle (also known as the Ornithine cycle) is a cycle of&#xA;  biochemical reactions occurring in many animals that produces urea&#xA;  ((NH&lt;sub&gt;2&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;CO) from ammonia (NH&lt;sub&gt;3&lt;/sub&gt;). This cycle was the first metabolic&#xA;  cycle discovered (Hans Krebs and Kurt Henseleit, 1932), five years&#xA;  before the discovery of the TCA cycle. In mammals, the urea cycle&#xA;  takes place primarily in the liver, and to a lesser extent in the&#xA;  kidney.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In chemical terms, urea synthesis is an irreversible, energy driven&#xA;  neutralization of the strong base HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;–&lt;/sup&gt; by the weak acid NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;, and the&#xA;  average daily excretion of 30 g of urea is equivalent to the disposal&#xA;  of about 1 mol of HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;–&lt;/sup&gt; per day. Thus, a major function of hepatic&#xA;  urea synthesis is to effect this neutralization, without which the&#xA;  body would otherwise be confronted by a major load of alkali.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Urea is excreted by the kidney, and is normally present in plasma and&#xA;  body fluids at a concentration of 3.0–6.5 mmol/L.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Urea_cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia - Ornithine cycle&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.gastrohep.com/ebooks/rodes.asp&quot; rel=&quot;nofollow noreferrer&quot;&gt;Textbook of Hepatology&lt;/a&gt; - &lt;a href=&quot;http://www.gastrohep.com/ebooks/rodes/Rodes_2_3_7.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ammonia, urea production and pH regulation - Dieter Häussinger&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1984 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0968000484902937&quot; rel=&quot;nofollow noreferrer&quot;&gt;The role of ureagenesis in pH homeostasis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The kidney reabsorbs urea in order to concentrate the urine&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2007 - &lt;a href=&quot;http://jasn.asnjournals.org/content/18/3/670.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Critical Role of Urea in the Urine-Concentrating Mechanism&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-10-31T12:28:13.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23358" PostTypeId="2" ParentId="23338" CreationDate="2014-10-22T04:12:45.643" Score="1" Body="&lt;p&gt;Your best bet might be the sub forum on reddit specialized in synthetic biology. Have a look &lt;a href=&quot;http://www.reddit.com/r/Synthetic_Biology/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Happy science!&lt;/p&gt;&#xA;" OwnerUserId="9890" LastActivityDate="2014-10-22T04:12:45.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23359" PostTypeId="2" ParentId="23353" CreationDate="2014-10-22T04:17:56.387" Score="2" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Discovery_and_development_of_HIV-protease_inhibitors&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;HIV protease inhibitors are peptide-like chemicals that competitively&#xA;  inhibit the action of the virus aspartyl protease. These drugs prevent&#xA;  proteolytic cleavage of HIV Gag and Pol polyproteins that include&#xA;  essential structural and enzymatic components of the virus. This&#xA;  prevents the conversion of HIV particles into their mature infectious&#xA;  form.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Competitive_inhibition&quot; rel=&quot;nofollow&quot;&gt;Competitive inhibition&lt;/a&gt; means that it just slows down the conversion, but it does not stop it. In the case of building a virus we are talking about a multi step process. By using multiple inhibitors we slow down multiple steps in this process. So it is much more effective than just using a single inhibitor for slowing down only a single step in the process...&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-22T04:17:56.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23360" PostTypeId="1" AcceptedAnswerId="23363" CreationDate="2014-10-22T05:12:49.130" Score="3" ViewCount="6802" Body="&lt;p&gt;So with the working definition of Eugenics: &quot;the aim to improve the human gene pool&quot;. What are key features that distinguish Eugenics from evolution by natural selection?  I mean, besides that natural selection occurs naturally.&lt;/p&gt;&#xA;" OwnerUserId="9891" LastEditorUserId="3624" LastEditDate="2014-10-22T09:08:47.157" LastActivityDate="2014-10-22T11:05:46.957" Title="What is the difference between eugenics and evolution by natural selection?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;human-genetics&gt;&lt;artificial-selection&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23361" PostTypeId="2" ParentId="23360" CreationDate="2014-10-22T05:56:21.263" Score="0" Body="&lt;p&gt;In principle, eugenics is just like selective breeding of animals and plants. For example, dogs have been bred for a variety of traits to fit into several niches, and corn has been bred to produce large yields in several climates. Eugenics would attempt to do the same for humans. However, no one agrees on how to &quot;improve&quot; the human gene pool, and far too often eugenecists have sought to remove criminals, the disabled, the jews, or whoever they feel is inferior. And the methods used to bring about their genetic utopia include forced sterilization and/or death camps. There is no moral way to implement eugenics, and I don't think humans should be in the business of deciding which people are superior or inferior and who is allowed to reproduce, it's always dangerous.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-10-22T05:56:21.263" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23362" PostTypeId="1" AcceptedAnswerId="23380" CreationDate="2014-10-22T08:44:08.177" Score="2" ViewCount="1230" Body="&lt;p&gt;Milk contains sugar and proteins which give energy. What compounds in alcoholic beverages &lt;em&gt;(edited)&lt;/em&gt; give energy? Are they more likely to turn into fat (as in beer belly) than blood glucose?&lt;/p&gt;&#xA;" OwnerUserId="9418" LastEditorUserId="9418" LastEditDate="2014-10-22T12:30:37.083" LastActivityDate="2014-10-22T15:30:36.303" Title="What are the sources of energy that alcohol provides?" Tags="&lt;food&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23363" PostTypeId="2" ParentId="23360" CreationDate="2014-10-22T08:50:49.043" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Selection&quot; rel=&quot;nofollow&quot;&gt;Selection&lt;/a&gt; is a mechanism of evolution which favours specific forms of traits over others, this can cause the spread of beneficial mutations through a population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Natural_selection&quot; rel=&quot;nofollow&quot;&gt;Natural selection&lt;/a&gt; is the spread of beneficial traits/genes through populations as a result of the natural variance in their effect on reproductive output (a function of life history traits like lifespan aging and reproductive rates). A classic example is that of &lt;a href=&quot;http://en.wikipedia.org/wiki/Darwin%27s_finches&quot; rel=&quot;nofollow&quot;&gt;Darwin's finches&lt;/a&gt;, where different variants of bill length and shape have evolved in populations based on what food resources (types of seed) are available to them and their ability to utilise those resources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Selective_breeding&quot; rel=&quot;nofollow&quot;&gt;Artificial selection&lt;/a&gt; is selection imposed on a population by humans to deliberately affect specific traits. Examples of this would be milk yield in cattle (we want more efficient production and better quality milk), dog breeds (selection on a whole host of traits like colour, beardedness, height, length) and crops like wheat and barley (selected for higher efficiency and  quality output).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Eugenics&quot; rel=&quot;nofollow&quot;&gt;Eugenics&lt;/a&gt;, coming from the greek for &quot;well-born&quot; or &quot;good&quot; race, is the application of artificial selection principles to humans. Just as with cattle or crops, there is an aim, it may be to increase height, remove genetic diseases, or promote a certain set of traits like blonde hair and blue eyes. Historically we can associate with a number of radical political ideologies, such as Nazism. Even &lt;a href=&quot;http://en.wikipedia.org/wiki/Compulsory_sterilization&quot; rel=&quot;nofollow&quot;&gt;here in Sweden&lt;/a&gt; (people tend to think of it as a very progressive and equality driven country) there was a program of eugenics until very recently, achieved by forcibly sterilising or coercing people in to it, for various reasons (racial purity, health, and antisocial behaviour). &lt;a href=&quot;http://www.pop.org/content/the-knife-in-the-closet-127&quot; rel=&quot;nofollow&quot;&gt;Here's an interesting example&lt;/a&gt; of a girl designated as being genetically inferior because her family had a history of alcoholism (that page gives a good history of eugenics too). The social and ethical problems of eugenics are obvious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under normal conditions a persons reproductive output is largely determined by their own choices and actions whereas under eugenics that choice is taken away and made by someone else and specifically with the aim of &quot;improving&quot; the quality of the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So in summary:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;natural selection is the result of natural variance in fitness linked to traits&lt;/li&gt;&#xA;&lt;li&gt;artificial selection leads to a change in traits, in a specifically targeted direction, decided and imposed by another organism (usually humans, I know of no other species which does this)&lt;/li&gt;&#xA;&lt;li&gt;eugenics is practice of artificial selection on humans enacted by humans with the specific aim of improving quality: often for social, economic, or political reasons and is generally accepted as being against human rights these days.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-10-22T09:31:02.643" LastActivityDate="2014-10-22T09:31:02.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23364" PostTypeId="2" ParentId="23360" CreationDate="2014-10-22T08:54:39.303" Score="3" Body="&lt;p&gt;First, you need to recognise the difference between &lt;strong&gt;Natural selection&lt;/strong&gt; and &lt;strong&gt;Artificial selection&lt;/strong&gt;. As a basic definition, you can say that in natural selection, selection is done on fitness (overall, long-term success of reproduction) and is determined by the complete living environment of the species. In artificial selection, selection is done by humans on a plant or animal species for specific attributes that are desired (see any Evolutionary textbook for more on the difference). So the two processes generally try to optimize completely different things, and artificial selection has a goal which is not the case for natural selection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally, &lt;strong&gt;Eugenics&lt;/strong&gt; can be likened to artificial selection, done by humans on humans. The methods used (selective breeding, culling, trunkated selection, sterilization etc.) are potentially the same. The difference between eugenics and articifial selection on plants and animals other than humans is purely moral and political (and therefore off-topic for Bio-SE).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, eugenics has also often been misguided in practice (if you ignore for a moment the usually horrible morals behind it). First, it relies on desired and undesired genotypes and phenotypes. Most people would not regard these as valid concepts, and even so, what will be desired/undesired will clearly differ between societies and over time. Second, eugenics does not appreciate the value of genetic diversity for the long-term success of a population (it will rather result in lower diversity). Third, eugenics is usually aimed for obvious physical traits and diseases, without much regard for their genetic background (e.g. heterozygious recessive carriers of disease). Fourth, eugenics usually devolve into a hunt for &quot;weaker&quot; groups of people, even if this has nothing to do with the gene pool of the population (for instance, many birth defects and the prevalence of Down's syndrome has almost nothing to do with the genetics of the population).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess you could argue that ongoing selection in humans is a form of eugenics since it is to a large extent determined by human interactions and choices (see e.g. &lt;a href=&quot;http://www.pnas.org/content/109/21/8044.abstract?etoc&quot; rel=&quot;nofollow&quot; title=&quot;Courtiol et al. 2012. Natural and sexual selection in a monogamous historical human population. PNAS&quot;&gt;Courtiol et al 2012&lt;/a&gt; &amp;amp; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15216422&quot; rel=&quot;nofollow&quot; title=&quot;Geary et al. 2004. Evolution of human mate choice. J Sex Res. 41(1):27-42&quot;&gt;Geary et al. 2004&lt;/a&gt;). However, this is definitely not a standard definition, and big difference compared to &quot;normal&quot; eugenics is that it is not guided by a common and explicit goal. I also know that some people label the collective outcome of individual decisions as a form of eugenics, which might be relevant for how you view &lt;a href=&quot;http://en.wikipedia.org/wiki/Preimplantation_genetic_diagnosis&quot; rel=&quot;nofollow&quot;&gt;Preimplantation genetic diagnosis&lt;/a&gt; (PGD) and &lt;a href=&quot;http://en.wikipedia.org/wiki/Prenatal_diagnosis&quot; rel=&quot;nofollow&quot;&gt;prenatal screening&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-10-22T11:05:46.957" LastActivityDate="2014-10-22T11:05:46.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23365" PostTypeId="1" CreationDate="2014-10-22T08:55:49.003" Score="1" ViewCount="296" Body="&lt;p&gt;Richard Dawkins famously advocated a &lt;a href=&quot;https://en.wikipedia.org/wiki/Gene-centered_view_of_evolution&quot; rel=&quot;nofollow&quot;&gt;gene-centric&lt;/a&gt; (as opposed to organism-centric) viewpoint on natural selection, most notably in &lt;a href=&quot;https://en.wikipedia.org/wiki/The_Extended_Phenotype&quot; rel=&quot;nofollow&quot;&gt;The Extended Phenotype&lt;/a&gt;. However, I have also heard &quot;on the grapevine&quot; that most professionals in biology and related areas do not take the gene-centric viewpoint altogether seriously.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is simple: how prominent is the gene-centric view of evolution among professional researchers in biology and related fields?&lt;/p&gt;&#xA;" OwnerUserId="8761" LastActivityDate="2014-10-23T14:19:36.840" Title="How prominent is the gene-centric view of evolution among professional researchers?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23366" PostTypeId="2" ParentId="23239" CreationDate="2014-10-22T09:02:36.587" Score="5" Body="&lt;p&gt;Hepatitis is a condition of the liver where the cells of the liver organ are inflamed. Most often it is caused by a viral infection, hepatitis &lt;a href=&quot;http://en.wikipedia.org/wiki/Hepatitis_A&quot; rel=&quot;noreferrer&quot;&gt;A&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Hepatitis_B&quot; rel=&quot;noreferrer&quot;&gt;B&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Hepatitis_C&quot; rel=&quot;noreferrer&quot;&gt;C&lt;/a&gt; are all viral forms of the disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria (and Fungi) can cause hepatitis of the liver, and two examples would be the &lt;a href=&quot;http://www.expertconsultbook.com/expertconsult/ob/book.do?method=display&amp;amp;type=bookPage&amp;amp;decorator=none&amp;amp;eid=4-u1.0-B978-1-4377-0881-3..00036-X--s0050&amp;amp;isbn=978-1-4377-0881-3&quot; rel=&quot;noreferrer&quot;&gt;Staphylococcal and Streptococcal bacteria&lt;/a&gt;. These can directly infect the liver, and are also responsible for some inflammations in other tissues of the &lt;a href=&quot;http://www.medicinejournal.co.uk/article/S1357-3039(06)00189-7/abstract&quot; rel=&quot;noreferrer&quot;&gt;skin and heart&lt;/a&gt; and elsewhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prolonged alcohol abuse is another cause of hepatitis (as well as cirrhosis) and is not associated with bacteria virus or fungi, but instead from a damaging effect on the liver.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="5144" LastEditDate="2014-10-22T09:04:51.737" LastActivityDate="2014-10-22T09:04:51.737" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23367" PostTypeId="1" AcceptedAnswerId="23373" CreationDate="2014-10-22T09:06:51.433" Score="1" ViewCount="366" Body="&lt;p&gt;There are some OTC paracetamol tablets, some with caffeine. Is this caffeine the same as the regular caffeine (found in a coffee)? Does it perform better than it in any way?&lt;/p&gt;&#xA;" OwnerUserId="3141" LastActivityDate="2014-10-22T10:36:58.110" Title="Difference between medicinal caffeine and regular caffeine" Tags="&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23368" PostTypeId="1" AcceptedAnswerId="23386" CreationDate="2014-10-22T09:44:34.910" Score="3" ViewCount="29827" Body="&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt; I was wondering if the amount of sperm increase with the amount of abstinence?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Side questions:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Is their a max amount of sperm?&lt;/li&gt;&#xA;&lt;li&gt;What happens with the excess amount? &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8116" LastActivityDate="2014-10-22T20:21:51.870" Title="Do you produce more sperm after 1 week of abstinence vs 1 year of abstinence" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ClosedDate="2016-01-31T02:01:46.480" ContentLicense="CC BY-SA 3.0" />
  <row Id="23369" PostTypeId="1" AcceptedAnswerId="23371" CreationDate="2014-08-27T14:51:17.577" Score="10" ViewCount="332" Body="&lt;p&gt;We were walking in the hills of snowdonia the other day and my girlfriend found this in the heather:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zitEU.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've never seen anything like it. Can anyone identify it? It was the biggest beetle I've ever seen.&lt;/p&gt;&#xA;" OwnerDisplayName="user9894" LastEditorUserId="3624" LastEditDate="2014-10-22T10:59:20.347" LastActivityDate="2014-10-22T11:31:23.250" Title="What is this beetle? Found in heather in snowdonia" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23370" PostTypeId="2" ParentId="23369" CreationDate="2014-08-27T15:37:26.333" Score="3" Body="&lt;p&gt;I would say that it is a &lt;strong&gt;Carabus coriaceus&lt;/strong&gt;. It might have a size of 30 to 40mm and is very common around Europe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5Q3ZT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately the English wikipedia article is rather tiny: &lt;a href=&quot;https://en.wikipedia.org/wiki/Carabus_coriaceus&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Carabus_coriaceus&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="Jon" LastActivityDate="2014-08-27T19:16:45.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23371" PostTypeId="2" ParentId="23369" CreationDate="2014-09-04T09:50:14.317" Score="9" Body="&lt;p&gt;I believe it's the &lt;a href=&quot;http://www.eakringbirds.com/eakringbirds5/insectinfocusvioletgroundbeetle.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Violet Ground Beetle&lt;/a&gt; - &#xA;&lt;em&gt;Carabus violaceus&lt;/em&gt;. This is a close relative to the &lt;em&gt;Carabus coriaceus&lt;/em&gt; posted by &lt;a href=&quot;https://outdoors.stackexchange.com/a/6595/2090&quot;&gt;Jon&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The purple colour is a give away, but as in many insect groups there are often very similar species. As pointed out in the comments to this anwer, this is the case for &lt;em&gt;C. violaceus&lt;/em&gt; and &lt;em&gt;C. problematicus&lt;/em&gt; (&lt;a href=&quot;http://www.thewcg.org.uk/idaids/cproblematicusviolaceus.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;differences&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are websites  like &lt;a href=&quot;http://observado.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;observado.org&lt;/a&gt; where sightings can be added as a species or for instance &quot;unknown beetle&quot;, where they are reviewed (depending on the availability of the volunteering experts) or identified. &lt;/p&gt;&#xA;" OwnerUserId="4684" OwnerDisplayName="Sdry" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:01.470" LastActivityDate="2014-10-22T11:31:23.250" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23372" PostTypeId="2" ParentId="23362" CreationDate="2014-10-22T09:58:59.587" Score="1" Body="&lt;h2&gt;Regarding energy:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Going off the assumption that you are using 'alcohol' in the sense of 'alcoholic beverage', it &lt;em&gt;really&lt;/em&gt; depends on what kind of beverage we're talking about, but all that information is on the label of the bottle, can or box.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for ethanol itself, some energy is freed by the metabolising of ethanol into ethanal and further into ethanoic acid, before finally being decomposed to carbon dioxide and water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, energy is energy: The source of the energy doesn't &lt;em&gt;really&lt;/em&gt; affect where the energy ends up, that depends mostly on external factors.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Regarding beer:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Ethanol gives roughly 7 kcal/g, compared to carbohydrates which give roughly 4 kcal/g.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;100 ml of beer contains (about) 4 grams of ethanol, beyond which the carbohydrate content varies according to the beer in question, but usually hovers around 3 g.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At a rough estimate the caloric contribution from ethanol is about 0.28 kcal/ml, and carbohydrates about 0.12 kcal/ml. When accounting for the traces of proteins, this gives roughly 0.4 kcal/ml, roughly the same as your common or garden variety soda.&lt;/p&gt;&#xA;" OwnerUserId="1095" LastEditorUserId="1095" LastEditDate="2014-10-22T13:12:46.373" LastActivityDate="2014-10-22T13:12:46.373" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23373" PostTypeId="2" ParentId="23367" CreationDate="2014-10-22T10:36:58.110" Score="3" Body="&lt;p&gt;From a pharmacology point of view, there is no difference between caffeine in caffeine pills and in a cup of coffee. It doesn't matter, how a chemical substance (in this case caffeine) is made, the effect of the substance is the same. What can make a difference is the presence of secondary plant ingredients.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For pure caffeine there are two possible sources: By chemical synthesis (&quot;&lt;a href=&quot;http://www.umich.edu/~chemh215/CHEM216/Honors%20Cup_old/HCProposal/caffeine.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;A Novel Method of Caffeine Synthesis from Uracil&lt;/a&gt;&quot;) and as a byproduct of the decaffeination process when producing decaffeinated coffee.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is also different is the amount of caffeine. While pills contain standardized amounts of caffeine, the amount for caffeine in brewed coffee varies between different kinds of coffee beans as well as for different brewing methods. See this figure (from &lt;a href=&quot;https://www.silverskincoffee.ie/articles/caffeine-content&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VsyIl.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-22T10:36:58.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23374" PostTypeId="1" CreationDate="2014-10-22T12:14:39.027" Score="2" ViewCount="109" Body="&lt;p&gt;the question is already in the title. If possible, it might be extended to:&#xA;Have animal taxa (mammal) who tend to live in a family structure have a monogamous sexuality? Or are there cases of these taxa, where the sexual partner is not the social one. &lt;/p&gt;&#xA;" OwnerUserId="9895" LastActivityDate="2014-12-22T13:58:31.823" Title="Do gibbons have a monogamous sexuality?" Tags="&lt;sexual-selection&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23375" PostTypeId="1" AcceptedAnswerId="23378" CreationDate="2014-10-22T13:10:33.650" Score="1" ViewCount="367" Body="&lt;p&gt;Can you find plasmodium parasites (malaria) in saliva under microscope from someone who's infected? Or it's only in the blood?&lt;/p&gt;&#xA;" OwnerUserId="1195" LastActivityDate="2014-10-22T14:45:35.683" Title="Can you find malaria parasites in saliva?" Tags="&lt;microscopy&gt;&lt;parasitology&gt;&lt;parasitism&gt;&lt;saliva&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23376" PostTypeId="2" ParentId="23264" CreationDate="2014-10-22T13:31:53.420" Score="3" Body="&lt;p&gt;I don't know if this qualifies as &quot;&lt;em&gt;incorporated ... into their lives&lt;/em&gt;&quot;, but &lt;a href=&quot;http://en.wikipedia.org/wiki/Hermit_crab&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hermit crabs&lt;/a&gt; use all sorts of man-made materials as housing/protection. If you do a google image search on &quot;&lt;a href=&quot;https://encrypted.google.com/search?q=hermit+crab+plastic&amp;amp;biw=1600&amp;amp;bih=773&amp;amp;source=lnms&amp;amp;tbm=isch&amp;amp;sa=X&amp;amp;ei=1q1HVN7OGOfmywOYrYL4Dg&amp;amp;ved=0CAkQ_AUoAg&quot; rel=&quot;nofollow noreferrer&quot;&gt;hermit crab plastic&lt;/a&gt; you will see many examples, including plastic waste.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also other animals that use random materials that are lying around to construct housing/cases, and I can imagine that e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Caddisfly&quot; rel=&quot;nofollow noreferrer&quot;&gt;Trichoptera&lt;/a&gt; larvae will occationally include pieces of plastic in their cases. At least they will use &lt;a href=&quot;https://biology.stackexchange.com/questions/15845/what-insect-is-this/15856#15856&quot;&gt;gold and pearls&lt;/a&gt; (when not given an option). However, these are not really examples of species that have adapted specifically to plastic to use it as a resource.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-10-22T13:31:53.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23377" PostTypeId="1" AcceptedAnswerId="23383" CreationDate="2014-10-22T14:44:29.160" Score="4" ViewCount="320" Body="&lt;p&gt;Found this living larva in broccoli from a store. It was about 10 mm long. It was in july this year, and I don't remember the country of origin for the broccoli. A bit of googling makes me think it could be a &lt;em&gt;Pieris rapae&lt;/em&gt;, but I don't know if there are any similar species.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Fis6z.jpg&quot; alt=&quot;&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/o7W9P.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;edit: Even if I don't know the origin of the broccoli, I assume (and hope) it was grown in Europe since I got it in Sweden.&lt;/p&gt;&#xA;" OwnerUserId="8630" LastEditorUserId="8630" LastEditDate="2014-10-22T23:35:05.987" LastActivityDate="2014-10-22T23:35:05.987" Title="Found a larva in my broccoli, is it a Small White (Pieris rapae)?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23378" PostTypeId="2" ParentId="23375" CreationDate="2014-10-22T14:45:35.683" Score="3" Body="&lt;p&gt;No.&lt;br&gt;&#xA;Although malaria is transmitted through the &lt;em&gt;saliva&lt;/em&gt; of a female &lt;em&gt;Anopheles&lt;/em&gt; mosquito, it stays in the bloodstream and doesn't pass over to the saliva of humans (otherwise it probably would be transmittable via humans directly). Once the parasites travel to the liver, it infects and bursts hepatocytes after reproducing (asexually). The burst cells then infect the bloodstream via red blood cells, where the parasites reproduce further and eventually burst their host cell, leading to a vicious cycle. This whole process only has to do with the bloodstream, since the parasites live in red blood cells.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are certain markers present in the saliva which can be used to detect the presence of malaria the most known of which is called &lt;em&gt;Pf&lt;/em&gt;HRP2, or &lt;em&gt;Plasmodium falciparum&lt;/em&gt; histadine-rich protein 2. This only applies to people infected by the type of parasite &lt;em&gt;P. falciparum&lt;/em&gt;, however it is this parasite type which is the cause for the vast overwhelming majority of deaths and complications during malaria infection. The range of &lt;em&gt;Pf&lt;/em&gt;HRP2 values in malaria-positive patients' saliva ranged from 17 to 1167 pg/mL in one study.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.malariajournal.com/content/11/1/175&quot; rel=&quot;nofollow&quot;&gt;http://www.malariajournal.com/content/11/1/175&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jstor.org/discover/10.2307/30086299?uid=3738432&amp;amp;uid=2&amp;amp;uid=4&amp;amp;sid=21104875852967&quot; rel=&quot;nofollow&quot;&gt;http://www.jstor.org/discover/10.2307/30086299?uid=3738432&amp;amp;uid=2&amp;amp;uid=4&amp;amp;sid=21104875852967&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8840" LastActivityDate="2014-10-22T14:45:35.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23379" PostTypeId="1" CreationDate="2014-10-22T14:47:57.957" Score="4" ViewCount="250" Body="&lt;p&gt;I have a matrix of sites where not all the environmental variables I want to assess were sampled. In other words, there are sites with the whole set of variables sampled, and there are other sites where just some variables were sampled. Does Canonical Correspondence Analysis work with missing data for the environmental variables? If it does, what would be the effect of not including the missing values?&lt;/p&gt;&#xA;" OwnerUserId="9897" LastActivityDate="2019-03-12T01:58:16.727" Title="Using Canonical Correspondence Analysis on matrices with missing data" Tags="&lt;ecology&gt;&lt;statistics&gt;&lt;environment&gt;&lt;species-distribution&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23380" PostTypeId="2" ParentId="23362" CreationDate="2014-10-22T14:50:23.313" Score="2" Body="&lt;p&gt;Ethanol is converted into &lt;a href=&quot;http://en.wikipedia.org/wiki/Acetyl-CoA&quot; rel=&quot;nofollow noreferrer&quot;&gt;AcKoA&lt;/a&gt;, which can be &quot;burned&quot; in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Citric_acid_cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;Krebs cycle&lt;/a&gt; or can be used to &lt;a href=&quot;http://en.wikipedia.org/wiki/Fatty_acid_synthesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;build fatty acids&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6QAdQ.jpg&quot; alt=&quot;ethanol - AcKoA conversion&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By chronic alcohol consumption there is another pathway involving &lt;a href=&quot;http://en.wikipedia.org/wiki/Microsomal_ethanol_oxidizing_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;MEOS&lt;/a&gt; which converts ethanol to AcKoA as well.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Are they more likely to turn into fat (as in beer belly) than blood&#xA;  glucose?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It won't turn into glucose, just into fat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Note:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is suspected that in extreme cases, like low glucose diets and starvation there is an &lt;strong&gt;AcKoA -&gt; glucose&lt;/strong&gt; pathway.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002116&quot; rel=&quot;nofollow noreferrer&quot;&gt;In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So in theory it is possible to convert ethanol to glucose, but there is not enough evidence of that yet. Normally this conversion (if it exists) does not happen, or it has a very low rate...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What compounds in alcoholic beverages (edited) give energy?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Mostly ethanol and sugar. E.g. sweet wine contains a lot of sugar, not just ethanol...&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-22T15:30:36.303" LastActivityDate="2014-10-22T15:30:36.303" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23381" PostTypeId="2" ParentId="23365" CreationDate="2014-10-22T16:26:02.880" Score="2" Body="&lt;p&gt;&lt;strong&gt;What do you mean by gene-centric view of evolution&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not totally sure you know what really means the gene centric view of evolution. Everybody agrees that selection (also) acts on genes and that selfish genetic elements exist. I think that what one calls the gene centric view of evolution is nothing but the &lt;a href=&quot;http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;modern synthesis of evolution&lt;/em&gt;&lt;/a&gt; (following the work of Ronald Fisher, Sewall Wright and some others such as Motoo Kimura).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or maybe by gene centric view you refer to the concept of &lt;em&gt;level of selection&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some people however argue that because of the gene centric view of evolution, we tend to underestimate the importance of some parameters in evolution and some are willing to rename the evolution theory into Extended Evolution Theory according to new insights about how parameters such as developmental bias for example influence the evolution of populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Modern snythesis of evolution theory&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will find more information in &lt;a href=&quot;http://www.zoology.ubc.ca/veg/LalandEtAl2014.pdf&quot; rel=&quot;nofollow&quot;&gt;this recent article&lt;/a&gt; that you may appreciate reading if it is not too complicated. I personally endorse the &quot;No, all is well&quot; opinion. It is important to understand that those who criticize the gene centric view in this article are NOT saying that selection do not act on genes neither that selfish genetic elements do not exist (thinks that R. Dawkins talk about in his books). They totally agree with those things. They just argue that the fisherian view of evolution in not enough and that according to recent findings we may want to rename our theory. The &quot;no, all is well&quot; opinion totally agrees with the importance of these new insights that do not come from what one may call the gene-centric view of evolution but they just don't think it is worth renaming the theory for that because our knowledge in evolution is just growing as it has always been growing and it doesn't seem that we are currently living a revolution in our understanding of evolution. I think that the main revolutions that happen to occur in evolution these days mostly have to do with the methodology of testing rather than with the theory itself. These revolutions have to do with increased computer power, better statistical methods and faster and cheaper sequencing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Level of selection&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, by gene-centric view of evolution you may refer to the concept of level of selection. To my knowledge everybody agree that selection occurs at different levels. Again, NOT everybody agree on the relative importance of selection acting at different level. The vast majority of research focus at evolution at the gene level, sometimes implicitly only.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;To conclude&lt;/strong&gt;, we all agree on the theoretical principles (I think) but not everybody agree on the relative importance of the different mechanisms. In saying this, I don't mean that everybody agree with everything that is written in R. Dawkins books!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-10-23T14:19:36.840" LastActivityDate="2014-10-23T14:19:36.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23383" PostTypeId="2" ParentId="23377" CreationDate="2014-10-22T18:03:20.123" Score="1" Body="&lt;p&gt;It definately looks like a &lt;em&gt;Pieris rapae&lt;/em&gt; larvae, which are distinct from larvae in closely related common species as e.g. &lt;em&gt;Pieris napi&lt;/em&gt; and &lt;em&gt;Pieris brassicae&lt;/em&gt;. However, I'm not a lepidopterist and there might be related rarer species I'm not aware of, especially since you don't know where the broccoli is from. However, &lt;em&gt;Pieris rapae&lt;/em&gt; is found basically all over the world as native or introduced (native in Europe, Asia, Africa and introduced in e.g. Ameria and Australia) and is a pest species of cabbage (including broccoli) so it is a very good fit.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2014-10-22T18:03:20.123" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23386" PostTypeId="2" ParentId="23368" CreationDate="2014-10-22T20:11:48.290" Score="1" Body="&lt;p&gt;There is an increase by abstinence.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The within-subject variability of the semen sperm count (n), volume&#xA;  (v) and the total number of spermatozoa (N) was studied on 220&#xA;  ejaculates from 36 normal subjects after an abstinence of 7 days or&#xA;  less.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The three semen characteristics for a given subject were highly&#xA;  correlated with the length of abstinence: for an increase in&#xA;  abstinence of 1 day there were mean increments of 13 × 106/ml for n,&#xA;  0·4 ml for v, and 87 × 106 for N.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1979 - &lt;a href=&quot;http://www.reproduction-online.org/content/57/2/391.short&quot; rel=&quot;nofollow&quot;&gt;Within-subject variability of human semen in regard to sperm count, volume, total number of spermatozoa and length of abstinence&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Semen analysis was performed on six men after various sexual&#xA;  abstinence periods (from 2 to 18 days). The variations in semen&#xA;  parameters were analyzed statistically as a function of the duration&#xA;  of abstinence.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Lengthy sexual abstinence was found to affect all semen&#xA;  characteristics. Semen volume and concentration and total sperm count&#xA;  showed significant increases, whereas motility and normal morphology&#xA;  decreased significantly with duration of abstinence. Significant&#xA;  changes in the percentage of normal sperm forms were observed after&#xA;  more than seven days' abstinence.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The study indicates that the influence of long sexual abstinence on&#xA;  semen quality varies with the variable considered. With regard to&#xA;  fertility, a long abstinence period might induce senescence of&#xA;  spermatozoa.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1994 - &lt;a href=&quot;http://europepmc.org/abstract/MED/7820161&quot; rel=&quot;nofollow&quot;&gt;Effect of long abstinence periods on human sperm quality.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Sperms can die of &quot;old age&quot;, as the previous quotes mentioned long abstinence period induces senescence. It is hard to find anything about their lifetime, it is at least 7 days I think.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For humans, entire process of spermatogenesis takes 74 days. Including&#xA;  the transport on ductal system, it takes 3 months. Testes produce 200&#xA;  to 300 million spermatozoa daily.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;according to &lt;a href=&quot;http://en.wikipedia.org/wiki/Spermatogenesis&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So there is a constant rate of sperm production.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the following differential equation can describe the change of the sperm count:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ \dot{x} = μ - Dx $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;x is the sperm count&lt;/li&gt;&#xA;&lt;li&gt;μ is the production rate regulated by testosteron (about 250 million per day)&lt;/li&gt;&#xA;&lt;li&gt;D is the death rate which depends on the age of the population (depends on the lifetime, production rate, elapsed time)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So there will be a maximum amount by abstinence. By that amount &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ μ = Dx $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ x_{max} = μ /D $$&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-22T20:21:51.870" LastActivityDate="2014-10-22T20:21:51.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23387" PostTypeId="1" CreationDate="2014-10-22T20:29:08.160" Score="3" ViewCount="250" Body="&lt;p&gt;I'm not much of an ornithologist but I know enough to distinguish most Central European birds of prey. To me it is amazing that there are so many species that seem to occupy the same niche. Especially the two native kite species (&lt;em&gt;Milvus milvus&lt;/em&gt; and &lt;em&gt;Milvus migrans&lt;/em&gt;) and the common buzzard (&lt;em&gt;Buteo buteo&lt;/em&gt;) are -- to my impression -- quite similar in terms of size, preferred prey, habitat etc. According to the competetive exclusion principle, these species would not coexist if they would exploit the exact same set of resources. So my question is: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the major differences between the mentioned species that allow coexistence? Are there more such examples from other geographical regions? &lt;/p&gt;&#xA;" OwnerUserId="8015" LastActivityDate="2014-10-22T20:29:08.160" Title="Niche differentiation in birds of prey" Tags="&lt;natural-selection&gt;&lt;ornithology&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23388" PostTypeId="1" AcceptedAnswerId="23405" CreationDate="2014-10-22T20:52:02.307" Score="4" ViewCount="2738" Body="&lt;p&gt;Sorry for a certainly naive question. &#xA;Some references (for example &lt;a href=&quot;https://faculty.washington.edu/chudler/nsdivide.html&quot; rel=&quot;nofollow&quot;&gt;https://faculty.washington.edu/chudler/nsdivide.html&lt;/a&gt;) seem to to indicate that the hypothalamus is part of the Central Nervous System. Others (for example &lt;a href=&quot;http://kidshealth.org/teen/your_body/body_basics/endocrine.html&quot; rel=&quot;nofollow&quot;&gt;http://kidshealth.org/teen/your_body/body_basics/endocrine.html&lt;/a&gt;) place it in the Endrocrine System. I would have said it is part of both, but then I read the two systems are distinct. Could anyone explain me to which one it belongs and why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gilles&lt;/p&gt;&#xA;" OwnerUserId="9901" LastActivityDate="2016-01-14T16:36:28.907" Title="Is the Hypothalamus part of the Central Nervous System or Endocrine System" Tags="&lt;neuroscience&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23389" PostTypeId="1" CreationDate="2014-10-22T21:30:32.607" Score="2" ViewCount="755" Body="&lt;p&gt;I know how they fold, but what causes some polypeptide chains to preferably fold into Alpha-helix rather than Beta-sheets (or vice-versa). What force makes it fold into one conformation over the other?&lt;/p&gt;&#xA;" OwnerUserId="9902" LastEditorUserId="9943" LastEditDate="2014-11-22T11:26:38.507" LastActivityDate="2014-12-05T18:28:20.573" Title="What causes a polypeptide to fold into an Alpha helix over a Beta pleated sheet" Tags="&lt;proteins&gt;&lt;protein-folding&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23390" PostTypeId="1" CreationDate="2014-10-22T22:49:13.110" Score="1" ViewCount="392" Body="&lt;p&gt;Diabetes patients need to conduct the “fingerstick” a few times a day. One of the mechanisms of &quot;fingerstick&quot; is to take small amount of blood sample and put it onto a test strip. The enzyme on the test strip reduces the glucose and the electronics of the glucose meter detect the redox species produced. However, this method is painful and increase the risk of infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photonic sensing technology opens up a new method for non-invasive blood glucose concentration. According to an article of &lt;a href=&quot;http://www.medgadget.com/2013/10/non-invasive-measurement-of-blood-glucose-levels-using-glucotrack-interview.html&quot; rel=&quot;nofollow&quot;&gt;medGadget&lt;/a&gt; in 2013 (The link follows &lt;a href=&quot;http://www.medgadget.com/2013/10/non-invasive-measurement-of-blood-glucose-levels-using-glucotrack-interview.html&quot; rel=&quot;nofollow&quot;&gt;http://www.medgadget.com/2013/10/non-invasive-measurement-of-blood-glucose-levels-using-glucotrack-interview.html&lt;/a&gt; ), the non-invasive kind was invented. By simply clipping onto the earlobe (without puncturing the skin), the blood glucose concentration could be measured. Does anybody knows the working principle for that? Or, suggest a paper describing that?&lt;/p&gt;&#xA;" OwnerUserId="9904" LastActivityDate="2014-10-23T02:08:00.147" Title="How non-invasive blood glucose concentration measurement work?" Tags="&lt;biophysics&gt;&lt;glucose&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23391" PostTypeId="1" CreationDate="2014-10-22T21:54:17.353" Score="2" ViewCount="63" Body="&lt;p&gt;Diabetes patients need to conduct the “fingerstick” a few times a day. One of the mechanisms of &quot;fingerstick&quot; is to take small amount of blood sample and put it onto a test strip. The enzyme on the test strip reduces the glucose and the electronics of the glucose meter detect the redox species produced. However, this method is painful and increase the risk of infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photonic sensing technology opens up a new method for non-invasive blood glucose concentration. According to an article of &lt;a href=&quot;http://www.medgadget.com/2013/10/non-invasive-measurement-of-blood-glucose-levels-using-glucotrack-interview.html&quot; rel=&quot;nofollow&quot;&gt;medGadget&lt;/a&gt; in 2013 (The link follows &lt;a href=&quot;http://www.medgadget.com/2013/10/non-invasive-measurement-of-blood-glucose-levels-using-glucotrack-interview.html&quot; rel=&quot;nofollow&quot;&gt;http://www.medgadget.com/2013/10/non-invasive-measurement-of-blood-glucose-levels-using-glucotrack-interview.html&lt;/a&gt; ), the non-invasive kind was invented. By simply clipping the earlobe (without puncturing the skin), the blood glucose concentration could be measured. Does anybody knows the working principle for that? Or, suggest a paper describing that?&lt;/p&gt;&#xA;" OwnerUserId="9904" OwnerDisplayName="aloha" LastActivityDate="2014-10-23T03:28:45.470" Title="How non-invasive blood glucose concentration measurement work?" Tags="&lt;biophysics&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-10-23T05:14:21.267" ContentLicense="CC BY-SA 3.0" />
  <row Id="23392" PostTypeId="2" ParentId="23239" CreationDate="2014-10-22T23:22:10.587" Score="3" Body="&lt;p&gt;The suffix '&lt;em&gt;-itis&lt;/em&gt;' (&lt;em&gt;-ῖτις&lt;/em&gt;, in ancient greek) usually is added to a word to represent a pathological condition called inflammation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, &lt;b&gt;haepatitis&lt;/b&gt; (or hepatitis) means generically inflammation of liver (&lt;em&gt;ἧπαρ&lt;/em&gt; épar, in ancient greek).&#xA;Usually it is &lt;a href=&quot;http://www.who.int/topics/hepatitis/en/&quot; rel=&quot;nofollow&quot;&gt; caused by viruses &lt;/a&gt; such as HAV, HBV, and HCV. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An haepatitis can be due also to &lt;a href=&quot;http://accessmedicine.mhmedical.com/content.aspx?bookid=331&amp;amp;sectionid=40727101&quot; rel=&quot;nofollow&quot;&gt; toxic agents or be autoimmune &lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, whaterver it is the cause of inflammation of liver cell, it is called haepatites; even if it is caused by less common pathogens as&lt;a href=&quot;http://accessmedicine.mhmedical.com/content.aspx?bookid=331&amp;amp;sectionid=40727101&quot; rel=&quot;nofollow&quot;&gt; bacteria; protists like &lt;em&gt;T Gondii&lt;/em&gt; ; minor hepatotropic viruses, like EBV, CMV, and herpetic viruses in general&lt;/a&gt;;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2007764&quot; rel=&quot;nofollow&quot;&gt; fungi&lt;/a&gt;, or &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/9781119950509.ch39/summary&quot; rel=&quot;nofollow&quot;&gt;protozoa and other parasites&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria can cause haepatitis, examples would be the Staphylococcal and Streptococcal haepatitis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ever the excessive intake of table salt (Na-Cl) or cronic alcoholism may cause  haepatitis or even a liver's cirrhosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, though it is less common, but &lt;a href=&quot;http://europepmc.org/abstract/MED/11677423&quot; rel=&quot;nofollow&quot;&gt;bacteria may cause haepatitis&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9899" LastEditorUserId="20608" LastEditDate="2015-12-15T01:58:04.970" LastActivityDate="2015-12-15T01:58:04.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23394" PostTypeId="2" ParentId="2602" CreationDate="2014-10-23T01:49:27.293" Score="2" Body="&lt;p&gt;Shear stress $\tau$ in this small sizes is usually measured in dyne/cm2 or N/m2 = Pa. The equations betweeen them: $1dyn/cm^2 = 10^{-5}N/cm^2 = 0.1N/m^2 = 0.1Pa$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What kind of damages zygotes can suffer by pipetting?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Using scanning electron microscopy, we found open holes on the surface&#xA;  of lysed eggs, indicating failure of the plasma membrane to reseal&#xA;  after microinjection. No holes were seen in unlysed eggs, but many of&#xA;  them had membrane alterations suggestive of healed punctures.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1987 - &lt;a href=&quot;http://www.biolreprod.org/content/37/4/957.short&quot; rel=&quot;nofollow&quot;&gt;Zygote viability in gene transfer experiments&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Even a small 1.2 dyn/cm2 shear stress induces apoptosis by pipetting zygotes. So zygotes have their critical shear stress level by 1.2 dyn/cm2 and pipetting involves greater forces than 1.2 dyn/cm2.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Shear stress at 1.2 dynes/cm2 induces stress-activated protein&#xA;  kinase/jun kinase phosphorylation that precedes and causes apoptosis&#xA;  in embryos (Xie et al., 2006b, Biol Reprod). Pipetting embryos is&#xA;  necessary for many protocols, from in vitro fertilization to&#xA;  collecting embryos prior to analyzing gene expression by microarrays.&#xA;  We sought to determine if pipetting upregulates phosphorylated MAPK8/9&#xA;  (formerly known as stress-activated protein kinase/jun&#xA;  kinase/SAPK/JNK1, 2). We found that phosphorylated MAPK8/9, a marker&#xA;  of MAPK8/9 activation, is upregulated in a dose-dependent manner by&#xA;  pipetting.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2007 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/mrd.20563/abstract&quot; rel=&quot;nofollow&quot;&gt;Pipetting causes shear stress and elevation of phosphorylated stress-activated protein kinase/jun kinase in preimplantation embryos&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The critical shear stress level is somewhere between 0.01 and 1000 dyn/cm2 by animal cells depending on the cell type and species. (I think the average is somewhere about 50 dyn/cm2, but it is very hard to differentiate between articles mentioning critical shear levels and most lethal shear levels, so the range and the average might be lower.) The death constant (1/h) increases exponentially by increasing the shear stress.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An apparatus for the detailed investigation of the influence of shear&#xA;  stress on adherent BHK cells was developed. Shear forces between 0.0&#xA;  and 2.5 N m−2 were studied. The influence on cell viability, cell&#xA;  morphology, cell lysis, and cell size was determined. Increasing shear&#xA;  forces as well as increasing exposure duration caused increasing&#xA;  changes in cell morphology and cell death. A “critical shear stress&#xA;  level” was determined.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1992 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/014102299290068Y&quot; rel=&quot;nofollow&quot;&gt;Determination of a “critical shear stress level” applied to adherent mammalian cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Shear stress related damage to a mouse hybridoma was examined by&#xA;  Abu-Reesh and Kargi under laminar and turbulent conditions in a&#xA;  coaxial cylinder Searle viscometer. Cells were exposed to 5 to 100&#xA;  N/m2 shear stress levels for 0.5 to 3.0 h. At a given shear stress and&#xA;  exposure time, turbulent shear was much more damaging than laminar&#xA;  shear as also reported in the past for protozoa and plant cells. Under&#xA;  turbulent conditions, damage occurred when shear stress exceeded 5&#xA;  N/m2. Respiratory activity of the cells was damaged earlier than the&#xA;  cell membrane, thus implying transmission of the stress signal to the&#xA;  interior of the cell. Cell damage followed first-order kinetics both&#xA;  in laminar and turbulent environments. For turbulent shear stress&#xA;  levels of 5 to 30 N/m2, the death rate constant (kd) increased&#xA;  exponentially with increasing stress level; the kd values varied over&#xA;  0.1 to 1.0 1/h.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2001 - &lt;a href=&quot;http://www.massey.ac.nz/~ychisti/HydroD.pdf&quot; rel=&quot;nofollow&quot;&gt;Hydrodynamic Damage to Animal Cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Subconfluent endothelial cultures continuously exposed to 1–5&#xA;  dynes/cm2 shear proliferate at a rate comparable to that of static&#xA;  cultures and reach the same saturation density (≃ 1.0–1.5 × 105&#xA;  cells/cm2 ). When exposed to a laminar shear stress of 5–10 dynes/cm2&#xA;  , confluent monolayers undergo a time-dependent change in cell shape&#xA;  from polygonal to ellipsoidal and become uniformly oriented with flow.&#xA;  Regeneration of linear “wounds” in confluent monolayer appears to be&#xA;  influenced by the direction of the applied force. Preliminary studies&#xA;  indicate that certain endothelial cell functions, including fluid&#xA;  endocytosis, cytoskeletal assembly and nonthrombogenic surface&#xA;  properties, also are sensitive to shear stress. These observations&#xA;  suggest that fluid mechanical forces can directly influence&#xA;  endothelial cell structure and function.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1981 - &lt;a href=&quot;http://biomechanical.asmedigitalcollection.asme.org/article.aspx?articleid=1395402&quot; rel=&quot;nofollow&quot;&gt;The Dynamic Response of Vascular Endothelial Cells to Fluid Shear Stress&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Shear stress above 0.25 dyne/cm(2) resulted in dramatic loss of&#xA;  podocytes but not of proximal tubular epithelial cells (LLC-PK(1)&#xA;  cells) after 20 h.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16684926&quot; rel=&quot;nofollow&quot;&gt;Podocytes are sensitive to fluid shear stress in vitro&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A series of careful studies has been made on blood damage in a&#xA;  rotational viscometer. Specific attention has been focused on the&#xA;  effects of solid surface interaction, centrifugal force, air interface&#xA;  interaction, mixing of sheared and unsheared layers, cell-cell&#xA;  interaction, and viscous heating. The results show that there is a&#xA;  threshold shear stress, 1500 dynes/cm2, above which extensive cell&#xA;  damage is directly due to shear stress, and the various secondary&#xA;  effects listed above are negligible.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1972 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006349572860855&quot; rel=&quot;nofollow&quot;&gt;Red Blood Cell Damage by Shear Stress&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The shear stress threshold of some dinoflagellates (microalgae) is&#xA;  even lower than that of erythrocytes (0.029 N/m2). For example, a&#xA;  continuous laminar shear stress level of only 0.0044 N/m2 (equivalent&#xA;  to a shear rate of 2.2 1/s) has proved lethal to the dinoflagellate&#xA;  Gonyaulax polyedra.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://books.google.hu/books?id=aaEeAAAAQBAJ&amp;amp;printsec=frontcover&amp;amp;hl=hu#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Upstream Industrial Biotechnology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Other cell types are not necessary as sensitive as animal cells and they don't necessary react with apoptosis (about 10 dyn/cm2) to shear stress, so you have to use necrotic (about 5000 dyn/cm2) forces to destroy them :&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;cell type                       size                shear sensitivity&#xA;microbial cells                 1-10μm              low&#xA;microbial pellets/clumps        up to 1cm           moderate&#xA;plant cells                     100μm               moderate/high&#xA;plant cell aggregates           up to 1-2cm         high&#xA;animal cells                    20μm                high&#xA;animal cells on microcarriers   80-200μm            very high&#xA;fungi cells                     2-10μm              moderate/high&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Table 1 - shear sensitivity by cells types  &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://books.google.hu/books?id=Z-N4SNmsYnMC&amp;amp;printsec=frontcover&amp;amp;hl=hu&amp;amp;source=gbs_ge_summary_r&amp;amp;cad=0#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Bioprocess Engineering Principles: table 8.6 - Pauline M. Doran&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1996 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/092304679503062X&quot; rel=&quot;nofollow&quot;&gt;Role of hydrodynamic shear in the cultivation of animal, plant and microbial cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1988 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0141022988900166&quot; rel=&quot;nofollow&quot;&gt;Effect of shear on the viability of plant cell suspensions&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2004 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bit.260440512/abstract&quot; rel=&quot;nofollow&quot;&gt;A quantitative analysis of shear effects on cell suspension and cell culture of perilla frutescens (plant) in bioreactors&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/9780470054581.eib543/abstract&quot; rel=&quot;nofollow&quot;&gt;Shear Sensitivity&lt;/a&gt; - the full text probably contains all the numbers&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Results show that Chinese Hamster Ovaries and Human Embryonic Kidney&#xA;  cells will enter the apoptotic pathway when subjected to low levels of&#xA;  hydrodynamic stress (around 2.0 Pa) in oscillating, extensional flow.&#xA;  In contrast, necrotic death prevails when the cells are exposed to&#xA;  hydrodynamic stresses around 1.0 Pa in simple shear flow or around&#xA;  500 Pa in extensional flow.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bit.22405/abstract&quot; rel=&quot;nofollow&quot;&gt;Induction of mammalian cell death by simple shear and extensional flows&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The shear sensitivity is not determined only by cell type and species, there are many other factors involved: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;type of cell and species&lt;/li&gt;&#xA;&lt;li&gt;composition and thickness of cell wall when present&lt;/li&gt;&#xA;&lt;li&gt;size and morphology of cell&lt;/li&gt;&#xA;&lt;li&gt;the intensity and nature of shear stress, whether turbulent or laminar, or associated with interfaces (e.g. during bubble rise and rupture)&lt;/li&gt;&#xA;&lt;li&gt;growth history, both short-term (e.g. starvation) and long term adaptation&lt;/li&gt;&#xA;&lt;li&gt;growth medium (trace elements, vitamins, carbon and nitrogen sources)&lt;/li&gt;&#xA;&lt;li&gt;growth rate&lt;/li&gt;&#xA;&lt;li&gt;growth stage&lt;/li&gt;&#xA;&lt;li&gt;type and concentration of shear protective agents if present&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Cells can be very sensitive to shear stress caused by turbulent flow, while not so sensitive to shear stress caused by laminar flow.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;On the basis of laminar flow viscometriy measurements, a critical&#xA;  shear stress level of 80-200 N/m2 has been suggested for Morindata&#xA;  citrifolia cells.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;... while for Daucus carota a shear stress level of 50 N/m2 has been&#xA;  associated with cell damage. In other study, carrot cells in a laminar&#xA;  flow Couette viscosimeter lost the ability to grow and divide in the&#xA;  shear stress range of 0.5-100 N/m2. The intracellular enzyme activity&#xA;  was impaired at shear stress levels above 3000N/m2, but significant&#xA;  lysis did not occur until a shear stress level of 10.000 N/m2 applied&#xA;  over a prolonged perioud (&gt;1h).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In contrast to the behavior in laminar flow, the cells were quite&#xA;  sensitive to turbulent impeller agitation. Impeller tip speeds of ~1.1&#xA;  m/s lysed a significant proportion of the cells within 40min.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://books.google.hu/books?id=-HDQZc_OftoC&amp;amp;printsec=frontcover&amp;amp;hl=hu#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Cell and Tissue Reaction Engineering&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://books.google.hu/books?id=aaEeAAAAQBAJ&amp;amp;printsec=frontcover&amp;amp;hl=hu#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Upstream Industrial Biotechnology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The bubble damage is severe (1000 cells by a single 3.5mm size bubble) because of the cell adherence to the interface of the bubble and the strong forces involved (&gt;1000 dyn/cm2 by stirred bioreactors). The adhesion and so the damage can be reduced with surfactants.  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2004 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15296446&quot; rel=&quot;nofollow&quot;&gt;Quantitative studies of cell-bubble interactions and cell damage at different pluronic F-68 and cell concentrations.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2004 - &lt;a href=&quot;http://journals.lww.com/anesthesiology/Abstract/2004/07000/Surfactant_Reduction_in_Embolism_Bubble_Adhesion.16.aspx&quot; rel=&quot;nofollow&quot;&gt;Surfactant Reduction in Embolism Bubble Adhesion and Endothelial Damage&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is proposed that when cells are either attached to, or very near, a&#xA;  rupturing bubble, the hydrodynamic forces associated with the rupture&#xA;  are sufficient to kill the cells.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;All experiments were conducted with Spodoptera frugiperda (SF-9)&#xA;  insect cells, in TNM-FH and SFML medium, with and without Pluronic&#xA;  F-68. Experiments indicate that approximately 1050 cells are killed&#xA;  per single, 3.5-mm bubble rupture in TNM-FH medium and approximately&#xA;  the same number of dead cells are present in the upward jet. It was&#xA;  also observed that the concentration of cells in this upward jet is&#xA;  higher than the cell suspension in TNM-FH medium without Pluronic F-68&#xA;  by a factor of two. It is believed that this higher concentration is&#xA;  the result of cells adhering to the bubble interface. These cells are&#xA;  swept up into the upward jet during the bubble rupture process.&#xA;  Finally, it is suggested that a thin layer around the bubble&#xA;  containing these absorbed cells is the “hypothetical killing volume”&#xA;  presented by other researchers.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1994 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bit.260430106/abstract&quot; rel=&quot;nofollow&quot;&gt;Quantification of damage to suspended insect cells as a result of bubble rupture&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For a hybridoma line, reported that exposure to laminar shear stress&#xA;  (208 N/m2) in unaerated flow in a cone and plate viscometer led to&#xA;  substantial loss in cell count and viability within 20 min. At a&#xA;  constant 180 s exposure, increasing shear stress over 100-350 N/m2&#xA;  linearly enhanced cell disruption, with &gt;90% of the cells being&#xA;  destroyed at 350 N/m2 stress level. Shear stres levels associated with&#xA;  bubble rupture at the surface of a bioreactor may range over 100-300&#xA;  N/m2. These values are remarkably consistent with shear rates that&#xA;  damaged hybridomas in unaerated laminar flow experiments.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://books.google.hu/books?id=aaEeAAAAQBAJ&amp;amp;printsec=frontcover&amp;amp;hl=hu#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Upstream Industrial Biotechnology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Smaller hole pipettes cause more damage.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We also examined aspects of the gene transfer procedure that might&#xA;  influence survival such as the size of injection pipettes and their&#xA;  taper relative to zygote diameter, possible toxicity of the injection&#xA;  medium, the timing of injection, and immediate vs. delayed pipette&#xA;  withdrawal. The only factors that significantly affected cell&#xA;  viability were pipette size and taper, and timing of injection in&#xA;  relation to first cleavage. This suggests that zygote viability&#xA;  correlates inversely with the size of the hole produced by the&#xA;  injection pipette and that damage to the membrane is less successfully&#xA;  repaired as the fertilized egg readies itself for division.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1987 - &lt;a href=&quot;http://www.biolreprod.org/content/37/4/957.short&quot; rel=&quot;nofollow&quot;&gt;Zygote viability in gene transfer experiments&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It is hard to find anything about the level of shear stress by pipetting. It can be certainly more than 1 dyn/cm2. It has a short duration (at most a few seconds). I think the following factors can influence the shear stress levels by pipetting:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;pipette type&lt;/li&gt;&#xA;&lt;li&gt;flow speed (faster flow can be more likely turbulent)&#xA;&lt;ul&gt;&#xA;&lt;li&gt;negative pressure by suction&lt;/li&gt;&#xA;&lt;li&gt;hole size (&lt;a href=&quot;http://en.wikipedia.org/wiki/Venturi_effect&quot; rel=&quot;nofollow&quot;&gt;bigger hole can reduce flow speed&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;liquid viscosity&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;bubble formation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Probably more factors are involved but I am not a pipetting expert. ;-) I agree with the others, it surely depends on the personal skills e.g. an amateur can create huge bubbles by pipetting, which can kill a lot of cells by formation and disruption...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I agree with Artem that this is an experiment to do especially if the result is important for you. What you need to create a model about pipette damage, are the shear stress levels by pipetting and the critical shear stress levels of the cells. I think it is hard to design and experiment in which you can measure the shear stress levels in your pipettes and there is no flow model for pipetting as far as I know, so it can be a good topic for a thesis or a diploma work. &lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-23T01:49:27.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23395" PostTypeId="2" ParentId="23390" CreationDate="2014-10-23T02:08:00.147" Score="1" Body="&lt;p&gt;This is not a new thing, by checking the articles about non-invasive glucose level measurement, it started in the early 90's.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Near-infrared (NIR) spectra of the human inner lip were obtained by&#xA;  using a special optimized accessory for diffuse reflectance&#xA;  measurements. The partial-least squares (PLS) multivariate calibration&#xA;  algorithm was applied for linear regression of the spectral data&#xA;  between 9000 and 5500 cm−1 (λ = 1.1-1.8 μm) against blood glucose&#xA;  concentrations determined by a standard clinical enzymatic method.&#xA;  Calibration experiments with a single person were carried out under&#xA;  varying conditions, as well as with a population of 133 different&#xA;  patients, with capillary and venous blood glucose concentration values&#xA;  provided. A genuine correlation between the blood glucose&#xA;  concentrations and the NIR-spectra can be proven. A time lag of about&#xA;  10 min for the glucose concentration in the spectroscopically probed&#xA;  tissue volume vs. the capillary concentration can be estimated.&#xA;  Mean-square prediction errors obtained by cross-validation were in the&#xA;  range of 45 to 55 mg/dL. An analysis of different variance factors&#xA;  showed that the major contribution to the average prediction&#xA;  uncertainty was due to the reduced measurement reproducibility, i.e.,&#xA;  variations in lip position and contact pressure. The results&#xA;  demonstrate the feasibility of using diffuse reflectance&#xA;  NIR-spectroscopy for the noninvasive measurement of blood glucose.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1993 - &lt;a href=&quot;http://www.opticsinfobase.org/as/abstract.cfm?uri=as-47-7-875&quot; rel=&quot;nofollow&quot;&gt;Noninvasive Blood Glucose Assay by Near-Infrared Diffuse Reflectance Spectroscopy of the Human Inner Lip&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are multiple approaches, mostly &lt;a href=&quot;http://en.wikipedia.org/wiki/Spectroscopy&quot; rel=&quot;nofollow&quot;&gt;spectroscopy&lt;/a&gt;, but &lt;a href=&quot;http://en.wikipedia.org/wiki/Dielectric&quot; rel=&quot;nofollow&quot;&gt;dielectric&lt;/a&gt; properties (e.g. conductivity) can depend on glucose levels too. Saliva can be used to measure glucose levels as well.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2014 - &lt;a href=&quot;http://inderscience.metapress.com/content/0486136372338670/&quot; rel=&quot;nofollow&quot;&gt;Non-invasive glucose monitoring using impedance spectroscopy&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2014 - &lt;a href=&quot;http://ieeexplore.ieee.org/xpl/login.jsp?tp=&amp;amp;arnumber=6777300&amp;amp;url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6777300&quot; rel=&quot;nofollow&quot;&gt;Broadband Tissue Mimicking Phantoms and a Patch Resonator for Evaluating Noninvasive Monitoring of Blood Glucose Levels&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2014 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0956566314007295&quot; rel=&quot;nofollow&quot;&gt;A paper strip based non-invasive glucose biosensor for salivary analysis&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The details of each technology you can find of wikipedia.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-23T02:08:00.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23396" PostTypeId="2" ParentId="23391" CreationDate="2014-10-23T03:28:45.470" Score="0" Body="&lt;p&gt;I'm not exactly sure how it is done non-invasively in the manner you describe but suspect that it has to do with IR absorption spectroscopy. Glucose has distinct bands in the near-IR frequency range. So by illuminating the ear lobe and the capillaries in the surface, picking off the refracted light, and spectrally analyzing you should be able to determine the amount of glucose relative to some reference calibration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I worked for a start-up company that did this semi-invasively for glucose measurements in the ICU. We drew a small blood sample and optically analyzed it in a glass cell using a scanning interferometer - then returned the blood to the patient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The optical method that draws blood probably is the best approach with regards to accuracy - where you would like to get within 10 mg/dL - but it also has its problems including response to 'interferents' in the blood that can pose as glucose not to mention high cost for the interferometer and fouling of the blood access system.&lt;/p&gt;&#xA;" OwnerUserId="9906" LastActivityDate="2014-10-23T03:28:45.470" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23398" PostTypeId="2" ParentId="23389" CreationDate="2014-10-23T05:51:38.100" Score="2" Body="&lt;p&gt;All the residues in a polypeptide chain tends to configure into their lowest potential energy state. except the peptide bond all the other bonds are free to rotate, alpha helix makes optimal use of internal H bonds. The overall structure is stabilized by H bond between the hydrogen atom attached to the electronegative nitrogen atom of peptide linkage and the electronegative carbonyl oxygen atom. The arrangement of amino acids in the peptide plays a very important role in forming alpha helix. Different combination of amino acids results in different combination of dihedral angels, hence it determines alpha helix conformation.&lt;/p&gt;&#xA;" OwnerUserId="8026" LastEditorUserId="3340" LastEditDate="2014-12-05T18:28:20.573" LastActivityDate="2014-12-05T18:28:20.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23399" PostTypeId="1" CreationDate="2014-10-23T07:25:23.013" Score="6" ViewCount="97" Body="&lt;p&gt;In quantitative traits we have many loci affecting a trait. If we took a bunch of parents where all mothers and fathers were of a certain value at the upper end of a trait range, and then looked at the offspring would we expect offspring from pairs of parents from more divergent populations to be even more extreme variance in their traits?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example: if we look at 2 men from East Africa, both 190 cm tall. They each have children with women who are 180 cm, one of whom is from East Africa and the other from Canada. We could assume that the Canadian woman is probably more unrelated to her male than the East African woman. I would therefore expect that it is quite likely that the East Africans in the example are tall because of &quot;tall-alleles&quot; in many of the same loci, whereas there is a greater probability that the Canadian female is tall thanks to mutations at different loci. Therefore would it be reasonable to expect greater variation in the offspring of the Canadian woman?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any evidence of this phenomenon?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Note: Ignore environmental and gene&lt;/em&gt; * &lt;em&gt;environment interaction variance, just go with a simple additive model, and assume populations have had some barriers to migration for some time&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-10-23T07:45:18.677" LastActivityDate="2021-05-09T00:03:40.363" Title="More extreme phenotypes when parents are from diverged populations" Tags="&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23400" PostTypeId="1" CreationDate="2014-10-23T07:32:21.300" Score="1" ViewCount="94" Body="&lt;p&gt;About four times in my life I have experienced the feeling of my eyelid fluttering for a few minutes by itself, and then it stops.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have talked to other people who have had the same experience so I presume there is no pathology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could someone please explain the physiology behind these random eye twiching experiences that I and many others have had?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2014-10-23T07:32:21.300" Title="Physiology of benign eye twitching?" Tags="&lt;physiology&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23401" PostTypeId="1" AcceptedAnswerId="23402" CreationDate="2014-10-23T09:03:41.833" Score="3" ViewCount="7705" Body="&lt;p&gt;All living things need water to survive. Worker ants can drink directly from the source. But a queen ant would need help from the colony to get its daily supply of food and water. I have seen ants carrying tiny bits of food, but I have not really seen them carrying water. Do they use their hands like how they carry food? Do they use a receptacle like us humans? Or are there some other innovative ways?&lt;/p&gt;&#xA;" OwnerUserId="1283" LastActivityDate="2019-04-18T00:43:07.810" Title="How do ants transport water?" Tags="&lt;ant&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23402" PostTypeId="2" ParentId="23401" CreationDate="2014-10-23T09:14:19.277" Score="4" Body="&lt;p&gt;The worker ants give water to the other ants in the nest. Also, they get most of their hydration out of the food anyway.&#xA;&lt;a href=&quot;http://blog.wildaboutants.com/2010/07/20/do-ants-drink-water/&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a blogpost with some references and nice humour about it.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2014-10-23T09:14:19.277" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23403" PostTypeId="1" AcceptedAnswerId="23431" CreationDate="2014-10-23T09:59:18.960" Score="3" ViewCount="546" Body="&lt;p&gt;I am looking for a good explanatory book concerning Neurobiology. I am interested on how the brain works but prior to this I believe that I have to start learning things about the biology of neurons. So I searched on the net and found a book called &quot;From Neuron to Brain&quot; from John G. Nicholls et. al.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually there are so many books out there and because I have never worked on that subject, all these results are confusing me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So i would like someone's opinion who has dealt with this subject to help me choose a book for beginners.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="6032" LastEditorUserId="9681" LastEditDate="2014-10-24T05:19:22.217" LastActivityDate="2014-10-30T18:01:32.730" Title="Book recommended for neurobiology" Tags="&lt;neuroscience&gt;&lt;book-recommendation&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23405" PostTypeId="2" ParentId="23388" CreationDate="2014-10-23T13:52:38.370" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Central_nervous_system&quot; rel=&quot;nofollow&quot;&gt;CNS&lt;/a&gt; refers to the brain and spinal cord. Its a very general term. Hypothalamus is part of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Central_nervous_system#Structure&quot; rel=&quot;nofollow&quot;&gt;CNS structure&lt;/a&gt; but its unique in a sense that it secretes many chemicals into the bloodstream like glands hence part of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Endocrine_system&quot; rel=&quot;nofollow&quot;&gt;endocrine system&lt;/a&gt;! so they are both correct!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2014-10-28T11:33:08.990" LastActivityDate="2014-10-28T11:33:08.990" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23406" PostTypeId="1" AcceptedAnswerId="27673" CreationDate="2014-10-23T15:41:07.037" Score="1" ViewCount="296" Body="&lt;p&gt;In all the examples I can think of, (mostly vertebrate), female meiosis, or oogenesis, only haploid gamete is produced while the other cell divisions result in polar bodies. While male meiosis results in 4 haploid gametes. This difference follows the fundamental definition of female and males being defined as resources committed into reproductive cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know if this asymmetrical gamete production is truly universal across all organisms. Are all meiosis in plants or unicellular organisms unequal between male and female?&lt;/p&gt;&#xA;" OwnerUserId="6134" LastEditorUserId="3340" LastEditDate="2015-01-15T05:57:30.947" LastActivityDate="2015-09-18T05:48:27.680" Title="Do all species have asymmetric female meiosis?" Tags="&lt;meiosis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23407" PostTypeId="1" CreationDate="2014-10-23T17:01:12.047" Score="1" ViewCount="345" Body="&lt;p&gt;I'm a programmer so I have little knowledge in the field of biology. However I have an interest in plants, GMOs and DNA (in terms of programming).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I want to know what kind of technology is necessary and what limitations there are involved in creating a DNA printer (that could print out a cell to be grown in a pot).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, how do we print the DNA of a plant? Can we print it all from the first pair of chromosomes? I have heard we are already able to print bacteria's DNA. Is this something we would be able to achieve outside of a lab? Could it be done on commercial scale?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, what conditions do we need to prepare the DNA if it is not that of a bacteria but rather of a plant that would grow into a multi-cellular organism? Can we really print a plant DNA, inject it into a cell and let it grow?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Third, what is the current understanding of DNA ? Can we analyze DNA strand with digital software yet? Can we simulate how the organism will do with the DNA? And how can I start working in this field? Are there any scientific papers I can learn from?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. My first goal is to make a Nepenthes Vine. I want to have a vine plant like Pothos creeping on my fence with a jugs to eat insects.&lt;/p&gt;&#xA;" OwnerUserId="9910" LastEditorUserId="9910" LastEditDate="2014-10-24T08:03:56.457" LastActivityDate="2014-10-24T08:17:59.903" Title="What kind of technology is required for plant seed DNA printing?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;bioinformatics&gt;&lt;botany&gt;" AnswerCount="2" CommentCount="3" ClosedDate="2014-10-24T18:13:04.013" ContentLicense="CC BY-SA 3.0" />
  <row Id="23408" PostTypeId="1" CreationDate="2014-10-23T18:08:23.400" Score="2" ViewCount="3799" Body="&lt;p&gt;I do not know if this question to suitable here or not. I posted it as I think biologists can help me in this question. If not suitable here, then I am sorry for that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have written paper which I spent about 3 years working on it and it has nice findings and original sequenced data (deposited in NCBI). I submitted the paper to &quot;Genome Biology&quot; and I got editorial rejection but they offered to transfer the paper to &quot;BMC Genomics&quot;. However, my supervisor refused this and suggested that we submit to &quot;Nature Scientific Report&quot;. I tried to convince him to go to BMC Genomics because it is more focused journal and it is better for my CV, however, he said the second one is better because it has better impact factor and it is Nature! (Impact factor: 5 for Scientific Reports vs 4.04 for BMC Genomics).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do you think as I am really confused which one to select?&lt;/p&gt;&#xA;" OwnerUserId="9911" LastEditorUserId="3624" LastEditDate="2014-10-25T21:29:32.787" LastActivityDate="2015-11-13T03:28:40.547" Title="Nature Scientific Reports vs. BMC Genomics" Tags="&lt;literature&gt;&lt;peer-review-journal&gt;&lt;publishing&gt;" AnswerCount="2" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="23409" PostTypeId="2" ParentId="23408" CreationDate="2014-10-23T18:42:45.607" Score="4" Body="&lt;p&gt;This is too long for a comment, so I post it here. And these are my personal views, someone else might handle this different. I would submit the paper to BMC Genomics for some reasons:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The editor offered to transfer the paper, so you get past the&#xA;editorial review. This is not guaranteed for Nature Scientific Report&#xA;(NSR). You still have to get through the peer review, but this is not&#xA;different between both journals.&lt;/li&gt;&#xA;&lt;li&gt;Honestly: Forget about the difference in the Impact Factor. Both are &#xA;medium range impact factor journals closely located together. My most&#xA;cited paper is published in such a medium impact journal, today you &#xA;find papers by a Medline search, so this doesn't matter anymore &#xA;(besides prestige). Additionally a lot of citations will raise the &#xA;journals impact factor in the future. I would understand this &#xA;argument when you would have to choose between Nature and BMC &#xA;Genomics, there is quite a difference.&lt;/li&gt;&#xA;&lt;li&gt;If your work fits better into BMC Genomics the chance for acceptance&#xA;is higher, so I would go there. This is of course always a point of&#xA;consideration. The same is true for your CV.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you have the chance to do the decision for yourself without angering your supervisor too much, I would go for it. Even better would be to convince him.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-23T18:42:45.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23411" PostTypeId="1" AcceptedAnswerId="23414" CreationDate="2014-10-23T19:24:21.110" Score="2" ViewCount="234" Body="&lt;p&gt;Caffeine is known to overcome &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18444173&quot; rel=&quot;nofollow&quot;&gt;G2/M&lt;/a&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16709440&quot; rel=&quot;nofollow&quot;&gt;(and possibly other types of)&lt;/a&gt; cell cycle arrest through its &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9870697&quot; rel=&quot;nofollow&quot;&gt;effects on DNA repair machinery&lt;/a&gt; and is used as a positive control in studies of cell cycle arrest. In &lt;a href=&quot;http://jvi.asm.org/content/79/4/2058.long#sec-9&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;, for example, researchers use concentrations of caffeine in the 1-4 mM range to overcome nocodazole-mediated arrest. Is this a physiologically relevant concentration?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found a lot of interesting caffeine data including the &lt;a href=&quot;http://en.wikipedia.org/wiki/Caffeine#Toxicity&quot; rel=&quot;nofollow&quot;&gt;LD50&lt;/a&gt; (estimated to be around 150-200 mg/kg) but have not been able to turn up any good numbers on reasonable concentrations that might be found in a human.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2017-04-21T03:06:53.980" Title="Concentration of caffeine in physiologically relevant setting" Tags="&lt;pharmacology&gt;&lt;cell-cycle&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23412" PostTypeId="1" AcceptedAnswerId="23433" CreationDate="2014-10-23T20:01:12.090" Score="5" ViewCount="1799" Body="&lt;p&gt;I often encounter the root &quot;&lt;em&gt;phyllum&lt;/em&gt;&quot; in binomial names in botany, but I've had trouble finding an actual definition for this root in any Latin dictionary outside of its taxonomic meaning. From context it seems to mean &quot;leaf&quot;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Acer macrophyllum&lt;/em&gt; - Bigleaf Maple&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Tsuga heterophylla&lt;/em&gt; - A Hemlock with distinct two-ranked needles&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;But the Latin for leaf should be &lt;em&gt;folium&lt;/em&gt;. Is there any real rhyme or reason to this? I don't know if this is a question better directed towards the Latin stackexchange, but I thought a botanist might have some insight on the subject. &lt;/p&gt;&#xA;" OwnerUserId="9914" LastEditorUserId="16866" LastEditDate="2017-06-22T14:03:16.363" LastActivityDate="2020-08-08T16:36:23.460" Title="What does the root &quot;phyllum&quot; mean used botanical binomial nomenclature" Tags="&lt;botany&gt;&lt;terminology&gt;&lt;nomenclature&gt;&lt;etymology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23414" PostTypeId="2" ParentId="23411" CreationDate="2014-10-23T20:31:32.627" Score="2" Body="&lt;p&gt;Let's figure it out. Suppose an adult with an average blood volume of 5 L (5000 mL) drinks a cup of strong coffee with 100 mg of caffeine in it. Given caffeine's formula weight of 194.19 g/mol, and assuming 100% of the caffeine is in the blood stream, its concentration (from &lt;a href=&quot;http://www.graphpad.com/quickcalcs/Molarityform.cfm&quot; rel=&quot;nofollow&quot;&gt;this awesome calculator page&lt;/a&gt; from Graphpad, the makers of Prism) would be approximately 103 &amp;micro;M, or 10-40 times &lt;strong&gt;less&lt;/strong&gt; than what's being used in the experiments you cite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, this is overcoming drug-mediated cell cycle arrest, so its possible that a lower concentration is needed to jump-start physiologically-arrested cells.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-10-23T20:31:32.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23415" PostTypeId="1" CreationDate="2014-10-23T22:17:37.657" Score="1" ViewCount="71" Body="&lt;p&gt;I did a mini-project on the drug azacitidine for my pharmacology class, and I learned that azacitidine has the ability to incorporate into both DNA and RNA. I think this is really unique because a similar drug, decitabine, is exclusively incorporated into DNA. Are there any specific physical/structural characteristics of azacitidine that allow it to affect the structure and function of DNA/RNA? Any help would be greatly appreciated!&lt;/p&gt;&#xA;" OwnerUserId="8977" LastActivityDate="2014-10-23T22:28:26.393" Title="What enables azacitidine to incorporate into both DNA and RNA?" Tags="&lt;biochemistry&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23416" PostTypeId="2" ParentId="23415" CreationDate="2014-10-23T22:28:26.393" Score="2" Body="&lt;p&gt;If you look at the very beginning of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Azacitidine&quot; rel=&quot;nofollow&quot;&gt;Wikipedia page&lt;/a&gt;, you'll see that azacitidine is an analog of cytidine, the &lt;code&gt;C&lt;/code&gt; letter of both DNA and RNA fame. Decitabine is a deoxy derivative, and hence would only be incorporated into deoxyribonucleic acid, or DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reading further, by structure azacitidine is ribonucleoside derivative, and is preferentially incorporated into RNA. However, it can be metabolized to 5-aza-2′-deoxycytidine-triphosphate and so be incorporated into DNA.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-10-23T22:28:26.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23417" PostTypeId="1" AcceptedAnswerId="23428" CreationDate="2014-10-23T22:57:37.620" Score="5" ViewCount="170" Body="&lt;p&gt;Please bear with me as I'm intruding into your world from a computer science background. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In programming, once you have created a program, you know all functions of that program. Thus, 100% knowledge is achieved. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, in the field of Biology, how much do we think we currently know about the human cell? Are all functions known (eg. 100%)? Are most functions known (60%)? Or do we know a miniscule proportion (1%~5%) of functions of a cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason I ask is I'm interested in the concept of simulating cells via computer. If we know about a given biological function of a cell, we could convert it into a mathematical function for use within a simulation. With simulations, you could simulate the cell's reactions to drugs, viruses, cell garbage cleanup, etc, based on it's defined functions. And the more functions we know about human cells, the better the simulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance.&lt;/p&gt;&#xA;" OwnerDisplayName="user9915" LastEditorDisplayName="user9915" LastEditDate="2014-10-23T23:05:48.723" LastActivityDate="2014-10-24T15:57:50.503" Title="Are all functions of a human cell known?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;cell-biology&gt;&lt;microbiology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ClosedDate="2014-10-24T10:02:57.720" ContentLicense="CC BY-SA 3.0" />
  <row Id="23418" PostTypeId="2" ParentId="23407" CreationDate="2014-10-23T23:11:08.190" Score="2" Body="&lt;p&gt;As Chris mentioned in his comment, 'printing' DNA from scratch (i.e. synthesizing a long strand &lt;em&gt;de novo&lt;/em&gt;) is expensive and difficult. Unfortunately, the process of GMO creation is not as simple as assembling a beautiful DNA sequence on the computer, printing it, and then inserting it into a cell. Here's a related &lt;a href=&quot;https://biology.stackexchange.com/questions/13819/how-easy-is-it-to-carry-out-de-novo-sequence-assembly?rq=1&quot;&gt;question&lt;/a&gt; about &lt;em&gt;de novo&lt;/em&gt; sequencing. Plant biologists, please correct me if I'm wrong but I don't think it's a trivial matter to grow a plant from a single cultured cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your third question reminds me of &lt;a href=&quot;http://www.dna-computing.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA programming&lt;/a&gt;, which is an amazingly cool, developing field. Many companies (including &lt;a href=&quot;http://research.microsoft.com/en-us/projects/dna/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Microsoft&lt;/a&gt;) are funding research into DNA circuitry and biological computing, making computers out of biomolecules. Here's an interesting &lt;a href=&quot;http://research.microsoft.com/apps/pubs/default.aspx?id=80784&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper&lt;/a&gt; that will tell you more. What you may be most interested in is the branch of DNA programming that seeks to identify discrete protein-coding and otherwise functional DNA that can be utilized as a sort of &quot;programming language&quot; to build a new organism. One of my past supervisors recently joined this field and I'm a little jealous. Overall, this is a very new field so there is much to be accomplished and very little is &lt;em&gt;technically&lt;/em&gt; possible, although the principle of GMOs is really just an optimization of an existing organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, the answer to all three of your questions is: &lt;strong&gt;No, not very well. But we're trying.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most likely this isn't something you'll be able to pick up in your spare time in order to have a cool plant to grow on your fence. It's very expensive and very difficult (in some cases, maybe even impossible). However, there are so many unknowns in this area of research and everything you propose is reasonable &lt;em&gt;in theory&lt;/em&gt;. Let me know if you figure it out. I would love to code my own garden.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-10-24T01:57:27.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23419" PostTypeId="2" ParentId="23407" CreationDate="2014-10-24T00:16:40.980" Score="2" Body="&lt;p&gt;The closest we have come to achieving this was probably when the J. Craig Venter institute &lt;a href=&quot;http://www.jcvi.org/cms/research/projects/first-self-replicating-synthetic-bacterial-cell/overview/&quot; rel=&quot;nofollow&quot;&gt;made a synthetic bacteria&lt;/a&gt;. They produced the genome for the smallest simplest bacteria they could find and it still took a large team of researchers several years and a LOT of money. Building a plant would be exponentially more difficult. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What complicates this is that you need more than DNA. You need the proteins that read the DNA and make RNA and more proteins. JCVI not only had to synthesize the DNA for the bacteria they wanted to make, but they had to take cells from another species of bacteria, remove all its DNA, then insert the new DNA. The leftover proteins from the previous species were able to read the new DNA, and make the proteins that built the new species. This only worked because the 2 species used were close enough that the same promoters and regulatory elements on the DNA could interact with the pre-existing protein. If you could make a plant genome and insert it into a bacteria, some plant proteins might be produced, but it would not be orchestrated well enough to actually produce a plant.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-10-24T00:16:40.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23421" PostTypeId="1" CreationDate="2014-10-24T05:14:46.830" Score="5" ViewCount="2545" Body="&lt;p&gt;Mammalian cell/tissue cultures sometimes require flasks coated with proteins. My uneducated guess is that these proteins mimic the ECM, perhaps the basal lamina, so finicky contact-dependent cells can attach to it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, I have a &lt;a href=&quot;http://www.atcc.org/products/all/CRL-9609.aspx&quot; rel=&quot;nofollow&quot;&gt;BEAS-2B&lt;/a&gt; tracheal culture which requires a coating of albumin, fibronectin and type I collagen. This is applied by incubating an empty plastic dish or flask with a solution of these proteins overnight. I give this as an example of what a &quot;coat&quot; constitutes. You answer should be general enough to apply to at least the most common coat types, or if it depends on the coat, you should explain how.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Likewise, there is some variation in how the trypsinization occurs. To have a starting point, let's say I am trypsinizing according to typical ATCC recommendations: 5 minutes with 0.25% Trypsin-0.53 mM EDTA, then inactivate with equal volume medium. I haven't worked with a cell that can withstand this noticeably (but then I haven't worked with any exotic cells).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;My question:&lt;/em&gt;&lt;/strong&gt; When I trypsinize the cells to passage, what happens to the coat?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since trypsin is a protease that cleaves even the attachment of cells to plastic, I am guessing that it will also destroy the coat. After the trypsin and cells are removed, the flask will have a tiny fraction of the protein coat that it had before, and will not support cells that require a coat any longer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I correct in thus deducing that coated flasks cannot be reused after trypsinization? Are any of the alternative detachment reagents an exception to this?&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-10-25T04:53:59.890" LastActivityDate="2018-12-14T11:09:52.773" Title="Does trypsin strip flask coating?" Tags="&lt;cell-biology&gt;&lt;cell-culture&gt;&lt;extra-cellular-matrix&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23422" PostTypeId="5" CreationDate="2014-10-24T05:17:30.733" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-10-24T05:17:30.733" LastActivityDate="2014-10-24T05:17:30.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23423" PostTypeId="4" CreationDate="2014-10-24T05:17:30.733" Score="0" Body="Molecules secreted by cells to provide structural support and biochemical support." OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-10-24T06:00:45.937" LastActivityDate="2014-10-24T06:00:45.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23424" PostTypeId="1" AcceptedAnswerId="23426" CreationDate="2014-10-24T05:53:25.477" Score="9" ViewCount="2153" Body="&lt;p&gt;Recently, CIDRAP at the University of Minnesota announced that &lt;a href=&quot;http://www.cidrap.umn.edu/news-perspective/2014/09/commentary-health-workers-need-optimal-respiratory-protection-ebola&quot;&gt;Ebola may be more transmissible through aerosols&lt;/a&gt; than previously thought.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I lack the familiarity with the field to critically evaluate this release. They also seem to more interested in making the point that &lt;em&gt;there is a risk&lt;/em&gt; of aerosol transmission, not to settle whether it does transmit by air or not.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What is the simple answer? Can Ebola really be transmitted by aerosols? &lt;/li&gt;&#xA;&lt;li&gt;If so, how come nobody realized this before? Is this a general phenomenon allowing any pathogen to become airborne? I don't see why you couldn't aerosolize a great many pathogenic objects, not just Ebola virus.&lt;/li&gt;&#xA;&lt;li&gt;How does the number of virions necessary for successful infection compare to what you could get from aerosols?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="540" LastEditorUserId="2949" LastEditDate="2014-10-24T18:29:17.683" LastActivityDate="2014-10-26T05:19:51.620" Title="To what extent is Ebola airborne? (aerosols)" Tags="&lt;virology&gt;&lt;infection&gt;&lt;epidemiology&gt;&lt;ebola&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23426" PostTypeId="2" ParentId="23424" CreationDate="2014-10-24T07:40:39.253" Score="15" Body="&lt;p&gt;Interesting question and hard to answer definitively. First of all: It seems still pretty clear that the major (and by far most important) infection route comes from direct contact with infected people or their body fluids and that aerosol transmission is of far less significance. Ebola is infecting cells of the immune system (mostly macrophages and dendritic cells) which are located in the skin which makes the route through the respiratory organs pretty uneffecient, but it is possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are reports for Ebola transmissions (or at least unclear cases in which a direct contact could be excluded), which suggest that the aerosl transmission is possible. There are reports of Ebola infections which spread among experimental animals between infected and non-infected (and without direct contact) control groups. This has been observed between rhesus monkeys and pigs. It was also possible for the pigs to infect non-human primates (see references 1-4 for details). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This results should be seen with some caution: At least for pigs an Ebola infection seems to be pretty much different than one in humans. There it looks more like a respiratory disease with all what comes along with it: Extended sneezing and coughing - which makes a lot of aerosol droplets. See reference 3 for the original paper and 5 and 6 for a summary and a classification. I think it is also possible that anatomical differences to the humans make such an infection route easier or harder.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally there are some reports of infected people which had no direct contact to people (see reference 7). However, this is rare and mostly restricted to people which where involved in health care for infected persons. These people come in close contact to the infected people which raises their chance of getting infected by aerosols. This underlines the importance for health care workers to get the right protective equipment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0140673695928413&quot;&gt;Transmission of Ebola virus (Zaire strain) to uninfected control&#xA;monkeys in a biocontainment laboratory.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://jid.oxfordjournals.org/content/204/2/200.long&quot;&gt;Replication, Pathogenicity, Shedding, and Transmission of Zaire&#xA;ebolavirus in Pigs&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/srep/2012/121115/srep00811/full/srep00811.html&quot;&gt;Transmission of Ebola virus from pigs to non-human primates&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1286457911001225&quot;&gt;Aerosol exposure to Zaire ebolavirus in three nonhuman primate&#xA;species: differences in disease course and clinical pathology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://scienceblogs.com/aetiology/2012/11/19/pig-to-monkey-ebola-is-there-something-in-the-air/&quot;&gt;Pig-to-monkey Ebola: is there something in the air?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://scienceblogs.com/aetiology/2014/08/08/new-paper-on-ebola-no-primate-to-primate-transmission-seen/&quot;&gt;New paper on Ebola–no primate-to-primate transmission seen&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://jid.oxfordjournals.org/content/179/Supplement_1/S92.long&quot;&gt;Ebola Hemorrhagic Fever, Kikwit, Democratic Republic of the Congo,&#xA;1995: Risk Factors for Patients without a Reported Exposure&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-10-24T11:34:00.597" LastActivityDate="2014-10-24T11:34:00.597" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23428" PostTypeId="2" ParentId="23417" CreationDate="2014-10-24T09:30:31.523" Score="3" Body="&lt;p&gt;As someone who has dabbled in both biology and programming, I assume you are referring to the theoritical ability  of functional programming to simulate organic behaviour from well defined input. From that point of view, our comprehension of the human cell behaviour is  currently near stone age level.&#xA;The astounding diversity of homeostatic and signaling parameters in our body makes a realistic simulation of human cell normal behaviour largely out of reach, so don't even think about patholgic states.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The more data we will acquire, the more precise our simulations will be. Currently, our data acquisition methods are too primitive, and clearly are not deterministic enough to base computed simulations upon them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, this answer reflects my own opinion, but I dare think that most of my colleagues will adhere to that view.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2014-10-24T15:57:50.503" LastActivityDate="2014-10-24T15:57:50.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23429" PostTypeId="1" AcceptedAnswerId="23436" CreationDate="2014-10-24T10:28:47.540" Score="11" ViewCount="25009" Body="&lt;p&gt;The spleen is considered a graveyard for red blood cells. So in case of &lt;strong&gt;Splenectomy&lt;/strong&gt; (complete surgical removal of the spleen), what would be the fate of red blood cells? Would this cause &lt;em&gt;Polycythemia&lt;/em&gt;?&lt;/p&gt;&#xA;" OwnerUserId="9919" LastEditorUserId="9099" LastEditDate="2014-10-24T14:21:14.337" LastActivityDate="2014-10-25T23:00:21.923" Title="Fate of erythrocytes after splenectomy" Tags="&lt;hematology&gt;&lt;red-blood-cell&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23430" PostTypeId="1" CreationDate="2014-10-24T11:29:09.680" Score="5" ViewCount="79" Body="&lt;p&gt;I would like to know if proteins expressed in higher quantities, such as DNA polymerase, would be better vaccine candidates for a T-cell based vaccine.&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="4717" LastEditDate="2015-08-16T12:14:32.917" LastActivityDate="2015-08-16T12:14:32.917" Title="Is viral protein expression important for peptide vaccine?" Tags="&lt;immunology&gt;&lt;virus&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23431" PostTypeId="2" ParentId="23403" CreationDate="2014-10-24T12:31:39.907" Score="6" Body="&lt;p&gt;I can highly recommend Kandel's &quot;Principles of neural science&quot;. I have not had any biology courses since highschool, but I was able to understand it well. It is really a book meant to teach. The style is beginner friendly, and not tedious/boring at all. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is an expensive buy and a very long read (I think the paper version is close to 2000 pages), but given the complexity of the subject matter, I find it reasonable. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you decide to go for it (or for any other neurobiology work, actually) get the newest edition. Getting an older one is a false economy here - our understanding of how this stuff works gets better by the year, and there is lots of missing (or sometimes even not-valid-any-longer) information in the older editions. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;A few examples of what might make the book hard to understand for beginners&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&quot;Principals of neural science&quot; does not require much preexisting biology knowledge. It is sufficient to roughly know that a cell has a nucleus, plasma with organelles swimming inside, and a membrane. But you have to be comfortable with a bit of biochemistry. This is an example passage concerning the behavior of ions in solution. I found this perfectly understandable with my prior knowledge, I don't know if you need brushing up on chemistry or not. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The cell membrane is selectively permeable to K+ because the otherwise impermeable membrane contains proteins that form pores called &lt;em&gt;ion channels&lt;/em&gt;. The channels that are active when the cell is at rest are highly permeable to K+ but considerably less permeable to Na+. The K+ ions tend to leak out of these open channels, down the ion's concentration gradient. As K+ ions exit the cell, they leave behind a cloud of unneutralized negative charge on the inner surface of the membrane, so that the net charge inside the membrane is more negative than that outside. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And then there are examples like this one: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Isoprenylation is another post-translational modification important for anchoring proteins to the cytosolic side of membranes. It occurs shortly after the synthesis of the protein is completed and involves a series of enzymatic steps that result in thioacylation by one of the two long-chain hydrophobic polyisoprenyl moieties (farnesyl, with 15 carbons, or geranyl-geranyl, with 20) of the dulfhydril group of a cysteine at the C-terminus of proteins. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here, my own chemistry is bad enough that I could only understand that a protein is modified by attaching some molecular structure to it, and this makes it possible to attach the protein to the cell membrane. The lack of understanding of the details (what is a geranyl-geranyl?) did not stop me from understanding the rest of the section, so I don't mind, but I know that there are readers who'd have a problem with that. Sadly, I don't know of a source which does not require such knowledge, and if you feel the need to know every single word, you might need to use a reference while reading, or start with a course in biochemistry first before switching to the neurobiology. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, if you don't have a life science background, there might be words outside of the chemistry you might have to look up, or understand from context, but they will be unfamiliar at first. For example, I was surprised to see the word &quot;process&quot; used in the meaning of a physical protrusion from the cell body. But this is not such a high hurdle, you have to either read ahead and puzzle such words out, or use a dictionary. They are not so frequent to prevent comfortable reading. &lt;/p&gt;&#xA;" OwnerUserId="1578" LastEditorUserId="1578" LastEditDate="2014-10-30T18:01:32.730" LastActivityDate="2014-10-30T18:01:32.730" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23432" PostTypeId="2" ParentId="23430" CreationDate="2014-10-24T12:49:39.700" Score="4" Body="&lt;p&gt;To find candidate proteins which can be used as peptide vaccine, these need to fulfill some criteria:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The most important is that the peptide (or protein) used for&lt;br&gt;&#xA;vaccination shall not have a closely relate sequence in the organism &#xA;in which the vaccination shall occur. Otherwise either no reaction&#xA;(due to immunologic tolerance to self) or an autoimmune reaction&#xA;might happen.&lt;/li&gt;&#xA;&lt;li&gt;The peptide/protein need to be expressed on the surface of the&#xA;microbe (either virus or bacteria) since otherwise it will not be&#xA;recognized by the immune system. Also domains of a potential vaccine&#xA;candidate which are inside of membrane are not useful.&lt;/li&gt;&#xA;&lt;li&gt;The epitope needs to be stable enough to be used as a vaccine and&#xA;also be present on the microbe (otherwise there is no immune&#xA;reaction).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you want to read further on this topic, there is an interesting Paper from the WHO available, which gives a nice introduction:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.who.int/biologicals/publications/trs/areas/vaccines/peptide/WHO_TRS_889_A1.pdf&quot; rel=&quot;nofollow&quot;&gt;Guidelines for the production and quality control of synthetic&#xA;peptide vaccines&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;To answer your question: No, these proteins cannot be used for this purpose, as they are relatively closely related to the same proteins in the human body. This will probably lead to no immunologic reaction at all. Additionally, these proteins are located inside of cells and thus not exposed to the immune system.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-24T12:49:39.700" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="23433" PostTypeId="2" ParentId="23412" CreationDate="2014-10-24T13:10:31.960" Score="9" Body="&lt;p&gt;Binomial names often use of greek words. Phyllum means -- as you correctly stated -- &quot;leaf&quot;, but is not derived from latin but from the greek φύλλον, 'phyllon'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, there are also lots of examples where the latin word 'folium' is used. To stick with the genus &lt;em&gt;Acer&lt;/em&gt; from your example, there is another species named &lt;a href=&quot;http://www.theplantlist.org/tpl1.1/record/kew-2615686&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Acer gracilifolium&lt;/em&gt;&lt;/a&gt;. So don't be confused by the linguistic chaos in binomial nomenclature. &lt;/p&gt;&#xA;" OwnerUserId="8015" LastEditorUserId="8015" LastEditDate="2014-10-24T14:13:03.407" LastActivityDate="2014-10-24T14:13:03.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23436" PostTypeId="2" ParentId="23429" CreationDate="2014-10-24T18:42:51.667" Score="3" Body="&lt;p&gt;The spleen is not the only organ which removes &quot;old&quot; erythrocytes, this happens as well in the liver and the lymph nodes. The whole process is termed &lt;a href=&quot;http://en.wikipedia.org/wiki/Red_blood_cell#Senescence&quot; rel=&quot;nofollow&quot;&gt;Eryptosis&lt;/a&gt;, the Apoptosis of Erythrocytes. During the aging of erythrocytes sialic acid on their outer membrane surface is removed. This leads to the recognition by macrophages and phagocytosis of this cells by macrophages which are located in liver and spleen. For more information see this article: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23801921&quot; rel=&quot;nofollow&quot;&gt;Physiology and Pathophysiology of Eryptosis&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Polycythemia is the state when you have an elevated number of red blood cells, characterized by an increased Hematokrit level. This is caused by the over-production of red blood cells, which can be caused by an overproduction of hematopietic cells in the bone marrow (so called &lt;a href=&quot;http://en.wikipedia.org/wiki/Myeloproliferative_syndrome&quot; rel=&quot;nofollow&quot;&gt;myeloproliferative syndrome&lt;/a&gt;, which are basically cancers), the exposure to permanently low oxygen-levels (this is what athletes exploit when the do training at high altitudes) or malignancies (usually lymphoma). It is also possible due to the mis-use of &lt;a href=&quot;http://en.wikipedia.org/wiki/Erythropoietin&quot; rel=&quot;nofollow&quot;&gt;Erythropoietin&lt;/a&gt; (EPO) which induces the production of red blood cells. Another possibility for having too much red blood cells is the over-transfusion during a blood transfusion. For further information have a look into the &lt;a href=&quot;http://en.wikipedia.org/wiki/Polycythemia&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;. The article there is pretty complete and contains a number of references.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-10-25T10:14:56.153" LastActivityDate="2014-10-25T10:14:56.153" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23437" PostTypeId="1" AcceptedAnswerId="23443" CreationDate="2014-10-24T19:55:52.280" Score="8" ViewCount="722" Body="&lt;p&gt;How long can a human cell live in a controlled environment, given all necessary nutrients, temperatures, mechanisms for waste removal, and other requirements are provided for? Put differently:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Can a human cell live on indefinitely?&lt;/li&gt;&#xA;&lt;li&gt;What's the longest known lifespan recorded for a human cell in a controlled environment?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerDisplayName="user9915" LastEditorDisplayName="user9915" LastEditDate="2014-10-25T13:42:23.280" LastActivityDate="2014-10-25T13:42:23.280" Title="Can a human cell live indefinetely in a controlled environment?" Tags="&lt;human-biology&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23438" PostTypeId="1" CreationDate="2014-10-24T20:48:09.357" Score="3" ViewCount="995" Body="&lt;p&gt;I started to think this definition of Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Microenvironment (biology), a small or relatively small usually&#xA;  distinctly specialized and effectively isolated biophysical&#xA;  environment (as of a nerve cell)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and I started to think which environments can be examples of its. &#xA;Joints, synovial joints with capsule, hyaline cartilage in capsules, ...?&#xA;I would like to get more examples of environments so I can think better definition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is Microenvironment?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-10-25T06:20:27.947" LastActivityDate="2016-10-04T14:45:39.877" Title="How is Microenvironment strictly defined?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23439" PostTypeId="1" AcceptedAnswerId="23442" CreationDate="2014-10-24T23:18:42.597" Score="11" ViewCount="11642" Body="&lt;p&gt;Dominant theory is that 'normal' dinosaurs went extinct from ether &lt;a href=&quot;http://www.wired.com/2008/12/deccantraps/&quot;&gt;super volcano&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/Cretaceous%E2%80%93Paleogene_extinction_event&quot;&gt;meteor impact&lt;/a&gt; or &lt;a href=&quot;https://www.youtube.com/watch?v=1iNcRJGzzxs&quot;&gt;combination of both&lt;/a&gt;. However there were &lt;a href=&quot;http://www.newscientist.com/article/dn26193-biggest-hunting-dinosaur-was-an-aquatic-sharkgobbler.html#.VErcdvnF8ms&quot;&gt;aquatic dinosaurs&lt;/a&gt; that are not present at this day. Was it one of the events above that caused them to go extinct, or was it something else?    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How did aquatic dinosaurs go extinct?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="8129" LastEditorUserId="107" LastEditDate="2014-10-25T00:25:52.260" LastActivityDate="2017-10-23T05:24:22.650" Title="How did aquatic dinosaurs go extinct?" Tags="&lt;palaeontology&gt;&lt;extinction&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23440" PostTypeId="2" ParentId="23438" CreationDate="2014-10-25T00:10:39.990" Score="1" Body="&lt;p&gt;The meaning of the term microenvironment depends on the scale of the system that you're looking at. It's a sort of weasel word that loosely means &quot;context&quot; or &quot;stuff in the immediate surroundings of the system of interest that has some kind of an effect on it&quot;. I've seen it used to describe everything from the chemical microenvironment of a cell (e.g. a hormone gradient) to the electrostatic microenvironment of a single amino acid residue in a protein (e.g. the field from nearby charged residues).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conceptually it's similar to the &quot;surroundings&quot; in the &quot;system and surroundings&quot; framework from statistical physics.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-10-25T00:10:39.990" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23441" PostTypeId="1" CreationDate="2014-10-25T00:18:10.743" Score="2" ViewCount="156" Body="&lt;p&gt;I have read somewhere that the live culture added to yogurt acting as &quot;healthy&quot; gut bacteria are actually synthetic and harmful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any truth to this? If so, what are some alternatives to getting good gut bacteria?&lt;/p&gt;&#xA;" OwnerUserId="9926" LastActivityDate="2014-10-25T10:04:57.850" Title="Are added yogurt cultures harmful to the gut?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23442" PostTypeId="2" ParentId="23439" CreationDate="2014-10-25T00:32:28.113" Score="5" Body="&lt;p&gt;Spinosaurs (like &lt;em&gt;Spinosaurus&lt;/em&gt;) are currently only known &lt;a href=&quot;http://dinosaurs.wikia.com/wiki/Spinosaurus&quot; rel=&quot;noreferrer&quot;&gt;from 112-97 million years ago&lt;/a&gt;, although isolated teeth push the origin possibly back to ~150 Mya. At least now, there isn't any definite spinosaur material younger than 97 Mya.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So spinosaurs were already extinct when the rest of the non-bird dinosaurs went extinct at the end of the Cretaceous, whether by meteor impact, volcanism, a combination, or something else completely.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2014-10-25T00:32:28.113" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23443" PostTypeId="2" ParentId="23437" CreationDate="2014-10-25T01:12:51.357" Score="7" Body="&lt;p&gt;This question is at least two questions. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Dividing cells&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;In terms of a dividing human cell line, every time a division occurs the telomeres capping the ends of the chromosomes get a little bit shorter. Once the telomeres get short enough they act as a signal that triggers apoptosis, destroying the cell. There is some human-to-human variation in the initial length of the telomeres, but the impression I've gotten from hanging around cell biologists is that the division limit is somewhere on the order of 10-100.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also cells in which the activity of a protein called telomerase is upregulated. Telomerase is a type of polymerase (an enzyme that synthesizes DNA) that acts to add extra length to telomeres. Telomerase+ cells are not affected by the division limit in the normal way. Some examples of telomerase+ cells are stem cells and many kinds of cancer cells. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Stationary cells&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;In a very real sense, a cell &quot;dies&quot; when it divides. Upon division a cell splits into two daughter cells, but it cannot be said that either daughter cell &quot;is&quot; the original cell. So a more satisfying way to answer to the original question would be to look at how long a single cell can be kept as-is and recognizably alive (i.e. in stationary phase).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you cheat and freeze the cell at liquid nitrogen temperatures (78 K), then there are plenty of examples of cells surviving for decades, in the sense that a culture can be stored and then thawed, and normal life processes will resume at least some of the time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sadly, there may not be a proper answer out there to this version of the question. A quick lit search did not turn up much. It is thought that at least some cells (in particular neurons) last for decades in the human body without dividing, although this is unsurprisingly hard to prove.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-10-25T01:12:51.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23444" PostTypeId="2" ParentId="23439" CreationDate="2014-10-25T03:02:19.787" Score="5" Body="&lt;p&gt;Not a lot of people realize how extreme and how sudden the dinosaur's extinction was. Radiolab did &lt;a href=&quot;http://www.youtube.com/watch?v=ZYoqtBEzuiQ&quot; rel=&quot;nofollow&quot;&gt;an episode&lt;/a&gt; with several geologists about the extinction of the dinosaurs. Basically, when the meteor hit the Earth, a humongous amount of material was ejected into space, and most of it fell back down to the surface all around the planet. As it fell it left an incredible amount of heat in the air, raising temperatures to as high as 1200 Farenheit (650 Celsius). Anything too large to hide under dirt died (dirt is a surprisingly good insulator). Even plankton and animals near the surface of the ocean would have been decimated by the heat, destroying the food chain that supported the large mesosaurs and plesiosaurs. The whole process is thought to have taken 2 hours. The fact that anything lived through that at all is dumb luck, and even if a semi-aquatic dinosaur was deep enough to avoid the worst of the heat, the food supply would have been destroyed and they would have starved shortly after the impact.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="1578" LastEditDate="2014-10-25T17:28:50.687" LastActivityDate="2014-10-25T17:28:50.687" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23445" PostTypeId="5" CreationDate="2014-10-25T05:24:51.593" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-10-25T05:24:51.593" LastActivityDate="2014-10-25T05:24:51.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23446" PostTypeId="4" CreationDate="2014-10-25T05:24:51.593" Score="0" Body="Covers both the Ebola virus and Ebola virus disease." OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-10-25T08:52:23.727" LastActivityDate="2014-10-25T08:52:23.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23448" PostTypeId="2" ParentId="23441" CreationDate="2014-10-25T10:04:57.850" Score="3" Body="&lt;p&gt;I'm not sure what you mean by 'synthetic' gut bacteria, so I can't address that. is yogurt harmful to the gut? I believe the answer is no.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Women (and their doctors) have long known that taking antibiotics can result in Candidia (a yeast infection). Physicians have been advising women taking antibiotics to eat yogurt with live cultures, including lactobacillus spp. and bifidus spp. In keeping with today's movement towards evidence based medicine, &lt;em&gt;Natural Medicines Comprehensive Database&lt;/em&gt; rates effectiveness based on scientific evidence according to the following scale: &lt;em&gt;Effective&lt;/em&gt;, &lt;em&gt;Likely Effective&lt;/em&gt;, &lt;em&gt;Possibly Effective&lt;/em&gt;, &lt;em&gt;Possibly Ineffective&lt;/em&gt;, &lt;em&gt;Likely Ineffective&lt;/em&gt;, &lt;em&gt;Ineffective&lt;/em&gt;, and &lt;em&gt;Insufficient Evidence to Rate&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The effectiveness ratings for (just) LACTOBACILLUS are as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Likely effective&lt;/em&gt; for:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Diarrhea in children caused by a certain virus (rotavirus). Children with rotaviral diarrhea who are being treated with lactobacillus seem to get over their diarrhea about a half day earlier than they would without this treatment. Larger doses of lactobacillus are more effective than smaller ones. At least 10 billion colony-forming units during the first 48 hours should be used.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Possibly effective&lt;/em&gt; for...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Preventing diarrhea in children caused by antibiotics.   &lt;/li&gt;&#xA;  &lt;li&gt;Preventing diarrhea in hospitalized adults. Drinking a specific beverage containing Lactobacillus casei, Lactobacillus bulgaricus, and Streptococcus thermophilus (Actimel, Danone) twice daily during antibiotic treatment and for a week afterwards significantly decreases the risk of developing diarrhea.&lt;br&gt;&#xA;  -Preventing diarrhea due to traveling. Taking a specific strain of Lactobacillus rhamnosus, Lactobacillus GG (Culturelle) seems to help prevent diarrhea in travelers.   &lt;/li&gt;&#xA;  &lt;li&gt;Preventing diarrhea due to cancer treatment (chemotherapy). There is some evidence that patients with cancer of the colon or rectum have less severe diarrhea, less stomach discomfort, shorter hospital care, and require fewer chemotherapy dose reductions due to GI side effects when they take a particular strain of Lactobacillus rhamnosus, Lactobacillus GG (Culturelle).&lt;/li&gt;&#xA;  &lt;li&gt;Colic in babies. Taking a specific Lactobacillus reuteri product seems to be more effective than using the drug simethicone.&lt;/li&gt;&#xA;  &lt;li&gt;Lung infections. Children ages 1 to 6 years who attend daycare centers seem to get fewer and less severe lung infections when given milk containing lactobacillus GG or a specific combination product containing both Lactobacillus acidophilus and Bifidobacterium (HOWARU Protect).&lt;/li&gt;&#xA;  &lt;li&gt;Treating a bowel condition called ulcerative colitis. Some research suggests that taking a specific combination product containing lactobacillus, bifidobacteria, and streptococcus might improve symptoms. &lt;/li&gt;&#xA;  &lt;li&gt;Treating irritable bowel syndrome (IBS). There is some research showing that certain strains of lactobacillus, but not others, can improve symptoms of IBS such as bloating, and stomach pain.&lt;/li&gt;&#xA;  &lt;li&gt;Treating vaginal infections caused by bacteria (bacterial vaginosis). &lt;/li&gt;&#xA;  &lt;li&gt;Treating and preventing eczema (atopic dermatitis) in infants and children who are allergic to cow’s milk. &lt;/li&gt;&#xA;  &lt;li&gt;Helping prescription medications treat Helicobacter pylori (H pylori) infection, which causes stomach ulcers.&lt;/li&gt;&#xA;  &lt;li&gt;&lt;strong&gt;Treating diarrhea caused by the bacterium Clostridium difficile.&lt;/strong&gt;&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Though some of the recommendations are for specific probiotic formulations, one can achieve similar results by reading yogurt packages and mixing types to assure coverage with the proper bacterial spp.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/druginfo/natural/790.html&quot; rel=&quot;nofollow&quot;&gt;National Institutes of Health&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-10-25T10:04:57.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23449" PostTypeId="1" AcceptedAnswerId="23461" CreationDate="2014-10-25T11:08:20.687" Score="4" ViewCount="3610" Body="&lt;p&gt;I found bunch of red worms coming out of sink. &#xA;It is rather unusual to find an overwhelmingly large number of worms. It doesn't seem like earthworm or horsehair worm. I don't know much about the worms though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could anyone please identify it for me.?  Notable features are&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Dark red in color. &lt;/li&gt;&#xA;&lt;li&gt;Has  a hook like structure at its rear end. &lt;/li&gt;&#xA;&lt;li&gt;Moves in both directions front and rear. &lt;/li&gt;&#xA;&lt;li&gt;It shrinks when it dwells in water.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/S1Wdc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9929" LastActivityDate="2015-11-17T11:16:32.690" Title="Please help me to identify this red worm" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23451" PostTypeId="1" CreationDate="2014-10-25T14:00:23.837" Score="1" ViewCount="199" Body="&lt;p&gt;If I flex my bicep and continue to contract it does it mean that the muscle cells are in depolarizing state and not repolarizing? &lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorDisplayName="user12874" LastEditDate="2015-01-13T15:29:18.573" LastActivityDate="2015-01-13T15:29:18.573" Title="Does repolarization of muscle fibers mean that the muscle bundle is relaxed?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;muscles&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23452" PostTypeId="1" AcceptedAnswerId="23501" CreationDate="2014-10-25T14:53:59.810" Score="9" ViewCount="5055" Body="&lt;p&gt;I am trying to find miRNAs that bind to the 3'UTR of a specific gene. What is the best way of doing that (that is, with a good scoring analysis that is most commonly used by researchers in this area)? I would also like to know the other possible methods if there are multiple ways of doing this. &lt;/p&gt;&#xA;" OwnerUserId="1843" LastEditorUserId="3340" LastEditDate="2014-10-27T08:44:29.627" LastActivityDate="2015-03-05T14:54:48.663" Title="How to find miRNA binding sites on a specific gene?" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;rna&gt;&lt;mrna&gt;&lt;microrna&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23453" PostTypeId="1" AcceptedAnswerId="23456" CreationDate="2014-10-25T15:38:02.217" Score="0" ViewCount="655" Body="&lt;p&gt;Assume that the heart is beating, but no pacemaker cells are working for at least 15 seconds. &#xA;This would be a very long compensatory pause if extrasystole started it. &#xA;There may be some low frequent cells working at lower frequency (less than 10 Hz) but I do not understand what. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the name of condition where main pacemaker cells are not beating?&lt;/strong&gt; &#xA;Main pacemakers are SA-node, AV-node and Purkinje-fibers/His-bundle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Raoul is correct. &#xA;This is called asystole. &#xA;It is temporal in the above case. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My definition in research but note the difference to current Clinics so you do not get confused&lt;/strong&gt;: Asystole is a state of no cardiac electrical activity from pacemaker cells when the conduction system and cardiomyocytes can be still functioning (so the case in my thread). The conduction system and cardiomyocytes of the ventricles are responsible for the bradycardia in my case for short-term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What do you think about this case?&lt;/strong&gt; &#xA;Some bradycardia?&#xA;Can you suspect asystole there between?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iDg4k.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please, do not make diagnoses based on just this picture (which is often the current standard). &#xA;Assume case where you see Time-Frequency of the heart perfectly and where you can see exactly the functioning of pacemaker cells at different frequency levels.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="9943" LastEditDate="2015-01-21T23:32:06.633" LastActivityDate="2015-01-21T23:32:06.633" Title="What is the name of the condition where no pacemaker cells are active in the heart for a short-time?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;electrocardiography&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23454" PostTypeId="2" ParentId="23451" CreationDate="2014-10-25T16:41:55.950" Score="1" Body="&lt;p&gt;No, macroscopically human muscle works by oscillation. This means that when a muscle is contracted (isometric contraction), some fibers alternatively contract through the actin/myosin process while some others relax at the same time. The end result is that the muscle as a whole keeps the same length, although it still does consume energy to stay in that state. That is why you get tired after some time of isometric contraction. To directly answer your question, it means that muscle in isometric contraction state will have some fibers depolarized, and others in resting state at any moment.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-10-25T16:41:55.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23455" PostTypeId="1" CreationDate="2014-10-25T16:46:33.523" Score="1" ViewCount="41" Body="&lt;p&gt;I am working on the solution to a worldwide problem: IBS or chronic diarrhea following a viral gastroenteritis infection. I think I have an answer. The only missing piece to the puzzle I found in a research paper discussing the genetic mutation of the Enterochromaffin cells by a gastroenteritis virus. I believe the paper was from Japan.  I had it, but I lost it.  Any help in finding this paper again would be greatly appreciated.&lt;/p&gt;&#xA;" OwnerUserId="9932" LastEditorUserId="57" LastEditDate="2014-10-25T18:00:04.483" LastActivityDate="2014-10-25T18:00:04.483" Title="Gastroenteritis virus causing mutation of the Enterochromaffin cells" Tags="&lt;neuroscience&gt;&lt;neurotransmitter&gt;&lt;literature&gt;&lt;gastroenterology&gt;&lt;neuromodulation&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23456" PostTypeId="2" ParentId="23453" CreationDate="2014-10-25T16:49:56.037" Score="7" Body="&lt;p&gt;If there are no pacemaker cells active, no muscle contraction will occur. This condition is named asystole. It can be a temporary or definitive condition. Some would call it &quot;extreme bradycardia&quot; in temporary cases, but this is just an euphemism.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Edit:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Ok, so let's try to clear up the confusion a bit. Technically, there is no asystole involved here (not even temporary). This rhythm is regularly irregular (irregular, but has a pattern), while asystole has no pattern by its very nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you are seeing here is not the consequence of low frequency firing from pacemaker cells. The supraventricular extrasystoles (every 3rd QRS complex) are a consequence of early ventricular depolarization not triggered by SA node activity. The P wave that would normally trigger the 3rd complex does in fact occur, but it is synchronous with the abnormal QRS complex, which is why you cannot see it. The compensatory pause is due to lengthening of the hyperpolarized state in pacemaker cells, and is a consequence of the addition of the hidden P wave and the extrasystole in a short time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In conclusion, this pattern is not the result of delayed pacemaker firing, but of&lt;/strong&gt; &lt;strong&gt;&lt;em&gt;early&lt;/em&gt;&lt;/strong&gt; &lt;strong&gt;depolarization of cardiomyocytes by an accessory pacemaker.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/v5lGR.png&quot; alt=&quot;strip with refractory time interval&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have marked on this strip the &lt;strong&gt;maximal&lt;/strong&gt; time interval of SA node hyperpolarization. Depending on when the P wave hidden in the extrasystole occurs, the real time may be shorter than the above interval.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2014-10-26T17:02:23.420" LastActivityDate="2014-10-26T17:02:23.420" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="23458" PostTypeId="1" AcceptedAnswerId="23470" CreationDate="2014-10-25T17:28:44.587" Score="6" ViewCount="148" Body="&lt;p&gt;I have two different papers. One claims that gut motility is reduced by stimulation of the Opioid κ and δ receptors. The receptors are activated by Morphine and certain derivatives, specifically Codeine, Fentanyl, Hydromophone, Methadone, and Oxycodone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second paper claims that gut motility is reduced by blocking the 5-HTb3 receptors.  Antagonists or competitors to the 5-HTb3 receptors being Morphine and certain derivatives.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these two different theories, two different action mechanisms, or am I missing something?&lt;/p&gt;&#xA;" OwnerUserId="9932" LastEditorUserId="57" LastEditDate="2014-10-25T17:30:33.720" LastActivityDate="2018-03-19T13:44:21.670" Title="What controls gut motility?" Tags="&lt;neuroscience&gt;&lt;neurotransmitter&gt;&lt;gastroenterology&gt;&lt;neuromodulation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23460" PostTypeId="2" ParentId="10550" CreationDate="2014-10-25T17:41:19.597" Score="1" Body="&lt;p&gt;At generation 1, the frequencies of $a^-$ is $p=0.35$ and the frequency of $a^+$ if $q=0.65$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming random mating (and no change in allele frequency) after any number of generation is given by $p^2$ (=0.1225), $2pq$ (=0.455) and $q^2$ (=0.4225).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-10-25T17:41:19.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23461" PostTypeId="2" ParentId="23449" CreationDate="2014-10-25T17:43:05.087" Score="1" Body="&lt;p&gt;Judging from the photo, it's an earthworm, some species of Lumbricidae. If the accident happened in India, &lt;a href=&quot;http://www.biodiversitylibrary.org/item/22498#page/251/mode/1up&quot; rel=&quot;nofollow&quot;&gt;this faunistic paper&lt;/a&gt; can be of some help.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastActivityDate="2014-10-25T17:43:05.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23463" PostTypeId="1" AcceptedAnswerId="23506" CreationDate="2014-10-25T17:53:40.060" Score="18" ViewCount="3107" Body="&lt;p&gt;I'm a runner (cross country) and I'm always amazed at how fast Olympic sprinters are. There's a lot of hype about those in the 100-meter dash being the fastest in the world, and we're constantly seeing the 100-meter time dropping. But is there a limit? How fast can human being, propelled only by its own energy (i.e. without any external assistance) run?&lt;/p&gt;&#xA;" OwnerUserId="9458" LastEditorUserId="3624" LastEditDate="2016-05-26T23:11:10.750" LastActivityDate="2016-05-26T23:11:10.750" Title="How fast can a human run?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;biophysics&gt;&lt;human-physiology&gt;&lt;bio-mechanics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23465" PostTypeId="2" ParentId="1506" CreationDate="2014-10-25T19:48:26.217" Score="1" Body="&lt;p&gt;Perhaps you're looking for these hanging inserts, for example: &lt;a href=&quot;http://www.emdmillipore.com/US/en/product/Millicell%C2%AE-Cell-Culture-Inserts,MM_NF-C10504#overview&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;Millicells&quot;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kaKfa.jpg&quot; alt=&quot;example of inserts&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="867" LastActivityDate="2014-10-25T19:48:26.217" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23466" PostTypeId="2" ParentId="23453" CreationDate="2014-10-25T20:03:40.553" Score="1" Body="&lt;p&gt;Bradycardia is a heart rate under 60 beats per minute. Your strip shows a heart rate of ~54 BPM (so, yes, it's bradycardia), and the rhythm is trigeminy. There is no asystole involved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the following rhythm strip, initially it shows supraventricular tachycardia (of &gt;150 BPM). After adenosine administration, a short period of asystole occurs, allowing the SA node to resume it's normal pacemaker rhythm., then resumption of sinus rhythm (at just under 100 BPM). Notice there are **no electrical complexes) during the asystole. It's not a matter &lt;em&gt;different guidelines&lt;/em&gt;. There is no asystole in your rhythm strip.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wv4Nt.jpg&quot; alt=&quot;rhythm strip showing tachycardia, a short period of asystole after adenosine administration, then resumption of sinus rhythm.&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-10-27T05:57:42.863" LastActivityDate="2014-10-27T05:57:42.863" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="23468" PostTypeId="2" ParentId="21241" CreationDate="2014-10-25T20:33:01.227" Score="1" Body="&lt;p&gt;The discussion you linked (&lt;a href=&quot;http://www.ecowalkthetalk.com/blog/2011/03/04/responses-how-effective-are-garbage-enzymes/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) shows that both researchers agree that 'garbage enzymes' are mostly acetic acid or vinegar, with a low pH(3-4). Fresh papayas contain papain, but roughly 2% of the enzyme self-digests per day in aqueous solution. &lt;a href=&quot;http://www.mpbio.com/detailed_info.php?family_key=02101142&amp;amp;country=223&quot; rel=&quot;nofollow&quot;&gt;Bromelain&lt;/a&gt; from pineapples is still active at acidic pH. Like most other proteases, it &lt;a href=&quot;http://download.springer.com/static/pdf/930/art%253A10.1007%252FPL00000936.pdf?auth66=1414266792_a815083294eaccc036b8194b1c9b706a&amp;amp;ext=.pdf&quot; rel=&quot;nofollow&quot;&gt;self-digests&lt;/a&gt; much more rapidly than papain. As a result, any digestive enzymes present when the mixture was made would destroy themselves by the time the mixture matured. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;((Those among you quick at math will note that perhaps 1/5 of the papain activity would remain after ninety days. While true, there's &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC348803/&quot; rel=&quot;nofollow&quot;&gt;evidence&lt;/a&gt; yeast cultures eat gluten for sustenance, and if they can digest gluten they'll digest papain. There's no reason to expect yeast to leave a delicious protein source unused.))&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the solution acquired proteases somehow, they would self-digest under the conditions the 'garbage enzyme' solution is stored at(room temperature, aqueous solution, nothing exotic like formaldehyde, months). The yeast itself by the time the fermentation is complete has died, destroyed by the acetic acid(or ethanol, depending) they created. Any digestive enzymes used by the yeast to dissolve proteins destroy themselves as the mixture matures and the yeast die off. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the mixture starts with no digestive enzymes, there's no mechanism to get appreciable amounts active digestive enzymes. If the mixture does start with digestive enzymes(papaya or pineapple), either the yeast will eat them and then die or they will digest themselves and the yeast will eat the byproducts. Finally, the yeast will die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a vinegar/alcohol blend, depending on how much oxygen is available during the fermentation, and it smells like whatever you put in it. If you used orange peels, it probably smells pretty okay. That's why it cleans. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are anxious to use real live proteases, there are powdered papaya/pineapple/etc powders you could reconstitute in water right before use. They are usually sold as meat tenderizer among other things. There are also blends of enzymes sold for pet urine deodorizing, and general purpose cleaning fluid with bacterial and enzymatic action. Formulating those at home is going to be fairly involved, but if you wanted an enzymatic cleaner you made yourself that's how to do it.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-10-25T20:33:01.227" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="23470" PostTypeId="2" ParentId="23458" CreationDate="2014-10-25T20:51:58.397" Score="4" Body="&lt;p&gt;They are two different mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Opium is arguably one of the oldest herbal medicines, being used as analgesic, sedative and antidiarrheal drug for thousands of years. These effects mirror the actions of the endogenous opioid system and are mediated by the principal μ-, κ- and δ-opioid receptors. In the gut, met-enkephalin, leu-enkephalin, β-endorphin and dynorphin occur in both neurons and endocrine cells. When released, opioid peptides activate opioid receptors on the enteric circuitry controlling motility and secretion. As a result, inhibition of gastric emptying, increase in sphincter tone, induction of stationary motor patterns and blockade of peristalsis ensue. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163293/&quot; rel=&quot;nofollow&quot;&gt;Opioid receptors in the gastrointestinal tract&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Roles of 5-HT in health include control of normal gut motor activity, secretion, and sensation, and regulation of food intake and cell growth. Abnormalities of serotonergic function contribute to symptom genesis in functional bowel disorders, inflammatory and infectious diseases of the gut, emetic responses to varied stimuli, obesity, and dysregulation of cell growth. Therapies acting as agonists or antagonists of 5-HT receptors or that modulate 5-HT reuptake play prominent roles in managing these conditions... &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19765366&quot; rel=&quot;nofollow&quot;&gt;Serotonin and the GI tract&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-10-25T20:51:58.397" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23471" PostTypeId="2" ParentId="23429" CreationDate="2014-10-25T23:00:21.923" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;So in case of Splenectomy (complete surgical removal of the spleen),&#xA;  what would be the fate of red blood cells? Would this cause&#xA;  Polycythemia?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;According to wikipedia none of the side effects are related to red blood cell count (just the quality of those cells).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As splenectomy causes an increased risk of sepsis due to encapsulated&#xA;  organisms (such as S. pneumoniae and Haemophilus influenzae) the&#xA;  patient should receive the pneumococcal conjugate vaccine (Prevnar),&#xA;  Hib vaccine, and the meningococcal vaccine; see asplenia. These&#xA;  bacteria often cause a sore throat under normal circumstances but&#xA;  after splenectomy, when infecting bacteria cannot be adequately&#xA;  opsonized, the infection becomes more severe.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;An increase in blood leukocytes can occur following a&#xA;  splenectomy.&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19331177&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt; The post-splenectomy platelet count may rise to&#xA;  abnormally high levels (thrombocytosis), leading to an increased risk&#xA;  of potentially fatal clot formation. There also is some conjecture&#xA;  that post-splenectomy patients may be at elevated risk of subsequently&#xA;  developing diabetes.&lt;a href=&quot;http://www.labex-grex.com/wp-content/uploads/2013/01/bjh12950.pdf&quot; rel=&quot;nofollow&quot;&gt;4&lt;/a&gt; Splenectomy may also lead to chronic&#xA;  neutrophilia. Splenectomy patients typically have Howell-Jolly&#xA;  bodies&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2141.2008.07155.x/abstract&quot; rel=&quot;nofollow&quot;&gt;5&lt;/a&gt; and less commonly Heinz bodies in their blood smears.&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7082831&quot; rel=&quot;nofollow&quot;&gt;7&lt;/a&gt;&#xA;  Heinz bodies are usually found in cases of G6PD (Glucose-6-Phosphate&#xA;  Dehydrogenase) and chronic liver disease.&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0891552005701598&quot; rel=&quot;nofollow&quot;&gt;8&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Splenectomy&quot; rel=&quot;nofollow&quot;&gt;wikipedia - Splenectomy&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Splenectomy can be recommended by inherited blood diseases (e.g. hereditary spherocytosis, thalassemia, etc...) which cause anaemia due to the destruction of abnormal red blood cells in the spleen. After surgery the RBC count is around normal in these cases, so removing the spleen does not cause polycythemia. If you check &lt;a href=&quot;http://en.wikipedia.org/wiki/Polycythemia&quot; rel=&quot;nofollow&quot;&gt;wikipedia - polycythemia&lt;/a&gt;, splenectomy or other spleen related diseases do not cause polycythemia, while polycythemia can cause enlarged spleen which may be removed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Erythropoiesis and so red blood cell count is regulated by &lt;a href=&quot;http://en.wikipedia.org/wiki/Erythropoietin&quot; rel=&quot;nofollow&quot;&gt;EPO&lt;/a&gt; which is regulated by blood oxygen level, so spleen does not regulate the production of red blood cells directly. Removing the spleen cannot cause upregulation of EPO and so polycythemia. Mean erythrocyte age is increased, so in long term there can be a slight increase of RBC count because of a function loss by old cells, but that is not significant enough to cause disease.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022346810009115&quot; rel=&quot;nofollow&quot;&gt;Partial splenectomy for hereditary spherocytosis: a multi-institutional review&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://www.labex-grex.com/wp-content/uploads/2013/01/bjh12950.pdf&quot; rel=&quot;nofollow&quot;&gt;The spleen and sickle cell disease: the sick(led) spleen&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://journal.frontiersin.org/Journal/10.3389/fphys.2013.00365/full&quot; rel=&quot;nofollow&quot;&gt;Red blood cell vesiculation in hereditary hemolytic anemia&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2007 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0609.2007.00818.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Erythropoietin after a century of research: younger than ever&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1982 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7082831&quot; rel=&quot;nofollow&quot;&gt;Glycosylated hemoglobins (GHb): an index of red cell survival.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To support the speculation that macrophages might also have a function&#xA;  in erythropoiesis in the context of disease and to further&#xA;  characterize their importance in erythropoiesis in vivo, Ramos and&#xA;  colleagues show that macrophages regulate erythroid development in&#xA;  polycythemia vera, β-thalassemia and anemia (Ramos et al., 2013).&#xA;  Chemical depletion of macrophages by clodronate liposome&#xA;  administration prevents mice from recovering from induced anemia,&#xA;  suggesting an essential function of macrophages in promoting stress&#xA;  erythropoiesis in vivo. Conversely, macrophage depletion not only&#xA;  improves the phenotype of polycythemia vera and reverses the&#xA;  pathological aspects of the disease, but also alleviates anemia caused&#xA;  by β-thalassemia. These results propose an important dual role of&#xA;  macrophages in physiological and pathological erythropoiesis in vivo.&#xA;  Both studies suggest that macrophages exert two seemingly&#xA;  contradictory actions on erythropoiesis. On one hand, macrophages are&#xA;  indispensable for stress erythropoiesis in vivo. In their absence&#xA;  erythroid production in the bone marrow and spleen in response to&#xA;  bleeding is impaired. However, macrophages can also be deleterious in&#xA;  the context of polycythemia vera and β-thalassemia, since depletion of&#xA;  macrophages leads to a decreased disease pathology. Moreover, ex vivo&#xA;  cultured human macrophages from polycythemia vera patients promote&#xA;  proliferation of human erythroblasts and diminish differentiation.&#xA;  This suggests a function for macrophages in disease progression since&#xA;  polycythemia vera is characterized by an overactive erythron and&#xA;  excessive erythropoiesis (Ramos et al., 2013). These findings might&#xA;  pave the way to future therapies implementing macrophage depletion in&#xA;  the treatment of erythroid disorders like polycythemia vera and&#xA;  β-thalassemia.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://journal.frontiersin.org/Journal/10.3389/fphys.2014.00009/full&quot; rel=&quot;nofollow&quot;&gt;Review article of macrophages and red blood cells; a complex love story&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Recovery after surgery is about 4-6 weeks. Liver and lymph nodes can take over the functions of the spleen partially. Every blood cell count may be elevated (esp. platelet count). The functions of the spleen are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;storing iron (in the form of ferritin or bilirubin, to protect it from pathogens)&lt;/li&gt;&#xA;&lt;li&gt;storing blood (for the case of blood loss e.g. injury)&lt;/li&gt;&#xA;&lt;li&gt;filtering out damaged or old blood cells (by inherited diseases abnormal red blood cells are removed from blood as well)&lt;/li&gt;&#xA;&lt;li&gt;filtering out phatogens, infected blood cells, etc... (to protect the body from sepsis)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And ofc. a lot of immune cells live there. Therefore in rare cases sepsis can occur after splenectomy immediately, and can cause life threatening conditions.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2001 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0891552005701598&quot; rel=&quot;nofollow&quot;&gt;Infectious complications in asplenic hosts&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;1996 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0891552005703226&quot; rel=&quot;nofollow&quot;&gt;Overwhelming postsplenectomy infection&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1975 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022346875800091&quot; rel=&quot;nofollow&quot;&gt;Immunological studies in the postsplenectomy syndrome&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1995 - &lt;a href=&quot;http://gut.bmj.com/content/36/5/684.abstract&quot; rel=&quot;nofollow&quot;&gt;Preservation of the spleen improves survival after radical surgery for gastric cancer.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19331177&quot; rel=&quot;nofollow&quot;&gt;Effect of splenectomy on antitumor immune system in mice.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22727971&quot; rel=&quot;nofollow&quot;&gt;Thrombocytosis in asplenia syndrome with congenital heart disease: a previously unrecognized risk factor for thromboembolism.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756197/&quot; rel=&quot;nofollow&quot;&gt;Vascular complications after splenectomy for hematologic disorders&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://journal.frontiersin.org/Journal/10.3389/fphys.2014.00009/full&quot; rel=&quot;nofollow&quot;&gt;Review article of macrophages and red blood cells; a complex love story&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Asplenic individuals are compromised not only in their ability to&#xA;  destroy infectious agents, but are at increased risk for death from&#xA;  autoimmune disease, certain tumors, and ischemic heart disease.&#xA;  Enhanced mortality is attributed to lack of phagocytes sequestered in&#xA;  spleen that efficiently engulf and destroy appropriate targets,&#xA;  although related cells are found elsewhere.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2012 - &lt;a href=&quot;http://www.jimmunol.org/content/188/9/4496.full&quot; rel=&quot;nofollow&quot;&gt;SIRPα/CD172a and FHOD1 Are Unique Markers of Littoral Cells, a Recently Evolved Major Cell Population of Red Pulp of Human Spleen&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2011 - &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0023164&quot; rel=&quot;nofollow&quot;&gt;Splenectomy Associated Changes in IgM Memory B Cells in an Adult Spleen Registry Cohort&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The spleen contains immune cells, from which macrophages phagocytose the senescent red blood cells. They degrade the hemoglobin into amino acids, bilirubin and iron. The iron is sent to the blood with transferrin, which can be captured and stored by the spleen or the liver or can be used to build new red blood cells in the red bone marrow. The amino acids can be used to build new proteins or they can be degraded by the liver or the kidney. The bilirubin is transported to the liver where it is conjugated and excreted into the bile. The other parts of the red blood cells are recycled as well. For the macrophages it is easier to do this kind of work if you have a dedicated organ which can help to filter out the cells for destruction, but it is not impossible without it, because macrophages live in other organs/tissues as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Red blood cells can get rid of damaged parts by creating microvesicles so they can elongate their lives. Vesiculation is facilitated by the spleen. These microvesicles can contain hemoglobin as well, and they are captured by the liver.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2004 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15095784&quot; rel=&quot;nofollow&quot;&gt;The red cell revisited--matters of life and death.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2141.2008.07155.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Microvesicles in haemoglobinopathies offer insights into mechanisms of hypercoagulability, haemolysis and the effects of therapy&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2003 - &lt;a href=&quot;http://www.bloodjournal.org/content/101/2/747.long?sso-checked=true&quot; rel=&quot;nofollow&quot;&gt;Hemoglobin loss from erythrocytes in vivo results from spleen-facilitated vesiculation&lt;/a&gt;  &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.mavietonsang.ch/scientifiques/node/26&quot; rel=&quot;nofollow&quot;&gt;RBC Storage&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18564399&quot; rel=&quot;nofollow&quot;&gt;RBC-derived vesicles during storage: ultrastructure, protein composition, oxidation, and signaling components.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The macrophages of the spleen have a remarkable function that enables&#xA;  them to remove unwanted damage from the RBC membrane, leaving the RBC&#xA;  intact (Crosby, 1957; Schnitzer et al., 1972). Removal of these&#xA;  intracellular inclusions seems to occur within the open circulation&#xA;  where the RBC are also checked for their loss of deformability to&#xA;  check for age. To achieve this, RBC must pass through the endothelial&#xA;  slits of the sinus to reenter the blood circulation. During this&#xA;  course, cells that are non-deformable will be removed from the&#xA;  circulation by residential macrophages. In the mean-time all inclusion&#xA;  bodies are also being removed. In splenectomized patients or in&#xA;  patients with a non-functional spleen, phagocytosis of the inclusion&#xA;  bodies fails and results in a retention of a variety of intracellular&#xA;  inclusions within the RBC, such as Howell-jolly bodies (inclusions of&#xA;  nuclear chromatin remnants) (Wilkins and Wright, 2000), Heinz bodies&#xA;  (inclusions of denatured hemoglobin caused by oxidative damage)&#xA;  (Wilkins and Wright, 2000) siderocytes (RBC containing granules of&#xA;  iron that are not part of the cell's hemoglobin) (Wilkins and Wright,&#xA;  2000) and Pappenheimer bodies inclusion bodies formed by phagosomes&#xA;  that have been engulfing excessive amounts of iron (Wilkins and&#xA;  Wright, 2000).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The molecular mechanism that underlies the removal of inclusion bodies&#xA;  is largely unknown. In Willekens et al. (2003) presented an analogy to&#xA;  the removal of Heinz bodies when discussing RBC that lose hemoglobin&#xA;  through vesiculation. Via the process of RBC vesiculation the RBC&#xA;  loses aggregated hemoglobin, which is important to maintain the&#xA;  homeostasis of RBC, increases in density and becomes smaller (Piomelli&#xA;  and Seaman, 1993). It was suggested that this process is also&#xA;  facilitated by the macrophages of the spleen, in which older cells&#xA;  vesiculate more than younger ones. Clearly, macrophages play a pivotal&#xA;  role in the clearance of damaged content from circulating RBC (Crosby,&#xA;  1957; Willekens et al., 2003) and vesiculation is an interesting and&#xA;  plausible mechanism to explain the efficient removal of damaged&#xA;  content while leaving the RBC intact (Wilson et al., 1987). The&#xA;  molecular mechanism by which macrophages in the spleen would be&#xA;  facilitating RBC vesiculation is still unknown.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://journal.frontiersin.org/Journal/10.3389/fphys.2014.00009/full&quot; rel=&quot;nofollow&quot;&gt;Review article of macrophages and red blood cells; a complex love story&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Aged or abnormal red blood cells with exposed phosphatidylserine&#xA;  (PS-RBCs) are cleared from the circulation by splenic macrophages. In&#xA;  asplenic patients, other mononuclear phagocytic cells in tissues and&#xA;  in circulation may function in this capacity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/ajh.21884/full&quot; rel=&quot;nofollow&quot;&gt;Activation of mononuclear phagocytes and its relationship to asplenia and phosphatidylserine exposing red blood cells in hemoglobin E/β-thalassemia patients&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Suicidal death of erythrocytes (eryptosis) is characterized by cell&#xA;  shrinkage, membrane blebbing, activation of proteases, and&#xA;  phosphatidylserine exposure at the outer membrane leaflet. Exposed&#xA;  phosphatidylserine is recognized by macrophages that engulf and&#xA;  degrade the affected cells. Eryptosis is triggered by erythrocyte&#xA;  injury after several stressors, including oxidative stress.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16910766&quot; rel=&quot;nofollow&quot;&gt;Mechanisms and significance of eryptosis.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;CD47 on erythrocytes inhibits phagocytosis through interaction with&#xA;  the inhibitory immunoreceptor signal regulatory protein alpha (SIRPα)&#xA;  expressed by macrophages. Thus, the CD47-SIRPα interaction constitutes&#xA;  a negative signal for erythrocyte phagocytosis. However, we recently&#xA;  reported that CD47 does not only function as a ‘don't eat me’ signal&#xA;  for uptake but can also act as an ‘eat me’ signal. In particular, a&#xA;  subset of old erythrocytes present in whole blood was shown to bind&#xA;  and to be phagocytosed via CD47- SIRPα interactions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/voxs.12038/full&quot; rel=&quot;nofollow&quot;&gt;CD47 functions as a removal marker on aged erythrocytes&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872327/&quot; rel=&quot;nofollow&quot;&gt;Mechanisms tagging senescent red blood cells for clearance in healthy humans&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.haematologica.org/content/97/7/994.short&quot; rel=&quot;nofollow&quot;&gt;Physiologically aged red blood cells undergo erythrophagocytosis in vivo but not in vitro&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1582-4934.2011.01310.x/full&quot; rel=&quot;nofollow&quot;&gt;Human red blood cell aging: correlative changes in surface charge and cell properties&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://link.springer.com/chapter/10.1007/978-1-4614-3461-0_6&quot; rel=&quot;nofollow&quot;&gt;Naturally Occurring Autoantibodies in Mediating Clearance of Senescent Red Blood Cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-25T23:00:21.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23472" PostTypeId="1" CreationDate="2014-10-25T23:08:24.647" Score="1" ViewCount="197" Body="&lt;p&gt;Suppose there is a person that has never used nicotine in any form in his/her life. Why does the person get dizzy after a few &quot;shots&quot; from a cigar(nicotine)? What's the difference between using other plants(e.g. marijuana)?&lt;/p&gt;&#xA;" OwnerUserId="6682" LastActivityDate="2014-10-26T01:19:14.703" Title="What are the reactions in the body that triggers dizziness after cigar(nicotine) smoking in non-smokers?" Tags="&lt;biochemistry&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23473" PostTypeId="2" ParentId="21535" CreationDate="2014-10-25T23:09:46.280" Score="1" Body="&lt;p&gt;My experience that it depends on it. You sleep in cycles, each cycle has about a 90 min duration. I think the quality depends on how many cycles you ended. It seems like you need to sleep more by an interruption.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sleep was recorded on 10 nights in each of seven older subjects (mean&#xA;  age 55) and nine younger normal subjects (mean age 22). The duration&#xA;  of the NREM-REM (non-rapid eye movement—rapid eye movement) sleep&#xA;  cycles was determined, starting from the onset of NREM sleep.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In the older group an intra-individual comparison was made between the&#xA;  mean duration of cycles interrupted by one period of spontaneous&#xA;  wakefulness, within their NREM part, and the duration of intact&#xA;  cycles. The interrupted cycles were found to be on average 20 min&#xA;  longer than the intact ones, despite the mean duration of intervening&#xA;  wakefulness being only 10 min.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In the younger group an intra-individual comparison was made between&#xA;  the mean duration of intact cycles ranked as containing a large amount&#xA;  of stages 3+4 and the mean duration of intact cycles ranked low for&#xA;  stages 3+4. Similar comparisons were made in respect of the amount of&#xA;  stage REM, and also the summed amount of stages 3+4 and REM. The&#xA;  cycles containing higher amounts of stages 3+4, REM, and of 3+4+REM&#xA;  were found to be on average 9, 18 and 18 min longer.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The effect of cycle content on cycle duration was most manifest for&#xA;  the first cycle, and least for the third cycle of the night.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The results demonstrate that whereas there may be an average cycle&#xA;  duration of about 90 min individual cycles are very variable. The&#xA;  contents of a cycle influence its duration, and the onset of the REM&#xA;  period is not a strictly time-locked phenomenon.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1974 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0013469474901692&quot; rel=&quot;nofollow&quot;&gt;Sleep cycle content and sleep cycle duration&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you wake up in the middle of a cycle or if you are interrupted often, then you will be tired. I think what happens by sleeping is much more complex, so this is just a short answer.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-25T23:09:46.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23474" PostTypeId="2" ParentId="21837" CreationDate="2014-10-25T23:32:40.967" Score="1" Body="&lt;p&gt;Every infectous disease works this way: if you had contact with x particles (virus, bacteria, etc...), then you have y% chance to get infected (depends on your immune system, luck, etc...), so it has a distribution. This is called virulence, and it can be measured with ID50 (infectious dose by 50% of subjects) and LD50 (lethal dose by 50% of subjects) values. According to animal studies the LD50 is very low by ebola, so it is highly virulent, but it highly depends on the mode of transmission. So this virulency is compensated by low transmissibility: people infected with ebola, but not showing symptoms release too small amount (or nothing) of the virus to infect others. By &lt;a href=&quot;http://en.wikipedia.org/wiki/Viral_hemorrhagic_fever&quot; rel=&quot;nofollow&quot;&gt;hemorrhagic fever&lt;/a&gt; you bleed out of every hole of your body, and that blood contains a lot of viruses, that's when it can infect others. So this is not a &lt;code&gt;&quot;Don't worry too much; we have the situation under control.&quot;&lt;/code&gt; case, it works this way currently. This can probably change due to mutations.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Symptoms usually begin with a sudden influenza-like stage&#xA;  characterized by feeling tired, fever, pain in the muscles and joints,&#xA;  headache, and sore throat.&lt;a href=&quot;http://en.wikipedia.org/wiki/Ebola_virus_disease&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;[12][13] The fever is usually greater&#xA;  than 38.3 °C (100.9 °F).[14] &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This is often followed by: vomiting, diarrhea and abdominal pain.[13]&#xA;  Shortness of breath and chest pain may occur next along with swelling,&#xA;  headaches and confusion.[13] In about half of cases the skin may&#xA;  develop a maculopapular rash (a flat red area covered with small&#xA;  bumps).[14]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In some cases, internal and external bleeding may occur.&lt;a href=&quot;http://en.wikipedia.org/wiki/Ebola_virus_disease&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt; This&#xA;  typically begins five to seven days after first symptoms.[15] All&#xA;  people show some decreased blood clotting.[14] Bleeding from mucous&#xA;  membranes or from sites of needle punctures is reported in 40–50% of&#xA;  cases.[16] This may result in the vomiting of blood, coughing up of&#xA;  blood, or blood in stool.[17] Bleeding into the skin may create&#xA;  petechiae, purpura, ecchymoses, or hematomas (especially around needle&#xA;  injection sites).[18] There may also be bleeding into the whites of&#xA;  the eyes. Heavy bleeding is uncommon and if it occurs is usually&#xA;  within the gastrointestinal tract.[14][19]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Recovery may begin between 7 and 14 days after the start of&#xA;  symptoms.[13] Death, if it occurs, is typically 6 to 16 days from the&#xA;  start of symptoms and is often due to low blood pressure from fluid&#xA;  loss.&lt;a href=&quot;http://jid.oxfordjournals.org/content/178/3/651.short&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt; In general, the development of bleeding often indicates a&#xA;  worse outcome and this blood loss can result in death.[12] People are&#xA;  often in a coma near the end of life.[13] Those who survive often have&#xA;  ongoing muscle and joint pain, liver inflammation, and decreased&#xA;  hearing among other difficulties.[13]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The time between exposure to the virus and the development of symptoms&#xA;  of the disease is usually 2 to 21 days.&lt;a href=&quot;http://en.wikipedia.org/wiki/Ebola_virus_disease&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;[10] Estimates based on&#xA;  mathematical models predict that around 5% of cases may take greater&#xA;  than 21 days to develop.[11]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;wikipedia - &lt;a href=&quot;http://en.wikipedia.org/wiki/Ebola_virus_disease&quot; rel=&quot;nofollow&quot;&gt;Ebola virus disease&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The LD50 of mouse-adapted EBO-Z virus inoculated into the peritoneal&#xA;  cavity was ~1 virion. Mice were resistant to large doses of the same&#xA;  virus inoculated subcutaneously, intradermally, or intramuscularly.&#xA;  Mice injected peripherally with mouse-adapted or intraperitoneally&#xA;  with non-adapted EBO-Z virus resisted subsequent challenge with&#xA;  mouse-adapted virus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1998 - &lt;a href=&quot;http://jid.oxfordjournals.org/content/178/3/651.short&quot; rel=&quot;nofollow&quot;&gt;A Mouse Model for Evaluation of Prophylaxis and Therapy of Ebola Hemorrhagic Fever&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Although outbreaks of Ebola virus have largely been confined to&#xA;  endemic regions, their high fatality rate, ability to transmit&#xA;  person-to-person, and low lethal infectious dose make Ebola virus a&#xA;  dangerous threat to public health and pose a great risk for&#xA;  researchers working with these viruses as well as health care&#xA;  personnel treating patients during outbreaks. Furthermore, their&#xA;  potential to be developed into aerosolized biological weapons also&#xA;  causes grave concern for their use as a bioterrorism agent ( Bray,&#xA;  2003).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S004268220800603X#bib4&quot; rel=&quot;nofollow&quot;&gt;Protection against lethal challenge by Ebola virus-like particles produced in insect cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Some interesting story about the topic (others were not so lucky):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In 2004, a virologist at USAMRIID was working in a BSL-4 laboratory&#xA;  with mice that had been infected 2 days before with a mouse-adapted&#xA;  variant of the Zaire species of Ebola virus (ZEBOV) (2). The virulence&#xA;  and infectious dose of this variant of ZEBOV are unknown in humans;&#xA;  wild-type virus has a case-fatality rate of up to 90% (3).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The person had been following standard procedure, holding the mice&#xA;  while injecting them intraperitoneally with an immune globulin&#xA;  preparation. While the person was injecting the fifth mouse with a&#xA;  hypodermic syringe that had been used on previous mice, the animal&#xA;  kicked the syringe, causing the needle to pierce the person’s&#xA;  left-hand gloves, resulting in a small laceration. The virologist&#xA;  immediately squeezed the site to force the extravasation of blood.&#xA;  After decontamination of the blue suit in the chemical shower, the&#xA;  injured site was irrigated with 1 liter of sterile water and then&#xA;  scrubbed with povidone-iodine for 10 minutes.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In terms of exposure risk, the needle was presumed to be contaminated&#xA;  with virus-laden blood, although it was suspected that low levels of&#xA;  virus were present on the needle. The animals had not yet manifested&#xA;  signs of infection, and much contamination may have been removed&#xA;  mechanically when the needle pierced the gloves. The local&#xA;  decontamination of the site also reduced potential for infection.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;USAMRIID medical, scientific, and executive staff concluded that the&#xA;  person with potential exposure warranted quarantine in the MCS.&#xA;  Contact plus airborne precautions (gown, gloves, N95 mask, eye&#xA;  protection) were used, with a plan to upgrade to BSL-4 precautions for&#xA;  signs or symptoms of illness. These extra precautions were instituted&#xA;  while the patient was asymptomatic for several reasons: 1) the timing&#xA;  of initial clinical manifestations with regard to potential for&#xA;  shedding virus were not known for this specific isolate in human&#xA;  infection; 2) there was interest in ensuring all infection control&#xA;  procedures were being followed appropriately in advance of clinical&#xA;  illness; and 3) there was interest in reducing any potential&#xA;  confounders, such as a caregiver transmitting a febrile respiratory&#xA;  infection to the patient, which might lead to unnecessary procedures&#xA;  or additional isolation. The person was monitored for routine vital&#xA;  signs; daily laboratory studies (coagulation studies, blood counts,&#xA;  chemistries, viral isolation, D-dimer) and regular physician&#xA;  assessments were performed.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Over the next several days, discussions were held with several&#xA;  internationally recognized filovirus experts regarding potential&#xA;  treatments or postexposure prophylaxis options. Local and state public&#xA;  health officials were also notified. The consensus opinion was that&#xA;  there was no safe, readily available source of immune plasma and&#xA;  little evidence existed to support its use. Emergency investigational&#xA;  new drug (IND) protocols were established for treatment with&#xA;  recombinant nematode protein (rNAPc2) and antisense oligomers, with&#xA;  the intention to consider implementation only if the patient&#xA;  demonstrated evidence of infection.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Ultimately, none of the 5 mice had confirmed viremia at the time of&#xA;  the incident. The patient did not become ill or seroconvert and was&#xA;  discharged after 21 days.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2600302/&quot; rel=&quot;nofollow&quot;&gt;Managing Potential Laboratory Exposure to Ebola Virus by Using a Patient Biocontainment Care Unit&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-26T04:58:02.013" LastActivityDate="2014-10-26T04:58:02.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23475" PostTypeId="2" ParentId="23452" CreationDate="2014-10-26T00:07:21.673" Score="1" Body="&lt;p&gt;I would thoroughly check the literature on the UTR you are interested in, a lot of this has already been done for many  genomic regions since nextgen seq began. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will want to first off use computational prediction algorithms to help guide you in getting a good Candidate list of miRNAs&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The interaction between a miRNA and its target mRNAs is usually studied by co-transfection of a reporter expression vector containing the 3'-UTR region of the mRNA and an inhibitory or precursor molecule for the miRNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, this does not measure the direct and physical interaction between a miRNA and a specific mRNA. To more specifically measure binding you will need to do a ElectroMobility Shift Assay.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a commercial tool which will work well if your just trying to identify it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.activemotif.com/catalog/905/lightswitch-synthetic-mirna-target-reporter-collection&quot; rel=&quot;nofollow&quot;&gt;http://www.activemotif.com/catalog/905/lightswitch-synthetic-mirna-target-reporter-collection&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think there are any other very effective/easy methods. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess you could do something like hybridize it, run the hyb on a gel, pop out the band and seq it&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-10-26T00:56:48.613" LastActivityDate="2014-10-26T00:56:48.613" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23476" PostTypeId="2" ParentId="23080" CreationDate="2014-10-26T00:12:57.143" Score="3" Body="&lt;p&gt;The difference has to do with the concept of &quot;thinning and heading&quot; and how plants respond to abiotic damage. Thinning refers to the removal of a branch or shoot all the way back to the node which it originated from. This is the primary type of pruning used on trees - either to limit growth or to increase the amount of light permeating to lower branches. Late winter is generally the best time to do this, just before the tree breaks dormancy, since plant pathogens are generally less abundant. By pruning in late winter, this also reduces the amount of time that the wound is exposed before the tree begins active growth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In contrast, &quot;heading&quot; refers to the partial removal of a branch, usually 1/2 to 1/3 back to the node.  The purpose of heading is to stimulate shoot growth on the remaining branch - hedges being a primary example. Because new shoots and leaves are desired, heading is usually performed at the height of stem growth (in most climates late spring to early summer). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biologic processes behind this are complex (botanists are just beginning to understand how plant behavior adapts to predation) but in very general terms, plants respond to damage in two ways: by compartmentalizing the wound; and by stimulating growth on the remaining tissue. Many types of woody plants produce latent (or adventitious) buds, which lie dormant within the cambium tissue. Normally these buds are suppressed by auxin hormones produced in the meristem by active shoots. When the meristem is removed (such as through heading the branch), these buds rapidly develop to produce new shoots and leaves. Most species used for hedges are selected because of this ability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So long story short: thinning is best performed in late winter, when the plant will quickly be able to seal off the damage while limiting the production of unwanted water sprouts and suckers. In contrast, heading is usually done in early summer, when the hedge can vigorously produce new growth and fill out any gaps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some resources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://extension.wsu.edu/maritimefruit/Pages/PruningBasics.aspx&quot; rel=&quot;nofollow&quot;&gt;http://extension.wsu.edu/maritimefruit/Pages/PruningBasics.aspx&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://puyallup.wsu.edu/~linda%20chalker-scott/horticultural%20myths_files/Myths/Wound%20sealer.pdf&quot; rel=&quot;nofollow&quot;&gt;http://puyallup.wsu.edu/~linda%20chalker-scott/horticultural%20myths_files/Myths/Wound%20sealer.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9914" LastEditorUserId="9914" LastEditDate="2014-10-26T00:22:50.410" LastActivityDate="2014-10-26T00:22:50.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23477" PostTypeId="1" AcceptedAnswerId="23483" CreationDate="2014-10-26T01:03:26.447" Score="2" ViewCount="278" Body="&lt;p&gt;First off, I'm new to bioinformatics and I am learning about DNA sequencing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say that I knew that a specific region of a genome which contained information about a disease (whether it a person had the disease or not).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would make sense that we would only want to sequence that part of the genome in order to make a detector for this disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would it be possible to 'cut-out' this region of the genome and only sequence that part (so we don't have to sequence the entire thing)? If not, how would we sequence only this part of the genome (it doesn't make sense to sequence the other parts as they don't give us information).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="9936" LastActivityDate="2014-10-26T08:08:34.633" Title="Sequencing a specific region of a genome" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23478" PostTypeId="2" ParentId="23472" CreationDate="2014-10-26T01:19:14.703" Score="1" Body="&lt;p&gt;It's all about the synapses, the places where separate neurons connect to one another. All psychoactive drugs act in some way so as to modulate the signals that are passed from one neuron to another. Nicotine acts by increasing the effect of signals that pass through a particular type of synaptic receptor called nicotinic acetylcholine receptors (they're named after the fact that they're affected by nicotine). The dizziness and other effects of nicotine are caused by this interference with normal neuronal communications.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason why regular users of nicotine don't get dizzy is because they've gained a tolerance to the drug. Tolerance isn't super well understood at the molecular level, but it has been associated with long term changes in the quantities and types of receptors that are present at synapses in certain regions of the brain, it particular the &lt;a href=&quot;http://www.nature.com/nrn/journal/v2/n2/abs/nrn0201_119a.html&quot; rel=&quot;nofollow&quot;&gt;nucleus accumbens&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Marijuana is similar to tobacco, only its main psychoactive component, THC, acts on the cannabinoid receptors.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-10-26T01:19:14.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23479" PostTypeId="2" ParentId="16987" CreationDate="2014-10-26T01:34:41.593" Score="4" Body="&lt;p&gt;Ebola enters the cells most probably using the &lt;a href=&quot;http://en.wikipedia.org/wiki/NPC1&quot; rel=&quot;nofollow&quot;&gt;NPC1 receptor&lt;/a&gt;, which is expressed by all cells. That receptor is important by other viruses as well e.g. by &lt;a href=&quot;http://en.wikipedia.org/wiki/Marburg_virus&quot; rel=&quot;nofollow&quot;&gt;Marburg virus&lt;/a&gt; entry, &lt;a href=&quot;http://www.fasebj.org/cgi/content/meeting_abstract/20/5/A853&quot; rel=&quot;nofollow&quot;&gt;HIV release&lt;/a&gt;, arenavirus entry, etc...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coreceptors are not necessary required, but they can enhance ebola virus entry. Such coreceptors are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/HAVCR1&quot; rel=&quot;nofollow&quot;&gt;TIM-1 (or HAVcr-1)&lt;/a&gt; - expressed mostly by epithelial cells,&lt;/li&gt;&#xA;&lt;li&gt;C-type lectins,&lt;/li&gt;&#xA;&lt;li&gt;β1 integrins,&lt;/li&gt;&#xA;&lt;li&gt;Tyro3 (TAM) family tyrosine kinase receptors - expressed by &lt;a href=&quot;http://en.wikipedia.org/wiki/Lymphopoiesis&quot; rel=&quot;nofollow&quot;&gt;lymphoid cells&lt;/a&gt;,&lt;/li&gt;&#xA;&lt;li&gt;Rab7&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It totally confuses the immune system with moves you can see only in Bruce Lee films e.g. by stimulate the expression of proinflammatory cytokines in the infected cells, so it can cause hemorrhagic fever.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By fighting the virus the &lt;a href=&quot;http://en.wikipedia.org/wiki/Adaptive_immune_system&quot; rel=&quot;nofollow&quot;&gt;adaptive immune system&lt;/a&gt; selects and proliferates the B- and T-cells which are specific to the virus and so B-cells can label the cell-free virus in the blood with antibodies for destruction, while T-cells can kill already infected cells. So if somebody manages to live through the symptoms her/his body will destroy the remaining virus after a few days maybe weeks.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://chandranlab.org/files/Miller_2012_b.pdf&quot; rel=&quot;nofollow&quot;&gt;Filovirus entry into cells – new insights&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315215/&quot; rel=&quot;nofollow&quot;&gt;Filovirus Entry: A Novelty in the Viral Fusion World&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://www.pnas.org/content/108/20/8426.short&quot; rel=&quot;nofollow&quot;&gt;T-cell immunoglobulin and mucin domain 1 (TIM-1) is a receptor for Zaire Ebolavirus and Lake Victoria Marburgvirus&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The gene is part of a 3-member transmembrane receptor kinase receptor&#xA;  family with a processed pseudogene distal on chromosome 15. The&#xA;  encoded protein is activated by the products of the growth&#xA;  arrest-specific gene 6 and protein S genes and is involved in&#xA;  controlling cell survival and proliferation, spermatogenesis,&#xA;  immunoregulation and phagocytosis. The encoded protein has also been&#xA;  identified as a cell entry factor for Ebola and Marburg viruses.&#xA;  [provided by RefSeq, May 2010]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/7301&quot; rel=&quot;nofollow&quot;&gt;TYRO3 protein tyrosine kinase&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Recent studies have revealed that the TAM receptor protein tyrosine&#xA;  kinases — TYRO3, AXL and MER — have pivotal roles in innate immunity.&#xA;  They inhibit inflammation in dendritic cells and macrophages, promote&#xA;  the phagocytosis of apoptotic cells and membranous organelles, and&#xA;  stimulate the maturation of natural killer cells. Each of these&#xA;  phenomena may depend on a cooperative interaction between TAM receptor&#xA;  and cytokine receptor signalling systems. Although its importance was&#xA;  previously unrecognized, TAM signalling promises to have an&#xA;  increasingly prominent role in studies of innate immune regulation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://www.nature.com/nri/journal/v8/n5/full/nri2303.html&quot; rel=&quot;nofollow&quot;&gt;Immunobiology of the TAM receptors&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://jvi.asm.org/content/80/20/10109&quot; rel=&quot;nofollow&quot;&gt;Tyro3 Family-Mediated Cell Entry of Ebola and Marburg Viruses&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We showed previously that Niemann-Pick C1 (NPC1), a lysosomal&#xA;  cholesterol transporter, is required for filovirus entry. Here, we&#xA;  demonstrate that NPC1 is a critical filovirus receptor. Human NPC1&#xA;  fulfills a cardinal property of viral receptors: it confers&#xA;  susceptibility to filovirus infection when expressed in non-permissive&#xA;  reptilian cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22395071&quot; rel=&quot;nofollow&quot;&gt;Ebola virus entry requires the host-programmed recognition of an intracellular receptor.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ebolaviruses cause a severe hemorrhagic fever syndrome that is rapidly&#xA;  fatal to humans and nonhuman primates. Ebola protein interactions with&#xA;  host cellular proteins disrupt type I and type II interferon&#xA;  responses, RNAi antiviral responses, antigen presentation,&#xA;  T-cell-dependent B cell responses, humoral antibodies, and&#xA;  cell-mediated immunity. This multifaceted approach to evasion and&#xA;  suppression of innate and adaptive immune responses in their target&#xA;  hosts leads to the severe immune dysregulation and “cytokine storm”&#xA;  that is characteristic of fatal ebolavirus infection. Here, we&#xA;  highlight some of the processes by which Ebola interacts with its&#xA;  mammalian hosts to evade antiviral defenses.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2014 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867414012938&quot; rel=&quot;nofollow&quot;&gt;Camouflage and Misdirection: The Full-On Assault of Ebola Virus Disease&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2011 - &lt;a href=&quot;http://glycob.oxfordjournals.org/content/21/6/806.short&quot; rel=&quot;nofollow&quot;&gt;Mouse LSECtin as a model for a human Ebola virus receptor&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://online.liebertpub.com/doi/abs/10.1089/jir.2013.0035&quot; rel=&quot;nofollow&quot;&gt;Ebola Virus-Like Particles Stimulate Type I Interferons and Proinflammatory Cytokine Expression Through the Toll-Like Receptor and Interferon Signaling Pathways&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-26T01:34:41.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23480" PostTypeId="1" CreationDate="2014-10-26T01:34:59.283" Score="1" ViewCount="97" Body="&lt;p&gt;My understanding of acute transplant rejection is that donor dendritic cells present donor antigens on MHC1 to host naive CD8+ T-cells resulting in an immune response against the graft. If you match MHC1 complexes between donor and host, wouldn't t-cell activation actually be more likely than the case where MHC1 complexes between donor and host are different? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reasoning: I imagine in the case where MHC1 complexes between donor and host are different that the  t-cell receptor is unable to bind the MHC1 complex in the first place..making the transplant essentially invisible. In the case where MHC1 complex between donor and host are the same, the t-cell receptor would bind the MHC1 complex, and increase the likelihood of an immune response. Given that HLA mismatch is a major cause of transplant rejection, something is wrong with my reasoning. Thoughts?&lt;/p&gt;&#xA;" OwnerUserId="9344" LastActivityDate="2014-12-03T13:26:58.080" Title="Why do physicians try to match HLA complexes for organ transplant?" Tags="&lt;immunology&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23481" PostTypeId="1" CreationDate="2014-10-26T01:40:58.283" Score="3" ViewCount="1174" Body="&lt;p&gt;I'm wondering if there are meant to be differences in DNA methylation between the forward and the reverse strand of the gene? I'm wondering because in primer design for bisulfite pyrosequencing one might only design primers for the forward strand. Should this matter for human/mouse DNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;cheers and thanks in advance for any advice.&lt;/p&gt;&#xA;" OwnerUserId="9937" LastActivityDate="2017-10-17T19:04:52.480" Title="DNA methylation on the forward vs reverse strand?" Tags="&lt;genetics&gt;&lt;transcription&gt;&lt;epigenetics&gt;&lt;dna-methylation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23482" PostTypeId="2" ParentId="23480" CreationDate="2014-10-26T02:35:57.577" Score="0" Body="&lt;p&gt;In short, if a T cell does not find its corresponding MHC 1 complex on a particular cell, its default behavior will be to attack it. Binding to the MHC complex will cause a period of anergy in the bound T cell.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-10-26T02:35:57.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23483" PostTypeId="2" ParentId="23477" CreationDate="2014-10-26T03:49:16.440" Score="1" Body="&lt;p&gt;Yes, it is possible to sequence a specific region of the genome. The method, as you mentioned, is called targeted sequencing. Resequencing is basically sequencing something that has already been sequenced. This means that instead of assembling all of your sequence reads from scratch, you can just align them to the reference sequence (in your case, the entire human genome has been sequenced). Targeted resequencing means you're sequencing a specific region, such as a gene. This requires concentration of the specific DNA you wish to sequence and can be done by PCR amplification (using primers that flank your desired sequence) or hybridisation (using probes complementary to your desired sequence that are fixed to a surface), among other methods. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For information on methods for enriching a DNA sequence, give this a read:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nmeth/journal/v7/n2/abs/nmeth.1419.html&quot; rel=&quot;nofollow&quot;&gt;Mamanova, L. et al. Target-enrichment strategies for next-generation sequencing. Nat. Methods. 7, 111-118 (2010).&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-10-26T08:08:34.633" LastActivityDate="2014-10-26T08:08:34.633" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23484" PostTypeId="2" ParentId="23424" CreationDate="2014-10-26T03:55:17.190" Score="1" Body="&lt;p&gt;It is not airborne, because if it had be we would have a really big problem.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Normal immunocompetent mice are not susceptible to non-adapted&#xA;  filoviruses. There are therefore two strategies available to establish&#xA;  a murine model of filovirus infection: adaptation of the virus to the&#xA;  host or the use of genetically modified mice that are susceptible to&#xA;  the virus. A number of knockout (KO) strains of mice with defects in&#xA;  either their adaptive or innate immunity are susceptible to&#xA;  non-adapted filoviruses. In this study, A129 α/β −/− interferon&#xA;  receptor-deficient KO mice, strain A129 IFN-α/β −/−, were used to&#xA;  determine the lethality of a range of filoviruses, including Lake&#xA;  Victoria marburgvirus (MARV), Zaire ebolavirus (ZEBOV), Sudan&#xA;  ebolavirus (SEBOV), Reston ebolavirus (REBOV) and Côte d’Ivoire&#xA;  ebolavirus (CIEBOV), administered by using intraperitoneal (IP) or&#xA;  aerosol routes of infection. One hundred percent mortality was&#xA;  observed in all groups of KO mice that were administered with a range&#xA;  of challenge doses of MARV and ZEBOV by either IP or aerosol routes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://jmm.sgmjournals.org/content/61/1/8.short&quot; rel=&quot;nofollow&quot;&gt;Lethality and pathogenesis of airborne infection with filoviruses in A129 α/β −/− interferon receptor-deficient mice&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ebola virus disease is not an airborne infection. Airborne spread&#xA;  among humans implies inhalation of an infectious dose of virus from a&#xA;  suspended cloud of small dried droplets.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This mode of transmission has not been observed during extensive&#xA;  studies of the Ebola virus over several decades.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://www.who.int/mediacentre/news/ebola/06-october-2014/en/&quot; rel=&quot;nofollow&quot;&gt;WHO - What we know about transmission of the Ebola virus among humans&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The virulence (ID50, LD50) is unkown for humans, but ebola is considered a highly virulent disease with low LD50 based on the studies with animals.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;INFECTIOUS DOSE: Viral hemorrhagic fevers have an infectious dose of 1&#xA;  - 10 organisms by aerosol in non-human primates Footnote 41.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1997 - &lt;a href=&quot;http://www.phac-aspc.gc.ca/lab-bio/res/psds-ftss/ebola-eng.php&quot; rel=&quot;nofollow&quot;&gt;EBOLAVIRUS - PATHOGEN SAFETY DATA SHEET - INFECTIOUS SUBSTANCES&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Although outbreaks of Ebola virus have largely been confined to&#xA;  endemic regions, their high fatality rate, ability to transmit&#xA;  person-to-person, and low lethal infectious dose make Ebola virus a&#xA;  dangerous threat to public health and pose a great risk for&#xA;  researchers working with these viruses as well as health care&#xA;  personnel treating patients during outbreaks. Furthermore, their&#xA;  potential to be developed into aerosolized biological weapons also&#xA;  causes grave concern for their use as a bioterrorism agent ( Bray,&#xA;  2003).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S004268220800603X#bib4&quot; rel=&quot;nofollow&quot;&gt;Protection against lethal challenge by Ebola virus-like particles produced in insect cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ebola virus is a highly virulent pathogen capable of inducing a&#xA;  frequently lethal hemorrhagic fever syndrome. Accumulating evidence&#xA;  indicates that the virus actively subverts both innate and adaptive&#xA;  immune responses and triggers harmful inflammatory responses as it&#xA;  inflicts direct tissue damage. The host immune system is ultimately&#xA;  overwhelmed by a combination of inflammatory factors and virus-induced&#xA;  cell damage, particularly in the liver and vasculature, often leading&#xA;  to death from septic shock. We summarize the mechanisms of immune&#xA;  dysregulation and virus-mediated cell damage in Ebola virus–infected&#xA;  patients. Future approaches to prevention and treatment of infection&#xA;  will be guided by answers to unresolved questions about interspecies&#xA;  transmission, molecular mechanisms of pathogenesis, and protective&#xA;  adaptive and innate immune responses to Ebola virus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2007 - &lt;a href=&quot;http://www.nature.com/ni/journal/v8/n11/abs/ni1519.html&quot; rel=&quot;nofollow&quot;&gt;Immunopathology of highly virulent pathogens: insights from Ebola virus&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The LD50 of mouse-adapted EBO-Z virus inoculated into the peritoneal&#xA;  cavity was ~1 virion. Mice were resistant to large doses of the same&#xA;  virus inoculated subcutaneously, intradermally, or intramuscularly.&#xA;  Mice injected peripherally with mouse-adapted or intraperitoneally&#xA;  with non-adapted EBO-Z virus resisted subsequent challenge with&#xA;  mouse-adapted virus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1998 - &lt;a href=&quot;http://jid.oxfordjournals.org/content/178/3/651.short&quot; rel=&quot;nofollow&quot;&gt;A Mouse Model for Evaluation of Prophylaxis and Therapy of Ebola Hemorrhagic Fever&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The high virulency is compensated by low transmissibility, that's why it is not a real threat currently for western countries (it is easy to quarantine). The current strain seems to be special, because it has about 100 times higher mutation rate than the old ones. It may mutate into a more transmissable strain, but I think there is not enough data and knowledge available to calculate the risk of such an event.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sequencing of 99 different Ebola isolates from patients in the 2014&#xA;  West African outbreak of Ebola showed the virus to be rapidly&#xA;  mutating,[15] with a mutation rate of 2.0 x 10-3 substitutions per&#xA;  site per year making it as fast changing as seasonal influenza.[16]&#xA;  This is likely to represent rapid adaptation to human hosts as the&#xA;  virus is repeatedly passed from human to human (as opposed to usually&#xA;  being passed between fruit bats and only occasionally crossing over&#xA;  into humans), and may pose challenges for the development of a vaccine&#xA;  to the virus.[17][18]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ebola_virus&quot; rel=&quot;nofollow&quot;&gt;wikipedia - Ebola virus&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Molecular evolutionary analyses for Ebola and Marburg viruses were&#xA;  conducted with the aim of elucidating evolutionary features of these&#xA;  viruses. In particular, the rate of nonsynonymous substitutions for&#xA;  the glycoprotein gene of Ebola virus was estimated to be, on the&#xA;  average, 3.6 x 10(-5) per site per year. Marburg virus was also&#xA;  suggested to be evolving at a similar rate. Those rates were a hundred&#xA;  times slower than those of retroviruses and human influenza A virus,&#xA;  but were of the same order of magnitude as that of the hepatitis B&#xA;  virus. When these rates were applied to the degree of sequence&#xA;  divergence, the divergence time between Ebola and Marburg viruses was&#xA;  estimated to be more than several thousand years ago.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1997 - &lt;a href=&quot;http://mbe.oxfordjournals.org/content/14/8/800.short&quot; rel=&quot;nofollow&quot;&gt;The origin and evolution of Ebola and Marburg viruses.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-26T05:19:51.620" LastActivityDate="2014-10-26T05:19:51.620" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="23485" PostTypeId="2" ParentId="23481" CreationDate="2014-10-26T04:27:58.537" Score="4" Body="&lt;p&gt;In most tissues, close to 100% of DNA methylation occurs at CpG sites. This provides a straightforward mechanism for epigenetic inheritance. Since C and G are complementary, both strands have the CpG site at the same locus and methylation is either present on both strands or on neither. During replication, each daughter DNA molecule inherits a parent strand with the (un)methylated CpG sites. Enzymes can recognise when there is asymmetrical CpG methylation and subsequently methylate the new strand where required. So, for CpG sites, both strands are methylated or not. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In embryonic and induced stem cells, however, ~25% of the total methylation occurs at non-CpG sites (especially CpA). Thus, methylation at a specific locus would only occur on one strand. As far as I know, how/if this methylation pattern is inherited has not yet been elucidated. Furthermore, this type of methylation occurs throughout the chromosome and is particularly high in exons whereas CpG methylation generally occurs upstream of a transcription start site.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-10-26T08:06:50.463" LastActivityDate="2014-10-26T08:06:50.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23486" PostTypeId="2" ParentId="23241" CreationDate="2014-10-26T04:49:36.233" Score="2" Body="&lt;p&gt;I found this safety sheet in the topic. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;SECTION IV – STABILITY AND VIABILITY&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;DRUG SUSCEPTIBILITY: Unknown. S-adenosylhomocysteine hydrolase&#xA;  inhibitors have been found to have complete mortality protection in&#xA;  mice infected with a lethal dose of Ebola virus (30).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;DRUG RESISTANCE: There are no known antiviral treatments available for&#xA;  human infections.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;SUSCEPTIBILITY TO DISINFECTANTS: Ebola virus is susceptible to sodium&#xA;  hypochlorite, lipid solvents, phenolic disinfectants, peracetic acid,&#xA;  methyl alcohol, ether, sodium deoxycholate, 2% glutaraldehyde, 0.25%&#xA;  Triton X-100, β-propiolactone, 3% acetic acid (pH 2.5), formaldehyde&#xA;  and paraformaldehyde, and detergents such as SDS (20, 21, 31-34).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;PHYSICAL INACTIVATION: Ebola are moderately thermolabile and can be&#xA;  inactivated by heating for 30 minutes to 60 minutes at 60ºC, boiling&#xA;  for 5 minutes, gamma irradiation (1.2 x106 rads to 1.27 x106 rads),&#xA;  and/or UV radiation (3, 6, 20, 32, 33).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;SURVIVAL OUTSIDE HOST: The virus can survive in liquid or dried&#xA;  material for a number of days (23). Infectivity is found to be stable&#xA;  at room temperature or at 4°C for several days, and indefinitely&#xA;  stable at -70°C (6, 20). Infectivity can be preserved by&#xA;  lyophilisation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://www.msdsonline.com/resources/msds-resources/free-safety-data-sheet-index/ebola-virus.aspx&quot; rel=&quot;nofollow&quot;&gt;Free Safety Data Sheet Index - Ebola virus&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;However there are no references on the site, so I checked the data provided. According to scientific articles it is trusty, however these articles are related to not the current West African strain, so it can be slightly different.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1982 - &lt;a href=&quot;http://jcm.asm.org/content/16/4/704.short&quot; rel=&quot;nofollow&quot;&gt;Inactivation of Lassa, Marburg, and Ebola viruses by gamma irradiation.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Clinical specimens from patients infected with Lassa, Ebola, or&#xA;  Marburg virus may present a serious biohazard to laboratory workers.&#xA;  We have examined the effects of heat, alteration of pH, and gamma&#xA;  radiation on these viruses in human blood and on the electrolytes,&#xA;  enzymes, and coagulation factors measured in laboratory tests that are&#xA;  important in the care of an infected patient. Heating serum at 60&#xA;  degrees C for 1 h reduced high titers of these viruses to&#xA;  noninfectious levels without altering the serum levels of glucose,&#xA;  blood urea nitrogen, and electrolytes. Dilution of blood in 3% acetic&#xA;  acid, diluent for a leukocyte count, inactivated all of these viruses.&#xA;  All of the methods tested for viral inactivation markedly altered&#xA;  certain serum proteins, making these methods unsuitable for samples&#xA;  that are to be tested for certain enzyme levels and coagulation&#xA;  factors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1984 - &lt;a href=&quot;http://jcm.asm.org/content/20/3/486.short&quot; rel=&quot;nofollow&quot;&gt;Physicochemical inactivation of Lassa, Ebola, and Marburg viruses and effect on clinical laboratory analyses.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ebola, Lassa, Venezuelan equine encephalitis, and Sindbis viruses were&#xA;  dried onto solid surfaces, incubated for various time periods under&#xA;  controlled conditions of temperature and relative humidity, and&#xA;  quantitatively eluted from surfaces, and viral titers in the recovered&#xA;  samples were determined. The viral inactivation kinetics that were&#xA;  obtained indicated that viral resistance to natural inactivation in&#xA;  the dark follows (in decreasing order of stability) alphavirus &gt; Lassa&#xA;  virus &gt; Ebola virus. The findings reported in this study on the&#xA;  natural decay in the dark should assist in understanding the&#xA;  biophysical properties of enveloped RNA viruses outside the host and&#xA;  in estimating the persistence of viruses in the environment during&#xA;  epidemics or after an accidental or intentional release.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://link.springer.com/article/10.1007/s00705-010-0791-0/fulltext.html&quot; rel=&quot;nofollow&quot;&gt;Persistence in darkness of virulent alphaviruses, Ebola virus, and Lassa virus deposited on solid surfaces&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our study has shown that Lake Victoria marburgvirus (MARV) and Zaire&#xA;  ebolavirus (ZEBOV) can survive for long periods in different liquid&#xA;  media and can also be recovered from plastic and glass surfaces at low&#xA;  temperatures for over 3 weeks. The decay rates of ZEBOV and Reston&#xA;  ebolavirus (REBOV) plus MARV within a dynamic aerosol were calculated.&#xA;  ZEBOV and MARV had similar decay rates, whilst REBOV showed&#xA;  significantly better survival within an aerosol.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2010.04778.x/abstract&quot; rel=&quot;nofollow&quot;&gt;The survival of filoviruses in liquids, on solid substrates and in a dynamic aerosol&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-26T05:03:23.287" LastActivityDate="2014-10-26T05:03:23.287" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23487" PostTypeId="2" ParentId="21481" CreationDate="2014-10-26T07:07:01.137" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I'm not an expert in the field, but it seems like there are almost&#xA;  countless ways in which an increased number of cases increases the&#xA;  risk of further exponential growth. It's encouraging to hear that in&#xA;  countries with better healthcare, death rates would likely be much&#xA;  lower, but at this point, isn't it inevitable that the outbreak will&#xA;  run its course as a global pandemic?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't think it is inevitable. The current strain has a high virulency, high mortality, but low transmissibility. It does not infect until the patient shows symptoms, but by most of that time she/he will be unable to move and spread the infection because of the 39°C degree fever. Only the people nursing the patient, e.g. family members, workers in the healthcare system, are in danger. So it spreads slowly compared to other diseases and that's why it is easy to quarantine and prevent. If it does not change attitude due to a mutation or anything else, I think we can avoid a more serious pandemic, at least I hope so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an already existing model for an older strain available here: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2870608/&quot; rel=&quot;nofollow&quot;&gt;Understanding the dynamics of Ebola epidemics&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Scared carriers not yet showing symptoms sneak or force their way&#xA;  across boarders to unaffected regions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I have the impression by listening and reading news, that most of the people know nothing about ebola in Africa, or they don't really care, because they cannot read, or they have bigger problems e.g. starving. For example Sierra Leone is one of the poorest countries in the world. They cannot move so easily, because travel requires money. So I think this is possible, but unlikely. If it happens, the infected person cannot spread the disease fast, because she/he will be unable to move after showing the symptoms. So she/he can be quarantined.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Objects, food, or water touched by the infected go unnoticed until&#xA;  they end up leaving the containment zone.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think in the current case this is unlikely either. But if a food contains virions, it does not necessary cause disease, e.g. microwave oven, or long shipment - usual by fruits like banana - can inactivate it.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If it can jump from bats or monkeys, thousands of infected humans&#xA;  increase points of contact to create vectors into other species,&#xA;  perhaps one that will travel unnoticed far beyond the containment&#xA;  zone.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, it needed 8 changes to fully adapt to guinea pigs. (It was possible to infect these animals, but the outcome was not lethal.) The virions contain 19kb of RNA, and the mutation rate is 2.0 x 10^-3 substitutions per site per year. Now I am not an expert of genetics (I always hated it), but as far as I understand it is possible to rougly estimate the risk based on this data. I guess it would take decades to adapt to another species, so it is not a fast process.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3763195/&quot; rel=&quot;nofollow&quot;&gt;Animal models for Ebola and Marburg virus infections&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Comparative sequence analysis of the complete genomes of the GP-adapted&#xA;  EBOV and wild-type virus showed 8 nucleotide differences, which led to&#xA;  5 amino acid substitutions; single amino acid mutations in NP and L&#xA;  and 3 mutations in VP24 (Volchkov et al., 2000). Using a reverse&#xA;  genetics approach, it was shown that VP24 had a critical role in the&#xA;  pathogenesis and the amino acid changes in VP24 were essential to&#xA;  achieve EBOV virulence in guinea pigs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://www.biomedcentral.com/1471-2180/3/6&quot; rel=&quot;nofollow&quot;&gt;Ebola virus infection inversely correlates with the overall expression levels of promyelocytic leukaemia (PML) protein in cultured cells&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ebola virus belongs to the family of negative strand RNA viruses&#xA;  (Mononegavirales) and together with the Marburg virus are the two&#xA;  known species of the Filoviridae family &lt;a href=&quot;http://www.biomedcentral.com/1471-2180/3/6&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;. Electron microscopy of&#xA;  Ebola virions produced in cell culture have shown them to be&#xA;  pleomorphic, appearing as either 6-shaped, circular or as long&#xA;  filamentous (and sometimes branched) forms with a length up to 14,000&#xA;  nm and a uniform diameter of 80 nm &lt;a href=&quot;http://en.wikipedia.org/wiki/Ebola_virus&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;. The 19 kb single-stranded RNA&#xA;  genome encodes seven viral proteins: the membrane associated (matrix)&#xA;  proteins VP24 and VP40, the viral glycoproteins, GP (that forms the 10&#xA;  nm long peplomers) and sGP (non-structural secreted form), the&#xA;  characteristic helical ribonucleocapsid that consists of the&#xA;  nucleoprotein (NP), VP30, VP35 and the L-protein that forms a&#xA;  RNA-dependent RNA polymerase &lt;a href=&quot;http://www.biomedcentral.com/1471-2180/3/6&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ebola_virus&quot; rel=&quot;nofollow&quot;&gt;wikipedia - Ebola virus&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sequencing of 99 different Ebola isolates from patients in the 2014&#xA;  West African outbreak of Ebola showed the virus to be rapidly&#xA;  mutating,[15] with a mutation rate of 2.0 x 10-3 substitutions per&#xA;  site per year making it as fast changing as seasonal influenza.[16]&#xA;  This is likely to represent rapid adaptation to human hosts as the&#xA;  virus is repeatedly passed from human to human (as opposed to usually&#xA;  being passed between fruit bats and only occasionally crossing over&#xA;  into humans), and may pose challenges for the development of a vaccine&#xA;  to the virus.[17][18]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After months of the same security precautions day in and day out,&#xA;  airport checkpoints, and other points of entry become lazy, and let&#xA;  infected through.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't think security works this way. Btw currently we have the technique to filter out people showing symptoms, for instance with IR detectors looking for elevated body temperature. We have e.g. ELISA for checking IgM or the presence of the virus itself in blood tests. So if these measures are needed, I think we will apply them. Currently they are not needed, according to &lt;a href=&quot;http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/case-counts.html&quot; rel=&quot;nofollow&quot;&gt;CDC&lt;/a&gt; there were only 5 cases outside Africa.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-26T07:07:01.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23488" PostTypeId="1" CreationDate="2014-10-26T08:55:36.037" Score="6" ViewCount="572" Body="&lt;p&gt;After a week of too little sleep, I slept about 12 hours last night to &quot;catch up&quot;. It made me wonder: what is happening physically that signals that I'm done sleeping,  or conversely,  that I need to sleep. I read this question and its answers, which explain how brain waves indicate different sleep stages: &lt;a href=&quot;https://biology.stackexchange.com/q/21177/4200&quot;&gt;Why sleep? No, actually, why wake?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what causes the changes in these brain waves? I'm curious about the mechanism by which my body determines that it needs sleep, and not just a set amount,  but a specific amount based on my previous week's lack of sleep. is it something in my brain or is it a hormone or something else?&lt;/p&gt;&#xA;" OwnerDisplayName="user4200" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-01-16T11:22:30.017" Title="What is happening physically when I get sleepy and when I wake up?" Tags="&lt;sleep&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23489" PostTypeId="1" AcceptedAnswerId="23490" CreationDate="2014-10-26T17:30:51.617" Score="2" ViewCount="1544" Body="&lt;p&gt;Huntington's disease can hit at any age, although it tends to hit middleaged people most often. What is the youngest and oldest person that has exhibited Huntington's?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clarification: By oldest I mean with no prior symptoms until the age. &lt;/p&gt;&#xA;" OwnerUserId="9941" LastActivityDate="2018-02-24T21:50:12.637" Title="Earliest and latest onset of Huntington's Disease(Chorea)?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23490" PostTypeId="2" ParentId="23489" CreationDate="2014-10-26T18:00:56.543" Score="6" Body="&lt;p&gt;Huntington's disease may become symptomatic starting from as low as 2 years old [1] and rarely after 55 years old [2] (yet there is evidence of onset at 65 years old [3] and even more according to newer studies).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mIPmN.png&quot; alt=&quot;Copyright © 2004, The American Society for Experimental NeuroTherapeutics, Inc.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Figure:&lt;/em&gt; Copyright © 2004, The American Society for Experimental NeuroTherapeutics, Inc.&lt;br&gt;&#xA;&lt;sup&gt;Richard H. Myers. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC534940/&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Huntington’s Disease Genetics&lt;/em&gt;&lt;/a&gt;. NeuroRx. Apr 2004; 1(2): 255–262. doi:  10.1602/neurorx.1.2.255. PMCID: PMC534940&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Factors [4]:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;CAG number (65%-71% of the variance in age of onset)&lt;/li&gt;&#xA;&lt;li&gt;siblingship (11%-19%)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] paternal age is negatively associated with age at onset of HD &lt;em&gt;(Huntington's disease)&lt;/em&gt;, particularly among subjects who inherit the mutant gene from grandfathers [5].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Huntington's Disease Society Of America. &lt;em&gt;What is Huntington's Disease (HD)?&lt;/em&gt; Available from &lt;a href=&quot;http://www.hdsa.org/about/our-mission/what-is-hd.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.hdsa.org/about/our-mission/what-is-hd.html&lt;/a&gt; (accessed 26.10.2014)&lt;/li&gt;&#xA;&lt;li&gt;National Institute of Neurological Disorders and Stroke. &lt;em&gt;Huntington's Disease: Hope Through Research&lt;/em&gt; Available from &lt;a href=&quot;http://www.ninds.nih.gov/disorders/huntington/detail_huntington.htm&quot; rel=&quot;noreferrer&quot;&gt;http://www.ninds.nih.gov/disorders/huntington/detail_huntington.htm&lt;/a&gt; (accessed 26.10.2014)&lt;/li&gt;&#xA;&lt;li&gt;Myers RH, Madden JJ, Teague JL, Falek A. &lt;em&gt;Factors related to onset age of Huntington disease.&lt;/em&gt; Am J Hum Genet. 1982 May;34(3):481-8. PMID: 6211092. Full text available from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1685335/&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1685335/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Rosenblatt A, Brinkman RR, Liang KY, Almqvist EW, Margolis RL, Huang CY, Sherr M, Franz ML, Abbott MH, Hayden MR, Ross CA. &lt;em&gt;Familial influence on age of onset among siblings with Huntington disease.&lt;/em&gt; Am J Med Genet. 2001 Jul 8;105(5):399-403. PMID: 11449389. Available from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11449389&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/11449389&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Farrer LA, Cupples LA, Kiely DK, Conneally PM, Myers RH. &lt;em&gt;Inverse relationship between age at onset of Huntington disease and paternal age suggests involvement of genetic imprinting.&lt;/em&gt; Am J Hum Genet. 1992 Mar;50(3):528-35. PMID: 1531729. Full text available from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1684271/&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1684271/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-10-26T18:23:17.547" LastActivityDate="2014-10-26T18:23:17.547" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23492" PostTypeId="2" ParentId="23488" CreationDate="2014-10-26T19:06:31.703" Score="4" Body="&lt;p&gt;During sleep the cerebrospinal fluid clears out the waste products of brains cells. Sleep fragmentation or sleep deprivation can prevent this process, or reduce its efficiency. So I think the accumulation of waste products cause that you have to sleep more after sleep deprivation and extreme sleep deprivation (e.g. by &lt;a href=&quot;http://en.wikipedia.org/wiki/Fatal_familial_insomnia&quot; rel=&quot;nofollow&quot;&gt;fatal insomnia&lt;/a&gt;) can cause death. Low quality sleep and sleep deprivation can cause or worsen both neural (e.g. Alzheimer's disease),  and metabolic diseases (e.g. diabetes mellitus, etc...), so you should avoid it, if you can (I cannot :D).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Daily sleep is regulated by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Circadian_clock&quot; rel=&quot;nofollow&quot;&gt;circadian clock&lt;/a&gt;. Many hormones can affect that clock, e.g. melatonin (dependent on blue light), insulin, etc...  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The conservation of sleep across all animal species suggests that&#xA;  sleep serves a vital function. We here report that sleep has a&#xA;  critical function in ensuring metabolic homeostasis. Using real-time&#xA;  assessments of tetramethylammonium diffusion and two-photon imaging in&#xA;  live mice, we show that natural sleep or anesthesia are associated&#xA;  with a 60% increase in the interstitial space, resulting in a striking&#xA;  increase in convective exchange of cerebrospinal fluid with&#xA;  interstitial fluid. In turn, convective fluxes of interstitial fluid&#xA;  increased the rate of β-amyloid clearance during sleep. Thus, the&#xA;  restorative function of sleep may be a consequence of the enhanced&#xA;  removal of potentially neurotoxic waste products that accumulate in&#xA;  the awake central nervous system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://www.sciencemag.org/content/342/6156/373&quot; rel=&quot;nofollow&quot;&gt;Sleep Drives Metabolite Clearance from the Adult Brain&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://online.liebertpub.com/doi/abs/10.1089/rej.2013.1530&quot; rel=&quot;nofollow&quot;&gt;Sleep Facilitates Clearance of Metabolites from the Brain: Glymphatic Function in Aging and Neurodegenerative Diseases&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;According to the traditional understanding of cerebrospinal fluid&#xA;  (CSF) physiology, the majority of CSF is produced by the choroid&#xA;  plexus, circulates through the ventricles, the cisterns, and the&#xA;  subarachnoid space to be absorbed into the blood by the arachnoid&#xA;  villi. This review surveys key developments leading to the traditional&#xA;  concept. Challenging this concept are novel insights utilizing&#xA;  molecular and cellular biology as well as neuroimaging, which indicate&#xA;  that CSF physiology may be much more complex than previously believed.&#xA;  The CSF circulation comprises not only a directed flow of CSF, but in&#xA;  addition a pulsatile to and fro movement throughout the entire brain&#xA;  with local fluid exchange between blood, interstitial fluid, and CSF.&#xA;  Astrocytes, aquaporins, and other membrane transporters are key&#xA;  elements in brain water and CSF homeostasis. A continuous&#xA;  bidirectional fluid exchange at the blood brain barrier produces flow&#xA;  rates, which exceed the choroidal CSF production rate by far. The CSF&#xA;  circulation around blood vessels penetrating from the subarachnoid&#xA;  space into the Virchow Robin spaces provides both a drainage pathway&#xA;  for the clearance of waste molecules from the brain and a site for the&#xA;  interaction of the systemic immune system with that of the brain.&#xA;  Important physiological functions, for example the regeneration of the&#xA;  brain during sleep, may depend on CSF circulation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://www.biomedcentral.com/content/pdf/2045-8118-11-10.pdf&quot; rel=&quot;nofollow&quot;&gt;A new look at cerebrospinal fluid circulation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sleep fragmentation is present in numerous sleep pathologies and&#xA;  constitutes a major feature of patients with obstructive sleep apnea.&#xA;  A prevalence of metabolic syndrome, diabetes and obesity has been&#xA;  shown to be associated to obstructive sleep apnea. While sleep&#xA;  fragmentation has been shown to impact sleep homeostasis, its specific&#xA;  effects on metabolic variables are only beginning to emerge. In this&#xA;  context, it is important to develop realistic animal models that would&#xA;  account for chronic metabolic effects of sleep fragmentation. We&#xA;  developed a 14-day model of instrumental sleep fragmentation in mice,&#xA;  and show an impact on both brain-specific and general metabolism. We&#xA;  first report that sleep fragmentation increases food intake without&#xA;  affecting body weight. This imbalance was accompanied by the inability&#xA;  to adequately decrease brain temperature during fragmented sleep. In&#xA;  addition, we report that sleep-fragmented mice develop glucose&#xA;  intolerance. We also observe that sleep fragmentation slightly&#xA;  increases the circadian peak level of glucocorticoids, a factor that&#xA;  may be involved in the observed metabolic effects. Our results confirm&#xA;  that poor-quality sleep with sustained sleep fragmentation has similar&#xA;  effects on general metabolism as actual sleep loss. Altogether, these&#xA;  results strongly suggest that sleep fragmentation is an aggravating&#xA;  factor for the development of metabolic dysfunctions that may be&#xA;  relevant for sleep disorders such as obstructive sleep apnea.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2012 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2869.2012.01029.x/full&quot; rel=&quot;nofollow&quot;&gt;Sustained sleep fragmentation affects brain temperature, food intake and glucose tolerance in mice&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2014 - &lt;a href=&quot;http://www.jneurosci.org/content/34/28/9179.extract&quot; rel=&quot;nofollow&quot;&gt;Sirtuin 3: A Molecular Pathway Linking Sleep Deprivation to Neurological Diseases&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Inadequate sleep simultaneously modulates the levels of multiple&#xA;  hormones that govern metabolism, In general, with sleep deprivation,&#xA;  the following hormones are decreased: insulin, growth hormone (GH),&#xA;  growth hormone releasing hormone (GHRH), and leptin levels. In&#xA;  contrast, ghrelin and somatostatin are increased. Essentially,&#xA;  hormones that signal that the body has plenty of energy are decreased,&#xA;  while those that signal energy need are increased. Experiments&#xA;  utilizing knockout animals as well as pharmacological agonists,&#xA;  antagonists, and immunodepletion of the proteins, illustrate that&#xA;  these hormones affect sleep regulation. Diabetic rats have decreased&#xA;  sleep time and consolidation while replacement of insulin increases&#xA;  increases slow-wave sleep.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.google.hu/books?id=yUIIAQAAQBAJ&amp;amp;printsec=frontcover&amp;amp;hl=hu#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;The Genetic Basis of Sleep and Sleep Disorders&lt;/a&gt; (book)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In humans, melatonin is produced by the pineal gland, a small&#xA;  endocrine gland[26] located in the center of the brain but outside the&#xA;  blood–brain barrier. The melatonin signal forms part of the system&#xA;  that regulates the sleep–wake cycle by chemically causing drowsiness&#xA;  and lowering the body temperature, but it is the central nervous&#xA;  system (specifically the suprachiasmatic nuclei, or SCN)[26] that&#xA;  controls the daily cycle in most components of the paracrine and&#xA;  endocrine systems[27][28] rather than the melatonin signal (as was&#xA;  once postulated).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Melatonin#Circadian_rhythm&quot; rel=&quot;nofollow&quot;&gt;wikipedia - melatonin&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-26T19:06:31.703" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23495" PostTypeId="2" ParentId="23403" CreationDate="2014-10-27T03:05:08.867" Score="2" Body="&lt;p&gt;I totally agree with Rumtscho. Kandel's Principles of Neural Science is excellent. Eric Kandel is a Nobel Laureate and one of the gurus in the field. As to the biology of neurons I can refer you to:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Part II: Cell and Molecular Biology of the Neuron, and Part III: Elementary interactions Between Neurons: Synaptic Transmission. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These sections cover the basics petfectly. The following sections bring the reader to higher level of processing in the brain, namely Part IV-IX that cover Cognition-Perception-Movement-Arousal-Development-and Language/Thought, respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it is a nice build-up to exactly the things you are looking for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But as Rumtscho says: it's quite a buy, but worth every penny. I have been using the book for about a decade during my studies as well as beyond.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-10-30T13:32:55.870" LastActivityDate="2014-10-30T13:32:55.870" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="23496" PostTypeId="1" CreationDate="2014-10-27T03:11:40.723" Score="4" ViewCount="1810" Body="&lt;p&gt;I made lemon juice 6 month ago.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I just washed the lemon using brush and then cut them into pieces.&lt;/li&gt;&#xA;&lt;li&gt;Then I put one layer of lemon in the bottle followed by one layer of&#xA;sugar&lt;/li&gt;&#xA;&lt;li&gt;Again one layer of lemon and one layer of sugar.&lt;/li&gt;&#xA;&lt;li&gt;Then I close the bottle and put it in the refrigerator.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;When I opened it, I observed some pink colored mold on the lemon slices.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone can identify the mold or tell me how to identify it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: in the 6 months, I never opened the bottle. The bottle was clean and I did not add water; just lemon and sugar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/glWBw.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MoSb2.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Rllhc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8972" LastEditorUserId="3340" LastEditDate="2014-10-27T09:44:21.947" LastActivityDate="2014-11-18T11:06:41.267" Title="Identify the pink mold infecting refrigerated lemons" Tags="&lt;biochemistry&gt;&lt;microbiology&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2014-11-18T16:26:11.423" ContentLicense="CC BY-SA 3.0" />
  <row Id="23497" PostTypeId="2" ParentId="21986" CreationDate="2014-10-27T03:27:42.033" Score="1" Body="&lt;p&gt;Neural axonal connections are physiologically one-way, in that an action potential would never back propagate. Since the signal is physiologically initiated near the cell body (dendritic input region) the normal flow of information therefore is dendritic-to-axonal. However, when axons are electrically activated (through neural implants such as auditory or sensory prosthetics etc), the signal will propagate both ways, i.e., to the axon terminal, but also to the cell body. It is by means of the ion channel opening-and-closing kinetics that action potentials travel only one way, namely away from the point of initiation. The axon itself is not gated in any way- it has no sense of directionality and sustains both directions.     &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-10-27T03:27:42.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23500" PostTypeId="2" ParentId="23150" CreationDate="2014-10-27T05:31:06.537" Score="8" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Yes, neural connections can be weakened.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Chemical connections between neurons (synapses) can certainly be strengthened or weakened, dependent on their input. Single synapses can undergo long term potentiation (LTP) or long term depression (LTD). As a typical example there are hippocampal neurons. High-frequency (tetanic) electrical stimulation in hippocampal neurons can result in long-term potentiation (strengthening) of synaptic connections in the hippocampus Moreover, when a synapse receives synchronous input from multiple incoming axons they can potentiate each other's responses &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10878/&quot; rel=&quot;nofollow&quot;&gt;(Purves &lt;em&gt;et al&lt;/em&gt;, 2001)&lt;/a&gt;. In contrast, low-frequency stimulation and  prolonged inactivity of synapses in the hippocampus can weaken them &lt;a href=&quot;http://www.annualreviews.org/doi/pdf/10.1146/annurev.ne.19.030196.002253&quot; rel=&quot;nofollow&quot;&gt;(Bear &amp;amp; Abraham, 1996)&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The connection between learning, let alone good and bad as you ask for in your question, is far from clear. However, LTP and LTD do provide plausible mechanisms that could underpin these processes at the cellular level &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10878/&quot; rel=&quot;nofollow&quot;&gt;(Purves &lt;em&gt;et al&lt;/em&gt;, 2001)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.annualreviews.org/doi/pdf/10.1146/annurev.ne.19.030196.002253&quot; rel=&quot;nofollow&quot;&gt;Bear &amp;amp; Abraham, &lt;em&gt;Ann Rev Neurosci&lt;/em&gt; (1996); &lt;strong&gt;19&lt;/strong&gt;: 437-62&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10878/&quot; rel=&quot;nofollow&quot;&gt;Purves &lt;em&gt;et al&lt;/em&gt;., eds. &lt;em&gt;Neuroscience&lt;/em&gt;, 2&lt;sup&gt;nd&lt;/sup&gt; ed., Sunderland (MA): Sinauer Associates; 2001&lt;/a&gt;&lt;/sub&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="19754" LastEditDate="2015-11-03T16:45:50.433" LastActivityDate="2015-11-03T16:45:50.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23501" PostTypeId="2" ParentId="23452" CreationDate="2014-10-27T07:22:46.250" Score="6" Body="&lt;p&gt;There are some tools for predicting the binding:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.targetscan.org/&quot; rel=&quot;nofollow&quot;&gt;TargetScan&lt;/a&gt; (based on seed match [primary], extra pairing, sequence context &lt;sup&gt;&lt;strong&gt;1&lt;/strong&gt;&lt;/sup&gt; — nucleotide composition around the site etc [secondary])&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.microrna.org/microrna/home.do&quot; rel=&quot;nofollow&quot;&gt;miRanda&lt;/a&gt; (based on hybridization stability and seed match[primary] and sequence context [secondary])&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://pictar.mdc-berlin.de/&quot; rel=&quot;nofollow&quot;&gt;PicTar&lt;/a&gt; (adds a layer of evolutionary conservation criteria)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;1&lt;/strong&gt;&lt;/sup&gt; &lt;em&gt;Context means the position of the target site in the 3'UTR and the surrounding nucleotide composition (which is also considered an indirect metric of secondary structure)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;miRanda and TargetScan also have classes called conserved and non-conserved targets. miRanda reports miRSVR scores and TargetScan reports context scores but these measures are based on few experimental results and &lt;strong&gt;may&lt;/strong&gt; not always be meaningful. miRSVR is based on change in target expression upon miRNA overexpression/knockdown. It also uses metrics for target site context. Context+ score of TargetScan includes many metrics which include target abundance and conservation along with the regular context scoring. Some of these metrics may be more useful than the others. But scores based just on miRNA OE/KD experiments can be misleading- especially if target expression is quantified just at the RNA level. Target abundance also varies between different cell types. For more details on these metrics refer to the papers corresponding to these tools.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some experimental procedures for target determination which mainly involve Protein-RNA crosslinking followed by immunoprecipitation of Ago and subsequent quantification by RNA sequencing. See &lt;a href=&quot;http://www.nature.com/nature/journal/v460/n7254/full/nature08170.html&quot; rel=&quot;nofollow&quot;&gt;HITS-CLIP&lt;/a&gt; and &lt;a href=&quot;http://www.cell.com/abstract/S0092-8674%2810%2900245-X&quot; rel=&quot;nofollow&quot;&gt;PAR-CLIP&lt;/a&gt;. These techniques &lt;strong&gt;do not&lt;/strong&gt; really find the targets. All they do is to correlate the levels of miRNA and their predicted targets attached to Ago (you won't exactly know if the ternary &lt;em&gt;mRNA-miRNA-Ago&lt;/em&gt; complex really formed or not). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S009286741300439X&quot; rel=&quot;nofollow&quot;&gt;CLASH&lt;/a&gt; is a more recent technique which tries to address this issue by ligating mRNA with miRNA. This way you can capture the miRNA-mRNA interaction. However, I am a little skeptical of CLASH; I myself was working on this principle some time back and faced this one challenge. CLASH roughly involves the following steps:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Crosslink protein-RNA&lt;/li&gt;&#xA;&lt;li&gt;Immunoprecipitate Ago&lt;/li&gt;&#xA;&lt;li&gt;Use RNAse to digest unbound regions of mRNA (and make it small enough for a short read sequencing experiment)&lt;/li&gt;&#xA;&lt;li&gt;Ligate miRNA and mRNA bound to Ago using RNA ligase&lt;/li&gt;&#xA;&lt;li&gt;Degrade Ago using protease&lt;/li&gt;&#xA;&lt;li&gt;Sequence the miRNA-mRNA ligated pair&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My doubt was how would miRNA and mRNA be ligated when the footprint of Ago is bigger than an miRNA (reported ~50-60 nt in HITS-CLIP and PAR-CLIP). When the RNA is nuclease protected then how can it be accessible to ligase. When I was thinking about it then I thought that a partial protein degradation was necessary (after RNAse step and before ligase step) to give some space for ligase to act. Eventually I did not work on it further. Three years later CLASH paper was published and I was happy that someone made it work. But the ligase issue was not addressed (It seems to have worked but I don't know how!!). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To test the predictions you can use a reporter assay (such as GFP or Luciferase) with the 3'UTR cloned downstream of the reporter. These can have artifacts too. Overexpressing the miRNA should be avoided and seed mutations should be done to ascertain the targetability. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another technique to determine a target mRNA is to mask its predicted miRNA binding site and see the effect on the expression. This has been done in zebrafish using morpholinos complementary to target sites but not on other models AFAIK. This seems to me as an elegant assay- no overexpression and you can precisely determine the target site.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-10-28T05:21:47.790" LastActivityDate="2014-10-28T05:21:47.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23502" PostTypeId="2" ParentId="23421" CreationDate="2014-10-27T08:10:03.253" Score="1" Body="&lt;p&gt;Generally the coating is of poly D-Lysine. Proteases act only on L-amino acids. So, I guess nothing should happen to the usual coated flasks. I have reused the flask even after 2 rounds of trypsinization, and the cells seemed to be fine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your case, the matrix is made of proteins isolated from animal sources. They are susceptible to proteolysis. You are right to assume that these flasks should not be reused. If you have a shortage of flasks then you can buy uncoated petriplates (which are cheaper) and coat them yourself.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-10-27T08:10:03.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23503" PostTypeId="2" ParentId="21986" CreationDate="2014-10-27T09:08:36.853" Score="1" Body="&lt;p&gt;The connection is one way, the input comes in the dendrites, while the output goes on the single axon in the neuron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/49mtc.png&quot; alt=&quot;neuron&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 1 - &lt;a href=&quot;http://en.wikipedia.org/wiki/Neuron&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia - neuron&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The axon of the presynaptic neuron can connect e.g. to the dendrite of a postsynaptic neuron, and so they can form &lt;a href=&quot;http://en.wikipedia.org/wiki/Synapse&quot; rel=&quot;nofollow noreferrer&quot;&gt;synapses&lt;/a&gt; in which they use &lt;a href=&quot;http://en.wikipedia.org/wiki/Neurotransmission&quot; rel=&quot;nofollow noreferrer&quot;&gt;neurotransmitters&lt;/a&gt; to transmit the signal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DbcGp.jpg&quot; alt=&quot;synapse&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 2 - &lt;a href=&quot;http://hplusmagazine.com/wp-content/uploads/neuron_structure2.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;synapse between two neurons&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DNKCI.jpg&quot; alt=&quot;neurotransmission&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 3 - &lt;a href=&quot;http://droualb.faculty.mjc.edu/Course%20Materials/Physiology%20101/Chapter%20Notes/Fall%202011/chapter_8%20Fall%202011.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;neurotransmission&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There can be different targets to an axon, not just dendrites, e.g. &lt;a href=&quot;http://droualb.faculty.mjc.edu/Course%20Materials/Physiology%20101/Chapter%20Notes/Fall%202011/chapter_8%20Fall%202011.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;another axon&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Neuromuscular_junction&quot; rel=&quot;nofollow noreferrer&quot;&gt;muscle cells&lt;/a&gt;, etc...&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-27T09:08:36.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23504" PostTypeId="2" ParentId="23150" CreationDate="2014-10-27T09:13:56.810" Score="3" Body="&lt;p&gt;What you are talking about called &lt;a href=&quot;http://en.wikipedia.org/wiki/Synaptic_plasticity&quot; rel=&quot;nofollow&quot;&gt;synaptic plasticity&lt;/a&gt;, and sure it is possible to weaken connection between neurons, that's why for instance you can forget things.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In neuroscience, synaptic plasticity is the ability of synapses to&#xA;  strengthen or weaken over time, in response to increases or decreases&#xA;  in their activity.&lt;a href=&quot;http://en.wikipedia.org/wiki/Synaptic_plasticity&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt; Plastic change also results from the alteration&#xA;  of the number of neurotransmitter receptors located on a synapse.&lt;a href=&quot;http://en.wikipedia.org/wiki/Synaptic_plasticity&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;&#xA;  There are several underlying mechanisms that cooperate to achieve&#xA;  synaptic plasticity, including changes in the quantity of&#xA;  neurotransmitters released into a synapse and changes in how&#xA;  effectively cells respond to those neurotransmitters.[3] Synaptic&#xA;  plasticity in both excitatory and inhibitory synapses has been found&#xA;  to be dependent upon postsynaptic calcium release.&lt;a href=&quot;http://en.wikipedia.org/wiki/Synaptic_plasticity&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt; Since memories&#xA;  are postulated to be represented by vastly interconnected networks of&#xA;  synapses in the brain, synaptic plasticity is one of the important&#xA;  neurochemical foundations of learning and memory.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Synaptic_plasticity&quot; rel=&quot;nofollow&quot;&gt;wikipedia - synaptic plasticity&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-27T09:13:56.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23505" PostTypeId="2" ParentId="23496" CreationDate="2014-10-27T09:30:43.737" Score="-1" Body="&lt;p&gt;I checked &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_citrus_diseases&quot; rel=&quot;nofollow&quot;&gt;citrus diseases&lt;/a&gt; on wikipedia, then &quot;ctrl+f&quot; and typed in &quot;pink mold&quot;. The result was &lt;a href=&quot;http://en.wikipedia.org/wiki/Clonostachys_rosea_f._rosea&quot; rel=&quot;nofollow&quot;&gt;Gliocladium roseum&lt;/a&gt; which is really a pink mold, but it is hard to find any image of it, where it is on fruits... So this is just a guess. Btw. I think it is rarely possible to identify microorganisms just by checking an image of them.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-27T09:30:43.737" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23506" PostTypeId="2" ParentId="23463" CreationDate="2014-10-27T10:36:33.027" Score="23" Body="&lt;p&gt;An older answer that &lt;a href=&quot;https://biology.stackexchange.com/a/9740/3624&quot;&gt;referred to the physiological feats of ancient humans&lt;/a&gt;, and why &lt;a href=&quot;http://www.independent.co.uk/news/science/modern-man-a-wimp-says-anthropologist-1802501.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;modern humans are wimps&lt;/a&gt; made me look up a couple of papers on running speeds a while ago. One of the examples used to support the statement that modern humans are &quot;wimps&quot; is a study of ancient fossilized footprints from Australia, which claim that the individuals making the footprints were running close to Olympic record times. The footprint studies (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0047248407000322&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Webb. 2007. Further research of the Willandra Lakes fossil footprint site, southeastern Australia. Journal of Human Evolution 52(6)&quot;&gt;Webb, 2007&lt;/a&gt;) basically attempts to describe the humans that have created the footprint paths, and also tries to calculate the speeds they were running at. For one of the individuals (T8), the estimated running speed is 37 km/h (i.e. 10.3 m/s). The interpretation by Peter McAllister in his book &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0733623913&quot; rel=&quot;nofollow noreferrer&quot;&gt;Manthropology&lt;/a&gt; seems to be (I haven't read the book) that these barefoot individuals running on mud could easily have outrun current day sprinters, especially with training and on a rubber track (also see this &lt;a href=&quot;http://www.huffingtonpost.com/peter-mcallister/pre-modern-man_b_836265.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;huffintonpost article&lt;/a&gt; on the book). If the estimates in &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0047248407000322&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Webb. 2007. Further research of the Willandra Lakes fossil footprint site, southeastern Australia. Journal of Human Evolution 52(6)&quot;&gt;Webb (2007)&lt;/a&gt; are close to accurate, it would seem that modern top-trained athletes might not have reached the edge of what is humanly possible when it comes to top speeds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also a biomechanical study on potential human running speeds (&lt;a href=&quot;http://jap.physiology.org/content/108/4/950.full-text.pdf+html&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Weyand et al. 2010. The biological limits to running speed are imposed from the ground up. Journal of Applied Physiology 108(4)&quot;&gt;Weyand et al., 2010) &lt;/a&gt;that you will probably find interesting. This paper looks at factors such as gait, stance, force application etc, and includes empirically estimated values from 10 subjects to discuss the limits to human speed. They conclude that (natural) human speeds are likely to be limited to ~50 km/h (as reference: &lt;a href=&quot;http://io9.com/the-physics-of-usain-bolts-world-record-100-meter-dash-924744818&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bolt's top speed&lt;/a&gt; during his 9.58 WR was ~44 km/h).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Consequently, human running speeds in excess of 50 km/h are likely to be limited to the&#xA;  realms of science fiction and, not inconceivably, gene doping.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They also look at different scenarios and e.g. point out how important limb length is for top speed: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Second, limbs lengthened through evolution or perhaps prosthetically could&#xA;  substantially increase the top running speed attained at the minimum period of foot-ground force application. For example, a relatively small increase in leg length of 10 cm would&#xA;  increase contact lengths by 9 cm and the top speeds of the subjects tested here from 9.1 to 9.8 m/s.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In general, important factors for maximum speed in animals are &lt;a href=&quot;http://en.wikipedia.org/wiki/Ground_reaction_force&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;ground  reaction force&lt;/em&gt;&lt;/a&gt; and &lt;em&gt;ground contact time&lt;/em&gt;. An earlier study by &lt;a href=&quot;http://jap.physiology.org/content/89/5/1991&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Weyand et al. 2002. Faster top running speeds are achieved with greater ground forces not more rapid leg movements. Journal of Applied Physiology 89(5): 1991-1999&quot;&gt;Weyand et al. (2002)&lt;/a&gt; also show how faster human runners in general have shorter ground contact times compared to slower runners. As a sidenote, this seems to be in contrast to cheetahs, which have longer ground contact times than greyhounds, while still being much faster (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22723482&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Hudson et al. 2012. High speed galloping in the cheetah (Acinonyx jubatus) and the racing greyhound (Canis familiaris): spatio-temporal and kinetic characteristics. J Exp Biol. 15&quot;&gt;Hudson et al. 2012&lt;/a&gt; and &lt;a href=&quot;http://www.rvc.ac.uk/SML/Projects/CheetahGalloping.cfm&quot; rel=&quot;nofollow noreferrer&quot;&gt;popular summary&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;View these as a couple of interesting examples and a starting point. This is not my area, and I do not know the literature well.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-10-30T15:16:27.257" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23507" PostTypeId="2" ParentId="23421" CreationDate="2014-10-27T10:54:02.720" Score="0" Body="&lt;p&gt;You should check the composition of the coating by using trypsin, e.g. poly-L-lysine or poly-D-lysine are usually applied:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Polymers of both D- and L-lysine are used to coat solid surfaces.&#xA;  Poly-L-lysine has been reported to improve the protein coating of&#xA;  ELISA plates. 6,7 However, in culture applications, certain cells can&#xA;  digest poly-L-lysine. In this situation, poly-D-lysine should be used&#xA;  as the attachment factor so that the cells are not disrupted by&#xA;  excessive uptake of L - lysine. The lower molecular weight&#xA;  poly-D-lysine (30,000 - 70,000) is easier to use because it is less&#xA;  viscous in solution, but the higher molecular weight poly-lysine&#xA;  (&gt;300,000) provides more attachment sites per molecul e. The molecular&#xA;  weight poly-D-lysine often preferred by users is the 70,000 - 150,000.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Product_Information_Sheet/1/p6407pis.pdf&quot; rel=&quot;nofollow&quot;&gt;Poly-D-lysine Hydrobromide&lt;/a&gt; - Sigma&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Trypsin does not seem like to hydrolise poly-D-lysine. Roughly it is specific to L-Lys and L-Arg, so if your coating contains these amino acids (in your case it does), than it will be degraded.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Trypsin (EC3.4.21.4) is part of the serine protease family. Trypsin&#xA;  cleaves lysine and arginine at the C-terminal side of the peptide. The&#xA;  hydrolysis rate is slower if an acidic residue is on either sides of&#xA;  the cleavage site and no cleavage occurs if a proline residue is on&#xA;  the carboxyl side of the cleavage site. Trypsin optimum pH is pH-7 to&#xA;  9. Trypsin will also hydrolyze ester and amide linkages of synthetic derivatives of amino acids such as: benzoyl L-arginine ethyl ester&#xA;  (BAEE), p-toluenesulfonyl- L-arginine methyl ester (TAME),&#xA;  tosyl-L-arginine methyl ester, N-α-benzoyl-L-arginine p-nitroanilide&#xA;  (BAPNA), L-lysyl-p-nitroanilide, and benzoyl-L-tyrosine ethyl ester&#xA;  (BTEE). Serine protease inhibitors that inhibit recombinant trypsin&#xA;  include TLCK (N-p-tosyl-L-lysine chloromethyl ketone), PMSF&#xA;  (phenylmethanesulfonyl fluoride), benzamidine, soybean trypsin&#xA;  inhibitor, and ovomucoid.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.prospecbio.com/Trypsin_Human_Yeast_10_222/&quot; rel=&quot;nofollow&quot;&gt;Trypsin Human, Yeast&lt;/a&gt; - ProSpec, or Sigma &lt;a href=&quot;http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/analytical-enzymes/trypsin.html#Specificity&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After incubation with 1mg/mL trypsin solution at 37°C for 1h, neither&#xA;  PLL nor PDL was found to be hydrolyzed, as indicated by the constant&#xA;  number of molecules found on the surface. The reason is that the&#xA;  entire polylysine chain was adsorbed to the surface, and steric&#xA;  hindrance and electrostatic repulsion prevented trypsin molecules from&#xA;  approaching the cleavange sites. To make polylysine exposed and&#xA;  available to trypsin digestion, a DSU SAM surface was created. A&#xA;  uniform coating of 5nm chromium and 30nm gold was first introduced on&#xA;  the slides. On top of that metal coating, an amine-active&#xA;  cross-linker, DSU SAM, was formed to covalently immobilize&#xA;  AF532-PLL/PDL molecules. After the free peptide molecules were&#xA;  removed, the slide was incubated with 1mg/mL trypsin at 37°C for 1h.&#xA;  The trypsin and cut polylysine fragments were then thorougly washed&#xA;  off. Intact PLL and PDL molecules had similar fluorescence intensities&#xA;  and surface number densities before trypsin was introduced. However,&#xA;  it is clear that trypsin digested PLL but not PDL. From over 30 images&#xA;  of different areas of the slides, for PLL the average numbers of&#xA;  molecules counted were 227±16 and 0 per frame before and after&#xA;  hydrolysis, respectively. In contrast, the corresponding numbers for&#xA;  PDL were 241±15 and 234±20 per frame, respectively. As explained in&#xA;  Emil Fisher's analogy of the lock and key, the L-isomer can fit the&#xA;  active site of trypsin bettern than the D-isomer. One reason is that&#xA;  only the L-isomer undergoes a coil to α-helix transition upon binding&#xA;  with the enzyme, while the D-isomer remains disordered.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://books.google.hu/books?id=qGZMh-9I2FkC&amp;amp;printsec=frontcover&amp;amp;hl=hu#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Applications of single-molecule detection in early disease diagnosis and enzymatic reaction study&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So the result depends on the type of the coating. Btw. I think the easiest way to decide would be to check it with an experiment. (Note that I know nothing about coatings, just trypsin.)&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-27T11:09:17.337" LastActivityDate="2014-10-27T11:09:17.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23508" PostTypeId="1" AcceptedAnswerId="23510" CreationDate="2014-10-27T11:24:15.730" Score="8" ViewCount="1387" Body="&lt;p&gt;One particular codon codes only for one amino acid, but an amino acid can be coded for by several different codons. Now according to the genetic code, the codon &lt;code&gt;UUU&lt;/code&gt; codes for the amino acid phenylalanine and &lt;code&gt;UUA&lt;/code&gt; codes for leucine. But, according to the Wobble Hypothesis, the base on the third position of the codon and that on the anticodon need not be complementary (which helps explain why there are very few types of tRNA molecules, inspite of there being 61 codons). If this hypothesis is true, then we could have a phenylalanine placed in a position which was meant to be for leucine, and vice versa (since the codons coding for them differ only in their third base). The same holds true for pairs like aspartic acid &amp;amp; glutamic acid and serine &amp;amp; arginine. So how does translation of a particular mRNA molecule result in the right polypeptide sequence?&lt;/p&gt;&#xA;" OwnerDisplayName="user9950" LastEditorUserId="22057" LastEditDate="2016-05-31T20:27:48.220" LastActivityDate="2016-07-16T14:50:22.953" Title="Redundancy of the genetic code" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;translation&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23509" PostTypeId="2" ParentId="23480" CreationDate="2014-10-27T11:27:54.620" Score="1" Body="&lt;p&gt;Cells with low MHC1 or non-recognizable MHC1 are destroyed by &lt;a href=&quot;http://en.wikipedia.org/wiki/Natural_killer_cell&quot; rel=&quot;nofollow&quot;&gt;NK cells&lt;/a&gt;, so e.g. viral infections, intracellular bacterial infections and cancer cells cannot hide with their &quot;abnormal&quot; proteins...&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-27T11:37:50.403" LastActivityDate="2014-10-27T11:37:50.403" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23510" PostTypeId="2" ParentId="23508" CreationDate="2014-10-27T12:05:37.803" Score="5" Body="&lt;p&gt;Wobble pairing is just a phenomenon and not a hard and fast rule. There are some justifications for why it should exist and that is why it is still called a hypothesis. And this statement is not true:&quot;&lt;em&gt;the base on the third position of the codon and that on the anticodon need not be complementary&lt;/em&gt;&quot;. The anticodon residue corresponding to the third residue of codon can be a &lt;em&gt;promiscuous&lt;/em&gt; base which can pair with two or many different bases.  The tRNA for Phenylalanine has an anticodon - &lt;code&gt;GAA&lt;/code&gt; which can pair with both &lt;code&gt;UUU&lt;/code&gt; and &lt;code&gt;UUC&lt;/code&gt; but not &lt;code&gt;UUA&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the statement of wobble hypothesis is that the first base of the anticodon (often is a modified/atypical nucleobase) can show promiscuity of binding.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-10-27T12:11:33.077" LastActivityDate="2014-10-27T12:11:33.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23511" PostTypeId="1" AcceptedAnswerId="23639" CreationDate="2014-10-27T13:12:24.580" Score="2" ViewCount="97" Body="&lt;p&gt;According to book Life Ascending: The Ten Great Inventions o Evolution.&#xA;(Lane, N.;2010), &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Motility has indeed transformed life on earth in ways that are not&#xA;  immediately apparent, from the complexity of ecosystems.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As I understand it, when animals had begun to actively use their bodies to locate resources and thus left the sedentary way of life the amount of information they received has increased exponentially. It induced the rapid evolution of additional physiological, morphological and behavioural adaptations such as specialized brain regions enabling spatial memory, vision or cognition⁠.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Was &lt;strong&gt;sociality&lt;/strong&gt; also additional adaption induced by motility?&#xA;&lt;strong&gt;Is sociality as a life strategy present only in mobile animal species, or they exist also a social sedentary organisms?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Working definition of sociality&lt;/em&gt;: Forming of animal group where information transfer enable cooperation among individuals.&lt;/p&gt;&#xA;" OwnerUserId="8500" LastEditorUserId="8500" LastEditDate="2014-10-27T15:56:31.440" LastActivityDate="2014-11-01T12:31:55.277" Title="Does sociality evolved before or after the ability of motility?" Tags="&lt;evolution&gt;&lt;adaptation&gt;&lt;sociality&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23512" PostTypeId="1" CreationDate="2014-10-27T14:14:22.200" Score="1" ViewCount="1334" Body="&lt;p&gt;How do the quantities of ATP formed during aerobic and anaerobic respiration compare? &lt;/p&gt;&#xA;" OwnerUserId="9951" LastEditorUserId="1306" LastEditDate="2014-10-27T15:30:20.743" LastActivityDate="2014-10-27T15:30:20.743" Title="How do the quantities of ATP formed during aerobic and anaerobic respiration compare?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-10-27T20:45:18.530" ContentLicense="CC BY-SA 3.0" />
  <row Id="23513" PostTypeId="2" ParentId="23208" CreationDate="2014-10-27T14:21:34.493" Score="7" Body="&lt;p&gt;Obviously, as you point out, some birds, such as waterbirds (ducks, puffins, auks, sandpipers) are perfectly fine in the rain, as they spend much of their time in the water anyhow and have oil glands that waterproof their feathers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For other birds, rain can increase heat loss. For instance, rain increases metabolism by up to 22% in eagles (&lt;a href=&quot;http://www.esajournals.org/doi/abs/10.2307/1942594&quot;&gt;Stalmaster &amp;amp; Gessaman, 1984&lt;/a&gt;), although the actual impact on average daily metabolism was 'negligible'. However, eagles were able to feed their offspring only half as much, and therefore had only half as many eaglets, when it rained (&lt;a href=&quot;https://sora.unm.edu/node/54147&quot;&gt;Elliott et al., 2005&lt;/a&gt;). (On the other hand, the authors point out that in the Tropics, eagles actually do better when it rains because there is more food available).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Migrating birds stop migrating, hide where they can, and wait until it dries up before they continue (&lt;a href=&quot;http://cat.inist.fr/?aModele=afficheN&amp;amp;cpsidt=13709895&quot;&gt;Erdi et al, 2002&lt;/a&gt;); those that don't, often end up far away from where they should be and, eventually, dead. In short, some birds don't mind the rain (e.g. seabirds), others sit it out in misery (e.g. nesting eagles) and others hunker down wherever they can find shelter (e.g. migrating birds).&lt;/p&gt;&#xA;" OwnerUserId="9952" LastEditorUserId="3624" LastEditDate="2014-10-28T08:59:27.373" LastActivityDate="2014-10-28T08:59:27.373" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23515" PostTypeId="2" ParentId="23512" CreationDate="2014-10-27T15:06:53.623" Score="3" Body="&lt;p&gt;You means fermentation and respiration? &#xA;In aerobic,1 mol glucose trough respiration and get about 38 ATP&#xA;In anaerobic, 1 mol glucose through fermentaion and get 2 ATP&lt;/p&gt;&#xA;" OwnerUserId="9029" LastActivityDate="2014-10-27T15:06:53.623" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23516" PostTypeId="2" ParentId="21821" CreationDate="2014-10-27T16:38:02.710" Score="3" Body="&lt;p&gt;First, when asking about a specific small term, it's best to check your spelling.  If you actually look at the sentience, you will note that you left out a very important hyphen:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pellequer compared several propensity scale methods using a dataset of&#xA;  14 &lt;strong&gt;epitope-annotated proteins&lt;/strong&gt;. [emphasis added]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The phrase means that the protein sequences (amino acid sequence) has the &lt;a href=&quot;https://en.wikipedia.org/wiki/Epitope&quot; rel=&quot;nofollow&quot;&gt;epitopes&lt;/a&gt; marked on them.  If you look at the &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/007668799103010E&quot; rel=&quot;nofollow&quot;&gt;cited paper&lt;/a&gt;, you will see the various tables and break downs of determined epitopes.  Pellequer's group did a lot of the early work when people were still working on techniques to &quot;map&quot; out the locations of epitopes (which are often not in linear segments of the protein sequence due to the protein structure).&lt;/p&gt;&#xA;" OwnerUserId="3971" LastActivityDate="2014-10-27T16:38:02.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23522" PostTypeId="1" CreationDate="2014-10-27T19:25:59.080" Score="2" ViewCount="1881" Body="&lt;p&gt;Note- I considered asking this on gardening.stackexchange.com but i believe it is better suited for this site since it deals with more complicated material. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I understand it, certain plants (&lt;em&gt;Camellia sinensis&lt;/em&gt;, &lt;em&gt;Coffea&lt;/em&gt;, etc.) grow best at higher altitudes. What factor, biologically speaking, is responsible for this? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that the oxygen concentration at higher altitudes is lower, is this the reason?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, is it possible to use machinery to alter the gas concentrations in a grow room and simulate the effects of high altitudes? Are there any other factors such as pressure or anything that can also be altered? Would simulating this environment be practical for large scale applications?&lt;/p&gt;&#xA;" OwnerUserId="1904" LastEditorUserId="16866" LastEditDate="2016-01-11T20:17:33.620" LastActivityDate="2016-01-11T20:17:33.620" Title="Is it possible to simulate the effects of high altitudes for plants?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;&lt;environment&gt;&lt;growth&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23523" PostTypeId="1" AcceptedAnswerId="23532" CreationDate="2014-10-27T22:15:34.460" Score="3" ViewCount="11377" Body="&lt;p&gt;By definition from Wikipedia, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hamming_distance&quot; rel=&quot;nofollow&quot;&gt;Hamming distance&lt;/a&gt; between two strings of equal length is the number of positions at which the corresponding symbols are different. In other words, it is the number of substitutions required to transform one string into another. Given two strings of equal length, compute the Hamming distance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to find the how many differences there are between two strings, say we have two DNA strings A and B:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;A = TGACCCGTTATGCTCGAGTTCGGTCAGAGCGTCATTGCGAGTAGTCGTTTGCTTTCTCAAACTCC &#xA;B = GAGCGATTAAGCGTGACAGCCCCAGGGAACCCACAAAACGTGATCGCAGTCCATCCGATCATACA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Throw them to two arrays A and B. Therefore, If &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;(= count 0)&#xA;(cond&#xA;   [(symbol=? A[1] B[1]) /do nothing just move on to the next pair of string] &#xA;   [else (add1 count)] ;; counter:= counter + 1; &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;output would be the counter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this the right logic flow to go with this problem? Any suggestion to write this on python or Scheme?&lt;/p&gt;&#xA;" OwnerUserId="9958" LastEditorUserId="6307" LastEditDate="2014-10-28T03:56:11.627" LastActivityDate="2014-10-28T05:50:09.017" Title="Hamming distance between two DNA strings" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23524" PostTypeId="2" ParentId="6966" CreationDate="2014-10-27T23:00:11.157" Score="10" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;The mechanism of action of serotonin-specific reuptake inhibitors, a commonly-prescribed class of antidepressants, is a downregulation of 5HT1A receptors through negative feedback. This downregulation of receptors takes time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.nhs.uk/conditions/SSRIs-(selective-serotonin-reuptake-inhibitors)/Pages/Introduction.aspx&quot; rel=&quot;nofollow&quot;&gt;Serotonin-specific reuptake inhibitors (SSRIs)&lt;/a&gt; are a class of antidepressants &lt;a href=&quot;http://www.uptodate.com/contents/depression-treatment-options-for-adults-beyond-the-basics&quot; rel=&quot;nofollow&quot;&gt;commonly prescribed to treat depression&lt;/a&gt;. Their therapeuric effects may need weeks of treatment &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC446220/&quot; rel=&quot;nofollow&quot;&gt;(Celada, 2004)&lt;/a&gt;, which can be explained by their action on 5HT1A receptors in the dendritic region of the serotoninergic neurons in the raphe nucleus. By blocking &lt;a href=&quot;https://en.wikipedia.org/wiki/Serotonin&quot; rel=&quot;nofollow&quot;&gt;serotonin (5HT)&lt;/a&gt; reuptake, negative feedback mechanisms cause the 5HT1A receptors to downregulate. This downregulation of the presynaptic modulatory 5HT1A receptors changes the firing pattern of the serotonergic neuron into a more fluttering mode, so that it releases more 5HT &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S089662730700623X/pdfft?md5=f8c0c9b791272a8f57fc804aa31f2f21&amp;amp;pid=1-s2.0-S089662730700623X-main.pdf&quot; rel=&quot;nofollow&quot;&gt;(Duman, 2007)&lt;/a&gt;. More 5HT makes you feel better. That is how it fits into the monoaminergic hypothesis. To have the 5HT1A receptors respond this way takes time, as it is an adaptive response that downregulates of 5HT1A receptors, &lt;em&gt;i.e.&lt;/em&gt;, less receptors are present on the cell's membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is only an expanation of delayed action of SSRIs, a specific subclass of antidepressants. For example, there are newer classes of antidepressants that seem to work faster (5HT4 action) &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S089662730700623X/pdfft?md5=f8c0c9b791272a8f57fc804aa31f2f21&amp;amp;pid=1-s2.0-S089662730700623X-main.pdf&quot; rel=&quot;nofollow&quot;&gt;(Duman, 2007)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC446220/&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;-&lt;/strong&gt; Celada &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;J Psychiatry Neurosci&lt;/em&gt; (2004); &lt;strong&gt;29&lt;/strong&gt;(4): 252–65&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S089662730700623X/pdfft?md5=f8c0c9b791272a8f57fc804aa31f2f21&amp;amp;pid=1-s2.0-S089662730700623X-main.pdf&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;-&lt;/strong&gt; Duman, &lt;em&gt;Neuron&lt;/em&gt; (2007); &lt;strong&gt;55&lt;/strong&gt;(5): 712-25&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-10-31T12:15:44.510" LastActivityDate="2016-10-31T12:15:44.510" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="23525" PostTypeId="1" AcceptedAnswerId="23534" CreationDate="2014-10-28T03:30:30.640" Score="7" ViewCount="387" Body="&lt;p&gt;Is it just by viruses or are there other means by which it gets into cells, such as plasmid uptake?&lt;/p&gt;&#xA;" OwnerUserId="8991" LastActivityDate="2014-10-28T10:39:56.550" Title="How exactly can dsRNA be introduced to a cell?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;microbiology&gt;&lt;virology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23526" PostTypeId="1" AcceptedAnswerId="23531" CreationDate="2014-10-28T03:36:19.430" Score="3" ViewCount="287" Body="&lt;p&gt;C. elegans can self fertilize, or they can mate with males. But are they able to mate with females? Or is there some kind of morphological barrier that prevents that?&lt;/p&gt;&#xA;" OwnerUserId="8991" LastActivityDate="2014-10-28T07:10:33.230" Title="If hermaphrodite C. elegans can reproduce with females?" Tags="&lt;genetics&gt;&lt;reproduction&gt;&lt;species&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23530" PostTypeId="1" CreationDate="2014-10-28T05:31:18.610" Score="6" ViewCount="5124" Body="&lt;p&gt;I'm wondering for how long a raven can stay continuously airborne, if strained to do so? If it makes a difference, I'm mostly interested in the Common raven, &lt;em&gt;Corvus corax&lt;/em&gt;. Are there for instance any information on long-distance dispersal (wind-blown individuals over sea?) that can be used to roughly estimate this? Information on other corvid species could also be interesting, as a rough proxy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are wondering, my motivation for asking is the biblical story in Genesis 6&amp;ndash;8 (the deluge of Noah). Here, Noah sends out a raven and a dove to look for land. From the story it appears as if the raven can stay airborne for a longer time than the dove, which returns to the ark to rest. Is there any realism in the claim that a raven can stay airborne for one or maybe even two weeks?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some background from Genesis 8 (&lt;a href=&quot;http://en.wikipedia.org/wiki/The_Living_Torah_and_Nach&quot; rel=&quot;noreferrer&quot;&gt;this translation&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After forty days, Noah opened the window he had made in the ark. He sent out the raven, and it departed. It went back and forth until the water had dried up from the land's surface. He then sent out the dove to see if the water had subsided from the land's surface. The dove could not find any place to rest its feet, and it returned to him, to the ark. There was still water over all the earth's surface. [Noah] stretched out his hand, and brought it to him in the ark. He waited another seven days, and once again sent the dove out from the ark. The dove returned to him toward evening, and there was a freshly-plucked olive leaf in its beak. Noah then knew that the water had subsided from the earth. He waited yet another seven days and sent out the dove [again]. This time it did not return to him any more.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So the raven couldn't find a place to land, and it flew around until it could do so. A week later, the dove still couldn't find a place to land, but a week later it could. Thus, either (a)&amp;nbsp;the raven was flying around for more than a week (as much as two weeks) or (b)&amp;nbsp;the raven could more readily land in a wet area than the dove. Can either of these be true?&lt;/p&gt;&#xA;" OwnerUserId="988" LastEditorUserId="3624" LastEditDate="2014-10-28T23:21:34.017" LastActivityDate="2019-06-27T14:16:22.063" Title="For how long can a raven stay airborne (a week or more)?" Tags="&lt;ethology&gt;&lt;ornithology&gt;&lt;flight&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="23531" PostTypeId="2" ParentId="23526" CreationDate="2014-10-28T05:49:18.603" Score="5" Body="&lt;p&gt;Since only the male tail is equipped with various specialized sensory and copulatory structures that enable him to locate the vulva and successfully inseminate the hermaphrodite.  Hermaphrodites can self-fertilize, but only males can cross-fertilize a hermaphrodite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;sources: &lt;a href=&quot;http://www.wormbook.org/chapters/www_maledevelopment/maledevelopment.html&quot;&gt;Wormbook: Male development&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK20094/&quot;&gt;C. elegans II (2nd edition): Sexual Dimorphism&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-10-28T07:10:33.230" LastActivityDate="2014-10-28T07:10:33.230" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23532" PostTypeId="2" ParentId="23523" CreationDate="2014-10-28T05:50:09.017" Score="3" Body="&lt;p&gt;Your logic on the problem seems correct. The wikipedia article about the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hamming_distance&quot; rel=&quot;nofollow&quot;&gt;Hamming distance&lt;/a&gt; describes both a python and a C &lt;a href=&quot;http://en.wikipedia.org/wiki/Hamming_distance#Algorithm_example&quot; rel=&quot;nofollow&quot;&gt;implementations&lt;/a&gt;. The python version assumes two strings of equal length:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;def hamming_distance(s1, s2):&#xA;    #Return the Hamming distance between equal-length sequences&#xA;    if len(s1) != len(s2):&#xA;        raise ValueError(&quot;Undefined for sequences of unequal length&quot;)&#xA;    return sum(ch1 != ch2 for ch1, ch2 in zip(s1, s2))&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="9099" LastActivityDate="2014-10-28T05:50:09.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23534" PostTypeId="2" ParentId="23525" CreationDate="2014-10-28T10:39:56.550" Score="5" Body="&lt;p&gt;Besides viral infections there are different pathways for cells to take up dsRNA. Inside the cells these dsRNA are processed by &lt;a href=&quot;http://en.wikipedia.org/wiki/Dicer&quot;&gt;Dicer&lt;/a&gt; which processes these RNAs into &lt;a href=&quot;http://en.wikipedia.org/wiki/Small_interfering_RNA&quot;&gt;small interfering RNA&lt;/a&gt;, which play an important role in the regulation of gene activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These pathways have mostly been researched in Drosophila and C. elegans, I am indicating where evidence for them in humans is available. The different possibilities for the uptake are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Uptake via transmembrane proteins:&lt;/strong&gt; In &lt;em&gt;C. elegans&lt;/em&gt; two different transmembrane proteins have been discovered which passively transport&#xA;dsRNA into the cells. They are called SID-1 and SID-2 (systemic RNA-interference defective protein), at least for&#xA;SID-1 a homologue exists in humans as well. These receptors are important for the uptake of systemic (produced by the own organism) dsRNA. See references 1-3 for&#xA;details.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Uptake via Endocytosis:&lt;/strong&gt; In drosophila cells active transport happens through the scavenger receptors SR-CI and Eater. They bind&#xA;the dsRNA and are then internalized. Knockdown of these genes&#xA;inhibited the import of dsRNA and inhibited the endocytosis mediated&#xA;knockdown of genes. This process seems to be evolutionary conserved,&#xA;as knockdown of the orthologous genes in C. elegans led to similar&#xA;results. This mechanism seems to be more important for the uptake of environmental dsRNA. See references 4 and 5 for more details.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Uptake via Phagocytosis:&lt;/strong&gt; At least for drosophila, there is evidence for a phagocytosis mediated uptake mechanism, which is&#xA;independent of endocytosis. See reference 6 for details.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;References&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21474576&quot;&gt;SID-1 is a dsRNA-selective dsRNA-gated channel.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488460/&quot;&gt;Uptake of extracellular double-stranded RNA by SID-2&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://download.bioon.com.cn/upload/month_0807/20080706_43c204a48553dce6acc28uzoFiKHYHz4.attach.pdf&quot;&gt;RNA interference: a mammalian SID-1 homologue enhances siRNA uptake&#xA;and gene silencing efficacy in human cells.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16862146&quot;&gt;The endocytic pathway mediates cell entry of dsRNA to induce RNAi&#xA;silencing.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jbc.org/content/281/20/14370.full&quot;&gt;Double-stranded RNA Is Internalized by Scavenger Receptor-mediated&#xA;Endocytosis in Drosophila S2 Cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21559499&quot;&gt;A phagocytic route for uptake of double-stranded RNA in RNAi&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-28T10:39:56.550" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23535" PostTypeId="2" ParentId="23388" CreationDate="2014-10-28T11:15:59.350" Score="1" Body="&lt;p&gt;It is part of the CNS and does &lt;em&gt;not&lt;/em&gt; secrete hormones into the bloodstream. Instead, it delivers input to the pituitary gland, which is an endocrine organ and secretes hormones into the bloodstream. Please refer to &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Hypothalamus&quot; rel=&quot;nofollow&quot;&gt;http://en.m.wikipedia.org/wiki/Hypothalamus&lt;/a&gt; and specifically the section &quot;Neural Connections&quot;. Otherwise, any basic neuroscience or endocrinology textbook covers this under hypothalamic-pituitary axis or the likes. Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-10-28T11:50:16.147" LastActivityDate="2014-10-28T11:50:16.147" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23538" PostTypeId="2" ParentId="10397" CreationDate="2014-10-28T12:41:26.087" Score="2" Body="&lt;p&gt;Consciousness is a difficult term to grasp in a short answer, and the question is as interesting as it is challenging. The reticular formation as mentioned by others before me is crucial, as the thalamus is the gateway of information to and from the brain. Therefore, subcortical structures such as the thalamus, when 'shut down', induce unconsciousness. Mircea Steriade &lt;a href=&quot;http://m.brodmannarea.info/readings/steriade-rtn-2005.pdf&quot; rel=&quot;nofollow&quot;&gt;(2005)&lt;/a&gt; has an excellent review on this and he is a leader in the field the field of sleep and absence epilepsy, thalamo-cortical interactions and consciousness. He describes there the cortical responses seen in the EEG during sleep: the sleep spindles, or related spike-and-wave discharges (SWDs) seen in the EEG during absence epileptic seizures, where patients temporarily loose consciousness. Sleep spindles and SWDs are highly synchronized responses that basically block out sensory input and cortical output. The blocking of sensory input and blocking of output to the body may be regarded as a loss of consciousness, as one is not able to sense the environment or undertake action in response to environmental stimuli (e.g., &lt;a href=&quot;http://nucleus.med.upatras.gr/NU/images/stories/physiology/articles/K_2000_CNP.pdf)&quot; rel=&quot;nofollow&quot;&gt;Kostopoulus (2000)&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, since the question is what part of the brain needs to shut down, it is technically the neocortex, as the neocortex holds the key to being aware of one's surroundings, i.e., processing of sensory input as well as driving motor neurons to move, talk and respond to stimuli &lt;a href=&quot;http://en.wikipedia.org/wiki/Neocortex&quot; rel=&quot;nofollow&quot;&gt;(see wiki page on neocortex)&lt;/a&gt;. So the end organ mainly associated with consciousness is the neocortex - as described in a review paper by Nobel laureate sir Francis Crick &lt;a href=&quot;http://authors.library.caltech.edu/40352/1/148.pdf&quot; rel=&quot;nofollow&quot;&gt;(1990)&lt;/a&gt;. The authors also indicate the thalamus and other structures as possible sites involved, but principally it is the neocortex. I hope this helps you a bit further.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-10-29T02:45:40.247" LastActivityDate="2014-10-29T02:45:40.247" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23539" PostTypeId="2" ParentId="8361" CreationDate="2014-10-28T12:54:55.307" Score="0" Body="&lt;p&gt;Another lead are sleep spindles, closely related to the RTN as mentioned before. Basically the thalamus enters a state of high-frequency firing to a low-frequency synchronous one, thereby taking the cortex with it. Sleep spindles are slow-wave potentials as apparent on the EEG that block out the normal flow of peripheral sensory information from thalamus to cortex. Basically this leads to a loss of consciousness as one is unaware of its environment. A similar thing occurs during absence epileptic seizures, where patients temporarily loose consciousness as marked by paroxysmal slow-wave EEG activity interrupting the high-frequency EEG associated with consciousness &lt;a href=&quot;http://nucleus.med.upatras.gr/NU/images/stories/physiology/articles/K_2000_CNP.pdf&quot; rel=&quot;nofollow&quot;&gt;Kostopaulus (2000)&lt;/a&gt;. Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-10-29T02:39:30.537" LastActivityDate="2014-10-29T02:39:30.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23540" PostTypeId="2" ParentId="21710" CreationDate="2014-10-28T13:01:42.763" Score="2" Body="&lt;p&gt;I think only b.) is true.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;a. I cannot find evidence that maltose is toxic to yeasts (and I would hardly believe it, because it is a glucose dimer), however I found evidence, that yeasts might need the presence of oxygen to process maltose.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;1977 - &lt;a href=&quot;http://mic.sgmjournals.org/content/106/2/277.short&quot; rel=&quot;nofollow&quot;&gt;The Requirement of Oxygen for the Utilization of Maltose, Cellobiose and D-Galactose by Certain Anaerobically Fermenting Yeasts (Kluyver Effect)&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;1994 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8012592&quot; rel=&quot;nofollow&quot;&gt;Effects of oxygen limitation on sugar metabolism in yeasts: a continuous-culture study of the Kluyver effect.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;b. Alcoholic fermentation is an anaerob process, so it won't work in the presence of oxygen.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;c. Alcoholic fermentation is for creating energy. Proteins are normally not involved as substrate (maybe by gluconeogenesis, but that's another story). If the yeast grows, then there is enough protein available to build fermentation enzymes as well.&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;d. I found some articles about the temperature dependency of alcoholic fermentation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Juices fermented at 10°C exhibited ethanol concentrations between 7.4&#xA;  and 13.4% and populations of K. apiculata, C. stellata and C. krusei&#xA;  in the range 106-108 cells/ml.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1988 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.1988.tb04312.x/abstract&quot; rel=&quot;nofollow&quot;&gt;The effects of temperature and pH on the growth of yeast species during the fermentation of grape juice&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At low temperatures, alcohol yield was higher. Secondary metabolites&#xA;  to alcoholic fermentation increased as the temperature increased.&#xA;  Glycerol levels were directly affected by temperature.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2003 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0168160502001447&quot; rel=&quot;nofollow&quot;&gt;Effects of fermentation temperature on the strain population of Saccharomyces cerevisiae&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The immobilized yeast showed an important operational stability&#xA;  without any decrease of its activity even at low temperatures (1−12&#xA;  °C). Specifically, at 6 °C the biocatalyst favored wine production&#xA;  within 8 days, which is less time than is required for the natural&#xA;  fermentation of grape must.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2001 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jf000942n&quot; rel=&quot;nofollow&quot;&gt;Wine Production Using Yeast Immobilized on Apple Pieces at Low and Room Temperatures&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It seems like low temperature does not necessary have an adverse effect, but this could depend on strain.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;e. Just the same as the previous answer. I think the main fermentation products will be always ethanol in the yeasts chosen for alcoholic fermentation (if the other conditions are right), so it is not temperature dependent in this case. A growing yeast will produce alcohol on both low and high temperatures. The ratio of ethanol and the byproducts can depend on the temperature, but not the presence of the ethanol itself. By too low or too high temperature the yeast will die or will stop to grow. (My experience that CO2 production is faster by high temperature, so it is because everything is faster or because the ethanol/CO2 ratio is lower.) An example of temperature dependence by wine making:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Temperature control is vital in the production of fine table wines as:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;High temperatures encourage the loss of alcohol and aroma and flavour compounds due to volatilisation. If the temperature goes above&#xA;  30 -35ºC, the yeast becomes sluggish and fermentation may stop.&lt;/li&gt;&#xA;  &lt;li&gt;Low temperatures will lead to a poor extraction of colour and tannins in red wines and can also cause sluggish fermentations and the&#xA;  production of high levels of ethyl acetate.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.wineskills.co.uk/winemaking/winemaking-knowledge-base/managing-alcoholic-fermentation&quot; rel=&quot;nofollow&quot;&gt;Managing the alcoholic fermentation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I think &quot;sluggish&quot; means stop growing in this case, and ofc. stop fermenting due to the death of the yeast cells.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-10-28T13:08:01.990" LastActivityDate="2014-10-28T13:08:01.990" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23541" PostTypeId="2" ParentId="23530" CreationDate="2014-10-28T14:32:09.173" Score="8" Body="&lt;p&gt;Can't be very sure about ravens but the maximum recorded flight duration is of Common Swift — &lt;a href=&quot;https://doi.org/10.1016/j.cub.2016.09.014&quot; rel=&quot;nofollow noreferrer&quot;&gt;10 months&lt;/a&gt;.&#xA;Alpine swifts also remain airborne for up to &lt;a href=&quot;http://dx.doi.org/10.1038/ncomms3554&quot; rel=&quot;nofollow noreferrer&quot;&gt;6 months&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pigeons can fly up to 1800km in a long flight. From &lt;a href=&quot;http://jeb.biologists.org/content/199/1/21.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; article (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9317262&quot; rel=&quot;nofollow noreferrer&quot;&gt;pubmed&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the United States, the longest pigeon races involve flights of 1800&#xA;  km and, because substantial financial rewards accrue to the owner of&#xA;  the fastest pigeon, there is severe selection for those pigeons that&#xA;  home the fastest.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Wikipedia article on pigeons says that they can fly at &lt;code&gt;80km/h&lt;/code&gt; but I suspect because the other wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_birds_by_flight_speed&quot; rel=&quot;nofollow noreferrer&quot;&gt;flight speeds&lt;/a&gt; says that average flight speed of peregrine falcon is &lt;code&gt;65-90km/h&lt;/code&gt;. So assuming that average speed of pigeon is &lt;code&gt;60km/h&lt;/code&gt; it should be able to fly for &lt;code&gt;30&lt;/code&gt;h. According to &lt;a href=&quot;http://jeb.biologists.org/content/49/3/527.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; paper, the speed with minimum power consumption is &lt;code&gt;8-9m/s (~30km/h)&lt;/code&gt;. At this speed they should be able to fly for 60 hours. In the same paper it is estimated that the maximum continuous power output is &lt;code&gt;~10.5 W&lt;/code&gt;; if a pigeon has &lt;code&gt;11g&lt;/code&gt; of stored fat (per 400g body weight — &lt;em&gt;assumptions from the same paper&lt;/em&gt;), and given the calorific value of fat — &lt;code&gt;38kJ/g&lt;/code&gt;, it can fly upto &lt;code&gt;38 × 11 ÷ 10.5 = ~40h&lt;/code&gt;. This means that the best trained ones can perhaps manage to fly for 2.5 days straight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now ravens are heavier (~3 times heavier) but are more aerodynamic and can fly faster. However, I guess they cannot perhaps fly 7 days straight.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2019-06-27T14:16:22.063" LastActivityDate="2019-06-27T14:16:22.063" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="23542" PostTypeId="1" CreationDate="2014-10-28T16:45:00.277" Score="5" ViewCount="7248" Body="&lt;p&gt;Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fish scales are dermally derived, specifically in the mesoderm. This&#xA;  fact distinguishes them from reptile scales paleontologically.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So aren't reptilia scales also dermally derived?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="3624" LastEditDate="2014-10-29T13:35:35.513" LastActivityDate="2019-08-05T18:31:56.760" Title="Are fish and reptilian scales homologous?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;development&gt;&lt;reptile&gt;&lt;scales&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23543" PostTypeId="1" CreationDate="2014-10-28T17:09:05.690" Score="4" ViewCount="120" Body="&lt;p&gt;I wonder whether developing deadly toxins in the organism's body is always or usually a defensive strategy rather than a by-product.&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="3703" LastEditDate="2014-10-28T22:42:47.673" LastActivityDate="2014-12-29T08:04:52.220" Title="Poisonous plants, animals, mushrooms: is this always a kind of defense?" Tags="&lt;evolution&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23545" PostTypeId="1" CreationDate="2014-10-28T17:46:29.247" Score="2" ViewCount="1995" Body="&lt;p&gt;Besides cooperativity between multiple active sites on an enzyme, what are the other reasons for the Eadie-Hofstee plot to be non-linear?&lt;/p&gt;&#xA;" OwnerUserId="9956" LastEditorUserId="4747" LastEditDate="2014-11-08T04:00:10.830" LastActivityDate="2014-11-14T00:02:19.313" Title="Why would an Eadie-Hofstee Plot be non-linear?" Tags="&lt;biochemistry&gt;&lt;enzyme-kinetics&gt;" AnswerCount="2" CommentCount="1" ClosedDate="2015-02-14T04:58:48.550" ContentLicense="CC BY-SA 3.0" />
  <row Id="23546" PostTypeId="2" ParentId="23542" CreationDate="2014-10-28T18:35:28.650" Score="8" Body="&lt;p&gt;No, fish scales are &lt;a href=&quot;https://en.wikipedia.org/wiki/Dermal_bone&quot; rel=&quot;nofollow&quot;&gt;dermal (= formed in derma) bones&lt;/a&gt; like &lt;a href=&quot;https://en.wikipedia.org/wiki/Skull_roof&quot; rel=&quot;nofollow&quot;&gt;skull roof&lt;/a&gt; bones. Scales in reptiles are formed by epidermis and are made primarily of protein (from &lt;a href=&quot;https://en.wikipedia.org/wiki/Keratinocyte&quot; rel=&quot;nofollow&quot;&gt;keratinocytes&lt;/a&gt;), being similar in derivation to hair, feather and nails.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, in reptiles one must differentiate between scales and osteoderms (= scutes). Scutes are widespread among reptiles and they &lt;em&gt;are&lt;/em&gt; similar to fish scales in that they are produced in derma and are ossified. Similar structures are found in some amphibians and in armadillo. Nevertheless, different types of osteoderms are currently &lt;a href=&quot;http://www.jstor.org/stable/1564085&quot; rel=&quot;nofollow&quot;&gt;considered as converges&lt;/a&gt;: &quot;it is essential to recognize that osteoderms represent non-homologous structures that have been independently evolved a number of times&quot; and have no direct homology with fish scales.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-10-29T11:21:33.280" LastActivityDate="2014-10-29T11:21:33.280" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="23547" PostTypeId="2" ParentId="23545" CreationDate="2014-10-28T19:37:05.350" Score="0" Body="&lt;p&gt;On Eadie-Hofstee plot, you can draw enzyme activity changes for example inhibition in a linear form:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/f2Kd0.jpg&quot; alt=&quot;inhibitions on EH plot&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Figure 1 - inhibitions on Eadie-Hofstee plot&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;left-top: &lt;a href=&quot;http://en.wikipedia.org/wiki/Competitive_inhibition&quot; rel=&quot;nofollow noreferrer&quot;&gt;competitive inhibition&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;right-top: &lt;a href=&quot;http://en.wikipedia.org/wiki/Non-competitive_inhibition&quot; rel=&quot;nofollow noreferrer&quot;&gt;non-competitive inhibition&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;left-bottom: &lt;a href=&quot;http://en.wikipedia.org/wiki/Uncompetitive_inhibitor&quot; rel=&quot;nofollow noreferrer&quot;&gt;uncompetitive inhibition&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;right-bottom: &lt;a href=&quot;http://en.wikipedia.org/wiki/Mixed_inhibition&quot; rel=&quot;nofollow noreferrer&quot;&gt;mixed inhibition&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;(Btw. they are linear on Hanes-Langmuir, Lineweaver-Burk plots too.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;edit:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to review &quot;enzymatic&quot; linked (2012 - &lt;a href=&quot;http://cdn.intechopen.com/pdfs/36518/InTech-Alternative_perspectives_of_enzyme_kinetic_modeling.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Alternative Perspectives&#xA;of Enzyme Kinetic Modeling&lt;/a&gt;) these plots were important only before the development of the unified enzymatic activity modulation equation (2007). (I had learned about this topic somewhere between 2004 and 2009 that's why I weren't up to date.)&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-11-14T00:02:19.313" LastActivityDate="2014-11-14T00:02:19.313" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23548" PostTypeId="1" CreationDate="2014-10-29T00:47:07.270" Score="4" ViewCount="2939" Body="&lt;p&gt;Given identical twin males, Michael and Douglas, Douglas and his wife have four children, all of whom are girls.  Michael and his wife have only one child, a boy, and are expecting another. What are the chances it will be another boy? If Michael and his wife have more children, what are the chances they will all be boys? Is there any support/evidence for, or a study about, one twin of an identical pair will have children all of the same gender and the other twin will have children all of the same (or opposite) gender?&lt;/p&gt;&#xA;" OwnerUserId="9967" LastEditorUserId="3624" LastEditDate="2014-10-29T09:53:13.827" LastActivityDate="2014-10-30T14:14:30.170" Title="The gender of offspring of Twins?" Tags="&lt;human-biology&gt;&lt;human-genetics&gt;&lt;reproductive-biology&gt;&lt;twins&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23549" PostTypeId="1" CreationDate="2014-10-29T00:54:32.663" Score="2" ViewCount="131" Body="&lt;p&gt;If there is ample amount of food, do &lt;em&gt;C. elegans&lt;/em&gt; worms know when to stop eating or do they store extra energy? Could they put this extra energy to use by moving faster or putting more eggs?&lt;/p&gt;&#xA;" OwnerUserId="9490" LastEditorUserId="3553" LastEditDate="2015-01-27T01:22:16.187" LastActivityDate="2015-01-27T13:03:05.723" Title="How do C. elegans manage nutrition?" Tags="&lt;molecular-biology&gt;&lt;nutrition&gt;&lt;animal-models&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23550" PostTypeId="2" ParentId="23548" CreationDate="2014-10-29T04:53:06.280" Score="2" Body="&lt;p&gt;The question you're asking is essentially a version of an old riddle:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;If you flip a coin ten times and it comes up heads each time, what are the odds that the coin will&#xA;come up heads when you flip it for an eleventh time?&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;And of course the answer is that the odds are fifty-fifty. You could instead argue that 10 heads in a row is evidence that the coin is weighted somehow, and the way you would deal with that is by flipping that same coin 1000 more times, or (somewhat less reassuringly) by finding 100 coins identical to your first one and then flipping them each 10 times.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's the same thing with children's genders. For every family with 6 girls there are hundreds more families with more mixed genders. The only effect known to skew the male-female sex ratio at birth significantly is wide scale sex-selective abortion (it tends to reduce the number of females).&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-10-29T04:53:06.280" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23553" PostTypeId="2" ParentId="23548" CreationDate="2014-10-29T09:28:48.387" Score="4" Body="&lt;p&gt;&lt;em&gt;Note: This is based on literature searches I've done a while ago out of general curiosity. I'm in no way an expert on human reproduction.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;If I understand you correctly you are basically asking if there are any evidence for sex biases in offspring between families, that has a heritable genetic basis. This has been an active research topic for a long time and there are a number of proposed mechanisms for how this can be achieved. Historical data sometimes shows deviations in sex ratios over time, e.g. in 20th centrury Europe after WWI and WWII (see data in &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs11692-008-9046-3&quot; rel=&quot;nofollow&quot; title=&quot;Gellatly. 2009. Trends in Population Sex Ratios May be Explained by Changes in the Frequencies of Polymorphic Alleles of a Sex Ratio. Evolutionary Biology 36(2): 190-200&quot;&gt;Gellatly, 2009&lt;/a&gt;). There are also other reported/hypothesized deviations in sex ratio e.g. trends in sex ratio due to paternal age (e.g. &lt;a href=&quot;http://humrep.oxfordjournals.org/content/14/12/3120&quot; rel=&quot;nofollow&quot; title=&quot;Jacobsen et al. 1999. Natural variation in the human sex ratio.  Hum. Reprod. 14(12): 3120-3125.&quot;&gt;Jacobsen et al, 1999&lt;/a&gt;), sex biases of offspring due to earlier insemination in the menstrual cycle, and the child rank. However, from what I've seen, the evidence hasn't been conclusive and different studies point in different directions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3455630/&quot; rel=&quot;nofollow&quot; title=&quot;Irving et al. 1999. The Ratio of X- and Y-Bearing Sperm in Ejaculates of Men with Three or More Children of the Same Sex. J Assist Reprod Genet. 16(9): 492–494.&quot;&gt;Irving et al (1999)&lt;/a&gt; point out, possible mechanisms for sex ratio biases can be:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;deviations in X/Y-ratio of sperm&lt;/li&gt;&#xA;&lt;li&gt;selection of sperm within the female reproductive tract&lt;/li&gt;&#xA;&lt;li&gt;biases in implantation success and/or survival for embryos of different sex&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Most evidence seems to point against explanation one, see tests in e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3455630/&quot; rel=&quot;nofollow&quot; title=&quot;Irving et al. 1999. The Ratio of X- and Y-Bearing Sperm in Ejaculates of Men with Three or More Children of the Same Sex. J Assist Reprod Genet. 16(9): 492–494.&quot;&gt;Irving et al (1999)&lt;/a&gt; and &lt;a href=&quot;http://humrep.oxfordjournals.org/content/14/11/2917.full&quot; rel=&quot;nofollow&quot; title=&quot;Graffelman et al. 1999. Human live birth and sperm–sex ratios compared.  Hum. Reprod. 14(11): 2917-2920.&quot;&gt;Graffelman et al (1999)&lt;/a&gt;. &lt;a href=&quot;http://humrep.oxfordjournals.org/content/14/11/2917.full&quot; rel=&quot;nofollow&quot; title=&quot;Graffelman et al. 1999. Human live birth and sperm–sex ratios compared.  Hum. Reprod. 14(11): 2917-2920.&quot;&gt;Graffelman et al (1999)&lt;/a&gt; also tests for an effect of male age, but do not find support for this idea. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another interesting study is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1685814/&quot; rel=&quot;nofollow&quot; title=&quot;Curtsinger et al. 1983. A two-generation study of human sex-ratio variation. Am J Hum Genet. 35(5): 951–961&quot;&gt;Curtsinger et al (1983)&lt;/a&gt;, which tries to look at vertical population transmission of sex ratio variation in Japan. They conclude that there is a marginally significant effect on the paternal side, which would support the idea that sex biases might run in families.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An analysis of vertical transmission of sex-ratio modifying factors that excludes effects of birth order in both the parental and offspring generations has detected a marginally significant paternal effect.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, they also conclude that the genetic variability in sex ratio is very small, if there is one. This study also does not find support for effects of e.g. paternal age or child birth order.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs11692-008-9046-3&quot; rel=&quot;nofollow&quot; title=&quot;Gellatly. 2009. Trends in Population Sex Ratios May be Explained by Changes in the Frequencies of Polymorphic Alleles of a Sex Ratio. Evolutionary Biology 36(2): 190-200&quot;&gt;Gellatly (2009)&lt;/a&gt; provides a model of how an autocorrelation in sex ratio between generations could be explaned (while still having a stable population-level sex ratio), using an autosomal gene modifying male sex ratio. Note thought that this is a proposed model, and not empirical evidence. However, &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs11692-008-9046-3&quot; rel=&quot;nofollow&quot; title=&quot;Gellatly. 2009. Trends in Population Sex Ratios May be Explained by Changes in the Frequencies of Polymorphic Alleles of a Sex Ratio. Evolutionary Biology 36(2): 190-200&quot;&gt;Gellatly (2009)&lt;/a&gt; also use genealogical/pedigree data from North America and Europe to show that there is an heritable component in the human sex ratio (an association between sex ratio in F1 and F2 generations). However, from what I can see the evidence is weak, and the models only explains 0.5% of the variance in the data. The introduction to this paper also has a useful overview of the subject with more references you might want to check out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All in all, my perception is that there are some evidence that certain sexes can be overrepresented in families, which could potentially mean that the sex ratio in the offspring of a twin brother can contain information on the probablility that his brother will have a son or daughter. However, to me, the evidence is far from conclusive and the estimated effects seem rather weak. So as a null hypothesis, you should definately go for a 50/50 chance of a son/daughter, irrespectively of what the sex ratio of the twin brother is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the general calculation of probabilities of different scenarios, you just use the product of probabilities and sometimes summation of birth orders. For instance (if assuming 50/50 sex ratio), the probability of having three sons is $0.5^3= 12.5\%$ (births: MMM) and the probability of having 2 sons and one daughter is $3*0.5^3= 37.5\%$ (births: FMM, MFM or MMF, i.e. three ways to achieve this scenario out of eight).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-10-30T14:14:30.170" LastActivityDate="2014-10-30T14:14:30.170" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23556" PostTypeId="2" ParentId="6947" CreationDate="2014-10-29T14:35:58.650" Score="0" Body="&lt;p&gt;SSRI's theoretically increase Serotonin levels.  Serotonin is an agonist to the 5HT-3 receptors. The 5HT-3a primarily associated with the upper gut and the 5HT-3b with the lower gut.  I would guess that theoretically again, SSRI's would tend to increase nausea, emesis, and diarrhea.  There may be other effects, but these are the ones I have researched.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The anti-emetics Dolasetron, Ondansetron, Granisetron, and Tropisetron are 5HT-3 antagonists.&lt;/p&gt;&#xA;" OwnerUserId="9932" LastActivityDate="2014-10-29T14:35:58.650" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23557" PostTypeId="1" CreationDate="2014-10-29T14:52:48.327" Score="6" ViewCount="4224" Body="&lt;p&gt;I am a senior in high school and I am studying cystic fibrosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't quite get the function of the CFTR gene as this is my first time dealing with this type of heavy scientific  info.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I had searched up its function on a website like this: &#xA;&lt;a href=&quot;http://omim.org/entry/602421?search=cystic%20fibrosis&amp;amp;highlight=fibrosi%20cystic&quot;&gt;http://omim.org/entry/602421?search=cystic%20fibrosis&amp;amp;highlight=fibrosi%20cystic&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By reading the gene functions section, I learned that CFTR regulate the formation of a chloride channel, changes the regulation of other transport pathways (i.e increase sodium ion absorption in sodium ion absortion). At the same time it also regulate the chloride-coupled bicarbonate receptor. And that is about all I got from that section.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would greatly appreciate if someone can summarize all the functions of the CFTR gene listed in layman terms (i.e grandma language)  and also explain to me why decreased  chloride channel leads to thicken mucus or increase sodium ion absorption leads to CF Symptoms. In addition I would also appreciate it if someone can tell me does decreased CFTR gene function also lead to other diseases on top of Cystic fibrosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="8279" LastActivityDate="2014-10-29T21:17:22.373" Title="Functions of the CFTR gene?" Tags="&lt;genetics&gt;&lt;medicine&gt;&lt;biomedical-technology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23558" PostTypeId="1" CreationDate="2014-10-29T15:01:27.423" Score="1" ViewCount="142" Body="&lt;p&gt;I have another question regarding cystic fibrosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that gene therapy is currently being talked about in the cure for cystic fibrosis. I know that Eric Alton at imperial college London is working on delivering genes using liposomes and viruses like lentiviruses but I am confused over the advantages and disadvantages of those two methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, is there an alternative 3rd method for injecting genes that don't involved viruses or liposomes. (An alternative type of vector) ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="8279" LastActivityDate="2015-01-15T04:33:53.343" Title="Gene Therapy for Cystic Fibrosis" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23559" PostTypeId="1" AcceptedAnswerId="23562" CreationDate="2014-10-29T16:22:28.013" Score="8" ViewCount="17267" Body="&lt;p&gt;I would like to understand what the term H+ Gradient means. I googled this question and found terms such as chemiosmosis and ion gradient being tossed around. I am very new to biology and I do not know any advanced terms or anything of the like. What I do understand is that the mitochondria produces ATP and has something called a proton pump.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance.&lt;/p&gt;&#xA;" OwnerUserId="8200" LastActivityDate="2018-05-30T14:54:16.033" Title="What is the H+ gradient in mitochondria?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23560" PostTypeId="2" ParentId="23557" CreationDate="2014-10-29T16:35:15.203" Score="7" Body="&lt;p&gt;CFTR is the gene which encodes the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cystic_fibrosis_transmembrane_conductance_regulator&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cystic fibrosis transmembrane conductance regulator&lt;/a&gt;&quot;, which is a membrane protein. Its function is to transport chloride and other negatively charged ion like thiocyanate ions from the inside of the cell to the outside (into the extra cellular space). This happens along a gradient, meaning the ions flow from the place of high concentration (inside the cell) to the place of low concentration (outside the cell). Since this would mean that a negative charge would build up on the outside of the cell, positively charged sodium ions follow the chloride ions by passive diffusion. This ions are secreted into the mucus in the extra cellular space.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leads to a higher concentrations of electrolytes (salts) outside of the cell, which causes water to leave the cell (following the higher concentration of electrolytes), which makes the mucus thinner. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the CFTR gene is mutated, this function is impaired and ions cannot be transported across the membrane. This causes a higher electrolyte concentration inside the cell and water stays there. This causes the mucus to get thicker (due to less influx of water), which then can block fine channels of the lung. Additionally bacteria can grow in the thicker mucus, which can cause severe problems as pneumonia. The process functions as shown in the figure below (from &lt;a href=&quot;https://www.bio.logis.de/pgs/produktnutzen/carrier-status&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;), the sodium ions are not shown here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0WJib.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to read further about cystic fibrosis, I recommend this &lt;a href=&quot;http://cyfbin.weebly.com/cyfb.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;website&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the immune system there are different functions affected. First, the reduced (or prevented) secretion if thiocyanate ions lead to a reduction in the production of &lt;a href=&quot;http://en.wikipedia.org/wiki/Hypothiocyanite#Relation_to_cystic_fibrosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hypothiocyanite&lt;/a&gt; ions which kill bacteria. Then different cells which are of importance to a proper immune reaction are impaired in their function, as shown in the figure below (from the first reference):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8Vz2Q.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The function of CFTR is impaired in all cell types, not only in epithelial cells in the lung (although these are the most obvious consequences). In the cells of the immune system (T-cells for example) the intracellular ion concentration is disturbed including Ca&lt;sup&gt;2+&lt;/sup&gt; which plays an important role in the regulation of other genes. Other observations show that the activation of the immune system itself is also affected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further informations can be found in the articles I linked below. They require some knowledge of immunology, but when there are question, ask.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.atsjournals.org/doi/full/10.1165/rcmb.2011-0399RT#.VFEWTVdAqYE&quot; rel=&quot;nofollow noreferrer&quot;&gt;Immune Responses in Cystic Fibrosis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jci.org/articles/view/6277&quot; rel=&quot;nofollow noreferrer&quot;&gt;The innate immune system in cystic fibrosis lung disease&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-10-29T21:17:22.373" LastActivityDate="2014-10-29T21:17:22.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23561" PostTypeId="2" ParentId="23545" CreationDate="2014-10-29T19:44:37.630" Score="4" Body="&lt;p&gt;The reason is that the inhibition models are inherently wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Inhibitors bind to enzymes with the same mass action principles as substrates do so the term that should describe their binding should mirror the form of the MM equation i.e. ([S]/([S]+km)).  However all the traditional equations use (1+([I]/Ki)) rather than ([I]/([I]+ki)).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To compound this problem the (1+([I]/Ki)) term multiplies into the Km in competitive inhibition but divides into the Vmax in the noncompetitive equation.  It is therefore not affecting these terms in the same way in these separate equations and leads to the conclusion it is upside down in the competitive equation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The plots above are deceiving as they allow the user to look at a linear plot and assume mechanism based on axis intercept pattern without analyzing the actual change in kinetic parameters produced by the inhibitor.  Kinetic models should be only fit using global data fitting to the proposed inhibition model.  This can be done quite easily using excel, for an example of how this can be done check out Kemmer and Keller 2010, or check youtube.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kemmer G, Keller S. 2010. Nonlinear least-squares data fitting in Excel spreadsheets. Nature Protocols 5:267-281.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By realizing that the change in enzyme kinetic properties relates directly to inhibitor binding the logical hyperbolic shift in values exactly like the hyperbolic curve of the MM equation must be acknowledged and finite changes in the kinetic parameters must be accounted for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;i.e. Km = Km-((delta Km)*([I]/([I]+Ki)))&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;  Vmax = Vmax-((delta Vmax)*([I]/([I]+Ki))) &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;While I have been told this may be over fitting as the competitive, noncompetitive, mixed noncompetitive equations define inhibition with one or two inhibition constant (Ki alphaKi), these terms eliminate the need for all of these equations and the family of equations that they spawned as they proved ineffective over the years (such as uncompetitive, partial competitive, partial noncompetitive, partial mixed noncompetitive, I could go on but I think you get the point).   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally the competitive, noncompetitive and mixed noncompetitive equations define the effect of the inhibitor with the equilibrium binding constants and do not allow for the possibility that complete inhibition may not occur (no delta terms), leading to the family of equation to try to make up for this, i.e. partial competitive and partial noncompetitive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Use empirical models and stop trying to force mechanistic models, the data will suggest the mechanism with good experimental design.&lt;/p&gt;&#xA;" OwnerUserId="9977" LastEditorUserId="9977" LastEditDate="2014-10-29T20:43:41.497" LastActivityDate="2014-10-29T20:43:41.497" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23562" PostTypeId="2" ParentId="23559" CreationDate="2014-10-29T19:51:55.040" Score="9" Body="&lt;p&gt;Lets start with a general definition: A gradient is the difference in the concentration of a substance (this can be a solutant in liquids, a gas or whatever) between two places. The image below shows the general definition. If nothing else happens what keeps the gradient stable, over time diffusion will cause an equilibrium between both places. The flow of substance always goes from the high concentration to the low (indicated by the arrows).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SltDs.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In biological systems the two parts of the gradient are usually divided by a membrane and are more stable. Gradients can be generated by active transport which requires the input of energy to work against the gradient. Examples would be the concentration gradient along a membrane like protons (positively charged hydrogen-ions), as this can be seen in the mitochondria. Here three complexes of the respiratory chain (I, III and IV) pump protons from the matrix in the intermembrane space, which requires energy. The fourth complex (V) pumps the protons back and uses the released energy from this process to make ATP. See the figure below which shows this process schematically (from &lt;a href=&quot;http://oregonstate.edu/instruction/bi314/summer09/mito.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xwhGf.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-29T19:51:55.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23564" PostTypeId="2" ParentId="23557" CreationDate="2014-10-29T20:31:48.553" Score="4" Body="&lt;p&gt;The CFTR &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene&quot; rel=&quot;nofollow noreferrer&quot;&gt;gene&lt;/a&gt; is coding a &lt;a href=&quot;http://en.wikipedia.org/wiki/Protein&quot; rel=&quot;nofollow noreferrer&quot;&gt;protein&lt;/a&gt; called CFTR (&lt;a href=&quot;http://en.wikipedia.org/wiki/Cystic_fibrosis_transmembrane_conductance_regulator&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cystic fibrosis transmembrane conductance regulator&lt;/a&gt;). This protein is an &lt;a href=&quot;http://en.wikipedia.org/wiki/Ion_channel&quot; rel=&quot;nofollow noreferrer&quot;&gt;ion channel&lt;/a&gt;, which allows &lt;a href=&quot;http://en.wikipedia.org/wiki/Passive_transport&quot; rel=&quot;nofollow noreferrer&quot;&gt;passive transport&lt;/a&gt; of the Cl- ions through the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_membrane&quot; rel=&quot;nofollow noreferrer&quot;&gt;cell membrane&lt;/a&gt; in both directions. This allows the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_%28biology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;cells&lt;/a&gt; to transport water due to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Active_transport&quot; rel=&quot;nofollow noreferrer&quot;&gt;active transport&lt;/a&gt; of Na+ ions. The Cl- ions follow the Na+ ions with passive transport to even up the &lt;a href=&quot;http://en.wikipedia.org/wiki/Electric_charge&quot; rel=&quot;nofollow noreferrer&quot;&gt;electric charges&lt;/a&gt;, while the water will follow the higher &lt;a href=&quot;http://en.wikipedia.org/wiki/Osmotic_concentration&quot; rel=&quot;nofollow noreferrer&quot;&gt;osmolarity&lt;/a&gt; created by both ions. (Something similar happens with &lt;a href=&quot;http://en.wikipedia.org/wiki/Glucose&quot; rel=&quot;nofollow noreferrer&quot;&gt;glucose&lt;/a&gt; when you put grapes into water. The glucose cannot go through the membrane of grape cells, but the water can. So the higher osmolarity in the grape cells will suck in water and the grapes will crack.)  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Without working CFTR the cells cannot transport too many Na+ ions, because their &lt;a href=&quot;http://en.wikipedia.org/wiki/Membrane_potential&quot; rel=&quot;nofollow noreferrer&quot;&gt;membrane potential&lt;/a&gt; changes too much when the Cl- ions cannot even up the charges, and so the cells would possibly die because of this. (Another possible explanation that the energy barrier would be too much for the Na+ transporter to send through another Na+ ion.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Without sufficient ion transport the water transport is not adequate in many regions of the body. By cystic fibrosis the most important affected organs are the skin, the lungs, the pancreas and the reproductive organs.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The skin cannot reabsorb Na+, so it will be salty.&lt;/li&gt;&#xA;&lt;li&gt;The lungs cannot send water to the mucus, so it will be too sticky, and because of that it prevents the cilias by cleaning out the pathogens from the lungs. The results are infections, probably pneumonia and &lt;a href=&quot;http://en.wikipedia.org/wiki/Cyst&quot; rel=&quot;nofollow noreferrer&quot;&gt;cysts&lt;/a&gt; in the lungs.&lt;/li&gt;&#xA;&lt;li&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Pancreas&quot; rel=&quot;nofollow noreferrer&quot;&gt;pancreas&lt;/a&gt; is usually not able to do its job as well. The result are poor digestion, and due to that vitamin absorption problems, e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Hypovitaminosis_D&quot; rel=&quot;nofollow noreferrer&quot;&gt;vitamin-D deficiency&lt;/a&gt; (and because of that &lt;a href=&quot;http://en.wikipedia.org/wiki/Osteoporosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;osteoporosis&lt;/a&gt;). In many cases the pancreas is completely cystic, and it loses the ability to produce insulin, which leads to &lt;a href=&quot;http://en.wikipedia.org/wiki/Cystic_fibrosis-related_diabetes&quot; rel=&quot;nofollow noreferrer&quot;&gt;diabetes&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;The reproductive organs are affected as well, most of the males with cystic fibrosis are infertile, and about every fifth female as well.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;As you already know this is a hereditary disease caused by mutations in the CFTR gene. What you probably don't know that only &lt;a href=&quot;http://en.wikipedia.org/wiki/Zygosity&quot; rel=&quot;nofollow noreferrer&quot;&gt;homozygotes&lt;/a&gt; are affected. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Prevalence&quot; rel=&quot;nofollow noreferrer&quot;&gt;prevalence&lt;/a&gt; of the mutant alleles is around 1/25 in my country (Hungary), so every 25th person is an asymptomatic carrier and by every 625th marriage there is a 25% chance that the child will be homozygote. The prevalence is dependent on the region, e.g. North- and West Europe is more affected than South- and East Europe. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Icjfu.jpg&quot; alt=&quot;CF birth prevalence&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 1 - cystic fibrosis homozygote prevalence - &lt;a href=&quot;https://www.cftrscience.com/epidemiology.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;Epidemiology: Mutational Diversity–Patterns of CFTR Mutations&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Because of the region dependent prevalence of the heterozygotes (and homozygotes) there are theories, which claim that probably there is (or was) a negative evolutionary pressure on the CFTR gene, and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Heterozygote_advantage&quot; rel=&quot;nofollow noreferrer&quot;&gt;heterozygotes have evolutionary advantage&lt;/a&gt;, just like by &lt;a href=&quot;http://en.wikipedia.org/wiki/Sickle-cell_disease&quot; rel=&quot;nofollow noreferrer&quot;&gt;sickle-cell anaemia&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Malaria&quot; rel=&quot;nofollow noreferrer&quot;&gt;malaria&lt;/a&gt;. The CFTR is target of many infectious diseases e.g. cholera, typhoid fever, tuberculosis, etc..., so &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2358959/&quot; rel=&quot;nofollow noreferrer&quot;&gt;there are many candidates&lt;/a&gt;. Afaik there is no decision yet in this topic.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-29T20:31:48.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23565" PostTypeId="2" ParentId="949" CreationDate="2014-10-29T22:40:57.833" Score="1" Body="&lt;p&gt;&lt;strong&gt;First the boring (but most important part) looking at the study:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important to critique the study design FIRST to see what kind of information we can actually obtain from this study. This is a meta-analysis of cross-sectional studies (meaning there is no record of change over time) that include a variety of age ranges of ADHD patients (some on treatment, some not) who were compared with age, gender and IQ-matched non-ADHD people to measure DAT levels in the stratum measured with PET and SPECT.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What they found:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There were very heterogeneous results from all the studies, there was no statistically significant difference between DAT in ADHD and normal (note that they use the word &quot;trends&quot;). The only thing statistically significant that they found was that there was a wide spread of DAT in the ADHD population, and that exposure to treatment accounted for half of this spread (variance).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What can we say about this?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not a very conclusive study, but studies like this are often necessary to merit doing higher resource intensive studies.  This study did not reach statistical significance in it's primary outcome, and on further search was able to only find a single outcome of significance. My summary of this would be: maybe this could represent a method of medication tolerance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;To answer your question&lt;/strong&gt;&#xA;If hypothetically this was the cause and I had to make up a possible method of transcription control, I would say something similar to your answer. I would guess there is some transcription factor that is inhibited by dopamine in the cell. When there isn't dopamine (b/c it is being blocked from returning), it would somehow become active and start transcribing the gene for DAT.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Disclaimer&lt;/strong&gt;&#xA;I am not a neurobiologist, this is my opinion after reading the article. Feel free to add to my comments&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Reference:&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Fusar-Poli, P., Rubia, K., Rossi, G., Sartori, G., &amp;amp; Balottin, U. (2012). Striatal dopamine transporter alterations in ADHD: pathophysiology or adaptation to psychostimulants? A meta-analysis. American Journal of Psychiatry, 169(3), 264-272.&lt;a href=&quot;http://journals.psychiatryonline.org/article.aspx?articleid=1028564#F4&quot; rel=&quot;nofollow&quot;&gt;[Link]&lt;/a&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9979" LastEditorUserId="57" LastEditDate="2014-11-02T08:02:43.223" LastActivityDate="2014-11-02T08:02:43.223" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23566" PostTypeId="2" ParentId="20647" CreationDate="2014-10-29T23:46:38.860" Score="1" Body="&lt;p&gt;Interesting question. I will dissect your question into its assumptions before giving my view on the overall question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) ..that nerves became larger.. : Why should there be a general tendency for nerves to increase in size during the course of evolution when there is no need to?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) ...that nerves became more myelinated...: A general tendency towards more myelination is not the case. Myelination is definitely a trait that has been acquired later in evolution, but &quot;the more the better&quot; does not apply. Imagine an electrical conductor - to insulate it a bit of plastic is enough. Adding more after that doesn't make a substantial difference. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) ...the order in which these receptors evolved...: myleine sheaths are made up of glial cells that wrap themselves around axons of neurons. Myeline makes neural transduction more efficient and faster. Hence, the amount of myelination tells you something about the efficiency and speed of transduction of the nerve (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0960982206025231/pdf?md5=6d1b10008c625c0ef51f98480f72b9e2&amp;amp;pid=1-s2.0-S0960982206025231-main.pdf&quot; rel=&quot;nofollow&quot;&gt;Hartline (2007)&lt;/a&gt;). For example, longer axons tend to be myelinated, short ones not. That, in turn, will have certain evolutionary benefits for the host, as more efficient communications means less energy required, lesser loss of information, and increased processing speeds. The amount of myelin hence tells you something about the importance of efficient communication of that sensory system. However, it does not tell you anything about when this receptor evolved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, the relation between myelination and receptor evolution is remote at best. In terms of evolution, amounts of myelination may tell you something about the evolutionary pressure placed on faster and more efficient workings of the receptor systems.     &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-10-29T23:46:38.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23568" PostTypeId="2" ParentId="19762" CreationDate="2014-10-30T02:33:44.253" Score="3" Body="&lt;p&gt;Organisms on Earth did not evolve in a homogenous environment. A critical part of speciation (when you go from a single species into two or more) is a reproductive barrier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can be a literal, physical barrier - mountain range appears between two populations, valley in the middle of habitat floods and isolates the two halves of the population, a small group is thrown by some catastrophe on a remote island and cannot escape, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It can also be a genetic barrier: Imagine a bird species where males compete for mates with their bright blue crests, and rare mutations occasionally lead to red-crested males which cannot mate at all. If some female birds happen to mate with undesirable red-crested males for a few generations, two parallel sub-populations may develop: Birds which prefer red crests and bird which prefer blue crests. These populations may be very unlikely to interbreed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There may be more complicated ways of erecting a barrier. For instance, a population of flowering plants that could previously interbreed arbitrarily may find that the ecosystem has experienced some crisis, and now the pollinating insects have become fastidious and only visit certain flowers and not others. Another example: While humans are currently a single species, because of culture (eg. language) certain human subpopulations (such as European nations) are much more likely to breed within themselves than between themselves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regardless of how the barrier comes to be, once a barrier can separate a species into sub-populations, the machinery of speciation is set in motion. All species evolve over time in different ways, especially if their environment does not have a very long history of unusual stability. As populations evolve, they try to stay somewhat coherent - the changes tend to be such that they still permit everyone in the population to mate with each other; otherwise they would impose a fitness cost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if two subpopulations are not in contact, there is nothing enforcing compatibility between them. Therefore, as evolution does its work, these are free to wildly diverge from each other. Recall the example of the bird species in which males with blue crests enjoy reproductive success. The color itself is not particularly important, but it is important that the males all have the same color crest and the females prefer the same color. So as these birds evolve, the crest color can slowly drift in hue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now let's say you took these birds, and set a few of them free in one continent, and another group free on another continent. Again, over time, the crest color will shift. However, there is nothing stopping from the color in continent A from shifting to red while the color in continent B shifts to green. There is, after all, no advantage to being compatible with a population you are not in contact with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The example above is largely behavioral, but non-behavioral examples are also possible. A very fundamental process is fertilization: Eggs have an ECM made up of proteins unique to that species, while sperm have enzymes to digest the coat of their own species. Because of this, cross-species fertilization is very difficult. Again, once you erect some kind of barrier between two populations, the systems of coat proteins and enzymes in the gametes of either population may evolve in divergent ways - they evolve in small steps, so that the interaction partner protein can always keep up, but compatibility with the isolated population is not selected for, and if the isolated groups are reunited after a very long time their gametes may end up becoming unable to fertilize each other.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-10-30T02:33:44.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23570" PostTypeId="1" AcceptedAnswerId="23573" CreationDate="2014-10-30T03:29:17.247" Score="0" ViewCount="52" Body="&lt;p&gt;I think Genetical Modification can be termed as 'Artificial Mutation'.&#xA;Is it possible that genes can be modified so much that it leads to the introduction of new Species i.e Can integration of large no. of Helpful mutations lead to quick evolution?&lt;/p&gt;&#xA;" OwnerUserId="9976" LastActivityDate="2014-10-30T11:26:16.003" Title="Does too much Genetical Modification leads to formation of new species?" Tags="&lt;speciation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23571" PostTypeId="1" AcceptedAnswerId="23572" CreationDate="2014-10-30T03:42:19.930" Score="27" ViewCount="43780" Body="&lt;p&gt;Why is the Krebs cycle considered a part of aerobic metabolism if molecular oxygen is not involved in any of the reactions in the cycle?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I originally thought that Krebs cycle was aerobic metabolism because it is in the process that oxygen is the final electron acceptor, but my teacher claims that glycolysis is anaerobic so what makes the Krebs cycle aerobic?&lt;/p&gt;&#xA;" OwnerUserId="9980" LastEditorUserId="9099" LastEditDate="2014-10-30T09:32:29.430" LastActivityDate="2021-02-02T21:02:44.310" Title="Why is the Krebs cycle considered a part of aerobic metabolism if molecular oxygen is not involved in any of the reactions in the cycle" Tags="&lt;metabolism&gt;&lt;cellular-respiration&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23572" PostTypeId="2" ParentId="23571" CreationDate="2014-10-30T04:02:36.353" Score="28" Body="&lt;p&gt;Oxygen is actually not needed in the Krebs cycle - it is needed in the electron transport chain that is downstream of the Krebs cycle to &lt;a href=&quot;http://www.austincc.edu/emeyerth/electrontrans.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;regenerate NAD&lt;sup&gt;+&lt;/sup&gt; from NADH&lt;/a&gt;. NAD&lt;sup&gt;+&lt;/sup&gt; is a co-enzyme and acts as an electron carrier in oxidizing reactions at various positions in the Krebs cycle. However, note that without O&lt;sub&gt;2&lt;/sub&gt;, NADH accumulates and the cycle cannot continue as it needs NAD&lt;sup&gt;+&lt;/sup&gt; to run.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;Krebs cycle - No O&lt;sub&gt;2&lt;/sub&gt; needed:&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GVQCY.jpg&quot; alt=&quot;Krebs cycle&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;Electron transport chain - O&lt;sub&gt;2&lt;/sub&gt; needed to regenerate NAD&lt;sup&gt;+&lt;/sup&gt; essential for the Krebs cycle:&lt;/strong&gt;&lt;/em&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Nk7Mn.gif&quot; alt=&quot;e- transport chain&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2021-02-02T21:02:44.310" LastActivityDate="2021-02-02T21:02:44.310" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="23573" PostTypeId="2" ParentId="23570" CreationDate="2014-10-30T04:36:59.290" Score="4" Body="&lt;p&gt;yes it possible, in one &lt;a href=&quot;http://www.sciencemag.org/content/270/5235/397.long&quot;&gt;article&lt;/a&gt; show a study for Mycoplasma genitalium which have 525 gene, however only 382 genes are essential for biological functions, they take out the nature gene and place the ' artifical gene' which synthsis in vitro, to test if the M. genitalium will survival when the No. of gene lower than 382. If it survival it will be a new species.&lt;/p&gt;&#xA;" OwnerUserId="9776" LastEditorUserId="3827" LastEditDate="2014-10-30T11:26:16.003" LastActivityDate="2014-10-30T11:26:16.003" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23574" PostTypeId="2" ParentId="23543" CreationDate="2014-10-30T06:41:14.530" Score="1" Body="&lt;p&gt;Developing anything by the body takes energy so generally only useful products are conserved. If some sort of mutation caused an organism to produce some sort of by-product that also happened to be toxic to its predators, then that organism is more favored to survive. No species ever starts producing something with the intention of toxicity in a predator/consumer of said species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These xenobiotics that the plant/animal produces then can either be selected for because they're useful in whatever pathway they are a by-product of. Or they can be conserved because then this by-product has a defense use, regardless of whether the pathway its part of is necessary. Or both could happen, it could be doubly selected for.&lt;/p&gt;&#xA;" OwnerUserId="9982" LastActivityDate="2014-10-30T06:41:14.530" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23575" PostTypeId="1" CreationDate="2014-10-30T07:13:16.433" Score="0" ViewCount="55" Body="&lt;p&gt;Different antigen detection triggers an immune system response that could perhaps stimulate mitochondria and such in killing cancer cells - something like chemo without the hair-loss? &lt;/p&gt;&#xA;" OwnerUserId="9636" LastActivityDate="2014-10-30T08:03:23.447" Title="Could transfusion of a different blood type cure blood-based cancers?" Tags="&lt;cancer&gt;&lt;hematology&gt;&lt;autoimmune&gt;&lt;antigen&gt;&lt;transfusion&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23577" PostTypeId="2" ParentId="23575" CreationDate="2014-10-30T08:03:23.447" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2265/&quot; rel=&quot;nofollow&quot;&gt;No&lt;/a&gt;. When a different blood type is introduced in the body, the host immune system recognizes the foreign blood as non-self and attacks it. The transfused blood becomes useless, and the potentially massive immune reaction can cause shock, which itself can be fatal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More details in the book &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2261/&quot; rel=&quot;nofollow&quot;&gt;Blood Groups and Red Cell Antigens&lt;/a&gt;, which can be found at the NCBI library.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastActivityDate="2014-10-30T08:03:23.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23579" PostTypeId="2" ParentId="22020" CreationDate="2014-10-30T10:19:57.667" Score="4" Body="&lt;p&gt;Good question. Just to set some stuff straight: In contrast to a comment placed earlier, there is definitely a current flow between electrodes in neural tissue, as long as the impedance is not too high. The potential difference between the electrodes and impedance determines how much current flows, basically following Ohm's law: I = U/R.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to your hypothesis (A) - I confirm  WYSIWYG's answer - electrodes indeed do not have to be coated, as long as they are conductive. For instance, Ag/AgCl coatings are used to electrically stabilize the electrode, mainly for sensitive reference electrodes used for recording purposes (&lt;a href=&quot;http://www.science-products.com/Products/CatalogG/AgAgCl-Pellets/ivm.html&quot; rel=&quot;nofollow&quot;&gt;see a commercial link here&lt;/a&gt;). For stimulation purposes chloride salts are a big no no, as AgCl or comparable chloride salts will be converted into metal (e.g. silver) + Cl&lt;sub&gt;2&lt;/sub&gt;, obviously a toxic gas.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to your hypothesis (B) - It is the electrical field that activates neurons (&lt;a href=&quot;http://www.researchgate.net/publication/11652216_New_currents_in_electrical_stimulation_of_excitable_tissues/file/79e4150cc73bab725f.pdf&quot; rel=&quot;nofollow&quot;&gt;Basser &amp;amp; Roth 2000&lt;/a&gt;) by means of inducing current flow. For example, imagine a cathode (negative electrode) placed close to a neuron. Normally in rest, a neuron's membrane is hyperpolarized (more negative ions inside the cell, the extracellular fluid can be considered to be neutral). The negative electrode will now cause the extracellular fluid to be negatively charged. Subsequently, positive current will flow out from the cell close to the electrode and into the electrode. According to Ohm's law, the membrane voltage is thus positive (note Ohm's law: U = IxR, with I being positive and R being always positive, means U is positive). Hence, the membrane is depolarized, as the resting state is a negatively charged state (hyperpolarized). With an anodic electrode neurons can also be depolarized but due to a slightly different mechanism. Basically, the flanking regions of the now negative current flow to the positive electrode become subject to positive current, as it counterbalances the negative flow to the electrode.  The chapter of two veterans in electrical stimulation, Abbas and Miller, in (&lt;a href=&quot;http://www.springer.com/biomed/neuroscience/book/978-0-387-40646-6&quot; rel=&quot;nofollow&quot;&gt;Cochlear implants&lt;/a&gt;) is particularly helpful, as is (&lt;a href=&quot;http://www.researchgate.net/publication/11652216_New_currents_in_electrical_stimulation_of_excitable_tissues/file/79e4150cc73bab725f.pdf&quot; rel=&quot;nofollow&quot;&gt;Basser &amp;amp; Roth 2000&lt;/a&gt;). I can't link a pdf to Abbas and Miller, excuse me for that. I bet your university library will have access to it. Hope this helps.   &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-10-30T10:31:00.820" LastActivityDate="2014-10-30T10:31:00.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23581" PostTypeId="2" ParentId="21241" CreationDate="2014-10-30T13:08:39.463" Score="1" Body="&lt;p&gt;There is some evidence that garbage enzymes have significant enzyme activity, so they really work.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The decomposable waste thrown into the environment can be used to&#xA;  produce value added bio-product which in turn reduces the production&#xA;  of greenhouse gas. Garbage enzyme is one such value added product&#xA;  produced by fermentation of organic solid waste. In the present study&#xA;  enzyme activity and disinfectant potential of garbage enzyme was&#xA;  evaluated and its influence on reduction of total solids, suspended&#xA;  solids and pathogens in dairy waste activated sludge were studied. The&#xA;  result showed the garbage enzyme possesses protease, amylase and&#xA;  lipase activity and reduced 37.2% of total solids, 38.6% of suspended&#xA;  solids and 99% of pathogens in dairy waste activated sludge. This&#xA;  significant result may be helpful for researchers to compare the&#xA;  effectiveness of earth-friendly garbage enzyme treatment of industrial&#xA;  sludge with various physical and chemical pre-treatment methods to&#xA;  improve the bio gas production from the sludge digestion unit.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2014 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0957582014001591&quot; rel=&quot;nofollow&quot;&gt;INVESTIGATION OF BIO CATALYTIC POTENTIAL OF GARBAGE ENZYME AND ITS INFLUENCE ON STABILIZATION OF INDUSTRIAL WASTE ACTIVATED SLUDGE&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2011 - &lt;a href=&quot;http://www.waset.org/publications/6989&quot; rel=&quot;nofollow&quot;&gt;A Study of the Garbage Enzyme’s Effects in&#xA;Domestic Wastewater&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This study was conducted to explore the feasibility of using Garbage&#xA;  Enzyme to treat sullage. The enzyme was prepared from fruits dregs,&#xA;  kitchen waste, molasses and water and capable of having reinforcing&#xA;  and cleaning function to work with nature. In this study, sullage was&#xA;  collected at open drainage at Arked Meranti, Arked Cengal and Kolej 9&#xA;  cafeteria?s and enzyme dosage determinations were done at laboratory&#xA;  scale. Sullage collected were analysed for BOD, COD, TSS and oil and&#xA;  grease. From the result obtained all samples treated using garbage&#xA;  enzyme prepared shows removal of BOD was 60% , COD and oil and grease&#xA;  almost 90%, then TSS was 80% after 7 days of treatment with different&#xA;  dosage of enzyme.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://eprints.utm.my/11581/&quot; rel=&quot;nofollow&quot;&gt;Garbage enzyme as an alternative method in treatment of sullage&lt;/a&gt; - &lt;a href=&quot;http://www.enzymesos.com/wp-content/uploads/2011/08/KhairulBariyahBakarMFKA2010.pdf&quot; rel=&quot;nofollow&quot;&gt;pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;To answer your questions:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So the question arises that does this recipe really have those&#xA;  cleaning enzymes and how are they generated?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Fruits, biological garbage etc... all contains cells, and those cells contain enzymes. By the fermentation process the cells are breaking down (&lt;a href=&quot;http://en.wikipedia.org/wiki/Lysis&quot; rel=&quot;nofollow&quot;&gt;lysis&lt;/a&gt;) and they release their enzymes.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Moreover if fruits like Pineapple and papaya are used does it make the&#xA;  solution more potent?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Pineapple and papaya contain proteases (e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Bromelain&quot; rel=&quot;nofollow&quot;&gt;bromelain&lt;/a&gt;). Enzymes are proteins, so these proteases can degrade them as well. (I think these proteases can be inhibited safely, but this would require a lot of research.) So I think it is not a good idea to ferment pineapple or papaya, because the result will be a significant loss of enzyme activity.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-30T13:08:39.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23583" PostTypeId="1" CreationDate="2014-10-30T13:44:54.097" Score="3" ViewCount="512" Body="&lt;p&gt;During an anatomy lecture I heard of the importance of the acidity of gastric acid (e.g., killing microorganisms, dissolving food, being a factor for triggering further processes). If a healthy person would eat a tsp. of Magnesia [Mg(OH)&lt;sub&gt;2&lt;/sub&gt;] suspension before a meal (lets say at least 30 min beforehand) and then eat normally, would it have a significant impact on the digestion? Like being unable to extract or produce certain products? Or having a higher risk for a yeast infection?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;This question also applies to proton channel inhibitors such as Omeprazole and other drugs like Ranitidine&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Background: The lecture was just a introduction to anatomy for informatics. We never went into greater details.)&lt;/p&gt;&#xA;" OwnerUserId="1807" LastEditorUserId="3340" LastEditDate="2014-10-31T04:52:37.543" LastActivityDate="2014-10-31T04:52:37.543" Title="Does eating antacid (such as Magnesia) before meal have any impact on digestion?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;digestive-system&gt;" AnswerCount="0" CommentCount="9" ClosedDate="2014-12-12T18:03:16.467" ContentLicense="CC BY-SA 3.0" />
  <row Id="23584" PostTypeId="1" CreationDate="2014-10-30T15:16:24.417" Score="0" ViewCount="498" Body="&lt;p&gt;How is the structure of DNA different from that of RNA?&lt;/p&gt;&#xA;" OwnerUserId="9988" LastEditorUserId="4747" LastEditDate="2014-10-30T16:22:15.857" LastActivityDate="2014-10-30T18:45:14.670" Title="What are the structual differences between DNA and RNA?" Tags="&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-10-30T17:52:32.497" ContentLicense="CC BY-SA 3.0" />
  <row Id="23586" PostTypeId="1" CreationDate="2014-10-30T16:04:18.383" Score="3" ViewCount="1715" Body="&lt;p&gt;Why are the amino acids - cysteine and tyrosine used in isoelectric point calculations for a protein sequence, yet neither of them are positively charged molecules? and are not used in net charge calculations.&lt;/p&gt;&#xA;" OwnerUserId="9990" LastActivityDate="2014-10-31T12:10:22.993" Title="Why is Cysteine and Tyrosine used to calculate a sequence isoelectric point?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;sequence-analysis&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23587" PostTypeId="2" ParentId="23584" CreationDate="2014-10-30T16:20:54.443" Score="3" Body="&lt;p&gt;DNA and RNA are similar, but different molecules. Both are made up of &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleic_acid&quot; rel=&quot;nofollow noreferrer&quot;&gt;nucleic acids&lt;/a&gt; attached to a backbone made of phosphate and a sugar forming a &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleotide&quot; rel=&quot;nofollow noreferrer&quot;&gt;nucleotide&lt;/a&gt;. DNA uses the nucleic acids Guanine, Cytosine, Adenine, and Thymine, while RNA replaces Thymine with Uridine. &#xA;&lt;img src=&quot;https://i.stack.imgur.com/1iPKG.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/MJ3qw.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;The nucleic acids can form pairs due to hydrogen bonding, which allows the DNA/RNA to store information, if one strand has a C, the other must have a G and vice versa. Same applies for A and T.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/gnJs1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While both molecules are capable of forming &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleic_acid_double_helix&quot; rel=&quot;nofollow noreferrer&quot;&gt;double helices&lt;/a&gt; by hydrogen bonding between G and C or A and T/U, the types of helix tend to be different. DNA prefers to form what is known as a B type helix, while RNA prefers the A type. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EeS63.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The left most helix is A type, the middle is B type, and the right helix is &lt;a href=&quot;http://en.wikipedia.org/wiki/Z-DNA&quot; rel=&quot;nofollow noreferrer&quot;&gt;Z type&lt;/a&gt;, a highly unusual form found only under certain conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA is almost always found as a double stranded molecule, and is primarily responsible for storing the information for making proteins and RNA and regulatory functions in cells. RNA is made by copying information from DNA through a process known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Transcription_%28genetics%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;transcription&lt;/a&gt; and performs a variety of roles. &lt;a href=&quot;http://en.wikipedia.org/wiki/Messenger_RNA&quot; rel=&quot;nofollow noreferrer&quot;&gt;Messenger RNA&lt;/a&gt;, or mRNA, carries information from DNA to &lt;a href=&quot;http://en.wikipedia.org/wiki/Ribosome&quot; rel=&quot;nofollow noreferrer&quot;&gt;ribosomes&lt;/a&gt; where it is used to build proteins through &lt;a href=&quot;http://en.wikipedia.org/wiki/Translation_%28biology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;translation&lt;/a&gt;. &lt;a href=&quot;http://en.wikipedia.org/wiki/Transfer_RNA&quot; rel=&quot;nofollow noreferrer&quot;&gt;Transfer RNA&lt;/a&gt;, or tRNA, carries amino acids to ribosomes to build proteins. The ribosome itself is made of RNA, known as rRNA, with proteins to help it function. Even through RNA is usually made up of only 1 strand, it can fold up and form complex shapes, such as the characteristic tRNA structure shown below. Some RNA molecules can even act as catalysts, carrying out chemical reactions such as cutting up other RNAs. These catalytic RNAs are known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Ribozyme&quot; rel=&quot;nofollow noreferrer&quot;&gt;ribozymes&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ADg4v.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2014-10-30T18:45:14.670" LastActivityDate="2014-10-30T18:45:14.670" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23589" PostTypeId="1" CreationDate="2014-10-30T17:58:57.017" Score="5" ViewCount="37066" Body="&lt;p&gt;I've looked in several sources, but I'm still confused. This is what I have so far:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A &lt;strong&gt;phosphotransferase&lt;/strong&gt; catalyzes the addition of a phosphate group.&lt;/li&gt;&#xA;&lt;li&gt;A &lt;strong&gt;kinase&lt;/strong&gt; is a type of phosphotransferase that transfers a phosphate group from ATP to a substrate.&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A &lt;strong&gt;phosphorylase&lt;/strong&gt; is a type of phosphotransferase that catalyzes the addition of a phosphate group from an inorganic phosphate (HPO4) to a substrate.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A &lt;strong&gt;hydrolase&lt;/strong&gt; catalyzes the hydrolysis of a chemical bond.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;A &lt;strong&gt;phosphatase&lt;/strong&gt; is a type of hydrolase that removes a phosphate group.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Is this right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&#xA;Also adding to the confusion is the enzyme &lt;a href=&quot;https://en.wikipedia.org/wiki/Phosphorylase_kinase&quot; rel=&quot;nofollow&quot;&gt;Phosphorylase kinase&lt;/a&gt;, which is the kinase that phosphorylates the enzyme &lt;a href=&quot;https://en.wikipedia.org/wiki/Glycogen_phosphorylase&quot; rel=&quot;nofollow&quot;&gt;Glycogen phosphorylase&lt;/a&gt;, which hydrolyzes glycogen.&lt;/p&gt;&#xA;" OwnerUserId="89" LastEditorUserId="89" LastEditDate="2014-10-30T20:21:58.320" LastActivityDate="2017-09-02T14:49:47.487" Title="What is the difference between a phosphotransferase, a phosphatase, a phosphorylase and a kinase?" Tags="&lt;enzymes&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23590" PostTypeId="2" ParentId="8355" CreationDate="2014-10-30T18:23:08.067" Score="-2" Body="&lt;p&gt;Simply put, evolution through natural selection is a process which occurs naturally. It will occur to any self-duplicating organism with: variations, hereditary traits and threats to propagation (e.g. all life forms we are familiar with). Evolutionary biologists study this, the same way astrophysicists study space, and studying black holes or life forms doesn't indicate anything other then knowing how it works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually, considering that most people in a certain field take interest in it (because logic), it is to be expected that biologists as a whole would rather see life doesn't go extinct then it does - again saying nothing about whether extinctions have or have not happened in the past.&lt;/p&gt;&#xA;" OwnerUserId="9993" LastEditorUserId="9993" LastEditDate="2015-02-06T02:57:04.257" LastActivityDate="2015-02-06T02:57:04.257" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23591" PostTypeId="1" CreationDate="2014-10-30T18:28:19.940" Score="1" ViewCount="5038" Body="&lt;p&gt;I am told that mutations are heritable changes to the genome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So this begs the question - what are non-heritable changes to genome? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DdCnK.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6759" LastEditorUserId="6759" LastEditDate="2014-10-30T19:33:34.023" LastActivityDate="2014-10-31T10:36:36.780" Title="What are non-heritable changes to genomes?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="23592" PostTypeId="1" AcceptedAnswerId="23600" CreationDate="2014-10-30T18:32:18.940" Score="1" ViewCount="351" Body="&lt;p&gt;As far as I understand, all life started as non-flying and flying came about by natural selection. What is the evolutionary advantageous &quot;path&quot; to flying? Or is there something else to explain this?&lt;/p&gt;&#xA;" OwnerUserId="9993" LastEditorUserId="5144" LastEditDate="2014-10-30T19:32:33.787" LastActivityDate="2014-10-31T00:31:26.183" Title="What is the progressive evolutionary advantage that leads to flying?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;adaptation&gt;&lt;flight&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="2" ClosedDate="2020-10-21T23:42:48.803" ContentLicense="CC BY-SA 3.0" />
  <row Id="23593" PostTypeId="2" ParentId="23591" CreationDate="2014-10-30T19:07:28.943" Score="3" Body="&lt;p&gt;I don't know what you really mean by &quot;heritable changes to the genome&quot;. I think you will understand why this sentence makes no sense after reading what follows. I start with some background and then try to address directly what confuses you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Short introduction to the concept of heritability&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concept of heritability may have two meanings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heritability is a concept defined at the &lt;em&gt;population level&lt;/em&gt; for &lt;em&gt;one given trait&lt;/em&gt;. The heritability ($h_B^2$) (in the broad sense) is the ratio of the genetic variance $V_p$ over the phenotypic variance $V_p$, where the phenotypic variance can itself be decomposed into environmental $V_e$ and genetic variance $V_g$ (and their covariance that we will neglect for the purpose of this question). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$h_B^2 = \frac{V_{g}}{V_{p}} = \frac{V_{g}}{V_{e} + V_{g}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When saying environmental variance $V_e$, we don't refer to the total variance in the environment (such as the variance in temperature for example) but we refer to the phenotypic variance (in a given population of a given trait of interest) that is caused by environmental variance. The same logic is true for the genetic variance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Inheritence&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the concept of heritability applies to phenotypic traits, the concept of inheritence can apply to DNA material. A mutation is inherited if the offspring receives the sequence from his/her mother or from his/her father (assuming we are talking about a species that have sexual reproduction with 2 genders).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Somatic versus germline mutations&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As pointed by @Chris in the comments. In multicellular organisms, not all mutations can be transmitted to the multicellular offspring. Most of the cells do not give rise to any other multicellular organisms. For example, imagine that while the biceps is under development at very low age, a mutation occurs that will be inherited by the daughter cells but not to the multicellular offspring. we call the line of cells that do not give rise to gametes (sperm and ovules), the soma line, by opposition to the germ line which gives rise to the gametes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;To answer your question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As soon as a given locus (position on the DNA) has some variance and that this variance explains some phenotypic variance, then the phenotypic trait it influences has a heritability greater than zero. If the variance at this locus has no effect on the phenotype, then it's heritability is zero (because $V_g = 0$, although there is some variance in the actual sequence). If the phenotypic trait of interest does not show any variance (in the population considered), then the concept of heritability is undefined for this trait!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think you may have a confusion between &quot;inherited trait&quot; and &quot;heritable trait&quot;. A mutation will necessarily be transmissible to the offspring (except if it happen to be in the somatic line in such case it will only be transmitted to daughter cells but not to the multicellular offspring) but it doesn't mean that this mutation will necessarily explain some variance in a phenotypic trait. A new much is necessarily heritable (pay attention to the soma vs germ line) but does not mean that a phenotypic will have higher heritability thanks to this mutation.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-10-30T19:56:31.887" LastActivityDate="2014-10-30T19:56:31.887" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23594" PostTypeId="1" CreationDate="2014-10-30T20:12:43.163" Score="0" ViewCount="153" Body="&lt;p&gt;&quot;Allelic combinations separate randomly. I.e. a parent might be Aa and Bb for two traits but that doesn't necessarily mean the gametes will strictly be AB or ab but any of a number of combinations. I.e. blue eyes does not imply short height or something.&quot;&lt;/p&gt;&#xA;" OwnerUserId="6759" LastActivityDate="2014-10-31T11:12:51.177" Title="Is this a valid definition of independent assortment?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23595" PostTypeId="1" CreationDate="2014-10-30T20:56:32.110" Score="0" ViewCount="404" Body="&lt;p&gt;From &lt;em&gt;Principles of Life&lt;/em&gt; by H. Craig Heller, David E. Sadava, Mary V. Price:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZoFBg.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I understand, Huntington's disease exhibits varying degrees of penetrance depending on &lt;em&gt;how many times the mutation is found&lt;/em&gt; in the person's genome. Penetrance is nearly complete if the incorrect base pair sequence is found over a certain number of times.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is what affects penetrance? Is it exclusively environmental? &lt;/p&gt;&#xA;" OwnerUserId="6759" LastEditorUserId="5198" LastEditDate="2014-10-31T04:44:58.767" LastActivityDate="2014-10-31T06:43:51.910" Title="What impacts penetrance of Huntington's disease?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="10" ClosedDate="2015-03-03T17:27:46.203" ContentLicense="CC BY-SA 3.0" />
  <row Id="23596" PostTypeId="2" ParentId="23594" CreationDate="2014-10-30T21:08:49.137" Score="1" Body="&lt;p&gt;That's a valid explanation, but not definition. Mendel's law of independent assortments states that during the formation of gametes, the alleles for one trait segregate independently of the alleles of another trait.&lt;/p&gt;&#xA;" OwnerUserId="28" LastActivityDate="2014-10-30T21:08:49.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23597" PostTypeId="2" ParentId="23586" CreationDate="2014-10-30T21:38:19.137" Score="2" Body="&lt;p&gt;Every amino acid has a different isoelectric point: a pH where they do not carry electric charge. This isoelectric point depends on the side chains:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;By glycine the side chain $-H$ is neutral (while the amino and carbonic acid groups are not) so the IEP is &lt;code&gt;5.97&lt;/code&gt;.&lt;/li&gt;&#xA;&lt;li&gt;By lysine the side chain $-(CH_2)_4\mbox{-}NH_2$ is alkaline $[R\mbox-NH_2 + H^+ \rightleftharpoons R\mbox-NH_3^+]$, so it will have a more alkaline IEP &lt;code&gt;9.74&lt;/code&gt; than glycine.&lt;/li&gt;&#xA;&lt;li&gt;By glutamic acid the side chain $-(CH_2)_2\mbox -COOH$ is acidic $[R\mbox -COOH \rightleftharpoons R\mbox -COO^- + H^+]$, so it will have a more acidic IEP &lt;code&gt;3.22&lt;/code&gt; than glycine.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Every side chain has more or less contribution to the IEP of the amino acid. In your question&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the side chain of cysteine $-CH_2\mbox-SH$ is a weak acid $[R\mbox-SH \rightleftharpoons R\mbox-S^- + H^+]$ so the IEP is &lt;code&gt;5.07&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;the side chain of tyrosine $-CH_2\mbox-Ph\mbox-{\scriptsize (p)}OH$ is an even weaker acid $[R\mbox-OH \rightleftharpoons R\mbox-O^- + H^+]$ so the IEP is &lt;code&gt;5.66&lt;/code&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And every amino acid has more or less contribution to the IEP of a protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.mhhe.com/physsci/chemistry/carey5e/Ch27/ch27-1-4-2.html&quot; rel=&quot;nofollow&quot;&gt;Table of pKa and pI values&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://academics.keene.edu/rblatchly/Chem220/hand/npaa/aawpka.htm&quot; rel=&quot;nofollow&quot;&gt;Amino Acids with Acidity Values&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.biochem.arizona.edu/classes/bioc460/spring/460web/lectures/LEC3_AAs/LEC3_AAs.html&quot; rel=&quot;nofollow&quot;&gt;Introduction to Proteins; Amino Acids, the Building Blocks of Proteins&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://chemwiki.ucdavis.edu/Wikitexts/UC_Davis/UCD_Chem_115_Lab_Manual/Lab_7%3A_Electrospray_Mass_Spectrometry&quot; rel=&quot;nofollow&quot;&gt;Electrospray Mass Spectrometry&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3340" LastEditDate="2014-10-31T12:10:22.993" LastActivityDate="2014-10-31T12:10:22.993" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23598" PostTypeId="2" ParentId="23589" CreationDate="2014-10-30T22:24:33.957" Score="4" Body="&lt;p&gt;Don't get caught in the linguistic trap of attaching too much significance to the precise meaning of any one piece of scientific jargon. Nomenclature, the system of naming things, utterly sucks in biology, and it sucks even harder for protein biology. There is no one universally accepted classification and naming system for proteins, although there have been plenty of attempts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, phosphotransferases are classified as EC number 2.7. However, Glycogen Phosphorylase is classed under 2.4, which might make you think &quot;well, clearly kinases are enzymes that transfer phosphate groups from organic substrates such as ATP and are classed as 2.7, whereas phosphorylases are enzymes that transfer from inorganic substrates and are therefore classed as 2.4&quot;. But wait! RNase PH is a phosphorylase that's classed under 2.7 &lt;em&gt;and&lt;/em&gt; uses inorganic phosphate, so um... yeah.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, don't get too hung up on the nomenclature. Unless you're working in an enzymology lab just say &quot;kinase&quot; and everyone will know what you're talking about.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-10-30T22:24:33.957" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23600" PostTypeId="2" ParentId="23592" CreationDate="2014-10-30T23:54:38.670" Score="2" Body="&lt;p&gt;The honest answer to this and many other similar evolutionary questions is that we don't know the answer. We can sample information from many different points along an organism's developmental timeline using the fossil record, genetics, etc. and reconstruct various states of said organism's development. The overwhelming evidence is that evolution is the process that connects these various states, but reconstructing the detailed trajectory that leads from one developmental state (e.g. flightless) to another (e.g. flying) is often formally impossible due to the low time resolution of the information that we have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, plenty of people have speculated as to the origins of flight, and there's an excellent &lt;a href=&quot;https://en.wikipedia.org/wiki/Flying_and_gliding_animals#Evolution_and_ecology_of_aerial_locomotion&quot; rel=&quot;nofollow&quot;&gt;wikipedia article on the subject&lt;/a&gt;. From the article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Powered flight has evolved only 4 times (birds, bats, pterosaurs, and insects)... Insects were the first to evolve flight, approximately 350 million years ago. The developmental origin of the insect wing remains in dispute, as does the purpose prior to true flight.  One suggestion is that wings initially were used to catch the wind for small insects that live on the surface of the water, while another is that they functioned in parachuting, then gliding, then flight for originally arboreal insects.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="784" LastEditorUserId="9993" LastEditDate="2014-10-31T00:31:26.183" LastActivityDate="2014-10-31T00:31:26.183" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23602" PostTypeId="2" ParentId="23595" CreationDate="2014-10-31T00:43:38.363" Score="3" Body="&lt;p&gt;Penetrance describes the frequency of a gene's &lt;a href=&quot;http://ghr.nlm.nih.gov/handbook/inheritance/penetranceexpressivity&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;expression&lt;/em&gt;&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Penetrance refers to the proportion of people with a particular genetic change (such as a mutation in a specific gene) who exhibit signs and symptoms of a genetic disorder. (&lt;em&gt;Genetics Home Reference&lt;/em&gt; nih.gov) &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;More specifically:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[P]enetrance is defined as the percentage of individuals with a given genotype who exhibit the phenotype associated with that genotype. For example, an organism may have a particular genotype but &lt;em&gt;may not express the corresponding phenotype, because of&lt;/em&gt; modifiers, epistatic genes, or suppressors in the rest of the genome or because of a modifying effect of the environment. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Note that the environment is only one factor affecting the expression of an allele.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Retinoblastoma and achondroplasia are often referred to in discussions about penetrance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Retinoblastoma is caused by mutations in the Rb gene. Not all people who carry this mutation suffer from retinoblastoma (about 90% do). There are numerous inherited diseases (including cancers) in which the same mutation is not expressed in all the individuals who carry it. Achondroplasia, on the other hand, has 100% penetrance: every person with the specific point mutation in the fibroblast growth factor receptor 3 gene always has abnormal bone growth and dwarfism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Huntingtons is a little different in that patients with 36 to 41 HD CAG repeats exhibit reduced penetrance; that is, &lt;em&gt;some&lt;/em&gt; may not develop HD in their lifetime; however 100% of those with the mutation produce the abnormal/polyQ/polyglutamine-enlarged &lt;em&gt;huntingtin&lt;/em&gt;. The age of onset is dependent on number of repeats but is affected by other modifiers (both genetic and environmental); this becomes less obvious in individuals with higher repeats sizes (e.g. greater than 44).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Huntington's is &lt;em&gt;not&lt;/em&gt; a genotype affected only by environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt; &lt;a href=&quot;https://www.inkling.com/read/thompson-genetics-in-medicine-nussbaum-7th/clinical-case-studies/case-22&quot; rel=&quot;nofollow&quot;&gt;Genetics in Medicine&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt; &lt;a href=&quot;http://scholar.google.com/scholar_url?hl=en&amp;amp;q=http://www.researchgate.net/publication/8674868_A_new_model_for_prediction_of_the_age_of_onset_and_penetrance_for_Huntington%27s_disease_based_on_CAG_length/file/d912f50c7b5514d383.pdf&amp;amp;sa=X&amp;amp;scisig=AAGBfm1I5kP6_bkgQtB8AUmM9IpCp7bU5Q&amp;amp;oi=scholarr&quot; rel=&quot;nofollow&quot;&gt;A new model for prediction of the age of onset and penetrance for Huntington’s disease based on CAG length&lt;/a&gt;&lt;/sub&gt; &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-10-31T06:43:51.910" LastActivityDate="2014-10-31T06:43:51.910" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23603" PostTypeId="2" ParentId="23334" CreationDate="2014-10-31T01:00:14.353" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Why can I feel this, when no forces are actually being applied to my&#xA;  stomach?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Acceleration sensors are in the ears and are part of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Vestibular_system&quot;&gt;vestibular system&lt;/a&gt;. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Vestibular_nuclei&quot;&gt;vestibular nuclei&lt;/a&gt; in the brain uses acceleration- and visual signals to decide what happens to your body. It can be fooled by visual signals without the presence of acceleration signals. The role of the vestibulo-autonomic reflex - you feel in your stomach - is probably to protect your inner organs from the damage they can possibly suffer by acceleration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same can happen by watching films with fast camera movements on a &lt;a href=&quot;http://en.wikipedia.org/wiki/Stereoscopy&quot;&gt;monoscopic&lt;/a&gt; display (e.g. normal films in the cinema or video games on an average LCD monitor, etc...), however not so often than by &lt;a href=&quot;http://en.wikipedia.org/wiki/Stereoscopy&quot;&gt;stereoscopic&lt;/a&gt; displays (e.g. 3d films in the cinema, &lt;a href=&quot;http://en.wikipedia.org/wiki/Stereoscopic_video_game&quot;&gt;stereoscopic video games&lt;/a&gt; on a &lt;a href=&quot;http://en.wikipedia.org/wiki/Head-mounted_display&quot;&gt;head-mounted display&lt;/a&gt; like Oculus Rift, etc...). This is because stereoscopic displays create the perfect illusion of depth (e.g. they can even be used by a therapy to overcome acrophobia), while monoscopic displays don't. So your vestibular nuclei is fooled much easier by stereoscopic displays.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These data show that a subset of PBN/KF neurons, whose activity is&#xA;  altered by a nauseogenic stimulus also respond to body motion and that&#xA;  irritation of the stomach lining can either cause an amplification or&#xA;  reduction in the sensitivity of the units to vestibular inputs. The&#xA;  findings imply that nausea and affective responses to vestibular&#xA;  stimuli may be modified by the presence of emetic signals from the GI&#xA;  system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2011 - &lt;a href=&quot;http://ajpregu.physiology.org/content/302/8/R965&quot;&gt;Integrative responses of neurons in parabrachial nuclei to a nauseogenic gastrointestinal stimulus and vestibular stimulation in vertical planes&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;1995 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7610884&quot;&gt;Study on vomiting related to the vestibulo-autonomic reflex.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This study describes the relation between the vection produced by&#xA;  optical flow and that created by galvanic vestibular stimulation.&#xA;  Vection is the illusion of self motion and is most often experienced&#xA;  when an observer views a large screen display containing a translating&#xA;  pattern. This illusion has only limited fidelity and duration unless&#xA;  it is reinforced by confirming vestibular information. Galvanic&#xA;  vestibular stimulation (GVS) can directly produce the sensation of&#xA;  vection.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2005 - &lt;a href=&quot;http://ieeexplore.ieee.org/xpl/login.jsp?tp=&amp;amp;arnumber=1492799&amp;amp;url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D1492799&quot;&gt;Virtual acceleration with galvanic vestibular stimulation in a virtual reality environment&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Neurons in the vestibular nuclei are not only activated by vestibular&#xA;  signals, but also by visual information. Consequently, the sensations&#xA;  of body motion derived from visual and vestibular signals are&#xA;  indistinguishable.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Sensations of body movement can also be generated by visual signals&#xA;  arriving at the vestibular nuclei. During unnatural movements of the&#xA;  body, conflict between visual and vestibular information leads to&#xA;  disorientation and nausea, as in the oculogyral illusion, the Coriolis&#xA;  effect, and vection.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.psypress.co.uk/mather/resources/topic.asp?topic=ch03-tp-02&quot;&gt;Foundations of Perception - The body senses - The vestibular system&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Three-dimensional movies presented via stereoscopic displays have&#xA;  become more popular in recent years aiming at a more engaging viewing&#xA;  experience. However, neurocognitive processes associated with the&#xA;  perception of stereoscopic depth in complex and dynamic visual stimuli&#xA;  remain understudied. Here, we investigate the influence of&#xA;  stereoscopic depth on both neurophysiology and subjective experience.&#xA;  Using multivariate statistical learning methods, we compare the brain&#xA;  activity of subjects when freely watching the same movies in 2D and in&#xA;  3D. Subjective reports indicate that 3D movies are more strongly&#xA;  experienced than 2D movies. On the neural level, we observe&#xA;  significantly higher intersubject correlations of cortical networks&#xA;  when subjects are watching 3D movies relative to the same movies in&#xA;  2D. We demonstrate that increases in intersubject correlations of&#xA;  brain networks can serve as neurophysiological marker for stereoscopic&#xA;  depth and for the strength of the viewing experience.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1053811914004856&quot;&gt;Stereoscopic depth increases intersubject correlations of brain networks&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Statistical differences in theta activity showed that the real and 3D&#xA;  environments caused similar cognitive processes, while the 2D caused&#xA;  an increase of anxiety indicating that perhaps participants were&#xA;  looking for the third dimension. Beta and gamma activity showed that&#xA;  participants perceived the third dimension of the stereoscopic&#xA;  environment as in the real one, something that did not happen in the&#xA;  2D environment. Our findings indicate that stereoscopic 3D virtual&#xA;  environments seem to approximate the real ones as far as it regards&#xA;  the cognitive processes they cause. Three dimensional stereoscopic&#xA;  environments increase users’ attention over the 2D and cause less&#xA;  mental effort.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://earthlab.uoi.gr/ojs/theste/index.php/theste/article/view/124&quot;&gt;Stereoscopic perception of women in real and virtual environments: A study towards educational neuroscience&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2001 - &lt;a href=&quot;http://jn.physiology.org/content/86/4/2054.short&quot;&gt;Human Cortical Activity Correlates With Stereoscopic Depth Perception&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In this study the effects of virtual reality exposure therapy (VRET)&#xA;  were investigated in patients with acrophobia. Feelings of presence in&#xA;  VRET were systematically varied by using either a head-mounted display&#xA;  (HMD) (low presence) or a computer automatic virtual environment&#xA;  (CAVE) (high presence). VRET in general was found to be more effective&#xA;  than no treatment. No differences were found in effectiveness between&#xA;  VRET using an HMD or CAVE. Results were maintained at 6 months&#xA;  follow-up. Results of VRET were comparable with those of exposure in&#xA;  vivo (Cyberpsychology and Behavior 4 (2001) 335). In treatment&#xA;  completers no relationship was found between presence and anxiety.&#xA;  Early drop-outs experienced less acrophobic complaints and&#xA;  psychopathology in general at pre-test. They also experienced less&#xA;  presence and anxiety in the virtual environment used in session one as&#xA;  compared to patients that completed VRET.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2004 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0005796703001396&quot;&gt;Treatment of acrophobia in virtual reality: The role of immersion and presence&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Despite the increasing use of virtual reality, the impact on cerebral&#xA;  representation of topographical knowledge of learning by virtual&#xA;  reality rather than by actual locomotion has never been investigated.&#xA;  To tackle this challenging issue, we conducted an experiment wherein&#xA;  participants learned an immersive virtual environment using a&#xA;  joystick. The following day, participants' brain activity was&#xA;  monitored by functional magnetic resonance imaging while they mentally&#xA;  estimated distances in this environment. Results were compared with&#xA;  that of participants performing the same task but having learned the&#xA;  real version of the environment by actual walking. We detected a large&#xA;  set of areas shared by both groups including the parieto-frontal areas&#xA;  and the parahippocampal gyrus. More importantly, although participants&#xA;  of both groups performed the same mental task and exhibited similar&#xA;  behavioral performances, they differed at the brain activity level.&#xA;  Unlike real learners, virtual learners activated a left-lateralized&#xA;  network associated with tool manipulation and action semantics. This&#xA;  demonstrated that a neural fingerprint distinguishing virtual from&#xA;  real learning persists when subjects use a mental representation of&#xA;  the learnt environment with equivalent performances.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/hbm.20917/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot;&gt;Impact of the virtual reality on the neural representation of an environment&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our main results are (1) stereoscopy in games increased experienced&#xA;  immersion, spatial presence, and simulator sickness; (2) the eff ects&#xA;  strongly differed across the three games and for both ge nders,&#xA;  indicating more affect on male users and with games involving depth&#xA;  animations; (3) results related to attention and cognitive involvement&#xA;  indicate more direct and less thoughtful interactions with&#xA;  stereoscopic games, pointing towards a more natural experience through&#xA;  stereoscopy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;https://www.uni-due.de/~hk0377/papers/Schild2012_CHI2012_User_Expericence_in_Stereoscopic_3D_Games.pdf&quot;&gt;Understanding User Experience in Stereoscopic 3D Games&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The results indicate that in a 2D movie viewers tended to look at the&#xA;  actors, as most of the eye movements were clustered there. The&#xA;  significance of the actors started at the beginning of a shot, as the&#xA;  eyes of the viewer focused almost immediately to them. In S3D movie&#xA;  the eye movement patterns were more widely distributed to other&#xA;  targets. For example, complex stereoscopic structures and objects&#xA;  nearer than the actor captured the interest and eye movements of the&#xA;  participants. Also, the tendency to first look at the actors was&#xA;  diminished in the S3D shots.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://www.researchgate.net/publication/252715479_What_do_people_look_at_when_they_watch_stereoscopic_movies&quot;&gt;What do people look at when they watch stereoscopic movies?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For the correlation between anxiety and presence, the results show&#xA;  very low correlation between anxiety and presence.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0097849310001263&quot;&gt;Using augmented and virtual reality for the development of acrophobic scenarios. Comparison of the levels of presence and anxiety&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Stereoscopic visualization in cinematography and VR creates an&#xA;  illusion of depth by means of two bidimensional images corresponding&#xA;  to different views of a scene. This perceptual “trick” is used to&#xA;  enhance the emotional response and the sense of presence and&#xA;  immersivity of the observers. An interesting question is if and how is&#xA;  possible to measure and analyze the level of emotional involvment of&#xA;  the observers during a stereoscopic visualization of a movie or of a&#xA;  virtual environment. The final goal of this research is a challenge,&#xA;  due to the large number of sensorial, physiological and cognitive&#xA;  stimuli involved. In this paper we begin this research by analyzing&#xA;  eventual differences in the brain activity of subjects during the&#xA;  observation of monoscopic or stereoscopic contents. To this aim, we&#xA;  have performed some experiments collecting EEG data using a&#xA;  Brain-Computer Interface device from two groups of users, during the&#xA;  observation of stereoscopic and monoscopic short movies inside the&#xA;  Virtual Theater of the University of Milan. From the analysis of the&#xA;  collected data, it seems that interesting differences are present in&#xA;  the average brain activity among the observers in the two groups, with&#xA;  a significative effect of stereoscopic visualization.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://spie.org/Publications/Proceedings/Paper/10.1117/12.906708&quot;&gt;Analysis of brain activity and response during monoscopic and stereoscopic visualization&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-10-31T01:00:14.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23606" PostTypeId="1" CreationDate="2014-10-31T03:21:21.427" Score="1" ViewCount="54" Body="&lt;p&gt;I understand that Fluorescence in situ hybridisation  can be used to measure the effectiveness of a gene therapy experiment/trial. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what are some other genetics techniques to measure the effectiveness of a gene therapy clinical trial. Would blotting (northern/southern) and PCR be a way to tell if a new genome have been integrated into existing cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="8279" LastActivityDate="2014-11-30T06:32:20.607" Title="Ways to measure effectiveness of a gene therapy trial?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23607" PostTypeId="1" AcceptedAnswerId="23608" CreationDate="2014-10-31T05:27:12.530" Score="-1" ViewCount="253" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Cells &quot;grown in LB broth to an OD600nm&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What does the OD stand for in this?&lt;/p&gt;&#xA;" OwnerUserId="10000" LastActivityDate="2014-10-31T05:41:22.373" Title="Cells &quot;grown in LB broth to an OD600nm&quot;" Tags="&lt;cell-culture&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-10-31T06:39:39.687" ContentLicense="CC BY-SA 3.0" />
  <row Id="23608" PostTypeId="2" ParentId="23607" CreationDate="2014-10-31T05:41:22.373" Score="1" Body="&lt;p&gt;&lt;strong&gt;OD&lt;/strong&gt; = &lt;strong&gt;O&lt;/strong&gt;ptical &lt;strong&gt;D&lt;/strong&gt;ensity&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you grow cells in broth, the broth becomes cloudy. The more cells there are, the cloudier it is. After you grow your cells for a while, you can measure their progress by shining a light through your sample. The more light your cell culture absorbs (higher absorbance is equivalent to higher OD) the more cells there are in it.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-10-31T05:41:22.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23609" PostTypeId="2" ParentId="23606" CreationDate="2014-10-31T05:59:05.093" Score="1" Body="&lt;p&gt;If all you cared about was genomic integration, then your best bet would be some kind of sequencing. If you sequence the modified region and the flanking regions you could be sure that the new sequence was present in the genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would probably be more interesting to look at how the new genes affect the cell. For example you could look at differences between protein expression in modified and unmodified cells. For that you could use RNAseq.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-10-31T05:59:05.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23610" PostTypeId="1" AcceptedAnswerId="70025" CreationDate="2014-10-31T08:04:12.970" Score="8" ViewCount="12861" Body="&lt;p&gt;I saw the chart in this post &lt;a href=&quot;https://biology.stackexchange.com/questions/8206/histidine-aromaticity&quot;&gt;Histidine aromaticity&lt;/a&gt;. Since I'm not allowed to comment and post a question instead of an answer, I have to ask my question in a separate thread. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can histidine be classified both as positively charged and hydrophobic?&lt;/p&gt;&#xA;" OwnerUserId="10001" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2018-01-31T13:49:19.113" Title="How can histidine be classified both as positively charged and hydrophobic?" Tags="&lt;molecular-biology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23612" PostTypeId="2" ParentId="23610" CreationDate="2014-10-31T08:55:19.780" Score="5" Body="&lt;p&gt;As @wysiwig stated, &lt;a href=&quot;http://en.wikipedia.org/wiki/Histidine&quot; rel=&quot;noreferrer&quot;&gt;Histidine&lt;/a&gt; is not hydrophobic. Depending on the pH different parts of the molecule can carry charges, see the image below (from &lt;a href=&quot;http://employees.csbsju.edu/cschaller/principles%20chem/acidity/acid%20pH.htm&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KHOaO.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nitrogen atoms can be protonated in an acidic environment, the carboxylgroup will loose it proton in a basic environment. All these forms are transferred into each other, when the pH changes.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-10-31T08:55:19.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23613" PostTypeId="1" AcceptedAnswerId="23614" CreationDate="2014-10-31T09:59:59.130" Score="12" ViewCount="633" Body="&lt;p&gt;I am currently writing a literature review in which I am talking about the old research on the subject. When this research was carried out the species I'm talking about were classed under a different genus (specifically, it used to be called &lt;em&gt;Vibrio fetus&lt;/em&gt; and is now called &lt;em&gt;Campylobacter fetus&lt;/em&gt;). What is the correct approach for choosing when to use the older name and when to use the newer name? I see three options, although there may be more:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Always use the modern name.&lt;/li&gt;&#xA;&lt;li&gt;Use the name used by the authors when discussing their work.&lt;/li&gt;&#xA;&lt;li&gt;Largely use the modern name but make reference to the fact a different name was employed where it is appropriate to do so.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I'm tending towards option 3, but it's sometimes a bit unwieldy. Is there an accepted convention I should be following?&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="3340" LastEditDate="2014-11-15T11:30:15.967" LastActivityDate="2014-11-15T11:30:15.967" Title="When writing about past research should I use the species name they employed or the modern version?" Tags="&lt;taxonomy&gt;&lt;nomenclature&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23614" PostTypeId="2" ParentId="23613" CreationDate="2014-10-31T10:30:21.160" Score="16" Body="&lt;p&gt;&lt;strong&gt;3.&lt;/strong&gt; is right thing to do. You can mention in the introduction that &quot;&lt;em&gt;Campylobacter fetus&lt;/em&gt;, which was previously known as &lt;em&gt;Vibrio fetus&lt;/em&gt; &lt;sup&gt;[Ref]&lt;/sup&gt; .........&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should not use the old name anywhere again (also for the sake of consistency), once you have made it clear that the species was renamed, in the Introduction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think there is any written convention like that (As such usage of any obsoleted terms is to be avoided and the standard nomenclature as described by ICZN/ICBN etc should be used). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-10-31T10:36:55.190" LastActivityDate="2014-10-31T10:36:55.190" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23615" PostTypeId="2" ParentId="23591" CreationDate="2014-10-31T10:36:36.780" Score="2" Body="&lt;p&gt;&lt;strong&gt;Most mutations to the DNA are heritable, but not all are inherited.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations occur in the DNA, DNA is then replicated and transmitted to offspring (cells or organisms). Generally all mutations are heritable because they can be inherited, but some aren't - either by random chance (drift) or deleterious fitness effects (selection). Any mutation which makes the cell less fit has a reduced chance of being inherited, but even mutations leading to cancer are inherited at some level (from mother cancer cell to daughter cancer cells) but at some point this lineage of inheritance will stop because it will kill the host (but this is no different to species/lineages of organism going extinct - if I carried a new novel mutation but didn't have children then that mutation is not inherited).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*I suppose a mutation which stops DNA from being replicated could be classed as not-heritable because the DNA is not going to be replicated, but that depends on there being no other sources of replication machinery (other cells perhaps) - a process I don't know well enough to offer any firm conclusions on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Non-heritable changes to the genome&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA can be altered beyond just sequence mutation, for example methylation- but this can be used as a heritable change to the genome (&lt;a href=&quot;http://en.wikipedia.org/wiki/Genomic_imprinting&quot; rel=&quot;nofollow&quot;&gt;genomic imprinting&lt;/a&gt;). Perhaps gene expression with strong environmental effects on gene expression could be considered as not heritable (because if the environment is not &quot;&lt;em&gt;inherited&lt;/em&gt;&quot; then parent-offspring regression would be 0) but maybe that's a change to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Transcriptome&quot; rel=&quot;nofollow&quot;&gt;transcriptome&lt;/a&gt; rather than genome.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-10-31T10:36:36.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23616" PostTypeId="2" ParentId="23610" CreationDate="2014-10-31T11:04:03.130" Score="5" Body="&lt;p&gt;As @Chris says, the charge depends on the pH: when the pH is different from the pH(I) of the molecule, this one is charged.(Take a look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Isoelectric_point&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt;).&#xA;Anyway, talking about Hys, its pH(I) is 7.47 (&lt;a href=&quot;http://www.chemie.fu-berlin.de/chemistry/bio/aminoacid/histidin_en.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;), so at a pH below its pI, the Histidine carry a net positive charge, otherwise it can be also in a netrual form. Obviously it's all a matter of equilibrium!&lt;/p&gt;&#xA;" OwnerUserId="3645" LastActivityDate="2014-10-31T11:04:03.130" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23617" PostTypeId="2" ParentId="23594" CreationDate="2014-10-31T11:12:51.177" Score="1" Body="&lt;pre&gt;&lt;code&gt;The Law of Independent Assortment:&#xA;Alleles for different traits are distributed to sex cells (&amp;amp; offspring) independently of one another.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This one is like written on the stone in my mind!&lt;/p&gt;&#xA;" OwnerUserId="3645" LastActivityDate="2014-10-31T11:12:51.177" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23619" PostTypeId="1" CreationDate="2014-10-31T15:12:30.477" Score="1" ViewCount="6714" Body="&lt;p&gt;The question is quite explanatory in it self, I used to think that both are same but then find somewhere that embryology is a part of developmental biology, can somebody please elucidate?&lt;/p&gt;&#xA;" OwnerUserId="9674" LastActivityDate="2018-02-05T09:44:01.703" Title="What is the difference between embryology and developmental biology?" Tags="&lt;reproduction&gt;&lt;development&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="23620" PostTypeId="1" CreationDate="2014-10-31T16:27:26.173" Score="1" ViewCount="72" Body="&lt;p&gt;There is no AAMI 12-lead ECG databases available online. &#xA;All of them have problems. &#xA;I and my friends finally finalised our tests with &lt;a href=&quot;https://biology.stackexchange.com/a/21870/86&quot;&gt;St Petersburg&lt;/a&gt;. &#xA;It is not AAMI. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the next step is to search any ECG databases with some leads (at least lead 2) with ECHO data. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any AAMI standarded ECG databases with ECHO data?&lt;/strong&gt;&#xA;This data need to be from the same patient. &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-06-17T22:40:15.997" Title="Any databases with AAMI ECG and ECHO?" Tags="&lt;cardiology&gt;&lt;database&gt;&lt;electrocardiography&gt;&lt;research-tools&gt;&lt;research-process&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23622" PostTypeId="1" AcceptedAnswerId="50704" CreationDate="2014-10-31T18:01:11.180" Score="8" ViewCount="187" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many models including the famous very first models derived by &lt;a href=&quot;http://en.wikipedia.org/wiki/Ronald_Fisher&quot; rel=&quot;nofollow&quot;&gt;Sir Ronald Fisher&lt;/a&gt; in his early career, assume infinite population size. In an infinite population, an allele can rise in frequency (if its fitness is greater than the fitness of its counterpart(s)). This increase follows a logistic curve that never exactly reach a frequency of 1. Therefore, the term fixation does not apply to these model and in consequence the concept of quasifixation has been created.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An allele is considered to be quasifixed if it reaches a frequency that is very close to 1. But how close? The decision is obviously arbitrary but when using a &lt;em&gt;continuous approximation model&lt;/em&gt; in a finite population the question is necessarily raised and a decision needs to be made. &lt;strong&gt;How close should the frequency of an allele be to 1 so that it is considered to be quasifxed?&lt;/strong&gt; The answer is probably a function of the population size $N$. What threshold do authors usually use in the theoretical population genetics literature? It would also be nice to have the definition of the author who first coined this term.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2016-08-06T17:21:04.457" LastActivityDate="2016-08-15T17:36:38.627" Title="How to define &quot;Quasifixation&quot; in continuous approximation of finite population?" Tags="&lt;evolution&gt;&lt;population-dynamics&gt;&lt;theoretical-biology&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23623" PostTypeId="1" CreationDate="2014-10-31T18:09:47.840" Score="6" ViewCount="360" Body="&lt;p&gt;I have a degree in Biology so I'm a little embarrassed that I never learned this, but...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do we know 1600 Pandas isn't enough?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that we have historical numbers (although I couldn't find them) which show the population has declined, but we also know the usable habitat has declined and it would be foolish to not consider that when trying to replenish the wild population. It seems to me that if there's only 1600 Pandas in the wild, that's probably the right number. How do we know it's not?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will accept answers about other endangered animals, if they show how we can calculate the approximate &quot;appropriate&quot; number for a species.&lt;/p&gt;&#xA;" OwnerUserId="10009" LastEditorUserId="1578" LastEditDate="2015-01-10T09:48:08.397" LastActivityDate="2015-11-30T16:20:26.527" Title="How can we calculate the minimum sustainable number of the panda population?" Tags="&lt;ecology&gt;&lt;population-dynamics&gt;&lt;conservation-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23625" PostTypeId="2" ParentId="23619" CreationDate="2014-10-31T18:20:09.057" Score="3" Body="&lt;p&gt;It's a simple sub-set relationship, embryology is a sub-set of developmental (it's a &quot;specialty&quot;). Embryology is only concerned with the embryo - developmental is a larger group, concerned with developments that may occur in other stages of life. Such as the development of secondary sexual characteristics in humans - a developmental thing, but not embryonic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are not purely objective definitions and the dividing lines are not well defined. Labels for various scientific fields are only generally applicable, and they are very flexible. For example, many Chemists also do a lot of physics. Many Biologists do a lot of Chemistry. Many Embryology studies dip into developmental stuff. These divisions are not always clear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Embryology is a part of Developmental Biology in the same way that Biology is part of &quot;Science&quot; - simple sub-set relationship. If you don't understand sub-sets very clearly, you'll want to study up on that relationship - it's very important in ALL sciences, so you can understand things like &quot;All squirrels are animals, but not all animals are squirells&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This statement would be reasonable - &quot;All Embrology is Developmental Biology, but some Developmental Biology is NOT Embryology&quot;&lt;/p&gt;&#xA;" OwnerUserId="10009" LastEditorUserId="10009" LastEditDate="2014-11-05T17:51:30.927" LastActivityDate="2014-11-05T17:51:30.927" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23627" PostTypeId="1" CreationDate="2014-10-31T21:46:18.767" Score="1" ViewCount="20" Body="&lt;p&gt;I just need a clarification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I am to talk about the physiological function of the CFTR gene product? Then what should I do research and talk about?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only physiological function that I can think of is the control of the thickness of mucus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any other ones?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On top of that, if i am to search for research paper for this topic. Do I just search for comparative study that compare the gene product in normal individuals and CF individuals in terms of mucus thickness?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="8279" LastActivityDate="2014-10-31T21:46:18.767" Title="Physiological function of CFTR gene product?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;homework&gt;&lt;medicine&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-11-01T13:25:53.517" ContentLicense="CC BY-SA 3.0" />
  <row Id="23630" PostTypeId="1" CreationDate="2014-10-31T23:38:07.483" Score="4" ViewCount="132" Body="&lt;p&gt;Humans and chimpanzees are related and thus have a most recent common ancestor. Of course pinning down this precise point is essentially impossible, so I'm interested in close ancestors of this most recent common ancestor. Also, I'd like to know things about it -- how it compares to common chimpanzees, bonobos, and humans in various ways -- so species known only from fragmentary evidence are less interesting to me. Ideally I'd ask for something with at least one near-complete skeleton and a separate (perhaps less complete) find, but as a non-expert I'd be happy to settle for whatever is considered to be well-attested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, what is the most recent well-attested common ancestor of chimpanzees and humans?&lt;/p&gt;&#xA;" OwnerUserId="10014" LastActivityDate="2021-05-08T14:05:10.947" Title="What is the most recent well-attested common ancestor of chimpanzees and humans?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;taxonomy&gt;&lt;phylogenetics&gt;&lt;cladistics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23632" PostTypeId="1" AcceptedAnswerId="25962" CreationDate="2014-11-01T02:49:46.767" Score="5" ViewCount="1455" Body="&lt;p&gt;What mechanism allows anadromous fish (like salmon) to switch from salt to fresh water and back?  How does the fish &quot;know&quot; to switch its physiology and do other fish possess the biochemical machinery for this?  How difficult would it be to genetically engineer salt tolerance into a freshwater fish?&lt;/p&gt;&#xA;" OwnerUserId="8387" LastEditorUserId="3340" LastEditDate="2014-12-06T11:53:33.680" LastActivityDate="2014-12-17T08:45:18.750" Title="How does anadromous fish physiology &quot;know&quot; to switch from salt to freshwater and back?" Tags="&lt;physiology&gt;&lt;ichthyology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23634" PostTypeId="1" CreationDate="2014-11-01T05:35:14.920" Score="6" ViewCount="86" Body="&lt;p&gt;If I enter a room with certain odor, I can sense the odor. However, if I stay there for some time I cannot sense it anymore. A new entrant to the room can still smell it or I have to leave the room for some time and upon returning I can sense it again. Does our nose detect only if there is change in odor? &lt;/p&gt;&#xA;" OwnerUserId="10017" LastEditorUserId="16866" LastEditDate="2016-01-11T20:17:40.027" LastActivityDate="2016-01-11T21:37:01.427" Title="Does our nose detect only if there is change in odor?" Tags="&lt;physiology&gt;&lt;senses&gt;&lt;olfaction&gt;&lt;nose&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23635" PostTypeId="1" AcceptedAnswerId="30332" CreationDate="2014-11-01T06:49:02.017" Score="1" ViewCount="82" Body="&lt;p&gt;I've noticed that the sound of water drops makes me wake up from sleep but other more strong sounds don't make me wake up. I can't find anything about this. The only reason I can think of is maybe because the sound of drops is continuous. Is there any research about the qualitative aspects of certain noises that affect the likelihood of causing arousal  from sleep?&lt;/p&gt;&#xA;" OwnerUserId="6927" LastEditorUserId="9268" LastEditDate="2014-11-01T15:32:18.990" LastActivityDate="2015-03-11T10:29:34.033" Title="What factors affect the likelihood of auditory stimuli causing arousal during sleep?" Tags="&lt;human-biology&gt;&lt;sleep&gt;&lt;hearing&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23636" PostTypeId="2" ParentId="23634" CreationDate="2014-11-01T09:20:00.443" Score="4" Body="&lt;p&gt;Senses in general &lt;a href=&quot;http://en.wikipedia.org/wiki/Neural_adaptation&quot; rel=&quot;nofollow&quot;&gt;adapt&lt;/a&gt; to continuous stimulation due to various processes. One such process is simply the exhaustion of the reserves of a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/mesh?term=Sensory+Receptor+Cells&quot; rel=&quot;nofollow&quot;&gt;receptor&lt;/a&gt;, or secondary neuron, due to a depletion of neurotransmitters. Entering a room activates a fresh pool of chemical receptors, thereby generating a clear sense of smell. However, this dims due to adaptation. Exiting and re-entering the room after a while revives the neuronal response. More &lt;a href=&quot;http://en.wikipedia.org/wiki/Neural_adaptation&quot; rel=&quot;nofollow&quot;&gt;central adaptive responses&lt;/a&gt; may also play a role. A comparable effect is seen in the tactile sense. For example, the awareness of wearing a ring or watch fades quickly. Changing its position revives the percept. So yes, sensory systems like olfaction and touch are more responsive to &lt;strong&gt;differential stimuli&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-01-11T21:37:01.427" LastActivityDate="2016-01-11T21:37:01.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23637" PostTypeId="1" CreationDate="2014-11-01T11:32:16.007" Score="15" ViewCount="573" Body="&lt;p&gt;The electroretinogram (ERG) is a measure of electrical activity of the retina. It is typically recorded from the cornea with a wire electrode or gold-foil electrode. Generally, the the ERG is considered to reflect the retinal processing of a light stimulus, typically a photoreceptor response followed by secondary neuronal activity and electrical activity evoked by supportive Muller cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering if the pupil response will add signal on top of the ERG? Firstly, there is the direct pupil response, which causes the pupil to constrict when the eye is subjected to bright light. Pupil constriction may, perhaps, induce &lt;strong&gt;electromyogram (EMG) activity&lt;/strong&gt; when the smooth sphincter muscle around the pupil contracts, which in turn could theoretically contaminate the ERG. Secondly, there is &lt;strong&gt;neuronal activity&lt;/strong&gt; involved in constricting the pupil, as light is processed in the retina by ganglion cells that in turn drive the pupil reflex. Furthermore, there is the consensual pupil response as well. This response causes the contralateral pupil to constrict when the ipsilateral eye is subjected to bright light. The consensual response is mediated by efferent input from the brain following stimulation of the other eye and causes both eyes to restrict. Hence, neural input arrives in the contralateral retina from the brain. This activity is not directly related to the processing of the light stimulus and may disturb the ERG proper when ERGs are recorded with a flash and both eyes are open. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Does a pupil-mediated EMG affects the ERG signal?&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Does neuronal activity involved in the pupil reflex affect the ERG, for example the  efferent input involved in the consensual response?&lt;/strong&gt; &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I have had no luck after extensive searches in text books, Scopus, Pubmed, Google, Google Scholar. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-11-03T01:02:28.093" LastActivityDate="2015-11-03T01:02:28.093" Title="Effect of pupil responses on the electroretinogram" Tags="&lt;neuroscience&gt;&lt;vision&gt;&lt;biophysics&gt;&lt;electrophysiology&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23638" PostTypeId="1" AcceptedAnswerId="28143" CreationDate="2014-11-01T11:37:41.123" Score="21" ViewCount="1331" Body="&lt;p&gt;Suppose you graft a piece of an existing 'old' plant onto a host plant. Will the graft continue to grow having the same biological age as its parent? In other words, would the graft die at the same time as its parent plant? Or would the process of grafting result in some sort of rejuvenation of the grafted daughter plant? Or alternatively, would the host plant carrying the graft determine the biological age of the graft primarily? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;PS: Personal experience-based (anecdotal) answers are more than welcomed&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2019-03-04T20:33:49.943" LastActivityDate="2019-03-04T20:33:49.943" Title="What is the biological age of grafted plants?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;development&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="6" ContentLicense="CC BY-SA 4.0" />
  <row Id="23639" PostTypeId="2" ParentId="23511" CreationDate="2014-11-01T12:31:55.277" Score="1" Body="&lt;p&gt;I'm going to hazard that primordial sociality by this definition and this question proceeded primordal motility in cells.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Algae started to form physically attached groups like these filaments, giving them some of the advantages of higher organization.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rKbNR.jpg&quot; alt=&quot;Filamentous Cyanobacteria&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its easy to see how this is a relatively simple adaptation - just have proteins or carbohydrates on the cell surface that stick together.  This might also have evolved from large cells compartmentalizing since we're talking about very ancient stages of life on earth. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-11-01T12:31:55.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23640" PostTypeId="1" CreationDate="2014-11-01T14:00:02.537" Score="2" ViewCount="192" Body="&lt;p&gt;During some cultivation experiments for my bachelor thesis I noticed that in liquid culture my bacteria (E. coli) grew differently, according to the position in the shaking incubator.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the goal was just to induce protein expression at a given OD, I altered the position of the flasks in the shaker, so the cultures were at a similar OD and I could add the IPTG to all of them at the same time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now I wonder if someone else noticed this phenomenon (Literature to cite would be great, I couldn't find anything until now) or if I did something wrong. Maybe it's also known and ignored for longer times?&#xA;The cultures more in the back of the incubator grew faster, so I think it's because of temperature alterations when opening the incubator to draw samples for growth kinetics, but I'm not sure about this at the moment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for helping me :-)&lt;/p&gt;&#xA;" OwnerUserId="10021" LastActivityDate="2014-11-01T14:00:02.537" Title="Effect of flask position in shaking incubator affects growth kinetics" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;cell-culture&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23641" PostTypeId="1" AcceptedAnswerId="24154" CreationDate="2014-11-01T16:12:33.350" Score="17" ViewCount="10450" Body="&lt;p&gt;I wonder why (especially human) sex lasts longer than just a few seconds?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My thought is that the shorter it takes a man to ejaculate, the lesser is the risk that he gets interrupted by a rival or a predator. Therefore, men who ejaculate quickly get an evolutionary advantage in the long-term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, as human sex lasts several minutes, I'm obvioulsy wrong with my argument. Anybody knows why?&lt;/p&gt;&#xA;" OwnerUserId="10022" LastActivityDate="2015-07-24T01:45:34.733" Title="Why does sex last so long?" Tags="&lt;evolution&gt;&lt;sex&gt;&lt;sexual-selection&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23643" PostTypeId="1" AcceptedAnswerId="26230" CreationDate="2014-11-01T23:49:00.147" Score="8" ViewCount="1240" Body="&lt;p&gt;I have been reading:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;William B. Whitman, David C. Coleman, and William J. Wiebe, &quot;Prokaryotes: The unseen majority&quot;, Proc. Natl. Acad. Sci. USA &lt;strong&gt;95&lt;/strong&gt;, pp. 6578–6583, June 1998.  &lt;a href=&quot;http://www.pnas.org/content/95/12/6578.full&quot;&gt;[Full Text]&lt;/a&gt; &lt;a href=&quot;http://www.pnas.org/content/95/12/6578.full.pdf+html&quot;&gt;[PDF]&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;wherein they estimate the number of prokaryote cells on Earth to be of the order of $10^{31}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't seem to find any equivalent data for eukaryote one-celled life. Are there any estimates for the number of one-celled eukaryotic living things on Earth? Do any other estimates confirm or tell against the reference I have cited above?&lt;/p&gt;&#xA;" OwnerUserId="5084" LastEditorUserId="57" LastEditDate="2014-11-02T08:16:21.387" LastActivityDate="2014-12-31T20:13:54.793" Title="How many eukaryotes are there on Earth?" Tags="&lt;microbiology&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23644" PostTypeId="1" AcceptedAnswerId="28032" CreationDate="2014-11-02T00:11:39.380" Score="8" ViewCount="529" Body="&lt;p&gt;I have been reading:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;M. Dröge, A. Pühler, W. Selbitschka, &quot;Horizontal gene transfer among bacteria in terrestrial and aquatic habitats as assessed by microcosm and field studies&quot;, Biol. Fertil. Soils (1999) &lt;strong&gt;29&lt;/strong&gt; pp221–245  &lt;a href=&quot;http://molecol.ifas.ufl.edu/education/webctvista/lectures/lgenetic/bsf29-3.pdf&quot; rel=&quot;nofollow&quot;&gt;[PDF]&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am not a biologist and am trying to get a feeling for how often prokaryotes make changes to their chromosomal DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How often is plasmid DNA successfully incorporated into chromosomal DNA?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to estimate either the number of gene changes (or, failing this, base pair changes) that a bacterium makes per unit time. Or, equivalently, the mean time between such changes.&lt;/p&gt;&#xA;" OwnerUserId="5084" LastEditorUserId="3553" LastEditDate="2015-11-30T05:49:06.637" LastActivityDate="2015-12-01T08:53:24.660" Title="How often does bacterial transformation happen?" Tags="&lt;genetics&gt;&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23646" PostTypeId="1" AcceptedAnswerId="23647" CreationDate="2014-11-02T04:17:03.497" Score="6" ViewCount="198" Body="&lt;p&gt;What causes phospholipids to flow so quickly in cell membranes? In Biology by Cambell et al. they state that a phospholipids can travel up to 2 micrometers per second. Is that a random movement or has anyone found that phospholipids have a current?&lt;/p&gt;&#xA;" OwnerUserId="10026" LastActivityDate="2014-11-02T05:30:45.870" Title="Phospholipid movement in cell membranes" Tags="&lt;biochemistry&gt;&lt;cell-membrane&gt;&lt;lipids&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23647" PostTypeId="2" ParentId="23646" CreationDate="2014-11-02T05:30:45.870" Score="5" Body="&lt;p&gt;There must be charge considerations in the movement of molecules in the lipid membrane. There is also a consideration that some species of phospholipids will migrate to &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0005273614001850&quot;&gt;portions of the membrane with sharper or smoother curvature&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Waves of electrical potential can propagate along a lipid bilayer as well, which is very important to nerve axons and extended structures like that.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general though the membrane is held together by vanDerWaals forces like other non-polar solvents.  As such, the movements of lipids and proteins and other amphipathic molecules in the membrane are still largely Brownian (random) in the 2D surface of the membrane. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2014-11-02T05:30:45.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23648" PostTypeId="1" AcceptedAnswerId="23650" CreationDate="2014-11-02T12:18:00.463" Score="6" ViewCount="1525" Body="&lt;p&gt;I wanted to know the chemical reaction involved in Fab synthesis. I looked everywhere for it. No luck. I know I will find it here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All I know for now is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fab is a monovalent fragment that is produced from IgG and IgM, consisting of the VH, CH1 and VL, CL regions, linked by an intramolecular disulfide bond. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Molecular basis of Fab will make more sense.&lt;/p&gt;&#xA;" OwnerUserId="10027" LastEditorUserId="9099" LastEditDate="2014-11-02T18:30:40.783" LastActivityDate="2014-11-02T18:30:40.783" Title="Synthesis of immunoglobulin Fab fragments: Where can I learn about Fab?" Tags="&lt;immunology&gt;&lt;antibody&gt;&lt;antigen&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23649" PostTypeId="2" ParentId="23648" CreationDate="2014-11-02T13:02:20.913" Score="2" Body="&lt;p&gt;FAbs are genetically engineered and not organically synthesized as such. This PNAS article nicely describes the construction of a phage (virus) library to generate a large amount of different FAbs and screen for FAbs with the wanted epitope (antigen) affinity: &lt;a href=&quot;http://www.pnas.org/content/95/11/6157.short&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/95/11/6157.short&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-02T13:02:20.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23650" PostTypeId="2" ParentId="23648" CreationDate="2014-11-02T13:07:17.267" Score="4" Body="&lt;p&gt;For the generation of Fab-fragments antibodies, (possibly genetically modified) which can be made in large quantities by cells or animals, are used. Antibodies as a whole are not synthesized. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Fab fragment is obtained from antibodies using the enzyme &lt;a href=&quot;http://en.wikipedia.org/wiki/Papain&quot; rel=&quot;nofollow noreferrer&quot;&gt;papain&lt;/a&gt;, which cleaves the antibody over the disulfide bonds in the hinge region. This results in two Fab fragments (which contain the antigen binding sites) and one Fc fragment (which contains the constant region of the antibody). See the image (from &lt;a href=&quot;https://www.bioscience.org/2001/v6/d/wittel/fulltext.php?bframe=figures.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RoZw9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to go further into the topic, read one of the references below.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.hgxb.com.cn/EN/article/downloadArticleFile.do?attachType=PDF&amp;amp;id=14298&quot; rel=&quot;nofollow noreferrer&quot;&gt;Preparation and separation of Fab and Fc fragments from human&#xA;immunoglobulin G with papain digestion&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://amrita.vlab.co.in/?sub=3&amp;amp;brch=70&amp;amp;sim=1349&amp;amp;cnt=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fragmentation of IgG Using Papain&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="9099" LastEditDate="2014-11-02T16:20:16.100" LastActivityDate="2014-11-02T16:20:16.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23651" PostTypeId="1" CreationDate="2014-11-02T15:05:31.987" Score="0" ViewCount="79" Body="&lt;p&gt;I'm get the confusion about  SYSTEM BIOLOGY filed.  &lt;code&gt;SBML&lt;/code&gt; is refer to as &lt;code&gt;SYSTEM BIOLOGY MARKUP LANGUAGE&lt;/code&gt; why we should called as &lt;code&gt;MARKUP LANGUAGE&lt;/code&gt;? In HTML,XML and other field Mark up language mean particular function is declare into the Angular bracket like &lt;code&gt;&amp;lt;H1&amp;gt; for Heading Tag&lt;/code&gt; this is displayed on the browser. Markup Language was actually developed for Wep application. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, MarkUp language only displayed what we want., not display the simple mathematical function. Like, I need add function 1 + 1 which is display on the browser Markup language is not add, which is done by the CGI programming Like PERL,PYTHON, javascript.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in SBML(System Biology MarkUp language) Tools are not only display the what we want it? and It is not run on the browser? So why we called it is MarkUp Language?&lt;/p&gt;&#xA;" OwnerUserId="9132" LastActivityDate="2014-11-02T22:43:07.180" Title="Why the name coined for MARKUP LANGUAGE for SBML?" Tags="&lt;bioinformatics&gt;&lt;systems-biology&gt;&lt;computational-model&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-11-02T22:35:56.943" ContentLicense="CC BY-SA 3.0" />
  <row Id="23653" PostTypeId="2" ParentId="23651" CreationDate="2014-11-02T16:43:15.350" Score="4" Body="&lt;p&gt;SBML follows in the same vein as XML, in that it provides a standardized and flexible method for structuring information. XML and its ilk aren't just for making web pages, they're for sending structured datasets between systems and programs (in fact, XML is a fairly common configuration format). Why? Because the structure makes parsing simple (well, simple-ish).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW, markup languages were not invented for the web, HTML was far from the first one. The origin of markup languages is typesetting and in fact one of the most common uses these days is still in writing papers (ask a local math/physics/CS person what he/she uses to write papers and the answer will be Latex...a markup language).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;: BTW, this really has nothing to do with biology and you could have at least read the &lt;a href=&quot;http://en.wikipedia.org/wiki/Markup_language&quot; rel=&quot;nofollow&quot;&gt;wikipedia page&lt;/a&gt; on what a markup language is.&lt;/p&gt;&#xA;" OwnerUserId="9523" LastEditorUserId="948" LastEditDate="2014-11-02T22:43:07.180" LastActivityDate="2014-11-02T22:43:07.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23655" PostTypeId="1" CreationDate="2014-11-02T21:20:08.437" Score="2" ViewCount="58" Body="&lt;p&gt;just curious. Are there any works or research results related to the influence of light color used for &lt;a href=&quot;http://en.wikipedia.org/wiki/Dawn_simulation&quot; rel=&quot;nofollow&quot;&gt;dawn simulation&lt;/a&gt;? I mean those wake-up lights which try to simulate dawn to make waking up better for you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cheap ones only use one color - those &quot;warm white&quot; LEDs - and only change brightness. However the more expensive ones also change color like the sun during sunrise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am just curious how much important could be the color change. :-)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks&lt;/p&gt;&#xA;" OwnerUserId="2961" LastActivityDate="2014-11-02T21:20:08.437" Title="Dawn simulation - does color change affect waking up?" Tags="&lt;human-biology&gt;&lt;sleep&gt;&lt;light&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23656" PostTypeId="1" AcceptedAnswerId="23671" CreationDate="2014-11-03T00:03:50.307" Score="8" ViewCount="436" Body="&lt;p&gt;The visually deprived brain undergoes extensive remodeling due to cross-modal plasticity. This leads to increased areas of the cortex being available for other purposes such as tactile processing. Now I am wondering if there is anything known about how long it takes for the blind to learn Braille as compared to normally sighted people? &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-04T02:18:04.977" LastActivityDate="2014-12-23T05:38:04.107" Title="Do blind people learn Braille equally fast as the sighted?" Tags="&lt;vision&gt;&lt;sensation&gt;&lt;learning&gt;&lt;language&gt;&lt;neuroplasticity&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23657" PostTypeId="1" AcceptedAnswerId="23673" CreationDate="2014-11-03T00:32:42.003" Score="3" ViewCount="48" Body="&lt;p&gt;Does the tannin level in plants go down or up after they die? Or does the tannin level stay the same regardless?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As they decay, do they release more tannins or does the production stop?&lt;/p&gt;&#xA;" OwnerUserId="10030" LastEditorUserId="57" LastEditDate="2014-11-03T07:25:00.007" LastActivityDate="2014-11-03T17:21:25.270" Title="Does the tannin level in plants go down or up after they die? Or does the tannin level stay the same regardless?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23658" PostTypeId="2" ParentId="23641" CreationDate="2014-11-03T01:51:38.453" Score="8" Body="&lt;p&gt;I'm going to give a tentative answer full of speculation and guesswork, but it's too long to fit in a comment so here goes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sex duration is possibly a sort of human reproductive &lt;a href=&quot;http://en.wikipedia.org/wiki/Handicap_principle&quot;&gt;handicap&lt;/a&gt;. Sexual arousal can soften the cervix, increasing fertility during lengthy sex sessions. Lengthy sex exposes them couple to predators and takes time and energy, so if you have the calories to burn you are probably a better mate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The more orgasms a male has had in the recent past the longer the average sex session takes to ejaculation. This kind of makes sense as an adaption strategy to different frequencies of sexual intercourse (if less sex happens it's more important to ejaculate quickly, if more sex happens you want to get as much fertility out of the sperm you produce as possible). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Comparing testicle size and penis size to other primates, humans have &lt;a href=&quot;http://en.wikipedia.org/wiki/Penis&quot;&gt;a large penis and relatively small testicles&lt;/a&gt;(compared to chimps, say) which implies we spend more energy on the sex and less energy on the ejaculation than chimps. It also implies a lower sexual frequency or smaller ejaculate sizes or larger vaginal depths or really a number of other things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The whole system kind of makes sense. Long sex durations are a sexual handicap system to show the fitness of partners, which are rewarded with slightly higher fertility. The whole post-sex evolutionary mechanism thing is a layer on top of the underlying mate selection which is beyond the scope of a book, nevermind a stack exchange answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's probably at least a little bit wrong. The handicap principle isn't super well accepted as a general evolutionary principle, even though it explains some things. &lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-11-03T01:51:38.453" CommentCount="2" CommunityOwnedDate="2014-11-03T01:51:38.453" ContentLicense="CC BY-SA 3.0" />
  <row Id="23659" PostTypeId="1" CreationDate="2014-11-03T01:55:35.997" Score="5" ViewCount="91" Body="&lt;p&gt;What is the effect of pasteurization and ultra-pasteurization on proteins, enzymes, and nutrients found in milk and other dairy products?&lt;/p&gt;&#xA;" OwnerUserId="8644" LastActivityDate="2014-11-03T22:12:56.120" Title="Ultra Pasteurization and Pasteurization" Tags="&lt;diet&gt;&lt;health&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23660" PostTypeId="2" ParentId="15937" CreationDate="2014-11-03T02:33:31.027" Score="4" Body="&lt;p&gt;I think that the distinction between carnivores and herbivores contains a gray area with a spectrum of omnivores in-between. Bears are placed in the order of carnivores, but are definitely truly omnivores &lt;a href=&quot;http://www.nhptv.org/natureworks/nwep10b.htm&quot; rel=&quot;nofollow&quot;&gt;see link&lt;/a&gt;. However, if you give them a choice between a salmon and blueberries, it's quite clear what will be devoured first. That's why it's a carnivore. The answer by @Dan S clearly shows that not all creatures may be in the spectrum. For example, domestic cats are indeed quite carnivorous and would not touch plant material. On the other hand, now we are talking pets (the SE where this question apparently came from) - dogs are truly omnivores despite being categorized as carnivorous. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-03T02:59:02.997" LastActivityDate="2014-11-03T02:59:02.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23661" PostTypeId="1" CreationDate="2014-11-03T03:31:14.827" Score="2" ViewCount="1279" Body="&lt;p&gt;The three common genotypes at the hemoglobin locus have very different phenotypes: SS individuals suffer from severe anemia, AS individuals have a relatively mild form of anemia but are resistant to malaria, and AA individuals have no anemia but are susceptible to malaria. The frequency of the S allele among the gametes produced by the first generation of a central African population is 0.2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(a) Assuming that mating occurs at random, what are the frequencies of the three genotypes among zygotes produced by this population?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that this is 0.2 for the S allele (q in the hardy weinberg equation)&#xA;and 0.8 for the A allele (p in the hardy weinberg equation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for the frequencies I got&#xA;AA = 0.64&#xA;AS = 0.32&#xA;SS = 0.04&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(b) In this area, no SS individuals survive to adulthood, 70% of the AA individuals survive, and all of the AS individuals survive. What is the frequency of each of the three genotypes among the second generation of adults?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know how to do this! I don't understand what to do! I tried multiplying &lt;/p&gt;&#xA;&#xA;&lt;p&gt;0.64 by 0.7 (because only 70% survive), but I know that is wrong answer. I know you have to divide 0.64 x 0.7 by the total that survived, but I don't understand why you have to do that. You didn't have to divide for part a, why do you have to divide for part b? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also for some reason the frequency of the AS is not 0.32 for the answer. I don't understand why! Please Please help me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(c) What is the frequency of the S allele among gametes produced by these adults?&#xA;I dont know this either!&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PLEASE EXPLAIN ALL OF THIS TO ME IN CLEAR STEPS! THANK YOU SO MUCH. &lt;/p&gt;&#xA;" OwnerUserId="10032" LastEditorUserId="1590" LastEditDate="2014-11-03T09:00:28.977" LastActivityDate="2014-11-03T13:46:04.500" Title="Hardy Weinberg problem help!" Tags="&lt;homework&gt;&lt;population-genetics&gt;&lt;hardy-weinberg&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23662" PostTypeId="2" ParentId="7384" CreationDate="2014-11-03T05:28:47.303" Score="1" Body="&lt;p&gt;As far as I know there are ongoing efforts to find genes that affect forensically relevant traits e.g. facial characteristics and fingerprint pattern type/ridge count, and it's definitely a topic of interest to some law enforcement agencies. However as previously mentioned, there are many factors that could influence complex traits, including in utero environments and other, postnatal effects, such as nutrition, as well as the interaction between those environments and genetic influences. Given past literature showing jury-eligible members tend to over-estimate the importance and statistical accuracy of DNA profiling, however, I think even with future technological and methodological advances in genetic research, this type of evidence should be used with caution, explained with extreme care and thoroughness, and never taken as the single determining factor in reaching a verdict.  &lt;/p&gt;&#xA;" OwnerUserId="10033" LastActivityDate="2014-11-03T05:28:47.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23664" PostTypeId="1" AcceptedAnswerId="30899" CreationDate="2014-11-03T08:46:04.490" Score="7" ViewCount="503" Body="&lt;p&gt;Does anyone know which direction the nucleosomes are wrapped? I wonder:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Relative to the B-DNA double helix twist direction (right-hand)&lt;/li&gt;&#xA;&lt;li&gt;Relative to the neighbor nucleosomes. Do they alternate to prevent supercoiling?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9687" LastEditorUserId="16460" LastEditDate="2017-04-01T08:18:46.230" LastActivityDate="2020-04-11T10:19:23.173" Title="Nucleosome wrapping direction" Tags="&lt;dna&gt;&lt;nucleic-acids&gt;&lt;histone&gt;&lt;structure-prediction&gt;&lt;supercoiling&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23665" PostTypeId="2" ParentId="23661" CreationDate="2014-11-03T08:51:10.167" Score="3" Body="&lt;p&gt;Your answer to &lt;strong&gt;a)&lt;/strong&gt; is correct (standard Hardy-Weinberg equation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For &lt;strong&gt;b)&lt;/strong&gt; you have to consider that you are calculating proportions of the population, which should sum to 1. Since 30% of the AA individuals and all SS individuals die, this is not the case after selection, which is why you should divide the frequencies by the total proportion that survive (also for the AS genotype), such as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;\begin{array}{c|cccc}&#xA;\text{genotype} &amp;amp; \text{freq before} &amp;amp; w_{survival} &amp;amp; \text{freq after selection} &amp;amp; \text{corrected freq}\\&#xA;&amp;amp;\text{selection}&amp;amp;&amp;amp;&amp;amp;\text{after selection}\\&#xA;\hline&#xA;AA &amp;amp; 0.64 &amp;amp; 0.7 &amp;amp; f(AA)\cdot w_{AA}=0.45 &amp;amp; 0.58\\&#xA;AS &amp;amp; 0.32 &amp;amp; 1 &amp;amp; f(AS)\cdot w_{AS}=0.32 &amp;amp; 0.42 \\&#xA;SS &amp;amp; 0.04 &amp;amp; 0 &amp;amp; f(SS)\cdot w_{SS}=0.0 &amp;amp; 0.0\\&#xA;\text{sum} &amp;amp; 1 &amp;amp; &amp;amp; 0.768 &amp;amp; 1&#xA;\end{array}&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;here $w$ is the fitness of genotypes. And for your comment on why you didn't have to divide by the sum of freqencies in &lt;strong&gt;a)&lt;/strong&gt;: you could do this, but since the sum of genotype frequencies is 1 it doesn't make a difference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For &lt;strong&gt;c)&lt;/strong&gt; you use the standard formula for calculating allele frequencies from genotypes, so that $f(A)=f(AA)+f(AS)/2= 0.79$ and $f(S)=f(SS)+f(AS)/2= 0.21$.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-11-03T13:46:04.500" LastActivityDate="2014-11-03T13:46:04.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23667" PostTypeId="1" CreationDate="2014-11-03T09:29:42.280" Score="9" ViewCount="1279" Body="&lt;p&gt;Phylogenetic trees with &gt;2 branches on a node are polytomic, and polytomy can appear on trees for two reasons. Firstly a lack of information in the data prevents proper resolution within a clade, called soft polytomy. Alternatively, hard polytomy may exist, this is when there truly is a simultaneous split from one lineage (species) in to more than two. &lt;a href=&quot;http://abacus.gene.ucl.ac.uk/CME/&quot; rel=&quot;noreferrer&quot;&gt;Yang&lt;/a&gt; states that &quot;it may be argued that hard polytomies do not exist&quot; but makes no citation or attempts at theoretical discussion. Are there any papers which discuss the theoretical possibility of hard polytomy and any evidence of it occurring?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YIEMM.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image from &lt;a href=&quot;http://biology.fullerton.edu/biol404/phylo/polytomies.html&quot; rel=&quot;noreferrer&quot;&gt;http://biology.fullerton.edu/biol404/phylo/polytomies.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-11-03T09:38:17.993" LastActivityDate="2014-11-04T00:06:36.073" Title="Evidence &amp; discussions of hard polytomy" Tags="&lt;phylogenetics&gt;&lt;molecular-evolution&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23668" PostTypeId="2" ParentId="23667" CreationDate="2014-11-03T10:52:07.357" Score="2" Body="&lt;p&gt;I think that changes in features that determine a node may happen in parallel or close together in a sequence. If the fossil record is not complete enough then the cladogram has to contain these stars. From a stochastic statistic point of view, although unlikely, it could actually happen that 2 or more  characteristics develop exactly during a similar time frame, so from a philosophical point of view, I disagree with yang. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-03T11:46:42.527" LastActivityDate="2014-11-03T11:46:42.527" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23669" PostTypeId="2" ParentId="10179" CreationDate="2014-11-03T14:52:15.820" Score="1" Body="&lt;p&gt;In addition to the arguments presented in the accepted answer, I would like to add that most species of mammals are red/green colour-blind. This has to do with the fact that for much of their evolutionary history, mammals were nocturnal creatures and so the ability to see different colours wasn't necessary. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This dates back to the mesozoic period when mammals had nocturnal lifestyles in order to avoid predation from dinosaurs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's an article that summarizes recent research on this topic: &lt;a href=&quot;http://www.utexas.edu/news/2012/10/29/effects-prehistoric-nocturnal-life-mammalian-vision/&quot; rel=&quot;nofollow&quot;&gt;http://www.utexas.edu/news/2012/10/29/effects-prehistoric-nocturnal-life-mammalian-vision/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9573" LastActivityDate="2014-11-03T14:52:15.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23670" PostTypeId="1" CreationDate="2014-11-03T15:04:15.917" Score="4" ViewCount="170" Body="&lt;ol&gt;&#xA;&lt;li&gt;The common cold and [some?] types of influenza are &lt;em&gt;self-limiting&lt;/em&gt;.&#xA;Some microorganisms cause &lt;em&gt;self-limiting&lt;/em&gt; diarrhea.&#xA;Is tuberculosis [potentially] self-limiting or not?&#xA;To put it another way, suppose that ONLY ONE &lt;strong&gt;&lt;em&gt;viable&lt;/em&gt;&lt;/strong&gt; cell of&#xA;&lt;em&gt;Mycobacterium tuberculosis&lt;/em&gt; enters the respiratory system of a&#xA;&lt;strong&gt;&lt;em&gt;healthy&lt;/em&gt;&lt;/strong&gt; human. Will the immune system of that healthy human be&#xA;able to defeat, on its own, that lone &lt;em&gt;Mycobacterium&lt;/em&gt; invading cell?&#xA;Is the human immune system capable of defeating &lt;em&gt;M. tuberculosis&lt;/em&gt;?&lt;/li&gt;&#xA;&lt;li&gt;If the answer to question number 1 is yes, then my follow up question&#xA;is this: Is the human immune system capable of defeating, on its own,&#xA;all other pathogenic microorganisms (bacteria)? How about pathogenic&#xA;viruses (except HIV)?&lt;/li&gt;&#xA;&lt;li&gt;As a non-medical professional (although I am a medical enthusiast), I&#xA;notice that self-limiting viral diseases are more common (both by&#xA;type and prevalence) than self-limiting bacterial diseases. Is this&#xA;observation correct?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To clarify: Yes Chris, for &quot;self-limiting&quot;, i mean an infection that resolves by itself without an external intervention (no antibiotics, antivirals, vaccines, etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested in the [theoretical] capabilities of the [unaided] human immune system. I live in a third world country where pulmonary TB is prevalent. Most of the self-limiting diseases i know are viral, and at this moment, i cannot name a bacterial infection that resolves without antibiotics. Nevertheless, i can't help but wonder why we humans can handle viral infections, but [apparently] not bacterial infections. And this got me asking long ago: is the human immune system incapable of defeating M. tuberculosis? Aside from bacteria that cause diarrhea, what are other examples of bacterial infections which the human immune system can clear on its own? What about fungal infections?&lt;/p&gt;&#xA;" OwnerUserId="10037" LastEditorUserId="107" LastEditDate="2014-11-11T19:12:53.927" LastActivityDate="2014-11-11T19:12:53.927" Title="human immune system" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23671" PostTypeId="2" ParentId="23656" CreationDate="2014-11-03T15:39:46.793" Score="4" Body="&lt;p&gt;I have had a very difficult time finding information that was well-written and what you were looking for. So, I did my best!&#xA;&lt;p&gt;&#xA;From what I have read it takes about four months - everyone is a little bit different and some take longer! Those of us with no visual impairment that try to learn it have no advantage and maybe a slight disadvantage with learning it... I know because I am trying to learn it. It does take a lot a patience and perseverance!&#xA;&lt;p&gt;&#xA;This is the article I referred to: &#xA;&lt;a href=&quot;http://www.quora.com/How-long-does-it-take-to-learn-Braille-and-does-it-get-harder-as-you-get-older/&quot; rel=&quot;nofollow&quot;&gt;Learning braille; how long does it take and does it get harder with age?&lt;/a&gt;&#xA;&lt;p&gt;&#xA;Hope this was helpful!&lt;/p&gt;&#xA;" OwnerUserId="6289" LastEditorUserId="6289" LastEditDate="2014-11-04T03:26:10.763" LastActivityDate="2014-11-04T03:26:10.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23672" PostTypeId="2" ParentId="21858" CreationDate="2014-11-03T16:03:25.177" Score="3" Body="&lt;p&gt;Plus lens therapy can indeed reverse myopia, but it does take time. Your eyes did not develop myopia in a few days.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The eye represents its environment. Fitting chicks, monkeys etc. with minus lenses always INCREASED the amount of myopia, while plus lenses always reduced myopia and resulted in hyperopia (lens compensation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Putting monkeys in a confined environment showed a myopic shift. Monkeys in an open &#xA;environment showed a refractive state about +1.00 diopters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;IMPORTANT: As I have said: Unfortunately, it does take time! Do not expect results after 1 week of plus lens therapy. That is why so many people give up and think that myopia is irreversible. You also do not build muscles after 1 week.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kind regards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Optical defocus and effects in HUMANS: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20592235&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/20592235&lt;/a&gt;&#xA;Defocus on chicks: &lt;a href=&quot;http://www.iovs.org/content/44/7/2818.full&quot; rel=&quot;nofollow&quot;&gt;http://www.iovs.org/content/44/7/2818.full&lt;/a&gt;&#xA;Monkeys in a confined environment: &lt;a href=&quot;http://www.iovs.org/content/2/6/571.short&quot; rel=&quot;nofollow&quot;&gt;http://www.iovs.org/content/2/6/571.short&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10039" LastEditorUserId="6511" LastEditDate="2014-12-05T20:36:14.403" LastActivityDate="2014-12-05T20:36:14.403" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23673" PostTypeId="2" ParentId="23657" CreationDate="2014-11-03T17:21:25.270" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Well maybe I'm confused, but do plants not produce tannins? If they do&#xA;  does the production of the tannins stop after death?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That depends on how you define death. Tannin is &lt;a href=&quot;http://en.wikipedia.org/wiki/Plant_secondary_metabolism&quot; rel=&quot;nofollow&quot;&gt;secondary product&lt;/a&gt;, so I don't think the plant cells will produce more tannin when they are starving probably because of cutting off the leaves, roots, etc... when the plant dies. The plant won't bother to degrade tannins (I guess it does not even have the pathway necessary to do that), because it is a defense mechanism against insects, mammalians, etc... and not an energy storage material. Tannins can be degraded by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24610854&quot; rel=&quot;nofollow&quot;&gt;microbes&lt;/a&gt;, heat, UV radiation, chemical reactions, etc... So if you can't protect the tannins from all of these then they will degrade. (Note: you can't, all you can do is slowing down the process.)&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-11-03T17:21:25.270" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23674" PostTypeId="2" ParentId="23670" CreationDate="2014-11-03T18:23:41.913" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;To put it another way, suppose that ONLY ONE viable cell of&#xA;  Mycobacterium tuberculosis enters the respiratory system of a healthy&#xA;  human. Will the immune system of that healthy human be able to defeat,&#xA;  on its own, that lone Mycobacterium invading cell? Is the human immune&#xA;  system capable of defeating M. tuberculosis?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, for example by vaccination you prepare the immune system for recognizing M. tuberculosis. After that it will have a greater chance to defeat the infection. Without vaccination it depends on the genetics, the immune system and the health state of the individual. E.g. starving people are more vulnerable to TBC.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.tandfonline.com/doi/abs/10.1080/15459620590918466#.VFe7HsnapqQ&quot; rel=&quot;nofollow&quot;&gt;minimum infectious dose of M. tuberculosis is very low&lt;/a&gt;, so it is possible that a single organism can cause infection. Be aware that the infectious dose depends on the type of the disease. So by other diseases your immune system can defeat a large amount of invaders and you don't even recognize it, because you don't get sick.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If the answer to question number 1 is yes, then my follow up question&#xA;  is this: Is the human immune system capable of defeating, on its own,&#xA;  all other pathogenic microorganisms (bacteria)? How about pathogenic&#xA;  viruses (except HIV)?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It depends on the individual. As far as I know for a certain disease some percent of the population is always resistant. Even &lt;a href=&quot;http://omicsonline.org/2155-9929/pdfdownload.php?download=2155-9929-2-108.pdf&quot; rel=&quot;nofollow&quot;&gt;by HIV about 1% of the population is resistant&lt;/a&gt;. I think it is even possible that somebody defeat HIV without special genetic resistance, however this happens rarely, because the minimum infectious dose is very low by HIV too. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As a non-medical professional (although I am a medical enthusiast), I&#xA;  notice that self-limiting viral diseases are more common (both by type&#xA;  and prevalence) than self-limiting bacterial diseases. Is this&#xA;  observation correct?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I guess you mean that diseases with low &lt;a href=&quot;http://en.wikipedia.org/wiki/Case_fatality_rate&quot; rel=&quot;nofollow&quot;&gt;fatality rate&lt;/a&gt; are more common. In western countries this is true, because the healthcare system prevents epidemics of lethal diseases with quarantines. In less fortunate countries I am not so sure about this...&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-11-03T18:23:41.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23675" PostTypeId="1" CreationDate="2014-11-03T18:48:03.657" Score="7" ViewCount="76" Body="&lt;p&gt;During the fall and winter season, a number of people are experiencing Seasonal Affective Disorder. One of the way it has traditionally been treated is with a dedicated lightbox - a very high intensity light (5k-15k lux) that is positioned somewhere the user can see it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the possible ways such light affect the brain is through being picked up by &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanopsin&quot; rel=&quot;nofollow noreferrer&quot;&gt;Melanopsin receptors&lt;/a&gt; in the eye and this info being &lt;a href=&quot;http://en.wikipedia.org/wiki/Suprachiasmatic_nucleus&quot; rel=&quot;nofollow noreferrer&quot;&gt;transmitted to the Suprachiasmatic Nucleus (SCN)&lt;/a&gt;. The SCN makes sleep/wake decisions by suppressing melatonin release.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has been tested that melanopsin receptors in the human eye respond most strongly to the light at around 470nm wavelength.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is about the mechanism by which this light influences the brain - &lt;strong&gt;which would have a stronger influence on the brain:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A &lt;strong&gt;constant, high intensity&lt;/strong&gt; source of light that is ignored by the conscious mind (fades into background)?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iHWO6.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;OR An &lt;strong&gt;alternating, moving or fading, less intense source of light&lt;/strong&gt; that the eye is drawn to, such as dancing light, a moving lamp or some other form of light that the conscious mind might be drawn to watch?&#xA;&lt;img src=&quot;https://i.stack.imgur.com/uV97Z.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;To clarify my question, I know that brain has a number of self-attenuating circuits (for example dopaminergic system), where extended release of some hormone numbs the sensitivity to the hormone. I'm interested - &lt;strong&gt;are SCN, melanopsin receptors or melatonin suppressing process are also self attenuating, where prolonged exposure to constant light would attenuate these processes?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2016-03-07T08:35:42.483" Title="Would constant light or fading light be registered as more wakefulness promoting by the Supra Chiasmatic Nucleus?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;vision&gt;&lt;circadian-rhythms&gt;&lt;melatonin&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23676" PostTypeId="1" AcceptedAnswerId="23677" CreationDate="2014-11-03T20:54:14.973" Score="4" ViewCount="149" Body="&lt;p&gt;I have a list of proteins formatted like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Protein Name        Gene Name&#xA;4E-BPI              EIF4EBP1&#xA;4E-BPI_pS65         EIF4EBP1&#xA;4E-BPI_PT37_T46     EIF4EBP1&#xA;53BP1               TP53BP1&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Its my job to pull the following from &lt;a href=&quot;http://www.uniprot.org/&quot; rel=&quot;nofollow&quot;&gt;Uniprot&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Subcellular Location information (this is easy)&lt;/li&gt;&#xA;&lt;li&gt;Information about phosphorylated forms&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The first thing I did was compile a list of Uniprot IDs for each gene's human form that I could plug into the Upload List function. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next, I used Uniprot's &quot;Customize Results Table&quot; &lt;a href=&quot;http://www.uniprot.org/uniprot/?query=EIF4EBP1&amp;amp;sort=score#customize-columns&quot; rel=&quot;nofollow&quot;&gt;page&lt;/a&gt;, to add the &quot;Subcellular Location&quot; column to the output. &lt;strong&gt;Do you know columns will provide information about the phosphorylated forms of these proteins?&lt;/strong&gt; I added columns PTM &gt; PhosSite and PTM &gt; PhosphoSite but they return the Uniprot ID or nothing at all. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there somewhere else in Uniprot that I can look for information about phosphorylated forms of proteins?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="8161" LastActivityDate="2014-11-03T21:03:16.177" Title="What information can Uniprot give me about phosphorylated forms of proteins?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;phosphorylation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23677" PostTypeId="2" ParentId="23676" CreationDate="2014-11-03T21:03:16.177" Score="6" Body="&lt;p&gt;You were looking in the wrong spot. The PTM section you clicked on is for post-translational modification databases such as &lt;a href=&quot;http://www.phosphosite.org&quot;&gt;PhosphoSite&lt;/a&gt;. To get the actual modified residues, click on &quot;PTM/Processsing&quot; (&lt;em&gt;sic&lt;/em&gt;) further up the page and then select &quot;Modified Residue&quot;, and in your results table you'll get a list of all phosphorylations, glycosylations, acetylations, etc.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-11-03T21:03:16.177" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23678" PostTypeId="2" ParentId="23659" CreationDate="2014-11-03T22:12:56.120" Score="3" Body="&lt;p&gt;This is an interesting question and it is rather hard to find reliable information. According to a review which also did a meta analysis of all available articles, pasteurization (and also ultra pasteurization) affects the vitamins to some degree. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the analysis, vitamin B1, B2, B6, B12, C, E and folate decreased. The author notes however, that with the exception of vitamin B2, where milk is an important dietary source, the other vitamins are not included in very high concentrations. See the first paper for all details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These findings are supported by another review (see reference 2), which shows some values in table 4:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/p6zZV.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This study finds proteins and amino acids not affected to a measurable degree, but data on protein behaviour is missing. My guess is that a part of the proteins are denaturated, but not all of them. There is some research which analyzes the effect of thermal treatment on milk in connection with other processes like the yoghurt or cheese production (have a look at reference 3). I haven't found any data on the proteins in milk which is directed to human consumption.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3795/lhak2qt6_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;A systematic review and meta-analysis of the effects of&#xA;pasteurization on milk vitamins, and evidence for raw milk&#xA;consumption and other health-related outcomes.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://scidoc.org/articles%20pdf/IJDSP/IJDSP-01-201.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Which Milk is Fresh?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.icef11.org/content/papers/aft/AFT992.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Effect of UHT and VAT Thermal Processing Systems on Whey Protein&#xA;Denaturation and Gel Strength of yoghurt&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-11-03T22:12:56.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23679" PostTypeId="2" ParentId="21410" CreationDate="2014-11-03T22:42:11.227" Score="5" Body="&lt;p&gt;There are some recipes available on the web, my answer is based on this &lt;a href=&quot;http://www.pickyourown.org/AppleCiderVinegarRecipe.php&quot; rel=&quot;noreferrer&quot;&gt;webpage&lt;/a&gt; and this &lt;a href=&quot;http://ohioline.osu.edu/hyg-fact/5000/pdf/5346.pdf&quot; rel=&quot;noreferrer&quot;&gt;information&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;p&gt;The process itself is rather easy and you can either use ready bought apple juice, homemade juice or apple cider (basically unfiltered apple juice). You will need some specially cultivated yeast, baker's yeast is generally not recommended since it might produce a lot of unwanted (and probably bad tasting) side products.&lt;/p&gt;&#xA;&lt;p&gt;For the fermentation itself you need some (very) clean vessels in which the process can take place. These should be from a material which is not corrosive, as the vinegar would otherwise react with the vessel. Food-grade plastic, glass or stainless steel should be ok.&lt;/p&gt;&#xA;&lt;p&gt;To have the reaction take place, the process need oxygen, otherwise the reaction will stop at the step of ethanol. This is also why acoholic fermentation is always sealed against the air, to avoid the oxidation of the alcohol the acetic acid. A cheese cloth will leave oxygen in, but keep insects and other contaminations out. If you need to filter the vinegar at the end of the process, a standard coffeefilter is good enough.&lt;/p&gt;&#xA;&lt;p&gt;The following step by step directions come from this &lt;a href=&quot;http://www.pickyourown.org/AppleCiderVinegarRecipe.php&quot; rel=&quot;noreferrer&quot;&gt;website&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Step 1 - Make or buy your apple cider or apple juice&lt;/p&gt;&#xA;&lt;p&gt;Apple juice or apple cider is the starting point for making apple&#xA;cider vinegar. You can make your own, or buy it ready made, fresh,&#xA;bottled or frozen.  You can use a mechanical or steam juicer to&#xA;produce the juice / cider. To make your own juice (which is the same&#xA;as plain unfermented apple cider), see this page. Keep in mind that&#xA;you want to select sweet apples, like Fuji, Delicious, Mutsu, Gala,&#xA;etc. Green, unripe and unsweet apples (like Granny Smith) do not have&#xA;enough sugar to make good cider vinegar. Tips about selecting apples:&lt;/p&gt;&#xA;&lt;p&gt;Apples used for cider don't have to be flawless. They do, however,&#xA;have to be free from spoilage. You can use blemished apples and small&#xA;sized apples. You can mix apple varieties together or use all one&#xA;variety. The only rule is to cut out any spoilage areas on otherwise&#xA;good apples. Spoiled areas will cause the juice to ferment too rapidly&#xA;and will ruin the cider. Don't use apples that appear brown, decayed&#xA;or moldy. Apples should be firm and ripe. Green, undermature apples&#xA;cause a flat flavor when juiced. The best cider comes from a blend of&#xA;sweet, tart and aromatic apple varieties. A bushel of apples yields&#xA;about 3 gallons of juice.&lt;/p&gt;&#xA;&lt;p&gt;Step 2 - Make your starter yeast&lt;/p&gt;&#xA;&lt;p&gt;Adding yeast to activate fermentation is not essential, but will speed&#xA;up the process and can produce a higher quality. Special cultivated&#xA;yeasts are available for this purpose at wine-making shops and&#xA;biological labs but bread yeasts are not recommended. To make a&#xA;starter, crumble one cake of yeast into one quart of cider and mix.&#xA;This makes enough starter for 5 gallons of cider; double the recipe&#xA;proportionately when making more.&lt;/p&gt;&#xA;&lt;p&gt;Steps 3 - Making Alcohol and Acetic Acid&lt;/p&gt;&#xA;&lt;p&gt;Pour all of the juice or cider into one or more containers to about&#xA;three-quarters capacity; do not close the lids on the containers.&#xA;Instead, cover the openings with cheesecloth secured with a rubber&#xA;band or string.&lt;/p&gt;&#xA;&lt;p&gt;Step 4 - Store out of direct light, but some place with constant temperature&lt;/p&gt;&#xA;&lt;p&gt;Stir the mixtures daily, making sure the cheesecloth is put back in&#xA;place. Keep the containers away from direct sunlight and maintain the&#xA;temperature at 60 to 80 degrees F.&lt;/p&gt;&#xA;&lt;p&gt;Step 5 - Keep stirring daily, monitoring and tasting for the next 3 to 4 weeks&lt;/p&gt;&#xA;&lt;p&gt;Full fermentation will take about 3 to 4 weeks. Near the end of this&#xA;period, you should notice a vinegar-like smell. Taste samples daily&#xA;until the desired strength is reached.&lt;/p&gt;&#xA;&lt;p&gt;Step 4 - Filter Mother of vinegar&lt;/p&gt;&#xA;&lt;p&gt;When the vinegar is fully fermented, filter the liquid through several&#xA;layers of fine cheesecloth or filter paper—a coffee filter works well&#xA;for this. This removes the mother of vinegar, shown at right,&#xA;preventing further fermentation or spoilage of the product. Mother of&#xA;vinegar is completely harmless and the surrounding vinegar does not&#xA;have to be discarded because of it. It can be filtered out using a&#xA;coffee filter, used to start a bottle of vinegar, or simply left in&#xA;and ignored.&lt;/p&gt;&#xA;&lt;p&gt;Step 6 - Done! Storing Your Vinegar&lt;/p&gt;&#xA;&lt;p&gt;The vinegar is now ready for storage in separate, capped containers.&#xA;Stored vinegar will stay in excellent condition almost indefinitely if&#xA;it is pasteurized. To pasteurize, heat the vinegar before pouring it&#xA;into sterilized bottles, or bottle, then place in a hot water bath. In&#xA;both cases, the temperature of the vinegar must reach at least 140&#xA;degrees F to pasteurize the product, and should not exceed 160 degrees&#xA;F. Use a cooking thermometer to ensure the correct temperature is met.&#xA;Cool the containers and store at room temperature out of direct&#xA;sunlight.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-11-03T22:42:11.227" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23680" PostTypeId="2" ParentId="23667" CreationDate="2014-11-04T00:06:36.073" Score="2" Body="&lt;p&gt;You might want to have a look at some of these: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21236789&quot; rel=&quot;nofollow&quot;&gt;Patterns of speciation and limits to phylogenetic resolution&lt;/a&gt;, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1055790300908972&quot; rel=&quot;nofollow&quot;&gt;Molecular polytomies&lt;/a&gt;, &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.1996.tb00198.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Problems with &quot;soft&quot; polytomies&lt;/a&gt;, and &lt;a href=&quot;http://scholar.google.com/scholar?q=Polytomies%2C%20the%20power%20of%20phylogenetic%20inference%2C%20and%20the%20stochastic%20nature%20of%20molecular%20evolution&amp;amp;btnG=&amp;amp;hl=en&amp;amp;as_sdt=0%2C38&quot; rel=&quot;nofollow&quot;&gt;Polytomies, the power of phylogenetic inference, and the stochastic nature of molecular evolution&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2014-11-04T00:06:36.073" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23681" PostTypeId="2" ParentId="23630" CreationDate="2014-11-04T03:32:20.493" Score="2" Body="&lt;p&gt;Two reasonably close relatives of the most recent chimpanzee-human ancestor (CHA) are &lt;em&gt;Sahelanthropus tchadensis&lt;/em&gt; and &lt;em&gt;Orrorin tugenensis&lt;/em&gt;, but both are poorly attested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One better candidate is &lt;em&gt;Ardipithecus ramidus&lt;/em&gt;, which has a fairly-complete skeleton (&quot;Ardi&quot;) among other fossils. It's a bit young (4.4 Ma), perhaps, to be a CHA but should be a close relative.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another reasonable candidate is &lt;em&gt;Oreopithecus bambolii&lt;/em&gt;. It is very well-attested. The trouble is that no one seems to know how it's related to humans; 'best guess' is that it's not actually an ancestor but a sister taxon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I'm not an evolutionary biologist, nor even a scientist, but I thought I'd leave what information I collected here as there is no better answer at this time.)&lt;/p&gt;&#xA;" OwnerUserId="10014" LastActivityDate="2014-11-04T03:32:20.493" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23682" PostTypeId="1" CreationDate="2014-11-04T04:10:16.717" Score="3" ViewCount="959" Body="&lt;p&gt;I generated a series of local BLAST databases using makeblastdb of metagenomic data and am searching for the presence of a particular gene. While I can do the normal BLAST analysis looking at e-values, % identity, etc. I haven't been able to figure out how to determine how many times a given sequence exists in the database.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So: given a BLAST database of metagenomic data where a particular gene may exist multiple times, how do I determine the copy number of a given BLAST hit?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="10043" LastActivityDate="2015-03-20T06:35:40.180" Title="Local BLAST Copy Number per Hit" Tags="&lt;bioinformatics&gt;&lt;biostatistics&gt;&lt;blast&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23683" PostTypeId="1" AcceptedAnswerId="23688" CreationDate="2014-11-04T06:04:00.173" Score="5" ViewCount="1277" Body="&lt;p&gt;For this reaction, found in typical biochemistry textbook:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$C_6H_{12}O_6 + 6O_2 \to 6CO_2 + 6H_2O$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested in where do the oxygen atoms of $6O_2$ go. I think they go to $6H_2O$, but this is not sufficient for balance. So Does oxygen atom from $6CO_2$ also get into the carbon dioxide. Experimentally these can be confirmed by iostope labeling experiments. Reference to any such experiments will be appreciated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested in this question because the central metabolism can be understood as a electron transfer process where glucose is donor and oxygen is acceptor. We need to calculate, effectively how many electrons glucose transfers to oxygen in case of full oxidation.&lt;/p&gt;&#xA;" OwnerUserId="1800" LastEditorUserId="3340" LastEditDate="2015-06-04T11:41:56.343" LastActivityDate="2015-06-04T11:41:56.343" Title="Tracking of oxygen molecules in glucose oxidation" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;bioenergetics&gt;&lt;glucose&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23684" PostTypeId="1" CreationDate="2014-11-04T06:16:12.780" Score="5" ViewCount="224" Body="&lt;p&gt;For example, the current largest known genome belongs to a tree: &lt;a href=&quot;http://motherboard.vice.com/read/the-largest-genome-ever-sequenced-belongs-to-a-tree&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://motherboard.vice.com/read/the-largest-genome-ever-sequenced-belongs-to-a-tree&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have heard that this could potentially be because trees require many duplicates of certain genes because they live their entire life exposed to direct sunlight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know of some specific scientific hypotheses for why this might be the case? &lt;/p&gt;&#xA;" OwnerUserId="10044" LastEditorUserId="22057" LastEditDate="2018-11-17T17:06:56.267" LastActivityDate="2018-11-17T17:06:56.267" Title="Why are the genomes of some trees so large?" Tags="&lt;genetics&gt;&lt;evolution&gt;&lt;botany&gt;&lt;trees&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="23685" PostTypeId="2" ParentId="23682" CreationDate="2014-11-04T06:18:45.520" Score="2" Body="&lt;ul&gt;&#xA;&lt;li&gt;Define a &quot;Hit&quot; (based on some cutoff- evalue, score etc)&lt;/li&gt;&#xA;&lt;li&gt;Get output in the tabular format&lt;/li&gt;&#xA;&lt;li&gt;Count number of hits per query — it is usually given in the header; if you want to look for some selected hits (based on some cutoff, then you can parse the file and find out)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Example file (header):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;# BLASTN 2.2.27+&#xA;# Query: TCONS_00036712 gene=XLOC_017996&#xA;# Database: ../nt_db/nt&#xA;# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score&#xA;# 1014 hits found&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;If you want to parse the header to look for number of hits then you can run this command in the terminal (if you have awk — there by default in linux and other unix based systems. For windows install gnuwin32).&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;awk -v OFS=&quot;\t&quot; '/^# Query/{q=$3 FS $4} /^# .* hits found/{h[q]=$2} END{for(i in h){print i,h[i]}}' blastoutput.txt&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;To get the number of hits for a given criterion (for e.g. I just defined bitscore [12th column] to be &gt;400) &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;awk -F &quot;\t&quot; '!/^#/ &amp;amp;&amp;amp; $12&amp;gt;400{a[$1]++} END{for(i in a){print i,a[i]}}' blastoutput.txt&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="1306" LastEditDate="2014-11-04T14:59:27.200" LastActivityDate="2014-11-04T14:59:27.200" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23686" PostTypeId="2" ParentId="23209" CreationDate="2014-11-04T06:30:40.647" Score="17" Body="&lt;p&gt;In short, it's because your brain processes external and self-produced stimuli differently. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If someone tickles you, you feel that ticklish feeling, but when trying to tickle yourself, there is a reduction in the sensation. When you are tickled by someone, a part of your brain activates causing you to laugh, etc., but it seems that when you trying tickling yourself, your brain doesn't react the same way and that section of the brain does not activate as if someone were tickling you.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Blakemore, S.J., D.M. Wolpert, and C.D. Frith. 1998. &lt;a href=&quot;http://wexler.free.fr/library/files/blakemore%20%281998%29%20central%20cancellation%20of%20self-produced%20tickle%20sensation.pdf&quot;&gt;Central cancellation of self-produced tickle sensation.&lt;/a&gt; &lt;em&gt;Nature Neuroscience&lt;/em&gt; 1(7): 635–640. doi:10.1038/2870&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6623" LastEditorUserId="5144" LastEditDate="2014-11-04T06:48:40.113" LastActivityDate="2014-11-04T06:48:40.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23687" PostTypeId="2" ParentId="23683" CreationDate="2014-11-04T06:46:18.557" Score="1" Body="&lt;p&gt;Glucose catabolism is a multistep process involving a series of reactions. The reaction you gave is simply the overall, balanced equation; it doesn't actually happen like that in living cells. All diatomic oxygen is converted to water in the electron transport chain, but water is also consumed and produced throughout the preceding steps, which is why the equation doesn't balance that way.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check out these images from Wikipedia and note all of the compounds entering and exiting the process. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/1/17/Glycolysis2.svg&quot; rel=&quot;nofollow&quot;&gt;Glycolysis&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/0/0b/Citric_acid_cycle_with_aconitate_2.svg&quot; rel=&quot;nofollow&quot;&gt;TCA Cycle&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/8/89/Mitochondrial_electron_transport_chain%E2%80%94Etc4.svg&quot; rel=&quot;nofollow&quot;&gt;Mitochondrial Electron Transport Chain&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-11-04T06:51:32.240" LastActivityDate="2014-11-04T06:51:32.240" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23688" PostTypeId="2" ParentId="23683" CreationDate="2014-11-04T06:55:17.450" Score="2" Body="&lt;p&gt;I think &lt;a href=&quot;http://www.jbc.org/content/180/2/803.full.pdf&quot; rel=&quot;nofollow&quot;&gt;this experiment (PDF file)&lt;/a&gt; will help you understand the basic concept about the fate of oxygen in aerobic respiration. Basically the result is:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The oxygen of respiratory carbon dioxide is in exchange equilibrium with body water.&lt;/li&gt;&#xA;&lt;li&gt;Utilized molecular oxygen is converted to body water. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In respect to calculation of electrons donated to oxygen, just calculating how many NADH2 and how many FADH2 is reduced in how many steps during ETC will be able to answer your question.&lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="9099" LastEditDate="2014-11-04T08:31:04.447" LastActivityDate="2014-11-04T08:31:04.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23689" PostTypeId="2" ParentId="23613" CreationDate="2014-11-04T07:07:29.713" Score="1" Body="&lt;p&gt;There actually is a rule, called the '&lt;a href=&quot;http://www.biocyclopedia.com/index/icbn.php&quot; rel=&quot;nofollow&quot;&gt;Principle of Priority&lt;/a&gt;', which states that the nomenclature of a taxonomic group is based upon priority of publication hence option 2 in your question is the correct approach. In the principle III (Principle of Priority) section of the link above it is stated that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This principle states, in essence, that if a taxonomic group has been&#xA;  given two or more names, the correct name is the first name that meets&#xA;  the Code’s standards for publication.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But here the rule doesn't seem to apply....instead there is a piece of literature regarding the reclassification of gen. &lt;em&gt;Vibrio&lt;/em&gt; to &lt;em&gt;Campylobacter&lt;/em&gt;. In the paper &quot;&lt;em&gt;Neotype Strain for the Type Species,Campylobacter fetus (Smith and Taylor) Sebald and Vkon&lt;/em&gt;&quot; (&lt;a href=&quot;http://ijs.sgmjournals.org/content/23/2/122.abstract&quot; rel=&quot;nofollow&quot; title=&quot;Veron &amp;amp; Chatelain. 1973. Taxonomic Study of the Genus Campylobacter Sebald and Véron and Designation of the Neotype Strain for the Type Species, Campylobacter fetus (Smith and Taylor) Sebald and Véron. INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY (now IJSEM) 23(9: 122-134&quot;&gt;Veron &amp;amp; Chatelain, 1973&lt;/a&gt;) they state that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A critical study of the present state of the classification of&#xA;  vibrio-like, curved, microaerophilic bacteria was made. The species&#xA;  originally described under the names Vibrio coli Doyle, V. jejuni&#xA;  Jones et al., V. sputorum PrCvot, and V. bubulus Florent are&#xA;  transferred to the genus Campylobacter Sebald and VCron&#xA;  1963. The authors suggest that the type species of this genus, C. fetus, be divided into two subspecies: &lt;strong&gt;C. fetus subsp. fetus (Smith&#xA;  and Taylor) comb. nov. (syn. V. fetus subsp. intestinalis Florent)&lt;/strong&gt;,&#xA;  which contains the neotype strain of the species, and C. fetus subsp.&#xA;  venerealis (Florent) comb. nov. The previously described subspecies V.&#xA;  fetus subsp. intermedius Elazhari is regarded as an infrasubspecific&#xA;  taxon with the name C. fetus subsp. venerealis biotype intermedius.&#xA;  CIP 5396 (=ATCC 27374=NCTC 10842) is proposed as the neotype strain of&#xA;  C. fetus subsp. fetus. This strain, then, is also the neotype strain&#xA;  of C. fetus (Smith and Taylor) Sebald and Vkron.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The highlighted words suggest how they have approached in naming the species...&lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="3624" LastEditDate="2014-11-06T10:09:18.427" LastActivityDate="2014-11-06T10:09:18.427" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="23690" PostTypeId="2" ParentId="23684" CreationDate="2014-11-04T07:46:24.240" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://www.genetics.org/content/196/3/891.long&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; study of the recently sequenced pine species states that 82% of genome is &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Repeated_sequence_(DNA)&quot; rel=&quot;nofollow&quot;&gt;repetitive&lt;/a&gt;. This is characteristic of any complex genome, including humans. Such sequences have often been considered &quot;&lt;a href=&quot;http://en.m.wikipedia.org/wiki/Noncoding_DNA#Junk_DNA&quot; rel=&quot;nofollow&quot;&gt;junk DNA&lt;/a&gt;&quot;, though any scientist will tell you that just because we don't know its purpose doesn't mean it doesn't have one. That said, a good portion of repeats are due to &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Transposable_element&quot; rel=&quot;nofollow&quot;&gt;transposable elements&lt;/a&gt;, effectively intracellular parasites, whose only purpose is presumably self-amplification and are more often than not deleterious. These interspersed repeats make up ~45% of the human genome. That paper mentions that, based on sequence homology, ~65% of the pine's genome is made of these repeats (that's 15 billion base pairs). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's interesting that, even though the pine's genome is ~7 times larger than a human's, it has only twice as many &lt;em&gt;predicted&lt;/em&gt; genes. The pine tree has ~50 000 hypothetical genes but only ~16 000 are what the authors call high confidence. When the human genome was first sequenced, there were ~35 000 hypothetical genes but now, some 10 odd years later, there are only ~21 000 predicted genes. It seems too early to compare the two. This also brings up the important point that the number of genes is not necessarily related to organismal complexity: the worm C. elegans has ~20 000 genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The large genome size has primarily been attributed to an extensive contribution of interspersed repetitive content (Morse et al. 2009; Kovach et al. 2010; Wegrzyn et al. 2013). Assembly of the Norway spruce genome has shown that LTR retrotransposons in particular are frequently nested within the long introns of some gene families (Nystedt et al. 2013). In addition, there is evidence for gene duplication, pseudogenes, and paralogs, although the extent of these is not clear (Kovach et al. 2010; Pavy et al. 2012).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I have never heard of the hypothesis you mention (not that that means anything), but it seems to me that it's far to early to tell. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-11-04T07:46:24.240" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="23693" PostTypeId="1" AcceptedAnswerId="23707" CreationDate="2014-11-04T12:06:22.927" Score="19" ViewCount="6837" Body="&lt;p&gt;The little amount of body hair humans have don't seem to be of much use for keeping warm.&#xA;Our Simian cousins on the other hand sport thick furs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At which point during the species evolution and why did humans lose their fur?&lt;/p&gt;&#xA;" OwnerUserId="8913" LastEditorUserId="948" LastEditDate="2014-11-04T15:55:53.533" LastActivityDate="2018-06-02T20:04:35.053" Title="Why did humans lose their fur?" Tags="&lt;evolution&gt;&lt;human-genetics&gt;&lt;hair&gt;" AnswerCount="4" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23694" PostTypeId="1" AcceptedAnswerId="23695" CreationDate="2014-11-04T13:16:27.750" Score="1" ViewCount="1150" Body="&lt;p&gt;I read that &quot;Bacteria are one-celled organisms that can multiply by division&quot;, are all one-celled organisms bacteria or are there any more narrow definitions?&lt;/p&gt;&#xA;" OwnerUserId="491" LastEditorUserId="3340" LastEditDate="2014-11-04T13:27:36.977" LastActivityDate="2016-08-17T08:59:21.027" Title="Are all single-celled organisms Bacteria?" Tags="&lt;immunology&gt;&lt;bacteriology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23695" PostTypeId="2" ParentId="23694" CreationDate="2014-11-04T13:23:14.593" Score="10" Body="&lt;p&gt;No, many &lt;a href=&quot;http://en.wikipedia.org/wiki/Unicellular_organism&quot;&gt;unicellular organisms&lt;/a&gt; are not bacteria. Examples include (but certainly not limited to); some fungi, &lt;a href=&quot;http://en.wikipedia.org/wiki/Chlorella&quot;&gt;chlorella&lt;/a&gt; algae, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Archaea&quot;&gt;archaea&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria are one of three domains in the classification of life. You can find more about the bacteria domain at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Bacteria#Classification_and_identification&quot;&gt;wikipedia&lt;/a&gt; page (It's a long and complex history which is hard to summarise here) and about &lt;a href=&quot;http://en.wikipedia.org/wiki/Three-domain_system&quot;&gt;the domains here&lt;/a&gt;. This last defines bacteria loosely consisting of &quot;&lt;strong&gt;prokaryotic cells possessing primarily diacyl glycerol (DAG) diester lipids in their membranes and bacterial rRNA, no nuclear membrane, traditionally classified as bacteria.&lt;/strong&gt;&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The composition of lipids in their membrane (DAG-esters) differentiates them from another major class of prokaryotes — Archaea, which have isoprenoid lipids in their membranes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Initially Archaea was called Archaebacteria. Because of significant differences, including the membrane composition, they are now grouped into a different kingdom.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="3340" LastEditDate="2014-11-04T13:37:23.140" LastActivityDate="2014-11-04T13:37:23.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23697" PostTypeId="1" AcceptedAnswerId="23708" CreationDate="2014-11-04T14:17:30.747" Score="7" ViewCount="1673" Body="&lt;p&gt;There's definitely something I'm missing here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since calories is a unit of measurement for energy, and caffeine seemingly gives you a lot, how can the labels on caffeinated products have such a low calory count?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would presume that caffeine doesn't really have as much energy as it seems to give you? In which case, what does it do?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance!&lt;/p&gt;&#xA;" OwnerUserId="10048" LastEditorUserId="3340" LastEditDate="2015-06-04T11:40:10.103" LastActivityDate="2015-06-04T11:40:10.103" Title="Why does caffeine give you so much energy, while being so low on calories?" Tags="&lt;pharmacology&gt;&lt;food&gt;&lt;ethnobiology&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23698" PostTypeId="2" ParentId="23694" CreationDate="2014-11-04T14:35:45.683" Score="6" Body="&lt;p&gt;No, as @rg255 already mentioned, bacteria are one of the main kingdoms of life:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/rh7Gt.png&quot; alt=&quot;Phylogenetic tree showing the three main domains of life (Bacteria, Archaea and Eukaryotes)&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;https://en.wikipedia.org/wiki/Bacteria&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bacteria&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Archaea&quot; rel=&quot;nofollow noreferrer&quot;&gt;Archaea&lt;/a&gt; are all unicellular organisms (though there are strange Archea like the &lt;a href=&quot;https://en.wikipedia.org/wiki/Pyrodictium&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pyrodictium&lt;/a&gt; genus that are borderline multicellular). The Eukaryota include all plants, fungi and animals but there are also unicellular Eukaryotes. For example, &lt;a href=&quot;https://en.wikipedia.org/wiki/Paramecium&quot; rel=&quot;nofollow noreferrer&quot;&gt;Paremecium&lt;/a&gt; is a unicellular animal, brewer's yeast (&lt;a href=&quot;https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;S. cerevisiae&lt;/em&gt;&lt;/a&gt;) is a unicellular fungus and &lt;a href=&quot;http://en.wikipedia.org/wiki/Chlorella&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chlorella&lt;/a&gt; is a unicellular plant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, all bacteria are unicellular but not all unicellular organisms are bacteria. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2016-08-17T08:59:21.027" LastActivityDate="2016-08-17T08:59:21.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23699" PostTypeId="2" ParentId="23697" CreationDate="2014-11-04T15:08:15.887" Score="6" Body="&lt;p&gt;Caffeine is a stimulant, which helps you release the energy your body stored. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Caffeine is a central nervous system and metabolic stimulant,[12] and&#xA;  is used both recreationally and medically to reduce physical fatigue&#xA;  and to restore alertness when drowsiness occurs. It produces increased&#xA;  wakefulness, faster and clearer flow of thought, increased focus, and&#xA;  better general body coordination.[13] The amount of caffeine needed to&#xA;  produce effects varies from person to person, depending on body size&#xA;  and degree of tolerance. Effects begin less than an hour after&#xA;  consumption, and a moderate dose usually wears off in about five&#xA;  hours.[13]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Caffeine has a number of effects on sleep, but does not affect all&#xA;  people in the same way. It improves performance during sleep&#xA;  deprivation but may lead to subsequent insomnia.[14] In shift workers&#xA;  it leads to fewer mistakes caused by tiredness.[15] In athletics,&#xA;  moderate doses of caffeine can improve sprint,[16] endurance,[17] and&#xA;  team sports performance,[18] but the improvements are usually not very&#xA;  large. Some evidence suggests that coffee does not produce the&#xA;  ergogenic effects observed in other caffeine sources.[19] High doses&#xA;  of caffeine, however, can impair athletic performance by interfering&#xA;  with coordination.[20] There is also evidence that caffeine may be&#xA;  helpful at high altitude.[21]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Caffeine#Stimulant_effects&quot; rel=&quot;noreferrer&quot;&gt;wikipedia - Caffeine&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;1980 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7369170&quot; rel=&quot;noreferrer&quot;&gt;Caffeine and coffee: their influence on metabolic rate and substrate utilization in normal weight and obese individuals.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2010 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0031938410000703&quot; rel=&quot;noreferrer&quot;&gt;Green tea catechins, caffeine and body-weight regulation&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;1985 - &lt;a href=&quot;http://europepmc.org/abstract/MED/4079741&quot; rel=&quot;noreferrer&quot;&gt;Influence of caffeine on the resting metabolic rate of exercise-trained and inactive subjects.&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2004 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1038/oby.2004.144/full&quot; rel=&quot;noreferrer&quot;&gt;Effect of a Dietary Herbal Supplement Containing Caffeine and Ephedra on Weight, Metabolic Rate, and Body Composition&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2006 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0031938406000540&quot; rel=&quot;noreferrer&quot;&gt;Metabolic effects of spices, teas, and caffeine&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2004 - &lt;a href=&quot;http://www.nature.com/clpt/journal/v75/n4/abs/clpt2004404a.html&quot; rel=&quot;noreferrer&quot;&gt;Enhanced Stimulant and Metabolic Effects of Combined Ephedrine and Caffeine&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2006 - &lt;a href=&quot;http://ajcn.nutrition.org/content/83/3/674.short&quot; rel=&quot;noreferrer&quot;&gt;Changes in caffeine intake and long-term weight change in men and women&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3340" LastEditDate="2014-11-05T04:05:21.710" LastActivityDate="2014-11-05T04:05:21.710" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23704" PostTypeId="2" ParentId="15514" CreationDate="2014-11-04T21:23:10.197" Score="5" Body="&lt;p&gt;You need to add Bell curves to your simulation. The most important curve to simulate is the nutritional quality of the prey though there are plenty more thing to curve like speed and virility for prey and predators both. Nature uses lots of Bell curves so they must be good for something, such as softening the harsh effects of pure exponential growth. I suspect that the more Bell curves you implement the more stable your populations will become. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the food value of your prey is all equal then there's no reason for your predators to not eat every last one. That's what I do with a plate full of foodstuffs, all equally delicious and with enough surplus that all the bad food can be thrown in the trash. Problems arise when you are forced to eat the trash because there's nothing else to eat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's eat our prey from all 3 sides of the curve. If we eat from the weakest and easiest to catch on the left this makes the prey population stronger and more resistant to the predator. If we eat from the most common on the top the prey rebound more rapidly. If we eat from the most desirable on the right the rapid quality (but not the virility) reduction of the prey population has serious negative health consequences for the predators. Notice how each direction we eat has the necessary corrective action against the predator as a response. Due to the wild randomness of genetics the weak population can always rebound in quality when the predatory pressure eases. Looks like Nature didn't screw that one up either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An easy example is seen in the human vs plant food supply. Population should rise with no detriment as we produce more and more food, and it would if the quality could stay the same. The population does rise but because the nutritional quality keeps dropping, the detriment is rapidly increasing on numerous health and population charts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When plants are forced to make do with what little they have, you are forced to make do with what little they provide.&lt;/p&gt;&#xA;" OwnerUserId="10053" LastActivityDate="2014-11-04T21:23:10.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23705" PostTypeId="1" CreationDate="2014-11-04T21:55:03.990" Score="3" ViewCount="182" Body="&lt;p&gt;Are there any connections between food allergen-related skin reactions causing intestinal (or more broadly, gastrointestinal) generalized inflammation? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If such a link exists, is it related to any of the inflammatory bowel diseases (Crohn's, colitis, irritable bowel syndrome)?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="16866" LastEditDate="2017-04-03T17:35:12.570" LastActivityDate="2017-04-03T17:35:12.570" Title="Food allergen-related skin reactions and intestinal inflammation?" Tags="&lt;immunology&gt;&lt;pathology&gt;&lt;food&gt;&lt;digestive-system&gt;&lt;allergies&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23706" PostTypeId="1" AcceptedAnswerId="31502" CreationDate="2014-11-04T22:20:32.417" Score="2" ViewCount="231" Body="&lt;p&gt;I am conducting an investigation into the topic of the intelligence of&#xA;animals, in particular farm animals. I would be interested to hear a scientific and biologic perspective as to what is perceived to be self-awareness, whether it be in a human or&#xA;not. Specifically, I am interested in the high-level self-awareness that we as humans experience and that is only now, beginning to be theorised as possible in other mammals (e.g. Dolphins).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is framed in a robotic context, where a being (natural or artificial) is defined to be self-aware if it can approximate enough human behaviour and thought, that it becomes indistinguishable from a human. This term we could label sentience, but this is a subjective term, and so I will avoid using it for the purpose of this question. I will define a being as self-aware in the robot context, as a being capable of both conscious reflection of itself and of its own conciousness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the problems I have found in my investigation, is a serious&#xA;misunderstanding about the nature of self-awareness, amongst&#xA;the general public.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that many people incorrectly assume that self-awareness is a product of&#xA;a being having a soul. This is rather unfortunate for animals as orthodox&#xA;Christianity teaches that animals do not have souls, and therefore are&#xA;incapable of attaining self-awareness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My investigation aims to bring to mainstream public attention, a new&#xA;definition of self-awareness, and to end the centuries-old misconception&#xA;that we are the only intelligent, self-aware creatures on the planet.&lt;/p&gt;&#xA;" OwnerUserId="10054" LastEditorUserId="5144" LastEditDate="2014-11-05T13:30:42.237" LastActivityDate="2015-04-19T17:11:44.313" Title="Is there biological evidence for self-awareness in animals?" Tags="&lt;intelligence&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23707" PostTypeId="2" ParentId="23693" CreationDate="2014-11-04T22:28:07.200" Score="23" Body="&lt;p&gt;This is an interesting question, and there are a number hypotheses available to explain this phenomenon. The short answer (as far as I can say after my literature search) is that we don't know the answer for sure. The long version follows below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main problem with all these hypotheses is that though they may have a valid point, a definitive hypothesis hasn't been demonstrated yet. All these hypotheses are listed in the first reference, with a ton of additional references in the paper. I will summarize the different hypotheses only briefly here; for details please read the paper. The second reference is also interesting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The point when this process started was after the last common ancestor of chimpanzee and humans when our two lines diverged. Chimpanzees are our closest relatives and still have hair coats, so this process must have started afterwards. Analyses of MC1R mutations (which affect pigmentation) suggest that human have been hairless for at least 1.2 million years. See reference 3 for details on this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Aquatic ape hypothesis (also known as aquatic ape theory):&lt;/strong&gt; This hypothesis states that modern humans spent some time semi-aquatic. In this lifestyle fur does not insulate very well and this led to an evolutionary disadvantage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cooling hypothesis:&lt;/strong&gt; This hypothesis states that the modern humans lost their hair when they left the forests and started to live on the savannah. There they got too warm with their fur and finally lost it. This hypothesis sounds logical at first thought, but has a few problems. Naked humans have two problems: during the day they collect quite some heat via their skin, which requires them to have a cooling system (we sweat to cool us), and during cold nights we need a lot of internal energy to keep our temperature stable. Insulation however works both ways (not only keeps the warmth in, but also can keep heat out), and indeed some savannah monkeys have denser fur than their relatives in the forest. The cooling system will also lead to water loss and potential dehydration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Hunting hypothesis:&lt;/strong&gt; This hypothesis states that humans started becoming carnivores and therefore had the need to run for extended periods of time to hunt for meat. This leads to thermal overload; without a fur they can release this heat much faster to avoid overheating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Bipedality hypothesis:&lt;/strong&gt; This hypothesis assumes that modern humans, walking on two feet, have a lower direct influx of solar radiation. This lowers the chance for overheating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Allometry hypothesis:&lt;/strong&gt; Allometry states that species which get bigger during evolution, do not have all their organs getting bigger at the same rate. The hypothesis states that humans got bigger, the number of hairs stayed the same, and finally got lost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Clothing hypothesis:&lt;/strong&gt; One of the more illogical hypotheses, this assumes that hair loss wasn't critical for humans as they managed to make themselves clothes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Vestiary hypothesis:&lt;/strong&gt; A mix of the cooling and the clothing hypothesis: Here it is assumed that hair loss is beneficial due to more cooling and that the negative effects of too much loss of heat were counteracted by the invention of artificial insulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Neoteny hypothesis:&lt;/strong&gt; Neoteny denotes the retention of of juvenile physical characteristics in adults. Humans are characterized as retarded in development (compared to the apes) and mature more slowly. Additionally, it is assumed that some characteristics (here loss of hair) of juvenile or fetal apes are maintained.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Carrion-eating hypothesis:&lt;/strong&gt; Another strange hypothesis, this assumes that man as a messy eater (like vultures and condors, which have naked necks) have an advantage of being hairless.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sex-related hypothesis:&lt;/strong&gt; This hypothesis assumes that hairless skin is more sensitive to stimuli like touch, temperature and pain. This would allow more sensitive social contacts, especially between man and woman, but also between woman and child. Pubic hair is not explained by this hypothesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Adaptation-against-ectoparasites hypothesis:&lt;/strong&gt; Here it is assumed that naked humans are less prone to harbour ticks, fleas and other parasites which hide and live within fur. Apes have great social rituals of removing these within their group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://users.utu.fi/mjranta/reprints/Rantala%202007.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evolution of nakedness in Homo sapiens&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://omicsonline.org/the-hairless-mutation-hypothesis-explains-not-only-the-origin-of%20humanization-from-the-human-ape-common-ancestor-but-also-immature-baby-delivery-2161-0436.1000111.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Hairless Mutation Hypothesis Explains Not Only the Origin of&#xA;Humanization from the Human/Ape Common Ancestor but also Immature&#xA;Baby Delivery&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://content.lib.utah.edu/cdm/ref/collection/uspace/id/682&quot; rel=&quot;nofollow noreferrer&quot;&gt;Genetic variation at the MC1R locus and the time since loss of human&#xA;body hair.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="231" LastEditDate="2018-06-02T20:04:35.053" LastActivityDate="2018-06-02T20:04:35.053" CommentCount="6" ContentLicense="CC BY-SA 4.0" />
  <row Id="23708" PostTypeId="2" ParentId="23697" CreationDate="2014-11-04T23:02:44.527" Score="10" Body="&lt;p&gt;I agree with @inf3rno: caffeine is a stimulant that acts on the brain and various other parts of the body &lt;a href=&quot;http://www.pnas.org/content/78/5/3260.short&quot;&gt;(Snyder et al., 1981)&lt;/a&gt; and I wish to elaborate on its psychopharmacology. Caffeine's effects in the brain are mediated through adenosine A&lt;sub&gt;1&lt;/sub&gt; and A&lt;sub&gt;2&lt;/sub&gt; receptors &lt;a href=&quot;http://link.springer.com/article/10.1007/BF00734999#page-1&quot;&gt;(Daly et al., 1983)&lt;/a&gt;. This results in a variety of actions &lt;a href=&quot;http://pharmrev.aspetjournals.org/content/51/1/83.long#title0&quot;&gt;(Fredholm et al., 1999)&lt;/a&gt;. Most notably, adenosine inhibits neurotransmitter release in various brain structures including the acetylcholine release in the mesopontine projection neurons. Caffeine blocks these adenosine receptors, in turn leading to an increase in acetylcholine release in the cortex and hippocampus. This increases vigilance and information processing. Increased acetylcholine release in the prefrontal cortex may lead to increased attentional abilities. Adenosine also inhibits the effects of dopamine released by the striatium, ultimately leading to disinhibition of motor output in the brainstem. This in turn increases motor activity &lt;a href=&quot;http://link.springer.com/article/10.1007/s00018-003-3269-3&quot;&gt;(Fisone et al., 1997)&lt;/a&gt;. In all, caffeine does not exert its stimulant effects through its metabolic energy content, but due to its pharmacologic effects on adenosine receptors.  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-05T01:12:28.827" LastActivityDate="2014-11-05T01:12:28.827" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23709" PostTypeId="1" AcceptedAnswerId="23810" CreationDate="2014-11-04T23:15:46.443" Score="8" ViewCount="10652" Body="&lt;p&gt;Presumably, as a whale or seal dives, its lungs get compressed by the increasing water pressure, and it gets less buoyant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under this model, for a given amount of air taken in at the surface, the animal has a very specific depth D at which it is neutrally buoyant. Any deeper, and the lungs shrink, making it negatively buoyant. Any shallower, and the lungs expand, making it positively buoyant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, until it reaches depth D, the animal is positively buoyant. To get to depth D, the animal would have to do a lot of work swimming down, fighting against its own floatiness. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The amount of air that keeps you neutrally buoyant at 10 meters will inflate to twice the volume once you surface, keeping you pinned there. Speaking as a scuba diver, I can say that it would take a lot of work to dive back down to 10 meters. (We deflate our air vests at the surface and re-inflate at depth from our incompressible tanks, something animals don't have.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For very deep divers like sperm whales, swimming down against positive buoyancy seems like a huge energy waste, the kind that one might expect wouldn't be tolerated long by evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So do marine mammals do anything to compensate for the effect of fluctuating lung size on their buoyancy? One guess is that they actually exhale fully before diving, thus making lung buoyancy a small player in the overall body buoyancy. Another guess is that they compress the air with their chest muscles at the surface in order to sink. These are just guesses; I'd love to hear the real story.&lt;/p&gt;&#xA;" OwnerUserId="10055" LastEditorUserId="10055" LastEditDate="2014-11-05T16:19:56.823" LastActivityDate="2018-04-09T03:50:56.037" Title="How do marine mammals control buoyancy?" Tags="&lt;zoology&gt;&lt;biophysics&gt;&lt;mammals&gt;&lt;marine-biology&gt;&lt;bio-mechanics&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23710" PostTypeId="1" AcceptedAnswerId="23714" CreationDate="2014-11-05T00:11:04.943" Score="2" ViewCount="251" Body="&lt;p&gt;I recently had a discussion with a statistician in my school about memory. Among other things, he told me that it has been experimentally demonstrated that when one extracts DNA from any organism and then induces a stressful condition on that organism, the same effects on DNA can be observed both in that organism and the DNA sample that was extracted before the stressful condition. From what I could tell it is as if he was suggesting that DNA has some kind of a telepathic property that enables this phenomenon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I am not a biologist (and neither was he) but I am heavily suspicious of this idea. Also, when I asked him for a specific paper on that, he simply told me that there are many and that it is fairly easy to find them. However, my efforts to find anything on google scholar were fruitless so far.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I want to know: Is such a thing possible and have there been any experimental studies on that?&lt;/p&gt;&#xA;" OwnerUserId="10056" LastActivityDate="2017-09-28T01:29:49.273" Title="Has DNA communication/interaction at a distance been empirically demonstrated?" Tags="&lt;dna&gt;&lt;memory&gt;&lt;communication&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23711" PostTypeId="1" AcceptedAnswerId="23719" CreationDate="2014-11-05T01:03:53.673" Score="4" ViewCount="654" Body="&lt;p&gt;&lt;strong&gt;Drake's rule&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Drake's rule states that the genome-wide mutation rate is more or less constant across all species — from &lt;em&gt;E.coli&lt;/em&gt; to the house sparrow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Data&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I think being Drake's &lt;a href=&quot;http://www.pnas.org/content/88/16/7160.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;original paper&lt;/a&gt; (table 1, page 4) on the subject (see here) is at the order of $3\times 10^{-3}$. When I look at &lt;a href=&quot;http://digitalcommons.wayne.edu/humbiol/vol85/iss4/1/&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;, I see that the genome-wide mutation rate is roughly around 30 for human. When I look at this paper, they cite some other papers suggesting a genome-wide mutation rate in the order of 0.1 to 1 in multicellular eukaryotes and typically at the order of 1 for vertebrates. Finally, when I look at &lt;a href=&quot;https://www.youtube.com/watch?v=jctvV5xrWw4&quot; rel=&quot;nofollow&quot;&gt;this speech&lt;/a&gt; (at the 60th minute), it seems however that the genome-wide mutation rate in human is 2.2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is going wrong?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do I mix-up different concepts or are there some very contradicting estimates depending on the article we look at? Isn't the genome-wide mutation rate, $U$, which is just the number of de novo mutations transmitted to one offspring on average? What is a correct estimate of $U$ for human for example (1, 2.2 or 30)?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-11-05T15:59:28.890" LastActivityDate="2014-11-05T22:09:14.330" Title="Drake's Law. What is the genome-wide mutation rate and what are the estimates?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;population-dynamics&gt;&lt;mutations&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23712" PostTypeId="2" ParentId="23705" CreationDate="2014-11-05T01:41:43.437" Score="2" Body="&lt;p&gt;Afaik the most probable trigger of IBDs (Crohn's, colitis ulcerosa) are changes in the gut microbiota due to western lifestyle (high intake of some nutrients e.g. milk fat). These changes cause an inflammation in the susceptible (genetic factors) people. So the cause of IBDs is very likely not an allergic reaction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Irritable_bowel_syndrome&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; IBS is not an IBD (inflammatory bowel disease). It is a functional disorder of the bowel, so not so serious as the IBDs. Its possible causes are low grade inflammation of the bowels and neuroendocrine disregulation. It has genetic factors as well. The pathomechanism is not fully understood yet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many bowel diseases which can be caused by specific foods, e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Coeliac_disease&quot; rel=&quot;nofollow&quot;&gt;celiac disease&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Lactose_intolerance&quot; rel=&quot;nofollow&quot;&gt;lactose intolerance&lt;/a&gt;, and so on, the list is long, &lt;a href=&quot;http://emedicine.medscape.com/article/931548-clinical&quot; rel=&quot;nofollow&quot;&gt;many of them can be caused by food protein intolerance&lt;/a&gt;. It is my understanding of protein sensitivity that skin conditions are caused by B-cell (IgE) mediated immune response, while bowel conditions are caused by T-cell mediated immune response. Ofc. there is connection between them, so it is possible that a certain type of protein induces skin symptoms and intestinal symptoms as well. Based on the current studies I think food sensitivity is not related to IBDs, and probably not related to IBS as well.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;CD is associated with dramatic changes in the gut microbiota and this&#xA;  was particularly evident for individuals with ileal CD.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://www.nature.com/ismej/journal/v2/n7/abs/ismej200837a.html&quot; rel=&quot;nofollow&quot;&gt;Molecular analysis of the gut microbiota of identical twins with Crohn's disease&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Molecular profiling of faecal bacteria revealed abnormalities of&#xA;  intestinal microbiota in UC and IBS patients, while different patterns&#xA;  of Bacteroides species loss in particular, were associated with UC and&#xA;  IBS.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://www.biomedcentral.com/1471-230X/10/134&quot; rel=&quot;nofollow&quot;&gt;Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of the gut microbiota&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Breakdown of the normal microbial community increases the risk of&#xA;  pathogen infection, the overgrowth of harmful pathobionts and&#xA;  inflammatory disease. Understanding the interaction of the microbiota&#xA;  with pathogens and the host might provide new insights into the&#xA;  pathogenesis of disease, as well as novel avenues for preventing and&#xA;  treating intestinal and systemic disorders.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://www.nature.com/nri/journal/v13/n5/full/nri3430.html&quot; rel=&quot;nofollow&quot;&gt;Role of the gut microbiota in immunity and inflammatory disease&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2014 - &lt;a href=&quot;http://www.wjgnet.com/1007-9327/pdf/v20/i5/1192.pdf&quot; rel=&quot;nofollow&quot;&gt;Role of the gut microbiota in inflammatory bowel disease&#xA;pathogenesis: What have we learnt in the past 10 years?&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Crohn's disease and ulcerative colitis are idiopathic, chronic,&#xA;  relapsing, inflammatory conditions that are immunologically mediated.&#xA;  Although their exact etiologies remain uncertain, results from&#xA;  research in animal models, human genetics, basic science and clinical&#xA;  trials have provided important new insights into the pathogenesis of&#xA;  chronic, immune-mediated, intestinal inflammation. These studies&#xA;  indicate that Crohn's disease and ulcerative colitis are heterogeneous&#xA;  diseases characterized by various genetic abnormalities that lead to&#xA;  overly aggressive T-cell responses to a subset of commensal enteric&#xA;  bacteria. The onset and reactivation of disease are triggered by&#xA;  environmental factors that transiently break the mucosal barrier,&#xA;  stimulate immune responses or alter the balance between beneficial and&#xA;  pathogenic enteric bacteria. Different genetic abnormalities can lead&#xA;  to similar disease phenotypes; these genetic changes can be broadly&#xA;  characterized as causing defects in mucosal barrier function,&#xA;  immunoregulation or bacterial clearance. These new insights will help&#xA;  develop better diagnostic approaches that identify clinically&#xA;  important subsets of patients for whom the natural history of disease&#xA;  and response to treatment are predictable.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2006 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16819502&quot; rel=&quot;nofollow&quot;&gt;Mechanisms of disease: pathogenesis of Crohn's disease and ulcerative colitis.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2011 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0016508511001697&quot; rel=&quot;nofollow&quot;&gt;Proinflammatory Cytokines in the Pathogenesis of Inflammatory Bowel Diseases&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2014 - &lt;a href=&quot;http://journals.lww.com/ibdjournal/Abstract/2014/02000/Role_of_Regulatory_B_Cells_in_Chronic_Intestinal.14.aspx&quot; rel=&quot;nofollow&quot;&gt;Role of Regulatory B Cells in Chronic Intestinal Inflammation: Association with Pathogenesis of Crohn's Disease&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://journals.lww.com/ibdjournal/Fulltext/2013/06000/Effects_of_Enteral_Nutrition_on_Crohn_s_Disease_.27.aspx&quot; rel=&quot;nofollow&quot;&gt;Effects of Enteral Nutrition on Crohn’s Disease: Clues to the Impact of Diet on Disease Pathogenesis&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The composite human microbiome of Western populations has probably&#xA;  changed over the past century, brought on by new environmental&#xA;  triggers that often have a negative impact on human health1. Here we&#xA;  show that consumption of a diet high in saturated (milk-derived) fat,&#xA;  but not polyunsaturated (safflower oil) fat, changes the conditions&#xA;  for microbial assemblage and promotes the expansion of a&#xA;  low-abundance, sulphite-reducing pathobiont, Bilophila wadsworthia2.&#xA;  This was associated with a pro-inflammatory T helper type 1 (TH1)&#xA;  immune response and increased incidence of colitis in genetically&#xA;  susceptible Il10−/−, but not wild-type mice. These effects are&#xA;  mediated by milk-derived-fat-promoted taurine conjugation of hepatic&#xA;  bile acids, which increases the availability of organic sulphur used&#xA;  by sulphite-reducing microorganisms like B. wadsworthia. When mice&#xA;  were fed a low-fat diet supplemented with taurocholic acid, but not&#xA;  with glycocholic acid, for example, a bloom of B. wadsworthia and&#xA;  development of colitis were observed in Il10−/− mice. Together these&#xA;  data show that dietary fats, by promoting changes in host bile acid&#xA;  composition, can markedly alter conditions for gut microbial&#xA;  assemblage, resulting in dysbiosis that can perturb immune&#xA;  homeostasis. The data provide a plausible mechanistic basis by which&#xA;  Western-type diets high in certain saturated fats might increase the&#xA;  prevalence of complex immune-mediated diseases like inflammatory bowel&#xA;  disease in genetically susceptible hosts.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.nature.com/nature/journal/v487/n7405/full/nature11225.html&quot; rel=&quot;nofollow&quot;&gt;Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10−/− mice&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The pathogenesis of IBS seems to be multifactorial, with the following&#xA;  factors playing a central role in the pathogenesis of IBS:&#xA;  heritability and genetics, dietary/intestinal microbiota, low-grade&#xA;  inflammation, and disturbances in the neuroendocrine system (NES) of&#xA;  the gut&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2012 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468846/&quot; rel=&quot;nofollow&quot;&gt;Irritable bowel syndrome: Diagnosis and pathogenesis&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2014 - &lt;a href=&quot;http://link.springer.com/article/10.1007/s10620-014-3299-8&quot; rel=&quot;nofollow&quot;&gt;Melatonin Regulation as a Possible Mechanism for Probiotic (VSL#3) in Irritable Bowel Syndrome: A Randomized Double-Blinded Placebo Study&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2012 - &lt;a href=&quot;http://ajpgi.physiology.org/content/303/7/G775&quot; rel=&quot;nofollow&quot;&gt;Irritable Bowel Syndrome: Methods, Mechanisms, and Pathophysiology. The confluence of increased permeability, inflammation, and pain in irritable bowel syndrome&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-11-05T01:41:43.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23714" PostTypeId="2" ParentId="23710" CreationDate="2014-11-05T04:37:11.260" Score="4" Body="&lt;p&gt;No — typical DNA extraction will not preserve information about the biochemical state of the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;During the process of DNA extraction, proteins are removed and DNA from a population of cells gets precipitated. Then you dissolve the DNA. In this process native conformational state cannot be preserved. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However there are techniques (see &lt;a href=&quot;https://biology.stackexchange.com/questions/20799/how-to-identify-the-genes-that-distal-enhancers-pair/20800#20800&quot;&gt;this&lt;/a&gt; post) that can capture long distance molecular interactions of DNA (which reflects a conformational state). To summarize in a line, these techniques &quot;lock&quot; the DNA in its conformation and downstream steps are carefully done so as prevent loss of information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stress is just a kind of biochemical response. This technique can be applied to study long range DNA-DNA interactions for different conditions (for e.g. Developmental stages).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stress can cause RNA in the cell to aggregate; however once you do the extraction you won't be able to know if it was aggregated in the cell before extraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;An Analogy: Sugar can be anhydrous powder or can be crystalline. But once you dissolve the sugar in water, there is no way to know in what form it existed before dissolution.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Certain processes (epigentic mechanisms) can lead to methylation (sometimes hydroxymethylation) of DNA (at cytosine; Bacteria also have adenine methylation). These modifications can be detected in the extracted DNA by different methods; one of the common techniques employed for this is &lt;a href=&quot;http://en.wikipedia.org/wiki/Bisulfite_sequencing&quot; rel=&quot;nofollow noreferrer&quot;&gt;bisulphite-sequencing&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Final word: all these claims about molecules having telepathic memory is pseudoscience. There is no evidence whatsoever for such proposed phenomena. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-11-05T09:33:24.770" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23715" PostTypeId="2" ParentId="23709" CreationDate="2014-11-05T05:11:10.397" Score="0" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/F9J2E.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This  scenario is called neutral buoyancy, and it's what marine mammals have, so it doesn't take energy for them to stay still in the water, and it's not particularly hard for them to go up or down when they want to either. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine an animal that is as dense as a rock trying to swim up for air, or one that has low density, like a balloon, trying to dive down to find food; it would take a lot more energy to counteract that net buoyancy-weight force (up or down) than it would if that net buoyancy-weight force was 0. So by having neutral buoyancy, marine mammals save energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And how do they achieve neutral buoyancy?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;They have more fat in their bodies&lt;/strong&gt; (fat is less dense than water), It also helps that saltwater is a little more dense than pure water, so the buoyant force is a little stronger. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So...as you predicted...neutral buoyancy helps them, but not by inhaling specific amount of air...instead one can say that's their inherent property...&lt;/p&gt;&#xA;" OwnerUserId="10045" LastActivityDate="2014-11-05T05:11:10.397" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="23716" PostTypeId="2" ParentId="9399" CreationDate="2014-11-05T05:12:54.660" Score="1" Body="&lt;p&gt;Non-coding transcripts can be as small as 10-15 nucleotides. Once the RNA polymerase initiates, the DNA is melted and the transcription bubble forms. This region is about 10 nucleotides long.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if you are asking the limit of mRNA length, then the answer is different. First of all, to get a protein, the ribosomes have to translate the transcript. To do that, they need some space to land on, and initiate the translation process. We know that ribosomes protect about ~30 nucleotides from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22153074&quot; rel=&quot;nofollow&quot;&gt; ribosome footprinting experiments&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, bacteria wouldn't need to utilize the genomic space and the ribosome machinery to produce small peptides (even if the peptides were useful), since the small peptides are already around as the degradation product of other proteins. Hence, once you add 3 times the shortest produced polyaminoacid length to the minimum length required for the ribosome landing, you get somewhat physical (or let's say physiological) limit of the transcript length.&lt;/p&gt;&#xA;" OwnerUserId="9687" LastActivityDate="2014-11-05T05:12:54.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23717" PostTypeId="2" ParentId="15469" CreationDate="2014-11-05T05:19:41.640" Score="4" Body="&lt;p&gt;$H_2S$ is the end product of sulfur related respirations (like sulfate respiration, sulfur respiration, etc...).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By aerob (oxygen) respiration the oxygen in $O_2$ has 0 &lt;a href=&quot;http://en.wikipedia.org/wiki/Oxidation_state&quot; rel=&quot;nofollow&quot;&gt;oxidation number&lt;/a&gt;, by $CO_2$ the oxygen has -2 oxidation number, so it was reduced while the carbon was oxidized.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the thiosulfate respiration of Salmonella enterica the following reaction happens by the reduction of thiosulfate: $S_2O_3^{2-} +2H^+ + 2e^- \to HS^- + HSO_3^{-}$. In this case the sulfur in $S_2O_3^{2-}$ has +2 oxidation number while the sulfur in $HS^-$ has -2 oxidation number, so the sulfur was reduced, it was an electron acceptor, just like oxygen by aerob respiration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in the case of Salmonella enterica $H_2S$ production is a byproduct of anaerob respiration. It makes growth faster.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sulfate-reducing bacteria are those bacteria that can obtain energy by&#xA;  oxidizing organic compounds or molecular hydrogen (H2) while reducing&#xA;  sulfate (SO2- 4) to hydrogen sulfide (H2S).&lt;a href=&quot;http://en.wikipedia.org/wiki/Oxidation_state&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt; In a sense, these&#xA;  organisms &quot;breathe&quot; sulfate rather than oxygen in a form of anaerobic&#xA;  respiration.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sulfate-reducing_bacteria&quot; rel=&quot;nofollow&quot;&gt;wikipedia - Sulfate-reducing bacteria&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Salmonella typhimurium produces H2S from thiosulfate or sulfite.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;1987 - &lt;a href=&quot;http://jb.asm.org/content/169/6/2391&quot; rel=&quot;nofollow&quot;&gt;The phs gene and hydrogen sulfide production by Salmonella typhimurium.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2011 - &lt;a href=&quot;http://jb.asm.org/content/194/2/475.full&quot; rel=&quot;nofollow&quot;&gt;Thiosulfate Reduction in Salmonella enterica Is Driven by the Proton Motive Force&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;S. enterica uses gut inflammation to enhance its sulfur related respiration to outgrow the resident microbes in the intestinal lumen (microbiota). The inflammation creates tetrathionate $S_4O_6^{2-}$ in which the sulfur has an average oxidation number of +2.5. This tetrathionate is reduced by the tetrathionate reductase into thiosulfate with sulfur having +2 oxidation number. So sulfur related respiration helps to make growth faster in order to colonize the gut.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Here we show that reactive oxygen species generated during&#xA;  inflammation react with endogenous, luminal sulphur compounds&#xA;  (thiosulphate) to form a new respiratory electron acceptor,&#xA;  tetrathionate. The genes conferring the ability to use tetrathionate&#xA;  as an electron acceptor produce a growth advantage for S. Typhimurium&#xA;  over the competing microbiota in the lumen of the inflamed gut. We&#xA;  conclude that S. Typhimurium virulence factors induce host-driven&#xA;  production of a new electron acceptor that allows the pathogen to use&#xA;  respiration to compete with fermenting gut microbes. Thus the ability&#xA;  to trigger intestinal inflammation is crucial for the biology of this&#xA;  diarrhoeal pathogen.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2010 - &lt;a href=&quot;http://www.nature.com/nature/journal/v467/n7314/abs/nature09415.html&quot; rel=&quot;nofollow&quot;&gt;Gut inflammation provides a respiratory electron acceptor for Salmonella&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2001 - &lt;a href=&quot;http://jb.asm.org/content/183/8/2463.full&quot; rel=&quot;nofollow&quot;&gt;The Alternative Electron Acceptor Tetrathionate Supports B12-Dependent Anaerobic Growth of Salmonella enterica Serovar Typhimurium on Ethanolamine or 1,2-Propanediol&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Since $H_2S$ is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Gasotransmitter&quot; rel=&quot;nofollow&quot;&gt;gasotransmitter&lt;/a&gt; in the human body, there can be other mechanisms which help S. enterica.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;in small amounts $H_2S$ has anti-inflammatory and anti-apoptotic effects&lt;/li&gt;&#xA;&lt;li&gt;in large amounts $H_2S$ has pro-inflammatory and pro-apoptotic effects&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So S. enterica can probably cause inflammation due to killing cells with a fast release of $H_2S$ or prevent inflammation and keep infected cells alive with a slow release of $H_2S$. I found many evidence of the pro-inflammatory theory. By the anti-apoptotic theory I wasn't so lucky, I found only a single review about anti-apoptotic strategies of intracellular pathogens, but it did not mention $H_2S$ production as a possible mechanism. So it might not be true, further studies needed...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the digestive system, H2S exerts potent anti-inflammatory actions,&#xA;  regulates blood flow and smooth muscle tone, modulates epithelial&#xA;  secretion and promotes healing of ulcers [4, 5].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs10620-012-2119-2?LI=true&quot; rel=&quot;nofollow&quot;&gt;Hydrogen Sulfide: A Rescue Molecule for Mucosal Defence and Repair&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hydrogen sulfide (H2S) is the most recent endogenous gasotransmitter&#xA;  that has been reported to serve many physiological and pathological&#xA;  functions in different tissues. Studies over the past decade have&#xA;  revealed that H2S can be synthesized through numerous pathways and its&#xA;  bioavailability regulated through its conversion into different&#xA;  biochemical forms. H2S exerts its biological effects in various&#xA;  manners including redox regulation of protein and small molecular&#xA;  weight thiols, polysulfides, thiosulfate/sulfite, iron-sulfur cluster&#xA;  proteins, and anti-oxidant properties that affect multiple cellular&#xA;  and molecular responses.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Understanding precise pathophysiological signaling mechanisms and the&#xA;  metabolism of H2S is a topic of active research. Unraveling H2S&#xA;  interactions within different tissues, with other biochemical&#xA;  molecules and various signaling mediators is becoming ever more&#xA;  complex.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;These results demonstrate that H2S donors can down-regulate adhesion&#xA;  molecule and proinflammatory cytokine expression, therefore&#xA;  identifying H2S, its synthesis enzymes, and molecular targets (e.g.,&#xA;  KATP channels) as potential targets for novel anti-inflammatory&#xA;  therapies.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Thus, all of the above findings demonstrate that H2S induces&#xA;  cytoprotection by an anti-apoptotic pathway.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1089860313002760&quot; rel=&quot;nofollow&quot;&gt;Hydrogen sulfide chemical biology: Pathophysiological roles and detection&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A short course of H2S infusion was associated with reduction of lung&#xA;  and kidney injury. Prolonged infusion did not enhance protection.&#xA;  Systemically, infusion of H2S increased both the pro-inflammatory&#xA;  response during endotoxemia, as demonstrated by increased TNF-α&#xA;  levels, as well as the anti-inflammatory response, as demonstrated by&#xA;  increased IL-10 levels. In LPS-stimulated whole blood of healthy&#xA;  volunteers, co-incubation with H2S had solely anti-inflammatory&#xA;  effects, resulting in decreased TNF-α levels and increased IL-10&#xA;  levels. Co-incubation with a neutralizing IL-10 antibody partly&#xA;  abrogated the decrease in TNF-α levels. In conclusion, a short course&#xA;  of H2S infusion reduced organ injury during endotoxemia, at least in&#xA;  part via upregulation of IL-10.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1043466612008010&quot; rel=&quot;nofollow&quot;&gt;A short course of infusion of a hydrogen sulfide-donor attenuates endotoxemia induced organ injury via stimulation of anti-inflammatory pathways, with no additional protection from prolonged infusion&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;H2S causes apoptosis in HPSCs by activating the mitochondrial pathway.&#xA;  It is suggested that H2S might be one of the factors modifying the&#xA;  pathogenesis of pulpitis by causing loss of viability of HPSCs through&#xA;  apoptosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0099239911000616&quot; rel=&quot;nofollow&quot;&gt;Hydrogen Sulfide Causes Apoptosis in Human Pulp Stem Cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The level ofendogenous H2S was increasing along with the infection&#xA;  occurrence and the gradient of infection aggravate. We can presume&#xA;  that endogenous H2S participated in inflammatory reaction of abdominal&#xA;  infection and could be one of the serology index which concerned with&#xA;  the gradient of infection.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1089860312003424&quot; rel=&quot;nofollow&quot;&gt;P53 The level changes and clinical significance of endogenous hydrogen sulfide of patients with acute abdominal infection&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The evidences showed that H2S has an obvious effect on colon smooth&#xA;  muscle contraction, and can increase the intestinal movements in slow&#xA;  transmit constipation. Our experiment states that H2S has&#xA;  anti-inflammation effect in prophase of acute peritoneal cavity&#xA;  infection.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2014 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1089860314001189&quot; rel=&quot;nofollow&quot;&gt;P48 Regulation of hydrogen sulfide in digestive stystem&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2010 - &lt;a href=&quot;http://www.atsjournals.org/doi/abs/10.1164/rccm.200907-1145OC#.VFmg78napqS&quot; rel=&quot;nofollow&quot;&gt;Hydrogen Sulfide Improves Neutrophil Migration and Survival in Sepsis via K+ATP Channel Activation&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2012 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3391661/&quot; rel=&quot;nofollow&quot;&gt;Hydrogen sulfide and resolution of acute inflammation: A comparative study utilizing a novel fluorescent probe&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2008 - &lt;a href=&quot;https://www.mh-hannover.de/fileadmin/institute/med_mikrobiologie/downloads/4_Faherty_TIM_2009_SKlos2.pdf&quot; rel=&quot;nofollow&quot;&gt;Staying alive: bacterial inhibition of apoptosis during infection&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;H2S is believed to have two contradicting roles in inflammation. It&#xA;  acts as both pro- and anti-inflammatory molecule(9). Li et al.&#xA;  reported that the physiological concentration of H2S has&#xA;  anti-inflammatory effects, while higher concentrations of H2S can&#xA;  produce pro-inflammatory effects(10). The H2S inflammatory role was&#xA;  also studied in different systems. In the gastrointestinal tract, the&#xA;  H2S regulating role functions by activating KATP channels in order to&#xA;  promote the inflammation response(57). The similar H2S function was&#xA;  observed in pancreas(7), but the actual mechanisms are largely&#xA;  unknown. In conclusion, H2S pathway is a possible route for targeting&#xA;  the inflammation treatment. However, much work needs to be done for&#xA;  understanding the mechanisms of the contradictory roles of H2S in&#xA;  inflammation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2012 - &lt;a href=&quot;http://scholar.uwindsor.ca/cgi/viewcontent.cgi?article=5848&amp;amp;context=etd&quot; rel=&quot;nofollow&quot;&gt;The Crosstalk between H2S and NO Signaling Pathways&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://f1000.com/prime/reports/b/5/28/pdf&quot; rel=&quot;nofollow&quot;&gt;Gasotransmitters, poisons, and antimicrobials: it’s a gas, gas, gas!&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Developing evidence suggests that dysbiosis (abnormal microbial&#xA;  composition or function) can contribute to if not cause chronic&#xA;  intestinal inflammation. 5,7 This inflammation can be caused either by&#xA;  an abnormal composition of entericbacteria with an elevated ratio of&#xA;  aggressive vs protective species, defective production of short-chain&#xA;  fatty acids and other protective microbial products, or enhanced&#xA;  production of hydrogen sulfide and nitrates that block butyrate&#xA;  metabolism and disrupt the mucosal barrier.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2010 - &lt;a href=&quot;http://images.abbottnutrition.com/ANHI2010/MEDIA/111th-conference-report-6-6-11.pdf#page=20&quot; rel=&quot;nofollow&quot;&gt;Inflammation and Nutrition in Chronic Disease&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://www.ingentaconnect.com/content/ben/cvp/2013/00000011/00000002/art00010&quot; rel=&quot;nofollow&quot;&gt;Potential Role of Hydrogen Sulfide in the Pathogenesis of Vascular Dysfunction in Septic Shock&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These results showed that physiological concentrations of H2S can&#xA;  induce apoptosis of PDL cells and HGFs in periodontitis, suggesting&#xA;  that H2S may play an important role in periodontal tissue damage in&#xA;  periodontal diseases.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2009 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0765.2009.01202.x/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;Hydrogen sulfide induces apoptosis in human periodontium cells&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2010 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006291X09023092&quot; rel=&quot;nofollow&quot;&gt;Bacteria-derived hydrogen sulfide promotes IL-8 production from epithelial cells&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We have shown that inactivation of H2S producing enzymes&#xA;  (cystathionine beta-synthase, cystathionine gamma lyase, or&#xA;  3-mercaptopyruvate sulfurtransferase) and NO-synthase in several Gram&#xA;  (+) and Gram (−) bacteria render them highly sensitive to different&#xA;  classes of antibiotics (Gusarov et al., Science 325 (2009) 1380–1384;&#xA;  Shatalin et al. Science 334 (2011) 986–990). We also presented&#xA;  evidence that Bacillus anthracis-derived NO is critical at the early&#xA;  stage of infection (Shatalin et al. PNAS 105 (2008) 1009–1013). Here&#xA;  we show that: (1) cbs/cse and nos mutations change Bacilli global gene&#xA;  transcription profile; (2) apore formation process in cbs/cse and nos&#xA;  mutants of B. anthracis is affected; (3) virulence of cbs/cse and nos&#xA;  mutants of B. anthracis is diminished. These results demonstrate that&#xA;  bacterial H2S and NO are an important virulence factors, and that&#xA;  enzymes generated these gases may serve as an attractive target for&#xA;  antimicrobial therapy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1089860314000561&quot; rel=&quot;nofollow&quot;&gt;S7-6 Role of H2S and NO in Bacillus anthracis spore formation and virulence&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Btw. there is non-hydrogen sulfide producing S. enterica too, which can probably (no study about this yet) cause salmonellosis. So using thiosulfate as electron acceptor and producing $H_2S$ might not be essential by the infection. (There are other non-sulfur electron acceptors e.g. nitrate, fumarate, etc... for the case of anaerob metabolism.) &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536232/&quot; rel=&quot;nofollow&quot;&gt;Genetic Analysis of Non-Hydrogen Sulfide-Producing Salmonella enterica Serovar Typhimurium and S. enterica Serovar Infantis Isolates in Japan&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2011 - &lt;a href=&quot;http://iai.asm.org/content/79/10/4105.short&quot; rel=&quot;nofollow&quot;&gt;Salmonella enterica Serovar Typhimurium Colonizing the Lumen of the Chicken Intestine Grows Slowly and Upregulates a Unique Set of Virulence and Metabolism Genes&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1003267&quot; rel=&quot;nofollow&quot;&gt;Salmonella Uses Energy Taxis to Benefit from Intestinal Inflammation&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2006 - &lt;a href=&quot;http://iai.asm.org/content/74/2/1130.short&quot; rel=&quot;nofollow&quot;&gt;Role of Gluconeogenesis and the Tricarboxylic Acid Cycle in the Virulence of Salmonella enterica Serovar Typhimurium in BALB/c Mice&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;1981 - &lt;a href=&quot;http://jb.asm.org/content/145/2/990.short&quot; rel=&quot;nofollow&quot;&gt;Aerotaxis in Salmonella typhimurium: role of electron transport.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2010 - &lt;a href=&quot;http://repository.tamu.edu/bitstream/handle/1969.1/ETD-TAMU-2010-05-7675/REYNOLDS-DISSERTATION.pdf?sequence=3&quot; rel=&quot;nofollow&quot;&gt;IDENTIFICATION OF NOVEL VIRULENCE GENES OF SALMONELLA ENTERICA&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2014 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0740002014000859&quot; rel=&quot;nofollow&quot;&gt;Increasing prevalence of hydrogen sulfide negative Salmonella in retail meats&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Overall hydrogen-sulfide and other gasotransmitters are important virulence factors of many pathogens.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3340" LastEditDate="2014-11-14T18:06:53.233" LastActivityDate="2014-11-14T18:06:53.233" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="23718" PostTypeId="1" AcceptedAnswerId="23724" CreationDate="2014-11-05T05:30:09.200" Score="12" ViewCount="760" Body="&lt;p&gt;How do marine mammals, whose very survival depends on regular diving, manage to avoid decompression sickness or &quot;the bends?&quot; Do they, indeed, avoid it?&lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="9943" LastEditDate="2014-11-06T04:19:42.483" LastActivityDate="2016-03-31T20:39:48.783" Title="How do diving marine mammals avoid decompression sickness?" Tags="&lt;physiology&gt;&lt;biophysics&gt;&lt;marine-biology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23719" PostTypeId="2" ParentId="23711" CreationDate="2014-11-05T05:59:03.830" Score="3" Body="&lt;p&gt;There are so many things that are implied in this paper, not explicitly said.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mutation rate here detected seems to be the emergence of chain-terminating (CT) mutations, which truncate protein coding genes, usually just one gene in a bacterium or phage, which would be possible to observe from inspecting a plate to see which colonies die or survive.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is only a specific kind of mutation, but Drake assumes that its frequency is related to the overall mutation rate.  Which is probably fine.  Mutations we infer from this work arise spontaneously from a similar mechanism in all organisms.  This is just ionizing radiation for the most part.  So at a first glance we still believe this.  That there are no specific mechanisms for mutation.  Since this is usually ionizing radiation we would expect that the rate would go up when there's more radiation around and it most certainly does. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are lots of reasons that animals and humans would have a smaller rate.  Drake is including in the paper the involvement of DNA repair mechanisms in the experiment as they are intrinsic to the survival of the yeast and bacterial cases and the phage may also enjoy the benefit thereof.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In some organisms there is a lot more DNA repair possible.  So that would mitigate the mutation rate in some cases like &lt;a href=&quot;https://en.wikipedia.org/wiki/Deinococcus_radiodurans&quot; rel=&quot;nofollow&quot;&gt;Deinococcus radiodurans&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Metazoans and diploid organisms which undergo meiosis for sexual reproduction have other methods for reducing the number of mutations they pass on.  Meiosis and recombination will allow the removal of many mutations by competition in gametes.  Since there are two copies of each chromosome, mutations are constantly being competed against their unmutated versions as gametes.  Then eukaryotes have their own repair enzymes and conditions.  Then lastly recombining into diploids, they also show mutations less often.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For these reasons and others, the mutation rate being even across the genome does not mean that that the mutations accumulate evenly.  Mutations still tend to accumulate in regions where positive selection is operational.  Here is an excerpt from &lt;a href=&quot;http://www.pnas.org/content/early/2014/10/31/1418307111.short&quot; rel=&quot;nofollow&quot;&gt;a recent genomic comparison of five strains of rice&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2014-11-05T22:09:14.330" LastActivityDate="2014-11-05T22:09:14.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23720" PostTypeId="1" AcceptedAnswerId="23723" CreationDate="2014-11-05T06:10:29.370" Score="63" ViewCount="10583" Body="&lt;p&gt;Is it possible for a woman to conceive from two different men and give birth to half-siblings?&lt;/p&gt;&#xA;" OwnerUserId="6124" LastEditorUserId="9943" LastEditDate="2015-01-11T13:01:03.473" LastActivityDate="2018-05-24T23:24:11.213" Title="Can a woman give birth to twins with different fathers?" Tags="&lt;twins&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="23721" PostTypeId="2" ParentId="19437" CreationDate="2014-11-05T06:10:50.520" Score="1" Body="&lt;p&gt;Generally speaking, heterochromatin or euchromatin structures mark specific regions to regulate the transcriptional activity and these marks carry the signature of developmental processes as they differ in different tissues (or cell types).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, we should not ignore the developmental processes if we want to understand how such epigenetic marks are formed. But first, we should reconsider the question as it assumes that the heterochromatin is produced. The assumption is somewhat valid, there are many enzymes responsible to shut the chromosome off thru the histone modifications. On the other hand, heterochromatin strucure comes as a default (or as the factory settings). Before the mid-blastula transition, where no (or negligable) transcription happens, all the genome is heterochromatin due to the excess amount of histones. After certain amount of division, the amount of histone per cell reduces but the genome per cell remains constant which then titrates the histones and some transcriptional activity kicks in. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then HATs, methyl transferases etc. help to clear up the necessary genomic regions depending on the extracellular developmental signaling. Then for many somatic cells, the ratio of heterochromatin and euchromatin regions more or less remain similar. &lt;/p&gt;&#xA;" OwnerUserId="9687" LastActivityDate="2014-11-05T06:10:50.520" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23722" PostTypeId="1" CreationDate="2014-11-05T07:59:09.523" Score="1" ViewCount="86" Body="&lt;p&gt;If a culture or sample of cells is such they all have no apoptosis mechanisms yet they have not been at present determined to be cancerous ; given such a cell culture is there a way to determine by their byproducts or how they signal themselves or other cells that they have no 'working' apoptosis mechanisms?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastActivityDate="2014-11-05T07:59:09.523" Title="Cells with no apoptosis mechanism and their 'byproducts'" Tags="&lt;cancer&gt;&lt;apoptosis&gt;" AnswerCount="0" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="23723" PostTypeId="2" ParentId="23720" CreationDate="2014-11-05T08:06:49.567" Score="69" Body="&lt;p&gt;Yes, this is possible through something called heteropaternal superfecundation (see below for further explanation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of all twin births, 30% are identical and 70% are non-identical (fraternal) twins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Identical twins result when a zygote (one egg, or ovum, fertilized by one sperm) splits at an early stage to become twins. Because the genetic material is essentially the same, they resemble each other closely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Typically during ovulation only one ovum is released to be fertilized by one sperm. However, sometimes a woman's ovaries release two ova. Each must be fertilized by a separate sperm cell. If she has intercourse with two different men, the two ova can be fertilized by sperm from different sexual partners. The term for this event is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1488855&quot;&gt;heteropaternal superfecundation&lt;/a&gt; (HS): twins who have the same mother, but two different fathers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has been proven in &lt;em&gt;paternity suits&lt;/em&gt; (in which there will be a bias selecting for possible infidelity) involving fraternal twins, where genetic testing must be done on each child. The frequency of heteropaternal superfecundation &lt;em&gt;in this group&lt;/em&gt; was found (in one study) to be 2.4%. As the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1488855&quot;&gt;study's authors&lt;/a&gt; state, &lt;em&gt;&quot;Inferences about the frequency of HS in other populations should be drawn with caution.&quot;&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="3624" LastEditDate="2014-11-06T12:43:09.377" LastActivityDate="2014-11-06T12:43:09.377" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="23724" PostTypeId="2" ParentId="23718" CreationDate="2014-11-05T11:00:52.507" Score="7" Body="&lt;p&gt;I think I got the answer....&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The primary anatomical adaptations for pressure of a deep-diving mammal such as the sperm whale center on air-containing spaces and the prevention of tissue barotrauma. Air cavities, when present, are lined with venous plexuses, which are thought to fill at depth, obliterate the air space, and prevent &quot;the squeeze.&quot; &lt;strong&gt;The lungs collapse, which prevents lung rupture and (important with regard to physiology) blocks gas exchange in the lung. Lack of nitrogen absorption at depth prevents the development of nitrogen narcosis and decompression sickness&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.scientificamerican.com/article/how-do-deep-diving-sea-cr/&quot; rel=&quot;nofollow&quot;&gt;Scientific American&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="19650" LastEditDate="2016-03-31T20:39:48.783" LastActivityDate="2016-03-31T20:39:48.783" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23725" PostTypeId="1" AcceptedAnswerId="23743" CreationDate="2014-11-05T12:02:09.077" Score="11" ViewCount="303" Body="&lt;p&gt;I always assumed colds ran on a 'no tagbacks' principle: once it's out of your system, it takes a while before you can get a cold again. Is there any truth to this, or can rhinoviruses hit you at any time?&lt;/p&gt;&#xA;" OwnerUserId="8642" LastActivityDate="2017-06-18T09:06:04.560" Title="Is there a period after you have had a cold when you cannot get a cold again?" Tags="&lt;virus&gt;&lt;infection&gt;" AnswerCount="4" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23726" PostTypeId="2" ParentId="23705" CreationDate="2014-11-05T13:20:59.230" Score="0" Body="&lt;p&gt;I doubt there can be causality in the direction &quot;irritation of skin by allergen&quot; --&gt; &quot;intestinal problems&quot;. I have seen several articles where skin prick testing was done on patients, but none of them mentioned intestinal problems as side effects. In rare cases, the skin testing may result in anaphylaxis, which is why it must be done in hospital with the help at hand. The possible warning symptoms are: low grade fever, lightheadedness or dizziness, wheezing or shortness of breath, extensive skin rash, swelling of face, lips or mouth, difficulty swallowing or speaking - again, the intestinal problems are not mentioned. ( &lt;a href=&quot;http://en.wikipedia.org/wiki/Skin_allergy_test&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Skin_allergy_test&lt;/a&gt; ). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disclaimer: I am not a doctor. I am a chemist / molecular biologist developing food analysis methods to detect allergenic materials undeclared on food label. The clinical papers are not my most focused field, but I have seen some.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Maybe I misunderstood the question. I thought that it was about whether the skin irritation from outside only and without actually consuming the food allergen can lead to digestive problems. I doubt that. On the other hand, eating the food allergen often results in digestive problems for allergic people. Skin and digestive problems can occur simultaneously. If these digestive problems are IBS or IBD-like or neither - I have no idea.&lt;/p&gt;&#xA;" OwnerUserId="5369" LastEditorUserId="5369" LastEditDate="2014-11-05T14:07:45.153" LastActivityDate="2014-11-05T14:07:45.153" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23727" PostTypeId="1" AcceptedAnswerId="23759" CreationDate="2014-11-05T13:31:54.583" Score="4" ViewCount="801" Body="&lt;p&gt;I don't know what I am asking is silly or not, but I have always heard that eating a banana after a meal helps in digestion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some people says before food while others say after.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it a fact or some silly myth?&lt;/p&gt;&#xA;" OwnerUserId="6802" LastEditorUserId="6511" LastEditDate="2014-11-06T22:54:09.007" LastActivityDate="2014-11-06T22:54:09.007" Title="Does eating bananas help digestion?" Tags="&lt;food&gt;&lt;digestion&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2014-11-12T06:39:13.543" ContentLicense="CC BY-SA 3.0" />
  <row Id="23728" PostTypeId="1" CreationDate="2014-11-05T13:43:49.047" Score="4" ViewCount="90" Body="&lt;p&gt;If an invasive species preys on native species, spreads widely and becomes dominant, should it not become extinct soon enough because of a lack of food?&lt;/p&gt;&#xA;" OwnerDisplayName="user6417" LastActivityDate="2014-12-05T18:19:54.547" Title="Do invasive species survive in the long run?" Tags="&lt;ecology&gt;&lt;invasive-species&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23729" PostTypeId="2" ParentId="23725" CreationDate="2014-11-05T13:44:32.207" Score="0" Body="&lt;p&gt;Just like that while a cell is infected with a virus, other virus can not enter that cell&#xA;As long as your body has not fully recovered and did not acquire full health so not be affected by another cold. The experience in cell culture and virus replication is observed exactly.&#xA;This includes all viral infections. When the cell (as conceptual you'r body) were infected with virus A, B virus unable to replication in the cell's and enter the host cell, untill host cell recovery.&#xA;The virus antigens that experss on the cell membrane prevents that other virus entering and until complete recovery those antigen is present in you'r cells membran's so cannot get a cold again, At least not the same cells infect&lt;/p&gt;&#xA;" OwnerUserId="9101" LastEditorUserId="9101" LastEditDate="2014-11-05T13:59:52.733" LastActivityDate="2014-11-05T13:59:52.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23730" PostTypeId="1" CreationDate="2014-11-05T13:47:02.127" Score="2" ViewCount="129" Body="&lt;p&gt;How come the pain in our body, primarily due to excessive physical exercises, vanishes after having a massage? What is the mechanism?&lt;/p&gt;&#xA;" OwnerUserId="3881" LastEditorUserId="948" LastEditDate="2014-11-05T16:05:01.940" LastActivityDate="2018-05-03T11:46:43.680" Title="Relieving pain by massage" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23731" PostTypeId="1" AcceptedAnswerId="23762" CreationDate="2014-11-05T13:55:41.070" Score="1" ViewCount="1066" Body="&lt;p&gt;Can a frog swim on its back, or it can use only the classic frog style? Does any (not specifically marine) animal exist with many different swimming styles, just like humans?&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-11-06T21:59:51.633" Title="Animal swimming styles" Tags="&lt;zoology&gt;&lt;behaviour&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23732" PostTypeId="2" ParentId="23725" CreationDate="2014-11-05T14:07:06.530" Score="2" Body="&lt;p&gt;If you are cured from the exact same virus, there is a less chance you will get it again. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Chris already mentioned in the comment, one part of the problem, that different species causes similar symptoms which you know as cold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another part of the problem that the same species can have different subtypes and different antigens, so the immune system does not necessary recognize the same species with different surface antigens. The most well known from this group is influenza (flu) surface antigens e.g. H5N1.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-11-05T14:07:06.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23733" PostTypeId="1" CreationDate="2014-11-05T16:25:32.987" Score="2" ViewCount="330" Body="&lt;p&gt;Is there a test method of proving a person being color-blind, without letting the test subject know, that he/she is being tested?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.g. showing the person cards with colored dots like depicted &lt;a href=&quot;https://en.wikipedia.org/wiki/Ishihara_Test&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; is not a valid answer.&lt;/p&gt;&#xA;" OwnerUserId="10064" LastEditorUserId="57" LastEditDate="2014-11-05T20:36:14.227" LastActivityDate="2014-11-06T09:15:00.127" Title="A subtle test for color-blindness" Tags="&lt;neuroscience&gt;&lt;pathology&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="10" ClosedDate="2014-11-08T15:29:54.160" ContentLicense="CC BY-SA 3.0" />
  <row Id="23734" PostTypeId="1" AcceptedAnswerId="23753" CreationDate="2014-11-05T16:35:36.553" Score="2" ViewCount="997" Body="&lt;p&gt;For the problem below I am aware of the statistics involved but just can't get my finger around the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In biology we use qPCR to measure gene expression or basically number of mRNA copies. It does this by counting how many cycles of amplification (2^) it needs to reach a threshold. So to simplify everything lets assume that 1024 copies would require 10 cycles (2^10). If there are more copies it would take less cycles to reach the threshold, therefore 2024 copies would take 9 cycles, 512 copies 11 cycles etc.. Now imagine the following scenario:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We have the following samples:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Sample 1. 1024 copies of gene A and 4096 copies of gene B&#xA;Sample 2. 1024 copies of gene A and 16384 copies of gene B&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Now we want to compare sample 2 to 1, with gene B in relation to gene A:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In absolute numbers this would be:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Sample 1. 4096 / 1024 = 4x more B&#xA;Sample 2. 16384 / 1024 = 16x more B&#xA;The average amount more B = (16 + 4) / 2 = 10x more B&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Now with qPCR the same samples from above would look like the following:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Sample 1. Gene A 10 cycles, Gene B 8 cycles.&#xA;Sample 2. Gene A 10 cycles, Gene B 6 cycles.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Now using the methods standard used for qPCR data we first take the difference between Gene B and A. Followed by the mean of the difference and this is taken 2^. &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Sample 1. 10 - 8 = 2 cycles&#xA;Sample 2. 10 - 6 = 4 cycles&#xA;The average amount more B = 2^((2 + 4)/2) = 8x more B&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;All publications / software tools etc will compute an average of 8x more B. And I am aware this originated from a log2 scale, however why does this statistically correct method differ in outcome from absolute numbers?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt;&#xA;I oversimplified my question therefore below some more details of my &quot;problem&quot;.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Condition 1 biorep 1. 1024 copies of ref and 1024 copies of gene X&#xA;Condition 1 biorep 2. 1024 copies of ref and 1024 copies of gene X&#xA;Condition 2 biorep 1. 1024 copies of ref and 4096 copies of gene X&#xA;Condition 2 biorep 2. 1024 copies of ref and 16384 copies of gene X&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So to compute in absolute numbers the average amount more of gene X in condition 2 versus 1:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;We can forget the reference gene here as cDNA amounts are the same, therefore: &#xA;Condition 1 biorep 1 &amp;amp; 2: average (1024 + 1024) / 2 = 1024 copies&#xA;Condition 2 biorep 1 &amp;amp; 2: average (4096 + 16384) / 2 = 10240 copies&#xA;Condition 2 vs 1: average 10240 / 1024 = 10x more gene X in condition 2 vs 1&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Now with qPCR CT values based on the numbers above:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Condition 1 biorep 1. Ref_CT 10 and GeneX_CT 10&#xA;Condition 1 biorep 2. Ref_CT 10 and GeneX_CT 10&#xA;Condition 2 biorep 1. Ref_CT 10 and GeneX_CT 8&#xA;Condition 2 biorep 1. Ref_CT 10 and GeneX_CT 6&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Now using the official qPCR calculations:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Condition 1, Ref_CT mean (10 + 10) / 2 = 10&#xA;Condition 2, Ref_CT mean (10 + 10) / 2 = 10&#xA;Condition 1, GeneX_CT mean (10 + 10) / 2 = 10&#xA;Condition 2, GeneX_CT mean (8 + 6) / 2 = 7&#xA;&#xA;Ref_deltaCT (10 - 10) = 0&#xA;GeneX_deltaCT (10 - 7) = 3&#xA;&#xA;delta_deltaCT (3 - 0) = 3&#xA;Difference Condition 2 vs 1 = (2^3) = 8x&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This equates to 8x more of Gene X on average in condition 2 compare to condition 1. Here now is the difference of 8x vs 10x. Also any program you will use to fill in these CT values it will result in a ratio of 8 compared to 10.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this perhaps as this method equating to 8 should only be used for technical replicates, and bioreps should use a different equation resulting into 10?&lt;/p&gt;&#xA;" OwnerUserId="10065" LastEditorUserId="3340" LastEditDate="2014-11-06T11:57:24.983" LastActivityDate="2014-11-10T04:41:38.233" Title="(Updated question) Problem with Fold-change mean compared to absolute data (in qPCR)" Tags="&lt;pcr&gt;&lt;statistics&gt;&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23736" PostTypeId="2" ParentId="23725" CreationDate="2014-11-05T17:03:57.610" Score="2" Body="&lt;p&gt;Technically, I would say no. There is no period after a cold in which you can't get a cold again. This is because as mentioned in the comment, there are many species of rhinoviruses which all give very similar symptoms (not to mention mild flu viruses), to which the body will have no immune response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it's important to remember how you get colds. It tends to be from people in your general area, and due to how colds spread this is all likely to be the same strain. Re-exposure to the strain that you have just recovered from would not cause the same infection again. It's also worth mentioning that the immune responses the body generates are in part non-specific (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Innate_immune_system&quot; rel=&quot;nofollow&quot;&gt;innate immune system&lt;/a&gt;), and as such may help in preventing reinfection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you were to be exposed to a different species it is possible get a second cold after only just clearing the first one, but within real-life this is unlikely to occur.&lt;/p&gt;&#xA;" OwnerUserId="10067" LastActivityDate="2014-11-05T17:03:57.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23737" PostTypeId="2" ParentId="23728" CreationDate="2014-11-05T17:33:00.517" Score="2" Body="&lt;p&gt;This potentially depends on what species you are referring to. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of plants, photosynthesis is used to as their source of energy, so will never run out of food as such. Assuming the conditions are favourable in terms of water and temperature (likely, otherwise the species wouldn't have flourished in the first place) and they stay that way, the only limiting factor is going to be nutrients in the soil. These are returned to the soil when the plant dies, so this is fairly self-limiting, when there's not enough then plants will die and the nutrients will return to the soil.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Animals face a slightly different situation, in that they need to eat to survive. As such, if the population that was introduced was large enough to eat all the prey (whether plants or other animals) in the area and carnivorous animals didn't partake in cannibalism even when times were tough, then the animal may die out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general however, predator and prey regulate fairly effectively, a decrease in prey causes a decrease in food availability which leads to a decline in predators. This allows an increase in prey, which gives a higher availability of food to predators so their numbers increase. This causes a decrease in prey numbers and so on. In general once an invasive species has been established, it will require intervention for it to be removed and it will not die out naturally.&lt;/p&gt;&#xA;" OwnerUserId="10067" LastActivityDate="2014-11-05T17:33:00.517" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23738" PostTypeId="1" AcceptedAnswerId="23740" CreationDate="2014-11-05T17:37:02.967" Score="2" ViewCount="95" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.uws.edu.au/newscentre/news_centre/more_news_stories/couch_potatoes_take_heart_-_watching_sport_can_make_you_fitter&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;, &quot;new research has found that viewing other people exercise actually increases your heart rate and other physiological measures, just as if you were working out yourself&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This got me thinking, can muscles be developed to be stronger and bigger from simply watching videos of people weightlifting from the point of view of the weightlifter?&lt;/p&gt;&#xA;" OwnerUserId="6343" LastActivityDate="2014-11-05T18:39:00.520" Title="Can you build muscles from watching point of view videos of people weightlifting?" Tags="&lt;development&gt;&lt;muscles&gt;&lt;human-physiology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23739" PostTypeId="2" ParentId="23738" CreationDate="2014-11-05T18:00:43.327" Score="0" Body="&lt;p&gt;I doubt it. Muscle growth comes from literally damaging muscle fibres by putting them under too much load. This is what causes the muscle pain after a workout. This triggers thickening and increase in number. Without the damage in the first place, there's no reason for the fibres to change.&lt;/p&gt;&#xA;" OwnerUserId="10067" LastActivityDate="2014-11-05T18:00:43.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23740" PostTypeId="2" ParentId="23738" CreationDate="2014-11-05T18:39:00.520" Score="6" Body="&lt;p&gt;That is highly unlikely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article to which you linked specifically states:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;While watching other people exercise may increase your heart rate and have other physiological effects, nothing can replace the health benefits of getting off the couch.&lt;/em&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;With proper nutrition, muscle is built through exercise by &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;adding sarcomeres [to muscle cells which is] physiologically determined by the degree of force a muscle can generate that is in turn dependent on the &lt;em&gt;degree of overlap of the thick and thin filaments&lt;/em&gt;. Thus, the amount of tension would control the number of in-series sarcomeres in a single muscle fiber.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Watching a show about cooking might stimulate hunger, but it won't put food into your stomach. Watching something that evokes a sympathetic response (fear, fighting, an attractive person exercising vigorously, an athlete in a competitive event, etc.) will elevate heart rate, sweat production, and resting muscle tension, but there is not &lt;em&gt;enough&lt;/em&gt; tension to produce muscle growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, there might be small deleterious effects to watching emotionally charged movies which elicit a sympathetic response: they cause stress. An effective horror film will elicit tension and maybe even a startle response - making you jump in your seat - but it will also elevate your blood pressure, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exercise is good for you physiologically. Simple stress without exercise is much less so.&lt;sup&gt;[2]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2222798&quot;&gt;Muscle growth and exercise&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://dujs.dartmouth.edu/fall-2010/the-physiology-of-stress-cortisol-and-the-hypothalamic-pituitary-adrenal-axis#.VFptgefTyto&quot;&gt;The Physiology of Stress: Cortisol and the Hypothalamic-Pituitary-Adrenal Axis&lt;/a&gt; (simplified but relevant)&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-11-05T18:39:00.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23741" PostTypeId="1" AcceptedAnswerId="23752" CreationDate="2014-11-05T18:43:43.047" Score="6" ViewCount="167" Body="&lt;p&gt;Adaptive plasticity involves sensing the environment and responding adaptively to it. Intuitively, I would think that this process may ask for a more or less complex genetic machinery of regulation of gene expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can you give me examples of genes and genetic pathways that are famous for their role in adaptive plastic response?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-12-06T17:56:24.133" LastActivityDate="2014-12-06T17:56:24.133" Title="Examples of genes involved in plastic responses" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;physiology&gt;&lt;molecular-genetics&gt;&lt;ecology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23743" PostTypeId="2" ParentId="23725" CreationDate="2014-11-05T21:58:34.183" Score="6" Body="&lt;p&gt;The short answer is no, there is no minimum time between two colds. The reasons for this are different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mostly it has to do with the viruses which cause the common cold. There is a bunch of them causing what we call a cold, including rhinoviruses, coronacviruses, adenoviruses, human parainfluenza viruses, human respiratory syncytial virus, enteroviruses other than rhinoviruses and metapneumovirus. As much as 200 different virus serotypes are connected to this disease, alone 99 from the rhinoviridae. See the references 1-3 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Different &lt;a href=&quot;http://en.wikipedia.org/wiki/Serotype&quot;&gt;serotypes&lt;/a&gt; means that two viruses of the same family (a rhinovirus for example) have different surface antigens on the virus and are not recognized by the same antibody. And this is what makes it difficult for the immune system. When it has learned to recognize and defeat one virus which causes a cold, it still has to learn how to do this with another (serotypically different) virus. So the adaptive immune system has to make highly specific antibodies every time it is faced with a new virus (which is of course not limited to cold viruses).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you have been infected with a virus and developed a sufficient immune reaction to develop antibodies, you are usually immune against this specific virus (with its specific serotype). Cold viruses live in communities, so when you move or travel, you will most likely encountered with different viruses, which your immune system doesn't know...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally there is another point which adds to the problem: Mutations of the viruses. The viruses are mutating constantly (RNA viruses at high rates) which changes their appearance and also their surface molecules (which are important for the recognition through the immune system). This leads to new serotypes, which are unknown to the immune system. See reference 4 for some more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://web.archive.org/web/20130314023306/http://integrativehealthconnection.com/wp-content/uploads/2011/11/Understanding-the-symptoms-of-the-common-cold-and-influenza.pdf&quot;&gt;Understanding the symptoms of the common cold and influenza.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19213880&quot;&gt;Sequencing and analyses of all known human rhinovirus genomes reveal&#xA;structure and evolution.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Common_cold&quot;&gt;Common cold&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC24164/&quot;&gt;Mutation rates among RNA viruses&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-11-06T08:13:28.427" LastActivityDate="2014-11-06T08:13:28.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23744" PostTypeId="2" ParentId="8048" CreationDate="2014-11-05T22:04:32.983" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is that correct that a complete DNA sequencing (the whole genome) need&#xA;  only to be done once (per person)?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Likely, yes.  But I think you vastly overestimate how often this is done.  If someone gets their DNA &quot;sequenced&quot; at 23andMe, for example, they are not getting their whole genome sequenced.  They are getting individual bits believed to be possibly clinically relevant sequenced.  It's a different technology than you would use to get the whole genome.  A whole mammalian genome is really big, therefore kind of expensive to sequence, and is mostly non-coding DNA of questionable relevance.  Therefore you can just genotype the exact bases of interest, or maybe do exome capture, which gets you full sequence for the 1% or so of the genome that is currently annotated to be coding.  Obviously either of those approaches would no be all-inclusive, so one might wish to redo them at a later date with new targeted regions of interest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if you did get a whole genome done with current technology, right now it has limitations, namely read length, that make it hard to work out certain details.  I could easily see someone needing to redo a genome using a longer read technology, when that technology arrives.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, we aren't really discovering that many new genes. Certainly not protein-coding ones.  What is more likely is that we discover that variants in this or that gene might be clinically relevant to some health parameter. &lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2014-11-05T22:04:32.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23745" PostTypeId="2" ParentId="13883" CreationDate="2014-11-05T23:34:56.560" Score="1" Body="&lt;p&gt;Hypomorphs (now commonly termed 'dominant negative') have a reduced (hypo) phenotype as compared the wildtype. Null (knockout) mutations, however, have the phenotype removed, so to say. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason that you would use null rather than hypomorph mutations to do double mutant analysis is because with the hypomorph, you would still see some effect of the phenotype you are trying to have eliminated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do you want to eliminate a phenotype? Let's say you want to try to find the pathway for the genetic interactions between A and B. You have 2 animals you want to cross (I work with C. elegans worms, and use double mutants often). If we look at the wildtype homozygous of both animals, they will be the same. Animal 1: +;+/+;+. Animal 2: +;+/+;+. (where + denotes wildtype, and ';' means they are not linked, so the genes are independent of each other). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We will use 'a' to denote null mutation A, and 'b' to denote null mutation B. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Animal 1 will have mutation A. Animal 2 will have mutation B. So now Animal 1 will look like a;+/a;+, and Animal 2 will look like +;b/+;b. Notice that each locus is corresponding with itself - ie: in the region where Animal 1 is still +, Animal 2 is b, and vice versa (for null mutation 'a'). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So then we cross Animal 1 with Animal 2 and get a;+/a;+ x +;b/+;b which will segregate in a 9:3:3:1 ratio (according to independent assortment of 2 independent genes - just draw a 4x4 punnet square to convince yourself). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We are interested in achieving the 1/16 a;b/a;b animal (also can be noted aabb, btw). And THAT is our double mutant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because we use a null allele, there is no chance of the wildtype phenotype &quot;leaking&quot; within our cross, giving us a false ratio or false assessment, as would be the case with a hypomorph (reduced, but not gone). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, when talking about genes in a pathway: I think this is what your professor was referring to. When we are mapping how genes interact, and in what order, we can either have the genes interacting in redundant or sequential pathways. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Redundant pathways: A -&gt; C and B -&gt; C. So either A or B can have an effect on C, meaning that having both is redundant, because one can do the job. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sequential pathway: A -&gt; B -&gt; C  OR  B -&gt; A -&gt; C. So both are existing in the pathway in sequence, and both are needed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just as a side note, whenever you are using double mutants to find out if your pathway is redundant or sequential, you MUST compare it to a single mutant!!! Otherwise you WILL NOT be able to tell the difference between your results. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a single mutant (A, for example), when using in a redundant pathway, you will still get phenotype C, since B is available. Just note that your C phenotype will be weaker. &#xA;When you then use a double mutant, knocking out both A and B, you will see NO expression of phenotype C. The same will apply if you knock out B instead of A. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, for a sequential pathway. If you use a single mutant (again, let's use A as the example) you will have no phenotype C, since A is needed to interact with B (whether upstream of downstream) in order to have an effect on C. And, if you use a double mutant (so knock out both A and B), then you will also have no expression of C, since both A and B are gone. (again, same applies if you use a B single mutant first)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, for a redundant pathway: single mutant will have C phenotype, double mutant will not have C phenotype. There IS a change!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a sequential pathway: single mutant will have no C phenotype, and double mutant will have no C phenotype. There is NO change!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you would have used a hypomorph to do these experiments, then you would probably see some percentage of C expression in your double mutant experiments, making your results inconclusive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;--&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[source: you can find this information in any genetics textbook (in my case, since i study worms, &lt;a href=&quot;http://www.wormbook.org/&quot; rel=&quot;nofollow&quot;&gt;WormBook&lt;/a&gt; is a great source); I have given this information from my own experience. I have an honours degree in Genetics (Biochemistry and Medical Genetics) and am currently continuing my education in grad school (biochemistry and molecular biology). &lt;/p&gt;&#xA;" OwnerUserId="10071" LastActivityDate="2014-11-05T23:34:56.560" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23746" PostTypeId="1" AcceptedAnswerId="23748" CreationDate="2014-11-06T02:32:58.167" Score="1" ViewCount="831" Body="&lt;p&gt;My teacher showed us an elaborate collection of graphs with one of them showing FSH and LH plasma levels during the menstrual cycle. LH level was almost 3 times higher than FSH level. Why? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this have anything to do with their synthesis or cellular responses?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastEditorUserId="9943" LastEditDate="2014-11-06T05:23:58.690" LastActivityDate="2014-11-06T08:40:51.023" Title="Why is LH level much higher than FSH level at ovulation?" Tags="&lt;physiology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23747" PostTypeId="1" CreationDate="2014-11-06T02:34:41.207" Score="4" ViewCount="58" Body="&lt;p&gt;&lt;em&gt;E. coli&lt;/em&gt; has two oxygen sensors: FNR (fumarate-nitrate reductase) and ArcBA (Anoxic Redox Control, two component control systems). FNR directly senses the oxygen, while the interaction of ArcB with oxygen is indirect one via quinone pool. Out of theree quionones in &lt;em&gt;E. coli&lt;/em&gt;, which one (oxidized and reduced forms of all three types)  play roles to what extent in what direction (inhibiting/activating) is much debatable. I would like to see some intuitive level arguments for why a cell, even in principle, need to have two sensors for oxygen?&lt;/p&gt;&#xA;" OwnerUserId="1800" LastEditorUserId="3340" LastEditDate="2014-11-06T06:24:54.330" LastActivityDate="2014-11-06T06:24:54.330" Title="Need for two oxygen sensors in E. coli" Tags="&lt;metabolism&gt;&lt;cellular-respiration&gt;&lt;ecoli&gt;&lt;anaerobic-respiration&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23748" PostTypeId="2" ParentId="23746" CreationDate="2014-11-06T03:07:19.437" Score="1" Body="&lt;p&gt;It is not the absolute plasma levels that are important, it is about their relative differences during the cycle. The steep rise in FSH during the first days induces follicle stimulation. The LH surge at day 12 induces maturation of the egg and stimulates its release (&lt;a href=&quot;http://en.wikipedia.org/wiki/Menstrual_cycle&quot; rel=&quot;nofollow&quot;&gt;see wiki page&lt;/a&gt;). The fact that LH's absolute plasma levels are higher may theoretically have to do with the fact that more LH is needed to elicit its physiolocal response. However, the differences of their &lt;em&gt;relative&lt;/em&gt; levels is way more important from a physiological point of view.  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-06T08:40:51.023" LastActivityDate="2014-11-06T08:40:51.023" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23749" PostTypeId="2" ParentId="23718" CreationDate="2014-11-06T03:36:29.260" Score="5" Body="&lt;p&gt;I concur with @souvik.bhattacharya but I wish to elaborate on it. The lung collapse indeed stops gas exchange in marine mammals by keeping the air away from the lung tissue that normally exchanges O&lt;sub&gt;2&lt;/sub&gt;, CO&lt;sub&gt;2&lt;/sub&gt; and N&lt;sub&gt;2&lt;/sub&gt;. Build up of N&lt;sub&gt;2&lt;/sub&gt; results in the bends after the pressure drops when re-surfacing (&lt;a href=&quot;http://rsbl.royalsocietypublishing.org/content/early/2012/09/11/rsbl.2012.0743&quot; rel=&quot;noreferrer&quot;&gt;McDonald &amp;amp; Ponganis, 2012&lt;/a&gt;). However, a study by Hooker et al. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3267154/&quot; rel=&quot;noreferrer&quot;&gt;2012&lt;/a&gt;) showed that beached whales, dolphins and seals did show signs of bubble formation in the internal organs, which was linked to exposure to noise and sonar, or other factors such as cold water that may disrupt the functionality of preventive measures such as the lung collapse. So to get back to your question - Yes they avoid it by lung collapse, but under certain conditions this mechanism may fail.        &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-06T03:46:26.223" LastActivityDate="2014-11-06T03:46:26.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23750" PostTypeId="1" CreationDate="2014-11-06T04:26:16.047" Score="2" ViewCount="98" Body="&lt;p&gt;I am currently writing a paper on irritable bowel syndrome, and I was wondering what the common diet of a patient with food-related IBS consists of. I've already begun discussing the pathogenesis of the disorder, but I want to start making a connection between food and IBS. I understand that most patients tend to be lactose intolerant, but I am also interested to see if there are any other common intolerances associated with IBS.&lt;/p&gt;&#xA;" OwnerUserId="8977" LastEditorUserId="8977" LastEditDate="2014-11-06T17:17:03.343" LastActivityDate="2018-06-26T05:32:15.850" Title="What is the common diet of food-related IBS patients? Besides most patients being lactose intolerant, what other intolerances do they face?" Tags="&lt;microbiology&gt;&lt;food&gt;&lt;nutrition&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23751" PostTypeId="2" ParentId="23750" CreationDate="2014-11-06T04:52:52.513" Score="1" Body="&lt;p&gt;Fermentable carbohydrates may cause problems in some IBS patients. Recent work suggests that restricting these foods may improve the symptoms in some patients.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nrgastro/journal/v11/n4/abs/nrgastro.2013.259.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nrgastro/journal/v11/n4/abs/nrgastro.2013.259.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More information can be found by looking for the FODMAP diet.&lt;/p&gt;&#xA;" OwnerUserId="6457" LastActivityDate="2014-11-06T04:52:52.513" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23752" PostTypeId="2" ParentId="23741" CreationDate="2014-11-06T05:47:42.143" Score="2" Body="&lt;p&gt;I assume that you mean gene expression regulation when you say genetic processes. The best example for your question would be that of synaptic plasticity in neurons. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The immediate responses are obviously that of protein modifications (cell signaling). These are fast responses that have immediate effects but are also quite short-lived. During the long term potentiation (LTP) some stable changes happen via gene regulatory mechanisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is to be noted that in a polarized cell such as neuron the distance between the nucleus and the point of action i.e. the synapses (at dendritic spines), is huge. Any event leading to transcription regulation would take a long time to act. Therefore there are post-transcriptional regulatory mechanisms in place. The mRNAs are localized at the spines and are kept in a repressed state; poised for translation when the signal is received. Finally, if the signal is sufficient enough, transcriptional regulation (sometimes stable due to epigenetic changes) takes place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can look for the genes involved in this pathway which also include ncRNAs (lncRNA and miRNAs).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other examples: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Acute stress response (such as Unfolded Protein Response [UPR])&lt;/li&gt;&#xA;&lt;li&gt;Acute inflammation&lt;/li&gt;&#xA;&lt;li&gt;Chemotaxis&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-11-06T05:55:00.963" LastActivityDate="2014-11-06T05:55:00.963" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23753" PostTypeId="2" ParentId="23734" CreationDate="2014-11-06T06:12:32.633" Score="2" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;Sample 1. 4096 / 1024 = 4x more B&lt;/p&gt;&#xA;&lt;p&gt;Sample 2. 16384 / 1024 = 16x more B&lt;/p&gt;&#xA;&lt;p&gt;The average amount more B = (16 + 4) / 2 = 10x more B&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;That is not the right way to go about. You are calculating average expression of &lt;code&gt;B&lt;/code&gt; in both samples. It does not mean there is &lt;code&gt;10x&lt;/code&gt; more &lt;code&gt;B&lt;/code&gt;. There is just &lt;code&gt;4x&lt;/code&gt; more &lt;code&gt;B&lt;/code&gt; in &lt;code&gt;Sample-2&lt;/code&gt; relative to &lt;code&gt;Sample-1&lt;/code&gt;.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;&lt;code&gt;Gene-A&lt;/code&gt; does not change its expression between samples and can be used as a reference gene.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;If you calculate by threshold cycle the fold change &lt;span class=&quot;math-container&quot;&gt;$ = 2^{8-6} = 4x$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;See &lt;a href=&quot;https://biology.stackexchange.com/questions/16228/real-time-pcr-normalization-algorithm&quot;&gt;this&lt;/a&gt; post too.&lt;/p&gt;&#xA;&lt;p&gt;The average is calculated between replicates, not between different experimental conditions.&lt;/p&gt;&#xA;&lt;p&gt;Sometimes the average of two experimental samples &lt;strong&gt;is&lt;/strong&gt; calculated — this is typically done in a MA-plot analysis which is done to filter out genes which show very high fold changes just because of their overall low expression (&lt;em&gt;1:4 vs 100:300&lt;/em&gt;).&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Answer to your Edit&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;You should not take the average (arithmetic mean) of Ct. They don't scale linearly with expression (and so is the converse).&lt;/p&gt;&#xA;&lt;p&gt;For any non-linear function &lt;span class=&quot;math-container&quot;&gt;$f(x)$&lt;/span&gt;:&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$f(x+y) \ne f(x)+f(y)$$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$f\left(\frac{x+y}{2}\right) \ne \frac{f(x)+f(y)}{2}$$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;Furthermore, for a convex function:&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$f(E[x]) \le  E[f(x)] $$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$ Jensen's\ inequality $$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;where &lt;span class=&quot;math-container&quot;&gt;$E[x]$&lt;/span&gt; is expected value of &lt;span class=&quot;math-container&quot;&gt;$x$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$a^x$&lt;/span&gt; is a convex function with respect to &lt;span class=&quot;math-container&quot;&gt;$x$&lt;/span&gt; (&lt;span class=&quot;math-container&quot;&gt;$a$&lt;/span&gt; is any real number &amp;gt; 1). So you can apply Jensen's inequality to Ct values and expression.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-11-10T04:41:38.233" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23754" PostTypeId="2" ParentId="23747" CreationDate="2014-11-06T06:24:24.360" Score="3" Body="&lt;p&gt;It is not uncommon for cells to have parallel pathways for same outcome. This ensures foolproof response and makes the system robust. &lt;em&gt;E.coli&lt;/em&gt; also has another sensor for aerotaxis (Aer and Tsr proteins). See my answer on your &lt;a href=&quot;https://biology.stackexchange.com/questions/20632/what-is-the-mechanism-of-oxygen-uptake-in-e-coli/22014#22014&quot;&gt;previous post&lt;/a&gt; and the linked paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also look for coherent feed forward network motifs. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2014-11-06T06:24:24.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23755" PostTypeId="2" ParentId="23733" CreationDate="2014-11-06T09:15:00.127" Score="1" Body="&lt;p&gt;I am colorblind, but I did not know that before I was 22 (!!). I got to know it by doing the Ishihara test. There are other tests you can do to test for colorblindness, such as the reverse colorblindness test (&lt;a href=&quot;http://www.cs.unm.edu/~aaron/creative/colorTest.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.cs.unm.edu/~aaron/creative/colorTest.htm&lt;/a&gt;), where a &quot;normal vision&quot; person will not see the two patterns shown there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, there is no test where you cannot ask &quot;what do you see?&quot; to the subject. On the other hand, I saw a photo where they were showing a northern light in both colorblind and normal vision (&lt;a href=&quot;https://www.facebook.com/nlblog/photos/pb.236481989828593.-2207520000.1415264974./416457851831005/?type=1&amp;amp;theater&quot; rel=&quot;nofollow&quot;&gt;https://www.facebook.com/nlblog/photos/pb.236481989828593.-2207520000.1415264974./416457851831005/?type=1&amp;amp;theater&lt;/a&gt;) -I hope facebook links are OK in this site-, where I see no difference between the two photos. You could for example show that photo pair to your test subject and ask a set of questions (e.g. which one do you like more?). If he/she is colorblind, then the answer will be &quot;they are the same&quot;, so you have a strong indication, or if they are able to point out differences, then they most likely have normal vision.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could think of an experiment where you just show several photos with different contrasts/saturations, and then add the northern light photo (maybe the author has some other photos you could use), so they are not aware of the underlying question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps &lt;/p&gt;&#xA;" OwnerUserId="10073" LastActivityDate="2014-11-06T09:15:00.127" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23756" PostTypeId="2" ParentId="21934" CreationDate="2014-11-06T09:45:42.240" Score="3" Body="&lt;p&gt;Interesting question! As this post has been sitting around for a while I am going for some speculations. First you talk chocolate, which essentially contains the alkaloid theobromine. Anise contains the propenylbenzene (E)-anethole (&lt;a href=&quot;http://www.lf1.cuni.cz/Data/files/PragueMedicalReport/PMR%2005-01%20Idle.pdf&quot; rel=&quot;nofollow&quot;&gt;Idle, 2005&lt;/a&gt;). Theobromine is a caffeine-derivative and basically produces alertness, but also restlessness and perhaps anxiety when administered in large amounts (&lt;a href=&quot;http://en.wikipedia.org/wiki/Theobromine&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;). In extremely high doses there can be LSD-like effects (&lt;a href=&quot;http://www.livestrong.com/article/547292-adverse-effects-of-raw-chocolate/&quot; rel=&quot;nofollow&quot;&gt;anecdotal report&lt;/a&gt;). Perhaps (speculative) your girlfriend is especially sensitive. Then (E)-anethole: the late Alexander Shulgin, Godfather of MDMA, has made the etheric oils (in)famous as precursors for amphetamine synthesis. In themselves the propenylbenzenes like (E)-anethole are quite harmless, as they do not contain an amine group (a prerequisite for being called an alkaloid). However, heating (E)-anethole in the presence of ammonia may lead to the production of PMA, a compound structurally and neuropsychopharmacologically related to MDMA (&lt;a href=&quot;http://www.lf1.cuni.cz/Data/files/PragueMedicalReport/PMR%2005-01%20Idle.pdf&quot; rel=&quot;nofollow&quot;&gt;Idle, 2005&lt;/a&gt;). Although a bit of chocolate and a sip of Sambuca do not meet any of these conditions, both chocolate and Sambuca do contain certain psychoactive compounds, or their immediate precursors.       &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-06T11:25:43.683" LastActivityDate="2014-11-06T11:25:43.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23758" PostTypeId="2" ParentId="23720" CreationDate="2014-11-06T11:26:20.233" Score="7" Body="&lt;p&gt;A search on Google will show you that there have been documented cases where twins had different fathers, including at least one case where a paternity lawsuit follows and the mother admitted to her husband that she had an affair. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also cases where twins look very different although they have the same parents. Including cases where one twin looks white and one twin looks black. This can happen when you have one white and one black parent, the children can end up being quite white or quite black and twins can look different. And it can happen if both parents are mixed race; they can have children that are lighter or darker than both parents, and twins can be one lighter and one darker. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Twins looking different by coincidence are much more common than twins with different fathers; as mentioned earlier in cases where there was a paternity lawsuit, only 2.4% turned out to have different fathers. That number will of course depend on the behaviour of people. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One newspaper article &lt;a href=&quot;http://www.theguardian.com/lifeandstyle/2011/aug/19/my-twins-have-different-fathers&quot;&gt;http://www.theguardian.com/lifeandstyle/2011/aug/19/my-twins-have-different-fathers&lt;/a&gt; describes a case with two days between sex with the two fathers which is more than I thought possible. As an example of dissimilar twins see &lt;a href=&quot;http://www.babycenter.com/0_strange-but-true-mixed-race-twins-one-black-one-white_10364936.bc&quot;&gt;http://www.babycenter.com/0_strange-but-true-mixed-race-twins-one-black-one-white_10364936.bc&lt;/a&gt; showing a family who actually has &lt;em&gt;two&lt;/em&gt; sets of twins with one quite light and one quite dark. &lt;/p&gt;&#xA;" OwnerUserId="10077" LastEditorUserId="10077" LastEditDate="2014-11-06T14:54:40.450" LastActivityDate="2014-11-06T14:54:40.450" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23759" PostTypeId="2" ParentId="23727" CreationDate="2014-11-06T11:57:33.203" Score="4" Body="&lt;p&gt;Bananas seem to contain lots of dietary fiber that help move consumed food through the intestines (&lt;a href=&quot;http://www.livestrong.com/article/429663-do-bananas-help-digestion/&quot; rel=&quot;nofollow&quot;&gt;popular article&lt;/a&gt;) thereby promoting digestion. Whether one should eat bananas before or after dinner is probably a debatable subject (&lt;a href=&quot;https://in.answers.yahoo.com/question/index?qid=20080513031420AA6QbDc&quot; rel=&quot;nofollow&quot;&gt;Yahoo forum&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-06T11:57:33.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23760" PostTypeId="1" CreationDate="2014-11-06T13:28:10.513" Score="3" ViewCount="138" Body="&lt;p&gt;Dosage compensation is used to make up for different copy numbers of the major sex chromosomes in males and females (One X or Z chromosome in one and two in the other). Two main mechanisms of dosage compensation exist, inactivation and upregulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But dosage compensation is not entirely perfect, the amount of gene product from an upregulated X/Z-linked genes in the heterogametic sex is not exactly that of the two in the homogametic sex. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674252/&quot; rel=&quot;nofollow&quot;&gt;In &lt;em&gt;Drosophila&lt;/em&gt;, the male-specific lethal (MSL) ribonucleoprotein&#xA;  complex mediates dosage compensation by upregulating transcription&#xA;  from the single male X chromosome &lt;strong&gt;approximately twofold.&lt;/strong&gt;&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;On average how well is dosage compensation performed? What is the variance like:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;within a single chromosome (between genes)? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;within species?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;between species?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-11-06T22:15:05.000" LastActivityDate="2014-11-06T22:15:05.000" Title="Imperfect dosage compensation" Tags="&lt;gene-expression&gt;&lt;sex-chromosome&gt;&lt;dosage-compensation&gt;" AnswerCount="0" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="23761" PostTypeId="2" ParentId="8048" CreationDate="2014-11-06T13:33:00.493" Score="0" Body="&lt;p&gt;Apart from what WYSIWYG said. &#xA;It might also be the case that you need to re-sequence because you're interested in seeing the changes that might have occurred since the last sequencing. Remember that cells keep dividing and therefore changing, so the DNA is slightly different from one cell to another (and from one population of cells or tissues to another). Single-cell sequencing is almost here.&#xA;The obvious example here is a tumour. It helps knowing what happened and if possible detect the driver (or drivers) mutation (cancer cells tend to increase their mutation rate).&lt;/p&gt;&#xA;" OwnerUserId="1739" LastActivityDate="2014-11-06T13:33:00.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23762" PostTypeId="2" ParentId="23731" CreationDate="2014-11-06T13:45:44.007" Score="2" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Don't know whether it was ever investigated, but I'm pretty sure, that frogs can in principle swim upside down (e.g. when escaping from predator), but they normally do not do it.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;One example of alternative swimming styles in animals is provided by some munnopsidid &lt;a href=&quot;https://en.wikipedia.org/wiki/Isopoda&quot; rel=&quot;nofollow noreferrer&quot;&gt;isopod&lt;/a&gt; crustaceans. Several genera are pelagic and have very elongated forelegs equipped with rows of setae and paddle-like hindlegs (see &lt;a href=&quot;http://web.qbi.uq.edu.au/ecovis/Images/Justin/1995%20Deep-sea%20spiders.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Marshall &amp;amp; Diebel 1995&lt;/a&gt; and &lt;a href=&quot;http://www.mbari.org/education/internship/98interns/98internpapers/98giver.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Giver 1998&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the forelegs are used to &quot;walk&quot; in the water column&lt;/li&gt;&#xA;&lt;li&gt;the same legs can be stretched out for passive parachuting&lt;/li&gt;&#xA;&lt;li&gt;the hindlegs are used for backward swimming&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Below is a photo of a parachuting specimen. And &lt;a href=&quot;https://www.youtube.com/watch?v=1VyaLPqJZsg&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; is a very nice video of a backward swimming specimen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cX8v2.jpg&quot; alt=&quot;Acanthamunnopsis&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Foto by Karen Osborn from &lt;a href=&quot;http://pelagics.lifedesks.org/node/29&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-11-06T20:50:05.623" LastActivityDate="2014-11-06T20:50:05.623" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23763" PostTypeId="1" AcceptedAnswerId="23917" CreationDate="2014-11-06T14:38:36.803" Score="7" ViewCount="20543" Body="&lt;p&gt;From literature the two terms seem to be interchangeable when discussing protein domains and motifs. But biochemically, what are the specific differences between these two terms? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example what is the difference in these sentences:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Generally globular protein cores have hydrophobic regions whilst the surface contains hydrophilic exterior facing residues.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Generally globular protein cores have non-polar regions whilst the surface contains polar exterior facing residues.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2014-11-07T11:56:40.970" LastActivityDate="2014-11-11T13:27:19.087" Title="Is there a difference between polarity and hydrophobicity?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23765" PostTypeId="1" CreationDate="2014-11-06T14:59:16.943" Score="1" ViewCount="48" Body="&lt;p&gt;I was in search in of list or detail about Insects and Birds which move their wings most but cover least distance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that in insects house fly moves its wings about 200/sec and covers 5mph (about 7.3 feet) distance and in birds Hummingbird moves its wings about 80/sec and covers 60mph (about 88 feet) distance, but I am in search of about 10 in each insects and birds. And also about their heart beats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have combine list, it will be much appreciated. If you know any book or website about same topic it will much helpful.&lt;/p&gt;&#xA;" OwnerUserId="8148" LastActivityDate="2014-11-06T14:59:16.943" Title="Insects or Birds covering least distance but most wing moves" Tags="&lt;entomology&gt;&lt;ornithology&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23766" PostTypeId="1" AcceptedAnswerId="23768" CreationDate="2014-11-06T17:12:43.897" Score="13" ViewCount="912" Body="&lt;p&gt;I had an interesting discussion today in which the question arose how insects survive in the winter. Since they need a high enough external temperature to be active, this seems a bit difficult in the winter. With frost they should completely freeze and I don't think they will survive this. Do they rely on eggs laid in the fall (which have to survive freezing temperatures as well) or do they employ other techniques for that?&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2017-04-11T20:58:11.117" Title="How do insects survive the winter?" Tags="&lt;entomology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23767" PostTypeId="2" ParentId="23766" CreationDate="2014-11-06T17:27:25.943" Score="8" Body="&lt;p&gt;The above answer is perfectly correct...except it deals with mainly ectothermic insects...now there are some endothermic insects as well..&amp;amp; many of them adopt this following curious technique to elevate their body temperature....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here the hawkmoth's capacity to elevate their body temperature depends on their powerful flight muscles which generate large amount of heat during when operating. The insects use shivering to warm off before they take flight..they contract their flight muscles in synchrony before flight, so that only slight wing movements occur but considerable heat is produced. Chemical reactions , &amp;amp; hence cellular respiration speed up their warmed-up flight motors &lt;strong&gt;enabling them to fly during cold days&lt;/strong&gt; &amp;amp; even during night....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/h8w30.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also some endothermic moths take help of 'time-trusted' countercurrent heat exchanger, that helps to maintain a high temperature in thorax...where majority of flight muscles are located...&lt;strong&gt;thus maintaining a constant temp. of about 30 degree celcius at the body core when the outside temperature is,sometimes ,even near subzero&lt;/strong&gt;...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sxBEa.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also...this particular mechanism is applied by insects &amp;amp; animals...ectotherms &amp;amp; endotherms alike...&#xA;Introduction of cholesterol in the cell membrane thus &lt;strong&gt;hindering solidification at low temperture&lt;/strong&gt; by disrupting the regular packing of phospholipids...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iwwFS.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="10045" LastEditDate="2014-11-08T03:30:45.783" LastActivityDate="2014-11-08T03:30:45.783" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23768" PostTypeId="2" ParentId="23766" CreationDate="2014-11-06T19:55:29.390" Score="13" Body="&lt;p&gt;As there are many insects, there are also a number of different strategies. As you already said, insects depend on the temperature of the environment and cannot produce enough heat with their metabolism. The major strategies are: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Migration, &lt;/li&gt;&#xA;&lt;li&gt;Communal living&lt;/li&gt;&#xA;&lt;li&gt;Cold tolerance (by means of &lt;a href=&quot;http://en.wikipedia.org/wiki/Antifreeze_protein&quot;&gt;antifreeze proteins&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Only some of the insects can opt for &quot; &lt;strong&gt;Migration&lt;/strong&gt;&quot; , those which are big enough to travel long distances. A good examples for this migration of insects is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Monarch_butterfly&quot;&gt;monarch butterfly&lt;/a&gt; which migrates from summer habitat in the north-eastern US and southern Canada to Mexico in the fall. Using this strategy the insects avoid live threatening temperatures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;&lt;strong&gt;Communal living&lt;/strong&gt;&quot; helps insects to get over the winter, as the colony produces enough heat to survive. A prominent example are &lt;a href=&quot;http://insects.about.com/od/antsbeeswasps/qt/How-Honey-Bees-Keep-Warm-In-Winter.htm&quot;&gt;bees&lt;/a&gt;, which maintain relatively high temperatures in their hives, another would be ants. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;&lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Antifreeze_protein&quot;&gt;Antifreeze proteins&lt;/a&gt;&lt;/strong&gt;&quot; are also employed by a few. Some insects contain special proteins or glycerol in their hemolymph (the equivalent to blood) which either prevents it from freezing and/or prevents the formation of ice crystals which destroy the cells. An example for such an animal would be the New Zealand &lt;a href=&quot;http://en.wikipedia.org/wiki/Weta&quot;&gt;Mountain Stone Weta&lt;/a&gt; which can stay frozen for month until the temperature gets high enough for living again. Some insects go into some kind of winter sleep, in which they survive the cold temperatures. Their living cycle is synchronized with the seasons of the year.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer is based on &lt;a href=&quot;http://en.wikipedia.org/wiki/Insect_winter_ecology&quot;&gt;this&lt;/a&gt; and &lt;a href=&quot;http://insects.about.com/od/adaptations/p/wintersurvival.htm&quot;&gt;this&lt;/a&gt; article, have a look for further information and references.&lt;/p&gt;&#xA;" OwnerUserId="8598" LastEditorUserId="10045" LastEditDate="2014-11-07T18:59:52.987" LastActivityDate="2014-11-07T18:59:52.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23769" PostTypeId="1" CreationDate="2014-11-06T20:29:57.773" Score="1" ViewCount="435" Body="&lt;p&gt;Why is the threshold between human embryo and human fetus defined as 8 weeks after fertilization? What's happening on the 8th week?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Note: definition of embryo based on &lt;a href=&quot;http://en.wikipedia.org/wiki/Embryo&quot; rel=&quot;nofollow&quot;&gt;Wikipedia's current definition&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="19073" LastEditorUserId="3624" LastEditDate="2014-11-07T08:35:44.350" LastActivityDate="2014-11-07T14:46:52.323" Title="Why is the threshold between human embryo and human fetus defined as 8 weeks after fertilization?" Tags="&lt;dna&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23770" PostTypeId="1" AcceptedAnswerId="24535" CreationDate="2014-11-06T20:33:52.023" Score="5" ViewCount="79" Body="&lt;p&gt;Sorry, I can not indicate the source, but I read that menstrual cycles of women who live in the same house over time sync. Is it true? How does it work?&lt;/p&gt;&#xA;" OwnerUserId="6124" LastActivityDate="2014-12-04T11:09:24.810" Title="How to evolutionary explain menstrural cycles synchronization?" Tags="&lt;human-biology&gt;&lt;adaptation&gt;" AnswerCount="1" CommentCount="6" ClosedDate="2014-12-04T14:49:42.120" ContentLicense="CC BY-SA 3.0" />
  <row Id="23774" PostTypeId="1" AcceptedAnswerId="23782" CreationDate="2014-11-06T20:57:17.540" Score="3" ViewCount="669" Body="&lt;p&gt;Each year, large volumes of crop are harvested from fields. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Where does this biomass get replenished from?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="10086" LastEditorUserId="10086" LastEditDate="2014-11-07T02:09:49.307" LastActivityDate="2014-11-07T02:09:49.307" Title="Where does crop biomass come from?" Tags="&lt;botany&gt;&lt;plant-anatomy&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23775" PostTypeId="1" CreationDate="2014-11-06T21:15:28.373" Score="5" ViewCount="174" Body="&lt;p&gt;I have a phobia of bugs (or other small creatures) living inside my pillow and crawling into my ear in the night. It might seem silly, but bare with me.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recently I got wondering, what organisms &lt;em&gt;could&lt;/em&gt; actually live inside a casual foam pillow?&lt;br&gt;&#xA;I machine-wash it every now and then to keep it clean.&lt;/p&gt;&#xA;" OwnerUserId="6433" LastEditorUserId="6433" LastEditDate="2014-11-06T22:57:01.533" LastActivityDate="2014-11-07T01:01:55.283" Title="What could live inside a pillow?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ClosedDate="2014-11-07T13:40:23.417" ContentLicense="CC BY-SA 3.0" />
  <row Id="23776" PostTypeId="2" ParentId="23731" CreationDate="2014-11-06T21:59:51.633" Score="1" Body="&lt;p&gt;Yes, creatures can swim different ways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you drop a frog into water while it is in the ventral up position, it will indeed swim upside down to escape before righting itself, which occurs by rotating while swimming. If the water is too shallow, it will flop and flip before jumping away. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Swimming on the surface ventral side up is kind of silly for a frog since it's eyes would be looking into the water, and it wouldn't see predators or prey on the surface. But I doubt if it is impossible. It's certainly not instinctual. To see an aquatic animal belly-up usually means something bad.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otters can float belly up and even swim that way:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NNk6U.jpg&quot; alt=&quot;otter swimming upside down under water.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While snorkeling, I have seen many fish (especially parrot fish) swimming completely sideways in order to keep an eye on me while I hover over them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Male orcas will swim upside down to mate, and will float upside down when semen is collected. Cetaceans have been taught to swim on their sides and expose one flipper to give the appearance of waving. In the documentary &lt;em&gt;Blackfish&lt;/em&gt;, you can see Tilicum doing just this thing, circling the enclosure on his side waving for two or three laps before killing one of his trainers. Other orca videos show Tilicum swimming upside down to show off their white ventral surface for the crowd. And dolphins, of course, can swim backwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dogs will do the &lt;em&gt;dog paddle&lt;/em&gt; on the surface of the water, but use a slightly different swimming technique to dive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XJdaq.jpg&quot; alt=&quot;dog swimming underwater to retrieve a ball on the bottom of a pool&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wish I could provide videos but I can't find them.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-11-06T21:59:51.633" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23777" PostTypeId="2" ParentId="23763" CreationDate="2014-11-06T22:15:10.507" Score="4" Body="&lt;p&gt;Hydrophilic means attracted to water, while polar means the molecule has electric pole(s).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A hydrophilic molecule or portion of a molecule is one that has a&#xA;  tendency to interact with or be dissolved by water and other polar&#xA;  substances.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;wikipedia - &lt;a href=&quot;http://en.wikipedia.org/wiki/Hydrophile&quot; rel=&quot;nofollow noreferrer&quot;&gt;hydrophile&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A polar molecule has a net dipole as a result of the opposing charges&#xA;  (i.e. having partial positive and partial negative charges) from polar&#xA;  bonds arranged asymmetrically.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Bonds can fall between one of two extremes — being completely nonpolar&#xA;  or completely polar. A completely nonpolar bond occurs when the&#xA;  electronegativities are identical and therefore possess a difference&#xA;  of zero. A completely polar bond is more correctly called an ionic&#xA;  bond and occurs when the difference between electronegativities is&#xA;  large enough that one atom actually takes an electron from the other.&#xA;  The terms &quot;polar&quot; and &quot;nonpolar&quot; are usually applied to covalent&#xA;  bonds, that is, bonds where the polarity is not complete. To determine&#xA;  the polarity of a covalent bond using numerical means, the difference&#xA;  between the electronegativity of the atoms is taken. On the Pauling&#xA;  scale, if the result is less than 0.4, the bond is generally nonpolar&#xA;  covalent. If the result is between 0.4 and 1.7, the bond is generally&#xA;  polar covalent. If the result is greater than 1.7 the bond is&#xA;  generally considered ionic.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;wikipedia - &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemical_polarity&quot; rel=&quot;nofollow noreferrer&quot;&gt;chemical polarity&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Water is polar. because oxygen (3.5) is more electronegative than hydrogen (2.2) and the difference (1.3) is between 0.4÷1.7. So the oxygen has a slight negative charge, while the hydrogens have slight positive charges in water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Polar molecules are hydrophile. e.g NH&lt;sub&gt;3&lt;/sub&gt;, EtOH, etc... Apolar (or nonpolar) molecules are usually hydrophobe, but there can be exceptions e.g. Cl&lt;sub&gt;2&lt;/sub&gt; is apolar, but more water soluble than CO or CO&lt;sub&gt;2&lt;/sub&gt;, because of a chemical reaction (Cl&lt;sub&gt;2&lt;/sub&gt; + H&lt;sub&gt;2&lt;/sub&gt;O → HOCl + HCl). Alcohols contain the polar -OH group. Short chain alcohols are water soluble and so hydrophile, while long chain alcohols are less water soluble, they are hydrophob, because most of the molecule contains apolar bonds. Molecules with ionic bonds, like NaCl are hydrophilic, but not necessary water soluble (e.g. AgCl is poorly soluble in water). So I think hydrophilicity and polarity are not synonyms. However these are just the exceptions, most of the hydrophilic compounds are polar and most of the hydrophobic compounds are apolar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Amino acid residues (and ofc. side chains) are no exceptions, so in the case of them these terms are synonyms (at least by the 20 common amino acid certainly).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Hydrophobic-polar_protein_folding_model&quot; rel=&quot;nofollow noreferrer&quot;&gt;HP (hydrophobic-polar) protein folding model&lt;/a&gt; comes from the article of Dill. He talks mostly about solvophobic and solvophilic residues. In the context of water use the terms hydrophobic, polar and charged amino acid residues. This kind of amino acid classification might be older, but (I assume) it was not so important before the HP model.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;solvent to a medium consisting of pure solvophobic residues. For the&#xA;  treatment of water-soluble proteins, -(q - 2)g thus describes the&#xA;  transfer of hydrophobic residues from water to a hydrophobic&#xA;  environment; for the treatment of membrane proteins,&#xA;  -(q - 2)g characterizes the transfer of polar or charged res idues from an apolar medium to a polar environment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1985 - &lt;a href=&quot;http://www.researchgate.net/publication/19176132_Theory_for_the_folding_and_stability_of_globular_proteins/file/9fcfd50c5e62fcabbd.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Theory for the folding and stability of globular proteins&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;According to Dill's article residues can be&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;charged (1 times)&lt;/li&gt;&#xA;&lt;li&gt;polar (2 times)&lt;/li&gt;&#xA;&lt;li&gt;hydrophilic (0 times)&lt;/li&gt;&#xA;&lt;li&gt;solvophilic (8 times)&lt;/li&gt;&#xA;&lt;li&gt;apolar (0 times)&lt;/li&gt;&#xA;&lt;li&gt;non-polar (0 times)&lt;/li&gt;&#xA;&lt;li&gt;water-insoluble (1 times)&lt;/li&gt;&#xA;&lt;li&gt;hydrophobic (3 times)&lt;/li&gt;&#xA;&lt;li&gt;solvophobic (23 times)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I checked the google either:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;google &lt;code&gt;&quot;* amino acid residue&quot;&lt;/code&gt; search&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ionic 7&lt;/li&gt;&#xA;&lt;li&gt;charged 104 000&lt;/li&gt;&#xA;&lt;li&gt;polar 42 000&lt;/li&gt;&#xA;&lt;li&gt;hydrophilic 917 000&lt;/li&gt;&#xA;&lt;li&gt;apolar 101 000&lt;/li&gt;&#xA;&lt;li&gt;nonpolar 326 000&lt;/li&gt;&#xA;&lt;li&gt;non-polar 44 000&lt;/li&gt;&#xA;&lt;li&gt;hydrophobic 111 000&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;google &lt;code&gt;&quot;* residue&quot; protein&lt;/code&gt; search&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;ionic 2 110&lt;/li&gt;&#xA;&lt;li&gt;charged 120 000&lt;/li&gt;&#xA;&lt;li&gt;polar 53 000&lt;/li&gt;&#xA;&lt;li&gt;hydrophilic 33 000&lt;/li&gt;&#xA;&lt;li&gt;apolar 4 690&lt;/li&gt;&#xA;&lt;li&gt;nonpolar 15 600&lt;/li&gt;&#xA;&lt;li&gt;non-polar 284 000&lt;/li&gt;&#xA;&lt;li&gt;hydrophobic 148 000&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So all of the hydrophilic, hydrophobic, nonpolar, polar, charged words are used frequently. I checked some books and articles, some of them use the &quot;hydrophobic-polar-charged +/-&quot; classification (just like Dill) which seems to be elder than the &quot;nonpolar - polar (neutral, acidic, alkaline)&quot; classification in other articles.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Amino_acid&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia - amino acid&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.proteinstructures.com/Structure/Structure/amino-acids.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Basics of Protein Structure - The 20 Amino Acids and Their Role in Protein Structures&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://condmat.lca.uc.pt/?page_id=1007&quot; rel=&quot;nofollow noreferrer&quot;&gt;condmat - Amino acids&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://chemistry.tutorvista.com/biochemistry/amino-acids.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;tutorvista - Amino Acids&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now the question still stands.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For example what is the difference in these sentences:&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;&lt;p&gt;Generally globular protein cores have hydrophobic regions whilst the surface contains hydrophilic exterior facing residues.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Generally globular protein cores have non-polar regions whilst the surface contains polar exterior facing residues.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't think there is any difference between the meaning of these two sentences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the more interesting question is which amino acids are in which groups. I checked some &lt;a href=&quot;http://en.wikipedia.org/wiki/Hydrophobicity_scales&quot; rel=&quot;nofollow noreferrer&quot;&gt;hydrophobicity scales&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kXSfW.png&quot; alt=&quot;hydrophobicity scale summary&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Figure 1 - hydrophobicity scale summary&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Amino Acid Hydrophobicity&lt;/a&gt; for the Kyte - Doolittle (kd), Wimley - White (ww), Hessa  - Heijne (hh)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/amino-acid-reference-chart.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hydrophobicity Index for Common Amino Acids&lt;/a&gt; for the two indexes&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://chemistry.tutorvista.com/biochemistry/amino-acids.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;tutorvista - Amino Acids&lt;/a&gt; for the pI values (pI can be used to filter the charged ones)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It seems to be far from obvious. As you already mentioned it is a continuous spectrum and hard to create groups. It was interesting that Trp (which is strongly apolar) had negative numbers on two scales (maybe the data was not reliable). What you can tell, which amino acids are certainly polar (hydrophilic) and which are certainly apolar (hydrophobic). Based on this information you can tell which residues will be in the apolar core (hydrophobic residues) and which will be on the polar exterior (hydrophobic residues) and which will create the backbone hydrogen bonds (polar residues) and probably salt bridges (polar, charged residues). Ofc. all of these can more or less depend on the pH...&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-11-11T13:20:57.507" LastActivityDate="2014-11-11T13:20:57.507" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23780" PostTypeId="2" ParentId="23769" CreationDate="2014-11-06T22:43:10.527" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;An embryo is called a fetus at a more advanced stage of development&#xA;  and up until birth or hatching. In humans, this is from the eighth&#xA;  week of gestation. However, animals which develop in eggs outside the&#xA;  mother's body are usually referred to as embryos throughout&#xA;  development; e.g. one would refer to a chick embryo, not a &quot;chick&#xA;  fetus&quot; even at late stages.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;wikipedia - &lt;a href=&quot;http://en.wikipedia.org/wiki/Embryo&quot; rel=&quot;nofollow noreferrer&quot;&gt;embryo&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I can answer what &quot;more advanced&quot; means with the following 2 pictures. I think you can see the difference. (Real photos were too disgusting for me.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JmpQq.jpg&quot; alt=&quot;7th week embryo&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 1 - 7th week embryo - &lt;a href=&quot;http://www.parents.com/pregnancy/week-by-week/&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DXtyZ.jpg&quot; alt=&quot;8th week fetus&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 2 - 8th week fetus - &lt;a href=&quot;http://www.parents.com/pregnancy/week-by-week/&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For the sake of blind people and google, the 8th week fetus has a face and a human form, while the 7th week embryo doesn't.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;From the 10th week of gestation (8th week of development), the&#xA;  developing organism is called a fetus.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;All major structures are already formed in the fetus, but they&#xA;  continue to grow and develop.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Since the precursors of all the major organs are created by this time,&#xA;  the fetal period is described both by organ and by a list of changes&#xA;  by weeks of gestational age.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Because the precursors of the organs are now formed, the fetus is not&#xA;  as sensitive to damage from environmental exposure as the embryo was.&#xA;  Instead, toxic exposure often causes physiological abnormalities or&#xA;  minor congenital malformation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;wikipedia - &lt;a href=&quot;http://en.wikipedia.org/wiki/Prenatal_development&quot; rel=&quot;nofollow noreferrer&quot;&gt;prenatal development&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So the scientific explanation of the threshold is that the precursors of all the major organs are created by that time.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-11-07T14:46:52.323" LastActivityDate="2014-11-07T14:46:52.323" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23781" PostTypeId="2" ParentId="23774" CreationDate="2014-11-06T22:57:41.337" Score="2" Body="&lt;p&gt;The matter in plants is mostly carbon, hydrogen, oxygen, and nitrogen, with various metal ions and some sulfur and phosphorus. The carbon, hydrogen, and oxygen are taken from carbon dioxide in the air and water from the soil through &lt;a href=&quot;http://en.wikipedia.org/wiki/Photosynthesis&quot; rel=&quot;nofollow&quot;&gt;photosynthesis&lt;/a&gt;. &lt;a href=&quot;http://en.wikipedia.org/wiki/Nitrogen_cycle&quot; rel=&quot;nofollow&quot;&gt;Nitrogen&lt;/a&gt; is taken up from the soil as ammonia or nitrates, or &lt;a href=&quot;http://en.wikipedia.org/wiki/Nitrogen_fixation&quot; rel=&quot;nofollow&quot;&gt;fixed&lt;/a&gt; from nitrogen gas, but this only happens in legumes. &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphorus_cycle&quot; rel=&quot;nofollow&quot;&gt;Phosphorus&lt;/a&gt; is also part of a nutrient cycle. Metal ions such as sodium, potassium, magnesium, and calcium are taken up through the roots with water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're asking about how this material is replenished, fertilizer is an important answer. For centuries, nitrogen was a limiting nutrient in farms because it would get removed faster than it was replaced, especially if crop rotation was not used or legumes weren't grown. Thanks to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Haber_process&quot; rel=&quot;nofollow&quot;&gt;Haber Process&lt;/a&gt; we can produce humongous amounts of ammonia from nitrogen gas, this has greatly increased the amount of nitrogen available for plants, but has also resulted in nitrate pollution in waterways and &lt;a href=&quot;http://en.wikipedia.org/wiki/Algal_bloom&quot; rel=&quot;nofollow&quot;&gt;algal blooms&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Eutrophication&quot; rel=&quot;nofollow&quot;&gt;eutrophication&lt;/a&gt;. Phosphate and potassium are also used in fertilizer and are usually mined, however phosphorus reserves are &lt;a href=&quot;http://en.wikipedia.org/wiki/Peak_phosphorus&quot; rel=&quot;nofollow&quot;&gt;limited&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2014-11-06T23:04:37.440" LastActivityDate="2014-11-06T23:04:37.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23782" PostTypeId="2" ParentId="23774" CreationDate="2014-11-06T23:05:50.847" Score="2" Body="&lt;p&gt;There are &lt;a href=&quot;http://en.wikipedia.org/wiki/Biogeochemical_cycle&quot; rel=&quot;nofollow&quot;&gt;biogeochemical cycles&lt;/a&gt; for the building stones of the biomass (e.g. hydrogen, carbon, nitrogen, oxygen, etc...), so all of these atoms are recycled. To recycle them the organisms need energy, which they get from sunlight, from chemical materials, etc... (check &lt;a href=&quot;http://en.wikipedia.org/wiki/Microbial_metabolism&quot; rel=&quot;nofollow&quot;&gt;microbial metabolism&lt;/a&gt; for further details).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants use sunlight as energy source, CO2 from air as carbon source, water and O2 from air as oxygen source, and so on... You can find more info about plant metabolism &lt;a href=&quot;http://en.wikipedia.org/wiki/Category:Plant_metabolism&quot; rel=&quot;nofollow&quot;&gt;on wikipedia&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-11-06T23:41:00.767" LastActivityDate="2014-11-06T23:41:00.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23783" PostTypeId="1" CreationDate="2014-11-06T23:38:50.803" Score="4" ViewCount="244" Body="&lt;p&gt;I was reading this article: &quot;&lt;a href=&quot;https://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=5&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CDgQFjAE&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fpublication%2F12196921_Overview_of_vector_design_for_mammalian_gene_expression%2Flinks%2F0912f50b859ea95140000000&amp;amp;ei=ygFcVKzCHteUsQSpm4LoAw&amp;amp;usg=AFQjCNHJpnMNYd2BQzxgF8-08QC2Mw9dTQ&amp;amp;sig2=3FJpi89PA0wj3WKu3eJmfQ&quot; rel=&quot;nofollow&quot;&gt;Overview of vector design for mammalian gene expression.&lt;/a&gt;&quot;  for an explanation of why mammalian cell lines are used for expressing cloned genes, and one of the reasons given is that &quot;DNA cloned from higher eukaryotic cells is readily expressed since the signals for transcription, mRNA processing, and translation are conserved in higher eukaryotic systems.&quot; What does it mean for the signals to be &quot;conserved,&quot; and why does this make mammalian cells a better host than other types of cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Follow-up question, in case the answer to that question doesn't make it clear: the article also says the machinery for protein folding and assembly are &quot;conserved&quot; - what does that mean (if not the same thing as in the first question) - and again, why does this make mammalian cells a superior choice of host for expressing cloned genes?&lt;/p&gt;&#xA;" OwnerUserId="6128" LastEditorUserId="5144" LastEditDate="2014-11-07T06:50:13.303" LastActivityDate="2014-11-07T12:01:14.297" Title="What does it mean for the signals for transcription and translation to be &quot;conserved&quot;?" Tags="&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;cell-culture&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23784" PostTypeId="2" ParentId="23774" CreationDate="2014-11-07T00:58:31.313" Score="1" Body="&lt;p&gt;The biomass of crops is definitely mostly carbon (from the air in the form of CO&lt;sub&gt;2&lt;/sub&gt;) and water. However, in terms of how it affects the environment: Crops use up trace elements that make up a tiny fraction of the biomass, but it is these trace elements that are not ubiquitously available. Most notably phosphorus and to a lesser extent nitrogen. The impact on the environment is that farming, and especially monocultures, deplete the environment of these essential trace elements. It is often these elements that restrict growth due to competition. Therefore, it may inhibit growth of native species. However, a far more devastating effect is that farmers will re-supply these trace elements in excessive amounts through artificial fertilizers, leading to surplus and run-off phosphates (phosphates are the main form in which phosphorus is applied in fertilizers) (&lt;a href=&quot;http://scholar.google.com.au/scholar_url?hl=en&amp;amp;q=http://www.jlakes.org/web/Phosphorus-runoff-agricultural-land-JEQ2004.pdf&amp;amp;sa=X&amp;amp;scisig=AAGBfm0CH05gfB4d7NIjhsCtrhHWheO5TA&amp;amp;oi=scholarr&amp;amp;ei=mxdcVNbRDYXm8AWii4LIBA&amp;amp;sqi=2&amp;amp;ved=0CBsQgAMoADAA&quot; rel=&quot;nofollow&quot;&gt;Hart et al, 2004&lt;/a&gt;). This in turn dramatically shifts the natural competition for this normally restricting element, in turn promoting growth of non-native plants and promoting the growth of P and N-tolerant plants while suppressing the growth of plants that are intolerant. As most plants are actually intolerant it will eventually lead to species loss and imbalance in the ecosystem (&lt;a href=&quot;http://homeguides.sfgate.com/negative-effects-nitrogenrich-fertilizer-environment-72041.html&quot; rel=&quot;nofollow&quot;&gt;popular link&lt;/a&gt;).           &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-07T00:58:31.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23785" PostTypeId="1" AcceptedAnswerId="23790" CreationDate="2014-11-07T01:00:26.553" Score="2" ViewCount="131" Body="&lt;p&gt;I just went to kill what I thought was a moth on the wall, and instead it fell on the floor and it sounded like dropping a coffee bean (because of the hard shell)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I live in the UK and have never seen one of these things before, I thought maybe it was a variant of a woodlouse, so I just crushed it in some kitchen roll I had over my hand and saw a little stain on the paper, but I assumed it was just blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I looked on the internet and discovered what it was, I smelled my hand and it stank (I'd literally washed my hands like a minute or two before killing this thing). Since I've touched my laptop keyboard and stuff, is that a problem? If I use my laptop and now eat something will it poison me or leave an awful taste in my mouth?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. If this seems OTT I do have slight OCD when it comes to hygiene and bugs.&lt;/p&gt;&#xA;" OwnerUserId="9106" LastActivityDate="2014-11-07T03:51:39.883" Title="Is the poison from Stink Bugs dangerous?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23786" PostTypeId="2" ParentId="23775" CreationDate="2014-11-07T01:01:55.283" Score="1" Body="&lt;p&gt;Bed bugs (&lt;a href=&quot;http://en.wikipedia.org/wiki/Bed_bug&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;)! However, you will definitely be able to notice when they are around by bite marks and blood residues.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-07T01:01:55.283" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23787" PostTypeId="2" ParentId="23730" CreationDate="2014-11-07T01:06:31.800" Score="3" Body="&lt;h1&gt;Short Answer&lt;/h1&gt;&#xA;&lt;p&gt;What you're referring to is called &lt;em&gt;&lt;strong&gt;Delayed Onset Muscle Soreness&lt;/strong&gt;&lt;/em&gt; (DOMS).&lt;/p&gt;&#xA;&lt;p&gt;We don't really know what causes DOMS, but it's most likely caused by a cascade effect started my muscle injury. Also, we aren't sure if massages (or what type of massages) really help relieve the pain.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h1&gt;What is &lt;em&gt;Delayed Onset Muscle Soreness&lt;/em&gt; (DOMS)?&lt;/h1&gt;&#xA;&lt;p&gt;Delayed onset muscle soreness (DOMS) is the sensation of muscular discomfort and pain during active contractions that occur 24–48 h after strenuous exercise. The initial symptoms are most evident at the muscle-tendon junction and thereafter spread throughout the entire muscle.&lt;a href=&quot;http://link.springer.com/referenceworkentry/10.1007/978-3-642-28753-4_1018&quot; rel=&quot;nofollow noreferrer&quot;&gt;(ref)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;h1&gt;Physiopathology of DOMS&lt;/h1&gt;&#xA;&lt;p&gt;The mechanism is not completely understood and several theories have been proposed, namely: &lt;a href=&quot;http://link.springer.com/article/10.2165/00007256-200333020-00005&quot; rel=&quot;nofollow noreferrer&quot;&gt;(ref)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;lactic acid&lt;/li&gt;&#xA;&lt;li&gt;muscle spasm&lt;/li&gt;&#xA;&lt;li&gt;connective tissue damage&lt;/li&gt;&#xA;&lt;li&gt;muscle damage&lt;/li&gt;&#xA;&lt;li&gt;inflammation&lt;/li&gt;&#xA;&lt;li&gt;enzyme efflux&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;The underlying cause is probably a conjunction of 2 or more of these theories. However, ultimately, the underlying transversal cause is &lt;strong&gt;muscle microtrauma&lt;/strong&gt;. There are a few interesting findings that support this:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;High-intensity eccentric contractions induce performance decrements and DOMS &lt;a href=&quot;http://www.clinsciusa.org/cs/064/0055/0640055.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(ref)&lt;/a&gt;,&lt;a href=&quot;http://www.tandfonline.com/doi/abs/10.1080/02701367.1985.10605375?journalCode=urqe20#.VFwGhvmsVB0&quot; rel=&quot;nofollow noreferrer&quot;&gt;(ref)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Concentric exercises seems to cause no soreness &lt;a href=&quot;http://www.tandfonline.com/doi/abs/10.1080/00140137208924444#.VFwHrfmsVB0&quot; rel=&quot;nofollow noreferrer&quot;&gt;(ref)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Eccentric contractions are high force and are associated with muscle damage &lt;a href=&quot;http://link.springer.com/article/10.1007/BF00635995&quot; rel=&quot;nofollow noreferrer&quot;&gt;(ref)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Creatinine, Potassium(K) (and sometimes Myoglobin) excretion (urine levels) and Creatine Kinase(CK), K and Neutrophil levels in blood are increased after intense exercise. This is also seen in &lt;a href=&quot;http://en.wikipedia.org/wiki/Rhabdomyolysis&quot; rel=&quot;nofollow noreferrer&quot;&gt;acute rhabdomyolysis&lt;/a&gt;, a condition in which damaged skeletal muscle tissue breaks down. (Ref: &lt;a href=&quot;https://rads.stackoverflow.com/amzn/click/com/0071466339&quot; rel=&quot;nofollow noreferrer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Harrison's Principles of Internal Medicine, 17th Ed, Chapter 273: Acute Renal Failure&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h1&gt;The effects of massage on DOMS&lt;/h1&gt;&#xA;&lt;p&gt;A massage MAY indeed reduce pain in DOMS &lt;a href=&quot;http://bjsm.bmj.com/content/37/1/72.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;(ref)&lt;/a&gt;, however, most studies' results are inconsistent and hindered by methodological flaws&lt;a href=&quot;http://bjsm.bmj.com/content/32/3/212.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;(ref)&lt;/a&gt; such as lack of control of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Placebo&quot; rel=&quot;nofollow noreferrer&quot;&gt;placebo effect&lt;/a&gt; or the subjectivity of pain.&lt;/p&gt;&#xA;&lt;p&gt;A study by &lt;em&gt;Smith et al&lt;/em&gt; suggests that sports massage will reduce DOMS when administered&#xA;2 hours after the termination of eccentric exercise. They also found lower CK levels, higher cortisol levels and a prolonged elevation of neutrophils in the blood of massaged groups &lt;a href=&quot;http://www.jospt.org/doi/abs/10.2519/jospt.1994.19.2.93#.VFwMYfmsVB0&quot; rel=&quot;nofollow noreferrer&quot;&gt;(ref)&lt;/a&gt;. This might mean lower muscle trauma and inflammation due to a reduced migration of neutrophils (to the muscle) and higher levels of serum cortisol.&lt;/p&gt;&#xA;&lt;p&gt;The increment in the blood flow to the muscles during a massage might also be implicated in the process, by restoring oxygen and nutrients required to muscle remodeling. However, there is no clinical evidence of this fact and a study strongly rebutes this &lt;a href=&quot;https://www.thieme-connect.com/products/ejournals/abstract/10.1055/s-2007-973041&quot; rel=&quot;nofollow noreferrer&quot;&gt;(ref)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Hyperstimulation of the nerve endings in the affected muscles might give a sense of pain relief, in a context of microtrauma. &lt;a href=&quot;http://link.springer.com/article/10.2165/00007256-200838060-00004&quot; rel=&quot;nofollow noreferrer&quot;&gt;(ref)&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6543" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-11-07T01:06:31.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23790" PostTypeId="2" ParentId="23785" CreationDate="2014-11-07T03:51:39.883" Score="4" Body="&lt;p&gt;Apparently there are no poisonous species (&lt;a href=&quot;http://animals.pawnation.com/stink-bugs-poisonous-7670.html&quot; rel=&quot;nofollow&quot;&gt;see this website&lt;/a&gt;), and some species are even eaten (&lt;a href=&quot;http://www.scienceinafrica.com/old/index.php?q=2003/october/stinkbug.htm&quot; rel=&quot;nofollow&quot;&gt;website&lt;/a&gt;). No worries. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-07T03:51:39.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23791" PostTypeId="1" AcceptedAnswerId="24136" CreationDate="2014-11-07T04:21:43.080" Score="1" ViewCount="107" Body="&lt;p&gt;I'm trying to think of places where a biofilm could develop other than on medical equipment or food processing equipment such as stainless steel mechanized blades or knives. I'm thinking more along the lines of biofilms on typical house hold things such as the bottoms of shower curtains&lt;/p&gt;&#xA;" OwnerUserId="8991" LastEditorUserId="3340" LastEditDate="2014-12-26T08:32:12.693" LastActivityDate="2014-12-26T08:32:12.693" Title="What are some places where biofilms could develop?" Tags="&lt;cell-biology&gt;&lt;microbiology&gt;&lt;nutrition&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ClosedDate="2014-12-26T17:21:58.063" ContentLicense="CC BY-SA 3.0" />
  <row Id="23793" PostTypeId="1" AcceptedAnswerId="23797" CreationDate="2014-11-07T06:28:59.523" Score="34" ViewCount="3345" Body="&lt;p&gt;I am a resident of the tropical island of Sri Lanka, and we have a strange traditional method to ripen our banana harvest quickly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What we do is this: We dig a pit in earth that is enough to put the whole banana cluster in. Then, after safely laying the bananas in the pit, we cover up the pit with a sheet such that only a small hole from a side remains: visualize a small 3-4 inch door to the pit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After that, we light a fire with semi-dry leaves just outside the pit's door. (&lt;em&gt;Semi-dry leaves are used to get as much smoke as possible. Dry leaves do not give that much smoke, because they completely oxidize quickly&lt;/em&gt;). And the smoke is sent through the door by blowing it with the aid of a bamboo.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OPOMi.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This sends a good amount of smoke and warms the inside of the pit considerably. And by experience I can tell you that this makes the bananas to ripen really quickly. I have done a controlled experiment where half of the cluster was not put into the pit. Bananas in the pit ripen overnight and the control sample took days to ripen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anybody explain what are the bio-mechanisms that are working here?&lt;/p&gt;&#xA;" OwnerUserId="9948" LastEditorUserId="9948" LastEditDate="2017-03-09T03:26:15.127" LastActivityDate="2017-03-09T03:26:15.127" Title="Ripening bananas artificially: What is the biological theory behind?" Tags="&lt;biochemistry&gt;&lt;botany&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23794" PostTypeId="1" CreationDate="2014-11-07T06:32:40.867" Score="1" ViewCount="124" Body="&lt;p&gt;I would like to know about the term stress response. For example &quot;some genes of a species under study is involved in stress response&quot;. What does that mean? I got this as a part of my assignment question.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/EAgAm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5669" LastEditorUserId="5669" LastEditDate="2014-11-07T14:05:17.730" LastActivityDate="2014-12-10T04:45:59.163" Title="What is meant by &quot;genes involved in the stress response&quot;?" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23795" PostTypeId="2" ParentId="23246" CreationDate="2014-11-07T08:15:01.567" Score="2" Body="&lt;p&gt;I investigated the topic too, so here is my answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To understand thermodinamic stability of water solved globulins or membrane proteins (all of them proteins hereafter) we have to understand protein folding. Proteins have a 3d structure (composed by their primary, secondary and tertiary structures). The structure of the proteins is constantly changing between the folded and unfolded states. The folded state has a lower free energy while the unfolded state has a higher. Between them there is a free energy barrier which determines the speed of the folding on a specific temperature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Changing structural on environmental factors can affect these free energies and can shift the equilibrium to the unfolded state. The unfolded protein can suffer irreversible changes (aggregation, disulphide exchange, proteolysis, irreversible subunit dissociation, chemical degradation, etc...), so the denaturation of the protein can be reversible or irreversible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that this is a very simplistic view, I think there are different degrees of unfoldedness, and so different things can happen when the protein is in one of these. For instance by a low degree of unfoldedness misfolding can happen which results a stable, but inactive folded state without coagulation (this can be more or less reversible). By a higher degree of unfoldedness coagulation can happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Folding mostly depends on one simple rule: all of the hydrogen bonds have to be satisfied, because a non-satisfied hydrogen bond has a very high energetic cost. The proteins have polar surfaces, which form hydrogen bonds with the water, and one or more apolar center, which have inner hydrogen bonds as backbones. Burial of an unpaired polar amino-acid (e.g. non-satisfied hydrogen bond) is very destabilizing and so it is non-existent in natural working proteins. Other factors, like salt bridges, aromatic-aromatic interactions, disulphide bonds, etc... can affect the stability as well, but hydrogen bonds and hydrophobic interactions are the major factors. The weights of these two major factors is most likely protein dependent (a study suggested 75% and 25%, while another 40% and 60%).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The backbone hydrogen bonds are usually most stable around room temperature, so the lowest free energy and the maximum stability is around 20°C by most proteins and both heating and cooling lowers the stability and can lead to denaturation. High temperatures (&gt;80°C) can cause covalent degradation, and so irreversible denaturation. Pressure has similar effect on the hydrogen bonds and the stability as cold denaturation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The osmolyte cosolvents like urea or TMAO contribute differently to the free energy of the folded and unfolded states and so shift the equilibrium between them. for example urea can cause denaturation, while TMAO protects the protein from denaturation. I think it is evident that changing pH and saltiness has strong effect on the charges of the amino acid side chains, and so the hydrogen bonds and the stability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both ultrasound and pulsed electric field (PEF) can cause denaturation. The effect seems strongly depending on the parameters of ultrasound/PEF and the type of the protein. Interesting that PEF can increase the enzyme activity too. It is hard to find studies about the denaturation mechanisms by these methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we want to increase the protein stability, the method we choose can depend on what we want to protect the protein from. One or more methods from the following list can help to increase the stability:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;increase of compactness and better packing (minimalization of surface/volume ratio)&lt;/li&gt;&#xA;&lt;li&gt;increase of electrostatic interactions (formation of additional ion pairs, e.g. more glutamic acid)&lt;/li&gt;&#xA;&lt;li&gt;additional hydrogen bonds&lt;/li&gt;&#xA;&lt;li&gt;additional disulphide bridges&lt;/li&gt;&#xA;&lt;li&gt;increasing hydrophobic interactions (greater proportion of buried hydrophobic residues)&lt;/li&gt;&#xA;&lt;li&gt;change protein microenvironment (use osmolytes, change pH, saltiness)&lt;/li&gt;&#xA;&lt;li&gt;glycosylate the protein surface&lt;/li&gt;&#xA;&lt;li&gt;decrease chain length&lt;/li&gt;&#xA;&lt;li&gt;change surface amino-acids (the effect can be completely unpredictable, but there are surface residue patterns with known effect on stability; add more ionisable amino acids to the surface; bury hydrophobic residues; etc...)&lt;/li&gt;&#xA;&lt;li&gt;protein fixation can change the stability as well&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Thermodynamic stability of a protein that unfolds and refolds rapidly,&#xA;  reversibly, cooperatively, and with a simple, two-state mechanism. The&#xA;  easiest proteins in which to study folding and stability are those&#xA;  that exhibit this sort of rapid reversibility. Both experimental&#xA;  design and also theoretical treatment of data are simplified by&#xA;  reversible systems. Thus, it is no surprise that most of the&#xA;  literature reports about stability discuss this type of reversible&#xA;  system. The stability of the protein is simply the difference in Gibbs&#xA;  free energy, dG, between the folded and the unfolded states. The only&#xA;  factors affecting stability are the relative free energies of the&#xA;  folded (Gf) and the unfolded (Gu) states. The larger and more positive&#xA;  Gu, the more stable is the protein to denaturation.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;If a protein unfolds reversibly it may be fully unfolded and inactive&#xA;  at high temperatures, but once it cools to room temperature, it will&#xA;  refold and fully recover activity. In the case of irreversible or&#xA;  slowly unfolding proteins, it is kinetic stability or the rate of&#xA;  unfolding that is important. A protein that is kinetically stable will&#xA;  unfold more slowly than a kinetically unstable protein. In a&#xA;  kinetically stable protein, a large free energy barrier to unfolding&#xA;  is required and the factors affecting stability are the relative free&#xA;  energies of the folded (Gf) and the transition state (Gts) for the&#xA;  first committed step on the unfolding pathway. Irreversible loss of&#xA;  protein folded structure is represented by: F &amp;lt;-&gt; U -&gt; I, where I is&#xA;  inactive due to aggregation, disulphide exchange, proteolysis,&#xA;  irreversible subunit dissociation, chemical degradation, etc...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1996 - &lt;a href=&quot;http://www.cryst.bbk.ac.uk/PPS2/projects/day/TDayDiss/index.html&quot; rel=&quot;nofollow&quot;&gt;The Source of Stability in Proteins&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1110/ps.051401905/full&quot; rel=&quot;nofollow&quot;&gt;Charge–charge interactions in the denatured state influence the folding kinetics of ribonuclease Sa&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://gmwgroup.harvard.edu/pubs/pdf/951.pdf&quot; rel=&quot;nofollow&quot;&gt;Why Are Proteins Charged? Networks of Charge–Charge Interactions in Proteins Measured by Charge Ladders and Capillary Electrophoresis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Evidence from proteins and peptides supports the conclusion that&#xA;  intrapeptide hydrogen bonds stabilize the folded form of proteins.&#xA;  Paradoxically, evidence from small molecules supports the opposite&#xA;  conclusion, that intrapeptide hydrogen bonds are less favorable than&#xA;  peptide–water hydrogen bonds. A related issue—often lost in this&#xA;  debate about comparing peptide–peptide to peptide– water hydrogen&#xA;  bonds—involves the energetic cost of an unsatisfied hydrogen bond.&#xA;  Here, experiment and theory agree that breaking a hydrogen bond costs&#xA;  between 5 and 6 kcal/mol. Accordingly, the likelihood of finding an&#xA;  unsatisfied hydrogen bond in a protein is insignificant. This&#xA;  realization establishes a powerful rule for evaluating protein&#xA;  conformations.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In their description of the alpha-helix, Pauling et al. (1951)&#xA;  asserted that the energy of the peptide N–H• • •O=C hydrogen bond was&#xA;  of order -8 kcal/mol, and that “such instability would result from the&#xA;  failure to form these bonds that we may be confident of their&#xA;  presence.” Pauling’s earlier estimate of the total protein hydrogen&#xA;  bond energy was -5 kcal/mol (Mirsky and Pauling 1936). From solution&#xA;  studies of urea dimers, Schellman estimated that an intrapeptide&#xA;  hydrogen bond would be enthalpically favored over a peptide–water&#xA;  hydrogen bond by ~1.5 kcal/mol (Schellman 1955). These and similar&#xA;  early studies led to the conclusion that the peptide hydrogen bond is&#xA;  a significant factor in stabilizing protein conformations.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This view was to change dramatically following a famous review by&#xA;  Kauzmann (1959), who invoked the thermodynamics of small model&#xA;  compounds to argue that stabilization of the folded state of a protein&#xA;  is due almost exclusively to the hydrophobic effect. Soon after&#xA;  Kauzmann’s proposal, Klotz and Franzen (1962) determined that the&#xA;  enthalpy of the interamide hydrogen bond of N-methyl acetamide in&#xA;  water was zero, and concluded that “the intrinsic stability of&#xA;  interpeptide hydrogen bonds in aqueous solution is small.” Similarly,&#xA;  hydrogen bonding involving another small molecule,&#xA;  epsilon-caprolactam, in dilute solution was shown to be negligible&#xA;  (Susi and Ard 1969). Kauzmann’s proposal, bolstered by these later&#xA;  studies, led to the widely held view that the hydrophobic effect makes&#xA;  the major energetic contribution to protein stability, with hydrogen&#xA;  bonds contributing little, or perhaps even opposing, the folding&#xA;  process. See Baldwin (2003) for a recent discussion of these issues.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Protein hydrogen bonds are ubiquitous, directional, and largely local,&#xA;  partitioning the polypeptide chain into alpha- and 3_10-helices,&#xA;  beta-sheet, and beta-turns. Together, these hydrogen-bonded backbone&#xA;  structures account for at least 75% of the conformation, on average,&#xA;  with remaining residues participating in both additional&#xA;  intramolecular hydrogen bonding and hydrogen bonding to water.&#xA;  Unsatisfied backbone polar groups are energetically expensive, to the&#xA;  degree that they almost never occur. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Force measurements between surfaces functionalized with lipids having&#xA;  hydrogen bonding headgroups (NTA, A, T, and MeT lipids) lead to a&#xA;  reproducible value of the energy of a single hydrogen bond in pure&#xA;  water: ~0.5 kcal/mol. It shows that it is energetically more favorable&#xA;  for the headgroups to make hydrogen bonds with each other than to make&#xA;  hydrogen bonds with water molecules. This is coherent with past&#xA;  studies made on proteins stability, which showed that intramolecular&#xA;  hydrogen bonds in a folded protein are energetically more favorable&#xA;  than bonds with water molecules in an unfolded protein with an average&#xA;  stabilization of ~1 kcal/mol per intramolecular hydrogen bond.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1996 - &lt;a href=&quot;http://www.fasebj.org/content/10/1/75.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;Forces contributing to the conformational stability of proteins.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2005 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253345/&quot; rel=&quot;nofollow&quot;&gt;Do all backbone polar groups in proteins form hydrogen bonds?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S002228361100355X&quot; rel=&quot;nofollow&quot;&gt;Backbone-Driven Collapse in Unfolded Protein Chains&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1476927106000296&quot; rel=&quot;nofollow&quot;&gt;Hydrophobic collapse in (in silico) protein folding&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2002 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022283602004655&quot; rel=&quot;nofollow&quot;&gt;Thermodynamic Consequences of Burial of Polar and Non-polar Amino Acid Residues in the Protein Interior&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2003 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006349503747195&quot; rel=&quot;nofollow&quot;&gt;Thermodynamics of Heat Activation of Single Capsaicin Ion Channels VR1&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2003 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/bi027184%2B&quot; rel=&quot;nofollow&quot;&gt;Temperature Range of Thermodynamic Stability for the Native State of Reversible Two-State Proteins&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ja8056419&quot; rel=&quot;nofollow&quot;&gt;Protein Cold Denaturation as Seen From the Solvent&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jo101075a&quot; rel=&quot;nofollow&quot;&gt;Construction of Peptoids with All Trans-Amide Backbones and Peptoid Reverse Turns via the Tactical Incorporation of N-Aryl Side Chains Capable of Hydrogen Bonding&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2002 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006349502753678&quot; rel=&quot;nofollow&quot;&gt;Energy of Hydrogen Bonds Probed by the Adhesion of Functionalized Lipid Layers&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0959440X11001783&quot; rel=&quot;nofollow&quot;&gt;How, when and why proteins collapse: the relation to folding&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002169#pcbi-1002169-g003&quot; rel=&quot;nofollow&quot;&gt;Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0959440X10001661&quot; rel=&quot;nofollow&quot;&gt;Membrane protein folding: how important are hydrogen bonds?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The main determinant of cold denaturation tendency is likely the&#xA;  stability decrease of backbone hydrogen bonds at low temperatures,&#xA;  which in turn is affected by the packing manner of the hydrophobic&#xA;  core cluster&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Using a newly developed pressure cell, we have now mapped pressure-&#xA;  and temperature-dependent changes of 31 hydrogen bonds in ubiquitin by&#xA;  measuring HBCs with very high precision. Short-range hydrogen bonds&#xA;  are only moderately perturbed, but many hydrogen bonds with large&#xA;  sequence separations (high contact order) show greater changes. In&#xA;  contrast, other high-contact-order hydrogen bonds remain virtually&#xA;  unaffected.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;We study the stability of globular proteins as a function of&#xA;  temperature and pressure through NPT simulations of a coarse-grained&#xA;  model. We reproduce the elliptical stability of proteins and highlight&#xA;  a unifying microscopic mechanism for pressure and cold denaturations.&#xA;  The mechanism involves the solvation of nonpolar residues with a thin&#xA;  layer of water. These solvated states have lower volume and lower&#xA;  hydrogen-bond energy compared to other conformations of nonpolar&#xA;  solutes. Hence, these solvated states are favorable at high pressure&#xA;  and low temperature, and they facilitate protein unfolding under these&#xA;  thermodynamical conditions.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;We further find that it is the changes in hydrophobic hydration with&#xA;  decreasing temperature that drive cold unfolding and that the overall&#xA;  process is enthalpically driven, whereas heat denaturation is&#xA;  entropically driven.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;As a consequence of a weaker penetration upon pressurizing, it was&#xA;  found that the pressure-denatured state was partially unfolded&#xA;  compared with the heat-denatured state. The mechanism of pressure&#xA;  denaturation was related to the disruption of the hydrogen-bond&#xA;  network of water onto a set of clusters characterized by strengthened&#xA;  O – H interactions, inducing a hardening of protein dynamics. The&#xA;  mechanism is opposite to that observed upon heating, i.e., the&#xA;  softening of the hydrogen bond network of water inducing a softer&#xA;  protein dynamics.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;We can conclude that the main driving force of protein denaturation at&#xA;  high pressures is the decrease of the hydrophobic effect as a&#xA;  consequence of the changes in water structure, without contradicting&#xA;  any of the current theories on the hydrophobic effect.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;For the pressure denaturation the weakening of the hydrophobic&#xA;  interaction between the bulky side chains is found to be crucial at&#xA;  lower temperatures, leading to an apparent destabilization of the&#xA;  folded backbone structure at elevated pressures.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23464178&quot; rel=&quot;nofollow&quot;&gt;Molecular dynamics simulation indicating cold denaturation of beta-hairpins.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0037270&quot; rel=&quot;nofollow&quot;&gt;Cold-Induced Changes in the Protein Ubiquitin&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.100.118101&quot; rel=&quot;nofollow&quot;&gt;Microscopic Mechanism for Cold Denaturation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://journals.aps.org/pre/abstract/10.1103/PhysRevE.79.030905&quot; rel=&quot;nofollow&quot;&gt;Hydrophobicity at low temperatures and cold denaturation of a protein&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 &lt;a href=&quot;http://www.nature.com/nchem/journal/v4/n9/abs/nchem.1396.html&quot; rel=&quot;nofollow&quot;&gt;Key stabilizing elements of protein structure identified through pressure and temperature perturbation of its hydrogen bond network&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.109.048104&quot; rel=&quot;nofollow&quot;&gt;Unifying Microscopic Mechanism for Pressure and Cold Denaturations of Proteins&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jp3039175&quot; rel=&quot;nofollow&quot;&gt;Role of Hydrophobic Hydration in Protein Stability: A 3D Water-Explicit Protein Model Exhibiting Cold and Heat Denaturation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1570963911002123&quot; rel=&quot;nofollow&quot;&gt;Molecular mechanisms of the anomalous thermal aggregation of green fluorescent protein&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jp2014836&quot; rel=&quot;nofollow&quot;&gt;Analysis of the Mechanism of Lysozyme Pressure Denaturation from Raman Spectroscopy Investigations, and Comparison with Thermal Denaturation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/anie.200802027/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;Cold- and Pressure-Induced Dissociation of Protein Aggregates and Amyloid Fibrils&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006349509061505&quot; rel=&quot;nofollow&quot;&gt;The Behavior of the Hydrophobic Effect under Pressure and Protein Denaturation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2004 - &lt;a href=&quot;http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.93.238105&quot; rel=&quot;nofollow&quot;&gt;Reversible Temperature and Pressure Denaturation of a Protein Fragment: A Replica Exchange Molecular Dynamics Simulation Study&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is found that the energetics involving backbone hydrogen bonding&#xA;  controls these shifts in protein stability almost entirely, with&#xA;  osmolyte cosolvents simply dialing between solvent-backbone versus&#xA;  backbone-backbone hydrogen bonds, as a function of solvent quality.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.biochem.77.061306.131357&quot; rel=&quot;nofollow&quot;&gt;Structure and Energetics of the Hydrogen-Bonded Backbone in Protein Folding&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://www.pnas.org/content/106/8/2595.short&quot; rel=&quot;nofollow&quot;&gt;Urea, but not guanidinium, destabilizes proteins by forming hydrogen bonds to the peptide group&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006349511001111&quot; rel=&quot;nofollow&quot;&gt;Backbone and Side-Chain Contributions in Protein Denaturation by Urea&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bip.21318/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;On the mechanism of SDS-induced protein denaturation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1995 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/bi00014a029&quot; rel=&quot;nofollow&quot;&gt;Hydrogen Bonds and the pH dependence of Ovomucoid Third Domain Stability&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2004 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/bi036106z&quot; rel=&quot;nofollow&quot;&gt;Effects of Chaotropic and Kosmotropic Cosolvents on the Pressure-Induced Unfolding and Denaturation of Proteins:? An FT-IR Study on Staphylococcal Nuclease&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2002 - &lt;a href=&quot;http://www.pnas.org/content/100/8/4557.short&quot; rel=&quot;nofollow&quot;&gt;The hydration structure of guanidinium and thiocyanate ions: Implications for protein stability in aqueous solution&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Overall, the sonication process had little effect on the structure of&#xA;  proteins in WPC solutions which is critical to preserving functional&#xA;  properties during the ultrasonic processing of whey protein based&#xA;  dairy products.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The data presented here suggest that among proteins of fibrinolytic&#xA;  systems, the fibrinogen is one of the most sensitive proteins to the&#xA;  action of ultrasound. It has been shown in vitro that ultrasound&#xA;  induced fibrinogen aggregates formation, characterized by the loss of&#xA;  clotting ability and a greater rate of plasminolysis than native&#xA;  fibrinogen in different model systems and under different mode of&#xA;  ultrasound treatment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1350417710002671&quot; rel=&quot;nofollow&quot;&gt;Effects of ultrasound on the thermal and structural characteristics of proteins in reconstituted whey protein concentrate&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.biomedcentral.com/content/pdf/1471-2091-12-60.pdf&quot; rel=&quot;nofollow&quot;&gt;Effects of low frequency ultrasound on some properties of fibrinogen and its plasminolysis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The results obtained with the different experimental protocols&#xA;  indicate, however, that the conformational equilibrium of GrpE is&#xA;  insensitive to electromagnetic fields in the tested range of frequency&#xA;  and field strength. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Effects of pulsed electric fields (PEF) treatment (0–547 µs and 0–40&#xA;  kV/cm) on physicochemical properties of soybean protein isolates (SPI)&#xA;  were studied. Solubility, surface free sulfhydryls (SHF) and&#xA;  hydrophobicity of SPI dispersions (20 mg/ml) increased with the&#xA;  increment of the PEF strength and treatment time at constant pulse&#xA;  width 2 µs, pulse frequency 500 pulse per second (pps) and sample flow&#xA;  rate (1 ml/s). When the PEF strength and treatment time were above 30&#xA;  kV/cm and 288 µs, solubility, surface SHF, and hydrophobicity of SPI&#xA;  decreased due to denaturation and aggregation of SPI by hydrophobic&#xA;  interactions and disulfide bonds. Size-exclusion chromatography and&#xA;  laser light scattering analyses demonstrated further that stronger PEF&#xA;  treatment-induced dissociation, denaturation and reaggregation of SPI.&#xA;  Circular dichroism analysis showed that PEF treatment did not produce&#xA;  significant secondary structure changes of SPI.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;A compact and low cost bench-top, pulsed electric field treatment&#xA;  system was designed and developed. The unit consisted of a&#xA;  high-voltage pulse generator (? 30 kV) and a treatment chamber with ?&#xA;  148 ml capacity. Over the set-up voltage range of 4–26 kV, 30 pulses&#xA;  (with instant charge reversal) were applied to eight different enzyme&#xA;  solutions using a 0.3-cm electrode distance, a 13–87 kV/cm field,&#xA;  0.5-Hz pulse frequency, 2-µs pulse width and 20 °C process temperature. For some enzymes, activities were reduced after the pulse&#xA;  treatments: lipase, glucose oxidase and heat-stable ?-amylase&#xA;  exhibited a vast reduction of 70–85%; peroxidase and polyphenol&#xA;  oxidase showed a moderate 30–40% reduction whereas alkaline&#xA;  phosphatase only displayed a slight 5% reduction under the conditions&#xA;  employed. On the other hand, the enzyme activities of lysozyme and&#xA;  pepsin were increased under a certain range of voltages. Electric&#xA;  pulse profile (instant charge reversal) played a very important role&#xA;  in reducing the activities of various enzymes.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Effects of high-voltage pulsed electric field (PEF) on native or&#xA;  thermal denatured enzyme activities were studied. When PEF was applied&#xA;  to various native enzymes, 105–120% of initial enzyme activities were&#xA;  observed after PEF treatment. It was suggested that an activation of&#xA;  enzyme would be possible by PEF treatment. We attempted a refolding of&#xA;  thermal denatured enzyme by using PEF. When PEF was applied to&#xA;  denatured peroxidase, enzyme refolding was accelerated in PEF and 60%&#xA;  of initial activity was observed after 12 kV/cm and 30 s of PEF&#xA;  treatment although spontaneous refolding of this enzyme resulted in&#xA;  40% of initial activity. On the other hand, when PEF was applied to&#xA;  thermal denatured lactate dehydrogenase (LDH), further PEF-induced&#xA;  inactivation was observed. It was suggested that the influence of PEF&#xA;  is dependent on the type of enzyme.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bem.21865/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;Real-time assessment of possible electromagnetic-field-induced changes in protein conformation and thermal stability&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2007 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0023643806002362&quot; rel=&quot;nofollow&quot;&gt;Effects of pulsed electric fields on physicochemical properties of soybean protein isolates&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1997 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0260877496000520&quot; rel=&quot;nofollow&quot;&gt;Effects of high field electric pulses on the activity of selected enzymes&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2007 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0304388606000738&quot; rel=&quot;nofollow&quot;&gt;Influence of pulsed electric field on various enzyme activities&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In halophiles, protein stability and function are maintained by&#xA;  increased ion binding and glutamic acid content, both allowing the&#xA;  protein inventory to compete for water at high salt. Acidophiles and&#xA;  alkalophiles show neutral intracellular pH; proteins facing the&#xA;  outside extremes of pH possess anomalously high contents in ionizable&#xA;  amino acids. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;These facts suggest that globular proteins should be maximally stable&#xA;  around room temperature. Twenty-six of these are unique, and 20 of the&#xA;  26 are maximally stable around room temperature irrespective of their&#xA;  structural properties, the melting temperature, or the living&#xA;  temperatures of their source organisms. Their average temperature of&#xA;  maximal stability is 293 ± 8 K (20 ± 8 °C).   The average energetic&#xA;  contribution of the individual amino acids toward protein stability&#xA;  decreases with an increase in protein size.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Analysed in terms of their effect on the protein structure, the ways&#xA;  in which thermophilic organisms obtain relative stabilization of their&#xA;  proteins can be classified as follows:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;increase of compactness and better packing&lt;/li&gt;&#xA;  &lt;li&gt;increase of electrostatic interactions&lt;/li&gt;&#xA;  &lt;li&gt;additional hydrogen bonds&lt;/li&gt;&#xA;  &lt;li&gt;additional disulphide bridges&lt;/li&gt;&#xA;  &lt;li&gt;increasing hydrophobic interactions&lt;/li&gt;&#xA;  &lt;li&gt;protein microenvironment&lt;/li&gt;&#xA;  &lt;li&gt;glycosylation&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;  &#xA;  &lt;p&gt;The rational modification of protein stability is an important goal of&#xA;  protein design. Protein surface electrostatic interactions are not&#xA;  evolutionarily optimized for stability and are an attractive target&#xA;  for the rational redesign of proteins. We show that surface charge&#xA;  mutants can exert stabilizing effects in distinct and unanticipated&#xA;  ways, including ones that are not predicted by existing methods, even&#xA;  when only solvent-exposed sites are targeted. Individual mutation of&#xA;  three solvent-exposed lysines in the villin headpiece subdomain&#xA;  significantly stabilizes the protein, but the mechanism of&#xA;  stabilization is very different in each case. One mutation&#xA;  destabilizes native-state electrostatic interactions but has a larger&#xA;  destabilizing effect on the denatured state, a second removes the&#xA;  desolvation penalty paid by the charged residue, whereas the third&#xA;  introduces unanticipated native-state interactions but does not alter&#xA;  electrostatics. Our results show that even seemingly intuitive&#xA;  mutations can exert their effects through unforeseen and complex&#xA;  interactions.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;These results suggest that surface charge-charge interactions are&#xA;  important for protein stability and that rational optimization of&#xA;  charge-charge interactions on the protein surface can be a viable&#xA;  strategy for enhancing protein stability. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;We have discovered a novel property of single-walled carbon nanotubes&#xA;  (SWNTs)their ability to stabilize proteins at elevated temperatures&#xA;  and in organic solvents to a greater extent than conventional flat&#xA;  supports. Experimental results and theoretical analysis reveal that&#xA;  the stabilization results from the curvature of SWNTs, which&#xA;  suppresses unfavorable protein-protein lateral interactions. Our&#xA;  results also indicate that the phenomenon is not unique to SWNTs but&#xA;  could be extended to other nanomaterials. The protein-nanotube&#xA;  conjugates represent a new generation of active and stable catalytic&#xA;  materials with potential use in biosensors, diagnostics, and bioactive&#xA;  films and other hybrid materials that integrate biotic and abiotic&#xA;  components. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The main chain to side chain salt bridge between the N-terminus and&#xA;  Glu 14 was, however, found to stabilize PFRD-XC4 by 1.5 kcal mol-1.&#xA;  The entropic cost of making a surface salt bridge involving the&#xA;  protein's backbone is reduced, since the backbone has already been&#xA;  immobilized upon protein folding.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2000 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0168165600002364&quot; rel=&quot;nofollow&quot;&gt;Stability and stabilization of globular proteins in solution&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2002 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/bi012154c&quot; rel=&quot;nofollow&quot;&gt;Maximal Stabilities of Reversible Two-State Proteins&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://www.tandfonline.com/doi/pdf/10.1080/02648725.1997.10647944&quot; rel=&quot;nofollow&quot;&gt;Enzyme Thermostabilization: the State of the Art&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.pnas.org/content/110/28/11337.full&quot; rel=&quot;nofollow&quot;&gt;Rational modification of protein stability by targeting surface sites leads to complicated results&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev-biophys-050511-102321&quot; rel=&quot;nofollow&quot;&gt;Disulfide Bonding in Protein Biophysics&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jp111448a&quot; rel=&quot;nofollow&quot;&gt;Methanol Strengthens Hydrogen Bonds and Weakens Hydrophobic Interactions in Proteins – A Combined Molecular Dynamics and NMR study&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022283611002324&quot; rel=&quot;nofollow&quot;&gt;Contribution of Hydrophobic Interactions to Protein Stability&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1997 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022283697910421&quot; rel=&quot;nofollow&quot;&gt;Protein thermal stability, hydrogen bonds, and ion pairs&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2005 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16533916&quot; rel=&quot;nofollow&quot;&gt;Thermal stability of proteins.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2004 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693406/&quot; rel=&quot;nofollow&quot;&gt;Protein structure, stability and solubility in water and other solvents.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2000 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/bi992091m&quot; rel=&quot;nofollow&quot;&gt;Rational Modification of Protein Stability by the Mutation of Charged Surface Residues&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/bi0600143&quot; rel=&quot;nofollow&quot;&gt;Protein Stability and Surface Electrostatics:? A Charged Relationship&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2003 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S002228360300233X&quot; rel=&quot;nofollow&quot;&gt;Contribution of Surface Salt Bridges to Protein Stability: Guidelines for Protein Engineering&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2000 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jf9911949&quot; rel=&quot;nofollow&quot;&gt;Influence of Sucrose on the Thermal Denaturation, Gelation, and Emulsion Stabilization of Whey Proteins&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/la0528450&quot; rel=&quot;nofollow&quot;&gt;Increasing Protein Stability through Control of the Nanoscale Environment&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2000 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/bi992257j&quot; rel=&quot;nofollow&quot;&gt;Contribution of Surface Salt Bridges to Protein Stability&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2003 - &lt;a href=&quot;http://www.pnas.org/content/101/12/4065.short&quot; rel=&quot;nofollow&quot;&gt;Elastic coupling of integral membrane protein stability to lipid bilayer forces&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-11-07T08:15:01.567" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23796" PostTypeId="2" ParentId="23791" CreationDate="2014-11-07T08:24:29.263" Score="3" Body="&lt;p&gt;They can certainly &lt;a href=&quot;http://www.biofilm.montana.edu/resources/pubs/98-025.html&quot; rel=&quot;nofollow&quot;&gt;develop in the toilet&lt;/a&gt;. Just try not to disinfect for a week...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another place is the surface of living organisms, e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Dental_plaque&quot; rel=&quot;nofollow&quot;&gt;dental plaque&lt;/a&gt; or the &lt;a href=&quot;http://www.open-access-biology.com/biofilms/biofilmsch12.pdf&quot; rel=&quot;nofollow&quot;&gt;leaves of a plant&lt;/a&gt;, etc...&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-11-07T08:24:29.263" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23797" PostTypeId="2" ParentId="23793" CreationDate="2014-11-07T08:33:21.747" Score="30" Body="&lt;p&gt;Ripening of bananas (and other fruits) is induced by acetylene and ethylene (Ethyne and Ethene) (see reference 1), which acts as a hormone and induces the ripening process. The incomplete combustion of the leaves produces ethylene, additionally the warmth of the process will help the enzymes as well. There is even a paper about this technique (although it is unfortunately not accessible), see reference 2 for more information. Smoking Chambers are routinely used in this process, see reference 3 and 4.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC549760/&quot; rel=&quot;nofollow&quot;&gt;Role of Ethylene in Fruit Ripening&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://ir.cftri.com/7272/&quot; rel=&quot;nofollow&quot;&gt;Effects of smoking on some physiological changes in bananas.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://agritech.tnau.ac.in/horticulture/fruit_ripening.pdf&quot; rel=&quot;nofollow&quot;&gt;Fruit Ripening&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.thehindu.com/sci-tech/agriculture/technology-for-ripening-fruits-as-important-as-marketing-them/article1991180.ece&quot; rel=&quot;nofollow&quot;&gt;Technology for ripening fruits as important as marketing them&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="9948" LastEditDate="2016-06-07T11:31:28.730" LastActivityDate="2016-06-07T11:31:28.730" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23798" PostTypeId="2" ParentId="23794" CreationDate="2014-11-07T10:18:28.477" Score="2" Body="&lt;p&gt;The comment by @fileunderwater is apt: stress-response-related genes are genes that are activated during stress, such as exposure to heat. In bacteria, for example, there are heat-shock proteins that are involved in keeping the tertiary structure of proteins (folding/3D shape) intact during periods of heat exposure. Genes encoding these heat shock proteins are then called to be upregulated, and you would find them back in a typical micro array experiment. Hope this helps. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-07T10:18:28.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23799" PostTypeId="2" ParentId="23783" CreationDate="2014-11-07T11:20:43.417" Score="2" Body="&lt;p&gt;I concur with @Bez but wish to elaborate on the meaning of 'conserved'. It is generally used in the context of evolution. A conserved characteristic or gene or protein means that it has 'survived' a long time without being altered. As @Bez mentions, certain parts of the protein machinery in eukaryotes is very different from prokaryotes, the latter being considered to have arisen much earlier in evolution. For example, some post-transcriptional processes (e.g. splicing &lt;a href=&quot;http://www.majordifferences.com/2013/10/difference-prokaryotic-and-vs.html#.VFyoRk0cTs0&quot; rel=&quot;nofollow&quot;&gt;and many more differences&lt;/a&gt;) only occur in eukaryotes. But there are many similarities as well, such as the basic use of mRNA etc (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK22531/&quot; rel=&quot;nofollow&quot;&gt;book section&lt;/a&gt;). The latter are examples of conserved mechanisms.  In the context of your question, it means that when you take eukaryotic DNA to express eukaryotic proteins it doesn't really matter which cell or host organism you take as it will be transcribed and folded correctly. For example, yeast is often used to express DNA from higher organisms as its protein synthesis is much the same across various eukaryotic species. However, expressing eukaryotic DNA in prokaryotes likely ends up in misfolded proteins without proper post-transcriptional modification and should be avoided. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to your follow-up question: Folding of proteins happens in the endoplasmatic reticulum (ER) in eukaryotes (&lt;a href=&quot;http://en.wikipedia.org/wiki/Endoplasmic_reticulum&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;), a cell organelle absent in prokaryotes as they lack a nucleus and associated organelles. Again, expression of eukaryotic genes in a prokaryotic expression system will end up in mis-folded proteins.     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To get back to your overall question - the 'signals': DNA transcription, splicing, protein synthesis, post translational modification and folding are all regulated by signals, such as specific DNA codons to start and stop transcription, RNA codes for splicing and start translation and protein tags that are placed on specific amino acid combinations. These signals are well conserved across eukaryotic species.  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-07T12:01:14.297" LastActivityDate="2014-11-07T12:01:14.297" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23801" PostTypeId="1" CreationDate="2014-11-07T13:21:46.170" Score="4" ViewCount="63" Body="&lt;p&gt;I'm looking for suggestions of the mechanistic level at which genotype*sex interactions can occur. These give different phenotypes from the same genotype dependent on the sex they are expressed in. For example, cis-acting sex-specific modifiers can affect gene expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What other mechanisms can create a gene*sex interaction?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2015-03-02T10:35:17.243" LastActivityDate="2015-03-02T10:35:17.243" Title="Mechanisms of genotype*sex interactions" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;population-genetics&gt;&lt;molecular-evolution&gt;&lt;quantitative-genetics&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ClosedDate="2015-03-29T18:49:04.403" ContentLicense="CC BY-SA 3.0" />
  <row Id="23802" PostTypeId="2" ParentId="23276" CreationDate="2014-11-07T14:09:58.943" Score="1" Body="&lt;p&gt;Interesting question. I concur with @Chris. Color constancy and size constancy are neural mechanisms and can therefore be imposed on visual input from the retina. In contrast, a blurry input cannot be neurally improved. As an analogy: Visual perceptions are processed and rendered by the brain and therefore represent &quot;photoshopped&quot; perceptions. In other words, perceptions are subjective representations manufactured by higher-level visual processing. However, focus is determined by optics. An out-of-focus picture, to push the analogy, cannot be fixed by fotoshop, nor the brain.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-06T11:47:04.897" LastActivityDate="2014-12-06T11:47:04.897" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23805" PostTypeId="1" CreationDate="2014-11-07T16:30:05.330" Score="2" ViewCount="256" Body="&lt;p&gt;I am currently working on a new tool for the analysis of (large) weighted networks. Association matrices (correlation matrices) as obtained from fMRI &lt;a href=&quot;http://www2.warwick.ac.uk/fac/sci/statistics/staff/academic-research/nichols/presentations/gsk-neurophysics/Vertes_GraphTheory.pdf&quot; rel=&quot;nofollow&quot;&gt;data&lt;/a&gt; are perfect examples of the kind of data I am looking for. Unfortunately I am only able to locate raw fMRI data and the task of converting them is way outside my expertise. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone point me to a place where such converted data can be found, or where I can download software which automatically converts the data? Preferably a dataset divided into control/disease. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="1576" LastEditorUserId="3340" LastEditDate="2014-11-26T12:09:26.343" LastActivityDate="2015-01-27T09:32:05.977" Title="Converting fmri data to association matrix" Tags="&lt;neuroscience&gt;&lt;network&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23806" PostTypeId="1" AcceptedAnswerId="23807" CreationDate="2014-11-07T16:42:36.560" Score="6" ViewCount="143" Body="&lt;p&gt;I am not sure if this is the right place to ask this question, but I guess that ornithology enthusiasts (or ornithologists) will have the best knowledge about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering if there is a website which would identify birds by their looks. For example, I would specify that the bird is similar to a sparrow in size (just a little bigger), it has a gray back and yellow-ish-orange-ish belly and it would tell me the exact species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does such a website exist?&lt;/p&gt;&#xA;" OwnerUserId="10098" LastActivityDate="2014-11-07T16:51:03.177" Title="A website for identifying birds" Tags="&lt;ornithology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23807" PostTypeId="2" ParentId="23806" CreationDate="2014-11-07T16:51:03.177" Score="7" Body="&lt;p&gt;There are actually a few, the problem with these websites is that they usually cover only a part of all birds on this planet. I use:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.rspb.org.uk/discoverandenjoynature/discoverandlearn/birdidentifier/&quot;&gt;Bird identifier&lt;/a&gt;: Usefull website for a lot of European birds.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://animals.nationalgeographic.com/animals/birding/backyard-bird-identifier/&quot;&gt;Backyard Bird Identifier&lt;/a&gt;: Useful for some European birds but&#xA;mostly for North American and Canadian birds.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.allaboutbirds.org/Page.aspx?pid=1189&quot;&gt;All about Birds&lt;/a&gt;: Useful, but needs more knowledge for the identification&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;What I also do is using Google with a description of the bird, which sometimes works surprisingly well.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-11-07T16:51:03.177" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23808" PostTypeId="1" AcceptedAnswerId="23815" CreationDate="2014-11-07T17:12:40.543" Score="3" ViewCount="228" Body="&lt;p&gt;Does eyesight primarily deteriorate 'naturally' due to genetics (genomic/epigenomic factors), or due to external factors such as normal wear and tear, or disease? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By normal wear and tear I include things like repetitive straining of the eyes by reading small text in a dim room night after night.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a background to my question: By dissecting the causes of visual deterioration into genetic factors versus external factors I hope to relate those causes to the age of onset, and rate of decay of visual acuity. &lt;/p&gt;&#xA;" OwnerUserId="10095" LastEditorUserId="9943" LastEditDate="2014-11-12T04:06:56.623" LastActivityDate="2014-11-12T04:06:56.623" Title="Do human visual functions degenerate due to genetic factors or by external factors?" Tags="&lt;genetics&gt;&lt;physiology&gt;&lt;human-anatomy&gt;&lt;vision&gt;&lt;epigenetics&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23810" PostTypeId="2" ParentId="23709" CreationDate="2014-11-07T17:41:58.247" Score="3" Body="&lt;p&gt;From what I can tell, &lt;strong&gt;marine mammals can't dynamically control buoyancy during a dive&lt;/strong&gt;. They ease the beginning of the dive by starting with a small lung volume to reduce buoyancy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pinnipeds like seals do this by &lt;a href=&quot;http://en.wikipedia.org/wiki/Pinniped#Diving_adaptations&quot; rel=&quot;nofollow&quot;&gt;exhaling half their breath before diving&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Deep-diving whales actually &lt;a href=&quot;http://bio.classes.ucsc.edu/bio131/Thometz%20Website/Ponganis%202011%20Diving%20Mammal%20Review.pdf&quot; rel=&quot;nofollow&quot;&gt;breathe in before diving&lt;/a&gt;, but their &lt;a href=&quot;http://www.catalyststudent.org.uk/dl/14429127b24f101e437528772fcc3a94b4508002/272-catalyst_22_2_500.pdf&quot; rel=&quot;nofollow&quot;&gt;lungs are small relative to body size&lt;/a&gt; to begin with. This makes their surface buoyancy weak enough to swim against without great difficulty (unlike humans).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As they dive their lungs compress rapidly with depth:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;V = Vs / (1 + D/10)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;V&lt;/code&gt; is lung volume, &lt;code&gt;Vs&lt;/code&gt; is lung volume at surface, and &lt;code&gt;D&lt;/code&gt; is depth in meters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At 90m, the lungs are already at 10% original volume. Pretty soon they've shrunk enough that their effect on buoyancy is negligible compared to the density of the incompressible tissues. Presumably, these are close to neutrally buoyant (though the fact that dead whales sink suggests that they're slightly negatively buoyant).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks to @souvik-bhattacharya for the ucsc.edu link.&lt;/p&gt;&#xA;" OwnerUserId="10055" LastEditorUserId="10055" LastEditDate="2014-11-07T17:56:18.933" LastActivityDate="2014-11-07T17:56:18.933" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23813" PostTypeId="1" AcceptedAnswerId="23833" CreationDate="2014-11-07T19:09:49.113" Score="2" ViewCount="50" Body="&lt;p&gt;If a liver cancer, for example, gives metastases. Will metastatic cells still have liver identity? I mean, if we mark liver cells, will we see the cancer cells too?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks a lot!&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="4747" LastEditDate="2014-11-08T21:04:50.507" LastActivityDate="2014-11-09T03:11:40.413" Title="Do metastatic cells still have their parent's identity?" Tags="&lt;cancer&gt;&lt;liver&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23814" PostTypeId="2" ParentId="2698" CreationDate="2014-11-07T19:19:21.010" Score="3" Body="&lt;p&gt;I realize this is an older topic, but I'd like to clarify some misconceptions:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1)  DAPI is usually referred to as a semi membrane-permanent dye because its penetration through viable cell membranes is concentration dependant.  At lower concentrations it is mostly excluded from viable cells, while at higher concentrations it stains live and dead cells about equally.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2)  Hoechst comes in both membrane permanent and impermanent varieties.  Make sure you order the correct one for your application!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3)  It is not necessarily true that Hoechst is preferred for viable cells.  Hoechst has very slow diffusion through thick tissue for instance, so for in vivo imaging applications (or in tissue sections), DAPI often stains viable cells much better than the (much heavier) 33342 because it is better able to diffuse through tissue.  For isolated cells however, Hoechst 33342 can much more rapidly stain viable nuclei (seconds vs. minutes for DAPI).  &lt;/p&gt;&#xA;" OwnerUserId="9561" LastActivityDate="2014-11-07T19:19:21.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23815" PostTypeId="2" ParentId="23808" CreationDate="2014-11-07T19:36:26.817" Score="4" Body="&lt;p&gt;Vision deteriorates for both reasons, but I'm not quite sure how to separate the effects of aging from &lt;em&gt;wear and tear&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cataracts are the leading cause of blindness in the world. Ways in which environment (which falls under the category of wear and tear in my book) affects cataract formation: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;UV light: people living at high altitudes (e.g. Tibet) have more cataracts 2° to increased UV light than those at lower altitudes (sunglasses with UV protection delays the process)&lt;/li&gt;&#xA;&lt;li&gt;lead exposure increases cataract formation.&lt;/li&gt;&#xA;&lt;li&gt;infections in infancy and childhood (rubella, toxoplasmosis, other)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Macular degeneration is another cause of vision loss. Environmental factors include:  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;smoking: speeds up age related macular degeneration.&lt;/li&gt;&#xA;&lt;li&gt;diet: diets low in antioxidants, and obesity increase degeneration.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Retinal damage caused by diabetic retinopathy:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Juvenile onset diabetes has long been thought to be associated with viral infections from coxsackievirus B, cytomegalovirus, adenovirus, rubella, and mumps.&lt;/li&gt;&#xA;&lt;li&gt;Type II diabetes is influences by obesity, lack of exercise, certain medications, (nicotinic acid, some diuretics, anti-epileptics, psychiatric drugs, and drugs to treat HIV (can impair beta cells or disrupt insulin action); Pentamidine (used to treat a type of pneumonia) can cause pancreatitis and diabetes; glucocorticoids/steroid hormones may impair insulin action. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Corneal opacities:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;infections: (Chlamydia trachomatis) bacteria that are spread by close contact with an infected person or by flies, especially common in Africa.  &lt;/li&gt;&#xA;&lt;li&gt;recurrent injury (soot and pathogens from indoor smoke, a dusty, windy environment).  &lt;/li&gt;&#xA;&lt;li&gt;vitamin A deficiency&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Nearsightedness:&#xA;- near-point work: reading, working with a computer all day, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glaucoma:&#xA;- diabetes, obesity, near-point work, other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nonenvironmental causes would be genetics and illnesses associated with aging.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;genetic predispositions associated with diabetes, nearsightedness and farsightedness&lt;/li&gt;&#xA;&lt;li&gt;decreased lens plasticity with age&lt;/li&gt;&#xA;&lt;li&gt;strokes secondary to hypertension, etc.&lt;/li&gt;&#xA;&lt;li&gt;amblyopia (“lazy eye”), strabismus (when eyes are aligned in different directions), astigmatisms &lt;/li&gt;&#xA;&lt;li&gt;hereditary causes of glaucoma and age-related macular degeneration&lt;/li&gt;&#xA;&lt;li&gt;retinitis pigmentosa, (degenerative disease of the retina)&lt;/li&gt;&#xA;&lt;li&gt;innumerable genetic disorders (Marfan's, Tay-Sachs, Albinism, Cone-rod dystrophy, various autoimune disorders, etc. &lt;/li&gt;&#xA;&lt;li&gt;retinoblastoma&lt;/li&gt;&#xA;&lt;li&gt;predisposition to glaucoma&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1314944/&quot; rel=&quot;nofollow&quot;&gt;Focusing on Vision Through an Environmental Lens&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt; &lt;a href=&quot;http://www.afb.org/info/about-afb/glossary-of-eye-conditions/25&quot; rel=&quot;nofollow&quot;&gt;Glossary of Eye Conditions&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt; &lt;a href=&quot;http://diabetes.niddk.nih.gov/dm/pubs/causes/&quot; rel=&quot;nofollow&quot;&gt;Causes of Diabetes&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt; &lt;a href=&quot;https://my.clevelandclinic.org/health/diseases_conditions/inherited_eye_disease&quot; rel=&quot;nofollow&quot;&gt;Inherited Eye Disease&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-11-07T19:36:26.817" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23817" PostTypeId="1" CreationDate="2014-11-07T21:53:46.073" Score="3" ViewCount="3709" Body="&lt;p&gt;The human brain is the most complicated human organ so it is hard to examine it completely but based on what we know do you think (or do you know from some source) if a human memory can be removed by emp(electromagnetic pulse) ? (If so do you think it would be pernament or temporary?)&lt;/p&gt;&#xA;" OwnerUserId="10111" LastActivityDate="2015-05-02T06:35:54.723" Title="Can human brain memory be removed by EMP?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;memory&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23818" PostTypeId="1" AcceptedAnswerId="23906" CreationDate="2014-11-07T21:54:49.913" Score="8" ViewCount="320" Body="&lt;p&gt;Let's say I have a DNA sequence with the following structure:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ 5' - N_n - S_1 - N_{1000} - S_2 - N_{1000} - S_3 - N_n - 3' $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here, the $N$s represent stretches of arbitrary sequence of the indicated length. $S_1$, $S_2$ and $S_3$ are all unique sequences 20 bp in length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I design a forward primer &lt;code&gt;PF&lt;/code&gt; that anneals to the positive strand at $S_1$. I design two reverse primers &lt;code&gt;PR1&lt;/code&gt; and &lt;code&gt;PR2&lt;/code&gt; that anneal to the negative strand at $S_2$ and $S_3$ respectively. Their annealing temperatures are reasonably close.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clearly, &lt;code&gt;PF&lt;/code&gt; and &lt;code&gt;PR1&lt;/code&gt; together will produce a 1040 bp PCR product, and &lt;code&gt;PF&lt;/code&gt; with &lt;code&gt;PR2&lt;/code&gt; will produce a 2060 bp product.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now let's say I add 0.2 μM &lt;code&gt;PF&lt;/code&gt; (standard concentration), 0.1 μM &lt;code&gt;PR1&lt;/code&gt; and 0.1 μM &lt;code&gt;PR2&lt;/code&gt; &lt;em&gt;all in the same reaction&lt;/em&gt;. I then run a PCR, with extension time sufficient for the 2 kb product.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can see the following possible outcomes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I get a 50/50 mix of 1 kb and 2 kb products.&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;PR1&lt;/code&gt; competes aggressively and I get hardly any 2 kb product and a lot of 1 kb product.&lt;/li&gt;&#xA;&lt;li&gt;After a few cycles, the 1 kb product that has accumulated serves as an efficient forward primer for &lt;code&gt;PR2&lt;/code&gt;, and I end up getting mostly 2 kb product and little 1 kb product.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Which one will happen? If it depends, what are the major factors &lt;em&gt;on which&lt;/em&gt; it depends? Primer concentrations, extension time, annealing temperature, dNTP amount, number of cycles?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question is basically a very simplified multiplex PCR. While much has been written about practical applications of multiplex PCR, I am hoping that answers will help me understand the considerations that go into deducing optimal multiplex PCR conditions without doing any empirical calibration. This isn't to circumvent the calibration, but to understand the process conceptually.&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="3340" LastEditDate="2014-11-10T10:27:17.283" LastActivityDate="2015-04-27T04:52:36.150" Title="Basic question about multiplex PCR" Tags="&lt;biochemistry&gt;&lt;pcr&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23819" PostTypeId="1" AcceptedAnswerId="23821" CreationDate="2014-11-07T23:56:11.173" Score="0" ViewCount="89" Body="&lt;p&gt;It is debated if omega-3 polyunsaturated fatty acids (N3PUFa) may be effective in preventing AF (atrial fibrillation), meta-analysis &lt;a href=&quot;http://www.mayoclinicproceedings.org/article/S0025-6196(13)00080-3/pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, much less has been considered this: &lt;strong&gt;Do N3-PUFAs prevent acute symptoms of periodic Atrial fibrillation?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The meta-analysis concentrate only in the long-term effects of prevention. &#xA;My proposal focuses on the short-term i.e. the fact that the user can recognise AF first and then uses N3-PUFAs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please, assume that there is a validation method by which the user can easily detect that he has AF - he does this if he suspect it, i.e. feels special discomfort and special wave-like-pain the chest. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;He takes each time in this case 20 ml of Müller omega-3 oil which has also vitamin D. &#xA;The effect of recovering is immediate in prophylaxis.&#xA;Assume the user has less than &amp;lt; 20 ng/ml vitamin D in blood each case, most of the time, 9 ng/ml so avitaminosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My conjecture is that N3-PUFAs can prevent the acute symptoms of periodic AF. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can N3-PUFAs prevent the acute symptoms of periodic AF?&lt;/strong&gt;&#xA;What is the role of vitamin D here? &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-26T09:22:56.557" LastActivityDate="2014-12-26T09:22:56.557" Title="Can Omega 3 Fatty Acids prevent chest pain in periodic Atrial Fibrillation?" Tags="&lt;biochemistry&gt;&lt;cardiology&gt;&lt;fat-metabolism&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23820" PostTypeId="2" ParentId="23817" CreationDate="2014-11-08T00:29:48.717" Score="10" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Electromagnetic_pulse&quot;&gt;http://en.wikipedia.org/wiki/Electromagnetic_pulse&lt;/a&gt; mentions the following natural sources of EMP, which I have ordered by frequency / period, from the shortest to the longest:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Electrostatic discharge from objects coming into contact (normally too small to be of any concern)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Lightning (milliseconds)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Solar flares (hours.) Such flares cause geomagnetic storms (more on this later.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Several artificial sources of EMP are mentioned, of which the only ones of interest are military:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Non-nuclear weapons. The page links to a general article on directed-energy weapons, which mentions microwave devices for causing pain and for targeted damaging of electronic equipment. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Nuclear weapons. &lt;a href=&quot;http://fas.org/nuke/intro/nuke/emp.htm&quot;&gt;http://fas.org/nuke/intro/nuke/emp.htm&lt;/a&gt; gives more information on this, listing three phases.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The EMP produced by the Compton electrons typically lasts for about 1 microsecond, and this signal is called HEMP. In addition to the prompt EMP, scattered gammas and inelastic gammas produced by weapon neutrons produce an “intermediate time” signal from about 1 microsecond to 1 second. The energetic debris entering the ionosphere produces ionization and heating of the E-region. In turn, this causes the geomagnetic field to “heave,” producing a “late-time” magnetohydrodynamic (MHD) EMP generally called a heave signal.  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The same reference also indicates:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...the region where the greatest damage can be produced is from about 3 to 8 km from ground zero. In this same region structures housing electrical equipment are also likely to be severely damaged by blast and shock.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As far as I am aware, memory loss was not a major recorded symptom among the survivors of Hiroshima and Nagasaki. The only recent data for sufferers of EMP would be from victims of lightning stikes. While the frequency spectrum is admittedly different from nuclear weapons, victims of lightning strikes are surely subjected to greater magnitudes of EMP than those who managed to survive nuclear bombings (who suffered many other traumas, such as blast waves and radiation.) Those who survive the immediate physical (burns) and neurological (cardiac arrest) effects of lightning strikes must surely be knocked unconscious and be disorientated when they regain consciousness. But again, I am not aware of medium or long term memory loss being a particular symptom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is worth comparing the structure of the brain (a fairly homogenous mass of tissue of high water content, relatively conductive) with the structure of electronic equipment (components of ever smaller size and greater resistance in order to save power, surrounded by a nonconductive medium such as air, and interconnected by wires, which serve to channel voltage.) It is unsurprising that the brain is less subsceptible to electrostatic damage than electronic components (electronics workers have to take precautions in order to avoid damaging sensitive components with static discharges from their bodies and clothing.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most widespread damage to equipment caused by EMP is from the long-period pulses, which are channeled by electric cables. These act over distances much larger than the size of the human body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the last reference:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...distortion of the geomagnetic field was observed worldwide in the case of the STARFISH test. ... the signal from this process is not large, but systems connected to long lines (e.g., power lines, telephone wires, and tracking wire antennas) are at risk&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first recorded EMP incident ... nuclear test over the South Pacific ... resulted in power system failures as far away as Hawaii.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Geomagnetic_storm&quot;&gt;http://en.wikipedia.org/wiki/Geomagnetic_storm&lt;/a&gt; mentions cases of damage caused by long period EMP, including electric shocks suffered by telegraph operators during solar flare events.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in conclusion, any amnesia caused by EMP is likely to be caused by normal biological shock mechanisms to individuals unfortunate enough to be electrocuted, and not by any direct electrical effect on the brain itself.&lt;/p&gt;&#xA;" OwnerUserId="9036" LastEditorUserId="9036" LastEditDate="2014-11-08T12:44:18.420" LastActivityDate="2014-11-08T12:44:18.420" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23821" PostTypeId="2" ParentId="23819" CreationDate="2014-11-08T04:47:05.710" Score="3" Body="&lt;p&gt;Omega 3 Fatty Acids cannot prevent the the acute symptoms of periodic A Fib, nor is there a role for vitamin D in the treatment of acute symptoms of periodic AF.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Atrial Fibrillation with the symptom of chest pain is very worrisome and requires urgent or emergent treatment. The most common treatments are heart rate control via IV antiarrhythmics, or cardioversion, either electrical or chemical, usually done in the emergency room. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There has never been a study wherein AFib accompanied by symptoms of chest pain was treated by Omega 3 Polyunsaturated Fatty Acids and there never will be, because N3PUFA does not cardiovert arrhythmias nor does it effect heart rate in AFib.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No medical body of any kind would support such a study. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, there is no convincing evidence that N3PUFAs decrease the incidence of AFib, and this has been studied often, because eating 4-5 servings of fish per week &lt;em&gt;has&lt;/em&gt; been shown to have a beneficial effect on A Fib. That gives reason to hope that N3PUFA supplements might be similarly beneficial. However:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The role of omega-3 polyunsaturated fatty acids in the setting of AF is controversial. Although some studies demonstrate a lower incidence of AF recurrence with omega-3 polyunsaturated fatty acids use, others have shown an &lt;em&gt;increased risk&lt;/em&gt;. Further studies are needed to assess the role of N3-PUFAs in the prevention of AF.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If N3PUFAs have not been proven to help AFib long term, there is no hope whatsoever that studies will be undertaken to shown their effect in the acute treatment of symptomatic AFib, which is the scenario you have described.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;Atrial Fibrillation becomes symptomatic when the arrhythmia results in decreased perfusion of various organs. If there is decreased perfusion to the heart, the presenting symptoms may be of ischemia (usually chest pain or pressure) or shortness of breath due to decreased cardiac output and decreased oxygenation in the lungs. If it is severe enough, fainting may occur from decreased blood pressure, and decreased perfusion of the brain. If it is not severe, it may result in a sensation of &lt;em&gt;flip-flopping&lt;/em&gt; in the chest, or palpitations (irregular, thumping, or pounding heartbeats). There are other symptoms of A Fib but since you mentioned chest pain, I won't elaborate.&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://www.mayoclinicproceedings.org/article/S0025-6196%2813%2900080-3/pdf&quot; rel=&quot;nofollow&quot;&gt;Atrial Fibrillation in the 21st Century: A Current Understanding of Risk Factors and Primary Prevention Strategies&lt;/a&gt;&lt;/sub&gt; &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-11-08T08:31:37.070" LastActivityDate="2014-11-08T08:31:37.070" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23822" PostTypeId="1" CreationDate="2014-11-08T04:56:41.240" Score="1" ViewCount="55" Body="&lt;p&gt;Is there a single word, or brief phrase, that denotes the state of the total genetic machinery (genome + transcriptome + proteome + ...) of a cell or organ or organism at a particular point in time?&lt;/p&gt;&#xA;" OwnerUserId="10110" LastActivityDate="2014-11-09T12:45:49.347" Title="Word denoting genetic state" Tags="&lt;genetics&gt;&lt;gene-expression&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23823" PostTypeId="1" CreationDate="2014-11-08T09:11:59.943" Score="2" ViewCount="60" Body="&lt;p&gt;Drug resistance can arise through a number of mechanisms. For instance, EGFR mutation when treating with EGFR inhibitors, or compensatory activation of alternative survival pathways. But does it occur at the level of a single cell, or would it be a population effect? In other words, would cells exposed to e.g. targeted kinase inhibitors slowly compensate with other pathways (and that would happen in every such cell) or would there be a sub-population of cells that is sensitive to inhibitors and another subpopulation inherently resistant and predisposed towards amplifying other pathways.&lt;/p&gt;&#xA;" OwnerUserId="10112" LastActivityDate="2016-11-22T22:34:02.810" Title="Tumour resistance: single-cell or population effect?" Tags="&lt;cancer&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23824" PostTypeId="1" CreationDate="2014-11-08T09:36:11.990" Score="7" ViewCount="27024" Body="&lt;p&gt;Amino acids with non‐ionizable side chains are zwitterions when they are at physiological pH, pH 7.4. This is what my book says. But I do not understand why. The Pka for a carboxyl group is around 3 and the pKa for an amino group is around 9. So the isoelectric point should be around ( 9+3) /2 = 6 for an amino acid with no ionizable side chain. At pH 7.4 it would be slightly negative, would it not?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also what exactly is a basic amino acid? Is that an amino acid that has a PI value of more than 7?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="10114" LastEditorUserId="5144" LastEditDate="2014-11-08T23:31:27.623" LastActivityDate="2016-12-21T21:26:36.007" Title="How are amino acids neutral at physiological pH?" Tags="&lt;amino-acids&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23826" PostTypeId="2" ParentId="23824" CreationDate="2014-11-08T13:53:59.477" Score="1" Body="&lt;p&gt;At pH 7.4 a carboxyl group is mostly present as COO&lt;sup&gt;-&lt;/sup&gt;, while an amino group is present as NH&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;. So when a molecule has both groups, such as an amino acid, the molecule as a whole is neutral. As it is a Zwitterion (equal + and - charges) the hydrogen can also flip flop between amino and carboxyl group. Making the molecule 'truly' neutral as both groups are not charged.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A basic amino acid has a basic group such as an amino group (Arginine) on its side chain.   &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="948" LastEditDate="2014-11-08T20:06:44.467" LastActivityDate="2014-11-08T20:06:44.467" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23827" PostTypeId="1" CreationDate="2014-11-08T15:31:49.327" Score="1" ViewCount="32" Body="&lt;p&gt;I have been cracking my fingers for 2-3 years and on the first year I was told that I'm going to get arthritis because of it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been researching this since the first year and I've never gotten an answer. Most people say either Yes, No or I don't know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Arthritis is mainly cause by bones rubbing together and cracking fingers is just air sockets poping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've asked my biology teacher and he said that he's not sure. He then explained to me that the cracking sound from people cracking their fingers is just air sockets poping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So can finger cracking cause arthritus?&lt;/p&gt;&#xA;" OwnerUserId="10115" LastActivityDate="2014-11-08T15:31:49.327" Title="Can cracking fingers cause Arthritis?" Tags="&lt;joints&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2014-11-08T23:44:28.930" ContentLicense="CC BY-SA 3.0" />
  <row Id="23828" PostTypeId="2" ParentId="23824" CreationDate="2014-11-08T16:00:57.813" Score="3" Body="&lt;p&gt;You are right, most of the amino acids have pI around 6, so they are slightly negative at pH 7.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.elcamino.edu/faculty/pdoucette/calculating-approximate-isoelectric-points.pdf&quot; rel=&quot;nofollow&quot;&gt;Calculating approximate isoelectric points for amino acids and peptides&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The isoelectric point depends on the amino and carboxylic-acid groups and the groups of the side chain. E.g. lysine has an amino group on the side chain, so it has a pI of 9.74.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-11-08T16:00:57.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23829" PostTypeId="2" ParentId="14063" CreationDate="2014-11-08T20:24:30.447" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Catalysis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Catalysis&lt;/a&gt; is about reducing the free energy barrier (aka. &lt;a href=&quot;http://en.wikipedia.org/wiki/Activation_energy&quot; rel=&quot;nofollow noreferrer&quot;&gt;activation energy&lt;/a&gt;) of a reaction, so it does not require any energy. In photolysis (e.g. splitting water) you get the energy from the absorbed photons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact process is called the Joliot-Kok cycle:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mCTlk.gif&quot; alt=&quot;Kok cycle&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 1 - Joliot-Kok cycle - &lt;a href=&quot;http://www.life.illinois.edu/crofts/bioph354/lect25.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So the photon separates the charges on the P680, after that the activated P680 activates the Yz intermedier, which forces the enzyme to the next step (Sx) in the reaction. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.protein.bio.msu.ru/biokhimiya/contents/v77/full/77091144.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Transmembrane Electric Potential Difference in the Protein–Pigment Complex of Photosystem 2&lt;/a&gt;  &lt;/li&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://www.chm.bris.ac.uk/motm/oec/motmc.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Manganese-calcium oxide cluster of Photosystem II and its assimilation by the Cyanobacteria&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The overall process comprises three types of reaction sequences: (a)&#xA;  light-induced charge separation leading to formation of the radical&#xA;  ion pair P680+&lt;em&gt;QA(-&lt;/em&gt;) ; (b) reduction of plastoquinone to plastoquinol&#xA;  at the QB site via a two-step reaction sequence with QA(-&lt;em&gt;) as&#xA;  reductant and (c) oxidative water splitting into O2 and four protons&#xA;  at a manganese-containing catalytic site via a four-step sequence&#xA;  driven by P680+&lt;/em&gt; as oxidant and a redox active tyrosine YZ acting as&#xA;  mediator.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2007 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17634752&quot; rel=&quot;nofollow noreferrer&quot;&gt;Photosystem II: structure and mechanism of the water:plastoquinone oxidoreductase.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So the process does not involve ATP or NAD or something like that just the &quot;redox active tyrosine YZ&quot;. ATP and NADPH are created after the PS2 part of photosynthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Lx4NR.png&quot; alt=&quot;light-dependent reactions of photosynthesis&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 2 - Light-dependent reactions of photosynthesis - electron transport chain - &lt;a href=&quot;http://cambridgecapp.wordpress.com/improving-photosynthesis/photosynthesis/light-dependent-reactions-of-photosynthesis/&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The photolysis of water is about storing the energy coming from the photons (light) in ATP and NADPH. In the Calvin cycle the cells use the stored energy to reduce CO2 into carbohydrates. For instance glucose can be delivered to the cells in the root, which can use it as food. &lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-11-08T21:18:51.370" LastActivityDate="2014-11-08T21:18:51.370" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23830" PostTypeId="1" CreationDate="2014-11-08T20:54:48.567" Score="2" ViewCount="149" Body="&lt;p&gt;I am extremely interested in science in general and in particular biology. Due to a different choice of career-path I probably will not be learning any more biology anytime soon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I would love to get my hands on a comprehensive textbook biology which hopefully will enable a goal in lifelong learning of biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are some good recommendations? I looked up biology textbooks on Google and found candidates such as &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0321831543&quot; rel=&quot;nofollow&quot;&gt;Campbell Biology&lt;/a&gt; by Reece and &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0321831543&quot; rel=&quot;nofollow&quot;&gt;Biology&lt;/a&gt; by Brooker. But as there are so many of them, I have no clue which one to get.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, biologists of stackexchange, can you help me out? &lt;/p&gt;&#xA;" OwnerUserId="10117" LastActivityDate="2014-11-09T04:26:39.460" Title="Searching for comprehensive textbook" Tags="&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23831" PostTypeId="2" ParentId="23824" CreationDate="2014-11-08T22:05:44.367" Score="2" Body="&lt;p&gt;If an amino acid has two amino groups and only one carboxyl group (like arginine and lysine), then they are positively charged (++ vs. -) at neutral pH. On the other hand, if amino acids have two carboxyl groups and only one amino group (like glutamic acid and aspartic acid), they are negatively charged at pH7 (-- vs. +). You are not correct that the groups are truly neutral. The carboxyl group is negatively charged in a solution much higher than the pKa of the carboxyl group (which is pH 2.48 for arginine). Same is true for the amino groups (pKb is at pH 11.5 for arginine). So, at pH 9.5, the ratio of the positively charged amino group to a neutral amino group is 100:1 (at the pKb it would be 50:50). At a pH of 4.48, the carboxyl group of arginine would be 1:100 negatively charged, versus neutral. So, at pH7, all of the carboxyl group is negatively charged (COO-) and all of the amino groups (2 of them) are fully positively charged (NH3+). Net charge is plus 1, in the case of arginine at pH7.&lt;/p&gt;&#xA;" OwnerUserId="10118" LastActivityDate="2014-11-08T22:05:44.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23833" PostTypeId="2" ParentId="23813" CreationDate="2014-11-09T03:11:40.413" Score="2" Body="&lt;p&gt;Welcome to stack. This is a good question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question: Generally, yes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Howeve like @user137 stated below it can depend on many factors most notably how many division cycles they go through, and also where they metastasize to. The immediate environment of a cell is very effective at altering gene expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I use Hepg2 cells regularly. These are hepatocellular carcinoma cells that can be cultured. These cells are known to express 3-hydroxy-3-methylglutaryl-CoA reductase and hepatic triglyceride lipase, two enzymes characteristically highly expressed in liver cells. If we want to do a quick quality control typing we will perform rtPCR for those enzymes. I have seen the expression drop off after about 4 months (~35 passages). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at gene expression (ideally through microarray) is a very valid way to identify/type a cells tissue of origin.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-11-09T03:11:40.413" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23834" PostTypeId="1" CreationDate="2014-11-09T03:13:03.163" Score="1" ViewCount="2680" Body="&lt;p&gt;What are best practices for naming newly created plasmids?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, a common format is &lt;code&gt;pABC123&lt;/code&gt;. What is the exact specification? Must there be 3 letters?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What databases of plasmid names exist? How much care is taken to avoid name &lt;a href=&quot;https://en.wikipedia.org/wiki/Collision_%28computer_science%29&quot; rel=&quot;nofollow&quot;&gt;collisions&lt;/a&gt;?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-11-09T03:34:02.763" Title="What are the rules for plasmid names?" Tags="&lt;synthetic-biology&gt;&lt;nomenclature&gt;&lt;plasmids&gt;&lt;database&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23835" PostTypeId="2" ParentId="23834" CreationDate="2014-11-09T03:20:13.963" Score="1" Body="&lt;p&gt;One of the most common methods (described by &lt;a href=&quot;http://blog.addgene.org/plasmids-101-how-to-name-your-plasmid-in-3-easy-steps&quot; rel=&quot;nofollow&quot;&gt;AddGene&lt;/a&gt;) is &lt;code&gt;p&lt;/code&gt; (for plasmid), followed by the name of the backbone, a dash, and inserts delimited by more dashes. From this we get things like: &lt;code&gt;pBluescript-CMV-mACT1-GFP&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another method which I prefer is to name all your plasmids in the format given in the question: &lt;code&gt;pABC123&lt;/code&gt;. Here &lt;code&gt;ABC&lt;/code&gt; is a 3 letter designation that the researcher should consistently use for every plasmid they create (often their initials), and the numbers are sequential (padded with zeros for better sorting by programs).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AddGene is one of the largest plasmid repositories out there. Unfortunately, collisions are a common problem - you should always search the name of a plasmid before assuming things based on the name. While the above two strategies help reduce the odds of collision, there are very few 3 letter combinations that haven't been taken.&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-11-09T03:34:02.763" LastActivityDate="2014-11-09T03:34:02.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23836" PostTypeId="2" ParentId="23834" CreationDate="2014-11-09T03:32:11.660" Score="2" Body="&lt;p&gt;So there are no rules per say (although I wish there were). But there are commonalities among plasmid names and they can help people identify them:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Include the empty backbone name in your plasmid name. This simple piece of information can often convey many important details. Once you know the backbone a plasmid is based on, you can usually derive: a) the bacterial antibiotic resistance, b) the promoter that drives the insert, and c) any other selection markers (for use in other cell types, e.g. eukaryotic cells).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Include information about the insert in your plasmid name. This is often a 3-6 letter representation of the gene (or DNA sequence).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Often researchers will add a lower case letter to the beginning of their insert abbreviation to specify what species it is. Example: ‘h’ is for Human (&lt;em&gt;homo sapiens)&lt;/em&gt;, ‘m’ is for mouse (&lt;em&gt;mus musculus)&lt;/em&gt;, ‘r’ is for rat (&lt;em&gt;rattus rattus or rattus norvegicus&lt;/em&gt;), etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Add any tags or fusions that are on your insert. Typically you would list any tag or fusion protein in the order they appear in the plasmid and their relative position to the insert. Example, if you have a Flag tag on the N-terminal of your insert, you would list it first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;e.g.   pBACKBONE-Flag-hGene&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there was also an EGFP fused to the C-terminal of your insert you would list it after the insert.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;pBACKBONE-Flag-hGene-EGFP&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your insert contains a mutation or modifcation, this should be included in the plasmid name.  Mutations are generally listed as the amino acid change and not a nucleotide change. The proper way to denote an amino acid mutation is to list the one letter abbreviation of the wild type amino acid immediately followed by its position (number) relative to the start Methionine (Met) followed by the one letter abbreviation of the mutated amino acid currently at that position.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Check for more information at &lt;a href=&quot;https://www.addgene.org/&quot; rel=&quot;nofollow&quot;&gt;Addgene.com&lt;/a&gt; they are the largest plasmid repository in the world.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By collisions I'm guessing you mean naming your plasmid something that is already &quot;taken.&quot; This is a benefit of submitting to a repository, they will ensure this doesn't happen.if your planning on filing a patent, your parent attorney will do it. &lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-11-09T03:32:11.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23837" PostTypeId="2" ParentId="23830" CreationDate="2014-11-09T03:32:17.980" Score="1" Body="&lt;p&gt;Try Campbell biology.....it covers almost all the topics under biology in a lucid way...also the book has packed quite a volume of info in it ranging from a beginner level to a fairly advanced level....excellent book also in matters of presentation &amp;amp; writing style so that one won't feel bored....&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Pros:&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Genetics ( both classical and modern)&lt;/li&gt;&#xA;&lt;li&gt;Ecology (including ethology)&lt;/li&gt;&#xA;&lt;li&gt;Evolutionary biology&lt;/li&gt;&#xA;&lt;li&gt;Animal classification&lt;/li&gt;&#xA;&lt;li&gt;Immunology&lt;/li&gt;&#xA;&lt;/ol&gt;&lt;/li&gt;&#xA;&lt;li&gt;Cons:&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Biochemistry ( it somewhat feels short)&lt;/li&gt;&#xA;&lt;li&gt;Plant anatomy ( not adequately covered)&lt;/li&gt;&#xA;&lt;li&gt;Plant classification ( same as above)&lt;/li&gt;&#xA;&lt;/ol&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&amp;amp; the rest of the chapters are like animal physiology etc. they are mixed...like some &#xA;principles they have gone thoroughly...some others not...but it's acceptable as they have to cover everything in one book...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But of course it's my personal opinion...so before considering it I would rather recommend downloading the book in pdf format &amp;amp; have a look at it yourself...but I feel you won't be disappointed....&lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="10045" LastEditDate="2014-11-09T04:26:39.460" LastActivityDate="2014-11-09T04:26:39.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23840" PostTypeId="1" CreationDate="2014-11-09T11:40:32.067" Score="2" ViewCount="269" Body="&lt;p&gt;In &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S2211124714002472&quot; rel=&quot;nofollow&quot;&gt;Wang et al.&lt;/a&gt;, the authors state on page 663 at the top that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Furthermore, &lt;strong&gt;Bax&lt;sup&gt;-/-&lt;/sup&gt; Bak&lt;sup&gt;-/-&lt;/sup&gt;&lt;/strong&gt; cells were completely&#xA;  resistant to paclitaxel-induced apoptosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What's the meaning of the &lt;code&gt;-/-&lt;/code&gt; notation? Bax and Bak are proteins involved in apoptosis.&lt;/p&gt;&#xA;" OwnerUserId="4971" LastEditorUserId="3340" LastEditDate="2014-11-10T06:27:38.430" LastActivityDate="2015-01-12T13:44:25.893" Title="What's the meaning of this notation?" Tags="&lt;apoptosis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23841" PostTypeId="2" ParentId="23840" CreationDate="2014-11-09T11:56:30.770" Score="8" Body="&lt;p&gt;-/- means both copies of the gene (both alleles) are knocked out &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-12T13:44:25.893" LastActivityDate="2015-01-12T13:44:25.893" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23842" PostTypeId="1" AcceptedAnswerId="23847" CreationDate="2014-11-09T12:57:43.417" Score="6" ViewCount="8162" Body="&lt;p&gt;Why does a cockroach not die after its head is cut off?&lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="948" LastEditDate="2014-11-09T18:55:37.987" LastActivityDate="2016-01-25T16:19:05.193" Title="Why does a cockroach not die even after decapitation?" Tags="&lt;entomology&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23843" PostTypeId="1" CreationDate="2014-11-09T13:35:21.777" Score="1" ViewCount="73" Body="&lt;p&gt;Endemism on islands is quite a common phenomenon, at least at the level of species or genera. Old continental fragments like Madagascar or New Caledonia may even harbour endemic families which went extinct on the continents. I also know of the odd example of Lactoridaceae that comprise only one species which is endemic to the Juan Fernandez Islands.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you know other instances of endemic &lt;strong&gt;families&lt;/strong&gt; on islands? What about Hawai'i, the Canaries or Galapagos? &lt;/p&gt;&#xA;" OwnerUserId="8015" LastActivityDate="2014-11-09T15:55:02.803" Title="Endemic plant families on islands?" Tags="&lt;botany&gt;&lt;taxonomy&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23844" PostTypeId="2" ParentId="21691" CreationDate="2014-11-09T14:13:06.183" Score="1" Body="&lt;p&gt;In cancer cells, the telomerase is not &quot;formed&quot; but activated, mainly due to an amplification and a gain of copy of the 5p chromosome arm, containing the gene coding for TERT. For example, a very common way to immortalize primary cells to establish a cell line is to stably express TERT.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Shortened telomeres initiates DNA damage response pathways, resulting in the activation of ATM and ATR, and downstream kinases CHK1 and CHK2, and phosphorylation of p53. Once activated, p53 upregulates genes that mediate cellular senescence and/or apoptosis.&lt;/p&gt;&#xA;" OwnerUserId="10126" LastActivityDate="2014-11-09T14:13:06.183" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23847" PostTypeId="2" ParentId="23842" CreationDate="2014-11-09T17:28:05.723" Score="9" Body="&lt;p&gt;Based on an article &lt;a href=&quot;http://www.scientificamerican.com/article/fact-or-fiction-cockroach-can-live-without-head/&quot;&gt;here&lt;/a&gt;, unlike humans, cockroaches have an open circulatory system. They don't have a huge network of blood vessels like that of humans, or tiny capillaries that you need a lot of pressure to flow blood through. Hence after you cut their heads off, very often their necks would seal off just by clotting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the article cockroaches breathe through spiracles, or little holes in each body segment. Plus, the roach brain does not control this breathing and blood does not carry oxygen throughout the body. Rather, the spiracles pipe air directly to tissues through a set of tubes called tracheae. In addition cockroaches are poikilotherms, or cold-blooded, meaning they need much less food than humans do. Hence cockroaches can survive decapitation.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-11-09T17:28:05.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23848" PostTypeId="2" ParentId="23817" CreationDate="2014-11-09T19:21:49.327" Score="8" Body="&lt;p&gt;The brain is not an electronic device.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An EMP is basically a large amount of electrons flying by all at once. They are negatively charged, and as they pass by they distort your local EM-field (hence the name). This distortion induces current in the wires (a phenomenon known since Faraday) - since most wires aren't made with a large tolerance, the sudden current spike overheats the wire and burns components. In the brain, there are no wires to induce current on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is true that electromagnetism plays a role in neuron function, and action potentials can be measured or manipulated with electrodes. However, this is just a consequence of the ion concentration being used for signaling - there is not a flow of electrons across a conducting wire that is driving the process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Memory is not stored electrically. The two major mechanisms of memory are strengthening of the synapses and the chemical state of the neurons (metabolites and proteins such as cAMP or CaMK, RNA levels, DNA methylation). These aren't very sensitive to electrons moving past - you're essentially trying to catalyze a chemical reaction by applying a strong EM field outside of the beaker.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I suspect the skull and tissue surrounding it may act as a Faraday cage to shield the brain itself from the EM field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure it is possible to create an electron flux so heavy that it manages to induce enough current in cells to kill them (or current in your bloodstream to cause cardiac arrest). However, the nuclear explosion that produces this would probably be much deadlier due to other effects, like blast shockwave or gamma rays. So to answer your question, a nuclear EMP would either kill you or not affect your memories, although if you had some exotic, very powerful, very precise pure EMP generator perhaps you could get some sort of stunning effect or give people a headache. I don't think it could erase memories without killing large parts of the brain.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-11-09T19:21:49.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23850" PostTypeId="1" AcceptedAnswerId="23870" CreationDate="2014-11-09T19:36:58.697" Score="5" ViewCount="508" Body="&lt;p&gt;Fish are often plagued by external parasites, which are presumably difficult for them to remove.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are well known cases where large fish come to coral reefs and allow smaller fish to pick off their parasites. See below a moray eel being &quot;cleaned&quot; by a shrimp.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Tq935.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some fish, like sunfish, even get cleaned up by birds: &lt;a href=&quot;https://www.youtube.com/watch?v=U60obmWODLQ&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.youtube.com/watch?v=U60obmWODLQ&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But on land, we have many social animals that solve this problem more directly by grooming each other. How come the fish never seem to do this? Many of them are already social, and I imagine they wouldn't have much trouble digesting the external parasites. Why don't they groom each other?&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-11-10T17:25:32.047" LastActivityDate="2014-11-10T17:25:32.047" Title="Why don't fish groom each other?" Tags="&lt;evolution&gt;&lt;ichthyology&gt;&lt;sociality&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23851" PostTypeId="1" CreationDate="2014-11-09T21:08:31.603" Score="4" ViewCount="36369" Body="&lt;p&gt;Gene expression involves transcribing only one strand of DNA molecule. So i was wondering what are some biological advantages of the double stranded DNA?&lt;/p&gt;&#xA;" OwnerUserId="10130" LastActivityDate="2018-05-08T10:49:19.500" Title="Importance of Double Helix DNA Structure" Tags="&lt;dna&gt;&lt;proteins&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23852" PostTypeId="1" CreationDate="2014-11-09T21:22:33.563" Score="1" ViewCount="1480" Body="&lt;p&gt;I'm posting this as a follow-up on &lt;a href=&quot;https://biology.stackexchange.com/questions/5470/what-to-look-for-when-buying-a-light-microscope&quot;&gt;What to look for when buying a light microscope?&lt;/a&gt;. The answerer states that you would need to use a an inverted microscope to count cell in the hemocytometer(counting chamber).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've read, partly, a book on lab diagnostics tests and it was not written that there. Moreover, they mentioned things about microscopes featuring a compound upright microscope both in words and picture.&lt;/p&gt;&#xA;" OwnerUserId="6682" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2017-04-24T16:10:27.700" Title="Can one use a hemocytometer on a compound upright microscope?" Tags="&lt;hematology&gt;&lt;microscopy&gt;&lt;red-blood-cell&gt;&lt;histology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23853" PostTypeId="2" ParentId="23850" CreationDate="2014-11-09T21:34:53.150" Score="1" Body="&lt;p&gt;Something from my imagination: Probably the first fishes were of small size with some of them evolving to be big. The variation in the sizes of the fishes is larger compared to the variation in the sizes of mammals(picture elephants and rats with whales and tiny fish). That being said, if you'd have bank of small fish staying in one place and all grooming each other, a bigger fish would swallow them with one bit(as whales eat). This does not happen on land with, say monkeys, because it would be too big of a load for  a tiger or an eagle to snatch both of them with one move. In conclusion, the ways of predators in oceans(trickier ambush tactics, faster speed attacks) and variations in sizes might have made this more of a disadvantage than an advantage underwater compared to on land.&lt;/p&gt;&#xA;" OwnerUserId="6682" LastEditorUserId="6682" LastEditDate="2014-11-10T04:18:23.837" LastActivityDate="2014-11-10T04:18:23.837" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23854" PostTypeId="2" ParentId="5470" CreationDate="2014-11-09T22:17:14.303" Score="2" Body="&lt;p&gt;Have you seen &lt;a href=&quot;http://www.microscopy.org/education/projectmicro/buying.cfm&quot; rel=&quot;nofollow&quot;&gt;http://www.microscopy.org/education/projectmicro/buying.cfm&lt;/a&gt;?&#xA;You can find your answer if you have such questions about buying a light microscope.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What kind of microscope should I buy?&lt;br/&gt; But I only have $50-100 to&#xA;spend; does that mean no microscopy?&lt;br/&gt; What type should I buy? What&#xA;features should I look for?&lt;br/&gt; I see a lot of other features advertised;&#xA;which ones are worthwhile?&lt;br/&gt; Can I check lens quality?&lt;br/&gt; What about&#xA;buying a used microscope?&lt;br/&gt; I see a lot of great deals on eBay. Where&#xA;do I find these microscopes?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="9101" LastEditorUserId="9101" LastEditDate="2014-11-09T22:29:06.093" LastActivityDate="2014-11-09T22:29:06.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23855" PostTypeId="1" CreationDate="2014-11-10T00:04:58.943" Score="4" ViewCount="2549" Body="&lt;p&gt;In terms of genetics, which type of reproduction is better against adverse mutations? I understand a bit of &lt;em&gt;Muller's Ratchet&lt;/em&gt;—in which asexual organisms accumulate a number of deleterious mutations in their genomes. However, doesn't the crossover process and corresponding genetic diversity in sexual-reproducing organisms make them more susceptible to these mutations?&lt;/p&gt;&#xA;" OwnerUserId="10132" LastActivityDate="2014-11-11T00:06:51.127" Title="Which is better against genetic mutations? Asexual or Sexual Reproduction?" Tags="&lt;genetics&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23856" PostTypeId="2" ParentId="23851" CreationDate="2014-11-10T00:18:05.817" Score="4" Body="&lt;p&gt;The structure allows for the DNA to be tightly packed into chromosomes. It also provides an extremely stable backbone with the negatively charged phosphates pointing to the outside of the molecule. This charge aids in the attachment of other molecules to the strand of DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA double helix allows it to be stable and it won't easily destroyed. &lt;/p&gt;&#xA;" OwnerUserId="8115" LastEditorUserId="10045" LastEditDate="2014-11-10T08:26:43.830" LastActivityDate="2014-11-10T08:26:43.830" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23857" PostTypeId="2" ParentId="23850" CreationDate="2014-11-10T04:08:42.343" Score="1" Body="&lt;p&gt;Perhaps it has something to do with fish slime coats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fish are covered in a thin layer of mucus which helps with immune system function, etc. According to &lt;a href=&quot;http://www.arkansasstripers.com/fish-slime-coat.htm&quot; rel=&quot;nofollow&quot;&gt;these guys&lt;/a&gt; at least, who admittedly are not exactly a scientific authority. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps grooming as a social behavior would disturb the slime coat more often than it would help remove parasites? Or it's dangerous for other reasons? (Some fish are very territorial)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some(most?) fish are just incapable of grooming other fish of the same size and shape. I mean look at &lt;a href=&quot;http://images.fineartamerica.com/images-medium-large-5/metal-marlin-realistic-carol-lynne.jpg&quot; rel=&quot;nofollow&quot;&gt;this guy&lt;/a&gt;. The moray eel above has a jaw much larger than that of the entire shrimp that is grooming it, so perhaps picking parasites off things with such a jaw is like cutting your fingernails with a meat cleaver?&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="4109" LastEditDate="2014-11-10T04:23:54.160" LastActivityDate="2014-11-10T04:23:54.160" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23859" PostTypeId="2" ParentId="23851" CreationDate="2014-11-10T04:38:13.200" Score="3" Body="&lt;p&gt;The &lt;strong&gt;most important&lt;/strong&gt; role of this peculiar double helix structure of DNA is to facilitate replication....in preparation of cell division each of the 2 strands acts as a template thus facilitating precise copying of genes....in the Nature(1953), Watson &amp;amp; Crick also suggested that &quot; &lt;em&gt;&lt;a href=&quot;http://www.nature.com/nature/dna50/watsoncrick.pdf&quot; rel=&quot;nofollow&quot;&gt;It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material&lt;/em&gt;&lt;/a&gt;&quot;...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, the extremely stable structure doesn't allow DNA to mutate rapidly, unlike RNA...thus converting it into an &quot;&lt;strong&gt;efficient information storage structure&lt;/strong&gt;&quot;....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;amp; lastly this double helix structure is also &lt;strong&gt;resistive against extreme physical changes&lt;/strong&gt;...as is evident from Griffith's experiment, where the heat-killed bacteria had their DNA intact...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also try this link- &quot;&lt;a href=&quot;http://www.nature.com/nature/dna50/watsoncrick2.pdf&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Genetic Implications of the Structure of Deoxyribonucleic Acid&lt;/a&gt;&quot;- Watson &amp;amp; Crick&lt;/em&gt;....as it always helps to learn from the very masters of DNA structure;) &lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="10045" LastEditDate="2014-11-10T06:07:14.560" LastActivityDate="2014-11-10T06:07:14.560" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23860" PostTypeId="1" CreationDate="2014-11-10T06:14:09.363" Score="0" ViewCount="296" Body="&lt;p&gt;Fish, as far as I know ( of course there &lt;strong&gt;may be&lt;/strong&gt; exceptions) , don't have any vocal organ...but they are proven to be social...so how do they manage to communicate with each other...on land, organisms like the honey-bee have their &quot;tail-wagging dance&quot;; ants have pheromones...so, what about fish?&lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="9943" LastEditDate="2014-11-10T09:42:46.680" LastActivityDate="2014-11-10T09:42:46.680" Title="How do fish communicate?" Tags="&lt;ichthyology&gt;&lt;communication&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23861" PostTypeId="2" ParentId="17940" CreationDate="2014-11-10T06:23:23.030" Score="15" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Photosynthesis&quot; rel=&quot;noreferrer&quot;&gt;Photosynthesis&lt;/a&gt; uses &lt;a href=&quot;http://en.wikipedia.org/wiki/Chlorophyll&quot; rel=&quot;noreferrer&quot;&gt;chlorophyll&lt;/a&gt; (or &lt;a href=&quot;http://en.wikipedia.org/wiki/Bacteriochlorophyll&quot; rel=&quot;noreferrer&quot;&gt;other pigments&lt;/a&gt;) for harnessing photons and water (or other compounds) as &lt;a href=&quot;http://en.wikipedia.org/wiki/Electron_donor&quot; rel=&quot;noreferrer&quot;&gt;electron donor&lt;/a&gt; $H_2O = 1/2O_2 + 2H^+ + 2e^-$. After &lt;a href=&quot;http://en.wikipedia.org/wiki/Oxygen-evolving_complex&quot; rel=&quot;noreferrer&quot;&gt;splitting the water&lt;/a&gt; it sends the electrons through the further steps of an &lt;a href=&quot;http://en.wikipedia.org/wiki/Electron_transport_chain&quot; rel=&quot;noreferrer&quot;&gt;electron transport chain&lt;/a&gt; and at the end it reduces $NADP^+$ into $NADPH$. Meanwhile it increases the $H^+$ concentration outside of a membrane, so it creates a &lt;a href=&quot;http://en.wikipedia.org/wiki/Electrochemical_gradient&quot; rel=&quot;noreferrer&quot;&gt;$H^+$ gradient&lt;/a&gt;. This gradient can be used to synthesize $ATP$ from $ADP$ using a &lt;a href=&quot;http://en.wikipedia.org/wiki/ATP_synthase&quot; rel=&quot;noreferrer&quot;&gt;$H^+$ pump&lt;/a&gt;. After that $NADPH$ and $ATP$ can be used to &lt;a href=&quot;http://en.wikipedia.org/wiki/Carbon_fixation&quot; rel=&quot;noreferrer&quot;&gt;fix $CO_2$&lt;/a&gt; at any time (so that part of the photosynthesis is not light dependent).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Lx4NR.png&quot; alt=&quot;Light-dependent reactions of photosynthesis&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 1 - Light-dependent reactions of photosynthesis - electron transport chain - &lt;a href=&quot;http://cambridgecapp.wordpress.com/improving-photosynthesis/photosynthesis/light-dependent-reactions-of-photosynthesis/&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Splitting $CO_2$ into $CO$ and $1/2O2$ is possible as well. It can be done &lt;a href=&quot;http://en.wikipedia.org/wiki/Carbon_monoxide_dehydrogenase&quot; rel=&quot;noreferrer&quot;&gt;enzymatically&lt;/a&gt; or due to &lt;a href=&quot;http://en.wikipedia.org/wiki/Photodissociation&quot; rel=&quot;noreferrer&quot;&gt;photolysis&lt;/a&gt;. You need similar energy to do that as by &lt;a href=&quot;http://en.wikipedia.org/wiki/Water_splitting&quot; rel=&quot;noreferrer&quot;&gt;water splitting&lt;/a&gt;.&#xA;After that $CO$ can be used e.g. by &lt;a href=&quot;http://en.wikipedia.org/wiki/Water-gas_shift_reaction&quot; rel=&quot;noreferrer&quot;&gt;shift reaction&lt;/a&gt; $CO + H_2O = CO_2 + H_2$ to create an electron donor ($H_2$) and play the same thing as normally. It is possible to reduce $CO$ with an electron donor ($_H2O$, $H_2$, $H_2S$, $NH_3$, etc...) further, and create for example ethanol or carbohydrates like glucose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Afaik only &lt;a href=&quot;http://en.wikipedia.org/wiki/Artificial_photosynthesis&quot; rel=&quot;noreferrer&quot;&gt;artificial photosynthesis&lt;/a&gt; use $CO_2$ splitting and natural ones prefer $NADPH$ and $ATP$ creation and usage for example in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Light-independent_reactions#Calvin_Cycle&quot; rel=&quot;noreferrer&quot;&gt;Calvin cycle&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/C4_carbon_fixation&quot; rel=&quot;noreferrer&quot;&gt;C4 pathway&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Crassulacean_acid_metabolism&quot; rel=&quot;noreferrer&quot;&gt;CAM pathway&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Reverse_Krebs_cycle&quot; rel=&quot;noreferrer&quot;&gt;reverse Krebs cycle&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Wood%E2%80%93Ljungdahl_pathway&quot; rel=&quot;noreferrer&quot;&gt;Wood pathway&lt;/a&gt;, etc... I think this is because &lt;a href=&quot;http://en.wikipedia.org/wiki/C4_carbon_fixation&quot; rel=&quot;noreferrer&quot;&gt;carbon fixation&lt;/a&gt; evolved before photosynthesis. So photosynthesis is just about plugging another energy source into the system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(In programmer terms the carbon fixation is loosely coupled to the implementation of the energy producing process and the common interface is described with ATP and NADPH creation.&#xA;In mobile phone user terms it is like charging your phone's battery (ATP and NADPH storage) from line power or using a solar charger. Both chargers provide electricity (ATP and NADPH) via USB.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is good, what you meant is possible, but afaik. in natural photosynthesis the $O_2$ always comes from the water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16453059&quot; rel=&quot;noreferrer&quot;&gt;Photosynthesis in the Archean era.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2606769/&quot; rel=&quot;noreferrer&quot;&gt;When did oxygenic photosynthesis evolve?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://arxiv.org/ftp/arxiv/papers/1212/1212.0872.pdf&quot; rel=&quot;noreferrer&quot;&gt;On the photosynthetic potential in the very Early Archean oceans&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://www.plantphysiol.org/content/154/2/434.full&quot; rel=&quot;noreferrer&quot;&gt;Early Evolution of Photosynthesis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1988 - &lt;a href=&quot;http://www.pnas.org/content/85/18/6577.abstract&quot; rel=&quot;noreferrer&quot;&gt;Photoreduction of carbon dioxide by aqueous ferrous ion: An alternative to the strongly reducing atmosphere for the chemical origin of life&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;wikipedia - &lt;a href=&quot;http://en.wikipedia.org/wiki/Anoxygenic_photosynthesis&quot; rel=&quot;noreferrer&quot;&gt;Anoxygenic photosynthesis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2002 - &lt;a href=&quot;https://web.anl.gov/PCS/acsfuel/preprint%20archive/Files/47_2_Boston_10-02_0274.pdf&quot; rel=&quot;noreferrer&quot;&gt;Kinetic study of the reverse water gas shift reaction in high-temperature, high-pressure homogeneous systems&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://depts.washington.edu/chemcrs/bulkdisk/chem456A_win04/info_Thermo_Chptr_10.pdf&quot; rel=&quot;noreferrer&quot;&gt;The Enthalpy, Entropy and Gibbs Energy of Ion Formation in Solutions&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;wikipedia - &lt;a href=&quot;http://en.wikipedia.org/wiki/Standard_enthalpy_of_formation&quot; rel=&quot;noreferrer&quot;&gt;Standard enthalpy of formation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.pnas.org/content/109/39/15606.full&quot; rel=&quot;noreferrer&quot;&gt;Splitting CO2 into CO and O2 by a single catalyst&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;2002 - &lt;a href=&quot;http://www.sciencemag.org/content/298/5599/1788.short&quot; rel=&quot;noreferrer&quot;&gt;Molecular Hydrogen as an Energy Source for Helicobacter pylori&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ja905797w&quot; rel=&quot;noreferrer&quot;&gt;Water-Gas Shift Reaction Catalyzed by Redox Enzymes on Conducting Graphite Platelets&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3627189/&quot; rel=&quot;noreferrer&quot;&gt;Leaf-architectured 3D Hierarchical Artificial Photosynthetic System of Perovskite Titanates Towards CO2 Photoreduction Into Hydrocarbon Fuels&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://aaqr.org/VOL14_No2_March2014/8_AAQR-13-09-OA-0283_533-549.pdf&quot; rel=&quot;noreferrer&quot;&gt;Comparison of CO2 Photoreduction Systems: A Review&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://www.ibp.ethz.ch/research/environmentalmicrobiology/teaching/Environmental_Microbiology_2013/Solids/Weber_2006&quot; rel=&quot;noreferrer&quot;&gt;Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1972 - &lt;a href=&quot;http://pubs.rsc.org/EN/content/articlelanding/1972/f1/f19726801550&quot; rel=&quot;noreferrer&quot;&gt;Flash photolysis of H2S&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://link.springer.com/referenceworkentry/10.1007/978-3-642-11274-4_300&quot; rel=&quot;noreferrer&quot;&gt;Anoxygenic Photosynthesis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2004 - &lt;a href=&quot;http://www.life.illinois.edu/govindjee/Part3/7_TimeLineBacteria.pdf&quot; rel=&quot;noreferrer&quot;&gt;Time line of discoveries: anoxygenic bacterial photosynthesis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1990 - &lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00032643?LI=true&quot; rel=&quot;noreferrer&quot;&gt;A reverse KREBS cycle in photosynthesis: consensus at last&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ar9001679&quot; rel=&quot;noreferrer&quot;&gt;Molecular Approaches to the Photocatalytic Reduction of Carbon Dioxide for Solar Fuels&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://www.nature.com/nature/journal/v508/n7497/full/nature13249.html&quot; rel=&quot;noreferrer&quot;&gt;Electroreduction of carbon monoxide to liquid fuel on oxide-derived nanocrystalline copper&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22487129&quot; rel=&quot;noreferrer&quot;&gt;Biological conversion of carbon monoxide to ethanol: effect of pH, gas pressure, reducing agent and yeast extract.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0014579311007101&quot; rel=&quot;noreferrer&quot;&gt;Hydrogen, metals, bifurcating electrons, and proton gradients: The early evolution of biological energy conservation&lt;/a&gt; - an exciting article&lt;/li&gt;&#xA;&lt;li&gt;2005 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0966842X0500199X&quot; rel=&quot;noreferrer&quot;&gt;Hydrogen-driven subsurface lithoautotrophic microbial ecosystems (SLiMEs): do they exist and why should we care?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev-micro-090110-102801&quot; rel=&quot;noreferrer&quot;&gt;Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1998 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1011134498001791&quot; rel=&quot;noreferrer&quot;&gt;Hydrogen metabolism in organisms with oxygenic photosynthesis: hydrogenases as important regulatory devices for a proper redox poising?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;1975 - &lt;a href=&quot;http://jb.asm.org/content/123/3/855.short&quot; rel=&quot;noreferrer&quot;&gt;Facultative anoxygenic photosynthesis in the cyanobacterium Oscillatoria limnetica.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2003 - &lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/358/1429/59.short&quot; rel=&quot;noreferrer&quot;&gt;On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells &lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/366/1580/2857.short&quot; rel=&quot;noreferrer&quot;&gt;Serpentinite and the dawn of life&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bies.200900131/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;noreferrer&quot;&gt;How did LUCA make a living? Chemiosmosis in the origin of life&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002455&quot; rel=&quot;noreferrer&quot;&gt;The Emergence and Early Evolution of Biological Carbon-Fixation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1751-1097.2012.01241.x/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;noreferrer&quot;&gt;Photosynthetic Electron Transport in an Anoxygenic Photosynthetic Bacterium Afifella (Rhodopseudomonas) marina Measured Using PAM Fluorometry&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.google.hu/books?id=lqJyvjW1DbYC&amp;amp;dq=Bacteriochlorophyll+alternative+electron+donors+anoxygenic+photosynthesis&amp;amp;lr=&amp;amp;hl=hu&amp;amp;source=gbs_navlinks_s&quot; rel=&quot;noreferrer&quot;&gt;Bacterial Energetics: A Treatise on Structure and Function&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0012821X11007540&quot; rel=&quot;noreferrer&quot;&gt;Depth variation of carbon and oxygen isotopes of calcites in Archean altered upperoceanic crust: Implications for the CO2 flux from ocean to oceanic crust in the Archean&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.sciencemag.org/content/339/6115/64.short&quot; rel=&quot;noreferrer&quot;&gt;Hydrogen-Nitrogen Greenhouse Warming in Earth's Early Atmosphere&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0019103510002708&quot; rel=&quot;noreferrer&quot;&gt;Aeronomical evidence for higher CO2 levels during Earth’s Hadean epoch&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://link.springer.com/chapter/10.1007/978-1-4939-1148-6_13&quot; rel=&quot;noreferrer&quot;&gt;From Ionizing Radiation to Photosynthesis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://pubs.rsc.org/en/content/articlelanding/2011/mt/c1mt00042j&quot; rel=&quot;noreferrer&quot;&gt;Metal centers in the anaerobic microbial metabolism of CO and CO2&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://specialpapers.gsapubs.org/content/504/1.abstract&quot; rel=&quot;noreferrer&quot;&gt;Evidence and arguments for methane and ammonia in Earth's earliest atmosphere and an organic compound–rich early ocean&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-11-10T06:23:23.030" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23862" PostTypeId="2" ParentId="23860" CreationDate="2014-11-10T06:24:22.980" Score="3" Body="&lt;p&gt;Be glad to answer your questions.&#xA;fish also sounds. The difference is that they are put in different positions by the body to sound.The sound of fish is about 20HZ. Difficult to discern the human ear. But you can rely on instruments to imitate and perceived. Of course, some fish also relies purely on action to exchange summarize a sound.Some fish by ultrasonic communication with dolphins is very similar (dolphins are not fish).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2 colors.&#xA;Some fish by changing the body color transfer information, are located in the tropical shallow water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3 flow.&#xA;Some fish to pass through the water with their fins flapping shaped courtship information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4 pheromone.&#xA;Release pheromone few fish, mostly deep-sea fish.。&lt;/p&gt;&#xA;" OwnerUserId="9029" LastActivityDate="2014-11-10T06:24:22.980" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23863" PostTypeId="1" CreationDate="2014-11-10T06:42:09.473" Score="3" ViewCount="371" Body="&lt;p&gt;It's a popular public sentiment that - GM foods like tomatoes (&lt;a href=&quot;http://en.wikipedia.org/wiki/Flavr_Savr&quot; rel=&quot;nofollow&quot;&gt;flavr savr&lt;/a&gt;) will affect our health.. Is there any logical scientific explanation behind this?&lt;/p&gt;&#xA;" OwnerUserId="9029" LastEditorUserId="5144" LastEditDate="2014-11-10T09:57:58.310" LastActivityDate="2018-11-19T12:32:48.177" Title="Will genetically modified food affect our health?" Tags="&lt;genetics&gt;&lt;food&gt;&lt;biotechnology&gt;&lt;health&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23865" PostTypeId="1" AcceptedAnswerId="35168" CreationDate="2014-11-10T11:28:42.130" Score="6" ViewCount="369" Body="&lt;p&gt;As opposed to action potential thresholds (which are binary yes/no events), electrophysiological thresholds of compound action potentials are arbitrary. Mostly a certain noise level is picked and when the neural signal crosses this 'threshold' it is said to be 'above-threshold'. I have come across various definitions of this threshold, such as SD-based values (2xSD, 4xSD etc), 'visual' thresholds (a bit iffy from my point of view) among other things. Is there a rule of thumb as to define threshold? Alternatively, a review article, book chapter, or a primary research article with considerable impact explicitly dealing with this matter would be very helpful.     &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-02-20T21:46:16.983" LastActivityDate="2016-02-20T21:46:16.983" Title="Criteria for compound action potential thresholds" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;&lt;biophysics&gt;&lt;electrophysiology&gt;&lt;signal-processing&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23866" PostTypeId="2" ParentId="21775" CreationDate="2014-11-10T12:40:01.137" Score="0" Body="&lt;p&gt;These channels are slow to respond. After depolarization they are activated, but only after a relatively long time. Their closing kinetics are also relatively slow. A definition is give &lt;a href=&quot;https://aaa-uruk04.cri.uchicago.edu/profiles/display/29640&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-10T12:40:01.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23867" PostTypeId="1" AcceptedAnswerId="23869" CreationDate="2014-11-10T13:09:20.477" Score="9" ViewCount="1149" Body="&lt;p&gt;I recently went walking in the highlands in Snowdonia, Wales and we came across this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LUD9h.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone explain what it is? My guess was some kind of fungus but I'm not positive. The ground was very water logged and boggy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It looked a lot like frog spawn, but it's autumn here and we wouldn't see frog spawn until Spring. There appeared to be no animals living inside or around it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's often called &lt;em&gt;star jelly&lt;/em&gt; and there's a whole wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Star_jelly&quot; rel=&quot;nofollow noreferrer&quot;&gt;Star Jelly&lt;/a&gt; talking about it:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;“Star jelly” (also called astromyxin, astral jelly, pwdr sêr, star&#xA;  rot, or star shot) is a gelatinous substance sometimes found on grass&#xA;  or even on branches of trees.&lt;a href=&quot;https://i.stack.imgur.com/LUD9h.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt; According to folklore, it is&#xA;  deposited on the earth during meteor showers. Star jelly is described&#xA;  as a translucent or grayish-white gelatin that tends to evaporate&#xA;  shortly after having “fallen.” Explanations have ranged from the&#xA;  material's being the remains of frogs, toads, or worms, to the&#xA;  byproducts of cyanobacteria, to the paranormal.[2][3][4][5] Reports of&#xA;  the substance date back to the 14th century and have continued to the&#xA;  present day.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerDisplayName="user9894" LastEditorDisplayName="user9894" LastEditDate="2016-08-30T08:09:29.307" LastActivityDate="2016-08-30T08:09:29.307" Title="Weird gelatinous substance in highland bog" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23868" PostTypeId="1" AcceptedAnswerId="23883" CreationDate="2014-11-10T13:47:32.960" Score="3" ViewCount="166" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jOmkF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I was moving to another house, I found this plastic bag on the top of the cabinet of my old house. It looks like someone cut it all with a scissor, but no one have access to my bedroom, and it was not me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't thing it could be rats. That bedroom was very tiny and closed, there's no way for a rat to enter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The house is very near &lt;a href=&quot;https://www.google.com.br/maps/place/Universidade+de+S%C3%A3o+Paulo/@-23.5671719,-46.7272143,2057m/data=!3m1!1e3!4m2!3m1!1s0x0:0x4f4f4d2c7e06e56&quot; rel=&quot;nofollow noreferrer&quot;&gt;a university with a little &quot;forest&quot;&lt;/a&gt;, there are many types of mosquito and little flying animals, but I can't imagine which could do this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm just curious. (and not sure if &quot;zoology&quot; is the correct tag here, but I had to choose one)&lt;/p&gt;&#xA;" OwnerUserId="10138" LastActivityDate="2014-11-10T20:43:03.877" Title="What kind of animal can do this?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23869" PostTypeId="2" ParentId="23867" CreationDate="2014-11-10T15:02:52.363" Score="6" Body="&lt;p&gt;So the &lt;a href=&quot;http://www.bbc.co.uk/programmes/b007tcw7&quot; rel=&quot;nofollow&quot;&gt;One show&lt;/a&gt; did a magazine piece on this the other day; a scientist did some DNA analysis of some of it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The conclusion was that it's &lt;strong&gt;frog jelly&lt;/strong&gt; (full of frog DNA). Apparently frogs have glands full of the components of the jelly in sacks in their bodies, when the sacks come into contact with moisture it expands massively (same process that allow them to produce frog spawn). When a frog is eaten (by a bird or fox) the jelly expands on contact with any moisture. The animal eating the frog either vomits it up or doesn't eat it in the first place and voila.&lt;/p&gt;&#xA;" OwnerDisplayName="user9894" LastEditorDisplayName="user9894" LastEditDate="2016-08-30T08:07:47.280" LastActivityDate="2016-08-30T08:07:47.280" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23870" PostTypeId="2" ParentId="23850" CreationDate="2014-11-10T15:16:54.483" Score="2" Body="&lt;p&gt;All cases of same species grooming I know of involve animals with a certain amount of dexterity. For example (images from &lt;a href=&quot;https://en.wikipedia.org/wiki/Social_grooming#In_non-human_animals&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Macaw beaks:&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/rgKMfm.jpg&quot; alt=&quot;Hyacinth Macaws, Anodorhynchus hyacinthinus at the Aquarium of the Americas in New Orleans, Louisiana.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Primate fingers:&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/ssdJdm.jpg&quot; alt=&quot;Macaques grooming each other at a foggy viewpoint near Lonavla, India.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Even ponies rubbing each other:&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/5QKdIm.jpg&quot; alt=&quot;Mutually grooming ponies at Turf Hill, New Forest, U.K.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In all of these cases, the animals involved have the right tools for the job. fingers, beaks and prehensile lips can all close in on a parasite and remove it with precision. how exactly would you expect a shark to do this (image from &lt;a href=&quot;http://www.theguardian.com/environment/2008/aug/04/wildlife&quot; rel=&quot;nofollow noreferrer&quot;&gt;the guardian&lt;/a&gt;)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/DiJ7um.jpg&quot; alt=&quot;shark jaws&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sharks can and do rub themselves against rocks to get rid of dead skin but they simply don't have the tools for the kind of detail work that the smaller fish can do for them. The same applies to other fish. I think you will find that at least in most cases, fish that use client species to groom themselves wouldn't be physically able to do the same job themselves. It's all a matter of the right size and the right tools. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Note that this is pure speculation, I have no references to back this up, it just seems reasonable. I would not be surprised if &lt;em&gt;some&lt;/em&gt; fish did actually indulge in social grooming, it's just harder for the reasons outlined above. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-11-10T15:26:01.840" LastActivityDate="2014-11-10T15:26:01.840" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23871" PostTypeId="1" AcceptedAnswerId="23889" CreationDate="2014-11-10T15:38:16.590" Score="9" ViewCount="7737" Body="&lt;p&gt;I have watched &lt;a href=&quot;https://www.youtube.com/watch?v=IGJ2jMZ-gaI&quot; rel=&quot;noreferrer&quot;&gt;video on youtube where guy pours molten aluminium into fire ant colony to make casing&lt;/a&gt;. In the comments below there's huge discussion on is that a right thing to do. I am on the side that one should not exterminate colony of living things to get aluminium shape of questionable artistic value. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Main argument on the opposing side is that ants do not feel pain - therefore it's ok. I have done &lt;a href=&quot;http://antfarm.yuku.com/reply/113498/Re-Can-ants-feel-pain-#.VGDXPvmsXuM&quot; rel=&quot;noreferrer&quot;&gt;some reading around&lt;/a&gt; and &lt;a href=&quot;https://answers.yahoo.com/question/index?qid=1006051630247&quot; rel=&quot;noreferrer&quot;&gt;opinions differ greatly&lt;/a&gt;.&lt;br&gt;&#xA;&lt;strong&gt;Do ants feel pain?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="8129" LastEditorUserId="8129" LastEditDate="2014-11-10T16:37:31.520" LastActivityDate="2019-12-10T02:38:17.687" Title="Do ants feel pain?" Tags="&lt;neuroscience&gt;&lt;entomology&gt;&lt;pain&gt;&lt;ant&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23872" PostTypeId="1" AcceptedAnswerId="23885" CreationDate="2014-11-10T15:39:53.463" Score="10" ViewCount="16706" Body="&lt;p&gt;Somewhere in the back of my mind, I have the claim that a muscle never increases its amount of cells but, if the muscle gets bigger, it's simply because individual cells get bigger.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The book Anatomy Trains on page 36 cites &quot;Changes in sarcomere length and physiological properties in immobilized muscle by  Williams et al&quot; when it makes the claim : &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Stretched, a muscle will attempt to recoil back to its &#xA;  resting length before giving up and adding more cells &#xA;  and sarcomeres to bridge the gap.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is that true? Do muscles increase the number of their cells in that way?&lt;/p&gt;&#xA;" OwnerUserId="152" LastEditorUserId="152" LastEditDate="2014-11-11T21:41:09.427" LastActivityDate="2017-09-07T06:18:23.863" Title="Does muscle get bigger by increase in size of individual cells or increase in number?" Tags="&lt;physiology&gt;&lt;muscles&gt;" AnswerCount="2" CommentCount="10" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23873" PostTypeId="1" AcceptedAnswerId="23882" CreationDate="2014-11-10T15:47:14.800" Score="5" ViewCount="3261" Body="&lt;p&gt;This is a cross-cutting question but I think its core is about biology. Our society's need for energy is dramatically growing and we are messing up with our environment to answer them. Maybe another way to proceed would be to use the primary energy source that is the sun in the same way as it has been used throughout the ages: photosynthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know the energy effiency is not as good as a solar panel's but it could clearly be compensated by volume. I found surprisingly little information about harvesting energy from photosynthesis which is why I began to wonder where we are at today. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;&#xA;I meant transforming the chemical energy generated by photosynthesis into electrical energy. For instance, the first algae powered building was unveiled at the International Building Exhibition hosted in Hamburg. This is a whole different approach.&#xA;The most basic example of what I would like to talk about seems to be the algae powered lamp that has (apparently) been developped. In other words, it seems that some sort of plant solar panels are under development and I don't understand how it's done.&lt;/p&gt;&#xA;" OwnerUserId="10139" LastEditorUserId="3340" LastEditDate="2015-06-04T11:39:39.330" LastActivityDate="2015-06-04T11:39:39.330" Title="Can we harvest energy from plants?" Tags="&lt;photosynthesis&gt;&lt;bioenergetics&gt;" AnswerCount="6" CommentCount="13" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23875" PostTypeId="2" ParentId="23873" CreationDate="2014-11-10T16:11:45.880" Score="6" Body="&lt;p&gt;It is not possible to do this directly. Indirectly, it is possible, this is actually done by harvesting fruits - they contain the energy of the sunlight conserved in chemical compounds like sugars or starch and their cellular structures. The basic process for this is &lt;a href=&quot;http://en.wikipedia.org/wiki/Photosynthesis&quot;&gt;photosynthesis&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The products from the fields are used technically to produce gas by fermentation, which then can be burned to produce electricity. Read reference 1 for more details.&#xA;What is also done is the use of sugar cane (done widely in Brazil) or &lt;a href=&quot;http://www.pjoes.com/pdf/19.2/323-329.pdf&quot;&gt;corn&lt;/a&gt; to produce ethanol which is then used in the fuel of cars. See references 2-4.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides these technical processes, there is of course still the possibility to simply burn whole plants or the wood of trees, which is also the result of the fixation of sun energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pjoes.com/pdf/19.2/323-329.pdf&quot;&gt;Biogas Production from Maize Grains and Maize Silage&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://journeytoforever.org/biofuel_library/Pimentel-Tadzek.pdf&quot;&gt;Ethanol Production Using Corn, Switchgrass, and Wood; Biodiesel&#xA;Production Using Soybean and Sunflower&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ethanol_fuel_in_Brazil&quot;&gt;Ethanol fuel in Brazil&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Corn_ethanol&quot;&gt;Corn ethanol&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-11-10T16:27:11.253" LastActivityDate="2014-11-10T16:27:11.253" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23876" PostTypeId="2" ParentId="23873" CreationDate="2014-11-10T16:20:16.483" Score="6" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;I found surprisingly little information about harvesting energy from&#xA;photosynthesis&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Photosynthesis does not produce energy as such, it produces &lt;strong&gt;sugars/carbohydrates/chemical energy&lt;/strong&gt;, which the plant then converts into energy via respiration.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DwZfS.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;You can burn the sugar to produce heat. But this is basically what your doing when you burn a plant. So no, photosynthesis cannot be used (directly) to produce electrical energy.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;In a &lt;a href=&quot;http://news.stanford.edu/news/2010/april/electric-current-plants-041310.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Standford university research&lt;/a&gt; they did successfully harvest electrictity from photosynthesis:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The Stanford research team developed a unique, ultra-sharp&#xA;nanoelectrode made of gold, specially designed for probing inside&#xA;cells. They gently pushed it through the algal cell membranes, which&#xA;sealed around it, and the cell stayed alive. From the&#xA;photosynthesizing cells, the electrode collected electrons that had&#xA;been energized by light and the researchers generated a tiny&#xA;electrical current.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;But it goes on to say:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Ryu said they were able to draw from each cell just one picoampere, an&#xA;amount of electricity so tiny that they would need a trillion cells&#xA;photosynthesizing for one hour just to equal the amount of energy&#xA;stored in a AA battery. In addition, the cells die after an hour.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So this is be no means practical at the moment&lt;/p&gt;&#xA;" OwnerDisplayName="user9894" LastEditorUserId="-1" LastEditorDisplayName="user9894" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-11-11T10:53:44.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23877" PostTypeId="1" AcceptedAnswerId="23888" CreationDate="2014-11-10T17:28:53.607" Score="4" ViewCount="187" Body="&lt;p&gt;This is the definition of a &lt;strong&gt;niche&lt;/strong&gt; from &lt;a href=&quot;http://en.wikipedia.org/wiki/Crash_Course_(YouTube)&quot; rel=&quot;nofollow&quot;&gt;Crash Course&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An area of the environment that requires a special set of skills or traits to extract food and reproduce.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Obviously, this version of the definition has been dummed so that it appeals to mass audiences, but after some research, I believe that the general concept remains the same.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is what I've learnt about species living in a niche:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The more the competition, the slower the evolutionary process.&lt;/li&gt;&#xA;&lt;li&gt;Lack of competition provides an ideal environment rapid evolution.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;But these points seem non-intuitive to me, because:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why would a increased competition slow down the evolutionary process? Shouldn't it speed it up, as different species will try to evolve the fastest in order to beat adversaries?&lt;/li&gt;&#xA;&lt;li&gt;Why does a lack of competition promote rapid evolution? Won't it slow down the evolution, as there is no reason to evolve?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I know that there is a logical reasoning behind this, and I would very much like to understand it. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;My source is &lt;a href=&quot;http://en.wikipedia.org/wiki/Crash_Course_(YouTube)&quot; rel=&quot;nofollow&quot;&gt;Crash Course&lt;/a&gt;, specifically &lt;a href=&quot;http://www.youtube.com/watch?v=92oHNd8vFwo&quot; rel=&quot;nofollow&quot;&gt;this  video&lt;/a&gt;. I've found it to be extremely reliable over the past, and highly doubt that they are supplying incorrect information. If anything, it is probably my inability to understand the concept.&lt;/p&gt;&#xA;" OwnerUserId="9282" LastEditorUserId="9282" LastEditDate="2014-11-10T18:16:32.690" LastActivityDate="2014-11-10T23:51:25.490" Title="Confusion regarding niches in evolution theory" Tags="&lt;evolution&gt;&lt;ecology&gt;&lt;species&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23880" PostTypeId="2" ParentId="23872" CreationDate="2014-11-10T20:02:24.070" Score="7" Body="&lt;p&gt;A tissue can undergo two types of quantitative growth:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;hypertrophy - cells increase in size&lt;/li&gt;&#xA;&lt;li&gt;hyperplasia - cells increase in number&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are tissues that grow as a result of one of the above processes and there are tissues that grow because both processes happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;https://www.google.com/?q=muscle+growth&quot;&gt;Google search&lt;/a&gt; for muscular growth yields as first result &lt;a href=&quot;http://en.wikipedia.org/wiki/Muscle_hypertrophy&quot;&gt;Muscle hypertrophy&lt;/a&gt;. And this is the process that happens to muscle tissue of an adult body under physical exercise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But muscle tissue can undergo hyperplasia too if stimulated by specific hormones like IGF-1 and human growth hormone (&lt;a href=&quot;http://en.wikipedia.org/wiki/Hyperplasia&quot;&gt;Wikipedia:Hyperplasia&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Muscle hyperplasia can occur also under physical activity in animals but this hasn't been proven for humans (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8107539&quot;&gt;Antonio J, Gonyea WJ. 1993&lt;/a&gt;). Stretch overload seems to be the most important trigger of hyperplasia (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8904572&quot;&gt;Kelley G., 1985&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-11-10T20:02:24.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23881" PostTypeId="1" CreationDate="2014-11-10T20:08:50.347" Score="2" ViewCount="2564" Body="&lt;p&gt;I amplified my DNA with real time PCR. The amplification curve shows good amplification but not a single band is observed in my gel after gel electrophoresis. What would be the possible reasons? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am attaching a photograph of my gel below. My ladder opened correctly but not a single band can be observed:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/wJPau.jpg&quot; alt=&quot;Gel&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10142" LastEditorUserId="3340" LastEditDate="2014-11-11T06:51:10.277" LastActivityDate="2015-10-20T15:54:16.927" Title="How can I get brighter DNA bands?" Tags="&lt;gel-electrophoresis&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="23882" PostTypeId="2" ParentId="23873" CreationDate="2014-11-10T20:40:44.880" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;The most basic example of what I would like to talk about seems to be&#xA;  the algae powered lamp that has (apparently) been developped.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think you misunderstood the idea. That lamp uses &lt;a href=&quot;http://en.wikipedia.org/wiki/Bioluminescence&quot;&gt;bioluminescence&lt;/a&gt; and not electric power. Normally living cells don't like to give you energy. The trick we use is anaerob fermentation. Without the presence of oxygen (good electron acceptor) they cannot extract more energy from compounds like ethanol, etc... so they get rid of them. After that we can &quot;burn&quot; these compounds with oxygen and get a lot of energy. So currently there is no solution which uses sunlight and microbes to produce electricity directly, however it might be possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many ways to use photosynthesis in order to produce energy.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The simplest way to burn the plant itself when it has grown enough. You can burn wood, energy plants (e.g. energy grass), etc... and use a generator.&lt;/li&gt;&#xA;&lt;li&gt;A more sophisticated approach to ferment biomass and produce methane, ethanol, etc... which you can burn. This works very well by starch (e.g. corn bioethanol), and there is active research about &lt;a href=&quot;http://en.wikipedia.org/wiki/Cellulosic_ethanol_commercialization&quot;&gt;cellulose conversion&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There is active research about &lt;a href=&quot;http://en.wikipedia.org/wiki/Artificial_photosynthesis&quot;&gt;artificial photosynthesis&lt;/a&gt; as well.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;You can feed microbes with electric power coming from a photovoltaic system (solar panel), so they can produce ethanol, methane, etc... This might be better than storing energy in batteries.&lt;/li&gt;&#xA;&lt;li&gt;You can use electric power coming from solar panels to split water. After that microbes can use the hydrogen as electron donor to fix $CO_2$, so they can create ethanol, etc... &lt;/li&gt;&#xA;&lt;li&gt;You can use light to split $CO_2$ into $CO$ and $1/2O_2$. You can use $CO$ in biological systems to create ethanol, etc... You can use $CO$ in shift reaction to create $H_2$. It is a new technology to use copper nanoparticles to convert $CO$ into ethanol in a completely artificial system.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You can use a photovoltaic system instead of photosynthesis if you need electric power instead of chemical compounds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Related articles:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/adma.201004393/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot;&gt;Light Absorption Enhancement in Thin-Film Solar Cells Using Whispering Gallery Modes in Dielectric Nanospheres&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1758-2229.2010.00211.x/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot;&gt;Powering microbes with electricity: direct electron transfer from electrodes to microbes&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0958166908001341&quot;&gt;The microbe electric: conversion of organic matter to electricity&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://aem.asm.org/content/77/9/2882.short&quot;&gt;Electrosynthesis of Organic Compounds from Carbon Dioxide Is Catalyzed by a Diversity of Acetogenic Microorganisms?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://pubs.rsc.org/en/content/articlelanding/2011/mt/c1mt00042j#!divAbstract&quot;&gt;Metal centers in the anaerobic microbial metabolism of CO and CO2&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://link.springer.com/chapter/10.1007/978-1-4939-1148-6_13&quot;&gt;From Ionizing Radiation to Photosynthesis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22487129&quot;&gt;Biological conversion of carbon monoxide to ethanol: effect of pH, gas pressure, reducing agent and yeast extract.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://www.nature.com/nature/journal/v508/n7497/full/nature13249.html&quot;&gt;Electroreduction of carbon monoxide to liquid fuel on oxide-derived nanocrystalline copper&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ar9001679&quot;&gt;Molecular Approaches to the Photocatalytic Reduction of Carbon Dioxide for Solar Fuels&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://aaqr.org/VOL14_No2_March2014/8_AAQR-13-09-OA-0283_533-549.pdf&quot;&gt;Comparison of CO2 Photoreduction Systems: A Review&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3627189/&quot;&gt;Leaf-architectured 3D Hierarchical Artificial Photosynthetic System of Perovskite Titanates Towards CO2 Photoreduction Into Hydrocarbon Fuels&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ja905797w&quot;&gt;Water-Gas Shift Reaction Catalyzed by Redox Enzymes on Conducting Graphite Platelets&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-11-10T20:40:44.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23883" PostTypeId="2" ParentId="23868" CreationDate="2014-11-10T20:43:03.877" Score="1" Body="&lt;p&gt;Although your plastic bag tears are most likely due to light damage as @Chris mentioned above, there is a type of ant that chews its way through plastic, rubber and other manufactured polymers: &lt;em&gt;Monomorium pharaonis&lt;/em&gt;, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Pharaoh_ant&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pharaoh ant&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/7/71/Monomorium_pharaonis_casent0173986_profile_1.jpg&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is &lt;a href=&quot;http://en.wikipedia.org/wiki/Pharaoh_ant#Invasiveness_and_extermination&quot; rel=&quot;nofollow noreferrer&quot;&gt;capable of destroying&lt;/a&gt; many manufactured materials and is a great example of &lt;a href=&quot;http://www.pestproducts.com/pharaohants.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;budding&lt;/a&gt;, a method by which new ant colonies form. They are very invasive and &lt;a href=&quot;http://combattermitespecialist.com/ants/&quot; rel=&quot;nofollow noreferrer&quot;&gt;difficult to control&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.753" LastActivityDate="2014-11-10T20:43:03.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23884" PostTypeId="2" ParentId="23881" CreationDate="2014-11-10T21:16:16.397" Score="1" Body="&lt;p&gt;As you can see from the bottom of the gel, the brightness of the bands have reduced even for the DNA ladder/marker. The main reason for this is that when you are running an agarose gel containing EtBr, due to the positive charge of the EtBr, the stain runs to the negative chamber, against the direction of the DNA migration as @Chris has pointed out! Although some of the DNA will stain but the rest of the EtBr will migrate towards the top of the gel (where the DNA is loaded).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A quick remedy for this is once you ran your gel is to soak your gel in a separate container containing your stain and running buffer such as TAE. I do this for one hour and that makes a huge difference!! Also make sure you regularly change the buffer in your agarose gel running apparatus and don't use the same buffer for a long time since again as @Chris has correctly pointed out there is a reduced conductivity in the older buffers when they heat up so migration does not work as well! Obviously this response assumes that you have a good degree (amount) of DNA in your gel bands, which can be calculated by nanodrop once you extracted the DNA using an extraction kit, or whatever method you normally use. I hope this helps!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This answer is more suited to the title of the question since after reading the main question a bit more carefully I'm slightly confused! So do you see anything at all or your product is far too faint? could you tell us where on the gel, relative to the ladder you expect to see this band? are they the ones at the button of the gel, below the loading buffer?&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="19277" LastEditDate="2015-10-20T15:54:16.927" LastActivityDate="2015-10-20T15:54:16.927" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23885" PostTypeId="2" ParentId="23872" CreationDate="2014-11-10T22:58:21.193" Score="10" Body="&lt;p&gt;The &quot;back of your mind&quot; is correct: &lt;em&gt;&quot;if the muscle gets bigger, it's simply because individual cells get bigger.&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Growth of muscle can occur in three ways: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;by an increase in muscle cell numbers&lt;/li&gt;&#xA;&lt;li&gt;by an increase in muscle fiber diameter&lt;/li&gt;&#xA;&lt;li&gt;by an increase in fiber length. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;However, growth in &lt;em&gt;cell numbers&lt;/em&gt; is &lt;strong&gt;limited to the prenatal and immediately postnatal period, with the animals and man being born with or soon reaching their full complement of muscle cells.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[G]rowth occurs by either hypertrophy of the existing muscle fibers by adding additional myofibrils to increase the muscle mass or by adding new sarcomeres to the ends of the existing muscle fibers to increase their length. Both of these mechanisms occur during the growth process. Growth in the girth of the muscle fibers... may be stimulated by development of stress creating an unequal pressure with splitting at the Z-band and development of additional SR and T-tubule systems. This adds to the diameter or girth of myofibers without any hyperplasia. The growth in length occurs at either end of the fibers and results in addition of new sarcomeres. In both cases, new myofibrillar protein must be synthesized and deposited in the muscle cells. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Adding or removing sarcomeres and myofibrils is determined by exercise, that is, the degree of force a muscle can generate which is in turn dependent on the degree of overlap of the thick and thin filaments. Thus, the amount of tension would control the number of in-series sarcomeres and the number of myofibrils in a single muscle fiber. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nutrition is also known to play an important role in muscle growth, but growth (that is, increase in girth) cannot occur without exercise. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact roles of GF and IGF-I are not completely clear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Muscle size does not increase by the addition of new muscle cells:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The results show that the &lt;em&gt;increase in muscle cross-sectional area from childhood to adult age is caused by an increase in mean fiber size.&lt;/em&gt; This is accompanied by a functional development of the fiber population: the proportion of type 2 fibers increases significantly from the age of 5 (approx. 35%) to the age of 20 (approx. 50%), which, &lt;strong&gt;in the absence of any discernible effect on the total number of fibers&lt;/strong&gt;, is most likely caused by a transformation of type 1 to type 2 fibers.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Activation of satellite cells&lt;/em&gt;, a claim made by body builders, is mis-represented by them. The &lt;em&gt;satellite cells&lt;/em&gt; seem only to &lt;em&gt;aid&lt;/em&gt; severely damaged muscle cells to heal, not to increase in number.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2222798&quot;&gt;Muscle growth and exercise&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Muscle_hypertrophy&quot;&gt;Muscle hypertrophy&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/mus.880150323/abstract&quot;&gt;Growth and development of human muscle: A quantitative morphological study of whole vastus lateralis from childhood to adult age&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2439518/&quot;&gt;Regulation of muscle mass by growth hormone and IGF-I&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-11-12T09:24:05.720" LastActivityDate="2014-11-12T09:24:05.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23886" PostTypeId="2" ParentId="23863" CreationDate="2014-11-10T23:25:12.030" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;It's a popular public sentiment that - GM foods like tomatoes (flavr&#xA;  savr) will affect our health.. Is there any logical scientific&#xA;  explanation behind this?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;GM organisms can have different genes and gene expression than natural ones, so they can create more protein or different proteins. Proteins can be toxic, can cause allergy and can catalyze reactions which can lead to toxic products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To create a GM plant you need dollar millions, so it is not a cheap business. The GMO food regulations are very strict (at least in the EU), so it is unlikely that you will eat a GMO which contains toxic compounds.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Whereas food safety organizations find nothing inherently unsafe in&#xA;  the process of genetic engineering, they note that new plant&#xA;  characteristics developed in the next wave of agricultural&#xA;  biotechnology could present new risks. At the same time, future&#xA;  generations of biotechnology may well provide food products with&#xA;  higher vitamin or protein content and lower allergenicity, yielding&#xA;  benefits to food consumers.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://www.pannonbiotech.hu/_upload/editor/GM_Economics.pdf&quot; rel=&quot;nofollow&quot;&gt;Agricultural Biotechnology: The Promise and Prospects of Genetically Modified Crops&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Despite all the effort to make GMO foods safe, there are issues:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pesticides associated to genetically modified foods (PAGMF), are&#xA;  engineered to tolerate herbicides such as glyphosate (GLYP) and&#xA;  gluphosinate (GLUF) or insecticides such as the bacterial toxin&#xA;  bacillus thuringiensis (Bt). The aim of this study was to evaluate the&#xA;  correlation between maternal and fetal exposure, and to determine&#xA;  exposure levels of GLYP and its metabolite aminomethyl phosphoric acid&#xA;  (AMPA), GLUF and its metabolite 3-methylphosphinicopropionic acid&#xA;  (3-MPPA) and Cry1Ab protein (a Bt toxin) in Eastern Townships of&#xA;  Quebec, Canada. Blood of thirty pregnant women (PW) and thirty-nine&#xA;  nonpregnant women (NPW) were studied. Serum GLYP and GLUF were&#xA;  detected in NPW and not detected in PW. Serum 3-MPPA and CryAb1 toxin&#xA;  were detected in PW, their fetuses and NPW. This is the first study to&#xA;  reveal the presence of circulating PAGMF in women with and without&#xA;  pregnancy, paving the way for a new field in reproductive toxicology&#xA;  including nutrition and utero-placental toxicities.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0890623811000566&quot; rel=&quot;nofollow&quot;&gt;Maternal and fetal exposure to pesticides associated to genetically modified foods in Eastern Townships of Quebec, Canada&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The study of combined effects of pesticides represents a challenge for&#xA;  toxicology. In the case of the new growing generation of genetically&#xA;  modified (GM) plants with stacked traits, glyphosate-based herbicides&#xA;  (like Roundup) residues are present in the Roundup-tolerant edible&#xA;  plants (especially corns) and mixed with modified Bt insecticidal&#xA;  toxins that are produced by the GM plants themselves. The potential&#xA;  side effects of these combined pesticides on human cells are&#xA;  investigated in this work. Here we have tested for the very first time&#xA;  Cry1Ab and Cry1Ac Bt toxins (10?ppb to 100?ppm) on the human embryonic&#xA;  kidney cell line 293, as well as their combined actions with Roundup,&#xA;  within 24?h, on three biomarkers of cell death: measurements of&#xA;  mitochondrial succinate dehydrogenase, adenylate kinase release by&#xA;  membrane alterations and caspase 3/7 inductions. Cry1Ab caused cell&#xA;  death from 100?ppm. For Cry1Ac, under such conditions, no effects were&#xA;  detected. The Roundup tested alone from 1 to 20 000?ppm is necrotic&#xA;  and apoptotic from 50?ppm, far below agricultural dilutions (50%&#xA;  lethal concentration 57.5?ppm). The only measured significant combined&#xA;  effect was that Cry1Ab and Cry1Ac reduced caspases 3/7 activations&#xA;  induced by Roundup; this could delay the activation of apoptosis.&#xA;  There was the same tendency for the other markers. In these results,&#xA;  we argue that modified Bt toxins are not inert on nontarget human&#xA;  cells, and that they can present combined side-effects with other&#xA;  residues of pesticides specific to GM plants.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jat.2712/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;Cytotoxicity on human cells of Cry1Ab and Cry1Ac Bt insecticidal toxins alone or with a glyphosate-based herbicide&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Though GM crops promises to meet the world's food need and eliminate&#xA;  the world hunger and starvation, the potent harmful effects cannot be&#xA;  overlooked and these need to be taken seriously. The long term impact&#xA;  on the society cannot be overruled as it includes the health risk of&#xA;  all the people involved be it producers (farmers) or the consumers&#xA;  along with the scientists who are working in the laboratory. Hence, it&#xA;  is the need of the hour to reach and try for sustainable development&#xA;  that meets the needs of humans and the balance of nature maintained.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0067079&quot; rel=&quot;nofollow&quot;&gt;Cry1Ab Treatment Has No Effects on Viability of Cultured Porcine Intestinal Cells, but Triggers Hsp70 Expression&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I think it is the same story as by food, pharma and plastic industry. The billion dollar profit can be more important than the consequences. Btw. if you check a regular food, which you can buy in the shop, you will find a lot of unhealthy components e.g. trans fatty acids, omega-6 fatty acids, fungicide remnants, etc... which can affect your health as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My conclusion is that in most of the cases it is safe, however in rare cases it might have a mild harmful effect. To filter out those cases and their causes we need further studies and better regulation.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-11-10T23:25:12.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23887" PostTypeId="1" CreationDate="2014-11-10T23:40:59.073" Score="3" ViewCount="293" Body="&lt;p&gt;I am looking for someone to identify this bug:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/I5eoy.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10144" LastEditorUserId="6561" LastEditDate="2015-10-12T23:49:57.393" LastActivityDate="2015-10-12T23:49:57.393" Title="Can Anyone Identify This Bug" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23888" PostTypeId="2" ParentId="23877" CreationDate="2014-11-10T23:51:25.490" Score="3" Body="&lt;p&gt;I think part of the confusion is that these terms are very loosely defined.  Also this discusses evolution in terms of taxanomic radiation, e.g. macroevolution at large spatial and temporal scales.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Problem 1 is that you haven't been clear about what kind of competition, inter or intraspecific competition?  These will have opposing effects generally which can counter balance each other &lt;a href=&quot;http://www.dx.doi.org/10.1098/rspb.2010.0018&quot; rel=&quot;nofollow&quot;&gt;[1]&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.dx.doi.org/10.1098/rspb.2013.1253&quot; rel=&quot;nofollow&quot;&gt;[2]&lt;/a&gt;.  When a species is free from interspecific competition, but under high intraspecific competition, that will promote an adaptive radiation, which concurrent morphological changes.  The most famous example of this would be Darwin's finches as studied by the Grants &lt;a href=&quot;http://www.dx.doi.org/10.1126/science.1070315&quot; rel=&quot;nofollow&quot;&gt;[3]&lt;/a&gt;.  With a lack of interspecific competition, the finches exhibited rapid morphological divergence.  Following the logic of this, you'll see that lack of competition will lead the kind of rapid taxanomic radiation the video is discussing, especially over a longer time scale.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However increased interspecific competition will have two effects. It will reduce the number of available niches for an existing species to expand into &lt;a href=&quot;http://www.dx.doi.org/10.1111/j.1558-5646.2010.01026.x&quot; rel=&quot;nofollow&quot;&gt;[4]&lt;/a&gt;, this generally will drive specialization of a species, which tends to limit genetic diversity which will lead to less &quot;raw material&quot; for evolution to work with. This specialization though is also technically evolution.  However with fewer niches, the new species tend to arise via replacement of existing species in an existing niche, as opposed to an adaptive radiation.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you can see how actually both conclusions are right depending on the type of evolution and competition being considered.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More interspecific competition -&gt; More specialization (one type of evolution), less adaptive radiation (another type of evolution)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More intraspecific competition -&gt; More adapative radiation, less specialization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope that helps answer your question.&lt;/p&gt;&#xA;" OwnerUserId="1097" LastActivityDate="2014-11-10T23:51:25.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23889" PostTypeId="2" ParentId="23871" CreationDate="2014-11-10T23:57:51.730" Score="9" Body="&lt;p&gt;I believe every living organism (even single cell ones) experience pain somehow, because it is important to stay alive. The scientific answer depends on how you define pain...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Related articles:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Evidence suggests that some, if not all, invertebrates have the&#xA;  potential to suffer through current practices that do not take into&#xA;  consideration that invertebrates may experience something like pain&#xA;  and stress and have the capacity for advanced and unexpected cognitive&#xA;  abilities.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.scielosp.org/scielo.php?pid=S0021-25712013000100004&amp;amp;script=sci_arttext&amp;amp;tlng=p&quot;&gt;Invertebrate welfare: an overlooked issue&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Genetic analysis of nociceptive behaviors in the nematode&#xA;  Caenorhabditis elegans and the fruit fly Drosophila melanogaster has&#xA;  led to the discovery of conserved sensory transduction channels and&#xA;  signaling molecules. These are embedded in neurons and circuits&#xA;  that generate responses to noxious signals. This article reviews the&#xA;  neurons and molecular mechanisms that underlie invertebrate&#xA;  nociception. We begin with the neurobiology of invertebrate&#xA;  nociception, and then focus on molecules with conserved functions in&#xA;  vertebrate nociception and sensory biology.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2004 - &lt;a href=&quot;http://www.rockefeller.edu/labheads/bargmann/pdf/TobinRev.pdf&quot;&gt;Invertebrate Nociception: Behaviors, Neurons and&#xA;Molecules&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Just to mention fire ants you possibly meet are invasive species, so you should not protect them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gXqxH.gif&quot; alt=&quot;fire ants worldwide&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The red imported fire ant, Solenopsis invicta Buren, is an invasive&#xA;  pest that has become widespread in the southern United States and&#xA;  Caribbean after accidental introduction from South America in the&#xA;  1930's. This species, which has diverse detrimental impacts on&#xA;  recipient communities, was recently discovered in Australia and New&#xA;  Zealand and has the potential to colonize numerous other regions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 1 - fire ants worldwide - &lt;a href=&quot;http://www.ars.usda.gov/Main/docs.htm?docid=9168&quot;&gt;source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-11-10T23:57:51.730" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23890" PostTypeId="2" ParentId="23855" CreationDate="2014-11-11T00:06:51.127" Score="2" Body="&lt;p&gt;Mutations can be caused by much more than just recombinatory events--polymerase fidelity, DNA damage repair, even environmental factors can have a huge impact on DNA damage. While most DNA polymerases have an error rate of around one mutation per billion, there are different levels of fidelity among different polymerases (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3639319/&quot; rel=&quot;nofollow&quot;&gt;McCulloch and Kunkel, 2008&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the fidelity of crossover/recombination events, it is true that these events increase the likelihood of a lethal or detrimental mutation. However, recombination is not a random process. &lt;a href=&quot;http://en.wikipedia.org/wiki/Recombination_hotspot&quot; rel=&quot;nofollow&quot;&gt;Recombination hotspots&lt;/a&gt; are chromosomal locations where the rate of recombination can be hundreds of times higher than other locations. These hotspots are generally in &quot;safe&quot; locations, not in the middle of a crucial gene, etc. There are also recombinase enzymes &lt;a href=&quot;http://en.wikipedia.org/wiki/Site-specific_recombination&quot; rel=&quot;nofollow&quot;&gt;specific to certain sites of recombination&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to &quot;which is better&quot;, I don't think the answer is as straightforward as you might think. You might think a sexually-reproducing eukaryote with a very high-fidelity DNA polymerase and safe, specific recombination hotspots would be ideal. That situation is generally what we find in nature, so you're (probably) correct. However, at the other extreme, think of a virus*. Viruses have a much, &lt;em&gt;much&lt;/em&gt;, &lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mutation_rate#Variation_in_mutation_rates&quot; rel=&quot;nofollow&quot;&gt;much&lt;/a&gt;&lt;/strong&gt; higher rate of mutation than eukaryotes--orders of magnitude higher. This is how a virus survives, basically out-evolving the host's defenses. A high rate of mutation works for a virus, and a low rate of mutation works for a multicellular eukaryote.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*Of course, there is always debate about &lt;a href=&quot;http://serc.carleton.edu/microbelife/yellowstone/viruslive.html&quot; rel=&quot;nofollow&quot;&gt;whether or not viruses are alive&lt;/a&gt;. However, they definitely reproduce.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2014-11-11T00:06:51.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23892" PostTypeId="2" ParentId="23887" CreationDate="2014-11-11T00:33:52.997" Score="3" Body="&lt;p&gt;It is an &lt;a href=&quot;http://hu.wikipedia.org/wiki/Orm%C3%A1nyosbog%C3%A1r-f%C3%A9l%C3%A9k&quot; rel=&quot;nofollow noreferrer&quot;&gt;ormányosbogár&lt;/a&gt; species. :D&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Curculionidae&quot; rel=&quot;nofollow noreferrer&quot;&gt;Curculionidae&lt;/a&gt; in Latin. I don't know the exact species, but it is common here in Hungary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is something like Mecinus janthinus, but it seems like shorter. Probably &lt;a href=&quot;https://www.flickr.com/photos/micks-wildlife-macros/4041408914/in/pool-britishbeetles|micks-wildlife-macros&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mecinus pyraster&lt;/a&gt; or another &lt;a href=&quot;http://claude.schott.free.fr/Mecininae/Mecininae_PL1.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mecinus species&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cFsyh.jpg&quot; alt=&quot;Mecinus janthinus&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 1 - Mecinus janthinus - &lt;a href=&quot;http://www.nhmus.hu/~podlussany/ormanyosfotok.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I think it is &lt;a href=&quot;http://en.wikipedia.org/wiki/Wheat_weevil&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sitophilus granarius&lt;/a&gt; aka. wheat weevil, but it is hard to decide because of the poor quality photo...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1LAho.jpg&quot; alt=&quot;Sitophilus granarius&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 2 - Sitophilus granarius - wheat weevil - &lt;a href=&quot;http://en.wikipedia.org/wiki/Wheat_weevil&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-11-11T01:03:39.997" LastActivityDate="2014-11-11T01:03:39.997" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23893" PostTypeId="1" CreationDate="2014-11-11T00:47:50.240" Score="2" ViewCount="51" Body="&lt;p&gt;I am taking a course on the nervous system and I am do not have any physics background. Therefore, I would like to know, what are we precisely talking about when we talk about current in the nervous system? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the same time what are we talking about when we talk about potential (i.e membrane potential or action potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I once heard an analogy about waterfall and water comparing current and potential (voltage), can someone elaborate on that for me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I know that electrical activity is the flow of electrons. Therefore does that mean that passive current in an axon/nerve is a flow of electrons? And is it also a flow of electrons when we have action potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance for all the help.&lt;/p&gt;&#xA;" OwnerUserId="8279" LastActivityDate="2014-11-11T21:42:38.663" Title="Confusion over role of current/potential in Nervous system?" Tags="&lt;neuroscience&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23894" PostTypeId="2" ParentId="23893" CreationDate="2014-11-11T01:04:20.923" Score="3" Body="&lt;p&gt;&lt;strong&gt;Current flow&lt;/strong&gt; is the movement of charged particles (ions in this case). The &lt;strong&gt;membrane potential&lt;/strong&gt; is the charge difference across the cell membrane. Usually there is more negative charge inside the cell than out, so the membrane potential is said to be negative. When ion channels open, typically positive ions (Na&lt;sup&gt;+&lt;/sup&gt;, K&lt;sup&gt;+&lt;/sup&gt;) will flow into the cell as they are flowing from a medium that is approximately uncharged (extracellular space) into an environment that is highly negatively charged. &lt;strong&gt;By analogy&lt;/strong&gt;, the positive ions can be viewed as water flowing down a gradient (waterfall). &lt;strong&gt;Electrical activity&lt;/strong&gt; is not a flow of electrons per definition, especially not so in nervous tissue where it is ions that move (it is indeed electrons in electric circuits and the likes). During an &lt;strong&gt;action potential&lt;/strong&gt;, therefore, it is &lt;em&gt;not&lt;/em&gt; electrons that are moving across the cell membrane, but ions, most notably Na&lt;sup&gt;+&lt;/sup&gt; and K&lt;sup&gt;+&lt;/sup&gt;, but also Ca&lt;sup&gt;+&lt;/sup&gt;, Cl&lt;sup&gt;-&lt;/sup&gt; among other charged particles. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-11T21:42:38.663" LastActivityDate="2014-11-11T21:42:38.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23896" PostTypeId="2" ParentId="23873" CreationDate="2014-11-11T01:25:12.360" Score="1" Body="&lt;p&gt;Another alternative is using plants to generate biomasse using photosynthesis and letting bacteria convert that into electricity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is research being done about this method and you can read more about it on the following websites:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plantpower.eu/&quot; rel=&quot;nofollow&quot;&gt;http://www.plantpower.eu/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://plant-e.com/technology.html&quot; rel=&quot;nofollow&quot;&gt;http://plant-e.com/technology.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="10145" LastActivityDate="2014-11-11T01:25:12.360" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23898" PostTypeId="1" CreationDate="2014-11-11T02:05:06.437" Score="3" ViewCount="433" Body="&lt;p&gt;I heard somewhere that activating any receptor results in the same intracellular response (signaling) which involves &lt;a href=&quot;http://en.wikipedia.org/wiki/NF-%CE%BAB&quot; rel=&quot;nofollow noreferrer&quot;&gt;NF-κB&lt;/a&gt;. If that is true, I hardly understand how the cells distinguish between different types of stimulis coming from different types of receptors. I guess I am missing the point... :S&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/d2mZ4.png&quot; alt=&quot;signal transduction&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 1 - signal transduction - &lt;a href=&quot;http://en.wikipedia.org/wiki/Signal_transduction&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If you check this picture about signal transduction. What you can see that there are about 10 arrows pointing to the inside of the nucleus, and there are about 10 receptor categories involved. Afaik. there are much more genes in the nucleus, so how is it possible to regulate the expression of so many genes with only a few signaling pathways?&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-11-11T02:33:54.667" LastActivityDate="2015-01-07T21:25:51.733" Title="Does the cellular response to every receptor work the same way?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cell-biology&gt;&lt;cell-signaling&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23900" PostTypeId="1" CreationDate="2014-11-11T02:15:34.977" Score="3" ViewCount="1430" Body="&lt;p&gt;I heard somewhere that cells use different nucleosides bound to triphosphates e.g. ATP, GTP, CTP and other modified compounds: NADH, NADPH to distinguish between different metabolic pathways and so they regulate where they use up the energy. I heard that kinases play an important role in the regulation. Is there a connection (I guess there is if I check NAD&lt;strong&gt;P&lt;/strong&gt;H)? Is this regulation mapped? I mean is there a simple map which contains the main processes and the energy carrier and regulatory compounds?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for something like this map (of receptor responses), but for metabolic regulation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kFkt1.png&quot; alt=&quot;signal transduction&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 1 - signal transduction - &lt;a href=&quot;http://en.wikipedia.org/wiki/Signal_transduction&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So it possibly contains mitochondria, O&lt;sub&gt;2&lt;/sub&gt;, CO&lt;sub&gt;2&lt;/sub&gt;, flows, ATP, NADPH, etc... I understand that different cell types can have different energy producer and consumer organelles and it is not possible to create something that is universally true, so I would be satisfied with a map of your favorite human cell type.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3340" LastEditDate="2014-11-11T13:09:18.223" LastActivityDate="2014-11-11T13:09:18.223" Title="How does the cell regulate different metabolic pathways?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;physiology&gt;&lt;metabolism&gt;&lt;cell-signaling&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23901" PostTypeId="1" CreationDate="2014-11-11T02:47:20.713" Score="6" ViewCount="342" Body="&lt;p&gt;When I was a child, my father showed me the classic essay &lt;a href=&quot;http://irl.cs.ucla.edu/papers/right-size.html&quot; rel=&quot;noreferrer&quot;&gt;&quot;On Being the Right Size&quot;, J. B. S. Haldane&lt;/a&gt;.  It talks (among other things) about how large animals need stockier legs to support their weight.  I weigh about the same per leg as a 350 lb deer, but my legs are closer in diameter to those of a 1500 lb horse. Why?&lt;/p&gt;&#xA;" OwnerUserId="840" LastEditorUserId="840" LastEditDate="2014-11-11T04:39:14.997" LastActivityDate="2014-11-11T17:56:40.203" Title="Comparative leg sizes" Tags="&lt;evolution&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23902" PostTypeId="1" AcceptedAnswerId="23903" CreationDate="2014-11-11T03:07:15.267" Score="0" ViewCount="81" Body="&lt;p&gt;Shampoo and conditioning products make claims to be the end all be all in hair care. I doubt that they are so advanced &quot;growth formula/anti-breakage/oily treatment&quot;. Have any of the claims been shown to be valid? Assuming a positive response do they have application for restoring the hairs used for hearing?&lt;/p&gt;&#xA;" OwnerUserId="9828" LastActivityDate="2014-11-11T09:08:53.793" Title="Do hairs in the ear respond to things like shampoo?" Tags="&lt;hearing&gt;&lt;hair&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23903" PostTypeId="2" ParentId="23902" CreationDate="2014-11-11T03:34:24.083" Score="2" Body="&lt;p&gt;You are mixing up hair cells and hair. Hair cells in the cochlea (&lt;a href=&quot;http://en.wikipedia.org/wiki/Organ_of_Corti&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;) have tiny stereocilia (subcellular organelles) that sense vibrations approaching the atomic scale. These are then translated in hyperpolarizing or depolarizing currents that drive the spiral ganglion cells of the auditory nerve. The 'hairs' on the hair cells will not readily benefit from shampoo I'm afraid. If you should want to test it, the shampoo should be intracochlearly administered in the scala media of the cochlea - so even if shampoo is beneficial it would be hard to utilize it without surgical intervention. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-11T09:08:53.793" LastActivityDate="2014-11-11T09:08:53.793" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23904" PostTypeId="2" ParentId="23900" CreationDate="2014-11-11T05:00:52.773" Score="0" Body="&lt;p&gt;Our body maintains a very delicate balance between the concentration of metabolites and substrates. If a pathway is not regulated, excess of a particular metabolite can disturb the whole process. Let's take cholesterol metabolism pathway for example. there are various means by which the cells control the production of cholesterol. For example AMP controlled kinase protein detects weather the concentration of ATP is high or not, if its low then the cell does not proceed with the production of it, by inhibiting the enzyme that catalysis the production of mevalonate. Other way is through transcription factor that is present  called SREBP. &lt;strong&gt;S&lt;/strong&gt;terol &lt;strong&gt;R&lt;/strong&gt;egulatory &lt;strong&gt;E&lt;/strong&gt;lement &lt;strong&gt;B&lt;/strong&gt;inding &lt;strong&gt;P&lt;/strong&gt;rotein regulate multiple genes that are involved in metabolism of cholesterol. Various protein denaturing components are present that upon receiving signal cleaves the intermediate's in the metabolism of cholesterol. &#xA;There are &lt;em&gt;n&lt;/em&gt;-number of pathways in our body and all are regulated by a complex network of signals that regulate them.&lt;/p&gt;&#xA;" OwnerUserId="8026" LastEditorUserId="3340" LastEditDate="2014-11-11T07:13:53.010" LastActivityDate="2014-11-11T07:13:53.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23906" PostTypeId="2" ParentId="23818" CreationDate="2014-11-11T06:17:27.053" Score="7" Body="&lt;p&gt;I haven't done this exact experiment. I am just deducing from the known facts about PCR. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The product of &lt;code&gt;PF&lt;/code&gt; and &lt;code&gt;PR2&lt;/code&gt; will serve as a template for both 1kb product (&lt;code&gt;P1&lt;/code&gt;) and 2kb product (&lt;code&gt;P2&lt;/code&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lets assume that after 2&lt;sup&gt;nd&lt;/sup&gt; cycle there is 1 copy each of &lt;code&gt;P1&lt;/code&gt; and &lt;code&gt;P2&lt;/code&gt; (Delay of 1 cycle to make a smaller length product. See &lt;a href=&quot;https://biology.stackexchange.com/questions/20266/how-are-dna-segments-selected-in-pcr/20267#20267&quot;&gt;here&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lets assume that the primer binding affinity is equal (and for just preliminaries consider that only one primer can bind a template — such as in overlapping binding sites). So half of &lt;code&gt;P2&lt;/code&gt; will bind to &lt;code&gt;PR2&lt;/code&gt; and half to &lt;code&gt;PR1&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Number of copies at n&lt;sup&gt;th&lt;/sup&gt; cycle is:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;P2&lt;sub&gt;(n)&lt;/sub&gt; = 1.5 × P2&lt;sub&gt;(n-1)&lt;/sub&gt;&#xA;&#xA;P1&lt;sub&gt;(n)&lt;/sub&gt; = 2 × P1&lt;sub&gt;(n-1)&lt;/sub&gt; + 0.5 × P2&lt;sub&gt;(n-2)&lt;/sub&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;However this is not really the scenario; the primers are not competing for the template.&#xA;Which means that both primers can bind to the substrate simultaneously. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/b2QKy.png&quot; alt=&quot;nested PCR&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA polymerases (except Klenow) will remove any DNA strand bound to the template, ahead of it. In that case &lt;code&gt;P1&lt;/code&gt; will not form. But when &lt;code&gt;PR2&lt;/code&gt; runs out, the unused &lt;code&gt;PR1&lt;/code&gt; can produce &lt;code&gt;P1&lt;/code&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now there are additional factors, such as the distance between &lt;code&gt;PR1&lt;/code&gt; and &lt;code&gt;PR2&lt;/code&gt; binding sites. If the distance between the primer binding sites is less than the smaller product then the abovementioned case occurs. If the inter-primer distance is larger than smaller product then both products will form (and just like the competing primers case, &lt;code&gt;P2&lt;/code&gt; will serve as a template for both products). In this case the copy numbers will be:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;P2&lt;sub&gt;(n)&lt;/sub&gt; = 2 × P2&lt;sub&gt;(n-1)&lt;/sub&gt;&#xA;&#xA;P1&lt;sub&gt;(n)&lt;/sub&gt; = 2 × P1&lt;sub&gt;(n-1)&lt;/sub&gt; + 1 × P2&lt;sub&gt;(n-2)&lt;/sub&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This means that &lt;code&gt;P1&lt;/code&gt; will dominate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other assumptions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;No limiting concentrations of dNTP, primers etc&lt;/li&gt;&#xA;&lt;li&gt;PCR efficiencies are equal for both primers and is equal to 2 (in non-competing cases)&lt;/li&gt;&#xA;&lt;li&gt;Primer annealing temperatures are same i.e binding affinities are same.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-04-27T04:52:36.150" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23908" PostTypeId="1" AcceptedAnswerId="23909" CreationDate="2014-11-11T07:08:01.970" Score="9" ViewCount="135585" Body="&lt;p&gt;What are the I-IV blood type descriptions shown below (commonly used in Eastern Europe), and how do you translate them into the ABO-system?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4RrW0.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10150" LastEditorUserId="3624" LastEditDate="2014-11-11T14:05:28.713" LastActivityDate="2019-02-14T00:07:29.090" Title="How to translate a blood type used in Eastern Europe?" Tags="&lt;hematology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23909" PostTypeId="2" ParentId="23908" CreationDate="2014-11-11T07:29:50.903" Score="19" Body="&lt;p&gt;It is a direct correlation between the ABO blood groups and the Roman numerals. &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; O: I&#xA;&#xA; A: II&#xA;&#xA; B: III&#xA;&#xA;AB: IV&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This numeric system was pioneered by Jan Jansky of Czechoslovakia in the early 20th century. Apparently it is still used in some former Soviet states. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC537907/?page=1&quot; rel=&quot;noreferrer&quot;&gt;Erb IH. 1940. Blood Group Classification (A Plea for Uniformity). Can Med Assoc J 42(5):418-421.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2019-02-14T00:07:29.090" LastActivityDate="2019-02-14T00:07:29.090" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="23910" PostTypeId="1" CreationDate="2014-11-11T07:33:05.673" Score="2" ViewCount="699" Body="&lt;p&gt;I want to separate 1600 Da peptide on SDS PAGE, on 20% GEL I didn't get any band, How can I separate on PAGE? Can I use 25% SDS PAGE?&lt;/p&gt;&#xA;" OwnerUserId="8423" LastEditorUserId="3340" LastEditDate="2014-11-11T11:53:31.453" LastActivityDate="2018-02-20T02:43:03.330" Title="How to separate peptide on SDS PAGE?" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="23912" PostTypeId="2" ParentId="23910" CreationDate="2014-11-11T09:48:01.790" Score="4" Body="&lt;p&gt;                                                   &lt;img src=&quot;https://i.stack.imgur.com/0fjzj.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Image is of an 18% Tris-tricine small-peptide SDS-polyacrylamide gel stained with coomassie blue dye &lt;sup&gt;&lt;a href=&quot;http://www.thermoscientificbio.com/protein-electrophoresis/pageruler-unstained-low-range-protein-ladder/&quot; rel=&quot;nofollow noreferrer&quot;&gt;[source]&lt;/a&gt;&lt;/sup&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Your peptide is 1.6 kDa; it would not run off in 20% gel if you don't run it for a long time. Also, try to prevent heating up of the gel (you can run it in a cold room or in front of an A/C vent).  However, it is better to use other techniques such as chromatography. You can also try dialysis if other unwanted peptides are much larger.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nprot/journal/v1/n1/full/nprot.2006.4.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Protocol for Tris-Tricine SDS-PAGE&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-11-11T11:51:01.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23913" PostTypeId="2" ParentId="9993" CreationDate="2014-11-11T09:58:09.943" Score="8" Body="&lt;p&gt;To add my 2 cents worth: Breathing rate and depth is regulated by chemoreceptors in the medulla in the brainstem. These chemoreceptors primarily respond to pH of the blood, but the pH is for an important part determined by the CO&lt;sub&gt;2&lt;/sub&gt;/HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; equilibrium as explained by @TomD. Essentially it is the increase in CO&lt;sub&gt;2&lt;/sub&gt; that is sensed by the medulla and which increases breathing frequency and the depth of inhalation. See this &lt;a href=&quot;http://gayyoga.gn.apc.org/Respiration.htm&quot; rel=&quot;noreferrer&quot;&gt;web page about respiratory control&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-26T22:06:02.063" LastActivityDate="2015-03-26T22:06:02.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23914" PostTypeId="2" ParentId="23898" CreationDate="2014-11-11T11:17:46.020" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I heard somewhere that activating any receptor results in the same intracellular response (signaling) which involves NF-κB.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't think all receptors activate NF-κB (Pro-growth signals activate it, mostly).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;how the cells distinguish between different types of stimulis coming from different types of receptors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The cell need not, sometimes, know where and how the signal came from, unless it has to interact back to the origin of signal (as in case of neural synapses). Some pathways such as growth and inflammation can be triggered by many kinds of signals; the responses generally converge to a common pathway (&lt;em&gt;If all that cell has to do is to boost up inflammation, then it would be costly for the cell to keep a unique pathway for each kind of trigger.&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;there are much more genes in the nucleus, so how is it possible to regulate the expression of so many genes with only a few signaling pathways?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Some genes are co-regulated because they fall in the same pathway. They collectively comprise what is known as a regulon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, it is possible that multiple signaling pathways have a different response in combination compared either of them individually. Such mechanisms exist in differentiation pathways during development (Can't think of an exact example; will provide one in a while). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-11T11:17:46.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23915" PostTypeId="2" ParentId="23900" CreationDate="2014-11-11T11:45:06.387" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I heard somewhere that cells ………………………… so they regulate where they use up the energy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes NADP/H is primarily employed in anabolic pathways such as fatty acid synthesis, while NAD/H is employed in catabolic pathways such as glycolysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think there is a general rule for other &quot;&lt;em&gt;energy-currency&lt;/em&gt;&quot; molecules (pyrimidine triphosphates are not used except in some rare cases such as glycogenesis).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I mean is there a simple map which contains the main processes and the energy carrier and regulatory compounds?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can search for the term &quot;&lt;em&gt;metabolic network&lt;/em&gt;&quot;. It would be too huge so it is better to look at specific sub-networks. KEGG is a good site for finding metabolic networks. There are other representations like hive plots, to visualize very huge graphs.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-11T11:45:06.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23916" PostTypeId="1" AcceptedAnswerId="24168" CreationDate="2014-11-11T12:46:04.210" Score="6" ViewCount="7005" Body="&lt;p&gt;Before anything else please pay attention of the double quotes on the &amp;quot;equal&amp;quot; in the title - I know they are not equal, but you will understand in a bit.&lt;/p&gt;&#xA;&lt;p&gt;If I look at the DNA codon table &lt;a href=&quot;http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; or in &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_codon_table&quot; rel=&quot;noreferrer&quot;&gt;wikipedia&lt;/a&gt;, and at the RNA codon table &lt;a href=&quot;http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; or in &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_code#RNA_codon_table&quot; rel=&quot;noreferrer&quot;&gt;wikipedia&lt;/a&gt;, their only difference is that the former has thymine (T) whereas the latter has uridine (U). But I am not understanding how all other nucleotides are the same. Bear in mind that transcription reads DNA from 3'-&amp;gt;5' and translation reads mRNA from 5'-&amp;gt;3'.&lt;/p&gt;&#xA;&lt;p&gt;Look at this example, focusing on the 3'-TAC-5' of the antisense strand.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7zTjz.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The 3'-TAC-5' codes for Tyrosine according to the DNA codon table. However, it transcribes and translates  3'-TAC-5' -&amp;gt; 5'-AUG-3' -&amp;gt; Methionine.&lt;/p&gt;&#xA;&lt;p&gt;Now focus on the corresponding codon in the sense strand, 5'-ATG-3', which codes for Valine according to the DNA table (it is read from 3' to 5'). This codon transcribes and translates 3'-GTA-5' -&amp;gt; 5'-CAU-3' -&amp;gt; Histidine, not Valine and not Methionine.&lt;/p&gt;&#xA;&lt;p&gt;So my questions are:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Why do DNA codon tables show the correspondence between codons and amino acids in the sense strands (5'-ATG-3'), if the only way to go from ATG to Met as in the figure is to consider the antisense strand?&lt;/li&gt;&#xA;&lt;li&gt;I can see that the AUG codon translates to Methionine, and it is translated by reading the 3'-TAC-5' codon in antisense strand, whose corresponding codon in sense strand is 5'-ATG-3'. But this last one is read from 3'-&amp;gt;5', so it reads 3'-GTA-5' -&amp;gt; 5'-CAU-3' -&amp;gt; His.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;I am guessing I'm getting many things wrongly in this... Maybe on the way that I'm reading  the tables: I always take into account that transcription is read 3'-&amp;gt;5' and this is the order I take to read DNA tables.&lt;/p&gt;&#xA;&lt;p&gt;Thank you and sorry if I was confusing.&lt;/p&gt;&#xA;" OwnerUserId="3324" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-11-20T14:57:51.570" Title="Why is the DNA codon table &quot;equal&quot; to the RNA codon table" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;transcription&gt;&lt;translation&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23917" PostTypeId="2" ParentId="23763" CreationDate="2014-11-11T12:59:13.393" Score="6" Body="&lt;p&gt;Hydrophobicity means aversion to water which results because of increase in entropy of the system due to the water-&quot;solute&quot; interaction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As already pointed out in by inf3rno, polarity of a molecule is because of its net dipole moment. It is true that polar molecules can dissolve in water (because they can interact with water via van der Waals' forces especially Keesom and Debye forces).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CO&lt;sub&gt;2&lt;/sub&gt; is apolar but dissolves in water (it actually reacts with water). Most apolar substances cannot interact with water via van der Waals forces.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To sum up, usually polar substances are not-hydrophobic (i.e they are hydrophilic), however some polar molecules such as nitriles, ketones and esters can be hydro-neutral (midway between hydrophobic and hydrophilic. See &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jp4029968&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;). Even large polar molecules are insoluble in water such as 1,2 dichlorobenzene and nitrobenzenes (For something to be soluble the solute-solvent interactions should be stronger than solute-solute interactions. &quot;Water insoluble&quot; may not be equivalent to &quot;hydrophobic&quot;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conversely, apolar substances are hydrophobic (unless they are reactive solutes such as Cl&lt;sub&gt;2&lt;/sub&gt; and CO&lt;sub&gt;2&lt;/sub&gt;).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-11-11T13:27:19.087" LastActivityDate="2014-11-11T13:27:19.087" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23918" PostTypeId="2" ParentId="23916" CreationDate="2014-11-11T13:08:12.217" Score="6" Body="&lt;p&gt;Genetic code and codons are always used with reference to RNA. When talking about DNA, the the sense strand of a gene is considered its sequence. The anti-sense strand though is the template for mRNA synthesis, does not represent the gene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA-codon table has simply U replaced by T. Apart from a wikipedia article, I don't find the term being popularly (not colloquially) used elsewhere.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-11-11T13:31:29.120" LastActivityDate="2014-11-11T13:31:29.120" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="23919" PostTypeId="2" ParentId="1269" CreationDate="2014-11-11T13:49:53.297" Score="2" Body="&lt;p&gt;In &lt;a href=&quot;http://www.jbc.org/content/278/11/9361.long&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; study, even though they have used fluorescence based method, they have reported concentrations.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When we studied basal intracellular calcium concentrations in acini from control rats they were in the low nanomolar range (140 ± 5 nmol).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For ATP concentrations you can see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20102715&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is it possible to find this information in a specific book or website, to avoid trawling though vast amounts of literature?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is the &lt;a href=&quot;http://www.hmdb.ca/metabolites/HMDB00538&quot; rel=&quot;nofollow&quot;&gt;human metabolome database&lt;/a&gt;. However, it doesn't have data for all cell types. Either more studies are required or the database needs updation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly there is the &lt;a href=&quot;http://www.ymdb.ca/&quot; rel=&quot;nofollow&quot;&gt;yeast metabolome database&lt;/a&gt; (&lt;em&gt;you may not require it for your query but just another piece of information that I thought is worth adding&lt;/em&gt;).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-11T13:49:53.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23920" PostTypeId="1" AcceptedAnswerId="23921" CreationDate="2014-11-11T14:02:51.153" Score="1" ViewCount="88" Body="&lt;p&gt;I read on a vitamin-D product (2000NE) that I should not use calcium and magnesium with it, because it can result crystal formation in the blood. I googled, but find anything about this. Is it true?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Somehow I doubt it, but I don't know the exact mechanism how vitamin-D works by building bones. Afaik. there are osteoblasts and osteoclasts which constantly build and degrade the Ca-Mg-PO&lt;sub&gt;4&lt;/sub&gt; depos, and I assume vitamin-D is just a cofactor of an enzyme or it is required to produce a hormone. I never heard of Ca/Mg - vitamin-D cross-reactions...)&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3340" LastEditDate="2014-11-11T14:15:36.723" LastActivityDate="2014-11-11T14:15:36.723" Title="Does vitamin D form crystals in the blood with calcium and magnesium?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23921" PostTypeId="2" ParentId="23920" CreationDate="2014-11-11T14:12:52.497" Score="2" Body="&lt;p&gt;Vitamin D does not bind to Calcium. It is a pre-hormone which is converted to calcitriol. Calcitriol has an intracellular receptor (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/7421&quot; rel=&quot;nofollow&quot;&gt;VDR&lt;/a&gt;) that, as a heterodimer with Retinoid-X receptor, regulates gene expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess the &quot;should not be had together&quot; is because of possible over-absorption of Calcium. There are commercially available supplements (e.g. &lt;a href=&quot;http://www.jamiesonvitamins.com/node/19&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;http://www.hollandandbarrett.com/shop/product/holland-barrett-calcium-and-magnesium-with-vitamin-d-tablets-60016154&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;) that have Vit-D + Ca + Mg.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-11T14:12:52.497" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23922" PostTypeId="2" ParentId="1750" CreationDate="2014-11-11T14:41:48.303" Score="1" Body="&lt;p&gt;The fastest will change as time passes and better technologies are developed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the fastest method existing at the moment is &lt;a href=&quot;http://www.integralmolecular.com/mapping.php&quot; rel=&quot;nofollow&quot;&gt;Shotgun Mutagenesis&lt;/a&gt; (provided by Integral Molecular Inc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This does not employ any new method of doing that. They just provide a set of plasmids, that has all the possible mutations. The set itself is generated by automated DNA synthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if you don't have a DNA synthesizer with you then simply order the kit from the company. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-11T14:41:48.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23923" PostTypeId="2" ParentId="23873" CreationDate="2014-11-11T15:19:57.587" Score="0" Body="&lt;p&gt;Everyone's looking at photosynthesis for direct energy conversion, but it's not the only approach. Another function of most plants is to pump water up to altitude, to serve its own needs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tap into that - picking plants where the sap is watery, not inconveniently sticky like maple syrup, resinous, or likely to congeal into rubber, and you have at least hypothetically, the potential for micro hydro power...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm making no claims for energy density or efficiency.&lt;/p&gt;&#xA;" OwnerUserId="10154" LastActivityDate="2014-11-11T15:19:57.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23925" PostTypeId="1" AcceptedAnswerId="23928" CreationDate="2014-11-11T17:46:50.593" Score="5" ViewCount="108" Body="&lt;p&gt;I would like to know the mode of action of mosquito repellent aerosols. Are these specific to mosquito or are other insects affected too?&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="9943" LastEditDate="2014-11-14T11:17:42.963" LastActivityDate="2014-11-14T11:17:42.963" Title="Do mosquito repellent sprays work on all insects?" Tags="&lt;zoology&gt;&lt;entomology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23926" PostTypeId="2" ParentId="23901" CreationDate="2014-11-11T17:56:40.203" Score="1" Body="&lt;p&gt;There is an interesting relationship between the length of an animals femur, the thickness and the mass of the thickness. A point that should be taken into account is that bones can different densities and so might be able to support varying amounts. The muscle in you leg also does nothing for the support of you weight it is (basically) all in the bone. Really looking purely at the leg won't tell you much you need to strip back the tissue and get you measurements straight from that. Given the different gate strategies of various animals this can lead to differing levels of muscle surrounding the leg and could be confounding your answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Walter Lewin a professor of physics at MIT did a lecture series where in the first lecture he went off on one about the relative sizes and thickness of animal femurs and it is really interesting (&lt;a href=&quot;http://www.youtube.com/watch?v=PmJV8CHIqFc&quot; rel=&quot;nofollow&quot;&gt;http://www.youtube.com/watch?v=PmJV8CHIqFc&lt;/a&gt; - between 11 minutes and 22 minutes). The short answer was that the ratio between the thickness and the length stays similar relative to the length.&lt;/p&gt;&#xA;" OwnerUserId="6811" LastActivityDate="2014-11-11T17:56:40.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23928" PostTypeId="2" ParentId="23925" CreationDate="2014-11-11T20:23:00.503" Score="2" Body="&lt;p&gt;The most common active ingredient in insect repellents is &lt;em&gt;N&lt;/em&gt;,&lt;em&gt;N&lt;/em&gt;-diethyl-3-methylbenzamide (other name: &lt;em&gt;N&lt;/em&gt;,&lt;em&gt;N&lt;/em&gt;-diethyl-&lt;em&gt;m&lt;/em&gt;-toluamide; abbreviated DEET). It provides protection against mosquitoes and many other insects. After various interesting hypotheses, it is currently assumed that mosquitoes simply smell DEET directly and avoid it.&lt;a href=&quot;http://www.pnas.org/content/early/2008/08/19/0805312105&quot; rel=&quot;nofollow&quot;&gt;&amp;#091;1&amp;#093;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user9516" LastEditorDisplayName="user9516" LastEditDate="2014-11-12T09:38:01.283" LastActivityDate="2014-11-12T09:38:01.283" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23929" PostTypeId="1" AcceptedAnswerId="23931" CreationDate="2014-11-11T20:35:24.433" Score="1" ViewCount="656" Body="&lt;p&gt;Is the nuclear envelope present in G1 of interphase of eukaryotic cell? If so how does a method like Calcium mediated transfection get DNA past the nuclear envelope?&lt;/p&gt;&#xA;" OwnerUserId="10026" LastActivityDate="2014-11-12T00:54:11.473" Title="Is the nuclear envelope present in G1 of interphase?" Tags="&lt;dna&gt;&lt;cell-cycle&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23930" PostTypeId="1" CreationDate="2014-11-11T22:16:56.337" Score="1" ViewCount="41" Body="&lt;p&gt;Where can I purchase a fly with tagged collagen?  My senior undergraduate research paper is observing the collagen in larvae with normal diet compared to larvae with an experimental diet.  I need flies that have the protein tagged so I can observe the collagen under a fluorescent microscope.  Instead of using an expensive antibody (my budget is $300) to tag the protein, my advisor suggested purchasing stock flies that already have the tagged protein.&lt;/p&gt;&#xA;" OwnerUserId="10158" LastEditorUserId="3340" LastEditDate="2014-11-12T04:51:30.643" LastActivityDate="2014-11-12T04:51:30.643" Title="Where do I purchase a fly with the collagen tagged?" Tags="&lt;genetics&gt;&lt;histology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23931" PostTypeId="2" ParentId="23929" CreationDate="2014-11-12T00:54:11.473" Score="0" Body="&lt;p&gt;To answer the question about nuclear envelope in G1 phase, yes it exists. The nuclear envelope is reformed at the end of &lt;a href=&quot;http://en.wikipedia.org/wiki/Telophase&quot; rel=&quot;nofollow noreferrer&quot;&gt;Telophase&lt;/a&gt; after the 2 copies of the DNA are pulled apart, but before the two daughter cells are separated by cytokinesis. We can see the new nuclear envelope in these images:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/2VLVX.jpg&quot; alt=&quot;reappearance of nucleus in telophase&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image from &lt;a href=&quot;http://en.wikipedia.org/wiki/Telophase&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/U8B5f.jpg&quot; alt=&quot;Nucleus present in cytokinesis&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nuclei visible near end of cytokinesis, centrosome still visible. Image from &lt;a href=&quot;http://en.wikipedia.org/wiki/Cytokinesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for how DNA gets into the nucleus without cellular division I don't have a good answer and I'm not sure anyone does right now. The nuclear envelope is a major barrier for non-viral gene delivery.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-11-12T00:54:11.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23932" PostTypeId="1" CreationDate="2014-11-12T01:43:10.360" Score="4" ViewCount="867" Body="&lt;p&gt;Does DNA polymerase I in bacteria use forward or reverse exonuclease activity to remove RNA primers? One of my books says it uses 5' to 3', but another says it uses 3' to 5' exonuclease activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update: I know RNase H can remove the primers, but the exonuclease activity of pol I can also remove them.&lt;/p&gt;&#xA;" OwnerUserId="9063" LastEditorUserId="9063" LastEditDate="2014-11-25T04:34:50.937" LastActivityDate="2014-11-25T04:34:50.937" Title="DNA polymerase I exonuclease activity" Tags="&lt;microbiology&gt;&lt;replication&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23933" PostTypeId="2" ParentId="23932" CreationDate="2014-11-12T02:01:10.383" Score="2" Body="&lt;p&gt;Googling your question showed that it is RNAse H that removes the RNA primer. DNA Pol I has both 3'-5' as well as 5'-3' exonuclease activity for proofreading and nick repair activities, respectively. See the &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_polymerase_I&quot; rel=&quot;nofollow&quot;&gt;wiki on Pol I&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-12T07:43:57.813" LastActivityDate="2014-11-12T07:43:57.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23934" PostTypeId="2" ParentId="23932" CreationDate="2014-11-12T02:01:30.403" Score="2" Body="&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_polymerase_I&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the replication process, RNAse H removes the RNA primer (created by Primase) from the lagging strand and then Polymerase I fills in the necessary nucleotides between the Okazaki fragments (see DNA replication) in 5' -&gt; 3' direction...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And elsewhere in the same article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pol I possesses four enzymatic activities:&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;A 5' -&gt; 3' (forward) DNA-Dependent DNA polymerase activity, requiring a 3' primer site and a template strand&lt;/li&gt;&#xA;  &lt;li&gt;A 3' -&gt; 5' (reverse) exonuclease activity that mediates proofreading&lt;/li&gt;&#xA;  &lt;li&gt;A 5' -&gt; 3' (forward) exonuclease activity mediating nick translation during DNA repair.&lt;/li&gt;&#xA;  &lt;li&gt;A 5' -&gt; 3' (forward) RNA-Dependent DNA polymerase activity. Pol I operates on RNA templates with considerably lower efficiency (0.1–0.4%) than it does DNA templates, and this activity is probably of only limited biological significance.&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So the answer to your question is neither. RNAse H removes the primers, and the exonuclease activity of DNA Pol I is irrelevant to primer removal, although it turns out it can operate in either direction depending on the context.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-11-12T02:01:30.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23935" PostTypeId="2" ParentId="19873" CreationDate="2014-11-12T02:06:57.413" Score="1" Body="&lt;p&gt;Not to forget that simple cross breeding your plants the Mendelian way also modifies their genetic make up, as @souvik bhattacharya indicates in his comment. No equipment necessary, no chemicals, no ethical issues.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-12T02:06:57.413" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23936" PostTypeId="1" CreationDate="2014-11-12T03:01:32.053" Score="6" ViewCount="216" Body="&lt;p&gt;This bush is in Tennessee, USA.:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/TLjx1.jpg&quot; alt=&quot;flower bush pic 1&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Lr6Cs.jpg&quot; alt=&quot;flower bush pic 2&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/GyGzZ.jpg&quot; alt=&quot;flower bush pic 3:&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/pmR7o.jpg&quot; alt=&quot;flower bush pic 4: &quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10159" LastEditorUserId="8186" LastEditDate="2014-11-12T05:08:23.280" LastActivityDate="2018-09-21T12:15:18.187" Title="Can someone identify this flowering bush from the US?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23939" PostTypeId="2" ParentId="23930" CreationDate="2014-11-12T04:51:01.920" Score="3" Body="&lt;p&gt;There are some more places other than what Bez has already mentioned.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://flybase.org/wiki/FlyBase:Stock_Collections&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, tagging collagen may be a problem. Collagen undergoes a lot of post-translational modifications including hydroxylation and end clipping. It forms a unique structure (triplex) and adding tags may compromise its structural integrity. You can try &lt;a href=&quot;http://en.wikipedia.org/wiki/Masson%27s_trichrome_stain&quot; rel=&quot;nofollow&quot;&gt;Masson's trichome stain&lt;/a&gt; instead, which is used to stain collagen — a very cheap alternative. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-12T04:51:01.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23940" PostTypeId="2" ParentId="2814" CreationDate="2014-11-12T05:25:31.930" Score="1" Body="&lt;p&gt;There is no literature report saying such a thing. However, I did a cursory check for &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000124.v2.p1&quot; rel=&quot;nofollow&quot;&gt;GWAS study on neuroblastoma&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Selected SNPs with p-value&gt;0.05&lt;/li&gt;&#xA;&lt;li&gt;Converted p-values to a score —  &lt;pre&gt;-log&lt;sub&gt;10&lt;/sub&gt;(p-value)&lt;/pre&gt;&lt;/li&gt;&#xA;&lt;li&gt;Mapped the SNPs to genes while calculating cumulative score for a gene&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I just sorted the genes based on their names, assuming that many paralogs have similar names. I know it is not the right way to go about it. However, I found many similar named groups in the list. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the next step is find actual paralogs and to score the cumulative score for a paralog-group. This is a little task:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Get sequences of the genes&lt;/li&gt;&#xA;&lt;li&gt;Run a BLAST search to find paralogs&lt;/li&gt;&#xA;&lt;li&gt;Assign genes to groups and find scores&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I can share the file with genes and scores. I would, however, continue only if someone is actually interested in pursuing this — this could be a research paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: If you want the file just comment your email id. Some IT admin idiot has blocked rapidshare/4shared etc&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-12T05:25:31.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23942" PostTypeId="1" CreationDate="2014-11-12T06:27:31.440" Score="1" ViewCount="80" Body="&lt;p&gt;Anyone know of any experiments that have knocked out the genes for producing centrioles in a worm, mouse, fish, fly or whatever animal? Are the genes for centrioles even identified? It has been shown that centrosomes form with out centrioles so I'm curious how lack of centrioles would effect the system of an animal as a whole.&lt;/p&gt;&#xA;" OwnerUserId="10026" LastEditorUserId="10026" LastEditDate="2014-11-12T07:03:44.817" LastActivityDate="2014-11-12T07:03:44.817" Title="Centriole genes Knock-out Experiment in Common experimental animals?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23943" PostTypeId="2" ParentId="23942" CreationDate="2014-11-12T06:57:21.773" Score="1" Body="&lt;p&gt;One of the chief components of centrosome is γ-Tubulin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15893303&quot; rel=&quot;nofollow&quot;&gt;study&lt;/a&gt; the authors have reported the effect of γ-Tubulin knockout in mice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quoting the abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Gamma-tubulin regulates the nucleation of microtubules, but knowledge&#xA;  of its functions in vivo is still fragmentary. Here, we report the&#xA;  identification of two closely related gamma-tubulin isoforms, TUBG1&#xA;  and TUBG2, in mice, and the generation of TUBG1- and TUBG2-deficient&#xA;  mice. TUBG1 was expressed ubiquitously, whereas TUBG2 was primarily&#xA;  detected in the brain. The development of TUBG1-deficient (Tubg1-/-)&#xA;  embryos stopped at the morula/blastocyst stages due to a&#xA;  characteristic mitotic arrest: the mitotic spindle was highly&#xA;  disorganized, and disorganized spindles showed one or two pole-like&#xA;  foci of bundled MTs that were surrounded by condensed chromosomes.&#xA;  TUBG2 was expressed in blastocysts, but could not rescue the TUBG1&#xA;  deficiency. By contrast, TUBG2-deficient (Tubg2-/-) mice were born,&#xA;  grew, and intercrossed normally. In the brain of wild-type mice, TUBG2&#xA;  was expressed in approximately the same amount as TUBG1, but no&#xA;  histological abnormalities were found in the Tubg2-/- brain. These&#xA;  findings indicated that TUBG1 and TUBG2 are not functionally&#xA;  equivalent in vivo, that TUBG1 corresponds to conventional&#xA;  gamma-tubulin, and that TUBG2 may have some unidentified function in&#xA;  the brain.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Another important gene is pericentrin. Fibroblasts from pericentrin knockout mice show abnormal spindles during mitosis have been &lt;a href=&quot;http://jcb.rupress.org/content/188/2/181.full&quot; rel=&quot;nofollow&quot;&gt;studied&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In agreement with a model in which pericentrin is required for correct&#xA;  spindle orientation, fibroblasts isolated from PCNT knockout mice show&#xA;  a significant increase in cells with disrupted astral microtubules and&#xA;  misoriented spindles (Fig. 2; unpublished data; Zheng, G., personal&#xA;  communication). Spindle misorientation is shown by an increase in the&#xA;  angle formed by the pole-to-pole spindle vector and the cell–substrate&#xA;  adhesion plane in pericentrin knockout compared with wild-type&#xA;  fibroblasts.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Apparently both &lt;em&gt;TUBG&lt;/em&gt; and &lt;em&gt;PCNT&lt;/em&gt; deletions (individually) are not lethal. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-12T06:57:21.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23944" PostTypeId="1" CreationDate="2014-11-12T06:58:33.223" Score="5" ViewCount="216" Body="&lt;p&gt;I read on this question &lt;a href=&quot;https://biology.stackexchange.com/questions/8513/what-is-in-the-space-between-neurons-in-a-brain&quot;&gt;What is in the space between neurons in a brain?&lt;/a&gt; that there is actually not much empty space in a brain. But my question is slightly different. Is there a visual demonstration I can see of approximately how &quot;packed full of cells&quot; the brain actually is? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously there wouldn't be a fixed answer as it is likely a continuum where the bigger you get the harder it is to swim through without being blocked by all the neurons/synapses. But what is a good ballpark size to be to swim through with relative ease? &lt;/p&gt;&#xA;" OwnerUserId="10162" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-08-28T11:21:20.170" Title="How small does a nanobot have to be to &quot;swim through the brain&quot; and access any neuron it wants to?" Tags="&lt;molecular-biology&gt;&lt;neuroscience&gt;&lt;microbiology&gt;&lt;brain&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23945" PostTypeId="1" CreationDate="2014-11-12T07:23:01.513" Score="1" ViewCount="33" Body="&lt;p&gt;Could a cell culture frozen in vitrified ice for CryoEM be effectively sliced into thin planes and resolved images produced? I was thinking if this could be done to get images from inside a cell.&lt;/p&gt;&#xA;" OwnerUserId="10026" LastActivityDate="2014-11-12T07:23:01.513" Title="Slicing cell cultures frozen in vitrified ice with a laser for CryoEM" Tags="&lt;cell-biology&gt;&lt;microscopy&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23946" PostTypeId="2" ParentId="23944" CreationDate="2014-11-12T07:23:20.053" Score="5" Body="&lt;pre&gt;&lt;b&gt;&lt;i&gt;Is there a visual demonstration I can see of approximately &#xA;how &quot;packed full of cells&quot; the brain actually is? &lt;/b&gt;&lt;/i&gt; &lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Yes. You can inject tracers in the CSF (Cerebrospinal fluid) or in the ventricles and monitor them. In &lt;a href=&quot;http://www.sciencemag.org/content/342/6156/373.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; study, the authors have injected a fluorescent tracer in the CSF and used a direct imaging.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We used in vivo two-photon imaging to compare CSF influx into the&#xA;  cortex of awake, anesthetized, and sleeping mice. The fluorescent&#xA;  tracers were infused into the subarachnoid CSF via a cannula implanted&#xA;  in the cisterna magna for real-time assessment of CSF tracer movement.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can also inject a radiolabeled tracer. The tracer should be a molecule that is not taken up by the cells. You can then visualize the space using Positron Emission Tomography (PET).&lt;/p&gt;&#xA;&#xA;&lt;pre&gt; &lt;b&gt;&lt;i&gt;But what is a good ballpark size to be to swim through with relative ease? &lt;/b&gt;&lt;/i&gt; &lt;/pre&gt;&#xA;&#xA;&lt;p&gt;You may find this interesting: the abovementioned study shows that the &quot;space&quot; expands during sleep and CSF percolates deeper into the brain. This allows clearing of toxic metabolites. Having said that, some interior regions would be difficult to reach. Apart from neurons, there are several glia which occupy the space. I am not entirely sure about this but in interior regions there would be very less of extracellular space (I am just guessing it would be less than ~1µm. See the black regions in the figure below). Extracellular space is 20% of total brain tissue but it is not constant throughout. For more details refer to this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2581/&quot; rel=&quot;nofollow noreferrer&quot;&gt;book&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MzTB4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-08-28T11:21:20.170" LastActivityDate="2015-08-28T11:21:20.170" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23947" PostTypeId="1" CreationDate="2014-11-12T10:57:41.470" Score="1" ViewCount="58" Body="&lt;p&gt;Are there any databases or papers that give recombination frequency as a function of position in the E coli genome?&lt;/p&gt;&#xA;" OwnerUserId="10163" LastActivityDate="2014-11-12T10:57:41.470" Title="Recombination frequency as a function of genomic location in E coli?" Tags="&lt;ecoli&gt;&lt;database&gt;&lt;recombination&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23948" PostTypeId="2" ParentId="15737" CreationDate="2014-11-12T11:54:35.360" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I have read that cohesin is one of such enzymes, but works as a&#xA;  transcription factor by binding specific DNA motifs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Cohesin binding is not motif dependent (like transcription factors) and is also dynamic. Though sequence may have a role it is, just as in the case of nucleosomes,  mostly the overall composition rather than a sequence based motif:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867400810193&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cohesin binding peaks correspond closely to peaks of high local AT&#xA;  composition, a base composition periodicity of ∼15 kb that is distinct&#xA;  from the ∼50 kb periodicity of base composition isochores, consistent&#xA;  with axis association of cohesins.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;DNA-protein complexes can be crosslinked and subsequently the loops can be pulled down. However, this is tricky. You would need to cut the DNA at the loop ends in order to ligate them together. I don't know how to do that (Perhaps by using an antibody linked to an endonuclease). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-04-12T10:47:07.967" LastActivityDate="2016-04-12T10:47:07.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23949" PostTypeId="2" ParentId="21605" CreationDate="2014-11-12T12:11:20.617" Score="1" Body="&lt;ul&gt;&#xA;&lt;li&gt;Verify where these transcripts are generally present (this should not be difficult for common organisms)&lt;/li&gt;&#xA;&lt;li&gt;If they are all expressed in a certain tissue use cDNA from that tissue&lt;/li&gt;&#xA;&lt;li&gt;If not then pool the cDNAs from different tissues such that all genes can be amplified&lt;/li&gt;&#xA;&lt;li&gt;cDNA libraries (including whole organism) are also available and you may obtain them from the nearest repository (I guess NCBI also provides).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Some other things you can do:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Ask the primer synthesis company to provide primer sets it in a&#xA;96well format.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;DNA synthesis is also a decent option (it takes something like $0.5 &#xA;per base pair), but that can be expensive if your cDNAs are huge.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-12T12:11:20.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23950" PostTypeId="1" CreationDate="2014-11-12T12:33:48.030" Score="3" ViewCount="50" Body="&lt;p&gt;Is there anything similar to &lt;a href=&quot;http://www.addgene.org/browse/sequence/13846/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; in Java (especially the circular map sequencing along with hover effect)? &lt;br/&gt;&#xA;For information I would like to convey that I am using Plasmapper and BioJava for achieving this, but, as the output is in image format, so I am not able to achieve the above said requirement.&lt;br/&gt;&#xA;Thanks...&lt;/p&gt;&#xA;" OwnerUserId="10164" LastEditorUserId="3340" LastEditDate="2014-11-12T16:16:43.707" LastActivityDate="2014-11-12T16:16:43.707" Title="Gene Sequencing and Plasmapper" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23951" PostTypeId="2" ParentId="23950" CreationDate="2014-11-12T12:44:53.630" Score="2" Body="&lt;p&gt;Check these out. They provide the functionality that you want:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://biologylabs.utah.edu/jorgensen/wayned/ape/&quot; rel=&quot;nofollow&quot;&gt;ApE&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.snapgene.com/products/snapgene_viewer/&quot; rel=&quot;nofollow&quot;&gt;SnapGene viewer&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-12T12:44:53.630" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23952" PostTypeId="1" AcceptedAnswerId="23956" CreationDate="2014-11-12T13:29:30.353" Score="4" ViewCount="137" Body="&lt;p&gt;I read that genetic drift is random variation in the relative allele frequencies of a population. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Yawyr.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question however seems to pin genetic drift down to increasing deleterious allele frequencies. Is the answer to this question correct? I don't think that increase of a deleterious allele necessarily indicates that genetic drift is operating; it suggests genetic drift, because one would think that such alleles should decrease in frequency rather than increase, but random chance in a large population can also increase the frequency of deleterious alleles. &lt;/p&gt;&#xA;" OwnerUserId="6759" LastActivityDate="2014-11-12T15:01:43.637" Title="Is genetic drift necessarily deleterious?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23953" PostTypeId="1" AcceptedAnswerId="23955" CreationDate="2014-11-12T13:31:12.763" Score="6" ViewCount="1202" Body="&lt;p&gt;I'm trying to find homologs of a set of proteins using BLASTp. I'm working with custom databases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm using evalue of 0.00001 as threshold. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to filter queries having hits with &gt;90% identities. Because BLASTp output is based on HSPs, I cannot filter by %identities/query, only by HSP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know how to do this and also if I'm following a reasonable strategy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Here is an alignment example: qcovs=100 but qcovhsp lower.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;qseqid           sseqid         pident length mismatch gapopen qstart   qend  sstart    send   evalue bitscore qcovs qcovhsp&#xA;HPNK_01698      HAPS_0519       81.88   596     75      5       630     1225    615     1177    0.0      889    100     49&#xA;HPNK_01698      HAPS_0519       49.17   301     115     8       84      366     201     481     2e-56    214    100     23&#xA;HPNK_01698      HAPS_0519       53.64   261     61      6       436     684     616     828     6e-49    191    100     20&#xA;HPNK_01698      HAPS_0519       46.61   251     62      3       332     510     584     834     6e-46    181    100     15&#xA;HPNK_01698      HAPS_0519       53.27   214     79      4       1       194     1       213     1e-45    180    100     16&#xA;HPNK_01698      HAPS_0519       55.96   218     60      8       550     764     643     827     1e-40    164    100     18&#xA;HPNK_01698      HAPS_0519       51.56   225     61      7       516     731     642     827     1e-38    157    100     18&#xA;HPNK_01698      HAPS_0519       49.57   230     77      6       484     713     643     833     1e-37    154    100     19&#xA;HPNK_01698      HAPS_0519       57.89   76      26      1       364     433     760     835     1e-13   76.3    100     6&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Code used&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Make database&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;makeblastdb -in $Hparasuisfastadatabase -out H_parasuis_strains_gb_ALL.fna_databaseBLAST -dbtype prot -parse_seqids &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Run BLAST&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;blastp -db H_parasuis_strains_gb_ALL.fna_databaseBLAST -query 'out_2.fasta' -out HPNK_selected_vs_H_parasuis_strainss.tblastn -evalue 0.00001 -outfmt &quot;6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovs qcovhsp&quot; -max_target_seqs 50&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Thanks, Bernardo&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="1306" LastEditDate="2014-11-12T14:02:09.603" LastActivityDate="2014-11-13T14:19:21.167" Title="Find protein homologs with BLASTp" Tags="&lt;bioinformatics&gt;&lt;blast&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23954" PostTypeId="2" ParentId="9323" CreationDate="2014-11-12T13:33:09.343" Score="1" Body="&lt;p&gt;As you have mentioned ions and temperature affect RNA structure. There are also different types of RNA structures and their dependence on ions are different. Mg&lt;sup&gt;2+&lt;/sup&gt;, as Mad Scientist mentioned, stabilizes duplexes; so do monovalent cations like K&lt;sup&gt;+&lt;/sup&gt; and Na&lt;sup&gt;+&lt;/sup&gt;. However, Mg&lt;sup&gt;2+&lt;/sup&gt; favors duplex over quadruplex if the same RNA can adopt both these conformations.&#xA;Dependence on temperature is a trivial case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ions and temperature should be more or less same for prokaryotes and eukaryotes unless we are talking about extremophiles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from these factors I can think of two other factors that can cause difference in RNA structure between prokaryotes and eukaryotes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Osmolytes&lt;/li&gt;&#xA;&lt;li&gt;RNA binding proteins/chaperones (Already mentioned in comments by Mad Scientist)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Osmolytes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has been &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20875423&quot; rel=&quot;nofollow&quot;&gt;shown&lt;/a&gt; that TMAO (Trimethylamine N-oxide) stabilizes RNA secondary structures. The metabolism of TMAO is different in prokaryotes and eukaryotes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3650111/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Although eukaryototes can endogenously produce L-carnitine, only&#xA;  prokaryotic organisms can catabolize L-carnitine&lt;sup&gt;11&lt;/sup&gt;. A role for&#xA;  intestinal microbiota in TMAO production from dietary carnitine was&#xA;  first suggested by studies in rats; moreover, while TMAO production&#xA;  from alternative dietary trimethylamines has been suggested in humans,&#xA;  a role for microbiota in production of TMAO from dietary L-carnitine&#xA;  in humans had not yet been demonstrated&lt;sup&gt;30-32&lt;/sup&gt;. The present studies&#xA;  reveal an obligatory role of gut microbiota in the production of TMAO&#xA;  from ingested L-carnitine in humans (Fig. 6c)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I cannot ascertain that this will affect RNA folding but is possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;RBP&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is something that you can be certain about. Some RNAs require protein counterparts to adopt a functionally capable structure. In the absence of the protein they may not form the relevant structure. So if an RNA needs &lt;em&gt;Hfq&lt;/em&gt; then you have to express it in the eukaryotic system where you want to use the RNA (and converse).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-12T13:33:09.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23955" PostTypeId="2" ParentId="23953" CreationDate="2014-11-12T14:22:03.500" Score="3" Body="&lt;p&gt;First of all, if you want &lt;code&gt;90%&lt;/code&gt; identity, you can discard this hit. None of the HSPs pass that threshold. What's more, since you're working with proteins, there are no splicing issues involved and you should be able to get a single HSP spanning most of the query and subject sequences. Assuming, of course, you have a true homolog.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your output, I see many small, overlapping HSPs, most of which have low identity. I can't be sure without seeing the sequence but it's a safe bet that what you have there are low complexity/repetitive regions and that's why you have so many separate HSPs. The only half way decent one starts at position 630 of the query sequence and is only 595 residues long, less than half your query protein. Either you have a very diverged N-terminal region or your HSP is just a conserved domain. Again, I would need to see the actual sequence alignment to be sure but that doesn't look like a true homolog (assuming your species are reasonably close which they must be if you're using a 90% identity threshold).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, always assuming that your species are close enough to expect decent homologs, I would simply ignore the shorter HSPs and deal with those that represent more than, say, 80% of my query's length at &gt;=90% identity. Shorter hits will most often be conserved domains or repetitive/low complexity regions. The thresholds you choose depend on the species you are studying. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your species are not that close, don't use BLASTP at all. Instead, you can use something like &lt;a href=&quot;http://hmmer.janelia.org/&quot; rel=&quot;nofollow&quot;&gt;&lt;code&gt;hmmer&lt;/code&gt;&lt;/a&gt;. Collect a set of homologs from various species for each of your query proteins, build a matrix using these and use that matrix to search your database. You could also use &lt;a href=&quot;http://big.crg.cat/services/selenoprofiles&quot; rel=&quot;nofollow&quot;&gt;Selenoprofiles&lt;/a&gt; which uses a similar approach.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-11-13T14:19:21.167" LastActivityDate="2014-11-13T14:19:21.167" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23956" PostTypeId="2" ParentId="23952" CreationDate="2014-11-12T15:01:43.637" Score="5" Body="&lt;p&gt;Drift is a random element of evolution from one generation to the next, it is equally likely to spread a deleterious mutation as a beneficial one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason the answer is D is because selection should remove a deleterious allele, while drift makes no distinction, and is therefore the only scenario where drift is expected to be a reasonable answer. However, it is possible for drift to contribute to all of those scenarios.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-11-12T15:01:43.637" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23957" PostTypeId="1" CreationDate="2014-11-12T16:22:37.697" Score="6" ViewCount="211" Body="&lt;p&gt;If a B cell contains two mu chains and two lambda chains and is self reactive can it go back and rearrange its kappa light chains? I'm not sure if it can only try to rearrange its lambda light chains or if it can go back and try to rearrange kappa chains as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Background info: the light chain is the smaller of the two types of polypeptide chain in an immunoglobulin molecule. There are two classes of light chain known as the kappa and lambda light chains. During B-cell development the light chain genes rearrange. First one kappa gene is rearranged; if this doesn't produce a functional protein then the kappa gene on the second chromosome is rearranged; if a functional protein is still not produced then the lambda gene is rearranged one chromosome at a time until a successful rearrangement is produced.&lt;/p&gt;&#xA;" OwnerUserId="9063" LastEditorUserId="9063" LastEditDate="2014-11-26T04:50:08.207" LastActivityDate="2014-12-24T00:03:35.593" Title="B cell receptor editing" Tags="&lt;genetics&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23959" PostTypeId="1" CreationDate="2014-11-12T19:06:07.427" Score="2" ViewCount="966" Body="&lt;p&gt;I've harvested IPTG induced E.coli BL21DE3 cells' suspension culture by spinning at 5000 rpm/15 min/4 degrees C. The pellet after spin looked pale pink colored. What could be the reasons?&lt;/p&gt;&#xA;" OwnerUserId="8142" LastActivityDate="2014-11-12T19:06:07.427" Title="Pink E.coli cell pellet. Reasons?" Tags="&lt;microbiology&gt;&lt;cell-culture&gt;&lt;recombinant&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2015-03-29T23:42:37.107" ContentLicense="CC BY-SA 3.0" />
  <row Id="23960" PostTypeId="1" CreationDate="2014-11-12T20:56:27.460" Score="0" ViewCount="450" Body="&lt;p&gt;I always assumed my brother and I were identical twins. Now my mother, in her eighties, says we are cisternal twins, but I cannot find any references on the matter. Is there such a thing? If so, what traits make them so?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;appended: also, we've been called mirror twins. In a study by a student, we learned that our fingerprints are nearly exact opposites.&lt;/p&gt;&#xA;" OwnerUserId="10168" LastEditorUserId="10168" LastEditDate="2014-11-13T13:59:17.297" LastActivityDate="2014-12-08T10:36:36.563" Title="Is &quot;Cisternal Twins&quot; an actual classification of twin types and if so, describe it" Tags="&lt;twins&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23962" PostTypeId="1" CreationDate="2014-11-12T22:39:39.850" Score="2" ViewCount="110" Body="&lt;p&gt;By lab work I mean urinalysis, blood work(live as well), fecals, cytologies, histologies and all other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read(partly) a book(from 2002) on lab diagnostics and the author did not mention anything about diagnostics. I've spent a lot of time searching on google as well and I did not get anything.&lt;/p&gt;&#xA;" OwnerUserId="6682" LastActivityDate="2014-11-13T00:02:14.210" Title="What are the features on a microscope one needs in order to do lab work?" Tags="&lt;pathology&gt;&lt;hematology&gt;&lt;microscopy&gt;&lt;histology&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23963" PostTypeId="1" CreationDate="2014-11-12T23:41:14.607" Score="1" ViewCount="378" Body="&lt;p&gt;I am reviewing some material on loop diuretics, and I am curious to know how these drugs are administered. Also, I am interested in knowing their time course of action once they are administered into the body. &lt;/p&gt;&#xA;" OwnerUserId="8977" LastActivityDate="2014-11-12T23:58:49.073" Title="What is the most common way of administering loop diuretics and what is their time course of action?" Tags="&lt;pharmacology&gt;&lt;pharmacokinetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23964" PostTypeId="2" ParentId="23963" CreationDate="2014-11-12T23:58:49.073" Score="1" Body="&lt;p&gt;I know that furosemide (there are &lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;sqi=2&amp;amp;ved=0CB0QFjAA&amp;amp;url=http%3A%2F%2Fen.wikipedia.org%2Fwiki%2FLoop_diuretic&amp;amp;ei=-fFjVMO7GMXvmAWWrILIDw&amp;amp;usg=AFQjCNGa7YEm02czkwGn6fnwmNsszHCmdA&amp;amp;sig2=7AlzGm-s7YhQOjetoXnYVQ&quot; rel=&quot;nofollow&quot;&gt;more types of loop diuretics&lt;/a&gt;) can be given intravenously (but can be orally given as well (&lt;a href=&quot;http://www.drugs.com/ppa/furosemide.html&quot; rel=&quot;nofollow&quot;&gt;furosemide info sheet&lt;/a&gt;)). Effects of i.v. furosemide are pretty much immediate as it is carried quickly to the kidneys via the blood. After i.v. administration the effects wear off in about half an hour. t&lt;sub&gt;1/2&lt;/sub&gt; is about 2 hours, but likely depending on route of administration.    &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-12T23:58:49.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23965" PostTypeId="2" ParentId="23962" CreationDate="2014-11-13T00:02:14.210" Score="2" Body="&lt;p&gt;It sounds like you need a microscope for standard microbiology lab tests. At a minimum, any standard wide-field/brightfield microscope would work. If most of your histology work involves colorimetric stains (e.g., H&amp;amp;E, gram staining), you don't need any fluorescence capability. If you are working with a lower budget, look at the new lines of LED-based miroscopes, which dramatically drop the cost (I think around $10,000).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you plan on doing a high volume, in particular of fixed histology/cytology slides, then you may want to invest in some of the automated slide scanner microscopes. They have a small benchtop footprint and can be programmed to image large areas automatically, for later analysis.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-11-13T00:02:14.210" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23966" PostTypeId="1" CreationDate="2014-11-13T00:35:23.813" Score="2" ViewCount="3428" Body="&lt;p&gt;There are probably a lot of really good answers that may vary significantly in terms of content.  I'm looking for a set of books that I can read in preparation for the &lt;a href=&quot;https://www.ets.org/gre/subject/about/content/biochemistry&quot; rel=&quot;nofollow&quot;&gt;GRE Subject Test In Biochemistry, Cell And Molecular Biology&lt;/a&gt;.  I have a Bachelors of Science degree, but never really studied any of the material on this exam (it's in a field which is not really related).  I'm interested in applying for a doctoral program in Biology, and would like to add something to my application so that it doesn't appear to come out of &quot;left-field&quot;, as they say.  When I look at the questions from the sample exam in the link above, I can't tell whether they are introductory in scope or would require advanced study in particular areas.  Could somebody recommend a set of textbooks that would cover all of the ground for this test?  If one textbook exists which is sufficient, that would be wonderful, but I'm guessing that multiple texts will be required.  My goal is to learn the material necessary to do well on the exam as thoroughly as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an aside, I tried looking for study materials in online bookstores, but wasn't able to find anything that consistently got good reviews.  I don't think Princeton Review or Barron's have books on this subject, unless I overlooked something.  At any rate, I'm okay reading through a set of undergraduate university textbooks, but I really have no idea which ones would be good.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;:  I just changed the word &quot;efficiently&quot; to &quot;thoroughly&quot;.  Sorry about that...  This more accurately reflects the goal.&lt;/p&gt;&#xA;" OwnerUserId="831" LastEditorUserId="831" LastEditDate="2014-11-13T00:41:03.803" LastActivityDate="2019-09-16T09:11:54.327" Title="Book Recommendations: GRE Subject Test In Biochemistry, Cell And Molecular Biology" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;book-recommendation&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23967" PostTypeId="2" ParentId="23966" CreationDate="2014-11-13T01:03:31.740" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.macmillanhighered.com/catalog/static/whf/stryer4/&quot; rel=&quot;nofollow&quot;&gt;Stryer's Biochemistry&lt;/a&gt; is a great book that pretty much covers all the requirements except those in A1 - Those are basic chemistry concepts which are not covered in Stryer. Any basic chemistry book will cover that. Make sure to verify, one-by-one, that all the test subjects are covered in Stryer. This answer is just a recommendation for a great Biochemistry book, not a guarantee for a one-shot success on the test.   &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-13T01:09:01.987" LastActivityDate="2014-11-13T01:09:01.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23969" PostTypeId="2" ParentId="23966" CreationDate="2014-11-13T04:20:59.747" Score="2" Body="&lt;p&gt;You can also try &lt;a href=&quot;http://bcs.whfreeman.com/lehninger5e/default.asp?s=&amp;amp;n=&amp;amp;i=&amp;amp;v=&amp;amp;o=&amp;amp;rau=0&quot; rel=&quot;nofollow&quot;&gt;Lehninger Principles of Biochemistry&lt;/a&gt;...It covers all the topic except the part about cell motility...&amp;amp; possibly, the 1-A-g ( I'm not too sure about it)...but the book is for pretty advanced levels...&amp;amp; I would not recommend it as a last minute reference book..but for thorough study it's great....&amp;amp; of course it's my personal opinion...so before you consider any book, I would rather advice you download a pdf copy of the same, to get a 1st hand experience...hope this helps &amp;amp; good luck for your exam...&lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="10045" LastEditDate="2014-11-13T04:32:48.213" LastActivityDate="2014-11-13T04:32:48.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23970" PostTypeId="1" CreationDate="2014-11-13T05:22:46.897" Score="1" ViewCount="153" Body="&lt;p&gt;In the BMI formula= (Weight)  X  703) / (Height^2) , what does 703 represent? What is a reliable source that I can cite for this answer? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;weight= lbs    height= inches &lt;/p&gt;&#xA;" OwnerUserId="8994" LastActivityDate="2014-11-13T07:55:45.377" Title="Clarification on BMI formula" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23971" PostTypeId="1" CreationDate="2014-11-13T05:33:42.950" Score="1" ViewCount="1455" Body="&lt;p&gt;I understand that apoptosis and necroptosis share the same upper part of the pathway, but I cannot seem to distinguish when is each one activated? From my readings, it seems that when procaspases 8 or 10 are unavailable, the cell will shift to necroptosis. What makes these procaspases unavailable and why does a cell second the necropotosis? &lt;/p&gt;&#xA;" OwnerUserId="8994" LastActivityDate="2014-11-13T08:28:54.217" Title="Apoptosis vs necroptosis" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;cell-signaling&gt;&lt;cell&gt;&lt;apoptosis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23972" PostTypeId="2" ParentId="21173" CreationDate="2014-11-13T06:00:54.240" Score="1" Body="&lt;p&gt;I am assuming that you understand this basic structure-&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XqhvT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, let's start with &lt;strong&gt;grana&lt;/strong&gt; which are &lt;code&gt;small discrete dark green bodies embedded in lighter coloured stroma&lt;/code&gt;...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, in evolutionarily primitive life forms like algae, there is no differentiation among individual granum....rather they consist of &lt;strong&gt;continuous layer or lamellae like the sheets of book parallel to each other&lt;/strong&gt;...like this....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RC4Wb.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;this lamellate form of chloroplast is found in all green plants&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;, but &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;in higher plants there are a no. of more or less separate piles of&#xA;  sheet or lamellae&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;( unlike algae, as previously mentioned, where the sheets of lamellae run through the whole chloroplast). &#xA;Each , of these lamellae is composed of double membranes joined at the ends &amp;amp; each membrane is 100-200 angstrom thick....&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;following Menke (1960) these double lamellae are known as&#xA;  &lt;strong&gt;Thylakoids&lt;/strong&gt;...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now, unifying all these- &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Lamellar system&lt;/strong&gt; consists of &lt;strong&gt;uniform thylakoids&lt;/strong&gt; , which sometimes are&#xA;  stacked up like pennies , &lt;strong&gt;each stack being called a granum&lt;/strong&gt; ( plu.&#xA;  grana)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&amp;amp; this is as simple explanation as I can give of this utterly confusing Q....please feel free to comment about any portion that needs to be elaborated...&lt;/p&gt;&#xA;" OwnerUserId="10045" LastActivityDate="2014-11-13T06:00:54.240" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23973" PostTypeId="2" ParentId="23971" CreationDate="2014-11-13T07:45:41.947" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;From my readings, it seems that when procaspases 8 or 10 are&#xA;  unavailable, the cell will shift to necroptosis. What makes these procaspases unavailable and why does a cell second the necropotosis?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This seems to be right.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mice with a conditional deletion of caspase-8 in the intestinal&#xA;  epithelium (Casp8ΔIEC) spontaneously developed inflammatory lesions in&#xA;  the terminal ileum and were highly susceptible to colitis. Casp8ΔIEC&#xA;  mice lacked Paneth cells and showed reduced numbers of goblet cells,&#xA;  indicating dysregulated antimicrobial immune cell functions of the&#xA;  intestinal epithelium. Casp8ΔIEC mice showed increased cell death in&#xA;  the Paneth cell area of small intestinal crypts. Epithelial cell death&#xA;  was induced by tumour necrosis factor (TNF)-α, was associated with&#xA;  increased expression of receptor-interacting protein 3 (Rip3; also&#xA;  known as Ripk3) and could be inhibited on blockade of necroptosis.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Caspase-8 is a cysteine protease critically involved in regulating&#xA;  cellular apoptosis. On activation of death receptors, including&#xA;  TNF-receptor and Fas, caspase-8 is activated by limited&#xA;  autoproteolysis and the processed caspase-8 subsequently triggers the&#xA;  caspase cascade that finally leads to apoptotic cell death.&#xA;  Caspase-mediated apoptosis is important for the turnover of IECs and&#xA;  for shaping the morphology of the gastrointestinal tract 4.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://hedricklab.ucsd.edu/documents/Gunther-Nature.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Caspase-8 regulates TNF-α-induced epithelial necroptosis and terminal ileitis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Caspase-8 has both prodeath and prosurvival roles, mediating apoptosis&#xA;  and/or preventing RIPK1-mediated necroptosis depending on cell type&#xA;  and stimulus. We found that inflammatory stimuli (LPS, lipoteichoic&#xA;  acid, or TNF-α) caused an increase in caspase-8 IETDase activity in&#xA;  primary rat microglia without inducing apoptosis. Inhibition of&#xA;  caspase-8 with either Z-VAD-fmk or IETD-fmk resulted in necrosis of&#xA;  activated microglia. Inhibition of caspases with Z-VAD-fmk did not&#xA;  kill non-activated microglia, or astrocytes and neurons in any&#xA;  condition. Necrostatin-1, a specific inhibitor of RIPK1, prevented&#xA;  microglial caspase inhibition-induced death, indicating death was by&#xA;  necroptosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23386613&quot; rel=&quot;nofollow noreferrer&quot;&gt;Caspase inhibitors protect neurons by enabling selective necroptosis of inflamed microglia.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Necrosis has long been described as a consequence of extreme&#xA;  physicochemical stress, such as heat, osmotic shock, mechanical&#xA;  stress, and freeze-thawing, which kill cells quickly and directly.&#xA;  Therefore, this cell death has been described as uncontrolled and&#xA;  accidental necrosis characterized by loss of plasmamembrane integrity&#xA;  and cellular collapse, though nuclei remain largely intact during this&#xA;  process (Krysko et al., 2008a,2008b; Vanden Berghe et al., 2010). Loss&#xA;  of membrane integrity and release of intracellular content grant&#xA;  necrotic cells the ability to induce an inflammatory response. These&#xA;  immunogenic endogenous molecules fall under the umbrella term&#xA;  ‘‘damage-associated molecular patterns’’ (DAMPs) (Garg et al., 2010;&#xA;  Kryskoet al., 2011). They include, in the case of accidental necrosis,&#xA;  HMGB1, IL-1a, uric acid, DNA fragments, mitochondrial content, and ATP&#xA;  (Tables 1and2)(Eigenbrod et al., 2008; Kono et al., 2010; Krysko et&#xA;  al., 2008a; Sauter et al., 2000). Because the nomenclature of DAMPs in&#xA;  the literature is confusing, here we define DAMPs as a family of&#xA;  molecules that are intracellular in physiological condition&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://ac.els-cdn.com/S1074761313000587/1-s2.0-S1074761313000587-main.pdf?_tid=02ed1bcc-6b04-11e4-a834-00000aacb360&amp;amp;acdnat=1415862750_46a1dd24c76c9f9c054452b9f4af69c5&quot; rel=&quot;nofollow noreferrer&quot;&gt;Necroptosis: The Release of Damage-Associated Molecular Patterns and Its Physiological Relevance&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Based on the articles above, I would say that capsase-8 is a signal that apoptosis works finely, and so the cell can kill itself whenever it wants. So if that signal is lost because of an infection, mutation or extensive cell damage, the cell has no choice, but to activate the necrotic pathway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KMljj.jpg&quot; alt=&quot;cell survival&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 1 - cell survival and programmed cell death - &lt;a href=&quot;http://www.nature.com/onc/journal/v31/n49/fig_tab/onc20127f4.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;During tumorigenesis, significant loss or inactivation of lead members&#xA;  in the caspase family leads to impairing apoptosis induction, causing&#xA;  a dramatic imbalance in the growth dynamics, ultimately resulting in&#xA;  aberrant growth of human cancers. Recent exploitation of apoptosis&#xA;  pathways towards re-instating apoptosis induction via caspase&#xA;  re-activation has provided new molecular platforms for the development&#xA;  of therapeutic strategies effective against advanced prostate cancer&#xA;  as well as other solid tumors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3721730/&quot; rel=&quot;nofollow noreferrer&quot;&gt;CASPASE CONTROL: PROTAGONISTS OF CANCER CELL APOPTOSIS&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These findings reveal that, although apoptotic/drug resistance is a&#xA;  formidable “stronghold” of cancer against chemotherapy, necroptotic&#xA;  susceptibility is an intrinsic “weak point” of cancer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2007 - &lt;a href=&quot;http://www.tandfonline.com/doi/abs/10.4161/auto.4592#.VGRjNMlc91Y&quot; rel=&quot;nofollow noreferrer&quot;&gt;Targeting the Weak Point of Cancer by Induction of Necroptosis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Playing a central role in cell death, caspases are targeted by&#xA;  different viruses in the aim of prolonging cell survival. For&#xA;  instance, viral IAPs (inhibitors of apoptosis) interact with and&#xA;  inhibit the processed active caspases, either by blocking the&#xA;  catalytic part of the enzymes, or through E3 ubiquitin ligase activity&#xA;  from RING domains, targeting caspases for rapid degradation via&#xA;  proteasome. Baculoviruses, asfiviruses or irridescent viruses encode&#xA;  such IAPs. Another class of caspase inhibitors frequently found among&#xA;  poxviruses include the serine proteinase inhibitors serpins:&#xA;  CrmA/SPI-2. Crma targets cysteine proteases such as host Caspase 1 and&#xA;  Caspase 8.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;viralzone - &lt;a href=&quot;http://viralzone.expasy.org/all_by_protein/912.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Inhibition of host caspases by virus&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pathogens specifically target both the caspase 8-dependent apoptotic&#xA;  cell death pathway and the necrotic cell death pathway that is&#xA;  dependent on receptor-interacting protein 1 (RIP1; also known as&#xA;  RIPK1) and RIP3 (also known as RIPK3). The fundamental co-regulation&#xA;  of these two cell death pathways emerged when the midgestational death&#xA;  of mice deficient in FAS-associated death domain protein (FADD) or&#xA;  caspase 8 was reversed by elimination of RIP1 or RIP3, indicating a&#xA;  far more entwined relationship than previously appreciated. Thus,&#xA;  mammals require caspase 8 activity during embryogenesis to suppress&#xA;  the kinases RIP1 and RIP3 as part of the dialogue between two distinct&#xA;  cell death processes that together fulfil reinforcing roles in the&#xA;  host defence against intracellular pathogens such as herpesviruses.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The MCMV protein vICA prevents caspase 8 activation, and this&#xA;  sensitizes cells to death receptor-induced necroptosis. In addition,&#xA;  the MCMV protein vIRA blocks necroptosis and MCMV-induced programmed&#xA;  necrosis by inhibiting RHIM (RIP homotypic interaction&#xA;  motif)-dependent interactions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.nature.com/nri/journal/v12/n2/fig_tab/nri3131_F2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Viral infection and the evolution of caspase 8-regulated apoptotic and necrotic death pathways&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One potential explanation for this is that this form of death evolved&#xA;  to provide a “backup” pathway. Indeed, cowpox virus produces the&#xA;  factor CrmA, a potent apical caspase inhibitor capable of blocking&#xA;  apoptosis (Ray et al., 1992; Gagliardini et al., 1994). Several viral&#xA;  encoded genes are similarly produced to prevent apoptosis, and thus it&#xA;  is clear that inhibition of apoptosis is an important means viruses&#xA;  have exploited to avoid immune clearance. Interestingly,&#xA;  cytomegalovirus induces RIP3-mediated necroptosis via the interferon&#xA;  regulatory factor DAI (Upton et al., 2012). This virus also produces a&#xA;  protein called viRA, a protein that disrupts assembly of RIP1/RIP3&#xA;  necrosomes and consequent necroptosis. Thus, while the physiological&#xA;  function(s) of necroptosis remains to be fully elaborated, it is clear&#xA;  that this cellular process has been around for a long time during&#xA;  evolution. It is likely that necroptosis may serve as an “Achille's&#xA;  heel” in tumor cells, and thus greater understanding of the process&#xA;  may reveal novel therapies for cancer therapeutics.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://journal.frontiersin.org/Journal/10.3389/fcell.2014.00003/full#h3&quot; rel=&quot;nofollow noreferrer&quot;&gt;Grand challenges in cell death and survival: apoptosis vs. necroptosis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It seems like there is a 3rd pathway too, it is called ferroptosis.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;TNF-induced necroptosis depends on receptor-interacting protein-1&#xA;  kinase, mitochondrial complex I and cytosolic phospholipase A2&#xA;  activities, whereas H2O2-induced necrosis requires iron-dependent&#xA;  Fenton reactions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://www.nature.com/cdd/journal/v17/n6/abs/cdd2009184a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Necroptosis, necrosis and secondary necrosis converge on similar cellular disintegration features&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The transition metal iron is essential for life, yet potentially toxic&#xA;  iron-catalyzed reactive oxygen species (ROS) are unavoidable in an&#xA;  oxygen-rich environment. Iron and ROS are increasingly recognized as&#xA;  important initiators and mediators of cell death in a variety of&#xA;  organisms and pathological situations. Here, we review recent&#xA;  discoveries regarding the mechanism by which iron and ROS participate&#xA;  in cell death. We describe the different roles of iron in triggering&#xA;  cell death, targets of iron-dependent ROS that mediate cell death and&#xA;  a new form of iron-dependent cell death termed ferroptosis. Recent&#xA;  advances in understanding the role of iron and ROS in cell death offer&#xA;  unexpected surprises and suggest new therapeutic avenues to treat&#xA;  cancer, organ dam&#xA;  - age and degenerative disease&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://www.columbia.edu/cu/biology/faculty/stockwell/StockwellLab/index/publications/Dixon_NatChemBiol_2013.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;The role of iron and reactive oxygen species in cell death&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2012 - &lt;a href=&quot;http://www.bloodjournal.org/content/119/10/2368?sso-checked=true&quot; rel=&quot;nofollow noreferrer&quot;&gt;Heme induces programmed necrosis on macrophages through autocrine TNF and ROS production&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Not just a 3rd, there are many more pathways (pyroptosis, MPT-RN, parthanatos, ferroptosis, NETosis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rFxBh.jpg&quot; alt=&quot;Signalling pathways of regulated cell death.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 2 - Signalling pathways of regulated cell death.&lt;br&gt;&#xA;2014 - &lt;a href=&quot;http://www.nature.com/nri/journal/v14/n11/full/nri3743.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Regulated cell death and inflammation: an auto-amplification loop causes organ failure&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-11-13T08:28:54.217" LastActivityDate="2014-11-13T08:28:54.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23974" PostTypeId="2" ParentId="23970" CreationDate="2014-11-13T07:55:45.377" Score="5" Body="&lt;p&gt;It's a conversion factor. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ 1~lbs = 0.453592~kg \\&#xA;1~in = 0.0254000~m $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ \frac{lbs}{in^2} = \frac{0.453592~kg}{(0.0254~m)^2} = \frac{703.069~kg}{m^2} $$&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-11-13T07:55:45.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23976" PostTypeId="1" AcceptedAnswerId="23979" CreationDate="2014-11-13T09:12:39.113" Score="23" ViewCount="7099" Body="&lt;p&gt;Humans (and other humanoid mammals) have five fingers in each hand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Curious to know, why five? Wouldn't more fingers be more useful?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any evidence that it used to be different and natural selection caused those with five fingers to survive?&lt;/p&gt;&#xA;" OwnerUserId="5563" LastEditorUserId="9943" LastEditDate="2015-01-06T12:26:42.947" LastActivityDate="2015-01-06T12:31:32.467" Title="Why do we have five fingers?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;human-evolution&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="23977" PostTypeId="1" AcceptedAnswerId="64188" CreationDate="2014-11-13T09:57:26.743" Score="10" ViewCount="8041" Body="&lt;p&gt;I was always curious, why do chameleons have this strange gait?&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="6623" LastEditDate="2014-11-14T11:37:41.627" LastActivityDate="2018-10-25T09:11:31.017" Title="Why do chameleons move back and forth?" Tags="&lt;zoology&gt;&lt;behaviour&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23979" PostTypeId="2" ParentId="23976" CreationDate="2014-11-13T12:14:00.573" Score="15" Body="&lt;p&gt;I found an interesting article in Scientific American (&lt;a href=&quot;http://www.scientificamerican.com/article/why-do-most-species-have/&quot;&gt;Coates, 2005&lt;/a&gt;), and I quote part of it:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The condition of having no more than five fingers or toes [...] probably evolved before the evolutionary divergence of amphibians (frogs, toads, salamanders and caecilians) and amniotes (birds, mammals, and reptiles in the loosest sense of the term). This event dates to approximately 340 million years ago in the Lower Carboniferous Period. Prior to this split, there is evidence of tetrapods from about 360 million years ago having limbs bearing arrays of six, seven and eight digits. Reduction from these polydactylous patterns to the more familiar arrangements of five or fewer digits accompanied the evolution of sophisticated wrist and ankle joints--both in terms of the number of bones present and the complex articulations among the constituent parts.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So Coates states that &lt;strong&gt;around 360 million years ago there were tetrapods with more digits&lt;/strong&gt; (6, 7, 8), but that &lt;strong&gt;this was reduced to 5 about 340 million years ago&lt;/strong&gt;. Losing things in evolution is generally relatively simple, yet re-gaining them is hard. So while there is still a tendency for evolution to create species with less digits, there are no examples of land dwelling species with more than 5 digits. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The author reasons that &lt;strong&gt;more digits do no good on land as more digits impair locomotion&lt;/strong&gt;. Most polydactylous species were indeed found to be aquatic.    &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-06T12:31:32.467" LastActivityDate="2015-01-06T12:31:32.467" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="23981" PostTypeId="1" AcceptedAnswerId="23984" CreationDate="2014-11-13T17:01:50.933" Score="1" ViewCount="56" Body="&lt;p&gt;I have two lists of proteins (including phosphorylated forms). I want to determine which members of each list act on which members of the other list. &lt;strong&gt;What online resources exist for finding out what a given protein binds or otherwise interacts with?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am aware of &lt;a href=&quot;http://www.uniprot.org/&quot; rel=&quot;nofollow&quot;&gt;Uniprot&lt;/a&gt; and &lt;a href=&quot;http://www.phosphosite.org/homeAction.do&quot; rel=&quot;nofollow&quot;&gt;Phosphosite&lt;/a&gt; which have proved useful but I am wondering if there are others that I am not aware of. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again: the question I am trying to answer is &quot;which proteins from list A interact with proteins from list B and vice-versa?&quot; &lt;/p&gt;&#xA;" OwnerUserId="8161" LastActivityDate="2014-11-13T21:23:29.337" Title="Resource for finding what proteins bind?" Tags="&lt;proteins&gt;&lt;database&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23982" PostTypeId="1" CreationDate="2014-11-13T17:14:46.587" Score="2" ViewCount="38" Body="&lt;p&gt;Are there any data on rodent populations per acre of different types of agricultural crops?&lt;/p&gt;&#xA;" OwnerUserId="864" LastActivityDate="2014-11-13T17:14:46.587" Title="Which agricultural crops attract rodents?" Tags="&lt;mammals&gt;&lt;agriculture&gt;&lt;rodents&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23983" PostTypeId="1" AcceptedAnswerId="24008" CreationDate="2014-11-13T17:25:19.383" Score="5" ViewCount="15881" Body="&lt;p&gt;I usually take my protein sample 0.8ml and sample buffer(2X) 0.2ml for my sample preparation in SDS PAGE. Am I using correct proportion? my protein sample concentration is 4.1mg/ml. What is the standard protocol?&lt;/p&gt;&#xA;" OwnerUserId="8423" LastEditorUserId="948" LastEditDate="2014-11-13T20:05:24.407" LastActivityDate="2017-02-24T07:18:58.757" Title="How to prepare sample for SDS PAGE?" Tags="&lt;lab-techniques&gt;&lt;western-blot&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23984" PostTypeId="2" ParentId="23981" CreationDate="2014-11-13T17:29:10.487" Score="1" Body="&lt;p&gt;Go to the NAR database site and look for protein domain databases. You have multiple options. &lt;a href=&quot;http://www.oxfordjournals.org/our_journals/nar/database/subcat/3/9&quot; rel=&quot;nofollow&quot;&gt;Here is the link&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="10118" LastEditorUserId="948" LastEditDate="2014-11-13T20:07:17.707" LastActivityDate="2014-11-13T20:07:17.707" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23985" PostTypeId="1" AcceptedAnswerId="23990" CreationDate="2014-11-13T19:57:38.400" Score="15" ViewCount="54275" Body="&lt;p&gt;&lt;em&gt;What is the maximum temperature that a beverage can be without burning the tongue?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect there's a maximum temperature that the surface tissue of a tongue can withstand without being damaged (causing the burning feeling that lasts even after the heat goes away). So let's say I want to setup a device to keep my coffee to the right temperature to drink without damaging my mouth - I'm interested to know the highest possible temperature that will not damage the surface tissue of the tongue in a way that will result in lingering pain after the heat is gone.&lt;/p&gt;&#xA;" OwnerUserId="19073" LastEditorUserId="19073" LastEditDate="2014-11-13T23:00:20.617" LastActivityDate="2019-01-17T10:14:09.730" Title="How hot can a beverage get without burning the tongue?" Tags="&lt;human-biology&gt;&lt;skin&gt;&lt;heat&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23986" PostTypeId="1" CreationDate="2014-11-13T20:06:10.080" Score="4" ViewCount="133" Body="&lt;p&gt;Why is the first phase of the pulse from a pacemaker cathodic?&lt;/p&gt;&#xA;" OwnerUserId="10179" LastEditorUserId="6289" LastEditDate="2014-11-13T21:50:23.190" LastActivityDate="2014-11-13T21:50:23.190" Title="Why does a pacemaker have a negative pulse?" Tags="&lt;human-biology&gt;&lt;cardiology&gt;&lt;electrophysiology&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ClosedDate="2014-12-12T16:54:10.637" ContentLicense="CC BY-SA 3.0" />
  <row Id="23987" PostTypeId="2" ParentId="23981" CreationDate="2014-11-13T21:23:29.337" Score="1" Body="&lt;p&gt;STRING is one available tool &lt;a href=&quot;http://string-db.org/&quot; rel=&quot;nofollow&quot;&gt;http://string-db.org/&lt;/a&gt; and allowes you to do multiple sequences/names. I would also take an indepth look at what expasy has to offer &lt;a href=&quot;http://www.expasy.org/proteomics&quot; rel=&quot;nofollow&quot;&gt;http://www.expasy.org/proteomics&lt;/a&gt;. It is a large collection of bioinformatics tools (far too many for me to go through) and almost always has the tool you want.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(As a side note Expasy also has tools in genomics, structural bioinformatics, and many more, check the left hand tabs on the website for the full list!).&lt;/p&gt;&#xA;" OwnerUserId="6811" LastActivityDate="2014-11-13T21:23:29.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23990" PostTypeId="2" ParentId="23985" CreationDate="2014-11-13T23:00:55.257" Score="10" Body="&lt;p&gt;Afaik the tongue is not more heat tolerant than other parts of the body, so the minimum temperature to cause burn is about drinking a beverage having 45°C temperature for a long time (more than 5 minutes). The pain threshold of tongue is around 47°C, so you will feel when it really burns.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to studies the hedonic value of coffee has a maximum by 60°C, and it is significantly lower by safe levels (45°C). Frequent burns of mouth increases the risk of oral cancer. So I think this will be a hard choice... ;-)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A burn is an injury which is caused by application of heat or chemical&#xA;  substances to the external or internal surfaces of the body, which&#xA;  causes destruction of tissues. The minimum temperature for producing a&#xA;  burn is about 44°C for an exposure of about 5-6 hours or about 65°C&#xA;  for two seconds are sufficient to produce burns.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.forensicpathologyonline.com/E-Book/injuries/thermal-injuries&quot;&gt;Thermal injuries&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I. With the object of producing standard low-temperature burns in&#xA;  animals, and of studying the area of tissue only partly damaged in a&#xA;  burn, a burning iron has been made capable of applying temperatures&#xA;  from 45°-80°C. to the skin; with this the amount of heat and&#xA;  temperature causing skin damage has been studied, and the macroscopic&#xA;  and microscopic damage due to graded temperatures have been&#xA;  delineated.&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;Graded temperatures of 45°-80°C. have been applied to the skin of shaved, anæsthetised guinea-pigs, and in some cases rats, for times&#xA;  varying from 10 sec. to 6 and 10 min. Observations have been made of&#xA;  the development of erythema, flare, blanching, blueing, heat fixation,&#xA;  incipient blister formation, œdema, and edge wheal, as also upon the&#xA;  later scab formation and rate of epithelium regeneration.&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Applications of 47°C. up to 6 minutes produce no visible change.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;At 50°-55°C. applied for 1 minute and over, there is a critical temperature for the development of permanent and irreversible damage;&#xA;  in animals good scab formation occurs after burning at this&#xA;  temperature.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;After temperatures of 60°-65°C. the epidermis can be peeled off from the exposed area, leaving a punched-out exposed surface area&#xA;  somewhat like the exposed human blister.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;1943 - &lt;a href=&quot;http://ep.physoc.org/content/32/1/67.short&quot;&gt;EXPERIMENTAL THERMAL BURNS, ESPECIALLY THE MODERATE TEMPERATURE BURN&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;According to Green the pain threshold of tongue is around 46-48°C.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1985 - &lt;a href=&quot;http://link.springer.com/article/10.3758/BF03198847&quot;&gt;Heat pain thresholds in the oral-facial region&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In all experiments, the chosen mean preferred temperature for drinking&#xA;  was around 60 °C (140 °F). Black coffee drinkers chose a slightly&#xA;  higher mean temperature than drinkers with added creamer, and they&#xA;  also chose a slightly lower mean temperature when the flavor was&#xA;  stronger. In all cases, consumers tended to choose, on average,&#xA;  temperatures for drinking coffee that were above the oral pain&#xA;  threshold and the burn damage threshold.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2621.2002.tb08814.x/abstract&quot;&gt;At What Temperatures Do Consumers Like to Drink Coffee?: Mixing Methods&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Overall, the available results strongly suggest that high-temperature&#xA;  beverage drinking increases the risk of EC. Future studies will&#xA;  require standardized strategies that allow for combining data, and&#xA;  results should be reported by histological subtypes of EC.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773211/&quot;&gt;High-temperature beverages and Foods and Esophageal Cancer Risk -- A Systematic Review&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-11-13T23:12:16.733" LastActivityDate="2014-11-13T23:12:16.733" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="23991" PostTypeId="2" ParentId="23985" CreationDate="2014-11-13T23:18:46.670" Score="5" Body="&lt;p&gt;This depends on a lot of factors, including how you take your first sip. If you sip with air, you are altering the temperature of the liquid as you sip, as well as decreasing the volume of hot liquid in your mouth, so that the increased surface area of your exposed tongue can quickly alter the temperature of a borderline scalding liquid into a non-scalding one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, there is part of the answer: it depends on volume, and time in contact with the tongue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most coffee pots keep coffee at about 170°F - hot enough to scald your mouth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.theguardian.com/lifeandstyle/wordofmouth/2013/sep/17/serving-temperature-affects-taste-food&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt;, while not scientific, does discuss why people like foods at temperatures that cause scalding, and what better temperatures are. But the public wants what it wants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Safety experts recommend that water heaters be set at 120°F because you will not sustain a first-degree burn on contact, which is important if one has mobility problems. At 120°F, it takes &lt;a href=&quot;http://www.antiscald.com/prevention/general_info/table.php&quot; rel=&quot;nofollow&quot;&gt;8 minutes of contact to acquire a second degree burn&lt;/a&gt;. At 155°F, it takes one second.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to guarantee no scald on contact with a small volume of coffee, I would think 145°F would be about right. (At 140°F, liquid will scald in 3 seconds. If you don't chug your coffee, this seems safe enough. If you chug, it will scald.)&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="3624" LastEditDate="2015-08-20T10:35:52.730" LastActivityDate="2015-08-20T10:35:52.730" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23992" PostTypeId="1" AcceptedAnswerId="24609" CreationDate="2014-11-14T01:20:06.670" Score="4" ViewCount="271" Body="&lt;p&gt;I was just eating a rather rare steak when I started wondering whether eating foods cooked was something I would instinctively want to do if the practice hadn't been taught to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, is cooking food an evolved behavior, inspired by nutritional value or health benefits, or is it a practice learned, and passed down through culture alone?&lt;/p&gt;&#xA;" OwnerUserId="19073" LastActivityDate="2021-02-01T14:55:07.603" Title="Is eating cooked food an evolved behavior or rather an intelligent one, passed down via culture?" Tags="&lt;evolution&gt;&lt;food&gt;" AnswerCount="4" CommentCount="12" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23993" PostTypeId="1" AcceptedAnswerId="30515" CreationDate="2014-11-14T05:27:10.000" Score="7" ViewCount="188" Body="&lt;p&gt;Retinitis pigmentosa (RP) patients typically become blind after a period of years in which their eye sight slowly deteriorates due to photoreceptor degeneration. Generally RP patients develop night-blindness first, then tunnel vision, after which finally the central eye sight diminishes leaving them with basically no eye sight, barred some crude residual light perception. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Retinitis_pigmentosa&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki page on RP&lt;/a&gt; has more information when needed. Typically, the process from diagnosis of RP to (near) complete loss of eye sight takes years to decades.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, Chebat et al. &lt;a href=&quot;http://www.researchgate.net/profile/Ron_Kupers/publication/5840241_Tactile-&amp;#39;visual&amp;#39;_acuity_of_the_tongue_in_early_blind_individuals/links/0c96052e83143d4bad000000.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(2007)&lt;/a&gt; make mention that their study group, consisting of congenitally blind subjects, includes one person with RP (see table 1 in the linked article). Hence, this implicates that this particular subject was blind from birth due to effects of RP. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is anyone familiar with &lt;strong&gt;newborns blinded by the effects of RP&lt;/strong&gt;?&#xA;&lt;br&gt;&#xA;&lt;br&gt;&#xA;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.researchgate.net/profile/Ron_Kupers/publication/5840241_Tactile-&amp;#39;visual&amp;#39;_acuity_of_the_tongue_in_early_blind_individuals/links/0c96052e83143d4bad000000.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chebat et al. &lt;em&gt;Neuroreport&lt;/em&gt; 2007;&lt;strong&gt;18&lt;/strong&gt;:1901-4&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2017-05-12T14:50:47.170" LastActivityDate="2017-05-12T14:50:47.170" Title="Congenital blindness due to retinitis pigmentosa - does it exist?" Tags="&lt;pathology&gt;&lt;vision&gt;&lt;perception&gt;&lt;neurophysiology&gt;&lt;neurodegenerative-disorders&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="23994" PostTypeId="1" AcceptedAnswerId="23998" CreationDate="2014-11-14T06:13:17.320" Score="4" ViewCount="1441" Body="&lt;p&gt;What is the definition of 'independent assortment'. I tried researching this term but came back with two results: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;alleles assort themselves independently of different alleles&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the alignment of homologous chromosomes is random along the metaphase plate; resulting in the daughter cell inheriting either maternal or paternal chromosome based on 50:50&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Which is the correct term?&lt;/p&gt;&#xA;" OwnerUserId="10132" LastActivityDate="2014-11-24T21:57:35.087" Title="What is 'independent assortment'?" Tags="&lt;human-biology&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23995" PostTypeId="1" CreationDate="2014-11-14T06:24:44.423" Score="3" ViewCount="4177" Body="&lt;p&gt;I have to perform a hydrolysis of BSA with the enzyme trypsin. As a control I want to inactivate the trypsin enzyme. Can I inactivate it permanently by boiling (100&lt;sup&gt;o&lt;/sup&gt;C) for 10 minutes, or does it it require 1 hour of boiling? After inactivation, I have to do a test (with an active enzyme) and a control with BSA at 37&lt;sup&gt;o&lt;/sup&gt;C). At this point the inactivated trypsin (the control) should not be re-activated. So my questions are (1) whether I can irreversibly inactivate trypsin by boiling, (2) how long I have to boil it, and (3) if the boiling process will irreversibly inactivate the trypsin.  &lt;/p&gt;&#xA;" OwnerUserId="8423" LastEditorUserId="9943" LastEditDate="2014-11-14T12:00:26.897" LastActivityDate="2014-11-15T08:59:39.487" Title="How to inactivate trypsin permanently by boiling?" Tags="&lt;enzymes&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23996" PostTypeId="1" CreationDate="2014-11-14T06:30:41.053" Score="7" ViewCount="487" Body="&lt;p&gt;I've read &lt;a href=&quot;http://en.wikipedia.org/wiki/V_formation&quot; rel=&quot;noreferrer&quot;&gt;on Wikipedia&lt;/a&gt; and in other sources that the lead position alternates due to flight fatigue, but does it alternate between a small cabal of of leadership birds, or does (almost) every bird get to sometimes go first?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the process different across different species?&lt;/p&gt;&#xA;" OwnerUserId="10184" LastEditorUserId="10184" LastEditDate="2014-11-14T08:09:26.203" LastActivityDate="2017-09-25T14:38:53.997" Title="When birds fly in V-formation, how is it decided which bird gets to be the 'lead bird'?" Tags="&lt;behaviour&gt;&lt;ornithology&gt;&lt;collective-behaviour&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="23997" PostTypeId="2" ParentId="23995" CreationDate="2014-11-14T07:20:01.190" Score="5" Body="&lt;p&gt;In my experience 10min at 100°C are sufficient, this is also supported by the paper linked below. Heat inactivation works by denaturing the protein and is therefore final. &#xA;Depending on what you want to do with you sample, it might be problematic, as this is probably also denaturated at least to some degree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also chemically inactivate trypsin, either by adding fetal bovine serum (which is done in cell culture), which contains protease inhibitors as α1-antitrypsin and α2-macroglobulin or by using commercially available inhibitors. Trypsin is also inhibited by calcium and magnesium ions, so your reaction buffers shouldn't contain any of them.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728467/&quot;&gt;A Simple Procedure for Effective Quenching of Trypsin Activity and&#xA;Prevention of 18O-Labeling Back-Exchange&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-11-14T07:20:01.190" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="23998" PostTypeId="2" ParentId="23994" CreationDate="2014-11-14T08:10:51.633" Score="2" Body="&lt;p&gt;The term was pioneered by Mendel, who had no knowledge of chromosomes, so definition 1 would perhaps be the best answer. However, we now know that definition 1 arises from definition 2 (chromosomes are inherited independently of each other) and from the fact that chromosomes recombine (cross-over). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, independent assortment does not apply to linked genes, which tend to be inherited together. That is, they are not independently assorted. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-11-24T21:57:35.087" LastActivityDate="2014-11-24T21:57:35.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="23999" PostTypeId="2" ParentId="21553" CreationDate="2014-11-14T08:21:26.713" Score="1" Body="&lt;p&gt;Things can certainly vary for different ligands and different levels of cascading but these are the reactions that you may consider.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Receptor activation&lt;/li&gt;&#xA;&lt;li&gt;Nuclear translocation (lets assume it is just a part of the receptor. You can assume secondary messengers; it will add an extra step)&lt;/li&gt;&#xA;&lt;li&gt;DNA-binding and Transcription activation&lt;/li&gt;&#xA;&lt;li&gt;Transcription&lt;/li&gt;&#xA;&lt;li&gt;Nuclear export of mRNA&lt;/li&gt;&#xA;&lt;li&gt;Translation&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Finally I guess what you really want is to know when steady state is reached. This will also depend on other factors such as:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Receptor deactivation rate&lt;/li&gt;&#xA;&lt;li&gt;mRNA and protein degradation rates&lt;/li&gt;&#xA;&lt;li&gt;Nuclear export of activated TF&lt;/li&gt;&#xA;&lt;li&gt;Network architecture (some networks can speed up response times). This factor can be ignored and we can consider an open loop.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Phosphorylation reactions are generally much faster than transcription/translation/translocation rates and can also assumed to be equilibrium with dephosphorylation reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nuclear import rates are also dependent on cell volumes and for polarized cells like neurons it will be much higher. The average import rate is around &lt;strong&gt;0.2 - 1.2 s&lt;sup&gt;-1&lt;/sup&gt; NPC&lt;sup&gt;-1&lt;/sup&gt; µM&lt;sup&gt;-1&lt;/sup&gt;(cargo)&lt;/strong&gt; [&lt;em&gt;where NPC is number of Nuclear pore complexes which is again on an average 120&lt;/em&gt; ] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2064595/table/tbl2/&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[&lt;strong&gt;1&lt;/strong&gt;]&lt;/sup&gt;&lt;/a&gt;. &#xA;It can be, for ease, assumed to be &lt;strong&gt;~0.02 min&lt;sup&gt;-1&lt;/sup&gt;&lt;/strong&gt; &lt;a href=&quot;http://www.biomedcentral.com/1752-0509/7/59/table/T2&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[&lt;strong&gt;2&lt;/strong&gt;]&lt;/sup&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In most modeling papers the transcription rate is assumed (based on experimental reports) to be &lt;strong&gt;1 per min&lt;/strong&gt; (Average polymerase speed of &lt;strong&gt;~1000nt/min&lt;/strong&gt; and gene length of &lt;strong&gt;1000nt&lt;/strong&gt;. This can vary with gene length)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Translation rates are somewhat trickier. The translation rate per ribosome translation elongation rate is &lt;strong&gt;~5 codons/sec&lt;/strong&gt; (15aa/sec)&lt;a href=&quot;http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002755&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[&lt;strong&gt;3&lt;/strong&gt;]&lt;/sup&gt;&lt;/a&gt; or perhaps may even be lower — &lt;strong&gt;3 - 9aa/s&lt;/strong&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022283609015496&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[&lt;strong&gt;4&lt;/strong&gt;]&lt;/sup&gt;&lt;/a&gt; ( &lt;em&gt;&lt;sup&gt;[&lt;strong&gt;3&lt;/strong&gt;]&lt;/sup&gt; is a more recent finding&lt;/em&gt;). However, the overall translation rate will be dependent on number of ribosomes (Ribosomes can be assumed to be infinite unless it is some condition like stress or starvation. By no of ribosomes I meant polysomes per mRNA, which can also vary). Also, the protein synthesis rate will depend on length of mRNA. This is one parameter that can have a broad range of values (&lt;strong&gt;0.6-100 min&lt;sup&gt;-1&lt;/sup&gt; × mRNA&lt;/strong&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can set up mathematical model (based on reaction rate equations) and calculate the response times (Depending on parameters it can be &lt;strong&gt;8-20&lt;/strong&gt; hours). Steady states can generally reach by &lt;strong&gt;8 hours&lt;/strong&gt; (based on my own experiment. But I used tetracycline to induce luciferase). Another experiment (unpublished) using IFNγ induction caused a peak in the reporter at &lt;strong&gt;~12h&lt;/strong&gt;. I am not linking all references (you can easily look up for these). Usually, for cell culture applications, there is some sort of unsaid rule to assume 12h as a general response time to persistent stimuli. Response times are also dependent on initial conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note&lt;/strong&gt;: Response time means the time required to achieve steady state. This does not mean the delay between signal onset and protein synthesis. Other metric that is used generally is max-peaking time. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-11-14T08:38:43.117" LastActivityDate="2014-11-14T08:38:43.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24000" PostTypeId="1" AcceptedAnswerId="24001" CreationDate="2014-11-14T08:30:10.933" Score="1" ViewCount="523" Body="&lt;p&gt;I just chanced upon a rather strange red bell pepper (or capsicum?):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ORjhj.jpg&quot; alt=&quot;bizarre bell pepper&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The green formation is bulbous to touch, just the like the outside of the bellpepper, and it has the same smell as one. I'm no biology expert, but I have a feeling that's a tiny ingrown bellpepper in there. My mom thinks it's a strange genetic experiment and wants me to throw it away! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is that strange growth, and what might have caused it? Is this safe to consume?&lt;/p&gt;&#xA;" OwnerUserId="10185" LastEditorUserId="16866" LastEditDate="2020-04-15T13:17:37.657" LastActivityDate="2020-04-15T13:17:37.657" Title="What is this bizarre in-growth in this red bell pepper?" Tags="&lt;genetics&gt;&lt;food&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24001" PostTypeId="2" ParentId="24000" CreationDate="2014-11-14T09:22:24.623" Score="6" Body="&lt;p&gt;This is very likely to be &lt;a href=&quot;http://www.gardeningknowhow.com/edible/vegetables/pepper/little-pepper-inside-pepper.htm&quot; rel=&quot;noreferrer&quot;&gt;parthenocarpy&lt;/a&gt;, which is an “internal proliferation” and varies from an irregular fruit to an almost carbon copy of the larger pepper. What is known is that it shows up in seed lines through natural selection and is unaffected by weather, pests, or other external conditions. Please see page 27 of &lt;a href=&quot;http://edepot.wur.nl/167546&quot; rel=&quot;noreferrer&quot;&gt;this document&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="10186" LastEditorUserId="6511" LastEditDate="2014-11-14T10:48:52.993" LastActivityDate="2014-11-14T10:48:52.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24002" PostTypeId="1" AcceptedAnswerId="51675" CreationDate="2014-11-14T09:26:18.857" Score="1" ViewCount="320" Body="&lt;p&gt;I wonder if we could try to see &lt;a href=&quot;http://en.wikipedia.org/wiki/Imaginary_color&quot; rel=&quot;nofollow&quot;&gt;imaginary&lt;/a&gt; &quot;supergreen&quot; color by directly stimulating M cones. For this I suppose we'd need:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Non-destructively scan specific human's retina to locate exact positions of M cone cells.&lt;/li&gt;&#xA;&lt;li&gt;Prepare a high-resolution image (on a &lt;a href=&quot;http://en.wikipedia.org/wiki/Retina_Display&quot; rel=&quot;nofollow&quot;&gt;retina&lt;/a&gt;-like display I guess), which would have light spots in some locations and dark in others, so that when the human we inspected looks at particular point of the image, these light spots were focused exactly on M cones.&lt;/li&gt;&#xA;&lt;li&gt;Track the eye movements and adjust the image so that S and L cones avoided significant exposure to prevent misperception.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Is anything of this hard to implement with current technology, given typical human retina properties (M cones density, their apparent color etc.)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is totally possible, has such an experiment already been performed?&lt;/p&gt;&#xA;" OwnerUserId="5119" LastActivityDate="2016-09-19T05:45:37.890" Title="Can we directly stimulate M cones in retina with current technology?" Tags="&lt;eyes&gt;&lt;vision&gt;&lt;experiment&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24003" PostTypeId="1" AcceptedAnswerId="24018" CreationDate="2014-11-14T09:35:14.747" Score="2" ViewCount="2545" Body="&lt;p&gt;As far as I know, lipids are defined as biomolecules which are hydrophobic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Triglycerides are composed of fatty acids and glycerol and are considered lipids but, are fatty acids alone or glycerol alone considered as lipids ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-11-17T06:09:22.520" Title="Are fatty acids and glycerol lipids?" Tags="&lt;biochemistry&gt;&lt;lipids&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24005" PostTypeId="2" ParentId="23925" CreationDate="2014-11-14T11:17:10.117" Score="1" Body="&lt;p&gt;Citronella oil is also used as an insect repellent and is seems effective on mosquitoes[&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1748-5967.2005.tb00146.x/abstract;jsessionid=48028622D4EDE52827A4E29ACC82E9CA.f04t03&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;] and head lice[&lt;a href=&quot;http://www.ima.org.il/IMAJ/ViewArticle.aspx?year=2004&amp;amp;month=12&amp;amp;page=75603&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;] as well. Though I was not able to find information on the mode of action, just the effectiveness of citronella.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/DEET&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; also says DEET is effective for fleas, ticks, and chiggers (though this lacks a references). Anecdotally, I know the Off brand of repellent is useful when the dogs get fleas to avoid getting all bitten up (Off contains DEET I believe).&lt;/p&gt;&#xA;" OwnerUserId="6623" LastActivityDate="2014-11-14T11:17:10.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24006" PostTypeId="1" CreationDate="2014-11-14T11:33:19.503" Score="3" ViewCount="210" Body="&lt;p&gt;I've seen sci-fi movies where the effects the body being unprotected in outer space are wildly different. In one movie, a guy radios for someone who's been ejected into space to breath all the air from his lungs immediately. In some movies, eyes are pulled from sockets. In others, ice crystals form, and the eyes begin to look a bit red... Sometimes the exposed person is a goner right away, sometimes they're shown to last for a minute or more. The Hollywood portrayals of space exposure just vary tremendously.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So I'm curious, what &lt;em&gt;really&lt;/em&gt; happens to the human body in the vacuum of outer space?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="19073" LastEditorUserId="19073" LastEditDate="2014-11-14T11:42:09.810" LastActivityDate="2019-03-12T02:05:42.160" Title="How does the body really react to exposure to the vacuum of space?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24007" PostTypeId="2" ParentId="24006" CreationDate="2014-11-14T11:42:51.877" Score="1" Body="&lt;p&gt;With regard to the vacuum - Apparently nothing happens as long as you don't hold your breath, just like you shouldn't hold your breath when ascending after scuba diving and the pressure drops. See &lt;a href=&quot;http://imagine.gsfc.nasa.gov/docs/ask_astro/answers/970603.html&quot; rel=&quot;nofollow&quot;&gt;NASA's answer to the same question&lt;/a&gt;. Of course there's the radiation that does other funny things in space, see the &lt;a href=&quot;http://imagine.gsfc.nasa.gov/docs/ask_astro/answers/970603.html&quot; rel=&quot;nofollow&quot;&gt;NASA link&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-14T11:42:51.877" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24008" PostTypeId="2" ParentId="23983" CreationDate="2014-11-14T11:58:35.500" Score="7" Body="&lt;p&gt;Sample preparation for protein gels is not a complex task. Simply mix the appropriate amount of sample buffer with your sample and load it. For a 2x sample buffer use equal amounts of sample and buffer, for 5x sample buffer use 4 parts of sample and 1 part of buffer (for examle 40µl + 10µl). Heat the mixed samples for 5 minutes at 95°C, cool them immediately on ice and load an appropriate amount of it on the gel. How much is possible really depends on the type of gel you use - 20-30µl should usually be possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do not load too much protein, otherwise you will not be able to seperate them appropriately. I usually use between 20-30µg of total protein per well or as little as 50ng for purified proteins (this depends on the antibodies as well).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a look on this &lt;a href=&quot;http://www.ruf.rice.edu/~bioslabs/studies/sds-page/gellab2.html&quot; rel=&quot;noreferrer&quot;&gt;webpage&lt;/a&gt; for some further information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For sample buffers I usually use the following recipes. I prefer the 5x, because I can load more protein, if the preparation is not very good. I also prefer the use of DTT to Mercaptoethanol, as it is much less smelly. If you have no DTT (or prefer mercaptoethanol) it can be replaced by an equal amount (200mM in the 2x, 500mM in the 5x buffer). If you use DTT, you need to make aliquots of the buffer and store it at -20°C, a working aliquot can be kept at 4°C for two weeks or so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2x sample buffer:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;4% SDS&lt;/li&gt;&#xA;&lt;li&gt;20% glycerol&lt;/li&gt;&#xA;&lt;li&gt;100 mM Tris-Cl, pH 6.8&lt;/li&gt;&#xA;&lt;li&gt;2 mM EDTA (ethylene diamine tetraacetic acid)&lt;/li&gt;&#xA;&lt;li&gt;200 mM DTT (dithiothreitol)&lt;/li&gt;&#xA;&lt;li&gt;0.1 % (w/v) bromphenol blue dye&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;5x sample buffer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;10% SDS&lt;/li&gt;&#xA;&lt;li&gt;50% glycerol&lt;/li&gt;&#xA;&lt;li&gt;250 mM Tris-Cl, pH 6.8&lt;/li&gt;&#xA;&lt;li&gt;5 mM EDTA (ethylene diamine tetraacetic acid)&lt;/li&gt;&#xA;&lt;li&gt;200 mM DTT (dithiothreitol)&lt;/li&gt;&#xA;&lt;li&gt;0.25 % (w/v) bromphenol blue dye&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-11-14T12:27:44.690" LastActivityDate="2014-11-14T12:27:44.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24011" PostTypeId="2" ParentId="23852" CreationDate="2014-11-14T12:34:15.640" Score="1" Body="&lt;p&gt;Yes it can. You will want to use a thin hemocytometer and the working distance of the objective (20x) needs to be long enough to focus both the cells under the cover glass and the grid under the hemocytometer. Because you are looking at it from the top it would be helpful probably to have some phase on the scope to increase your contrast so that you can more clearly see the grid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hemocytometers are most commonly used with inverted microscopes because inverted microscopes are the most convenient microscope for performing tissue culture, and 's a commonly used to count cells when passaging or setting up an experiment etc, as they allow you to view cells in a culture plate. Upright microscopes require that you make a slide.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-11-14T12:34:15.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24012" PostTypeId="2" ParentId="15743" CreationDate="2014-11-14T13:08:52.603" Score="1" Body="&lt;p&gt;Being a typical molecular biologist, I am a little uncomfortable with classical genetics terms. I might redefine some symbols (perhaps to mean the same) [&lt;em&gt;It is like talking to oneself while thinking&lt;/em&gt;]. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;There are four DNA-blocks : A&lt;sub&gt;1&lt;/sub&gt;, B&lt;sub&gt;1&lt;/sub&gt;, A&lt;sub&gt;2&lt;/sub&gt; and B&lt;sub&gt;2&lt;/sub&gt;. A&lt;sub&gt;k&lt;/sub&gt; and B&lt;sub&gt;k&lt;/sub&gt; are adjacent blocks. [&lt;em&gt;Perhaps this is same as what you defined the symbols as&lt;/em&gt;]. A and B are contiguous DNA regions whereas 1 and 2 are different chromosomes (homologous regions). See the figure below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/YA7us.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The formula: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;D=X&lt;sub&gt;11&lt;/sub&gt;X&lt;sub&gt;22&lt;/sub&gt; - X&lt;sub&gt;12&lt;/sub&gt;X&lt;sub&gt;21&lt;/sub&gt;&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;basically means that the difference between the probability that the loci are in &lt;code&gt;configuration I&lt;/code&gt; (&lt;code&gt;11 &amp;amp; 22&lt;/code&gt;) or &lt;code&gt;configuration II (swapped)&lt;/code&gt; (&lt;code&gt;12 &amp;amp; 21&lt;/code&gt;). Lets say there is a third region (3) which is homologous to the two &lt;em&gt;alleles&lt;/em&gt; which has DNA-blocks A&lt;sub&gt;3&lt;/sub&gt; and B&lt;sub&gt;3&lt;/sub&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As LD is defined it is a difference in probabilities. Depending on how you define, it will take a negative or a positive value. When you have 3 recombinationally feasible &lt;em&gt;alleles&lt;/em&gt; then there can be six cases:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;C&lt;sub&gt;1&lt;/sub&gt;: [A&lt;sub&gt;1&lt;/sub&gt;B&lt;sub&gt;1&lt;/sub&gt;] [A&lt;sub&gt;2&lt;/sub&gt;B&lt;sub&gt;2&lt;/sub&gt;] [A&lt;sub&gt;3&lt;/sub&gt;B&lt;sub&gt;3&lt;/sub&gt;]&lt;/li&gt;&#xA;&lt;li&gt;C&lt;sub&gt;2&lt;/sub&gt;: [A&lt;sub&gt;1&lt;/sub&gt;B&lt;sub&gt;1&lt;/sub&gt;] [A&lt;sub&gt;2&lt;/sub&gt;B&lt;sub&gt;3&lt;/sub&gt;] [A&lt;sub&gt;3&lt;/sub&gt;B&lt;sub&gt;2&lt;/sub&gt;]&lt;/li&gt;&#xA;&lt;li&gt;C&lt;sub&gt;3&lt;/sub&gt;: [A&lt;sub&gt;1&lt;/sub&gt;B&lt;sub&gt;3&lt;/sub&gt;] [A&lt;sub&gt;2&lt;/sub&gt;B&lt;sub&gt;2&lt;/sub&gt;] [A&lt;sub&gt;3&lt;/sub&gt;B&lt;sub&gt;1&lt;/sub&gt;]&lt;/li&gt;&#xA;&lt;li&gt;C&lt;sub&gt;4&lt;/sub&gt;: [A&lt;sub&gt;1&lt;/sub&gt;B&lt;sub&gt;2&lt;/sub&gt;] [A&lt;sub&gt;2&lt;/sub&gt;B&lt;sub&gt;1&lt;/sub&gt;] [A&lt;sub&gt;3&lt;/sub&gt;B&lt;sub&gt;3&lt;/sub&gt;]&lt;/li&gt;&#xA;&lt;li&gt;C&lt;sub&gt;5&lt;/sub&gt;: [A&lt;sub&gt;1&lt;/sub&gt;B&lt;sub&gt;2&lt;/sub&gt;] [A&lt;sub&gt;2&lt;/sub&gt;B&lt;sub&gt;3&lt;/sub&gt;] [A&lt;sub&gt;3&lt;/sub&gt;B&lt;sub&gt;1&lt;/sub&gt;]&lt;/li&gt;&#xA;&lt;li&gt;C&lt;sub&gt;6&lt;/sub&gt;: [A&lt;sub&gt;1&lt;/sub&gt;B&lt;sub&gt;3&lt;/sub&gt;] [A&lt;sub&gt;2&lt;/sub&gt;B&lt;sub&gt;1&lt;/sub&gt;] [A&lt;sub&gt;3&lt;/sub&gt;B&lt;sub&gt;2&lt;/sub&gt;]&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In this case there is no single measure for &lt;em&gt;difference&lt;/em&gt;. You can also do something like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;LD&lt;sub&gt;1'&lt;/sub&gt; = P(C&lt;sub&gt;1&lt;/sub&gt;) + P(C&lt;sub&gt;2&lt;/sub&gt;) - (P(C&lt;sub&gt;3&lt;/sub&gt;) + P(C&lt;sub&gt;4&lt;/sub&gt;) + P(C&lt;sub&gt;5&lt;/sub&gt;) + P(C&lt;sub&gt;6&lt;/sub&gt;))&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Where LD&lt;sub&gt;1'&lt;/sub&gt; is LD of region 1 and P(C&lt;sub&gt;m&lt;/sub&gt;) is the frequency of m&lt;sup&gt;th&lt;/sup&gt; configuration.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, if there are 3 or more adjacent DNA blocks, you can only define LD, pairwise. It however, makes sense because linkage reduces with distance and you can calculate LD&lt;sub&gt;AC&lt;/sub&gt; = LD&lt;sub&gt;AB&lt;/sub&gt; x LD&lt;sub&gt;BC&lt;/sub&gt; &lt;br&gt;(&lt;em&gt;A,B and C are contiguous in alphabetical order. If A and B are not linked then A and C cannot be linked.&lt;/em&gt;)&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-11-21T16:44:47.623" LastActivityDate="2014-11-21T16:44:47.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24013" PostTypeId="1" CreationDate="2014-11-14T13:38:40.053" Score="2" ViewCount="102" Body="&lt;p&gt;The result of a vision test by my oculist yielded a result of more than 100% while wearing prescription glasses. I wonder, how can a person see better using eyeglasses?&lt;/p&gt;&#xA;" OwnerUserId="10064" LastActivityDate="2014-11-14T13:38:40.053" Title="How can eyeglasses improve vision beyond 100%?" Tags="&lt;vision&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-11-26T17:51:57.567" ContentLicense="CC BY-SA 3.0" />
  <row Id="24014" PostTypeId="1" AcceptedAnswerId="24015" CreationDate="2014-11-14T14:13:31.630" Score="21" ViewCount="21763" Body="&lt;p&gt;This is a two-part question:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;What is the point of fruit if not to be eaten? It’s my understanding that organisms will adapt to survive and thrive. I understand that being eaten can spread seeds, but this just seems like too much of a risky tactic to rely on.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Following on from part one: If being eaten is the best way to spread seed, why do some plants avoid this (such as by being poisonous or thorny)?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6179" LastEditorUserId="16866" LastEditDate="2017-04-13T04:17:45.877" LastActivityDate="2017-05-17T15:16:43.193" Title="Why do plants fruit?" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;development&gt;&lt;fruit&gt;&lt;seeds&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="24015" PostTypeId="2" ParentId="24014" CreationDate="2014-11-14T14:45:43.507" Score="22" Body="&lt;p&gt;&lt;strong&gt;Seeds are spread by many mechanisms&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wind dispersal: When air currents used to spread seeds. Often these plants have evolved features to facilitate wind catching, for example &lt;a href=&quot;https://www.google.se/webhp?sourceid=chrome-instant&amp;amp;ion=1&amp;amp;espv=2&amp;amp;ie=UTF-8#q=dandelion%20seeds&quot;&gt;dandelions&lt;/a&gt;. Aka, &lt;a href=&quot;http://www.thefreedictionary.com/anemochory&quot;&gt;anemochory&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Propulsion &amp;amp; bursting: When seeds are propelled from the plant in an such as in &lt;a href=&quot;https://www.youtube.com/watch?v=8iyKAq_s7-M&quot;&gt;these videos&lt;/a&gt;. This is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Seed_dispersal#Autochory&quot;&gt;Ballochory&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Water: Similarly to wind dispersal plants can spread seeds by water movement/currents, aka &lt;a href=&quot;http://en.wiktionary.org/wiki/hydrochory&quot;&gt;Hydrochory&lt;/a&gt;. This is used by many algae and water living plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sticky Seeds: There are many ways a seed can attach to the outside of an animal - by using hooks, barbs, sticky excretions, hairs. Seeds then get carried by an animal and fall off later. This is &lt;a href=&quot;http://en.wiktionary.org/wiki/epizoochory&quot;&gt;epizoochory&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fruiting: Plants can use seed-bearing fruit to encourage animals to eat the seeds. They will then be spread when the waste is excreted after digestion. This is a process of &lt;a href=&quot;http://en.wiktionary.org/wiki/endozoochory&quot;&gt;endozoochory&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;More than one way to spread a seed&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From above you can see there are many ways to spread a seed. This means that many plants (those that do not use fruit) will want (from an evolutionary perspective) to avoid being eaten at all costs, and therefore evolve poison/taste cues that reduce the frequency of this. However, if investing in producing fruit bears a net benefit, ie many seeds are spread and successfully propagate, then the cost of fruit production is not a risk. A fruiting plant can minimize the risk by limiting reward (making fruit taste good and be nutritious) to only the right spatiotemporal moment when the seeds are primed for dispersal, if the fruit is eaten before the seeds are ready/present in the fruit then there will be no benefit of producing the fruit. (I expect this is why unripe fruit doesn't tend to taste so nice - it doesn't taste nice unless it's ripe because those where mutations made fruit taste good before the seeds were ready had no offspring, and those that time the ripening well were much more successful).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Producing an edible fruit is not necessarily the &lt;em&gt;best&lt;/em&gt; way but is the way many plant species have evolved to spread their seeds. Evolution works by random mutation and selection, which can only work with the variation it has available - only if a mutation to produce fruit arises in a species and it improves fitness is it then likely to spread. &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1600-048X.2013.00271.x/abstract&quot;&gt;It appears that endozoochory could be a very good methods of long distance dispersal&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Some interesting stuff&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, &lt;a href=&quot;http://awesci.com/cranberry-migration/&quot;&gt;according to this blog post&lt;/a&gt;, unripe fruits taste bitter because they are full of tanins. Cranberries are an odd fruit because they taste bitter which means they are unattractive to animals, but they do float - which is a good dispersal method - because of an air-pocket inside the fruit that evolved. It could be the case then that once a mutation arrived for the air-pocket the fruit could just float away on water to a new location, and then using resources to make the fruit sweet and tasty became an unnecessary cost so was lost (to some degree).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://phys.org/news/2010-11-benefits-bitter-cranberry-evolution-thanksgiving.html&quot;&gt;This article&lt;/a&gt; contains this text:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Like many species of plants native to North America, the cranberry is specially adapted to wetlands -- water-soaked areas that create transition points between dry land and open water. But cranberries do not grow directly in the water. Instead, they typically lay their roots at its edge, taking advantage of the rich soils created by alternating layers of peat, sand, clay and rock.&#xA;  Other fruits are dependent on hungry creatures to spread their seed,&#xA;  so sweetness can help their chance of being eaten and transported&#xA;  elsewhere. Not cranberries. Because of their little air pockets, the&#xA;  fruit falls from the plant's long vines when ripe and lets the water&#xA;  transport it to distant beds.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This advantage dictated the fruit we eat today.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Blueberries and cranberries are close cousins and are in fact not&#xA;  berries at all; they belong instead to a class of fruits known as&#xA;  epigynous or false berries. Unlike a true berry, the fruit grows from&#xA;  beneath the rest of the flower parts and as the fruit ripens the&#xA;  flower stays attached and ripens as well.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Vorsa believes that at some point during the last ice age there were&#xA;  fewer animals to eat the fruits, and this might have driven the two&#xA;  species to diverge. The cranberries developed an acidity level five&#xA;  times higher than blueberries because it came to rely on water for&#xA;  seed dispersal. Cranberries did not need to produce large amounts of&#xA;  sugar that their blue-colored relatives required to entice consumption&#xA;  by animals in order to spread their seeds.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-11-14T20:40:18.240" LastActivityDate="2014-11-14T20:40:18.240" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24017" PostTypeId="1" CreationDate="2014-11-14T17:39:30.187" Score="10" ViewCount="1892" Body="&lt;p&gt;There are obviously good reasons that explain why you cannot tickle yourself (see e.g. &lt;a href=&quot;https://biology.stackexchange.com/questions/23209/why-can-you-not-tickle-yourself&quot;&gt;here&lt;/a&gt;). This got me thinking why it is possible to masturbate...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wouldn't it make more sense to &lt;em&gt;not&lt;/em&gt; being able to do that so that you are more inclined to have &lt;em&gt;real&lt;/em&gt; sex. Individuals who were not able to relieve themselves in this manner should have been more actively producing offspring. And the tickling example shows that self-produced sensations &lt;em&gt;can&lt;/em&gt; be inhabited.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this make sense? I know that it is always hard to reconstruct evolutionary processes but are there reasons that explain this?&lt;/p&gt;&#xA;" OwnerUserId="10193" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2017-01-15T04:45:04.037" Title="Evolutionary reasons why you cannot tickle yourself but masturbate" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;sex&gt;&lt;sensation&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24018" PostTypeId="2" ParentId="24003" CreationDate="2014-11-14T18:17:46.290" Score="5" Body="&lt;p&gt;From &lt;a href=&quot;http://goldbook.iupac.org/L03571.html&quot; rel=&quot;nofollow&quot;&gt;IUPAC Goldbook&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A loosely defined term for substances of biological origin that are&#xA;  soluble in nonpolar solvents. They consist of saponifiable lipids,&#xA;  such as glycerides (fats and oils) and phospholipids, as well as&#xA;  nonsaponifiable lipids, principally steroids.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That means that lipid does not mean any hydrophobic molecule.&#xA;Lipids can be amphipathic as you already know about fatty acids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glycerol is &lt;strong&gt;not&lt;/strong&gt; a lipid; neither is it hydrophobic. Glycerol, if to be classified into one of biomolecular classes, it would be that of monosaccharides (in the form of sugar alcohol like sorbitol and xylitol). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-11-17T06:09:22.520" LastActivityDate="2014-11-17T06:09:22.520" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24019" PostTypeId="1" CreationDate="2014-11-14T21:25:55.400" Score="4" ViewCount="261" Body="&lt;p&gt;There are many softwares such as SnapGene, Geneious, Vector NTI, ApE, Gentle and others for assistance with cloning. Their key functions are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Making maps of plasmids&lt;/li&gt;&#xA;&lt;li&gt;Annotating plasmids with common features&lt;/li&gt;&#xA;&lt;li&gt;Finding restriction sites&lt;/li&gt;&#xA;&lt;li&gt;Mapping Sanger sequencing reads&lt;/li&gt;&#xA;&lt;li&gt;Showing sequence, reverse complement of the sequence, translations in different frames&lt;/li&gt;&#xA;&lt;li&gt;Designing primers for specific applications (such as Gibson cloning)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Is there a tool that does functions such as these, but runs from a command line?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Note:&lt;/em&gt;&lt;/strong&gt; My intent is not so much to get recommendations for what to use, but to get an idea of what software is currently available. Obviously there exist many CLI tools which can be made to serve &lt;em&gt;also&lt;/em&gt; these purposes, up to and including general purpose text editors like &lt;code&gt;vi&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested in what effort has already been made to produce CLI software specifically intended for cloning (by which I mean the functions described above).&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-11-15T23:52:12.980" LastActivityDate="2014-11-16T00:04:08.463" Title="Is there a command line molecular cloning tool?" Tags="&lt;cloning&gt;&lt;software&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24020" PostTypeId="1" AcceptedAnswerId="24023" CreationDate="2014-11-14T23:21:25.157" Score="12" ViewCount="21949" Body="&lt;p&gt;You know how your cells die all the time and new ones are made to replace them, so you practically have a new body every maybe 5 years?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many people say you become a completely different person every several years, but what about neural cells, do they get replaced?&lt;br&gt;&#xA;I believe it would cause a lot of information to get lost if this happened.&lt;/p&gt;&#xA;" OwnerUserId="4080" LastActivityDate="2020-04-27T12:14:00.840" Title="Are brain cells replaced over time?" Tags="&lt;neuroscience&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24021" PostTypeId="1" CreationDate="2014-11-15T02:17:26.220" Score="1" ViewCount="1018" Body="&lt;p&gt;If an individual has no lens like Claude Monet (who had them removed).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They should be able to still focus the images they see in a well light area if they shrink their pupils to a very small size like the Moken people right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But they won't be able to see well at all in dim light, as focusing would require them to dilate their pupils which would make everything  very blurred.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this right?&lt;/p&gt;&#xA;" OwnerUserId="8279" LastEditorUserId="9943" LastEditDate="2014-11-23T13:56:41.893" LastActivityDate="2014-12-23T14:53:44.347" Title="Does pupil size affect image focus in persons with no lens?" Tags="&lt;physiology&gt;&lt;eyes&gt;&lt;vision&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24022" PostTypeId="2" ParentId="9276" CreationDate="2014-11-15T03:01:13.510" Score="7" Body="&lt;p&gt;The first differentiation in human embryogenesis is from early blastomeres into trophoblast, which forms the outer layer of the blastocyst, and inner cell mass (ICM). It may be unsurprising then that cells on the inside of the 8-16 cell stage morula &#xA;differentiate into ICM whereas those on the outside differentiate into trophoblast. However it is currently unclear whether this is a causal relationship (the inside-outside model) or whether blastocyst patterning is set-up earlier in cleavage (such as in the apicobasal polarity model) or if it is some combination of the two. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You were correct in imagining that tissue patterning is determined by chemical substances: a very broad class called morphogens. Cells don't necessarily count how many times they have divided but cell division can certainly affect morphogen concentration and localisation. I suppose in some sense you could describe this as a clock. I wouldn't though, especially because mammalian cleavage is asynchronous. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One line of studies showed that a transcription factor called Tead4 specifies trophoblast&lt;a href=&quot;http://dev.biologists.org/content/134/21/3827.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;$^{ref}$&lt;/a&gt;. It was then shown that Tead4 can be regulated by cell-cell contact (mediated by Hippo signalling) &lt;a href=&quot;http://www.cell.com/developmental-cell/abstract/S1534-5807(09%2900077-X&quot; rel=&quot;noreferrer&quot;&gt;$^{ref}$&lt;/a&gt;. They hypothesised that the magnitude of cell-cell contact could provide a mechanism by which Tead4 localisation could be controlled in presumptive trophoblast and ICM. This could explain why the cells have different fates because inner cells are completely surrounded (more cell junctions) whereas outer cells are largely exposed to the medium. Note that I only provided that as an example of a possible mechanism. It is not confirmed and, as with any model, the real picture is incredibly more complex and likely involves many factors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm reluctant to go into too much detail on this because you're asking about a complex process that is still under active study and I'm unclear as to how much information you actually want. A book could be written on this subject alone, and many review papers have been published. Here's a recent one:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822(12%2901253-5&quot; rel=&quot;noreferrer&quot;&gt;Development: Do Mouse Embryos Play Dice?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suggest you read that and then if you have further, more specific questions, we can try and answer them for you. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-11-16T13:56:33.223" LastActivityDate="2014-11-16T13:56:33.223" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24023" PostTypeId="2" ParentId="24020" CreationDate="2014-11-15T03:27:48.647" Score="13" Body="&lt;p&gt;By brain cells, I'll assume you mean neurons (the other type are called glial cells). Yes, new neurons arise in a least certain parts of the brain, and yes, they do cause memories to weaken or disappear. This has been shown in mice, guinea pigs and degus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be wrong to assume that neurogenesis occurs with the frequency of, say, gastric cell or skin turnover. Up until recently, it was not thought to occur at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Learning and remembering use various cortical structures, including the hippocampus.Throughout life, new neurons (neurogenesis) are continuously added to the dentate gyrus. These additions remodel hippocampal circuits, and when this occurs after memory formation, this neurogenesis leads to degradation or forgetting of established memories. This was shown in adult mice. Conversely, decreasing neurogenesis after memory formation decreased forgetting.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not only plasticity that makes the brain adaptable to continuous changes in environmental demands. Adult-born neurons integrate into preexisting neuronal networks and participate in information processing. Adult neurogenesis itself is a type of circuit plasticity required for hippocampus-dependent learning and memory recall. Adult hippocampal neurogenesis may also promote forgetting.&lt;sup&gt;[2]&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The more neurogenesis there is, the more memories are broken down. Since we retain many memories over our lifetime, it's pretty safe to say out brains don't &quot;turn over&quot; every five years (or even over longer periods); some parts of our brain don't seem to undergo neurogenesis at all.&lt;sup&gt;[3]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://www.sciencemag.org/content/344/6184/598&quot;&gt;Hippocampal Neurogenesis Regulates Forgetting During Adulthood and Infancy&lt;/a&gt; &lt;em&gt;Science&lt;/em&gt; 9 May 2014&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://www.sciencemag.org/content/344/6184/594.summary&quot;&gt;A Price to Pay for Adult Neurogenesis&lt;/a&gt; &lt;em&gt;Science&lt;/em&gt; 9 May 2014&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://www.jneurosci.org/content/22/3/612.full.pdf&quot;&gt;Neurogenesis in the Adult Brain&lt;/a&gt; &lt;em&gt;The Journal of Neuroscience&lt;/em&gt; February 1, 2002&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-11-15T03:27:48.647" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24024" PostTypeId="2" ParentId="19526" CreationDate="2014-11-15T04:30:33.333" Score="0" Body="&lt;p&gt;You can fairly easily substitute peptides (short proteins) from the outside of the body, but you have to supply them by injection. They don't survive the low pH of the stomach unless you encapsulate them into an acid-resistant matrix. Short peptides are often very local and short acting, present only during specific times of the embryonic development (for example, morphokines). However, assuming that you have a peptide hormone like insulin, you can administer it systemically and it will work. There is however over 350 peptides/short protein that are extracellular and many of them are locally restricted. So, you should not just inject them. The problem with larger proteins is, that they do not cross the cell barrier like these small peptides (which have a receptor for crossing/uptake). Many of the broken genes carriers (patients) of genetic diseases have in their genome, are coding for large intracellular proteins, often even tissue-specifically expressed. You cannot get them easily to the right destination, nor can you get them easily into the cell. You have to use a virus that encodes them and infects the cell. Read some Cell / Molecular Biology textbook if you want to learn more details.&lt;/p&gt;&#xA;" OwnerUserId="10118" LastActivityDate="2014-11-15T04:30:33.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24025" PostTypeId="1" CreationDate="2014-11-15T04:34:20.547" Score="0" ViewCount="114" Body="&lt;p&gt;What are the plasmids composed of? Are they composed of genomic or non-genomic DNA? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess the answer is &quot;genomic DNA&quot; but I'm not sure.&lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="14782" LastEditDate="2015-03-05T19:13:23.183" LastActivityDate="2015-03-05T19:13:23.183" Title="What is the nature of plasmids?" Tags="&lt;genetics&gt;&lt;bacteriology&gt;&lt;plasmids&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-11-16T03:16:13.703" ContentLicense="CC BY-SA 3.0" />
  <row Id="24026" PostTypeId="2" ParentId="19548" CreationDate="2014-11-15T04:54:52.507" Score="1" Body="&lt;p&gt;Let me see whether I can explain this quickly. The eye size is tightly regulated genetically. Babies don't have big eyes, they have exactly the same sized eyes like adults, only their head is smaller. Myopic eyes are larger than normal and hyperopic eyes are smaller than normal, even though the difference is only 1 to a few millimeters. When you focus to the far point, the light focusses to the nearest point possible in the back of your eye. When you come closer to an object, the focus point inside the eye moves further out. Thus, the farsighted person with the small eye can only see when the object is away. Moving closer moves the focal point inside the eye to behind the retina. The opposite is true for myopic people with too large eyes. When a person gets old, the lens gets stiff and cannot adjust the focal point inside the eye to the distance of the retina. Thus, the lens remains stiff in the most relaxed state (extended), or - in other words - at the most distant focal point the person had when it was young. A normal-sighted person has his old-age focal point at the horizon and since his lens is stiff, can only see sharp from the horizon to a few meters in front of him (depending on the intensity and wavelength of the light - blue light better than red). A short-sighted person is of disadvantage when old, since his far point remains to be at short distance. He gains a little sharpness over the normal sighted person in the short distance, but loses it in the distance like he always did. You can calculate this nicely, actually. All physics.&lt;/p&gt;&#xA;" OwnerUserId="10118" LastActivityDate="2014-11-15T04:54:52.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24027" PostTypeId="2" ParentId="24003" CreationDate="2014-11-15T05:18:19.950" Score="1" Body="&lt;p&gt;Glycerol is not lipid (short chain &lt;a href=&quot;http://en.wikipedia.org/wiki/Polyol&quot; rel=&quot;nofollow&quot;&gt;polyol&lt;/a&gt;, so it is &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemical_polarity&quot; rel=&quot;nofollow&quot;&gt;polar&lt;/a&gt; and water soluble), but fatty acids (&lt;a href=&quot;http://en.wikipedia.org/wiki/Amphiphile&quot; rel=&quot;nofollow&quot;&gt;amphiphilic&lt;/a&gt;) and triglycerides (&lt;a href=&quot;http://en.wikipedia.org/wiki/Hydrophobe&quot; rel=&quot;nofollow&quot;&gt;hydrophobic&lt;/a&gt;) are.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Lipids may be broadly defined as hydrophobic or amphiphilic small&#xA;  molecules; the amphiphilic nature of some lipids allows them to form&#xA;  structures such as vesicles, multilamellar/unilamellar liposomes, or&#xA;  membranes in an aqueous environment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;wikipedia - &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipid&quot; rel=&quot;nofollow&quot;&gt;lipid&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-11-15T05:18:19.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24028" PostTypeId="2" ParentId="24019" CreationDate="2014-11-15T05:46:13.687" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Making maps of plasmids Annotating plasmids with common features&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Plasmapper works through commandline&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Finding restriction sites&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Simple regex searches can do that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mapping Sanger sequencing reads&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;BLAST will do it. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Showing sequence, reverse complement of the sequence, translations in&#xA;  different frames &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;EMBOSS has a collection of tools for these things. (&lt;code&gt;getorf&lt;/code&gt; is a tool for finding ORFs)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Designing primers for specific applications (such as&#xA;  Gibson cloning)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Primer3 works through commandline&lt;br&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&#xA;You can just download the entire &lt;a href=&quot;http://emboss.sourceforge.net/&quot; rel=&quot;nofollow&quot;&gt;EMBOSS&lt;/a&gt; collection. It has many useful tools.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-15T05:46:13.687" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24029" PostTypeId="1" CreationDate="2014-11-15T07:00:25.753" Score="1" ViewCount="92" Body="&lt;p&gt;I'm using cDNA AFLP teq.. I extracted 670 bp band from polyacrylamide (urea) gel and I have amplified with PCR  but on agarose gel it stops at nearly 350 bp.it happened for most of other bands before. I always extracted the precise bands.  I repeated with both pre and selective primers with the same PCR program before done for amplification of digested cDNA and same size bands observed in agarose gel.I wonder maybe secondary structure causes losses in band size (before running in polyacrylamide samples treated in 94 degree for 5 min), but how I can recognize?  i should notice 350 bp band i mentioned above is very sharp. what other thing I'm wondering is can dye uses in agarose gel alternate the DNA charge and reduces the speed of movement . The big  matter is the rate of losses in band size almost is same for almost all of the bands for one primer. Is it happened for anyone before? can i trust on my extracted bands for doing cloning?&lt;/p&gt;&#xA;" OwnerUserId="10202" LastEditorUserId="3340" LastEditDate="2014-11-15T12:17:36.933" LastActivityDate="2014-11-15T12:17:36.933" Title="Loss in DNA band size extracted from polyacrylamide gel" Tags="&lt;molecular-genetics&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24030" PostTypeId="2" ParentId="24025" CreationDate="2014-11-15T08:24:42.187" Score="4" Body="&lt;p&gt;You probably mean genomic and non-genomic DNA - &lt;a href=&quot;http://en.wikipedia.org/wiki/Plasmid&quot; rel=&quot;nofollow noreferrer&quot;&gt;Plasmids&lt;/a&gt; are small rings of non-genomic double-stranded DNA in Bacteria. They replicate mostly indepently of the genomic DNA can can occur from a few to several hundred copies per cell. See the illustration from the Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FGXPy.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-11-15T10:58:33.007" LastActivityDate="2014-11-15T10:58:33.007" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24031" PostTypeId="2" ParentId="23995" CreationDate="2014-11-15T08:59:39.487" Score="2" Body="&lt;p&gt;You can consider these also:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Add 2-mercaptoethanol and heat at 95⁰ for 10 min &lt;sup&gt;[&lt;a href=&quot;http://www.jbc.org/content/225/2/1061.full.pdf&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;]&lt;/sup&gt; &lt;/li&gt;&#xA;&lt;li&gt;Add PMSF, incubate for some time and then heat for some time (lets say 70⁰ for 10min) to inactivate residual PMSF.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-15T08:59:39.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24032" PostTypeId="2" ParentId="9788" CreationDate="2014-11-15T10:22:29.683" Score="2" Body="&lt;p&gt;Some of the criteria, I guess are difficult to find (Also for my lack of understanding of those terms). For the rest you can search these databases:-&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Growth substrate: &lt;em&gt;I don't really know what you are asking here — growth rate in minimal media/optimal growth medium ?&lt;/em&gt; Nevertheless, see the &lt;a href=&quot;https://mediadb.systemsbiology.net/defined_media/&quot; rel=&quot;nofollow&quot;&gt;Media Database&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Methanogenesis: Ortholog Table - KEGG MODULE &lt;a href=&quot;http://www.kegg.jp/kegg-bin/view_ortholog_table?md=M00567&quot; rel=&quot;nofollow&quot;&gt;M00567&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;Nitrogen fixation: Ortholog Table - KEGG MODULE &lt;a href=&quot;http://www.kegg.jp/kegg-bin/view_ortholog_table?md=M00175&quot; rel=&quot;nofollow&quot;&gt;M00175&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-15T10:22:29.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24034" PostTypeId="1" AcceptedAnswerId="24035" CreationDate="2014-11-15T10:32:09.130" Score="2" ViewCount="666" Body="&lt;p&gt;I'm trying to use miRBase database to annotate some microRNA sequences in length 22-24bp. I highly appreciate if someone let me know whether I should do this BLAST against mature miRNA or stem-loop sequence database? and the other main question is that which number of E-value is reasonably accepted as a lowest E-Value in the miRNA BLAST results? Also, what tool you suggest to perform miRNA enrichment analysis? for example we can use DAVID for gene (coding sequence) enrichment analysis. Using such analysis we are able to assign probable functions and biological roles to a group of miRNA (not only one miRNA). Any comments and idea is welcomed. &lt;/p&gt;&#xA;" OwnerUserId="10205" LastEditorUserId="10205" LastEditDate="2014-11-15T11:47:34.947" LastActivityDate="2014-11-17T04:21:12.173" Title="what the best E-value cutoff in the miRNA homology search" Tags="&lt;bioinformatics&gt;&lt;blast&gt;&lt;microrna&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24035" PostTypeId="2" ParentId="24034" CreationDate="2014-11-15T10:49:44.877" Score="0" Body="&lt;p&gt;If you are using BLAST for short nucleotide searches then you should reduce your word size to &amp;lt;=7. It is better to align with mature sequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E-value depends on the database size. If your target database is huge then you should increase the e-value cutoff. If miRBase (for a few organisms) is your database then there is no need to run BLAST, also. You can simply run SSEARCH (Smith-Waterman Local alignment algorithm). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are running BLAST against miRbase you can set the e-value cutoff at 10. This is fine because there are many similar looking miRNAs with different function. If you reduce the e-value cutoff then you may lose these. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some other criteria for miRNA conservation- e.g there should be very high (almost exact) similarity at the seed region. After the BLAST, make sure that seed region is conserved.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Can we can use DAVID for miRNA functional analysis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't think DAVID can be directly used (miRNAs have to be annotated in their database). What you can do is that you can predict the targets of your miRNA and then pass them to DAVID. DAVID won't do the predictions but there are other programs (see &lt;a href=&quot;https://biology.stackexchange.com/questions/23452/how-to-find-mirna-binding-sites-on-a-specific-gene&quot;&gt;this&lt;/a&gt; post). You can also try BioMart (provided by ENSEMBL) for getting GO details. Even BioMart does not provide functional annotation for miRNAs (I just tried, to verify). So best thing is to check for the targets.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-11-17T04:21:12.173" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="24036" PostTypeId="2" ParentId="24020" CreationDate="2014-11-15T11:12:25.030" Score="4" Body="&lt;p&gt;Addition to anongoodnurse's answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Different organisms have different numbers of neurogenic niches (regions where neurons form). For example zebrafish&lt;sup&gt;[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22318736&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]&lt;/sup&gt; has six niches compared to two in mammals and it is known to have active neurogenesis throughout life. In mammals, apart from the dentate gyrus (subgranular zone) of hippocampus, the other prominent neurogenic niche is the subventricular zone (SVZ) - the region adjoining the ventricles. Immature neurons born at the SVZ migrate to olfactory bulb via the rostral migratory stream&lt;sup&gt;[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11681836&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2917621&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also refer to this detailed review&lt;a href=&quot;http://dx.doi.org/10.1016/j.neuron.2011.05.001&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt; [4]&lt;/sup&gt;&lt;/a&gt; on Adult Neurogenesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;&lt;sup&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;br&gt;&lt;br&gt;&#xA;[1] Lindsey, Benjamin W., Audrey Darabie, and Vincent Tropepe. &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22318736&quot; rel=&quot;nofollow&quot;&gt;The cellular composition of neurogenic periventricular zones in the adult zebrafish forebrain.&lt;/a&gt;&quot; Journal of Comparative Neurology 520.10 (2012): 2275-2316.&lt;br&gt;&#xA;[2] Pencea, Viorica, et al. &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11681836&quot; rel=&quot;nofollow&quot;&gt;Neurogenesis in the subventricular zone and rostral migratory stream of the neonatal and adult primate forebrain.&lt;/a&gt;&quot; &lt;em&gt;Experimental neurology&lt;/em&gt; 172.1 (2001): 1-16.&lt;br&gt;&#xA;[3] Bath KG, Lee FS. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2917621&quot; rel=&quot;nofollow&quot;&gt;&quot;Neurotrophic Factor Control of Adult SVZ Neurogenesis&quot;&lt;/a&gt;. &lt;em&gt;Developmental neurobiology&lt;/em&gt;. 2010;70(5):339-349&lt;br&gt;&#xA;[4] Ming, Guo-li, and Hongjun Song. &quot;&lt;a href=&quot;http://dx.doi.org/10.1016/j.neuron.2011.05.001&quot; rel=&quot;nofollow&quot;&gt;Adult neurogenesis in the mammalian brain: significant answers and significant questions&lt;/a&gt;.&quot; &lt;em&gt;Neuron&lt;/em&gt; 70.4 (2011): 687-702.&#xA;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-04-12T10:41:19.217" LastActivityDate="2016-04-12T10:41:19.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24039" PostTypeId="2" ParentId="23273" CreationDate="2014-11-15T16:01:00.967" Score="2" Body="&lt;p&gt;I remember going to a chemistry lecture which mentioned this (the lecture was on blood transfusion in general).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main reasons are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Hemoglobin is toxic to the human body: Hb in RBCs is a tetramer, but in the plasma it breaks into two dimers --&gt; toxicity in the kidneys. Hb needs modification by cross-linking or recombination. Wikipedia states that this is Acute Tubular Necrosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Hb in plamsa decreases osmotic pressure&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Hemoglobin removes the NO from the vessel walls causing vasoconstriction, shrinkage of the vessels.  --&gt; &lt;em&gt;this was the main focus of the chemistry lecture; there was a lot of talk about free radicals and stuff but I've unfortunately forgotten the details&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've also searched a bit on the web and some people (one yahoo answers) confirm rhill45's answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think searching failed blood transfusion products (people have tried transfusing Hb directly) will be of great help.&lt;/p&gt;&#xA;" OwnerUserId="10207" LastActivityDate="2014-11-15T16:01:00.967" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24040" PostTypeId="1" CreationDate="2014-11-15T16:43:12.443" Score="1" ViewCount="1049" Body="&lt;p&gt;I've read that the human's unfertilized oocyte ( stuck at metaphase 2 of meiosis ) lacks centrioles and that it completes meiosis 2 after fertilization as sperm gives its proximal centriole. Then what about the centrioles required for mitosis of zygote?? How does proximal centriole function?&lt;/p&gt;&#xA;" OwnerUserId="10208" LastActivityDate="2019-03-11T12:03:40.853" Title="How does proximal centriole of human sperm function?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24043" PostTypeId="2" ParentId="24019" CreationDate="2014-11-16T00:04:08.463" Score="1" Body="&lt;p&gt;For protein alignment you have things like &lt;a href=&quot;http://www.clustal.org&quot; rel=&quot;nofollow&quot;&gt;Clustal W/Clustal X&lt;/a&gt;. Many, including myself use R for bioinformatics related work and I have came across &lt;a href=&quot;http://bioconductor.org/packages/release/bioc/html/ecolitk.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; package which can be found in Bioconductor, which can address one of your points but I don't know of any unified CLI for the points you have said.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't worked with that specific package itself but if you have R or RStudio, which is my preferred IDE, you simply have to enter the command &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;source(&quot;bioconductor.org/biocLite.R&quot;) &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;command to upload the biocLite package and prepare R for download from the bioconductor database/depository and then execute the command &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;biocLite(&quot;ecolitk&quot;)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;It's mostly for plotting functions to work with circular genomics and can be used with other genomes/plasmids according to the &lt;a href=&quot;http://www.bioconductor.org/packages/release/bioc/manuals/ecolitk/man/ecolitk.pdf&quot; rel=&quot;nofollow&quot;&gt;package description&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-11-16T00:04:08.463" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24045" PostTypeId="1" AcceptedAnswerId="24050" CreationDate="2014-11-16T00:19:39.280" Score="6" ViewCount="2054" Body="&lt;p&gt;Many breeds of domestic dogs seem to like burying food, presumably in preparation for leaner times.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that dogs evolved from animals similar to the modern wolves through a mix of natural and artificial selection, is this burying behavior novel in dogs, or inherited from wild wolves? Do wild wolves also habitually bury food, and return to their caches when hungry?&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="338" LastEditDate="2014-11-16T04:20:02.440" LastActivityDate="2014-11-16T04:20:02.440" Title="Do wolves bury food like dogs?" Tags="&lt;evolution&gt;&lt;food&gt;&lt;ethology&gt;&lt;dogs&gt;&lt;instinct&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24046" PostTypeId="1" AcceptedAnswerId="24048" CreationDate="2014-11-15T17:42:55.200" Score="15" ViewCount="11414" Body="&lt;p&gt;A normal camera can capture a rectangular image. If human eyes watch an area, what's the shape of the captured region? Rectangular? Half-spherical?&lt;/p&gt;&#xA;" OwnerUserId="10230" OwnerDisplayName="padman" LastEditorUserId="2949" LastEditDate="2014-11-21T19:55:00.823" LastActivityDate="2018-11-16T23:32:16.283" Title="If human eyes watch an area, what's the shape of its capturing shape? Rectangular? Half spherical?" Tags="&lt;human-biology&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24047" PostTypeId="2" ParentId="24046" CreationDate="2014-11-15T17:52:02.280" Score="4" Body="&lt;p&gt;One eye captures a roughly circular area.  Because we have two overlapping fields of vision for depth perception, between our two eyes we capture a roughly elliptical shape.&lt;/p&gt;&#xA;" OwnerDisplayName="Dave Coffman" LastActivityDate="2014-11-15T17:52:02.280" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24048" PostTypeId="2" ParentId="24046" CreationDate="2014-11-15T19:05:47.987" Score="25" Body="&lt;p&gt;The capture area of the eye is a bit fuzzier and harder to define than that of a camera.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A camera captures consistent, fully detailed data right up to the edge of its sensor, and no data at all beyond it. Captured data is clipped by an ideally uniform sensor, augmented a bit by the lens, and is well-defined during design and manufacturing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The eye can capture higher &quot;resolution&quot; near the center of its capture area and also has very little information about color near the edges (see also &lt;a href=&quot;http://en.wikipedia.org/wiki/Peripheral_vision&quot; rel=&quot;nofollow noreferrer&quot;&gt;Peripheral Vision&lt;/a&gt;); so it's not quite as clean cut depending on your goal of &quot;capture area&quot;. The eye also has a bit of a &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Blind_spot_(vision)&quot; rel=&quot;nofollow noreferrer&quot;&gt;blind spot&lt;/a&gt;&quot; near the middle, which our brains basically Photoshop out. Additionally, it varies from person to person. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;effective&lt;/em&gt; capture area would really depend on your application (e.g. the &quot;capture area&quot; for, say, reading text, would be narrower than the area for, say, detecting motion).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a typical diagram for a single eye, showing just the ability to see something in that area (does not show details related to peripheral vision quality):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0zByD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a typical diagram for both eyes combined, the solid white area is the overlap:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LfiSe.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both of those images are from a &lt;a href=&quot;https://web.archive.org/web/20170124045754/https://vision.arc.nasa.gov/personnel/al/papers/64vision/17.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;1964 NASA report&lt;/a&gt; detailing aspects of the human visual field. If you want the detailed answer to your question and more, you probably want to take a look at that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that our field of vision is very wide, those diagrams may not do it justice. As an experiment, close one eye, stare straight ahead and hold your arms straight out to the sides. Wiggle your fingers and slowly bring your arms forward until you can just see your wiggling fingers in your peripheral vision, and you will get an idea. As an added experiment, hold a piece of paper with text on it, and repeat the same experiment until you can read the text - this region will be extremely narrow and will give you an idea of how the quality of vision changes across the field. Also try with a colored object and bring it in until you can clearly identify the color.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also some simplified mentions of it in wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Field_of_view#Humans_and_animals&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Field_of_view#Humans_and_animals&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Human_eye#Field_of_view&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Human_eye#Field_of_view&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Visual_field#Normal_limits&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Visual_field#Normal_limits&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;A good set of search keywords is &lt;a href=&quot;https://www.google.com/search?q=human+field+of+vision&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;human field of vision&quot;&lt;/a&gt;. There is also a nice related article entitled &lt;a href=&quot;http://petapixel.com/2012/11/17/the-camera-versus-the-human-eye/&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Camera Versus the Human Eye&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8218" OwnerDisplayName="Jason C" LastEditorUserId="8218" LastEditDate="2018-11-16T23:32:16.283" LastActivityDate="2018-11-16T23:32:16.283" CommentCount="7" ContentLicense="CC BY-SA 4.0" />
  <row Id="24050" PostTypeId="2" ParentId="24045" CreationDate="2014-11-16T04:09:43.197" Score="5" Body="&lt;p&gt;The habit of burying food in modern dogs is an instinct that came from the grey wolf (&lt;a href=&quot;http://en.wikipedia.org/wiki/Gray_wolf&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Canis lupus&lt;/em&gt;&lt;/a&gt;) long ago, and originates from a phenomenon called &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-7998.1972.tb04087.x/abstract&quot; rel=&quot;noreferrer&quot;&gt;surplus killing&lt;/a&gt;, where a carnivore would kill more than it could eat, and often use it at a later time.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many, if not all, carnivores possess behaviour patterns which allow utilization of a kill at a later time, or allow other members of the same social unit or offspring to use the food.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;When the prey is small enough to transport, and there are pups, it is often &lt;a href=&quot;http://www.wolfhowl.org/behavior.php&quot; rel=&quot;noreferrer&quot;&gt;returned to the den&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pups will usually remain in their den for the first three or four weeks of their lives before mother allows them to venture forth into the light. During this time the mother is quite dependant on her mate and other pack members to bring her food in the form of meat that is often regurgitated for her.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is then fed on by the litter, and the excess &lt;a href=&quot;http://books.google.com/books?id=AhlvmkSkxeYC&amp;amp;pg=PA226&amp;amp;lpg=PA226&amp;amp;dq=food%20hoarding%20in%20animals%20table%208.4&amp;amp;source=bl&amp;amp;ots=AuVX5o1F9u&amp;amp;sig=Bn0jY_QCby4H9ovSER678OU_CH4&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=eCFoVMvKDYqNyATInYB4&amp;amp;ved=0CB4Q6AEwAA#v=onepage&amp;amp;q=food%20hoarding%20in%20animals%20table%208.4&amp;amp;f=false&quot; rel=&quot;noreferrer&quot;&gt;buried for later use&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is called &lt;a href=&quot;http://wolfcenter.org/site/wolf-behavior/cache-behavior.html#.VGgX0_nF-3Q&quot; rel=&quot;noreferrer&quot;&gt;'caching'&lt;/a&gt;, and is &lt;a href=&quot;http://www.mmilani.com/dog-covers-food.html&quot; rel=&quot;noreferrer&quot;&gt;still seen today&lt;/a&gt; in the domestic dog (&lt;a href=&quot;http://en.wikipedia.org/wiki/Dog&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Canis familiaris&lt;/em&gt;&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2014-11-16T04:09:43.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24051" PostTypeId="2" ParentId="20264" CreationDate="2014-11-16T08:39:56.477" Score="0" Body="&lt;p&gt;&lt;strong&gt;Problems with the davson danielli model :&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;em&gt;freeze-etched micrographs&lt;/em&gt;:&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This is a technique of rapidly freezing the cell and then fracturing them. The fracture occurs along lines of weakness and in these micrographs there were two prominent dark lines which indicate the phospholipid bilayer and but there were transmembrane proteins even in between the phospholipid bilayer unlike what the davson danielli model suggested (that the phospholipid bilayers contained two layers of proteins on top and on bottom.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OH8I1.jpg&quot; alt=&quot;enter image description here&quot;&gt;                 &lt;img src=&quot;https://i.stack.imgur.com/xw8cr.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2)&lt;em&gt;structure of membrane proteins :&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;improvements in biochemical tech allowed people to extract proteins from the membranes. They were different sizes and globular in structure.They were unlike the type that would form continuous layers on the periphery of the membrane. Proteins were hydrophilic in nature and hence should have been attracted to the tails and not the heads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3)&lt;em&gt;Fluorescent anti-body tagging&lt;/em&gt; :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;red and green markers were attached to the antibodies that bind to membrane proteins. these two cells were fused together and 40 minutes later it was seen that the red and green markers were mixed throughout the membrane of the fused cells. therefore the proteins were free to move within the membrane rather than being fixed in a peripheral layer.&lt;/p&gt;&#xA;" OwnerUserId="10218" LastActivityDate="2014-11-16T08:39:56.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24052" PostTypeId="1" CreationDate="2014-11-16T11:11:50.207" Score="2" ViewCount="59" Body="&lt;p&gt;I consistently read in non-scientific resources that I have to put my rosemary to low temperature (about 10°C) in winter (unless I don't want it to freeze). I googled, but I fail to find a scientific resource about why room temperature is not good for it. Do you have any explanation (with scientific references ofc.)?&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2016-05-09T17:38:05.533" Title="Rosemary room temperature at winter" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="0" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="24054" PostTypeId="2" ParentId="24021" CreationDate="2014-11-16T13:29:20.867" Score="1" Body="&lt;p&gt;Very nice question! You are right, in that small pupils will help to reduce the blurriness of vision caused by &lt;a href=&quot;http://www.who.int/features/qa/45/en/&quot; rel=&quot;nofollow noreferrer&quot;&gt;refractive errors&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Removal of the lens (&lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;sqi=2&amp;amp;ved=0CB0QFjAA&amp;amp;url=http%3A%2F%2Fen.wikipedia.org%2Fwiki%2FAphakia&amp;amp;ei=nqFoVJP-IceNmwW-54CQDg&amp;amp;usg=AFQjCNEXe77XNDui-EnjZkaYEQXZtbUtGg&amp;amp;sig2=S_tiQvjCEOlvB7dGtFkgxg&quot; rel=&quot;nofollow noreferrer&quot;&gt;aphakia&lt;/a&gt;) results in farsightedness. It is caused by a focus point that falls behind the retina as the absence of the lens prevents focusing of the image, causing a blurred image. The amount of blur is proportional to the pupil size (&lt;a href=&quot;https://jrm.phys.ksu.edu/papers/2008/pinhole-glasses-tpt.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Colichia et al., 2008&lt;/a&gt;). See their figure 2 below:&lt;img src=&quot;https://i.stack.imgur.com/Cu6qv.png&quot; alt=&quot;&quot;&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the upper part you see a hyperopic eye, which has a lens that cannot accommodate sufficiently, comparable to an aphakic eye. the bottom part shows the result of when a pinhole is applied, namely a reduction of the blurred circle and improvement of the focus. This could also be achieved by having very small pupils such as when ambient light is very bright (and a characteristic of the Moken peoples when diving (&lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822(03)00290-2&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gislén et al., 2003&lt;/a&gt;). And indeed, under conditions of low lighting the pupil size will increase and hence blurring will be worse. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-16T13:29:20.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24055" PostTypeId="1" CreationDate="2014-11-16T14:27:10.957" Score="5" ViewCount="1224" Body="&lt;p&gt;I understand that there will be many other factors that affect rate of evolution/innovation. However, other things being equal, how will the rate of evolution vary between two populations of different sizes? Does doubling the population size double the rate of introduction of new traits?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this answerable for evolving life in general, or do different forms of life have different scaling laws? For example, is it different for sexual and asexual life?&lt;/p&gt;&#xA;" OwnerUserId="10223" LastActivityDate="2015-06-08T21:14:27.830" Title="How does rate of evolution/innovation scale with population size?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24056" PostTypeId="1" AcceptedAnswerId="24073" CreationDate="2014-11-16T15:21:11.720" Score="9" ViewCount="1416" Body="&lt;p&gt;We are all familiar with the examples of symbiotic relationships in nature consisting of two agents, like lichen or the co-evolvement between certain birds and flowering plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do we know of any mutually symbiotic relationships that has three of a even higher number of agents?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: To make a implicit distinction clear, let's specify that the agents in question have distinctive and fully interdependent roles in the symbiosis. In contrast to a scenario where a range of bird species might co-evolve for a single specific flower and have the same role as pollinators in the symbiosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This image represents my current models in thinking about this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/s7jBI.png&quot; alt=&quot;conceptual network types&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The type I'm searching for here is mainly the &quot;3-agent symbiosis&quot;, but the bidirectional one is of interest as well.&lt;/p&gt;&#xA;" OwnerUserId="9124" LastEditorUserId="9124" LastEditDate="2014-11-17T05:39:33.487" LastActivityDate="2014-11-19T09:08:42.993" Title="Are there any known mutual symbiotic relationships that has more than two agents?" Tags="&lt;evolution&gt;&lt;ecology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24057" PostTypeId="1" AcceptedAnswerId="24064" CreationDate="2014-11-16T15:49:24.873" Score="2" ViewCount="161" Body="&lt;p&gt;Mammals have external qualifying characteristics like body hair, ear pinna, etc. But a whale has none of that. So, can it be identified as a mammal just by external observations?&lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="9943" LastEditDate="2014-11-16T23:24:46.677" LastActivityDate="2018-10-28T18:21:14.947" Title="How to determine externally that a whale is a mammal?" Tags="&lt;mammals&gt;&lt;morphology&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24058" PostTypeId="1" CreationDate="2014-11-16T17:05:40.233" Score="3" ViewCount="102" Body="&lt;p&gt;Drinking sea water can be deadly as it contains too much salt, basically de-hydrating the body. Normal tap water contains little salt and is good for re-hydration. My question: How much salt needs to be dissolved in water such that it does not hydrate nor de-hydrate? For instance, would a physiologic saline solution (9 grams of salt per liter of water) meet this criterion? &lt;/p&gt;&#xA;" OwnerUserId="10226" LastEditorUserId="9943" LastEditDate="2014-11-17T11:47:35.923" LastActivityDate="2014-11-17T17:30:20.827" Title="What proportion of salt in water would make it not dehydrate nor hydrate someone?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;" AnswerCount="0" CommentCount="14" FavoriteCount="1" ClosedDate="2015-07-03T09:21:18.913" ContentLicense="CC BY-SA 3.0" />
  <row Id="24059" PostTypeId="2" ParentId="24056" CreationDate="2014-11-16T17:50:32.247" Score="2" Body="&lt;p&gt;The human body contains a few billion microbes (more than human cells), so we live in symbiosis with many different species. Some of them protect us from infections, some of them help in the digestion, and so on... So I think the human body fulfills your requirements.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;wikipedia - &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_microbiome&quot; rel=&quot;nofollow&quot;&gt;human microbiome&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Normally we don't live in sterile environment. So we depend on our microflora in order to protect us against pathogens by preventing them to colonize e.g. our intestines. So without a sterile environment we would die in the lack of our microflora e.g. in a C. difficile infection. In exchange we give our microbes shelter (e.g. we protect them from oxygen, UV radiation, temperature changes) and food (e.g. carbohydrates we cannot digest, for example xylitol). So the human-microbiome relationship is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Mutualism_%28biology%29&quot; rel=&quot;nofollow&quot;&gt;mutualism&lt;/a&gt;. Some of these microbes are not detected outside of the (not necessary human) host, so these relationships can be obligate. These microbes do not only support us, but each other as well. E.g. they help each other to digest nutritients (syntrophy), so they can live in mutualism with each other as well. So multipartite symbiosis certainly exists in the human body, and it seems like much more common in the nature than we previously thought.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://link.springer.com/article/10.1186%2F2049-2618-1-17&quot; rel=&quot;nofollow&quot;&gt;Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2003 - &lt;a href=&quot;http://www.pnas.org/content/100/18/10452.full&quot; rel=&quot;nofollow&quot;&gt;Honor thy symbionts&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3989713/&quot; rel=&quot;nofollow&quot;&gt;Cooperation, communication, and co-evolution: grand challenges in microbial symbiosis research&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2007 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2007.01281.x/full&quot; rel=&quot;nofollow&quot;&gt;Interactions and competition within the microbial community of the human colon: links between diet and health&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2005 - &lt;a href=&quot;http://www.sciencemag.org/content/307/5717/1915.short&quot; rel=&quot;nofollow&quot;&gt;Host-Bacterial Mutualism in the Human Intestine&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.pnas.org/content/110/31/12804.short&quot; rel=&quot;nofollow&quot;&gt;Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www2.fiu.edu/~makemson/SeniorSeminar/MultipartiteMutualsimAnnRev-13.pdf&quot; rel=&quot;nofollow&quot;&gt;It Takes a Village: Ecological and Fitness Impacts of Multipartite Mutualism&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1559669/&quot; rel=&quot;nofollow&quot;&gt;Entente cordiale: Multiple symbiosis illustrates the intricate interconnectivity of nature&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="10045" LastEditDate="2014-11-17T12:09:44.833" LastActivityDate="2014-11-17T12:09:44.833" CommentCount="17" ContentLicense="CC BY-SA 3.0" />
  <row Id="24061" PostTypeId="1" CreationDate="2014-11-16T21:56:42.750" Score="1" ViewCount="63" Body="&lt;p&gt;What kind of biosensor is made by Phages?&#xA;I need a list of published paper that used Phages for make LCR(inductance (L), capacitance (C), and resistance (R) of a component) biosensor for detection. for example detection of E.coli&lt;/p&gt;&#xA;" OwnerUserId="9101" LastEditorUserId="9101" LastEditDate="2014-11-19T23:14:01.480" LastActivityDate="2014-11-19T23:14:01.480" Title="Phage base Biosensor" Tags="&lt;biotechnology&gt;" AnswerCount="0" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24062" PostTypeId="1" AcceptedAnswerId="24068" CreationDate="2014-11-16T22:31:07.460" Score="4" ViewCount="6554" Body="&lt;p&gt;Do all Gram negative bacteria cause septic shock? If they don't could they if you attacked them with an antibiotic that could lyse the cell? For example any antibiotic that attacks the cell wall, although I suppose that could be difficult with the gram negative wall, not to many gram negatives are susceptible to a wall attack.&lt;/p&gt;&#xA;" OwnerUserId="10026" LastActivityDate="2014-11-17T01:11:37.083" Title="Do all Gram negative bacteria cause septic shock?" Tags="&lt;microbiology&gt;&lt;medicine&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24063" PostTypeId="1" AcceptedAnswerId="24070" CreationDate="2014-11-16T22:45:22.413" Score="3" ViewCount="332" Body="&lt;p&gt;At which temperature is the Tick-Borne Encephalitis Virus destroyed? If there is no data specifically for TBEV, is there any data for typical temperatures at which other Flaviviruses / Flaviviridae / other similar viruses are destroyed? (Or if there's nothing specific at all, then viruses in general?)&lt;/p&gt;&#xA;" OwnerUserId="10228" LastActivityDate="2014-11-17T11:34:39.360" Title="At which temperature is the Tick-Borne Encephalitis Virus destroyed?" Tags="&lt;virus&gt;&lt;virology&gt;&lt;parasitology&gt;&lt;temperature&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24064" PostTypeId="2" ParentId="24057" CreationDate="2014-11-16T23:15:50.500" Score="4" Body="&lt;p&gt;A whale has a horizontal tail fin which is a typical feature of mammalian marine animals &lt;a href=&quot;http://sciencefocus.com/qa/why-do-fish-have-vertical-tail-fins-and-whales-have-horizontal-ones&quot; rel=&quot;nofollow&quot;&gt;see link&lt;/a&gt;. Mammalian sea animals typically have a vertical movement of the tail fin for swimming. Fishes like sharks have a vertically oriented tail fin and move it side-ways for locomotion.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-16T23:15:50.500" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24065" PostTypeId="2" ParentId="24002" CreationDate="2014-11-16T23:57:30.073" Score="1" Body="&lt;p&gt;Technology is not advanced enough to achieve receptor-specific stimulation. Regarding your defined needs:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Identifying M cones: It is already challenging to distinguish cones from rods in the retina (&lt;a href=&quot;http://link.springer.com/chapter/10.1007%2F978-3-642-24085-0_51#page-1&quot; rel=&quot;nofollow&quot;&gt;Turpin et al, 2011&lt;/a&gt;), let alone identify the three classes of cones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Your retinal-mosaic image would theoretically be possible, although very small pixels would be needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Eye tracking is doable, but not at this level of accuracy. Delays in the system will almost certainly result in transient activation of other receptors.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-16T23:57:30.073" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24066" PostTypeId="2" ParentId="24062" CreationDate="2014-11-17T00:45:17.333" Score="2" Body="&lt;p&gt;The major factor defining Gram-negative (vs. Gram-positive) bacteria is the structure of the cell wall, outer membranes, and the moieties that extend out into the environment:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2yYGZ.png&quot; alt=&quot;Gram+ vs. Gram-&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=File:Gram-Cell-wall.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/w/index.php?title=File:Gram-Cell-wall.svg&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gram+ bacteria have an inner plasma membrane and an outer, thick layer of &lt;a href=&quot;http://en.wikipedia.org/wiki/Peptidoglycan&quot; rel=&quot;nofollow noreferrer&quot;&gt;peptidoglycans&lt;/a&gt;. This is what takes up &lt;a href=&quot;http://en.wikipedia.org/wiki/Gram_staining&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gram's stain&lt;/a&gt;. Gram-, on the other hand, have a plasma membrane, a thinner peptidoglycan wall, then an outer membrane consisting of &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipopolysaccharide&quot; rel=&quot;nofollow noreferrer&quot;&gt;lipopolysaccharides&lt;/a&gt; (also known as LPS or endotoxin) anchored into the membrane's phospholipids, along with various proteins within the membrane:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DGchn.png&quot; alt=&quot;Gram- outer membrane structure&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Gram_negative_cell_wall.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://commons.wikimedia.org/wiki/File:Gram_negative_cell_wall.svg&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sepsis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sepsis&lt;/a&gt;, a systemic inflammatory response syndrom (&lt;a href=&quot;http://en.wikipedia.org/wiki/Systemic_inflammatory_response_syndrome&quot; rel=&quot;nofollow noreferrer&quot;&gt;SIRS&lt;/a&gt;) can be caused by both Gram-positive and -negative bacteria, as well as viruses and fungi. In the case of Gram-negatives, the immune system is activated in response to the presence of LPS from extracellular lysed and intracellular &lt;a href=&quot;http://en.wikipedia.org/wiki/Antigen_processing&quot; rel=&quot;nofollow noreferrer&quot;&gt;antigen-processed&lt;/a&gt; bacteria, through the &lt;a href=&quot;http://en.wikipedia.org/wiki/Toll-like_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;Toll-like receptor&lt;/a&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/TLR4&quot; rel=&quot;nofollow noreferrer&quot;&gt;TLR4&lt;/a&gt;/&lt;a href=&quot;http://en.wikipedia.org/wiki/CD14&quot; rel=&quot;nofollow noreferrer&quot;&gt;CD14&lt;/a&gt;/&lt;a href=&quot;http://en.wikipedia.org/wiki/Lymphocyte_antigen_96&quot; rel=&quot;nofollow noreferrer&quot;&gt;MD-2&lt;/a&gt; pathway. One can have a local infection, and still not develop sepsis. However, if the infection becomes large enough or the bacteria enter the blood stream in significant numbers, sepsis can occur. Not all patients with sepsis develop &lt;a href=&quot;http://en.wikipedia.org/wiki/Septic_shock&quot; rel=&quot;nofollow noreferrer&quot;&gt;septic shock&lt;/a&gt;, which is characterized not only by a microorganism-caused SIRS and organ dysfunction/hypoperfusion, but also by chronic hypotension (low blood pressure) even after administration of IV fluids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Structurally, LPS contains the highly-conserved &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipid_A&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lipid A&lt;/a&gt;, which anchors the molecule into the outer membrane, a &lt;a href=&quot;http://en.wikipedia.org/wiki/Core_oligosaccharide&quot; rel=&quot;nofollow noreferrer&quot;&gt;core oligosaccharide&lt;/a&gt;, and the outer &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipopolysaccharide#O-antigen&quot; rel=&quot;nofollow noreferrer&quot;&gt;O-antigen&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VEMGJ.png&quot; alt=&quot;LPS structure&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:LPS.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://commons.wikimedia.org/wiki/File:LPS.svg&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lipid A is actually the most toxic segment of LPS (the portion &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20404851/&quot; rel=&quot;nofollow noreferrer&quot;&gt;recognized by TLR4 and MD-2&lt;/a&gt;), and while it is generally highly-conserved among different bacterial strains and species, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3569842/&quot; rel=&quot;nofollow noreferrer&quot;&gt;studies have shown&lt;/a&gt; that different human-pathogenic species of bacteria have altered Lipid A from the &quot;canonical&quot; structure derived from &lt;em&gt;E. coli&lt;/em&gt;. This can cause variations in the downstream signaling from TLR4 to &lt;a href=&quot;http://en.wikipedia.org/wiki/NF-%CE%BAB&quot; rel=&quot;nofollow noreferrer&quot;&gt;NF-κB&lt;/a&gt;, potentially leading to immune system evasion. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to directly address your question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Do all Gram negative bacteria cause septic shock?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They can, if present in sufficient quantities, but not necessarily through the same mechanisms. The immune system recognizes many different &lt;a href=&quot;http://en.wikipedia.org/wiki/Pathogen-associated_molecular_pattern&quot; rel=&quot;nofollow noreferrer&quot;&gt;pathogen-associated molecular patterns&lt;/a&gt; (PAMPs) through a variety of TLRs and other &lt;a href=&quot;http://en.wikipedia.org/wiki/Pattern_recognition_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;pattern recognition receptors&lt;/a&gt; (PRRs) like C-type lectin receptors, Nod1 and Nod-like receptors, etc. Some work on intact bacteria, others recognize intracellular epitopes. Therefore, sepsis and, in severe cases, septic shock, can be caused by Gram-negative bacteria through LPS-independent pathways. While it's possible that lysing these bacteria chemically by antibiotics could potentially enhance the immune response, cells like &lt;a href=&quot;http://en.wikipedia.org/wiki/Macrophage&quot; rel=&quot;nofollow noreferrer&quot;&gt;macrophages&lt;/a&gt; are very good at recognizing foreign invaders and lysing them on their own, giving plenty of substrates to the various receptors. Also, keep in mind that dead cells may auto-lyse, so the antibiotics need not necessarily attack the cell wall itself, just kill the bacteria.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-11-17T00:45:17.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24067" PostTypeId="1" CreationDate="2014-11-17T01:00:31.283" Score="1" ViewCount="76" Body="&lt;p&gt;How would you test the effect of antioxidants on &lt;em&gt;C.elegans&lt;/em&gt; lifespan?&#xA;Is this done through feeding &lt;em&gt;E.coli&lt;/em&gt; with antioxidants and then &lt;em&gt;C.elegans&lt;/em&gt; with E.coli, or is there another method?&lt;/p&gt;&#xA;" OwnerUserId="9490" LastActivityDate="2014-11-21T03:57:43.697" Title="C.elegans and antioxidants" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24068" PostTypeId="2" ParentId="24062" CreationDate="2014-11-17T01:11:37.083" Score="4" Body="&lt;p&gt;all Gram negative bacteria can potentially cause septic shock, but septic shock is not limited to Gram negative cell wall lipopolysaccharides. Any infectious agent can cause septic shock, including gram positive and gram negative bacteria, fungi and even viruses (this is quite evident in the recent Ebola outbreak).&lt;sup&gt;[1]&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The causative agents for sepsis/septic shock have evolved. Originally strongly considered to be related to Gram-negative bacteria, that is no longer the case. About 25 years ago, sepsis was considered to be a response to endotoxin thought to be relatively specific for Gram-negative bacteria. That Gram-negative bacteria were the most common causes of sepsis&lt;sup&gt;[2]&lt;/sup&gt; resulted in trials that focused on  specific therapies for G negative endotoxins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is now recognized that sepsis may occur from bacterial, fungal and viral organisms. More recent epidemiology studies reveal that Gram-positive bacteria have become the most common cause of sepsis in the past 25 years. According to the most recent estimates in sepsis, there are approximately 200,000 cases of Gram-positive sepsis each year, compared with approximately 150,000 cases of Gram-negative sepsis.&lt;sup&gt;[3]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fungal causes of sepsis have also grown at a rapid pace. Why this occurs may be two-fold: a general increase in nosocomial (hospital acquired) cases of sepsis, and more effective treatment of bacterial infections, thus promoting fungal infections to a more leading role. The increase of fungal nosocomial infections has also shifted away from the common Candida albicans organism to the more recalcitrant torulopsis, glabrata and krusei subspecies.&lt;sup&gt;[4]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So while the Gram negative Lipopolysaccharide or “endotoxin” is unique to Gram negative bacteria, cell components of Gram positive bacteria have been identified that appear to be biologically equivalent to endotoxin in stimulating the inflammatory response associated with sepsis and septic shock. These include a peptidoglycan layer outside the cell membrane of Gram positive bacteria as well as non-peptidoglycan polymers (such as the teichoic acids). They have been shown to stimulate the release of cytokines, specifically tumor necrosis factor and interleukin-1.&lt;sup&gt;[5]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://www.npr.org/blogs/goatsandsoda/2014/08/26/342451672/how-ebola-kills-you-its-not-the-virus&quot; rel=&quot;nofollow&quot;&gt;How Ebola Kills You: It's Not The Virus&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2197912&quot; rel=&quot;nofollow&quot;&gt;Septic shock in humans. Advances in the understanding of pathogenesis, cardiovascular dysfunction, and therapy&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12700374&quot; rel=&quot;nofollow&quot;&gt;The epidemiology of sepsis in the United States from 1979 through 2000.&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[4] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7763123&quot; rel=&quot;nofollow&quot;&gt;Nosocomial bloodstream infections. Secular trends in rates, mortality, and contribution to total hospital deaths.&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[5] &lt;a href=&quot;http://www.columbia.edu/itc/hs/medical/pathophys/id/2009/sepsisNotes.pdf&quot; rel=&quot;nofollow&quot;&gt;Sepsis and Septic Shock&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488423/&quot; rel=&quot;nofollow&quot;&gt;Sepsis, severe sepsis and septic shock: changes in incidence, pathogens and outcomes&lt;/a&gt;&lt;/sub&gt; &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-11-17T01:11:37.083" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24069" PostTypeId="2" ParentId="24055" CreationDate="2014-11-17T03:41:15.110" Score="4" Body="&lt;p&gt;Interesting question (+1) but not that easy to answer. I'll give a try! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, the rate of evolution and rate of adaptation are two different things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two main thing processes that quantitatively differ in populations of different sizes. 1) &lt;em&gt;population-wide mutation rate&lt;/em&gt; and 2) &lt;em&gt;genetic drift&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1. Population-wide mutation rate&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Large populations create more mutations at each generation and therefore if the rate of evolution or the rate of adaptation is limited by the genetic variance, then one can expect large population to have higher rate of evolution and higher rate of adaptation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;--&gt; Large populations may have higher rate of evolution and higher rate of adaptation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. Genetic drift&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, small population have higher drift, resulting in a higher probability of fixation for new neutral (or slightly deleterious) mutations. It results that a small population will fix (fixed: frequency = 1) a higher proportions of the new mutations through time than large populations.nActually the probability of fixation of a neutral mutation is \frac{1}{2N}. Therefore, the rate at which neutral alleles fix is $\mu\cdot 2N \frac{1}{2N} = \mu$, where $\mu$ is the mutation rate. So, the rate of fixation of neutral alleles is independent of the population size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;--&gt; Small populations have more drift but this doesn't necessarily yield to higher rate of evolution&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other and comments&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Shifting balance theory&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If adaptation is limited by the genetic architecture, that is, only mutation of very big effect on phenotype can be advantageous, then small population have the advantage to be able to accumulate slightly deleterious mutations, so that they can get off a local peak on the adaptive landscape and eventually manage to evolve toward a new higher fitness peak.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;--&gt; Small population may have higher rate of adaptation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Population-wide mutation rate &lt;strong&gt;vs&lt;/strong&gt; genetic drift&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Weighting the relative importance of rate of production of neutral (or quasi-neutral) mutations (See &lt;em&gt;population-wide mutation rate&lt;/em&gt; above and the probability of fixation of neutral (or quasi-neutral) mutations (See &lt;em&gt;Genetic drift&lt;/em&gt; above) depends also on the probability distribution of mutational effects (=probability distribution of the effect on fitness of a given new mutation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Ceteris Paribus&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The comparison between large and small populations are dependent on the state of other parameters. So even when saying all else being equal (ceteris paribus), we need to know what these other parameters are equal to, in order to answer the question because there are interactions between populations size and other parameters in explaining the rate of adaptation and rate of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other impact of population size on genetic features&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Population size has many impacts on various genetic features, such as pattern of genetic diversity, distribution of per locus Fst between subpopulation, and other things. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?Db=pubmed&amp;amp;Cmd=Retrieve&amp;amp;list_uids=11794777&amp;amp;dopt=abstractplus&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; is likely of interest&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-06-08T21:14:27.830" LastActivityDate="2015-06-08T21:14:27.830" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24070" PostTypeId="2" ParentId="24063" CreationDate="2014-11-17T04:58:14.447" Score="4" Body="&lt;p&gt;A very basic model of virus inactivation is &lt;a href=&quot;http://en.wikipedia.org/wiki/Exponential_decay&quot; rel=&quot;nofollow noreferrer&quot;&gt;exponential decay&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can describe exponential decay with the $N(t) = N_0e^{-\lambda t}$ equation, of if you want to use half-time, then with the $N(t) = N_02^{-t/t_{1/2}}$, where $N$ is the value which reduces by time, $t$ is the time, $\lambda$ is the exponential decay constant and $t_{1/2}$ is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Half-life&quot; rel=&quot;nofollow noreferrer&quot;&gt;half-life&lt;/a&gt; (the time required to reduce the actual value to its half).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exponential decay looks like this on diagrams:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7SCP4.png&quot; alt=&quot;exponential decay&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 1 - exponential decay&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZQg9Y.png&quot; alt=&quot;exponential decay on log scale&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 2 - exponential decay on log scale is linear&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In the case of your TBEV virus, the $N_0$ will be the initial virus titer, the $N(t)$ will be the virus titer by a specific time, the $t$ will be the time and the $t_{1/2}$ will be the half-life, which depends on many things; TBEV strain, temperature, dry/moist heat, pH, etc... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now real life logarithmic diagrams of TBEV thermal inactivation are linear only by the first 30 mins or so (the inactivation is exponential during that period) as you can see on Figure 3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nKSnu.png&quot; alt=&quot;virus inactivation at 60°C&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Figure 3 - virus inactivation at 60°C&lt;br&gt;&#xA;2004 - &lt;a href=&quot;http://www.researchgate.net/publication/8085123_West_Nile_virus_recent_experience_with_the_model_virus_approach/file/9fcfd508e8667c6ae2.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;West Nile virus: recent experience with the model virus approach.&lt;/a&gt;&lt;br&gt;&#xA;where $TCID_50$ is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Virus_quantification#Endpoint_dilution_assay&quot; rel=&quot;nofollow noreferrer&quot;&gt;tissue culture infective dose&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;By virus inactivation most of the articles like to use &lt;a href=&quot;http://www.criver.com/files/pdfs/bps/bioprocessing_journal_jan2014.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;log 10 reduction factors&lt;/a&gt;. For example $3 lg$ or $3 log 10$ means in this context, that lowering the initial value to $10^3 = 1000$ fold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to this article most of the checked TBEV strains has an inactivation index (the reduction factor difference between two temperatures) around 1.7lg between 50°C and 37°C for 15 mins. So you need 15 mins at 50°C to reduce them at least $10^{1.7}=50$ fold. The reduction factor by this study was around 4lg by 37°C for 15mins (so the virus count reduces certainly not just because the heat, but other environmental factors).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Thermoresistance (Т50) of TBEV strains was tested by Ovchinnikova et&#xA;  al. method [17] using 24-hour cell culture grown in 96-hole plates at&#xA;  the presence of СО2. The thermoresistance was determined by&#xA;  inactivation index – difference in lg of titers of virus samples&#xA;  heated at 50°С during 15 minutes or unheated (4°С). In case of titers&#xA;  difference equal or less than 2.0 lg the strain was characterized as&#xA;  Т50+, from 2.1 to 3.0 lg – as medium, equal or more than 3.1 lg – as&#xA;  Т50-.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The values of lgTCD50/ml at 37ºС varied from 3.5 to 8.26. According to&#xA;  the thermoresistanse feature all tested strains were divided into&#xA;  three group: thermostable (Т50+) - nine strains; thermolabile (Т50-) –&#xA;  one strain; strains with medium thermoresistance – three strains. It&#xA;  should be noted that all strains isolated from I. persulcatus ticks&#xA;  collected in Krasnochikoiskiy district of Transbaikalia were&#xA;  thermostable.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.intechopen.com/books/encephalitis/genetic-and-biological-properties-of-original-tbev-strains-group-circulating-in-eastern-siberia#SEC7&quot; rel=&quot;nofollow noreferrer&quot;&gt;Genetic and Biological Properties of Original TBEV Strains Group Circulating in Eastern Siberia&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;According to another study TBEV required 6 hours of moist heat at 60°C for inactivation of 6.6 lg. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Vapor heating of a FVII concentrate in another study (which used&#xA;  lyophilization, followed by adding water to achieve homogenous&#xA;  moistening, then heating at 60°C for 10 hours, followed by heating at&#xA;  80°C for one hour in an airtight container under nitrogen gas&#xA;  atmosphere) was evaluated for its ability to inactivate HAV, HIV-1,&#xA;  TBEV, PRV, and MVM. HAV was readily inactivated within one hour at&#xA;  60°C (5.9 log 10 ). TBEV required six hours of this treatment for&#xA;  inactivation of 6.6 log 10 , and three hours were required to&#xA;  inactivate&#xA;  6.2 log 10 of HIV-1 and 6.9 log 10 of PRV.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2002 - &lt;a href=&quot;http://www.biopharminternational.com/biopharm/data/articlestandard//biopharm/282003/62862/article.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Part 3a, Plasma and Plasma Products - Heat and Solvent/Detergent Treatments&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;According to this study TBEV is considered not heat resistant, so if you are worried for example about raw milk pasteurization, then I think boiling the milk for a few minutes is enough.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Due to the lipid envelope, TBEV is readily inactivated by heat&#xA;  treatment, detergents and organic solvents. Even though a viremic&#xA;  phase is common during a TBEV infection in several animal species,&#xA;  foodborne infection via contaminated meat or organs is unlikely due to&#xA;  the fast virus inactivation at elevated temperatures.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.efsa.europa.eu/en/efsajournal/doc/2190.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Scientific Opinion on an update on the present knowledge on the&#xA;occurrence and control of foodborne viruses&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-11-17T11:34:39.360" LastActivityDate="2014-11-17T11:34:39.360" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24071" PostTypeId="2" ParentId="24067" CreationDate="2014-11-17T05:15:36.047" Score="1" Body="&lt;p&gt;You can simply add the molecule of interest in the NGM or Liquid medium. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058345#s2&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The worms were bleach-synchronized as follows: 2 mL of 6% NaOCl were&#xA;  mixed with 1 mL of 5 M NaOH per 7.5 mL of concentrated worm&#xA;  suspension, and shaken for 4–7 minutes until the carcasses dissolved&#xA;  as monitored by direct observation. The remaining eggs were then&#xA;  washed 3 times by pelleting at ~1150 g for 2 minutes at room&#xA;  temperature, followed by aspiration of the supernatant and&#xA;  resuspension in 50 mL of 0.1 M NaCl. A final pellet of eggs was&#xA;  obtained by centrifugation at ~1150 g for 2 minutes at room&#xA;  temperature, followed by aspiration of the supernatant. Eggs were then&#xA;  added to a 250 mL liquid culture, as described above. For experiments&#xA;  without RNAi treatment, bacteria were heat killed at 80°C for 60&#xA;  minutes. The worms were cultured at 20°C and monitored until they&#xA;  reached adulthood (~72 h), at which time FUdR was added to a final&#xA;  concentration of 400 µM. Worm viability was scored every two days by&#xA;  taking ten 10 µL drops (initially ~20 worms per drop) of the culture&#xA;  and counting the living worms under a microscope. The average number&#xA;  of living worms was then calculated. &lt;strong&gt;S medium or deionized water&lt;/strong&gt;&#xA;  &lt;strong&gt;containing 10 mM malate, succinate, or fumarate was added back every&lt;/strong&gt;&#xA;  three days to compensate for metabolism of the compounds and&#xA;  evaporation, and S medium containing FUdR and bacteria was replaced&#xA;  every 6 days. At least two replicates of each experiment were&#xA;  performed.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-17T05:15:36.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24072" PostTypeId="2" ParentId="15743" CreationDate="2014-11-17T05:29:40.960" Score="2" Body="&lt;p&gt;LD describes the associations among alleles at different loci. For anything more than two bi-allelic loci, you need more than just one number to fully describe the associations. For instance, if we have three bi-allelic loci 1-3, we need the three pairwise LD coefficients, plus one extra three-way coefficient. In general, if we have $K$ loci, and the $k^\text{th}$ locus has $n_k$ alleles, there are $\prod_k n_k$ possible haplotypes, so to fully describe the state of the population we need $\prod_k n_k-1$ haplotype frequencies. If we instead want to use allele frequencies and associations, we'll therefore need $$\prod_k n_k-1-\sum_k(n_k-1)=\prod_k n_k-\sum_k n_k+k-1$$ LD coefficients. (Note that each locus is described by $n_k-1$ allele frequencies.) This means that things get complicated pretty quickly with many loci! If you want to dive into the details, check out &lt;a href=&quot;http://www.genetics.org/content/127/1/229.short&quot; rel=&quot;nofollow&quot;&gt;Barton and Turelli (1991)&lt;/a&gt; and &lt;a href=&quot;http://www.genetics.org/content/161/4/1727.short&quot; rel=&quot;nofollow&quot;&gt;Kirkpatrick, Johnson, and Barton (2002)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6313" LastActivityDate="2014-11-17T05:29:40.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24073" PostTypeId="2" ParentId="24056" CreationDate="2014-11-17T06:11:26.183" Score="5" Body="&lt;p&gt;I think what you are asking for is &amp;quot;&lt;em&gt;Multiple Mutualism&lt;/em&gt;&amp;quot;. Normally,&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Most of the known cases of multiple mutualism involve relationships in&#xA;which two of the partners are at the same organizational level—usually&#xA;two bacteria that might be interacting directly—but are both essential&#xA;for the survival of the host&lt;/p&gt;&#xA;&lt;p&gt;&lt;sup&gt;— &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1559669/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Entente cordiale: Multiple symbiosis illustrates the intricate interconnectivity of nature -Philip Hunter&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;For example, the &lt;a href=&quot;http://farm8.staticflickr.com/7165/6739167807_2ece1d4c8e_z.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;glassy-winged sharpshooter (&lt;em&gt;Homalodisca coagulata&lt;/em&gt;)&lt;/a&gt; primarily feeds on xylem-fluid which is low on organic nutrients…so it depends on 2 bacteria, &lt;a href=&quot;http://4.bp.blogspot.com/_V32jx77vvh0/S5LGSV7WYRI/AAAAAAAAAjk/_6nhB4HG4P4/s800/F3.large.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Baumannia cicadellinicola&lt;/em&gt;&lt;/a&gt; and &lt;em&gt;Sulcia muelleri&lt;/em&gt;. The sharpshooter provides these with raw carbon skeletons present in the xylem fluid, and those bacteria in return synthesizes vitamins, essential amino acids, etc. For more detailed study, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1472245/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wu et al, 2006&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;However, there are also examples of three-way mutualistic symbioses in which all the partners are at different organizational levels. One known case involving a virus, a bacterium and an insect, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1287993/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Moran NA, Degnan PH, Santos SR, Dunbar HE, Ochman H (2005) The players in a mutualistic symbiosis: insects, bacteria, viruses, and virulence genes. Proc Natl Acad Sci USA 102: 16919–16926&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Anyway, the essence as stated by Andreas Brune, Professor of Biogeochemistry at the Max Planck Institute for Terrestrial Microbiology in Marburg, Germany:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Multiple symbiosis is probably more widespread than we think, especially in view of the symbiotic systems involving different organizational levels, for example between bacterium, nematode and insect, or bacterium, protozoan and insect.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-11-18T19:05:47.107" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24074" PostTypeId="1" AcceptedAnswerId="24077" CreationDate="2014-11-17T12:48:48.060" Score="7" ViewCount="2627" Body="&lt;p&gt;I watched this movie, where they rented hearts to people for a year. I wonder if it is possible to transplant a heart indefinitely from person to person, or does the heart have a lifetime? So, do human organs age and eventually die, or is it possible to transplant organs indefinitely? What is the limiting factor for life of human organs?&lt;/p&gt;&#xA;" OwnerUserId="10234" LastEditorUserId="3340" LastEditDate="2014-11-17T13:53:37.267" LastActivityDate="2017-11-21T23:00:33.740" Title="Can human organs be transplanted indefinitely?" Tags="&lt;physiology&gt;&lt;senescence&gt;&lt;organs&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24075" PostTypeId="2" ParentId="24074" CreationDate="2014-11-17T14:14:50.527" Score="5" Body="&lt;p&gt;The median lifetime of an organ transplant is &lt;a href=&quot;http://en.wikipedia.org/wiki/Transplant_rejection&quot; rel=&quot;nofollow&quot;&gt;some 5 to 10 years&lt;/a&gt; mainly due to chronic rejection mediated by host-versus-graft immune responses.  Hence long-term transplants definitely have a limited half life. However, this graft rejection is relatively slow and early explantation and re-implantation in a new host may actually &quot;reset&quot; this process? With re-setting I mean that the new host's immune system must start the slow graft rejection process (immunization) all over again, including antigen recognition and build up of the humoral and cellular immunity (&lt;a href=&quot;http://en.wikipedia.org/wiki/Transplant_rejection#Immunologic_mechanisms_of_rejection&quot; rel=&quot;nofollow&quot;&gt;see wiki on graft rejection&lt;/a&gt;). So in theory the organ-lifetime may actually surpass the recipient lifetime as mentioned earlier when grafts are explanted and re-implanted. As this scenario has never been tried as far as I am aware - due to the obvious risks associated with repeated complex surgeries - it becomes speculative at this point.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-17T22:54:56.213" LastActivityDate="2014-11-17T22:54:56.213" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24076" PostTypeId="1" CreationDate="2014-11-17T16:00:22.730" Score="4" ViewCount="193" Body="&lt;p&gt;This question is related to &lt;a href=&quot;https://cogsci.stackexchange.com/questions/8582/what-causes-introverts-to-lose-energy-in-social-settings-and-require-recovery&quot;&gt;this question about introverts becoming exhausted after extended social events on cognitive sciences stack exchange&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I read more on the topic of human extraversion-introversion, I keep seeing the mention of &quot;&lt;strong&gt;energy&lt;/strong&gt;&quot; which extraverts draw from social engagements and introverts expend in such engagements. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;When energy is drained, the state can be called &quot;&lt;strong&gt;exhaustion&lt;/strong&gt;&quot;, depletion, being drained&lt;/li&gt;&#xA;&lt;li&gt;When enough energy is accumulated, the state can be called &quot;&lt;strong&gt;elation&lt;/strong&gt;&quot;, being energized&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The idea makes sense, and I see many diverse writers use it, but nobody defines what this energy is in a biological sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the biological mechanism behind &quot;energy&quot; spent/gained in social interactions - what is it in brain terms?&lt;/strong&gt; I'm looking for an answer like: Dopamine in X part of the brain? Mirror neuron activation? Amygdala overreacting? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found a &lt;a href=&quot;http://www.selfgrowth.com/articles/The_Mind_of_the_Introvert_Why_We_Act_the_Way%20_We_Do.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;quote from this article on introversion&lt;/a&gt;, although it does not seem to have any sources listed&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Research has shown that the mind of an introvert works differently&#xA;  than the mind of an extrovert. Introverts have more pronounced&#xA;  &lt;strong&gt;activity in the parts of the brain that deal with long term memory,&#xA;  planning, complex thinking and organizing&lt;/strong&gt;. Our introverted mind is&#xA;  always turning and running and because of this, we need very little&#xA;  outside stimulation. The extrovert's brain has more pronounced&#xA;  activity in the &lt;strong&gt;areas associated with sensing and processing&#xA;  information from the outside&lt;/strong&gt;. That's why extroverts seek outside&#xA;  stimulation&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What are the scientific names of the brain regions described in the quote above?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="-1" LastEditDate="2017-04-13T12:56:15.910" LastActivityDate="2015-06-04T11:39:16.537" Title="What is the biological basis of &quot;energy&quot; that extraverted humans draw from social engagements and introverts expend?" Tags="&lt;human-biology&gt;&lt;brain&gt;&lt;endocrinology&gt;&lt;behaviour&gt;&lt;bioenergetics&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24077" PostTypeId="2" ParentId="24074" CreationDate="2014-11-17T16:25:07.920" Score="6" Body="&lt;p&gt;First of all, it will be practically impossible to make an estimation of how long a transplanted organ will live and how many times it could be transplanted. However, it is relatively safe to say that it will not live forever. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be able to receive an organ transplantation, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_leukocyte_antigen&quot; rel=&quot;nofollow&quot;&gt;HLA MHC-complexes&lt;/a&gt; of donor and receiver need to be matched very carefully, to limit the &lt;a href=&quot;http://en.wikipedia.org/wiki/Transplant_rejection&quot; rel=&quot;nofollow&quot;&gt;host-vs-graft&lt;/a&gt; reaction. This limits the number of possible donor-receiver patient pars drastically. So to be able to do a &quot;row transplantation&quot; (one receiver to the next and so on), they need to have matching MHC-complexes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise the immune system of the receiver turns against the transplanted organ and will eventually destroy it. To avoid this reaction, transplantation patients also receive drugs, which severely suppress their immune system, thus making other infections potentially dangerous. This reaction will still take place, since you cannot shut down the immune system of the receiver completely (for obvious reasons), though it happens at a much slower rate. Transplanted organs will only live for a certain time (see estimates from a number of transplantations below) and it is possible that people need to receive transplants twice in their life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For this reason, no doctor will put their patient at risk by giving them an organ which might have a reduced lifetime. The risk of the operation itself is also substantial.  Additionally, the original receiver needs to be dead to do this, as he would otherise need another organ in exchange.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What we can do is to take the average number of a lot of transplantations together and calculate some average life-years for a transplant. According to table 2 in this paper (&quot;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1600-6143.2005.01021.x/full&quot; rel=&quot;nofollow&quot;&gt;The Life-Years Saved by a Deceased Organ Donor&lt;/a&gt;&quot;) the &quot;average benefit by type of transplant (life-years)&quot; is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Kidney: 7.2 years&lt;/li&gt;&#xA;&lt;li&gt;Liver: 16.9 years&lt;/li&gt;&#xA;&lt;li&gt;Lung: 2.1 years&lt;/li&gt;&#xA;&lt;li&gt;Heart: 14.5 years&lt;/li&gt;&#xA;&lt;li&gt;Kidney-Pancreas: 12.9 years&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;These numbers are not definite, since the life style of the donor and the receiver as well as infections of the transplated patient (who has a severely suppressed immune system – this is critical) also play an important role in determining the lifetime of the organ.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="4040" LastEditDate="2014-11-18T05:51:20.930" LastActivityDate="2014-11-18T05:51:20.930" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="24078" PostTypeId="1" AcceptedAnswerId="24080" CreationDate="2014-11-17T18:10:25.920" Score="5" ViewCount="440" Body="&lt;p&gt;This is just a homework question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Q: Let’s assume that there is an unknown set of E. coli genes that are required for biofilm formation. Describe a genetic experiment you could perform to try to identify those genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The one idea that I can think of is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Compare strains that produce biofilm against strains that do not produce biofilm. Sequence genes, find differences, interrupt genes in biofilm producing strains and confirm biofilm ability is impaired.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Is there a better approach than this?&lt;/p&gt;&#xA;" OwnerUserId="5100" LastActivityDate="2014-11-18T17:09:00.047" Title="How to identify genes required for biofilm formation" Tags="&lt;genetics&gt;&lt;bacteriology&gt;&lt;experimental-design&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24079" PostTypeId="1" CreationDate="2014-11-17T18:47:20.977" Score="0" ViewCount="187" Body="&lt;p&gt;I first thought that action potentials of His-bundle i.e. Purkinje fibers are Cardiac. &#xA;However, I started to think that this is not enough. &#xA;I think now that they are neuronal and cardiac. &#xA;&lt;strong&gt;My conjecture&lt;/strong&gt;. They have first short-acting neuronal part and then long-acting cardiac part. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are Purkinje Action Potentials Neuronal and Cardiac?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-26T09:21:48.930" LastActivityDate="2014-12-26T09:21:48.930" Title="Are Purkinje Action Potentials Neuronal and Cardiac?" Tags="&lt;cardiology&gt;&lt;neurology&gt;&lt;action-potential&gt;&lt;electrophysiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24080" PostTypeId="2" ParentId="24078" CreationDate="2014-11-17T18:52:14.183" Score="7" Body="&lt;p&gt;You could do different things: First you could, as you say yourself, sequence the complete genomes of the strains from a biofilm and compare these with some, which do not form biofilms. This may give you an idea which genes are involved when they are present in the &quot;biofilm genome&quot; but not in the other. The proof would be to disrupt these genes either by removing or mutating them or by gene silencing techniques and see what the outcome is. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also possible that only a mutation in a gene which exists in the sample and the control genome makes the difference. Then site-directed mutagenesis would help to identify the important genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second possibility is that there is no real difference in the sample and the control genome and the difference for developing a biofilm &quot;simply&quot; lies in the difference of gene expression. Then the isolation of RNA (either total or mRNA only) would help to find involved genes. If the environment makes the difference for the development of a biofilm, then the biofilm and the control cells should have show no (or almost no) difference in their gene expression profiles when they are cultivated under identical conditions. You then need to test the gene expression for different environmental conditions (including those that favor the development of biofilms) to find genes which are involved. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This comparison of the different conditions will then deliver genes which are uniquely or more highly expressed in the biofilm group, a lot of genes which are comparable in expression to the control sample, and some genes which have a lower expression than the control. It is now worth looking at the higher (or unique) and lower expressed genes, find out their function and then start mutating them to check their function for the formation of a biofilm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally there is the chance that the gene(s) which is necessary for the biofilm formation is located on an extra-chromosomal plasmid. I would also check the plasmids present in the biofilm and the control sample, sequence them (if present) and see which genes they express. The function for the biofilm formation can easily be tested with a simple transformation.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-11-18T17:09:00.047" LastActivityDate="2014-11-18T17:09:00.047" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24083" PostTypeId="1" CreationDate="2014-11-17T21:59:38.423" Score="4" ViewCount="492" Body="&lt;p&gt;Walking  by the lake and watching the ducks the other day a thought struck me; there are lots of aquatic birds but all remain at least somewhat terrestrial, nesting on land. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is it that no birds have taken the evolutionary route of the dolphins and whales and returned to the sea?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there something in avian biology that means this is not possible?&lt;/p&gt;&#xA;" OwnerUserId="10239" LastEditorDisplayName="user24284" LastEditDate="2018-01-13T10:58:25.050" LastActivityDate="2018-01-15T11:50:24.250" Title="Why are there no marine birds?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;ornithology&gt;&lt;eggs&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24084" PostTypeId="1" AcceptedAnswerId="24102" CreationDate="2014-11-17T23:02:23.740" Score="9" ViewCount="1617" Body="&lt;p&gt;There are many sports restricted to players of a certain age (e.g. 16 and under, 18 and under, etc.) What if a person is older and fakes his birth certificate to say that he is younger? Is there any way to expose this person?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can we determine such a person's age by radiocarbon dating methods or other means?&lt;/p&gt;&#xA;" OwnerUserId="10241" LastEditorUserId="5198" LastEditDate="2014-11-18T07:32:15.020" LastActivityDate="2014-11-18T07:55:28.787" Title="Can we determine a person's age by dating methods or other means?" Tags="&lt;radiation&gt;&lt;imaging&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24085" PostTypeId="2" ParentId="24084" CreationDate="2014-11-17T23:11:17.540" Score="2" Body="&lt;p&gt;To grab this opportunity to sum up the comments for the C-14 dating method, including those of of @MattDMo and @canadier: Theoretically spoken - Yes we can! But only after (1) killing the person and (2) waiting a few hundred years. As carbon keeps on being recycled in a living carbon-based organism, it has to be dead first. Secondly, because the margin or error is about 80 years, mainly due to the relatively long half-life of C14 (5730 years) and the variability in the C14 dating method (&lt;a href=&quot;http://en.wikipedia.org/wiki/Radiocarbon_dating#Errors_and_reliability&quot; rel=&quot;nofollow&quot;&gt;see wiki on C14 dating&lt;/a&gt;) one should wait, ideally between 1k and 1000k years. But given the error margin a few hundred years may suffice to get a rough idea. So to sum up - practically this test, although it is objective and free of subjectivity and robust to false pretenses, makes no sense as (a) a human life is about the same a the error margin of the test and (b) the competitor cannot participate in the contest after his or her life has being taken.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not aware of any biologoical methods to objectively measure age. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-18T01:53:28.903" LastActivityDate="2014-11-18T01:53:28.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24086" PostTypeId="1" CreationDate="2014-11-17T23:37:16.463" Score="3" ViewCount="45" Body="&lt;p&gt;Are there any validated SNPs that are either predictive of developing bipolar spectrum disorder or are associated with its pathophysiology?&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastEditorUserId="9943" LastEditDate="2014-11-17T23:42:39.030" LastActivityDate="2020-07-06T21:35:35.513" Title="Predictive Single Nucleotide Polymorphisms (SNPs) for Bipolar Disorder" Tags="&lt;psychology&gt;&lt;pathophysiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24087" PostTypeId="2" ParentId="24083" CreationDate="2014-11-18T00:33:35.453" Score="6" Body="&lt;p&gt;Apart from one isolated group of birds in Australia (i.e., mound nesters found in Australia that use external heat for incubation - see &lt;a href=&quot;http://yongergnow.com.au/about-us/malleefowl/&quot; rel=&quot;noreferrer&quot;&gt;link&lt;/a&gt;), all birds incubate their eggs (&lt;a href=&quot;http://www.newton.dep.anl.gov/natbltn/400-499/nb456.htm&quot; rel=&quot;noreferrer&quot;&gt;see link&lt;/a&gt;). All species that returned from land to sea have retained their reproductive cycle (marine mammals still give live birth and suckle their young) and still rely on air for oxygen intake. Extrapolating this mammalian evolution to birds would result in a creature that returns to sea, with all ties to land cut off, but that still has to incubate their eggs under water. As they would still rely on air, this is not very feasible as they would need to go up often to breath. This would leave the eggs vulnerable to predation. Even worse, it would leave the eggs at the mercy of a relatively cold ocean cooling them down quickly. Incubation means that the eggs are pretty much kept at body temperature which is difficult in the sea regardless of breathing parents. In all, while there may be certain benefits of underwater life for birds, it will require some drastic evolutionary changes in terms of the reproductive cycle. A more parsimonious way of colonizing the sea is to go back to land once and a while to lay eggs, incubate them, and raise the young until they are sea-worthy, like penguins do as @MattDMo mentioned.     &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-18T00:42:03.807" LastActivityDate="2014-11-18T00:42:03.807" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24089" PostTypeId="1" CreationDate="2014-11-18T01:27:53.093" Score="1" ViewCount="87" Body="&lt;p&gt;I am bioinformatician trying to support some small RNA-seq experiments. All bioanalyzer traces that I have seen for RNA at the small RNA range show at peak at 22. But probably it depends on the protocol for the RNA purification (in this case only experience with RNeasy Qiagen).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know if some of you have some examples/experience of good bioanalyzer results after RNA purification that have been sequenced and got a big percentage of miRNA detected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Currently I have a example where there is a broad peak at 25 and in some cases a small peak at 22. After sequencing there is almost not data. So at some point we lost the data. Trying to figure out if the bioanalyzer was good at that point, or already was something wrong. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks.&lt;/p&gt;&#xA;" OwnerUserId="10245" LastActivityDate="2014-11-18T01:27:53.093" Title="small RNA bioanalyzer traces showing miRNA enrichment for sRNA-seq" Tags="&lt;small-rnaseq&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24090" PostTypeId="1" AcceptedAnswerId="24101" CreationDate="2014-11-18T02:55:14.623" Score="10" ViewCount="3404" Body="&lt;p&gt;Corneas are donated and transplanted, but not the eyeball. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't understand. What is the purpose of donating a cornea without an eyeball to a blind person?&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="9943" LastEditDate="2015-03-23T13:32:39.387" LastActivityDate="2015-03-23T13:32:39.387" Title="What is the use of eye banks, if eyeball transplants do not exist at present?" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;vision&gt;&lt;human-eye&gt;&lt;tissue-repair&gt;" AnswerCount="6" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24091" PostTypeId="2" ParentId="24079" CreationDate="2014-11-18T02:59:41.520" Score="1" Body="&lt;p&gt;On the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cardiac_action_potential&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt; they are called cardiac action potentials. As the generation of the action potentials in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sinoatrial_node&quot; rel=&quot;nofollow&quot;&gt;sinoatrial node&lt;/a&gt; is mediated by muscle cells, as is the conduction of the action potentials through the purkinje network (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Cardiac_action_potential&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;), the action potentials are not neural in nature, but cardiac.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-18T03:23:37.813" LastActivityDate="2014-11-18T03:23:37.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24092" PostTypeId="2" ParentId="24090" CreationDate="2014-11-18T03:09:47.353" Score="2" Body="&lt;p&gt;The eyeball is basically the sclera that surrounds the delicate inner structures of the eye (&lt;a href=&quot;http://en.wikipedia.org/wiki/Eye&quot; rel=&quot;nofollow&quot;&gt;see wiki on the eye&lt;/a&gt;). The cornea is the transparent window in front of the pupil that transmits light to the retina. It needs replacement when it turns opaque, often due to damage or infections. The cornea can be replaced on its own, without the need for transplanting other tissues of the eye, as an opaque or otherwise damaged cornea does not necessarily mean that other structures of the eye are damaged. If the light-sensitive parts are damaged, including the exceptionally rare case that the entire eye ball is missing, corneal transplants have obviously no use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eye banks are necessary to properly retrieve and store eyes. They extract, preserve, and dispatch corneas when necessary (&lt;a href=&quot;http://en.wikipedia.org/wiki/Eye_bank&quot; rel=&quot;nofollow&quot;&gt;eye bank wiki&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-18T03:34:49.683" LastActivityDate="2014-11-18T03:34:49.683" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24093" PostTypeId="2" ParentId="24067" CreationDate="2014-11-18T03:23:19.233" Score="4" Body="&lt;p&gt;base on a &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S004763740800050X&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; they do the test of nano-Pt, kind of SOD, and they do the experiment in several steps, first choose C. elegans strains and growth conditions, meanwhile prepare the nano-pt. then, do the lifespan assay. thired is Oxidative stress resistance. the last step is Fluorescence microscopy. in the mictoscopy they do several steps, include Measurement of lipofuscin accumulation, Detection of ROS, Measurement of SOD/catalase activit, Thermotolerance and Effects of dietary restriction&lt;/p&gt;&#xA;" OwnerUserId="9776" LastEditorUserId="9776" LastEditDate="2014-11-21T03:57:43.697" LastActivityDate="2014-11-21T03:57:43.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24095" PostTypeId="1" CreationDate="2014-11-18T04:57:00.483" Score="8" ViewCount="331" Body="&lt;p&gt;As I understand it, the ejecta resulting from the &lt;a href=&quot;http://www.livescience.com/26933-chicxulub-cosmic-impact-dinosaurs.html&quot; rel=&quot;nofollow&quot;&gt;K-T impact&lt;/a&gt; (also known as the end-Cretaceous or Cretaceous-Tertiary extinction event) re-entered the atmosphere all over the world; the heat from friction with the atmosphere raised the air temperature to a few hundred degrees C. All organisms all around the World were incinerated, except those that could bury underground or move into water.Now birds don't bury underground, nor do they   bury their eggs. So, how come birds didn't go extinct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To clarify, I'm not considering the longer term cooling effect (which was in turn followed by a longer term warming effect due the CO2 dumped in the atmosphere). What happened just after the impact was that a sizable fraction of the entire volume involved on the collision would be on ballistic trajectories. Most of these would fall back to Earth, while a small fraction would escape Earth's gravity. Now, these ejecta actually contain a significant fraction of the total energy of the impact and almost all of that in then dissipated as heat when they re-enter the atmosphere. This leads to shock heating of the atmosphere to at least a few hundred degrees celcius, but &lt;a href=&quot;http://www.livescience.com/28582-asteroid-extinction-firestorm.html&quot; rel=&quot;nofollow&quot;&gt;much higher temperatures are also possible&lt;/a&gt;, see also &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jgrg.20018/full&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8202" LastEditorUserId="8202" LastEditDate="2016-08-17T00:27:15.457" LastActivityDate="2016-08-17T00:27:15.457" Title="How did birds survive the KT impact?" Tags="&lt;ornithology&gt;&lt;palaeontology&gt;" AnswerCount="1" CommentCount="14" FavoriteCount="1" ClosedDate="2016-05-10T03:06:37.810" ContentLicense="CC BY-SA 3.0" />
  <row Id="24099" PostTypeId="1" CreationDate="2014-11-18T05:49:32.963" Score="-1" ViewCount="118" Body="&lt;p&gt;Generally &lt;a href=&quot;http://en.wikipedia.org/wiki/Longevity&quot; rel=&quot;nofollow&quot;&gt;living longer&lt;/a&gt; and with a better &lt;a href=&quot;http://en.wikipedia.org/wiki/Quality_of_life_%28healthcare%29&quot; rel=&quot;nofollow&quot;&gt;quality of life&lt;/a&gt; is considered a good thing, if not for ourselves then for our family and friends who care about us. Some factors that influence human longevity are outside our control or only currently exist in a research laboratory; others factors we can control but vary in their impact and effectiveness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;What interventions (preventative or curative) applied by individuals have been proven to increase human longevity, ranked by their effectiveness?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The interventions can be ranked by the ratio of &lt;em&gt;Time Spent vs. Time Gained&lt;/em&gt; or &lt;em&gt;Money Spent vs Time Gained&lt;/em&gt;. A centuries' worth of data driven medicine and longitudinal studies should provide some answer as to what works and what doesn't. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For purposes of this question, please exclude future interventions that have not yet or never been tested on a sizable portion of population. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the biggest improvements in collective aggregate life expectancy in a society have been communal solutions such as elimination of pathogens. As these either exist or don't exist for a given community - I'd like to narrow the scope to interventions applied or chosen by individuals (such what they personally do or don't do). That is, interventions that supplement communal improvements.&lt;/p&gt;&#xA;" OwnerUserId="4788" LastEditorUserId="4788" LastEditDate="2014-11-18T06:07:11.780" LastActivityDate="2014-11-18T06:07:11.780" Title="Human longevity interventions ranked by effectiveness" Tags="&lt;lifespan&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-11-18T16:25:48.193" ContentLicense="CC BY-SA 3.0" />
  <row Id="24100" PostTypeId="2" ParentId="24099" CreationDate="2014-11-18T05:58:25.117" Score="1" Body="&lt;p&gt;&lt;em&gt;Time Spent vs. Time Gained&lt;/em&gt; is not a concept I'm familiar with, because much of the time, the gain was an &lt;em&gt;entire lifetime&lt;/em&gt;. I don't know that any studies have averaged it out for entire populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Four generations ago, the average Swede had the same probability of dying as a hunter-gatherer, but improvements in our living conditions through medicine, better sanitation and clean drinking water (considered &quot;environmental&quot; changes) decreased mortality rates to modern levels in just 100 years, researchers found. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most significant advances which promoted health and longevity include (as mentioned above):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;improved sanitation.&lt;/li&gt;&#xA;&lt;li&gt;improved water quality.&lt;/li&gt;&#xA;&lt;li&gt;vaccines.&lt;/li&gt;&#xA;&lt;li&gt;antibiotics.&lt;/li&gt;&#xA;&lt;li&gt;improved living conditions.&lt;/li&gt;&#xA;&lt;li&gt;improved nutrition.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Since you posted a comment indicating a change in your question, I'll stop here.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-11-18T05:58:25.117" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24101" PostTypeId="2" ParentId="24090" CreationDate="2014-11-18T06:11:33.023" Score="9" Body="&lt;p&gt;No-one can re-implant an entire eye, because the optic nerve has been severed in one who has lost an eye. A cornea can't be grafted to a glass eye. But blindness isn't only caused by loss of the entire orbit. It's also caused by cloudy corneas, which is the purpose of eye-banks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The optic nerve is a cable of nerve fibers that carry  visual information from the eye to the brain. In adult mammals, any damage to the optic nerve caused by injury or disease tends to be permanent, because the cells that form the optic nerve cannot regenerate. Any injury or disease that involves optic nerve damage can lead to permanent loss of vision. Obviously the loss of an eye would sever the optic nerve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if the future holds success for optic nerve regeneration, it would also open the door for entire-eye transplantation. In which case, a new cornea might come in handy.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-11-18T06:17:03.637" LastActivityDate="2014-11-18T06:17:03.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24102" PostTypeId="2" ParentId="24084" CreationDate="2014-11-18T06:34:46.950" Score="6" Body="&lt;p&gt;No, one can't confirm age by carbon dating. That doesn't mean we can't make a decent guess by other methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an interesting case of a 33 year old Texas woman who enrolled in 10th grade in Texas. She said she had no transcripts because she had been homeschooled. She looked like a teenager and acted like a one too. She even fooled her new 23 year old boyfriend. So it happens. It also happened in the Little Leagues World Series, if I remember correctly. A twenty-something guy passed himself off as a 14 year old. He was a star (for a while).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In children and adolescents, the combination of a dental exam, dental films and bone X-rays can narrow a one's biological age well. Once the bones are done growing in length, that avenue is closed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After that, someone might have to provide a tooth. Chemical analysis of tooth dentin, such as aspartic acid racemization, has shown reproducible and fairly precise results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Global levels of carbon-14 (14C) have been carefully recorded over time. In one 2010 study, forty-four teeth from 41 individuals (one per individual) were analyzed &#xA;using aspartic acid racemization analysis of tooth crown dentin or radiocarbon analysis of enamel. Teeth from individuals with dates of birth ranging from 1936 through 1994 (aged 13–70 years) were analyzed, and where the date of birth was known, yielded a 14C-based &lt;em&gt;date of birth estimation accuracy of 1.3 years&lt;/em&gt; (S.D. = 0.9 years). In one case, a date of birth was determined to be &lt;strong&gt;1948.4&lt;/strong&gt;. In another, it was determined to be &lt;strong&gt;1988&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[T]en of these were split and subjected to both radiocarbon and racemization analysis. Combined analysis showed that the two methods correlated well (R2 = 0.66, p &amp;lt; 0.05). &lt;em&gt;Radiocarbon analysis showed an excellent precision with an overall absolute error of &lt;strong&gt;1.0 ± 0.6 years&lt;/strong&gt;.&lt;/em&gt; Aspartic acid racemization also showed a good precision with an overall absolute error of 5.4 ± 4.2 years. Whereas radiocarbon analysis gives an estimated year of birth, racemization analysis indicates the chronological age of the individual at the time of (tooth extraction).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;During the course of aging, l-forms of amino acids are transformed by racemization to the d-forms. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[T]he extent of racemization of amino acids may be used to estimate the age of various tissues. Of all stable amino acids, aspartic acid has one of the fastest racemization rates and is therefore the amino acid most commonly used for age estimation....[T]eeth are the tissue of choice for age estimation analysis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Both methods have strengths and limitations. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The radiocarbon birth dating method can tell the birth date of the person regardless of the time of (extraction). However, the time window for this analysis is limited to subjects born after the early 1940s because the calculations are based on the measurement of bomb pulse-derived 14C. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Clearly this wouldn't be of too much use in people trying to pass themselves off as teens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some studies of aspartic acid racemization report accuracies of age ±3 years. The radiocarbon and racemization can further narrow it down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.buzzfeed.com/katiejmbaker/why-did-charity-johnson-pretend-to-be-a-teenager-for-20-year&quot; rel=&quot;nofollow&quot;&gt;Why did Charity Johnson pretend to be a teenager for 20 years?&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871409/&quot; rel=&quot;nofollow&quot;&gt;Age Estimation in Forensic Sciences APPLICATION OF COMBINED ASPARTIC ACID RACEMIZATION AND RADIOCARBON ANALYSIS&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16225206&quot; rel=&quot;nofollow&quot;&gt;Strategy for the estimation of chronological age using the aspartic acid racemization method with special reference to coefficient of correlation between D/L ratios and ages&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-11-18T07:55:28.787" LastActivityDate="2014-11-18T07:55:28.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24103" PostTypeId="2" ParentId="24078" CreationDate="2014-11-18T06:57:16.750" Score="4" Body="&lt;p&gt;Addition to Chris' answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you do not have a strain that doesn't produce biofilm then you would have to screen for the genes that are involved in biofilm production (this goes for any phenotype).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In earlier times people used to do this by random mutagenesis with mutagens such as EMS (Ethyl Methanesulphonate) or UV. Nowadays it is possible to build a library of targeted mutagens against each gene for e.g. Library of &lt;a href=&quot;http://www.nature.com/nbt/journal/v31/n3/fig_tab/nbt.2508_F5.html&quot; rel=&quot;nofollow&quot;&gt;CRISPR-Cas&lt;/a&gt; nucleases. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-18T06:57:16.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24104" PostTypeId="2" ParentId="24079" CreationDate="2014-11-18T07:21:44.180" Score="2" Body="&lt;p&gt;The His-Purkinje fiber system is a network of &lt;strong&gt;one type&lt;/strong&gt; of specialized conducting &lt;strong&gt;cardiac&lt;/strong&gt; cells that carry an action potential in the heart. There are other cells which perform this function in different parts of the heart. The initiation time, shape, and duration of the action potential are distinctive for different parts of the heart, reflecting their different functions. These distinctions arise because the &lt;strong&gt;myocytes&lt;/strong&gt; in each region of the heart have a characteristic set of channels and anatomy. You can completely dissociate the nervous system from the heart, and the heart will still pace itself. Think of what happens with heart transplants. This completely eliminates neuronal influence. See the following brief excerpt which explains one type of cells conduction method. Please note there is no reference to neurons.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The positive charge that enters cell A not only depolarizes cell A but also produces a flow of positive charge to cell B—intracellular current. This flow of positive charge discharges the membrane capacitance of cell B, thereby depolarizing cell B and releasing extracellular positive charges that had been associated with the membrane. The movement of this extracellular positive charge from around cell B toward the extracellular region around cell A constitutes the extracellular current. The flow of intracellular current from cell A to cell B and the flow of extracellular current from around cell B to around cell A are equal and opposite. It is the flow of this extracellular current in the heart that gives rise to an instantaneous electrical vector, which changes with time. Each point on an electrocardiogram (ECG) is the sum of the many such electrical vectors, generated by the many cells of the heart.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This has been extensively studied, so much so that cardiac electrophysiologists can pinpoint the location of a small group of cells that are misfiring by the nature of the impulse they are giving off. The annual median salary for an electrophysiologist in the US is $480,000. :-( There is a lot of grant money in this area. It's a big deal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For in-depth study of electrophysiology of cardiac cells, please see &lt;a href=&quot;https://www.inkling.com/read/medical-physiology-boron-boulpaep-2nd/chapter-21/electrophysiology-of-cardiac&quot; rel=&quot;nofollow&quot;&gt;Electrophysiology of Cardiac Cells&lt;/a&gt; or any other of a number of reliable sources.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-11-18T07:26:55.887" LastActivityDate="2014-11-18T07:26:55.887" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24105" PostTypeId="2" ParentId="24090" CreationDate="2014-11-18T07:43:31.057" Score="17" Body="&lt;p&gt;You are asking two questions that you think are connected but are actually not.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Question 1 - What is the use of eye banks?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Answer: It's to store corneas for transplant for people with cornea damage.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Question 2 - What use is cornea transplant to a completely blind person?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Answer: It depends. If the blindness is due to clouded cornea (several diseases cause this) then replacing the cornea will reverse the blindness. If the blindness has other causes then cornea transplant is of no use to the person.&lt;/p&gt;&#xA;" OwnerUserId="8918" LastActivityDate="2014-11-18T07:43:31.057" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24106" PostTypeId="1" CreationDate="2014-11-18T08:31:55.043" Score="5" ViewCount="286" Body="&lt;p&gt;We are starting a metagenomics project in our research group to study microbiota in the respiratory tract. Since the are no books yet about metagenomics, seems reading some reviews and online tutorials is the only alternative.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could you suggest me essential papers, websites or other resources useful for my purpose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="4717" LastEditDate="2014-11-21T07:16:19.757" LastActivityDate="2019-03-08T14:32:17.330" Title="Publicly available resources for learning metagenomics" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24107" PostTypeId="1" AcceptedAnswerId="24110" CreationDate="2014-11-18T09:30:10.213" Score="4" ViewCount="319" Body="&lt;p&gt;Following up from this question: &lt;a href=&quot;https://biology.stackexchange.com/questions/15226/does-recombination-increase-the-additive-genetic-variance-for-fitness&quot;&gt;Does recombination increase the additive genetic variance for fitness?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;(I'm thinking about the evolution of additive genetic variance and differences between the sex chromosomes and autosomes. Assume males are heterogametic (XY) and females XX, recombination occurs on the X in females, but not between X and Y in males. This means X chromosomes recombine at 2/3rds the rate of autosomes. Answers need not necessarily relate to sex chromosomes as many other factors should be affecting their evolution and additive genetic variance)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I can tell, recombination should improve the efficiency of selection as variance in fitness of the population of chromosomes increases (because favourable mutations can combine more easily and deleterious ones do too) which should in turn reduce additive genetic variance (right?). But then recombination means many more combinations occurs which means additive genetic variance might be higher.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if I sample the additive genetic variance in a trait in a population where chromosomes that do recombine and a population where chromosomes do not recombine, where should we see the most variance (the recombiners or non-recombiners)?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-11-18T14:17:34.120" Title="Effect of recombination on the rate of loss of genetic variation" Tags="&lt;recombination&gt;&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24109" PostTypeId="2" ParentId="24090" CreationDate="2014-11-18T13:32:25.363" Score="15" Body="&lt;p&gt;I used to work at an eye bank so I have a bit of knowledge about this, though some of it may be out of date.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several aspects to an eye bank.  The corneas are one of the primary things that are kept for transplantation.  Of course, this will not repair blindness in someone that has problems in other areas of the eye, but corneal transplants are helpful for people who have corneal damage for one reason or another (such as a foreign object, age, or disease damaging the cornea.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beyond this, small parts of the sclera (the white part of the eye) are also sometimes used to patch damage (though generally this is not because of unexpected trauma, but because of reconstruction from other surgeries, such as valve implantation because of glaucoma.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, of course, many people would not understand what the purpose of the organization was if it was called a &quot;Cornea Bank&quot;.  &quot;Eye Bank&quot; is more descriptive.&lt;/p&gt;&#xA;" OwnerUserId="6602" LastEditorUserId="6602" LastEditDate="2014-11-18T16:26:52.877" LastActivityDate="2014-11-18T16:26:52.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24110" PostTypeId="2" ParentId="24107" CreationDate="2014-11-18T14:05:29.580" Score="2" Body="&lt;p&gt;I found a key paper for myself from an issue of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066956/&quot; rel=&quot;nofollow&quot;&gt;Nature Reviews Genetics last year&lt;/a&gt;. It discusses and reviews how recombination affects the rate of genetic variation at the sequence level. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A key concept is that of selective interference, which is what I had stumbled across in the question, this is when the efficacy of selection is reduced because &quot;recombination fails to break down linkage disequilibrium at selected loci.&quot; Simply, a beneficial mutation in a system of no recombination is only as fit as the background it is in, if recombination is extremely high (no LD whatsover) then the fitness is defined only by it's own effects. This means that recombination can reduce polymorphism because selective interference will reduce the speed at which non-neutral alleles are fixed or lost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, recombination maintains polymorphism, because without it there is a greater potential for hard sweeps, soft sweeps, partial sweeps, and background selection to all remove genetic variance. For sweeps a beneficial mutation will drag any mutations it is linked with to fixation, the further from the allele the weaker that effect is. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that over riding effect of recombination is to maintain genetic variance despite the increased rate at which an mutation can fix when there is no selective interference because it reduces the polymorphism reducing effects of sweeps and background selection.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;It is expected that neutral genetic variation will be systematically&#xA;  depleted in genomic regions with little recombination.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-11-18T14:17:34.120" LastActivityDate="2014-11-18T14:17:34.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24111" PostTypeId="1" AcceptedAnswerId="24112" CreationDate="2014-11-18T14:31:18.947" Score="2" ViewCount="22070" Body="&lt;p&gt;Assuming there were 20 different amino acids and less than 40 types of different tRNAs found in this alien organism. How many amino acids would be found in the translational product of a 600-nucleotide mRNA?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I am very confused over how I should solve this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we assume 1 codon = 1 nucleotide, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;20 amino acids require 20 different codons = 20 different nucleotides &amp;lt; 40 different tRNAs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we assume 1 codon = 2 nucleotides,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;20 amino acids require 20 different codons = 5 x 5 combination of nucleotides? (considering A, T, C, G, U)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5 x 5 = 25 &amp;lt; 40 different tRNAs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The correct answer is to consider 1 codon = 2 nucleotides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My question&lt;/strong&gt;,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since both 1 codon = 1 nucleotide and 1 codon = 2 nucleotides fit the requirement of this question, why is 1 codon = 2 nucleotides the correct answer?&lt;/p&gt;&#xA;" OwnerUserId="10251" LastEditorUserId="3340" LastEditDate="2014-11-19T06:06:34.747" LastActivityDate="2017-11-28T20:12:27.617" Title="Calculating number of amino acids in mRNA" Tags="&lt;dna&gt;&lt;homework&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24112" PostTypeId="2" ParentId="24111" CreationDate="2014-11-18T15:37:49.810" Score="0" Body="&lt;p&gt;I think I have this figured out. Had to do some math. With our 4 nucleotide system, the number of possible codons is 4&lt;sup&gt;3&lt;/sup&gt; = 64. That is number of nucleotides to the codon length power. The question asks us to determine codon length while giving us the number of amino acids and an upper limit on tRNAs. Using the same formula, &lt;pre&gt; #Nucleotides&lt;sup&gt;(Codon-Length)&lt;/sup&gt; = #Codons,&lt;/pre&gt; we must find a combination of nucleotide number and codon length that gives between 20 and 40 codons.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;                               Codon Length&#xA;Nucleotides    1         2        3        4        5&#xA;     2         2         4        8        16       32&#xA;     3         3         9        27       81       243&#xA;     4         4         16       64       256      1024&#xA;     5         5         25       125      625      3125&#xA;     6         6         36       216      1296     7776&#xA;     7         7         49       343      2401     16807&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So using this table we see that a few different combinations of Nucleotide number and codon length will fit in that range. A 2-nucleotide system could work if each codon was 5 bases long. A 3-nucleotide system could work with 3 base long codons. A 4-base system cannot work, it goes from less than 20 to more than 40. A 5-base system can work with 2 base codons. A 6-base system can also work with 2-base codons. 7 or more bases fails because even a 2-base codon will make more than 40 codons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A codon length of 1 nucleotide would require at least 20 nucleotides, so it would not be a good answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5 is probably the correct answer because it works with the shortest codon length, though I don't know how you'd get base pairing with an odd number of bases. Perhaps the 5th base pairs with itself. A 6 base system can also work with the same codon length and wouldn't need a self pairing base. However that table shows several combinations could work, so this question might have been to see how you defend your answer.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="3340" LastEditDate="2014-11-19T06:05:48.330" LastActivityDate="2014-11-19T06:05:48.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24114" PostTypeId="1" AcceptedAnswerId="24115" CreationDate="2014-11-18T18:54:20.840" Score="1" ViewCount="136" Body="&lt;p&gt;According to Wikipedia &lt;a href=&quot;http://en.wikipedia.org/wiki/Peptide_bond&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Peptide_bond&lt;/a&gt; , when a peptide bond is made a water molecule is released as a secondary product.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, my question is simple (perhaps silly). Considering that proteins are being made every time in our organisms and this water molecule is being released in every peptide bond, why our bodies are not flooded of water?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks! &lt;/p&gt;&#xA;" OwnerUserId="9236" LastActivityDate="2014-11-18T19:02:29.197" Title="Does the Peptide bond produce water in our organism?" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24115" PostTypeId="2" ParentId="24114" CreationDate="2014-11-18T19:02:29.197" Score="4" Body="&lt;p&gt;The simple answer is that there are literally thousands of chemical reactions (mediated by enzymes) going on in the cell. Some produce H&lt;sub&gt;2&lt;/sub&gt;O, others consume it. For example, when proteins are broken down into their individual amino acids as part of normal turnover in the cell, a water molecule is necessary to break the peptide bond. Therefore, the overall balance of water produced vs. water consumed is fairly equal, especially when you take into consideration the consumption of water and its excretion via urine and sweat.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-11-18T19:02:29.197" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24117" PostTypeId="1" AcceptedAnswerId="24140" CreationDate="2014-11-18T21:02:35.663" Score="2" ViewCount="428" Body="&lt;p&gt;During bridge amplification, when sequences attached to adapters on the surface form &quot;bridges&quot; and are replicated, it seems like sequences with either end attached to the surface will be created. &#xA;For instance, in this &lt;a href=&quot;http://res.illumina.com/documents/products/techspotlights/techspotlight_sequencing.pdf&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt; in figure 7, there are sequences facing both ways on the plate. In step 8, all the sequences are oriented in the same direction (pink end attached to the surface)&#xA;How are does this occur? How are the other sequences removed?&lt;/p&gt;&#xA;" OwnerUserId="10256" LastEditorUserId="4747" LastEditDate="2014-11-18T21:35:50.737" LastActivityDate="2014-11-19T05:56:48.133" Title="During bridge amplification of DNA sequences, why aren't sequences amplified in both orientations?" Tags="&lt;genetics&gt;&lt;dna-sequencing&gt;&lt;rna-sequencing&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24118" PostTypeId="2" ParentId="24090" CreationDate="2014-11-18T21:03:41.180" Score="2" Body="&lt;p&gt;In addition to providing tissue for transplant, eye banks also provide tissue from all parts of the eye to medical schools and universities for teaching and research purposes. There are many medically relevant questions that can only be answered by examining human tissue, and eye banks facilitate this research.&lt;/p&gt;&#xA;" OwnerUserId="10257" LastActivityDate="2014-11-18T21:03:41.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24119" PostTypeId="2" ParentId="24090" CreationDate="2014-11-18T21:05:40.083" Score="2" Body="&lt;p&gt;It seems to me that really your whole question seems to be much simpler than it seems and it is just&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;why are eye banks called eye banks when they can't transplant eyes, just bits of them like corneas&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the english language and in various cultures, the names of things often have a loose and not entirely accurate relationship to the product at question.  For example a person might be a screw loose mentally but that doesn't mean a physical screw, etc, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;English is not a consistent scientific logical language for describing the world.&lt;/p&gt;&#xA;" OwnerUserId="10258" LastActivityDate="2014-11-18T21:05:40.083" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24120" PostTypeId="1" CreationDate="2014-11-18T21:21:13.817" Score="5" ViewCount="16517" Body="&lt;p&gt;This is similar to another post but not quite the same... At work, our ventilation system produces a constant low pitched sound - like a rumble - as well as the sound of air blowing through the vents. It's not very loud, we can certainly talk, even whisper to each other, but when it shuts off, it's like a huge weight off my shoulders. My ears don't really pop but there's sort of a slight &quot;tingling&quot; sensation - like when the blood starts flowing to a hand or foot that fell asleep. You can usually hear several people in the same room say &quot;Ahhh&quot; as in we are all glad the noise has stopped. I have worked in this location for over 10 years and in that time I have developed tinnitus which is probably attributed to a number of bad behaviors as a youth. But I was wondering if this constant noise could contribute to the decline in hearing? Also, that sense of relief when the noise stops makes me wonder if the constant noise adds to our stress levels?&lt;/p&gt;&#xA;" OwnerUserId="10259" LastActivityDate="2019-04-08T13:34:43.403" Title="Does prolonged exposure to low pitch but low volume noise affect hearing or stress?" Tags="&lt;hearing&gt;&lt;human-ear&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24121" PostTypeId="2" ParentId="24117" CreationDate="2014-11-18T21:53:49.180" Score="0" Body="&lt;p&gt;Presumably they removed one set of fragments from their figures for clarity of demonstration. In reality, both fragments remain immobilized on the chip. The sequencing primer only anneals to one adapter which allows selective extension of one of the sets in each run. For fragments of sufficient length, this provides an easy mechanism for creating paired end sequence reads as you can use one primer to read one strand and, subsequently, another primer to read the other strand. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-11-18T21:53:49.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24123" PostTypeId="1" AcceptedAnswerId="24125" CreationDate="2014-11-18T23:40:08.533" Score="2" ViewCount="202" Body="&lt;p&gt;There were a lot of odd-toed ungulate animals in the ancient times but now just few of them survived. What is the reason for that?&lt;/p&gt;&#xA;" OwnerUserId="10263" LastEditorUserId="3340" LastEditDate="2014-11-19T05:40:04.287" LastActivityDate="2014-11-19T05:40:04.287" Title="Why did many odd-toed ungulates become extinct?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24125" PostTypeId="2" ParentId="24123" CreationDate="2014-11-19T00:26:18.607" Score="2" Body="&lt;p&gt;there are two suborder under perissodactyla that are still suvival, Hippomorpha and Ceratomorpha. many perissodactyla species become extinct may bacause the member of perissodactyla animals have sample stomach, compared with artiodactyla, so after the plant change on the earth, they cannot adapt it. and also hinting was one part of reason. &#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Odd-toed_ungulate&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Odd-toed_ungulate&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9776" LastActivityDate="2014-11-19T00:26:18.607" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24126" PostTypeId="1" AcceptedAnswerId="24127" CreationDate="2014-11-19T01:25:42.410" Score="13" ViewCount="13002" Body="&lt;p&gt;Does each cell contain only a single copy of its genome? Or are there ever 'extra' copies present. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reason behind question&lt;/strong&gt;: &lt;em&gt;Wondering whether gene mutations could be corrected by referencing a 'backup copy'.. If such a thing exists..&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user9915" LastEditorUserId="3340" LastEditDate="2014-11-19T05:35:48.243" LastActivityDate="2014-12-03T15:59:28.343" Title="Do human cells contain only one copy of the genome?" Tags="&lt;genetics&gt;" AnswerCount="5" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24127" PostTypeId="2" ParentId="24126" CreationDate="2014-11-19T01:34:18.040" Score="13" Body="&lt;p&gt;As a quick answer, yes, most human cells carry 2 copies of the genome and are known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Ploidy#Diploid&quot;&gt;diploid&lt;/a&gt; cells. One copy comes from each of your parents, so they aren't identical, but usually pretty close. Sperm and egg cells only carry one copy of the genome and are known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Ploidy#Haploid_and_monoploid&quot;&gt;haploid&lt;/a&gt;. During fertilization the 2 cells merge their copies and make a diploid zygote. At the &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosome#Human_chromosomes&quot;&gt;chromosomal&lt;/a&gt; level, humans have 23 chromosomes, so a diploid cell has 2 copies of each so a total of 46.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as repairing damaged DNA, using one chromosome to repair its damaged counterpart is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Homologous_recombination&quot;&gt;Homologous Recombination&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-11-19T01:34:18.040" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24128" PostTypeId="2" ParentId="24126" CreationDate="2014-11-19T02:29:02.100" Score="5" Body="&lt;p&gt;Diploid cells contain two copies of the genome. Additionally, each copy of the genome can have multiple copies of certain genes. Which can provide a level of protective redundancy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are a number of potential problems with having multiple copies of portions of the genome such as trisomy disorders (e.g. Down Syndrome). Which is why therapy like you describe is still highly experimental.&lt;/p&gt;&#xA;" OwnerUserId="10257" LastActivityDate="2014-11-19T02:29:02.100" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24129" PostTypeId="1" AcceptedAnswerId="24138" CreationDate="2014-11-19T02:30:46.833" Score="2" ViewCount="347" Body="&lt;p&gt;The Tobacco Mosaic Virus (TMV) capsid consists of many copies of one protein (&lt;a href=&quot;http://www.rcsb.org/pdb/101/motm.do?momID=109&quot; rel=&quot;nofollow&quot;&gt;http://www.rcsb.org/pdb/101/motm.do?momID=109&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which other viral capsids consist of only one kind of coat protein?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does each copy of the protein in these also have the same tertiary structure?&lt;/p&gt;&#xA;" OwnerUserId="160" LastActivityDate="2014-11-19T09:29:06.077" Title="Which virus capsids consist of only one type of capsid protein?" Tags="&lt;virus&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24130" PostTypeId="1" AcceptedAnswerId="24135" CreationDate="2014-11-19T02:44:26.673" Score="1" ViewCount="348" Body="&lt;p&gt;I know the clavicle of the cat floats freely as opposed to be attached as in humans. This is supposed to allow them to be able to squeeze through spaces, according to a quick google search. But how does that allow them to move through tight spaces in comparison with humans? &lt;/p&gt;&#xA;" OwnerUserId="8991" LastActivityDate="2014-11-19T04:40:48.470" Title="The suspended cat clavicle" Tags="&lt;anatomy&gt;&lt;vertebrates&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24132" PostTypeId="1" CreationDate="2014-11-19T03:21:05.203" Score="3" ViewCount="1095" Body="&lt;p&gt;I'm quite curious on how animals view incestual pairings. Given there are enough mates around, i have quite observed that most females (subjects are dogs, cats, pigeons and chickens) would go choose another mate that is not a direct family member (parent, sibling, offspring). How does this work? Is it instinct to not favor family members or does it still revolve around who's the fittest mate?&lt;/p&gt;&#xA;" OwnerUserId="10265" LastEditorUserId="10265" LastEditDate="2014-11-21T00:49:37.933" LastActivityDate="2015-01-20T02:18:24.583" Title="Incestual Reproduction in Animals" Tags="&lt;reproduction&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24133" PostTypeId="2" ParentId="24120" CreationDate="2014-11-19T04:02:36.273" Score="4" Body="&lt;p&gt;Basically you are asking: (1) does the low-pitch noise affect my hearing sensitivity; (2) has the noise aggravated hearing loss acquired earlier in life; (3) if the noise can induce stress and (4) if the noise may cause tinnitus (kind of a hidden question).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) Is the ventilator noise damaging?: Noise-induced hearing loss typically occurs at high sound levels. Occupational safe noise levels are set at around 85 dB SPL &lt;a href=&quot;http://www.safeworkaustralia.gov.au/sites/swa/about/publications/Documents/278/NationalStandardForOccupationalNoise_NOHSC1007-2000_PDF.pdf&quot; rel=&quot;nofollow&quot;&gt;(Nat. Stand. Occupational Noise&lt;/a&gt;). This is comparable to listening to traffic on a busy road from 10 meters away for 8 hours/day for 5 days/week (&lt;a href=&quot;http://en.wikipedia.org/wiki/Sound_pressure&quot; rel=&quot;nofollow&quot;&gt;see wiki on sound levels&lt;/a&gt;), or a diesel truck at 15 meters going 64 km/h. If you can still talk normally, the noise cannot be much more than 60 dB SPL, which is normal conversational level (&lt;a href=&quot;http://www.ccohs.ca/oshanswers/phys_agents/noise_basic.html&quot; rel=&quot;nofollow&quot;&gt;see sound chart&lt;/a&gt;). So the ventilation noise is not bad for your ears as it is well below 85 dB SPL.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) Does the noise aggravates present damage?: Similarly to the answer under (1), the noise is not loud enough to be regarded damaging even with existing hearing loss.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3) Does it cause stress? As @anongoodnurse suggested: yes it causes stress, apparently. Every unpleasant sensation will do so to a certain level.         &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(4) Effects of the noise on tinnitus: Typically, tinnitus is caused by hearing loss (&lt;a href=&quot;http://www.tinnitus.asn.au/tinnitus.htm&quot; rel=&quot;nofollow&quot;&gt;see cause of tinnitus&lt;/a&gt;) and the pitch of tinnitus often coincides with the lost frequencies (&lt;a href=&quot;http://www.randombio.com/tinnitus.html&quot; rel=&quot;nofollow&quot;&gt;see cause and effect of tinnitus&lt;/a&gt;). So if your &quot;bad behaviors&quot; at youth refer to loud music, then it is probably noise-induced hearing loss that has resulted in a dip at your hearing acuity at 4 kHz (the &lt;a href=&quot;http://emedicine.medscape.com/article/857813-clinical&quot; rel=&quot;nofollow&quot;&gt;4-kHz notch&lt;/a&gt;). In effect, the tinnitus you are experiencing will be around this frequency and therefore high-pitched. As the loudness of the ventilator is too low to cause damage, it is probably unrelated to your tinnitus. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-19T04:08:21.940" LastActivityDate="2014-11-19T04:08:21.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24135" PostTypeId="2" ParentId="24130" CreationDate="2014-11-19T04:40:48.470" Score="1" Body="&lt;p&gt;Based on what I learned from my comp vert anatomy class, the clavicle does not articulate with other skeletal elements, thus allowing the scapulae to retract further along with the forelimbs&lt;/p&gt;&#xA;" OwnerUserId="10266" LastActivityDate="2014-11-19T04:40:48.470" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24136" PostTypeId="2" ParentId="23791" CreationDate="2014-11-19T04:46:37.387" Score="0" Body="&lt;p&gt;Try thinking about places that are not very often cleaned and disinfected such as the toilet. Not only that, but the bottoms of shower curtains and in drains. Plaque on teeth is a biofilm, catheters, in/on wounds.&lt;/p&gt;&#xA;" OwnerUserId="10266" LastActivityDate="2014-11-19T04:46:37.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24137" PostTypeId="2" ParentId="24132" CreationDate="2014-11-19T05:16:35.377" Score="1" Body="&lt;p&gt;Anecdotally I have never observed a preference in lab mice, but we have never made a detailed study of it. Males do not seem to favor non-incestuous over incestuous breeding. Though inbreeding does tend to produce smaller litter sizes over generations and inbred strains of lab mice do tend to be less hearty. Though lab mice are a bit removed from the situation in the wild.&lt;/p&gt;&#xA;" OwnerUserId="10257" LastActivityDate="2014-11-19T05:16:35.377" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24138" PostTypeId="2" ParentId="24129" CreationDate="2014-11-19T05:20:45.913" Score="2" Body="&lt;p&gt;Interestingly, the fact that viruses might be made up of repeating subunits was a &lt;a href=&quot;http://www.nature.com/nature/journal/v177/n4506/abs/177473a0.html&quot; rel=&quot;nofollow&quot;&gt;hypothesis&lt;/a&gt; by the famous Watson and Crick in 1956.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A useful resource for this is the &lt;a href=&quot;http://viralzone.expasy.org/&quot; rel=&quot;nofollow&quot;&gt;Viral Zone&lt;/a&gt; website maintained at by the ExPASy bioinformatics system. It contains an easily browsable and human interpretable list of viral families and their characteristics. In particular, you can &quot;&lt;a href=&quot;http://viralzone.expasy.org/all_by_species/750.html&quot; rel=&quot;nofollow&quot;&gt;browse by virion&lt;/a&gt;&quot; which will show you different structural classifications of viruses; make sure to look at all the different genetic classes of viruses (single-strand RNA, double-strand RNA, DNA, etc). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From my preliminary investigation, it appears that many capsids are composed of only a single subunit; in addition to TMV, some other examples I found are the &lt;a href=&quot;http://viralzone.expasy.org/all_by_species/161.html&quot; rel=&quot;nofollow&quot;&gt;totiviridae&lt;/a&gt; family of viruses which infect single-celled eukaryotes such as &lt;em&gt;Giardia lamblia&lt;/em&gt;, the human-infecting &lt;a href=&quot;http://viralzone.expasy.org/all_by_species/27.html&quot; rel=&quot;nofollow&quot;&gt;astroviridae&lt;/a&gt; and &lt;a href=&quot;http://viralzone.expasy.org/all_by_species/32.html&quot; rel=&quot;nofollow&quot;&gt;calciviridae&lt;/a&gt; families, and (as far as I can tell) the &lt;a href=&quot;http://viralzone.expasy.org/all_by_species/9.html&quot; rel=&quot;nofollow&quot;&gt;Heptatitis B virus&lt;/a&gt;. It also appears that &lt;a href=&quot;http://www.pnas.org/content/101/10/3414.full&quot; rel=&quot;nofollow&quot;&gt;Dengue&lt;/a&gt; virus has a single capsid protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the tertiary structure of capsid subunits, you might find &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767311/&quot; rel=&quot;nofollow&quot;&gt;this review&lt;/a&gt; of interest. Basically, due to symmetries in the shape of icosahedra (or helices or other geometric shapes adopted by capsids), you can argue that the structure of subunits in certain symmetrical parts of the capsid has to be the same (because they are copies of the same protein and, by positional symmetry, they have to be experiencing the same forces). When there are asymmetries in the structure of the icosahedron, then it is often hypothesized that there exists a state of &quot;quasi-equivalence;&quot; that is, the deviation from symmetry is small enough that the tertiary structure of each subunit is not affected very much. The review goes into these points in much greater detail.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastEditorUserId="4840" LastEditDate="2014-11-19T09:29:06.077" LastActivityDate="2014-11-19T09:29:06.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24139" PostTypeId="2" ParentId="24126" CreationDate="2014-11-19T05:35:17.423" Score="5" Body="&lt;p&gt;Addition to other answers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually a human cell is diploid. Sometimes there might be extra copies of a chromosome and this phenomenon is called aneuploidy (Downs Syndrome, Klinefelter's syndrome etc). This always has deleterious effects because of changes in stoichiometries of different gene products (dosage effect). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some other organisms also tolerate polyploidy (more than two copies of the entire genome) — salamanders and a lizard whose name I can't remember right now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would an extra copy help in providing a functional gene when the other copy is mutated?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes and it is the case with all recessive mutations. The effect of loss of function is not seen because the other allele is providing a functional copy (sometimes the dosage is reduced and it affects the system in subtle ways).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it the mutation is dominant then extra copies won't help much. For example, a mutation that leads to the formation of a toxic or hyperactive protein (gain of function), then extra copies may at best reduce the overall relative concentration of the bad allele but cannot eliminate its ill effects. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-11-19T10:51:41.020" LastActivityDate="2014-11-19T10:51:41.020" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24140" PostTypeId="2" ParentId="24117" CreationDate="2014-11-19T05:56:48.133" Score="2" Body="&lt;p&gt;See &lt;a href=&quot;https://ncifrederick.cancer.gov/atp/cms/wp-content/uploads/2010/08/CustomerIlluminaTechExplanation.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; document on how Illumina sequencing works. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you are doing a single end sequencing, the reverse strands produced after the bridge amplification + denaturation (&lt;em&gt;step-7&lt;/em&gt;) are specifically removed (clipped at the junction of primer and the &quot;insert&quot; region). Furthermore, the free 3' ends are blocked (by chemical modification) to ensure that there is no unwanted priming. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For paired end sequencing, both strands are sequenced; so in one flow cell the forward strand is cleaved while in the other the reverse strand is cleaved. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-19T05:56:48.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24142" PostTypeId="1" CreationDate="2014-11-19T06:56:06.077" Score="0" ViewCount="349" Body="&lt;p&gt;Chlorine is usually mixed in water to make it safe for consumption. What is a safe quantity of chlorine that can be consumed? What are the side effects of chlorine and does this include hair loss? &lt;del&gt;What are some common chemicals utilized for water purification?&lt;/del&gt; Thank you.&lt;/p&gt;&#xA;" OwnerUserId="10269" LastEditorUserId="3340" LastEditDate="2014-11-19T11:59:37.453" LastActivityDate="2014-11-19T12:03:59.513" Title="Safe level of chlorine in water" Tags="&lt;human-biology&gt;&lt;food&gt;&lt;hair&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-11-19T12:08:14.140" ContentLicense="CC BY-SA 3.0" />
  <row Id="24143" PostTypeId="1" AcceptedAnswerId="24147" CreationDate="2014-11-19T07:51:18.023" Score="1" ViewCount="2428" Body="&lt;p&gt;This is for AP Biology, but the assigned textbook chapter doesn't contain any information about the question.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What are some difficulties animals had to overcome to reproduce on land? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Some disadvantages I brainstormed are&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the formation of bones—need for vertical structure and support against gravity (?)&lt;/li&gt;&#xA;&lt;li&gt;development of lungs&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Are there any more?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,&lt;/p&gt;&#xA;" OwnerUserId="10132" LastActivityDate="2018-12-03T18:53:48.567" Title="What are some difficulties animals had to overcome to reproduce on land?" Tags="&lt;reproduction&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24144" PostTypeId="2" ParentId="24056" CreationDate="2014-11-19T09:03:36.037" Score="1" Body="&lt;p&gt;I can think of an example for the 3rd picture in your image &quot;Common Agent With Multiple Symbiotic Relationships.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We have: 1.) a species of parasitoid wasp 2.) a species of plant and 3.) a species of moth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The moth provides pollination activity for the plant. The plant provides a place for the moth to lay its eggs, and a food source for caterpillars once they hatch. Once the plant begins undergoing herbivory it releases Volatile Organic Compounds (VOCs) which attract the wasp and inform it that there are potential hosts nearby. The parasitoid parasitizes either the eggs or the larvae (depending on the species of wasp) and helps the plant by limiting the damage it sustains due to herbivory (like a body guard).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Common example species could be:&#xA;1.) Wasps of the genus &lt;em&gt;Cotesia&lt;/em&gt; (parasitize caterpillars) or of the genus &lt;em&gt;Trichogramma&lt;/em&gt; (parasitize eggs).&#xA;2.) Plants of the family Solanaceae (Datura, tomatoes, or potatoes)&#xA;3.) Sphinx moths of the genus &lt;em&gt;Manduca&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a lot of literature on the subject of VOCs and parasitoids, but if you need a quick reference here is one: &lt;a href=&quot;http://chemse.oxfordjournals.org/content/30/9/739.short&quot; rel=&quot;nofollow&quot;&gt;http://chemse.oxfordjournals.org/content/30/9/739.short&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="10270" LastEditorUserId="10270" LastEditDate="2014-11-19T09:08:42.993" LastActivityDate="2014-11-19T09:08:42.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24145" PostTypeId="2" ParentId="23264" CreationDate="2014-11-19T09:20:34.910" Score="3" Body="&lt;p&gt;One example: The Satin Bowerbird (&lt;em&gt;Ptilonorhynchus violaceus&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The males of this species build structures out of sticks (suprisingly called bowers) that they decorate with blue items to attract potential mates. Recent research has shown that the males have began incorporating plastics into these structures for courtship.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A google image search can confirm pictures of this. In this study: &quot;&lt;a href=&quot;http://science.umd.edu/biology/borgialab/UyandBorgiaEvol2000.pdf&quot; rel=&quot;nofollow&quot;&gt;Sexual selection drives rapid divergence in Bowerbird display traits&lt;/a&gt;&quot; &#xA;researchers provided the birds with square plastic tiles, that were ultimately incorporated into bowers. &lt;/p&gt;&#xA;" OwnerUserId="10270" LastEditorUserId="5144" LastEditDate="2014-11-19T09:24:46.110" LastActivityDate="2014-11-19T09:24:46.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24146" PostTypeId="2" ParentId="23873" CreationDate="2014-11-19T09:32:42.757" Score="1" Body="&lt;p&gt;I can highly recommend Prof David MacKay's online book &lt;a href=&quot;http://www.withouthotair.com/&quot; rel=&quot;nofollow&quot;&gt;http://www.withouthotair.com/&lt;/a&gt;&#xA;where puts things into perspective. You can find him on YouTube and TED too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;e.g. &lt;a href=&quot;http://www.withouthotair.com/c18/page_103.shtml&quot; rel=&quot;nofollow&quot;&gt;http://www.withouthotair.com/c18/page_103.shtml&lt;/a&gt; &quot;Can we live on renewables&quot;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;POWER PER UNIT LAND OR WATER AREA&#xA;Wind            2 W/m2&#xA;Offshore wind   3 W/m2&#xA;Tidal pools     3 W/m2&#xA;Tidal stream    6 W/m2&#xA;Solar PV panels 5-20 W/m2&#xA;Plants          0.5 W/m2&#xA;Rain-water&#xA;  (highlands)   0.24 W/m2&#xA;Hydroelectric&#xA;  facility      11 W/m2&#xA;Geothermal      0.017 W/m2&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Table 18.10. Renewable facilities have to be country-sized because all renewables are so diffuse.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it doesn't look good for plants  as direct energy source (except for food) (in UK at least)...(or most renewable things for that matter).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essential reading for anyone interested in energy.&lt;/p&gt;&#xA;" OwnerUserId="10271" LastEditorUserId="10271" LastEditDate="2014-11-19T09:38:33.283" LastActivityDate="2014-11-19T09:38:33.283" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24147" PostTypeId="2" ParentId="24143" CreationDate="2014-11-19T09:49:41.040" Score="1" Body="&lt;p&gt;The disadvantages you mention have not much to do with reproduction, but with locomotion and oxygen absorption.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Difficulties to reproduce on land are the fact that aquatic egg-producing creatures typically lay soft eggs with porous shells to promote exchange of water and waste products with the surrounding water. Water is essential for growth as a typical creature consists for some 70% of water. Soft-shelled porous eggs when laid on on land dry out very quickly and are prone to predation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main adaptation to reproduce on land instead of water has been the development of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Amnion&quot; rel=&quot;nofollow&quot;&gt;amnion&lt;/a&gt;. The amnion is basically a membrane filled with water (the amniotic sac) in which the embryo is immersed during development. Hence, you could argue that the transition to land in terms of embryonic development has never taken place, as the embryos develop in a protected aqueous environment contained within the amnion! The early &lt;a href=&quot;http://en.wikipedia.org/wiki/Amniote&quot; rel=&quot;nofollow&quot;&gt;amniotes&lt;/a&gt; laid eggs on land where the embryos develop, while the later ones such as humans carry their embryos/fetuses around. But early as well as late amniotes are characterized by a developing embryo immersed in a watery environment contained in the amnion. Other structures that aided the transition to land were &lt;a href=&quot;http://en.wikipedia.org/wiki/Amniote&quot; rel=&quot;nofollow&quot;&gt;eggs with hard shells&lt;/a&gt;, and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Allantois&quot; rel=&quot;nofollow&quot;&gt;allantois&lt;/a&gt;. A hard outer shell in amniotes that lay their eggs on land  helps to protect them against drying out, the harsh terrestrial environment and predators. The allantois helps to exchange and store waste products produced by the embryo, a structure not needed when eggs are immersed in water and waste products can diffuse freely through a weak and porous shell.      &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-19T22:23:46.840" LastActivityDate="2014-11-19T22:23:46.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24148" PostTypeId="2" ParentId="24126" CreationDate="2014-11-19T10:46:03.160" Score="2" Body="&lt;p&gt;To address the &quot;reason behind the question&quot; - no, this doesn't work as you seem to assume it does. It is the whole point of sexual reproduction to have two slightly different copies of the genome. Mutations are not &quot;corrected&quot; within an organism, because they are not considered a bad thing per se. Mutations are &quot;corrected&quot; across generations, in the sense that maladaptive mutations are selected out of the gene pool, because their carriers don't manage to reproduce well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there were a mechanism in the cell which would decide that &quot;this copy of the genome is 'correct', this is 'incorrect', I will replace all differing places in the 'incorrect' copy with the information from the 'correct' copy&quot;, evolution would never have happened. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An individual has two genome copies, and each of them gets transcribed from. If one of them contains a mutation with negative effects, then it's bad luck for the individual. The purpose of the two genome copies is to increase genetic variability, not to reduce it. &lt;/p&gt;&#xA;" OwnerUserId="1578" LastActivityDate="2014-11-19T10:46:03.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24149" PostTypeId="2" ParentId="24142" CreationDate="2014-11-19T11:58:45.570" Score="1" Body="&lt;p&gt;Chlorine is a reactive substance and an oxidizing agent. It can cause damage to surfaces exposed to it such as eyes, skin etc but it cannot penetrate deeper. Chlorine can damage your hair by oxidation — hair becomes rough and brittle. This is not same as hair loss — chlorine doesn't cause hair to fall out because it cannot penetrate to the follicles. See &lt;a href=&quot;http://www.hairdr.com/news/press-releases/dr-robert-leonard-exposes-the-truths-and-myths-surrounding-hair-loss-in-men-and-women/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://water.epa.gov/drink/contaminants/basicinformation/disinfectants.cfm&quot; rel=&quot;nofollow&quot;&gt;EPA&lt;/a&gt; has set maximum residual disinfectant level for chlorine (as Cl&lt;sub&gt;2&lt;/sub&gt; and other chlorinating agents such as chloramine [NH&lt;sub&gt;2&lt;/sub&gt;Cl] and chlorine dioxide [Cl&lt;sub&gt;2&lt;/sub&gt;O]) beyond which it is considered unsafe.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Chloramine       :  4.0 mg/L or 4 ppm&#xA;Chlorine         :  4.0 mg/L or 4 ppm&#xA;Chlorine Dioxide :  0.8 mg/L or 800 ppb&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-11-19T12:03:59.513" LastActivityDate="2014-11-19T12:03:59.513" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24150" PostTypeId="2" ParentId="23842" CreationDate="2014-11-19T12:18:38.077" Score="2" Body="&lt;p&gt;Cockroaches are insects which means their brain is distributed.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The predominant characteristics of the cockroach central nervous&#xA;  system (CNS) are its segmented nature and decentralization of control&#xA;  processes (&lt;strong&gt;Ganihar et al., 1994; Pipa &amp;amp; Delcomyn, 1981&lt;/strong&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;.&#xA; There is a pair of ganglion on each segment- head, thorax and abdomen. The ganglion on head is controlling the antennae inputs,proboscis,mandibles,eyes etc. When we cut off its head the ability to control all the above described organs fails(although, that doesn't matter because these organs are also decapitated) &amp;amp; it can't eat.. but the ganglion on the thorax is actually responsible for the breathing and digestion of food(with the help of ganglion on the abdomen). So if there is any food in the gut it will be normally digested and cockroach can live days consuming this energy. Also when head is gone there is no need to provide resources for the organs in head. So it can live more days by saving these resources.Plus, it can copulate if it is placed properly and this copulation is controlled by the ganglion on the abdomen.&lt;/p&gt;&#xA;" OwnerUserId="10273" LastEditorUserId="10045" LastEditDate="2014-11-19T18:37:09.923" LastActivityDate="2014-11-19T18:37:09.923" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24151" PostTypeId="2" ParentId="23887" CreationDate="2014-11-19T12:24:24.407" Score="0" Body="&lt;p&gt;This is definitely Sitophilus granarius [wheat weevil].It is a common pest in India, as it mostly attacks wheat grains stored in sacks.When we buy plain grains of wheat from shops we can see these pests inside and there may be plenty of them drilling the wheat and leave the empty crest of wheat behind.&lt;/p&gt;&#xA;" OwnerUserId="10273" LastActivityDate="2014-11-19T12:24:24.407" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24153" PostTypeId="2" ParentId="24120" CreationDate="2014-11-19T13:28:14.547" Score="1" Body="&lt;p&gt;Noises over 75dB can cause temporary damage (temporary threshold shift), noises over 85dB can cause both temporary and permanent damage (permanent threshold shift). The size of the permanent damage depends on the intensity of the noise, the duration, and many other parameters e.g. genetics, antioxidants, time between two exposures, etc... For example daily 8h of 80dB is considered safe, while daily 8h of 85dB or 20mins of 100dB is considered unsafe. Tinnitus is a sign of hearing loss, so it can be both temporary and permanent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should measure the noise levels. For example install &lt;a href=&quot;https://play.google.com/store/apps/details?id=kr.sira.sound&quot; rel=&quot;nofollow&quot;&gt;Sound Meter&lt;/a&gt; to your mobile phone. (The results can depend on the microphone. Most of the mobile phones cannot measure 100dB+ sounds, but I think this is not your case.) For example the ventilator of my computer is 35dB. I agree with Chris Stronks, that it is unlikely that your noisy ventilator caused your tinnitus or has any effects on it.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://sdngnet.com/Files/Lectures/FUTA-ARC-507/Assignments/2007%20Assignments/Term%20Papers/Noise%20Induced%20Hearing%20Damage.pdf&quot; rel=&quot;nofollow&quot;&gt;A TERM PAPER ON NOISE - INDUCED HEARING DAMAGE&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.noiseandhealth.org/article.asp?issn=1463-1741;year=2013;volume=15;issue=62;spage=55;epage=66;aulast=Pawlaczyk-Luszczynska&quot; rel=&quot;nofollow&quot;&gt;Noise induced hearing loss: Research in central, eastern and south-eastern Europe and newly independent states&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.nidcd.nih.gov/health/hearing/pages/noise.aspx&quot; rel=&quot;nofollow&quot;&gt;Noise-Induced Hearing Loss&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sound is measured in units called decibels. Sounds of less than 75&#xA;  decibels, even after long exposure, are unlikely to cause hearing&#xA;  loss. However, long or repeated exposure to sounds at or above 85&#xA;  decibels can cause hearing loss. The louder the sound, the shorter the&#xA;  amount of time it takes for NIHL to happen.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;1953 - &lt;a href=&quot;http://www.tinnitus.tinnitus.org/HB_Nov00.pdf&quot; rel=&quot;nofollow&quot;&gt;TINNITUS AURIUM IN NORMALLY HEARING PERSONS&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;1974 - &lt;a href=&quot;http://scitation.aip.org/content/asa/journal/jasa/56/5/10.1121/1.1903482&quot; rel=&quot;nofollow&quot;&gt;Hearing loss due to continuous exposure to steady‐state broad‐band noise&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The limit of permissible noise exposure, defined as the maximal level&#xA;  which did not cause measurable noise‐induced shift in hearing levels&#xA;  of workers exposed to it irrespective of exposure years, was shown to&#xA;  be NR 75 or 80 dBA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2012 - &lt;a href=&quot;http://oem.bmj.com/content/early/2012/06/11/oemed-2011-100578.short&quot; rel=&quot;nofollow&quot;&gt;10-Year prospective study of noise exposure and hearing damage among construction workers&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://office.wjgnet.com/2218-6247/full/v3/i3/58.htm&quot; rel=&quot;nofollow&quot;&gt;Noise-induced hearing loss in the 21st century: A research and translational update&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2014 - &lt;a href=&quot;http://oem.bmj.com/content/early/2014/07/25/oemed-2014-102200.short#aff-1&quot; rel=&quot;nofollow&quot;&gt;Early prognosis of noise-induced hearing loss&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At this occasion, a standardised noise exposure was applied (20 min,&#xA;  200–500 Hz, 100 dBA) and the TTS at 4 kHz was determined during at&#xA;  least 10 min after exposure.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;1989 - &lt;a href=&quot;http://scitation.aip.org/content/asa/journal/jasa/86/5/10.1121/1.398609&quot; rel=&quot;nofollow&quot;&gt;Noise level, inner hair cell damage, audiometric features, and equal‐energy hypothesis&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;According to new studies continuous exposure to low dB (65-70) sound (which don't damage inner hair cells) can cause neural changes in sound processing. Constant noise can cause annoyance, concentration disturbance, etc... as well.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23154196&quot; rel=&quot;nofollow&quot;&gt;Effects of passive, moderate-level sound exposure on the mature auditory cortex: spectral edges, spectrotemporal density, and real-world noise.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2014 - &lt;a href=&quot;http://www.nature.com/nrn/journal/v15/n7/full/nrn3744.html&quot; rel=&quot;nofollow&quot;&gt;Is the din really harmless? Long-term effects of non-traumatic noise on the adult auditory system&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;People are increasingly being exposed to environmental noise from&#xA;  traffic, media and other sources that falls within and outside legal&#xA;  limits. Although such environmental noise is known to cause stress in&#xA;  the auditory system, it is still generally considered to be harmless.&#xA;  This complacency may be misplaced: even in the absence of cochlear&#xA;  damage, new findings suggest that environmental noise may&#xA;  progressively degrade hearing through alterations in the way sound is&#xA;  represented in the adult auditory cortex.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2012 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22532192&quot; rel=&quot;nofollow&quot;&gt;Effects of repeated &quot;benign&quot; noise exposures in young CBA mice: shedding light on age-related hearing loss.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2012 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22588305&quot; rel=&quot;nofollow&quot;&gt;Environmental noise exposure degrades normal listening processes.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Here we show that exposing adult rats to structured noise at a sound&#xA;  pressure level of 65 dB, which is markedly below the broadly accepted&#xA;  safety level standard, results in behavioural impairments and&#xA;  substantially impairs the function of the auditory cortex. The strong&#xA;  deterioration in cortical processing of acoustic inputs is independent&#xA;  of the modulation rates of structured noises. Almost equally strong&#xA;  effects result from 10-h daily versus 24-h daily exposure regimens.&#xA;  These results indicate that there can be substantial negative&#xA;  consequences for the auditory system documented at the cortical level,&#xA;  attributable to environmental exposure to structured noises delivered&#xA;  under conditions that do not directly impact hearing sensitivity.&#xA;  These noises are deemed to be 'safe' and are often present in modern&#xA;  human environments.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;2013 - &lt;a href=&quot;http://www.noiseandhealth.org/article.asp?issn=1463-1741;year=2013;volume=15;issue=64;spage=153;epage=159;aulast=van&quot; rel=&quot;nofollow&quot;&gt;Noise and health in vulnerable groups: A review&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A cross-sectional study in Nigeria [36] among children frequenting a&#xA;  school near a major road (noise range: 68-85 dBA) found at least some&#xA;  annoyance and concentration disturbance in 70% of the children.&#xA;  Fatigue and lack of concentration came forward as the most prevalent&#xA;  noise-related health problems.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-11-19T13:36:45.570" LastActivityDate="2014-11-19T13:36:45.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24154" PostTypeId="2" ParentId="23641" CreationDate="2014-11-19T13:57:24.690" Score="12" Body="&lt;p&gt;There are plenty of animals with brief procreative periods, as you suggest. In chimps, sex takes 10 to 15 seconds - much less time than humans. So the question is really why have humans evolved to be different?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think any of the answers based on fitness are particularly compelling. It's not like sex feels like running a marathon or less physically fit people can't manage to ejaculate in their partners so it seems unlikely that the lengthy sex act serves to distinguish fitter individuals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead, I think the difference probably lies in the pair-bonding role of sexual activity. Humans form unusually long-lasting, typically monogamous or largely monogamous, bonds that function to provide the support needed during the lengthy childhood that humans undergo. The prolonged, and highly pleasurable, sex act likely functions to help maintain these bonds in order to keep the couple together and provide the stable support needed to maximise the chances of successfully raising a child to adulthood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, to the best of my knowledge, there is no high quality empirical evidence that would convincingly answer the question so any answer must be somewhat speculative.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2014-11-19T13:57:24.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24161" PostTypeId="1" AcceptedAnswerId="24164" CreationDate="2014-11-19T17:26:30.013" Score="3" ViewCount="4328" Body="&lt;p&gt;What was possibly wrong in my gel electrophoresis when I didn't see bands of DNA ladder, and genomic DNA sample on gel ? I could see bands of genomic PCR and RNA solution.&lt;img src=&quot;https://i.stack.imgur.com/GUtPW.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you all of guys for sharing your opinions. From some opinions, I found out the possible error that my genomic DNA didn't show up because it was not pure (I forgot the detail that our group used a sample of DNA which was extracted from a previous lab and we didn't obtain an expected ratio for the purity of DNA. Then, we also used the impure DNA sample to do PCR, and finally used the amplified DNA for gel electrophoresis lab). However, the reason for DNA ladder didn't show up I'm not sure. I just can suppose that my groupmate who handled with DNA ladder solution possibly contaminated it.&lt;/p&gt;&#xA;" OwnerUserId="9944" LastEditorUserId="107" LastEditDate="2014-11-22T14:37:08.480" LastActivityDate="2014-11-22T14:37:08.480" Title="What is possibly wrong in my gel electrophoresis when I didn't see bands of DNA ladder on gel?" Tags="&lt;gel-electrophoresis&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="1" ClosedDate="2014-11-22T04:12:51.583" ContentLicense="CC BY-SA 3.0" />
  <row Id="24164" PostTypeId="2" ParentId="24161" CreationDate="2014-11-19T22:29:15.237" Score="0" Body="&lt;p&gt;Possibly You don't mix ladder containing microtube by Sampler. You should slowly Fill and emptying Sampler for several times when pick it for use, mix it well, but do it without creating a bubble.one more thing, check your ladder by &quot;NanoDrop&quot;&lt;/p&gt;&#xA;" OwnerUserId="9101" LastEditorUserId="3340" LastEditDate="2014-11-22T05:04:34.170" LastActivityDate="2014-11-22T05:04:34.170" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24166" PostTypeId="2" ParentId="23842" CreationDate="2014-11-19T22:55:19.613" Score="7" Body="&lt;p&gt;Although the answers to date are all factual and sufficient to answer the question why cockroaches would live without its head, some answers don't seem to be necessary as explanations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Summarizing the given answers so far.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Roaches' simple  circulation would still function without its head.&lt;/li&gt;&#xA;&lt;li&gt;Roaches' decentralized respiratory system can still function without its head.&lt;/li&gt;&#xA;&lt;li&gt;Roaches are cold-blooded and demand less energy.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;However, &lt;a href=&quot;http://en.wikipedia.org/wiki/Mike_the_Headless_Chicken&quot; rel=&quot;noreferrer&quot;&gt;chickens can live without its head&lt;/a&gt; as long as the injury does not significantly damage its brain stem, which controls the animal's vital reflexes such as respirations.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Chickens do have complex network of blood vessels and capillaries.&lt;/li&gt;&#xA;&lt;li&gt;Chickens don't breathe via spiracles and do have centralized respiration system like us.&lt;/li&gt;&#xA;&lt;li&gt;Chickens are warm-blooded.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Thus, an animal (such as a cockroach) can live headless if its remaining organs can still control its &quot;vital functions&quot;.&lt;/p&gt;&#xA;" OwnerUserId="9731" LastEditorUserId="9731" LastEditDate="2014-11-20T05:01:37.320" LastActivityDate="2014-11-20T05:01:37.320" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24167" PostTypeId="1" AcceptedAnswerId="24201" CreationDate="2014-11-20T00:41:01.093" Score="4" ViewCount="3024" Body="&lt;p&gt;I know that many labs use either &lt;a href=&quot;http://www.flowjo.com/&quot; rel=&quot;nofollow&quot;&gt;FlowJo&lt;/a&gt; or &lt;a href=&quot;http://www.denovosoftware.com/&quot; rel=&quot;nofollow&quot;&gt;FCS Express&lt;/a&gt; to plot and analyze their flow data. These seem like the two standards for most labs (and I have used FlowJo before). However, my current funding does not cover software licenses and I'm not keen to pay $500-2000 out-of-pocket for a license. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there alternatives that approach the quality of FlowJo/FCS Express but are open-source/free with an academic license? I'm looking for an approach which will allow me to fit G1/S/G2-M curves to my data.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="9829" LastEditDate="2014-12-21T03:41:40.990" LastActivityDate="2018-09-24T11:50:19.207" Title="Alternatives to commercially available flow cytometric analysis software for use in cell cycle analysis?" Tags="&lt;flow-cytometry&gt;&lt;cell-cycle&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24168" PostTypeId="2" ParentId="23916" CreationDate="2014-11-20T02:32:35.850" Score="3" Body="&lt;p&gt;I can understand your confusion but it all makes sense. The basic idea is that what we call the &quot;antisense&quot; strand is actually the one being transcribed. However, since that is in effect a mirror image, it is much simpler to think in terms of the sense strand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To take a very simple example:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;5' ATG 3' &amp;lt;-- sense strand&#xA;3' TAC 5' &amp;lt;-- antisense strand&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The antisense strand will be read in a 3' to 5' direction:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;3' TAC 5' &amp;lt;-- antisense strand&#xA;5' AUG 3' &amp;lt;-- mRNA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Since the mRNA is a mirror image, it has the sequence of the sense strand. It is this mRNA that is then translated and this is read in a 5' to 3' direction. So, AUG is translated as Met. To illustrate, have a look at this image from &lt;a href=&quot;http://en.wikipedia.org/wiki/Translation_%28biology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt; (click on it for a larger version), &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;a href=&quot;http://upload.wikimedia.org/wikipedia/commons/9/94/Protein_translation.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/GMIf5.gif&quot; alt=&quot;protein translation animation&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the image above you can see the growing polypeptide (protein) chain snaking its way through the ribosome. The flying blue things are &lt;a href=&quot;http://en.wikipedia.org/wiki/Transfer_RNA&quot; rel=&quot;nofollow noreferrer&quot;&gt;tRNA molecules&lt;/a&gt; and the black chain at the bottom is the mRNA being translated. You can't really see it very well in this image but if you look at the original you can clearly see it is moving from the right towards the left. The right hand side is the 5' end and the left is the 3'. Or, in a more static version (adapted from &lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/organic/translation.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/YJL3J.gif&quot; alt=&quot;protein translation&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the &lt;em&gt;antisense&lt;/em&gt; strand is read, transcribed to RNA (which has the sequence of the sense strand but with T converted to U) and it is this mRNA which is read (in a 5' to 3' direction) to produce the protein.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-11-20T02:32:35.850" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24170" PostTypeId="1" AcceptedAnswerId="24174" CreationDate="2014-11-20T03:22:44.967" Score="2" ViewCount="174" Body="&lt;p&gt;I was reading a book on radiation biology, and the book describes the process of &quot;indirect action&quot;, where radiation can first ionize a water molecule forming a free radical, which then may interact with important cellular molecules, such as DNA.  This contrasts with &quot;direct action&quot; which involves direct ionization of a key cellular molecule.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The book states that as hydration increases, the probability of indirect action occurring increases.  Given that indirect action normally predominates over direct action in cells, could this mean that over-hydration could be a risk factor for developing cancer in humans? Has there been any research into this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, would larger humans, who obviously have a larger bodily water content, have an increased risk of developing cancer compared with smaller humans?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="1472" LastEditDate="2014-11-20T03:50:41.827" LastActivityDate="2014-11-20T05:48:00.493" Title="Is excessive hydration a risk factor for cancer in humans?" Tags="&lt;cancer&gt;&lt;radiation&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24171" PostTypeId="1" CreationDate="2014-11-20T03:27:35.840" Score="2" ViewCount="414" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/1447/why-does-rigor-mortis-occur-after-death&quot;&gt;&lt;em&gt;Rigor mortis&lt;/em&gt;&lt;/a&gt; sets in due to non-functional &quot;&lt;a href=&quot;http://www.cs.stedwards.edu/chem/Chemistry/CHEM43/CHEM43/Projects04/ATPASES/PTYPE_CALCIUM.HTM&quot; rel=&quot;nofollow noreferrer&quot;&gt;ATP powered calcium pumps&lt;/a&gt;&quot; as a result of which the calcium ions stream out &amp;amp; the muscles remain in a suspended animation state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, it's a frequent observation (as can be seen from a coroner's report) that the time for rigor mortis to set in depends on external temperature, like it's earlier in summer, but late during winter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why this fluctuation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Rigor_mortis#Physical_changes&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt; has got an answer, but it's too brief.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When conditions are warm, the &lt;strong&gt;onset&lt;/strong&gt; and pace of rigor mortis are sped&#xA;  up by providing a conducive environment for the metabolic processes&#xA;  that cause decay. Low temperatures, however, slow them down.&#xA;  Therefore, for a person who dies outside in frozen conditions rigor&#xA;  mortis may last several days more than normal.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-11-20T15:29:07.297" Title="Time for rigor mortis to set in" Tags="&lt;human-physiology&gt;&lt;forensics&gt;" AnswerCount="0" CommentCount="5" FavoriteCount="0" ClosedDate="2014-11-27T04:53:05.403" ContentLicense="CC BY-SA 3.0" />
  <row Id="24172" PostTypeId="2" ParentId="24106" CreationDate="2014-11-20T03:57:29.013" Score="2" Body="&lt;p&gt;The Coursera &lt;a href=&quot;https://www.coursera.org/course/bioinfomethods1&quot; rel=&quot;nofollow&quot; &gt;Bioinformatic Methods&lt;/a&gt; courses include classes on metagenomics and, more importantly, tools to use when applying these methods. I have not taken this particular course, but Coursera is generally very good with getting hands-on experience using computational tools. A course-like setting may also be conducive to group learning. &lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2014-11-20T03:57:29.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24174" PostTypeId="2" ParentId="24170" CreationDate="2014-11-20T05:48:00.493" Score="3" Body="&lt;p&gt;In the most technical sense, yes. In a practical sense, no. Average background radiation dose from food and water sources is ~.3 mSv &lt;a href=&quot;http://www.unscear.org/unscear/en/publications/2008_1.html/&quot; rel=&quot;nofollow&quot;&gt;according to the UN&lt;/a&gt;. Given that it takes 1 full Sv to increase cancer risk by ~5-6%, it seems unlikely that, under normal conditions, variability in consumption of water will change risk in a significant fashion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, when dealing with highly contaminated water, there may be a more exaggerated effects, scaling with an increased concentration of radioactive particles per unit of water. Of course, in highly radioactive situations the risk of radiation poisoning may be a more immediate worry.&lt;/p&gt;&#xA;" OwnerUserId="10257" LastActivityDate="2014-11-20T05:48:00.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24175" PostTypeId="1" CreationDate="2014-11-20T06:29:20.777" Score="2" ViewCount="565" Body="&lt;p&gt;Imagine that horses, dogs, bears, and gorillas had teeth as unreliable as humans do, The interruption in behaviour and stress brought by teeth would cause them to be more prone to sinus infections, jaw abscesses, and general poor performance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The stress from cavities and wisdom teeth growing sideways would affect their survival rates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans have evolved slow maturation times, including teeth, have shortened jaws with compressed teeth, and errored, unvariable, DNA from inbreeding after near extinction 100k years ago (lake toba caldera) which makes us biologically quirky and unreliable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does our jaw have to be so short that we could live with impacting wisdom teeth? because it places strain on the neck to have a long jaw?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why didnt face infections and tooth misalignment cause humans to select each other strongly with straight teeth? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are wonky teeth a feature of cold climates, where people dont have so much fruit, and in hot countries, ethnicities have straigher teeth?&lt;/p&gt;&#xA;" OwnerUserId="8952" LastActivityDate="2014-11-20T07:51:13.040" Title="Why do humans have irregular teeth and impacting wisdom teeth?" Tags="&lt;teeth&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24176" PostTypeId="2" ParentId="14864" CreationDate="2014-11-20T06:45:27.960" Score="-2" Body="&lt;p&gt;From the statistical point of view, this question is rather vague. One would need a mathematical definition for the term &quot;genetic variance&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In one extreme, if the &quot;genetic variance&quot; merely means the categorial variations of nucleotides (i.e. ACTG) in the pooled genomes of interest, then the distribution of total &quot;genetic variance&quot; vs. loci variation is uniform and only depends on the size of the locus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In another extreme (among many dimensions of extremes), if the &quot;genetic variance&quot; is only manifest by the organism's immediate &quot;fitness&quot; and only has two values: life and death (on birth), then all the &quot;essential genes&quot; are &quot;the most important&quot; loci. If you're interested in the n most important loci where n &gt; the number of essential genes, then you would first look at the binary genetic interactions in the database such as &lt;a href=&quot;http://wiki.thebiogrid.org/doku.php/statistics&quot; rel=&quot;nofollow&quot;&gt;BioGrid&lt;/a&gt; where two non-essential genes would &quot;interact&quot; and change the organism's fitness (in life and death).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course none of the two extremes is very interesting in population genetics or evolution, but a statistical question is best phrased by statistical terms. I would try to find the mathematical definition for &quot;fitness variance&quot;, too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;---EDIT---&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a semi-empirical/informatics study, I think you could start with the simplest organism whose genome is well studied.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Choose an organism (e.g. yeast)&lt;/li&gt;&#xA;&lt;li&gt;Assume uniform inheritability&lt;/li&gt;&#xA;&lt;li&gt;Choose a specific measurable phenotype/environment (e.g. the ability to grow on a specific sugar x)&lt;/li&gt;&#xA;&lt;li&gt;Scan each gene in the yeast genome and see its quantitative impact on growth (They're documented in various database)&lt;/li&gt;&#xA;&lt;li&gt;Ignore genetic interaction&lt;/li&gt;&#xA;&lt;li&gt;(Or scan each gene pair/triplet/.../n-cluster to see its impact on growth on x)&lt;/li&gt;&#xA;&lt;li&gt;Try to model your empirical distribution. It's only valid for that specific phenotype/environment&lt;/li&gt;&#xA;&lt;li&gt;Define your &quot;TOTAL genetic variance in fitness&quot; meaningfully and rigorously. &quot;Additivity&quot; would be a very drastic assumption.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My guess as a non-geneticist is that, as rg255 suggested, for each phenotype as a function of the environment, the distribution would follow a &lt;a href=&quot;http://en.wikipedia.org/wiki/Power_law&quot; rel=&quot;nofollow&quot;&gt;power law&lt;/a&gt;. They would not have the properties that would allow you to use central limit theorem to &quot;add them up&quot;. But for a specific phenotype, your empirical cumulative distribution function (cdf) would answer your question.&lt;/p&gt;&#xA;" OwnerUserId="9731" LastEditorUserId="1590" LastEditDate="2016-08-17T08:50:24.443" LastActivityDate="2016-08-17T08:50:24.443" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24182" PostTypeId="2" ParentId="24175" CreationDate="2014-11-20T07:51:13.040" Score="2" Body="&lt;p&gt;Teeth first:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The vast majority of people have no problems with their wisdom teeth, whether they emerge or not. Impacted wisdom teeth are &lt;em&gt;very&lt;/em&gt; common and are usually painless. They do, however, sometimes mess around with other teeth and throw off our bites (which will always readjust, not necessarily in a cosmetically pleasing manner, but the bite will adjust). Today, because we value straight teeth, impacted wisdom teeth are often removed prophyllactically, even if we have no proof that it/they will cause any problems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since impacted wisdom teeth are not evident until well after reproductive ability is attained, there is no reason to believe that malocclusion from wisdom teeth &lt;em&gt;should&lt;/em&gt; be evolutionarily selected against. If problem teeth are so bad as to cause disability for an individual, that individual is removed from the gene pool. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given two equivalent males, there's no reason &lt;em&gt;not&lt;/em&gt; to entertain the notion that a female &lt;em&gt;did not&lt;/em&gt; choose the one with better occlusion. So, it &lt;em&gt;is&lt;/em&gt; theoretically possible that what we have now is an improvement over what was the state of our occlusions long ago. But there is rarely only one reason for two individuals to choose each other as partners, so... the teeth are &lt;em&gt;relatively&lt;/em&gt; unimportant evolutionarily.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or, if impacted wisdom teeth hurt enough to interfere with reproduction (&quot;Not tonight, Og, I have a killer toothache.&quot;) the individuals who don't reproduce because of it will be dropped from the gene pool. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There may have been selection against wisdom teeth, because there are populations who have a lower incidence of third molars.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;80% of all people will have problems with their backs at some point in their lifetime, which is a direct result of bipedalism in humans. You might ask why we became bipedal with that painful trade off. But bipedalism gave us &lt;em&gt;some&lt;/em&gt; distinct advantages in survival. So did the expansion of our brains. The greater advantage has precedence in evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/001057.htm&quot; rel=&quot;nofollow&quot;&gt;Impacted tooth&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.telegraph.co.uk/science/evolution/9873352/Evolution-to-blame-for-bad-backs-dropped-arches-and-impacted-wisdom-teeth-say-scientists.html&quot; rel=&quot;nofollow&quot;&gt;Ancient Mutation Explains Missing Wisdom Teeth&lt;/a&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-11-20T07:51:13.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24183" PostTypeId="2" ParentId="10022" CreationDate="2014-11-20T08:19:37.950" Score="0" Body="&lt;p&gt;It is commonly called as &quot;Robber fly&quot; or &quot;assassin fly&quot;. Scientifically it is &quot;Asilidae&quot; of the order &quot;Diptera&quot; and it is a fast attacking predator mostly preying on grasshopper nymphs and damsel flies. It is strongly built for kill.&#xA;&lt;a href=&quot;http://www.robberflies.info/keyger/htmle/didpic.html&quot; rel=&quot;nofollow&quot;&gt;http://www.robberflies.info/keyger/htmle/didpic.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10273" LastEditorUserId="10273" LastEditDate="2014-11-20T09:52:31.873" LastActivityDate="2014-11-20T09:52:31.873" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24185" PostTypeId="1" AcceptedAnswerId="31787" CreationDate="2014-11-20T11:16:36.730" Score="7" ViewCount="783" Body="&lt;p&gt;I've been reading the &lt;a href=&quot;http://explore.georgetown.edu/publications/index.cfm?Action=View&amp;amp;DocumentID=77894&quot;&gt;chapter by Haig et al in The Genetics and Biology of Sexual Conflict.&lt;/a&gt; I think this chapter has them quite unclearly defined. Could anyone describe these two phenomenon more clearly than the chapter does? Real or hypothetical examples would be good to give clarification, and clarification of how they are distinct from sexual conflict and antagonism.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Parental Conflict will refer to phenotypic interactions in which&#xA;  matrigenes and patrigenes prefer different outcomes&quot;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&quot;Parental Antagonism occurs when an allele has a relative advantage&#xA;  when inherited from one sex but a relative disadvantage when inherited&#xA;  from the other.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-11-20T13:34:17.910" LastActivityDate="2015-04-27T17:36:40.557" Title="What are parental antagonism &amp; parental conflict?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24187" PostTypeId="2" ParentId="23977" CreationDate="2014-11-20T11:57:19.863" Score="-1" Body="&lt;p&gt;Predators are very good at spotting moving targets, as movements will easily stand out from inanimate objects and vegetation.&#xA;Most prey will prefer to hide or just run if they are spotted by predators.&#xA;But the chameleons prefer to blend in with the vegetation instead. This gives them the advantage that they may move in plain sight, and still not be recognized as prey.&lt;/p&gt;&#xA;" OwnerUserId="10276" LastActivityDate="2014-11-20T11:57:19.863" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24188" PostTypeId="1" CreationDate="2014-11-20T16:46:43.897" Score="2" ViewCount="1852" Body="&lt;p&gt;I use methanol fixation (@ -20⁰C for 10 minutes) when performing immunofluorescence assays on cultured cells. Generally speaking, this results in very good antibody staining. However, the cells tend to look markedly different than they did under phase contrast microscopy prior to fixation. This has my PI worried about how these images will be received by reviewers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does a methanol fixative work, and why does it cause a change in cell morphology? Are there parameters that can be adjusted to mitigate this effect? &lt;/p&gt;&#xA;" OwnerUserId="10257" LastEditorUserId="3971" LastEditDate="2014-11-21T16:57:23.410" LastActivityDate="2015-02-19T19:20:25.583" Title="Does methanol fixation deform cultured cells?" Tags="&lt;lab-techniques&gt;&lt;microscopy&gt;&lt;histology&gt;&lt;fluorescent-microscopy&gt;&lt;staining&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24189" PostTypeId="1" AcceptedAnswerId="24196" CreationDate="2014-11-20T16:51:17.987" Score="10" ViewCount="25631" Body="&lt;p&gt;I noticed that my cat which is only 6 months old has started stretching its body from time to time. Then I thought that this motion doesn't seem very natural from another cat's viewpoint, so my cat probably didn't try to imitate some other cat all of a sudden and learned it like that. This action must have been caused by something else then. Or at least that's what I think.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both animals and people stretch their muscles from time to time, but it doesn't seem to be caused by memory of others doing it. So how does this action originate in them?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastEditorUserId="3624" LastEditDate="2014-11-21T09:15:55.257" LastActivityDate="2016-10-16T00:12:37.457" Title="Why do people and animals stretch out their bodies and what is causing this behaviour?" Tags="&lt;human-biology&gt;&lt;zoology&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24190" PostTypeId="1" AcceptedAnswerId="24199" CreationDate="2014-11-20T17:24:42.520" Score="1" ViewCount="110" Body="&lt;p&gt;How can I obtain per site log-likelihoods for a topology against an alignment without optimising branch lengths? (which software can I use to do this)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Per site log-likelihoods can be used for various tests of whether a topology fits the data in a multiple sequence alignment well using e.g. the Shimodaira-Hasagawa test, the AU test etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RAxML, Garli and FastTree and other software packages can calculate per site log-likelihoods given a tree, alignment and substitution model but all will automatically optimise branch lengths first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to test a tree in which a pair of sequences (A and B) are monophyletic, where in the maximum likelihood topology they are not. My problem is that when I infer a tree with a constraint requiring A and B to be monophyletic, the edge length is set to the minimum within the allowed precision. But having an edge length so close to zero does not make biological sense if the tree is describing a monophyletic clade for A and B: the minimum length of the edge must be equivalent to one substitution or character change, else A and B are in a polytomy containing clade with other sequences which is not the biological scenario I'd like to test (in that case there would be ambiguity regarding the relationship of A and B to other groups emerging from that polytomy).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So . . . I'd like to edit my constrained tree and increase the edge length to the A and B clade to the minimum one substitution length, then perform the AU test against the per site log likelihoods for that topology. But the above software optimises the edge lengths, resetting the edge length to A and B to effectively 0!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks&lt;/p&gt;&#xA;" OwnerUserId="10285" LastActivityDate="2014-11-21T02:57:48.717" Title="Testing monophyly from per site log-likelihoods without optimising branch lengths" Tags="&lt;evolution&gt;&lt;phylogenetics&gt;&lt;sequence-analysis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24191" PostTypeId="1" AcceptedAnswerId="24192" CreationDate="2014-11-20T17:55:00.340" Score="0" ViewCount="77" Body="&lt;p&gt;As you know using RNAi we are able to prevent gene expression. so why we do not use it to stop viral genes expression? &lt;/p&gt;&#xA;" OwnerUserId="1916" LastActivityDate="2014-11-20T19:20:56.333" Title="Why we do not use RNAi to control ebola?" Tags="&lt;gene-expression&gt;&lt;ebola&gt;&lt;gene&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24192" PostTypeId="2" ParentId="24191" CreationDate="2014-11-20T19:20:56.333" Score="1" Body="&lt;p&gt;Delivering siRNA in vivo is a difficult prospect, but has been overcome in research environments and several commercial in vivo solutions are on the market &lt;a href=&quot;http://www.lifetechnologies.com/us/en/home/life-science/rnai/introduction-to-in-vivo-rnai.html&quot; rel=&quot;nofollow&quot;&gt;see examples from Life Technologies here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bigger problems come from potential off-target effects. siRNA tend to be double stranded and both the 'guide' and 'passenger' strand can occasionally target multiple sequences that you did not intend. Additionally, siRNA tend to activate the body's immune system in ways that would inhibit therapy or cause excess inflammation and cell death. See the detailed review &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21125490&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, it is a good idea, and the current research in the field is working to overcome technical challenges, but we are not there yet.&lt;/p&gt;&#xA;" OwnerUserId="10257" LastActivityDate="2014-11-20T19:20:56.333" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24193" PostTypeId="1" CreationDate="2014-11-20T19:25:40.777" Score="1" ViewCount="35" Body="&lt;p&gt;Assuming humans could use all of their muscle strength at once, with no need of cooling or energy, how fast could we theoretically run?&lt;/p&gt;&#xA;" OwnerUserId="10286" LastEditorUserId="3624" LastEditDate="2014-11-20T19:30:57.407" LastActivityDate="2014-11-20T19:30:57.407" Title="What's the max speed that humans could run?" Tags="&lt;human-biology&gt;&lt;theoretical-biology&gt;&lt;muscles&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="2" ClosedDate="2014-11-20T20:03:50.243" ContentLicense="CC BY-SA 3.0" />
  <row Id="24195" PostTypeId="1" AcceptedAnswerId="24241" CreationDate="2014-11-20T20:04:03.537" Score="0" ViewCount="443" Body="&lt;p&gt;I've been trying to figure out a systematic way to count the number of hydrogen bonds for multiple PDB files.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DSSP shows me the total number of hydrogen bonds when I make &lt;code&gt;dssp.exe 1A11.pdb&lt;/code&gt;, giving me the total number of &lt;code&gt;24&lt;/code&gt; (am I correct, ok?)&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;24 96.0   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)--&amp;gt;H-N(J)  , SAME NUMBER PER 100 RESIDUES&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;But when I run this command in R:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt; require(biod3d)&#xA;&amp;gt; x=dssp(read.pdb(&quot;1A11&quot;), full=T)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;it doesn't look to have the number of hydrogen bonds. It shows this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt; x$hbonds&#xA;     BP1 BP2 NH-O.1   E1 O-HN.1   E2 NH-O.2   E3 O-HN.2   E4 ChainBP1 ChainBP2 Chain1 Chain2 Chain3 Chain4&#xA;1-A   NA  NA     NA  0.0      5 -2.1     NA  0.0      4 -0.3     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;   &amp;lt;NA&amp;gt;      A   &amp;lt;NA&amp;gt;      A&#xA;2-A   NA  NA      3 -0.2      6 -1.5      4 -0.2      7 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;3-A   NA  NA      4 -0.2      7 -1.8      5 -0.2      2 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;4-A   NA  NA      1 -0.3      8 -1.5      6 -0.2      7 -0.6     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;5-A   NA  NA      1 -2.1      9 -1.9      6 -0.2     10 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;6-A   NA  NA      2 -1.5     10 -1.3      1 -0.3      5 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;7-A   NA  NA      3 -1.8     11 -1.3      4 -0.6      5 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;8-A   NA  NA      4 -1.5     12 -1.2      3 -0.2      6 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;9-A   NA  NA      5 -1.9     13 -1.1      4 -0.2      7 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;10-A  NA  NA      6 -1.3     14 -2.3      5 -0.2     13 -0.4     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;11-A  NA  NA      7 -1.3     15 -1.8     12 -0.2     16 -0.3     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;12-A  NA  NA      8 -1.2     16 -1.8     13 -0.2     11 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;13-A  NA  NA      9 -1.1     17 -2.4     10 -0.4     18 -0.5     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;14-A  NA  NA     10 -2.3     18 -1.6     15 -0.2     13 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;15-A  NA  NA     11 -1.8     19 -1.8     17 -0.2     20 -0.5     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;16-A  NA  NA     12 -1.8     20 -0.8     17 -0.3     14 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;17-A  NA  NA     13 -2.4     21 -1.9     19 -0.2     16 -0.3     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;18-A  NA  NA     14 -1.6     22 -2.0     13 -0.5     21 -1.0     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;19-A  NA  NA     15 -1.8     23 -2.0     20 -0.3     24 -0.3     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;20-A  NA  NA     16 -0.8     24 -1.5     15 -0.5     19 -0.3     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;21-A  NA  NA     17 -1.9     25 -1.0     18 -1.0     19 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;22-A  NA  NA     18 -2.0     25 -0.3     23 -0.2     20 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;23-A  NA  NA     19 -2.0     22 -0.2     18 -0.3     21 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;24-A  NA  NA     20 -1.5     23 -0.2     19 -0.3     22 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;25-A  NA  NA     21 -1.0     23 -0.2     22 -0.3     24 -0.2     &amp;lt;NA&amp;gt;     &amp;lt;NA&amp;gt;      A      A      A      A&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So, my question: Is the total number of hydrogen bonds hidden somewhere in this output or somewhere else (or doesn't exist)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I manage to count the number of hydrogen bonds in a single PDB using Bio3D and R, then I can create a loop and iterate over all remainder PDB files.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for all!&lt;/p&gt;&#xA;" OwnerUserId="9236" LastEditorUserId="9236" LastEditDate="2014-11-22T19:54:22.990" LastActivityDate="2014-11-22T19:54:22.990" Title="Counting the number of hydrogen bonds of multiple PDB files" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;pdb&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24196" PostTypeId="2" ParentId="24189" CreationDate="2014-11-20T23:04:49.520" Score="10" Body="&lt;p&gt;Humans and other animals have lots of innate behaviors that are not learned from observation, i.e. behaviors that are hard-wired into our nervous system, and this is one of them. &lt;a href=&quot;http://en.wikipedia.org/wiki/Primitive_reflexes#Sucking_reflex&quot;&gt;Suckling reflexes&lt;/a&gt; in mammals and the &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/003293.htm&quot;&gt;Moro reflex&lt;/a&gt; is human babies (which we grow out of) are other simple examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The stretching behaviours you are referring to are usually labelled &lt;em&gt;pandiculation&lt;/em&gt; in humans (defined as involuntary stretching of the soft tissues), and yawning is often considered a special case of this. These kinds of behaviours are also normally related to transition periods between high-low activity in animals (&lt;a href=&quot;http://www.medical-hypotheses.com/article/S0306-9877%2806%2900060-0/abstract&quot;&gt;Walusinskie, 2006&lt;/a&gt;). In practice, stretching functions as a way to reverse the muscular atonia during REM sleep, and is in this sense a way to restore homeostatic functions (&lt;a href=&quot;http://www.appliedanimalbehaviour.com/article/0168-1591%2889%2990117-2/abstract&quot;&gt;Fraser, 1989&lt;/a&gt;; &lt;a href=&quot;http://www.medical-hypotheses.com/article/S0306-9877%2806%2900060-0/abstract&quot;&gt;Walusinskie, 2006&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A paper by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20109487&quot;&gt;Rial et al (2010)&lt;/a&gt; deals with the evolution of sleep and wakefulness in mammals from our reptile predecessors, and indicates that stretching behaviours might have originated/evolved from post-basking activities, more specifically risk-assessment behaviours, such as: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...risk assessment behaviour (RAB) and consists of the suspension of current behaviour, to be replaced by head dipping movements, eye scanning, rearing and&#xA;  adopting stretch attending postures...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is most likely much more to be said about this, and the paper cited above contains many references that can provide further clarification and evidence. A short comparative discussion of pandiculation is found in &lt;a href=&quot;http://www.appliedanimalbehaviour.com/article/0168-1591%2889%2990117-2/abstract&quot;&gt;Frasier (1989)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-11-21T00:11:26.287" LastActivityDate="2014-11-21T00:11:26.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24199" PostTypeId="2" ParentId="24190" CreationDate="2014-11-21T01:38:06.910" Score="0" Body="&lt;p&gt;If you have the budget for it, I highly recommend &lt;a href=&quot;http://www.geneious.com/&quot; rel=&quot;nofollow&quot;&gt;Geneious&lt;/a&gt; for topology work.  It was a real saver for me on an epi paper last year.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, they allow for testing per-log likelihood without adjusting edge length.  If you want to throw up some dummy data somewhere I can throw up an example. &#xA;I have no connection or stake with the company, just happy with it.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2014-11-21T02:57:48.717" LastActivityDate="2014-11-21T02:57:48.717" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24200" PostTypeId="2" ParentId="24188" CreationDate="2014-11-21T01:57:16.297" Score="2" Body="&lt;p&gt;Yes, fixation of almost any kind can have effects on morphology.  When you take a free flowing, protein spiked fat-blob (ie cell membrane), and make it rigid, you are going to get some differences.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A fun visualization of this can be done by wrapping cellophane/shrink wrap around a serological pipette and dipping it in a dry ice and methanol bath.  It's something I show students all the time before getting into histology work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Back to what you need.  What cells are you using and what are you growing them on?  Have you tried acetone fixation and you know it destroyed your plastic?  The amount of time and concentration needed for acetone fixation is low enough that most modern chamber slides can handle it.  Do you need the membrane to be permeabilized in fixation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I don't know the main effect you are measuring, but assuming you have good controls, you should be able to see it past the fixation.&lt;/strong&gt;  The effect in your controls should be similar to your treated groups, unless the treatment is specifically effected by your fixative.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moving to some more general recommendations.  I think you should reconsider the fixative’s you’ve ruled out, because I am unconfident about their application.  The base source I always recommend students to turn to is the Wiley &quot;Current Protocols in X&quot; book that is relevant to the task at hand.  In this case, I think the most relevant text is &lt;em&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/book/10.1002/0471142735&quot; rel=&quot;nofollow noreferrer&quot;&gt;Current Protocols in Immunology&lt;/a&gt;&lt;/em&gt;, and the appropriate unit is 21.4 &quot;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/0471142735.im2104s103/abstract#&quot; rel=&quot;nofollow noreferrer&quot;&gt;Immunohistochemistry&lt;/a&gt;.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think a particularly useful, and relevant to this question if you are concerned with formalin masking, is Table 21.4.3.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YFfJo.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is for human antigens, but the “&lt;a href=&quot;http://www.ihcworld.com/_technical_tips/antigen_retrieval_tips.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;antigen retrieval&lt;/a&gt;” process works for murine cells in most cases.  You are right that you antigen could be blocked by formalin, but the solution is often unmasking as MtOH are often more harsh to morphology.  To support protocol 1:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Formalin or paraformaldehyde fixation cross-links protein, often&#xA;  making antigens inaccessible to specific antibodies. The antigen&#xA;  retrieval protocol, which combines high temperature with buffers at&#xA;  different pH, has been very effective in unmasking antigenic&#xA;  determinants which may be masked in fixed tissue or fixed cell&#xA;  preparations, particularly determinants within the nucleus or&#xA;  cytoplasm (Taylor and Shi, 2013).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My modification of the protocol is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sodium citrate buffer: 0.1 M citric acid/0.1 M sodium citrate, pH 6.0&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wash sample on a liner rocker for 5 min w/2x culture volume of d.i. H2O&lt;/li&gt;&#xA;&lt;li&gt;Place your slides in 1mM citrate buffer in Coplin jars with the lid slightly off&lt;/li&gt;&#xA;&lt;li&gt;Weigh the jar in final state so you know how much water to add back&lt;/li&gt;&#xA;&lt;li&gt;Microwave 4-7 min.  You don’t want it to go to a boil, and you need to remember to allow for venting&lt;/li&gt;&#xA;&lt;li&gt;Weigh the jar again and add back water&lt;/li&gt;&#xA;&lt;li&gt;Microwave another 4-7 min, again you don’t want a boil&lt;/li&gt;&#xA;&lt;li&gt;Take out of the oven and allow it to come to room temp by sitting it on the bench.  If you do it too fast you’re going to disrupt the membrane.&lt;/li&gt;&#xA;&lt;li&gt;After it’s back to room temp, wash 2x PBS+0.05% Tween20 for 10 min each&lt;/li&gt;&#xA;&lt;li&gt;Try your IHC again, it will probably work now.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2014-11-21T16:43:45.293" LastActivityDate="2014-11-21T16:43:45.293" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24201" PostTypeId="2" ParentId="24167" CreationDate="2014-11-21T02:31:33.947" Score="3" Body="&lt;p&gt;Sounds like you should look into &lt;a href=&quot;http://master.bioconductor.org/help/course-materials/2007/BioC2007/labs/flowcore1/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bioconductor's flow suite&lt;/a&gt;.  I actually really like doing flow analysis in R, but it takes some practice and getting used to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biggest problem you will run into (in my opinion) is gating.  It's not easy to setup a GUI point and click gate.  Rather, you'll be more forced and inclined to set limits with algorithms or hard value limits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found &lt;a href=&quot;https://bio.codeplex.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;.Net Bio&lt;/a&gt; to be fun, but not nearly as powerful as Bioconductor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Meta note, couldn't think of a less opinion oriented way to answer other than just to say &quot;It can be done in R utilizing Bioconductor.&quot;  If this is still off, I'm fine with deletion. &lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="-1" LastEditDate="2018-09-24T11:50:19.207" LastActivityDate="2018-09-24T11:50:19.207" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="24203" PostTypeId="1" AcceptedAnswerId="24278" CreationDate="2014-11-21T05:09:53.173" Score="4" ViewCount="341" Body="&lt;p&gt;Is there any survival benefit in humans that can be obtained from chronic exposure to low dose radiation, or is any dose of radiation a potential harm?  Has any research been done into this?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="1472" LastEditDate="2014-11-21T07:41:36.517" LastActivityDate="2018-03-18T12:24:49.513" Title="Any benefit to low dose radiation?" Tags="&lt;radiation&gt;" AnswerCount="2" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="24204" PostTypeId="1" CreationDate="2014-11-21T05:51:54.160" Score="2" ViewCount="194" Body="&lt;p&gt;One day I had found some bees have come around the light source like other positively photo tropic insects, I hadn't seen any bees coming over light before. I think bees are diurnal and they don't leave their nest at nights, I also read from an article that parasitic wasps may attack bees and these attacked bees would lose their mind and leave their nest at nights.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this possible or any other reason behind the night travel of bees and their positive photo tropism ? &#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Apocephalus_borealis&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Apocephalus_borealis&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10294" LastActivityDate="2014-11-21T06:33:36.290" Title="Are bees positively phototropic" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24205" PostTypeId="2" ParentId="24204" CreationDate="2014-11-21T06:33:36.290" Score="2" Body="&lt;p&gt;Honey bees rely on the position of the sun (and the ephemeris function) to navigate and communicate (i.e. the waggle dance). If they are out too late in the day to return to the hive (occasional), or if they are disturbed at night in the hive, they will fly towards a light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Beekeepers and bee renters have learned that if you are going to disturb a hive at night, do so with minimal light so as not to lose bees. Also, they avoid lights in the vicinity of the hive in general.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a number of parasites and insecticides that cause bees to behave erratically. Colony Collapse Disorder is a major threat to the honeybee's survival.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why are bees attracted to light? I don't know if anyone knows that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://animals.howstuffworks.com/insects/bee5.htm&quot; rel=&quot;nofollow&quot;&gt;Dinner and Dancing: Bee Navigation&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.forbes.com/sites/ericmack/2014/05/12/the-cause-of-colony-collapse-disorder-disappearing-bees-becoming-more-clear/&quot; rel=&quot;nofollow&quot;&gt;The Cause Of Colony Collapse Disorder, Disappearing Bees Becoming More Clear&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-11-21T06:33:36.290" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24208" PostTypeId="1" AcceptedAnswerId="24210" CreationDate="2014-11-21T09:21:06.227" Score="9" ViewCount="7615" Body="&lt;p&gt;Like other animals, why don't humans have species &amp;amp; breeds ?&#xA;&lt;br/&gt; Even my pet dog is one type of breed, but we (humans) lack breeds &amp;amp; species?  What is the main reason?&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="9943" LastEditDate="2014-11-21T10:52:28.050" LastActivityDate="2016-12-26T18:31:22.207" Title="Like other animals, why humans don't have species &amp; breeds?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;human-genetics&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24210" PostTypeId="2" ParentId="24208" CreationDate="2014-11-21T12:03:43.243" Score="9" Body="&lt;p&gt;If you with 'humans' refer to our genus &lt;em&gt;Homo&lt;/em&gt; (which is often the case), we do have multiple species, see &lt;a href=&quot;http://en.wikipedia.org/wiki/Homo#Species&quot;&gt;wikipedia for an overview&lt;/a&gt;. The difference to many other organism groups is just that all species except &lt;em&gt;Homo sapiens&lt;/em&gt; are extinct. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, taxonomic ranks below the species level - such as breed, subspecies, population and race - are very poorly definined and are usually used in different ways in different taxonomic groups. It is therefore difficult to draw one-to-one comparisons between these types of ranks across taxonomic groups. It is even relatively meaningless to compare e.g. taxonomic families between taxonomic orders, since they are used in such different ways, and compared to ranks below the species level taxonomic 'order' and 'family' have much clearer definitions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if you with breeds of dogs are referring to distict phenotypes (which is basically what they are), you can easily see that some human populations also have distict phenotypes, so in this sense they are similar. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason why the concept of human races is largely obsolete and controversial (along with breeds) is clearly our human collective history of racism, nazism and eugenics.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2014-11-21T12:03:43.243" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24215" PostTypeId="1" AcceptedAnswerId="24233" CreationDate="2014-11-21T14:07:54.223" Score="1" ViewCount="130" Body="&lt;p&gt;The heart pumps the blood to supply tissues and kidney always filters the blood to remove urea,extra water and etc. And all these are vital,so the kidney is as important as heart:&#xA;and my question is:&#xA;Why is heart failure treated as more critical than kidney failure?&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="3340" LastEditorDisplayName="user14640" LastEditDate="2016-02-10T16:29:53.107" LastActivityDate="2016-02-10T16:29:53.107" Title="Why is heart failure treated as more critical than kidney failure?" Tags="&lt;cardiology&gt;&lt;kidney&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24217" PostTypeId="2" ParentId="24195" CreationDate="2014-11-21T14:47:44.483" Score="1" Body="&lt;p&gt;The number of hydrogen bonds cannot actually be said from software only inferred. But you could try using STRIDE (&lt;a href=&quot;http://structure.usc.edu/stride/&quot; rel=&quot;nofollow&quot;&gt;http://structure.usc.edu/stride/&lt;/a&gt;) which takes the file name with a -h flag to output the number of hydrogen bonds. You could then write a small shell script which would pass in each file and store the data you wanted in whatever format you liked.&lt;/p&gt;&#xA;" OwnerUserId="6811" LastActivityDate="2014-11-21T14:47:44.483" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24218" PostTypeId="2" ParentId="21258" CreationDate="2014-11-21T14:57:02.770" Score="6" Body="&lt;p&gt;This is a general answer for all three of your related questions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;This one&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/21424/how-does-temperature-influences-the-rate-of-protein-turnover&quot;&gt;How does Temperature influences the rate of protein turnover?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/21198/how-is-the-rate-of-transcription-influenced-by-temperature&quot;&gt;How is the rate of transcription influenced by temperature?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Since you said:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I want to simulate the evolution of genetic architecture when after a&#xA;  sudden change in temperature or in an environment that is temporally&#xA;  heterogeneous in terms of the temperature&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You should see this &lt;a href=&quot;http://www.pnas.org/content/108/26/10591.full.pdf?with-ds=yes&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper&lt;/a&gt;. They have studied the dependence of growth rate on temperature. This was measured for different organisms (all poikilotherms). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this figure: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/UcZXO.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Figure S1 from Dell et. al 2011. PNAS&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The unimodal thermal response of radial growth rate of sac fungi (m/(colony*s)). Green and brown curves are OLS regressions to the Boltzmann-Arrhenius model (Eq. 1) for the subset of data that are the rise and fall components, respectively. These components were extracted by the algorithm described in the Materials and Methods. For&#xA;  this particular response, the rise was obtained by the algorithm&#xA;  through removal of the measurements at the 4 highest temperatures and&#xA;  the fall through removal of measurements at the 5 lowest temperatures.&#xA;  The blue curve is the best fit to the Johnson &amp;amp; Lewin model (SI&#xA;  Methods) (1). Values shown are estimated activation energies with 95%&#xA;  confidence intervals for the respective response components. Dotted&#xA;  vertical arrows are estimated temperatures for T&lt;sub&gt;opt&lt;/sub&gt; –the temperature&#xA;  at which the trait value is optimal–calculated from the direct method&#xA;  (red) and Johnson &amp;amp; Lewin model (blue). See SI for more details. Data&#xA;  are from Fargues et al. (9)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As you can see, the curve is skewed. The left side of the curve from T&lt;sub&gt;opt&lt;/sub&gt; follows the activation energy model (Arrhenius/Boltzmann). The right side, though they say in the figure legend also fits the model, it seems to me that the phenomenon is somewhat different. The steepness of the curve is perhaps because of denaturation of enzyme active site and therefore a loss of activity. For different enzymes the denaturation kinetics would vary. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I happened to stumble into the author of this paper and that is how I got to know of this work. He seemed to agree that the right half steepness might be because of enzyme denaturation.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also have a look at &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1110/ps.ps.05801/full&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt; which is about the temperature dependence of the activity of the proteasome of a thermophile (same principles apply for mesophiles). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 2 of the article:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/qhyT7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Normalized Cbz-Ala-Ala-Leu-pNA hydrolysis activity of (filled squares)&#xA;  purified native and (filled circles) 70°C heat-purified recombinant (α&#xA;  + β) Mj proteasome. To normalize recombinant activity to native activity a multiplier of 1.92 was used. Error bars for the native&#xA;  sample represent one standard deviation for triplicate assays.&#xA;  Measured temperature errors were ±2°C.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Bottomline&lt;/strong&gt; (From my comments)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can assume that the enzymes are at their optimum. You can model the loss of activity due to increased temperature (protein denaturation) as gamma/chi square or exponential function (or the fitted function on the denaturation kinetics) and the effect of low temperature using the chemical thermodynamic equations. But the point is that we don't know if they are at their optimum or not or how each of they may perform at different temperatures.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-06-30T06:47:34.507" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24219" PostTypeId="2" ParentId="21326" CreationDate="2014-11-21T15:41:40.343" Score="1" Body="&lt;p&gt;I'm not sure if they will be useful for your application, but you should look into software used to visualize ecological networks (and maybe also software used for drawing electrical charts). The type of data used there is very similar to what you want to plot, with nodes and links along with metadata for links on e.g. rates or connection strenghts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can point you to &lt;strong&gt;mangal&lt;/strong&gt; by ecologist Tim Poisot (blogpost on mangal &lt;a href=&quot;http://timotheepoisot.fr/2014/01/09/mangal-in-action/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;), &lt;a href=&quot;http://www.sbgn.org/Main_Page&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;SBGN&lt;/strong&gt;&lt;/a&gt; (Systems Biology Graphical Notation), and there is also the R-package &lt;a href=&quot;http://cran.r-project.org/web/packages/diagram/index.html&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;diagram&lt;/strong&gt;&lt;/a&gt;. However, I haven't used them much so I cannot say how useful they will be.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-11-23T23:21:07.080" LastActivityDate="2014-11-23T23:21:07.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24220" PostTypeId="1" CreationDate="2014-11-21T16:13:27.253" Score="7" ViewCount="4567" Body="&lt;p&gt;When a cytotoxic T cell (CTL) recognizes a peptide presented in the MHC-1 of a dendritic cell (APC), why it doesn't kill this cell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that initially, in the lymph node, the T cell is inactivated. But eventually it becomes activated and travels to the tissue, where it again finds APCs presenting the offending antigen. So why doesn't the CTL kill the APC at this point?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, not all MHC-1's of the dendritic cell present antigens from phagocytized cells. Some MHC-1's present peptides coming from the dendritic cell itself, so that if the dendritic cell itself becomes infected with virus or bacteria, it can be killed by a CTL that recognizes the peptide. So in this case, the CTL does indeed kill the dendritic cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is, when exactly does the CTL kill the APC? How does the CTL knows that should or shouldn't kill the APC?&lt;/p&gt;&#xA;" OwnerUserId="561" LastEditorUserId="948" LastEditDate="2014-11-21T16:31:56.967" LastActivityDate="2021-02-04T17:26:53.820" Title="Why cytotoxic T cells don't kill dendritic cells when they present antigen?" Tags="&lt;immunology&gt;&lt;mhc&gt;" AnswerCount="5" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24221" PostTypeId="2" ParentId="19939" CreationDate="2014-11-21T16:36:23.347" Score="2" Body="&lt;p&gt;Please consider this a sort of comment — I tried looking up for articles related to MSMA mode of action but almost all the articles are about its toxicity in mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By what I understand, trivalent arsenates act as phosphate analogs and therefore interfere in phosphorylation reactions including DNA synthesis &lt;a href=&quot;http://ipmworld.umn.edu/chapters/whitacreherb.htm&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[Ref]&lt;/sup&gt;&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The weed is affected perhaps because of its relatively higher growth rate. Also the already established lawn grasses would have good population size to regrow out of the damage.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-22T10:54:48.240" LastActivityDate="2014-12-22T10:54:48.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24222" PostTypeId="2" ParentId="19864" CreationDate="2014-11-21T18:12:03.503" Score="0" Body="&lt;p&gt;Actin is required for the neurite architecture and is present throughout the shaft (along the direction of the neurite process)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See these images.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &lt;img src=&quot;https://i.stack.imgur.com/K77Hp.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &amp;nbsp; &lt;a href=&quot;http://cornellcelldevbiology.org/sung/researchunconventional.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;[Source]&lt;/strong&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp; &amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/5GXBz.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&amp;nbsp; &amp;nbsp;&lt;a href=&quot;http://www.uni-leipzig.de/~pwm/web/?section=introduction&amp;amp;page=neurons&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;[Source]&lt;/strong&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are not from research papers but the sources are trustworthy. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-21T18:12:03.503" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24224" PostTypeId="2" ParentId="7537" CreationDate="2014-11-21T18:31:58.370" Score="1" Body="&lt;p&gt;You can use the PCR purification kit for cleaning up the DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can use the primers that you used for RTPCR for sequencing. The universal primers would work only if the sequence complementary to it is there in the 3' end of your amplicon.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-21T18:31:58.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24225" PostTypeId="2" ParentId="3432" CreationDate="2014-11-21T18:44:00.997" Score="1" Body="&lt;p&gt;&lt;em&gt;E.coli&lt;/em&gt; strains that have &lt;em&gt;dam&lt;/em&gt; or &lt;em&gt;dcm&lt;/em&gt; methylases can methylate plasmid at adenines or cytosines respectively. See &lt;a href=&quot;https://www.neb.com/tools-and-resources/usage-guidelines/dam-and-dcm-methylases-of-e-coli&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; — It is a NEB web page but has links to the cited references.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DH5α has both the methylases- &lt;em&gt;dam&lt;sup&gt;+&lt;/sup&gt; dcm&lt;sup&gt;+&lt;/sup&gt;&lt;/em&gt; , BL21 is &lt;em&gt;dam&lt;sup&gt;+&lt;/sup&gt; dcm&lt;sup&gt;−&lt;/sup&gt;&lt;/em&gt; and ET12567 is &lt;em&gt;dam&lt;sup&gt;−&lt;/sup&gt; dcm&lt;sup&gt;−&lt;/sup&gt;&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-21T18:44:00.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24226" PostTypeId="1" CreationDate="2014-11-21T20:01:58.757" Score="2" ViewCount="103" Body="&lt;p&gt;I am studying ECGs of heart transplant patients. &#xA;The difficult thing is that there is so little available data publicly. &#xA;I must apply for data in my universities. &#xA;It would be also great if something is public. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have searched several databases and contacted some authors directly. &#xA;Some findings&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;No heart transplant data in Physionet, online search tool &lt;a href=&quot;http://physionet.org/cgi-bin/atm/ATM&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;No heart transplant data of ECGI with Dr Rudy (personal email)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am waiting answers or working with application for&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Dr Rudy's &lt;a href=&quot;http://www.cardioinsight.com&quot; rel=&quot;nofollow&quot;&gt;company&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;University of Helsinki's database (under process for application)&lt;/li&gt;&#xA;&lt;li&gt;Some technical universities in Finland (these have connections where are good data but they do not hold data themselves)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any ECG data about heart transplant patients?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-11-22T20:30:34.967" LastActivityDate="2014-11-22T20:30:34.967" Title="ECG of heart transplant patients" Tags="&lt;cardiology&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24227" PostTypeId="1" AcceptedAnswerId="24228" CreationDate="2014-11-21T20:46:56.280" Score="3" ViewCount="125" Body="&lt;p&gt;Obviously, I barely know what I am talking about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I want to find the &lt;strong&gt;&quot;MUC5B promoter polymorphism &lt;code&gt;rs35705950&lt;/code&gt;&quot;&lt;/strong&gt; in my RAW genetic data from 23andMe. (see this paper  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23695349&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/23695349&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think &lt;code&gt;rs35705950&lt;/code&gt; is the SNP number...   When I search I get no results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I search for &lt;code&gt;MUC5B&lt;/code&gt; I get 9 results, but the SNP numbers doesn't match.  &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;My question(s)&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Is it possible that I just don't have this gene (&lt;code&gt;rs35705950&lt;/code&gt;)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does 23andMe not have ALL of my genetic information?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I doing something wrong or misunderstanding what I am looking for?&lt;/p&gt;&#xA;" OwnerUserId="10298" LastActivityDate="2014-11-21T23:03:25.913" Title="Looking for a gene in my raw genetic data. What are the possible causes for this?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24228" PostTypeId="2" ParentId="24227" CreationDate="2014-11-21T21:49:30.510" Score="3" Body="&lt;p&gt;Let's set things straight. The genomes of humans are highly similar and in general everyone shares the same genes. &lt;em&gt;SNPs&lt;/em&gt;, or &lt;em&gt;Single Nucleotide Polymorphisms&lt;/em&gt;, are single basepair positions in the genome in which there tend to be differences between people. This means, that instead of measuring the whole genome sequence for a person, which is very expensive and difficult, we can just examine a subset of the genome (the SNP positions) and capture most of the unique characteristics of that genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;23andMe do exactly that. They measure a large set of SNPs (but not all of them), and thus give you some useful information about your unique DNA sequence. So you would need to look in the output given to you by 23andMe and see if they measure the SNP in question (rs35705950).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do SNPs have to do with genes then? Well, if one of these SNPs occurs inside a gene, it could affect the gene, for example by producing a slightly different protein that could lead to some phenotype. So, studies link SNPs to different phenotypes such as disease or hair color. Usually the link is not one-to-one, but given as a probability.&lt;/p&gt;&#xA;" OwnerUserId="1441" LastEditorUserId="1441" LastEditDate="2014-11-21T22:30:00.187" LastActivityDate="2014-11-21T22:30:00.187" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24231" PostTypeId="2" ParentId="13986" CreationDate="2014-11-22T05:29:10.060" Score="3" Body="&lt;p&gt;The Hodgkin-Huxley model:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$I=C_m\frac{dV}{dt} + g_k(V_m - V_k) + g_{Na}(V_m - V_{Na}) + g_l(V_m- V_l)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where $C_m$ is membrane capacitance per unit area and $g_i$ are membrane conductances.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reducing the number of channels does not affect capacitance; it basically reduces membrane conductance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Myelination causes reduction of number of channels (concentrating them only at the nodes of Ranivier) and also increases the effective membrane thickness. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Capacitance decreases as an inverse function of &quot;inter-plate distance&quot; (of parallel plates) which is the membrane thickness. This reduces the capacitative current.It also prevents the build up charge and thereby allowing it to propagate forward (Longitudinal current). IMO, the effect of myelination of capacitance would be much less than that of its effect on conductance. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-07-06T06:43:06.413" LastActivityDate="2015-07-06T06:43:06.413" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24233" PostTypeId="2" ParentId="24215" CreationDate="2014-11-22T06:55:26.050" Score="4" Body="&lt;p&gt;I don't know that one &lt;em&gt;is&lt;/em&gt; treated as more critical than the other. Both are potentially life-threatening conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One in five people over 40 will develop heart failure (HF). That makes it a very common disease of aging, and as more people survive other events (e.g. MI), it will continue to be prevalent, if not to rise.&lt;sup&gt;[1][2]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a patient presents with heart failure (HF), whether it is to a PCP, an urgent care center, or the ER, it is treated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the US, the prevalence of CKD (chronic kidney disease) in people ages 60 and older approximately the same as of congestive heart failure (CHF): 18.8 to 24.5 percent. Between 1980 and 2009, the prevalent rate for end-stage renal disease (ESRD) increased nearly 600 percent, from 290 to 1,738 cases per million.&lt;sup&gt;[3]&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a patient presents with renal failure (RF), whether it is to a PCP, an urgent care center, or the ER, it is treated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That makes both conditions much more common (and less emergent) in presentation than, say, anaphylaxis (life-threatening allergies).&lt;sup&gt;[4]&lt;/sup&gt; Known rates or cases of anaphylaxis were 0.0004% for food (e.g. peanuts), 0.7% to 10% for penicillin, 0.22% to 1% for radiocontrast media, and 0.5% to 5% after insect stings. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Emergencies are emergencies, and are triaged for care based on risk, with standardized acuity scales that have five levels (e.g., 1- resuscitation, 2- emergent, 3- urgent, 4- less urgent, 5- nonurgent).&lt;sup&gt;[5]&lt;/sup&gt; To claim that one is treated as more emergent than another, one would need to present evidence that, e.g. HF is rated as emergent more often than RF. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12473553&quot; rel=&quot;nofollow&quot;&gt;Lifetime risk for developing congestive heart failure: the Framingham Heart Study&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813829/&quot; rel=&quot;nofollow&quot;&gt;Chronic Heart Failure: Contemporary Diagnosis and Management&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://kidney.niddk.nih.gov/kudiseases/pubs/kustats/&quot; rel=&quot;nofollow&quot;&gt;Kidney Disease Statistics for the United States&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[4] &lt;a href=&quot;http://archinte.jamanetwork.com/article.aspx?articleid=646961&quot; rel=&quot;nofollow&quot;&gt;Anaphylaxis in the United States&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;Considering the 1999 US population of 272 million, the population at risk for anaphylaxis from food is 1099, from penicillin is 1.9 million to 27.2 million, from radiocontrast media is 22 000 to 100 000, from latex is 220, and from insect stings is 1.36 million to 13.6 million. These calculations yield a total of 3.29 million to 40.9 million individuals &lt;em&gt;at risk&lt;/em&gt; of anaphylaxis.&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[5] &lt;a href=&quot;http://www.ahrq.gov/professionals/systems/hospital/esi/esi1.html&quot; rel=&quot;nofollow&quot;&gt;Emergency Severity Index (ESI): A Triage Tool for Emergency Department&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-11-22T07:00:40.820" LastActivityDate="2014-11-22T07:00:40.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24234" PostTypeId="1" AcceptedAnswerId="24235" CreationDate="2014-11-22T06:55:38.630" Score="1" ViewCount="1108" Body="&lt;p&gt;Was out walking in the park today, came across a tree, and me being me I thought &quot;Hey lets try climbing this thing for fun.&quot; But something strange struck me, the tree was completely devoid, as in COMPLETELY, of any bark. On the trunk, on the branch, no bark anywhere, pure albino. Well, I reasoned, maybe it's just born that way. But then I look down, and I see the remnants of some bark wrapping around the tree's base. (Greyish colour). Huh. And I also saw approximately 7 massive slightly orange ants tumbling through an ant hole. I'm not a large fan of ants, especially since I had pretty much been standing on their nest for a couple of minutes, so I hastily backed off.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's where my mind kicked in though, how did the tree become barkless? For some background, I live in Sydney, NSW, Australia, and it's pretty darn hot here, nearly Summer. MAYBE the wind blew it off? (but there hasn't been any wind lately) Only logical explanation was THE ANTS DID IT. Do ants really eat the bark off trees like this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.imgur.com/ZthlQ1Z.jpg&quot; alt=&quot;barkless tree&quot;&gt;&#xA;Dang that's a big picture. You can sort of see if you look closely the remains of the bark at the bottom. Been to this park before, and I'm 75% sure the tree was not albino back then.&lt;/p&gt;&#xA;" OwnerUserId="10302" LastEditorUserId="3340" LastEditDate="2014-11-22T07:51:47.280" LastActivityDate="2014-11-22T07:54:26.590" Title="Ants eating bark" Tags="&lt;botany&gt;&lt;species-identification&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ClosedDate="2014-12-06T08:55:29.320" ContentLicense="CC BY-SA 3.0" />
  <row Id="24235" PostTypeId="2" ParentId="24234" CreationDate="2014-11-22T07:33:23.657" Score="2" Body="&lt;p&gt;Trees have different kinds of bark. If your tree was not moist and seeping, it had bark. Since that tree is clearly alive, it's likely that it has a smooth, light-colored naturally peeling bark.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jDR20.jpg&quot; alt=&quot;stewartia pseudocamillia bark close-up&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Japanese Stewartia (&lt;em&gt;Stewartia pseudocamillia&lt;/em&gt;) has a beautiful bark that is constantly shedding in patches of tan, green, orange and brown. It always has bark, however.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Crepe Myrtle is also used in landscaping for it's beautiful, peeling bark.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To know if this condition is normal for that tree, identification (using range, habitat, bark, leaves, twigs, and sometimes flowers, fruits and seeds) is needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Eucalyptus grandis&lt;/em&gt; is native to your area. Eucalyptus species also shed bark and the picture in your question definitely looks like eucalyptus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EFIiz.jpg&quot; alt=&quot;eucalyptis grandis&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When it is finished peeling, it's very light. This might be your tree.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="3340" LastEditDate="2014-11-22T07:54:26.590" LastActivityDate="2014-11-22T07:54:26.590" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24236" PostTypeId="1" CreationDate="2014-11-22T11:37:45.693" Score="1" ViewCount="122" Body="&lt;p&gt;How could I compare what a normal eye can see to a camera lens?&#xA;I just went through a very comprehensive article @ &lt;a href=&quot;http://www.cambridgeincolour.com/tutorials/cameras-vs-human-eye.htm&quot; rel=&quot;nofollow&quot; title=&quot;CambridgeInColour&quot;&gt;CambridgeInColor&lt;/a&gt;, but I'm still not really clear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I take a picture with a SLR camera from an object about 30m from me: what focal length do I need to use, how should I present this picture to truly capture what the eye can see (because of the 40-60° that we see 100% everything)? And how should I print it to scale?&#xA;Are there any options so I can put a ruler, or a human being at a certain point to be able to show the differences?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope I'm clear here, but if not, please comment and I'll try to explain better!&#xA;What I'm aiming for is that I need a picture, but not a picture in itself, but more like what the eye will see at that position. Not what the camera registers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="10303" LastActivityDate="2014-11-22T11:37:45.693" Title="How to compare a camera and an eye" Tags="&lt;eyes&gt;&lt;human-eye&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24238" PostTypeId="1" AcceptedAnswerId="24240" CreationDate="2014-11-22T13:59:38.497" Score="4" ViewCount="69" Body="&lt;p&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=sRv19gkZ4E0&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; video suggests that the first cell to be the victim of viral infection of ebola is the dendritic cell which acts as the leader of immune system cells.But I am unable to understand how the dendritic cells get infected if they are the leaders?&lt;/p&gt;&#xA;" OwnerUserId="3881" LastActivityDate="2014-12-22T15:38:44.250" Title="Action of Ebola Viruses" Tags="&lt;immunology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24240" PostTypeId="2" ParentId="24238" CreationDate="2014-11-22T14:58:25.530" Score="1" Body="&lt;p&gt;Viruses can infect any cell:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a virus must have a host cell (bacteria, plant or animal) in which to live and make more viruses. Outside of a host cell, viruses cannot function. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;a href=&quot;http://science.howstuffworks.com/life/cellular-microscopic/virus-human1.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This includes the dendritic cells:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dendritic cells are antigen-presenting cells of the immune system. Their main function is to process antigen material and present it on the cell surface to the T cells of the immune system. They act as messengers. They don't actually release any antibodies.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dendritic_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quite simply, at the beginning of an infection, the viruses / bacteria will be destroyed by macrophages. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FrXQb.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The dendritic cell will &quot;pick up&quot; some of the leftover pieces.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1dtY1.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When it finds a T-Cell that has the same configuration, it orders lots of identical T-Cells to be made. These T cells have multiple jobs, one of which is activating the B cells. It is the B cells that release the antibodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ViRDm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/929BQ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So Ebola.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the dendritic cells are &quot;invaded&quot;, then the only line of defence is the macrophages. This is often not enough to stop an attack, and it multiplies out of control.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason the Dendritic cells can be invaded is because they are just as vulnerable as other cells. They haven't activated the T cells, and they haven't activated the B cells, so there is nothing protecting them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=zQGOcOUBi6s&quot; rel=&quot;nofollow noreferrer&quot;&gt;Images Source (YouTube video)&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="10304" LastActivityDate="2014-11-22T14:58:25.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24241" PostTypeId="2" ParentId="24195" CreationDate="2014-11-22T19:53:47.237" Score="0" Body="&lt;p&gt;This an initial solution, but can be improved:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;out = system2(&quot;f:/stride/stride.exe&quot;, &quot;f:/stride/1a11.pdb -h&quot;, stdout=T)&#xA;nh  = strsplit(out[grepl(&quot;HBT&quot;, out)], &quot;  &quot;)[[1]][2]&#xA;print(nh) # Output: 26 (hydrogen bonds)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I compiled an Windows version of Stride and uploaded here:&#xA;&lt;a href=&quot;http://lcrserver.icmc.usp.br/~daniel/bin/stride.exe&quot; rel=&quot;nofollow&quot;&gt;http://lcrserver.icmc.usp.br/~daniel/bin/stride.exe&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9236" LastActivityDate="2014-11-22T19:53:47.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24247" PostTypeId="1" AcceptedAnswerId="24250" CreationDate="2014-11-22T23:24:09.750" Score="1" ViewCount="513" Body="&lt;p&gt;I got a statuette of a bird, carved of semi-precious minerals, but with its tail broken off. I'd like to restore it, rebuild the tail, but I'd first need to know how it should look like. Can you help me identify the species this is modelled after? (...unless it's just artistic license of the anonymous author...)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BCWAr.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously, the tail is missing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you would need the photos from a different angle or whatever description I could provide of its features, just tell me what you need, and I'll add the extra data.&lt;/p&gt;&#xA;" OwnerUserId="6512" LastEditorUserId="9943" LastEditDate="2017-02-05T19:33:51.673" LastActivityDate="2017-02-05T19:33:51.673" Title="Bird identification" Tags="&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="2" CommentCount="3" ClosedDate="2014-11-23T14:05:06.410" ContentLicense="CC BY-SA 3.0" />
  <row Id="24248" PostTypeId="2" ParentId="23182" CreationDate="2014-11-22T23:27:41.310" Score="0" Body="&lt;p&gt;Your teacher was passing on a myth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This false belief might be related to the equally false belief that hot exerted horses should not be fed cold water. It could also be down to someone downing a big glass of ice-cold water in one go as a child, get a brief stomach ache and spin a health-advice on it. &lt;/p&gt;&#xA;" OwnerUserId="9583" LastEditorUserId="9583" LastEditDate="2014-11-23T12:54:03.663" LastActivityDate="2014-11-23T12:54:03.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24249" PostTypeId="2" ParentId="24247" CreationDate="2014-11-23T01:17:00.653" Score="-2" Body="&lt;p&gt;It might be the Green Catbird (Ailuroedus crassirostris)&lt;/p&gt;&#xA;" OwnerUserId="10309" LastActivityDate="2014-11-23T01:17:00.653" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24250" PostTypeId="2" ParentId="24247" CreationDate="2014-11-23T01:26:38.163" Score="4" Body="&lt;p&gt;I think it's a kingfisher. Luckily the tail is short.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mGbUV.jpg&quot; alt=&quot;kingfisher bird&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some are larger, some smaller, yellow-, orange-, or brown-billed, but all with an intense stare, especially when they spot prey.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-11-23T01:26:38.163" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24252" PostTypeId="2" ParentId="23295" CreationDate="2014-11-23T02:58:10.930" Score="2" Body="&lt;p&gt;Excellent question! The difference is the fact that the &lt;strong&gt;rheobase&lt;/strong&gt; is an example of a &lt;strong&gt;threshold&lt;/strong&gt; measure. The &lt;strong&gt;threshold&lt;/strong&gt;, as you correctly suggest, is the minimal energy (typically current level and not voltage as you suggest) to excite neural tissue. The threshold applies only under the specific experimental parameter settings used. These parameters include the type of electric stimulus (for example, a biphasic current pulse), the electrode configuration (for example, bipolar stimulation) and the stimulus duration (for example 200 microseconds).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rheobase is the minimal current level needed to excite a tissue when an &lt;strong&gt;infinitely long stimulus would be applied&lt;/strong&gt;. The rheobase is typically found by plotting the threshold level (as defined above) as a function of stimulus duration. The reason for developing this measure is the fact that excitable membranes integrate the injected current, so charge builds up in the tissue. In other words, increasing the pulse duration decreases the threshold current level needed. Hence, the rheobase is a convenient threshold measure because it incorporates the duration parameter of the stimulus. It will still depend on things like electrode configuration and stimulus shape.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The function of the strength-duration relationship can be fitted with a decaying exponential: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I = I&lt;sub&gt;th&lt;/sub&gt; / ( 1-e&lt;sup&gt;(-t/Tsd)&lt;/sup&gt; )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where I= Threshold current level; &#xA;I&lt;sub&gt;rh&lt;/sub&gt; = rheobase&#xA;t = stimulus duration&#xA;Tsd = Tau = exponential&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a picture of a theoretical strength-duration curve copied from the wiki page on rheobase. [NB: I find the wiki page needlessly complicated].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fhfLz.png&quot; alt=&quot;hypothetical strength-duration curve&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rheobase is the horizontal asymptote. An often used parameter to characterize the function is chronaxie, which is the pulse duration equivalent to two times the rheobase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The explanation given here was adapted from the book &quot;Cochlear Implants&quot;, chapter 5 &quot;Biophysics and Physiology&quot; by Abbas and Miller, two veterans in cochlear implant electrophysiology. Unfortunately I cannot give you a link to the pdf as I own the work in hard copy. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-23T22:46:54.093" LastActivityDate="2014-11-23T22:46:54.093" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24257" PostTypeId="1" CreationDate="2014-11-23T12:31:00.577" Score="0" ViewCount="168" Body="&lt;p&gt;I first thought that this is because of prolonged depolarisations. &#xA;However, I am not sure anymore, because after reading &lt;a href=&quot;http://pubchem.ncbi.nlm.nih.gov/compound/suxamethonium#section=DrugBank-Interactions&quot; rel=&quot;nofollow&quot;&gt;PubChem&lt;/a&gt;, the only possible pathways are are Choline agonist. &#xA;So I would say that succinylcholine cause myorelaxation by some cholino-receptor agonists. &#xA;I do not think it is about depolarisation and how long it is. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can succinylcholine cause myorelaxation?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-11-25T21:40:56.827" LastActivityDate="2015-06-12T16:06:34.607" Title="How can succinylcholine cause myorelaxation?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24260" PostTypeId="2" ParentId="13986" CreationDate="2014-11-23T13:15:53.577" Score="4" Body="&lt;p&gt;Very nice question! I'll go through your three questions sequentially.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Q1: Why does lower capacitance increase &quot;the effectiveness of nearby nodes&quot; or allow the depolarizing voltage to &quot;travel not by ion diffusion, but as an electric field&quot;?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A: Capacitance basically results in sequestering of charge of opposite polarities along the cell membrane, which basically results in a neutralization of charge differences. The effect of this is explained on the website of &lt;a href=&quot;http://amrita.vlab.co.in/?sub=3&amp;amp;brch=43&amp;amp;sim=137&amp;amp;cnt=1&quot; rel=&quot;nofollow&quot;&gt;Amrita&lt;/a&gt; and I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] a higher capacitance results in a lower potential difference. In a cellular sense, increased capacitance requires a greater ion concentration difference across the membrane.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What myelin does is insulating the neuron, thereby decreasing its capacitance. You could say that by increasing the thickness of the membrane, the negative insides of the cell do not attract positive charge outside the cell. It's a bit simplified, yet it effectively describes what myelin does (&lt;a href=&quot;http://www.pdn.cam.ac.uk/teaching/part1a/intro_to_circuits/Capacitors3.html&quot; rel=&quot;nofollow&quot;&gt;see cambridge web page on capacitance&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in a myelinated axon, when Na&lt;sup&gt;+&lt;/sup&gt; enters the cell in a node of Ranvier, the positive charge entering the cell is not counterbalanced by outside negative charge and hence, the charge is not or at least less counterbalanced. This allows for the depolarizing potential to be transmitted by electric charge. If there were no myelin, the depolarizing potential would fade out pretty quickly along the axon by neutralizing charges outside the cell. Without myelin the opening of more sodium channels in the direct vicinity are necessary not only to transmit the action potential across the axon, but it is also necessary to amplify the signal to prevent it from dying out. In a myelinated axon, hence, the depolarizing potential reaches much farther and in answer to your next question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Q2:This allows us to say that λ, or the rate of spatial decay of potential, increases, decreasing the effective length of the neuron. Why should its decrease help faster conduction?)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One could say that myelination effectively decreases the length of the axon (the lamba parameter) as the depolaring potential reaches further along the axon.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fact that the depolarizing potential reaches further means that voltage-operated sodium channels can be activated at larger distances from a certain depolaring potential. Hence, adjacent nodes of Ranvier can be spaced by as much as 1.5 mm. Due to the fact that the next node is activated by passive spread of an electric field, which is pretty much instant, it skips the intervening distance with about light speed, greatly enhancing conduction velocity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Q3: And another question is, how would reduced density of sodium voltage gated channels cause a decreased capacitance?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically there are no ion channels below a myelin sheath as they are totally useless there. It is the myelin that decreases capacitance and there happen to be no channels underneath.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-11-23T13:15:53.577" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24261" PostTypeId="1" AcceptedAnswerId="24262" CreationDate="2014-11-23T16:36:37.803" Score="11" ViewCount="17783" Body="&lt;p&gt;DNA is made up of pairs on AT and GC base pairs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that A only pairs with T and G only with C. Does this apply just to humans, or are there animals where T will pair with G?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, surely there would be more possible combinations if A could pair with G or T or C, and DNA would have a better information density - less would be needed to hold the information?&lt;/p&gt;&#xA;" OwnerUserId="10304" LastEditorUserId="10304" LastEditDate="2014-11-24T10:38:49.100" LastActivityDate="2018-05-17T21:34:46.687" Title="Why does A pair with T and G with C?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24262" PostTypeId="2" ParentId="24261" CreationDate="2014-11-23T17:05:28.607" Score="17" Body="&lt;p&gt;There is no difference in base pairing between different kinds of organisms. Humans, animals and bacteria all share the same fundamental mechanisms as they all use DNA. Which bases can pair is determined by the chemistry of the individual bases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bases in DNA form the following hydrogen bonds when they are paired:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kAkBW.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/jGPqM.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you would try to combine other bases than the canonical Watson-Crick pairs, the hydrogen bond donors and acceptors wouldn't match. You need a donor/acceptor pair at each position.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are different base pairs possible, but these situations don't really occur in DNA but in RNA. You can find G/U wobble base pairs and even base pairs that use different parts of the bases than the canonical base pairs, e.g. Hoogsteen base pairs.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-11-23T17:05:28.607" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24263" PostTypeId="1" AcceptedAnswerId="24315" CreationDate="2014-11-23T17:18:45.703" Score="2" ViewCount="145" Body="&lt;p&gt;I know that it has alpha1, alpha2 and beta1 effects. &#xA;It has beta2 receptor where epinephrine can effect. &#xA;However, to say that it is beta adrenomimetic, I am not sure. &#xA;That is ligand binding beta2 receptor causes a stimulatory effect. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is norepinephrine beta2 adrenomimetic?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-11-23T18:08:58.220" LastActivityDate="2014-11-26T17:43:01.753" Title="Is Norepinephrine beta2 adrenomimetic?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;physiology&gt;&lt;pharmacology&gt;&lt;neurotransmitter&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24264" PostTypeId="1" AcceptedAnswerId="24316" CreationDate="2014-11-23T18:06:02.310" Score="0" ViewCount="79" Body="&lt;p&gt;I started to think this problem by first thinking if the alpha2 mimetism is possible in either case. &#xA;It seems to be indirectly in either one. &#xA;Ephedrine seems to have more prominent effect in CNS. &#xA;So I propose that Ephedrine has indirect central alpha2 mimetic effect. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is ephedrine central alpha2 mimetic?&lt;/strong&gt; &#xA;I think one evidence about that would be if there is a alpha2 receptor which is activated by ephedrine somehow indirectly. &lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-11-25T21:26:25.293" Title="Ephedrine or pseudoephedrine indirectly central alpha2 mimetic?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24265" PostTypeId="1" AcceptedAnswerId="24267" CreationDate="2014-11-23T18:34:56.597" Score="0" ViewCount="647" Body="&lt;p&gt;E. coli lives in lower intestine. But exactly where can we find E. coli, and where is there none (or a really small amount) of it?&#xA;I need the exact names of parts of the lower intestine where we can find E. coli.&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="3624" LastEditDate="2014-11-24T08:54:15.993" LastActivityDate="2014-11-24T08:54:15.993" Title="Exact location of E. coli in human body" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;ecoli&gt;&lt;gastroenterology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24266" PostTypeId="1" AcceptedAnswerId="24453" CreationDate="2014-11-23T20:56:28.440" Score="0" ViewCount="55" Body="&lt;p&gt;T-cells are important for efficient vaccination since they have:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A. T-cell receptor (TCR)&lt;/li&gt;&#xA;&lt;li&gt;B. CD4+&lt;/li&gt;&#xA;&lt;li&gt;C. CD8+&lt;/li&gt;&#xA;&lt;li&gt;D. Memory&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My gut is telling me it's A since the TCR would recognize the antigens but I want to make sure. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="10318" LastEditorUserId="948" LastEditDate="2014-11-23T21:36:35.453" LastActivityDate="2014-12-02T05:57:41.980" Title="T-cells Question" Tags="&lt;human-biology&gt;&lt;homework&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24267" PostTypeId="2" ParentId="24265" CreationDate="2014-11-23T21:25:18.937" Score="0" Body="&lt;p&gt;In &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC127545/&quot; rel=&quot;nofollow&quot;&gt;Gastrointestinal Tract Location of Escherichia coli O157:H7 in Ruminants&lt;/a&gt; (Grauke &lt;em&gt;et al.&lt;/em&gt; 2002):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;in the lower GIT digesta, specifically the cecum, colon&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's about O157:H7, but I think the standard act a same.&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="9829" LastEditDate="2014-11-23T22:22:51.810" LastActivityDate="2014-11-23T22:22:51.810" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24268" PostTypeId="1" CreationDate="2014-11-23T21:34:46.643" Score="5" ViewCount="17428" Body="&lt;p&gt;Can it be that the adult eye can change color? Specifically my question is about a unilateral color change, such that the color of one eye remains constant, while the other changes color over time. Can this happen? Or can it be related to light-scattering, or an illusion of some sort?&lt;/p&gt;&#xA;" OwnerUserId="10320" LastEditorUserId="9943" LastEditDate="2014-11-24T04:58:42.990" LastActivityDate="2018-08-24T08:40:29.280" Title="Is it biologically possible for an adult's eye color to change?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;eyes&gt;&lt;human-eye&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24269" PostTypeId="1" CreationDate="2014-11-23T23:20:54.613" Score="12" ViewCount="18889" Body="&lt;p&gt;Does one parent transmit more DNA to the offspring than the other one? Or do both parents always transmit the same amount of genetic material to their offspring?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, can a baby be provided with a gene from the mother without an &quot;opposite gene&quot; from the father?&lt;/p&gt;&#xA;" OwnerUserId="10324" LastEditorUserId="9225" LastEditDate="2014-11-24T17:47:48.060" LastActivityDate="2019-03-28T15:53:05.677" Title="Does one parent transmit more DNA to the offspring than the other one?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24270" PostTypeId="2" ParentId="21326" CreationDate="2014-11-24T01:47:56.770" Score="1" Body="&lt;p&gt;The basic problem is one of prior knowledge. The information you have about E. coli metabolism is in the form of a simple network, i.e. a list of nodes and the edges (along with their weights) that connect them. From this information alone it's impossible to know, for example, that the reactions in the TCA cycle should be plotted as a perfect circle (that's the circle in the middle of your example graph). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only source for that information that's likely to be compatible with all of the metabolite/reaction names in your SBML file is the &lt;a href=&quot;http://bigg.ucsd.edu/&quot; rel=&quot;nofollow&quot;&gt;BiGG database&lt;/a&gt;. You can download maps that contain, among other things, x-y coordinates for all of the nodes in a metabolic network so that when you plot them they're not arranged in a big sloppy mess. You can then use a tool like &lt;a href=&quot;http://opencobra.sourceforge.net/openCOBRA/Welcome.html&quot; rel=&quot;nofollow&quot;&gt;COBRA&lt;/a&gt; to make the actual plots (look up the documentation for &lt;code&gt;readCbMap&lt;/code&gt; and &lt;code&gt;drawFlux&lt;/code&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even this won't be as pretty as you'd like. The best answer, unfortunately, is a piece of software called Simpheny, which is commercial software that costs about a zillion dollars and is not freely available.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-11-24T01:47:56.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24271" PostTypeId="2" ParentId="24269" CreationDate="2014-11-24T02:13:34.270" Score="17" Body="&lt;p&gt;&lt;strong&gt;SHORT ANSWER&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two parents transmit the same amount of genetic material to their offspring ....or almost&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;LONG ANSWER&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Nuclear versus Cytoplasmic DNA&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All &lt;a href=&quot;http://en.wikipedia.org/wiki/Eukaryote&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eukaryotes&lt;/a&gt; (everything that is neither a &lt;em&gt;Bacteria&lt;/em&gt; nor an &lt;em&gt;Archeabacteria&lt;/em&gt;) have nuclear and cytoplasmic DNA. Most of the DNA is nuclear DNA. As its name indicates, nuclear DNA is found in the nucleus. The cytoplasmic DNA is found in the cytoplasm, that is, outside of the nucleus. More specifically, in all eukaryotes, cytoplasmic DNA can be found in the mitochondrion. In plants (which are eukaryotes), you can find cytoplasmic DNA in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitochondrion&quot; rel=&quot;nofollow noreferrer&quot;&gt;mitochondrion&lt;/a&gt; and in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Plastid&quot; rel=&quot;nofollow noreferrer&quot;&gt;plastids&lt;/a&gt; (including the &lt;a href=&quot;http://en.wikipedia.org/wiki/Chloroplast&quot; rel=&quot;nofollow noreferrer&quot;&gt;chloroplasts&lt;/a&gt; (plastids active in photosynthesis)). See &lt;a href=&quot;http://en.wikipedia.org/wiki/Symbiogenesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for more information about the origin of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Organelle&quot; rel=&quot;nofollow noreferrer&quot;&gt;organelles&lt;/a&gt; (≈ organ of a cell) who carry DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nuclear and cytoplasmic DNA doesn't have the same mode of inheritance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Inheritance of Nuclear Genes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the diploid (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Ploidy&quot; rel=&quot;nofollow noreferrer&quot;&gt;ploidy&lt;/a&gt;) phase (phase during which each individual carries two copies of each gene), an individual carries one copy from his/her mother and one from his/her father.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above sentence assumes that a diploid phase exists (which is not the case of all species) and that genders (male vs female) exist which is by far not the case of each species. It also assumes that we are talking about autosomes (non-sexual chromosomes, see below for sexual chromosomes). These assumptions hold for humans for example. Note that the diploid phase is much longer in human than the haploid phase (spermatozoid, ovule). We say that humans are diplontic. Some species are haplontic (longer haploid phase) and some are haplo-diplontic. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_life_cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;life-cycle&lt;/a&gt; for more info.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short: Inheritance of nuclear genes is bi-parental, each offspring necessarily carry one copy of a given gene from his/her father and the other copy from his/her mother.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: there are some exceptions to this perfect bi-parental transmission (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Intragenomic_conflict#Segregation_distortion&quot; rel=&quot;nofollow noreferrer&quot;&gt;segregation distorter and intra-genomic conflict&lt;/a&gt;). Also, have a look at the short section on sexual chromosomes below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Inheritance of Cytoplasmic Genes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many exceptions to what I am about to write...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Globally speaking, offspring inherit cytoplasmic DNA for their mothers only. That means that your mitochondrion is those of your mother only. Therefore, mothers transmit slightly more genes than fathers because of the concern of cytoplasmic genes.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;To complete the picture...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Inheritance of Sexual Chromosomes (Nuclear DNA)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all sexual species have sex chromosomes but some do. In these species, it is not rare that one of the two sexual chromosomes is shorter than the other (In mammals, the &lt;span class=&quot;math-container&quot;&gt;$Y$&lt;/span&gt; chromosome is shorter than the &lt;span class=&quot;math-container&quot;&gt;$X$&lt;/span&gt; chromosome). In such a case, the male transmits slightly less DNA to their male offspring than to their female offspring. Also, in such case, fathers transmit less DNA to their male offspring than do mothers but males transmit as much DNA to their female offspring than do mothers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The evolution of sex chromosomes is a very interesting subject as well and you will find tons of information on this website or on different sites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Non-genetic inheritance&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Nutrient in eggs&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not only genes are transmitted. Parents also transmit proteins and nutrients in the egg. Females transmit more nutrients to their offspring than males.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Epigenetic&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not only genes are transmitted. Parents also transmit modifications on the DNA that are not modifications in the DNA sequence per se. These modifications are called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Epigenetics&quot; rel=&quot;nofollow noreferrer&quot;&gt;epigenetic&lt;/a&gt; modifications&quot;. Not all species can produce epigenetic modifications. In species who can transmit epigenetic modifications, both males and females can produce them. It is possible that in some species mother have a higher variance in the modifications that they transmit than males (or vice-versa) but I am not aware of such things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Environment and Cultural transmission&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not only genes are transmitted. Parents also offer an environment in which the offspring grow. Some species typically feed or protect their offsprings. Depending on the species males or females may have more influence on the environment experienced by the offsprings. Finally, in some species (human, chimps and orca for example) a set of traditions (culture) are transmitted to the offsprings from the parents. And depending on the species the father or the mother may have more influence in the culture transmitted to the offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Length of chromosomes may differ between two randomly sampled individuals&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all variants between two chromosomes in a population is caused by substitutions of one nucleotide by another. Some variation is due to deletions of nucleotides or insertions of nucleotides. You can even a very long piece of DNA who get inserted, duplicated or deleted. Therefore between two given individuals, the exact amount of DNA that is transmitted may also differ only because they happen to have different variants. However, this is not a systematic difference in the quantity of DNA that is transmitted by one sex or another unlike the other cases presented above.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-28T15:53:05.677" LastActivityDate="2019-03-28T15:53:05.677" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="24273" PostTypeId="2" ParentId="9819" CreationDate="2014-11-24T05:13:14.937" Score="1" Body="&lt;p&gt;This is not a proper answer. Bear with me. I'm in a hurry; will edit the answer to a decent form when I find time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the abstract of &lt;a href=&quot;http://classic.physrev.physiology.org/content/77/3/731.short&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Of the 80% of oxygen consumption coupled to ATP synthesis,&#xA;  approximately 25-30% is used by protein synthesis, 19-28% by the&#xA;  Na&lt;sup&gt;+&lt;/sup&gt;-K&lt;sup&gt;+&lt;/sup&gt;-ATPase, 4-8% by the Ca&lt;sup&gt;2+&lt;/sup&gt;-ATPase, 2-8% by the actinomyosin&#xA;  ATPase, 7-10% by gluconeogenesis, and 3% by ureagenesis, with mRNA&#xA;  synthesis and substrate cycling also making significant contributions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also check &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006349502751503&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; out.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-24T05:13:14.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24274" PostTypeId="2" ParentId="11078" CreationDate="2014-11-24T06:34:51.430" Score="2" Body="&lt;p&gt;The best way for scaling up these kinds of reactions is to set up many reactions. Prepare a mastermix for lets say 20 reactions. You can pool them together, precipitate the RNA and dissolve to appropriate concentration in nuclease free water. Also, use gene specific primer instead of oligo-dT and don't add poly-A tails (poly-A does not affect the in-vitro stability of RNA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Mad Scientist already indicated, you would not need to make DNA again from RNA. Simply take 1:2 molar ratio of your IVT template dsDNA (restriction digested) and the RNA (post IVT). Heat and anneal slowly. DNA-RNA hybrids are stronger then DNA-DNA hybrids and the former is more likely to form after annealing. You can digest the unpaired strands using enzymes like mung bean nuclease. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-11-24T06:34:51.430" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24275" PostTypeId="1" CreationDate="2014-11-24T10:11:16.453" Score="1" ViewCount="698" Body="&lt;p&gt;I had came across an insect  near my backyard in India(Kerala). I haven't seen this one before and I searched web to find out what insect is this and found its image which saying its a &quot;Giraffe Weevil&quot; (Trachelophorus giraffa). The link below says that this insect is endemic to Madagascar.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Abht5.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/vPQvG.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Giraffe_weevil&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Giraffe_weevil&lt;/a&gt; and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are herbivore insects, with adults feeding on a tree that is commonly known as the &quot;giraffe beetle tree&quot;&#xA;(Dichaetanthera arborea)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This states that these insects need the &quot;giraffe beetle tree&quot;(Dichaetanthera arborea) which is also native to Madagascar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how come this insect could be found in India(Kerala), and further more all the above links state that the long neck of these dimorphic insects are evolved for fighting and nest making but they do tell that after mating the females will make the nest and lay one egg inside, So did the male insect make any nest in reality, if so then why the male have to perform both nest making and fighting.[Sorry for the errors,also there are more links to this]&lt;/p&gt;&#xA;" OwnerUserId="10294" LastActivityDate="2014-11-24T23:38:06.143" Title="Do &quot;Giraffe Weevil&quot; males build Nests" Tags="&lt;entomology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24276" PostTypeId="2" ParentId="13573" CreationDate="2014-11-24T10:11:29.160" Score="2" Body="&lt;p&gt;&lt;em&gt;Note: not my area of expertise&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;First of all, heterochromia can be &lt;a href=&quot;http://en.wikipedia.org/wiki/Heterochromia_iridum&quot; rel=&quot;nofollow noreferrer&quot;&gt;congenital (found at birth) or acquired&lt;/a&gt;, and from your question it is not clear if you are asking about one specific type or the overall frequency (if so, at what age?). Since acquired heterochromia is often due to injury or disease, the overall frequency is likely to increase with age. Also see answers to the question &quot;&lt;a href=&quot;https://biology.stackexchange.com/a/24277/3624&quot;&gt;&lt;em&gt;Is it biologically possible for an adult's eye color to change?&lt;/em&gt;&lt;/a&gt;&quot; for more on reasons for acquired heterochromia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to an Austrian study (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/485098&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Stelzer. 1979. Iris heterochromia: variations in form, age changes, sex dimorphism. Anthropol Anz. 37(2):107-16&quot;&gt;Stelzer, 1979&lt;/a&gt;), the overall frequency in the Vienna population was 0.26% (males: 0.16; females: 0.37). However, &lt;a href=&quot;http://www.medicinenet.com/heterochromia_iridis/page2.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Medicine.net&lt;/a&gt; reports a frequency of 0.6% for only congenial heterochromia, but this number lacks a clear reference. A thorough review of different reasons for heterochomia can be found in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3259577/&quot; rel=&quot;nofollow noreferrer&quot; title=&quot; Rennie. 2012. Don&amp;#39;t it make my blue eyes brown: heterochromia and other abnormalities of the iris. Eye 26(1): 29–50.&quot;&gt;Rennie (2012)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-12-02T13:22:27.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24277" PostTypeId="2" ParentId="24268" CreationDate="2014-11-24T10:33:08.963" Score="9" Body="&lt;p&gt;Short answer: The genes that encode eye color do not change, but the pigments in the eye can change due to external factors like diseases of medication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Long answer: Yes, it is possible that the eye color of adults can change, and it can also only happen to one eye. It is then called &lt;a href=&quot;http://en.wikipedia.org/wiki/Heterochromia_iridum&quot; rel=&quot;nofollow&quot;&gt;Heterochromia&lt;/a&gt;. There are two possibilities for different colored eyes, either congenitial (genetic) or acquired. Since you ask only for eye color changes in adults, we can skip here the genetic reasons, as these show up in kids already. If you are interested in them, have a look into the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Heterochromia_iridum&quot; rel=&quot;nofollow&quot;&gt;Heterochromia&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The basis for our eye color is genetically determined, changes can later occur due to diseases (so if one experiences a change in eye color, it is always a good idea to consult a doctor) and also due to medications. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The eye undergoing a change in pigmentation can either lighten up or darken.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fuchs_heterochromic_iridocyclitis&quot; rel=&quot;nofollow&quot;&gt;Fuchs’ Heterochromic iridocyclitis&lt;/a&gt;:&lt;/strong&gt; (also known as Fuchs’ Heterochromic uveitis) The change is caused by an eye infection with different microorganisms like Toxoplasma gondii, Herpes simplex virus or Rubella (an probably others) but it can also have an autoimmune pathology. See reference 1 and 2 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Horner's Syndrome:&lt;/strong&gt; This is a syndrome which mostly occurs in kids after damages to some nerves. This can lead to insufficient signals towards the pigment production and heterochromia. Rarely this can occur also in adults, where this is called acquired Horner's syndrome, see reference 3 for details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Pigment_dispersion_syndrome&quot; rel=&quot;nofollow&quot;&gt;Pigmentary Glaucoma&lt;/a&gt;:&lt;/strong&gt; In this disease (also known as Pigment dispersion syndrome) pigment cells from the back of the iris float are seperated from the original place and float through the aqueous humor of the eye where they can produce pigment which over time changes the appearance of the eye. See reference 4 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Medications:&lt;/strong&gt; Some of the medications against glaucoma (the prostaglandins latanoprost and bimatoprost) can cause a deeper pigmentation which will not always diminish after the end of the treatment. See reference 5 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cancers:&lt;/strong&gt; Some cancers as melanoma can also cause heterochromia, either when they are darker pigmented that the eye or when they are not pigmented. In both cases they influence the eye color. See reference 6 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC504771/&quot; rel=&quot;nofollow&quot;&gt;Fuchs' heterochromic cyclitis: review of the literature on the&#xA;pathogenetic mechanisms.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.joii-journal.com/content/pdf/1869-5760-3-14.pdf&quot; rel=&quot;nofollow&quot;&gt;Associations of Fuchs heterochromic iridocyclitis in a South Indian&#xA;patient population&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://content.lib.utah.edu/cdm/ref/collection/ehsl-nam/id/5365&quot; rel=&quot;nofollow&quot;&gt;Acquired Heterochromia with Horner's Syndrome in Two Adults&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3816/a9w8nlnz_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Pigment dispersion syndrome and pigmentary glaucoma – a major review&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1771317/&quot; rel=&quot;nofollow&quot;&gt;Incidence of iris colour change in latanoprost treated eyes&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701136/&quot; rel=&quot;nofollow&quot;&gt;Diffuse iris melanoma: Report of a case with review of the&#xA;literature&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-11-25T08:21:28.353" LastActivityDate="2014-11-25T08:21:28.353" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24278" PostTypeId="2" ParentId="24203" CreationDate="2014-11-24T11:30:50.600" Score="3" Body="&lt;p&gt;This is an interesting - and highly debated question. Generally there are two completely different directions of thinking when talking about dangerous substances (this applies to dangerous chemicals as well): &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Linear_no-threshold_model&quot; rel=&quot;nofollow noreferrer&quot;&gt;linear no-threshold model&lt;/a&gt; (LNT).&lt;/li&gt;&#xA;&lt;li&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Hormesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;hormesis&lt;/a&gt; model, in our case the model of &lt;a href=&quot;http://en.wikipedia.org/wiki/Radiation_hormesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;radiation&#xA;hormesis&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Summarizing the models the LNT model says that every dose has a negative response, so there is nothing like a stimulating dose and exposure should be avoided at any means. This reflects the policy in the handling of radioactive substances. If you look at the figure below, the curves a + b (supra-linear and linear) reflect the LNT model (the figure comes from &lt;a href=&quot;http://en.wikipedia.org/wiki/Linear_no-threshold_model&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BpvNM.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The radiation hormesis model says that there is a dose range in which the radiation above the background level is not only not harmful, but beneficial. High doses are (in line with the LNT model) also considered harmful. This can be seen in the curves c (linear-quadratic) and d (hormesis) in the figure above. The benefits are thought to take place through the activation of repair mechanisms (which are only activated by radiation) which protect against changes in the genome and thus also protect, once activated, against changes which are caused by other agents and reasons. See reference 1 for more details about radiation hormesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a number of studies which observe this effects in the laboratory and this is also one of the major critic points: To my knowledge it is currently unknown if these effects can also be seen outside a controlled laboratory environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other critique points are low study publications (which makes studies prone to statistical errors), using wrong models (cell culture) or too high doses. See references 2 and 3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since our environment contains naturally radioactive substances as well as cosmic and UV radiation, we have developed pretty efficient mechanisms to deal with these problem. Additionally measurable effect of radiation on the activity repair mechanisms can be seen (and this is not debated at all), but the main question is if these effects can also have a beneficial effect. It is also not known, if all radiation ($\alpha, \beta$ and $\gamma$) have the same effect, or if some of these like $\alpha$-radiation is more dangerous. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I think it may be possible that there is some positive effect, but until this is proven, I would rather be safe than sorry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://radiationhormesis.com/RadiationHormesis/Evidence%20for%20beneficial%20low%20level%20radiation%20effects%20and%20radiation%20hormesis.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evidence for beneficial low level radiation effects and radiation&#xA;hormesis.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://iopscience.iop.org/0952-4746/30/2/E02/pdf/0952-4746_30_2_E02.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Uncertainties in studies of low statistical power&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://download.nap.edu/login.php?record_id=11340&amp;amp;page=http%3A%2F%2Fwww.nap.edu%2Fdownload.php%3Frecord_id%3D11340&quot; rel=&quot;nofollow noreferrer&quot;&gt;Health Risks from Exposure to Low Levels of Ionizing Radiation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-11-24T11:30:50.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24279" PostTypeId="2" ParentId="23083" CreationDate="2014-11-24T11:42:08.653" Score="1" Body="&lt;p&gt;I assume that the figure comes from a section on genetic drift (since this seems likely), and it shows how the allele frequency will change over time under drift in a diploid population. So in short, each line represents the distribution of allele frequencies in different hypothetical populations, that all started with the allele frequencey p=0.5. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your specific questions, as the comment from @remi.b says, t is expressed as &lt;strong&gt;generation time&lt;/strong&gt; since this is the relevant time scale for evolutionary changes. The reason why it is a &lt;strong&gt;function of population size&lt;/strong&gt;, N, is that genetic drift acts more stongly in small populations, since it is essentially a sampling effect. You can see it as a repeated application of &lt;a href=&quot;http://en.wikipedia.org/wiki/Binomial_distribution&quot; rel=&quot;nofollow&quot;&gt;binomial sampling&lt;/a&gt;. So in small populations different populations will quicky drift away from the starting point of p=0.5, while this takes a longer time in larger populations. The effect of population size is clearly shown in &lt;a href=&quot;http://www.nature.com/scitable/topicpage/genetic-drift-and-effective-population-size-772523&quot; rel=&quot;nofollow&quot; title=&quot;Kliman, R., Sheehy, B. &amp;amp; Schultz, J. (2008) Genetic Drift and Effective Population Size. Nature Education 1(3):3&quot;&gt;this article&lt;/a&gt; from Nature education, where you can see the distribution of allele frequencies after one generation in populations of different sizes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The change in allele frequencies over time under drift has been modelled by a diffussion approximation (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528040/&quot; rel=&quot;nofollow&quot; title=&quot;Kimura. 1955. SOLUTION OF A PROCESS OF RANDOM GENETIC DRIFT WITH A CONTINUOUS MODEL. Proc Natl Acad Sci 41(3): 144–150.&quot;&gt;Kimura, 1955&lt;/a&gt; for the original results). His results show that heterozygozity decreases at the rate of $1/(2N)$ per generation, and after 2N generations the distribution of allele frequencies is essentially flat (if you started at p=0.5). The degree of heterozygocity at time t is given by:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$H_t = H_0*e^{-(\frac{1}{2N})t}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, your graph does not show populations where fixation has occured (only heterozygous populations), and this proportion will increase over time in the absence of new mutations. So what is missing are bars at 0 and 1, and these will become higher as time goes by (more populations will have become fixed for one of the alleles). It should also be mentioned that these results deal with the effective population size, so $N$ is really equal to $N_e$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the confusion of &lt;strong&gt;frequency/frequencies&lt;/strong&gt;; the graph shows the frequency of one allele in different populations (so the &lt;em&gt;allele frequency&lt;/em&gt; on the x-axis), but each line shows the distribution of &lt;em&gt;allele frequencies&lt;/em&gt; in different populations. This is probably why you found this confusing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, your question is a bit unclear since you haven't described from where you got the graph and exactly what it is supposed to represent.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-11-24T23:32:50.677" LastActivityDate="2014-11-24T23:32:50.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24281" PostTypeId="2" ParentId="24275" CreationDate="2014-11-24T13:42:01.947" Score="2" Body="&lt;p&gt;As the comment by @terdon says, the most likely explanation is that your species identification is mistaken. The superfamily Curculionoidea, which contains the weevils (Curculionidae are the true weevils) is also extremely species rich. Without seeing a picture of what you found, there are many other similar species with long necks in the family &lt;a href=&quot;http://en.wikipedia.org/wiki/Attelabidae&quot; rel=&quot;nofollow noreferrer&quot;&gt;Attelabidae&lt;/a&gt;, which is the family of &lt;em&gt;Trachelophorus giraffa&lt;/em&gt;. For instance, the wikipedia page includes a picture &lt;em&gt;Apoderus longicollis&lt;/em&gt; which is very similar to the Giraffe weevil from Madagaskar, and it is supposed to be found in India (see &lt;a href=&quot;http://www.gbif.org/species/1171902&quot; rel=&quot;nofollow noreferrer&quot;&gt;GBIF info&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uFD1T.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Paracycnotrachelus&lt;/em&gt; is another genus found in Asia where some species have long necks. Another giraffe-necked species is also found in New-Zealand - see &lt;a href=&quot;http://en.wikipedia.org/wiki/Lasiorynchus_barbicornis&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Lasiorynchus barbicornis&lt;/em&gt;&lt;/a&gt; - so the overall body shape is not that unique (note that much of the elongation in this species is of the snout though):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6K6vO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if we should never rule out the possibility of range changes/introductions, this must be based on close examinations of the specimen, and it is even more unlikely in this case since &lt;em&gt;Trachelophorus giraffa&lt;/em&gt; seems to be a very specialized species.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-11-24T23:38:06.143" LastActivityDate="2014-11-24T23:38:06.143" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24282" PostTypeId="2" ParentId="24275" CreationDate="2014-11-24T13:45:06.900" Score="1" Body="&lt;p&gt;First of all, the beetle you found likely doesn't belong to &lt;em&gt;Trachelophorus giraffa&lt;/em&gt;. There are &lt;a href=&quot;http://szmn.sbras.ru/persons/legalov/legalov128.pdf&quot; rel=&quot;nofollow&quot;&gt;lots of&lt;/a&gt; of species in the family Attelabidae, many of them having long necks in males and some were described or are known known from India.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I couldn't find any primary source on the nesting behavior of &lt;em&gt;Trachelophorus giraffa&lt;/em&gt;, and I suspect that most of the web-pages mentioning the male participation in creating the cradle by rolling leaves stem from &lt;a href=&quot;http://books.google.de/books?id=9GO9RKIj-SwC&amp;amp;pg=PP20&quot; rel=&quot;nofollow&quot;&gt;this popular book&lt;/a&gt;, while in at least &lt;a href=&quot;http://books.google.de/books?id=UMq-2xYmCwQC&amp;amp;pg=PA64&quot; rel=&quot;nofollow&quot;&gt;another popular book&lt;/a&gt; it is explicitly written that &lt;em&gt;females&lt;/em&gt; make the cradle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As attested &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1748-5967.2011.00359.x/abstract&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, &quot;all females of the species Attelabidae make their host-plant leaves into cradles where they oviposit&quot;, so I suspect that &lt;em&gt;Trachelophorus giraffa&lt;/em&gt; is no exception to this rule. &lt;a href=&quot;http://www.costam.org.my/publications/Vol%204%20No%202%20Dec%202008.pdf#page=5&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a very detailed description of mating behavior of a species with similarly long neck: males take no part in building the nest and seem to utilize their necks only when competing for female.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-11-24T14:31:49.970" LastActivityDate="2014-11-24T14:31:49.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24283" PostTypeId="2" ParentId="24220" CreationDate="2014-11-24T14:01:33.953" Score="2" Body="&lt;p&gt;The presentation of antigens on the cell surface is done by two different molecule complexes: The MHCI and the MHCII complexes. These are coupled to different pathways and are recognized by different T cell populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The MHCI molecule presents all proteins which are present in the cell on the surface. To do so, peptides coming from the proteasome (where long proteins are digested) are transported in the the endoplasmatic reticulum (ER) by a special transporter called Transporter associated with Antigen Processing (TAP). By doing so, a profile of all proteins expressed in the cell is presented on its surface, including proteins which arise due to an infection of the cell. MHCI is recognized by cytotoxic (or CD8 positive) T cells which subsequently kill all cells which show foreign antigens on their surface (since this is a sign for an infection).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The MHCII complex only presents proteins on its surface which have been taken up by phagocytosis (so here only external proteins are presented). To prevent binding of cellular proteins in the ER (like for MHCI), the binding pocket of the receptor is blocked by the invariant chain. This chain dissociates only when the MHCII complex enter the phagolysosome with its acidic conditions. This makes sure that only proteins which have been taken up by phagocytosis are presented. MHCII complexes are recognized by helper (or CD4 positive) T cells, which in turn can activate B cells to raise a proper immune response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In theory this should prevent all problems. In the practical life this is different for dendritic cells in a mechanism called &quot;cross presentation&quot;. In this mechanism antigens which are taken up by phagocytosis are exported from the phagolysosme and imported into the ER. This pathway also involves the TAP protein. By choosing this way, APC can activate naive CTL which will kill all cells which present this antigen. See references 1 and 2 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This pathway is important for the immune response to a number of viruses as well as tumors which evade the MHCII mediated immune response by suppressing the MHCII antigen presentation. See references 3 and 4.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also important for the stability of the self-tolerance by the deletion of auto-reactive CTL. See reference 5 for details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3816/99y5nwg4_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Outside looking in: the inner workings of the crosspresentation&#xA;pathway within dendritic cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://ac.els-cdn.com/S0952791506002494/1-s2.0-S0952791506002494-main.pdf?_tid=5307b164-7421-11e4-a888-00000aacb35f&amp;amp;acdnat=1416864900_c529833ed101d317c69b5391ed9b4d4a&quot; rel=&quot;nofollow&quot;&gt;Cross-talk between the endocytic pathway and the endoplasmic&#xA;reticulum in cross-presentation by MHC class I molecules&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3816/86teuzcg_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Role of bone marrow-derived cells in presenting MHC class I-restricted tumor antigens.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.uiowa.edu/~immuno/classMaterial/Immunology%20I%202003/Sigal.pdf&quot; rel=&quot;nofollow&quot;&gt;Cytotoxic T-cell immunity to virus-infected non-haematopoietic cells&#xA;requires presentation of exogenous antigen.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9221753&quot; rel=&quot;nofollow&quot;&gt;Exogenous class I-restricted cross-presentation of self antigens can&#xA;lead to deletion of autoreactive CD8+ T cells.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-11-24T21:45:09.350" LastActivityDate="2014-11-24T21:45:09.350" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24287" PostTypeId="1" CreationDate="2014-11-24T18:40:37.243" Score="2" ViewCount="627" Body="&lt;p&gt;I study physics but I have got interested about biology too. Surfing around the web, I have found out that in buying microscopes one needs to decide between the cheaper no-name brands vs. the four big ones: Zeiss, Nikon, Leica, and Olympus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the four big ones, only Zeiss delivers directly to my country. The price for Primo Star with phototube and Full-Kohler illumination is 1.8k euro or 2.3k usd. It has only bright-field optics but dark-field (if I got it correctly) is easy to add, as well as phase-contrast.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, I was wondering how much I would get out of the scope as a home user. I would probably do plant biology. I would also like to learn some staining techniques.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How difficult it would be to run some mini-studies at home? Do research? I would know about imaging quite a lot.. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(There was some other similar questions but they did not mention home use.)&lt;/p&gt;&#xA;" OwnerUserId="10333" LastActivityDate="2017-05-23T13:42:24.493" Title="Is Zeiss Primo Start microscope worth the price for student use?" Tags="&lt;microscopy&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2017-05-25T20:02:42.810" ContentLicense="CC BY-SA 3.0" />
  <row Id="24288" PostTypeId="1" CreationDate="2014-11-24T19:26:27.843" Score="1" ViewCount="713" Body="&lt;p&gt;Imagine the scenario. My friend and I are playing a game of chess near a highway. Initially, I notice the sound of the highway. While I'm playing chess, however, I do not notice it. After the game my friend asks me if I can hear the highway, and I regain my ability to notice it. This seems to be different for smells.&#xA;If we were playing chess in a room filled with garbage, the smell would gradually fade away. If my friend asked me if I could smell the garbage, I would not be able to smell the garbage as severely. What is the cause of this difference?&#xA;It seems that visual and touch follows the same pattern as hearing. What makes smell unique?&lt;/p&gt;&#xA;" OwnerUserId="9448" LastEditorUserId="9943" LastEditDate="2015-11-05T12:52:36.607" LastActivityDate="2015-11-05T12:52:36.607" Title="Sensory adaptation regarding smell and hearing" Tags="&lt;brain&gt;&lt;perception&gt;&lt;adaptation&gt;&lt;senses&gt;&lt;sensory-systems&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24290" PostTypeId="2" ParentId="24288" CreationDate="2014-11-24T22:47:58.557" Score="1" Body="&lt;p&gt;Adaptation occurs in every sensory system. For example in &lt;strong&gt;vision&lt;/strong&gt; there is the &lt;a href=&quot;http://psylux.psych.tu-dresden.de/i1/kaw/diverses%20Material/www.illusionworks.com/html/motion_aftereffect.html&quot; rel=&quot;nofollow&quot;&gt;motion after effect&lt;/a&gt; that occurs through adaptation of visual neurons in the cortex. Also, the visual system strongly adapts to low and high lighting conditions through &lt;a href=&quot;http://users.ipfw.edu/abbott/120/adaptation.html&quot; rel=&quot;nofollow&quot;&gt;light and dark adaptation&lt;/a&gt;. The &lt;strong&gt;tactile system&lt;/strong&gt; also shows substantial adaptation, as touch receptors in the skin fail to convey information after prolonged stimulation (you won't feel a watch/ring/band aid etc after wearing it for a while). For example, mechanoreceptors in the skin such as the &lt;a href=&quot;http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Mechanoreceptors.html&quot; rel=&quot;nofollow&quot;&gt;Pacinian corpuscles&lt;/a&gt; fail to transmit tactile stimuli when activated for a prolonged time. The &lt;strong&gt;auditory system&lt;/strong&gt; also adapts to loud sounds by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2504588/&quot; rel=&quot;nofollow&quot;&gt;cortical mechanisms&lt;/a&gt; as well as  &lt;a href=&quot;http://users.ipfw.edu/abbott/120/adaptation.html&quot; rel=&quot;nofollow&quot;&gt;peripheral mechanisms&lt;/a&gt; through the middle ear muscles. Lastly, as you correctly identified, the &lt;strong&gt;olfactory system&lt;/strong&gt; adapts to stimulation as well through &lt;a href=&quot;http://www.intropsych.com/ch04_senses/olfactory_adaptation.html&quot; rel=&quot;nofollow&quot;&gt;metabolic mechanisms&lt;/a&gt; that decrease the responsiveness of chemical receptors. The list of adaptational mechanisms provided is not comprehensive, but I just used some obvious examples to show that adaptation occurs in all the senses in a variety of ways. In fact, one of the hallmarks of &lt;em&gt;any&lt;/em&gt; physiological intact sensory system is the capability to operate over a wide range of stimulus levels. For example, vision operates over a range of intensities differing 8 orders of magnitude, while hearing operates in an intensity range of 10&lt;sup&gt;13&lt;/sup&gt;. To maintain such an impressive range of input intensities sensory systems have to adapt at various levels. As an analogy, the same applies to your photo camera in which the exposure time has to be regulated in order to take pictures under different lighting conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to come back to your suggestion that smell cannot be revived after continued stimulation while it can be revived with other senses is not true I think. The attentional revival you are talking about is not so much adaptation but has more to do with the attentional shift, which may occur with any sensory modality.          &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-11-25T00:21:43.753" LastActivityDate="2014-11-25T00:21:43.753" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24291" PostTypeId="1" AcceptedAnswerId="24304" CreationDate="2014-11-25T01:10:56.680" Score="7" ViewCount="287" Body="&lt;p&gt;In &lt;a href=&quot;https://worldbuilding.stackexchange.com/questions/4521/how-can-i-kill-every-human-on-earth/4533#4533&quot;&gt;an answer&lt;/a&gt; to a recent question on Worldbuilding, I suggested that an organism convert $\ce{H2O}$ into $\ce{H2O2}$. I suggested a few processes that yielded the desired final result ($\ce{2H2O \rightarrow H2O2 + H2}$ and $\ce{H2O + O3 \rightarrow H2O2 + O2}$). I noted that both were mere guesses. The feasibility of it was debated because hydrogen peroxide is a rocket fuel and contains a lot of energy (I heavily modified the answer and set it on an entirely different track after another mistake was pointed out).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could some process similar to this ever happen in an organism?&lt;/p&gt;&#xA;" OwnerUserId="9458" LastEditorUserId="-1" LastEditDate="2017-04-13T12:52:23.867" LastActivityDate="2016-08-09T18:40:45.807" Title="Can an organism process H₂O into H₂O₂?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24292" PostTypeId="1" AcceptedAnswerId="24299" CreationDate="2014-11-25T01:18:07.097" Score="1" ViewCount="2785" Body="&lt;p&gt;Sometimes I see in my house there are flipped cockroaches whose lose their heads. I used to have a cat, but there is no pet in my house anymore so I think it's only ants can be involved in this. But if so, the headless cockroach should be preyed already. Is there any explanation for this?&lt;/p&gt;&#xA;" OwnerUserId="6786" LastEditorUserId="6786" LastEditDate="2017-06-06T12:43:07.623" LastActivityDate="2017-06-06T12:43:07.623" Title="Why do flipped cockroaches sometimes lose their heads?" Tags="&lt;entomology&gt;&lt;death&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24293" PostTypeId="1" AcceptedAnswerId="24295" CreationDate="2014-11-25T03:38:13.353" Score="1" ViewCount="58" Body="&lt;p&gt;Which cell type cannot process and present antigen peptide in association with MHC-I when it is infected?&lt;/p&gt;&#xA;" OwnerUserId="9063" LastActivityDate="2014-11-25T04:07:16.687" Title="MHC-I presentation during infection" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24294" PostTypeId="2" ParentId="24203" CreationDate="2014-11-25T04:05:20.200" Score="0" Body="&lt;p&gt;I would be inclined to say yes based on the current wording of your question. There is more than one type of radiation out there, so I'm not exactly sure which you are interested in. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultraviolet is the one I will focus on though. Within the ultraviolet spectrum there are three types of ultraviolet radiation. The types are UVA, UVB, and UVC. UVC is primarily blocked by the atmosphere, so it never reaches us on the Earth's surface. UVB is perhaps best known for causing sun burns and skin cancer. UVA is the least powerful of the three. In chronic doses as you suggest it is probably far from good, but it can be beneficial at low doses.  UVA is linked with the production of Vitamin D which strengthens bones. It also stimulates tanning of the skin, which helps to protect the body from UV damage. Here is a link to The WHO describing some of UV's health benefits: &#xA;www.who.int/uv/faq/.../en/index1.html&lt;/p&gt;&#xA;" OwnerUserId="10270" LastActivityDate="2014-11-25T04:05:20.200" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24295" PostTypeId="2" ParentId="24293" CreationDate="2014-11-25T04:07:16.687" Score="2" Body="&lt;p&gt;All nucleated cell (cells with defined nucleus) are able to present MHC-1 on their surface.  Since red blood cells do not have nucleus, they are not able to represent antigins in MHC-1 molecule.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Major_histocompatibility_complex&quot; rel=&quot;nofollow&quot;&gt;check wikipedia for reference&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10334" LastActivityDate="2014-11-25T04:07:16.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24296" PostTypeId="2" ParentId="24291" CreationDate="2014-11-25T04:23:39.197" Score="9" Body="&lt;p&gt;Actually, there's a lot of animals, plants and microbes can do it. However, it is just an Intermediate process in general. Here's a strong example. In the condition with the absence of catalase, glucose oxidase can catalyze glucose + H&lt;sub&gt;2&lt;/sub&gt;O + O&lt;sub&gt;2&lt;/sub&gt; become gluconic acid + H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt;. Another process can also generate H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; catalyzed by Ero1. &lt;/p&gt;&#xA;" OwnerUserId="9790" LastEditorUserId="3340" LastEditDate="2014-11-25T11:42:25.193" LastActivityDate="2014-11-25T11:42:25.193" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24298" PostTypeId="1" AcceptedAnswerId="24301" CreationDate="2014-11-25T04:59:29.130" Score="8" ViewCount="4647" Body="&lt;p&gt;Why it is difficult to control orgasm in male humans? How are orgasms controlled and what is different between males and females?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can control urine for few minutes, but we can't control orgasm for more than a few seconds, but both are discharging though same organ (penis).&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="1590" LastEditDate="2014-11-26T07:08:10.673" LastActivityDate="2014-11-26T07:08:10.673" Title="In males, why it is difficult to control orgasm?" Tags="&lt;human-biology&gt;&lt;sex&gt;&lt;reflexes&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24299" PostTypeId="2" ParentId="24292" CreationDate="2014-11-25T05:19:18.723" Score="0" Body="&lt;p&gt;In all likelihood, it is your cat who crunches the cockroach's head once it catches it and/or finishes playing with it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ants do eat bugs but they are usually not so selective that they'll carry off the head alone. With more manageable insects, they carry the whole thing off; otherwise they take it apart and carry it away in pieces if they're interested in it as a food source.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you watch a cat with a mouse, chipmunk, bird, large insect, etc, they often seek to kill the animal with a throat or nape bite if they are done 'playing' with it. I've found headless prayer mantises and other large insects in my garage many times, and have seen my cats beheading them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://wec.ufl.edu/faculty/BranchL/research/Branch%20papers/Viz_obs_pred_Mammalia95.pdf&quot; rel=&quot;nofollow&quot;&gt;The techniques that cats use to kill prey vary with prey size&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-11-25T05:19:18.723" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24301" PostTypeId="2" ParentId="24298" CreationDate="2014-11-25T05:55:56.843" Score="5" Body="&lt;p&gt;The sphincter of the bladder is under voluntary control (that's what toilet training is about). That's why you can hold your urine even when the stretched bladder is sending messages to your brain that you really have to go. That's not to say there aren't involuntary effects on the bladder during orgasm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Orgasm is a separate entity. It is a complex neurological response with four stages. Orgasm is controlled by the autonomic nervous system and is a response that can be controlled as easily as pupillary dilation/contraction in response to light (that is, &lt;em&gt;not at all&lt;/em&gt;). However, there is some measure of voluntary control over the plateau phase of orgasm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a bit more detail,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;expulsion is a spinal cord reflex that occurs as the ejaculatory process reaches a ‘point of no return’. During expulsion, the smooth muscle fibers of the bladder neck contract to prevent the backward flow of semen into the bladder; the pelvic floor muscles, along with the bulbospongiosus and ischiocavernosus muscles, have primary roles in this function, and display stereotypical rhythmic contractions to propel semen distally throughout the bulbar and penile urethra. During this process, the external urinary sphincter is normally relaxed. The bladder neck and proximal portion of the urethra, which both contain abundant smooth muscle fibers, receive dual sympathetic and parasympathetic innervation. Besides the cholinergic and noradrenergic components, the principal mediators found in these nerve terminals are NPY, VIP, and NO. The external urethral sphincter and pelvic floor striated muscles are solely regulated by the somatic nervous system, but &lt;strong&gt;there is no definitive evidence that a voluntary control of the expulsion phase exists in humans&lt;/strong&gt;.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Human_sexual_response_cycle#Orgasmic_phase&quot; rel=&quot;nofollow&quot;&gt;Human sexual response cycle&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7356224&quot; rel=&quot;nofollow&quot;&gt;Physiology of male sexual function&lt;/a&gt;&lt;br&gt;&#xA;[1] &lt;a href=&quot;http://www.medscape.org/viewarticle/569396_2&quot; rel=&quot;nofollow&quot;&gt;Ejaculatory Disorders: Pathophysiology and Management: Physiology of Ejaculation&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-11-25T08:04:45.740" LastActivityDate="2014-11-25T08:04:45.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24303" PostTypeId="1" AcceptedAnswerId="24309" CreationDate="2014-11-25T08:02:31.397" Score="1" ViewCount="602" Body="&lt;p&gt;I'm not sure if this is physics, biology or chemistry related so I will start here.&#xA;I'm from a city (Baku, Azerbaijan) where crude oil is known to be extracted since ancient times. Oil is no longer being produced within city limits however soil is still heavily contaminated in some parts of the city. &#xA;Recently a major project has started to turn one of the most contaminated parts of the century old oilfield (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Black_City_(Baku)&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Black_City_(Baku)&lt;/a&gt; for more) into urban territory.&#xA;Developer promises that all contaminated soil is being removed and recultivated but I still have some doubts about it. I also don't trust official reports so would like to conduct my own investigation.&#xA;What is the health hazard of soil contamination? Are hydrocarbon vapors direct health hazard? Or may be it's radon that surfaces with oil? What and how to check? Would I be ok if I just check radioactive contamination with dosimeter/radiometer?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can ignore water contamination and direct contact with chemicals. I'm talking only about vapors during hot season.&lt;/p&gt;&#xA;" OwnerUserId="10339" LastEditorUserId="10339" LastEditDate="2014-11-25T08:19:45.393" LastActivityDate="2016-03-31T09:59:36.933" Title="Crude oil contamination hazard" Tags="&lt;health&gt;&lt;soil&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24304" PostTypeId="2" ParentId="24291" CreationDate="2014-11-25T08:17:40.513" Score="11" Body="&lt;p&gt;Hydrogen peroxide as a reactive oxygen species (ROS) is a highly problematic molecule for the processes inside of cells (it can spontaneously oxidize and damage cellular components). With &lt;a href=&quot;http://en.wikipedia.org/wiki/Catalase&quot;&gt;Catalase&lt;/a&gt;, organisms have a very effective enzyme which degrades the peroxide into water and oxygen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, although the molecule is problematic, it is still produced by organisms in traces. For its production by the NADPH oxidase, first NADPH is oxidized and &lt;a href=&quot;http://en.wikipedia.org/wiki/Superoxide&quot;&gt;superoxide&lt;/a&gt; is formed. The reaction looks like the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$NADPH + O_2 \rightarrow NADP^+ + H^+ + O_2^-$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a second step the &lt;a href=&quot;http://en.wikipedia.org/wiki/Superoxide_dismutase&quot;&gt;superoxide dismutase&lt;/a&gt; uses two molecules of superoxide and H&lt;sup&gt;+&lt;/sup&gt; to generate H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt;, the total reaction (which is divided into several steps) looks like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$2O_2^- + 2 H^+ \rightarrow H_2O_2 + O_2$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; is then usually degraded by the catalase (or used in immunological processes like the &lt;a href=&quot;http://en.wikipedia.org/wiki/Respiratory_burst&quot;&gt;respiratory burst&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="6" LastEditDate="2014-11-25T12:12:10.033" LastActivityDate="2014-11-25T12:12:10.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24305" PostTypeId="1" AcceptedAnswerId="24306" CreationDate="2014-11-25T08:45:08.857" Score="1" ViewCount="1632" Body="&lt;p&gt;I read on Wikipedia about this: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/King_cobra#Venom&quot; rel=&quot;nofollow&quot;&gt;King Cobra - Wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Thailand, a concoction of alcohol and the ground root of turmeric is ingested, which has been clinically shown to create a strong resilience against the venom of the king cobra, and other snakes with neurotoxic venom. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though, I have been in the village parts of India where King Cobra is frequently encountered, I have never heard of this knowledge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can somebody please explain the scientific basis of this statement and possible reasons for this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[PS]: Can somebody also please create a tag for &quot;Snakes&quot;?&lt;/p&gt;&#xA;" OwnerUserId="10337" LastEditorUserId="3624" LastEditDate="2014-11-25T14:42:36.747" LastActivityDate="2015-11-20T01:19:07.017" Title="Resilience to the neurotoxins of Indian King Cobra" Tags="&lt;physiology&gt;&lt;herpetology&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24306" PostTypeId="2" ParentId="24305" CreationDate="2014-11-25T09:51:02.743" Score="3" Body="&lt;p&gt;Well, turmerin, the compound in turmeric has been medically proven to help neutralize venom from King Cobras in snakes (&lt;a href=&quot;http://jcpronline.com/final/098457ck.pdf&quot; rel=&quot;nofollow&quot;&gt;reference1&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1440627&quot; rel=&quot;nofollow&quot;&gt;reference2&lt;/a&gt;). It has also been used in ayurveda for snake bite treatment (&lt;a href=&quot;http://www.ayurvedacollege.com/articles/students/turmeric&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) The alcohol I guess is just used to help ingest the turmeric and act as a pain reliever, though it strangely seems counter-productive since most snakebite help guides advice against the consumption of alcohol after getting bitten (&lt;a href=&quot;http://www.auroville.org/contents/1675&quot; rel=&quot;nofollow&quot;&gt;reference1&lt;/a&gt;, &lt;a href=&quot;http://arachnophiliac.info/burrow/snakebite_advice.htm&quot; rel=&quot;nofollow&quot;&gt;reference2&lt;/a&gt;) due to its blood thinning properties. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having said that, I guess personally, I would go for anti-venom rather than ingest turmeric. As a quick remedy until you get the anti-venom you should be able to depend on turmeric. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-11-25T09:51:02.743" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24307" PostTypeId="2" ParentId="8550" CreationDate="2014-11-25T10:25:58.247" Score="7" Body="&lt;p&gt;There are a number of things to clarify here; &lt;strong&gt;Fecundity&lt;/strong&gt; is the number of offspring that is produced by an individual, and this can be separated into &lt;strong&gt;potential fecundity&lt;/strong&gt; (maximum reproductive capacity) and &lt;strong&gt;realized fecundity&lt;/strong&gt; (number of offspring actually produced). &lt;strong&gt;Realized fecundity&lt;/strong&gt; is very similar to &lt;strong&gt;fertility&lt;/strong&gt;, which is defined as the number of viable offspring that are produced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Potential fecundity&lt;/strong&gt; can sometimes be a good proxy for future fertility, and this is especially true for species where all eggs are present after metamorphosis of the adult insect (&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.ento.47.091201.145300&quot;&gt;Awmack &amp;amp; Leather, 2002&lt;/a&gt;). However, in some species the formation of eggs is a continuous process in adult individuals, and this is relatively common in beetles. Therefore, the number of immature eggs might be a poor proxy of both potential and realized fecundity in these species (&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.ento.47.091201.145300&quot;&gt;Awmack &amp;amp; Leather, 2002&lt;/a&gt;), and this is more likely in relatively long-lived species that feed extensively as adults. In beetle species that do not feed as adults (often lacking functional mouthparts), immature eggs is probably a better approximation of potential fecundity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It should also be mentioned that the quality of host plants will often affect the maturation of eggs (&lt;a href=&quot;http://hilgardia.ucanr.edu/Abstract/?a=hilg.v29n10p411&quot;&gt;Sterns &amp;amp; Smith, 1960&lt;/a&gt;; &lt;a href=&quot;http://link.springer.com/article/10.1007/PL00008823&quot;&gt;Hopkins &amp;amp; Ekbom, 1999&lt;/a&gt;), and will therefore also determine to what extent the number of immature eggs is a good indication of potential fecundity. When feeding on poor quality hosts eggs may e.g. be reabsorbed by females to use for other purposes (see references in &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.ento.47.091201.145300&quot;&gt;Awmack &amp;amp; Leather, 2002&lt;/a&gt; &amp;amp; &lt;a href=&quot;http://link.springer.com/article/10.1007/PL00008823&quot;&gt;Hopkins &amp;amp; Ekbom, 1999&lt;/a&gt; for further information).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The review paper by &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.ento.47.091201.145300&quot;&gt;Awmack &amp;amp; Leather, 2002&lt;/a&gt; is very comprehensive, and contains a wealth of useful references on this topic.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2014-11-25T10:25:58.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24308" PostTypeId="2" ParentId="24305" CreationDate="2014-11-25T10:28:26.723" Score="2" Body="&lt;p&gt;As The Last Word said turmeric is a suggested medicine for cobra bites in India,also Bromelain found in Pineapple and Papain in Papaya fruit are also suggested medicines by folks. Although they are unaware of these chemicals they do use these fruits for venom treatment.&#xA;Also oral administration of garlic is said as a prophylactic tool against cobra venom.&#xA;Azadirachta indica(Neem) is also a prescribed medicine for Indian Cobra bites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.google.co.in/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=9&amp;amp;ved=0CE8QFjAI&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fpublication%2F51064057_Herbs_and_herbal_constituents_active_against_snake_bite%2Flinks%2F0912f50a48bd135b2c000000&amp;amp;ei=AlF0VImNFoaNuASv8YCICw&amp;amp;usg=AFQjCNE9BJ_rGjd3eG2TH-rSJh4-bIaq6w&amp;amp;sig2=1iP7DTk7Z34YZ4vWiQnvbg&amp;amp;bvm=bv.80185997,d.c2E&amp;amp;cad=rja&quot; rel=&quot;nofollow&quot;&gt;http://www.google.co.in/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=9&amp;amp;ved=0CE8QFjAI&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fpublication%2F51064057_Herbs_and_herbal_constituents_active_against_snake_bite%2Flinks%2F0912f50a48bd135b2c000000&amp;amp;ei=AlF0VImNFoaNuASv8YCICw&amp;amp;usg=AFQjCNE9BJ_rGjd3eG2TH-rSJh4-bIaq6w&amp;amp;sig2=1iP7DTk7Z34YZ4vWiQnvbg&amp;amp;bvm=bv.80185997,d.c2E&amp;amp;cad=rja&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cipadessa baccifera leaves have powerful anti venom properties, especially for the treatment of cobra poison.&#xA;  &lt;a href=&quot;http://indiabiodiversity.org/species/show/31204&quot; rel=&quot;nofollow&quot;&gt;http://indiabiodiversity.org/species/show/31204&lt;/a&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Aristolochia taxa have also been used as reptile repellents. Aristolochia  serpentaria (Virginia snakeroot) is thus named because the root was used to treat snakebite, as &quot;so offensive to these reptiles, that they not only avoid the places where it grows, but even flee from the traveler who carries a piece of it in his hand&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I couldn't find if there is any remedy for snake bites exist in Thailand as you said but i found this,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A hospital in Thailand hooked up with Mahasarakham University and brewed up a remedy. It’s a mix of betel nut, lime juice and the root of Trigonstemon reidiodes. &quot;&#xA;  &lt;a href=&quot;https://hughpaxton.wordpress.com/tag/kap-choeng-hospital-develops-herbal-cure-for-cobra-snake-bite/&quot; rel=&quot;nofollow&quot;&gt;https://hughpaxton.wordpress.com/tag/kap-choeng-hospital-develops-herbal-cure-for-cobra-snake-bite/&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Without references I would suggest a traditional snake bite remedy used in my place called &quot;Vishakallu&quot;[Venom Stone] with ingredients&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ocimum sanctum (Tulsi leaves),&#xA;Anisomeles malabarica(Perumthumba),&#xA;Sandal wood&lt;/p&gt;&#xA;&#xA;&lt;p&gt;these medicines are treated with a stone and this stone is used for healing and it is then placed in cow milk and stored in cow dung ash and can be reused 15+ times.&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="10294" LastEditDate="2014-12-02T13:42:59.307" LastActivityDate="2014-12-02T13:42:59.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24309" PostTypeId="2" ParentId="24303" CreationDate="2014-11-25T11:19:09.960" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Soil contamination or soil pollution is caused by the presence of xenobiotic (human-made) chemicals or other alteration in the natural soil environment. It is typically caused by industrial activity, agricultural chemicals, or improper disposal of waste. The most common chemicals involved are petroleum hydrocarbons, polynuclear aromatic hydrocarbons (such as naphthalene and benzo(a)pyrene), solvents, pesticides, lead, and other heavy metals. Contamination is correlated with the degree of industrialization and intensity of chemical usage.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Soil_contamination&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Soil_contamination&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The acute health effects of hydrocarbon mixtures are generally associated with exposure concentrations at thousands of ppm. However, the exposure concentration and exposure duration leading to the onset of acute health effects varies between individual hydrocarbons, and this may influence the effects of exposure to mixtures.Health effects associated with a single exposure to hydrocarbons are asphyxiation, narcosis (ie depression of the central nervous system; anaesthesia), cardiac arrest and aspiration. Of these, the first two are probably the most significant in the offshore context.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.hse.gov.uk/offshore/notices/sn_04_04.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.hse.gov.uk/offshore/notices/sn_04_04.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In relation to the assessment of vapour risk,petroleum hydrocarbons and chlorinated hydrocarbons differ in their potential forvapour intrusion (VI) risks, primarily because petroleum hydrocarbons (PHCs) readily&#xA;  biodegrade in the subsurface when sufficient oxygen is available(USEPA 2011,2012a). Hence while a number of aspects of this guidance are general and can beapplied to a range of volatile compounds, the guidance is intended to specificallyaddress PVI and should not be applied to sites contaminated with other compounds&#xA;  including chlorinated hydrocarbons and landfill gas. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://clu-in.org/download/issues/vi/CRCCARETechreport23-PetroleumhydrocarbonvapourintrusionassessmentAustralianguidance2.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://clu-in.org/download/issues/vi/CRCCARETechreport23-PetroleumhydrocarbonvapourintrusionassessmentAustralianguidance2.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Organic compounds can be a major pollution problem in groundwater. Their presence in water can create a hazard to public health and the environment. This page will focus on the BTEX's which makes up one of the main groups of soluble organic compounds that find their way into our soil and groundwater. One of the most common sources for BTEX-contamination of soil and groundwater are spills involving the release of petroleum products such as gasoline, diesel fuel and lubricating and heating oil from leaking oil tanks. Because of their polarity and very soluble characteristics, the organic chemicals (BTEX's) of petroleum products will be able to enter the soil and groundwater systems and cause serious pollution problems.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.webapps.cee.vt.edu/ewr/environmental/teach/gwprimer/btex/btex.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.webapps.cee.vt.edu/ewr/environmental/teach/gwprimer/btex/btex.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jp7Tf.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Petroleum vapours at percentage concentrations are flammable, potentially explosive&#xA;  and acutely toxic; lower explosive limits (LEL) for many volatile hydrocarbons are in the&#xA;  low percentage range. Petroleum vapours are denser than air. Some components of&#xA;  petroleum vapour are also chronically toxic at trace concentrations and as such are also&#xA;  considered under the heading VOCs [volatile organic compounds ].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.epa.nsw.gov.au/resources/clm/120932GroundGas.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.epa.nsw.gov.au/resources/clm/120932GroundGas.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This document contains site investigation details which describes how to find traces of compounds in soil and water.&#xA;. &lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="3624" LastEditDate="2014-12-01T10:44:26.867" LastActivityDate="2014-12-01T10:44:26.867" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24312" PostTypeId="1" AcceptedAnswerId="24313" CreationDate="2014-11-25T18:31:45.487" Score="1" ViewCount="6182" Body="&lt;p&gt;The chapter by Douglas Futuyma in 'Evolution' (Losos et al 2013, Princeton) states that natural selection can occur at the species level. Futuyma states that if natural selection occurs at the species level it does not occur at the individual level: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Neither gene selection nor species selection has molded the advantageous characteristics of individual organisms; rather, they have affected properties at the gene level or at the species level. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But how does natural selection occuring at the species level not affect individuals? Surely any selective advantage of a particular species must occur among particular individuals of that species. For example, if Species A is selected because it is browner than Species B, this will be because individuals of Species A are browner than individuals of Species B. &lt;/p&gt;&#xA;" OwnerUserId="1216" LastEditorUserId="948" LastEditDate="2014-11-25T22:44:45.580" LastActivityDate="2017-11-02T17:49:11.597" Title="How can natural selection occur at species level whilst not occuring at the individual level?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24313" PostTypeId="2" ParentId="24312" CreationDate="2014-11-25T19:18:12.073" Score="2" Body="&lt;p&gt;I think you have misunderstood the passage. Here is a larger section (found at &lt;a href=&quot;http://books.google.se/books?id=_XitAAAAQBAJ&amp;amp;pg=PA190#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;google books&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Natural selection can also occur at the level of species, for certain characteristics enhance the rate of origin of new species or diminish the likelihood of species extinction. For instance, the number of species in lineages of herbivorous insects has generally increased faster than in closely related lineages that have other feeding habits. Neither gene selection nor species selection has molded the advantageous characteristics of individual organisms; rather, they have affected properties at the gene level or at the species level. But individual selection, selection among individual organisms within populations, is at the center of evolutionary theory. It is at this level that selection explains most of the adaptive features of organisms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Going through this part-by-part; the first two sentences state that lineage/species selection can occur, in the sense that species traits can enhance the speciation rate of a lineage or decrease their risk of extinction, relative to other lineages (e.g. in herbivorous insects). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;He is then saying that the traits that are the target of this selection are not traits of individuals but traits/properties of the species/lineage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example might help to explain the point. For instance, it has been argued that pelagic larvae in sessile ocean species will lead to higher dispersal rates, which means that species can colonize new environments, and this can lead to speciation through adaptive radiation (&lt;a href=&quot;http://www.jstor.org/stable/10.1086/507994&quot; rel=&quot;nofollow&quot; title=&quot;Jablonski &amp;amp; Hunt. 2006. Larval Ecology, Geographic Range, and Species Survivorship in Cretaceous Mollusks: Organismic versus Species-Level Explanations. American Naturalist 168(4)&quot;&gt;Jablonski &amp;amp; Hunt, 2006)&lt;/a&gt;. A larger range will also correspond to lower extinction rates (everything else equal). The trait might also be fixed within a lineage (so there is no variance at the individual level within-species), and if so, this lineage as a whole could have higher speciation rates and lower extinction rates compared to a sister lineage that lacks pelagic larvae. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The individuals within species will naturally have the underlying traits (pelagic larvae), but the traits that are selected at the lineage level (extinction risk &amp;amp; speciation rate) are not properties of individuals but are traits of the lineage/species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;He then ends by continuing with &quot;normal&quot; individual selection, and states that processes at this level is responsible for most adaptive features of organisms. It should also be noted that lineage selection is still considered controversial, and it has been shown that it is inherently much weaker than selection at the individual level. Personally, I think there are some very good examples of how species/lineage selection can function, but to what extent it is an important process for species and organisms is an open empirical question. If you are interested to look further, &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.39.110707.173510&quot; rel=&quot;nofollow&quot; title=&quot;Jablonski D (2008) Species Selection: Theory and Data. Annu Rev Ecol Evol S 39: 501–524.&quot;&gt;Jablonski (2008)&lt;/a&gt; and &lt;a href=&quot;https://global.oup.com/academic/product/evolution-and-the-levels-of-selection-9780199267972?cc=se&amp;amp;lang=en&amp;amp;&quot; rel=&quot;nofollow&quot; title=&quot;Okasha. 2007. Evolution and the Levels of Selection. Oxford university press&quot;&gt;Okasha (2007)&lt;/a&gt; are two good starting points.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-11-26T08:47:34.673" LastActivityDate="2014-11-26T08:47:34.673" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24314" PostTypeId="2" ParentId="24312" CreationDate="2014-11-25T19:18:27.640" Score="1" Body="&lt;p&gt;I think there is some misunderstanding there, natural selection does act on an individual and can be determined by its genes (assuming there is genetic variance underlying the variance in trait). Those with more favourable genes will have more favourable phenotypes and thus be more likely to survive/reproduce. However, (genetic) evolution does not occur within an individual, evolution occurs at the population level as the frequencies of existing and new mutations changes over time or space.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following from your example: Two morphs of a species exist, brown and white (like the &lt;a href=&quot;http://en.wikipedia.org/wiki/Peppered_moth_evolution&quot; rel=&quot;nofollow&quot;&gt;classic peppered moth&lt;/a&gt;), which is genetically determined, and one has a selective advantage - let's say brown. Thus all individuals of the brown morph are more likely to survive and reproduce. Over time the genes causing the brown phenotype will increase in frequency in the population and frequency of brown (white) moths will have increased (decreased).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect it would be helpful if you included more of the text preceding the statement. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Edit: having seen @fileunderwaters answer, which arrived seconds before I posted mine, I see that I was right, more of the text was useful :)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So going back to the moths, an individual moth would not be able to change it's trait in response to selection.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-11-25T19:26:34.083" LastActivityDate="2014-11-25T19:26:34.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24315" PostTypeId="2" ParentId="24263" CreationDate="2014-11-25T21:21:22.797" Score="1" Body="&lt;p&gt;The answer can be found in &lt;a href=&quot;http://pubchem.ncbi.nlm.nih.gov/compound/norepinephrine#section=DrugBank-Interactions&quot; rel=&quot;nofollow noreferrer&quot;&gt;PubChem&lt;/a&gt;, which is linked in the comment by anongoodnurse. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would not say that &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Norepinephrine is beta2 adrenomimetic&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;because norepinephrine has many roles such as neurotransmitter. &#xA;I would just say that &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Norepinephrine is alpha, beta adrenoagonist.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;More pieces of information about it from PubChem:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6ELA7.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-11-26T17:43:01.753" LastActivityDate="2014-11-26T17:43:01.753" CommentCount="0" CommunityOwnedDate="2014-11-25T21:21:22.797" ContentLicense="CC BY-SA 3.0" />
  <row Id="24316" PostTypeId="2" ParentId="24264" CreationDate="2014-11-25T21:26:25.293" Score="0" Body="&lt;p&gt;Anongoodnurse provide an excellent comment in other discussion about how to search PubChem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ephedrine is not alpha2 mimetic. &#xA;Pseudoephedrine is alpha2 mimetic, &lt;a href=&quot;http://pubchem.ncbi.nlm.nih.gov/compound/pseudoephedrine#section=DrugBank-Interactions&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/R928l.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-11-25T21:26:25.293" CommentCount="0" CommunityOwnedDate="2014-11-25T21:26:25.293" ContentLicense="CC BY-SA 3.0" />
  <row Id="24320" PostTypeId="1" AcceptedAnswerId="24352" CreationDate="2014-11-26T03:11:00.527" Score="5" ViewCount="3238" Body="&lt;p&gt;How do gory images lead to nausea?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yesterday my friend visited shock sites (a website). He said that he got nauseous sensation within seconds after viewing the gory images. However, I don't understand how seeing such sights can lead to nausea? Eyes are present at the top of the head and the digestive tract is present below the mouth. They aren't physically connected.&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="6289" LastEditDate="2014-11-26T16:59:07.303" LastActivityDate="2015-08-24T18:14:30.690" Title="How do gory images lead to nausea?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24321" PostTypeId="1" AcceptedAnswerId="24322" CreationDate="2014-11-26T03:43:16.963" Score="1" ViewCount="79" Body="&lt;p&gt;Which type of RNA molecule is coded for in intergenic regions? I think it must be a non-coding RNA but I'm unsure which type.&lt;/p&gt;&#xA;" OwnerUserId="9063" LastEditorUserId="3340" LastEditDate="2014-11-26T05:24:16.170" LastActivityDate="2014-11-26T05:25:00.310" Title="RNAs arising from intergenic regions" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;genomics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24322" PostTypeId="2" ParentId="24321" CreationDate="2014-11-26T04:37:11.110" Score="2" Body="&lt;p&gt;The term intergenic is more or less obsolete now. In fact it is ironical to say that a gene, which can give rise to a functional protein or an RNA, is expressed from an intergenic region. However the usage continues for both lncRNAs and miRNAs (other major type of ncRNA in metazoans&lt;sup&gt;&lt;strong&gt;1&lt;/strong&gt;&lt;/sup&gt; - piRNAs have different classification). lncRNAs are vaguely classified as sense-overlapping (expressed in the same direction as a known gene but not completely overlapping), antisense (expressed from the antisense strand of a known gene) or intergenic; similarly miRNAs are classified as intronic or intergenic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not necessary that the intergenic RNA has to be strictly non-coding, it can be coding as well; a novel protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In all these cases the term intergenic means - not overlapping with a &lt;strong&gt;known&lt;/strong&gt; gene. Better nomenclature is necessary as the field of genomics makes more progress. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this &lt;a href=&quot;http://genome.cshlp.org/content/17/6/669.full&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;1&lt;/strong&gt;&lt;/sup&gt; Most metazoans.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-11-26T05:25:00.310" LastActivityDate="2014-11-26T05:25:00.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24324" PostTypeId="2" ParentId="15346" CreationDate="2014-11-26T08:03:47.137" Score="1" Body="&lt;p&gt;Nepeta cataria(Catnip, Catmint, Catnep) is a plant belongs to the family Lamiaceae.It is a  herb that has been recognized for its medicinal properties for many centuries. Over time it has been used in remedies to cure internal cancer, smallpox and scarlet fever.Also it was believed that a dense growth bordering fields helped to protect crops because of its ability to repel rats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Major Active Constituents of catnip includes a and ß nepetalactone  citronella , a and ß citral , limonene , geraniol , thymol , and carvacrol  epideoxyloganic acid and 7-deoxyloganic acid&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nepeta cataria has a carminative, anti-spasmodic, astringent and anti-flatulent effect on the gastrointestinal system, particularly on the stomach . It is also a diaphoretic and antipyretic in times of fever . Nepeta cataria is similarly recognized as a tonic, mild nervine, and sedative, with a slightly emmenagogue action . With respects to cats, Nepeta cataria produces an aphrodisiac effect. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://scu.edu.au/scps/index.php/125/&quot; rel=&quot;nofollow&quot;&gt;http://scu.edu.au/scps/index.php/125/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A research paper published in 1994 states that, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Catnip was  the most promising candidate lures tested. The 'catnip-response' is &#xA;  inherited as an autosomal dominant (Todd 1962). In trials, behavioural observations showed &#xA;  that 50% of the subjects (including all four domestic cats and 8 of 20 feral cats) showed the full catnip response (B. K. Clapperton, unpublished data). This includes sniffing, licking, rubbing and head-over rolling (Tucker and Tucker 1988). Nine of the remaining 12 feral cats approached and sniffed at the catnip samples. This suggests that, although not all cats are genetically determined to respond to catnip , these odours may act as more general attractants.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.southwestnrm.org.au/sites/default/files/uploads/ihub/clapperton-bk-et-al-1994-development-and-testing-attractants-feral-cats-felis-catus.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.southwestnrm.org.au/sites/default/files/uploads/ihub/clapperton-bk-et-al-1994-development-and-testing-attractants-feral-cats-felis-catus.pdf&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When cats inhales nepetalactone it stimulates the olfactory bulb, the part of the brain that processes odors. The olfactory bulb then interacts with the amygdala, the brain region associated with emotion and decision-making, and hypothalamus, which controls a variety of bodily functions. From the hypothalamus, nepetalactone stimulates a sexual response in cats that are genetically predisposed to sensitivity to catnip. (About 20 to 30 percent of cats don't seem to react to the plant.)this is why mostly adult cats shows significant addiction to catnip.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.compoundchem.com/2014/06/08/catnip/&quot; rel=&quot;nofollow&quot;&gt;http://www.compoundchem.com/2014/06/08/catnip/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The catnip stimulates an Innate Releasing Mechanism(IRM) in domestic cats that elicits a predictably playful behaviour pattern apparently independent of experience and learning(Ewer,1973 and Leyhausen,1975) ,trans-nepetalactone is reported to produce behavioral respondse in cats.It has been verified by Todd in 1963 that capnip is mediated by Olfactory and not gustatory stimuli.Catnip sensitivity has been related to a dominant autosomal geneand to the estrous cycle by Todd.The reports shows catnip elicits behavioral respondses in domestic and wild cats, but these responses are not shown by female sex.In addition, it has been suggested that catnip mimics a pheromone found in cat urine, however evidence supporting this theory is scant.(Todd 1962)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00987747#page-1&quot; rel=&quot;nofollow&quot;&gt;http://link.springer.com/article/10.1007%2FBF00987747#page-1&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="10294" LastEditDate="2014-12-01T10:58:15.033" LastActivityDate="2014-12-01T10:58:15.033" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24326" PostTypeId="1" CreationDate="2014-11-26T09:54:54.520" Score="0" ViewCount="68" Body="&lt;p&gt;I'd like to know which chemical compounds form hyphae in Actinobacteria. Is it the same structure of the cell wall?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you&lt;/p&gt;&#xA;" OwnerUserId="5686" LastEditorUserId="20392" LastEditDate="2016-12-06T07:57:11.287" LastActivityDate="2016-12-06T07:57:11.287" Title="What's the composition of Actinobacteria's hyphae?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24327" PostTypeId="1" CreationDate="2014-11-26T11:07:05.260" Score="1" ViewCount="21" Body="&lt;p&gt;Rhizobium infection can be triggered at root hairs of legumes, creating infection threads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can these infections threads be colonized by more than one type of Rhizobium (e.g. Fixing and non-fixing)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about when the infection is inside the plant cells? Can symbiosomes be co-inhabited by different bacteria?&lt;/p&gt;&#xA;" OwnerUserId="659" LastActivityDate="2014-11-26T11:07:05.260" Title="Can different strains of Rhizobium share an infection thread or symbiosome?" Tags="&lt;bacteriology&gt;&lt;plant-physiology&gt;&lt;ecology&gt;&lt;infection&gt;&lt;agriculture&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24329" PostTypeId="1" AcceptedAnswerId="24335" CreationDate="2014-11-26T13:29:51.043" Score="0" ViewCount="366" Body="&lt;p&gt;Salbutamol is a very commonly used direct-acting β2-agonist. &#xA;This suggests me that it is sympatholytic. &#xA;However, it has sympathomimetic pathways, see &lt;a href=&quot;http://pubchem.ncbi.nlm.nih.gov/compound/salbutamol#section=Biological-Test-Results&quot; rel=&quot;nofollow&quot;&gt;PubChem&lt;/a&gt; for Sympathomimetic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am trying to think the group of Salbutamol. &#xA;Sympathomimetic or sympatholytic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can you classify Salbutamol into a group?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2021-04-28T23:05:03.267" Title="Salbutamol's Pathways of Interaction and Classification" Tags="&lt;pharmacology&gt;&lt;autonomic-nervous-system&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24330" PostTypeId="2" ParentId="20425" CreationDate="2014-11-26T14:12:08.337" Score="2" Body="&lt;p&gt;Lets summarize the comments into a real answer: When the only chemical changed in your reaction is the DNA, which came from a fresh Phenol/Chloroform preparation, I would suspect it. From there, we have a few possibilities, what could have gone wrong.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The most likely cause of an enzymatic reaction not working with&#xA;Phenol/Chloroform prepared DNA are left-overs (or carry-over) of the&#xA;organic solvents from the reaction. The inhibit (especially Phenol)&#xA;enzymatic reactions very efficiently. It would help to do another&#xA;round of DNA precipitation.&lt;/li&gt;&#xA;&lt;li&gt;It is possible that your DNA didn't got dissolved after the drying&#xA;step in the precipitation. Depending on the conditions, DNA can form&#xA;a pellet which is hardly to see and even harder to dissolve. So your&#xA;DNA concentration would be too low to get amplification. To prevent&#xA;this measure the concentration of your DNA.&lt;/li&gt;&#xA;&lt;li&gt;It is possible that the water you used is contanminated with DNAses&#xA;(although it shouldn't) and your DNA got degraded by them. Here only&#xA;new aliquots will help.&lt;/li&gt;&#xA;&lt;li&gt;Depending on the size of your amplicon, it is possible that overly&#xA;harsh condition during the preparation led to the shearing of the&#xA;DNA leaving not enough intact DNA to get a proper amplification. If&#xA;this is the case, be more gentle with the extraction.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Additionally your primers can be a problem. It would be good to keep the 100x stock solutions permanently at -20°C and prepare 10x working solutions. These can undergo freezing and thawing (which will degrade them over time) but they can be replaced easily.&#xA;I would also try the new DNA prep (if possible side by side with one that is working) with new primers to test if they are the problem.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-11-26T14:12:08.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24333" PostTypeId="1" CreationDate="2014-11-26T15:10:37.527" Score="0" ViewCount="85" Body="&lt;p&gt;I was having a discussion with a colleague and this question came up...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is commonplace in molecular genetics studies to only genotype one of a pair of monozygotic twins (and then implicitly impute the other's genotype by assuming the pair is genetically identical). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is this: assuming a quantitative trait study, what should the phenotype be? Should it be the phenotype of the genotyped twin OR should it be an average of the two twins' phenotypes? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I genotype Twin A &lt;/li&gt;&#xA;&lt;li&gt;Twin A has a phenotype score of 4 &lt;/li&gt;&#xA;&lt;li&gt;Twin B has a phenotype score of 6&lt;/li&gt;&#xA;&lt;li&gt;Should Twin A's phenotype for the genotype-phenotype test be 4 (the individual's phenotype) or 5 (the average phenotype of the genome)? &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Answers from experience and from theory welcome!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="10347" LastEditorUserId="10347" LastEditDate="2014-11-27T09:28:15.793" LastActivityDate="2015-02-03T07:41:26.387" Title="Phenotype choice for one of a MZ twin pair in a genetic association study" Tags="&lt;genetics&gt;&lt;twins&gt;&lt;gwas&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24334" PostTypeId="1" CreationDate="2014-11-26T16:56:49.310" Score="2" ViewCount="4268" Body="&lt;p&gt;Beginning with 600 template DNA molecules after 25 cycles of PCR how many amplicons will be produced?&lt;/p&gt;&#xA;" OwnerUserId="10350" LastActivityDate="2014-11-26T21:36:26.807" Title="PCR processes number of amplicons produced" Tags="&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-11-27T05:16:34.553" ContentLicense="CC BY-SA 3.0" />
  <row Id="24335" PostTypeId="2" ParentId="24329" CreationDate="2014-11-26T17:02:48.120" Score="3" Body="&lt;p&gt;An &lt;em&gt;agonist&lt;/em&gt; works with the receptor: a substance that initiates a physiological response when combined with a receptor; in the case of salbutamol (or albutarol in the US) they activate the beta-2 receptor on the muscles surrounding the airways. They are also known as sympathomimetics, as they imitate β2 adrenergics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;em&gt;blocker&lt;/em&gt; (or antagonist) is one that that blocks the action of endogenous catecholamines; for that reason, they are also called sympatholytic: antagonistic to or inhibiting the transmission of nerve impulses in the sympathetic nervous system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears you have experienced a simple confusion in terms. Salbutamol/albuterol is definitely a sympathomimetic, used extensively on asthma and COPD.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://pharmrev.aspetjournals.org/content/64/3/450.full&quot; rel=&quot;nofollow&quot;&gt;Pharmacology and Therapeutics of Bronchodilators&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-11-26T17:02:48.120" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24336" PostTypeId="1" CreationDate="2014-11-26T17:21:31.877" Score="-2" ViewCount="8239" Body="&lt;p&gt;Bigger animals, like Elephants, or Dinosaurs for example, are in need for more oxygen than the amount of oxygen that small animals need? (humans, dogs, cats, etc)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="10351" LastActivityDate="2016-12-19T03:09:35.607" Title="Bigger animals needs bigger amount of oxygen?" Tags="&lt;breathing&gt;&lt;growth&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ClosedDate="2016-12-19T04:45:11.313" ContentLicense="CC BY-SA 3.0" />
  <row Id="24338" PostTypeId="2" ParentId="24336" CreationDate="2014-11-26T17:50:07.237" Score="3" Body="&lt;p&gt;I'm not an expert but I think it's pretty obvious.. Bigger animals do require more energy and thus more oxygen for cellular respiration. They also have bigger lungs, although the rythm of the breathing is slower.&lt;/p&gt;&#xA;" OwnerUserId="5686" LastActivityDate="2014-11-26T17:50:07.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24339" PostTypeId="1" CreationDate="2014-11-26T19:16:18.000" Score="9" ViewCount="26381" Body="&lt;p&gt;I am reading about dopamine, and I have realized that dopaminergic neurons can fire phasically or tonically. What is the difference between these two modes of firing?&lt;/p&gt;&#xA;" OwnerUserId="10353" LastActivityDate="2018-04-11T09:53:54.547" Title="What is the difference between tonic and phasic firing?" Tags="&lt;dopamine&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24341" PostTypeId="2" ParentId="24334" CreationDate="2014-11-26T21:36:26.807" Score="2" Body="&lt;p&gt;This is a theoretical consideration, as PCR depends on a number of factors as optimal priming, salt concentration, enzyme activity, available dNTPs and so on. Ideally the number of DNA molecules is doubled with every cycle. So the general formula to calculate the number is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$ n \times 2^{cycles} = $ number of DNA molecules at the end of the PCR&lt;/p&gt;&#xA;&#xA;&lt;p&gt;n is the number of molecules set into the reaction&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for our 600 DNA molecules with 25 cycles this would give:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$600 \times 2^{25} = 20.132.659.200$ or roughly 20.1 billion molecules of DNA.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-11-26T21:36:26.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24342" PostTypeId="1" CreationDate="2014-11-26T23:51:21.573" Score="4" ViewCount="242" Body="&lt;p&gt;I am reading &lt;a href=&quot;http://www.openanesthesia.org/ABA:Heart_transplant_-_autonomic_effect&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; and &lt;a href=&quot;http://web.squ.edu.om/med-Lib/MED_CD/E_CDs/anesthesia/site/content/v04/040240r00.HTM&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; where I am considering this sentence&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[N]o baseline parasympathetic innervation [in transplanted heart].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Does this sentence imply that the heart work then in full sympaticus all the time?&lt;/strong&gt; &#xA;Probably, through altered systems, but still. &#xA;At least the regulation of blood pressure strongly supports this, &lt;a href=&quot;http://www.cts.usc.edu/ht-pg-medications.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for the generic medication plan.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Does transplanted heart have full sympaticus without medication?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Notification of terminology.&lt;/em&gt; I tend to use overloading in writing. &#xA;For instance, I can say that there is sympathetic and parasympathetic supply to the heart i.e. innervations of S and PS through endocrine system to the heart. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not yet completely sure how the recipient's body can target the alpha and beta receptors of donors in heart. &lt;strong&gt;Are there any variations of these receptors?&lt;/strong&gt; If yes, then the effect of sympathetic stimulation would also differ from the original stimulation. &#xA;So full sympaticus (or original) may not be present. &#xA;The new stimulation may lead to greater or smaller activation of sympaticus.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2015-01-08T09:52:17.487" LastActivityDate="2015-01-08T10:32:08.167" Title="Does transplanted heart have full sympaticus without medication?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24343" PostTypeId="2" ParentId="24320" CreationDate="2014-11-27T00:25:20.087" Score="-1" Body="&lt;p&gt;The connection is almost certainly psychological.  For me, I can watch Grey's Anatomy, Spartacus, or any number of bloody shows while eating, but while researching microsurgery I came across an image of a hand cut in half and it bothered me for an entire day.  Therefore, for me at least (and likely others) nausea from gore is context dependent and therefore likely psychological.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then again, there may be some biological basis.  From &lt;a href=&quot;https://en.wikipedia.org/wiki/Disgust#Neural_basis&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Disgust#Neural_basis&lt;/a&gt; :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Functional MRI experiments have revealed that the anterior insula in the brain is particularly active when experiencing disgust, when being exposed to offensive tastes, and when viewing facial expressions of disgust.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That Wikipedia article links to this Letter to Nature: &lt;a href=&quot;http://www.nature.com/nature/journal/v389/n6650/full/389495a0.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nature/journal/v389/n6650/full/389495a0.html&lt;/a&gt; which provides more detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, the part of the brain that actually controls vomiting is called the Area postrema.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So...  in short, my answer is &quot;The &lt;a href=&quot;https://en.wikipedia.org/wiki/Insular_cortex&quot; rel=&quot;nofollow&quot;&gt;insular cortex&lt;/a&gt; of the brain is responsible, though there is a large psychological component.&quot;&lt;/p&gt;&#xA;" OwnerUserId="10343" LastEditorUserId="10343" LastEditDate="2014-11-27T06:05:33.430" LastActivityDate="2014-11-27T06:05:33.430" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24346" PostTypeId="1" CreationDate="2014-11-27T01:38:42.627" Score="1" ViewCount="67" Body="&lt;p&gt;In A level Bio today we talked about abcesic acid as a stress hormone, and its ability to reduce osmotic potential around guard cells to close stomata.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, is abscesic acid in sorghum bicolor leaves responsible for its ability to roll up in lack of water?&lt;/p&gt;&#xA;" OwnerUserId="10357" LastEditorUserId="3624" LastEditDate="2014-11-27T12:08:39.440" LastActivityDate="2014-11-27T12:08:39.440" Title="Why do Sorghum Bicolor leaves roll up?" Tags="&lt;botany&gt;&lt;homework&gt;&lt;plant-physiology&gt;&lt;endocrinology&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24349" PostTypeId="1" CreationDate="2014-11-27T04:03:45.577" Score="4" ViewCount="1700" Body="&lt;p&gt;Here are two images from Google. Afferent neurons receive input and send it to the central nervous system. Input is received by the neuron's dendritic end and send away centrally via axon terminals that are sheathed with Schwann cells. Axon terminals synapse to motor neurons (muscles and glands). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is it possible that Merkel cells, which supposed to be a sensory cell, synapse with an axon, and not with a dendritic end? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HHWMu.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eBPRW.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="9943" LastEditDate="2015-07-31T14:20:27.493" LastActivityDate="2017-11-21T10:18:25.747" Title="Why are Merkel cells innervated by an axon, and not a dendrite?" Tags="&lt;neurophysiology&gt;&lt;skin&gt;&lt;histology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24350" PostTypeId="1" CreationDate="2014-11-27T04:12:48.803" Score="0" ViewCount="38" Body="&lt;p&gt;Are there certain biochemical processes that would normally cause a cell to self-destruct but if the cell being tested has apoptosis mechanisms that have malfunctioned or been 'turned off' the cell will not 'malfunction' because of the induced process ? Are there such biochemical processes that could indirectly indicate which cells have no functioning apoptosis mechanisms? If so would this be a possible test for cancerous cells?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastActivityDate="2015-01-14T13:22:12.133" Title="About artificially induced processes that would normally cause a cell to self-destruct" Tags="&lt;cancer&gt;&lt;apoptosis&gt;&lt;treatment&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24351" PostTypeId="1" AcceptedAnswerId="24358" CreationDate="2014-11-27T06:35:05.693" Score="2" ViewCount="77" Body="&lt;p&gt;If all the cells in a cancerous tumour had their apoptosis mechanisms 'turned back on' or reactivated or repaired by some 'yet to be discovered' process would this cause the tumour to 'self destruct' or be destroyed? Are there known processes that can repair or reactivate the apoptosis mechanisms in a cell?&lt;/p&gt;&#xA;" OwnerUserId="6195" LastEditorUserId="948" LastEditDate="2014-11-28T21:23:17.880" LastActivityDate="2014-11-29T13:12:14.270" Title="Regarding the apoptosis mechanisms in cells and cancer" Tags="&lt;cancer&gt;&lt;apoptosis&gt;&lt;treatment&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24352" PostTypeId="2" ParentId="24320" CreationDate="2014-11-27T08:25:49.760" Score="4" Body="&lt;p&gt;The connection between eyes and food pipe had to do nothing with the motion sickness because the visual inputs and outputs to these sensory information are processed in the brain itself, So there is not need for eyes and food pipe to be connected together in order to cause nausea.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Vasovagal response or vasovagal response or vasovagal attack (also called neurocardiogenic syncope) is a malaise mediated by the vagus nerve. When it leads to syncope or &quot;fainting&quot;, it is called a vasovagal syncope, which is the most common type of fainting. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(from &lt;a href=&quot;http://en.wikipedia.org/wiki/Vasovagal_response&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Vasovagal_response&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This case is most commonly seen in adults and adolescents. There are several syndromes which comes under the vasovagal syncope which consists of symptoms like loss of consiusness,lightheadness,nausea,sweating,tinnitus,confusion,altered heart rate,fuzzy thoughts,cloud like spots in vision etc.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Vasovagal syncope occurs in response to a trigger, with a corresponding malfunction in the parts of the nervous system that regulate heart rate and blood pressure. When heart rate slows, blood pressure drops, and the resulting lack of blood to the brain causes fainting and confusion.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(from &lt;a href=&quot;http://en.wikipedia.org/wiki/Vasovagal_response&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Vasovagal_response&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several pshychiatric disorders can cause vasovagal response like,&#xA;&lt;strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Agoraphobia&lt;/li&gt;&#xA;&lt;li&gt;Obsessive–compulsive disorder&lt;/li&gt;&#xA;&lt;li&gt;Social anxiety disorder&lt;/li&gt;&#xA;&lt;li&gt;Blood-injury phobia&lt;/li&gt;&#xA;&lt;li&gt;Hemophobia&lt;/li&gt;&#xA;&lt;li&gt;Traumatophobia&lt;/li&gt;&#xA;&lt;li&gt;Trypanophobia&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nwocc.com/Pt%20Education/neuro_syncope.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.nwocc.com/Pt%20Education/neuro_syncope.pdf&lt;/a&gt; &lt;br&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Vasovagal_response&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Vasovagal_response&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When it comes to seeing red, the faint feelings could be tied to a phenomenon called blood-injury phobia. According to WebMD, this condition evolved as a way for humans to cope with threats:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&quot;The idea is that back in time, when someone was coming at someone else with a sharp stick or rock, a kind of genetic variation allowed certain people to faint in response,&quot; explains Tyler C. Ralston, PsyD, a clinical psychologist in Honolulu,&lt;strong&gt; who treats people with blood-injury phobias. Warriors who fainted looked dead and were passed over during battle. The blood pressure drop also might have helped those who were wounded avoid bleeding to death. Survivors then passed on the &quot;fainting&quot; gene.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(from: &lt;a href=&quot;http://www.popsugar.com/fitness/Why-Sight-Blood-Makes-You-Feel-Faint-3061135&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.popsugar.com/fitness/Why-Sight-Blood-Makes-You-Feel-Faint-3061135&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Overcoming Obstacles in CBT&quot; written by Yvonne Tone and Michael McDonough states a condition about&lt;strong&gt; a patient having similar psychological problem described in the question. Here the patient's panic is associated with &quot;gory images&quot; of injury or illness, and his responses included intense nausea, pale skin, sweat and sometime fainting. He also reports avoiding gory scenes on TV/filim and medical programmes. The problem is identified as co-morbid panic/agoraphobia and blood injury phobia. &lt;/strong&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Iv6RO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;a href=&quot;http://books.google.co.in/books?id=1uIYqkKgKRYC&amp;amp;pg=PA44&amp;amp;dq=nausea+and+gory+images&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=qLZ2VJPMJ420uAS8qoHIBA&amp;amp;ved=0CB0Q6AEwAA#v=onepage&amp;amp;q=nausea%20and%20gory%20images&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://books.google.co.in/books?id=1uIYqkKgKRYC&amp;amp;pg=PA44&amp;amp;dq=nausea+and+gory+images&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=qLZ2VJPMJ420uAS8qoHIBA&amp;amp;ved=0CB0Q6AEwAA#v=onepage&amp;amp;q=nausea%20and%20gory%20images&amp;amp;f=false&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="3624" LastEditDate="2014-12-01T10:22:30.857" LastActivityDate="2014-12-01T10:22:30.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24353" PostTypeId="2" ParentId="17265" CreationDate="2014-11-27T08:34:47.410" Score="8" Body="&lt;p&gt;There was a paper that attempted to assess this published in 2010&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/107/52/22454.full&quot;&gt;There’s plenty of time for evolution&lt;/a&gt; - Herbert S. Wilf and Warren J. Ewens&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also a layman's explanation of this &lt;a href=&quot;http://whyevolutionistrue.wordpress.com/2010/12/29/theres-plenty-of-time-for-evolution/&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically when we account for the fact that genes evolve in parallel under a number of simultaneous trials, it appears that there is indeed enough time for species to have evolved as far as they have.&lt;/p&gt;&#xA;" OwnerUserId="8112" LastActivityDate="2014-11-27T08:34:47.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24357" PostTypeId="2" ParentId="24339" CreationDate="2014-11-27T12:19:19.000" Score="10" Body="&lt;p&gt;Tonic firing typically occurs without presynaptic input and can be viewed at as background activity. Tonic activity is often characterized by a steady action potential firing at a constant frequency. Note that not all neurons may have tonic activity at rest. It may serve as keeping a steady background level of a certain neurotransmitter or it can serve as a mechanism where both an inhibition or increase in presynaptic input can be transmitted. When a neuron is silent at rest, only an increase in presynaptic activity can be transmitted postsynaptically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In contrast, phasic firing occurs after a neuron is activated due to presynaptic activity and it incurs activity on top of any background activity a neuron may have. It is typically restricted to one, a few, or a short burst of action potentials, whereafter the activity quickly returns to the resting state. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://med.stanford.edu/content/dam/sm/delecea/documents/Tsai_2009_Science.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tsai &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Science&lt;/em&gt; (2017); &lt;strong&gt;324&lt;/strong&gt;: 1080-4&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2018-04-11T09:53:54.547" LastActivityDate="2018-04-11T09:53:54.547" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24358" PostTypeId="2" ParentId="24351" CreationDate="2014-11-27T14:25:21.177" Score="1" Body="&lt;p&gt;The processes of apoptosis is not so simple, there is a lot of genes and proteins that participate in it. In cancer cells some of them mutate and not working properly. &lt;br&gt;&#xA;Lack of apoptosis is the main problem in cancer. If cell not working properly, it dies. But not in cancer.&lt;br&gt;&#xA;So theoretically, yes. If we will fix the apoptosis, the cell probably will die. &lt;br&gt;&#xA;It's gene engineering direction. You need to target the cancer cell, and to change problem genes. It's really difficult processes. And every type of cancer has different mutations ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Read this for example http://www.jeccr.com/content/30/1/87&#xA;(Journal of Experimental &amp; Clinical Cancer Research )&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="10104" LastEditDate="2014-11-29T13:12:14.270" LastActivityDate="2014-11-29T13:12:14.270" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24360" PostTypeId="1" CreationDate="2014-11-27T17:57:07.070" Score="-2" ViewCount="762" Body="&lt;p&gt;As the title says, i've been wondering if there are any similarities between the DNA of humans and the DNA of animals?&#xA;Like, maybe monkeys are more similiar in their DNA to humans, than dogs are (to humans)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance, sorry if there are any english mistakes.&lt;/p&gt;&#xA;" OwnerUserId="10351" LastActivityDate="2014-11-27T18:43:09.507" Title="Are there any similarities in the DNA of a humans and animals?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-11-28T10:36:25.963" ContentLicense="CC BY-SA 3.0" />
  <row Id="24361" PostTypeId="2" ParentId="24360" CreationDate="2014-11-27T18:43:09.507" Score="4" Body="&lt;ul&gt;&#xA;&lt;li&gt;Genome-wide variation from one &lt;b&gt;human being&lt;/b&gt; to another can be up to 0.5% (99.5% similarity)&lt;br /&gt;&#xA;&lt;br /&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;b&gt;Chimpanzees&lt;/b&gt; are 96% to 98% similar to humans, depending on how it is calculated. (&lt;a href=&quot;http://genome.wellcome.ac.uk/doc_WTD020730.html&quot; rel=&quot;nofollow&quot;&gt;http://genome.wellcome.ac.uk/doc_WTD020730.html&lt;/a&gt;)&lt;br /&gt;&#xA;&lt;br /&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;b&gt;Cats &lt;/b&gt;have 90% of homologous genes with humans, 82% with dogs, 80% with cows, 79% with chimpanzees, 69% with rats and 67% with mice. (&lt;a href=&quot;http://genome.cshlp.org/content/17/11/1675.full&quot; rel=&quot;nofollow&quot;&gt;http://genome.cshlp.org/content/17/11/1675.full&lt;/a&gt;)&lt;br /&gt;&#xA;&lt;br /&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;b&gt;Cows &lt;/b&gt;(&lt;i&gt;Bos taurus&lt;/i&gt;) are 80% genetically similar to humans (&lt;a href=&quot;http://www.sciencemag.org/cgi/content/full/324/5926/522&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencemag.org/cgi/content/full/324/5926/522&lt;/a&gt;)&lt;br /&gt;&#xA;&lt;br /&gt;&lt;/li&gt;&#xA;&lt;li&gt;75% of &lt;b&gt;mouse&lt;/b&gt; genes have equivalents in humans (&lt;a href=&quot;http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000112&quot; rel=&quot;nofollow&quot;&gt;http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000112&lt;/a&gt;), 90% of the mouse genome could be lined up with a region on the human genome (&lt;a href=&quot;http://www.genome.gov/page.cfm?pageID=10005831&quot; rel=&quot;nofollow&quot;&gt;http://www.genome.gov/page.cfm?pageID=10005831&lt;/a&gt;) 99% of mouse genes turn out to have analogues in humans (&lt;a href=&quot;http://www.nature.com/nature/journal/v420/n6915/full/420509a.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nature/journal/v420/n6915/full/420509a.html&lt;/a&gt;)&lt;br /&gt;&#xA;&lt;br /&gt;&lt;/li&gt;&#xA;&lt;li&gt;The &lt;b&gt;fruit fly&lt;/b&gt; (&lt;i&gt;Drosophila&lt;/i&gt;) shares about 60% of its DNA with humans (&lt;a href=&quot;http://www.genome.gov/10005835&quot; rel=&quot;nofollow&quot;&gt;http://www.genome.gov/10005835&lt;/a&gt;).&lt;br /&gt;&#xA;&lt;br /&gt;&lt;/li&gt;&#xA;&lt;li&gt;About 60% of &lt;b&gt;chicken&lt;/b&gt; genes correspond to a similar human gene. (&lt;a href=&quot;http://www.sciencedaily.com/releases/2004/12/041208230523.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedaily.com/releases/2004/12/041208230523.htm&lt;/a&gt;)&lt;br /&gt;&#xA;&lt;br /&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="10104" LastActivityDate="2014-11-27T18:43:09.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24364" PostTypeId="1" CreationDate="2014-11-27T21:27:24.517" Score="2" ViewCount="4620" Body="&lt;p&gt;Ok let me start with the definitions of incomplete dominance and codominance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;incomplete dominance - The situation in which the phenotype of heterozygotes is intermediate between the phenotypes of individuals homozygous for either allele.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;codominance - The situation in which the phenotypes of both alleles are exhibited in the heterozygote because both alleles affect the phenotype in separate, distinguishable ways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is the standard textbook example of incomplete dominance to show a cross of red and white Snapdragons of pure bread. Which yields the phenotypic ratio of 1 red : 2 pink : 1 white. The standard text example of codominance is AB blood type where the A glycoprotein and B glycoprotein together produce a distinguishable phenotype apart from AA or BB.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I really don't understand the distinction between intermediate phenotypes and distinguished phenotypes. How is pink not distinguished from white and red. Consider a hypothetical example of some insect that interprets red, white and pink as distinguishable signals where perhaps red is a safe flower, white is ignored, and pink is dangerous. Say these signal recognitions have evolved based on the insects contrast against the flower pigment and the probability of being eaten by a predator because of increased exposure while getting nectar from the flower. I suppose I have a misunderstanding but wouldn't the red, white, and pink phenotypes be distinguishable rather than intermediates in that case? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I'm probably just being an idiot but how is incomplete dominance different from codominance?&lt;/p&gt;&#xA;" OwnerUserId="10026" LastEditorUserId="10026" LastEditDate="2014-11-27T21:33:10.307" LastActivityDate="2015-10-13T21:32:17.833" Title="How is incomplete dominance different from codominance?" Tags="&lt;genetics&gt;" AnswerCount="5" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24365" PostTypeId="2" ParentId="23805" CreationDate="2014-11-27T22:08:22.700" Score="0" Body="&lt;p&gt;I would suggest you to learn the basics of fMRI data analysis. It is not easy to understand everything in depth, that is for sure. Anyway, luckily, you can start with some good software (e.g. &lt;a href=&quot;http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/&quot; rel=&quot;nofollow&quot;&gt;http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/&lt;/a&gt;) that does many things for you. Knowing just the basics can get you far then.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the data, try to have a look at &lt;a href=&quot;http://www.humanconnectome.org/data/&quot; rel=&quot;nofollow&quot;&gt;http://www.humanconnectome.org/data/&lt;/a&gt;. I think they have even preprocessed datasets.&lt;/p&gt;&#xA;" OwnerUserId="10364" LastActivityDate="2014-11-27T22:08:22.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24368" PostTypeId="1" CreationDate="2014-11-28T03:08:30.230" Score="2" ViewCount="320" Body="&lt;p&gt;Why did Henrietta Lacks die when her cells didn't die? As I understand it only the cells from her cervix were immortal so perhaps the cervical cancer took her life and the cells never died.&lt;/p&gt;&#xA;" OwnerUserId="8730" LastEditorUserId="3553" LastEditDate="2014-11-30T20:04:25.123" LastActivityDate="2014-11-30T20:04:25.123" Title="Henrietta Lacks and HeLa cells" Tags="&lt;cancer&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24369" PostTypeId="2" ParentId="24368" CreationDate="2014-11-28T03:25:48.147" Score="10" Body="&lt;p&gt;The cells never died in the sense that they kept replicating, individual cells still died. They were safely cultured in petri dishes before &lt;a href=&quot;http://en.wikipedia.org/wiki/Henrietta_Lacks&quot;&gt;Henrietta Lacks&lt;/a&gt; died. The cells came from a tumor that developed from her cervix. The &lt;a href=&quot;http://en.wikipedia.org/wiki/HeLa&quot;&gt;cervical cancer cells&lt;/a&gt; had developed high telomerase activity. &lt;a href=&quot;http://en.wikipedia.org/wiki/Telomerase&quot;&gt;Telomerase&lt;/a&gt; builds telomeres on the ends of DNA, protecting the chromosomes. In normal cells, telomeres tend to get shorter as the cells divide, eventually the DNA is damaged and the cells die. HeLa cells are protected because their telomeres are well maintained.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There was nothing special about Henrietta lacks that made her tissues immortal, so digging her up wouldn't be worth it. Her family would probably get mad too.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-11-28T03:25:48.147" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24370" PostTypeId="1" AcceptedAnswerId="24372" CreationDate="2014-11-28T05:09:39.400" Score="9" ViewCount="320" Body="&lt;p&gt;Circumcision removes the foreskin of the penis which mainly acts as a cover to the penis. Normally removing the foreskin makes more vulnerable to any STD, so how could circumcision reduce the risk of a HIV infection?&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="10045" LastEditDate="2014-11-29T07:19:19.530" LastActivityDate="2014-11-30T06:34:39.733" Title="How Circumcision could reduce the chance for a HIV infection?" Tags="&lt;human-biology&gt;&lt;hiv&gt;&lt;aids&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24371" PostTypeId="1" CreationDate="2014-11-28T09:52:39.780" Score="5" ViewCount="687" Body="&lt;p&gt;I am currently hearing a lecture about human machine interaction. The lecturer is not a biologist (neither am I, we are both computer scientists), but he makes some statements about biology which I think are questionable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One statement was that the energy of the lowest perceivable signal for eyes is &lt;img src=&quot;https://i.stack.imgur.com/GcmmD.png&quot; alt=&quot;enter image description here&quot;&gt; and the energy of the lowest perceivable signal for ears is &lt;img src=&quot;https://i.stack.imgur.com/AXm2D.png&quot; alt=&quot;enter image description here&quot;&gt;. He cites those values from the following (German) source:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Schmidtke, H. et al. Handbuch der Ergonomie mit ergonomischen&#xA;  Konstruktionsrichtlinien und Methoden. Koblenz: Bundesamt für&#xA;  Wehrtechnik und Beschaffung (BWB)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;HdE (2002): 2.4.1, Abb. 2&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;[KIT-Bibliothek: 2007 E 1808-1(2) (Präsenzexemplar)]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is clear that those values vary from person to person. Assuming they don't vary too much, it is interesting to know &lt;strong&gt;why the human ear can detect signals with lower energy than the human eye&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to my lecturer, the reason is because we can hear in all directions, but see only in one direction. He argues that hearing is much more important for this reason to detect predators, even if they are silent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this argumentation seems very weak to me. I would rather think that there is a range in which &quot;interesting&quot; signals occur. If the interesting signals have lower energy for sound than for visual signals the ear adapted to this range.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess if the hypothesis of my lecturer is correct, then animals which can see in all directions would (always / very often) have much worse ears. If my hypothesis is correct, then there would be no significant difference in animals with &quot;panorama-vision&quot; and animals without in terms of lowest perceivable energy for ears and eyes (assuming fair comparisions; unfair would be comparing fish with land animals as the medium might play a big role).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any source (written by somebody from biology, not form computer science) which makes a claim about this question?&lt;/p&gt;&#xA;" OwnerUserId="8014" LastEditorUserId="9099" LastEditDate="2014-11-28T13:12:43.000" LastActivityDate="2015-03-03T17:21:06.207" Title="Why do human ears have a lower boundary for the lowest energy perceivable signal than eyes?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;sensation&gt;&lt;human-eye&gt;&lt;human-ear&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24372" PostTypeId="2" ParentId="24370" CreationDate="2014-11-28T10:29:54.627" Score="7" Body="&lt;p&gt;This is an interesting question, which has not been answered yet. It is also questionable, if this protective effect is present at all. There are around 40 studies on the topic available which have subsequently undergone meta-analysis. In a meta-analysis all data from recent studies which meet certain quality criteria are analysed together. This gives a much bigger dataset and stronger statistical data. It also helps eliminating the effects of too small test groups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of these meta-analysis identified circumcision to have a positive effect on the prevention of HIV infections (reference 1). The authors recommended considering it as a preventive measure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two other meta-analysis were more cautious on the topic and either found only a weak link (reference 2) or that only &quot;randomized control studies&quot; (reference 3) would provide clear data. The problem with all these studies is, that they are observational studies, where unknown other effects can play a bigger role than the supposed main effect. It is ethically very difficult to make controlled trials on the transmission of deadly diseases in humans. This is also the reason why all trials on this have been stopped.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a hypothesis on how circumcision may help preventing the infection with HIV (when you not get infected in the operation itself due to improper hygienic standards). The skin in the penis contains a large number of immune cells (dendritic cells, CD4/CD8-T-cells) which are the target cells of the HIV virus. It is thought that the virus can more easily penetrate the relatively thin skin of the foreskin. It is also possible, that the surface size is important here, as there are reports which show that men with a larger foreskin also have a larger risk of getting infected. See reference 4.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another hypothesis has to do with the with the bacteria which live under the foreskin. The number of different strains present is much lower in circumcised men, which led to the conclusion that the dendritic cells, which present these to the immune system have an easier job in the circumcised men and are more likely to prevent the infection with HIV.&#xA;See reference 5 and 6 for more information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://journals.lww.com/aidsonline/pages/articleviewer.aspx?year=2000&amp;amp;issue=10200&amp;amp;article=00018&amp;amp;type=abstract&quot;&gt;Male circumcision and risk of HIV infection in sub-Saharan Africa: a&#xA;systematic review and meta-analysis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://apps.who.int/rhl/reviews/langs/CD003362.pdf&quot;&gt;Male circumcision for prevention of heterosexual acquisition of HIV&#xA;in men&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3820/6krnh2wf_pdf.htm&quot;&gt;HIV and male circumcision--a systematic review with assessment of&#xA;the quality of studies.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21042054&quot;&gt;Male circumcision for HIV prevention: current research and&#xA;programmatic issues.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://healthland.time.com/2013/04/17/why-circumcision-lowers-risk-of-hiv/&quot;&gt;Why Circumcision Lowers Risk of HIV&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://mbio.asm.org/content/4/2/e00076-13.full&quot;&gt;Male Circumcision Significantly Reduces Prevalence and Load of&#xA;Genital Anaerobic Bacteria&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-11-28T10:29:54.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24374" PostTypeId="1" AcceptedAnswerId="24379" CreationDate="2014-11-28T15:09:00.360" Score="5" ViewCount="3394" Body="&lt;p&gt;I have trouble in solving this exercise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Exercise&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A circular plasmid of 10,000 base pairs (bp) is digested with two restriction enzymes,A and B, to produce a 3000 bp and a 2000 bp bands when visualised on an agarose gel. when digested with one enzyme at a time, only one band is visible at 5000 bp. If the first site for enzyme A(A1) is present at the 100th base, the order in which the remaining sites (A2,B1 and B2) are present is?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why I struggle with this exercise&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can a 10,000bp plasmid produce 3000bp and 2000bp only on agarose gel. I mean where are the remaining 5000bp? I dont know if my concept is right.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Linearised bands on an agarose gel may be doublet. That can clear the doubts in problem. But still I dont know how to do a reasonable restriction mapping and find out sites of different enzymes.&lt;/p&gt;&#xA;" OwnerDisplayName="user10367" LastEditorUserId="5144" LastEditDate="2014-11-28T19:55:38.680" LastActivityDate="2014-11-28T19:55:38.680" Title="Restriction Mapping - Homework question" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24377" PostTypeId="2" ParentId="21863" CreationDate="2014-11-28T18:26:22.783" Score="1" Body="&lt;p&gt;Cloning of animals typically involves:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Taking nucleus from healthy adult cell of animal to clone&lt;/li&gt;&#xA;&lt;li&gt;Taking a healthy egg and replace the egg's nucleus with nucleus from source animal.&lt;/li&gt;&#xA;&lt;li&gt;Implanting egg in female, stimulating the pregnancy process.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This same process should work on humans BUT:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&quot;Is it really possible to create humans in lab?&quot; No. Animal cloning doesn't work this way, so human cloning wouldn't either. Animals aren't &quot;created&quot; in lab. The one artificial step is the modifying the nucleus of the egg cell before the pregnancy process initiates. The rest of the egg-&gt;embryo-&gt;infant pregnancy process is traditional nature and there is no working lab process available to replace natural pregnancies.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Cloning animals is very high risk, it involves lots of trial and error, and involves lots of mistakes, botched pregnancies, abortions, and birth defects. The core concept of replacing the nucleus in an egg cell makes sense, but the practical reality of that procedure involves cell damage and pregnancy risks. With non-human animals, no one cares. With humans, purposefully causing lots of botched pregnancies, miscarriages, and birth defects will make most people squeamish.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Donor Eggs: If the process worked perfectly, a single donor egg would suffice. Since the process doesn't work perfectly, many donor eggs are required. Getting those donor eggs is a very invasive process that I would not want my wife, sisters, or daughters to subject themselves to. With lab animals, who cares, scientists can be as invasive as they want, and harvest all the eggs that they need. Humans have rights which really impedes this type of risky work.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Today, cloning humans is possible, but at prohibitively high cost and risk. It is inevitably going to happen, but the costs and risks will impede its popularity. Process improvements that deliver more safety and reliability will allow human cloning to become more popular.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE: &quot;Why cant it be attempted..?&quot; It definitely is being attempted. Panayiotis Zavos is one doctor who has been very public about his attempts to clone humans:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;In April 2009, he claimed to have cloned 14 human embryos and transferred 11 of those to wombs.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AFAIK, none of these efforts led to a live birth. I'm sure other doctors have attempted and even more are considering it and waiting until it's a little more practical and realistic.&lt;/p&gt;&#xA;" OwnerUserId="5100" LastEditorUserId="5100" LastEditDate="2014-11-28T19:54:03.560" LastActivityDate="2014-11-28T19:54:03.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24378" PostTypeId="1" CreationDate="2014-11-28T19:42:09.843" Score="3" ViewCount="276" Body="&lt;p&gt;Parasitic infections lead to the production of parasite-specific IgE, but they also lead to the activation of nonspecific, polyclonal B-cells and T-cells. How do parasites trigger non-specific activation?&lt;/p&gt;&#xA;" OwnerUserId="9063" LastActivityDate="2015-04-12T19:33:13.993" Title="B-cell and T-cell activation by parasites" Tags="&lt;immunology&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24379" PostTypeId="2" ParentId="24374" CreationDate="2014-11-28T19:54:49.320" Score="5" Body="&lt;p&gt;This is not as hard, as it first seems. Lets have a look at the single enzyme digests first: The digest with enzyme A and B only leads to products which are 5kB (5000 bp) away from each other. Since they are of the same size, both equally sized restriction fragments appear as one band. So each enzyme cuts the plasmid exactly in half.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The double digest is a bit more tricky, but not much. You get two products from it, with 2kb and 3kB. This means that enzyme B cuts between the restriction sites for enzyme A, resulting in these two fragments. Have a look at the sketch I made below (only a quick one and not to scale):&#xA;&lt;img src=&quot;https://i.stack.imgur.com/LyPuL.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A1 and A2 are the cutting sites for enzyme A, B1 and B2 the sits for enzyme B. The numbers on the outside are the positions on the DNA sequence. You can see that a single digest leads to two fragments of 5kB (doesn't matter which) and that both A and both B sites are located 5kB from each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A1 is at position 100, A2 has to be at position 5100, B1 is located 2kB behind A1 (and therefore at position 2100), and B2 2kB behind position A2 (and therefore at position 7100). To get the same restriction pattern it is also possible that B1 and B2 are located 3kB behind their respective enzyme A position (so at 3100 and 8100) and you still get the same pattern of 2kB and 3kB on the gel.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-11-28T19:54:49.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24380" PostTypeId="1" CreationDate="2014-11-28T20:58:53.410" Score="1" ViewCount="141" Body="&lt;p&gt;I saw &lt;a href=&quot;https://www.google.cz/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCcQyCkwAA&amp;amp;url=http%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3Dx4I9mmd-2Rc&amp;amp;ei=ld14VNnKIuGvygPIwoDoDw&amp;amp;usg=AFQjCNHHA_YBdjKTH6WMI21GHG0yD9_eJA&amp;amp;sig2=w_bSWYdGHwITN9fViyBYeg&amp;amp;bvm=bv.80642063,d.bGQ&quot; rel=&quot;nofollow&quot;&gt;this video&lt;/a&gt; created by Derek Muller and he says there that it is very unusual to evolutionary develop the colour of the skin without the pigment. That sounds reasonable but if so, what nutrients have to get animals with pigment to get colored? Is it an active job of the cells or skin cells are just full of colorful minerals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case of giraffes: How does skin correct the shape of the spots? (For instance in cause of zebras it is clear according to &lt;a href=&quot;https://www.google.cz/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCIQtwIwAA&amp;amp;url=http%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DBD6h-wDj7bw&amp;amp;ei=FOF4VKjnG8rfOJWigYgG&amp;amp;usg=AFQjCNG7tEk0UgTfpgmhS8tZjIB90KOgbA&amp;amp;sig2=cgt9BA33uEJ_eKiqVCjDRA&amp;amp;bvm=bv.80642063,d.ZWU&quot; rel=&quot;nofollow&quot;&gt;this video&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And what about purposely colorful flowers? What nutrients do they need?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you very much.&lt;/p&gt;&#xA;" OwnerUserId="6124" LastEditorUserId="22859" LastEditDate="2016-04-08T16:32:17.030" LastActivityDate="2016-04-08T16:32:17.030" Title="What is different between the pigment of giraffes and the pigment of flowers?" Tags="&lt;evolution&gt;&lt;skin&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24381" PostTypeId="2" ParentId="24380" CreationDate="2014-11-28T22:37:54.997" Score="3" Body="&lt;p&gt;Pigmentation in most animals which is between black, brown, red, yellow and which is made up by the mixture of two pigments: Eumelanin (yellow to red) and Pheomelanin (black to brown). The ratio between these two makes a color. These are pigmental colors which are made by a special kind of cells in the skin, in mammals they are called melanocytes (and I will only look into mammals here, as this is already complicated enough). Additionally there are other colors, especially in fish and insects iridescent color play an important role.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This pigmentation is made by a cascade of enzymes from the oxidation and polymerization of the amino acid tyrosinase. So there are no minerals involved in the process. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanin&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the pattern: As far as I know the literature, these pattern by x-inactivation are only present in &lt;a href=&quot;http://en.wikipedia.org/wiki/Cat_coat_genetics&quot; rel=&quot;nofollow noreferrer&quot;&gt;cats&lt;/a&gt;. Here one of the enyzmes which is important for the generation of the dark pigment is encoded on the x-chromosome of the animals. Gene defects on this chromosome then lead to pigmentory defects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pigmentation patterns can be explained by a model which was formulated by Alan Turing and which is called &quot;Reaction Diffusion Model&quot;. You can find an interesting article about this in reference 1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically two different morphogens (different pigment cells) influence each other with positive and negative signals. If these signals would occur independently, than only relative incomplex two-dimensional colorations would be possible. See the figure from reference 2:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mMTay.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://mosaicscience.com/story/how-zebra-got-its-stripes-alan-turing&quot; rel=&quot;nofollow noreferrer&quot;&gt;How the zebra got its stripes, with Alan Turing&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.fbs.osaka-u.ac.jp/labs/skondo/paper/science%20review2010.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reaction-Diffusion Model as a Framework for Understanding Biological&#xA;Pattern Formation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-11-28T22:37:54.997" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24383" PostTypeId="2" ParentId="24371" CreationDate="2014-11-29T03:50:56.910" Score="1" Body="&lt;p&gt;I can't check the sources, but I think they must estimate the relative energy of a threshold-sensitivity signal. I don't think the energy of a sound wave can be assigned an arbitrary value the way a photon can...certainly only a photon can propagate in a vacuum...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both light and sound waves scatter less, as they propagate, if they're higher frequency/energy. So all things being equal blue light scatters less than red light, and ultrasound scatters less than infrasound. So audible sound is less directional than visible light, and any sound receptor provides information that is less directional compared to any light receptor. So of course sound's a good thing to pick up for alert signals, that doesn't really mean it's been prioritized over vision through evolutionary processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since most of vertebrate evolution occurs in the ocean, where sound and light propagation are quite different than in the terrestrial milieu, the lecturer's conjecture is likely irrelevant. Our sense organs are far more influenced by their evolutionary history than considerations of &quot;best possible&quot; (globally optimal) function.&lt;/p&gt;&#xA;" OwnerUserId="3336" LastActivityDate="2014-11-29T03:50:56.910" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24384" PostTypeId="1" AcceptedAnswerId="24397" CreationDate="2014-11-29T03:53:45.883" Score="7" ViewCount="4155" Body="&lt;p&gt;If a razor cuts only the hair, then how does hair thicken and become more rough with a razor shave and not after one using a trimmer? If both are used for hair removal, why is there a difference in hair growth?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been using a trimmer for 1 year, but the growth of hair remained unchanged.  When I started shaving with a razor, the hair growth thickened.&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="57" LastEditDate="2014-11-30T12:02:11.870" LastActivityDate="2014-11-30T20:05:56.323" Title="Why does hair thicken and become more rough after a razor shave but not after one using a trimmer?" Tags="&lt;human-biology&gt;&lt;hair&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ClosedDate="2014-11-30T18:12:29.133" ContentLicense="CC BY-SA 3.0" />
  <row Id="24385" PostTypeId="1" CreationDate="2014-11-29T04:38:12.373" Score="1" ViewCount="23854" Body="&lt;p&gt;I've just watched Breaking Bad Season 01 Episode 03. In that Walter gives the chemical composition of human body. The conversation is as follows&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Walter White: Let's break it down. Hydrogen. What does that give us?&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Gretchen Schwartz: We're looking at 63%.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Walter White: Sixty-three, that is a big bite. My next step's gotta be&#xA;  oxygen.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Gretchen Schwartz: Oxygen, 26%.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Walter White: Twenty-six. There you have your water.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Gretchen Schwartz: Carbon, 9%.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Walter White: Carbon, 9.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Gretchen Schwartz: For a total of 98%.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Walter White: Right.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Gretchen Schwartz: Nitrogen, 1.25%.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Walter White: One-point-two-five.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Gretchen Schwartz: That brings you to 99 and a quarter. Which only&#xA;  leaves you with the trace elements down where the magic happens.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Walter White: Oh, wait a minute. What about calcium? Calcium's not a&#xA;  trace. Got a whole skeleton to account for.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Gretchen Schwartz: You would think, right? Calcium's only 0.25%.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Walter White: What? That low? Seriously? Damn, I never would've&#xA;  thought that. Okay, so where does iron fit in.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Gretchen Schwartz: Iron. 0.00004%&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Walter White: What? You can't have hemoglobin without iron.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Gretchen Schwartz: Apparently, it don't take take much. No doubt. Go&#xA;  figure.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Walter White: Sodium.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Gretchen Schwartz: Sodium, 0.04%. Phosphorus, 0.19%.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Walter White: Point-one-nine. There we go. So the whole thing adds up&#xA;  to... 99.888042%. We are 0.111958%. Shy.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Gretchen Schwartz: Supposedly that's everything.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Walter White: Yeah? I don't know, it just... it seems like something's&#xA;  missing, doesn't it? There's got to be more to a human being than&#xA;  that.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Gretchen Schwartz: What about the soul?&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Walter White: The soul? There's nothing but chemistry here.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;When I searched for it, Wikipedia has &lt;a href=&quot;http://en.wikipedia.org/wiki/Composition_of_the_human_body&quot; rel=&quot;nofollow&quot;&gt;something different&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which one is correct?&lt;/p&gt;&#xA;" OwnerUserId="10368" LastEditorUserId="57" LastEditDate="2014-11-29T12:53:33.083" LastActivityDate="2014-11-29T12:53:33.083" Title="What is the exact chemical composition of human body?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ClosedDate="2014-11-30T07:15:20.277" ContentLicense="CC BY-SA 3.0" />
  <row Id="24387" PostTypeId="1" AcceptedAnswerId="24522" CreationDate="2014-11-29T06:15:38.800" Score="3" ViewCount="1047" Body="&lt;p&gt;Is there any stem cell or biogel method that exist for muscle and tendon lengthening?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is known that height surgery is limit to six inches with two surgeries and three inches each, it is also true that there is limit because the muscle and tendons could stretch no more. Is there some research about this? &lt;/p&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="630" LastEditDate="2019-05-08T12:32:01.640" LastActivityDate="2019-05-08T12:32:01.640" Title="Is there any stem cell or biogel method that exist for muscle and tendon lengthening?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;muscles&gt;&lt;tendons&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="24388" PostTypeId="2" ParentId="24385" CreationDate="2014-11-29T07:15:16.250" Score="2" Body="&lt;p&gt;That conversation is strange. While different tables exist, the very first elements seem messed up. If the body is 60 (some sources say 70)% water, then oxygen has to be the most abundant element by &lt;em&gt;weight&lt;/em&gt; (water - H&lt;sub&gt;2&lt;/sub&gt;O - has a molecular weight of ~18 g/mol, with hydrogen contributing only 2g/mol of that weight).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The usual figures are roughly Oxygen (65%), Carbon (18%), Hydrogen (10%), Nitrogen: (3%), Calcium (1.5%), etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the writers of Breaking Bad weren't stupid. So, they weren't discussing percentages of the mass of each element, but rather the frequency of that atom in the body. The number of hydrogen atoms does indeed exceed the number of oxygen atoms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, by &lt;strong&gt;atomic percent&lt;/strong&gt;, Oxygen is 25.6%, Carbon: 9.5%, Hydrogen: 63%, Nitrogen: 1.3%, Calcium: 0.24%, etc. So yes, the numbers are approximately correct for a normal, average, youthful (more water) 70 kg male.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So &lt;a href=&quot;http://pyrolysium.org/body-composition/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; is a table incorporating both percent by weight and percent by abundance. The writers were pretty well informed.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-11-29T07:15:16.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24392" PostTypeId="1" AcceptedAnswerId="24402" CreationDate="2014-11-29T08:12:23.440" Score="6" ViewCount="12066" Body="&lt;p&gt;If other animals have more than 2 nipples, then why do humans have only 2 nipples? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even my pet dog has more than 2 nipples.&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="57" LastEditDate="2014-11-29T12:37:09.923" LastActivityDate="2018-03-12T15:00:01.137" Title="Why do humans have only two nipples?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24393" PostTypeId="2" ParentId="24392" CreationDate="2014-11-29T10:03:20.603" Score="3" Body="&lt;p&gt;Your pet dog needs more than two nipples because she can have up to 11 or more puppies. If she had two nipples, most of them sound starve. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Twins are rare enough in humans. Two nipples are fine, and fit with bilateral symmetry. All primates have two nipples. So do many animals with one, two, and rarely three offspring at a time. Elephants: 2 teats, 1 calf (usually). Goats: 2 teats, 2 kids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why a cow has four teats, I'm sure I don't know, but I'm sure that's what made them valuable as a milk source to man.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-11-29T10:03:20.603" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24397" PostTypeId="2" ParentId="24384" CreationDate="2014-11-29T13:26:55.033" Score="6" Body="&lt;p&gt;Hair does not grow back thicker when it is cut. This is somewhat of an optical illusion because when you shave with a razor it leaves the top of the hair flat rather than pointed so it appears thicker. For instance see this picture:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/U7g9A.png&quot; alt=&quot;Hair being cut&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;As you can see the hair is tapered at the top and when cut loses this taper to leave a large cross-sectional area. I would say that for your question with with the trimmer that it is probably cutting the hair further up the taper where the hair is 'thinner' to begin with. A razor cuts closer to the base and thus gives a thicker appearance.&lt;/p&gt;&#xA;&lt;p&gt;Evidence: &lt;a href=&quot;http://www.scientificamerican.com/article/fact-or-fiction-if-you-shave-or-wax-your-hair-will-come-back-thicker/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.scientificamerican.com/article/fact-or-fiction-if-you-shave-or-wax-your-hair-will-come-back-thicker/&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0190962299701817&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0190962299701817&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6811" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-11-30T20:05:56.323" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24398" PostTypeId="1" AcceptedAnswerId="24399" CreationDate="2014-11-29T15:04:34.130" Score="2" ViewCount="1842" Body="&lt;p&gt;I think I have a wrong concept about viral mutation process. First of all what is mutation actually? I mean, I know it's a sudden change in DNA, happening when subjected to mutagenic agents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But can it occur due to internal urge of an organism, say virus? If not then how can virus like Ebola undergo rapid mutations so that no vaccination can be given as specificity for antigen is lost?&#xA;What accounts for such a viral behaviour?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In evolution, internal urge for survival causes development of  some beneficial characters. What is meant by this at molecular level. like gradual mutation!! &lt;/p&gt;&#xA;" OwnerDisplayName="user10367" LastEditorUserId="5144" LastEditDate="2014-11-29T17:21:54.967" LastActivityDate="2016-03-23T01:47:22.240" Title="Viral Mutation Mechanism" Tags="&lt;evolution&gt;&lt;molecular-genetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24399" PostTypeId="2" ParentId="24398" CreationDate="2014-11-29T17:17:05.583" Score="3" Body="&lt;p&gt;A mutation is a change in the genomic sequence - this can either be in the DNA or for viruses also in the RNA which carries their genetic information. This can either happen due to external influences (chemicals, radiation) or internal (mistakes while copying the information) reasons. See the figure below which shows the principle:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Jf8QR.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA based lifeforms usually have pretty good proof reading functions which eliminate most mutations, as they are often causing problems. RNA based viruses (as the flu virus or the ebola virus) do not have a proof reading function which raises their mutation rate drastically. See the figure below, which shows the mutation rates of several organism groups (image from this &lt;a href=&quot;http://www.sciencemag.org/content/323/5919/1308.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AQb6X.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These higher mutation rates indeed produce high number of mutated viruses which are different from the original form. This leads to a high number of viruses which are non-functional due to this mutations, but also to a few which are better adapted or look different due to this mutation. This can help in evading the immune system (when surface proteins of the virus change) or to adapt better to a host.&#xA;Since the number of viruses in an infected individual is very high (billions of viruses) it doesn't matter and the the mutations which are beneficial for the virus are positively selected for. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can lead to difficulties in the production of vaccines when the proteins used in the vaccine mutate. Usually this is accounted for by using proteins for immunization which only mutate slowly or not (because their function is important and mutations disrupt it). For more information have a look at the following review:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.uni-leipzig.de/~biophy09/Biophysik-Vorlesung_2009-2010_DATA/QUELLEN/LIT/A/B/3/Domingo_1997_rna_virus_mutations.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;RNA virus mutations and fitness for survival.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="22057" LastEditDate="2016-03-23T01:47:22.240" LastActivityDate="2016-03-23T01:47:22.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24400" PostTypeId="2" ParentId="24364" CreationDate="2014-11-29T19:32:07.403" Score="1" Body="&lt;p&gt;Certainly if you are talking about signals, red, white, and pink phenotypes are distinguishable rather than intermediates...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But inheriting a character is far away from the concept of distinguishing signals. As genotype of an organism decides its phenotype, you should know that in a hybrid both the paternal and maternal traits would exist. If one is dominant then it is expressed and the recessive is not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However if the dominant gene is unable to express itself independently in presence of the recessive and if the recessive is partially expressed, then both the dominant and recessive give rise to an intermediate phenotype which &quot;only one of them cannot produce&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is what we call blending. In case of Snapdragons, pink is a phenotype that allele responsible for red or white alone could not have produced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case of co dominance you can notice multiple dominance. i.e., no recessive character is there. All alleles are expressed &quot;independently of one another&quot; in an organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eg:- AB blood group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also consider cross between black coat coloured cat and white cat. The offspring produced has black and white patched coat colour. i.e., Black and white didnt blend to give rise to grey. I mean, alleles responsible for these traits are independently expressed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that clears your doubt. :-)&lt;/p&gt;&#xA;" OwnerDisplayName="user10367" LastActivityDate="2014-11-29T19:32:07.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24401" PostTypeId="2" ParentId="24364" CreationDate="2014-11-29T19:44:32.027" Score="0" Body="&lt;p&gt;AB blood group is the best example one can give about co dominance. What matters is both A and B are dominant and are expressed independently of one another. The quantity they are produced is not important here as our genetic make up cannot do relatively very large difference between synthesis of the two.&lt;/p&gt;&#xA;" OwnerDisplayName="user10367" LastActivityDate="2014-11-29T19:44:32.027" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24402" PostTypeId="2" ParentId="24392" CreationDate="2014-11-29T22:22:55.233" Score="11" Body="&lt;p&gt;Questions of the type, &quot;why does organism X have feature A?&quot; invite teleological (&lt;a href=&quot;https://en.wikipedia.org/wiki/Just-so_story&quot;&gt;just so&lt;/a&gt;) explanations which are difficult to substantiate. For example, the number of teats on a cow are difficult to explain in terms of providing milk to humans!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We should look to evolutionary history to explain human traits, not &quot;just so&quot; stories. The simple answer is that humans are primates, and primates have similar bodies and lifestyles. If there's a single pressure that lead to the number of teats in primates, it's likely the arboreal niche, not the mean litter size. Indeed, litter size is &lt;a href=&quot;http://www.int-res.com/articles/esr2009/8/n008p201.pdf&quot;&gt;usually a plastic trait&lt;/a&gt;, even in primates, and is certainly not an accurate predictor of the number of teats. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are no strict restrictions on nipple numbers in humans; they can occur &lt;a href=&quot;https://en.wikipedia.org/wiki/Milk_line&quot;&gt;anywhere on the milk line.&lt;/a&gt; So humans &lt;em&gt;tend&lt;/em&gt; to have two nipples because that's what primates &lt;em&gt;tend&lt;/em&gt; to have, because of our evolutionary history.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A better answer than this one would locate a candidate common ancestor to the primate and non-primate lineages and make reference to the embryonic development of the mammary tissue.&lt;/p&gt;&#xA;" OwnerUserId="3336" LastEditorUserId="3336" LastEditDate="2014-11-30T01:54:27.820" LastActivityDate="2014-11-30T01:54:27.820" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="24403" PostTypeId="1" CreationDate="2014-11-30T01:27:14.723" Score="1" ViewCount="251" Body="&lt;p&gt;I would like to find a method of increasing the biomass of my D&lt;sub&gt;2&lt;/sub&gt;O cultures because my current method is not yielding enough protein. I would like to also minimize the amount of H&lt;sub&gt;2&lt;/sub&gt;O in my culture. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My current methodology is a small scale growth of 3mL with 75% D&lt;sub&gt;2&lt;/sub&gt;O and LB grown for approximately 9hrs. This culture is then used to seed a 20mL 100% D&lt;sub&gt;2&lt;/sub&gt;O and M9 culture overnight and this entire culture is used to seed a 1L D&lt;sub&gt;2&lt;/sub&gt;O and M9 culture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your time.&lt;/p&gt;&#xA;" OwnerUserId="8979" LastEditorUserId="3340" LastEditDate="2014-11-30T07:00:45.553" LastActivityDate="2014-11-30T07:00:45.553" Title="Optimization of E. coli growth in D₂O (heavy water)" Tags="&lt;microbiology&gt;&lt;experimental-design&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24404" PostTypeId="2" ParentId="24403" CreationDate="2014-11-30T01:50:28.603" Score="1" Body="&lt;p&gt;It looks like you're very stringently avoiding $^1\mathrm{H}$. You may want to consider replica plating your transformations onto $\mathrm{D}_2\mathrm{O}$ plates (selecting for $\mathrm{D}_2\mathrm{O}$ tolerance earlier.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume you're doing protein NMR and want &quot;triple labeling.&quot; Depending on how specific your carbon labelling is, you may want to grow your starter cultures on triple labeled agal hydrolyzate (something like &quot;Bioexpress.&quot;) You can buy some unlabeled stuff for fairly cheap (\$55 USD at &lt;a href=&quot;http://shop.isotope.com/category.aspx?id=10032221&quot; rel=&quot;nofollow&quot;&gt;CIL&lt;/a&gt; for 10 mL of 10X stock) and if your starters grow well you can spring for the same quantity of $^2\mathrm{H}$,$^{13}\mathrm{C}$,$^{15}\mathrm{N}$ for around \$405. &lt;/p&gt;&#xA;" OwnerUserId="3336" LastActivityDate="2014-11-30T01:50:28.603" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="24405" PostTypeId="1" CreationDate="2014-11-30T02:12:10.590" Score="7" ViewCount="6255" Body="&lt;p&gt;In regards to the body metabolizing and excreting THC: if urination is increased as a result of drinking lots of fluids, does that mean that more THC is leaving the body? To rephrase the question, is metabolism required for urination? Or can you simply urinate as a body process without metabolizing toxins from your body?&lt;/p&gt;&#xA;" OwnerUserId="10373" LastEditorUserId="9268" LastEditDate="2014-11-30T05:06:57.527" LastActivityDate="2014-12-01T13:19:29.067" Title="Does THC excretion increase if urine volume increases?" Tags="&lt;metabolism&gt;&lt;toxicology&gt;&lt;pharmacokinetics&gt;&lt;renal-physiology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24406" PostTypeId="2" ParentId="24405" CreationDate="2014-11-30T04:31:08.003" Score="9" Body="&lt;p&gt;This question asks about the urinary excretion of THC. Before answering the question I think you're getting at, I'll first note that &lt;a href=&quot;http://en.wikipedia.org/wiki/Cannabinoid&quot; rel=&quot;nofollow&quot;&gt;cannabinoids&lt;/a&gt; (of which THC is one) are primarily metabolized by hepatic cytochromes rather than being excreted directly. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=3012605&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; is a classical pharmacokinetic paper on the topic if you’re able to access it; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570572/&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt; is a more recent general review accessible on Pubmed Central. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cannabinoid metabolites are excreted both renally (via kidneys) and in the feces, so I’ll understand your question to refer to the renally excreted portion. When considering renal excretion of any substance we think in terms of &lt;a href=&quot;http://en.wikipedia.org/wiki/Renal_function#Glomerular_filtration_rate&quot; rel=&quot;nofollow&quot;&gt;glomerular filtration rate&lt;/a&gt;, which refers to the volume of blood filtered through the glomerular capillaries per unit time, often estimated as &lt;a href=&quot;http://www.webmd.com/a-to-z-guides/creatinine-and-creatinine-clearance-blood-tests&quot; rel=&quot;nofollow&quot;&gt;creatinine clearance&lt;/a&gt;. The question then boils down to: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Does excess hydration increase GFR?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And the basic answer is: no. The  kidneys control both volume and osmolality more distally, i.e. after the event of glomerular filtration.&lt;sup&gt;1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the scenario you posit – drinking a lot of dilute fluid – &lt;a href=&quot;http://en.wikipedia.org/wiki/Osmoreceptor&quot; rel=&quot;nofollow&quot;&gt;osmoreceptors&lt;/a&gt; in the hypothalamus will sense the decreased plasma osmolality and suppress ADH (&lt;a href=&quot;http://en.wikipedia.org/wiki/Vasopressin&quot; rel=&quot;nofollow&quot;&gt;antidiuretic hormone&lt;/a&gt;, a.k.a. arginine vasopressin), the hormone that acts on the distal nephron to control water reabsorption. If ADH is completely suppressed, the kidneys can produce up to 25 L/day of urine with an osmolality as low as 60 mOsm/kg.&lt;sup&gt;2,3&lt;/sup&gt; This huge volume of urine, however, reflects water homeostasis achieved at the distal tubule rather than increased glomerular filtration. It does not correlate with increased excretion of THC metabolites or anything else at the level of the glomerulus. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;Notes and References&#xA;&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;1. If this makes no sense to you, you may want to check out &lt;a href=&quot;http://cnx.org/contents/14fb4ad7-39a1-4eee-ab6e-3ef2482e3e22@7.16:175/Anatomy_&amp;amp;_Physiology&quot; rel=&quot;nofollow&quot;&gt;this basic introduction to renal physiology&lt;/a&gt; that is available online. The referenced textbook in #3 below is more comprehensive but requires a library or purchase for access.&#xA;&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;2. &quot;Normal&quot; urine osm ~300-800 mOsm/kg; plasma Osm ~280-290 mOsm/kg.&#xA;&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;3. Christopher Lote. (2012). &lt;em&gt;Principles of Renal Physiology.&lt;/em&gt; Springer New York.&#xA;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;P.S. If the question you really wanted to ask was, &quot;Will drinking lots of water make my tox screen negative faster?&quot;.... I'm not answering that question. For reasons largely unrelated to the discussion here (but see references in paragraph #1), I suggest assuming that THC metabolites will be &lt;em&gt;forever&lt;/em&gt; detectable via tox screen. ;-)&#xA;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-12-01T13:19:29.067" LastActivityDate="2014-12-01T13:19:29.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24407" PostTypeId="2" ParentId="24370" CreationDate="2014-11-30T06:29:03.763" Score="2" Body="&lt;p&gt;Unfortunately overlaying all of this is a social aspect that is difficult to eliminate. Virtually any male researcher into this topic has a vested interest in vindicating his own penile condition. Men feel strongly about the perfection of their own penises, however they find them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is very clear from the discussion and tone of many of these studies that the researchers are themselves circumcised, and want circumcision to be treated as the norm. The same effect is possible in the other direction, but seems to occur to a lesser extent because intactness is the biological norm and requires no action to make it so. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For that reason, studies out of the USA (including those led by American researchers in Africa) disproportionately favour circumcision, while those out of Europe do not. One reason this bias can creep in is that it is difficult to do double-blinded and/or placebo-controlled trials of circumcision. Thus experimenter and experimentee effects can creep in at every stage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Circumcision is an intervention with deep social, religious, historical and cultural roots, and once it has become customary, rationality about it is difficult to achieve. Especially considering the operation on healthy infants, the fact that the foreskin is an integral part of an adult sexual organ gets lost from sight. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is very common for the circumcised penis to be treated as the norm (with terms like &quot;uncircumcised&quot; common, where &quot;normal&quot; &quot;whole&quot; or &quot;intact&quot; would apply to any other body part that had not been surgically reduced). After that, circumcision may be treated as equal and opposite to the alternative of doing nothing, when it is no such thing. Thus the yawning gap between &quot;circumcision [somewhat] reduces the incidence of X disease&quot; and &quot;all male babies should be circumcised&quot; can be leapt in a single bound.&lt;/p&gt;&#xA;" OwnerUserId="10375" LastEditorUserId="10375" LastEditDate="2014-11-30T06:34:39.733" LastActivityDate="2014-11-30T06:34:39.733" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24408" PostTypeId="2" ParentId="9297" CreationDate="2014-11-30T06:32:04.273" Score="2" Body="&lt;p&gt;The mirror test is definitely useful, but clearly biased toward animals with social intelligence (a notion of self is only useful if there's a notion of other) and also toward highly visual animals.  A mole-rat, no matter how intelligent, is unlikely to use a mirror for much of anything.  Using the same test for animals with very different sensory modalities is bound to fail. For example, see &lt;a href=&quot;https://www.youtube.com/watch?v=Q-_5XN6lIf0&quot; rel=&quot;nofollow&quot;&gt;the comments&lt;/a&gt; of the following YouTube video.  The user Sluchesi notes:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;sticking a piece of post-it paper on my tom cat's head where he couldn't see it without a mirror and while petting him, waited until I was sure he didn't notice it (he didn't respond to it), showed him the mirror and he instantly started trying to get the paper off his head (not the image in the mirror, his own), shaking it and using his paws.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A second user (M. Ransom) did the same test and verified it.  Not quite to the level of scientific proof that you would want to see, but certainly worth a follow-up study by someone who focuses on the topic.  If true, it would indicate that cats probably do have a conception that the reflection in the mirror is them, but place little value on introspection or visual self-concepts.  This might indicate that what cats (and many other animals) lack is not the ability to have a model of self, but to have a model of some other being modeling yourself (i.e., 2nd-order model of self).  This is actually a quite complicated level of modeling: even humans are quite bad at guessing what other people think about them.  However, basically all humans try to do it, even if their guess is often mirror-bias (i.e., other people think about them like they think about themselves).  Given that this is nearly at the limit of average human cognition (3rd order models of other/self are rare and usually limited to strategic games like poker), it seems reasonable that most animals lack this ability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having a model of another's conception of oneself is necessary for a being to care what they look like, for instance.  After all, if you can't comprehend that the world attaches importance to how you look, you would be unlikely to develop mechanisms to attach importance to it either.  In that second case, the mirror test may be accurate (i.e., it measures higher order thought), but it is in fact measuring something very different (and more advanced) than what it has been assumed to measure.&lt;/p&gt;&#xA;" OwnerUserId="10374" LastActivityDate="2014-11-30T06:32:04.273" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24409" PostTypeId="1" CreationDate="2014-11-30T06:59:06.097" Score="3" ViewCount="674" Body="&lt;p&gt;A new life form discovered on a distant planet has a genetic code consisting of five unique nucleotides and only one stop codon. If each codon has four bases,what is the maximum number of unique amino acids this life form can use ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried this and got 624 (Using permutation method 5×5×5×5 = 625). But the answer given was 3124. Please help.&lt;/p&gt;&#xA;" OwnerDisplayName="user10367" LastEditorUserId="3340" LastEditDate="2014-12-03T04:28:37.720" LastActivityDate="2014-12-03T04:28:37.720" Title="Problem on number of amino acids that an alien can use" Tags="&lt;homework&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24411" PostTypeId="1" CreationDate="2014-11-30T11:13:13.613" Score="1" ViewCount="2106" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;In the last century, even during the past decades of the present century, students of systematics could not have thought of any fundamental distinctions among &lt;strong&gt;Taxonomy&lt;/strong&gt; &amp;amp; &lt;strong&gt;Systematics&lt;/strong&gt; . These terms appeared to them more or less synonymous and hence often misunderstood until G.S.Simpson(1961) analysed each of the terms separately &amp;amp; gave a comprehensive definition of each term and its workable areas so that their underlying fundamentals became clear.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is what I found in my book. But what is actually Systematics? And what is the difference between it and taxonomy??&lt;/p&gt;&#xA;" OwnerUserId="10378" LastActivityDate="2016-06-02T09:11:17.830" Title="What is actually systematics? What is the difference between it &amp; taxonomy?" Tags="&lt;taxonomy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24412" PostTypeId="1" CreationDate="2014-11-30T12:59:27.113" Score="1" ViewCount="11041" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Lysosomes are irregularly shaped membrane bound organelles containing 50 different types of enzymes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But how are they formed? How are they produced??&lt;/p&gt;&#xA;" OwnerDisplayName="user10379" LastActivityDate="2014-11-30T16:49:16.773" Title="How are lysosomes formed?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24413" PostTypeId="2" ParentId="24412" CreationDate="2014-11-30T16:45:55.260" Score="3" Body="&lt;p&gt;Cells take up external material in the process pf phagocytosis. This involves creating a vesicle from plasma membrane that will contain the external material. The vesicle enters the cytoplasm where it is called (early) endosome. The cellular membrane components of this endosome are recycled and gave back to the plasma membrane. The endosome pH decreases and it is now called late endosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Meanwhile, peptides (which will form the future hydrolases) are produced in the ribosomes of the endoplasmic reticulum and mannose 6-phosphate is added to these peptides. They are further transported to the Golgi apparatus which &quot;packs&quot; them into lysosomal vesicles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lysosomal vesicles fuse with a late endosome and due to the acidic medium of the endosome, the peptides dissociate from mannose 6-phosphate. This process turns the late endosome into a mature lysosome that is capable to digest material taken up via endocytosis.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;My book wrote: lysosomes are formed from ER or golgibodies.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;ER and Golgi help supply the enzymes to endosomes, thus turning them into lysosomes.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Lysosome,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Lysosome&amp;amp;oldid=635272974&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Lysosome&amp;amp;oldid=635272974&lt;/a&gt; (accessed November 30, 2014).&lt;/li&gt;&#xA;&lt;li&gt;Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000. Lysosomes. Available from: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK9953/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK9953/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-11-30T16:49:16.773" LastActivityDate="2014-11-30T16:49:16.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24414" PostTypeId="2" ParentId="24411" CreationDate="2014-11-30T16:55:51.120" Score="2" Body="&lt;p&gt;Systematics studies the diversification and relationships of past and present living forms. Taxonomy is only a part of systematics as defined by Michener &lt;em&gt;et al.&lt;/em&gt; in 1970:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Systematic biology (hereafter called simply systematics) is the field that (a) provides scientific names for organisms, (b) describes them, (c) preserves collections of them, (d) provides classifications for the organisms, keys for their identification, and data on their distributions, (e) investigates their evolutionary histories, and (f) considers their environmental adaptations. This is a field with a long history that in recent years has experienced a notable renaissance, principally with respect to theoretical content. Part of the theoretical material has to do with evolutionary areas (topics e and f above), the rest relates especially to the problem of classification. Taxonomy is that part of Systematics concerned with topics (a) to (d) above.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Source:&lt;/strong&gt; Michener, Charles D., John O. Corliss, Richard S. Cowan, Peter H. Raven, Curtis W. Sabrosky, Donald S. Squires, and G. W. Wharton (1970). Systematics In Support of Biological Research. Division of Biology and Agriculture, National Research Council. Washington, D.C. 25 pp.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;via&lt;/strong&gt; Wikipedia contributors, &quot;Systematics,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Systematics&amp;amp;oldid=635316421&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Systematics&amp;amp;oldid=635316421&lt;/a&gt; (accessed November 30, 2014).&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-11-30T16:55:51.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24415" PostTypeId="2" ParentId="21460" CreationDate="2014-11-30T20:04:49.213" Score="0" Body="&lt;p&gt;In performing a cursory Google Scholar search using the terms &quot;keeping tempo&quot;, I found these articles that seem to cover your topic of interest:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.iapsych.com/iqclock2/LinkedDocuments/schulze2005.pdf&quot; rel=&quot;nofollow&quot;&gt;Schulze, Cordes, and Vorberg (2005) Keeping Synchrony While Tempo Changes: Accelerando and Ritardando&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://mykal.free.fr/synthesis/detectrythm.pdf&quot; rel=&quot;nofollow&quot;&gt;Scheirer (1997) Tempo and beat analysis of acoustic musical signals&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jstor.org/stable/10.1525/mp.2006.24.2.155%20.&quot; rel=&quot;nofollow&quot;&gt;McKinnet and Moelants (2006) Ambiguity in Tempo Perception: What Draws Listeners to Different Metrical Levels?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully, these papers are a help to you. It doesn't hurt to conduct experiments that others have conducted. All that really does is add more information and data to what is currently available/known.&lt;/p&gt;&#xA;" OwnerUserId="8979" LastActivityDate="2014-11-30T20:04:49.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24420" PostTypeId="1" AcceptedAnswerId="24432" CreationDate="2014-12-01T02:43:53.850" Score="3" ViewCount="1623" Body="&lt;p&gt;I was reading in my pharmacology textbook on lithium in treating bipolar disorder, and I was curious to know if there was any specific action lithium takes to produce symptoms such as polyuria and polydipsia. Any help would be great. Also, what is the most common way to monitor lithium levels in the body? &lt;/p&gt;&#xA;" OwnerUserId="8977" LastEditorUserId="9268" LastEditDate="2014-12-01T16:42:08.707" LastActivityDate="2014-12-01T16:44:21.080" Title="What is the mechanism of action of lithium-induced polyuria?" Tags="&lt;biochemistry&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24421" PostTypeId="1" AcceptedAnswerId="24425" CreationDate="2014-12-01T03:12:59.953" Score="4" ViewCount="35126" Body="&lt;p&gt;After vasectomy, where does the sperm go?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vasectomy Procedure cuts only vas deferens, But Our Testes still produces sperm, if there is no output for sperm, where does it go?&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="1590" LastEditDate="2014-12-01T09:51:36.310" LastActivityDate="2019-02-21T20:48:42.107" Title="After vasectomy, where does the sperm go?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24423" PostTypeId="1" AcceptedAnswerId="24431" CreationDate="2014-12-01T05:39:54.527" Score="2" ViewCount="130" Body="&lt;p&gt;What initiates primase to add an RNA primer to a DNA strand and what makes it stop adding RNA nucleotides? Is there tags added to the DNA back-bone?  &lt;/p&gt;&#xA;" OwnerUserId="10026" LastActivityDate="2014-12-01T13:57:20.143" Title="What initiates primase to add an RNA primer to a DNA strand and what makes it stop?" Tags="&lt;biochemistry&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24424" PostTypeId="1" AcceptedAnswerId="24438" CreationDate="2014-12-01T05:43:18.927" Score="1" ViewCount="23" Body="&lt;p&gt;A population given inhabiting an area. I can trace every individual and I've got the hypothesis there is a break in distribution like individuals born in the upper half of the area will rarely move to the lower half and vice versa.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tracking each individual how can I determine the line/border which divides the population in a upper and lower half. What's the math or algorithm behind to draw this imaginary line?&lt;/p&gt;&#xA;" OwnerUserId="10384" LastActivityDate="2014-12-04T05:54:47.377" Title="Determining break/border of movement" Tags="&lt;ecology&gt;&lt;species-distribution&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24425" PostTypeId="2" ParentId="24421" CreationDate="2014-12-01T07:55:27.213" Score="2" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;A vasectomy [...] is a contraceptive procedure in men in which the vas deferens, or sperm duct, is cut and the cut ends are sealed in order to prevent the transportation of sperm. Sperm is still produced, but does not leave the body. Vasectomy is usually done as a means of sterilization and is sometimes reversible.&lt;br&gt;&#xA;(from &lt;a href=&quot;http://urology.med.miami.edu/specialties/male-urologic-health/vasectomy&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://urology.med.miami.edu/specialties/male-urologic-health/vasectomy&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;br&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;When the vasectomy is complete, sperm cannot exit the body through the penis. Sperm are still produced by the testicles, but they are soon broken down and absorbed by the body. Much fluid content is absorbed by membranes in the epididymis, and much solid content is broken down by the responding macrophages and re-absorbed via the blood stream. Sperm is matured in the epididymis for about a month before leaving the testicles. After vasectomy, the membranes must increase in size to absorb and store more fluid; this triggering of the immune system causes more macrophages to be recruited to break down and re-absorb more solid content.&lt;br&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Vasectomy&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Vasectomy&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;br&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;A vasectomy only blocks sperm and does not affect your sexual drive, your ability to have an erection, orgasm or ejaculation or your ability to have and enjoy sex. Sperm is only a small fraction of the total liquid in your semen(almost 4-5 %). The amount of fluid, intensity – even color and texture – does not appear to change when sperm is absent.&lt;br&gt;&#xA;...&lt;br&gt;&#xA;The body absorbs unused sperm cells normally – whether or not you’ve had a vasectomy. After the procedure, the testicles will continue to produce sperm, but they will not leave the body in the semen. They dissolve and are simply and naturally absorbed by the body.&#xA;&lt;br&gt;(from &lt;a href=&quot;http://urology.med.miami.edu/specialties/male-urologic-health/vasectomy&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://urology.med.miami.edu/specialties/male-urologic-health/vasectomy&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;br&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Sperm are produced in the testicles.  They are stored and reach maturation in the epididymis, a tightly coiled, muscular tube that is 15 to 18 feet long and leads into the vas deferens.   The muscle of the epididymis and the vasdeferens contract to propel the sperm through these structures and into the urethra at the base of the penis so the sperm eventually can fertilize an egg.&#xA;&lt;a href=&quot;http://vasectomyreversalcenterofamerica.com/microsurgical-vasectomy-reversal/faqs/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://vasectomyreversalcenterofamerica.com/microsurgical-vasectomy-reversal/faqs/&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Sperm are produced in the seminiferous tubules of the testes, and this does not change. A vasectomy does not affect the function of the testes. It is a physical separation of the vas deferens from each testis, so that the sperm cells cannot be ejaculated. However, the rest of the semen, which is made in the seminal vesicles behind the bladder and which is stored in the prostate, is ejaculated so the male reproductive experience will not change. He can still ejaculate, but there will be no sperm cells in the semen, so there can be no fertilization of an egg cell during intercourse.&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-01T10:38:51.977" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24426" PostTypeId="1" CreationDate="2014-12-01T11:10:50.037" Score="2" ViewCount="1138" Body="&lt;p&gt;here is my question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In certain plants, tall is dominant to short. If a heterozygous plant is crossed with a homozygous tall plant, what is the probability that the offspring will be short?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My Solution:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let T be the allele for the tall phenotype and t be the allele for the short phenotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then the parental cross would be Tt x TT = 100% tall phenotype (1/2 Tt, 1/2 TT).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence the probability of having short offspring should be $\fbox{0}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the answer key for this question says the answer is $\fbox{$\frac{1}{2}$}$. How can this be??? It really bothers me when the answer key is potentially incorrect because it makes me very unsure, and I end up wasting time trying to figure out if the key is wrong or if I am. Can somebody please let me know if what I did was correct/incorrect?? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="9762" LastEditorUserId="3624" LastEditDate="2014-12-01T11:32:47.760" LastActivityDate="2015-02-24T19:06:44.883" Title="Simple Mendelian Genetics Question" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24427" PostTypeId="1" CreationDate="2014-12-01T11:36:18.097" Score="2" ViewCount="81" Body="&lt;p&gt;I was reading the topic of 'The concentration of the molecule can be adjusted quickly only if the lifetime of a molecule is short' from &lt;em&gt;Molecular Biology of the Cell&lt;/em&gt; by Alberts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the end of pg-837 (this part can also be found &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26813/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;), the author says - &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;In fact, after a molecule's synthesis rate has been either increased&#xA;  or decreased abruptly, the time required for the molecule to shift&#xA;  halfway from its old to its new equilibrium concentration is equal to&#xA;  its normal half-life—that is, equal to the time that would be required&#xA;  for its concentration to fall by half if all synthesis were stopped.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What do they exactly mean by 'shift halfway'? I am not able to understand quite clearly what the above sentence means. I hope some of you may be able to help me. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="10392" LastEditorUserId="3340" LastEditDate="2014-12-01T14:11:55.997" LastActivityDate="2016-02-08T06:04:07.353" Title="Change in synthesis rate of a molecule changes equilibrium concentration" Tags="&lt;biochemistry&gt;&lt;kinetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24428" PostTypeId="1" CreationDate="2014-12-01T12:35:14.743" Score="3" ViewCount="160" Body="&lt;p&gt;Additive genetic variance can be estimated in a number of ways, and is a key concept in evolutionary biology and quantitative genetics. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the typical methods (experimental designs) used to estimate this variance? How are they done?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found papers &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2011.01267.x/full&quot; rel=&quot;nofollow&quot;&gt;such as this&lt;/a&gt;, which use paternal half sib breeding designs and the fit a model to estimate genetic variance and then multiply the values by 4 to estimate the G-matrix.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Of particular importance is the sire-level covariance matrix because, when multiplied by four, it provides an estimate of G.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am interested in this because I am working on &lt;a href=&quot;http://jessicakabbott.com/documents/Obtainingsnapshotsofgeneticvariationusinghemiclonalanalysis.pdf&quot; rel=&quot;nofollow&quot;&gt;hemiclones&lt;/a&gt; and want to think about the differences, strengths, and weaknesses of classical methods compared to hemiclonal analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*note, I mean to estimate the &lt;em&gt;standing&lt;/em&gt; additive genetic variation within a population&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-12-17T17:19:26.683" LastActivityDate="2014-12-17T17:19:26.683" Title="What are the common methods to estimate additive genetic variance?" Tags="&lt;evolution&gt;&lt;quantitative-genetics&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24429" PostTypeId="2" ParentId="24427" CreationDate="2014-12-01T13:06:51.160" Score="1" Body="&lt;p&gt;&lt;em&gt;Note: The term &lt;strong&gt;equilibrium&lt;/strong&gt; is different from &lt;strong&gt;steady-state&lt;/strong&gt; w.r.t chemical reactions. Steady state is the right term for the above example. Equilibrium is used in the sense of forward and reverse reactions in a single reversible reaction. The above example considers two irreversible reactions — production and degradation.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... ... the time required for the molecule to shift halfway from its old to its new equilibrium concentration is equal to its normal half-life&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is not true if the degradation reaction is zeroth order or if these reactions are nonlinear. But for a linear production degradation set of reactions ($X$ is a biomolecule formed at a constant rate $\alpha$ and degraded at a first order rate  $\beta$ ), the reaction rate can be represented by the following equation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{d[X]}{dt}\bigg|_1=\alpha _1 - \beta [X]$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At steady state $\frac{d[X]}{dt}=0$, which means $[X_{ss_1}]=\Large\frac{\alpha _1}{\beta}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Half life as defined, by setting $\alpha$=0 and solving the differential equation = ${\Large \frac{log(2)}{\beta}}$  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the formation rate is changed to a new value:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{d[X]}{dt}\bigg|_2=\alpha _2 - \beta [X]$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and $[X_{ss_2}]=\Large\frac{\alpha _2}{\beta}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the above equation following equation can be deduced (by integrating the differential equation):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$-\frac{1}{\beta}.log(\alpha _2 - \beta [X]){\large|}_{X_{initial}} ^{X_{final}}= t_{\frac{1}{2}} $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;when you substitute $X_{initial}=X_{ss_1}=\frac{\alpha _1}{\beta}$ and $X_{final}=\Large\frac{\frac{\alpha _2}{\beta} - \frac{\alpha _1}{\beta}}{2}$ (halfway between new steady state and old steady state)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;you would obtain: $$t_{\frac{1}{2}}= -\frac{1}{\beta}log\left(\frac{\alpha _2 -\beta\frac{\alpha _1}{\beta}}{\alpha _2 - \beta \frac{\frac{\alpha _2}{\beta} - \frac{\alpha _1}{\beta}}{2}}\right) = \frac{log(2)}{\beta} $$&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-02-08T06:04:07.353" LastActivityDate="2016-02-08T06:04:07.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24430" PostTypeId="1" AcceptedAnswerId="24451" CreationDate="2014-12-01T13:35:30.960" Score="4" ViewCount="421" Body="&lt;p&gt;I know I can use bleach to kill most of the spores that live on my walls. I know I have to keep humidity below a certain level and temperature above another to prevent the spread of mold. I have read tons of websites on how to treat 'wall infestations'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's the mold that affects my books that worries me the most.&#xA;Especially now that I've discovered a very enticing market for used books. You can find bargains but sometimes the books smell &quot;of mold&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know more about the kind of molds (and/or fungi or other bio-monsters) that usually feast on paper. The paper that makes the pages of a book.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone point me to any kind of resource with answers to the following questions?&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;What are the most common biological causes of page deterioration?&#xA;1b. Can they be identified without lab instrumentation?&lt;/li&gt;&#xA;&lt;li&gt;Can they spread from one book to another, and if yes how and how fast?&lt;/li&gt;&#xA;&lt;li&gt;Can they be neutralized in some way (stopping the spread), or should one just burn the moldy books to avoid contagion?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I seek knowledge to protect knowledge. &lt;/p&gt;&#xA;" OwnerUserId="10393" LastEditorUserId="3340" LastEditDate="2014-12-01T14:00:50.133" LastActivityDate="2014-12-04T08:48:41.620" Title="Molds and fungi usually found on book pages: identifying and preventing further spread" Tags="&lt;botany&gt;&lt;mycology&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24431" PostTypeId="2" ParentId="24423" CreationDate="2014-12-01T13:57:20.143" Score="1" Body="&lt;p&gt;Prokaryotic primases are activated by DNA helicase [1, 2] while the eukaryotic ones are triggered when they form a complex with DNA polymerase alpha and its accessory B subunit [2].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I couldn't find too much information about what exactly triggers activation, but according to De Falco M &lt;em&gt;et al.&lt;/em&gt; (2004):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] synthetic function &lt;em&gt;(of the prokaryotic primase)&lt;/em&gt; is specifically activated by thymine-containing synthetic bubble structures that mimic early replication intermediates. [3]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It stops when it finishes reading a DNA template:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Sso DNA primase utilizes poly-pyrimidine single-stranded DNA templates with low efficiency for de novo synthesis of RNA primers [3].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wikipedia contributors, &quot;Primase,&quot; Wikipedia, The Free Encyclopedia, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Primase&amp;amp;oldid=593928284&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/w/index.php?title=Primase&amp;amp;oldid=593928284&lt;/a&gt; (accessed December 1, 2014).&lt;/li&gt;&#xA;&lt;li&gt;David N. Frick, and Charles C. Richardson. &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.biochem.70.1.39&quot; rel=&quot;nofollow&quot;&gt;DNA PRIMASES.&lt;/a&gt; Annual Review of Biochemistry. Vol. 70: 39-80 (Volume publication date July 2001). DOI: 10.1146/annurev.biochem.70.1.39&lt;/li&gt;&#xA;&lt;li&gt;De Falco M, Fusco A, De Felice M, Rossi M, Pisani FM. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15459292&quot; rel=&quot;nofollow&quot;&gt;The DNA primase of Sulfolobus solfataricus is activated by substrates containing a thymine-rich bubble and has a 3'-terminal nucleotidyl-transferase activity.&lt;/a&gt; Nucleic Acids Res. 2004 Sep 30;32(17):5223-30. Print 2004.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2014-12-01T13:57:20.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24432" PostTypeId="2" ParentId="24420" CreationDate="2014-12-01T14:23:11.423" Score="3" Body="&lt;p&gt;Lithium changes the effect of at least three substances that play a role in diuresis:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;aldosterone:&lt;/strong&gt;  lithium partially inhibits its ability to increase the &lt;strong&gt;expression of ENaC receptors&lt;/strong&gt; on apical membrane thus increasing sodium losses [1].&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;arginine vasopressin (AVP):&lt;/strong&gt; because lithium can induce hyperparathyroidism, parathyroid hormone can act as partial agonist to AVP, inhibiting its &lt;strong&gt;hydroosmotic action&lt;/strong&gt; [2].&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;antidiuretic hormone (ADH):&lt;/strong&gt; lithium blocks its stimulatory effect on adenilate cyclase. The result is a &lt;strong&gt;decrease of cAMP levels&lt;/strong&gt; in the cells from collecting tubules. cAMP promotes formation of water channels, thus improving absorption from collecting tubules. Because lithium decreases cAMP levels, diuresis is stimulated [1].&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;All these result in polyuria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lithium levels can be determined from the blood. Usually the test should be performed 12 hours after last dose of Lithium [3].&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Eleanor Lederer, MD; &lt;em&gt;Lithium Nephropathy&lt;/em&gt; on &lt;a href=&quot;http://emedicine.medscape.com/article/242772-overview#a0104&quot; rel=&quot;nofollow&quot;&gt;http://emedicine.medscape.com/article/242772-overview#a0104&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Carney SL, Ray C, Gillies AH. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8840263&quot; rel=&quot;nofollow&quot;&gt;Mechanism of lithium-induced polyuria in the rat.&lt;/a&gt; Kidney Int. 1996 Aug;50(2):377-83.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://labtestsonline.org/understanding/analytes/lithium/tab/sample/&quot; rel=&quot;nofollow&quot;&gt;http://labtestsonline.org/understanding/analytes/lithium/tab/sample/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2014-12-01T16:44:21.080" LastActivityDate="2014-12-01T16:44:21.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24433" PostTypeId="2" ParentId="24426" CreationDate="2014-12-01T14:33:56.837" Score="3" Body="&lt;p&gt;Assuming you have stated the question correctly, the answer key is incorrect for exactly the reasons you have given and your reasoning and consequent answer are correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would double-check you have read the question correctly and then conclude the answer key is incorrect. It happens.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2014-12-01T14:33:56.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24434" PostTypeId="1" AcceptedAnswerId="24521" CreationDate="2014-12-01T17:29:00.983" Score="1" ViewCount="180" Body="&lt;p&gt;I am little confused here. &#xA;I used the term &lt;em&gt;adrenoagonist&lt;/em&gt; and &lt;em&gt;sympatholytic&lt;/em&gt; to describe the compound. &#xA;However, my teacher says that the correct term here is adrenomimetic -term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding of Terms&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Adrenoagonist says that to bind to adrenoreceptor which prolongs the effect of NE in receptor.&lt;/li&gt;&#xA;&lt;li&gt;Sympatholytic - inhibition of postganglionic fibers of sympathetic nervous system&lt;/li&gt;&#xA;&lt;li&gt;Adrenomimetic - mimic effects of sympathetic nerve stimulation on pre- / postganglionic fibers. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I still think clonidine is sympatholytic i.e. adrenolytic (not adrenomimetic). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can clonidine be adrenomimetic?&lt;/strong&gt; &#xA;Why not adrenolytic?&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-05T21:41:51.223" LastActivityDate="2014-12-05T21:41:51.223" Title="Clonidine's adrenonergic nature?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;pharmacology&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24435" PostTypeId="1" AcceptedAnswerId="24439" CreationDate="2014-12-01T17:52:29.130" Score="-1" ViewCount="171" Body="&lt;p&gt;Assume you have a drug &lt;strong&gt;&lt;a href=&quot;https://pubchem.ncbi.nlm.nih.gov/compound/2405#section=Biomolecular-Interactions-and-Pathways&quot; rel=&quot;nofollow noreferrer&quot;&gt;nebivolol&lt;/a&gt;&lt;/strong&gt;.&#xA;When nebivolol is used as beta1 selective drug, beta2 is mostly for side effects, but this is not clear from PubChem.&#xA;I do not know any cases where nebivolol is used as beta1 and beta2 selective in the treatment.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Its first two pathways of interaction from PubChem.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Assume this pathway to be selective for some indication&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2hOrI.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and this nonselective (where side-effects stems mostly with large doses)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jtApy.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There no such differences in this section. &#xA;No explanations when side-effects come in each case of treatment plan (dose). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can you understand side-effects of this adrenoblocker from selective beta1 pathway in PubChem?&lt;/strong&gt; &#xA;Like in which cases beta2 selection becomes possible when beta1 is selective. &#xA;When beta2 is nonselective when beta1 is kept selective?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, &lt;strong&gt;how can you read pharmacodynamics of this adrenoblocker in PubChem?&lt;/strong&gt;&#xA;I.e. what the drug does to the body at any given dose. &#xA;I think there is little pieces of informations about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Implicitly, the side-effect can be read from &lt;strong&gt;Mechanism of Action&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AAekk.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where it refers at high doses to bronchospasm. &#xA;However, I would refer explicit discussion about side-effects and what we are trying to find and what are suspected as side-effects. &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-02T14:58:09.763" LastActivityDate="2014-12-02T14:58:09.763" Title="To understand side-effects for nebivolol's beta1 selective pathway in PubChem?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ClosedDate="2014-12-02T06:41:44.507" ContentLicense="CC BY-SA 3.0" />
  <row Id="24436" PostTypeId="1" AcceptedAnswerId="24480" CreationDate="2014-12-01T19:38:50.757" Score="2" ViewCount="117" Body="&lt;p&gt;I would appreciate any suggestion regarding self-studying experimental techniques used in biology for a theoretical scientist (candidate).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe I should be more specific. I'm a biology major, but took as little experimental courses as possible, and I didn't paid much attention to those I took. (shame on me, right). Then I got a MS in applied math. When I revisit my molecular biology/genetics and biochemistry textbooks, I realized that they are mostly descriptive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An experiment/technique oriented textbook would be very helpful for me, especially if it will also provide an overview of the methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My purpose is not the make up for the lost undergrad years, change my research orientation or master experimental skills. I'm aware that this is not achievable by reading some texts. My sole purpose is to not get lost on theory/experiment interface. When someone asks how something could be proven experimentally, I want to know what options are there in the field.&lt;/p&gt;&#xA;" OwnerUserId="1458" LastEditorUserId="1458" LastEditDate="2014-12-01T20:08:27.630" LastActivityDate="2014-12-02T20:22:54.707" Title="Suggestions for self-studying experimental techniques" Tags="&lt;experiment&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24437" PostTypeId="1" CreationDate="2014-12-01T21:25:55.167" Score="2" ViewCount="866" Body="&lt;p&gt;Assume you have been in non-gluten diet 20 years. &#xA;You built mass 8 mass with substances containing gluten (endogenous gluten stored in fat). &#xA;Then, celiac disease is diagnosed. &#xA;You have been 3 months in gluten free diet. &#xA;After mass period, you go to fat burning period. &#xA;The challenge starts: endogenous gluten stored in fat. &#xA;It is painful if too intensive training program. &#xA;Even little amount of gluten causes enteropathy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the protectant methods for burning fat containing gluten?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can you prove that there are no gluten-derived peptides that accumulate somewhere?&lt;/strong&gt; &#xA;Since the cellular receptors for gluten have been identified, I think this may be over-complicating things. - &lt;em&gt;Ryan's answer&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have not found any good solution for this, since I do not understand the pathophysiology enough well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Toxic factors related to celiac disease&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://pubchem.ncbi.nlm.nih.gov/compound/17787981&quot; rel=&quot;nofollow&quot;&gt;gliadin&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How is endogenous gluten released from fat?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-02T14:49:53.803" LastActivityDate="2014-12-02T14:49:53.803" Title="How to manage fat-gluten oxidation in celiac disease?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;physiology&gt;&lt;celiac-disease&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24438" PostTypeId="2" ParentId="24424" CreationDate="2014-12-01T21:35:22.440" Score="0" Body="&lt;p&gt;There are a lot of approaches to this kind of problem. Starting with the simplest approach I think you'd benefit from using a &lt;a href=&quot;https://en.wikipedia.org/wiki/K-means_clustering&quot; rel=&quot;nofollow&quot;&gt;K-means classification&lt;/a&gt;, with K=2 (or higher numbers to address @Luigi's concerns about model bias.) Once you've defined the geometric center of each population, you can treat them as foci, and use the equidistant points between each focus to define the boundary of interest. That does import another assumption (that the boundary is equidistant to the two points).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A more sophisticated way to divide two clusters is with a &lt;a href=&quot;https://en.wikipedia.org/wiki/Support_vector_machine&quot; rel=&quot;nofollow&quot;&gt;support vector machine&lt;/a&gt; but because this is a machine learning approach, you'd need to manually annotate a number of training data sets as &quot;group 1&quot; or &quot;group 2.&quot; But after training, the SVM will define the optimal boundary (hypersurface) between these groups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two types of approaches (clustering versus machine learning) differ in where the manually-imported assumptions lie. One can combine them fruitfully -- using K-means to define the populations and SVM to define the dividing boundary.&lt;/p&gt;&#xA;" OwnerUserId="3336" LastEditorUserId="3336" LastEditDate="2014-12-04T05:54:47.377" LastActivityDate="2014-12-04T05:54:47.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24439" PostTypeId="2" ParentId="24435" CreationDate="2014-12-01T22:59:01.030" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;How can you differentiate between effects and side-effects of this adrenoblocker in PubChem?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think PubChem will list all sites (receptors) at which a drug reacts, rather than the preferred sites, which I think is appropriate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pharmacological properties are listed in Section 8: Pharmacology and Biochemistry:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pharmacology&#xA;  Bisoprolol is a competitive, cardioselective β1-adrenergic antagonist. Activation of β1-receptors (located mainly in the heart) by epinephrine increases heart rate and the blood pressure causing the heart to consume more oxygen. β1-adrenergic blocking agents such as bisopolol lower the heart rate and blood pressure and may be used to reduce workload on the heart and hence oxygen demands. They are routinely prescribed in patients with ischemic heart disease. In addition, β1-selective blockers prevent the release of renin, a hormone produced by the kidneys causes constriction of blood vessels. Bisoprolol is lipophilic and exhibits no intrinsic sympathomimetic activity (ISA) or membrane-stabilizing activity...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From this, one cal tell that if there is activity at a beta-2 receptor, it is not the major intended site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PubChem is a valuable resource, but it's not a one-stop-shopping site. That's the reason there are extensive references given for sites of interaction. It's a great starting place for investigation of a drug.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-01T22:59:01.030" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24440" PostTypeId="2" ParentId="24437" CreationDate="2014-12-01T23:45:16.510" Score="6" Body="&lt;p&gt;Gluten is a protein. The textbook answer is that &lt;strong&gt;protein is not stored in fat cells.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Proteins are hydrolyzed into amino acids through digestion; some amino acids are &lt;a href=&quot;https://en.wikipedia.org/wiki/Ketogenic_amino_acid&quot; rel=&quot;nofollow&quot;&gt;ketogenic&lt;/a&gt;, and can contribute carbon towards fat biosynthesis. So some of the carbon that originates in gluten &lt;em&gt;may&lt;/em&gt; be incorporated into a fatty acid. But the carbon has no 'memory' of its previous role in a gluten molecule, and could not act as gluten when the fat is subsequently oxidized.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One can imagine an undigested gluten molecule (or its peptide fragments) binding to the exterior of a fat cell, but there's no mechanism for it to get incorporated &lt;em&gt;into&lt;/em&gt; fat as an intact protein. &lt;/p&gt;&#xA;" OwnerUserId="3336" LastEditorUserId="3336" LastEditDate="2014-12-02T12:59:52.193" LastActivityDate="2014-12-02T12:59:52.193" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24441" PostTypeId="1" CreationDate="2014-12-02T00:19:29.110" Score="5" ViewCount="4141" Body="&lt;p&gt;When reading about how green / leafy plants work,&#xA;I saw that they have chlorophyll A &amp;amp; B, which allow the plant to use the energy from light by capturing and transforming. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When reading about Chlorophyll, I saw some charts showing &quot;peak points&quot; for each type for light wavelengths. Apparently, each chlorophyll type has both peak points.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since from further reading I learn that plants can use all the light in the visible spectrum for photosynthesis, I'm wondering (&lt;strong&gt;my questions &gt;&gt;&lt;/strong&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What do &quot;peak points&quot; of wavelength correspond to / stand for?&lt;/li&gt;&#xA;&lt;li&gt;How does light peaking in red spectrum (say around 630nm) differ to (or affect plants) compared to light in red spectrum peaking at 680nm (which I gather is Chlorophyll A peak-ish)?&lt;/li&gt;&#xA;&lt;li&gt;When same amount of radiant flux is projected to leaves on different wavelengths, one far from a chlorophyll peak the other near, which one gives more energy to plant and why?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="10395" LastActivityDate="2019-03-16T18:54:02.930" Title="What does &quot;chlorophyll photosynthesis peak&quot; mean in relation to photon wavelength?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;photosynthesis&gt;&lt;light&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24445" PostTypeId="2" ParentId="24387" CreationDate="2014-12-02T04:39:51.320" Score="4" Body="&lt;p&gt;Limb lengthening surgery is usually used to treat sequelae caused by bone disease, trauma, pygmyism or inflammation. I personally do not recommend to use surgical methods to increase height. Typically Limb Lengthening requires Achilles pre-lengthening surgery and a lot of postoperative rehabilitation. Moreover, Limb lengthening surgery may cause pain, infection, muscle atrophy, joint stiffness and delayed bone healing. There's a lot of related research cause this study is timely for some patients.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ALDEGHERI, R., RENZI-BRIVIO, L., &amp;amp; AGOSTINI, S. (1989). The callotasis method of limb lengthening. Clinical Orthopaedics and Related Research, 241, 137-145.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;De Bastiani, G., Aldegheri, R., Renzi-Brivio, L., &amp;amp; Trivella, G. (1987). Limb lengthening by callus distraction (callotasis). Journal of Pediatric Orthopaedics, 7(2), 129-134.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Paley, D. (1988). Current techniques of limb lengthening. Journal of Pediatric Orthopaedics, 8(1), 73-92.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Paley, D. (1990). Problems, obstacles, and complications of limb lengthening by the ilizarov technique. Clinical Orthopaedics and Related Research, 250, 81-104.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Szoke, G., Lee, S. H., Simpson, A. H., &amp;amp; Prescott, J. (2005). Response of the tendon during limb lengthening. The Journal of Bone and Joint Surgery.British Volume, 87(4), 583-587.&lt;/p&gt;&#xA;" OwnerUserId="9790" LastActivityDate="2014-12-02T04:39:51.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24447" PostTypeId="1" CreationDate="2014-12-02T04:49:33.857" Score="-1" ViewCount="3086" Body="&lt;p&gt;What is the charge on the nucleotide 5'pGpGpApCpT 3' @ pH 7.00?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought adenine has 1 &lt;code&gt;NH&lt;/code&gt; group and Guanine has &lt;code&gt;NH&lt;/code&gt; and &lt;code&gt;OH&lt;/code&gt; groups and cytosine and thymine  has &lt;code&gt;OH&lt;/code&gt; groups on it and phosphate at 5' end an &lt;code&gt;OH&lt;/code&gt; at 3' end .so at pH 2.00-3.00 &lt;code&gt;OH&lt;/code&gt; will give away an electron and becomes negatively charged.so is it +2+2-1-1-1 which is -1? please explain?&lt;/p&gt;&#xA;" OwnerUserId="10350" LastEditorUserId="3340" LastEditDate="2014-12-02T05:11:40.050" LastActivityDate="2020-06-21T19:01:36.217" Title="What is the charge on oligonucleotide 5' pGpGpApCpT 3' at pH 7.00?" Tags="&lt;biochemistry&gt;" AnswerCount="3" CommentCount="4" ClosedDate="2020-06-24T07:16:20.457" ContentLicense="CC BY-SA 3.0" />
  <row Id="24449" PostTypeId="2" ParentId="24266" CreationDate="2014-12-02T05:24:27.957" Score="0" Body="&lt;p&gt;I think T cell when presented to antigen (here vaccine) will produce memory T cell, which on next encounter with the same organism may act much faster and efficiently .so i think the correct answer is option D&lt;/p&gt;&#xA;" OwnerUserId="10350" LastActivityDate="2014-12-02T05:24:27.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24450" PostTypeId="2" ParentId="24441" CreationDate="2014-12-02T05:31:53.900" Score="4" Body="&lt;p&gt;First thing to note is that the absorption spectrum of chlorophyll A and chlorophyll B is similar but not the same. The reason for the appearance of absorption spectra is because the light is composed of photons of light.  Different photon has different  oscillation frequency and energy. The essence of Chlorophyll absorption is absorbing photons. After chlorophyll absorption of a photon, the electron transition from the ground state to the excited state, and get water electronic from the water cause decomposition. Only phonton that has resonant vibration frequency with electrons, and can meet the energy requirements of electronic transitions in order to be absorbed by chlorophyll. The Photon energy of different wavelengths of light is different. This is also the reason of different wavelengths of light affect chlorophyll light absorption.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Simply explain the absorption spectrum:  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;280 ~ 315nm  has small effect of plant morphology and physiological processes&lt;/li&gt;&#xA;&lt;li&gt;315 ~ 400nnm absorption rate is small, impact the photoperiod, prevent stem elongation&lt;/li&gt;&#xA;&lt;li&gt;400 ~ 520nm (blue) Absorption ratio of of chlorophyll and carotenoid in this light is maximum, it has the greatest impact on photosynthesis&lt;/li&gt;&#xA;&lt;li&gt;520 ~ 610nm absorption rate is not high&lt;/li&gt;&#xA;&lt;li&gt;610 ~ 720nm (red) low absorption rate.  It has a significant effect on photosynthesis and light cycle effect of  chlorophyll.&lt;/li&gt;&#xA;&lt;li&gt;720 ~ 1000nm Low absorption rate, stimulate cell elongation, impact of flowering and seed germination&lt;/li&gt;&#xA;&lt;li&gt;1000nm converted into heat&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;p.s. white light is a mixture of light&lt;/p&gt;&#xA;" OwnerUserId="9790" LastEditorUserId="10395" LastEditDate="2014-12-02T19:31:46.057" LastActivityDate="2014-12-02T19:31:46.057" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24451" PostTypeId="2" ParentId="24430" CreationDate="2014-12-02T05:43:41.147" Score="5" Body="&lt;p&gt;Mold can grow in Extreme environments: they can live in very low water activity level, sometimes as lower as 0.71, live in refrigerator temperatures, these characteristics make it difficult to kill them thoroughly. &#xA;You can search &quot;paper deterioration&quot; in Google or library, then you can find lots article about this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1) Causes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Foxing and other white, fluffy coating or light yellow powder on paper caused by: Eurotium rubrum, E. repens, Aspergillus versicolor, Penicillium solitum, and Penicillium decumbens. (Karbowska-Berent, Joanna, Joanna Jarmiłko, and Jolanta Czuczko. &#xA;Source: &lt;em&gt;&quot;Fungi in Fox Spots of a Drawing by Leon Wyczółkowski.&quot; Restaurator. International Journal for the Preservation of Library and Archival Material 35.2 (2014): 159-179.)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Black spots: Monilia, Aspergillus, Penicillium, Mucor, Stemphylium, Hormodendrum, Fusarium, Chaetomium, Byssochlamys &#xA;Source: &lt;em&gt;Beckwith, Theodore Day, Wilbur Harold Swanson, and Thomas Marion Iiams. &quot;Deterioration of paper: the cause and effect of foxing.&quot; Publ. Univ. Calif., biol Sci. 1.13 (1940): 299-356&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2) Spreading&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For their spread, I think the mold can spread everywhere, but i did not find any resource about it.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;3) Method that kill the mold&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Drying the affected paper objects and applying 70% ethanol are the most preferred options to stop active fungal growth. &#xA;Source: &lt;em&gt;Sequeira, Sílvia O., Eurico J. Cabrita, and Maria F. Macedo. &quot;Fungal Biodeterioration of Paper: How are Paper and Book Conservators Dealing with it? An International Survey.&quot; Restaurator. International Journal for the Preservation of Library and Archival Material 35.2 (2014): 181-199&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8972" LastEditorUserId="3340" LastEditDate="2014-12-04T08:48:41.620" LastActivityDate="2014-12-04T08:48:41.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24453" PostTypeId="2" ParentId="24266" CreationDate="2014-12-02T05:57:41.980" Score="1" Body="&lt;p&gt;vaccination is injecting the low or non-toxic substances that having a pathogen's identifying characteristics into human or animal body. When the animals exposed to the non-injurious pathogens, the immune system will produce a protective material, such as immune hormones, physiologically active substances and specific antibodies. When the animal re-exposure to this pathogen, the animal's immune system will follow its memory and create more protective material to prevent damage from the pathogen.&#xA;So choose D&lt;/p&gt;&#xA;" OwnerUserId="9790" LastActivityDate="2014-12-02T05:57:41.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24454" PostTypeId="2" ParentId="24409" CreationDate="2014-12-02T06:05:13.977" Score="1" Body="&lt;p&gt;I also got 624. Maybe the answer is incorrect.&#xA;My processing is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each codon has four bases, the species contain five unique nucleotides, so for the first position in the codon, there are 5 possible results, also, for the second position in the codon, there are 5 possible results, it is same in third and forth position,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so the result should be  5*5*5*5-1=624&lt;/p&gt;&#xA;" OwnerUserId="8972" LastEditorUserId="5144" LastEditDate="2014-12-02T10:18:14.267" LastActivityDate="2014-12-02T10:18:14.267" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24457" PostTypeId="2" ParentId="24387" CreationDate="2014-12-02T07:25:17.700" Score="2" Body="&lt;p&gt;It seems that just a Russian researcher named Dr Alexander Teplyashin has made any progress into using stem cells for LL (Limb lengthening). Conventional way to go about it would always be surgeries which are detailed in Wikipedia (&lt;a href=&quot;http://en.wikipedia.org/wiki/Limb_lengthening_methods&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). This is a relatively new development, so I could not find any relative publications to support the claim of this particular researcher. There is however a website detailing the news in English, most others being in Russian (&lt;a href=&quot;http://www.naturalheightgrowth.com/2014/05/31/believe-alexander-teplyashin-got-stem-cell-technique-successfully-work/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) Here are a few publications of his (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?term=Tepliashin%20AS%5BAuthor%5D&amp;amp;cauthor=true&amp;amp;cauthor_uid=17918338&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). There are already lengthening methods available which is a combination of both surgery and stem cells (&lt;a href=&quot;http://www.telegraph.co.uk/health/healthnews/8033218/Stem-cells-used-to-save-womans-leg.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). As far as there is some credible proof, I would take the claims of that Russian researcher with a pinch of salt. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-12-02T07:25:17.700" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24458" PostTypeId="1" AcceptedAnswerId="35334" CreationDate="2014-12-02T08:49:36.393" Score="1" ViewCount="286" Body="&lt;p&gt;I searched on &lt;a href=&quot;http://bionumbers.hms.harvard.edu/search.aspx?log=y&amp;amp;task=searchbytrmorg&amp;amp;trm=flicker+fusion+&amp;amp;time=2014/12/02+03:46:43.943&quot; rel=&quot;nofollow&quot;&gt;bio-numbers&lt;/a&gt; for flicker-fusion threshold of insect eyes in general and for flies in particular. &lt;a href=&quot;http://www.jstor.org/stable/1539540&quot; rel=&quot;nofollow&quot;&gt;Ruck, 1961&lt;/a&gt; gives values for some flies. Is there any database maintained for these values? Is there any comparative study done for many flies/insects?&lt;/p&gt;&#xA;" OwnerUserId="6228" LastEditorUserId="9829" LastEditDate="2015-06-18T22:36:14.003" LastActivityDate="2015-06-20T20:27:35.583" Title="Flicker fusion threshold for insect eyes" Tags="&lt;eyes&gt;&lt;visual-system&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24459" PostTypeId="2" ParentId="21645" CreationDate="2014-12-02T09:01:30.723" Score="2" Body="&lt;p&gt;You can start with deterministic model using ODEs for reaction rates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if you are considering diffusion then you would have to use Partial differential equations for Fick's diffusion law.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can, however, assume that there is no &quot;diffusion&quot; but just transport of the signal molecule from a well mixed system (medium) to another well mixed system (cytosol). In this case you can use an ODE for &quot;conversion&quot; of extracellular signal to intracellular signal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The model becomes simple and easy to analyze if you reduce the number of steps. Certain steps can be removed by making certain assumptions such as Equilibrium approximation (EA) or Quasi-Steady-State approximation (QSSA).&lt;br&gt; If a reversible reaction is extremely fast compared to all other reactions (such as binding-unbinding of the activator to DNA), you can assume that reaction to be in equilibrium and represent the concentration of some species using equilibrium constants. &lt;br&gt;&#xA;In Quasi-Steady-State approximation, you assume that certain species are in steady state with respect to others i.e their concentrations do not change over time. In the model you just set $\frac{d[X]}{dt}=0$ for that species. Then obtain the concentration relationships as a function of reaction rate parameters. I'll explain QSSA and EA using the Michaelis-Menten (MM) kinetics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MM considers following steps:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Enzyme-Substrate binding (Reversible): $ E + S \rightleftharpoons ES $ with forward rate constant &lt;strong&gt;&lt;em&gt;k&lt;sub&gt;1&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; and reverse rate constant &lt;strong&gt;&lt;em&gt;k&lt;sub&gt;2&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;Enzyme-Substate complex converting to Product and Enzyme (Irreversible): $ ES \to P + E$ with rate constant &lt;strong&gt;&lt;em&gt;k&lt;sub&gt;3&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt; &lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EA&lt;/strong&gt; (The actual MM model): &lt;br&gt;&#xA;Assuming step 1 is in equilibrium. $k_1[E][S]=k_2[ES]$&#xA;&lt;br&gt; Get &lt;strong&gt;[&lt;em&gt;ES&lt;/em&gt;]&lt;/strong&gt; in terms of &lt;strong&gt;[&lt;em&gt;E&lt;/em&gt;]&lt;/strong&gt; and &lt;strong&gt;[&lt;em&gt;S&lt;/em&gt;]&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;QSSA&lt;/strong&gt; (The revised MM mddel):&lt;br&gt;&#xA;Assuming &lt;strong&gt;[&lt;em&gt;ES&lt;/em&gt;]&lt;/strong&gt; is in steady state. ${\Large \frac{d[ES]}{dt}}=k_1[E][S]-k_2[ES]-k_3[ES] = 0$ &lt;br&gt; which means $[ES] = \Large \frac{k_1[E][S]}{k_2+k_3}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This way you have removed certain reactions from the model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can do stochastic modeling as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For simulations you can use Matlab or Fortran. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-02T12:35:08.077" LastActivityDate="2014-12-02T12:35:08.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24460" PostTypeId="1" CreationDate="2014-12-02T09:53:11.450" Score="1" ViewCount="44" Body="&lt;p&gt;Are there any mammals whose males can feed the offsprings with milk from the breasts?&lt;/p&gt;&#xA;" OwnerUserId="408" LastActivityDate="2014-12-02T09:53:11.450" Title="Are there any mammals whose males can feed with milk?" Tags="&lt;zoology&gt;&lt;mammals&gt;&lt;sexual-dimorphism&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2014-12-02T11:34:15.477" ContentLicense="CC BY-SA 3.0" />
  <row Id="24463" PostTypeId="2" ParentId="21497" CreationDate="2014-12-02T11:32:30.200" Score="2" Body="&lt;p&gt;There are two possibilities:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Do not use the sequences per se but a scalar metric of sequence similarity for distance values&lt;/li&gt;&#xA;&lt;li&gt;Introduce gaps in the alignment. You can also do an end to end gapped alignment such as the Needleman-Wunsch and use the alignment scores for the distance matrix. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-02T11:32:30.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24464" PostTypeId="2" ParentId="15629" CreationDate="2014-12-02T11:53:45.130" Score="2" Body="&lt;p&gt;It doesn't seem like a homogenization problem. Nonetheless you can try this:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Suspend the heads in trizol&lt;/li&gt;&#xA;&lt;li&gt;Homogenize by passing through &lt;strong&gt;30/31G&lt;/strong&gt; needles (&lt;a href=&quot;http://www.bd.com/us/diabetes/page.aspx?cat=7001&amp;amp;id=7253&quot; rel=&quot;nofollow&quot;&gt;insulin syringe&lt;/a&gt;) up to 10-15 times.&lt;/li&gt;&#xA;&lt;li&gt;Heating a little might help but I think it is unnecessary for these tissues. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Insulin syringe is much better than the hand held homogenizer. Freeze-thaw 1-2 times if you want (helps in homogenization).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During extraction you can add 5M LiCl (100µl) + Ethanol (1ml) to 400µl aqueous phase (instead of isopropanol), keep at -20⁰C for 1-2h before centrifuging. Alternatively you can add a little RNAse free glycogen to Isopropanol during precipitation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: the liquid Nitrogen trick that rg255 mentioned is for quickly getting heads and avoiding the pain of dissecting each head.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="1590" LastEditDate="2016-08-17T08:49:25.950" LastActivityDate="2016-08-17T08:49:25.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24465" PostTypeId="2" ParentId="1938" CreationDate="2014-12-02T12:13:46.630" Score="1" Body="&lt;p&gt;There are always exceptions but you can consider some general rules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A is 1 i.e the sequence that is perfectly complementary (2 is complementary but direction is parallel — cannot base-pair), then B would be 1 (siRNA). Reasons (some are just based on general rules of siRNA design):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;siRNAs have to be perfectly complementary&lt;/li&gt;&#xA;&lt;li&gt;The size is also perfect for a siRNA (21nt)&lt;/li&gt;&#xA;&lt;li&gt;U/A (2-3 residues) at the 5' of the siRNA&lt;/li&gt;&#xA;&lt;li&gt;U at 10th position&lt;/li&gt;&#xA;&lt;li&gt;GC content 43% (ideal 30-50%)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://www.lifetechnologies.com/in/en/home/references/ambion-tech-support/rnai-sirna/general-articles/-sirna-design-guidelines.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for guidelines for siRNA design.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-02T12:13:46.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24466" PostTypeId="1" CreationDate="2014-12-02T12:18:56.723" Score="2" ViewCount="2040" Body="&lt;p&gt;In course of evolution (possibly), mammary glands became vestigial in male mammals, but became fully developed in females. Is there any plausible explanation for this characteristic?&lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="948" LastEditDate="2014-12-02T15:12:43.993" LastActivityDate="2014-12-02T16:42:08.907" Title="Why only female mammals have well developed mammary glands?" Tags="&lt;mammals&gt;&lt;sexual-dimorphism&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24467" PostTypeId="2" ParentId="21129" CreationDate="2014-12-02T12:21:49.480" Score="1" Body="&lt;p&gt;Pretreat the enzyme at high temperature before carrying out the assay at the standard temperature –  Alan Boyd&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-02T12:21:49.480" CommentCount="0" CommunityOwnedDate="2014-12-02T12:21:49.480" ContentLicense="CC BY-SA 3.0" />
  <row Id="24468" PostTypeId="2" ParentId="19829" CreationDate="2014-12-02T12:27:13.483" Score="1" Body="&lt;p&gt;From &lt;a href=&quot;http://genesdev.cshlp.org/content/27/23/2602.long&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We chose to test for Cas9-driven targeted mutagenesis on the&#xA;  endogenous Trp53 gene in mouse embryonic fibroblasts (MEFs), a cell&#xA;  line in which the biology of p53 has been thoroughly characterized and&#xA;  where the gene is structurally intact.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Furthermore:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Seventy-two hours post-transduction, cells were cultured in the&#xA;  presence or absence of Nutlin-3a, a specific inhibitor of the MDM2–p53&#xA;  interaction (Tovar et al. 2006). Cells were scored for the fraction of&#xA;  GFP+ cells after 4 d of Nutlin-3a exposure using flow cytometry (Fig.&#xA;  2B). Nutlin-3a potently activates a p53-dependent anti-proliferative&#xA;  cellular response, which strongly and specifically selects for any&#xA;  cells with disrupted Trp53 function (Efeyan et al. 2007). Much like&#xA;  MLP-p53.1224 infected cells, the pQCiG-p53 GFP+ cells were rapidly&#xA;  enriched for in the presence of Nutlin-3a, suggesting that&#xA;  CRISPR-mediated gene disruption had initially occurred in at least a&#xA;  proportion of the initial Cas9-expressing cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-02T12:27:13.483" CommentCount="0" CommunityOwnedDate="2014-12-02T12:27:13.483" ContentLicense="CC BY-SA 3.0" />
  <row Id="24469" PostTypeId="2" ParentId="24466" CreationDate="2014-12-02T13:21:51.490" Score="-1" Body="&lt;p&gt;The mammary glands in human males is not vestigial but rudimentary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human females have XX chromosomes and males have XY chromosome,here the &quot;Y&quot; chromosome is provided by father and &quot;X&quot; by the mother. At the time of fertilization, the father can provide either X or Y chromosome. If he provides Y chromosome the child will be male and if he provides X then child will be female. The mother always provides X chromosome. So the Y chromosome in the male child is responsible for the development of male sex organs and due to the presence of X chromosome the female sex organs are suppressed. Note that the female organs are suppressed but they are not eliminated. At the time of puberty males don't receive hormones which initiate the development of female sex organs. As a result the mammary glands stay in males as nipples but the hormone effects are only present in females and cause the formation of large amounts of fatty tissue near the nipples and develop as breasts.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A distinguishing characteristic of the class Mammalia is the presence of mammary glands. The mammary glands are modified sweat glands that produce milk, which is used to feed the young for some time after birth. Only mammals produce milk. Mammary glands are most obvious in humans, as the female human body stores large amounts of fatty tissue near the nipples, resulting in prominent breasts.&#xA;  &lt;a href=&quot;http://en.wikipedia.org/wiki/Female&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Female&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;While estrogens are present in both men and women, they are usually present at significantly higher levels in women of reproductive age. They promote the development of female secondary sexual characteristics, such as breasts.&#xA;  &lt;a href=&quot;http://en.wikipedia.org/wiki/Estrogen&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Estrogen&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="3553" LastEditDate="2014-12-02T16:42:08.907" LastActivityDate="2014-12-02T16:42:08.907" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="24471" PostTypeId="2" ParentId="24447" CreationDate="2014-12-02T16:10:35.847" Score="3" Body="&lt;p&gt;I didn't quite understand where you're getting all your OH groups, maybe from the enol tuatomers of the nucleotides. I tried to look up the pKa's for the keto tautomers of the nucleotides on Wikipedia&lt;a href=&quot;http://en.wikipedia.org/wiki/Guanine&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;,&lt;a href=&quot;http://en.wikipedia.org/wiki/Thymine&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;,&lt;a href=&quot;http://en.wikipedia.org/wiki/Adenine&quot; rel=&quot;nofollow noreferrer&quot;&gt;3&lt;/a&gt;,&lt;a href=&quot;http://en.wikipedia.org/wiki/Cytosine&quot; rel=&quot;nofollow noreferrer&quot;&gt;4&lt;/a&gt;.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/rfrXm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, if pH is below a functional group's pKa, that group will be protonated, and if pH is above pKa, it will be deprotonated, though this is an equilibrium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we assume pH of 7 and assume I have the pKas right ( these values are for the free nucleic acids, no deoxyribose attached ), then the primary amines on A, G, and C will be protonated NH3 groups with positive charges.The amides on G and T should remain deprotonated and uncharged.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So with the sequence GGACT, we have 4 primary amines, so 4 positive charges. However, we also have 5 phosphates, each carrying a negative charge, so +4 plus -5 is -1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course all of this goes out the window once we bind that oligonucleotide to another oligonucleotide, I assume the hydrogen bonding will alter the pKas and charges. For all I know, simply attaching the nucleic acids to a deoxyribose and stacking them together changes the pKas.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-12-02T16:10:35.847" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24472" PostTypeId="2" ParentId="24466" CreationDate="2014-12-02T16:18:37.950" Score="4" Body="&lt;p&gt;It comes down to investment in offspring. Males invest little in offspring only a little sperm whilst females have to develop the more expensive egg and the energy used through its development. In the mammalian line, this investment has increased in amount, initially through viviparity and then through the secretion of feeding fluids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In species, such as humans, where there is a lasting pair bond and both male and female invest in rearing the young then I suppose there could be a situation where it makes equal sense for both males and females to nurse - although the cost of mammaries on other functions may favour specialisation anyway - but remember that, in many mammals, it is the mother alone that rears the offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may also find the answer to this question useful: &lt;a href=&quot;https://biology.stackexchange.com/questions/5127/do-any-birds-beside-the-family-columbidae-or-any-reptile-or-mammal-feed-their&quot;&gt;Do any birds beside the family Columbidae (or any reptile or mammal) feed their young “Crop Milk”&lt;/a&gt;. What I hadn't realised is that there actually two species of bats where the male lactates.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-12-02T16:18:37.950" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24473" PostTypeId="2" ParentId="23254" CreationDate="2014-12-02T17:54:23.617" Score="1" Body="&lt;p&gt;Different components of the ECM can be stained differently but since you asked about hyaluronic acid (HA) I'll limit my answer to its staining. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3201155/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper. They use Hyaluran Binding Protein (HABP) as a specific probe for HA. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because HA has a very simple, conserved composition and is&#xA;  ubiquitously expressed in all animals that have a developed immune&#xA;  response, HA is not immunogenic. Therefore, there are no antibodies&#xA;  that specifically recognize HA, and traditional immunohistochemical&#xA;  methods of detection of HA are not possible. Fortunately, a very&#xA;  specific and tightly binding protein, the hyaluronan binding protein&#xA;  (HABP), which is composed of the HA binding domain with the link&#xA;  module from aggrecan, was isolated (Hascall and Heinegård 1974;&#xA;  Tengblad 1979) and adapted as an HA probe (Ripellino et al. 1985).&#xA;  HABP is now widely employed for specific detection of HA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Biotin tagged HABP can be used for IHC based visualization procedures.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-02T17:54:23.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24474" PostTypeId="2" ParentId="23342" CreationDate="2014-12-02T18:07:30.797" Score="1" Body="&lt;p&gt;To know if the ends are compatible see compatible cohesive ends (isoschizomers) from NEB website. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are unsure then do a blunt end ligation. For blunting a sticky end (From the comments):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Use Klenow or Pfu polymerase (or any proofreading/high fidelity polymerase).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can use Taq if you intend to to a TA cloning. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-02T18:07:30.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24475" PostTypeId="1" AcceptedAnswerId="24479" CreationDate="2014-12-02T19:02:11.637" Score="1" ViewCount="222" Body="&lt;p&gt;I have heard about &lt;a href=&quot;https://en.wikipedia.org/wiki/Human_anti-mouse_antibody&quot; rel=&quot;nofollow&quot;&gt;human anti-mouse antibodies (HAMAs)&lt;/a&gt; and read that HAMAs neutralize murine antibodies, therefore decreasing the effectiveness of those murine antibodies. Is this true that HAMAs neutralize the murine antibodies? How?&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="5144" LastEditDate="2014-12-02T19:19:32.660" LastActivityDate="2014-12-02T20:09:55.173" Title="human anti-mouse antibody" Tags="&lt;immunology&gt;&lt;antibody&gt;&lt;antigen&gt;&lt;mouse&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24477" PostTypeId="2" ParentId="23254" CreationDate="2014-12-02T19:34:43.747" Score="0" Body="&lt;p&gt;The book &quot;Basic Histology&quot; by Junqueira and Carneiro acknowledge the problem in histologic fixation of ground substance. They recommend freeze drying in liquid nitrogen and  then removing water by high vacuum at a temperature of -30 celcius, which will cause sublimation (ice--&gt;vapor). Then fixing the sample with a nonpolar solvent. Afterwards you can use stains like PAS technic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've never done this, I'm just copying from the book. If you already happen to have liquid nitrogen, high vacuum, and PAS in your lab this might be cheaper than HABP.&lt;/p&gt;&#xA;" OwnerUserId="4433" LastActivityDate="2014-12-02T19:34:43.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24478" PostTypeId="2" ParentId="24475" CreationDate="2014-12-02T20:03:44.057" Score="3" Body="&lt;p&gt;It's common for the human immune system to create antibodies against many proteins, even some human proteins. Hemophiliacs who receive regular doses of clotting factor proteins often develop neutralizing antibodies against the clotting factor proteins, even though they are a human protein&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25435742&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore it's not surprising that antibodies would be developed against mouse antibodies. There are differences between mouse and human antibodies, and human antibodies may bind to these different regions. I found the amino acid sequences for human&lt;a href=&quot;http://www.uniprot.org/uniprot/A0A087WV47&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt; and mouse&lt;a href=&quot;http://www.uniprot.org/uniprot/Q91Z05&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt; immunoglobulin gamma heavy chain constant region and aligned them by hand and marked the matching amino acids:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Human: MELGLSWVFLVAILEGVQCEVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWMSWVRQAPGKGLEWVANIKQDGSEKYYVDSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARECDNWF DPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT CPPC      PAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK&#xA;       |   |  |||| || |||||||||||||||| ||||  ||||||||||| | | |||||| ||||||| |       || | |||||||||||||| |  || ||| |||| ||||||      | |||||  ||||| |  ||| ||||    | |    |||||| |||| ||| |||| | | |||||| ||| |||  || ||||||    ||  | | |  | | |||| ||     |   ||||      ||| | |||||| |||  || |||| || |||||||||  || |   | |  |||| | |    | |||| |||| |   ||||  ||| |||| || || ||| |||| ||  | |||| |||    |    ||||||| || | || ||| ||   | ||| | |||||||| | ||||    | |     ||| | || | | |  |  | ||||&#xA;Mouse: MDSRLNLVFLVLILKGVQCEVQLVESGGGLVKPGGSRKLSCAASGFTFSDYGMHWVRQAPEKGLEWVAYINSGSTTIYYADTVKGRFTISRDNAKNTLFLQMTSLRSEDTAMYYCARELWLRRIDYWGQGTTITVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQS GLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCPAPNLEGGPSVFIFPPNIKDVLMISLTPKVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHREDYNSTIRVVSALPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPPPAEQLSRKDVSLTCLVVGFNPGDISVEWTSNGHTEENYKDTAPVLDSDGSYFIYSKLDIKTSKWEKTDSFSCNVRHEGLKNYYLKKTISRSPGK&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;As you can see, there are a lot of matching residues, but several differences. Keep in mind that antibodies also contain light chains, and that there are several other types of antibodies, I just used the IgG heavy chain as an example.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-12-02T20:03:44.057" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24479" PostTypeId="2" ParentId="24475" CreationDate="2014-12-02T20:09:55.173" Score="2" Body="&lt;p&gt;As mentioned in the comment, all antibodies have constant regions and variable regions. The variable regions are the binding sites on the ends of the two arms, and the constant regions are the rest of the molecule. When humans are injected with murine antibodies, the immune system recognises and sets up an immune response to them, through generation of HAMA. This affects the efficacy of the antibody because it is attacked the same way a pathogenic substance would be. Antibodies have different effects, but the most important one in this instance is through opsonisation (&lt;a href=&quot;http://en.wikipedia.org/wiki/Opsonin#Examples&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Opsonin#Examples&lt;/a&gt;). Because antibodies have two arms, they can bind multiple targets and cause a grouping and clumping. This also causes activation and phagocytosis through phagocytes (generally macrophages) which will ingest and destroy the therapeutic antibodies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antibodies that are mostly human with just mouse variable regions have been created to try and counter this problem, known as chimeric antibodies. Humanised antibodies are also available, which are entirely human with only the very tips of the variable regions (known as the hypervariable regions) are from mice. This reduces the problem as far as possible (&lt;a href=&quot;http://en.wikipedia.org/wiki/Fusion_protein#Chimeric_protein_drugs&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Fusion_protein#Chimeric_protein_drugs&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="10067" LastActivityDate="2014-12-02T20:09:55.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24480" PostTypeId="2" ParentId="24436" CreationDate="2014-12-02T20:14:17.830" Score="3" Body="&lt;p&gt;I cannot more highly recommend &lt;a href=&quot;http://www.molecularcloning.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Molecular Cloning 4 ed.&lt;/a&gt;. It is a really comprehensive text which covers numerous molecular biology experimental techniques including different types of PCR. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Also, there are some great suggestions for other books and websites that also cover molecular biology techniques in the answers to this question: &lt;a href=&quot;https://biology.stackexchange.com/questions/21750/short-concise-practical-manual-for-doing-experimental-biology?rq=1&quot;&gt;Short, concise, practical manual for doing experimental biology&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8979" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-12-02T20:22:54.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24481" PostTypeId="1" AcceptedAnswerId="24544" CreationDate="2014-12-03T00:43:50.103" Score="14" ViewCount="531" Body="&lt;p&gt;Our color vision is based on three types of receptors (cones) which are sensitive to three distinct locations on the spectrum:  420–440 nm, 534–555 nm, and 564–580 nm.  We label them &quot;red&quot;, &quot;green&quot;, and &quot;blue&quot;, but these names are arbitrary.  However, their locations on the spectrum may not be arbitrary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I notice that they correspond to the colors of the three most important things in our natural habitat:  sky (the above), vegetation (the below), and blood (the sign of potential food or alarm, depending upon whether you are the hunter or the prey).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I on to something here, or am I just dreaming in technicolor?&lt;/p&gt;&#xA;" OwnerUserId="10405" LastEditorUserId="9943" LastEditDate="2014-12-18T01:13:26.543" LastActivityDate="2016-09-15T06:23:15.547" Title="Is our color vision calibrated to sky, vegetation, and blood?" Tags="&lt;vision&gt;&lt;neurophysiology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="24482" PostTypeId="1" AcceptedAnswerId="24495" CreationDate="2014-12-03T00:52:27.740" Score="13" ViewCount="328" Body="&lt;p&gt;I would guess there is a theory in biology which states that the population size for a given species is inversely proportional to the body mass of individuals in that species.  In other words, there are zillions of ants, billions of mice, millions of deer, and just a few elephants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If humans existed in a &quot;state of nature&quot; (i.e., were not able to manipulate their environment more than any other mammal), what population size would be predicted by their ~70 kg body mass?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Assume that the human population has spread globally.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I imagine we would fall somewhere between the wolf and bear populations.&lt;/p&gt;&#xA;" OwnerUserId="10405" LastEditorUserId="3624" LastEditDate="2014-12-03T10:33:09.117" LastActivityDate="2020-05-26T16:06:04.867" Title="How big should the human population be, as predicted by body mass?" Tags="&lt;ecology&gt;&lt;population-dynamics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24483" PostTypeId="1" CreationDate="2014-12-03T01:35:49.920" Score="3" ViewCount="125" Body="&lt;p&gt;Is there a way to inhibit an antibody response to a specific antigen using immunosupression? I am interested in reducing the anti-antibody formation to animal antibodies such as murine antibodies in antisera. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read that there are ways to decrease the immune response to antisera but haven't found a detailed paper on how they work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update 12/3/2014: Would this work? &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374127/pdf/0100491.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374127/pdf/0100491.pdf&lt;/a&gt;&#xA;Although it is streptavidin, could a similar process be used for antibodies? &lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="10401" LastEditDate="2014-12-03T22:56:20.203" LastActivityDate="2014-12-11T00:24:46.310" Title="How to inhibit formation of specific antibodies (to antisera)?" Tags="&lt;immunology&gt;&lt;biotechnology&gt;&lt;antibody&gt;&lt;antigen&gt;&lt;mouse&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24487" PostTypeId="2" ParentId="24364" CreationDate="2014-12-03T03:42:59.733" Score="1" Body="&lt;p&gt;incomplete dominance are more likely mean blend, like you make juice contain apple and pear by blender, you can not distinguish them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;codominance can be think as mix, like you a salad that contain apple and pear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;like the example of incomplete dominance: pink flower, pink is differ from white and red, but it related to the two color,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;as the example of codominance ABO blood type, blood type AB means it contain A antigen and B antigen, we can distinguish them &lt;/p&gt;&#xA;" OwnerUserId="8972" LastActivityDate="2014-12-03T03:42:59.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24489" PostTypeId="1" AcceptedAnswerId="24491" CreationDate="2014-12-03T06:17:39.813" Score="11" ViewCount="2827" Body="&lt;p&gt;In ancient days, there were &lt;strong&gt;no&lt;/strong&gt; birth control methods like condoms or contraceptive pills available. How did they control pregnancy?&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="9943" LastEditDate="2014-12-03T12:58:03.847" LastActivityDate="2015-07-07T04:05:13.267" Title="How was birth control realized in ancient days?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;&lt;reproductive-biology&gt;" AnswerCount="2" CommentCount="2" ClosedDate="2014-12-06T18:43:24.900" ContentLicense="CC BY-SA 3.0" />
  <row Id="24490" PostTypeId="2" ParentId="24489" CreationDate="2014-12-03T06:47:24.590" Score="2" Body="&lt;p&gt;Condoms have been around for a long long time. Supposedly, condoms made from such materials as fish bladders, linen sheaths, and animal intestines where in use around 3000 BC (&lt;a href=&quot;http://www.ourbodiesourselves.org/health-info/a-brief-history-of-birth-control/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;a href=&quot;http://en.wikipedia.org/wiki/Coitus_interruptus&quot; rel=&quot;nofollow&quot;&gt;Coitus interruptus&lt;/a&gt; was tried before that which may or may not be successful. Infanticide was also practiced where an unwanted child was born in ancient societies (&lt;a href=&quot;https://birthpsychology.com/journals/volume-9-issue-1/pre-and-perinatal-anthropology-iii-birth-control-abortion-and-infanticide-#.VH6zYN-jm1I&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). You can read all about the &lt;a href=&quot;http://en.wikipedia.org/wiki/History_of_birth_control&quot; rel=&quot;nofollow&quot;&gt;history of birth control&lt;/a&gt; on wiki.  &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-12-03T06:47:24.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24491" PostTypeId="2" ParentId="24489" CreationDate="2014-12-03T08:47:40.057" Score="12" Body="&lt;p&gt;The need for birth control has been a concept for thousands of years and remains an important issue for men and women today, the need for contraception helped humans to achieve control over our population and healthy sexual relationships without having the fear of pregnancy.&lt;/p&gt;&#xA;&lt;p&gt;The medieval contraception methods mostly relies on plant based oral contraceptives and also plant based suppositories. There is always an element of myth in the usage of these medicines to control child birth, but due to the overusage of Silphion, the plant was gone extinct.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Silphion was a plant that grew in the hills near the Greek city-state of Cyrene located in North Africa. This plant was one example of an oral contraceptive in ancient times, based partly on Pliny's statement that it could be used &amp;quot;to promote the menstrual discharge&amp;quot; but since then has been harvested into extinction.&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Medieval_contraception&quot; rel=&quot;noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Asafoetida is widely used as a  contraceptive in medieval period, Asafoetida or asafetida is the dried latex exuded from the rhizome or tap root of several species of Ferula.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;One of the earliest contraceptive pioneers was Soranus of Ephesus, a Greek physician of the 2nd century C.E. who practiced in Rome and wrote extensively on obstetrics, gynecology and pediatrics. Many of his texts exist to this day which describes plants that were recommended for use as oral contraceptives, suppositories and abortifacients: galbanum, silphium, opopanax, myrtle, rue, white pepper, cow parsnip and pomegranate.&#xA;&lt;a href=&quot;http://www.medievalists.net/2012/06/28/of-lemons-yams-and-crocodile-dung-a-brief-history-of-birth-control/&quot; rel=&quot;noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Also condom is not a modern mechanism it was used in ancient times, but the usage was to protect oneself from sexually transmitted diseases, but an unknown chemical used  which is a spermicide and this resulted in contraception.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Records of condom use dates back to 3000 B.C. where King Minos of Crete, son of Zeus and Europa, utilized the bladders of goats to protect himself during intercourse.&lt;/p&gt;&#xA;&lt;p&gt;In the 1500s, a syphilis epidemic spread across Europe. It was at this time that Gabriel Fallopius,created a linen&#xA;condom as a means to protect from the continuing spread of disease . This proved especially effective when soaked in an unknown chemical solution acting as a spermicide.&#xA;&lt;a href=&quot;https://drive.google.com/viewerng/viewer?a=v&amp;amp;pid=sites&amp;amp;srcid=bWVkaWNpbmFlLm9yZ3xoaXN0b3JpYS1tZWRpY2luYWV8Z3g6MjA5ODJiZTA0YjRmODFlMQ&quot; rel=&quot;noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The medieval contraception methods includes,&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Condoms&lt;/li&gt;&#xA;&lt;li&gt;Female Barrier Methods&lt;/li&gt;&#xA;&lt;li&gt;Herbs and Rituals&lt;/li&gt;&#xA;&lt;li&gt;Intrauterine devices&lt;/li&gt;&#xA;&lt;li&gt;Male methods&lt;/li&gt;&#xA;&lt;li&gt;The Pill&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;These methods are widely described in &lt;a href=&quot;https://drive.google.com/viewerng/viewer?a=v&amp;amp;pid=sites&amp;amp;srcid=bWVkaWNpbmFlLm9yZ3xoaXN0b3JpYS1tZWRpY2luYWV8Z3g6MjA5ODJiZTA0YjRmODFlMQ&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; article.&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-07-07T04:05:13.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24492" PostTypeId="1" AcceptedAnswerId="24498" CreationDate="2014-12-03T09:06:27.093" Score="1" ViewCount="949" Body="&lt;p&gt;Anger is an emotion generated by neural processes in the brain and is associated with elevated blood pressure. How can an emotion, which is totally related to brain, result in blood pressure changes?&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="9943" LastEditDate="2014-12-03T11:39:39.167" LastActivityDate="2017-12-27T19:23:20.480" Title="How does anger relate to blood pressure?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;psychology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24494" PostTypeId="2" ParentId="16220" CreationDate="2014-12-03T09:40:50.010" Score="2" Body="&lt;p&gt;I assume that we are talking about eukaryotic genomes which are split into introns and exons. Depending on what you want to do with your cloned gene, you need different strategies. The method is based on the assumption that the gene sequence has only very little differences to the known sequences of other organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to express your gene from a vector, you need to find the right processed mRNA which is then processed into cDNA and then cloned. Here two strategies are possible: If you have a gene, which is strongly expressed, you can design a primer primer (based on the orthologous sequences) which is anchored in the poly-A tail and has a gene specific seuqence next to it. With this it should be possible to amplify your gene specifically and isolate it. If the gene is not strongly expressed (the resulting amount of cDNA would be very small, since there is no amplification involved), I would opt for making cDNA from total mRNA (use anchored polyA primers) and then amplify the sequence from the cDNA pool with two primers (again based on the orthologous sequences) to amplify the gene sequence. I would go for TA-cloning here, since you do not know, which restriction enzyme recognition sites are present on your gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you need the complete sequence containing introns and exons, there are two possible strategies. First you can use primers to amplify the gene and subsequently clone it. Then it is possible (and this is probably what I would do) to use a set of primers which bind to the end of the gene (and also the reverse strand) to amplify the sequences at the end and then sequence these PCR products. This gives you the exact sequences at the 5' and 3' end of the gene and allows you to include possible regulatory sites, since you then can design exactly matching primers for this region. Again, I would go for TA cloning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And finally you could start by sequencing the whole region based on homologous sequence primers first and then with primers designed on the newly analyzed sequences. This is the most exact way, but is also costly and takes some time (since you need to make new primers after each round of sequencing until you are done).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-03T09:40:50.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24495" PostTypeId="2" ParentId="24482" CreationDate="2014-12-03T09:50:52.933" Score="12" Body="&lt;p&gt;It is certainly possible to use general relationships to predict human population density or abundance. The relationship between population density/abundance and body size is an old topic in ecology that falls within the field of allometrics (how different features of organisms scale with body size). A closely related allometric relationship is &lt;a href=&quot;https://en.wikipedia.org/wiki/Kleiber&amp;#39;s_law&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kleiber's law&lt;/a&gt;, which deals with the relationship between body size and metabolic rate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your assumption of a generally negative relationship between body size and abundance is correct, and the relationship is approximately linear on a log-log scale. As mentioned in the comments, the exact shape of the regression will depend on what organism groups are included, since the scaling relationship is known to differ between taxa. However, to get a reasonable ballpark figure we can look at a the classic paper by &lt;a href=&quot;http://www.nature.com/nature/journal/v290/n5808/abs/290699a0.html&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Damuth. 1981. Population density and body size in mammals. Nature 290: 699-700&quot;&gt;Damuth (1981)&lt;/a&gt;, which include 307 mammal herbivores. The scaling relationship found there is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$D = 10^{4.23}*W^{-0.75}$$&lt;/span&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where density (D) is in individuals per km&lt;sup&gt;2&lt;/sup&gt; and body weight is adult body mass in grams. Using your example of 70kg for humans would result in a predicted density of 3.9 individuals/km&lt;sup&gt;2&lt;/sup&gt;. The scaling coefficient -0.75 (or -3/4) is often labelled &quot;Damuth's rule&quot;, and is usually also found when pooling both ectotherms and endotherms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, remember that this regression was based on primary consumers, i.e. mainly herbivore grazers. Alternative data for groups of mammals can be found in &lt;a href=&quot;http://www.jstor.org/stable/2461591&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Peters &amp;amp; Raelson. 1984. Relations between Individual Size and Mammalian Population Density. Am Nat&quot;&gt;Peters &amp;amp; Raelson (1984)&lt;/a&gt;. That paper presents regressions for both carnivores+omnivores as well as for all groups of mammals (herbivores, carnivores, omnivores). The relationship for carnivores + omnivores (CO) is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$D = 15.7*W^{-1.15}$$&lt;/span&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and the regression with all groups is (HCO):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$D = 40.7*W^{-0.859}$$&lt;/span&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In both of these regressions body weight is expressed in kg. Using the CO regression results in a predicted human density of 0.1 individuals/km&lt;sup&gt;2&lt;/sup&gt;, and the HCO regression gives a human density of 1.1 individuals/km&lt;sup&gt;2&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at these values, it is reasonable to assume that the predicted &quot;natural&quot; population density of humans lies in the range 0.1 - 4 individuals/km&lt;sup&gt;2&lt;/sup&gt;, but certainly biased towards the lower part of the range. I suspect that a regression looking only at primates would predict an even lower value, so I would not rule out values below 0.1 individuals/km&lt;sup&gt;2&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To get a grasp of what this means in actual population numbers, we can extrapolate the densities to the entire earth. If we use the predicted density from the carnivore+omnivore model in &lt;a href=&quot;http://www.jstor.org/stable/2461591&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Peters &amp;amp; Raelson. 1984. Relations between Individual Size and Mammalian Population Density. Am Nat&quot;&gt;Peters &amp;amp; Raelson (1984)&lt;/a&gt; and the entire land area of the earth, which is ~150 million km&lt;sup&gt;2&lt;/sup&gt; (&lt;a href=&quot;https://en.wikipedia.org/wiki/Earth&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia: Earth&lt;/a&gt;), the predicted human population would be about &lt;strong&gt;18 million&lt;/strong&gt;. Using the high estimate from &lt;a href=&quot;http://www.nature.com/nature/journal/v290/n5808/abs/290699a0.html&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Damuth. 1981. Population density and body size in mammals. Nature 290: 699-700&quot;&gt;Damuth (1981)&lt;/a&gt; would correspond to about &lt;strong&gt;600 million&lt;/strong&gt; people. However, remember that this is using the entire land area, including deserts, mountain ranges and arctic areas.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another point of reference is the estimated historical human population density during the Paleolithic, when we lived as hunter-gatherers. I have often seen population densities in the area of 1 per mile&lt;sup&gt;2&lt;/sup&gt;, i.e. 2.6 individuals per km&lt;sup&gt;2&lt;/sup&gt;. These estimates are naturally very uncertain, but shows that the allometric scaling relationships seem to provide at least reasonable order-of-magnitude estimates of &quot;natural&quot; human population density.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also somewhat enlightening to consider that our current human population size of 7 billion corresponds to the predicted population size of a 380 gram carnivorous mammal (using the CO relationship from &lt;a href=&quot;http://www.jstor.org/stable/2461591&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Peters &amp;amp; Raelson. 1984. Relations between Individual Size and Mammalian Population Density. Am Nat&quot;&gt;Peters &amp;amp; Raelson (1984)&lt;/a&gt;), making the unrealistic assumption that this mammal has managed to colonize all land areas on earth. This shows pretty clearly what an outlier modern humans represent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The generality of these types of relationships for predicting densities of individual species can however be questioned. For instance, the regression relationships also differ between climatic regions (see &lt;a href=&quot;http://www.jstor.org/stable/2461591&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Peters &amp;amp; Raelson. 1984. Relations between Individual Size and Mammalian Population Density. Am Nat&quot;&gt;Peters &amp;amp; Raelson (1984)&lt;/a&gt; for more), and, as indicated in the comment by @remi.b, it is also unclear what population states that should be included. For instance, should only population densities in &quot;ideal&quot; habitats be used, when we know that population densities of the same species can differ by orders of magnitude in different habitats? It is also unclear if/how to consider the effects of modern humans. &lt;a href=&quot;http://www.jstor.org/stable/2462997&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Silva &amp;amp; Downing. 1995. The Allometric Scaling of Density and Body Mass: A Nonlinear Relationship for Terrestrial Mammals. Am Nat 145(5)&quot;&gt;Silva &amp;amp; Downing (1995)&lt;/a&gt; also argue that the scaling relationship is nonlinear on the log scale, with a more shallow slope for larger species, and also find essentially no relationship between body size and density within some groups of species. More recent papers have also highlighted that studies on global relationships between density and body size often mix-up several different processes and relationships, see &lt;a href=&quot;http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347%2807%2900098-5&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;White et al. 2007. Relationships between body size and abundance in ecology. TREE 22(6): 323–330&quot;&gt;White et al (2007)&lt;/a&gt; for an overview on this.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="46609" LastEditDate="2020-05-26T16:06:04.867" LastActivityDate="2020-05-26T16:06:04.867" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="24496" PostTypeId="2" ParentId="19175" CreationDate="2014-12-03T09:51:04.820" Score="5" Body="&lt;p&gt;As far as I am aware, there are no commercially available re-usable microarrays. The reason for this is most likely that the arrays are really sensitive and you run into the trouble with false positive signals. I have once seen a microarray which has been stripped and still delivered quite some signals in areas which had a strong signal before. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You have to make sure to strip all the hybridized samples from the chip without damaging the probes which are bound on the surface. I think the trade-off between &quot;everything is off&quot; and &quot;some sample is still bound&quot; is not good enough. Who wants to risk false positive signals and possibly retract publications on this basis? You may also loose weak signals which are hidden under false-positive signals.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="1590" LastEditDate="2014-12-03T09:55:04.247" LastActivityDate="2014-12-03T09:55:04.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24497" PostTypeId="1" CreationDate="2014-12-03T10:43:44.597" Score="1" ViewCount="102" Body="&lt;p&gt;Colchicine is a chemical usually used to cause polyploidy mutant by inhibiting chromosome segregation. &lt;br&gt;It is synthesized in the Colchicum Autumnale. &lt;br&gt;But what mechanism prevent C. Autumnale from being affected by the Colchicine?&lt;/p&gt;&#xA;" OwnerUserId="8834" LastActivityDate="2014-12-03T10:43:44.597" Title="What mechanism prevent Colchicum Autumnale from being affected by Colchicine" Tags="&lt;cell-division&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24498" PostTypeId="2" ParentId="24492" CreationDate="2014-12-03T11:15:37.783" Score="3" Body="&lt;p&gt;Anger is a common emotion in most animals and it is highly related to stress. At time of anger body usually releases stress hormones and  the body's way to respond to stress is by sympathetic nervous system activation which results in the fight-or-flight response.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Anger is an emotional response related to one's psychological interpretation of having been threatened. Often it indicates when one's basic boundaries are violated. Sheila Videbeck describes anger as a normal emotion that involves a strong uncomfortable and emotional response to a perceived provocation.&lt;/p&gt;&#xA;&lt;p&gt;Anger may have physical correlates such as increased heart rate, blood pressure, and levels of adrenaline and noradrenaline. Some view anger as an emotion which triggers part of the fight or flight brain response.&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Anger&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Anger&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Stress and anger trigger the release of stress hormone Cortisol in the body. Mild releases of Cortisol can give the body a sudden burst of energy,it also may increase the heart rate to 180 times a minute and  blood pressure from 120 over 80 to 220 over 130.&lt;/p&gt;&#xA;&lt;p&gt;Anger is processed in hypothalamus and amygdala,the roles of two peptide hormones, corticotropin-releasing hormone (CRH) is responsible for the production of Cortisol (Primary stress hormone) and  arginine-vassopressin (AVP) produces Vasopressin, which triggers blood pressure by increases reabsorption of water by the kidneys, this results in contraction of blood vessels which raises blood pressure.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The human stress response involves a complex signaling pathway among neurons and somatic cells. While our understanding of the chemical interactions underlying the stress response has increased vastly in recent years, much remains poorly understood. The roles of two peptide hormones, corticotropin-releasing hormone (CRH) and arginine-vassopressin (AVP), have been widely studied. Stimulated by an environmental stressor, neurons in the hypothalamus secrete CRH and AVP.&lt;/p&gt;&#xA;&lt;p&gt;CRH, a short polypeptide, is transported to the anterior pituitary, where it stimulates the secretion of corticotropin (4). Consequently, corticotropin stimulates increased production of corticosteroids including cortisol, the primary actor directly impacting the stress response (5). Vasopressin, a small hormone molecule, increases reabsorption of water by the kidneys and induces vasoconstriction, the contraction of blood vessels, thereby raising blood pressure.&#xA;&lt;a href=&quot;http://dujs.dartmouth.edu/fall-2010/the-physiology-of-stress-cortisol-and-the-hypothalamic-pituitary-adrenal-axis#.VH7k8cnQoX0&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://dujs.dartmouth.edu/fall-2010/the-physiology-of-stress-cortisol-and-the-hypothalamic-pituitary-adrenal-axis#.VH7k8cnQoX0&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bmqcb.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-03T11:15:37.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24500" PostTypeId="2" ParentId="19435" CreationDate="2014-12-03T11:56:51.653" Score="1" Body="&lt;p&gt;It is possible to tag molecular motors with fluorescent proteins. It may impede with its movement but as &lt;a href=&quot;http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000216&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper describes, a variant can be created that doesn't have cargo binding ability. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Constitutively active kinesin motors can be generated by truncations&#xA;  that remove autoinhibitory and cargo-binding regions of the&#xA;  polypeptide. For this work, we generated KHC(1-560) (Figure 1A), a&#xA;  dimeric motor that has been well characterized in vitro and in vivo&#xA;  [16],[18],[19]. KHC(1-560) motors were tagged with three tandem copies&#xA;  of monomeric Citrine (mCit), a variant of enhanced yellow fluorescent&#xA;  protein (FP) (Figure 1A), and expressed in COS cells (Figure 1B).&#xA;  Single Kinesin-1 motors were tracked in live cells using a modified&#xA;  TIRF microscope (Figure 1C) in which the angle of illumination was&#xA;  varied to enable deeper imaging as described [17]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, if your objective is just &lt;em&gt;to determine the density distribution of Kinesin and Dynein in a Neuron&lt;/em&gt;, you can simply fix the cells and do IHC staining for the motor proteins followed by high resolution imaging.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-03T11:56:51.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24501" PostTypeId="1" AcceptedAnswerId="24513" CreationDate="2014-12-03T13:04:58.847" Score="1" ViewCount="157" Body="&lt;p&gt;What happens when an allogeneic organ transplant is performed on an immunocompetent recipient vs. when it is performed on an immunosuppresed recipient using a donated organ with immunocompetent cells?&lt;/p&gt;&#xA;" OwnerUserId="9063" LastActivityDate="2014-12-03T18:00:57.017" Title="allogeneic organ transplant and the immune response" Tags="&lt;immunology&gt;&lt;organs&gt;&lt;transplantation&gt;&lt;hla&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24502" PostTypeId="2" ParentId="23480" CreationDate="2014-12-03T13:26:58.080" Score="0" Body="&lt;p&gt;T-cells are selected against self reactivity so those that react to self-MHC are selected against and die by anergy. That's why they try to match the donor and the recipient's MHC molecules, to diminish the immune response.&lt;/p&gt;&#xA;" OwnerUserId="9063" LastActivityDate="2014-12-03T13:26:58.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24504" PostTypeId="2" ParentId="19226" CreationDate="2014-12-03T15:03:38.673" Score="2" Body="&lt;p&gt;I'm no expert at this but I don't think you need a Turing machine to achieve this, at least for DNA, since in conventional sense (not including carcinogenic factors such as UV) the most probable stage in which a DNA mutation can happen is during DNA replication so &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_polymerase&quot; rel=&quot;nofollow&quot;&gt;DNA polymerase&lt;/a&gt; engages in proofread to ensure accurate DNA replication, and then the DNA can get back into being heterochromatic (eventually). This will be more difficult for RNA as they are single stranded although they do fold onto themselves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also there many many strands of RNA that are produced through alternative splicing, VDJ recombination and RAG imprecise rearrangements for antibody production, which can give rise to infinite possible RNA productions. So how would you know what is &quot;good&quot; and what is &quot;bad&quot; in terms of RNA and its production. Half the time we don't even know what they do and what their roles are and the only reason we call something as a &quot;bad&quot; or &quot;faulty&quot; RNA is because it is having a negative effect not because we understand the precise role of the sequence, which means a theoretical table would be useless.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in short, a turing style protein machinery is neither possible (due to almost infinite potential number of RNA produced) nor feasible (since the number of proteins that would have to check each RNA sequence would in turn have to be almost infinite). And none of these takes into account SNPs i.e. individual variations, which can produce proteins with different sequence but identical structure/function, since obviously any lethal variations would be selected against but thats a whole different argument.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-12-03T15:03:38.673" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24505" PostTypeId="1" CreationDate="2014-12-03T15:25:19.640" Score="1" ViewCount="2881" Body="&lt;p&gt;I am studying the limitations of Theranos &lt;a href=&quot;http://www.theranos.com/&quot; rel=&quot;nofollow&quot;&gt;device&lt;/a&gt;. &#xA;They have 238 documents in Google Patents Search (Inassignee as Theranos), &lt;a href=&quot;https://www.google.com/search?tbm=pts&amp;amp;hl=en&amp;amp;q=inassignee%3A%22Theranos%2C%20Inc.%22&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. &#xA;&lt;strong&gt;Which patents are relevant for their device?&lt;/strong&gt; &#xA;They have 70 tests which are not necessary to consider now. &#xA;Just the basics of the device.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My intuition says that it uses PCR to multiply the microliter of blood for the analysis. &#xA;&lt;strong&gt;What are limiations of multiplying so little blood?&lt;/strong&gt; &#xA;I think this is where their engineering work applies. &#xA;&lt;strong&gt;What components do you need to multiply?&lt;/strong&gt; &#xA;I think all is not necessary. &#xA;Otherwise, the specificity and accuracy can be difficult to hold. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can Theranos blood test's be specific and accurate compared to conventional full blood test?&lt;/strong&gt; &#xA;I suspect if you can do the conventional full blood test with Theranos device with the same accuracy and specificity as the conventional one.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-04T07:31:24.937" LastActivityDate="2014-12-04T09:39:38.063" Title="Theranos blood test's Specificity and Accuracy?" Tags="&lt;hematology&gt;&lt;research-process&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24506" PostTypeId="1" AcceptedAnswerId="24514" CreationDate="2014-12-03T15:46:37.090" Score="6" ViewCount="13543" Body="&lt;p&gt;In the back of my mind I have the idea that human eyes can't notice the color of objects in the far periphery, and that any subjective perception of colors is done by the brain that tries to fill in the color percept.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is that true? &lt;/p&gt;&#xA;" OwnerUserId="152" LastEditorUserId="9943" LastEditDate="2014-12-04T10:56:21.073" LastActivityDate="2014-12-04T10:56:21.073" Title="Can the human eye distinguish colors in the periphery?" Tags="&lt;neuroscience&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24507" PostTypeId="2" ParentId="24126" CreationDate="2014-12-03T15:59:28.343" Score="0" Body="&lt;p&gt;Most of the above answers are incorrect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The definition of the genome is all of the encoding genetic material. An individual human genome includes two full sets of 23 chromosomes as well as mitochondrial DNA. There is one copy of this genome in most human cells. A few exceptions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Red blood cells don't have nucleuses and have no chromosomes. They don't have a copy of the genome.&lt;/li&gt;&#xA;&lt;li&gt;Human sperm cells have only one set of 23 chromosomes. This is not the complete genome of the individual.&lt;/li&gt;&#xA;&lt;li&gt;Despite comments above, human egg cells have a full two sets of chromosomes until ovulation. The fertilized zygote gets one set of chromosomes from an egg cell and one set from a sperm cell. However, the actual egg cell in the ovaries has a full two sets of chromosomes which don't all get transferred to the zygote.&lt;/li&gt;&#xA;&lt;li&gt;There is genetic variation between cells due to damage and copying mistakes.&lt;/li&gt;&#xA;&lt;li&gt;Some living humans are chimeric and are often unaware of this. They are individuals formed from distinct egg/sperm combinations. That adds extra complexity to this answer.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5100" LastActivityDate="2014-12-03T15:59:28.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24508" PostTypeId="2" ParentId="24506" CreationDate="2014-12-03T16:08:51.257" Score="3" Body="&lt;p&gt;There are two types of photoreceptor in the eye, known as rods and cones. Rods are spread equally throughout the whole retina, whereas cones are focussed in one spot known as the fovea:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/EXacI.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cones are the only type of photoreceptor that can sense colour, so rods can only sense black and white. However, rods can work in much lower light and will also work when not being focussed on. Due to what is known as 'summation of action potentials', through which nerve impulses from multiple rods add together to cause a signal to be sent to the brain, rods are much more effective than cones at sending impulses. If you've ever seen something flickering in the corner of your eye and not been able to see what it is when you've looked properly, this is probably why (&lt;a href=&quot;http://en.wikipedia.org/wiki/Peripheral_vision#Characteristics&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia: Peripheral vision characteristics&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: Further information on how vision is perceived can be found in &lt;a href=&quot;https://biology.stackexchange.com/a/20764/10067&quot;&gt;this answer&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the question of whether or not the brain tries to guess the colour I don't know. I would suggest yes, the brain compensates as much as possible for a lack of information. It's known that the brain can compensate for the blind spot where the optic nerve passes out of the eye and compensates for it using the other eye and other information (&lt;a href=&quot;http://io9.com/5804116/why-every-human-has-a-blind-spot---and-how-to-find-yours&quot; rel=&quot;nofollow noreferrer&quot;&gt;Why every human has a blind spot, and how to find yours&lt;/a&gt;). However that is just my opinion, I haven't been able to find any research relating to the idea.&lt;/p&gt;&#xA;" OwnerUserId="10067" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-12-03T16:08:51.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24509" PostTypeId="2" ParentId="24505" CreationDate="2014-12-03T16:15:38.240" Score="-1" Body="&lt;p&gt;&lt;em&gt;I haven't seen their device and I won't want to see it, I want to first understand the concept better independently. I am not an expert in biology but I have feeling how such device could be done.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;Noname covers sensitivity and new concept &lt;em&gt;&amp;quot;amplification&amp;quot;&lt;/em&gt; raising a new puzzle: &lt;em&gt;is amplification done by analog methods (op-apms), digital methods, dilution or/and some other methods?&lt;/em&gt;&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h2&gt;&lt;strong&gt;Summarising the Noname to sensitivity, amplification and background&lt;/strong&gt;&lt;/h2&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;em&gt;(I added bolding)&lt;/em&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;&lt;strong&gt;&amp;quot;Theranos is working on modular micofluidic devices/cartridges&amp;quot;&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;&amp;quot;regardless of how good your device is, at some point you start amplifying junk. The better the primers and other reagents the less junk you amplify, but at the end of the day &lt;strong&gt;you want more sample to be more sensitive&lt;/strong&gt;.&amp;quot;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;&amp;quot;they aren't/can't multiply the analyte of interest. In these tests, they rely more on dilution or small volumes to perform detection. This is where their ability to reliably dilute and correct for the dilution comes into play. -- if you had perfect detection you might be ok, but &lt;strong&gt;you generally want to analyze more blood so that statistics work in your favor and your performance goes up&lt;/strong&gt;. Most of the other chemistries, proteins, and as mentioned earlier, electrolytes will probably be ok for dilution and detection and in fact this is why there are plenty of small devices already out there that use a drop of blood and perform the same tests.&amp;quot;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;&amp;quot;They don't publicize that &lt;strong&gt;they may need to draw a venous sample (needle in your arm) for some tests&lt;/strong&gt; and depending on what tests you order, you may need a separate finger prick for each test.&amp;quot;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;where by (2) &lt;em&gt;more sensitivity can actually be a good thing&lt;/em&gt;; by (3) same tests already done by other devices in small size: &lt;em&gt;what is so special with Theranos device?&lt;/em&gt; and by (4) &lt;em&gt;one drop of blood not enough for all tests&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;h2&gt;&lt;em&gt;&lt;strong&gt;&amp;quot;What are limiations of multiplying so little blood?&amp;quot;&lt;/strong&gt;&lt;/em&gt;&lt;/h2&gt;&#xA;&lt;hr /&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Decision Analysis (DA) and Compositional Blood Analysis (CBA)&lt;/strong&gt;: I see such a device as a Decision Analysis (DA) device where you need to do compositional blood analysis (CBA). You get a lot of vague information on which you do &lt;em&gt;sensitivity analysis&lt;/em&gt;. Conventional full blood tests can be seen as devices where the sensitivity is very very low to other factors. It is not surprising that development has lasted about 10 years, sensitivity analysis is very low research project. For example, Chevron's DA model started 1990 and continuing, implementation takes time. For example, scale hydration level to some level in all samples. When you have low-quality information, you need to use ad hoc models (often based on high-quality samples) such as supposed correlations between things to improve prediction accuracy.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;1.1. What are &lt;strong&gt;Decision factors&lt;/strong&gt;?&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;1.1.1. Rheology of blood? Dry or liquid phase samples?&lt;/p&gt;&#xA;&lt;p&gt;1.1.2. Correlation of red/white shells: I don't use the word &lt;em&gt;&amp;quot;approximation&amp;quot;&lt;/em&gt; because the number of red shells correlated with the number of white shells&lt;/p&gt;&#xA;&lt;p&gt;1.1.3. Density (~1.05 kg/l)&lt;/p&gt;&#xA;&lt;p&gt;1.1.4. Colour of blood&lt;/p&gt;&#xA;&lt;p&gt;1.1.5. Hydration level&lt;/p&gt;&#xA;&lt;p&gt;1.1.6. other factors?&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h2&gt;&lt;em&gt;&lt;strong&gt;&amp;quot;How can Theranos blood test's be specific and accurate compared to conventional full blood test?&amp;quot;&lt;/strong&gt;&lt;/em&gt;&lt;/h2&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;I think this question mis-framed. It is better to ask &lt;em&gt;&amp;quot;How much extra value does such a device can offer?&amp;quot;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;Smaller size and less blood mean convenience. It may be useful with athletes, new markets. More convenient to patients/users even though suffering from some abnormalities due to its intrinsic limitations related to its small-volume measurement method.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h2&gt;&lt;strong&gt;What components do you need to multiply?&lt;/strong&gt;&lt;/h2&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;I think this is an important insight: is it possible to multiply blood somehow ensuring its quality for testing? This would make blood tests less painful for patients. Perhaps this is related to stem-cell research? Perhaps not, the Noname covers this in terms of dilution more closely.&lt;/p&gt;&#xA;" OwnerUserId="1705" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-04T09:39:38.063" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24510" PostTypeId="2" ParentId="13822" CreationDate="2014-12-03T16:52:32.290" Score="1" Body="&lt;p&gt;Renin angiotensin is for regaining homeostasis. If you have lost salts, blood pressure and blood volume will decrease due to loss of fluids. But the renin angiotensin mechanism will try to undo this by stimulating uptake of Na&lt;sup&gt;+&lt;/sup&gt; and water. But still, they can not fully compensate for loss of Na&lt;sup&gt;+&lt;/sup&gt;, INTAKE of Na&lt;sup&gt;+&lt;/sup&gt; is NECESSARY. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, the main stimulus for triggering renin angiotensin is Blood volume and pressure rather than Osmolarity of blood. In conditions like hemorrhage where blood loss occurs but there is no change in osmolarity, Renin-Angiotensin will still respond (but ADH(vasopressin) will not as ADH responds only to change in osmolarity.) &amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;— &amp;nbsp;biogirl&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-03T16:52:32.290" CommentCount="0" CommunityOwnedDate="2014-12-03T16:52:32.290" ContentLicense="CC BY-SA 3.0" />
  <row Id="24512" PostTypeId="1" AcceptedAnswerId="24518" CreationDate="2014-12-03T17:16:05.123" Score="0" ViewCount="551" Body="&lt;p&gt;I am thinking how &lt;a href=&quot;https://pubchem.ncbi.nlm.nih.gov/compound/4991#section=Biological-Half-Life&quot; rel=&quot;nofollow&quot;&gt;pyridostigmine&lt;/a&gt; can be used in the treatment of myasthenia gravis.&#xA;Its similar compound (neostigmine) is also anticholine esterase. &#xA;This compound has the indication of myasthenia gravis but with the stimulation of the nicotinic receptor. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I cannot understand how pyridostigmine is causing the effect. &#xA;Probably, pyridostigmine is similar to neostigmine in structure, which can be why more pieces of information is about neostigmine than pyridostigmine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can pyridostigmine have the indication of myasthenia gravis?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-12-03T22:15:54.810" Title="How can Pyridostigmine have the indication of Myasthenia?" Tags="&lt;human-biology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24513" PostTypeId="2" ParentId="24501" CreationDate="2014-12-03T17:47:37.597" Score="1" Body="&lt;p&gt;The situation is just as you'd imagine. In an immunocompetant recipient, a host-versus-graft reaction occurs. This is called &lt;em&gt;transplant rejection&lt;/em&gt;. Single episodes (acute rejection) are easy to treat and rarely lead to organ failure. Chronic rejection is the leading cause of organ transplant failure. The organ slowly loses its function and symptoms start to appear. This type of rejection cannot be effectively treated with immunosuppressants. Some people may need another transplant.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In bone marrow and other transplants, T cells in the allografts reconstitute T-cell immunity in the recipient. Unfortunately, these T cells recognize the recipient as 'non-self' and employ a wide range of immune mechanisms to attack recipient tissues in a process known as graft-versus-host disease (GVHD).&lt;sup&gt;[2]&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Acute GVHD&lt;/em&gt; describes a distinctive syndrome of dermatitis, hepatitis, and enteritis developing within 100 days after allogeneic hematopoietic-cell transplantation (HCT). &lt;em&gt;Chronic GVHD&lt;/em&gt; describes a more diverse syndrome developing after day 100. In addition to allogeneic HCT, &lt;em&gt;procedures associated with high risk of GVHD include transplantation of solid organs containing lymphoid tissue and transfusion of unirradiated blood products.&lt;/em&gt;&lt;sup&gt;[3]&lt;/sup&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;GVHD is increasing due to the increasing number of allogeneic hematopoietic cell transplantations (HCT). More than 25,000 allogeneic transplantations performed annually. Given current trends, the number of transplants from unrelated donors is expected to double within the next five years, significantly increasing the population of patients with GVHD.&lt;sup&gt;[4]&lt;/sup&gt; Yet the major complication, GVHD, remains lethal and limits the use of this important therapy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Long-term immunosuppressants are usually the treatment regimen for chronic GVHD. Fungal, bacterial, and viral infections are a major risk with this treatment since the immune system will be suppressed for a very long time.&lt;sup&gt;[5]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000815.htm&quot; rel=&quot;nofollow&quot;&gt;Transplant rejection&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://www.nature.com/nri/journal/v7/n5/full/nri2000.html&quot; rel=&quot;nofollow&quot;&gt;Graft-versus-host disease&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://emedicine.medscape.com/article/429037-overview&quot; rel=&quot;nofollow&quot;&gt;Graft Versus Host Disease&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[4] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735047/?iframe=true&amp;amp;width=95%&amp;amp;height=95%&quot; rel=&quot;nofollow&quot;&gt;Graft-versus-Host Disease&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[5] &lt;a href=&quot;http://my.clevelandclinic.org/health/treatments_and_procedures/hic_Bone_Marrow_and_Transplantation/hic-graft-vs-host-disease-an-overview-in-bone-marrow-transplant&quot; rel=&quot;nofollow&quot;&gt;Graft vs Host Disease: An Overview in Bone Marrow Transplant&lt;/a&gt;&lt;/sub&gt;   &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-12-03T18:00:57.017" LastActivityDate="2014-12-03T18:00:57.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24514" PostTypeId="2" ParentId="24506" CreationDate="2014-12-03T19:03:53.783" Score="7" Body="&lt;p&gt;It depends to some degree on what you define as peripheral vision. Until relatively recently, color vision in the peripheral field has been thought to be substantially less developed than color vision in the central field. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most estimates of peripheral color perception place the limit of trichromatic (RBG) vision at no more than 30 degrees from fixation; the visual field was thought to be completely color blind at about 50 degrees of eccentricity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within the last 30 years, an increased understanding of the changing spatial scale in the peripheral field has led researchers to reevaluate what is believed about peripheral function. Virtually every measure of peripheral color perception can be improved by using a suitably large stimulus in the peripheral field.&lt;sup&gt;&lt;a href=&quot;https://i.stack.imgur.com/jjsDG.jpg&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a schematic of distribution of cones in the retina. While cones are decreased in number at 60°, they do exist.&lt;sup&gt;&lt;a href=&quot;https://i.stack.imgur.com/faOv5.gif&quot; rel=&quot;noreferrer&quot;&gt;2&lt;/a&gt;&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jjsDG.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a schematic of angles on peripheral vision.&lt;sup&gt;&lt;a href=&quot;https://i.stack.imgur.com/faOv5.gif&quot; rel=&quot;noreferrer&quot;&gt;2&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/faOv5.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Previous measured sensitivity curves farther into the periphery than thought. In one paper, detection thresholds for colored disks showed that color vision, in particular color vision mediated by the L – M cone-opponent channel (luminance or blue–yellow colors), persists up to at least 50 deg. The larger the color disc, the better the peripheral color vision.&lt;sup&gt;[3]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The range of eccentricities over which red–green color vision is still possible is larger than previously thought. Color stimuli can be reliably detected and identified by chromatically opponent mechanisms even at 50 deg eccentricity. Earlier studies most probably underestimated this range. Differences could be caused by technical limitations and &lt;em&gt;the use of stimuli of non-optimal size.&lt;/em&gt; (Emphasis mine) In agreement with previous studies we found that the decline in reddish-greenish L − M color sensitivity was greater than for luminance and bluish-yellowish S − (L + M) signals. We interpret our findings as being consistent with a functional bias in the wiring of cone inputs to ganglion cells (Buzás et al., 2006) that predicts a decrease but not a lack of cone-opponent responses in the retinal periphery.  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;https://i.stack.imgur.com/jjsDG.jpg&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3953765&quot; rel=&quot;noreferrer&quot;&gt;Color vision in the peripheral retina&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;https://i.stack.imgur.com/faOv5.gif&quot; rel=&quot;noreferrer&quot;&gt;2&lt;/a&gt; &lt;a href=&quot;http://www.sharp-sighted.org/index.php?option=com_content&amp;amp;task=view&amp;amp;id=58&amp;amp;Itemid=120&quot; rel=&quot;noreferrer&quot;&gt;The Retina: Rods and Cones&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.journalofvision.org/content/9/4/26.full&quot; rel=&quot;noreferrer&quot;&gt;3 Color perception in the intermediate periphery of the visual field&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-03T19:03:53.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24515" PostTypeId="1" AcceptedAnswerId="24529" CreationDate="2014-12-03T19:37:41.997" Score="1" ViewCount="7700" Body="&lt;p&gt;I expressed a yeast vector in &lt;em&gt;E.coli&lt;/em&gt; and purified about 13µg of it. I then linearized it using a restriction enzyme, and attempted to gel purify it. I attempted this twice. The gel showed a clear bright band at the right spot, but after gel purification I end up with only 0.7µg of linear plasmid. I doubt I made the same mistake twice. What is the best way to purify a linear plasmid after digest?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The plasmid is about 3.5 kb. I incubate an overnight culture of E. coli, miniprep the following morning, elute into water. I end up with 13µg of DNA in 200µl of H&lt;sub&gt;2&lt;/sub&gt;O. I add the PmeI (10µl) and the CutSmart buffer (23µl) from NEB, incubate overnight. The following day, I run the 230µl through a 1% gel and get a single band around 3.5 kb. I excise the band, and perform a gel purification using the Biobasic kit, add denaturant (probably guanidine hydrochloride), wait for 10 minutes for the gel to dissolve, run through column, wash 2X with wash buffer with ethanol added, elute in water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,&#xA;Max &lt;/p&gt;&#xA;" OwnerUserId="10411" LastEditorUserId="3340" LastEditDate="2014-12-04T06:18:12.127" LastActivityDate="2017-08-03T19:51:30.150" Title="Purifying a linear plasmid after restriction digest?" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;" AnswerCount="2" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="24516" PostTypeId="1" CreationDate="2014-12-03T19:41:49.687" Score="4" ViewCount="211" Body="&lt;p&gt;Is there an online library that includes all known genes in stored in their nucleotide form of all living organisms? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm presuming that such a database doesn't exist. So to kick of my search, how can I find a gene amongst all the other databases? Where is a good place to start looking for information about my gene given that it is a well studied sequence? The issue is that I have been provided with the sequence, but I just don't know what organism the sequence belongs to or what it codes for.&lt;/p&gt;&#xA;" OwnerUserId="9733" LastEditorUserId="3553" LastEditDate="2016-02-29T04:30:57.390" LastActivityDate="2017-04-04T13:06:29.233" Title="Where should I start looking for an online gene library?" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;database&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24517" PostTypeId="2" ParentId="24516" CreationDate="2014-12-03T20:21:44.840" Score="8" Body="&lt;p&gt;NCBI is a good option. &#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're looking for a gene sequence,  you can search for the gene name in the nucleotide database. For example, here is the annotated human insulin gene;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/J00265.1&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/nuccore/J00265.1&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-12-03T20:52:21.063" LastActivityDate="2014-12-03T20:52:21.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24518" PostTypeId="2" ParentId="24512" CreationDate="2014-12-03T22:15:54.810" Score="2" Body="&lt;p&gt;Pyridostigmine is an analog of neostigmine, so has the same basic mechanism of action. Please forgive me for repeating information you may already know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two main families of acetylcholine receptors: muscarinic and nicotinic. Acetylcholine receptors at the neuromuscular junction (NMJ) are exclusively nicotinic (N&lt;sub&gt;1&lt;/sub&gt; or N&lt;sub&gt;M&lt;/sub&gt;), so that's the only receptor I'll address.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Myasthenia Gravis is caused by an immune response to nicotinic postsynaptic receptors on skeletal muscle. An antibody can either destroy or block the receptor site. The antibodies destroy the receptor sites more rapidly than the body can replace them. In MG, there can be as much as an 80% reduction in the number of these receptor sites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Acetylcholinesterase (AChE) is an enzyme that breaks down acetylcholine (ACh) at the synaptic cleft. AChE has a remarkably high specific catalytic activity: each molecule of AChE degrades about 25000 molecules of ACh per second. Any drug which serves to inhibit AChE will increase ACh concentration at the N&lt;sub&gt;1&lt;/sub&gt; receptor. AChE inhibitors can be irreversible or reversible. Reversible inhibitors, (competitive or noncompetitive) have therapeutic applications; irreversible AChE  modulators are toxic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carbamates are organic compounds derived from carbamic acid (NH2COOH). They are reversible AChE inhibitors. This group includes neostigmine, pyridostigmine and physostigmine. Pyridostigmine is an analog of neostigmine, so has the same basic mechanism of action. Because they are not lipid soluble, they are selective for the NMJ; both also have direct action on Nm Receptors. The major difference between them is that pyridostigmine has a slight but significantly longer duration of action.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.drugbank.ca/drugs/DB00545&quot; rel=&quot;nofollow&quot;&gt;Drug Bank: Pyridostigmine&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://neurolex.org/wiki/Category:Pyridostigmine&quot; rel=&quot;nofollow&quot;&gt;NeuroLex.org&lt;/a&gt; (get's it's info from PubChem)&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-03T22:15:54.810" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24519" PostTypeId="2" ParentId="24516" CreationDate="2014-12-03T22:41:41.197" Score="9" Body="&lt;h1&gt;Databases&lt;/h1&gt;&#xA;&lt;p&gt;There are too many databases to list here, but Wikipedia has a decent list of the &lt;a href=&quot;https://en.wikipedia.org/wiki/List_of_biological_databases#Genome_Databases&quot; rel=&quot;nofollow noreferrer&quot;&gt;genome databases&lt;/a&gt;. For example, there are databases dedicated to genes of individual species, like &lt;a href=&quot;http://www.wormbase.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wormbase&lt;/a&gt;, &lt;a href=&quot;http://www.yeastgenome.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;SGDB&lt;/a&gt; and countless others. Alternatively, as others mention a great place to kick off your search is the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/&quot; rel=&quot;nofollow noreferrer&quot;&gt;NCBI&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;h1&gt;Finding your nucleotide sequence in databases&lt;/h1&gt;&#xA;&lt;p&gt;It sounds like you already have your sequence. If you want to see if your sequence has been found elsewhere or if there are any similar sequences, you can use &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi&quot; rel=&quot;nofollow noreferrer&quot;&gt;BLAST&lt;/a&gt; from NCBI. Although it is not strictly a database in itself, it looks to align your sequence to similar sequences in external NCBI databases and quantifies the sequence similarity. It will reveal the species for you to go to a more appropriate database along with a lot of other information about the gene.&lt;/p&gt;&#xA;&lt;p&gt;There are plenty of parameters to alter to suit your specific needs, but generally, the default settings are a great place to start analysing your gene. You'll need to run a nucleotide test since you want to find the DNA sequence. The results might be difficult to interpret.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2017-04-04T02:10:07.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24520" PostTypeId="2" ParentId="24516" CreationDate="2014-12-04T00:31:36.750" Score="3" Body="&lt;p&gt;SwissProt is a human-annotated database of genes/proteins with known functions.&lt;/p&gt;&#xA;" OwnerUserId="10420" LastActivityDate="2014-12-04T00:31:36.750" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24521" PostTypeId="2" ParentId="24434" CreationDate="2014-12-04T00:53:04.357" Score="3" Body="&lt;p&gt;Clonidine is an agonist on the α2 receptor... but then again norepinephrine is also an agonist on the α2 receptor. Then the physiologic ligand of the a2 receptor, norepinephrine is autocrine (meaning it is released from a cell then binds on a receptor on the same cell) causing negative feed back and it inhibits further release of norepinephrine from the neuron thus preventing overstimulation. Clonidine is quite specific to the α2 receptor and it doesn't really stimulate α1/β1/β2. Given a situation  where only the α2 receptor is stimulated and none of the other epinephrine receptors, you would have a net decrease of sympathetic effects since the amount of norepinephrine being released is begin decreased by the stimulation of the α2 receptor on the presynaptic membrane of the sympathetic neuron. Hence clonidine is an α2 agonist that is sympatholytic&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have no clue what the difference are between these&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;agonist vs mimetic  &lt;/li&gt;&#xA;&lt;li&gt;adreno vs sympatho&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="3340" LastEditDate="2014-12-05T17:49:47.903" LastActivityDate="2014-12-05T17:49:47.903" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24522" PostTypeId="2" ParentId="24387" CreationDate="2014-12-04T01:18:52.023" Score="4" Body="&lt;p&gt;In doing search into muscle stem cells, I found some articles which discuss roles of &lt;a href=&quot;https://en.wikipedia.org/wiki/Myosatellite_cell&quot; rel=&quot;nofollow&quot;&gt;satellite stem cells&lt;/a&gt; and non satellite cells  involved in muscle regeneration: (&lt;a href=&quot;http://physrev.physiology.org/content/93/1/23.short&quot; rel=&quot;nofollow&quot;&gt;Yin, Price and Rudnicki, 2013&lt;/a&gt;,&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0012160699995659&quot; rel=&quot;nofollow&quot;&gt;Seale and Rudnicki, 2000&lt;/a&gt;, and &lt;a href=&quot;http://www.nature.com/ncb/journal/v12/n3/full/ncb2025.html&quot; rel=&quot;nofollow&quot;&gt;Mitchell et al, 2010&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other articles, that I found discussed the splicing of &lt;a href=&quot;https://en.wikipedia.org/wiki/Insulin-like_growth_factor&quot; rel=&quot;nofollow&quot;&gt;insulin-like growth factors&lt;/a&gt; (IGF-1) into the satellite stem cells rodent muscles and the subsequent expression of the gene were studied to understand how is plays a role in muscle repair (&lt;a href=&quot;http://jp.physoc.org/content/549/2/409.short&quot; rel=&quot;nofollow&quot;&gt;Hill and Goldspink, 2003&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC337031/&quot; rel=&quot;nofollow&quot;&gt;Musaro et al, 2004&lt;/a&gt;). Another study looked at how &lt;a href=&quot;https://en.wikipedia.org/wiki/Transforming_growth_factor_beta&quot; rel=&quot;nofollow&quot;&gt;transforming growth factor-&amp;beta;&lt;/a&gt; (TGF-&amp;beta;) and its interaction in the &lt;a href=&quot;https://en.wikipedia.org/wiki/Notch_signaling_pathway&quot; rel=&quot;nofollow&quot;&gt;Notch signaling pathway&lt;/a&gt; play a role in smooth muscle repair &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/stem.319/full&quot; rel=&quot;nofollow&quot;&gt;(Kurpiinski et al, 2010)&lt;/a&gt;( &lt;a href=&quot;http://www.nature.com/mt/journal/v15/n5/full/6300145a.html&quot; rel=&quot;nofollow&quot;&gt;Review Articles by Péault et al, 2007 &lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/nature/journal/v451/n7181/full/nature06800.html&quot; rel=&quot;nofollow&quot;&gt;Seagers and Lee, 2008&lt;/a&gt; )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for current methods on the application of stem cells to myogeneration or myoregeneration, there are a few papers that I found but, it seems like we are still too far away from anything that is medically feasible (&lt;a href=&quot;http://www.nature.com/cr/journal/v24/n10/full/cr201491a.html&quot; rel=&quot;nofollow&quot;&gt;Zhu et al, 2014&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23224711&quot; rel=&quot;nofollow&quot;&gt;Milner and Cameron, 2013&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully that answered your question or at least put you on the right track in your research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;b&gt;EDIT&lt;/b&gt;: I found some papers on tendon repair and growth, but the conclusions are the same, in that there is much more research and technology improvements to be done (&lt;a href=&quot;http://online.liebertpub.com/doi/abs/10.1089/ten.1999.5.267&quot; rel=&quot;nofollow&quot;&gt;Awad et al, 2007&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25266738&quot; rel=&quot;nofollow&quot;&gt;Breidenbach et al, 2014&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="8979" LastEditorUserId="8979" LastEditDate="2014-12-04T03:24:59.040" LastActivityDate="2014-12-04T03:24:59.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24523" PostTypeId="1" AcceptedAnswerId="24530" CreationDate="2014-12-04T01:37:15.453" Score="3" ViewCount="71" Body="&lt;p&gt;I need a dye that will stain stem cells (for this purpose the stem cells will proquired from chicken bone marrow).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This will be an educational hands on activity for young teenagers so ideally the dye should be:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Safe&lt;/li&gt;&#xA;&lt;li&gt;Easy to handle&lt;/li&gt;&#xA;&lt;li&gt;Stain quickly&lt;/li&gt;&#xA;&lt;li&gt;Be relatively cheap&lt;/li&gt;&#xA;&lt;li&gt;Present an obvious colour change under a low zoom microscope or the naked eye&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I vaguely remember using a dye years ago that fits this bill, but cannot recall the name or company.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastActivityDate="2015-10-17T20:43:18.160" Title="Is there a stem cell dye for education purposes?" Tags="&lt;stem-cells&gt;&lt;staining&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24524" PostTypeId="2" ParentId="11025" CreationDate="2014-12-04T03:07:26.553" Score="1" Body="&lt;p&gt;Afaik. RA and psoriasis are probably caused by a malfunction of genes which regulate IL-23 production. IL-23 is required for Th17 cells to survive. Th17 cells produce a lot of things which result in inflammation and since TNF-α is a key mediator in inflammation and break down of joints, reducing the amount of available TNF-α reduces the inflammation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;(Th17 cells produce IL-17, IL-21, IL-22, IL-6 and TNF-α. Th17 cells are playing against Treg cells, which try to protect self cells. IL-17 promote osteoclastogenesis, and osteoclasts break down bone. According to serveral wikipedia articles IL-17 induces the production of other cytokines such as IL-6, IL-1β, TNF-α. IL-21 is required for sustained CD8+ T cell effector activity. IL-22 is a mediator of cellular inflammatory responses. IL-6 modulates the resistance of T cells against apoptosis, induces activation of T helper cells and promotes osteoclastogenesis. TNF-α is an endogenous pyrogen which is able to induce fever, apoptotic cell death, cachexia, inflammation and inhibits tumorigenesis and viral replication. IL-1β is a mediator of the inflammatory response, and it is involved in the regulation of apoptosis as well.)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adalimumab is an immunoglobulin, which binds to TNF-α, and so it prevents it to bind TNF-α receptors and cause inflammation. After it is bound to its target you cannot reuse it, that's why you need daily doses of it. It is degraded by liver and kidney cells, or probably by phagocytes as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other TNF-α blocking pharmaceuticals as well. There are IL-23 inhibitors, one of them is called ustekinumab. It is an immunoglobulin too and it is used by treating psoriasis. By RA it is currently under clinical trial, but I guess it will work by RA as well. There is an IL-23 inhibitor which is not an immunoglobulin and can be taken orally, it is called apilimod. Sadly it failed the clinical trials, it had only mild effect. It probably does not reach the inflammation in sufficient amount. Maybe later there will be an effective delivery method and so a drug which can be taken orally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are alternative natural therapies: TNF-α inhibitors which you can take orally, for example γ-linolenic acid, ω−3 fatty acids, chondroitin sulfate, etc... These can be useful by mild cases of RA. Probably fever therapy works by mild cases as well. Afaik. cryotherapy has nice results in treating RA and its positive effect lasts much longer than the effects of any drugs, so if you aren't afraid of cold, that is a nice alternative therapy as well.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2013 - &lt;a href=&quot;https://www.oapublishinglondon.com/article/494&quot; rel=&quot;nofollow&quot;&gt;The interleukin-23/interleukin-17 axis and the role of Treg/Th17 cells in rheumatoid arthritis and joint destruction&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2010 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3083.2009.02361.x/pdf&quot; rel=&quot;nofollow&quot;&gt;IL-23 in the pathogenesis of rheumatoid arthritis.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2003 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2567.2003.01749.x/full&quot; rel=&quot;nofollow&quot;&gt;Dihomo-γ-linolenic acid inhibits tumour necrosis factor-α production by human leucocytes independently of cyclooxygenase activity&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0889159111004685&quot; rel=&quot;nofollow&quot;&gt;Omega-3 supplementation lowers inflammation and anxiety in medical students: A randomized controlled trial&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/ja061906t&quot; rel=&quot;nofollow&quot;&gt;Discovery of a TNF-α Antagonist Using Chondroitin Sulfate Microarrays&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://clinicaltrials.gov/ct2/show/NCT01645280&quot; rel=&quot;nofollow&quot;&gt;A Study of the Effectiveness and Safety of Ustekinumab (STELARA) and CNTO 1959 Administered Under the Skin of Patients With Active Rheumatoid Arthritis, Despite Existing Methotrexate Therapy&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://informahealthcare.com/doi/abs/10.1586/1744666X.2014.870036&quot; rel=&quot;nofollow&quot;&gt;Cryotherapy in inflammatory rheumatic diseases: a systematic review&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/art.34339/pdf&quot; rel=&quot;nofollow&quot;&gt;A Phase IIa, Randomized, Double-Blind, Placebo-Controlled Trial of&#xA;Apilimod Mesylate, an Interleukin-12/Interleukin-23 Inhibitor, in Patients With&#xA;Rheumatoid Arthritis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-12-04T03:07:26.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24525" PostTypeId="2" ParentId="10846" CreationDate="2014-12-04T03:29:22.217" Score="2" Body="&lt;p&gt;There are other histocompatibility antigens on the surface of blood cells, e.g. A, B, Rh, etc... (There are probably a lot more which change less by person to person, so they have lower effect on the outcome of blood transfusion.) These antigens can be recognized by immune cells as self, that's why they don't destroy them. Before complete differentiation RBCs have nuclei, so they can have MHC1 remnants on their surface from that period of their development. RBCs are relatively well tolerated by the immune system especially with coverage.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;wikipedia - &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood_type&quot; rel=&quot;nofollow&quot;&gt;Blood type&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2012 - &lt;a href=&quot;http://www.bloodjournal.org/content/119/6/1566&quot; rel=&quot;nofollow&quot;&gt;Transfusion in the absence of inflammation induces antigen-specific tolerance to murine RBCs&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2014 - &lt;a href=&quot;http://ijbiotech.neoscriber.com/29889.pdf&quot; rel=&quot;nofollow&quot;&gt;Simultaneous Camouflage of Major and Minor Antigens on Red Blood Cell&#xA;Surface With Activated mPEGs&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2014-12-04T03:59:44.567" LastActivityDate="2014-12-04T03:59:44.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24526" PostTypeId="2" ParentId="14067" CreationDate="2014-12-04T03:47:04.763" Score="2" Body="&lt;p&gt;There can be many responses. They are important for alloimmunity (so by transfusion, transplantation, etc...), for recognizing pathogens, cancer, virus, etc... By T cell activation, the regulator T cells recognize these antigens as self, and prevent the autoimmune reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess they were thinking on MHC1 and MHC2. MHC1 shows the inside of the cells, so e.g. by viral infection or cancer non-self oligopeptides (from degraded proteins) bind to MHC1. These non-self antigens are recognized by CD8+ T cells, which destroy the affected cells. MHC2 is used by APCs to present possible pathogens to CD4+ T cells in a similar way.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="11841" LastEditDate="2015-01-07T00:59:12.783" LastActivityDate="2015-01-07T00:59:12.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24528" PostTypeId="1" CreationDate="2014-12-04T05:44:54.157" Score="2" ViewCount="89" Body="&lt;p&gt;In one of my courses, we were discussing a paper by &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1467-2979.2006.00210.x/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Muller and van Leeuwen (2006)&lt;/a&gt; which made a lot of comparisons the differences between &lt;a href=&quot;https://en.wikipedia.org/wiki/Fish_locomotion&quot; rel=&quot;nofollow noreferrer&quot;&gt;carangiform (mullet) and anguilliform (eel)&lt;/a&gt; locomotion. While reading the text, one of the passages stood out to me:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;When comparing the estimates of vortex ring height with those of ring width, mullet and mackerel shed approximately round vortex rings, whereas eel vortex ring are almost twice as wide as they are tall. Such distorted rings are less likely to form and once formed, they are more likely to break up, all of which results in a different vortex pattern in the wake. &lt;img src=&quot;https://i.stack.imgur.com/ynn5A.png&quot; alt=&quot;Differences in Vortex Patterns (credit Muller and van Leeuwen)&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The time-resolved flow fields of eels indeed support the notion that the vortices in its wake break up: two independent studies, visualizing horizontal cross-sections through the eel’s wake, observed that individual vortex cores elongate and split into two (Muller et al. 2001; Tytell 2004a). We can therefore conclude that the shape of the propeller, and hence implicitly the propulsion mechanism, might affect wake shape. This observation also implies that a propeller shape that promotes the formation of a suboptimal wake is less efficient, and therefore the absence or presence of a wake that is predicted to maximize efficiency is a valuable indicator for the hydrodynamic efficiency of a fish’s swimming design.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So, essentially during carangiform locomotion the body of the fish moves 1/2 wavelength whereas anguiliform swimmers make 1 wavelength. My questions are how can they make such a statement when &lt;a href=&quot;https://en.wikipedia.org/wiki/Particle_image_velocimetry&quot; rel=&quot;nofollow noreferrer&quot;&gt;particle image velocimetry&lt;/a&gt; (PIV) does not adequately measure the movements of anguiliform swimmers, let alone their efficiency, when they are essentially swimming through their own vortexes? Are there any studies that address this issue in anguiliforms?&lt;/p&gt;&#xA;" OwnerUserId="8979" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-04T20:15:47.513" Title="How do you accurately measure anguiliform (eel) locomotion?" Tags="&lt;physiology&gt;&lt;ichthyology&gt;&lt;movement&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24529" PostTypeId="2" ParentId="24515" CreationDate="2014-12-04T06:09:57.213" Score="4" Body="&lt;p&gt;Can't exactly say what problem you are facing but you can follow these steps for efficient restriction digestion and elution.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Never set up a digestion reaction with more than 1µg DNA per 20µl; if you require more digested DNA, then set up multiple 20µl reactions with maximum of 1µg DNA in each (500-700ng is ideal).&lt;/li&gt;&#xA;&lt;li&gt;10µl enzyme for a 230µl reaction: bad idea. Set up 10×20µl reactions with not more than 0.5µl enzyme per reaction tube. &lt;/li&gt;&#xA;&lt;li&gt;Avoid overnight incubations; 4 hours should be sufficient (NEB PmeI is 10 units/µl and 1 unit is the amount required to cleave 1µg DNA in 1h in a 50µl reaction. You are adding 5 units in 20µl. Overnight incubation is too much)&lt;/li&gt;&#xA;&lt;li&gt;Deactivate the enzyme after the reaction.&lt;/li&gt;&#xA;&lt;li&gt;Just run a little bit of sample from one tube in the gel to see if digestion has happened. After confirming digestion simply use the PCR purification kit. You can pool your tubes. &lt;/li&gt;&#xA;&lt;li&gt;Optional: Elute in Tris-Cl pH 7.5 instead of water or use warm (60⁰C) water.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-04T06:09:57.213" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="24530" PostTypeId="2" ParentId="24523" CreationDate="2014-12-04T06:31:18.647" Score="5" Body="&lt;p&gt;There is no specific dye for stem cells. You would have to do an immuno-histochemical staining for stem cell markers such as Sox2/Oct4 etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually stem cells have a distinct morphology (round and clustered). You can use Leishman's (or Romanowsky-Giemsa) stain.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-02-09T03:50:15.083" LastActivityDate="2015-02-09T03:50:15.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24531" PostTypeId="2" ParentId="24505" CreationDate="2014-12-04T06:32:06.660" Score="2" Body="&lt;p&gt;&lt;strong&gt;Which patents are relevant for their device?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;They currently only have about 27 issued patents (US) &lt;/li&gt;&#xA;&lt;li&gt;Of those patents about 10 of them are related to network/internet/health record/algorithm (so not really about their device)&lt;/li&gt;&#xA;&lt;li&gt;The remaining patents focus on a few areas: sample acquisition (getting the blood drop and handling of it), Patch based technology (before they pivoted), sample quality analysis (this is key to making sure the small sample is good quality), microfluidics/modular device (these are the patents relating to the actual testing and device)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the limitations of multiplying so little blood?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;From a molecular standpoint (PCR) the smaller sample you start with, the less of the original nucleic acid template you have to start with.  Lower end PCR testing uses 10uL of sample.  This is ok when you are trying to bring molecular diagnostics to the point of care or developing markets, but the best PCR tests use 50uL of sample (more than a drop of blood which is traditionally 25uL or so),  regardless of how good your device is, at some point you start amplifying junk. The better the primers and other reagents the less junk you amplify, but at the end of the day you want more sample to be more sensitive.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;From a NON-molecular standpoint (chemistries, cellular analysis, coag, etc.), they aren't/can't multiply the analyte of interest.  In these tests, they rely more on dilution or small volumes to perform detection.  This is where their ability to reliably dilute and correct for the dilution comes into play. Although there is certain limits to this.  Coagulation tests would not be representative if you diluted the sample so in this case they will have to rely on working with a small volume.  Cellular analysis can only be diluted so much as you get to a point where you miss important but less common cell types.  Take eosinophils (a type of WBC) while they can get to 15 or 20 percent of all WBC cell types, in general they only make up a couple percent.  Assume that 2% of all your WBCs are eosinophils.  If you only have 3500 WBCs per 1uL of blood (which is on the lower end of normal), you have approximately only 70 of these cells in that same volume.  If you dilute the sample so that way there is more of it available for other tests like electrolytes, but you still analyze 1uL, The number of those cells is even less.  If you had perfect detection you might be ok, but you generally want to analyze more blood so that statistics work in your favor and your performance goes up. Most of the other chemistries, proteins, and as mentioned earlier, electrolytes will probably be ok for dilution and detection and in fact this is why there are plenty of small devices already out there that use a drop of blood and perform the same tests.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Their issue in diluting or amplifying analytes of interest is that biology still is governed by the laws of physics and even though technology may allow you to analyze samples down to 10nL, that just isn't use full in biology, and limits their their capability to perform the supposed menu of tests from one microtainer of blood.  They don't publicize that they may need to draw a venous sample (needle in your arm) for some tests and depending on what tests you order, you may need a separate finger prick for each test. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How can Theranos blood test's be specific and accurate compared to conventional full blood test?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;If they reliably control dilution of the small sample, they maybe able to provide high quality results for some tests.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Finger pricks actually can be easily skewed via technique.  Theranos has specially trained people to draw these samples, but it is time consuming &gt;5 mins and until it is fully automated this is one variable that no matter how good sensors are, you can't correct for variation pre-analytically when you have that small sample.  Finger pricks also skew certain tests even when technique is good such as platelet and WBC values in the CBC.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I discussed the sample volume issue above regarding PCR amplification and how good tests use up to 50uL.  So if they compare to a 10uL test, they may be able to compete, but not full lab quality.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A lot of the future techniques they have regarding small techniques (in their applications) like their coagulation tests work great in an academic setting, but they fail to be able to handle the full range of blood samples they will see, so it will be interesting to see how that plays out.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Takeaway&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Theranos is working on modular micofluidic devices/cartridges that will use small sample&lt;/li&gt;&#xA;&lt;li&gt;There are certain biological limitations that stand in the way of them performing all the tests in their catalog with only a drop of blood&lt;/li&gt;&#xA;&lt;li&gt;The FDA will eventually be requiring them to submit their tests for approval as they are currently doing tests that are available on commercially and FDA approved devices already (this makes sense because LDTs were never ment to be used in place of standard tests and equipment and since there is NO published data on their performance it can be worrisome to providers and payer)&lt;/li&gt;&#xA;&lt;li&gt;Their true business plan has yet to be elucidated, but if they really did have a box that did all this, they would be selling them to physicians and clincs where those results could actually be used in diagnosis rather than 4 hours later.&lt;/li&gt;&#xA;&lt;li&gt;I hope they succeed, but there is just way too much hype to buy in on it yet.    &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am sorry I don't have sources, most of this is from intimate knowledge of the space and from the little info available on them so I could definitely be wrong on some of this.  I hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="10424" LastActivityDate="2014-12-04T06:32:06.660" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24533" PostTypeId="1" CreationDate="2014-12-04T09:08:11.123" Score="0" ViewCount="3186" Body="&lt;p&gt;Norepinephrine is less beta2 adrenomimetic than epinephrine so more selective so less bronchospasm so may be therofore better in treatment of cardiac failure and different shocks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I am not sure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have some intuition that some of them is somehow analog of the other one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PubMed about norepinephrine in Pharmacology&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Sympathomimetics&lt;/li&gt;&#xA;&lt;li&gt;Adrenergic alpha-Agonists&lt;/li&gt;&#xA;&lt;li&gt;Vasoconstrictor Agents&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;PubMed about epinephrine in Pharmacology&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Bronchodilator Agents (beta2)&lt;/li&gt;&#xA;&lt;li&gt;Mydriatics (beta2)&lt;/li&gt;&#xA;&lt;li&gt;Adrenergic alpha-Agonists&lt;/li&gt;&#xA;&lt;li&gt;Sympathomimetics&lt;/li&gt;&#xA;&lt;li&gt;Adrenergic beta-Agonists (this causes those two first indications)&lt;/li&gt;&#xA;&lt;li&gt;Vasoconstrictor Agents&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;which is logical because epinephrine is nonselective beta2.&#xA;However, I am not sure if those properties include all accepted indications.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This proposes me that norepinephrine can be used better in acute situations. &#xA;However, I know that epinephrine injections are more given to allergic people to carry for anaphylactic shock.&#xA;&lt;strong&gt;Why so?&lt;/strong&gt;&#xA;Probably, because of price.&#xA;&lt;strong&gt;How does the indications of norepinephrine differ from those in epinephrine?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-04T09:13:35.753" LastActivityDate="2014-12-04T10:54:16.527" Title="Differentiation of norepinephrine and epinephrine in indications" Tags="&lt;pharmacology&gt;&lt;autonomic-nervous-system&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24534" PostTypeId="2" ParentId="14951" CreationDate="2014-12-04T09:25:29.517" Score="0" Body="&lt;p&gt;There is a single basal body per cilium. During cell division the centrosome has two centrioles, however, during the differentiation of citiated cells, there is an amplification of basal bodies that nucleate from the centrioles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In multiciliated cells the basal bodies arise from two pathways- 1. &lt;em&gt;de-novo&lt;/em&gt; / deuterosomal / acentriolar pathway and 2. centriolar pathway. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a work carried out by &lt;a href=&quot;http://dx.doi.org/10.1038/nature13770&quot; rel=&quot;nofollow noreferrer&quot;&gt;Al Jord et al (2014)&lt;/a&gt;, the interplay of these two pathways had been studied in the brain ependymal cells. The study shows that post division, when the cell begins to differentiate, the daughter centriole serves as a site for creation of deuterosomes. During this stage deuterosome independent procentrioles also nucleate (the centriolar pathway) on both mother and daughter centrioles. However, the contribution to basal bodies is predominantly from the deuterosomes. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;more than 90% of the centrioles were generated via deuterosomes and&#xA;  less than 10% directly from centrosomal centriole&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Following figure explains the process nicely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;img src=&quot;https://i.stack.imgur.com/Ckdl0.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not really sure about multiciliated unicellular organisms. My guess is that they retain old basal bodies and new ones are created by a similar mechanism. Most ciliates can also undergo sexual reproduction. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-01-27T10:56:12.210" LastActivityDate="2016-01-27T10:56:12.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24535" PostTypeId="2" ParentId="23770" CreationDate="2014-12-04T09:58:38.657" Score="4" Body="&lt;p&gt;This is a myth which most likely came from methological flaws in the original study. It could never be reproduced. This paper (&quot;&lt;a href=&quot;http://www.directupload.net/file/d/3801/7pifeij3_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Darwin’s Legacy: An Evolutionary View of Women’s Reproductive and Sexual Functioning&lt;/a&gt;&quot;) deals with it. The interesting part starts from page 30 and says (the references can be ressolved in the article):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Critiques of MSH Studies&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Wilson (1992) and Yang and Schank (2006),&#xA;  among others, have criticized the study design, methods, and&#xA;  statistics used by McClintock (1971) and others who have claimed&#xA;  evidence of MS. For example, McClintock &#xA;  incorrectly used the Page test for ordered hypotheses with multiple&#xA;  treatments (she used the same groups of women repeatedly instead of&#xA;  independent treatments), making it impossible to evaluate the true&#xA;  level of significance of her reported findings. Likewise, reports of&#xA;  greater estrous synchrony in chimpanzees caged together than in those&#xA;  caged apart (Wallis, 1985) and synchronization of estrogen peaks in a&#xA;  sample of five golden lion tamarins (French &amp;amp; Stribley, 1987) are&#xA;  rendered moot by the use of unsuitable statistical tests (Schank,&#xA;  2001). Furthermore, computer simulations suggested that the null&#xA;  hypothesis of no synchronization could not be rejected in either the&#xA;  chimpanzee or tamarin samples (Schank, 2001).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-12-04T11:09:24.810" LastActivityDate="2014-12-04T11:09:24.810" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24536" PostTypeId="2" ParentId="24483" CreationDate="2014-12-04T10:12:47.833" Score="1" Body="&lt;p&gt;If you are referring to reducing the titer in the immunized animal, you could give the animal a drug that has immunosuppressive properties. Velcade (PS-341) is a drug that effectively reduces plasma cell counts. There are many immunosuppressive drugs available.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you  want to reduce the antibodies affinity, you are undertaking a much more delicate process. Affinity can be transiently affected by introducing a  unfavorable environment for the antibody. You can accomplish this by changing the temp, salt conditions, pH or introducing a denaturing agent like guanidine HCL.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Changing any of these conditions in just a little excess could also result in a permanent reduction in affinity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are attempting to tailor the affinity constant of the Ab by changing the architecture of the antigen, you are correct this can be done using site directed mutagenesis. However I think it would be more effective to perform a random mutagenesis and then screen the mutants for the &lt;em&gt;Ka&lt;/em&gt; value you want.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly the antigen could also be post-translationally modified. After performing &lt;em&gt;in vitro&lt;/em&gt; transcription and translation you could modify your antigen using different strategies such as ubiquination, phosphorylation, prenylation etc... All these could potentially affect &lt;em&gt;Ka&lt;/em&gt; as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A Hybridoma system to produce a monoclonal antibody should also be explored. Here is a reputable company that produces monoclonal antibodies:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sdix.com/Products/Custom-Antibody-Services/Ab-Production-and-Services/mAb-Antibody-Development/Hybridoma-Development.aspx&quot; rel=&quot;nofollow&quot;&gt;http://www.sdix.com/Products/Custom-Antibody-Services/Ab-Production-and-Services/mAb-Antibody-Development/Hybridoma-Development.aspx&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-12-11T00:24:46.310" LastActivityDate="2014-12-11T00:24:46.310" CommentCount="15" ContentLicense="CC BY-SA 3.0" />
  <row Id="24537" PostTypeId="2" ParentId="21812" CreationDate="2014-12-04T10:19:37.590" Score="3" Body="&lt;p&gt;As WYSIWYG wrote, energy is the answer, but to clarify the dependence of energy from momentum... sorry, the dependence of frequency from wavelength, have a look at the animation on this web page: &lt;a href=&quot;http://www.acs.psu.edu/drussell/Demos/wave-x-t/wave-x-t.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.acs.psu.edu/drussell/Demos/wave-x-t/wave-x-t.html&lt;/a&gt;, posted here in what I believe complies with fair use legislation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xRmLX.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It represents a sinusoidal wave, the basic component of any disturbance (as long as you can count on linearity, but that's another matter...).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Frequency tells you how fast the red dot goes up and down. This is what a receptor put in that specific position will sense: a disturbance (here it's the height of a string, in your case the amplitude of the electric field) changing $\nu$ times per second.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wavelength, on the other hand, tells you how far the maxima and minima of the sinusoid are separated in the medium. In this case, two subsequent crests are separated by $\lambda$ meters. For a given disturbance frequency, this number depends on how fast the wave is allowed to travel in the medium. A slow wave will have a shorter wavelength (because it will travel a smaller distance in space during the time the red dot completes a cycle); conversely, a fast wave will have a longer wavelength.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: the speed can depend on the frequency of the disturbance - in that case the medium is said to be 'dispersive' and the relation between frequency and wavelength (or energy and momentum, or - if you are into quantum physics - between energy E and wavenumber k) is called a '&lt;a href=&quot;http://en.wikipedia.org/wiki/Dispersion_relation&quot; rel=&quot;nofollow noreferrer&quot;&gt;dispersion relation&lt;/a&gt;'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In an isotropic homogeneous medium, the speed is the same in every point and in any direction and you can write&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\lambda(\nu) = c(\nu) / \nu $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The frequency is determined by the physical process in the source. It's very hard to change the frequency (i.e. the color, in the visible) of a light wave - you have to resort to nonlinear effects to do that. The wavelength is the result of the interaction with the medium, and changes all the time. But it's customary to express a sort of implied equivalence between frequency and wavelength based on the behavior the light wave would have in vacuum. Hence, when one says 550 nm photon, he is usually implying a photon with en energy corresponding to &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$E = h \ \nu = h \ c_0 /\lambda = 4.226 10^-19 \ J = 2.64 \ eV$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where $c_0$ is the speed of light in vacuo.&#xA;(Note: the latter value is computed from the one before diving by the charge of the electron).&lt;/p&gt;&#xA;" OwnerUserId="10393" LastEditorUserId="10393" LastEditDate="2014-12-04T10:26:25.207" LastActivityDate="2014-12-04T10:26:25.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24538" PostTypeId="2" ParentId="24533" CreationDate="2014-12-04T10:22:12.097" Score="1" Body="&lt;p&gt;The differences in the action/indication is because of differential affinity of the two molecules to different adrenergic receptors. The wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Adrenergic_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ardenergic receptor&lt;/a&gt; has a table which summarizes this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia doesn't cite references for it. You may have a look at some of the following old articles.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.2165/00003495-198400282-00002&quot; rel=&quot;nofollow noreferrer&quot;&gt;α- and β-Adrenergic Receptor Subtypes&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the periphery, α1-receptors are located postsynaptically, mediating the excitatory effects of catecholamines at α-receptors. α2-Adrenoceptors, on the other hand, are autoreceptors involved in the regulation of noradrenaline (norepinephrine) release. In the central nervous system, both α1- and α2-receptors exist on postsynaptic cells; there are also 2 principal subtypes of β-adrenoceptors. β1-Receptors have a high affinity for both noradrenaline and adrenaline (epinephrine) and are found in the heart, brain, and adipose tissue. β2-Receptors have a low affinity for noradrenaline and are involved in mediation of relaxation of vascular and other smooth muscles and in many of the metabolic effects of catecholamines.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/pdf/10.1146/annurev.ne.04.030181.002223&quot; rel=&quot;nofollow noreferrer&quot;&gt;β-Adrenergic Receptor Subtypes: Properties, Distribution, and Regulation&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/UriSH.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;strong&gt;NE&lt;/strong&gt;=Norepinephrine, &lt;strong&gt;EPI&lt;/strong&gt;=Epinephrine, &lt;strong&gt;ISO&lt;/strong&gt;=Isoprenaline&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-04T10:54:16.527" LastActivityDate="2014-12-04T10:54:16.527" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24539" PostTypeId="1" AcceptedAnswerId="24541" CreationDate="2014-12-04T10:38:12.893" Score="1" ViewCount="426" Body="&lt;p&gt;I have a plasmid with the P15A origin which apparently has a low copy number (see &lt;a href=&quot;http://www.qiagen.com/resources/technologies/plasmid-resource-center/growth%20of%20bacterial%20cultures&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;). This would explain why my purification yeilds for subsequent digestion are low (gel shows the plasmid after digestion and clean-up with 5µl being loaded). I am currently growing my E. coli containing plasmid up in 5mls overnight before doing a miniprep. My question is should I grow my 5ml cultures up for longer (2 days) or just give it up and do a larger amount for Midiprep.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/2lh0z.jpg&quot; alt=&quot;plasmid gel&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am also curious as to what actually controls the plasmid copy number inside cells. An explanation of the regulation of plasmid copy number would be much appreciated.&lt;/p&gt;&#xA;" OwnerUserId="6811" LastEditorUserId="3340" LastEditDate="2014-12-04T11:14:30.573" LastActivityDate="2014-12-05T09:30:26.673" Title="Low copy numbers of plasmids" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;plasmids&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24541" PostTypeId="2" ParentId="24539" CreationDate="2014-12-04T11:23:34.720" Score="3" Body="&lt;ul&gt;&#xA;&lt;li&gt;I am sure you have done it; just a note to others: do a PCR screen to&#xA;ascertain that the plasmid is there.&lt;/li&gt;&#xA;&lt;li&gt;For minipreps you generally do not need a starter culture. &lt;/li&gt;&#xA;&lt;li&gt;If you have screened your clones and now just want to amplify and keep the plasmid for cloning purposes then go for a maxiprep with 200-400ml cultures. &lt;/li&gt;&#xA;&lt;li&gt;Do not overgrow the cells, your extraction becomes difficult and you would get even worse yields. Just set up a huge culture and pool the cells before extraction. Always seed and harvest cells that are in exponential growth phase.&lt;/li&gt;&#xA;&lt;li&gt;If you need to screen the plasmid for clones or something then do a colony PCR, keep the colony inoculated in a small culture (make a temporary glycerol stock if your screening is taking time). If screen is positive then incoulate the &lt;strong&gt;starter culture&lt;/strong&gt; for maxiprep/gigaprep culture with this stock. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-05T09:30:26.673" LastActivityDate="2014-12-05T09:30:26.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24542" PostTypeId="2" ParentId="24441" CreationDate="2014-12-04T11:31:38.747" Score="3" Body="&lt;p&gt;Lets start with the absorption spectrum first (image from the Wikipedia page in &lt;a href=&quot;https://en.wikipedia.org/wiki/Chlorophyll&quot; rel=&quot;nofollow noreferrer&quot;&gt;chlorophyll&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oi8Yk.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you see in the figure is the absorption of light thoughout the visible spectrum by chlorophyll a (blue) and b (red). The higher the peaks get, the higher the absorption is. What we can see, is that chlorophyll absorbs light roughly until 500 nanometers (nm) and from 620 nm. The light between this is not absorbed, but reflected. This is the green light and the reason why leafs are green. Above 700 nm the light is reflecxcted again, this is the reason why green leafs are visible white in infrared photography.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The peaking of the both chlorophylls ensures that light of the wavelength can be used efficiently for photosynthesis. Since leafs contain both chlorophylls, this gives a wider range for energy absorption than with only one. Additionally both absorption maxima are far enough from each other to prevent one chlorophyll from &quot;stealing&quot; light from the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The light closer located to the peak transmits more energy because it will absorbed better. The closer you get to the maxima of the absorption curves, the higher the absorption and the energy transfer will be.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-04T11:31:38.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24544" PostTypeId="2" ParentId="24481" CreationDate="2014-12-04T13:39:47.590" Score="16" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Color vision is not based on a calibration to the sky, vegetation and blood. The current leading theory of the development of trichromatic vision in humans is based on the foraging of fruit in our primate ancestors.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The places of red, green and blue wavelengths in the &lt;strong&gt;spectrum&lt;/strong&gt; are physically defined and, therefore, not arbitrary; see &lt;a href=&quot;https://biology.stackexchange.com/questions/21812/is-human-vision-sensitive-to-frequency-or-wavelength&quot;&gt;this question on Biology SE&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before continuing, it is good to mention that &lt;strong&gt;trichromacy&lt;/strong&gt; (the presence of red, green and blue cones in the retina) is typical for &lt;strong&gt;primates&lt;/strong&gt;. For example, dichromacy (&amp;lt;500 and &gt;500 nm cones) is the most common configuration in mammals. The split in red and green photopigment in primates developed relatively late in evolution (30-40 mln years ago), inferring trichromacy in primates from a dichromatic ancestor. Note that many avian and aquatic species may be tetrachromats or up (4 or more photopigments) (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0896627300808454&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nathans et al. 1999&lt;/a&gt;), with the mantis shrimp featuring no less than 10(!) different photopigments (&lt;a href=&quot;http://web.qbi.uq.edu.au/ecovis/Images/Justin/1989%20A%20retina%20with%20at%20least%20ten%20spectral%20types.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cronin &amp;amp; Marshall, 1989&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is believed that the red-green-blue system in primates has evolved due to its benefits for &lt;strong&gt;identifying fruit on a background of foliage, and to assess the ripeness of fruits&lt;/strong&gt;. The food of monkeys typically consists of fruit, and young leaves. Young leaves are light-green, while ripe fruits are often yellow (e.g., bananas) and orange (e.g. oranges, mangos) (&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/263/1370/593.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Osorio &amp;amp; Vorobyev, 1996&lt;/a&gt;). Unripe fruits typically contain chlorophyll and resemble the color of foliage (green). Hence, to discern ripe, nutritious fruits (yellow-orange or 570-620 nm) from foliage (green or 495-570 nm - frequencies mentioned were copied from &lt;a href=&quot;http://en.wikipedia.org/wiki/Visible_spectrum&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;), it makes sense to have good resolution in the red-green area. The red opsin has its maximum at 530, and the green at 560 nm. The blue has its peak a lot lower at 425 nm (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0896627300808454&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nathans et al. 1999&lt;/a&gt;). Hence, the red and green opsins, which evolved late in evolution, are both right in the &quot;ripe fruit area&quot; and have absorption spectra very close together. Hence, there is a lot of color sensitivity (high color resolution) in the red-green area, which covers reds, oranges, yellows and greenish colors. This gives primates a very high sensitivity to recognize fruits, and especially ripe fruits in a green background. The resolution in the green-blue range is smaller (blues, purples). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a background: color vision in trichromats works by color opponency, and specifically a yellow-blue and red-green color opponency. This means there exists no yellowish blue hue, or a reddish green (&lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CB8QFjAA&amp;amp;url=http%3A%2F%2Ffaculty.washington.edu%2Fsbuck%2F545ColorClass%2FDeValois.DeValois.1993.pdf&amp;amp;ei=MGGAVJHGNs_k8AXckYKIDQ&amp;amp;usg=AFQjCNGsOvlT1CU4N19IDDES5NN1Ip7mvg&amp;amp;sig2=I2xYLmDhgEGJyXefYMNhiQ&amp;amp;bvm=bv.80642063,d.dGc&quot; rel=&quot;nofollow noreferrer&quot;&gt;De Valois &amp;amp; De Valois, 1993&lt;/a&gt;). The red-green opponency means that we have exquisite sensitivity in the red-green pathway, as red cones suppress green cone output and vice versa. In other words, there is a high color acuity in the red-green area that helps to recognize fruits.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note: The trichromat color vision scenario in primates supports the notion that cats (for example), being predators with dichromatic vision, do not benefit from being able to identify ripe and unripe fruits, as mentioned by @GoodGravy. In contrast, cats need excellent night vision and motion sensitivity, being nocturnal hunters. Indeed, color vision versus night vision, and color vision versus high motion sensitivity are both trade-offs that do not go hand in hand (&lt;a href=&quot;http://lup.lub.lu.se/record/131377/file/624203.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kelber et al, 2002&lt;/a&gt;).                        &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://web.qbi.uq.edu.au/ecovis/Images/Justin/1989%20A%20retina%20with%20at%20least%20ten%20spectral%20types.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cronin &amp;amp; Marshall, &lt;em&gt;Nature&lt;/em&gt; (1989); 137-40&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CB8QFjAA&amp;amp;url=http%3A%2F%2Ffaculty.washington.edu%2Fsbuck%2F545ColorClass%2FDeValois.DeValois.1993.pdf&amp;amp;ei=MGGAVJHGNs_k8AXckYKIDQ&amp;amp;usg=AFQjCNGsOvlT1CU4N19IDDES5NN1Ip7mvg&amp;amp;sig2=I2xYLmDhgEGJyXefYMNhiQ&amp;amp;bvm=bv.80642063,d.dGc&quot; rel=&quot;nofollow noreferrer&quot;&gt;De Valois &amp;amp; De Valois, &lt;em&gt;Vis Res&lt;/em&gt; (1993); &lt;strong&gt;33&lt;/strong&gt;(8): 1053-65&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://lup.lub.lu.se/record/131377/file/624203.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kelber &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Biol Rev&lt;/em&gt; (2003); &lt;strong&gt;78&lt;/strong&gt;: 81–118&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0896627300808454&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nathans &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Neuron&lt;/em&gt; (1999); &lt;strong&gt;24&lt;/strong&gt;(2): 299–312&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2016-09-12T22:10:29.823" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24545" PostTypeId="2" ParentId="24515" CreationDate="2014-12-04T14:23:27.030" Score="3" Body="&lt;p&gt;Why do a gel purification? you can just use a kit similar to QIAGEN gel extraction kit and do a non gel based plasmid purification and elution, using the buffers used as usual! PCR DNA clean up kits will do as well!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-12-04T14:23:27.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24546" PostTypeId="1" CreationDate="2014-12-04T13:32:53.977" Score="3" ViewCount="614" Body="&lt;p&gt;I am aware of satiety only through experience, rules-of-thumb and possibly myths. For example: white bread is not filling, a pasta meal can be filling but because we &quot;burn&quot; carbs quickly pasta itself is not, and I personally find fruit in the melon family filling. (But that could be because I hate them ;) )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a formal measure of satiety? How does it work?&lt;/p&gt;&#xA;" OwnerUserId="11526" OwnerDisplayName="d3vid" LastEditorUserId="3128" LastEditDate="2014-12-11T22:31:34.613" LastActivityDate="2014-12-11T22:31:34.613" Title="How is satiety measured?" Tags="&lt;digestive-system&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24548" PostTypeId="1" AcceptedAnswerId="24558" CreationDate="2014-12-04T15:39:58.903" Score="1" ViewCount="114" Body="&lt;p&gt;I recently read of a study that investigated the ethics of child's biological sex choice in humans, and now I want to find out how this can/could be done. Does anyone know of scientific papers or journals that describe the methods in some detail? The answers I was finding in my own search were not as specific as I would like.&lt;/p&gt;&#xA;" OwnerUserId="9018" LastEditorUserId="6511" LastEditDate="2014-12-05T00:02:09.760" LastActivityDate="2014-12-05T00:58:39.757" Title="(how) is it possible to choose the biological sex of a child?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="8" ClosedDate="2014-12-05T23:24:43.763" ContentLicense="CC BY-SA 3.0" />
  <row Id="24549" PostTypeId="1" CreationDate="2014-12-04T15:51:55.297" Score="3" ViewCount="857" Body="&lt;p&gt;Take two people Sam (average human) and Jack. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Jack says to Sam &quot;I'm going to show you some skittles (or other object) and I want you to tell me as quick as you can how many I'm holding.&quot; He opens his hands and there are three. Sam can instantly tell there are three. Then Jack shows five to Sam, who takes a little longer, as he knows there are around 4/5 but can't tell so has to count. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the number of skittles increases, Sam takes longer and longer to answer to the point where he needs to count the skittles one at a time to be sure, and sometimes to even recount them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is it that we can instantly if we are looking at three maybe four objects but any more than this we cant? It gets harder and harder to estimate?&lt;/p&gt;&#xA;" OwnerUserId="6179" LastEditorUserId="5198" LastEditDate="2014-12-04T18:35:39.710" LastActivityDate="2019-01-25T13:08:23.093" Title="What are limitations on the number of objects the eye determine at a glance?" Tags="&lt;brain&gt;&lt;vision&gt;&lt;memory&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24550" PostTypeId="1" AcceptedAnswerId="24551" CreationDate="2014-12-04T16:18:20.887" Score="0" ViewCount="46" Body="&lt;p&gt;Do diploids such as humans end up with a mixture of two different shaped proteins where the appropriate gene is expressed differently in the two halves of a chromosome pair or is there some governing factor that dictates that only one of the alleles is ever used to direct protein synthesis?&lt;/p&gt;&#xA;" OwnerUserId="6951" LastActivityDate="2014-12-04T16:35:10.367" Title="If gene differs between chromosome pair does individual get a mixture of protein shapes?" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;protein-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24551" PostTypeId="2" ParentId="24550" CreationDate="2014-12-04T16:35:10.367" Score="0" Body="&lt;p&gt;Yes, that mixture of shapes can happen.  Differences in the nucleotide base sequences between the two alleles of a gene can lead to differences in amino acid sequence, which in some cases large differences in protein shape.  One example would be if one allele changed a cystine codon to any other codon, leading to loss of a disulfide bond needed to stabilize the tertiary structure of a protein.  For an extreme example, consider a mutation causing sickle-cell anemia; in this case, the disease-causing allele leads to altered shape of the entire red blood cell.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a heterozygote carries a healthy allele and a disease-causing recessive allele, the protein produced by the healthy allele provides enough activity to mask the lack of activity of the &quot;broken&quot; protein provided by the recessive allele.  If, instead of being a true recessive, the disease-causing allele is partially penetrant, then the heterozygote would suffer from the reduced level of the active protein (only one allele is providing the good stuff).&lt;/p&gt;&#xA;" OwnerUserId="10430" LastActivityDate="2014-12-04T16:35:10.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24552" PostTypeId="2" ParentId="24546" CreationDate="2014-12-04T17:41:28.857" Score="10" Body="&lt;p&gt;Satiety is complex, and there are several kinds of satiety, all of which come into play in different circumstances. &lt;strong&gt;Things that decrease or halt our eating are called &lt;em&gt;satiety signals&lt;/em&gt;.&lt;/strong&gt; Different satiety signals are put out by different substances (carbohydrates, fats and proteins) as well as by things like gut stretching and other signals. There is also a psychological component to override satiety signals (company during meals, appearance of food, cost, etc.). The best measure of satiety may well be &lt;em&gt;when a person stops eating a given meal&lt;/em&gt;. In lab conditions, the meals are carefully calibrated, but people (and animals) can feed as long as they desire to (&lt;em&gt;ad lib&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Historically, satiety was thought to be the end product of serum glucose, available energy based on body heat, fat utilization by the liver, and the generation of ATP and other energy-rich molecules by the liver and/or brain. For the most part, these hypotheses have not withstood the test of time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Three major signals influence food intake: satiety signals, adiposity signals, and central effectors. For the sake of simplicity, I'll deal only with satiety signals. Satiety signals (SS) arise from the GI tract and related organs during a meal, and influence eating behavior by activating peripheral nerves passing from the GI tract to the brain, or by recognition by brain receptors.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As food interacts with the lining of the stomach and intestine, gut peptides and other signals that coordinate/optimize the digestive process are secreted. The signals that inform the CNS function as satiety signals. Different signals are secreted in response to carbohydrates, fats, and proteins, and it's the specific mix of signals that informs the brain as to what precisely has been eaten.&lt;sup&gt;[2]&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cholecystokinin (CCK) is the most extensively studied gastrointestinal satiety hormone. It is secreted by cells in the duodenum and jejunum in response to ingested fat and protein in chyme (food plus gastric fluid). Giving CCK IV decreases ad lib meal size, while blocking CCK receptor sites will increase ad lib eating per meal.&lt;sup&gt;[3]&lt;/sup&gt;&lt;sup&gt;[4]&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carbohydrates and fats as the most effective stimulators of Glucagon-Like Peptide (GLP-1) and Peptide YY (PYY). IV GLP-1 decreases meal size by promoting early satiety.&lt;sup&gt;[5]&lt;/sup&gt; Within the CNS, PYY is detectable in the hypothalamus, medulla, pons, and spinal cord.&lt;sup&gt;[6]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Enterostatin is a protein which is broken down into a digestive lipase and a five-peptide fragment (Ala-Pro-Gly-Pro-Arg (APGPR) in humans). The appetite regulating effects of APGPR in the brain are specific to high-fat or fat diets but not towards diets rich in protein or carbohydrate.&lt;sup&gt;[6]&lt;/sup&gt;&lt;sup&gt;[7]&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Amylin decreases meal size in rats, probably through the same pathway as CCK. Oxyntomodulin (OXM) and pancreatic polypeptide (PP) are also meal terminators. Pre-prandial subcutaneous administration of OXM to overweight and obese humans over a 4-week period resulted in a significant reduction in body weight of 2.3 kg, compared with 0.5 kg for the placebo arm.&lt;sup&gt;[9]&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a growing field, and there is more suspected, and more to prove. But one can see that there is no one measure of satiety.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] That satiety signals come from the stomach and beyond was shown by &quot;fake eating&quot;, that is, diverting swallowed food from the stomach by creating a fistula. If food is allowed to enter the stomach, satiety signals are elicited; if not, eating continues for a long time.&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://ajpgi.physiology.org/content/286/1/G7&quot;&gt;Gastrointestinal Satiety Signals I. An overview of gastrointestinal signals that influence food intake&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://www.siumed.edu/~astrader/Docs/Gastrointestinal%20hormones%20and%20Satiety.pdf&quot;&gt;Gastrointestinal hormones and satiety&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[4] Rats with spontaneous mutations of the CCK-1 receptor (called&#xA;OLETF -Otsuka Long Evans Tokushima Fatty- rats) eventually become obese&#xA;during their lifespan.&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[5] &lt;a href=&quot;http://ajpregu.physiology.org/content/276/5/R1541&quot;&gt;Glucagon-like peptide-1 promotes satiety and reduces food intake in patients with diabetes mellitus type 2&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[6] &lt;a href=&quot;http://themedicalbiochemistrypage.org/gut-brain.php#pyy&quot;&gt;Introduction to Gut-Brain Interactions&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[7] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12855414&quot;&gt;Enterostatin inhibition of dietary fat intake is dependent on CCK-A receptors.&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[8] &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0031938495020675&quot;&gt;Amylin decreases meal size in rats&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[9] &lt;a href=&quot;http://themedicalbiochemistrypage.org/gut-brain.php#enterostatin&quot;&gt;Gut-Brain Interrelationships and Control of Feeding Behavior&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-04T17:41:28.857" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24553" PostTypeId="1" CreationDate="2014-12-04T18:06:03.617" Score="6" ViewCount="1575" Body="&lt;p&gt;I have been reading about the human liver and zebra fish heart muscle having the ability to regenerate. It seems to me that these organs have very little chance to become damaged or worn out. At the very least their chances of being damaged are comparable to other internal organs. So why those particular organs have the regenerative capability?&lt;/p&gt;&#xA;" OwnerUserId="1766" LastEditorUserId="1766" LastEditDate="2014-12-05T18:33:53.403" LastActivityDate="2014-12-24T12:00:34.133" Title="Why do some internal organs regenerate?" Tags="&lt;cell-biology&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="24554" PostTypeId="2" ParentId="24549" CreationDate="2014-12-04T18:30:12.917" Score="3" Body="&lt;p&gt;The answer to this question is complicated, but assume it's not for the moment. The easy answer is that our eyes can detect patterns we're familiar with and &quot;produce&quot; an answer in the form of a number. Unfamiliar patterns do not produce this 'number'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take a die. We are immediately aware of the number of dots in the typical arrangement of one to six. We need expend no counting to do so. If the skittles are arranged in the familiar die pattern, we will have no problem knowing if there are 4 or 6 skittles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given a pair of dice, any gambler can tell you what number any two faces adds up to without counting the spots. Do it long enough, and your brain is on auto-recognize. In your example, if Sam is a gambler, and the skittles are arranged like the spots on two dice, again, no problem telling between 2-12 skittles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you arrange things in a comfortable pattern, this can go on into the hundreds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9EQGr.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above was easily recognized by you as nine, I presume.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EYGEG.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/rcSex.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Someone good with pattern recognition will know that the above left is 25 dots. However, they will not know that there are 25 dots in the above right.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the easy answer is that the eye can grasp high numbers of things if they are presented in a familiar pattern. The normal mind, however, is not able to do so with higher numbers arranged in a random pattern. And, random is how most things present themselves. So, we need to count.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-04T18:30:12.917" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24555" PostTypeId="1" AcceptedAnswerId="25856" CreationDate="2014-12-04T19:30:53.813" Score="11" ViewCount="2119" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/a/2280/3885&quot;&gt;This answer&lt;/a&gt; explains the sensation of extremities &quot;falling asleep&quot; as a result of sustained pressure on a nerve. The answer links to an external web page that says that the feeling &quot;quickly goes away once the pressure is relieved.&quot;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my experience, however, it doesn't usually go exactly like this.  For me at least, usually what happens is I will start feeling a tingling sensation in my feet after sitting in an awkward position for an extended period of time. If I ignore the sensation for long enough, it continues to get worse until I finally do stand up.  But after I stand up, rather than the sensation quickly disappearing, I find that usually it suddenly gets much worse for a period of time.  What started as an annoying tingling when I was sitting quickly turns into something quite uncomfortable upon standing up, even to the point where I am not able to walk around properly until the sensation passes a few minutes later.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But once I am standing up, the nerve shouldn't be pinched anymore, so why does the sensation of my foot being &quot;asleep&quot; remain for a few minutes after standing up, and why does it actually seem to briefly get worse &lt;em&gt;after&lt;/em&gt; I have already stood up and &quot;unpinched&quot; the nerve?&lt;/p&gt;&#xA;" OwnerUserId="3885" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-12-14T21:39:35.467" Title="What causes feeling of feet falling asleep to be delayed?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24556" PostTypeId="1" CreationDate="2014-12-04T19:45:37.363" Score="2" ViewCount="106" Body="&lt;p&gt;I feel there is a part of the theory of evolution I'm not understanding correctly or maybe I'm missing it, but would like cleared up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I understand, over time random mutations occur which in some cases provide an advantage allowing that animal to survive and reproduce. Its children will have that mutation allowing them to survive and so on over many many years until it evolves into a new species and / or the old ones become extinct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example the rock pocket mouse.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The part I'm getting stuck on is that unless these mutations happen instantly and in a large number, given its over such a big time scale how do animals who are not well adapted get enough time to evolve to survive?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example is fish that evolve to be able to &quot;walk&quot; out of the sea to escape predators.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If moving out allowed them to survive how did they get enough time to evolve and not be made extint in the time they didn't not have these limbs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully I have explained myself clearly :)&lt;/p&gt;&#xA;" OwnerUserId="10431" LastEditorUserId="3340" LastEditDate="2014-12-05T08:37:44.157" LastActivityDate="2015-04-15T00:49:13.847" Title="Duration of selection and survival of the fittest" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24557" PostTypeId="2" ParentId="24556" CreationDate="2014-12-04T20:05:09.993" Score="3" Body="&lt;p&gt;Could not fit in a comment..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Welcome to Biology.SE! Here are a bunch of comments.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The sentence &lt;code&gt;until it evolves into a new species and / or the old ones become extinct&lt;/code&gt; sounds weird and there seems to be some confusion between evolution and speciation. Also it seems that you have a very static view of what is a species, as if species were predetermined categories into which evolution came to show itself!&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I am not sure but I think your question has to do with &quot;valley crossing&quot;, that is &quot;how can a population evolve toward some phenotypic trait if intermediate phenotypic traits are not fit?&quot; Is that your question? You may be interested in &quot;shifting balance theory&quot; but it might be a bit too advanced. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It is common to overconsider the valley to cross (the deleterious impact of interemediate traits) and those traits are not necessarily so deleterious&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Mutations do not always have small effects on traits. One mutation may have some very important impact and therefore, one mutation alone might be enough to cross a whole valley! You amy be interested in Fisher's geometric model. Fisher's geometric model is just some very arbitrary model and is not much inspired by any biological observation but it helps getting the concept of how mutations impact fitness (=function of survival and reproductive fitness).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When you say &lt;code&gt;how do animals who are not well adapted get enough time to evolve to survive?&lt;/code&gt; I may use the word &lt;code&gt;animals&lt;/code&gt; to refer to populations or to individuals in a population (extinction of genotype is a population and extinction of populations are two different things). If you referred to individuals then, your interest seems to be into &quot;valley crossing&quot; and &quot;mutational effect&quot;(effect of a mutation on phenotype or fitness). If you referred to populations, then you may be interested in &quot;evolutionary rescue&quot; or more broadly speaking in the so-called &quot;theory of extinction&quot;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There are probably other posts (or part of answers) on this site that will help you. A very good answer would be very very long. But maybe a moderately good answer may be relatively short!&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2014-12-04T20:05:09.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24558" PostTypeId="2" ParentId="24548" CreationDate="2014-12-04T22:58:27.377" Score="2" Body="&lt;p&gt;The main technique is sperm separation or sorting, where you separate sperm by gender, and only use the gender that you want. Existing techniques aren't perfect. AFAIK, they are typically less than 90% accurate, but it is still better than 50%. Typically, this involves some type of cell sorting device often with some kind of fluorescent tag marker.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second technique is embryo screening. Often, with IVF, you screen and can confirm the gender that you want before implanting the embryo in the mother.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Links:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.fertility-docs.com/programs-and-services/gender-selection/select-the-gender-of-your-baby-using-pgd.php&quot; rel=&quot;nofollow&quot;&gt;http://www.fertility-docs.com/programs-and-services/gender-selection/select-the-gender-of-your-baby-using-pgd.php&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.in-gender.com/Gender-Selection/MicroSort/&quot; rel=&quot;nofollow&quot;&gt;http://www.in-gender.com/Gender-Selection/MicroSort/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5100" LastActivityDate="2014-12-04T22:58:27.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24559" PostTypeId="1" CreationDate="2014-12-04T23:28:11.360" Score="1" ViewCount="72" Body="&lt;p&gt;I have had a look at previous inhaled anesthetics and many of them appear to be fluorocarbons. What could be the mechanism behind fluorine's anesthetic properties? Is it the specific bonding pattern or the molecules involved? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize anesthetics are rather unknown I just wondered what people have as a hypothesis?&lt;/p&gt;&#xA;" OwnerUserId="10433" LastActivityDate="2014-12-05T03:08:42.443" Title="Anesthetics, specifically inhaled anesthetics" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;pharmacology&gt;&lt;pharmacokinetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24560" PostTypeId="1" AcceptedAnswerId="24596" CreationDate="2014-12-04T23:29:41.730" Score="4" ViewCount="13251" Body="&lt;p&gt;Why do we have to exhale in order to talk? From looking on Wikipedia, it seems like it has something to do with the glottis, but I'm not clear on the mechanism that makes speech sound so different when air is coming in.&lt;/p&gt;&#xA;" OwnerUserId="10432" LastActivityDate="2020-05-13T14:22:50.267" Title="Why can't people talk while inhaling?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;breathing&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24561" PostTypeId="1" AcceptedAnswerId="24570" CreationDate="2014-12-04T23:34:14.883" Score="8" ViewCount="217" Body="&lt;p&gt;I can't remember which question it was, but in the past here, it was explained to me that memory is actively stored in the brain, rather than &quot;physically&quot;. Meaning, memories are made up of the brain's activity, not its physical cell structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure I have that right though. I mean, that, for one thing seem inefficient and overly complex. It seems like a vast amount of energy would be required to store so much information in the form of activity patterns. Maybe I misunderstood. So I'm asking. If my brain lost all of its energy (activity) for a moment (for example, one second), would my memory be gone too? &lt;/p&gt;&#xA;" OwnerUserId="19073" LastEditorUserId="19073" LastEditDate="2014-12-05T03:17:34.030" LastActivityDate="2014-12-05T08:15:03.487" Title="If my brain lost all of its activity for a moment, would my memory be gone too?" Tags="&lt;neuroscience&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24564" PostTypeId="1" AcceptedAnswerId="24581" CreationDate="2014-12-05T01:33:28.800" Score="4" ViewCount="101" Body="&lt;p&gt;I know that there is a variable region on antibodies which can recognize a wide variety of antigens, and that germinal centers create more &quot;fit&quot; antibodies to respond to an infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I was just wondering:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Does this process itself evolve? Only vertebrates have this type of immune system if I understand correctly, do we actually get better (faster/more efficient) at responding to disease?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is there any antigen which antibodies don't recognize?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Can an organism be so efficient at this process of immune response, that it essentially never gets sick or dies of disease?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There are cases where organisms contain viruses which do not harm them. Could an organism have this relationship with all viruses? As in, no virus is actually a disease to them?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="10435" LastActivityDate="2014-12-05T10:28:02.417" Title="A few questions regarding immunology" Tags="&lt;molecular-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-12-05T11:41:21.403" ContentLicense="CC BY-SA 3.0" />
  <row Id="24567" PostTypeId="2" ParentId="24561" CreationDate="2014-12-05T02:47:05.817" Score="1" Body="&lt;p&gt;I found the answer to my question &lt;a href=&quot;https://biology.stackexchange.com/questions/5405/do-memories-have-mass/5408#5408&quot;&gt;here&lt;/a&gt;, however not linked to a duplicate question, so I'll quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Memories are represented in the brain as patterns of firing neurons.&#xA;  Let's say, for simplicity, that each neuron can either be on or off.&#xA;  Since there are 86 billion neurons in the brain, we can experience&#xA;  2^86bn possible brain states. That's a lot.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Of course there are a lot of simplifications here--most notably, there&#xA;  is a lot of structure to the brain, and so i'm not suggesting you can&#xA;  store 2^86bn memories--but the logic is the same. Even with only 1,000&#xA;  neurons, we can store a ridiculous amount of information (2^1000). &#xA;  - Jeff&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And from the comments, I understand that this quote is not totally accurate, as a brain state is not a memory, and we just simply dont know enough about memory to do this kind of calculation, but the start of this quote is the key to the question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Memories are represented in the brain as patterns of firing neurons.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Meaning yes, if the brain lost activity for a moment, its stored information would likely deteriorate tremendously, if not completely. That is, if my cited information (and interpretation of its effect)  is correct.&lt;/p&gt;&#xA;" OwnerUserId="19073" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2014-12-05T03:21:14.990" CommentCount="15" ContentLicense="CC BY-SA 3.0" />
  <row Id="24569" PostTypeId="1" AcceptedAnswerId="24575" CreationDate="2014-12-05T02:56:50.763" Score="13" ViewCount="2224" Body="&lt;p&gt;We have two eyes, but we don't have two hearts.&#xA;Why do humans have two of some organs, but not all? &lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="3553" LastEditDate="2014-12-05T03:42:15.867" LastActivityDate="2018-03-20T08:11:03.367" Title="Why do we have two of some organs, but not all?" Tags="&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24570" PostTypeId="2" ParentId="24561" CreationDate="2014-12-05T02:59:46.467" Score="3" Body="&lt;p&gt;&lt;strong&gt;Summary&lt;/strong&gt;&#xA;Working memory on a current task could be distorted, but I cannot find a reason to suggest sudden loss of electrical information would permanently alter short or long term memory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully a neuroscientist can answer with a more electro-chemical oriented answer, but fundamentally I think the experts aren't sure what a memory actually is (there are only a handful of theories each that are understudied or flawed). This is also a fairly hypothetically question. Baring these points in mind, treat not only this, but all answers skeptically and take with a pinch of salt!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;LTP&lt;/strong&gt;&#xA;A &lt;a href=&quot;http://ac.els-cdn.com/S1074742710002017/1-s2.0-S1074742710002017-main.pdf?_tid=e6b4b2b8-7c28-11e4-879e-00000aacb35f&amp;amp;acdnat=1417747764_0543a96073c94a049e76bfe2eacd3508&quot; rel=&quot;nofollow&quot;&gt;recent review&lt;/a&gt; by Baudry &lt;em&gt;et al&lt;/em&gt; covers the modern biochemical view on  long-term potentiation (LTP) of the hippocampus that is probably responsible for things like learning and memory. It is a complex protein formation involving BDNF, calpain, and synaptic modifications. If hypothetically you became 'brain dead' for a moment, this way of looking at memory probably wouldn't take a hit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Engrams&lt;/strong&gt;&#xA;Something I have less of a grasp on is Richard Semon's &lt;a href=&quot;http://en.wikipedia.org/wiki/Engram_%28neuropsychology%29&quot; rel=&quot;nofollow&quot;&gt;Engram&lt;/a&gt;, but was more heavily studied by Richard Thompson. Even the &lt;a href=&quot;http://www.theguardian.com/science/neurophilosophy/2012/apr/06/1&quot; rel=&quot;nofollow&quot;&gt;most modern&lt;/a&gt; studies describe this kind of brain mapping as chemical and cellular rather than electrical. So again perhaps nothing other than the unstored would be lost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Working Memory loss&lt;/strong&gt;&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S089662731300038X&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; rather technical article discusses primate prefrontal cortex neurone firing as a persistent stream needed for a &quot;working memory&quot;. I am out of my depth here, but it seems like some &quot;forming&quot; memories may be lost if there was momentary activity loss, but I don't see why the underlying biochemical state that cause this effect would be lost, so very little information would be directly lost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Memory loss.&lt;/strong&gt; Diseases that cause memory loss involve tissue and protein changes along with other physiological changes. Memory loss induced by trauma is likely caused by swelling where the neurones are damaged by swelling or the trauma itself on a cellular level. It seems to be the case that the electrical information isn't the important factor to memory loss.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Note: I think memory would be lost indirectly, perhaps removed in a similar way as when you wake up from a dream or in cases of trauma. I am also ignoring that there would be a reasonable probability that this would induce seizure, stroke, or other bad health effects!&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2014-12-05T03:49:02.483" LastActivityDate="2014-12-05T03:49:02.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24571" PostTypeId="1" CreationDate="2014-12-05T03:08:10.950" Score="3" ViewCount="176" Body="&lt;p&gt;I'm studying modified Mendelian ratios. I've got a theoretical problem that I'm stumped on:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A species of bird may have normal wings, or a mutation that causes frazzled wings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do 15 identical breeding pairs, crossing a male bird with frazzled wings to a normal winged female. The progeny obtained are 46 with normal wings (22 male/24 female) and 23 frazzled, all male.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Afterwards, I mate the normal winged females to the normal winged males obtained from the above cross. The progeny obtained all have normal wings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I figured out a possible solution, and would like to know if it makes sense:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Z(f)&lt;/code&gt; = Z sex chromosome with normal wing gene, recessive&lt;br&gt;&#xA;&lt;code&gt;Z(F)&lt;/code&gt; = Z sex chromosome with frazzled wing gene, dominant&lt;br&gt;&#xA;&lt;code&gt;W&lt;/code&gt; =  W sex chromosome&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;code&gt;Z(F)/W&lt;/code&gt; = abnormal wing female bird (does not survive as not enough&#xA;gene product produced)&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;Z(f)/W&lt;/code&gt; = normal wing female bird&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;Z(F)/Z(F)&lt;/code&gt; = abnormal wing male bird (does not survive as not enough gene product produced, or possibly survives as just enough is produced by 2 mutant genes, doesn't matter anyway)&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;Z(F)/Z(f)&lt;/code&gt; = abnormal wing male bird (survives as wildtype gene produces enough product)&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;Z(f)/Z(f)&lt;/code&gt; = normal winged male bird&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My crosses:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P1: &lt;code&gt;Z(F)/Z(f) × Z(f)/W&lt;/code&gt; &lt;br&gt;&#xA;Progeny: &lt;code&gt;Z(F)/Z(f)&lt;/code&gt;, &lt;code&gt;Z(f)/Z(f)&lt;/code&gt;, &lt;code&gt;Z(F)/W&lt;/code&gt; (fails to survive), &lt;code&gt;Z(f)/W&lt;/code&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;F1: &lt;code&gt;Z(F)/Z(f)&lt;/code&gt;, &lt;code&gt;Z(f)/Z(f)&lt;/code&gt;, &lt;code&gt;Z(f)/W&lt;/code&gt; in 2:1 normal:frazzled wings &lt;br&gt;&#xA;F2: &lt;code&gt;Z(f)/Z(f) × Z(f)/W&lt;/code&gt; produces &lt;code&gt;Z(f)/Z(f)&lt;/code&gt;, &lt;code&gt;Z(f)/W&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;This would account for the phenotypic ratios seen in the problem, and also uses the &lt;code&gt;ZW&lt;/code&gt; sex chromosome system found in birds. The genetic explanation would be that a single &lt;code&gt;Z(F)&lt;/code&gt; does not produce enough product to thrive, for whatever reason. The trait is sex-linked dominant on the Z chromosome.&lt;/p&gt;&#xA;" OwnerUserId="10436" LastEditorUserId="3340" LastEditDate="2014-12-05T14:37:44.413" LastActivityDate="2014-12-05T14:37:44.413" Title="Modified Mendelian Ratios Problem" Tags="&lt;genetics&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24572" PostTypeId="2" ParentId="24559" CreationDate="2014-12-05T03:08:42.443" Score="3" Body="&lt;p&gt;The following is one of the many elegant statements in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866459/&quot; rel=&quot;nofollow&quot;&gt;General Anesthetic Actions on GABA&lt;sub&gt;A&lt;/sub&gt; Receptors&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is the fervent view of the authors that general anesthesia is no different from any other pharmacological process: exogenously administered drugs interact with key sites on cellular proteins in the body which results directly in the alteration in the function of these proteins, in the present case, neuronal proteins that control how information is conveyed through the nervous system. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Isoflurane, Sevoflurane, and Desflurane, the current inhalation general anesthetics, along with Halothane and the intravenous anesthetics Propofol, Etomidate, Methohexital and Thiopental, enhance the function of GABA&lt;sub&gt;A&lt;/sub&gt; receptors (GABA&lt;sub&gt;A&lt;/sub&gt;Rs), the most abundant fast inhibitory neurotransmitter receptor in the CNS (ligand-gated chloride ion channels) by increasing the affinity of the receptor for GABA. Since these receptors are abundant in parts of the CNS that process higher-order brain functions, it stands to reason that GABA&lt;sub&gt;A&lt;/sub&gt;R function is central to memory, awareness and consciousness. GABA&lt;sub&gt;A&lt;/sub&gt;Rs are involved in mediating hypnosis, depression of spinal reflexes, and amnesia, three of the classical components of general anesthesia. Isoflurane, Sevoflurane, and Desflurane enhance the amplitude of responses to low concentrations of GABA and prolong the duration of GABA mediated synaptic inhibition. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A very good starting point for your investigations can be found by clicking on the linked article above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11176100/&quot; rel=&quot;nofollow&quot;&gt;Agent-selective effects of volatile anesthetics on GABA&lt;sub&gt;A&lt;/sub&gt; receptor-mediated synaptic inhibition in hippocampal interneurons&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12195434/&quot; rel=&quot;nofollow&quot;&gt;The sedative component of anesthesia is mediated by GABA(A) receptors in an endogenous sleep pathway&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-05T03:08:42.443" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24573" PostTypeId="1" CreationDate="2014-12-05T03:22:05.967" Score="9" ViewCount="18446" Body="&lt;p&gt;When restriction enzymes jaggedly cut double stranded DNA it results in so called sticky ends. What is the substance that makes the DNA sticky?&lt;/p&gt;&#xA;" OwnerUserId="8730" LastEditorUserId="3553" LastEditDate="2016-11-25T10:08:36.607" LastActivityDate="2016-11-25T10:08:36.607" Title="What makes DNA sticky-ends sticky?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;restriction-enzymes&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24574" PostTypeId="2" ParentId="24573" CreationDate="2014-12-05T03:30:20.433" Score="10" Body="&lt;p&gt;&lt;strong&gt;What are sticky ends.&lt;/strong&gt;&#xA;There is no substance that is attached making the DNA ends &quot;sticky&quot;. What has actually happened is an overhang of at least a few nucleotides. Blunt ends are another kind of cut, but have no overhanging residues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/66iks.jpg&quot; alt=&quot;sticky end recombination&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why are sticky ends sticky?&lt;/strong&gt;&#xA;Restriction enzymes usually cut these ends deliberately so that a four nucleotides are overhanging on the 5' end of the double strand. These are complementary to other overhangs and because they are less stable than a bound double strand region, and are able to hydrogen bond easily with complementary bases, they are easier to attach with a ligase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below is an image of the base pairs interacting via H bonds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/H9xV0.gif&quot; alt=&quot;ATCG base pair complementing with H bonds&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2014-12-05T17:42:23.420" LastActivityDate="2014-12-05T17:42:23.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24575" PostTypeId="2" ParentId="24569" CreationDate="2014-12-05T03:37:21.267" Score="11" Body="&lt;p&gt;&lt;em&gt;Here is my overly succinct answer.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I doubt we will ever know this for sure. But, it basically comes down to &lt;strong&gt;ancestral bilateral symmetry&lt;/strong&gt; in development; this defaults to two organs and is broadly symmetrical except where the organs are central. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2176165/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt; for a more thorough answer regarding bilateral symmetry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/mGwer.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/mGwer.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further exceptions to symmetry occur where evolution pressured the body into not bothering to grow the second of an organ due to a waste of resources for the body, or functional advantages emerged from asymmetrical evolution. I always like the ears of an owl for an excellent example of two asymmetrical features that provided a discrete advantage when it comes to locating the source of a sound. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/FW2zV.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/FW2zV.jpg&quot; alt=&quot;skull of an owl showing one ear hole is higher on the skull than the other.&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2016-05-14T05:04:35.820" LastActivityDate="2016-05-14T05:04:35.820" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="24576" PostTypeId="2" ParentId="24561" CreationDate="2014-12-05T08:15:03.487" Score="4" Body="&lt;p&gt;Memories are dynamic; that is not equivalent to &quot;memories are evanescent&quot;. Cellular structure and composition controls memory, not just a continuous passage of signals. This point is already discussed in the comments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Loss of energy (in the form of ATP) would cause memory deterioration and in some cases neuronal cell death too— strokes, which happen due to lack of blood supply to brain (and hence unavailability of nutrients and oxygen) can cause amnesia. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But one second will practically not affect anything. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-05T08:15:03.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24577" PostTypeId="2" ParentId="10774" CreationDate="2014-12-05T08:57:22.737" Score="2" Body="&lt;p&gt;This specific experiment has not been done. Fusing cells is difficult and it also leads to polyploidy. Cells are immortalized by overexpressing oncogenes (or viral replication genes); for example HEK293 cell line was established by transforming embryonic kidney cells with adenovirus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now transforming a neuron would immortalize it but would also make it lose its function; for a cell like neuron, replication would compromise its activity for e.g. loss of established synapses. As mentioned in the comments by har-wradim, it &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23087000&quot; rel=&quot;nofollow&quot;&gt;was shown&lt;/a&gt; that transforming neurons with oncogenes leads to their de-differentiation. Another experiment of transforming neurons gave a contrasting result. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/089662739290247B&quot; rel=&quot;nofollow&quot;&gt;Feddersen et al&lt;/a&gt; transformed purkinje cells in mice by expressing SV40 viral t-antigen from a purkinje-cell specific promoter and surprisingly it lead to degeneration of cerebellar tissue. Also have a look at &lt;a href=&quot;http://www.jneurosci.org/content/24/42/9232.full&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-05T08:57:22.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24578" PostTypeId="2" ParentId="11333" CreationDate="2014-12-05T09:22:10.953" Score="2" Body="&lt;ol&gt;&#xA;&lt;li&gt;You are right but a small correction: &lt;strong&gt;P&lt;/strong&gt; represents primary producers. So the answer is just dead plants or tissues such as broken branches. &lt;/li&gt;&#xA;&lt;li&gt;Death, excretion because of turnover (which includes urine or other metabolites), tissue turnover (shedding of dead cells, molting etc)&lt;/li&gt;&#xA;&lt;li&gt;Maintenance, locomotion, repair, immunity &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-05T09:22:10.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24579" PostTypeId="2" ParentId="14076" CreationDate="2014-12-05T09:27:53.417" Score="2" Body="&lt;p&gt;Yes. Freezing would practically stop all biochemical reactions. Household freezer can maintain -15⁰C so that would work. However, freezing also damages the cells if cryoprotectants are not used. But I guess that is not your concern. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-05T09:27:53.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24580" PostTypeId="2" ParentId="14872" CreationDate="2014-12-05T10:00:55.620" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Does it mean that e-NOS and n-NOS are synthesized by mediation of Ca&#xA;  and calmodulin?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Calmodulin is activated by binding to calcium and NOS is activated by binding to Ca&lt;sup&gt;2+&lt;/sup&gt;-calmodulin. The binding changes the structural conformation which renders the enzyme active. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22486744&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Are e-NOS and n-NOS expressed on macrophages after induction [...]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Macrophages generally express iNOS upon induction by cytokines. The activity of iNOS is shown to be different in humans compared to mice; humans have low activity&lt;sup&gt; [&lt;a href=&quot;http://www.jleukbio.org/content/81/3/579.full&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;]&lt;/sup&gt;. However mouse macrophages have &lt;a href=&quot;http://www.jbc.org/content/278/29/26480.full&quot; rel=&quot;nofollow&quot;&gt;been shown&lt;/a&gt; to express eNOS constitutively and eNOS-knockout mice show reduced NFkB production and iNOS induction.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-05T10:00:55.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24581" PostTypeId="2" ParentId="24564" CreationDate="2014-12-05T10:28:02.417" Score="1" Body="&lt;p&gt;This is a pretty broad question, but I will try to give an answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This process will undergo further evolution over time, no question. It has evolved into the current state and there is no reason to assume that this ended. When there are mutations which prove advantageous, they will evolve. This may also involve a faster response time for example, but we can of course make not definite claims about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are antigens which are not recognized by the immune system, the process is called molecular mimicry. In it, microorganisms mimic molecules or structures which are found inside the body of the infected person and which are therefore not recognized by the immune system (if the immune system recognized self-antigens, this leads to autoimmune diseases). Have a look at the references 1 and 2 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a rather theoretical question. Our immune system is really efficient in clearing potential threats before you get a real infection. You can see the difference when you compare healthy individuals with persons which are immuno suppressed because of a transplantation. These persons need to be very careful about their environment in avoiding the exposure to potential pathogens. And they easily get infections. Additionally microbes evolve to evade our immune system. So I think the answer here is no.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are viruses which co-evolved with the organism, an example would be the ebola virus in certain fruit bats. Here it does no harm, while it is a big problem for humans. As there is a really, really big number of viruses available in nature, it is quite unlikely that we learn to tolerate all of them. Additionally viruses mutate and change over time, so we would have to learn again to live with them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Molecular_mimicry&quot; rel=&quot;nofollow&quot;&gt;Molecular mimicry&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9761770&quot; rel=&quot;nofollow&quot;&gt;Molecular mimicry and immune-mediated diseases.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-05T10:28:02.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24582" PostTypeId="2" ParentId="16766" CreationDate="2014-12-05T10:34:30.970" Score="1" Body="&lt;p&gt;If the gene is supposed to be well conserved then you can use the sequence from the related species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For protein coding genes target the ISH probe to the coding region which is more likely to be conserved. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you can also do subsequently is to:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;amplify the CDS&lt;/li&gt;&#xA;&lt;li&gt;do 3' and 5' RACE&lt;/li&gt;&#xA;&lt;li&gt;Clone in a plasmid (do a blunt end or TA cloning)&lt;/li&gt;&#xA;&lt;li&gt;Sequence the insert&lt;/li&gt;&#xA;&lt;li&gt;Design exact primers&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;are there any other good databases for gene sequences?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;EMBL and DDBJ&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-05T10:34:30.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24584" PostTypeId="2" ParentId="14232" CreationDate="2014-12-05T11:20:31.360" Score="2" Body="&lt;p&gt;In situation A) there is no mention of growth, so there is no reason to assume something is cultured. If we assume that in A) a germ plant arises, it is no tissue culture but a regularly bred plant. It is no tissue culture, because a seed is typically formed after pollination, which involves the recombination of parent genes to form reproductive cells (pollen) and the fusion of these reproductive cells after pollination. Because the definition of plant tissue culture is: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;&quot;... a form of cloning in which the plants are all genetically the same - similar to taking cuttings.&quot;&lt;/strong&gt; &lt;em&gt;(quoted from: &lt;a href=&quot;http://www.rbgsyd.nsw.gov.au/science/Herbarium_and_resources/laboratories/tissue_culture&quot; rel=&quot;nofollow&quot;&gt;Royal botanical gardens, NSW, australia&lt;/a&gt;).&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;it follows that seedlings are not clones of their parents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Situation B) therefore meets the criterion of tissue culture, as new tissue grows out of a single progenitor cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the answer is: they are &lt;strong&gt;not&lt;/strong&gt; 2 examples of tissue culture, the difference being that A) is the result of a normal breeding and B) meets the criteria of tissue culture.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-05T11:47:20.293" LastActivityDate="2014-12-05T11:47:20.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24586" PostTypeId="2" ParentId="10292" CreationDate="2014-12-05T12:20:32.370" Score="2" Body="&lt;p&gt;Removal of 5' cap is essential for degradation by 5'→3' exonucleases such as Xrn1/2. Xrn1/2 is constitutive and degradation of uncapped RNAs would be quite fast (don't have a reference for the exact lifetime). Deadenylation generally precedes 3'→5' degradation by exosome but I am not sure if that is a prerequisite. However tailless mRNAs can be stabilized by tethering Pab1p (Poly-A binding protein) to the 3'UTR. See &lt;a href=&quot;http://genesdev.cshlp.org/content/12/20/3226.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 4 of the linked paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/pjDrI.jpg&quot; alt=&quot;Figure-4&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Tethered Pab1p stabilizes mRNAs that do not receive a tail. (A)&#xA;  Strategy. The HDV self-cleaving ribozyme was inserted into the 3′ UTR&#xA;  of MFA2/MS2 RNA, yielding an mRNA without a poly(A) tail (A0) in vivo.&#xA;  (B) Oligo(dT) cellulose chromatography. RNAs were extracted from cells&#xA;  carrying the ribozyme-containing construct depicted inA, or the&#xA;  control plasmid used in previous figures. RNAs were fractionated by&#xA;  oligo(dT) cellulose chromatography, then analyzed by Northern&#xA;  blotting. The ribozyme-containing RNA is not retained by the column,&#xA;  whereas the control RNA is retained. (T) Total RNA prior to&#xA;  fractionation; (+) retained by the column; (−) not retained by the&#xA;  column. The mRNA runs slightly faster in the oligo(dT) retained (+)&#xA;  sample than in the total (T) RNA, because less RNA is loaded per lane.&#xA;  (C) S1 nuclease analysis. The 3′ end of mRNA prepared from a strain&#xA;  carrying the ribozyme-containing RNA was determined by S1 nuclease&#xA;  mapping. The position of undigested probe (65 nucleotides) and of the&#xA;  protected species (43 nucleotides) are shown. The prominent 3′&#xA;  terminus lies at the expected position for ribozyme cleavage. (D)&#xA;  Decay of ribozyme-cleaved RNA by a transcriptional pulse-chase&#xA;  experiment and Northern blotting. The turnover rate of&#xA;  ribozyme-cleaved reporter mRNAs was determined in strains with (left)&#xA;  or without (right) MS2/Pab1p. Time (in min) following transcriptional&#xA;  repression are given directly at top; half-lives are at bottom. (E)&#xA;  Quantitation of results. Amounts of mRNA were normalized to the level&#xA;  of 18S rRNA, at bottom of each lane in D. (•) MS2/Pab1p; (○) vector&#xA;  alone.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Prokaryotic UTRs do not have any general paradigm. To have a controlled inactivation of a mRNA in a prokaryotic system you can use riboswitches or  cis-repressive RNA (RBS complementary RNAs). RNA-guided RNA degradation is also possible in prokaryotes using the CRISPR-Cas system. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951265/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; paper. Proteins Cmr-1,2,3,4 &amp;amp; 6 are required for this activity. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-05T12:33:38.713" LastActivityDate="2014-12-05T12:33:38.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24587" PostTypeId="2" ParentId="24573" CreationDate="2014-12-05T12:50:21.940" Score="10" Body="&lt;p&gt;The sticky ends are sticky because they have complementary bases. Typically used restriction enzymes cut the two complementary DNA strands at different spots, generating 'overhang', or sticky ends:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3rehz.jpg&quot; alt=&quot;Sticky ends&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These overhangs allow for perfect base pairing (C with G, A with T), which is the result of hydrogen bonding. Just like water molecules show strong affinity to each other or other molecules with -OH and -H groups (e.g., alcohol), hydrogen bonds between nucleotides glues the ends together. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The principles of base-pairing has been nicely answered by @MadScientist in &quot;&lt;a href=&quot;https://biology.stackexchange.com/a/24262/3624&quot;&gt;&lt;em&gt;Why does A pair with T and G with C?&lt;/em&gt;&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-12-05T13:01:48.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24588" PostTypeId="2" ParentId="1525" CreationDate="2014-12-05T13:05:03.630" Score="1" Body="&lt;p&gt;Kozak consensus sequence (KCS) is present near or overlapping with the start codon. I am not sure what you mean by distance between that and A-site. Start codon is localaized at P-site at the time of translation initiation. Distance between start codon/KCS and A-site at initiation is same as distance between P- and A- sites (I guess ~20Å). A-site keeps moving during translation and hence the distance keeps increasing. Crystal study is available; See &lt;a href=&quot;http://www.cell.com/cell/fulltext/S0092-8674%2814%2901281-1&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this figure from the abovementioned study for the relative positions of start-codon, P-site (exit) and A-site (entry).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/ytJrQ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-05T13:05:03.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24589" PostTypeId="1" AcceptedAnswerId="24614" CreationDate="2014-12-05T15:01:42.897" Score="9" ViewCount="4850" Body="&lt;p&gt;If the eye sees an object, but the object is out of focus, the eye could be focusing too near or too far. How does the eye (or the brain) distinguish one situation from the other?&#xA;How does it know whether to focus closer or further?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested in the case when:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;only one eye is open (There must be another way besides parallax clues). &lt;/li&gt;&#xA;&lt;li&gt;The object is an unfamiliar size&lt;/li&gt;&#xA;&lt;li&gt;The object is an unknown distance from the eye.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Ideas so far&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the eye try focusing either a little nearer or further and then if that doesn't help to make the object clearer then the eye focuses in the opposite direction?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is there some light-sensitive apparatus that is always a focused a little nearer or further than the rest of the eye, and so for instance if the cells which are focused further out are giving a clearer picture than the other cells then the eye knows to focus further out?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is the blurriness of a object closer than the focal point a distinguishably different sort of blurriness than an object beyond than the focal point?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is there some other mechanism altogether?&lt;/p&gt;&#xA;" OwnerUserId="9879" LastEditorUserId="9879" LastEditDate="2014-12-05T18:00:16.710" LastActivityDate="2014-12-07T11:39:36.017" Title="How does the eye know whether to focus further out or nearer in order to bring a blurry object into focus?" Tags="&lt;eyes&gt;&lt;vision&gt;&lt;human-eye&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24591" PostTypeId="2" ParentId="24589" CreationDate="2014-12-05T17:59:48.270" Score="6" Body="&lt;p&gt;The neurology of vision is an extremely complex subject and is difficult to describe with any brevity, because there is so very much going on in so many parts of the brain. It is estimated that about 50% of the pathways of the brain, and about 30% of the cortex are involved in vision (where only 8% of the cortex is devoted to touch, and 3% to hearing). Some research estimates that eighty to eighty five percent of our perception, learning, cognition and activities are mediated through vision.&lt;sup&gt;&lt;a href=&quot;https://i.stack.imgur.com/o6e3z.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ability to accurately focus on an object, sustain that focus, and to change focusing when looking at different distances is called accommodation. That happens with the pupil size, the lens shape, etc. but it doesn't tell us &lt;em&gt;how&lt;/em&gt; the brain chooses on what to focus. The short answer is that it's much more than focusing like a camera lens. We have retinal areas that &lt;em&gt;simultaneously&lt;/em&gt; pay attention to further and closer areas, light/dark, edges, and more, all going on at once. That and much more information carried to the brain is processed, and efferently focus is honed. It's even more complex when two eyes are involved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are so many aspects to sight that an enormous number of kinds of optical illusions exist. They are involuntary. That's why they're fun. In fact, if you weren't tricked, it would indicate a problem in part of your brain. Here's one that relies on processing contrast:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/o6e3z.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you scan looking at the white dots, your peripheral vision seems to be able to see black dots, but it's clear on scanning them one row at a time that there are no black dots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the following illusion, the red vertical lines are parallel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/d0iO1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following are summaries of the neuroanatomy of vision.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://hubel.med.harvard.edu/book/bcontex.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eye, Brain and Vision&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://brighamandwomens.org/Departments_and_Services/neurology/services/NeuroOphthamology/Images/SelectedPublications/VisualSystem.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Anatomy and physiology of the afferent visual system&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;https://i.stack.imgur.com/o6e3z.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt; &lt;a href=&quot;http://www.brainline.org/content/2008/11/vision-our-dominant-sense_pageall.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Vision Is Our Dominant Sense&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-05T17:59:48.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24592" PostTypeId="2" ParentId="16596" CreationDate="2014-12-05T20:18:55.600" Score="0" Body="&lt;p&gt;Methylation played different roles for different types of organisms throughout evolution. For bacteria, methylation protects against self-digestion of DNA by restriction enzymes. In eukaryotes, methylation assumes many different roles (e.g., mutation-rate regulator, gene expression regulator, chromatin structure regulator, etc.). Insects have very little methylation and it is not entirely clear what they use it for. Viruses don't encode for methyltransferases that modify DNA. However, when a virus integrates into a host genome that is methylated, the viral DNA usually assumes the methylation pattern of the integration locus.&lt;/p&gt;&#xA;" OwnerUserId="10118" LastActivityDate="2014-12-05T20:18:55.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24593" PostTypeId="2" ParentId="21858" CreationDate="2014-12-05T20:54:23.133" Score="2" Body="&lt;p&gt;The human eye is dynamic and always represents its visual environment. Thus, why was myopia so rare in early mankind, but now so present?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It can not be only caused by genetics. The worst thing you could do is wearing your full minus lens prescription while doing near work. When you think of how your myopia initially started (a lot of near work) and then you wear your minus (unfortunately, often over-prescribed), you are in your &quot;initial&quot; state again. And the cycle repeats itself - over and over again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By reversing myopia, you must also consider prevention. When you do a lot of near work (long-term), wear plus lens to protect your eyes. It makes your eyes as if they are looking in the distance and thus relaxing your eyes effectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Try the following: Measure your &lt;a href=&quot;http://en.wikipedia.org/wiki/Snellen_chart&quot; rel=&quot;nofollow&quot;&gt;Snellen&lt;/a&gt; score, then do near work for 3 hours or so and then check your Snellen again. You will see your sight will get worse (in this case &lt;a href=&quot;http://en.wikipedia.org/wiki/Pseudomyopia&quot; rel=&quot;nofollow&quot;&gt;temporarily&lt;/a&gt;). If you continue, your eyes will adapt and become myopic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, plus lens therapy is not mainstream. Often people say &quot;it does not help&quot; or &quot;it causes cataracts&quot; and so forth. But therapy needs to be applied over a long-timeframe. Consider it as a &quot;long-term diet&quot;.&lt;/p&gt;&#xA;" OwnerUserId="10444" LastEditorUserId="4788" LastEditDate="2014-12-06T00:36:30.997" LastActivityDate="2014-12-06T00:36:30.997" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24595" PostTypeId="2" ParentId="24573" CreationDate="2014-12-06T01:19:47.933" Score="6" Body="&lt;p&gt;The &quot;substance&quot; is hydrogen bonds (H-bonds), or rather the potential to form them. Each of the unpaired A/T bases in the sticky ends have the potential to form 2 H-bonds with a complementary T/A, and each of the unpaired G/C bases have the potential to form 3 H-bonds with a complementary C/G.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the perspective of a biophysicist, H-bonds are often thought of as being the strongest intermolecular interactions. I personally think that it's a little bit lazy and unphysical to see things this way, but the prevailing view in the field is that H-bonds determine specificity in all macromolecular interactions (e.g. the specificity that causes a single DNA strand to bind mostly to complementary DNA strands and poorly to random DNA strands).&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-12-06T01:19:47.933" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24596" PostTypeId="2" ParentId="24560" CreationDate="2014-12-06T01:54:16.687" Score="10" Body="&lt;p&gt;Via deep scientific analysis (i.e. trying it myself 5 seconds ago), I have determined that you can in fact speak while breathing in, it just sounds funny.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think of the vocal chords as being like the body of a flute. As air passes by them, they vibrate and make sounds. Through careful modulation of their shape, specific sounds can be reproducibly made (this is equivalent to opening and closing the stops on the metaphorical flute). The way the pressure in your throat changes when you inspire (breathe in) is very different from the way in which the pressure changes when you expire (breathe out). These pressure differences are a large part of the reason why you sound different when you speak during inspiration as opposed to expiration, just like breathing into a flute differently would produce different sounds (although potentially the same notes). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other physiological, neurological, etc. effects probably also cause differences in the vocal cords during expiration/inspiration and thus also contribute somewhat to the differences in the sound.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2014-12-06T03:08:04.713" LastActivityDate="2014-12-06T03:08:04.713" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24597" PostTypeId="1" AcceptedAnswerId="24598" CreationDate="2014-12-06T02:27:02.720" Score="0" ViewCount="52" Body="&lt;p&gt;Today we had our exam. There was a punnet square for two genes. and when I multiplied , for example, &lt;code&gt;Ry × rY&lt;/code&gt; I wrote the answer as &lt;code&gt;RyrY&lt;/code&gt;. When I returned back home I realized that I may have made a mistake because the book used to write them as &lt;code&gt;RrYy&lt;/code&gt;. So is my answer write or wrong? why? I also freaked out because there were 16 boxes in the punnet square so does that mean that I'll lose 16 points? I got everything else in the exam correctly. So I'm freaking out because I don't know if I'm getting a 100 or 86 which will throw all my work the entire semester. Please respond as soon as you can. I feel like I'm having a panic attack.&lt;/p&gt;&#xA;" OwnerUserId="9460" LastEditorUserId="3340" LastEditDate="2014-12-06T10:42:54.530" LastActivityDate="2014-12-06T10:43:36.370" Title="Intro Bio question: dihybrid punnet square" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24598" PostTypeId="2" ParentId="24597" CreationDate="2014-12-06T04:14:36.107" Score="1" Body="&lt;p&gt;Hah! You can relax. There's no difference between &lt;code&gt;RyrY&lt;/code&gt; and &lt;code&gt;RrYy&lt;/code&gt;, as there is no fundamental ordering of genes like that. That being said, the standard convention would be to write &lt;code&gt;RrYy&lt;/code&gt; (or at least &lt;code&gt;RryY&lt;/code&gt;), so if your grader is a pedantic hardass they might take off a couple of points, but probably not the whole 16.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="3340" LastEditDate="2014-12-06T10:43:36.370" LastActivityDate="2014-12-06T10:43:36.370" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24599" PostTypeId="1" CreationDate="2014-12-06T05:38:07.567" Score="2" ViewCount="309" Body="&lt;p&gt;I would like to get suggestions for the books related to &lt;strong&gt;General time reversible model of evolution&lt;/strong&gt; and &lt;strong&gt;Felsenstein model&lt;/strong&gt; etc. Specifically the mathematical treatment of these topics and concepts related to &lt;strong&gt;general balance&lt;/strong&gt; and &lt;strong&gt;detailed balance&lt;/strong&gt; etc. Can someone point out any books, links etc related to these.&lt;/p&gt;&#xA;" OwnerUserId="5669" LastEditorUserId="3340" LastEditDate="2014-12-06T10:40:35.993" LastActivityDate="2020-07-13T21:11:52.213" Title="General time reversible model of evolution and Felsenstein model" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;book-recommendation&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24600" PostTypeId="1" AcceptedAnswerId="24603" CreationDate="2014-12-06T05:54:33.703" Score="-2" ViewCount="278" Body="&lt;p&gt;How does the said body treat heat-resistant pathogenic bacteria? If fever is the body's response to foreign microbial invasion, then what happens if the bacteria is heat-resistant but the body's own cells and enzymes start to denature due to the excess heat? Are there other mechanisms that the multicellular, eukaryotic body can use to defeat foreigners?&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastActivityDate="2014-12-06T06:37:59.577" Title="How does a multicellular, eukaryotic body treat heat-resistant pathogenic bacteria?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24602" PostTypeId="2" ParentId="21350" CreationDate="2014-12-06T06:11:22.543" Score="1" Body="&lt;p&gt;γ-Tubulin is specifically &lt;a href=&quot;http://jcb.rupress.org/content/131/1/207.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;localized&lt;/a&gt; to the minus end of microtubules. GFP labeled γ-Tubulin can be used to label the minus ends in-vivo and without the requirement of staining. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022283696903228&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fan et al&lt;/a&gt; have developed a phage display antibody specific to α-Tubulin that can be used to visualize minus ends. See the figure below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/sKkDS.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image is an electron-micrograph but it is certainly possible to do a fluorescent microscopy after IHC staining.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-06T06:11:22.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24603" PostTypeId="2" ParentId="24600" CreationDate="2014-12-06T06:37:59.577" Score="1" Body="&lt;p&gt;The usual 'heat resistant' bacteria or thermophiles are free living organisms with specific niche and are not pathogenic. Most pathogens are mesophiles and that is why they are grow in the body temperature. Spores are thermotolerant but spores are dormant and are not actively growing microbes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having said that, different mesophiles can have different levels of thermotolerance. Pyrexia (fever) is not necessarily a defensive mechanism and is more of a by-product of a systemic inflammatory response. Moreover bacteria are more tolerant to temperature changes than our body; there are definitely other mechanisms to combat infection. Read about innate and acquired immune response. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-06T06:37:59.577" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24606" PostTypeId="1" AcceptedAnswerId="24612" CreationDate="2014-12-06T06:53:31.790" Score="2" ViewCount="41" Body="&lt;p&gt;I have to separate two proteins of 86kDa and 80kDa respectively, however, I just cannot get a decent separation even in 6% polyacrylamide gel. To make matters worse, these two proteins are isoforms and there is no commercially available antibodies to differentiate either one. I am pretty sure raising an antibody against one of the isoform is not an option for me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am tying with the idea of reducing the gel to 4% (I am pretty sure I am pushing it already) or a 2D gel (both isoforms seem to have the same IP though).&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="3340" LastEditDate="2014-12-06T07:13:51.570" LastActivityDate="2014-12-06T11:30:04.290" Title="Separation of closely-sized isoforms" Tags="&lt;molecular-biology&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24607" PostTypeId="2" ParentId="10235" CreationDate="2014-12-06T06:54:38.350" Score="5" Body="&lt;p&gt;There are various mechanisms through which membrane proteins can remain localized in the membrane. See the below figure from MBOTC (book):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/xAhyD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(A) They can aggregate together so that their relative positions are constant. &lt;br&gt;&#xA;(B) They can be anchored to the Extracellular Matrix &lt;br&gt;&#xA;(C) They can be anchored to the cytoskeleton &lt;br&gt;&#xA;(D) They can be anchored via cell-cell interactions (adherens junctions, hemidesmosomes etc)&lt;br&gt;&#xA;(E) &lt;em&gt;Not mentioned in the figure; mentioned in the comments&lt;/em&gt;. Lipid rafts are membrane regions which are composed of rigid lipids like cholesterol and sphingolipids. Lipid rafts are thicker than regular membrane and do not diffuse into the latter. Some proteins are specifically anchored to/incorporated into the lipid rafts (T-Cell receptor, IgE receptor) and their relative position with adjacent proteins (co-receptors) remains constant.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why is the noncytosolic layer not able to do lateral movements between&#xA;  domains but cytosolic layer is able to do so?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Where did you read this. Both layers can do lateral movements; if proteins are specifically &quot;anchored&quot; to one side of the membrane then the concept of domain applies to that side only. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-06T11:26:05.263" LastActivityDate="2014-12-06T11:26:05.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24609" PostTypeId="2" ParentId="23992" CreationDate="2014-12-06T10:08:05.100" Score="2" Body="&lt;p&gt;Cooked food is a learnt trait rather than an evolutionary one. On a certain psychological level its a society norm so you would be hard pressed to find an individual who wouldn't mind eating completely raw meat/steak.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, say if you chuck a few humans into the wilderness at an early age and not teach them how to cook meat they may not actually cook their food. As early prehistoric humans discovered fire they eventually noticed/learnt to cook food and passed on the knowledge . You would have to research the history of that since I don't actually know the details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cooking food makes more sense on a psychological level as we cook food based on our cultural upbringing, and our memories and knowledge. A human would prefer cooked meat based on his upbringing or understanding that eating processed meat is safer as it means food contains less pathogens. The way we cook food depends on where we are from (eg.An Indian would cook meat differently from, lets say an Italian because their environment provides them with different ingredients and/or devices, pans/pots)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope that wasn't too confusing.&lt;/p&gt;&#xA;" OwnerUserId="10448" LastActivityDate="2014-12-06T10:08:05.100" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24610" PostTypeId="2" ParentId="21058" CreationDate="2014-12-06T10:35:19.130" Score="5" Body="&lt;p&gt;I am presenting a speculative approach since nobody has mentioned about any existent models yet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that selection is based on performance in certain tasks; performance is a function of traits which in-turn is a function of genotype. Performance is a non-linear function of genotype and selection imposes a cutoff/bandpass filter on the performance vector. So selection causes some individuals to perish — which genotypes are selected out depends on their relative contribution to the performance function. As you already mentioned in the question, selection would lead to reduction in variance; some of the diagonal terms would reduce. Now if your traits are truly independent (as in case of additive variances) and also uncorrelated then then extradiagonal terms would be very small and their contribution to the eigenvalues would be minimal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall the eigenvalues and hence the determinant of the G-matrix would decrease upon selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Addition based on the points mentioned in rg255's answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3229175/&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper&lt;/a&gt; mentioned by rg255 talks about the shape of the distribution corresponding to G-matrix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/73ixA.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The eigenvalues correspond to the axes of the ellipse. In the first case eigenvalues are 0.5 and 0.5; in the second case they are 0.05 and 0.95.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Alternatively, assuming a normal (Gaussian) bivariate distribution of&#xA;  values, we can represent the cloud with a 95% confidence ellipse whose&#xA;  axes represent the principal components or eigenvectors of the&#xA;  G-matrix (Fig. 2). The length of each axis is determined by the&#xA;  corresponding eigenvalues of the G-matrix.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Selection may reduce the area of the ellipse if the boundary points get selected out, hence causing eigenvalues and determinant to reduce. However, if the central points are removed (some kind of inverse-bandpass filter), then the limits of variation would not change. In other words the shape or size of the ellipse would not change — it would just become sparse. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-08-17T08:49:06.987" LastActivityDate="2016-08-17T08:49:06.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24611" PostTypeId="2" ParentId="10553" CreationDate="2014-12-06T11:10:56.373" Score="3" Body="&lt;p&gt;See these three sites:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://clinicaltrials.gov/&quot; rel=&quot;nofollow&quot;&gt;ClinicalTrials.gov&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://datashare.nida.nih.gov/&quot; rel=&quot;nofollow&quot;&gt;NIDA&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://clinicalstudydatarequest.com/&quot; rel=&quot;nofollow&quot;&gt;ClinicalStudyDataRequest&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For clinical trials conducted by other agencies (in different countries), you may have to contact those authorities. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-05-03T14:15:35.467" LastActivityDate="2015-05-03T14:15:35.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24612" PostTypeId="2" ParentId="24606" CreationDate="2014-12-06T11:14:59.353" Score="1" Body="&lt;p&gt;6kDa are usually enough to seperate two proteins in my experience. Try the other way, use a 7 or even 8% gel. They run longer but have a higher separation capacity. If you look at this figure from the &lt;a href=&quot;http://lifescience.roche.com/wcsstore/RASCatalogAssetStore/Articles/12115972001_10.11.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;LabFaQ&lt;/a&gt;, you see that you can use a higher percentage gel:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XKDKi.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other thing are the antibodies: Where are your isoforms different? 6kDa are 55 to 60 amino acids more for the long form, so there should be enough possibilities to make specific antibodies.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-12-06T11:30:04.290" LastActivityDate="2014-12-06T11:30:04.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24613" PostTypeId="2" ParentId="1368" CreationDate="2014-12-06T11:47:26.953" Score="2" Body="&lt;p&gt;RHEB does not sense amino acids. See the abstract of &lt;a href=&quot;http://www.nature.com/onc/journal/v25/n5/full/1209106a.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Activation of this pathway requires inhibition of the tumor suppressor&#xA;  complex TSC1/2. TSC2 is a GTPase-activating protein for the small&#xA;  GTPase Ras homologue enriched in brain (Rheb), GTP loading of which&#xA;  activates mTOR by a yet unidentified mechanism. The level at which&#xA;  this pathway senses the availability of amino acids is unknown but is&#xA;  suggested to be at the level of TSC2. Here, we show that amino-acid&#xA;  depletion completely blocks insulin- and TPA-induced Rheb activation.&#xA;  &lt;strong&gt;This indicates that amino-acid sensing occurs upstream of Rheb.&lt;/strong&gt;&#xA;  Despite this, amino-acid depletion can still inhibit mTOR/S6 kinase&#xA;  signaling in TSC2-/- fibroblasts. Since under these conditions&#xA;  Rheb-GTP levels remain high, a second level of amino-acid sensing&#xA;  exists, affecting mTOR activity in a Rheb-independent fashion.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;RHEB also doesn't have any &lt;a href=&quot;http://www.uniprot.org/uniprot/Q921J2&quot; rel=&quot;nofollow&quot;&gt;amino-acid binding&lt;/a&gt; (or any small molecule binding) domain. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-06T11:47:26.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24614" PostTypeId="2" ParentId="24589" CreationDate="2014-12-06T13:27:05.907" Score="6" Body="&lt;p&gt;Interesting question! Determining the focus of a visual image is carried out in the &lt;a href=&quot;http://neuroscience.uth.tmc.edu/s3/chapter07.html&quot;&gt;visual association area&lt;/a&gt; of the brain. Ultimately, this process results in focusing of the retinal image by adjustment of the shape of the lens in the eye. Lens shaping to focus the image is called &lt;strong&gt;accommodation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The neuronal circuitry involved in accommodation includes the following structures:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The input to the accommodation response is provided by the retina, optic nerve, thalamus, and visual cortex. The visual cortex projects to the association cortex. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The (simplified) output scheme is the following: The association cortex projects to the supraoculomotor nuclei, which in turn generates motor control signals that initiate the accommodation response. The signal is then sent bilaterally to the oculomotor complex, and hence input from one eye is enough to focus both eyes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The motor output regulates the ciliary muscles that control the shape of the crystalline lens. Negative accommodation  adjusts the eye for long distances by relaxation of the ciliary muscles. Positive accommodation  adjustment of the eye for short distances by contraction of the ciliary muscles &lt;a href=&quot;http://medical-dictionary.thefreedictionary.com/accommodation&quot;&gt;Medical Dictionary&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the second part of your question: how out-of-focus images are functionally recognized:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are at least three mechanisms responsible for accommodation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Detection of &lt;strong&gt;image blur&lt;/strong&gt;: if an image is blurred / out of focus the edges are not clearly defined. Retinal blur can be detected (edge detection) and assessed in the brain. Correction is then initiated as described above, and is basically done by trial and error. If adjustment results in a change of blur, the accommodation response (lens deformation) is detected as useful and accommodation is initiated. The accommodation itself is also based on trial-and-error: if blur increases the accommodation is reversed, if it decreases accommodation is increased in the same direction. (&lt;a href=&quot;http://link.springer.com/article/10.1007/BF01569293&quot;&gt;Philips &amp;amp; Stark, 1977&lt;/a&gt;). Image blur operates monocularly and is sufficient for accommodation to occur and is likely the most important mechanism for accommodation. It can occur without prior knowledge of distance, size etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two more specific cases also result in accommodation, with likely similar neural circuitry involved:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) &lt;strong&gt;Vergence / retinal disparity&lt;/strong&gt;. This stimulus is generated when the eyes move both in opposite directions, i.e. when focus shifts toward objects closer or farther away. The temporary displacement on binocular retinal images is detected and leads to initiation of accommodation &lt;a href=&quot;http://jp.physoc.org/content/137/3/488.full.pdf&quot;&gt;Fincham &amp;amp; Walton, 1977&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3). The &lt;strong&gt;near response&lt;/strong&gt;: While 1) and 2) are retinotopic responses, the near-response is initiated by spatiotopic stimuli, including perceived depth and distance of objects, which are derived from cues such as relative size, overlap, perspective, shading and texture gradients as well as small timevarying dynamic depth cues which include motion&#xA;parallax, loom and motion in depth. Dynamic cues provide time-varying references for perception of relative depth whereas static cues allow simultaneous comparison&#xA;of separate absolute distances from which relative depth is perceived (&lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CB8QFjAA&amp;amp;url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F1454368&amp;amp;ei=ZQODVKXKKcrf8AXL14HoDQ&amp;amp;usg=AFQjCNFhgMm1PGqccg-tGT9lvCxOxHc7bw&amp;amp;sig2=5xzOa3FSHTgVd_RJ49pPsQ&amp;amp;bvm=bv.80642063,d.dGc&quot;&gt;Schor et al., 1991&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-07T11:39:36.017" LastActivityDate="2014-12-07T11:39:36.017" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24618" PostTypeId="1" CreationDate="2014-12-06T16:26:56.813" Score="5" ViewCount="691" Body="&lt;p&gt;Our biology teacher says that peacocks will soon become extinct because of bigger and bigger (and heavier and heavier) tails. Why natural selection did not eliminate sexual selection?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HTIDv.jpg&quot; alt=&quot;peacock evolution&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6124" LastEditorUserId="6124" LastEditDate="2015-06-25T13:41:02.363" LastActivityDate="2015-10-08T20:17:52.333" Title="Is sexual selection evolutionarily advantageous?" Tags="&lt;evolution&gt;&lt;ornithology&gt;&lt;sexual-selection&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24620" PostTypeId="1" AcceptedAnswerId="24670" CreationDate="2014-12-06T18:08:29.057" Score="7" ViewCount="2186" Body="&lt;p&gt;Photosensitive epilepsies are characterized by visually-induced seizures. Flashing-light stimuli are known to induce seizures in some (but not all) patients. My question is whether people with this type of epilepsy can self-induce seizures by rapid eye blinking?  &lt;/p&gt;&#xA;" OwnerUserId="10453" LastEditorUserId="9943" LastEditDate="2014-12-07T12:22:34.947" LastActivityDate="2014-12-13T10:49:45.487" Title="Can rapid eye blinking induce epileptic seizures?" Tags="&lt;neuroscience&gt;&lt;vision&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24623" PostTypeId="2" ParentId="24618" CreationDate="2014-12-06T19:20:32.967" Score="7" Body="&lt;p&gt;&lt;strong&gt;What does &quot;evolutionary advantageous&quot; mean?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First note that &lt;code&gt;is sexual selection evolutionarily advantageous?&lt;/code&gt; is a question that makes no sense. An allele or a trait can be evolutionarily advantageous if it increases the fitness of its carrier. If an allele, an evolutionary process or an environmental change decreases the risk of extinction for a species, then you cannot talk about evolutionary advantage. Selection (whether natural, sexual, artificial or whatever) does not (necessarily) minimize the risk of extinction of species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/239/is-there-any-evidence-that-sexual-selection-may-lead-to-extinction-of-species&quot;&gt;This post&lt;/a&gt; is very related to your question and is definitely worth reading.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope your teacher didn't really say that! Assuming he did say that, then know that it is really not as easy as he's suggesting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a number of studies that address the question on whether &lt;a href=&quot;http://en.wikipedia.org/wiki/Sexual_selection&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sexual Selection&lt;/a&gt; (SS) and Natural Selection (NS) have opposite or antagonist effects. The subject is not easy and as SS is not my field of expertise my answer will not be complete. I will talk about two possible hypotheses for explaining the existence of SS and what they mean in terms of probability of extinction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Good Genes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under the &quot;&lt;a href=&quot;http://www.britannica.com/EBchecked/topic/1512494/good-genes-hypothesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Good Gene&lt;/a&gt;&quot; hypothesis, females' preference (we'll assume that females are choosy but there are many species where males are choosy) of some traits evolve because those traits are correlated with the global health of the male. In consequence, by choosing a male carrying some trait, the female makes sure that her offsrping will receive good genes from their father. This hypothesis assumes that poor males cannot produce fancy phenotype, while good males can. This is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Handicap_principle&quot; rel=&quot;nofollow noreferrer&quot;&gt;Zahavi's Handicap Principle&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under this hypothesis, if a trait become too costly for a given male, the male will just die, therefore limiting the evolution of secondary sexual traits. As a result, the population will no get extinct. Furthermore, under this hypothesis, SS may actually increase the effect of NS making sure that only the best male reproduce. In results the mean absolute fitness of the population should increase faster in a population where &quot;Good gene&quot;-SS occurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sexy Son&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Females preference for some trait may also evolve because mating with a sexy male means having sexy sons. This is called the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sexy_son_hypothesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;sexy son&lt;/a&gt;&quot; hypothesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under this hypothesis, again if a sexy male has a low enough survival, then a female has better to mate with a less sexy male (even though her offspring won't be very sexy) so to increase the survival of her offspring. After a bunch of generations, all females will end up preference mating with non-sexy male, changing the concept of what we call sexy in this population and therefore reversing the effects of SS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may also want to read about &lt;a href=&quot;http://en.wikipedia.org/wiki/Fisherian_runaway&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fisher's runaway processes&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Just an article among others&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aneil Agrawal has some nice articles on SS that may interest you. &lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822(11)01397-2?cc=y&quot; rel=&quot;nofollow noreferrer&quot;&gt;This article&lt;/a&gt; for example discusses how sexual antagonist genes influence whether SS has an antagonist or parallel effect to NS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is SS really different from NS?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question &lt;code&gt;Why natural selection did not eliminate sexual selection?&lt;/code&gt; assumes that NS and SS are two different things! This is a very old-style point of view. Charles Darwin coined these two terms thinking of two, unrelated processes. Today, most authors see SS as being part of NS (if a chestnut tree is a type of tree, SS is a type of NS). And many of the processes that are termed SS has actually not much to do with &quot;competition to access a mate&quot; but only has to do with NS. For example, many people talk about SS when talking about sexually antagonist genes or sexual conflicts. In short, the concepts are kind a mixed up. You may want to read about the work of Hannah Kokko about the semantics of terms related to SS.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-10-08T20:17:52.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24628" PostTypeId="1" AcceptedAnswerId="24629" CreationDate="2014-12-07T02:17:34.260" Score="0" ViewCount="842" Body="&lt;p&gt;Yes, I know, not two, but THREE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Yes, sorry but I did quite a bit of research, searching my notes and textbook for the answer, but all I could find was TWO functional groups as a opposed to the three my guide said there should be. Trust me, I looked quite a bit and there were many conflicting sources with different answers.&lt;/p&gt;&#xA;" OwnerUserId="10458" LastEditorUserId="10458" LastEditDate="2014-12-07T23:29:22.960" LastActivityDate="2014-12-08T03:15:35.253" Title="Which three functional groups are found in the general structure of amino acids?" Tags="&lt;genetics&gt;&lt;amino-acids&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2014-12-07T07:44:50.083" ContentLicense="CC BY-SA 3.0" />
  <row Id="24629" PostTypeId="2" ParentId="24628" CreationDate="2014-12-07T03:01:34.067" Score="1" Body="&lt;p&gt;Amine, alkyl, and carboxylate.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vLoUD.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;I'd guess the part that you're having trouble on is that the alpha carbon in the center of the generic AA structure is part of an alkyl functional group&lt;/p&gt;&#xA;&lt;h2&gt;Edit&lt;/h2&gt;&#xA;&lt;p&gt;The original answer that I gave might have been too clever for its own good. Depending on how one looks at the question, the third functional group could instead be the functional group of the particular side chain, i.e. for Alanine it would be a methyl group, for Tryptophan it would be an indole group, etc.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-08T03:15:35.253" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24631" PostTypeId="1" AcceptedAnswerId="24632" CreationDate="2014-12-07T04:21:06.407" Score="10" ViewCount="6156" Body="&lt;p&gt;And vice versa, do the left-handed people tend to use the left side teeth of their jaw to chew food more often than the right-handed people?&lt;br&gt;Or the frequency of food chewing distribute fairly to both sides of the jaw?&lt;/p&gt;&#xA;" OwnerUserId="8834" LastActivityDate="2018-02-04T02:37:21.857" Title="Do the right-handed people tend to use the right side teeth of their jaw to chew food more often than the left-handed people?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24632" PostTypeId="2" ParentId="24631" CreationDate="2014-12-07T05:38:23.043" Score="11" Body="&lt;p&gt;Individuals have not only hand dominance but also a dominant foot, eye and ear. There has also been a belief that this sidedness applies to chewing as well. However, the short answer is that no one is sure, but that it &lt;em&gt;may&lt;/em&gt; be related to handedness. I only looked at studies done after 2000.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One large study&lt;sup&gt;[1]&lt;/sup&gt; found a questionable to weak correlation, not consistently maintained through different dentition (baby teeth, mixed, and permanent). A slightly smaller study showed a correlation; in 78% chewing side preference correlated with other tested lateralities (footedness, handedness, eyedness and earedness).&lt;sup&gt;[2]&lt;/sup&gt; Another similar sized study found none.&lt;sup&gt;[3]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A small 2012 study found that there was a preference for right sidedness when chewing hard food (73.68%) and for soft food (57.89%) but failed to correlate this with hand/other-sidedness.&lt;sup&gt;[4]&lt;/sup&gt; Another small study tested for sidedness, finding that 55% of subjects did not have any side preference, 30% preferred to chew on right and 15% preferred the left side, and this was reproducible in 90% of subjects &lt;em&gt;only with almonds&lt;/em&gt; (a medium hardness food) as opposed to jerky or asparagus. Unfortunately they did not measure sidedness. Their findings were that chewing-side preference is not a fixed characteristic, and texture &lt;em&gt;seemed&lt;/em&gt; to affect sidedness.&lt;sup&gt;[5]&lt;/sup&gt; A review article determined that a person's dental condition to a large extent dictates how they chew.&lt;sup&gt;[6]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The studies were mostly designed very differently, making good comparisons difficult. I think it's safe to say it's possible but not known with certainty.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22469391&quot;&gt;Absence or weak correlation between chewing side preference and lateralities in primary, mixed and permanent dentition&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15140165/&quot;&gt;Chewing side preference as a type of hemispheric laterality&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18947820&quot;&gt;Relationship between chewing side preference and handedness and lateral asymmetry of peripheral factors&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[4] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443888/&quot;&gt;Chewing side preference in first and all mastication cycles for hard and soft morsels&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[5] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16409510&quot;&gt;Chewing-side determination of three food textures&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[6] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17402223&quot;&gt;Adaptation of mastication in response to the characteristics of the individual or the food&lt;/a&gt;&lt;/sub&gt;   &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-12-07T09:17:07.040" LastActivityDate="2014-12-07T09:17:07.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24633" PostTypeId="1" AcceptedAnswerId="24644" CreationDate="2014-12-07T09:34:36.083" Score="2" ViewCount="1027" Body="&lt;p&gt;First of all, I'm no expert in biology. I failed a lot in high school. Please bear with it if it's a stupid question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the past few days, I got a rotten smell as if an animal died in my kitchen. I cleaned and didn't find anything until I found the culprit today: leakage of rotten eggs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There were two eggs in a hard plastic container, and one of them leaked a bit. Then I saw around 4-5 insects-kind of thing lurking around. It looks like a worm and if you ask me how those things look like, it's as if the egg yolk itself separated into the shape of worms and started moving. If I remember correctly, I believe I saw a pair of white dots (their eyes) in each.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Did those eggs (which was stored in a warm place) actually hatched and gave to a life? I threw all of them away, but I still feel really sick. Is it because of my carelessness that the egg yolk actually became alive in such shape?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks beforehand.&lt;/p&gt;&#xA;" OwnerUserId="10461" LastEditorUserId="10461" LastEditDate="2014-12-07T09:39:38.093" LastActivityDate="2014-12-07T21:21:51.657" Title="Can a rotten egg actually hatches to a real life?" Tags="&lt;eggs&gt;&lt;chickens&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24635" PostTypeId="1" AcceptedAnswerId="24661" CreationDate="2014-12-07T14:14:38.610" Score="4" ViewCount="135" Body="&lt;p&gt;I live in Northern Virginia, USA. As I am sitting here there is a large flock of small (blackish) birds in a tree. They are quite prevalent here. For the sake of brevity I will call these birds &quot;sparrows.&quot; I don't believe it matters what they really are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also several medium-sized blackish birds perched on the eaves of the townhouses. Again, I'll call these birds &quot;crows&quot;. (We have a committee of large vultures (yes, really) in the neighborhood as well, which is why I call the crows medium-sized.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The crows (tend to) lay their eggs in the sparrow's nests. Little crow hatchlings are then &quot;raised by&quot; the sparrow parents, along side thier smaller &quot;siblings&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the now adult crow think it's just an oversized sparrow? (IOW, do all of the crows I see have identity issues and feelings of inadequacy due to their extreme gigantism? :) )&lt;/p&gt;&#xA;" OwnerUserId="8928" LastEditorUserId="8928" LastEditDate="2014-12-07T14:25:30.540" LastActivityDate="2014-12-08T04:33:36.953" Title="Does a bird know it's different?" Tags="&lt;ornithology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ClosedDate="2014-12-08T02:24:23.207" ContentLicense="CC BY-SA 3.0" />
  <row Id="24638" PostTypeId="1" CreationDate="2014-12-07T17:45:19.727" Score="0" ViewCount="431" Body="&lt;p&gt;Thallaesemic patients are advised to have only &quot;&lt;a href=&quot;http://nbts.gov.eg/pages/Phenotyping.html&quot; rel=&quot;nofollow&quot;&gt;phenotypically matched blood&lt;/a&gt;&quot;.I mean the transfusion problems arise mainly due to &quot;grouping problems&quot; like mismatch b/w ABO &amp;amp; Rh+/- so what do this phenotyping mean? Isn't &quot;grouping&quot; of blood enough? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Statutory declaration- the link provided in the q is only to clarify in which context the q is asked &amp;amp; nothing more, like promoting Egyptian Gov. Health Service&lt;/em&gt;...(or any other CRAZY INTERPRETATIONS like that)** &lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="10045" LastEditDate="2014-12-08T05:04:20.803" LastActivityDate="2014-12-08T05:04:20.803" Title="What is phenotyping of blood during transfusion process?" Tags="&lt;hematology&gt;&lt;blood-transfusion&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24640" PostTypeId="1" CreationDate="2014-12-07T18:36:05.410" Score="6" ViewCount="11884" Body="&lt;p&gt;Suppose you want to stand on one leg. Doing it eyes open is not that difficult, but doing it eyes closed seems to be difficult. Why?&lt;/p&gt;&#xA;" OwnerUserId="10463" LastEditorUserId="9943" LastEditDate="2015-05-22T01:52:00.153" LastActivityDate="2015-05-22T01:52:00.153" Title="Effect of closed eyes on balance?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;vision&gt;&lt;balance&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24642" PostTypeId="1" CreationDate="2014-12-07T20:53:19.180" Score="2" ViewCount="847" Body="&lt;p&gt;So I was in class and my professor was explaining western blotting. It seems as though there's more than one way to increase or decrease the signal intensity. He presented us the challenge to discover different ways this can happen. As hard as I look all I can find on the internet or even in google scholar is just certain chemicals like 'signal enhancer' and that's it, nothing remotely specific. Legitimately I do not propose this as actual homework, in fact it's just a curiosity I have. Therefore I ask the scientific community what, if any, are conditions that one could increase or decrease the signal intensity in western blotting? I understand what western blotting is, anyone can find this on wikipedia, but conditions that could increase or decrease signal intensity?&lt;/p&gt;&#xA;" OwnerUserId="10459" LastEditorUserId="9689" LastEditDate="2014-12-08T20:56:04.460" LastActivityDate="2014-12-08T20:56:04.460" Title="Increasing/decreasing signal intensity in Western blotting" Tags="&lt;biochemistry&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24643" PostTypeId="1" AcceptedAnswerId="24647" CreationDate="2014-12-07T21:06:15.857" Score="8" ViewCount="2065" Body="&lt;p&gt;I would like to know if it's possible for a human to acquire an animal memory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I mean, animals store their memories in their brain, right? And so do we, humans, store our memory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So, is it possible to cut off an inch (or something like that) of an animal brain,&#xA;also to cut off an inch of a human brain, and to replace that animal brain-piece in the missing part of the human's brain?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="10351" LastEditorUserId="9943" LastEditDate="2014-12-08T12:04:40.363" LastActivityDate="2014-12-08T21:43:41.180" Title="Can a human acquire a memory of an animal?" Tags="&lt;human-biology&gt;&lt;zoology&gt;&lt;brain&gt;&lt;memory&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ClosedDate="2014-12-19T21:48:52.060" ContentLicense="CC BY-SA 3.0" />
  <row Id="24644" PostTypeId="2" ParentId="24633" CreationDate="2014-12-07T21:21:51.657" Score="8" Body="&lt;p&gt;A chick can't develop outside of it's egg, so you won't see an embryonic chick growing and wiggling in a pool of substance leaked from a cracked egg.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Centuries ago, people believed in &lt;em&gt;spontaneous generation&lt;/em&gt;: that life can arise from non-living things. A common example of this was the fact that maggots would &quot;arise&quot; from rotting meat if left to rot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although this theory was disproved, it is not rare to find someone that still believes it, because they seem to see it happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the 1800's, before DNA was discovered, it became accepted that &quot;like gives rise to like&quot; - that is, chicken eggs will hatch chicks (not peacocks or mice), pea seeds will always give rise to peas, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA was 'discovered' in the late 1800's by Johann Friedrich Miescher. He extracted a new king of organic moleculr out of cell nuclei, which he called &quot;nuclein&quot;. Although Miescher did develop some hypotheses about how &quot;nuclein&quot; might be involved in heredity, he ascribed to the view at the time that any one type of molecule would be too simple to account for all the variation seen within species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be about 75 years before the magnitude of Miescher's discovery would be fully understood, and that DNA is the basis for heredity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chicken eggs, if they give rise to anything (which will depend on if it is fertilized and properly incubated) can only give rise to chickens. Whether they are fertilized or not, they can't give rise to worms. A chick can't develop outside of it's egg, so you won't see an embryonic chick growing and wiggling in a pool of substance leaked from a cracked egg.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you buy bananas and let them ripen and rot on your kitchen counter, you will suddenly find a lot of fruit flies in the house. The fruit flies did not spontaneously arise from the bananas; they came from eggs laid on the bananas before you bought them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you buy bananas and wash them well when you get home, and let them rot, you will not find fruit flies buzzing around them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is why your rotten egg didn't give rise to those little worm things.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-07T21:21:51.657" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24645" PostTypeId="1" AcceptedAnswerId="24648" CreationDate="2014-12-07T21:24:43.260" Score="1" ViewCount="52" Body="&lt;p&gt;I was wondering... If Ebola attacks immune cells and causes immunosupression, then shouldn't we see death in Ebola patients due to secondary infection?&lt;/p&gt;&#xA;" OwnerUserId="10401" LastActivityDate="2014-12-07T21:42:06.463" Title="Ebola immunosupression and infection" Tags="&lt;immunology&gt;&lt;ebola&gt;&lt;immunosuppression&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24646" PostTypeId="2" ParentId="24642" CreationDate="2014-12-07T21:25:39.387" Score="2" Body="&lt;p&gt;There are several different places in a typical &lt;a href=&quot;http://www.cellsignal.com/common/content/content.jsp?id=western&quot; rel=&quot;nofollow&quot;&gt;Western blotting protocol&lt;/a&gt; where conditions can be altered to modulate signal intensity. The first is the amount of protein loaded - more protein will give a stronger signal, less will give a weaker signal. However, too much protein can result in indistinct bands, increased background, lane distortion, and other issues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The next condition to change is the amount of primary antibody and the incubation buffer. More primary may lead to an increased signal, but too much can give higher background. Some antibodies give a better signal when diluted in BSA, others when diluted in nonfat dry milk. Generally, milk will give you a cleaner blot, but may reduce the signal. Incubation time can also affect specificity and signal intensity - some antibodies will fully bind with a 1-2 hour incubation at room temperature, others require an overnight incubation at 4°C.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The third condition to alter is the amount and type of secondary antibody. Increasing the amount of secondary may increase signal, but again may result in increased background. There are also different types of secondaries, depending on your detection system - HRP for chemiluminescent detection, AP for colorimetric, fluorescent tags for imaging systems, etc. These have different sensitivities, but can also result in increased background, depending on the other conditions of the protocol.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, the type of detection system can affect sensitivity. For example, when using standard HRP-conjugated secondaries, there are numerous different ECL substrates with widely varying sensitivities. &lt;a href=&quot;http://www.piercenet.com/cat/western-blotting-substrates&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a list of different systems available from Thermo/Pierce, ranging from standard ECL to Femto.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, while Western blotting seems like a fairly straightforward procedure, there are many places to optimize the conditions to get the results you're looking for.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-12-07T21:25:39.387" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24647" PostTypeId="2" ParentId="24643" CreationDate="2014-12-07T21:32:27.243" Score="21" Body="&lt;p&gt;No, it can't be done for a lot of reasons. Here are just a few.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Memories are stored in electrical pathways, not the the cells themselves. You don't have 1000 memories in a chunk of brain that contains 1000 neurons. If you don't get the entire pathway, you won't get the memory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Once a nerve is cut, it won't &lt;em&gt;fuse&lt;/em&gt; with another cut nerve. All you'll have is a chunk of dying animal brain in your head. Even if a skilled neurosurgeon united the blood vessels of your brain to those of the chunk to keep it alive, the nerves themselves wouldn't become a working part of your brain. All you'd have (at best) is a useless chunk of another animal's brain sitting where your now-missing chunk was.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Animals are different from us. Your body would recognize the different-animal brain matter as foreign, and would make antibodies to it and reduce it to mush (if one didn't die of infection before then).&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-12-08T09:17:13.387" LastActivityDate="2014-12-08T09:17:13.387" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="24648" PostTypeId="2" ParentId="24645" CreationDate="2014-12-07T21:42:06.463" Score="1" Body="&lt;p&gt;Yes, we should. But Ebola doesn't completely immunosuppress us, or there would be no survivors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ebola kills by overwhelming the body before enough antibodies are formed to fight it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're one of the survivors (as about 40-50% are, more with good care), you'll have antibodies to Ebola in your blood which might help someone else infected with Ebola.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're not one of the survivors, it's still likely you'll have some antibodies, but the shock your body goes into from all the dead cell products in your blood (which - overly simplified - causes a &lt;em&gt;cytokine storm&lt;/em&gt; -&gt; leaky capillaries -&gt; fluid balance problems -&gt; end organ failure -&gt; death).&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-07T21:42:06.463" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24652" PostTypeId="2" ParentId="24642" CreationDate="2014-12-07T22:14:22.970" Score="1" Body="&lt;p&gt;Additionally to the points in the answer @mattdmo has given, it is possible to enrich the protein of choice before the gel run. This can either be done by using tagged proteins (possibly with the cleavage of the tag before loading) or by doing an immunoprecipitation of your protein. The later is interesting when you have only low concentrations of your protein present in the cell. What you basically do is to bind an antibody to the protein, the bind the protein-antibody-complex to a column or beads, wash away (in theory, practically you are not getting all the other proteins away) and then load the sample. Depending on the enrichment, you will be able to see a band, where this is not possible without immunoprecipitation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then washing and blocking of the blot plays an important role. Usually you use milk powder to prepare the blocking solution, as this is quite cheap and works pretty well. But it can give quite a high background and make problems with phosphoproteins (not necessarily though). Sometimes it's better to use more expensive solutions like BSA for blocking the membrane. The washing is also critical, depending on how stringent you wash, you will loose signal and influence the background. Here you can play with different concentrations of detergents as well as with different detergents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally you can get a lot of different signals in the detection. For chemolumincence based detection you can either use x-ray films (which are rather unsensitive) and have problems with strong bands outshining neighbouring weak ones. They are also harder to quantify, as the linear range in which more intensity corresponds with more signal is limited. With chemoluminescence you can also use special highly sensitive CCD-cameras (which are more sensitive and have a much higher linear detection range) or phospho-imager plates (special plates, which store the chemoluminecent signal on a light sensitive plate and which are read out with a special scanner).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The latest development in the detection technology are infrared scanners for which you use secondary antibodies coupled to a dye which fluoresces at infrared wavelength. These scanner are extremely sensitive and also allow the usage of two differently labelled secondary antibodies at the same time, which can be very handy in analyzing protein interactions. You will need primary antibodies from different species, though. The modern detection techniques also have the advantage of delivering digital files, while films need to be scanned before further use in publications.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2014-12-08T09:12:40.387" LastActivityDate="2014-12-08T09:12:40.387" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24653" PostTypeId="1" CreationDate="2014-12-07T22:22:22.867" Score="4" ViewCount="114" Body="&lt;p&gt;I have lost count of how many protocols I've seen, including those supposed to be professionally written (such as manuals that come with kits from well known brands, or methods sections of papers in respected journals), that outright fail to give unambiguous instructions. Some common examples are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Give centrifuge speed in RPM instead of RCF, and not say what rotor or centrifuge it is.&lt;/li&gt;&#xA;&lt;li&gt;Say to spin a sample at &quot;maximum speed&quot;.&lt;/li&gt;&#xA;&lt;li&gt;Use subjective time periods, e.g. &quot;incubate briefly&quot; (is one minute brief enough or does it have to be five seconds?)&lt;/li&gt;&#xA;&lt;li&gt;Subjective quantities, such as &quot;get a good amount of cells&quot; (!!!)&lt;/li&gt;&#xA;&lt;li&gt;Give time ranges without explaining the consequences of the choice, such as &quot;5-10 minutes&quot; (is it 5 or 10? which one???).&lt;/li&gt;&#xA;&lt;li&gt;Say &quot;mix well&quot;, without specifying if vortexing is okay.&lt;/li&gt;&#xA;&lt;li&gt;Say &quot;mix well, don't vortex&quot;, and don't explain what mixing technique I'm supposed to use.&lt;/li&gt;&#xA;&lt;li&gt;Give urgent-sounding warnings, such as &quot;don't touch the pellet!&quot;, without explaining what happens if I do it or how to fix it (do I need to start over? will I just get 5% lower yield?).&lt;/li&gt;&#xA;&lt;li&gt;Give urgent-sounding warning, without explaining how to actually heed the warning (&quot;dry the pellet, but do not over-dry it!&quot;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It is in fact extremely rare that I ever see a protocol that has none of these issues. It almost never happens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is extremely important that scientific results be reproducible, and it seems like you are &lt;a href=&quot;http://blogs.nature.com/news/2014/03/acid-bath-stem-cell-team-releases-tip-sheet.html&quot; rel=&quot;nofollow&quot;&gt;opening yourself up to a lot of trouble with an ambiguous protocol&lt;/a&gt;. What if somebody fails to reproduce your results, not because your experiment wasn't legitimate, but simply because you left out some crucial detail from the protocol you gave them? You would look bad, and for no good reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why is it so common for protocols to be ambiguous? Is there some nuance to this that escapes me, or do people just not care? How do you follow a protocol that left out crucial information so as to be impossible to follow? Or are you supposed to have amassed a sufficiently vast reservoir of practical knowledge that you can draw on it to &quot;fill in the blanks&quot; on the fly?&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-12-07T22:28:18.837" LastActivityDate="2014-12-07T22:45:20.503" Title="What's up with all the vague protocols?" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;protocol&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2014-12-08T02:19:17.343" ContentLicense="CC BY-SA 3.0" />
  <row Id="24656" PostTypeId="2" ParentId="24653" CreationDate="2014-12-07T22:45:20.503" Score="3" Body="&lt;p&gt;This is too long for a comment, so I post my thoughts about this here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This falls into different important parts here: One is an insufficient understanding of the techniques on which the method is based. This makes it hard to decide which steps are important and which are not. One prominent example would be the use of EDTA in DNA gel running buffers. This recipe originated from RNA research (where you need the EDTA) which where then simply used for DNA as well. Since it worked somehow, it was never really changed.I have seen enough people in the lab clinging to old photocopies of protocols without knowing why they do certain steps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And the other (connected) issue is that protocols are usually passed down through labs. Things are then done in a certain way because they have always done in this way (with some changes in the protocol probably not even documented) and are not changed. People are even told to use the exact routine, even if this makes absolutely no sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In publications there may also be another thing which comes into play: The fear that someone uses the own methods and will then be faster than the own group. At least some groups only publish incomplete and vague methods because of this reason. Then it's a thing of space: There are character limitations in publications and when you need to save a few hundred characters when the article is too long, it's much easier to shave the methods than the discussion. &lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-07T22:45:20.503" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24658" PostTypeId="2" ParentId="24640" CreationDate="2014-12-07T23:16:47.843" Score="7" Body="&lt;p&gt;Balance is tricky and depends on a lot of things, including, to some degree, your sight. Balance is achieved and maintained by a complex set of sensorimotor control systems that include &lt;em&gt;sensory input from vision (sight)&lt;/em&gt;, proprioception (touch), and the vestibular system (motion, equilibrium, spatial orientation); integration of that sensory input; and motor output to the eye and body muscles. Your vision helps you see where your head and body are in relationship to the world around you and to sense motion between you and your environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Very simply put, &lt;strong&gt;to blindfold someone is to take out the contribution of vision to balance.&lt;/strong&gt; So, if the other systems involved in balance are off even a bit, blindfolding someone will interfere with their ability to keep their balance, even on two legs, let alone one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are those systems in more detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Proprioception&lt;/strong&gt;. In your joints, muscles, tendons, skin, and other areas, you have proprioceptors, that tell your brain where yoor aody parts (arms, legs, etc) are in relation to self in space. Because we live on a planet with  gravity, even if we are blindfolded, if we are standing correctly, our feet will sent our brain signals that will in turn allow the brain to judge our position in space with regard to gravity and we will keep our feet firmly planted on the ground in a way which will maintain us upright in a constantly regulated position (if we sense less pressure from the bottom of our right great toe, we will adjust by leaning forward and to the right a bit until out=r brain says, &quot;ok, right there!&quot; This happens from all the skin and joint proprioceptors responding at the same time. Notice that once vision is blocked, our bodies become relatively very still; we focus on our balance. We move tentatively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As people age, they lose some of their propioceptive abilities. That's one of the reasons for falls in the elderly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Inner ear&lt;/strong&gt;. In our inner ear are the semi-circular canals, three on each side, which are oriented at ~90° to each other so we cover 3 dimensions. In these canals is fluid which sloshes about when we move our heads, change directions, bend over, etc. The fluid moving about is detected by fine hair-like projections on the sensory cells lining the canal called &lt;em&gt;stereocilia&lt;/em&gt; - like a wave would be detected by your leg in shallow ocean water. These semicircular canals help us to remain oriented in space. Now, the semicircular canals are also attached to &lt;em&gt;otolith organs&lt;/em&gt; - two chambers which are concerned with gravity. They have fine crystals in them - called otoconia - which move according to our head's position with relationship to &quot;down&quot;, or gravity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we stand perfectly still (probably not possible without support), everything is read by the vestibular system (the semicircular canals and the otolithic organs) as normal, and we stay upright (there is a constant communication between our vestibular system and our brain). So, when blindfolded, we can stay upright even if we shake our heads, bend them forward or back, etc (within reason). As we age, things can degenerate in this vestibular system, which affects our balance, and results in more falls in the elderly. (Diseases in the young can also affect this.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Vestibulo-ocular Reflex&lt;/strong&gt;. A complicated system which reflexly coordinated input from your vestibular system and your vision in head movement. If someone suddenly turns your head, your eyes will move in the equal and opposite manner, that is, your eyes will stay focused on the object on which they were focused just before your head was moved. This system is what allows you to easily keep reading something while you shake your head from side to side (not the case if you move the print side to side).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When things start going wrong (in a very slow manner) with your vestibular or proprioception systems, your eyes can &lt;em&gt;help compensate&lt;/em&gt; by orienting you to the horizon, etc., in a manner, correcting for some 'off' calculations in your vestibular system. Vision helps us to identify orientation with respect to gravity, determine direction and speed of movement, etc., to a much lesser degree than the other systems described but enough to have an impact. So, in people whose vision is failing, either their other systems have to be in really good working order (e.g. why young blind people aren't always falling over) or they have problems with falling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://vestibular.org/understanding-vestibular-disorder/human-balance-system&quot;&gt;The Human Balance System&lt;/a&gt; (easy)&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ucdmc.ucdavis.edu/publish/news/newsroom/7895&quot;&gt;Researchers find diminished balance in those with poor vision&lt;/a&gt; (easy)&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.cbass.com/Balance.htm&quot;&gt;Balance&lt;/a&gt; (easy)&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;ved=0CCUQFjAB&amp;amp;url=http%3A%2F%2Fwww.engineering.pitt.edu%2FWorkArea%2FDownloadAsset.aspx%3Fid%3D2147497203&amp;amp;ei=G9yEVIusHMHLsASslYG4Cg&amp;amp;usg=AFQjCNEe1Htq6qVrQ_O7d_g8Ri5MTPmPJA&amp;amp;sig2=KtQ6NV4wrEMVBL2L3uTXyw&amp;amp;bvm=bv.80642063,d.aWw&quot;&gt;Visual influences on balance&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://books.google.com/books?hl=en&amp;amp;lr=&amp;amp;id=bCuHZgwSRC4C&amp;amp;oi=fnd&amp;amp;pg=PP2&amp;amp;dq=vestibulo+ocular+reflex+and+physiologic+vertigo&amp;amp;ots=A5rMJ0X1Ks&amp;amp;sig=XobkDjkD-jId7DnUhQpBQouCGlc#v=onepage&amp;amp;q=vestibulo%20ocular%20reflex%20and%20physiologic%20vertigo&amp;amp;f=false&quot;&gt;Baloh and Honrubia's Clinical Neurophysiology of the Vestibular System&#xA; By Robert William Baloh, Kevin Kerber, MD&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://neuroscience.uth.tmc.edu/s2/chapter02.html&quot;&gt;Somatosensory Systems&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://kin450-neurophysiology.wikispaces.com/Vestibular+Occular+Reflex&quot;&gt;Vestibular Occular Reflex&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-07T23:16:47.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24661" PostTypeId="2" ParentId="24635" CreationDate="2014-12-08T00:40:03.793" Score="6" Body="&lt;p&gt;Crows don't lay their eggs in sparrows' nests - they lay them in crows' nests. What you're describing, though, here is &lt;em&gt;brood parasitism&lt;/em&gt;. This relieves the parasitic parent of the responsibility of rearing young, building nests, protecting the eggs, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brood parasitism is seen in a number of duck species, with females laying their eggs in the nests of others. One example is the goldeneye, Bucephala &lt;em&gt;clangula&lt;/em&gt;. Interspecific brood-parasites include the most cuckoos and cowbirds, black-headed ducks, and indigobirds, whydahs, and honeyguides. About 1% of all known bird species are obligate brood parasites (never make nests, need a host). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a picture of a reed warbler feeding a cuckoo which was a parasite, its egg having been laid in the warbler's nest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Parasite nestlings suffer a relatively high mortality, either from rejection by the host (host bird will not feed the parasite) or rejection before fledgling (once nestling graduates to tree branch, the hosts stop feeding it). However, clearly since cowbirds and cuckoos are still alive and well, enough of them do survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1b4ID.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do they think they are of the host species? There was no literature I could find on this. While the parasite messes up the host parents and 'siblings' (when there are surviving 'siblings'), there is much less follow-up done on the behavior of the parasite once fledged. Common sense will therefore need to come into play.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a cowbird thought it was an indigo bunting, it would not be able to reproduce, as it would try to attract a bunting mate and fail. Since the hosts continue to experience parasitism over many generations, and the population of parasites does not necessarily decline in a given area over several generations (in some areas, it is the host population that declines), I would have to say, &lt;strong&gt;yes, the bird 'knows' it's different (probably only on an instinctual - not cognitive - level); the parasite bird feels nothing about its bad behavior, and does not learn their own behavior from their host parents.&lt;/strong&gt; Instinct takes over; they mate with their own kind, and continue to parasitize the host birds' nests.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Brood_parasite&quot; rel=&quot;nofollow noreferrer&quot;&gt;Brood parasite&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/early/2012/05/24/rspb.2012.0612&quot; rel=&quot;nofollow noreferrer&quot;&gt;Host–parasite coevolution beyond the nestling stage? Mimicry of host fledglings by the specialist screaming cowbird&lt;/a&gt;&lt;/sub&gt; &#xA;&lt;sub&gt;&lt;a href=&quot;http://www.lsa.umich.edu/ummz/birds/publications/pdf/RBP.156.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Brood parasitism by cowbirds: risks and effects on reproductive success and survival in indigo bunting&lt;/a&gt;&lt;/sub&gt; &#xA;&lt;sub&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Brood_parasite&quot; rel=&quot;nofollow noreferrer&quot;&gt;Brood parasite&lt;/a&gt;&lt;/sub&gt; &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-12-08T04:33:36.953" LastActivityDate="2014-12-08T04:33:36.953" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24663" PostTypeId="1" AcceptedAnswerId="24682" CreationDate="2014-12-08T01:41:14.760" Score="3" ViewCount="2764" Body="&lt;p&gt;Gunnar von Heijne's Positive-inside Rule seems to have been around for a couple of decades and underpins a lot of what we know about transmembrane topology. It is used to predict the topology of a given transmembrane domain, typically a helix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is &lt;strong&gt;what are the physicochemical, or biochemical explanations for this rule?&lt;/strong&gt; Although the literature talks about it in depth and has many examples of the rule being employed, I can't seem to find anything about the &quot;behind the scenes&quot; explanation.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2014-12-08T01:55:21.937" LastActivityDate="2015-11-16T10:54:25.193" Title="Why does the 'Positive-inside Rule' exist?" Tags="&lt;proteins&gt;&lt;cell-membrane&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24666" PostTypeId="2" ParentId="24642" CreationDate="2014-12-08T04:23:25.360" Score="2" Body="&lt;p&gt;One thing that others have not mentioned yet is that the time of the wash can affect the signal. If its washed longer than the usually required 5 minute three time wash, this could result in a reduced (decreased) signal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&#xA;&lt;a href=&quot;http://www.cellsignal.com/common/content/content.jsp?id=western-trouble&quot; rel=&quot;nofollow&quot;&gt;http://www.cellsignal.com/common/content/content.jsp?id=western-trouble&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9002" LastActivityDate="2014-12-08T04:23:25.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24667" PostTypeId="1" CreationDate="2014-12-08T04:49:28.697" Score="3" ViewCount="63" Body="&lt;p&gt;I have an indoor fountain with lots of water. What are the most common microorganisms in this kind of moist environment, and what are the standard way to prevent biofilm formation by them? I thought of copper and/or salt as general cheap disinfectants so far. &lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2015-01-08T00:20:14.643" Title="Prevent biofilm formation on moist surfaces" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24668" PostTypeId="1" AcceptedAnswerId="24672" CreationDate="2014-12-08T04:49:48.210" Score="9" ViewCount="63205" Body="&lt;p&gt;I've learned that plants transform glucose into sucrose before sending it into phloem. But the process seems to be complex and energy comsuming. Why should plants do it? Is it really necessary?&lt;/p&gt;&#xA;" OwnerUserId="10330" LastActivityDate="2019-01-11T13:47:15.300" Title="Why should plants transform glucose into sucrose before transporting it to other parts?" Tags="&lt;plant-anatomy&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24669" PostTypeId="2" ParentId="24638" CreationDate="2014-12-08T04:58:08.703" Score="1" Body="&lt;p&gt;In response to the above q. many have commented that the process is &lt;em&gt;only limited to Middle Eastern countries&lt;/em&gt;....I think the term '&lt;em&gt;only&lt;/em&gt;' will be better substituted by '&lt;em&gt;mainly&lt;/em&gt;', the reason to which , is explained later ....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the main clarification lies in the fact that, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;....there are more than 600 known antigens besides A and B that&#xA;  characterize the proteins found on a person's red cells. A combination&#xA;  of some of these less familiar but commonly occurring antigens are&#xA;  absent from the blood of an extremely small percentage of the&#xA;  population. There are also a few antigens that almost all people have&#xA;  on their red cells but that some lack. - &lt;a href=&quot;http://web.archive.org/web/20080621091025/http://www.newenglandblood.org/medical/rare.htm&quot; rel=&quot;nofollow&quot;&gt;One In A Million&#xA;  American Rare Donor Program&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now patients receiving a 1st time transfusion normally do not show any reactions or cross-matching problems with these blood subgroups but during repeated transfusion process like in case of thallaesemia , the receiver's blood gets sensitized against the donor's blood &amp;amp; the problems ensues...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.blood.co.uk/the-donor/summer2014/phenotyping/&quot; rel=&quot;nofollow&quot;&gt;Dr Therese Callaghan&lt;/a&gt; said, “All other antibodies are unexpected and&#xA;  are of two distinct types, alloantibodies (which target an antigen&#xA;  that is not present on your own red blood cells) and autoantibodies&#xA;  (which target an antigen that is present on your own cells).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;“Patients receiving a transfusion for the first time do not normally&#xA;  have problems with matching blood types and antigens. However it is&#xA;  during subsequent transfusions when more care needs to be taken. If,&#xA;  during a later transfusion, the blood contains the same antigens as an&#xA;  earlier one, the patient’s immune system recognises the transfused&#xA;  blood cells as ‘foreign’ and the antibodies (formed after the first&#xA;  transfusion) will destroy the blood cells the patient has been given.&#xA;  This is called a transfusion reaction and can cause serious illness or&#xA;  even death if not treated quickly. That is why matching the blood&#xA;  phenotype is so important.”&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now coming to &quot;&lt;strong&gt;Why mainly in Middle-East ??&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These rare blood groups are distributed into major 30 discrete system, which &lt;strong&gt;mainly  are present in different ethnic groups &amp;amp; communities&lt;/strong&gt;...mainly living in Middle-Eastern states &amp;amp; Asia...&amp;amp; also in African countries...&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353626/table/T3/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353626/table/T3/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intersted people may also check the following articles (or simply search Google)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://scabb.org/blog/to-provide-phenotype-matched-red-blood-cells-or-not-%E2%80%93-that-is-the-question/&quot; rel=&quot;nofollow&quot;&gt;To Provide Phenotype-Matched Red Blood Cells or Not – That is the Question!&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.transfusionguidelines.org.uk/red-book/chapter-13-patient-testing-red-cell-immunohaematology/13-3-pre-transfusion-testing&quot; rel=&quot;nofollow&quot;&gt;13.3: Pre-transfusion testing&lt;/a&gt;- Joint United Kingdom (UK) Blood Transfusion and Tissue Transplantation Services Professional Advisory Committee&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;amp; for a complete picture plz browse through- &lt;a href=&quot;http://www.cartercenter.org/resources/pdfs/health/ephti/library/lecture_notes/med_lab_tech_students/LN_Immunohaematology_final.pdf&quot; rel=&quot;nofollow&quot;&gt;Immunohaematology&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10045" LastActivityDate="2014-12-08T04:58:08.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24670" PostTypeId="2" ParentId="24620" CreationDate="2014-12-08T05:22:37.820" Score="6" Body="&lt;p&gt;“Self-induction” in photosensitive epilepsy is a well-described and fascinating  phenomenon. Photosensitivity itself is rare, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=renite+KN.+Photosensitivity+in+epilepsy%3A+electrophysiological+and+clinical+correlates.+Acta+Neurologica+Scandinavica+1989%3B+80+%28Suppl+125%29%3A3%E2%80%93149&quot;&gt;occurring in only ~5% of patients with epilepsy&lt;/a&gt;.&lt;sup&gt;1&lt;/sup&gt; Among this group it &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12169155&quot;&gt;has been estimated&lt;/a&gt;&lt;sup&gt;2&lt;/sup&gt; that 25% self-induce epileptiform activity. The most common methods appear to be passing a hand with open fingers repeatedly across the visual field and, as you query, blinking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quoting from a classical paper on the topic by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=13861141&quot;&gt;Andermann et al&lt;/a&gt;:&lt;sup&gt;3&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The method of inducing seizures varies&#xA;  both in detail and in principle. Light contrasts are always brought about, but they may either be applied to and alternate for the whole visual field—an effect produced by blinking or batting the eyelids and induced by any flickering light—or else the attack is elicited by the spatial displacement of brightness and darkness  over the retina. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This phenomenon is most common in epileptics with established photic triggers, and the scenario triggering an attack is often in the context of bright sunlight. However, this has also been described in epileptics who are not otherwise photosensitive. See, for example, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=3084713&quot;&gt;“Seizures triggered by blinking in a non-photosensitive epileptic.”&lt;/a&gt;&lt;sup&gt;4&lt;/sup&gt;&#xA;Notably, some authors have questioned whether blinking and other “triggers” are actually themselves ictal phenomena (i.e. representing the initial phase of an epileptic event) rather than a form of voluntary self-induction. For more on that hypothesis, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=5132972&quot;&gt;Ames, 1971&lt;/a&gt;.&lt;sup&gt;5&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Presuming that this is, in fact, self-induction as has been traditionally postulated, the question of why such patients repeatedly self-induce seizures is perhaps the most interesting aspect of this. There &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12169155&quot;&gt;has been some research&lt;/a&gt;&lt;sup&gt;2&lt;/sup&gt; considering the psychiatric factors underlying the behavior. Quoting &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=13861141&quot;&gt;Andermann&lt;/a&gt;&lt;sup&gt;3&lt;/sup&gt; again:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The reward a patient seeks by self-stimulation may lie in escape from unwanted situations, in attracting attention, in punishing those around him, or, indeed, in deriving pleasure from the attack.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Kasteleijn-Nolst Trenité DG. &lt;em&gt;Photosensitivity in epilepsy. Electrophysiological and clinical correlates.&lt;/em&gt; Acta Neurol Scand Suppl. 1989;125:3-149.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Ng BY. &lt;em&gt;Psychiatric aspects of self-induced epileptic seizures.&lt;/em&gt; Aust N Z J Psychiatry. 2002 Aug;36(4):534-43.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Andermann K, et al. &lt;em&gt;Self-induced epilepsy. A collection of self-induced epilepsy cases compared with some other photoconvulsive cases.&lt;/em&gt; Arch Neurol. 1962 Jan;6:49-65.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Rafal RD, Laxer KD, Janowsky JS. &lt;em&gt;Seizures triggered by blinking in a non-photosensitive epileptic.&lt;/em&gt; J Neurol Neurosurg Psychiatry. 1986 Apr;49(4):445-7.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Ames FR. &lt;em&gt;&quot;Self-induction&quot; in photosensitive epilepsy.&lt;/em&gt; Brain. 1971;94(4):781-98.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-12-08T07:43:13.063" LastActivityDate="2014-12-08T07:43:13.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24671" PostTypeId="1" AcceptedAnswerId="24677" CreationDate="2014-12-08T06:46:37.587" Score="10" ViewCount="13343" Body="&lt;p&gt;The cornea is not supplied with blood vessels and so exchanges gases directly with the atmosphere. So how does it breathe during sleep when our eyes are closed?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="6" LastEditDate="2014-12-08T10:04:01.413" LastActivityDate="2014-12-08T11:46:19.210" Title="How does the cornea breathe during sleep?" Tags="&lt;human-biology&gt;&lt;eyes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24672" PostTypeId="2" ParentId="24668" CreationDate="2014-12-08T07:52:55.043" Score="13" Body="&lt;p&gt;Glucose, fructose and galactose are the three dietary monosaccharides. Glucose and Fructose are  simple monosaccharides found in plants. A monosaccharide is the basic unit of carbohydrate and the simplest form of sugar, glucose are aldose and Fructose are ketose.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If the carbonyl is at position 1 (that is, n or m is zero), the molecule begins with a formyl group H(C=O)-, and is technically an aldehyde. In that case, the compound is termed an aldose. Otherwise, the molecule has a keto group, a carbonyl -(C=O)- between two carbons; then it is formally a ketone, and is termed a ketose. Ketoses of biological interest usually have the carbonyl at position 2.&#xA;  &lt;a href=&quot;http://en.wikipedia.org/wiki/Monosaccharide&quot;&gt;http://en.wikipedia.org/wiki/Monosaccharide&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Whereas Sucrose is a disaccharide composed of glucose and fructose. A disaccharide is more complex than monosaccharide, more complex compounds like oligosaccharides and polysaccharides exists. Sucrose synthesised within the cytosol of photosynthesizing cells is then available for general distribution and is commonly trans located to other carbon-demanding centers via the phloem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sucrose and starch are more efficient in energy storage when compared to glucose and fructose, but starch is insoluble in water. So it can't be transported via phloem and the next choice is sucrose, being water soluble and energy efficient sucrose is chosen to be the carrier of energy from leaves to different part of the tree. Another problem exists,   glucose is highly reactive and this may result in some intermediate reactions while transporting glucose. Being a complex structure, sucrose is not as much reactive as glucose. So plants uses the sucrose as a medium to transfer energy. Inside the cells, sucrose is converted back to glucose and fructose. Energy is yielded when it is needed. So plants transfer glucose and fructose in the form of sucrose in order to:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Increase energy storage&lt;/li&gt;&#xA;&lt;li&gt;Efficient energy transfer&lt;/li&gt;&#xA;&lt;li&gt;Removing in between reactions&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;References&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://chemed.chem.purdue.edu/genchem/topicreview/bp/1biochem/carbo5.html&quot;&gt;Carbohydrates&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plantphysprimer.com/sucrose-starch-biosynthesis/&quot;&gt;Sucrose &amp;amp; Starch Biosynthesis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.els.net/WileyCDA/ElsArticle/refId-a0021259.html&quot;&gt;Sucrose Metabolism&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://plantsinaction.science.uq.edu.au/edition1/?q=content/2-1-3-sucrose-and-starch-synthesis&quot;&gt;Sucrose and starch synthesis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Disaccharide&quot;&gt;Disaccharide&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="5144" LastEditDate="2014-12-08T09:54:28.617" LastActivityDate="2014-12-08T09:54:28.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24673" PostTypeId="2" ParentId="21058" CreationDate="2014-12-08T09:44:40.600" Score="6" Body="&lt;p&gt;First of all, &lt;a href=&quot;http://www.bio.tamu.edu/users/ajones/gmatrixonline/gevolving.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here is a program&lt;/a&gt; which simulates the evolution of the G-matrix over multiple generations, it's a few years old (they seem to have stopped developing it) and I've only played with it briefly. This could solve &lt;em&gt;how&lt;/em&gt; to model the evolution of the G-matrix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fisher's fundamental theorem is a great place to start off with the theory of this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The rate of increase in fitness of any organism at any time is equal to its genetic variance in fitness at that time.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What this means (as I am sure you realise but I will put in so the answer can help others too) is that evolution by selection depends not only on the strength and form of selection, but the genetic variation underlying the selected trait. This is captured in the breeders equation $\Delta \bar z = G \beta$  where $\Delta \bar z$ is the response (in a multivariate space), $G$ is a matrix of the genetic variance within traits covariance between traits (different traits, the same traits in either sex, or the same traits in multiple environments) and $\beta$ is the vector of selection gradients on all of those contexts. It seems reasonable to &lt;a href=&quot;https://biology.stackexchange.com/questions/21021/did-darwin-ever-reach-the-conclusion-that-selection-will-remove-variation&quot;&gt;expect that given enough time selection will erode variation&lt;/a&gt; because standing genetic variance is a finite resource and selection removes polymorphism while not adding any new variants (that's for mutation &amp;amp; migration).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.genetics.org/content/180/4/2151.full.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;This paper discusses the effects of both selection and drift on the G-matrix, they also deal with some modelling to support their results.&lt;/a&gt; &lt;strong&gt;More specific to simulation,&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3229175/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article by Arnold et al&lt;/a&gt; (a number of the big players in the G-matrix circle). It reviews &quot;empirical, analytical, and simulation studies of the G-matrix with a focus on its stability and evolution.&quot; It would be a really good read for you on this subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This paragraph captures the essence of your question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Focusing on a longer time scale, we find that the G-matrix evolves in expected ways to the AL [adaptive landscape] and the pattern of mutation. In the absence of correlational selection (rω = 0) and mutational correlation (rμ = 0), the average G-ellipse is nearly circular, although the ellipse fluctuates wildly about this average (first row in Fig. 6). At the opposite extreme, when the leading eigenvectors of the AL and the M-matrix [mutation matrix] are both inclined at an angel of 45°, the leading eigenvector of G is pitched at the same angle (last row in Fig. 6). Between these two extremes, G tends to evolve to a shape and orientation that represents an intermediate compromise between the AL and M. In other words, the simulation results confirm our intuition and theoretical expectations (Lande 1980b) that G should evolve toward alignment with the AL and M.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Simulation studies of the G-matrix:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Bürger R, Wagner GP, Stettinger J. How much heritable variation can be maintained in finite populations by mutation-selection balance. Evolution. 1989;43:1748–1766.&lt;/li&gt;&#xA;&lt;li&gt;Multivariate mutation-selection balance with constrained pleiotropic effects.&#xA;Wagner GP&#xA;Genetics. 1989 May; 122(1):223-34.&lt;/li&gt;&#xA;&lt;li&gt;On the distribution of the mean and variance of a quantitative trait under mutation-selection-drift balance.&#xA;Bürger R, Lande R&#xA;Genetics. 1994 Nov; 138(3):901-12.&lt;/li&gt;&#xA;&lt;li&gt;Predicting long-term response to selection.&#xA;Reeve JP&#xA;Genet Res. 2000 Feb; 75(1):83-94.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The &lt;a href=&quot;http://people.sc.fsu.edu/~pbeerli/bsc5932/reeve-2000.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;last article there by Reeve&lt;/a&gt; is probably the best paper for your question because it describes in some detail the simulation model they use and how it is all set up.&lt;/strong&gt; Briefly they simulate a population of 4000 diploid individuals with three genetically correlated traits with separate but identical sexes, random mating, and discrete generations. 20000 generations are simulated to allow mutation-selection-drift equilibrium (almost like a burn-in time on an MCMC chain). They then shift the optimum for one trait by 10 standard deviations and simulate 1500 generations in five replicates. There are 100 unlinked loci underlying the traits, with 50 loci affecting each trait (randomly assigned) meaning there is likely some degree of genetic correlation though it is not perfectly correlated &lt;em&gt;(for some reading on genetic correlations and the evolution of differences you can read &lt;a href=&quot;http://www.bonduriansky.net/E-2005b.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bonduriansky &amp;amp; Rowe 2005&lt;/a&gt;, &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2009.00793.x/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Poissant et al 2010&lt;/a&gt;, and &lt;a href=&quot;http://mbe.oxfordjournals.org/content/30/9/2168.full.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Griffin et al 2013&lt;/a&gt;)&lt;/em&gt;. The model then assigns phenotypic values to individuals, and fitness is derived. Figure two shows how the mean, skew, and kurtosis of the variance distributions changed for those 1500 generations.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Addition&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22487403&quot; rel=&quot;nofollow noreferrer&quot;&gt;Roff 2012:&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;While the mean trait values change under selection, so also will the&#xA;  G matrix, its orientation tending to shift in the direction of&#xA;  selection. ... Genetic drift may also play a role in changing the G&#xA;  matrix, but in this case the change will be random though on average&#xA;  producing a proportional change in the constituent variances and&#xA;  covariances.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2016-08-17T08:48:18.300" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24674" PostTypeId="2" ParentId="7912" CreationDate="2014-12-08T09:46:19.440" Score="2" Body="&lt;p&gt;I have gone through quite a number of papers using this virus, but I haven't found any definite answer on the maximum insert length. There is an indirect answer, though. The two articles cited below both report possible insert length of up to 3.7kb without any experimental problems. This insert length results in a viral genome which is about 1.9kb longer than naturally occurring. So at least 3.7kb insert length are possible, if longer inserts can also be used, needs to be tested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23887178&quot; rel=&quot;nofollow&quot;&gt;Design and generation of recombinant rabies virus vectors.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21867879/&quot; rel=&quot;nofollow&quot;&gt;New rabies virus variants for monitoring and manipulating activity&#xA;and gene expression in defined neural circuits.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-08T09:46:19.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24675" PostTypeId="2" ParentId="5405" CreationDate="2014-12-08T10:03:15.007" Score="0" Body="&lt;p&gt;We already remove old memories (well, more properly unimportant ones) partially in order to make room for new ones&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are 3 different levels of storage, but none of them involve an increase of mass. (Distribution of mass, in one sense, but not amount thereof.) I'm not a neuroscientist, but there are one or two lurking around here who can correct anything wrong that I say, so don't take me as an authority. As I understand it: the first level is strictly electrochemical and very short-lived (except in some savants), such as what was the last word that you heard or the last time that you cracked your knuckles. Once the experience is over, it is forgotten. The second is just chemical, as proteins or whatever organize themselves into patterns that are essentially &quot;books&quot;. That is what happens with stuff that you need to keep, such as school lessons, tax laws, or whatever. The third is DNA transcription, wherein a memory becomes an intrinsic part of your existence and might be inherited (as in &quot;instinct&quot; or even transplanted to another person.&lt;/p&gt;&#xA;" OwnerDisplayName="user9033" LastActivityDate="2014-12-08T10:03:15.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24676" PostTypeId="2" ParentId="23960" CreationDate="2014-12-08T10:31:06.960" Score="2" Body="&lt;p&gt;Cisternal doesn't make sense in this context, so either your mother is using an obscure term (quite possible, these things change a lot) or just has the wrong word. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, mirror twins are a known thing (and quite cool): &lt;a href=&quot;http://www.twinsuk.co.uk/twinstips/4/140/twin-pregnancy--multiple-births/types-of-twins--identical-fraternal--unusual-twinning/&quot; rel=&quot;nofollow&quot;&gt;http://www.twinsuk.co.uk/twinstips/4/140/twin-pregnancy--multiple-births/types-of-twins--identical-fraternal--unusual-twinning/&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;She may have meant something like &quot;chiral twins&quot; or &quot;&lt;em&gt;cis&lt;/em&gt;-&lt;em&gt;trans&lt;/em&gt; twins&quot;, which would be borrowing from a similar concept in chemistry to describe your mirror-image nature (but is, again, not a phrase I've heard in the twin literature.)&lt;/p&gt;&#xA;" OwnerUserId="10347" LastEditorUserId="10347" LastEditDate="2014-12-08T10:36:36.563" LastActivityDate="2014-12-08T10:36:36.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24677" PostTypeId="2" ParentId="24671" CreationDate="2014-12-08T10:33:26.723" Score="11" Body="&lt;p&gt;As you noted, the cornea needs oxygen, yet it's not vascular. It needs to get it's oxygen supply from diffusion. In the daytime, diffusion occurs from air through the tear film covering the cornea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cornea spends about a third of it's lifetime under closed lids. At night, the tear film remains intact and is continuously replenished. The inner aspect of your eyelids, called the palpebral conjunctiva, are &lt;em&gt;highly&lt;/em&gt; vascularized, with capillaries just below the surface (and accessory tear ducts and tiny mucosal glands to keep it moist). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you sleep, oxygen (and nutrients) diffuses from the palpebral conjunctival capillaries through the tear film to your cornea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The blood vessels in the palpebral conjunctiva are more permeable than most other capillaries and contribute fluid and nutrients to tears by leaking plasma. The surface epithelial cells are also a source of tear fluid because of a special arrangement of the cells such that there is more intercellular space allowing fluid, antibodies, and other plasma constituents to the surface of the conjunctiva. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This very issue was of great concern to ophthalmologists when people started wearing extended-wear contact lenses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;The Conjunctiva and Lacrimal System (www.eyecalcs.com/DWAN/pages)&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.karger.com/Article/Abstract/267143&quot;&gt;Organization of Capillaries in the Primate Conjunctiva&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;The Conjunctiva—Structure and Function (oftalmologia/enciclopedias)&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.readcube.com/articles/10.1111%2Fj.1755-3768.1985.tb05225.x?r3_referer=wol&amp;amp;tracking_action=preview_click&amp;amp;show_checkout=1&quot;&gt;The oxygen tension and temperature of the superior palpebral conjunctiva&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;https://www.nei.nih.gov/health/cornealdisease&quot;&gt;Facts About the Cornea and Corneal Disease&lt;/a&gt; (cool article)&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="9943" LastEditDate="2014-12-08T11:46:19.210" LastActivityDate="2014-12-08T11:46:19.210" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24680" PostTypeId="2" ParentId="19804" CreationDate="2014-12-08T12:21:28.067" Score="3" Body="&lt;p&gt;It would not be possible to differentiate CSC from normal population non-invasively and select them out. You may do a single cell expression analysis to say if a CSC is present in a population or not but there is no magic bullet method for eliminating them. Also there are several oncogenes and some of them are also required for usual stem cell function. HAT kind of methods will not be able to eliminate potential cancer cells. Also, usual cancer chemotherapeutic drugs also affect other actively growing cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bottomline: Not possible with the current level of knowledge and technology.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-08T12:21:28.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24681" PostTypeId="2" ParentId="7945" CreationDate="2014-12-08T12:42:37.317" Score="1" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.drugbank.ca/drugs/DB01403&quot; rel=&quot;nofollow&quot;&gt;Drugbank&lt;/a&gt; and the articles cited below, Levomepromazine is an antagonist of several different receptors: These include dopaminergic 2, dopaminergic 4, alpha-1 adrenoceptor, 5HT-2, histamine type 1 and muscarinic-cholinergic receptors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.biomedcentral.com/1472-684X/12/2&quot; rel=&quot;nofollow&quot;&gt;Evidence for the use of Levomepromazine for symptom control in the&#xA;palliative care setting: a systematic review&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/002432058890519X&quot; rel=&quot;nofollow&quot;&gt;Muscarinic cholinergic and histamine H1 receptor binding of&#xA;phenothiazine drug metabolites&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0447.1993.tb03391.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Levomepromazine receptor binding profile in human brain—implications&#xA;for treatment—resistant schizophrenia&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0014299986907934&quot; rel=&quot;nofollow&quot;&gt;Phenothiazine drug metabolites: Dopamine D2 receptor, α1-and&#xA;α2-adrenoceptor binding&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-08T12:42:37.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24682" PostTypeId="2" ParentId="24663" CreationDate="2014-12-08T13:04:35.607" Score="2" Body="&lt;p&gt;There are not much explanations available, as far as I can see. The best explanation that I have found is that the positive charge allows the orientation of the protein in the membrane. The orientation for membrane proteins is important as a lot of them are transporters which have a dedicated transportation direction. The same is true for receptors, which transport a signal from the outside to the inside of the cell. Most of the positively charged arginine and lysine residues are found in loop regions which are located between transmembrane regions (often hydrophobic helices).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3134198&quot; rel=&quot;nofollow&quot;&gt;Topogenic signals in integral membrane proteins.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://mbe.oxfordjournals.org/content/early/2013/09/28/molbev.mst169&quot; rel=&quot;nofollow&quot;&gt;Positive charge loading at protein termini is due to membrane protein&#xA;topology, not a translational ramp&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022283614002812&quot; rel=&quot;nofollow&quot;&gt;The Positive Inside Rule Is Stronger When Followed by a Transmembrane&#xA;Helix&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.mathmed.org/ray/biophysics-702/bp702-2010-11/dalbey/von_Heijne.pdf&quot; rel=&quot;nofollow&quot;&gt;Membrane-protein topology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-08T13:04:35.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24683" PostTypeId="2" ParentId="1132" CreationDate="2014-12-08T13:15:28.257" Score="2" Body="&lt;p&gt;&lt;a href=&quot;https://www.unitedchem.com/catalog/sample-prep/manifolds/universal-vacuum-manifold&quot; rel=&quot;nofollow&quot;&gt;This company&lt;/a&gt; sells a vacuum manifold for 24, 48 and 96 well plate formats. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-08T13:15:28.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24684" PostTypeId="1" AcceptedAnswerId="24691" CreationDate="2014-12-08T13:20:13.013" Score="3" ViewCount="262" Body="&lt;p&gt;Are nerves and/or neurons able to grow and repair after damage, but not regenerate? Is this specific to humans? I have heard of people being paralyzed, but after much therapy are able to use their legs again. Is this just through the creation of new connections from healthy nerves, or is there nerve repair to an extent?&lt;/p&gt;&#xA;" OwnerUserId="9018" LastActivityDate="2014-12-08T15:20:57.713" Title="Neuron Growth and Regeneration" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24686" PostTypeId="1" AcceptedAnswerId="24690" CreationDate="2014-12-08T14:01:01.780" Score="0" ViewCount="179" Body="&lt;p&gt;IF I began a PCR cycle with 5 copies of a particular DNA section, and copied the section by PCR, for 6 cycles, how many copies of the DNA (include the originals) would I have by the end of these cycles? Explain or sketch out your reasoning. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: I think it is 315 copies (5+10+20+40+80+160 = 315) after 6 cycles right?&lt;/p&gt;&#xA;" OwnerUserId="10481" LastEditorUserId="5144" LastEditDate="2014-12-08T16:32:42.403" LastActivityDate="2014-12-08T16:32:42.403" Title="PCR cycle problem" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;homework&gt;&lt;pcr&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="0" ClosedDate="2014-12-08T18:44:02.890" ContentLicense="CC BY-SA 3.0" />
  <row Id="24687" PostTypeId="1" AcceptedAnswerId="24715" CreationDate="2014-12-08T14:18:37.570" Score="3" ViewCount="6558" Body="&lt;p&gt;Data I am trying to get my hands on:  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What types of &lt;a href=&quot;http://en.wikipedia.org/wiki/Synesthesia&quot; rel=&quot;nofollow&quot;&gt;synesthesia&lt;/a&gt; (e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Grapheme%E2%80%93color_synesthesia&quot; rel=&quot;nofollow&quot;&gt;Grapheme-color synesthesia&lt;/a&gt;,  &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromesthesia&quot; rel=&quot;nofollow&quot;&gt;Chromesthesia&lt;/a&gt;, etc.) are most common across the population?&lt;/li&gt;&#xA;&lt;li&gt;What percent of population has that type of synesthesia?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It would also be great if there's geographical (genealogical) data on what types of synesthesia are more common to what areas.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What percent of the population has what type of synesthesia?&lt;/strong&gt;   &lt;/p&gt;&#xA;" OwnerUserId="8129" LastEditorUserId="5144" LastEditDate="2018-03-09T11:31:51.583" LastActivityDate="2018-03-09T11:31:51.583" Title="What percent of the population has some form of synesthesia?" Tags="&lt;neuroscience&gt;&lt;sensation&gt;&lt;epidemiology&gt;&lt;synesthesia&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24688" PostTypeId="5" CreationDate="2014-12-08T14:19:32.583" Score="0" Body="&lt;p&gt;Synesthesia (also spelled synæsthesia or synaesthesia; from the Ancient Greek σύν syn, &quot;together&quot;, and αἴσθησις aisthēsis, &quot;sensation&quot;) is a neurological phenomenon in which stimulation of one sensory or cognitive pathway leads to automatic, involuntary experiences in a second sensory or cognitive pathway. People who report such experiences are known as synesthetes.&lt;br&gt;&#xA;Forms of Synesthesia:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Grapheme-color synesthesia&lt;/li&gt;&#xA;&lt;li&gt;Chromesthesia&lt;/li&gt;&#xA;&lt;li&gt;Spatial sequence synesthesia&lt;/li&gt;&#xA;&lt;li&gt;Number form&lt;/li&gt;&#xA;&lt;li&gt;Auditory-tactile synesthesia&lt;/li&gt;&#xA;&lt;li&gt;Misophonia&lt;/li&gt;&#xA;&lt;li&gt;Mirror-touch synesthesia&lt;/li&gt;&#xA;&lt;li&gt;Lexical-gustatory synesthesia&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There are many more other forms of synesthesia.&lt;/p&gt;&#xA;" OwnerUserId="8129" LastEditorUserId="8129" LastEditDate="2014-12-08T14:50:17.497" LastActivityDate="2014-12-08T14:50:17.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24689" PostTypeId="4" CreationDate="2014-12-08T14:19:32.583" Score="0" Body="Synesthesia is a neurological phenomenon in which stimulation of one sensory or cognitive pathway leads to automatic, involuntary experiences in a second sensory or cognitive pathway. " OwnerUserId="8129" LastEditorUserId="8129" LastEditDate="2014-12-08T14:49:50.027" LastActivityDate="2014-12-08T14:49:50.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24690" PostTypeId="2" ParentId="24686" CreationDate="2014-12-08T14:39:21.537" Score="2" Body="&lt;p&gt;PCR ideally doubles the number of amplified DNA molecules in each cycle. So after the first step you have 10 molecules, after the second 20, the third 50 and so on. The formula for the calculation is: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;n × 2&lt;sup&gt;cycles&lt;/sup&gt; = number of molecules&lt;/p&gt;&#xA;&#xA;&lt;p&gt;n is the number of molecules you start your PCR with, cycles is the number of cycles used. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your case this would be: 5 × 2&lt;sup&gt;6&lt;/sup&gt; = 320 molecules of DNA.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="3340" LastEditDate="2014-12-08T15:11:45.793" LastActivityDate="2014-12-08T15:11:45.793" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24691" PostTypeId="2" ParentId="24684" CreationDate="2014-12-08T15:00:56.667" Score="0" Body="&lt;p&gt;&lt;em&gt;the following is true for humans, I dunno about other animals&lt;/em&gt;: &#xA;&lt;strong&gt;schwann cells&lt;/strong&gt; in peripheral nervous system can rebuild a severed &lt;strong&gt;axon&lt;/strong&gt; if the &lt;strong&gt;perineurium&lt;/strong&gt; of the &lt;strong&gt;nerve fibers&lt;/strong&gt; are sutured together ... the same is not true for &lt;strong&gt;oligodendrocytes&lt;/strong&gt; in the central nervous system. Thus only peripheral nerves can regenerate and not nerves located in the central nervous system (ie. spinal cord or brain).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;surgical nerve regeneration after a nerve is severed is not the only possible form of nerve regeneration, another example would be when the &lt;strong&gt;facial nerve&lt;/strong&gt; is damaged by &lt;strong&gt;bells palsy&lt;/strong&gt; and then it regenerates itself. so a fun example of what can go wrong is when some of the nerves switch when they regenerate, so your brain thinks it's doing one thing, but since the nerves switched when they regenerated, it does the other. The example would be &quot;crocodile tears syndrome&quot;, it has nothing to do with crocodiles (thats just the name) but rather this is where the facial nerves salivation fibers get switched with the crying fibers... so when they eat they cry...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;as for neuro-rehabilitation in people suffering paralysis, this is a broad question. As I understand it, if it's the spinal cord thats cut then it will never regenerate, but if its a nerve that left the spinal cord (a peripheral nerve) than it may possibly regenerate. Here are some specific conditions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also it could be a temporary thing like &lt;strong&gt;Guillain-Barré syndrome&lt;/strong&gt; where the immune system (hyper sensitized by a previous campylobacter bacteria or CMV virus, or for some other reason) temporarily injures the peripheral nerves and then after about 2 weeks they recover)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;also there is there are &lt;strong&gt;drugs and toxins&lt;/strong&gt; which are temporary, so one your body metabolizes/excretes (bile or urine) it is gone: &lt;strong&gt;botulinum toxin&lt;/strong&gt; (from bacteria Clostridium botulinum), &lt;strong&gt;curare&lt;/strong&gt; (south american plant poison), the many chemically modified versions of curare produced by pharmaceutical used in surgery to relax the muscles, and the list goes on for drugs/toxins. Again, drugs/toxins are temporary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Stroke&lt;/strong&gt;, though in the central nervous system, might be able to be rehabilitated since maybe everything wasn't destroyed (even though what was destroyed was destroyed permanently), and the patient can salvage what is left and use their neuroplasticity to try and use their brains slightly differently to be able to recover.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;ALS&lt;/strong&gt;, affects the ventral horn of the spinal cord... this one is irreversible at least today.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;there are many other causes of paralysis which may nbe reversible or irreversible&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;glossary&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;schwann cell&lt;/strong&gt;= the fatty cell that wraps around an individual nerve in order to myelin ate it... myelination being the fatty insulating of axon so they send electric signals faster...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;axon&lt;/strong&gt;= a projection off of the cell body that sends an electrical impulse to the end of the nerve that ultimately communicates with the target nerve/muscle/gland/etc&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;perineurium&lt;/strong&gt;= outside protective sheath composed of connective tissue covering many nerve fibers&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;oligodendrocytes&lt;/strong&gt;= the equivalent of a schwann cell, but in the central nervous system, it myelinates many nerves, unlike the schwann cell which only myelinates 1 nerve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;nerve fibers&lt;/strong&gt;= a collection of many nerves running together&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;facial nerve&lt;/strong&gt;= facial nerve innervated the muscles of the face and there are 2 facial nerves, one for each side of the face. the facial nerve doesn't only do face muscles, but also taste, salivation, and tear formation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;bell's palsy&lt;/strong&gt;= when the facial nerve stops working and half the face gets droopy... there are a lot of possible causes, like virus bacteria, and many many noninfectious causes...&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2014-12-08T15:20:57.713" LastActivityDate="2014-12-08T15:20:57.713" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24692" PostTypeId="2" ParentId="9000" CreationDate="2014-12-08T15:05:27.190" Score="2" Body="&lt;p&gt;As dd3 said the density of mechanoreceptors dictates skin sensitivity to touch (also look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Cortical_homunculus&quot; rel=&quot;nofollow&quot;&gt;penfield map&lt;/a&gt;. It is a nice illustration of how different senses are mapped to the brain and to what extent each region is sensitive to stimulus). Skin thickness is also different in different regions. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2793095/&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; article says that Dikkopf1 (a Wnt pathway antagonist) controls skin thickness. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-08T15:05:27.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24693" PostTypeId="1" CreationDate="2014-12-08T15:23:00.480" Score="5" ViewCount="6274" Body="&lt;p&gt;I am on a number of reptile groups and I often hear freezing recommended as a humane way to get rid of surplus feeder insects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, they can also &lt;a href=&quot;http://cricket-breeding.com/how-frozen-crickets-stay-alive/&quot; rel=&quot;noreferrer&quot;&gt;revive&lt;/a&gt; if you don't leave them in there long enough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I had a bag of crickets and put them in the freezer, how long would it take for them to die in this way? &lt;/p&gt;&#xA;" OwnerUserId="10482" LastActivityDate="2018-09-14T12:59:21.997" Title="How long does it take for a cricket to die at subzero temperatures?" Tags="&lt;entomology&gt;&lt;death&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24694" PostTypeId="2" ParentId="23817" CreationDate="2014-12-08T16:46:31.570" Score="5" Body="&lt;p&gt;This isn't a ridiculous idea; Transcranial Magnetic Stimulation is used in research and even has some use as treatment for depression (&lt;a href=&quot;http://www.mayoclinic.org/tests-procedures/transcranial-magnetic-stimulation/basics/definition/prc-20020555&quot;&gt;http://www.mayoclinic.org/tests-procedures/transcranial-magnetic-stimulation/basics/definition/prc-20020555&lt;/a&gt;) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In TMS a strong, localized magnetic field can disrupt normal functioning of regions of the brain. For instance it can be used on the visual cortex to cause temporary blindness (actually, can cause a condition called blindsight: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2234142/&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2234142/&lt;/a&gt;) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for memory though, TMS does not seem to be able to cause &lt;em&gt;permanent&lt;/em&gt; memory loss (in fact, there is research indicating that it may be able to boost memory). Plus, the magnetic pulse would have to be either extremely strong, or very close, for it to have an appreciable effect.&lt;/p&gt;&#xA;" OwnerUserId="10484" LastActivityDate="2014-12-08T16:46:31.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24696" PostTypeId="2" ParentId="24693" CreationDate="2014-12-08T17:08:19.470" Score="5" Body="&lt;p&gt;The &lt;a href=&quot;http://www.pnas.org/content/109/50/20750.full&quot; rel=&quot;noreferrer&quot;&gt;actual paper&lt;/a&gt; that the linked article cites never mentioned about freezing the crickets:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We examined CCR (Chill Coma Recovery) in G. pennsylvanicus exposed to 0 °C. The time&#xA;  required for crickets to recover movement of the abdomen and legs&#xA;  increased exponentially with the duration of exposure to 0 °C; after&#xA;  more than 12 h of cold exposure, recovery time reached a plateau at&#xA;  ca. 15 min&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And this is how CCR is performed&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A total of 60 crickets were placed individually into 14-mL plastic&#xA;  tubes and cooled from 25 °C at 0.25 °C⋅min−1 and held at 0 °C for 2–42&#xA;  h. At 2-h intervals (first 24 h), and every 6 h thereafter, four&#xA;  crickets were placed on their dorsum in a Petri dish at room&#xA;  temperature. Times of four indices of chill-coma recovery were&#xA;  recorded: (i) first foreleg movement, (ii) first hind leg movement,&#xA;  (iii) initiation of abdominal contractions (active ventilation), and&#xA;  (iv) righting. Foreleg and hind leg movement were identified as a&#xA;  coordinated directional movement of the limbs, distinct from twitches&#xA;  of the limbs observed during rewarming. If crickets had not righted&#xA;  within 3 h of removal from the cold, they were considered to have&#xA;  incurred chilling injury that precluded recovery.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, the crickets were never actually subjected to subzero temperatures or freezing or even cold shocks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How long it takes to die depends on the freezer temperature; based on personal experience I can say that they die in ~10min @ -20⁰C. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Didn't find much information on crickets but according to &lt;a href=&quot;http://jeb.biologists.org/content/148/1/245.short&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; paper Drosophila will die in less than 2 hours at -5⁰C upon transferring them to the cold temperature directly (cold shock). However, if the larvae are &quot;hardened&quot; by keeping at +5⁰C before cold shock, their survival chance increased — the temperature required for killing them in 2h (Lowest Lethal Temperature) reduced. Now cricket is bigger than Drosophila but the surface area is also higher. I cannot do more than speculate at this moment (you can apply complex heat transfer equations and see how the rate changes with the size).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-08T18:21:24.297" LastActivityDate="2014-12-08T18:21:24.297" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24697" PostTypeId="1" AcceptedAnswerId="24727" CreationDate="2014-12-08T18:13:52.343" Score="9" ViewCount="337" Body="&lt;p&gt;Humans and apes have somewhat obvious similarities, these must have been apparent to natural philosophers before the possibility of a common ancestry was first proposed in the mid-1800's. These proposals were not formally made in Darwin's &lt;em&gt;On the Origin of Species&lt;/em&gt; (1859), but his general ideas of common ancestry were built upon in Thomas Huxley's &lt;em&gt;Evidence as to Man's Place in Nature&lt;/em&gt; (1863) and then Darwin's &lt;em&gt;The Descent of Man&lt;/em&gt; (1871). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How was the resemblance between apes and humans explained prior to this shift in thinking?&lt;/p&gt;&#xA;" OwnerUserId="5825" LastEditorUserId="1590" LastEditDate="2014-12-09T08:45:07.470" LastActivityDate="2015-12-15T09:55:39.187" Title="How was the resemblance between apes and humans explained in pre-Darwinian biology?" Tags="&lt;evolution&gt;&lt;history&gt;&lt;human-evolution&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24698" PostTypeId="1" AcceptedAnswerId="24710" CreationDate="2014-12-08T19:25:03.047" Score="1" ViewCount="199" Body="&lt;p&gt;Why are nausea and dizziness such common side effects from medication?  If you go through your medicine cabinet and look at side effects, those might just be on every single bottle.  Is there some system in the human body that is very sensitive to any disturbance and causes nausea and dizziness?&lt;/p&gt;&#xA;" OwnerUserId="10343" LastActivityDate="2015-01-24T17:45:06.860" Title="Why are nausea and dizziness such common side effects from medication?" Tags="&lt;medicine&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24703" PostTypeId="1" AcceptedAnswerId="24714" CreationDate="2014-12-08T22:15:23.627" Score="1" ViewCount="2140" Body="&lt;p&gt;Is there any scientific evidence supporting the hypothesis that physical exercise following lack of sleep increases the risk of sudden cardiac death (SCD)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only relevant research I could find is: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725925/&quot; rel=&quot;nofollow&quot;&gt;Reddy PR, Reinier K, Singh T, et al. Physical activity as a trigger of sudden cardiac arrest: The Oregon Sudden Unexpected Death Study. &lt;em&gt;International journal of cardiology&lt;/em&gt; 2009;131(3):345-349. doi:10.1016/j.ijcard.2007.10.024.&lt;/a&gt; However, it only points out that 5% of the SCD cases in the sample took place during vigorous physical activity, which does not directly answer my question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not a biology professional, so please pardon me for any misunderstanding, and, when possible and reasonable, please avoid using too many biological jargons in the answer.&lt;/p&gt;&#xA;" OwnerUserId="10493" LastActivityDate="2017-10-30T08:08:04.473" Title="Does physical exercise following lack of sleep increase the risk of sudden cardiac death (SCD)?" Tags="&lt;cardiology&gt;&lt;sleep&gt;&lt;health&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24704" PostTypeId="1" CreationDate="2014-12-08T22:22:06.470" Score="3" ViewCount="251" Body="&lt;p&gt;Can maybe someone share knowledge or guesses on the following questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Does the prolonged use of antihistamines cause long-term effects on mind or CNS?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are there any known evidences of their influence of formation of CNS or personality when taken at a young age?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Generation-II antihistamines are said to be next to devoid of sedative effects since they selectively block just the H1-receptors. However, they are reportedly potentially mind-altering. How is this possible? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="10490" LastEditorUserId="9943" LastEditDate="2014-12-15T03:11:11.747" LastActivityDate="2014-12-15T03:11:11.747" Title="Long-term effects of antihistamines on mind and CNS" Tags="&lt;psychology&gt;&lt;central-nervous-system&gt;&lt;histamine&gt;&lt;antihistamines&gt;" AnswerCount="0" CommentCount="14" FavoriteCount="1" ClosedDate="2014-12-08T22:31:50.150" ContentLicense="CC BY-SA 3.0" />
  <row Id="24707" PostTypeId="2" ParentId="24667" CreationDate="2014-12-08T23:31:47.113" Score="1" Body="&lt;p&gt;You can use some antibiotics or germicide or alcohol...they prevent the formation by interfering with the attachment or adhesion and expansion of immature biofilms..&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="10401" LastEditDate="2014-12-08T23:37:06.337" LastActivityDate="2014-12-08T23:37:06.337" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="24708" PostTypeId="1" AcceptedAnswerId="26063" CreationDate="2014-12-09T00:18:18.737" Score="4" ViewCount="4658" Body="&lt;p&gt;I have come up with what I thought was a clever idea: Store the agarose gels I pour, and only cut as many lanes as I need to run later, minimizing wasted agarose (and wasted effort/time) when I need to make many electrophereses using a small number of lanes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realized that over time, the EtBr would diffuse out of my gel into the buffer that the gels are kept in. Since I add 2 µl of EtBr to 50 ml gel, and the gels were kept in 400 ml TAE buffer, I added 16 µl EtBr to the buffer, reasoning that now concentrations are equal and no net diffusion will take place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, after several weeks, I noticed that the EtBr signal from the gel is severely weakened. What can I do to fix this? I can see the following options:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Use higher concentration of EtBr in the buffer (how much?)&lt;/li&gt;&#xA;&lt;li&gt;Change buffer weekly, adding fresh EtBr every time&lt;/li&gt;&#xA;&lt;li&gt;Cover the transparent container with aluminum foil to prevent hypothetical photobleaching&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Which one is most likely to solve my problem? Should I just give up, and throw away gels that are older than a day or two (I want to avoid this option, because of the record keeping needed to track when the gel was last made)?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-12-20T04:17:28.083" Title="Long term storage of agarose-ethidium bromide gels that have already been cast" Tags="&lt;lab-techniques&gt;&lt;gel-electrophoresis&gt;&lt;lab-reagents&gt;" AnswerCount="3" CommentCount="10" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24709" PostTypeId="1" AcceptedAnswerId="24712" CreationDate="2014-12-09T00:36:04.603" Score="3" ViewCount="214" Body="&lt;p&gt;I stumbled upon a few hundred of these swarming around two different places in my living room today. They kind of look like a carpenter ant to me, but I'm not sure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I'd love to know how you identified the ant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;// EDIT, per a helpful suggestion, I'm in Los Angeles, CA, US. We just had rain come through within the last 4-5 days and it has since dried up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sxVP0.jpg&quot; alt=&quot;winged ant that is black in color&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10497" LastEditorUserId="10497" LastEditDate="2014-12-09T00:46:33.380" LastActivityDate="2018-04-02T01:40:36.287" Title="Is this a carpenter ant?" Tags="&lt;entomology&gt;&lt;species-identification&gt;&lt;ant&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24710" PostTypeId="2" ParentId="24698" CreationDate="2014-12-09T01:55:03.003" Score="3" Body="&lt;p&gt;Some medications because they are taken orally do cause nausea. Many medications, because they have an effect on blood pressure, or are central acting in some way, do cause dizziness. However, nausea and dizziness in particular are two highly subjective symptoms which are difficult to quantitate or verify, and which can occur with simple anxiety or stress. Several more such highly subjective and difficult-to-verify symptoms are numbness, tingling, headache, insomnia, fatigue and difficulty concentrating, all of which can be brought on by stress.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Switching for a moment to a drug with a measurable side effect of beta-blockers: erectile dysfunction (ED). In a study of men treated with beta blockers, the patients were separated into three groups with the following results:&lt;br&gt;&#xA;a) the group who were not told the name of the medicine nor informed of the ED side effect had the lowest incidence of ED (3.1%)&lt;br&gt;&#xA;b) the group who were told the name of the medicine but not informed about the ED side effect had a 15.6% incidence of ED&lt;br&gt;&#xA;c) the group who were told the name of the medicine and informed of the ED side effect had the highest incidence of ED (31.2%)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Hypervigilance&lt;/em&gt; is an increase in attention to bodily cues or symptoms for any reason. It has been well documented in many studies that if you give one group of people a list of possible negative side effects, and another group a list of possible beneficial effects, then give both groups placebos (usually a small coated sugar or cornstarch tablet), the first group will experience negative effects while the second will feel better. The negative expectation producing a negative side effect is called the &lt;strong&gt;nocebo effect&lt;/strong&gt; (the opposite of the &lt;em&gt;placebo effect&lt;/em&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Interestingly, recent studies where anti-anxiety medications were administered before the nocebo dramatically decreased the nocebo effect.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For ethical reasons, in all clinical trials of drugs, patients in the treatment group and the placebo group must be given an extensive list (standardized) of possible negative side effects, introducing a negative expectation into both populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two of the most common negative side effects &lt;em&gt;in both groups&lt;/em&gt; are dizziness and nausea. Therefore, they must be reported as possibly occurring side effects with the medication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not to say we're all imagining things. Nocebo effects have been correllated with reproducible effects on functional MRIs. They have a basis in reality, even if it's caused by negative expectations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a problem being discussed a lot now by medical ethicists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=4&amp;amp;ved=0CDkQFjAD&amp;amp;url=http%3A%2F%2Fwww.dovepress.com%2Fgetfile.php%3FfileID%3D14399&amp;amp;ei=Wk6GVMSQKpSEyQTr2IHQDw&amp;amp;usg=AFQjCNEEuRlbxHGRyfEvDj_-YsW7b-wXeg&amp;amp;sig2=3PxkuQ4vhb13kApFqnDXhg&amp;amp;bvm=bv.80642063,d.aWw&quot; rel=&quot;nofollow&quot;&gt;The influence of the nocebo effect in clinical trials&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://jama.jamanetwork.com/article.aspx?articleid=1887491&quot; rel=&quot;nofollow&quot;&gt;Avoiding Nocebo Effects to Optimize Treatment Outcome&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-09T01:55:03.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24712" PostTypeId="2" ParentId="24709" CreationDate="2014-12-09T06:12:34.420" Score="2" Body="&lt;p&gt;No, this is not a carpenter ant...it's possibly a &lt;a href=&quot;http://en.wikipedia.org/wiki/Pavement_ant&quot; rel=&quot;nofollow&quot;&gt;Pavement Ant&lt;/a&gt; (&lt;em&gt;Tetramorium&#xA;caespitum&lt;/em&gt;) - only it's a male &amp;amp; hence winged....for identification...follow these &lt;a href=&quot;http://www.wvu.edu/~exten/infores/pubs/pest/hpm3002.pdf&quot; rel=&quot;nofollow&quot;&gt;guidelines&lt;/a&gt;-&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pavement ant workers are small, l/8-inch to 3/16-inch&#xA;  long, and blackish brown with light-colored legs and two spines at the&#xA;  end of the thorax. A distinguishing character, visible with a hand&#xA;  lens or microscope, is the series of fine parallel groves on the head&#xA;  and thorax&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="10045" LastEditDate="2014-12-09T06:19:49.633" LastActivityDate="2014-12-09T06:19:49.633" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24713" PostTypeId="1" CreationDate="2014-12-09T06:41:15.577" Score="1" ViewCount="71" Body="&lt;p&gt;I am a Pharmacology and Toxicology major at a large state school. I was only required to take physics I and II. (algebra based)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At first I thought that was fine, but I soon began to realize that I can't just memorize like my professor and book asks me too, but I need to go in-depth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is this, I am looking for a way to learn the &quot;physics and chemistry behind physiology&quot; or deeper that what we are taught?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, say we are taught that atherosclerosis can cause aneurysms and that aneurysms can rupture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what we aren't taught is that blood flow through a closed vessel is constant, so any dilatation in the mid-length will increase the cross-sectional area and decrease the fluid velocity to maintain flow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In accordance with Bernoulli's principle, the decrease in velocity is met with an increase in pressure, which increases wall tension. Vessel integrity is already compromised from the three layer degradation. So now you start to see this great positive feedback loop whereby atherosclerosis damages the vessel wall causing it to dilate, which increases the pressure, which causes it to dilate further, which damages the vessel wall further, etc, etc, until the aneurysm finally ruptures. (I did not write this example, but it is an example of how I would like to learn it.  I would like to know how the author of that explanation came to that conclusion or what kind of book would explain in heavy detail.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question I am asking how can I learn the &quot;science&quot; behind the physiology?  I'm a type of learner that needs to know the how and why.  Will I need to take more physics classes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;** Sorry if I posted in the wrong section, I am new to stack exchange!&lt;/p&gt;&#xA;" OwnerUserId="10498" LastActivityDate="2014-12-09T09:40:43.187" Title="Deeper Learning in Physiology?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-12-09T10:27:42.537" ContentLicense="CC BY-SA 3.0" />
  <row Id="24714" PostTypeId="2" ParentId="24703" CreationDate="2014-12-09T07:18:11.107" Score="1" Body="&lt;p&gt;Sleep is an important aspect of our life. Sleep disorders are acute due to their effects in physiological and mental health of a person.Sleep occupies nearly 30% of our daily life and people were gradually decreasing the sleep time in order to adjust their busy schedule. According to the United States National Sleep Foundation, adults need to sleep 7-9 hours each night. The decrease in sleep time contribute mostly towards cardiovascular disease, including hypertension, coronary artery disease(CAD),risk of arrhythmia, stroke etc.&lt;/p&gt;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Circadian_rhythm&quot; rel=&quot;nofollow noreferrer&quot;&gt;circadian&lt;/a&gt; and dirurnal rhythms influence the neural circulatory control causing the changes in heart rate, vascular tone and blood pressure. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Rapid_eye_movement_sleep&quot; rel=&quot;nofollow noreferrer&quot;&gt;REM&lt;/a&gt;(Rapid Eye Movement)sleep and nonREM sleep affects the cardiovascular system. Researchers found it important that normal sleep is a complex and dynamic process with profound effects on cardiovascular homeostasis.&#xA;Insufficient sleep is a stress stimulator that acts through the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sympathetic_nervous_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;sympathetic nervous system&lt;/a&gt; elicit changes in blood pressure, heart rate and barroreflex setpoint.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sleep_deprivation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sleep deprivation&lt;/a&gt; is a state of having less or no sleep which is a major reason for cardiovascular diseases.Which may cause&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Inflammation&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Cardiovascular disease is mainly driven by &lt;a href=&quot;http://www.sanofi.com/Images/21177_Atherothrombosis_backgrounder.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;atherothrombosis&lt;/a&gt;, which is an &lt;a href=&quot;http://en.wikipedia.org/wiki/Inflammation&quot; rel=&quot;nofollow noreferrer&quot;&gt;inflammatory&lt;/a&gt; process. Increased levels of &lt;a href=&quot;http://en.wikipedia.org/wiki/C-reactive_protein&quot; rel=&quot;nofollow noreferrer&quot;&gt;C-reactive protein&lt;/a&gt;(CRP) and &lt;a href=&quot;http://en.wikipedia.org/wiki/Interleukin_6&quot; rel=&quot;nofollow noreferrer&quot;&gt;interleukin-6&lt;/a&gt;(IL6) have been implicated as the predictors of cardiovascular disease risk.Both CRP and IL6 have been found elevated in both totally and partially sleep-deprived subjects.Inflammatory cells such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Monocyte&quot; rel=&quot;nofollow noreferrer&quot;&gt;monocytes&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Neutrophil_granulocyte&quot; rel=&quot;nofollow noreferrer&quot;&gt;neutrophils&lt;/a&gt; were also found to be elevated during acute sleep deprivation, supporting that sleep deprivation is an inflammatory process.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Endothelial Dysfunction&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Endothelial_dysfunction&quot; rel=&quot;nofollow noreferrer&quot;&gt;Endothelial Dysfunction&lt;/a&gt; has been reported after a combination of sleep deprivation and stress, also increased heart rate, blood pressure are reported in sleep deprived subjects may result in Endothelial Dysfunction.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Hypertension and Stress&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Hyper tension and &lt;a href=&quot;http://en.wikipedia.org/wiki/Stress_hormone&quot; rel=&quot;nofollow noreferrer&quot;&gt;stress hormones&lt;/a&gt; are released by the body when lack of sleep occurs, this results in elevated bloop pressure and may lead to CAD.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;CardioArtery Disease&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;The American Cancer Society , the Almeda County study and Partinen also showed an increased risk of CAD in subjects who reported sleeping 4-6 hours a day.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Diabetes Mellitus(DM)&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Diabetes_mellitus&quot; rel=&quot;nofollow noreferrer&quot;&gt;Diabetes Mellitus&lt;/a&gt; is a major risk factor for CAD and it has been underlined from several studies across past decades that sleeplessness can result in DM.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;A &lt;a href=&quot;http://en.wikipedia.org/wiki/Sudden_cardiac_death&quot; rel=&quot;nofollow noreferrer&quot;&gt;sudden cardiac death&lt;/a&gt; is highly probable for a person who follows increased physical exercise and decreased sleep durations. For a sleep deprived person the risk of cardiac diseases are so high, then for some one who spend lot of time exercising can cause chronic cardiac problems. Physical exercise and over training can cause more stress hormones and increased heart rates, these factors along with prolonged sleep deprivation can cause serious cardiac diseases or even sudden cardiac death.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Levels of cortisol (the &amp;quot;stress&amp;quot; hormone) are elevated for long periods of time.&#xA;The body spends more time in a catabolic state than an anabolic state (perhaps as a result of elevated cortisol levels).&#xA;Excessive strain to the nervous system during training.&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Overtraining&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Overtraining&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Critical Care Nursing: Synergy for Optimal Outcomes - Roberta Kaplow&lt;/p&gt;&#xA;&lt;p&gt;Sleep Deprivation and Disease: Effects on the Body, Brain and Behavior - Matt T. Bianchi&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-09T08:29:39.123" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24715" PostTypeId="2" ParentId="24687" CreationDate="2014-12-09T07:23:56.290" Score="3" Body="&lt;p&gt;&lt;strong&gt;The phenomenon&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Synesthesia is a neurological phenomenon in which a stimulus in one sensory or cognitive pathway triggers an experience in another.  Some hallmarks:&lt;sup&gt;1&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;It tends to be developmental, arising early in childhood. &lt;/li&gt;&#xA;&lt;li&gt;It is involuntary.&lt;/li&gt;&#xA;&lt;li&gt;It is stable over time (i.e. the same stimulus leads to the same sensory experience).  &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Epidemiology&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best paper I found on the issue is by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17076063&quot; rel=&quot;nofollow noreferrer&quot;&gt;Simner et al, 2006&lt;/a&gt;.&lt;sup&gt;2&lt;/sup&gt; The authors first review prior literature on the topic and then describe their own methodology and study addressing the question of prevalence. Regarding prior research:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Estimates of the prevalence of synesthesia have diverged widely....estimates range from 1 in 4.....to 1 in 25000 - 100 000.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not so helpful. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They point out some problems with prior studies: one group of surveys relied on self-referral and made the (conservative) assumption that all non-responders to an invitation to participate were non-synesthetes. Another set of studies avoided this problem by questioning every member of a participant pool but established the prevalence only “subjectively” (their wording, although I note that this is an inherently subjective phenomenon!). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Simner's own group used a validated survey questionnaire about specific synesthetic experiences (the specificity and prior validation of this overcoming the  &quot;subjective&quot; aspect in their view). They found an overall prevalence of 4.4% for any type of synesthesia. Importantly, the male: female ratio was not significantly different from 1 in this group, in contrast to many prior studies which have found a marked female predominance, ranging from 2:1 to 5:1 (references in Simner's paper for those interested).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Modalities of experience&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To address your question about the types of sensory experience involved, I turn to a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=22428428&quot; rel=&quot;nofollow noreferrer&quot;&gt;more recent review article&lt;/a&gt;&lt;sup&gt;1&lt;/sup&gt; that compiled results from multiple studies. In this report, grapheme-color type synesthesia was most common (86%). These participants see a number or letter and experience a particular color in association. This was followed by followed by time-space type (62%), a group who associates units of time with a particular space relative to their body.  The third most common was music-color type (41%), which is fairly straightforward. The majority experienced more than one type (clearly, given the percentages). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a graph showing the percentage of the cohort who reported particular synesthetic experiences, grouped according to the category of inducer: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZQmjq.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the most common type mentioned above, grapheme-color, includes all three of the first categories - &quot;digits,&quot; &quot;letters,&quot; and  &quot;words&quot; on this graph. Although only the inducers are listed here, the most common associated perceptions were indeed color (97%), followed by spatial configurations (62%). In most cases the color was static (73%) but in some people it moved in a specific direction (16%).  &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Niccolai V1, Jennes J, Stoerig P, Van Leeuwen TM. &lt;em&gt;Modality and variability of synesthetic experience.&lt;/em&gt; Am J Psychol. 2012 Spring;125(1):81-94.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Simner J1, Mulvenna C, Sagiv N, Tsakanikos E, Witherby SA, Fraser C, Scott K, Ward J. &lt;em&gt;Synaesthesia: the prevalence of atypical cross-modal experiences.&lt;/em&gt; Perception. 2006;35(8):1024-33.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-12-09T09:14:48.060" LastActivityDate="2014-12-09T09:14:48.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24716" PostTypeId="5" CreationDate="2014-12-09T08:52:08.180" Score="0" Body="&lt;p&gt;Questions often incorporate the study of our nearest ancestors, both the extant primates and extinct pre- &lt;em&gt;Homo sapiens&lt;/em&gt;. Users should read the guidance on questions related to the relevant tags &lt;a href=&quot;/questions/tagged/evolution&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;evolution&amp;#39;&quot; rel=&quot;tag&quot;&gt;evolution&lt;/a&gt; and &lt;a href=&quot;/questions/tagged/adaptation&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;adaptation&amp;#39;&quot; rel=&quot;tag&quot;&gt;adaptation&lt;/a&gt; and see meta where &quot;on-topicness&quot; of evolution questions are discussed.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-03-23T11:16:33.673" LastActivityDate="2016-03-23T11:16:33.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24717" PostTypeId="4" CreationDate="2014-12-09T08:52:08.180" Score="0" Body="The study of evolution with a particular focus on questions about the evolution of modern humans. " OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-03-23T11:16:29.440" LastActivityDate="2016-03-23T11:16:29.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24718" PostTypeId="1" CreationDate="2014-12-09T09:05:06.037" Score="3" ViewCount="387" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;RELATED:&lt;/strong&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/16749/why-does-rabies-cause-hydrophobia&quot;&gt;Why does rabies cause hydrophobia?&lt;/a&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/7554/agony-hydrophobia-and-viruses-in-the-light-of-evolutionary-principles&quot;&gt;Agony, Hydrophobia and viruses in the light of evolutionary principles&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Has hydrophobia been found outside of rabies?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have only seen it being mentioned as a &lt;em&gt;symptom&lt;/em&gt; of rabies.&lt;/p&gt;&#xA;" OwnerUserId="6818" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2016-10-11T17:23:13.973" Title="Hydrophobia Outside of Rabies?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;pathology&gt;&lt;virology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24719" PostTypeId="2" ParentId="24718" CreationDate="2014-12-09T09:31:40.847" Score="4" Body="&lt;p&gt;You are correct that hydrophobia is often considered &lt;a href=&quot;http://en.wikipedia.org/wiki/Pathognomonic&quot; rel=&quot;nofollow&quot;&gt;pathognomonic&lt;/a&gt; of rabies. However, I offer for your consideration: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12121215&quot; rel=&quot;nofollow&quot;&gt;Hydrophobia as a rare presentation of Cotard's syndrome: a case report.&lt;/a&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cotard's syndrome itself is a bizarre psychiatric condition that the authors of the above paper define well:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cotard’s syndrome is a rare condition where the central symptom is a nihilistic delusion, which, in its complete form, leads the patient to deny his own existence and that of the external world.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The patient described in this case report harbored delusions that his internal organs were shrinking. He asserted that his abdomen would rupture if he internalized anything. The hydrophobia was secondary to this concern. When given a glass of water he showed a panic reaction and attempted to keep away. Orientation and memory remained intact. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors go to length to point out that this was not, in fact, a case of rabies (as thought that were in question at this point!). Also, the patient himself was not aware of symptoms of rabies, ruling out &quot;rabies hysteria&quot; (a hypochondriacal delusion that one has rabies).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hydrophobia, then, is a rare manifestation of a rare psychiatric disease in addition to the more frequent and well-known association with rabies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;1. Nejad AG. Acta Psychiatr Scand. 2002 Aug;106(2):156-8; discussion 158.&#xA;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2014-12-10T16:32:09.880" LastActivityDate="2014-12-10T16:32:09.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24720" PostTypeId="2" ParentId="24713" CreationDate="2014-12-09T09:40:43.187" Score="1" Body="&lt;p&gt;It is very easy, use google + pathophysiology and read some articles in the actual topic. There are a lot of &lt;a href=&quot;http://www.amazon.com/Best-Sellers-Books-Pathophysiology/zgbs/books/227602&quot; rel=&quot;nofollow&quot;&gt;pathophysiology books&lt;/a&gt; as well (some of them pretty expensive). Another way to do &lt;a href=&quot;https://www.coursera.org/courses?query=physiology&quot; rel=&quot;nofollow&quot;&gt;an online course&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just a simple search about your example:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is known that AAAs are characterized by destruction of elastin and&#xA;  collagen in the media and adventitia, loss of medial smooth muscle&#xA;  cells with thinning of the vessel wall, and transmural infiltration of&#xA;  lymphocytes and macrophages. Atherosclerosis is a common underlying&#xA;  feature of aneurysms. However, atherosclerosis is not the primary&#xA;  driving factor in the development of AAAs. Atherosclerosis is a&#xA;  disease that is widespread throughout the vasculature, however&#xA;  aneurysms only form in specific locations and only in certain&#xA;  individuals. Additionally, atherosclerosis is primarily a disease of&#xA;  the intima, while aneurysm formation primarily affects the media and&#xA;  adventitia.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://www.vascularweb.org/research/Pages/the-pathogenesis-of-abdominal-aortic-aneurysms.aspx&quot; rel=&quot;nofollow&quot;&gt;The Pathogenesis of Abdominal Aortic Aneurysms&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2014-12-09T09:40:43.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24722" PostTypeId="2" ParentId="24718" CreationDate="2014-12-09T10:34:15.377" Score="0" Body="&lt;p&gt;Hydrophobia is mostly attributed to rabies, most of the sources refer rabies as hydrophobia. Technically Hydrophobia is the intense fear of water.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.allaboutcounseling.com/library/hydrophobia/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hydrophobia&lt;/a&gt; is an intense, irrational fear of water that can be commonly diagnosed at childhood and should be treated as soon as possible. Certain types of hydrophobia may also appear in later stages of contracting rabies, which would require treatment on an immediate basis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Also the Wikipedia link for &lt;a href=&quot;http://en.wikipedia.org/wiki/Rabies&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rabies&lt;/a&gt; states that&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Signs and symptoms may soon expand to slight or partial paralysis, anxiety, insomnia, confusion, agitation, abnormal behavior, paranoia, terror, and hallucinations, progressing to delirium. The person may have hydrophobia.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So rabies and hydrophobia are distinct and hydrophobia is a symptom of rabies.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://books.google.co.in/books?id=CRYDAAAAQAAJ&amp;amp;pg=PA722&amp;amp;dq=non%20rabid%20hydrophobia&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=gsKGVLumO461uATMgIGQCg&amp;amp;ved=0CCAQ6AEwAQ#v=onepage&amp;amp;q=non%20rabid%20hydrophobia&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hydrophobia&lt;/a&gt; may, however, more readly be confronted with hysteria, acute mania and tetanus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Hydrophobia is incidental to other diseases, it can be observed, occassionally, in tetanus,hysteria,cynanche,tonsillaris,tracheitis and certain inflammations in stomach. Tetanus is strongly believed to cause intense hydrophobia conditions.How ever, there is always a belief of hydrophobia linked with rabies.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The pathology of Hydrophobia and Tetanus is found to have great similarities and there is a great similarity in the distribution of lesion in the central nervous system as well as a certain analogy in the kind of lesion. The &lt;strong&gt;special localization of symptoms of both disease, in the tongue,throat and neck was associated with the special prevalence of the lesions in the medulla oblongata&lt;/strong&gt; and especially in the neighborhood of the nuclei in the fourth ventricle etc.&lt;/p&gt;&#xA;&lt;p&gt;Reference :&lt;strong&gt;THE Medical Times and Gazette - J &amp;amp; A Churchill&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So it is possible to cause hydrophobic conditions when Tetanus is affected and also hydrophobia can occur from mental disorders.&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-09T10:34:15.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24724" PostTypeId="2" ParentId="24708" CreationDate="2014-12-09T11:32:09.250" Score="0" Body="&lt;p&gt;I'm not quite sure what you are doing. Are you running the whole gel each time and cutting off the lanes you've used, or only putting the lanes you desire into the tank and leaving the rest outside?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the former then the ethidium bromide will be leaching out of the gel because it is positively charged so each time you apply a current to it some of it leaves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the latter, I'm not sure why you are storing your gel in buffer at all. Wrap it in clingfilm to stop it drying out and store it away from UV light to avoid the ethidium degrading.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Frankly, however, I'm not sure why you think this will be a big timesaver? You can store pre-melted agarose with ethidium bromide added for a period of weeks and pouring a fresh gel doesn't take a significant amount of time.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2014-12-09T11:32:09.250" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24726" PostTypeId="2" ParentId="19887" CreationDate="2014-12-09T13:08:36.063" Score="2" Body="&lt;p&gt;Simple answer is no:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$Ants \neq Aphids$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, they &lt;em&gt;could&lt;/em&gt; be used as evidence that aphids are there depending on the reliability of the coexistence. Ants and aphids are independent entities and do not rely on each other so can exist in non-overlapping populations. Applying this idea to the correct species of ant and aphid is, of course, important for it to work as an indicator - it will only be true in those combinations where this &quot;aphid protection&quot; occurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't find any information on the reliability of the relationship, especially not knowing which species you are looking at. If there was a high positive correlation of ant density and aphid density then one would expect the presence of ants to be a good indicator to the presence of aphids. If the correlation is low there is a higher chance of a false positive (where a false positive = when you see ants, conclude there must be aphids, and there are no aphids).&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-12-09T13:21:07.720" LastActivityDate="2014-12-09T13:21:07.720" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24727" PostTypeId="2" ParentId="24697" CreationDate="2014-12-09T13:19:56.333" Score="5" Body="&lt;p&gt;The time before Darwinism, people believed life as an entity which is created rather evolved. But there were great biologists interested in the relationship between species, who deliberately thought of evolution ideas and some of them believed in ape-human similarities and placed humans and apes in same group. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;In 1699, Edward Tyson, an English anatomist, dissected an ape specimen(chimpanzee) and showed that its anatomy closely approaches ours.But he didn't established any relationships between humans and apes. It was first done in 1738 by Swedish scientist  &lt;a href=&quot;http://en.wikipedia.org/wiki/Carl_Linnaeus&quot;&gt;Linnaeus&lt;/a&gt; in his book &lt;a href=&quot;http://en.wikipedia.org/wiki/Systema_Naturae&quot;&gt;Systema Naturae&lt;/a&gt; .After that in 1759, &lt;a href=&quot;http://en.wikipedia.org/wiki/Jean-Baptiste_Lamarck&quot;&gt;Lamarck&lt;/a&gt;, a French naturalist  who was Darwin's predecessor in general theory of evolution, stated that humans were derived from up-right walking apes.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In 1759, just half a century before Darwin was born and precisely one hundred years before he published his famous book , &quot;Origin of Species&quot;, Linnaeus, the great Swedish scientist, discovered that man was a mammal. He then placed man in the Order of primates, which means literary the first, or the highest,order of mammals.It comprises all the monkey like forms, including the man-like apes.&#xA;  &lt;a href=&quot;http://books.google.co.in/books?id=CCgDAAAAMBAJ&amp;amp;pg=PA32&amp;amp;dq=man%20and%20apes%20before%20darwin&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=gOyGVOq1LM-fugSlpoDIBA&amp;amp;ved=0CDkQ6AEwBQ#v=onepage&amp;amp;q=man%20and%20apes%20before%20darwin&amp;amp;f=false&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Primate Evolution and Human Origins&lt;/strong&gt; - Russel L. Ciochon &amp;amp; John G.Fleagle&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Human Evolution: A Guide to the Debates&lt;/strong&gt; - Brian Regal&lt;/p&gt;&#xA;" OwnerUserId="10294" LastActivityDate="2014-12-09T13:19:56.333" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24728" PostTypeId="1" AcceptedAnswerId="24731" CreationDate="2014-12-09T13:31:09.843" Score="5" ViewCount="337" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;We then fitted a linear regression including all three life-history&#xA;  traits to estimate the vector of linear selection gradients, β, for&#xA;  each sex (Lande and Arnold 1983). A quadratic regression model&#xA;  incorporating all linear, quadratic, and cross-product terms was then&#xA;  used to estimate the matrix of nonlinear selection gradients, γ, for&#xA;  each sex. &quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is from the paper &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2011.01267.x/full&quot; rel=&quot;nofollow&quot;&gt;Evidence for strong intralocus sexual conflict in the Indian meal moth, &lt;em&gt;Ploida interpunctella&lt;/em&gt;&lt;/a&gt;. I am not sure why they estimate these gradients separetly rather than taking them just from the one full model - any suggestions? Is this normal or have they done it for a reason?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For some similar work see these two papers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2012.01579.x/pdf&quot; rel=&quot;nofollow&quot;&gt;Gosden et al&lt;/a&gt; which seems to use only the linear gradients from one model with sex as an effect.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/279/1748/4836&quot; rel=&quot;nofollow&quot;&gt;Stearns et al&lt;/a&gt; which uses linear, quadratic and correlational estimated from one multiple regressions model per sex (similar to the main paper I cite first but not using a linear terms only model for the linear coefficient).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I have mailed the corresponding author on the quoted paper to ask why, I will let you know what he says &lt;strong&gt;if&lt;/strong&gt; he replies&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="3624" LastEditDate="2014-12-11T13:42:27.317" LastActivityDate="2014-12-11T13:42:27.317" Title="Why estimate linear and full (linear, quadratic, and correlational) selection coefficients separately?" Tags="&lt;natural-selection&gt;&lt;statistics&gt;&lt;population-genetics&gt;&lt;sexual-selection&gt;&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24729" PostTypeId="2" ParentId="13469" CreationDate="2014-12-09T13:46:58.387" Score="1" Body="&lt;p&gt;I think the answer should be C because when it is submerged, cutaneous respiration takes place and hence right atrium receives more oxygenated blood.&lt;/p&gt;&#xA;" OwnerUserId="3615" LastActivityDate="2014-12-09T13:46:58.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24731" PostTypeId="2" ParentId="24728" CreationDate="2014-12-09T14:05:36.340" Score="4" Body="&lt;p&gt;This is directly following the advice of &lt;a href=&quot;http://www.jstor.org/stable/2408842&quot; rel=&quot;nofollow&quot; title=&quot;Lande &amp;amp;Arnold. 1983. The Measurement of Selection on Correlated Characters. Evolution&quot;&gt;Lande &amp;amp; Arnold (1983)&lt;/a&gt;, saying: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Linear multiple&#xA;  regression can be used first to estimate the forces of directional selection, $\beta$, and their standard errors. Then a quadratic multiple regression (16) or (Al), can be used to estimate the forces of stabilizing selection, $\gamma$, with their standard errors. The regression (16) provides the best quadratic approximation to the selective surface (although valid estimates of $\beta$ can be obtained&#xA;  only from a purely linear regression, or by using the orthogonal regression (Al)).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The reason is that the estimates of direction selection is influenced by the higher order terms in the full model that includes quadratic and correlational selection, and the linear model therefore has the best estimates of the change in mean value over a generation of selection ($s = \bar{z}_{after} - \bar{z}_{before}$). However, the full model is the better representation of the fitness surface. There are also other methods to approximate the fitness surface.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the record, I used the same approach in my master's thesis many years ago.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-12-09T14:17:33.680" LastActivityDate="2014-12-09T14:17:33.680" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24732" PostTypeId="1" CreationDate="2014-12-09T15:51:41.473" Score="2" ViewCount="2100" Body="&lt;p&gt;While grocery shopping I was thinking that we restrict ourselves in regard to which animals we eat. I surely don't want to eat spiders and ants, for example, but I know that this is just because of my upbringing. But a lot of plants are actually inedible. So, is my idea correct that we can eat far more animal species than plant species? And if so, why? The reasons why certain plants are inedible seem to me also as rather diverse, like most plants&#xA;developed their own special molecule(s) to avoid being eaten by us. :)&#xA;I would be interested in some more educated opinion on this thought than mine. Thx in advance.&lt;/p&gt;&#xA;" OwnerUserId="10507" LastActivityDate="2020-09-24T08:28:14.377" Title="Are more animal species edible than plants?" Tags="&lt;food&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24735" PostTypeId="2" ParentId="24732" CreationDate="2014-12-09T17:28:57.137" Score="2" Body="&lt;p&gt;It is estimated by some that on earth there are&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;7.77 million species (of which 953,434 have been described and cataloged) of animals&lt;/li&gt;&#xA;  &lt;li&gt;298,000 species (of which 215,644 have been described and cataloged) of plants&lt;/li&gt;&#xA;  &lt;li&gt;611,000 species (of which 43,271 have been described and cataloged) of fungi&lt;/li&gt;&#xA;  &lt;li&gt;36,400 species (of which 8,118 have been described and cataloged) of protozoa. &lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;with 6.5 million species found on land and 2.2 million (about 25 percent of the total) dwelling in the ocean depths.&lt;sup&gt;[1]&lt;/sup&gt;&lt;sup&gt;[2]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite the existence of toxic plants and animals, from the numbers alone it is clear that there are more animal species we can eat than plant species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This does not take into account population or individual sizes, just species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001127&quot; rel=&quot;nofollow&quot;&gt;How Many Species Are There on Earth and in the Ocean?&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://www.sciencedaily.com/releases/2011/08/110823180459.htm&quot; rel=&quot;nofollow&quot;&gt;How many species on Earth? About 8.7 million, new estimate says&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-09T17:28:57.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24737" PostTypeId="1" AcceptedAnswerId="24745" CreationDate="2014-12-09T19:04:06.533" Score="5" ViewCount="2539" Body="&lt;p&gt;Every time we speak, sing, or make any other kind of advanced noise with our throats, we exhale, or to put it that way, blow air through our throats. Why is this required? After all, speakers do not need any air blowing through them, they simply vibrate the air and create the vibrations (sounds) they're supposed to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why can't humans create (intelligible) sound just by having an organ that vibrates the air around us? Also, are there any animals that can? (None that I can think of at least). Would it be an evolutionary gain, or just rather pointless?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS:&#xA;Obvoiusly we can clap out hands and the like, but that's not what I'm talking about. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;: The question is not about exhaling/inhaling, but rather why we need airflow in the first place; why we cannot use a mechanism similar to that of speakers.&lt;/p&gt;&#xA;" OwnerUserId="9400" LastEditorUserId="3624" LastEditDate="2014-12-10T09:17:30.403" LastActivityDate="2014-12-10T09:17:30.403" Title="Why do we have to exhale (or inhale) in order to speak?" Tags="&lt;evolution&gt;&lt;human-anatomy&gt;&lt;anatomy&gt;&lt;organs&gt;&lt;communication&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24738" PostTypeId="2" ParentId="24737" CreationDate="2014-12-09T19:42:09.243" Score="4" Body="&lt;p&gt;Here is a &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_woodwind_instruments&quot; rel=&quot;nofollow&quot;&gt;list of woodwind instruments&lt;/a&gt;. Do you know of any (non-open) reed instrument that produces a note without anyone blowing air through them? Imagine a clarinet &lt;em&gt;being played on someone's lap&lt;/em&gt; pouring out a melody. That would be very, very remarkable indeed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our ability to produce sound from our throats is in theory like a reed instrument  in music. Let's take the flute.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The flutist blows a rapid &lt;em&gt;jet of air&lt;/em&gt; across the embouchure hole. In the flute, the air jet produces an oscillating (vibrating) component to the air flow. Once the air is vibrating, the energy is radiated as &lt;em&gt;sound out of the end and any open holes.&lt;/em&gt; The column of air in the flute vibrates much more easily at some frequencies than at others (i.e. it resonates at certain frequencies). These resonances largely determine the playing frequency and thus the pitch, and the player in effect chooses the desired set of resonances by choosing a suitable combination of keys. (More on that &lt;a href=&quot;http://newt.phys.unsw.edu.au/jw/fluteacoustics.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our vocal chords don't vibrate without the movement of air through them. They just tense and relax to different degrees. There is no sound made if you go through all the motions of saying &lt;em&gt;yes&lt;/em&gt; but don't move any air. The moment you move even a small amount of air, you'll get a &lt;em&gt;sound&lt;/em&gt;. Furthermore, vibration of the vocal chords is not enough for speech. The noise must go through a chamber where a particular noise will be made to change to resemble speech. Say &lt;em&gt;ahhhhhh&lt;/em&gt; and touch the tip of your tongue to the roof of your mouth. The sound is changed significantly. Now, add your cheeks, lips, teeth, and pharynx all changing shapes and you have language.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our voices are a wind instrument (not like an electronic speaker. For that, look to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Electrolarynx&quot; rel=&quot;nofollow&quot;&gt;electrolarynx&lt;/a&gt;). The air column moving across the vocal chords is the air jet. The vocal chords are what sets the air to vibrate. Our &quot;mouth&quot; (all of those I mentioned above&quot; affect the vibrations to produce the desired sound. That's speech.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-12-09T19:47:48.090" LastActivityDate="2014-12-09T19:47:48.090" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="24739" PostTypeId="2" ParentId="13524" CreationDate="2014-12-09T20:09:04.057" Score="3" Body="&lt;p&gt;Tracing it backwards this was the earliest reference I found via google scholar, it's &lt;a href=&quot;http://www.jstor.org/stable/2461940?seq=7&quot; rel=&quot;nofollow&quot;&gt;from 1988 and uses the $r B C$ notation&lt;/a&gt; in the format we are used to.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Hamilton's rule states that for a social&#xA;  action to be favored under natural selection, rb - c &gt; 0, where c is the cost to the&#xA;  actor in terms of the effect on (usually a reduction in) his expected number of&#xA;  future offspring, bis the benefit to the recipient in terms of the effect on (usually&#xA;  an increase in) his expected number of future offspring, and r is the relatedness of&#xA;  the actor to the recipient&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, I've traced back a bit further by going through the references and found &lt;a href=&quot;http://www.jstor.org/stable/2097061?seq=2&quot; rel=&quot;nofollow&quot;&gt;this Michod paper from 1978&lt;/a&gt; where they defined terms $b_i$ and $c_i$ as the &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;fitness effect of genotype $i$'s behaviour on others&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;fitness effect of genotype $i$'s behaviour on self&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;respectively, which was the first such notation I could find which could be interpreted as $b$ = benefit via the increased fitness of others and $c$ as a cost to self.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;As far as I can tell&lt;/strong&gt; this leaves a 14 year gap between Hamilton's long version and the beginnings of the current notation by Michod in 1978, with the first &quot;rB - c &gt; 0&quot; type of notation appearing in 1988. Obviously my search is not exhaustive - many papers from this period will be hard to find and text search (e.g. using &quot;rB&quot; as a search term) - but it's a good start. If I find an older reference any time I will update.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-12-09T20:09:04.057" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24744" PostTypeId="2" ParentId="17064" CreationDate="2014-12-09T21:27:57.200" Score="3" Body="&lt;p&gt;This is a question which is not easy to answer, especially the 50.000bp number (which I haven't found anywhere in there literature). However, I found some evidence, partly derived from plant and mammal artificial chromosomes (references 1 and 2), partly from the original publication from Murray and colleagues (reference 3).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problems with small chromosomes seems to be their passage through mitosis and meiosis, where smaller artificial chromosomes tend to get lost. They are also not controlled very well in their number.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Murray states that YACs of 55kB in size are relatively stable in the yeast cells are relatively stable, but have a lower stability than natural chromosomes. When you are interested in the deeper details, I recommend reading the article. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.google.de/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCYQFjAA&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fpublication%2F13221095_Construction_of_mammalian_artificial_chromosomes_prospects_for_defining_an_optimal_centromere%2Flinks%2F0fcfd505d7426cf5ab000000&amp;amp;ei=x2eHVNLBDc6xPM6agYgP&amp;amp;usg=AFQjCNGQU_Te_mhEPBN-IB4jUgX0DXJTPA&amp;amp;bvm=bv.81449611,d.ZWU&quot; rel=&quot;nofollow&quot;&gt;Construction of mammalian artificial chromosomes: prospects for&#xA;defining an optimal centromere&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3831/3h98yits_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Alteration of chromosome numbers by generation of minichromosomes –&#xA;Is there a lower limit of chromosome size for stable segregation?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3831/skvpifuw_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Contruction of artificial chromosomes in yeast.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-09T21:27:57.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24745" PostTypeId="2" ParentId="24737" CreationDate="2014-12-09T21:52:17.920" Score="5" Body="&lt;p&gt;As part of your question, you ask if other animals can create sound without continuous airflow. Many insects (e.g. cicadas and moths) do exactly this by using &lt;a href=&quot;http://en.wikipedia.org/wiki/Tymbal&quot; rel=&quot;nofollow&quot;&gt;tymbals&lt;/a&gt;. A tymbal/timbal is an external membrane organ that is controlled by muscles or wing movements, that cause the membrane to flip back and forth, creating clicks or other sounds. So in many ways it produces sound in a similar way as loudspeakers, by creating sounds using a vibrating membrane. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One example can be found in this clip, which nicely shows how the organ functions:&lt;br&gt;&#xA;&lt;a href=&quot;http://youtu.be/SJGrkXGTSLg&quot; rel=&quot;nofollow&quot;&gt;Moth Making Sonar Jamming Sounds&lt;/a&gt; (youtube)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On &lt;a href=&quot;http://www.slu.se/sv/institutioner/ekologi/research/ovrigt/fjarilsljud/mindre-batspinnare-/&quot; rel=&quot;nofollow&quot;&gt;this page&lt;/a&gt; (in Swedish) you can also listen to slowed-down butterfly sounds from four species.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-12-09T22:12:47.627" LastActivityDate="2014-12-09T22:12:47.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24750" PostTypeId="1" CreationDate="2014-12-10T01:14:23.997" Score="2" ViewCount="42" Body="&lt;p&gt;This question is regarding the conversation that took place here: &lt;a href=&quot;https://biology.stackexchange.com/q/21772/9018&quot;&gt;Why don&amp;#39;t mammals have more than 4 limbs?&lt;/a&gt;. I'm not sure if someone mentioned this and I just missed it, but everyone is talking about two pairs of limbs for all terrestrial vertebrates; what about the case of kangaroos? If we are analyzing this from a locomotion point of view, and tails are being considered limbs, then wouldn't the kangaroo be considered to have five? They use their tail for balance and to push forward in &quot;walking&quot; (not exactly a walk, but I am lacking the proper term at the moment), resting only on the tail and forelimbs as the hind limbs swing forward. Does anyone have thoughts on this?&lt;/p&gt;&#xA;" OwnerUserId="9018" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2014-12-10T01:14:23.997" Title="Terrestrial Vertebrate Limbs" Tags="&lt;anatomy&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24751" PostTypeId="1" CreationDate="2014-12-10T01:43:49.080" Score="2" ViewCount="1965" Body="&lt;p&gt;For studying diseases, such as chronic obstructive pulmonary disease (COPD), cells are often grown in air liquid interface.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that the common way of establishing this these days is to grow cells in culture well inserts with a permeable bottom, then put medium only in the well and not the insert.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is an image from Stemcell Technologies:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/vjR1e.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The last images implies that the level of the medium is just high enough to cover only the basal side of cells. Is this realistic? Given that the monolayer is a few microns thick, is it really just a matter of carefully pipetting just enough medium? It seems like the error of a pipette is too high for this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practice, I am getting the impression that the level of liquid is actually higher than the apical surface of the cells, but it is somehow prevented from seeping out of the well and into the insert. If so, how? The bottom of the insert is permeable; even if you grow cells to confluence, surely there will be a small hole or two somewhere which causes a leak?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2016-08-04T04:56:59.533" Title="How does air-liquid interface (ALI) culture work?" Tags="&lt;lab-techniques&gt;&lt;cell-culture&gt;&lt;tissue&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24752" PostTypeId="2" ParentId="8539" CreationDate="2014-12-10T02:14:25.300" Score="2" Body="&lt;p&gt;There are, indeed, several such mAb based treatments. From the &lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/cancer/in-depth/monoclonal-antibody/art-20047808?pg=1&quot; rel=&quot;nofollow&quot;&gt;Mayo Clinic&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The monoclonal antibody drug rituximab (Rituxan) attaches to a specific protein (CD20) found only on B cells, one type of white blood cell. Certain types of lymphomas arise from these same B cells. When rituximab attaches to this protein on the B cells, it makes the cells more visible to the immune system, which can then attack.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(...)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cetuximab (Erbitux), a monoclonal antibody approved to treat colon cancer and head and neck cancers, attaches to receptors on cancer cells that accept a certain growth signal (epidermal growth factor). Blocking this signal from reaching its target on the cancer cells may slow or stop the cancer from growing.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(...)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The monoclonal antibody bevacizumab (Avastin) targets a growth signal called vascular endothelial growth factor (VEGF) that cancer cells send out to attract new blood vessels. Bevacizumab intercepts a tumor's VEGF signals and stops them from connecting with their targets.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(...)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ibritumomab (Zevalin), approved for non-Hodgkin's lymphoma, combines a monoclonal antibody with radioactive particles. The ibritumomab monoclonal antibody attaches to receptors on cancerous blood cells and delivers the radiation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(...)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ado-trastuzumab emtansine (Kadcyla) is one such drug approved to treat HER2-positive breast cancer. Ado-trastuzumab emtansine contains an antibody that attaches to the HER2 receptors on the breast cancer cells. The cancer cells then ingest the antibody, which releases a few molecules of chemotherapy.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It does eliminate side effects, although the treatment is not side effect-free.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally, my suspicion with this approach is this: At its heart, cancer is a problem of uncontrolled cell division. Most cells in the body do not divide rapidly, and this slowing down of proliferation is integrated into differentiation into whatever tissue the cells are in. The most obvious cells that divide rapidly are stem cells (themselves carcinogenic!). Furthermore, it seems to be a common theme in cancer that the less differentiated (or more de-differentiated) you are, the more easily you divide, and hence the nastier the cancer you generate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As such, the worst cancers out there are going to be very undifferentiated, and express few eligible surface markers. What's more, &lt;a href=&quot;https://en.wikipedia.org/wiki/Somatic_evolution_in_cancer#Natural_selection_in_cancer&quot; rel=&quot;nofollow&quot;&gt;tumors evolve&lt;/a&gt;. If you start selecting against cells which express your marker, you will encourage the tumor to simply evolve and stop expressing that marker. Back to the benchside to look for a new marker - meanwhile your patient gets worse and worse.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is why generalized chemotherapies (or radiotherapy) are so attractive. They attack the rapid division of cancer cells, and the cancer cells cannot evolve to lose this property, because if they did, they would not be cancer cells.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-12-10T02:14:25.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24753" PostTypeId="1" CreationDate="2014-12-10T02:34:00.537" Score="1" ViewCount="78" Body="&lt;p&gt;I'm curious how health risks (mortality, lifetime probability of cancer, etc) change with cigarette consumption.  Specifically, treatring cigarette consumption like a continuous variable, rather than a binary for &quot;smokers&quot; and &quot;nonsmokers&quot;.  I've got access to academic literature, but I'm not a doctor or a PhD health researcher.  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2223525/&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; states in the abstract that the dose-response relationship between cigarettes and incidence of lung cancer is linear.  &lt;a href=&quot;http://www.cdc.gov/tobacco/data_statistics/fact_sheets/health_effects/effects_cig_smoking/index.htm&quot; rel=&quot;nofollow&quot;&gt;This website&lt;/a&gt; (CDC) states that &quot;smokers&quot; have a 25-fold increase in risk of lung cancer.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How to reconcile the two?  The latter reports odds ratios, which means that they did a logistic regression, which means that the raw logistic regression coefficient was 3.2.  If the average smoker smokes 20 cigarettes a day, and the dose-response relationship is linear, then the relative risk for someone who smokes one per day should be exp(0.32) = 1.37.  So someone who smokes one cigarette per day would be 1.37 times more likely to get lung cancer than someone who never smoked (on average).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this a reasonable estimate?  I can certainly understand why public health types wouldn't promote this sort of conclusion, as smoking one cigarette can be a slipper slope to smoking a lot more cigarettes.  &lt;/p&gt;&#xA;" OwnerUserId="10512" LastEditorUserId="10512" LastEditDate="2014-12-10T03:43:45.673" LastActivityDate="2014-12-10T03:43:45.673" Title="Cigarette consumption dose-response function WRT health outcomes" Tags="&lt;human-biology&gt;&lt;cancer&gt;&lt;statistics&gt;&lt;health&gt;&lt;smoking&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24755" PostTypeId="2" ParentId="9089" CreationDate="2014-12-10T02:52:45.853" Score="1" Body="&lt;p&gt;If you have access to a centrifuge, either spin columns or phenol:chloroform will give very pure, high-quality DNA. Even with &lt;a href=&quot;http://misterguch.brinkster.net/MLX031.pdf&quot; rel=&quot;nofollow&quot;&gt;dirty methods&lt;/a&gt;, you can re-extract the product several times, to sacrifice yield for purity. Just be very clean. Whatever method you use should remove salts and proteins, which are the major contaminants. I won't go too much into how to extract DNA, as that's a whole separate question - but the most important thing is that purer is better.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should resuspend in Tris-EDTA. Tris buffer maintains pH at slightly acidic (best for DNA) and EDTA chelates metal ions which can catalyze oxidative damage of DNA. Very pure distilled water works too, but if you get contaminants they will do more damage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Afterwards you can store the DNA for quite some time provided it's frozen. At -20C you can store DNA for years. It may not be perfect quality when you pull it out a decade later, but most of it will be good, and I'm sure it will be okay if you use a good sequencing method (and I'm sure sequencing technology will advance more in 10 years than the degradation of your DNA). The good news is that you can simply store it in your freezer, and it will be okay. -20C particularly is not hugely important, you can probably get away with -10C or so - the crucial thing is for it to be frozen, not liquid (this vastly reduces diffusion).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to do it like a pro, you would put it under -80C. This is considered very safe for multiple years. You can do even better by precipitating it with ethanol, and then storing at -80C. In my opinion, this -80C is overkill - DNA is fine, for the most part, stored at -20C and even 4C, especially if you work reasonably clean and contamination-free. If you had some extremely valuable, very sensitive DNA, sure, do the -80. But just personal sequencing/genotyping? Just extract a bit extra DNA  (a couple micrograms).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The really safe method is liquid nitrogen, which stops practically all chemical activity. Higher temperatures are too cold for most DNA-damaging reactions to proceed at a significant rate, but the molecules still move around. At -200C, they stop dead. But, once again, overkill unless you are saving very critical DNA for centuries later.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ogt.com/resources/literature/403_dna_storage_and_quality&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Three simple things I can recommend that are less obvious: First, do not handle your sample with hands, even gloved. Use some kind of plastic tweezers. Hands are warm and will locally warm up the sample. I would go as far as to put the sample tube in another box so that there is no direct contact. Second, avoid freeze/thawing. Whatever your storage system is, make sure it is very reliable. Third, wrap it in something opaque, to minimize light exposure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Note as per Chris's comments:&lt;/em&gt;&lt;/strong&gt; Always consult the MSDS of the substances you work with and take appropriate safety precautions! Always make sure to receive proper training before working with hazardous materials, and never purchase illegal contraband without appropriate authorization!&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="540" LastEditDate="2014-12-11T18:31:02.313" LastActivityDate="2014-12-11T18:31:02.313" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="24757" PostTypeId="2" ParentId="21881" CreationDate="2014-12-10T04:18:12.467" Score="2" Body="&lt;p&gt;yea the hox genes are essential for the the specification of the location but the actual growing of the limbs are determined by a series of protein and other factors. proximal limb contains fgf(fibroblast growth factors) wnt(look up wnt pathway) and high levels of retonic acid where distal limbs shows high fgf's high wnt and little to none RA. the sonic the hedgehog gene talked about in the other answer has to to do with the anteriorizing(up)/posteriozing(down) of the autopod(digits, carpals). as to dorsal ventral wnt would be the culprit&lt;/p&gt;&#xA;" OwnerUserId="10513" LastActivityDate="2014-12-10T04:18:12.467" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24761" PostTypeId="1" CreationDate="2014-12-10T11:59:34.517" Score="6" ViewCount="24259" Body="&lt;p&gt;I've extracted DNA using a kit and final step is eluted with buffer. If I must dilute my DNA samples, do I use the same elution buffer or can I use milliq water?&lt;/p&gt;&#xA;" OwnerUserId="10516" LastEditorUserId="6" LastEditDate="2014-12-10T12:19:39.747" LastActivityDate="2018-04-24T07:31:19.400" Title="Should I dilute DNA with water or elution buffer?" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24762" PostTypeId="2" ParentId="24761" CreationDate="2014-12-10T12:11:17.927" Score="10" Body="&lt;p&gt;I would generally recommend using the elution buffer (which is typically Tris-EDTA buffer) or TE-Buffer, as the pH and the conditions stabilize the DNA for a longer time, which is especially interesting when you want to store your DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also dependent on your downstream application - when they recommend diluting the sample in water (or another buffer) I would follow this advice. In my experience TE buffer is perfect for all molecularbiology applications (cloning, digestion, amplification, PCR, etc.). The EDTA will of course complex bivalent cations, but since the concentration in the buffer is only 1mM and the DNA solution is usually diluted further in PCR or digests, this plays no role in real life applications.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-10T12:11:17.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24763" PostTypeId="2" ParentId="24761" CreationDate="2014-12-10T12:15:53.490" Score="7" Body="&lt;p&gt;The Quiagen kits I'm familiar with explicitly state that you can use water instead of elution buffer for elution. The choice of continuing to use buffer or water is yours and depends on what you want to do with the DNA and whether the buffer interferes with later steps. Using the buffer is probably safer for long-term storage, but I don't know how much this really matters (I never had any problem storing DNA in water).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you dilute with water you'll obviously end up with a weaker buffer that might not be able to keep the pH at the specified value. So if you need your DNA at the elution buffer pH, you shouldn't dilute it. &lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-12-10T12:15:53.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24764" PostTypeId="2" ParentId="24761" CreationDate="2014-12-10T12:18:37.870" Score="6" Body="&lt;p&gt;Just to add to the above responses, you are better off not use MQ because if it is contaminated with DNases, then it will digest your construct if it reaches room temperature or 37 oC as you are melting the frozen construct in your hand! TE-buffer is the standard buffer for DNA elusions but make sure your column is compatible with it. For transfection based experiments TE works fine for me!&lt;/p&gt;&#xA;" OwnerUserId="6511" LastActivityDate="2014-12-10T12:18:37.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24766" PostTypeId="1" CreationDate="2014-12-10T16:11:20.277" Score="5" ViewCount="503" Body="&lt;p&gt;This idea came to my mind when thinking about how many people become ill in many locations with similar symptoms (fever and rough cough) from Influenza. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are of course different types of influenza virus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can Influenza A virus work as a vector for other upper respiratory infections?&#xA;That is, much the same as the mosquito being a vector of malaria, can an influenza virus carry other infections with it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, how? If not, why do some people get so sick from viral influenza, and not others?&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="4101" LastEditDate="2015-06-02T14:36:37.157" LastActivityDate="2015-06-16T07:48:41.817" Title="Can an influenza virus carry other infectors with it?" Tags="&lt;microbiology&gt;&lt;virology&gt;&lt;infection&gt;&lt;influenza&gt;" AnswerCount="5" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24767" PostTypeId="1" CreationDate="2014-12-10T16:47:27.013" Score="1" ViewCount="66" Body="&lt;p&gt;I am looking for any database about pacemakers with the leads&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;atria A &lt;/li&gt;&#xA;&lt;li&gt;right ventricle VR&lt;/li&gt;&#xA;&lt;li&gt;left ventricle VL&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I did not find any in Physionet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any anonymous data about different situations online or accessible by request?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-12-10T16:47:27.013" Title="Public Pacemaker database online?" Tags="&lt;cardiology&gt;&lt;research-process&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24768" PostTypeId="2" ParentId="24766" CreationDate="2014-12-10T16:56:37.377" Score="3" Body="&lt;p&gt;I wouldn't call influenza a vector here, but yes, an infection with the flu virus which results in a full infection can have secondary infections as complications. There are often caused by bacteria which usually live in the respiratory pathway and kept under control by the immune system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This includes pneumonia (either viral or bacterial), inflammation of muscles and the heart muscle (myositis and myocarditis) as well as pericarditis. Less severe complications include infections like ear infections and sinusitis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See the references for more details:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://download.thelancet.com/flatcontentassets/H1N1-flu/pathogenesis/pathogenesis-8.pdf&quot; rel=&quot;nofollow&quot;&gt;Complications of Viral Influenza&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedaily.com/releases/2010/01/100122002334.htm&quot; rel=&quot;nofollow&quot;&gt;Double trouble: Bacterial super-infection after the flu&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://ajp.amjpathol.org/article/S0002-9440%2810%2960393-8/fulltext&quot; rel=&quot;nofollow&quot;&gt;A Mouse Model of Lethal Synergism Between Influenza Virus and&#xA;Haemophilus influenzae&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-10T16:56:37.377" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24769" PostTypeId="2" ParentId="24766" CreationDate="2014-12-10T17:30:40.983" Score="1" Body="&lt;p&gt;While a viral infection such as influenza can lead to secondary infections, it is inappropriate to call it a vector for those other infections. It is not the means by which those other infections are acquired. If a bacterial sinus infection follows upon a bout with the flu, that bacteria was not carried to the patient by the influenza virus. A single bacterium is immense compared to any virus. No, the bacteria most likely resided within the host before the infection, but it was under control. Or it might be introduced during the infection and find a foothold it would not have likely found in a healthy host. In a situation like this, the immune system is distracted and weakened enough to present an opportunity for this bacteria to grow out of control into an infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bacteria in this scenario are a little bit like the annoying hordes of roofing contractors that recently swarmed my neighborhood after a hail storm. These guys are always around, looking for the occasional roof that might be getting old and need repair. But right after a hail storm, they find a lot more of the opportunities they are looking for. So suddenly they are all over the place. They didn't literally fall from the sky with the hail. But the hail presented the opportunity they needed to thrive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Malaria is a microscopic germ which hitches a ride inside a comparably enormous mosquito to find it's way eventually into a human blood stream. An influenza virus is too small for &lt;em&gt;anything&lt;/em&gt; infectious to hitch a ride inside it.&lt;/p&gt;&#xA;" OwnerUserId="5018" LastEditorUserId="5018" LastEditDate="2014-12-10T17:36:43.907" LastActivityDate="2014-12-10T17:36:43.907" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="24770" PostTypeId="2" ParentId="21881" CreationDate="2014-12-10T17:44:05.813" Score="6" Body="&lt;p&gt;I wanted to add some helpful references. The 6th edition of the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK9983/&quot; rel=&quot;noreferrer&quot;&gt;Gilbert Developmental Biology textbook is available on NCBI bookshelf&lt;/a&gt;. It's a bit old (2000), but much of the information is still relevant. You can search this textbook for specific terms but not browse.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also a collaborative science/fashion project between the Storey sisters, called &lt;a href=&quot;http://www.primitive-streak.org/fertilisation.html&quot; rel=&quot;noreferrer&quot;&gt;Primitive Streak&lt;/a&gt;, which documents the early stages of human development.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For any given developmental process, there are a number of genes being activated and/or inactivated at that stage that determine how and when structures grow. Events can determine axes too; for instance, the dorsal/ventral axis of the embryo is determine by how the embryo blastocyst implants in the uterine wall. The left-right axis of the body is determined by the direction that fluid travels through a structure called the node, which is directed by hair-like structures called cilia. If nodal flow is backwards, your internal organs will switch sides, called situs inversus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Back to the limb example... in tetrapods, or animals with 4 limbs, the area where limbs emerge is based on Hox gene expression, and whether or not it will become a forelimb (arms) or hindlimb (legs) is determined by either Tbx5 or Tbx4 gene expression, respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The proximal-distal axis (proximal = towards the trunk; distal = away from the trunk) is determined by FGF gene expression, which induces formation of a structure called the apical ectodermal ridge (AER).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The anterior-posterior axis (head to tail) is determined by Sonic hedgehog gene expression in a region called the zone of polarizing activity (ZPA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The dorsal-ventral axis (back-front; or back of the hand/arm - palm/inside of arm) is determined by the Wnt7a gene being expressed on the dorsal side.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The outgrowth of the limb is determined by Hox gene expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Digit (finger) formation is dependent on cell death between the fingers - hands start webbed, kind of like ducks, and then genes such as the BMPs cause cells between the fingers to die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Terms to look up for more detail, since I don't have enough street cred here to post more than 2 links yet:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Snapshot Summary: The Tetrapod Limb (Gilbert book)&lt;/li&gt;&#xA;&lt;li&gt;apical ectodermal ridge (AER)&lt;/li&gt;&#xA;&lt;li&gt;zone of polarizing activity (ZPA)&lt;/li&gt;&#xA;&lt;li&gt;situs inversus&lt;/li&gt;&#xA;&lt;li&gt;Hox genes&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="10518" LastActivityDate="2014-12-10T17:44:05.813" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24771" PostTypeId="1" CreationDate="2014-12-10T18:39:28.287" Score="3" ViewCount="767" Body="&lt;p&gt;Given an in vivo sample from an experimental infection, I would like to see if a bacterial protein is present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been thinking about Western Blot using sera from animals infected with the bacteria. However, this strategy needs a positive control that requires prior gene cloning and expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is maybe a shorter path.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="4717" LastEditDate="2014-12-10T18:54:30.423" LastActivityDate="2014-12-11T19:37:28.653" Title="Western blot alternatives" Tags="&lt;western-blot&gt;&lt;protein-expression&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24773" PostTypeId="2" ParentId="7570" CreationDate="2014-12-10T22:22:01.007" Score="7" Body="&lt;p&gt;No, it is not true, see references 1 and 2 for this purpose. From these articles which followed up booster vaccinations for pertussis it seems that there is at least some protection 5 and 8 years after the boost. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is another study, which says that 10 years are relatively safe to assume, as the reduction in antibody levels over time estimated from the 5 year study would still allow protective levels of antibodies. See reference 3 for details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the problems to make statements about the duration of the protection is the lack of data. Additionally there was a change in the vaccine from whole cell (which is pretty immungenic, but has higher number unwanted side effects) against a acellular vaccine. This change happened in the 90s, so there are no longterm data available. See reference four for more details. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The common recommendation at the moment for adults is to repeat the booster vaccination every 10 years (together with tetanus and diphteria) and for people which have close contact to unvaccinated persons every 5 years to prevent infections (see reference 4).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17443462&quot; rel=&quot;noreferrer&quot;&gt;Immunity to pertussis 5 years after booster immunization during&#xA;adolescence.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3832/wwdif25k_pdf.htm&quot; rel=&quot;noreferrer&quot;&gt;Immune responses to pertussis antigens eight years after booster&#xA;immunization with acellular vaccines in adults.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2532581/&quot; rel=&quot;noreferrer&quot;&gt;How long can we expect pertussis protection to last after the&#xA;adolescent booster dose of tetanus-diphtheria-pertussis (Tdap)&#xA;vaccines?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3832/48fgi993_pdf.htm&quot; rel=&quot;noreferrer&quot;&gt;Acellular pertussis vaccine use in risk groups (adolescents,&#xA;pregnant women, newborns and health care workers): A review of&#xA;evidences and recommendations&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-10T22:22:01.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24774" PostTypeId="2" ParentId="24766" CreationDate="2014-12-10T22:51:40.847" Score="2" Body="&lt;p&gt;A vector transmits a disease or parasite from one animal or plant to another. Fruit bats are vectors for Ebola. They are a host to the virus, which can then be passed on to humans. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Influenza A, the virus responsible for human seasonal epidemics, is not a vector for other pathogens, although &lt;em&gt;co-infection&lt;/em&gt; with two different strains of influenza can give rise to progeny viruses with mixtures of genes derived from the parental strains. If anything, that would make humans, other mammals and birds the vectors for Influenza A.&lt;sup&gt;[1]&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Influenza A doesn't carry plasmids, and it does not insert it's genes into cell DNA as does a retrovirus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most frequent serious complications of influenza are pulmonary and fall into 4 categories or groups: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;primary influenza pneumonia  &lt;/li&gt;&#xA;&lt;li&gt;secondary bacterial pneumonia (also called co-infection, but from different sources)  &lt;/li&gt;&#xA;&lt;li&gt;pneumonia due to unusual pathogens or in immunocompromised hosts  &lt;/li&gt;&#xA;&lt;li&gt;exacerbations of chronic pulmonary diseases   &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Typically, the first group is smaller than the second (except for Avian Influenza A). No additional infection is necessary in this group to cause pneumonia or death.&lt;sup&gt;[2]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the second (and largest) group, typically viral influenza infection is followed by near resolution of symptoms, subsequently complicated 4 to 14 days later by a recurrence of fever, dyspnea, productive cough, and pulmonary consolidation. Common pathogens are &lt;em&gt;S. pneumoniae&lt;/em&gt;, &lt;em&gt;S. aureus&lt;/em&gt; (methicillin-sensitive [MSSA] or methicillin-resistant [MSSA]), S. pyogenes, H. influenzae, and some others.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pathogenetic mechanisms of viral-bacterial co-infections result from virus induced alteration in pulmonary epithelial cells (e.g. reduced ciliary function, cell death/decreased epithelial barrier function, etc.), virus-mediated inhibition of innate immune cells (e.g., suppressed phagocytosis, impaired microbial killing, etc.), dysregulated inflammation (e.g. increased inflammation due to chemokines) and other mechanisms.&lt;sup&gt;[2]&lt;/sup&gt;&lt;sup&gt;[3]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pneumonia due to unusual pathogens or in immunocompromised hosts, and exacerbations of chronic pulmonary diseases are less common than the second group but carry a high mortality. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second reference is an exhaustive review which you might find quite helpful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933150/&quot; rel=&quot;nofollow&quot;&gt;1 FluGenome: a web tool for genotyping influenza A virus&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://download.thelancet.com/flatcontentassets/H1N1-flu/pathogenesis/pathogenesis-8.pdf&quot; rel=&quot;nofollow&quot;&gt;2 Complications of Viral Influenza&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24590244&quot; rel=&quot;nofollow&quot;&gt;3 The co-pathogenesis of influenza viruses with bacteria in the lung&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-12-11T11:08:20.730" LastActivityDate="2014-12-11T11:08:20.730" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24775" PostTypeId="1" AcceptedAnswerId="25806" CreationDate="2014-12-10T23:12:32.113" Score="2" ViewCount="388" Body="&lt;p&gt;So, fastq-dump has the ability to be run on just an SRA file accession number, such that the SRA is converted to FASTQ on-the-fly, and the SRA doesn't have to be written to disk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm curious whether it would be possible to use fastq-dump to write to a named pipe (using mkfifo) and feed that into another program, for example Trinity, to run an assembly on the FASTQ file without ever having to write all that data to disk. For large datasets, this could actually save quite a bit of time in aggregate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has anyone done something similar? I am going to try and experiment with the technique soon, but I a) don't know much about the mkfifo process to begin with and b) am unsure of how this procedure would work for paired-end data where fastq-dump is splitting the SRA file as it goes. How would one specify which output would go to which pipe?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: A (hypothetical) example:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;mkfifo fileStream&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;fastq-dump SRR123456 &gt; fileStream&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Trinity --single fileStream misc_args&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That should take the fastq-dump data and stream it into the named pipe &quot;fileStream&quot;, which can then be used to stream data into Trinity. I don't know enough about all of the commands, however, to know if this makes any sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would welcome any thoughts from more experienced users!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Added update as an answer below.&lt;/p&gt;&#xA;" OwnerUserId="5598" LastEditorUserId="5598" LastEditDate="2014-12-12T20:17:51.103" LastActivityDate="2014-12-19T19:18:20.597" Title="fastq-dump using mkfifo to stream data" Tags="&lt;bioinformatics&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24776" PostTypeId="1" CreationDate="2014-12-11T00:54:04.140" Score="1" ViewCount="39" Body="&lt;p&gt;I've heard the claim that because farmers would be using the same seed, you would end up with an entire crop population that could be susceptible to a disease. Like if you had a diverse population of potatoes, not many of them could become blighted, but if you have only one kind of potato on your farm and that kind is susceptible to Phytophthora infestans, then all your potatoes would become blighted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Is this really how it works? Like once a seed with a desired characteristic is found, is it cloned? Or would they implement the same gene into many different crops?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If they do clone them, why couldn't they implement the same gene into a diversity of crops? Is it too costly?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Could one use mutagenesis to create diversity? If the seeds are cloned, could a certain number of the seeds be modified to try to account for natural diversity?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="10435" LastActivityDate="2014-12-11T00:54:04.140" Title="Would biotechnology in agriculture actually decrease biodiversity, as many people say? Does it have to?" Tags="&lt;biotechnology&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24777" PostTypeId="1" AcceptedAnswerId="25786" CreationDate="2014-12-11T00:55:48.680" Score="9" ViewCount="5705" Body="&lt;p&gt;Why is DNA called deoxyribonucleic acid and not something else? I get the nucleic acid part (because that's what DNA is made of) but what about the deoxyribo- part, especially the ribo- part. Maybe because DNA doesn't have oxygen, hence the &quot;deoxy-&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Also, please tell me what is wrong with my question or whether there was a duplicate I didn't find so I can fix this question or delete it.)&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="10401" LastEditDate="2014-12-11T01:08:53.287" LastActivityDate="2017-02-24T06:11:45.060" Title="Why does DNA have its name?" Tags="&lt;dna&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24778" PostTypeId="2" ParentId="24771" CreationDate="2014-12-11T01:00:12.687" Score="3" Body="&lt;p&gt;I think that enzyme-linked immunosorbent assay (or ELISA) is the best way to do so, given you have an antibody against the protein to coat the sample wells with... You could use mice to create polyclonal antibodies against your protein by injecting the protein and collecting the serum and purifying it...as long as there isn't similar proteins to the bacterial one in the sample you are testing for...but to diagnose an infection you could use something like q-PCR assuming you can get the bacterial DNA from the sample (you could use typical bacterial DNA extraction techniques).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more on ELISA go &lt;a href=&quot;https://en.wikipedia.org/wiki/ELISA&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. Here is a good animation on ELISA:&#xA;&lt;a href=&quot;http://highered.mheducation.com/sites/0072556781/student_view0/chapter33/animation_quiz_1.html&quot; rel=&quot;nofollow&quot;&gt;http://highered.mheducation.com/sites/0072556781/student_view0/chapter33/animation_quiz_1.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="10401" LastEditDate="2014-12-11T19:37:28.653" LastActivityDate="2014-12-11T19:37:28.653" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24779" PostTypeId="2" ParentId="16041" CreationDate="2014-12-11T02:25:07.120" Score="9" Body="&lt;p&gt;Not all cat predatory behavior is innate. Researchers found that cats predatory behavior for birds vs. mice depends to a significant degree on training by the mother: if the mother taught predatory behavior with birds, the kittens grew up to be better at catching birds than at catching mice and vice versa. Supportive data shows that aside from monkeys and other primates, cats are among the most adept at learning &lt;em&gt;by observing the successes and failures of other animals&lt;/em&gt; attempting to complete tasks to obtain a reward. This might influence, therefore, a cat's response to and attraction for objects in the air or on the floor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Blindfolded cats can hunt mice by vibration. Paul Leyhausen, a German animal behaviorist studied domestic cats (and related felines) from the 1950's through the 1970's, and much of what is known about their predatory behavior is thanks to him. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although their vision is not especially keen, domestic cats see well in dim light and readily perceive motion. According to Leyhausen, prey movement and the direction of movement are the only factors which innately release crouching, stalking, and catching behaviors in cats. When presented with quail, cats were far more likely to go after active quail than those stilled by tonic immobility. Cats are also more likely to go after smaller prey (mice &gt; rats) and mice were much more likely to elicit play pawing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Leyhausen also demonstrated that rodents were probably the natural prey of cats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though there has been much study of cats and predation, little is available on detail of the kind you are interested in.  My best guess for a good toy for a cat would be a smaller object that moved along the floor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More information can be obtained from Leyhausen's book, Cat Behavior: The Predatory and Social Behavior of Domestic and Wild Cats. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0163104780924565&quot; rel=&quot;noreferrer&quot;&gt;Effects of the mother, object play, and adult experience on predation in cats&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA; &lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0163104780924425&quot; rel=&quot;noreferrer&quot;&gt;The effects of experience on the predatory patterns of cats&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA; &lt;sub&gt;&lt;a href=&quot;http://link.springer.com/article/10.3758/BF03212037#page-3&quot; rel=&quot;noreferrer&quot;&gt;Tonic immobility in Japanese quail can reduce the probability of sustained attack by cats&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA; &lt;sub&gt;&lt;a href=&quot;http://homepage.psy.utexas.edu/HomePage/Group/AnimPersInst/Animal%20Personality%20PDFs/A/Ademac%201975.pdf&quot; rel=&quot;noreferrer&quot;&gt;The behavioral bases of prolonged suppression of predatory attack in cats&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-11T02:25:07.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24780" PostTypeId="2" ParentId="21881" CreationDate="2014-12-11T02:31:31.447" Score="7" Body="&lt;p&gt;Embryonic cells &quot;know&quot; where they are relative to each other by chemical signals, same as in adults. These molecules are known as morphogens (specific examples include the sonic hedgehog and β-catenin). The amount of morphogen in a region of cells determines which gene gets turned on and thus what it develops into. And the amount varies by how far they are from the source of the morphogen. Though AFAIK, scientists don't fully understand their mechanisms yet (like how they are dispersed, how the different concentrations are kept rigidly, etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for arms, etc., the earliest cells are unspecialized (stem cells). They &quot;define&quot; which becomes what early on by how they are arranged. Remember that their &quot;up, down, left, and right&quot; is relative to them, not to their surroundings. The first multicellular hollow ball of stem cells, the blastula, separates into distinct germ layers during gastrulation - the ectoderm, mesoderm, endoderm. Each of these layers develop into something different upon further division. What develops after that is basically a worm, composed of a series of repeating &quot;segments&quot; (somites) with a distinct head and tail area. Somites are initially undifferentiated. The job of determining which segment becomes what falls on Hox genes. So that for example, one segment becomes the head, another becomes the arm and pectoral girdle, another becomes a rib+vertebra, etc. Hox genes are arranged in clusters within the DNA relative to which gets expressed first. The first hox gene is for the head for example, while the last is for the tip of the tail (the tipmost segment of the coccyx in humans). Though these clusters themselves are often repeated into a kind of redundant failsafes. &lt;a href=&quot;http://learn.genetics.utah.edu/content/variation/hoxgenes/&quot;&gt;This page from the University of Utah explains it pretty well&lt;/a&gt;. It helps if you view embryogenesis as more or less echoes of evolution in fast forward.&lt;/p&gt;&#xA;" OwnerDisplayName="user9033" LastActivityDate="2014-12-11T02:31:31.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="24782" PostTypeId="1" AcceptedAnswerId="25855" CreationDate="2014-12-11T02:44:33.883" Score="11" ViewCount="16165" Body="&lt;p&gt;So I was cleaning out my car and found a McDonalds French fry. as I don't eat anything in my car I know exactly who and when this fry is a result of. The when is + 10 months old and it could pass off as one just prepared. How could this be?&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-12-12T00:57:06.407" LastActivityDate="2018-02-13T18:29:54.343" Title="Why don't McDonald's fries decompose?" Tags="&lt;lipids&gt;&lt;fatty-acid-synthase&gt;&lt;carbohydrates&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="24783" PostTypeId="2" ParentId="21867" CreationDate="2014-12-11T02:47:31.450" Score="1" Body="&lt;p&gt;&lt;strong&gt;Why&lt;/strong&gt; nature has done it this way around is difficult to explain. What is certain, however, is that the &lt;em&gt;membrane potential&lt;/em&gt; which results from the imbalance of these ions across the membrane is used for a variety of purposes, such as transport of other ions and molecules, action potential generation in neurons among many other things. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How&lt;/strong&gt; it is accomplished is mainly through the Na&lt;sup&gt;+&lt;/sup&gt;,K&lt;sup&gt;+&lt;/sup&gt;-Atpase pump and secondarily through Cl&lt;sup&gt;-&lt;/sup&gt; channels that exchange Na&lt;sup&gt;+&lt;/sup&gt; for Cl&lt;sup&gt;-&lt;/sup&gt; to lift the amount of Cl&lt;sup&gt;-&lt;/sup&gt; outside the cell. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-11T03:12:44.177" LastActivityDate="2014-12-11T03:12:44.177" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="24784" PostTypeId="2" ParentId="8577" CreationDate="2014-12-11T03:34:11.123" Score="5" Body="&lt;p&gt;Hand sweating has been fairly well-studied, both because sweating from the hands is one of the main mechanisms of heat dissipation at higher temperatures and because there is a significant effect on palmar sweating by the autonomic nervous system (the main cause of hyperhydrosis of the palms).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disregarding autonomic effects (stress response), the single most important determinant of hand and foot blood flow is the thermal status of the body core. Heat dissipation is more marked in the hands than feet, and remains so as temperature increases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Studies have been done of palmar sweating in extremes of temperatures, palmar sweating changes with aging (decreases), palmar sweating in disease, etc. But what has not been studied is the effect of localized heat on sweating of the palms, which would be of interest to you if sweating was a result of the insulating capacity of the gloves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is known about palmar sweating is that it is an ongoing and important process in both genders, at all temperatures, and at all ages. The most reasonable assumption then, given the limits of the literature, is that your hands sweat continuously and steadily at a given temperature, and it is highly likely that you are noticing it when wearing gloves only because the vapor barrier caused by the gloves prohibits evaporation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://ro.uow.edu.au/cgi/viewcontent.cgi?article=1201&amp;amp;context=hbspapers&quot; rel=&quot;nofollow&quot;&gt;The roles of hands and feet in temperature regulation in hot and cold environments&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://jp.physoc.org/content/133/1/132.full.pdf&quot; rel=&quot;nofollow&quot;&gt;OBSERVATIONS ON THE ACTIVITY OF SWEAT GLANDS WITH SPECIAL REFERENCE TO THE INFLUENCE OF AGEING&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://health.howstuffworks.com/wellness/men/sweating-odor/sweaty-palms.htm&quot; rel=&quot;nofollow&quot;&gt;Why do I get sweaty palms?&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-12-11T09:07:51.060" LastActivityDate="2014-12-11T09:07:51.060" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="24786" PostTypeId="1" AcceptedAnswerId="25789" CreationDate="2014-12-11T04:18:55.250" Score="24" ViewCount="62804" Body="&lt;p&gt;Why is DNA made out of deoxyribose and RNA made of ribose? Why can't they both use ribose or deoxyribose? I think that the deoxyribose gives an advantage in storing genes, the job of DNA and ribose is better dealt with outside the nucleus...but why?&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="3340" LastEditDate="2014-12-12T06:38:13.120" LastActivityDate="2016-04-29T13:21:38.907" Title="Why deoxyribose for DNA and ribose for RNA?" Tags="&lt;dna&gt;&lt;rna&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="25784" PostTypeId="2" ParentId="9835" CreationDate="2014-12-11T06:28:34.760" Score="2" Body="&lt;p&gt;Most of the time, calcium is not the most important ion in terms of active propagation of an action potential along an axon. It is usually sodium and potassium which play the key roles here. In most living things the concentrations of ions for the intracellular and extracellular solutions are similar. For an action potential, you usually have an influx of sodium followed by an efflux of potassium. The sodium influx depolarizes the membrane and the potassium efflux re-polarizes it. The speed of conduction is determined by the membrane resistance and its &quot;leakage&quot;. That is to say, how easily can a single travel along an axon? This is determined by the diameter of the axon, the greater the diameter, the faster the conduction. The leakage refers to ease with which ions leak out of the axon as the signal is propagating. Insulation via myelin sheaths help in preventing this, and, less leakage, the greater the signal at the next propagation site.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Calcium is the most important ion for the transmission of a signal from a pre to post synaptic cell. Without calcium, you have no neurotransmitter release. This is because the influx of calcium triggers a series of events involving the snare complex which eventually leads to vesicular release of neurotransmitter in quantal units. If you remove calcium from the extracellular solution, you will have no neurotransmitter release. If you block the calcium channels, you will have no neurotransmitter release.&lt;/p&gt;&#xA;" OwnerUserId="11525" LastActivityDate="2014-12-11T06:28:34.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25785" PostTypeId="2" ParentId="21867" CreationDate="2014-12-11T07:06:08.393" Score="0" Body="&lt;p&gt;Your question isn't all that precise but I think looking at individual ionic equilibrium potentials begins to give us some understanding.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at the equilibrium potentials(EK for potassium and ENA for sodium) for these two ions and their channels you have that EK = -90mV and ENA = +60mV in a typical neuron. This means that at these voltages you will have no NET flow of that ion across the membrane. Inside a cell you will have a certain amount of negatively charged ions called anions which will not diffuse, or move across the membrane regardless of the concentration gradient. To compensate for this (because the inside and outside of the cells like to have equal charges when there are not action potentials) you need a certain amount of a positively charged ion on the inside. NOW, there is no NET flow of EK at a negative voltage, this is around the same voltage of the entire membrane resting potential (this varies). If you look at the numbers and consider the voltage at which an action potential occurs, then you cannot have sodium be the cation inside the membrane since ENA = +60 since an action potential propagates when the membrane is driven towards a positive voltage. &lt;/p&gt;&#xA;" OwnerUserId="11525" LastEditorUserId="11525" LastEditDate="2014-12-11T15:26:14.837" LastActivityDate="2014-12-11T15:26:14.837" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="25786" PostTypeId="2" ParentId="24777" CreationDate="2014-12-11T07:39:42.860" Score="15" Body="&lt;p&gt;The name is derived from the sugar which is bound to the base. For RNA it is &lt;a href=&quot;http://en.wikipedia.org/wiki/Ribose&quot; rel=&quot;noreferrer&quot;&gt;Ribose&lt;/a&gt; (that why it is called ribonucleic acid) and for DNA it is &lt;a href=&quot;http://en.wikipedia.org/wiki/Deoxyribose&quot; rel=&quot;noreferrer&quot;&gt;Deoxyribose&lt;/a&gt; (hence the name deoxynucleic acid). The deoxyribose is missing an OH-group at positition 2 of the sugar ring, the name literally means &quot;without oxygen&quot;. See the image below (from &lt;a href=&quot;http://www.siumed.edu/~bbartholomew/course_material/nucleic_acids.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;) for further clarification:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3Tqaf.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-11T07:39:42.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25787" PostTypeId="2" ParentId="10015" CreationDate="2014-12-11T08:16:03.753" Score="3" Body="&lt;p&gt;When you look at the development of the embryo, at the beginning all cells are totipotent, meaning they can develop into any cell type of the body. This changes relatively fast by &lt;a href=&quot;http://en.wikipedia.org/wiki/Cellular_differentiation&quot; rel=&quot;nofollow noreferrer&quot;&gt;differentiation&lt;/a&gt;, which means that the totipotent cells develop into more specialized cell types, which then can not give rise to all cell types. So the different &lt;a href=&quot;http://en.wikipedia.org/wiki/Germ_layer&quot; rel=&quot;nofollow noreferrer&quot;&gt;germ layers&lt;/a&gt; (meso, ecto- and endoderm) develop and from these all the cell types in our body. See the first figure for clarification (from &lt;a href=&quot;http://stemcellres.com/content/2/5/42/figure/F1?highres=y&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nRA21.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lineage restriction means that you have a differentiated cell line, which can only further develop into cells of this line. So hematipoietic stem cells can only further develop into cells of the hematopietic line (lymphocytes, erythrocytes, basophiles and so on), like shown in the figure below (taken from &lt;a href=&quot;http://vectorblog.org/2014/10/a-double-shot-of-good-news-for-scid-promising-transplant-and-gene-therapy-data/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eip5i.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-11T08:16:03.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25788" PostTypeId="2" ParentId="17116" CreationDate="2014-12-11T08:45:22.403" Score="4" Body="&lt;p&gt;&lt;strong&gt;Recap of the question:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at a single locus trait ($A$) controlled by two alleles, $A_1$ and $A_2$, the phenotypic mean is only affected by inbreeding depression, $f$ (Wright's inbreeding coefficient), if there is some degree of dominance, $d$. Why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Answer:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we take inbreeding as a higher than expected frequency of homozygotes, such that if the frequencies of alleles $A_1$ and $A_2$ are $p = q = 0.5$ the expected frequencies of the genotypes in an outbred population, $P_{outbred}$, would be $p^2 = 0.25$, $2pq = 0.50$, and $q^2 = 0.25$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each genotype has the following phenotypic result on a trait $A_1A_1 = 5$, $A_1A_2 = 7.5$, $A_2A_2 = 10$... this is an additive trait with allele $A_1$ having an additive effect of 2.5, and $A_2$ an additive effect of 5.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can then compare an inbred population of 100 individuals, $P_{inbred}$ where the frequency of $A_1A_1 = 0.5$, $A_1A_2 = 0$, $A2_A2 = 0.5$, to $P_{outbred}$ , where I use $\bar{X}$ to symbolise trait means.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\bar{X}_{inbred} = \frac{(50 \cdot 5) + (0 \cdot 7.5) + (50 \cdot 10)}{100} = 7.5$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\bar{X}_{outbred} = \frac{(25 \cdot 5) + (50 \cdot 7.5) + (25 \cdot 10)}{100} = 7.5$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when the trait is additive the population means are equal. It is onlt when we add dominance to the situation that the population means will differ as a result of inbreeding. Continuing from the above example, the populations are the same size and structure, but $A_2$ is now completely dominant to $A_1$ such that $A_1A_2$ individuals now have a trait value of 10. Now&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\bar{X}_{inbred} = \frac{(50 \cdot 5) + (0 \cdot 10) + (50 \cdot 10)}{100} = 7.5$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\bar{X}_{outbred} = \frac{(25 \cdot 5) + (50 \cdot 10) + (25 \cdot 10)}{100} = 8.75$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus inbreeding has affected the population mean in a trait which has dominance, it is basically because the heterozygotes are less common in an inbreeding population and this is where dominance effects are seen.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;there is a linear decline in the mean of a trait with increasing f... with overdominance (di &gt; ai)&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is because in the case of overdominance, the outbred population mean becomes even more elevated - if we say now the $A_1A2$ trait is a phenotype of 15 the means become&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\bar{X}_{inbred} = \frac{(50 \cdot 5) + (0 \cdot 15) + (50 \cdot 10)}{100} = 7.5$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\bar{X}_{outbred} = \frac{(25 \cdot 5) + (50 \cdot 15) + (25 \cdot 10)}{100} = 11.25$&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot; there is a linear decline in the mean of a trait with increasing f... if the allele associated with an increased value of the trait is dominant or partially dominant (ai ≥ di &gt; 0)&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The mean will increase if the dominant allele produces a smaller phenotype. Here we say $A_1$ is now completely dominant,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\bar{X}_{inbred} = \frac{(50 \cdot 5) + (0 \cdot 5) + (50 \cdot 10)}{100} = 7.5$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\bar{X}_{outbred} = \frac{(25 \cdot 5) + (50 \cdot 5) + (25 \cdot 10)}{100} = 6.25$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I hope that answers the question, I tried to answer last night but was too tired to think - this is just what I came up with on the walk to work today so I haven't had the time to check it/overthink it&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2014-12-12T08:50:33.610" LastActivityDate="2014-12-12T08:50:33.610" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25789" PostTypeId="2" ParentId="24786" CreationDate="2014-12-11T09:41:05.203" Score="17" Body="&lt;p&gt;Nice question which leads to the fundamentals of DNA and RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/DNA&quot; rel=&quot;noreferrer&quot;&gt;DNA&lt;/a&gt; (Deoxyribonucleic acid) is the core of life in Earth, every known living organism is using DNA as their genetic backbone. DNA is so precious and vital to &lt;a href=&quot;http://en.wikipedia.org/wiki/Eukaryote&quot; rel=&quot;noreferrer&quot;&gt;eukaryotes&lt;/a&gt; that its kept packaged in cell nucleus, its being copied but never removed because it never leaves the safety of nucleus. DNA directs all cell activity by delegating it to RNA. &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA&quot; rel=&quot;noreferrer&quot;&gt;RNA&lt;/a&gt; (Ribonucleic acid ) have varied sort of biological roles in coding, decoding, regulation, and expression of genes. RNA carries messages out of the cell nucleus to cytoplasm.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The structure of RNA nucleotides is very similar to that of DNA nucleotides, with the main difference being that the ribose sugar backbone in RNA has a hydroxyl (-OH) group that DNA does not. This gives DNA its name: DNA stands for deoxyribonucleic acid. Another minor difference is that DNA uses the base thymine (T) in place of uracil (U). Despite great structural similarities, DNA and RNA play very different roles from one another in modern cells.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;http://exploringorigins.org/rna.html&quot; rel=&quot;noreferrer&quot;&gt;http://exploringorigins.org/rna.html&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;RNA has three main characteristics that differs it from DNA&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;RNA is very unstable and decomposes rapidly.&lt;/li&gt;&#xA;&lt;li&gt;RNA contains Uracil in place of Thymine&lt;/li&gt;&#xA;&lt;li&gt;RNA is almost always single stranded.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;DNA and RNA use a ribose sugar as a main element of their chemical structures, ribose sugar used in DNA is deoxyribose, While RNA uses unmodified ribose sugar.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Ribose and Deoxyribose&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TvpOf.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;From the fig above we can see that the principal difference between&#xA;  the two molecules is the presence of OH in ribose (2' tail) and absence&#xA;  in deoxyribose. There is a difference in one Oxygen atom as the name&#xA;  stands de-oxy ribose. Both Ribose and deoxyribose have an Oxygen(O)&#xA;  atom  and a Hydrogen (H) atom (an OH group) at their 3' sites. The OH&#xA;  groups are very reactive in nature, so the 3' OH tail is required for&#xA;  phosphodiester bonds to form between &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleotide&quot; rel=&quot;noreferrer&quot;&gt;nucleotides&lt;/a&gt; in both ribose&#xA;  and deoxyribose atoms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA is such an important molecule so it must be protected from decomposition and further reactions. The absence of one Oxygen is the key for extending DNA's longevity. When the 2' Oxygen is absent in deoxyribose, the sugar molecule is less likely to get involved in chemical reactions( the aggressive nature of Oxygen in chemical reactions are famous). &lt;strong&gt;So by removing the Oxygen from deoxyribose molecule, DNA avoids being broken down&lt;/strong&gt;. In an RNA's point of view the Oxygen is helpful, unlike DNA, RNA is a short-term tool used by the cell to send messages and manufacture proteins as a part of gene expression. Simply speaking mRNA (Messenger RNA) has the duties of turning genes ON and OFF, when a gene needed to be put ON mRNA is made and to keep it OFF the mRNA is removed. So &lt;strong&gt;the OH group in 2' is used to decompose the RNA quickly thereby making those affected genes in OFF state.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, &lt;strong&gt;the ribose sugar is placed in RNA for easily decomposing it and DNA uses deoxyribose sugar for longevity.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;References&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Flesh and Bones of Metabolism -  Marek H. Dominiczak&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Genetics For Dummies -  Tara Rodden Robinson&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="3340" LastEditDate="2014-12-12T06:35:59.433" LastActivityDate="2014-12-12T06:35:59.433" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="25790" PostTypeId="1" AcceptedAnswerId="25795" CreationDate="2014-12-11T11:28:29.850" Score="1" ViewCount="40396" Body="&lt;p&gt;There is a common saying in my place: &lt;em&gt;If you eat your skin, hair or nails, it will be deposited in the cecal (Vermiform) appendix, and can cause appendicitis.&lt;/em&gt; (This is mostly told to children to discuourge them from eating their own.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any reality in this statement? In the case of hair and nails they are dead cells, but what is the issue with skin? Skin is normally living and the cells are active.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So is there any problem digesting ones own skin?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do nails, skin and hair must be trapped in Vermiform appendix?&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="5198" LastEditDate="2014-12-11T18:25:49.343" LastActivityDate="2016-01-13T19:39:13.167" Title="Can swallowed fingermails, hair, or skin get caught in your appendix?" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2014-12-12T01:38:04.630" ContentLicense="CC BY-SA 3.0" />
  <row Id="25792" PostTypeId="2" ParentId="24786" CreationDate="2014-12-11T13:25:04.517" Score="9" Body="&lt;p&gt;Addition to Jvrek's answer based on the comments. Most RNA degradation mechanisms catalysed by different RNAses (RNAse-A and RNAse-S, for example), involve the 2'-OH. Therefore the repertoire of RNAses is selective towards RNA and not DNA because of the 2'-OH. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/m1u6g.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/cc4uU.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-13T06:38:49.533" LastActivityDate="2014-12-13T06:38:49.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25794" PostTypeId="1" AcceptedAnswerId="25803" CreationDate="2014-12-11T16:03:10.897" Score="0" ViewCount="77" Body="&lt;p&gt;I heard this clause from my teacher one week ago:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Chicken are grown in half a year until eaten in Baltic countries - Estonia, Latvia and Lithuania, for instance, [probably in other parts of Europe, too]. How do you imagine this to happen so fast? - - Growth hormones are used to grow them fast. This affects your endocrine system and can replace its natural function. We cannot even know the withdrawal symptoms when you stop eating food of growth hormones. - - Eat pork instead. No growth hormones used in their life cycle because not needed and not so useful in practice.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I started to think what. Can this really be true that the effect of growth hormones is big economically on poultry but not on pork so it is not used. &#xA;The size of chicken is small compared to pork so they have different muscular structure. &#xA;So probably more musculature in chicken and bigger effect therefore. &#xA;&lt;strong&gt;Why does growth hormones have bigger growth effect on chicken?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is it true that growth hormones are used more in the growth of chicken than pork in Western countries?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not understand the critique presented against poultry industry here, in favour of pork industry. &#xA;Probably, there is some truth too.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-12-12T03:06:42.703" Title="Effect of Western chicken and GH" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ClosedDate="2014-12-12T11:18:26.613" ContentLicense="CC BY-SA 3.0" />
  <row Id="25795" PostTypeId="2" ParentId="25790" CreationDate="2014-12-11T18:19:25.547" Score="6" Body="&lt;p&gt;Skin is safe to chew, and digestible. Fingernails are not digestible, so really shouldn't be swallowed if avoidable. In the medical literature, there are at least 225 cases of foreign bodies in the appendix. They include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;a metal drill bit that was ingested unintentionally 3 months earlier&lt;/li&gt;&#xA;&lt;li&gt;pins (81  cases)&lt;/li&gt;&#xA;&lt;li&gt;lead shot (81 cases) &lt;/li&gt;&#xA;&lt;li&gt;seeds (34 cases)&lt;/li&gt;&#xA;&lt;li&gt;bones (16 cases) &lt;/li&gt;&#xA;&lt;li&gt;eggshell&lt;/li&gt;&#xA;&lt;li&gt;glass&lt;/li&gt;&#xA;&lt;li&gt;teeth&lt;/li&gt;&#xA;&lt;li&gt;nails (hair causes problems with bezoar formation)&lt;/li&gt;&#xA;&lt;li&gt;a die (dice)&lt;/li&gt;&#xA;&lt;li&gt;the clinical end of a thermometer. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Most (71%) patients were symptomatic, typically with intermittent abdominal pain for months or years. Pins were most likely to elicit symptoms (93% of cases).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it seems there is some truth to this nugget of folk wisdom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above were found over many, many years. Since most cases are asymptomatic, it's likely there are many cases that never come to light, but not remarkably so (lots of appendices are removed and examined every year!). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://archsurg.jamanetwork.com/article.aspx?articleid=571167&quot; rel=&quot;nofollow&quot;&gt;Foreign Bodies in the Appendix&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="19650" LastEditDate="2016-01-13T19:39:13.167" LastActivityDate="2016-01-13T19:39:13.167" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="25797" PostTypeId="1" CreationDate="2014-12-11T22:01:48.793" Score="2" ViewCount="28" Body="&lt;p&gt;I have a list of genes for each of which I'd like to find:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;A list of transcription factors that up-regulate the gene&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A list of inhibitory factors that down-regulate it.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I used this tool on &lt;a href=&quot;http://www.sabiosciences.com/chipqpcrsearch.php&quot; rel=&quot;nofollow&quot;&gt;Qiagen's&lt;/a&gt; website to find transcription factors (and will be thrilled if someone can share a better tool). Its less than ideal for my purposes because I need to search each gene individually and there doesn't seem to be anyway of downloading or copy/pasting the transcription factors it returns; but it works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I really need now though, is &lt;strong&gt;a way to find inhibitory factors by gene&lt;/strong&gt;. Does anyone know how I can do this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have already tried using  &lt;a href=&quot;http://www.wikipathways.org/index.php/WikiPathways&quot; rel=&quot;nofollow&quot;&gt;wikipathways&lt;/a&gt; and found it to show almost none of the transcription factors I found on Qiagen's website leading me to conclude that their data is far from comprehensive. I have applied for access to &lt;a href=&quot;http://www.ingenuity.com/&quot; rel=&quot;nofollow&quot;&gt;Ingenuity&lt;/a&gt; only to discover that I will not be granted access soon enough to make use of it. &lt;/p&gt;&#xA;" OwnerUserId="8161" LastEditorUserId="3340" LastEditDate="2014-12-12T06:33:29.100" LastActivityDate="2014-12-12T06:33:29.100" Title="Resource for finding Repressive/Inhibitory factors for a given gene?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;research-tools&gt;&lt;transcription-factor&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25798" PostTypeId="1" AcceptedAnswerId="25809" CreationDate="2014-12-11T23:41:41.630" Score="4" ViewCount="3286" Body="&lt;p&gt;I've been living in my apartment for a year now, and noticed something lately. During spring and summer I have quite a lot of midges indoors, and even now there are some. But there are no spiders! So my question is a bit of the opposite of what all spider/house related articles are about: how do I get more spiders to my house?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some info about my place: I live in a 40 year old apartment in Rotterdam, Netherlands on the second floor. It's always between 17 and 20°C, and the place is poorly isolated; plenty of cracks for visitors to crawl through. Also, I usually have a window open a bit. I have quite a lot of plants, and an aquarium, so I guess air humidity is relatively high. There is a large backyard with lots of weeds and some trees, however people use it for dumping old furniture so it is not a real garden (it's most likely the source of the midges).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can I do something to stimulate spiders to come to my house?&lt;/p&gt;&#xA;" OwnerUserId="4802" LastEditorUserId="10401" LastEditDate="2014-12-12T02:31:47.813" LastActivityDate="2019-12-09T14:39:52.150" Title="How to attract spiders to my house?" Tags="&lt;entomology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25799" PostTypeId="1" AcceptedAnswerId="25808" CreationDate="2014-12-12T01:34:51.320" Score="8" ViewCount="1201" Body="&lt;p&gt;What is the number of the transcription factor genes present in the human genome? Does this value differ compared to Mus musculus, Drosophila melanogaster, Arabidopsis thaliana, C. elegans and S. cerevisiae? Additionally, does the proportion change between eukaryotes and prokaryotes?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="9099" LastEditDate="2014-12-12T10:33:52.840" LastActivityDate="2014-12-15T08:07:06.567" Title="Number of transcription factor genes in the human genome" Tags="&lt;transcription&gt;&lt;human-genome&gt;&lt;genomes&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="25802" PostTypeId="2" ParentId="10168" CreationDate="2014-12-12T02:14:29.480" Score="2" Body="&lt;p&gt;Amalgam fillings are made from an alloy. The properties of the chemical elements bound into an alloy are different than the properties of those elements in different forms. The fillings do not release any biologically significant form or biologically significant amount of either silver or mercury. They are essentially inert.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plus silver antibacterial effects are quite modest. The existence of fine cracks and gaps between amalgam and tooth provide wonderful hiding places for bacteria - and that shelter is probably more important to the bacteria than any negative effects of the silver. &lt;/p&gt;&#xA;" OwnerDisplayName="user9033" LastActivityDate="2014-12-12T02:14:29.480" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25803" PostTypeId="2" ParentId="25794" CreationDate="2014-12-12T02:31:16.763" Score="3" Body="&lt;p&gt;Poultry raised for meat in the US (called &lt;em&gt;broilers&lt;/em&gt;) reach butchering size in 5 to 8 weeks (compared to 10 weeks for half the size 40 years ago. It's not a GH miracle; it's a result of generations of selective breeding (as cows have undergone for unhealthy udder size).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GH use is illegal in the US and many other countries. Honestly, it's an unnecessary additive/expense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I raised poultry for more than a decade, mostly chickens and ducks (but almost everything else as well). Once I bought 25  1-day-old broiler chicks (early broilers were a Plymouth Rock X Cornish) alongside my usual mix.  Within 2 weeks the broilers were at least 3 or 4 times the size of the other chicks, and more than a couple of them died (under ideal conditions - all free-range outside, cooped only at night). By 10 weeks, they were enormous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They were also dumber than a bag of hammers, unfortunately. I felt so sorry for them that I let them live out their natural lives, which wasn't terribly long, partly because of their docile stupidity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Growth hormone is unnecessary in the poultry industry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;https://www.mcmurrayhatchery.com/jumbo_cornish_x_rocks.html&quot; rel=&quot;nofollow&quot;&gt;Murray McMurray Hatchery: Jumbo Cornish X Rocks&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://extension.psu.edu/animals/poultry/topics/general-educational-material/the-chicken/modern-meat-chicken-industry&quot; rel=&quot;nofollow&quot;&gt;Modern Meat Chicken Industry&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-12-12T03:06:42.703" LastActivityDate="2014-12-12T03:06:42.703" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25806" PostTypeId="2" ParentId="24775" CreationDate="2014-12-12T06:45:33.577" Score="6" Body="&lt;p&gt;fastq-dump can write to stdout ; the &lt;code&gt;-Z&lt;/code&gt; option allows you to do that. This, you can pipe to any downstream process. [&lt;a href=&quot;http://codextechnicanum.blogspot.in/2014/06/sra-to-gzipped-fastq.html&quot; rel=&quot;nofollow&quot;&gt;An example&lt;/a&gt;]. Also see the SRA-toolkit &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&amp;amp;f=fastq-dump&quot; rel=&quot;nofollow&quot;&gt;manual&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I guess someone asked this question &lt;a href=&quot;https://www.biostars.org/p/123320/&quot; rel=&quot;nofollow&quot;&gt;in biostar&lt;/a&gt; too.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-14T09:18:01.403" LastActivityDate="2014-12-14T09:18:01.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25807" PostTypeId="2" ParentId="24555" CreationDate="2014-12-12T09:45:07.300" Score="1" Body="&lt;p&gt;Paresthesia is defined as the abnormal sensation of the skin, such as numbness, tingling, pricking or burning. Paresthesia is a diverse medical condition and the definitions seems too vague. Most of the books define Paresthesia as a symptom of some other disease. Mostly Paresthesia is categorized as transient or permanent. Paresthesia can arise from several causes like artery related, nerve related, migraine, vitamin B deficiency, brain related and may cause from side effects of other drugs.&lt;/p&gt;&#xA;&lt;p&gt;Classification of transient and chronic Paresthesia is described in detail &lt;a href=&quot;http://cdn.intechopen.com/pdfs-wm/29764.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Nerve impulses require a healthy energy supply, known as the axonal transport system.  This well developed micro-vascular distribution method provides the blood flow needed to maintain the cells in good working order. If pressure is put on the correct spot, though, all the tiny arteries, veins and capillaries that supply the nerves’ nutrients become pinched off and the nerve cells begin to function abnormally.&lt;/p&gt;&#xA;&lt;p&gt;Compression isn’t the only thing that can cause limbs to fall asleep. Excessive vibration will also lead to paresthesia. Operating hand-held vibrating tools is an extremely common cause of this&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.todayifoundout.com/index.php/2012/01/what-causes-arms-legs-and-feet-to-fall-asleep/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;As simulation level increases transient Paresthesia may occur, usually disappearing with in a few second&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Localized paresthesia or pain occasionally results from a specific&#xA;mechanism. Mechanical irritation of a peripheral nerve can project&#xA;such sensations to their periphery.If the pressure on a peripheral&#xA;nerve provokes paresthesia, then a neuroma or chronic compression&#xA;occurs. If the pain is initiated by the movement of a joint, there may&#xA;be a ganglion affected by the process.&lt;/p&gt;&#xA;&lt;p&gt;Reference : Neurological Differential Diagnosis -- Marco Mumenthaler&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The paresthesia mentioned in the question is transient, mostly paresthesia can happen in cold weather conditions or can happen when sitting in a particular position for long time. Several types of paresthesia exist and there are several reasons for the occurrence. But most of them are attributed to the strain in  peripheral nerve. When we stand up, the itching effects get increase and it slowly fades out, this is because when the nerve resulted in the formation of paresthesia is stressed more when we take a stand up poster. As some paresthesia is caused by the lack of blood supply, blood supply itself is not always causes paresthesia but there are cases when blood circulation to the nerve is interrupted and this may result in stress of nerve and which may cause paresthesia. These kinds of paresthesia is common and it only last for minutes. So when we stand up the tension to the nerve increases, also the blood pressure increases and blood is slowly available to the nerve. &lt;strong&gt;When we try to stand, the nerves are burdened with more tension and paresthesia increases but after sometime the blood flow become natural and paresthesia  diminishes slowly. Paresthesia   can be reduced by massage or applying pressure on the affected areas&lt;/strong&gt;, all these are helpful for people having transient paresthesia. Chronic paresthesia and paresthesia due to other medical conditions need more complex treatments.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Causes for paresthesia&lt;/strong&gt;&lt;br /&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/yXAO8.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;References&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://books.google.co.in/books?id=PhdtLQVtCMMC&amp;amp;pg=PA438&amp;amp;dq=why%20paresthesia%20occurs&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=ZX6KVJnEBoPhuQSDiILoAg&amp;amp;ved=0CB0Q6AEwAA#v=onepage&amp;amp;q=why%20paresthesia%20occurs&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Clinical Guide&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Clinical Neurology of the Older Adult --  Joseph I. Sirven, Barbara L. Malamut&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://books.google.co.in/books?id=fs6sQlM0z9UC&amp;amp;pg=PA63&amp;amp;dq=working%20of%20paresthesia&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=SnqKVLaUF5CTuASnzoKIAg&amp;amp;ved=0CCwQ6AEwAw#v=onepage&amp;amp;q=working%20of%20paresthesia&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Paresthesia and Dysesthesia&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-12T09:45:07.300" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25808" PostTypeId="2" ParentId="25799" CreationDate="2014-12-12T10:06:45.793" Score="13" Body="&lt;p&gt;Here I will assume we are talking about eukaryotic &lt;a href=&quot;http://en.wikipedia.org/wiki/Transcription_factor&quot;&gt;sequence specific transcription factors&lt;/a&gt; (ssTFs) and try to answer your first and part of the second question. There is in any case not definitive answer yet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An estimate of ssTFs genes in humans is given in the 2009 &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19274049&quot;&gt;Nature Reviews Genetics&lt;/a&gt; paper by Vaquerizas, JM et al, &lt;em&gt;A census of human transcription factors: function, expression and evolution&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An excerpt from the abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Here, we present an analysis of 1,391 manually curated sequence-specific DNA-binding transcription factors, their functions, genomic organization and evolutionary conservation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The numbers are somewhat higher now. Wingender et al. have counted 1,558 human genes in their &lt;a href=&quot;http://tfclass.bioinf.med.uni-goettingen.de/tfclass&quot;&gt;TFClass&lt;/a&gt; database &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23180794&quot;&gt;2013 NAR paper&lt;/a&gt;. In their &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25361979&quot;&gt;2014 NAR paper&lt;/a&gt; they included 1,557 human, 1,147 mouse and 1,105 rat orthologs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way to look for this information is to see the number of entries listed in TF databases, like for example &lt;a href=&quot;http://jaspar.genereg.net&quot;&gt;JASPAR&lt;/a&gt;. This has the advantage of including other species. However, the coverage here depends on the availability of position weight matrices (PWMs) for the binding specificities. Many uncharacterized TFs may not be found.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;To try to answer your third question, that is, what is the proportion of TFs in the different species, a naive approach would be to divide the number of predicted TFs by the number of predicted genes in the target genome. For example, taking the latest estimates above with the predicted number of coding genes from &lt;a href=&quot;http://www.ensembl.org&quot;&gt;Ensembl&lt;/a&gt; database (version 78) will return these percentages:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;# Human&#xA;100 * 1557 / 20364 = 7.64%&#xA;# Mouse&#xA;100 * 1147 / 22606 = 5.07%&#xA;# Rat&#xA;100 * 1105 / 22777 = 4.85%&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This suggests humans have a slightly higher proportion of TFs than rodents. However, these differences are not too big and may be dependent on the accuracy of the different estimates on TFs and gene numbers. An in itself, these numbers are not so interesting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A much more interesting question is whether TF families have expanded more or less in different species (that is, whether the number of  proteins within each family has increased, regardless of the proportion to the total number of genes in the genome). I could find at least &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16166257&quot;&gt;one paper&lt;/a&gt; where this has been done systematically for several eukaryotic species, covering animals, plants and fungi, and focusing on TFs common to the ones found in plants. The main conclusion of the paper is that some TFs families have expanded more in plants than in other organisms. Quoted from the abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To investigate if differences exist in the expansion patterns of TF gene families between plants and other eukaryotes, we first used Arabidopsis (Arabidopsis thaliana) TFs to identify TF DNA-binding domains. These DNA-binding domains were then used to identify related sequences in 25 other eukaryotic genomes. Interestingly, among 19 families that are shared between animals and plants, more than 14 are larger in plants than in animals. After examining the lineage-specific expansion of TF families in two plants, eight animals, and two fungi, we found that TF families shared among these organisms have undergone much more dramatic expansion in plants than in other eukaryotes. Moreover, this elevated expansion rate of plant TF is not simply due to higher duplication rates of plant genomes but also to a higher degree of expansion compared to other plant genes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9099" LastEditorUserId="9099" LastEditDate="2014-12-15T08:07:06.567" LastActivityDate="2014-12-15T08:07:06.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25809" PostTypeId="2" ParentId="25798" CreationDate="2014-12-12T10:50:40.430" Score="4" Body="&lt;p&gt;Spiders are naturally attracted to areas where preys are abundant, insects are primary source of spider prey. So you must create proper environment for insects in your home,  lights to attract nocturnal insects, flowers to attract butterflies and moths are attracted towards decaying vegetation(It may make your place smelly). Once insects are abundant then spiders are attracted towards these areas. Some parasitic wasps are predator to spiders like those belonging to Ichneumonidae, try to avoid these species. Also you can collect spider eggs and place it inside your home, so they will hatch out in your place.Some times you can see web full of spider nymphs, take it out and place it in your home.&lt;/p&gt;&#xA;&lt;p&gt;Attracting spider to home can be achieved through buying some spider traps like poison free spider glue, which contains pheromones. Spiders are attracted to it and they will stick on them and eventually die, so you need to be careful and use the phenomenal effect of the spider trap to attract spiders or it will be dead and become useless.&lt;/p&gt;&#xA;&lt;p&gt;The analysis revealed that the wasp spider pheromone is methylcitric acid trimethyl ester, a derivative of citric acid.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Some other techniques to attract spiders&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;An unspecified Cheiracanthium species is attracted to the smell of petroleum and has caused problems by weaving webs inside the canister vent of particular models of Mazda vehicles, resulting in blockages and build-up of pressure that could potentially cause fuel leakage from the fuel tank and an increased risk of fire. Mazda issued a voluntary recall of Mazda 6 models built between 2010-2012, to fit them with software which would alert drivers if problems were developing.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cheiracanthium&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;A spider that preys on the malaria-carrying mosquito is attracted to the odour of people's smelly socks, say scientists.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://news.bbc.co.uk/earth/hi/earth_news/newsid_9398000/9398408.stm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Eugenol baited traps we found seven individuals of two species of Thomisidae. In contrast, with the control traps, no Thomisidae were caught . Since Thomisidae were caught only in traps baitedwith eugenol, whereas no crab spiders were attracted to control traps, we postulate that eugenol served as an attractant for these spiders.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.americanarachnology.org/joa_free/joa_v26_n1/joa_v26_p117.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-12T10:50:40.430" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="25810" PostTypeId="2" ParentId="16045" CreationDate="2014-12-12T13:18:38.007" Score="3" Body="&lt;p&gt;Interesting question!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There has been at least one study that bypassed a spinal lesion site with autografted neuronal tissue (&lt;a href=&quot;http://online.liebertpub.com/doi/abs/10.1089/089771502320317069&quot; rel=&quot;nofollow&quot;&gt;Tadie et al., 2004 - doi:10.1089/089771502320317069&lt;/a&gt;). The study participant regained voluntary motor skills 8 months after bypass surgery. The surgery involved the implantation of nerve autografts between the rostral spinal ventral horn and the caudal ventral roots. Regain of motor function was observed after the patient had been paralyzed for 3 years. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2014-12-12T13:18:38.007" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25811" PostTypeId="2" ParentId="24775" CreationDate="2014-12-12T13:52:11.310" Score="2" Body="&lt;p&gt;As WYSIWYG pointed out, fastq-dump can output to STDOUT, so if you want to combine it with named pipes, you'd do:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;mkfifo mydata.fifo&#xA;fastq-dump -Z mydata.sra &amp;gt; mydata.fifo &amp;amp;&#xA;cat mydata.fifo # or whatever&#xA;rm mydata.fifo&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;If you try to catch the output from fastq-dump without &lt;code&gt;-Z&lt;/code&gt; it fails with the &lt;code&gt;Illegal seek(29)&lt;/code&gt; error:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;mkfifo mydata.fastq&#xA;fastq-dump mydata.sra &amp;amp;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;By the way, be careful with your downstream analyses: if the input is to be read more than once, respective program will fail to re-read from your pipe. For single-end data and Trinity that's probably not the case, but I suspect that for paired-end data Trinity will attempt to read the input files at more than one step.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-12-12T14:20:08.437" LastActivityDate="2014-12-12T14:20:08.437" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25815" PostTypeId="1" AcceptedAnswerId="27640" CreationDate="2014-12-12T16:51:32.830" Score="3" ViewCount="196" Body="&lt;p&gt;We have an old BioRad ICycler Thermal Cycler with MyIQ single color fluorescent detector. While it's meant for RT-PCR, we've been using it for melt curves and binding assays for different types of RNA using thiazole orange as the intercalating fluorophore. However, when we tried to get serious about this assay and do things in triplicate we noticed that the well to well variation was terrible, making statistical significance difficult to get.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After reading through the manual I tried to get &quot;persistent well factors&quot; for the instrument to correct for this variation. However, the instrument's protocol for this requires heating to 95⁰C, so intercalating fluorophores won't work, the RNA melts and fluorescence is lost, so I tried with fluorescein. This didn't solve the variation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I tried to make my own well factors by making 10mL of Poly(rA) Poly(rU) RNA solution with thiazole orange and filling 96 PCR tubes with 100µL each and measuring fluorescence. Then I calculate the average fluorescence and divided the average by the value for each well to determine a factor, F, for each well. Then I tried to normalize subsequent experiments by multiplying each well's fluorescence by its F to get a corrected value. However, while this reduces the variation a little, it's still pretty bad.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you have any suggestions to reduce the well to well variation in these experiments or otherwise correct the data?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have no prior experience with RT-PCR instruments, everything I know about it comes from playing around with the instrument. I don't know if I'm missing something really basic. &lt;br&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Step by step protocol&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Prepared 1xSSC buffer, 150mM NaCl, 15mM Sodium Citrate, pH 7.5&lt;/li&gt;&#xA;&lt;li&gt;Weighed 5mg Thiazole Orange, dissolved in 1mL Methanol&lt;/li&gt;&#xA;&lt;li&gt;Diluted Thiazole Orange 1000 fold in 1xSSC&lt;/li&gt;&#xA;&lt;li&gt;Took 71.4µL (100µg) Poly(rU) Poly(rA) solution, 1.4µg/uL&lt;/li&gt;&#xA;&lt;li&gt;Diluted RNA with 8.93mL 1xSSC&lt;/li&gt;&#xA;&lt;li&gt;Added 100µL diluted Thiazole Orange to diluted RNA, final volume 10mL&lt;/li&gt;&#xA;&lt;li&gt;Set up 96 PCR tubes, used 8 channel pipette and trough to transfer&#xA;100µL RNA solution to each&lt;/li&gt;&#xA;&lt;li&gt;Placed PCR tubes in all 96 positions of thermal cycler&lt;/li&gt;&#xA;&lt;li&gt;Ran melt curve protocol, start at 25⁰C, increase 1⁰C every cycle,&#xA;60 cycles, so final temp is 85⁰C. Each cycle is 10 seconds. &#xA;Measure fluorescence every cycle.&lt;/li&gt;&#xA;&lt;li&gt;Repeated melt curve 3 times, total of 4 curves.&lt;/li&gt;&#xA;&lt;li&gt;Put data from each curve into spreadsheet. 96 data points at each temperature. &lt;/li&gt;&#xA;&lt;li&gt;Averaged fluorescence across the whole plate at each temperature.&#xA;Used this average, standard deviation, maximum, and minimum &#xA;values to make the plots below.&lt;/li&gt;&#xA;&lt;li&gt;Calculated correction factors for each well at each temperature by &#xA;dividing the whole plate average fluorescence by each well's &#xA;fluorescence for melt curves 2, 3, and 4. Averaged correction factors from each curve.&lt;/li&gt;&#xA;&lt;li&gt;Calculated corrected fluorescence for curves 1, 2, 3, and 4 by &#xA;multiplying the averaged correction factor for each well by the &#xA;observed fluorescence for that well.&lt;/li&gt;&#xA;&lt;li&gt;Replotted the corrected values to show reduced variation.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Data is shown below. I repeated the melt curve 4 times because the first melt usually has a lower intensity than subsequent melts. Y axis is fluorescence, X axis is temperature in celsius, and I plotted the average fluorescence at each temperature with the standard deviation along with the minimum and maximum to show how far outside the standard deviation some wells are falling. I calculated the correction factors for melt curves 2, 3, and 4 and averaged them. When I used these averaged factors on melt curves 2, 3, and 4 it did a good job at eliminating variation. When I applied the correction factors to melt curve 1, it reduced the variation, but not by much.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IoJGX.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="3340" LastEditDate="2014-12-14T06:34:17.803" LastActivityDate="2015-01-13T13:04:06.490" Title="Well to well variation in thermal cycler fluorescence?" Tags="&lt;lab-techniques&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="25820" PostTypeId="2" ParentId="24775" CreationDate="2014-12-12T20:17:08.147" Score="1" Body="&lt;p&gt;Okay, so just for others who might stumble upon this, here is a brief description of one implementation of this technique to run with paired-end RNA-seq data:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;fastq-dump SRA_file --split-files -I -Z | tee &amp;gt;(grep '@.*\.1\s' -A3 --no-group-separator &amp;gt; namedPipe_1) &amp;gt;(grep '@.*\.2\s' -A3 --no-group-separator &amp;gt; namedPipe_2) &amp;gt;/dev/null&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This first requires the creation of two named pipes using mkfifo. For paired-end data, the &lt;code&gt;-Z&lt;/code&gt; flag becomes problematic because it forces the data into a single stream. There are many ways to regain the two pairs, but the way I've elected to do it is to use &lt;code&gt;--split-files&lt;/code&gt; to break up the stream beforehand, &lt;code&gt;-I&lt;/code&gt; to append either &quot;.1&quot; or &quot;.2&quot; to the end of each header, and then use &lt;code&gt;tee&lt;/code&gt; to duplicate the stream plus grep with a regex to parse the info from each pair back out into separate pipes for downstream use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tested this with Trinity, running on each named pipe just as I would with a FASTQ file, and it seems to be working fine. While I am not 100% sure that Trinity won't try and go back to the original FASTQ files, the first thing Trinity does is take those FASTQ files and parse them into FASTA format, which it later concatenates into &quot;both.fa&quot;, and so I'm pretty confident that this will work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE: This implementation will not work (at least, not as far as I can tell) with the Trimmomatic plugin for Trinity. Something seems to get screwed up because of the way Trimmomatic pulls from the streams - just a cautionary note, I haven't figured out the cause.&lt;/p&gt;&#xA;" OwnerUserId="5598" LastEditorUserId="5598" LastEditDate="2014-12-19T19:18:20.597" LastActivityDate="2014-12-19T19:18:20.597" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25822" PostTypeId="2" ParentId="13942" CreationDate="2014-12-12T21:16:49.797" Score="1" Body="&lt;p&gt;Problems:&#xA;Where are the anti-antibodies created? In a mouse or in a human? Well, of course, you can't use humans to create antibodies so we are left with mice. So what's  wrong with that?&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Anti-antibodies &lt;strong&gt;will&lt;/strong&gt; be created to the Fc (the constant section of the antibody) region of the antibody because the antibody is foreign and is treated as a foreign antigen. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;So, you would have to use chimeric (or humanized) antibodies... I believe they are pretty expensive and takes a long time to make. Let's see that in current time. By now, I am sure you have heard about ZMapp, the drug that treats Ebola. Well, creating that drug is similar to this because they are creating antibodies as well. But I heard that a few doses of this drug takes &lt;strong&gt;3-6 months&lt;/strong&gt; to make! In this &lt;a href=&quot;http://www.latimes.com/science/la-sci-ebola-zmapp-20140903-story.html#page=1&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; , it mentions that it takes half a year to make ZMapp! &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In conclusion, it's a real challenge, which is why we haven't found drugs that work like how you describe out in the market... But it's nice that you are thinking about this stuff...&lt;/p&gt;&#xA;" OwnerUserId="10401" LastActivityDate="2014-12-12T21:16:49.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25823" PostTypeId="1" CreationDate="2014-12-12T21:18:40.420" Score="0" ViewCount="93" Body="&lt;p&gt;In a previous post of mine, I asked how to supress the creation of anti-antibodies in vivo. In the answer, it was mentioned that site-directed mutagenesis could be used. Currently, I can't find mcuh on how to do so... How does this work?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update: As people want to know where this idea is coming from, here is the link to my previous question about it.. look in the answer for more info:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/24483/how-to-inhibit-formation-of-specific-antibodies-to-antisera&quot;&gt;How to inhibit formation of specific antibodies (to antisera)?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-12-12T22:00:33.013" Title="How can site-directed mutagenesis be used to suppress the production of anti-antibodies?" Tags="&lt;immunology&gt;&lt;biotechnology&gt;&lt;antibody&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="25825" PostTypeId="1" AcceptedAnswerId="27614" CreationDate="2014-12-12T22:17:28.090" Score="4" ViewCount="773" Body="&lt;p&gt;One can classify the effects of Transcription Factors (TF) on gene expression into two types: it either enhance or repress the gene expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have always been told that most of transcription factors functions act to enhance gene expression rather than repress gene expression. &lt;em&gt;Assuming this is true&lt;/em&gt;, my question is &lt;strong&gt;why are activators more common than repressors?&lt;/strong&gt;. Is there for example a mechanistic explanation for that (cost less energy to enhance or the enhancement pathway is easier to evolve)?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Transcriptional_regulation#Enhancers&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;While activators can interact directly or indirectly with the core machinery of transcription through enhancer binding, repressors predominantly recruit co-repressor complexes leading to transcriptional repression by chromatin condensation of enhancer regions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The mechanisms are different and it sounds a likely cause of the overrepresentation of enhancement function of transcription factors in genomes but it is not obvious to me why activators and repressors have to have use different mechanisms and it is not obvious to me either why these different mechanisms would yield to a ratio of repressors to activators other than $\frac{1}{2}$.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-12-12T23:43:26.863" LastActivityDate="2015-01-12T16:23:43.437" Title="Why are most transcription factors enhancing the expression rather than repressing?" Tags="&lt;transcription&gt;&lt;gene-regulation&gt;&lt;transcription-factor&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="25826" PostTypeId="1" CreationDate="2014-12-12T22:46:20.217" Score="5" ViewCount="996" Body="&lt;p&gt;I am wondering about the logistics of a simple experiment with say 3 types of alcohols, and various concentrations of each, with a control(s)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to research the effects of alcohol on mitosis. Do I need any expensive equipment or is it do-able with standard equipment? I am looking specifically at what I expect to be a negative impact on cell growth. Potential cell death and slowing of mitosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;We expect mitosis to slow and stop entirely or become corrupted as the amount of alcohol used increases. Of the three alcohols we will be testing, we expect some to be more damaging than others. The 3 chosen alcohols, listed in order of their hypothesised toxicity are Methanol, Ethanol and 2-methyl-2-butanol.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am basically trying to see if tertiary alcohols are safer due to ethanols main metabolites acetaldehyde &amp;amp; acetic acid being more harmful/toxic? Since Tertiary alcohols for example, aren't metabolised into aldehydes. Which makes them less toxic than ethanol in theory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now I am unsure as to which cells to use to test upon, I'm also unsure as to the legitimacy of my hypothesis. Budget, time and a lack of knowledge is against me. I am researching as much as possible as quick as possible. Thankfully I have help available soon or I would be totally out my depth. This is me out of practice in the field trying to get a head start and help a friend out as best I can. I'll be his assistant and feel thats more than appropriate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realise I can't test for too many things. I need one clear goal. If we choose to test certain cells over others do you have any suggestions? and why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The liver processes ethanol into acetaldehyde &amp;amp; acetic acid. So I would need these chemicals potentially in order to properly test ethanols effects on cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am so out of my depth I feel right now I'm hoping for a prod in the right direction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The 3 chosen alcohols, listed in order of their hypothesized toxicity are Methanol, Ethanol and 2-methyl-2-butanol. - concentrations of each yet to be considered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suffer from dyslexia and my wording is bad at the best of times. But please realize this is a very first draft / ideas on the table. Any help at all is appreciated, apologies for my lack of knowledge in the field. I'm trying to refresh my studies from 10 years ago in 2 days.&lt;/p&gt;&#xA;" OwnerUserId="11539" LastEditorUserId="10401" LastEditDate="2014-12-12T23:44:57.647" LastActivityDate="2014-12-14T08:53:55.390" Title="Studying effects of alcohol on cells" Tags="&lt;cell-culture&gt;&lt;mitosis&gt;&lt;cell-biology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25828" PostTypeId="2" ParentId="25826" CreationDate="2014-12-12T23:48:35.427" Score="4" Body="&lt;p&gt;Great idea! It seems that this research has been done before and your hypothesis is correct, but testing a wide variety of alcohols and testing your hypothesis for each one of them would be a great project.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, to do this, I would expect you would need to check the growth of the cells after certain periods of time. How would you do this? Well, the best device would be a hemocytometer. It looks like the price varies from 10.00 - 400.00 which is pretty cheap. Of course, there would be mitosis if there is growth during periods of time, which means there would be more cells after certain periods of time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What cells to choose? I would choose something easy to work with, such as &lt;em&gt;E.coli&lt;/em&gt;. It is safe and easy to work with. It needs minimal resources. Here's a link to a simple culture you can probably make at home:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://makezine.com/projects/how-to-make-bacterial-brothagar/&quot; rel=&quot;nofollow&quot;&gt;http://makezine.com/projects/how-to-make-bacterial-brothagar/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Later, however, when you get good data, you can use mammalian and human cells to show that the research is relevant to human beings. However, mammalian cells are harder to grow because mammalian cells grow slower than bacteria and fungi and moreover contamination can cause problems. You would also need biosafety cabinets or laminar flow hoods and learn of aseptic and sterile technique.&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="3340" LastEditDate="2014-12-14T07:02:06.553" LastActivityDate="2014-12-14T07:02:06.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25829" PostTypeId="2" ParentId="25826" CreationDate="2014-12-13T00:08:58.353" Score="4" Body="&lt;p&gt;Based on T Abraham's answer, a hemocytometer would work. However, a hemocytometer requires a microscope, but if you are in a cell lab, you probably have access to a microscope. I would recommend using mammalian cells instead of bacteria, they're larger and easier to see, and more relevant to human health. If you're interested in liver toxicity in particular, try getting HepG2 cells. These are human liver cancer cells, but extra paperwork might be involved because they can potentially carry hepatitis virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Should also use trypan blue staining with your hemacytometer to mark live and dead cells. Dead cells can't export the dye and turn dark.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, an &lt;a href=&quot;http://en.wikipedia.org/wiki/MTT_assay&quot; rel=&quot;nofollow&quot;&gt;MTT assay&lt;/a&gt; is a nice way to measure cell viability if you have access to 96 well plates and plate readers. Using a cuvette based spectrophotometer is possible with this assay if you can grow your cells in larger containers, such as 10cm dishes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hemacytometer assay can get you total cells and percent of cells that are alive. The MTT assay tells you number of live cells. To get percent of cells that are alive you need a control that represents 100% viable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neither of these can tell you much about mitosis specifically, just the number of cells and percent viability. &lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2014-12-14T07:18:35.037" LastActivityDate="2014-12-14T07:18:35.037" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25830" PostTypeId="1" CreationDate="2014-12-13T00:15:40.003" Score="3" ViewCount="4237" Body="&lt;p&gt;I understand that too much close reading will strain the ciliary muscles of the eyes. But what about small fonts? The contraction of the ciliary muscles is dependent on the distance not font size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, it is better to read from a closer monitor with bigger font or from a further monitor with smaller font?&lt;/p&gt;&#xA;" OwnerUserId="11541" LastEditorUserId="3553" LastEditDate="2014-12-13T08:14:36.087" LastActivityDate="2014-12-13T17:01:33.443" Title="Why do small fonts strain the eyes?" Tags="&lt;eyes&gt;&lt;vision&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25840" PostTypeId="1" AcceptedAnswerId="25846" CreationDate="2014-12-13T09:01:19.283" Score="9" ViewCount="741" Body="&lt;p&gt;If the bones are not connected to the brain, how is their growth controlled?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question is not a duplicate of the question &lt;a href=&quot;https://biology.stackexchange.com/questions/21650/mechanisms-of-bone-growth&quot;&gt;Mechanisms of bone growth&lt;/a&gt;, as this question deals with &lt;em&gt;how&lt;/em&gt; bone growth is &lt;em&gt;controlled&lt;/em&gt;, and not &lt;em&gt;which bone structures or bone tissues&lt;/em&gt; are involved.&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2014-12-15T01:56:51.763" Title="How are bones growing, if bones are not connected to the brain?" Tags="&lt;human-biology&gt;&lt;neuroanatomy&gt;&lt;bone-biology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25845" PostTypeId="1" CreationDate="2014-12-13T11:15:21.467" Score="1" ViewCount="56" Body="&lt;p&gt;I'm a computer scientist and implementing a heart-rate monitor for physical exercise. While I try to improve my code, I stumbled over the question how fast the heart rate can change within a given time slot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say someone in rest has a pulse of 60bpm. If he now gets physically active and exploits himself, how much time will it take at least to reach his maximum pulse of (supposed) 200? How long will it take, after hitting that point to slow down his heart rate again?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or to rephrase the question, so it fit's more to my specific code-problem.&#xA;How much can the pulse change (increase/decrease) within a small time-slot of, let's say 8 seconds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Annotation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Susan pointed out, that might be dependent on the trainings-state of each individual. If so, what is (might be) the highest possible increase/decrease?&#xA;I suppose the pulse increase of a bad trained person might be faster then that of a well trained person, whereas the the decrease of the pulse should be way faster of that trained person.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Annotation 2:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question was already posted here: &lt;a href=&quot;https://biology.stackexchange.com/questions/5021/how-quickly-can-the-human-heart-rate-rise-and-fall&quot; title=&quot;How quickly can the human heart rate rise and fall&quot;&gt;How quickly can the human heart rate rise and fall&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But not really answered. The answer here says, the rate can change within one beat. But it does not say by how much it can change, which bothers me. Especially &lt;em&gt;how much it can change within a given period.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="11548" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-12-13T14:40:53.890" Title="Maximum heart rate increase/decrease while physically active" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2014-12-13T20:23:35.967" ContentLicense="CC BY-SA 3.0" />
  <row Id="25846" PostTypeId="2" ParentId="25840" CreationDate="2014-12-13T13:07:06.673" Score="7" Body="&lt;p&gt;The &lt;strong&gt;developmental growth&lt;/strong&gt; of bone tissue is hormonally controlled. It is, as far as I know, not under direct neuronal control. Before reaching adolescence, the long bones (mainly in the arms and legs) grow in the epiphyseal plate, the area of the bone where cartilage is formed and ossified on the diaphyseal side, thereby lengthening the bone. The longitudinal growth of long bones continues until early adulthood at which time the chondrocytes in the epiphyseal plate stop proliferating and the epiphyseal plate transforms into the epiphyseal line as bone replaces the cartilage (&lt;a href=&quot;https://www.boundless.com/biology/textbooks/boundless-biology-textbook/the-musculoskeletal-system-38/bone-216/growth-of-bone-818-12061/&quot; rel=&quot;nofollow noreferrer&quot;&gt;boundless website&lt;/a&gt;). The growth and stop of growth in adulthood is hormonally controlled. Bone tissue growth is controlled by various hormones including &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12433064&quot; rel=&quot;nofollow noreferrer&quot;&gt;parathyroid hormone&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12868124&quot; rel=&quot;nofollow noreferrer&quot;&gt;growth hormone&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Growth hormone (GH) is secreted by the pituitary, in turn controlled by the hypothalamus in the brain. So although the brain is involved, it is not directly involved, in that it regulates growth, and cessation of it through hormone release. Growth hormone is probably the most important hormone and is released by the pituitary, but parathyroid hormone released by the thyroid, among other hormones, may play a role as well.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: Your question implies bone growth, which at first seemed to point toward developmental growth to me. However, there is also the more dynamic control of bone mass due to the forces that act on them in everyday life, referred to as &lt;strong&gt;bone mass accrual&lt;/strong&gt;. This process is controlled by the sympathetic and parasympathetic system (&lt;a href=&quot;http://www.pnas.org/content/109/38/15455.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bajayo et al., 2012&lt;/a&gt;): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ESoQx.gif&quot; alt=&quot;direct neuroal control of bone growth&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This system acts through direct neural innervation of bone tissue and stimulates bone formation when needed (after imposed strain on the skeletal system), but by default stimulates the breakdown (resorption) of bones to salvage its components for other uses (use it or loose it principle). So yes, the skeletal system is directly connected to the brain (with credits to @anongoodnurse). &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-14T12:33:29.387" LastActivityDate="2014-12-14T12:33:29.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25848" PostTypeId="1" AcceptedAnswerId="25849" CreationDate="2014-12-13T15:43:57.853" Score="4" ViewCount="12255" Body="&lt;p&gt;So I found this tiny bug on my wall in the bedroom of my apartment. I estimate it is about 3mm long by 1mm wide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1CTK8.jpg&quot; alt=&quot;Unknown Bug&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/aA6pE.jpg&quot; alt=&quot;Close up unknown bug&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it a bed bug? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It does not seem to match any of the pictures I've seen online.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The apartment is very clean by most standards. The only other bug I've seen in here is the odd stink bug.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Northeast coast of USA. &lt;/p&gt;&#xA;" OwnerUserId="11550" LastEditorUserId="16866" LastEditDate="2017-12-08T04:31:33.247" LastActivityDate="2017-12-08T04:31:33.247" Title="Bug Identification: Is this small tubular, black bug a bed bug?" Tags="&lt;species-identification&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="25849" PostTypeId="2" ParentId="25848" CreationDate="2014-12-13T16:01:15.320" Score="6" Body="&lt;p&gt;I'm going to suggest it is the larvae of a carpet beetle. Initially I thought possibly the Varied carpet beetle because of the lighter patches near the posterior end similar to this picture from the wiki page on this species:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/z0c08.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having said that the geographical range might not be correct so it could be a similar species so I've dug a bit deeper. There are some 120 species in North America, from this &lt;a href=&quot;https://books.google.se/books?id=aWVi0IF_jcQC&amp;amp;pg=PA210&amp;amp;lpg=PA210&amp;amp;dq=carpet%20beetle%20species%20america&amp;amp;source=bl&amp;amp;ots=N11Rs5NL7D&amp;amp;sig=pVhd_eSpUfmy5ARXSpUX7md_fW8&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=f2KMVM3VO8jKO-PQgKgN&amp;amp;ved=0CFwQ6AEwDA#v=onepage&amp;amp;q=carpet%20beetle%20species%20america&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;link&lt;/a&gt; I'd say that the Buffalo carpet beetle is a contender.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carpet beetles are classified as a pest species:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;larvae feed on natural fibers and can damage carpets, furniture, clothing and insect collections&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not all bad though, the larvae are also known as &lt;em&gt;wooly bears&lt;/em&gt;, how nice.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2014-12-13T16:01:15.320" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25850" PostTypeId="1" CreationDate="2014-12-13T16:34:58.040" Score="3" ViewCount="84" Body="&lt;p&gt;I'm attempting to replicate a cell biology method from a 1958 &lt;em&gt;Laboratory Investigation&lt;/em&gt; paper. The protocol is for the isolation of an extracellular matrix protein, and a key step is a centrifugation carried out for 2 hours at 2300 rpm. Apparently it was not common practice to list make, model, and rotor size of centrifuges, so I am a little lost as to what settings to use on my own centrifuge to get the same rcf.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any good starting points for estimating the proper settings? e.g. who the major centrifuge suppliers were at the time or what models would be seen as 'standard' for a cell biology lab?&lt;/p&gt;&#xA;" OwnerUserId="10257" LastActivityDate="2015-01-13T07:34:28.337" Title="Estimating RPM to RCF in Methods from Older Papers" Tags="&lt;cell-biology&gt;&lt;cell-culture&gt;&lt;protocol&gt;&lt;centrifugation&gt;&lt;extra-cellular-matrix&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="25852" PostTypeId="1" AcceptedAnswerId="25853" CreationDate="2014-12-13T20:52:55.507" Score="4" ViewCount="138" Body="&lt;p&gt;Nowadays it is possible to sequence the DNA of extinct species, such as the Neanderthals, the Denisovans, and others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to determine, solely from the sequenced DNA or from known bone fragments, how many chromosomes the individual (or the species represented by the individual) had?&lt;/p&gt;&#xA;" OwnerUserId="11546" LastActivityDate="2014-12-14T00:03:40.247" Title="Does DNA analysis allow determining amount of chromosomes?" Tags="&lt;dna-sequencing&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25853" PostTypeId="2" ParentId="25852" CreationDate="2014-12-13T21:01:23.870" Score="6" Body="&lt;p&gt;This depends completely on the quality of the DNA. Since each chromosome is essentially a very long strand of DNA, breakages and missing sections are very common in extinct species due to degradation over time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a full DNA read is absent, no determination of chromosomal number can be performed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming a full read (covering all breakages) of the DNA is present, the telomeres of each chromosome can be found, and since chromosomes usually only have one set of telomeres each, this may be useful for chromosomal number determination. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Caveat 1: &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosome_2_%28human%29&quot; rel=&quot;nofollow&quot;&gt;Chromosome 2 (human)&lt;/a&gt; is an example of how this method may fail, since a recently fused chromosome will still possess the tandem repeats characteristic of telomeres. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Caveat 2: Telomeres may vary in length due to the age of the cell, as well as be broken in multiple regions. Due to the tandem repeat nature of telomeres, it is nearly impossible to tell these different states apart experimentally. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2014-12-14T00:03:40.247" LastActivityDate="2014-12-14T00:03:40.247" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="25855" PostTypeId="2" ParentId="24782" CreationDate="2014-12-13T21:41:16.420" Score="16" Body="&lt;p&gt;This &lt;a href=&quot;http://aht.seriouseats.com/archives/2010/11/the-burger-lab-revisiting-the-myth-of-the-12-year-old-burger-testing-results.html&quot;&gt;controlled experiment of burger decomposition&lt;/a&gt; explains in detail why fast food burgers do not decompose easily. The same can be applied to fries, which are smaller and come dehydrated from the frying.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main take-aways from this experiment are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1: Dehydration is the main reason why fast food fries/burgers do not decompose easily. Placing the burgers in a ziplock bag, preventing dehydration, causes the burgers to decompose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2: Since an unsalted, home-made burger did not decompose, preservatives, chemicals, saturated fats, and other components are unlikely to be the case of the fast food burgers not rotting. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2014-12-13T21:41:16.420" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25856" PostTypeId="2" ParentId="24555" CreationDate="2014-12-13T22:17:18.407" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.orthochirurg.com/resources/journals/Current%20Concepts%20Review/Pathophysiology%20of%20nerve%20compression%20syndromes%20response%20of%20peripheral%20nerves%20to%20loading.pdf&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt;, while mainly dealing with chronic nerve compression, appears to explain the effects of nerve compression on the blocking the transmission of neural impulses (causing the &quot;sleeping limb&quot; syndrome).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC491778/pdf/jnnpsyc00044-0059.pdf&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; describes how the application of pressure on a nerve causes a miniature case of &lt;a href=&quot;http://en.wikipedia.org/wiki/Compartment_syndrome&quot; rel=&quot;nofollow&quot;&gt;compartment syndrome&lt;/a&gt;, where the pressure causes the intraneuron pressure to increase, leading to paresthesia. Edema also occurs within the neuron, causing pain signals to be sent out. In the experimental rats which were unable to relieve this pressure, permanent nerve damage resulted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the effects from the nerve compression exceeds a certain level, the pain/tingling will result in you releasing the pressure from the limb in order to prevent nerve damage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the nerves are still blocked from transmitting their impulses due to the  compression blockage described in Paper 1. When the blockage is resolved, the neurons are now capable of transmitting their pain signals, which continue for a period of time until the pressure within the limb falls sufficiently below the pain threshold. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2014-12-13T22:17:18.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25858" PostTypeId="1" AcceptedAnswerId="26064" CreationDate="2014-12-14T03:07:29.590" Score="6" ViewCount="3013" Body="&lt;p&gt;(Apologies if this is a too weird/inappropriate question in this forum. I only thought that I ask it since it happens to be part of human life.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The skin on a human typically blocks many substances that could be harmful for the organism. One area that is not covered by skin, however, is the &quot;glans penis&quot; (the tip of the penis). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering that the surface on this area seems to become more stretched during erection, it would look like erection causes the tip to allow more substances to pass through than otherwise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any studies about how erection affects the porosity in this area of the body?&lt;/p&gt;&#xA;" OwnerUserId="11546" LastEditorUserId="11546" LastEditDate="2014-12-14T03:20:25.333" LastActivityDate="2016-11-30T15:57:41.997" Title="Skin porosity in glans penis when erect" Tags="&lt;sex&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25859" PostTypeId="1" AcceptedAnswerId="25907" CreationDate="2014-12-14T05:18:42.943" Score="5" ViewCount="647" Body="&lt;p&gt;I have read that weight loss is an effective lifestyle modification for people with hypertension, and systolic pressure may be reduced by up to 1-2 mmHg for every 1kg of weight lost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the physiological reason for weight loss reducing blood pressure or weight gain increasing it?  Please provide a physiologically detailed response rather than simply saying that more weight means the body must work harder to pump blood.  I understand this but I want to know the mechanisms of how the body detects the increased weight and adjusts the blood pressure accordingly.  Thanks!&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2018-08-09T06:13:57.320" Title="Why does weight loss lower blood pressure?" Tags="&lt;blood-pressure&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25860" PostTypeId="1" AcceptedAnswerId="25861" CreationDate="2014-12-14T05:24:34.337" Score="8" ViewCount="693" Body="&lt;p&gt;Anticipation whereby symptoms of genetic disorders occur earlier and with more severity as it is passed from one generation to the next.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So wouldn't these inherited diseases over a few hundred generations affect offspring before they can reproduce and thus shouldn't these diseases like Huntington's disease no longer be with us today?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or are most of these genetic diseases generated through sporadic mutations at a high enough rate to persist?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2014-12-14T19:31:12.177" Title="Why do we still have genetic disorders that show anticipation?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25861" PostTypeId="2" ParentId="25860" CreationDate="2014-12-14T06:00:19.667" Score="5" Body="&lt;p&gt;I can think of 3 explanations (not mutually exclusive) for the maintenance of important genetic disorders that prevent the sick carrier to reproduce.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Following what you said, the frequency of a given allele in a population is influenced by selection, drift, migration and mutation. Some disease present at low frequency can typically spontaneously de novo appear in a population. This is typically the case of cancer and trisomy 21 where new mutations (mutation in the broad sense) likely explain a big part of why such disease do not disappear through time. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Many genetic disease are carried out by recessive alleles. In consequence, only homozygotes for the recessive allele express the disease and the disease can persist through drift. Note the interesting case of hemophilia and Malaria resistant where the heterozygote actually has higher fitness than any homozygote (heterozygote advantage), particularly in regions where there is a high prevalence of malaria. In this case, the disease is not washed out of the population not only due to drift but also due positive selection on the heterozygotes.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Many so-called genetic disease actually have an important environmental component. For the Huntington's disease, the carrier of the autosomal dominant mutation does not necessarily express the disease. From &lt;a href=&quot;http://en.wikipedia.org/wiki/Huntington%27s_disease&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;:&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The disease is caused by an autosomal dominant mutation in either of an individual's two copies of a gene called Huntingtin, which means any child of an affected person typically has a 50% chance of inheriting the disease.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As a result the Huntington's disease can still segregate thanks to drift in the healthy heterozygotes.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-12-14T19:31:12.177" LastActivityDate="2014-12-14T19:31:12.177" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25862" PostTypeId="2" ParentId="25850" CreationDate="2014-12-14T06:45:52.060" Score="1" Body="&lt;p&gt;I am not sure about what they used in 1958 (perhaps Sorvall). However you may look at recent papers for ECM protein isolation (if that was your objective).&lt;/p&gt;&#xA;&lt;p&gt;Have a look at &lt;a href=&quot;http://link.springer.com/article/10.1134%2FS1990519X09050137&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; article.&lt;/p&gt;&#xA;&lt;p&gt;From materials and methods:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;ECM protein isolation&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Fibroblasts or A431 cells were removed from the&#xA;surface of the culture plate with 2 mM EDTA in PBS for 3–5 min at&#xA;37⁰C. Detached cells were discarded, and remaining ECM proteins&#xA;attached to the surface of culture plates were washed with the same&#xA;solution. Cell removal was controlled under the microscope. After&#xA;cells were completely removed, matrix proteins were covered with 5%&#xA;acetic acid and incubated at 4⁰C overnight. Then, acetic acid was&#xA;removed and exchanged with a buffer containing 125 mM Tris-HCl, pH&#xA;6.8, 0.1% SDS, 10% glycerol, 1% DDT, 0.05 mM PMSF, protease inhibitor cocktail (Roche, Germany), and incubated at 37⁰C for 1 h. Proteins&#xA;were removed with a scraper. The procedure was repeated three times.&#xA;All protein extracts, including acetic acid, were combined and ECM&#xA;proteins were precipitated by five volumes of acetone. After&#xA;incubation at –20⁰C overnight and centrifugation at 7000 g for 15 min,&#xA;the protein pellets were dissolved in an appropriate buffer for&#xA;further analysis by one- or two-dimensional gel electrophoresis.&lt;/p&gt;&#xA;&lt;p&gt;In addition, we obtained a Triton X-100-soluble fraction of ECM&#xA;proteins. Cells were removed as described above; dishes were filled&#xA;with 1% Triton X-100 and incubated at 37⁰C for 30 min. The extraction&#xA;was repeated three times. The following procedure of ECM extraction&#xA;was the same as described above. Samples obtained from both fractions&#xA;were dissolved in a buffer for one-dimensional (Laemmli) or&#xA;two-dimensional (rehydration buffer containing 8 M urea, 2% CHAPS, 20&#xA;mM DDT, 0.1% Triton X-100) electrophoresis. Proteins that remained&#xA;after Triton X-100 extraction were dissolved in Laemmli sample buffer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-14T06:45:52.060" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25863" PostTypeId="2" ParentId="25826" CreationDate="2014-12-14T07:16:07.273" Score="3" Body="&lt;p&gt;For assaying effect of alcohol on cell growth: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;strong&gt;Prokaryotic Cells&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Take ~5ml medium (LB for &lt;em&gt;E.coli&lt;/em&gt;) in test-tubes/plastic tubes and add appropriate concentration of alcohol(s) in these.&lt;/li&gt;&#xA;&lt;li&gt;Inoculate 1% bacteria from a starter culture (OD~0.6)&lt;/li&gt;&#xA;&lt;li&gt;After different time intervals or a fixed time point take some culture, dilute and spread plate it (for each tube).&lt;/li&gt;&#xA;&lt;li&gt;Count colonies (CFU)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;strong&gt;Eukaryotic Cells&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;You can try this in a 6-well plate.&lt;/li&gt;&#xA;&lt;li&gt;Seed the cells such that they attain 60% confluency in 24 hours&lt;/li&gt;&#xA;&lt;li&gt;After 24 hours: Change the medium and add the medium with appropriate concentration of alcohol&lt;/li&gt;&#xA;&lt;li&gt;Wait for at least one division time (varies for different types of cells). 24 hours would be a fine interval for the treatment.&lt;/li&gt;&#xA;&lt;li&gt;As mentioned in the other answer, you can use MTT assay or Trypan blue to detect viable cells (It would be difficult to differentiate inviable cells from the viable ones by just looking in the haemocytometer without staining)&lt;/li&gt;&#xA;&lt;li&gt;You can use indirect assays similar in principle to bacterial spread plating; split the cells (if the cells are adherent) and inoculate a small percentage of them into another flask/plate. Count the number of cells in the new flask after 24hours.&lt;/li&gt;&#xA;&lt;li&gt;You can also do flow cytometry of cells stained with propidium iodide to identify cells in different stages of mitosis.&lt;/li&gt;&#xA;&lt;li&gt;For yeast you can simply grow them as you would grow bacteria and assess cell viability by either colony based methods or flow cytometry&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-14T08:53:55.390" LastActivityDate="2014-12-14T08:53:55.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25864" PostTypeId="1" AcceptedAnswerId="25865" CreationDate="2014-12-14T08:01:34.237" Score="3" ViewCount="1249" Body="&lt;p&gt;In the explanation of the sulfur cycle, it is often said that sulfur moves from the atmosphere to the ground by acid rain in the form of sulfuric acid. Can plants directly use sulfuric acid to assimilate sulfur?&lt;/p&gt;&#xA;" OwnerUserId="11555" LastActivityDate="2014-12-14T08:06:48.133" Title="Can plants directly use sulfuric acid?" Tags="&lt;biochemistry&gt;&lt;ecology&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25865" PostTypeId="2" ParentId="25864" CreationDate="2014-12-14T08:06:48.133" Score="2" Body="&lt;p&gt;Plants have &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20460185&quot; rel=&quot;nofollow&quot;&gt;sulfate transporters&lt;/a&gt; which they use to assimilate sulfur. Since sulfate is the conjugate base of sulfuric acid, this &lt;strong&gt;could&lt;/strong&gt; be construed as a &quot;yes&quot; for your question. Sulfuric acid would be present in its conjugate base form at physiological pH values.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it would be unwise to water your plants with sulfuric acid, as many plants have an &lt;a href=&quot;http://www.ces.ncsu.edu/depts/hort/consumer/quickref/soil/pHplants.html&quot; rel=&quot;nofollow&quot;&gt;optimal pH range&lt;/a&gt; which will quickly cause death when sulfuric acid lowers the pH of the soil below that range. As a result, areas afflicted by acid rain may require &lt;a href=&quot;http://www.elmhurst.edu/~chm/vchembook/196soil.html&quot; rel=&quot;nofollow&quot;&gt;treatment with alkaline limestone&lt;/a&gt; to resolve this issue. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2014-12-14T08:06:48.133" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="25869" PostTypeId="1" CreationDate="2014-12-14T10:15:36.603" Score="8" ViewCount="169" Body="&lt;p&gt;My algorithm learns regulatory interaction between genes using Bayesian Network approach from gene expression data. After the algorithm has converged to a network of interacting genes, how to validate that the interactions are correct? I have used Lung Cancer dataset from NCBI GEO with ID: GDS2771. Also, how to get the set of genes responsible for a disease (in this case lung cancer) , and how to quantify their expression levels as over or under expressed?&lt;/p&gt;&#xA;" OwnerUserId="11558" LastEditorUserId="3340" LastEditDate="2014-12-16T15:29:52.753" LastActivityDate="2014-12-17T08:39:00.370" Title="How to validate the regulatory interactions inferred from gene expression data?" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;gene-expression&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25870" PostTypeId="2" ParentId="25869" CreationDate="2014-12-14T10:36:33.533" Score="11" Body="&lt;p&gt;You can validate the interactions by knockding down (KD) or overexpressing (OE) a gene and checking the change in expression levels of the downstream nodes. You can do this in a high throughput fashion using microarray or RNAseq. For protein you can do an LC-MS. However this method cannot help you in:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Differentiating direct vs indirect interactions&lt;/li&gt;&#xA;&lt;li&gt;Finding regulation in case of loops and other non-linear interactions in the network&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Loops are tricky but sampling at multiple time intervals can let you know if oscillations exist or not. For most usual cases this approach works out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually this is followed by another round of validation using a relatively low throughput but sensitive technique such as &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Real-time PCR (KD vs OE)&lt;/li&gt;&#xA;&lt;li&gt;Western blots (KD vs OE)&lt;/li&gt;&#xA;&lt;li&gt;Reporter assays (KD vs OE) would detect direct interactions. For e.g. possible promoter for a (Transcription Factor) TF (upstream of gene-Y) is used to express GFP to see if GFP responds to the TF; thereby validating the effect of TF on Gene-Y via the promoter.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In some cases you may have to do ChIP-seq to find out if a gene has binding sites for a TF in its promoter/enhancer. You may also use predictions for TF binding sites. For finding regulation by miRNAs you can see &lt;a href=&quot;https://biology.stackexchange.com/questions/23452/how-to-find-mirna-binding-sites-on-a-specific-gene&quot;&gt;this&lt;/a&gt; post.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For finding complex dynamics such as pulses and oscillations you have to collect time-course data. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;how to quantify their expression levels as over or under expressed?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For that you first need to define your control (up/down regulated wrt what?). Having done that you can compare the expression and use right statistical tests to check differential regulation. If you have just one sample then most tests won't work. For RNAseq,  EM algorithms are used which use a bayesian model to obtain likelihoods and p-value (I have used cufflinks and eXpress). Then a FDR correction can be performed when comparing the test vs control. I am not very sure about algorithms used for comparing LC-MS data for proteins.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-12-17T08:39:00.370" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25871" PostTypeId="2" ParentId="2786" CreationDate="2014-12-14T13:56:38.710" Score="3" Body="&lt;p&gt;Proteins that are membrane localized or secreted would take time to become active or even become poised for activity. Membrane receptors may remain inactive until triggered by the appropriate ligand. Nonetheless proteins won't remain (inactive or active) for a very long time as constant turnover happens in the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One example, similar to what MarchHo mentioned in their answer (pre-proteins) is that of fibrinogen. Fibrinogen gets converted to fibrin when there is an injury and haemostasis reaction cascade is initiated. Fibrinogen has a biological half life (in its latency) of ~100 hours &lt;a href=&quot;http://qjmed.oxfordjournals.org/lookup/ijlink?linkType=ABST&amp;amp;journalCode=bloodjournal&amp;amp;resid=74/2/743&amp;amp;atom=%2Fqjmed%2F96%2F10%2F711.atom&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[&lt;strong&gt;ref&lt;/strong&gt;]&lt;/sup&gt;&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-15T04:56:26.567" LastActivityDate="2014-12-15T04:56:26.567" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25872" PostTypeId="2" ParentId="2786" CreationDate="2014-12-14T14:13:57.907" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Chymotrypsinogen&quot; rel=&quot;nofollow&quot;&gt;Chymotrypsinogen&lt;/a&gt; is a proteolytic protein that is translated and stored in the pancreas in an inactive form. They are only activated when they are secreted from the pancreas. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other zymogens such as apoptotic &lt;a href=&quot;http://en.wikipedia.org/wiki/Caspase&quot; rel=&quot;nofollow&quot;&gt;caspases&lt;/a&gt; have similar lengths of time between translation and use.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2014-12-14T14:13:57.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25874" PostTypeId="2" ParentId="21794" CreationDate="2014-12-14T18:46:51.783" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dihydrouracil_oxidase&quot; rel=&quot;nofollow&quot;&gt;Dihydrouracil oxidase&lt;/a&gt; can catalyse the reduction of uracil to dihydrouracil in the presence of hydrogen peroxide. The reduction of uracil to dihydrouracil can also be catalysed by &lt;a href=&quot;http://en.wikipedia.org/wiki/Dihydrouracil_dehydrogenase_(NAD%2B)&quot; rel=&quot;nofollow&quot;&gt;dihydrouracil dehydrogenase&lt;/a&gt; using NADH. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1146717/&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;, 5,6-dihydroxycytosine can be formed by treating cytosine or DNA with osmium tetroxide, an extremely strong oxidising agent. Since they are both pyrimidines (and in fact cytosine often &lt;a href=&quot;http://en.wikipedia.org/wiki/Deamination#Cytosine&quot; rel=&quot;nofollow&quot;&gt;spontaneously hydrolyses&lt;/a&gt; to uracil), uracil will also be affected by the same oxidation. 5,6-dihydroxyuracil was also detected within the oxidised DNA sample as a result of oxidation and demethylation of thymine.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The presence of 5,6-dihydroxyuracil (peak 11 in&#xA;  Fig. 1) can be explained analogously to the formation&#xA;  of 5-hydroxy-5-methylbarbituric acid from thymine on&#xA;  permanganate oxidation (lida &amp;amp; Hayatsu, 1970, 1971)&#xA;  (Scheme 2). The actual oxidation products ofcytosine, i.e.&#xA;  structures (I) and (II), were not observed in DNA. As the&#xA;  calf thymus DNA used in this work did not contain uracil,&#xA;  the uracil derivatives discussed above could not have been&#xA;  formed from uracil in DNA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2014-12-14T18:46:51.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25875" PostTypeId="2" ParentId="24555" CreationDate="2014-12-14T21:39:35.467" Score="0" Body="&lt;p&gt;According to the post you linked, paresthesia causes the &quot;falling asleep&quot; notion. According to Wikipedia, there are two types of paresthesia, transient and chronic. Transient paresthesia is the type you are describing.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Paresthesias of the hands, feet, legs and arms are common, transient symptoms. The most common, everyday cause is temporary restriction of the blood supply to an area of nerves, commonly caused by leaning or resting on parts of the body such as the legs; other causes include conditions such as hyperventilation syndrome and panic attacks. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Other places like &lt;a href=&quot;http://cdn.intechopen.com/pdfs-wm/29764.pdf&quot; rel=&quot;nofollow&quot;&gt;this link&lt;/a&gt; mention that parethesia is caused by:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;• Obdormition: Obdormition is a numbness caused by prolonged pressure on a nerve,&#xA;  such as when a leg falls asleep if the legs are crossed for a prolonged period. It&#xA;  disappears gradually as the pressure is relieved (1).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;• Whiplash: Paresthesias in the upper extremity may occur after&#xA;  whiplash injury (2), a type of cervical soft tissue injury (3). Pujol&#xA;  et al showed that 13% of patients with whiplash had associated&#xA;  paresthesias (4). Recovery usually arises within 6 months after injury&#xA;  (5).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;• Hyperventilation syndrome: Paresthesia constitutes 35% of presenting&#xA;  complaints in patients with hyperventilation syndrome (6) and may&#xA;  begin after as little as threeminute of hyperventilation (7). After&#xA;  increasing the depth or frequency of respiration, www.intechopen.com72&#xA;  Paresthesia the alkaline shift produced selectively increases Na+&#xA;  conductance and ectopic discharges in normal cutaneous afferent nerves&#xA;  can be induced (8). Other electrolytes, i.e. magnesium, potassium,&#xA;  chloride, phosphate and bicarbonate, also demonstrated significant&#xA;  changes in concentration (7).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;• Panic attack: Paresthesiae of the mouth, hands and feet are common,&#xA;  transient symptoms of the related conditions of hyperventilation&#xA;  syndrome and panic attacks. Ietsugu et al demonstrated that&#xA;  paresthesia can be used as a reliable indicator of severe panic&#xA;  attacks (9).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;• Transient ischemic attack (TIA): TIA may be manifested by&#xA;  paresthesias. Several reasons may cause TIA such as thrombosis,&#xA;  embolus, intravascular debris and blood vessels disruption. Perez et&#xA;  al. reported the initial manifestation of cardiac myxoma can be&#xA;  paresthesias caused by TIA (10). Post-ischemic paresthesia occurs when&#xA;  hyper polarization by the Na+/K+ pump is transiently halted by&#xA;  elevated extracellular K+. The electrochemical gradient for K+ is&#xA;  reversed and inward transport of K+ triggers regenerative&#xA;  depolarization (8).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;• Seizures: Paresthesia may happen during and after a partial seizure&#xA;  (11). Treatment of seizures with vagus nerve stimulation can also&#xA;  trigger paresthesias and is considered an adverse event associated&#xA;  with this treatment modality (12).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;• Dehydration: At around 5% to 6% cumulative water loss, paresthesia&#xA;  may occur.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;• Insufficient blood supply: Circulatory disorders could lead to&#xA;  transient or chronic paresthesia.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As you can see, there are many causes for paresthesia. The most common is the pressure on the nerves and the loss of loss supply.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually, the feeling quickly goes away once the pressure is relieved. But in your case, the paresthesia is delayed because it's caused by restriction of blood flow. Because it is caused by restriction of blood flow, it may take time  for the blood the reach the area and oxygenate the nerves. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does it get worse? Well, because the action of standing up causes the blood pressure and heart rate to increase, decreasing blood flow to the nerves (read the abstract of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2625838&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;). Another reason is that when standing up, there is increased pressure on the nerves, causing paresthesia. Together, these effects, may increase paresthesia for a few seconds. But when the blood flow becomes normal and the pressure on the nerve decreases, the paresthesia goes away.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There you have it! Nice and concise hopefully... @Daniel if you have more questions, you can ask them by adding a comment to this post.&lt;/p&gt;&#xA;" OwnerUserId="10401" LastActivityDate="2014-12-14T21:39:35.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25878" PostTypeId="1" AcceptedAnswerId="25896" CreationDate="2014-12-15T04:38:49.213" Score="0" ViewCount="86" Body="&lt;p&gt;In my neuro-anatomy course notes I found that the facial nerve &quot;uses&quot; the trigeminal nerve to reach its targets. However, I have yet to find any diagram or reference that indicates how this is done. How is the trigeminal nerve &quot;used&quot; by the facial nerve?&lt;/p&gt;&#xA;" OwnerUserId="5427" LastEditorUserId="9943" LastEditDate="2014-12-15T05:02:09.567" LastActivityDate="2015-01-14T22:03:12.593" Title="Relation between trigeminal and facial nerve in sympathetic response" Tags="&lt;anatomy&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25879" PostTypeId="1" AcceptedAnswerId="25881" CreationDate="2014-12-15T06:10:21.537" Score="6" ViewCount="1477" Body="&lt;p&gt;In the nitrogen cycle (ecology), it is usually described that plants can use nitrogen in the form of ammonium (NH&lt;sub&gt;4&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;) and nitrate (NO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt;). Do plants prefer one form of nitrogen over the other?&lt;/p&gt;&#xA;" OwnerUserId="11555" LastActivityDate="2015-11-13T05:10:07.380" Title="Do plants have preference for the form of nitrogen as nutrient?" Tags="&lt;biochemistry&gt;&lt;ecology&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25880" PostTypeId="1" AcceptedAnswerId="25889" CreationDate="2014-12-15T06:35:33.913" Score="42" ViewCount="3982" Body="&lt;p&gt;I was discussing this with my brother. I'm pretty sure I read somewhere that they can move.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: By movement I mean long distance migration (preferably within the brain only).&lt;/p&gt;&#xA;" OwnerUserId="11562" LastEditorUserId="16651" LastEditDate="2015-12-16T15:42:48.550" LastActivityDate="2015-12-18T16:34:19.170" Title="Can brain cells move?" Tags="&lt;cell-biology&gt;&lt;neuroscience&gt;&lt;brain&gt;&lt;development&gt;&lt;stem-cells&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="25881" PostTypeId="2" ParentId="25879" CreationDate="2014-12-15T07:32:02.780" Score="5" Body="&lt;p&gt;Quoting verbatim from &lt;a href=&quot;http://www.kno3.org/product-features-a-benefits/nitrate-no3-versus-ammonium-nh4&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; site. &lt;em&gt;The reference is not really a scientific article but you can check the references it cites. Some were not in English so I did not check. However these points are fairly logical&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nitrates are the preferred nitrogen source:  &lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;&lt;p&gt;Non-volatile: unlike ammonium, nitrate is non-volatile, so there is    no need to incorporate it in the soil when applied by top- or side dressing, which makes it a convenient source for application.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Mobile in the soil - direct uptake by the plant, highest efficiency.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;Nitrates synergistically promote the uptake of cations, such as K, Ca    and Mg, while ammonium competes for the uptake with these cations.&lt;/li&gt;&#xA;  &lt;li&gt;Nitrates can be readily absorbed by the plant and do not need to    undergo any further conversion, as is the case with urea and ammonium, before plant uptake.&lt;/li&gt;&#xA;  &lt;li&gt;No acidification of the soil if all the nitrogen is applied as    nitrate-nitrogen.&lt;/li&gt;&#xA;  &lt;li&gt;Nitrates limit the uptake of harmful elements, such as chloride, into    large quantities.&lt;/li&gt;&#xA;  &lt;li&gt;The conversion of nitrates to amino acids occurs in the leaf. This    process is fuelled by solar energy, which makes it an energy-efficient process. Ammonium has to be converted into organic N compounds in the roots. This process is fuelled by carbohydrates, which are at the expense of other plant life processes, such as plant &#xA;  growth and fruit fill.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Many plants can carry out nitrification but this is not universal. From &lt;a href=&quot;http://www.annualreviews.org/doi/pdf/10.1146/annurev.py.12.090174.001035&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nitrification is sometimes considered so universal and rapid that&#xA;  applications of NH&lt;sub&gt;4&lt;/sub&gt;-N are considered equivalent to&#xA;  NO&lt;sub&gt;3&lt;/sub&gt;-N. This is not true in many forest, orchard, and&#xA;  grassland soils.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, nitrate being more soluble is susceptible to leaching and wash off, care has to be taken when using nitrate based fertilizers. From the previously mentioned paper:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Unlike the positively charged ammonium ion, which is relatively&#xA;  stationary because of its adsorption to organic matter or clay&#xA;  particles, the negatively charged nitrate ion is freely mobile in the&#xA;  soil solution (166). Thus, leaching and denitrification primarily&#xA;  involve a loss of NO&lt;sub&gt;3&lt;/sub&gt;-N (171). Inhibition or retardation of&#xA;  nitrification of applied NH&lt;sub&gt;4&lt;/sub&gt;-N can reduce nitrogen losses,&#xA;  increase efficiency of applied N, and establish a predominantly&#xA;  ammoniacal form of nitrogen available for plant uptake (105, 171,222,&#xA;  232).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-11-13T05:10:07.380" LastActivityDate="2015-11-13T05:10:07.380" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25882" PostTypeId="2" ParentId="2786" CreationDate="2014-12-15T08:26:27.170" Score="1" Body="&lt;p&gt;One example that may interest you Rory M are the so-called toxin - antitoxin pairs in bacteria. Interestingly enough, many bacterial species need a way to protect themselves from their own toxins. Thus, for a particular toxin, a corresponding antitoxin is synthesized (most often both are proteins, but the antitoxin may be RNA as well, three types of toxin - antitoxin systems are known; check out &lt;a href=&quot;http://en.wikipedia.org/wiki/Toxin-antitoxin_system&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Toxin-antitoxin_system&lt;/a&gt;). The antitoxin remains bound to the toxin until the latter is secreted into its designated location. If the antitoxin decouples prematurely, cellular death may occur. I'm not too sure how long the two are &quot;stored&quot; within the cell; I imagine this could vary greatly between species. &lt;/p&gt;&#xA;" OwnerUserId="10001" LastActivityDate="2014-12-15T08:26:27.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25885" PostTypeId="1" AcceptedAnswerId="25886" CreationDate="2014-12-15T09:43:42.303" Score="2" ViewCount="5657" Body="&lt;p&gt;Since we &lt;em&gt;homo sapiens&lt;/em&gt; (and all other species) are continuously evolving, are humans undergoing speciation based on our environment? OR has there been any difference across people that could say speciation has already happened?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: I am asking this question because I have recently seen a documentary in which some Chinese anthropologists claim that Chinese people are a different species altogether. Ref: &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Incredible_Human_Journey&quot; rel=&quot;nofollow&quot;&gt;Incredible human journey&lt;/a&gt; (Section &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Incredible_Human_Journey#2._Asia&quot; rel=&quot;nofollow&quot;&gt;Asia&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="9764" LastEditorUserId="1590" LastEditDate="2014-12-15T10:11:50.050" LastActivityDate="2017-09-21T22:22:10.897" Title="Speciation of humans?" Tags="&lt;evolution&gt;&lt;speciation&gt;&lt;human-evolution&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ClosedDate="2014-12-15T15:31:08.577" ContentLicense="CC BY-SA 3.0" />
  <row Id="25886" PostTypeId="2" ParentId="25885" CreationDate="2014-12-15T10:05:36.873" Score="2" Body="&lt;p&gt;While its possible humans could speciate into two distinct groups at some point in the future, it hasn't happened recently (100 kya) and it doesn't seem to be happening now. If it were happening we would see two or more distinct populations that didn't interbreed and over time accumulated increasing differences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://johnhawks.net/graphics/skin_color_cline.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;These&lt;/a&gt; skin colors track most of the evolution we've done in the last hundred thousand years or so, and none of the people from different parts of the globe have any difficulty reproducing with any of the others. If speciation is happening it hasn't happened yet. I doubt speciation could happen given how much gene transfer there was between populations just on foot and boat, never mind planes and trains. Although, speciation does not require physical isolation to occur. See Wallace Effect and sympatric speciation. If there's enough pressure agaist hybridization, human speciation could occur. Think blue collar versus white collar worker and the disappearing middle class.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Speciation has certainly happened with humans before. Not with 'evolutionarily modern' humans, but 'evolutionarily modern' is mostly defined as 'humans since the last speciation event', so that's tautological. But Homo erectus, the neanderthals, the denisovans, et cetera(seriously, there's a lot of Homo species) were all descendants from one common ancestor. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the idea that Chinese people are a different species, or descended from Homo erectus? See the geneticist from the documentary who mapped out the genetics of the Chinese population. Archeological and skeletal evidence is easily blurred, but the genetics can't be explained without an out of africa theory. &lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="-1" LastEditDate="2017-09-21T22:22:10.897" LastActivityDate="2017-09-21T22:22:10.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25887" PostTypeId="2" ParentId="5007" CreationDate="2014-12-15T10:25:00.853" Score="3" Body="&lt;p&gt;Modern humans are continuing to evolve. Let me give you an example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before cattle were domesticated over 99% of all adults were lactose-INtolerant (i.e., they did not produce the enzyme needed to break down lactose (lactase) and could not digest it, i.e. got diarrhoea if they drank milk). All infants produce this enzyme, but in lactose-intolerant people the gene that codes the enzyme responsible for breaking down lactose becomes suppressed after the age of 1 or so. Before domestication of cattle, lactose-intolerant people were by far the majority in any human population. Why? Because if you never consume milk, constantly producing an unneeded enzyme is a huge waste of protein, especially in conditions of limited food supply. With the domestication of cattle, people who could utilize lactose suddenly had a huge advantage - they had another source of protein and calcium. They quickly became bigger and stronger than people who could not consume dairy products in adulthood. Thus, people in Europe and Africa (where cattle were domesticated) quickly became lactose-tolerant, unlike people in Asia, where to this day most people are lactose-intolerant. The evolutionary pressure at that time was huge - people in Europe and Africa went from mostly lactose-intolerant to mostly lactose-tolerant in 10 000 years or so. Interestingly enough, in this respect cats evolved in parallel to humans and now cats in Europe are predominantly lactose-tolerant, whereas cats in Asia are mostly lactose-intolerant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, this is not the only change that has occurred within the last 10 000 years and it surely is not the last one that will take place. It is just an illustrative (and hopefully interesting) example of evolution and natural selection in modern humans. In what direction humans will evolve in the future is very speculative.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As requested, a couple of references: &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/news/070401_lactose&quot; rel=&quot;nofollow&quot;&gt;http://evolution.berkeley.edu/evolibrary/news/070401_lactose&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.smithsonianmag.com/arts-culture/lactose-tolerance-and-human-evolution-56187902/?no-ist&quot; rel=&quot;nofollow&quot;&gt;http://www.smithsonianmag.com/arts-culture/lactose-tolerance-and-human-evolution-56187902/?no-ist&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10001" LastEditorUserId="10001" LastEditDate="2014-12-16T00:52:45.623" LastActivityDate="2014-12-16T00:52:45.623" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25889" PostTypeId="2" ParentId="25880" CreationDate="2014-12-15T11:29:02.487" Score="60" Body="&lt;p&gt;The question is relatively broad and one should take into account that the brain not only consists of &lt;em&gt;neurons&lt;/em&gt;, but also &lt;em&gt;glial cells&lt;/em&gt; (supportive cells) and &lt;em&gt;pre-mitotic neuronal stem cells&lt;/em&gt;. Furthermore, as critical fellow-scientists have indicated, developmental stage is very important, as the developing embryonic brain is very different from the adult brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, after sifting through various publications, the answer to the question is actually remarkably simple: &lt;strong&gt;Yes, brain cells migrate.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In  the &lt;strong&gt;adult brain&lt;/strong&gt; glial cells migrate in the brain (&lt;a href=&quot;http://www.nature.com/nrn/journal/v10/n11/abs/nrn2720.html&quot;&gt;Klämbt, 2009&lt;/a&gt;). Glial cells are involved in a myriad of functions, but a notable example of migrating glial cells are the oligodendrocytes that migrate relative long distances to find their target axons onto which they wrap themselves to form the insulating myelin sheath (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0166223600020968&quot;&gt;Tsai and Miller, 2002&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neuronal stem cells migrate over long distances in response to injury (&lt;a href=&quot;http://www.pnas.org/content/101/52/18117.full.pdf+html&quot;&gt;Imitola et al., 2004&lt;/a&gt;) and they migrate from specific stem-cell locations (e.g., hippocampus and subventricular zone) to other regions (&lt;a href=&quot;http://www.nature.com/bmt/journal/v32/n1s/full/1703937a.html&quot;&gt;Clarke, 2003&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, post-mitotic (fully differentiated, not-dividing) neurons can also be migratory in the adult brain. Specifically, newly formed neurons can migrate over hundreds of microns in fish (&lt;a href=&quot;http://www.jneurosci.org/content/32/4/1436.full&quot;&gt;Scott et al., 2012&lt;/a&gt;) and neuronal migration has been shown in the human cortex as well (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0896627300806510&quot;&gt;Fox et al., 1998&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not surprisingly, glial cells, stem cells and neurons also migrate during &lt;strong&gt;embryonic development&lt;/strong&gt;. Most notably, post-mitotic neurons destined to fulfill peripheral functions have to migrate over relatively long distances from the neural crest to their target locations (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10831/&quot;&gt;Neuroscience, 2&lt;sup&gt;nd&lt;/sup&gt; ed, Neuronal Migration&lt;/a&gt;).  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-16T04:22:53.143" LastActivityDate="2014-12-16T04:22:53.143" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="25890" PostTypeId="1" CreationDate="2014-12-15T13:58:04.640" Score="3" ViewCount="355" Body="&lt;p&gt;Circulating factors present in young &lt;strong&gt;mice&lt;/strong&gt; have been shown to promote rejuvenation of aged mice, suggesting that tissues have inherent capabilities to regenerate, and circulating factors may be promoting/inhibiting this [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24988454&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically; supplementation of GDF11 (growth and differentiation factor 11) can reverse some effects of ageing (muscle tissue rejuvenates, and some degree of cognitive improvements) [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24797481&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;]; conversely circulating CCL11 impairs neurogenesis in aged mice and causes cognitive impairment [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21886162&quot; rel=&quot;nofollow noreferrer&quot;&gt;3&lt;/a&gt;]. GDF11 decreases with age, CCL11 increases with age. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4t9lW.png&quot; alt=&quot;from Bitto et al 2014&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Image from Bitto et al 2014, [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24988454&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;])&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These factors (well, GDF11 at least) are not as highly expressed in humans as in mice [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18927237&quot; rel=&quot;nofollow noreferrer&quot;&gt;4&lt;/a&gt;], so the specific mechanisms may differ. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What other circulating factors been shown to affect health or longevity?&lt;/strong&gt; Particularly in humans, but other mouse (or 'higher' organisms, e.g. primates) experiments would be interesting too.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24988454&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bitto, A., and Kaeberlein, M., “Rejuvenation: it’s in our blood.,” Cell Metab., vol. 20, no. 1, pp. 2–4, Jul. 2014.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24797481&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sinha, M., &lt;em&gt;et al&lt;/em&gt;, “Restoring systemic GDF11 levels reverses age-related dysfunction in mouse skeletal muscle.,” Science, vol. 344, no. 6184, pp. 649–52, May 2014.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21886162&quot; rel=&quot;nofollow noreferrer&quot;&gt;Villeda, S., &lt;em&gt;et al&lt;/em&gt;, “The ageing systemic milieu negatively regulates neurogenesis and cognitive function.,” Nature, vol. 477, no. 7362, pp. 90–4, Sep. 2011.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18927237&quot; rel=&quot;nofollow noreferrer&quot;&gt;Souza, T., &lt;em&gt;et al&lt;/em&gt;, “Proteomic identification and functional validation of activins and bone morphogenetic protein 11 as candidate novel muscle mass regulators.,” Mol. Endocrinol., vol. 22, no. 12, pp. 2689–702, Dec. 2008.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2014-12-16T12:53:57.807" LastActivityDate="2015-01-14T07:00:15.487" Title="Circulating factors affecting human health/longevity" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;senescence&gt;&lt;health&gt;&lt;growth&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25892" PostTypeId="1" CreationDate="2014-12-15T15:00:24.853" Score="8" ViewCount="13686" Body="&lt;p&gt;Anxiety sometimes cause diarrhea, sometimes constipation, and sometimes both. It's interesting because it seems their underlying neurophysiology is somehow different. What are underlying physiological processes that lead to these two symptoms in anxious people? Particularly in terms of the activity of sympathetic and parasympathetic nervous system? &lt;/p&gt;&#xA;" OwnerUserId="4206" LastEditorUserId="6289" LastEditDate="2014-12-15T23:44:43.693" LastActivityDate="2017-02-14T07:35:32.960" Title="Why does anxiety cause diarrhea or constipation?" Tags="&lt;physiology&gt;&lt;neuroscience&gt;&lt;digestive-system&gt;&lt;autonomic-nervous-system&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25894" PostTypeId="1" CreationDate="2014-12-15T18:27:47.113" Score="3" ViewCount="67" Body="&lt;p&gt;&lt;strong&gt;Is this statement applicable to any known plant/region combinations?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Plant species X, Y, and Z are truly indigenous to region R. Other &quot;immigrant&quot; species can be destroyed by drought or harsh weather, but these species will always be part of the region R.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(all species in question are &quot;benign&quot; - like wheat; please disregard climate change and other global disasters like nuclear wars).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS. Background: I heard this statement (with specific X,Y,Z,R) attributed to a &quot;leading botanist&quot; (probably 20th century), but I don't really see how this can be true (my biology education ended in high school though; I am a mathematician by training).&lt;/p&gt;&#xA;" OwnerUserId="4152" LastEditorUserId="3624" LastEditDate="2014-12-16T14:12:17.533" LastActivityDate="2014-12-16T14:12:17.533" Title="Native vs Immigrant plants" Tags="&lt;botany&gt;&lt;ecology&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="1" ClosedDate="2014-12-16T17:24:36.057" ContentLicense="CC BY-SA 3.0" />
  <row Id="25896" PostTypeId="2" ParentId="25878" CreationDate="2014-12-15T21:20:43.980" Score="1" Body="&lt;p&gt;Certain parts of the facial nerve cooperatively share structure of trigeminal nerve. For example, to reach the sublingual gland, the chorda tympani of the facial nerve joins the mandibular branch of the lingual nerve. Additionally, to reach the lacrimal gland of the eye, the greater petrosal nerve branch of the facial nerve joins the structure of the maximallary branch of the trigeminal nerve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a pictorial demonstration of this, please refer to page 1069 of Clinically Oriented Anatomy 7th edition by Moore.&lt;/p&gt;&#xA;" OwnerUserId="5427" LastActivityDate="2014-12-15T21:20:43.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25898" PostTypeId="1" AcceptedAnswerId="25910" CreationDate="2014-12-15T23:26:59.550" Score="6" ViewCount="1018" Body="&lt;p&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/pdf/10.1146/annurev.ecolsys.37.091305.110224&quot; rel=&quot;nofollow&quot;&gt;Hansen (2006)&lt;/a&gt; in his review uses the concept of &lt;code&gt;environmental robustness&lt;/code&gt; independently of the other concepts of robustness (at pages 139 and 140) without defining it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How is the term &lt;code&gt;environmental robustness&lt;/code&gt; usually defined?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concept of robustness (aka genetic robustness) can be further decoupled into mutational robustness, developmental robustness and maybe some others. I think envirnmental robustness is one of these sub-categories of (genetic) robustness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intuitively, I understand environmental robustness as something that is very close to &lt;code&gt;plasticity in the broad sense&lt;/code&gt;. What I call &lt;code&gt;plasticity in the broad sense&lt;/code&gt; is any phenotypic response to an environment whether or not the response is adaptive or not. Therefore, &lt;code&gt;plasticity in the broad sense&lt;/code&gt; is &lt;code&gt;adaptive plasticity&lt;/code&gt; + &lt;code&gt;non-adaptive plasticity&lt;/code&gt;. I would intuitively think that a genotype is environmentally robust if the phenotype it produces varies little with environment, that is if this genotype has low plasticity (in the broad sense). Am I using a more or less standard definition of &lt;code&gt;environmental robustness&lt;/code&gt;?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-12-16T19:54:35.073" LastActivityDate="2014-12-16T19:54:35.073" Title="What is Environmental Robustness? Is it different from plasticity?" Tags="&lt;evolution&gt;&lt;ecology&gt;&lt;population-dynamics&gt;&lt;population-genetics&gt;&lt;definitions&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25899" PostTypeId="1" CreationDate="2014-12-16T00:09:40.023" Score="3" ViewCount="172" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A well-known test for consciousness in an organism is to observe its ability to recognise itself in a mirror (see wikipedia article: &lt;a href=&quot;http://en.wikipedia.org/wiki/Mirror_test&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;Mirror test&quot;&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why haven't I come across a &quot;non-visual&quot; mirror test? I.e. one that involves one of the other senses?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, how about testing for consciousness in bats by using an &quot;audio mirror&quot;, the premise being that perhaps bats may recognise themselves through &lt;a href=&quot;http://en.wikipedia.org/wiki/Animal_echolocation&quot; rel=&quot;nofollow noreferrer&quot;&gt;echolocation&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ylKTj.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;(image adapted from &lt;a href=&quot;http://scienceinseconds.com/cmsFiles/pageImages/echolocation.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;here&lt;/strong&gt;&lt;/a&gt;)&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="5005" LastActivityDate="2016-08-09T05:33:01.157" Title="Why not use non-visual self-recognition to test for consciousness in an organism?" Tags="&lt;ethology&gt;&lt;behaviour&gt;&lt;sensation&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25900" PostTypeId="2" ParentId="25899" CreationDate="2014-12-16T00:26:10.103" Score="1" Body="&lt;p&gt;Here are my thoughts.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;An animal does not chose to emit some light while they have more control over other signals they emit and may likely just not emit it. So it would not be an easy trait to study.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;More importantly, animals (almost) always receive feedback for signals they emit. When a dog barks, it can hear itself! Animals are not used to receive feedback of their appearance through a mirror and therefore they cannot evolve to respond adaptively to the signal they emitted. Any adaptive response to a new signal is either due to luck or to cognitive abilities. The advantage of the (visual) mirror is that it is uncommon and their response therefore necessarily reflects cognitive abilities. Typically, if a bat can response to the sound it produces, it doesn't mean it is able of self consciousness (Theory of Mind), it just mean that bats evolved to recognize the sound they produce.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-12-16T04:13:46.180" LastActivityDate="2014-12-16T04:13:46.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25903" PostTypeId="1" CreationDate="2014-12-16T03:42:29.113" Score="7" ViewCount="448" Body="&lt;p&gt;I'm an undergraduate currently writing a thesis on RNA secondary structure prediction, specifically building upon analysis done by the &lt;em&gt;RNAStructure&lt;/em&gt; and &lt;em&gt;Unafold&lt;/em&gt; software packages by modifying certain algorithms here and there. I'm actually not a biologist, however. I've taken all of my classes in physics and computer science, and I sort of stumbled into my current research, and since it seemed to be a good fit for my skill set I stuck with it. However this leaves me curious of a motivation for my current work. Why is RNA secondary structure prediction important and what are some of its applications?&lt;/p&gt;&#xA;" OwnerUserId="11575" LastEditorUserId="6307" LastEditDate="2014-12-16T20:16:32.930" LastActivityDate="2014-12-17T01:04:36.600" Title="Use cases of RNA secondary structure prediction" Tags="&lt;rna&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="25904" PostTypeId="2" ParentId="25903" CreationDate="2014-12-16T05:25:34.853" Score="5" Body="&lt;h1&gt;Short answer&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;I can think of at least a dozen applications for which it would be useful to know the secondary structure of a given sequence of RNA off of the top of my head. In no particular order:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Simulation/visualization of RNA&lt;/li&gt;&#xA;&lt;li&gt;Riboswitches&lt;/li&gt;&#xA;&lt;li&gt;MicroRNA&lt;/li&gt;&#xA;&lt;li&gt;RNA interference (RNAi)&lt;/li&gt;&#xA;&lt;li&gt;RNA-RNA interactions&lt;/li&gt;&#xA;&lt;li&gt;RNA-DNA interactions&lt;/li&gt;&#xA;&lt;li&gt;RNA-protein interactions&lt;/li&gt;&#xA;&lt;li&gt;Ribosomal protein expression&lt;/li&gt;&#xA;&lt;li&gt;Ribozymes&lt;/li&gt;&#xA;&lt;li&gt;Forced evolution of RNA aptamers&lt;/li&gt;&#xA;&lt;li&gt;Synthetic tRNAs with four and five base-pair codons&lt;/li&gt;&#xA;&lt;li&gt;Termination of transcription (the process that makes mRNA from DNA)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Basically anything to do with RNA, which is one of the fundamental building blocks of all living creatures.&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;More in-depth&lt;/h1&gt;&#xA;&#xA;&lt;h2&gt;Simulation/visualization of RNA&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Secondary structure (2°) forms the second (yep) level in the standard 4 level hierarchy of macromolecular structure, and consists of short-range interactions between and among residues. In RNA, 2° is usually thought of as being loosely identical with base-pairing interactions. In order to do a proper simulation/visualization you'll probably also need at least the 3° information, but 2° is important too.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Riboswitches&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;As an mRNA gets translated by a ribosome, in many cases it can form into a complex 3D structure that will affect the translation process. For example, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3454353/pdf/nihms-405790.pdf&quot; rel=&quot;nofollow&quot;&gt;some of the mRNAs that encode proteins related to the metabolism of metal ions have a riboswitch that will themselves bind to metal ions&lt;/a&gt; and inhibit/upregulate expression of the related protein. For various reasons it's usually extremely difficult to get the full 3D structure of a riboswitch, so getting to know the 2° remains an important source of information about them.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2014-12-16T18:29:02.930" LastActivityDate="2014-12-16T18:29:02.930" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="25907" PostTypeId="2" ParentId="25859" CreationDate="2014-12-16T07:21:56.433" Score="3" Body="&lt;p&gt;Weight gain increases blood pressure, the reason for this process is due to the effect of hormone called &lt;a href=&quot;http://en.wikipedia.org/wiki/Leptin&quot; rel=&quot;nofollow noreferrer&quot;&gt;Leptin&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Leptin is made by fat and circulates in the bloodstream to reach the brain, where it acts as a signal for energy reserves, adjusting both energy expenditure and the sensation of hunger – hence it is sometimes referred to as the ‘satiety hormone’.&lt;/p&gt;&#xA;&lt;p&gt;The group showed that some obese people who were lacking the hormone leptin because of a genetic disorder had low blood pressure despite being very heavy. This was also the case for people lacking the gene for the leptin receptor in the brain, meaning that the brain was unable to respond to the hormone.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cam.ac.uk/research/news/satiety-hormone-leptin-links-obesity-to-high-blood-pressure&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The team lead by Professor Michael Cowley, Monash University, Australia, in collaboration with Professor Sadaf Farooqi, from the University of Cambridge, UK suggests that the leptin signalling is necessary for obesity-induced increased blood pressure. The clinical studies in severely obese humans showed that these observations are relevant to humans.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Professor Cowley said: “High blood pressure is a well-known consequence of obesity. Our study explains the mechanism behind this link, showing that leptin, a hormone secreted by fat, increases blood pressure.”&lt;/p&gt;&#xA;&lt;p&gt;Professor Farooqi, from the Wellcome Trust-Medical Research Council Institute of Metabolic Science added: “We now know that leptin regulates both our weight and our blood pressure through its action on the brain. Targeting this action could offer a useful way of helping people fight obesity and associated problems such as high blood pressure and heart disease.”&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cam.ac.uk/research/news/satiety-hormone-leptin-links-obesity-to-high-blood-pressure&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It is thought that Leptin's only task is to activate the sympathetic nervous system connected to the brown fat and there by directly burns energy. But it is also behind the activation of sympathetic nervous system of heart and kidney, thereby increase the blood pressure.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Genetic and drug experiments in mice, they have pinpointed an area in the mouse brain that increases blood pressure when it is exposed to high leptin levels.&#xA;This region is called the dorsomedial hypothalamus, and is thought to be involved in controlling energy consumption. Their findings show that high levels in leptin do indeed boost blood pressure, via this brain region.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://ndt.oxfordjournals.org/content/15/8/1115.full.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://ndt.oxfordjournals.org/content/15/8/1115.full.pdf+html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-16T07:21:56.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25908" PostTypeId="1" AcceptedAnswerId="25963" CreationDate="2014-12-16T08:49:00.830" Score="4" ViewCount="429" Body="&lt;p&gt;&lt;strong&gt;EURASIAN MAGPIE&lt;/strong&gt; VS &lt;strong&gt;GORILLA&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lXEQK.jpg&quot; alt=&quot;Eurasian magpie&quot;&gt;   &lt;strong&gt;VS&lt;/strong&gt;   &lt;img src=&quot;https://i.stack.imgur.com/pHRs2.jpg&quot; alt=&quot;Gorilla&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How could be the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Eurasian_magpie&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eurasian magpie&lt;/a&gt;&quot; bird won the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mirror_test&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mirror Test&lt;/a&gt;&quot; where &lt;a href=&quot;http://en.wikipedia.org/wiki/Gorilla&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gorillas&lt;/a&gt; failed ?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In 1982, mirror tests on two, zoo-reared gorillas failed to demonstrate self-recognition. The authors wrote &quot;[These studies]...suggest that the gorilla may be the only great ape which lacks the conceptual ability necessary for self-recognition.&quot; In 1993, a report was published that although six gorillas had previously failed to exhibit self-recognition.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The Eurasian magpie is the only bird to pass the mirror test. Researchers applied a small red, yellow or black sticker to the throat of five Eurasian magpies where they could be seen by the bird only by using a mirror. The birds were then given a mirror. The feel of the sticker on their throats did not seem to alarm the magpies, however, when the birds with colored stickers caught a glimpse of themselves in the mirror, they scratched at their throats - a clear indication that they recognized the image in the mirror as their own. Those that received a black sticker, invisible against the black neck feathers, did not react.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mirror_test&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Birds lacks neocortex, the area where self-recognition was thought to reside. Then which part of the brain do birds like Magpies uses to process these complex cognition ?&#xA;Why do Gorillas failed the mirror test ? &lt;/p&gt;&#xA;" OwnerUserId="10294" LastActivityDate="2014-12-17T09:41:50.207" Title="How could be the &quot;Eurasian magpie&quot; bird won the &quot;Mirror Test&quot; where Gorillas failed" Tags="&lt;brain&gt;&lt;intelligence&gt;&lt;cognition&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="25909" PostTypeId="2" ParentId="25903" CreationDate="2014-12-16T09:36:39.567" Score="1" Body="&lt;p&gt;Knowing the secondary structure of nucleic acids is very useful in many cases when working with them. The simplest case, and probably the most often used case is when you order or synthesize a small RNA or DNA and actually don't want this to have any stable secondary structure. There are many methods where you use a small nucleic acid that can bind to a complementary part of another nucleic acid (hybridization). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example in PCR, which is used to amplify small amounts of DNA, you use small DNAs called primers that bind to specific parts of a larger DNA template. If those primers can form stable secondary structures by themselves, those structures would have to be broken up before the primer can bind to the template. Such competing structures can drastically reduce the efficiency of such experiments and are something that people try to avoid, e.g. by predicting secondary structures before choosing primers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also methods that use short nucleic acids with attached labels such as fluorophores. Those labeled probes bind to specific target sequences, and you can then e.g. determine with a microscope where those probes are bound. In all such techniques you don't really want secondary structures in your probes as they interfere with the binding to the actual target.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When RNA is introduced first, it is often said to be single-stranded and secondary structure is not even mentioned. But even when acting as messenger RNA, secondary structure of RNA does play a role. One mechanism for transcription termination works by forming a stem-loop within a certain range of stability, and predicting those is necessary to predict the site where transcription is terminated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also many types of regulatory RNAs, this is a very active and hot topic at the moment. The most well known are probably RNA interference (siRNA and miRNA), but there are also many ribozymes and especially in bacteria also riboswitches. I won't try to list the different types of regulatory RNAs here, there is a large number of different classes that are known, and new ones are still discovered. To understand those it is often necessary to know the secondary or tertiary structure of the RNAs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can often at least create some hypotheses on how an RNA could work by looking at the secondary structure. In riboswitches for example you typically have an on- and an off-conformation, and those can often be explained by secondary structures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the secondary structure is often not enough to understand how a specific RNA works, you still start by predicting it in most cases. In many cases you would additionally use experimental data to verify the prediction (e.g. SHAPE or inline probing). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Determining the actual three-dimensional structure of RNA is pretty hard. How hard depends heavily on the exact RNA, but it can easily take years to do this. If you're lucky you can crystallize it easily, but RNAs with flexible parts tend to not crystallize well. In that case you can do NMR to determine the structure, but that has a rather severe size-limitation and can easily take years for larger RNAs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case of NMR, knowing the secondary structure is very useful in pretty much every case. You need to assign your signals to specific bases, and this is much easier if you know the secondary structure. You can also use NMR to support or disprove specific secondary structure predictions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More reliable secondary structure prediction would be pretty nice, the current methods still fail often enough. Though there is probably a limit on how good you can get such methods for RNAs with extensive tertiary structure. &lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-12-16T09:36:39.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25910" PostTypeId="2" ParentId="25898" CreationDate="2014-12-16T09:43:02.370" Score="3" Body="&lt;p&gt;I think robustness and plasticity are different concepts, although related to each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would define plasticity as the property of a system to adapt to external changes. As defined in the wikipedia page for &lt;a href=&quot;http://en.wikipedia.org/wiki/Phenotypic_plasticity&quot; rel=&quot;nofollow&quot;&gt;phenotypic plasticity&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Phenotypic plasticity is the ability of an organism to change its phenotype in response to changes in the environment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think this definition agrees with the one in your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Robustness in biological systems, however, is defined as (&lt;a href=&quot;http://en.wikipedia.org/wiki/Robustness_(evolution)&quot; rel=&quot;nofollow&quot;&gt;wikipedia article&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Robustness of a biological system (also called biological or genetic robustness) is the persistence of a certain characteristic or trait in a system under perturbations or conditions of uncertainty.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From this article three references are cited, all of which give some definition of robustness in their introductions/abstracts:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17167519&quot; rel=&quot;nofollow&quot;&gt;Felix and Wagner (Heredity 2008):&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Robustness, the persistence of an organismal trait under perturbations, is a ubiquitous property of complex living systems.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15520792&quot; rel=&quot;nofollow&quot;&gt;Kitano (Nature Reviews Genetics 2004):&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Robustness is a property that allows a system to maintain its functions despite external and internal perturbations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15369668&quot; rel=&quot;nofollow&quot;&gt;Stelling et al. (Cell 2004):&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Robustness, the ability to maintain performance in the face of perturbations and uncertainty, is a long-recognized key property of living systems.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;All these definitions imply that robustness is the ability to remain &lt;em&gt;unperturbed&lt;/em&gt; under external or environmental perturbations. In a sense this looks like the opposite to plasticity, which is the ability to change under external perturbations. Personally, I think that robustness is accomplished because biological plasticity allows organisms to compensate (with some limits) the external perturbation in order to maintain their state.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastActivityDate="2014-12-16T09:43:02.370" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="25911" PostTypeId="2" ParentId="25892" CreationDate="2014-12-16T11:12:41.027" Score="2" Body="&lt;p&gt;Hraish is right about the relationship between emotions and &lt;a href=&quot;http://en.wikipedia.org/wiki/Gut%E2%80%93brain_axis&quot; rel=&quot;nofollow&quot;&gt;gut-brain axis&lt;/a&gt;. &lt;a href=&quot;http://en.wikipedia.org/wiki/Stress_hormone&quot; rel=&quot;nofollow&quot;&gt;Stress hormones&lt;/a&gt; released by the brain are responsible for the gut-brain reflexes. Anxiety is related to stress and stress hormones are released when anxiety is expressed by the individual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Irritable_bowel_syndrome&quot; rel=&quot;nofollow&quot;&gt;Irritable bowel syndrome&lt;/a&gt;(IBS)  symptom-based diagnosis, which is having symptoms such as chronic abdominal pain, discomfort, bloating, alteration of bowel habits, diarrhea, constipation etc.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Irritable bowel syndrome (IBS) is a functional digestive disorder characterized by abdominal pain, bloating and altered bowel habits without any organic cause.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(&lt;strong&gt;Drossman 1999b; Mulak and Bonaz 2004)&lt;/strong&gt;.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In addition, stress is able to increase visceral sensitivity either at the central and/or peripheral level. &lt;strong&gt;(Mulak and Bonaz 2004; Larauche, et al. 2011)&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Stress is enabled through the  corticotrophin-releasing factor (CRF) system (CRF, urocortins and their receptors CRF1,2), is a key factor involved in the pathophysiology of IBS.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Stress is able to modify visceral sensitivity as well as GI motility, permeability, intestinal microbiota, and immunity of the GI tract, all mechanisms that are involved in the pathophysiology of IBS. In addition, stress is able to modulate the hypothalamic pituitary adrenal (HPA) axis and the autonomic nervous system (ANS) which is the link between the gut and the CNS and an imbalance of the ANS is observed in IBS patients. The main brain areas involved in stress are the prefrontal cortex, the limbic system (e.g. the hippocampus and the amygdala) and the hypothalamus. Relations between the prefrontal cortex and the limbic system are important in the management of stress response. &#xA;  &lt;strong&gt;(Pellissier, et al. 2010a; Mazurak, et al. 2012)&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One of the most common gut related conditions seen&#xA;  by GPs and Gastroenterologists is Irritable Bowel Syndrome (IBS), previously known as&#xA;  colitis,mucous colitis, spastic colon, and spastic bowel disease.Around 10-20% of adolescents and adults have symptoms consistent with IBS (with females twice as likely as males to report IBS symptoms).&#xA;  IBS is associated with 12 months of abdominal pain or discomfort which is (1) relieved with&#xA;  defecation; and/or (2) associated with change in stool frequency and/&#xA;  or form (i.e., constipation and/or diarrhoea). IBS is also associated with other gut-related symptoms including: bloating,nausea,and excessive gas. Non-gut related symptoms include fatigue, headaches, sleep problems,and pain conditions, such as fibromyalgia.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Individuals who experience IBS also identify that their gut problems increase doing times&#xA;  of stress.Itcan become a vicious cycle-IBS is exacerbated by stress and stress is inturn increased by symptoms of IBS.With anxiety comes increased muscle tension around the gut&#xA;  (affecting gutmotility) and activation of the flight fight response, reducing blood in the gut (this is what causes butterflies in the tummy!). These physical changes cause the &#xA;  gut-brain to send signals to the brain which in turn promote further stress and distress, most commonly in the form of anxiety.For individuals with IBS (or actually most gut conditions), the ongoing worry about their gut and unproductive patterns can be very&#xA;  debilitating. It can also be the starting point for their anxiety&#xA;  and/or depression. &#xA;  &lt;a href=&quot;http://www.arcvic.org.au/component/docman/doc_view/111-the-battle-of-two-brains-simon-knowles&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;From the above definitions &lt;strong&gt;it is clear that anxiety and brain-gut relationships are valid and IBS is an important reason for gut related disorders when stress is been experienced by the person. Over 10-20 % of adults have symptoms related to IBS, which means a common type of disorder in the general public&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;http://www.intechopen.com/books/the-amygdala-a-discrete-multitasking-manager/the-irritable-bowel-syndrome-how-stress-can-affect-the-amygdala-activity-and-the-brain-gut-axis&quot; rel=&quot;nofollow&quot;&gt;Stress Affects the Amygdala Activity&lt;/a&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;http://www.arcvic.org.au/component/docman/doc_view/111-the-battle-of-two-brains-simon-knowles&quot; rel=&quot;nofollow&quot;&gt;Anxiety and the Brain-Gut-Axis&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastActivityDate="2014-12-16T11:12:41.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25912" PostTypeId="1" CreationDate="2014-12-16T12:19:09.673" Score="10" ViewCount="262" Body="&lt;p&gt;There is a dataset that contains body mass ($x$) and metabolic rate ($y$) from many different organisms. It is common to fit the data to the model of the form $y=ax^b$ and estimate the parameters $a$ and $b$ (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Kleiber%27s_law&quot;&gt;Kleiber's law&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Metabolic_theory_of_ecology&quot;&gt;The Metabolic theory of ecology&lt;/a&gt;). In doing so, it is also common to log transform $y$ and $x$ and create the linear relationship log($y$)=log($a$)+$b$log($x$) and perform linear regression analysis based on the log transformed data. Is this approach better than directly estimating $a$ and $b$ based on nonlinear regression for $y=ax^b$ (because results are different)?&lt;/p&gt;&#xA;" OwnerUserId="11555" LastEditorUserId="3624" LastEditDate="2014-12-16T14:31:49.450" LastActivityDate="2017-11-28T21:37:13.470" Title="Statistical method for characterizing the relationship between body mass and metabolic rate" Tags="&lt;metabolism&gt;&lt;statistics&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25913" PostTypeId="1" AcceptedAnswerId="25978" CreationDate="2014-12-16T15:25:42.103" Score="6" ViewCount="346" Body="&lt;p&gt;I have worked with the optimization of several viral proteins, from different viruses/families, with different results.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When &lt;a href=&quot;http://dx.doi.org/10.1186%2F1475-2859-10-15&quot; rel=&quot;nofollow noreferrer&quot;&gt;Menzella, 2011&lt;/a&gt; was published I tried that method.  I found quite the contrary result, in that randomization did far poorer than straight maximization of codon usage.  I chucked this up to working within the context of viral infection (though it was also true in transient expression from plasmid transfection under CMV promotion).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was quite excited by Pechmann and Frydman's &lt;a href=&quot;http://dx.doi.org/10.1038/nsmb.2466%20M3&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nature article&lt;/a&gt; which highlighted the importance of the location of the codon within the protein when regarding optimal vs suboptimal codon selection. Oddly enough we were able to deploy this information most successfully with the purposeful deoptimization of a protein.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pairing a locational awareness, screening for secondary structure, and then maximizing codon optimization has had the best results for more than a year.  By maximization, I mean choosing the most optimal codon in every instance that doesn't violate:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Needed restriction sites&lt;/li&gt;&#xA;&lt;li&gt;Predicated Secondary Structure&lt;/li&gt;&#xA;&lt;li&gt;Location gradient to a lesser extent (&lt;a href=&quot;http://dx.doi.org/10.1038/nsmb.2466%20M3&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;ibid.&lt;/em&gt;&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This is all well and good, but we've been having problems with my institutions preferred vendor for gene synthesis.  A post-doc that just joined my lab recommended a company I had never heard of before, and they posed an optimization strategy I had never considered before.  Instead of maximizing codon optimization, they propose a &quot;balanced&quot; codon optimization that matches the normal distribution of codons in the target organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, the codon bias for alanine in humans breaks down (roughly) as follows:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;GCC 65% &lt;/li&gt;&#xA;&lt;li&gt;GCT 20% &lt;/li&gt;&#xA;&lt;li&gt;GCA 11% &lt;/li&gt;&#xA;&lt;li&gt;GCG 4%&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;As opposed to a maximization strategy which would seek to use &quot;GCC&quot; when ever possible and only when there was an issue switch to &quot;GCT,&quot; the balanced stratgy would seek to replicate the above distribution as closely as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Has anyone tried a balanced codon approach, especially when compared to a maximization technique?&lt;/strong&gt;  My overall goal is to maximize expression of naturally poorly expressing protein.  I know that straight maximization can occasionally lead to poor expression for a variety of reasons (often fatal secondary structure), but this seems like it would hardly increase expression at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be further interested if anyone else had experience within a viral context.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that there have been a few &lt;a href=&quot;https://biology.stackexchange.com/questions/1152/which-is-more-important-for-protein-expression-mrna-structure-or-codon-optimizat&quot;&gt;related questions&lt;/a&gt;, mostly in the context of &lt;a href=&quot;https://biology.stackexchange.com/questions/836/dna-synthesis-companies-cost-per-base-turn-around-time-codon-optimization-alg/876#876&quot;&gt;E. Coli.&lt;/a&gt;  I don't think this is a duplicate, but would be willing to remove if it is seen as such.  If I run into some extra funds I may test this empirically, but often when I'm trying such a test it's only in relation to 2-3 proteins, which might not be representative.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2016-02-29T22:20:47.257" Title="Balanced vs Maximized Codon Optimization" Tags="&lt;gene-expression&gt;&lt;virology&gt;&lt;synthetic-biology&gt;" AnswerCount="2" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="25914" PostTypeId="1" AcceptedAnswerId="26010" CreationDate="2014-12-16T16:02:18.447" Score="1" ViewCount="124" Body="&lt;p&gt;&lt;a href=&quot;http://string-db.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;STRING&lt;/a&gt; has protein (amino acid sequences) mapped to a single gene ID.&#xA;I have these doubts with respect to STRING ID.&#xA;I find that&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;1.All alleles of a single gene share the same STRING ID and&lt;/p&gt;&#xA;&lt;p&gt;2.Especially in Eukaryotes, splice variants of the single gene(which might translate to different proteins) share the same STRING ID.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Does STRING take into account these two things like UniProt and have different IDs based on allelic differences and splice variants?If so,how?&lt;/p&gt;&#xA;" OwnerUserId="8135" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-18T16:19:51.767" Title="STRING ID - allelic differences and splice variants" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="25915" PostTypeId="2" ParentId="25898" CreationDate="2014-12-16T16:25:41.873" Score="0" Body="&lt;p&gt;I am just summarizing ddiez's answer with a small addition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Robustness is the ability of the system to maintain its steady state or at the very least qualitative nature of the steady state with minor changes in the parameters of the system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is different from stability which actually means the ability of the system to return to its steady state when it is slightly displaced from there. A stable system will reach the steady state irrespective of the initial condition. In multistable systems the state where the system eventually converges, will depend on the initial condition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So &lt;strong&gt;stability&lt;/strong&gt; is meant in the sense of perturbation in the &lt;strong&gt;state&lt;/strong&gt; and &lt;strong&gt;robustness&lt;/strong&gt;, of perturbation in the system &lt;strong&gt;parameters&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if you have a model and you do a random sampling of parameters drawn from a uniform distribution of lets say ±2×mean, you will end up with a many sets of parameters with fluctuations from the mean values. Now, if you solve for the steady state at each parameter value you will get a distribution. Less the variance of this distribution, more robust is the system (based on the model).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We had discussed plasticity &lt;a href=&quot;https://biology.stackexchange.com/questions/21728/definitions-of-robustness-and-canalization?rq=1&quot;&gt;in this&lt;/a&gt; post. Plasticity may be in a way synonymous with adaptive; if a system takes an input and gives an output then &lt;em&gt;how plastic a system is&lt;/em&gt; can be defined as how fast or easily does a system reach the new steady state. In this case the input is a parameter of the model and only that is changed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I put these concepts in the perspective of an organism's metabolism then:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Robustness would refer to how (in)sensitive the metabolic flux is to the minor changes in rates of different reactions (by changes in the enzyme structures perhaps). &lt;/li&gt;&#xA;&lt;li&gt;Stability would refer to whether the system gets back (or how fast it gets back) to its original state if you add some extra or remove a metabolite. &lt;/li&gt;&#xA;&lt;li&gt;Plasticity would refer to how fast would the system adapt or reach the new steady state when there is a change of diet/available nutrients. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Having said that I also feel, as fileunderwater said, that definitions are not universal and different people mean different things. Mathematically speaking environment is  an extrinsic parameter i.e. Input. Environmental robustness should mean the maintenance of the steady state response to changes in the input. This makes sense for example in the case of maintenance of body temperature in homeotherms. &lt;em&gt;Environmental plasticity&lt;/em&gt; is also important in certain situations. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-12-16T16:56:20.300" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="25916" PostTypeId="1" AcceptedAnswerId="26188" CreationDate="2014-12-16T17:00:49.857" Score="2" ViewCount="438" Body="&lt;p&gt;According to &lt;a href=&quot;https://biology.stackexchange.com/questions/16032/what-causes-paresthesia-pins-and-needles-at-a-cellular-level&quot;&gt;this excellent answer&lt;/a&gt;, the difference between &quot;pain&quot; and &quot;pins and needles&quot; (neuropathy) is that different receptors (sensory nerves) trigger in reaction to different stimuli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Different types of pain receptors (hot/cold, pressure, etc.) send pain signals to the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Different receptors are responsible for sending neuropathy signals to the brain. These receptors are usually triggered when the nerve receives a shortage of blood flow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sensory_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia Article on Sensory Receptors&lt;/a&gt;, there don't appear to be &lt;em&gt;any&lt;/em&gt; nerves that produce pins-and-needles sensations to the brain...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I ask: &lt;strong&gt;What are the specific types of nerves/receptors that send &quot;pins and needles&quot; signals to the brain?&lt;/strong&gt; What are they called?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would imagine that it either has to be a specific, specialized receptor that (perhaps) starts firing if its senses &quot;something is wrong&quot; (such as decreased bloodflow to the area, etc.), &lt;strong&gt;or&lt;/strong&gt; it's that &lt;em&gt;all&lt;/em&gt; sensory receptors are capable of firing &quot;pins and needles&quot; signals under special circumstances.&lt;/p&gt;&#xA;" OwnerUserId="11581" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-01-25T01:06:13.847" Title="What specific sensory nerves act as receptors for &quot;pins and needles&quot; (neuropathy)?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;human-anatomy&gt;&lt;pain&gt;&lt;central-nervous-system&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="25918" PostTypeId="1" CreationDate="2014-12-16T17:11:33.390" Score="0" ViewCount="134" Body="&lt;p&gt;I am definitely pro vaccination, and the question is a bit morbid because people would die, but assuming that we didn't treat or vaccinate people for fatal diseases such as Ebola or the black death, would the surviving people pass along a trait that eventually would lead to near immunity for that disease?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any examples of diseases that humans &quot;contract&quot; but they are immune to? Or any examples of immunity through human evolution?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about in animals? Are there diseases that have been naturally eradicated?&lt;/p&gt;&#xA;" OwnerUserId="11582" LastActivityDate="2014-12-16T19:09:39.427" Title="Would humans eventually evolve to fight off fatal diseases if we didn't treat/vaccinate for them?" Tags="&lt;evolution&gt;&lt;pathology&gt;&lt;epidemiology&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2014-12-16T19:10:50.777" ContentLicense="CC BY-SA 3.0" />
  <row Id="25919" PostTypeId="2" ParentId="25918" CreationDate="2014-12-16T17:29:23.603" Score="1" Body="&lt;p&gt;Sure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the Europeans settled the Americas, 90%+ of the native American inhabitants were wiped out due to diseases like smallpox that the Europeans clearly had developed resistance to. Clearly, the surviving native americans had resistance, and the Europeans had gone through some similar event previously in history.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bubonic plague that was the cause behind the black death wiped out large percentages of populations, but selected for survivors with resistance:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://news.sciencemag.org/biology/2014/02/black-death-left-mark-human-genome&quot; rel=&quot;nofollow&quot;&gt;Black Death Left a Mark on Human Genome&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Caveats:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Often evolving to fight off disease involves mass death, like with &gt;90% of the native american population dying.&lt;/li&gt;&#xA;&lt;li&gt;There is always the chance that a future pandemic can come that human biology fails to simply evolve a resistance for and gets wiped out.&lt;/li&gt;&#xA;&lt;li&gt;The Earth is changing rather quickly. The past is not a guarantee for the future.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5100" LastEditorUserId="5144" LastEditDate="2014-12-16T19:09:39.427" LastActivityDate="2014-12-16T19:09:39.427" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="25920" PostTypeId="1" CreationDate="2014-12-16T17:37:27.970" Score="2" ViewCount="545" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At least in Britain you normally come across distinct kinds of cough medicine &quot;chesty&quot;, &quot;dry&quot; and &quot;tickly&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Fvu9K.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Are &quot;chesty&quot;, &quot;dry&quot; and &quot;tickly&quot; coughs always due to microoganisms?&lt;/li&gt;&#xA;&lt;li&gt;For the types of cough that are infectious, are differences due to different species of micro-organism or the same micro-organism at different stages of its development?&lt;/li&gt;&#xA;&lt;li&gt;Do the alternative treatments (e.g. levomenthol, squill, liquorice for chesty vs. glycerol for dry/tickly) merely deal with symptoms or do they actually help fight the infection? &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Related&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A related question is: &lt;a href=&quot;https://biology.stackexchange.com/questions/17121/what-is-the-cause-of-dry-cough&quot;&gt;What is the cause of dry cough?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-04-19T11:27:52.417" Title="Do distinctions between dry, tickly and chesty coughs have any medical basis?" Tags="&lt;pathology&gt;&lt;medicine&gt;&lt;pathogenesis&gt;&lt;treatment&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25921" PostTypeId="1" CreationDate="2014-12-16T17:50:44.197" Score="1" ViewCount="37" Body="&lt;p&gt;I know people with SAD (Seasonal Affective Disorder) benefit from blue light in the winter as night-time comes much earlier (in the UK, sunset is around 4pm in December, compared to 9pm in June).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, during winter (say the UK), would the average person also benefit from more blue light in the late afternoon/early-evening than standard light bulbs currently supply?&lt;/p&gt;&#xA;" OwnerUserId="11583" LastActivityDate="2014-12-16T17:50:44.197" Title="Would blue light be effective to help average people when sunsets come much earlier in the day?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;brain&gt;&lt;light&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25922" PostTypeId="1" AcceptedAnswerId="25927" CreationDate="2014-12-16T18:12:12.587" Score="11" ViewCount="3364" Body="&lt;p&gt;I've seen snakes get captured in sacks and I've wondered if the snake would get dizzy if the sack were twirled around.  I have not done any tests (and don't plan to) because snakes scare me.  &lt;/p&gt;&#xA;" OwnerUserId="11584" LastEditorUserId="11584" LastEditDate="2015-01-05T16:25:38.760" LastActivityDate="2015-01-06T04:31:37.553" Title="Do snakes get dizzy?" Tags="&lt;physiology&gt;&lt;neuroscience&gt;&lt;reptile&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25924" PostTypeId="1" AcceptedAnswerId="25929" CreationDate="2014-12-16T18:13:31.990" Score="0" ViewCount="469" Body="&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/s10682-013-9639-x&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; uses Pied Flycatcher as a study species. For the population of Pied Flycatchers they studied, 'pedigree information' was available. What exactly does this 'pedigree information' mean?&lt;/p&gt;&#xA;" OwnerUserId="1216" LastActivityDate="2014-12-16T19:47:35.820" Title="What does 'pedigree information' mean?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25925" PostTypeId="1" AcceptedAnswerId="25928" CreationDate="2014-12-16T18:34:06.477" Score="3" ViewCount="30715" Body="&lt;p&gt;So I know that the major/minor groove arise from the offset pairing of the two strands in the helix.  All my textbook tells me is that &quot;pitch causes the off-set pairing of DNA and this gives rise to the major and minor grooves.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not too sure what this is saying.  What exactly is pitch and how does it give rise to the grooves?&lt;/p&gt;&#xA;" OwnerUserId="10470" LastActivityDate="2014-12-16T19:14:54.013" Title="Why do the major and minor groove exist in DNA?" Tags="&lt;dna&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25926" PostTypeId="1" CreationDate="2014-12-16T18:44:29.720" Score="2" ViewCount="152" Body="&lt;p&gt;I am interested in understanding how pain receptors send signals to the somatosensory cortex (the part of the brain that registers various nerve signals such as pain, presure, temperatures, etc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, I'm interested in whether or not two distinct nerves/receptors share, or don't share, &quot;channels of communication&quot; to the cortex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, say I touch the very tip of my finger to a hot stove, and, say, only 10 &quot;temperature-sensing nerves&quot; are triggered to transmit pain signals to my brain:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Do each of these 10 nerves send 10 distinct signals to my brain, traveling down 10 completely 10 channels?; or&lt;/li&gt;&#xA;&lt;li&gt;Do each of these 10 nerves send 10 distinct signals to, say, my spinal cord, where they are then combined into 1 large pain signal and forwarded on to the brain?; or&lt;/li&gt;&#xA;&lt;li&gt;Something else entirely?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Here's an awful illustration of the question I'm asking:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Uv36q.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Scenario #1, both nerves send 2 distinct signals to the brain, and those signals are kept distinct/isolated throughout the course of their entire journey to the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Scenario #2, both nerves send 2 distinct signals to the spinal cord, but the spine then combines them and only forwards 1 signal on to the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I''m sure in reality it's neither of these scenarios, and is something much more complex. But I'm curious and want to know!&lt;/p&gt;&#xA;" OwnerUserId="11581" LastActivityDate="2015-01-25T00:06:13.923" Title="How and where do nerves share pathways to the brain?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;brain&gt;&lt;pain&gt;&lt;central-nervous-system&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25927" PostTypeId="2" ParentId="25922" CreationDate="2014-12-16T18:50:12.690" Score="14" Body="&lt;p&gt;Probably don't do any experiments that involve shoving reptiles in a sack and swinging them around your head, as someone will surely call the ASPCA on you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The type of dizziness that is associated with spinning around is called &quot;vertigo&quot;. From &lt;a href=&quot;http://en.wikipedia.org/wiki/Vertigo&quot;&gt;wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Repetitive spinning, as in familiar childhood games, can induce short-lived vertigo by disrupting the inertia of the fluid in the vestibular system&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So then from a physiological perspective the question is, do snakes have fluid in their ears like people do? And a quick review of snake physiology seems to suggest that they do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, I'm going to put forward the tentative hypothesis that yes, snakes can get dizzy, but it's still probably very different from you think of as dizziness.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-12-16T18:50:12.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25928" PostTypeId="2" ParentId="25925" CreationDate="2014-12-16T18:58:17.030" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Screw_thread#Lead.2C_pitch.2C_and_starts&quot; rel=&quot;noreferrer&quot;&gt;Pitch&lt;/a&gt; is not a great word for this, as its meaning is ambiguous. It's hard to find a universal nomenclature for DNA geometry, but see the &quot;Base pair geometry&quot; section of &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleic_acid_double_helix&quot; rel=&quot;noreferrer&quot;&gt;this wikipedia page&lt;/a&gt;. The relevant property is what they call &quot;opening&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the biochemistry textbook by Berg:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9KgFS.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To explain in words, if the glycosidic bonds (which attach the nucleic base to the sugar in the backbone) stuck straight out at 90 angles on both sides, then the grooves in double-stranded DNA would be symmetrical. Because the glycosidic bonds are at an angle (relative to the interface between the AT or GC pairs), one of the &quot;faces&quot; of the base pair is larger than the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Words and flat pictures, however, will never really give you a good intuitive sense of what's going on with the 3D structure of the grooves. A &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/B000O8Z7UQ&quot; rel=&quot;noreferrer&quot;&gt;good modeling kit&lt;/a&gt; will be of great help to you.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2014-12-16T19:14:54.013" LastActivityDate="2014-12-16T19:14:54.013" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25929" PostTypeId="2" ParentId="25924" CreationDate="2014-12-16T19:47:35.820" Score="3" Body="&lt;p&gt;It means that they &lt;a href=&quot;http://en.wikipedia.org/wiki/Pedigree_chart&quot; rel=&quot;nofollow&quot;&gt;recorded family information&lt;/a&gt; for the traits that they were investigating in the paper, i.e., they had plumage characteristics for siblings or parent-offspring pairs. Look for this phrase in the paper: &quot;phenotypic data usually available for one or two generations, mostly from parent-offspring pairs or siblings.&quot;&lt;/p&gt;&#xA;" OwnerUserId="10518" LastActivityDate="2014-12-16T19:47:35.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25930" PostTypeId="1" AcceptedAnswerId="26187" CreationDate="2014-12-16T20:28:39.213" Score="2" ViewCount="159" Body="&lt;p&gt;When I touch my hand on a hot stove, I feel pain. I'm interested in knowing all the main &quot;endpoints&quot; (components/parts of the body) that are involved in relaying this pain signal. As I understand it so far, they are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Nerve (thermoreceptor)&lt;/li&gt;&#xA;&lt;li&gt;Fibers&lt;/li&gt;&#xA;&lt;li&gt;Spinal cord&lt;/li&gt;&#xA;&lt;li&gt;Brain stem (medula =&gt; pons =&gt; midbrain)&lt;/li&gt;&#xA;&lt;li&gt;???&lt;/li&gt;&#xA;&lt;li&gt;Somatosensory Cortex&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;A special sensory nerve in my hand, called a &lt;strong&gt;thermoreceptor&lt;/strong&gt;, receives a thermal input (the hot stove) and fires a pain signal to my spinal cord.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My spinal cord then sends the signal up into the brain stem, where the signal travels through the medula, the pons and the midbrain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At this point the signal is somehow wired to my somatosensory cortex; the part of the brain that ultimately processes the signal and interprets it as &quot;pain&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Have I identified all the key players here?&lt;/strong&gt; What connects the midbrain/brainstem to the somatosensory cortex?&lt;/p&gt;&#xA;" OwnerUserId="11581" LastEditorUserId="9943" LastEditDate="2016-03-10T21:00:51.773" LastActivityDate="2016-03-10T21:00:51.773" Title="Anatomy of nervous system's sensory pathways" Tags="&lt;neuroscience&gt;&lt;central-nervous-system&gt;&lt;peripheral-nervous-system&gt;&lt;sensory-systems&gt;&lt;brain-stem&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25932" PostTypeId="1" AcceptedAnswerId="25936" CreationDate="2014-12-16T21:10:52.967" Score="5" ViewCount="1226" Body="&lt;p&gt;Normally I wash/detect with one primary/secondary-HRP antibody pair, strip, then wash/detect with the other primary/secondary-HRP pair which works well. However, I recently started working with a HRP-conjugated primary antibody for my protein of interest and wondered if I might add this together with the secondary antibody for my loading control to save the stripping and second washing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any general guidelines for Western blotting with multiple antibodies at the same time, i.e. changing antibody dilution? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An obvious first step is to make sure the HRP-conjugated primary isn't from the animal recognized by the secondary. I anticipate blotting with mouse HRP-conjugated anti-GFP and a secondary rabbit anti-mouse would not be a very good decision.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2014-12-16T22:24:26.643" Title="Western blotting with multiple antibodies" Tags="&lt;molecular-biology&gt;&lt;antibody&gt;&lt;western-blot&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="25933" PostTypeId="1" AcceptedAnswerId="25960" CreationDate="2014-12-16T22:01:49.273" Score="0" ViewCount="189" Body="&lt;p&gt;Suppose you haven't hit your nails so the white spots are due to Leukonychia. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are the discoloration i.e. the white spots due to lower porosity (less minerals absorbing) or some other factor? I cannot understand their physiobiological chareterisation and why are they created due to evolutionary terms? To show a person that he is lacking minerals? Or why do some people have them?&lt;/p&gt;&#xA;" OwnerUserId="1705" LastActivityDate="2014-12-17T07:46:47.230" Title="What is the evolutionary purpose of white spots in nails and how can they be characterised due to Leukonychia?" Tags="&lt;evolution&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ClosedDate="2014-12-17T09:54:07.550" ContentLicense="CC BY-SA 3.0" />
  <row Id="25935" PostTypeId="1" CreationDate="2014-12-16T22:23:18.370" Score="3" ViewCount="925" Body="&lt;p&gt;There is a tendency of some animals (including people!) to be &quot;copy-cats&quot; and try to imitate members of their own, and sometimes other, species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most obvious example is a parrot copying human speech. Humans also try to copy the speech of their parents when they are little. &quot;ma-ma, da-da&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The less obvious examples, I'm not even really sure are occurring. Like when a gorilla at the zoo assumes the same posture as a person sitting on just the other side of the glass. Like my cat, who tries to chew on bones similar to the two dogs we have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure there are more/better examples I'm not aware of.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is it that creates this behavior? Is it something that was learned, or is it some natural tendency? Is there such a thing as behaviors that are &quot;encoded in the dna&quot;?&lt;/p&gt;&#xA;" OwnerUserId="9700" LastActivityDate="2016-04-16T01:13:47.483" Title="Why do some animals try to imitate other animals?" Tags="&lt;genetics&gt;&lt;ethology&gt;&lt;behaviour&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25936" PostTypeId="2" ParentId="25932" CreationDate="2014-12-16T22:24:26.643" Score="4" Body="&lt;p&gt;What you can do depends on your proteins: If both proteins (your target protein and the loading control) are seperated far enough, you can detect both of them in the same step by adding both primary antibodies and both secondary ABs into the buffer at the same time. They will bind only to their specific epitope and you will get nice signals. This is something I have done several time. This avoids the stripping process (which can be tricky sometimes) and you have both signals on the same film. Additionally you save chemicals, film and time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is another way with which you can come around the stripping: Do you first primary/secondary antibody combination and then incubate the blot with a buffer containing sodium azide. This inhibits the enzyme irreversibly, you have to make to wash very carefully afterwards. Then you can proceed with the second antibody combination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want work with a marked primary antibody (which is unusual, but will of course work) and your loading control at the same time, I would definitely make sure that the secondary antibody with the HRP is not binding to your marked primary, otherwise the signal might get very strong (from the primary and also from the bound secondary), but I don't think it would cause other problems.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-16T22:24:26.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25937" PostTypeId="2" ParentId="25922" CreationDate="2014-12-16T22:30:26.247" Score="12" Body="&lt;p&gt;Dizziness is caused by a continuing rotation of the fluids in the semi-circular canals of the vestibular system that transmit rotation information to the brain. After prolonged rotation of the body, the circular canal fluids are engaged in a rotating motion. This fluid motion continues even when the body has stopped moving. The persistent fluid rotation is detected by the hair cells lining the canals that in turn send this aberrant information to the brain that interprets it as continuous motion of the body. A picture from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Vestibular_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki page on the vestibular system&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/13pLG.gif&quot; alt=&quot;Wiki page image of the labyrinth of the inner ear showing the semicircular canals&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All jawed vertebrates, including snakes, have this basic system of a horizontal, posterior and anterior canal filled with fluid (&lt;a href=&quot;http://en.wikipedia.org/wiki/Vestibular_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki on the vestibular system&lt;/a&gt;). Based on this common anatomy, hence, it is reasonable to assume snakes do get dizzy. However, as @tel rightfully indicates, dizziness is a subjective perceptual phenomenon and the assumption of snakes getting dizzy needs experimental verification. Ethically, however, this would (and should) never get through a review board as it is a curiosity-based question only.      &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-17T05:47:12.120" LastActivityDate="2014-12-17T05:47:12.120" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="25938" PostTypeId="1" AcceptedAnswerId="25939" CreationDate="2014-12-16T23:29:04.407" Score="0" ViewCount="101" Body="&lt;p&gt;For part of an exam question, &quot;why do cells grown in liquid cause turbidity?&quot; I answered that cells &lt;em&gt;refract&lt;/em&gt; light. The correct answer was that cells scatter light. Isn't the light scattering ultimately caused by lots of refraction events? Is the grader correct to take off full points?&lt;/p&gt;&#xA;" OwnerUserId="5100" LastActivityDate="2014-12-16T23:55:22.557" Title="Cells scatter light in solution. Do they refract?" Tags="&lt;cell-culture&gt;&lt;light&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25939" PostTypeId="2" ParentId="25938" CreationDate="2014-12-16T23:55:22.557" Score="0" Body="&lt;p&gt;You're both correct. Turbidity is causes by excessive light reflection events from all of the particles, and is actually how it is measured in a sample. As to cells, they both both reflect light that is incident on a membrane, but they will also refract light that does manage to enter the cell because of the difference in refractive indices. A portion of the light will also be absorbed by the cells.&lt;/p&gt;&#xA;" OwnerDisplayName="user560" LastActivityDate="2014-12-16T23:55:22.557" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25940" PostTypeId="1" CreationDate="2014-12-17T00:28:10.643" Score="1" ViewCount="100" Body="&lt;p&gt;There is information about decontamination times &lt;a href=&quot;http://www.cdc.gov/biosafety/publications/bmbl5/BMBL5_appendixI.pdf&quot; rel=&quot;nofollow&quot;&gt;here on pages 6 and 7&lt;/a&gt;. My specific question is how persistent botulinum toxin is in a natural environment, or alternatively, what is the half life of this toxin? &lt;/p&gt;&#xA;" OwnerUserId="3016" LastEditorUserId="9943" LastEditDate="2014-12-18T21:55:08.557" LastActivityDate="2014-12-19T00:20:43.783" Title="Persistency of botulinum toxin in environment" Tags="&lt;toxicology&gt;&lt;environment&gt;&lt;bacterial-toxins&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25941" PostTypeId="1" AcceptedAnswerId="25942" CreationDate="2014-12-17T00:37:31.390" Score="25" ViewCount="5597" Body="&lt;p&gt;I know that it is common to say, &quot;use hot water when washing your hands&quot; or when you've got a cut, &quot;wash your hands with warm water,&quot; etc. I was wondering, why is this the case? Since bacteria grow in warm environments, you would think that it might be beneficial for bacteria. Is this just another myth or is this actually true?&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="9829" LastEditDate="2015-04-23T15:49:41.227" LastActivityDate="2015-04-23T15:49:41.227" Title="Hot water and bacteria" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25942" PostTypeId="2" ParentId="25941" CreationDate="2014-12-17T00:47:57.530" Score="36" Body="&lt;p&gt;The bacteria wouldn't see any benefit from the warm water in the ~30-60 seconds you're washing your hands, neither would hot water &quot;sterilize&quot; your hands at temperatures you could tolerate. The reason you wash your hands with hot water is because the hot water+detergent soap mix is better for removing oil and dirt than cold water+detergent, which is supposedly where bacteria reside.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, there was a study published saying that washing with hot water doesn't have much of an effect on bacterial load. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15824636&quot;&gt;Hot water for handwashing--where is the proof?&lt;/a&gt; (Laestadius and Dimberg, 2005). I'd be interested to look more into their methods but the paper is behind a paywall and I don't have access at home.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, this paper, &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1471-5740.2002.00043.x/full&quot;&gt;Water temperature as a factor in handwashing efficacy&lt;/a&gt; by Michaels &lt;em&gt;et al&lt;/em&gt;. is open and shows no evidence that hot water is any better than cold water for removal of microbes.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[W]ater temperature exhibits no effect on transient or resident bacterial reduction during normal handwashing with bland soap.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="9829" LastEditDate="2014-12-21T03:46:47.650" LastActivityDate="2014-12-21T03:46:47.650" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25943" PostTypeId="2" ParentId="25941" CreationDate="2014-12-17T00:49:58.580" Score="10" Body="&lt;p&gt;The goal of hand washing is to remove surface debris, including foreign pathogens. Most things that most people encounter on a daily basis dissolve more easily in hot water than in cold water. Thus, hot water around 100° F is used to facilitate this debris removal process, although the ideal culture temperature for E coli and a raft of related bacteria is around there too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hand_washing#Water_temperature&quot; rel=&quot;nofollow&quot;&gt;wikipedia on hand washing&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Contrary to popular belief however, scientific studies have shown that using warm water has no effect on reducing the microbial load on hands&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2014-12-18T10:10:55.720" LastActivityDate="2014-12-18T10:10:55.720" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="25944" PostTypeId="1" CreationDate="2014-12-17T00:50:08.737" Score="2" ViewCount="434" Body="&lt;p&gt;I was reading about Fab fragment and about using them to fight of viral infections. It seems that the Fab attaches to the viral receptors, which stops the viruses from attacking the cells. It seems that it has been done before. I was wondering, since Fab fragments can't activate immune response, what happens to the Fab-virus complex in the blood?&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="10401" LastEditDate="2015-01-04T03:02:21.790" LastActivityDate="2015-01-04T03:02:21.790" Title="Fab fragments of antibodies to fight viral infections" Tags="&lt;antibody&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="25945" PostTypeId="2" ParentId="25941" CreationDate="2014-12-17T00:50:11.683" Score="6" Body="&lt;p&gt;It makes no difference at all. To sterilize your hands you would need to wash them with water at around 115 degrees C at 1.2 atmospheres of pressure for over 30 minutes &amp;ndash; that's obviously not going to happen. The bacteria that normally reside on your skin can easily tolerate tap water, no matter whether the faucet is set to maximum hot or maximum cold, or just average. Even if the temperature of the water could appreciably slow down bacterial growth (which it can't), once you've washed your hands your skin temperature goes back to as it was before the washing in a minute or so.&lt;/p&gt;&#xA;" OwnerUserId="10001" LastEditorUserId="948" LastEditDate="2014-12-17T17:08:45.773" LastActivityDate="2014-12-17T17:08:45.773" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25948" PostTypeId="1" AcceptedAnswerId="25951" CreationDate="2014-12-17T01:20:25.097" Score="1" ViewCount="2208" Body="&lt;p&gt;My &lt;em&gt;understanding&lt;/em&gt; of the &quot;sensory pathway&quot; is that its a linear, directional pipeline as follows:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Nerves (fire various signals depending on the type of sensors they are)&lt;/li&gt;&#xA;&lt;li&gt;Fibers (transmit signals from nerves to spinal cord)&lt;/li&gt;&#xA;&lt;li&gt;Spinal cord (transmits signals from fibers to brainstem)&lt;/li&gt;&#xA;&lt;li&gt;Brainstem (transmits signals from spinal cord to brain)&lt;/li&gt;&#xA;&lt;li&gt;Brain (the somatosensory cortex register signals as pain/pressure/temperature/etc.)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So again, my &lt;em&gt;understanding&lt;/em&gt; is that sensory nerves are 1-way sensors, and that once they fire a signal, its 1 and only ultimate destination is the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, as a precursor to my question, if anything I have stated is incorrect, please begin by correcting me!&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I read that pinched nerves in the back and neck can cause &lt;em&gt;neuropathy&lt;/em&gt; (&quot;pins and needles&quot;) all over the body: hands, feet, face, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;But how can this be?&lt;/strong&gt; If my understanding of the sensory pathway is correct, then a pinched nerve in one's neck should only send &quot;pins and needles&quot; signals directly to the brain; it should not at any point forward/relay signals on to any other areas of the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To state that a pinched nerve in one's neck could possibly cause neuropathy in their arm, then that insinuates there is some connection between the pinched &quot;neck nerve&quot; and the nerve(s) in the arm that are experiencing the pins and needles sensation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, unless I completely misunderstand the entire sensory pathway and how pain signals transmit, this implies that a pinched nerve sends signals out to the spinal cord, &lt;strong&gt;down the spinal cord and into, say, an arm&lt;/strong&gt;, and that the sensory receptors in the arm subsequently react to these signals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is this possible?!? Is there some kind of feedback mechanism at play where nerves in the neck and back can relay signals on to other areas of the body, instead of just feeding directly into the &quot;&lt;em&gt;spinal cord =&gt; brainstem =&gt; cortex&lt;/em&gt;&quot; pipeline?&lt;/p&gt;&#xA;" OwnerUserId="11581" LastActivityDate="2014-12-17T04:15:06.490" Title="Can signals travel &quot;backwards&quot; in the sensory pathway?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;brain&gt;&lt;pain&gt;&lt;central-nervous-system&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25949" PostTypeId="2" ParentId="25944" CreationDate="2014-12-17T01:25:43.460" Score="2" Body="&lt;p&gt;There are three pathways by which soluble antibodies (which is what the Fab fragments arise from) can inactivate viruses (from Janeway's Immunobiology):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xziHP.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you describe with the Fab binding to the viral receptors is a type of neutralization. Janeway claims that the type of naturally occurring antibody primarily responsibly for neutralization, IgA, is mostly exported to mucous secretions, so presumably it gets digested/excreted along with the rest of the mucous proteins.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-12-17T01:25:43.460" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="25950" PostTypeId="2" ParentId="19246" CreationDate="2014-12-17T01:26:11.100" Score="13" Body="&lt;p&gt;There is a &amp;quot;anti-virus,&amp;quot; although many call it a virophage.In 2008, a paper in Nature was published about the observations of a new strain of a virus known as Acanthamoeba polyphaga mimivirus. This virus mainly attacks amoeba. It was discovered in 1992. It was one of the biggest viruses ever found.Later, a related virus called the mamavirus was discovered. But, after observing this specimen under an electron microscope, scientist found tiny viral particles attacking the mamavirus. It was called Sputnik. The Sputnik virus hijacks the mamvirus's machinery and depends on the mamavirus to survive. It made scientists wonder if the mamavirus is a living thing.&lt;/p&gt;&#xA;&lt;p&gt;Here is a picture of it attacking the mamavirus:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sHpRQ.jpg&quot; alt=&quot;mamavirus&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;You can see small subviral particles attacking the bigger virus. That is Sputnik.&#xA;Note that it is a virus that &lt;strong&gt;coinfects&lt;/strong&gt; other organisms but needs a virus infecting an organism to survive. According to Wikipedia:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Sputnik virophage&lt;/strong&gt; is a subviral agent that reproduces in amoeba cells that are already infected by a certain helper virus; Sputnik uses the helper virus's machinery for reproduction and inhibits replication of the helper virus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It seems that there are more species of virophages, including one that infects the marine phagotropic flagellate &lt;em&gt;Cafeteria roenbergensis&lt;/em&gt; in the presence of a second virus — Cafeteria roenbergensis virus and another one known as the Organic Lake virophage but not much detail is known about this virus.&lt;/p&gt;&#xA;&lt;p&gt;Here is the link to the Nature article on the Sputnik virophage, published in 2008:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v455/n7209/full/nature07218.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.nature.com/nature/journal/v455/n7209/full/nature07218.html&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;It may be possible to synthesize one in the future. However using this to kill viruses would not make sense because the virophage technically still attacks the host of the virus it is hijacking, plus, from what I understand, it only uses the virus's machinery.&lt;/p&gt;&#xA;&lt;p&gt;Hopefully this was helpful. If you have questions, you can comment on this answer...&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-17T01:31:36.867" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="25951" PostTypeId="2" ParentId="25948" CreationDate="2014-12-17T02:03:37.487" Score="2" Body="&lt;p&gt;Reverse signals (dendrite -&amp;gt; axon) do occur in neurons, and are called &lt;a href=&quot;http://jp.physoc.org/content/485/Pt_1/1.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;back propagating action potentials&lt;/a&gt; (bAPs). However, whatever role bAPs play in the nervous system at large is subtle/small enough that we don't really understand them at all.&lt;/p&gt;&#xA;&lt;p&gt;In any case, as @luigi points out, pinched nerves don't have anything to do with bAPs. The reason why a pinch in one place (the neck) feels like it has an effect in another place (the arm) is because some neurons trace long (on the order of several feet) pathways through the body. Ultimately, the sensory input of everything below your head passes through neurons in your neck at some point. If there is a pinch in the neuron in your neck that relays sense information from your arm, that neuron in your neck can activate spuriously, even in the absence of any stimulus acting on your arm. In that case your brain will interpret the spurious activation of that neck neuron as being the result of some kind of strange arm stimulus, and so you feel pins and needles.&lt;/p&gt;&#xA;&lt;p&gt;See &lt;a href=&quot;http://en.wikipedia.org/wiki/Somatosensory_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for more information on the sensory cortex in your brain and the &amp;quot;sense image&amp;quot; it maintains of your body.&lt;/p&gt;&#xA;&lt;h1&gt;Edit&lt;/h1&gt;&#xA;&lt;p&gt;To clarify what I mean by a &amp;quot;pathway&amp;quot;,&#xA;&lt;img src=&quot;https://i.stack.imgur.com/iZHSE.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The part marked &amp;quot;proprioceptors or mechanoreceptors&amp;quot; is what's buried in your skin. If you poke a mechanoreceptor, it evokes a signal in the neuron marked &amp;quot;first-order&amp;quot;. In some cases, that first-order neuron will reach all the way to brainstem (as in the picture above), and in some cases that first-order neuron will interface with an intermediate neuron in the spine, but the effect is the same in any case. A first-order neuron stimulates a second-order neuron, which in turn stimulates a third-order neuron, etc., all the way until the original signal arising from the mechanoreceptor reaches the somatosensory cortex. A pinch in any of those first, second, etc. order neurons will potentially send spurious signals to the somatosensory cortex.&lt;/p&gt;&#xA;&lt;h1&gt;Second edit:&lt;/h1&gt;&#xA;&lt;p&gt;Rereading your question, I think a lot of the trouble that you're having has to do with your understanding of how the brain assembles sense information. In order to feel pain in your arm, it is not necessary for anything to be happening to the arm itself. Your arm could be perfectly healthy and normal, but as long as your brain is receiving a signal equivalent to the one produced by a damaged arm you will still feel the same sensation of pain.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-17T04:15:06.490" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="25952" PostTypeId="2" ParentId="25920" CreationDate="2014-12-17T02:18:55.880" Score="1" Body="&lt;p&gt;If I may add to what Resonating has said, when it comes to infections, dry cough is usually associated with a viral infection, whereas wet cough is usually caused by bacteria. The two are treated very differently - dry cough is remedied with cough-supressing drugs (antivirals are rarely needed), whereas bacterial infections are medicated with antibiotics (antivirals are NOT antibiotics) and drugs that help clear the mucus from the respiratory pathway. Treating wet cough with dry cough medications is not only ineffective, it can also be dangerous. One more thing - not all bacterial infections necessitate antibiotics which should be used sparingly because the world is running out of antibiotics.&lt;/p&gt;&#xA;" OwnerUserId="10001" LastEditorUserId="-1" LastEditDate="2015-04-19T11:27:52.417" LastActivityDate="2015-04-19T11:27:52.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25954" PostTypeId="1" AcceptedAnswerId="25955" CreationDate="2014-12-17T03:12:17.640" Score="0" ViewCount="79" Body="&lt;p&gt;I am not sure if this question is better suited CogSci.SE so please tell me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is why are we satisfied when we get things that aren't useful in any important way? For example, relating to Stack exchange, why are we satisfied and happy when we get badges because badges don't increase reputation or help you get privileges in Stack Exchange. Similar with Winter Bash. Why are we happy when we get hats? They are just for decorations. Is there a biological explanation for this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What chemical leads to us getting that feeling of satisfaction?&lt;/strong&gt;  &lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="5762" LastEditDate="2014-12-18T08:35:02.827" LastActivityDate="2014-12-18T08:35:02.827" Title="Satisfication with irrelevant things" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ClosedDate="2014-12-17T09:54:51.317" ContentLicense="CC BY-SA 3.0" />
  <row Id="25955" PostTypeId="2" ParentId="25954" CreationDate="2014-12-17T04:41:27.047" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dopamine&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dopamine&lt;/a&gt; is one of many neurotransmitters which modulate information passage between one brain area to another. Dopamine is thought to play important role in  pleasure, addiction,&#xA;and learning.Massive increase in the&#xA;amount of dopamine released in the brain during video game play, the releasing of dopamine&#xA;are in areas thought to control reward and learning.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/10HJS.png&quot; alt=&quot;enter image description here&quot; /&gt;&#xA;&lt;a href=&quot;https://books.google.co.in/books?id=pNWPfbZ2s0IC&amp;amp;pg=PA53&amp;amp;dq=dopamine%20and%20video%20games&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=6fmQVNCtJNijugTY6oDoCQ&amp;amp;ved=0CDYQ6AEwBA#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Certain neural structures, called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Reward_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;reward system&lt;/a&gt;, are critically involved in mediating the effects of reinforcement. A reward is an appetitive stimulus given to a human or some other animal to alter its behavior. Rewards typically serve as reinforcers. A reinforcer is something that, when presented after a behavior, causes the probability of that behavior's occurrence to increase. Note that, just because something is labelled as a reward, it does not necessarily imply that it is a reinforcer. A reward can be defined as reinforcer only if its delivery increases the probability of a behavior.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The reason why we are happy when we get these decorative items is because they are things which we can possess. Reward system is responsible for this kind of behavior, when we gain or achieve something in life its usually gets rewarded in the form of a pleasure. Foraging ants and bees are provided with these reward systems and which in turn makes these animals to derive a pleasure out of their daily achievements. Whether in life, video game or stack exchange or anything, an achievement is something brain thinks relevant and rewards it with a pleasure in mind.&lt;/p&gt;&#xA;&lt;p&gt;Considering badges in stack exchange, really badges are an analogy to reputation. When we have more badges usually our charisma increases like in the case of reputation. Also levels and scores in games,achievements in office, stack exchange badges and hats all fall under the same analogy. So when we have more badges we are meant to be more successful and brain will reward us to attain more badges and also people like hats too.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;References&lt;/p&gt;&#xA;&lt;p&gt;Digital Media: Transformations in Human Communication - Paul Messaris, Lee Humphreys&lt;/p&gt;&#xA;&lt;p&gt;Cyber Junkie: Escape the Gaming and Internet Trap - Kevin Roberts&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-17T04:41:27.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25956" PostTypeId="1" CreationDate="2014-12-17T05:56:06.797" Score="5" ViewCount="519" Body="&lt;p&gt;Is it possible to dock multiple ligands with a target? If so, what is the suitable software used for? -- Is it possible to fix specific docking region for the target (or) automatic?&lt;/p&gt;&#xA;" OwnerUserId="11593" LastActivityDate="2014-12-17T06:49:27.573" Title="Is it possible to dock multiple ligands with the target?" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25958" PostTypeId="2" ParentId="25935" CreationDate="2014-12-17T06:28:01.927" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.britannica.com/EBchecked/topic/383252/mimicry&quot; rel=&quot;nofollow&quot;&gt;Mimicry&lt;/a&gt;, in biology, phenomenon characterized by the superficial resemblance of two or more organisms that are not closely related taxonomically. This resemblance confers an advantage—such as protection from predation—upon one or both organisms through some form of “information flow” that passes between the organisms and the animate agent of selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://books.google.co.in/books?id=i9ITMiiohVQC&amp;amp;pg=PA2398&amp;amp;dq=evolution%20of%20mimicry&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=ARSRVMy_IdC9uATm9oHACg&amp;amp;ved=0CCIQ6AEwAQ#v=onepage&amp;amp;q=evolution%20of%20mimicry&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; link describes different types of animal mimicry&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The two step mechanism of mimicry evolution states that,  &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;1) Mutations at genes of major effect first allow a phenotypic leap&#xA;  achieving an approximate resemblance to a particular model.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;2) Once these mutations have increased in the population, resemblance can be enhanced through the gradual selection of epistatic&#xA;  modifiers.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Considering the case of butterflies, the working of two step mechanism evolved through different types of natural selection process. Experiments show that birds associate certain patterns in the butterfly wings to identify the specie and generalize those features, but a small deviation from the exact pattern is neglected. The increased resemblance is advantageous to species having imperfect mimics. So the species which displays/perform imperfect mimics can some how fall under the list of rejection and manages to survive, thereby passing genes to next generation.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Largesse of the Genome&quot;, an idea put forward by J.R.G.Turner states that, it is believed that the modification of a trait can be achieved by so many different genes that some of them will inevitably happen to be linked.Amoung the many possible combinations of the loci, selection could simply sieve out the ones that involve linked genes.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Encyclopedia of Insects by Vincent H. Resh, Ring T. Cardé&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Although the exact mechanisms of mimicry is still a questionable area, experiments are giving hopes regarding the two step mechanism and more over natural selection is the predominant factor which makes a mimicry successful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://books.google.co.in/books?id=Jk0Hym1yF0cC&amp;amp;pg=PA640&amp;amp;dq=mimicry%20and%20genes&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=hBSRVPjyF4uVuATGpYLADQ&amp;amp;ved=0CCAQ6AEwAQ#v=onepage&amp;amp;q=mimicry%20and%20genes&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; link describes insect mimicry and two step mechanism in detail.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;https://books.google.co.in/books?id=k_7UBAAAQBAJ&amp;amp;pg=PA353&amp;amp;dq=mimicry%20in%20birds&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=Fx2RVOaqEoO6uATcwoCQDA&amp;amp;ved=0CCEQ6AEwAQ#v=onepage&amp;amp;q=mimicry%20in%20birds&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;A Dictionary of Birds&lt;/a&gt; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;https://books.google.co.in/books?id=YRcAVvmE6eMC&amp;amp;pg=PA274&amp;amp;dq=evolution%20of%20bird%20mimicry&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=QhKRVN7RIoTGuAT54oG4DA&amp;amp;ved=0CDAQ6AEwBA#v=onepage&amp;amp;q=evolution%20of%20bird%20mimicry&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Encyclopedia of Evolution&lt;/a&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;https://books.google.co.in/books?id=Nr3cj_ER07sC&amp;amp;pg=PA259&amp;amp;dq=mimicry%20and%20genes&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=hBSRVPjyF4uVuATGpYLADQ&amp;amp;ved=0CBsQ6AEwAA#v=onepage&amp;amp;q=mimicry%20and%20genes&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Rapidly Evolving Genes and Genetic Systems&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="107" LastEditDate="2016-04-16T01:13:47.483" LastActivityDate="2016-04-16T01:13:47.483" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25959" PostTypeId="2" ParentId="25956" CreationDate="2014-12-17T06:41:36.453" Score="3" Body="&lt;p&gt;Huameng Li and Chenglong Li have done multiple ligand docking in two (AFAIK) of their works:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jcc.21486/full&quot; rel=&quot;nofollow&quot;&gt;Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of protein&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jm401144z&quot; rel=&quot;nofollow&quot;&gt;Drug Design Targeting Protein–Protein Interactions (PPIs) Using Multiple Ligand Simultaneous Docking (MLSD).....&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The method is called Multiple Ligand Simultaneous Docking (MLSD). I am not at all an expert in this field and you should read the first paper for details on how they implemented this. This algorithm was implemented on AutoDock. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-17T06:49:27.573" LastActivityDate="2014-12-17T06:49:27.573" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25960" PostTypeId="2" ParentId="25933" CreationDate="2014-12-17T07:46:47.230" Score="3" Body="&lt;p&gt;This is a common misunderstanding from newcomers in evolutionary biology. Not every trait is the result of an adaptation. Evolution is way more than just natural selection and is not as deterministic as you may think. There is stochasticity inherent to mutational processes and there is stochasticity in reproductive success (called genetic drift). &lt;a href=&quot;https://biology.stackexchange.com/questions/21772/why-dont-mammals-have-more-than-4-limbs&quot;&gt;This&lt;/a&gt; seemingly totally unrelated post may help you getting a quick grasp of what are the stochastic processes in evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The white spots you observe very likely do not result from an adaptive process but it just happen to be the way it is. For the physiology part (but this would be the subject of another question) I have no idea what drives these white spots.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2014-12-17T07:46:47.230" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25961" PostTypeId="1" CreationDate="2014-12-17T08:19:25.613" Score="2" ViewCount="3679" Body="&lt;p&gt;According to the Mayo Clinic, stress/anxiety can cause &quot;pins and needles&quot; (neuropathy) sensations all over the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;But how can this be?&lt;/strong&gt; My &lt;em&gt;understanding&lt;/em&gt; of the sensory pathway is that sensory receptors (nerves) fire &quot;pins and needles&quot; signals to the brain whenever there is a lack of blood flow to them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So does stress reduce blood flow to nerves? Is it a chemical reaction, perhaps where stress releases hormones that prevent the nerves from functioning correctly? Something else?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking for a biological/physiological/scientific explanation of what stress does to make nerves misbehave.&lt;/p&gt;&#xA;" OwnerUserId="11581" LastActivityDate="2014-12-17T08:19:25.613" Title="Physiologically, how can stress/anxiety cause neuropathy?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;brain&gt;&lt;central-nervous-system&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25962" PostTypeId="2" ParentId="23632" CreationDate="2014-12-17T08:45:18.750" Score="2" Body="&lt;p&gt;Osmoregulation is a homeostasis regulation mechanism followed by salmons to adapt on both salt and fresh water.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Osmoregulation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Osmoregulation&lt;/a&gt; is the active regulation of the osmotic pressure of an organism's fluids to maintain the homeostasis of the organism's water content; that is, it keeps the organism's fluids from becoming too diluted or too concentrated. Osmotic pressure is a measure of the tendency of water to move into one solution from another by osmosis. The higher the osmotic pressure of a solution, the more water tends to move into it. Pressure must be exerted on the hypertonic side of a selectively permeable membrane to prevent diffusion of water by osmosis from the side containing pure water.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;In order to reduce the dehydrating effects of salt water, salmons drink several liters of water per day, but in fresh water salmons doesn't drinks at all. The only water it consumes is that which goes down when it feeds. When an ocean-dwelling salmon drinks, it takes in a lot of salt(NaCl), which exacerbates the salt-loading problem.&#xA;In fresh water, the salmon's kidneys produce large volumes of dilute urine, while in the ocean , the kidneys' urine production rates drop dramatically and produce a very concentrated urine.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Salmon use to deal with the NaCl fluxes driven by the gradients between the salmon and its surroundings. In their gill epithelial cells, salmon have a special enzyme that hydrolyzes ATP and uses the released energy to actively transport both Na+ and Cl- against their concentration gradients. In the ocean, these Na+-Cl- ATPase molecules 'pump' Na+ and Cl- out of the salmon's blood into the salt water flowing over the gills, thereby causing NaCl to be lost to the water and offsetting the continuous influx of NaCl. In fresh water, these same Na+-Cl- ATPase molecules 'pump' Na+ and Cl- out of the water flowing over the gills and into the salmon's blood, thereby offsetting the continuous diffusion-driven loss of NaCl that the salmon is subject to in fresh water habitats with their vanishingly low NaCl concentrations.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.unm.edu/%7Etoolson/salmon_osmoregulation.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wXzam.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rohlB.png&quot; alt=&quot;enter image description here&quot; /&gt;&#xA;&lt;a href=&quot;http://www.nzqa.govt.nz/assets/qualifications-and-standards/qualifications/ncea/NCEA-subject-resources/Biology/91604-B/91604-EXP-B-student3-001.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-17T08:45:18.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25963" PostTypeId="2" ParentId="25908" CreationDate="2014-12-17T09:22:43.583" Score="3" Body="&lt;p&gt;I think this &lt;a href=&quot;http://people.eku.edu/ritchisong/birdbrain.html&quot; rel=&quot;nofollow&quot;&gt;website&lt;/a&gt; provides a pretty surprisingly thorough breakdown of avian brain anatomy, including historical contexts and debate around what exactly is homologous and what is not, and whether 'homologous' is a useful bit of information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short: It was thought until recently that the bird brain was just the core of the mammal brain with some layers peeled off, but it turns out to be more like a scale model, with many of the same parts. Roughly. Sort of.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So birds do not technically have a neocortex. They have a structure that looks like a neocortex, but it also looks like some other things. Gorillas do have a prefrontal cortex etc (&lt;a href=&quot;http://www.sciencephoto.com/media/301286/view&quot; rel=&quot;nofollow&quot;&gt;even if they are smaller than in humans&lt;/a&gt;). The knowledge that structure X performs function Y in an organism generally implies little about a second organism, with or without structure X. Even features like 'wings are for flying' and 'fins are for swimming' have exceptions.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="1590" LastEditDate="2014-12-17T09:41:50.207" LastActivityDate="2014-12-17T09:41:50.207" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="25964" PostTypeId="2" ParentId="25899" CreationDate="2014-12-17T09:36:55.820" Score="1" Body="&lt;p&gt;It's got to be because optical mirrors are relatively easy to produce and field, and it's obvious that it presents a duplicate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be interested in designs for a 'sound mirror' that doesn't just look like a wall under echolocation. Maybe a system to dynamically reproduce a 'sound hologram' of the bat?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A 'scent mirror' would be really difficult to build, not to mention 'ability to recognize your own smell' doesn't really imply higher brain function. Perhaps storing urine from dogs in estrus or stress or something to see if their own scents provoke behavior changes as if it was another dog?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A 'touch mirror'? A 'taste mirror'?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nearly everything can see, and mirrors are way easier than the alternatives.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-12-17T09:36:55.820" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25965" PostTypeId="1" CreationDate="2014-12-17T09:42:34.403" Score="3" ViewCount="395" Body="&lt;p&gt;I sometimes use denaturing gel electrophoresis on a preparative scale to purify RNA produced by in vitro transcription. The major issue with this is that the sample after extraction from the gel still contains significant amounts of acrylamide, or acrylamide oligomers/polymers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Exchanging the buffer using Vivaspins doesn't reliably remove it, precipitating the RNA also only reduces the amount, but can't remove the acrylamide entirely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In some cases the acrylamide doesn't interfere much with the later experiments, but there are some experiments that won't work with acrylamide in the sample.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the options to purify the RNA after gel electrophoresis that would reliable eliminate acrylamide from the sample? Preferably they should be simple and fast, not something like a full FPLC/HPLC run.&lt;/p&gt;&#xA;" OwnerUserId="11595" LastActivityDate="2014-12-17T10:18:34.053" Title="How can I purify RNA after gel electrophoresis to remove residual acrylamide?" Tags="&lt;rna&gt;&lt;lab-techniques&gt;&lt;gel-electrophoresis&gt;&lt;purification&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25967" PostTypeId="1" AcceptedAnswerId="25969" CreationDate="2014-12-17T09:52:26.563" Score="6" ViewCount="17266" Body="&lt;p&gt;Here is a simple diagram of a neuron:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AfmsJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few (very closely related) questions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Where are receptors located (for pain, pressure, temperature, etc.): in the axon terminals or the dendrite tree?&lt;/li&gt;&#xA;&lt;li&gt;Please confirm: for sensory nerves, signals travel from axon terminal to dendrite tree, yes?&lt;/li&gt;&#xA;&lt;li&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Nerve&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt;, axons communicate with each other across synapses, and nerves are chained bundles of axons (basically forming a cable with each other). However, if sensory signals travel from axon to dendrite, then how can axons be chained together? In other words, if axons are a &quot;male&quot; recepticle, and dendrites are a &quot;female&quot; recepticle, then how can you have a chain of all-male recepticles?&lt;/li&gt;&#xA;&lt;li&gt;Please confirm: a nerve is just the cabling that houses bundles of long, individual strands of neurons, yes?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11581" LastEditorUserId="9943" LastEditDate="2014-12-17T10:12:06.687" LastActivityDate="2018-11-05T13:40:05.970" Title="Nerves, Neurons, Axons and Dendrites by Example" Tags="&lt;neuroanatomy&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25968" PostTypeId="2" ParentId="25965" CreationDate="2014-12-17T09:53:22.907" Score="2" Body="&lt;p&gt;If you don't want acrylamide in your preparation, don't use it, as you will always have some carry-over in the solution. And you will not get rid of it completely, as it at least partly co-precipitated with the nucleic acids (it's used as a co-precipitation agent for this purpose). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the best solution is to use chromatography, either size-exclusion or charged resins. See these two papers for more information:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370578/&quot; rel=&quot;nofollow&quot;&gt;Large-scale preparation and purification of polyacrylamide-free RNA&#xA;oligonucleotides&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2822929/&quot; rel=&quot;nofollow&quot;&gt;Rapid, non-denaturing RNA purification using weak anion-exchange fast&#xA;performance liquid chromatography&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="3340" LastEditDate="2014-12-17T10:18:34.053" LastActivityDate="2014-12-17T10:18:34.053" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="25969" PostTypeId="2" ParentId="25967" CreationDate="2014-12-17T10:08:58.417" Score="4" Body="&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Receptors are typically not located in a neuron. Instead, receptors generally synapse onto a primary neuron, and specifically on the primary neuron's dendrite;  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Within the neuron&lt;/strong&gt; physiological signals are received in the dendrite and are transmitted uni-directionally via the axon to the axon terminal. &lt;strong&gt;Between neurons&lt;/strong&gt; the signal is transmitted from axon to dendrite via the synapse (see figure).  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Although axo-axonal communication exists, it is not the typical way of neural communication (they are regulatory in nature and do not convey information as such). Typically, axons synapse onto another neuron via the dendrite of that second neuron.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The typical connection is the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eJpbb.gif&quot; alt=&quot;synapses&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Nerves typically do not contain cell bodies, only the elongated parts of neurons, i.e. the axons. A nerve is a bundle of axons that contain closely related signals from closely related structures in the body.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-17T10:38:45.977" LastActivityDate="2014-12-17T10:38:45.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25970" PostTypeId="5" CreationDate="2014-12-17T10:13:08.953" Score="0" Body="&lt;p&gt;The study of the physiology of the nervous system, with emphasis on transcellular communication, and cellular and molecular processes involved in neural communication.&lt;/p&gt;&#xA;" OwnerUserId="28834" LastEditorUserId="28834" LastEditDate="2017-03-27T09:47:21.223" LastActivityDate="2017-03-27T09:47:21.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25971" PostTypeId="4" CreationDate="2014-12-17T10:13:08.953" Score="0" Body="The study of the physiology of the nervous system, with emphasis on transcellular communication, and cellular and molecular processes involved in neural communication." OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-18T04:08:28.033" LastActivityDate="2014-12-18T04:08:28.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25972" PostTypeId="1" CreationDate="2014-12-17T10:23:50.473" Score="1" ViewCount="100" Body="&lt;p&gt;The Period/Cryptochrome (PER/CRY) complex is a heterodimer that transcriptionally regulates circadian rhythm. When it is phosphorylated, it is transported to the nucleus and it inhibits a transcription factor that regulates the synthesis of its own subunits (negative feedback).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Research on the circadian molecular clock speaks of an accumulation of PER/CRY complex in the cytoplasm during the day phase (see review &lt;a href=&quot;http://www.nature.com/nrc/journal/v3/n5/full/nrc1072.html&quot; rel=&quot;nofollow&quot;&gt;The circadian clock: pacemaker and tumour suppressor&lt;/a&gt;, Fu and Lee, 2003). Why does this complex not move to nucleus during the day? In other words how is the phosphorylation-dephosphorylation switch controlled?&lt;/p&gt;&#xA;" OwnerUserId="11597" LastEditorUserId="3340" LastEditDate="2014-12-18T17:08:23.273" LastActivityDate="2014-12-18T17:56:20.437" Title="How do PER/CRY complexes accumulate in the cytoplasm?" Tags="&lt;proteins&gt;&lt;circadian-rhythms&gt;&lt;light&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="25973" PostTypeId="1" CreationDate="2014-12-17T10:32:12.427" Score="2" ViewCount="66" Body="&lt;p&gt;I know that there are &lt;a href=&quot;http://en.wikipedia.org/wiki/Nuclear_localization_sequence&quot; rel=&quot;nofollow&quot;&gt;Nuclear Localisation Sequencenes (NLS)&lt;/a&gt;. They can be taken from endogenous or viral proteins and fused to the N or C terminus of my recombinant protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which is the best one? Which the best short one (so that it can be more easily added with a Primer)? Should it be attached to the N or the C terminus?&#xA;Do they influence expression?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have heard that &lt;em&gt;size does matter&lt;/em&gt; (Too large wont fit through the nuclear pore, too smalll will diffuse out again). What is the range of protein sizes that can be targeted efficiently?&lt;/p&gt;&#xA;" OwnerUserId="3042" LastEditorUserId="948" LastEditDate="2014-12-17T17:11:03.663" LastActivityDate="2014-12-17T17:11:03.663" Title="How do I get recombinant proteins into the nucleus of mammal cells?" Tags="&lt;cell-biology&gt;&lt;proteins&gt;&lt;mammals&gt;&lt;synthetic-biology&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="25974" PostTypeId="1" AcceptedAnswerId="27494" CreationDate="2014-12-17T12:40:10.167" Score="9" ViewCount="1421" Body="&lt;p&gt;&lt;em&gt;Based on the comments in &lt;a href=&quot;https://biology.stackexchange.com/questions/21137/can-a-single-axon-propagate-multiple-simultaneous-action-potentials/22015#comment41492_22015&quot;&gt;this&lt;/a&gt; post and also &lt;a href=&quot;http://chat.stackexchange.com/rooms/19544/long-axons-vs-serial-neurons&quot;&gt;this&lt;/a&gt; chat. For discussions and speculations please comment in the chat.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The basic question is what is the advantage of having a single long axon such as that of sciatic nerve (~1m) compared to a series of neurons? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The primary advantage is surely the conduction speed which will get affected because of chemical synapses. However, gap junction synapses can reduce that delay. The larger volume of the soma of the post synaptic neuron may also reduce the conduction speed, but signal strengthening can also happen. Cell architecture can be adjusted to minimize the loss of speed.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The obvious disadvantage of having a single large cell is that there would be tremendous burden on the nucleus for the cellular maintenance. There would be delays in transfer of non-electrical signals such as biomolecules from axon termini to soma and vice versa. Long axons also means continuous transport along them which in turn demands large number of molecular motors and therefore ATP. Moreover, a small injury can disable the entire conduction channel. It can be imagined that this trait (long axons) can also be selected against; injury leading to inability to move and thereby causing perishment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt; (&lt;em&gt;Based on comments to Anne's answer&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Time is of course a valid advantage for having a single axon as an information conduction channel. However, the energy or the maintenance cost is the factor that I am actually interested in. Maintenance cost would increase with cell volume (in fact surface area) and having serial neurons would demand more energy (cumulative) than a single axon (including costs of maintaining a nucleus). However a long cell would need much higher number of molecular motors to maintain the traffic flow rate. All responses that require transcriptional control would be slow (such as response to injury). Moreover a single soma also imposes a limit on the number of mitochondria. There should be a limit on how long an axon can be. I am especially interested in case of big animals (with long hindlimbs) that also have a good reflex (perhaps camels, even horses). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has someone tried to analyse the tradeoffs of having a long axon vs series of neurons connected by gap junctions? If not is this problem worth modeling or quite trivial? &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Saw this in &lt;a href=&quot;https://www.quora.com/What-is-the-longest-axon-in-the-world&quot; rel=&quot;nofollow noreferrer&quot;&gt;Quora&lt;/a&gt;&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;My first thought mostly agreed with the question details, except I'm&#xA;  pretty sure that the dorsal root ganglion (DRG) has a longer axon than&#xA;  the motor information carried in the sciatic nerve (which is the&#xA;  longest nerve in the body, but not axon).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Does this mean that sciatic nerve has serial neurons?&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-01-09T18:25:17.977" Title="Single long axon vs serial neurons" Tags="&lt;cell-biology&gt;&lt;neuroscience&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25975" PostTypeId="2" ParentId="7927" CreationDate="2014-12-17T15:31:32.720" Score="3" Body="&lt;p&gt;ImageJ is a multi platform piece of software that has a cell counter module that might be of some use, and hey its &lt;strong&gt;free!&lt;/strong&gt; Its easy to use and so ludicrously crude that it is very  versatile. I remember using it in undergrad to count cells under the microscope automatically after a few image contrast tweaks. I don't see why this couldn't be reapplied to count eggs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Download:&lt;/em&gt; &lt;a href=&quot;http://rsb.info.nih.gov/ij/download.html&quot; rel=&quot;nofollow&quot;&gt;http://rsb.info.nih.gov/ij/download.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Cell Counter documentation:&lt;/em&gt; &lt;a href=&quot;http://imagej.nih.gov/ij/plugins/cell-counter.html&quot; rel=&quot;nofollow&quot;&gt;http://imagej.nih.gov/ij/plugins/cell-counter.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2014-12-17T18:11:48.003" LastActivityDate="2014-12-17T18:11:48.003" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25976" PostTypeId="1" AcceptedAnswerId="25979" CreationDate="2014-12-17T15:57:54.120" Score="3" ViewCount="13350" Body="&lt;p&gt;I live in Canada and tap water is drinkable, as a matter of fact, the government puts a little bit of flouride in the tap water so it cleans your teeth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My wife and mom always tells me not to drink the tap water when it's warm/hot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there something in the water that's bad for the body or is this a myth? (bacterias in warm/hot water vs cold)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Added info: The water is heated in the water heater which is in the basement of my house. It is a new water heater, only a year old. My house is built 7 years ago, which for a house it's not old. I don't know about the pipes though&lt;/p&gt;&#xA;" OwnerUserId="11602" LastEditorUserId="11602" LastEditDate="2014-12-17T16:30:49.187" LastActivityDate="2014-12-17T16:30:49.187" Title="Can I drink warm/hot tap water?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ClosedDate="2014-12-17T17:45:36.957" ContentLicense="CC BY-SA 3.0" />
  <row Id="25977" PostTypeId="2" ParentId="25976" CreationDate="2014-12-17T16:03:30.593" Score="3" Body="&lt;p&gt;The reason for this worry is chemical--as water warms up, more contaminants can dissolve in the water. With water pipes specifically, people worry about lead contamination. Modern pipes are not as likely to corrode (or even be made of lead) as old pipes, so this is more of a concern in older buildings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this &lt;a href=&quot;http://www.nytimes.com/2008/01/29/health/29real.html?_r=0&quot; rel=&quot;nofollow&quot;&gt;NYT article&lt;/a&gt; for more information.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2014-12-17T16:03:30.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25978" PostTypeId="2" ParentId="25913" CreationDate="2014-12-17T16:08:04.423" Score="3" Body="&lt;p&gt;Codon usage optimization is still pretty much heurestic. The most common factor we think are important in E. Coli are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;optimization to highly expressed genes, i.e. maximization of codon adaptation index &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19359587/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/19359587/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;keeping the optimal GC content &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0107319&quot; rel=&quot;nofollow&quot;&gt;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0107319&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;not introducing motifs that are somehow detrimental, e.g. restriction enzymes, or some dinucleotides &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056642&quot; rel=&quot;nofollow&quot;&gt;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056642&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;adapting to available tRNA &lt;a href=&quot;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007002&quot; rel=&quot;nofollow&quot;&gt;http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007002&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;minimizing folding energy (in the first ca. 30 codons) and minimizing the amount of hairpins at the 5' end &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0014579305010719&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0014579305010719&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;optimization of 'codon context' e.g. dicodons but also using nonoptimal codons between secondary structure for more accurate folding &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15772378&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/15772378&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;optimization of codon balance and also maybe the introduction of a 'ramp of slow codons' in the beginning of a gene to avoid 'traffic jams' of ribosomes later on. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20403329&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/20403329&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Most probably it's a mixture of all of those.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disclaimer: We are working on a codon optimization strategy for e.coli/yeast/hela and it works in e. coli but is yet untested in human cells. If you want to take a long shot just shoot me a message and we could try it. Apart from this, I would also offer you to have a look at your sequence and see if there is anything 'strange' from the codon usage point of view and what I think what be the best optimization strategy.&lt;/p&gt;&#xA;" OwnerUserId="11603" LastEditorUserId="3971" LastEditDate="2015-03-12T14:33:27.593" LastActivityDate="2015-03-12T14:33:27.593" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="25979" PostTypeId="2" ParentId="25976" CreationDate="2014-12-17T16:14:08.467" Score="4" Body="&lt;p&gt;This actually depends on how your tap water is warmed. &#xA;If you have a personal water heater, which is connected to your tap with non-corrodable pipes, then there is essentially no difference. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if the heating comes from a common source, then it would be very difficult to verify that the heater-tap connection does not contain any corrodable pipes. In this case, it might be better to not use the warm water for direct drinking, especially if the building is old.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A 7-year old house should not have lead pipes installed, since the &lt;a href=&quot;http://www.hc-sc.gc.ca/ewh-semt/pubs/water-eau/lead-plomb-eng.php&quot; rel=&quot;nofollow&quot;&gt;Canadian Plumbing Code&lt;/a&gt; has banned lead pipes since 1975. As such, I believe that your warm water is safe to drink. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The National Plumbing Code allowed lead as an acceptable material for pipes until 1975 and in solder until 1986. All provinces and territories use the National Plumbing Code as a basis for their own regulations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2014-12-17T16:14:08.467" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="25980" PostTypeId="1" AcceptedAnswerId="26001" CreationDate="2014-12-17T16:52:11.067" Score="3" ViewCount="47" Body="&lt;p&gt;If certain cells or tissue in a specific part of the body are for some reason overworked; like the cases of severe acid reflux damaging the throat repeatedly and the cells in the throat having to do growth and repair a lot more than they would with a healthy person -- or problems in the stomach attacking the stomach lining a lot, causing 'extra' growth and repair; could these situations of 'extra' growth and repair cause various cells used in these processes to mutate with all the cellular division and replication required? And maybe some of these extra-growth-and-repair induced mutations might cause the apoptosis mechanisms to malfunction?&lt;/p&gt;&#xA;" OwnerUserId="11605" LastEditorUserId="948" LastEditDate="2014-12-17T17:07:10.747" LastActivityDate="2014-12-18T02:35:21.700" Title="Regarding tumors and their developement" Tags="&lt;cancer&gt;&lt;apoptosis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25981" PostTypeId="2" ParentId="14671" CreationDate="2014-12-17T17:12:16.630" Score="3" Body="&lt;p&gt;It depends on the seed and fruit you're talking about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The amount of DNA in your crushed up sample of plant matter depends on only one thing--how many cells are in your sample. Look at this diagram of a kernel of corn (&lt;a href=&quot;http://courses.bio.indiana.edu/L104-Bonner/&quot; rel=&quot;nofollow noreferrer&quot;&gt;U of Indiana&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zsLYKm.jpg&quot; alt=&quot;corn&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are different cell densities in each area--in the endosperm, the cells can be huge (and therefore have a lower density of DNA when compared with the embryo).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's look at a stained mustard seed (&lt;a href=&quot;http://www.seedbiology.de/structure.asp&quot; rel=&quot;nofollow noreferrer&quot;&gt;U of London&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bX8Qk.jpg&quot; alt=&quot;mustard seed histology&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, the cells here are very dense. More dense means more DNA &lt;em&gt;per unit sample&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as fruit is concerned, the same rule of thumb applies. &lt;a href=&quot;http://naldc.nal.usda.gov/download/IND43969103/PDF&quot; rel=&quot;nofollow noreferrer&quot;&gt;Verner, 1938&lt;/a&gt; shows some cool apple tissue histology that might give you an idea of cell density in fruit tissue (again, it will be different in different fruits--search for &lt;code&gt;&quot;fruitname histology&quot;&lt;/code&gt; if you're interested).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, now that we've talked about density, we need to actually think about getting the DNA out. The extraction process is actually &lt;strong&gt;much&lt;/strong&gt; more important in terms of your final yield.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many plant seeds contain polyphenolics, which can cause DNA degradation. This protocol (&lt;a href=&quot;http://www.hort.cornell.edu/reisch/grapegenetics/DNA_Protocol.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cornell U&lt;/a&gt;) details many of the possible shortcomings:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These compounds have also been reported to cause difficulty in DNA purification in other plant species; polysaccharides (Murray and Thompson, 1980; Fang et al., 1992); polyphenolic compounds (Katterman and Shattuck, 1983; Couch and Fritz, 1990; Howland et al. 1991; Collins and Symons, 1992); and sticky and resinous materials (Webb and Knapp, 1990).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These contaminants can degrade DNA, but also render it unusable in PCR amplification and endonuclease digestion (&lt;a href=&quot;http://nar.oxfordjournals.org/content/25/5/1085.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kim &lt;em&gt;et al.&lt;/em&gt; 1997&lt;/a&gt;, &lt;a href=&quot;http://www.hort.cornell.edu/reisch/grapegenetics/DNA_Protocol.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cornell U&lt;/a&gt;, &lt;a href=&quot;http://www.epibio.com/docs/default-source/forum-archive/forum-16-1---rapid-dna-extraction-from-plant-seeds-for-pcr.pdf?sfvrsn=4&quot; rel=&quot;nofollow noreferrer&quot;&gt;EPICENTRE Biotechnologies&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall, there are definitely species-specific differences in fruit/seed plant DNA content. &lt;strong&gt;Practically&lt;/strong&gt;, however, the most important factor in DNA yield and viability for future experimentation is sample purity and contamination. Specific fruits and seeds may contain one or more of the above contaminants, so the answer to &quot;Seeds or fruits?&quot; definitely depends on the species of plant you're working with.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2014-12-17T17:12:16.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25982" PostTypeId="1" AcceptedAnswerId="36814" CreationDate="2014-12-17T18:05:48.237" Score="1" ViewCount="941" Body="&lt;ol&gt;&#xA;&lt;li&gt;A multivalent antibody molecule such as Immunoglobulin M Immunoglobulin A etc bind to more than one antigens or epitopes but I am confused about that wheather these multivalent antibodies bind to identical epitopes or can bind to different epitopes? means if one molecule of Immunoglobulin M being pentameric can bind to 10 epitopes at a time the 10 epitopes that it binds Will be identical or can be different..? Confused about that..       2. And also another Question I want to ask that as Immunoglobulin G,Immunoglobulin D and Immunoglobulin E are monomers but all of them have 2 antigen binding sites so we consider them as Mutivalent antibodies or not and if we cnsider them as multivalent antibodies then what are the Examples of monovalent antibody that Specifically only bind to One antigen molecule or epitope? Because as far as i Have studied Antibody or Immunoglobulin molecule hae specific &quot;Y&quot; structure that contains 2 binding sites. Similarly in this case also want answer that these momomeric ImmunoglobulinsG,D,E each binds to 2 identical antigens or epitopes or can bind to two different epitopes. Means that if Immunoglobulin G is binding to two epitopes these epitopes will be identical or can be different...??? :/&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5729" LastEditorUserId="5729" LastEditDate="2014-12-17T18:32:07.913" LastActivityDate="2015-08-13T14:27:02.210" Title="Binding of Multivalent Antibody to mutiple epitopes?" Tags="&lt;biochemistry&gt;&lt;immunology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25983" PostTypeId="2" ParentId="21431" CreationDate="2014-12-17T18:21:46.143" Score="1" Body="&lt;p&gt;In some types of cancer cells, an enzyme called telomerase can actually rebuild the telomeres, making a cell appear &quot;younger&quot; than it actually is and preventing it from senescing (reaches a point where it stops dividing).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Telomerase, a eukaryotic ribonucleoprotein (RNP) complex, helps to stabilize telomere length in human stem cells, reproductive cells and cancer cellsby adding TTAGGG repeats onto the telomeres using its intrinsic RNA as a template for reverse transcription.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://hmg.oxfordjournals.org/content/10/7/677.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Shay &lt;em&gt;et al&lt;/em&gt;. 2001&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This Myerson review from 2000, &lt;a href=&quot;http://jco.ascopubs.org/content/18/13/2626.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;Role of Telomerase in Normal and Cancer Cells&lt;/a&gt;,&#xA; provides a good overview of telomeres in normal and cancerous cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's not that telomeres (shown in image below) are more &lt;em&gt;robust&lt;/em&gt; in cancer cells, they are actually &lt;em&gt;rebuilt&lt;/em&gt; by the telomerase enzyme.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Incla.jpg&quot; alt=&quot;telomere&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(&lt;a href=&quot;http://socratic.org/questions/how-does-the-dna-sequence-change-with-distance-from-the-telomere&quot; rel=&quot;nofollow noreferrer&quot;&gt;Socratic&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2014-12-17T18:21:46.143" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25984" PostTypeId="2" ParentId="25982" CreationDate="2014-12-17T18:32:30.790" Score="5" Body="&lt;p&gt;Non-engineered IgM (such as is produced &lt;em&gt;in vivo&lt;/em&gt;) has the same binding domain on all &quot;arms&quot; of the pentamer. They don't bind to more than one &lt;a href=&quot;http://en.wikipedia.org/wiki/Antigen&quot; rel=&quot;noreferrer&quot;&gt;antigen&lt;/a&gt;, instead they can bind to multiple copies of the same &lt;a href=&quot;http://en.wikipedia.org/wiki/Epitope&quot; rel=&quot;noreferrer&quot;&gt;epitope&lt;/a&gt;. Due to steric hindrance, a single IgM molecule generally will not bind at all 10 binding sites.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2014-12-17T18:32:30.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25985" PostTypeId="1" AcceptedAnswerId="26004" CreationDate="2014-12-17T18:51:55.003" Score="5" ViewCount="11942" Body="&lt;p&gt;I heard that irises are different and unique for every person. According &lt;a href=&quot;http://research.ijcaonline.org/volume44/number7/pxc3878434.pdf&quot; rel=&quot;nofollow&quot;&gt;this link&lt;/a&gt;, probability of two irises having identical pattern is 1 in 10 to the 78th power. That's how &lt;a href=&quot;https://en.wikipedia.org/wiki/Iris_recognition&quot; rel=&quot;nofollow&quot;&gt;iris scanners&lt;/a&gt; identify the identity of people. This technology is becoming very evident. So I ask, why are irises for each person different and unique?&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="10401" LastEditDate="2014-12-18T03:17:35.620" LastActivityDate="2014-12-18T06:10:19.637" Title="Why are irises unique?" Tags="&lt;eyes&gt;&lt;human-genetics&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25986" PostTypeId="1" AcceptedAnswerId="25987" CreationDate="2014-12-17T19:04:11.793" Score="8" ViewCount="506" Body="&lt;p&gt;I am interested in understanding what &quot;pain&quot; and &quot;hot/cold&quot; &lt;em&gt;look&lt;/em&gt; like, as far as waves signatures (signal processing) go.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My general &lt;em&gt;understanding&lt;/em&gt; of how pain (nociceptive pathways) and hot/cold (thermoreceptive pathways) works are as follows:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A sensory receptor (nociceptor for pain and thermoreceptor for temperature) responds to analog stimuli, and synapses an appropriate signal onto a first-order neuron (the neuron it directly connects to); then&lt;/li&gt;&#xA;&lt;li&gt;The signal travels up the nerve, neuron to neuron, through the spinal cord, up into the brainstem, and finally into the somatosensory cortex; then&lt;/li&gt;&#xA;&lt;li&gt;That cortex decodes the signal and interprets it as &quot;pain&quot; or &quot;hot/cold&quot;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Further, my &lt;em&gt;understanding&lt;/em&gt; is that these signals are electrochemical in nature:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;While passing through a neuron (dendrite -&gt; axon) the signal is of a purely electrical form, no different than the electricity racing around the motherboard of my laptop right now; but...&lt;/li&gt;&#xA;&lt;li&gt;To synapse from the axon of one neuron to the dendrite of the next sequential neuron, the electrical signal is transformed (somehow, this is where I'm fuzzy) into a chemical signal, and essentially hormones/messenger chemicals ferry the preserved signal to the next neuron's dendrite. At that point, the dendrite converts the chemical signal back into electricity, and on and on this goes until we reach the cortex.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, only because I am a total neophyte here, I have to preface my actual question by asking the greater community at large: &lt;strong&gt;is my general understanding here correct?&lt;/strong&gt; If not, please begin by correcting me!&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;The question at hand&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;If everything I've currently stated is more or less correct, then this implies that, while traveling &lt;em&gt;inside&lt;/em&gt; a neuron (dendrite -&gt; axon), neurological signals such as pain or temperature exist as waves of electricity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm wondering:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What do these waves look like? Do they have special names? Are they sinusoidal in nature? Do they travel with known periods/frequencies/amplitudes? &lt;strong&gt;Can I represent these waves as trigonometric functions?&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;I'm sure this differs based on genetics and all sorts of other factors, but what are the general power ratings for the central nervous system? &lt;strong&gt;How much Watts/Volts/Amps travel with these signals?&lt;/strong&gt; Are there standard ranges?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Please note&lt;/strong&gt;: This is not homework! I am a grown man who works as a software engineer by day and I migrated here from the Stack Overflow community. I am asking this question because I have absolutely zero background in biology, and after scouring the internet for an answer to this, I could find nothing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please don't hold back with lofty, low-level explanations. Give me &lt;strong&gt;science&lt;/strong&gt; here! Though I am not a biologist, I'm certainly no dummy either.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;" OwnerUserId="11581" LastEditorUserId="9943" LastEditDate="2014-12-18T00:02:14.853" LastActivityDate="2015-02-21T20:22:19.643" Title="What does pain look like in wave form?" Tags="&lt;pain&gt;&lt;electrophysiology&gt;&lt;neurophysiology&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="25987" PostTypeId="2" ParentId="25986" CreationDate="2014-12-17T19:18:13.387" Score="5" Body="&lt;p&gt;I don't want to comment about the nature of electric signals in neurons (as I know only little about physiology and neurophysiology). But here is a short answer that may already help you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neuronal electric signals are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Action_potential&quot; rel=&quot;nofollow noreferrer&quot;&gt;action potential&lt;/a&gt;. If you register the voltage at a given location on the axon of a neuron through time you will see something like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lI36e.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This picture shows one action potential. Of course when you feel pain it lasts for more than 5 milliseconds. In such case, if you record the voltage for a longer period of time you will just see a series of action potentials. You should have a look to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Action_potential&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki page&lt;/a&gt; for more information.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-02-21T20:22:19.643" LastActivityDate="2015-02-21T20:22:19.643" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="25988" PostTypeId="2" ParentId="21431" CreationDate="2014-12-17T19:44:27.860" Score="3" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Telomere&quot; rel=&quot;nofollow noreferrer&quot;&gt;Telomeres&lt;/a&gt; are at the end of the chromosomes and get shorter with every cell division, since the lagging strand is missing a start point for the DNA polymerase. This limits the number of cell divisions to 40 to 60 before the cells go into &lt;a href=&quot;http://en.wikipedia.org/wiki/Senescence&quot; rel=&quot;nofollow noreferrer&quot;&gt;senescence&lt;/a&gt; and stop dividing (they are not dying at this point). This phenomenon is called the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hayflick_limit&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hayflick limit&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cell populations which need to divide more often or cells which need to maintain a long telomer status (stem cells) because they give rise to other cell populations, have an enzyme called &lt;a href=&quot;http://en.wikipedia.org/wiki/Telomerase&quot; rel=&quot;nofollow noreferrer&quot;&gt;telomerase&lt;/a&gt; which has it's own (RNA) template and can enlarge the length of the telomere. See the figure how this works (from the Wikipedia article on Telomerase):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vdftI.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question: Younger cells have longer telomeres (compared to older cells). Usually cells stop dividing, when their telomeres get too short to avoid chromosomal damage, due to the progressive shortening of the chromosomes. In cancer cells the pathways controlling this (for example &lt;a href=&quot;http://en.wikipedia.org/wiki/P53&quot; rel=&quot;nofollow noreferrer&quot;&gt;p53&lt;/a&gt; and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Retinoblastoma_protein&quot; rel=&quot;nofollow noreferrer&quot;&gt;retinoblastoma&lt;/a&gt; pathway) are often mutated, so that the cells divide forever. This leads to chromosomal instability, further mutations and chromosomal disarrangements, which can cause real havoc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also happens for some cancers that they manage to reactivate their telomerase, thus keeping their telomers at a healthy length and preventing chromosomal damage. By this activation they get around reaching the Hayflick limit for the maximum number of cell divisions and are truly capable of living forever. The famous HeLA cell line for example is telomerase positive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The activity of the telomerase in one cell has no effect on the neighboring cells.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-17T19:44:27.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25989" PostTypeId="2" ParentId="25986" CreationDate="2014-12-17T19:51:52.860" Score="2" Body="&lt;p&gt;Since the action potential question has already been answered, I will attempt to answer &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I'm sure this differs based on genetics and all sorts of other factors, but what are the general power ratings for the central nervous system? How much Watts/Volts/Amps travel with these signals? Are there standard ranges?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You are right in that there is a large amount of variation in the electrical variables, however neurons generally have an action potential voltage of ~70mV, give and take 30. I could not find any papers in a cursory search on the power of neurons. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your &quot;comment question&quot; due to lack of space, (1) neurons encode data in a binary fashion due to their on or off mechanism of impulse transmission, and there have been studies done in deciphering what these pulses mean. However, it is still an active field of research with many questions. (2) However, pain signals are only transmitted on sensory neurons containing nociceptors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should also read up on how an action potential is generated, as that would help you understand the concept better. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2014-12-17T19:51:52.860" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="25990" PostTypeId="1" AcceptedAnswerId="26000" CreationDate="2014-12-17T20:10:05.123" Score="0" ViewCount="185" Body="&lt;p&gt;I am studying the treatment plan of adrenergic agents for heart failure. &#xA;Then, in the group discussion, spironolactone was included. &#xA;But I cannot understand how it is relevant when considering adrenergic agents for treatment of heart failure.&#xA;It is probably that it was only mentioned because adrenergic agents are usually used in combination with ABC therapy (antiplatelet, beta blockers, ...). &#xA;This includes also diuretics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Spironolactone is diuretic and antihypertensive. &#xA;But I cannot understand how one can classify it adrenergic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the role of spironolactone with adrenergic agents in heart failure?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-18T07:53:33.667" LastActivityDate="2014-12-18T07:53:33.667" Title="Spironolactone's role with adrenergic agents in heart failure?" Tags="&lt;human-biology&gt;&lt;pharmacology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25991" PostTypeId="2" ParentId="17557" CreationDate="2014-12-17T20:10:22.540" Score="5" Body="&lt;p&gt;There are three worms which have been found in the sediment of the mediterranean seafloor, which not only live without oxygen but also do not tolerate the exposure to oxygen. They belong to the metazoans, for more details see either the report (reference 1) or the original article (reference 2). They reach a size og about 1mm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://phys.org/news189836027.html&quot;&gt;Scientists discover first multicellular life that doesn't need&#xA;oxygen&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.biomedcentral.com/1741-7007/8/30/abstract&quot;&gt;The first metazoa living in permanently anoxic conditions&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-17T20:10:22.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25992" PostTypeId="1" AcceptedAnswerId="25999" CreationDate="2014-12-17T20:54:46.687" Score="3" ViewCount="7468" Body="&lt;p&gt;I am looking for the names of the nerves in 3 specific locations of the human body:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The nerve running along the &quot;top&quot; (opposite side of the palm) portion of the thumb, from knuckle to fingernail (see 1st picture below); and&lt;/li&gt;&#xA;&lt;li&gt;The nerve running along the anterior tibia (also see 1st picture below); and&lt;/li&gt;&#xA;&lt;li&gt;The nerve(s) of the face running along the eyebrows and outer edges of the eye sockets (see 2nd picture below)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;After looking &lt;a href=&quot;https://bedahunmuh.files.wordpress.com/2010/05/facial-nerve-schema.jpg?w=800&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;, &lt;a href=&quot;http://www.innerbody.com/image/nerv01.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.bartleby.com/107/illus788.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;, the best I could muster was:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The &lt;strong&gt;median nerve&lt;/strong&gt; is the nerve that carries sensory signals from the top of my thumb; and&lt;/li&gt;&#xA;&lt;li&gt;The &lt;strong&gt;superficial peroneal nerve&lt;/strong&gt; is the nerve that carries sensory signals from my anterior tibia&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;But in every diagram of the face's nerves, there are simply too many for the article/blog/diagram to enumerate, and I can't discern which specific nerve or nerves runs outside of the eyes and across the brows.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any ideas? Here are the pics to solidify the specific areas I'm looking for:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XlI2F.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/F81wi.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please note: this is not homework! And although it may be considered by some to be a rudimentary question, I have actively tried to research this myself and have come up short. Below, I explain all the failed methods I attempted to figure this out on my own. So all this to say: if you do down/closevote this, please don't do it because you think it's homework or because you think it shows a lack of research!&lt;/p&gt;&#xA;" OwnerUserId="11581" LastEditorUserId="9943" LastEditDate="2014-12-17T23:50:19.273" LastActivityDate="2014-12-18T01:48:49.093" Title="Names of nerves in hands, shins and face" Tags="&lt;human-anatomy&gt;&lt;cranial-nerves&gt;&lt;peripheral-nervous-system&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="25993" PostTypeId="2" ParentId="17400" CreationDate="2014-12-17T20:55:40.413" Score="5" Body="&lt;p&gt;In biochemistry the K&lt;sub&gt;i&lt;/sub&gt; is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Dissociation_constant&quot; rel=&quot;nofollow noreferrer&quot;&gt;dissociation constant&lt;/a&gt; of a complex and molecules bound to it. It is a measure for the  functional strength of the inhibitor. This can for example be an enzyme and its substrate, the K&lt;sub&gt;i&lt;/sub&gt; defines the stability of the complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/IC50&quot; rel=&quot;nofollow noreferrer&quot;&gt;IC&lt;sub&gt;50&lt;/sub&gt;&lt;/a&gt; on the other hand is the halfmaximal inhibitory concentration of a substance on a biochemical process. This can be an inhibitor of an enzyme. &#xA;See this figure (from the Wikipedia article on the IC&lt;sub&gt;50&lt;/sub&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/x4qHu.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The K&lt;sub&gt;i&lt;/sub&gt; plays an important role in the calculation of the IC&lt;sub&gt;50&lt;/sub&gt;, as it defines the strength of the enzyme-inhibitor complex.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-17T20:55:40.413" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25994" PostTypeId="1" AcceptedAnswerId="25995" CreationDate="2014-12-17T21:23:12.063" Score="4" ViewCount="10778" Body="&lt;p&gt;Are all children born with only either male or female body parts (other than exceptions), or is there actually a natural third gender with the physical characteristics of both genders, e.g. the child has the genitalia, or reproductive organs, of both sexes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Wikipedia they are only either male or female &lt;a href=&quot;http://en.wikipedia.org/wiki/Sex_assignment&quot; rel=&quot;noreferrer&quot;&gt;when born&lt;/a&gt;. They only &lt;a href=&quot;http://en.wikipedia.org/wiki/Gender_identity&quot; rel=&quot;noreferrer&quot;&gt;feel&lt;/a&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/Trans_woman&quot; rel=&quot;noreferrer&quot;&gt;different&lt;/a&gt; later on in life.&lt;/p&gt;&#xA;" OwnerUserId="11608" LastEditorUserId="14629" LastEditDate="2017-03-20T18:11:52.047" LastActivityDate="2017-06-14T03:13:24.460" Title="Are transgender people born physically different from others?" Tags="&lt;human-anatomy&gt;&lt;gender&gt;&lt;sexuality&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="25995" PostTypeId="2" ParentId="25994" CreationDate="2014-12-17T22:17:29.090" Score="12" Body="&lt;p&gt;The concept of &lt;a href=&quot;http://en.wikipedia.org/wiki/Transgender&quot; rel=&quot;nofollow noreferrer&quot;&gt;transgenders&lt;/a&gt; has nothing to do with sexual organs at birth. Transgenders is a concept that has to do with sociology, not biology. See the wiki link.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Intersex&quot; rel=&quot;nofollow noreferrer&quot;&gt;intersex&lt;/a&gt; (previously called Hermaphroditism) has to do with biology. The wiki link makes a great job at defining intersex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short: A transgender person is born anatomically either male or female (with eventually exception of intersex who go on to become transgender) and they then identify themselves to the opposite sex (or a third sex) rather than identifying themselves to their actual anatomic sex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that &lt;a href=&quot;https://biology.stackexchange.com/questions/52149/how-is-trangender-female-different-from-normal-female-biologically&quot;&gt;this post&lt;/a&gt; is closely related.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2017-06-14T03:13:24.460" LastActivityDate="2017-06-14T03:13:24.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25996" PostTypeId="1" AcceptedAnswerId="26021" CreationDate="2014-12-17T22:38:58.193" Score="4" ViewCount="170" Body="&lt;p&gt;Related: &lt;a href=&quot;https://biology.stackexchange.com/questions/17557/whats-the-biggest-obligate-anaerobic-organism-discovered-till-now&quot;&gt;What&amp;#39;s the biggest obligate anaerobic organism discovered till now?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I had always assumed that the &lt;em&gt;Riftia&lt;/em&gt; tube worms were obligately anaerobic since they lived next to anoxic volcanic vents, but a quick literature search showed it to be a facultative anaerobe, &lt;a href=&quot;http://www.int-res.com/articles/meps/174/m174p151.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;being able to survive at least 60 hours&lt;/a&gt; without oxygen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If &quot;facultative anaerobe&quot; is defined as being able to survive at least 24 hours in the absence of molecular oxygen in an otherwise normal environment, are there any metazoal organisms larger than &lt;em&gt;Riftia&lt;/em&gt; (which are up to 1.5m long)?&lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-12-18T19:26:05.330" Title="What is the biggest facultative anaerobic metazoan known to science?" Tags="&lt;metabolism&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="25997" PostTypeId="5" CreationDate="2014-12-18T00:12:50.960" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-12-18T00:12:50.960" LastActivityDate="2014-12-18T00:12:50.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25998" PostTypeId="4" CreationDate="2014-12-18T00:12:50.960" Score="0" Body="The discipline of biomedical engineering of the nervous system. Notable device examples include the pacemaker, cochlear implants and retinal implants." OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-18T04:08:17.883" LastActivityDate="2014-12-18T04:08:17.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="25999" PostTypeId="2" ParentId="25992" CreationDate="2014-12-18T01:48:49.093" Score="2" Body="&lt;p&gt;You are looking for the Trigeminal nerve, the largest nerve in the face. Here it is with its branches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FwYaB.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is both afferent and efferent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/q7HMw.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/310889&quot; rel=&quot;nofollow noreferrer&quot;&gt;Afferent and efferent components of the facial nerve in the bullfrog (Rana catesbeiana)&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.bmc.med.utoronto.ca/cranialnerves/?page_id=26&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cranial Nerves Illustrated: Figure V-4 General sensory component of the trigeminal nerve, ophthalmic (V1) division.&#xA;General sensory afferent (blue-green)&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-18T01:48:49.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26000" PostTypeId="2" ParentId="25990" CreationDate="2014-12-18T02:34:33.590" Score="1" Body="&lt;p&gt;Spironolactone works through a mechanism different than the adrenergics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You said of the ABC approach, &quot;This includes also diuretics.&quot; That's why Spironolactone was included.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Spironolactone is a specific pharmacologic antagonist of aldosterone, acting primarily through competitive binding of receptors at the aldosterone-dependent sodium-potassium exchange site in the distal convoluted renal tubule. Spironolactone causes increased amounts of sodium and water to be excreted, while potassium is retained. &lt;strong&gt;Spironolactone acts both as a diuretic and as an antihypertensive drug by this mechanism.&lt;/strong&gt; It may be given alone or with other diuretic agents which act more proximally in the renal tubule. Aldosterone interacts with a cytoplasmic mineralocorticoid receptor to enhance the expression of the Na+, K+-ATPase and the Na+ channel involved in a Na+ K+ transport in the distal tubule . Spironolactone bind to this mineralcorticoid receptor, blocking the actions of aldosterone on gene expression. Aldosterone is a hormone; its primary function is to retain sodium and excrete potassium in the kidneys.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The lack of a decrease in the neuroendocrine prognostic markers, norepinephrine and endothelin-1, suggests that &lt;strong&gt;the beneficial effects of spironolactone are mainly related to mechanisms independent of the adrenergic and endothelin systems.&lt;/strong&gt; The escape of AII and aldosterone, probably reflecting activated feedback mechanisms, confirms the specific activity of spironolactone on the &lt;em&gt;renin-angiotensin-aldosterone system&lt;/em&gt; and supports the hypothesis that the beneficial effects of spironolactone on the progression of heart failure are mediated by the blockade of aldosterone receptors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://pubchem.ncbi.nlm.nih.gov/compound/spironolactone#section=Interactions&quot; rel=&quot;nofollow&quot;&gt;PubChem&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://content.onlinejacc.org/article.aspx?articleid=1130466&quot; rel=&quot;nofollow&quot;&gt;Beneficial neurohormonal profile of spironolactone in severe congestive heart failure: Results from the RALES neurohormonal substudy&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2014-12-18T06:45:26.357" LastActivityDate="2014-12-18T06:45:26.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26001" PostTypeId="2" ParentId="25980" CreationDate="2014-12-18T02:35:21.700" Score="1" Body="&lt;p&gt;There is indeed a positive correlation between gastric reflux disease and esophageal cancer, and also between stomach ulcerations and stomach cancer. There are more than one possible mechanisms for these correlations to arise, but what you are proposing is definitely a prime suspect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.webmd.com/heartburn-gerd/news/20130523/chronic-heartburn-may-raise-odds-for-throat-cancer-study&quot; rel=&quot;nofollow&quot;&gt;http://www.webmd.com/heartburn-gerd/news/20130523/chronic-heartburn-may-raise-odds-for-throat-cancer-study&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10658066&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/10658066&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10001" LastActivityDate="2014-12-18T02:35:21.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26003" PostTypeId="1" CreationDate="2014-12-18T05:10:00.287" Score="2" ViewCount="106" Body="&lt;p&gt;So my major is in pharmacy but both my master and my (currently in progress) doctoral degree are both in theoretical chemistry. My thesis is about quantum chemistry and proteins, but it has a certain amount of phylogeny and evolutionary biology such that I've had to learn some phylogenic analysis methodology and have had my share of experience using sequence databases and analysis tools around the web. Although I do not focus particularly in the human genome, or even human proteins for that matter, I got myself thinking about a rather curious question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am by no means a specialist in molecular and evolutionary biology, but I do understand that chromosomes and genes come up in the population by several mechanisms. Now, it is interesting to me that all the information regarding biological sex in humans is contained within a single chromosomal switch, the Y chromosome. Given that fact, I asked myself &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Do we have some order in the arrangement of our genes in their chromosomes?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So now I turn that question to you people, who seem to be more well-equipped to tackle theses questions than I certainly am. Forgive my ignorance and indulge my curiosity!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[EDIT FOR CLARIFICATION]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Okay, clarifying some points that were raised in the comments:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is about whether there is a pattern in the organization of genes into chromosomes. For example, the Y chromosome clearly contains a lot of genes associated with sexual dimorphism in humans. I was wondering if chromosomes in general follow that general pattern. If, for example, Chromosome 1 contains such and such kinds of genes, as if it had hints of an overarching &quot;theme&quot; to it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is that clearer?&lt;/p&gt;&#xA;" OwnerUserId="11613" LastEditorUserId="11613" LastEditDate="2014-12-18T17:28:12.097" LastActivityDate="2014-12-18T17:28:12.097" Title="Are the Chromosomes organized in any meaningful way?" Tags="&lt;genetics&gt;&lt;human-genetics&gt;&lt;human-genome&gt;" AnswerCount="0" CommentCount="7" ClosedDate="2014-12-18T16:22:43.033" ContentLicense="CC BY-SA 3.0" />
  <row Id="26004" PostTypeId="2" ParentId="25985" CreationDate="2014-12-18T06:10:19.637" Score="5" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Iris_%28anatomy%29&quot; rel=&quot;noreferrer&quot;&gt;Iris&lt;/a&gt; is a thin, circular structure in the eye, responsible for&#xA;controlling the diameter and size of the pupil and thus the amount of&#xA;light reaching the retina. The color of the iris gives the eye its&#xA;color. In optical terms, the pupil is the eye's aperture and the iris&#xA;is the diaphragm that serves as the aperture stop.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Color and structure of iris is greatly depended upon genetic links, but the patterns are not. Iris is developed by the prenatal(before birth) growth through a process of tight forming and folding of the tissue membrane.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The human iris begins to form during the third month of gestation. The structures creating its distinctive pattern are complete by the eighth month of gestation, but pigmentation continues into the first years after birth. The layers of the iris have both ectodermal and mesodermal embryological origin, consisting of (from back to front): a darkly pigmented epithelium; pupillary dilator and sphincter muscles; heavily vascularized stroma (connective tissue of interlacing ligaments containing melanocytes); and an anterior layer of chromataphores and melanocytes with a genetically determined density of melanin pigment granules. The combined effect is a visible pattern displaying various distinctive features such as arching ligaments, crypts, furrows, ridges, and a zigzag collarette. Iris colour is determined mainly by the density of the stroma and its melanin content, with blue irises resulting from an absence of pigment: longer wavelengths differentially penetrate while shorter wavelengths are reflected and scattered, a phenomenon resembling that which makes the sky blue. The heritability and ethnographic diversity of iris colour have long been studied, but until the present research, little attention had been paid to the achromatic pattern complexity and textural variability of the iris among individuals.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cl.cam.ac.uk/%7Ejgd1000/anatomy.html&quot; rel=&quot;noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Iris Recognition vs. Retina Scanning&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Iris and retinal scanning are ocular based biometric identifiers. Iris recognition uses a camera to capture image of the iris. Iris is the only internal organ visible from outside the body. Iris scanners can acquire an image of the eye from a distance of 3 to 10 inches.&#xA;In retinal scanning, the device send a beam of light deep inside the eye to capture the image of retina, which is located on the back of the eye. retinal scanning is not widely used due to the intrusive methods used to capture the image.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Factors which enhance the iris scanning system&lt;/strong&gt;,&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8JTxd.png&quot; alt=&quot;enter image description here&quot; /&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/sXX1H.png&quot; alt=&quot;enter image description here&quot; /&gt;&#xA;&lt;a href=&quot;http://www.irisid.com/irisrecognitiontechnology&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-18T06:10:19.637" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26008" PostTypeId="2" ParentId="5749" CreationDate="2014-12-18T07:53:20.563" Score="2" Body="&lt;p&gt;Sometimes cancer arises when you have crossing over between non-homologous chromosomes. In the process, a chimeric protein arises. A chimeric protein is a protein that consists of parts of two separate proteins spliced together. In this way, cancer cells end up producing a substance (in this case a protein) that is absent in a healthy person. A good example is the fusion gene bcr-abl whose product leads to chronic myelogenous leukemia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://en.wikipedia.org/wiki/Philadelphia_chromosome&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Philadelphia_chromosome&lt;/a&gt; for more details on bcr-abl.&lt;/p&gt;&#xA;" OwnerUserId="10001" LastActivityDate="2014-12-18T07:53:20.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26009" PostTypeId="1" AcceptedAnswerId="26186" CreationDate="2014-12-18T09:18:20.647" Score="3" ViewCount="393" Body="&lt;p&gt;I'm looking for the &quot;earliest&quot; specific site where the 3 following nerves' sensory signals &quot;converge&quot;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Trigeminal nerve&lt;/li&gt;&#xA;&lt;li&gt;Median nerve&lt;/li&gt;&#xA;&lt;li&gt;Superficial peroneal nerve&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;By &quot;earliest&quot;, I really mean the first location in the sensory pathway (to the brain) at which these 3 nerves' sensory signals converge.  And by &quot;converge&quot;, I mean &quot;feed into each other&quot;. My &lt;em&gt;understanding&lt;/em&gt; is that, with sensory nerves, all &lt;em&gt;tactile reception&lt;/em&gt; roads lead to the somatosensory cortex, and so, I would imagine all the nerve signals converge/merge into one another at some point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would imagine the location I'm looking for is the brainstem, probably the &lt;strong&gt;pons&lt;/strong&gt;, but I'm not a biologist and am looking for either correction or confirmation here. This uneducated guesstimate comes from two sources:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cranial_nerves&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; - which states that the cranial nerves feed into the pons; and&lt;/li&gt;&#xA;&lt;li&gt;The fact that the median and peroneal nerves are spinal nerves, which ultimately feed into the medula, which then turns into the pons.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Am I right or way off track?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Please note&lt;/strong&gt;: this is not homework!&lt;/p&gt;&#xA;" OwnerUserId="11581" LastEditorUserId="11581" LastEditDate="2014-12-18T13:38:29.220" LastActivityDate="2014-12-25T22:57:02.513" Title="Specific location where nerves converge" Tags="&lt;neuroanatomy&gt;&lt;central-nervous-system&gt;&lt;brain-stem&gt;&lt;peripheral-nervous-system&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26010" PostTypeId="2" ParentId="25914" CreationDate="2014-12-18T09:44:18.767" Score="2" Body="&lt;p&gt;STRING does not distinguish between different products of the same gene. E.g. for human, the protein identifier you see (&lt;code&gt;ENSP...&lt;/code&gt;) corresponds to the longest splice form for each gene (&lt;code&gt;ENSG...&lt;/code&gt;). Therefore, STRING won't help you if you need to distinguish between splice forms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Splice forms are merged because for most sources of evidence, there is little data for the interactions of individual splice forms. &lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2014-12-18T09:44:18.767" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26012" PostTypeId="1" AcceptedAnswerId="26013" CreationDate="2014-12-18T11:46:59.130" Score="12" ViewCount="754" Body="&lt;p&gt;After listening to a scientific talk, I had this question that why in the natural selection process, are the L-amino acids selected over the D- form. However, we still we produce D-amino acids; specifically in the brain there is a higher concentration of D- amino acids. One possible reason is that they act as neurotransmitters.&lt;/p&gt;&#xA;" OwnerUserId="11619" LastEditorUserId="3340" LastEditDate="2014-12-18T14:45:41.580" LastActivityDate="2016-04-20T15:13:12.637" Title="Is there any evolutionary advantage of selection of L-amino acid over D-amino acid?" Tags="&lt;evolution&gt;&lt;amino-acids&gt;&lt;chirality&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26013" PostTypeId="2" ParentId="26012" CreationDate="2014-12-18T12:06:58.217" Score="6" Body="&lt;p&gt;As you say yourself, biological molecules are usually available in both chiralic possibilities, yet nature uses only one of the two possibilities. At some point in our molecular evolution (and at a very early one) L-amino acids were stochastically &quot;chosen&quot; over their D-equivalents (I think that the choices would have been equiprobable). There is no reason why D-amino acids shouldn't work here as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is some discussion on why L-amino acids are used, see the references for some ideas. It might be that the proteins made from it where slightly more stable or because they were more abundant. D-amino acids are in use today as a protective step - most proteases for example cannot hydrolyse the D-amino acids in the peptidoglycan wall of bacteria. Using this &quot;unusual&quot; amino acids gives some protection here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00932495&quot;&gt;Mirror symmetry breaking in biochemical evolution&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pnas.org/content/93/21/11435.full.pdf&quot;&gt;Mirror symmetry breaking at the molecular level&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dirac.ruc.dk/~st/articles/article35print.pdf&quot;&gt;Origin of homochirality in biological systems&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="3340" LastEditDate="2014-12-18T12:32:58.990" LastActivityDate="2014-12-18T12:32:58.990" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26014" PostTypeId="1" AcceptedAnswerId="26027" CreationDate="2014-12-18T15:12:59.163" Score="7" ViewCount="1277" Body="&lt;p&gt;If I go into a green room (all walls are semitransparent and green) and spend some time - around 10+ min - in there, when I come out all my eyes see is white as pink. I see no (or very few other) colors due to this for a while - around 2 minutes. What is the science behind this? Why do eyes lose color perception in this case?&lt;/p&gt;&#xA;" OwnerUserId="11622" LastEditorUserId="9943" LastEditDate="2014-12-18T23:14:39.213" LastActivityDate="2014-12-19T02:23:09.647" Title="What is the science behind the inaccurate perception of colors?" Tags="&lt;eyes&gt;&lt;perception&gt;&lt;neurophysiology&gt;&lt;senses&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26015" PostTypeId="2" ParentId="26014" CreationDate="2014-12-18T15:25:59.590" Score="12" Body="&lt;p&gt;First recall that &lt;strong&gt;pink is white minus green&lt;/strong&gt;, more or less.&#xA;Now, your perception can be explained by adaptation: Neurons try to control their gain (amplification factor) to have roughly the same range of output. So if there's a lot of stimuli they like, they will reduce their gain, and vice versa. It can be thought of as a form of fast time-scale homeostasis in this case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While you were in the green room, your neurons that represent 'green' gets less sensitive to green stimuli due to strong green input (adaptation). Additionally, the 'non-green' representing neurons become more sensitive, since there's less visual stimuli that they like. When you suddenly come out of that room, now the green neurons do not respond as strongly as the non-green neurons in response to white, hence your perception of pink.&lt;/p&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2014-12-18T16:31:43.290" LastActivityDate="2014-12-18T16:31:43.290" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26016" PostTypeId="2" ParentId="14700" CreationDate="2014-12-18T16:00:43.857" Score="3" Body="&lt;p&gt;It is definitely possible to include antibodies and other biological molecules in formula to better approximate that of its mother's milk.  &lt;strong&gt;However&lt;/strong&gt;, there's no way you could mass-produce this. Every mother has unique antibodies, even horomones that are the same in different people are present at different concentrations. The current &quot;formula&quot; on the market is good for as many people as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isolating antibodies from a mother to include in formula milk would be insanely, &lt;em&gt;insanely&lt;/em&gt; expensive. Think thousands of dollars for a carton of formula. Not to mention the hassle of frequent blood and serum draws from the mother for antibody isolation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, yes, this is possible (and I wouldn't be surprised if someone with a lot of money to burn has tried it). It's not remotely cost-effective or feasible, though.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2014-12-18T16:00:43.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26017" PostTypeId="2" ParentId="21592" CreationDate="2014-12-18T16:46:41.613" Score="3" Body="&lt;p&gt;inf3rno's comment provides a great example, in the production of vinegar (&lt;a href=&quot;http://www.foodsafetymagazine.com/magazine-archive1/februarymarch-2005/beating-back-biofilms-in-food-processing/&quot; rel=&quot;nofollow&quot;&gt;Food Safety Magazine&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the production of some fermented foods, biofilms are an essential element for optimum production. During the production of vinegar, acetic acid bacteria are allowed to grow on wood chips. The biofilm that is formed helps make the conversion of substrate to acid more efficient.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This paper, &lt;a href=&quot;http://link.springer.com/referenceworkentry/10.1007%2F978-90-481-3585-1_262&quot; rel=&quot;nofollow&quot;&gt;Biofilms in the Food Environment&lt;/a&gt; (Czaczyk &amp;amp; Myszka, 2014) also provides examples of biofilm use in industrial food production (on page 75, 14th page in the linked PDF):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Bioreactors&#xA;  with biofilms (biofilms represent a natural form of cell immobilization) are used to obtain acetic acid, citric acid, ethanol, and polysaccharides.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can also check out Chapter 7 of this book of the same name, &lt;a href=&quot;http://books.google.com/books?id=fHVZOLQVaEMC&quot; rel=&quot;nofollow&quot;&gt;Biofilms in the Food Environment&lt;/a&gt;, for more information, if you're interested. It's not available for free online but you may be able to find it in a library.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="9829" LastEditDate="2015-01-05T20:50:59.513" LastActivityDate="2015-01-05T20:50:59.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26018" PostTypeId="2" ParentId="14231" CreationDate="2014-12-18T17:00:41.410" Score="3" Body="&lt;p&gt;These hormones are progesterone and estrogens. They are actually secreted by the placenta, in increasing amounts as the fetus matures:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CZ85O.png&quot; alt=&quot;placental hormones&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(&lt;a href=&quot;http://www.vivo.colostate.edu/hbooks/pathphys/reprod/placenta/endocrine.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Colorado State, R. Bowen&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see that the placenta produces both types of hormone in increasing amounts until birth. Additionally, the hormone &lt;strong&gt;relaxin&lt;/strong&gt; is secreted by the placenta and thought to aid in parturation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Relaxin is a hormone thought to act synergistically with progesterone to maintain pregnancy. It also causes relaxation of pelvic ligaments at the end of gestation and may therefore aid in parturation. In some of the species in which relaxin is known to be produced, it is produced by the placenta, while in others, the major source is the corpus luteum. In some species, relaxin is produced by both the corpus luteum and placenta. - &lt;a href=&quot;http://www.vivo.colostate.edu/hbooks/pathphys/reprod/placenta/endocrine.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;R. Bowen&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="9829" LastEditDate="2015-01-05T18:46:06.903" LastActivityDate="2015-01-05T18:46:06.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26020" PostTypeId="2" ParentId="26014" CreationDate="2014-12-18T18:05:35.930" Score="3" Body="&lt;p&gt;The shift in color is caused by the proteins in your photoreceptors being used up and thus no longer being able to absorb the light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you stare at a green wall, you're using up green sensing proteins. When you switch to a white wall you're now seeing more red and blue compared to green, and thus it appears pinkish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your brain somewhat tricks you into thinking that the green you're seeing is the same was it was when you first looked at it, but you're actually sensing less of it the longer you look.&lt;/p&gt;&#xA;" OwnerUserId="11624" LastActivityDate="2014-12-18T18:05:35.930" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26021" PostTypeId="2" ParentId="25996" CreationDate="2014-12-18T19:26:05.330" Score="1" Body="&lt;p&gt;I think a tapeworm is your best bet. For tapeworms specifically, I found this textbook, &lt;a href=&quot;https://books.google.com/books?id=I6X8G8YPdv4C&amp;amp;pg=PA57&amp;amp;lpg=PA57&amp;amp;dq=tapeworm%20facultative%20anaerobes&amp;amp;source=bl&amp;amp;ots=O7lBX-2-pq&amp;amp;sig=o9ev1ApBYPcSi3OClOJGi0vGblo&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=ZSiTVPXBGou1ggS3gIPACw&amp;amp;ved=0CEIQ6AEwBw#v=onepage&amp;amp;q=tapeworm%20facultative%20anaerobes&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Animal Physiology: From Genes to Organisms&lt;/a&gt;, which claims:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Active facultative anaerobes include some parasitic worms such as tapeworms that can survive without oxygen indefinitely...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I was not able to find any primary research on the subject either @WYSIWYG (other than a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14844373&quot; rel=&quot;nofollow&quot;&gt;paper from 1951&lt;/a&gt; that doesn't seem to be available anywhere), but if the textbook's claim holds, I can't think of anything larger than a tapeworm.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2014-12-18T19:26:05.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26022" PostTypeId="1" AcceptedAnswerId="26024" CreationDate="2014-12-18T20:34:24.470" Score="2" ViewCount="1244" Body="&lt;p&gt;So I'm reading about how mutations in DNA can be caused by oxidative damage. An example of a product of oxidative damage is given: 8-oxo-7-hydrodeoxyguanosine&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My textbook says that this product frequently mispairs with A, resulting in a high level of &lt;strong&gt;G--&gt;T transversions&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm not understanding is why it's a G--&gt;T transversion. If the 8-oxo-G is pairing with A, resulting an an A-G pair, isn't this a T--&gt;G transversion? Or does the order not matter?&lt;/p&gt;&#xA;" OwnerUserId="11626" LastActivityDate="2015-02-16T22:22:58.317" Title="G&gt;T transversion VS. T&gt;G transversion?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;molecular-genetics&gt;&lt;dna-damage&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26023" PostTypeId="2" ParentId="7647" CreationDate="2014-12-18T20:42:23.303" Score="0" Body="&lt;p&gt;To a certain extent how much people like various foods is a relative thing. Vegetables are indeed more desirable as food over, say, rocks, but often less desirable than, say, cake. Our bodies get more energy from sugar than vegetable matter, so evolutionarily we prefer the taste of sugar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is complicated by the fact that our tastes are often learned/environmental. Like, I love clams but I know many people hate clams; there isn't some biological reason for this, it just comes down to I grew up near the coast and they grew up inland.&lt;/p&gt;&#xA;" OwnerUserId="10329" LastActivityDate="2014-12-18T20:42:23.303" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26024" PostTypeId="2" ParentId="26022" CreationDate="2014-12-18T21:07:26.657" Score="1" Body="&lt;p&gt;Originally the position had a G:C pair. After the mutation, there is an oxoG:C pair. Upon replication, the strand with C will pair to G and the original pair will be created as expected. However, since oxoG can also pair with A, the strand with oxoG may form an oxoG:A pair. Another round of replication gives the products T:A and oxoG:A. Thus the G in the original strand is replaced by T (ie it is a G$\ce{-&amp;gt;}$T transversion). &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-12-18T21:13:00.163" LastActivityDate="2014-12-18T21:13:00.163" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26025" PostTypeId="1" CreationDate="2014-12-18T21:56:48.533" Score="8" ViewCount="1322" Body="&lt;p&gt;Let's say I want to evolve a bacterium that is resistant to an antibiotic. I want to do this by growing initially clonal populations of bacteria in presence of this antibiotic for a long time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have two options:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Make one 50 ml flask culture&lt;/li&gt;&#xA;&lt;li&gt;Make ten 5 ml tube cultures&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;What are the comparative advantages and disadvantages of these two? Clearly, the ten culture version is better at probing the space of all possible resistance mechanisms. However, what about the rate of evolution? If I just want to get a resistant strain as fast as possible, which one should I use?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that &quot;antibiotic&quot; is just a proxy for any selective pressure, and &quot;bacteria&quot; is proxy for any organism. If possible, I think it will be interesting to address the effects of sexual vs. asexual reproduction in the organism that is being evolved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is already a question, &lt;a href=&quot;https://biology.stackexchange.com/questions/24055/how-does-rate-of-evolution-innovation-scale-with-population-size&quot;&gt;How does rate of evolution/innovation scale with population size?&lt;/a&gt; that is very similar. I think mine is different, because it is not one small population vs. one big population, but one big population vs. many small populations. In other words, I am attempting to control for number of selection/mutation events, and focus only on the stratification of the total population.&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-12-19T13:25:15.613" Title="Evolution: One big population vs. many small populations" Tags="&lt;evolution&gt;&lt;population-biology&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26026" PostTypeId="1" AcceptedAnswerId="26038" CreationDate="2014-12-18T22:27:10.877" Score="5" ViewCount="15312" Body="&lt;p&gt;What is the purpose of segments in citrus fruit? In my experience, each segment usually contains from zero to two seeds. I may have seen more but only rarely, if I remember correctly. What is the significance of having more than one seed in a section (twinning, perhaps)?&lt;/p&gt;&#xA;" OwnerUserId="11628" LastActivityDate="2019-03-18T16:33:30.740" Title="What is the purpose of segments in citrus fruit?" Tags="&lt;reproduction&gt;&lt;fruit&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26027" PostTypeId="2" ParentId="26014" CreationDate="2014-12-18T22:59:46.063" Score="7" Body="&lt;p&gt;To explain the neurophysiological background to the existing answers I would like to add the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The effect you are describing (pinkish appearance of white) is generally referred to as a &lt;strong&gt;negative after image&lt;/strong&gt; and it is a direct reflection of the color opponency in the retina. The effect is caused by &lt;strong&gt;adaptation&lt;/strong&gt; of the (in this case green) cones in the retina. This adaptation occurs through &lt;strong&gt;photobleaching&lt;/strong&gt;, which means that the chromophore (cis-retinal) in the visual pigment in the cones is converted to the inactive state (trans-retinal). The conversion of retinal forms the basis of the detection of photons by the cones. When you look at a green stimulus for a long time, the photopigment in the green cones is progressively converted to the inactive trans-retinal state and the green cones will stop responding to the green light stimulus. Why then does this lead to a pink'ish (magenta) perception of white? This is because color vision is based on color opponency. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The visual system in the retina is based on &lt;strong&gt;three cones&lt;/strong&gt;: red, green and blue cones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These cones feed into three channels: a &lt;strong&gt;red-green&lt;/strong&gt;, a &lt;strong&gt;yellow-blue&lt;/strong&gt; and an achromatic (&lt;strong&gt;luminance&lt;/strong&gt;) channel. Note that yellow is formed by adding the red-green color signal, while the achromatic channel is formed by adding the red and green cones as well, where only light intensity information is extracted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The red-green and yellow-blue channels are opponent channels. For your specific example, the latter is important. Red-green opponency means that at the neural level, red responses cancel green responses and vice versa. Therefore, we are not able to perceive a &quot;reddish green&quot;. White is perceived when light activates all cones, such that red cancels green, green cancels red and yellow cancels blue. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if the green cone system is adapted due to the green pigment being bleached, the opponency of green is diminished and the red response will dominate. In addition, as the yellow channel will be reduced as well, there will be a bit of blue added as well due to reduced blue suppression, explaining the pink'ish (i.e., magenta) appearance you describe. A nice example of the negative after-effect is the following: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stare at the colored dots on the girl's nose in the negative photo image below for 30 seconds. Then look at a white surface and start blinking. You should see a non-negative image of the girl (see &lt;a href=&quot;https://fstoppers.com/other/mindfreak-staring-black-and-white-sony-ad-will-make-you-see-color-6946&quot; rel=&quot;nofollow noreferrer&quot;&gt;here for image source&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2uzdV.jpg&quot; alt=&quot;blinking&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference on the opponency model: &#xA;&lt;strong&gt;Mather, Foundations of Perception, chapter 12 Colour Vision.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-19T02:23:09.647" LastActivityDate="2014-12-19T02:23:09.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26028" PostTypeId="1" AcceptedAnswerId="26034" CreationDate="2014-12-18T23:29:12.190" Score="10" ViewCount="2283" Body="&lt;p&gt;I have mass spectrometry data (LC-MS/MS) from rat cortices under either drug or control treatments. The results were performed in triplicate (three pairs of rats, drug or control per pair). In addition to some of the bioinformatics analysis I am doing, I will have to validate some of the fold-changes from the mass spectrometry by Western blot in order to have my results published. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the proteins I have chosen to to validate work very nicely by Western blot which captures the same trend as the mass spectrometry. However, other proteins that I have attempted to validate go in the exact opposite direction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;In general, how accurate is mass spectrometry compared to Western blotting?&lt;/li&gt;&#xA;&lt;li&gt;Is it unusual to have a lot of variability between the results of the two methods? I am worried that I might have to try multiple proteins before I see the results replicated and this seems problematic to me. That leads me to the third question.&lt;/li&gt;&#xA;&lt;li&gt;Which result should I trust?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Other information - Some of the proteins I have chosen for validation come from lower in the list where not as many peptide fragments were detected. In some cases, fragments were detected in only 2 of the 3 biological replicates. I did not chose to validate proteins where the 2 or 3 replicates varied widely in normalized spectral count values so I would expect these readings to be accurate. Additionally, the mass spectrometry part of the experiment was performed by a reputable lab that has filtered erroneous data using FDR cutoffs. There is a high correlation overall between all three replicates for a particular treatment and low standard error between samples across the population so, statistically, I trust the mass spec results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you need more information please ask - I don't know what exactly will be useful to answer my questions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT :&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mcponline.org/content/12/9/2381&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; article discusses the justification for using western blotting to validate mass spec results. It suggests using selected reaction monitoring assays as an alternative. Some of the points made by commenters in this thread are reiterated in this article.&lt;/p&gt;&#xA;" OwnerUserId="11630" LastEditorUserId="11630" LastEditDate="2014-12-22T06:13:47.553" LastActivityDate="2014-12-22T06:13:47.553" Title="Mass spectrometry versus western blotting for validation" Tags="&lt;bioinformatics&gt;&lt;western-blot&gt;&lt;mass-spectrometry&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="26029" PostTypeId="2" ParentId="26012" CreationDate="2014-12-18T23:43:11.157" Score="7" Body="&lt;p&gt;The current thinking amongst biophysicists is that if we all woke up tomorrow to find that someone had edited the book of life so as to exchange all of the L-'s and D-'s (and made similar mirroring changes to all of the molecules that any protein interacts with), everything would be exactly the same. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://academic.evergreen.edu/curricular/m2o2006/mcbiology/hiv%20protease.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Milton, et al. (Science, 1992)&lt;/a&gt; lent supporting empirical evidence to this view by carrying out the total chemical synthesis of a D-enzyme, D-HIV-1 protease. They showed that the L- and D- versions of the enzyme had identical and reciprocal activity, meaning that L-enzyme cut the L-substrate well and the D-substrate poorly, and vice-versa for the D-enzyme:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/uquIF.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They also showed that the structures the L-enzyme and D-enzyme were mirror images of one another:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/nunwQ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The preference for L- forms over D- emerged sometime early in evolutionary history, and there's a lot of speculation as to how the preference arose (it could have been &lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF01809580&quot; rel=&quot;nofollow noreferrer&quot;&gt;cosmic rays&lt;/a&gt;!), but the evidence is thin.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-12-18T23:43:11.157" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26030" PostTypeId="1" CreationDate="2014-12-19T00:44:09.373" Score="3" ViewCount="417" Body="&lt;p&gt;Ordinal response variables show up often in biology, but I'm not sure how they are best analysed. Some examples are qualitative assessments (little, many, a lot) or risk assessments (low risk, medium risk, high risk).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My study is about correlation between pain and depression levels. We are measuring pain on an ordinal &lt;a href=&quot;http://en.wikipedia.org/wiki/Likert_scale&quot; rel=&quot;nofollow&quot;&gt;Likert&lt;/a&gt; scale. This is a number scale running from 10 (severe pain) to 0 (no pain). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We will also measure depression on a similar scale (scale: 4 - 0).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What statistical test should I use?&lt;/p&gt;&#xA;" OwnerUserId="11632" LastEditorUserId="3624" LastEditDate="2014-12-19T14:04:19.720" LastActivityDate="2015-03-13T18:52:55.423" Title="Choosing appropriate statistical test for ordinal data" Tags="&lt;statistics&gt;&lt;biostatistics&gt;" AnswerCount="2" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="26032" PostTypeId="2" ParentId="26030" CreationDate="2014-12-19T02:04:49.263" Score="1" Body="&lt;p&gt;The testing of an ordinal scale requires non-parametric statistical tests. Mean and standard deviation are invalid parameters for descriptive statistics whenever data are on ordinal scales, as are any parametric analyses based on the normal distribution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The report of &lt;a href=&quot;http://asq.org/quality-progress/2007/07/statistics/likert-scales-and-data-analyses.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Allen &amp;amp; Seaman, 2007&lt;/a&gt; describes a number of possible tests:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nonparametric procedures—based on the rank, median or range—are appropriate for analyzing these data, as are chi-squared statistics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notably, Kruskall-Wallis models can be used to replace a standard parametric analysis of variance, as it is based on the ranks and not the means of the responses. Given these scales are representative of an underlying continuous measure, one recommendation is to analyze them as interval data as a pilot prior to gathering the continuous measure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, non-parametric tests are notoriously low in statistical power. There is a way of making an ordinal Likert scale like the ones you use continuous by using a ruler or slider, see the following figure (taken from &lt;a href=&quot;http://asq.org/quality-progress/2007/07/statistics/likert-scales-and-data-analyses.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Allen &amp;amp; Seaman, 2007&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8dUAN.gif&quot; alt=&quot;slider&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This trick makes it continuous and normal parametric tests can be used, ramping up statistical power substantially. It is a lot more work though to analyze the data. Especially when the subjects indicate their perceived pain/depression by physically putting a mark on a paper ruler, as you have to manually measure the responses. A digital slider can make your life easier. If you are planning to do hundreds of subjects you should carefully think about the possible options.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good luck!&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-19T04:31:47.853" LastActivityDate="2014-12-19T04:31:47.853" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26034" PostTypeId="2" ParentId="26028" CreationDate="2014-12-19T04:53:47.677" Score="4" Body="&lt;p&gt;It is a common practice to prove a result using an orthogonal technique. Like RNAseq followed by qRT-PCR etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Western blotting is not a robust technique and cross comparisons are difficult because of difference in the avidities/affinities of different antibodies. So comparisons can be made only with one protein-control pair in different conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;LC-MS is more sensitive and less biased(IMO). So the general trick is- don't do westerns for all proteins just report the ones that behave well (say that you &quot;chose&quot; these because they are important). I know this is a wrong practice and I should not be advocating it. For your own scientific validation try it with another MS technique; if you used ESI-Quadrupole/ion-Trap etc then try with MALDI-TOF or iTRAQ. Some luddites will continue to cling to westerns.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it is better to not test the proteins that have low peptide counts. See what is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/MA_plot&quot; rel=&quot;nofollow&quot;&gt;MA plot&lt;/a&gt;. This is frequently used for microarrays. Here &lt;code&gt;M&lt;/code&gt; denotes fold change and &lt;code&gt;A&lt;/code&gt; denotes total expression in both samples. Don't pick proteins that are low in expression in both samples; they might not be meaningful. For example if you have &lt;code&gt;2&lt;/code&gt; molecules of &lt;code&gt;X&lt;/code&gt; and &lt;code&gt;100&lt;/code&gt; molecules of &lt;code&gt;Y&lt;/code&gt; in control condition and &lt;code&gt;5&lt;/code&gt; molecules of &lt;code&gt;X&lt;/code&gt; and &lt;code&gt;200&lt;/code&gt; molecules of &lt;code&gt;Y&lt;/code&gt; in test; then the fold change in &lt;code&gt;X&lt;/code&gt; would seem important; however this change may not be relevant and can be a result of stochastic fluctuation/measurement error. If you have many samples you can see if something is stochastic or not but the limitation is the number of samples. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Note: I am not saying that 2→5 molecule increment should be meaningless. But to know if they have a meaning or not you would require more complex models; better avoid them at this moment.&lt;/em&gt; &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-19T05:51:47.263" LastActivityDate="2014-12-19T05:51:47.263" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26037" PostTypeId="2" ParentId="19024" CreationDate="2014-12-19T06:45:30.730" Score="0" Body="&lt;p&gt;Is it possible to clone your gene of interest onto a new plasmid (preferably with a GST/avidin/alternative tag)? If all else fails, this would probably remove the problem with elution. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2014-12-19T06:45:30.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26038" PostTypeId="2" ParentId="26026" CreationDate="2014-12-19T07:12:04.123" Score="4" Body="&lt;p&gt;The citrus fruits belongs to the type &lt;a href=&quot;http://en.wikipedia.org/wiki/Hesperidium&quot; rel=&quot;nofollow noreferrer&quot;&gt;hesperidium&lt;/a&gt;, which is a highly specialised form of berry specific to citrus fruit.The hesperidium is derived entirely from the ovary, other features of hesperidium includes leathery exocarp, spongy mesocarp and juice filled endocarp.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;A hesperidium has an aromatic, leathery exocarp (the &amp;quot;rind&amp;quot;) and mesocarp and endocarp compartmentalized into sections (each representing a carpel), each of which contains one to several seeds. This type of berry is unique to the genus Citrus, which produces fruits such as oranges, grapefruit, lemons, limes and tangerines.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bio.miami.edu/dana/226/226F09_22print.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The edible flesh of a mature citrus fruit is divided into segments, each derived from an ovary locule.The number of segments varies widely but is typically between 10-15.Each segment is surrounded by tough endocarp membrane and filled with tightly packed juice sacks or vesticles.&#xA;&lt;a href=&quot;https://books.google.co.in/books?id=Jh_LiAVmSNQC&amp;amp;pg=PA146&amp;amp;lpg=PA146&amp;amp;dq=hesperidium%20%20ovary&amp;amp;source=bl&amp;amp;ots=weCgrjj8go&amp;amp;sig=zC8gLEcuj9DMygrfrPPcRTolH2g&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=NMqTVLXfJYTFmwWcioDQDw&amp;amp;ved=0CEQQ6AEwCQ#v=onepage&amp;amp;q=hesperidium%20%20ovary&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;There are several major ways that plants have evolved for constructing&#xA;fleshy fruits.  Oranges etc. belong to the family Rutaceae, which is&#xA;unique in filling its &amp;quot;locules&amp;quot; (the spaces in which seeds are produced)&#xA;with &amp;quot;juice sacs&amp;quot; that are attached to the outer walls.  Each of the&#xA;locules probably represents a structure, known as a &amp;quot;carpel&amp;quot; that was&#xA;at one time distinct, but now has fused together with its neighbors.&#xA;The outer skin of most citrus fruits shows no sign that the interior&#xA;is sectioned, but this is a result of the fusion occurring early in&#xA;the development of each individual fruit (rather than early in the&#xA;evolution of the Rutaceae).&#xA;&lt;a href=&quot;http://www.bio.net/mm/plantbio/1994-July/003704.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;strong&gt;Segmentation inside the citric fruits are due to its development from the ovary, as each of the segment is evolved from the ovary locule, the number of segments varies according to species&lt;/strong&gt;(also there are variations in single species). The evolutionary advantage of segmentation inside the fruit is a debated topic.A digestible theory is that, each segment of the fruit contains 1-3(in the case of orange) seeds, due to the evolution by mammalian resources, keeping segments inside the fruits helps in the dispersal of seeds by different agents. When a ripe fruit falls down, its individual segments are broken apart and eaten by different animals/birds, this in turn helps in dispersal of seeds to geographically distinct(distant) locations. &lt;strong&gt;With each segments featuring seeds inside them, its a good adaptation to produce a single fruit which can be distributed by different agents.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-19T08:51:45.940" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="26039" PostTypeId="2" ParentId="26025" CreationDate="2014-12-19T08:27:07.570" Score="2" Body="&lt;p&gt;With very large population sizes like this the effect of genetic drift goes to zero, which is greatly simplifying. I'm also assuming selection is very strong, so that fixation times are small, and that mutation rates and population size more or less cancels out, so there are a finite number of mutations and the selection space is relatively unexplored. If selection is weak everything takes longer, but I'm pretty sure the results are the same. There's greater exploration of alternatives, but that doesn't affect our thought experiment comparing population size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In asexual populations: 10 cultures will give you ten answers to your selection criteria, one of which will be 'best'. One culture will give you the best solution a little bit later (larger populations take longer to reach fixation). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In sexual populations: One culture is better. The space of alleles is larger, and positive or conditionally positive mutations will be tested against more possible synergistic partners.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider that there are ten positive mutations split across your population. A sexual population in ten sub-populations has a tiny chance of getting all ten mutations into the same gene pool, but all ten sub-populations combined make it near-certainty that all ten mutations will make it into the same organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's a limit to sexual population size above which evolution doesn't accelerate with additional individuals, because any additional mutations they bring to the table are eventually guaranteed to already exist in the gene pool. That limit is related to the genome size and mutation rate and probably other things, but for biological species it is enormous. &lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2014-12-19T08:27:07.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26040" PostTypeId="1" AcceptedAnswerId="26044" CreationDate="2014-12-19T09:12:36.917" Score="1" ViewCount="6722" Body="&lt;p&gt;Some books says the dominant plant form in tropical rainforest biome is broad leaved evergreen trees. Other books say it is broad leaved evergreen trees and deciduous trees. What is the most accepted way (or the truth)? Also how do you explain the deciduousness adaptation in tropical rainforest (e.g., when do they shed leaves)?&lt;/p&gt;&#xA;" OwnerUserId="11555" LastActivityDate="2014-12-19T10:27:11.867" Title="Deciduous trees in tropical rainforest" Tags="&lt;evolution&gt;&lt;ecology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26043" PostTypeId="2" ParentId="26025" CreationDate="2014-12-19T10:22:17.083" Score="4" Body="&lt;p&gt;&lt;em&gt;Note: This is not an area where I know the litterature well&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Where are many counteracting processes to consider for this question. For instance, the rate of evolution will be affected by the rate of mutation, the distribution of positive and deleterious mutations, strength of selection, whether the fitness effects are small or large, if fitness effects depend on interactions between multiple mutations or single mutations with large effect, asexual vs. sexual populations, and processes such as genetic drift.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A recent review that is useful for your question is &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0169534713002322#&quot; rel=&quot;nofollow&quot; title=&quot;Lanfear et al. 2014. Population size and the rate of evolution. TREE 29(1): 33–41&quot;&gt;Lanfear et al (2014)&lt;/a&gt;. They focus on how substitution rate is affected by effective population size, and go through both theoretical and empirical evidence. They conclude that in most cases, most mutations are deleterious, and that drift and selection are the most important effects in determining rates of evolution. They also state the effect of effective population size (N&lt;sub&gt;e&lt;/sub&gt;) is likely to depend if mutations are dominated by deleterious or advantagious mutations, and they expect the rate of evolution to be negatively correlated with N&lt;sub&gt;e&lt;/sub&gt; when deletious mutations dominate evolution and a positive correlation to N&lt;sub&gt;e&lt;/sub&gt; when advantagious mutations dominate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A paper by &lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001715&quot; rel=&quot;nofollow&quot; title=&quot;Rozen et al. 2008. Heterogeneous Adaptive Trajectories of Small Populations on Complex Fitness Landscapes . Plos One. DOI: 10.1371/journal.pone.0001715&quot;&gt;Rozen et al (2008)&lt;/a&gt; indicates that while large populations are more effective in fixing mutations with large positive effects, small populations can be more effective in complex &quot;rugged&quot; adaptive landscapes.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;While such determinism speeds adaptation on the smooth adaptive landscape represented by the simple environment, it can limit the ability of large populations from effectively exploring the underlying topography of rugged adaptive landscapes characterized by complex environments.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, this does not deal directly with the rate of evolution, but mostly about attaining the highest possible fitness in a particular fitness landscape. Another interesting paper is &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0960982207009840&quot; rel=&quot;nofollow&quot; title=&quot;Desai et al. 2007. The Speed of Evolution and Maintenance of Variation in Asexual Populations. Current Biology 17(5)&quot;&gt;Desai et al. (2007)&lt;/a&gt;, but I haven't looked through this yet.  However, they find (for asexual bacteria) that the speed of adaptation scales less than linearly with population size, and similar results have also been found in studies from Lenski's group. Their interpretation is that evolution is driven by multiple concurrent mutations of small effect and not one-by-one fixation of single mutations (which would favour large populations more).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For your case of evolution of resistance, I think &lt;strong&gt;one crucial thing is if you expect resistance to be driven by a few single mutations or combinations of many mutations&lt;/strong&gt; that interact (related to whether resistance is &quot;easy&quot; or &quot;hard&quot; to evolve). From what I understand, the first case should favour a single large population (since they will fix mutations for resistance more quickly), while the second case might favour many smaller populations (since you might get more effective exploration of combinations of mutations)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are just a few starting points in a very large field, and I hope that you find them useful.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-12-19T10:27:37.560" LastActivityDate="2014-12-19T10:27:37.560" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26044" PostTypeId="2" ParentId="26040" CreationDate="2014-12-19T10:27:11.867" Score="1" Body="&lt;p&gt;Deciduous trees are those which shed their leaves once a year at the time of winter season and later grow new leaves, plants those keep their foliage throughout the year are called evergreens. Deciduous trees usually have broad leaves e.g., ash, beech, birch, maple and oak. There is a confusion exists over the dominance of trees in rain forest, but most of the resources suggests broad leaf evergreen trees as the most dominant. But deciduous trees are equally important because the difference may be negligible.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Deciduous trees shed their leaves usually as an adaptation to a cold or dry season. Evergreen trees do lose leaves, but each tree loses its leaves gradually and not all at once. &lt;strong&gt;Most tropical rainforest plants are considered to be evergreens&lt;/strong&gt;, replacing their leaves gradually throughout the year as the leaves age and fall, whereas species growing in seasonally arid climates may be either evergreen or deciduous.&lt;a href=&quot;http://en.wikipedia.org/wiki/Evergreen&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;The dominant plants in the tropical rain forest are broadleaf evergreen trees&lt;/strong&gt;. Unlike evergreens that grow in colder parts of the United States, those of the tropical rain forest have no protection against cold weather or droughts.&lt;a href=&quot;http://teacher.scholastic.com/scholasticnews/indepth/rainforest/figs.asp&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;strong&gt;Adaptations of Deciduous trees&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Broad green leaves capture sunlight needed to make food through photosynthesis.&lt;/li&gt;&#xA;&lt;li&gt;They cuts off the supply of water to the leaves and seals off the area between the leaf stem and the tree trunk, as sunlight and water become scarce, the leaves are unable to continue producing chlorophyll and this produce vibrant colors in the leaves.&lt;/li&gt;&#xA;&lt;li&gt;In winter, they simply loose their leaves and seal up the places where the leaves attach to the branch. Losing their leaves helps trees to conserve water loss through transpiration.&lt;/li&gt;&#xA;&lt;li&gt;In spring the trees grows back their leaves and start the cycle once more.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;hr /&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In the spring, deciduous trees begin producing thin, broad, light-weight leaves. This type of leaf structure easily captures the sunlight needed for food production (photosynthesis). The broad leaves are great when temperatures are warm and there is plenty of sunlight. However, when temperatures are cold, the broad leaves expose too much surface area to water loss and tissue damage. To help prevent this damage from occurring, deciduous trees make internal and physical adaptations that are triggered by changes in the climate.&lt;/p&gt;&#xA;&lt;p&gt;Cooler temperatures and limited sunlight are two climatic conditions that tell the tree to begin adapting. In the Fall, when these conditions occur, the tree cuts off the supply of water to the leaves and seals off the area between the leaf stem and the tree trunk. With limited sunlight and water, the leaf is unable to continue producing chlorophyll, the &amp;quot;green&amp;quot; stuff in the leaves, and as the chlorophyll decreases the leaves change color. The beautiful display of brilliant red, yellow, and gold leaves, associated with deciduous forests in the fall, is a result of this process. Most deciduous trees shed their leaves, once the leaves are brown and dry.&#xA;&lt;a href=&quot;http://www.cotf.edu/ete/modules/msese/earthsysflr/dforestP.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-19T10:27:11.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26046" PostTypeId="1" CreationDate="2014-12-19T11:05:21.087" Score="4" ViewCount="4081" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;If I bathe a squid axon in a fluid that has high sodium concentration , why does the duration of action potential decrease compared to a control experiment in low sodium bath but maintained at the same osmotic pressure with choline chloride? Why does the amplitude of action potential increase in the experimental set ? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;In short&lt;/em&gt;-  In the experiment, when the neurons are bathed in low sodium fluid but constant osmotic pressure, amplitude of action potential decreased, but duration of action potential increased.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I wanted to validate this with Nernst equation and/or GHK equation .&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The increase is action potential amplitude with high extracellular sodium ( more sodium influx,more depolarization ? ) is intuitive? &#xA;But again I am confused because the membrane is only slightly permeable to sodium such that increases in extracellular sodium won't really alter the membrane potential enough to generate an action potential. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Also how does the action potential duration decrease in high sodium ?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What should be done if I want to increase duration of action potential while keeping the axons in high sodium bath ?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;The duration of action potential is not the time to reach threshold voltage. It is the overall time the membrane stays depolarized.&lt;/li&gt;&#xA;  &lt;li&gt;In other words, why are the axons slowly repolarized when bathed in low sodium concentration(and also maintained at constant osmotic pressure with choline chloride ) compared to high sodium bath axons that are rapidly repolarized ?&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;How do you think the answer would've changed if choline chloride was not used ?&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="6497" LastEditorUserId="6497" LastEditDate="2014-12-19T12:40:19.450" LastActivityDate="2014-12-19T14:44:59.153" Title="Action potential changes in low sodium concentrations but constant osmotic pressure" Tags="&lt;neuroscience&gt;&lt;electrophysiology&gt;&lt;neurophysiology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26047" PostTypeId="2" ParentId="25858" CreationDate="2014-12-19T11:20:34.323" Score="0" Body="&lt;p&gt;I do not think that it is a correct statement to proclaim that the &quot;glans penis&quot; is uncovered by skin. This would be true only if the penis is circumcised. Under foreskin section of this article it is clearly stated&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The foreskin in the adult male either partially or completely covers&#xA;  the glans penis (&lt;a href=&quot;http://www.cirp.org/library/sex_function/#n40&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, it would be safe to say that unless erect, the penis is completely protected by the foreskin against the entry of foreign particles (&lt;a href=&quot;http://www.cirp.org/library/hygiene/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). The second part deals with the porosity of the penis while erect. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Some males, well endowed with a generous foreskin, have the glans&#xA;  fully covered even when the penis is fully erect (&lt;a href=&quot;http://www.drmomma.org/2009/09/functions-of-foreskin-purposes-of.html&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I couldn't find any studies that compared the entry of bacteria in an erect or a flaccid penis but I would say that even if circumcised, your chances of getting an infection without indulging in unsafe sexual practices remain quite slim. Of course, in case of cuts or abrasions on the penis, chances of infection increase. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2014-12-19T11:20:34.323" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26050" PostTypeId="2" ParentId="26046" CreationDate="2014-12-19T12:01:04.277" Score="4" Body="&lt;p&gt;High sodium extracellularly means an &lt;strong&gt;increased sodium concentration gradient&lt;/strong&gt; across the membrane. This means there is a &lt;strong&gt;larger driving force for sodium to enter the cell&lt;/strong&gt; once the sodium channels open at the start of the action potential, and hence a larger depolarization takes place &lt;strong&gt;increasing the action potential amplitude&lt;/strong&gt;. The enhanced depolarization leads to an &lt;strong&gt;increased proportion of activated voltage-operated potassium channels&lt;/strong&gt; that open upon depolarization. When more potassium channels open, more potassium will exit the cell, thereby repolarizing the cell to a larger extent, in turn stopping the depolarization step of the action potential faster. In all, the action potential develops quicker, as the depolarization is increased as well as the repolarization step, and hence the time it takes to execute an action potential is diminished. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your subquestion as to the &lt;strong&gt;small sodium conductance is not valid&lt;/strong&gt;, as during an action potential it is actually very high.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To increase the action potential duration you can increase the re-polarization step by &lt;strong&gt;increasing the extracellular potassium concentration&lt;/strong&gt;, thereby diminishing the potassium concentration gradient and prolonging the repolarization step.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-19T12:32:51.047" LastActivityDate="2014-12-19T12:32:51.047" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="26051" PostTypeId="1" CreationDate="2014-12-19T12:03:45.887" Score="1" ViewCount="218" Body="&lt;p&gt;I'm trying to produce a haplotype network and so have decided to use the software haploview. However I'm having some problems importing my sequences into the software.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I Have my sequences in a FASTA format but I can't find a way to convert this into a &lt;a href=&quot;http://www.broadinstitute.org/science/programs/medical-and-population-genetics/haploview/input-file-formats-0&quot; rel=&quot;nofollow&quot;&gt;format that haploview accepts&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have any ideas how I can get from a FASTA format file (e.g. &gt;Az01|Female|Azores AGGATCT...) to a phased haplotype format (Az01    Azores    0    4    2    2)?&lt;/p&gt;&#xA;" OwnerUserId="3382" LastEditorUserId="3340" LastEditDate="2014-12-19T12:20:34.027" LastActivityDate="2014-12-19T12:20:34.027" Title="How do I import FASTA files into Haploview?" Tags="&lt;bioinformatics&gt;&lt;population-genetics&gt;&lt;software&gt;" AnswerCount="0" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="26052" PostTypeId="2" ParentId="26025" CreationDate="2014-12-19T12:34:46.097" Score="0" Body="&lt;p&gt;Both have its benefits and drawbacks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The single big culture would have a bigger risk of contamination, but a bigger chance that the resistant mutated individuals are present, so in this case you would have a lower risk of complete extermination of your culture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The smaller several cultures on the other hand will let you try several dosages of the antibiotic without fearing exterminating your culture. On the other hand each individual culture probably will have lower diversification, so lowers the chance of new strains.&lt;/p&gt;&#xA;" OwnerUserId="11641" LastActivityDate="2014-12-19T12:34:46.097" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26053" PostTypeId="2" ParentId="26030" CreationDate="2014-12-19T13:00:06.820" Score="2" Body="&lt;p&gt;You can use ordinal multinomial regression (also known as ordered logit) if the response is ordered. These methods are basically extensions of logistic regressions, but using e.g. a cumulative logit instead of the logit. However, there are a number of different assumptions you need to consider. For instance, are you going to use a proportional-odds assumption (which is commonly used), which means that there is an equal probability of going from e.g. class 1 -&gt; 2 and class 5 -&gt; 6? You can also evaluate the proportional odds assumption using plots or a score test. If the response cannot be ordered, there are &lt;a href=&quot;http://en.wikipedia.org/wiki/Multinomial_logistic_regression&quot; rel=&quot;nofollow&quot;&gt;multinomial nominal methods&lt;/a&gt; that you can use, and you can also evaluate the results from an ordered analysis by comparing the predictions with ones from a multinomial nominal analysis. I have used these kinds of methods for the analysis is Red list classifications, which are clearly ordered but cannot simply be transformed into a numerical response (similar to your situation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The book &lt;a href=&quot;http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470082895.html&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Analysis of Ordinal Categorical Data&lt;/em&gt; (Agresti. 2010)&lt;/a&gt; is a really good starting point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In R you can look at the packages &lt;code&gt;polr&lt;/code&gt; and &lt;code&gt;vgam&lt;/code&gt; for ways to perform different types of analyses on ordinal data. The author of the book above has also published some examples for categorical data analysis in R, using the packages I mentioned: &lt;a href=&quot;http://www.stat.ufl.edu/~aa/ordinal/R_examples.pdf&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Examples of Using R for Modeling Ordinal Data&lt;/em&gt;&lt;/a&gt;. In SAS similar analyses can be done using &lt;code&gt;Proc Genmod&lt;/code&gt; and &lt;code&gt;Proc Logistic&lt;/code&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-12-19T13:26:42.993" LastActivityDate="2014-12-19T13:26:42.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26054" PostTypeId="2" ParentId="26046" CreationDate="2014-12-19T14:00:38.967" Score="2" Body="&lt;p&gt;&lt;strong&gt;Not different from @ChrisStronks answer. Just in different words.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just for everyone's knowledge — you are referring to the &lt;a href=&quot;https://en.wikipedia.org/wiki/Voltage_clamp&quot; rel=&quot;nofollow&quot;&gt;Voltage-clamp&lt;/a&gt; experiment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Situation 1: Sodium is depleted in the ECF. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite the fact that Na&lt;sup&gt;+&lt;/sup&gt; conductance is much less than that of K&lt;sup&gt;+&lt;/sup&gt; and the equilibrium membrane potential (hyperpolarized) is closer to Nernst potential of K&lt;sup&gt;+&lt;/sup&gt;, absence of Na&lt;sup&gt;+&lt;/sup&gt; would move the equilibrium potential closer to the K&lt;sup&gt;+&lt;/sup&gt; Nernst potential. This would result in increase in the response time of action potential (AP).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Situation 2: Sodium is increased in the ECF&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The consequence of this would depend on how much is the concentration of Na&lt;sup&gt;+&lt;/sup&gt;. You can calculate the changed Nerst potential of Na&lt;sup&gt;+&lt;/sup&gt; using the Nernst-Plank equation. &lt;br&gt; &lt;strong&gt;How would it decrease the response time of AP?&lt;/strong&gt; &lt;br&gt;&#xA;It would increase Nernst potential of Na&lt;sup&gt;+&lt;/sup&gt; causing an increase in the sodium current. This would increase the rate of AP and therefore decrease the response time. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-19T14:44:59.153" LastActivityDate="2014-12-19T14:44:59.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26056" PostTypeId="1" AcceptedAnswerId="26068" CreationDate="2014-12-19T15:30:50.657" Score="1" ViewCount="172" Body="&lt;p&gt;Since all bacteria have one circular chromosome, there is no designated origin to start the systematic gene locus numbering. Therefore, what is the rule to start the numbering at a particular point (i.e. why is in the &lt;em&gt;E.coli&lt;/em&gt; K12 strain the thrL gene given the ordered locus number b0001? If the answer is: It is the first Gene downstream of basepair-1, then why is basepair-1 at this particular position)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why the question? Since bacteria show frequently functional synteny between genes, should I be surprised to find a gene frequently associated with the (arbitrary?) annotation origin? If the annotation origin is i.e. the origin of replication that would be an interesting case of synteny, but if no such rule exists, then such a case would most likely just reflect the historic sequence of Genome Sequencing&lt;/p&gt;&#xA;" OwnerUserId="11643" LastEditorUserId="3340" LastEditDate="2014-12-19T15:48:57.373" LastActivityDate="2014-12-21T17:58:54.387" Title="Is there a rule for the annotation of the basepair or gene locus origin in bacterial genomes?" Tags="&lt;phylogenetics&gt;&lt;genomes&gt;&lt;gene-annotation&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="26057" PostTypeId="1" AcceptedAnswerId="26070" CreationDate="2014-12-19T16:23:48.030" Score="1" ViewCount="77" Body="&lt;p&gt;Reading the &lt;a href=&quot;http://www.nice.org.uk/guidance/cg127/resources/guidance-hypertension-pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;NICE clinical guideline for Hypertension&lt;/a&gt; it says...&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;For people aged under 40 years with stage 1 hypertension and no evidence of target organ damage, cardiovascular disease, renal disease or diabetes, consider seeking specialist evaluation of secondary causes of hypertension and a more detailed assessment of potential target organ damage.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However it is not clear in the guidelines exactly what &amp;quot;specialist evaluation of secondary causes of hypertension and a more detailed assessment of potential target organ damage&amp;quot; would entail.&lt;/p&gt;&#xA;&lt;p&gt;I understand that it is typical to carry out blood tests to look at kidney function, thyroid function, cholesterol and glucose levels; and that further tests such as a 12-lead ECG, echocardiography and renal ultrasound scan may be ordered if necessary to test for organ damage.&lt;/p&gt;&#xA;&lt;p&gt;My question is what further tests would be performed by a specialist on a patient aged under 40 years with stage 1 hypertension and no evidence of target organ damage, cardiovascular disease, renal disease or diabetes? I have done several searches on Google but most of the papers I've read relate to patients who already have signs of organ damage or existing disease.&lt;/p&gt;&#xA;" OwnerUserId="11644" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-20T12:35:31.937" Title="Specialist evaluation for people aged under 40 years with stage 1 hypertension" Tags="&lt;human-biology&gt;&lt;blood-pressure&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26058" PostTypeId="1" CreationDate="2014-12-19T19:48:38.087" Score="7" ViewCount="379" Body="&lt;p&gt;Red light plus green light makes yellow light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose I shone a pure red light, say 650nm, onto the same spot as a pure green light, say 550nm. The eye sees this two-peak spectrum as yellow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This presumably means we are tricking the eye, since a pure yellow light source would also be perceived as yellow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do the cells on our retina treat composite spectra equivalently to corresponding single-peak spectra? If not, how do we quantify the gap?&lt;/p&gt;&#xA;" OwnerUserId="3511" LastActivityDate="2014-12-31T18:39:48.020" Title="Can the eye distinguish between pure and composite colours and how do we measure this?" Tags="&lt;vision&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26059" PostTypeId="2" ParentId="26058" CreationDate="2014-12-19T21:02:43.857" Score="7" Body="&lt;p&gt;Yes, we do perceive a composite spectrum in a way which is analogous to how we perceive the corresponding single-peak spectrum. Human beings have trichromatic vision, meaning that there are 3 types of specialized cells in our eyes for seeing color. Each one has a different color of light which produces peak stimulus, although they all perceive a range of colors:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JKEca.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;(&lt;a href=&quot;http://en.wikipedia.org/wiki/Trichromacy&quot; rel=&quot;nofollow noreferrer&quot;&gt;the axes are wavelength and normalized response&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;None of the color-sensing cells has a peak color of yellow. In order to perceive something as being yellow it either has to be pure yellow or stimulate the 3 types of color sensing cells in a very similar way as pure yellow would. However, if you took very careful readings of the output signals from the color sensing cells you might see some subtle differences in the exact waveforms of the responses.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2014-12-31T18:39:48.020" LastActivityDate="2014-12-31T18:39:48.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26060" PostTypeId="2" ParentId="24708" CreationDate="2014-12-20T01:05:37.637" Score="2" Body="&lt;p&gt;I think I have some evidence that the key factor is light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since asking this question, I changed the buffer for fresh TAE-EtBr (same concentration as in my gels) moved my gels from a well-lit area into a closed, opaque box so that they remain in darkness. After 1 week, I ran equal amounts of my ladder in the stored gel, as well as a fresh gel. The &lt;a href=&quot;https://i.stack.imgur.com/PqokH.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;results&lt;/a&gt; (old gel on left, new gel on right) show very little difference in signal - I conclude that blocking the light is sufficient.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2014-12-20T01:05:37.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26062" PostTypeId="1" CreationDate="2014-12-20T03:40:16.053" Score="2" ViewCount="389" Body="&lt;p&gt;In temperate rainforest, the dominant plant form is often coniferous trees (&lt;a href=&quot;http://en.wikipedia.org/wiki/Temperate_rainforest&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;). However, coniferous trees are also the dominant plant form in a very different climate and form a different biome (boreal forest). Why are broad leaved evergreen trees not so adapted in temperate rain forests as in tropical rainforests? What is the advantage of needle-shaped leaves in the climate with temperate rainforest?&lt;/p&gt;&#xA;" OwnerUserId="11555" LastActivityDate="2015-01-10T05:37:03.480" Title="Coniferous trees in temperare rain forests" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;ecology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26063" PostTypeId="2" ParentId="24708" CreationDate="2014-12-20T04:02:18.940" Score="3" Body="&lt;p&gt;To increase storage life: after gel solidifies, dampen it with running buffer. Wrap the gel in polyvinyl chloride. Place in plastic container with a lid. Store in fridge in dark. It will last for a year as long as you re-dampen it with buffer each time you access it. &lt;strong&gt;Don't keep it submerged in buffer as the etbr will diffuse out.&lt;/strong&gt; this is probably the cause of your problem. Notice when you order precast gels (either agarose or acrylamide) they are sealed and only a small vol of buffer is added to keep it hydrated. Additionally, the etbr and EDTA in the buffer helps prevent most mold growth although I have seen black mold grow a few times at around a year.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can always spike the buffer with etbr adding it directly to the electrophoresis chamber before you run the gel (etbr doesn't even need to even be in the gel for it to work) although I find you get a little more sensitivity with the etbr in the gel. If you spike it be sure to mix and let it sit for about 20 min for the etbr to diffuse.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are trying to cut down on cost you are probably using a higher grade agarose than you really need for the application your doing so I would take a look at that&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you end up needing to store gels for rna work, add plain old Clorox bleach to a final concentration of 1% to your TAE gel just after microwaving. It sounds crazy but it works extremely well. You will completely inhibit RNAse and your rna bands will look nice!!!. The bleach also helps  with storage of the gel.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2014-12-20T04:17:28.083" LastActivityDate="2014-12-20T04:17:28.083" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26064" PostTypeId="2" ParentId="25858" CreationDate="2014-12-20T06:31:58.903" Score="5" Body="&lt;p&gt;So if you're interested in the detailed anatomy of the glans penis, I &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3697758&quot; rel=&quot;nofollow noreferrer&quot;&gt;recommend this&lt;/a&gt; as a nice article to go to after you've checked &lt;a href=&quot;https://books.google.com/books?id=hB6nqQCPKBoC&amp;amp;lpg=PA384&amp;amp;dq=Glans%20penis&amp;amp;pg=PA384#v=onepage&amp;amp;q=Glans%20penis&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;general references&lt;/a&gt;.  Opening two sentences are worth quoting here:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The human glans penis is covered by stratified squamous epithelium and&#xA;  a dense layer of connective tissue equivalent to the dermis of typical&#xA;  skin. Rete ridges of the epidermis are irregular and vary in height&#xA;  depending on location, age, and presence or absence of a foreskin. The&#xA;  papillary layer of the dermis blends into and is continuous with the&#xA;  deep connective tissue forming the tunica albuginea of the corpus&#xA;  spongiosum of the glans penis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And as &lt;a href=&quot;https://biology.stackexchange.com/a/26047/9694&quot;&gt;pointed out in The Last Word's answer&lt;/a&gt;, foreskin covers the penis if you look at humans in an evolutionary scale of time.  The exception being an erection, which should lead to foreskin retraction (at least at some level).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the question then becomes if the squamous epithelium and connective tissue are more prone to infection than the dermis. First, it's worth pointing out that the epidermis is not equally protective across the body. Think about the skin on your face vs. the bottom of your foot, or vs. a baby's.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think comparing the glans penis directly to the surrounding tissue -- the prepuce (foreskin), fossa navicularis, and urethra -- makes the most sense. To make a plumbing analogy, is it the pipe (urethra), the fitting (glans penis), hole (fossa navicularis), or insulation (prepuce) that is most prone to infection?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well, first we need to look at our pathogen, &quot;what's doing the infecting?&quot; For HIV, probably &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23187317&quot; rel=&quot;nofollow noreferrer&quot;&gt;the urethra&lt;/a&gt;, but if you're interested in bacterial infection, the best things to look into are balanitis and balanoposthitis.  That would be the inflammation of the glans or glans &amp;amp; prepuce. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1195642/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here is a good review&lt;/a&gt; on infectious causes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, there is going to a strong sampling bias due to circumcision rates.  Also most studies are not going to be asking the the specific question we are trying to answer here. And it would be hard to prove that infection occurred during the erection, not immediately before or after.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found little evidence of bacterial infection of the prepuce but not the glans penis.  I do know of cases of the reverse however, which may indicate that the glans has a greater infection rate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I think it's worth pointing out the difference is not likely to be drastic, and that the surface of glans has many similarities to skin.  For example, it has an epidermis and dermis. It stretches quite well, and I think dryness will be an issue far before porosity.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2016-11-30T15:57:41.997" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26066" PostTypeId="1" AcceptedAnswerId="26084" CreationDate="2014-12-20T11:27:49.653" Score="8" ViewCount="282" Body="&lt;p&gt;It's about 5 or 6 cm long. It's on the outside (north facing) wall of my garage about a metre above ground level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photo taken in Thailand near Hua Hin (about 12N 100E) in December 2014.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jLeic.jpg&quot; alt=&quot;unknown chrysalis&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="11648" LastEditorUserId="11648" LastEditDate="2014-12-21T06:32:43.427" LastActivityDate="2014-12-21T06:32:43.427" Title="Can anyone identify this chrysalis? (Identified)" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26067" PostTypeId="1" CreationDate="2014-12-20T11:51:06.047" Score="10" ViewCount="1173" Body="&lt;p&gt;I've recently seen the following image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FqhQ1.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Hoerflaeche.svg&quot; rel=&quot;noreferrer&quot;&gt;https://commons.wikimedia.org/wiki/File:Hoerflaeche.svg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Translation (from German):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The upper boundary (Schmerzgrenze) is where it starts to hurt&lt;/li&gt;&#xA;&lt;li&gt;&quot;Musikwahrnehmbarkeit&quot; is where you can hear music&lt;/li&gt;&#xA;&lt;li&gt;&quot;Sprachwahrnehmbarkeit&quot; is where you can recognize speech&lt;/li&gt;&#xA;&lt;li&gt;&quot;Hörschwelle&quot; is absolute threshold of hearing (ATH)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;While the ATH seems to be relatively smooth, there is a noticeable &quot;gap&quot; between 2kHz and 5kHz. Does anybody know why this is the case?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some possible explanations I've heard are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Evolution: Hearing a baby cry&lt;/li&gt;&#xA;&lt;li&gt;Evolution: Hearing leafs rustling&lt;/li&gt;&#xA;&lt;li&gt;Coincidence: There is no good reason for that.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The image is from wikipedia commons and has no references. It might be wrong. Do you know similar graphs? Do you eventually have this kind of information for other animals?&lt;/p&gt;&#xA;" OwnerUserId="8014" LastEditorUserId="8014" LastEditDate="2014-12-20T11:56:42.300" LastActivityDate="2021-01-08T07:06:51.253" Title="Why do humans hear better between 2kHz and 5kHz?" Tags="&lt;human-ear&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26068" PostTypeId="2" ParentId="26056" CreationDate="2014-12-20T12:27:59.647" Score="1" Body="&lt;p&gt;[I'm sure we have a skilled microbiologist somewhere here, so he would correct my answer.]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The necessity to designate gene locations in classical bacterial model species predated the genomic era, so traditional maps were normally neither bound to origin of replication, nor were they necessarily expressed in base-pairs. In &lt;em&gt;E. coli&lt;/em&gt;, for example the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98936/&quot; rel=&quot;nofollow&quot;&gt;traditional map&lt;/a&gt; was created based on the F-pili-mediated DNA transfer experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When whole genome sequences became available it was only natural to continue the traditionally defined numeration in terms of placing the &quot;base-pair one&quot;. Thus, in &lt;em&gt;E. coli&lt;/em&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98937/&quot; rel=&quot;nofollow&quot;&gt;&quot;the traditional and physical maps ... linkage map are closely correlated&quot;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding of the current situation with bacteria without genetic prehistory is that their genomes are numerated either respective to classic closely-related species (if any) or according to the presumed location of ori. Just to give an example of how the dilemma was solved for the &lt;em&gt;Buchnera&lt;/em&gt; genome: it was &quot;assumed the DnaA box upstream of the gidA gene is the replication origin&quot; and the authors decided to designate &quot;&lt;a href=&quot;http://www.nature.com/nature/journal/v407/n6800/full/407081a0.html&quot; rel=&quot;nofollow&quot;&gt;the start of the DnaA box as base pair one&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you see, still, even if the authors try to define &quot;base-pair one&quot; based on the position of ori, the problem is that this point depends on the ori-searching tool one uses and on the contemporary understanding of how ori-sites look like (direct determination of origins of replications are in many cases not easy). See e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC156607/table/T1/&quot; rel=&quot;nofollow&quot;&gt;this table&lt;/a&gt; with a revision of ori locations in a set of genomes: while most of the genomes received their numeration irrespective of ori, some of them were indeed bound to it, but the new analysis showed that these locations were inaccurate.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2014-12-21T17:58:54.387" LastActivityDate="2014-12-21T17:58:54.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26070" PostTypeId="2" ParentId="26057" CreationDate="2014-12-20T12:35:31.937" Score="2" Body="&lt;p&gt;Alongside full guidance released by NICE they also produce treatment pathways which give further advice - here is the &lt;a href=&quot;http://pathways.nice.org.uk/pathways/hypertension&quot; rel=&quot;nofollow&quot;&gt;treatment pathway for hypertension&lt;/a&gt;.  You've listed most of the investigations that would be considered in your original question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Investigations that &lt;em&gt;may&lt;/em&gt; be considered as appropriate include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Urine dipping for proteinuria or haematuria indicative of renal damage&lt;/li&gt;&#xA;&lt;li&gt;Measuring of plasma urea and electrolytes and estimation of glomerular filtration rate, again as an indicator of renal damage&lt;/li&gt;&#xA;&lt;li&gt;Measuring of plasma glucose, total cholesterol and LDL/HDL cholesterol to rule out additional risk factors as part of cardiovascular risk assessment - e.g. diabetes, hypercholestrolaemia&lt;/li&gt;&#xA;&lt;li&gt;Fundoscopy to examine the retina for damage resulting from hypertension &lt;/li&gt;&#xA;&lt;li&gt;12 lead ECG to show any changes compatible with left ventricular hypertrophy &lt;/li&gt;&#xA;&lt;li&gt;Scanning for the presence of a &lt;a href=&quot;http://en.wikipedia.org/wiki/Pheochromocytoma&quot; rel=&quot;nofollow&quot;&gt;phaeochromocytoma&lt;/a&gt; if clinically suspected&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You may also find the &lt;a href=&quot;http://www.patient.co.uk/doctor/hypertensive-emergencies&quot; rel=&quot;nofollow&quot;&gt;professional reference page on hypertension&lt;/a&gt; from patient.co.uk useful.&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2014-12-20T12:35:31.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26074" PostTypeId="1" AcceptedAnswerId="35283" CreationDate="2014-12-20T19:35:35.760" Score="12" ViewCount="175" Body="&lt;p&gt;Humans use &quot;language.&quot; By language, I mean the thing I am using right now to talk to you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know dolphins and orcas have very complex communication systems and also seem to process linguistic and gestural commands. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But do they have their own languages? Where is the evidence for or against? If we take two group of dolphins Group A and Group B, would Group A speak one language and Group B speak another?&lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="11657" LastEditDate="2014-12-21T08:57:29.557" LastActivityDate="2017-03-12T12:29:05.500" Title="Can dolphins actually communicate linguistically?" Tags="&lt;ethology&gt;&lt;mammals&gt;&lt;language&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26075" PostTypeId="1" AcceptedAnswerId="26081" CreationDate="2014-12-20T20:15:56.513" Score="6" ViewCount="179" Body="&lt;p&gt;This plant was found growing in Colombia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://habrastorage.org/files/23e/2bf/9f6/23e2bf9f635f45e983729aad992c9b34.jpg&quot; alt=&quot;Foto&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="11529" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.787" LastActivityDate="2014-12-20T23:25:28.450" Title="What is the name of this plant (see pic)?" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26076" PostTypeId="1" CreationDate="2014-12-20T21:00:52.310" Score="2" ViewCount="2801" Body="&lt;p&gt;Often do I hear people speaking of how the domestic house cats are more friendly, less ferocious, less savage-like, and smarter and/or than their distinct but equivalent feline-species friends, like lions, tigers, jaguars, panthers, leopards, cheetahs, etc. &lt;strong&gt;Is this provably true in any form or way&lt;/strong&gt;? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are domesticated animals really &quot;smarter&quot; or less ferocious, or are some simply, but assumption of lessened threat potential, more so inclined to deem the house cat/dog as less ferocious simply because it's not such a big threat? Look at it this way:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RJU5C.jpg&quot; alt=&quot;Typical house cat; domesticated and homegrown-type.&quot;&gt;&#xA;This little beast here is &quot;very cute&quot; because he/she is small and barely 9 lbs. When playing, he/she isn't directly threatening to many human's safety, and many people are not afraid of cats; &lt;strong&gt;however, is he/she really smarter because he/she is safer and less dangerous to us humans only&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Yl5HY.jpg&quot; alt=&quot;Somewhat &amp;quot;typical&amp;quot; tiger.&quot;&gt;&#xA;This beast, however, is hundreds of pounds heavier and many feet longer. Is it considered more savage-like because it can seriously harm and possibly kill humans by playing a little rough, which is like how a 9 lb. house cat would play equivalently, &lt;strong&gt;but would give you some light scratches at worst&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've also heard arguments about &quot;friendliness&quot; of felines, usually claiming that house cats are friendlier due to evolution and nurturing/upbringing; lions/tigers, on the other hand, are claimed to be naturally unfriendly and have &quot;more wild&quot; in the, and incapable of being as &quot;friendly&quot; or &quot;trustworthy&quot; as a house cat. Point is, I'm probably not the only person who's heard this. Also, consider other animals, like dogs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dogs come from the grey wolf, &lt;strong&gt;&lt;em&gt;to put it simply&lt;/em&gt;&lt;/strong&gt;. Compare both a typical house dog and a wild grey wolf, and it's pretty obvious that many would assume the house dog is safer, friendlier, and less harmful, despite the fact that some domesticated dog breeds can pack a greater bite than the wild grey wolf. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Comparing the house dog's behavior to the wild grey wolf is also not a good measure of &quot;friendliness&quot;, as compare a savage Homo sapiens from an uncivilized territory to a common city person, and you'd think the same thing: that the savage human is &quot;less intelligent&quot; and the city person is more so.&lt;/p&gt;&#xA;" OwnerDisplayName="user11653" LastEditorUserId="3340" LastEditDate="2014-12-22T05:01:12.870" LastActivityDate="2014-12-22T08:16:15.240" Title="Are domesticated animals really &quot;more intelligent,&quot; or is that a myth/misunderstanding?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;zoology&gt;&lt;ethology&gt;&lt;behaviour&gt;" AnswerCount="3" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="26077" PostTypeId="1" AcceptedAnswerId="26078" CreationDate="2014-12-20T22:06:49.100" Score="2" ViewCount="253" Body="&lt;p&gt;What is the relationship between deletion or insertion of nucleotide in the gene sequence and the protein's length that is coded out from the mutated gene?&lt;/p&gt;&#xA;" OwnerUserId="9976" LastEditorUserId="948" LastEditDate="2014-12-20T23:37:20.713" LastActivityDate="2014-12-20T23:37:20.713" Title="Will gene mutations give rise to a protein that is shorter than the full length protein?" Tags="&lt;genetics&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26078" PostTypeId="2" ParentId="26077" CreationDate="2014-12-20T22:40:42.293" Score="4" Body="&lt;p&gt;It depends on the nature of the insertion or deletion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many mutations are &lt;em&gt;point&lt;/em&gt; mutations, where one single nucleotide is changed:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ATGACTACGCTATTCAGT&#xA;M  T  T  L  F  S&#xA;&#xA;ATGTCTACGCTATTCAGT&#xA;M  S  T  L  F  S&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Notice that changing the fourth A to a T caused a T-&gt;S change in the final protein, and didn't change its length. However, an insertion/deletion is different. Starting with this sequence:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ATGTCTATTGACGCTATTCAG&#xA;M  S  I  D  A  I  Q&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Let's have an insertion, an A after the A in position 7:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ATGTCTAATTGACGCTATTCAG&#xA;M  S  N  STOP&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Notice we now have a stop codon (TGA). This means the protein will be truncated, and will be much smaller. That isn't always the case. Rather than adding an A at position 7, let's add it after position 9:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ATGTCTATTAGACGCTATTCA&#xA;M  S  I  R  R  Y  S&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The protein is about the same length, but the AAs are completely different than the original version after the insertion:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;M  S  I  D  A  I  Q&#xA;M  S  I  R  R  Y  S&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This is called a frameshift mutation. Biologically, these mutations are harmful because they change all the amino acids after the mutation, the protein is often not functional and can end up being different sizes (if a stop codon is now in frame or out of frame) and the protein can even end up being unstable and rapidly degraded.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, to answer your question about the length of the protein, it'll increase/decrease by one AA every time 3 nucleotides are added/removed, but can increase or decrease &lt;strong&gt;drastically&lt;/strong&gt; if a stop codon is added or removed by a frameshift mutation.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2014-12-20T22:40:42.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26079" PostTypeId="2" ParentId="26076" CreationDate="2014-12-20T23:00:24.913" Score="7" Body="&lt;p&gt;Domestication has little, if anything, to do with intelligence.  From &lt;a href=&quot;http://en.wikipedia.org/wiki/Jared_Diamond&quot; rel=&quot;noreferrer&quot;&gt;biologist Jared Diamond&lt;/a&gt;, the 6 criteria for domestication are as follows:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;Flexible diet – Creatures that are willing to consume a wide variety of food sources and can live off less cumulative food from the food pyramid (such as corn or wheat), particularly food that is not utilized by humans (such as grass and forage) are less expensive to keep in captivity. Carnivores by definition feed primarily or only on flesh, which requires the expenditure of many animals, though they may exploit sources of meat not utilized by humans, such as scraps and vermin.&lt;/li&gt;&#xA;  &lt;li&gt;Reasonably fast growth rate – Fast maturity rate compared to the human life span allows breeding intervention and makes the animal useful within an acceptable duration of caretaking. Some large animals require many years before they reach a useful size.&lt;/li&gt;&#xA;  &lt;li&gt;Ability to be bred in captivity – Creatures that are reluctant to breed when kept in captivity do not produce useful offspring, and instead are limited to capture in their wild state. Creatures such as the panda, antelope and giant forest hog are territorial when breeding and cannot be maintained in crowded enclosures in captivity.&lt;/li&gt;&#xA;  &lt;li&gt;Pleasant disposition – Large creatures that are aggressive toward humans are dangerous to keep in captivity. The African buffalo has an unpredictable nature and is highly dangerous to humans; similarly, although the American bison is raised in enclosed ranges in the Western United States, it is much too dangerous to be regarded as truly domesticated. Although similar to the domesticated pig in many ways, Africa's warthog and bushpig are also dangerous in captivity.&lt;/li&gt;&#xA;  &lt;li&gt;Temperament which makes it unlikely to panic – A creature with a nervous disposition is difficult to keep in captivity as it may attempt to flee whenever startled. The gazelle is very flighty and it has a powerful leap that allows it to escape an enclosed pen. Some animals, such as the domestic sheep, still have a strong tendency to panic when their flight zone is encroached upon. However, most sheep also show a flocking instinct, whereby they stay close together when pressed. Livestock with such an instinct may be herded by people and dogs.&lt;/li&gt;&#xA;  &lt;li&gt;Modifiable social hierarchy – Social creatures whose herds occupy overlapping ranges and recognize a hierarchy of dominance can be raised to recognize a human as the pack leader.&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From his Pulitzer prize-winning &lt;a href=&quot;http://en.wikipedia.org/wiki/Guns,_Germs,_and_Steel&quot; rel=&quot;noreferrer&quot;&gt;book&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We (as a species) domesticated animals (and plants) by selecting traits we sought, and then breeding to keep alive/emphasize these traits. In hunting animals (retrievers, for example), intelligence may be one of those traits. Others might include obedience, speed, agility, even dark-colored coats for camouflage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's not really correct to say &quot;more evolved&quot; as @MarchHo explains in his comment. Rather, you might say &quot;more docile&quot;, or &quot;less aggressive&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Keep in mind that less aggressive, domesticated animals are not necessarily more intelligent than their wild counterparts.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;/questions/tagged/status-myth&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged 'status-myth'&quot; rel=&quot;tag&quot;&gt;status-myth&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="9829" LastEditDate="2014-12-21T02:44:08.020" LastActivityDate="2014-12-21T02:44:08.020" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26080" PostTypeId="2" ParentId="7647" CreationDate="2014-12-20T23:09:12.870" Score="0" Body="&lt;p&gt;I would suspect there are many reasons from behavioral to genetics to anthropological. I think the answer you are looking for (as you have posted it here) is sensitivity to phenylthiocarbamide or PTC. PTC is an organosulpher thiourea. It has a very bitter taste and the ability to taste PTC is determined by ones genetics. It I s a dominant trait and about 2/3 of the population can taste it. Although it is not found in food there is a large body of evidence linking the ability to taste other thiourea compounds with dietary habits. For example, smokers and coffee nuts are more likely able to taste PTC. They also more often dislike certain vegetables. If you ever want to find out if you have the ability to taste it you can try tasting &lt;a href=&quot;http://www.spectrum-scientifics.com/ProductDetails.asp?ProductCode=1363&amp;amp;click=2&quot; rel=&quot;nofollow&quot;&gt;test strips&lt;/a&gt; that contain PTC. &lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2014-12-20T23:09:12.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26081" PostTypeId="2" ParentId="26075" CreationDate="2014-12-20T23:25:28.450" Score="4" Body="&lt;p&gt;That looks like a member of genus &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Lupinus&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lupinus&lt;/a&gt;&lt;/em&gt;, flowering plants native to North and South America:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Jp3qzm.jpg&quot; alt=&quot;Lupine&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I couldn't find a good resource for species of &lt;em&gt;Lupinus&lt;/em&gt; in Columbia so I can't help you with the species, unfortunately.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2014-12-20T23:25:28.450" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26082" PostTypeId="2" ParentId="23374" CreationDate="2014-12-21T01:25:21.230" Score="1" Body="&lt;p&gt;Regarding gibbons, yes. According to &lt;a href=&quot;http://animals.nationalgeographic.com/animals/mammals/gibbon/&quot; rel=&quot;nofollow&quot;&gt;National Geographic&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Gibbons are monogamous and live in family groups consisting of an adult pair and their young offspring.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There isn't a generalized answer for &quot;family living&quot;, although specific family types are indicative of relationship type. Nuclear families (parents and children) tend to be monogamous, families with multiple males and one female tend to be polyandrous, and families with one male and multiple females tend to be polygynous. See this page on &lt;a href=&quot;http://anthro.palomar.edu/behavior/behave_2.htm&quot; rel=&quot;nofollow&quot;&gt;primate social structure&lt;/a&gt; for more information.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="9829" LastEditDate="2014-12-22T13:58:31.823" LastActivityDate="2014-12-22T13:58:31.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26083" PostTypeId="2" ParentId="26076" CreationDate="2014-12-21T05:57:56.540" Score="5" Body="&lt;p&gt;It's not entirely clear what you're asking.  If you're asking whether domestic animals are more friendly to humans than wild animals, the answer is generally yes.  However, this does not make them &quot;more evolved&quot;.  Domestic and wild animals are ultimately derived from a shared common ancestor, so they have been evolving for an equal period of time.  In general, domesticated animals have been &lt;a href=&quot;https://en.wikipedia.org/wiki/Selective_breeding&quot; rel=&quot;noreferrer&quot;&gt;selectively bred&lt;/a&gt; for traits that make them useful or appealing to humans, so it is to be expected that they possess more of these traits than their wild relatives.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An interesting detail is that, in addition to behavioral traits like increased tameness, many domestic animals tend to display certain physical traits such as floppy ears, shorter faces, and coloration differences, which were not present in their wild ancestors.  A &lt;a href=&quot;http://dx.doi.org/10.1534/genetics.114.165423&quot; rel=&quot;noreferrer&quot;&gt;recent article&lt;/a&gt; has proposed that these traits are the result of mild developmental defects which have been selected for by the process of domestication.  A &lt;a href=&quot;https://en.wikipedia.org/wiki/Domesticated_silver_fox&quot; rel=&quot;noreferrer&quot;&gt;long-running experiment&lt;/a&gt; on domesticating silver foxes has lent some evidence to this idea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, comparing cats to tigers is not really a meaningful comparison.  The closest wild relative to the housecat is the wildcat, &lt;em&gt;Felis silvestris&lt;/em&gt;, which looks like this:&#xA;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/b/b6/Scottish_wildcat_%26_kitten.jpg&quot; alt=&quot;Wildcat, Felis silvestris&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="11657" LastActivityDate="2014-12-21T05:57:56.540" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26084" PostTypeId="2" ParentId="26066" CreationDate="2014-12-21T06:31:38.437" Score="4" Body="&lt;p&gt;&lt;strong&gt;I've found it&lt;/strong&gt; - it's a Common Rose Swallowtail (Pachliopta aristolochiae)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few images on this page.&#xA;&lt;a href=&quot;http://flickrhivemind.net/Tags/aristolochiae,butterfly/Interesting&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://flickrhivemind.net/Tags/aristolochiae,butterfly/Interesting&lt;/a&gt; including these two&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ayLFs.jpg&quot; alt=&quot;Pupa&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vMWjX.jpg&quot; alt=&quot;Pupa and butterfly&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a picture also at &lt;a href=&quot;http://en.wikipedia.org/wiki/Pachliopta_aristolochiae&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Pachliopta_aristolochiae&lt;/a&gt; but this one is upside down compared to mine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nitwu.jpg&quot; alt=&quot;Wikipedia image&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mystery solved.&lt;/p&gt;&#xA;" OwnerUserId="11648" LastActivityDate="2014-12-21T06:31:38.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26086" PostTypeId="1" AcceptedAnswerId="26099" CreationDate="2014-12-21T09:50:51.740" Score="22" ViewCount="4980" Body="&lt;blockquote&gt;&#xA;  &lt;h1&gt;Origin of the word &quot;cancer&quot;&lt;/h1&gt;&#xA;  &#xA;  &lt;p&gt;The disease was first called cancer by Greek physician Hippocrates (460-370 BC). He is considered the “Father of Medicine”. Hippocrates used the terms &lt;em&gt;carcinos&lt;/em&gt; and &lt;em&gt;carcinoma&lt;/em&gt; to describe non-ulcer forming and ulcer-forming tumors. In Greek this means a crab. The description was names after the crab because the finger-like spreading projections from a cancer called to mind the shape of a crab. &amp;ndash; &lt;a href=&quot;http://www.news-medical.net/health/Cancer-History.aspx&quot;&gt;source&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bpsjN.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the cancer cells spread in a way that tumor looks like a crab. Why? Why doesn't it, for example, have a potato-like spread in which cancer cells form a sphere?&lt;/p&gt;&#xA;" OwnerUserId="11607" LastEditorUserId="11607" LastEditDate="2015-12-02T23:53:54.897" LastActivityDate="2020-12-08T22:17:45.403" Title="Why should a tumor look like a crab?" Tags="&lt;cancer&gt;&lt;terminology&gt;&lt;history&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26088" PostTypeId="1" CreationDate="2014-12-21T19:14:39.563" Score="1" ViewCount="616" Body="&lt;p&gt;I have calculated the probability that any child will have a particular blood type from both the genotype level and the phenotype level assuming the human ABO Rh system is followed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are the genotype probabilities:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;AA+/+ 49/1764&#xA;AA+/- 98/1764&#xA;AA-/- 49/1764&#xA;AO+/+ 98/1764&#xA;AO+/- 196/1764&#xA;AO-/- 98/1764&#xA;BB+/+ 49/1764&#xA;BB+/- 98/1764&#xA;BB-/- 49/1764&#xA;BO+/+ 98/1764&#xA;BO+/- 196/1764&#xA;BO-/- 98/1764&#xA;AB+/+ 98/1764&#xA;AB+/- 196/1764&#xA;AB-/- 98/1764&#xA;OO+/+ 49/1764&#xA;OO+/- 98/1764&#xA;OO-/- 49/1764&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Here are the phenotype probabilities:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;A+ 441/1764&#xA;A- 147/1764&#xA;B+ 441/1764&#xA;B- 147/1764&#xA;AB+ 294/1764&#xA;AB- 98/1764&#xA;O+ 147/1764&#xA;O- 49/1764&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Here is the frequency of the blood types in the 1st generation by genotype:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;AA+/+ 5/101&#xA;AA+/- 5/101&#xA;AA-/- 5/101&#xA;BB+/+ 5/101&#xA;BB+/- 5/101&#xA;BB-/- 5/101&#xA;AB+/+ 5/101&#xA;AB+/- 10/101&#xA;AB-/- 5/101&#xA;OO+/+ 5/101&#xA;OO+/- 5/101&#xA;OO-/- 5/101&#xA;AO+/- 10/101&#xA;AO+/+ 5/101&#xA;AO-/- 5/101&#xA;BO+/+ 4/101&#xA;BO+/- 4/101&#xA;BO-/- 4/101&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Here are the numbers and their genders; a number represents an individual from a population of 101:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&#xA;&lt;b&gt;Male:&lt;/b&gt; &#xA;0,2,5,10,11,17,20,22,23,31,34,40,41,44,46,47,50,55,59,61,62,68,71,79,80,82,85,88,89,92,94,100&#xA;&#xA;&lt;b&gt;Hermaphroditic(and fertile):&lt;/b&gt;&#xA;4,8,16,25,32,64 &lt;/pre&gt;&#xA;&#xA;&lt;p&gt;all the rest are female&lt;/p&gt;&#xA;&#xA;&lt;p&gt;M/F mating: 11,904 offspring in 2nd generation H/A mating(hermaphrodites can mate with other hermaphrodites, males, females, and even themselves): 3636 offspring in 2nd generation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you divide these by 6 you will get the amount per operation. The operations I am taking into consideration are +, -, *, /, ^, nth root, and arrow arrow(tetration).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how can I take the frequency of blood types at the genotype level, probability of blood type at genotype and phenotype levels, and total number of offspring to get a 1st order estimate of the frequency of these blood types in the 2nd generation?&lt;/p&gt;&#xA;" OwnerUserId="5851" LastEditorUserId="5851" LastEditDate="2014-12-23T05:08:52.343" LastActivityDate="2014-12-23T05:08:52.343" Title="Blood type frequency given probability" Tags="&lt;genetics&gt;" AnswerCount="0" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="26089" PostTypeId="2" ParentId="26067" CreationDate="2014-12-21T21:19:20.453" Score="9" Body="&lt;p&gt;Acoustically, we hear better in the 2-5 kHz range because our auditory canal resonates in that range (specifically, around 3 kHz). Our ear looks something like this (&lt;a href=&quot;http://www.music.miami.edu/programs/mue/Research/mescobar/thesis/web/Psychoacoustics.htm&quot; rel=&quot;noreferrer&quot;&gt;U Miami&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iJFIA.png&quot; alt=&quot;ear&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The auditory canal is part of the outer ear, which amplifies sound so that it can be converted into electrochemical signals by the middle and inner ear. We hear better in the 2-5 kHz range because the &lt;a href=&quot;http://en.wikipedia.org/wiki/Resonance&quot; rel=&quot;noreferrer&quot;&gt;resonant frequency&lt;/a&gt; of the auditory canal is in that range.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanical question of &quot;how does this work&quot; is usually easier to answer than the &quot;why did this evolve?&quot; question. Since reproductive fitness is the driving force of evolution, hearing babies crying (&lt;a href=&quot;http://www.simonheather.co.uk/pages/articles/science_hearing.pdf&quot; rel=&quot;noreferrer&quot;&gt;between 1-5 kHz&lt;/a&gt;) is the best guess I can come up with.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2014-12-21T21:19:20.453" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26090" PostTypeId="5" CreationDate="2014-12-21T21:51:37.977" Score="0" Body="&lt;p&gt;The peripheral nervous system (PNS) is the part of the nervous system consisting of the nerves and ganglia outside of the brain and spinal cord.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="9829" LastEditDate="2014-12-21T22:51:55.940" LastActivityDate="2014-12-21T22:51:55.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26091" PostTypeId="4" CreationDate="2014-12-21T21:51:37.977" Score="0" Body="The peripheral nervous system (PNS) is the part of the nervous system consisting of the nerves and ganglia outside of the brain and spinal cord." OwnerUserId="9829" LastEditorUserId="9829" LastEditDate="2014-12-21T22:51:47.690" LastActivityDate="2014-12-21T22:51:47.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26093" PostTypeId="1" CreationDate="2014-12-22T00:14:46.683" Score="0" ViewCount="896" Body="&lt;p&gt;I heared somewhere, I cannot remember where, that there has not been an evolution observed in our lifetime. In life science class, right at the start, we was doing the usual MRSGREN (how to tell if something is a living organism), and the tutor said that you can also tell something is a living organism if it evolves. So I asked if there has been an observed evolution in our lifetime. She said that there had been many but could not recite any off the top of her head, so the next week she handed me a piece of paper with 8 or so websites that aparrently corroborated her claim. I have not got the paper anymore but I recall there been on there the peppered moth or something. So I set out to look for a chronological list of evolution but could not find an authoritative one. I could only find something on wikipedia that indicated that species have been dying out for the past thousand years, but nothing saying that any have evolved. &lt;/p&gt;&#xA;" OwnerUserId="11659" LastActivityDate="2014-12-22T18:58:49.670" Title="Evolutionary chronology - if any, which species have evolved in the last 100 years" Tags="&lt;evolution&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26094" PostTypeId="1" CreationDate="2014-12-22T00:28:52.937" Score="4" ViewCount="145" Body="&lt;p&gt;Could a prion be used to sufficiently deform a viral protein in order to make the virus it is a part of incapable of reproducing? For example, take the common cold's VP1 protein and turn it into a prion, then inject that prion into someone with a cold. Would this prion ever come into contact with the virus? Would it actually deform the virus? Can we make prions?&lt;/p&gt;&#xA;" OwnerUserId="11660" LastActivityDate="2014-12-23T09:19:39.713" Title="Potential to destroy viruses using prions?" Tags="&lt;proteins&gt;&lt;pathology&gt;&lt;prion&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2014-12-27T11:48:24.523" ContentLicense="CC BY-SA 3.0" />
  <row Id="26096" PostTypeId="1" AcceptedAnswerId="26100" CreationDate="2014-12-22T02:42:03.107" Score="10" ViewCount="2126" Body="&lt;p&gt;Little odd question here. I was told that DNA was read in groups of three. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming this, my question is: Which way would better describe how the DNA is read. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(123)456789 to 123(456)789 to 123456(789) &#xA;or &#xA;(123)456789 to 1(234)56789 to 12(345)6789&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that the string of numbers 123456789 represents a DNA sequence. &lt;/p&gt;&#xA;" OwnerUserId="11661" LastEditorUserId="3340" LastEditDate="2014-12-22T13:06:05.247" LastActivityDate="2014-12-23T03:06:58.127" Title="How is DNA Read" Tags="&lt;dna&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26097" PostTypeId="2" ParentId="26096" CreationDate="2014-12-22T02:43:22.613" Score="10" Body="&lt;p&gt;Assuming the first coding position is 1, the DNA will be read as: (123)456789 to 123(456)789 to 123456(789). There are fairly few exceptions to this, e.g. some viruses (e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1966841&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/1966841&lt;/a&gt;), where reading frames overlap like in your second example. This is because the viral genome is much smaller and needs to code all of its proteins into as little nucleic acid as possible. Note that there is more than one way for frames to overlap.&lt;/p&gt;&#xA;" OwnerUserId="10001" LastEditorUserId="10001" LastEditDate="2014-12-22T02:48:57.903" LastActivityDate="2014-12-22T02:48:57.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26098" PostTypeId="2" ParentId="26086" CreationDate="2014-12-22T03:08:58.520" Score="1" Body="&lt;p&gt;&quot;Cancer&quot; is so named because the cancers Hippocrates first observed looked like crabs to him. If he had first observed cancers that most resembled potatoes, cancer probably would have been named differently today. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cancerous growths reminded Hippocrates of a moving crab, which led to&#xA;  the terms carcinoma (malignant tumor) and cancer (ulcerated malignant&#xA;  tumor).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Reference &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/cncr.25553/full&quot; rel=&quot;nofollow&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1002/cncr.25553/full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My point is, there is no &quot;need&quot; for a tumor to look like a crab or any other particular shape. Most tumors are probably irregular in shape. Most often they just look like lumps. I think breast cancer turns out to look like a crab fairly often (not sure why) and it was precisely breast cancer that Hippocrates was studying, probably because it's fairly close to the surface of the body, and, hence, fairly accessible and easy to observe. That's not irrelevant when there are no proper surgical techniques and anaesthetics. &lt;/p&gt;&#xA;" OwnerUserId="10001" LastEditorUserId="10001" LastEditDate="2014-12-22T08:49:52.583" LastActivityDate="2014-12-22T08:49:52.583" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26099" PostTypeId="2" ParentId="26086" CreationDate="2014-12-22T04:44:56.453" Score="16" Body="&lt;p&gt;Such projections are more formally known as &lt;em&gt;spiculations.&lt;/em&gt; Most commonly, we talk about spiculations with respect to the radiographic appearance of malignant breast and lung lesions. &lt;a href=&quot;http://pubs.rsna.org/doi/pdf/10.1148/radiographics.13.4.8356272&quot; rel=&quot;noreferrer&quot;&gt;This paper&lt;/a&gt;* describes the correlation between the mammorgraphic appearance of spiculated breast lesions and their pathology (microscopic appearance), which is a reasonable start at addressing the &quot;why&quot; question you pose. The authors define spiculations as follows:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A spiculated breast lesion is defined as a mass or an architectural distortion characterized by thin lines radiating from its margins.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here is a picture taken from that paper which shows the mammographic appearance on the left and the microscopic appearance on the right, with the arrows pointing to the spiculations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Cf7lP.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The linked paper gives many other examples of the microscopic and radiographic analysis of such tumors. It also explains that the two primary reasons for the spiculated shape are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Desmoplasia&quot; rel=&quot;noreferrer&quot;&gt;desmoplastic response&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;tumor infiltration (which occurs along anatomic ductal structures)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;According to this report, the first explanation is more common. To understand the &lt;em&gt;why&lt;/em&gt; behind the shape, we need to know the mechanism of this desmoplastic response. As described in the linked Wikipedia article, desmoplasia is not actually the tumor itself but dense fibrous tissue that is induced with malignant tumors invade healthy tissue. The mechanism of this is not entirely clear, but the Wikipedia article sets forth two theories:  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The &lt;strong&gt;reactive stroma hypothesis&lt;/strong&gt; postulates that tumor cells cause the proliferation of fibroblasts and subsequent secretion of collagen that acts as a scaffold. This scaffold apparently forms the outline of the &quot;crablegs&quot;.  &lt;/li&gt;&#xA;&lt;li&gt;The &lt;strong&gt;tumor-induced stromal change hypothesis&lt;/strong&gt; states that tumor cells themselves differentiate into fibroblasts and secrete the collagen that forms the spiculated scaffold.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;*Franquet T, De Miguel C, Cozcolluela R, Donoso L. Radiographics. &lt;em&gt;Spiculated lesions of the breast: mammographic-pathologic correlation.&lt;/em&gt; 1993 Jul;13(4):841-52.&#xA;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="3340" LastEditDate="2014-12-23T06:11:06.483" LastActivityDate="2014-12-23T06:11:06.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26100" PostTypeId="2" ParentId="26096" CreationDate="2014-12-22T04:49:09.260" Score="11" Body="&lt;p&gt;DNA codes for proteins via &lt;a href=&quot;http://www.nature.com/scitable/definition/codon-155&quot; rel=&quot;nofollow&quot;&gt;codons&lt;/a&gt;. A codon is a combination of three nucleotides. As there are 4 different nucleotides available in DNA, there are 64 permutations possible. These 64 codons code for the 20 amino acids and 3 stop codons. Hence, many amino acids are coded by several different codons - the genetic code is said to be redundant.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Typically DNA sequences have a single reading frame (but see @user3790338's answer for an interesting exception to this rule). The reading frame is, basically, defined by the first amino acid of the protein that it decodes. Thereafter, each subsequent triplet is one codon, in a non-overlapping way (123 - 456 - 789 - etc.). Note that DNA sequences contain so-called introns that intervene the coding DNA. These regions are eliminated post-transcriptionally. For clarity-sake I have disregarded them in my answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, one has to realize that this coding of DNA is only important phsyiologically during translation, i.e., when mRNA is being translated into a protein. It is the ribosome that actually reads the codons and stop codons to determines which amino acid is to be incorporated in the growing protein and when to stop translation. Hence, although we read DNA sequences in terms of codons, the cellular machinery doesn't read DNA, it reads mRNA. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-23T03:06:58.127" LastActivityDate="2014-12-23T03:06:58.127" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26101" PostTypeId="1" AcceptedAnswerId="26102" CreationDate="2014-12-22T05:32:36.727" Score="0" ViewCount="204" Body="&lt;p&gt;I need to read this article — &lt;a href=&quot;https://www.dropbox.com/s/2d8gyme0jv584mj/color%20vision%20evolution.pdf&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;&quot;Beyond the rainbow&quot;&lt;/strong&gt;&lt;/a&gt; by&#xA;&lt;em&gt;Marie-Claire Koschowitz et al.&lt;/em&gt;, for an exam. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following are some questions for which I could not figure the answer out after reading. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Why does this miniaturization necessitates insulation ? Following is quote from article: &quot;&lt;em&gt;For fast-growing, presumably warm- blooded animals , such miniaturization would only have been possible with sufficient body insulation.&lt;/em&gt; &quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Dinosaurs suppose to have tetrachromacy. The article mentions &quot;&lt;em&gt;dinosaurs were endowed with the highly differentiated color vision of birds&lt;/em&gt;&quot;. Does this mean Dinosaur's &quot;inherited&quot; their tetrachromacy from birds ? Why does the article mention reptiles before that ? Are birds reptiles ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) The article starts talking about h&lt;em&gt;ow mammals develop fur and lost their highly differentiated color vision because they gave up structural color signaling&lt;/em&gt;. What is the direct connection between mammals and the dinosaurs ? I don't see the parallel here....why bring the mammals into the discussion ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) What is the connection between &lt;em&gt;pennaceous feather and planar feathers&lt;/em&gt; ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any or all questions answered is welcome ! Thanks !&lt;/p&gt;&#xA;" OwnerUserId="11662" LastEditorUserId="3340" LastEditDate="2014-12-23T06:07:04.923" LastActivityDate="2016-01-25T12:37:35.740" Title="Can someone help me analyze this article?" Tags="&lt;evolution&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="13" FavoriteCount="1" ClosedDate="2016-01-30T19:14:17.150" ContentLicense="CC BY-SA 3.0" />
  <row Id="26102" PostTypeId="2" ParentId="26101" CreationDate="2014-12-22T05:51:09.877" Score="6" Body="&lt;p&gt;I will answer the questions one by one-&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Why does this miniaturization necessitates insulation ?&lt;/strong&gt;&#xA;An organism's volume determines the total amount of heat that can be stored. The loss (exchange) of heat between the body and external environment mainly occurs on the skin's surface. Hence, body volume determines &lt;em&gt;how much&lt;/em&gt; heat is stored, while body surface determines &lt;em&gt;how fast&lt;/em&gt; that heat is dissipated to the environment. Volume increases with a power of three with radius, while surface increases with a power of two. Hence, smaller animals have large surface-to-volume ratios, which decreases rapidly with body size. Hence, small animals will dissipate relatively more heat per unit of time.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Dinosaurs suppose to have tetrachromacy. The article mentions &quot;dinosaurs were endowed with the highly differentiated color vision of birds&quot;. Does this mean Dinosaur's &quot;inherited&quot; their tetrachromacy from birds ?&lt;/strong&gt; &#xA;No, birds are the closest living relatives to dinosaurs, and birds can be said to have inherited tetrachromacy from dinosaurs - see the cladogram below.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KVibI.jpg&quot; alt=&quot;cladogram&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Why does the article mention reptiles before that ? Are birds reptiles ?&lt;/strong&gt;&#xA;Birds are not reptiles, they are separate classes within the animal kingdom.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;What is the direct connection between mammals and the dinosaurs ? ... why bring the mammals into the discussion ?&lt;/strong&gt;&#xA;Here below is another cladogram; there is no obvious, direct (evolutionary) connection between dinosaurs and mammals. The thing is that dinosaurs ruled the world before the last mass extinction, thereafter it were the mammals. That's why the authors discuss them both, I guess. Especially since we are mammals it may make sense to draw parallels. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nmMD8.jpg&quot; alt=&quot;mammals dinos&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;What is the connection between pennaceous feather and planar feathers&lt;/strong&gt;&#xA;As far as I could track the two down, they are the same (&lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CB8QFjAA&amp;amp;url=http%3A%2F%2Fwww.actazool.org%2Fdownloadpdf.asp%3Ffiletype%3Dpdf%26id%3D5012&amp;amp;ei=GtqYVPHtMMX98QWm6YGAAQ&amp;amp;usg=AFQjCNF_k4RgBrxSReVmtRC9_lCrpznZag&amp;amp;sig2=OmT6ci-WSCCa1tj96Rc_4w&amp;amp;bvm=bv.82001339,d.dGc&quot; rel=&quot;nofollow noreferrer&quot;&gt;Prum, 2006&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Lastly, in response to your original question, before edits: &lt;a href=&quot;http://www3.uni-bonn.de/Press-releases/seeing-dinosaur-feathers-in-a-new-light&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here is a link&lt;/a&gt; with a plain-English popular-scientific web article published online by the first author.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-01-25T12:37:35.740" LastActivityDate="2016-01-25T12:37:35.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26103" PostTypeId="2" ParentId="26076" CreationDate="2014-12-22T07:57:09.940" Score="1" Body="&lt;h2&gt;&quot;More intelligent&quot; as more capable of learning&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Domesticated varieties of animals generally aren't &quot;smarter&quot; as per objective measurements of brain power, however, I'd argue that they would &lt;em&gt;feel&lt;/em&gt; smarter for us because they have different patterns of learning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For most living beings, there is a general shift of the &quot;explore vs exploit&quot; behavior balance as the individual ages - juvenile individuals observe and absorb new behaviors, often by imitating their parents and siblings, while adult individuals tend to lock in the behaviors they already have instead of exploring new options.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans differ from other animals in that this &quot;juvenile&quot; behavior lasts much longer, and the same applies for many domesticated animals - a mid-age dog in many behavioral aspects is more similar to a wolf cub than a wolf of the same age. Such an animal would be more capable and willing to learn new patterns of interaction and tricks than a similar wild animal, and thus feel &quot;more intelligent&quot; to a human observer - while it's an entirely different difference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, as far as I understand, this doesn't neccessarily apply to all domesticated animals which we raise for food and resources, but to 'companion' animals like cats, dogs and horses.&lt;/p&gt;&#xA;" OwnerUserId="5727" LastEditorUserId="5727" LastEditDate="2014-12-22T08:16:15.240" LastActivityDate="2014-12-22T08:16:15.240" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26104" PostTypeId="2" ParentId="26093" CreationDate="2014-12-22T08:10:36.100" Score="-1" Body="&lt;h2&gt;Short generation cycles&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;By definition, we shouldn't expect to observe within our lifetimes the evolution of any species with a generational cycle comparable to our lifetime (mammals and such) since species differentiation requires a multitude of generations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The directly observed evolution thus is limited to short lived organisms such as bacteria, viruses, plants or insects, with an emphasis on the first two.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible to directly observe evolution in an experimental laboratory setting by taking a strain of bacteria that doesn't possess a certain capability (e.g. resistance to some chemical compound), periodically introducing this compound and accelerating the mutation rate by e.g.  radiation, observing the formation of a new species of bacteria that is able to resist this chemical.&lt;/p&gt;&#xA;" OwnerUserId="5727" LastActivityDate="2014-12-22T08:10:36.100" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26105" PostTypeId="1" CreationDate="2014-12-22T10:57:31.507" Score="2" ViewCount="14327" Body="&lt;p&gt;What is the difference between breed, variant, sub-species and species? Are there any similarities between sub-species and sub-population of a region? &lt;/p&gt;&#xA;" OwnerUserId="11650" LastEditorUserId="3340" LastEditDate="2014-12-22T12:15:37.573" LastActivityDate="2017-07-03T20:42:02.143" Title="What is difference between breed, variant, subspecies and species?" Tags="&lt;taxonomy&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26106" PostTypeId="2" ParentId="26093" CreationDate="2014-12-22T11:38:26.950" Score="6" Body="&lt;p&gt;Every single species in existence has &quot;evolved&quot; over the past 100 years. Evolution is a constant process. You are asking whether we can observe evolutionary change in a given species over a short time span, not whether evolution is occurring. I know this sounds like pedantry but it is a very important distinction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, yes, of course we've seen evolution in action in short time spans. The classic example is the various bacterial species that have developed resistance to antibiotics. As very nicely illustrated by Garry Trudeau: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/9PkaG.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want more rigorous evidence than a comic strip, have a look at Wikipedia's page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Antibiotic_resistance&quot; rel=&quot;nofollow noreferrer&quot;&gt;antibiotic resistance&lt;/a&gt; or read &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC518544/pdf/jbacter00647-0081.pdf?origin=publication_detail&quot; rel=&quot;nofollow noreferrer&quot;&gt;Demerec, 1948&lt;/a&gt;(1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example is described by &lt;a href=&quot;http://www.pnas.org/content/109/51/21010.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yona &lt;em&gt;et al.&lt;/em&gt;&lt;/a&gt;(2) who show that subjecting yeast to high temperatures (heat stress) for a few generations causes genetic changes that help the cells deal with the stress. This is, clearly, evolution in action. In fact, they even show that the first response is the duplication of an entire chromosome (think of it as a crude, bludgeon-like solution) which is later suppressed by other, more subtle, compensatory mechanisms which arise to replace it. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC518544/pdf/jbacter00647-0081.pdf?origin=publication_detail&quot; rel=&quot;nofollow noreferrer&quot;&gt;Demerec, Milisav, &quot;Origin of bacterial resistance to antibiotics.&quot; Journal of bacteriology 56(1), 1948&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pnas.org/content/109/51/21010.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yona &lt;em&gt;et al&lt;/em&gt;., &quot;Chromosomal duplication is a transient evolutionary solution to stress&quot;, PNAS, 109(51), 2012.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2014-12-22T18:58:49.670" LastActivityDate="2014-12-22T18:58:49.670" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26107" PostTypeId="1" AcceptedAnswerId="26111" CreationDate="2014-12-22T12:15:40.183" Score="1" ViewCount="73" Body="&lt;p&gt;Is the ATP molecule which is bound to the myosin head for relaxation of the muscle (i.e., to break the cross bridge) also utilized for active transport of calcium to the sarcoplasmic reticulum during muscle relaxation? &lt;/p&gt;&#xA;" OwnerUserId="11647" LastEditorUserId="9943" LastEditDate="2014-12-22T13:35:37.120" LastActivityDate="2014-12-23T18:57:14.857" Title="Double use of ATP in relaxing myosin &amp; active transportation of calcium?" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26108" PostTypeId="2" ParentId="26093" CreationDate="2014-12-22T12:17:24.990" Score="1" Body="&lt;p&gt;As Peteris claimed, we cannot witness the complete evolution of a specie in our life time. Our life, being a frozen moment in the eternal journey of evolution, not always gives us the pleasure to completely understand the process of evolution(also the purposes). But we can witness some minute details, which we can consider as the sub sets of a complete evolution. By evolution, most people think of the complete development from one specie to another, but this kind of evolution to develop a completely different specie will take a millions of years. So we could conclude that those kind of evolutions cannot be witnessed in our life time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But there are those evolutions which are more dramatic and came into existence within a period of some decades, so considering these minor evolutions(or we can call it variations) we have a couple of cases were some species develop,&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Resistance over chemicals(pesticides,insecticides)&lt;/li&gt;&#xA;&lt;li&gt;Adaptions to withstand predations&lt;/li&gt;&#xA;&lt;li&gt;Cope with available resources(veg/non veg diets)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1. Resistance over chemicals(pesticides,insecticides)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Reappearence of tougher bedbugs that are harder to kill&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Entomologist Dini Miller of Virginia Tech says bedbugs probably developed thicker, denser, waxlike exoskeletons, also called cuticles, that repel chemicals in pesticides. To test the hypothesis, her group is comparing cuticle-coding genes in both insecticide-resistant and susceptible bedbugs, as well as measuring their cuticle thickness and hydrocarbon content, which indicates how much wax is present.&#xA;  &lt;a href=&quot;http://www.popsci.com/science/article/2011-05/bedbugs-are-harder-ever-kill&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Evolution of Microgadus tomcod&lt;/strong&gt;&#xA;  After General Electric dumped polychlorinated biphenyls (PCBs) in the Hudson River from 1947 through 1976, tomcod living in the river were found to have evolved an increased resistance to the compound's toxic effects.&lt;a href=&quot;http://www.popsci.com/science/article/2011-05/bedbugs-are-harder-ever-kill&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt; Scientists identified the genetic mutation that conferred the resistance, and found that the mutated form was present in 99 percent of the tomcods in the river, compared to fewer than 10 percent of the tomcods from other waters.&#xA;  &lt;a href=&quot;http://en.wikipedia.org/wiki/Microgadus_tomcod&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. Adaptions to withstand predations&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Lizards are Evolving to be Dancers&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Take the southeast fence lizard, for example. When fire ants were accidentally introduced to the States about 70 years ago, the fence lizard found itself defenseless against them. The ants had no natural enemies, and it only took 12 of them to take a lizard down in about a minute. Seventy years later, the lizards that live closest to the port where the ants were first introduced have evolved an unlikely strategy for dealing with their antagonists. How unlikely? Well, there's a dance involved, which makes these animals the first on record to employ the West Side Story method of self-defense.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;While other lizards respond to ant attacks by &quot;sitting still, just hoping the ants would go away,&quot; these smooth operators developed an ant-shaking shimmy that they've passed on to their kids. And those kids have longer legs for quicker get-aways. Just so we're clear: Nature, not weird daddy issues, has created leggy lizards that thwart attackers through shaking what their mommas gave them.&#xA;  &lt;a href=&quot;http://www.cracked.com/article_19213_7-animals-that-are-evolving-right-before-our-eyes.html&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;3. Cope with available resources(veg/non veg diets)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Lizards are Rewiring Their Own Guts, Right Now&lt;/strong&gt;&#xA;  In 1971, scientists introduced 10 Italian wall lizards to an island in Croatia, but right after they dropped them off, the Croatian War for Independence prevented the researchers from following up on their little lizard guinea pigs. In fact, the scientists couldn't get back to the island until 2004. When they did, they found 5,000 lizard descendants who had not only annihilated the entire indigenous lizard population, but also rewired the shape of their own innards to accommodate the local diet.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Before their introduction to the island, the wall lizards were carnivores, so their digestive systems weren't built for leaf-eating. But on an island short on insects and long on plants, a strictly carnivorous stomach would be a one-way ticket to Deadville. So the lizards developed things called cecal valves, which were muscles that slowed down the process of food digestion and gave them more time to break down plant cellulose. But growing new gut muscles wasn't all the lizards had up their sleeves. They also grew bigger heads for stronger bites, and dropped territorial defenses.&#xA;  &lt;a href=&quot;http://www.cracked.com/article_19213_7-animals-that-are-evolving-right-before-our-eyes_p2.html&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Evolution is an aggregation of all these combined traits and mostly evolution is accelerated when the species are &lt;a href=&quot;http://en.wikipedia.org/wiki/Allopatric_speciation&quot; rel=&quot;nofollow&quot;&gt;geographically separated&lt;/a&gt;, time is a crucial factor  with evolution. We are unlucky to witness a complete evolution in our neighborhood, but all these accumulating traits which change a specie to adapt with a diverse environment is a powerful evidence towards evolution and its working.&lt;/p&gt;&#xA;" OwnerUserId="10294" LastActivityDate="2014-12-22T12:17:24.990" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26109" PostTypeId="1" AcceptedAnswerId="26117" CreationDate="2014-12-22T12:34:08.633" Score="0" ViewCount="7652" Body="&lt;p&gt;How does the mango tree perceive the summer season, so tree starts producing the fruits? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Every tree requires sunlight to grow but what limits the production of fruits to a certain season?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example: Mango only grows in summer season, whereas banana grows in all seasons.&lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorUserId="1590" LastEditDate="2014-12-22T15:36:22.520" LastActivityDate="2020-07-21T16:32:18.047" Title="Why are some vegetables/fruits seasonal?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26110" PostTypeId="1" AcceptedAnswerId="27656" CreationDate="2014-12-22T12:38:02.250" Score="3" ViewCount="4560" Body="&lt;p&gt;Why does our voice change when we get affected by cold or cough? I observed the voice change thing in so many people including me. &lt;/p&gt;&#xA;" OwnerDisplayName="user10246" LastEditorDisplayName="user12874" LastEditDate="2015-01-13T22:31:55.763" LastActivityDate="2015-01-14T00:46:17.823" Title="Why does our voice change when we get affected by cold or cough?" Tags="&lt;human-biology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="26111" PostTypeId="2" ParentId="26107" CreationDate="2014-12-22T13:52:47.483" Score="2" Body="&lt;p&gt;ATP is used (hydrolyzed) by ion pumps to transport ions such as calcium against their concentration gradient. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Molecular motors (such as myosin and kinesin) also couple ATP hydrolysis with movement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However both these processes are separate and just because calcium flux changes happen during muscle contraction doesn't mean that it is the same ATP that drives some kind of a bifuntional enzyme to perform both tasks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover calcium is released during the contraction phase from the sarcoplasmic reticulum (SR); pumping back the calcium to the SR happens during the repolarization (there is no myosin movement at this stage).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-22T13:52:47.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26112" PostTypeId="1" AcceptedAnswerId="26113" CreationDate="2014-12-22T15:03:37.510" Score="2" ViewCount="60" Body="&lt;p&gt;I quite understand why thymine is present in DNA. So we can mark it out where cytosine undergoes a reaction and is converted to uracil. Then we can repair the DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But how can we make that out in RNA ??&lt;/p&gt;&#xA;" OwnerUserId="11647" LastEditorUserId="3340" LastEditDate="2014-12-22T16:25:01.277" LastActivityDate="2014-12-26T07:05:14.167" Title="How are lesions in the RNA corrected?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26113" PostTypeId="2" ParentId="26112" CreationDate="2014-12-22T15:57:05.820" Score="3" Body="&lt;p&gt;RNA is shortlived and need not undergo repair. A &quot;mutated&quot; RNA will degrade and will be replaced by the correct RNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even though RNAs are shortlived compared to DNA (which does not really undergo turnover), some RNAs are stable and have low turnover. Nonetheless RNA would be present in multiple copies it is improbable that all of them would have undergone mutation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover RNA with certain mutated codons e.g. non-sense mutations are cleared off by the exosome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks to har-wradim for pointing out about RNA repair mechanisms. There are few reports that say that methylations in the RNA can be corrected by the enzymes AlkB (in &lt;em&gt;E.coli&lt;/em&gt;) and its eukaryotic homologue hABH3. These enzymes were known to repair methyl lesions in the DNA (1-methyladenine and 3-methylcytosine), but it was subsequently shown that they can act on RNA as well &lt;strong&gt;&lt;sup&gt;[&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1097276504005209&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;,&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0306452206015156&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]&lt;/sup&gt;&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However there seems to be no mechanism for repairing deamination damage; &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/anie.201206489/abstract&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; study has demonstrated an artificially designed system which is capable of targeted RNA deamination (but there is no system yet that can fix a deaminated base in RNA). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1568786412000444&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; article comments that AlkB is tightly regulated because if uncontrolled it can demethylate functional methylations too. Overexpression of AlkB is actually toxic to the cells unless they are under alkylation stress by agents such as EMS/MMS (Ethyl/Methyl MethaneSulphonate).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But IMO RNA repair is not as essential as DNA repair because of aforementioned reasons. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-26T07:05:14.167" LastActivityDate="2014-12-26T07:05:14.167" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="26115" PostTypeId="2" ParentId="5586" CreationDate="2014-12-22T20:19:28.693" Score="8" Body="&lt;p&gt;First of all, this observation is the norm across human perception. While humans react in roughly the same way to similar stimuli (e.g. both a cranberry and a tomato are seen as &lt;em&gt;red&lt;/em&gt;, the destruction of tissue is felt as &lt;em&gt;painful&lt;/em&gt;), the intensity tends to be different. Also, many stimuli elicit not just a knowledge of the state of the world or one's body, but also a reaction (e.g. shivering when cold, or emotions like fear when physical pain is felt), and these reactions differ between humans too. So, on a very general level, it can be answered with &quot;Because that's how human perception works&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that this is a very unsatisfactory answer, so here are some factors off the top of my head. For any given case, one or more of them will cause the difference, and you cannot tell which ones from casual observation. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Your observation of &quot;&lt;em&gt;similar clothing&lt;/em&gt;&quot; could have been incorrect. For example, an acrylic sweater can look exactly like a sheep wool sweater, but warms much less. Or, slightly shorter sleeves can cause much cooling if they leave the wrist exposed. Layering is also very important, and we generally only notice the uppermost clothing layer. &lt;/li&gt;&#xA;&lt;li&gt;Your observation of &quot;&lt;em&gt;similar body structure&lt;/em&gt;&quot; could have been not precise enough. People who have the same appearance can have different amounts and distributions of body fat. Maybe one person is simply better insulated than another one. &lt;/li&gt;&#xA;&lt;li&gt;The state of their &lt;em&gt;circulatory system&lt;/em&gt; was different. Vasoconstriction and vasodilation will change the skin temperature, which is sensed by peripheral thermoreceptors. &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Estrogen&lt;/em&gt; is involved in thermal perception. The gender of the person and the current point in the menstrual cycle (or pregnancy) in women will make a difference. &lt;/li&gt;&#xA;&lt;li&gt;The &lt;em&gt;circadian cycle&lt;/em&gt; of the two people is probably not perfectly synchronised. Core body temperature varies during the cycle, and thermoperception depends on core body temperature too, not just skin temperature. &lt;/li&gt;&#xA;&lt;li&gt;A different &lt;em&gt;metabolism&lt;/em&gt; will cause one person to create more body heat than another&lt;/li&gt;&#xA;&lt;li&gt;Other &lt;em&gt;hormones&lt;/em&gt; (beyond estrogen and the ones ruling the circadian cycle and metabolism) probably have an effect on thermoperception, but I can't tell you details here. Temperature is regulated in the hypothalamic-pituitary-adrenal axis, so the hormones from it are likely to have an influence. &lt;/li&gt;&#xA;&lt;li&gt;Normal variations in the two people's &lt;em&gt;neural networks&lt;/em&gt; will change the intensity of signal perception. People are born with very unconnected neurons, and build unique connections depending on the environment they encounter while growing up. As a result, each person's brain functions slightly differently when given the same input. &lt;/li&gt;&#xA;&lt;li&gt;Differences in &lt;em&gt;neurotransmitter sensitivity&lt;/em&gt; can account for the difference in intensity of perception. People sometimes react differently to the same level of neurotransmitter, or also their brains secrete different amounts of neurotransmitter as a response to the same stimulus. These differences exist on an average level (e.g. glutamate can potentially &quot;do&quot; more for me than for you) but are also affected by drugs and illness. &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Attention&lt;/em&gt; is a major part of perception. The CNS can suppress information from sensory organs at a very low level if the brain is focusing elsewhere. &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Habit&lt;/em&gt;: people can intentionally or unintentionally learn to disregard or misinterpret their body sensations. &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Psychological stress&lt;/em&gt; increases the core body temperature &lt;/li&gt;&#xA;&lt;li&gt;The above reasons all assumed differences between a pair of healthy individuals. Some conditions, for example running a &lt;em&gt;fever&lt;/em&gt;, but also &lt;em&gt;neurological disorders&lt;/em&gt; anywhere along the complex pathways from sensors to cortex (and the other way round!) or diseases which for some reason alter thermoregulation, will all change the feeling of hot or cold. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This list is probably incomplete. Also, some of the factors I listed will overlap to some extent (e.g. vasodilation is frequently mediated through hormones, and ingrained habits are reflected in neural network connections). But the take away point is: &lt;strong&gt;Human perception is an active process, very far removed from simple &quot;reporting&quot; of the state of the environment. It is unrealistic to expect two individuals to have the same perception when exposed to the same stimuli.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an in-depth description of how thermoperception and thermoregulation work physiologically, see &lt;a href=&quot;http://ajpregu.physiology.org/content/301/5/R1207&quot;&gt;this summarizing paper&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="1578" LastActivityDate="2014-12-22T20:19:28.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26116" PostTypeId="2" ParentId="26058" CreationDate="2014-12-22T20:57:07.913" Score="1" Body="&lt;p&gt;What tel explained is correct. I wanted to add that we actually see pure light in a composite way too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note for example that the M receptor has a peak at around 550nm, and a symmetric response curve. So, if you shine a 540nm light, the response of the M cone is the same as the response at 560nm. So, how do we know that it's a cool, bluish green and not a warm, yellowish green? By the response of the other cones. The ganglion cells in the retina combine the response of several cones to represent the wavelength of the light perceived by the photoreceptors (as well as some other attributes of the image within their receptive field). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for &quot;tricking&quot; the eye, we're doing it all the time. Higher levels of visual processing will interpret colors depending on everything else perceived in the picture, such as light intensity, texture, and even cultural knowledge about colors. A mostly unbiased representation of wavelengths is only present at very early stages of visual processing. &lt;/p&gt;&#xA;" OwnerUserId="1578" LastActivityDate="2014-12-22T20:57:07.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26117" PostTypeId="2" ParentId="26109" CreationDate="2014-12-22T21:01:40.550" Score="1" Body="&lt;p&gt;Many plants start flowering (and subsequent seed / fruit production) based on light, temperature, and / or humidity changes, which tell them summer is near. That is when they need to grow fruit. Surely, there are plants trying to look for sunlight, pollinators, good conditions for seedlings, in the winter, but they are specially adapted, and thrive in their niche only through some season sensing similar to the summer-flowering plants.&lt;/p&gt;&#xA;&lt;p&gt;At the Equator there isn't much difference between seasons and days, and there  should be no need for such mechanism. Bananas are suited to the Equator, meaning banana trees don't know what seasons are.&lt;/p&gt;&#xA;&lt;p&gt;Plants in temperate climates care about seasons a lot. We put them in greenhouses and we play with their light, in order to force off-season flowering. Tomatoes are kept in the greenhouse not because we don't like them shivering outside, but because we want to fool their temperature-sensing organs that summer is here.&lt;/p&gt;&#xA;&lt;p&gt;At the Tropics there is an important difference in the amount of rain water and a smaller change in day duration. Mangoes are more suited to the Tropics, meaning they care about seasons. People who grow mangoes in greenhouses try to fool them by adjusting humidity, but I couldn't find any evidence that it is humidity rather than day length.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastEditorUserId="10337" LastEditDate="2020-07-21T16:32:18.047" LastActivityDate="2020-07-21T16:32:18.047" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="26119" PostTypeId="1" AcceptedAnswerId="26122" CreationDate="2014-12-23T07:06:45.950" Score="7" ViewCount="1155" Body="&lt;p&gt;Since I started learning about molecular cell biology, I have witnessed an increasing amount of attention to this thing called a &quot;histone code.&quot; However, unlike the central dogma of molecular cell biology (i.e. DNA RNA Protein), I still feel very confused about what exactly constitutes the histone code. Is this term code being used rigorously like it is for the central dogma? That is,  is there an actual code? If so, what is its alphabet (e.g. GTAC for DNA, GUAC for RNA, the amino acids for  proteins)? What kind of words does it encode (e.g. codons for RNA to protein)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If these things are not known, how do we know it's actually a code then?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="3340" LastEditDate="2014-12-23T08:40:28.140" LastActivityDate="2014-12-26T06:59:55.300" Title="In what sense is the &quot;histone code&quot; a code?" Tags="&lt;molecular-biology&gt;&lt;histone&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26120" PostTypeId="1" AcceptedAnswerId="26144" CreationDate="2014-12-23T07:15:31.757" Score="5" ViewCount="4162" Body="&lt;p&gt;I am working on 20% SDS PAGE. I want to know optimum polymerization time for 20% resolving gel and 6% stacking gel. If I increase the time then would it affect the band pattern?&lt;/p&gt;&#xA;" OwnerUserId="8423" LastEditorUserId="948" LastEditDate="2014-12-23T17:03:55.097" LastActivityDate="2015-01-03T12:06:27.517" Title="What is SDS PAGE gel polymerization time?" Tags="&lt;molecular-biology&gt;&lt;sds-page&gt;" AnswerCount="4" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26121" PostTypeId="2" ParentId="26119" CreationDate="2014-12-23T08:14:30.280" Score="0" Body="&lt;p&gt;It's not a code in the strict sense of the word. With proteins and nucleic acids you have a strictly defined set of letters and strict rules for them to match one another (note that in some cases atypical base pairing occurs in nucleic acids). The &quot;code&quot; part in histone code is meant to convey the notion that modifications in the histone proteins influence the expression of genetic information. The main mechanisms of histone modification are methylation, acetylation, and ubiquitilation. In a very rough analogy, these would be the &quot;letters&quot; of the histone code (NOTE that this is a very imprecise analogy).&lt;/p&gt;&#xA;" OwnerUserId="10001" LastActivityDate="2014-12-23T08:14:30.280" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26122" PostTypeId="2" ParentId="26119" CreationDate="2014-12-23T08:26:19.267" Score="8" Body="&lt;p&gt;As already mentioned by Stefan, the &quot;histone&quot; code is not really a universal code; it is restricted to eukaryotic systems and even then, not unambiguous. It is, at present related to two kinds of histone modifications and their correlation with the transcriptional activity at that locus:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Methylation&lt;/li&gt;&#xA;&lt;li&gt;Acetylation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Other modifications such as phosphorylation and ubiquitylation also exist but they are not generally considered in this &quot;code&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Acetylation masks the histone's positive charge and thereby loosens the chromatin (DNA wrapped around the histones), which in turn facilitates transcription. Therefore acetylation is almost always activating in the sense of gene expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Methylation, on the other hand has different effects. Methylation on Histone-3 at 4th lysine (H3K4) and H3K36 causes activation whereas H3K9 and H3K27 are repressive. There is also some difference between different extent of methylation i.e monomethylation, dimethylation and trimethylation. The effect of methylation is executed by proteins that have domains such as chromodomain and PHD fingers, that identify these modified histones. Sometimes the histone can carry both kinds of methylation marks H3K4me3 and H3K27me3 and these are called &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S095506741200052X&quot; rel=&quot;nofollow&quot;&gt;bivalents&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other histones of the octameric nucleosome can also be modified. However as with other kinds of modifications that I mentioned previously they do not seem to be very common and are therefore not generally considered in this &quot;code&quot;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-26T06:59:55.300" LastActivityDate="2014-12-26T06:59:55.300" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26123" PostTypeId="1" AcceptedAnswerId="26130" CreationDate="2014-12-23T08:51:31.140" Score="5" ViewCount="4670" Body="&lt;p&gt;Is the empty space inside a bamboo stem a xylem? And why is the space so large?&lt;/p&gt;&#xA;" OwnerUserId="10330" LastEditorUserId="3624" LastEditDate="2014-12-24T00:01:33.873" LastActivityDate="2014-12-24T00:10:43.440" Title="What does the empty space in the bamboo stem do?" Tags="&lt;botany&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26124" PostTypeId="2" ParentId="26120" CreationDate="2014-12-23T08:54:49.753" Score="4" Body="&lt;p&gt;The polymerization time is strongly dependent on APS and TEMED concentrations. I do not think that the increased time for polymerization would somehow influence the division of the proteins in negative way. Actually the time varies from 20 min to 1 h, but I personally leave the gel to polymerize longer. Unpolymerized Acrylamide could build adducts with some proteins which could result in multiple bands. In addition acrymamide itself is toxic, so I always give it additional time to polymerize. Good luck!&lt;/p&gt;&#xA;" OwnerUserId="11671" LastEditorUserId="9943" LastEditDate="2014-12-23T11:23:04.393" LastActivityDate="2014-12-23T11:23:04.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26125" PostTypeId="2" ParentId="26120" CreationDate="2014-12-23T09:04:08.337" Score="9" Body="&lt;p&gt;There is nothing like a general polymerization time, as this is a chemical reaction which depends on many factors. The most important are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;APS:&lt;/strong&gt; Concentration and and the age of the chemical are important. APS decomposes over time when it is not stored completely dry (which it is not on most benches) and also with freezing thawing cycles in storage. APS provides the free radicals necessary for the reaction; without it no polymerization will happen. In my experience APS is the most critical part of the reaction, with old solutions making the polymerization really slow. I would make a stock solution, freeze it in aliquots. For making gels I thaw on aliquot and keep it in the fridge afterwards for a week and then discard it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;TEMED:&lt;/strong&gt; Is the catalyst for the reaction, too much of it will start the reaction very fast. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Temperature:&lt;/strong&gt; The warmer it is, the faster the polymerization will be. In the cold room you will not get complete reaction, if any.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you can do is to store the remaining acrylamide in the beaker and wait until it is polymerized. Then your gel should also be ok to use. A longer polymerization time (assuming that your gel was completely polymerized before) will not change the resolving capacity of your gel.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="3340" LastEditDate="2014-12-23T12:12:57.290" LastActivityDate="2014-12-23T12:12:57.290" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26126" PostTypeId="2" ParentId="26119" CreationDate="2014-12-23T09:04:27.947" Score="4" Body="&lt;p&gt;The histone code isn't a sequence of letters like you see in DNA and RNA but rather refers to the pattern of post-translational modification of histones. This is then, by definition, an epigenetic control of gene expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Histones are basic DNA binding proteins around which DNA is wound to form chromatin. For transcription to occur, transcription factors and RNA polymerase must bind DNA, which generally cannot happen if DNA is wrapped tightly around histones. DNA must therefore be able to come off from and translocate relative to histones in order to expose bare regions. Based on the level of compaction, chromatin can be generally classified as two types:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;euchromatin&lt;/strong&gt;: loosely bound, transcriptionally active&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;heterochromatin&lt;/strong&gt;: tightly bound, transcriptionally repressed&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The state of chromatin compaction is determined by specific  post-translational modifications to the residues in the histones' amino-terminal tail. This is the histone code. One commonly talked about and perhaps easiest to understand modifications is acetylation of lysine residues: this is generally considered to activate transcription since it neutralizes the positive charge of the amino acid so the negatively charged DNA isn't attracted as tightly. Phosphorylation of serine or threonine can have a similar effect by introducing negative charges. Other modifications include mono-, di- and trimethylation of lysine and arginine, ubiquitinylation and others that I haven't memorised. Each histone monomer can be modified independently and each has several residues that can be modified; this leads to staggeringly large number of ways in which just a single nucleosome can be modified. Importantly, these modifications can recruit proteins including transcription factors, histone modifiers and chromatin remodellers (which can condense or loosen the chromatin). All of these serve to tightly regulate gene expression. This is an active field of research and what all discovered combinations of modifications do is largely unknown, but certain modifications are often characteristic of active and repressed transcription.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a standard convention for conveying histone modifications. For example, if lysine 23 of histone H3 was acetylated, you would write H3K23Ac. For trimethylation of arginine 3 on histone H4, you would write H4R3Me3. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-12-23T09:11:28.293" LastActivityDate="2014-12-23T09:11:28.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26127" PostTypeId="2" ParentId="26094" CreationDate="2014-12-23T09:19:39.713" Score="0" Body="&lt;p&gt;Prions are misfolded &quot;versions&quot; of proteins already present in the genome. These tend to bind to their properly folded counterparts and catalyze their misfolding into prions. Although unlikely, it is not impossible to imagine that they might interact with other macromolecules. That being said, injecting a human with prionic particles for any reason (especially in a clinical trial for the common cold) is EXTREMELY unlikely. Even if you prove that it works in animal models, injecting a person would be considered too risky. Additionally, the &quot;benefit&quot; of that would be marginal - curing the common cold, from which &gt; 99% of people recover even without any medication. Given that there is great risk and very little benefit, we will most likely never know for sure how feasible this is (at least for the common cold). As a concept, it could work, but would be extremely difficult to get right. &lt;/p&gt;&#xA;" OwnerUserId="10001" LastActivityDate="2014-12-23T09:19:39.713" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26129" PostTypeId="2" ParentId="26120" CreationDate="2014-12-23T11:01:16.420" Score="6" Body="&lt;p&gt;Others have already explained the effect of different factors on polymerization time. This answer is mostly about: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If I increase the time then would it affect the band pattern?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It may.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some tips: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Make a little extra mix so that you can leave some in the beaker to know if polymerization has happened.&lt;/li&gt;&#xA;&lt;li&gt;Always layer the poured resolving gel with water so that the gel doesn't get dried up. &lt;/li&gt;&#xA;&lt;li&gt;Don't leave the gel for long time after polymerization. Not only it wastes time, it also may cause the gel to dry up and SDS/Urea to precipitate/crystallize.&lt;/li&gt;&#xA;&lt;li&gt;Wash the gels with the running buffer after removing the comb/before loading the sample. You can use a fine needled (high gauge) to do that.&lt;/li&gt;&#xA;&lt;li&gt;Pre-run the gel to equilibriate it; this not generally necessary and as Nick Sandor said, would destroy stacking gel. However it is important for big urea gels and somewhat important for continuous SDS-gels if you have left it for a quite some time post polymerization. So it is better to not leave the gel for a long time &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-24T04:38:35.937" LastActivityDate="2014-12-24T04:38:35.937" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26130" PostTypeId="2" ParentId="26123" CreationDate="2014-12-23T11:34:31.943" Score="8" Body="&lt;p&gt;No, its not xylem. Bamboo is a grass, and the stem (culm) of many grasses are hollow in the middle (see e.g. &lt;a href=&quot;http://www.fsl.orst.edu/forages/projects/regrowth/print-section.cfm?title=Grass%20Structures&quot;&gt;&lt;em&gt;Grass Structures&lt;/em&gt;&lt;/a&gt; from Oregon state for some more info).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact reason for why Bamboo have hollow stems is most likely due to evolutionary contingencies. However, from a mechanical stability point of view, a hollow stem is much more rigid and stable than a solid (but much thinner) stem composed of the same amount of biomass (&lt;a href=&quot;https://books.google.se/books?id=XeLmGmWl3-IC&amp;amp;pg=PA191#v=onepage&amp;amp;q&amp;amp;f=false&quot;&gt;Niklas &amp;amp; Spatz, 2012&lt;/a&gt;, p. 191ff). So from the perspective of efficiency, the hollow stems of grasses are very useful. The solid node discs found in grass stems (and in other plants with hollow stems) are however really important for increasing overall stability and ability of stems to resist deformations, while only contributing to a very small amount of the total biomass.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2014-12-24T00:10:43.440" LastActivityDate="2014-12-24T00:10:43.440" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26133" PostTypeId="5" CreationDate="2014-12-23T12:54:50.793" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2014-12-23T12:54:50.793" LastActivityDate="2014-12-23T12:54:50.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26134" PostTypeId="4" CreationDate="2014-12-23T12:54:50.793" Score="0" Body="The study of the adaptability of the nervous system. It includes changes in neural pathways and synapses due to changes in behavior (e.g., learning), environment (e.g., stressors) and bodily injury (e.g., brain damage)." OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-23T14:30:56.550" LastActivityDate="2014-12-23T14:30:56.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26135" PostTypeId="1" AcceptedAnswerId="26137" CreationDate="2014-12-23T13:51:40.743" Score="6" ViewCount="255" Body="&lt;p&gt;Since a human woman is born with a set number of eggs, and meiosis is the process by which sex cells are produced, would meiosis in a woman happen before she is born or soon after she was born?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If meiosis creates sex cells and women are born with a set number of sex cells, when in the development of a woman are her sex cells created?&lt;/p&gt;&#xA;" OwnerUserId="11674" LastEditorUserId="9829" LastEditDate="2014-12-23T16:58:21.527" LastActivityDate="2014-12-23T16:58:21.527" Title="When are a female's eggs created?" Tags="&lt;human-biology&gt;&lt;development&gt;&lt;meiosis&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26137" PostTypeId="2" ParentId="26135" CreationDate="2014-12-23T15:12:56.257" Score="6" Body="&lt;p&gt;Oocytes, or immature female eggs, develop in the fetus's ovaries during pregnancy. This graph (&lt;a href=&quot;https://embryology.med.unsw.edu.au/embryology/index.php/Oocyte_Development#Oogenesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;U. New South Wales&lt;/a&gt;) shows the oocyte population over time in a human female:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QiFQl.jpg&quot; alt=&quot;graph of oocytes in human body&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although the x-scale is kind of confusing (months when negative, years when positive), you can see that the fetus has all the oocytes it will ever have at the peak 18-22 weeks after conception. Since age 0 is birth, meiosis in a woman happens long before she is born.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2014-12-23T15:12:56.257" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26138" PostTypeId="1" AcceptedAnswerId="26140" CreationDate="2014-12-23T15:56:36.957" Score="4" ViewCount="29157" Body="&lt;p&gt;I'm curious what the exact cause is of dramatic heat generation that comes along with muscle activity. Can anybody explain this in understandable language?&lt;/p&gt;&#xA;" OwnerUserId="11675" LastEditorUserId="3340" LastEditDate="2015-06-24T08:56:36.510" LastActivityDate="2015-06-24T08:56:36.510" Title="What causes muscles to generate heat on contraction?" Tags="&lt;metabolism&gt;&lt;muscles&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="26139" PostTypeId="2" ParentId="26138" CreationDate="2014-12-23T17:17:51.263" Score="4" Body="&lt;p&gt;This is oversimplified, but hopefully clear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When we eat food, &lt;a href=&quot;http://www.merriam-webster.com/dictionary/metabolism&quot; rel=&quot;nofollow noreferrer&quot;&gt;metabolic&lt;/a&gt; processes break down larger, multi-carbon molecules (like glucose) into smaller molecules. This process is called &lt;a href=&quot;http://www.rsc.org/Education/Teachers/Resources/cfb/metabolism.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;catabolism&lt;/a&gt;, and it releases energy. Here's a simple example of a catabolic reaction:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;AB -&amp;gt; A + B + energy&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;For more on this principle, look at the section on Le Châtelier's Principle on &lt;a href=&quot;http://www.chemistry.wustl.edu/~edudev/LabTutorials/Buffer/Buffer.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this page&lt;/a&gt; from Washington University.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our body can use the energy released to drive more chemical reactions. Specifically, our cells make a molecule called ATP, which is used all over the cell when energy is needed. However, our cells can't convert 100% of the energy from catabolic processes into chemical energy, some of it is lost as heat (or &lt;a href=&quot;http://en.wikipedia.org/wiki/Entropy&quot; rel=&quot;nofollow noreferrer&quot;&gt;entropy&lt;/a&gt;). When we use ATP, a high energy phosphate group is hydrolyzed (chemically split) from the ATP molecule (&lt;a href=&quot;http://apbrwww5.apsu.edu/thompsonj/Anatomy%20&amp;amp;%20Physiology/2010/2010%20Exam%20Reviews/Exam%201%20Review/Ch02%20Nucleic%20Acids%20and%20ATP.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;ASPU&lt;/a&gt;, look at the arrow on the right for energy release):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HjlXb.png&quot; alt=&quot;atp hydrolysis&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This releases energy, some of which (during exercise) is used to make muscles contract, but much of it is lost as heat. We heat up when we exercise because the muscles are being used more than at rest, which means more ATP is being used to contract the muscles, which means more heat is being released by the ATP hydrolysis reaction.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="9829" LastEditDate="2014-12-23T17:57:26.820" LastActivityDate="2014-12-23T17:57:26.820" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="26140" PostTypeId="2" ParentId="26138" CreationDate="2014-12-23T17:39:27.307" Score="7" Body="&lt;p&gt;First, it might be helpful to talk briefly about what heat is. It is a form of energy - molecular energy. Basically, heat is the amount of jiggliness of the molecules of a substance or object. When we look at a hot object, it doesn't apear to be moving any more than a cold object, but on a scale much smaller than we can see, it's molecules are moving faster than in a colder object. &lt;a href=&quot;http://www.physicsclassroom.com/class/thermalP/Lesson-1/What-is-Heat&quot;&gt;Read this&lt;/a&gt; for more information if you want.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are at least two things going on in muscle contraction (as well as in other metabolic processes) which produce heat. The first is the chemical reaction that powers muscle contraction. You probably don't want to get into great detail, but basically there is a molecule which your cells use to store power, which we abbreviate as ATP. When our muscles use that power, an &lt;a href=&quot;http://en.wikipedia.org/wiki/Exothermic_reaction&quot;&gt;exothermic&lt;/a&gt; chemical reaction occurs that &quot;burns&quot; ATP, breaking it into two pieces (ADP and phosphate). That reaction releases energy. Some of that energy is used in the actual movement of the muscle. But some of it just &quot;jiggles&quot; the nearby molecules. Again that jiggling is the very definition of heat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second source of heat is probably much smaller: friction. In short, just about any time &lt;em&gt;anything&lt;/em&gt; moves, nearby molecules get jiggled some more. Imagine trying to walk through a room packed full of harps. Everywhere you move, some of those strings get plucked and vibrate. It's a little bit like that. When your muscle fibers tighten and flex, they rub past each other and jiggle each others atoms. All of that jiggliness &lt;em&gt;is heat,&lt;/em&gt; and the jiggling continues until it can transfer to some other medium, as when, &lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/thermo/sweat.html&quot;&gt;sweat evaporates&lt;/a&gt; from your skin.&lt;/p&gt;&#xA;" OwnerUserId="5018" LastActivityDate="2014-12-23T17:39:27.307" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26141" PostTypeId="1" CreationDate="2014-12-23T19:26:04.970" Score="5" ViewCount="454" Body="&lt;p&gt;In an experiment by Pollard, T.D. and R.R. Weihing, amoeba cells injected with  Cytochalasin B were inhibited of movement, while the control group amoeba cells did move. A hypothesis was made that Cytochalasin B blocked polymerization of actin monomers into actin filaments, thus preventing the cell from moving. To validate this hypothesis the experiments were made again with cycloheximide (inhibits new protein synthesis), and dinitrophenol (inhibits new ATP formation), and colchicine (inhibits polymerization of microtubules Here are the results:$\\$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\begin&#xA;Condition:                                  % of cells that didn't move&#xA;No drug                                      3&#xA;Cycochalasin B                            95&#xA;Colchicine                                   4&#xA;Cycloheximide                             3&#xA;Cycloheximide + Cycochalasin B    94&#xA;Dinitrophenol                               5&#xA;Dinitrophenol + Cycochalasin B      85$&#xA;$\\$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt; Why were these control important? How did they help validate the hypothesis?&#xA;Note: this is for self-study.                                 &lt;/p&gt;&#xA;" OwnerUserId="11676" LastActivityDate="2014-12-25T22:04:45.990" Title="Cytochalasin B in cell movement" Tags="&lt;cytoskeleton&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26142" PostTypeId="2" ParentId="26141" CreationDate="2014-12-23T19:44:35.157" Score="2" Body="&lt;p&gt;When you work with living cells, there are usually more pathways which can be affected, when you start treating the cell a drug. To make sure, which pathway is specifically inhibited, you need these controls, as an inhibition of any of them could theoretically have the same effect: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Protein synthesis (cycloheximide) as this provides new actin monomers which are important for the enlongation.&lt;/li&gt;&#xA;&lt;li&gt;ATP synthesis (dinitrophenol) as ATP is necessary for the movement&#xA;along actin filaments. &lt;/li&gt;&#xA;&lt;li&gt;Inhibition of microtubuli (colchicine) inhibits the microtubuli found&#xA;in the flagella of amoeba, which also provide a form of movement&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The controls show that only the addition of Cytochalasin B to the culture inhibits the movement by inhibiting the enlongation of the actin filaments which proves the hypothesis of the group.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-23T19:44:35.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26143" PostTypeId="1" CreationDate="2014-12-23T22:18:05.580" Score="5" ViewCount="275" Body="&lt;p&gt;Does the venom of the &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Sydney_funnel-web_spider#Venom&quot; rel=&quot;nofollow&quot;&gt;Sydney funnel web spider&lt;/a&gt; have to be injected into the bloodstream to have an effect? If the venom was swallowed (e.g. if a spider was eaten), would it still have an effect? Or wouldn't it be able to pass through the gut lining, or be broken down in the gut?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that the funnel web's venom is different to most spiders', but would this answer apply to spider venom in general?&lt;/p&gt;&#xA;" OwnerUserId="461" LastEditorUserId="1306" LastEditDate="2014-12-27T13:00:20.183" LastActivityDate="2014-12-27T13:00:20.183" Title="Is funnel web spider venom poisonous?" Tags="&lt;toxicology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26144" PostTypeId="2" ParentId="26120" CreationDate="2014-12-23T23:02:49.313" Score="3" Body="&lt;p&gt;APS and TEMED concentrations matter a lot. Even with that standardized, your polyacrylamide on the shelf is losing reactive groups as we speak. Who know how long it sat in the warehouse? It all adds up to the fact that the minimum required time is practically impossible to predict.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, once polymerized, a gel is stable for days without apparent loss of quality. Overnight polymerization will be &quot;optimal&quot; in the sense that the gel won't get any better with longer or shorter polymerization. But so will be a two-days old gel. People used to cast gels every Friday, and leave them in wet paper towels in the cold room for the next week.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastActivityDate="2014-12-23T23:02:49.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26145" PostTypeId="2" ParentId="23957" CreationDate="2014-12-23T23:52:25.143" Score="2" Body="&lt;h1&gt;The short answer is no.&lt;/h1&gt;&#xA;&lt;p&gt;Here's a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077556/&quot; rel=&quot;nofollow noreferrer&quot;&gt;review article with some evidence&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;h2&gt;B cell receptor editing in tolerance and autoimmunity&lt;/h2&gt;&#xA;&lt;h3&gt;Section: Receptor Editing in Mice with Conventional Autoantibody Transgenes&lt;/h3&gt;&#xA;&lt;p&gt;If multiple κ rearrangements fail to yield a suitable L chain, the κ&#xA;locus undergoes rearrangement to a non-coding gene called RS in mice&#xA;(RS is referred to as the κ deleting element in humans). RS&#xA;rearrangement results in either deletion or inversion of Cκ,&#xA;consequently inactivating κ L chain expression on that allele. In cell&#xA;lines with λ rearrangements, one or usually both κ alleles are&#xA;deleted, whereas in κ-expressing B cells the fraction of RS&#xA;rearrangements is approximately 15%.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;In summary: After a point with (probably multiple) κ rearrangement failures, both κ loci (usually) get deleted, leaving only λ.&lt;/strong&gt; So if a B cell expressing a BCR with λ is self-reactive, it won't have the chance to rearrange its κ.&lt;/p&gt;&#xA;&lt;p&gt;However, there's a lot more involved. For one, it's possible to get a functional and non-self-reactive λ chain BCR without repeated κ rearrangement failures.&lt;/p&gt;&#xA;&lt;p&gt;Since the quoted passage might be confusing out of context, I'd like to mention briefly that your question's description of light chain recombination is very simplified. In reality, there are many additional mechanisms involved and many different paths to get a functional κ rearrangement, a functional λ rearrangement, neither, or even both. Moreover, there's a lot we don't know, since we learn one experiment at a time, and we can't always directly measure what we'd like to.&lt;/p&gt;&#xA;&lt;p&gt;First, rearrangement &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9550405&quot; rel=&quot;nofollow noreferrer&quot;&gt;has been observed to occur simultaneously in  κ and λ&lt;/a&gt;. This fact might explain why it's possible to get a functional λ chain BCR right away as mentioned above. Second, allelic exclusion (between both κs and both λs) doesn't always work as you and I might expect it to, and a developing B cell can express different BCRs simultaneously (even one with κ and the other with λ). Third, due to receptor editing, a B cell has multiple opportunities for a functional κ chain rearrangement on a single chromosome, meaning that neither λ nor the second κ is needed despite an initially nonfunctional κ rearrangement.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;I highly recommend reading the review article!&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="9652" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-24T00:03:35.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26146" PostTypeId="2" ParentId="26143" CreationDate="2014-12-24T00:29:57.020" Score="3" Body="&lt;p&gt;The Sydney Funnel Web Spider's venom is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Delta_atracotoxin&quot; rel=&quot;nofollow noreferrer&quot;&gt;δ-atracotoxin&lt;/a&gt; and it is especially toxic to primates. It is a peptide toxin, which means that it has the potential to be digested in the stomach before having any physiological affect. However, many peptide toxins are not inactivated by swallowing--you don't want to be eating any &lt;a href=&quot;http://en.wikipedia.org/wiki/Botulinum_toxin#Sources&quot; rel=&quot;nofollow noreferrer&quot;&gt;Botulinum toxin&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.scielo.br/scielo.php?script=sci_arttext&amp;amp;pid=S1678-91992006000200005&quot; rel=&quot;nofollow noreferrer&quot;&gt;Characterization of insecticidal peptides from venom Australian funnel-Web spiders&lt;/a&gt; (Vonorax &lt;em&gt;et al.&lt;/em&gt; 2006) harvested venom from &lt;a href=&quot;http://en.wikipedia.org/wiki/Hadronyche_infensa&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Hadronyche infensa&lt;/em&gt;&lt;/a&gt;, the Darling Downs funnel-web spider. This spider is closely related to the Sydney Funnel Web spider and also produces δ-atracotoxin.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;An oral ingestion activity test was undertaken using crude &lt;em&gt;H. infensa&lt;/em&gt; venom.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The ingestion test was performed with insect larvae, which are susceptible to the venom when injected. (Aside: there's a lot of &lt;a href=&quot;http://www.jbc.org/content/279/42/44133.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;interesting&lt;/a&gt; research on the toxin's effect in insects). They didn't find much:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Oral ingestion activity test of crude H. infensa venom&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;No effect was observed in this test, even though approximately 4 times the dose required for lethality by injection was orally consumed by the larvae.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I don't think anyone has performed a study of toxin ingestion in primates (if they have, I couldn't find it). The researchers don't speculate as to why the toxin has no effect when ingested. As expected, the toxin had no effect on (non-primate) mice:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Effect of atracotoxin-Hv1 on newborn mice&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;All mice in both test and control groups survived without apparent toxic effect beyond 24h post injection.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Whether this is applicable to other spider venom depends on the nature of the venom. A non-peptide, low molecular weight venom able to be absorbed by the lining of the esophagus could be very toxic by ingestion.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;Further reading:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jbc.org/content/279/42/44133.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Scanning Mutagenesis of ω-Atracotoxin-Hv1a Reveals a Spatially Restricted Epitope That Confers Selective Activity against Insect Calcium Channels&lt;/a&gt; (Tedford &lt;em&gt;et al.&lt;/em&gt; 2004)&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0014579300013399&quot; rel=&quot;nofollow noreferrer&quot;&gt;Isolation and pharmacological characterisation of δ-atracotoxin-Hv1b, a vertebrate-selective sodium channel toxin&lt;/a&gt; (Szeto &lt;em&gt;et al.&lt;/em&gt; 2000)&lt;/p&gt;&#xA;&lt;p&gt;(for more info on peptide toxins): &lt;a href=&quot;http://monographs.iarc.fr/ENG/Monographs/vol94/mono94-7.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cyanobacterial Peptide Toxins&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-24T00:49:43.670" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26147" PostTypeId="1" AcceptedAnswerId="26154" CreationDate="2014-12-24T06:22:09.600" Score="5" ViewCount="85" Body="&lt;p&gt;With radiation therapy, could some of the radiation used cause new mutations in non-cancerous cells that are near the tumour that is being irradiated? If so could these new mutations lead to new cancerous cell colonies (which might later metastasize)?&lt;/p&gt;&#xA;" OwnerUserId="11605" LastEditorUserId="3340" LastEditDate="2014-12-25T09:10:56.077" LastActivityDate="2014-12-25T09:10:56.077" Title="About radiation therapy" Tags="&lt;radiation&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26148" PostTypeId="1" AcceptedAnswerId="26152" CreationDate="2014-12-24T06:45:06.633" Score="2" ViewCount="119" Body="&lt;p&gt;I have 6 genes of &lt;em&gt;Candida albicans&lt;/em&gt; yeast namely &lt;code&gt;orf19.723&lt;/code&gt;, &lt;code&gt;orf19.5908&lt;/code&gt;, &lt;code&gt;orf19.610&lt;/code&gt;, &lt;code&gt;orf19.2119&lt;/code&gt;, &lt;code&gt;orf19.4998&lt;/code&gt; and &lt;code&gt;orf19.4056&lt;/code&gt;. And I have found the corresponding ortholog genes from &lt;a href=&quot;http://www.broadinstitute.org/regev/orthogroups/&quot; rel=&quot;nofollow&quot;&gt;Broad Institute website&lt;/a&gt; of other 16 species of yeast. So I have all gene names. Now how would I specifically download these genes and &lt;strong&gt;from where&lt;/strong&gt; can I do this, preferably in an automated manner?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also is there any standard naming convention? Because the ORF names given have other names too like BCR1, EFG1 and NDT80.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The list of gene names I have :&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;The orthologs of C. Albicans with S. cerevisiae&#xA;orf19.2119  YHR124W &#xA;orf19.4998  YBR033W YKL034W &#xA;orf19.5908  YBR083W &#xA;orf19.610   YMR016C YKL043W &#xA;orf19.723   NONE&#xA;orf19.4056  YMR136W &#xA;&#xA;The orthologs of C. Albicans with S. paradoxus&#xA;orf19.2119  spar33-g1.1 &#xA;orf19.4998  spar197-g23.1   spar324-g3.1    &#xA;orf19.5908  spar200-g4.1    &#xA;orf19.610   spar184-g1.1    spar324-g10.1   &#xA;orf19.723   NONE&#xA;orf19.4056  spar165-g2.1&#xA;&#xA;The orthologs of C. Albicans with S. mikatae&#xA;orf19.2119  NONE&#xA;orf19.4998  smik146-g12.1   smik109-g17.1   &#xA;orf19.5908  smik83-g2.1 &#xA;orf19.610   smik571-g2.1    smik109-g10.1   &#xA;orf19.723   NONE&#xA;orf19.4056  smik1535-g1.1   &#xA;&#xA;The orthologs of C. Albicans with S. bayanus&#xA;orf19.2119  sbayc514-g9.1   &#xA;orf19.4998  sbayc611-g22.1  sbayc652-g20.1  &#xA;orf19.5908  sbayc678-g131.1 &#xA;orf19.610   sbayc638-g23.1  sbayc652-g27.1  &#xA;orf19.723   NONE&#xA;orf19.4056  sbayc657-g41.1&#xA;&#xA;The orthologs of C. Albicans with S. castellii&#xA;orf19.2119  Scas697.24  &#xA;orf19.4998  Scas625.4   &#xA;orf19.5908  Scas718.27  Scas635.12  &#xA;orf19.610   Scas106.1   Scas709.52  Scas625.8   &#xA;orf19.723   NONE&#xA;orf19.4056  Scas680.22d &#xA;&#xA;The orthologs of C. Albicans with C. glabrata&#xA;orf19.2119  CAGL0L13090g    &#xA;orf19.4998  CAGL0L01947g    &#xA;orf19.5908  CAGL0M01716g    CAGL0F04081g    &#xA;orf19.610   CAGL0M07634g    CAGL0L01771g    &#xA;orf19.723   NONE&#xA;orf19.4056  CAGL0I00902g    CAGL0L06776g    &#xA;&#xA;The orthologs of C. Albicans with S. kluyveri&#xA;orf19.2119  SAKL0E11330g    &#xA;orf19.4998  SAKL0A09812g    &#xA;orf19.5908  SAKL0B06578g    &#xA;orf19.610   SAKL0D13442g    &#xA;orf19.723   SAKL0A03476g    &#xA;orf19.4056  SAKL0E04862g    &#xA;&#xA;The orthologs of C. Albicans with K. lactis&#xA;orf19.2119  KLLA0F24420g    &#xA;orf19.4998  KLLA0F25674g    &#xA;orf19.5908  KLLA0E12507g    &#xA;orf19.610   KLLA0F04840g    &#xA;orf19.723   NONE&#xA;orf19.4056  KLLA0F17116g    &#xA;&#xA;The orthologs of C. Albicans with A. gossypii&#xA;orf19.2119  AGR347W &#xA;orf19.4998  AFR275W &#xA;orf19.5908  AER177W &#xA;orf19.610   ABR055C &#xA;orf19.723   NONE&#xA;orf19.4056  ADR249W &#xA;&#xA;The orthologs of C. Albicans with K. waltii&#xA;orf19.2119  Kwal33.14699    &#xA;orf19.4998  Kwal26.8099 &#xA;orf19.5908  Kwal27.12423    &#xA;orf19.610   Kwal26.8176 &#xA;orf19.723   NONE&#xA;orf19.4056  Kwal47.17849    &#xA;&#xA;The orthologs of C. Albicans with C. tropicalis&#xA;orf19.2119  CTRG01097.3 &#xA;orf19.4998  CTRG03636.3 &#xA;orf19.5908  CTRG02294.3 &#xA;orf19.610   NONE&#xA;orf19.723   CTRG00608.3 &#xA;orf19.4056  CTRG04523.3 &#xA;&#xA;The orthologs of C. Albicans with L. elongosporus&#xA;orf19.2119  LELG01178   &#xA;orf19.4998  NONE&#xA;orf19.5908  LELG02666   &#xA;orf19.610   LELG05390   &#xA;orf19.723   LELG03123   &#xA;orf19.4056  LELG01761   &#xA;&#xA;The orthologs of C. Albicans with C. parapsilosis&#xA;orf19.2119  CPAG04608   &#xA;orf19.4998  NONE&#xA;orf19.5908  CPAG01691   &#xA;orf19.610   CPAG00178   &#xA;orf19.723   CPAG00564   &#xA;orf19.4056  CPAG05034   &#xA;&#xA;The orthologs of C. Albicans with D. hansenii&#xA;orf19.2119  DEHA2A07282g    &#xA;orf19.4998  NONE&#xA;orf19.5908  DEHA2G13794g    &#xA;orf19.610   DEHA2E10978g    &#xA;orf19.723   DEHA2E05984g    &#xA;orf19.4056  DEHA2E07172g    DEHA2F25916g    &#xA;&#xA;The orthologs of C. Albicans with C. guilliermondii&#xA;orf19.2119  PGUG02096.1 &#xA;orf19.4998  NONE&#xA;orf19.5908  PGUG04378.1 &#xA;orf19.610   PGUG03651.1 &#xA;orf19.723   PGUG05571.1 &#xA;orf19.4056  PGUG05533.1 &#xA;&#xA;The orthologs of C. Albicans with C. lusitaniae&#xA;orf19.2119  CLUG00404   &#xA;orf19.4998  NONE&#xA;orf19.5908  CLUG04694   &#xA;orf19.610   CLUG02047   &#xA;orf19.723   CLUG00627   &#xA;orf19.4056  CLUG05535&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="5669" LastEditorUserId="3340" LastEditDate="2014-12-24T11:26:16.533" LastActivityDate="2014-12-25T09:17:58.770" Title="Downloading specific yeast genes in an automated manner?" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;database&gt;&lt;yeast&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="26150" PostTypeId="2" ParentId="26148" CreationDate="2014-12-24T09:15:06.983" Score="1" Body="&lt;p&gt;OK, the first step must be to map all these IDs to the same database. Try using &lt;a href=&quot;http://uniprot.org&quot; rel=&quot;nofollow&quot;&gt;http://uniprot.org&lt;/a&gt; if you want protein sequences else, look for each of them and find the corresponding Refseq ID. Since you have IDs from multiple databases, you might need to google them individually. If you know the ID type of each identifier you have, you can use a tool like DAVID's &lt;a href=&quot;http://david.abcc.ncifcrf.gov/conversion.jsp&quot; rel=&quot;nofollow&quot;&gt;gene name converter&lt;/a&gt; to automate it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you have a list of IDs from the same database, save them in a file (one ID per line). Then, for UniProt accessions, you can get the FASTA protein sequence by running:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;while read name; do wget -O - http://uniprot.org/$name.fasta; done &amp;lt; names.txt&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;For RefSeq IDs, you can use the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/sites/batchentrez&quot; rel=&quot;nofollow&quot;&gt;batch retrieval&lt;/a&gt; tool of Entrez. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-12-24T09:15:06.983" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26152" PostTypeId="2" ParentId="26148" CreationDate="2014-12-24T10:50:23.663" Score="2" Body="&lt;p&gt;These sequences do not have any standard i.d. The information in Saccharomyces Genome Database is also obsolete (2005) and does not have these identifiers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These sequences can be found &lt;a href=&quot;http://www.broadinstitute.org/regev/orthogroups/index.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; (in the same site).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each species has a short name:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&#xA;&lt;b&gt;ORGANISM        Short Name&lt;/b&gt;&#xA;&lt;i&gt;S.cerevesiae    Scer&#xA;S. bayanus      Sbay&#xA;S. paradoxus    Spar&#xA;A. gossypii     Agos&#xA;&#xA;.... and so on.&lt;/i&gt; &lt;/pre&gt;&#xA;&#xA;&lt;p&gt;First letter of genus name in uppercase + first 3 letters of species name in lowercase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fasta file (for all ORFs) is:&#xA;&lt;br&gt; &lt;code&gt;www.broadinstitute.org/regev/orthogroups/nt/&amp;lt;Shortname&amp;gt;.fasta&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From there you can use grep to retrieve the sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, if you have saved shortnames and gene names two separate files you can do something like this: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;for shortname in `cat shortname.txt`; do wget -O tmp.fa &quot;http://www.broadinstitute.org/regev/orthogroups/nt/&quot;$shortname.fasta; grep -A 1 -f ids.txt tmp.fa &amp;gt;&amp;gt; $shortname&quot;_Select.fa&quot;; done&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-25T09:17:58.770" LastActivityDate="2014-12-25T09:17:58.770" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="26153" PostTypeId="2" ParentId="24553" CreationDate="2014-12-24T12:00:34.133" Score="2" Body="&lt;p&gt;It is not really essential that all vital organs should have regenerative potential (for example brain). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cellular composition of a tissue is a big factor in deciding if the organ/tissue will regenerate or not. Some cells divide while others do not; highly specialized and polarized cells like neurons do not divide perhaps because the act of division itself will compromise their function. That doesn't mean these tissues cannot regenerate; they would need stem cells that can differentiate into the type of cells that died.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So regeneration can happen via:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Division of the tissue cells (skin healing, liver regeneration)&lt;/li&gt;&#xA;&lt;li&gt;Differentiation of stem cells (erythropoesis, muscle regeneration)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Organs that do not have non-dividing cells can regenerate by simply proliferating whereas others would need to maintain a stem cell niche- which is not possible in all tissues. Maintenance of stem cells also adds up to the cost of metabolism; so there is some tradeoff. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-24T12:00:34.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26154" PostTypeId="2" ParentId="26147" CreationDate="2014-12-24T12:14:09.523" Score="4" Body="&lt;p&gt;Yes, this can happen, although the risk is low. The problem is that some tumors need to be irradiated since the cannot be operated (this is true for some brain tumors). Here the radiation therapy is the therapy of choice. The effect of the therapy is that the tumor cells get a high radiation dose which either kills them or drives them into apoptosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem the irradiation is that you will always affect healthy cells, of which most will die. This causes some of the negative effects of the radiation therapy, but it is also possible that a healthy cell receives a dose which is &quot;only&quot; damaging and causes a secondary tumor. Here a benefit analysis needs to be done to see if the benefit from the therapy is woth taking the risk of acquiring more damages. See the references for some more background.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cancerresearchuk.org/about-cancer/type/brain-tumour/treatment/radiotherapy/long-term-side-effects-of-brain-tumour-radiotherapy&quot; rel=&quot;nofollow&quot;&gt;Long term side effects of brain tumour radiotherapy&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cancer.org/cancer/cancercauses/othercarcinogens/medicaltreatments/secondcancerscausedbycancertreatment/second-cancers-caused-by-cancer-treatment-toc&quot; rel=&quot;nofollow&quot;&gt;Second Cancers Caused by Cancer Treatment&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK13999/&quot; rel=&quot;nofollow&quot;&gt;Therapy-Related Secondary Cancers&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2014-12-24T12:14:09.523" CommentCount="18" ContentLicense="CC BY-SA 3.0" />
  <row Id="26155" PostTypeId="2" ParentId="16982" CreationDate="2014-12-24T12:48:35.393" Score="1" Body="&lt;p&gt;If you supply heat to a system, the entropy increases which results in destabilization of order. This is a general thermodynamic principle and you can refer any basic book on that topic. However, it is not essential that all molecules would be affected equally. There are heat-stable enzymes in thermophiles such as &lt;em&gt;Thermus aquaticus&lt;/em&gt; which are resistant to heat. Also the membranes in these organisms are made up of stronger and more rigid isoprenoid lipids.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even in mesophiles, lipid membranes with higher content of cholesterol are rigid and more resistant to thermal movements. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On Breakdown of thermostat:&#xA;The body can regulate the temperature only in a certain range; at higher temperatures these mechanisms will fail as well. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-01-14T08:32:28.800" LastActivityDate="2015-01-14T08:32:28.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26156" PostTypeId="2" ParentId="17340" CreationDate="2014-12-24T13:32:03.017" Score="1" Body="&lt;p&gt;The process is not clearly understood. Calcium helps in capacitation: During capacitation calcium enters the spermatozoa through ion channels; blocking these channels inhibits the acrosome reaction but what calcium does inside the spermatozoa is not very clear. &lt;a href=&quot;http://www.biolreprod.org/content/68/1/207.full&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; paper says that calcium activates a certain tyrosine kinase in the spermatozoa which in turn activates a protein called p32. This they say occurs &quot;&lt;em&gt;concomitantly with capacitation&quot;&lt;/em&gt;. Other papers cited by this article talk about involvement of calcium dependent adenylate cyclase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jcs.biologists.org/content/116/10/1981.abstract&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; article also says that protein tyrosine phosphorylations are important for capacitation but doesn't describe how.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could not find a more precise information on this topic. I shall update the answer if I find one.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-26T08:37:46.000" LastActivityDate="2014-12-26T08:37:46.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26157" PostTypeId="2" ParentId="7782" CreationDate="2014-12-24T14:05:22.057" Score="7" Body="&lt;p&gt;This phenomenon is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Bokeh&quot; rel=&quot;nofollow noreferrer&quot;&gt;bokeh&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XbMxG.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are right in the hexagonal shape being produced by the iris (of the camera), and from this, it is clear why this happens: The iris blocks out some of the light travelling into it, and a shape approximating that of the camera's iris aperture is projected onto the CCD. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same thing happens for the eye. The iris will block out a portion of the light, causing the bokeh to approximate the shape of the iris aperture (aka the pupil), which is roughly circular for humans. Animals with non-circular pupils will perceive differently shaped bokeh. If the lens suffers from astigmatism, it will also result in non-spherical bokeh being projected onto the retina.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://photo.stackexchange.com/questions/21459/whats-the-difference-between-bokeh-and-gaussian-blur&quot;&gt;This stackexchange link&lt;/a&gt; goes into greater detail on Gaussian blur vs bokeh. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="-1" LastEditDate="2017-04-13T12:44:06.640" LastActivityDate="2015-01-20T17:19:26.860" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26158" PostTypeId="1" CreationDate="2014-12-24T14:11:29.380" Score="1" ViewCount="186" Body="&lt;p&gt;An acute instance of anxiety can cause a sudden sharp chest pain for a very brief period of time.  What is the mechanism behind anxiety leading to chest pain?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the pain coming from the heart itself, or surrounding muscles?  What structure is in pain and what is the physiology behind it?&lt;/p&gt;&#xA;" OwnerUserId="1472" LastActivityDate="2014-12-24T14:11:29.380" Title="How does anxiety cause chest pain?" Tags="&lt;pain&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26159" PostTypeId="2" ParentId="23791" CreationDate="2014-12-24T14:14:21.060" Score="0" Body="&lt;p&gt;biofilms also form in almost all systems with water flow (e.g. water tap, central heating), which also include environments outside of the household such as &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6941.2003.tb01050.x/full&quot; rel=&quot;nofollow&quot;&gt;rivers&lt;/a&gt; and the famous yellowstone park hot &lt;a href=&quot;http://aem.asm.org/content/75/8/2464.short&quot; rel=&quot;nofollow&quot;&gt;springs&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="11680" LastActivityDate="2014-12-24T14:14:21.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26161" PostTypeId="2" ParentId="14163" CreationDate="2014-12-24T14:59:44.910" Score="2" Body="&lt;p&gt;generally, &lt;a href=&quot;http://en.wikipedia.org/wiki/Lactobacillales&quot; rel=&quot;nofollow&quot;&gt;lactic acid bacteria&lt;/a&gt; (LAB) are the ones you should be looking at for milk-based fermentation products. although sometimes species like bifidobacterium are added, which is of a completely different phylum. also, for cheese production, or the Dutch variety I am familiar with anyway, you would need fungi as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;the lactobacillales order is not monophyletic, as you can see on the wiki page there are at least two different clades.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the wikipedia page 'Yogurt' speculates on the ecological niche of LAB: &quot;Analysis of the L. delbrueckii subsp. bulgaricus genome indicates that the bacterium may have originated on the surface of a plant. Milk may have become spontaneously and unintentionally infected through contact with plants, or bacteria may have been transferred via the udder of domestic milk-producing animals.&quot; (&lt;a href=&quot;http://www.livescience.com/10502-yogurt-culture-evolves.html&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;EDIT: the LAB are an order, they have been around for quite some time before the humans showed up.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="11680" LastActivityDate="2014-12-24T14:59:44.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26162" PostTypeId="2" ParentId="21555" CreationDate="2014-12-24T15:02:38.580" Score="1" Body="&lt;p&gt;lactic acid bacteria ferment the disaccharide lactose present in high amounts in milk to the three-carbon compound lactic acid, which acidifies the milk. this causes the proteins also present in milk to denaturate and coagulate, forming curdles. other causes/methods of curdling can be application of heat, salts or by adding the enzyme chymosin (rennin).&lt;/p&gt;&#xA;" OwnerUserId="11680" LastEditorUserId="11680" LastEditDate="2014-12-24T18:38:34.107" LastActivityDate="2014-12-24T18:38:34.107" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26163" PostTypeId="1" CreationDate="2014-12-24T15:52:47.913" Score="2" ViewCount="107" Body="&lt;p&gt;The vector product obtained by ligation between a vector previously digested with antarctic phosphatase lacks 5' phosphate groups. T4 ligase can ligate it to an insert with complementary sticky ends which provides 2 phosphate groups. But there are still 2 nicks in the vector product! How are these normally repaired ?&lt;/p&gt;&#xA;" OwnerUserId="4746" LastActivityDate="2015-04-30T10:19:58.637" Title="Repair of cloning vector nicks digested with antarctic phosphatase and ligated with T4 enzyme" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26165" PostTypeId="1" AcceptedAnswerId="26167" CreationDate="2014-12-24T17:55:44.930" Score="6" ViewCount="746" Body="&lt;p&gt;My understanding is that PCR is carried out until a fluorescent nucleotide halts replication. The segments of DNA are fed through the capillary tube based on size, sifting through the segments from smallest to largest; subsequently, the sequence is read from one end to the other. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm confused as to how we know that each nucleotide in the sequence has been accounted for, or if a nucleotide has been counted twice. If two fragments of the same size, ending with the same ddNTP, pass through the capillary tube at slightly different times, how do we know if that specific nucleotide hasn't been double-counted?&lt;/p&gt;&#xA;" OwnerUserId="5179" LastEditorUserId="3340" LastEditDate="2014-12-25T09:07:57.277" LastActivityDate="2014-12-25T09:07:57.277" Title="Why doesn't Sanger (fluorescent) DNA sequencing double count nucleotides?" Tags="&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26166" PostTypeId="2" ParentId="26163" CreationDate="2014-12-24T17:58:32.563" Score="1" Body="&lt;p&gt;The nicks are not repaired during preparation. Instead, the vector (which is circular, despite the nicks) is transformed into the host where it is repaired by endogenous mechanisms, likely through base excision.  &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2014-12-24T17:58:32.563" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26167" PostTypeId="2" ParentId="26165" CreationDate="2014-12-24T18:24:26.437" Score="6" Body="&lt;p&gt;In chain-termination sequencing, a population of molecules is detected as opposed to a single one. The readout looks like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0X2w0.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;[ &lt;a href=&quot;http://seqcore.brcf.med.umich.edu/doc/dnaseq/trouble/badseq.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://seqcore.brcf.med.umich.edu/doc/dnaseq/trouble/badseq.html&lt;/a&gt; ]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The peaks represent intensity of the four different fluorophores at the detector. Every fragment that is terminated at the same spot will have the same fluorophore and the same length. Because capillary gel electrophoresis separates molecules by size, these fragments will pass through at approximately the same time. &quot;Approximately the same time&quot; is why you see broad-ish and overlapping peaks on the readout as opposed to sharp and distinct lines. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ideally, the readout will appear like the left half of the image, where there's minimal overlap between peaks. However, often you will see overlapping peaks, as in the right half of the image. The link above explains many reasons for why this occurs. Whether or not a peak is correctly assigned is determined by Phred scores, which is a statistical analysis of the shape and resolution of each peak. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2014-12-24T18:46:21.573" LastActivityDate="2014-12-24T18:46:21.573" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26168" PostTypeId="1" CreationDate="2014-12-24T19:11:44.070" Score="1" ViewCount="24" Body="&lt;p&gt;Although the Bacteriological Code is an important guideline for taxonomists and microbiologists, describing the criteria for delineating species and higher taxa of the prokaryotes, I, and plenty of other microbiologists with me, would not be able to describe the main rules by heart. I am also not able to find a clear summary anywhere on the web, and reading and understanding the Code itself is currently taking quite some time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, does the Code say anything about taxa mainly or solely composed of uncultured strains based on 16S sequences, apart from the addition of &lt;em&gt;Candidatus&lt;/em&gt; to currently uncultured single species? I am specifically referring to higher taxa, large groups of sequences.&lt;/p&gt;&#xA;" OwnerUserId="11680" LastEditorUserId="3340" LastEditDate="2014-12-25T08:45:25.077" LastActivityDate="2014-12-25T08:45:25.077" Title="What are the main principles of the Bacteriological Code?" Tags="&lt;microbiology&gt;&lt;taxonomy&gt;&lt;phylogenetics&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26169" PostTypeId="1" CreationDate="2014-12-24T19:51:33.483" Score="1" ViewCount="80" Body="&lt;p&gt;I am enriching RNA-seq data for the fungus &lt;em&gt;Neurospora crassa&lt;/em&gt; and would like to be able to search the genome by functional category, determine similarity of genes by category membership, and any other information I find interesting in Python or R. There are many websites that have this information, but the most comprehensive appears to be &lt;a href=&quot;http://pedant.helmholtz-muenchen.de/pedant3htmlview/pedant3view?Method=start_method&amp;amp;Db=p3_p13841_Neu_crass_MIPS&quot; rel=&quot;nofollow&quot;&gt;Pedant&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to download a SQL database, a JSON file, or even a text file that contains the information on these sites without having to use a web interface for everything.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The data I need access to is gene code, gene description, DNA sequence, FunCat category, GO category, and maybe others on the Pedant site.  Is there anyway to to programmatically access these fields or download all of them in bulk?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note&lt;/strong&gt;: I have been using the python &lt;a href=&quot;https://pythonhosted.org/bioservices/&quot; rel=&quot;nofollow&quot;&gt;bioservices module&lt;/a&gt;, but it only gives access to KEGG, which is missing information on many of the genes in the &lt;em&gt;N. Crassa&lt;/em&gt; genome.&lt;/p&gt;&#xA;" OwnerUserId="4619" LastEditorUserId="3340" LastEditDate="2014-12-25T08:58:54.637" LastActivityDate="2014-12-25T08:58:54.637" Title="Download FunCat Database for Programmatic Access" Tags="&lt;bioinformatics&gt;&lt;database&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26171" PostTypeId="1" CreationDate="2014-12-24T23:11:46.107" Score="4" ViewCount="63" Body="&lt;p&gt;What is a good minimal medium for &lt;em&gt;Pseudomonas&lt;/em&gt; bacteria? Do I need different media for different &lt;em&gt;Pseudomonas&lt;/em&gt; species?&lt;/p&gt;&#xA;" OwnerUserId="11680" LastEditorUserId="9829" LastEditDate="2015-05-20T14:47:14.950" LastActivityDate="2015-05-20T14:47:14.950" Title="Medium for Pseudomonas?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;experimental-design&gt;&lt;medium&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26172" PostTypeId="1" CreationDate="2014-12-24T23:14:25.430" Score="3" ViewCount="59" Body="&lt;p&gt;I can't seem to find one of the best demos I've seen of color vs brightness perception. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It consisted of a rotating animation of earth made of red of bright red points on a dark green background. As the animation plays, the red points slowly get darker while the green background gets brighter. At some point they are of the same brightness (but different colors), which is where something very cool happens; your brain no longer perceives the red points as a 3D object, and they just look like a jumble of points bouncing around the screen. When the red points are darker than the background, the 3D object appears again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know what is this animation called, or where to find it? It's hard to find on google without knowing what to call it.&lt;/p&gt;&#xA;" OwnerUserId="810" LastEditorUserId="3340" LastEditDate="2014-12-25T09:25:14.563" LastActivityDate="2014-12-25T09:25:14.563" Title="Color perception vs shade perception demo" Tags="&lt;vision&gt;&lt;terminology&gt;&lt;perception&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26173" PostTypeId="1" AcceptedAnswerId="26194" CreationDate="2014-12-25T03:21:47.797" Score="5" ViewCount="199" Body="&lt;p&gt;As a freshman biochemistry major, I find myself befuddled by our body's ability to perform complex chemical reactions to break down foreign substances. I can see how we would evolve explicit pathways to deal with substances we would find often in our environment of evolutionary adaptedness, but we also process things we would never have encountered before. How does the human (or any organism's) body do that without explicit programming?&lt;/p&gt;&#xA;" OwnerUserId="11686" LastActivityDate="2014-12-26T04:49:38.043" Title="How does the body &quot;know&quot; how to metabolize foreign substances" Tags="&lt;evolution&gt;&lt;biochemistry&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26174" PostTypeId="1" CreationDate="2014-12-25T06:06:21.693" Score="4" ViewCount="197" Body="&lt;p&gt;I want to chemically synthesize a GFP gene for expressing in rice.I am using the IDT Codon Optimization program and found that not all the codons are 100% optimized. Some of them are the 2nd or 3rd in frequency of usage. Also, the stop codon in the gene optimized is the least used in rice. I don't think all the codons can be the ones that are the most used in rice as there is need of translational pauses to get optimal protein expression. But how do I decide which codons are to be used in what positions to get maximum efficiency. Do I just use the automatic codon optimized gene given by IDT or further optimize it manually?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So should the stop codon used be the one which is the most frequently used in rice for proper mRNA termination?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please help me as I am new to this and want tips and suggestions for getting optimized codons in this gene.&lt;/p&gt;&#xA;" OwnerUserId="8617" LastEditorUserId="3340" LastEditDate="2015-05-01T13:08:51.830" LastActivityDate="2016-11-15T02:05:17.560" Title="Need help in codon optimization" Tags="&lt;molecular-biology&gt;&lt;biotechnology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26175" PostTypeId="2" ParentId="16043" CreationDate="2014-12-25T06:28:31.663" Score="3" Body="&lt;p&gt;It uses a gonet matrix to compare each of these two sequences. Since you you could have insertions and extensions as well as substitutions, it becomes a 3 parameter problem. 1*open + 6*penalty + substitution_penalty = X. X can be solved by a linear combination of substitution_penalties, extensions, and insertions. So I think this will be really really hard&lt;/p&gt;&#xA;&#xA;&lt;p&gt;with that being said. Clustal outputs the multiple sequence alignment. Why don't you just look at sequence 1 and sequence 2 and see what the insertions and substitutions are! &lt;/p&gt;&#xA;" OwnerUserId="3887" LastEditorUserId="3340" LastEditDate="2014-12-25T08:39:55.497" LastActivityDate="2014-12-25T08:39:55.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26176" PostTypeId="2" ParentId="26174" CreationDate="2014-12-25T08:05:59.787" Score="3" Body="&lt;p&gt;Generally the codon optimization is the most frequent tRNA found in your species of interest. However, your codon must not result in something that disrupts standard molecular biology practices. For instance, if your codon places a restriction site in a unique cloning vector, then the algorithm will just look for the next best codon which does not cause unwanted addition or elimination of a cloning site. Places like IDT will also weigh the cost of the codon vs. the ease of manufacturing in their algorithm (see &lt;a href=&quot;https://www.idtdna.com/pages/decoded/decoded-articles/web-tools/decoded/2013/10/22/codon-optimization-tool-makes-synthetic-genes-easy&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you describe as translational pausing that is 'needed' by the organism to optimize proper gene expression is a &lt;em&gt;consequence&lt;/em&gt; and not a &lt;em&gt;necessity&lt;/em&gt; of infrequent codons (to my full understanding). See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22806127&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. That means you don't want to add this translational pausing in optimized gene expression. It is a simply an evolutionary byproduct. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question more bluntly, I can tell you with some experience to trust the codon optimization algorithms from biotech companies like IDT. I find they work very well. Rice is a common enough organism :) &lt;/p&gt;&#xA;" OwnerUserId="3887" LastEditorUserId="3340" LastEditDate="2014-12-26T06:11:54.440" LastActivityDate="2014-12-26T06:11:54.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26177" PostTypeId="2" ParentId="17635" CreationDate="2014-12-25T10:18:48.430" Score="3" Body="&lt;p&gt;The skeletal muscle is not isotropic and therefore the effect of stress would be different from different axes. The strength also depends on the density of fibers and the composition of tendons (aponeurosis) that connect the muscle tissues; these can change (positively) with long term exercise &lt;sup&gt;[&lt;a href=&quot;http://jap.physiology.org/content/90/1/164&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;ref&lt;/strong&gt;&lt;/a&gt;]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2772832/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; article the authors show the effect of different mechanical stresses on the skeletal muscle tissue — digitorum longus, from rabbit hindlimbs.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Tests were performed on extensor digitorum longus (EDL) muscles,&#xA;  chosen for its regular cross-section and low pennation angle (Lieber&#xA;  and Blevins, 1989). To ensure that only muscle tissue was tested,&#xA;  aponeuroses were carefully dissected away&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/NjxVM.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Figure from the same article by Morrow et al. (2010)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can notice that the yielding point to longitudinal extension is somewhere near 180kPa. It can be assumed that a hook into the tissue on pulling would generate longitudinal extension stress (unless the hook pierces through the muscle tissue or has sharp edges that can rip the muscle transversely). The stress in the Bobby situation would be: $$\frac{\text{weight (mass)}\times \text{gravitational acceleration}\ (9.8\ ms^{-2})}{\text{area of the muscle covered by the hook} \times \text{number of hooks}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the best I can answer your question based on data; this cannot be directly extrapolated to the Bobby situation because:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The muscle tissue is different&lt;/li&gt;&#xA;&lt;li&gt;The strength of the tissue depends on how much has Bobby exercised his muscles. &lt;/li&gt;&#xA;&lt;li&gt;There would be additional mechanical stresses in other directions because of his movement while being suspended from the hook. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Ribs are not very strong bones and attempt to hook something on it may cause punctured lungs, not pneumothorax. Death will depend on the severity of the wound. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-01T15:54:49.483" LastActivityDate="2015-06-01T15:54:49.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26178" PostTypeId="1" AcceptedAnswerId="26198" CreationDate="2014-12-25T10:45:25.420" Score="4" ViewCount="791" Body="&lt;p&gt;To my understanding, an allergic response is a non-adaptive response of the immune system to some molecule. The molecule in question is therefore &quot;thought by the immune system&quot; to be infectious although it is not. An allergic response is triggered by immunoglobulin of type E (&lt;code&gt;$IG_E$&lt;/code&gt;) and causes an immune reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd expect immune responses to not be instataneous, that is I would expect that it takes some time in order for the immune system to achieve some reaction peak. In consequences, I have been wondering whether someone that is under an allergic reaction is more resistant to early development of infectious disease because the immune system is already &quot;switched on&quot; prior to the infection. On the other hand, I would have thought that the body resistance to anything is lowered during an allergic reaction 1) because the allergy diminishes &quot;general health&quot; and 2) because &lt;a href=&quot;https://biology.stackexchange.com/questions/7129/does-an-allergic-reaction-kill-body-cells&quot;&gt;allergic response may kill body cells&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are we more/less resistant to infectious diseases during an allergic reaction?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-12-27T09:32:29.113" Title="Are we more/less resistant to infectious diseases during an allergic reaction?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;immunology&gt;&lt;medicine&gt;&lt;allergies&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26179" PostTypeId="1" CreationDate="2014-12-25T11:34:48.040" Score="2" ViewCount="62" Body="&lt;p&gt;I am not a biologist. I am a software developer interested in genetic algorithms therefore i am probably talking to biologists who also have a knowledge of genetic algorithms. I need to &quot;breed&quot; different solutions to a problem while allowing the number of genes in my solution to vary because i don't know in advance how many genes i need. This is why i need to be able to cross solutions with N genes with solutions with M genes and this is a serious problem. If N and M are very different the problem would be even more serious. I want to know what happens in the biological world. I am trying to understand how much difference in genome is &quot;enough&quot; to prevent interbreeding between different organisms. Would it be possible to say that if less than (approximately) X% of the genes of two organisms are different then they can probably mate and have offspring?&#xA;Thank you&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wentu&lt;/p&gt;&#xA;" OwnerUserId="11691" LastEditorUserId="11691" LastEditDate="2014-12-26T10:24:06.393" LastActivityDate="2014-12-26T10:24:06.393" Title="How much difference in genome is enough to prevent interbreeding?" Tags="&lt;evolution&gt;&lt;chromosome&gt;&lt;speciation&gt;" AnswerCount="0" CommentCount="5" FavoriteCount="1" ClosedDate="2014-12-26T05:07:06.160" ContentLicense="CC BY-SA 3.0" />
  <row Id="26180" PostTypeId="1" CreationDate="2014-12-25T12:22:17.690" Score="7" ViewCount="687" Body="&lt;p&gt;The Wikipedia page on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Estrous_cycle&quot;&gt;Estrous cycle&lt;/a&gt; says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Humans have menstrual cycles instead of estrous cycles. They shed their endometrium instead of reabsorbing it. Unlike animals with estrous cycles, human females are sexually receptive throughout their cycles.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The page on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Menstrual_cycle&quot;&gt;menstrual cycles&lt;/a&gt; says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The cycle occurs only in fertile female humans and other female primates&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Do we know how many million years ago that switch happened and our female ancestors got sexually receptive throughout their cycles? &lt;/p&gt;&#xA;" OwnerUserId="152" LastEditorUserId="9268" LastEditDate="2014-12-25T20:14:35.590" LastActivityDate="2014-12-25T21:55:33.493" Title="When did our ancestors switch to a menstrual cycle instead of the estrous cycle?" Tags="&lt;endocrinology&gt;&lt;sex&gt;&lt;human-physiology&gt;&lt;human-evolution&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26183" PostTypeId="2" ParentId="26180" CreationDate="2014-12-25T17:37:22.503" Score="2" Body="&lt;p&gt;Menstruation occurs only in most of the primates, and a handful of other mammals. It is tempting to speculate that place the switch to menstrual cycles evolved right after the split between non-menstruating primates (tarsiers and their relatives) and menstruating relatives (almost all others), which is about 63 million years ago.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other menstruating animals, so I am not sure if nature reinvented menstruation whenever social conditions required unproductive sex, or menses are in fact a more archaic trait.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I doubt we have material evidence about all these speculations.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastEditorUserId="8809" LastEditDate="2014-12-25T21:55:33.493" LastActivityDate="2014-12-25T21:55:33.493" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26184" PostTypeId="2" ParentId="26141" CreationDate="2014-12-25T17:53:57.723" Score="3" Body="&lt;p&gt;The other inhibitors work on other processes, as you already noticed. There is almost no difference between the conditions when they are added and the corresponding condition when they are missing, suggesting those other processes play no role in the observed phenomenon. Eliminating those other processes makes it more believable that actin polymerization is important, rather than being &lt;strong&gt;one of multiple&lt;/strong&gt; factors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, often cell will adapt to an inhibitor by increasing or decreasing other kinds of activity. For example, it could be that actin polymerization inhibition prevents amoeba from eating. In this case, because any imaginable motive mechanism requires energy, starving amoeba may become unable to move, even though it was not using actin for movement. In order to refute such scenarios, where actin polymerization is not directly inducing movement, and where cytochalazine does not inhibit movement directly mechanism, supplementary experiments were performed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNP induces something similar to starvation, yet, in these experiments, did not abolish movements when given alone. Nor did DNP rescue movement, because the combination (DNP + cytochalazine) is virtually identical to cytochalazine alone. In both circumstances, DNP did nothing, thus showing that ATP depletion is not influencing movement. This is proof that actin polymerization is &lt;strong&gt;directly&lt;/strong&gt; causing amoeba movement, and not an indirect ATP-mediated effect. Similarly, cytochalazin's effect is independent of protein synthesis, once more supporting the hypothesis that actin polymerization is important on its own.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastEditorUserId="8809" LastEditDate="2014-12-25T22:04:45.990" LastActivityDate="2014-12-25T22:04:45.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26185" PostTypeId="2" ParentId="25880" CreationDate="2014-12-25T19:19:16.767" Score="11" Body="&lt;p&gt;To add to Christiaan's answer, I'll mention one striking example of long-distance neuronal migration in the adult mammalian brain: the so-called &lt;strong&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Rostral_migratory_stream&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rostral Migratory Stream&lt;/a&gt;&lt;/strong&gt; found in rodents, in rabbits and both the squirrel and rhesus monkey. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neuronal precursors originating in the subventricular zone (SVZ) of the brain migrate to reach the main olfactory bulb (OB), and it's quite a distance for the small cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KmAvj.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5009" LastEditorUserId="9943" LastEditDate="2015-12-18T16:34:19.170" LastActivityDate="2015-12-18T16:34:19.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26186" PostTypeId="2" ParentId="26009" CreationDate="2014-12-25T22:57:02.513" Score="3" Body="&lt;p&gt;By reasoning, we can make the following distinction: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the trigeminal nerve is a cranial nerve. &lt;/li&gt;&#xA;&lt;li&gt;the 2 others are peripheral&#xA;nerves.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Cranial nerves take their origin into their respective &lt;em&gt;nuclei&lt;/em&gt;, and bypass the dorsal columns (main spinal tract for sensory information). Peripheral sensory nerves stem from the spinal roots, and from there go up through the dorsal columns. This would bring you to the thalamus, where all sensory information is regrouped. However, &lt;strong&gt;somatosensory information from the face and the rest of the body happen to travel through different thalamic nuclei&lt;/strong&gt; (&lt;a href=&quot;http://en.wikipedia.org/wiki/Ventral_posterior_nucleus&quot; rel=&quot;nofollow&quot;&gt;ventroposterolateral for the body, ventroposteromedian for the face&lt;/a&gt;, If my neuroanatomy is not too far behind me...). This leaves us with the internal capsula (fibers that link the thalamus to the cortex), but I do not think much signal integration occurs there. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In conclusion, the first anatomical level of convergence between the 3 above-cited nerves would indeed be the somatosensory cortex.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-12-25T22:57:02.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26187" PostTypeId="2" ParentId="25930" CreationDate="2014-12-25T23:06:36.643" Score="1" Body="&lt;p&gt;The key player you are lacking is the &lt;strong&gt;thalamus&lt;/strong&gt;, which integrates a lot of stimuli, and pre-processes them before sending them to the cortex&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-12-25T23:06:36.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26188" PostTypeId="2" ParentId="25916" CreationDate="2014-12-25T23:15:28.680" Score="2" Body="&lt;p&gt;&lt;strong&gt;Pins-and-needles (PAN) sensation and pain stem from the same nerves&lt;/strong&gt;. The pathophysiologic process is different, though. PAN is characteristic of nerve lesion, and is therefore a pathologic reaction. Pain is a physiologic reaction to a stimulus perceived as ominous.&#xA;Pathophysiologically speaking, the PAN sensation is a distortion in somatosensory stimulus processing due to injury to peripheral nerves.&#xA;Of course, the PAN sensation will stem from somatosensory nerves. Pure motor nerves will not cause such a sensation.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-12-25T23:15:28.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26189" PostTypeId="1" AcceptedAnswerId="26222" CreationDate="2014-12-25T23:26:40.003" Score="23" ViewCount="53693" Body="&lt;p&gt;During a biology experiment at school, where we would look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Elodea&quot;&gt;waterweeds&lt;/a&gt; under a microscope, my teacher said something about that it's impossible for the human eye to see the cells without a magnifying glass of some sort. So, I saw that as a challenge, and decided to check if I could see the cells. And after holding the leaves really close to my face, I was indeed able to see tiny rectangles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since I was curious about it now, I decided to look some more things up. First, I tried to find out the actual size of waterweed cells. Based on &lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Waterpest_celstructuur.jpg&quot;&gt;this 640x enlarged image&lt;/a&gt;, which features cells of 5mm wide and 10 - 15mm long in the picture (which corresponds with of roughly 8µm wide and 15µm long).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I left this in the back of my head for a long time then, but I just looked at my cotton sleeve, and noticed tiny fibers. Not the ones that are woven together, but ones that are standing out from it. So, after looking it up, it turns out that &lt;a href=&quot;http://en.wikipedia.org/wiki/10_micrometres&quot;&gt;cotton fibers are 10 µm wide&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I wondered, &lt;strong&gt;what is the smallest size a human eye can actually see&lt;/strong&gt;? According to a whole bunch of sources all across the internet, it's either &lt;a href=&quot;http://www.sciencefocus.com/qa/how-small-can-naked-eye-see&quot;&gt;200-400µm&lt;/a&gt;, &lt;a href=&quot;https://www.youtube.com/watch?v=htPXMQ5s-yo#t=26&quot;&gt;100µm&lt;/a&gt;, or &lt;a href=&quot;http://en.wikipedia.org/wiki/Naked_eye#Small_objects_and_maps&quot;&gt;58-75µm&lt;/a&gt;. I also hear 'the width of a human hair' very often, but those can range &lt;a href=&quot;http://hypertextbook.com/facts/1999/BrianLey.shtml&quot;&gt;from 17 to 181µm&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="11695" LastEditorUserId="10401" LastEditDate="2014-12-26T00:12:13.700" LastActivityDate="2017-07-25T21:48:10.277" Title="What's the smallest size a human eye can see?" Tags="&lt;human-biology&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="26190" PostTypeId="2" ParentId="25926" CreationDate="2014-12-25T23:28:15.340" Score="1" Body="&lt;p&gt;The first layer of sensory integration from neural interconnection lies in the spinal dorsal horns (for somatosensory stimuli), and the spinal anterolateral system (for painful stimuli). It resembles option #2 much more than option #1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Addenda: Since you are asking a lot about neuroanatomy and neurophysiology, I suggest those 2 beginner books:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0071603964&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Neuroanatomy Text and Atlas&lt;/em&gt;, John Martin&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0878936955&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Neuroscience&lt;/em&gt;, Dale Purves&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2014-12-25T23:28:15.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26191" PostTypeId="1" AcceptedAnswerId="26195" CreationDate="2014-12-25T23:35:40.807" Score="4" ViewCount="736" Body="&lt;p&gt;In learning about how cofactors are essential to proper enzyme function, my textbook mentioned catalase and its relation to the human body. According to my textbook, catalase is similar to hemoglobin in that it has 4 hemes which cradle an Fe (iron) atom; the iron atom is used to neutralize free radicals when it &quot;pulls on the substrate's electrons, which brings on the transition state&quot; after catalase is holding a substrate in its active site. I already know that free radicals have one or more unpaired electrons which make them dangerous as they &quot;seek out&quot; an electron to complete its pair on any molecule, atom, or ion it can find, perhaps causing significant tissue damage in the process. I also know that the transition state is a key point in a reaction in which the activation energy required has been met and the reaction will continue spontaneously until it ends. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;My question is, what exactly is happening here that helps to neutralize a free radical, and what is the part after the transition state doing?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I had to guess, based on that cofactors generally can be affected during a reaction, perhaps Iron somehow binds with the free radical and share its electrons, effectively neutralizing the unpaired electron as well as using up the Iron atom? I imagine the &quot;pulling&quot; in the book could fit a description of a weak chemical bond/attraction, but I'm still unsure.&lt;/p&gt;&#xA;" OwnerUserId="11696" LastEditorUserId="11696" LastEditDate="2014-12-26T00:14:31.507" LastActivityDate="2014-12-26T05:38:24.867" Title="How do catalase and other antioxidants neutralize free radicals?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26192" PostTypeId="1" AcceptedAnswerId="26197" CreationDate="2014-12-25T23:50:22.533" Score="1" ViewCount="3817" Body="&lt;p&gt;According to my textbook, &quot;Too much or too little salt can interfere with the hydrogen bonds that hold an enzyme in its three-dimensional shape&quot;. I know that NaCl is held together by an ionic bond, meaning that one atom is strongly positive (in this case sodium) and one atom is strongly negative (in this case chlorine). I would guess the polarity of salt has something to do with its effect on hydrogen bonds, which consist of a hydrogen atom which bonds weakly to a strongly electronegative atom, resulting in a similar behavior to its ionization in glass of water, since water molecules are also polar and form hydrogen bonds with one another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;My question is, how exactly does salinity affect the bonds of an enzyme?&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="11696" LastEditorUserId="11696" LastEditDate="2014-12-26T00:13:58.357" LastActivityDate="2014-12-27T06:18:50.437" Title="How does salinity affect the bonds of an enzyme?" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26193" PostTypeId="1" CreationDate="2014-12-26T02:45:45.653" Score="1" ViewCount="135" Body="&lt;p&gt;There was apparently a hibernating yellow jacket queen in my stack of firewood outside.  An hour or so after bringing in the firewood, we saw the queen fly off into the house, where we can't find her.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What will happen?  Will she lay her eggs and start a nest somewhere in our house?  Will she just find somewhere and go back to sleep?&lt;/p&gt;&#xA;" OwnerUserId="11697" LastActivityDate="2014-12-26T02:45:45.653" Title="I brought a hibernating yellow jacket queen into my house accidentally. What will happen?" Tags="&lt;entomology&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="26194" PostTypeId="2" ParentId="26173" CreationDate="2014-12-26T04:49:38.043" Score="2" Body="&lt;p&gt;One strategy for xenobiotic metabolism seems to be making a lot of similar enzymes with different substrate specifities. Lets take the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cytochrome_P450&quot; rel=&quot;nofollow noreferrer&quot;&gt;cytochrome p450s&lt;/a&gt; as an example. These are a class of enzymes with 57 genes identified for humans, and I don't know how many alternative splicing products are made from those genes. As a class, they are responsible for about 75% of drug metabolism and are predominantly found in the liver. They work by using a heme group with a carbon monoxide to add oxygens to xenobiotics. Here is a diagram of the mechanism:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TCeE1.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's been too long since my drug metabolism class to go into more detail on these enzymes, but there are other classes of enzyme that fit this multiple enzyme strategy such as the 2 &lt;a href=&quot;http://en.wikipedia.org/wiki/Monoamine_oxidase&quot; rel=&quot;nofollow noreferrer&quot;&gt;monoamine oxidases&lt;/a&gt;, 5 &lt;a href=&quot;http://en.wikipedia.org/wiki/Flavin-containing_monooxygenase&quot; rel=&quot;nofollow noreferrer&quot;&gt;flavin containing mono-oxygenases&lt;/a&gt;, and 4 &lt;a href=&quot;http://en.wikipedia.org/wiki/Epoxide_hydrolase&quot; rel=&quot;nofollow noreferrer&quot;&gt;epoxide hydrolases&lt;/a&gt;. So the body doesn't really know how to break down xenobiotics, but has a wide array of enzymes with broad and overlapping substrate specificities that work on whatever they happen to bind to, whether it's an endogenous hormone or pharmaceutical compound or toxin.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-12-26T04:49:38.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26195" PostTypeId="2" ParentId="26191" CreationDate="2014-12-26T05:38:24.867" Score="3" Body="&lt;p&gt;Catalase (hydrogen peroxide oxidoreductase) does not actually quench free radicals. It catalyzes the conversion of hydrogen peroxide to water; the former is a &lt;strong&gt;source&lt;/strong&gt; of a free radical, not a free radical in itself. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the &lt;a href=&quot;http://biology.kenyon.edu/BMB/Chime/catalase/frames/cattx.htm#Proposed%20Mechanism%20of%20Catalase&quot; rel=&quot;nofollow&quot;&gt;proposed mechanism&lt;/a&gt; of action of catalase: First one of the oxygens is deprotonated by at the active site of the enzyme. Then the Iron atom that is bound to heme forms a co-ordination complex with the deprotonated oxygen and pulls it away from the other oxygen. As a result the O-O bond breaks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Free radical quenchers/antioxidants react with the free radicals and form non-toxic products. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-26T05:38:24.867" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26197" PostTypeId="2" ParentId="26192" CreationDate="2014-12-26T06:02:41.980" Score="4" Body="&lt;p&gt;Sodium Chloride is not &quot;polar&quot;. It is an ionic compound and dissociates into the respective ions in water (because of the latter's high dielectric constant). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hydrogen bonds are similar to of dipole-dipole interactions (van der Waals) but much stronger and are therefore classified as a separate type of bond. However excess salt can lead to ion-dipole interactions (which are stronger than H-bond) that may prevent the formation of the hydrogen bond.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ions such as Cl&lt;sup&gt; -&lt;/sup&gt; can act as chaotropes (cause disorder)&lt;sup&gt;[&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006349597786478#&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;ref&lt;/strong&gt;&lt;/a&gt;]&lt;/sup&gt;. K&lt;sup&gt;+&lt;/sup&gt; is also chaotropic while Na&lt;sup&gt;+&lt;/sup&gt; is kosmotropic (reduces disorder). However both Na&lt;sup&gt;+&lt;/sup&gt; and Cl&lt;sup&gt; -&lt;/sup&gt; affect the entropy of water very slightly. So the effect of NaCl should be mostly due to ion-dipole interactions. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-27T06:18:50.437" LastActivityDate="2014-12-27T06:18:50.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26198" PostTypeId="2" ParentId="26178" CreationDate="2014-12-26T10:05:21.300" Score="3" Body="&lt;p&gt;There are a number of issues with your question, and the short answer is &lt;em&gt;no&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Immunity to pathogens is conferred by antibodies, but not usually of the IgE group. Pathogens usually stimulate IgM -&gt; IgG; IgAs are present in mucosal surfaces.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are multiple kinds of &quot;allergic responses&quot;, and each carries its own risks.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Type I reactions (ie, immediate hypersensitivity reactions) involve immunoglobulin E (IgE)–mediated release of histamine and other mediators from mast cells and basophils.  &lt;/li&gt;&#xA;  &lt;li&gt;Type II reactions (ie, cytotoxic hypersensitivity reactions) involve immunoglobulin G or immunoglobulin M antibodies bound to cell surface antigens, with subsequent complement fixation.&lt;/li&gt;&#xA;  &lt;li&gt;Type III reactions (ie, immune-complex reactions) involve circulating antigen-antibody immune complexes that deposit in postcapillary venules, with subsequent complement fixation.&lt;/li&gt;&#xA;  &lt;li&gt;Type IV reactions (ie, delayed hypersensitivity reactions, cell-mediated immunity) are mediated by T cells rather than by antibodies. &lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Limiting ourselves to allergic responses mediated by IgE, we have anaphylaxis, allergic asthma, urticaria, angioedema, allergic rhinitis, some types of drug reactions, and atopic dermatitis. These reactions can result in something as mild as urticaria or as life-threatening as anaphylaxis. None of these conditions carries an increased or decreased general immunological response to pathogens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If allergy affected immunocompetency, one would expect to see, for example, an increased incidence of &lt;em&gt;fungal infections&lt;/em&gt; in allergic individuals, but this is not the case. Allergy does not result in an immunocompromised condition, nor does it result in a &lt;em&gt;primed&lt;/em&gt; response (an idea popular in the 90's). They are mediated by different pathways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK27112/&quot; rel=&quot;nofollow&quot;&gt;Effector mechanisms in allergic reactions&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK27117/&quot; rel=&quot;nofollow&quot;&gt;The production of IgE&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.direct-ms.org/pdf/HygienePrinciples/YazdanbakshHygieneHypothesis.pdf&quot; rel=&quot;nofollow&quot;&gt;Allergy, Parasites, and the Hygiene Hypothesis&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15060206&quot; rel=&quot;nofollow&quot;&gt;Immunocompetence and allergy&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-26T10:05:21.300" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="26200" PostTypeId="2" ParentId="19246" CreationDate="2014-12-26T11:27:42.633" Score="2" Body="&lt;p&gt;Since most answers have already covered multicellular immune systems, I will try to explore the concept of unicellular immune systems. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The now famous &lt;a href=&quot;http://en.wikipedia.org/wiki/CRISPR&quot; rel=&quot;nofollow noreferrer&quot;&gt;CRISPR-CAS&lt;/a&gt; system originally evolved as a bacterial immune system to protect itself against phages. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QxZ0k.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Much like computer-based antivirus solutions, CRISPR CAS relies on a &quot;signature&quot; system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Known targets for the CRISPR CAS system are encoded on bacterial DNA, and these known signatures are then transcribed and processed into short guide RNAs known as crRNAs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These crRNAs are then used by the CAS protein complex to target and cut up (therefore inactivating) these DNA strands that match. This therefore allows the cells to possess a native antivirus system that can &quot;receive live updates&quot; just like a commercial software antivirus program by simply modifying their &quot;signature list&quot; of possible pre-crRNAs.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2014-12-26T11:27:42.633" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26201" PostTypeId="1" CreationDate="2014-12-26T13:07:56.543" Score="2" ViewCount="540" Body="&lt;p&gt;I wonder why is it called &lt;strong&gt;plasma&lt;/strong&gt; membrane - what's the biological meaning of the word 'plasma'? &lt;/p&gt;&#xA;" OwnerUserId="11676" LastEditorUserId="16866" LastEditDate="2020-04-15T13:05:54.737" LastActivityDate="2020-04-15T13:05:54.737" Title="What's the meaning of 'plasma' in 'plasma membrane'?" Tags="&lt;terminology&gt;&lt;cell-membrane&gt;&lt;etymology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26202" PostTypeId="2" ParentId="26201" CreationDate="2014-12-26T14:50:01.653" Score="1" Body="&lt;p&gt;I thought it was a no-brainer, apparently it's more of a historical journey into the origins of Botany. But I have a hypothesis: During the debate of whether the cell or the fluid within it was the origin of life, that fluid was called 'protoplasm' - first formed, i.e. it's the origin of life. The plasma membrane, then, is simply that which surrounds the 'plasma' - the protoplasm.&lt;/p&gt;&#xA;" OwnerUserId="11676" LastActivityDate="2014-12-26T14:50:01.653" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26203" PostTypeId="5" CreationDate="2014-12-26T16:55:57.800" Score="0" Body="&lt;p&gt;Ants are social insects in the family Formicidae, a member of the Hymenoptera, which also includes the wasps and bees.&lt;/p&gt;&#xA;" OwnerUserId="4821" LastEditorUserId="4821" LastEditDate="2014-12-26T19:51:16.057" LastActivityDate="2014-12-26T19:51:16.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26204" PostTypeId="4" CreationDate="2014-12-26T16:55:57.800" Score="0" Body="Ants are social insects in the family Formicidae, a member of the Hymenoptera, which also includes the wasps and bees." OwnerUserId="4821" LastEditorUserId="4821" LastEditDate="2014-12-26T19:51:19.707" LastActivityDate="2014-12-26T19:51:19.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26206" PostTypeId="1" CreationDate="2014-12-26T16:59:45.963" Score="3" ViewCount="1535" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Metapleural_gland&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; describes how antibiotics are produced in ants:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Metapleural glands ... are responsible for the production of an&#xA;  antibiotic fluid that then collects in a reservoir ... also referred&#xA;  to as the bulla ... From the bulla, ants can groom the secretion onto&#xA;  the surface of their exoskeleton. This helps to prevent the growth of&#xA;  bacteria and fungal spores on the ants and inside their nest.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So how are ants often cited as an important problem in hospitals, spreading infections from garbage and through the patients? Shouldn't their natural antibiotics prevent that?&lt;/p&gt;&#xA;" OwnerUserId="4821" LastActivityDate="2016-02-01T20:56:40.640" Title="If ants have an antibiotic gland, how can they spread hospital infections?" Tags="&lt;infection&gt;&lt;epidemiology&gt;&lt;antibiotics&gt;&lt;ant&gt;" AnswerCount="3" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26207" PostTypeId="1" CreationDate="2014-12-26T17:24:01.027" Score="8" ViewCount="729" Body="&lt;p&gt;I read about the &lt;a href=&quot;http://en.wikipedia.org/wiki/Windkessel_effect&quot; rel=&quot;nofollow&quot;&gt;Windkessel effect&lt;/a&gt;. Then I read about pulse pressure waves getting reflected from the periphery. If the pulse pressure wave is reflected during diastole and at the same time blood is being pumped forward by the aorta due to the Windkessel effect, then we have two opposite forces acting which should create turbulence even in a normal aorta. Why doesn't this happen?&lt;/p&gt;&#xA;" OwnerUserId="11702" LastEditorDisplayName="user13010" LastEditDate="2015-01-14T14:16:45.213" LastActivityDate="2015-01-14T14:16:45.213" Title="Why don't we see turbulence in the aorta even in normal situations?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;&lt;blood-circulation&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26208" PostTypeId="2" ParentId="26206" CreationDate="2014-12-26T19:13:31.067" Score="6" Body="&lt;p&gt;Ants can and do carry loads that are several times their own weight. I grew up in an area with a lot of ants, and a common scene was a long trail of ants acting as a food supply line. Once a morsel is located, they create a long feremone trail to that morsel. A large clump of ants is always working to break the food into smaller pieces, and several ants are usually on their way back to the colony carrying large crumbs. Often these crumbs are the first thing you notice, rather than the actual ants, because they are often so much larger than the ants themselves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a hospital, most of the food that ants would scavenge would have fallen from the plate of a human being. Many of those human beings would be carriers of disease. I would expect that the trail that these ants walk is littered with plenty of crumbs-of-crumbs that fall off of their load along the way. If these were large enough for us to see, they would get the attention of the ants and they would carry them back to their colony. But a particle of the microscopic crumb dust they do leave behind might carry several specimens of the germ that sickened some messy patient, even if the ant that dropped it was relatively sterile.&lt;/p&gt;&#xA;" OwnerUserId="5018" LastEditorUserId="5018" LastEditDate="2016-02-01T20:56:40.640" LastActivityDate="2016-02-01T20:56:40.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26209" PostTypeId="2" ParentId="26206" CreationDate="2014-12-26T19:36:34.413" Score="3" Body="&lt;p&gt;Other than the fact that ants carry bacteria on their food particles, there could also be alternative reasons that they can spread infections.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just like antibiotics derived from bacteria and fungi have caused resistant pathogen strains to evolve (MRSA for example), it could also be the case that the bacteria naturally living around the ants have evolved some degree of resistance to the &lt;em&gt;ant&lt;/em&gt;ibiotics, perhaps by effluxing sufficient amounts of them by overexpressing pump proteins to the levels that the &lt;em&gt;ant&lt;/em&gt;ibiotics are only mildly bacteriostatic instead of bacteriocidal. These bacteria can then fall off the ants while in the hospital and lead to disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is reasonable to assume that this could evolve, since the ants frequently communicate socially with one another, and any resistant bacteria or fungi can then quickly colonise a previously empty niche, thus creating significant evolutionary pressure for this. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2014-12-26T19:36:34.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26210" PostTypeId="2" ParentId="26206" CreationDate="2014-12-26T19:36:40.817" Score="9" Body="&lt;p&gt;I have worked in hospitals (US) most of my life, treating both community-acquired, and more pertinently to this question, &lt;em&gt;nosocomial&lt;/em&gt; (hospital acquired) infections, and have read many articles on the subject. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have &lt;strong&gt;never, ever&lt;/strong&gt; seen &lt;em&gt;ants&lt;/em&gt; mentioned anywhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;People, flies, cockroaches and rats, yes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ants, no.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, ants are vectors in a few foreign studies. The key word in these studies is &lt;em&gt;potential&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you stated,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;From the bulla, ants can groom the secretion onto the surface of their exoskeleton. This helps to prevent the growth of bacteria and fungal spores on the ants and inside their nest.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No antibiotic covers all organisms. Also, the secretions are to protect the ants against infection, not against the carrier state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pathogenic bacteria is cultured from ants themselves. The ant can be thought of as similar to a human: humans make antibodies to pathogens but are vectors of many diseases. Ants protect themselves via secretions, but are hosts to potential pathogens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.cdc.gov/hicpac/2007IP/2007ip_part1.html&quot;&gt;Part I: Review of Scientific Data Regarding Transmission of Infectious Agents in Healthcare Settings&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.who.int/water_sanitation_health/medicalwaste/148to158.pdf&quot;&gt;Hospital hygiene and infection control&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.tsusinvasives.org/dotAsset/5c7555bc-4758-4e49-aa20-b193e838ba65.pdf&quot;&gt;Ants associated with pathogenic microorganisms in brazilian&#xA;hospitals: attention to a silent vector&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.researchgate.net/publication/258854189_Ants_in_a_hospital_environment_and_their_potential_as_mechanical_bacterial_vectors&quot;&gt;Ants in a hospital environment and their potential as mechanical bacterial vectors&lt;/a&gt;&lt;/sub&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://cdn.intechopen.com/pdfs-wm/26469.pdf&quot;&gt;Insect/Bacteria Association&#xA;and Nosocomial Infection&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-26T19:36:40.817" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26211" PostTypeId="2" ParentId="26207" CreationDate="2014-12-26T19:53:27.407" Score="2" Body="&lt;p&gt;There is turbulence in the normal aorta, which is thought to be one mechanism of endothelial injury leading to atherosclerosis and thrombus formation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.academia.edu/2957731/Blood_Flow_in_the_Healthy_Aorta_Turbulent_or_not&quot; rel=&quot;nofollow&quot;&gt;Blood Flow in the Healthy Aorta: Turbulent or not?&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19463611&quot; rel=&quot;nofollow&quot;&gt;Flow velocity and turbulence in the transverse aorta of a proximally directed aortic cannula: hydrodynamic study in a transparent model&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.diva-portal.org/smash/get/diva2:453413/FULLTEXT01.pdf&quot; rel=&quot;nofollow&quot;&gt;WALL SHEAR STRESS IN A SUBJECT SPECIFIC HUMAN&#xA;AORTA - INFLUENCE OF FLUID-STRUCTURE INTERACTION&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-26T19:53:27.407" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="26212" PostTypeId="2" ParentId="26207" CreationDate="2014-12-26T22:20:10.890" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Why don't we see turbulance in Aorta even in normal situations?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are different parts of aorta where turbulence is possible and where not. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is often said that &lt;em&gt;in normal situations, we cannot see turbulence in aorta because aorta is very stiff and its surface is very smooth&lt;/em&gt;. &#xA;However, this is a simplification and involves an average person (middle aged) which has stiff aortic arch too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the elasticity of arcus aortae is responsible for &lt;em&gt;50% of the volume to the peripheral circulation, thus creating a nearly continuous peripheral blood flow&lt;/em&gt; as anongoodnurse says, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7786838&quot; rel=&quot;nofollow noreferrer&quot;&gt;this publication&lt;/a&gt;.&#xA;However, not all of this blood travel to the backward direction. &#xA;It would be interesting to see how much blood is travelling backward. &#xA;This would help to understand what is the likely hood for turbulences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Those models linked by Anongoodnurse's answer are a few models used to locate places of possible turbulences discretely but they do not seem to consider the amount of blood capable of creating turbulences, just discrete models:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Stalder et al.&lt;/strong&gt; I do not like the first publication because it is using Reynold's number that is designed originally for laminar flow. Problem with viscosity etc. There are better ways to the same thing and consider explicitly the creation of turbulence. It does much simplifications there. Fitting the equation to the physiological ranges of some set of data is bad procedure.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Fukuda et al.&lt;/strong&gt; I like the second publication. High velocity and turbulence and nonlinear streamlines in the ascending aorta in normal situation. In other words, high magnitude of the strain rate tensor along aortic curvatures. So we need nonlinear distribution of at least 4D (later 6D) to quantify the amount and degree of nonlinear processes in turbulences.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Lantz et al.&lt;/strong&gt; Third publication. Linear model for nonlinear situation. I am not convinced by their Mesh selection. Only in Mechanics' journal. Very far from Medical publication or from Mathematical. Not rigorous.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In summary, there are many models and publications to answer the question where are the turbulences. However, they try to answer nonlinear problem by linear models. &#xA;I have not seen any models where they do this rigorously.&#xA;I think we should narrow this problem even more, like Fukuda et al has done. &#xA;They manage to provide some good pieces of information by just considering an intervention with least turbulence in the aorta.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally speaking, we can see some turbulence in arcus aortae in the diastole when blood bounces back from the aortic valve. &#xA;The walls of arcus aortae can store about 50% of left ventricular volume. &#xA;However, I do not know how much of this blood is travelling backward and reflecting back from the atrial valve and causing possibility for turbulences. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[P]ulse pressure wave getting reflected from periphery. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Pulse pressure is systolic minus diastolic pressure. &#xA;Pulse wave is those small waves inside respiratory waves:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FhEZc.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where vasomotor waves are controlling the big picture.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If the pulse pressure wave is reflected during diastole and at the same time blood is being pumped forward by aorta - -. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Wrong! Blood is pumped by heart. Aorta is just a vessel for transportation. &#xA;Generally speaking, Some blood is reflected back from arcus aortae which bounches back from the aortic valve.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[Because] windkessel effect then we have two opposite forces acting which should&#xA;  create turbulance even in normal aorta. Why doesn't this happen?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You confuse here different terms and processes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Generally speaking.&lt;/strong&gt; &#xA;Arcus aortae stretches during systole. &#xA;It is coils back in diastole (left atrium relaxing), blood crashing off aortic valve, possibly creating a heart sound and increasing diastolic pressure. Like anongoodnurse says, in this phase, you can see some turbulence in the aorta but little, since the wall of the aorta is very smooth and only small portion of blood is travelling backward from the walls of aorta:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nu9j5.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where see the aorta coils part.&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2014-12-27T21:14:56.453" LastActivityDate="2014-12-27T21:14:56.453" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="26214" PostTypeId="1" CreationDate="2014-12-27T01:26:23.997" Score="6" ViewCount="348" Body="&lt;p&gt;DNA holds genetic information and holds the key to the evolution of living organisms. Transcription and translation mechanisms enable living cells to process information encoded in DNA. To that end, transcription and translation are fundamental mechanisms needed to enable the evolution of organisms. Molecular machines (enzymes) carry out these mechanisms by reading the information in DNA and using it to construct proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Did the first living cell contain the machinery needed for translation and transcription? or  Did they evolve over time? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt; Edited the question to narrow the scope.&lt;/p&gt;&#xA;" OwnerUserId="3820" LastEditorUserId="3347" LastEditDate="2014-12-30T08:36:33.990" LastActivityDate="2014-12-30T08:36:33.990" Title="The origin of molecular machines" Tags="&lt;evolution&gt;&lt;molecular-evolution&gt;&lt;abiogenesis&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26215" PostTypeId="1" AcceptedAnswerId="26221" CreationDate="2014-12-27T03:24:08.183" Score="1" ViewCount="115" Body="&lt;p&gt;The apoptosis mechanisms in a cell are like a type of 'self-destruction mechanism': is this correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As with any type of complex system with various necessary functions, if it has a set of self-destruction mechanisms for 'shutting down' the whole system, it would require some sort of 'internal programming' that can somehow 'target' each of the system's necessary functions and 'disrupt' each of them simultaneously or in some 'order'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words a self-destruction system in order to be effective would have to be able to 'target' each necessary function in the system. And if a biological system has a mutation or a set of mutations that 'distort' some parts of the system then the self-destruct mechanisms might not be able to 'target' all of the functions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So maybe the cellular mutation 'automatically' makes it hard or impossible for the self-destruct mechanisms to work. Is this possible??&lt;/p&gt;&#xA;" OwnerUserId="11605" LastEditorUserId="3340" LastEditDate="2014-12-27T06:32:45.337" LastActivityDate="2014-12-27T12:41:48.700" Title="About the apoptosis mechanisms in a cell" Tags="&lt;cancer&gt;&lt;mutations&gt;&lt;apoptosis&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26216" PostTypeId="1" AcceptedAnswerId="26228" CreationDate="2014-12-27T06:22:09.580" Score="8" ViewCount="1433" Body="&lt;p&gt;Opponent process is a color theory that states that the human visual system interprets information about color by processing signals from cones and rods in an antagonistic manner (&lt;a href=&quot;https://en.wikipedia.org/wiki/Opponent_process&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the advantage of opponent color against RGB color? For example, in object recognition or edge detection?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can we say that it provides some level of invariance to changes in brightness?&lt;/p&gt;&#xA;" OwnerUserId="11707" LastEditorUserId="9943" LastEditDate="2015-01-09T01:08:00.723" LastActivityDate="2020-04-13T09:26:51.617" Title="Advantage of opponent color?" Tags="&lt;neuroscience&gt;&lt;vision&gt;&lt;neurophysiology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26217" PostTypeId="1" CreationDate="2014-12-27T06:37:54.817" Score="1" ViewCount="735" Body="&lt;p&gt;Why is that bonobos skin color on the areas not covered by hair are dark throughout life unlike the chimpanzee? &lt;/p&gt;&#xA;" OwnerUserId="11679" LastEditorUserId="11679" LastEditDate="2014-12-28T11:28:24.950" LastActivityDate="2014-12-28T11:28:24.950" Title="The skin color of bonobos" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;skin&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26218" PostTypeId="2" ParentId="26178" CreationDate="2014-12-27T09:32:29.113" Score="1" Body="&lt;p&gt;This is a very good question which is an active research topic! &#xA;I can just say that we do not know the correct answer to it but we have some evidences that some allergies are connected with autoimmune diseases. &#xA;You called this &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;1) the allergy diminishes &quot;general health&quot; and 2) because allergic response may kill body cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would say that there can be a mechanism between allergies and autoimmune diseases.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4126025/&quot; rel=&quot;nofollow&quot;&gt;IgE Mediated allergy to wheat in a child with celiac disease&lt;/a&gt;. There has been later found other cases on this but not published in PubMed. &#xA;The link between coeliac disease and IgE-mediated allergy is not very clear.&#xA;Pharmacological intervention with Montelukast (a leukotriene-antagonist) can possibly in all sorts of ways. However, research is going on about this because the mechanism is unknown.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I picked celiac disease here because it is been connected to many other autoimmune diseases and is the most undiagnosed disease. &#xA;I consider Montelukast because its mechanism in IgE and because of its latest research findings with childhood asthma (about 2001), see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?cmd=Link&amp;amp;LinkName=pubmed_pubmed&amp;amp;from_uid=23126384&quot; rel=&quot;nofollow&quot;&gt;this search&lt;/a&gt; in PubMed, and in successful treatment of opportunistic diseases in HIV/AIDS, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17151039&quot; rel=&quot;nofollow&quot;&gt;this publication&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2014-12-27T09:32:29.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26221" PostTypeId="2" ParentId="26215" CreationDate="2014-12-27T12:41:48.700" Score="3" Body="&lt;p&gt;Not at all. In order to self destruct, you don't need to disable all necessary functions, you just need to disable one. That's why the functions are called &quot;essential&quot;. To take a very simple example, in every movie you've seen where the self destruct has been activated, that self destruct mechanism was almost certainly a bomb that blew the ship/installation/planet or whatever up. The self destruct did not go around disabling individual processes, it just activated a bomb and destroyed everything.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apoptosis is quite similar. While there are many essential processes in a cell whose failure can activate apoptosis, the mechanism of apoptosis itself usually involves the straightforward destruction (&lt;a href=&quot;http://en.wikipedia.org/wiki/Lysis&quot; rel=&quot;nofollow&quot;&gt;lysis&lt;/a&gt;) of the cell. Simply put, the cell digests itself, breaking down its various constituent parts and, finally, destroying the cell membrane and breaking up the cell itself. For a summary see &lt;a href=&quot;http://en.wikipedia.org/wiki/Apoptosis#Execution&quot; rel=&quot;nofollow&quot;&gt;this Wikipedia page&lt;/a&gt; or &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26873/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Briefly, when apoptosis is triggered, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Caspase#Caspase_cascade&quot; rel=&quot;nofollow&quot;&gt;caspase cascade&lt;/a&gt; is initialized which results in the breakdown of various proteins in the cell and, finally, in cell lysis. It really is analogous to setting of the bomb that destroys the facility of the bad guys. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2014-12-27T12:41:48.700" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26222" PostTypeId="2" ParentId="26189" CreationDate="2014-12-27T12:45:04.603" Score="32" Body="&lt;p&gt;Very nice question!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, the 'smallest size' that a human eye can perceive is called &lt;strong&gt;visual acuity&lt;/strong&gt;, and can be expressed in various ways. It cannot simply be expressed by means of size measures, as objects with a fixed size are perceived as smaller when viewed from a distance (&lt;em&gt;perspective&lt;/em&gt;). A familiar example is the train track:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KKV3V.jpg&quot; alt=&quot;perspective&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, visual acuity has to be measured as a function of viewing distance, i.e,  in degrees of visual view. Measured in degrees, the visual acuity of the average normally sighted person is &lt;sup&gt;1&lt;/sup&gt;/&lt;sub&gt;60&lt;/sub&gt; degree, or 1 minute of arc (1 MAR) (&lt;a href=&quot;http://webvision.med.utah.edu/book/part-viii-gabac-receptors/visual-acuity/&quot; rel=&quot;noreferrer&quot;&gt;Webvision, chapter &quot;Visual Acuity&quot;, by Kalloniatis &amp;amp; Luu&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using the basic structure of the eye and some trigonometry one can deduce the smallest visible size :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/H0yS8.jpg&quot; alt=&quot;basic structure of the eye&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The trigonometric formula becomes: $2d \times tan(\frac{\alpha}{2})$ with &lt;em&gt;d&lt;/em&gt; being the viewing distance and alpha ($\alpha$) the visual acuity expressed in radians ($\pi \times \frac{degrees}{180}$) (&lt;a href=&quot;https://www.nde-ed.org/EducationResources/CommunityCollege/PenetrantTest/Introduction/visualacuity.htm&quot; rel=&quot;noreferrer&quot;&gt;NDT resource center&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming the closest distance an adult can focus (~100 mm) and an average maximal acuity of 1 MAR, the smallest visible size boils down to &lt;strong&gt;29 microns&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A young child can focus at distances down to ~50 mm, and can have a visual acuity of 0.4 MAR, which yields &lt;strong&gt;6 microns&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that 1 MAR encompasses 288 microns on the retina, and some 180 photoreceptors. The optical limitations of the eye (such as diffraction by the lens and light scatter by the neural cells in the retina) limits the resolution of the human eye below the theoretical 'pixel limit' of the eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to sum up, depending on one's age, one should be able to see targets in the order of 6 - 29 microns. The lower bounds of this range are indeed in the range of the waterweed cells and cloth fibers you describe. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS - the values described are representative under ideal conditions, i.e., under situations of abundant lighting and high contrast.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="16866" LastEditDate="2017-03-14T17:03:51.997" LastActivityDate="2017-03-14T17:03:51.997" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26223" PostTypeId="1" AcceptedAnswerId="26250" CreationDate="2014-12-27T15:01:22.603" Score="3" ViewCount="402" Body="&lt;p&gt;Been struggling with this for the past few days even after reading half of the acid base tutorial &lt;a href=&quot;http://www.anaesthesiamcq.com/AcidBaseBook/ABindex.php&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, if someone could help me that'd be great. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I don't understand is how HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; is supposed to buffer the blood. I know that HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; is a base and can accept H&lt;sup&gt;+&lt;/sup&gt;, but the way that the HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; came to fruition is by donating a H&lt;sup&gt;+&lt;/sup&gt; to the surrounding water, so there's a net zero change in H&lt;sup&gt;+&lt;/sup&gt; thus no buffering action took place. Let's say a HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; accepts a H&lt;sup&gt;+&lt;/sup&gt;, now the CO&lt;sub&gt;2&lt;/sub&gt; produced by H&lt;sub&gt;2&lt;/sub&gt;CO&lt;sub&gt;3&lt;/sub&gt; → CO&lt;sub&gt;2&lt;/sub&gt; + H&lt;sub&gt;2&lt;/sub&gt;O leaves the blood because the P&lt;sub&gt;&lt;em&gt;venous&lt;/em&gt;&lt;/sub&gt;CO&lt;sub&gt;2&lt;/sub&gt; gets higher than the CO&lt;sub&gt;2&lt;/sub&gt; pressure in the air in the lungs, and you exhale. Now you're in the exact same situation as before the CO&lt;sub&gt;2&lt;/sub&gt; got attached to H&lt;sub&gt;2&lt;/sub&gt;O. &#xA;Still the text calls it as an buffer, with a very large buffering capacity as well. How does this work?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To me it seems that buffering blood using HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; makes as much sense as using HCl, Cl&lt;sup&gt; -&lt;/sup&gt; can accept H&lt;sup&gt;+&lt;/sup&gt;, right? Nevermind that HCl is a very strong acid.. Surely no one would think of using HCl to buffer blood. &lt;/p&gt;&#xA;" OwnerUserId="11709" LastEditorUserId="3340" LastEditDate="2014-12-28T16:21:53.457" LastActivityDate="2014-12-31T17:54:50.010" Title="How do CO₂ and carbonic acid (H₂CO₃) work in buffering the blood?" Tags="&lt;biochemistry&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26224" PostTypeId="1" CreationDate="2014-12-27T17:06:11.510" Score="1" ViewCount="54" Body="&lt;p&gt;I was reading an article on MIT Technology review about superpatients for low cholesterol that got me thinking whether such patients exist for cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article is &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.technologyreview.com/featuredstory/532421/the-search-for-exceptional-genomes/&quot; rel=&quot;nofollow&quot;&gt;http://www.technologyreview.com/featuredstory/532421/the-search-for-exceptional-genomes/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I had also previously read an article on naked mole rats and the hyaluronan in the ECM.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.wired.com/2013/06/naked-mole-rat-cancer/&quot; rel=&quot;nofollow&quot;&gt;http://www.wired.com/2013/06/naked-mole-rat-cancer/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, I am wondering whether there are any current studies, that is trying to discover the genetic outliers for cancers. Ie, humans that have hyaluronan in their ECM that is almost naked mole rat like. Since I understand that with a genetic pool of 7+ billion there has to be at least one outlier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="8279" LastActivityDate="2014-12-27T17:06:11.510" Title="Superpatients for Cancer resistance" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;cancer&gt;&lt;dna-sequencing&gt;&lt;biotechnology&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26228" PostTypeId="2" ParentId="26216" CreationDate="2014-12-28T00:46:52.087" Score="4" Body="&lt;p&gt;RGB color is a more direct representation of the &quot;raw input&quot; received by the (human) eye, since the three types of cone cell have responsivity spectra that roughly correspond to red, green, and blue light:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/1/1e/Cones_SMJ2_E.svg&quot; alt=&quot;Human cone response curves&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Opponent color decomposes color into three &quot;dimensions&quot; of opposing properties: dark or light, yellow or blue, and red or green.  This provides some brightness invariance, since changing the intensity of light will change the brightness but not the yellow/blue or red/green balance of the color, even though the stimulation level of all three types of cone cell will change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One could speculate that opponent color perception is more &quot;meaningful&quot; in real-world environments.  The dark/light axis represents the overall amount of light, the yellow/blue axis indicates which end of the visible spectrum is predominant, and the red/green axis provides a finer distinction for low-frequency light.&lt;/p&gt;&#xA;" OwnerUserId="11657" LastActivityDate="2014-12-28T00:46:52.087" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="26229" PostTypeId="2" ParentId="26105" CreationDate="2014-12-28T01:40:57.687" Score="6" Body="&lt;p&gt;A &lt;strong&gt;species&lt;/strong&gt; is commonly defined as the largest group within which interbreeding produces viable offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;strong&gt;sub-species&lt;/strong&gt; is a subgroup below the level of a species.  One definition is a group which can interbreed successfully with other subspecies, but does not do so in practice (e.g. due to geographical isolation).  Other terms like &lt;strong&gt;variety&lt;/strong&gt;, &lt;strong&gt;form&lt;/strong&gt;, etc., may be used in some domains to indicate various groupings below the species level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;strong&gt;breed&lt;/strong&gt; usually refers to a population of a domestic animal that has been selectively bred for specific characteristics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;strong&gt;population&lt;/strong&gt; is a set of individuals within a species that live in the same geographical region.  Depending on rates of gene flow, different populations within a species may eventually differentiate into subspecies or distinct species — this is known as &lt;a href=&quot;https://en.wikipedia.org/wiki/Allopatric_speciation&quot; rel=&quot;noreferrer&quot;&gt;allopatric speciation&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="11657" LastActivityDate="2014-12-28T01:40:57.687" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26230" PostTypeId="2" ParentId="23643" CreationDate="2014-12-28T08:17:11.737" Score="4" Body="&lt;p&gt;Could not fit in a comment....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;To make sure we all understand your question...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is your question &lt;code&gt;how many (eukaryote) species are currently living?&lt;/code&gt; or &lt;code&gt;How many (eukaryote) cells are currently living?&lt;/code&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Just a hint to answer the question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Micheal Lynch, in his book (&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0878934847&quot; rel=&quot;nofollow&quot;&gt;On the Origin of Genome Architecture&lt;/a&gt;) at page 3, Box 1.1 tries to answer the question &lt;code&gt;How much DNA is there on earth?&lt;/code&gt;. He ends up with an estimation of a total length of DNA on earth of $10^{24}$ km for procaryotes, $10^{25}$ km for eukaryote (of which $\frac{1}{1000}$% is accounted to humans). This sums up to a total DNA length of $10^{12}$ light-years, or 10 times the diameter of the known universe!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In his calculations, he estimates that the total number of procaryote cells at $10^{30}$ (citing Whitman et al. 1998 as you did). He estimates the total number of eukaryote species to $10^7$, i.e. 6 times the number of known eukaryote species. However, he doesn't directly give any reference for this estimate but he refers to different chapters in the book that contain lots of references.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;...I hope that helps...&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2014-12-31T20:13:54.793" LastActivityDate="2014-12-31T20:13:54.793" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26231" PostTypeId="1" AcceptedAnswerId="26238" CreationDate="2014-12-28T09:14:56.557" Score="10" ViewCount="239" Body="&lt;p&gt;Related to but distinct from &lt;a href=&quot;https://biology.stackexchange.com/questions/681/how-will-rising-carbon-dioxide-levels-in-the-troposphere-affect-photosynthetic-p&quot;&gt;this question&lt;/a&gt; due to the concentrations involved. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While small carbon dioxide concentration increases can &lt;a href=&quot;http://www.sciencedaily.com/releases/2009/02/090209205202.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;positively impact&lt;/a&gt; plant growth under &lt;a href=&quot;http://www.nature.com/scitable/knowledge/library/effects-of-rising-atmospheric-concentrations-of-carbon-13254108&quot; rel=&quot;nofollow noreferrer&quot;&gt;some circumstances&lt;/a&gt; and at the same time &lt;a href=&quot;http://news.stanford.edu/pr/02/jasperplots124.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;negatively affect it&lt;/a&gt; under other circumstances, these changes are relatively small (doubling CO&lt;sub&gt;2&lt;/sub&gt; from 0.04% to 0.08%). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any research on plants grown at extremely high (&gt;1%) carbon dioxide concentrations in the air, assuming Earth atomspheric pressure? For the purpose of this question, assume that the plants are supplied with pH modifiers such as limestone in the soil to prevent soil acidification. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="24354" LastEditDate="2018-03-14T16:06:05.917" LastActivityDate="2018-03-14T16:06:05.917" Title="Can plants grow under extreme (&gt;1%) carbon dioxide concentrations?" Tags="&lt;botany&gt;&lt;photosynthesis&gt;&lt;climate-change&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26232" PostTypeId="2" ParentId="23805" CreationDate="2014-12-28T09:18:03.477" Score="1" Body="&lt;p&gt;You can get raw FMRI data from &lt;a href=&quot;https://openfmri.org/&quot; rel=&quot;nofollow&quot;&gt;https://openfmri.org/&lt;/a&gt; on that website you'll also download your conditions files for the experimental design (you'll need this in creating your matrix). This is a link to an experiment(it's data) with &quot;healthy&quot; participants and participants diagnosed with schizophrenia: &lt;a href=&quot;https://openfmri.org/dataset/ds000115&quot; rel=&quot;nofollow&quot;&gt;https://openfmri.org/dataset/ds000115&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Raw image files from a scanner will be in .dcm format. You can use &lt;a href=&quot;http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html&quot; rel=&quot;nofollow&quot;&gt;http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html&lt;/a&gt; to convert the multiple &quot;.dcm&quot; images of a scan into a 3 single 4D images for anatomicals, also known as T1 images. That converter will also convert the BOLD images into a single 4D image. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After conversion, the images you will want and need to load into whichever fmri data analysis software you're using will be in &quot;.nii.gz&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question suggest that you don't need data analysis software but if you do,  I'm only familiar with FSL, you can find information on FSL from here &lt;a href=&quot;http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/&quot; rel=&quot;nofollow&quot;&gt;http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps. &lt;/p&gt;&#xA;" OwnerUserId="11525" LastActivityDate="2014-12-28T09:18:03.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26233" PostTypeId="1" AcceptedAnswerId="26247" CreationDate="2014-12-28T10:59:13.743" Score="5" ViewCount="171" Body="&lt;p&gt;I have trouble identifying a tree that I saw on a vacation. This is the image:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ISdqx.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know the name of the tree, I only know that its not European.&lt;/p&gt;&#xA;" OwnerUserId="11715" LastEditorUserId="3340" LastEditDate="2014-12-29T08:47:19.917" LastActivityDate="2015-01-02T14:13:14.713" Title="Identifying a tree with an image" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26234" PostTypeId="2" ParentId="26233" CreationDate="2014-12-28T13:44:21.170" Score="2" Body="&lt;p&gt;The fruit strongly resembles immature &lt;a href=&quot;http://en.wikipedia.org/wiki/Lychee&quot; rel=&quot;nofollow noreferrer&quot;&gt;lychee&lt;/a&gt; (&lt;em&gt;Litchi chinensis&lt;/em&gt;). Since I have only seen the fruit, I cannot comment on whether the flower looks correct. The flowers appear to be slightly different from those in Wikipedia, especially in the number of &quot;stamens&quot;(?) per flower. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dhAk5.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1Av5s.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2014-12-28T13:44:21.170" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26235" PostTypeId="1" CreationDate="2014-12-28T14:52:43.453" Score="7" ViewCount="61" Body="&lt;p&gt;The internet says a million things about what to eat and what not to eat in regards to impacts on acne. For instance:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Refrain from dairy products.&lt;/li&gt;&#xA;&lt;li&gt;Refrain from food heavy in unsaturated fat.&lt;/li&gt;&#xA;&lt;li&gt;Refrain from too much sweet.&lt;/li&gt;&#xA;&lt;li&gt;Consume fresh food (raw fruits &amp;amp; vegetables) but no cabbage and cauliflower.&lt;/li&gt;&#xA;&lt;li&gt;No Alcohol&lt;/li&gt;&#xA;&lt;li&gt;Etc. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there really any relation between food consumed and the occurrence of acne?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="11717" LastEditorUserId="16866" LastEditDate="2017-04-03T18:02:12.610" LastActivityDate="2017-04-03T18:02:12.610" Title="Is there any conclusive study relating the food consumed and the occurrence of acne?" Tags="&lt;human-biology&gt;&lt;food&gt;&lt;skin&gt;&lt;diet&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26236" PostTypeId="2" ParentId="5586" CreationDate="2014-12-28T14:55:57.487" Score="1" Body="&lt;p&gt;Human body temperature is a measure of the body's ability to keep, generate, or get rid of heat as the need arises. The body is very adept at maintaining temperature within a narrow and safe range, despite occasional huge variations in the room temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But some bodies are more efficient than others. Even bodies of the same height and weight may differ dramatically in the ability to maintain body temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans also differ in their preferred room temperature. Some like it warmer, some cooler. This is called thermal comfort. Thermal comfort is not merely physical, but psychological too. In one's choice of preferred temperature, besides psychology, other personal factors come into the equation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also the feeling of cold or hot depends upon the DIFFERENCE between one's normal body temperature and outside temperature. And contrary to popular belief, different people have different normal body temperatures. It also depends upon the amount of muscle mass and fat, as fat stores heat (decreasing the normal temperature) while muscles dissipate it (increasing the normal temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following links might help:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mnn.com/health/fitness-well-being/stories/why-are-some-people-colder-than-others&quot; rel=&quot;nofollow&quot;&gt;http://www.mnn.com/health/fitness-well-being/stories/why-are-some-people-colder-than-others&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.medicalnewstoday.com/releases/5711.php&quot; rel=&quot;nofollow&quot;&gt;http://www.medicalnewstoday.com/releases/5711.php&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="11716" LastActivityDate="2014-12-28T14:55:57.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26237" PostTypeId="1" AcceptedAnswerId="26239" CreationDate="2014-12-28T16:04:39.657" Score="11" ViewCount="3009" Body="&lt;p&gt;I read that the length of telomeres in Dolly was shorter, because the DNA was taken from an old sheep. Shorter telomeres may lead to early aging. What is happening now with cloning? Do we use a telomerase to restore the length in a donor cell? &lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="948" LastEditDate="2014-12-28T16:12:31.640" LastActivityDate="2014-12-29T23:09:36.593" Title="Cloning and Telomeres" Tags="&lt;cloning&gt;&lt;telomere&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26238" PostTypeId="2" ParentId="26231" CreationDate="2014-12-28T16:06:17.620" Score="11" Body="&lt;p&gt;Yes they can, but their normal growth is somewhat impaired. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0273117794903069&quot;&gt;A study by Bugbee and collaborators&lt;/a&gt; showed that while the yield of rice and wheat increases with CO&lt;sub&gt;2&lt;/sub&gt; up to about 0.1% CO&lt;sub&gt;2&lt;/sub&gt;, yield decreases sharply as CO&lt;sub&gt;2&lt;/sub&gt; climbs from 0.1% to 0.25%. There is a smaller loss in yield as CO&lt;sub&gt;2&lt;/sub&gt; is further increased from 0.25% to 2%.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One interesting thing to note about the study is that the above results turn somewhat on how &quot;yield&quot; is defined. Bugbee defines yield in terms of the mass of the parts of the plant that people can actually eat. They make a note in the study that the vegetative growth of the plants (the green leafy parts humans can't eat) was not affected by the jump from optimal to super-optimal CO&lt;sub&gt;2&lt;/sub&gt; levels.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="3340" LastEditDate="2014-12-29T08:45:25.853" LastActivityDate="2014-12-29T08:45:25.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26239" PostTypeId="2" ParentId="26237" CreationDate="2014-12-28T16:30:29.457" Score="13" Body="&lt;p&gt;No, it doesn't seem to be common practice. A telomerase treatment would probably do more harm than good, and may be completely unnecessary in the first place.&lt;/p&gt;&#xA;&lt;p&gt;Betts and coworkers published &lt;a href=&quot;http://www.pnas.org/content/98/3/1077.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;a study in which they examined telomere length in cloned cattle&lt;/a&gt;. They found that while telomere length in cloned embryos does start out somewhat shorter than in naturally produced embryos, by the time that the normal processes of embryonic development were in full swing telomere length in cloned and natural embryos was equivalent.&lt;/p&gt;&#xA;&lt;p&gt;Betts' results make sense in light of the fact that telomerase activity (and the activity of many, many related proteins) is normally upregulated in embryonic cells.&lt;/p&gt;&#xA;&lt;p&gt;As for Dolly, while it is true that her telomeres were shorter than those of an average age-matched sheep at the time of her death, it's far from clear that those short telomeres had anything to do with her decline. Also keep in mind that she didn't just keel over suddenly in the night, she was euthanized. A subsequent autopsy showed that she had a form of lung cancer caused by a retrovirus common in sheep.&lt;/p&gt;&#xA;&lt;h3&gt;Edit: why were Dolly's telomeres shortened?&lt;/h3&gt;&#xA;&lt;p&gt;This is a good question, as the findings of shortened telomeres in Dolly's case do contradict the findings in the Betts paper. Clearly we need more citations:&lt;/p&gt;&#xA;&lt;p&gt;-&lt;a href=&quot;http://www.nature.com/nature/journal/v399/n6734/full/399316b0.html&quot; rel=&quot;noreferrer&quot;&gt;&amp;quot;Analysis of telomere lengths in cloned sheep.&amp;quot; Shiels et al, 1999&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;This is the original citation for the claim that Dolly's telomeres were shortened. There isn't too much extra information to be had as it's a very short paper (1 page letter). They did look at other cloned sheep created from types of cells other than skin cells (as Dolly was) and saw the same kind of telomere shortening relative to controls. They also make a point of mentioning that Dolly's telomere length may be within the normal variation for sheep.&lt;/p&gt;&#xA;&lt;p&gt;-&lt;a href=&quot;http://www.biolreprod.org/content/66/6/1649.long&quot; rel=&quot;noreferrer&quot;&gt;&amp;quot;Remarkable differences in telomere lengths among cloned cattle derived from different cell types.&amp;quot; Miyashita et al, 2002&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;The investigators found that telomere length in cloned cattle was strongly dependent on the type of cell from which the clone was derived. For example, clones made from mammary cells tended to have shortened telomeres, whereas those derived from muscle cells had normal length telomeres.&lt;/p&gt;&#xA;&lt;p&gt;-&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/mrd.20279/abstract&quot; rel=&quot;noreferrer&quot;&gt;&amp;quot;The analysis of telomere length and telomerase activity in cloned pigs and cows.&amp;quot;, Jeon, 2005&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;This group found that cloned cattle had normal length telomeres, whereas cloned pigs had elongated telomeres. By way of explaining these results, they found that telomerase activity was upregulated in cloned pigs relative to control pigs, whereas telomerase activity in cloned cattle matched that of control cattle.&lt;/p&gt;&#xA;&lt;p&gt;How should we take all of this information? At the very least we can say that telomere length in clones is highly dependent on species and on source tissue, and that telomere length can increase, decrease, or stay the same in cloned animals relative to control animals. Clearly telomere length in cloned animals is a fiddly property. It is very likely that it also depends on the exact details of the cloning protocol as it was carried out (i.e. how much did the experimenter's hands shake when they inserted the needle to suck out the nucleus?, etc.).&lt;/p&gt;&#xA;&lt;p&gt;So I would say not to read too much into Dolly's shortened telomeres. They may have been a result of her being a clone, or they may have been a result of natural variation. In either case the shortened telomeres were not linked to her ill-health, and it's likely that small tweaks to the cloning protocol would eliminate any telomere length discrepancies in future clones.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-29T23:09:36.593" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26240" PostTypeId="1" CreationDate="2014-12-28T16:36:14.077" Score="1" ViewCount="103" Body="&lt;p&gt;is the vascular cambium equivalent to interfascular cambium or intrafascular cambium?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;isn't the vascular cambium similar to the intrafascular cambium because both occur inside the vascular bundle&lt;/p&gt;&#xA;" OwnerUserId="11780" LastEditorUserId="11780" LastEditDate="2014-12-28T17:34:59.863" LastActivityDate="2014-12-28T17:34:59.863" Title="what's the vascular cambium?" Tags="&lt;botany&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26241" PostTypeId="2" ParentId="1675" CreationDate="2014-12-28T18:18:23.860" Score="7" Body="&lt;p&gt;I'll contradict the answer posted here (ages ago) and say &lt;strong&gt;no&lt;/strong&gt;, it isn't possible. Growing an organ wthout MHC proteins &lt;em&gt;might&lt;/em&gt; be achievable, but it would be rejected &lt;em&gt;for not having&lt;/em&gt; MHC1. NK cells instruct all cells without MHC1 to perform apoptosis. In this case, MHC1 antigens are &lt;em&gt;required&lt;/em&gt; on cells for proper self-identification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Keeping MHC1-less cells alive could be achieved by&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;equipping them with whatever is keeping erythrocytes and thrombocytes (also lacking MHC1) from being destroyed on sight. (A good idea, but see next paragraph)&lt;/li&gt;&#xA;&lt;li&gt;disabling their apoptosis mechanism (Cells with disabled apoptosis mechanisms are commonly referred to as cancer, so we might want to &lt;em&gt;not do&lt;/em&gt; this.)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;MHC1 also has a function; it presents &quot;peptide shreddings&quot; from proteosomes to T cells; this way T cells can check if the cell contains internal foreign proteins (sign of a virus infection or cancerous transformation). Thus, removing MHC from the cells would make them very liable to become nearly unstoppable virus factories or tumor cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(On a side note, while everyone technically can receive 0 Rh negative blood, group-identical blood is used always, except in rare emergency cases. A and B antigens here, as far as I know, do not have function.)&lt;/p&gt;&#xA;" OwnerUserId="11718" LastActivityDate="2014-12-28T18:18:23.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26242" PostTypeId="1" CreationDate="2014-12-28T18:54:32.290" Score="1" ViewCount="287" Body="&lt;p&gt;I'm using Arelquin to look at the genetic structure between a number of different populations. I  want to compare the populations by producing pairwise FST values, however I don't know what model for the genetic distances I should use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two models provided are Slatkin's distance or Reynold's distance. They both aim to linearize the FST values by transforming them [Slatkin's = FST/(1-FST), Reynold's = -ln(1-FST)]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do I know if the FST values need to be transformed, and if they do need to be transformed, what model should I use?&lt;/p&gt;&#xA;" OwnerUserId="3382" LastActivityDate="2014-12-28T18:54:32.290" Title="What genetic distance model should be used when calculating genetic differences in Arelquin?" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;molecular-genetics&gt;&lt;molecular-evolution&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26244" PostTypeId="1" AcceptedAnswerId="26246" CreationDate="2014-12-28T20:33:55.577" Score="4" ViewCount="148" Body="&lt;p&gt;I am continually surprised at the items my pet dog is willing to ingest.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand part of the consumption is driven by nutritional instincts (licking salty liquids such as sweat) or nurturing instincts (eating baby faeces to prevent predators) but why does an animal with a sense of smell many thousands of times greater than our own not become nauseated by the same substances, smells or conditions that humans do? &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Sweat&lt;/li&gt;&#xA;&lt;li&gt;Faeces&lt;/li&gt;&#xA;&lt;li&gt;Decayed foodstuffs&lt;/li&gt;&#xA;&lt;li&gt;Assorted garbage &lt;/li&gt;&#xA;&lt;li&gt;Untreated and/or dirty water&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I have known my dog to bury a piece of rotting pork only to dig it up several months later for consumption.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition I watched dogs refuse to eat certain items (spicy meat etc) until their owner makes a move to take it back at which point the animal will swallow the item causing a gag, hacking couch or nasal clearance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a biological mechanism that suppresses the gag reflex in canines, is the need to consume overpowering their distaste or do they simply not find such substances unpalatable?&lt;/p&gt;&#xA;" OwnerUserId="11722" LastActivityDate="2014-12-28T23:26:36.310" Title="Why are canines not nauseated by similar foodstuffs/state of decay as human beings?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26246" PostTypeId="2" ParentId="26244" CreationDate="2014-12-28T23:26:36.310" Score="8" Body="&lt;p&gt;Your dog finds these things palatable, I assure you, and no gag-reflex suppression is needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I had a dog that would steal duck eggs from my flock, bury them all over the place, and dig them up when properly rotted to enjoy as a treat, and no, I'm not making this up. I saw her do it, ran across many buried duck eggs while gardening, and could immediately smell when she was enjoying one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All that to say what smells good to a dog has nothing to do with what is acceptable to you. Many of your &quot;dislikes&quot; are &lt;em&gt;conditioned&lt;/em&gt;: living in a society where cleanliness is valued and clean water is available, humans in such societies can afford to snub their noses at less sanitized things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Manure may well elicit a completely different reaction to a farmer, who saves it carefully before spreading it on his fields to enrich the soil. To him, it might be the smell of a good crop next summer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many species exhibit corprophagia. It's not known why dogs (some, far from all) do this. Rabbits, for instance, eat their own feces after their first movement of the day. This is normal and nutritional for them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eating the feces of &lt;em&gt;other species, particularly herbivores&lt;/em&gt;, is common among dogs and isn’t considered abnormal, just undesirable. My (same) dog followed my goats around like they were Pez dispensers. Since dogs can't digest cellulose, they get some of the advantage of eating plants this way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Capybara, rabbits, hamsters and other related species do not have a complex ruminant digestive system. Instead they extract more nutrition from grass by giving their food a second pass through the gut. Soft fecal pellets of partially digested food are excreted and generally consumed immediately. Consuming these cecotropes is important for adequate nutritional intake of Vitamin B12. They also produce normal droppings, which are not eaten.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Young elephants, pandas, koalas, and hippos eat the feces of their mother to obtain the bacteria required to properly digest vegetation found on the savanna and in the jungle. When they are born, their intestines do not contain these bacteria (they are completely sterile). Without them, they would be unable to obtain any nutritional value from plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eating garbage and human feces is thought to be one function of dogs during their early domestication, some 12,000 to 15,000 years ago. They served as our first waste management workers, helping to keep the areas around human settlements clean. A study of village dogs in Zimbabwe revealed that feces made up about 25% of the dogs’ overall diet, with human feces making up a large part of that percentage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;Coprophagia&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9882606&quot;&gt;Daily rhythms of food intake and feces reingestion in the degu, an herbivorous Chilean rodent: optimizing digestion through coprophagy&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.2042-3306.1977.tb04010.x/abstract;jsessionid=67F2A980089E9959F36A20ACE36D917E.f01t03&quot;&gt;Coprophagia as seen in Thoroughbred Foals&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2014-12-28T23:26:36.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26247" PostTypeId="2" ParentId="26233" CreationDate="2014-12-29T00:20:44.197" Score="2" Body="&lt;p&gt;I think you should look into trees in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Rubiaceae&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rubiaceae&lt;/a&gt; family (which is very large with ~6500 species in total). Many species there have spherical inflorescences, and some are somewhat similar-looking to the ones in your picture, e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Neolamarckia_cadamba&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Neolamarckia cadamba&lt;/em&gt;&lt;/a&gt; or species in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nauclea&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Nauclea&lt;/em&gt;&lt;/a&gt; genus. This is however just a suggestion to guide you, and not a species determination. Note also that spherical inflorescences are relatively common in many plant taxa, so it might be found in another family than Rubiaceae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is what Nauclea orientalis (photo from Wikipedia) looks like, just to give you a sense of the basic similarity:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/QhkQv.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The individual flowers are however much smaller than the flowers in your picture.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2014-12-29T00:20:44.197" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26249" PostTypeId="1" AcceptedAnswerId="26257" CreationDate="2014-12-29T06:49:25.943" Score="1" ViewCount="70" Body="&lt;p&gt;I’m trying to reconcile structures  in PDB entries with their  sequences as reported in their &lt;code&gt;chemList.polymer.dbref&lt;/code&gt; entries.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.g.: considering structures for HIV integrase:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;PDB:3OS0&lt;/code&gt; references &lt;code&gt;UNP:P14350&lt;/code&gt;, focusing on integrase (len=391)&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&gt;sp|P14350|752-1143&#xA;CNTKKPNLDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKIVLQ…NRTVSIDNLKPTSHQNGTTNDTATMDHLEKNE &lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;PDB:2B4J&lt;/code&gt; references &lt;code&gt;UNP:P12497&lt;/code&gt;, focusing on integrase (len=287)&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&gt;sp|P12497|1148-1435&#xA;FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGI…LLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Why should these sequences be so different?!  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;and in case you think I'm focused on a bit of noise: there are &lt;strong&gt;42 other&lt;/strong&gt; HIV integrase structures all referencing &lt;code&gt;UNP:P14350&lt;/code&gt;, and &lt;strong&gt;43 other&lt;/strong&gt; structures referencing &lt;code&gt;UNP:12497&lt;/code&gt; (and 79 others referencing &lt;code&gt;UNP:Q76353&lt;/code&gt;, very similar to &lt;code&gt;UNP:12497&lt;/code&gt;), 22 referencing an entirely different &lt;code&gt;UNP:Q72498&lt;/code&gt;.&lt;/p&gt;&#xA;" OwnerUserId="11729" LastEditorUserId="3340" LastEditDate="2015-06-19T07:15:11.930" LastActivityDate="2015-06-19T07:15:11.930" Title="how to reconcile PDB structures' sequences via Uniprot references?" Tags="&lt;bioinformatics&gt;&lt;sequence-analysis&gt;&lt;pdb&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26250" PostTypeId="2" ParentId="26223" CreationDate="2014-12-29T07:15:29.203" Score="2" Body="&lt;p&gt;What do you mean by &quot;there's a net zero change in $\ce{H+}$ thus no buffering action took place&quot;? The property of a buffer system IS to prevent drastic change in pH. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Buffer capacity, a measure of how much a buffer system can sustain a change in $\ce{[H+]}$ (aka. pH), (mostly) depends on two parameters -- the concentration of that buffer, and how close the desired pH is to its pKa. $\ce{H2CO3}$ has pKa's of 6.4 and 10.3. Given that the pH of blood is about 7.4 and better to stay that way, the base/acid pair, $\ce{[HCO3_^{-}]/[H2CO3]}$ (pKa=6.4) (plus a whole bunch of various proteins such as albumins in blood, all of which has its own pKa) does provide a good buffer capacity around that pH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;True, $\ce{CO2}$ is constantly removed through respiration, but it is also constantly generated by cellular respiration, making $\ce{H2CO3&amp;lt;=&amp;gt;CO2 + H2O}$ a &quot;volatile equilibrium&quot; and keeping both $\ce{HCO3_^{-}}$ and $\ce{H2CO3}$ in high enough concentration to sustain its buffer capacity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HCl has a pKa of about -7 so it &lt;i&gt;would&lt;/i&gt; make a good buffer around pH of -7. In an aqueous environment, all HCl molecules will 100% dissociate, and no $\ce{H+}$ will ever bind to $\ce{Cl-}$ because water itself will first &quot;hijack&quot; the proton as  $\ce{H3O+}$ (pKa=-1.74) before $\ce{Cl-}$ by about five order of magnitude. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;---EDIT---&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may be thinking that when cells release $\ce{CO2}$ to the blood, $\ce{H2CO3}$ would be the first product, and in order for $\ce{H2CO3}$'s conjugate base to work as a base to absorb any extra $\ce{H+}$, first it must release a $\ce{H+}$, resulting in no net change in free $\ce{H+}$ and hence no capacity in balancing extra or insufficient $\ce{H+}$ to maintain the pH. Indeed, if $\ce{H2CO3}$ is the &lt;i&gt;ONLY&lt;/i&gt; chemical species in the blood when it would not be a buffer. A buffer requires at least two species -- a potential proton donor and a potential proton acceptor, both of which in high and comparable concentration. pH is a measure of external free $\ce{H+}$, a result of final proton balance of all the acid and base in the blood, dictated by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Henderson%E2%80%93Hasselbalch_equation&quot; rel=&quot;nofollow&quot;&gt;Henderson–Hasselbalch equation&lt;/a&gt;. Thus when $\ce{H2CO3}$ is released in the blood, the blood's basic pH will causes most of $\ce{H2CO3}$ to become $\ce{HCO3_^{-}}$, releasing free proton. Again IF that's all the $\ce{HCO3_^{-}}$ in the blood after being made from $\ce{H2CO3}$, the blood's pH will drop, but there is already abundant amount of $\ce{HCO3_^{-}}$ in the blood, helping the system to reach new equilibrium. Of course, the buffer capacity of blood is not infinite. If there is so much metabolic acid being produced that it shifts the ratio of $\ce{[HCO3_^{-}]/[H2CO3]}$ toward excessive acid, acidosis would occur.&lt;/p&gt;&#xA;" OwnerUserId="9731" LastEditorUserId="9731" LastEditDate="2014-12-31T17:54:50.010" LastActivityDate="2014-12-31T17:54:50.010" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="26251" PostTypeId="1" CreationDate="2014-12-29T09:25:55.017" Score="22" ViewCount="8259" Body="&lt;p&gt;Polar bears are white in color and white color is not a good absorbant of heat. Why then didn't they evolve a black color to absorb more heat?&lt;/p&gt;&#xA;" OwnerUserId="11730" LastEditorUserId="9943" LastEditDate="2014-12-29T12:27:15.117" LastActivityDate="2015-03-24T21:47:55.913" Title="Why didn't the polar bear change its color from white to black during evolution to absorb heat?" Tags="&lt;evolution&gt;" AnswerCount="9" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26252" PostTypeId="2" ParentId="26214" CreationDate="2014-12-29T09:30:54.823" Score="2" Body="&lt;p&gt;The main hypothesis is that all starts from RNA. &quot;The RNA world&quot;. There was no DNA and no proteins. Both function was performed by RNA. Now there are no living organism that carrying information in RNA (only viruses...), but there is &quot;enzymes&quot; from RNA - ribozymes. &lt;br&gt;&#xA;The evolution to DNA was later, according to this hypothesis.&lt;br&gt;&#xA;There is really good article in wiki. &lt;br&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_world_hypothesis&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/RNA_world_hypothesis&lt;/a&gt;&lt;br&gt;&#xA;or if you want something more look here&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26876/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK26876/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;b&gt;Summary&lt;/b&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;From our knowledge of present-day organisms and the molecules they contain, it seems likely that the development of the directly autocatalytic mechanisms fundamental to living systems began with the evolution of families of molecules that could catalyze their own replication. With time, a family of cooperating RNA catalysts probably developed the ability to direct synthesis of polypeptides. DNA is likely to have been a late addition: as the accumulation of additional protein catalysts allowed more efficient and complex cells to evolve, the DNA double helix replaced RNA as a more stable molecule for storing the increased amounts of genetic information required by such cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="10104" LastEditDate="2014-12-29T19:54:04.357" LastActivityDate="2014-12-29T19:54:04.357" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26253" PostTypeId="1" AcceptedAnswerId="26435" CreationDate="2014-12-29T11:09:28.750" Score="6" ViewCount="125" Body="&lt;p&gt;Is there a type of blood cell that can reach &lt;strong&gt;all other&lt;/strong&gt; body cells? By &quot;reach&quot;, I mean to &quot;touch&quot; the surface of the target cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we look at the red blood cell for example, that moves in blood vessels, there are cells close by - after the wall of blood vessel - that get oxygen by diffusion and not by direct contact, as far as I know.&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="9829" LastEditDate="2015-01-06T18:49:58.813" LastActivityDate="2015-01-06T18:49:58.813" Title="Blood cells penetration" Tags="&lt;immunology&gt;&lt;hematology&gt;&lt;blood-circulation&gt;" AnswerCount="1" CommentCount="10" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26254" PostTypeId="2" ParentId="26251" CreationDate="2014-12-29T11:15:15.217" Score="10" Body="&lt;p&gt;Bears initially were dark. But in snow it is really poor camouflage, their victims will see them to early. So they evolved to white color.&lt;br&gt;&#xA;They have a lot of fat and good fur to keep the temperature, they don't really need more sun energy. They need more food.&lt;br&gt;&#xA;In the same way - in the forest all bears are dark - for camouflage.&lt;br&gt;&#xA;Read here &lt;br&gt;&#xA;&lt;a href=&quot;http://www.polarbearsinternational.org/about-polar-bears/essentials/fur-and-skin&quot;&gt;http://www.polarbearsinternational.org/about-polar-bears/essentials/fur-and-skin&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="10104" LastEditDate="2014-12-29T11:37:06.140" LastActivityDate="2014-12-29T11:37:06.140" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26255" PostTypeId="1" AcceptedAnswerId="26259" CreationDate="2014-12-29T12:47:07.477" Score="6" ViewCount="402" Body="&lt;p&gt;As far as I understand, evolution is nowadays pretty much analyzed through phylogenetic trees, that is cladograms. These are constructed using the available records and taking some key structures and deduce whether species acquired or lost it, thereby generating a node. By  this approach, chronology is of utmost importance, but chronological &lt;strong&gt;time&lt;/strong&gt; is not. Hence, cladograms are not 'Darwinian' evolutionary trees as the latter are based on chronological &lt;em&gt;time&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I cannot help myself when analyzing a cladogram and interpreting the accumulation of various nodes along a branch as moving through time. Isn't evolution all about time? At the risk of pitfalling myself into a 'this is a primarily opinion based question': &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isn't it just so that along a certain branch, &lt;strong&gt;each successive node has taken time to develop&lt;/strong&gt;? Would it not be plausible to determine and assign a certain '&lt;strong&gt;standard evolutionary time unit&lt;/strong&gt; (a SETU if you like) representing the average time it takes for any organism to loose or acquire a certain trait, thereby allowing &lt;strong&gt;each node to be interpreted as time&lt;/strong&gt;? Of course, the SETU would be a gross estimate, but could still potentially re-animate the Darwinian look on modern-day evolution.   &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2014-12-29T13:52:49.443" LastActivityDate="2015-01-07T23:17:39.427" Title="Phylogenetics and the Tree of Life" Tags="&lt;evolution&gt;&lt;phylogenetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26256" PostTypeId="2" ParentId="26251" CreationDate="2014-12-29T13:01:42.763" Score="28" Body="&lt;p&gt;Polar bears do not have white fur - they don't have pigments in their fur hairs which makes them clear and translucent. The outer fur consists of hollow fibres, which shatter a part of the incoming light (the visible part) which makes them look white. This gives a very good camouflage in a white environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was initially thought (see reference 1) that the hollow fibers work in the same way as fiber optic cables and direct the UV part of the light (the visible was thought to be shattered) towards the black skin of the bears where it generates heat, but this hypothesis has been disproved. The UV part of the light is simply absorbed by the bears outer fur and doesn't reach the skin (see reference 2 for details).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hollow hair helps with the insulation of the skin and can change the color due to environmental influences. The tend to get yellow after feeding on seals due to the fatty substances from the animals. There have also been reports from zoos that algae lived inside the hollow part of the fur making the animals more grey and sometimes even green (see reference 3).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3851/scn26x9s_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Light collection and solar sensing through the polar bear pelt&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.uvm.edu/rsenr/nr385se/mod4/polarBearfurdata.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Is polar bear hair fiber optic?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3851/8tk4qeno_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;The greening of polar bears in zoos&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="15051" LastEditDate="2015-03-22T21:18:53.790" LastActivityDate="2015-03-22T21:18:53.790" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26257" PostTypeId="2" ParentId="26249" CreationDate="2014-12-29T13:25:11.503" Score="1" Body="&lt;p&gt;None of them is integrase:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;b&gt;P12497&lt;/b&gt;&#xA;Protein    Gag-Pol polyprotein&#xA;Gene       gag-pol&#xA;Organism   Human immunodeficiency virus type 1 group M subtype B (isolate NY5) (HIV-1)&lt;/pre&gt;&#xA;&#xA;&lt;pre&gt;&lt;b&gt;P14350&lt;/b&gt;&#xA;Protein    Pro-Pol polyprotein&#xA;Gene       pol&#xA;Organism   Human spumaretrovirus (SFVcpz(hu)) (Human foamy virus)&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Even if you meant the integrase product of the polyprotein, the second one is not even HIV.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;https://en.wikipedia.org/wiki/Human_foamy_virus&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Human Foamy Virus (HFV) is a retrovirus and specifically belongs to&#xA;  the genera Spumavirus. The spumaviruses are complex and significantly&#xA;  different from the other six genera of retroviruses in several ways.&#xA;  The foamy viruses derive their name from the characteristic ‘foamy’&#xA;  appearance of the cytopathic effect (CPE) induced in the cells.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-29T13:25:11.503" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26258" PostTypeId="1" CreationDate="2014-12-29T13:48:23.607" Score="7" ViewCount="1728" Body="&lt;p&gt;What is an operon in a eukaryotic cell, and how does it regulate the expression of genes? I've already read Wikipedia, but it is not enough clear to me. Unfortunately my knowledge in genetics are very poor! &lt;/p&gt;&#xA;" OwnerUserId="11731" LastEditorUserId="784" LastEditDate="2014-12-29T16:05:51.917" LastActivityDate="2020-01-15T20:03:10.357" Title="What is an operon?" Tags="&lt;genetics&gt;&lt;cell-biology&gt;&lt;operons&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26259" PostTypeId="2" ParentId="26255" CreationDate="2014-12-29T14:50:21.300" Score="8" Body="&lt;p&gt;Let's start with a short comment. You say &lt;code&gt;[..]evolution is nowadays pretty much analyzed through phylogenetic trees[..]&lt;/code&gt;. Many evolutionary biologist make extensive use of phylogenetic methods but a good part of evolutionary biologist (most of them I would say) do not work directly with phylogenetic methods.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I am not sure I understand your question but I hope the following may help you either to understand the issue or to edit your question. Note that I am NOT a phylogeneticist (not sure this word exist).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the definition of &quot;Node&quot; in Phylogenetics&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think your definition of a &lt;code&gt;node&lt;/code&gt; might be unusual. In phylogeny, a node is the most recent common ancestor shared by two sister lineages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Time in a phylogenetic tree&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, when you look at a phylogenetic tree, the axis along which lineages diversify represent the time (real time in years). Now, we use different methods in order to make estimation of this real time such as the rate of neutral substitutions. You may want to read about &lt;a href=&quot;http://en.wikipedia.org/wiki/Molecular_clock&quot; rel=&quot;nofollow&quot;&gt;molecular clock&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;each successive node has taken time to develop?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am not sure what you mean by &quot;develop&quot; here. Develop usually means the process by which a given individual/organism change phenotypically through its lifetime. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Developmental_biology&quot; rel=&quot;nofollow&quot;&gt;Developmental Biology&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;average time it takes for any organism to loose or acquire a certain trait&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Again, I am not sure whether you talk about development or evolution here as you talk about &quot;any organism&quot; and not about &quot;any population&quot;. In any case, an average time for a population to acquire a given arbitrary trait is a concept that 1) is valid only for discrete trait, 2) that is very dependent on the kind of trait you want to consider, 3) that will varies a lot from one given trait to another and 4) is extremely dependent on when you consider being the starting point of the evolutionary process toward the creation of the given trait. Therefore, it doesn't makes much sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Currently used &quot;standard evolutionary time unit&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, you can use similar concept for quantitative traits. &lt;a href=&quot;http://en.wikipedia.org/wiki/Darwin_(unit)&quot; rel=&quot;nofollow&quot;&gt;The Darwin (d)&lt;/a&gt; is a unit of evolutionary change (invented by Haldane and named after C. Darwin). It is defined as the e-fold (e≈2.7) in a mean of individual's trait in a population over million of years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, the Haldane is a unit of evolutionary change (I don't know who invented it and it is obviously named after JBS Haldane) and correspond to the number of standard deviation (of the distribution of individual trait in the population) change in the mean of individuals trait in a population per generation. The Haldane unit is therefore dependent on the selection pressure, the additive and non-additive genetic variance and environmental variance (therefore the heritability) and the mutational pressures.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-01-07T23:17:39.427" LastActivityDate="2015-01-07T23:17:39.427" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26260" PostTypeId="2" ParentId="26255" CreationDate="2014-12-29T16:24:28.593" Score="3" Body="&lt;p&gt;Something like what you describe does exist, and is called a &lt;a href=&quot;http://en.wikipedia.org/wiki/Molecular_clock&quot; rel=&quot;nofollow&quot;&gt;molecular clock&lt;/a&gt;. The rate of change in certain genes and non-coding sequences has been correlated to other evidence (fossil record, etc.) in such a way as to allow you to estimate in absolute terms how long a given set of mutations would take to occur naturally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Keep in mind that only certain genes have the required property of accumulating mutations at a more or less constant rate with respect to time. Most genes accumulate mutations in a more stochastic fashion.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-12-29T16:24:28.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26261" PostTypeId="1" AcceptedAnswerId="26262" CreationDate="2014-12-29T17:57:36.640" Score="6" ViewCount="15788" Body="&lt;p&gt;The original question was to predict the basic requirements for information storage. Then the discussion moved to why is it necessary to include mRNA in the protein translation process. Why can't there be a similar chemical molecule like tRNA which can directly read from DNA and exclude the mRNA intermediate. Also is the current translation process optimal in the sense that can there be a system which does not need mRNA or a similar intermediate altogether. Or is the presence of an intermediate a necessary requirement.&lt;/p&gt;&#xA;" OwnerUserId="5808" LastActivityDate="2015-08-30T11:26:10.663" Title="Why is mRNA needed in the Protein translation?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;molecular-evolution&gt;&lt;information-theory&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26262" PostTypeId="2" ParentId="26261" CreationDate="2014-12-29T18:27:59.097" Score="6" Body="&lt;p&gt;One reason is that an intermediate like mRNA allows for higher amounts of protein expression. You can have multiple mRNA molecules that are translated simultaneously. If you read directly from DNA you can have at most two translations in parallel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure about this, but I would imagine that having to unwind the DNA double strand every time for translation could be a drawback to directly reading from DNA as well. The mRNA is also subject to various forms of regulation, which might be an advantage as well for the added intermediary.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-12-29T18:27:59.097" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="26263" PostTypeId="2" ParentId="26261" CreationDate="2014-12-29T18:28:14.773" Score="4" Body="&lt;p&gt;I don't have a lot of references for this, but it's too long for a comment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Separating the roles of RNA and DNA helps to better control protein production and gene replication. If ribosomes worked directly on DNA, it would probably be very hard to replicate that DNA, as the DNA polymerases would collide with the ribosomes. You'd have to stop protein production and move the ribosomes out of the way before you could copy the DNA. Keeping mRNA separate allows the ribosomes to keep making protein while the DNA is being replicated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, transcription of DNA would be similar, where the DNA replication could collide with the transcription machinery. I can't find anything about that situation so I don't know how its regulated or how often it happens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, having mRNA allows amplification and further regulation. Every mRNA copy can make several protein copies, so the amount of protein produced from a single round of transcription can be higher than if the DNA were read directly by a ribosome. mRNA also has many binding sites for miRNA and other regulatory RNAs. If DNA were read directly, that wouldn't be possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also some cases where mRNA is stored and used later, such as immediately after &lt;a href=&quot;http://mmbr.asm.org/content/63/2/446.long&quot; rel=&quot;nofollow&quot;&gt;fertilization&lt;/a&gt;, or in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3027201/&quot; rel=&quot;nofollow&quot;&gt;platelets&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24751163&quot; rel=&quot;nofollow&quot;&gt;erythrocytes&lt;/a&gt; where translation can happen even after transcription stops due to loss of the nucleus.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2014-12-29T18:28:14.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26264" PostTypeId="2" ParentId="26251" CreationDate="2014-12-29T19:14:03.857" Score="7" Body="&lt;p&gt;How much energy could an Arctic-dwelling creature be expected to capture from sunlight?  I think not very much.  How much can it gain from having coloration that allows it to capture prey more easily?  Quite a bit.  Also, given the size of the polar bear, they will probably be generating more than enough waste heat from metabolic activity.  Indeed, if you do a little research, you might discover that the polar bear's problem is, indeed, getting rid of heat:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In bears, the basal metabolic rate varies with climate and season;&#xA;  Polar Bear has highest BMR.  Overheat easily when running; can't&#xA;  travel any great distance at speeds more than a walk.  Low&#xA;  surface-area to volume ratio favors heat retention. Tendency to&#xA;  overheat enhanced by layer of fat 11 cm (4.5in) thick.  Young cubs up&#xA;  to 6 months old, with little body fat, are susceptible to cold.   Use&#xA;  more than twice the predicted energy for moving at a given speed,&#xA;  perhaps due to bulky body.   Fat and fur both insulate.   As long as&#xA;  bear isn't exposed to wind, body temperature and metabolic rate remain&#xA;  normal at -37 degrees C (-35 degrees F).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;From &lt;a href=&quot;http://library.sandiegozoo.org/factsheets/polar_bear/polar.htm&quot; rel=&quot;nofollow&quot;&gt;http://library.sandiegozoo.org/factsheets/polar_bear/polar.htm&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, even if the polar bear was a perfect absorber, it could get at most ~1kW/m^2 of energy from the sun, and that only on a clear day in the summer.  And that heat would be on the outside of its insulating fur &amp;amp; fat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there's the answer: a strong selective pressure towards white, little or none towards black.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Re waste heat: What is meant here is that when the polar bear (or any animal) consumes food, part of it goes to producing heat as an unavoidable byproduct of metabolism.  Larger animals usually have to get rid of excess heat, thanks to the surface/volume relationship mentioned in the comments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a reference, try thinking about this: &lt;a href=&quot;http://en.wikipedia.org/wiki/Thermoregulation&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Thermoregulation&lt;/a&gt;  And remember that not all answers are written down in a book (or web site, these days).  Sometimes you have to actually think and reason out your own answers :-)&lt;/p&gt;&#xA;&#xA;&lt;hr /&gt;&#xA;&#xA;&lt;p&gt;Added: I think the problem with this question is the assumption that polar bears (or indeed, any boreal mammal) need to absorb heat.  Maybe that's down to anthropocentrism, since humans evolved from ancestors that lived in tropical climes, and so have adaptations (like sweating &amp;amp; nearly hairless skin) for cooling.  But if you read the links, you discover that more often the problem is getting rid of excess metabolic heat, and most boreal mammals seem quite comfortable in what we primates consider cold.  (I write this after coming in from playing with my two dogs, who love to run around in the fresh snow.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might also think about why almost all (non-domesticated) mammals have evolved protective or camouflaging coloration.  (The only exception I can think of offhand is the skunk.)  Indeed, a number of boreal mammals have evolved seasonal color changes (e.g. &lt;a href=&quot;http://srel.uga.edu/outreach/ecoviews/ecoview130106.htm&quot; rel=&quot;nofollow&quot;&gt;http://srel.uga.edu/outreach/ecoviews/ecoview130106.htm&lt;/a&gt; ), having darker summer colors (like their more southerly relatives), but turning white in winter.  That suggests that the benefits of camouflage strongly outweigh any possible benefit from solar heat gain.&lt;/p&gt;&#xA;" OwnerUserId="11736" LastEditorUserId="331" LastEditDate="2014-12-31T00:25:04.993" LastActivityDate="2014-12-31T00:25:04.993" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26265" PostTypeId="2" ParentId="26258" CreationDate="2014-12-29T20:03:28.087" Score="10" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Operon&quot; rel=&quot;nofollow noreferrer&quot;&gt;Operons&lt;/a&gt; were once thought to appear only in prokaryotes (and viruses of prokaryotes), but there are now known to be a number examples in eukaryotic organisms. These are mostly seen in nematodes and insects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally an operon is a functional DNA unit which contains a cluster of genes which are regulated by one promoter/repressor element and which are transcribed together. These are genes which functionally work together in a close context. A good example for this is the &lt;a href=&quot;https://en.wikipedia.org/wiki/Lac_operon&quot; rel=&quot;nofollow noreferrer&quot;&gt;lac operon&lt;/a&gt; in bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In prokaryotes the expression of the operon leads to &lt;a href=&quot;https://en.wikipedia.org/wiki/Messenger_RNA#Monocistronic_versus_polycistronic_mRNA&quot; rel=&quot;nofollow noreferrer&quot;&gt;polycistronic&lt;/a&gt; (multiple open reading frames on the same transcript) mRNA, which is then translated into proteins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Operons in eukaryotes are also gene clusters (often of functional closely related proteins), which are regulated by one regulatory unit (promoter). See figure 1 from reference 1:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UMqU1.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are different ways of mRNA arising from this phenomenon. First the mRNA can be dicistronic and most likely has internal ribosome entry sites (IRES) which allows the initiation (or re-initiation) of the translation of the second gene. Another possibility is the cleavage of the primary mRNA strand into two (or more) monocistronic mRNAs. And finally it is also possible that the dicistronic transcript is alternatively spliced to get different (monocistronic) mRNAs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in the details of eukaryotic operons, I strongly recommend reading at least the first reference (and probably also following up some of the related citations (on the right on the NIH website)).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/15642184&quot; rel=&quot;nofollow noreferrer&quot;&gt;Blumenthal, T. (2004). Operons in eukaryotes. Briefings in Functional Genomics, 3(3), 199-211.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.551.4059&amp;amp;rep=rep1&amp;amp;type=pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pi, H., Lee, L. W., &amp;amp; Lo, S. J. (2009). New insights into polycistronic transcripts in eukaryotes. Chang Gung Med. J, 32, 494-498.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="46609" LastEditDate="2020-01-15T20:03:10.357" LastActivityDate="2020-01-15T20:03:10.357" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="26266" PostTypeId="1" CreationDate="2014-12-29T20:57:51.800" Score="5" ViewCount="39" Body="&lt;p&gt;I've been taking a few walks in the countryside in Scotland and England this winter (end of December 2014). Some parts of England haven't had &lt;em&gt;any&lt;/em&gt; frosts yet, which is very unusual, and it's been generally quite warm since summer ended.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My friends and I agree that there's quite a lot of stuff putting out shoots and buds, as if it's April already. I can imagine that this means a lot of small fragile plants could get killed if a hard frost comes in the next few weeks. If so, it seems natural to expect that next summer will be marked by an absence of these plants, and, being dead, they won't put out seeds or otherwise reproduce for next year. In other words, we're expecting some species to experience localised die-off.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this plausible or are we just imagining it? If it's actually happening, is it something to actually be worried about? i.e. will a large portion of the seeds/shoots/buds/whatever refrain from growing even if some are being tricked by the mild winter, or will they be cold-resistant if they're coming up now, or is some other mechanism going to make it all okay? Alternatively, is this winter likely to trigger a large ecological change?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realise this question doesn't single-out any particular species for attention, and perhaps it's too much of an open question for StackExchange's taste, but I'd very much appreciate some insight into how fragile or robust is the distribution of British plant life when the weather is abnormal, as it is right now.&lt;/p&gt;&#xA;" OwnerUserId="3511" LastActivityDate="2014-12-29T21:18:43.050" Title="Is there a risk of localised die-off when plants bud too early?" Tags="&lt;ecology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26267" PostTypeId="2" ParentId="26266" CreationDate="2014-12-29T21:03:14.377" Score="2" Body="&lt;p&gt;If you're talking about shoots or buds coming out of individual seeds, then those plants are probably doomed. Most seeds are &quot;designed&quot; as one-shot delivery packages. In this case, they'll bud, be killed off by a frost at some point during the winter, and then be spent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a perennial plant like a tree that buds year after year, the impact of an early blooming will depend on the species. As per a Q&amp;amp;A from Cornell (&lt;a href=&quot;http://www.gardening.cornell.edu/warm_winter/warm_weather.pdf&quot; rel=&quot;nofollow&quot;&gt;Will Warm Winter Wither Plants?, 2007&lt;/a&gt;), most plants growing in a temperate climate (like that of Britain) will have experienced warm winters before and will have at least some evolutionary adaptations to help them deal with occasional aberrant weather. For example, even if you do see some fresh buds on a tree this time of year it is likely that the majority of its bud primordia (the parts of the plant that will someday become buds) have not developed. Although you won't see regrowth in the spring of most of the buds that opened early, you will see normal development of the buds that stayed dormant during the winter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the question of wider ecological change, one anomalous year isn't going to make a difference because, as you say, &lt;code&gt;a large portion of the seeds/shoots/buds/whatever refrain from growing even if some are being tricked by the mild winter&lt;/code&gt;. However, if a string of mild winters cause significant die-off year after year you would start to see changes in the ecosystem. It works the same way for many with loosing their hair...&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2014-12-29T21:18:43.050" LastActivityDate="2014-12-29T21:18:43.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26268" PostTypeId="2" ParentId="26251" CreationDate="2014-12-29T21:42:26.690" Score="2" Body="&lt;p&gt;In addition to camouflage, consider that during the colder parts of the year, when they need the heat the most, the nights are longer than the day.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Darker fur would radiate more heat away from the body than the lighter fur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it's possible that they did evolve the white fur for heat - but in their environment, the coldest part of the year heat retention is more critical than heat gathering, and this would bias towards white fur, not black.&lt;/p&gt;&#xA;" OwnerUserId="5940" LastActivityDate="2014-12-29T21:42:26.690" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26269" PostTypeId="1" AcceptedAnswerId="26279" CreationDate="2014-12-29T21:53:54.407" Score="5" ViewCount="7943" Body="&lt;p&gt;I knew that mature red blood cells (RBCs) lacked nuclei, but I wasn't aware until just now that they also lacked ribosomes and mitochondria. Most cells in the human body all contain a common laundry list of housekeeping proteins and RNAs (including mitochondrial proteins and ribosomal RNAs), but I guess RBCs lack a number of them. Do they still have all of the other organelles? Obviously hemoglobin (and to a lesser extent carbonic anhydrase) makes up a large portion of the dry weight of RBCs, but are other proteins still present? If so, what are their relative abundances?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, do red blood cells have any of the normal metabolic (i.e. ATP producing) proteins? Obviously they don't have any of the TCA cycle proteins, but do they still have the glycolysis ones?&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="3340" LastEditDate="2014-12-30T08:32:36.550" LastActivityDate="2014-12-30T12:40:18.657" Title="Besides hemoglobin, what proteins are present in red blood cells?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;hematology&gt;&lt;red-blood-cell&gt;&lt;human-physiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26271" PostTypeId="1" AcceptedAnswerId="26272" CreationDate="2014-12-30T00:12:46.980" Score="3" ViewCount="47" Body="&lt;p&gt;I was thinking about crazy uses for engineered bacteria. Nano-assembly of Graphene seems like a potentially excellent target for the technology. Have any research/full-blown labs worked on this? Any papers on it?&#xA;What would be some of the difficulties?&lt;/p&gt;&#xA;" OwnerUserId="8619" LastEditorUserId="8619" LastEditDate="2015-03-13T03:05:54.003" LastActivityDate="2015-03-13T03:05:54.003" Title="Has any research lab done serious work to engineer new bacteria which assemble graphene wafers?" Tags="&lt;recombinant&gt;&lt;protein-engineering&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26272" PostTypeId="2" ParentId="26271" CreationDate="2014-12-30T00:47:02.650" Score="5" Body="&lt;p&gt;Surprisingly, the answer is yes. In 2012 Tanizawa et al published a paper titled &lt;a href=&quot;http://iopscience.iop.org/1742-6596/352/1/012011&quot;&gt;Microorganism mediated synthesis of reduced graphene oxide films&lt;/a&gt;. The gist of it is that most of the steps (including the structuring of the graphene sheet) were carried out with chemical synthesis, but a final reduction step from graphene oxide to graphene was carried out using bacteria from a local river.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably not quite what you were thinking of, but I imagine this is the closest you'll get for right now.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-12-30T00:47:02.650" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26273" PostTypeId="1" AcceptedAnswerId="26278" CreationDate="2014-12-30T02:24:17.507" Score="2" ViewCount="741" Body="&lt;p&gt;I'm a little embarrassed to ask but when you have for example four degenerate primers and the end protocol says that the final primer concentration should be 10 µM working stock, should you make the primers 10µM total (2.5 µM each) or 10 µM for each degenerate primer?&lt;/p&gt;&#xA;" OwnerUserId="3887" LastEditorUserId="3340" LastEditDate="2014-12-30T05:44:08.803" LastActivityDate="2014-12-30T05:58:22.890" Title="Concentration of degenerate primers should you dilute to?" Tags="&lt;molecular-biology&gt;&lt;pcr&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26274" PostTypeId="1" CreationDate="2014-12-30T02:43:19.533" Score="6" ViewCount="362" Body="&lt;h2&gt;Short summary&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I am a researcher in origins of life, a field that deals with hypotheses about evolutionary processes that took place before LUCA (the last universal common ancestor), and with the chemical processes that gave rise to life and evolution in the first place. This is very hard to study empirically, and as a consequence there are many competing hypotheses. However, I've noticed that many of them have a common form, which I will describe below. My question is about whether hypotheses of this particular form exist (and have been investigated, for example using phylogenetic methods) in post-LUCA evolutionary biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My reason for asking is that my colleagues and I were not able to think of a good example. If no example is known in post-LUCA evolutionary biology then it casts doubt on the plausibility of this type of hypothesis in pre-LUCA evolution. I suspect this is the case, and therefore my ideal answer would provide me with bibliographic material to support a claim that there just aren't any good examples of this in evolutionary biology. However, I would also be happy to be proven wrong with a really good example.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Longer explanation&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Hypotheses regarding the origins of life are difficult to test empirically, because phylogenetic methods can give us little direct evidence about anything before LUCA, and because there are no fossils dating from that time. (The entirety of Earth's surface has since been replaced by plate tectonics.) Consequently there are a number of competing hypotheses that differ from one another in almost every way. However, I've noticed that many of them have a common form: they say that &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;one or more of the features of a modern (i.e. post-LUCA) cell were originally provided by an external mechanism, in the form of abiotic chemical processes that took place in some very specific microenvironment, and&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;evolution eventually provided a solution that very closely echoed the one that had originally been provided by the environment.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Point (1) seems relatively easy to satisfy in an evolutionary scenario; it's point (2) that I'm specifically interested in. The two most popular hypotheses in the field both have this form:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Some forms of the The &lt;a href=&quot;https://en.wikipedia.org/wiki/RNA_world_hypothesis&quot; rel=&quot;nofollow&quot;&gt;RNA-World hypothesis&lt;/a&gt; hold that originally, RNA nucleotides were produced by purely chemical processes in the environment, and that life evolved from self-replicating RNA molecules made up from these abiotically-produced monomers. Later, life evolved a cellular metabolism by which it could construct its own RNA monomers. This satisfies point (2) because it says that the environment provided RNA rather than some other heteropolymer with catalytic properties; the evolutionary solution echoes the environmental one in that it uses the same complex molecule.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wächterschäuser's &lt;a href=&quot;https://en.wikipedia.org/wiki/Iron%E2%80%93sulfur_world_theory&quot; rel=&quot;nofollow&quot;&gt;Iron-Sulphur World&lt;/a&gt; theory, and many of its descendants, including Russel's &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2442388/&quot; rel=&quot;nofollow&quot;&gt;alkaline vent theory&lt;/a&gt;, hold that the reductive tricarbolic acid cycle (rTCA cycle, aka reverse citric acid cycle) was originally catalysed by mineral surfaces. This enabled the formation of the first cells, which eventually evolved enzymes that could be used to catalyse the rTCA cycle without the mineral catalysts. This satisfies point (2) because it says that the first evolved solution used essentially the same chemical pathway as the one provided by the environment, just with different catalysts.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;(Not all hypotheses in origins of life have this form. Some versions of the RNA World theory hold that RNA-based life was preceded by life based on some other heteropolymer, for example. But the hypotheses described above are very popular.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From an evolutionary biology point of view, point (2) seems rather an odd feature for a hypothesis to have. Evolution is great at producing novel solutions to problems, but to my knowledge it isn't good at copying old ones. (Mimicry doesn't provide a counterexample to this, since it's about appearance rather than mechanism, and often the mimic produces the same visual effect through a very different mechanism. For example, although the treehopper Cyphonia clavata mimics the outward appearance of an ant, it does so not by being anatomically similar to an ant but by &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0960982211004222&quot; rel=&quot;nofollow&quot;&gt;having a face on its butt&lt;/a&gt;.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consequently I'm looking for known examples from evolutionary biology that satisfy both point (1) and point (2). That is, I'm looking for examples where a species originally relied on some relatively complex process in its environment, and became less dependent on its environment &lt;em&gt;by evolving a mechanism that closely echoes the one originally provided by the environment&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example that might fit the bill would be a species that was originally unable to produce a key metabolite (e.g. an amino acid), but then later evolved the ability to produce the metabolite for itself. Evidence for this might be constituted by finding a species that produces the metabolite using a novel set of proteins, indicating that the capability to produce the metabolite was lost and then re-evolved. It would make an even better example if the novel proteins catalyse substantially the same chemical pathway that other species use to produce the same metabolite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It may be that no good examples of this exist, which is actually better for me than if they do. More than any particular example, the main thing I want to know is whether ideas along these lines have been discussed in evolutionary biology at all (perhaps outside the context of the origins of life), and if so where I can find the literature on it.&lt;/p&gt;&#xA;" OwnerUserId="3347" LastEditorUserId="3347" LastEditDate="2015-01-05T03:40:07.127" LastActivityDate="2015-01-06T09:35:32.187" Title="Are there known examples where an evolved mechanism &quot;echoes&quot; one originally provided by the environment?" Tags="&lt;evolution&gt;&lt;abiogenesis&gt;" AnswerCount="4" CommentCount="15" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26276" PostTypeId="2" ParentId="1133" CreationDate="2014-12-30T04:56:11.787" Score="9" Body="&lt;p&gt;I don't agree with the accepted answer which seem to assume that food is chewed. I don't think that can be assumed if generally talking about animals and choking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in addition to Larry's statement of dogs and cats:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fish regularly chokes on prey.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6SFdc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Birds can choke.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/qjrPC.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.businessinsider.com/dolphins-are-choking-to-death-on-fish-2013-6&quot; rel=&quot;noreferrer&quot;&gt;Even dolphins choke&lt;/a&gt;:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/PiA2E.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9124" LastEditorUserId="9124" LastEditDate="2014-12-30T07:09:54.687" LastActivityDate="2014-12-30T07:09:54.687" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26277" PostTypeId="1" CreationDate="2014-12-30T05:53:19.537" Score="18" ViewCount="1249" Body="&lt;p&gt;I have a general interest in complex adaptive systems and I have found that nature and the organisms within it is a perfect natural case of a rich adaptive system with a lot of possibilities for gaining insight in general about the nature of complex adaptive systems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My mind accidentally started thinking about the common human feeding pattern breakfast-lunch-dinner and I sought reference points in nature, realizing that I'm not aware of any specific cases where the feeding pattern of animals other then humans follow a distinct pattern, in contrast to a constant, stochastic or mainly opportunistic search for food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of humans there is probably a very strong cultural cause for our very distinct feeding pattern, but that is not necessarily to say that these patterns &lt;em&gt;only&lt;/em&gt; can occur in species with a highly developed culture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does the scientific body of observations look like here? Is there any research or empirical observations about the feeding pattern of animals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, I would of the top of my head assume that some common reasons for these patterns to develop could be connected to e.g. the 24h circadian rhythm, dependencies to availability of food, or internal dependencies on behavioural organization in social species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course it's likely that many organisms do not have the luxury of spending a significant time on other activities then acquiring food, but nevertheless we can see that some animals have evolved into a situation where they don't have to constantly be in the search for food, but instead can spend time on other activities increasing their fitness, like engaging in social interactions, searching for and seducing sexual mates, exploring their environment and migrating, building nests and so on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To clarify what kind of observations I'm imagining could happen, take these &lt;strong&gt;speculative&lt;/strong&gt; examples: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Some species of birds have a significantly higher feeding activity in the morning, where they after a night of inactivity have depleted their daily energy resource and when the insects, their main source of food, starts to activate after a cold night and are still cold and slower/easier prey. After this the birds only have an opportunistic approach to feeding which is enough to satisfy their energy need, and they spend more energy on pruning, calling for potential mates and engaging in territorial battles. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many primates engage in collective feeding sessions where they as a group travel to a known area rich with food where they spend a couple of hours before they retreat back to a different location for socializing and digesting the food. One reason for this behaviour can be that there is a high risk of predation at these food-rich areas, as the predators learn that these places are frequently visited by prey.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Feline predators on the savannah are usually concentrating their hunting in the night as the darkness gives them an advantage of stealth and surprise. This is why they in daytime instead spend a considerable amount of time on resting, engaging in activities regarding social hierarchies, order and bonding with the pride, while most often only opportunistically engaging in hunting.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Do we have a body of knowledge here? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While it would be close to hand to start trying making lists of observations like this, which certainly would be interesting in itself, the intention of this question is to get a &lt;strong&gt;good overview on the subject&lt;/strong&gt;. Are patterns like these common or uncommon? In the cases where they are found, what are the common factors and what can be identified as the underlying causes?&lt;/p&gt;&#xA;" OwnerUserId="9124" LastEditorUserId="9124" LastEditDate="2015-01-03T03:35:13.410" LastActivityDate="2019-02-21T01:40:56.497" Title="Do species other than humans have distinct daily feeding patterns?" Tags="&lt;zoology&gt;&lt;food&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="10" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26278" PostTypeId="2" ParentId="26273" CreationDate="2014-12-30T05:58:22.890" Score="2" Body="&lt;p&gt;You can just add 2µl from each working stock (10µM) to your PCR mix of 20µl.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can check &lt;a href=&quot;http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=725&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; protocol. &#xA;&lt;br&gt;&lt;strong&gt;Caution&lt;/strong&gt;: The author has used $l$ instead of $\mu l$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He uses 5µl of each primer (20µM) in a 50µl reaction. This is double of what I mentioned. IMO it is best to try with a lower concentration and then increase it if necessary. Excess primer concentration can give rise to some nonspecific binding and amplification if the primers are not perfectly designed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://stanxterm.aecom.yu.edu/wiki/index.php?page=Degenerate_primer_design&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; site:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Using degenerate primers&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Because a degenerate primer is really a mix of different primers, only&#xA;  a fraction of the degenerate 'primer' will actually work in the PCR.&#xA;  One would therefore need to increase the primer concentration in PCR,&#xA;  sequencing reactions, etc. If a primer is 8-fold degenerate, the&#xA;  concentration should be raised 4-8-fold, and so on. However, for&#xA;  higher degeneracies, e.g., 64-fold, one cannot increase the primer&#xA;  concentration 64-fold and would have to try their luck with a&#xA;  5-10-fold increase only.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-30T05:58:22.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26279" PostTypeId="2" ParentId="26269" CreationDate="2014-12-30T06:26:51.160" Score="8" Body="&lt;p&gt;Reticulocyte stage is when the ribosomes are still present and after that no new protein synthesis occurs. However RBCs have a lot of proteins and major proteins other than haemoglobin are cytoskeletal proteins and ion channels/pumps (In fact, cytoskeletal proteins are more abundant than haemoglobin). It is the Na&lt;sup&gt;+&lt;/sup&gt;-K&lt;sup&gt;+&lt;/sup&gt;-ATPase that consumes most ATP. As you correctly identified the RBCs produce ATP via glycolysis and glycolytic enzymes are also present. Note that deficiency of pyruvate kinase leads to haemolytic anaemia. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a detail on the proteins present in human RBSs, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14963112&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper. They have studied the RBC proteome by ion-trap MS. The top 5 proteins (from &lt;a href=&quot;http://www.mcponline.org/content/3/5/501/T1.expansion.html&quot; rel=&quot;nofollow&quot;&gt;Table-1&lt;/a&gt;) are:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;b&gt;No.    Protein description              Molecular mass (Da)    Gi Number    Sequence     No. of identified &#xA;                                                                           coverage(%)      peptides&lt;/b&gt; &#xA;&lt;hr&gt;1      Spectrin α chain, erythrocyte         279,916.5          1174412       48.0           77*&#xA;2      Spectrin β chain, erythrocyte         246,468.1          17476989      48.0           76*&#xA;3      Ankyrin 1, splice form 2              206,067.9          105337        45.0           55&#xA;4      Ankyrin 1, isoform 4, erythrocytic    203,416.6          10947036      45.0           50&#xA;5      Ankyrin 1, isoform 2, erythrocytic    189,011.2          10947042      46.0           48&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Although in this table you cannot find glycolytic enzymes other than GAPDH and Aldolase, but other enzymes are also present. They are perhaps not detected in this experiment because of overwhelming levels of structural proteins. You can check &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC291039/pdf/jcinvest00315-0067.pdf&quot; rel=&quot;nofollow&quot;&gt;this old paper&lt;/a&gt; that shows a study of different glycolytic enzymes from erythrocytes. It is also to be noted that the glycolytic pathway flux is not as smooth as in other cells. So some accumulated metabolites are probably exported out of the cells to keep the flux smooth&lt;sup&gt;[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1856577&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt; &lt;em&gt;Full text not found&lt;/em&gt;]&lt;/sup&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2014-12-30T12:40:18.657" LastActivityDate="2014-12-30T12:40:18.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26281" PostTypeId="2" ParentId="26261" CreationDate="2014-12-30T07:56:16.407" Score="0" Body="&lt;p&gt;In lay man terms you need your DNA to remain intact and protected. so instead of shipping it to the cytoplasm where a lot can happen to it, the cell makes an intermediate mRNA. if anything does wrong with mRNA, the cell can discard it and make another copy and after translation the copy of mRNA is also discarded.You also have the amplification; instead of making one protein from one gene on a DNA strand, and then one more and the another, we can just make a bunch of copies of mRNA and send them to the nucleus where we can make as many proteins as we need. by doing this there is minimal manipulation of the original DNA strand and the cell get a lot of product over a short period.&lt;/p&gt;&#xA;" OwnerUserId="11747" LastEditorUserId="3340" LastEditDate="2014-12-30T08:02:10.200" LastActivityDate="2014-12-30T08:02:10.200" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26282" PostTypeId="2" ParentId="26251" CreationDate="2014-12-30T08:18:27.020" Score="-1" Body="&lt;p&gt;Well, Polar bears do have black skin; But, living in the harsh arctic conditions they've adapted several traits such as thick layer of blubber, wide paws etc. But their most peculiar trait is having a &lt;em&gt;white fur coat;&lt;/em&gt; unlike other bears, polar bears have evolved to have white fur with hollow hairs which easily allows their black skin to absorb the radiations from the sun. So there's no problem with the heat intake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the reason behind their white fur lies in their quest to food. The white fur enables them to easily hide/blanket in their surrounding (the &lt;em&gt;white&lt;/em&gt; masses of snow) i.e. it helps them in camouflage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And, I guess that's it! Thanks!&lt;/p&gt;&#xA;" OwnerUserId="11746" LastEditorUserId="5144" LastEditDate="2015-03-24T21:47:55.913" LastActivityDate="2015-03-24T21:47:55.913" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26284" PostTypeId="2" ParentId="26251" CreationDate="2014-12-30T11:21:08.527" Score="1" Body="&lt;p&gt;Although black is a better absorber of (heat) radiation, it is also a better emitter too. As Polar bears live in a cold environment, having black hair would cause them to radiate their body heat away more quickly. Their colour helps them to retain heat better - dark objects equilibrate to the temperature of their surrounding faster, lighter objects more slowly. If they were darker, they would require more food to survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their black skin is irrelevant as the light has already been scattered/reflected away by the white/colourless hairs - as they look white, it's the reflected light that you are seeing.&lt;/p&gt;&#xA;" OwnerUserId="11750" LastActivityDate="2014-12-30T11:21:08.527" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26285" PostTypeId="2" ParentId="26274" CreationDate="2014-12-30T11:57:26.733" Score="4" Body="&lt;p&gt;It was getting long for a comment:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;&lt;p&gt;A species that was originally parasitic, but then evolved to survive     independently of its host by independently evolving the&#xA;  same       metabolic functions&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;A predator that originally relied on its prey to synthesise some vital metabolite, but later evolved the ability to produce the&lt;br&gt;&#xA;  missing metabolite for itself through a similar pathway&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A parasite is generally evolved from a free living form. It has a reduced genome and cannot synthesize many vital nutrients. It is unlikely that it would acquire a gene that would enable it to live freely. A parasite, in general does not require to synthesize nutrients; so it is not under any pressure to acquire that function as long as its host is surplus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Same is in the case of predators.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, in higher organisms it is difficult to conjure a new gene; it is a slow process and happens via gene modification. However, in lower (basically unicellular) organisms lateral gene transfers are much easier and it is possible that they can acquire new metabolic pathways from other organisms. Have a look at &lt;a href=&quot;http://www.nature.com/nature/journal/v405/n6784/full/405299a0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; article. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In lower eukaryotes endosymbiosis, is another way by which new metabolic pathways can be acquired relatively fast. A diatom called &lt;em&gt;Rhopalodia gibba&lt;/em&gt;, which already had a red alga derived secondary plastid, acquired another cyanobacteria derived green plastid for nitrogen fixation. You can have a look at &lt;a href=&quot;https://biology.stackexchange.com/questions/17676/a-photosynthesizing-mouse/17682#17682&quot;&gt;this&lt;/a&gt; post too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For your question on independent acquisition of traits; almost all metabolic pathways are evolved like that only. Enzymes isoforms that can bind to a slightly different substrate gave rise to another step in the pathway. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also possible to &lt;strong&gt;engineer&lt;/strong&gt; a new trait:&lt;br&gt;&#xA;Nucleotide analogs have been created to make a 6-letter nucleotide system which can be replicated by PCR&lt;sup&gt;[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427765/&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;http://www.pnas.org/content/109/30/12005&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;]&lt;/sup&gt;. Earlier this year this was demonstrated in-vivo&lt;sup&gt;[&lt;a href=&quot;http://www.nature.com/nature/journal/v509/n7500/full/nature13314.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;3&lt;/a&gt;]&lt;/sup&gt;. It has been shown that these new nucleotides can also be transcribed (see cross references in &lt;sup&gt;[3]&lt;/sup&gt;).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2014-12-30T13:11:28.953" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26286" PostTypeId="2" ParentId="26274" CreationDate="2014-12-30T13:02:16.967" Score="2" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment#Evolution_of_aerobic_citrate_usage_in_one_population&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;E. coli&lt;/em&gt; long term evolution experiment&lt;/a&gt; showed that &lt;em&gt;E. coli&lt;/em&gt; had evolved a function (the metabolism of citrate) which was not required in the ancestral environment, but which evolved naturally and was selected for in this new artificial environment. AFAIK, this is the only example of a function that has been observed naturally evolving under controlled conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason we are unlikely to see any metazoans evolving new metabolic pathways is due to the fact that they have long lifespans and therefore reproduction times. However, as WYSIWYG has already mentioned, almost all metabolic pathways evolved that way, it is just hard to observe due to the long time spans involved.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2014-12-30T13:02:16.967" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26287" PostTypeId="1" CreationDate="2014-12-30T13:52:20.500" Score="3" ViewCount="453" Body="&lt;p&gt;As far as I know proteins are built by sequentially reading triplets of nucleotides.&lt;br&gt;&#xA;But if at a certain point a nucleotide is inserted in the sequence, the following sequence of triplets is completely different.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;For example:&#xA;&#xA;AATACGGTACCATTA ...&#xA;&#xA;AAT ACG GTA CCA TTA ...&#xA;&#xA;But inserting a nucleotide B at second place we get&#xA;&#xA;ABA TAC GGT ACC ATT ...&#xA;&#xA;Which is completely different. &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;However I know from theory that a single nucleotide insertion is not dangerous in most cases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could someone clarify my mind about this?&lt;/p&gt;&#xA;" OwnerUserId="5642" LastEditorUserId="6" LastEditDate="2014-12-30T14:14:29.407" LastActivityDate="2014-12-30T14:14:29.407" Title="Why isn't the insertion of a single nucleotide destructive for DNA?" Tags="&lt;genetics&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26288" PostTypeId="2" ParentId="26287" CreationDate="2014-12-30T14:14:10.920" Score="9" Body="&lt;p&gt;A single &lt;strong&gt;substitution&lt;/strong&gt; can often be silent, or at least not impact the structure and function of the resulting protein in a significant way. But what you describe is a frameshift, and that is one of the most destructive mutations. It will completely change the sequence of the protein after this mutation and disrupt the function of those parts of the protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Insertions or deletions that result in a frameshift are absolutely destructive mutations.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2014-12-30T14:14:10.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26292" PostTypeId="2" ParentId="26251" CreationDate="2014-12-30T16:19:29.580" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Why then didn't they evolve a black color to absorb more heat?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This assumes that evolution is an active process, working by organisms' will or need. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do not forget that the theory of evolution works from generation to generation, by random (imperfect and chaotic) mutations, most of which are unfavorable. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The polar bears did not evolve a black color because they can't decide that. If you believe in evolution, and you believe that a black color would draw more heat, increasing the animal's chances of survival over its white peers (so much that the white peers would eventually die off), then we are simply waiting for the black color to come around. Evolution is never finished.&lt;/p&gt;&#xA;" OwnerUserId="11754" LastActivityDate="2014-12-30T16:19:29.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26293" PostTypeId="1" CreationDate="2014-12-30T21:57:25.973" Score="4" ViewCount="79" Body="&lt;p&gt;I have noticed that when I eat something sweet, then afterwards, I eat something else that is sweet, the second sweet food is not as sweet as it usually is. I am pretty sure many others have a similar experience before too. Why does this happen?&lt;/p&gt;&#xA;" OwnerUserId="10401" LastActivityDate="2014-12-30T22:50:34.057" Title="Relative sweetness" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;senses&gt;&lt;taste&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26294" PostTypeId="2" ParentId="26293" CreationDate="2014-12-30T22:28:09.117" Score="3" Body="&lt;p&gt;What you describe is an example of neural adaptation, whereby neural response to a consistent stimuli becomes reduced with repetition. This occurs not just with sweetness (as shown empirically in &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/dev.20000/abstract&quot; rel=&quot;nofollow&quot;&gt;this study on sucrose consumption by rats&lt;/a&gt;), but with many other types of stimuli (the feeling of clothes on your skin, the particular smell of your own home) as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, our senses are tuned to detect relative changes in our environment rather than absolute values. For example, if I were to place an unmarked 10 kg weight in one of your hands and a 12 kg weight in your other hand, you might have some trouble telling me what the exact mass of each weight is. You would have no trouble whatsoever telling me which weight was heavier. Neural adaptation allows us to maintain the ability to make these kinds of distinctions over a wide range of stimuli intensities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no scientific consensus as to the exact mechanism of neural adaptation (and there probably isn't just one), but there are many candidate processes at the level of individual neurons, such as long term depression. Grill-Spector et al published a widely cited paper a few years ago called &lt;a href=&quot;http://vpnl.stanford.edu/papers/Grill-SpectorTICS06.pdf&quot; rel=&quot;nofollow&quot;&gt;&quot;Repetition and the brain: neural models of stimulus-specific effects&quot;&lt;/a&gt; in which they put forth several potential mechanistic models of neural adaptation.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2014-12-30T22:50:34.057" LastActivityDate="2014-12-30T22:50:34.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26295" PostTypeId="2" ParentId="26251" CreationDate="2014-12-30T23:46:34.780" Score="0" Body="&lt;p&gt;I think an important point hasn't been mentioned yet.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why then didn't they evolve a black color&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;The changes introduced by evolution initially are random&lt;/em&gt;.  Only the persistence of those changes over generations can be thought of in a &quot;smart&quot; way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Technically, evolution can lead to some things getting worse!  For example, if mutations improve a creatures eye-sight but at the same time worsen it's hearing, both traits may end up surviving assuming the improved eye-sight makes more of a difference than the worsened hearing.&lt;/p&gt;&#xA;" OwnerUserId="3906" LastActivityDate="2014-12-30T23:46:34.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26298" PostTypeId="1" AcceptedAnswerId="26299" CreationDate="2014-12-31T02:02:02.393" Score="6" ViewCount="605" Body="&lt;p&gt;In the January Issue of SciAm (discussing Haemophilia):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When damage occurs to blood vessels, exposure of the blood to collagen in the cell walls and material released by the cells triggers the activation of clotting factors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I read the original in print, but it is available online &lt;a href=&quot;http://www.scientificamerican.com/article/a-primer-on-haemophilia-graphic/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This seems to imply that animal cells (in this example, those of humans) have cell walls.  I sometimes see similar implications in other resources.  However, in elementary biology, one is taught that animal cells never have cell walls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, my question: &lt;strong&gt;Are references to animal cell cell walls (such as the above, for human animal cells) simple mistakes--or are they exceptions to a generalization?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="9804" LastEditorUserId="9804" LastEditDate="2014-12-31T10:56:31.923" LastActivityDate="2018-03-14T16:07:39.547" Title="Are There Exceptions to Animal Cells not Having Cell Walls?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26299" PostTypeId="2" ParentId="26298" CreationDate="2014-12-31T02:12:02.810" Score="5" Body="&lt;p&gt;Humans, as well as the rest of the metazoans (i.e. animals), absolutely do not have cell walls. What humans do have is extracellular matrix (ECM), which is the sort of fibrous, sort of gel-like material in which cells in many of the tissues are embedded. Collagen is a major component of ECM.&lt;/p&gt;&#xA;&lt;p&gt;From the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26810/&quot; rel=&quot;noreferrer&quot;&gt;old copy of &lt;em&gt;Alberts&lt;/em&gt; that is hosted on the NCBI website&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Tissues are not made up solely of cells. A substantial part of their volume is extracellular space, which is largely filled by an intricate network of macromolecules constituting the extracellular matrix (Figure 19-33). This matrix is composed of a variety of proteins and polysaccharides that are secreted locally and assembled into an organized meshwork in close association with the surface of the cell that produced them...&lt;/p&gt;&#xA;&lt;p&gt;Two main classes of extracellular macromolecules make up the matrix: (1) polysaccharide chains of the class called glycosaminoglycans (GAGs), which are usually found covalently linked to protein in the form of proteoglycans, and (2) fibrous proteins, including collagen, elastin, fibronectin, and laminin, which have both structural and adhesive functions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="784" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-31T03:14:42.280" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26302" PostTypeId="2" ParentId="3448" CreationDate="2014-12-31T11:44:06.303" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;If I were discussing a SNP of FOO that gives rise to foo in a tumor&#xA;  cell of an organism, I wouldn't say that the organism has foo, but I&#xA;  might say that the tumor has it.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can call it a somatic mutation. See &lt;a href=&quot;http://www.nature.com/nature/journal/v446/n7132/full/nature05610.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper. They report such mutations in cancer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can use the term like this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Carcinoma tissue had a &lt;strong&gt;somatic mutation&lt;/strong&gt; in &lt;strong&gt;XYZ&lt;/strong&gt; oncogene, thereby making it constitutively active.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If I were discussing a chimeric or mosaic organism in which some&#xA;  fraction of the chimera had foo and the other fraction had FOO&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In this case you can say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;The organism is chimeric for gene-X, expressing variants X1 and X2&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://atvb.ahajournals.org/content/27/2/380.full&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Effects of AngII-Infusion Into LDL Receptor−/− Mice That Were Chimeric&#xA;  for AT1a Receptors&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-31T11:44:06.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26303" PostTypeId="2" ParentId="17149" CreationDate="2014-12-31T12:03:45.193" Score="3" Body="&lt;p&gt;The primary difference between a benign tumor and a malignant tumor is that the former cannot metastasize; therefore they remain within the tissue boundaries.They grow slowly and are are not very de-differentiated thereby retaining some of the tissue organization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another point to be considered is that benign tumors do not cause vascularization (formation of blood vessels in the tumor tissue; triggered by secretion of VEGF), which also limits its growth.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2014-12-31T12:03:45.193" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="26304" PostTypeId="1" CreationDate="2014-12-31T15:53:07.887" Score="4" ViewCount="1549" Body="&lt;p&gt;Proteins are formed by stringing together different amino acids.  Different amino acids have different properties (such as being attracted to or repelled by water, positively or negatively charged, large, small, etc.).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I would like to know is if there are any rules or principles which determine how amino acids are strung together to form proteins?  If so, what are those rules and can anyone recommend any resources where I can learn more about this subject?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;MORE DETAILS&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me try and explain what I am trying to ask.  I understand that there are rules of grammar that I need to follow in order to put together a well formed English sentence.  I am wondering if there is something akin to that for stringing together amino acids in order to create a 'well-formed' protein. (I am NOT referring to how DNA codes for amino acids).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, imagine that I wanted to create a new protein and I had a pile of amino acids at my disposal.  It seems to me that if I understood the principles and rules by which amino acid chains work then I could know which amino acids to string together and the order in which to string them together in order to create the particular type of protein that I wish to create.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is similar to how I can string together letters and words to form well formed sentences or how I can string together well-formed sentences to create logical arguments.  There's a logic to how to form a sentence and a different logic for how to form an argument -- and it is possible to discern that logic by studying syntax and reasonable arguments.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume the same is true for proteins.  There must be some sort of logic or system for how amino acids are strung together -- some sort of connection between the 3-dimension, functional protein and the nature of the properties of the individual amino acids and how they are organized together.  What I am wondering is whether or not we have any idea what that system of logic is.&lt;/p&gt;&#xA;" OwnerUserId="11767" LastEditorUserId="11767" LastEditDate="2015-01-04T16:48:04.930" LastActivityDate="2016-10-24T05:15:51.763" Title="Are There Rules for How Proteins Are Formed?" Tags="&lt;proteins&gt;&lt;amino-acids&gt;&lt;protein-folding&gt;&lt;protein-structure&gt;" AnswerCount="5" CommentCount="9" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26306" PostTypeId="2" ParentId="26304" CreationDate="2014-12-31T18:07:23.457" Score="2" Body="&lt;p&gt;I suppose you are not asking how does DNA code for mRNA which has codons (sets of 3 nucleic acids) when read in the correct reading frame (where 3 base pairs each are read beggining from the start codon) a ribosome then translates this into protein... theres a lot more details then what I said... that is called translation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Translation_%28biology%29&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Translation_%28biology%29&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Afterwords the protein is folded into a 3d shape&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Folding_funnel&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Folding_funnel&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other stuff (other than amino acids) can be added, like a a lipid for anchoring into the membrane (GPI anchor or prenylation) or sugar (glycosylation) amoung other things, this is called post translational modification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Posttranslational_modification&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Posttranslational_modification&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;if you are asking about the evolution of proteins, here is another article:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Protein_family&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Protein_family&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;wikipedia can get pretty detailed, also there might not be a lot of pictures... lippincott's illustrated biochemistry has lots of great pictures... but it's a book for health science students, not very abstract/theoretical/philosophical so you won't get much on evolution of protein families among different life forms...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are asking which amino acids can go together and which stuff can't, I dunno, I'm not a biochemist...&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2014-12-31T18:59:29.453" LastActivityDate="2014-12-31T18:59:29.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26307" PostTypeId="2" ParentId="26304" CreationDate="2014-12-31T18:50:18.200" Score="3" Body="&lt;p&gt;I'm going to assume that you mean &quot;are there any rules for which amino acids can follow which amino acids in a protein?&quot; The answer is no. In terms of a protein's chemistry, there is no restriction on the amino acid sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, not all amino acid sequences will fold into a definite 3D structure, and not all amino acid sequences will be soluble in water. For these reasons some amino acid sequences cannot be produced via the standard &lt;em&gt;in vivo&lt;/em&gt; process (i.e. by a ribosome), but there's no reason they couldn't be produced through chemical synthesis.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2014-12-31T18:50:18.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26308" PostTypeId="1" AcceptedAnswerId="26310" CreationDate="2014-12-31T20:21:42.377" Score="11" ViewCount="785" Body="&lt;p&gt;Once upon a time, binomial nomenclature was expected to follow Latin rules: the genus had to be a noun and the species had to be an adjective that agreed with the genus according to Latin rules of adjectival agreement with the noun modified by it. That’s why we have species names like &lt;em&gt;sativus, sativa,&lt;/em&gt; and &lt;em&gt;sativum&lt;/em&gt; seen again and again, the exact form depending on the genus’s gender.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if knew a bit of Greek and Latin, you could figure out something about what binomials such as &lt;em&gt;Stegosaurus armatus&lt;/em&gt; or &lt;em&gt;Dodecatheon pulchellum&lt;/em&gt; might be about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Enter 2014, and with it such new binomials as the ponderous &lt;a href=&quot;http://en.wikipedia.org/wiki/Dreadnoughtus&quot;&gt;&lt;em&gt;Dreadnoughtus schrani&lt;/em&gt;&lt;/a&gt;.  That looks more like &lt;a href=&quot;http://en.wikipedia.org/wiki/Dog_Latin&quot;&gt;Dog Latin&lt;/a&gt; than Classical Latin: just tack a few Latinate-looking suffixes to words that cannot be decoded using any known roots from Greek or Latin.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I first read about it, I honestly thought somebody was making a bad joke. It’s not like the Greeks and Romans never thought of fearing nothing; one might imagine a taxon built out of actual classical roots — perhaps like &lt;i&gt;*Timendumnihil&lt;/i&gt; — would have been more universally understandable than the Dog-Latin form &lt;em&gt;Dreadnoughtus&lt;/em&gt; we’ve been stuck with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there no requirement that new taxa have classical forms?  Was there ever, and if so, when and why did this change?  Or, if there was not, then why did everybody seem to go along with the scheme for so long?&lt;/p&gt;&#xA;" OwnerUserId="8869" LastEditorUserId="8869" LastEditDate="2014-12-31T21:24:16.563" LastActivityDate="2014-12-31T21:35:58.107" Title="Dreadnoughtus: Why are new taxa named using Dog Latin?" Tags="&lt;taxonomy&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26310" PostTypeId="2" ParentId="26308" CreationDate="2014-12-31T21:35:58.107" Score="13" Body="&lt;p&gt;There is an International Commission on Zoological Nomenclature, to which submissions for new organisms' names is strongly recomended. The discoverer does have some leeway within this system if there is no Latin name that well-describes this species. Your example is one of many.&lt;/p&gt;&#xA;&lt;p&gt;Chapter 31, for example, clearly states:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;31.1.1. A species-group name, if a noun in the genitive case formed from a personal name that is Latin, or from a modern personal name that is or has been latinized, is to be formed in accordance with the rules of Latin grammar.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Examples. Margaret, if latinized to Margarita or Margaretha, gives the genitives margaritae or margarethae; similarly Nicolaus Poda, even though the name of a man, if accepted as a Latin name, gives podae; Victor and Hercules, if accepted as Latin names, give victoris and herculis; the name of Plinius, a Roman, even though anglicized to Pliny, gives plinii; Fabricius and Sartorius, if treated as Latin names, give fabricii and sartorii, but if treated as modern names give fabriciusi and sartoriusi; Cuvier, if latinized to Cuvierius, gives cuvierii.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;31.1.2. A species-group name, if a noun in the genitive case (see Article 11.9.1.3) formed directly from a modern personal name, is to be formed by adding to the stem of that name -i if the personal name is that of a man, -orum if of men or of man (men) and woman (women) together, -ae if of a woman, and -arum if of women; the stem of such a name is determined by the action of the original author when forming the genitive.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Example. Under this provision, the species-group names podai from Poda, victori from Victor, and cuvieri from Cuvier are admissible. The names puckridgei and puckridgi may be formed from Puckridge.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Similar rules apply for genus and family names.&lt;/p&gt;&#xA;&lt;p&gt;Since your example was a new genus and species, it didn't &amp;quot;fit&amp;quot; into previous categories (in the future, if and when similar discoveries are made that shed light on the genus' relation to others, the name can and will be changed accordingly, with or without the authors' approval).&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;According to the research team that discovered the taxon, the genus name Dreadnoughtus &amp;quot;alludes to the gigantic body size of the (which presumably rendered healthy adult individuals nearly impervious to attack)&amp;quot; and to the two dreadnought battleships of the Argentine Navy, the ARA Rivadavia and ARA Moreno. Thus, the genus name also honors the country (Argentina) in which Dreadnoughtus schrani was discovered. The name of the type species, schrani, was given in recognition of the American entrepreneur Adam Schran for his financial support of the project. - Wikipedia&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;A &amp;quot;good&amp;quot; or &amp;quot;useful&amp;quot; taxon is commonly taken to be one that reflects evolutionary relationships. Since this one does not, in a few decades, this name may well be gone.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2014-12-31T21:35:58.107" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26311" PostTypeId="2" ParentId="26251" CreationDate="2014-12-31T22:05:34.813" Score="1" Body="&lt;p&gt;This is a brief expansion on DrAlchemist's response; one that I intended to make myself, but saw that s/he had already covered the basics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To see that black is a better emitter of heat we have to leave biology and go to physics, specifically quantum mechanics, even more specifically black body radiation. Like most things, absorption and radiation are equally balanced when it comes to a given material/color. A white object is slow to absorb heat and a black object is quick to absorb heat, as we have likely all seen demonstrated in elementary school. What my teacher (and likely yours) did not mention is that the white object cools slowly when taken out of the sun, but the black object will cool much more quickly. Black heats up quickly, and radiates just as quickly when the temperature differential inverts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a mental exercise, consider an idealized object that absorbs electromagnetic energy perfectly, called a black body. Turn a heat lamp on it, and it will absorb all the heat it receives. Turn the lamp off and, as in the argument above, it will become a perfect emitter of the radiation it absorbed.&lt;/p&gt;&#xA;" OwnerUserId="11757" LastActivityDate="2014-12-31T22:05:34.813" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26312" PostTypeId="1" AcceptedAnswerId="26324" CreationDate="2014-12-31T23:11:55.753" Score="5" ViewCount="296" Body="&lt;p&gt;This is about devices like that sold by &lt;a href=&quot;http://www.foc.us/&quot; rel=&quot;nofollow&quot;&gt;foc.us&lt;/a&gt; that allows user to apply a small current on a specific part of the forehead.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the sake of this question I use the foc.us &quot;gamer&quot; model as example. This device has:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;a headset with two (moist)electrodes that are positioned on the forehead&lt;/li&gt;&#xA;&lt;li&gt;a controller unit that is used to apply a (selectable) current between 0.1mA - 2.0mA through the electrodes&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;[Update:] the electrodes have a surface area of 35mm x 35mm (they are 12mm thick).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to information received from the company this device is a &quot;micro current signal generator&quot; and can be operated in &quot;tDCS&quot; mode (I am not sure what &quot;tDCS&quot; means). The device has a timer so that it can be set to provide this current between 1 - 40 minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They sell this device with an (explicit or implicit) claim that is helps the wearer improve their ability to focus (on, for example, a game that the wearer is playing).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any known health benefits (such as improved ability to focus) or dangers (damage on the nerve system?) from applying a current on the forehead?&lt;/p&gt;&#xA;" OwnerUserId="11546" LastEditorUserId="9943" LastEditDate="2015-08-05T14:18:33.020" LastActivityDate="2015-08-05T14:18:33.020" Title="Are there any known health benefits / risks from milliampere current (0.1-2 mA) on forehead?" Tags="&lt;neuroscience&gt;&lt;psychology&gt;&lt;biomedical-engineering&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26313" PostTypeId="1" CreationDate="2014-12-31T23:38:13.110" Score="0" ViewCount="100" Body="&lt;p&gt;I had a question relating to chemistry and biology, so please tell me if this is suited better for the Chemistry website. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question was, if water dissolves salt by separating the two ions, the Na&lt;sup&gt;+&lt;/sup&gt; ion and the Cl&lt;sup&gt; -&lt;/sup&gt; ion, then why do we still taste salt in the water? The ions in the salt are still separated, so wouldn't the water not taste like salt?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Any help on fixing this question would be appreciated)&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="3340" LastEditDate="2015-01-02T04:23:13.697" LastActivityDate="2016-06-22T18:26:48.293" Title="Taste of salt water" Tags="&lt;biochemistry&gt;&lt;salt&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26315" PostTypeId="1" AcceptedAnswerId="26352" CreationDate="2015-01-01T00:10:25.183" Score="4" ViewCount="2920" Body="&lt;p&gt;Recently, I have been reading Janeway's immunobiology and had a question on immunoglobin A. I read that IgA activates the complement pathway using the Fab fragment of the IgA. How does IgA do that? I can't seem to find an information on that in  the book or online.&lt;/p&gt;&#xA;" OwnerUserId="10401" LastActivityDate="2015-11-23T18:40:28.410" Title="IgA complement activation" Tags="&lt;immunology&gt;&lt;antibody&gt;&lt;immunoglobin&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26316" PostTypeId="1" CreationDate="2015-01-01T00:57:40.837" Score="9" ViewCount="600" Body="&lt;p&gt;It is well known that sleep deprivation causes considerable discomfort in humans (and has even &lt;a href=&quot;https://en.wikipedia.org/wiki/Sleep_deprivation#Interrogation&quot;&gt;used as a form of torture&lt;/a&gt;), but nevertheless there have been &lt;a href=&quot;https://en.wikipedia.org/wiki/Randy_Gardner_%28record_holder%29&quot;&gt;people who went through protracted sleep deprivation&lt;/a&gt;, apparently with no long term consequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've noticed that sleep deprivation seems to trigger an intense sense of &quot;this is bad for me&quot; - yet given the apparent lack of ill effects (beyond the obvious) I cannot say whether this is merely anxiety over discomfort, as opposed to a genuine perception of physiological damage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What if you were to go without sleep for as long as possible, despite the discomfort? Is it possible to commit suicide in this way (and what would be the cause of death)? Would you fail because you eventually ignore whatever stimulus was preventing sleep, and sleep anyway? Would artificially counteracting the temporary debilitating physiological effects (such as loss of body temperature) allow you to survive sleep deprivation of arbitrary length?&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorDisplayName="user12874" LastEditDate="2015-01-10T17:16:50.597" LastActivityDate="2018-07-17T01:42:26.440" Title="What's the worst that can happen from too much sleep deprivation? Can you die?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;neuroscience&gt;&lt;sleep&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26317" PostTypeId="2" ParentId="26316" CreationDate="2015-01-01T02:43:04.620" Score="8" Body="&lt;p&gt;The short answer is: Yes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fatal_familial_insomnia&quot; rel=&quot;nofollow&quot;&gt;Fatal familial insomnia&lt;/a&gt; is a genetically passed down disease that at some random point in a carriers life will suddenly stop them from sleeping, ever, they die within 7 to 18 months &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know you did not ask about the disease, but it shows (even without illegal war tests) that it will kill you eventually, even in humans. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe in humans without the disease a complete lack of sleep may kill them within weeks, but who knows? maybe it was the drug.&lt;/p&gt;&#xA;" OwnerUserId="11758" LastEditorUserId="5144" LastEditDate="2015-01-02T08:55:56.703" LastActivityDate="2015-01-02T08:55:56.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26320" PostTypeId="1" CreationDate="2015-01-01T10:15:49.080" Score="2" ViewCount="72" Body="&lt;p&gt;I tried reading by light from a neighbouring room and felt sleepier than if my own lights were on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a &lt;strong&gt;formula&lt;/strong&gt; for the intensity of light vs physiological preparation for sleep(calcium, melatonin)? Or is there a &lt;strong&gt;threshold&lt;/strong&gt; intensity below which the body goes to &quot;sleepy mode&quot;?&lt;/p&gt;&#xA;" OwnerUserId="9418" LastEditorUserId="16866" LastEditDate="2016-02-27T17:36:36.730" LastActivityDate="2016-02-27T17:36:36.730" Title="awakening effects of light" Tags="&lt;human-biology&gt;&lt;sleep&gt;&lt;human-physiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26324" PostTypeId="2" ParentId="26312" CreationDate="2015-01-01T13:10:10.347" Score="6" Body="&lt;p&gt;Interesting question!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You ask 3 questions if I am correct:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;What is &lt;strong&gt;tDCS&lt;/strong&gt;;&lt;/li&gt;&#xA;&lt;li&gt;What are the &lt;strong&gt;adverse effects&lt;/strong&gt; of tDCS (at 0.1 - 2 mA);&lt;/li&gt;&#xA;&lt;li&gt;What are the health benefits (&lt;strong&gt;enhanced focus&lt;/strong&gt;);&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I will answer your questions one by one:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) &lt;strong&gt;What is tDCS&lt;/strong&gt;: tDCS devices are &lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCsQFjAA&amp;amp;url=http%3A%2F%2Fthebrainstimulator.net%2F&amp;amp;ei=tjilVNIZ19fyBbHSgrgM&amp;amp;usg=AFQjCNEflwIpSFOadQ22x9xcdMjR8drQOg&amp;amp;sig2=5JT4lVWCFZHPT0WeBbzeNg&quot; rel=&quot;nofollow noreferrer&quot;&gt;TransCranial Direct Current Stimulation (tDCS) devices&lt;/a&gt;. They send &lt;em&gt;direct current&lt;/em&gt; through (&lt;em&gt;trans&lt;/em&gt;) the skin and skull (&lt;em&gt;cranial&lt;/em&gt;) to the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) &lt;strong&gt;Adverse effects&lt;/strong&gt;: &lt;strong&gt;&lt;em&gt;EDITED:&lt;/em&gt;&lt;/strong&gt; A review by one of the leaders in the field (&lt;a href=&quot;http://www.aipass.org/files/TDCS_State%20of%20the%20art.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nitsche et al. &lt;strong&gt;Transcranial direct current stimulation: State of the art 2008&lt;/strong&gt;; &lt;em&gt;Brain Stim&lt;/em&gt;. (1) 206-23&lt;/a&gt;) mentions that current densities between &lt;strong&gt;0.029 and 0.08 mA/cm&lt;sup&gt;2&lt;/sup&gt;&lt;/strong&gt; are regularly applied in humans, with session durations of up to 40 min. Side effects are summarized in Table 1 in the cited review. Side effects are mostly nonexistent, though quite a few studies report some itching or tingling sensations under the electrode surface. Very rarely headaches or more serious side effects are reported. The authors predict that the limits will probably increase in the coming years (i.e., after 2008). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A more recent review, however, mentions a slightly lower upper limit of regularly applied current densities, namely &lt;strong&gt;0.066 mA/cm&lt;sup&gt;2&lt;/sup&gt;&lt;/strong&gt; in humans, using stimulation times of up to 20 min. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;highest upper safe current limit&lt;/strong&gt; I could find is mentioned in a 2009 paper by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754807/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bikson et al.&lt;/a&gt; that mentions &lt;strong&gt;0.14 mA/cm&lt;sup&gt;2&lt;/sup&gt;&lt;/strong&gt; based on &lt;strong&gt;animal data&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that it is not current level &lt;em&gt;per se&lt;/em&gt; that determines safety, it is the &lt;strong&gt;density of the current&lt;/strong&gt; that matters. Moreover, the duration of stimulation will be an important factor to take into account. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To go back to your device: in case of 3.5 x 3.5 cm square electrodes (i.e., 12 cm&lt;sup&gt;2&lt;/sup&gt;) as mentioned in the question, the current level range (0.1 - 2 mA) represents a current density range of &lt;strong&gt;0.008 - 0.16 mA/cm&lt;sup&gt;2&lt;/sup&gt;&lt;/strong&gt;. However, I skimmed the website and they mention 3 cm square sponges or 3.5 cm diameter circular sponges, which brings the upper limit to &lt;strong&gt;0.22&lt;/strong&gt; and &lt;strong&gt;0.28 mA/cm&lt;sup&gt;2&lt;/sup&gt;&lt;/strong&gt;, respectively. The website says the device can be used up to &lt;a href=&quot;http://www.foc.us/index.php/v2-tdcs-developer-edition&quot; rel=&quot;nofollow noreferrer&quot;&gt;40 min&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In all, based on this literature review on tDCS and despite the company claiming their &lt;a href=&quot;http://www.foc.us/index.php/v2-tdcs-developer-edition&quot; rel=&quot;nofollow noreferrer&quot;&gt;device is safe&lt;/a&gt;, I would conclude the upper limit of &lt;strong&gt;2 mA not advisable&lt;/strong&gt;, as its assciated current density exceeds the upper limits that I was able to find (Note, my answer is by no means a comprehensive review on safety of tDCS !). Dependent on the exact electrode surface you could calculate your own safety limit based upon the references cited.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3) &lt;strong&gt;tDCS and enhanced focus&lt;/strong&gt;: Health benefits in terms of ability to focus: I searched Google Scholar using the search term &quot;TransCranial Direct Current Stimulation attention&quot;, which yielded no useful hits. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way to go for your focus question is to look at what cortex is situated underneath the 'forehead' that is stimulated by this device. Basically it is the prefrontal cortex: &#xA;&lt;img src=&quot;https://i.stack.imgur.com/LzVxY.png&quot; alt=&quot;pFC&quot;&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stimulating the prefrontal cortex reportedly increases &lt;strong&gt;working memory&lt;/strong&gt; (&lt;a href=&quot;http://www.gwern.net/docs/dnb/2005-fregni.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fregni et al., 2005&lt;/a&gt;) and &lt;strong&gt;motor learning&lt;/strong&gt; (&lt;a href=&quot;http://www.researchgate.net/publication/10710628_Facilitation_of_implicit_motor_learning_by_weak_transcranial_direct_current_stimulation_of_the_primary_motor_cortex_in_the_human/file/79e4150ae2024da0f0.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nitsche et al., 2003&lt;/a&gt;). Working memory basically allows a person to use acquired information (let's say seconds or perhaps minutes ago) in subsequent tasks. Motor learning is essentially training of motor skills. Both motor learning and working memory are essential in gaming(!). However, one should carefully read the cited articles (and perhaps related ones, I gave just a few) in terms of effect size, electrode placement and stimulus conditions (including, but not limited to: current level, stimulus duration, stimulus waveforms, stimulus frequency, session duration etc.) to extrapolate their findings onto your device.      &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-02T13:39:52.057" LastActivityDate="2015-01-02T13:39:52.057" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26327" PostTypeId="1" AcceptedAnswerId="26348" CreationDate="2015-01-01T14:36:34.193" Score="2" ViewCount="885" Body="&lt;p&gt;Genetically-engineered bacteria are used to produce insulin in industry, but as far as I know, the bacteria can produce only proinsulin. Why is that? What happens in the human body in order to make functional insulin, that can't happen in some microorganisms? In the body proteases cut some at amino acids, and cleave the polypeptide while other enzymes create disulfide bonds.  Why is there no bacteria in the industry that can do the same? It's not possible for some reason or in other words — can such a bacterial strain not be engineered? &lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="10104" LastEditDate="2015-01-04T08:21:12.883" LastActivityDate="2015-01-04T08:21:12.883" Title="Production of processed Insulin in bacteria" Tags="&lt;bacteriology&gt;&lt;insulin&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26329" PostTypeId="1" CreationDate="2015-01-01T17:18:50.017" Score="1" ViewCount="1555" Body="&lt;p&gt;To my current understanding, stenosis or narrowing of the arteries would mean higher blood pressure, similar to atherosclerosis. So the Renin system should be suppressed to counter the high blood pressure. But..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read in a textbook that renal artery stenosis means lower blood flow in the kidney due to the narrowing of the artery. Thus the Renin system is activated to increase blood pressure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why does narrowing of the renal artery cause a decrease in blood pressure, and not increase?&lt;/p&gt;&#xA;" OwnerUserId="11781" LastEditorUserId="3340" LastEditDate="2015-01-03T05:06:13.280" LastActivityDate="2015-01-03T05:06:13.280" Title="Why does renal artery stenosis lead to activation of Renin-Angiotensin system?" Tags="&lt;renal-physiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26330" PostTypeId="2" ParentId="9791" CreationDate="2015-01-01T18:02:45.150" Score="0" Body="&lt;p&gt;This is a great question and one we should all be asking. Given that our closest relatives the great apes are all quadrupedal, our ancestors at one point must have also been quadrupedal. In fact we as humans are mainly quadrupedal between our first nine to fifteen months of postnatal life. As adults we still engage in quadrupedal behaviors from time to time. For instance, humans often copulate, climb steep hills and walk through thick underbrush on all fours. Because all great apes also engage in bipedal behaviors the difference between us and them is one of frequency. As adults we are much more likely to be bipedal while great apes are much more likely to be on all fours. Because changes in behavior precede changes in structure, to diagnose fossil behaviors we use characters that change during the individual's lifetime in response to practiced behaviors (i.e if we used characters that are mainly inherited to diagnose behaviors we would not know if it is the fossil in question that practiced these behaviors or an ancestor of the fossil that did). In the case of Lucy we can use the x-sectional area of the arm bone vs the x-sectional area of the lumbar vertebra. Bone x-sections change during our lifetime in response to the loads placed on them.  Because bipeds place all their upper body weight on their lower back vertebrae and none on their arms, while quadrupeds distribute their upper body weight on their arms, it would be expected that a biped have a much larger lumbar and smaller arm x-sectional area than a quadruped. This expectation is confirmed in comparisons of humans to great apes, or to baboons and other large monkeys. Notably, Lucy shows ratios that are most similar to baboons (a small lower back and large arms) suggesting it wasn't mainly a biped but often practiced quadrupedal behaviors. Lucy does not preserve a foramen magnum and shows no pelvic characters that are exclusive to bipeds. As you note it only preserves a thigh bone, a leg bone, a single foot bone and two toe bones, none of which show exclusively bipedal characters. The foot bones of the first family fossils which are ~200,000 yrs older than Lucy and have been assumed to be the same as Lucy(but may not be) show a gorilla-like foot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, paleontologist would not gain as much fame or money if they found a possible ape ancestor.  As such to be able to claim it is human they claim these fossils are bipeds using whatever human-like characters they exhibit to associate the fossil to bipedality. More than likely Lucy represents an African great ape that diverged from the common human African ape group around the time of the chimpanzees/gorilla/human split. Lucy is thus a human ancestor and a biped for convenience sake and not based on facts.  &lt;/p&gt;&#xA;" OwnerUserId="11782" LastActivityDate="2015-01-01T18:02:45.150" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26331" PostTypeId="2" ParentId="445" CreationDate="2015-01-01T18:15:10.087" Score="2" Body="&lt;p&gt;Rhinorrhea, or runny nose is a response used by our nasal membrane to get rid of foreign particles including pollen dust and infection. As such we get runny noses when we have a cold, allergy or are exposed to high densities of air-born particles. Cold air may irritate our nasal membranes, both because of temperature differences relative to our body and due to the lower amounts of moisture cold air holds. Cold air thus also results in a runny nose. &lt;/p&gt;&#xA;" OwnerUserId="11782" LastActivityDate="2015-01-01T18:15:10.087" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26332" PostTypeId="1" AcceptedAnswerId="27851" CreationDate="2015-01-01T18:40:46.117" Score="0" ViewCount="648" Body="&lt;p&gt;What triggers programmed cell death in humans? Is it decided by the brain (for the entire body)? Or is it a local decision of a cell by its environment? Something else?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize that there might be different cases. But I'd like to get a general idea of where (and why, actually) does this happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bsp.med.harvard.edu/node/168&quot; rel=&quot;nofollow&quot;&gt;As linked to&lt;/a&gt; by a comment below - one type of cell-death (Necrosis) just &quot;happens&quot; to a cell. And perhaps there are other types that are decided by the cell.&#xA;What I'm asking about (and trying to understand more) is about the idea that cell-death might be &lt;em&gt;initiated&lt;/em&gt; externally to the cell because it would be beneficial to the whole organism. Such as &quot;the separation of fingers and toes&quot; mentioned in &lt;a href=&quot;http://en.wikipedia.org/wiki/Apoptosis&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;  .   &quot;Who&quot; would initiate it? Are there examples of the CNS initiating it? Notifying the cell by nerves? By hormones? Are they initiated by neighboring cells? (And if so - what cells have the &quot;clout&quot; to send such signals?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm trying to understand is who decides when a cell dies in those cases where it's &lt;em&gt;not&lt;/em&gt; the cell itself.&lt;/p&gt;&#xA;" OwnerUserId="8055" LastEditorUserId="8055" LastEditDate="2015-01-18T20:41:10.337" LastActivityDate="2015-01-20T00:29:26.223" Title="What triggers programmed cell death in humans (from outside the cell)?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;neuroscience&gt;&lt;apoptosis&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26333" PostTypeId="1" CreationDate="2015-01-01T20:43:11.473" Score="5" ViewCount="703" Body="&lt;p&gt;Blood fructose levels are not regulated by insulin in the human body. This means that the body absorbs &lt;strong&gt;pure&lt;/strong&gt; fructose very fast, and it raises the blood fructose levels rapidly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do fruits/ vegetation contain compounds, which help the digestive system to &lt;strong&gt;regulate the absorption of fructose&lt;/strong&gt;? If so, what are they?&lt;/p&gt;&#xA;" OwnerUserId="8644" LastEditorUserId="8644" LastEditDate="2015-01-06T01:19:41.993" LastActivityDate="2015-01-30T05:15:02.303" Title="Which fruit compounds affect the speed of fructose absorption?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="3" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26336" PostTypeId="2" ParentId="26313" CreationDate="2015-01-02T04:44:29.117" Score="4" Body="&lt;p&gt;Perception of saltiness is because of the sodium ion. At concentrations ≤ 100mM, sodium ions elicit a taste response pathway which is inhibited by a small molecule called amiloride. Other monovalent cations do not elicit this &quot;amiloride-sensitive&quot; response. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At higher concentrations sodium ions elicit a non-amiloride sensitive response; other ions like K&lt;sup&gt;+&lt;/sup&gt; also elicit this response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Epithelial sodium channel — ENaC, is responsible for sodium taste perception (amiloride sensitve) and there are distinct population of taste receptor cells that express this channel (&lt;a href=&quot;http://dx.doi.org/10.1038/nature08783&quot; rel=&quot;nofollow&quot;&gt;Chandrashekar et al., 2010&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So other sodium salts like NaNO&lt;sub&gt;3&lt;/sub&gt; would also taste salty (the anions can surely have some role in the difference of taste)&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-06-22T18:26:48.293" LastActivityDate="2016-06-22T18:26:48.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26337" PostTypeId="2" ParentId="26329" CreationDate="2015-01-02T05:35:10.527" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;So why does narrowing of the renal artery cause a decrease in blood pressure, and not increase?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It doesn't. It causes an increase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the blood flow to the kidney is decreased for any reason (for example, hemorrhage or dehydration), the kidney is one of the organs that will protect it's perfusion by causing an increase in BP through the renin-angiotensin-aldosterone system (RAAS).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Very briefly: decr. blood flow -&gt; renin secretion by juxtaglomerular cells -&gt; conversion of serum Angiotensinogen into Angiotensin I (+ ACE) -&gt; Angiotensin II =&gt; elevated BP (by a host of mechanisms).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is renal artery stenosis, the kidney will try to compensate for this (&lt;em&gt;locally&lt;/em&gt;) reduced blood flow by activating the RAAS. The kidney doesn't 'know' that the blood flow/pressure is only locally reduced. It will cause systemic hypertension as a way to increase it's blood flow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Atherosclerosis is a whole different ball of wax. &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-02T05:35:10.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26340" PostTypeId="1" CreationDate="2015-01-02T10:52:25.477" Score="5" ViewCount="195" Body="&lt;p&gt;The mean population fitness as given by mutation load theory depends only on the genome-wide mutation rate ($U$). My question is: &lt;strong&gt;How many generations is needed to reach a new mutation load equilibrium after a change in $U$?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Following is an article were they perform the kind of calculations I am interested in:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let $U$ be the genome-wide mutation rate, $\delta U$ a change (between two time steps) in the genome-wide mutation rate and $s$ the mutational effect (effect on fitness) of a given mutation. In &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev-ecolsys-110411-160257&quot; rel=&quot;nofollow noreferrer&quot;&gt;Agrawal and Whitlock (2012)&lt;/a&gt;, page 13 (or 127 in the journal), $3^{rd}$ paragraph, the authors say:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[After a change in $U$,] it can take a long time to approach mutation-selection balance. For example, if the mutation rate is increased by $\delta U = 1$ deleterious mutation per genome per generation, then it would take ∼120 generations for fitness to decline 80% of its expected amount if s = 0.01. However, by obtaining a time series of data, one could infer the equilibrium load after tens or hundreds of generations even if equilibrium is not reached&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How were these ~120 generations estimated/calculated?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="13405" LastEditDate="2017-03-29T22:10:54.917" LastActivityDate="2017-03-29T22:10:54.917" Title="How does the population fitness change after a change in mutation rate?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26341" PostTypeId="1" AcceptedAnswerId="26354" CreationDate="2015-01-02T11:30:14.643" Score="6" ViewCount="257" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Survival_function&quot;&gt;survival curve/function&lt;/a&gt; describes the probability of a given individual to survive to age $x$. In humans, today's survival function is very much influenced by medicine. This leads me to wonder what the survival function looked like before modern medicine. Typically I wonder what the survival function looked like during the paleolithic age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What did the survival function looked like during the paleolithic age?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why did the survival function looked like that? What were the major causes of mortality for males and for females?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3624" LastEditDate="2015-01-02T23:18:59.707" LastActivityDate="2015-01-02T23:55:09.977" Title="Survival curve in early humans" Tags="&lt;human-biology&gt;&lt;natural-selection&gt;&lt;population-dynamics&gt;&lt;medicine&gt;&lt;demography&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26342" PostTypeId="1" AcceptedAnswerId="26379" CreationDate="2015-01-02T11:32:32.323" Score="4" ViewCount="583" Body="&lt;p&gt;Today, about 10 to 20 percent of known pregnancy end in miscarriage. Pregnancy is a biological process that has been very well studied by medicine. As a result, modern medicine helps a lot to prevent miscarriages and to prevent death of pregnant women.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What was the percentage of pregnancy ending in miscarriage before modern medicine? Typically, what was the percentage pregnancy ending in miscarriage in early Homo sapiens, during the paleolithic age?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2015-01-03T23:46:08.133" Title="Miscarriage in early humans" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;medicine&gt;&lt;pregnancy&gt;&lt;human-evolution&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26343" PostTypeId="1" AcceptedAnswerId="26353" CreationDate="2015-01-02T11:34:16.767" Score="3" ViewCount="668" Body="&lt;p&gt;The average fecundity per woman varies a lot from country to country. I call average fecundity per woman the average number of born children per woman. In Homo sapiens, what was the average fecundity per woman during the paleolithic age for example? Is it about 2 offspring per woman or about 12 offsprings per woman?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3624" LastEditDate="2015-01-02T23:25:48.703" LastActivityDate="2016-02-25T09:59:52.617" Title="Fecundity per woman in early humans" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;natural-selection&gt;&lt;human-evolution&gt;&lt;demography&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26344" PostTypeId="2" ParentId="26233" CreationDate="2015-01-02T14:13:14.713" Score="1" Body="&lt;p&gt;In what season was the picture taken?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you give an idea of the size of the objects present on the photo?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on the rough surface of the fruits, I would suggest having a look at Moraceae, and in particular at the &lt;a href=&quot;http://en.wikipedia.org/wiki/Artocarpeae&quot; rel=&quot;nofollow&quot;&gt;Artocarpeae&lt;/a&gt; tribe within this family.&lt;/p&gt;&#xA;" OwnerUserId="1486" LastActivityDate="2015-01-02T14:13:14.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26347" PostTypeId="1" CreationDate="2015-01-02T17:31:08.170" Score="2" ViewCount="185" Body="&lt;p&gt;What is the minimum needed equipment to perform simple plant electrophysiology? I am looking for some simple experiments that I could run at home for learning. Ideally, I would transfer the skills to stud neuroscience later on (the skills could be related to operating a microscope, doing recordings with microelectrodes, signal processing, statistics, etc). How expensive this would be?&lt;/p&gt;&#xA;" OwnerUserId="11795" LastEditorUserId="9943" LastEditDate="2015-01-26T14:25:20.473" LastActivityDate="2015-01-26T14:25:20.473" Title="What equipment is needed to perform simple plant electrophysiology?" Tags="&lt;plant-physiology&gt;&lt;electrophysiology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26348" PostTypeId="2" ParentId="26327" CreationDate="2015-01-02T18:40:01.910" Score="3" Body="&lt;p&gt;Insulin is processed from &lt;a href=&quot;https://en.wikipedia.org/wiki/Proinsulin&quot; rel=&quot;nofollow noreferrer&quot;&gt;proinsulin&lt;/a&gt; by folding the peptide and forming 3 disulfide bonds before cleaving the peptide in 2 positions, leaving 2 peptide chains held in place by the disulfide bonds. This process is summarized in this image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/H1cyb.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This only works because the peptide is packaged in a secretory vesicle during synthesis. This protects the peptide against the reductive environment of the cytoplasm, where &lt;a href=&quot;https://en.wikipedia.org/wiki/Glutathione&quot; rel=&quot;nofollow noreferrer&quot;&gt;glutathione&lt;/a&gt; is likely to reduce the disulfide bonds that hold insulin together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When industrial insulin production moved from extracting the hormone from animal pancreases (pancreai?) to bacterial production of human recombinant insulin, glutathione was likely to cause a problem because simple protein production in bacteria just builds the protein in the cytoplasm, where glutathione is present. It is possible to export the protein into the periplasm during synthesis, similar to how proinsulin is moved into the endoplasmic reticulum during synthesis in human cells, but this can complicate protein purification (larger volumes of media, if protein is inside cells you can spin the cells down and work with a smaller volume). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that &lt;a href=&quot;https://en.wikipedia.org/wiki/Insulin_%28medication%29#Principles&quot; rel=&quot;nofollow noreferrer&quot;&gt;more recent methods&lt;/a&gt; use yeast to make insulin, potentially allowing production of actual insulin instead of proinsulin. And modern purification methods can extract insulin from animal sources that is just as good as recombinant sources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know from personal experience that it can be very hard to produce proteins with multiple disulfide bonds in bacteria. We attempted to produce mutants of bee venom PLA2 in E. coli, but the protein was misfolded and wound up in inclusion bodies. We purified the inclusion bodies, unfolded the proteins, then slowly refolded them by dialysing the protein in a glutathione solution. We aimed at making a protein with a free thiol for later chemical modification, but that free thiol just picked up a glutathione we couldn't remove without ruining enzyme activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also please note that I am not fully aware of how insulin is made on the industrial scale and I could be wrong. That's why this was originally a comment.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2015-01-02T18:40:01.910" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="26350" PostTypeId="2" ParentId="5558" CreationDate="2015-01-02T19:27:36.683" Score="1" Body="&lt;p&gt;If one looks at the sequence map in detail, at the fusion point we find both telomere and pre-telomere sequences. And what is particularly compelling, is that these main groups occur in the correct order.  That is, first you see a pre-telomere sequence, then a telomere sequence. Then we see the telomeres inverted and the inverted pre-telomeres after that. This is exactly what would be predicted for a chromosome fusion.  Yes, one can quibble (as Tomkins does) that within a particular group that the sequences don't &quot;look exactly as they should&quot;.  But this would be consistent with ideas proposed here.  That these sequences MUST have undergone significant mutation in order for the fusion to even occur!  And then of course one would expect mutations to continue after the fusion event as part of normal evolution.&lt;/p&gt;&#xA;" OwnerUserId="11797" LastActivityDate="2015-01-02T19:27:36.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26351" PostTypeId="1" CreationDate="2015-01-02T20:12:08.130" Score="1" ViewCount="6370" Body="&lt;p&gt;If I were to do a blue/white selection of transformed &lt;em&gt;E. coli&lt;/em&gt; on LB agar ampicillin plates at &lt;strong&gt;room temperature (23⁰C)&lt;/strong&gt; for about 2 days and 18 hours, will I run into the issue of satellite colonies or any other issues?&lt;/p&gt;&#xA;" OwnerUserId="11799" LastEditorUserId="3340" LastEditDate="2015-01-03T05:01:35.797" LastActivityDate="2015-02-07T00:00:07.643" Title="Growing E. coli at room temperature?" Tags="&lt;molecular-biology&gt;&lt;microbiology&gt;&lt;molecular-genetics&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="26352" PostTypeId="2" ParentId="26315" CreationDate="2015-01-02T22:40:27.667" Score="6" Body="&lt;p&gt;I found some reports on it (like reference 1) but there is an oddly little amount of publications on this topic. then I found this review in Mucosal Immunology (reference 2, interesting to read) which doubts this activation. It says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Interaction with complement&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;IgA lacks the residues identified in the Fc regions of IgG or IgM that&#xA;  bind to C1q, and consequently IgA does not activate the classical&#xA;  complement pathway. Although several papers have reported activation&#xA;  of the alternate pathway by heat-aggregated, denatured, or&#xA;  recombinantly generated IgA, this seems to be essentially artifactual,&#xA;  and intact native IgA antibodies complexed with antigen inhibit&#xA;  complement activation induced by IgG or IgM antibodies. This&#xA;  effect is also replicated by Fabα fragments generated by cleavage of&#xA;  IgA1 antibodies with IgA1 protease. It is telling that mixed&#xA;  aggregates of heat-denatured IgG and IgA activate the alternate&#xA;  pathway in proportion to the content of IgG, and that C3b becomes&#xA;  covalently linked to the IgG heavy chains, not to IgA. Intriguing&#xA;  reports that IgA antibodies promote complement-dependent lysis or&#xA;  opsonization of encapsulated bacteria probably also arise from&#xA;  facilitation of alternate pathway activation by bacterial&#xA;  polysaccharides&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It names three papers to underline this (which are number 45-47 in the reference list of the article), which can be found as references 3-5. So the question here is not only how the mechanism looks like, but also if this is real or an artefact.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.filedropper.com/showdownload.php/hiemstra1988&quot;&gt;Activation of complement by human serum IgA, secretory IgA and IgA1&#xA;fragments.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/mi/journal/v4/n6/full/mi201139a.html&quot;&gt;Structure and function relationships in IgA&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3855/j4jz8n5e_pdf.htm&quot;&gt;Anti-inflammatory activity of human IgA antibodies and their Fabα&#xA;fragments: inhibition of IgG-mediated complement activation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6854021&quot;&gt;IgA blocks IgM and IgG-initiated immune lysis by separate molecular&#xA;mechanisms.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11342648&quot;&gt;Activity of human IgG and IgA subclasses in immune defense against&#xA;Neisseria meningitidis serogroup B.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-01-02T22:40:27.667" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26353" PostTypeId="2" ParentId="26343" CreationDate="2015-01-02T22:56:16.593" Score="2" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/26341/survival-curve-in-early-humans&quot;&gt;Infant mortality was high during the paleolithic&lt;/a&gt;, so the fecundity of females had to be quite a bit higher than 2 to sustain viable populations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A recent paper by &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/ajpa.22495/full&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;White. 2014. Mortality, fertility, and the OY ratio in a model hunter–gatherer system. American Journal of Physical Anthropology 154(2): 222–231&quot;&gt;White (2014)&lt;/a&gt; that explores how the ratio of young and old individuals in a population relates to demographic rates compiles data on hunter-gatherer societies from previous studies that you will probably find useful. Among other statistics, that paper reports a range in total fertility of 2.6–8.0. One of the source papers (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12317265&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Hewlett. 1991. Demography and childcare in preindustrial societies. J Anthropol Res. 47(1):1-37.&quot;&gt;Hewlett, 1991&lt;/a&gt;, &lt;a href=&quot;http://anthro.vancouver.wsu.edu/media/PDF/demo_childcare.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf here&lt;/a&gt;) has data for individual hunter-gatherer societies (along with data from other types of pre-industrial societies). Many populations lie in the range 4-7 offspring. Note however that most (all?) of these values are from current or recent hunter-gatherer societies and not paleolithic societies. However, to give a ballpark estimate they are probably useful and fairly accurate. Also note that the child mortality rate of these societies are often between 40-50% (infant mortality ~10-30%)&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2016-02-25T09:59:52.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26354" PostTypeId="2" ParentId="26341" CreationDate="2015-01-02T23:14:21.337" Score="4" Body="&lt;p&gt;To obtain a full survival curve (basically a full life table) you would need to make quite a number of assumptions, since the data for paleolithic societies is scattered and probably biased. This is however not a field I know well, but I can point you to one recent paper (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/ajpa.22495/full&quot; rel=&quot;nofollow&quot; title=&quot;White. 2014. Mortality, fertility, and the OY ratio in a model hunter–gatherer system. American Journal of Physical Anthropology 154(2): 222–231&quot;&gt;White, 2014)&lt;/a&gt; that explores how the ratio of young and old individuals in a population relates to demographic rates, using agent-based models. Using such a model you can obtain smooth survival curves and also explore how different assumptions will affect the survival curves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also data from recent or current hunter-gatherer societies that can be used to approximate what the survival curves looked like during the paleolithic. For instance,  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12317265&quot; rel=&quot;nofollow&quot; title=&quot;Hewlett. 1991. Demography and childcare in preindustrial societies. J Anthropol Res. 47(1):1-37.&quot;&gt;Hewlett (1991)&lt;/a&gt; (&lt;a href=&quot;http://anthro.vancouver.wsu.edu/media/PDF/demo_childcare.pdf&quot; rel=&quot;nofollow&quot;&gt;pdf here&lt;/a&gt;) has compiled survival rate data for individual hunter-gatherer societies (along with other demographic rates and data from other types of pre-industrial societies). The child mortality rate (deaths before age 15) often lie in the range 40-50% in active (mobile) and sedentary hunter-gatherer societies, with an infant mortality rate usually between 10-30% (death before 12 months of age). This indicates a fairly steep survival curve, which is the reason why the average age of paleolithic people is often estimated to ~25 years. This doesn't mean that most people died around the age of 25, just that the distribution of ages was very skewed and non-normal. Many died young, but people that survived to adulthood could become much older than 25.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-01-02T23:55:09.977" LastActivityDate="2015-01-02T23:55:09.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26355" PostTypeId="1" CreationDate="2015-01-03T00:26:20.350" Score="0" ViewCount="68" Body="&lt;p&gt;Is it common for an undergraduate to run their thesis (evolutionary genomics) in a supercomputer? In my country, few supercomputers exist, but I'm not sure how it is for bachelors in the US or Europe. I am writing my application to graduate school abroad and I want to know if it is a remarkable point I can use as hook to begin my statement.&lt;/p&gt;&#xA;" OwnerUserId="11801" LastEditorUserId="3340" LastEditDate="2015-01-03T06:53:52.773" LastActivityDate="2015-01-03T06:53:52.773" Title="Supercomputer and undergraduates" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;genomics&gt;&lt;computational-model&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ClosedDate="2015-01-03T07:12:54.340" ContentLicense="CC BY-SA 3.0" />
  <row Id="26356" PostTypeId="2" ParentId="26355" CreationDate="2015-01-03T00:32:45.637" Score="2" Body="&lt;p&gt;IMO irrespective of country and level (undergrad/Masters), if you can run a job on a High Performance Computing cluster or a supercomputer, you should mention that on your resume. And sure, you can use that in your statement, especially given the fact that not many have access to it, you had the rare opportunity and made full use of it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my experience, I haven't seen many undergrads here in the US that can run a job on a HPC - not without prior computing experience!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All the best to you!&lt;/p&gt;&#xA;" OwnerUserId="9665" LastEditorUserId="3340" LastEditDate="2015-01-03T05:04:17.190" LastActivityDate="2015-01-03T05:04:17.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26357" PostTypeId="1" CreationDate="2015-01-03T02:17:49.257" Score="1" ViewCount="123" Body="&lt;p&gt;I know each element of the central dogma is a code in the mathematical sense of finite-state machines. That is, DNA is transcribed into RNA, and RNA into proteins.  What other examples are there of codes that exist naturally in organisms? &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="11652" LastEditDate="2015-01-03T03:08:03.677" LastActivityDate="2015-01-03T05:09:31.600" Title="Are there more true codes found in biology besides the central dogma?" Tags="&lt;information-theory&gt;&lt;information&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26358" PostTypeId="2" ParentId="26357" CreationDate="2015-01-03T02:46:08.467" Score="1" Body="&lt;p&gt;DNA is a code that occurs via stepwise polymerization, like all major macromolecules. In respects to DNA, it is Nucleic Acid sequences that polymerize to create the DNA. In eukaryotic cells this happens at multiple replicons (regions of replication). So you can look DNA as code for itself. You also have rRNA, mRNA, and tRNA. All of these code for and do specific things. rRNA facilitates the creation and movement of the ribosome, where mRNA and tRNA &quot;code&quot; for the final protein. tRNA serves as the principle code strand for the correct Amino Acids. This is read as a series of three N.A's (codons) One codon for a respective Amino Acid. mRNA actually guides the synthesis of these polypeptide chains. You also have something called operons. These are groups of genes with related functions that are clustered together. This allows for rapid initiation and termination of gene expression. Im sure there are a few others but these are those that come off the top of my head. The term &quot;code&quot; and molecular bio are very much intertwined. &lt;/p&gt;&#xA;" OwnerUserId="8059" LastEditorUserId="8059" LastEditDate="2015-01-03T02:55:18.040" LastActivityDate="2015-01-03T02:55:18.040" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="26360" PostTypeId="2" ParentId="26357" CreationDate="2015-01-03T05:09:31.600" Score="0" Body="&lt;p&gt;I am not very familiar with them, but I hear that bacterial non-ribosomal peptide synthases are made of catalytic modules, lined up in series, paralleling their product. My suspicion is that there is some promiscuity / ambiguity in the nonribosomal code.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, N-glycosylation in the ER / Golgi occurs in a defined series of events, but that includes backtracking (that is, sugar cleavage), which I am not sure would belong in a finite state machine.&lt;/p&gt;&#xA;" OwnerUserId="8809" LastActivityDate="2015-01-03T05:09:31.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26361" PostTypeId="1" CreationDate="2015-01-03T05:28:53.753" Score="8" ViewCount="61162" Body="&lt;p&gt;There are many references to eagle pushing their young off the nest to make them know how to fly, for example &lt;a href=&quot;http://www.youtube.com/watch?v=_ap8u-xD8xc&quot; rel=&quot;noreferrer&quot;&gt;this motivational video&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;It is also described in &lt;a href=&quot;http://www.eagleflight.org/cyberstudies/actions-and-attitudes-of-a-growing-church/157-with-eagles-wings&quot; rel=&quot;noreferrer&quot;&gt;this website&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Let me show you &amp;quot;the ways of an eagle&amp;quot; in the nest, and give you a picture of our lives as well. After the eaglets get to a certain size, or maturity, everything changes! One day the mother eagle comes back from being gone, but this time there’s no food in her beak, and she doesn’t land on the edge of the nest. Instead, she hovers over the nest.&lt;/p&gt;&#xA;&lt;p&gt;You may not know this, but an eagle can do almost what a hummingbird can do. Even though they are great birds, they can remain almost motionless in midair with those great wings just undulating in the breeze. They do this about three feet above the nest. I’m sure if little eagles could talk to one another—and maybe they can—one would certainly say, &amp;quot;My, what strong wings Mommy has.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;Why does the mother do this? She is demonstrating that those curious appendages on the babies’ backs have a useful function. Eagles, of course, were meant to fly, but they don’t know that. If we take an eagle and separate it at birth from its parents, it will never learn to fly. It will just grovel around in the dirt like a chicken. It might even look up and see eagles soaring overhead and never guess that it was meant to soar in the heavens.&lt;/p&gt;&#xA;&lt;p&gt;Eagles have to be taught, and that’s the mother’s job. So first she just demonstrates.&lt;/p&gt;&#xA;&lt;p&gt;The next thing she does is come down into the nest and surprise her young. One can imagine how warm it must normally be for the little eagles to snuggle with their mother and be enshrouded with her feathers, but this time she puts her head up against one of the little ones, and pushes that little one closer and closer to the edge of the nest. (&amp;quot;Hey mom, mom, what are you doing?&amp;quot;)&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;All at once she pushes the little one out of the nest, and the eaglet falls down the face of the cliff, surely to be destroyed. But not so! In a flash the great mother eagle flies down, catches the little one on her back, and flies up and deposits it in the nest. (&amp;quot;Whew! Mom, that must have been an accident.&amp;quot;) But it wasn’t an accident. The mother bird pushes the little one out again, and again, over and over.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Why would a mother do that to her young? Does she hates the little one? Not at all. It’s just that those little birds were made to fly, and they don’t know it, so she is going to push them out of the nest. She never lets them hit bottom, but she does let them fall, because they have to learn something they don’t know.&lt;/p&gt;&#xA;&lt;p&gt;The next time the mother bird comes back she decides to clean house, and so she stands on the edge of the nest. The first things to go are the feathers inside; she drops them over the edge. Then the leaves go over the edge—heave ho! While this is going on, she’s not very talkative, either. (&amp;quot;Mom, what are you doing?&amp;quot;) She pays no attention. Since she built the house, she knows how to take it apart.&lt;/p&gt;&#xA;&lt;p&gt;Next she decides to take the sticks out of the middle of the nest, and with her great strong beak and feet, she’s able to break them off and stand them straight up. (&amp;quot;Mom, it’s not comfortable in here anymore.&amp;quot;) Then she takes certain key sticks out of the nest and throws them over the edge. (&amp;quot;What are you doing, Mom? You are wrecking my room.&amp;quot;)&lt;/p&gt;&#xA;&lt;p&gt;She seemingly pays no attention to the concerns of her young as she prepares to pull the nest apart, for she is determined that those little ones will fly, and she knows something they don’t. She knows they will never fly as long as they remain in the nest.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However, looking at &lt;a href=&quot;https://www.youtube.com/watch?v=Fx1-Os0l7Ac&quot; rel=&quot;noreferrer&quot;&gt;this very interesting documentary on white-tailed eagle&lt;/a&gt;, the young eagles don't learn to fly by getting pushed as described in the motivational video, but they learned flying by practicing their wings on good winds.&lt;/p&gt;&#xA;&lt;p&gt;Looking from the nesting place (cliff), I read that it might be &lt;a href=&quot;http://en.wikipedia.org/wiki/Golden_eagle&quot; rel=&quot;noreferrer&quot;&gt;Golden Eagle&lt;/a&gt;. But the section describing the fledgling doesn't say anything about the parent eagle pushing the young, although it does say about &amp;quot;jumping off&amp;quot;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The first attempted flight departure can be abrupt, with the young jumping off and using a series of short, stiff wing-beats to glide downward or being blown out of nest while wing-flapping. The initial flight often includes a short flight on unsteady wings followed by an uncontrolled landing.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Does Golden Eagle really push their young to teach them flying? If not, which species is it?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;In case it's not clear, I am also interested in references that describes the eagle behavior in more details. It would be good if there is a video documentary, but considering that capturing this moment on tape might be difficult, that's not my utmost concern.&lt;/p&gt;&#xA;" OwnerUserId="11790" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-10-25T09:09:52.710" Title="What species of eagle pushes their young to teach them flying?" Tags="&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26363" PostTypeId="2" ParentId="26361" CreationDate="2015-01-03T07:06:04.700" Score="3" Body="&lt;p&gt;I am pretty sure this doesn't happen with eagles, and I have no idea why this would be written. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But not so! In a flash the great mother eagle flies down, catches the little one on her back, and flies up and deposits it in the nest. (&quot;Whew! Mom, that must have been an accident.&quot;) But it wasn’t an accident.&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is flight, alright: a pure &lt;em&gt;flight of fancy&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been many hundreds of videocams set up in all kinds of remote locations so that behavior in the wild can be studied. Some of the most popular cams in recent years have been the eagle cams (e.g. at eagles.org). They are live during nesting season and record for all the behavior of eagles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the parents did not feed their young, as described in the fabrication above, the young would starve to death, as it takes time to learn to fly. If anything, the eagle parents must increase the feeding to keep up with the nutritional needs of the growing chicks, and the muscle building taking place. The parents don't stop feeding until a while after they're flying well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eagles don't learn &quot;learn&quot; why they have wings by observing the mother eagle hovering above them (pure anthropomorphizing). They leave the nest and start roaming on the branches, practicing hopping, landing, and building up their wing strength. Eventually flying, they still come back to the nest to feed. In &lt;a href=&quot;https://www.youtube.com/watch?v=kxDMtRqYbhc&quot; rel=&quot;nofollow&quot;&gt;this video&lt;/a&gt; from British Columbia (not the most exciting in the world) you can see exactly this happening with bald eagles. Eventually the young eagles scavenge and learn to hunt for themselves. It takes time. &lt;a href=&quot;http://www.hornbyeagles.com/eaglefaq.htm#E&quot; rel=&quot;nofollow&quot;&gt;This page&lt;/a&gt; describes the fledgling feeding and flight behavior.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While I am not going to try to find an eagle that behaves in the bizarre manner you've found and asked about, I will say that eagles are eagles and more or less behave pretty similarly. The most common eagle in the world is the bald eagle. The Golden behaves like the Bald. Eagle behavior is influenced by habitat, etc. Wikipedia has a page listing 60 species of eagles. Picking a random eagle from another part of the world (in this case, the Sub-Saharan &lt;a href=&quot;http://en.wikipedia.org/wiki/Martial_eagle&quot; rel=&quot;nofollow&quot;&gt;Martial eagle&lt;/a&gt;, this information seems to confirm that attentiveness of adult eagles and fledgling behavior is &lt;em&gt;similar&lt;/em&gt; though not without species variation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Martial eagles have a slow breeding rate, laying usually one egg (rarely two) every two years. The egg is incubated for 45 to 53 days and the chick fledged at 96 to 104 days. Despite increasing signs of independence (such as flight and beginning to practice hunting), juvenile birds will remain in the care of their parents for a further 6 to 12 months. Due to this long dependence period, these eagles can usually only mate in alternate years.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm sure I'm not the first to warn you not to believe everything you read on the internet.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-01-03T08:32:20.550" LastActivityDate="2015-01-03T08:32:20.550" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26364" PostTypeId="1" CreationDate="2015-01-03T07:53:06.017" Score="6" ViewCount="557" Body="&lt;p&gt;I'm looking for any studies that show a positive curve in respects to music sessions in humans and neurotransmitter release (specifically dopamine, epinephrine, and serotonin.) Any direct links would be great as I attempted googling and cannot find any at all for some reason.  &lt;/p&gt;&#xA;" OwnerUserId="8059" LastEditorDisplayName="user13145" LastEditDate="2016-10-18T05:27:21.237" LastActivityDate="2021-04-20T17:53:08.637" Title="Dopamine and other neurotransmitter release during music listening" Tags="&lt;brain&gt;&lt;neurotransmitter&gt;&lt;dopamine&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26368" PostTypeId="1" CreationDate="2015-01-03T10:55:00.893" Score="5" ViewCount="258" Body="&lt;p&gt;We got this task:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are 3 genes (acb) on one chromosome (linked inheritance). Distance a-c = 12cM, a-b=16cM. Probability for double crossing-over (&lt;em&gt;CO&lt;/em&gt;) is 0,6%. Find ratio of genotypes of descendants (AcB/acb X acb/acb).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know whether the 0,6% for double &lt;em&gt;CO&lt;/em&gt; is included in the 16% (16cM) probability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it is not, so I got these ratios:&#xA;No &lt;em&gt;CO&lt;/em&gt; and double &lt;em&gt;CO&lt;/em&gt;: 42% AcB/acb, 42% acb/acb,&#xA;1x &lt;em&gt;CO&lt;/em&gt;: 8% Acb/acb, 8% acB/acb&lt;/p&gt;&#xA;" OwnerUserId="11805" LastEditorUserId="3340" LastEditDate="2015-01-03T11:25:46.517" LastActivityDate="2015-04-02T08:57:47.043" Title="Is probability for double crossing over included in distance cM? [task]" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26369" PostTypeId="1" CreationDate="2015-01-03T11:12:49.800" Score="0" ViewCount="6443" Body="&lt;p&gt;At what phase does this occur in mitosis (or even meiosis); some text books say prophase while others say metaphase.&lt;/p&gt;&#xA;" OwnerUserId="11780" LastEditorUserId="3340" LastEditDate="2015-01-03T11:29:06.640" LastActivityDate="2018-11-27T22:44:48.477" Title="When do the spindle fibers attach to the chromosome" Tags="&lt;genetics&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26371" PostTypeId="1" CreationDate="2015-01-03T15:13:24.193" Score="3" ViewCount="886" Body="&lt;p&gt;Is it possible to get either a false positive or a false negative from a DNA paternity test and what would be the likely mechanisms behind this?  For example, is it possible that a father's DNA could have changed during his lifetime enough to be unrecognisable to that of his children?&lt;/p&gt;&#xA;" OwnerUserId="11807" LastEditorUserId="69" LastEditDate="2015-01-03T17:33:28.660" LastActivityDate="2015-01-03T18:55:20.277" Title="How fallible are DNA paternity tests?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26373" PostTypeId="2" ParentId="26371" CreationDate="2015-01-03T18:55:20.277" Score="4" Body="&lt;p&gt;Discounting lab error and other kinds of human incompetence, there aren't very many things that can confound a paternity test. Normal DNA damage cannot, but there are kinds of genetic chimeras that get strange results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Normal human DNA damage can't add up fast enough to change the results without killing you several times over, but there are a surprisingly large number of people who are chimeras. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The relevant particular flavor of chimerism is &lt;a href=&quot;http://en.wikipedia.org/wiki/Chimera_%28genetics%29#Tetragametic_chimerism&quot; rel=&quot;nofollow&quot;&gt;tetragametic chimerism&lt;/a&gt;, where essentially parts of your body are sibling-related to the rest. This occasionally is discovered during paternity testing, in one vivid instance when &lt;a href=&quot;http://www.businessinsider.com/lydia-fairchild-is-her-own-twin-2014-2&quot; rel=&quot;nofollow&quot;&gt;a woman was provably not the mother of the newborn that she had just given birth to.&lt;/a&gt; Technically I suppose the baby was her skin's niece.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The incidence of this was thought to be very low, but it's almost impossible to detect without DNA testing. We know the incidence is much higher than we thought, but we don't know how high.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-01-03T18:55:20.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26374" PostTypeId="1" CreationDate="2015-01-03T19:00:12.417" Score="10" ViewCount="46362" Body="&lt;p&gt;The blood of persons of blood group O contains antibodies against antigens A and B. The red blood cells of persons of blood group A have A antigen on their surface. If someone with blood group A receives blood from a donor of group O, then anti-A antibodies in the donor blood should attack the A antigens on the recipient's red cells. Shouldn’t this be a problem?&lt;/p&gt;&#xA;" OwnerUserId="11812" LastEditorUserId="22057" LastEditDate="2017-12-27T16:23:22.647" LastActivityDate="2019-03-08T19:08:29.560" Title="Why can blood group O be given to all blood groups?" Tags="&lt;immunology&gt;&lt;red-blood-cell&gt;&lt;blood-group&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="26376" PostTypeId="1" AcceptedAnswerId="34128" CreationDate="2015-01-03T22:16:38.077" Score="1" ViewCount="77" Body="&lt;p&gt;I know there is a specific term for insects that need to consume protein to produce viable eggs, as well as a term for those insects that don't need to consume protein to produce viable eggs.&lt;/p&gt;&#xA;" OwnerUserId="3382" LastActivityDate="2015-05-09T22:55:15.363" Title="What term describes insects that must eat protein to reproduce?" Tags="&lt;entomology&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26377" PostTypeId="2" ParentId="26351" CreationDate="2015-01-03T23:08:17.830" Score="1" Body="&lt;p&gt;Since b/w screening is a means to  selection, you want maximum selection pressure. This will be obtained by incorporating all optimal conditions. The many enzymes of the lac operon are going to function best at their optimal temp.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why would you do this? If it is because you can't go in the next day it's better to do it when you're available. You're only going to doubt your results when you get them.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2015-02-07T00:00:07.643" LastActivityDate="2015-02-07T00:00:07.643" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26378" PostTypeId="2" ParentId="16287" CreationDate="2015-01-03T23:21:53.160" Score="1" Body="&lt;p&gt;A good post about &quot;mixing&quot;, which means that a population generally harbors multitude of different versions of a gene, called alleles. So one organism, like a human, has a unique combination of which two alleles out of thousands possible represent each gene in its body. Besides this, major changes are often made not so much by mutations as by changes in the level of gene expression. For example, a mutation in one gene that produces a protein important for regulation of the expression of 50 other genes can cause a lot of change in body development (morphology) and physiology by simply affecting the expression level (amount of protein produced) by these 50 genes. In turn, changed levels of these 50 proteins can make substantial changes in the whole protein interaction network in cells. If you think why sharks look different than elephants, for instance, it's much more because of differential gene expression (including the timing of the expression during body development) than differences brought about by mutations causing functional changes in the coding regions of multiple genes.&#xA;And yes, mutations only provide raw material for evolution - diversity to select from. Mutations are a supermarket for evolution, selection is what evolution tends to buy more frequently in this supermarket or what's in demand currently. It is thus selection and drift that work to increase the frequency of certain mutant alleles that actually result in evolution.&#xA;The mechanism of selection is simple. The functional diversity in populations created by mutations in particular creates different survival rates for particular phenotypes/genotypes based on how well the combination of the alleles representing its genome can create a phenotype that matches environment. For example, in a bacterial population adapted to neutral media there's still a random diversity in the range of pH tolerance. If the medium becomes more acidic, cells that happen to have better tolerance to low pH gradually increase in frequency over time.&#xA;The difference between prokaryotes, like bacteria, and eukaryotes (like humans) mostly lies in that due to meiosis eukaryotes randomly shuffle alleles, so that they &quot;intermix&quot; in a population creating more possible phenotypes to select from. Bacteria do not have this mechanism and can only diverge by cell division, creating diversity only by mutations. However, it is not completely true, as now it is well known that bacteria share a lot of genes via horizontal gene transfer - direct exchange of genes between bacterial cells. This process is often aided by viruses. Horizontal gene transfer, just like meiosis, works to shuffle genes in the population, creating more diversity.&lt;/p&gt;&#xA;" OwnerUserId="11816" LastEditorUserId="11816" LastEditDate="2015-01-03T23:39:40.040" LastActivityDate="2015-01-03T23:39:40.040" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26379" PostTypeId="2" ParentId="26342" CreationDate="2015-01-03T23:39:38.637" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Pregnancy is a biological process that has been very well studied by medicine. As a result, modern medicine helps a lot to prevent miscarriages and to prevent death of pregnant women.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;While the latter clause is correct (maternal - and infant - mortality is reduced with medical care), the former is not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Miscarriages have been a problem as far back as recorded history. The written record includes medicinal recipes to prevent miscarriages. The problem then, as now, is that it just can't be done very well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a 2000 Obstetrics journal article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Human reproduction is extraordinarily wasteful. The reasons for this have taxed all of the contributors to this book. As we move into the 21st century &lt;em&gt;it is sobering to reflect on the fact that we have failed to harness the power of the evolving revolution in molecular medical biology to answer the fundamental question: why is the fate of a fertilized egg so hazardous and so unsuccessful?&lt;/em&gt; The following account summarizes our limited knowledge of the epidemiology of miscarriage and then moves on to consider some of the medical causes of miscarriage...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Miscarriage is difficult to study, and the causes difficult to establish, so the literature showing that any interventions help (antibiotics, bed rest, supplements, etc.) is not plentiful. Smoking seems to have a deleterious effect on pregnancy. How this relates to early populations is a matter of conjecture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some good studies do exist, however. &lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJM199906103402304#t=articleResults&quot; rel=&quot;nofollow&quot;&gt;One good study&lt;/a&gt; in the New England Journal of Medicine followed an ideal group: women who had no history of infertility, who were trying to become pregnant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of 221 couples followed for 6 months, a total of 199 pregnancies were detected, of which 126 ended in live birth (therefore a 37% miscarriage rate). Because of the methodology, failure of blastocysts to implant could not be measured. The findings of this study were supported by others (&lt;a href=&quot;http://www.nejm.org/doi/pdf/10.1056/NEJM198807283190401&quot; rel=&quot;nofollow&quot;&gt;31%&lt;/a&gt;), etc.: early loss increased when implantation occurred later than 10 days after ovulation. While the authors were hopeful (&quot;There may be opportunities to increase fertility by extending the time during which implantation can occur.&quot;), they were also realistic (&quot;Such interventions should be approached cautiously, however, because they may have unintended consequences with respect to the quality of surviving embryos.&quot;) Basically, you can't fool around too much with Mother Nature in this realm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has modern medicine been able to change this rate? Not really. Even with IVF, where thousands of dollars are spent trying to preserve a single pregnancy (certainly not the norm), miscarriage is common. The best way to increase the viability of IVF pregnancy is to select better oocytes, embryos, etc. In other words, maternal factors remain refractory to manipulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even things obstetricians long took for gospel (for example, bedrest with pre-eclampsia) have &lt;a href=&quot;http://journals.lww.com/greenjournal/Abstract/1998/02000/Treatment_of_Miscarriage__Current_Practice_and.17.aspx&quot; rel=&quot;nofollow&quot;&gt;little evidence of benefit to the fetus&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The literature is vast in this area (reproduction is an important field to study). I can write a book on how little can be manipulated on average (I will consider spending thousands of dollars on one pregnancy &lt;em&gt;not average&lt;/em&gt;), but it wouldn't sell. What does sell are false claims, this one being as good as any claimed today:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To prevent miscarrying or if one that is apt to miscarrie goe a journey let her take this powder morning and evening whilst shee journeys: Take of Dragons Blood the weight of a silver two-pence, a dram of red corrall powdered, the weight of 2 barly corns of Ambergrease, Besar ye weight of 3 barly corns, mix all these together and keep them close stoped in little vial glasse when you use take as much of it as lie upon a penny in a little clary water at nighte when you goe to bed, and in ye morning fasting and sleep after it to use it till you are out of danger.   &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-01-03T23:46:08.133" LastActivityDate="2015-01-03T23:46:08.133" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26380" PostTypeId="1" CreationDate="2015-01-04T00:55:57.457" Score="0" ViewCount="579" Body="&lt;p&gt;A fetus can now be screened for some of the more common genetic diseases and its sex determined from just a whole blood sample from the pregnant mother. Fetal DNA is abundant enough in the systemic circuit to be able to be purified and sequences analyzed. Question is, in the case of fraternal twins, could the procedure discern between the two fetus's...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a clearer example, can it distinguish between:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scenario 1: if one fetus was male and one fetus female&#xA;And scenario 2: both male?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears the test would just look for presence of Y chromosome using certain markers. But it could then look at SNP to distinguish individuals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking for clarification here&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2015-01-04T03:37:35.303" Title="Can cfDNA testing distinguish results in the case of twins?" Tags="&lt;dna&gt;&lt;molecular-genetics&gt;&lt;pregnancy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26381" PostTypeId="1" AcceptedAnswerId="26394" CreationDate="2015-01-04T03:08:32.960" Score="1" ViewCount="610" Body="&lt;p&gt;After reading about complement pathway and the complement components, I was wondering, does the C1q component attach to the Fab fragment or to the Fc fragment? The pictures in Janeway's Immunobiology are confusing and the text don't mention about this. &lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="9943" LastEditDate="2015-01-04T23:53:46.177" LastActivityDate="2015-01-07T01:18:43.960" Title="C1q attachment to antibodies" Tags="&lt;immunology&gt;&lt;antibody&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26382" PostTypeId="2" ParentId="26380" CreationDate="2015-01-04T03:37:35.303" Score="1" Body="&lt;p&gt;I think you are overestimating how these cfDNA tests work.  Maybe I read the paper wrong, but from what I read of one technique (Sequenom's MaterniT21 test) there is no purification of fetal DNA.  They do restriction digests to assess the percentage of fetal DNA,  but I don't think they enrich for the fetal DNA when they sequence.  The library they make is mostly maternal, they are just looking for slight deviations in how many reads come from each chromosome, if too many come from chromosome 21, they conclude it's because the fetus has too many copies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And as for SNPs, coverage is way to low for that.  We're talking about 40 million reads, even if that were mostly fetal DNA, which I don't think it is, that's not enough coverage to call SNPs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if there were two fetuses, and they were not identical, then the signal from each would be half what would be expected based on the restriction digests assay. So maybe you would have enough counts that you could tell that the Y chromosome counts were too low, and the X chromosome a bit too high, but since these tests almost certainly have not been clinically tested on multiple fetuses well enough for verify their accuracy, no company is going to report results.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2015-01-04T03:37:35.303" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26383" PostTypeId="1" AcceptedAnswerId="26419" CreationDate="2015-01-04T11:33:38.237" Score="15" ViewCount="5896" Body="&lt;p&gt;&lt;strong&gt;Note: question rewritten to prevent misunderstanding and make it more answerable&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that some small animals like C. elegans display surprising sophistication with a very small number of cells. But I wonder, among the animals with known/estimated cell count, which has the fewest cells? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To make the question answerable, please note these constraints: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I'm only asking about members of the kingdom &lt;em&gt;Animalia&lt;/em&gt;, so single cell organisms and colonials like Vovox are excluded. If there are single cell organisms which are classified under Animalia (I think there aren't, but not 100% sure), I still want to know about the smallest multicellular animal. &lt;/li&gt;&#xA;&lt;li&gt;I'm only asking about species where we can distinguish &lt;em&gt;individuals&lt;/em&gt;. If some kind of polyp or sponge is just a bunch of cells which can merge with or separate from other cells and remain a viable organism, it's not interesting. &lt;/li&gt;&#xA;&lt;li&gt;Please only consider species where the adult form reaches some size and &lt;em&gt;stops growing&lt;/em&gt;. (Macroscopic) examples like the tapeworm, which continues building more proglottides throughout life, or fish which continue getting larger as they age, are excluded.&lt;/li&gt;&#xA;&lt;li&gt;If the species consists of distinctive, stable &quot;subgroups&quot; of different sizes, &lt;em&gt;the smallest size subgroup&lt;/em&gt; counts. For dogs, the size of the average chihuahua counts. For C. elegans, the size of the hermaphrodite (959 cells vs 1031 in the male) counts. &lt;/li&gt;&#xA;&lt;li&gt;What counts is the number of cells in a &lt;em&gt;healthy adult&lt;/em&gt; of the species or the relevant subgroup. For non-eutelic animals, make that the average healthy adult. Not the smallest ever observed exemplar, and also not amputated or stunted exemplars.&lt;/li&gt;&#xA;&lt;li&gt;I am aware that we haven't discovered all microscopic animals yet, and haven't counted the cells of all discovered ones. Still, I'd like info on the &lt;em&gt;current level of knowledge&lt;/em&gt;, including current known cell count, evidence that something has less than the current lowest known-for-sure count, and other relevant information. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1578" LastEditorUserId="1578" LastEditDate="2015-01-04T19:55:13.210" LastActivityDate="2015-04-15T23:11:41.263" Title="How many cells does the smallest animal have?" Tags="&lt;zoology&gt;&lt;anatomy&gt;" AnswerCount="3" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26384" PostTypeId="2" ParentId="26369" CreationDate="2015-01-04T12:04:04.533" Score="1" Body="&lt;p&gt;Your confusion comes from the inconsistent terminology in the literature. The attachement of the spindles to the chromosomes happens in the &lt;strong&gt;Prometaphase&lt;/strong&gt; &lt;a href=&quot;https://books.google.de/books?id=Cg4WAgAAQBAJ&amp;amp;lpg=PP1&amp;amp;dq=essential%20cell%20biology&amp;amp;hl=de&amp;amp;pg=PA624#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;[1&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Prometaphase&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]. The name already suggests that this is not one of the classical phases is cell division, but lies somewhere between Pro- and metaphase. Wikipedia states:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Prometaphase is sometimes simply included as part of the end of prophase and early metaphase.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you really need to stick to the classical scheme of pro-, meta-, ana- and telophase, I would personally suggest to treat the attachement (not the formation!) of spindles as a part of the metaphase.&lt;/p&gt;&#xA;" OwnerUserId="8015" LastActivityDate="2015-01-04T12:04:04.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26385" PostTypeId="2" ParentId="26383" CreationDate="2015-01-04T12:36:26.320" Score="10" Body="&lt;p&gt;I don't know about all known animals, or actual cell count. However, males of the wasp &lt;a href=&quot;http://en.wikipedia.org/wiki/Dicopomorpha_echmepterygis&quot;&gt;&lt;em&gt;Dicopomorpha echmepterygis&lt;/em&gt;&lt;/a&gt; are considered the smallest known insects with a body size of 139 μm. This should at least be a contender for smallest animal. As a reference point, &lt;em&gt;C. elegans&lt;/em&gt; are usually about 1mm long.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, given that we know only about 10% of the estimated number of species, and the ones we know are biased towards larger animal species, the smallest animal is most likely undescribed. In the case of parasitic wasps (or other insect parasites) these are extremely poorly known and new species are often described. Our knowledge of soil communities are also poorly known and includes many extremely small animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the record, answers to a question like this depends alot on exactly what you include and how size is calculated. Could it be either sex or the average between sexes?&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2015-01-04T12:36:26.320" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26387" PostTypeId="2" ParentId="26383" CreationDate="2015-01-04T15:35:54.550" Score="0" Body="&lt;p&gt;Some of the smallest animals have only one cell. Paramecium Aurelia &lt;img src=&quot;https://i.stack.imgur.com/c5YRP.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2015-01-04T16:15:54.260" LastActivityDate="2015-01-04T16:15:54.260" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="26388" PostTypeId="1" AcceptedAnswerId="26391" CreationDate="2015-01-04T16:50:12.487" Score="3" ViewCount="134" Body="&lt;p&gt;I have seen on the internet that prolonged steriod treatment can result in the development of steroid drug tolerance leading to decreased hormone secretion. In turn this may lead to drug dependence, as you need to keep taking that drug to keep your body to function normally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can steroid treatment lead to drug dependency&lt;/strong&gt;, and if yes, &lt;strong&gt;how&lt;/strong&gt;?  &lt;/p&gt;&#xA;" OwnerUserId="11824" LastEditorUserId="9943" LastEditDate="2015-01-05T00:04:46.307" LastActivityDate="2020-11-08T22:25:31.877" Title="How does steroid dependence occur?" Tags="&lt;pharmacology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26389" PostTypeId="1" CreationDate="2015-01-04T20:45:44.653" Score="0" ViewCount="860" Body="&lt;p&gt;I really want to know what the second phase of photosynthesis (in the dark) is. I have a fair understanding of the first cycle where molecular oxygen is generated under the influence of light, but I don't understand the second cycle which can take place in the dark. It would greatly help to have a graphic of the second phase of photosynthesis.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: it is not for my homework, but for my own understanding. My textbook doesn't explain things very well.&lt;/p&gt;&#xA;" OwnerUserId="11826" LastEditorUserId="9943" LastEditDate="2015-01-05T22:43:37.680" LastActivityDate="2015-01-06T08:32:04.740" Title="What is the second phase of photosynthesis?" Tags="&lt;cell-biology&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26390" PostTypeId="2" ParentId="26304" CreationDate="2015-01-04T20:53:13.207" Score="2" Body="&lt;p&gt;I hope that I got what are you asking. You give the example of words, it's not good one. Look on the protein like a machine or maybe cupboard. You bought one in Ikea and now you need to follow the instruction to bring together all the elements. If you just paste together all the parts you will not get a working cupboard. What rules the parts of cupboard following? Physic.&#xA;&lt;br&gt;&lt;br&gt;&#xA;Take for beginning the Bohr model of atom. If you want simpler example - planets in solar system. After that put 10 atoms together to from the simplest amino acid. What structure will they get? Bring near another amino acid. How will they interact together? &#xA;&lt;br&gt;&lt;br&gt;&#xA;The rules comes from physics. And they are very very very very complected. To understand what structure some protein will get or how it will interact with another protein - you need to take all the atoms in the system and to know how they will act one with another. Only huge computers can calculate such things - and only the simplest of them.&#xA;&lt;br&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit: answer to the comment:&lt;/strong&gt;&lt;br&gt;&#xA;Thats what so amazing in the nature. The evolution found the way to build all the body proteins just from approximately 20 amino acids. By the way that doesn't mean that there is just 20 a.c. There are more that 500. 240 Of them can be found free in nature and other only only as intermediates in metabolism. (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/anie.198308161/abstract&quot; rel=&quot;nofollow&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1002/anie.198308161/abstract&lt;/a&gt;) &#xA;&lt;br&gt;&lt;br&gt;&#xA;If you want another example - take Lego. You have - lets say - 20 types of different peaces but you can make a lot of different things from them.&lt;br&gt;&#xA;&lt;br&gt;&#xA;The nature must use a minimal amount of building blocks. This giving advantage in the evolution cause it is simpler. Look at the DNA. Its build just from 4 building blocks! And caring all the information of how to form entire body. Isn't it amazing? :)  &lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="10104" LastEditDate="2015-01-05T11:57:50.070" LastActivityDate="2015-01-05T11:57:50.070" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26391" PostTypeId="2" ParentId="26388" CreationDate="2015-01-04T21:37:45.033" Score="2" Body="&lt;p&gt;All classes of drugs react differently in the body. Some bind to receptors, some clean receptors, some drugs cause re-uptake inhibition in the brain, and others destroy viral and bacterial infections. Classifying drugs and how the human body would develop a tolerance to them in a post on this website would take pages upon pages to answer. When you say steroids, i'm assuming you are talking about anabolic steroids. That is the male sex hormone testosterone and its multitudes of derivatives. (DHT and non-DHT). Your body does not in fact develop a &quot;dependance&quot; on the drugs, rather it is a checks and balances system that your endocrine system establishes. Lets say you take a dosage of Testosterone Cypionate at 200mg a week for a 20 week interval from your G.P (common treatment for andropause). In laymans terms, your body senses the increase of testosterone and tells your Leydig Cells in the testes to stop signaling LH (responsible for testosterone production). Because it sees that there is already an abundance of the hormone. Now, once treatment stops, there are a series of protocols one could take to stimulate the natural production of testosterone again. Other forms of AAS are much harder on the HPTA than others however. (Trenbolone Acetate)&lt;/p&gt;&#xA;" OwnerUserId="8059" LastEditorUserId="8059" LastEditDate="2015-01-04T23:08:00.403" LastActivityDate="2015-01-04T23:08:00.403" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26392" PostTypeId="2" ParentId="26304" CreationDate="2015-01-04T22:42:29.580" Score="4" Body="&lt;p&gt;&lt;strong&gt;&lt;em&gt;Disclaimer:&lt;/strong&gt; This is an interesting question if I have understood what you are trying to ask. But unfortunately the case is that there are so many different cases its impossible to cover them here. Other answers talk about folding and modification, but these are still heavily dependant on the &quot;2d&quot; DNA sequence and aren't useful if all one has is a final protein, so I'll discuss the 'rules' of a final structure. This started as a comment and got too long!&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, &lt;strong&gt;no&lt;/strong&gt;, there are not many examples in the grand scheme of things where rules at a protein level exist in any sort of grammatical way. Its all about 3D chemistry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Protein Structure in relation to Function.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Functional areas in a protein are often made up of structures like alpha helices and beta sheets linked by very flexible looping regions. The way these structural elements are connected is generally different in every protein. However some motifs that perform similar tasks can be identified by their 3D shape and order of connection (which I think is what you're asking about). For example the OB motif (images and good starting point &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0959440X02003925&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) has a strict order that the beta sheets follow, whereas the helix is optional. Although this is a neat example of protein &quot;grammar&quot;, its very much exceptional when motifs like this are identified.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;No Obvious Rules.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;This following answer is educated guessing, and other peoples comments would be helpful.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Proteins are much more complex than a 2 dimensional language like English or DNA. One way to think about why your question is difficult to answer is considering that protein biochemistry happens in 3D space whereas our other examples, language and DNA, operate linearly in a 2D line. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any evidence of a linear ordering in a finished protein implies very simple folding and post-translational processing. Most biochemical tasks are not simple and require complex nuances in the enzymes' chemistry (which comes from 3D chemistry, not 2D sequence). DNA is complicated too, but like our language, it is designed to be simple and read quickly in a line. This means if a sequence wants to do something a bit more sophisticated, it needs a specific order. This isn't a problem in 3D space as there is a lot more to variation other than sequence.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2016-10-24T05:15:51.763" LastActivityDate="2016-10-24T05:15:51.763" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26393" PostTypeId="2" ParentId="26274" CreationDate="2015-01-04T23:03:55.013" Score="2" Body="&lt;p&gt;&lt;em&gt;See this more as a comment than an answer, since it became too long for a comment. However, I think some of the examples should be relevant to refine your question.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;One thing that I find vague in this question is what exactly constitutes a &quot;process&quot;/&quot;function&quot;? To me, this can be almost anything. You seem to be focusing on molecular biology and biological pathways, but I think it is just as reasonable to think in terms of large scale processes. If so, there are lots of processes that seem valid in my mind, relating to e.g. reproduction and dispersal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, in primitive plants (and other taxa) fertilization is external and dependent on environmental moisture to transport gametes. Organisms with internal fertilization has bypassed this by providing their own mechanism for fertilization, which does not depend on environmental processes (to the same extent). The evolutionary forces behind this was maybe/probably that it was more efficient and allowed colonization of new environments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another similar example is seed dispersal in plants, where some are wind dispersed (&quot;primitive&quot; state) and others use active measures to eject seeds (ballochory). By doing this they have bypassed the dependence of wind to disperse their seeds. The same kinds of mechanisms can also be found in groups of mosses. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In both these cases a function that was previously external and environmentally mediated is now provided by the organisms themselves, and they involve quite complicated morphological and anatomical adaptations. Do you find them valid for your question? These are just two examples, but there are lots of similar cases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More in the line of comments to your question, I think you should provide one or two references to the hypothesis you are referring to (i.e. where it has been used/discussed), which would make it easier to understand exactly what you are after (and also provide an entry into the literature). This could maybe also help explain why the &quot;&lt;em&gt;...evolved solution 'echoes' the one provided by the environment&lt;/em&gt;&quot;. At the moment I don't understand at all why this should be the case in general. Adaptive evolution happen because of selection that acts on differences in fitness, and it is indifferent to whether the mechanism echoes a previous solution to a similar problem (except for the fact that evolution is constrained by the evolutionary history of organisms).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2015-01-04T23:03:55.013" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26394" PostTypeId="2" ParentId="26381" CreationDate="2015-01-04T23:55:40.643" Score="1" Body="&lt;p&gt;Complement factor &lt;strong&gt;c1q&lt;/strong&gt; binds to the constant &lt;strong&gt;Fc portion of an antibody&lt;/strong&gt; (&lt;a href=&quot;http://www.nature.com/nature/journal/v332/n6166/abs/332738a0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Duncan &amp;amp; Winter, 1988&lt;/a&gt;). Indeed, the constant (Fc) tail of the antibody is where other proteins involved in immune responses typically bind, most notably the Fc receptors (e.g., &lt;a href=&quot;http://www.nature.com/nm/journal/v6/n4/full/nm0400_443.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Clynes et al., 2000&lt;/a&gt;) found on immune cells such as B lymphocytes. Fc receptors mediate the recruitment of immune cells to a site of infection. The primary role of the Fab region is antigen binding as it contains the highly variable antigen binding domain. See the following figure (from the site of &lt;a href=&quot;http://www.invivogen.com/review-antibody-generation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Invivogen&lt;/a&gt;) for the Fab and Fc region showing the constant and variable regions of antibodies:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/D2d1M.gif&quot; alt=&quot;Ab&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Figure legend from &lt;a href=&quot;http://www.invivogen.com/review-antibody-generation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Invivogen&lt;/a&gt;): The Fc region mediates effector functions, such as antibody-dependent cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC). In ADCC, the Fc region of an antibody binds to Fc receptors (FcγRs) on the surface of immune effector cells such as natural killers and macrophages, leading to the phagocytosis or lysis of the targeted cells. In CDC, the antibodies kill the targeted cells by triggering the complement cascade at the cell surface. I&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The constant regions of antibodies are located on the heavy chain (CH1,2,3) and the light chain (CL). These constant regions are potential binding sites for other immune molecules as they are constant between antibodies, irrespective of the variable region in Fab. Most of the constant regions are found on the Fc region explaining its major role in binding other molecules involved in the immune response, including complement factor c1q. However, the constant regions in Fab (CL) may also provide binding sites for other proteins and indeed some bacterial compounds are known to bind to this region (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7927988&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bouvet, 1994&lt;/a&gt;). However, I have not found evidence of c1q binding the Fab region.  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-07T01:18:43.960" LastActivityDate="2015-01-07T01:18:43.960" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26395" PostTypeId="2" ParentId="26389" CreationDate="2015-01-05T00:38:46.960" Score="4" Body="&lt;p&gt;Here's an overview of both the Light and Dark cycles of photosynthesis, which looked particularly useful to me as it shows that the energy-carriers ATP and NADPH&lt;sub&gt;2&lt;/sub&gt; generated through solar energy are used in the dark cycle to generate sugars. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RrOA2.jpg&quot; alt=&quot;PhotoSynthesis&quot;&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is another one that shows more details on the precursors involved in the Calvin cycle:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hLlvt.png&quot; alt=&quot;CalvinCycle&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As commented by others, googling 'dark cycle' or its synonyms will give thousands of optional images to choose from if these don't suffice. The first one is taken from tutorvista.com the second one from users.rcn.com.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-05T12:39:54.737" LastActivityDate="2015-01-05T12:39:54.737" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26396" PostTypeId="1" AcceptedAnswerId="26446" CreationDate="2015-01-05T03:16:47.357" Score="7" ViewCount="133" Body="&lt;p&gt;In his 1970 paper &quot;Selfish and Spiteful Behaviour in an Evolutionary Model&quot;, Hamilton uses Price's equation to derive his well-known rule $rb -c &amp;gt;0$. My question is about one of the steps in his derivation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hamilton considers a population of $n$ individuals. Let $s_{ij}$ be the effect of individual $i$ on the fitness of $j$. The fitness of an individual $j$ is defined as $w_j = 1 + \sum_i s_{ij}$, $w=1/n \sum_j w_j$ is the mean fitness in the population, and $q=1/n \sum_j q_j$ is the average frequency of a certain allele. Using Price's equation, we get &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w \Delta q = Cov (q_j, \sum_i s_{ij})$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far so good. But Hamilton then says that this equation can be rewritten as&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w\Delta q = \sum_i 1/n \sum_j (q_j - q)s_{ij}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on the definition of covariance (i.e., $Cov (X,Y) = E((X-E(X))(Y-E(Y)))$, this seems to only be the case if $E(\sum_i s_{ij}) = 1/n \sum_j \sum_i s_{ij} = 0$. But this would imply that the average fitness wouldn't change over time, which sounds odd for me. In sum, I don't understand this step in Hamilton's paper. What am I missing?&lt;/p&gt;&#xA;" OwnerUserId="11829" LastEditorUserId="11829" LastEditDate="2015-01-06T01:26:57.610" LastActivityDate="2015-01-07T01:51:23.873" Title="Hamilton's derivation of direct fitness from his 1970 paper" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;population-genetics&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26397" PostTypeId="2" ParentId="26304" CreationDate="2015-01-05T03:37:25.897" Score="6" Body="&lt;p&gt;It sounds like your question is &quot;what are the rules to protein folding?&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's not the only way to read your question.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Protein Folding is a unique problem - a 1D sequence maps to a 3D object.  Since proteins mediate nearly all biochemical transformations and therefore mediate life's processes, protein folding one of the great unsolved problems in science today. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see in the example folded structure above there are helices and flat sheets of connected strands.  You can see below in the schematic alpha beta barrel motif of triose phosphate isomerase (TIM) how elegant these structures can be.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sy3y7.png&quot; alt=&quot;the TIM alpha beta barrel&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although the combinations and overall organization of the beta sheets and the alpha helices are boundless, there are some unifying motifs in these structures. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Long ago, a couple of researchers tabulated the amino acids probability of being in alpha helices or beta strands.  The &lt;a href=&quot;http://en.wikipedia.org/wiki/Chou%E2%80%93Fasman_method&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chou-Fasman model&lt;/a&gt; is important in that it has approximately ~70% chance of detecting alpha helices and beta strands.  Its not a great accuracy but what's really amazing about these algorithms is that they show that local forces - the interaction of amino acids near each other in the sequence have something to do with the formation of at least alpha-helices and beta strands. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been pounds worth of papers written since then.  In general, statistical surveys of protein sequences have been able to identify folds or motifs by a long list of string and machine learning algorithms.  Hidden Markov Models and Bayesian profiles are popular. Of course all these are similar to Chou-Fasman in that they work on the sequence in short segments more or less.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a while it was thought that molecular dynamics and other discrete simulations might help to solve protein folding by allowing long distance interactions to be involved.  Just simulating the entire protein molecule in a computer program as it moves into a folded conformation, but this has not proven to be possible for a couple of reasons: (1) it takes a long time for a protein to fold relative to the length of a tractable simulation (2) the forces involved in protein folding and molecular size scales are not really easy to simulate - they do not precisely simulate the forces and behavior experienced by molecules and they involve many more solvent molecules than most computations can involve - even today's server farms would get clogged up with respectable protein folding simulation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since 1994 the &lt;a href=&quot;http://predictioncenter.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Critical Assessment of Structure Prediction (CASP)&lt;/a&gt; have provided an open competition every 2 years where 3D structures that have been determined experimentally is held from publication.  While its well attended &lt;a href=&quot;http://www.nature.com/nature/journal/v405/n6782/abs/405039a0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;a new class of algorithms showed up around 2000&lt;/a&gt;.  These algorithms work on the assumption that local forces are important to protein folding, but often incorporating molecular dynamics.  Using MD or statistics based on protein structures (see the &lt;a href=&quot;http://www.rcsb.org/pdb/home/home.do&quot; rel=&quot;nofollow noreferrer&quot;&gt;RCSB&lt;/a&gt; for the repository), segments of the protein sequence are tested for structural tendencies.  chaining these predictions together, initial protein folds are put together.  Once put together long term interactions can assemble a protein structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW that is not to say that Protein folding is solved - the solutions that come out often produce a structure that is really similar to the final structure, but often there are substantial differences.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just looking at the individual sequence there are no simple rules to decide how the protein fold - ultimately molecular physics of the individual sequence determines where the fold will go.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is incredibly terse, but it could get you started.  Study of protein without any helices or beta strands is a topic in itself - they can be treated the same way as above.  Then there are also proteins who do not have a single fold, but are dynamic and flop around all the time, or only have a shape when in contact with a surface of some kind.  So there's even more.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2015-01-05T15:47:24.847" LastActivityDate="2015-01-05T15:47:24.847" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26399" PostTypeId="2" ParentId="2650" CreationDate="2015-01-05T08:52:50.733" Score="2" Body="&lt;p&gt;Its not known what the consensus is but there is definitely a decline in the race concept. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The concept of biological race has declined significantly in frequency of use in physical anthropology in the United States during the 20th century. We present three kinds of evidence of this rejection of what was a core concept: (1) The frequency of articles using the race concept in the AJPA declined from 60 percent in 1918 to 4 percent in 2001 (r = -.89, p = .01). (2) Content analysis of university level textbooks of introductory physical anthropology for 1980-99 found only one textbook which supported the race concept. (3) A series of mailed questionnaires to members of the American Anthropological Association found that while 37 percent of responding physical anthropologists rejected the race concept in 1978, this rose to 69 percent in 1999.”&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Section - Summary, paragraph 1&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://anthro.amu.edu.pl/pdf/paar/vol066/01lieb.pdf&quot; rel=&quot;nofollow&quot;&gt;&quot;The decline of race in American physical anthropology&quot;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="11679" LastActivityDate="2015-01-05T08:52:50.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26403" PostTypeId="1" AcceptedAnswerId="26404" CreationDate="2015-01-05T14:34:00.943" Score="1" ViewCount="174" Body="&lt;p&gt;Sugars are found ubiquitously in plants and are regulated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For sucrose it's pretty straightforward - it's basically kept at a low ish level, and put into storage or other intermediate compounds. These act to inhibit or promote other parts of the calvin cycle of sugar production (fructose 2,6 bisphosphate especially iirc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fructose is a bit more obscure. What are the regulatory feedback loops involved?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastActivityDate="2015-01-05T14:34:00.943" Title="What controls Fructose regulation in plants?" Tags="&lt;biochemistry&gt;&lt;plant-physiology&gt;&lt;sugar&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26404" PostTypeId="2" ParentId="26403" CreationDate="2015-01-05T14:34:00.943" Score="1" Body="&lt;p&gt;&lt;strong&gt;Preamble&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, fructose kinases &lt;em&gt;(like Fru6P,2-kinase)&lt;/em&gt; and fructose phosphotases &lt;em&gt;(such as Fru2,6bisP)&lt;/em&gt; regulate and are in turn regulated by fructose &lt;em&gt;(specifically Fru6P)&lt;/em&gt;  levels in plants. There are also several metabolites that regulate the rate at which those fructose enzymes function creating quite a complex fructose regulatory network. This phosphorylation can make fructose unavailable or available to proteins as well as providing energy in the process (and aparently the rate of this can be controlled effectively &lt;em&gt;in vivo&lt;/em&gt; (Stitt, 1990)).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't come across any cell uptake regulation, but remember plants are physiologically very different to humans and there may not be a like for like system in this case. Although I suspect there will be since in plants fructose can be concencentrated in fruiting bodies. Perhaps another answer, or a major edit to this answer can explain that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fructose is often referred to as a regulatory metabolite in plants &lt;em&gt;i.e&lt;/em&gt; levels of fructose affect other pathways due to its phosphorylated state. However, there are lots of sugar regulating systems in plants. Although &lt;a href=&quot;http://www.plantphysiol.org/content/124/4/1532.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article focuses more on glucose and galactose, it emphasises the idea of a regulatory web rather than a cycle when it comes to plants and sugar regulation. Below the studies are based on plants such as spinach and other leafy vegetation, not fruiting plants I'm afraid!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Kinase Control&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3PGA, 2PGA, PEP, dihydroxyacetone P, and the 2-carbon intermediate glycollate-2-P are all metabolites that control phosphorylation that inhibit the kinase, whilst Pi activates the kinase. Interestingly PPi also inhibits the kinase by competing with ATP. As one can imagine, this causes sigmoidal ATP saturation kinetics and is clearly indicative of regulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Phosphorylation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fru6P and Pi both inhibit Fru2,6bisP hydrolysis by FRU2,6PASE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/pdf/10.1146/annurev.arplant.47.1.185&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; from 1996 has a figure showing just how complex sugar pathways can be. To expand on your question, we can see how fructose phosphorylation plays a role in regulating in Sucrose and Starch glycolysis (Plaxton, 1996).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Disclaimer: I haven't studied this since undergraduate level, so constructive comments are welcome and I encourage people to edit this answer to improve it and help it more aptly answer the question!&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3553" LastActivityDate="2015-01-05T14:34:00.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26405" PostTypeId="2" ParentId="26274" CreationDate="2015-01-05T14:54:49.100" Score="1" Body="&lt;p&gt;After considering this question some more, I think a key feature for this hypothesis to work is that the original function must be so integrated and vital for the biology of the organism that it must be mimicked/echoed to some extent. In terms of your RNA-example, it was not enought to evolve the ability to synthesize any complex molecule that could function as an enzyme and information carrier, but had to be RNA since this was already used in the biological pathways of the primitive organism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With this in mind I think that you should look closely at vitamins (or other essential nutrients) for evidence of similar processes. The key think about vitamins is that they are often large complex molecules that are vital nutrients and the ability to synthesize vitamins differs widely between taxa. In a sense, the nucleotides were essential nutrients for the organisms in the proposed RNA-world, so vitamins/essential nutrients should be a relevant analog to look for similar evolutionary processes. However, keep in mind that molecular biology is not at all my field, and I might be mistaken on some aspects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take the example of &lt;strong&gt;Vitamin C&lt;/strong&gt;. This cannot be synthezised by humans, but by most other mammals (vitamin C synthesis is considered ancestral in mammals). It can also be synthesized by plants, yeast and many other animals. However, vitamin C is used in different ways in different organisms. Plants use it e.g. for photosynthesis, photoprotection, cell wall growth and in the synthesis of plant hormones, while humans and other mammals use it as enzyme cofactors and for immune responses. Another key aspect is that plants, yeast and animals all use different pathways to synthezise vitamin C (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145266/#R2&quot; rel=&quot;nofollow&quot; title=&quot;Drouin et al. 2011. The Genetics of Vitamin C Loss in Vertebrates. Curr Genomics 12(5): 371–378.&quot;&gt;Drouin et al, 2011&lt;/a&gt;), which indicates that the synthesis of vitamin C is not ancestral to all these taxa (i.e. not an ancestral feature of all eukaryotic life). In mammals, the synthesis of vitamin C has also switched between organs multiple times, which also indicates novel adaptations that results in the same molecule. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To me, it seems very likely that vitamin C was initially obtained by animals from plants (which have very high concentrations of vitamin C) as part of their diet (i.e. environmentally provided) and became an essential component in many biological pathways. If this is the case, animals later gained the ability to synthesize vitamin C themselves, using a different biological pathway than plants. This feature has later been secondarily lost (e.g. humans and teleost fish) and regained multiple times in different taxa. However, this is speculation on my part, and I don't know this literature well enought to say if there are studies on the origin of vitamin C synthesis in animals, or if the pathways of vitamin C synthesis in plants and animals are fundamentally related. A review by &lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.arplant.52.1.437&quot; rel=&quot;nofollow&quot; title=&quot;Smirnoff et al. 2001. BIOSYNTHESIS OF ASCORBIC ACID IN PLANTS: A Renaissance. Annual Review of Plant Physiology and Plant Molecular Biology 52: 437-467&quot;&gt;Smirnoff et al (2001)&lt;/a&gt; indicates that there are some similarities between the enzymes involved in the final stages of vitamin C synthesis:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The gene and/or cDNAs encoding GalLDH, GulLO, and AraLO have been isolated and described from several organisms including cauliflower, sweet potato (GalLDH, 54, 121), rat (GulLO, 70), and Saccharomyces cerevisiae (53). In addition, complete nucleotide coding sequences of the A. thaliana and Nicotiana tabacum GalLDH genes (Accession No. AB042279.1, AB024527.1), and the Candida albicans AraLO gene (Accession No. AF031228) have been submitted directly to GenBank and associated databases. The predicted amino acid sequences of these related proteins share substantial amounts of identity. The mature cauliflower GalLDH amino acid sequence shares 28% overall identity with the rat GulLO and 26% identity with the Candida albicans AraLO (using the J Hein method with PAM250 residue weight table).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, this doesn't necessarily mean that the synthesis of vitamin C is ancestral to both plants and animals. I haven't been able to find any papers on the origin of vitamin C synthesis, and if there is evidence that it is ancestral to all modern life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In either case, I think it could be useful for you to look closely at vitamins in animals or other organisms for possible examples of the type of processes you are looking for, since they are (by definition) essential nutrients that some animals can and others cannot synthesize. They should therefore be good potential targets to find similar processes as your RNA-example. &lt;em&gt;Vitamin B12&lt;/em&gt; is an extreme to the other end, since it is essential for most animals but can only be synthesized by bacteria (so the main source is through bacterial symbiosis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also possible that I'm mistaken, and that synthesis of all vitamins is ancestral to modern life, and that there has only been subsequent loss of the ability to synthesize certain vitamins/nutrients. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S016895251300053X#&quot; rel=&quot;nofollow&quot; title=&quot;Helliwell et al. 2013. Widespread decay of vitamin-related pathways: coincidence or consequence? Trends in Genetics 29(8):  469–478&quot;&gt;Helliwell et al (2013)&lt;/a&gt; mentions this as a possibility in relation to the RNA-world, but also points out that the pathways for biosynthesis often differs between taxa, which would suggest that there has indeed been secondary acquisition:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The fundamental nature of vitamins is illustrated by the close structural relation of many vitamins to nucleotides (Figure 1), reflecting the likelihood that they were present in the ancient RNA world. Yet, their biosynthetic pathways appear to have arisen via the patchwork model of pathway evolution [31], resulting in the recruitment of unrelated proteins in any one pathway. Indeed, many vitamins are synthesized by different routes in different organisms [20]. For example, alternative pathways are found for thiamine biosynthesis in prokaryotes and among different eukaryotes (Figure 2) [20]. Despite this diversity in biosynthetic pathways, there appear to be common trends in the causes and mechanisms underlying pathway loss.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-01-06T09:35:32.187" LastActivityDate="2015-01-06T09:35:32.187" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26406" PostTypeId="2" ParentId="21244" CreationDate="2015-01-05T17:11:49.367" Score="4" Body="&lt;p&gt;While your question asking about birds, reptiles and fish (oh my!) may be too broad, hopefully looking at frog oogenesis can show some differences in large offspring number v. small offspring number. Some frogs even give birth to live offspring (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25551466&quot; rel=&quot;nofollow noreferrer&quot;&gt;Iskandar &lt;em&gt;et al.&lt;/em&gt; 2014&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;p&gt;Much of this explanation can be found in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK9983/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Developmental Biology, 6th edition&lt;/a&gt; by Gilbert SF.&lt;/p&gt;&#xA;&lt;p&gt;In frogs, meiosis happens in stages (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10008/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Developmental Biology&lt;/a&gt;):&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/au6Td.jpg&quot; alt=&quot;frog oogenesis&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;This shows that different &amp;quot;cohorts&amp;quot; of oocytes form, develop, and are released, rather than a single group of mitotic events that are released gradually (as in humans). When the eggs have undergone &lt;a href=&quot;http://en.wikipedia.org/wiki/Vitellogenesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;vitellogenesis&lt;/a&gt; (yolk development), they are ready for fertilization.&lt;/p&gt;&#xA;&lt;p&gt;As far as this question is concerned:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;I am mainly interested in this to understand how the mother's chromosomes are represented in the offspring. Are all of her chromosomes guaranteed to be represented in at least one offspring?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;If you're asking whether or not all of the mother's chromosomes will be represented in her &lt;em&gt;total&lt;/em&gt; offspring, perhaps--with a large number of offspring (and a high ratio of fertilized eggs) the probability is very high.&lt;/p&gt;&#xA;&lt;p&gt;No &lt;em&gt;single&lt;/em&gt; offspring will contain &lt;strong&gt;all&lt;/strong&gt; of its mother's chromosomes. Let's look at a diploid organism with two pairs of chromosomes: A and B. At the beginning of meiosis I, a cell will have one &lt;em&gt;copy&lt;/em&gt; of both &lt;em&gt;pairs&lt;/em&gt;:&lt;/p&gt;&#xA;&lt;pre&gt;&lt;code&gt;A1 A2 B1 B2&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;p&gt;Then comes synthesis, duplicating all chromosomes. Now we have two &lt;em&gt;copies&lt;/em&gt; of each &lt;em&gt;pair&lt;/em&gt;:&lt;/p&gt;&#xA;&lt;pre&gt;&lt;code&gt;A1A1 A2A2 B1B1 B2B2&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;p&gt;In prophase, chromosomes are condensed and the duplicated pairs connect in a process called synapsis:&lt;/p&gt;&#xA;&lt;pre&gt;&lt;code&gt;A1A1-A2A2 B1B1-B2B2&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;p&gt;In anaphase, the pairs are pulled apart so that each daughter cell has &lt;em&gt;two&lt;/em&gt; copies of a &lt;em&gt;single&lt;/em&gt; member of the pair:&lt;/p&gt;&#xA;&lt;pre&gt;&lt;code&gt;daughter Y: A1A1 B2B2&#xA;daughter Z: A2A2 B1B1&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;p&gt;&lt;em&gt;Note that at this point it is &lt;strong&gt;not possible&lt;/strong&gt; for either of the daughter cells to contain &lt;strong&gt;all&lt;/strong&gt; of the mother's chromosomes.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;With meiosis II, these &lt;em&gt;copies&lt;/em&gt; are pulled apart, making four daughter cells:&lt;/p&gt;&#xA;&lt;pre&gt;&lt;code&gt;daughter Y1: A1 B2&#xA;daughter Y2: A1 B2&#xA;daughter Z1: A2 B1&#xA;daughter Z2: A2 B1&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;p&gt;These are now haploid, and await the male's sperm to make them diploid once more. Also note that daughters Y1/Y2 and Z1/Z2 are chromosomally identical (they can be different in practice with crossing over).&lt;/p&gt;&#xA;&lt;p&gt;Here is a prettier representation of what I just described (&lt;a href=&quot;http://en.wikipedia.org/wiki/Meiosis#Prophase_I&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;):&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KapcI.png&quot; alt=&quot;meiosis&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The key is to remember that &lt;em&gt;pairs&lt;/em&gt; of chromosomes and &lt;em&gt;copies&lt;/em&gt; of chromosomes are different and to keep track of how they segregate during meiosis.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt; To address your clarification:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;I am not talking about whether or not any of the daughter cells contains all of the mothers genetic material by itself, but rather whether every segment of genetic material is found in at least one offspring.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This is more of a probability question. If all oocytes mature, and are fertilized, the answer is clearly yes. However, not all oocytes are fertilized. Let's look at the same four daughter cells from my earlier example:&lt;/p&gt;&#xA;&lt;pre&gt;&lt;code&gt;daughter Y1: A1 B2&#xA;daughter Y2: A1 B2&#xA;daughter Z1: A2 B1&#xA;daughter Z2: A2 B1&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;p&gt;Let's say 2/4 (50%) are fertilized by the male frog. Going through all possible fertilizations, let's see how many combinations result in all of the mother's genetic material being passed down:&lt;/p&gt;&#xA;&lt;pre&gt;&lt;code&gt;Y1, Y2 - No&#xA;Y1, Z1 - Yes&#xA;Y1, Z2 - Yes&#xA;Y2, Z1 - Yes&#xA;Y2, Z2 - Yes&#xA;Z1, Z2 - No&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;p&gt;The answer to your question really depends on what proportion of oocytes make it to maturity, and what proportion of mature oocytes are fertilized. The probability of all the mother's genetic material being passed down increases with increasing fertilization ratio/egg number, so given the high number of offspring produced by many species of frog, I'd say that there is a good chance of all the mother's genetic material making it to the next generation, although it is not guaranteed.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-01-05T18:42:48.350" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26407" PostTypeId="1" AcceptedAnswerId="26410" CreationDate="2015-01-05T17:23:02.503" Score="2" ViewCount="369" Body="&lt;p&gt;I am going to give a rough presentation on twin studies.&#xA;The terms heritability and concordance are included already, but I struggle with understanding the difference of the genetic material of dizygotic twins and ordinary siblings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While ordinary siblings evolved from different sperm and egg cells, I only know that dizygotic twins form when two different sperm cells fertilize egg cells of the same cycle. However, I'm not sure if these cells are identical products of the same meiosis process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I appreciate your help and time.&lt;/p&gt;&#xA;" OwnerUserId="11837" LastEditorUserId="9829" LastEditDate="2015-01-07T16:48:12.413" LastActivityDate="2015-01-07T16:48:12.413" Title="How does the genetic material differ between dizygotic twins and ordinary siblings?" Tags="&lt;human-biology&gt;&lt;twins&gt;&lt;oogenesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26408" PostTypeId="2" ParentId="21244" CreationDate="2015-01-05T18:30:04.587" Score="6" Body="&lt;p&gt;I'm not sure about the ubiquity of this but, in many animals, each primary oocyte that undergoes oogenesis only produces one mature egg. The other products of meiosis are polar bodies, which are not fertilised. These cells often degenerate but can sometimes play supportive roles in embryogenesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Of7Z4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question, each mature egg is necessarily from a different meiosis event and so it is not guaranteed that all of the mother's chromosomes are represented in her offspring. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-04-19T17:10:49.770" LastActivityDate="2015-04-19T17:10:49.770" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26409" PostTypeId="2" ParentId="16577" CreationDate="2015-01-05T18:39:47.333" Score="2" Body="&lt;p&gt;I'd like to add a few books to to the above suggestions. The book by Sean Rice &quot;Evolutionary Theory: Mathematical and Conceptual Foundations&quot; covers a lot of ground, including allele-based models, quantitative genetics, Price's formalism, and MLS. If you're interested in social evolutionary models, I found R. McElreath and R. Boyd &quot;Mathematical Models for Social Evolution&quot; to be extremely accessible for those that don't have a solid math background. Another great book on social evolution is S. Frank's &quot;Foundations of Social Evolution&quot; but it is not as easy to follow as McElreath and Boyd's book.&lt;/p&gt;&#xA;" OwnerUserId="11829" LastActivityDate="2015-01-05T18:39:47.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26410" PostTypeId="2" ParentId="26407" CreationDate="2015-01-05T18:56:05.430" Score="4" Body="&lt;p&gt;Differences in genetic material between dizygotic twins and siblings are likely to be very similar.  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dizygotic twins, or so-called fraternal twins, on the other hand, are no more genetically similar than any other set of siblings. - &lt;a href=&quot;http://www.hci.utah.edu/eihg/perinatal/gentwin.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Utah.edu&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Since &lt;a href=&quot;https://biology.stackexchange.com/questions/26135/when-are-a-females-eggs-created/26137#26137&quot;&gt;all oocytes are all synthesized during fetal development&lt;/a&gt;, dizygotic twins are no more likely to come from a single mitotic division than siblings are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also note that in human females, only one egg comes from the a full mitotic division:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iWeSC.gif&quot; alt=&quot;meiosis&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-01-05T18:56:05.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26412" PostTypeId="2" ParentId="26171" CreationDate="2015-01-05T19:42:24.123" Score="6" Body="&lt;p&gt;&lt;em&gt;Pseudomonas&lt;/em&gt; bacteria are generally not difficult to grow:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Rugged and opportunistic, &lt;em&gt;Pseudomonas&lt;/em&gt; use a wide range of nutritional sources, even very simple nutritional environments without any organic compounds. - &lt;a href=&quot;http://www.sigmaaldrich.com/technical-documents/articles/analytix/pseudomonas-media.html&quot; rel=&quot;noreferrer&quot;&gt;Sigma&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;For specific species, you'll want to use a selection medium. Sigma-Aldrich has a number of  &lt;a href=&quot;http://www.sigmaaldrich.com/technical-documents/articles/analytix/pseudomonas-media.html&quot; rel=&quot;noreferrer&quot;&gt;commercial products&lt;/a&gt; for selection and I'm sure you can find a recipe that suits your species with a Google search.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;Related reading:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://aem.asm.org/content/33/5/1222.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;Medium for the Selective Isolation of Members of the Genus Pseudomonas from Natural Habitats&lt;/a&gt; (Grant and Holt, 1977)&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22365238&quot; rel=&quot;noreferrer&quot;&gt;Evaluation of various selective media for the detection of Pseudomonas species in pasteurized milk&lt;/a&gt; (Van Tassell &lt;em&gt;et al.&lt;/em&gt;, 2012)&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-01-05T19:42:24.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26413" PostTypeId="1" AcceptedAnswerId="26414" CreationDate="2015-01-05T21:34:06.827" Score="35" ViewCount="12467" Body="&lt;p&gt;I'm just curious, how many mosquito &quot;bites&quot; (mosquitoes which have removed blood from a person) would it take to remove enough blood to put a person into shock? (Putting aside all reasons why it wouldn't happen, how many would it take?)&lt;/p&gt;&#xA;" OwnerUserId="11525" LastEditorUserId="9943" LastEditDate="2015-01-06T12:29:13.777" LastActivityDate="2017-06-06T18:58:33.197" Title="How many mosquitoes would it take to &quot;drain&quot; enough blood to put a person into shock?" Tags="&lt;entomology&gt;&lt;blood-circulation&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="26414" PostTypeId="2" ParentId="26413" CreationDate="2015-01-05T22:14:02.343" Score="57" Body="&lt;p&gt;This question falls into different subquestions: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1. How much blood does a mosquito take when feeding?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not so easy to answer, but there are publications which measure the volume of different mosquito species. Reference 1 lists volumes between 2.85 and 11.99µL per meal and mosquito. Reference 2 lists 3.07 and 5.71µL. To make the approximation a bit easier, let's assume that mosquitoes drink about 5µL per bite (which should be near enough).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. How much blood does a human have?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood_volume&quot;&gt;Wikipedia&lt;/a&gt;, humans have around 77mL blood per kilogram of body weight. If we take a 70kg human, we get around 5L of blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;3. How many mosquitos does it take to get a human into shock, and how many to suck him out completely?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the Medline, &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000167.htm&quot;&gt;Hypovolemic shock&lt;/a&gt; occurs when a human loses about 1/5 (or more) of his blood volume. 1/5th of 5L is one litre. Since each mosquito sucks 5µL, this would take about 200.000 mosquitoes. To suck out all blood would take 1 million mosquitoes. (This is not possible since mosquitoes depend on an existing blood pressure, as reference 3 shows. If a capillary is empty due to massive blood sucking, they change to another.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides this theoretical (but interesting) calculation, there are some real problems about getting biten by so many mosquitos. First, this is a question of available skin. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_skin#Skin_components&quot;&gt;human skin&lt;/a&gt; is about 2 square meters in size, which would require 100.000 bites per square meter. To break this down further, a square meter has 10.000 square centimeters, so there would be 10 mosquitos which need to bite you per square centimeter. Rather unlikely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then each mosquito injects a mix of anti-coagulants, pain killers etc. prior to sucking to keep the blood from clotting and also to make sure you won't notice the bite immediately. As pointed out in the comments, this would already cause a lot of trouble and probably cause massive bleeding, since the effect of the anti-coagulants would sum up when biten by thousands of mosquitos. Additionally the body reacts by releasing histamines and since the amount would also be massive, this would cause real trouble and probably kill you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3858/k7varb48_pdf.htm&quot;&gt;Regulation of blood meal size in the mosquito&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3551617/&quot;&gt;La Crosse Virus Infection Alters Blood Feeding Behavior in Aedes&#xA;triseriatus and Aedes albopictus (Diptera: Culicidae)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0050464&quot;&gt;Visualizing Non Infectious and Infectious Anopheles gambiae Blood&#xA;Feedings in Naive and Saliva-Immunized Mice&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-01-07T12:30:25.627" LastActivityDate="2015-01-07T12:30:25.627" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="26416" PostTypeId="1" AcceptedAnswerId="26417" CreationDate="2015-01-06T00:35:38.480" Score="4" ViewCount="134" Body="&lt;p&gt;Is it possible to perform real-time blood glucose monitoring using a wearable non-invasive device (similar to a fitness band measuring heart rate)? I'm aware that there are some devices in the market developed by medical companies but most of them require you to stick a needle in your body and it also requires you to switch needles and reapply it every few days.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can blood glucose be measured in a non-invasive way?&lt;/p&gt;&#xA;" OwnerUserId="9667" LastEditorUserId="1590" LastEditDate="2016-01-06T08:08:59.307" LastActivityDate="2016-01-06T08:08:59.307" Title="How would real-time blood glucose monitoring work?" Tags="&lt;diabetes-mellitus&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26417" PostTypeId="2" ParentId="26416" CreationDate="2015-01-06T01:52:58.660" Score="5" Body="&lt;p&gt;If you browse the on-line patent data bases - either www.uspto.gov or www.freepatentsonline.com for &quot;glucose monitor&quot; you'll find there are at least half a dozen technologies that have been proposed including the most non-invasive technologies such as using light - similar to the pulse oximeters used in hospitals to measure the pulse and PaO2 through the skin to more invasive methods that periodically pump small samples of blood outside the body for chemical or optical analysis. But in terms of accuracy, the best way to measure BG is by some means that can analyze arterial blood in vivo. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Companies that are trying to develop these devices are shooting for accuracies better than 12 mg/dL, but that's very hard to do with the noninvasive methods. There is a very new technology that uses a contact lens as the sensor, measuring from the iris and transmitting to remote electronics for processing, but that's still probably year's away. I believe the best products that are available today may be those developed by Dexcom in San Diego, CA. See their website here: &lt;a href=&quot;http://www.dexcom.com/&quot; rel=&quot;noreferrer&quot;&gt;http://www.dexcom.com/&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The journal Science just published its year end Breakthroughs and that includes an article that shows hope in restoring the B cells in the pancreas for type I diabetics see &lt;a href=&quot;http://www.sciencemag.org/content/346/6216/1444.full&quot; rel=&quot;noreferrer&quot;&gt;http://www.sciencemag.org/content/346/6216/1444.full&lt;/a&gt; . This of course is the best solution - a cure. I hold hope scientists are less than 5 years away from that goal.&lt;/p&gt;&#xA;" OwnerUserId="9906" LastActivityDate="2015-01-06T01:52:58.660" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26418" PostTypeId="1" AcceptedAnswerId="26424" CreationDate="2015-01-06T04:16:08.877" Score="15" ViewCount="1674" Body="&lt;p&gt;Does photosynthesis occur only in the visible spectrum? If there is a way to completely remove all other electromagnetic bands from the sunlight, including infrared (IR), will photosynthesis continue to occur?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any known plant (algae, fungi, bryophytes, pteridophytes, gymnosperms and angiosperms) that utilises the other wavelengths for photosynthesis?&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="9943" LastEditDate="2015-01-06T05:05:27.320" LastActivityDate="2015-06-02T20:10:37.163" Title="Do electromagnetic waves outside the visible spectrum have any role in photosynthesis?" Tags="&lt;botany&gt;&lt;photosynthesis&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="26419" PostTypeId="2" ParentId="26383" CreationDate="2015-01-06T04:22:03.810" Score="12" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Rotifer&quot;&gt;Rotifers&lt;/a&gt; are microscopic protostomes with around 1000 cells apiece.  &lt;a href=&quot;http://www.elasmo-research.org/education/topics/r_matter_of_scale.htm&quot;&gt;This website&lt;/a&gt; claims the smallest rotifers have less than 100 cells, but I couldn't confirm this.  Most rotifers are eutelic — within a given species, each adult individual has the same number of cells (&lt;a href=&quot;http://eol.org/pages/6851/details&quot;&gt;Encyclopeia of Life: Rotifers&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/2/2d/Bdelloid_Rotifer.jpg&quot; alt=&quot;Bdelloid rotifer&quot;&gt;&#xA;(&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Bdelloid_Rotifer.jpg&quot;&gt;Source&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt; &lt;a href=&quot;https://en.wikipedia.org/wiki/Myxozoa&quot;&gt;Myxozoans&lt;/a&gt; might be even smaller.  These are microcsopic parasites that have been classified as cnidarians based on molecular studies.  They have complicated life cycles including a single-celled stage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/3/3b/Fdl17-9-grey.jpg&quot; alt=&quot;Myxobolus cerebralis&quot;&gt;&#xA;(&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Fdl17-9-grey.jpg&quot;&gt;Source&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="11657" LastEditorUserId="3624" LastEditDate="2015-01-06T23:01:55.137" LastActivityDate="2015-01-06T23:01:55.137" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26420" PostTypeId="2" ParentId="26333" CreationDate="2015-01-06T04:28:15.400" Score="1" Body="&lt;p&gt;Yes they do. The answer is glucose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's begin at the beginning: you eat a piece of fruit. The fruit contains many different kinds of sugars, including fructose and glucose. One of the immediate effects your digestion of this fruit has is to raise the levels in your blood of every type of sugar that was present, and the blood levels of many other types of nutrients as well. This has nothing to do with how well your body does/doesn't absorb fructose, it is simply a normal step in digestion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next, &lt;a href=&quot;http://ressources.unisciel.fr/biocell/chap2/res/glucose_transporter_family_Wood.pdf&quot; rel=&quot;nofollow&quot;&gt;GLUT2 transporters in the insulin producing cells in your pancreas import glucose&lt;/a&gt;. This acts as a signal that tells those cells to start producing insulin. Insulin then diffuses around the body and produces myriad effects, including upregulation of GLUT4  activity across the body. These GLUT4 transporters are present on cells in many parts of your body and are what are responsible for taking up most of the glucose from your blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now on to fructose. GLUT5 is the main fructose transporter. Just like GLUT4, GLUT5 activity is also regulated by insulin, but in a less quick and dramatic fashion than with GLUT4. Although there's a large body of work showing that GLUT5 does not respond quickly to insulin, recent work has shown that, for example, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12914929&quot; rel=&quot;nofollow&quot;&gt;high levels of insulin lead to increased GLUT5 activity in skeletal muscle over a period of 24 hours&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if what your trying to get at is some reason why eating an apple is better for you than chugging an equivalent volume of Auntie Jemimah's pure corn syrup, it's always going to be some reason like this where you have co-metabolism of several nutrients that tend to show up together in &quot;natural&quot; food. It is unlikely that there are any complex plant substances that would be primarily responsible for the health benefit of fresh fruit in general.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2015-01-06T23:03:07.360" LastActivityDate="2015-01-06T23:03:07.360" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="26421" PostTypeId="2" ParentId="25922" CreationDate="2015-01-06T04:31:37.553" Score="2" Body="&lt;p&gt;It is impossible to objectively answer this question, as there is no defined method to objectively tell if the animal is dizzy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All that is known is the existence of vestibular system. Vestibular system helps to define ones orientation with respect to gravity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The response of a reptile to such a stimuli would most probably be freezing as opposed to a four-footed or two-footed beings. This is due to the stabilty of posture present in reptiles which have either their entire body opposed to the ground (in the which the center of gravity touches the ground) or have their centre of gravity very very close to the ground. As the reptile is already stable there would be no movement in the form of corrective reflexes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bipedal or quadipedal beings on the other hand have a high center of gravity and when the vestibular system is stimulated, the dizziness will kick in some corrective reflexes which can be objectively measured.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the answer can only be derived based on observations on humans or other creatures with quantifiable response to the stimulation of vestibular system.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-01-06T04:31:37.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26423" PostTypeId="2" ParentId="24342" CreationDate="2015-01-06T05:40:52.593" Score="5" Body="&lt;p&gt;The parasympathetic supply to the heart is by nerves and that is truncated during surgery as pointed out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sympathetic supply to the heart is by two means: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Through sympathetic nerves from the sympathetic trunk&lt;/li&gt;&#xA;&lt;li&gt;From the adrenal medulla which secretes both adrenaline and nor-adrenaline directly into the blood stream&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The heart contains the beta receptors for the sympathetic system, especially the ventricles and nodes (SA) and conducting fibers. These receptors respond to the presence of adrenaline and nor-adrenaline in blood. Thus the sympathetic response is preserved while the parasympathetic responce is lost. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a minimal level of nor-epinephrine in blood at all times which thus influences the heart. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Receptors in Heart:  &lt;img src=&quot;https://i.stack.imgur.com/tnlLa.gif&quot; alt=&quot;Receptors in Heart&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heart contains adrenergic (sympathetic) and cholinergic (Parasympathetic) receptors. When the heart is transplanted, the donor heart also contains the same receptors. The only thing missing are the nerves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sympathetic system does not suffer as much as the parasympathetic system, because of the adrenal medulla which secretes the nor-epinephrine (same as nor-adrenaline) into the blood, which upon reaching the heart can stimulate the beta receptors on the heart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no organ which releases acetyl-choline into blood, (fortunately, as such a release would be disastrous leading to shock and rigor, possibly death). So the parasympathetic receptors in the heart do not receive any stimuli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit 1:&#xA;In response to your edit, yes there are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12519093&quot; rel=&quot;nofollow noreferrer&quot;&gt;polymorphisms&lt;/a&gt; in all receptors. But the structure of adrenaline and nor-adrenaline are pretty much constant. This means that the donor heart will be at a similar level of sympaticus as it was in the donor when (s)he was alive. Although this will not be the same as the recipients pre-surgery sympaticus state of the now removed heart.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-01-08T10:32:08.167" LastActivityDate="2015-01-08T10:32:08.167" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="26424" PostTypeId="2" ParentId="26418" CreationDate="2015-01-06T07:52:32.190" Score="17" Body="&lt;p&gt;Photosynthesis only occurs in the visible light.have a look at the absorption spectra of the different pigments involved in photosynthesis, you see that all these pigments absorb light between 400 and 700nm (from a diagram from &lt;a href=&quot;https://www.supergrowled.com/full-spectrum-led-grow-lighting/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FXbmH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You see that the absorption spectra of &lt;a href=&quot;http://en.wikipedia.org/wiki/Chlorophyll&quot; rel=&quot;nofollow noreferrer&quot;&gt;chlorophyll&lt;/a&gt; a and b are located from 400 to 500nm and again from 630 to 700nm. The maxima for both molecules are different so that the light is used more efficiently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other three important light harvesting pigments involved in photosynthesis (in cyanobacteria and plants) are: &lt;a href=&quot;http://en.wikipedia.org/wiki/Carotene&quot; rel=&quot;nofollow noreferrer&quot;&gt;Beta Carotene&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Phycoerythrin&quot; rel=&quot;nofollow noreferrer&quot;&gt;Phycoerythrin&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Phycocyanin&quot; rel=&quot;nofollow noreferrer&quot;&gt;Phycocyanin&lt;/a&gt;. These use different parts of the visible spectrum (hence the different color of cyanobacteria), but they still only use the visible part of the light between 400 and 700nm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for this can be seen in the figure when you look at the intensity of the sunlight (plotted in black). All photosynthesis occurs in the area of the highest intensity. Wavelengths shorter than 350nm are efficiently blocked by our atmosphere, wavelengths much longer are not transporting much energy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To shortly answer your question: If we could &quot;switch off&quot; all other wavelengths from the spectrum, there would still be photosynthesis on earth.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="284" LastEditDate="2015-06-02T20:10:37.163" LastActivityDate="2015-06-02T20:10:37.163" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="26425" PostTypeId="2" ParentId="26418" CreationDate="2015-01-06T09:17:28.903" Score="20" Body="&lt;p&gt;Photosynthesis is &lt;strong&gt;nearly&lt;/strong&gt; all visible light. There's usually not enough UV and thermodynamics more or less rules out infrared. Chris covered that pretty spectacularly, but that nearly is significant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is &lt;a href=&quot;http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0000457&quot; rel=&quot;noreferrer&quot;&gt;some evidence&lt;/a&gt; that certain kinds of fungi can use gamma rays or other ionizing radiation for energy, but they're not particularly common. Melanin is used instead of chlorophyll, but apparently 'tooling up' for radiosynthesis(is that a word?) is fairly hard on the cell. It was assumed the melanin was a protective pigment(like it is in humans) and produced only when necessary(also like humans), but these particular ones were discovered growing in the Chernobyl reactor and apparently evolved to continuously produce melanin and absorb ionizing radiation for food. They don't stop producing melanin even on the verge of starvation. Other melanized fungi live in high-radiation environments, like mountaintops and the poles, where there is more UV and cosmic rays and things. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fun fact aside: Fossilized melanized fungal spores turn up at the K-T boundary when the earth had no magnetic field and therefore higher radiation flux at the surface (see paper linked above and &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0012821X03001304&quot; rel=&quot;noreferrer&quot; title=&quot;Hulot G, Gallet Y (2003) Do superchrons occur without any palaeomagnetic warning? Earth Planetary Sci. Lett. 210: 191–201&quot;&gt;Hulot &amp;amp; Gallet, 2003&lt;/a&gt; for more). &lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="3624" LastEditDate="2015-01-13T13:01:13.583" LastActivityDate="2015-01-13T13:01:13.583" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="26430" PostTypeId="2" ParentId="21440" CreationDate="2015-01-06T11:54:21.103" Score="6" Body="&lt;p&gt;Tumors can be benign (they don't bother you at all eg: a mole which does not change) and malignant (also called cancer).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The difference is based on:-&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Degree of differentiation - How much the tumor cells resemble the normal cells&lt;/li&gt;&#xA;&lt;li&gt;Rate of growth - In general (over generalised) benign tumors are slow growing while malignant tumors are fast growing&lt;/li&gt;&#xA;&lt;li&gt;Spread to nearby tissues - Benign growth don't cross tissue planes as defined by basement membranes/fascias, while malignant tumors invade across tissue planes&lt;/li&gt;&#xA;&lt;li&gt;Metastasis - Spread to a remote location in the body through blood, lymph vessels, transcoelomic (peritoneal, pleural, pericardial spaces) routes - This is ONLY seen in malignant tumors.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Coming specifically to rate of growth, these factors must be considered:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;What is stated above in 2 is the general case:&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Malignant tumors a.k.a cancers grow fast&lt;/li&gt;&#xA;&lt;li&gt;Benign tumors are slow growing&#xA;That being said some benign tumors grow faster that malignant tumors. Eg: Fibroid - grows very rapid under the influence of estrogen as in pregnancy&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;The rate of growth of malignant cancers depend on their degree of differentiation (look point 1 above).&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Well differentiated cancers grow slow - Cancers that are very similar to normal cells are considered to be well differentiated&lt;/li&gt;&#xA;&lt;li&gt;Poorly differentiated cancers grow faster based on the &quot;poorness&quot; of differentiation,i.e. the worse the degree of differentiation, the faster the growth. Totally undifferentiated (unidentifiable as any tissue type) are called anaplastic cancers and these grow the fastest&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;The rate of growth of cancers may vary over time &#xA;&lt;ul&gt;&#xA;&lt;li&gt;Due to excessive division probability of mutation is high and a sub-clone may emerge with faster rate of division thus a previously slow growing cancer could suddenly start growing fast &lt;/li&gt;&#xA;&lt;li&gt;Due to the same process some cancers may suddenly decrease in their growth rate and may eventually even vanish! (become necrotic and get cleared away)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This is taken from Robbin's Text book of Pathology,Ed.8, chapter 6&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit 1: &#xA;To know the numbers you need, you have to find out the rate of increase in volume (by measuring size at two points in time) and divide it by the approximate volume of one cell. This will give you the number of cells that has newly divided within the two measured points (growth in interval). Which can then be converted to cell divisions per second. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As pointed out, the rate is going to vary extremely, based on the cancer type. &lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-01-09T00:56:42.193" LastActivityDate="2015-01-09T00:56:42.193" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26432" PostTypeId="1" AcceptedAnswerId="26434" CreationDate="2015-01-06T16:30:49.830" Score="3" ViewCount="260" Body="&lt;p&gt;I found this insect today in front of my room. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am just curious to know what kind of insect it is? And, is it poisonous?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Location: India&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Mfojd.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="11856" LastEditorUserId="6561" LastEditDate="2017-03-28T21:47:07.393" LastActivityDate="2017-03-28T21:47:07.393" Title="What is this insect in India?" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26433" PostTypeId="1" AcceptedAnswerId="26442" CreationDate="2015-01-06T17:34:00.343" Score="1" ViewCount="183" Body="&lt;p&gt;I wish to find an order of magnitude for the binding/unbinding constants of mRNA and RNA-binding proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose molecules &lt;strong&gt;A&lt;/strong&gt; and &lt;strong&gt;B&lt;/strong&gt; reversibly associate to give the complex &lt;strong&gt;C&lt;/strong&gt;. Assuming the diffusion is large enough such that no concentration gradient exist, the reaction equation at equilibrium is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&#xA;&lt;strong&gt;&lt;sub&gt;➕&lt;/sub&gt;[A][B] — &lt;sub&gt;➖&lt;/sub&gt;[C] = 0&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;with &lt;strong&gt;&lt;sub&gt;➕&lt;/sub&gt;&lt;/strong&gt; the binding constant (units: &lt;em&gt;concentration&lt;sup&gt;-1&lt;/sup&gt;.time&lt;sup&gt;-1&lt;/sup&gt;&lt;/em&gt;), &lt;strong&gt;&lt;sub&gt;➖&lt;/sub&gt;&lt;/strong&gt; the unbinding constant (units: &lt;em&gt;time&lt;sup&gt;-1&lt;/sup&gt;&lt;/em&gt;), and &lt;strong&gt;[A], [B], [C]&lt;/strong&gt; the concentrations of the molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found many papers assessing the equilibrium constant &lt;strong&gt;K&lt;/strong&gt; = &lt;sub&gt;+&lt;/sub&gt; / &lt;sub&gt;➖&lt;/sub&gt; but I am interested in &lt;sub&gt;+&lt;/sub&gt; and &lt;sub&gt;➖&lt;/sub&gt; independently.&lt;/p&gt;&#xA;" OwnerUserId="9662" LastEditorUserId="3340" LastEditDate="2015-01-07T11:16:58.133" LastActivityDate="2015-01-07T11:16:58.133" Title="Kinetic binding / unbinding constants of protein + mRNA ⇌ mRNP" Tags="&lt;protein-binding&gt;&lt;enzyme-kinetics&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="26434" PostTypeId="2" ParentId="26432" CreationDate="2015-01-06T17:37:49.623" Score="3" Body="&lt;p&gt;Its a black Cricket .&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Crickets, (family &lt;strong&gt;Gryllidae&lt;/strong&gt;) are related to the Grasshoppers Family.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It should have grasshopper like hind legs .&#xA;Crickets usually emit  noise from its body.&lt;/p&gt;&#xA;" OwnerUserId="9929" LastActivityDate="2015-01-06T17:37:49.623" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26435" PostTypeId="2" ParentId="26253" CreationDate="2015-01-06T18:46:26.737" Score="4" Body="&lt;p&gt;No, there is not. Cells in the bloodstream reach most areas in the body, but there are certain &lt;a href=&quot;http://en.wikipedia.org/wiki/Immune_privilege&quot; rel=&quot;nofollow&quot;&gt;privileged&lt;/a&gt; areas which stop cells, drugs and macromolecules from leaving the bloodstream and entering the tissue. These privileged areas are thought to exist in sensitive or important areas for their own protection:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Immune privilege is thought to be an evolutionary adaptation to protect vital structures from the potentially damaging effects of an inflammatory immune response. (&lt;a href=&quot;http://en.wikipedia.org/wiki/Immune_privilege&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The most common example of such an area is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood%E2%80%93brain_barrier&quot; rel=&quot;nofollow&quot;&gt;blood-brain barrier&lt;/a&gt;, but there other barriers to privileged areas, including the &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood%E2%80%93testis_barrier&quot; rel=&quot;nofollow&quot;&gt;blood–testis barrier&lt;/a&gt;, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood%E2%80%93retinal_barrier&quot; rel=&quot;nofollow&quot;&gt;blood-retinal barrier&lt;/a&gt; and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood%E2%80%93ocular_barrier&quot; rel=&quot;nofollow&quot;&gt;blood-ocular barrier&lt;/a&gt;. Cells do not pass from the blood through these barriers, except in disease (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S001457931100336X&quot; rel=&quot;nofollow&quot;&gt;Larochelle &lt;em&gt;et al.&lt;/em&gt; 2011&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Related reading:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2263/&quot; rel=&quot;nofollow&quot;&gt;first chapter&lt;/a&gt; of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2261/&quot; rel=&quot;nofollow&quot;&gt;Blood Groups and Red Cell Antigens&lt;/a&gt; has a decent high-level overview of different types of blood cells and their roles in the bloodstream and the immune system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S001457931100336X&quot; rel=&quot;nofollow&quot;&gt;How do immune cells overcome the blood–brain barrier in multiple sclerosis?&lt;/a&gt; Larochelle &lt;em&gt;et al.&lt;/em&gt; 2011&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-01-06T18:46:26.737" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="26436" PostTypeId="2" ParentId="19692" CreationDate="2015-01-06T19:11:40.747" Score="1" Body="&lt;p&gt;Regarding the equivalence of MLS and kin selection, here is how I see the equivalence between these two approaches to selection. &#xA;MLS says that cooperation is favored when the response to&#xA;between-group selection outweighs within-group selection. Price's&#xA;equation tells us that this happens when the genetic variance&#xA;between-groups is higher than the genetic variance within-groups.&#xA;This is equivalent to saying that altruists tend to interact&#xA;with other altruists and, accordingly, that the coefficient of&#xA;relatedness increases.&lt;/p&gt;&#xA;" OwnerUserId="11829" LastActivityDate="2015-01-06T19:11:40.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26437" PostTypeId="1" AcceptedAnswerId="26439" CreationDate="2015-01-06T19:37:04.203" Score="7" ViewCount="5098" Body="&lt;p&gt;Does a pulp cell contain all the elements that a 'normal' plant cell contains?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've searched for an hour to find more information about this but couldn't find anything useful. Is the pulp cell the exception from the general size range of most eukaryotic plant cells, normally between &lt;em&gt;10 - 100 µm&lt;/em&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please include link to a reputable website.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sqZXb.jpg&quot; alt=&quot;orange pulp cell&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="11864" LastEditorUserId="15950" LastEditDate="2019-02-10T15:32:03.403" LastActivityDate="2019-02-10T15:32:03.403" Title="Are pulp cells (in oranges) normal plant cells?" Tags="&lt;cell-biology&gt;&lt;botany&gt;&lt;fruit&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="26439" PostTypeId="2" ParentId="26437" CreationDate="2015-01-06T20:48:58.693" Score="11" Body="&lt;p&gt;They are not individual cells. In fact, the &quot;juice sacs&quot; (as they are known) are actually specialized, multicellular hairs:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Juice sacs originate as multicellular hairs in which the interior of the enlarged distal part breaks down and fills with liquid. The juice sacs constitute the fleshy, edible pulp of an orange and are the source of the sweet juice. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MS0uq.jpg&quot; alt=&quot;pulp dissection&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Quote and image from &lt;a href=&quot;http://waynesword.palomar.edu/termfr4.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fruit Terminology&lt;/a&gt;, palomar.edu)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is from a botany course; if for some reason that isn't reputable enough, check out the book &lt;a href=&quot;http://books.google.com/books/about/Anatomy_of_seed_plants.html?id=WWMZtVy1734C&quot; rel=&quot;nofollow noreferrer&quot;&gt;Anatomy of Seed Plants&lt;/a&gt; by Katherine Esau (1960).&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="9829" LastEditDate="2015-01-07T14:19:32.620" LastActivityDate="2015-01-07T14:19:32.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26441" PostTypeId="2" ParentId="26433" CreationDate="2015-01-06T23:47:04.640" Score="1" Body="&lt;p&gt;Ridgeway and coworkers designed a really neat microfluidic device for making these kinds of kinetic binding measurements on RNA and protein &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790880/pdf/gkp733.pdf&quot; rel=&quot;nofollow&quot;&gt;(Ridgeway et al. 2009)&lt;/a&gt;. Their device works sort of like a stop-flow, and they used a FRET based scheme to detect binding and unbinding events. They took measurements for one particular rRNA/ribosomal protein pair and got &lt;strong&gt;(6 ± 0.4) × 10&lt;sup&gt;5&lt;/sup&gt; &lt;em&gt;M&lt;sup&gt;-1&lt;/sup&gt;s&lt;sup&gt;-1&lt;/sup&gt;&lt;/em&gt;&lt;/strong&gt; for the bimolecular on-rate &lt;strong&gt;&lt;em&gt;k&lt;sub&gt;on&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; and &lt;br&gt; &lt;strong&gt;(5 ± 0.9) × 10&lt;sup&gt;-3&lt;/sup&gt; &lt;em&gt;s&lt;sup&gt;-1&lt;/sup&gt;&lt;/em&gt;&lt;/strong&gt; for the unimolecular off-rate &lt;strong&gt;&lt;em&gt;k&lt;sub&gt;off&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ridgeway cites references 23,24,26, and 33 when talking about experiments with &quot;similar constructs and buffer conditions&quot;, so those would probably be a good place to start looking if you want to assemble a diverse set of &lt;strong&gt;&lt;em&gt;k&lt;sub&gt;on&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt;  and &lt;strong&gt;&lt;em&gt;k&lt;sub&gt;off&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt;&amp;nbsp; values.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2015-01-07T10:28:45.023" LastActivityDate="2015-01-07T10:28:45.023" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26442" PostTypeId="2" ParentId="26433" CreationDate="2015-01-07T00:29:11.063" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1046202302000129&quot; rel=&quot;nofollow noreferrer&quot;&gt;Katsamba PS, Park S, Laird-Offringa IA. 2002. Kinetic studies of RNA–protein interactions using surface plasmon resonance. Methods 26(2):95-104&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many methods for studying kinetics, I only mention this one because the lab I'm in has used it for studying protein-ligand interactions. That article has a good explanation of SPR and how it works, so I won't offer to much detail other than to say it basically measures the change of refractive index as one molecule binds to another, which is immobilized on a chip. This allows direct measurement of on- and off-rates. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The researches studied two RNA binding proteins: HuD and U1A, as well as several mutants. Here are their results (Table 1 in the article):&#xA;&lt;img src=&quot;https://i.stack.imgur.com/f8kkD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I really couldn't tell you if those rates are generally representative of RNA-protein interactions, but I suppose that's not what you're asking. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-01-07T00:29:11.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26443" PostTypeId="2" ParentId="14067" CreationDate="2015-01-07T00:40:52.610" Score="2" Body="&lt;p&gt;Self-antigens are not recognized by the body. This is due to self-antigens being presented to the immune system of the body during the embryological development. Any immune cell which recognize the pattern are destroyed during the intrauterine period, preventing the emergence of Auto-immunity in the Life-time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Self-antigens become important in the following situations: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;There are self-antigens, called cryptic antigen, which are not presented to the immune system during embryologic development. These antigens generally are not present on the cell surface or they are present behind a barrier which is usually not penetrated by the immune cells. Eg.: The sperm antigens are not usually exposed to immune system as the sperms are behind the blood-testis barrier. Other such barriers are blood brain barrier, blood retina barrier, etc... &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;This is important because if for some reason (infection, trauma, etc...) such antigens get into the general circulation they will cause an immune reaction leading to autoimmunity&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Self antigens play a role in graft rejection and transfusion reactions. This is mediated specially by the T-cells. This is the reason why transplant patients receive life-long immune supressants and cross-match is done before transfusion&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Self-antigen non-recognition also means non-self antigen recognition. This is the basis of cells infected with viruses or tumor cells getting destroyed. As the new protein peptides (viral or mutated regular proteins) presented by the MHC 1 are not recognised as self, such cells are destroyed protecting the body&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The corollary of 3 is that any pathogen which resembles the self-antigen are tolerated and active immunity does not come into play i.e. the epitopes that are recognized as self do not cause any immune response&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Some pathogens have antigens that closely resemble human antigens. When T-cells mount response against such antigens, a specific sub-clone of T-cell or B-cell (which are activated by the T-cell) may gain the ability to act against the body cells (due to mutations in the hotspots of the anti-topes) that have antigEns resembling the pathogens. This is called molecular mimicry. A well established disease that is due to this mechanism is the Rheumatic Heart Disease. Post-streptococcal Glomerulonephritis is also another example. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-01-07T00:40:52.610" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="26444" PostTypeId="1" AcceptedAnswerId="27456" CreationDate="2015-01-07T01:25:40.590" Score="15" ViewCount="378" Body="&lt;p&gt;Originally, life evolved from non-living matter. Why is life only generated from other life nowadays, and why doesn't it evolve from inanimate matter, like it did originally billions of years ago, when life evolved on Earth?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe I should reword this further. Living organisms reproduce other living organisms but the first living organism came from non living material or chemicals. So could life be created in a laboratory as it originally was ? Originally the process leading to a life form took one billion years, so would this be the answer to my question that it takes too long and that is why it is not being repeated again ?&lt;/p&gt;&#xA;" OwnerUserId="11869" LastEditorUserId="11657" LastEditDate="2015-01-08T04:04:34.107" LastActivityDate="2017-07-07T05:42:13.683" Title="Formation of Life" Tags="&lt;evolution&gt;&lt;biochemistry&gt;&lt;molecular-evolution&gt;&lt;abiogenesis&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="26446" PostTypeId="2" ParentId="26396" CreationDate="2015-01-07T01:51:23.873" Score="3" Body="&lt;p&gt;Actually the derivation is pretty straightforward. It's easier to use the fact that $Cov(X,Y) = E(XY) - E(X)E(Y)$ to derive this result. Suppose&#xA;$x_{j} = \sum_{i} s_{ij}$.&lt;br&gt;&#xA;\begin{align*} &#xA;  Cov (x_j, q_{j}) &amp;amp;= E (x_{j}q_{j}) - E (x_{j}) E (q_{j}) \\&#xA;                    &amp;amp;= \frac{1}{n}\sum x_{j} q_{j} - \frac{1}{n}\sum&#xA;                      x_{j} q \\&#xA;                    &amp;amp;= \frac{1}{n} \sum x_{j} (q_{j} - q)&#xA;\end{align*}&lt;/p&gt;&#xA;" OwnerUserId="11829" LastActivityDate="2015-01-07T01:51:23.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="26447" PostTypeId="1" CreationDate="2015-01-07T02:19:12.117" Score="1" ViewCount="54" Body="&lt;p&gt;I'm a very lazy person. I spend most of my time in a chair, at a computer; I eat more than three meals a day. I don't do any sport, at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I want to know is: why do I need to sleep 8-12 hours daily since I don't waste myself physically during the day?!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wouldn't 3-5 hours be more reasonable? With an increase to 7-10 if I were a bodybuilder or a construction worker.. something that would actually deplete my body of energy?&lt;/p&gt;&#xA;" OwnerUserId="11871" LastActivityDate="2015-01-07T02:19:12.117" Title="How much does sleeping correlate with daily activity?" Tags="&lt;sleep&gt;&lt;movement&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="27442" PostTypeId="2" ParentId="26444" CreationDate="2015-01-07T04:49:33.063" Score="3" Body="&lt;p&gt;There are two questions here:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why does life only generate life?&lt;/li&gt;&#xA;&lt;li&gt;Why doesn't life continue to be generated on Earth?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The first one is easy. We don't only generate life. If that were true, it might be illegal to flush toilets. Life forms of some kind would occupy all the space in our atmosphere. Babies - or some living things - would rise up from our graves. Conceivably none of the millions/billions of people who have died from the beginning of history (and well before that) would be dead. Add to that animals, and everything in the other Kingdoms included in &lt;em&gt;Life&lt;/em&gt;, and there would be nothing left perhaps &lt;em&gt;except&lt;/em&gt; for life. To be honest, life generates heat, death and simple substances much more commonly than it generates life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you mean, why does &lt;strong&gt;like&lt;/strong&gt; produce &lt;strong&gt;like&lt;/strong&gt; (in your case, a life generates a similar life form*, that's because of genetic material. New life is based on the genetic material of the preceding life form. People don't give birth to zebras, zebras do. When the genetic material is damaged enough, we give birth to a non-viable or diseased child. If a mutation is favorable, it is (under the right circumstances) spread through an advantage. An example of this is the appearance of lactase, an enzyme which allows adults to derive continued nutrition from animal milk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to your second question: why doesn't life continue to be generated on Earth? Are you 100% sure that it isn't happening? How would you recognize a life form foreign to our own? How many different &lt;em&gt;kinds&lt;/em&gt; of life can evolve under the same planetary conditions, the same planetary element ratios, etc.? If a &lt;em&gt;very rudimentary&lt;/em&gt; silicon-based life form evolved in, say, the last 2,000,000 years, would you know how to look for it? In other words, are you defining life only as we now know it - a carbon based, DNA-propigated form?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, if a non-carbon based life form could only evolve on &lt;em&gt;this&lt;/em&gt; planet to a very basic, simple level, would you give credence to it as a newly evolved &quot;life&quot; form? Intelligent life is rare. I would guess that &lt;em&gt;very&lt;/em&gt; simple life forms are far less rare in the Universe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How would you classify (or explain) the chemosynthetic bacteria that oxidize sulfur instead of oxygen?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize that there are a lot of questions here and not many answers. But part of finding an answer is asking the right questions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000491&quot; rel=&quot;nofollow&quot;&gt;The Origins of Lactase Persistence in Europe&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-07T04:49:33.063" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="27444" PostTypeId="1" AcceptedAnswerId="27445" CreationDate="2015-01-07T10:41:39.193" Score="3" ViewCount="11681" Body="&lt;p&gt;In sample buffer preparation we add EDTA, but if SDS-PAGE is for protein then is it necessary to add EDTA in sample buffer? What is role of EDTA in sample buffer for protein separation for SDS-PAGE. &lt;/p&gt;&#xA;" OwnerUserId="8423" LastEditorUserId="3340" LastEditDate="2015-01-08T05:23:29.013" LastActivityDate="2017-10-12T07:04:07.000" Title="Does sample buffer require EDTA for protein separation on SDS PAGE?" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27445" PostTypeId="2" ParentId="27444" CreationDate="2015-01-07T10:53:32.733" Score="3" Body="&lt;p&gt;EDTA is a complexing agent for bivalent cations and is usually used to inhibit enzymes (proteases, nucleases) which need these ions in their active center to work. Without it they do not attack the sample. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The presence of EDTA in the sample buffer is interesting, since Laemmli's original paper from 1970 (&quot;&lt;a href=&quot;http://www.directupload.net/file/d/3860/l6eqjwqh_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Cleavage of structural proteins during the assembly of the head of bacteriophage T4.&quot;&lt;/a&gt;) doesn't use it and I think it is not necessary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for this is simple: Protein samples are usually generated in buffers which contain different protease inhibitors, which protects the samples. Additionally the purpose of the sample buffer is to denaturate (at least for the standard SDS gels) the protein sample completely, so it will run uniformly. Both steps ensure that proteases are either inhibited or completely denaturated, which will both protect the sample.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only reason I can think of for using EDTA is that it can help to destabilize your target protein, when a co-factor which is important for the structure is complexed by EDTA and thus keep it in solution after the denaturation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are of course ressources which state that EDTA is necessary for protein integrity, but they only say it is there to inhibit proteases by complexing metal ions (see &lt;a href=&quot;https://books.google.de/books?id=TbVtbD51FxgC&amp;amp;pg=PA98&amp;amp;lpg=PA98&amp;amp;dq=edta%20in%20sds%20sample%20buffer&amp;amp;source=bl&amp;amp;ots=FD8RkmOf1W&amp;amp;sig=9TVhxu1mNQncO5wCwGtowkRN76g&amp;amp;hl=de&amp;amp;sa=X&amp;amp;ei=j06tVO-MLczuUIKmhEg&amp;amp;ved=0CGQQ6AEwCA#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for example).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a 2x sample buffer, I use the following recipe (this can also be made 5x if necessary), which contains EDTA, but can also be done without. If you prefer β-Mercaptoethanol, you can use it in the same concentration as the DTT (which has the advantage of being less smelly):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2x sample buffer:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;4% SDS&lt;/li&gt;&#xA;&lt;li&gt;20% glycerol&lt;/li&gt;&#xA;&lt;li&gt;2 mM EDTA (ethylene diamine tetraacetic acid) - &lt;em&gt;can be made without&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;100 mM Tris-Cl, pH 6.8&lt;/li&gt;&#xA;&lt;li&gt;200 mM DTT (dithiothreitol)&lt;/li&gt;&#xA;&lt;li&gt;0.1 % (w/v) bromphenol blue dye&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-01-08T10:26:42.707" LastActivityDate="2015-01-08T10:26:42.707" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="27449" PostTypeId="1" CreationDate="2015-01-07T13:23:31.337" Score="3" ViewCount="753" Body="&lt;p&gt;We can see length, and other physical quantities. We can perceive through our other senses like (temperature through thermoreceptors, weight through pressure receptors etc.). But how do we &quot;sense&quot; time?&lt;/p&gt;&#xA;" OwnerUserId="12872" LastEditorUserId="6289" LastEditDate="2015-01-07T16:10:38.287" LastActivityDate="2015-01-07T17:16:11.497" Title="How do humans perceive time?" Tags="&lt;human-biology&gt;&lt;neurology&gt;&lt;circadian-rhythms&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27450" PostTypeId="1" AcceptedAnswerId="27451" CreationDate="2015-01-07T14:25:31.563" Score="7" ViewCount="1203" Body="&lt;p&gt;In the wiki page of &lt;a href=&quot;https://en.wikipedia.org/wiki/Biophysics&quot;&gt;Biophysics&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Biophysics spans all scales of biological organization, from the molecular scale &lt;strong&gt;to whole organisms and ecosystems.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But after searching on the internet; the dominant application of physics in biology that I see is at the molecular scale. In the wiki page &lt;a href=&quot;https://en.wikipedia.org/wiki/Mathematical_and_theoretical_biology#Mathematical_biophysics&quot;&gt;Mathematical biophysics&lt;/a&gt;, there is a lot of interesting information, but it is only about mathematical knowledge applied to biophysics, not physics itself. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What, if any, physics knowledge (based on principles and laws of physics) can be applied to biology in the sense of organisms and ecosystems?&lt;/p&gt;&#xA;" OwnerUserId="6786" LastEditorUserId="3340" LastEditDate="2015-01-08T05:43:54.553" LastActivityDate="2015-01-08T05:43:54.553" Title="What physics knowledge can be applied to biology of organisms and ecosystems?" Tags="&lt;biophysics&gt;&lt;theoretical-biology&gt;&lt;ecosystem&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27451" PostTypeId="2" ParentId="27450" CreationDate="2015-01-07T14:59:05.523" Score="7" Body="&lt;p&gt;This question is really asking for examples, and the list of ways that knowledge of physics can be used in biology could be very long. However, here are a couple of examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Systems ecology, especially with regard to energy and nutrient flow.&lt;/strong&gt;&lt;br&gt;&#xA;This type of ecology can be strongly influenced by physics. For one example see the book &lt;a href=&quot;http://www.cambridge.org/ar/academic/subjects/life-sciences/ecology-and-conservation/theoretical-ecosystem-ecology-understanding-element-cycles&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Theoretical Ecosystem Ecology: Understanding Element Cycles&lt;/em&gt;&lt;/a&gt; by Ågren &amp;amp; Bosatta (Ågren was originally a physicist)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Physical limitations to growth and transport&lt;/strong&gt;&lt;br&gt;&#xA;This can include for instance mechanical contraints on plant growth (see e.g. the book &lt;a href=&quot;https://books.google.se/books?id=XeLmGmWl3-IC&amp;amp;pg=PA191#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Plant Physics&lt;/em&gt;&lt;/a&gt; by Nicklas &amp;amp; Spatz), water transport in trees (see e.g. &lt;a href=&quot;https://biology.stackexchange.com/questions/11044/how-do-trees-lift-water-higher-than-10-meters/&quot;&gt;this BioSE question&lt;/a&gt;) or the biomechanics of movement (see e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22723482&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hudson et al (2012)&lt;/a&gt; on the speed and movement of cheetahs or &lt;a href=&quot;http://en.wikipedia.org/wiki/Biomechanics&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia: Biomechanics&lt;/a&gt;).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Allometric relationships between organisms, e.g. with regard to metabolism&lt;/strong&gt;&lt;br&gt;&#xA;To explain these types of relationships knowledge in physics is useful. See e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Kleiber%27s_law&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kleiber's law&lt;/a&gt; for more.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;MAXENT as a general approach to ecological patterns or to model species distributions&lt;/strong&gt;&lt;br&gt;&#xA;This is basically a tool lifted from physics that can be applied to ecological problems. There are many papers to look at, but &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0169534714001037&quot; rel=&quot;nofollow noreferrer&quot;&gt;Harte &amp;amp; Newman (2014)&lt;/a&gt; (Harte is another previous physicist) and &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1472-4642.2010.00725.x/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Elith et al (2010)&lt;/a&gt; are two good starting points. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Dynamical modelling of populations and communities&lt;/strong&gt;&lt;br&gt;&#xA;This field use many of the same tools for analysis as physics, e.g. systems of differential equations. One of the pioneers in this field (among many) were &lt;a href=&quot;http://en.wikipedia.org/wiki/Robert_May,_Baron_May_of_Oxford&quot; rel=&quot;nofollow noreferrer&quot;&gt;Robert May&lt;/a&gt; (also started with a PhD in physics), and his classical book &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0199209995&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Theoretical Ecology: Principles and Applications&lt;/em&gt;&lt;/a&gt; is still a good starting point.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Energy harnessing and conversion by organisms&lt;/strong&gt;&lt;br&gt;&#xA;This can refer both to how organsims convert prey to energy (e.g. conversion efficiencies) and the physics of photosynthesis (which is an interesting intersection between physics and molecular biology). See &lt;a href=&quot;http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.92.218301&quot; rel=&quot;nofollow noreferrer&quot;&gt;Jang et al (2004)&lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/ncomms/2014/140109/ncomms4012/full/ncomms4012.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;O'Reilly &amp;amp; Olaya-Castro (2013)&lt;/a&gt; for examples of the how quantum mechanics can inform us about photosynthesis. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Hopefully this will give you a sense of some different ways that knowledge in physics can be useful for biology.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-01-07T22:43:13.377" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27452" PostTypeId="2" ParentId="27449" CreationDate="2015-01-07T15:53:00.440" Score="3" Body="&lt;p&gt;Humans and many other organisms have a &lt;a href=&quot;http://en.wikipedia.org/wiki/Circadian_clock&quot; rel=&quot;nofollow noreferrer&quot;&gt;circadian clock&lt;/a&gt;, a biological system that oscillates every 24 hours (but is also sensitive to external stimuli). There are many components to the human circadian clock that are not known. On the molecular level, &lt;a href=&quot;http://en.wikipedia.org/wiki/Circadian_clock#Mammalian_clocks&quot; rel=&quot;nofollow noreferrer&quot;&gt;gene regulation&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Circadian_clock#Post-transcriptional_modification&quot; rel=&quot;nofollow noreferrer&quot;&gt;post-transcriptional&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Circadian_clock#Post-translational_modification&quot; rel=&quot;nofollow noreferrer&quot;&gt;post-translational&lt;/a&gt; modification are all implicated. There is also evidence of a &lt;a href=&quot;http://en.wikipedia.org/wiki/Circadian_clock#Systems_biology_approaches_to_elucidate_oscillating_mechanisms&quot; rel=&quot;nofollow noreferrer&quot;&gt;systemic network&lt;/a&gt; through which the oscillation propogates, probably via hormones or other intercellular signals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many of the molecular mechanisms are not well-understood (and to go into all of them would take all week), but I'll give an example of one fairly self-contained negative feedback loop mediated by the Period/Cryptochrome &lt;a href=&quot;http://en.wikipedia.org/wiki/Period_(gene)&quot; rel=&quot;nofollow noreferrer&quot;&gt;PER/CRY complex&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PER/CRY is a heterodimeric transcriptional regulator. During the day, it is located in the cytoplasm, unphosphorylated (and sometimes as independent subunits). However, upon phosphorylation, it enters the nucleus and negatively regulates many genes, &lt;em&gt;including itself&lt;/em&gt;. This is a negative feedback loop, more PER/CRY in the nucleus means that less will be produced. Here's a hopefully simple figure to illustrate this (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0968000406002726&quot; rel=&quot;nofollow noreferrer&quot;&gt;Belden &lt;em&gt;et al.&lt;/em&gt; 2006&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Gnrpy.jpg&quot; alt=&quot;per/cry&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phosphorylated PER/CRY also regulates &lt;a href=&quot;http://en.wikipedia.org/wiki/Vasopressin#Central_nervous_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;vasopressin&lt;/a&gt;, a hormone that helps the CNS regulate circadian rhythm (&lt;a href=&quot;http://thebrain.mcgill.ca/flash/a/a_11/a_11_m/a_11_m_hor/a_11_m_hor.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;McGill University&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ipOXC.jpg&quot; alt=&quot;per/cry vasopressin&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully this is clear. Remember that this is only part of the entire circadian clock system and that there is more detail even in relation to the PER/CRY complexes themselves (&lt;a href=&quot;http://thebrain.mcgill.ca/flash/a/a_11/a_11_m/a_11_m_hor/a_11_m_hor.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;McGill University&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9OI4W.jpg&quot; alt=&quot;crying&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-01-07T15:53:00.440" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27454" PostTypeId="2" ParentId="26444" CreationDate="2015-01-07T16:54:04.050" Score="-2" Body="&lt;p&gt;Abiogenisis, where imperfect micelles (spheres) of hydrophobic carbon chain formatiions leads to potentials for capturing and mixing elements and molecules forming peptides, polypeptides and protiens that can then catalyze enzymes to patterns to the micelle to a cell of sorts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Was it inside a terrestrial micelle that life formed or Did amazing spiraling symetry of life get help or even need it from galactic wave patterns, crystal energy of minerals or was it just a mixing up microscopic pieces of Pythogerian parts and geometry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Either and anyway, given low energy potentials needed for effeciency of a new life form, unless it was non carbon based, it would have practically zero chance of survival where energetic mass of life that already exists just chews it up and mutates spin offs. Only a dynamic shift in genetics as we know it would allow us to detect divergent life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, got to love the ugly waterbear. &lt;/p&gt;&#xA;" OwnerUserId="12875" LastActivityDate="2015-01-07T16:54:04.050" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27455" PostTypeId="2" ParentId="27449" CreationDate="2015-01-07T17:16:11.497" Score="4" Body="&lt;p&gt;The nature of time has been discussed for millenia. We don't know exactly why or where time perception exists, but we do have some information on how it is perceived.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The circadian rhythm is basically in place to help us sleep, wake and perform tasks in a 24 hour cycle of light. Robbed of light, and the melatonin it's absence produces, the rhythm shifts considerably.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vision is a powerful cue for the passage of time. Bees have an extremely sophisticated ability to predict the sun's location at a given moment (they can count the moments). While I doubt the same is true for humans, our eyes give us a great deal of information about the passage of time: the time in a 24 hour period (the position of the sun, moon, stars, shadows, etc), and the time in a year, the time in a lifetime. Witnessing the passage of time, according to physicist Paul Davies, we observe how the &lt;em&gt;“later states of the world differ from earlier states that we still remember.”&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides the important input from our eyes and memories, we also have internal timekeepers.  A study decades ago on short order cooks (I can't seem to find it) found that an experienced cook can keep internal time to the second, and can keep multiple &quot;stopwatches&quot; going in his head: the scrambled eggs, the toast, the pancakes, the grilled cheese sandwiches all take a certain amount of time, and short order cooks can tell when that time has passed with extraordinary precision.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fact that the fluids flow at different rates tells us that we perceive time differently under different circumstances. Time perception is surprisingly prone to measurable distortions and illusions. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The importance of our temporal experiences for daily living is strikingly documented in individual neurological cases where patients report of an accelerated progression of time and, consequently, have troubles in adequately interacting with the environment, i.e. driving a car. Psychological research has shown that cognitive functions such as attention, working memory as well as long-term memory determine our temporal judgements. Moreover, drive states, moods and emotions, as well as factors of personality influence duration estimates. For example, time intervals are judged to be longer when we pay more attention to time and when the load of varying experiences stored in memory is higher. Our subjective well-being also strongly influences how time is experienced. Time speeds up when we are involved in pleasant activities, but it drags during periods of boredom. Thus, our sense of time is a function of the intricate interplay between specific cognitive functions and of our momentary mood states.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Where exactly time is perceived by the brain is unknown, but several areas keep appearing, most prominently, the cerebellum, the right posterior parietal cortex, the right prefrontal cortex, as well as &lt;em&gt;fronto-striatal circuits&lt;/em&gt;. All have been implicated as the neural substrates of a potential timekeeping mechanism. The inner experience of time&lt;sup&gt;[1]&lt;/sup&gt; gives a broad overview. The conclusion is worth reading.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To further support that the &lt;em&gt;where&lt;/em&gt; is not known, consider the following:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Studies done in humans also support the hypothesis that &lt;em&gt;striatum&lt;/em&gt; and its afferents are involved in interval timing. Recent fMRI data showed that timing network could involve cortico-striatal loops, including premotor and supplementary motor areas, frontal operculum and dorsolateral prefrontal cortex, and temporal and parietal cortices, as well as the putamen. Imaging studies in humans, lesion studies in humans and rodents, and drug studies in rodents all point towards a central role of the &lt;em&gt;basal ganglia&lt;/em&gt; in interval timing. The anatomy of the basal ganglia suggests that information is proceeded through &lt;em&gt;cortico-striato-thalamic loops&lt;/em&gt;. Severe deficiencies in reproducing temporal intervals were also found in Parkinson’s patients, therefore, further supporting the hypothesis of basal ganglia involvement in interval timing. There are also lesions data suggesting that the timing network is much widely distributed. Lesions of the nucleus basalis magnocellularis, a cholinergic nucleus in the basal forebrain with projections to the frontal cortex, induced a progressive, proportional, delay in peak time response (memory pattern). This effect is believed to be related to altered temporal memories [42,43] due to change in acetylcholine (ACh) level. Lesions of the frontal cortex produce similar memory patterns, whereas lesions of the hippocampus or fimbria fornix, a basal forebrain cholinergic nucleus with projections to the hippocampus, result in memory effects translated into an advance of the peak time response. These experimental findings undoubtedly support the hypothesis of a distributed interval timing neural network.&lt;sup&gt;[2]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For a fun but non-scientific look at time, the NYT has written an understandable article.&lt;sup&gt;[3]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The final answer is that no one knows for sure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://plato.stanford.edu/entries/time-experience/&quot; rel=&quot;nofollow&quot;&gt;The Experience and Perception of Time&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;1 &lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/364/1525/1955&quot; rel=&quot;nofollow&quot;&gt;The inner experience of time&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;2 &lt;a href=&quot;http://europepmc.org/articles/pmc3751097&quot; rel=&quot;nofollow&quot;&gt;Why noise is useful in functional and neural mechanisms of interval timing?&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;3 &lt;a href=&quot;http://www.nytimes.com/2010/01/05/health/05mind.html?_r=0&quot; rel=&quot;nofollow&quot;&gt;Where Did the Time Go? Do Not Ask the Brain&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA; &lt;sub&gt;&lt;a href=&quot;http://www.jneurosci.org/content/25/45/10369.full&quot; rel=&quot;nofollow&quot;&gt;Time and the Brain: How Subjective Time Relates to Neural Time&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866156/&quot; rel=&quot;nofollow&quot;&gt;Human time perception and its illusions&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-07T17:16:11.497" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27456" PostTypeId="2" ParentId="26444" CreationDate="2015-01-07T17:22:34.257" Score="9" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Abiogenesis&quot;&gt;Abiogenesis&lt;/a&gt;, the development of living things from non living matter, is not something we know much about, since it happened about 4 billion of years before we were around and haven't reproduced it in the lab. My guess is that it's not easy. However, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment&quot;&gt;Miller-Urey&lt;/a&gt; experiment and others have told us something about abiogenic production of organic compounds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first living organism on Earth ( Let's imaging some &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_world_hypothesis&quot;&gt;self-replicating RNA&lt;/a&gt; ) was probably very inefficient, copied itself slowly and made a lot of errors. At the time it could survive because there wasn't any competition. However, as time went on some of these copies were more efficient and copied themselves more quickly, outnumbering the original sequences and driving them into extinction. Wait another 3.5 - 4 billion years and you have modern life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If abiogenesis were to occur on Earth today, the resulting organism would likely be inefficient like the first organism. However, now it would face immense competition from very efficient modern organisms and would probably be eaten. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is speculation, but I assume that any new type of life on Earth would be carbon based, since organic carbon based building blocks are abundant. If anything, abiogenesis might be easier on modern earth than early earth because the starting materials (nucleotides, amino acids) are readily available, but competition from modern life and reactive oxygen in the atmosphere would hinder any new abiogenesis.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2015-01-07T17:22:34.257" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27458" PostTypeId="2" ParentId="26333" CreationDate="2015-01-07T18:46:44.600" Score="0" Body="&lt;p&gt;I'm unsure currently about the empirical data surrounding inhibition of GLUT5, but with regards to GLUT2, some data exists to point out flavonoids and phloretin as potential inhibitors found in diet. The following articles should provide some sort of starting point to dig a little deeper on the matter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17699876&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/17699876&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17172639&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/17172639&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-01-07T18:46:44.600" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27459" PostTypeId="1" CreationDate="2015-01-07T19:24:31.347" Score="1" ViewCount="1379" Body="&lt;p&gt;What is the importance of urea in mass spectrometry? We use 8M urea to FASP our proteins prior to mass spectrometry.  What is the significance of using 8M urea? and how does it affect the proteins?&lt;/p&gt;&#xA;" OwnerUserId="12880" LastActivityDate="2016-05-20T10:12:29.173" Title="What is the importance of urea in mass spectrometry?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;mass-spectrometry&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27462" PostTypeId="2" ParentId="27459" CreationDate="2015-01-07T20:56:24.037" Score="2" Body="&lt;p&gt;8M urea is a denaturant, as @Chris mentioned. Denaturing proteins is important for molecular (aka classical) mass spectrometry. If you analyzed a non-denatured protein, you'd get information not only on the primary structure, but also on noncovalent interaction (2+°):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The classical MS approach, so-called “molecular MS,” analyzes, in the gas phase of the mass spectrometer, individual species initially present in solution after destruction of the noncovalent framework. On the other hand, “supramolecular MS” or “nondenaturing MS” aims at transferring intact noncovalent complexes that preexist in solution into the gas phase of the instrument.&lt;/p&gt;&#xA;&lt;p&gt;(&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18592183&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sanglier &lt;em&gt;et al.&lt;/em&gt; 2008&lt;/a&gt;, Methods Mol. Biol.)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Denaturing proteins is important for molecular/classical mass spec because it ensures your analysis only reflects the covalent bonds (primary structure) present in your target protein.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-01-07T20:56:24.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27464" PostTypeId="2" ParentId="23898" CreationDate="2015-01-07T21:25:51.733" Score="2" Body="&lt;p&gt;It's a complicated answer. More than 200 cell types, each type of cell inherits a unique expression of receptors, internal and external. Diffusion of signals through the plasma membrane and/or nuclear compartment may act directly as cofactors, activators, etc. The specific sequestration, and pattern of expression of external receptors also influence what signals become bound and relayed. The cell will also have a motif of internal/cytoplasmic/nuclear proteins expressed that complex or become directly activated by interaction with any of the above, etc. So the currently expressed set of internal, and external proteins determine not only how the cell interprets the signal, but also how they respond. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the actual genetic material, you'll find inherited motifs like DNA methylation, histone acetylation patterns etc. influence what parts of the DNA can actually be accessed. Per the above schema of signaling pathways, the signals received by each individual cell differ based on the actual cell type. In any case there are patterns of activators/repressors, enhancers/silencers that are switched on or off by these signals. Some journals are also introducing evidence insoluble receptors like EGFR+ligand can actually internalize and translocate to the nucleus and act as transcription regulators. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The final note, is that due to alternative splicing and transcription of proteins that promote or repress splicing sites, in a combination with the above concepts a cell can regulate for thousands of genes. This is a very general answer, however. The concept to take home, though, is that differentiated cells have their own specific motifs they express that make &quot;reading&quot; different signals possible, and also makes differing responses to what could be the same signal possible. These motifs also allow for the accurate expression of the relevant portions of the genome (not all genes are expressed at all times in all cells).&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-01-07T21:25:51.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27465" PostTypeId="1" CreationDate="2015-01-07T23:56:16.877" Score="2" ViewCount="299" Body="&lt;p&gt;I've been looking around the net looking for a nice protocol to validate micropipette calibrations using absorbance readings of a dye in solution. Does anyone have one they can share? I'd highly appreciate it!&lt;/p&gt;&#xA;" OwnerUserId="12887" LastEditorUserId="9943" LastEditDate="2015-01-08T04:08:58.620" LastActivityDate="2017-04-27T18:41:40.043" Title="Protocol for checking pipette calibrations using absorbance readings of a dye in solution?" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27466" PostTypeId="2" ParentId="27465" CreationDate="2015-01-08T04:31:17.927" Score="2" Body="&lt;p&gt;I see what you are getting at however this would be a very WRONG way of calibrating such an instrument. If dyes varied among trials it would throw off your calibration. Also, you would need to generate some sort of standard curve to equate absorbance to weight, since true calibration of these instruments is done by weighing the volumes they dispense (1g = 1ml water). The weight of water and the weight of your dye solution will not increase the same in terms of moles/g. Also a scale is far easier to calibrate that the detector in any spectrophotometer. Calibrate pipettes by weighing the volume of water they dispense. It should be done in a chamber that inhibits evaporation and you need a precision scale. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a reliable guide for pipette calibration&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=3&amp;amp;ved=0CEEQFjAC&amp;amp;url=http%3A%2F%2Fwww.pipettecalibration.net%2Fpipette-calibration-files%2Fguide-to-pipetting-2.pdf&amp;amp;ei=1AeuVP_wB8algwT6voFA&amp;amp;usg=AFQjCNGiSECuPthCsHxGLnl_Y2aGNkE9pw&amp;amp;sig2=x4b2RaC6dIUlmTnXF6c_6Q&amp;amp;bvm=bv.83134100,d.eXY&quot; rel=&quot;nofollow&quot;&gt;enter link description here&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2015-01-08T04:31:17.927" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27468" PostTypeId="1" AcceptedAnswerId="27471" CreationDate="2015-01-08T07:56:55.243" Score="4" ViewCount="4981" Body="&lt;p&gt;This move was seen in Pitch Black and i wonder if it is possible at all. Say you are handcuffed to a pole, hands in the back, and the pôle is a little higher than your head. You just want to do a complete loop with your hands, going above your head, so they end up in front of you and you are free of the pole.&lt;/p&gt;&#xA;&lt;p&gt;Now, putting horrible pain aside, is it possible to perform this move alone?&lt;/p&gt;&#xA;&lt;p&gt;If not, maybe with a small surface to rely on, for a lever effect?&lt;/p&gt;&#xA;&lt;p&gt;Would it cause minor / major damage at all or just pain ?&lt;/p&gt;&#xA;&lt;p&gt;I am also curious if performing this move slightly turned sideways help ( as much as you could at least, considering the situation). In the movie he goes one shoulder at a time.&lt;/p&gt;&#xA;&lt;p&gt;Anyway, i hope im clear enough !&lt;/p&gt;&#xA;&lt;p&gt;Exactly what i mean is this &lt;a href=&quot;http://youtu.be/TF-NhH4NpTc?t=1m34s&quot; rel=&quot;nofollow noreferrer&quot;&gt;video&lt;/a&gt; at 1:35&lt;/p&gt;&#xA;" OwnerUserId="12892" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-02-13T02:24:24.677" Title="Is it possible to move your arms above your head when handcuffed in the back?" Tags="&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27469" PostTypeId="2" ParentId="27468" CreationDate="2015-01-08T08:36:57.380" Score="1" Body="&lt;p&gt;Depending on the situation (i.e. orientation/rigidity of cuffed hands and the height of the pole), you could potentially escape, but getting your arms flipped around where your hands are in front of you would involve serious damage.&#xA;It may be technically possible to achieve alone with some way to continue wedge your arms further, but the pain would probably knock you out before you succeeded.&lt;/p&gt;&#xA;" OwnerUserId="12894" LastActivityDate="2015-01-08T08:36:57.380" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27471" PostTypeId="2" ParentId="27468" CreationDate="2015-01-08T10:33:24.733" Score="4" Body="&lt;p&gt;This is not normally possible or would be extremely painful if done. But there are special cases.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ol start=&quot;2&quot;&gt;&#xA;  &lt;li&gt;&lt;p&gt;Atraumatic dislocation. &#xA;  This occurs when the shoulder dislocates with minimal force such as reaching up for an object or turning over in bed. Usually it will 'pop' back in itself or with a little help. Normally this type of dislocation does not need reducing in A&amp;amp;E. It can occur regularly throughout the day and will be associated with certain positions the arm is placed into. This type of dislocation is associated with people that have 'lax' joints, for example people who hyper-extend their knees and elbows and can get the palms of both hands onto the floor with ease.  This joint laxity is normal for these people and the onset of dislocation can be associated with a change in how the muscles around the shoulder are interacting with each other or a change in posture/ position of the arm. This can produce an imbalance in the control of the joint. Referral for appropriate physiotherapy is the initial form of management. The physiotherapist should look at the way in which the muscles and shoulder joint is moving and posture aiming to restore the balance. Treatment can 'cure' the problem as long as the exercises and advice is continued, but in some cases there is only minimal or nil benefit. At this point surgical intervention is indicated. &lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Positional Non-traumatic dislocations. &#xA;  This group of people can dislocate their shoulders without any form or history of trauma. Some may have started out dislocating their shoulder as a party trick; others may have always had shoulders that just 'fall' out of joint. This type of dislocation is usually painless and can be put back in easily. Both shoulders are typically involved. The cause of this type of dislocation is usually a result of what we call 'abnormal muscle patterning' which means the strong muscles around the shoulder joint are not working in the correct order causing them to pull the shoulder out of joint with active movement in the particular direction such as lifting the arm forward above the head or out to the side and above the head.  The main treatment for this is physiotherapy that looks at re-sequencing the muscles in order to prevent further dislocations.  Occasionaly surgery in the form of thermal capsular shrinkage or plication may be neccessary.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Taken from &lt;a href=&quot;http://www.shoulderdoc.co.uk/articletile.asp?article=50&amp;amp;section=12&amp;amp;tile=3&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; such people would be able to dislocate then get their hands in front and relocate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The body can be trained to be quite flexible through training like gymnastics etc...&lt;/p&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-01-08T10:33:24.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27472" PostTypeId="2" ParentId="19303" CreationDate="2015-01-08T10:38:32.400" Score="8" Body="&lt;p&gt;Very simply putting, irregular heat beat means that the pulse is not regular. It can be diagnosed by checking your pulse clinically. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Irregularities are further classified as: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Regularly Irregular: this occurs in heart blocks where every second or third beat is skipped regularly causing a pattern. Usually as time progresses the degree of block worsens and result in the final form which is complete block (fourth degree heart block)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Irregularly Irregular: this occurs in arrhythmia where there is total dissociation between atria and ventricles and the ventricles beat very irregularly with no pattern. The ventricles don't follow intrinsic rhythm because every SA nodal impulse that occurs at the end of latency of AV node will get conducted. Thus the heart rate is very high without any pattern. (Here heart rate means ventricular rate)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-01-09T06:27:07.277" LastActivityDate="2015-01-09T06:27:07.277" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="27474" PostTypeId="1" CreationDate="2015-01-08T12:27:29.037" Score="3" ViewCount="921" Body="&lt;p&gt;I define persistent hypothermia in &lt;a href=&quot;https://biology.stackexchange.com/q/27467/86&quot;&gt;this thread&lt;/a&gt; about the mechanisms of persistent hypothermia. &#xA;The Graph of Katzung et al. in Pharmacology about Heart Failure:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/B5MBQ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am thinking which parts here are critical on temperature. &#xA;Temperature has a direct effect of reaction rates of chemical reactions here, for instance NE, AII and probably chemical reactions in endothelin such as ET. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, I am thinking that the relationship between temperature and cardiac performance cannot be linear at all. &#xA;Some have said me that low temperature can decrease metabolism and oxygen consumption. &#xA;However, I started to think differently when time goes enough far that is when heart cannot anymore supply enough blood with oxygen. Thus, hypoxia can occur and asymptomatic exodus may occur. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Physiological case&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Based on physiology, I can propose that the cardiac output curve shifts to the left (CO1 $\to$ CO2), due to less oxygen being supplied to the heart, similarly EDV1 (end-diastolic volume) shifts $\to$ EDV2 and SV1 (stroke volume) $\to$ SV2. &#xA;However, the venous return (VR) curve can shift much more, since I propose that the effect of temperature on smooth musculature is relatively bigger than on heart because of proportional size of tissue. &#xA;So the VR1 shifts to VR2, so EDV2 $\to$ EDV3 and SV2 $\to$ SV3.&#xA;Consequently, SV3 &gt; SV1, while EDV3 &amp;lt; EDV1. &#xA;See my draft figure about this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PKSEA.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where EDV (End Diastolic Volume) in the x-axis and SV (Stroke Volume) in the y-axis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a healthy person, who have no hypertrophy of ventricles and elastic myocardium, the heart can tolerate this. So such a condition of cardiac failure as in the figure 13-3 is possible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if flexibility of the myocardium, for instance, is not possible, such a pathway may not be possible. &#xA;The autonomic nervous system may enter the picture and increase vagus nerve stimulation (PS more). &#xA;However, not sure about the exact pathway. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the effect of temperature on cardiac performance?&lt;/strong&gt; &#xA;How can temperature decrease cardiac performance?&lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2016-02-16T05:48:55.080" Title="What is the effect of persistent hypothermia on cardiac performance?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;temperature&gt;&lt;heart-failure&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27475" PostTypeId="1" AcceptedAnswerId="28245" CreationDate="2015-01-08T13:32:13.737" Score="14" ViewCount="15964" Body="&lt;p&gt;Somewhere in evolutionary history &lt;em&gt;homo&lt;/em&gt; started walking upright and became bipedal. You hear these hypotheses that, by walking upright, they could see better across the grassy savannas to escape predators, find food, find fellow humans etc. However, the most parsimonious way to accomplish looking farther across the grassy plains is by growing taller - much less adaptations necessary and hence more favorable from an evolutionary perspective. Other hypotheses say &lt;em&gt;homo&lt;/em&gt; freed his hands to carry things. Quite fine, but some apes are known to carry around stuff. Moreover, walking on all fours increases running speed (you don't have to see far if you can escape faster) and apes climb trees better (what's a better place to hide from predators?). Hence my question: &lt;strong&gt;Why has bipedalism been favored in evolution?&lt;/strong&gt;      &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="10022" LastEditDate="2015-02-02T21:16:47.233" LastActivityDate="2015-02-03T13:14:46.357" Title="Why did humans become bipedal?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27476" PostTypeId="2" ParentId="1972" CreationDate="2015-01-08T13:53:01.893" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I'm not clear what &quot;Locus&quot;, &quot;Main locus&quot;, and &quot;IGMT group&quot; mean here&#xA;  exactly. Specifically, what is the difference between &quot;Locus&quot; and&#xA;  &quot;Main locus&quot;?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From the same site:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A locus is a set of IG or TR genes that are ordered and are localized&#xA;  in a same chromosomal location, in a given species. […]&lt;br&gt; &#xA;   A locus comprises the genes of different groups which participate&#xA;  potentially to the synthesis of a polypeptide of the same 'chain&#xA;  type'.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Main locus&lt;/code&gt; should have been &lt;code&gt;Locus&lt;/code&gt; minus the &lt;code&gt;orphons&lt;/code&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A chromosomal orphon set is a set of IG or TR orphons (genes outside&#xA;  from the main loci) belonging to a same group and localized on the&#xA;  same chromosome in a given species.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&#xA;However the &lt;code&gt;Main Locus&lt;/code&gt; and &lt;code&gt;Locus&lt;/code&gt; have the same options; Options for the &lt;code&gt;Locus&lt;/code&gt; should have been chromosomes. They must have made a revision in the site but forgot to change the help. I tried setting all the options except &lt;code&gt;any&lt;/code&gt; in &lt;code&gt;Locus&lt;/code&gt; and selecting &lt;code&gt;all&lt;/code&gt; for the &lt;code&gt;Orphons&lt;/code&gt;; it yields no result. It works only if you set &lt;code&gt;any&lt;/code&gt; in &lt;code&gt;Locus&lt;/code&gt;. So it seems &lt;code&gt;Locus&lt;/code&gt; option is useless; you can set the &lt;code&gt;Locus&lt;/code&gt; as &lt;code&gt;any&lt;/code&gt; by default.&#xA;&lt;br&gt; &lt;em&gt;For confirmation it is best to ask the authors&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the changelog:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;16 April 2012&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;&lt;p&gt;Update of the IMGT/GENE-DB Query page:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The search criteria are organized according to the axioms IDENTIFICATION, LOCALIZATION and CLASSIFICATION of IMGT-ONTOLOGY.&#xA;  Addition of new search criteria:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;MolecularComponent (IDENTIFICATION)&lt;/li&gt;&#xA;  &lt;li&gt;Locus (LOCALIZATION): includes main loci and chromosomal orphon sets&#xA;  Main locus: &quot;all&quot; value allows to search genes of all main loci.&#xA;  Chromosomal orphon set: &quot;all&quot; value allows to search genes of all chromosomal orphon sets&lt;/li&gt;&#xA;  &lt;/ul&gt;&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For details on the IMGT classification you should refer to &lt;a href=&quot;http://bioinformatics.oxfordjournals.org/content/15/12/1047.abstract&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fixing a &lt;code&gt;Locus&lt;/code&gt; option does not change the &lt;code&gt;IMGT&lt;/code&gt; dropdown box option but the results are different. If you try your example and set &lt;code&gt;Main Locus&lt;/code&gt; as &lt;code&gt;IGH&lt;/code&gt; and &lt;code&gt;IMGT Group&lt;/code&gt; as &lt;code&gt;IGKJ&lt;/code&gt; you would get no results. It is just a problem of the web interface. Apparently the search works fine.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Running the search&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I searched with the exact same criterion as you mentioned and did not get any sequences smaller than 38nt. There must have been some bug which seems to be fixed. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-01-08T15:42:05.530" LastActivityDate="2015-01-08T15:42:05.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27477" PostTypeId="2" ParentId="26277" CreationDate="2015-01-08T14:46:52.237" Score="4" Body="&lt;p&gt;&lt;strong&gt;Preamble&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a very interesting question one which I don't immediately know an answer to. I think this overly succinct answer and the fact nobody else has answered highlights the degree to which the age old darwinian assumptions play a role in the field. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Zoological POV&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not an expert in this area so I went to a zoology lab technician and this is what they had to say (I'm paraphrasing here):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Most animals are opportunistic and can't afford the luxury of a late&#xA;  brunch... The only animals that spring to mind that appear to 'plan' for&#xA;  meals are the hoarders (squirrels for example). But they don't&#xA;  typically cache food in the same way we would for a weekly shop, but&#xA;  do so for fear of food scarcity (overwintering, rival competition);&#xA;  Not unlike the mad dash for bread and loo roll when it starts snowing&#xA;  slightly!&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Maybe animals do have their diet set to a circadian rhythm, or maybe not. We can't say for sure. Darwin implied, even a peaceful meadow is full of starving ravenous animals clinging to survival. There is no real time for luxury. If food is there, they eat it. Many animals don't even get full the same way we do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Scarcity of Literature&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem lies in that there is no body of literature around animal eating times since animals seldom have enough food in their natural environment to monitor any regularity. If you want specific questions on a particular species for optimum feeding times, I would recommend opening another question as lab animals do have recommended diets. Many predators have optimum hunting times (for example nocturnal, or dusk). However one could argue this is to do with success rates/effective hunting strategy and not necessarily scheduled eating times.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2015-01-09T11:30:19.230" LastActivityDate="2015-01-09T11:30:19.230" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="27478" PostTypeId="1" AcceptedAnswerId="31357" CreationDate="2015-01-08T15:56:20.347" Score="7" ViewCount="286" Body="&lt;p&gt;The underlying intuition of Hamilton's model of inclusive fitness is that we should study social behaviors from the point of view of actors -- rather than the recipients. To build his model, Hamilton expresses the genotype of the actor $j$ in terms of the genotype of the recipient of&#xA;the behavior, $i$. The genotype of $j$ is decomposed in two parts,&#xA;``genes which are copies by direct replication of genes in $i$; the&#xA;other part consists of non-replica genes'' (Hamilton 1970, p. 1219).&#xA;Hamilton (1970) further defines $q_{i}$ as the gene frequency of the&#xA;replica part, $b_{ij}$ represents the replica fraction, and $q$ is the average gene frequency in the population. From these definitions Hamilton (1970) jumps to the equality:&#xA;\begin{equation}&#xA;      E (q_{j}) = \frac{1}{1-b_{i}}\left\{ (b_{ij} - b_{i})q_{i} + (1-b_{ij})q\right\}&#xA;\end{equation}&#xA;where&#xA;\begin{align*}&#xA;  b_{i} = \frac{1}{n}\sum_{j}b_{ij}&#xA;\end{align*}&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How did Hamilton derive the above equation?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Here is what &lt;em&gt;I think&lt;/em&gt; Hamilton is doing. My impression is that the above equation expresses $E(q_j | q_i)$ as a linear regression on $q_i$. In other words, I think the above equation is equivalent to:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$E(q_j | q_i) = E(q_j) + \beta (q_i - E(q_i))$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$E(q_j | q_i) = q + \beta (q_i - q)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, this equation is equivalent to Hamilton's equation if the regression coefficient is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\beta = (b_{ij} - b_i) / (1 - b_i)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I haven't been able to derive this regression coefficient. Given that $\beta = Cov (q_j, q_i)/Var (q_i)$, I suspect that the way to go is to rewrite $q_j$ and $q_i$ in terms of $b_{ij}$ and $b_i$ and calculate the regression coefficient.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hamilton 1970 &quot;Selfish and Spiteful Behaviour in an Evolutionary Model&quot; &#xA;&lt;a href=&quot;http://www.nature.com/nature/journal/v228/n5277/abs/2281218a0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.nature.com/nature/journal/v228/n5277/abs/2281218a0.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qOtTC.png&quot; alt=&quot;Excerpt from Hamilton&amp;#39;s paper&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="11829" LastEditorUserId="11829" LastEditDate="2015-01-20T21:11:44.477" LastActivityDate="2015-04-15T00:28:26.067" Title="Hamilton's inclusive fitness approach" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;mathematical-models&gt;&lt;population-genetics&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27479" PostTypeId="1" CreationDate="2015-01-08T17:35:13.460" Score="4" ViewCount="241" Body="&lt;p&gt;I always hear people saying that the mutation rate is around $10^{-6}$ or $10^{-7}$. I don't even know if this number is the mutation rate of genes or of a single nucleotides and I actually (almost) never seen a referenced estimation of the mutation rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know there is an impressive variance in mutation rate depending on the species we look at and depending on the genomic region we look at. Various other factors also influence the mutation rate such as ecological factors (thermal stress for example).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In multicellular eukaryotes, what is a good estimate of the mutation rate per nucleotide, per gene and per genome? How does real values vary around these estimates?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-01-18T00:12:23.250" LastActivityDate="2015-01-18T00:12:23.250" Title="Mutation Rate in Multicellular Eukaryotes" Tags="&lt;evolution&gt;&lt;population-dynamics&gt;&lt;mutations&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27481" PostTypeId="1" AcceptedAnswerId="27504" CreationDate="2015-01-08T22:56:07.370" Score="1" ViewCount="166" Body="&lt;p&gt;I have a list of ~200 DNA sequences, representing probably 50 different genomic regions but they're all mixed up. For example, if I have &lt;code&gt;seq1, seq2.... seq10&lt;/code&gt;, &lt;code&gt;seq1&lt;/code&gt; might align to &lt;code&gt;seq3&lt;/code&gt; and &lt;code&gt;seq8&lt;/code&gt;, but be completely unrelated to the others. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also some differences in the lengths sampled, so the above example might represent:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Seq1-------------------------------------------------&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Seq3----------------------   seq8-----------------&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such that &lt;code&gt;seq3&lt;/code&gt; and &lt;code&gt;seq8&lt;/code&gt; don't align to each other, but both align to &lt;code&gt;seq1&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what I'd like to do is go through and somehow generate a list of groups of sequences that align to each other, as well as the alignments. eg:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Group 1&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Seq1-------------------------------------------------&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Seq3----------------------   seq8-----------------&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Group 2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;seq2------------------------------------&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;.       seq6-----------------------------&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;.   seq7--------------------------xxxxxx&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Group 3&lt;/strong&gt;... etc &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trying ClustalW or MUSSLE to align everything doesn't work (or takes an unreasonable amount of time), I'm guessing because there are so many sequences that don't align at all. I tried making a custom BLAST database and then BLASTed each sequence against it, but then I get multiple hits for the same alignment (with the group 2 example above, &lt;code&gt;seq2:seq6&lt;/code&gt;, &lt;code&gt;seq2:seq7&lt;/code&gt;, &lt;code&gt;seq6:seq2&lt;/code&gt;, &lt;code&gt;seq6:seq7&lt;/code&gt;, &lt;code&gt;seq7:seq2&lt;/code&gt; and &lt;code&gt;seq7:seq6&lt;/code&gt; all get returned as 6 unique hits, when they should be grouped together.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My current coding knowledge is fairly basic, but I'm willing to read docs and figure stuff out, I just don't want to reinvent the wheel. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit2:&lt;/strong&gt; &#xA;Really, the grouping is the important part - once I have the groups, I can do the alignment separately with little effort. I'd just like to have groups where each sequence is in a single group.&lt;/p&gt;&#xA;" OwnerUserId="12905" LastEditorUserId="3340" LastEditDate="2015-01-09T10:40:12.820" LastActivityDate="2015-01-10T09:08:41.780" Title="Aligning multiple sequences in heterogeneous group" Tags="&lt;bioinformatics&gt;&lt;blast&gt;&lt;sequence-alignment&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27483" PostTypeId="2" ParentId="27481" CreationDate="2015-01-08T23:14:50.223" Score="0" Body="&lt;p&gt;Do you really need BLAST?  That is, are the sequences different enough from each other that you need an algorithm that looks for large differences between them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe you could use something like Phrap, which should put together contigs for you, if the sequences which should go together are very close to identical.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2015-01-08T23:14:50.223" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27484" PostTypeId="2" ParentId="3256" CreationDate="2015-01-08T23:19:38.240" Score="4" Body="&lt;p&gt;As with so many things, it depends. Also, I'm a bit unclear when you say antibody-receptor interaction, do you mean that you have an antibody that's specific for a receptor, or that you're studying Fc receptors binding to antibodies? (for the following, I assume the former)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For most cell types and most cell surface molecules, simple antibody binding isn't going to induce endocytosis, and keeping the cells on ice is sufficient to prevent most background endocytosis (i'd do the assays in a cold room as well so that even when you take tubes out of the ice bucket they stay cold).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, if you're using highly phagocytic cells (like macrophages), and/or you're triggering a receptor through cross-linking or some other mechanism, you might get some endocytosis that affects your results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanism (clathrin vs non) can also vary, again depending on what's being bound. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should do some optimization - ie: do the same assay on a set of samples, with or without  inhibition and see if your antibody binding is affected. But be aware that a lot of drugs for inhibiting endocytosis can do other stuff too, so watch out for artifacts. Maybe read this: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18369934&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/18369934&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12905" LastActivityDate="2015-01-08T23:19:38.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27485" PostTypeId="1" CreationDate="2015-01-09T00:33:43.070" Score="4" ViewCount="846" Body="&lt;p&gt;Here is its usage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;there is sufﬁcient genetic control to make nonmetric traits useful in anthropological work, and such variables have successfully assigned individuals from distinct geographic regions to their correct groups (for example, ... As such, nonmetric traits are an appropriate means for studying biological distances&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;a href=&quot;https://www.academia.edu/5201951/Sahara_Barrier_or_corridor_Nonmetric_cranial_traits_and_biological_affinities_of_North_African_Late_Holocene_populations&quot; rel=&quot;nofollow&quot;&gt;https://www.academia.edu/5201951/Sahara_Barrier_or_corridor_Nonmetric_cranial_traits_and_biological_affinities_of_North_African_Late_Holocene_populations&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="11679" LastActivityDate="2015-01-09T02:19:56.083" Title="What do biologists mean when they use the term &quot;biological distance&quot;?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27486" PostTypeId="2" ParentId="26216" CreationDate="2015-01-09T00:54:54.983" Score="4" Body="&lt;p&gt;The first question, namely what is the &lt;em&gt;advantage of color opponency 'against' RGB&lt;/em&gt;, is technically incorrect. The opponent system (Red/Green; Blue/Yellow and brightness channels) is physiologically situated in the neuronal retinal layer and higher visual structures such as the lateral geniculate nucleus and receives input from the RGB system (photoreceptors in the retina: Red, Green, Blue cones). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sGqRR.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then the question becomes &quot;&lt;strong&gt;&lt;em&gt;what is the advantage of adding the opponent channels on top of the RGB system?&lt;/em&gt;&lt;/strong&gt; The advantage of opponency may in fact not be the negative opponent effect so often stressed in the Hering model (and shown in the figure: e.g., blue suppressing yellow etc). The advantage lies in the finding that activity of one opponent pair &lt;em&gt;increases activity&lt;/em&gt; of the opponent color in adjacent areas in the retina. This effect results in a &lt;strong&gt;sharpening of color contrasts&lt;/strong&gt; between the opponent colors (&lt;a href=&quot;http://jraissati.com/PHIL256/09_HurvichJameson_AnOpponentTheoryOfColorVision.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hurvich and Jameson, 1957&lt;/a&gt;). Indeed, the poor spatial color-contrast, as provided by the sparsely placed cones in the retina, is enhanced by this mechanism. Especially the blue cones are present in isolated patches in the retina. Because one color in an opponent pair increases the other's activity directly adjacent to it in the retina, the resolution of the blurry retinal image is greatly increased. Hence, as you rightfully say, &lt;em&gt;edge detection&lt;/em&gt; and in particular &lt;strong&gt;color contrast perception&lt;/strong&gt; is enhanced. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Object recognition&lt;/em&gt;, as you mention in your question, is a process that is facilitated by the visual system through many stages including the higher visual cortices. Enhanced color contrast will likely facilitate object perception, but indirectly since color contrasting makes up just a small portion of a much bigger and complicated neural system devoted to object recognition, namely the visual 'ventral' stream (&lt;a href=&quot;http://www.pnas.org/content/96/16/9379.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ishai et al., 1999&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly you ask whether opponent colors may facilitate &lt;em&gt;invariance to brightness&lt;/em&gt;. Assuming you mean color invariance under varying luminance (referred to as &lt;strong&gt;color constancy&lt;/strong&gt;) the answer is &lt;strong&gt;no&lt;/strong&gt;. The RGB cone system can deal with this easily, as the &lt;strong&gt;ratio of cone activation&lt;/strong&gt; yields enough information to code the hue under various luminances. If a certain object reflection activates twice as many red cones than green cones, it will also activate the same ratio when the luminance is increased (&lt;a href=&quot;http://www.psypress.com/cw/mather-9781841696997/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mather, 2006 - Chapter 12&lt;/a&gt;).      &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-18T13:03:38.743" LastActivityDate="2015-03-18T13:03:38.743" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27487" PostTypeId="2" ParentId="27485" CreationDate="2015-01-09T01:56:54.220" Score="4" Body="&lt;p&gt;&lt;em&gt;Biological distance&lt;/em&gt; is pretty much what you'd guess: how &lt;strong&gt;closely&lt;/strong&gt; related are &lt;em&gt;x&lt;/em&gt; and &lt;em&gt;y&lt;/em&gt; based on genetic (phenotype or genotype) studies?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is &lt;em&gt;zero&lt;/em&gt; biological distance between identical twins. There is &lt;em&gt;extremely little&lt;/em&gt; biological distance between family members (for most intents and purposes, none, no matter where they live). It goes on and on in this manner.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Biological distance, or degree of genetic relatedness, will be assessed by a comparison of dental nonmetric trait frequencies.&lt;sup&gt;1&lt;/sup&gt;  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The phrase has been used in Theoretical Population Biology for decades. Back then, they had phenotypes to measure the degree of biological distance.&lt;sup&gt;2&lt;/sup&gt; Today, actual genetic determination of kinship is possible.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Biological distance, or biodistance, is the measure of biological relatedness (or divergence) between and within human groups, living and past, based on human skeletal and dental variation.&lt;sup&gt;3&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://online.sfsu.edu/mgriffin/Weston.pdf&quot; rel=&quot;nofollow&quot;&gt;1 Dental Variation of Prehistoric Amerindian Populations&#xA;from Eastern Tennessee&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0040580975900192&quot; rel=&quot;nofollow&quot;&gt;2 Kinship, information and biological distance&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.academia.edu/3482164&quot; rel=&quot;nofollow&quot;&gt;3 Biological Distance in Bioarchaeology and Human Osteology&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-09T01:56:54.220" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27488" PostTypeId="2" ParentId="27485" CreationDate="2015-01-09T01:57:25.327" Score="4" Body="&lt;p&gt;I think this is more of a Biological Anthropology question, and my guess is the question could be rephrased as &quot;&lt;strong&gt;&lt;em&gt;What do anthropologists mean when they use the term “biological distance?&lt;/em&gt;&lt;/strong&gt;” &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Anthropology Stack Exchange is still under construction so that is a dead end for now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.academia.edu/3482164/Biological_Distance_in_Bioarchaeology_and_Human_Osteology&quot; rel=&quot;nofollow&quot;&gt;Pietrusewsky (2014)&lt;/a&gt; gives the following definition, and I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Biological distance&lt;/strong&gt;, or biodistance, is a measure of relatedness or divergence among groups separated by time and/or geography based on morphological variation (Buikstra et al. 1990). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Pietrusewsky continues with elaborating on Biodistance research:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Biological distance studies, which are undertaken to reconstruct population history and to assess ancestry, dominated bioarchaeological research during the 19th and early 20th centuries. [...] These early attempts were flawed due to limitations of the approach, which included the mistaken belief that humanity could be divided into a finite number of pure races, and the lack of adequate quantitative methods. Advances in evolutionary theory, including quantitative and population genetics, and improvements in computing and statistical procedures in the early 20th century provided a much sounder basis for measuring and interpreting morphological variation within and between human groups.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These elaborations may explain the rather defensive stature the authors take in your cited article to back up their methods, and I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In any case, there is sufficient genetic control to make nonmetric traits useful in anthropological work, and such variables have successfully assigned individuals&#xA;  from distinct geographic regions to their correct groups (for example, Winder, 1981; Prowse and Lovell, 1995; Blom et al., 1998; Christensen, 1998; Donlon, 2000;&#xA;  Hanihara et al., 2003). As such, nonmetric traits are an appropriate means for studying biological distances among North African populations and the implications of&#xA;  the patterning of these distances in assessing the relative role of the Sahara Desert as a barrier to gene flow.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-09T02:19:56.083" LastActivityDate="2015-01-09T02:19:56.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27490" PostTypeId="1" CreationDate="2015-01-09T02:52:34.707" Score="2" ViewCount="1020" Body="&lt;p&gt;There are &lt;a href=&quot;http://mentalfloss.com/article/60243/tree-flowers-40-different-fruits&quot; rel=&quot;nofollow&quot;&gt;multi-fruit trees with as many as 40 different fruit&lt;/a&gt;, but would it be possible to graft a vegetable onto a tree?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or maybe something in between, like grafting onto an apple tree a fruits in the botanical sense, but one of those often eaten as savory food, similar to vegetables: tomato, squash, avocado?&lt;/p&gt;&#xA;" OwnerUserId="5972" LastEditorUserId="5972" LastEditDate="2015-01-09T06:57:34.680" LastActivityDate="2015-01-09T06:57:34.680" Title="Grafting vegetables onto fruit-bearing trees" Tags="&lt;botany&gt;&lt;fruit&gt;&lt;vegetable&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27492" PostTypeId="2" ParentId="27474" CreationDate="2015-01-09T03:55:19.370" Score="-2" Body="&lt;p&gt;Both pictures you posted show that increased peripheral vascular resistance decrease cardiac output. If you are talking about someone outdoors not properly dressed in a Scandinavian winter, then their cutaneous vasculature would constrict and Also their extremities would get less blood flow. That would increase peripheral vascular resistance and thus decrease cardiac output. These articles were the first to pop up for me (&lt;a href=&quot;http://circres.ahajournals.org/content/7/3/366&quot; rel=&quot;nofollow&quot;&gt;http://circres.ahajournals.org/content/7/3/366&lt;/a&gt; &amp;amp; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10215232&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/10215232&lt;/a&gt;) and it seems to say that the primary cause of increased vascular resistance is actually caused by decreased cardiac output as well as local control.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This may seem contradictory to therapeutic use of hypothermia, where it is used to decrease metabolic needs (I don't know what is the mechanism for this) to help compensate for hypoxia (in cardiac tissue and the brain?). Cooling the heart would decrease it's metabolic needs (less perfusion, increased metabolic demands resulting from sympathetic input to heart. I guess the same thing probably happens when doctors prescribe a beta-blocker or non-dihydropyridine calcium channel blocker (CCB), the vascular resistance probably increases (except for the CCB diltiazem which dilates blood vessels in addition to it's effects on the heart). But the main thing is the sympathetic output to the heart, which is blocked by these drugs, and cold; this is more important than the increased peripheral vascular resistance. But &lt;strong&gt;remember that afterload is not identical to peripheral vascular resistance&lt;/strong&gt;!!! The decreased cardiac output would probably decrease blood pressure and afterload, I'm guessing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the slowing of reactions related to vasoconstriction (transmission of nervous signal from hypothalamus via pre ganglionic sympathetic fiber, then synapse in sympathetic chain, then transmission via post ganglionic nerve; release of NE, Epi, AT-II; rate of diffusion to receptor; effect of cold on membrane fluidity; effect on the alpha adrenergic receptor; rate of second messenger signalling cascade; effect of cAMP formation by G stimulator protein or breakdown by phosphodiesterase; effect of Ca++ release; effect on PLC mediated IP3/DAG release; effect on NO release and receptor stimulation of guanylate cyclase;  and the various other factors regulating endothelial function and smooth muscle contraction), I don't know. I also assume that an increase in viscosity (a factor included in the calculation of vascular resistance) could be another factor leading to increased vascular resistance, but even if this happens, this is less important than the decrease of the hearts metabolic rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally I'm not acquainted with the literature on therapeutic use of hypothermia, aside from the ethical debates about using Nazi hypothermia research. I'm just going at it with the same physiology knowledge you have, and relaying your confusion back at you. I'm just as lazy as you and I don't feel like spending hours delving into review articles on hypothermia research, but I agree that it is an interesting question, and it is also relevant to other very important topics in medicine (ie. use of beta blockers, non-dihydropyridine CCBs other than diltiazem).&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2015-01-09T05:29:03.707" LastActivityDate="2015-01-09T05:29:03.707" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="27494" PostTypeId="2" ParentId="25974" CreationDate="2015-01-09T04:54:07.230" Score="10" Body="&lt;p&gt;First, I must clarify that a nerve is not the same as a neuron. A nerve is a collection of axons (with each axon a part of an individual neuron) in the peripheral nervous system. Thus, when you mention “single long axon such as the sciatic nerve”, this is technically an incorrect phrase as the sciatic nerve is a collection of many long axons. If one of these axons is nonfunctional, this would not severely affect the function of the entire sciatic nerve. However, you are right that if the entire sciatic nerve is severed, then there would be serious consequences downstream. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, the primary advantage of conduction velocity is less dependent on length and more dependent on presence and degree of myelination (directly proportional to fiber diameter) and presence of nodes of Ranvier. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regards to the content of your question, the advantage of length is exactly what one might think--- greater distance. The sciatic nerve is the longest nerve in the body in order for our nervous system to innervate as far as the tip of our toes. Having hundreds of side-by-side series of neurons compared to hundreds of side-by-side axons seems like a far less efficient system in a couple of ways in exactly the two ways you mention: energy and time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Energy: Having serial neurons would require an increase the number of neurons needed to transmit a message. Having more neurons requires more Na+, K+ and Na/K pumps and individual channels, requiring more energy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Time: Having serial neurons would also require an increase in the number of synapses between neurons— either electrical or chemical. If the synapses are chemical, then time is increased many-many fold. If the synapses are electrical, then time is slightly increased by 10-fold per synapse compared to chemical synapses, but this would still take more time compared to having a single axon with myelination and nodes of Ranvier which by about 100-fold faster than a single electrical synapse. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, having longer nerves made up of axons rather than serial neurons is beneficial by improving energy and time efficiency, which allows our bodies to effectively innervate structures farther away.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ref: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Regarding delay of conduction: Chemical v. Electrical/Gap  Ch 10 of Principles of Neuroscience- &quot;Synaptic Integration in the Central Nervous System&quot; (Siegelbaum,&#xA;Kandel, Yuste) 5th ed. McGraw-Hill Medical, c2013.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10921/&quot; rel=&quot;noreferrer&quot;&gt;Regarding conduction velocity of myelinated versus nonmyelinated&#xA;cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Regarding the ATPase absolute number increase in serial vs one long axon, I assume this will depend on the number of neurons in series. However, I read &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23022068&quot; rel=&quot;noreferrer&quot;&gt;this paper&lt;/a&gt;, which says that increased length between each node of Ranvier has been physiologically associated with increased conduction velocity. This suggests fewer needed nodes, despite concentrated ATPases at these locations, and thus fewer ATPases. I haven't been able to find studies which compare ATPase concentration in the soma compared to nodes of Ranvier within axons. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding energy use in soma vs axon, mitochondria are not only made in the soma but are concentrated in pre- and post-synaptic membranes (and growth cones). The more of these structures there are (as in serial neurons), the more presumed mitochondria. See &lt;a href=&quot;http://ajpcell.physiology.org/content/292/2/C641&quot; rel=&quot;noreferrer&quot;&gt;mitochondria and neuronal activity&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, my literature search could not find studies which showed longest possible energetically feasible length for myelinated or unmyelinated neurons. &lt;/p&gt;&#xA;" OwnerUserId="11631" LastEditorUserId="11631" LastEditDate="2015-01-09T18:25:17.977" LastActivityDate="2015-01-09T18:25:17.977" CommentCount="17" ContentLicense="CC BY-SA 3.0" />
  <row Id="27496" PostTypeId="1" AcceptedAnswerId="27502" CreationDate="2015-01-09T05:59:41.457" Score="3" ViewCount="1299" Body="&lt;p&gt;I know that H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; is a chemical with high oxidative potential. It can deliver nascent oxygen which can destroy bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that open wounds have cells that are dividing at a fast rate to effect healing. Is it good to add a substance that can cause damage to cell membrane and possibly cause mutation in the DNA of these fast growing tissues?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; be safely used to sterilize wounds?&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2019-01-24T02:12:53.853" LastActivityDate="2019-01-24T02:12:53.853" Title="Hydrogen Peroxide on Open Wounds" Tags="&lt;physiology&gt;&lt;healing&gt;&lt;sterilisation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="27497" PostTypeId="2" ParentId="27490" CreationDate="2015-01-09T06:15:22.803" Score="1" Body="&lt;p&gt;For grafting to &quot;take&quot;, the the two plants' vasculatures have to be organized similarly. This is not possible for two such differently organized stems as a pepper and an apple.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a cross section of a young woody stem (such as an apple, though this example is a tilia):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WzQeb.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a cross section of an herbaceous stem (such as a pepper):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PHvDJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see there is dissimilarity in organization. Furthermore, herbaceous plant stems die back in the winter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if possible, grafting an herbaceous (non-woody) stem onto a woody stem (e.g. apple) would not confer any advantage for the green pepper, a tender annual, and would be disadvantageous to the woody stemmed tree (pruning for no reason, when the branch would otherwise have produced apples, and the leaves performed their useful functions.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-09T06:15:22.803" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27501" PostTypeId="2" ParentId="14140" CreationDate="2015-01-09T08:17:46.100" Score="1" Body="&lt;p&gt;This problem is rampant and has been plaguing the research community for a decade. I can explain how exactly do these companies make these fake kits, how to experimentally verify what I said is true, and how to spot them by just looking at their website. I can even point fingers and name a few known and notorious companies that do this malpractice. What I ask from anyone who reads this is to recognize that these companies are the bad apples in Chinese companies and you shall not generalize all Chinese biotech companies. Generalization, not a good thing, and I trust all the years of training in scientific critical thinking has taught you better :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now how do these companies make fake ELISA kits? Simple. They use a universally present protein target, initially TGF beta--I do not know what they have shifted to lately--to make one type of ELISA kit, and label it as anything and everything. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How to actually prove it? Run a western using a trusted third party antibody. If nothing shows up, you know the standard is not what they claim it is. Or you can also run a third party recombinant protein on the kit. Same core concept. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do not want to bother with all that? Then just keep an eye out for this signature: one company that has thousands sometimes tens of thousands of ELISA kits, covering all kinds of species--sometimes ridiculous ones like whales, giraffes, tadpoles, sharks etc.--nothing against giraffes, they are awesome and all but seriously... These companies are literally like Noah's Ark. How can one company you never heard of come up with so many ELISA kits while established companies who have been making kits for decades are dangling on the level of hundreds or thousands? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe, one thinks, that someone went hard core and just made them all, that maybe this is real? After all there are no other choices, they are the only ones selling this ELISA kit, wouldn't hurt too much to give it a try...?? &#xA;And that is why these companies still exist today. That is why so many papers got pulled, and so many clinically promising indications turned out to be false. That is what cost millions of dollars of tax payers money. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the end I want to point out that, if researchers did their due diligence, or if there are some more effective forms of media where researchers can get information like this, these companies would have died a decade ago. Instead they just keep coming up with different company names and pulling the same scam. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to put examples of these companies by directly referencing their names but I am not sure about the forum rules would allow it so for this post, I would not do so. The signature described above should be clear enough for you to spot these companies. Wish you all the luck in 2015. &lt;/p&gt;&#xA;" OwnerUserId="12912" LastEditorUserId="3340" LastEditDate="2015-01-09T08:27:49.700" LastActivityDate="2015-01-09T08:27:49.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27502" PostTypeId="2" ParentId="27496" CreationDate="2015-01-09T08:42:10.047" Score="4" Body="&lt;p&gt;There will be few rapidly-dividing cells in a fresh wound (which is the wound to which H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; is applied). In general, it is a good idea to avoid applying irritants to rapidly dividing tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hydrogen peroxide is a weak mutagen. It is produced in many body tissues, ingested in drinks, produced by mouth bacteria, etc. It may well cause some cancers. Some OSHA-mandated literature does warn that it is a mutagen and must be handled with care, but these are warnings to people who work with concentrated solutions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, a relatively weak hydrogen peroxide solution, even if it is mutagenic, would need to be left in place and active (or renewed) for a long period of time to produce skin cancer. As it has been a staple of first aid kits for decades, and this association has never been made clinically, my best guess is that the benefit (as a bacterocidal agent) far outweighs the risk in the treatment of minor wounds. As in all things, however, prudence is advised. (I myself don't use it because soap and a lot of water is quite effective. Nor is it used in the care of wounds in Emergency Rooms where it is considered to be detrimental to wound healing. If I were in a country where clean water and soap were in short supply, I might well use it if necessary.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because it is an irritant (and many irritants can be considered mutagenic), it is actually used to treat precancerous skin lesions, the finding being that it affects the more rapidly dividing pre-cancerous cells than the rest of the epithelium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Far more potent peroxides have been used topically, which may increase the risk of skin cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, one of the responses of skin cells to H2O2 is the generation of an oxygenase to fight the effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19180893&quot; rel=&quot;nofollow&quot;&gt;Topical sulindac combined with hydrogen peroxide in the treatment of actinic keratoses&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.nature.com/jid/journal/v79/n1/abs/5615395a.html&quot; rel=&quot;nofollow&quot;&gt;Effects of Peroxides on Rodent Skin: Epidermal Hyperplasia and Tumor Promotion&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.pnas.org/content/86/1/99.short&quot; rel=&quot;nofollow&quot;&gt;Heme oxygenase is the major 32-kDa stress protein induced in human skin fibroblasts by UVA radiation, hydrogen peroxide, and sodium arsenite&lt;/a&gt;&lt;br&gt;&#xA;Recent Advances in Wound Care, Michael K. Abraham, MD, MS, and Jason S. Oh, MD &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-01-09T09:05:10.197" LastActivityDate="2015-01-09T09:05:10.197" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="27503" PostTypeId="1" CreationDate="2015-01-09T08:52:11.520" Score="0" ViewCount="52" Body="&lt;p&gt;For my course project, I am thinking of listing out major chemical reactions that occur at synapses, along with their temporal characteristics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could not find any textbooks to use as a starting point, and Google did not help me either. I was hoping to receive help in finding a review paper or textbook about chemical computations at the synapse. &lt;/p&gt;&#xA;" OwnerUserId="6228" LastEditorUserId="9943" LastEditDate="2015-01-10T12:22:11.663" LastActivityDate="2015-01-10T12:22:11.663" Title="Chemical reactions at the synapse" Tags="&lt;literature&gt;&lt;synapses&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27504" PostTypeId="2" ParentId="27481" CreationDate="2015-01-09T09:28:10.740" Score="2" Body="&lt;p&gt;You can try this:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;BLAST each sequence to every other sequence (pairwise).&lt;/li&gt;&#xA;&lt;li&gt;Every alignment (with some defined cutoff) denotes a connection. &lt;/li&gt;&#xA;&lt;li&gt;Map all connections.&lt;/li&gt;&#xA;&lt;li&gt;If a sequence is connected to some other directly or indirectly, it falls in a group. Put all the sequences that &lt;code&gt;seq1&lt;/code&gt; aligns to, in &lt;strong&gt;Group-1&lt;/strong&gt;, then go to the alignments of these sequences; put all the sequences that these align to again in &lt;strong&gt;Group-1&lt;/strong&gt;; so keep populating the group like this. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Methodology:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Install &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;amp;PAGE_TYPE=BlastDocs&amp;amp;DOC_TYPE=Download&quot; rel=&quot;nofollow&quot;&gt;standalone blast&lt;/a&gt; (if you don't have many sequences then you can run online BLAST as well)&lt;/li&gt;&#xA;&lt;li&gt;Make a blast database from your sequences using &lt;code&gt;makeblastdb&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;Align these sequences against the database. If you are using online BLAST use BL2seq (align two sequences). &lt;em&gt;It is much better and convenient to use standalone.&lt;/em&gt; You can also mention if you want plus-plus or plus-minus or both alignments. You might in some cases want only either of the two.&lt;/li&gt;&#xA;&lt;li&gt;In the standalone BLAST you can specify the output format (which fields to include etc- the format you choose just depends on your requirements).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;A tabular output format looks something like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;# BLASTN 2.2.27+&#xA;# Query: TCONS_00036712 gene=XLOC_017996&#xA;# Database: ../nt_db/nt&#xA;# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score&#xA;# 1014 hits found&#xA;TCONS_00036712  gi|191174875|emb|CU655970.6|    95.54   202 9   0   423 624 16680   16479   8e-85    324&#xA;TCONS_00036712  gi|51491599|gb|AC144709.2|  95.02   201 10  0   424 624 28443   28243   1e-82    316&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Ignore the commented (&lt;code&gt;#&lt;/code&gt;) lines; the first field is query ID, the second is the subject ID and there is an alignment between the two; the other fields provide information about the alignment (You can choose these fields). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For parsing I use a fast and easy scripting language called awk which is included in all UNIX based systems. It is also available for windows in GNUWin32 package.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you have to do is check the first two fields and update the group. &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&#xA;# MakeGroups.awk&#xA;&#xA;BEGIN{FS=&quot;\t&quot;}     # Declaring Field separator as Tab&#xA;&#xA;!($1 in grp){          # Check if the seq is a parent group. If not...&#xA;    k=1&#xA;    for(i in grp){ &#xA;        if($1 in grp[i]){    # Check if the seq is part of any other groups&#xA;            parentgrp[$1]=i&#xA;            if(!($2 in grp[i]))   # Check if the second field i.e subject already present in the parentgroup&#xA;                grp[i][$2]        # if not assign the second field to the parent group&#xA;            k=0&#xA;            break    # stop checking further&#xA;        }&#xA;    }&#xA;    if(k==1)        # There is no parent group with this label and the seq is not a part of any other group&#xA;        grp[$1][$1] # Make a group with the query-id as the label and add this query to this group.&#xA;}  &#xA;&#xA;$1 in grp{&#xA;    if(!($2 in grp[$1]))&#xA;        grp[$1][$2]    # If the second field is not a part of the group with first field as label then assign it to that&#xA;}&#xA;&#xA;END{&#xA;    for(i in grp){&#xA;        x++&#xA;        print &quot;Group-&quot;x&quot;\n----------&quot;&#xA;        for(j in grp[i])&#xA;            print j&#xA;    }&#xA;    print &quot;\n&quot;&#xA;}&#xA;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Run this script like this in the terminal: &#xA;&lt;br&gt;&lt;code&gt;gawk -f MakeGroups.awk blastalignmentfile.txt&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Note:&lt;/strong&gt; This script contains multidimensional arrays. It will not work with all versions of awk. Use &lt;code&gt;gawk version &amp;gt;4.0&lt;/code&gt;&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As swarnbes mentions in their answer, there are faster algorithms which do this kind of stuff and are used for sequence assembly. What many of them do is to make a graph (networks called deBruijn graphs), where each connection is an alignment, and compute an Eulerian Path. See &lt;a href=&quot;http://www.nature.com/nbt/journal/v29/n11/full/nbt.2023.html&quot; rel=&quot;nofollow&quot;&gt;this review&lt;/a&gt; by Pavel Pevzner for details. Overlapping sequences form contigs and you can easily trace back which sequence came from which contig (which you can call a Group). Each contig/Group is a disjoint deBruijn sub-graph.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-01-10T09:08:41.780" LastActivityDate="2015-01-10T09:08:41.780" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="27505" PostTypeId="2" ParentId="7566" CreationDate="2015-01-09T10:25:16.797" Score="3" Body="&lt;p&gt;I know two databases for such information: The &quot;National Nutrient Database for Standard Reference&quot; (reference 1) from the United States Department of Agriculture (which you list yourself) and the &quot;Nutrition Data&quot; (reference 2) Database. Both allow searching for specific foods and give the values back. I like the second more, since it gives you the complete output it has and you don't have to choose three single nutrients like for the USDA database.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://ndb.nal.usda.gov/&quot; rel=&quot;nofollow&quot;&gt;USDA National Nutrient Database for Standard Reference&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://nutritiondata.self.com/&quot; rel=&quot;nofollow&quot;&gt;Nutrition Data&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-01-09T10:25:16.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27506" PostTypeId="2" ParentId="27503" CreationDate="2015-01-09T12:05:21.203" Score="1" Body="&lt;p&gt;If you are interested it from the point of view of &quot;chemical computations&quot;, you probably want literature which looks at signal transduction in detail. I would suggest &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0815342152&quot; rel=&quot;nofollow&quot;&gt;Marks' et al textbook on signal transduction&lt;/a&gt;. I have not yet read it through (it is on my list), but I liked the clear writing style of the introduction, and, as you can see from the table of contents, it does have chapters which address synapses and their neurotransmitters specifically. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I doubt that it will contain a complete list (there are several hundreds of compounds which can be considered to be neurotransmitters), but as an introductory textbook, it is likely to contain the major ones. &lt;/p&gt;&#xA;" OwnerUserId="1578" LastActivityDate="2015-01-09T12:05:21.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27507" PostTypeId="1" CreationDate="2015-01-09T13:58:47.313" Score="2" ViewCount="291" Body="&lt;p&gt;I am quite a fan of the recent oculus rift VR glasses, but it does have several flaws over normal vision, most notably a much less wide field of view, the so-called screen door effect because of too low resolution (&lt;a href=&quot;https://i.imgur.com/8WnDnmt.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;example 1&lt;/a&gt;, &lt;a href=&quot;http://mkeblx.net/uploads/oculus-sim.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;example 2&lt;/a&gt;) and often also a certain latency between head movements and corresponding view angle change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could one, in theory, create glasses which have these limitations to wear during everyday life to adapt to them, and later have the benefit of a more &quot;realistic&quot; experience?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know making the glasses is not trivial, I'm just asking about whether the perceptual adaptation part would even work as intended, what timeframe I could expect to adapt in, and how stringent the wearing of them has to be (is waking up without them ok, or should sleep be blindfolded, etc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have experience/advice/knowledge on the subject, maybe even links to prior applications?&lt;/p&gt;&#xA;" OwnerUserId="12917" LastActivityDate="2015-01-13T00:35:31.533" Title="Using perceptual adaptation for enhancing realism of VR/other entertainment" Tags="&lt;vision&gt;&lt;perception&gt;&lt;neuroplasticity&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27508" PostTypeId="1" CreationDate="2015-01-09T14:52:09.643" Score="8" ViewCount="795" Body="&lt;p&gt;For example, why do I love paprika while my girlfriend hates it? Why do I find broccoli disgusting and she adores it? As humans, there are things we'd all agree on being awful, like rotten meat, for obvious evolutionary reasons - those things are damaging to our body and we should not eat those. But when asked about delicious food, everyone would pick something slightly (or completely) different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder, is it because our tongues are different and the food does indeed taste different, or is it our brains that interpret the same taste differently? Also, what evolutionary purpose does this serve? To me it only makes planning the dinner a pain without really adding anything to our lives. &lt;/p&gt;&#xA;" OwnerUserId="12919" LastActivityDate="2015-05-29T00:12:52.433" Title="Why do we find some things disgusting and others delicious?" Tags="&lt;evolution&gt;&lt;food&gt;&lt;taste&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27509" PostTypeId="2" ParentId="27479" CreationDate="2015-01-09T17:57:29.230" Score="3" Body="&lt;p&gt;The real mutation rate of any organism depends by too many factors both external, like the environment, and internal, like the error rate of the DNA polymerases and DNA-repair enzymes and even from different region in the same genome (the mutation rate of non-coding DNA tend to be higher than the one of actively used DNA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general however it is possible to determine an average mutation rate for a given organism and usually it is expressed in &lt;strong&gt;mutation per base pair (or single nucleotide) per generation&lt;/strong&gt;.&#xA;If you want to know roughly the mutation rate per gene or per genome you just need to multiply the mutation rate by the number of bases of the gene or genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good papers on the topic are:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Drake JW, Charlesworth B, Charlesworth D, Crow JF (April 1998). &quot;Rates&#xA;  of spontaneous mutation&quot;. Genetics 148 (4): 1667–86.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Ossowski S, Schneeberger K, Lucas-Lledó JI, et al. (January 2010).&#xA;  &quot;The rate and molecular spectrum of spontaneous mutations in&#xA;  Arabidopsis thaliana&quot;. Science 327 (5961): 92–4.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Nachman MW, Crowell SL (September 2000). &quot;Estimate of the mutation&#xA;  rate per nucleotide in humans&quot;. Genetics 156 (1): 297–304.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you want to know about some specific organism you have to dig into the literature...&lt;/p&gt;&#xA;" OwnerUserId="12923" LastEditorUserId="3340" LastEditDate="2015-01-09T18:18:31.363" LastActivityDate="2015-01-09T18:18:31.363" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="27511" PostTypeId="1" AcceptedAnswerId="27513" CreationDate="2015-01-09T20:37:08.003" Score="17" ViewCount="4199" Body="&lt;p&gt;I know for instance some cells are sexual, so, this got me wondering, do the males of all species that have distinct sexes have Y chromosomes? &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="3553" LastEditDate="2015-01-10T02:25:35.773" LastActivityDate="2019-03-30T03:30:26.503" Title="Do males of all sexual species have Y chromosomes?" Tags="&lt;sex&gt;&lt;sex-chromosome&gt;&lt;sex-determination&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27512" PostTypeId="2" ParentId="27511" CreationDate="2015-01-09T20:49:32.473" Score="13" Body="&lt;p&gt;No. There are many &lt;a href=&quot;https://en.wikipedia.org/wiki/Sex-determination_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;sex-determination systems&lt;/a&gt;. Mammals and fruitflies use the XX/XY sex-determination system — except for the platypus, which has 10 sex chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ZW sex-determination system is used by birds and some reptiles. It's similar but with the male having two of the same chromosome (ZZ) and the female being the heterogametic sex (ZW). There's several other variations, such as X0 (XX for females, X for males, with no Y).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also animals with temperature-dependent sex determination and others use reverse their sex.&lt;/p&gt;&#xA;" OwnerUserId="8564" LastEditorUserId="8564" LastEditDate="2019-03-30T03:30:26.503" LastActivityDate="2019-03-30T03:30:26.503" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27513" PostTypeId="2" ParentId="27511" CreationDate="2015-01-09T21:04:34.437" Score="29" Body="&lt;h1&gt;Very short answer&lt;/h1&gt;&#xA;&lt;p&gt;No, not all males of all sexual species have &lt;code&gt;Y&lt;/code&gt; chromosomes. You might want to have a look to the Wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Sex-determination_system&quot; rel=&quot;noreferrer&quot;&gt;sex-determination systems&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;h1&gt;Long answer&lt;/h1&gt;&#xA;&lt;p&gt;&lt;strong&gt;Diversity among the species that reproduce sexually&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Not all species that have sexual reproduction have sexes. Yeasts, for example, have mating types but no sex.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Diversity among the species that have sexes&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Sex is determined by both genetic and environmental factors. In some species, genetic factors are more important than environmental factors in other species it is the reverse. Species which sex is mostly determined by the genetics are said to have GSD (Genetic Sex Determination). For example, humans are GSD, as the female is &lt;code&gt;XX&lt;/code&gt; and the male is &lt;code&gt;XY&lt;/code&gt;. The species where sex is mostly determined by the environment are called ESD (Environmental Sex Determination). For examples, crocodiles are ESD as sex is determined by temperature. It is important to understand however that there is a whole continuum between these two extremes.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Diversity among the species that are GSD&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Among the species that are GSD, some have sexual chromosomes some don't. Some have one locus  (locus=position on a chromosome) that determines the sex, some have many loci (loci=plural of locus). Humans, for example, have sexual chromosomes (&lt;code&gt;X&lt;/code&gt; and &lt;code&gt;Y&lt;/code&gt;) and have only one locus which determines the sex. This locus is called SRY and it codes for a protein called &lt;a href=&quot;http://en.wikipedia.org/wiki/Testis_determining_factor&quot; rel=&quot;noreferrer&quot;&gt;TDF&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Now you can split GSD with sexual chromosomes into two more categories (it is a bit more complex in reality): &lt;code&gt;XY&lt;/code&gt; and &lt;code&gt;ZW&lt;/code&gt;. &lt;code&gt;XY&lt;/code&gt; are those species where the male is heterogametic (&lt;code&gt;XY&lt;/code&gt;), while the female is homogametic (&lt;code&gt;XX&lt;/code&gt;). In &lt;code&gt;ZW&lt;/code&gt; systems, the male is homogametic (&lt;code&gt;ZZ&lt;/code&gt;) and the female is heterogametic (&lt;code&gt;ZW&lt;/code&gt;). Birds and some plants have ZW systems for example, while mammals (except &amp;quot;basal&amp;quot; mammals) and Drosophila have &lt;code&gt;XY&lt;/code&gt; system.&lt;/p&gt;&#xA;&lt;p&gt;See also the post &lt;a href=&quot;https://biology.stackexchange.com/questions/68007/what-determines-sex-in-birds&quot;&gt;What determines sex in birds?&lt;/a&gt;&lt;/p&gt;&#xA;&lt;h1&gt;Extra Information&lt;/h1&gt;&#xA;&lt;p&gt;&lt;strong&gt;Dosage Compensation&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;In species that have sex chromosomes, there is a difference in the number of copy of genes between the sexes. In eutherian mammals, for example, females have two copies of all the genes on the X chromosomes, while males only have one copy of most of these genes (plus a few Y chromosome genes). The set of methods to deal with this issue is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Dosage_compensation&quot; rel=&quot;noreferrer&quot;&gt;Dosage Compensation&lt;/a&gt; and there is also an impressive diversity dosage compensations.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Comments on this diversity of sexual systems&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;The diversity in a sex-determination system, dosage compensation and other things related to sex are impressive. It is even more impressive when we look at how many independent origins there are. Below are some other examples.&lt;/p&gt;&#xA;&lt;p&gt;The Amazon molly (a fish) is a species that have sexual reproduction but there are no males. The females have to seek for sperm in a sister species in order to activate the development of the eggs but the genes of the father from the sister species are not used. (see &lt;a href=&quot;http://classic.rspb.royalsocietypublishing.org/content/275/1636/817.short&quot; rel=&quot;noreferrer&quot;&gt;this article&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;p&gt;There are also &lt;a href=&quot;http://en.wikipedia.org/wiki/Hermaphrodite&quot; rel=&quot;noreferrer&quot;&gt;hermaphrodites&lt;/a&gt; including sequential hermaphrodites (first male, then females or the opposite) in plants and animals. There are also species where populations are made of hermaphrodites and females and others where there are hermaphrodites and males (very uncommon).&lt;/p&gt;&#xA;&lt;p&gt;In some species, the sex is determined by social factors. In clownfish, the sex is determined by comparing its own size with the size of the other fishers living in the same anemone.&lt;/p&gt;&#xA;&lt;p&gt;In an ant species (or two species actually), males and females can both reproduce by parthenogenesis (some kind of cloning but with meiosis and cross-over) but they the meet they reproduce together and their offsprings are sterile workers. So males and females are just like two sister species that reproduce sexually to create an army to protect and feed them. See more information in &lt;a href=&quot;http://www.nature.com/nature/journal/v435/n7046/abs/nature03705.html&quot; rel=&quot;noreferrer&quot;&gt;this paper&lt;/a&gt;&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;Here is a nice figure from &lt;a href=&quot;http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001899&quot; rel=&quot;noreferrer&quot;&gt;Bachtrog et al. 2014&lt;/a&gt; that offers an idea of the diversity of sex determination system (thank to @rg225 for pointing out this figure).&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/7YzPz.png&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/7YzPz.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/a&gt;&#xA;&lt;strong&gt;Book suggestion&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.amazon.ca/Evolution-Sex-Determination-Leo-Beukeboom/dp/0199657149/ref=sr_1_fkmr0_1?ie=UTF8&amp;amp;qid=1420837818&amp;amp;sr=8-1-fkmr0&amp;amp;keywords=sex-determination%20system%20perrin%20beukeboom&quot; rel=&quot;noreferrer&quot;&gt;The Evolution of Sex-Determination&lt;/a&gt; is a great book that may interest you.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-03-27T07:07:48.840" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="27514" PostTypeId="2" ParentId="23312" CreationDate="2015-01-09T21:56:52.087" Score="4" Body="&lt;p&gt;Your logic looks correct to me. Essentially, what you are doing is uniformly distributing the regulator among the available mRNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that even when using Hill functions to model transcription, the ratio of transcription factor (TF) concentration to the number of TF binding sites must be large - otherwise, you would have to consider binding ratios even at the level of transcription modeling, similarly to what you are doing now for translation. E.g. consider a hypothetical situation where 10 TF molecules compete for binding to 5 different promoter regions, each having 10 binding site repeats - you need to somehow distribute the available 10 TF molecules among 50 target binding sites. Clearly, this is not something accounted for by the standard Hill equation, which would in such case wrongly assume that 10 TF molecules are regulating each construct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your specific case, introducing the ratio of the regulator per each mRNA may not even be necessary if this ratio is large, effectively leading to saturation levels anyway. Note that the maximum level that $m_x$ can reach (at steady state) is equal to $max(m_X) = \frac{\alpha_{mX}}{\beta_{mX}}$. If you can ensure this value to be much smaller than your translational regulator concentration, you will get similar results even if you use simply $\frac{K}{K+R}$ for translation modeling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the latter assumption cannot be made, then your reasoning makes sense. For each individual mRNA molecule:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\text{X produced per mRNA} = \alpha_{X} .\frac{K}{K+R'}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $R'$ is the amount of mRNA bound to this molecule. If $R$ is the total available regulator concentration and uniform binding affinity is assumed, this means that $R'=\frac{R}{m_X}$. Summing this over a total of $m_X$ mRNA and considering degradation yields exactly your final ODE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that another important assumption you are making is that regulator binding/unbinding to/from mRNA is fast compared to translation, and that no cooperative interactions are present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to verify things further, you could establish system reactions, then derive Hill-free ODE equations according to the law of mass action. You could then compare this model to the one you propose. Furthermore, performing a stochastic simulation might make sense. If you want to go down this road but don't want to implement Gillespie's algorithm on your own, you can use e.g. &lt;a href=&quot;http://www.cs.tut.fi/~sanchesr/SGN/SGNSim.html&quot; rel=&quot;nofollow&quot;&gt;SGNSim&lt;/a&gt; or &lt;a href=&quot;http://www.copasi.org/tiki-view_articles.php&quot; rel=&quot;nofollow&quot;&gt;COPASI&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3583" LastEditorUserId="3583" LastEditDate="2015-01-09T22:25:51.053" LastActivityDate="2015-01-09T22:25:51.053" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27516" PostTypeId="2" ParentId="15763" CreationDate="2015-01-10T00:11:09.973" Score="3" Body="&lt;p&gt;This is a classic Brown-Sequard syndrome well- studied in the field of neurology. To answer your question, you would need to know what tracts are being severed and what sensations each tract is responsible for. A clean R hemi-section of the spinal cord at the level of T6 would affect the 1) R lateral corticospinal tract, 2) R spinothalamic tract, and 3) R dorsal columns. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The R lateral corticopsinal tract is an upper motor neuron (UMN) pathway, which relays messages from your brain to the periphery. If severed, it would lead to paralysis of muscles below the lesion on the ipsilateral side. This would result in UMN signs such as increased reflexes, increased spasticity, and muscle weakness. &lt;/li&gt;&#xA;&lt;li&gt;The spinothalamic tract is a sensory pathway connecting peripheral sensations and bringing them up to the brain. Specifically, it communicates sensations of pain, temperature, and gross touch. If severed on the R side, these sensations would be lost on the contralateral side a few levels below the site of the lesion. The reason for this is due to the decussation, or crossing over, of the tract at or slightly above the level of entry of the nerve fibers into the spinal cord from the periphery. &lt;/li&gt;&#xA;&lt;li&gt;The dorsal columns are similar to the spinothalamic tract, except the sensations communicated are vibration, fine touch, and proprioception. If severed, this would cause loss of these sensations below the level of the lesion but on the same side. A patient would not be able to balance himself/herself without support. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Regarding what areas of the body would be affected based on a lesion in T6, C1, or L5, just as mentioned by jonsca, one would need a dermatome to understand what areas of skin sensation would be affected, and know the nerve root origins of different nerves of muscles. A great book to read to locate these answers in a table format is &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/145111768X&quot; rel=&quot;nofollow&quot;&gt;Neurology BluePrints&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise, feel free to open any Neurology textbook for a reference, and look for Brown-Sequard Syndrome to read in more detail. &lt;/p&gt;&#xA;" OwnerUserId="11631" LastActivityDate="2015-01-10T00:11:09.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27517" PostTypeId="2" ParentId="13982" CreationDate="2015-01-10T00:21:28.323" Score="2" Body="&lt;p&gt;If it is not water-soluble (lipophobic or hydrophilic), the only other alternative would be that it is fat-soluble (lipophilic or hydrophobic). Consider adding the powder to fatty solids or liquids which can be absorbed from the GI tract into the vascular system, if that is where you'd like the drug to go to be distributed throughout the body. Ideally, you would need to look up the target concentration of the drug within the blood in order to be effective, its volume of distribution, its bioavailability, its half-life, mechanism of metabolism, and calculate from there how much you would really need in order to last the full 2 weeks. &lt;/p&gt;&#xA;" OwnerUserId="11631" LastActivityDate="2015-01-10T00:21:28.323" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27519" PostTypeId="1" AcceptedAnswerId="27551" CreationDate="2015-01-10T04:21:32.893" Score="2" ViewCount="184" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SKFl8.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose that the x-axis represents time, and the y-axis vessel diameter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then this graph is claimed to roughly describe what happens when the blood pressure increases, then decreases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the blood pressure first increases, the vessel diameter expands to its maximum radius. Then it contracts. What I don't understand is why it keeps on expanding and contracting after its initial expansion - does this model still make sense after its initial expansion and contraction?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone explain?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="9943" LastEditDate="2015-01-10T12:19:32.667" LastActivityDate="2015-01-10T18:28:42.300" Title="Why can blood vessel contraction be described as a second order system?" Tags="&lt;mathematical-models&gt;&lt;blood-pressure&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27521" PostTypeId="2" ParentId="7450" CreationDate="2015-01-10T04:49:00.610" Score="1" Body="&lt;p&gt;One can sometimes notice street lights delaying the annual shedding of leaves in some species (a well-lit branch will be mostly green while the rest of the tree is turning). So at least &lt;em&gt;part&lt;/em&gt; of it would be day/night length in at least &lt;em&gt;some&lt;/em&gt; species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would expect, however, that the answer varies based on species, genus, and/or family, and that there are probably multiple causes at work (one obvious alternate cause being temperature). Just going from memory of my personal observations, years when autumn weather patterns start earlier do tend to have trees turn and lose leaves earlier, so it's not &lt;em&gt;all&lt;/em&gt; day/night length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Drought is also a factor. I live in a seasonal-rainfall part of the world (US Pacific Northwest), and if summer is drier than normal (and normal is pretty dry), by mid-August many of the native deciduous trees will be starting to drop leaves. (Not all of them, but some of them, definitely more than just a few, will be turning and dropping.)&lt;/p&gt;&#xA;" OwnerUserId="12927" LastActivityDate="2015-01-10T04:49:00.610" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27524" PostTypeId="2" ParentId="26062" CreationDate="2015-01-10T05:37:03.480" Score="2" Body="&lt;p&gt;The largest area of temperate rain forest in the world is on the west coast of North America, which has a summer dry season. In other words, at precisely what would be the best time for plants to grow (based on temperature), there's a shortage of water. (Summer vacation visitors to the rain forests on the Olympic Peninsula are often wondering &quot;where's the rain?&quot;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conifers have small, waxy, and (generally, with a few exceptions) evergreen leaves. All the conifers in the rain forests of western North America are evergreen; that allows them to grow in the cooler months of the year, when there can occasionally be hard frosts (and when deciduous trees are dormant). The waxy, small leaves help them conserve water in the dry summers. A double advantage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;North of about central BC, there's no longer the summer dry season, but by that point the growing season is getting short enough that conifers have an advantage despite the perhumid climate (Prince Rupert, BC is further north than Edmonton, Alberta).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll add that this is not the only non-boreal climate where conifers are abundant: consider for example the piñon-juniper woodlands of the American Southwest or the Piney Woods of the Deep South.&lt;/p&gt;&#xA;" OwnerUserId="12927" LastActivityDate="2015-01-10T05:37:03.480" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27525" PostTypeId="2" ParentId="23936" CreationDate="2015-01-10T06:06:16.580" Score="4" Body="&lt;p&gt;Polygonum cuspidatum, common name Japanese knotweed. A notorious invasive species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's actually a herbaceous perennial (those stems grew in just one season, and will die back to the ground at the first hard freeze), not a shrub. The red things are ripening seeds, not flowers.&lt;/p&gt;&#xA;" OwnerUserId="12927" LastActivityDate="2015-01-10T06:06:16.580" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27527" PostTypeId="1" AcceptedAnswerId="27561" CreationDate="2015-01-10T07:23:01.220" Score="2" ViewCount="14327" Body="&lt;p&gt;The title says it all. Why is it that patients are placed in the trendelenburg position when a catheter is inserted in the sub clavian vein? What would happen if the patient wasn't placed in the trendelenburg position when placing the catheter?&#xA;Thanks in advance for the help.&lt;/p&gt;&#xA;" OwnerUserId="5318" LastEditorUserId="11631" LastEditDate="2015-01-11T02:05:19.537" LastActivityDate="2015-01-11T02:05:19.537" Title="Why is the Trendelenburg position used when placing and removing Central Venous Line catheters in the sub-clavian vein?" Tags="&lt;blood-circulation&gt;&lt;circulatory-system&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27528" PostTypeId="1" CreationDate="2015-01-10T09:01:04.887" Score="25" ViewCount="27540" Body="&lt;p&gt;Some hair especially body hair regrows after trimming but stops growing after a while. What is the mechanism behind control of hair growth and how is the length limit determined?&lt;/p&gt;&#xA;" OwnerUserId="12930" LastEditorUserId="3340" LastEditDate="2015-01-10T15:05:17.223" LastActivityDate="2017-07-17T06:46:07.227" Title="Why does hair grow after trimming but remains at a constant length after a while?" Tags="&lt;human-biology&gt;&lt;hair&gt;&lt;human-physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="27529" PostTypeId="2" ParentId="27528" CreationDate="2015-01-10T09:37:29.083" Score="21" Body="&lt;p&gt;Hair grows from the follicle; there is no way for the follicle to determine if the hair tip is trimmed or not. This is unlike plant shoot/root growth that happens at the tip. Also there is no signaling from tip to follicle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hair growth has four stages: Anagen (Initiation), Catagen, Telogen (resting) and Exogen (falling off). Initially the primary follicle is formed during development of the skin, after that the hair growth continues in a cycle. In other words the old hair shaft is replaced by a new one. The period of the cycle (or how fast it happens determines the final hair length); the faster is the cycle the shorter will be the hair (you may note that certain people have a very short head hair even when they do not trim). This is because the old shaft doesn't get time to grow before it is shed and replaced by the new one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; &lt;img src=&quot;https://i.stack.imgur.com/kp67k.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;From: &lt;a href=&quot;http://physrev.physiology.org/content/81/1/449.short&quot; rel=&quot;noreferrer&quot;&gt;Stenn &amp;amp; Paus (2001)&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the same source&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because there is a limit to the time a follicle stays in anagen, there&#xA;  is also a limit to the length of its product, the hair shaft. The&#xA;  anagen phase has been divided into six subphases (64, 359). Except for&#xA;  the last subphase, anagen VI (the duration of which dictates the shaft&#xA;  length), the length of the anagen subphases I–V does not differ&#xA;  substantially between follicles from different regions (490, 565). &#xA;  &lt;br&gt;[…]&lt;br&gt;&#xA;   Because the actual length of a hair follicle does not appear to&#xA;  dictate the length of its shaft (rather the duration of anagen&#xA;  determines hair shaft length), it is tempting to speculate that the&#xA;  subcutis offers optimal growth conditions…&#xA;  &lt;br&gt;[…]&lt;br&gt;Although influenced by environment (light, temperature, and&#xA;  nutrition) and systemic (endocrinological factors) parameters, it is&#xA;  generally believed that there is considerable innate local control of&#xA;  hair shedding; each fiber grows to a specific length, for a specific&#xA;  period of time, before being shed&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-01-10T15:14:46.847" LastActivityDate="2015-01-10T15:14:46.847" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="27531" PostTypeId="2" ParentId="19258" CreationDate="2015-01-10T11:18:29.703" Score="1" Body="&lt;p&gt;It is known that Grizzly bears catching salmon during times of plenty only eat the head (the fish brain, as any brain, is rich in fats, easy to digest and basically luxury food). However, in times of shortage they consume pretty much the whole fish, as every scrap of food, even untasty and non-nutricious tail fins and the likes are better than nothing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your cat will chase, hunt and catch prey following its hunting instincts. When its well-fed, however, your cat is not really hungry and will eat only the tastiest and easiest parts (say liver etc), but will definitely skip smelly intestines with undigested plant material. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can try to find a reference to the Grizzly study (pretty interesting study :-)   &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-10T12:08:44.933" LastActivityDate="2015-01-10T12:08:44.933" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27532" PostTypeId="1" AcceptedAnswerId="27559" CreationDate="2015-01-10T12:42:49.210" Score="8" ViewCount="4444" Body="&lt;p&gt;The right atrium  is one of four chambers (two atria and two ventricles) in the hearts of mammals (including humans) and archosaurs (which include birds and crocodilians). It receives deoxygenated blood from the superior and inferior venae cavae, the coronary sinus, and the anterior and smallest cardiac veins, and pumps it into the right ventricle through the tricuspid valve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can humans survive without right atrium? In this condition blood would fill the right ventricle directly, comparable to some animals like  frogs, toads, snakes and lizards. What advantages does the normal human heart have to this anatomy ? If we had this anatomy, where would the best place for pacemakers be, like the sinus node?&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorDisplayName="user12874" LastEditDate="2015-01-12T12:29:29.817" LastActivityDate="2018-05-14T19:05:46.860" Title="Can humans live without their right atrium?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27533" PostTypeId="1" AcceptedAnswerId="27534" CreationDate="2015-01-10T12:51:32.610" Score="15" ViewCount="5685" Body="&lt;p&gt;I've noted that every time a house fly is resting on a surface, it appears to &quot;rub&quot; or &quot;scrub&quot; its front legs in a repetitive movement. And they do it continuously. Why?&lt;/p&gt;&#xA;" OwnerUserId="12933" LastEditorUserId="9943" LastEditDate="2017-01-18T19:24:39.990" LastActivityDate="2020-03-14T17:42:33.627" Title="Why do flies &quot;rub&quot; their front legs when resting?" Tags="&lt;entomology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27534" PostTypeId="2" ParentId="27533" CreationDate="2015-01-10T12:53:24.467" Score="15" Body="&lt;p&gt;Flies rubbing their legs are &lt;strong&gt;cleaning themselves&lt;/strong&gt;. They can also often be seen rubbing their back legs often. Additionally, flies also often clean their &lt;a href=&quot;http://www.howitworksdaily.com/why-do-flies-rub-their-legs-together/&quot;&gt;&lt;strong&gt;wings, compound eyes and bodily bristles&lt;/strong&gt;&lt;/a&gt;. Legs and wings are used as a primary means of &lt;strong&gt;locomotion&lt;/strong&gt; and means of escape. Eyes and bristles are sensory organs and hence also essential for their survival. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below a picture of a tachinid fly showing the bristles and compound eyes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cj6uj.jpg&quot; alt=&quot;fly&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The eyes need to be clean as they are essential for the &lt;strong&gt;detection of visual stimuli&lt;/strong&gt;. The bristles, as a commenter rightfully stated, contain &lt;strong&gt;chemoreceptors&lt;/strong&gt; &lt;a href=&quot;http://berkeley.edu/news/media/releases/2004/06/25_flies.shtml&quot;&gt;reminiscent of receptors on the human tongue that sense sweet and bitter tastes&lt;/a&gt;. These taste receptors alert the fly for sweet (food) and bitter (poisons) substances. Hence, cleaning of the legs may not only serve hygienic purposes, but may well be important for keeping the bristles and hence the associated sensory organs clean and free of prior encountered substances. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-11T13:40:51.483" LastActivityDate="2015-01-11T13:40:51.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27535" PostTypeId="1" CreationDate="2015-01-10T13:01:01.740" Score="13" ViewCount="1533" Body="&lt;p&gt;We always prefer to be in 20-25° C, although our core temperature is about 37°? Why is our skin temperature lower than our core temperature? &lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorUserId="4901" LastEditDate="2015-01-11T02:31:35.127" LastActivityDate="2015-02-13T03:55:09.730" Title="Why do we experience temperatures below 37 degrees Celsius as 'hot'?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;sensation&gt;&lt;temperature&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2015-01-12T01:57:05.557" ContentLicense="CC BY-SA 3.0" />
  <row Id="27536" PostTypeId="1" CreationDate="2015-01-10T13:19:22.760" Score="9" ViewCount="64013" Body="&lt;p&gt;The hematocrit, also known as packed cell volume (PCV) or erythrocyte volume fraction (EVF), is the volume percentage (%) of red blood cells in blood. It is normally 45% for men and 40% for women.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so,Why do we have hematocrit for men? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First,I thought it might be caused by different hormones but I couldn't find adequate evidence to prove this Hypothesis.Therefore I decided to share it.&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorDisplayName="user13010" LastEditDate="2015-01-14T14:52:26.373" LastActivityDate="2016-06-23T09:03:11.117" Title="Why do men have a higher hematocrit (red blood cell count) than women?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;endocrinology&gt;&lt;hematology&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27537" PostTypeId="1" CreationDate="2015-01-10T13:37:36.327" Score="1" ViewCount="137" Body="&lt;p&gt;Ewing's sarcoma or Ewing sarcoma is a malignant small, round, blue cell tumor. It is a rare disease in which cancer cells are found in the bone or in soft tissue. It is more common in right heart than left heart? Why? Which one is more dangerous? &lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorDisplayName="user12874" LastEditDate="2015-01-24T16:43:53.033" LastActivityDate="2015-01-24T16:43:53.033" Title="Why is sarcoma more prevalent and common in right heart?" Tags="&lt;cardiology&gt;&lt;pathophysiology&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27539" PostTypeId="1" CreationDate="2015-01-10T13:53:23.927" Score="2" ViewCount="233" Body="&lt;p&gt;Please help to choose Bioconductor R packages and other software for the whole genome sequence data analysis and, in particlular, the goals of false discovery mutation rate, mutations exclusion, mutation contribution and data dimensionality reduction. I could find Expander, MeV, Genesis software for the microarray experiments, however, could not find similar tools for the whole genome sequence analysis of mycobacteria. Sorry, that my question has no code.&lt;/p&gt;&#xA;" OwnerUserId="12935" LastActivityDate="2015-01-10T14:07:06.970" Title="Whole genome sequence analysis software" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;&lt;genomes&gt;&lt;sequence-analysis&gt;&lt;sequence-alignment&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27540" PostTypeId="2" ParentId="27539" CreationDate="2015-01-10T14:07:06.970" Score="3" Body="&lt;p&gt;There are couple of them. First if you want to sequence analysis basic packages are :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bioconductor.org/help/workflows/high-throughput-sequencing/&quot; rel=&quot;nofollow&quot;&gt;http://www.bioconductor.org/help/workflows/high-throughput-sequencing/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, Maqweb seems promising.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://maqweb.sourceforge.net&quot; rel=&quot;nofollow&quot;&gt;http://maqweb.sourceforge.net&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2015-01-10T14:07:06.970" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27541" PostTypeId="2" ParentId="2955" CreationDate="2015-01-10T14:08:46.460" Score="29" Body="&lt;p&gt;This is due to the fact that skin is the interface where heat is lost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our body due to constant functioning, produces heat constantly as a by-product (due to exothermic reaction of ATP break mainly). The excess heat needs to be conducted away from the body, or it will cause a decrease in the body metabolism to prevent temperature rise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heat is lost mainly through the skin by:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Sweating - Through evaporation&lt;/li&gt;&#xA;&lt;li&gt;Radiation - As heat waves (IR rays - That's why IR camera captures people at night)&lt;/li&gt;&#xA;&lt;li&gt;Conduction - Directly through objects that touch skin&lt;/li&gt;&#xA;&lt;li&gt;Convection - Through air circulation&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;When the ambient temperature rises, the heat lost through radiation, conduction, and convection drastically decreases. And often when the temperature is high, there is a accompanying rise in the relative humidity which decreases the heat loss through sweating (as the amount of water vapor is high in the atmosphere, the sweat does not evaporate, so no heat is lost).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the heat which is not lost is felt as the &quot;hot sensation&quot;. It relieves by stopping any activity, seeking shade or a cool place, etc... all of which increases the heat lost or decreases the heat produced.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;You have to note that the temperature of skin is lower than the body temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UGOFW.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Skin temperature is lower than the core body temperature for two reasons:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The skin acts as a medium through which the external temperature is measured - as such the skin temperature is at equilibrium with the external temperature. The brain regulates the core-body temperature in response to temperature measured through skin. If a person is exposed suddenly to cold environment, skin looses much of its heat in the form of radiation (radiation is direclty proportional to the temperature difference) this will cause perception of cold and the body starts shivering even though no actual heat loss has occured from the core body thermal load (only skin looses heat, not the body core). The brain anticipates that the core will loose its heat when exposed to such low temperature for prolonged periods and starts the warming mechanism &lt;strong&gt;before&lt;/strong&gt; the actual cooling occurs such that the cooling is &lt;strong&gt;either prevented or minimized&lt;/strong&gt;. This is called &lt;strong&gt;Anticipatory control&lt;/strong&gt; and the temperature of skin being close to the ambient temperature within physiological limits is needed for this.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Skin is the medium (almost the only medium) through which the excessive heat produced by the body core during activity is expelled. The skin temperature is lower so that a constant gradient can be created between the body core and body surface to maintain the flow of heat. (Heat losses through urine and feces is minimal)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;For more details see &lt;a href=&quot;https://biology.stackexchange.com/questions/28520/do-humans-perceive-temperature-or-heat-flux-or-both&quot;&gt;this question&lt;/a&gt;. All the answers in this question are good and will increase your understanding of what actually happens.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-02-13T03:55:09.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27542" PostTypeId="1" CreationDate="2015-01-10T14:11:57.167" Score="1" ViewCount="208" Body="&lt;p&gt;Oxygen is transferred by hemoglobin from the lungs to tissues, while carbon dioxide is transferred by hemoglobin from tissues to lungs. How is this regulated bidirectional transfer mediated?&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorDisplayName="user12874" LastEditDate="2015-01-10T15:05:22.553" LastActivityDate="2015-01-10T15:05:22.553" Title="How is oxygen and carbon dioxide exchange mediated by hemoglobin?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;physiology&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ClosedDate="2015-01-11T10:05:37.630" ContentLicense="CC BY-SA 3.0" />
  <row Id="27543" PostTypeId="1" AcceptedAnswerId="27657" CreationDate="2015-01-10T14:39:04.007" Score="14" ViewCount="1362" Body="&lt;p&gt;LDL particles pose a risk for cardiovascular disease when they invade the endothelium and become oxidized, since the oxidized forms are more easily retained by the proteoglycans. A complex set of biochemical reactions regulates the oxidation of LDL particles, chiefly stimulated by presence of necrotic cell debries and free radicals in the endothelium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cN99N.jpg&quot; alt=&quot;enter image description here&quot;&gt;  &lt;img src=&quot;https://i.stack.imgur.com/wMPwr.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why doesn't HDL cause diseases like LDL ? What's the reason?&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorDisplayName="user13010" LastEditDate="2015-01-14T15:38:19.447" LastActivityDate="2015-01-14T15:38:19.447" Title="Why doesn't HDL cause diseases like LDL?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;physiology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="5" ClosedDate="2015-03-14T04:04:25.143" ContentLicense="CC BY-SA 3.0" />
  <row Id="27544" PostTypeId="2" ParentId="27542" CreationDate="2015-01-10T14:41:11.193" Score="2" Body="&lt;p&gt;Under conditions of high CO&lt;sub&gt;2&lt;/sub&gt; (in tissues such as muscle) and hence high acidity hemoglobin binds preferentially CO&lt;sub&gt;2&lt;/sub&gt;, thereby mediating CO&lt;sub&gt;2&lt;/sub&gt; removal. Under conditions of low CO&lt;sub&gt;2&lt;/sub&gt; (high pH) and high O&lt;sub&gt;2&lt;/sub&gt; (conditions met in the lungs), it preferably binds O&lt;sub&gt;2&lt;/sub&gt;, thereby releasing CO&lt;sub&gt;2&lt;/sub&gt;. Hence, the specific characteristics of hemoglobin allow for CO&lt;sub&gt;2&lt;/sub&gt; uptake in the body, and O&lt;sub&gt;2&lt;/sub&gt; uptake and CO&lt;sub&gt;2&lt;/sub&gt; release in the lungs. Info from &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemoglobin&quot; rel=&quot;nofollow&quot;&gt;wikipedia on hemoglobin&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-01-10T14:41:11.193" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27545" PostTypeId="2" ParentId="27536" CreationDate="2015-01-10T14:58:03.340" Score="2" Body="&lt;p&gt;Reference values for hematocrit are identical in male and female children and as well in elderly men and women. Differences in hematocrit between fertile women and men are caused by repetitive loss of blood - and therefore iron - in menstruating women.&lt;/p&gt;&#xA;" OwnerUserId="3865" LastActivityDate="2015-01-10T14:58:03.340" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27546" PostTypeId="1" AcceptedAnswerId="27549" CreationDate="2015-01-10T16:03:47.240" Score="6" ViewCount="3604" Body="&lt;p&gt;I have learned that Cyanosis presents with blue skin and nails. What is the reason for the blue coloration of the skin and nails? Why wont the skin and nails turn another color in the visible spectrum such as green for instance? How is this disease diagnosed?&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorUserId="12909" LastEditDate="2015-01-22T23:13:22.020" LastActivityDate="2015-01-23T00:28:33.603" Title="Why do skin and nail go blue in cyanosis?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;pathology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27547" PostTypeId="1" AcceptedAnswerId="27560" CreationDate="2015-01-10T16:10:45.500" Score="8" ViewCount="3076" Body="&lt;p&gt;This is about the possibility (or lack thereof) for a person to re-grow a new &quot;permanent tooth&quot; or set of teeth, to replace the teeth that grew after their milk teeth fell out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I had earlier seen some anecdotal evidence on the internet that this would have happened to some people. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, what I wanted to ask is if there is any scientific evidence (e.g. properly recorded unusual medical phenomena) that shows that a person has grown a tooth (or a set of teeth) to replace their permanent teeth?&lt;/p&gt;&#xA;" OwnerUserId="11546" LastEditorUserId="6061" LastEditDate="2015-01-10T17:56:27.630" LastActivityDate="2016-01-26T06:30:09.367" Title="Is there any scientific evidence that a human has ever grown a third set of teeth?" Tags="&lt;human-biology&gt;&lt;development&gt;&lt;stem-cells&gt;&lt;teeth&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27548" PostTypeId="1" CreationDate="2015-01-10T16:29:22.660" Score="0" ViewCount="144" Body="&lt;p&gt;It looks like most things (or everything?) that we consume, whether it is a food, drink, or something we smoke (like e.g. some drug like marijuana) ends up in some amounts in our hair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is the case, is it theoretically possible that there exists some compound that, when ingested, could affect the color of our hair?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or alternatively, would it be possible for an ingested chemical to weaken or strengthen the disulfide bonds present in hair structure?&lt;/p&gt;&#xA;" OwnerUserId="12939" LastActivityDate="2015-01-10T16:29:22.660" Title="If what we eat can be seen in our hair, then to what degree can our food affect the &quot;look and feel&quot; of our hair?" Tags="&lt;human-biology&gt;&lt;hair&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27549" PostTypeId="2" ParentId="27546" CreationDate="2015-01-10T17:19:25.943" Score="5" Body="&lt;p&gt;The skin appears blue due to the diffraction of light through the skin. Blood is either bright red (sufficiently oxygenated) or dark red. &quot;The blue appearance of surface veins is caused mostly by the scattering of blue light away from the outside of venous tissue if the vein is at 0.5 mm deep or more. Veins and arteries appear similar when skin is removed and are seen directly&quot; &lt;a href=&quot;http://en.wikipedia.org/wiki/Venous_blood&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;a href=&quot;https://i.stack.imgur.com/aXWIW.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;&lt;/a&gt;. The color of blood is due to the difference in color between deoxyhemoglobin and oxyhemoglobin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's consider the &quot;blue fugates&quot; of Kentucky. The ancestors of this family have different shades of blue skin tones. Dr. Madison Cawein discovered that the family had a high concentration of FE$^{3+}$ brown methemoglobin. This form is useless to the body so the enzyme diaphorase reduces the methemoglobin to FE$^{2+}$ (hemoglobin that can carry oxygen) &lt;a href=&quot;http://courses.chem.indiana.edu/c122/documents/Experiment10_BloodandHemoglobin.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;[2]&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically the skin color comes down to light diffraction not the blood changing from red to blue.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/aXWIW.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cyanosis is the appearance of a blue or purple coloration of the skin or mucous membranes due to the tissues near the skin surface having low oxygen saturation &lt;a href=&quot;http://en.wikipedia.org/wiki/Cyanosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;[3]&lt;/a&gt;. Cyanosis is a clinical sign diagnosed visually. Cyanosis is an indication for &lt;a href=&quot;http://www.webmd.com/lung/arterial-blood-gases&quot; rel=&quot;nofollow noreferrer&quot;&gt;blood gas testing&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Venous_blood&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Venous_blood&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://courses.chem.indiana.edu/c122/documents/Experiment10_BloodandHemoglobin.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://courses.chem.indiana.edu/c122/documents/Experiment10_BloodandHemoglobin.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cyanosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Cyanosis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.webmd.com/lung/arterial-blood-gases&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.webmd.com/lung/arterial-blood-gases&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="12909" LastActivityDate="2015-01-10T17:19:25.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27550" PostTypeId="1" CreationDate="2015-01-10T17:21:11.430" Score="4" ViewCount="1844" Body="&lt;p&gt;I have heard that birds have exceptional eyesight. How far does this mean they can see? What's the resolution like? Are we talking about just vague shapes or something like, at 100 feet, seeing individual hairs on a dog's fur coat? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've also read that, in general,  primates are the only mammals that have color vision. I know birds are not mammals. Is it common for birds to have color vision as well, like primates?&lt;/p&gt;&#xA;" OwnerUserId="11652" LastActivityDate="2015-01-10T17:21:11.430" Title="How far can birds see?" Tags="&lt;vision&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ClosedDate="2015-01-26T07:30:53.480" ContentLicense="CC BY-SA 3.0" />
  <row Id="27551" PostTypeId="2" ParentId="27519" CreationDate="2015-01-10T17:59:39.823" Score="2" Body="&lt;p&gt;Many systems have this property. The plot you are looking at is the plot of the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3961098/&quot; rel=&quot;nofollow noreferrer&quot;&gt;transfer function&lt;/a&gt; for blood vessel diameter vs time. A trick in mathematics or engineering is to understand a system is to sometimes look at at different system with the same properties that you do understand. For instance, a mass springer damper system is similar to a RLC circuit. That is, if we understand the mass spring damper system, we view the RLC circuit as the analog to the mechanical system and vice versa. In the case of blood pressure, we also have a driven force (the heart). Thus, an extremely simple model would be&#xA;$$&#xA;m\ddot{x} + c\dot{x} + kx = F(t)&#xA;$$&#xA;As we see below, the mass spring damper model produces the a similar plot of the transfer function. If you understand the mechanical system or RLC circuit, you can look at your plot parameters as an analog to one of these systems to understand the dynamics occurring in the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/aSeee.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A more interesting question is can we use &lt;a href=&quot;http://ctms.engin.umich.edu/CTMS/index.php?example=Introduction&amp;amp;section=ControlPID&quot; rel=&quot;nofollow noreferrer&quot;&gt;PID control&lt;/a&gt; to manage the overshoot, rise time, and settling time of the vessel diameter in the body?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The differential equation that models this process is probably related to a Bernoulli differential equation.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Bernoulli%27s_principle&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Bernoulli%27s_principle&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;page 15 &lt;a href=&quot;http://www.physics.usyd.edu.au/~jbryant/Fluids/Fluidslect4.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.physics.usyd.edu.au/~jbryant/Fluids/Fluidslect4.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bme.ccny.cuny.edu/faculty/bfu/blood%20flow%20permeability%20in%20microvessels.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://bme.ccny.cuny.edu/faculty/bfu/blood%20flow%20permeability%20in%20microvessels.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;A precise differential equation will need to account for pressure (Bernoulli), fluids (Navier-Stokes), and the elasticity of the vessel walls. &lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-01-10T18:28:42.300" LastActivityDate="2015-01-10T18:28:42.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27553" PostTypeId="1" CreationDate="2015-01-10T20:21:44.757" Score="1" ViewCount="34" Body="&lt;p&gt;What proportion of the total number of proteins in E. coli could be fluorescently labelled for PALM/STORM imaging?&lt;/p&gt;&#xA;" OwnerUserId="12944" LastActivityDate="2015-01-10T20:40:22.187" Title="Could the proteome of E. coli be fluorescently labelled?" Tags="&lt;genomics&gt;&lt;fluorescent-microscopy&gt;&lt;protein-engineering&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27554" PostTypeId="2" ParentId="27553" CreationDate="2015-01-10T20:35:03.767" Score="1" Body="&lt;p&gt;One at a time, you could potentially label all of them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're asking how many proteins you could label at once, your biggest limitation is probably your microscope. In order to distinguish between different types of proteins you need different color fluorescent labels (dyes, fluorescent proteins, etc). Even the fanciest fluorescent microscopes tend to be set up to excite/record labels in &amp;lt;10 distinct wavelengths.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practice I've only seen experiments where there were tracking 3 distinct types of proteins at one time.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2015-01-10T20:40:22.187" LastActivityDate="2015-01-10T20:40:22.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27555" PostTypeId="1" CreationDate="2015-01-10T21:04:25.927" Score="3" ViewCount="342" Body="&lt;p&gt;It is an important gene expressed in &lt;em&gt;E. coli&lt;/em&gt; that represses the SOS response and also the expression of lambda lytic phase genes. UV light and damage to DNA is responsible for its breakdown and hence the expression of repair genes and, if present, lambda phage genes. However I couldn't find a reference for its original name. &lt;/p&gt;&#xA;" OwnerUserId="12945" LastEditorUserId="6307" LastEditDate="2015-01-15T02:31:09.677" LastActivityDate="2019-05-29T20:32:01.037" Title="What does the gene name &quot;lexA&quot; stand for?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;bacteriology&gt;&lt;virology&gt;&lt;gene&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27556" PostTypeId="2" ParentId="27537" CreationDate="2015-01-10T23:23:31.770" Score="8" Body="&lt;p&gt;Ewing's sarcoma is a &lt;a href=&quot;http://www.webmd.com/cancer/ewings-sarcoma&quot;&gt;&lt;strong&gt;bone&lt;/strong&gt; cancer&lt;/a&gt;. As such, it does not arise as a primary tumor in the heart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ewing's sarcoma does metastasize. Like any metastatic cancer, it seeds along it's venous return to the heart, &quot;taking root&quot; in suitable tissue. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cardiac metastases of Ewing's sarcoma are exceedingly rare, with only a few reported cases. Since all blood returns to the right side of the heart first, then the lungs, this is where distant metastases of Ewing's sarcoma are found. The side doesn't matter; it's never good.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Primary heart tumors do occur, about 1/20th as often as metastatic tumors. Of these, myxomas are the most common. Of sarcomatous types, which are very rare, they can occur anywhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.webmd.com/cancer/ewings-sarcoma&quot;&gt;Ewing's Sarcoma&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232596/&quot;&gt;Metastatic Ewing's Sarcoma to the Right Ventricle&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;https://theoncologist.alphamedpress.org/content/12/9/1134.full&quot;&gt;Primary Malignant Sarcomas of the Heart and Great Vessels in Adult Patients — A Single-Center Experience&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0167527302001365&quot;&gt;Echocardiographic and pathologic characteristics of primary cardiac tumors: a study of 149 cases&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2559.1999.00636.x/abstract&quot;&gt;Primary cardiac sarcomas: an immunohistochemical and grading study with long-term follow-up of 24 cases&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-10T23:23:31.770" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27557" PostTypeId="1" CreationDate="2015-01-10T23:52:51.833" Score="1" ViewCount="20" Body="&lt;p&gt;Colour perception goes out to 50 degrees but is the sensitivity to RGB. Question is it the same in the four quadrants of the retinal field? That is if the red colour sensitivity eg is 30 temporal retina 50 degree nasal retina etc. And what are the eccentric limits for each colour [frequency]in the four quadrants.&lt;/p&gt;&#xA;" OwnerUserId="12948" LastActivityDate="2015-01-10T23:52:51.833" Title="Retinal eccentricity to colour sensitivity" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ClosedDate="2015-01-11T18:56:04.297" ContentLicense="CC BY-SA 3.0" />
  <row Id="27558" PostTypeId="2" ParentId="27555" CreationDate="2015-01-11T00:10:52.263" Score="4" Body="&lt;p&gt;I'd go with Lambda Excision A. Terms like &lt;em&gt;lex&lt;/em&gt; or &lt;em&gt;rec&lt;/em&gt; often stand for what'd be termed a mnemonic, where for example &lt;em&gt;rec&lt;/em&gt; may stand for recombination, or &lt;em&gt;umu&lt;/em&gt; for UV mutator. The naming conventions can be difficult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: A 1981 study by Roger Brent and Mark Ptashne notes some data from initial studies that showed the lexA repressor downregulated a number of genes including himA, which they note to be required for integration of lambda phage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/78/7/4204.full.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/78/7/4204.full.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-01-14T22:19:28.857" LastActivityDate="2015-01-14T22:19:28.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27559" PostTypeId="2" ParentId="27532" CreationDate="2015-01-11T00:24:19.410" Score="2" Body="&lt;p&gt;This is an interesting theoretical question, but several things would need to be clarified:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Does removing the R atrium relocate the SA node to the R ventricle or remove it completely from the picture? &lt;/li&gt;&#xA;&lt;li&gt;Does the remaining R ventricle have a tricuspid valve? &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Technically, the R atrium is the home of the sino-atrial node, which provides natural pacing of the human heart between 60-80 beats/min. Without this natural pacing, our hearts would rely on back-up pacer systems such as atrioventricular node, His-Purkinje systems or the intrinsic but ectopic pacing of individual atrial or ventricular cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CdxoC.jpg&quot; alt=&quot;Automaticity Foci&quot;&gt;&#xA;&lt;a href=&quot;http://quizlet.com/32212304/ekg-stuff-flash-cards/&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible for humans to survive without the SA node because of these back-up systems. However, our heart rates would be lower, or bradycardic. Although there are many individuals who survive with bradycardia ranging from top athletes to the elderly, this condition could lead to negative symptoms including fatigue, dizziness, lightheadedness, syncope, and even cardiac arrest &lt;a href=&quot;http://www.heart.org/HEARTORG/Conditions/Arrhythmia/AboutArrhythmia/Bradycardia-Slow-Heart-Rate_UCM_302016_Article.jsp&quot; rel=&quot;nofollow noreferrer&quot;&gt;[2]&lt;/a&gt;. Ideally, the SA node would be located at or near the area of blood entry into a chamber (or, put another way, opposite from the side where blood exits the chamber), so that blood is pushed synchronously out of the chamber rather than against a wall or the entry, causing turbulence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The R atrium also provides a chamber through which venous blood can sit before it is pumped into the R ventricle to be pumped again into the pulmonary vasculature to be oxygenated. This function allows blood to enter the pumping ventricle quickly, a physiologic benefit &lt;a href=&quot;http://cardiac-output.info/1967AHJ.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;[3]&lt;/a&gt;. In a heart without a R atrium, if the R ventricle still had valves to be able to keep blood from backing up into the vena cava system, then this function of filling and pumping would still be preserved, although it would not be as efficient as if there was a preceding atrium. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In nature, there are three-chamber hearts found in certain amphibians and reptiles. However, usually it is made of 2 atria and one ventricle, rather than 1 atrium and 2 ventricles. In this model, deoxygenated blood and oxygenated blood are mixed (to different degrees, based on the animal), which is not ideal. However, these animals usually have other modes of oxygenation such as through the skin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary, the short answer is- yes, probably, humans can survive without the R atria but it would not be without serious consequences in quality of life. &lt;/p&gt;&#xA;" OwnerUserId="11631" LastActivityDate="2015-01-11T00:24:19.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27560" PostTypeId="2" ParentId="27547" CreationDate="2015-01-11T00:44:59.007" Score="8" Body="&lt;p&gt;There are legitimate case reports in credited journals of hyperdontia, or the condition of having supernumerary teeth. Such cases are often associated with congenital syndromes-- cleft lip and palate, trichorhinophalangeal syndrome, cleidocranial dysplasia, and Gardner's syndrome. I included a case report and a comprehensive review for you below. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21967947&quot;&gt;Case Report&lt;/a&gt; from American Journal of Orthodontic Dentofacial Orthopedics, 2011.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25500927&quot;&gt;Comprehensive Review&lt;/a&gt; from Journal of Oral Science, 2014.&lt;/p&gt;&#xA;" OwnerUserId="11631" LastEditorUserId="11631" LastEditDate="2015-01-11T01:10:25.523" LastActivityDate="2015-01-11T01:10:25.523" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27561" PostTypeId="2" ParentId="27527" CreationDate="2015-01-11T00:58:06.513" Score="5" Body="&lt;p&gt;There are 2 main reasons for using the Trendelenburg position when placing and removing a central venous line catheter into the subclavian or even internal jugular vein.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Exactly what C Rags mentioned-- to increase the size of the vein. This position utilizes the force of gravity to pool blood towards the head from the lower extremities. This makes the vein of interest easier to visualize compared to surrounding structures, to palpate since this increases pressure within the vein, and to ultimately puncture. &lt;/li&gt;&#xA;&lt;li&gt;To avoid air embolisms, which are particularly more damaging if they get into the brain causing a stroke than if they travel inferiorly to the leg, for example. Air embolisms can be introduced when inserting or removing a line. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Ref:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://emedicine.medscape.com/article/422189-overview#showall&quot;&gt;http://emedicine.medscape.com/article/422189-overview#showall&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11631" LastEditorUserId="11631" LastEditDate="2015-01-11T01:03:21.860" LastActivityDate="2015-01-11T01:03:21.860" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27562" PostTypeId="2" ParentId="27555" CreationDate="2015-01-11T01:20:24.807" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://ecoliwiki.net/colipedia/index.php/lexA:Gene&quot; rel=&quot;nofollow noreferrer&quot;&gt;According to this website&lt;/a&gt;, it is a mnemonic for &amp;quot;lambda excision&amp;quot;. I have also found this usage in scientific literature (eg. Harami et al., 2013). However, neither of these sources reference anything and I cannot find any defining paper. Almost all papers simply refer to it as lexA.&lt;/p&gt;&#xA;&lt;p&gt;As far as I can find (it's difficult to dig up these old papers), this is how the locus (not necessarily gene) was originally described (Howard-Flanders and Boyce, 1966):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;There is a ... locus, &lt;em&gt;lex&lt;/em&gt; (locus for X-ray sensitivity), in &lt;em&gt;E. coli&lt;/em&gt; K-12 ... [A] mutation at this locus increases the extent of UV-induced DNA breakdown. This effect is similar to, but less extreme than, that of the &lt;em&gt;rec&lt;/em&gt; locus ...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It's possible that as this locus was better characterised, the name lex was retained for consistency with previous literature but redefined to reflect a better understanding of its function (although I don't think that &amp;quot;lambda excision&amp;quot; does this very well at all).&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Harami GM, Gyimesi M, Kovacs M. 2013. From keys to bulldozers: expanding roles for winged helix domains in nucleic-acid-binding proteins. Trends Biochem Sci 38(7):364-371&lt;/p&gt;&#xA;&lt;p&gt;Howard-Flanders P, Boyce RP. 1966. DNA Repair and Genetic Recombination: Studies on Mutants of &lt;em&gt;Escherichia coli&lt;/em&gt; Defective in These Processes. Radiat Res Supp 6:156-184&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-05-29T20:32:01.037" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="27565" PostTypeId="2" ParentId="17498" CreationDate="2015-01-11T07:50:21.650" Score="4" Body="&lt;p&gt;Remember that except for the concluding pathway through the A-V bundle, the atrial muscle mass is separated from the ventricular muscle mass by fibrous tissue. Therefore, ventricular fibrillation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanism of atrial fibrillation, except that the process occurs only in atrial muscle mass instead of the ventricular mass. A frequent cause of atrial fibrillation is atrial enlargement resulting from heart valve lesions that prevent the atria from emptying adequately into the ventricles, or from ventricular failure with excess damming of blood in the atria. the dilated atrial walls provide ideal conditions of along conductive pathway as well as slow conduction, both of which predispose to atrial fibrillation.&#xA;For the same reasons that the ventricle will not pump blood during ventricle fibrillation. Neither do the atria pump blood in atrial fibrillation. therefore, the atria become useless as primer pumps for the ventricles. Even so, blood flow passively through the atria into the ventricles, and the efficiency of ventricular pumping is decreased only 20-30 percent. Therefore, in contrast to the lethality of ventricular fibrillation, a person can live for months or even years with atrial fibrillation, although at reduced efficiency of overall heart pumping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;numerous small depolarization waves spread in all directions through the atria during atrial fibrillation. Because the waves are weak and many of them are opposite polarity at any given time, they usually almost completely electrically neutralize one another. Therefore, in the electrocardiography, one can see either no P waves from the atria or only a fine, high-frequently, very low voltage wavy record. conversely, the QRS-T complexes are normal unless there is some pathology of the ventricles, but their timing is irregular.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/seiZX.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9nxVD.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastActivityDate="2015-01-11T07:50:21.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27567" PostTypeId="1" AcceptedAnswerId="27764" CreationDate="2015-01-11T08:16:27.540" Score="10" ViewCount="352" Body="&lt;p&gt;I found it in Western Turkey.It was growing on a rock so what's it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9EaQ0.jpg&quot; alt=&quot;sorry for picture quality&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8692" LastEditorUserId="5144" LastEditDate="2015-01-11T11:17:09.500" LastActivityDate="2015-01-17T02:08:13.227" Title="What is the name of this plant? (found in a rock)" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27569" PostTypeId="1" CreationDate="2015-01-11T10:39:32.863" Score="7" ViewCount="458" Body="&lt;p&gt;Alleles refer to duplicate genes, where one allele can be dominant over the other. What makes an allele dominant or recessive, given that both code for a single protein?. &lt;/p&gt;&#xA;" OwnerUserId="4806" LastEditorUserId="9943" LastEditDate="2015-01-11T11:57:44.693" LastActivityDate="2015-01-11T17:00:16.313" Title="Why is an allele dominant or recessive?" Tags="&lt;genetics&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2015-01-11T20:11:06.937" ContentLicense="CC BY-SA 3.0" />
  <row Id="27573" PostTypeId="1" AcceptedAnswerId="27737" CreationDate="2015-01-10T03:01:06.017" Score="8" ViewCount="407" Body="&lt;p&gt;At night when they roost, do chickens experience a state of sleep (meaning do they move from NREM1 to NREM2, NREM3 and REM) or are they in a state of torpor (reduced metabolic rate and decreased physiological activity)?&lt;/p&gt;&#xA;" OwnerUserId="12982" OwnerDisplayName="Ben Plont" LastEditorUserId="12909" LastEditDate="2015-01-16T04:03:34.143" LastActivityDate="2015-01-16T04:07:01.750" Title="Chickens roosting, is it sleep or torpor?" Tags="&lt;zoology&gt;&lt;sleep&gt;&lt;chickens&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27574" PostTypeId="2" ParentId="2902" CreationDate="2015-01-11T11:07:32.023" Score="5" Body="&lt;p&gt;The iris has 2 sets of muscles:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The circular muscle (Sphincter iris) - This causes iris constriction and is supplied by the parasympathetic system - Acetyl Choline muscarinic receptors&lt;/li&gt;&#xA;&lt;li&gt;The radial dilator muscle - This causes dilation of the iris and is supplied by the sympathetic system - The Adrenergic receptors (Alpha 1)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Theoretically speaking, there can be four sets of drugs:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Alpha 1 adrenergic stimulators - will cause midriasis&lt;/li&gt;&#xA;&lt;li&gt;Alpha 1 adrenergic blockers/antagonists - will cause miosis&lt;/li&gt;&#xA;&lt;li&gt;Muscarinic blockers - will cause midriasis&lt;/li&gt;&#xA;&lt;li&gt;Muscarinic agonists/stimulators - will cause miosis&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In practice,&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.globalrph.com/ophthalmic_mydriatics.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Midriatics&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Alpha 1 agonists: Phenylephrine&lt;/li&gt;&#xA;&lt;li&gt;Muscarinic antagonists: Atropine, Homatropine, cyclopentolate, tropicamide    &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Miotics (mainly used for Glaucoma):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Muscarinic agonists: Pilocarpine, carbachol, etc...        &lt;/li&gt;&#xA;&lt;li&gt;In practice alpha 1 antagonists are not usually used to effect miosis&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/C4QyH.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two ways to achieve either midriasis:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Stimulate the Adrenergic receptors&lt;/li&gt;&#xA;&lt;li&gt;Inhibit the Muscarinic receptors&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Similarly miosis can also be achieved vice-versa.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer to your question is yes, when given the proper counter-acting agent, depending on the concentration of the agents and the mechanism of actions opposite effects are achieved. This is primarily because the drugs act on different sets of muscles. If a adrenergic stimulator - phenylephrine is instilled with a muscarinic stimulator - cyclopentolate, both sets of muscles will be acted upon and based on the concentration of the drugs, the decay rate and the efficacy, the iris diameter will either increase or decrease to variable degree. The point is that both the drugs will affect the final diameter of the iris (which is based on the autonomic state of the patient and the strength of drugs administered)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the special cases will be to administer a inhibitor of a receptor followed by an stimulator of the same receptor or vice-versa - In this scenario, the duration of action and the affinity of the given drugs to the receptor in question will play a decided role in determining the final action as both drugs act on the same muscle. If the inhibition is permanent or long-acting then inhibition of the muscle action is predominant. This may change if the stimulator has a very high affinity to the receptor - Higher affinity will result in tighter binding of stimulator and remove the chance for the inhibitor to work - i.e. increase the probability of the clearance of inhibitor. As you can see from above statement, if the clearance rate of inhibitor is slow (takes too long to metabolize), then the effect will ultimately be inhibitory effect. Similarly in case of poisonings where the stimulating effect is permanently achieved (Organo Phosphorous poisoning will cause permanent damage to acetylcholinestrase the enzyme responsible to remove acetyl choline) the reversal will depend on the affinity of the inhibitors (in this case, of acetyl choline) to the receptors (muscarinic). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus the question must be more specific to get a proper answer, as &lt;strong&gt;the effect is totally dependent on the drugs administered.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="5198" LastEditDate="2015-01-15T08:51:26.933" LastActivityDate="2015-01-15T08:51:26.933" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27577" PostTypeId="2" ParentId="14902" CreationDate="2015-01-11T12:57:30.737" Score="1" Body="&lt;p&gt;Two main types of action potentials occur in the heart . One type, the fast response, occurs in normal atrial and ventricular myocytes and in the specialized conducting fibers (Purkinje fibers of the heart)and is divided into five phases. The rapid upstroke of the action potential is designated phase 0.The upstroke is followed by a brief period of partial, early repolarization (phase 1) and then by a plateau (phase 2) that persists for about 0.1 to 0.2 second. The membrane then repolarizes(phase 3) until the resting state of polarization (phase 4) is again attained (at point e). Final repolarization (phase 3) develops more slowly than depolarization (phase 0).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genesis of the Upstroke (Phase 0)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The action potential amplitude (the potential change during phase 0) is dependent on [Na+ ]o.&#xA;The Na+ channels open very rapidly or activate (in about 0.1 msec), thereby resulting in an abrupt increase in gNa . However, once open, the Na+ channels inactivate (time course ˜1 to 2 msec), and gNa rapidly decreases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genesis of Early Repolarization (Phase 1)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In many cardiac cells that have a prominent plateau, phase 1 is an early, brief period of limited repolarization. This brief repolarization results in the notch between the end of the upstroke and the beginning of the plateau . Repolarization is brief because of activation of a transient outward current (ito ) carried mainly by K+ . Activation of K+ channels during phase 1 causes a brief efflux of K+ from the cell because the cell interior is positively charged and [K+ ]i greatly exceeds [K+ ]o . The cell is briefly and partially repolarized as a result of this transient efflux of K+ .The size of the phase 1 notch varies among cardiac cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genesis of the Plateau (Phase 2)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During the action potential plateau, Ca++ enters myocardial cells through calcium channels During the flat portion of phase 2 , this influx of Ca++ is counterbalanced by the efflux of K+ . K+ exits through channels that conduct mainly the ito , iK , and iK1 currents. The ito current is responsible for phase 1, as described previously, but it is not completely inactivated until after phase 2 has expired.&#xA;During the plateau (phase 2) of the action potential, the concentration gradient for K+ across the cell membrane is virtually the same as it is during phase 4. However, Vm is now positive. Therefore, there is a large gradient that favors efflux of K+ from the cell. If gK were the same during the plateau as it is during phase 4, efflux of K+ during phase2 would greatly exceed the influx of Ca++ , and a sustained plateau could not be achieved. However, as Vm approaches and then attains positive values near the peak of the action potential upstroke, gK suddenly decreases . The diminished K+ current associated with the reduction in gK&#xA;prevents excessive loss of K+ from the cell during the plateau. This reduction in gK at both positive and low negative values of Vm is called inward rectification. Inward rectification is a characteristic of several K+ currents, including the iK1 current For these channels, large K+ currents flow at negative values of Vm (i.e., gK is large). However, when Vm is near 0 mV, or positive, as occurs during the plateau (phase 2), little or no K+ current flows (i.e., gK is low). Thus, the substantial gK that prevails during phase 4 of the cardiac action potential is largely due to the iK1 channels, but current through these channels is greatly diminished during the plateau.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sv0GC.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other K+ channels play a role in phase 2 of the action potential. These are characterized as delayed rectifier (iK ) channels. These K+ channels are closed during phase 4 and are activated very slowly by the potentials that prevail toward the end of phase 0. Hence, activation of these channels tends to increase gK very gradually during phase 2. These channels play only a minor role during phase 2, but they contribute to the process of final repolarization (phase 3), as described later. Two types of iK channels exist, depending on their rates of activation. The more slowly activating channel is designated the iKs channel, whereas the more rapidly activating channel is designated the iKr channel . The duration of the action potential in myocytes in various regions of the ventricular myocardium is determined in part by the relative distributions of these iKr and iKs channels.&#xA;Genesis of Final Repolarization (Phase 3)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The process of final repolarization (phase 3) starts at the end of phase 2, when efflux of K+ from the cardiac cell begins to exceed influx of Ca++ . As noted, at least three outward K+ currents (ito , iK , and iK1 ) contribute to the final repolarization (phase 3) of the cardiac cell.&lt;br&gt;&#xA;Restoration of Ionic Concentrations (Phase 4)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The steady inward leak of Na+ that enters the cell rapidly during phase 0 and more slowly throughout the cardiac cycle would gradually depolarize the resting membrane voltage were it not for Na+ ,K+ -ATPase, which is located in the cell membrane. Similarly, most of the excess Ca++ ions that had entered the cell mainly during phase 2 are eliminated principally by a 3Na+ -1Ca++ antiporter, which exchanges 3 Na+ ions for 1 Ca++ ion. However, some of the Ca++ ions are eliminated by an ATP-driven Ca++ pump.&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorDisplayName="user12874" LastEditDate="2015-01-11T15:35:45.940" LastActivityDate="2015-01-11T15:35:45.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27578" PostTypeId="2" ParentId="26374" CreationDate="2015-01-11T13:21:30.433" Score="17" Body="&lt;p&gt;Good question! Let's start with an overview and explanation of the ABO blood grouping system (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2267/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dean, 2005&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/N4Kyn.jpg&quot; alt=&quot;ABO&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Blood groups, antigens and antibodies&lt;/strong&gt;: Subjects with blood group A carry the A antigen on their red blood cells (RBCs) and have antibodies to antigen B; subjects with blood group B have the B antigen and anti-A antibodies, blood group AB carries both the A and B antigens and have no antibodies, and finally folks with group O have no antigens but both antibodies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Blood groups and transfusion&lt;/strong&gt;: Circulating antibodies in a person's blood will attack transfused RBCs from unmatching blood groups. These antibodies fix complement and cause rapid intravascular hemolysis, triggering an acute hemolytic transfusion reaction that can cause disseminated intravascular coagulation, shock, acute renal failure, and death (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2267/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dean, 2005&lt;/a&gt;). As people with blood group AB have no antibodies, they can receive all blood groups without issues. People with blood group O can only receive RBCs of blood group O, because they carry both antibodies. Blood group A can receive A and O, and blood group B can recive B and O. Hence, blood group O can be received by all other groups, and is therefore the universal donor. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Typically, literature on transfusion deals with the haplotyping the antigens of the donor RBCs. The question whether the &lt;strong&gt;antibodies in the donor's blood&lt;/strong&gt; with blood group O would &lt;strong&gt;start attacking cells&lt;/strong&gt; in recipient with blood group A, B and AB is, therefore, a very good question. And the answer is: &lt;strong&gt;yes, they will&lt;/strong&gt;. Why then is O still the universal donor as they have both anti-A and anti-B antibodies?   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, whole blood is not used for &quot;routine&quot; blood transfusions (&lt;a href=&quot;http://www.bloodbook.com/products.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Torrens University Website&lt;/a&gt;). Instead, blood component therapy has largely replaced the use of whole blood (&lt;a href=&quot;http://www.patient.co.uk/doctor/Blood-Transfusion-and-Blood-Products.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Patient.co.uk website&lt;/a&gt;). For routine transfusions, only the fraction containing packed red blood cells is transfused (&lt;a href=&quot;http://www.mayoclinic.org/tests-procedures/blood-transfusion/basics/why-its-done/prc-20021256&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mayo Clinic website&lt;/a&gt;). Hence, in these cases, the &lt;strong&gt;blood plasma containing the antibodies is (virtually) removed&lt;/strong&gt; after centrifugation. Since O-type red blood cells contain no antigens (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2267/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dean, 2005&lt;/a&gt;), and the plasma with the antibodies are not transfused, it can be donated to everyone, barred that the rhesus factor matches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, even if plasma is transfused, antibodies in the donor's plasma are a minor problem, because of the &lt;strong&gt;small amount of antibody&lt;/strong&gt; present in the donated plasma, which is further diluted on transfusion into the recipient's circulation (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2267/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dean, 2005&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2267/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dean (2005) &lt;em&gt;Blood Groups and Red Cell Antigens&lt;/em&gt;. Chapter 5.The ABO Blood Group&lt;/a&gt;&lt;/sub&gt;     &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2019-03-08T19:08:29.560" LastActivityDate="2019-03-08T19:08:29.560" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="27579" PostTypeId="1" CreationDate="2015-01-11T13:31:52.820" Score="2" ViewCount="486" Body="&lt;p&gt;The key feature of adipocytes seems to be energy storage. Today humans in Western countries don't have to hunger and have therefore less need to store energy in fat cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do adipocytes have additional functions that still make them valuable?&#xA;Wikipedia &lt;a href=&quot;http://en.wikipedia.org/wiki/Body_fat_percentage&quot; rel=&quot;nofollow&quot;&gt;lists&lt;/a&gt; 10–13% and 2-5% for men as essential body fat percentage for woman. What functions don't get fulfilled if the body fat percentage drops below that level?&lt;/p&gt;&#xA;" OwnerUserId="152" LastEditorUserId="152" LastEditDate="2015-01-18T12:43:38.130" LastActivityDate="2015-01-18T16:37:52.683" Title="Is there any disadvantage to having a really low adipocyte count in our times?" Tags="&lt;human-biology&gt;&lt;fat-metabolism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27580" PostTypeId="1" CreationDate="2015-01-11T13:40:49.890" Score="7" ViewCount="655" Body="&lt;p&gt;I'm struggling with a question I've been asked.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Why is double stranded genetic material more 'durable' than single stranded one?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that double stranded genetic material is more stable due to multople strands. The single stranded isn't as stable as the double stranded since it lacks the second strand and therefore the bases are open.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stable isn't the same as durable, and I've never heard in class that one is more durable than the other one. Did I miss something or is this just a mistake?&lt;/p&gt;&#xA;" OwnerUserId="12955" LastEditorUserId="9829" LastEditDate="2015-05-13T19:55:44.190" LastActivityDate="2015-05-13T19:55:44.190" Title="Double stranded nucleic acids are more 'durable' than single stranded nucleic acids?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;rna&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27581" PostTypeId="1" CreationDate="2015-01-11T15:27:39.140" Score="1" ViewCount="45" Body="&lt;p&gt;There is a detailed and, to my inexpert eyes, plausible description of the etiology of celiac disease and other autoimmune disorders posted here: &lt;a href=&quot;http://no-gluten.org/CeliacDisease.htm&quot; rel=&quot;nofollow&quot;&gt;http://no-gluten.org/CeliacDisease.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it is at all accurate? If any of it is speculative or incorrect, which parts are those? Red flags to me are that it cites no sources and is much more detailed than any other description of celiac that I've seen. But, again, it does coincide with what little I do know of human immune biology.&lt;/p&gt;&#xA;" OwnerUserId="8922" LastEditorUserId="8922" LastEditDate="2015-01-16T00:11:33.040" LastActivityDate="2015-01-16T00:11:33.040" Title="Is this description of etiology of celiac disease correct?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;proteins&gt;&lt;autoimmune&gt;&lt;celiac-disease&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27582" PostTypeId="1" CreationDate="2015-01-11T15:49:49.657" Score="16" ViewCount="1325" Body="&lt;p&gt;For every 104 male babies, we have 100 female babies and there are statistics which are more reliable. (Those tell us that we have 997 female infants born per 1000 male infants born.) What is the reason for that? Why do we have more male babies than female babies?&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorUserId="5925" LastEditDate="2017-08-08T11:44:38.553" LastActivityDate="2019-02-08T14:04:00.183" Title="Why do we have more male infants born?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;&lt;human-genetics&gt;&lt;sexual-selection&gt;" AnswerCount="2" CommentCount="10" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27583" PostTypeId="2" ParentId="27569" CreationDate="2015-01-11T15:56:15.790" Score="1" Body="&lt;p&gt;There are several hypotheses about the evolution of dominance. It is important first of all, to note that empirical observations show that &lt;em&gt;beneficial alleles tend to be more dominant than detrimental alleles&lt;/em&gt;. Among the two main hypotheses to explain the evolution of dominance, one has been formulated by &lt;a href=&quot;http://en.wikipedia.org/wiki/Ronald_Fisher&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ronald Fisher&lt;/a&gt; and one by &lt;a href=&quot;http://en.wikipedia.org/wiki/Sewall_Wright&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sewall Wright&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fisher's hypothesis&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Fisher's hypothesis, between two equally beneficial alleles, if one is more dominant than the other than it's heterozygote carrier will have higher fitness. In consequence, beneficial alleles evolve to become more dominant while detrimental alleles evolve to be recessive (so that they can hide from selection in heterozygotes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Wright's hypothesis&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Wright's hypothesis, beneficial alleles are more dominant because of the kinetic of biochemical reactions. The rate of a biochemical reaction is a function of the concentration in the substrates of interest. The function is called &quot;Michaelis-Menten function&quot; after the name of the authors. The Michaelis-Menten function looks like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rFgql.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think about a knock-out mutation. Such mutation will decrease by half the concentration of protein the gene in question produce in heterozygotes. Imagine, the concentration of proteins in the wildtype homozygote was 3 (see above graph). The rate of reaction of this homozygote is therefore about 3. The heterozygote would have a concentration of 1.5 and the rate of the reaction is therefore about 2.5-2.75. Assuming that the rate of this biochemical reaction is directly related to fitness, then a the locus of interest, benefical alleles are necessarily dominant and detrimental alleles are necessarily recessive. Selection for dominance is not involved in Wirght's model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is Fisher's or Wright's hypothesis correct?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Current state of the art is to consider Wright's model to be correct and Fisher's model to be wrong. In reality, the truth probably lies somewhere in between these two extremes. Note also that some other alternative explanations may exist in the literature but Wright and Fisher original hypotheses are by far the most considered hypotheses for the evolution of dominance. During my undergrad, I remember a speaker (but I forgot his name, sorry!) who showed that some alleles actually have some domain that are directly responsible for decreasing the expression of the other allele on the sister chromosome suggesting that Fisher's hypothesis might sometime be a good explanation as well.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-01-11T17:00:16.313" LastActivityDate="2015-01-11T17:00:16.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27584" PostTypeId="1" AcceptedAnswerId="27597" CreationDate="2015-01-11T16:31:43.227" Score="5" ViewCount="7662" Body="&lt;p&gt;I once read that it was because of osmotic pressure that it returns to the blood stream, by entering the venules. But why? If lymph originated as plasma how come that the solute concentration is higher in the venule? Doesn't plasma contain solutes such as salts, nutrients, oxygen, etc. ?&lt;/p&gt;&#xA;" OwnerUserId="12958" LastActivityDate="2015-01-11T21:20:37.190" Title="How does most of lymph get back into the blood stream? (I don't mean the lymphatic system)" Tags="&lt;circulatory-system&gt;&lt;lymphatic-system&gt;&lt;veins&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27585" PostTypeId="2" ParentId="27582" CreationDate="2015-01-11T17:02:33.807" Score="9" Body="&lt;p&gt;There is an article in the &lt;a href=&quot;https://books.google.com/books?id=ByIDAAAAMBAJ&amp;amp;pg=PA325&amp;amp;lpg=PA325&amp;amp;dq=female+births+compared+to+males+when+food+is+scarce&amp;amp;source=bl&amp;amp;ots=giX27EcMmG&amp;amp;sig=hThg-7JQSmeCrk5F54E0s4sELkI&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=jqayVIK6KIq1sQTchoHgDA&amp;amp;ved=0CDEQ6AEwBA#v=onepage&amp;amp;q=female%20births%20compared%20to%20males%20when%20food%20is%20scarce&amp;amp;f=false&quot; rel=&quot;noreferrer&quot;&gt;Journal of Popular Science&lt;/a&gt; from 1885. However, I do know there is at least one more recent article floating around some where since I read it. At the moment, I can't find it but will update if or when I do.&lt;/p&gt;&#xA;&lt;p&gt;The article goes on to state that during times of scarcity the number of male births outweighs the number of females whereas in times of plenty, the number of female birth outweighs the number of males. I will let you read linked article but give you the information I recall from the more recent article I can't locate at the moment.&lt;/p&gt;&#xA;&lt;p&gt;The reason for the differences in births has to do with the lifestyles men and women lead. Men tend to do more dangerous activities at younger ages which causes unnatural deaths early on. Due to these unnatural deaths, in times of scarcity, the reproducing population converges to 1:1 (not exactly) male to females due to the lifestyle choices of men. It was also hypothesized that women are almost guaranteed to find a mate so having less females during rough times wont hurt the population since they should all find a mate.&lt;/p&gt;&#xA;&lt;p&gt;Additionally, the phenomenon of environmental factors influencing male and female births is well documented in &lt;a href=&quot;http://www.nature.com/nature/journal/v296/n5860/abs/296850a0.html&quot; rel=&quot;noreferrer&quot;&gt;alligators&lt;/a&gt;. The first linked article also goes on to examine this occurring with other species as well.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;Thanks to @Anne, who sent me a discover article, we have the name of two sets of researchers on this topic. Here is an exert from the article &lt;a href=&quot;http://discovermagazine.com/2013/nov/08-sex-ratios&quot; rel=&quot;noreferrer&quot;&gt;Famine Can Tilt the Sex Ratio of Future Generations. But Why?&lt;/a&gt; (Discover, Nov. 2013). Additionally, we can look up the articles by the respected researchers now. I believe the research by Robert Trivers and mathematician Dan Willard will be the most applicable.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;While demographers were struggling to understand sex ratio anomalies in the context of culture, evolutionary biologists had largely embraced an idea put forth in 1973 by biologist Robert Trivers and mathematician Dan Willard. The Harvard-based pair theorized that as the physical condition of a female declines — if she’s nutritionally deprived, for example — she’ll tend to produce a lower ratio of male to female offspring. Evidence of the theory came from red deer and humans; in both species, adverse conditions in the mother’s environment during pregnancy are correlated with a shift toward female births.&lt;/p&gt;&#xA;&lt;p&gt;Although natural selection ideally favors a 50/50, or .500, sex ratio in a population, mammals typically produce slightly more males than females. Because sex ratio is biased toward males, the figure is expressed by dividing male births by total births. It’s estimated that women give birth to 3 percent more boys, for a standard .515 sex ratio (with 48.5 percent female births). When fewer boys and more girls are born than that, it’s described as a sex ratio decline.&lt;/p&gt;&#xA;&lt;p&gt;Evolutionary biologists say male mortality, which is overall higher than that of females, explains the male bias in sex ratio: A slightly skewed sex ratio at birth that favors males ensures that there are roughly an equal number of males and females of reproductive age. (Theoretically, a .500 sex ratio at birth may be possible if the gender difference in mortality is eliminated.)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;Again thanks to @Anne, who provide this link as well, we see that men do outpace female births. We can see the world data &lt;a href=&quot;https://www.cia.gov/library/publications/the-world-factbook/fields/2018.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2017-12-16T05:12:54.820" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="27586" PostTypeId="2" ParentId="5088" CreationDate="2015-01-11T18:05:04.970" Score="6" Body="&lt;p&gt;As salt accumulates in thebody, it also indirectly increases the extracellular fluid volume for two basic reasons:&#xA;1. When there is excess salt in the extracellular fluid,the osmolality of the fluid increases, and this in turn stimulates the thirst center in the brain, making the person drink extra amounts of water to return the extracellular salt concentration to normal. This increases the extracellular fluid volume.&#xA;2. The increase in osmolality caused by the excess salt in the extracellular fluid also stimulates the hypothalamic-posterior pituitary gland secretory mechanism to secrete increased quantities of antidiuretic hormone. The antidiuretic hormone then causes the&#xA;kidneys to reabsorb greatly increased quantities&#xA;of water from the renal tubular fluid, thereby diminishing the excreted volume of urine but&#xA;increasing the extracellular fluid volume.&#xA;Thus, for these important reasons, the amount of salt that accumulates in the body is the main determinant of the extracellular fluid volume. Because only small increases in extracellular fluid and blood volume can often increase the arterial pressure greatly, accumulation of even a small amount of extra salt in the body can lead to considerable elevation of arterial pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/q2kTJ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Progressive changes in important circulatory system variables during the first few weeks of&#xA;volume-loading hypertension.&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorDisplayName="user12874" LastEditDate="2015-01-12T17:01:46.970" LastActivityDate="2015-01-12T17:01:46.970" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27587" PostTypeId="1" AcceptedAnswerId="27595" CreationDate="2015-01-11T18:08:27.970" Score="2" ViewCount="366" Body="&lt;p&gt;Suppose one would do &lt;a href=&quot;http://en.wikipedia.org/wiki/Spectrophotometry&quot; rel=&quot;nofollow&quot;&gt;spectrophotometry&lt;/a&gt; on biological materials. What would be the minimum requirements for the measuring device so that the results could be published in a reputable journal? I suppose that two important properties are &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;resolution of the spectrum (would e.g. 25 nm be enough? 15 nm? 5 nm?)&lt;/li&gt;&#xA;&lt;li&gt;measurement error (10%, 5%, 1%, ..?)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;What else (if anything) should be taken into consideration?&lt;/p&gt;&#xA;" OwnerUserId="12961" LastActivityDate="2015-01-11T20:33:20.680" Title="What are the requirements for a spectrometer to be used in biological research?" Tags="&lt;measurement&gt;&lt;peer-review-journal&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27588" PostTypeId="1" AcceptedAnswerId="27599" CreationDate="2015-01-11T18:12:09.490" Score="3" ViewCount="102" Body="&lt;p&gt;I have asked a similar question in Biology.SE (&lt;a href=&quot;https://biology.stackexchange.com/questions/27450/what-physics-knowledge-can-be-applied-to-biology-of-organisms-and-ecosystems&quot;&gt;What physics knowledge can be applied to biology of organisms and ecosystems?&lt;/a&gt;), but it just about organisms and ecosystems, not evolution. After watching a clip that Richard Dawkin talks about &lt;a href=&quot;https://www.youtube.com/watch?v=lRTfgQG5Yn8&quot; rel=&quot;nofollow noreferrer&quot;&gt;applying Darwinian evolution to physics&lt;/a&gt;, I would like to ask a vice versa question: &lt;strong&gt;is there any knowledge of physics can be applied in to evolution?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="6786" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-01-12T04:41:14.843" Title="Is there any knowledge of physics can be applied in to evolution?" Tags="&lt;evolution&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27589" PostTypeId="1" AcceptedAnswerId="27592" CreationDate="2015-01-11T18:20:25.297" Score="4" ViewCount="3445" Body="&lt;p&gt;I know Ginkgo is a gymnosperm, but I was wondering whether Ginkgo is also technically a conifer. I did a Google search, and found several confident authoritative-sounding answers. Unfortunately, those answers were divided between &quot;is&quot; and &quot;is not&quot;. So which is it? Is a Ginkgo a conifer?&lt;/p&gt;&#xA;" OwnerUserId="12962" LastActivityDate="2015-01-11T20:54:19.283" Title="Is a Ginkgo tree a conifer?" Tags="&lt;botany&gt;&lt;taxonomy&gt;&lt;dendrology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27592" PostTypeId="2" ParentId="27589" CreationDate="2015-01-11T19:33:56.033" Score="5" Body="&lt;p&gt;The scientific answers are pretty clear: Gingkos are not closely related to the conifers, they are closer related to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cycad&quot; rel=&quot;nofollow noreferrer&quot;&gt;cycads&lt;/a&gt;. See this phylogenetic tree based on the 18S RNA from paper 2:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/17lft.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It shows that conifers and Ginkgos are relative close related, but not on the same sub-branch of the tree. The last common ancestor between Ginkgos and Conifers is older than the one between Ginkgo and Cycadales. This classification has been made on the basis of genome comparisions and also based on an analysis of the chloroplasts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://gbe.oxfordjournals.org/content/5/1/243.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chloroplast Phylogenomics Indicates that Ginkgo biloba Is Sister to&#xA;Cycads&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3864/g7om6biq_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Molecular Phylogeny of Ginkgo biloba: Close Relationship Between&#xA;Ginkgo biloba and Cycads&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.academicjournals.org/article/article1380807405_Mohanta.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Advances in Ginkgo biloba research: Genomics and metabolomics pe&#xA;rspectives&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-01-11T20:54:19.283" LastActivityDate="2015-01-11T20:54:19.283" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27593" PostTypeId="1" CreationDate="2015-01-11T19:47:22.877" Score="1" ViewCount="1647" Body="&lt;p&gt;I reading that orsomucoid (alpha-1-acid glycoprotein) is the major carrier of positively charged (basic) drugs in the blood, while &lt;strong&gt;albumin carries negatively charged (acidic) and drugs with neutral charge&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand I've read that albumin is excluded by the basement membrane in the glomeruli, and in general by negatively charged glycosaminoglycans in the interstitial space, because &lt;strong&gt;albumin is negatively charged&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did a quick search online and I couldn't &lt;strong&gt;find the information explaining this contradiction&lt;/strong&gt;. Does anyone have an explaination?&lt;/p&gt;&#xA;" OwnerUserId="4433" LastActivityDate="2015-01-11T19:47:22.877" Title="negatively charged albumin as major carrier of acidic/negative charged drugs in blood" Tags="&lt;proteins&gt;&lt;pharmacology&gt;&lt;pharmacokinetics&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27594" PostTypeId="2" ParentId="1294" CreationDate="2015-01-11T20:14:05.777" Score="3" Body="&lt;p&gt;Below are some insights about the evolution of dominance. It does not directly answers your question but understanding how it is thought to evolve also help understand the mechanism governing dominance relationship between alleles.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;There are several hypotheses about the evolution of dominance. It is important first of all, to note that empirical observations show that &lt;em&gt;beneficial alleles tend to be more dominant than detrimental alleles&lt;/em&gt;. Among the two main hypotheses to explain the evolution of dominance, one has been formulated by &lt;a href=&quot;http://en.wikipedia.org/wiki/Ronald_Fisher&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ronald Fisher&lt;/a&gt; and one by &lt;a href=&quot;http://en.wikipedia.org/wiki/Sewall_Wright&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sewall Wright&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fisher's hypothesis&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Fisher's hypothesis, between two equally beneficial alleles, if one is more dominant than the other than it's heterozygote carrier will have higher fitness. In consequence, beneficial alleles evolve to become more dominant while detrimental alleles evolve to be recessive (so that they can hide from selection in heterozygotes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Wright's hypothesis&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Wright's hypothesis, beneficial alleles are more dominant because of the kinetic of biochemical reactions. The rate of a biochemical reaction is a function of the concentration in the substrates of interest. The function is called &quot;Michaelis-Menten function&quot; after the name of the authors. The Michaelis-Menten function looks like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rFgql.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think about a knock-out mutation. Such mutation will decrease by half the concentration of protein the gene in question produce in heterozygotes. Imagine, the concentration of proteins in the wildtype homozygote was 3 (see above graph). The rate of reaction of this homozygote is therefore about 3. The heterozygote would have a concentration of 1.5 and the rate of the reaction is therefore about 2.5-2.75. Assuming that the rate of this biochemical reaction is directly related to fitness, then a the locus of interest, benefical alleles are necessarily dominant and detrimental alleles are necessarily recessive. Selection for dominance is not involved in Wirght's model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is Fisher's or Wright's hypothesis correct?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Current state of the art is to consider Wright's model to be correct and Fisher's model to be wrong. In reality, the truth probably lies somewhere in between these two extremes. Note also that some other alternative explanations may exist in the literature but Wright and Fisher original hypotheses are by far the most considered hypotheses for the evolution of dominance. During my undergrad, I remember a speaker (but I forgot his name, sorry!) who showed that some alleles actually have some domain that are directly responsible for decreasing the expression of the other allele on the sister chromosome suggesting that Fisher's hypothesis might sometime be a good explanation as well.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2015-01-11T20:14:05.777" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27595" PostTypeId="2" ParentId="27587" CreationDate="2015-01-11T20:33:20.680" Score="3" Body="&lt;p&gt;For all the common uses of a spectrophotometer in biology, any commercial one should be sufficient. For all the routine stuff, the quality of the spectrophotometer is usually of negligible importance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are no general rules on what errors and resolution are acceptable, that always depends on what you're measuring. The error should be significantly smaller than size of the effect you're looking at, otherwise you get no useable data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many sources of error with biological systems, the spectrophotometer is really one of the last ones you would think of. Simply the error of pipetting is likely far larger than the error of the spectrophotometer, and differences in the preparation of your biological samples might introduce an even larger error. Unless you're doing something beyond the routine uses of UV/Vis spectrometry, you probably don't need to worry about this.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2015-01-11T20:33:20.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27596" PostTypeId="1" AcceptedAnswerId="27598" CreationDate="2015-01-11T20:59:27.860" Score="8" ViewCount="436" Body="&lt;p&gt;I would like to know what is this plant ? Does anybody have an idea ? Somebody offered it to me but there is no explanation about how to care about it... &#xA;Some purple flowers appeared, during 2-3 days. And now it seems it lacks something, but I don't really know what to do :(&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/id517.jpg&quot; alt=&quot;unknown plant&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any idea ?&#xA;Thank you very much !&lt;/p&gt;&#xA;" OwnerUserId="12966" LastActivityDate="2015-01-11T21:31:25.310" Title="What is this plant ...?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27597" PostTypeId="2" ParentId="27584" CreationDate="2015-01-11T21:20:37.190" Score="7" Body="&lt;p&gt;Technically 'lymph' is used to refer to the fluid found within the lymphatic system. If it's not in the lymphatic system, it is not lymph fluid. Thus, your question is really asking about interstitial fluid or the plasma that was filtered out of blood capillaries.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer to your question is based on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Starling_equation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Starling equation&lt;/a&gt;. Normally fluid leaves a capillary due to a net pressure that favors the interstitium. This net pressure is based on the hydrostatic pressure within the capillary being greater than the interstitial pressure of the surrounding tissues, and the oncotic pressure of the capillary (that draws fluid in) being weaker than the hydrostatic pressure of the capillary (that pushes fluid out). At the venule end of this system, the capillary oncotic pressure is stronger than the capillary hydrostatic pressure, drawing fluid back into the circulatory system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4irFO.png&quot; alt=&quot;Filtration in Systemic Capillaries&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remember that albumin is the most important component which establishes the oncotic pressure within a vessel, and that this protein is normally NOT released out of a vessel during filtration. Thus, it passes from the capillary into its corresponding venule directly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/z3MBy.jpg&quot; alt=&quot;Microcirculation&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, plasma that enters the interstitium contains many of the same components as when it is in the blood, but the main difference is the protein content, losing the majority of proteins as it enters the interstitium. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, if you are asking how the majority of LYMPH fluid re-enters the blood stream, the answer is through the R lymphatic and L lymphatic (aka thoracic) ducts, at the location of the R subclavian or R internal jugular, and L subclavian veins, respectively. Once fluid enters lymphatic capillaries, it goes through a system of lymphatic vessels, trunks, and finally, the above mentioned ducts to rejoin blood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.biog1445.org/demo/06/lymphaticsys.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.biog1445.org/demo/06/lymphaticsys.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://intranet.tdmu.edu.ua/data/kafedra/internal/in_mow/classes_stud/uk/med/medprof/ptn/%D0%B0%D0%BD%D0%B3%D0%BB%D1%96%D0%B9%D1%81%D1%8C%D0%BA%D0%B0%20%D0%BC%D0%BE%D0%B2%D0%B0%20%D0%B7%D0%B0%20%D0%BF%D1%80%D0%BE%D1%84%D0%B5%D1%81%D1%96%D0%B9%D0%BD%D0%B8%D0%BC%20%D1%81%D0%BF%D1%80%D1%8F%D0%BC%D1%83%D0%B2%D0%B0%D0%BD%D0%BD%D1%8F%D0%BC/2/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://intranet.tdmu.edu.ua/data/kafedra/internal/in_mow/classes_stud/uk/med/medprof/ptn/англійська%20мова%20за%20професійним%20спрямуванням/2/&lt;/a&gt;№%2003.%20Heart...htm&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11631" LastActivityDate="2015-01-11T21:20:37.190" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27598" PostTypeId="2" ParentId="27596" CreationDate="2015-01-11T21:31:25.310" Score="7" Body="&lt;p&gt;That is a beautiful Pink Quill, or Tillandsia cyanea. I have included two websites below about this plant, both of which include care tips. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://home-and-gardening.info/2009/09/18/a-guide-on-growing-tillandsia/&quot;&gt;http://home-and-gardening.info/2009/09/18/a-guide-on-growing-tillandsia/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://houseplants.about.com/od/bromeliads/a/Bromeliads.htm&quot;&gt;http://houseplants.about.com/od/bromeliads/a/Bromeliads.htm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11631" LastActivityDate="2015-01-11T21:31:25.310" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27599" PostTypeId="2" ParentId="27588" CreationDate="2015-01-12T00:38:08.923" Score="3" Body="&lt;p&gt;There's some. The basic idea is that entropy, as rigorously defined in statistical physics, can be equated to complexity. This is an idea that has been around since at least the &lt;a href=&quot;http://bayes.wustl.edu/etj/articles/theory.1.pdf&quot; rel=&quot;nofollow&quot;&gt;1957 paper by Jaynes&lt;/a&gt;. In a fairly hand-wavey way, one can then say that a system that is being fed a large quantity of free energy (as the earth is by the sun) tends to become more complex over time (i.e. evolve).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thinking this through a bit, the above argument applies as easily to weather patterns as it does to living creatures. Recently, with the rise of computers and modeling there have been attempts to apply these kinds of general ideas (increasing free energy leading to increasing complexity) to living creatures in a more systematic way. Jeremy England is one researcher working on this problem, and &lt;a href=&quot;https://www.quantamagazine.org/20140122-a-new-physics-theory-of-life/&quot; rel=&quot;nofollow&quot;&gt;this link goes to a pretty good pop-science-style writeup of his work on the topic&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2015-01-12T04:41:14.843" LastActivityDate="2015-01-12T04:41:14.843" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27600" PostTypeId="2" ParentId="1294" CreationDate="2015-01-12T00:47:29.953" Score="5" Body="&lt;p&gt;A gene is dominant (lets call it B) when its presence in combination with a recessive allele (heterozygotic Bb) leads to the same phenotype as homozygotic BB. A recessive allele leads only to phenotypic expression when it is present twice (homozygotic bb).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To illustrate this rather abstract definition of dominant and recessive alleles let's look at a striking example, namely a gene mutation responsible for &lt;em&gt;albinism&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the causes that can lead to albinism is a mutation  in the gene that encodes &lt;em&gt;tyrosinase&lt;/em&gt; (TYR). Tyrosinase is used by &lt;em&gt;melanocyte cells&lt;/em&gt; to convert the amino acid tyrosine into the pigment &lt;em&gt;melanin&lt;/em&gt; that colors the skin, hair, and eyes (&lt;a href=&quot;http://www.scientificamerican.com/article/killing-albinos-tanzania-albinism/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ballantine, 2009&lt;/a&gt;). Animals lacking tyrosinase have white skin and hair and red eyes, such as the kangaroo in the picture below (source: &lt;a href=&quot;http://listverse.com/2014/02/12/10-amazing-color-mutations-in-animals/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Listverse&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xXVJG.jpg&quot; alt=&quot;Albino Roo&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One functional gene (B) is enough to allow for pigmentation to occur and hence it is dominant. The other mutated allele (b) produces nonfunctional enzyme, but is recessive as one functional allele produces sufficient enzyme to allow for normal pigmentation in a Bb individual. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your question you mention blue and brown eyes. AS @Larry_Parnell indicates, in blue eyes the eyes do not contain the pigment melanin and are therefore blue (the blue color is caused by non-pigmented optic effects). Brown eyes are therefore dominant as the melanine colors the eyes such that the blue color is masked (it is still there though). The phenotype of blue eyes is therefore recessive, as one allele for brown eyes is enough to bring pigment into the iris.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that other interactions also exist, such as co-dominance (e.g., the ABO blood group system where the genes for A and B antigens are both dominant over O) and incomplete dominance. I refer to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Dominance_%28genetics%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki page on dominance&lt;/a&gt; here, as the question is not specifically about these interactions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;sub&gt;references&lt;/sub&gt;&lt;/strong&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.scientificamerican.com/article/killing-albinos-tanzania-albinism/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ballantine. &lt;em&gt;Sci Am&lt;/em&gt; February 2009&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dominance_%28genetics%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Wikipedia&lt;/em&gt; - Dominance (genetics)&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-12T12:18:53.190" LastActivityDate="2015-01-12T12:18:53.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27601" PostTypeId="1" CreationDate="2015-01-12T01:48:24.670" Score="3" ViewCount="152" Body="&lt;p&gt;Why does human hair behave differently depending on its location? For instance, head hair grows to an indefinite length, but eyebrows maintain a particular length and appearance. Head hair and eyebrows may exhibit balding, but not ear, arm, nose, and facial hair (etc). Why is this so?&lt;/p&gt;&#xA;" OwnerUserId="12970" LastActivityDate="2015-01-12T01:48:24.670" Title="Why does human hair grow and behave differently depending on its location?" Tags="&lt;human-biology&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27602" PostTypeId="1" CreationDate="2015-01-12T03:06:10.153" Score="9" ViewCount="4874" Body="&lt;p&gt;I understand this question might fall into opinion based, but I'm trying to write it so that it meets the &quot;Many good questions generate some degree of opinion based on expert experience&quot; part and not get closed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;https://biology.stackexchange.com/questions/14812/can-you-answer-ray-comforts-question-on-biological-evolution&quot;&gt;closed creationist question&lt;/a&gt; about directly observing the evolution of new species made me think about just declaring dog breeds as new species just to provide an answer to that question. Turns out &lt;a href=&quot;http://www.scientificamerican.com/article/an-immodest-proposal/?page=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;I'm not the first one to think of it&lt;/a&gt;, and to be honest I probably read that article and forgot about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That article quotes geneticist Jerry Coyne as saying:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;“If somehow the recognized [dog] breeds existed only as fossils,&#xA;  paleontol­ogists would consider them not one species but&#xA;  many—certainly more than the thirty-six species of wild dogs that live&#xA;  in nature today.”&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is also &lt;a href=&quot;https://biology.stackexchange.com/questions/2483/are-there-dog-breeds-that-are-so-far-apart-genetically-that-they-cant-produce-v&quot;&gt;this question&lt;/a&gt; about breeds of dogs being different enough they can't breed. The answer posted to that question discusses attempts to breed beagles with irish setters, and having great difficulty.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm aware that the commonly used definition of different species is individuals who can't interbreed and make a fertile offspring. However the Scientific American article I referred to above mentions that animals are often classified as separate species because they are separated by a geographical barrier, and if they could mingle they would make fertile hybrid offspring. The same articles mentions fruit fly research that bred two different species of fruit fly and made fertile offspring, even though they would never interbreed in the wild. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is speculation, but let's imagine taking an island and putting several breeds of dogs on that island. Many of those breeds would easily interbreed and create mutts. But I'm pretty sure there would some sorting, the large dogs like st. bernards and great danes aren't going to easily interbreed with tiny dogs like chihuahuas. If we came back to this island after 50 or 100 years, we'd probably see small dogs and large dogs (assuming the island had decent ecological niches for both sizes of dogs to survive in)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Creationists like to ask why we haven't observed the evolution of a new species and don't want to listen to arguments about the fossil record or DNA sequences. If we just define some dog breeds as different species, we'd have an easy answer. I think some dogs would at least come close to meeting that definition for these reasons:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Dog breeds with large size differences would have great difficulty breeding.&lt;/li&gt;&#xA;&lt;li&gt;Some pairs of breeds seem to have trouble interbreeding (Beagles + Irish Setter). &lt;/li&gt;&#xA;&lt;li&gt;Some animals recognized as different species can create fertile hybrid offspring.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So why don't we recognize some dog breeds as different species?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-09-23T15:31:52.250" Title="Why can't we call dog breeds different species?" Tags="&lt;evolution&gt;&lt;species&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27603" PostTypeId="2" ParentId="19055" CreationDate="2015-01-12T04:15:19.707" Score="1" Body="&lt;p&gt;Pan is referring to all. So a pan-caspase inhibitor is a molecule that inhibits all caspases indiscriminately.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Pan&quot; rel=&quot;nofollow&quot;&gt;pan&lt;/a&gt; means all in Greek.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastActivityDate="2015-01-12T04:15:19.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27605" PostTypeId="2" ParentId="27507" CreationDate="2015-01-12T04:39:23.490" Score="1" Body="&lt;p&gt;Adaptation to altered vision is probably most well-investigated using prism-glasses. Prism glasses can shift the visual horizontally, for example by 20 degrees (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0149763405000059&quot; rel=&quot;nofollow noreferrer&quot;&gt;Redding et al., 2005&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YiZ7T.jpg&quot; alt=&quot;Prism goggles&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The use of horizontal shifting goggles has been investigated intensively to treat the symptoms of attentional neglect. Neglect occurs due to unilateral parietal brain lesions. For example, a lesion in the right hemisphere may induce left-sided neglect, where the left part of the visual field is seen, but simply not processed and neglected (&lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCcQFjAB&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGilles_Rode%2Fpublication%2F13542141_Prism_adaptation_to_a_rightward_optical_deviation_rehabilitates_left_hemispatial_neglect%2Flinks%2F09e4150dc9e1cbad95000000.pdf&amp;amp;ei=d0SzVNvVGYiN8QWoq4G4CA&amp;amp;usg=AFQjCNFFgi6hAQXMNrya4lXzWajDikfKpA&amp;amp;sig2=YHJbnlbc06fdQrrN2jsacA&amp;amp;bvm=bv.83339334,d.dGc&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rosetti et al., 1998&lt;/a&gt;). Wearing prism goggles for approximately 6.5 hours/day, over the course of 2 weeks has been shown to reduce the symptoms of neglect significantly by as long as 17 weeks(!) after treatment (&lt;a href=&quot;http://www.cisi.unito.it/neuropsicologia/didattica/materiali/approfondimenti/neglect/2002/frassinetti.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Frasinetti et al., 2002&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the treatment of a neurological disorder such as neglect adaptation to prism glasses is great. However, treating healthy controls with comparable methods may induce unwanted side effects. 15 min of prism exposure has been shown to lead to several degrees of error in pointing tasks, for up to two weeks after the adaptation in normally sighted controls (&lt;a href=&quot;http://link.springer.com/article/10.3758%2FBF03213965?LI=true&quot; rel=&quot;nofollow noreferrer&quot;&gt;Klapp et al., 1974&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To mention some studies closer to your question: in a virtual reality experiment subjects wore a head-mounted display that shifted the virtual position of their eyes. Their performance on a hand-eye coordination task first decreased by ~40% and then increased again with ~30% after adapting to the display. After taking the display off, there were transient after-effects, that impacted eye-hand performance (&lt;a href=&quot;http://www.creol.ucf.edu/Research/Publications/1502.PDF&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rolland et al, 1995&lt;/a&gt;; &lt;a href=&quot;http://www.mitpressjournals.org/doi/pdfplus/10.1162/105474698565703&quot; rel=&quot;nofollow noreferrer&quot;&gt;Biocca &amp;amp; Rolland, 1998&lt;/a&gt;). In other studies wearing a head-mounted display longer lasting discomfort was reported in 5% of the subjects (&lt;a href=&quot;http://ieeexplore.ieee.org/xpl/login.jsp?tp=&amp;amp;arnumber=6788197&amp;amp;url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6788197&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cobb et al., 1999&lt;/a&gt;) as well as binocular stress after removal of the display (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1475-1313.1993.tb00496.x/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mark Mon-Williams et al., 1993&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although the latter studies did not report serious after-effects, the more rigorously performed studies with the prism glasses have shown long-standing effects after visual adaptation. Hence, although the performance with virtual-reality head-mounted displays and comparable devices will undoubtedly increase after adapting to them, visual functions in everyday life may correspondingly be compromised. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So although this answer may not be addressing all your practical questions, I would say it is not advisable to let one actively adapt to head-mounted displays, or other wearable virtual-reality glasses that change visual function in the first place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.mitpressjournals.org/doi/pdfplus/10.1162/105474698565703&quot; rel=&quot;nofollow noreferrer&quot;&gt;Biocca &amp;amp; Rolland, &lt;em&gt;Presence&lt;/em&gt; 1998; &lt;strong&gt;7&lt;/strong&gt;:262-77&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://ieeexplore.ieee.org/xpl/login.jsp?tp=&amp;amp;arnumber=6788197&amp;amp;url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6788197&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cobb et al., &lt;em&gt;Presence&lt;/em&gt; 1999; &lt;strong&gt;8&lt;/strong&gt;:169-86&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1475-1313.1993.tb00496.x/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Frasinetti et al., &lt;em&gt;Brain&lt;/em&gt; 2002; &lt;strong&gt;125&lt;/strong&gt;:608-23 &lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://link.springer.com/article/10.3758%2FBF03213965?LI=true&quot; rel=&quot;nofollow noreferrer&quot;&gt;Klapp et al., &lt;em&gt;Perception &amp;amp; psychophysics&lt;/em&gt; 1974; &lt;strong&gt;15&lt;/strong&gt;: 399-400&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0149763405000059&quot; rel=&quot;nofollow noreferrer&quot;&gt;Redding et al. &lt;em&gt;Neurosci Biobehav Rev&lt;/em&gt; 2005; &lt;strong&gt;29&lt;/strong&gt;:3, 431-44&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.creol.ucf.edu/Research/Publications/1502.PDF&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rolland et al., IEEE Proceedings of VRAIS 1995&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCcQFjAB&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGilles_Rode%2Fpublication%2F13542141_Prism_adaptation_to_a_rightward_optical_deviation_rehabilitates_left_hemispatial_neglect%2Flinks%2F09e4150dc9e1cbad95000000.pdf&amp;amp;ei=d0SzVNvVGYiN8QWoq4G4CA&amp;amp;usg=AFQjCNFFgi6hAQXMNrya4lXzWajDikfKpA&amp;amp;sig2=YHJbnlbc06fdQrrN2jsacA&amp;amp;bvm=bv.83339334,d.dGc&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rosetti et al. &lt;em&gt;Nature&lt;/em&gt; 1999; &lt;strong&gt;365&lt;/strong&gt;:166*9&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-13T00:35:31.533" LastActivityDate="2015-01-13T00:35:31.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27606" PostTypeId="1" CreationDate="2015-01-12T05:45:25.313" Score="2" ViewCount="273" Body="&lt;p&gt;In dissociated live cells, does staining them with an antibody block the protein's function? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am sorting cells based on their expression of a few marker genes, and culturing them post-sort for several days.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can one assess if the protein is still functional?&lt;/p&gt;&#xA;" OwnerUserId="12971" LastEditorUserId="12971" LastEditDate="2015-07-20T00:37:12.883" LastActivityDate="2015-07-20T00:37:12.883" Title="Does antibody staining / immunolabeling block or inhibit protein function?" Tags="&lt;antibody&gt;&lt;experimental-design&gt;&lt;protein-binding&gt;&lt;research-process&gt;&lt;research-tools&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27607" PostTypeId="2" ParentId="27602" CreationDate="2015-01-12T05:57:56.860" Score="8" Body="&lt;p&gt;I don't enjoy the idea of comparing people to dogs, but this is a bit akin (please note the &lt;strong&gt;bit&lt;/strong&gt;) to asking if people who are genetically short (or &quot;little people&quot;, both proportionate and disproportionate dwarfism), pygmies, short people, normal sized people, tall people, very tall people, and people with acromegaly (gigantism) can be called different species. I compare because it's fairly clear to most individuals that we are all the same species: homo sapiens. About breeding, it is very likely that a reproductive specialist would be quite concerned (I certainly would be) about a woman with drarfism carrying the child of a very tall person (who had very tall parents), but not the opposite pairing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below is a photograph of the wedding of Tom Thumb and Lavinia Warren. That union produced no children. Her bridesmaid Minnie, (her sister), who was only 27 inches tall, also married a little person (Edward Newell). She became pregnant with a normal-sized child, but died during the birthing of a 6 pound baby (her baby died as well).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CItC1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are they a different species? No. A paleontologist (a good one) would be able to tell that the bones of a little person was actually of the same species based on certain conformations, just as I believe paleontologists today could distinguish prehistoric small cats from very large cats. Size matters, but not nearly as much as the type and distribution of teeth, the shape of the jaw, etc.  In other words, I strongly disagree with the following:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If somehow the recognized [dog] breeds existed only as fossils, paleontol­ogists would consider them not one species but many—certainly more than the thirty-six species of wild dogs that live in nature today.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That statement is based on a fairly profound error in thinking: a cognitive bias that is mistrustful of science in general due to a lack of familiarity with the rigors involved in the scientific methods of paleontologists in particular. I say this without rancor or animus of any kind; where I settled down (in the deeply religious region), the vast majority of my children's friends' parents are creationists, and the vast majority of our friends are fundamentalists. We argue about science all the time; I know the basic arguments. I'm familiar with their websites. I personally find myself in the camp of Christian thinkers like geneticist Francis Collins, M.D., Ph.D., the director of the Human Genome Project, who understand genetics and find no threat to their faith in evolution or science. (E.g. Creationists reject all science which indicates the age of the Earth is &gt;~6000 years.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The truth is that the definition of a species is not that easy, even for prokariotes. Difficult as well is a pure definition of life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, about size. &lt;strong&gt;The domestic dog exhibits greater diversity in body size than any other terrestrial vertebrate.&lt;/strong&gt; This is due to a small number of (or perhaps even a single) alleles: the IGF1 Allele. It's hard to argue difference of species on the basis of a small number of alleles: we allow much more variability for other alleles without wanting to classify as &lt;em&gt;different species&lt;/em&gt;: eye color, hair color, hair length, straight vs. curly coat, degree of tail curl, ear morphology, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.sciencemag.org/content/316/5821/112.short&quot; rel=&quot;noreferrer&quot;&gt;A Single IGF1 Allele Is a Major Determinant of Small Size in Dogs&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0168952507003058&quot; rel=&quot;noreferrer&quot;&gt;Lessons learned from the dog genome&lt;/a&gt;&lt;/sub&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0169534795900314&quot; rel=&quot;noreferrer&quot;&gt;A species definition for the modern synthesis&lt;/a&gt;&lt;/sub&gt; &#xA;&lt;sub&gt;&lt;a href=&quot;http://www.genetics.org/content/179/2/1033.short&quot; rel=&quot;noreferrer&quot;&gt;Single-Nucleotide-Polymorphism-Based Association Mapping of Dog Stereotypes&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;https://scholar.google.com/scholar?start=10&amp;amp;q=canis+familiaris+genetic+determinant+size&amp;amp;hl=en&amp;amp;as_sdt=0,39&quot; rel=&quot;noreferrer&quot;&gt;Canine Genetics Facilitates Understanding of Human Biology&lt;/a&gt;&lt;/sub&gt; &#xA;&lt;sub&gt;&lt;a href=&quot;http://www.pnas.org/content/99/16/10234.full&quot; rel=&quot;noreferrer&quot;&gt;How many species of prokaryotes are there? (PNAS)&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.pnas.org/content/102/suppl_1/6600.short&quot; rel=&quot;noreferrer&quot;&gt;Ernst Mayr and the modern concept of species (PNAS)&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/363/1506/2971.short&quot; rel=&quot;noreferrer&quot;&gt;Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/s11084-010-9192-3&quot; rel=&quot;noreferrer&quot;&gt;Is it Useful to Have a Clear-cut Definition of Life? On the Use of Fuzzy Logic in Prebiotic Chemistry&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-12T05:57:56.860" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="27608" PostTypeId="1" CreationDate="2015-01-12T06:11:09.687" Score="6" ViewCount="3963" Body="&lt;p&gt;I've got a His-tagged protein in 6M urea, 500 mM imidazole buffer that needs to be quantified before dialysis to ensure there's enough protein worth dialysing. I ran out of my elution buffer which should be used for blanking. I made a fresh buffer with the same contents, it started giving me false results. I could interpret that problem is with the buffer (probably because of change in chemical batch) from the readings I got in BCA and Bradford assays. Hence, I ran a gel to get an idea of presence of protein. Are there ways to estimate protein concentration quantitatively from the gel?&lt;/p&gt;&#xA;" OwnerUserId="8142" LastActivityDate="2016-08-19T22:33:43.287" Title="Can concentration of a protein be determined from a gel quantitatively (rough estimation)?" Tags="&lt;molecular-biology&gt;&lt;proteins&gt;&lt;purification&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27609" PostTypeId="2" ParentId="27608" CreationDate="2015-01-12T07:24:18.607" Score="6" Body="&lt;p&gt;Yes, you can use SDS-PAGE as a semiquantitative estimate of protein concentration. You need to create a standard curve with a protein of known concentration to compare against. Quantification is done by densitometry. It's a quick and easy process, but keep in mind some limitations:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Band intensity depends not only on the amount of protein but also on the amino acid composition of the proteins and the dye used&lt;/li&gt;&#xA;&lt;li&gt;The unknown protein and standard should be run on the same gel to remove variations in gels, electrophoresis, staining, destaining and imaging&lt;/li&gt;&#xA;&lt;li&gt;Densitometry can be quite qualitative depending on how it's done&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I'm not sure if you're looking for a protocol, but it's relatively straight forward. I usually load 2, 4, 6, 8 and 10 uL of 100 ng/uL BSA as a standard and 2, 4 and 6 uL of the protein of interest (based on past experience with my proteins and their purification). The gel is stained with Coomassie and the band intensity estimated with a program called ImageJ. A standard curve is created by plotting intensity as a function of mass, from which the concentration of the unknown can be found. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-01-12T07:30:35.147" LastActivityDate="2015-01-12T07:30:35.147" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27610" PostTypeId="2" ParentId="27582" CreationDate="2015-01-12T09:16:33.847" Score="21" Body="&lt;p&gt;&lt;em&gt;Note: This is based on literature searches I've done a while ago out of general curiosity. I'm in no way an expert on human reproduction.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;First, I'm not sure if you are asking about &lt;em&gt;evolutionary reasons&lt;/em&gt; or the  &lt;em&gt;developmental causes&lt;/em&gt; for for a difference in sex ratio. Here, I will focus on the &lt;em&gt;developmental causes&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is much evidence for a male bias in human sex ratio at birth (secondary sex ratio), and the ratio have been shown to change over time, e.g. as in 20th centrury Europe after WWI and WWII (see data in &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs11692-008-9046-3&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Gellatly. 2009. Trends in Population Sex Ratios May be Explained by Changes in the Frequencies of Polymorphic Alleles of a Sex Ratio. Evolutionary Biology 36(2): 190-200. DOI: 10.1007/s11692-008-9046-3&quot;&gt;Gellatly, 2009&lt;/a&gt;),in relation to environmental or parental factors (see e.g. &lt;a href=&quot;http://humrep.oxfordjournals.org/content/14/12/3120&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Jacobsen et al. 1999. Natural variation in the human sex ratio.  Hum. Reprod. 14(12): 3120-3125.&quot;&gt;Jacobsen et al, 1999&lt;/a&gt;), or between ethnic groups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A bias in sex ratio can be due to (at least) three different mechanisms (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3455630/&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Irving et al. 1999. The Ratio of X- and Y-Bearing Sperm in Ejaculates of Men with Three or More Children of the Same Sex. J Assist Reprod Genet. 16(9): 492–494.&quot;&gt;Irving et al (1999)&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;deviations in X/Y-ratio of sperm&lt;/li&gt;&#xA;&lt;li&gt;selection of sperm within the female reproductive tract&lt;/li&gt;&#xA;&lt;li&gt;biases in implantation success and/or survival for embryos of different sex&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I guess that success of fertilization/zygote formation could maybe be considered a separate step (between 2-3). From what I've seen, there is little evidence for explanation one, see tests in e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3455630/&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Irving et al. 1999. The Ratio of X- and Y-Bearing Sperm in Ejaculates of Men with Three or More Children of the Same Sex. J Assist Reprod Genet. 16(9): 492–494.&quot;&gt;Irving et al (1999)&lt;/a&gt; and &lt;a href=&quot;http://humrep.oxfordjournals.org/content/14/11/2917.full&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Graffelman et al. 1999. Human live birth and sperm–sex ratios compared.  Hum. Reprod. 14(11): 2917-2920.&quot;&gt;Graffelman et al (1999)&lt;/a&gt;. &lt;a href=&quot;http://humrep.oxfordjournals.org/content/14/11/2917.full&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Graffelman et al. 1999. Human live birth and sperm–sex ratios compared.  Hum. Reprod. 14(11): 2917-2920.&quot;&gt;Graffelman et al (1999)&lt;/a&gt; also tests for an effect of male age, but do not find support for this idea. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A problem is that it is extremely difficult to study these factors under natural conditions (practically and ethically). Interestingely, there is also evidence for an excess loss of male fetuses in recognized pregnancies (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1471-0528.2003.00022.x/abstract;jsessionid=C12E828425BF6DB14C1699ECE1F567D1.f01t01&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Ingmarsson. 2003. Gender aspects of preterm birth. BJOG: An International Journal of Obstetrics &amp;amp; Gynaecology 110: 34–38&quot;&gt;Ingmarsson, 2003&lt;/a&gt;, &lt;a href=&quot;http://humrep.oxfordjournals.org/content/20/3/583.long&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Boklage. 2005. The epigenetic environment: secondary sex ratio depends on differential survival in embryogenesis. Human reproduction&quot;&gt;Boklage, 2005&lt;/a&gt;), and this would indicate that the sex ratio close to conception is even more skewed towards males than the sex ratio at birth. This is even more curious with the background of an unbiased sex ratio in sperm (explanation 1 above). However, it is very problematic to study what happens in the first part of pregnancies, since a number of weeks have usually passed before the pregnancy is even recognized. I haven't found any papers reporting the human primary sex ratio (sex ratio at conception), which could be affected by factor 1 &amp;amp; 2 above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even so, the most likely explanation seems to be a strong bias during embryogenesis, as mentioned in &lt;a href=&quot;http://humrep.oxfordjournals.org/content/20/3/583.long&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Boklage. 2005. The epigenetic environment: secondary sex ratio depends on differential survival in embryogenesis. Human reproduction&quot;&gt;Boklage (2005)&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The usual excess of males is present through pregnancy beyond clinical recognition, but not present at fertilization. The difference, therefore, must arise between fertilization and clinical recognition, through a preferential loss of females during embryogenesis. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The same paper also points out that fewer than 25% of natural human fertilizations go full term (probably even less), and 2/3 of these fail before the pregnancies have been clinically recognized. By back-calculating from the secondary sex ratio and the excess of failed male pregnancies, the sex ratio close to conception has been estimated to 125-135 male:100 female (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1472648310615969#&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Pergament et al. 2002. Sex ratio: a biological perspective of ‘Sex and the City’. Reproductive BioMedicine Online 5(1): 43–46&quot;&gt;Pergament et al, 2002)&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact causes for such a bias during is not entirely known from what I've seen. However, &lt;a href=&quot;http://humrep.oxfordjournals.org/content/20/3/583.long&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Boklage. 2005. The epigenetic environment: secondary sex ratio depends on differential survival in embryogenesis. Human reproduction&quot;&gt;Boklage (2005)&lt;/a&gt; mentions a couple of different explanations. For instance, among mammals in general, the earliest stages of embryogenesis proceeds more rapidly in male embryos:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Since some of the products of these earliest stages are signals from one part of the embryo to another, or from the embryo to the maternal physiology, signals which are required for continuation and maintenance of the pregnancy, the establishment of viable, clinically recognizable pregnancy is correspondingly more efficient in general for male embryos (Krackow, 1995; Kochhar et al., 2003). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The same issue is also mentioned in &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1471-0528.2003.00022.x/abstract;jsessionid=C12E828425BF6DB14C1699ECE1F567D1.f01t01&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Ingmarsson. 2003. Gender aspects of preterm birth. BJOG: An International Journal of Obstetrics &amp;amp; Gynaecology 110: 34–38&quot;&gt;Ingvarsson (2003)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Studies in recent years indicate that sex differentiation begins at conception. The SRY gene on the Y-chromosome is already transcribed at the 2-cell stage and triggers growth acceleration in the XY embryos. This accelerated growth is believed to be important for the male embryo as it allows complete testicular differentiation before the levels of oestrogenic hormones become too high as pregnancy progresses.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://humrep.oxfordjournals.org/content/20/3/583.long&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Boklage. 2005. The epigenetic environment: secondary sex ratio depends on differential survival in embryogenesis. Human reproduction&quot;&gt;Boklage (2005)&lt;/a&gt; also mentions genomic imprinting and chromosome X–Y segregation as possible explanations for a bias (see references in paper for more).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, &lt;strong&gt;in summary&lt;/strong&gt;; there is evidence for an male bias in secondary sex ratio (sex ratio at birth), even though there is usually a excess of failed male fetuses in recognized pregnancies, which means that the male bias must be even higher very early in pregnancies. There is some evidence that this might be due to a higher success of embryogenesis of male fetuses, but the evidence isn't strong and the issue is difficult to study.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The evidence provided by these results is indirect. That is unlikely to change. Ethical, technical and financial considerations argue against the destruction for karyotyping of statistically sufficient numbers of products of natural human fertilizations. Granted, any bias of the sort we seek to discover and understand might, after all, operate differently, or not at all, in sham fertilizations of hamster oocytes, versus oocytes from artificially induced human ovulations, versus naturally fertilized human oocytes. The best evidence we have, or are likely to have in the foreseeable future, indicates that the consistent excess of males observed in human births does not originate in a consistent bias in spermatogenesis or in fertilization. &#xA;  (&lt;a href=&quot;http://humrep.oxfordjournals.org/content/20/3/583.long&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Boklage. 2005. The epigenetic environment: secondary sex ratio depends on differential survival in embryogenesis. Human reproduction&quot;&gt;Boklage, 2005&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Finally, it should also be mentioned that the bias in sex ratio at birth can be partially due to sex-selective abortion and infanticide, but to what extent is not entirely known (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Sex-selective_abortion&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia: Sex-selective abortion&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might also find this related question on the heritability of sex ratio interesting: &lt;a href=&quot;https://biology.stackexchange.com/questions/23548/the-gender-of-offspring-of-twins/23553#23553&quot;&gt;The gender of offspring of Twins?&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2019-02-08T14:04:00.183" LastActivityDate="2019-02-08T14:04:00.183" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="27612" PostTypeId="1" CreationDate="2015-01-12T11:22:48.790" Score="1" ViewCount="59" Body="&lt;p&gt;I was reading &lt;a href=&quot;https://biology.stackexchange.com/questions/21829/what-determines-the-autumn-leaf-color&quot;&gt;this question&lt;/a&gt; about autumn leaf colors. One of the answers &lt;a href=&quot;http://www.biology.upatras.gr/attachments/article/650/Archetti%20et%20al%20Trends%20in%20Ecology%20and%20Evolution.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;refers&lt;/a&gt; to an article by Archetti et al. In the article, box 4 (page 5) shows the reflectance spectra of leaves of different color. How is the reflectance spectrum of such solid materials measured? There was a recent question about &lt;a href=&quot;https://biology.stackexchange.com/questions/27587/what-are-the-requirements-for-a-spectrometer-to-be-used-in-biological-research/27595#27595&quot;&gt;spectrophotometers&lt;/a&gt; but it appears to assume the sample is in a liquid form.&lt;/p&gt;&#xA;" OwnerUserId="12973" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-01-16T08:48:44.497" Title="How is the reflectance spectrum of solids measured?" Tags="&lt;botany&gt;&lt;measurement&gt;&lt;phenology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27613" PostTypeId="1" CreationDate="2015-01-12T13:01:39.043" Score="0" ViewCount="144" Body="&lt;p&gt;I'm looking for tutorials and software that can help me study whole genome sequence data is and genome wide associations. I have Matlab and Bioconductor R so anything involving those packages would be preferable. &lt;/p&gt;&#xA;" OwnerUserId="12935" LastEditorUserId="3553" LastEditDate="2015-11-26T02:55:08.333" LastActivityDate="2015-11-26T02:55:08.333" Title="How to do a whole genome analysis of Multidrug-resistant Mycobacterium tuberculosis" Tags="&lt;bioinformatics&gt;&lt;sequence-analysis&gt;&lt;gwas&gt;&lt;tuberculosis&gt;&lt;data&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27614" PostTypeId="2" ParentId="25825" CreationDate="2015-01-12T13:10:02.050" Score="2" Body="&lt;p&gt;&lt;em&gt;I can answer this question only based on guesses because I am not really sure about your claim that activators are higher in number than repressors. So consider this as an extended comment.&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;While activators can interact directly or indirectly with the core&#xA;  machinery of transcription through enhancer binding, repressors&#xA;  predominantly recruit co-repressor complexes leading to&#xA;  transcriptional repression by chromatin condensation of enhancer&#xA;  regions&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not really true. A repressor can simply sit on the the promoter and prevent RNAP from binding the to the latter. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11282469&quot; rel=&quot;nofollow&quot;&gt;Abstract&lt;/a&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Transcriptional repressors are usually viewed as proteins that bind to&#xA;  promoters in a way that impedes subsequent binding of RNA polymerase.&#xA;  Although this repression mechanism is found at several promoters,&#xA;  there is a growing list of repressors that inhibit transcription&#xA;  initiation in other ways. For example, several repressors allow the&#xA;  simultaneous binding of RNA polymerase to the promoter, but interfere&#xA;  with subsequent events of the initiation process, eventually&#xA;  inhibiting transcription initiation. The recent increase in the number&#xA;  of repressors for which the repression mechanism has been&#xA;  characterized in detail has shown an amazing variety of strategies to&#xA;  repress transcription initiation. It is not surprising to find that&#xA;  the repression mechanism used is usually exquisitely adapted to the&#xA;  characteristics of the promoter and of the repressor involved.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Some justification on why the number activators would be more:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A network perspective:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lets assume an that gene-&lt;strong&gt;A&lt;/strong&gt; somehow causes the repression of the gene-&lt;strong&gt;B&lt;/strong&gt;. This repression can be either direct (&lt;strong&gt;A&lt;/strong&gt; being a repressor of &lt;strong&gt;B&lt;/strong&gt;) or indirect via some other genes. In the case of indirect regulation you just need one repressor in the network path &lt;strong&gt;A → B&lt;/strong&gt; to result in repression of the latter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So all repressive paths would minimally require only one repressor, all other steps in the path can be activation; whereas in an activating path you would need &lt;em&gt;'n'&lt;/em&gt; activators for &lt;em&gt;'n'&lt;/em&gt; steps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Post-transcriptional Regulation:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now if you include post-transcriptional regulation then you can find more number of repressors: miRNAs (2588 reported in humans: miRbase-21) and many proteins as well (For an e.g. see &lt;a href=&quot;http://www.jneurosci.org/content/26/27/7135.full&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;). Most cases of events leading to translational activation are actually derepression. It is logical in a way because an mRNA is a temporary product; it should not by default require an additional signal to start producing proteins. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-01-12T16:23:43.437" LastActivityDate="2015-01-12T16:23:43.437" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27615" PostTypeId="2" ParentId="27613" CreationDate="2015-01-12T15:17:32.387" Score="1" Body="&lt;p&gt;You've picked a fascinating and very important organism to study. Unfortunately there are many many steps with many software packages that you'll need and each next step will depend on what you find making any particular tutorial nigh on pointless. I'm sorry to say that I don't think anyone will dump an entire project proposal or workflow as an answer. I'll give you an answer to get you started on your research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Example&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An excellent example of such a study is &lt;a href=&quot;http://www.sciencemag.org/content/317/5840/944.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fellay &lt;em&gt;et al.&lt;/em&gt;, 2007&lt;/a&gt; and you can find their materials and methods supplement &lt;a href=&quot;http://www.sciencemag.org/content/suppl/2007/07/17/1143767.DC1/Fellay-SOM.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;An introduction to this kind of research&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First you need to find the sequences of proteins that you think are significant. There are a bunch of ways of doing this, but I suggest standing on the shoulders of giants and scouring the literature (regardless, find an example where this has been done elsewhere). If there isn't much out there or for an entirely new viewpoint on something, &lt;a href=&quot;https://biology.stackexchange.com/questions/7190/finding-proteins-in-dna-sequence/7192#7192&quot;&gt;this answer&lt;/a&gt; might help for finding proteins in the DNA sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sequence alignments against other strains is your best bet of identifying mutations (and possibly an indicator of resistance, which is what I guess you're after). There are plenty to choose from, but &lt;a href=&quot;http://www.uniprot.org/blast/&quot; rel=&quot;nofollow noreferrer&quot;&gt;BLAST&lt;/a&gt; is a good tool to start with. You should compare your resistant strain with non resistant strains. Be very careful when analysing the data, not every mutation will be significant.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-01-12T15:25:32.230" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27616" PostTypeId="1" CreationDate="2015-01-12T16:09:20.610" Score="0" ViewCount="190" Body="&lt;p&gt;I am studying RNA-binding proteins involved in RNA granules. I am searching the literature for an order of magnitude of the absolute global concentration in the cytoplasm. Although I am aware this quantity can vary greatly from proteins to proteins, I would be happy if I find some papers having estimated it for some given proteins.&lt;/p&gt;&#xA;" OwnerUserId="9662" LastEditorUserId="9662" LastEditDate="2015-01-12T16:14:37.200" LastActivityDate="2015-01-12T16:14:37.200" Title="Typical in-vivo protein concentration" Tags="&lt;proteins&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27617" PostTypeId="1" CreationDate="2015-01-12T16:27:25.010" Score="0" ViewCount="38" Body="&lt;p&gt;I was wondering which kind of plants would survive longest without CO&lt;sub&gt;2&lt;/sub&gt; : plants with fatty, thick leaves or plants with thinner, less fatty leaves? &#xA;And can we conclude that the plant species that are more dependent on CO&lt;sub&gt;2&lt;/sub&gt; levels, would benefit from the greenhouse effect?&lt;/p&gt;&#xA;" OwnerUserId="12976" LastEditorUserId="3340" LastEditDate="2015-01-12T18:08:57.680" LastActivityDate="2015-01-12T18:29:10.393" Title="Plant dependence on CO₂ levels" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;climate-change&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27620" PostTypeId="1" AcceptedAnswerId="27627" CreationDate="2015-01-12T17:55:47.960" Score="0" ViewCount="3212" Body="&lt;p&gt;Which sex of trees bears fruit? The males or females? And what specifically cause that one to bear fruit. Is it the same as it is with blossoms in trees?&lt;/p&gt;&#xA;" OwnerUserId="11855" LastActivityDate="2015-01-12T23:24:09.380" Title="Which sex of trees bears fruit?" Tags="&lt;botany&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2015-01-12T23:58:47.487" ContentLicense="CC BY-SA 3.0" />
  <row Id="27621" PostTypeId="1" AcceptedAnswerId="27622" CreationDate="2015-01-12T18:11:12.713" Score="16" ViewCount="3903" Body="&lt;p&gt;Taking my current profile picture as a prominent example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/U8P3C.jpg?s=256&amp;amp;g=1&quot; alt=&quot;Dog&amp;#39;s eyes glowing green in camera&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This photo has been taken with flash. As I gather, this is the same effect that makes a human's eyes glow red on photos, namely the reflection of the flash at the choroid and then passing back through the retina.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The retina is full of bloodvessels and the blood inside them gives the reflected light it's reddish color.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it's the same effect, why is the color different?&lt;/p&gt;&#xA;" OwnerUserId="12979" LastActivityDate="2017-01-28T09:52:17.940" Title="Why do dog's eyes glow green on a photo?" Tags="&lt;eyes&gt;&lt;light&gt;&lt;pets&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27622" PostTypeId="2" ParentId="27621" CreationDate="2015-01-12T18:18:36.737" Score="10" Body="&lt;p&gt;Dogs, cats, and many other mammals have a &lt;a href=&quot;http://en.wikipedia.org/wiki/Tapetum_lucidum&quot;&gt;Tapetum lucidum&lt;/a&gt; which reflects light back through the retina to help with night vision. Humans don't have this layer. The tapetum is probably reflecting green light that would have normally been absorbed.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2015-01-12T18:18:36.737" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27623" PostTypeId="2" ParentId="27617" CreationDate="2015-01-12T18:29:10.393" Score="1" Body="&lt;p&gt;Plants do not need CO&lt;sub&gt;2&lt;/sub&gt; for survival. They need it just for photosynthesis; if you supply them with alternate carbon source such as glucose then they would survive (See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC429343/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for non-CO&lt;sub&gt;2&lt;/sub&gt; Carbon-source utilization). There are non-photosynthetic plants which are totally dependent on carbon sources other than CO&lt;sub&gt;2&lt;/sub&gt;; some are carnivorous like venus fly-trap. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure what you intend when you correlate leaf thickness to CO&lt;sub&gt;2&lt;/sub&gt;-dependence. Leaf morphology can affect photosynthesis rates but afaik there is no relationship between leaf morphology and CO&lt;sub&gt;2&lt;/sub&gt;-&lt;strong&gt;dependence&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;can we conclude that the plant species that are more dependent on&#xA;  CO&lt;sub&gt;2&lt;/sub&gt; levels, would benefit from the greenhouse effect&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Greenhouse effect is not equivalent to increase in CO&lt;sub&gt;2&lt;/sub&gt;; increased CO&lt;sub&gt;2&lt;/sub&gt; levels can cause greenhouse effect which is a physical phenomenon of entrapment of IR radiation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;CO&lt;sub&gt;2&lt;/sub&gt; is fixed by an enzyme called Rubisco; like most enzyme catalyzed reactions this will reach a saturation limit i.e. addition of more CO&lt;sub&gt;2&lt;/sub&gt; will not increase the rate of photosynthesis. However the rate of photosynthesis is limited at the Rubisco step because of low levels of CO&lt;sub&gt;2&lt;/sub&gt; (See &lt;a href=&quot;http://link.springer.com/chapter/10.1007%2F978-1-4020-6709-9_191&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) and it can be expected that most photosynthetic plants will be benefited by increase in CO&lt;sub&gt;2&lt;/sub&gt;. However, not all plants would be resistant to increased temperatures and moreover the rate of enzyme catalysis would also change with temperature. So it is not that easy to predict. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-01-12T18:29:10.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27624" PostTypeId="2" ParentId="5088" CreationDate="2015-01-12T18:32:53.260" Score="2" Body="&lt;p&gt;Salt will cause high blood pressure, &lt;em&gt;but only under certain circumstance.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;physiologic hormonal compensations for increased blood volume:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Atrial natriuretic peptide&lt;/strong&gt; -- increases sodium excretion, hence this is &lt;strong&gt;INCREASED&lt;/strong&gt; with high blood volume&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Antidiuretic horomone&lt;/strong&gt; -- ADH increases water reabsorption in the kidney, hence this will be &lt;strong&gt;DECREASED&lt;/strong&gt; with high blood volume&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Renin/Aldosterone&lt;/strong&gt; -- increases sodium reabsorption from ultrafiltrate back into blood, hence it will be &lt;strong&gt;DECREASED&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;these explainations are a bit reverse (saying that these horomones have these effects and that is why they are released) for the sake of simplicity, and I'm not discussing the mechanism of release of these horomones (aka under what circumstances they are released in the place where they are released from)... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;while these horomones help with the kidney regulation of sodium balance and blood volume, this still depends on the kidneys being given the circumstance where they can be effective.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Pathologic circumstances, when elimination of excess sodium fails:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some people simply have a higher sodium sensitivity and there are a variety of factors that have been statistically correlated to sodium sensitivity, but often the mechanism is unknown. Here are various factors statistically correlated to affect salt sensitivity:&#xA;&lt;a href=&quot;http://physrev.physiology.org/content/85/2/679&quot; rel=&quot;nofollow&quot;&gt;http://physrev.physiology.org/content/85/2/679&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the above article shows that no organ systems need be compromised for excess sodium to raise blood pressure, but just for the sake of discussing more macroscopic things I want to discuss these organ systems based reasons for the kidney being unable to compensate for excess sodium in the diet=&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The kidney:&#xA;A patient with renal disease may not be able to regulate the excretion of sodium. Even in normal humans, the kidney's capacity to excrete sodium declines with age, and smaller increases in salt intake induce a rise in arterial pressure, as GFR (the renal filtration of the blood sent to the kidney) falls by about 40%, though individual variations are wide and some people lose less. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Other than the kidney:&#xA;Other diseases can also interfere with renal excretion of sodium. A problem with maintaining blood volume will cause constriction of the renal artery. This would occur before a drop in blood pressure would occur, as this is a way of preventing a drop in blood pressure. This occurs in congestive heart failure and liver cirrhosis.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A patient with congestive heart failure may not have adequate renal&#xA;perfusion.  Hence, to maintain adequate blood pressure the renal artery is constricted.&lt;/li&gt;&#xA;&lt;li&gt;Also, liver cirrhosis may decrease renal perfusion&#xA;because of the lack of blood proteins (proteins found inside the&#xA;blood vessels that keep water in the blood vessels via osmosis)&#xA;holding fluids in the intravascular space and having them escape into&#xA;the extra-vascular (outside the blood vessels but still outside the&#xA;cells of the body) space. Again, to maintain adequate blood pressure the renal artery is constricted.&lt;/li&gt;&#xA;&lt;li&gt;burns, also because of loss of blood proteins--&gt; leakage of intravascular fluid to extravascular space--&gt; decreased blood volume and increased sympathetic nervous system output--&gt; reduction of renal blood flow... same as for cirrhosis&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In addition to reduction of salt in the diet, diuretics (ex. loop and thiazide) can help the body excrete even more sodium into the urine than what your body can do on it's own.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;this article describes the renal handling of excess salt in the diet:&#xA;&lt;a href=&quot;http://booksite.elsevier.com/brochures/thekidney/PDFs/TheKidneyCh36_P088488.pdf&quot; rel=&quot;nofollow&quot;&gt;http://booksite.elsevier.com/brochures/thekidney/PDFs/TheKidneyCh36_P088488.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2015-05-04T00:22:37.877" LastActivityDate="2015-05-04T00:22:37.877" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27626" PostTypeId="1" AcceptedAnswerId="27661" CreationDate="2015-01-12T20:16:46.747" Score="5" ViewCount="1510" Body="&lt;p&gt;I'm interested in what humans can do to speed up the rate of growth in a plant. I'm interested in both the context of home gardening and large-scale, institution-backed projects. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously, optimal growing conditions are one factor that can be modified. I imagine that there are also genetic mutations that can be done (&lt;a href=&quot;https://biology.stackexchange.com/questions/19873/is-it-possible-to-genetically-modify-a-plant-at-home&quot;&gt;possibly even at home!&lt;/a&gt;). Botany is not my field so what I'm looking for here is are the basics and some good resources for further reading. &lt;/p&gt;&#xA;" OwnerUserId="8161" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-01-14T04:13:03.823" Title="Are there ways to speed up the growth of plants?" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;botany&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27627" PostTypeId="2" ParentId="27620" CreationDate="2015-01-12T23:24:09.380" Score="2" Body="&lt;p&gt;The distinction between male and female is not that clear in plants, at least at the level of individuals. Actually the details may be rather complicated (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Plant_reproductive_morphology#Terminology&quot; rel=&quot;nofollow&quot;&gt;[1]&lt;/a&gt;), but in general we can distinguish between plants that have:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;male and female individuals (dioecy)&lt;/li&gt;&#xA;&lt;li&gt;male and female flowers on the same individual (monoecy)&lt;/li&gt;&#xA;&lt;li&gt;flowers that have both male and female structures (bisexuality)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In the first case, only female individuals produce flowers that -- when fertilized by the pollen from the flowers of a male individual -- develop into a fruit. Examples are Hazelnut, common nettle and a few other species &lt;a href=&quot;http://en.wikipedia.org/wiki/Category:Dioecious_plants&quot; rel=&quot;nofollow&quot;&gt;[2]&lt;/a&gt;. However, dioecy is rather rare among extant flowering plants [3]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Monoecious plant species are somewhat different. A good example is maize. The male flowers of a maize plant are located in the tassels at the apex of the stem, wheres the female flowers are are in the leaf axils. Note that each corn developed from a single flower and that the cob is actually the infructescense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there are bisexual plants. In these, every flower has the potential to be fertilized and develop into a fruit, which is why they are also called perfect flowers. Plants have developed several strategies to prevent self-fertilization, e.g. the temporally delayed expression of female/male structures within the same flower.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Resources:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;[3]: Bawa, K. S. (1980). Evolution of dioecy in flowering plants. Annual review of ecology and systematics, 15-39.&lt;/p&gt;&#xA;" OwnerUserId="8015" LastActivityDate="2015-01-12T23:24:09.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27628" PostTypeId="1" CreationDate="2015-01-12T23:38:44.487" Score="4" ViewCount="347" Body="&lt;p&gt;I recently heard about the evolution of the &lt;a href=&quot;http://en.wikipedia.org/wiki/London_Underground_mosquito&quot; rel=&quot;nofollow&quot;&gt;London Underground mosquitoes&lt;/a&gt;, and how they have changed genetically enough that they almost can no longer reproduce with above ground mosquitos. Since this change in the mosquitos occurred over a relatively short time frame, how many years/generations would it take for a similar process to happen with humans?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thought experiment that comes to mind is this. Assuming we sent a colony of humans to a distant planet and didn't have any physical contact with them for x number of years, how many years would it take for the colony of humans to branch off enough genetically to be no longer be able to reproduce with Earth humans? This is assuming the planet is habitable but different enough to change the course of human evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, what would be an expected minimum number of years it would take for this colony's descendants to be removed from Earth humans to one day again be reunited and not be able to produce offspring between the now different species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, what would be an expected minimum number of years the would need to pass before they are reunited and are no longer enough of the same species to produce offspring together?&lt;/p&gt;&#xA;" OwnerUserId="12984" LastEditorUserId="9943" LastEditDate="2015-01-13T11:02:24.537" LastActivityDate="2015-01-13T11:02:24.537" Title="A colony of humans are sent to an alien world, at what point would the descendants evolve to be genetically incompatible with Earth humans?" Tags="&lt;evolution&gt;&lt;human-genetics&gt;&lt;theoretical-biology&gt;&lt;astrobiology&gt;&lt;human-evolution&gt;" AnswerCount="1" CommentCount="20" ClosedDate="2015-01-13T10:40:16.200" ContentLicense="CC BY-SA 3.0" />
  <row Id="27630" PostTypeId="1" AcceptedAnswerId="27642" CreationDate="2015-01-13T01:59:56.000" Score="3" ViewCount="207" Body="&lt;p&gt;I read &lt;a href=&quot;http://www.theweedblog.com/marijuana-mother-plants-more-susceptible-to-viral-infections-over-time/&quot; rel=&quot;nofollow&quot;&gt;an article by a gardener&lt;/a&gt; describing how a virus had transmitted a negative trait to his plants. It rather shocked me, because I hadn't realized that a virus could transform an adult plant. I was aware of dipping arabadopsis flowers in agrobacterium tumefaciens, but the concept of non-reproductive structures being transformed seems fascinating. What kind of virus is capable of that? &lt;/p&gt;&#xA;" OwnerUserId="146" LastEditorUserId="3624" LastEditDate="2015-01-13T14:29:35.320" LastActivityDate="2015-01-13T21:59:33.353" Title="What virus transforms full grown plants?" Tags="&lt;botany&gt;&lt;virus&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27631" PostTypeId="1" CreationDate="2015-01-13T03:20:20.773" Score="0" ViewCount="282" Body="&lt;p&gt;I am working on building a real time PCR machine. Is there any chemistry set that I can purchase online to:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Identify if PCR amplification was successfully done.  &lt;/li&gt;&#xA;&lt;li&gt;Test fluorescence dyes that could be used to validate if the fluorescence detector optics worked; i.e. something I could excite with a specific wavelength and monitor for fluorescence. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I am looking for something that is not dangerous and only serves the single purpose of validating the real time PCR machine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Mods please advise if I need to move to Chemistry StackExchange&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="12985" LastEditorUserId="3340" LastEditDate="2015-01-13T06:27:20.173" LastActivityDate="2016-07-08T09:45:16.390" Title="Real Time PCR Test Chemistry" Tags="&lt;pcr&gt;&lt;diy-biology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="27633" PostTypeId="2" ParentId="27630" CreationDate="2015-01-13T06:09:19.760" Score="5" Body="&lt;p&gt;Viruses can infect just about any living thing, so that it could infect a plant is no surprise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your article describes how a small virus-infected part of a plant had been cloned and consequently the entire cloned plant was infected, and it infected plants grown hydroponically in the same water. No surprise there either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plant viruses have been known for centuries. One of the earliest recorded descriptions of a virus-infected plant can be found in a poem written by the Japanese Empress Kōken (718–770), in which she describes a plant with yellowing leaves in summer. The plant (a Eupatorium) was described as &quot;autumnal&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The top 10 plant viruses (in one paper) in molecular plant pathology were listed as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(1) Tobacco mosaic virus, (2) Tomato spotted wilt virus, (3) Tomato yellow leaf curl virus, (4) Cucumber mosaic virus, (5) Potato virus Y, (6) Cauliflower mosaic virus, (7) African cassava mosaic virus, (8) Plum pox virus, (9) Brome mosaic virus and (10) Potato virus X, with honourable mentions for viruses just missing out on the Top 10, including Citrus tristeza virus, Barley yellow dwarf virus, Potato leafroll virus and Tomato bushy stunt virus. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Some plant virologists even care enough to argue about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One paper describes how a plant was &lt;em&gt;improved&lt;/em&gt; by a viral infection:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In all cases, virus infection delayed the appearance of drought symptoms. Beet&#xA;  plants infected with CMV* also exhibited significantly improved tolerance to freezing. Metabolite profiling analysis showed an increase in several osmoprotectants and antioxidants in BMV**-infected rice and CMV-infected beet plants before and after drought stress.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;*Cucumber mosaic virus&lt;br&gt;&#xA;**Brome mosaic virus&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v422/n6934/full/422831a.html&quot;&gt;Aetiology: The earliest recorded plant virus disease&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22017770&quot;&gt;Top 10 plant viruses in molecular plant pathology&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://rybicki.wordpress.com/2012/01/12/the-real-top-10-for-plant-viruses/&quot;&gt;The REAL Top 10 for Plant Viruses&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.apsnet.org/edcenter/intropp/PathogenGroups/Pages/PlantViruses.aspx&quot;&gt;&#xA;Introduction to Plant Viruses, the Invisible Foe&#xA;&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://tracysfeldman.com/XuNew%20Phytologist%20Xu%20et%20al.pdf&quot;&gt;Virus infection improves drought tolerance&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-13T06:09:19.760" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27634" PostTypeId="2" ParentId="27612" CreationDate="2015-01-13T07:12:00.573" Score="3" Body="&lt;p&gt;As the name implies, reflectance spectra are measured from light reflected off an object. Any object with reflects light, such as any opaque object) will work for this technique; to me this seems like solids are ideally suited for reflectance spectrphotometry. You might be used to &lt;em&gt;transmission&lt;/em&gt; or &lt;em&gt;absorbance&lt;/em&gt; spectrophotometry, which measures the amount of light transmitted or lost after passing through a sample. These methods are typically used for liquids which allow passage of light to some extent. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/276/1654/121.long&quot; rel=&quot;nofollow&quot;&gt;The paper (1)&lt;/a&gt; cited by the review you mention says that they used a &quot;&lt;a href=&quot;http://www.trios.de/index.php?option=com_content&amp;amp;view=article&amp;amp;id=196&amp;amp;catid=47&amp;amp;Itemid=76&amp;amp;lang=en&quot; rel=&quot;nofollow&quot;&gt;RAMSES-ARC hyperspectral radiance sensor&lt;/a&gt;,&quot; which is probably just as awesome as it sounds. In principle reflection spectrophotometry works very similarly to transmission-based spectrophotometry: generate monochromatic light, shine it at the sample, and measure the intensity of light that comes back at that wavelength (or over a range of wavelengths)$^†$. If you do this for many different wavelengths of light, you have a reflectance spectrum. &lt;a href=&quot;http://www.labint-online.com/uploads/tx_ttproducts/datasheet/principles-and-applications-ofreflectance-spectrophotometry.pdf&quot; rel=&quot;nofollow&quot;&gt;This link&lt;/a&gt; might have some useful information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$^†$ &lt;strong&gt;Edit&lt;/strong&gt;: Modern-day spectrophotometers use a more efficient method in which broad-band light is passed onto the sample and the response at a single wavelength can later be mathematically reconstructed. If you're interested in these types of details, refer to &lt;a href=&quot;http://en.wikipedia.org/wiki/Fourier_transform_spectroscopy&quot; rel=&quot;nofollow&quot;&gt;Fourier Transform spectroscopy&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/276/1654/121.long&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt;: Doring TF, Anchetti M, Hardie J. (2009). Autumn leaves seen through herbivore eyes. &lt;em&gt;Proc. R. Soc. B&lt;/em&gt; 282(1801): 121-127.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastEditorUserId="4840" LastEditDate="2015-01-16T08:48:44.497" LastActivityDate="2015-01-16T08:48:44.497" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27635" PostTypeId="2" ParentId="27628" CreationDate="2015-01-13T07:21:08.090" Score="4" Body="&lt;p&gt;That's an interesting model, because mosquitoes are vectors for serious illnesses, so are pretty well studied.  One team of scientists are working on genetically altering mosquitoes in Africa to make them unable to transmit the parasite that causes malaria. As the mosquitoes breed, it spreads through the population. In an interview, the lead researcher stated:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the lab, we saw the mutation spread to more than half the population of mosquitoes we had living in cages. This happened in a time span of 12 to 16 generations of mosquitoes (each generation being between 18 to 30 days in the wild). So it's quite efficient.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;12 to 16 generations&lt;/strong&gt; for one mutation to spread to half of a contained population. In human generations, 16 = 320 years, and that doesn't take into account fertility rates, miscarriages, etc. (Not a problem for mosquitoes, I presume).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How many mutations would it take to make two humans incapable of reproducing without endangering their own health or fertility? &lt;em&gt;Excluding&lt;/em&gt; all of the harmful mutations that might just result in disease or decreased fertility? &lt;em&gt;And add to that&lt;/em&gt; that the males need to change as well as the females? No one knows. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine a cystic-fibrosis type mutation (one gene) that increased the viscosity of cervical mucus such that normal sperm could not fertilize the egg. There would need to be another mutation in males that would make sperm stronger, or secrete an enzyme that breaks down mucus, or something to that effect. However, look at Cystic Fibrosis. People used to die before adulthood. Most men with CF are sterile. Women with CF, living longer now because of better care and treatment, are getting pregnant, but many have a decreased lifespan post-pregnancy, and almost all the babies are premature. You can't predict &quot;when&quot; a series of beneficial mutations so dramatic as to change a being so dramatically. The answer might be never.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Try to give me a single or a few mutations that would prevent the ability of people from one population and another to mate. Say one mutation led to a smaller pelvis. Most women with that mutation would die in childbirth before a mutation arose to make smaller babies (which would most likely be a deleterious mutation as well).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not a geneticist (which is really the person who should be answering this question) but I think the odds of this scenario ever occurring are very low. I just can't imagine mutations making reproduction impossible between two populations being beneficial and selected in one population rather than harmful. Keep in mind that different humans from populations that were isolated for many thousands of years have no problem reproducing.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-01-13T09:45:21.923" LastActivityDate="2015-01-13T09:45:21.923" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27638" PostTypeId="1" CreationDate="2015-01-13T11:03:18.420" Score="7" ViewCount="1530" Body="&lt;p&gt;The amino acid leucine, is used in proteins more than others. Leucine with 9.1 percent (its average in more than 1.150 different proteins) is used most and tryptophan with 1.4 percent is used less than all other amino acids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is leucine used more than tryptophan?&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorUserId="14709" LastEditDate="2015-03-07T19:32:35.647" LastActivityDate="2015-08-03T19:53:53.667" Title="Why is leucine amino acid used the most in proteins and tryptophan the least?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;amino-acids&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27639" PostTypeId="2" ParentId="27638" CreationDate="2015-01-13T11:31:13.707" Score="3" Body="&lt;p&gt;&lt;em&gt;This is a guess.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tryptophan is a bulky amino acid. Having a lot of if would make the protein bulky. It is anyways hydrophobic and cannot be present on protein exteriors; high tryptophan may distort hydrophobic core possibly because of its bulkiness and ability to form pi-stacking interactions. &lt;br&gt;&#xA;However, tryptophan is an essential amino acid and cannot be made &lt;em&gt;de novo&lt;/em&gt; in humans. Indeed, it has only one codon perhaps because of its limited usage. &lt;br&gt;&#xA;Nonetheless, tryptophan, despite its low abundance, is important in stabilization of protein structures such as β-hairpin &lt;sup&gt;[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20564027&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]&lt;/sup&gt; and it is also required for synthesizing serotonin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Leucine is present in the hydrophobic core and β-regions. It also surrounds active sites which causes exclusion of water; this in turn facilitates catalysis by allowing polar residues to bind to the substrates &lt;sup&gt;[&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0022283673903720&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]&lt;/sup&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't have any comment on why not isoleucine or valine instead of leucine.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-01-14T06:57:49.747" LastActivityDate="2015-01-14T06:57:49.747" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27640" PostTypeId="2" ParentId="25815" CreationDate="2015-01-13T13:04:06.490" Score="1" Body="&lt;p&gt;There can be several reasons for variability and since you said that the machine has not been serviced for a long time, I guess that should be one main source of errors. Multichannel pipettes can also sometimes cause problems (based on personal experience) and it is mostly because the tips don't fit properly in all channels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Try varying some parameter (for e.g. concentration of RNA) and see the effect on melting temperature; if the inter-replicate variability is not high enough to make the inter-sample difference insignificant then you can continue with your experiment. Take more number of replicates to minimize variance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the variability is very high then I guess you would need to get your machine repaired or use more sensitive equipments designed specifically for these kind of studies. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-01-13T13:04:06.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27641" PostTypeId="2" ParentId="25890" CreationDate="2015-01-13T13:38:44.777" Score="3" Body="&lt;p&gt;&lt;strong&gt;Oxytocin&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has been shown that oxytocin signaling helps in muscle regeneration by activating MAP Kinase/ERK pathway in skeletal muscles.&lt;sup&gt;[&lt;a href=&quot;http://www.nature.com/ncomms/2014/140610/ncomms5082/full/ncomms5082.html&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;1&lt;/strong&gt;&lt;/a&gt;]&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oxytocin is also known to promote adult neurogenesis.&lt;sup&gt;[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21692136&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;2&lt;/strong&gt;&lt;/a&gt;]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Myostatin&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is a paralog of GDF and like GDF prevents hypertrophy of cardiac muscles.&lt;sup&gt;[&lt;a href=&quot;http://circres.ahajournals.org/content/115/2/296.long&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;3&lt;/strong&gt;&lt;/a&gt;]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Leptin&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though leptin is not really connected to ageing but it regulates appetite and thereby the metabolism &lt;sup&gt;[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17212793&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;4&lt;/strong&gt;&lt;/a&gt;]&lt;/sup&gt;. It &lt;em&gt;may&lt;/em&gt; contribute indirectly to ageing by reducing food intake and preventing obesity and other metabolic syndromes.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://pubs.acs.org/doi/pdf/10.1021/cb4008277&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt; summarizes different soluble small (synthetic) molecules that have potential to induce regeneration.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-01-14T07:00:15.487" LastActivityDate="2015-01-14T07:00:15.487" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27642" PostTypeId="2" ParentId="27630" CreationDate="2015-01-13T14:28:12.543" Score="3" Body="&lt;p&gt;These are just a couple of short examples, but Witch's broom structures in trees can sometimes be caused by viruses - see &lt;a href=&quot;http://en.wikipedia.org/wiki/Witch%27s_broom&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Wikipedia: Witch's broom&lt;/em&gt;&lt;/a&gt; (fungi is maybe the most common cause though). In rose species you also have the similar &lt;em&gt;Rose rosette disease&lt;/em&gt; (also called witches’-broom of rose), which is &lt;a href=&quot;http://www.missouribotanicalgarden.org/gardens-gardening/your-garden/help-for-the-home-gardener/advice-tips-resources/pests-and-problems/diseases/viruses/rose-rosette.aspx&quot; rel=&quot;nofollow&quot;&gt;caused by a virus&lt;/a&gt;. The same webpage from &lt;a href=&quot;http://www.missouribotanicalgarden.org/gardens-gardening/your-garden/help-for-the-home-gardener/advice-tips-resources/pests-and-problems/diseases/viruses.aspx&quot; rel=&quot;nofollow&quot;&gt;Missouri Botanical Garden&lt;/a&gt; also includes a list of other plant viruses that you might find interesting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plant viruses that infect non-reproductive structures are common though - a overview can be found here: &lt;a href=&quot;http://www.apsnet.org/edcenter/intropp/PathogenGroups/Pages/PlantViruses.aspx&quot; rel=&quot;nofollow&quot;&gt;The American Phytopathological Society: Introduction to Plant Viruses, the Invisible Foe&lt;/a&gt;. More indepth information can be found in &lt;a href=&quot;https://books.google.se/books?id=xLdSrKhThNEC&amp;amp;&quot; rel=&quot;nofollow&quot; title=&quot;Agrios. 2012. Plant Pathology. Elsevier&quot;&gt;&lt;em&gt;Plant Pathology&lt;/em&gt; (Agrios, 2012)&lt;/a&gt; (see ch. 12: &quot;&lt;em&gt;Plant diseases caused by viruses&lt;/em&gt;&quot;).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-01-13T21:59:33.353" LastActivityDate="2015-01-13T21:59:33.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27643" PostTypeId="1" AcceptedAnswerId="27644" CreationDate="2015-01-13T15:15:36.150" Score="6" ViewCount="2451" Body="&lt;p&gt;Is it true that people become gradually shorter as they age?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it is, is it more common in one gender than the other?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And is it known what triggers this? (Considering that the &quot;shortening&quot; probably does not start immediately after the person stops growing?)&lt;/p&gt;&#xA;" OwnerUserId="11546" LastActivityDate="2015-09-18T10:40:16.827" Title="Do people grow shorter as they age, how common is it, and what triggers it?" Tags="&lt;senescence&gt;&lt;growth&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27644" PostTypeId="2" ParentId="27643" CreationDate="2015-01-13T16:07:09.380" Score="6" Body="&lt;p&gt;Short answer: Yes, we do shrink with age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most important reason is that the cartilage in the joints between our bones gets worn out and thinner, as well as disks between the vertebrae of the spine. This results in a compression of the spine and also to a loss in height. Shrinking bones due to osteoporosis can also play a role, as well as &lt;a href=&quot;https://en.wikipedia.org/wiki/Sarcopenia&quot; rel=&quot;nofollow&quot;&gt;muscular atrophy&lt;/a&gt; due to ageing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &quot;The Baltimore Longitudinal Study of Aging&quot; (reference 1) adults start shrinking by the age of 30 by 5-8mm per decade. This is relatively short after you completely stop growing. This process gets faster with increasing age, the study says it goes faster after 70.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Men and women do not shrink equally, men loose around 3cm between 30-70 and a total of 5cm by the age of 80. Women loose about 5cm between 30 and 70 and a total of 4.5cm by the age of 80 (these are average numbers from reference 1). Reference 2 also has a nice summary of this original article.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This effect can be attenuated by regulary excercising as the study listed in reference 3 shows.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://aje.oxfordjournals.org/content/150/9/969.short&quot; rel=&quot;nofollow&quot;&gt;Longitudinal Change in Height of Men and Women: Implications for&#xA;Interpretation of the Body Mass Index: The Baltimore Longitudinal&#xA;Study of Aging&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.google.de/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=1&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCEQFjAA&amp;amp;url=http%3A%2F%2Fwww.wsj.com%2Farticles%2FSB10001424053111904194604576580720025344668&amp;amp;ei=kTu1VJ2mGYbB7Aai0IHQBg&amp;amp;usg=AFQjCNEFuE87mw8Oq2RBT55ylJVtuHY5qw&amp;amp;bvm=bv.83339334,d.ZGU&quot; rel=&quot;nofollow&quot;&gt;Yes, You Are Getting Shorter&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10965182&quot; rel=&quot;nofollow&quot;&gt;Role of physical activity training in attenuation of height loss&#xA;through aging.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-01-14T07:46:09.903" LastActivityDate="2015-01-14T07:46:09.903" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27645" PostTypeId="1" AcceptedAnswerId="27646" CreationDate="2015-01-13T16:10:02.997" Score="5" ViewCount="294" Body="&lt;p&gt;What happens in the human body when someone is stung by a jellyfish; namely a box jelly. Judging by what I have heard about the stings I'm guessing that they involve a neurotoxin. &#xA;&lt;p&gt;&#xA;But what is actually happening? What are the symptoms and what happens after the sting (treatments and survivability)?&lt;/p&gt;&#xA;" OwnerUserId="6289" LastActivityDate="2015-04-04T22:15:59.343" Title="What happens when someone is stung by a jellyfish?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;toxicology&gt;&lt;ichthyology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27646" PostTypeId="2" ParentId="27645" CreationDate="2015-01-13T16:47:17.790" Score="7" Body="&lt;p&gt;The problem is that &lt;a href=&quot;http://en.wikipedia.org/wiki/Box_jellyfish&quot; rel=&quot;nofollow&quot;&gt;box jellyfish&lt;/a&gt; doesn't specify one jellyfish but a group of different jellyfish. Some of these are highly venomous - I pick here &lt;a href=&quot;http://en.wikipedia.org/wiki/Chironex_fleckeri&quot; rel=&quot;nofollow&quot;&gt;Chironex fleckeri&lt;/a&gt;, as this is often called &quot;the most venomous jellyfish in the world&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chironex fleckeri has long tentacles which are covered with millions of explosive cells called &lt;a href=&quot;http://en.wikipedia.org/wiki/Cnidocyte&quot; rel=&quot;nofollow&quot;&gt;Cnidocytes&lt;/a&gt; which inject a dart with the very powerful toxin upon touch. It is therefore very dangerous to touch the tentacles with bare hands to remove them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The toxin is a mix of different bioactive proteins which have cytolytic, cytotoxic, inflammatory or hemolytic activity. Case reports (you can find information in reference 3 about it) show that the tentacles &quot;burn&quot; though all skin layers causing immediate strong pain and lasting scars (if the victims survive) which tend to show signs of necrosis. The toxins itself paralyze the muscles of the heart and the respiration and also causes hypokalemia by hemolyzing red blood cells (one of the toxin acts as a membrane pore in the blood cells). This causes further problems and often a cardiac arrest. See reference 1 and 2 for details on the toxins. Especially 2 is interesting, as this is a PhD-Thesis on this topic with a lot of references.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Treatment depends on how severe the injury is - in severe cases an antivenom can be used. Besides this typical measures are CPR, giving oxygen and removing the tentacles (with appropriate protection). See reference 3 (good overview) to 5 for details on this topic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jbc.org/content/early/2014/01/08/jbc.M113.534149&quot; rel=&quot;nofollow&quot;&gt;Chironex fleckeri (Box Jellyfish) Venom Proteins: Expansion of a&#xA;Cnidarian Toxin Family that Elicits Variable Cytolytic and&#xA;Cardiovascular Effects&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://researchonline.jcu.edu.au/5682/&quot; rel=&quot;nofollow&quot;&gt;The molecular and biochemical characterisation of venom proteins&#xA;from the box jellyfish, Chironex fleckeri&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.marine-medic.com.au/pages/medical/chironex.asp&quot; rel=&quot;nofollow&quot;&gt;Chironex fleckeri (Multi-tentacled Box Jellyfish)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23434796&quot; rel=&quot;nofollow&quot;&gt;Jellyfish stings and their management: a review.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24379089&quot; rel=&quot;nofollow&quot;&gt;Cytotoxic and cytolytic cnidarian venoms. A review on health&#xA;implications and possible therapeutic applications.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-04-04T22:15:59.343" LastActivityDate="2015-04-04T22:15:59.343" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27647" PostTypeId="1" AcceptedAnswerId="27654" CreationDate="2015-01-13T18:01:38.847" Score="5" ViewCount="1909" Body="&lt;p&gt;According to some information, in the ancient past (at least some) animals grew larger due to a higher levels of oxygen in the atmosphere. So for example there is &lt;a href=&quot;http://www.sciencedaily.com/releases/2010/10/101029132924.htm&quot;&gt;this study regarding dragonflies&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can higher levels of atmospheric oxygen also lead to larger plants? For example, would it be possible to grow gigantic strawberries in a hermetically sealed greenhouse that maintains a higher atmospheric oxygen concentration?&lt;/p&gt;&#xA;" OwnerUserId="11546" LastEditorUserId="9943" LastEditDate="2015-01-13T23:52:48.283" LastActivityDate="2015-01-14T18:52:12.057" Title="If higher levels of atmospheric oxygen can lead to larger animals, can it also lead to larger plants?" Tags="&lt;botany&gt;&lt;cellular-respiration&gt;&lt;growth&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27648" PostTypeId="1" AcceptedAnswerId="27652" CreationDate="2015-01-13T18:07:58.550" Score="11" ViewCount="8105" Body="&lt;p&gt;I was looking into the following problem:&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/R5KaR.png&quot; alt=&quot;Who would win? 1 trillion lions or the sun?&quot;&gt;&#xA;Obviously, the solution lies in how much energy either can output per unit of time.&lt;br&gt;&#xA;The total energy output of the sun is $3.8×10^{26} \frac{J}{s}$.&lt;br&gt;&#xA;The number of lions alone pales in comparison ($10^{12}$).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I'm now trying to figure out how many lions it would take to have an output equal to the sun, but I seem to be having a hard time finding good data.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the peak energy output of a lion per second (or where/how can I find such information)?&lt;/p&gt;&#xA;" OwnerUserId="6433" LastEditorUserId="6433" LastEditDate="2015-01-14T08:18:21.090" LastActivityDate="2015-01-15T16:29:17.407" Title="How much energy does a lion contain?" Tags="&lt;zoology&gt;&lt;literature&gt;" AnswerCount="3" CommentCount="17" FavoriteCount="2" ClosedDate="2015-01-14T20:10:26.263" ContentLicense="CC BY-SA 3.0" />
  <row Id="27649" PostTypeId="2" ParentId="27648" CreationDate="2015-01-13T19:12:45.323" Score="5" Body="&lt;p&gt;The sun will win until you have enough lions to form a star sized mass.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that your lions have an average mass of &lt;strong&gt;200kg&lt;/strong&gt;, which is &lt;a href=&quot;http://www.scribd.com/doc/15574755/Relative-Body-Mass-of-the-Lion-and-Tiger&quot; rel=&quot;nofollow&quot;&gt;probably pretty close&lt;/a&gt;, 1 trillion lions has a mass of &lt;strong&gt;2×10&lt;sup&gt;14&lt;/sup&gt; &lt;em&gt;kg&lt;/em&gt;&lt;/strong&gt;, which is pretty close to the mass of &lt;a href=&quot;https://en.wikipedia.org/wiki/Remus_%28moon%29&quot; rel=&quot;nofollow&quot;&gt;Remus&lt;/a&gt;, a moon around the asteroid Sylvia. The mass of the sun is about &lt;a href=&quot;https://en.wikipedia.org/wiki/Sun&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;2×10&lt;sup&gt;30&lt;/sup&gt; &lt;em&gt;kg&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So your lions would have enough mass to become gravitationally crushed into an object, but probably not enough to become rounded. Once crushed they won't be able to carry out any metabolism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if we considered the sum of 2 trillion individual lions the sun would still win because nuclear fusion completely outclasses chemical reactions in terms of energy released, and the mass of the sun is still much much much larger.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if we somehow converted the lions into energy by &lt;strong&gt;E=mc&lt;sup&gt;2&lt;/sup&gt;&lt;/strong&gt;, we get about &lt;strong&gt;1.8×10&lt;sup&gt;31&lt;/sup&gt; &lt;em&gt;J&lt;/em&gt;&lt;/strong&gt;. So if you managed that you could release more energy than the sun for a very short time.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="3340" LastEditDate="2015-01-14T06:54:02.313" LastActivityDate="2015-01-14T06:54:02.313" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27650" PostTypeId="1" AcceptedAnswerId="27653" CreationDate="2015-01-13T21:10:15.247" Score="8" ViewCount="2489" Body="&lt;p&gt;In the UK at present, one of the examination boards has set a &quot;controlled assessment&quot; (an experiment that pupils do at school under exam conditions) that involves testing a hypothesis that vitamin C is removed from fruit juice by heating it (i.e. in the pasteurisation process).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am massively skeptical about this. The teacher guidance suggests &quot;Treating fresh orange juice in boiling water for between 10 and 30 mins gives an easily measurable decrease in vitamin C levels&quot;. Leaving aside that this hardly represents a simulation of the pasteurisation process(!), does anybody know of any solid, academic studies of the effect of pasteurisation on the vitamin C content of fruit juice? I have tried (as a scientist, but non-biologist) my usual routes to reliable information and they fail miserably - the www is &lt;em&gt;full&lt;/em&gt; of crackpots on this one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a follow-up to that, is it not the case anyway that the oxidation of the orange juice when it is boiled in this experiment, plus simple exposure to light could also be responsible for any decrease in vitamin C observed?&lt;/p&gt;&#xA;" OwnerUserId="12993" LastActivityDate="2017-12-19T14:00:16.810" Title="Pasteurisation of orange juice and Vitamin C" Tags="&lt;vitamins&gt;&lt;heat&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27652" PostTypeId="2" ParentId="27648" CreationDate="2015-01-13T21:33:17.837" Score="22" Body="&lt;p&gt;Wow, as an astrophysicist who has just logged into biology SE for the first time, I didn't think I'd have a question I could immediately answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are correct about the Sun's output, so what about the lion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the lion is in its usual passive state, i.e. lying around as shown in your picture, then you would not go far wrong in treating them as black body radiators (well this will give you an upper limit, though the emissivity of human skin is quite high, so it should be a reasonable approximation.). To estimate a power I need a lion's temperature and its surface area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.felineconservation.org/feline_species/lion.htm&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt; the body temperature of a lion is 311.33 Kelvin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found a calculator that used the DuBois formula for surface area (for humans) and put in 440 pounds and 7 feet 10 for the weight and &quot;height&quot; of a (male, adult) lion - this returned a surface area of $3.6\ m^2$ (about twice a, male human, so sounds roughly ok).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now using the Stefan-Boltzmann formula $P = \sigma A T^4$, I get the power output of a &quot;black body&quot; lion to be about 2 kW.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus $10^{12}$ lions have a power output of $2\times 10^{15}\ W$, which is 11 orders of magnitude less than the Sun.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But now take the question at its most basic. Compared to the Sun, the lion is a pretty effective power generation unit. The Sun only generates $2\times 10^{-4}\ W/kg$, whereas a lion-based power source weighs in with a massive $10\ W/kg$! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Note that the calculation just assumes the Lion can produce this kind of power output whatever environment it is in. In practice a Lion absorbs a large fraction of this power from its surroundings and its internal metabolism does not need (and probably cannot) supply 2kW. Thus the 2kW should be reduced to some extent, though I'm not sure a simplistic $T^4 - T_{\rm env}^{4}$ calculation can be correct, unless one of you biologists tells me that a Lion's metabolism shuts down once the ambient (African) temperature approaches 311K (I guess in a human a lot of it goes in evaporating sweat?) Whatever, the order of magnitude of the answer is unchanged.&lt;/p&gt;&#xA;" OwnerUserId="12993" LastEditorUserId="12993" LastEditDate="2015-01-15T16:29:17.407" LastActivityDate="2015-01-15T16:29:17.407" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="27653" PostTypeId="2" ParentId="27650" CreationDate="2015-01-13T22:20:48.237" Score="10" Body="&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2621.2002.tb09543.x/abstract&quot; rel=&quot;noreferrer&quot;&gt;Hodgins AM, Mittal GS, Griffiths MW. 2002. Pasteurization of Fresh Orange Juice Using Low-Energy Pulsed Electrical Field. J Food Sci 67(6):2294-2299&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a study of non-thermal food preservation, but it cites two studies that measured ascorbate loss from pasteurisation. I can't cite the studies directly because I can't find them online. According to these authors, they reported losses of 7.0-15.0% and 18.0% after 95°C for 15s. This is high compared to the pulsed electrical field method. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/9Szhd.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jf000306p&quot; rel=&quot;noreferrer&quot;&gt;Yeom HW, Streaker CB, Zhang QW, Min DB. 2000. Effects of Pulsed Electric Fields on the Quality of Orange Juice and Comparison with Heat Pasteurization. J Agric Food Chem 48(10):4597-4605&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This study compared ascorbate loss during storage after PEF or thermal treatment. While no difference was observed when stored at 22°C, PEF treated orange juice maintained significantly higher ascorbate concentration than thermally treated orange juice when stored at 4°C. The authors attribute this to the &quot;higher processing temperature&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/8gcBo.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They also say (and reference other studies):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ascorbic acid is a typically heat sensitive nutrient. High temperatures during processing and storage cause loss of ascorbic acid. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="3340" LastEditDate="2015-01-14T06:25:21.057" LastActivityDate="2015-01-14T06:25:21.057" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27654" PostTypeId="2" ParentId="27647" CreationDate="2015-01-13T22:42:07.317" Score="5" Body="&lt;p&gt;Oxygen is good for animals because our basic metabolism is this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;High energy carbon molecules + O&lt;sub&gt;2&lt;/sub&gt; → energy + H&lt;sub&gt;2&lt;/sub&gt;O + CO&lt;sub&gt;2&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Plants do that too at night, but during the day, they mostly do this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;High energy photons + H&lt;sub&gt;2&lt;/sub&gt;O + CO&lt;sub&gt;2&lt;/sub&gt; → High energy carbon molecules + O&lt;sub&gt;2&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Rubisco, one of the most important enzymes in photosynthesis, can bind to O&lt;sub&gt;2&lt;/sub&gt;, leading to less efficient photorespiration, instead of photosyntheis.  Rubisco is often a bottleneck in photosynthesis, in large part for that reason.  So high oxygen isn't helpful to plants.  In fact, C&lt;sub&gt;4&lt;/sub&gt; plants and CAM plants have evolved more complicated physiology to minimize the effect of O&lt;sub&gt;2&lt;/sub&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastEditorUserId="5148" LastEditDate="2015-01-14T17:38:05.913" LastActivityDate="2015-01-14T17:38:05.913" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27655" PostTypeId="1" CreationDate="2015-01-14T00:00:28.620" Score="1" ViewCount="185" Body="&lt;p&gt;I don't know if this is a physics or a biology question but this might be better orientated around the element of how the human eye works in a 3D visual situation than physics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given the rise of 3D virtual reality headsets such as the Oculus Rift. I have a question about eye strain relating to these.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Often on a computer, eye strain comes from staring at the monitor for too long of which is the same continuous distance that your eyes have to focus on... thus causing computer vision syndrome (as well as lack of blinking). Meaning you should look at an object far away every X amount of minutes to rest the eyes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How ever in a virtual headset, although the monitor is much closer, it is in 3D (or a fake 3D). So i wondered, does the eye muscles adjust based on this trick of fake 3D. Or will your eyes still focus on the fixed distance to the screen display regardless of the fake 3D perception, meaning you still get eye strain either way?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you imagine looking through a 3D VR Headset, staring at a 3D object in the distance, is that going to create the same change in muscle adjustment in the eye as looking at a physical object in the real world of the same distance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially - 3D VR headsets could reduce the amount of eye strain. Because the eye is busy adjusting all the time for these &quot;fake&quot; distance illusions, rather than forced to focus in one way for a long length of time such as a 2D monitor. It might help people who struggle with computer vision syndrome perhaps?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has any studies been done on this?&lt;/p&gt;&#xA;" OwnerUserId="12996" LastEditorUserId="12996" LastEditDate="2015-01-14T05:10:05.217" LastActivityDate="2015-01-14T05:10:05.217" Title="Eye strain using 3D screens" Tags="&lt;eyes&gt;&lt;perception&gt;&lt;human-eye&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27656" PostTypeId="2" ParentId="26110" CreationDate="2015-01-14T00:46:17.823" Score="3" Body="&lt;p&gt;The important point is that your voice is influenced by airflow, and your vocal cords. When we're sick, and it depends on what it is, a number of factors change the sound of your voice by influencing the two of these, either: By changing airflow due to respiratory tract swelling or fluid buildup, or by damage/swelling/alterations to the vocal cords. In a couple  of examples: A weak airflow might produce a higher pitch or weaker voice, or perhaps swollen vocal cords produce that hoarseness associated with decreased frequency of vibration.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-01-14T00:46:17.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27657" PostTypeId="2" ParentId="27543" CreationDate="2015-01-14T01:50:23.517" Score="12" Body="&lt;p&gt;Thank you for the fascinating question! It was tough to research but very worthwhile.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;LDL is actually not such a bad molecule. It is formed from VLDL/IDL after VLDL/IDL distribute triglycerides, phospholipids, cholesterol and cholesterol esters to peripheral cells. With less to give, LDL subsequently tries to be helpful by providing any needy peripheral cell with leftover cholesterol necessary for plasma membrane synthesis and other cellular functions. In fact, even endothelial cells, which line the vasculature, have LDL receptors to welcome any cholesterol packages from LDL. Another function of LDL is to make HDL even ‘healthier’ by removing cholesteryl ester from HDL molecules in the periphery and returning it to the liver. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remember that LDL does not contain exactly the same components as its precursors. LDL does not have the ApoE &amp;amp; C proteins that VLDL and IDL have. LDL has only ApoB-100 and a concentrated level of cholesterol. LDL-family receptors generally recognize ApoE and ApoB, which are located on VLDL and IDL, thus easily pulling them into the liver out of the bloodstream, via endocytosis. Because LDL contains only the ApoB protein, it is less easily recognized. Thus, more LDL lingers in the blood. This is supported by the lengths of their half-lives--- with VLDL and IDL half-lives being about 6 hours and LDL half-life being about 3 days. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YiB2a.jpg&quot; alt=&quot;Lipoprotein Content&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where disease comes in is with an imbalance of fat in our diet. This is explained in detail by this extensive article on &lt;a href=&quot;http://www.medscape.org/viewarticle/582014&quot; rel=&quot;noreferrer&quot;&gt;Managing Dyslipidemia: The Triglyceride/High-Density Lipoprotein Axis&lt;/a&gt;. The article explains that disease cannot solely be blamed on LDL alone. A high fat diet leads to elevated triglycerides in the blood stream, which increases blood viscosity, interference with endothelial function, stimulation of arterial inflammation, and interference with normal blood coagulation. These conditions can predispose to atherosclerotic lesions. In addition, there is an up-regulation of protein ApoC-III, which subsequently increases the half-lives of VLDL and IDL particles. It even increases the activity of an enzyme called cholesteryl ester transfer protein (CETP), which can exchange cholesteryl ester in HDL and LDL for triglycerides in VLDL and IDL, and vice versa. This leads to change in composition of HDL and LDL, making them more triglyceride-rich, physically smaller, and less interactive with their respective membrane receptors. With HDL even smaller, it is also easily filtered through the kidneys, leading to lower levels. All this means there is more circulating LDL in the blood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;LDL enters the endothelium via breaks in the endothelial wall created naturally (by dying or dividing cells) or through injury (by inflammatory processes including infections, chemical exposures) or it leaks in through junctions between endothelial cells when there is high intraluminal pressure (such as in hypertension). From there, LDL can become oxidized and ingested by macrophages, forming foam cells, which can rupture spewing its contents into the surrounding arterial wall, leading to the beginning of atherosclerotic lesion. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why can’t HDL cross through endothelial wall, too? Actually, it can! According to the above-mentioned article, “HDL particles [in its native form] appear to have the potential to delipidate cholesterol from foam cells” at the site of a lesion. With HDL being smaller, it can enter the endothelium to interact with foam cells. Its interaction, however, is the opposite of LDL. Cholesterol is transferred back from the foam cell to HDL, reversing the oxidized LDL-induced process. In addition, “HDL protects LDL from oxidation by [using] metal ions” before oxidized LDL can lead to further damage. This mechanism is still unknown. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why can’t HDL become oxidized, too? Indeed, this can also happen! However, it appears again than oxidized HDL behaves oppositely to oxidized LDL. “Oxidative tyrosylation of high density lipoprotein by peroxidase enhances cholesterol removal from cultured fibroblasts and macrophage foam cells [5].” There is a caveat though. This function seems to depend on how HDL is oxidized. If oxidized by copper or hypochlorous acid, HDL “loses its ability to remove cholesterol from cultured cells [6].” &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, given the very same conditions including oxidative environment and entry into the endothelial cell, HDL inherently behaves oppositely to LDL. This likely is related to their inherently different composition, but we have yet to understand how this occurs at a molecular level. However, HDL could technically be 'bad' under the right oxidative conditions. In the end, LDL is given a bad reputation because its relatives IDL/VLDL easily escape into other cells via receptors and HDL concentration is lowered partially by renal filtration. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;References: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://books.google.com/books?id=j2BNM6Bv_BEC&amp;amp;pg=PA621&amp;amp;lpg=PA621&amp;amp;dq=how+does+ldl+enter+an+endothelial+cell?&amp;amp;source=bl&amp;amp;ots=7GF1P9kFB7&amp;amp;sig=C0ytpD4Fi3ksIfehL6g7rXWut-w&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=76O0VMO8G-mxsAS3t4K4Cw&amp;amp;ved=0CGIQ6AEwCQ#v=onepage&amp;amp;q=how%20does%20ldl%20enter%20an%20endothelial%20cell%3F&amp;amp;f=false&quot; rel=&quot;noreferrer&quot;&gt;Mera, Steven L. Understanding Disease: Pathology and Prevention.&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19592615&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/19592615&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nrmicro/journal/v8/n2/fig_tab/nrmicro2269_F1.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.nature.com/nrmicro/journal/v8/n2/fig_tab/nrmicro2269_F1.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Libby, P (2006). &quot;Inflammation and cardiovascular disease mechanisms&quot;. American Journal of Clinical Nutrition. 83(suppl) (2): 456S–460S. 994471841.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.medscape.org/viewarticle/582014&quot; rel=&quot;noreferrer&quot;&gt;http://www.medscape.org/viewarticle/582014&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://atvb.ahajournals.org/content/23/9/1488.full#ref-16&quot; rel=&quot;noreferrer&quot;&gt;http://atvb.ahajournals.org/content/23/9/1488.full#ref-16&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11631" LastEditorUserId="11631" LastEditDate="2015-01-14T02:07:33.093" LastActivityDate="2015-01-14T02:07:33.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27660" PostTypeId="2" ParentId="27648" CreationDate="2015-01-14T03:56:06.097" Score="3" Body="&lt;p&gt;I'm going to work this from the angle of power the animals could produce for an extended (e.g. 1 hour) time. I'll assume that a lion produces power somewhere between that of a human and a horse, since the typical weight of a lion &lt;a href=&quot;https://en.wikipedia.org/wiki/Lion&quot; rel=&quot;nofollow&quot;&gt;(180 kg/400 lb-ish for males)&lt;/a&gt; is between that of a human &lt;a href=&quot;https://en.wikipedia.org/wiki/Body_weight&quot; rel=&quot;nofollow&quot;&gt;(80 kg/180 lb-ish for males)&lt;/a&gt; and a horse &lt;a href=&quot;https://en.wikipedia.org/wiki/Horse#Size_and_measurement&quot; rel=&quot;nofollow&quot;&gt;(850 kg/1800 lb-ish for draft horses)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Human: &lt;a href=&quot;https://en.wikipedia.org/wiki/Human_power&quot; rel=&quot;nofollow&quot;&gt;100 W&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Horse: &lt;a href=&quot;https://en.wikipedia.org/wiki/Horsepower&quot; rel=&quot;nofollow&quot;&gt;746 W&lt;/a&gt; (&quot;1 horsepower&quot;, or 746 W, is based off of how much work a draft horse can do for an extended period of time)&lt;/li&gt;&#xA;&lt;li&gt;Lion: 200 W?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So you would need 3.8×10&lt;sup&gt;26&lt;/sup&gt;/200, or 1.9×10&lt;sup&gt;24&lt;/sup&gt; lions. That's not a trillion, but about 2 trillion &lt;em&gt;trillion&lt;/em&gt; lions. The exact amount of power produced won't change this too drastically, e.g. if our lions produce 800 W instead, it'd be 475 billion trillion lions.&lt;/p&gt;&#xA;" OwnerUserId="6664" LastEditorUserId="6664" LastEditDate="2015-01-14T13:18:11.657" LastActivityDate="2015-01-14T13:18:11.657" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27661" PostTypeId="2" ParentId="27626" CreationDate="2015-01-14T04:13:03.823" Score="1" Body="&lt;p&gt;Yes.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The research team, led by the Durham Centre for Crop Improvement Technology, and including experts at the University of Nottingham, Rothamsted Research and the University of Warwick, have discovered that plants have the natural ability to regulate their growth independently of Gibberellin, particularly during times of environmental stress.&lt;/p&gt;&#xA;&lt;p&gt;They found that plants produce a modifier protein, called SUMO that interacts with the growth repressing proteins.&lt;/p&gt;&#xA;&lt;p&gt;The researchers believe that by modifying the interaction between the modifier protein and the repressor proteins they can remove the brakes from plant growth, leading to higher yields, even when plants are experiencing stress.&lt;a href=&quot;https://www.dur.ac.uk/news/newsitem/?itemno=19764&quot; rel=&quot;nofollow noreferrer&quot;&gt;[1]&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Bacterization is the process by which bacteria applied to the soil and plant parts. Under certain conditions yields were able to increase 10 to 13 percent. However, not all results were able to be reproduced so this is something you can look into more as well. &lt;a href=&quot;https://ucanr.edu/repositoryfiles/ca3311p15-62691.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;[2]&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Another option is to artificial increase the amount of CO&lt;span class=&quot;math-container&quot;&gt;$_2$&lt;/span&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Over the years there have been numerous laboratory experiments which conclude that increases levels of CO2 result in increased plant growth no matter how that plant growth is quantified. Sylvan Wittwer in Food, Climate and Carbon Dioxide tabulates the results. &lt;a href=&quot;http://www.sjsu.edu/faculty/watkins/CO2plants.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;[3]&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Lastly, you can look into genetically modified organisms (GMOs) which is a hotly debated topic.&lt;/p&gt;&#xA;&lt;p&gt;With a Google search, you will see that that there are numerous articles on methods to increase plant growth, to numerous for me to give a blurb about them all. Therefore, I linked a few that seems promising as well as interesting.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-01-14T04:13:03.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27662" PostTypeId="1" CreationDate="2015-01-14T04:26:39.003" Score="14" ViewCount="7898" Body="&lt;p&gt;What is the smallest sound duration that the human can hear? In other words, what is the lower duration limit for a sound to be translated into electrical signals by the ear?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose the human ear can discern or distinguish between 18 kHz and 20 kHz sounds, this would mean that, if a single wave could  be processed at 20 KHz, the sound duration would be 1 / (20KHz) = 0.00005 second, which would be next to incredible (and probably impossible).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am particularly interested in the lower duration limit as depending on frequency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am expecting something like this (I am not sure)&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; Freq   Duration needed to be aware of the sound&#xA; 20KHz  0.05S (50 mS)&#xA; 10KHz  0.04S (40 mS)&#xA;  5KHz  0.03S (30 mS)&#xA;2.5KHZ  0.02S (20 mS)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="13003" LastEditorUserId="9943" LastEditDate="2015-01-14T13:47:05.180" LastActivityDate="2017-09-28T09:03:57.507" Title="What is the human ear's temporal resolution?" Tags="&lt;human-biology&gt;&lt;hearing&gt;&lt;human-ear&gt;" AnswerCount="2" CommentCount="10" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27663" PostTypeId="2" ParentId="27662" CreationDate="2015-01-14T04:46:33.013" Score="-2" Body="&lt;p&gt;The average human auditory range is between $20$ Hz to $20$ kHz &lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/sound/earsens.html&quot; rel=&quot;nofollow&quot;&gt;[1]&lt;/a&gt;. How this relates to time is by the definition of frequency.&#xA;$$&#xA;f = \frac{1}{\text{time in sec}} = \frac{\omega}{2\pi}&#xA;$$&#xA;where $\omega$ is angular frequency. So if a human can hear a sound frequency of $18$ kHz, then &#xA;$$&#xA;(18\cdot 1000)^{-1} = 0.000056\text{ sec}&#xA;$$&#xA;where $18$ kHz is $18000$ Hz.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Abel (1972) reported duration DLs ranging from approximately 0.4 to 80ms for stimulus durations of 0.2 and 1000 ms, respectively. The lowest frequency on average is $20$ kHz but all people are different and some people may hear at a lower frequency.[1]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;A different type of auditory temporal resolution can be assessed by measuring the minimum detectable duration of a gap in a continuous sound. The gap detection is in the order of 2 to 3 ms for tones at moderate and high sound&#xA;  pressure levels (Exner, 1875; Ostroff et al., 2003; Plomp, 1964). Zwicker and Feldtkeller (1967) reported values of 1.5 ms and 5.0 ms for gap detection in tonal signals and noise, respectively.[1]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.usaarl.army.mil/publications/HMD_Book09/files/Section%2019%20-%20Chapter%2011%20Auditory%20Perception%20and%20Cognitive%20Performance.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.usaarl.army.mil/publications/HMD_Book09/files/Section%2019%20-%20Chapter%2011%20Auditory%20Perception%20and%20Cognitive%20Performance.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-01-14T05:45:40.107" LastActivityDate="2015-01-14T05:45:40.107" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="27667" PostTypeId="2" ParentId="21467" CreationDate="2015-01-14T09:13:36.147" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;epitope in immunomic microarray DNA microarrays measure one response&#xA;  value for each gene per sample; that is, mRNA concentration produced&#xA;  by the gene but a single epitope can generate different response&#xA;  values corresponding to different epitopes in peptide–MHC chips.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The excerpt looks grammatically incorrect and is therefore confusing. I guess what it tries to convey is — like there can be several probes for a single mRNA in a normal gene-expression microarray, there can be several antibodies binding to different epitopes in the same protein. Different antibodies will bind to their cognate epitopes with different affinities. This is what is referred to as &quot;response value&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By quality I guess what the authors mean is that for the same epitope it is possible to quantify the binding interactions between that epitope and antibodies of different classes (but same antigen binding site). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having looked at this excerpt, I would not recommend this book to anyone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also have a look at these two articles:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ploscompbiol.org/article/metrics/info:doi/10.1371/journal.pcbi.0020081&quot; rel=&quot;nofollow&quot;&gt;From Functional Genomics to Functional Immunomics: New Challenges, Old Problems, Big Rewards&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev-micro-090110-102922&quot; rel=&quot;nofollow&quot;&gt;Prospects for the Future Using Genomics and Proteomics in Clinical Microbiology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-01-15T05:54:21.560" LastActivityDate="2015-01-15T05:54:21.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27668" PostTypeId="2" ParentId="23558" CreationDate="2015-01-14T09:44:49.933" Score="3" Body="&lt;p&gt;There are many other methods that are used for transfecting cells in culture. These include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Cationic lipid mediated (as mentioned by user137)&lt;/li&gt;&#xA;&lt;li&gt;Calcium Phosphate mediated transfection&lt;/li&gt;&#xA;&lt;li&gt;Biolistic methods&lt;/li&gt;&#xA;&lt;li&gt;Electroporation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Newer techniques include optical transfection (using lasers to bore a hole through membrane) and impalefection (using nanotubes). &lt;a href=&quot;http://en.wikipedia.org/wiki/Transfection&quot; rel=&quot;nofollow&quot;&gt;Wikipedia page&lt;/a&gt; on transfection nicely summarizes these techniques.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Induced pluripotent stem cells can be cultured from a patient, transformed using the plasmid and transplanted back to the tissue where it can replace the old cells with &quot;corrected&quot; cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is another somewhat recent technique called &lt;a href=&quot;http://dx.doi.org/10.3791/2847&quot; rel=&quot;nofollow&quot;&gt;in-vivo electroporation&lt;/a&gt; using which Nucleic Acid can be delivered directly in to the desired tissue. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, to fix a mutation or introduce a transgene, just transfection is not enough; you have to make sure that the desired gene is inserted in the chromosome at the right location. Faulty gene can be replaced by the transfected functional gene via homologous recombination(HR), but rates of recombination are generally very low. Targeted gene insertion methods using genome editing tools such as Zinc-Finger Nuclease (ZFN), TALEN, and Crispr-Cas can increase this rate by introducing a break in the DNA at that region; this causes DNA repair systems to &quot;repair&quot; the break using HR.&#xA;&lt;br&gt;There is another type of DNA repair system called NHEJ (Non-Homologous End Joining), and this is not what we are interested in. NHEJ can, in fact cause mutation through indels. Presence of the transfected DNA would shift the preference towards HR, however it has also been shown that different stages of cell cycle have different preference towards HR and NHEJ (cant find the reference as of now but I am sure about it because I was thinking at some point of time, to work on this). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having said that, I would add that it is essential to screen the cells to see if the gene is incorporated or not. If some optimal protocol is devised then one can proceed to in-vivo electroporation.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-01-15T04:33:53.343" LastActivityDate="2015-01-15T04:33:53.343" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="27669" PostTypeId="2" ParentId="21183" CreationDate="2015-01-14T09:44:50.653" Score="3" Body="&lt;p&gt;The paper &quot;&lt;a href=&quot;http://www.directupload.net/file/d/3867/8ikapqur_pdf.htm&quot; rel=&quot;nofollow&quot;&gt;Modified method for combined DNA and RNA isolation from peanut and other oil seeds.&lt;/a&gt;&quot; has a nice protocol for isolating DNA and RNA (which later can either be differentially digested or precipitated) from oil seeds for PCR. You can find the complete paper in the link above, the materials and methods sections says the following for the extraction method:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;RNA and DNA isolation&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Approximately 1–1.2 g of dried seed of each genotype was utilized in&#xA;  extraction. Seeds were frozen with liquid nitrogen and pulverized by&#xA;  grinding with mortar and pestle until a fine powder. Tissue was placed&#xA;  into 10 mL solution I (100 mM Tris, 150 mM LiCl, 50 mM EDTA, 1.5 %&#xA;  SDS, 2 % PVP-40, 1.5 % b-mercaptoethanol) buffer, pH 7.5, and mixed&#xA;  thoroughly by vortexing or inversion. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;To the homogenized tissue, a 5&#xA;  mL acid phenol, pH 4.3 (Fisher Scientific, Pittsburg, PA) was added&#xA;  and tissue was mixed thorough for 5 min, followed by the addition of 5&#xA;  mL chloroform:isoamyl alcohol (24:1) and mixed for an additional 5&#xA;  min. The homogenate was centrifuged for 10 min and the upper aqueous&#xA;  layer (around 9 mL) was transferred to a fresh 40 mL tube containing 9&#xA;  mL of solution II (2 M guanidinium thiocyanate, 0.5 M sodium citrate,&#xA;  1.5 M ammonium acetate, 1 % N-lauroylsarcosine) buffer, pH 5.2, mixed by gentle inversion, and allowed to incubate for 10 min at room&#xA;  temperature. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;After incubation, a 4.5 mL phenol:chloroform:isoamyl&#xA;  alcohol (25:24:1), pH 6.7 was added, mixed thoroughly for 5 min,&#xA;  centrifuged for 10 min at 13,000g, and the aqueous layer (around 16&#xA;  mL) was transferred to a new 40 mL tube. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;To the transferred solution,&#xA;  9 mL 1.2 M NaCl and 9 mL isopropanol were added, mixed, placed on ice&#xA;  for at least 1 h, and centrifuged for 15 min at 13,000g. The liquid&#xA;  was discarded and the resulting pellet was washed with 2 mL cold 70 %&#xA;  ethanol, dried, and resuspended in 4 mL RNase-free water. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;4 mL 4 M&#xA;  LiCl was added, mixed, placed on ice in the refrigerator for at least&#xA;  1 h, and centrifuged for 15 min at 4°C at 13,000g. The supernatant&#xA;  (around 8 mL) was transferred to a new 40 mL tube for DNA isolation&#xA;  and the pellet was retained for RNA isolation. For RNA isolation, the&#xA;  pellet was washed with 2 mL ice-cold 70 % ethanol, dried, and&#xA;  resuspended in 750 lL RNase-free water. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;For DNA isolation, 8 mL&#xA;  isopropanol was added to the transferred supernatant tube, mixed well,&#xA;  centrifuged for 5 min, discarded the liquid, washed pellet with 2 mL&#xA;  ice-cold 70 % ethanol, dried, and resulting pellet was resuspended in&#xA;  500 lL 10 mMTris, pH7.5. The amount of DNA or RNA was determined using&#xA;  Nanodrop 2000c spectrophotometer (Thermo Scientific, Wilmington, DE).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-01-14T09:44:50.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27670" PostTypeId="1" AcceptedAnswerId="27709" CreationDate="2015-01-14T10:30:24.317" Score="4" ViewCount="544" Body="&lt;p&gt;I could find a way which could find it by body oxygen consumption and there is another way to measure it by injecting drugs — measuring cardiac output by the so-called “indicator dilution method,” a small amount of indicator, such as a dye, is injected into a large systemic vein or, preferably,into the right atrium.&#xA;I read about it but didn't understand it very well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you explain it and Which one is mostly used in clinics to measure cardiac output?&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorUserId="3340" LastEditDate="2015-01-14T15:58:55.270" LastActivityDate="2015-02-18T13:06:22.120" Title="How can we measure cardiac output?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;&lt;heart-output&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27672" PostTypeId="2" ParentId="27662" CreationDate="2015-01-14T12:00:12.480" Score="10" Body="&lt;p&gt;I will provide an answer in 2 parts. The first part is a theoretical approach based on the absolute possible minimum (my original answer). The second part focuses on experiments in the peripheral auditory system (added edited answer).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;PART I: Absolute theoretical minimum (original answer)&lt;/strong&gt;&#xA;As you inquire about electrical signals in the auditory human system I have to say that electrophysiological data at such a fundamental level is scarce in humans. That having said, we can start off by looking at &lt;strong&gt;auditory clicks&lt;/strong&gt;, which are generally the shortest possible well-defined auditory stimuli. The shortest auditory click I was able to find, and which was used in a psychophysical context (i.e., audible to a human) was &lt;strong&gt;10 microseconds&lt;/strong&gt; (&lt;a href=&quot;http://scitation.aip.org/content/asa/journal/jasa/49/2B/10.1121/1.1912374&quot; rel=&quot;nofollow noreferrer&quot;&gt;Leshowitz, 1971&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, (1) assuming 10 microseconds is the lower duration limit of a click (it may well be lower), and (2) assuming this click duration is representative of the lower limit of a tonal burst duration limit (it may well not be), and (3) assuming you indeed wish to know about/use auditory tones and not clicks, and finally (4) assuming we need at least one wavelength of a tone to fit in this window, then we could present a frequency of 100 kHz, or higher. As 20 kHz is the upper frequency limit of the human ear, we would need at &lt;strong&gt;least 50 microseconds&lt;/strong&gt; for one wavelength, i.e., basically what @Dustin concluded, but it does not end here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Frequency splatter&lt;/em&gt; (&lt;a href=&quot;http://www.math.tau.ac.il/~hezy/papers/j28.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fishbach et al., 2001&lt;/a&gt;) limits the lower limit of tonal stimuli. To prevent spectral splatter one needs to incorporate rise and fall times (ramps) onto the tonal stimulus. Hence, again assuming you do want tonal stimuli, an onset and offset ramp of one wavelength each would be advisable (at the very least) and hence 3 wavelengths are needed, increasing the duration of a 20 kHz tone to 3 wavelengths, i.e., &lt;strong&gt;150 microseconds&lt;/strong&gt; (spectral splatter may not be prevented, but at least reduced).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On top of this theoretical approach, it has to be noted that I started off with taking a click as a starting point. A click, being an impulse signal, basically stimulates the entire cochlea (the inner ear), and hence represents the most powerful auditory stimulus. Pure-tone bursts are, as a consequence, weak stimuli as they stimulate a small proportion of the available hair cells. High sound levels may therefore be necessary for short tonal stimuli, in turn degrading the frequency resolution in the cochlea as excitation spreads away from the characteristic frequencies. Mostly, several milliseconds are used as tone bursts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, taking 20 khz is kind of an upper limit, and many folks are not even able to hear 16 khz. An upper limit of, say, 12 kHz would be advisable when grownups are used. This means a wavelength of 83 microseconds and for 3 wavelengths (for ramp times) that means &lt;strong&gt;250 microseconds&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If lower frequencies are needed, this number would increase further.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT: PART II. Phsyiological experiments.&lt;/strong&gt;&#xA;As you are also interested in electrical signals, we might take another approach and start looking at experimental (animal) data. The temporal limits of the auditory system are generally assumed to reside in the ribbon synapse that is situated between the inner hair cells and the auditory nerve fiber (&lt;a href=&quot;http://www.nature.com/nature/journal/v444/n7122/fig_tab/4441013a_F1.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Parsons, 2006&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/S4hZg.jpg&quot; alt=&quot;RibonSynapse&quot;&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This synapse is considered to be the limiting factor in the temporal characteristics of the auditory system (&lt;a href=&quot;http://www.nature.com/nature/journal/v434/n7035/abs/nature03418.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Khimich, 2005&lt;/a&gt;). By analyzing this synapse using very short tone bursts, it was shown that the vesicles of glutamate (the neurotransmitter activating the auditory nerve fibers that lead the signal to the brain) were released as shortly as &lt;strong&gt;2 ms after tone onset&lt;/strong&gt;. Tone bursts were 8 - 16 kHz, 10 ms plateau, 1 ms&#xA;rise/fall (&lt;a href=&quot;http://www.nature.com/nature/journal/v434/n7035/abs/nature03418.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Khimich, 2005&lt;/a&gt;). Note the tone burstduration and rise fall times mentioned in answer PART I. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed, when first spike times in auditory nerve fibers were determined, spikes with the shortest latency occurred just under 2 ms (&lt;a href=&quot;http://jn.physiology.org/content/78/5/2438.long#F12&quot; rel=&quot;nofollow noreferrer&quot;&gt;Heil and Irvine, 1997&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eoO3y.gif&quot; alt=&quot;First spike times&quot;&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;SR in the figure means spike rate, showing that higher spike rates are accompanied by shorter latencies. A1 means auditory cortex neurons, which obviously have longer latencies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Hence, from these experiments I dare say that 2 ms would be sufficient to elicit at least one spike.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why then leave part I of the answer? The problem is that the experimental data do not show that a spike wouldn't have been generated at shorter stimuli. The data merely show that with an ongoing stimulus the first spike appears at 2 ms. It does not show whether &lt;strong&gt;2 ms of temporal summation&lt;/strong&gt; is necessary, and that is why I have left part I of my answer in place, as a theoretical lower bound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note: the spike rates are highly dependent on loudness levels. Lower sound levels result in longer latencies. Specificaly, acceleration of the stereocilia on the inner hair cells in the cochlea is the primary parameter. The faster the cilia move, the faster the spike response.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://jn.physiology.org/content/78/5/2438.long#F12&quot; rel=&quot;nofollow noreferrer&quot;&gt;Heil &amp;amp; Irvine. J Physiol 1997; 78:2438-54&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.math.tau.ac.il/~hezy/papers/j28.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fishbach et al. J Neurophysiol 2001; 85:2303-23&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.nature.com/nature/journal/v434/n7035/abs/nature03418.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Khimich et al. Nature 2005; 434:889-94&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://scitation.aip.org/content/asa/journal/jasa/49/2B/10.1121/1.1912374&quot; rel=&quot;nofollow noreferrer&quot;&gt;Leshowitz et al. J Acoust Soc Am 1971; 49, Suppl 2:462-6&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;https://i.stack.imgur.com/S4hZg.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Parsons. Nature 2006; 444:1013-4&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2017-09-28T09:03:57.507" LastActivityDate="2017-09-28T09:03:57.507" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27673" PostTypeId="2" ParentId="23406" CreationDate="2015-01-14T13:16:19.287" Score="1" Body="&lt;p&gt;Plant meiosis gives rise to four megaspores but usually upto three of them die by apoptosis leaving only one megaspore. But they are symmetric and three of them need not die all the time as it seems &lt;sup&gt;[&lt;a href=&quot;http://dx.doi.org/10.1530/rep.1.00306&quot; rel=&quot;nofollow&quot;&gt;REF&lt;/a&gt;]&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plasmodium being a haploid organism undergoes meiosis after fusion of gametocytes. Sexual differentiation is initiated at some point during the merozoite stage (See &lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052480&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and also the cross references).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chlamydomonas is also haploid during its vegetative phase, and produces four flagellated haploid gametocytes. Sexual differentiation is apparently stochastic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps there are more examples of organisms that do not undergo asymmetric division as seen in metazoa. There may be some stochastic asymmetry which leads to differentiation of sexes in the haploid unicellular eukaryotes and apoptosis in plant megaspores; these stochastic events may happen later as well. For plasmodium this is not really known; others I am not sure of.  &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-09-18T05:48:27.680" LastActivityDate="2015-09-18T05:48:27.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27674" PostTypeId="2" ParentId="24350" CreationDate="2015-01-14T13:22:12.133" Score="1" Body="&lt;p&gt;In some cases yes — when there is a mutation in apoptotic regulators such as Bcl2 family of proteins. In other cases it is difficult to identify and only identification is that those cells are growing rapidly; in other words failure to undergo apoptosis is not the cause but the effect of the cancerous transformation (as in case of p53, Ras, Myc mutations etc). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-01-14T13:22:12.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27676" PostTypeId="1" CreationDate="2015-01-14T14:09:01.143" Score="0" ViewCount="119" Body="&lt;ol&gt;&#xA;&lt;li&gt;Is the molecule nitric oxide responsible for healing blood vessels?&lt;/li&gt;&#xA;&lt;li&gt;How does nitric oxide heal the blood vessels?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I watched a documentary about the healing effects of nitric oxide. In the video I saw a cardiologist show an X-ray picture of one of his damaged heart blood vessels, and then another X-ray picture showing the same heart blood vessel completely healed. He claimed it was due to a radical change in his diet of consuming lots of nitrogen rich vegetables which the body in turn converted to nitric oxide. Is this possible?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources : &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The original source was the youtube video Forks Over Knifes, however it was recently taken down. I have provide the following links which provide a little bit of information :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.happyhealthylonglife.com/happy_healthy_long_life/2010/06/esselstyn-session.html&quot; rel=&quot;nofollow&quot;&gt;http://www.happyhealthylonglife.com/happy_healthy_long_life/2010/06/esselstyn-session.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.happyhealthylonglife.com/happy_healthy_long_life/2010/12/no.html&quot; rel=&quot;nofollow&quot;&gt;http://www.happyhealthylonglife.com/happy_healthy_long_life/2010/12/no.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dr. Caldwell Esselstyn was the one who made the statement about heart health and nitric oxide, also showing the xray pictures of one of his colleague cardiologists in the documentary.&lt;/p&gt;&#xA;" OwnerUserId="9107" LastEditorUserId="9107" LastEditDate="2015-01-14T17:23:51.177" LastActivityDate="2018-06-15T12:47:26.813" Title="Is the molecule nitric oxide responsible for healing blood vessels?" Tags="&lt;cardiology&gt;&lt;blood-circulation&gt;&lt;health&gt;&lt;blood-pressure&gt;&lt;healing&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27677" PostTypeId="1" CreationDate="2015-01-14T14:20:32.117" Score="5" ViewCount="55" Body="&lt;p&gt;Well i was flying kites today I saw a tree and its branches were spread around in random directions... I would like to know that how do these trees know to nourish their branches in some direction so as it doesn't fall off due to gravity. I know it can get its strength from the roots inside the soil so that it does not fall. But if this strength were not enough the tree may fall due to weight of its own branches. Can this happen??&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am new to this site I don't know much about the rules here. Feel free to edit if I have done any mistakes(especially about tags)&lt;/p&gt;&#xA;" OwnerUserId="13013" LastEditorUserId="3340" LastEditDate="2015-01-14T14:59:02.487" LastActivityDate="2015-01-14T14:59:02.487" Title="How does trees know to balance themselves so that they never fall down" Tags="&lt;botany&gt;&lt;plant-anatomy&gt;&lt;bio-mechanics&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2015-01-14T21:20:23.680" ContentLicense="CC BY-SA 3.0" />
  <row Id="27678" PostTypeId="1" CreationDate="2015-01-14T14:34:18.913" Score="4" ViewCount="596" Body="&lt;p&gt;The size of the phase 1 notch varies among cardiac cells. It is prominent in myocytes in the&#xA;epicardial and midmyocardial regions of the left ventricular wall  and in ventricular Purkinje fibers. However, the notch is negligible in myocytes from the endocardial region of the left ventricle.&#xA;What's the reason?&lt;/p&gt;&#xA;" OwnerDisplayName="user13010" LastEditorDisplayName="user12874" LastEditDate="2015-01-14T15:16:38.897" LastActivityDate="2015-01-15T11:50:19.973" Title="Why do the size of the phase 1 notch vary among cardiac cells?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27679" PostTypeId="2" ParentId="21687" CreationDate="2015-01-14T15:33:09.027" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Alloy&quot; rel=&quot;nofollow&quot;&gt;Alloys&lt;/a&gt; have completely different chemical properties than their component elements. Elemental mercury is liquid, and is toxic, but when alloyed into &lt;a href=&quot;http://en.wikipedia.org/wiki/Amalgam_%28chemistry%29&quot; rel=&quot;nofollow&quot;&gt;amalgam&lt;/a&gt; with silver, tin, and some other elements it is perfectly safe, and has been &lt;a href=&quot;http://en.wikipedia.org/wiki/Amalgam_%28dentistry%29&quot; rel=&quot;nofollow&quot;&gt;used&lt;/a&gt; in dental fillings for a &lt;a href=&quot;http://en.wikipedia.org/wiki/Amalgam_%28dentistry%29#History_of_use&quot; rel=&quot;nofollow&quot;&gt;very long time&lt;/a&gt; with no negative effects. The same is true of cobalt and chromium alloys - they are chemically bonded to the other elements in the alloy, making a new molecule, and cannot &quot;leach out&quot; without the chemical bonds being broken, which cannot happen in the mouth or at standard cooking temperatures. Hence, they are safe for food prep and for fillings/implants.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-01-14T15:33:09.027" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="27681" PostTypeId="1" AcceptedAnswerId="27743" CreationDate="2015-01-14T15:53:06.257" Score="8" ViewCount="14227" Body="&lt;p&gt;Why do persons with &lt;a href=&quot;http://en.wikipedia.org/wiki/Turner_syndrome&quot; rel=&quot;noreferrer&quot;&gt;Turner syndrome&lt;/a&gt; have  developmental abnormalities, when normal XX-females do not, even though they only have 1 active X chromosome? From what I know, one X-chromosome is inactivated into a Barr body in normal XX-females, but these obviously don't show the symptoms of Turner syndrome. What function does the inactive chromosome have?&lt;/p&gt;&#xA;" OwnerUserId="8834" LastEditorUserId="3624" LastEditDate="2015-01-16T23:22:29.017" LastActivityDate="2015-01-16T23:22:29.017" Title="What effect does the Barr body have, in relation to female Turner syndrome?" Tags="&lt;human-biology&gt;&lt;human-genetics&gt;&lt;chromosome&gt;&lt;sex-chromosome&gt;&lt;dosage-compensation&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27683" PostTypeId="1" AcceptedAnswerId="27700" CreationDate="2015-01-14T16:43:54.777" Score="6" ViewCount="2429" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/aHamW.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this image while reading optical instruments in physics. If we look at the uncorrected rays, we see that the image they outline gets inverted. So why don't people with myopic vision see images as inverted representations?&lt;/p&gt;&#xA;" OwnerUserId="12872" LastEditorUserId="9943" LastEditDate="2015-01-15T01:48:16.347" LastActivityDate="2016-11-24T20:57:44.797" Title="Why don't myopic people see the world upside-down?" Tags="&lt;vision&gt;&lt;human-eye&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27684" PostTypeId="2" ParentId="27546" CreationDate="2015-01-14T17:01:25.610" Score="2" Body="&lt;p&gt;When haemoglobin takes on oxygen the colour will shift from blue to red. the reason for this is a change in orientation of the Nitrogen ligans of the haemoglobin molecule.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The red cells pass through the veins in the lung(s) to the aevioli; the blue haem (pH~7.2) exchanges CO2 for O2 (now pH~7.4) 98% saturation and goes from blue to red.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We see the colour(s) because the haemoglobin's Fe in the centre of the ring goes in and out of plane to the ring. The colour comes for this phenomenon due to the 4 Nitrogen atoms and the electron states that exist without and with oxygen. This takes place within about 12milliseconds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="13017" LastActivityDate="2015-01-14T17:01:25.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27685" PostTypeId="1" AcceptedAnswerId="55857" CreationDate="2015-01-14T17:31:14.447" Score="2" ViewCount="1163" Body="&lt;p&gt;I see that myofibrils (muscle cells) contain not one, but multiple nuclei.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Why is this so?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Do all the nuclei participate in cell division?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9906" LastActivityDate="2017-02-02T00:07:08.690" Title="Why do some cells like myofibrils have multiple nuclei?" Tags="&lt;cell-biology&gt;&lt;dna&gt;&lt;muscles&gt;&lt;mitosis&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27686" PostTypeId="1" AcceptedAnswerId="27689" CreationDate="2015-01-14T18:23:10.140" Score="4" ViewCount="539" Body="&lt;p&gt;We mostly can defibrillate the heart before 1 min of ventricular fibrillation by electroshock.Then we often can't do defibrillate it with electroshock.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the reason and What's the best way to defibrillate heart within 1 min after ventricular fibrillation?&lt;/p&gt;&#xA;" OwnerDisplayName="user13018" LastEditorUserId="9943" LastEditDate="2015-01-15T12:59:28.557" LastActivityDate="2015-01-15T12:59:28.557" Title="Why can't we defibrillate the heart within 1 minute after ventricular fibrillation by electroshock?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27687" PostTypeId="2" ParentId="27685" CreationDate="2015-01-14T18:32:35.397" Score="1" Body="&lt;p&gt;In the case of myofibrils this is the case because of the syncytial nature of that given structure. It means that in developing muscle tissue after a certain stage the cell divisions become somewhat different in that the final step, being separation of the daughter cells via invagination of cell membranes, does not happen. The nuclei though keep dividing after that. In the end what we have is a big membrane coated structure (basically a cell), with lots of nuclei in it.&lt;/p&gt;&#xA;" OwnerUserId="9638" LastActivityDate="2015-01-14T18:32:35.397" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27688" PostTypeId="2" ParentId="27647" CreationDate="2015-01-14T18:47:02.117" Score="1" Body="&lt;p&gt;The already given answers are correct, but I think explaining basic metabolism does not answer the problem of how big organisms can grow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The argument about metazoan body size and the growing athmospheric O2 levels is that this latter process makes the diffusion of oxygen through animal tissue faster (because of the growing partial pressure of O2). This, in turn, made it possible for metazoans, which at the time had no elaborate body structures and no developed respiratory apparatuses, to actually &lt;em&gt;grow&lt;/em&gt; larger, since it was possible for cells further away from the surface of an organism to respirate as well. Or, to put it differently, cell masses could grow bigger without risking anoxy in deeper parts of the tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem with plants is not a very easy one to tackle, and I don't think there's a clear answer to this based on current knowledge. One must experiment with this and see what happens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My guess is that the response of a plant lineage to grown O2 levels would be very dependent on the exact habitat the plant lives in, since for an evolutionary change to happen fast, there must be a clear evolutionary-ecological adaptive value it provides, and that is very dependent on environmental givens. Also, in recent (current) plants, respiration is a solved problem, so I'm not sure a plant would benefit in any way from elevated O2 levels. It would surely affect the working of RuBisCO as mentioned. Maybe an immediate response would be the spread of C4 metabolism within plants.&lt;/p&gt;&#xA;" OwnerUserId="9638" LastEditorUserId="9638" LastEditDate="2015-01-14T18:52:12.057" LastActivityDate="2015-01-14T18:52:12.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27689" PostTypeId="2" ParentId="27686" CreationDate="2015-01-14T18:54:02.950" Score="4" Body="&lt;p&gt;Unless defibrillated within 1 minute after fibrillation begins, the heart is usually too weak to be revived by defibrillation because of the lack of nutrition from coronary blood flow. However, it is still possible to revive the heart by preliminarily pumping the heart by hand (intermittent hand squeezing) and then defibrillating the heart later. In this way, small quantities of blood are delivered into the aorta and a renewed coronary blood supply develops. Then, after a few minutes of hand pumping, electrical defibrillation often becomes possible. Indeed, fibrillating hearts have been pumped by hand for as long as 90 minutes followed by successful defibrillation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A technique for pumping the heart without opening the chest consists of intermittent thrusts of pressure on the chest wall along with artificial respiration. This, plus defibrillation, is called cardiopulmonary resuscitation, or CPR.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lack of blood flow to the brain for more than 5 to 8 minutes usually causes permanent mental impairment&#xA;or even destruction of brain tissue. Even if the heart is revived, the person may die from the effects of&#xA;brain damage or may live with permanent mental impairment.&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastActivityDate="2015-01-14T18:54:02.950" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27690" PostTypeId="2" ParentId="27681" CreationDate="2015-01-14T19:15:21.557" Score="1" Body="&lt;p&gt;Very interesting question!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And I don't think either that the linked Wikipedia article answers the question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately I do not know the answer for sure, but I might have some relevant information to add. So, from my studies I know that Barr-bodies are not totally inactive, they, in fact, do have some very limited transcriptional activity. It might be low in intensity, but still vital? I'm just guessing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My other guess is linked to the development of a Barr-body in a cell with two active XX chromosomes early during fetal development. So this happens via a process called X-inactivation in which a gene called Xist becomes active on both X chromosomes, then another gene, the Tsix also becomes active on one of the chromosomes and suppresses Xist on the other. The one with the suppressed Xist remains active, the other becomes the Barr-body (the process of selecting which chromosome becomes the Barr-body is random, hence &lt;a href=&quot;http://en.wikipedia.org/wiki/Calico_cat&quot; rel=&quot;nofollow&quot;&gt;female mosaicism&lt;/a&gt;). So, the point is, that for correct X-inactivation, the interplay of two X chromosomes are needed, and people with Turner syndrome have only one. That might be the problem, e.g. the Xist becomes active on the one X they have and starts interfering with the normal functioning of the chromosome, and there's no Tsix to suppress it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, again, I'm just making educated guesses here.&lt;/p&gt;&#xA;" OwnerUserId="9638" LastEditorUserId="9638" LastEditDate="2015-01-14T19:21:11.193" LastActivityDate="2015-01-14T19:21:11.193" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27691" PostTypeId="1" CreationDate="2015-01-14T19:15:21.463" Score="3" ViewCount="481" Body="&lt;p&gt;Are the human bones about equal in density? Or is there any published data on the mean + s.d. density for a given bone available?&lt;/p&gt;&#xA;" OwnerUserId="13019" LastActivityDate="2015-01-14T22:13:28.210" Title="Mean and standard deviation of human bone density?" Tags="&lt;bone-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27692" PostTypeId="1" AcceptedAnswerId="27745" CreationDate="2015-01-14T19:21:51.353" Score="2" ViewCount="746" Body="&lt;p&gt;Do bacteria with multiple flagella move faster than bacteria with a single flagella? Assuming the flagella are at the same length.&lt;/p&gt;&#xA;" OwnerUserId="11855" LastEditorUserId="948" LastEditDate="2015-01-14T19:22:52.197" LastActivityDate="2015-01-16T10:08:57.057" Title="Do bacteria with multiple flagella move faster than bacteria with a single flagella?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27693" PostTypeId="2" ParentId="27691" CreationDate="2015-01-14T22:13:28.210" Score="3" Body="&lt;p&gt;Interesting question that I'd not considered before.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bone density is commonly measured by assessing the bone mineral density (BMD) using dual-energy x-ray absorptiometry (DMA), literally the g/cm2 of minerals in the bone. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having had a search I can only find values for a small number of bones commonly measured when testing for osteoporosis (characterised by reduced BMD). Unsurprisingly the age and sex of the individual has a large effect on BMD; after puberty males have higher BMD (1) and during ageing this then declines, sometimes dramatically (2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These values are from a Vietnamese study (3) show that the hip and the spine are different.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Men [ mean (SD) ]&lt;/h3&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Femoral neck: 0.85 (0.13)&lt;/li&gt;&#xA;&lt;li&gt;Total hip: 1.00 (0.13)&lt;/li&gt;&#xA;&lt;li&gt;Lumbar spine: 1.05 (0.12)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h3&gt;Women  [ mean (SD) ]&lt;/h3&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Femoral neck: 0.80 (0.11)&lt;/li&gt;&#xA;&lt;li&gt;Total hip: 0.95 (0.12)&lt;/li&gt;&#xA;&lt;li&gt;Lumbar spine: 0.96 (0.11)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;There must be other reference values for other bones in different populations but I don't have time to look them up now! Good luck in your own research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found &lt;a href=&quot;http://www.niams.nih.gov/Health_Info/Bone/Bone_Health/bone_mass_measure.asp&quot; rel=&quot;nofollow&quot;&gt;this website&lt;/a&gt; by the US National Institute of Health and &lt;a href=&quot;http://whqlibdoc.who.int/trs/WHO_TRS_921.pdf&quot; rel=&quot;nofollow&quot;&gt;this PDF&lt;/a&gt; by the World Health Organisation immeasurably enlightening. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Bonjour JP, Rizzoli R. Bone acquisition in adolescence. In: Marcus R, Feldman D, Kelsey J, eds. Osteoporosis. San Diego, CA, Academic Press, 1996:465–476&lt;/li&gt;&#xA;&lt;li&gt;Cummings SR, Kelsey JL, Nevitt MC, O’Dowd KJ (1985) Epidemiology of osteoporosis and osteoporotic fractures. Epidemiol Rev 7:178–208&lt;/li&gt;&#xA;&lt;li&gt;Ho-Pham, et al. (2011) Reference Ranges for Bone Mineral Density and Prevalence of Osteoporosis in Vietnamese Men and Women. BMC Musculoskeletal Disorders, 12:182  doi:10.1186/1471-2474-12-182&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastActivityDate="2015-01-14T22:13:28.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27694" PostTypeId="1" AcceptedAnswerId="27698" CreationDate="2015-01-14T22:32:14.580" Score="5" ViewCount="617" Body="&lt;p&gt;Industrial water taps are present in most biology laboratories I have been too. There are accompanied by a sign stating &quot;do not drink&quot;. So obviously it is not a good idea to drink it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However I could not find any information or reference concerning its safety for body use. The only indication I could find is that eye wash stations are using potable water instead of industrial water, suggesting that industrial water is not suitable for eye contact - at least.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question: &lt;em&gt;is it safe to use industrial water available in labs for hand washing, multiple times per day over the course of several years?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for a precise answer about the possible long term harm of industrial water in this context, if possible with references.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/T2kyH.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="13022" LastEditorUserId="13022" LastEditDate="2015-01-14T23:26:27.233" LastActivityDate="2015-01-15T00:14:56.947" Title="Safety of using industrial water for hand washing" Tags="&lt;lab-techniques&gt;&lt;safety&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27695" PostTypeId="2" ParentId="27678" CreationDate="2015-01-14T22:48:17.150" Score="2" Body="&lt;p&gt;Between at least the endocardial and epicardial regions, I believe the transient outward current is facilitated much more in epicardial cells. &lt;a href=&quot;http://circ.ahajournals.org/content/88/6/2903.full.pdf&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; article demonstrates the differences in Ito between the two cell types in dogs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm also recommending the following article about Ito phenotypes: &quot;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.2005.086223/pdf&quot; rel=&quot;nofollow&quot;&gt;Transient outward potassium current, ‘I&lt;sub&gt;to&lt;/sub&gt;’, phenotypes&#xA;in the mammalian left ventricle: underlying molecular,&#xA;cellular and biophysical mechanisms&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="8598" LastEditDate="2015-01-15T11:50:19.973" LastActivityDate="2015-01-15T11:50:19.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27697" PostTypeId="2" ParentId="27683" CreationDate="2015-01-14T23:56:15.867" Score="4" Body="&lt;p&gt;&lt;strong&gt;Overview&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Myopia does not cause image inversion. @mgkrebbs provides an answer with a clearer diagram than the one you have provided that illustrates how only the focussing ability, not the orientation, of an object changes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, an image can be inverted by special inversion glasses. Furthermore is that the brain can convert the image to the right way around. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although myopic vision can't cause the inversion, the answer you're looking for is probably that &lt;a href=&quot;http://en.wikipedia.org/wiki/Perceptual_adaptation&quot; rel=&quot;nofollow noreferrer&quot;&gt;perceptual adaptation&lt;/a&gt;, a phenomenon that occurs to correct our vision, comes into play in cases of inversion. The brain &quot;gets used to&quot; inverted images and what you visualise becomes the correct orientation. So lets say myopia did cause inversion, the person with naturally inverted vision wouldn't experience anything unusual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Experimental Evidence&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The below text from the wikipedia entry describes an experiment with inverting glasses. These glasses contained prisms that flipped the real world image before it reached the eye. Note the experiment was carried out in the in the late 1800s.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;On a later experiment, Stratton wore the glasses for eight whole days. By day four, the images seen through the instrument were still upside down. However, on day five, images appeared upright until he concentrated on them; then they became inverted again. By having to concentrate on his vision to turn it upside down again, especially when he knew images were hitting his retinas in the opposite orientation as normal, Stratton deduced his brain had reprocessed his vision and adapted to the changes in vision.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://wexler.free.fr/library/files/linden%20(1999)%20the%20myth%20of%20upright%20vision.%20a%20psychophysical%20and%20functional%20imaging%20study%20of%20adaptation%20to%20inverting%20spectacles.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;A more recent study by Linden &lt;em&gt;et al.&lt;/em&gt;, 1999&lt;/a&gt; confirmed the same thing happening with more up to date inverting glasses. The subjects reported slightly different results. Rather than the image being inverted, it was more the case that the subject felt their reality became inverted to match the inverted image. I can't see someone suffering with myopic vision being able to make this distinction since they would only be used to one orientation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Figure 1&lt;/em&gt; from Linden &lt;em&gt;et al.&lt;/em&gt;, 1999&lt;img src=&quot;https://i.stack.imgur.com/ivmn2.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On removal of the glasses, the world becomes temporarily re-distorted, but normal vision and perception returns. &lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2015-01-15T03:33:27.647" LastActivityDate="2015-01-15T03:33:27.647" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27698" PostTypeId="2" ParentId="27694" CreationDate="2015-01-15T00:14:56.947" Score="7" Body="&lt;p&gt;The water from taps labelled &quot;Industrial Water, Do Not Drink&quot; comes from the same potable water line as domestic taps. The line should be split somewhere in the building, with the industrial line containing multiple backflow inhibitors to prevent cross contamination of potable or domestic water. Based on that fact, the water should be safe for hand washing, however, should be tested in the case of objective concern.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-01-15T00:14:56.947" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27699" PostTypeId="1" AcceptedAnswerId="27701" CreationDate="2015-01-15T02:57:51.740" Score="10" ViewCount="382" Body="&lt;p&gt;Does the peripheral nervous system have a system of routers that decide where a message is meant to go based on some kind of address, or does a signal from the brain follow a single, unbroken chain of neurons that starts at the brain and ends at one destination?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, let's say my brain wants to send a message to my left pinky, telling it to contract. In the first model, a series of action potentials travel down my spinal cord, reaching a node in my chest. The action potentials encode the &quot;contract&quot; command as well as an address. The node in my chest reads the address, and routes the signal down my left arm. It reaches my left hand, where another node reads the address and sends the signal to my left pinky, where the signal reaches the appropriate muscle, telling it to contract. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the second model, every single muscle in my body has a particular chain of neurons that runs in parallel to my brain. If my brain wants to send that signal, it doesn't have to specify an address, it just sends the &quot;contract&quot; command down the path that says &quot;Leads directly to left pinky and nowhere else&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the second model is true, does that mean that the large, visible structures that we call &quot;nerves&quot;, such as the vagus nerve, are actually bundles of point-to-point connections?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anywhere I can find more information about this would be awesome. I'm a comp sci/biochem double major, and really love reading about the body as an information system.&lt;/p&gt;&#xA;" OwnerUserId="11686" LastEditorUserId="9943" LastEditDate="2015-01-15T12:00:36.093" LastActivityDate="2015-01-15T12:10:44.193" Title="Does the nervous system have &quot;routers&quot;?" Tags="&lt;neurophysiology&gt;&lt;peripheral-nervous-system&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27700" PostTypeId="2" ParentId="27683" CreationDate="2015-01-15T03:04:56.667" Score="13" Body="&lt;p&gt;You have misinterpreted the nature of the light rays shown in the diagram in the question.  The two rays are representing light coming from the same (distant) point in the environment, that is, some small feature on an object is reflecting (or emitting) light in slightly different directions and reach the eye separated by a small amount (less than the width of the pupil).  The rays are almost, but not quite, parallel.  The two rays, coming from the same point, should be focused on the same point on the retina (as are the red rays corrected by the external lens).  The spread of the uncorrected rays in myopia or hyperopia sends them to different places of the retina, causing the image to be out of focus, not upside down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The path of light from an entire scene can be illustrated like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/frMbN.jpg&quot; alt=&quot;Moisey CC BY-SA 3.0 via commons.wikimedia.org&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As this diagram shows, the image is upside down for all of us, in focus or not.  That the image top is at the bottom of the retina is not especially important -- the cells doing the interpretation could have been located physically located anywhere as needed.&lt;/p&gt;&#xA;" OwnerUserId="231" LastEditorUserId="231" LastEditDate="2015-01-15T03:11:31.730" LastActivityDate="2015-01-15T03:11:31.730" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27701" PostTypeId="2" ParentId="27699" CreationDate="2015-01-15T03:09:01.483" Score="8" Body="&lt;p&gt;The second model is the one. No tags, flags, or routers, just a 1-to-1 system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A striking example of this is are the different effects of spinal cord injury, which depend on the place &lt;a href=&quot;http://www.apparelyzed.com/paralysis.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;where the injury occurs&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ONZ9e.jpg&quot; alt=&quot;paralysis&quot;&gt;  &lt;img src=&quot;https://i.stack.imgur.com/Plcph.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And I quote from the &lt;a href=&quot;http://www.apparelyzed.com/paralysis.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;apperalyzed website&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Spinal Cord Injury Overview&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;When a person suffers a spinal cord injury, information traveling&#xA;  along the spinal nerves below the level of injury will be either&#xA;  completely or partially cut off from the brain, resulting in&#xA;  Quadriplegia (Tetraplegia) or Paraplegia.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;[...] The brain will still be trying to send messages downwards to the&#xA;  muscles in the body, known as motor messages. These messages however,&#xA;  will be blocked by the damage in the spinal cord at the level of&#xA;  injury. Nerves joining the spinal cord above the level of injury will&#xA;  be unaffected and continue to work as normal.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Quadriplegia / Tetraplegia&lt;/strong&gt; [occurs] when a person has a spinal cord injury above &#xA;  the first thoracic vertebra. Paralysis usually affects&#xA;  the cervical spinal nerves resulting in paralysis of all four limbs.&#xA;  [...]&#xA;  &lt;strong&gt;Paraplegia&lt;/strong&gt; [occurs] when the level of spinal cord injury [is] below the first thoracic spinal nerve [and leads to] paralysis of the legs and abdomen up to the nipple line, [but] paraplegics have full use of their arms and hands&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This example shows that there are &lt;em&gt;strict one-to-one connections&lt;/em&gt; (2&lt;sup&gt;nd&lt;/sup&gt; model) and that messages are not simply flagged and routed to their destination via the shortest or quickest route available among a bunch of redundant, ill-defined pathways (1&lt;sup&gt;st&lt;/sup&gt; model). Hence, &lt;strong&gt;there is only one way from the brain to the periphery; once severed the message cannot be simple re-routed via parallel lines&lt;/strong&gt;.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example is the make-up of the sensory-motor cortex:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jloYK.jpg&quot; alt=&quot;homunculi&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The picture shows that the motor cortex (muscle control/motor output) as well the sensory cortex (sensory input) contain a complete image of the body. Each part of the motor cortex and sensory cortex is devoted to the control or sense of one specific part of the body, respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nerves are indeed typically bundles of 1-to-1 fibers. For example, the optic nerve contains fibers that carry info from one, and only one well-defined and localized pixel from the retina to the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Principles of Neuroscience by &lt;a href=&quot;http://en.wikipedia.org/wiki/Principles_of_Neural_Science&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kandel and Schwartz&lt;/a&gt; is a great book with a wealth of info. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-15T12:10:44.193" LastActivityDate="2015-01-15T12:10:44.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27702" PostTypeId="2" ParentId="26235" CreationDate="2015-01-15T03:29:22.180" Score="4" Body="&lt;p&gt;The short and unsatisfying answer is no-- it remains controversial due to lack of high quality randomized clinical trials. According to an article in UptoDate, a reliable resource for many physicians, last updated September 2014, there is an association between acne and intake of milk in which milk components could exacerbate acne. Unfortunately, there have been no randomized clinical trials on this subject. According to the same article, &quot;there is no reliable evidence that ingestion of chocolate is associated with an increased prevalence or severity of acne.&quot; In a similar light, the article continues on to say that &quot;data on favorable effects of dietary factors such as zinc, omega-3 fatty acids, antioxidants, vitamin A, and dietary fiber on acne vulgaris are limited. Further studies are necessary to determine the roles of these supplements in acne vulgaris.&quot;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.uptodate.com/contents/pathogenesis-clinical-manifestations-and-diagnosis-of-acne-vulgaris?source=search_result&amp;amp;search=acne+and+food&amp;amp;selectedTitle=1%7E150#H8&quot; rel=&quot;nofollow&quot;&gt;http://www.uptodate.com/contents/pathogenesis-clinical-manifestations-and-diagnosis-of-acne-vulgaris?source=search_result&amp;amp;search=acne+and+food&amp;amp;selectedTitle=1%7E150#H8&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11631" LastEditorUserId="11631" LastEditDate="2015-01-15T04:44:33.667" LastActivityDate="2015-01-15T04:44:33.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27704" PostTypeId="2" ParentId="27686" CreationDate="2015-01-15T05:23:57.913" Score="7" Body="&lt;p&gt;To say that there is a cutoff of one minute at which time shocking becomes ineffective is incorrect. The best way to defibrillate a heart within one minute of VFib onset is with electric shock. In fact, short of certain drugs in certain instances, it's &lt;em&gt;the only way to defibrillate Vfib, regardless of the amount of time that has passed&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the one minute cut-off were true, survival rates of out-of-hospital arrests would be more dismal than they are. Even with the availability of automated external defibrillators (AEDs) to treat out-of-hospital arrest, the collapse to response time is well over a minute. Someone has to notice a collapse, feel for a pulse, and call for a defibrillator (or get it themselves), expose the chest, apply the paddles, wait for the monitor to display the rhythm, clear the area and shock. If you were told that this usually occurs in under a minute, you were misinformed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Seattle is the best city in the US (probably the world) in which to have a heart attack.&lt;sup&gt;[1]&lt;/sup&gt; The population has a high rate of training in CPR, a highly trained corps of paramedics and EMTs, and a quick response time. So it's logical to do studies about factors affecting survival of out-of-hospital arrests in Seattle.&#xA;&lt;strong&gt;A study published in 1999 found that CPR did not have any effect on outcomes of out-of-hospital arrests unless the interval time (from arrest to defibrillation) was greater than 4 minutes&lt;/strong&gt;.&lt;sup&gt;[2]&lt;/sup&gt; (In other words, shocking without CPR was no different in outcome than shocking &lt;em&gt;preceded by&lt;/em&gt; CPR; both resulted in cardioversion to a stable rhythm and a return of of spontaneous circulation &lt;strong&gt;in the same percentage of patients&lt;/strong&gt;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, that is not to say that CPR (chest compressions +/- respirations) are unimportant. A 2003 study found an unacceptable level of CPR was performed when AED paddles were connected (i.e. there was an over-reliance on shocking).&lt;sup&gt;[3]&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The new Advanced Cardiac Life Support guidelines call for CPR to be initiated immediately, regardless of witnessed or unwitnessed arrest (i.e. down time).&lt;sup&gt;[4]&lt;/sup&gt; It needs to be noted, though, that this recommendation does not rest on defibrillation with the aim of &lt;em&gt;return of spontaneous circulation&lt;/em&gt;(ROSC), but &lt;strong&gt;on improved neurological outcomes&lt;/strong&gt;.&lt;sup&gt;[5]&lt;/sup&gt; This, not ROSC, is what the new ACLS recommendations are based on, because ACLS is not considered highly successful if the patient leaves the hospital only to be hospitalized elsewhere in a persistent vegetative state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://www.komonews.com/news/health/King-County-may-be-the-best-place-to-have-a-heart-attack-210592381.html&quot; rel=&quot;nofollow&quot;&gt;King County may be the best place to have a heart attack&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://jama.jamanetwork.com/article.aspx?articleid=189314&quot; rel=&quot;nofollow&quot;&gt;Influence of Cardiopulmonary Resuscitation Prior to Defibrillation in Patients With Out-of-Hospital Ventricular Fibrillation&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://www.annemergmed.com/article/S0196-0644%2803%2900383-4/abstract&quot; rel=&quot;nofollow&quot;&gt;Interruption of cardiopulmonary resuscitation with the use of the automated external defibrillator in out-of-hospital cardiac arrest&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[4] &lt;a href=&quot;http://acls-algorithms.com/vfpulseless-vt/&quot; rel=&quot;nofollow&quot;&gt;VF/Pulseless VT&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[5] &lt;a href=&quot;http://jama.jamanetwork.com/article.aspx?articleid=196200&quot; rel=&quot;nofollow&quot;&gt;Delaying Defibrillation to Give Basic Cardiopulmonary Resuscitation to Patients With Out-of-Hospital Ventricular Fibrillation A Randomized Trial&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-01-15T12:20:06.000" LastActivityDate="2015-01-15T12:20:06.000" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="27708" PostTypeId="2" ParentId="8079" CreationDate="2015-01-15T07:00:43.567" Score="2" Body="&lt;p&gt;An interesting question! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am attaching the picture from Boron &amp;amp; Boulpaep, Medical Physiology, 2nd Ed, p921 here to clarify the details left out in the hand drawn picture. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XUmpa.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The flow of the digestive pancreatic enzymes increase mainly during food consumption. This is brought about by a number of redundant systems. The fasting secretion of pancreatic enzymes depends on the &lt;a href=&quot;http://www.vivo.colostate.edu/hbooks/pathphys/digestion/stomach/mmcomplex.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;MMC&lt;/a&gt; (migrating motor complex). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PTGxJ.png&quot; alt=&quot;Secretion rates during 24 hour period&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bicarbonate ions are exchanged with chlorine ions in the apical membrane of the acinar cells through a Chloride Bicarbonate Exchanger. This process is driven by:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Secretin - most important humoral factor - Increases secretion&lt;/li&gt;&#xA;&lt;li&gt;ACh through muscarinic receptors - Increases secretion&lt;/li&gt;&#xA;&lt;li&gt;GRP (Gastrin Releasing Peptide) - Increases secretion&lt;/li&gt;&#xA;&lt;li&gt;Substance P - Decreases secretion&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Mechanism of action of secretin seems to be through activation of cAMP. However even small amounts of secretin which do not raise the cAMP levels measurably can stimulate bicarbonate secretion. This suggests secretin response may be by &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Unmeasurably small amount of increase in cAMP&lt;/li&gt;&#xA;&lt;li&gt;Raise in cAMP levels in localised compartments&lt;/li&gt;&#xA;&lt;li&gt;Activation of alternative second messenger pathways&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In case of GRP the second messenger is not known.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer to your question is that when secretin is secreted, the Bicarbonate-Chloride transporter is accelerated to achieve the result displayed. This mainly happens when food enters the small intestine so as to neutralize the acid permitting the digestive enzymes to function at the optimal pH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Chloride-Bicarobonate Transporter is an exchange transporter which explains why there is a sharp fall in the chloride levels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/plgk2.jpg&quot; alt=&quot;Mechanism of bicarbonate ion secretion&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-01-15T07:00:43.567" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27709" PostTypeId="2" ParentId="27670" CreationDate="2015-01-15T07:04:06.393" Score="3" Body="&lt;p&gt;Drs. Swan and Ganz developed a direct method of measuring cardiac output by thermodilution. They invented a multilumen catheter with a thermal resistor on the end (a Swan Ganz catheter) which could be advanced into the pulmonary artery. Through another lumen, a cold saline solution of known temperature and volume is injected into the right atrium. Using a computer model, the temperature of the blood at the catheter tip is used to determine stroke volume. Stroke volume x heart rate = cardiac output.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The injectate mixes with the blood as it passes through the ventricle and into the pulmonary artery, thus cooling the blood. The blood temperature is measured by a thermistor at the catheter tip, which lies within the pulmonary artery, and a computer is used to acquire the thermodilution profile; that is, the computer quantifies the change in blood temperature as it flows over the thermistor surface. The cardiac output computer then calculates flow (cardiac output from the right ventricle) using the blood temperature information, and the temperature and volume of the injectate. The injection is normally repeated a few times and the cardiac output averaged.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pLyqr.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same principle is used with a dye study but measuring the concentration of dye downstream.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although this is considered to be the &quot;gold standard&quot;, because it is so invasive and carries a serious risk of complications, it has largely been replaced by echocardiography and Doppler techniques.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0002914972906352&quot; rel=&quot;nofollow noreferrer&quot;&gt;Measurement of blood flow by thermodilution&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.cvphysiology.com/Cardiac%20Function/CF021.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Measurement of Cardiac Output&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.internationaljournalofcaringsciences.org/docs/Vol1_Issue3_02_Lavdaniti.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Invasive and non-invasive methods for cardiac output measurement&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-15T07:04:06.393" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27710" PostTypeId="2" ParentId="11090" CreationDate="2015-01-15T11:07:33.953" Score="0" Body="&lt;p&gt;I think Dawkins answers this in the book as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The point was that most strategies are not stable because the &quot;random&quot; introduction/mutation/evolution of some alternate strategies will disrupt a population of the first strategy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The example was a group of doves being invaded by a single hawk (the conspiracy of doves). Because the hawk does relatively better (by winning every conflict against a dove), than even after generations of entirely doves, the random addition of a hawk (say by mutation) will take hold because the hawk always wins against a dove. Whatever feature/gene that created a hawk in the pool of doves will be passed to some offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I remember correctly, the only stable case was prober-retaliator, since all others get invaded by someone else.&lt;/p&gt;&#xA;" OwnerUserId="13028" LastActivityDate="2015-01-15T11:07:33.953" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27711" PostTypeId="1" AcceptedAnswerId="27721" CreationDate="2015-01-15T12:55:57.720" Score="8" ViewCount="3823" Body="&lt;p&gt;There was this interesting discussion on CPR and defib in response to the question &lt;a href=&quot;https://biology.stackexchange.com/questions/27686/why-cant-we-defibrillate-heart-within-1-minute-after-ventricular-fibrillation-b&quot;&gt;&quot;Why can't we defibrillate the heart within 1 minute after ventricular fibrillation by electroshock?&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now I was wondering &quot;&lt;strong&gt;How long can the brain cope without O&lt;sub&gt;2&lt;/sub&gt;?&lt;/strong&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And to specify this question to a realistic situation: &quot;&lt;strong&gt;How long can the brain survive a cardiac arrest without (gross) neurological symptomatic consequences?&lt;/strong&gt;&quot;    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would define &quot;gross symptomatic consequences&quot; as &quot;noticeable and debilitating&quot; in one way or another to the subject. This opposed to minute changes in, e.g., motor response latencies measured in a laboratory task designed to pick up the slightest results of asphyxia. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;As background: I did these CPR and defib courses and the first thing they tell you to do is (1) call 911 / 000 whatever alarm number and (2) arrange a partner in crime to help with CPR;  or in case of a defib situation, (call alarm nr), make your way to the defib, unpack, apply electrodes, look at the manual, casually wait for instructions/warning lights etc. But..but... there is a person here without oxygen supply to his brain! And I know professional staff should be brought to the scene, but what struck me most is that starting up the defib (which inherently takes time) is more important than CPR (which is immediate)? In other words, loosing precious minutes is advantageous over diving straight away into CPR and pumping blood around?&lt;/em&gt;    &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-01-16T01:19:41.307" Title="How long can the brain survive during ongoing cardiac arrest?" Tags="&lt;neurology&gt;&lt;blood-circulation&gt;&lt;breathing&gt;&lt;central-nervous-system&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27713" PostTypeId="1" AcceptedAnswerId="27725" CreationDate="2015-01-15T13:59:39.940" Score="7" ViewCount="630" Body="&lt;p&gt;I recently started making all kinds of bacteria-processed foods by myself (such as yoghurt, but also Sauerteig and so on), and I found myself wondering how much of the weight of these products is actually due to the bacteria themselves in the end. But I couldn't find anything useful on the internet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, specifically for yoghurt, how much of its weight is due to the bacteria, i.e. dead and/or living bacterial cells, but not including the products of their metabolism outside the cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would also be happy about numbers on other bacteria- or fungi-processed foods, but I wanted to keep the question simple.  &lt;/p&gt;&#xA;" OwnerUserId="5439" LastEditorUserId="5439" LastEditDate="2019-06-26T07:19:59.333" LastActivityDate="2019-06-26T07:19:59.333" Title="How much of the weight of yoghurt is due to bacteria?" Tags="&lt;bacteriology&gt;&lt;food&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27714" PostTypeId="1" AcceptedAnswerId="27720" CreationDate="2015-01-15T14:16:44.273" Score="7" ViewCount="1169" Body="&lt;p&gt;Mothers transmit their mitochondria (and therefore mtDNA) to their offspring and fathers don't. Lets assume that father had a mutation of the gene that encodes mtDNA, would then be his offspring at risk? Why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also found the following statement:&#xA;&quot;The current genetic advice is that fathers with mtDNA mutations are at no risk of transmitting the defect to their offspring.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can that be true? Is it because of gene silencing? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance!&lt;/p&gt;&#xA;" OwnerUserId="6214" LastEditorUserId="14735" LastEditDate="2015-04-26T08:43:51.620" LastActivityDate="2015-04-26T08:43:51.620" Title="Father with mutated mtDNA- why isn't his offspring at risk?" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;human-genetics&gt;&lt;mitochondria&gt;&lt;gene&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27715" PostTypeId="1" CreationDate="2015-01-15T14:21:35.723" Score="0" ViewCount="703" Body="&lt;p&gt;Need advice: how to approach discrepancy in differential microarray gene expression test results: what to do if ANOVA, ttest, SAM and Limma procedures show different results and especially more discrepant when using log transformations and normalization operations?&lt;/p&gt;&#xA;" OwnerUserId="12935" LastActivityDate="2015-01-15T14:48:02.463" Title="What to do if microarray t-test, ANOVA, SAM and LImma show various selected significant genes?" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;microarray&gt;&lt;gene&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27717" PostTypeId="2" ParentId="27715" CreationDate="2015-01-15T14:48:02.463" Score="1" Body="&lt;p&gt;I wouldn't expect different methods to give the same results. Further, why are you even testing non-normalized datasets, the results of that are completely and utterly useless for any purpose other than showing that normalization is important. In addition, an T-test is a special case of an ANOVA (and of course limma is itself using a moderated T-test, though it's going to have significantly more power than the others), so I have to ask myself exactly what sort of design you're using that it's appropriate to substitute one for the other and still get apparently vastly different results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, I would strongly encourage you to work with a local bioinformatician or statistician for what is presumably your first microarray analysis, particularly if you don't have a strong statistics background.&lt;/p&gt;&#xA;" OwnerUserId="9523" LastActivityDate="2015-01-15T14:48:02.463" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27720" PostTypeId="2" ParentId="27714" CreationDate="2015-01-15T14:53:39.293" Score="11" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;...would then be his offspring at risk? Why?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No. Generally speaking, fathers do not pass on their mtDNA (Mitochondrial DNA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why? Because the mitochondria present in oocytes (egg cell) is the mother's, as every oocyte directly inherits the mother's mitochondria when they are made in the reproductive organs. The mitochondria that the sperm from the father carry to the egg do not enter the egg cell or are destroyed in the process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also worth mentioning that, in general, mtDNA does &lt;strong&gt;NOT&lt;/strong&gt; reside in the nucleus of cells, but in the mitochondria itself. It is not condensed during cell division, it is not spliced during Meiosis II, and it does not undergo recombination with another cell's mtDNA. Instead, when a cell divides, each cell takes about half of the mitochondria present in the cell and maintains them. That way &lt;em&gt;only&lt;/em&gt; the mitochondria present in the cell before division will be inherited by the daughter cells, and thus only the maternal mitochondria present in oocytes (egg cells) before sperm instigate cell division will be inherited by any offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qfP3c.jpg&quot; alt=&quot;From vignette2.wikia.nocookie.net&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2015-01-15T14:53:39.293" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27721" PostTypeId="2" ParentId="27711" CreationDate="2015-01-15T15:44:53.290" Score="10" Body="&lt;p&gt;From Boron and Boulpaep textbook of Medical Physiology, second edition, p.289:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because of falling ATP levels in the brain, consciousness is lost within 10 seconds of a blockade in cerebral blood flow. Irreversible nerve cell injury can occur after only 5 minutes of interrupted blood flow.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If conscious is lost within 10 seconds of blockade in cerebral blood flow, I guess a person will not be conscious to do any action in only 10 seconds!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brain ischemia is divided into &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Focal ischemia which signifies stroke. &lt;/li&gt;&#xA;&lt;li&gt;Global ischemia which occurs in cardiac arrest. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Permanent neural injury means that once perfusion is restored, the symptoms don't relieve as the part of brain which caused those symptoms becomes dead irreversibly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a list of symptoms check this &lt;a href=&quot;http://www.columbianeurosurgery.org/conditions/cerebral-ischemia/&quot; rel=&quot;noreferrer&quot;&gt;page&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-01-16T01:19:41.307" LastActivityDate="2015-01-16T01:19:41.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27725" PostTypeId="2" ParentId="27713" CreationDate="2015-01-15T17:02:47.303" Score="8" Body="&lt;p&gt;Interesting question and it will only be possible to do some estimation. The problem is to know the exact bacterial composition as well as the mass of the bacteria. To start, it is necessary to know the number of bacteria in a defined amount of yoghurt. There are scientific publications on this topic, but the numbers in fresh produced yoghurt are in the area of 10&lt;sup&gt;8&lt;/sup&gt; bacteria per gram yoghurt and declines over time. Based on the numbers in  reference 1 and 2 I use 2x10&lt;sup&gt;8&lt;/sup&gt; bacteria per gram fresh yoghurt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other number we need is the mass of one bacterium. This is complicated, as bacteria are very light due to their size and cannot be easily weighted. There are some numbers available (we imply here that all bacteria weight the same, which is of course not the case), and according to them, one bacterium weighs about 1x10&lt;sup&gt;-12&lt;/sup&gt; grams.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutiplying both numbers gives the amount of bacteria in one gram of yoghurt, around 0.0002 gram or 0.2mg. One typical sized yoghurt of 150 gram therefore contains about 30mg of bacteria. The weight of the bacteria can thus be neglected against the total weight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1489325/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Survival of Yogurt Bacteria in the Human Gut&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://books.google.de/books?id=uV2Oi0g_TB4C&amp;amp;pg=PA171&amp;amp;lpg=PA171&amp;amp;dq=cfu%20yogurt&amp;amp;source=bl&amp;amp;ots=df6xr8ykgA&amp;amp;sig=lUcjh8RQlN31KktcP4oxYUoJp-M&amp;amp;hl=de&amp;amp;sa=X&amp;amp;ei=xu-3VL7aA4SuUaGtgrAC&amp;amp;ved=0CEoQ6AEwBTgK#v=onepage&amp;amp;q=cfu%20yogurt&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Handbook of Food and Beverage Fermentation Technology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://hypertextbook.com/facts/2003/LouisSiu.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mass of a Bacterium&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2019-06-21T15:57:29.943" LastActivityDate="2019-06-21T15:57:29.943" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="27727" PostTypeId="2" ParentId="27714" CreationDate="2015-01-15T19:33:19.267" Score="5" Body="&lt;p&gt;&lt;strong&gt;TL;DR: Ubiquitin.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Occasional occurrence of &lt;em&gt;paternal inheritance of mtDNA&lt;/em&gt; has been suggested in mammals &lt;em&gt;including humans&lt;/em&gt;. Clearly, spermatozoa have mitochondria; they make the energy needed for motility. Paternal mitochondrial DNA (mtDNA) does enter oocytes. It is a persisting fallacy that only maternal mtDNA is present in humans because only oocyte mitochondria are present in the product of conception.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has been known for some time. According to an article in the Proceedings of the National Academy of Sciences, Nov. 1996, under &lt;em&gt;Evolution&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In vertebrates, inheritance of mitochondria is thought to be predominantly maternal, and mitochondrial DNA analysis has become a standard taxonomic tool. In&#xA;  accordance with the prevailing view of strict maternal inheritance, many sources assert that during fertilization, the sperm tail, with its mitochondria, gets excluded from the embryo. This is incorrect. In the majority of mammals — including humans — the midpiece mitochondria can be identified in the embryo even though their ultimate fate is unknown. The &quot;missing mitochondria&quot; story seems to have&#xA;  survived — and proliferated — unchallenged in a time of contention between hypotheses of human origins, because it supports the &quot;African Eve&quot; model of recent radiation of &lt;em&gt;Homo sapiens&lt;/em&gt; out of Africa.&lt;sup&gt;[1]&lt;/sup&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, what happens to paternal mtDNA if it is indeed present in embryonic cells? Paternal mitochondria are targeted and destroyed.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;While some confusion may still persist in popular science, research data clearly document that the paternal sperm-borne mitochondria of most mammalian species enter the ooplasm at fertilization and are specifically targeted for degradation by the resident ubiquitin system. Ubiquitin is a proteolytic chaperone that forms covalently linked polyubiquitin chains on the targeted proteinaceous substrates....Prohibitin, the major protein of the inner mitochondrial membrane, appears to be ubiquitinated in the sperm mitochondria.&lt;sup&gt;[2]&lt;/sup&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A finding of a patient with severe exercise intolerance in whom the mutated mtDNA in muscle was shown to be paternally inherited challenged the concept of strict maternal inheritance of mtDNA (the mtDNA harboring the mutation was paternal in origin and accounted for &lt;strong&gt;90 percent&lt;/strong&gt; of the patient's muscle mtDNA.)&lt;sup&gt;[3]&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Paternal mtDNA inheritance may have gone unrecognized in cases of mitochondrial disease with no clear maternal pattern of inheritance because mitochondrial haplotypes are rarely investigated in diagnostic analyses.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, a small study of 12 patients with mitochondrial myopathy failed to show Paternal mtDNA.&lt;sup&gt;[4]&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is too simplistic to say paternal inheritance of mtDNA does not occur. It has been shown in mice and other mammals.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The mitochondrial DNA of 172 sheep from 48 families were typed by using PCR-RFLP, direct amplification of the repeated sequence domain and sequencing analysis. The mitochondrial DNA from three lambs in two half-sib families were found to show paternal inheritance. Our findings provide direct evidence of paternal inheritance of mitochondria DNA in sheep. A total of 12 highly polymorphic microsatellite markers, which mapped on different chromosomes, were employed to type the sheep population to confirm family relationships. Possible mechanisms of paternal inheritance are discussed.&lt;sup&gt;[4]&lt;/sup&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;We should not believe everything we read without more investigation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;[1] Misconceptions about mitochondria and mammalian fertilization:&#xA;Implications for theories on human evolution&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1472648310604956&quot;&gt;Degradation of paternal mitochondria after fertilization: implications for heteroplasmy, assisted reproductive technologies and mtDNA inheritance&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMoa020350&quot;&gt;Paternal Inheritance of Mitochondrial DNA&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[4] &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022510X03003563&quot;&gt;No evidence for paternal inheritance of mtDNA in patients with sporadic mtDNA mutations&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;[5] &lt;a href=&quot;http://www.nature.com/hdy/journal/v93/n4/abs/6800516a.html&quot;&gt;Further evidence for paternal inheritance of mitochondrial DNA in the sheep (Ovis aries)&lt;/a&gt;&lt;/sub&gt;    &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-15T19:33:19.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27731" PostTypeId="1" AcceptedAnswerId="27732" CreationDate="2015-01-15T23:12:05.887" Score="1" ViewCount="87" Body="&lt;p&gt;The iGEM &lt;a href=&quot;http://parts.igem.org/Help:2014_DNA_Distribution#DNA_Kit_Plate_Instructions&quot; rel=&quot;nofollow&quot;&gt;DNA Kit Plate Instructions&lt;/a&gt; say that there is only 2-3ng of DNA per well, which is already miniprepped and in plasmids.  Then it says that &quot;there is not enough DNA in each well to perform anything but transformations&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Couldn't PCR be performed on an amount of DNA that small, given appropriate primers?  Is transformation &lt;em&gt;truly&lt;/em&gt; the only thing that could be done with that DNA?  If PCR could be done on the DNA, why might they suggest otherwise?&lt;/p&gt;&#xA;" OwnerUserId="13040" LastActivityDate="2015-01-16T16:39:20.233" Title="Can iGEM distribution parts be directly PCR'd?" Tags="&lt;pcr&gt;&lt;transformation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27732" PostTypeId="2" ParentId="27731" CreationDate="2015-01-15T23:16:27.177" Score="1" Body="&lt;p&gt;You probably could do PCR on that amount of DNA, but if you screw something up you don't get a second chance. Transforming bacteria and doing a miniprep turns your 3ng into a few micrograms, which is enough to tolerate a few mistakes.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2015-01-15T23:16:27.177" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27734" PostTypeId="1" CreationDate="2015-01-16T00:43:30.143" Score="1" ViewCount="117" Body="&lt;p&gt;I've had our home fumigated, but the silverfish seem to return unaffected. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are their eggs unaffected?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the best way to eliminate them from your home?&lt;/p&gt;&#xA;" OwnerUserId="9906" LastActivityDate="2015-01-16T21:18:45.277" Title="What is the most effective way to eliminate silverfish (g. Thysanura) from walls and floorboards?" Tags="&lt;entomology&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27735" PostTypeId="2" ParentId="27711" CreationDate="2015-01-16T00:56:06.487" Score="3" Body="&lt;p&gt;If we consider another case, there is blood flow, but no new oxygen is coming into the system, the brain cells &lt;strong&gt;may&lt;/strong&gt; begin to die after about four minutes &lt;a href=&quot;http://www.med.nyu.edu/content?ChunkIID=96472&quot; rel=&quot;nofollow&quot;&gt;[1]&lt;/a&gt;. However, this depends on the person not the amount of time. Consider &lt;a href=&quot;http://en.wikipedia.org/wiki/Freediving&quot; rel=&quot;nofollow&quot;&gt;free divers&lt;/a&gt; and more specifically &lt;a href=&quot;http://en.wikipedia.org/wiki/Tom_Sietas&quot; rel=&quot;nofollow&quot;&gt;Tom Sietas&lt;/a&gt;. These men and women, in this sport, can go well beyond the 5 minute mark with no debilitating brain damage. Now, Tom Sietas holds the world record for &lt;a href=&quot;http://en.wikipedia.org/wiki/Static_apnea&quot; rel=&quot;nofollow&quot;&gt;static apnea&lt;/a&gt; with the time of 22mins and 22sec under water without air and yes he survived. &lt;a href=&quot;http://www.dailymail.co.uk/news/article-2157442/How-CAN-man-hold-breath-22-minutes-The-amazing-feat-world-record-holder-Tom-Sietas-explained.html&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a news article about Tom but it goes on to say Pearl divers go about 7mins without air.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastActivityDate="2015-01-16T00:56:06.487" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="27736" PostTypeId="1" AcceptedAnswerId="27750" CreationDate="2015-01-16T02:56:04.773" Score="13" ViewCount="2429" Body="&lt;p&gt;This question is brought on by a Sci Fi novel I am thinking about writing. The plot device involves a colonist in charge of building a population on a new planet who loses his supply of embryos and so forth in the landing. With the artificial &quot;wombs&quot; intact, he populates the planet with clones of himself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If he wanted to introduce enough variation (without making up new genes, only rearranging) in the population to allow them to be able to reproduce naturally without inbreeding problems, would he be able to? In particular, could he make a woman? &#xA;Alternately, could a woman (without a Y chromosome) do the the inverse?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the risk of introducing bias into the answers, the plot as it stands assumes he is a male and he CAN'T do any of the above and he is restricted to clones.&lt;/p&gt;&#xA;" OwnerUserId="13043" LastEditorUserId="13054" LastEditDate="2015-01-16T21:37:18.620" LastActivityDate="2015-12-06T17:12:30.100" Title="Does a man contain all the genes needed to make a woman?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;dna&gt;&lt;molecular-genetics&gt;&lt;cloning&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27737" PostTypeId="2" ParentId="27573" CreationDate="2015-01-16T03:05:59.943" Score="5" Body="&lt;p&gt;When birds sleep, they do experience NREM sleep &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17452279&quot;&gt;[1]&lt;/a&gt;. Furthermore, Kavanau (2002) concluded that NREM has evolved in warm blooded animals &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S014976340200088X&quot;&gt;[2]&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Birds provide a unique opportunity to evaluate current theories for the function of sleep. Like mammalian sleep, avian sleep is composed of two states, slow-wave sleep (SWS) and rapid eye-movement (REM) sleep that apparently evolved independently in mammals and birds. Despite this resemblance, however, it has been unclear whether avian SWS shows a compensatory response to sleep loss (i.e., homeostatic regulation), a fundamental aspect of mammalian sleep potentially linked to the function of SWS. Here, we prevented pigeons (Columba livia) from taking their normal naps during the last 8 h of the day. Although time spent in SWS did not change significantly following short-term sleep deprivation, electroencephalogram (EEG) slow-wave activity (SWA; i.e., 0.78-2.34 Hz power density) during SWS increased significantly during the first 3 h of the recovery night when compared with the undisturbed night, and progressively declined thereafter in a manner comparable to that observed in similarly sleep-deprived mammals. SWA was also elevated during REM sleep on the recovery night, a response that might reflect increased SWS pressure and the concomitant 'spill-over' of SWS-related EEG activity into short episodes of REM sleep. As in rodents, power density during SWS also increased in higher frequencies (9-25 Hz) in response to short-term sleep deprivation. Finally, time spent in REM sleep increased following sleep deprivation. The mammalian-like increase in EEG spectral power density across both low and high frequencies, and the increase in time spent in REM sleep following sleep deprivation suggest that some aspects of avian and mammalian sleep are regulated in a similar manner &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18321247&quot;&gt;[3]&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From the Abstract and reference &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18321247&quot;&gt;[3]&lt;/a&gt; above, we see that EEGs have been taking on birds and show that birds enter REM and SWS similarly to mammals. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;In response to Chris Stronks, researchers have also studied chickens see &lt;a href=&quot;https://books.google.com/books?id=8wM35EdLbwQC&amp;amp;pg=PA204&amp;amp;lpg=PA204&amp;amp;dq=do+chickens+have+rem+sleep&amp;amp;source=bl&amp;amp;ots=wgrsZfX2VX&amp;amp;sig=WD39hxVyBYRzw4WlEWb3bVa11uo&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=koy4VPueL8i1sQScxIHICg&amp;amp;ved=0CEIQ6AEwBQ#v=onepage&amp;amp;q=do%20chickens%20have%20rem%20sleep&amp;amp;f=false&quot;&gt;Evolution of Sleep: Phylogenetic and Functional Perspective&lt;/a&gt; by Patrick McNamara, Robert A. Barton, Charles L. Nunn. In the section for REM sleep in birds, the studies were conducted on pigeons and chickens see pages 204-205.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-01-16T04:07:01.750" LastActivityDate="2015-01-16T04:07:01.750" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="27738" PostTypeId="1" CreationDate="2015-01-16T04:18:47.717" Score="2" ViewCount="4808" Body="&lt;p&gt;I will be planting Papaya fruit seeds and I understand that there is a female and a male plant, so how can one distinguish which are the ones that will bear fruit and which I should just rip up by its roots as I have limited planting space?&lt;/p&gt;&#xA;" OwnerUserId="13044" LastEditorUserId="9943" LastEditDate="2015-01-16T04:29:29.367" LastActivityDate="2016-05-14T15:51:08.443" Title="Which Papaya (Lechosa) plant (male or female) bears fruit?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27739" PostTypeId="2" ParentId="27738" CreationDate="2015-01-16T04:23:25.480" Score="2" Body="&lt;p&gt;Male flowers have no ovary and do not produce a fruit but females need to be pollinated or the fruits will be aborted falling off when they are about golf ball size &lt;a href=&quot;http://www.ctahr.hawaii.edu/oc/freepubs/pdf/F_N-5.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(1)&lt;/a&gt;. Therefore, you will need at least one male or hermaphrodite plant with your female plants so you can manually pollinate the female plants. Also, note that hermaphrodites can pollinate themselves so you will not need another one or a male for fruit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article goes on to say that hermaphrodites are the preferred type but under certain circumstances a hermaphrodite can shift to a female.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cool winter weather or high soil moisture can lead to a shift toward femaleness, where the stamens fuse to the carpels or ovary wall. The re­&#xA;  sulting fruits become severely ridged (carpelloid, or “cat­ faced”) and hence are deformed and unmarketable &lt;a href=&quot;http://www.ctahr.hawaii.edu/oc/freepubs/pdf/F_N-5.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(1)&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qb9qa.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Home gardeners should take steps to avoid having only a single papaya plant, in case it turns out to be a female. One way to accomplish this is have several plants in the garden, to ensure the possibility that at least one will be&#xA;  a hermaphrodite with pollen. If space is limited, allow several seedlings to grow to flowering stage in the same planting spot, and then remove all but the healthiest her­maphrodite plant &lt;a href=&quot;http://www.ctahr.hawaii.edu/oc/freepubs/pdf/F_N-5.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(1)&lt;/a&gt;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-01-16T04:36:44.207" LastActivityDate="2015-01-16T04:36:44.207" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="27740" PostTypeId="1" AcceptedAnswerId="27741" CreationDate="2015-01-16T04:39:49.387" Score="0" ViewCount="2862" Body="&lt;p&gt;Is it true that some organs (such as the liver or the intestines) are less active at certain times of the day, regardless of whether the individual is awake or not?&lt;/p&gt;&#xA;" OwnerUserId="11546" LastEditorUserId="3340" LastEditDate="2015-01-17T09:05:47.017" LastActivityDate="2015-01-17T09:05:47.017" Title="Is it true that some organs &quot;sleep&quot; at certain times of the day and does this affect dieting or when to take medicine?" Tags="&lt;human-biology&gt;&lt;sleep&gt;&lt;chronobiology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27741" PostTypeId="2" ParentId="27740" CreationDate="2015-01-16T05:28:22.910" Score="4" Body="&lt;p&gt;No, this is not true. The only &quot;organ&quot; (if you will) that needs to &quot;sleep&quot; is the brain, and even then it is still quite active. The body needs to rest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When blood is needed in a prioritized manner in certain areas of the body - for example, during a marathon the muscles and the heart need more oxygen - mechanisms are in place to shunt some of the blood away from organs that need it less (the stomach and intestines, for example) to those that need it more. But that doesn't mean the GI tract is sleeping, or even resting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no organ that &quot;sleeps&quot;. The brain as a whole is highly active during sleep, even secreting certain hormones predominantly during that time.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-16T05:28:22.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27742" PostTypeId="2" ParentId="27736" CreationDate="2015-01-16T05:40:26.947" Score="8" Body="&lt;p&gt;A woman (assuming no mosaicism) has two X chromosomes in the nuclei of her cells (except for oocytes). A man, in every cell with a nucleus (except for spermatocytes), has only one, pluripotent or not. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only way he could make a female would be to either manipulate cells by  duplicating the X chromosome (very difficult to do) or remove/inactivate the Y (giving rise to an XO female). That in itself would introduce problems in the female.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.genetics.edu.au/Publications-and-Resources/Genetics-Fact-Sheets/FactSheet32&quot;&gt;Turner Syndrome XO Syndrome&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-01-16T06:51:04.450" LastActivityDate="2015-01-16T06:51:04.450" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="27743" PostTypeId="2" ParentId="27681" CreationDate="2015-01-16T09:40:24.707" Score="9" Body="&lt;p&gt;The reason is that X-inactivation is not complete (&lt;a href=&quot;http://www.nature.com/nature/journal/v434/n7031/full/nature03479.html&quot; rel=&quot;noreferrer&quot; title=&quot;Carrell &amp;amp; Willard. 2005. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434, 400-404&quot;&gt;Carrell &amp;amp; Willard, 2005&lt;/a&gt;; &lt;a href=&quot;http://www.nature.com/scitable/topicpage/x-chromosome-x-inactivation-323&quot; rel=&quot;noreferrer&quot; title=&quot;Ahn, J. &amp;amp; Lee, J. 2008. X chromosome: X inactivation. Nature Education 1(1):24&quot;&gt;Ahn &amp;amp; Lee, 2008&lt;/a&gt;), and as many as 15-25% of X-linked genes escape silencing (&lt;a href=&quot;http://www.nature.com/nature/journal/v434/n7031/full/nature03479.html&quot; rel=&quot;noreferrer&quot; title=&quot;Carrell &amp;amp; Willard. 2005. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434, 400-404&quot;&gt;Carrell &amp;amp; Willard, 2005&lt;/a&gt;; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0531513106005206&quot; rel=&quot;noreferrer&quot; title=&quot;Cheng et al. 2008. Dosage compensation of the X chromosome and Turner syndrome. International Congress Series, Volume 1298 (Wellness for Girls and Women with Turner Syndrome. Proceedings of the Consensus Conference)&quot;&gt;Cheng et al, 2005&lt;/a&gt;). This means that some genes on the Barr body are expressed in XX-females, although often at lower levels compared to the active X-chromosome, and this is part of the normal gene dosage. The &quot;purpose&quot; of X-inactivation is usually dosage compensation, so that genes are expressed equally in males and females (and then actually upregulated in both sexes to balance autosomal genes, see e.g. &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bies.080149/abstract&quot; rel=&quot;noreferrer&quot; title=&quot;Dementyeva et al. 2009. X-chromosome upregulation and inactivation: two sides of the dosage compensation mechanism in mammals. Bioessays 31(1)&quot;&gt;Dementyeva et al, 2009&lt;/a&gt;). However, this is not true for all genes, and the ones that normally escape X-inactivation will be expressed in the incorrect dosage in X0 females. Some of these genes are thought to contribute to the symptoms of Turner syndrome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also likely that the genes that escape silencing are involved in sex-linked traits, as stated in &lt;a href=&quot;http://www.nature.com/nature/journal/v434/n7031/full/nature03479.html&quot; rel=&quot;noreferrer&quot; title=&quot;Carrell &amp;amp; Willard. 2005. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434, 400-404&quot;&gt;Carrell &amp;amp; Willard (2005)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Such genes are potential contributors to sexually dimorphic traits, to phenotypic variability among females heterozygous for X-linked conditions, and to clinical abnormalities in patients with abnormal X chromosomes.&lt;br&gt;&#xA;  ... ...&#xA;  &lt;br&gt;However, as many of the genes that escape from inactivation do not have Y-linked homologues, strict dosage compensation may not be necessary for all genes on the chromosome. Such characteristic genomic differences should be recognized as a factor for explaining sex-specific phenotypes both in complex disease as well as in normal, sexually dimorphic traits.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0531513106005206&quot; rel=&quot;noreferrer&quot; title=&quot;Cheng et al. 2008. Dosage compensation of the X chromosome and Turner syndrome. International Congress Series, Volume 1298 (Wellness for Girls and Women with Turner Syndrome. Proceedings of the Consensus Conference)&quot;&gt;Cheng et al (2005)&lt;/a&gt; also point out that the expression of the genes that escape silencing is tissue-dependent, which suggests that the role these genes play in the symptoms of Turner syndrome is also tissue dependent.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-01-16T12:00:26.743" LastActivityDate="2015-01-16T12:00:26.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27744" PostTypeId="2" ParentId="27736" CreationDate="2015-01-16T09:44:16.127" Score="5" Body="&lt;p&gt;Theoretically this should be possible as men carry both sex chromosomes. You would have to find a way to make haploid cells and then have them form a diploid cell with two X chromosomes. Your population would go through a genetic bottleneck which would soon cause a lot of other genetic problems as there is not enough variety.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But besides this rather theoretical approach, there is a real problem with this kind of reproduction: it won't work because of &lt;a href=&quot;http://en.wikipedia.org/wiki/Genomic_imprinting&quot; rel=&quot;nofollow&quot;&gt;genetic imprinting&lt;/a&gt;. This takes place in the egg and as well in the sperm cell and consists of small modifications added to the DNA. This silences this gene and allows the expression of genes specifically either from the mother's or the father's copy of the chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example for this would be the loss of a part of chromosome 15. Depending on which copy is lost, this either causes the &lt;a href=&quot;http://en.wikipedia.org/wiki/Prader%E2%80%93Willi_syndrome&quot; rel=&quot;nofollow&quot;&gt;Prader-Willi Syndome&lt;/a&gt; (inherited from the father) or the &lt;a href=&quot;http://en.wikipedia.org/wiki/Angelman_syndrome&quot; rel=&quot;nofollow&quot;&gt;Angelman Syndrome&lt;/a&gt; (inherited from the mother). This &lt;a href=&quot;http://genetics.thetech.org/ask-a-geneticist/imprinting&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; goes deeper into imprinting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Due to the missing maternal imprinting, the cells constructed from the father will not be viable since the expression of some genes (which would come from the mother) is missing. Nevertheless it has been shown in mice that it is possible to overcome this problem. The researchers deleted the maternal imprinting on one copy of the chromosomes they used, mimicked the fathers imprinting and where able to breed viable off-springs from two female mice without a father. But this approach is rather technical and also error prone since you have to know the imprinting of the mother. The article can be found &lt;a href=&quot;http://www.biol.uw.edu.pl/embrio/lib/exe/fetch.php/dydaktyka/birth_of_parthenogenetic_mice.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="16985" LastEditDate="2015-12-06T17:12:30.100" LastActivityDate="2015-12-06T17:12:30.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27745" PostTypeId="2" ParentId="27692" CreationDate="2015-01-16T10:08:57.057" Score="3" Body="&lt;p&gt;Note: in the following I'm going to focus on &lt;em&gt;E. coli&lt;/em&gt;, which is the best understood system for bacterial flagellar movement. It would be interesting to compare uniflagellate bacteria and bacteria that have a fixed number of flagella. However, I know about &lt;em&gt;E. coli&lt;/em&gt; and I think there is something interesting to be learned just from them, so I'll continue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You're in luck that you asked this question when you did: &lt;a href=&quot;http://elifesciences.org/content/3/e01916#F12&quot; rel=&quot;nofollow&quot;&gt;a very cool paper (1)&lt;/a&gt; was published just last year addressing your question. They find that the number of flagella has only a small effect on bacterial motion, but to understand why requires some background (A lot of the following background comes from this paper, which summarizes it pretty well). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would argue that &lt;em&gt;E. coli&lt;/em&gt; movement is one of the best-understood examples of cell movement we have, with excellent, high-resolution, quantitative data being generated for over 40 years now (the king in this field is Howard Berg at Harvard, if you want to learn more just read a recent review from him). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;E. coli&lt;/em&gt; have a variable number of flagella, from one to ten or so. They operate in a bundle, but this bundle is highly dynamic due to the way &lt;em&gt;E. coli&lt;/em&gt; moves. Rather than proceeding continually a straight line like a car, &lt;em&gt;E. coli&lt;/em&gt; moves by a series of starts and stops called a &lt;a href=&quot;http://www.cellsalive.com/animabug.htm&quot; rel=&quot;nofollow&quot;&gt;run-and-tumble&lt;/a&gt;: the bacteria moves in a straight line for a &lt;em&gt;short&lt;/em&gt; amount of time (a &lt;em&gt;run&lt;/em&gt;), and then it stops in its tracks and changes direction (a &lt;em&gt;tumble&lt;/em&gt;) before starting off again &lt;a href=&quot;http://jb.asm.org/content/182/10/2793.abstract&quot; rel=&quot;nofollow&quot;&gt;(2)&lt;/a&gt;. At a first pass this run-and-tumble behavior is essentially diffusion, the bacteria covers a lot of ground without going anywhere &lt;em&gt;on average&lt;/em&gt; unless there's some food nearby, in which case the run-and-tumble is slightly biased so that the bacteria drifts toward the food. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I said, during runs the flagella are bundled together and all turning counter-clockwise. A tumble happens when the bacteria sends a signal to the flagella to start turning clockwise. This breaks apart the flagellar bundle and sends all the flagella in different directions. Up until the paper I mention above, it was still not clear exactly how many flagella need to start turning clockwise before the bundle breaks up and a tumble commences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now you can see why having more flagella might not necessarily be a good thing: you might be able to move faster during the run (though this is not obvious to me, given the sometimes &lt;a href=&quot;http://jilawww.colorado.edu/perkinsgroup/Purcell_life_at_low_reynolds_number.pdf&quot; rel=&quot;nofollow&quot;&gt;unintuitive nature (3)&lt;/a&gt; of &lt;a href=&quot;http://en.wikipedia.org/wiki/Reynolds_number&quot; rel=&quot;nofollow&quot;&gt;low-Reynolds number fluid dynamics&lt;/a&gt;) but at the same time the flagellar bundle will be more sensitive to break-up because with more flagella come more opportunities for one to start moving counter-clockwise and mess things up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the authors of the above paper &lt;a href=&quot;http://elifesciences.org/content/3/e01916#F12&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt; find, it turns out that there are correlations between the actions of different flagella in a bundle, so that a bacteria with many flagella effectively acts like a bacteria with fewer flagella. The result is that the overall pattern of run-and-tumble is not much affected by the number of flagella; you might argue that number of flagella has a minor effect on bacterial movement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, you might be interested not in the net movement of a bacteria, but just on its speed when it's moving forward, in the run phase. Unfortunately I wasn't able to find any good measurements of the run velocity of a bacterial cell as a function of number of flagella. But hopefully given this recent paper, maybe such measurements are on the horizon! &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://elifesciences.org/content/3/e01916#F12&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt; Mears PJ &lt;em&gt;et al.&lt;/em&gt; (2014) Escherichia coli swimming is robust against variations in flagellar number. &lt;em&gt;eLife&lt;/em&gt; 3:e01916.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jb.asm.org/content/182/10/2793.abstract&quot; rel=&quot;nofollow&quot;&gt;(2)&lt;/a&gt; Turner L &lt;em&gt;et al.&lt;/em&gt; (2000). Real-time imaging of fluorescent flagellar filaments. &lt;em&gt;J. Bacteriol&lt;/em&gt;. 182(10): 2793-2801&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jilawww.colorado.edu/perkinsgroup/Purcell_life_at_low_reynolds_number.pdf&quot; rel=&quot;nofollow&quot;&gt;(3)&lt;/a&gt; Purcell EM. (1977). Life at low Reynolds number. &lt;em&gt;Am. J. Phys.&lt;/em&gt; 45: 3-11.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2015-01-16T10:08:57.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27746" PostTypeId="1" AcceptedAnswerId="27747" CreationDate="2015-01-16T10:15:27.180" Score="3" ViewCount="1416" Body="&lt;p&gt;I came across a species name that contains &quot;x&quot; in its name, namely &lt;em&gt;Miscanthus&lt;/em&gt; × &lt;em&gt;giganteus&lt;/em&gt;. What does this symbol stand for and is it commonly used in taxonomic nomenclature?&lt;/p&gt;&#xA;" OwnerUserId="6875" LastEditorUserId="1560" LastEditDate="2015-01-16T14:52:09.013" LastActivityDate="2015-01-16T15:59:36.897" Title="What does x in &quot;Miscanthus × giganteus&quot; name stand for?" Tags="&lt;botany&gt;&lt;taxonomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27747" PostTypeId="2" ParentId="27746" CreationDate="2015-01-16T10:24:34.620" Score="4" Body="&lt;p&gt;It means that the plant is a hybrid. Having it in the middle means that it is between species of the same genus, else the × (it's not the letter x but the multiplication symbol ×) would have been in front. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is very commonly used in taxonomic nomenclature, namely every time you have a hybrid. This means you'll usually see it with plants, as animals very rarely interbreed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia says that your plant is a hybrid from Miscanthus sinensis and Miscanthus sacchariflorus. It is an easy place to look up most hybrids you might encounter. &lt;/p&gt;&#xA;" OwnerUserId="1578" LastEditorUserId="1578" LastEditDate="2015-01-16T15:59:36.897" LastActivityDate="2015-01-16T15:59:36.897" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="27748" PostTypeId="1" CreationDate="2015-01-16T12:16:34.903" Score="1" ViewCount="1194" Body="&lt;p&gt;In &lt;a href=&quot;http://www.askamathematician.com/2012/05/q-is-the-final-step-in-evolution-an-ascension-into-an-energy-based-lifeform/&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;, the author says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Evolution isn’t “leading up” to anything, it just drunkenly limps along using the same set of tricks in slightly different orders.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;On other occasions, however, the term &quot;evolution&quot; is often deployed as a process that develops gradually, typically from a simple to a more complex form, or from not adapted to more specialized and &quot;fit&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These contrasting interpretations of evolution make me wonder how I should interpret &quot;to evolve&quot; and &quot;evolution&quot; in the context of processes involved in speciation? &lt;/p&gt;&#xA;" OwnerUserId="6786" LastEditorUserId="9943" LastEditDate="2015-01-17T12:15:09.663" LastActivityDate="2015-01-17T12:15:09.663" Title="What does to &quot;evolve&quot; exactly mean?" Tags="&lt;evolution&gt;&lt;terminology&gt;" AnswerCount="2" CommentCount="17" FavoriteCount="0" ClosedDate="2015-01-16T15:08:53.603" ContentLicense="CC BY-SA 3.0" />
  <row Id="27749" PostTypeId="2" ParentId="27748" CreationDate="2015-01-16T12:33:59.113" Score="3" Body="&lt;p&gt;A couple of comments, but maybe not an answer; I think misuse is the wrong word - alternative meaning is better. '&lt;em&gt;Evolve&lt;/em&gt;' as a word is much older than the theory of evolution, and has its origin in the Latin &lt;em&gt;evolvere&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;evolve&lt;/strong&gt; (v.) &#xA;      1640s, &quot;to unfold, open out, expand,&quot; from Latin evolvere &quot;to unroll, roll out, roll forth, unfold,&quot; especially of books; figuratively &quot;to make clear, disclose; to produce, develop,&quot;&lt;br&gt;&#xA;  from assimilated form of ex- &quot;out&quot; (see ex-) + volvere &quot;to roll&quot; (see volvox). Meaning &quot;to develop by natural processes to a higher state&quot; is from 1832. Related: Evolved; evolving.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;from &lt;a href=&quot;http://www.etymonline.com/index.php?allowed_in_frame=0&amp;amp;search=evolve&amp;amp;searchmode=none&quot; rel=&quot;nofollow&quot;&gt;Online Etymology Dictionary&lt;/a&gt;. Implicit in that definition is the laying out of something predetermined, which can relate to going from simpler to more complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also note that Darwin only used the word '&lt;em&gt;evolve&lt;/em&gt;' once in &lt;em&gt;On the Origin of Species&lt;/em&gt; (1859), in the final sentence: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There is grandeur in this view of life, with its several&#xA;  powers, having been originally breathed into a few forms or into one;&#xA;  and that, whilst this planet has gone cycling on according to the fixed&#xA;  law of gravity, from so simple a beginning endless forms most beautiful&#xA;  and most wonderful have been, and are being, evolved. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The implication of progress was one reason why Darwin disliked the word '&lt;em&gt;evolve&lt;/em&gt;' and preferred &quot;&lt;em&gt;descent with modification&lt;/em&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same root was then used as a name to the theory of Evolution, but then in a much more specific sense than the older, general meaning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look back at the etymology above, it is quite clear that biological evolution (The Modern synthesis version) emphazise the connotations '&lt;em&gt;expand&lt;/em&gt;', '&lt;em&gt;produce&lt;/em&gt;' and '&lt;em&gt;develop&lt;/em&gt;', but not the '&lt;em&gt;unroll&lt;/em&gt;' and '&lt;em&gt;unfold&lt;/em&gt;' parts (which both to some extent imply something predetermined).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-01-16T13:21:23.290" LastActivityDate="2015-01-16T13:21:23.290" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="27750" PostTypeId="2" ParentId="27736" CreationDate="2015-01-16T12:53:49.520" Score="9" Body="&lt;p&gt;&lt;em&gt;This answer also involves some speculations as the question is about a good theoretical framework for a science fiction.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find in &lt;a href=&quot;https://biology.stackexchange.com/questions/17410/could-a-sperm-be-altered-to-contain-a-females-genetics/17435#17435&quot;&gt;this&lt;/a&gt; post about how sperm can be used to produce embryonic stem cells. It would still require an oocyte for doing that. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question now is- Can you produce oocytes from a male?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may fuse two &lt;code&gt;X&lt;/code&gt; bearing haploid spermatids to form a diploid cell with &lt;code&gt;XX&lt;/code&gt;. This cell will also have mitochondria and ribosomes — seems like a decent candidate. Gametogenesis has not been shown to happen in-vitro. Moreover a zygote will need a lot more cytoplasmic resources that you can get from a fused spermatid. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plus there are imprinting issues as already pointed out by Chris. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Conclusion&lt;/strong&gt;: Next to impossible&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For your question &quot;&lt;strong&gt;Does a man contain all the genes needed to make a women&lt;/strong&gt;&quot;: yes he has but does not have the biological machinery to do that (exclusive of the womb). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However if you choose to send a female astronaut for this mission then there may be some hope. As Chris said, there are problems with homotypic fusions because of imprinting issues. But with a supply of ova there can be other ways:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Make clones using SCNT&lt;/strong&gt;: limitation is that there would be very little variability.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Erase imprinting marks and fuse two oocytes&lt;/strong&gt;: This has not been done yet but this is possible. At this moment we have technology (still incipient for therapy grade), for targeted genome editing. The basic principle involves fusing a DNA-endonuclease with a sequence specific DNA Binding Domain (DBD). Examples include Zinc Finger Nuclease, TALENs and Crispr-Cas. &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/anie.201206489/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;This&lt;/a&gt; study demonstrates an engineered system that can deaminate RNA in a sequence specific manner. Based on a similar principle it should be possible to link DNA-(cytosine/adenine)- methyltransferase or DNA-(cytosine/adenine)-demethylase to a sequence specific DBD &lt;sup&gt;&lt;strong&gt;1&lt;/strong&gt;&lt;/sup&gt;. This system can be used for targeted epigenetic modification. This would have a little more variation than cloning because of meiotic recombination. Limitation is that there won't be any males, this would perhaps become an Amazonian Planet.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Make sure that your space-shuttle has a good biolab facility :P&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;1&lt;/strong&gt;&lt;/sup&gt; Imprinting is generally implemented by DNA methylation which happens mostly on cytosines. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-01-16T13:04:28.070" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27751" PostTypeId="2" ParentId="27748" CreationDate="2015-01-16T13:03:27.693" Score="1" Body="&lt;p&gt;&lt;strong&gt;Great question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think evolution and its derivatives are among the most &lt;em&gt;misconceived&lt;/em&gt; and &lt;em&gt;abused&lt;/em&gt; terms in Biology. Evolution is often seen as the driving force that pushes life to perfection. For example, what I often encounter are things along the line: &quot;Organism A has trait X, A has been evolving for Y years, thus X is evolved into a useful and optimal token for survival, so we have been exploring X... bladibla&quot;. &lt;em&gt;No&lt;/em&gt; - the trait X is there because it may be useful at present, or it has been useful in the past, or perhaps it is simply there because it occurred by chance and hasn't proved detrimental in Y years. Evolution is not only survival of the fittest (X is optimized), it is, and probably even more so, the &lt;strong&gt;extermination of the unfit&lt;/strong&gt; (X is not detrimental). The &quot;termination of the unfit&quot; may, in fact, be more apt than &quot;survival of the fittest&quot;, as survival depends on out-competing (and hence terminating) others. The interpretation of evolution as &quot;survival of the fittest&quot; is, however, the most encountered interpretation, perhaps unfortunately.    &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-16T14:05:15.787" LastActivityDate="2015-01-16T14:05:15.787" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="27753" PostTypeId="1" CreationDate="2015-01-16T13:37:49.390" Score="5" ViewCount="95" Body="&lt;p&gt;Are there any known viruses that have managed to infect all of humankind either in the past or presently, either benign or otherwise?&lt;/p&gt;&#xA;" OwnerUserId="13047" LastActivityDate="2015-01-16T13:37:49.390" Title="Are there any viruses that have infected all humans in the past or present?" Tags="&lt;virology&gt;" AnswerCount="0" CommentCount="6" ClosedDate="2015-01-18T13:08:42.063" ContentLicense="CC BY-SA 3.0" />
  <row Id="27755" PostTypeId="2" ParentId="27731" CreationDate="2015-01-16T16:39:20.233" Score="1" Body="&lt;p&gt;Here is the feedback I got from iGEM HQ:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Yes, we estimate there would be a total of ~3ng (on average) for a part sample in a well, and assuming a suspension with 10ul, there would be more than enough for PCR reactions. However, transformations are recommended over PCRing directly from the kit, because you can now store that part long term in glycerol form and you can prepare more of that part easily.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So the reason to prefer transformation over PCR seems to be long-term storage and future amplification.&lt;/p&gt;&#xA;" OwnerUserId="13040" LastActivityDate="2015-01-16T16:39:20.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27756" PostTypeId="1" AcceptedAnswerId="27758" CreationDate="2015-01-16T18:37:39.300" Score="0" ViewCount="232" Body="&lt;p&gt;So I believe (and correct me if I'm wrong--it's logic, not research) that the human body is pretty much all just processed sunlight based on the food chain.  How much, if any, of the human body is made up of materials that did not originate from the sun (e.g., various minerals or other trace elements)?  &lt;/p&gt;&#xA;" OwnerUserId="13052" LastActivityDate="2015-01-16T23:18:32.007" Title="How much of the human body is processed sunlight?" Tags="&lt;human-biology&gt;&lt;food&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27757" PostTypeId="1" CreationDate="2015-01-16T19:55:02.347" Score="14" ViewCount="1650" Body="&lt;p&gt;Grapefruit juice contains furanocoumarins, which irreversibly inhibit CYP3A4.  For this reason, when one is taking certain medications it is necessary to not eat grapefruits because the inhibition of CYP3A4 can reduce how much of the drug is metabolized before it can get used, resulting in an overdose.   It apparently takes 24 hours after eating a grapefruit before the enzyme level is 50% and up to 72 hours for it to be completely normal.  So, it seems that eating one grapefruit a day would substantially impair one's CYP3A4 levels indefinitely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia says, &lt;a href=&quot;http://en.wikipedia.org/wiki/CYP3A4&quot;&gt;the purpose of CYP3A4&lt;/a&gt; is &quot;to oxidize small foreign organic molecules (xenobiotics), such as toxins or drugs, so that they can be removed from the body.&quot;   It seems like inhibiting CYP3A4, from a biological standpoint, would reduce one's immune system or at least the ability to tolerate and eliminate certain toxins.   Are there other enzymes that take up the slack, or is there something in grapefruit itself which does the job instead, or is a daily grapefruit just a bad idea?  What are the effects of extended inhibition of CYP3A4?  Will the body perhaps build up a tolerance or immunity, or (perhaps with negative effects) pump out more CYP3A4 to try to compensate?&lt;/p&gt;&#xA;" OwnerUserId="9450" LastEditorUserId="15136" LastEditDate="2015-04-20T06:56:08.167" LastActivityDate="2017-08-13T21:28:37.447" Title="Grapefruits and CYP3A4" Tags="&lt;metabolism&gt;&lt;enzymes&gt;&lt;toxicology&gt;&lt;liver&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27758" PostTypeId="2" ParentId="27756" CreationDate="2015-01-16T21:08:14.683" Score="2" Body="&lt;p&gt;I think that Carl Sagan &lt;a href=&quot;https://www.goodreads.com/author/quotes/10538.Carl_Sagan&quot; rel=&quot;nofollow&quot;&gt;said it best&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The nitrogen in our DNA, the calcium in our teeth, the iron in our blood, the carbon in our apple pies were made in the interiors of collapsing stars. We are made of starstuff.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The current view of cosmology is that every atom that isn't hydrogen, helium, or lithium was created in the fusion furnace in  the hearts of giant stars. These heavy atoms were then spread about the place by supernovas.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there's a lot more to the matter that makes up living creatures than just the atoms. The vast majority of the free energy that allows for the creation of intricate organic molecules with complex patterns of chemical bonds (e.g. protein, DNA, etc.) does indeed originate with our sun.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2015-01-16T23:18:32.007" LastActivityDate="2015-01-16T23:18:32.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27759" PostTypeId="2" ParentId="27734" CreationDate="2015-01-16T21:18:45.277" Score="2" Body="&lt;p&gt;They feed on fungi, which grow wherever there's high humidity levels. So the best way to get rid of them would be to lower the air humidity. For example, by increasing the temperature in your (presumably) bathroom. &lt;/p&gt;&#xA;" OwnerUserId="13055" LastActivityDate="2015-01-16T21:18:45.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27760" PostTypeId="1" CreationDate="2015-01-16T21:43:18.133" Score="1" ViewCount="560" Body="&lt;p&gt;Does the size or mass of a body affect the time it takes for rigor mortis to sets in? For example: compare a 300 pound man to 100 pound girl to 5 pound animal.&lt;/p&gt;&#xA;" OwnerUserId="11855" LastEditorUserId="11855" LastEditDate="2015-01-18T18:39:03.920" LastActivityDate="2015-01-19T07:27:28.793" Title="Does the size or mass of a body affect the time it takes for rigor mortis to sets in?" Tags="&lt;human-anatomy&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27761" PostTypeId="1" AcceptedAnswerId="27762" CreationDate="2015-01-16T22:02:03.033" Score="4" ViewCount="686" Body="&lt;p&gt;I'm wondering what effects are &lt;em&gt;known&lt;/em&gt; to happen to a person's cells when a person is cryogenically frozen, especially those that need to be overcome in order to &quot;bring them back to life.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a cellular and maybe even molecular level, is the person exactly the same as before?&lt;/p&gt;&#xA;" OwnerUserId="9700" LastEditorUserId="9700" LastEditDate="2015-01-16T22:10:45.390" LastActivityDate="2017-11-08T18:48:11.570" Title="What effects does being cryogenically frozen have on a person's body?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="3" ClosedDate="2015-01-17T11:52:02.840" ContentLicense="CC BY-SA 3.0" />
  <row Id="27762" PostTypeId="2" ParentId="27761" CreationDate="2015-01-16T23:32:34.287" Score="5" Body="&lt;h3&gt;Short Answer&lt;/h3&gt;&#xA;&lt;p&gt;Death!&lt;/p&gt;&#xA;&lt;h3&gt;Longer Explanation&lt;/h3&gt;&#xA;&lt;p&gt;In terms of the cellular and molecular level, many of the relatively weak interactions holding a person together are disrupted by cold temperatures. As a cell freezes, most of its  proteins and lipid membrane content will denature and &amp;quot;fall apart&amp;quot;, the same as if you boiled it.&lt;/p&gt;&#xA;&lt;p&gt;As with many things in biology, the problem is water. At room temperature, the lipid bilayers and proteins of a cell are held together largely by way of a complex network of interactions with the surrounding water. If the cell gets too hot or too cold this network of interactions between biomolecules and water falls apart. This leads to a disruption of the cell's overall organization*, which in turn can cause problems up to and including complete cell rupture and death.&lt;/p&gt;&#xA;&lt;p&gt;So in order to preserve a living creature under cryonic conditions you need to replace the water in and around its cells with a different molecule that will maintain most of the normal intermolecular interactions even under conditions of extreme cold. There are protocols for freezing cell cultures that use various different substances as replacements for water, such as glycerol or &lt;a href=&quot;http://www.med.umn.edu/starrlab/prod/groups/med/@pub/@med/@starrlab/documents/content/med_content_370794.html&quot; rel=&quot;noreferrer&quot;&gt;DMSO&lt;/a&gt;, and there's a &lt;a href=&quot;http://scienceline.org/2008/06/ask-mahan-frogfreeze/&quot; rel=&quot;noreferrer&quot;&gt;frog that loads its own blood with carbohydrates at low temperatures&lt;/a&gt; in order to turn it into a better cryonic medium.&lt;/p&gt;&#xA;&lt;h3&gt;footnote&lt;/h3&gt;&#xA;&lt;p&gt;*The disruption of a cell's organization at extreme cold is likely to persist even if the cell is brought back to room temperature. See &lt;a href=&quot;http://www.ingentaconnect.com/contentone/cryo/cryo/2013/00000034/00000001/art00007&quot; rel=&quot;noreferrer&quot;&gt;Gulevsky, et al&lt;/a&gt; for a complete review of the thermodynamics of cold denaturation.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2017-11-08T18:48:11.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27763" PostTypeId="2" ParentId="2721" CreationDate="2015-01-17T00:29:23.310" Score="5" Body="&lt;p&gt;A group of tightly linked genes that are involved in similar molecular pathway is called a &lt;a href=&quot;http://en.wikipedia.org/wiki/Supergene&quot; rel=&quot;nofollow noreferrer&quot;&gt;supergene&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the pleasure to formulate a slight opposition to @shigeta's answer, I will give some examples of supergenes in eukaryotes.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;In &lt;em&gt;Primula&lt;/em&gt;, heterostyly is controlled by a supergene.&lt;/li&gt;&#xA;&lt;li&gt;In &lt;a href=&quot;http://en.wikipedia.org/wiki/Papilio_memnon&quot; rel=&quot;nofollow noreferrer&quot;&gt;Papilio memno&lt;/a&gt;, mimicry is controlled by a supergene.&lt;/li&gt;&#xA;&lt;li&gt;In some species of ants, some social behaviour is caused by a supergene.&lt;/li&gt;&#xA;&lt;li&gt;Sexual chromosomes (and this is quite common) can be considered as supergenes.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Globally speaking, every locus that is under antagonist sexual in different sex/castes/ecotype/whatever is likely to start forming a supergene as soon as another locus that has antagonist effect appears in its vicinity because the presence of two such genes on the same chromosomal region will select for arrest of recombination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But of course, those represent exceptions (however common these exceptions might be) but in general, I don't think you should expect that adjacent genes would have similar functions.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2017-02-17T15:37:28.567" LastActivityDate="2017-02-17T15:37:28.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27764" PostTypeId="2" ParentId="27567" CreationDate="2015-01-17T01:42:25.297" Score="11" Body="&lt;p&gt;I have been looking into this for days, but this plant is difficult to identify without its flower. I reached out to a botanist at Dartmouth, who suggests that it is either one of two species-- a nasturtium (Tropaeoleum sp.) or a geranium (pelargonium). The leaves are what are called peltate, meaning shield-like with the stem attached directly underneath. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZP01A.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Botanist at Dartmouth&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://etc.usf.edu/clipart/48400/48426/48426_peltate_leaf.htm&quot; rel=&quot;noreferrer&quot;&gt;http://etc.usf.edu/clipart/48400/48426/48426_peltate_leaf.htm&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;On further research, specifically of peltate leaves, this plant looks more like Umbilicus rupestris, which is commonly found in southern Europe and grows in damp rock crevices!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Umbilicus_rupestris&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Umbilicus_rupestris&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11631" LastEditorUserId="11631" LastEditDate="2015-01-17T02:08:13.227" LastActivityDate="2015-01-17T02:08:13.227" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27766" PostTypeId="1" CreationDate="2015-01-17T08:26:30.080" Score="2" ViewCount="64" Body="&lt;p&gt;Could it be that a given pathway of enzymes (or proteins in general) may fulfill different purposes in a cell by for shifting partners? Say protein A activates B, B activates C and C has a specific action X (e.g. X = phosphorylation of protein D). Now do pathways exist where, e.g., A can activate C directly resulting in action Y (e.g. dephosphorylation of protein D)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At this time I am in need of real-world examples of this scenario, but I can't find any. Can anyone help? &lt;/p&gt;&#xA;" OwnerUserId="13057" LastEditorUserId="11841" LastEditDate="2015-01-17T15:09:58.297" LastActivityDate="2015-03-31T01:15:43.780" Title="Is it possible that a set of functionally related proteins in a pathway fulfill different functions?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="6" ClosedDate="2015-03-31T08:57:53.690" ContentLicense="CC BY-SA 3.0" />
  <row Id="27778" PostTypeId="1" CreationDate="2015-01-17T15:47:47.723" Score="3" ViewCount="39" Body="&lt;p&gt;I am looking for a statistical approach to inter-codon mutations. For example a 64*64 (64*63 actually) table, that contain the possibility of mutation from one codon to another codon (CCA to CAA or CGG... for example).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any articles, databases or others that provide such table?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please comment if my question is not completely clear.&#xA;I searched but didn't find an answer for this question in Google Scholar.&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="14826" LastEditDate="2015-03-29T17:54:37.183" LastActivityDate="2015-03-29T17:54:37.183" Title="Inter-codon mutations statistical analysis" Tags="&lt;dna&gt;&lt;dna-sequencing&gt;&lt;mutations&gt;&lt;nucleic-acids&gt;&lt;codon&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27779" PostTypeId="1" AcceptedAnswerId="27789" CreationDate="2015-01-17T15:57:15.377" Score="8" ViewCount="670" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphene&quot;&gt;Phosphene&lt;/a&gt; from rubbing the closed eyes where first described at least &lt;a href=&quot;http://dx.doi.org/10.1007%2Fbf00165665&quot;&gt;since Ancient Greece&lt;/a&gt;, but I caught myself thinking that I wouldn't want to try it out. So I wonder, how safe it is to actually rub closed eyes or put pressure on the human eye in general? Can frequent but small, or rare but sharp, application of pressure cause myopia or other eye disorders? What is the maximum pressure before the eye is damaged? What happens with the eye if you accidentally hit it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I remember several times during my childhood accidentally poking myself in the eye with a finger—the experience was very uncomfortable, I couldn't even open the eye for several minutes, but I don't think anything happened to my eyes since then, and my myopia was probably caused by any other factor than pressure damage.&lt;/p&gt;&#xA;" OwnerUserId="13062" LastActivityDate="2015-01-17T22:46:18.337" Title="Is it dangerous to rub closed eyes?" Tags="&lt;human-eye&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27780" PostTypeId="1" CreationDate="2015-01-17T17:45:34.350" Score="0" ViewCount="783" Body="&lt;p&gt;I need to perform tuberculosis mutation analysis. First step I need to do is to align sequences in fasta format against one reference file. i tried CLC genomics workstation --- it hangs on 60 000 lines of fasta reference file for entire day. Please advise what technology and tutorial to use to do that task.&lt;/p&gt;&#xA;" OwnerUserId="12935" LastActivityDate="2015-01-18T16:17:33.067" Title="How to do whole genome sequence alignment in R or Ruby/C++, any good language?" Tags="&lt;bioinformatics&gt;&lt;mutations&gt;&lt;sequence-alignment&gt;&lt;gwas&gt;" AnswerCount="2" CommentCount="2" ClosedDate="2015-01-20T10:58:28.323" ContentLicense="CC BY-SA 3.0" />
  <row Id="27781" PostTypeId="2" ParentId="27780" CreationDate="2015-01-17T18:09:47.537" Score="3" Body="&lt;p&gt;Found a tool:  MUMmer is a system for rapidly aligning entire genomes.  The current&#xA;version (release 3.0) can find all 20 base pair maximal exact matches between&#xA;two bacterial genomes of ~5 million base pairs each in 20 seconds, using 90 MB&#xA;of memory, on a typical 1.8 GHz Linux desktop computer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you know a better programmatic approach, let me know, please&lt;/p&gt;&#xA;" OwnerUserId="12935" LastActivityDate="2015-01-17T18:09:47.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27783" PostTypeId="1" AcceptedAnswerId="27786" CreationDate="2015-01-17T19:14:03.390" Score="1" ViewCount="12958" Body="&lt;p&gt;When you open up a chicken leg or a clam and you remove the meat, there is this little part that is connected to the bone and is not easily scraped off. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is this part called and what mechanism does it use to connect to the bone or the shell?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorDisplayName="user24284" LastEditDate="2017-10-29T05:29:53.973" LastActivityDate="2017-10-29T05:29:53.973" Title="What do you call that part of the muscle that connects directly to the bone?" Tags="&lt;human-anatomy&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27784" PostTypeId="1" CreationDate="2015-01-17T19:23:59.413" Score="5" ViewCount="9836" Body="&lt;p&gt;During cardiac cycle, there are two periods in which the heart volume doesn’t change, but there is a change in tension/pressure. It takes about 0.25-0.35 second to achieve this change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I searched in Google and Wikipedia, but could not find the reason, so I decided to ask this question.&lt;/p&gt;&#xA;" OwnerDisplayName="user13058" LastEditorUserId="11841" LastEditDate="2015-01-25T05:46:49.217" LastActivityDate="2018-01-13T09:42:19.567" Title="What’s the reason for isovolumic contraction and isovolumic relaxation?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27786" PostTypeId="2" ParentId="27783" CreationDate="2015-01-17T20:02:56.740" Score="4" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Tendon&quot; rel=&quot;nofollow noreferrer&quot;&gt;tendon&lt;/a&gt; is the part of the muscle that connects directly to the bone.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A tendon (or sinew) is a tough band of fibrous connective tissue that usually connects muscle to bone and is capable of withstanding tension. Tendons are similar to ligaments and fasciae; all three are made of collagen. Ligaments join one bone to another bone; fasciae connect muscles to other muscles. Tendons and muscles work together to move bones.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kfyak.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image was taken from the wikipedia link.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastActivityDate="2015-01-17T20:02:56.740" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27787" PostTypeId="2" ParentId="27780" CreationDate="2015-01-17T20:31:52.113" Score="4" Body="&lt;p&gt;I think you incorrectly identified what type of analysis you want.  You mention that you have numerous sequences in a fasta file (you mention at least 60,000) that need to be aligned to a single genome.  So your not doing a pairwise alignment, your aligning DNA sequences to a reference genome.  The fastest known algorithm for this is burrow-wheeler transformation mappings which can be accomplished with tools such as bowtie, bowtie2, BWA, etc...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm assuming your experimental design is something like this: You have sequencing data from a number of tissue samples with half or some number of samples being a disease state, the other being normal.  So you want to create alignment files for each sample, and than determine where these alignments differ.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After alignment, you will need to create a variant file (VCF) which can be accomplished using samtools or GATK.  The VCF file will give you all bp locations with alternative alleles from your reference genome.  Which seems to be what your looking for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Citations that could be useful:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Li H.&lt;em&gt;, Handsaker B.&lt;/em&gt;, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.broadinstitute.org/gatk/about/cited-by&quot; rel=&quot;nofollow&quot;&gt;https://www.broadinstitute.org/gatk/about/cited-by&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The last url contains 145 publications that used GATK to look at population-scale variant differences.  These publications could be very useful to see how other papers have accomplished variant discovery for the use for scientific inference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For User137 - since I can't comment on this board yet; you want to use a program called muscle.  There is an MS-DOS version and it can align short sequences extremely fast.&lt;/p&gt;&#xA;" OwnerDisplayName="user11727" LastEditorDisplayName="user11727" LastEditDate="2015-01-18T16:17:33.067" LastActivityDate="2015-01-18T16:17:33.067" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27788" PostTypeId="1" CreationDate="2015-01-17T21:16:36.427" Score="4" ViewCount="161" Body="&lt;p&gt;The TCA cycle intermediate Isocitrate dehydrogenase commonly undergoes point mutations in cancers. This allows IDH to reduce a-Ketogluterate to 2Hydoxygluterate, causing a reduction in pVHLs ability to hydroxylate HIF-1a, and a subsequent accumulation of HIF-1a. This leads to angiogenesis via VEGF. If the cancer cell is converting its a-KG away form the TCA cycle, how does the cell make up for the loss of TCA function, and subsequent ETC function for energy production? Why would the cancer cell prefer to lose high yield energy production in exchange for low yield energy production?&lt;/p&gt;&#xA;" OwnerUserId="12883" LastActivityDate="2015-12-08T18:02:34.320" Title="Energy metabolism in Cancer cells" Tags="&lt;cell-biology&gt;&lt;metabolism&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27789" PostTypeId="2" ParentId="27779" CreationDate="2015-01-17T22:46:18.337" Score="5" Body="&lt;p&gt;The answer is both yes and no, depending on how often and how hard one rubs his or her own eyes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Occasional light rubbing is not a problem-- it stimulates tear production and relieves stress by lowering heart rate via the oculocardiac reflex. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Frequent hard rubbing is a problem-- it can worsen eyesight in people who already have progressive myopia, and worst-case-scenario lead to retinal detachment. For those with glaucoma, can interrupt blood flow and even cause nerve damage. It can (but rarely) scratch, tear, or deform the cornea leading to pain and distorted vision. It can lead to damage of small delicate vessels, causing a subconjunctival hemorrhage, which is benign despite its worrisome appearance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is generally recommended to just avoiding rubbing the eyes altogether! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;www.abc.net.au/health/talkinghealth/factbuster/stories/2012/09/18/3592456.htm&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.visioneyeinstitute.com.au/dangers-rubbing-eyes/&quot; rel=&quot;noreferrer&quot;&gt;http://www.visioneyeinstitute.com.au/dangers-rubbing-eyes/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11631" LastActivityDate="2015-01-17T22:46:18.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27790" PostTypeId="1" CreationDate="2015-01-18T00:22:16.923" Score="2" ViewCount="476" Body="&lt;p&gt;As I understand it, in yeast ageing there is daughter cell and mother cell. The daughter cell is has newly &quot;fresh&quot; DNA and mother cell dies after some counts of replication. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens to the accumulated DNA damage in the yeast mother cell? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of theory of human ageing is accumulation of damage in nuclear DNA. The daughter yeast cell is clone of mother, and has same DNA. What happens with this damage?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;b&gt;Edit to simplify:&lt;/b&gt; Why is the DNA damage not transferred at all to the daughter cell? The repair mechanism in humans is evidently not perfect, because DNA damage is one of major ageing theories. So if we die from this, how do yeast get around the detrimental affects of DNA damage that cause ageing in humans?&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="3553" LastEditDate="2015-01-26T12:38:55.640" LastActivityDate="2015-09-29T11:38:29.197" Title="How does DNA damage cause ageing in yeast?" Tags="&lt;yeast&gt;&lt;dna-damage&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27791" PostTypeId="1" CreationDate="2015-01-18T00:51:05.880" Score="4" ViewCount="2804" Body="&lt;p&gt;When I took a course on genetics and evolution, I learned that recombination and sexual reproduction is advantageous compared to asexual reproduction. Sexual reproduction allows more combinations of DNA because of recombination, allowing more variations of species, causing natural selection to &quot;choose&quot; different variations of species to reproduce and share their genes to help the species from dying out. On the other hand, asexual reproduction doesn't allow recombination. So species can only rely on mutational changes to keep a species safe from extinction. Therefore, why don't we see more sexually reproducing species than asexually reproducing species? Sexually reproducing species have an advantage, don't they?&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="3624" LastEditDate="2016-01-21T16:11:01.587" LastActivityDate="2016-09-21T21:57:40.383" Title="Why asexual reproduction?" Tags="&lt;genetics&gt;&lt;evolution&gt;&lt;reproduction&gt;&lt;recombination&gt;&lt;asexual-reproduction&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27792" PostTypeId="1" AcceptedAnswerId="27803" CreationDate="2015-01-18T01:03:53.343" Score="6" ViewCount="5921" Body="&lt;p&gt;How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The book's answer is $20^{12}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I disagree. This result distinguishes the following two polypeptides even though they are exactly the same polypeptide:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Met)x11-Glu&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glu-(Met)x11&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I right? How would I otherwise answer this question? My background in probabilities is very weak.&lt;/p&gt;&#xA;" OwnerUserId="8516" LastActivityDate="2015-01-18T04:14:58.710" Title="How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids?" Tags="&lt;molecular-biology&gt;&lt;proteins&gt;&lt;amino-acids&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27793" PostTypeId="1" AcceptedAnswerId="27795" CreationDate="2015-01-18T01:17:45.073" Score="2" ViewCount="70" Body="&lt;p&gt;I know that by now this is old new but I heard that a cell that used a synthetic pair of nucleotides, called X and Y, have been made. My question was, how did the cell understand the X and Y nucleotides during translation and how was it even represented in mRNA? It must have been represented differently, possibly using X and Y nucleotides only. That's the only way I can think of that causes the cell to make 172 amino acids instead of the usual 20. By the way I read this in the Discover magazine, January issue.&lt;/p&gt;&#xA;" OwnerUserId="10401" LastActivityDate="2015-07-18T19:20:12.990" Title="How semi-synthetic cell with artificial DNA works" Tags="&lt;dna&gt;&lt;cell&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27794" PostTypeId="2" ParentId="27792" CreationDate="2015-01-18T01:23:51.473" Score="6" Body="&lt;p&gt;Think of the amino acid choices as 12 seats. In the first seat, we have 20 choices. In the next seat, we have 20 choices, and this continues. Therefore, we have that &#xA;$$&#xA;\underbrace{20\cdots 20}_{12\text{ times}} = 20^{12}&#xA;$$&#xA;For your question about the the polypeptides, (Met)x11-Glu is not the same as Glu-(Met)x11, order matters.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Up to this point, we have considered the sequence of amino acids that make up a protein. This is the first of several levels of protein structure, illustrated in Fig. 4.4. The sequence of amino acids in&#xA;  a protein is its primary structure. The sequence of amino acids&#xA;  ultimately determines how a protein folds &lt;a href=&quot;http://www.macmillanhighered.com/catalog/static/whf/biologyhowlifeworks/media/rethinking/assessment/HLWChapter4.pdf&quot;&gt;[1]&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="12909" LastActivityDate="2015-01-18T01:23:51.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27795" PostTypeId="2" ParentId="27793" CreationDate="2015-01-18T01:39:02.493" Score="2" Body="&lt;p&gt;The altered E Coli still only made use of the regular 20 amino acids (presumably).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at the &lt;a href=&quot;http://www.nature.com/nature/journal/v509/n7500/full/nature13314.html&quot; rel=&quot;nofollow&quot;&gt;original citation&lt;/a&gt;, Malyshev et al didn't characterize the RNA in their altered E Coli at all. All they did was add free X and Y to the E Coli's growth medium and add a gene to the E Coli that expressed an &lt;code&gt;algal nucleotide triphosphate transporter&lt;/code&gt;. Malyshev et al then demonstrated that replication (copying of the DNA) proceeds normally and in such a way as to preserve the X and Y content.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So no information as to whether any of the products downstream from the DNA (ie mRNA, proteins, etc) were affected by their modifications.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2015-07-18T19:20:12.990" LastActivityDate="2015-07-18T19:20:12.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27796" PostTypeId="2" ParentId="27791" CreationDate="2015-01-18T01:51:40.943" Score="11" Body="&lt;p&gt;When you say, why don't we see more sexually reproducing species than asexual, I presume you are referring to bacteria, protists, archaea, some fungi, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most multicellular organisims do reproduce sexually, which makes sense since an organism would need to be multicellular to have cells specialized for gametes. As you stated, the advantage is that sexual reproduction offers an advantage by allowing more rapid generation of genetic diversity, allowing adaptation to changing environments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, look at the single-celled organisms that reproduce asexually. Asexual reproduction is beneficial in many circumstances in that it can create individuals rapidly and in large quantities. For example, yeast can duplicate every hour under the proper conditions. For yeast, that means survival by sheer numbers. For us, it means we can make bread in a few hours.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you believe asexually reproducing organisms are at a disadvantage due to lack of genetic diversity, consider bacteria and antibiotic resistance. The rapid generation times allow mutations to be selected for in particular circumstances. Penicillin was introduced in 1941. Two years after this landmark event, strains of Penicillin-resistant S. aureus had already emerged. Now, perhaps 2% of Staph. aureus (SA) is susceptible to penicillin, and some SA are &quot;superbugs&quot; with multidrug resistance: good for Staph, bad for us.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, it is possible for single-celled organisms to &quot;share&quot; DNA through mechanisms sometimes likened to sexual reproduction; lateral gene transfer occurs through conjugation, transformation and transduction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, both asexually and sexually reproducing organisms are well-suited to their ecological niches.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-18T01:51:40.943" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27797" PostTypeId="2" ParentId="27792" CreationDate="2015-01-18T02:07:59.780" Score="3" Body="&lt;p&gt;The individual amino acids are not symmetrical. Thus, your two example peptides are not chemically equivalent, and the $20^{12}$ figure is correct.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2015-01-18T02:07:59.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27799" PostTypeId="1" AcceptedAnswerId="27800" CreationDate="2015-01-18T02:35:15.177" Score="42" ViewCount="82825" Body="&lt;p&gt;Why draw blood from veins rather than arteries? Is it more convenient or safer?&lt;/p&gt;&#xA;" OwnerUserId="11855" LastActivityDate="2015-09-23T10:38:57.880" Title="Why draw blood from veins rather than arteries?" Tags="&lt;hematology&gt;&lt;blood-circulation&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="17" ContentLicense="CC BY-SA 3.0" />
  <row Id="27800" PostTypeId="2" ParentId="27799" CreationDate="2015-01-18T02:54:30.000" Score="54" Body="&lt;p&gt;Veins have several advantages over arteries. From a purely practical standpoint, veins are easier to access due to their superficial location compared to the arteries which are located deeper under the skin. They have thinner walls (much less smooth muscle surrounding them) than arteries, and have less innervation, so piercing them with a needle requires less force and doesn't hurt as much. Venous pressure is also lower than arterial pressure, so there is less of a chance of blood seeping back out through the puncture point before it heals. Because of their thinner walls, veins tend to be larger than the corresponding artery in the area, so they hold more blood, making collection easier and faster. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, it is somewhat safer if a small embolism (bubble in the blood) is introduced into a vein rather than an artery. Blood flow in veins always goes to larger and larger vessels, so there is very little chance of a vessel being blocked by the embolism before the bubble reaches the heart/lungs and is hopefully destroyed. Blood flow in an artery, on the other hand, always moves into smaller and smaller vessels, eventually ending in capilllaries, and there is a chance that a bubble introduced by a blood draw (generally rare) or more commonly an intravenous line (IV) could block a small blood vessel, potentially leading to hypoxia in the affected tissues.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2015-01-24T15:00:07.330" LastActivityDate="2015-01-24T15:00:07.330" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27801" PostTypeId="2" ParentId="27799" CreationDate="2015-01-18T02:55:18.823" Score="16" Body="&lt;p&gt;Right of the bat, veins are superficial so it is much easier to hit a vein than an artery. Arterial sticks are very difficult if you are not practiced at them while veins are much much easier. Also arterial sticks have a very specific purpose usually for example arterial blood gas. Also veins are low pressure compared to the higher pressure of arteries so less chance of bleeding. &lt;/p&gt;&#xA;" OwnerUserId="13066" LastActivityDate="2015-01-18T02:55:18.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27802" PostTypeId="2" ParentId="27791" CreationDate="2015-01-18T03:03:43.853" Score="6" Body="&lt;p&gt;This just in addition to @anongoodnurse's excellent answer. It was mentioned in the OP that asexual organisms do not undergo recombination; this is not true. Recombination is used for integration of foreign DNA into prokaryotic chromosomes and for repair. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, don't underestimate the power of mutational change in rapidly reproducing organisms. While mutation rate is low, consider the effect when it is applied to millions of individuals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, just an interesting example of the ability of bacteria to evolve. Many organisms can rearrange foreign DNA for their benefit. I will mention the specific example (because it's what I work with) of transforming &lt;em&gt;B subtilis&lt;/em&gt; with a plasmid containing an antibiotic resistance marker and somewhat toxic gene. Often you will find transformed bacteria that have rearranged the plasmid to delete or inactivate the toxic gene while still retaining the resistance gene. Thus they can still grow in the selective medium and manage to be of no use to me whatsoever!&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-01-18T03:03:43.853" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27803" PostTypeId="2" ParentId="27792" CreationDate="2015-01-18T04:14:58.710" Score="7" Body="&lt;p&gt;Judging from what you have said, I assume that combinatorics is not a problem to you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe your problem is that you think Glu-(Met)x11 is equivalent to (Met)x11-Glu, just turned around. However, that is not a correct mindset. Amino acids are not symmetrical molecules, therefore reversed linear combination does not create a turned-around (be it chiral or not) form of a similar amino acid. My guess is that you write amino acid names in consecution when representing peptides. This method has a small problem that it does not incorporate directionality of molecules. Drawing the whole molecule may be a solution, but that is too much chore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My solution is to add a small mark (perhaps an arrow, or a &gt; mark) to represent a specific side of the amino acid molecule (amine group or carboxyl group), so that mirroring the sequence (so that the mark would be at the &quot;other&quot; side of each amino acid) would actually create a peptide molecule different from reversing the sequence (so that the mark is still at the &quot;normal&quot; side of each amino acid). If you think that doesn't look good, you can draw a frame around each amino acid, where one side of the amino acid has a dent and the other side has a bump (to represent the amine and carboxyl groups) so that only a bumped side can connect to a dented side. Mirroring the sequence would also reverse the positions of the bumps and dents, thereby creating a different peptide molecule than merely reversing the sequence while keeping the positions of the bumps and dents in place.&lt;/p&gt;&#xA;" OwnerUserId="13067" LastActivityDate="2015-01-18T04:14:58.710" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27804" PostTypeId="2" ParentId="20400" CreationDate="2015-01-18T04:53:26.673" Score="2" Body="&lt;p&gt;As the siphuncle pumps cameral liquid out of a chamber, the pressure of the chamber falls and nitrogen, oxygen, and some carbon dioxide diffuse into the chamber.  Sea water gas pressures are in equilibrium with atmospheric gases (oxygen and nitrogen) and are in equilibrium with nautilus blood.  Hence as cameral liquid is pumped out of the chamber, gases enter from the blood.  But it would make no difference to the buoyant state of the animal if gases entered or if there were a vacuum.  The emptying mechanism relies on sodium pumps transporting salt out of the cameral liquid.  There is no way to duplicate this biological mechanism in a mechanical system.  &lt;/p&gt;&#xA;" OwnerUserId="13068" LastActivityDate="2015-01-18T04:53:26.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27806" PostTypeId="2" ParentId="27784" CreationDate="2015-01-18T07:42:06.970" Score="6" Body="&lt;p&gt;To put it in very simple words the reason for isovolumetric contaction and relaxation is to make the necessary pressure changes that is necessary to allow blood to flow into or flow out of the ventricles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The basic formula you need to remember to understand this is:-&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Fluids flow from high pressure area to low pressure area along the pressure gradient (Eg: Injecting a drug into blood stream - as the pressure in the syringe is higher than the pressure in blood vessel, the drug flows into the blood vessel)&lt;/li&gt;&#xA;  &lt;li&gt;Pressure is inversely proportional to volume (when temperature is constant) - this is Boyle's law. In a container with a fixed amount of fluid an increase in the volume of container will cause a proportionate amount of fall in the pressure in the container and vice-versa&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4AzmC.jpg&quot; alt=&quot;flow pressure relationship&quot;&gt;  &lt;img src=&quot;https://i.stack.imgur.com/04bTW.jpg&quot; alt=&quot;Boyle&amp;#39;s Law&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Isovolumetric contraction&lt;/strong&gt;: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The end-diastolic pressure in the aorta is in the range of approximately 90-100 mm of Hg. For blood to flow from left ventricle to aorta, the pressure in the left ventricle should exceed the pressure in the aorta. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As long as the pressure in the left ventricle is lesser than the pressure in the left atrium, the blood flows from Left Atrium to Left Ventricle. When Left Ventricle starts contracting the pressure in the LV rapidly overcomes the pressure in left atrium leading to closure of the mitral valve. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the pressure in the LV is greater than the pressure in the LA. So no blood flows in. At the same time the pressure in the LV is not sufficient to overcome the pressure in the aorta. So the semilunar valve remains closed. The ventricle continues contracting causing a time period in which there is increase in pressure without volume change as both inlet and outlet are closed. This period is called period of isovolumic contraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The isovolumic contraction ends when the pressure in the left ventricle becomes higher than the pressure in the aorta, which will cause the semilunar valves to open and blood to flow from left ventricle to aorta.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Isovolumic Relaxation&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reverse happens in isovolumic relaxation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the blood volume in the ventricle decreases and the left ventricle starts relaxing the pressure in the left ventricle falls. When the pressure gets below that of the aorta, the semilunar valve closes. But the pressure in the ventricle is still higher than the pressure in the left atrium. So the mitral valve remains closed. So here too both the inlet and outlet are closed but as the ventricle is relaxing the pressure keeps falling. So till the pressure in the left ventricle falls below that of the left atrium, there is a time period volume is constant and the pressure keeps falling - this is called Isovolumic Relaxation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This period is followed by opening of the mitral valve (as the pressure in the LV falls below that of the LA) and blood flows into the ventricle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take a look at the phonocardiogram linked in Majid's answer. It will help you understand what I explained.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this explains your question&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-01-18T07:47:44.240" LastActivityDate="2015-01-18T07:47:44.240" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27808" PostTypeId="2" ParentId="9920" CreationDate="2015-01-18T08:30:01.293" Score="4" Body="&lt;p&gt;The frequency fluctuations will be determined by a standard model of selection as found in any basic population genetics text. In this scenario they take a very basic form: during each long period $i$ the frequency of $A_1$ increases from $f_i$ to $f_i\cdot (1+s_1)^{n_1}$ and during each short period $j$ the frequency of $A_1$ decreases from $f_j$ to $f_j\cdot (1/(1+s_2))^{n_2}.$ Thus over each pair of periods the frequency of $A_1$ changes by $(1+s_1)^{n_1}/(1+s_2)^{n_2}$. If this quantity exceeds 1, $A_1$ goes to fixation; if it is less than one $A_2$ goes to fixation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More generally, for an infinite population in a fluctuating environment, the allele with the higher geometric mean fitness will go to fixation. Early discussions of these results are due to Dempster (1955; &lt;em&gt;Cold Spring Harbor Symp. Quant. Biol.&lt;/em&gt;), Haldane and Jayakar (1963; &lt;em&gt;J. Genetics&lt;/em&gt;), and Lewontin and Cohen (1969; &lt;em&gt;PNAS&lt;/em&gt;).&lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="13072" LastEditDate="2015-01-22T03:44:08.897" LastActivityDate="2015-01-22T03:44:08.897" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27809" PostTypeId="1" CreationDate="2015-01-18T10:29:42.597" Score="7" ViewCount="319" Body="&lt;p&gt;The heterochromatin is generally localized at the nuclear periphery (also near nuclear lamina), whereas active genes are preferentially found in the nuclear interior. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Children with Hutchinson-Gilford syndrome have a mutation in a LMNA gene, which codes lamin A and C, therefore, mutation in a LMNA gene causes overexpression of genes near nuclear lamina, this shows that nuclear lamina has something to do with gene expression regulation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the mechanism by which lamins regulate gene expression?&lt;/p&gt;&#xA;" OwnerUserId="6214" LastEditorUserId="6307" LastEditDate="2015-04-01T21:32:32.670" LastActivityDate="2015-10-18T20:03:00.010" Title="What is the mechanism by which lamins regulate gene expression?" Tags="&lt;cell-biology&gt;&lt;gene-regulation&gt;&lt;chromatin&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27812" PostTypeId="2" ParentId="27579" CreationDate="2015-01-18T16:24:42.910" Score="2" Body="&lt;p&gt;You mentioned something odd in the tittle &quot;adipocyte count&quot;, this was likely a mistake, but I will address it anyway. I recall something about liposuction not being preventative for&#xA;   diabetes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can have more adipocytes with less lipids in each cell, or fewer&#xA;   adipocytes with more lipid in each cell. Hypertrophy vs hyperplasia, just like in the question you asked on muscles elsewhere on this forum. Anyway, when a patient gets liposuction they decrease the number of&#xA;   adipocytes. Then if s/he gains the weight back the size of their&#xA;   individual adipocytes will be larger than it was before the&#xA;   liposuction. Somehow this was bad, and it increased insulin resistance. &lt;strong&gt;in a way, decreased &lt;em&gt;&quot;adipocyte count&quot;&lt;/em&gt; is dangerous.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;here is the other, obvious stuff on endocrine function of adipose tissue that you surely already know since your profile is very endocrine based, but anyway, here goes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adipose tissue has hormonal functions, secreting horomones (leptin, adiponectin, and resisting... these modify appetite as well as insulin resistance) and modifying them (converting testosterone to estrogen vi the enzyme aromatase). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The adipose-derived hormones are quite mysterious to me, I don't know much about them. The effects of the aromatase in adipose tissue are more obvious:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;men will have increased estrogen levels (for example leading to gynecomastia aka man boobs, as a chubby guy I know this all to well)&lt;/li&gt;&#xA;&lt;li&gt;women will have higher estrogen which will stimulate LH secretion from the pituitary stimulating theca intern cells in the ovary which will increase testosterone levels. The condition in women is known as PCOS.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In a person with little adipose tissues, there will be less conversion of testosterone to estrogen, so men will have less estrogen. Women will also have less estrogen, and less testosterone, aka they will not have PCOS in those women that already have PCOS, but thats not saying much :)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&#xA;I may be wrong on some of this information, anyone please correct me.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2015-01-18T16:37:52.683" LastActivityDate="2015-01-18T16:37:52.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27815" PostTypeId="1" CreationDate="2015-01-18T18:51:22.993" Score="4" ViewCount="1131" Body="&lt;p&gt;how do macrophages  have the capacity to digest pathogen in opsonization but not in the            first time when the pathogen is new  and they play the role of antigen presenting cells(APCs) first they digest polypeptide of antigen and then let the plasma cells first secrete an antibody and after that they can destroy antigens?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastActivityDate="2015-01-18T23:37:52.720" Title="how do macrophages have the capacity to digest pathogen in opsonization" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27816" PostTypeId="1" AcceptedAnswerId="27823" CreationDate="2015-01-18T19:12:59.543" Score="1" ViewCount="272" Body="&lt;p&gt;Why would some genes have more than two modes in their expression distribution? What external factors would cause this anomaly?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm referring to the expression distribution of a gene across different tissue samples. For example, if one was to download a bunch of data from NCBI GEO, and pinpoint one gene and plot the expression level versus the frequency for that gene across all those data sets, some genes would have more than 2 modes (2 expression levels with very high frequency). This is the only case I'm interested in: more than 2 modes - not bimodal. So what would cause more than two modes?&lt;/p&gt;&#xA;" OwnerUserId="13082" LastEditorUserId="13082" LastEditDate="2015-01-19T05:21:41.590" LastActivityDate="2015-01-19T05:21:41.590" Title="Multi-modal distribution for gene expression data" Tags="&lt;gene-expression&gt;&lt;biostatistics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27817" PostTypeId="2" ParentId="27815" CreationDate="2015-01-18T19:54:04.917" Score="2" Body="&lt;p&gt;It's a simple matter of ionic charge&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Opsonization works because it is masking negative charge with positive charge. Phagocytosis works on positively charged things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your right though, the sequence seems odd. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;First something is phagocytosed (by a macrophage or another monocyte-derivative, these are the APCs... but neutrophils, which are not APCs or monocyte-derivates also perform phagocytosis but they dot not have the MHC-II to be described)&lt;/li&gt;&#xA;&lt;li&gt;then digested in endosome/lysosomal, &lt;/li&gt;&#xA;&lt;li&gt;then presented on the MHC class II, &lt;/li&gt;&#xA;&lt;li&gt;recognized by TCR on T-cell, &lt;/li&gt;&#xA;&lt;li&gt;then much more complicated stuff to get to B cells to convert to plasma cells &lt;/li&gt;&#xA;&lt;li&gt;plasma cells secrete the antibody, in order for opsonization of the pathogen to be phagocytosis more easily. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Yet it was the initial phagocytosis that led to this. A bit of a circle.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are three answers: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;one is cytokines&lt;/li&gt;&#xA;&lt;li&gt;another one is about how the TLR receptor mediates phagocytosis&lt;/li&gt;&#xA;&lt;li&gt;a third is how complements act as opsonins&#xA;&lt;hr&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;local presence of &lt;strong&gt;cytokines&lt;/strong&gt; (ex. interleukins, interferon, TNF) from either innate or adaptive &quot;&lt;em&gt;immune system&lt;/em&gt;&quot; (by &quot;&lt;em&gt;immune system&lt;/em&gt;&quot; I mean immune cells other than macrophage, but also epithelium which secretes types of interferons) that lead to &quot;&lt;em&gt;signal transduction&lt;/em&gt;&quot; (&quot;&lt;em&gt;signal transduction&lt;/em&gt;&quot; is the intracellular chain reaction in response to the activation of the cytokine (or other ligand) binding to the receptor, too complicated for me to explain) that alters the behavior of macrophage to enhance phagocytosis.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;On the other hand, &lt;strong&gt;PAMPs&lt;/strong&gt; activate the &lt;strong&gt;TLR&lt;/strong&gt; which could permit phagocytosis without prior activation &lt;em&gt;from sources &quot;other&quot; than the thing being phagocytosis&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By &quot;&lt;em&gt;other&quot; things&lt;/em&gt; I mean opsonins and cytokines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;PAMPs&lt;/strong&gt; (pathogen associated molecular pattern) are things on the pathogen that are distinctively foreign to the host, like flagella or LPS [which is the outer membrane from gram (-) bacteria]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;TLR&lt;/strong&gt; is the receptor on the macrophage that recognizes PAMPs. I think that TLR simply enhances phagocytosis via signal transduction much like cytokines. As an interesting side note, the TLR is quite ancient in kingdom animalia, having it's origin in sponges  as close to the beginning as you get). Other aspects of the immune system evolved later on specifically in vertebrate. In fact the lymphocytes is unique to jawed vertebrate (aka absent in agnathans and invertebrate) and i don't know much about antibody production in non-mammals. Also in lower vertebrate and invertebrate, phagocytosis is done by hemocytes. In other words, the TLR is pretty fundamental as far as immune stuff goes, more so than cell types doing their things (ex. plasma cell making antibodies, macrophages doing phagocytosis).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;But there is also &lt;strong&gt;complement mediated opsonization&lt;/strong&gt;, primarily C3b but other complement proteins as well. Finally there are yet more (less important) opsonins, Mannose-binding lectin and C-reactive protein (CRP). all of these things are &quot;Acute phase reactants&quot; that are secreted by the liver under inflammatory conditions, mediated by cytokines. Complement is not always activated by the immunoglobulins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Complement is activated by &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;classical pathway, again Fc region of antibody (IgG/IgM), just like antibody mediated opsonization. In addition, classical pathway can be activated by CRP binding to microbial polysaccharides&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;&lt;p&gt;alternative pathway, which is the spontaneous hydrolysis of C3. Under normal (non-infected) circumstances, this is normally prevented by a variety of mechanisms.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;activation by mannose binding lectin. MVL recognizes certain sugars that are found in certain positions that are unique to bacteria, fungi, viruses.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I'm saying all these things as explanations of &lt;strong&gt;human&lt;/strong&gt; immune system. It's probably different in different animals, the more different the further away from human. The complement system has been discovered in primitive vertebrate (agnathans) and invertebrate (specifically in deuterostomes like protocordates and echinoderms) but there are variations. &lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2015-01-18T23:37:52.720" LastActivityDate="2015-01-18T23:37:52.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27819" PostTypeId="1" AcceptedAnswerId="27820" CreationDate="2015-01-19T01:30:16.717" Score="0" ViewCount="2776" Body="&lt;p&gt;Also, what is the definition of polar in this case? (9th Grade)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it have to do with the bonds it makes?&lt;/p&gt;&#xA;" OwnerUserId="13087" LastActivityDate="2015-01-19T02:36:46.537" Title="Why is water a polar molecule?" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ClosedDate="2015-01-19T03:31:22.260" ContentLicense="CC BY-SA 3.0" />
  <row Id="27820" PostTypeId="2" ParentId="27819" CreationDate="2015-01-19T01:44:17.317" Score="3" Body="&lt;p&gt;Polar means there's a higher density of electron on the oxygen and a lower density of electrons on the hydrogens. This has to do with the electronegativity of the elements in question. Hydrogen is in group 1 which likes to lose it's electron and oxygen in group 16 which likes to get two electrons (in this case one from each hydrogen) in order to complete the octet in it's valence shell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also it has to do with the shape, water molecules are not linear, but rather bent in a 'v' shape. the two sides are positively charged and the middle is negatively charged. if it were linear then the middle wouldn't matter, but because it is bent, on side has a negative charge and the other side has positive charge. It's not an negative/positive change the way it is in an ion, just a slight negative/positive charge.&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2015-01-19T01:55:33.690" LastActivityDate="2015-01-19T01:55:33.690" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="27821" PostTypeId="2" ParentId="27819" CreationDate="2015-01-19T02:36:46.537" Score="2" Body="&lt;p&gt;Polar simply means the electron density is not distributed evenly across a molecule. In water this is caused by the comparatively higher electronegativity of the Oxygen (you can think of this like Oxygen wants the electrons it shares in the covalent bond a lot more than the Hydrogen does so it keeps them closer but this is an oversimplification). This translates to the Oxygen having a partial negative charge (higher electron density) and the Hydrogen being slightly positive (lower electron density). The individual water molecules will form Hydrogen bonds between each other, with the positive Hydrogen of one molecule forming a weak bond with the negative Oxygen of another molecule. A molecule being polar has an effect on many of physical and chemical properties of the molecule.&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Electronegativity&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Electronegativity&lt;/a&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hydrogen_bond&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Hydrogen_bond&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="11858" LastActivityDate="2015-01-19T02:36:46.537" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27822" PostTypeId="1" AcceptedAnswerId="27824" CreationDate="2015-01-19T03:34:00.000" Score="24" ViewCount="31626" Body="&lt;p&gt;Children and teens can hear high pitched sounds that adults can't hear anymore. Why do adults lose high-frequency hearing?&lt;/p&gt;&#xA;" OwnerUserId="11855" LastEditorUserId="10055" LastEditDate="2015-01-19T12:54:56.860" LastActivityDate="2015-07-09T14:53:21.623" Title="Why do adults lose hearing at high frequencies?" Tags="&lt;hearing&gt;&lt;neurophysiology&gt;&lt;neurodegenerative-disorders&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="27823" PostTypeId="2" ParentId="27816" CreationDate="2015-01-19T04:43:17.980" Score="1" Body="&lt;p&gt;One trivial situation in which this can happen is when the tissue used for expression studies is heterogeneous. Different cells express different levels of the gene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bimodality can be observed when the system can actually occupy two stable states; i.e. a gene can either have a high expression or a low expression. When you sample the population you would get two peaks. Bistablity (two stable steady states) is a common phenomenon in biological systems and positive feedbacks generally exhibit such behavior. In bistable systems there is also an unstable steady state which lies &quot;between&quot; the two stable states (like a mountain separating two valleys). If the system is in the unstable state, it can fall to either of the two stable states. (See &lt;a href=&quot;http://jb.asm.org/content/194/5/1088.full&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article for an example). This concept can be extended to multistable systems but they are a little more complex than the simple feedbacks. However they can theoretically exist (I don't know of a biological example yet). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bimodality/multimodality can be also observed in the absence of a deterministic bistability in the system. This happens because of the expression noise due to stochasticity and is observed in case of transcription bursts (See &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006349512007837&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-01-19T04:43:17.980" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="27824" PostTypeId="2" ParentId="27822" CreationDate="2015-01-19T04:53:17.137" Score="31" Body="&lt;p&gt;Hearing declines with age and, typically, high frequencies are affected first. &lt;strong&gt;Age-related hearing loss&lt;/strong&gt; (or &lt;strong&gt;&lt;em&gt;presbyacusis&lt;/em&gt;&lt;/strong&gt; (&lt;a href=&quot;http://www.jneurosci.org/content/26/7/2115.full.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kujawa &amp;amp; Liberman, 2006&lt;/a&gt;)) is progressive and starts at the highest frequencies and as a person ages the lower frequencies are affected. The reduction in hearing sensitivity is caused by the &lt;strong&gt;loss of hair cells&lt;/strong&gt;. Hair cells are sensory cells in the inner ear that convert acoustic vibrations into electrical signals. These signals are transmitted to the brain via the auditory nerve.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of the &lt;strong&gt;tonotopic organization&lt;/strong&gt; of the inner ear (the &lt;em&gt;cochlea&lt;/em&gt;) one can conclude that presbyacusis develops from the basal to apical region. The following schematic of the cochlea from &lt;a href=&quot;http://www.britannica.com/EBchecked/media/537/The-analysis-of-sound-frequencies-by-the-basilar-membrane&quot; rel=&quot;nofollow noreferrer&quot;&gt;Encyclopædia Britannica, Inc.&lt;/a&gt; nicely shows the cochlear tonotopy (i.e., high frequencies in the base, low frequencies in the apex); &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ERAIB.jpg&quot; alt=&quot;cochlea&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to your question &lt;strong&gt;why the basal region is more sensitive to aging&lt;/strong&gt; - that is a very good and interesting question that has &lt;strong&gt;not been answered, as far as I am aware&lt;/strong&gt;. What is known, however, is that the basal regions of the cochlea are also more sensitive to the damaging effects of &lt;strong&gt;ototoxic antibiotics&lt;/strong&gt; such as kanamycin (&lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=3&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCkQFjAC&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fprofile%2FHuib_Versnel%2Fpublication%2F47660604_Effects_of_electrical_stimulation_on_the_acoustically_evoked_auditory-nerve_response_in_guinea_pigs_with_a_high-frequency_hearing_loss%2Flinks%2F0c96053cd1c55581f2000000&amp;amp;ei=JYe8VJjTO-PPmwX_4oGQCA&amp;amp;usg=AFQjCNHO_pbdR5L3pW2btsnZGDdtEo-iLA&amp;amp;sig2=S1nw5B9anvl__Iwy7eNgLA&amp;amp;bvm=bv.83829542,d.dGY&quot; rel=&quot;nofollow noreferrer&quot;&gt;Stronks &lt;em&gt;et al&lt;/em&gt;., 2011&lt;/a&gt;) and other aminoglycosides, and some &lt;strong&gt;chemotherapeutics&lt;/strong&gt; such as cisplatin (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596108/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Schacht &lt;em&gt;et al&lt;/em&gt;., 2012&lt;/a&gt;). In low doses these compounds specifically target the basal regions over the apical ones (at high doses the whole cochlea is affected). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps the &lt;strong&gt;specific anatomy and circulation&lt;/strong&gt; causes the basal region to be affected more by these chemicals. For example, blood flow may be enhanced basally whereby environmental and food-based chemicals may enter the basal region more readily (educated guesses, I can dig up references of authors posing these possibilities if necessary). This scenario may also contribute to presbyacusis, since it is quite imaginable that years of exposure to various substances may cause accumulation damage specifically to the basal parts of the cochlea. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, since high frequencies are coded in the basal region, and given that sound enters the cochlea in the basal region (see picture below), &lt;strong&gt;all sounds&lt;/strong&gt;, including damaging loud low-frequency stimuli &lt;strong&gt;first travel to the base&lt;/strong&gt; on their way to their point of processing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/M9fxb.jpg&quot; alt=&quot;Cochlea structure&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because sound is analyzed as a travelling wave, sound travel stops at that point where the frequency matches the cochlear characteristic frequency. There the wave quickly dies out due to cochlear filtering (&lt;a href=&quot;http://www.psypress.com/cw/mather-9781841696997/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mather, 2006&lt;/a&gt;); see the first picture above. In effect, more apical parts of the cochlea are exposed less frequently to (damaging) sound stimuli, while the &lt;strong&gt;base of the cochlea is exposed to all sounds entering the inner ear&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, &lt;strong&gt;chemical exposure and acoustic wear and tear&lt;/strong&gt; may be more prominent in the cochlear base, which can explain why &lt;strong&gt;presbyacusis starts at the very high frequencies and progresses to low frequencies&lt;/strong&gt; (upward in the cochlea) from there.         &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.britannica.com/EBchecked/media/537/The-analysis-of-sound-frequencies-by-the-basilar-membrane&quot; rel=&quot;nofollow noreferrer&quot;&gt;Encyclopedia Brittanica* The-analysis-of-sound-frequencies-by-the-basilar-membrane&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.jneurosci.org/content/26/7/2115.full.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kujawa &amp;amp; Liberman, &lt;em&gt;J Neurosci&lt;/em&gt; 2006; 26:2115-23&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.psypress.com/cw/mather-9781841696997/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mather, Foundations of Perception, 2009&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596108/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Schacht et al, Anat Rec Hoboken 2013; 295:1837-50&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=3&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCkQFjAC&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fprofile%2FHuib_Versnel%2Fpublication%2F47660604_Effects_of_electrical_stimulation_on_the_acoustically_evoked_auditory-nerve_response_in_guinea_pigs_with_a_high-frequency_hearing_loss%2Flinks%2F0c96053cd1c55581f2000000&amp;amp;ei=JYe8VJjTO-PPmwX_4oGQCA&amp;amp;usg=AFQjCNHO_pbdR5L3pW2btsnZGDdtEo-iLA&amp;amp;sig2=S1nw5B9anvl__Iwy7eNgLA&amp;amp;bvm=bv.83829542,d.dGY&quot; rel=&quot;nofollow noreferrer&quot;&gt;Stronks et al, Hear Res 2011; 272:95-107&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-09T14:53:21.623" LastActivityDate="2015-07-09T14:53:21.623" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27825" PostTypeId="2" ParentId="27760" CreationDate="2015-01-19T05:35:48.630" Score="1" Body="&lt;p&gt;One of the main factors that impacts rigor mortis is temperature. Basically, a smaller body would slow down the metabolic processes behind rigor more substantially. Also, one of the first things that happens in rigor is the stiffening of muscles. An increase in muscle mass would increase the time for rigor as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Refer to these links: &lt;a href=&quot;http://en.wikipedia.org/wiki/Rigor_mortis&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; and &lt;a href=&quot;http://www.crimewatchcanada.com/index.php?option=com_content&amp;amp;view=article&amp;amp;id=79:changes-to-a-body-after-death&amp;amp;catid=41:january-february-2010-issue-76&amp;amp;Itemid=53&quot; rel=&quot;nofollow&quot;&gt;another that talks about rigor mortis within the scope of forensic pathology&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;n.i.&lt;/p&gt;&#xA;" OwnerUserId="13082" LastEditorUserId="13082" LastEditDate="2015-01-19T07:27:28.793" LastActivityDate="2015-01-19T07:27:28.793" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27827" PostTypeId="1" CreationDate="2015-01-19T09:48:00.787" Score="1" ViewCount="231" Body="&lt;p&gt;After reading the answer to &lt;a href=&quot;https://biology.stackexchange.com/questions/10710/does-our-dna-change-during-our-lives&quot;&gt;Does our DNA change during our lives?&lt;/a&gt;, I was wondering if and how it would be possible to change the structure of the 13 loci that are used in the CODIS database, in such a way that forensic biometrics would not be able to identify/verify you anymore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read about DNA chimeras, and cases exist where a bone marrow transplantation altered the DNA, depending on the sample that was taken. However, are there any other known ways to alter DNA, such as cancer, radiation, etc?&lt;/p&gt;&#xA;" OwnerUserId="13091" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2016-12-01T09:38:46.850" Title="Known ways to modify the genetic structure of the 13 loci used in CODIS" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;senescence&gt;" AnswerCount="0" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="27830" PostTypeId="1" AcceptedAnswerId="27831" CreationDate="2015-01-19T13:08:37.430" Score="4" ViewCount="462" Body="&lt;p&gt;I'm not sure if this will be a simple question that is almost a natural law for an ecologist, or a complex serious of assumptions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I vaguely remember from school that only 10% of the energy is converted to biomass at each 'level up' however I have never seen any academic support of this. Lets say we have a fairly representative model ecosystem. In a pyramid of biomass, &lt;strong&gt;what percentage of biomass would I expect to see at each level&lt;/strong&gt; (top predator, primary predator, herbivores, plant mass)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An additional part I would like to know is does this ever correlate to the ecosystem of any given tier. i.e typically 5 predators will be found in the same area as 20 herbivores rather than 10% of predator biomass for 100% of prey.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;There are plenty of diagrams available on google, but I have yet to see anything that looks credible. Any citations to academic sources would be greatly appreciated.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/u5N6h.gif&quot; alt=&quot;Bird ecosystem&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2016-08-23T04:37:27.243" LastActivityDate="2016-08-23T04:37:27.243" Title="In a typical model ecosystem, what might the percentage of plants be to top predators and everything inbetween?" Tags="&lt;ecology&gt;&lt;ecosystem&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27831" PostTypeId="2" ParentId="27830" CreationDate="2015-01-19T13:25:24.100" Score="4" Body="&lt;p&gt;The percentage of biomass at each stage will vary tremendously, based on the following factors: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1: Relative turnover rate of the biomass. When biomass turnover is very high (for example in plankton and whales), it is possible for whale biomass to exceed that of the plankton, even through the whales feed on plankton. Therefore, it is better to use a pyramid of energy, where the total energy flux through a specific trophic level is used. See the article &lt;a href=&quot;http://www.globalchange.umich.edu/globalchange1/current/lectures/kling/energyflow/highertrophic/trophic2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for more detail. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Just as with the inverted pyramid of numbers, in some rare exceptions, there could be an inverted pyramid of biomass, where the biomass of the lower trophic level is less than the biomass of the next higher trophic level. The oceans are such an exception because at any point in time the total amount of biomass in microscopic algae is small. Thus a pyramid of biomass for the oceans can appear inverted (see image part b). You should now ask &quot;how can that be?&quot; If the amount of energy in biomass at one level sets the limit of energy in biomass at the next level, as was the case with the hares and foxes, how can you have less energy at the lower trophic level? This is a good question, and can be answered by considering, as we discussed in the last lecture, the all important aspect of &quot;time&quot;. Even though the biomass may be small, the RATE at which new biomass is produced may be very large. Thus over time it is the amount of new biomass that is produced, from whatever the standing stock of biomass might be, that is important for the next trophic level.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Z7O6l.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2: Biomass conversation rate in each trophic stage. For example, the &lt;a href=&quot;https://en.wikipedia.org/wiki/Entomophagy#Environmental_benefits&quot; rel=&quot;nofollow noreferrer&quot;&gt;article on entomophagy&lt;/a&gt; cites a number of papers that insects convert vegetation to biomass approximately 10 times more efficiently than cattle. A population of humans that fed on cattle would have a different biomass (and energy) pyramid than a population of humans that fed on locusts, for example. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-01-19T13:25:24.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27832" PostTypeId="2" ParentId="20075" CreationDate="2015-01-19T14:22:12.780" Score="1" Body="&lt;p&gt;The PRANK and PAGAN algorithms have both come out of the Loytynoja lab in Finnland, and are stirring up the pot a bit. They use inferred phylogenetic relationships as a parameter, and tend to yield a much more 'gappy' alignment, supposedly due to more accurate handling of indels. For easy alignments the method doesn't matter so much, but if the sequences are highly divergent it might be worth while checking out &lt;a href=&quot;http://wasabiapp.org/software/pagan/&quot; rel=&quot;nofollow&quot;&gt;PAGAN&lt;/a&gt; and &lt;a href=&quot;http://wasabiapp.org/software/prank/&quot; rel=&quot;nofollow&quot;&gt;PRANK&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="13093" LastActivityDate="2015-01-19T14:22:12.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27833" PostTypeId="1" AcceptedAnswerId="27854" CreationDate="2015-01-19T15:19:27.087" Score="2" ViewCount="935" Body="&lt;p&gt;On &lt;a href=&quot;http://en.wikipedia.org/wiki/Eye&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; it is explained that the human eye has a certain 'resolution'. Does this mean that the retinal image consists of pixels? If yes, what shape would these pixels have?&lt;/p&gt;&#xA;" OwnerUserId="9588" LastEditorUserId="9943" LastEditDate="2015-01-20T09:50:13.237" LastActivityDate="2015-01-20T10:22:55.937" Title="Parallels between pixelized image and the human retina" Tags="&lt;neuroscience&gt;&lt;vision&gt;&lt;human-eye&gt;&lt;neurophysiology&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27835" PostTypeId="2" ParentId="26332" CreationDate="2015-01-19T15:55:49.487" Score="0" Body="&lt;p&gt;One event that comes to mind is the use of radiation on cancer patients. Radiation is an external event that can trigger apoptosis in humans &lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=4&amp;amp;ved=0CEAQFjAD&amp;amp;url=http%3A%2F%2Fwww.mdpi.com%2F1422-0067%2F14%2F11%2F22409%2Fpdf&amp;amp;ei=VSW9VO6mI8KlgwSNs4O4Aw&amp;amp;usg=AFQjCNEPIcnAdY-Vc6uBisES5gec7HNrrw&amp;amp;sig2=Uq6Ulv0UTgbR6yt4L_-elg&amp;amp;bvm=bv.83829542,d.eXY&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;. When cancer patients receive radiation, the treatment is localized. The brain isn't telling the cells to die it is the radiation effects on the cell.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Ionizing radiation can also induce apoptosis via the generation of free radical oxygen species &lt;a href=&quot;http://www.nature.com/icb/journal/v77/n3/full/icb199934a.html&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Free radical oxygen species does this by searching for an electrons in the molecular make up of the cell &lt;a href=&quot;http://www.vivo.colostate.edu/hbooks/pathphys/misc_topics/radicals.html&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-01-19T16:04:33.070" LastActivityDate="2015-01-19T16:04:33.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27836" PostTypeId="1" CreationDate="2015-01-19T19:11:38.140" Score="3" ViewCount="156" Body="&lt;p&gt;Out of all of the nucleoside triphosphates what makes ATP the most used? Is it its structure? The amount of energy it contains? Why is GTP not used as much? What is the deal with the other nucleoside triphosphates (dATP, dGTP, dTTP, dCTP, UTP, CTP)? Are there any artificial NTPs that can substitute for ATP? (like something that could cure Cyanide poisoning or a disease/illness that somehow de-functionalizes the Electron Transport Chain)&lt;/p&gt;&#xA;" OwnerUserId="13098" LastActivityDate="2015-01-19T19:11:38.140" Title="Why is ATP the main nucleoside triphosphate used to exchange energy?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;energy&gt;&lt;cell-biology&gt;" AnswerCount="0" CommentCount="14" FavoriteCount="1" ClosedDate="2015-01-20T16:36:54.720" ContentLicense="CC BY-SA 3.0" />
  <row Id="27837" PostTypeId="1" CreationDate="2015-01-19T21:24:35.707" Score="2" ViewCount="430" Body="&lt;p&gt;I suspect both language-use and upright-posture have anatomical consequences. So does the fossil record show which came first?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NOTE: To the folks who marked this question &quot;homework&quot;: This is certainly not an actual homework question. I have been an accomplished biologist for over 30 years and I am genuinely interested in the evidence for the timing of these critical human attributes. If you feel that the answer is so trivially obvious, that I should have been able to find out with only modest research, could you please leave a comment explaining, as if to a child, exactly how it is so obvious?&lt;/p&gt;&#xA;" OwnerUserId="12962" LastEditorUserId="12962" LastEditDate="2015-01-24T14:08:23.177" LastActivityDate="2015-01-24T14:08:23.177" Title="Which came first in hominid evolution: language or bipedalism?" Tags="&lt;evolution&gt;&lt;human-evolution&gt;&lt;language&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="3" ClosedDate="2015-01-23T23:55:22.097" ContentLicense="CC BY-SA 3.0" />
  <row Id="27838" PostTypeId="1" CreationDate="2015-01-19T21:29:06.527" Score="4" ViewCount="308" Body="&lt;p&gt;Why is Glycerol 3-phosphate named in such way? Shouldn't it be named as Glycerol 1-phosphate by proper IUPAC- nomenclature?&lt;/p&gt;&#xA;" OwnerUserId="13101" LastActivityDate="2016-06-24T08:15:23.007" Title="Glycerol 3-phosphate nomenclature" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27839" PostTypeId="1" AcceptedAnswerId="27840" CreationDate="2015-01-19T21:35:41.450" Score="18" ViewCount="14276" Body="&lt;p&gt;My biology textbook mentions that DNA is antiparallel and it got me wondering... Can DNA be parallel? What would happen if it was parallel? could DNA still replicate right?&lt;/p&gt;&#xA;" OwnerUserId="13098" LastActivityDate="2017-10-02T13:09:09.087" Title="why is DNA antiparallel? Can it be parallel?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;dna&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="27840" PostTypeId="2" ParentId="27839" CreationDate="2015-01-19T22:01:51.600" Score="15" Body="&lt;p&gt;Interestingly the answer is yes. The problem with parallel strands is that the DNA is not pairing in the known way it does when it is combined anti-parallel (or Watson-Crick-pairs). &#xA;I have found different images illustrating the problems:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/t3prj.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/maass.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both images are from this &lt;a href=&quot;http://scienceblogs.com/digitalbio/2007/07/13/its-still-a-dna-puzzle-but-this-is-the-answer/&quot;&gt;blog post&lt;/a&gt; (originally from a publication cited there which is not available online). Both pictures show a distorted DNA structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This article (&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC101824/&quot;&gt;NMR structure of a parallel-stranded DNA duplex at atomic resolution&lt;/a&gt;&quot;) shows a more schematic solution of this problem by showing the single pairings. C and G cannot build up 3 hydrogen bonds as they do this in the Watson-Crick-pairing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LEWN2.jpg&quot; alt=&quot;The hydrogen bonding schemes for antiparallel and parallel DNA duplexes. The antiparallel DNA duplexes are stabilized by Watson–Crick base pairing, while other schemes are possible for parallel duplexes. (A) Watson–Crick G:C base pair, (B) Hoogsteen G:C+ base pair, (C) Donohue G:C base pair, (D) Watson–Crick A:T base pair, (E) Hoogsteen A:T base pair, (F) Donohue A:T base pair and (G) C:C+ base pair.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Subfigure A and C show the Watson-Crick-pairs, the others come from parallel bindings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This changes in structure disrupts the function of the DNA (which for example depends on the reverse strand for proof reading). Enzymes which replicate, transcribe, repair etc. DNA will not work on this changed structure, as their function depends on the structural features of the DNA.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-01-19T22:01:51.600" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27841" PostTypeId="1" AcceptedAnswerId="27844" CreationDate="2015-01-19T22:02:53.563" Score="2" ViewCount="478" Body="&lt;p&gt;Although this page (&lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/IIIE5aNotadaptation.shtml&quot; rel=&quot;nofollow&quot;&gt;http://evolution.berkeley.edu/evosite/evo101/IIIE5aNotadaptation.shtml&lt;/a&gt;) denounces the idea that blood's redness is not an adaptation, I remain inquisitive on the matter since no scientific research has been performed in studying its possible advantages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have any ideas on the advantages of having red blood?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your time and effort&lt;/p&gt;&#xA;" OwnerUserId="4819" LastActivityDate="2015-01-20T07:39:47.277" Title="What are the advantages of blood's redness?" Tags="&lt;hematology&gt;&lt;red-blood-cell&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ClosedDate="2015-01-20T04:16:09.350" ContentLicense="CC BY-SA 3.0" />
  <row Id="27842" PostTypeId="1" CreationDate="2015-01-19T22:15:16.123" Score="3" ViewCount="7585" Body="&lt;p&gt;Many sci fi movies produce interesting ideas and technologies that we seem to be able to realize in real life at some point. &quot;Lucy&quot; was not one of those movies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But Morgan Freeman's speech in the movie on cell evolution did interest me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The speech claimed that cells in harsher environments evolve towards immortality, while cells in favorable environments evolve toward reproduction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is this idea accurate?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="13102" LastActivityDate="2016-10-20T17:14:22.853" Title="Cell evolution: immortality vs reproduction" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="27843" PostTypeId="1" AcceptedAnswerId="27845" CreationDate="2015-01-19T22:22:02.343" Score="5" ViewCount="474" Body="&lt;p&gt;When we are self-conscious of our own breathing, its rate changes very easily. Therefore, if it changes so easily, what is the point in measuring it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your time and effort&lt;/p&gt;&#xA;" OwnerUserId="4819" LastActivityDate="2015-01-20T09:18:39.853" Title="If we change our breathing rate so easily, then what is the point of measuring it?" Tags="&lt;breathing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27844" PostTypeId="2" ParentId="27841" CreationDate="2015-01-19T22:26:09.640" Score="5" Body="&lt;p&gt;The reason why blood is red is rather simple: It is the iron atom in the middle of the heme, which plays the central part in binding oxygen. Depending on the oxidation state the blood looks either dark or light red. The structure is the following (taken from here):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BD46i.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That the color only depends on the coordinated metal atom is shown by another related molecule, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemocyanin&quot; rel=&quot;nofollow noreferrer&quot;&gt;hemocyanin&lt;/a&gt;, which is the oxygen carrying molecule in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hemolymph&quot; rel=&quot;nofollow noreferrer&quot;&gt;hemolymph&lt;/a&gt; of insects. It contains copper which is colorless in one oxidation state and blue-green in the other. The function is the same, the color is different.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="11841" LastEditDate="2015-01-20T07:39:47.277" LastActivityDate="2015-01-20T07:39:47.277" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="27845" PostTypeId="2" ParentId="27843" CreationDate="2015-01-19T22:37:51.143" Score="7" Body="&lt;p&gt;We may be able to voluntarily control our respiratory rate, but only for a short while. The buildup or depletion of CO&lt;sub&gt;2&lt;/sub&gt; will force us, against our will, to either speed up our respiration or slow it down. So, you can't effectively &quot;fake&quot; your respiratory rate for long, nor, to an astute observer, convincingly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Normal breathing patterns are &quot;normal&quot; for a reason. Aberrations from normal do occur in pathological states, but they are compensatory mechanisms driven by a number of factors your blood chemistries: the &lt;em&gt;pH&lt;/em&gt; and the intimately linked CO&lt;sub&gt;2&lt;/sub&gt;/H-CO&lt;sub&gt;3&lt;/sub&gt; concentrations, etc. You can pretend any way you like: you won't be able to keep it up comfortably. Also, normal breathing isn't simply &quot;breathe in/breathe out&quot;. It is a more complex thing characterized by an inspiratory phase of certain duration, an expiratory phase of a different relative duration, and a normal, periodic deeper breath (close to a sigh), all done physiologically and unconsciously. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With certain illnesses come certain breathing patterns. You might be able to fool one person's quick assessment, but not more than that. If the faked breathing pattern (largely unsustainable anyway) doesn't appear physiological, you will be quickly found out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For that reason, a sustained increased or decrease in respiratory rate is indicative of particular pathologies, whereas a normal respiratory rate is a helpful sign.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-01-20T09:18:39.853" LastActivityDate="2015-01-20T09:18:39.853" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27846" PostTypeId="2" ParentId="27838" CreationDate="2015-01-19T22:39:48.573" Score="5" Body="&lt;p&gt;You're right, according to standard rules of nomenclature it would be called glycerol 1-phosphate. It comes back to the outdated D/L configuration nomenclature. A more thorough explanation is quoted below. &#xA;&lt;img src=&quot;https://i.stack.imgur.com/e1bOj.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When the R/S system (sequence rule) is applied, substitution of one of the primary hydroxyl groups often leads to changes in the configurational prefix, thus obscuring chemical and biogenetical relationships; it is generally inapplicable to the steric description of such mixtures as occur in triacy1glycerols isolated from natural sources. The stereospecific numbering of glycerol and its derivatives as proposed by Hirschmann [9], described above and in &lt;a href=&quot;https://i.stack.imgur.com/e1bOj.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;, avoids these difficulties; it has proved useful and is widely accepted.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.chem.qmul.ac.uk/iupac/lipid/lip1n2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2016-06-24T08:15:23.007" LastActivityDate="2016-06-24T08:15:23.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27847" PostTypeId="1" AcceptedAnswerId="27855" CreationDate="2015-01-19T22:45:38.580" Score="0" ViewCount="243" Body="&lt;p&gt;What shows how healthy someone is by their heart rate - how low it is at resting pulse or how low it is during exercise or how large the difference is between the resting rate and rate with load? Any ideas?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clarification:&#xA;Essentially, how does the heart rate reflect healthiness and in which ways (is it the resting pulse, pulse during exercise, differences, etc.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your time and effort&lt;/p&gt;&#xA;" OwnerUserId="4819" LastEditorUserId="4819" LastEditDate="2015-01-20T00:03:59.120" LastActivityDate="2015-01-20T05:48:18.117" Title="What shows how healthy someone is by their heart rate?" Tags="&lt;cardiology&gt;&lt;health&gt;" AnswerCount="1" CommentCount="14" ClosedDate="2015-01-20T09:30:53.727" ContentLicense="CC BY-SA 3.0" />
  <row Id="27848" PostTypeId="2" ParentId="27842" CreationDate="2015-01-19T23:26:41.850" Score="3" Body="&lt;p&gt;You'll see that in many cases, when any sort of cell enters a zone of intolerance or zone of physical stress, the replication machinery gets put on the backburner (and thus replication). Expression of stress-response proteins like heat shock proteins is increased as a result (1). If a cell isn't within acceptable parameter to undergo division at G1 or G2 (anoxic environment, etc.), you'll find mechanisms like G0 phase or sporulation are preferred until the environment returns to something less stressful (2). I wouldn't say cells would rather be immortal, &lt;em&gt;per se&lt;/em&gt;, but longevity or even apoptosis/entosis/etc. would be preferable to replication if nothing is going right (3, 4).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be clear, when we're talking about evolution that's a tough one. Sure, some sort of stress-response transient signal could induce some lasting cell memory selecting toward a specific function. I simply don't have the data to quote you in that aspect, however.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372250/&quot; rel=&quot;nofollow&quot;&gt;Biology of the heat shock response and protein chaperones: budding yeast (Saccharomyces cerevisiae) as a model system.&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Slonczewski, J., &amp;amp; Foster, J. (2011). Microbiology: An evolving science (2nd ed., p. 143). New York: W.W. Norton. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/onc/journal/v23/n16/full/1207532a.html&quot; rel=&quot;nofollow&quot;&gt;DNA damage-induced apoptosis&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.hindawi.com/journals/ijcb/2010/214074/&quot; rel=&quot;nofollow&quot;&gt;Cellular Stress Responses: Cell Survival and Cell Death&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;As a footnote, while replication does occur in sporulation, the replicated chromosome is destroyed in the process of forming the actual spore.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-01-20T19:29:55.920" LastActivityDate="2015-01-20T19:29:55.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27850" PostTypeId="2" ParentId="27837" CreationDate="2015-01-19T23:47:42.677" Score="3" Body="&lt;p&gt;This article by Philip Lieberman &lt;a href=&quot;http://edoc.bbaw.de/volltexte/2006/188/pdf/25nzvtXxXJA_188.pdf&quot; rel=&quot;nofollow&quot;&gt;On the subcortical bases of the evolution of language&lt;/a&gt;, page 22, he asserts the neurons associated with language may have developed based on the demands of bipedal posture. While there's no concrete data to support when we see the first languages, &lt;a href=&quot;http://www.sciencemag.org/content/331/6018/750.abstract&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; we see evidence of arches (and presumably bipedal posture) in &lt;em&gt;Australopithecus afarensis&lt;/em&gt;. So there are still some dots that need connecting.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-01-19T23:47:42.677" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27851" PostTypeId="2" ParentId="26332" CreationDate="2015-01-20T00:29:26.223" Score="1" Body="&lt;p&gt;The answer is, in part, it depends. Let's think of the PI3K/AKT pathway. Akt actively phosphorylates BAD which abrogates the Bax/Bak apoptosis pathway. RTK's at the plasma membrane activate this pathway when bound with survival factors. In the absence of survival factors, Akt would become dephosphorylated and you'd have a net movement toward apoptosis. In a particular form of cell death called anoikis, this could be as simple as detaching from the extracellular matrix. So anything that halts the binding of survival factors could play a role.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of immune response, activated Tc cells can induce apoptosis by secreting pore-forming enzymes as well as enzymes that directly activate caspases. The Tc cells also express Fas on their membrance which is involved in the extrinsic apoptosis pathway. TNF (tumor necrosis factor) may also bind cell surface receptors as sort of a death factor, and push towards apoptosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are just examples, some generic searches about apoptosis, necroptosis, entosis, and a myriad of other programmed death mechanisms will yield a very comprehensive overview.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-01-20T00:29:26.223" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27854" PostTypeId="2" ParentId="27833" CreationDate="2015-01-20T04:58:17.260" Score="4" Body="&lt;p&gt;The pixels of the visual system are represented by the photoreceptors. Their shape is the following (adapted from &quot;&lt;a href=&quot;https://www.google.com.au/url?sa=i&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=images&amp;amp;cd=&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CAUQjhw&amp;amp;url=http%3A%2F%2Fthebrain.mcgill.ca%2Fflash%2Fd%2Fd_02%2Fd_02_m%2Fd_02_m_vis%2Fd_02_m_vis.html&amp;amp;ei=W9y9VL3_KYS48gWM74LQCQ&amp;amp;bvm=bv.83829542,d.dGY&amp;amp;psig=AFQjCNFrEBtog8di_gHO96241fju8JuKbw&amp;amp;ust=1421815254578217&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Brain from Top to Bottom, MgGill University&quot;&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gfBeK.jpg&quot; alt=&quot;Cones, rods&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are about a 180 photoreceptors packed on 288 microns on the retina (see &quot;&lt;a href=&quot;https://biology.stackexchange.com/questions/26189/whats-the-smallest-size-a-human-eye-can-see&quot;&gt;What's the smallest size a human eye can see?&lt;/a&gt;&quot;) so about 1 pixel per 2 microns. The rods and cones are packed closely together on the retina, referred to as the retinal mosaic. This retinal mosaic is not unlike a photosensitive chip, as can be seen on the folllowing image (&lt;a href=&quot;http://labs.nri.ucsb.edu/reese/benjamin/PubsRetinalMosaics.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Developmetal Neurobiology lab, UCLA, Santa Barbara&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/63g5R.jpg&quot; alt=&quot;Retinal Mosaic&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We do not visually perceive this mosaic, as the optics of the eye (e.g., light diffraction by the cornea and the lens, and distortions due to the relatively large pupil size) prevents optimal use of the photoreceptor density (the maximal resolution). Furthermore, especially outside the field of view (the foveal region), the output of many photoreceptors are funneled onto one single optic nerve fiber, thereby fusing the output of many photoreceptors (See the question &quot;&lt;a href=&quot;https://cogsci.stackexchange.com/questions/6265/why-can-we-not-see-around-our-point-of-focus-of-our-eyes/8481#8481&quot;&gt;Why can we not see around our point of focus of our eyes?&lt;/a&gt;&quot;). Lastly, the brain actively 'glues' any gaps in the visual field together. Most strikingly, the blind spot, which is the place where the optic nerve exits the eye is fairly large, is normally not visible to us: see the following picture (&lt;a href=&quot;http://www.pnas.org/content/95/3/811/F3.expansion.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;PNAS online content&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Pz9E5.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, any gaps in the retinal image are in fact actively smoothened out by the brain.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:56:15.910" LastActivityDate="2015-01-20T09:54:08.993" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27855" PostTypeId="2" ParentId="27847" CreationDate="2015-01-20T05:48:18.117" Score="1" Body="&lt;p&gt;A healthy heart and cardiovascular system distributes oxygenated blood more efficiently than a less healthy one. Therefore, for a given level of exertion, a healthy heart will need to pump fewer times than a less healthy one to provide the same quantity of oxygenated blood to the rest of the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's pretty much that simple. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the whole patient has to be considered. A low heart rate in and of itself doesn't mean someone is fit since there are many drugs and medical conditions that can create a low heart rate. Person A sitting in front of you appears fit and healthy, is on no relevant medications, and has a heart rate of 50? Fitness almost certainly explains it. Person B sitting in front of you is overweight, on several meds and not very fit? Fitness almost certainly doesn't explain it.&lt;/p&gt;&#xA;" OwnerUserId="4729" LastActivityDate="2015-01-20T05:48:18.117" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27856" PostTypeId="1" CreationDate="2015-01-20T07:49:43.050" Score="2" ViewCount="93" Body="&lt;ol&gt;&#xA;&lt;li&gt;Why do we sympathize in general when we see something or someone dying even if we personally don't know it/them?&lt;/li&gt;&#xA;&lt;li&gt;Is there any species which sympathize with the death of its own species?&lt;/li&gt;&#xA;&lt;li&gt;Is there any species which sympathize with the death of other species?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-01-20T07:49:43.050" Title="Death Psychology" Tags="&lt;psychology&gt;&lt;death&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ClosedDate="2015-01-20T14:21:04.873" ContentLicense="CC BY-SA 3.0" />
  <row Id="27860" PostTypeId="2" ParentId="27833" CreationDate="2015-01-20T09:29:05.997" Score="3" Body="&lt;p&gt;If you by pixels are referring to the photoreceptors (&lt;a href=&quot;https://en.wikipedia.org/wiki/Rod_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;rods&lt;/a&gt; &amp;amp; &lt;a href=&quot;https://en.wikipedia.org/wiki/Cone_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;cones&lt;/a&gt;), their density differs over the retina, and we can only see sharp images at high resolution in a small region of our eye (fovea). So the resolution varies over the retina. The image we actually see is also a continiously interpreted and updated, and the brain is very creative in this process by basically &quot;filling in the blanks&quot;. We therefore don't see in pixels, and our resolution is influenced by (at least) light conditions, contrast, photoreceptor density, signal merging and interpretation of the visual signals by the &lt;a href=&quot;https://en.wikipedia.org/wiki/Visual_cortex&quot; rel=&quot;nofollow noreferrer&quot;&gt;visual cortex&lt;/a&gt; in the brain. However, our eye is also constantly scanning the visual field (see &lt;a href=&quot;https://en.wikipedia.org/wiki/Saccade&quot; rel=&quot;nofollow noreferrer&quot;&gt;saccade&lt;/a&gt;), so even if the &quot;static&quot; visual resolution (when we focus constantly on a single point) is drastically different over the visual field, this does not match our visual perception. As a sidenote, saccades are possibly the fastest human motions, and can reach speeds well above 400°/s (&lt;a href=&quot;http://www.iovs.org/content/13/8/619.full.pdf+html&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Boghen et al. 1975. Velocity Characteristics of Normal Human Saccades. Invest. Ophthalmol. Vis. Sci. 13(8)&quot;&gt;Boghen et al, 1975&lt;/a&gt;) - wikipedia reports 900°/s but without a clear reference - and takes place several times per second.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we focus at the resolution in terms of photoreceptor density (densities of rods/cones), this is drastically different over regions of the retina. For instance, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1427131&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Jonas et al 1992. Count and density of human retinal photoreceptors. Graefes Arch Clin Exp Ophthalmol.&quot;&gt;Jonas et al. (1992)&lt;/a&gt; reports ~150,000 cones/mm&lt;sup&gt;2&lt;/sup&gt; close to the center of the fovea to 2500-6000 cones/mm&lt;sup&gt;2&lt;/sup&gt; towards the periphery. The approximate density of rods goes from 150,000 rods/mm&lt;sup&gt;2&lt;/sup&gt; to 30,000 in the periphery. Cone &amp;amp; rod diameter also differs over the retina, with larger diameters towards the retinal periphery, which relates to light sensitivity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A nice summary of the flexibility and limitations of human vision can be seen in this xkcd comic (click for larger version):&#xA;&lt;a href=&quot;http://xkcd.com/1080/large/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/mNwBc.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&#xA;(from &quot;&lt;em&gt;xkcd: Our central visual field&lt;/em&gt;&quot; at &lt;a href=&quot;http://xkcd.com/1080/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://xkcd.com/1080/&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-01-20T10:22:55.937" LastActivityDate="2015-01-20T10:22:55.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27865" PostTypeId="1" CreationDate="2015-01-20T14:24:03.610" Score="1" ViewCount="549" Body="&lt;p&gt;I'm frequently getting electric shocks in my office when touching things. I basically know why this happens and how to avoid it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still I started to wonder what would be the best way to touch something if you knew you will be shocked. I know that fingertips have more nerve endings but I guess they also have more callus. What are &lt;strong&gt;factors for sensitivity to electric shock&lt;/strong&gt; and what &lt;strong&gt;part of the hand is therefore the least unpleasant&lt;/strong&gt; to be shocked?&lt;/p&gt;&#xA;" OwnerUserId="13116" LastEditorUserId="13116" LastEditDate="2015-01-21T07:45:19.393" LastActivityDate="2015-01-21T07:45:19.393" Title="Factors for sensitivity to electric shock" Tags="&lt;pain&gt;&lt;senses&gt;" AnswerCount="0" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="27866" PostTypeId="1" CreationDate="2015-01-20T14:52:54.237" Score="9" ViewCount="161" Body="&lt;p&gt;I'm curious about the origin of the neural network. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm thinking perhaps once life evolved beyond the single cell organism, it needed a simple neural network to coordinate those cells, and cell functions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What were the first neural systems like?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More specifically: What kind of cell did the first neurons evolve from and how did they work at first? (assuming there were few, if any, neural connections in the first organisms to develop neurons of some sort) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I understand about a neural system, it needs a few neurons linked together to keep firing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps the first neurons had triggers other than dendrite connections? &lt;/p&gt;&#xA;" OwnerUserId="13102" LastEditorUserId="13102" LastEditDate="2015-01-20T23:40:10.730" LastActivityDate="2015-12-10T13:43:27.143" Title="What were the first neural systems like?" Tags="&lt;evolution&gt;&lt;cell-biology&gt;&lt;neuroscience&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="27867" PostTypeId="2" ParentId="27478" CreationDate="2015-01-20T16:08:21.783" Score="2" Body="&lt;p&gt;From the limited information, I can provide the following but I am not sure if this is what you are looking for. Also, I still don't see the statement where the author concludes we get the Linear regression model $E(q_i) = Aq_i + C$ which is odd notation since it says the expected value is a linear regression. In fact, if it is a linear regression, it should say $q_j = Aq_i + C$.&#xA;$$&#xA;A = \frac{\text{cov}(q_i,q_j)}{\text{var}(q_i)}\quad\text{and}\quad C = E[q_j] - \frac{\text{cov}(q_i,q_j)}{\text{var}(q_i)}E[q_i].&#xA;$$&#xA;Now, we can write the variance and covariance as&#xA;\begin{align}&#xA;\text{var}(q_i) &amp;amp;= E[q_i^2]-E^2[q_i]\\&#xA;\text{cov}(q_i,q_j) &amp;amp;= E[q_iq_j]-E[q_i]E[q_j]&#xA;\end{align}&#xA;where the expected value of a discrete random variable $X$ is calculated as&#xA;$$&#xA;E[X] = \sum_{i=1}^Nx_ip_X[x_i]&#xA;$$&#xA;where $p_X[x_i]$ is probability of $x_i$ and $N$ can be countable infinite.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The mean of conditional PDFs comes up in optimal prediction where the minimum mean square error is $E_{Y\mid X}[Y\mid x]$. This optimal prediction covers linear and nonlinear. For the standard Gaussian PDF, the optimal prediction will be linear since $E_{Y\mid X}[Y\mid x]=\rho x$ where $\rho$ is the correlation coefficient. I am going to short hand $E_{Y\mid X}[Y\mid x]$ to $E[Y\mid x]$&#xA;$$&#xA;E[Y\mid x] = \mu_Y + \frac{\rho\sigma_Y}{\sigma_X}(x-\mu_X)&#xA;$$&#xA;where $\mu_i$ $i=X,Y$ is the mean and $\sigma_i$ is the standard deviation. If $X$ and $Y$ are not Gaussian, then the model can be nonlinear. Are there examples of non Gaussian be linear probably.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-01-20T17:04:19.720" LastActivityDate="2015-01-20T17:04:19.720" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27868" PostTypeId="5" CreationDate="2015-01-20T16:45:47.273" Score="0" Body="&lt;p&gt;related tag: &lt;a href=&quot;/questions/tagged/biochemisry&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;biochemisry&amp;#39;&quot; rel=&quot;tag&quot;&gt;biochemisry&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please use specific tags for the following carbs: &lt;a href=&quot;/questions/tagged/glucose&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;glucose&amp;#39;&quot; rel=&quot;tag&quot;&gt;glucose&lt;/a&gt;, &lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="16866" LastEditDate="2020-01-02T19:41:14.550" LastActivityDate="2020-01-02T19:41:14.550" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="27869" PostTypeId="4" CreationDate="2015-01-20T16:45:47.273" Score="0" Body="A carbohydrate is a diverse group of biological molecules that contain carbon (C), hydrogen (H) and oxygen (O) atoms. They are commonly used in biological metabolism and catabolism. " OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2015-01-20T18:31:26.373" LastActivityDate="2015-01-20T18:31:26.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27870" PostTypeId="1" CreationDate="2015-01-20T16:56:59.050" Score="5" ViewCount="4167" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;: I am coming at this question from an electrical engineering background, and I feel like I am missing certain assumptions that are going into the statement found in my physiology textbook, &quot;vasoconstriction increases blood pressure&quot;.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Consider a simple series circuit and a parallel circuit run by a battery/heart&lt;/strong&gt; [you will find the parallel and series circuit in any physiology book description of the vasculature, yet I can't find any exploration of the assumptions made when applying these circuit models]:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;In the series circuit, if I have an increase in resistance across&#xA;one of my resistors, this will basically redistribute the pressure&#xA;drops across the resistors, but it will not alter the total pressure&#xA;drop across all the resistors [fixed by the heart].&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In the parallel circuit, if I have an increase in resistance across&#xA;    one of my resistors, this will redistribute the flow to different&#xA;    branches, but the pressure drop will not change as again this is&#xA;    fixed by the heart.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This analysis seems to suggest that if the resistance across an organ [branch of parallel circuit] changes, the flow changes, not the pressure. The heart, I would assume, then responds by increasing the pressure to increase flow ie actually injecting energy into the system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Here is the problem with the circuit model though:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;it assumes that the battery/heart is the only source of energy in&#xA;the system, and the resistors are passive re distributors of that&#xA;energy.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the controllers of vascular resistance are smooth muscle which must actively put energy into the system to vasoconstrict. This could be&#xA;a source of pressure increase as the smooth muscle would be actively&#xA;constricting against an incompressible fluid, but I am really not&#xA;sure.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;it does not account for the compliance of the vasculature.&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;-the tubing the heart is hooked up to modifies the blood pressure the heart has to generate to inject fluid into that tube. If the tubing was stiff, the heart would have to generate very high systolic pressures that would then rapidly decrease during the diastolic phase. The more compliant the tubing, the less pressure the heart has to generate to inject fluid into the tube. Intuitively though, there would seem to some relationship between the ability of a fluid to flow and vessel compliance. A highly compliant vessel with a fluid injection will simply expand and hold the fluid while a less compliant vessel will maintain a pressure necessary to push the fluid along.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sparknotes in the form of questions:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Is the only source of energy in the cardiac circuit the heart? Or&#xA;does artiole smooth muscle actually inject energy into the system,&#xA;        and result in systemic increases in the pressure available in the&#xA;        closed circuit.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I don't think vascular compliance ie expansion of the artery walls&#xA;due to volume filling results in any active injections of&#xA;        energy into the system..it should simply transfer the energy&#xA;        available to push fluid to elastic energy in the connective tissue&#xA;        of the artery walls. Is this correct?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Does vessel compliance partly determine the pressure the heart has to inject into the system?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;What is the relationship between compliance and flow if there is one?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="13119" LastActivityDate="2015-01-22T00:21:56.680" Title="How does vasoconstriction/vasodilation change blood pressure?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;medicine&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27871" PostTypeId="2" ParentId="27790" CreationDate="2015-01-20T17:06:55.623" Score="5" Body="&lt;p&gt;In eukaryotic cells there is no difference between a mother and a daughter cell - the later is an exact copy of the mother cell. This is true for yeasts as well for example for human cells. The only thing that happens over time is that the telomeres at the end of the chromosomes get shorter (unless the cell has an active telomerase which most cells doesn't) and it reaches the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hayflick_limit&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hayflick limit&lt;/a&gt; where every further division will lead to a shortage of coding chromosmal regions and thus cause problems. If cells do not acquire any other chromosomal damage and have enough ressources, this would be the limit for their lifetime.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course there are DNA damages occuring over time. Most of them are either repaired by the highly efficient DNA damage repair system of eukaryotic cells, which consists of different checkpoints during the cell cycle. These checkpoints are located at transition between the different  phases of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;cell cycle&lt;/a&gt;. If a DNA damage is identified, the cell cycle is stopped to enable a DNA damage repair by special proteins and to prevent that damaged cells undergo mitosis (here the &lt;a href=&quot;http://en.wikipedia.org/wiki/G2-M_DNA_damage_checkpoint&quot; rel=&quot;nofollow noreferrer&quot;&gt;G2-M checkpoint&lt;/a&gt; is important). This works schematically like in this figure (from the Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_repair&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA repair&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9MwBD.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the DNA damage cannot be resolved, cells will either go into senescence (basically go into a permanent dormant state) or undergo apoptosis. If there are damages which are (for whatever reasons) are either not spotted or occur during the repair of DNA double strand breaks by non-homologous end joining, these are then replicated and inherited by further generations. Unless these errors occur during the replication process mother and daughter cells are genetically identical.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So eukaryotic cells acquire DNA damage over time (one of the reasons why late pregnancies pose a greater risk than early), but we are different from yeast in one point: Yeast has an active telomerase, which is not active in most of our cells (mainly except in stem cells). If the cells collect too much chromosmal damages than they will die.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The references listed below go deeper into the topic and are interesting to read.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://nar.oxfordjournals.org/content/26/6/1487.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Negative regulation of yeast telomerase activity through an&#xA;interaction with an upstream region of the DNA primer&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3879/6827pimy_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cell cycle control in the kidney.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3873/yxu4u4se_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;The evolution of diverse biological responses to DNA damage:&#xA;insights from yeast and p53&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3873/8dbvh7hd_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA damage and decisions: CtIP coordinates DNA repair and cell cycle&#xA;checkpoints&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3873/oli52vv2_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cellular Responses to DNA Damage: One Signal, Multiple Choices&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-01-26T10:09:24.117" LastActivityDate="2015-01-26T10:09:24.117" CommentCount="17" ContentLicense="CC BY-SA 3.0" />
  <row Id="27873" PostTypeId="2" ParentId="27870" CreationDate="2015-01-20T18:28:13.847" Score="4" Body="&lt;p&gt;The circulatory system is a dynamic system which cannot be adequately explained by your example (at least not by me). You need to understand it, not seek to make it fit your (especially) &lt;em&gt;electrical circuits with resistors&lt;/em&gt;. Blood isn't electricity. At least try a fluid dynamics model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's take this very simple model: Blow up a balloon four-fifths of the way, and put a wide inflatable cuff around its middle. Inflate the cuff so that the balloon bulges just a tiny bit at the ends, then stuff it all into a plexiglass box so that the balloon has no room to expand. The plexiglass box represents our body. Lets call the pressure inside the balloon now normal blood pressure. The air in the balloon represents your total blood volume. It can't change from moment to moment; it's fixed. The box can't change it's volume moment to moment either. It's fixed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cuff represents arterial smooth muscle. Vasoconstriction can be represented by inflating the cuff further. Constriction (inflation of the cuff) will increase the pressure throughout inside the balloon, because the same amount of gas now has to exist in a smaller space. Vasodilation (deflating the cuff) decreases the pressure inside the balloon, because the gas can now inhabit a larger amount of space.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's it, really. If the same volume must inhabit a smaller, constricted space, the pressure exerted by blood in that space will be higher. If the blood vessles dilate, the pressure in the blood vessels falls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now add about 20 layers of complexity to that simple model, and you have a working model of the circulatory system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sparknote answers&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Arterial and arteriolar smooth muscle &quot;injects energy into the system&quot;, resulting in systemic increases in the pressure existing in the vascular &quot;circuit&quot; (meaning somewhat elastic tubing) if &lt;em&gt;resistance&lt;/em&gt; requires energy. (So I have misunderstood: see @Raoul's answer.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Sorry, I didn't read this properly the first time around. Yes, the heart supplies the energy. The contribution of the elastic walls of the arteries is not active, but passive.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Absolutely. The more elastic/compliant the arteries are, the less work the heart must exert to pump the blood through the circuits. The stiffer and narrower the arteries are, the harder the heart must work to pump blood through the circuits. The result of that increased work is a thickening of the muscular walls of the heart, called &lt;em&gt;ventricular hypertrophy&lt;/em&gt;, which is a sign of elevated pressure in the system.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I'm not sure I want to commit here to your lingo, but the answer should be inferable from numbers 1-3. Elastic vessels help (by rebound compression) to propel the blood through the circuits. Stiff vessels hinder it, making the heart do more of the work.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I am not an engineer, so I may be misusing some of the terms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edited to add&lt;/strong&gt;: Please see @Raoul's answer for a better explanation.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-01-21T15:59:19.150" LastActivityDate="2015-01-21T15:59:19.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27875" PostTypeId="1" CreationDate="2015-01-20T21:30:09.300" Score="1" ViewCount="64" Body="&lt;p&gt;Why don't stem cell therapies use a virus to deliver gene editing sequences to stem cells instead of the harvesting-transformation-transplant route. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought it might be because of a lack of specificity on the part of the viruses, but then I saw phage display techniques that would seem to make that a non-issue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought it might be trans-cytosis or getting the phages out of the blood-stream and into contact with the stem cells. I haven't found an easy solution to this hurdle, but it doesn't seem to be insurmountable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the main issue is regulatory? Perhaps a lack of precedents in this area. What do you think of my analysis? Is this idea even feasible?&lt;/p&gt;&#xA;" OwnerUserId="146" LastActivityDate="2015-01-21T17:48:19.080" Title="Why don't stem cell therapies use viruses?" Tags="&lt;virus&gt;&lt;stem-cells&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27876" PostTypeId="2" ParentId="27875" CreationDate="2015-01-20T22:44:17.547" Score="2" Body="&lt;p&gt;Stem cell therapies &lt;em&gt;do&lt;/em&gt; in fact utilise viruses. In the examples cited, the stem cells were infected by viruses in vitro, genetically modified, and then reintroduced into the target as autologous transplants. The main issue at hand is that live viruses introduced directly would be targeted and destroyed by the immune system, which greatly reduces their efficacy in causing transformation of cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://www.nature.com/mt/journal/v20/n4/full/mt2011310a.html&quot; rel=&quot;nofollow&quot;&gt;a recent Nature paper&lt;/a&gt;, zinc finger nucleases were used to target and disrupt the CCR5 or CXCR4 gene, which greatly reduces the efficiency of HIV binding to CD4+ T cells. The zinc finger nucleases were introduced into the cells using an adenovirus vector.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Generation of cxcr4 ZFN adenovirus and CGW-siX4s lentiviral vectors. The CXCR4 targeting locations of siX4s and ZFN are shown in Supplementary Figure S1.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This technique was then used in a number of clinical trials to modify hematopoietic stem cells using zinc finger nucleases, as summarised in &lt;a href=&quot;http://www.mdpi.com/1999-4915/6/3/1395/pdf&quot; rel=&quot;nofollow&quot;&gt;this review paper&lt;/a&gt;. The recent advent of CRISPR-Cas systems will probably lead to an increase in similar techniques, due to the higher specificity and ease of engineering of Cas9-based nucleases.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-01-20T22:44:17.547" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27877" PostTypeId="1" CreationDate="2015-01-20T23:17:24.043" Score="3" ViewCount="565" Body="&lt;p&gt;I'm performing FACS on e coli, but the cells are clumping together so each event is multiple cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I ran a control where I had one flask of e coli expressing GFP, and one flask expressing RFP. Run separately, I got a clean population of either high-GFP fluorescent events, or high RFP fluorescent events. If I mix 10uL of each population into 200uL TE buffer and immediately run that sample, all the events have high RFP AND high GFP fluorescence, indicating the cells are sticking together immediately upon mixing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cell line: ER2566 (NEB)&#xA;F- λ- fhuA2 [lon] ompT lacZ::T7 gene 1 gal sulA11 Δ(mcrC-mrr)114::IS10 R(mcr-73::miniTn10-TetS)2 R(zgb-210::Tn10)(TetS) endA1 [dcm]&#xA;Host strain for the expression of a target gene cloned in the pTYB vectors.&#xA;Carry a chromosomal copy of the T7 RNA polymerase gene inserted into lacZ gene and thus under the control of the lac promoter. In the absence of IPTG induction expression of T7 RNA polymerase is suppressed by the binding of lac I repressor to the lac promoter.&#xA;Deficient in both lon and ompT proteases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Growth media: M9 minimal media&lt;/p&gt;&#xA;&#xA;&lt;p&gt;FACS running media: TE&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know there are anti-clumping agents for yeast and mammalian cells, but I haven't come across one for bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone recommend:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;an e coli protein expression strain that is known to not clump&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;an anti-clumping agent for bacteria&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;any other possible solutions&#xA;?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="13123" LastActivityDate="2015-01-20T23:17:24.043" Title="How to prevent e coli from clumping (for FACS)?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;ecoli&gt;&lt;fluorescent-microscopy&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27878" PostTypeId="1" AcceptedAnswerId="27882" CreationDate="2015-01-20T23:47:09.783" Score="1" ViewCount="329" Body="&lt;p&gt;I can sometimes feel quite drowsy after some &quot;meals&quot; (e.g. a cold cut &amp;amp; cheese sandwich with juice on the side) and less drowsy (or maybe less often) after others (such as a salad).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This drowsiness sometimes affects my work at the office, so I wanted to ask these questions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What biological factors lead to the body getting tired after eating?&lt;/li&gt;&#xA;&lt;li&gt;Are there any strategies that can be used to minimize this effect?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="12939" LastEditorUserId="12939" LastEditDate="2015-01-20T23:58:31.490" LastActivityDate="2015-01-21T00:21:50.467" Title="What is the biological basis for tiredness after eating?" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;&lt;energy&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ClosedDate="2015-03-07T20:27:59.623" ContentLicense="CC BY-SA 3.0" />
  <row Id="27882" PostTypeId="2" ParentId="27878" CreationDate="2015-01-21T00:15:04.417" Score="0" Body="&lt;p&gt;High carbohydrate meals will undoubtedly increase the relative levels of insulin, increase the shuttling of glucose from the blood to the cells, and leave you fatigued in wake of that. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Reactive_hypoglycemia&quot; rel=&quot;nofollow&quot;&gt;reactive hypoglycemia&lt;/a&gt;. Reducing carbohydrate consumption should, to some level, reduce this effect. Caffeine should just as likely increase blood glucose levels by increasing glycogenolysis through PKA activation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Chris Stronks pointed out, &lt;a href=&quot;http://www.health.harvard.edu/newsletters/Harvard_Heart_Letter/2010/July/eating-can-cause-low-blood-pressure&quot; rel=&quot;nofollow&quot;&gt;eating can cause low blood pressure via redistribution of blood&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-01-21T00:21:50.467" LastActivityDate="2015-01-21T00:21:50.467" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27884" PostTypeId="1" AcceptedAnswerId="27885" CreationDate="2015-01-21T00:41:56.350" Score="2" ViewCount="1280" Body="&lt;p&gt;I wanted to ask a couple questions related to pituitary giants (people who are giants because of some anomaly, such as a tumor, in their pituitary gland).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of these giants seem to keep growing and growing until the tumor (or the gland) is removed. Is this because the fusing of the growth plates is controlled by the amount of growth hormone in blood?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for this question is that many of the giants have been described to grow past when the growth plates should probably have fused. For example (all heights in meter, m):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Bernard_Coyne_(giant)&quot; rel=&quot;nofollow&quot;&gt;Bernard Coyne&lt;/a&gt; This giant is described as having been 2.36m at the age of 20, but 2.54m at the time of his death at the age of 23.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Edouard_Beaupr%C3%A9&quot; rel=&quot;nofollow&quot;&gt;Edouard Beaupré&lt;/a&gt; At the age of 17, this giant was measured as 2.16m tall and at the age of 21, he was measured at 2.50m tall. At the time of his death, at the age of 23, he was listed (in his death certificate) as having been 2.51m tall and &quot;still growing&quot;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/V%C3%A4in%C3%B6_Myllyrinne&quot; rel=&quot;nofollow&quot;&gt;Väinö Myllyrinne&lt;/a&gt; This giant was 2.22m at the age of 21 but is described as having &quot;experienced a second phase of growth in his late thirties&quot;, attaining a height of 2.51m by the time of his death at 54.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Adam_Rainer&quot; rel=&quot;nofollow&quot;&gt;Adam Rainer&lt;/a&gt; This giant was, unusually enough, a &quot;dwarf&quot; at the age of 18, reaching a height of 1.22m. However he had a growth spurt afterwards, reaching a height of 2.18m at the age of 30 and 2.34m by the time of his death at age 49.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Also, in some cases the giant individuals facial (bone) structure changes as he/she ages. Considering that the human skull does not have any growth plates, or anything that would (as far as I know) put a stop to the skull bones response to growth hormone, can changes in face structure also happen to &quot;regular&quot; people who take growth hormones? &lt;/p&gt;&#xA;" OwnerUserId="12939" LastEditorUserId="12939" LastEditDate="2015-01-21T04:27:02.930" LastActivityDate="2015-01-21T11:08:26.913" Title="Pituitary giants - is the fusing of growth plates dependent on amount of growth hormone in blood?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;growth&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27885" PostTypeId="2" ParentId="27884" CreationDate="2015-01-21T01:04:01.180" Score="2" Body="&lt;p&gt;&lt;em&gt;Gigantism&lt;/em&gt; is caused by too much growth hormone (GH) and causes increased growth in kids (&lt;a href=&quot;http://www.healthline.com/health/gigantism#Overview1&quot; rel=&quot;nofollow&quot;&gt;healthline website&lt;/a&gt;). After adulthood, increased GH leads to &lt;em&gt;acromegaly&lt;/em&gt; which leads to continuing growth of fingers, feet, forehead, jaw, nose, and lips (&lt;a href=&quot;http://pituitary.ucla.edu/body.cfm?id=89&quot; rel=&quot;nofollow&quot;&gt;UCLA Health website&lt;/a&gt;). Note that structures like the nose and ears also keep on growing in healthy folks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, &lt;strong&gt;GH does not prevent closure of the growth plates&lt;/strong&gt;, which happens normally as far as I am aware. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taking GH during childhood will likely lead to gigantism, and to acromegaly in healthy individuals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;: In answer to the &lt;strong&gt;QUESTION EDIT&lt;/strong&gt;: the comment by @Raoul is interesting here, as the first guy Bernard Coyne was an eunich. Perhaps that was why his plates never fused as he will have had no testosterone production. I couldn't find specifics in the other 3 cases, but my guess is they are also exceptional cases (otherwise they wouldn't have made it in the record books). As to the question title I dare say that GH is not involved in plate fusion. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-21T11:08:26.913" LastActivityDate="2015-01-21T11:08:26.913" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27886" PostTypeId="1" AcceptedAnswerId="27895" CreationDate="2015-01-21T01:51:43.263" Score="1" ViewCount="1989" Body="&lt;p&gt;This question is from &quot;Concepts of Genetics,&quot; Klug &amp;amp; Cummings, 10e.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Thalassemia is an inherited anemic disorder in humans. Affected&#xA;individuals exhibit either a minor anemia or a major anemia.&#xA;Assuming that only a single gene pair and two alleles are&#xA;involved in the inheritance of these conditions, is thalassemia a&#xA;dominant or recessive disorder?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know from a quick Google search that the disorder is recessive, but how would I come to this conclusion based on the question alone?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: I've spoken to my professor, and he shared his opinion that is essentially the same as canadiener's answer. Thanks to everyone that replied!&lt;/p&gt;&#xA;" OwnerUserId="13127" LastEditorUserId="13127" LastEditDate="2015-01-23T17:20:36.190" LastActivityDate="2015-01-23T17:20:36.190" Title="How to determine if this blood disorder is recessive or dominant?" Tags="&lt;homework&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="27887" PostTypeId="1" AcceptedAnswerId="27888" CreationDate="2015-01-21T02:04:49.827" Score="5" ViewCount="1713" Body="&lt;p&gt;My sister is in 9th grade biology and her teacher avoided answering the question of how we actually study the inside of a cell. I haven't taken biology in a while but I'd like to give her an answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone roughly summarize how we actually learn about what goes on inside a cell? Just mentioning a few of the most common or used techniques would be fine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: I hope this isn't a bad question. It's a bit vague. But I didn't want to leave her without a decent answer.&lt;/p&gt;&#xA;" OwnerUserId="11652" LastActivityDate="2015-01-21T12:23:10.783" Title="How do we look inside the cell?" Tags="&lt;cell-biology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27888" PostTypeId="2" ParentId="27887" CreationDate="2015-01-21T02:48:01.993" Score="7" Body="&lt;p&gt;Techniques to look at whole cells are: &lt;strong&gt;Light microscopy&lt;/strong&gt; (cells, large organelles), &lt;strong&gt;electron microscopy&lt;/strong&gt; (detailed analysis of subcellular structures and even proteins) and &lt;strong&gt;confocal fluorescence miscroscopy&lt;/strong&gt; (look at particular cellular planes, reconstruct 3D images).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And of course you can analyze the insides by Biochemistry by breaking the cell membranes and look at individual proteins and DNA/RNA by &lt;strong&gt;extraction&lt;/strong&gt; and &lt;strong&gt;electrophoresis&lt;/strong&gt; followed by &lt;strong&gt;Western&lt;/strong&gt; / &lt;strong&gt;Northern&lt;/strong&gt; / &lt;strong&gt;Southern blotting&lt;/strong&gt;, or isolate organelles by &lt;strong&gt;centrifugation&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is a broad question, and I just gave the most obvious examples of techniques (not anywhere near exhaustive). By googling the bold-out terms you may provide some details to your sis.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-21T03:45:06.520" LastActivityDate="2015-01-21T03:45:06.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27889" PostTypeId="2" ParentId="27887" CreationDate="2015-01-21T04:26:50.357" Score="4" Body="&lt;p&gt;Beyond the conventional methods listed by Chris Stronks, Berkley Labs have far advanced the state of the art in probing the internal structures of cells using x-ray tomography. See:&#xA;&lt;a href=&quot;http://ncxt.lbl.gov/&quot; rel=&quot;nofollow&quot;&gt;http://ncxt.lbl.gov/&lt;/a&gt; . The images obtained are absolutely incredible and allow researchers to probe the cell layer by layer and visually contrast specific organelles for study much in the same manner that organisms are examined using CT scanners.&lt;/p&gt;&#xA;" OwnerUserId="9906" LastActivityDate="2015-01-21T04:26:50.357" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27890" PostTypeId="5" CreationDate="2015-01-21T04:50:49.853" Score="0" Body="&lt;p&gt;Respiration deals with the exchange of gases across organs that facilitate transport of the gases to and from the cells of the organism, especially in higher organisms. Breathing and ventilation are related terms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the cellular metabolic process that convert nutrients into chemical energy the tag &lt;a href=&quot;/questions/tagged/cellular-respiration&quot; class=&quot;post-tag&quot; title=&quot;show questions tagged &amp;#39;cellular-respiration&amp;#39;&quot; rel=&quot;tag&quot;&gt;cellular-respiration&lt;/a&gt; should be used.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2016-03-23T09:12:34.570" LastActivityDate="2016-03-23T09:12:34.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27891" PostTypeId="4" CreationDate="2015-01-21T04:50:49.853" Score="0" Body="The exchange of gases across organs that facilitate transport of the gases to and from the cells of the organism." OwnerUserId="9906" LastEditorUserId="3624" LastEditDate="2015-01-21T10:14:08.733" LastActivityDate="2015-01-21T10:14:08.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27892" PostTypeId="2" ParentId="27799" CreationDate="2015-01-21T05:02:06.543" Score="7" Body="&lt;p&gt;Blood is not always drawn from the veins depending on the medical need and situation. For example critically ill ICU patients will often have an arterial catheter placed to provide an accurate measure of blood pressure. Blood is sometimes sampled from this line to provide a more accurate measure of blood gases and cardiac performance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the risks of dealing with arterial blood are greater as others have mentioned.&lt;/p&gt;&#xA;" OwnerUserId="9906" LastActivityDate="2015-01-21T05:02:06.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27894" PostTypeId="2" ParentId="27870" CreationDate="2015-01-21T06:24:32.357" Score="2" Body="&lt;p&gt;I just want to add a few points to the above answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heart is not the only organ which helps blood flow. The following structures also help:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The action of muscles on deep veins acts as a pump - Soleus is called peripheral heart for that matter&lt;/li&gt;&#xA;&lt;li&gt;The compliance itself adds to the flow - Infact the compliance of the blood vessels is what makes the blood flow continuous instead of pulsatile like a system with stiff tubes would be expected to act when the pump is pulsatile in nature&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Some Critical Points to keep in mind:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The circulatory system is made in such a way that the total sum of cross sections of all the vessels at a particular level is as follows:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The sumtotal of cross-sections of all capillaries is the largest cross section ~ 11308 cm&lt;sup&gt;2&lt;/sup&gt;, (approximately only 1/4 are open under normal pressure, so effective cross section is ~ 2827 cm&lt;sup&gt;2&lt;/sup&gt;)&lt;/li&gt;&#xA;&lt;li&gt;The sumtotal of cross-sections of venules followed by arterioles (~141 cm&lt;sup&gt;2&lt;/sup&gt;) (venules more than arterioles as arterioles normally are under a tonal contraction) &lt;/li&gt;&#xA;&lt;li&gt;Sumtotal of cross-sections of veins followed by arteries (~63 cm&lt;sup&gt;2&lt;/sup&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Cross-section of Vena Cava ~ 1.38 cm&lt;sup&gt;2&lt;/sup&gt; followed by Aorta ~ 1.13 cm&lt;sup&gt;2&lt;/sup&gt; &#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So if the cross sections are added up: Capillaries &gt; Venules &gt; Arterioles &gt; Veins &gt; Arteries&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The Pressure Blood Pressure we measure is not exactly the flow pressure aka the pressure gradient. We measure the &lt;strong&gt;radial pressure&lt;/strong&gt; not the pressure gradient. Special equipment is needed to measure pressure gradient.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The volume of fluid inside a parallel circuit (artery to capillary to vein) is not constant as plasma diffuses out at the small arterioles and capillary levels and diffuses back in at the venous side. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The pressure flow curve is not linear due to the compliance of the blood vessels. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The heart contributes very little to the blood flow in the veins. (To re emphasize that heart is not the only organ driving circulation). It is mainly through postural drainage and muscle action. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Coming to your question I like to point out one thing:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is a need to increase perfusion, the vasoconstriction occurs at the venular side. The capillary pressure is responsible for perfusion.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;$$P_c = \frac{(R_{post}/R_{pre}).P_a + P_v}{1 + (R_{post}/R_{pre})}$$&#xA;  Where P - pressure and the characters a, v and c denotes artery, vein and capillary&#xA;  resistance&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;R&lt;sub&gt;post&lt;/sub&gt; - Post-capillary resistance&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;R&lt;sub&gt;pre&lt;/sub&gt; - Pre-capillary resistance&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EJsjW.jpg&quot; alt=&quot;Effect of pre and post capillary pressure on capillary pressure&quot;&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The equation and picture are taken from Boron and Boulpaep textbook of Medical Physiology, 2nd Edition, Chapter 19: Arteries and Viens.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;When there is a need to increase the perfusion to an organ the post capillary pressure is raised by venoconstiction (or in the case of glomeruli of kidney constriction of efferent arterioles). As you can see from the above equation, such a rise will cause rise in the capillary pressure and increase the perfusion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise vasoconstriction occurs to do exactly what you assumed would happen: to redirect blood flow. In fact this happens at several levels: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Vasoconstriction of periphery (limbs) occur in cold conditions which causes cyanosis (meaning the flow is so reduced that most oxygen is used up)&lt;/li&gt;&#xA;&lt;li&gt;Vasoconstriction of Splanchnic vessels occur when muscles need more blood (during exercise, flight, fight, etc...)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;If you can read this chapter you will understand the equation much better. This book explains the physics behind physiology in a beautiful manner.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-01-22T00:21:56.680" LastActivityDate="2015-01-22T00:21:56.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27895" PostTypeId="2" ParentId="27886" CreationDate="2015-01-21T06:31:44.630" Score="2" Body="&lt;p&gt;Given that this is a text book question about classical genetics, you can safely disregard any reality about the disorder.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd argue that the two alleles show incomplete dominance. The mild anemia, which is intermediate between healthy individuals and those with severe anemia, can be attributed to heterozygous individuals. In this case, the expression of the functional allele is not enough to compensate for the nonfunctional allele, producing the mutant phenotype. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-01-21T07:38:54.387" LastActivityDate="2015-01-21T07:38:54.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27896" PostTypeId="1" CreationDate="2015-01-21T07:01:28.107" Score="2" ViewCount="122" Body="&lt;p&gt;Once in a math congress someone presented a paper on a mathematical model used to predict the impact of certain measures that could be taken in order to control some pest/plague. A guy in the audience interrupted the speaker and asked why not to &quot;kill them all&quot;(referring to the specimens of the pest/plague) and put a stop to the problem. The speaker observed that we were thinking that kind of things because almost all of us were mathematicians and so we were not aware that it would be a big problem to do that. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From my point of view, he was suggesting that &quot;the right way to control a plague is not to kill them all&quot; is a standard, uncontroversial fact that all biologists would agree. My question is about this last point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is that a scientific thesis or an ideological one? I mean, do biologists have theories that allow them to know that the &quot;right&quot; way to control a plague is not to kill every specimen of the species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is it the case that we can assure that exterminating a species is necessarily going to affect, directly or not, humankind? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it a matter of chance and, as we are not completely certain of what may happen after exterminating the species, then we don't want to take a risk?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks! And feel free to edit tags :)&lt;/p&gt;&#xA;" OwnerUserId="13128" LastEditorUserId="13128" LastEditDate="2015-01-21T20:52:55.460" LastActivityDate="2017-07-12T19:52:50.623" Title="Almost philosophical question about controlling a pest/plague" Tags="&lt;ecology&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="27897" PostTypeId="2" ParentId="24257" CreationDate="2015-01-21T09:14:03.627" Score="3" Body="&lt;p&gt;Succinycholine, as its name might suggest, is a cholinergic agonist indeed. It acts on the neural plate of skeletal muscles, where it activates the muscle cholinergic receptors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phase 1 block due to succinylcholine thus occurs by activating so many receptors at once, that the whole muscle gets desensitized and therefore paralyzed. A corollary of that is that muscle will twitch during activation, thus accounting for the reason why people twitch shortly before becoming paralyzed after a succinycholine iv injection. This phase 1 block will resolve in 2-5 minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now an interesting phenomenon is that if you go on stimulating the muscle with more cholinergic agonists (for example, a second iv dose of succinylcholine), you may end up provoking endocytosis and degradation of the cholinergic receptors. This is called phase 2 block, and in contrast to phase 1, it will take at least several hours to resolve. This is why we never use a second dose in the clinics, except in very special cases.&#xA;You can also read about it all on &lt;a href=&quot;http://en.wikipedia.org/wiki/Suxamethonium_chloride&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2015-01-21T09:14:03.627" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="27898" PostTypeId="1" CreationDate="2015-01-21T11:34:41.847" Score="37" ViewCount="36397" Body="&lt;p&gt;In the never-ending debate &lt;a href=&quot;http://people.xiph.org/~xiphmont/demo/neil-young.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;raging in the audiophile community&lt;/a&gt; about sound quality and what humans can or cannot hear, it is &lt;a href=&quot;http://hypertextbook.com/facts/2003/ChrisDAmbrose.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;very&lt;/a&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/Sense#Hearing&quot; rel=&quot;nofollow noreferrer&quot;&gt;very&lt;/a&gt; &lt;a href=&quot;https://sound.stackexchange.com/questions/25070/what-is-the-resolution-of-human-hearing&quot;&gt;very&lt;/a&gt; &lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/Sound/earsens.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;very&lt;/a&gt; &lt;a href=&quot;https://sound.stackexchange.com/questions/23537/how-is-it-possible-to-hear-something-at-44-1khz&quot;&gt;incredibly&lt;/a&gt; often cited that the upper-limit of the audible range of human hearing is 20&amp;nbsp;kHz, give or take. &lt;a href=&quot;http://hypertextbook.com/facts/2003/ChrisDAmbrose.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;Some&lt;/a&gt; indicate that this is a conservative estimate, and that the actual upper-limit is actually lower than that (~18&amp;nbsp;kHz). While &lt;a href=&quot;https://en.wikipedia.org/wiki/Sampling_(signal_processing)#Sampling_rate&quot; rel=&quot;nofollow noreferrer&quot;&gt;others&lt;/a&gt; suggest that sounds could be heard or otherwise perceived up to about 25&amp;nbsp;kHz-30&amp;nbsp;kHz:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sampling rates higher than about 50 kHz to 60 kHz cannot supply more usable information for human listeners.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And some &lt;a href=&quot;https://en.wikipedia.org/wiki/Hearing_range&quot; rel=&quot;nofollow noreferrer&quot;&gt;others&lt;/a&gt; suggest that there is substantial variation between individuals around the upper limit:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The human range is commonly given as 20 to 20,000 Hz, though there is considerable variation between individuals, especially at high frequencies&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So is there &lt;strong&gt;any&lt;/strong&gt; biological evidence whatsoever that young, healthy humans can hear or otherwise perceive (or sense) sound waves above 20&amp;nbsp;kHz? And what would be a conservative estimate of the absolute upper limit of the audible spectrum for humans (i.e. usable sound information for human ears and senses)?&lt;/p&gt;&#xA;" OwnerUserId="5782" LastEditorUserId="-1" LastEditDate="2017-04-13T12:59:01.713" LastActivityDate="2016-03-01T20:17:56.390" Title="Can humans perceive sounds above 20 kHz?" Tags="&lt;hearing&gt;&lt;human-ear&gt;&lt;ultrasound&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="27899" PostTypeId="2" ParentId="9101" CreationDate="2015-01-21T11:40:24.620" Score="4" Body="&lt;p&gt;The quick and dirty answer is: fMRI doesn't perform well in the temporal domain, but excels in the spatial domain among non-invasive imaging methods. If you need an answer as to &lt;em&gt;where&lt;/em&gt; the action is, use fMRI. If you need answers to temporal questions, I recommend using electrophysiology such as EEG, which excels in the temporal domain, or MEG for a combination of good temporal and spatial resolution.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to what the limit exactly is, I would say a few seconds. fMRI measures blood oxygentaion responses, (See the answer on the question: &quot;&lt;a href=&quot;https://cogsci.stackexchange.com/questions/8650/what-does-fmri-measure-exactly/8654#8654&quot;&gt;What does fMRI measure exactly&lt;/a&gt;&quot;), which are inherently slow. Neural processes in local neural networks occur in milliseconds, in larger networks in the order of hundreds of milliseconds. Blood flow differences, in contrast, occur in the order of seconds. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2018-12-22T23:10:58.590" LastActivityDate="2018-12-22T23:10:58.590" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="27900" PostTypeId="2" ParentId="27887" CreationDate="2015-01-21T12:23:10.783" Score="0" Body="&lt;p&gt;One technique that I like is &lt;em&gt;Immunofluorescence&lt;/em&gt;. You get images like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KVQFE.jpg&quot; alt=&quot;Immunoflourescence: The nuclei are stained blue (command centre of the cell), the cytoplasm green&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The staining are caused by applying antibodies with an flourescent probe. The antibody 'sticks' to certain parts of the cell, &amp;amp; the probe produces the light patterns you see.&lt;/p&gt;&#xA;" OwnerDisplayName="user13131" LastActivityDate="2015-01-21T12:23:10.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27901" PostTypeId="2" ParentId="27898" CreationDate="2015-01-21T12:23:11.840" Score="46" Body="&lt;p&gt;&lt;strong&gt;Yes, we can&lt;/strong&gt;. By means of &lt;em&gt;bone conduction&lt;/em&gt; we can hear up to 50 kHz, and values up to 150 kHz have been reported in the young (&lt;a href=&quot;http://www.nature.com/nature/journal/v166/n4222/abs/166571b0.html&quot; rel=&quot;noreferrer&quot;&gt;Pumphrey, 1950&lt;/a&gt;). However, it is indeed generally agreed that 20 kHz is the upper acoustical hearing limit through air conduction. The reason for this is debated, but the &lt;strong&gt;transfer function of the ossicle chain in the middle ear&lt;/strong&gt; is a suspected culprit in setting the upper frequency limit to 20 kHz (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/037859559500031X&quot; rel=&quot;noreferrer&quot;&gt;Hemila et al., 1995&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, using normal speakers or headphones &lt;strong&gt;20 kHz is a very reasonable absolute upper limit&lt;/strong&gt;. Note that the Nyquist criterium necessitates higher sampling rates (at least 40 kHz), so your statement of using 50k-60k sound cards is correct. If you decide on using bone conduction aids, you might start to think on using higher sampling rates still.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is an example of a commercially available bone conduction head set (&lt;a href=&quot;http://www.google.com.au/aclk?sa=l&amp;amp;ai=CkvizVZ-_VJj7DNei9AWT1YDoAcjBo_UE4M_17fYBo-7dg_QBCAkQASDezc8eKBRgpfiIgIwBoAHYkajyA8gBB6kCT6rj00h0qz6qBCdP0NpvCahllnJ8FoYQ9Ys3zOY6nF49ISPnVUh7VSQgD_Kp6T1mKGjABQWgBiaAB5Du1w2IBwGQBwKoB6a-G-AS5Ovp3tOx15muAQ&amp;amp;sig=AOD64_1z0NcdVwArFW6YE2me6GrZNEEqJA&amp;amp;adurl=http://www.wildfiresports.com.au/aftershokz-bluez-2-wireless-bone-conduction-headph&amp;amp;ctype=5&amp;amp;rct=j&amp;amp;q=&amp;amp;ei=VZ-_VLW9CpHv8gX-woHwCw&amp;amp;ved=0CGUQpyswAA&quot; rel=&quot;noreferrer&quot;&gt;AfterShockz&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lUjM2.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These devices have the potential to increase the upper limit because they &lt;strong&gt;bypass the middle ear&lt;/strong&gt; and hence circumvent the limiting transfer function of the middle ear. They induce vibrations onto the temporal bone, that travel via the bone directly to the inner ear. See the following picture from &lt;a href=&quot;http://thehightechsociety.com/bone-conduction/&quot; rel=&quot;noreferrer&quot;&gt;The High Tech Society&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RFXSD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note: when you grow older the hearing sensitivities at high frequencies  are severely reduced, and even the 6 kHz range is severely affected in the elderly (picture from &lt;a href=&quot;http://www.linuxfocus.org/English/March2003/article271.meta.shtml&quot; rel=&quot;noreferrer&quot;&gt;John Perr's website&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UD8we.png&quot; alt=&quot;HFHL&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;em&gt;Disclaimer: I haven't looked into the capabilities in terms of upper frequency limits of bone conduction head sets. I am just talking theoretical limits.&lt;/em&gt;&lt;/sub&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.nature.com/nature/journal/v166/n4222/abs/166571b0.html&quot; rel=&quot;noreferrer&quot;&gt;Pumphrey, &lt;em&gt;Nature&lt;/em&gt; 1950; &lt;strong&gt;166&lt;/strong&gt;:571&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/037859559500031X&quot; rel=&quot;noreferrer&quot;&gt;Hemila et al., &lt;em&gt;Hear Res&lt;/em&gt; 1995; &lt;strong&gt;85&lt;/strong&gt;:31-44&lt;/a&gt;&lt;/sub&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-03-01T20:17:56.390" LastActivityDate="2016-03-01T20:17:56.390" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="27902" PostTypeId="1" CreationDate="2015-01-21T13:19:30.383" Score="5" ViewCount="557" Body="&lt;p&gt;I want to measure metabolism rates in &lt;a href=&quot;http://en.wikipedia.org/wiki/Tardigrade&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Tardigrades&lt;/em&gt;&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Pja5q.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Metabolic rates will be assessed immediately following their exit from cryptobiosis (an animal dormant state).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that oxygen levels is the usual way to measure metabolism, but tardigrades are extremely small and hence oxygen level differences will be minute. Is there any other way to characterize metabolic rates, or is there a way to make the oxygen method viable?&lt;/p&gt;&#xA;" OwnerUserId="13132" LastEditorUserId="3340" LastEditDate="2015-01-22T09:10:09.337" LastActivityDate="2015-01-22T12:52:29.217" Title="How to measure metabolic rates of microscopically small animals?" Tags="&lt;metabolism&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27903" PostTypeId="2" ParentId="27870" CreationDate="2015-01-21T13:37:44.437" Score="2" Body="&lt;p&gt;I'll try a brief answer myself.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;No, the heart is not the only energy provider, as others have stated above. Does vasoconstriction inject energy into the system? Not really. Arteriolar constriction will increase the resistance of the system. Therefore, &lt;strong&gt;more energy will be required to keep flow at a constant level when vasocontriction occurs.&lt;/strong&gt; Arteriolar vasoconstriction forces the system to function at a higher energy level, yet it does not inject energy targeted at facilitating flow.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Yes, your assumption is correct.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;@anongoodnurse answered correctly.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There is no direct relationship between compliance and flow. They are independent factors. The important point is the following: &lt;strong&gt;during diastole, the heart is isolated from the vessels.&lt;/strong&gt; The higher the vessel compliance is, the more potential elastic energy will be transferred from the heart to the vessels during systole, to then ensure good flow during diastole. In elderly persons for example, arteries are usually stiff, systolic pressure is high, and diastolic pressure is low (as is flow).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;To conclude, I would say that the most important lesson that is to be learned here is that although a higher blood pressure means a higher energy state and more work for the heart, &lt;strong&gt;it is incorrect to assume that blood flow is physiologically adequate because pressure is high!&lt;/strong&gt; This is a common mistake made in the emergency room.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2015-01-21T20:15:02.890" LastActivityDate="2015-01-21T20:15:02.890" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27904" PostTypeId="1" CreationDate="2015-01-21T14:42:52.363" Score="0" ViewCount="329" Body="&lt;p&gt;A) Amino acids and triglycerides that have a carbon-carbon double bond&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or                                                                                &lt;/p&gt;&#xA;&#xA;&lt;p&gt;B) proteins and fatty acids &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think they are both true, but I should choose only one&#xA;I think that because since amino acids have COOH and C-H group, proteins do too and fatty acids have these groups too just like triglycerides with a double bond. But since I have to choose one I would choose B. Am I right?&lt;/p&gt;&#xA;" OwnerUserId="13133" LastEditorUserId="13133" LastEditDate="2015-01-21T16:50:32.220" LastActivityDate="2015-01-21T17:27:21.480" Title="Which of these components has C-H and COOH groups" Tags="&lt;lipids&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-01-22T09:09:45.353" ContentLicense="CC BY-SA 3.0" />
  <row Id="27905" PostTypeId="2" ParentId="23074" CreationDate="2015-01-21T14:57:55.753" Score="21" Body="&lt;h1&gt;Overview.&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;This is a very interesting question. The ideas behind this have been around for a while and the methods are covered in great detail elsewhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The overall answer to the hypothetical question is rather surprising. There may be actually potential benefits to perpetual liquid ventilation for people with certain diseases. Trials so far have not found side effects in fluorocarbon liquid breathing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So lets talk about the history of liquid breathing and case studies, then we will move onto the hypothetical situation of liquid breathing indefinitely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A great review (Shaffer &lt;em&gt;et al&lt;/em&gt;, 1992) covers the field in great depth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;@MCM pointed out in the comments that my original answer did no emphasise that animal diaphragms are not powerful enough to move the liquid in and out of the lungs. I should mention now that the below cases all use ventilators to pump the fluid into and out of the lungs. The difficulty of breathing this without a ventilator is emphasised by &lt;a href=&quot;http://www.ted.com/talks/david_blaine_how_i_held_my_breath_for_17_min?language=en&quot; rel=&quot;nofollow noreferrer&quot;&gt;David Blaine at 4:54 in this TED talk&lt;/a&gt; who said it was like trying to breathe with an elephant standing on your chest.&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Case studies.&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;As early as the 1920s, poisonous gas research that lead to the infamous mustard gas found that lungs could tolerate large quantities of saline briefly without damage.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Animals.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Kylstra, the first pioneer introducing the idea of land animals breathing liquids (Kylstra &lt;em&gt;et al.,&lt;/em&gt; 1962), found mice could withstand 4 hours of 160 atmospheres of pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clark found that mice and rats could breathe oxygen bubbled silicone oils and survive for a few hours after emersion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In 1965, he discovered that the fluorocarbon known as FC75 not only supported respiration during total immersion but the mice &lt;strong&gt;survived indefinitely in apparent good health.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most recent study I can find is the partial use of fluorocarbon liquid ventilation in adult respiratory distress syndrome (ARDS) of rabbits. The same improvements in breathing were not observed in saline liquid breathing or conventional ventilators.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Humans.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;In humans PFCs were first used successfully in 1989 for the ventilation of young infants near death.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Marked improvement in lung compliance, without a compromise of cardiovascular status was noted in all three patients. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;All three infants died of their severe preexisting respiratory complications, but the trial showed liquid breathing can support gas exchange in humans. However developing lungs of infants cannot rely on mechanical ventilators for prolonged periods as nearly a quarter of premature infants of those that do later developed chronic breathing problems. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Biomedical application.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There are a fair few researches and doctors who believe fluorocarbon liquid ventilation has some advantages over gas ventilation. It reduces stress at the area of interfacial surface tension in the distressed, surfactant-deficient lung. This would be ideal and appropriate for ARDS in human adults. A more sophisticated use would be using fluorocarbons as a drug delivery system straight to damaged lung tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(All the above can be found in the &lt;a href=&quot;http://onlinelibrary.wiley.com/store/10.1002/ppul.1950140208/asset/1950140208_ftp.pdf?v=1&amp;amp;t=i56t8bq6&amp;amp;s=159dd8f9de838c216066607ce22a03bf16bf0092&quot; rel=&quot;nofollow noreferrer&quot;&gt;1992 review.&lt;/a&gt; There is also data on the different properties of suitable FCs)&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Real world potential.&lt;/h1&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is perpetual liquid breathing possible? ...And healthy?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So this is where we stand with the case studies; mice can breath liquids indefinitely and stay in good health, rabbits with ARDS survive where breathable gas would not help, and there is a contingency in the biomedical community that it can be better than gas ventilation for medical treatment. To me it seems that there is nothing to suggest a fully grown adult would suffer from breathing liquids. The inertness of the fluorocarbons implies any toxicity would only reveal itself in a timescale of years, and everything else about the compounds pose no danger and may make gas transfer across the lungs easier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This relatively modest success is perhaps no surprise. The exchange interface of our lungs relies on a mucous (liquid) so the gases can permeate the lung tissue. Expanding on that idea should certainly not rule out the possibility of liquid breathing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biggest drawback, besides the cost of a long term experiment and being dependent on a mechanical ventilator, is that these are very small case studies of success. Given the massive amounts of unknowns (particularly for long term studies), switching to  purely liquid ventilation in an adult human could have unforeseen risks and would be considered dangerous by any ethics board (or insurance company)! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a lighter note, &lt;a href=&quot;https://www.youtube.com/watch?v=l7oytGfPQw4&quot; rel=&quot;nofollow noreferrer&quot;&gt;here is a YouTube video of what Maddie&lt;/a&gt;, a biology podcaster from the BBC, had to say on the matter of living in total submersion. Lots of skin problems, risk of infection after a few days etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, a very interesting, albeit understudied, topic!&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2019-05-29T11:23:35.700" LastActivityDate="2019-05-29T11:23:35.700" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="27907" PostTypeId="2" ParentId="24371" CreationDate="2015-01-21T16:48:08.117" Score="0" Body="&lt;p&gt;It is my understanding that the dark-adapted eye can perceive single photons. Those have a well-defined range of energies in the visible spectrum. Also, as others have pointed out, light is very directional and localized: if you are not looking at the source, it will not be perceived. Sound comes to the ears from all directions at all times. The waves are so large that low frequencies cannot even &quot;fit&quot; inside a typical room, so direction is meaningless. Trying to define a particular energy for them when they can vary in both frequency and intensity (unlike photons, which only vary in frequency and number of them impinging) is not likely to be exact. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I was told that two completely unlike forces differed by a factor of 4, I would say, &quot;could be that one is actually more or less than the other, too close to tell.&quot; In electronics, component values can vary over a range of half to twice as much and be in specification. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally speaking, the senses evolved to the point where any further sensitivity would result in perceiving noise. Then, quite reasonably, they stopped. If you could hear the air molecules banging on your eardrums (if ears were 10 dB more sensitive) you would go mad. Light does not have this noise characteristic, so we can see the lowest possible value: one photon.&lt;/p&gt;&#xA;" OwnerDisplayName="user13135" LastActivityDate="2015-01-21T16:48:08.117" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27908" PostTypeId="2" ParentId="27875" CreationDate="2015-01-21T16:49:25.407" Score="0" Body="&lt;p&gt;Thanks to you guys I googled, &amp;quot;&lt;a href=&quot;https://www.google.com/search?q=stem%20cell%20virus%20animals&amp;amp;oq=stem%20cell%20virus%20animals&amp;amp;aqs=chrome..69i57.8314j0j7&amp;amp;client=ubuntu-browser&amp;amp;sourceid=chrome&amp;amp;es_sm=117&amp;amp;ie=UTF-8&quot; rel=&quot;nofollow noreferrer&quot;&gt;stem cell virus animals&lt;/a&gt;&amp;quot; and found some promising links! I appreciate you guys emphasizing immunological response. I was hoping that the virus would be effective enough to work on the first shot and thereby avoid most of the immunological complications. However it seems that the second generation of adenovirus vectors in animal models was abandoned for just that reason: &lt;a href=&quot;http://atvb.ahajournals.org/content/20/6/1452.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;source - NCBI&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Here is a nice excerpt regarding animal models:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;“&lt;strong&gt;third-generation adenovirus vectors&lt;/strong&gt;”: This research focuses on the development of improved production systems for gutless adenovirus vectors and their use for the efficient introduction of large or multiple transgenes into human progenitor and stem cells with minimal vector-related toxicity. In addition to the use of regular third-generation adenovirus vectors for the transient genetic modification of target cells, we have embarked on the generation of new vector types for stable transgene expression in transduced target cells using locus/site-specific transgene integration or homologous recombination. For example, we have generated new adenovirus/adeno-associated virus vectors. These vectors stably integrate into a specific locus on human chromosome 19 and are capable of genetically complementing dystrophin-deficient human myoblasts.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.lumc.nl/org/moleculaire-celbiologie/research/Virus-and-Stem-cell-biology/&quot; rel=&quot;nofollow noreferrer&quot;&gt;-Leeds Universitair (NZ)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="146" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-01-21T17:48:19.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27909" PostTypeId="2" ParentId="27896" CreationDate="2015-01-21T16:55:32.330" Score="5" Body="&lt;p&gt;Biologists are certainly not afraid to exterminate pests and plagues in the wild. See: smallpox and polio. However, such exterminations are nearly impossible and very expensive. See: smallpox and polio. In both cases extinction is through  extensive vaccination, preventing the disease from having any hosts to live in. To achieve this you need to vaccinate a huge fraction of the human population for quite some time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Practically, how would you go about exterminating an agricultural pest? A beetle, for example? Perhaps an army of men, forming a cordon the width of the united states, turning over every rock and every tree from the west coast to the east coast. With a high net or something to prevent beetles from flying over the cordon. And some method for dealing with cities and roads and tunnels and things, because if you miss only five or six they'll be back soon, depending on life cycle and offspring numbers. Or if you forget Canada. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And to use a biological solution to a biological problem, consider myxomatosis and the Australian rabbit problem. Rabbits were(and are) a pest, myxomatosis is a rabbit plague that has a 99.99% fatality rate and is fiercely infectious. Sure enough, myxomatosis wiped out the rabbit population. A few years later the rabbits were back but now the survivors were resistant to myxomatosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would argue that it's a scientific thesis based on hard lessons biologists have learned about doing 100% of anything. There are many biologists with moral precepts against the extinction of pest species. It's a bit of a moot point, however. The only reliable method of extinction is habitat destruction. Whether that's immunizing all the humans or cutting down the rainforests, it does work. It's just usually impractical.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-01-21T16:55:32.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27910" PostTypeId="2" ParentId="27898" CreationDate="2015-01-21T17:16:38.730" Score="8" Body="&lt;p&gt;If all the processes through which a signal passes are linear, then it makes sense to speak in terms of a maximum useful-content frequency. If a signal passes through non-linear stages, however, it is possible that frequency content which would in and of itself be above the range of hearing, may interact with other frequency content which is also above that range, in such a fashion as produce artifacts which are well within the range of hearing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A rather annoying example of that may be observed when a &lt;a href=&quot;http://en.wikipedia.org/wiki/GSM&quot;&gt;GSM&lt;/a&gt; cell phone is located near audio equipment. All of the frequency content transmitted by the phone exceeds the upper limit of human hearing by multiple orders of magnitude, and yet the annoying buzz picked up by the audio equipment clearly does not.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens is that the frequency content of the cell phone's transmissions contains numerous frequencies which are separated by tens or hundreds of hertz, and many amplifier stages don't completely filter out the radio-frequency content, but are unable to process it without distortion. This distortion causes the amplifier to output sum and difference frequencies, some of which are very much in audible range.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many kinds of objects and materials will reflect sound waves in a fashion which varies in non-linear fashion with the sounds being reflected. If a diaphragm which had more freedom of movement in one direction than the other were hit with a mixture of 100,000&amp;nbsp;Hz and 100,100&amp;nbsp;Hz tones, it would &quot;buzz&quot; at 100&amp;nbsp;Hz, whereas it would not do so if hit by either tone alone; further, a conventional recording of the combined tones by a high-quality microphone would detect nothing, so playing it back in the presence of the diaphragm would yield no buzz.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be rare for aesthetically-pleasing audio content to have frequency content over 20&amp;nbsp;kHz which contributed materially to its aesthetic aspects.  It would certainly be possible, however, to construct frequency content over 20&amp;nbsp;kHz, however, which could be heard in many common environments, and whose perceived sound would vary in ways that would not be possible using only frequencies below 20&amp;nbsp;kHz, and would not be implausible that some kinds of musical instruments (e.g. handbells) might produce mixtures of high frequency content which would sound different to different people who found them pleasing, in ways which could not be mimicked using only directly-audible frequencies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It may be possible for an audio technician working with a &lt;a href=&quot;http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging&quot;&gt;functional MRI&lt;/a&gt; team to create, for an individual, a sound which was indistinguishable from the original, but for another individual that recreated sound might sound nothing like the original.&lt;/p&gt;&#xA;" OwnerUserId="13136" LastEditorUserId="355" LastEditDate="2015-01-21T21:19:08.207" LastActivityDate="2015-01-21T21:19:08.207" CommentCount="18" ContentLicense="CC BY-SA 3.0" />
  <row Id="27911" PostTypeId="1" AcceptedAnswerId="27916" CreationDate="2015-01-21T17:21:32.000" Score="2" ViewCount="52" Body="&lt;p&gt;Are there any generic ways to determine if a person is infected with a parasite?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With &quot;generic ways&quot; I mean ways that do not rely on symptoms caused by a particular parasite. Also I am mainly concerned by parasites that are too large for the immune system to completely handle on its own (such as worms).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, can parasites be seen in x-rays, MRI scans, or through some body fluid samples?&lt;/p&gt;&#xA;" OwnerUserId="12939" LastActivityDate="2015-01-21T20:00:50.317" Title="Are there any generic (not dependent on symptoms) ways to find parasite infections?" Tags="&lt;human-biology&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27912" PostTypeId="2" ParentId="27904" CreationDate="2015-01-21T17:27:21.480" Score="3" Body="&lt;p&gt;Answer A is wrong because triglycerides are esters not carboxylic acids so they have -COOR group, not -COOH. Amino acids and fatty acids have -COOH groups and proteins too - on C-termini and in side chains.&lt;/p&gt;&#xA;" OwnerUserId="13094" LastActivityDate="2015-01-21T17:27:21.480" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27913" PostTypeId="1" CreationDate="2015-01-21T18:15:06.430" Score="2" ViewCount="690" Body="&lt;p&gt;I've got control region sequence data from a population of shark and I'm looking to convert this from FASTA to FSTAT in order to calculated the effective population size of females. The software I want to use only accepts FSTAT or Genepop files.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to convert FASTA to FSTAT or even Genepop? &lt;/p&gt;&#xA;" OwnerUserId="3382" LastActivityDate="2015-05-07T09:33:23.773" Title="How do you convert mtDNA sequences in FASTA to FSTAT format?" Tags="&lt;bioinformatics&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27914" PostTypeId="2" ParentId="27913" CreationDate="2015-01-21T18:26:57.420" Score="1" Body="&lt;p&gt;Check out &lt;a href=&quot;http://www.cmpg.unibe.ch/software/PGDSpider/&quot; rel=&quot;nofollow&quot;&gt;PGDSpider&lt;/a&gt;. The &lt;a href=&quot;http://www.cmpg.unibe.ch/software/PGDSpider/#Input_and_output_formats&quot; rel=&quot;nofollow&quot;&gt;inputs and outputs table&lt;/a&gt; indicates that it supports conversion between FASTA and FSTAT formats, among many others.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-01-21T18:26:57.420" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27915" PostTypeId="2" ParentId="27898" CreationDate="2015-01-21T19:27:25.570" Score="2" Body="&lt;p&gt;Taken from &lt;a href=&quot;http://people.xiph.org/%7Exiphmont/demo/neil-young.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&amp;quot;24/192 Music Downloads... and why they make no sense&amp;quot;&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Sampling rate and the audible spectrum&lt;/p&gt;&#xA;&lt;p&gt;I'm sure you've heard this many, many times: The human hearing range spans 20Hz to 20kHz. It's important to know how researchers arrive at those specific numbers.&lt;/p&gt;&#xA;&lt;p&gt;First, we measure the 'absolute threshold of hearing' across the entire audio range for a group of listeners. This gives us a curve representing the very quietest sound the human ear can perceive for any given frequency as measured in ideal circumstances on healthy ears. Anechoic surroundings, precision calibrated playback equipment, and rigorous statistical analysis are the easy part. Ears and auditory concentration both fatigue quickly, so testing must be done when a listener is fresh. That means lots of breaks and pauses. Testing takes anywhere from many hours to many days depending on the methodology.&lt;/p&gt;&#xA;&lt;p&gt;Then we collect data for the opposite extreme, the 'threshold of pain'. This is the point where the audio amplitude is so high that the ear's physical and neural hardware is not only completely overwhelmed by the input, but experiences physical pain. Collecting this data is trickier. You don't want to permanently damage anyone's hearing in the process.&lt;/p&gt;&#xA;&lt;p&gt;The upper limit of the human audio range is defined to be where the absolute threshold of hearing curve crosses the threshold of pain. To even faintly perceive the audio at that point (or beyond), it must simultaneously be unbearably loud.&lt;/p&gt;&#xA;&lt;p&gt;At low frequencies, the cochlea works like a bass reflex cabinet. The helicotrema is an opening at the apex of the basilar membrane that acts as a port tuned to somewhere between 40Hz to 65Hz depending on the individual. Response rolls off steeply below this frequency.&lt;/p&gt;&#xA;&lt;p&gt;Thus, 20Hz - 20kHz is a generous range. It thoroughly covers the audible spectrum, an assertion backed by nearly a century of experimental data.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PuhtK.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Above: Approximate equal loudness curves derived from Fletcher and Munson (1933) plus modern sources for frequencies &amp;gt; 16kHz. The absolute threshold of hearing and threshold of pain curves are marked in red. Subsequent researchers refined these readings, culminating in the Phon scale and the ISO 226 standard equal loudness curves. Modern data indicates that the ear is significantly less sensitive to low frequencies than Fletcher and Munson's results.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;This seems to imply that it's highly, highly improbable that anything above 20 kHz could be heard by the human ear, and that in most realistic conditions even that threshold would never be reached. I'm curious if others more knowledgeable can confirm or contradict this...&lt;/p&gt;&#xA;" OwnerUserId="5782" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-01-21T19:27:25.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27916" PostTypeId="2" ParentId="27911" CreationDate="2015-01-21T20:00:50.317" Score="3" Body="&lt;p&gt;The first thing that comes to mind would be eosinophils numeration. It is a specific type of white blood cell that handles parasitic infections. So in most cases, a blood sample would show an increase in this type of cell.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2015-01-21T20:00:50.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27919" PostTypeId="1" AcceptedAnswerId="74012" CreationDate="2015-01-21T23:05:55.123" Score="4" ViewCount="233" Body="&lt;p&gt;So far, I've found eleven species of Cerapoda that lived during the Jurassic period. Are there any other known species that I've missed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The eleven that I've found out about are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Agilisaurus&lt;/li&gt;&#xA;&lt;li&gt;Albalophosaurus&lt;/li&gt;&#xA;&lt;li&gt;Camptosaurus&lt;/li&gt;&#xA;&lt;li&gt;Chaoyangsaurus&lt;/li&gt;&#xA;&lt;li&gt;Dryosaurus&lt;/li&gt;&#xA;&lt;li&gt;Heterodontosaurus&lt;/li&gt;&#xA;&lt;li&gt;Othnielosaurus&lt;/li&gt;&#xA;&lt;li&gt;Uteodon&lt;/li&gt;&#xA;&lt;li&gt;Xuanhuaceratops&lt;/li&gt;&#xA;&lt;li&gt;Yandusaurus&lt;/li&gt;&#xA;&lt;li&gt;Yinlong&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am a game board designer working on a game related to dinosaurs. The &quot;only&quot; research i did is Wikipedia + the DK book &quot;Prehistoric&quot; + Dino Directory web site + several more lesser sites. I would appreciate any information on other species if my list isn't exhaustive, or literature suggestions that might help me.&lt;/p&gt;&#xA;" OwnerUserId="11691" LastEditorUserId="3624" LastEditDate="2015-01-22T09:44:07.963" LastActivityDate="2018-06-09T21:26:54.567" Title="What species of Cerapoda lived during the Jurassic?" Tags="&lt;palaeontology&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="27921" PostTypeId="1" AcceptedAnswerId="27924" CreationDate="2015-01-22T00:41:46.577" Score="1" ViewCount="2783" Body="&lt;p&gt;I can't find the exact definition of Mendelian segregation. In addition, I am wondering how it is related to the Hardy-Weinberg equilibrium? &lt;/p&gt;&#xA;" OwnerUserId="13143" LastEditorUserId="9943" LastEditDate="2015-01-22T01:21:44.277" LastActivityDate="2019-06-21T16:46:48.443" Title="What is Mendelian Segregation and how is it related to the Hardy-Weinberg equilibrium?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27922" PostTypeId="1" AcceptedAnswerId="27932" CreationDate="2015-01-22T00:45:22.603" Score="3" ViewCount="1365" Body="&lt;p&gt;This isn't exactly homework but I'd like to treat it as such. I'm asked to find the probability that both (III: 2) and (III: 3) are carriers given that (II: 7) and (III: 1) exhibited the recessive trait (affected individuals are marked black in the pedigree below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Denoting the affected individuals with $aa$ (and so the dominant allele is denoted $A$), I was able to determine the following:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Both (II: 1) and (II: 2) are carriers.&lt;/li&gt;&#xA;&lt;li&gt;Both (I: 3) and (I: 4) are carriers.&lt;/li&gt;&#xA;&lt;li&gt;At least one of (I: 1) and (I: 2) must be a carrier.&lt;/li&gt;&#xA;&lt;li&gt;The probability that (II: 6) is a carrier is $\frac{2}{3}$.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YcxQD.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer is supposed to be $\frac{1}{3}\times\frac{1}{4}=\frac{1}{12}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm mostly confused as to how to approach this one case at a time. Suppose (II: 6) is indeed a carrier. Then if (II: 5) is homozygous for $A$, then (III: 3) has a $\frac{1}{2}$ probability of being a carrier; if (II: 5) is also a carrier, then (III: 3) has a $\frac{2}{3}$ probability of being a carrier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the event that (II: 5) is homozygous is mutually exclusive from the event that he is heterozygous, would I just add these probabilities (i.e. $\frac{1}{2}+\frac{2}{3}$)? Then multiply by the $\frac{2}{3}$ of (II: 6)? This would give $\frac{7}{9}$, which doesn't seem to get me any closer to the right answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A different approach I tried was multiplying the respective probabilities for the (II: 5) events above, which gives $\frac{1}{3}$ and thus one factor of the provided answer. If this is right, and it seems to be, I'm not sure how to apply this to the (III: 2) side of the pedigree.&lt;/p&gt;&#xA;" OwnerUserId="13127" LastActivityDate="2015-01-22T06:01:05.097" Title="Assessing probability from a pedigree" Tags="&lt;homework&gt;&lt;genetic-diagrams&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27923" PostTypeId="1" CreationDate="2015-01-22T01:11:29.827" Score="2" ViewCount="52" Body="&lt;p&gt;Phenotypes such as; skin color, eye color, nose shape, lip size, limb proportions, and skull shape. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Im trying to find a source for this quote.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;If you ask what percentage of your genes is reflected in your external appearance, the basis by which we talk about race, the answer seems to be in the range of .01 percent,&quot; said Dr.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Harold P. Freeman&quot; From - &lt;a href=&quot;http://astro.temple.edu/~ruby/opp/racesnyt.html&quot; rel=&quot;nofollow&quot;&gt;http://astro.temple.edu/~ruby/opp/racesnyt.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="11679" LastEditorUserId="740" LastEditDate="2015-01-23T15:00:36.423" LastActivityDate="2015-01-23T15:00:36.423" Title="Is it possible to estimate how much variation in common phenotypes is predicted by genetics?" Tags="&lt;human-biology&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27924" PostTypeId="2" ParentId="27921" CreationDate="2015-01-22T01:19:27.097" Score="3" Body="&lt;p&gt;&lt;strong&gt;Mendelian segregation&lt;/strong&gt; is defined on the &lt;a href=&quot;http://www.nature.com/scitable/definition/principle-of-segregation-law-of-segregation-mendel-301&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nature&lt;/a&gt; site, and I quote:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The Principle of Segregation describes how &lt;strong&gt;pairs of gene variants are separated into reproductive cells&lt;/strong&gt;. The segregation of gene variants, called alleles, and their corresponding traits was first observed by Gregor Mendel in 1865. Mendel was studying genetics by performing mating crosses in pea plants. He crossed two heterozygous pea plants, which means that each plant had two different alleles at a particular genetic position He discovered that the traits in the offspring of his crosses did not always match the traits in the parental plants. This meant that the pair of alleles encoding the traits in each parental plant had &lt;strong&gt;separated or segregated&lt;/strong&gt; from one another during the formation of the reproductive cells. [...] We now know that the segregation of genes occurs during meiosis in eukaryotes, which is a process that produces reproductive cells called gametes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Likewise, the &lt;strong&gt;Hardy-Weinberg equilibrium&lt;/strong&gt; is explained on &lt;a href=&quot;http://www.nature.com/scitable/definition/hardy-weinberg-equilibrium-122&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nature's website&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The Hardy-Weinberg equilibrium is a principle stating that the &lt;strong&gt;genetic variation in a population will remain constant from one generation to the next in the absence of disturbing factors&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So in case of Mendell's experiments, his pea plants showed no disturbance and quite perfect ratios, for example 3:1 green:yellow seed pods:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/I1g3W.gif&quot; alt=&quot;seed pods&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The Nature site continues on the Hardy-Weinberg principle:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;When mating is random in a large population with no disruptive circumstances, the law predicts that both genotype and allele frequencies will remain constant because they are in equilibrium.&lt;/p&gt;&#xA;&lt;p&gt;The Hardy-Weinberg equilibrium can be disturbed by a number of forces, including mutations, natural selection, nonrandom mating, genetic drift, and gene flow. [...]. This occurs because certain alleles help or harm the reproductive success of the organisms that carry them. [...]. Because [...] of these disruptive forces [...] the Hardy-Weinberg equilibrium rarely applies in reality. Therefore, the Hardy-Weinberg equilibrium describes an idealized state [...].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So to get back to your question on the relation between Mendelian segregation and the Hardy-Weinberg equilibrium: The &lt;strong&gt;Hardy-Weinberg equilibrium is necessary for the Mendelian segregation to become phenotypically apparent&lt;/strong&gt;. So in Mendell's controlled experiments the 3:1 green:yellow pods became nicely apparent as both phenotypes had equal chance of survival.&lt;/p&gt;&#xA;&lt;p&gt;And to continue the seed pod example, if there were to be introduced a disturbing factor, such as a pest that wrecks havoc in plants with yellow pods, but not in green, the &lt;strong&gt;Hardy-Weinberg equilibrium&lt;/strong&gt; (i.e., Mendell's 3:1 green:yellow) would be disturbed and &lt;strong&gt;Mendelian segregation&lt;/strong&gt; would become less apparent as aberrant phenotpyic ratios would emerge (&amp;gt;3 : &amp;lt;1).&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-01-22T02:24:22.487" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27928" PostTypeId="2" ParentId="23189" CreationDate="2015-01-22T02:34:00.320" Score="3" Body="&lt;p&gt;Unfortunately at this time, there are no known glucosepane breakers which can feasibly be used in a living organism.  There is a small (very small) amount of research being done on the topic by Yale university in cooperation with the SENS foundation, but the focus is extremely early stage - nothing more than synthesis and detection of artifical glucosepane and precursors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is a rather frustrating situation, as there are very good arguments indicating glucosepane as an almost universal 'bad thing that should be fixed', and the molecule itself isn't particularly complicated.  It seems that this would be a low effort/high reward research area.&lt;/p&gt;&#xA;" OwnerUserId="13147" LastActivityDate="2015-01-22T02:34:00.320" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27929" PostTypeId="1" CreationDate="2015-01-22T03:52:20.253" Score="2" ViewCount="2060" Body="&lt;ol&gt;&#xA;&lt;li&gt;A ribosome is where amino acids are linked together by peptide bonds.&lt;/li&gt;&#xA;&lt;li&gt;A virus is NOT considered prokaryotic because it does not have a membrane.&lt;/li&gt;&#xA;&lt;li&gt;The nucleotide ATP is one of the most used energy molecules of a cell. &lt;/li&gt;&#xA;&lt;li&gt;Sugar phosphates are the type of lipid moved through the blood.&lt;/li&gt;&#xA;&lt;li&gt;A compound that lowers the pH is called an acid.&lt;/li&gt;&#xA;&lt;li&gt;The cell wall is a carbohydrate covering of all cells.&lt;/li&gt;&#xA;&lt;li&gt;The term cytosol is only applied to (blank) cells?&lt;/li&gt;&#xA;&lt;li&gt;An A-U base pair is part of the (blank) found in RNA.&lt;/li&gt;&#xA;&lt;li&gt;The major form of usable energy in animals is (what)?&lt;/li&gt;&#xA;&lt;li&gt;A polypeptide is a subunit of a what? &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This is what I said &#xA;1. True&#xA;2.True&#xA;3. True&#xA;4. False (cholesterol)&#xA;5. True less than 7 acidic&#xA;6. False&#xA;7. Don't know&#xA;8.complementary &#xA;9. ATP&#xA;10. Protein or amino acid? Don't know &lt;/p&gt;&#xA;" OwnerUserId="13149" LastEditorUserId="9943" LastEditDate="2015-01-22T12:45:48.950" LastActivityDate="2015-01-22T15:55:48.253" Title="True or false &amp; fill in the blanks" Tags="&lt;biochemistry&gt;&lt;homework&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27930" PostTypeId="2" ParentId="27929" CreationDate="2015-01-22T04:11:28.820" Score="4" Body="&lt;p&gt;1-6: OK;&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;7&quot;&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;prokaryotes&lt;/strong&gt;. Cytosol is the portion of cytoplasm which is devoid of any organelles, i.e., cytoplasm = cytosol + organelles. As prokaryotes don't have any organelles in their cytoplasm, they have only cytosol. So the answer would be prokaryotes (their cytoplasm consist of cytosol only). For a special case in eukaryotes see Crags answer below. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Double strand&lt;/strong&gt;;  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;Glucose? (but not ATP, fat would also be a suitable alternative specially in animal living in cold regions thanks to @CRags);  &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;protein&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-22T14:21:41.643" LastActivityDate="2015-01-22T14:21:41.643" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="27932" PostTypeId="2" ParentId="27922" CreationDate="2015-01-22T04:21:55.743" Score="3" Body="&lt;ul&gt;&#xA;&lt;li&gt;II:6 has a $2/3$ probability of being a carrier Aa.&lt;/li&gt;&#xA;&lt;li&gt;II:3 has a $1/2$ probability of being a carrier Aa. &lt;/li&gt;&#xA;&lt;li&gt;Assuming, just like canadianer&#xA;suggested, that the recessive gene is rare, autosomal, and&#xA;non-x-linked, this means II:5 and II:4 are both homozygous (AA).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;If parents of III:2 are therefore Aa and AA, this gives III:2 the probability of being a carrier of $1/2$. However, we must multiply this value by $1/2$, because III:2's father has a $1/2$ probability of being Aa. Therefore $\frac{1}{2}\frac{1}{2}= 1/4 =$ probability of III:2 being a carrier. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly for III:3, if her parents are Aa and AA, this gives III:3 the probability of being a carrier of $1/2$. However, we must multiple this value by $2/3$, because III:3's mother has a $2/3$ probability of being Aa. Therefore $\frac{1}{2}\frac{2}{3}= 1/3 =$ probability of III:3 being a carrier. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The probability of both III:2 and III:3 being carriers is the product of both their probabilities: $\frac{1}{3}\frac{1}{4}= 1/12$. &lt;/p&gt;&#xA;" OwnerUserId="11631" LastEditorUserId="12909" LastEditDate="2015-01-22T04:28:48.153" LastActivityDate="2015-01-22T04:28:48.153" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="27934" PostTypeId="1" CreationDate="2015-01-22T05:26:52.780" Score="3" ViewCount="697" Body="&lt;p&gt;As I sit here after eating too much chocolate, I wonder:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the biological mechanisms behind eating too much candy candy causing nausea in a healthy individual?  Is it a spike in blood sugar, or does the stomach run out of a particular chemical, or is it a pH shift?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it the same reason that greasy meals can cause nausea?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From an evolutionary perspective, candy causing nausea seems counter-intuitive since candy is easy calories.  Then again, candy and concentrated carbs are modern inventions...&lt;/p&gt;&#xA;" OwnerUserId="10343" LastEditorUserId="19099" LastEditDate="2017-06-24T14:40:15.167" LastActivityDate="2017-06-25T07:34:43.507" Title="Why does too much candy cause nausea?" Tags="&lt;biochemistry&gt;&lt;stomach&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27935" PostTypeId="1" AcceptedAnswerId="28221" CreationDate="2015-01-22T05:46:37.163" Score="4" ViewCount="1567" Body="&lt;p&gt;If a certain set of cells or tissue are undergoing a lot of reproduction and repair cycles for some reason, does this inevitably lead to cancerous growths? If the mutation rate exceeds the normal 'background' mutation rate for the tissue will these extra mutations eventually cause cancer?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As user Luke said below; does an increased rate of replication increase the rate of mutations.&lt;/p&gt;&#xA;" OwnerUserId="11605" LastEditorUserId="4109" LastEditDate="2015-01-31T10:45:53.407" LastActivityDate="2019-06-25T12:14:55.230" Title="Does increased cell turnover cause cancerous mutations?" Tags="&lt;cancer&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27936" PostTypeId="2" ParentId="27922" CreationDate="2015-01-22T06:01:05.097" Score="1" Body="&lt;p&gt;I can answer your question from the comments. In the second case, we have that one set of parents carry the following probabilities: $AA=1/2$, $Aa = 1/2$, and $AA = 1$. The second set of parents are the following: $AA = 1$, $Aa=2/3$, and $AA = 1/3$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the first set, we have the probability of $AA = \frac{1 + 1/2}{2} = \frac{3}{4}$. For the second set, we have $AA = \frac{1 + 1/3}{2} = \frac{2}{3}$. Now the probability of a child being $AA = \frac{3}{4}\frac{2}{3} = \frac{1}{2}$.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastActivityDate="2015-01-22T06:01:05.097" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="27937" PostTypeId="1" CreationDate="2015-01-22T07:45:12.213" Score="2" ViewCount="2113" Body="&lt;p&gt;Cnidaria, such as jelly fish and sea anemones are radial symmetric en feature a simple body plan. One notable aspect is the lack of a brain. Hence, there is no central guiding structure, no mind or will if you like. Nonetheless, they are known to be predatory (such as the sea anemones), and are quite effective in defending themselves as well (such as stinging jelly fish). &lt;strong&gt;How does a diffuse nervous system allow Cnidaria to feed and defend themselves?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sea anemone devouring a crab:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Rpwx9.jpg&quot; alt=&quot;Sea Anemone Devouring Crab&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="13152" LastEditorUserId="9943" LastEditDate="2015-01-23T00:04:26.117" LastActivityDate="2015-01-23T03:21:32.043" Title="How can a brainless Cnidarian hunt and defend itself?" Tags="&lt;marine-biology&gt;&lt;neurophysiology&gt;&lt;peripheral-nervous-system&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27938" PostTypeId="1" CreationDate="2015-01-22T10:34:00.317" Score="3" ViewCount="49" Body="&lt;p&gt;What has to duplicate before cell enters M phase?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;DNA&lt;/li&gt;&#xA;&lt;li&gt;histones&lt;/li&gt;&#xA;&lt;li&gt;centrosome&lt;/li&gt;&#xA;&lt;li&gt;mitochondria (any other organelles?)&lt;/li&gt;&#xA;&lt;li&gt;condensins (not sure?)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;have I forgotten anything?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance!&lt;/p&gt;&#xA;" OwnerUserId="6214" LastEditorUserId="6214" LastEditDate="2015-01-22T10:43:19.767" LastActivityDate="2015-01-22T10:43:19.767" Title="What has to duplicate before cell enters M phase?" Tags="&lt;cell-biology&gt;&lt;meiosis&gt;&lt;cell&gt;&lt;mitosis&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="2" ClosedDate="2015-04-02T00:23:20.820" ContentLicense="CC BY-SA 3.0" />
  <row Id="27939" PostTypeId="1" AcceptedAnswerId="27950" CreationDate="2015-01-22T11:49:43.480" Score="0" ViewCount="918" Body="&lt;p&gt;Water and carbon are lost through perspiration and breathing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much mass is lost in this way in a single day for a typical person?&lt;/p&gt;&#xA;" OwnerUserId="13156" LastActivityDate="2015-01-22T23:28:23.350" Title="How much mass does a person lose in a day through breathing and perspiration?" Tags="&lt;biochemistry&gt;&lt;breathing&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27940" PostTypeId="2" ParentId="27929" CreationDate="2015-01-22T11:56:13.727" Score="2" Body="&lt;p&gt;Cytosol is the fluid portion of cytoplasm.  All organelles are suspended in the cytosol but they do not form a part of cytosol. See &lt;a href=&quot;https://www.google.co.in/url?sa=t&amp;amp;source=web&amp;amp;rct=j&amp;amp;ei=dvvAVIneDaalmQWgmoCQCw&amp;amp;url=http://www.saylor.org/site/wp-content/uploads/2010/11/BIO101-Difference-Between-Cytosol-and-Cytoplasm.pdf&amp;amp;ved=0CCcQFjAC&amp;amp;usg=AFQjCNGoxSNppwoKdETuuQe1WNKc-Qx3ZQ&quot; rel=&quot;nofollow&quot;&gt;here for a detailed explanation&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Chris Stronks mentioned all cells have cytosol, but the red blood cells specifically do not have any organelles. The cytoplasm of RBC has only cytosol in which hemoglobin is suspended. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So even though all cells have cytosol, RBCs are a special case. That &lt;em&gt;may&lt;/em&gt; be the answer to your question. &lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-01-22T14:07:15.967" LastActivityDate="2015-01-22T14:07:15.967" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="27941" PostTypeId="2" ParentId="27937" CreationDate="2015-01-22T11:59:57.603" Score="6" Body="&lt;p&gt;Sea anemones are members of the phylum of &lt;em&gt;Cnidaria&lt;/em&gt;. Distinguishing features of this phylum are radial symmetry and the presence of &lt;em&gt;cnidocytes&lt;/em&gt;, or stinging cells (like the ones found in jelly fish). These cells have a mechanical trigger and if activated a subcellular harpoon is fired and paralyzing and painful toxin is injected. A cnidocyte diagram is shown below (from &lt;a href=&quot;http://en.wikipedia.org/wiki/Cnidocyte#mediaviewer/File:Nematocyst_discharge.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uDdLw.png&quot; alt=&quot;Cnidocyre&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Cnidarian nervous system is relatively simple indeed. The Cnidarian nervous system is decentralized and diffuse, and it basically consists of reflex arches. It is referred to as a &quot;nerve net&quot; as shown in the following schematic of a sea-anemone's nervous system (picture from &lt;a href=&quot;http://bioserv.fiu.edu/~walterm/GenBio2004/new_chap45_nervous/sp07_nervous_system.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Florida Int. University&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/70mX5.gif&quot; alt=&quot;Nerve net&quot;&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The presence of cnidocytes and a mesh nervous system basically answer your question: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) &lt;strong&gt;Feeding&lt;/strong&gt;: Whenever a prey touches the sting cells, it gets harpooned and paralyzed. The mechano-sensory cells sense touch, and drive nervous cells in the mesh. The nervous cells activate contractile epithelial cells in the arms of the anemone that push the prey inside the mouth. Then digestion takes place and the mouth serves as anus once digestion is complete.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) &lt;strong&gt;Defense&lt;/strong&gt;: the cnidocytes operate by mechanical triggering and no nerve cells are necessary. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-23T03:21:32.043" LastActivityDate="2015-01-23T03:21:32.043" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27942" PostTypeId="2" ParentId="27902" CreationDate="2015-01-22T12:52:29.217" Score="3" Body="&lt;p&gt;Metabolism in other small organisms, such as bacteria, are measured by taking the metabolism of a very large population of organisms, and then dividing that by the count of organisms in order to obtain the metabolic rate of a given individual. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://mic.sgmjournals.org/content/151/3/693.long&quot; rel=&quot;nofollow&quot;&gt;this paper on the metabolism of E. coli&lt;/a&gt;, they looked at the various input and output chemicals. Glucose, biomass, oxygen, and carbon dioxide were all observed. Observation of multiple variables also helps in the reduction of errors by using the stoichiometric balance to make sure that no errors have occurred in the measurements. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The methodology section of the paper had the following techniques:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Continuous cultivations were performed at 28 °C, at a stirring speed&#xA;  of 800 r.p.m., and the pH was controlled at pH 6·6 with 2·5 mol NaOH&#xA;  l−1. The 2-l bioreactor (model SGI 7F-Set2; Setric) was equipped with&#xA;  standard measuring and control units (temperature, pH, dissolved&#xA;  oxygen, stirrer speed). A constant aeration rate of 1·33 v.v.m. was&#xA;  achieved by a mass flow controller (Brooks). Continuous cultivation&#xA;  was performed for at least eight residence times at a given dilution&#xA;  rate; steady-state conditions were verified by constant optical&#xA;  density and oxygen and carbon dioxide transfer rates. Except for&#xA;  glucose, all other substrates were in excess. The concentration of&#xA;  dissolved oxygen was always maintained above 20 % of air saturation.&#xA;  Analytical techniques.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Culture liquid was withdrawn from the bioreactor into an ice-cooled&#xA;  beaker. Cell dry mass was determined gravimetrically after&#xA;  centrifugation of a known sample volume. The pellet was washed twice&#xA;  with 0·9 % w/v NaCl and dried at 40 °C under vacuum for 48 h.&#xA;  Elemental biomass composition was analysed with a PE 2400 II elemental&#xA;  analyser (Perkin Elmer). Glucose was measured enzymically by a YSI&#xA;  glucose analyser (model 2700; Yellow Springs Instrument Co.). Organic&#xA;  acids, i.e. acetic acid, formic acid, lactic acid and pyruvic acid,&#xA;  were analysed by HPLC using an HPX-87H Aminex ion-exclusion column&#xA;  (Bio-Rad). The column, connected to a UV detector (λ=210 nm) and RI&#xA;  detector, was eluted at 50 °C with 5 mmol H2SO4 l−1 at a flow rate of&#xA;  0·5 ml min−1.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If the tardigrades are grown in solution, an identical methodology can be used to measure respiration rate. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-01-22T12:52:29.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27943" PostTypeId="2" ParentId="27929" CreationDate="2015-01-22T15:55:48.253" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;A ribosome is where amino acids are linked together by peptide bonds.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;True.    &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A virus is NOT considered prokaryotic because it does not have a membrane.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Some have capsules or envelopes, the latter of which are composed of the host cell's membrane. A virus would not be considered a prokaryote because it is not strictly alive -- prokaryotes do not have membrane-bound organelles, but they still produce the cellular machinery necessary to process nutrients and create proteins &lt;em&gt;de novo&lt;/em&gt; without hijacking another cell. I would say &lt;strong&gt;False&lt;/strong&gt; on this one, because the presence of a membrane doesn't define either viruses or prokaryotes, ergo the lack of one wouldn't either.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The nucleotide ATP is one of the most used energy molecules of a cell.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;True. The other extremely common one is GTP, an ATP analogue.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sugar phosphates are the type of lipid moved through the blood.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;False. Sugars are phosphorylated to make sure they stay &lt;em&gt;inside&lt;/em&gt; the cell and don't enter the blood (first thing that happens to glucose and fructose is phosphorylation in energy metabolism). They are also &lt;em&gt;not&lt;/em&gt; lipids; they are not composed of long carbon chains of varying saturation. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A compound that lowers the pH is called an acid.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;True. Since pH is a measurement of the available H+ ions in solution and acids contribute available H+ ions to the solution, the more acidic the compound the lower the pH will be.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The cell wall is a carbohydrate covering of all cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Generally speaking, True -- of plant, some bacteria, and some archae cells. Eukaryotes do not have cell walls. The cell walls of plants are composed of a carbohydrate (sugar) polymer called cellulose (aka - dietary fiber).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The term cytosol is only applied to (blank) cells?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Prokaryotic -- for reasons listed by others.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An A-U base pair is part of the (blank) found in RNA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm a bit confused on this one. RNA is generally single-stranded, not double-stranded. It should not be base-pairing with itself unless specifically designed to. However, the Uracil is the RNA &lt;strong&gt;complement&lt;/strong&gt; (my best guess) to Adenosine and replaces Thymine found in regular DNA. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The major form of usable energy in animals is (what)?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Either ATP or sugars/carbohydrates. Sugars are eventually used to regenerate ATP, and fats are broken down into sugars or further down-stream metabolic components of sugars.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A polypeptide is a subunit of a what?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A protein. Proteins are composed of many polypeptide strands which usually come together to compose discrete formations (alpha-helices or beta-sheets) that then eventually form proteins.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2015-01-22T15:55:48.253" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="27944" PostTypeId="1" CreationDate="2015-01-22T15:55:59.303" Score="2" ViewCount="374" Body="&lt;p&gt;The protein I am purifying needed an elution buffer with 2% Triton X-100. I formulated the elution buffer not keeping the CMC in mind. My goal is to make my protein sample triton free to check its stability and quantify its concentration. Lately, I learnt that micelles can be broken down upon dilution. So, I've diluted my protein sample below triton's CMC and tried concentrating it using Sartorius Vivaspin 5K (PES resin). I loaded 500 ul of diluted sample and was left with 100 ul after concentration using vivaspin. But, this sample gave an abnormal reading of above 3 OD after blanking against the buffer it is in. I presume, triton's interference is causing these discrepant readings.&lt;/p&gt;&#xA;" OwnerUserId="8142" LastActivityDate="2015-01-22T15:55:59.303" Title="Can protein sample be made 2% Triton X-100 free?" Tags="&lt;proteins&gt;&lt;purification&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27946" PostTypeId="1" CreationDate="2015-01-22T19:28:26.547" Score="3" ViewCount="1316" Body="&lt;p&gt;Riboswitches are a rather elegant way to regulate gene expression without any additional machinery. A small ligand binds to the mRNA and directly influences transcription or translation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the known riboswitches are found in bacteria, there are few examples of riboswitches in eukaryotes. There are no classical riboswitches in humans as far as I know (there is one example, but triggered by a protein and not a metabolite), it seems that more complex organisms tend to use other methods of gene regulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any known reasons for this? What are the drawbacks of regulating gene expression with riboswitches compared to using regulatory proteins? Is there an explanation for the lack of riboswitches in more complex organisms?&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2017-08-17T22:29:55.707" Title="Why are riboswitches mostly present in bacteria and not in eukaryotes?" Tags="&lt;rna&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27947" PostTypeId="1" AcceptedAnswerId="27948" CreationDate="2015-01-22T20:22:04.807" Score="15" ViewCount="1498" Body="&lt;p&gt;This insect bumbled into my bedroom last night - can someone ID it for me? I'm mainly curious because I'd like to know if it poses any danger to my cats (who were very eager to add it to the menu).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3OrUc.png&quot; alt=&quot;cape town insect&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was about an inch and a half to two inches long, and when I picked it up to toss it outside it made a loud squeaking noise. I live just outside of Cape Town, South Africa (but I'm not a native, so I don't know all the species here). &lt;/p&gt;&#xA;" OwnerUserId="13163" LastActivityDate="2016-03-16T21:59:16.427" Title="Species ID: Cape Town mystery insect" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27948" PostTypeId="2" ParentId="27947" CreationDate="2015-01-22T21:11:23.560" Score="14" Body="&lt;p&gt;It appears to be a &lt;a href=&quot;http://en.wikipedia.org/wiki/Longhorn_beetle&quot; rel=&quot;nofollow noreferrer&quot;&gt;longhorn borer beetle&lt;/a&gt;. A more comparable picture is found &lt;a href=&quot;http://www.whatsthatbug.com/2013/03/20/bycid-from-south-africa/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;. Are there fig trees nearby?&#xA;&lt;img src=&quot;https://i.stack.imgur.com/TBmuR.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.google.com/search?q=beetles+in+south+africa&amp;amp;client=ubuntu&amp;amp;hs=gYl&amp;amp;channel=fs&amp;amp;source=lnms&amp;amp;tbm=isch&amp;amp;sa=X&amp;amp;ei=ombBVNCxBIqdNpbYgsAL&amp;amp;ved=0CAgQ_AUoAQ&amp;amp;biw=1366&amp;amp;bih=673#channel=fs&amp;amp;tbm=isch&amp;amp;q=longhorn+borer+beetle&amp;amp;imgdii=_&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; you will find numerous images of Longhorn beetles.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastActivityDate="2015-01-22T21:11:23.560" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27950" PostTypeId="2" ParentId="27939" CreationDate="2015-01-22T23:28:23.350" Score="2" Body="&lt;p&gt;The simplest route to your answer would be through the kcal consumed/expended equation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1kg (2.2lbs) of fat has ~7700 kcal of energy. The average person requires roughly 2000kcal per day if they perform mild physical labor throughout their day - 25.9% of the total energy available in 1kg of fat. So you could say that if a person did not eat for a day they would lose ~1/4kg or 1/2lb of fat-mass.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I calculated the above in &quot;fat&quot; because it's the number I knew off-hand, but truth be told the amount of &quot;mass&quot; you'd lose also depends on density. Fat (9kcal/g) is more energy dense than alcohol (7kcal/g), carbohydrates/sugars (4kcal/g), and protein (4kcal/g). For the same energy expenditure of 2000kcal in a single day you would metabolise more than 1/2kg or 1lb of either carbohydrates or proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In reality you will burn roughly equal amounts of fats and carbohydrates (assuming you're not forcing your body into a ketogenic state) at about a 55% fat/45% carbs ratio IIRC.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, with the assumption that the person isn't on a keto diet, has sufficient fat reserves, and expends 2000kcal of energy in a single day while drinking enough water to replace what is used in the energy metabolism, you will lose ~.14kg of fat and ~.63kg of carbohydrates for a grand total of &lt;strong&gt;&lt;em&gt;~.77kg (~1.69lbs)&lt;/em&gt;&lt;/strong&gt; of mass expended per day.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since humans vary greatly, however, that is going to vary wildly. Personally speaking, it's easy for me to expend &gt;3000kcal per day with an hour of moderate exercise since I'm simply &lt;em&gt;bigger&lt;/em&gt; than the average person and require more energy to do anything. If you're shorter than average, do less work than average (i.e. - are sedentary), or hormonal conditions (which are &lt;strong&gt;rare&lt;/strong&gt; and &lt;em&gt;cannot&lt;/em&gt; be self-diagnosed) modify calorie expenditure, your numbers will be different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also worth it to note: Ghrelin, a major hunger-regulating hormone, changes its tonic behavior significantly if you go more than 2 days consuming less than 1200kcal. After 2 days fasting it will instigate changes that will result in more fat &lt;em&gt;retained&lt;/em&gt; after you resume a regular eating schedule &lt;em&gt;for up to 5 years&lt;/em&gt;... So starving yourself for a week to lose 5kg seems great until you realize you'll gain 10kg once you go back to a normal diet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As always, if you're unsure of any diets please go to a qualified professional for consultation.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2015-01-22T23:28:23.350" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27952" PostTypeId="1" AcceptedAnswerId="27957" CreationDate="2015-01-23T02:48:16.017" Score="2" ViewCount="504" Body="&lt;p&gt;&lt;strong&gt;TLDR? Just read the bold bits!&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I started with Darwin's &lt;em&gt;Origin of Species&lt;/em&gt;, and then read Dawkins's first three books &lt;em&gt;The Selfish Gene&lt;/em&gt;, &lt;em&gt;The Extended Phenotype&lt;/em&gt;, and &lt;em&gt;The Blind watchmaker&lt;/em&gt; (I just started &lt;em&gt;River out of Eden&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dawkins talks of Gradualists and Punctuationalists as if their views are incompatible but my initial understanding of Darwin was that &lt;strong&gt;both of these are true&lt;/strong&gt;. My understanding is that if you look at an individual line of heredity then you will see a very &lt;strong&gt;consistent and gradual change&lt;/strong&gt; through the generations (at the mutation rate), but if you look at the population as a whole you will see &lt;strong&gt;&quot;periods of rapid evolution&quot;&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To me this seems easy to reconcile. Imagine &lt;strong&gt;a gene for fur thickness&lt;/strong&gt; in polar bears, if each n&lt;sup&gt;th&lt;/sup&gt; generation has a 'random' mutation for thicker or thinner then for each line of heredity &lt;strong&gt;you'll see a random walk about the starting point&lt;/strong&gt;. Most of them will go up a bit, then down a bit, and end up close to where they started, some will be a bit further away, and a small number will be far away (much thicker or thinner fur) &lt;strong&gt;in a Gaussian distribution&lt;/strong&gt;. So any random sample from the population that happens to become &lt;strong&gt;a fossil is most likely to be in the middle&lt;/strong&gt; (i.e. unchanged over many generations).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now if there's a &lt;strong&gt;sudden environmental change&lt;/strong&gt;, or a one-off freak event such as a very cold winter, say that only the 10% with the thickest fur survived this cold winter (and perhaps a very small number of others who got lucky). Now very quickly within a few generations, that &lt;strong&gt;thick fur gene will dominate&lt;/strong&gt; and as the population grows back to whatever size the environment can sustain it will be &lt;strong&gt;present in much greater absolute numbers than before the selection event&lt;/strong&gt;. When looking at random samples of the population throughout this period, you might conclude that there has been a &quot;period of rapid evolution&quot;. If the change is more gradual than a single sudden event, for example it gets colder over 500 years, each year the ones with the thinnest fur die off and the thicker fur genes get more popular in the population. &lt;strong&gt;This would appear to be a very rapid period of evolution, but really all the evolving happened gradually, long before the selection event&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question really is what's wrong with this view of things? Dawkins seemed to anticipate all my thoughts and objections while I read his books and provided explanations, except for this one. This kept nagging at me the whole time and he never mentions it at all. I can't imagine I'm the first person to think this way (especially since Darwin himself pretty much said this) so &lt;strong&gt;why doesn't Dawkins explain it&lt;/strong&gt; (either as correct or as incorrect with the reasons why)? &lt;strong&gt;Can someone please explain it to me either way?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="13166" LastEditorUserId="13166" LastEditDate="2015-01-23T03:44:31.653" LastActivityDate="2015-01-23T06:00:38.687" Title="Gradualism vs. Punctuationalism" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27957" PostTypeId="2" ParentId="27952" CreationDate="2015-01-23T06:00:38.687" Score="2" Body="&lt;p&gt;If I understand your question correctly, you are essentially distinguishing between the timescale on which the variation in the character of interest is generated, and the timescale on which selection prunes the population based upon that variation. The argument is then that &quot;all the evolving happened gradually, long before the selection event&quot; because that is when the variation was generated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To me, this seems to be a misuse of the term &quot;evolution&quot;, which is usually defined as a change in trait or allele frequencies in a population over time. Under that definition, much of the evolution does occur via the selection event. Before, you have a wide range of trait values; after, only a narrow selected set of trait values. In such a model, selection indeed is the major cause of allele frequency or trait value change. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practice, both processes are usually acting in concert; variation is being produced by mutation and recombination and eliminated by selection at comparable rates so that the net amount of variation in the population is at an approximate steady state. This is essentially the model Darwin espouses, though note that Darwin does not have our modern understanding of heredity and therefore is not able to explain how variation is generated or preserved. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additional note: When thinking about models of the kind that you describe, it is also key to understand that if you have a large number of loci affecting your trait (e.g. coat thickness), then the Gaussian distribution prior to strong selection will not include the extreme phenotypic values. If there are 20 diploid loci interacting additively to determine coat thickness and the mean individual has 20 thickness alleles and 20 thinness alleles, no individuals in a reasonably sized population will initially have all 40 thickness alleles, or even 39 or 38 etc. Selection for thickness will change the mean, and will also result in individuals outside of the initial range of variation. If the mean is 30, you may well get an individual with 38 or 39 or even all 40 thickness alleles. So once selection occurs, new more extreme phenotypes will suddenly appear. Nothing strange has happened in terms of rates of generating new variation; in fact this is just a consequence of reassorting the current alleles under the new allele frequencies. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-01-23T06:00:38.687" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="27959" PostTypeId="2" ParentId="27947" CreationDate="2015-01-23T09:21:50.243" Score="13" Body="&lt;p&gt;It is definitely a longhorn beetle (Cerambycidae), most probably from the subfamily &lt;a href=&quot;http://en.wikipedia.org/wiki/Lamiinae&quot; rel=&quot;nofollow&quot;&gt;Lamiinae&lt;/a&gt; (Flat-Faced Longhorns, &gt; 10000 species worldwide). I'm however mostly familiar with longhorn beetles from northern Europe, and there might be taxa that I'm unaware of. The overall morphology (e.g. downward facing head, robust build, spined pronotum) is however very suggestive of Lamiinae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The species suggested by @dustin also belongs to this subfamily and is probably correct, especially since it seems to be a common species where you find fig trees. &lt;a href=&quot;http://www.thegardeningblog.co.za/gardening/fig-tree-damage/&quot; rel=&quot;nofollow&quot;&gt;This blog&lt;/a&gt; and &lt;a href=&quot;http://www.biodiversityexplorer.org/beetles/cerambycidae/phryneta_spinator.htm&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Biodiversity Explorer - South Africa&lt;/em&gt;&lt;/a&gt; both label &lt;em&gt;Phryneta spinatorthem&lt;/em&gt; as a pest species in Cape town and have nice pictures that are very similar to yours (also pics of larvae and larval galleries).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sound you heard comes from &lt;a href=&quot;http://en.wikipedia.org/wiki/Stridulation&quot; rel=&quot;nofollow&quot;&gt;stridulation&lt;/a&gt; of the scutellum against the back edge of the pronotum (similar to the sounds emitted by grasshoppers), and it is common in many longhorn beetles (especially from Lamiinae). It is believed to be a defence mechanism (they stridulate a lot when handled), but might also serve other purposes. Large species of longhorn beetles can have a painful bite, but they are not poisonous (I have at least never heard of a poisonous longhorn beetle) and not dangerous to your cats.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="19521" LastEditDate="2016-03-16T21:59:16.427" LastActivityDate="2016-03-16T21:59:16.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27960" PostTypeId="1" CreationDate="2015-01-23T10:25:05.440" Score="1" ViewCount="83" Body="&lt;p&gt;I read about the molecular biology of cancer, and I have a mess on my head and a lot of questions.. .&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My primary question is-&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The damage of the cancer cells is in the dna sequence or in the gene expression(microRNAs)? or even something else?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks:)&lt;/p&gt;&#xA;" OwnerUserId="13171" LastActivityDate="2015-01-23T16:02:20.127" Title="The damage of cancer cells" Tags="&lt;dna&gt;&lt;microbiology&gt;&lt;cancer&gt;&lt;mutations&gt;&lt;dna-damage&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27961" PostTypeId="1" CreationDate="2015-01-23T11:13:12.833" Score="4" ViewCount="411" Body="&lt;p&gt;This bagworm was found in Singapore (near McRitchie Reservoir) some time in June 2012. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the plant from which the bagworms were obtained:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/WKj3O.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few examples of the bagworms:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/gIxQn.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/5RmHD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bagworm when dissected out of its bag:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/BwhUJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/VjuHw.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-01-23T11:27:27.710" Title="Identification of unknown bagworm (Singapore)" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27962" PostTypeId="2" ParentId="27961" CreationDate="2015-01-23T11:27:27.710" Score="1" Body="&lt;p&gt;Is the plant Banana (looks similar)? If so, the bagworm (Psychidae) &lt;em&gt;Kophene cuprea&lt;/em&gt; could be a possibility, since it is considered a pest on banana (&lt;a href=&quot;https://books.google.se/books?id=I4siBAAAQBAJ&amp;amp;pg=PA606#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Mosich &amp;amp; Larsen, 1978&lt;/a&gt;). The larval case is also supposed to be conical, but I cannot find an online picture for comparison.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2015-01-23T11:27:27.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27964" PostTypeId="1" CreationDate="2015-01-23T12:38:57.280" Score="4" ViewCount="306" Body="&lt;p&gt;I am able to grow mycelium successfully on the spent coffee grounds. And mycelium is successfully fruiting once/twice on the same substrate. I am cloning by taking mycelium from the existing one (which is fruiting at present) and transfer to the new jar and run it for 8-10 days and use it in new box for fruiting next generation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I am growing is 4th generation(I mean the transfer cycle).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I am Newbie, I have done some sort of research and started with a master spawns (got it from govt. mushroom labs). But I am not able to understand one thing is.&#xA;Is it ok to clone using mycelium or do I need to do spore cloning or need to go for master spawn spawns now and then or its ok to continue to nth generation and keep eating the fruits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any serious issues with my cloning?&lt;/p&gt;&#xA;" OwnerUserId="13113" LastEditorUserId="13113" LastEditDate="2015-01-23T12:55:50.840" LastActivityDate="2015-02-16T05:39:42.413" Title="How Many Generation We can Run a Mycelium of Pleurotus ostreatus/Pearl Oyster?" Tags="&lt;mycology&gt;&lt;cloning&gt;&lt;mushroom&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27966" PostTypeId="1" AcceptedAnswerId="27969" CreationDate="2015-01-23T14:15:36.450" Score="6" ViewCount="336" Body="&lt;p&gt;This is about products such as:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The &quot;&lt;a href=&quot;http://www.theradome.com/frequently-asked-questions/#i31&quot; rel=&quot;nofollow&quot;&gt;Theradome&lt;/a&gt;&quot; laser helmet (this claims to stimulate hair growth through lasers)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Theradome™, a biomedical engineering company based in the Silicon Valley, is the proud designer, developer and manufacturer of the Theradome™ LH80 PRO, the first and most powerful FDA cleared OTC wearable laser hair helmet for laser hair growth treatment. At last, millions of people suffering hair loss can enjoy clinically effective laser hair restoration treatments at home, at an affordable price, with a simple push of a button.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/B00HX27AM4&quot; rel=&quot;nofollow&quot;&gt;Silk'n Flash&amp;amp;Go Hair Removal Device&lt;/a&gt; (claims to remove hair using lasers)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Silk'n Flash&amp;amp;Go™ is a revolutionary light-based system for permanent results at home. Now you can remove unwanted hair forever on your body and face – all with gentle pulses of light that disable hair growth. It's the safe way to get smooth, beautiful skin.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From the information on the website, it would appear that the products are safe for all; however, both products seem to be &lt;strong&gt;not&lt;/strong&gt; recommended for the two darkest skin colors on the Fitzpatrick Skin Tone Classification Scale on a variety of different product feedback websites. What is the reasoning behind this?&lt;/p&gt;&#xA;" OwnerUserId="12939" LastEditorUserId="12909" LastEditDate="2015-01-23T18:40:35.930" LastActivityDate="2015-01-23T18:40:42.533" Title="Why are particular laser-related skin products not recommended for darker skin tones?" Tags="&lt;skin&gt;&lt;health&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27967" PostTypeId="2" ParentId="27960" CreationDate="2015-01-23T14:18:58.653" Score="4" Body="&lt;p&gt;Cancer is commonly defined as uninhibited cellular replication caused by mutations to the genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genes where cancer-causing mutations have been identified are known as &lt;strong&gt;oncogenes&lt;/strong&gt;; the COSMIC (Catalogue Of Somatic Mutations In Cancer) database lists all of the known oncogenes (547 to date - 23rd Jan 2015 - 1% of all human genes!) [&lt;a href=&quot;http://cancer.sanger.ac.uk/cancergenome/projects/census/&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;em&gt;effect&lt;/em&gt; of a particular mutation would be to alter in some way the expression of a gene or genes. This may be directly, for instance rendering a tumour-suppressing gene unable to fulfil its role [&lt;a href=&quot;http://www.nature.com/ncb/journal/v15/n1/full/ncb2641.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;], or indirectly, for instance by affecting epigenetic mechanisms that in turn affect expression of genes involved in cell cycle regulation [&lt;a href=&quot;http://www.nature.com/nrc/journal/v15/n2/abs/nrc3884.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;3&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To my knowledge cancer is not 'caused' by just a change in expression of a gene, although it may be mediated by it. The change in expression or effectiveness of a gene (such as tumour suppressor p53) resulting in uncontrolled cell division is &lt;em&gt;caused&lt;/em&gt; by mutations at the genomic level. &lt;/p&gt;&#xA;&#xA;&lt;h3&gt;What causes the mutations?&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Lots of factors can cause mutations, from chemicals (e.g. from cigarette smoke, not just restricted to the lungs either [&lt;a href=&quot;http://www.cancerresearchuk.org/cancer-info/healthyliving/smoking-and-cancer/smoking-and-cancer&quot; rel=&quot;nofollow noreferrer&quot;&gt;4&lt;/a&gt;]) to mistakes in the DNA replication machinery as somatic cells undergo normal cell division [&lt;a href=&quot;http://www.sciencemag.org/content/347/6217/78.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;5&lt;/a&gt;]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The last reference there provides very compelling evidence for the reason that some tissues are more predisposed to cancer than others; tissues with higher cell turnover (and thus require more cell division) have higher incidences of cancer - see the below figure from [&lt;a href=&quot;http://www.sciencemag.org/content/347/6217/78.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;5&lt;/a&gt;]! This figure separates &quot;lung cancer&quot; into two groups to show that even non-smokers have risk of developing lung cancer, but not as high a risk as those who smoke.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kFUaM.png&quot; alt=&quot;Figure 1 from reference 5, showing the relationship between cell turnover and cancer incidence&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://cancer.sanger.ac.uk/cancergenome/projects/census/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://cancer.sanger.ac.uk/cancergenome/projects/census/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Muller, P.A.J.; Vousden, K.H. (2013) &lt;a href=&quot;http://www.nature.com/ncb/journal/v15/n1/full/ncb2641.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;p53 mutations in cancer&lt;/strong&gt;&lt;/a&gt;. &lt;em&gt;Nat Cell Biol&lt;/em&gt;. 15:2-8&lt;/li&gt;&#xA;&lt;li&gt;Hamamoto, R.; Saloura, V.; Nakamura, Y. (2015) &lt;a href=&quot;http://www.nature.com/nrc/journal/v15/n2/abs/nrc3884.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Critical roles of non-histone protein lysine methylation in human tumorigenesis&lt;/strong&gt;&lt;/a&gt;. &lt;em&gt;Nat Rev Cancer&lt;/em&gt;. 15:110-124&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cancerresearchuk.org/cancer-info/healthyliving/smoking-and-cancer/smoking-and-cancer&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cancer research UK report on smoking and cancer&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Tomasetti, C. &amp;amp; Vogelstein, B. (2015) &lt;a href=&quot;http://www.sciencemag.org/content/347/6217/78.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Variation in cancer risk among tissues can be explained by the number of stem cell divisions&lt;/strong&gt;&lt;/a&gt;. &lt;em&gt;Science&lt;/em&gt; &lt;strong&gt;347&lt;/strong&gt;, 78-81&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2015-01-23T16:02:20.127" LastActivityDate="2015-01-23T16:02:20.127" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="27968" PostTypeId="2" ParentId="27923" CreationDate="2015-01-23T14:49:18.323" Score="2" Body="&lt;h2&gt;Height&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;This is just a single example, but &quot;height&quot; has received a lot of GWAS (genome-wide association study) attention, and last year the GIANT consortium published results of an analysis on 250,000 people looking at the genetic influences of height [&lt;a href=&quot;http://www.nature.com/ng/journal/v46/n11/full/ng.3097.html&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using just 2,000 genetic variants they could statistically account for 20% of the phenotypic variation in height. Using 9,500 genetic variants this rose to 29%.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What this emphasises is that common traits (such as height) are highly polygenic; there is no &quot;height gene&quot; that controls it - instead it is the combination of many small-effect variants that cumulatively give rise to an individuals final phenotype (height, in this case).&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Pigmentation&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Pigmentation (of eyes, skin and hair) on the other hand is not nearly as polygenic. A 2013 review [&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1084952113000499&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;] discussed the known genetic variation for these traits. Prediction of eye colour using genetics, for instance, requires only six genetic variants &quot;to be suitable to predict blue, intermediate, and brown colors with an overall accuracy of 0.91, 0.72, and 0.93, respectively&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in contrast to height where even with 9,500 variants measured you would still only have 29% accuracy, you can be 91% sure that someone will have blue eyes if you know the individuals genotype at only 6 positions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in short the quote you reference is incorrect - we can predict many common traits with reasonable accuracy - although for some phenotypes the individual predictive capability of a specific genotype may be around 0.01% (e.g. some of the height variants).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Wood, A. R. et al. (2014) &lt;a href=&quot;http://www.nature.com/ng/journal/v46/n11/full/ng.3097.html&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Defining the role of common variation in the genomic and biological architecture of adult human height&lt;/strong&gt;&lt;/a&gt;. &lt;em&gt;Nat Genet&lt;/em&gt; &lt;strong&gt;46&lt;/strong&gt;, 1173-1186, doi:10.1038/ng.3097&lt;/li&gt;&#xA;&lt;li&gt;Liu, F., Wen, B. &amp;amp; Kayser, M. (2013) &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1084952113000499&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Colorful DNA polymorphisms in humans&lt;/strong&gt;&lt;/a&gt;. &lt;em&gt;Seminars in Cell &amp;amp; Developmental Biology&lt;/em&gt; &lt;strong&gt;24&lt;/strong&gt;, 562-575&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastActivityDate="2015-01-23T14:49:18.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27969" PostTypeId="2" ParentId="27966" CreationDate="2015-01-23T16:59:56.757" Score="5" Body="&lt;p&gt;The reason for laser hair removal/growth products not being safe for darker skin tones is the ability for darker skin tones to absorb more light from the laser than lighter skin does BEFORE the light is able to reach the depth at which the hair follicle is located. Light from lasers must pass through the epidermis where melanocytes are located before they reach the hair follicle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uSEe1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More melanin means increased ability to absorb wavelengths as seen in the curve below. Laser products such as Theradome (678nm) and Silk'N (475-1200 nm) have shorter wavelengths, which are highly absorbed by melanin, and therefore can damage skin in darker skin tone patients. Safer products like Nd:YAG are those that have higher wavelengths at 1064nm and can penetrate the skin without over-absorption by melanin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NUwMP.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disclosures: I own no stock in any of these companies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.theradome.com/press-release/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.theradome.com/press-release/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/B0093BOR4W&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.amazon.com/Silkn-Flash-Removal-Device-Cartridge/dp/B0093BOR4W&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/jid/journal/v122/n2/full/5602198a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.nature.com/jid/journal/v122/n2/full/5602198a.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11631" LastActivityDate="2015-01-23T16:59:56.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27970" PostTypeId="1" AcceptedAnswerId="27974" CreationDate="2015-01-23T17:26:00.227" Score="2" ViewCount="392" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cwi1x.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The photo above shows the effects of the R allele of the pea shape gene on the synthesis of an enzyme that converts unbranched starch into branched starch. The r allele of this gene determines an inactive form of the enzyme, leading to a buildup of linear, unbranched starch that ultimately causes seed wrinkling. My question is, &lt;strong&gt;How does the r allele &lt;em&gt;specifically&lt;/em&gt; prohibit the activity of the enzyme?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Does the DNA/Gene sequence simply code for proteins that create an enzyme which cannot bind to its respective substrate ?&lt;/li&gt;&#xA;&lt;li&gt;Is the substrate in the above illustration the unbranched starch itself ?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8059" LastActivityDate="2015-01-23T19:02:21.173" Title="Mode of Enzymatic Inhibition via R-Allele" Tags="&lt;molecular-genetics&gt;&lt;enzymes&gt;&lt;allele&gt;&lt;enzyme-kinetics&gt;&lt;gene&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27971" PostTypeId="1" AcceptedAnswerId="27972" CreationDate="2015-01-23T18:05:58.957" Score="1" ViewCount="886" Body="&lt;p&gt;Why do humans have eyebrows? It seems that it isn't necessary but only humans have them, correct? So what is the use of them for humans? I hear that they protect our eyes. However, isn't that what eyelashes do? What other functions do eyelashes have?&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="12909" LastEditDate="2015-01-23T18:44:52.317" LastActivityDate="2015-01-23T18:44:52.317" Title="Why do humans have eyebrows?" Tags="&lt;evolution&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ClosedDate="2015-01-24T07:01:44.790" ContentLicense="CC BY-SA 3.0" />
  <row Id="27972" PostTypeId="2" ParentId="27971" CreationDate="2015-01-23T18:29:19.607" Score="1" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;Eyebrows function to protect the eyes from perspiration and provide shade.&lt;/p&gt;&#xA;&lt;p&gt;Eyelids function to protect the eyes from foreign objects and sunlight.&lt;/p&gt;&#xA;&lt;p&gt;Eyelashes function to protect the eyes from foreign objects, produce sebum (a lubriant that the eyelids) and acts as protection for the eyes from tears &lt;a href=&quot;http://www.emergencymedicalparamedic.com/what-is-the-function-of-eyebrows-eyelids-and-eyelashes/&quot; rel=&quot;nofollow noreferrer&quot;&gt;[1]&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The above seems to be backed up by &lt;a href=&quot;http://health.howstuffworks.com/human-body/systems/eye/question520.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;health how stuff works&lt;/a&gt; and &lt;a href=&quot;http://www.emedicinehealth.com/anatomy_of_the_eye/page3_em.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;the anatomy of the eye&lt;/a&gt; from emedicinehealth.&lt;/p&gt;&#xA;&lt;p&gt;However, note that biologist dont have any concrete reasons for the eyebrow. This is just what many of them agree on I suppose. Here is another resource from &lt;a href=&quot;http://www.sciencefocus.com/qa/why-do-we-have-eyebrows&quot; rel=&quot;nofollow noreferrer&quot;&gt;sciencefocus&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-01-23T18:29:19.607" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27974" PostTypeId="2" ParentId="27970" CreationDate="2015-01-23T18:56:28.957" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8329688&quot; rel=&quot;nofollow&quot;&gt;Bhattacharyya M, Martin C, Smith A. 1993. The importance of starch biosynthesis in the wrinkled seed shape character of peas studied by Mendel. Plant Mol Bio 22(3):525-531&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The wrinkled-seed mutant (rr) of pea (Pisum sativum L.) arose through mutation of the gene encoding starch-branching enzyme isoform I (SBE1) by insertion of a transposon-like element into the coding sequence. Two isoforms of starch-branching enzyme have been documented in the developing pea embryo. The second isoform, SBEII, is expressed towards the later stages of embryo development while SBEI is expressed highly in the early stages. Due to mutation of SBEI the total amount of starch and the proportion of amylopectin, a branched starch polymer, are greatly reduced in the wrinkled (rr) line as compared to that in the wild-type, round (RR) line. Consequently, the level of sucrose in the rr line is nearly two fold that of the RR line. Increased sucrose concentration in the developing embryos of this mutant line causes increased uptake of water and thereby increases the cell size and fresh weight. During seed maturation in these mutant seeds a greater loss of water occurs. As a result, the wrinkled seed phenotype develops. Besides this morphological variation, the mutation also causes changes in the amount of lipid and of one storage protein, legumin. This review article discusses the role of the SBEI enzyme in causing such metabolic changes in the developing embryos with the implication that metabolism can play a central role in plant development.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These authors claim that the mutant protein is not present in peas, so the wrinkled phenotype is not due to an inability of the protein to bind its substrate (amylose and amylopectin - the linear and branched components of starch, respectively) but rather its complete absence. The mutant is due to an 800 bp transposon insertion into the coding sequence of SBE1. If it was expressed, it would be reasonable to expect that it wouldn't be able to bind its substrate. The authors also discuss mutations at other loci that have been shown to be responsible for the wrinkled phenotype, but it is believed that these are relatively newer and would not have been observed by Mendel. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-01-23T19:02:21.173" LastActivityDate="2015-01-23T19:02:21.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27975" PostTypeId="1" CreationDate="2015-01-23T19:02:19.630" Score="3" ViewCount="302" Body="&lt;p&gt;What is the time taken to form a peptide bond &lt;em&gt;in vivo&lt;/em&gt; or &lt;em&gt;in vitro&lt;/em&gt;? It isn't mentioned in my course on protein structures. I was just curious to find out  if any  time scale is known?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that prokaryotic and eukaryotic cells have difference ribosome structures, is there any chance that the time might vary between species or even within species? &lt;/p&gt;&#xA;" OwnerUserId="9767" LastEditorUserId="3553" LastEditDate="2015-01-25T19:13:42.540" LastActivityDate="2015-01-27T14:53:37.993" Title="How long does it take to form a peptide bond?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27976" PostTypeId="1" CreationDate="2015-01-23T19:42:28.663" Score="2" ViewCount="118" Body="&lt;p&gt;Aloha, I live in Hawaii working with sharks and their sensitivity to magnetism but here we also have large cockroaches. Has anyone worked with cockroaches and magnetism?  I wonder if placing high magnetic fields near food and anywhere else, would repel cockroaches. Mahalo and aloha.&lt;/p&gt;&#xA;" OwnerDisplayName="user13084" LastActivityDate="2015-01-23T19:42:28.663" Title="Cockroaches and magnetic fields" Tags="&lt;entomology&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27977" PostTypeId="2" ParentId="14458" CreationDate="2015-01-23T23:28:13.313" Score="0" Body="&lt;p&gt;It is a question of transmembrane potential. Ca++ being a cation, means that if you decrease the amount of ionized calcium in the extra cellular fluid, it conceptually is nearly equivalent to having a more positively charged intracellular fluid. This in turn means that the cell will be closer to its threshold potential for depolarization, therefore accounting for its hyper excitability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you should keep in mind, is that when we say something as: &quot;this cell has a transmembrane potential of -70 mV&quot;, we always define it &lt;strong&gt;relatively to the extra cellular fluid.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;edit: I am leaving this incorrect answer because of the interesting comments below.&lt;/h1&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2017-06-19T01:20:12.657" LastActivityDate="2017-06-19T01:20:12.657" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="27980" PostTypeId="1" AcceptedAnswerId="27986" CreationDate="2015-01-24T01:57:57.193" Score="3" ViewCount="2296" Body="&lt;p&gt;There are many programmed cell death pathways, but some cells show a greater preference for some over the other. I'm wondering as to why if necrosis is an inflammatory response that causes damage to neighboring cells, why some cells would prefer this as opposed to a more controlled mechanism such as apoptosis or even autophagy. &lt;/p&gt;&#xA;" OwnerUserId="12891" LastActivityDate="2015-01-25T11:44:30.430" Title="why do some cells in the body prefer necrosis to apoptosis as a means of cell death?" Tags="&lt;cell-biology&gt;&lt;apoptosis&gt;&lt;autophagy&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27981" PostTypeId="1" CreationDate="2015-01-24T02:33:41.373" Score="1" ViewCount="43" Body="&lt;p&gt;I know that ammonia is toxic for the body since it disturbs enzymes of mitochondria. &#xA;I want to know that why the ammonotelic animals don't get affected by it?&#xA;I mean that even if there is plenty of water to remove ammonia from their body, does ammonia not cause any damage till it's inside body? &#xA;Does toxicity depends on concentration level?&#xA;Can anyone tell me its evolutionary significance? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry for the previous question. .&#xA;Actually it was a easy one and I got the answer.&#xA;Sorry for the unclarity.;)&lt;/p&gt;&#xA;" OwnerUserId="11647" LastEditorUserId="11647" LastEditDate="2015-01-30T06:56:35.897" LastActivityDate="2015-01-30T06:56:35.897" Title="Relation between a compound's toxicity and it's concentration level" Tags="&lt;evolution&gt;&lt;osmoregulation&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27982" PostTypeId="1" CreationDate="2015-01-24T04:57:02.707" Score="1" ViewCount="20" Body="&lt;p&gt;I'm not sure if this is best in Biology or Physics, but on Earth we decay to skeletons and then eventually to dust.  What would happen in space in a space suit?&lt;/p&gt;&#xA;" OwnerUserId="13181" LastActivityDate="2015-01-24T04:57:02.707" Title="What would happen to a body in an astronaut suit over time if floating free?" Tags="&lt;biochemistry&gt;&lt;decay&gt;" AnswerCount="0" CommentCount="6" ClosedDate="2015-01-24T11:32:45.257" ContentLicense="CC BY-SA 3.0" />
  <row Id="27983" PostTypeId="2" ParentId="27980" CreationDate="2015-01-24T06:37:33.797" Score="2" Body="&lt;p&gt;Necrosis can be described as accidental cell death or damage, triggered possibly from external environmental factors such as exposure to radiation, toxins, excessive heat and etc...whereas, Apoptosis is a programmed form of a cell death mechanism. This process may be used to recycle unwanted cells in the body. Therefore, the particular stimulus that the cell receives may be a key determinant of the cell death mechanism observed. &lt;/p&gt;&#xA;" OwnerUserId="12876" LastActivityDate="2015-01-24T06:37:33.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27986" PostTypeId="2" ParentId="27980" CreationDate="2015-01-24T11:01:14.937" Score="6" Body="&lt;p&gt;There is actually no preference for apoptosis or necrosis in cells of the human body - both types can occur in all cells and they have different triggers. The main differences can be seen in this figure (from &lt;a href=&quot;https://en.wikipedia.org/wiki/Necrosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dTHb4.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apoptosis (also called programmed cell death) has three different triggers (intrinsic, extrinsic and Perforin/Granzyme pathways), see the image below for details (from reference 1):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hF4G8.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All three activate different components and caspases in the beginning but finally all activate Caspase 3, which finally activates endonucleases (which degrade the chromosomal DNA), Proteases (which degrade the proteins in the nucleus and the cytoskeleton) which leads to the degradation of the cell. In the end apoptotic bodies are formed from the cell. Additionally the mitochondria break down and release cytochrome c and ATP. Their release from the cell attracts macrophages which take up and eliminate the apoptotic bodies and in turn release cytokines which suppress an inflammatory response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apoptosis goes on in a ordered way and does not trigger any further reactions in neighbouring cells (except these receive the same signal). See also reference 1 and 2 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Necrosis is triggered by external stimuli of the cell as injury of tissues or toxins from infections. Necrotic cells swell, while there internal structures are in a state of unregulated degradation. Finally the membrane will burst and set free cytochrome c and phosphatidylserines from the membranes which cause inflammation in the affected tissue. The necrotic cells are not removed by macrophages which allows the released interior of the cell to spread further and cause problems.  See reference 2 and 3 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Necrosis is usually not as a beneficial process, but there are also publications which see &#xA;the process as a specific form of cell death (see reference 4).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://tpx.sagepub.com/content/35/4/495.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Apoptosis: A Review of Programmed Cell Death&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.diffen.com/difference/Apoptosis_vs_Necrosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Apoptosis vs. Necrosis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.crch.org/PDF/jc/Elise2_12-05-08.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cell death by necrosis: towards a molecular definition&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.bioparadigma.spb.ru/files/Proskuryakov-2003-Necrosis.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Review Necrosis: a specific form of programmed cell death?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-01-24T11:01:14.937" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27988" PostTypeId="1" CreationDate="2015-01-24T12:24:35.047" Score="4" ViewCount="1834" Body="&lt;p&gt;&lt;em&gt;Pseudomonas aeruginosa&lt;/em&gt; is the fifth most written about¹ binomial name of all species. I'm having trouble coming to terms with the possibility that such a well researched and studied organism has never been given a shorter vernacular name. I can't find one listed anywhere. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any short common name for it? Even a colloquial one? Maybe a pet name common to microbiologists or students in the labs of some particular region? I'm mostly interested in English but how about in other languages?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am aware it can be abbreviated to &lt;em&gt;P. aeruginosa.&lt;/em&gt; I don't consider that a common name. &lt;em&gt;Pseudomonas&lt;/em&gt; by itself refers to a genus of around 191 species.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;¹ &lt;em&gt;&quot;most written about&quot; meaning mentioned in the most books or volumes of Google Books' English corpus (ngram data), according to my own research. The top five are: Homo sapiens, Escherichia coli, Staphylococcus aureus, Candida albicans, Pseudomonas aeruginosa.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8564" LastEditorUserId="8564" LastEditDate="2015-01-25T01:12:20.810" LastActivityDate="2015-05-28T08:21:10.793" Title="Does Pseudomonas aeruginosa have any common name at all?" Tags="&lt;bacteriology&gt;&lt;taxonomy&gt;" AnswerCount="1" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="27989" PostTypeId="1" AcceptedAnswerId="27990" CreationDate="2015-01-24T13:24:11.267" Score="18" ViewCount="27508" Body="&lt;p&gt;I found this picture online claiming it was a grass cell. Clearly it is a cross section image but I was hoping you could tell me if this is actually grass, or something else if anything.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/7949z.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/7949z.jpg&quot; alt=&quot;grass cross section&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9482" LastEditorUserId="5403" LastEditDate="2019-02-19T00:00:14.060" LastActivityDate="2019-02-19T00:00:14.060" Title="Is this a grass cell?" Tags="&lt;species-identification&gt;&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="27990" PostTypeId="2" ParentId="27989" CreationDate="2015-01-24T14:08:29.690" Score="19" Body="&lt;p&gt;It's not a single grass &lt;em&gt;cell&lt;/em&gt;, but this does indeed appear to be a micrograph of a &lt;em&gt;leaf&lt;/em&gt; of grass&amp;mdash;so it actually contains numerous cells. Here's another image I was able to find with a much more clear description of exactly what you're seeing:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/T85Fe.png&quot; alt=&quot;http://www.sciencephoto.com/media/30161/view&quot;&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Marram grass leaf. Light micrograph of a cross section through a closed (unravelled) leaf of Marram grass, Ammophila arenaria. The deeply grooved leaf is thrown into folds (seen here) and it uncurls when mature so that the folds do not face the centre. The folds conserve water and withstand salt, and prevent excessive evaporation. &lt;strong&gt;Round vascular bundles are visible inside each fold, serving to transport food and water through the leaf&lt;/strong&gt;. Spines on the surface discourage animals from eating the leaf. Marram grass is important in coastal ecology, since it is one of the commonest grass species in Britain to stabilize sand dunes. Magnification: x22 at 35mm size. (Emphasis added)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;sup&gt;Source: &lt;a href=&quot;http://www.sciencephoto.com/media/30161/view&quot; rel=&quot;noreferrer&quot;&gt;http://www.sciencephoto.com/media/30161/view&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And here's another:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WTwgR.png&quot; alt=&quot;http://www.eplantscience.com/index/principles_of_horticulture/minerals.php&quot;&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Transverse section of Marram Grass leaf , showing adaptations to prevent water loss; outer thick cuticle, curling by means of hinge cells to protect inner epidermis, stomata&#xA;  sunken into surface to maintain high humidity&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;sup&gt;Source: &lt;a href=&quot;http://www.eplantscience.com/index/principles_of_horticulture/minerals.php&quot; rel=&quot;noreferrer&quot;&gt;http://www.eplantscience.com/index/principles_of_horticulture/minerals.php&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The coloration yielding the yellow 'happy faces' is artificial, either due to staining or direct post-processing of the image.&lt;/p&gt;&#xA;" OwnerUserId="6703" LastEditorUserId="6703" LastEditDate="2015-01-24T14:16:19.730" LastActivityDate="2015-01-24T14:16:19.730" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27991" PostTypeId="1" CreationDate="2015-01-24T15:29:36.273" Score="3" ViewCount="285" Body="&lt;p&gt;In many papers one can read that telomeres may play an important role in longevity. According to Calado et al.&lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23956466&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;&lt;/sup&gt; the telomeres of mice are much longer than the telomeres of humans. However, mice have an average life expectancy of about 2 years and humans about 80 years. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the metabolic rate therefore determine how fast the telomeres shorten? Can one say that the higher the metabolic rate, the faster the telomere shorten?&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23956466&quot; rel=&quot;nofollow&quot;&gt;Telomere dynamics in mice and humans&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="13179" LastEditorUserId="13179" LastEditDate="2015-01-24T18:50:32.897" LastActivityDate="2015-01-24T18:50:32.897" Title="Does the metabolic rate determine how fast the telomeres shorten?" Tags="&lt;metabolism&gt;&lt;telomere&gt;&lt;lifespan&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27992" PostTypeId="1" CreationDate="2015-01-24T15:44:38.900" Score="3" ViewCount="2107" Body="&lt;p&gt;Going back the genealogical lineage from present humans to the beginning of life, what was the biggest - in terms of body size or mass - animal in this sequence?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More generally, what would a time vs. size graph look like? Obviously the first ones were tiny microbes, but do we have &quot;deep valleys&quot; and high peaks one after the other? I know that our ancestors at the time of the dinosaurs were very small rodents. Were there some even smaller ones earlier (not referring to the microbes)?&lt;/p&gt;&#xA;" OwnerUserId="6316" LastEditorUserId="19650" LastEditDate="2015-12-22T12:01:30.853" LastActivityDate="2015-12-23T08:28:50.703" Title="Largest direct ancestor of humans" Tags="&lt;evolution&gt;&lt;human-evolution&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27993" PostTypeId="1" CreationDate="2015-01-24T17:20:26.147" Score="12" ViewCount="8944" Body="&lt;p&gt;What are the differences between cancer and tumour? I mean is it in the DNA or shape or something else... And how can a benign tumour turn into a malignant tumour? The body has a lot of tumours all the time, however not all of them become cancerous, why is this so?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my main question is: What is so special about cancer cells that they can get out of control unlike an ordinary benign tumour?&lt;/p&gt;&#xA;" OwnerUserId="13171" LastEditorUserId="11631" LastEditDate="2015-01-25T05:06:54.450" LastActivityDate="2015-08-08T08:31:44.170" Title="What are the differences between cancer and tumour?" Tags="&lt;cell-biology&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="27994" PostTypeId="2" ParentId="27993" CreationDate="2015-01-24T17:33:40.747" Score="19" Body="&lt;p&gt;A &lt;strong&gt;tumour&lt;/strong&gt; is simply a space-occupying lesion (something that should not be there, that is; a &quot;lump&quot;) caused by abnormal cell replication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(In medicine, the word &quot;tumour&quot; literally means &quot;swelling&quot;, and can sometimes refer to that instead, but that's a different story).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cancer&lt;/strong&gt; is a disease in which cell replication is &lt;em&gt;totally out of control&lt;/em&gt;. What causes cancer is damage to the genes (DNA) which normally &lt;em&gt;stop&lt;/em&gt; cell replication when it needs to be stopped.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's no such thing as an &quot;ordinary tumour&quot;; all tumours are abnormal. However, what makes a &lt;em&gt;benign&lt;/em&gt; (harmless) tumour different from a &lt;em&gt;cancerous&lt;/em&gt; tumour is that there is still some mechanisms stopping the cells inside the tumour from replicating; they are doing it more than they should, but they are not &lt;em&gt;totally&lt;/em&gt; out of control. When those last mechanisms are broken too, the tumour is cancerous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(This is a simplified explanation; the actual explanation is a semester-long university course. It's mostly accurate for the layman, though)&lt;/p&gt;&#xA;" OwnerUserId="13187" LastEditorUserId="13187" LastEditDate="2015-01-25T08:05:50.257" LastActivityDate="2015-01-25T08:05:50.257" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="27995" PostTypeId="2" ParentId="24698" CreationDate="2015-01-24T17:45:06.860" Score="0" Body="&lt;p&gt;anongoodnurse's answer is very thorough, but I would like to add one additional thing:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nausea is in many ways the body's &quot;default reaction&quot; to anything being out of order with the body's chemistry; since most such things would once have been caused, the vast majority of the time of the time, by eating something toxic (or at least biologically active, and therefore probably toxic in large doses), which means that regurgitating stomach contents had a decent chance to expel the toxin and therefore save the person's life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the effects of the medication are fairly light compared to toxic doses, the body rarely goes as far as actually throwing up (although people on prophylactic antiretrovirals, as one example, may disagree); the stimulus to do so is weak, so we feel only weak to moderate nausea rather than nausea strong enough to throw up.&lt;/p&gt;&#xA;" OwnerUserId="13187" LastActivityDate="2015-01-24T17:45:06.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27996" PostTypeId="1" AcceptedAnswerId="28003" CreationDate="2015-01-24T19:38:02.703" Score="5" ViewCount="351" Body="&lt;p&gt;Can methylation of a promoter induce gene expression in some rare cases? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've read somewhere that methylation of an intron can induce gene expression (eg. Igf2). How is that even possible? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance!&lt;/p&gt;&#xA;" OwnerUserId="6214" LastEditorUserId="5144" LastEditDate="2015-01-24T19:44:57.847" LastActivityDate="2015-01-26T02:10:09.667" Title="Can methylation of a promoter induce gene expression in some rare cases?" Tags="&lt;cell-biology&gt;&lt;gene-expression&gt;&lt;gene&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="27997" PostTypeId="1" CreationDate="2015-01-24T19:53:04.377" Score="3" ViewCount="49" Body="&lt;p&gt;According to the book &quot;Primer of The Molecular Biology of Cancer&quot; by Vincent, Theodore and Ateven, the tumour cell is &lt;strong&gt;changed depending on its environment.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;performed genome-wide analysis on three tumor samples: a patient's primary breast tumor; her metastatic brain tumor, which formed despite therapy; and a xenograft tumor in a mouse, originating from the patient's breast tumor. They find that the primary tumor &lt;strong&gt;differs&lt;/strong&gt; from the metastatic and xenograft tumors mainly in the prevalence of genomic mutations&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why the tumour cell changing on different places?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;why suddenly the breast tumour cells changes on the xenograft tumour and why the metastasis on the brain are now different from the place they came from?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How does this alteration obtained? in the DNA or microRNA or something else?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="13171" LastEditorUserId="948" LastEditDate="2015-01-24T23:32:54.123" LastActivityDate="2015-01-24T23:32:54.123" Title="Why does a tumour's genome change depending on the environment?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;gene-expression&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="27999" PostTypeId="1" CreationDate="2015-01-24T21:41:13.757" Score="9" ViewCount="1961" Body="&lt;p&gt;As far as I am aware, the saccades of the eye are central to visual perception. If the eye is held still, the human stops seeing, even if light is reaching the retina and the visual pathway is intact. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But we recently had a question on UX.stackexchange about possible improvements to a visual+EEG interface used for communication with locked-in patients. The designer asking it mentioned that eye tracking devices are unlikely to work, because the patients' eyes can't move. This surprised me, as I would have thought that the patients must be able to move their eyes if they are able to read the device's screen. But I have never had contact with a locked-in person, and assume that the asker knew more about them than I do. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, are there situations in which a human's eye muscles are paralyzed, so the eyeballs cannot be moved in their orbits, but this human still has visual perception and can mentally process information in his/her field of view?&lt;/p&gt;&#xA;" OwnerUserId="9471" LastEditorUserId="9943" LastEditDate="2015-05-25T12:40:59.820" LastActivityDate="2015-05-26T03:47:32.953" Title="Can people with paralyzed eye muscles see?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;pathology&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28001" PostTypeId="2" ParentId="27999" CreationDate="2015-01-24T22:09:18.853" Score="8" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Visual perception persists in the absence of functional eye movement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;An example case would be retinal implants wearers. Retinal implants like the Argus II consist of a set of electrodes placed onto the degenerate retina of blind folks. Electrical stimulation of the electrode array elicits flashes of light (&lt;em&gt;phosphenes&lt;/em&gt;). Visual input is provided via a head-mounted camera, and the device translates the camera images into patterned electrode stimuli. Hence, because the camera is head worn, Argus II wearers cannot use eye movements to scan the world. They have to use head-scanning techniques. &lt;strong&gt;Still they are able to perceive flashes of light (phosphenes) and can recognize simple shapes and perceive motion&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In fact, eye movements such as saccades are &lt;em&gt;detrimental&lt;/em&gt; in Argus II wearers&lt;/strong&gt;, because the oculomotor system feedbacks muscle movements to the brain when a saccade is made to stabilize the perceptual field of view. In normally sighted people the oculomotor feedback system is important, as it tells the brain to compensate the retinal image position shift when a saccade is made. Compensation occurs through a shift in the brain representation of the retinal image to the opposite direction, thereby stabilizing the image representation. However, this is detrimental in Argus II wearers, because the position of the electrode array and hence retinal position of the image is unaffected by eye position. Hence, when subjects use their implant, any saccades will disrupt visual processing, because the oculomotor system will abberantly compensate the perceived location of the object being viewed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More importantly, perhaps, are &lt;strong&gt;micro-saccades&lt;/strong&gt;. Micro- saccades are small, involuntary eye movements. When images are present stably to the retina the images fade very quickly due to adaptive processes in retinal neurons. &lt;strong&gt;Micro-saccades are thought to prevent fading&lt;/strong&gt;, as they constantly produce small, involuntary fluctuations in gaze, thereby shifting the image quickly over the retina, and thereby refreshing the retinal image and preventing adaptation (&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/280/1757/20130077&quot; rel=&quot;nofollow&quot;&gt;Stingl, 2013&lt;/a&gt;). When Argus II wearers stop scanning the image, images indeed fade within seconds &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676187/&quot; rel=&quot;nofollow&quot;&gt;(Stronks, 2013)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To get back to your question and summarize:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Title question: &lt;strong&gt;No, eye muscles are not needed for sight&lt;/strong&gt;, given that Argus II wearers have sight (though artificial, crude vision). However, &lt;strong&gt;a functional saccade system in normally sighted folks improves scanning, and anecdotally micro-saccades prevent image fading&lt;/strong&gt; by constantly refreshing the retinal image.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Body question: Argus II implant wearers are an example of vision without oculomotor control. &lt;strong&gt;Although they cannot use their eye muscles for scanning, they still have functional vision&lt;/strong&gt;.&#xA; However image fading is a problem in Argus II users and folks without functional eye muscles alike, so &lt;strong&gt;head scanning techniques will be needed&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: Other implant systems, such as the Alpha-IMS use light-capturing methods inside the eye. Hence these subjects can use normal eye scanning and saccades for scanning. Also, albeit anecdotally, fading is reduced in Alpha-IMS wearers, because of the micro-saccades preventing adaptation (&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/280/1757/20130077&quot; rel=&quot;nofollow&quot;&gt;Stingl, 2013&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/280/1757/20130077&quot; rel=&quot;nofollow&quot;&gt;Stingl et al., &lt;em&gt;Proc Royal Soc B&lt;/em&gt; (2013); &lt;strong&gt;280&lt;/strong&gt;(1757)&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676187/&quot; rel=&quot;nofollow&quot;&gt;Stronks et al., &lt;em&gt;IOVS&lt;/em&gt; (2013); &lt;strong&gt;54&lt;/strong&gt;(6): 3891–901.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-26T03:47:32.953" LastActivityDate="2015-05-26T03:47:32.953" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="28002" PostTypeId="2" ParentId="27997" CreationDate="2015-01-24T23:31:44.073" Score="2" Body="&lt;p&gt;Tumor cells can have very unstable genomes, as much of the &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_repair&quot; rel=&quot;nofollow&quot;&gt;error repair machinery&lt;/a&gt; is damaged or missing. Since the cells are rapidly dividing and the DNA gets duplicated each time a cell splits, more and more mutations accumulate as the tumor grows and metastasizes. Just like in evolution as a whole, mutations that are either neutral or help the cell survive better in its environment are kept, whereas cells that develop deleterious mutations (perhaps killing the cell outright, making it more visible to the immune system, or just giving it a growth disadvantage as compared to neighboring cells) either die out or get outnumbered by other cells. This is why, over time, tumors can become resistant to therapies intended to kill them, as their cells accumulate mutations that help it evade the treatment and keep growing. There may be a disadvantage that the cells might grow more slowly than the original ones, but since the original ones were killed by the treatment, the resistant ones survive. So, this means that a tumor is rarely homogeneous, with all the cells having the exact same genome. &lt;a href=&quot;http://en.wikipedia.org/wiki/Deep_sequencing&quot; rel=&quot;nofollow&quot;&gt;Deep sequencing&lt;/a&gt; using &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_sequencing#Next-generation_methods&quot; rel=&quot;nofollow&quot;&gt;next-generation methods&lt;/a&gt; is being used to gather information on all the different mutations throughout a tumor, which can help doctors learn which mutations are most common and prescribe patient-specific &lt;a href=&quot;http://en.wikipedia.org/wiki/Combination_therapy&quot; rel=&quot;nofollow&quot;&gt;combination therapy&lt;/a&gt; which can kill all the various cell populations at once.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why are metastatic and xenografted tumors different from the parent? Metastases can arise from single cells or very small clumps of cells, and xenografts are generally made with very small pieces of tumor, so both may start with a different set of mutations than is common in the original tumor. As they grow and divide, as described above, they will become different from their parents. The surrounding environment definitely affects this: the amount of oxygen present, degree of vascularization and blood supply, number and kind of immune cells present, etc. With all these and more factors, a metastasis or xenograft will evolve differently than its parents.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-01-24T23:31:44.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28003" PostTypeId="2" ParentId="27996" CreationDate="2015-01-25T00:12:46.013" Score="4" Body="&lt;p&gt;There is nothing intrinsic to DNA methylation itself that requires it to repress transcription. Simply, it affects sequence recognition by proteins. CpG methylation can prevent transcription factor binding and/or recruit proteins that inhibit transcription, either competitively or through chromatin condensation. This is why it's generally associated with transcriptional repression. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found some articles which describe methylation in intergenic regions and introns activating transcription but, since you're asking specifically about promoters, I'll limit the examples to methylation in the 5' flanking region. Please note that I'm grossly oversimplifying these articles, you should actually read them to get the full picture. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25016019&quot; rel=&quot;nofollow&quot;&gt;Bahar HK, Vana T, Walker MD. 2014. Paradoxical role of DNA methylation in activation of FoxA2 gene expression during endoderm development. J Biol Chem 289(34):23882-23892&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This study reports that, during development, high levels of methylation of a CpG island in the FoxA2 promoter is present in expressing tissues and absent in non-expressing tissues. Their hypothesis is that CpG methylation prevents binding of a protein that represses transcription by condensing chromatin through histone modifications.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17343736&quot; rel=&quot;nofollow&quot;&gt;Hantusch B, Kalt R, Krieger S, Puri C, Kerjaschki D. 2007. Sp1/Sp3 and DNA-methylation contribute to basal transcriptional activation of human podoplanin in MG63 versus Saos-2 osteoblastic cells. BMC Mol Bio 8(20)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here, PDPN expression was associated with CpG methylation. They hypothesize that methylation could affect chromatin state or recruit, what they term, a methylation dependent factor, which activates transcription. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16166088&quot; rel=&quot;nofollow&quot;&gt;Niesen MI, Osborne AR, Yang H, Rastogi S, Chellappan S, Cheng JQ, Boss JM, Blanck G. 2005. Activation of a methylated promoter mediated by a sequence-specific DNA-binding protein, RFX. J Biol Chem 280(47):38914-38922&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This study describes a DNA binding protein (RFX) that can recognize and activate the methylated promoter of MHC. They suggest that RFX can competitively inhibit binding of methyl-DNA binding domain proteins that condense chromatin.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-01-26T02:10:09.667" LastActivityDate="2015-01-26T02:10:09.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28004" PostTypeId="2" ParentId="27980" CreationDate="2015-01-25T00:52:47.690" Score="3" Body="&lt;p&gt;The answer given above by Chris is correct, but does leave out one relatively recently discovered method of cell death, somewhere between the two responses of apoptosis and necrosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's called pyroptosis. It's a form of programmed cell death (in immune cells, e.g. macrophages), so it is similar to apoptosis. However, instead of a neat and tidy non-phlogistic (inflammatory) death as is the case in apoptosis, the cell purposefully upregulates inflammatory cytokines, swells, and bursts, releasing the cytokines and other inflammatory mediators out into the extracellular space. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UXbHF.jpg&quot; alt=&quot;Pyroptosis activation&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Pyroptosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;The wikipedia page on this is quite good&lt;/a&gt;, and for this image and more information you can check out &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910423/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this study&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a response to certain Pathogen Associated Molecular Patterns (PAMPs). These are patterns that are present on pathogens - in this case particular bacterial species - and trigger an immune response. Read more about them &lt;a href=&quot;http://www.nature.com/scitable/content/pamps-and-damps-in-the-inflammatory-response-14464749&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;. This pro-inflammatory response attracts other immune cells to the area, and helps to drive an immune response, containing and aiding in the elimination of the invading pathogens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: OP may also be interested to know that if an apoptotic cell is not cleared by a macrophage, eventually it will become &quot;secondarily necrotic&quot;, meaning the membrane eventually falls apart and the cell releases it's contents (&lt;a href=&quot;http://cshperspectives.net/content/5/1/a008748.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;). This turns it from non-inflammatory to an inflammatory response. Neutrophils are particularly adept at keeping their membranes intact, due to the harmful nature of the cell contents. There is a pubmed entry &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18453112&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; regarding it, but the actual book I've taken this information from isn't available without subscription.&lt;/p&gt;&#xA;" OwnerUserId="10067" LastEditorUserId="10067" LastEditDate="2015-01-25T11:44:30.430" LastActivityDate="2015-01-25T11:44:30.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28006" PostTypeId="1" AcceptedAnswerId="28031" CreationDate="2015-01-25T03:25:03.957" Score="4" ViewCount="1955" Body="&lt;p&gt;I'm aware that melanocytes produce melanin, giving color to the skin, but why are these cells recruited or overactive when healing skin abrasions, lesions and sores when T-cells and inflammatory cytokines of the immune response help with healing. I'm just wondering why the production of color is associated with the healing of the wound and if it proves beneficial, or if it just a side effect so to speak.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: In this study, it explains the recruitment of melanocytes after the initially response of innate immune cells and inflammatory cytokines, however, it does not delve into how this is beneficial to the cell.  &lt;br&gt;&#xA;[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597032/&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;]&lt;/p&gt;&#xA;" OwnerUserId="12891" LastEditorUserId="3340" LastEditDate="2015-01-25T05:32:37.147" LastActivityDate="2015-01-29T15:59:03.420" Title="Why is hyper pigmentation the common aftermath of skin lesions and abrasions?" Tags="&lt;skin&gt;&lt;melanin&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28007" PostTypeId="1" AcceptedAnswerId="28008" CreationDate="2015-01-25T03:39:39.263" Score="4" ViewCount="1412" Body="&lt;p&gt;For an assignment I have to differentiate the three types of muscle tissues in these three pictures&#xA;&lt;img src=&quot;https://i.imgur.com/60ZPX9q.png&quot; alt=&quot;Muscle cells&quot;&gt;.&#xA;I'm having difficulty seeing the striations and branches etc. because the pictures are so small. Am I missing something?&lt;/p&gt;&#xA;" OwnerUserId="13193" LastEditorUserId="13193" LastEditDate="2015-01-25T03:58:43.430" LastActivityDate="2015-01-25T05:04:00.370" Title="Trying to differentiate between the three muscle tissues with small pictures" Tags="&lt;cell-biology&gt;&lt;muscles&gt;&lt;histology&gt;&lt;eukaryotic-cells&gt;&lt;tissue&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28008" PostTypeId="2" ParentId="28007" CreationDate="2015-01-25T05:04:00.370" Score="5" Body="&lt;p&gt;Without answering the problem for you, because you have not shown work yet to try to figure out which is which, let me tell you that you have &lt;a href=&quot;http://courseweb.edteched.uottawa.ca/Medicine-histology/English/SS_BasicTissues/muscle_tissue.htm&quot;&gt;three options&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Skeletal Muscle- striated, peripherally located nuclei, same thickness along length, non-branching &lt;/li&gt;&#xA;&lt;li&gt;Cardiac Muscle- striated, few centrally located nuclei, branches and anastamosis&lt;/li&gt;&#xA;&lt;li&gt;Smooth Muscle- non-striated, centrally located single nucleus per cell, tapering ends&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now, hopefully, based on your pictures, which are indeed sufficient for you to figure out which is which, you can answer your own question. Good luck! &lt;/p&gt;&#xA;" OwnerUserId="11631" LastActivityDate="2015-01-25T05:04:00.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28009" PostTypeId="1" AcceptedAnswerId="28012" CreationDate="2015-01-25T07:59:58.383" Score="1" ViewCount="1156" Body="&lt;p&gt;Does the heart no longer function? Does it go into ventricular fibrillation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What happens?&lt;/p&gt;&#xA;" OwnerUserId="4819" LastActivityDate="2015-01-25T08:55:05.993" Title="What happens when the brain is no longer capable of co-ordinating or regulating the heart and breathing rates?" Tags="&lt;brain&gt;&lt;cardiology&gt;&lt;breathing&gt;" AnswerCount="2" CommentCount="4" ClosedDate="2015-01-25T22:41:35.913" ContentLicense="CC BY-SA 3.0" />
  <row Id="28010" PostTypeId="2" ParentId="28009" CreationDate="2015-01-25T08:33:53.267" Score="1" Body="&lt;p&gt;The heart beats are initiated by the pacemaker cells which are located in the heart itself. So absence of neural input will not affect heart function by much. Though heart can function without neural input, it will not be able to respond to stimuli. The human heart rate is regulated beat by beat through the vagus nerve. This would be lost. The sympathetic system would be able to influence heart rate through the adrenal gland. But even this is delayed. Plus till the levels of noradrenaline falls to normal heart rate will be high. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The contractility control also will be lost pretty much. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The respiratory centers are located in the medulla and in the absence  of brain stem outflow the person will be under respiratory arrest which is a medical emergency. &lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-01-25T08:55:05.993" LastActivityDate="2015-01-25T08:55:05.993" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28011" PostTypeId="2" ParentId="27993" CreationDate="2015-01-25T08:45:23.340" Score="1" Body="&lt;p&gt;Tl;dr answer, tumors are &lt;strong&gt;abnormal&lt;/strong&gt; growth (or swelling, thanks to Malic for pointing out) of any kind. The &lt;em&gt;kinds&lt;/em&gt; of tumors are benign and malignant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Benign tumors are usually slow growing and harmless. Example would be a lipoma. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Malignant tumors are otherwise called cancers. They generally have a bad prognosis. Very few cancers are &lt;em&gt;curable&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Swelling over an injury (which is also called tumor) is due to local transudation (shift of plasma from capillaries). This is temporary and usually goes down one the injury heals. &lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-01-25T09:39:27.027" LastActivityDate="2015-01-25T09:39:27.027" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="28012" PostTypeId="2" ParentId="28009" CreationDate="2015-01-25T08:45:54.660" Score="3" Body="&lt;p&gt;Damage to the brainstem - the part of the brain responsible for controlling breathing and the heart - has different effects on the heart and the lungs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Every heartbeat is not directed by the brain. Instead, the brain has a &quot;throttle&quot; to the heart, by which it can regulate the heart rate up and down, but the actual heartbeat is initiated by special cells in the heart, called pacemaker cells. In the absence of signals from the brainstem, the heart will continue pumping; this is (one of the reasons) why people who need ventilators to breath for them do not also need their heart pumped for them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Breathing, however, &lt;em&gt;is&lt;/em&gt; directly controlled by the brain. Without signals from the brain, breathing will stop completely (the technical term is &quot;respiratory arrest&quot;, but that literally just means &quot;breathing-stuff stopped-ness&quot;). Survival time without breathing depends on a number of factors, but at room temperature, without medical intervention (ie. rescue breaths or a ventilator) and barring any special circumstances, is only a few minutes. Permanent brain damage sets in a few minutes later, even if the person can be resuscitated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, without any breathing, the heart will stop beating due to a lack of oxygen before long. The general progression will be from sinus (&quot;normal&quot;) rhythm, to ventricular tachycardia, to ventricular fibrillation, to asystole (&quot;flatlining&quot;).&lt;/p&gt;&#xA;" OwnerUserId="13187" LastActivityDate="2015-01-25T08:45:54.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28013" PostTypeId="2" ParentId="20946" CreationDate="2015-01-25T09:06:38.027" Score="0" Body="&lt;p&gt;I think the body would undergo decay. While it is true that the moon does not contain living organisms capable of decaying a dead human body, the human body itself contains huge load of bacteria→ on skin surface and gut which will continue to grow. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The aerobic bacteria will die out as soon as oxygen is removed which is very soon. The anaerobic bacteria will continue to grow and proliferate till substrate (dead human body) will cease to exist. This will be regulated as anongoodnurse has pointed out by the heat and light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further, the infectious status of the dead person will also matter. Any fungal infection can alter the rate of decay. &lt;/p&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-01-25T09:06:38.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28015" PostTypeId="1" AcceptedAnswerId="28029" CreationDate="2015-01-25T13:10:09.253" Score="6" ViewCount="114" Body="&lt;p&gt;If there are wrong DNA pair, for example A=G, is there mechanism that could repair such things - &lt;strong&gt;after&lt;/strong&gt; the replication was &lt;strong&gt;finished&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or it happens only during replication?&lt;/p&gt;&#xA;" OwnerUserId="10104" LastActivityDate="2015-01-26T17:03:16.987" Title="Repair wrong DNA pair after ending replication?" Tags="&lt;dna&gt;&lt;dna-damage&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28017" PostTypeId="1" AcceptedAnswerId="28018" CreationDate="2015-01-25T13:24:35.177" Score="3" ViewCount="10838" Body="&lt;p&gt;I have encountered comparisons of the Michaelis-Menten constant (&lt;span class=&quot;math-container&quot;&gt;$K_m$&lt;/span&gt;) a few times. Generally speaking if the &lt;span class=&quot;math-container&quot;&gt;$K_m$&lt;/span&gt; of an enzyme is higher, then its affinity to its substrate is lower. How does this make sense?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe the maximum velocity (&lt;span class=&quot;math-container&quot;&gt;$V_{\mathrm{max}}$&lt;/span&gt;) of higher &lt;span class=&quot;math-container&quot;&gt;$K_m$&lt;/span&gt; enzymes is higher? Then of course, &lt;span class=&quot;math-container&quot;&gt;$K_m$&lt;/span&gt; can have a higher value. Because &lt;span class=&quot;math-container&quot;&gt;$K_m$&lt;/span&gt; is the substrate concentration at half of the &lt;span class=&quot;math-container&quot;&gt;$V_{\mathrm{max}}$&lt;/span&gt;. But I think we cannot determine affinity with &lt;span class=&quot;math-container&quot;&gt;$K_m$&lt;/span&gt;.&lt;/p&gt;&#xA;" OwnerDisplayName="user13196" LastEditorUserId="31955" LastEditDate="2018-11-30T02:03:23.900" LastActivityDate="2018-11-30T02:03:23.900" Title="Making sense of enzyme Km comparisons" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;&lt;enzyme-kinetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="28018" PostTypeId="2" ParentId="28017" CreationDate="2015-01-25T13:39:05.053" Score="4" Body="&lt;p&gt;Since the Michaelis-Menton constant Km is the concentration of substrate at 0.5Vmax, it is an inverse measure of its substrate affinity, because a lower Km indicates that less substrate is needed to reach a certain reaction speed. Hence, a low Km means a high substrate affinity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your statement&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Maybe the maximum velocity (Vmax) of higher-Km enzymes is higher? Then of course Km can have a higher value.&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;is incorrect. &lt;strong&gt;Km characterizes how steep reaction speed increases with substrate availability&lt;/strong&gt;; it does not determine maximum speed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, to address your title question, &lt;strong&gt;comparing affinities can make a lot of sense&lt;/strong&gt;. For example, consider the case where enzymes catalyzing similar reactions in different species of organisms are compared. Very low Km means optimal use of small substrate levels, while a high Vmax shows optimized reaction speeds. This in turn may tell you something about optimal habitats and evolutionary pressure.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-25T15:25:09.070" LastActivityDate="2015-01-25T15:25:09.070" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28019" PostTypeId="2" ParentId="14458" CreationDate="2015-01-25T15:07:34.177" Score="2" Body="&lt;p&gt;From Uptodate on Clinical Manifestations of Hypocalcemia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Acute hypocalcemia directly increases peripheral neuromuscular irritability [ 1 ]. As measured electromyographically, tetany consists of repetitive high-frequency discharges after a single stimulus. Hyperexcitability of peripheral neurons is probably the most important pathophysiologic effect of hypocalcemia, but hyperexcitability occurs at all levels of the nervous system, including motor end-plates, the spinal reflexes, and the central nervous system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Guyton and Hall Textbook of Physiology:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The concentration of&#xA;  calcium ions in the extracellular fluid also has a profound&#xA;  effect on the voltage level at which the sodium&#xA;  channels become activated. When there is a deficit of&#xA;  calcium ions, the sodium channels become activated&#xA;  (opened) by very little increase of the membrane potential&#xA;  from its normal, very negative level. Therefore, the&#xA;  nerve fiber becomes highly excitable, sometimes discharging&#xA;  repetitively without provocation rather than&#xA;  remaining in the resting state. In fact, the calcium ion&#xA;  concentration needs to fall only 50 per cent below&#xA;  normal before spontaneous discharge occurs in some&#xA;  peripheral nerves, often causing muscle “tetany.”This is&#xA;  sometimes lethal because of tetanic contraction of the&#xA;  respiratory muscles.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The probable way in which calcium ions affect the&#xA;  sodium channels is as follows:These ions appear to bind&#xA;  to the exterior surfaces of the sodium channel protein&#xA;  molecule. The positive charges of these calcium ions&#xA;  in turn alter the electrical state of the channel protein&#xA;  itself, in this way altering the voltage level required to&#xA;  open the sodium gate.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-01-25T15:07:34.177" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28021" PostTypeId="1" CreationDate="2015-01-25T17:45:16.880" Score="3" ViewCount="892" Body="&lt;p&gt;I seached for endosymbiotic theory in Wiki and I found this about endosymbiotic theory:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Symbiogenesis, or endosymbiotic theory, is an evolutionary theory&#xA;  which explains the origin of eukaryotic cells from prokaryotes. It&#xA;  states that several key organelles of eukaryotes originated as&#xA;  symbiosis between separate single-celled organisms. According to this&#xA;  theory, mitochondria and plastids (e.g. chloroplasts), and possibly&#xA;  other organelles, represent formerly free-living bacteria that were&#xA;  taken inside another cell as an endosymbiont, around 1.5 billion years&#xA;  ago.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But I couldn't find any answer for my question, so I decided to ask:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to this theory and differences between inner and outer mitochondria and plastid membranes, which membranes (outer or inner membranes) of mitochondria and plastids (e.g. chloroplasts) relate to bacteria?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And why do mitochondria need to have a double membrane?&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorUserId="9943" LastEditDate="2015-01-25T22:26:37.187" LastActivityDate="2015-01-25T22:26:37.187" Title="Which of the two mitochondorial membranes relate to bacteria according to the endosymbiotic theory?" Tags="&lt;evolution&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28022" PostTypeId="1" CreationDate="2015-01-25T18:12:12.193" Score="8" ViewCount="2842" Body="&lt;p&gt;I was confronted by this question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biological evolution of life on Earth, from simple prokaryote-like cells to large, multicellar eukaryotic organisms,&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A) has occurred in accordance with the laws of thermodynamics.&lt;/li&gt;&#xA;&lt;li&gt;B) has caused an increase in the entropy of the planet.&lt;/li&gt;&#xA;&lt;li&gt;C) has been made possible by expending Earth's energy resources.&lt;/li&gt;&#xA;&lt;li&gt;D) has occurred in accordance with the laws of thermodynamics, by expending Earth's energy resources and causing an increase in the entropy of the planet.&lt;/li&gt;&#xA;&lt;li&gt;E) violates the laws of thermodynamics because Earth is a closed system.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Answer:  A&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I do not understand. Biological evolution does cause the system (living organisms)'s entropy to decrease. So, by the second law of thermodynamics, the entropy of the universe (in this case Earth), must have overall increased.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would answer D... Where am I going wrong?&lt;/p&gt;&#xA;" OwnerUserId="8516" LastEditorUserId="11631" LastEditDate="2015-01-26T05:35:35.873" LastActivityDate="2021-05-02T04:45:33.777" Title="Relationship Between Evolution and the Increase of Entropy of Earth" Tags="&lt;evolution&gt;&lt;thermodynamics&gt;" AnswerCount="7" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28024" PostTypeId="2" ParentId="28021" CreationDate="2015-01-25T18:45:05.913" Score="3" Body="&lt;p&gt;The inner membrane is that of the engulfed bacteria. The bacterium would have been phagocytosed by a larger cell. Hopefully you can see in this image the smaller cell being engulfed in the membrane of the larger cell:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fKiSO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[ &lt;a href=&quot;http://commons.m.wikimedia.org/wiki/File:Chloroplast_primary_endosymbiosis.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt; ]&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-01-25T20:15:34.770" LastActivityDate="2015-01-25T20:15:34.770" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28025" PostTypeId="1" CreationDate="2015-01-25T18:52:48.097" Score="3" ViewCount="3680" Body="&lt;p&gt;This question is causing great confusion in my head.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which of the following is an example of potential rather than kinetic energy?&#xA;A) the muscle contractions of a person mowing grass&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B) water rushing over Niagara Falls&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C) light flashes emitted by a firefly&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D) a molecule of glucose&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E) the flight of an insect foraging for food&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Answer:  D&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A) Muscle contractions is caused by the use of potential energy in ATP used by actin and myosin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B) This is a classic example of what potential energy means.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C) Bioluminescence is a process caused by the use of chemical (potential) energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D) Yes, the molecule of glucose does contain potential energy. BUT, it is not potential energy itself...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E) Flight is kinetic energy. However, you can still boil this down to ATP in actin and myosin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do I approach this problem? My teacher said this is the type of problem she would give us. But this is so ambiguous. Am I lost?&lt;/p&gt;&#xA;" OwnerUserId="8516" LastEditorUserId="3340" LastEditDate="2015-06-04T11:38:51.200" LastActivityDate="2015-06-04T11:38:51.200" Title="Kinetic Vs Potential Energy in Biochemical Contexts" Tags="&lt;thermodynamics&gt;&lt;bioenergetics&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28026" PostTypeId="2" ParentId="28022" CreationDate="2015-01-25T18:55:25.843" Score="10" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;However, I do not understand. Biological evolution does cause the system (living organisms)'s entropy to decrease. So, by the second law of thermodynamics, the entropy of the universe (in this case Earth), must have overall increased.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The universe and the earth are not equatable. Earth is not an isolated system. Life causes entropy of the earth to decrease. This is offset by increased entropy of the sun, which is the primary source of energy for the earth. Overall, the entropy of the universe increases. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-01-25T18:55:25.843" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28029" PostTypeId="2" ParentId="28015" CreationDate="2015-01-25T19:52:53.230" Score="6" Body="&lt;p&gt;DNA mismatches and indels can be repaired after replication through an aptly named mechanism called &lt;a href=&quot;http://en.m.wikipedia.org/wiki/DNA_mismatch_repair&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA mismatch repair&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll briefly describe the mechanism in &lt;em&gt;Escherichia coli&lt;/em&gt;, but it's similar in other organisms. A protein called MutS scans DNA for lesions caused by mismatched nucleotides incorporated during replication that escaped DNA polymerase proofreading. These are detected by the kink they produce in the DNA backbone. MutS recruits MutL and MutH; the former activates the latter, which is an endonuclease. MutH cuts the DNA backbone near the lesion in the newly synthesized strand (the one containing the misincorporated nucleotide). This strand can be identified because it has not yet been methylated, while the parent strand contains the original methylation. After cleavage, UvrD helicase unwinds the strand and an exonuclease digests it. The gap around the former lesion can then be filled by DNA polymerase III and DNA ligase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Z1lHQ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[ &lt;a href=&quot;http://commons.m.wikimedia.org/wiki/File:DNA_mismatch_repair.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;image adapted from&lt;/a&gt; ]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's an interesting review in a Nature publication that discusses it in more depth, as well as the mechanism in humans:&#xA;&lt;a href=&quot;http://www.nature.com/cr/journal/v18/n1/full/cr2007115a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Guo-Min L. 2008. Mechanisms and functions of DNA mismatch repair. Cell Res 18:85-98&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-01-26T17:03:16.987" LastActivityDate="2015-01-26T17:03:16.987" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28030" PostTypeId="2" ParentId="28022" CreationDate="2015-01-25T21:32:12.390" Score="1" Body="&lt;p&gt;The Second Law is one of the most misunderstood and misapplied laws of thermodynamics. It has a scope largely confined to physics, nothing more should be read into it. Simply put, it states that &quot;Heat cannot spontaneously flow from a colder location to a hotter location&quot;. (&lt;a href=&quot;https://en.wikipedia.org/wiki/Thermodynamics#Laws_of_thermodynamics&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;) There is nothing about life that violates that, or creates &quot;negative entropy&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you get into the details, you need to consider closed vs systems, and equilibrium vs non-equilibrium systems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, life contributes to positive entropy, like everything else. Energy at high potential is transformed to low potential, at the same time creating useful work and waste heat. Note that &quot;useful work&quot; can include storing energy in a form useful for future use.&lt;/p&gt;&#xA;" OwnerUserId="13199" LastEditorUserId="9458" LastEditDate="2015-01-25T22:06:23.157" LastActivityDate="2015-01-25T22:06:23.157" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28031" PostTypeId="2" ParentId="28006" CreationDate="2015-01-25T22:38:44.917" Score="2" Body="&lt;p&gt;The upper layer of the skin (or the epidermis) is formed mostly by keratinocytes and some melanocytes (about 30-40 times more keratinocytes) and also fibroblasts (although they are not shown here). The melanocytes are found in the basal cell layer at the border between epidermis and dermis as shown in the figure below (from &lt;a href=&quot;http://www.dermnetnz.org/terminology.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wyAQw.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The melanocytes spread out their dendrites between the keratinocytes and transport the melanosomes (pigment containing vacuoles) to them to pigment these cells. This is a highly regulated process and depends strongly on the interaction between keratinocytes and melanocytes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the so-called paracrine pathway the keratinocytes secret substances which regulate the production of melanin. These are for example &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanocyte-stimulating_hormone&quot; rel=&quot;nofollow noreferrer&quot;&gt;alpha-MSH&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/Adrenocorticotropic_hormone&quot; rel=&quot;nofollow noreferrer&quot;&gt;ACTH&lt;/a&gt;, which stimulate the melanocytes to produces more melanin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This regulation is the key to the hyperpigmentation. During the proliferation or the inflammation chemokines and hormones are produced (and secreted) in the skin which stimulate keratinocytes and fibroblasts. These are for example the keratinocyte growth factor (KGF), as well as the chemokines IL1-alpha and TNF-alpha. This stimulation leads to the production of ACTH (and derived peptides) by the keratinocytes and the secretion of stem cell factor (SCF) and hepatocyte growth factor (HGF) by the fibroblasts which all induce pigmentation. The chemokine secretion is also enhanced from the keratinocytes by KGF. If you are interested in a deeper view at this topic, have a look at reference 1 (and the references in the paper). Reference 2 goes deeper into the regulation of the paracrine signalling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In an injury (especially in larger areas of the skin) a lot of cells are damaged and need to be replaced. This functions via cell division but also via the migration of cells into the affected area. This is described by the paper you link - here melanocytes and melanoblasts (melanocyte stem cells which can divide and then differentiate into melanocytes) migrate into the injured region to replace the destroyed melanocytes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3878/zhza8z6x_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mechanisms underlying post- inflammatory hyperpigmentation: lessons&#xA;from solar lentigo&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/jid/journal/v127/n11/full/5700938a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hepatocyte Growth Factor Establishes Autocrine and Paracrine&#xA;Feedback Loops for the Protection of Skin Cells after UV Irradiation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-01-29T15:59:03.420" LastActivityDate="2015-01-29T15:59:03.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28032" PostTypeId="2" ParentId="23644" CreationDate="2015-01-25T22:40:08.813" Score="5" Body="&lt;p&gt;Transformation underpins a lot of lab modern projects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This will be a very unsatisfying answer, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Transformation_efficiency&quot; rel=&quot;nofollow&quot;&gt;this wikipedia entry&lt;/a&gt; explains why. The time, and success, of bacterial transformation of competent cells varies greatly depending on a few things mainly:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the length of nucleic acid sequence for insertion (or more accurately, the plasmid)&lt;/li&gt;&#xA;&lt;li&gt;the species of target organism (or more accurately, the genotype of the target organism)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Transformation_efficiency#Factors_affecting_transformation_efficiency&quot; rel=&quot;nofollow&quot;&gt;a host of other things&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;With a specific plasmid and organism you would be able to get a more satisfying answer, but I imagine the answer would even differ from lab to lab.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I worked with a microbiologist that provided me with a protein as a part of my honours project, and I can give you a broad impression I got from them: it does not happen often. Sometimes none of the cultures you are trying to transform will incorporate the new sequence into their genome, other times the cloning process goes very well and all your cultures will be transformed successfully. For our project, valid colonies only presented after a week with reasonable success (more than half the attempts were successful). But you don't know if the transformation worked until way after the first transformation happened.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanisms behind this are grossly understudied. If we take some thing &lt;em&gt;B. subtilis&lt;/em&gt;, arguably the most academically studied organism in the field of transformation, it can take up the DNA as food or incorporate it into its genome but nobody knows exactly how this happens at a molecular level (Chen &amp;amp; Dubnau, 2004)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Chen, I., &amp;amp; Dubnau, D. (2004). &lt;a href=&quot;http://faculty.fmcc.suny.edu/freeman/webpages/micro/readings/DNA%20UPTAKE%20DURING%20BACTERIAL.pdf&quot; rel=&quot;nofollow&quot;&gt;DNA uptake during bacterial transformation.&lt;/a&gt; &lt;em&gt;Nature Reviews.&lt;/em&gt; Microbiology, &lt;strong&gt;2&lt;/strong&gt;(3), 241–9&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2015-12-01T08:53:24.660" LastActivityDate="2015-12-01T08:53:24.660" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28033" PostTypeId="2" ParentId="27790" CreationDate="2015-01-25T23:02:17.343" Score="4" Body="&lt;h1&gt;Background to the different theories of ageing.&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=jc4yK0zZ-cQ&quot; rel=&quot;nofollow&quot;&gt;This video, from a senior lecturer at the University of Liverpool who specialises in ageing&lt;/a&gt;, discusses the theories of ageing. He touches on the DNA damage theory. &lt;/p&gt;&#xA;&#xA;&lt;h1&gt;DNA damage theory of ageing.&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;Note that when talking about DNA damage theory, we are specifically talking about damage to the process of cell renewal by DNA damage repair mechanisms in stem cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Mutation ageing is not the same as DNA damage causing ageing and cannot really cause ageing in yeast.&lt;/strong&gt; The idea that cells &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_damage_theory_of_aging#Mutation_theories_of_aging&quot; rel=&quot;nofollow&quot;&gt;acquire damage over time due to mutated DNA&lt;/a&gt; is fundamentally different to the DNA damage theory of ageing. The mechanisms that lead to DNA damage are covered very well in @Chris' answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The suggested systemic effect that DNA damage has in the human body causes an inability to renew cells due to a lack of viable stem cells. This contributes to the process of ageing in the organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In yeast, this stem cell depletion process does not happen (they are single cellular mostly). &lt;em&gt;In the comments it appears that you are actually talking about mutation based ageing in your original question.&lt;/em&gt; Mutations are passed to daughter cells. But these daughter cells don't appear to age or to die quicker (If the parental cell is 5 days old, the daughter cell does not appear to be 5 days old). This is the fundamental reason why this form of ageing remains less studied - &lt;strong&gt;it doesn't really make sense that general mutations cause ageing.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Summary&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;To directly answer the question: &lt;strong&gt;&quot;How does DNA damage cause ageing in yeast?&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question doesn't quite capture the whole picture and confuses DNA damage theory of animal ageing with general DNA damage at a cellular level. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many theories of ageing. Nobody knows which ones have more or less influence on ageing. Yeast is a good model for some kinds of age theory modelling, but perhaps not in the case of DNA damage based ageing. Although they experience DNA damage in the form of mutation, this doesn't cause ageing in the same way that DNA damage might cause ageing in humans because they are single celled organisms, and don't experience the same inter-tissue relationships that more complex organisms have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&#xA; &lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&#xA;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Edits&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;This answer has been changed extensively since its first draft based on additional questions and queries from the OP in the comments. I decided to keep some important points that were raised and dismissed.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why there is no DNA damage transfer at all, to daughter cell?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;DNA damage can occur and &lt;strong&gt;&lt;em&gt;is&lt;/em&gt;&lt;/strong&gt; transferred to the daughter cell. Damage is very rare though. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So how yeast survive? Human stem cells aging and die, or get cancer. But yeast no. Human start from one cell. And die. Yeast start from one cell and live forever (dividing again and again) &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Edit After Comments:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Single cell&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In yeast there are no inter-tissue systems. Mutated damage is simply passed on if the cell is viable. Also the assumption that they live forever isn't entirely accurate. But the DNA is passed on in its mutated or damaged form.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Multi cell&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA damage based ageing is a big problem for animals. (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/acel.12071/full&quot; rel=&quot;nofollow&quot;&gt;Dolle &lt;em&gt;et al&lt;/em&gt; 2013&lt;/a&gt;) Showed that DNA damage to a single repair pathway causes accelerated ageing, (but note that there was not an increase in mutation during this ageing).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;but you talking about cancer, it's not so good example, my mistake.  But in humans aging NOT like cancer - it occur in ALL the body and all the cells. So in all cells there are some DNA damage.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Another edit:&lt;/strong&gt; You were right to talk about cancer in this context. The DNA damage theory of ageing is that small changes (damage) in our DNA accumulate over time and damage cell types by damaging various DNA repair pathways. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Damage accumulates and over time less &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_damage_theory_of_aging#Long-lived_stem_cells&quot; rel=&quot;nofollow&quot;&gt;stem cells for renewal are viable and cellular repair of other damaged cells slows down&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also this same fundamental principle of mutation damage happening over time can lead to mutations that switch off cell control mechanisms and lead to cancer. Although these these mutations do not increase in rate with age (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15690342&quot; rel=&quot;nofollow&quot;&gt;Hill &lt;em&gt;et al.,&lt;/em&gt; 2005&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example the naked mole rat lives 10 times that of comparable species (less ageing) and have not been observed to naturally acquire cancer (less cancer). The theory implies that the two things are quite linked because of the way DNA changes, but not that specifically mutation is a cause or result of ageing. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I talking more about aging. Because there is aging in yeast. And one of aging theories for human - accumulating DNA damage. So what &lt;em&gt;Chris&lt;/em&gt; writing is that it's really rare. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;**Stem cells are damaged. ** I'm no longer entirely sure of what you mean by ageing in yeast. Yeast aren't reliant on a limited number of stem cells for cellular renewal, they don't age in the way you might be thinking. They simply proliferate the mutated cell type. There is no impact to a larger organism like in human ageing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;DNA damage.&lt;/strong&gt; Yeast is a very helpful organism for understanding the underlying biochemistry and genetics of ageing, not the overall ageing systems. These are two different fields of study. It is unclear which you are talking about at this point.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Also there is aging in places where no stem cells - like brain - no renew of cells, just existing cells age, damaged, die, and not replaced. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Dolle 2006 found that spontaneous DNA damage in relation to age happened in the liver but not the brain.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2015-09-29T11:38:29.197" LastActivityDate="2015-09-29T11:38:29.197" CommentCount="16" ContentLicense="CC BY-SA 3.0" />
  <row Id="28034" PostTypeId="1" CreationDate="2015-01-25T23:42:39.470" Score="6" ViewCount="37116" Body="&lt;p&gt;I read these two from various books, and got confused. The confusion is -&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reticulospinal tracts control gamma motor neurons. Gamma motor neurons control tone of muscle. &#xA;In decerebrate rigidity, the reticulospinal tracts are cut, so the gamma motor neurons start firing excessively, and SPASTICITY develops. I understood this part and why Decerebrate Rigidity is a misnomer as it is actually spasticity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Question is, in decorticate rigidity, the cerebral cortex is damaged. The basal ganglia are intact. One explanation I found is that the basal ganglia keep the reticulospinal tract activated so gamma motor neuron is under control. But if basal ganglia have no direct communication with brainstem or spinal cord, and their efferents pass through cerebral cortex, then even in decorticate rigidity, the reticulospinal tract should not be working, and thus the gamma motor neurons should fire excessively, in which case the decorticate rigidity also becomes a spasticity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I missing anything? I am keeping red nucleus and vesticular nuclei out of this just to make matter simple. My question is about activity of gamma motor neurons in these two conditions. I hope you got the question. Thank you. &lt;/p&gt;&#xA;" OwnerUserId="11702" LastActivityDate="2017-07-26T04:11:45.300" Title="Mechanism of Decorticate &amp; Decerebrate Posturing? Also why is only Decorticate Rigidity a misnomer?" Tags="&lt;neurology&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28035" PostTypeId="2" ParentId="18985" CreationDate="2015-01-26T00:08:20.413" Score="1" Body="&lt;p&gt;Hot spots on the human body caused by cell phones are caused by the EMF/RF (ElectroMagnetic Frequency/Radio Frequency) emitted from the phones (or any mobile wireless device). (There is much conjecture about the safety of  these frequencies and whatnot... That is not what I am here to talk about).&#xA;&lt;p&gt;&#xA;In this case, the term hot spot does &lt;em&gt;not&lt;/em&gt; refer to you being a WiFi hot spot! It simply means that since the frequencies are similar to that of a microwave, you will absorb them and they will cause heating internally. These areas will remain warm for a time - whether you can feel it or not, some people can, some can't. Shown &lt;a href=&quot;https://media.licdn.com/mpr/mpr/p/2/005/060/0ea/3ff9e3d.jpg&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; is a thermal image of someone who recently used a cell phone and one who had not.&lt;/p&gt;&#xA;" OwnerUserId="6289" LastEditorUserId="6289" LastEditDate="2015-01-27T15:28:52.680" LastActivityDate="2015-01-27T15:28:52.680" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28036" PostTypeId="2" ParentId="28034" CreationDate="2015-01-26T00:27:05.800" Score="1" Body="&lt;p&gt;1) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;a. &lt;strong&gt;Decorticate posturing&lt;/strong&gt; means &lt;strong&gt;rubrospinal tract&lt;/strong&gt; is the dominant output to the motor neurons of the body... maybe dominant is the wrong word, I am not all that knowledgable on this subject, but it is certainly altering the standard reticulospinal tract based extensor posturing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Rubrospinal_tract&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Rubrospinal_tract&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is responsible for the strange flexion of upper limbs (aka arms). I say strange because when you think coma you think extension, not flexion. The lower limbs (aka legs), as always is extensor. Why the upper limb but not the lower limb? The red nucleus may play an additional role in controlling muscles of the shoulder and upper arm via projections of its magnocellular part.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b. In &lt;strong&gt;decerebrate posturing&lt;/strong&gt; the rubrospinal tract is also cut, since the lesion is below the red nucleus. In this scenario the &lt;strong&gt;reticular activating system&lt;/strong&gt; (aka &lt;strong&gt;reticulospinal tract&lt;/strong&gt;) is the dominant output to the motor neurons of the body. Here you get the classic extensor pose, for both upper and lower limbs...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;The point is&lt;/em&gt;: Rubrospinal tract was what you were missing. The red nucleus is the specific part of the basal ganglia that is involved...&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;2) &#xA;the difference between spasticity vs rigidity:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;spasticity is an increased resistance to the passive movement of a&#xA;joint due to abnormally high muscle tone (hypertonus) which varies&#xA;with the amplitude and speed of displacement of a joint.  &lt;/li&gt;&#xA;&lt;li&gt;rigidity is an increased resistance to the passive movement of a joint which is&#xA;constant throughout the range of joint displacement and not related&#xA;to the speed of joint movement. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;your supposed to test this out on patients to get a feel for what's the difference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;spaciticity is the case for upper motor neurons lesions (ex. stroke), since the spinal reflexes are not being inhibited from above...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;an example of rigidity in neurology is Parkinson's disease, which is the loss of the substantial nigra, which like the red nucleus is also in the midbrain... while the the substantial nigra and basal ganglia loop do influence the motor control of the body... they are not upper motor neurons. Upper motor neuron is specific to the corticospianl tract, it is the neuron going from cortex to anterior horn of spinal cord. Basal ganglia does influence the motor cortex but it isn't part of the corticospinal tract, hence not an upper motor neuron lesion.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;3)&#xA;Role of muscle spindles in spasticity from upper motor neuron lesions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am using this website for this part of my answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.d.umn.edu&quot; rel=&quot;nofollow&quot;&gt;http://www.d.umn.edu&lt;/a&gt;&#xA;it's from university of minnisota, which is funny because their acronym is UMN&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;high resistance to stretch occurs when the spindles are overactive&#xA;  (usually due to high rate of gamma motor neuron discharge) --&gt;&#xA;  HYPERTONIC (SPASTIC) &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;removing inhibitory inputs to the gamma motor&#xA;  neurons increases their discharge rate, and increases spindle output&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;this can happen when there is an UPPER MOTOR NEURON lesion&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It seems that with an upper motor neuron lesion, the gamma motor neuron is uninhibited, thus the gamma fibers have a constitutively increased discharge rate and muscle spindles are overactive. The machanoreceptors in the spindles then decrease their afferent sign, which should lead to relaxation of a/g-motor neurons, and well, I dunno, I am thoroughly confused on the precise mechanism of UMN lesion causing spasticity. Reflexes are intact so the a/g-motor neurons should relax, since only UMN damaged and not any part of the reflex arc. I seem to be missing something here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm calling for back up, someone please help!&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2015-01-26T17:07:29.153" LastActivityDate="2015-01-26T17:07:29.153" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28037" PostTypeId="2" ParentId="28025" CreationDate="2015-01-26T00:36:55.000" Score="2" Body="&lt;p&gt;I think you are right and many examples are ambiguous.  Even D) is ambiguous as a molecule is always in motion due to entropy except, perhaps, at absolute zero (0 Kelvin). But normally, it does contain kinetic energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, as you already identified the ambiguity, look at the &lt;em&gt;best&lt;/em&gt;, or in this case &lt;em&gt;least incorrect&lt;/em&gt; answer; The only option without any physical movement explicitly mentioned in the question description is D). All the others mention 'emit', 'flight', 'rushing down', etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also ask your teacher :)&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-26T00:49:41.400" LastActivityDate="2015-01-26T00:49:41.400" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28038" PostTypeId="1" CreationDate="2015-01-26T02:08:52.273" Score="2" ViewCount="643" Body="&lt;p&gt;Have there been any experiments that have kept neurons alive (stationary), without preserving methods such as freezing? If yes, then how long were the cells kept alive for? &lt;/p&gt;&#xA;" OwnerUserId="13179" LastEditorUserId="16651" LastEditDate="2015-11-18T01:51:00.913" LastActivityDate="2015-11-18T01:51:00.913" Title="How long can a human neuron live outside the body in a controlled environment?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;lab-techniques&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28039" PostTypeId="1" AcceptedAnswerId="28049" CreationDate="2015-01-26T03:39:16.247" Score="6" ViewCount="667" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6lnvp.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does predation surge with mass extinction? It is caused by extreme selective pressures over resource competition that forces certain species to adapt to predatory niches?&lt;/p&gt;&#xA;" OwnerUserId="10132" LastEditorUserId="3624" LastEditDate="2015-02-05T10:24:02.690" LastActivityDate="2015-02-05T10:24:02.690" Title="Why do the proportion of predators increase at mass extinction events?" Tags="&lt;evolution&gt;&lt;ecology&gt;&lt;palaeontology&gt;&lt;extinction&gt;&lt;predation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28040" PostTypeId="2" ParentId="28022" CreationDate="2015-01-26T03:40:00.170" Score="-2" Body="&lt;p&gt;Evolution increases complexity (entropy)&#xA;e.g., developing a new citrate path way in &lt;a href=&quot;http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment#Evolution_of_aerobic_citrate_usage_in_one_population&quot; rel=&quot;nofollow&quot;&gt;E. coli&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It does this process by of expending energy.&#xA;i.e., via lifeforms's metabolism &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to answer your question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A,B,C are all correct (or part of a correct answer) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However D is the most correct answer (It is an all of the above type answer)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E is a none of the above answer (and most incorrect)&lt;/p&gt;&#xA;" OwnerUserId="13203" LastEditorUserId="13203" LastEditDate="2015-01-27T19:16:29.823" LastActivityDate="2015-01-27T19:16:29.823" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28041" PostTypeId="2" ParentId="28022" CreationDate="2015-01-26T05:14:25.107" Score="3" Body="&lt;p&gt;I would say A or D are acceptable, but A is probably the better answer: firstly, the entropy of the planet system alone is probably not increasing (indeed, it's probably near to constant) and as noted elsewhere, you need to consider a closed system to apply the Second Law, so you need to think about everything that &lt;em&gt;comes to&lt;/em&gt; and &lt;em&gt;leaves&lt;/em&gt; the Earth. This is the key to understanding why life on Earth doesn't violate the second law: Earth absorbs and re-radiates roughly the same amount of light, but that light's state is radically changed as this happens, and this state change and the huge entropy increase it brings about overwhelmingly offsets the decrease in Earth's organisms' entropy as they build themselve whilst making use of that light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's look at the radiation balance in more detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thermodynamic entropy of a system is basically the system's &lt;a href=&quot;http://en.wikipedia.org/wiki/Conditional_entropy&quot; rel=&quot;nofollow&quot;&gt;conditional information content&lt;/a&gt; (also known evocatively as &lt;em&gt;equivocation&lt;/em&gt; in information theoretic circles) conditioned on the given macroscopic properties of a system. It's the logarithm of the number of ways a system's internal microstates can be arranged consistent with the observed outward properties. A simple explanation of the logarithm is that when you add two systems together, the number of ways that they can be arranged multiplies (think of two car number plate letters: one letter yields 26 different number plates, two letters $26^2$ number plates, three letters $26^3$ number plates, three letters and two digits yields $26^3\times 10^2$ number plates and so forth). So the entropies add when the possibilities multiply.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The entropy of a system of identical particles is proportional to the number of particles in that system. Think of each particle as like a letter in an alphabet of its states and then think of long &quot;number plates&quot; of concatenated particle states.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So now: let's look at the input to the Earth: around about $1{\rm kg}$ of energy in the form of sunlight per second is available to Earth systems to do work. It comes as $\frac{c^2}{h\,\nu}$ photons per second, where $\lambda = \frac{c}{\nu}$ is of the order of 500nm so $\nu\approx600{\rm THz}$. That is, about $2\times 10^{35}$ photons per second. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The energy &lt;em&gt;output&lt;/em&gt; of the Earth is basically infrared heat: it's the same amount of energy as comes in, but it is now composed of many more photons, because now $\nu$ in the photon number $\frac{c^2}{h\,\nu}$ is of the order of $30{\rm THz}$ (corresponding to $\lambda=10{\rm \mu\,m}$). The Earth therefore radiates roughly twenty times more photons than it absorbs: about $4\times 10^{36}$ photons per second. Each photon can encode the same amount of information, so the entropy increase is roughly &lt;em&gt;twentyfold&lt;/em&gt;. Life systems on Earth use about one thousandth of the incident Solar energy: it has been estimated that photosynthesis fixes energy for use by life systems at the rate of about $100{\rm TW}=10^{14}{\rm J\,s^{-1}}$, compared with an input of $1{\rm kg\,s^{-1}}\approx 10^{17}{\rm J\,s^{-1}}$. So, no matter how complex life organisms get, this barely makes a dint on the massive entropy &quot;production&quot; of the total Earth energy cycle: the nett production of entropy by the whole Earth system is still strongly positive notwithstanding the presence and evolution of life, and therefore in keeping with the Second Law.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An interesting calculation has been done on how much Solar energy is needed to evolve life on Earth to the present day. This is presented in the paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://arxiv.org/abs/0903.4603&quot; rel=&quot;nofollow&quot;&gt;Emory F. Bunn, &quot;Evolution and the second law of thermodynamics&quot;, Accepted for Publication Amer. J Phys.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bunn calculates that &lt;em&gt;less than a year&lt;/em&gt; of sunlight would be enough to power the evolution of &lt;em&gt;all&lt;/em&gt; life on Earth over the last four billion years and still be in keeping with the Second Law.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I should cite where I first saw this idea for explaining the life versus second law problem: I took this line of argument from:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0679776311&quot; rel=&quot;nofollow&quot;&gt;Roger Penrose, &quot;The Road To Reality: A Complete Guide to the Laws of the Universe&quot;, 2004 Chapter 27, &quot;The Big Bang and its Thermodynamic Legacy&quot;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;but I have heard it used in several lay explanations of physics since.&lt;/p&gt;&#xA;" OwnerUserId="5084" LastEditorUserId="5084" LastEditDate="2015-01-26T06:06:16.640" LastActivityDate="2015-01-26T06:06:16.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28042" PostTypeId="1" CreationDate="2015-01-26T07:16:56.243" Score="5" ViewCount="7833" Body="&lt;p&gt;Descendant of n generation has on average 1/2&lt;sup&gt;n&lt;/sup&gt; DNA of ancestor. (For example children have 1/2 DNA of parents and 1/4 DNA of Grandparents, After 10 Generation 1/1024 DNA and after 100 Generations 1/2&lt;sup&gt;100&lt;/sup&gt; DNA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a point (value of n) when descendant is no more related to ancestor and is similarly related to random individual from an ancestral population.&lt;/p&gt;&#xA;" OwnerUserId="11639" LastEditorUserId="13219" LastEditDate="2015-01-27T15:48:08.007" LastActivityDate="2017-01-24T15:12:04.133" Title="After how many generations descendant is not more related to ancestor, than to a random individual in an ancestral population?" Tags="&lt;genetics&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28043" PostTypeId="2" ParentId="28022" CreationDate="2015-01-26T08:02:15.960" Score="1" Body="&lt;p&gt;My 2 pennies on this &lt;em&gt;discussion&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Entropy in general is the total number of states a system can occupy which is also called degrees of freedom (so is with the supply of heat, the molecules vibrate and can occupy more states). Any system tries to avoid confinement and maximize the number of states it can occupy. However if the system is in a stable state and any movement would cost it energy, then it would remain in the present state at the cost of reduced degree of freedom. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This relationship is described by this equation: &lt;strong&gt;ΔG = ΔH -TΔS&lt;/strong&gt; &lt;br&gt;Where &lt;strong&gt;ΔG&lt;/strong&gt; is change in the Gibbs free energy, &lt;strong&gt;ΔH&lt;/strong&gt; is change in enthalpy, &lt;strong&gt;ΔS&lt;/strong&gt; is change in entropy and &lt;strong&gt;T&lt;/strong&gt; is the temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though the process of natural selection destroys the number of phenotypic states that life can occupy, thereby causing a decrease in entropy, there are other processes which lead to gain in entropy (for example population growth and migration). Note that the process of reproduction itself creates order from disordered molecules, but as the population expands and spreads entropy is again maximized. As already pointed out by bobc, catabolic processes which fuel life processes increase entropy but anabolic processes do the opposite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my opinion is that the process of &lt;strong&gt;Natural Selection&lt;/strong&gt; reduces entropy, so is the formaton of the eukaryotic cell. A free living bacteria has more freedom than a cell-locked mitochondria. However there are other energetic benefits that balance this reduction of entropy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For earth I would &lt;em&gt;guess&lt;/em&gt; that the overall entropy has reduced because the earth has cooled down since its birth. Since heat is removed entropy has reduced. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no violation of the second law in any of these cases. It is a universal law. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-01-26T08:02:15.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28044" PostTypeId="2" ParentId="28025" CreationDate="2015-01-26T08:13:12.273" Score="2" Body="&lt;p&gt;Going by the answer, the key to interpret this question seems to be the &lt;strong&gt;absence of kinetic energy&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Total Energy (mechanical) = Potential + Kinetic (let's ignore the pressure component as this question does not involve it).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the key to answer this question would be a system where the full energy is represented by the Potential energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a contracting muscle - let's consider gross dynamics - the muscle is in motion (the myofibrils are moving) ~ Kinetic Energy&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Water moving in a falls - Definitely kinetic energy (In fact this system is one where the potential energy is constantly decreasing while the kinetic energy is increasing constantly)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bioluminescence - Light Energy which is neither kinetic nor potential (as I understand physics, so correct me if I am wrong)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glucose as a source of energy - In its unutilised state (only during which it is called glucose) is purely potential energy. When glucose is talked in terms of potential energy, the movement of glucose inside a medium is not what is being talked about.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-01-26T08:13:12.273" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28045" PostTypeId="1" CreationDate="2015-01-26T08:16:22.507" Score="7" ViewCount="381" Body="&lt;p&gt;This question is not to discuss whether substances that have anti-&lt;em&gt;H. pylori&lt;/em&gt; activity work or not, or to discuss the pros and cons of such but from a medical perspective.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that one is able to control, reduce, or eliminate &lt;em&gt;H. pylori&lt;/em&gt; via foods containing natural anti-bacterial activity targeted at &lt;em&gt;H. pylori&lt;/em&gt; without the consumption of antibiotics, what is the possibility of reinfection or an overgrowth with &lt;em&gt;H. pylori&lt;/em&gt;?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In this study, the bactericidal activity of Korean and Japanese wasabi roots, stems and leaves against Helicobacter pylori were examined... All parts of wasabi showed bactericidal activities against H. pylori strain NCTC 11637, YS 27 and YS 50. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My questions are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;If this method was carried out &lt;em&gt;in vivo&lt;/em&gt; and the results were found to be consistent with the research mentioned above, what is the chance of developing resistance to &lt;em&gt;H. pylori&lt;/em&gt;?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Will developing resistance prevent recolonization of the stomach lining with &lt;em&gt;H. pylori&lt;/em&gt;?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15246236&quot; rel=&quot;nofollow&quot;&gt;Bactericidal activity of wasabi (Wasabia japonica) against Helicobacter pylori&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9748" LastEditorUserId="16299" LastEditDate="2016-01-01T01:30:11.517" LastActivityDate="2017-04-07T21:57:15.780" Title="Can Helicobacter pylori be eradicated naturally?" Tags="&lt;immunology&gt;&lt;bacteriology&gt;&lt;antibiotics&gt;&lt;gastroenterology&gt;" AnswerCount="3" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="28046" PostTypeId="1" CreationDate="2015-01-26T08:37:05.417" Score="5" ViewCount="4533" Body="&lt;p&gt;Following &lt;a href=&quot;https://biology.stackexchange.com/questions/7019/what-nutrients-can-humans-absorb-in-the-mouth&quot;&gt;this question&lt;/a&gt; regarding absorption in human &lt;em&gt;oral cavity&lt;/em&gt; (sadly not yet fully answered), I'm curious if any nutrient absorption occurs during the descent of food through the &lt;em&gt;esophagus&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if so, what requirements must a nutrient meet for that.&lt;/p&gt;&#xA;" OwnerUserId="13206" LastEditorUserId="9943" LastEditDate="2015-01-26T12:41:13.580" LastActivityDate="2016-09-12T20:05:19.920" Title="Are nutrients absorbed in human esophagus?" Tags="&lt;human-biology&gt;&lt;food&gt;&lt;digestive-system&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28047" PostTypeId="1" AcceptedAnswerId="28051" CreationDate="2015-01-26T09:40:01.787" Score="10" ViewCount="885" Body="&lt;p&gt;This &lt;a href=&quot;http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CancerCellsInCulture.html&quot; rel=&quot;nofollow&quot;&gt;website on cultured cancer cells&lt;/a&gt; () says cancer cells &lt;em&gt;may be immortal&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering if there has been any research done to find if cancer cells are really immortal. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;How old is the still maintained living oldest culture of cancer cells?&lt;/li&gt;&#xA;&lt;li&gt;Has there been any research done on replicative senescence of Cancer Cells invitro?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Edit 1:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is some data relating to the number of replications the cells have undergone, it will be very useful&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="9943" LastEditDate="2015-05-25T12:50:13.290" LastActivityDate="2015-07-19T06:06:17.470" Title="Have there been studies done to test Immortality of cancer cells in culture?" Tags="&lt;cancer&gt;&lt;senescence&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28048" PostTypeId="1" CreationDate="2015-01-26T10:25:34.147" Score="4" ViewCount="1754" Body="&lt;p&gt;What are the differences between a benign tumor and an injury related swelling?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And can swellings due to injury turn into a benign tumor?&lt;/p&gt;&#xA;" OwnerUserId="13171" LastEditorUserId="9943" LastEditDate="2015-01-27T12:59:57.850" LastActivityDate="2015-01-29T13:20:22.673" Title="What are the differences between a benign tumor and swelling?" Tags="&lt;human-biology&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28049" PostTypeId="2" ParentId="28039" CreationDate="2015-01-26T10:32:34.557" Score="3" Body="&lt;p&gt;The data used in the graph you posted seems to be from &lt;a href=&quot;http://www.yale.edu/ypmip/predation/Chapter_12.pdf&quot; rel=&quot;nofollow&quot;&gt;Bambach. 2002. Supporting predators: changes in the global ecosystem inferred from changes in predator diversity&lt;/a&gt; (in &lt;a href=&quot;http://www.museumoftheearth.org/publications/pubdetails.php?pubID=526&amp;amp;back=catID%3D81%26page%3D2%26buy%3D2&quot; rel=&quot;nofollow&quot;&gt;Kowalewski &amp;amp; Kelley. The Fossil Record of Predation&lt;/a&gt;) - see fig 19b - and, if so, is specifically dealing with marine predators.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't have time to look at that paper closely (it is quite long), and paleoecology is not my field, but a couple of relevant sections are:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;However, the diversity of predators and the proportion&#xA;  of total faunal diversity composed of predators have both increased over time, implying that ecosystems have&#xA;  increased their ability to support either more predators or more specialization among predators. Also, turnover&#xA;  in diversity dominance among predator groups, with more energetic predator taxa replacing or being added to a&#xA;  fauna of less energetic groups, implies that the energy available in marine food webs has increased. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If&#xA;  the efficiency of energy transfer between levels in&#xA;  the food pyramid has stayed nearly constant (and&#xA;  there is no evidence that it has not), then a reasonable&#xA;  hypothesis for the increased proportional diversity&#xA;  of predators is that either the biomass of prey species&#xA;  has increased or the populations of prey taxa have&#xA;  become more stable (or both), permitting greater&#xA;  specialization by predators on more reliable food&#xA;  supplies. Thus, predators could increase their&#xA;  proportional share of total diversity by specializing&#xA;  on fewer prey taxa.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So according to the author, energetics, energy flow and predator specialization seems like likely reasons for the change. However, the paper also discuss factors such as rates of fossilization and also the fact that predators are generally rarer than prey means that there is probably more stochasticity in the fossil occurence process, which could affect estimated turnover rates and maybe also the proportion between predator and prey. You'll have to look at the entire paper for a fuller picture, and maybe somebody more knowledgeable can fill in later. I also think that you need to look at radiation patterns in certain taxa to fully understand these stepwise changes, and also to consider oxygenetion events as possible underlying reasons, but these are just my speculations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reasons given above also in one sense echoes the &quot;&lt;em&gt;biotic&lt;/em&gt;&quot; explanation for the latitudunal diversity gradient (see e.g. &lt;a href=&quot;http://www.nature.com/nature/journal/v405/n6783/full/405220a0.html&quot; rel=&quot;nofollow&quot; title=&quot;Gaston. 2000. Global patterns in biodiversity. Nature 405: 220-227&quot;&gt;Gaston, 2000&lt;/a&gt; and &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2007.01020.x/abstract&quot; rel=&quot;nofollow&quot; title=&quot;Mittelbach et al. 2007. Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecology letters 10(4): 315–331&quot;&gt;Mittelbach et al, 2007&lt;/a&gt;), where high levels of primary production can support more specialized predators/parasites in more complex food webs, then leading to higher species diversity. So there might be interesting connections to contemporary patterns and processes of biodiversity as well. However, I haven't seen a compilation of %predators over different biomes or latitudes to match the graph in the question. Also, the &quot;&lt;em&gt;biotic&lt;/em&gt;&quot; explanation for the latitudunal diversity gradient has been criticized and is not without problems (see papers above for more).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-01-26T11:43:52.937" LastActivityDate="2015-01-26T11:43:52.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28051" PostTypeId="2" ParentId="28047" CreationDate="2015-01-26T10:49:13.313" Score="15" Body="&lt;p&gt;The HeLa cell line is undoubtedly the most used and investigated &lt;strong&gt;human&lt;/strong&gt;  immortal tumor cell line. Extracted from a cervical tumor from Henrietta Lacks in 1951 at Johns Hopkins hospital, Baltimore, MD these cells proved immortal and are still used in many, many labs worldwide today. It is the oldest human cell line in use and, therefore, the &lt;strong&gt;oldest human tumor cell line&lt;/strong&gt; &lt;a href=&quot;http://www.nature.com/news/deal-done-over-hela-cell-line-1.13511&quot; rel=&quot;nofollow&quot;&gt;(Callaway, 2013)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of &lt;strong&gt;senescence&lt;/strong&gt; of immortal cells; HeLa cells are immortal, and hence do not grow old as such. However, they are subject to mutations and the &lt;strong&gt;genetic profile of HeLa cells does change over time&lt;/strong&gt;. Hence, although they may not be growing old, they do age in the sense that mutations are accumulating in continuous cell lines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.nature.com/news/deal-done-over-hela-cell-line-1.13511&quot; rel=&quot;nofollow&quot;&gt;Callaway, &lt;em&gt;Nature&lt;/em&gt; (2013); &lt;strong&gt;500&lt;/strong&gt;: 132-3&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-25T12:47:55.053" LastActivityDate="2015-05-25T12:47:55.053" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="28055" PostTypeId="1" AcceptedAnswerId="28125" CreationDate="2015-01-26T13:40:39.060" Score="1" ViewCount="252" Body="&lt;p&gt;The wikipedia article on &lt;a href=&quot;https://en.wikipedia.org/wiki/Canine_transmissible_venereal_tumor&quot; rel=&quot;nofollow&quot;&gt;CTVT&lt;/a&gt; says that the tumor cell has 57-64 chromosome while a normal dog has 78 chromosomes. Similarly while all chromosomes in dogs except the X and Y chromosomes are acrocentric, many of the CTVT chromosomes are sub-metacentric or metacentric. Reference is given for the data in Wikipedia though a subscription is needed to view the referred articles themselves, so I was unable to confirm the data. (Wikipedia is sufficient for me, though popular opinion seem otherwise)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition there seems to be numerous (in the order of thousands) differences in sequences. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Their study showed that the cancer cells all originated from a common ancestor cell, not from the dogs themselves. Comparisons of the cancer DNA with dog DNA from reference samples held by the US Kennel Club and Crufts showed that it most likely originated at least 250 years ago from a wolf or an &quot;old&quot; Asian dog breed such as a husky or Shih Tzu, and spread like wildfire thereafter.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This was taken from &lt;a href=&quot;http://www.newscientist.com/article/dn9713#.VMZB9TXT7MI&quot; rel=&quot;nofollow&quot;&gt;Riddle of Infectious Dog Cancer Solved&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;How is the conclusion arrived at in cases like this in general? What percentage / degree of genetic similarity is needed to identify something as belonging to a specific species?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How was the conclusion arrived at in this specific case? (I know I am greedy!)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-01-28T23:59:00.123" Title="How was the origin of CTVT parasitic cancer determined?" Tags="&lt;genetics&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28056" PostTypeId="2" ParentId="23170" CreationDate="2015-01-26T14:02:34.443" Score="1" Body="&lt;p&gt;The most important features are the eyes, followed by the nose and mouth, respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An elaborate answer can be found on the duplicate question on Cognitive Sciences SE:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://cogsci.stackexchange.com/questions/8393/are-some-facial-features-more-important-than-others-in-human-facial-recognition/8906#8906&quot;&gt;Are some facial features more important than others in human facial recognition?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:56:15.910" LastActivityDate="2015-03-26T23:34:02.803" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28057" PostTypeId="2" ParentId="26347" CreationDate="2015-01-26T14:23:44.143" Score="1" Body="&lt;p&gt;Electrophysiology on plant cells means single-cell recordings, as there are no gross compound action potentials.  As you correctly say, this means &lt;strong&gt;micro-electrodes&lt;/strong&gt;; this in turn means &lt;strong&gt;computerized manipulation of the pipettes&lt;/strong&gt;, a decent &lt;strong&gt;microscope&lt;/strong&gt;, &lt;strong&gt;signal amplifier&lt;/strong&gt;, &lt;strong&gt;recording software&lt;/strong&gt;, &lt;strong&gt;stimulator slash voltage/current control&lt;/strong&gt;, &lt;strong&gt;Faraday cage&lt;/strong&gt;, &lt;strong&gt;analysis software&lt;/strong&gt; (Matlab), and not unimportantly a &lt;strong&gt;vibration-free workbench&lt;/strong&gt; (whole departments have moved house due to micrometer vibrations in the building). I guess you should think anywhere between 10k - 100k (dollars, euros whatever) as a reasonable estimate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A student internship would be advisable finance-wise, but especially because single cell recordings, and electrophysiological skills in general, are relatively difficult to master.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-01-26T14:23:44.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28059" PostTypeId="1" CreationDate="2015-01-26T15:44:18.133" Score="3" ViewCount="745" Body="&lt;p&gt;Why is excess glucose, synthesized to glycogen, stored only in limited amounts, as compared with lipids/triglycerides that are stored in our body? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is mature glycogen arranged (polymerized) in 12 tiers polymer?&lt;/p&gt;&#xA;" OwnerUserId="13213" LastEditorUserId="16651" LastEditDate="2015-12-26T23:17:59.143" LastActivityDate="2015-12-26T23:17:59.143" Title="Conversion and storage of glucose to glycogen" Tags="&lt;biochemistry&gt;&lt;metabolism&gt;&lt;glucose&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28062" PostTypeId="2" ParentId="28059" CreationDate="2015-01-26T16:15:44.667" Score="0" Body="&lt;p&gt;In &lt;a href=&quot;http://cmgm.stanford.edu/biochem200/glycogen/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; presentation from stanford.edu, it's stated that the number of granules is directly dependent on the number of glycogenin molecules available, and the size of the granule is directly dependent on the need for physical association b/t the glycogen synthase, and glycogenin.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-01-26T16:15:44.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28063" PostTypeId="1" CreationDate="2015-01-26T17:07:37.730" Score="6" ViewCount="101" Body="&lt;p&gt;&lt;a href=&quot;https://english.stackexchange.com/questions/222304/plural-of-dibamus#comment473277_222304&quot;&gt;&lt;em&gt;Migrated from English site.&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dibamus&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Dibamus&lt;/em&gt;&lt;/a&gt; is a genus of legless lizards in the family &lt;em&gt;Dibamidae&lt;/em&gt;, of the infraorder &lt;em&gt;Dibamia&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genera are usually given in singular, so what is the correct plural of &lt;em&gt;Dibamus&lt;/em&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Families and orders are usually given in plural, so what are the correct singulars of &lt;em&gt;Dibamidae&lt;/em&gt; and &lt;em&gt;Dibamia&lt;/em&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bonus question: What is the etymology of the root &lt;em&gt;dibam-&lt;/em&gt;?&lt;/p&gt;&#xA;" OwnerUserId="13215" LastEditorUserId="16866" LastEditDate="2017-04-26T19:15:27.983" LastActivityDate="2017-04-26T19:15:27.983" Title="Plural of &quot;dibamus&quot;" Tags="&lt;species-identification&gt;&lt;nomenclature&gt;&lt;species&gt;&lt;reptile&gt;&lt;etymology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28064" PostTypeId="2" ParentId="28046" CreationDate="2015-01-26T17:24:28.983" Score="7" Body="&lt;p&gt;For several reasons, I seriously doubt that this has been studied extensively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a good reason to study absorption through oral mucosa because a drug or glucose can be held there by people who needing rapid absorption of a drug (e.g. sublingual nitroglycerine) or by people who may be unable to swallow (e.g. a hypoglycemic individual who has lost consciousness). Where there is a reason to know, there is a reason to study something.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The esophagus, on the other hand, is normally an area of rapid transport (a pill, or a fluid, for instance, is in the esophagus less than 10 seconds). While it's assumed that some pregastric absorption through the esophagus occurs and might be beneficial to avoid a &quot;first pass&quot; metabolism of the drug by the liver, there is no good method to keep a drug in the esophagus. With that in mind, absorption from the sublingual mucosa (where a pill might be held) is more valuable than what might get absorbed in as little as 6 seconds in transit to the stomach. From that point, it will spend significant amounts of time in the stomach, the various sections of the small intestine, and the large intestine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Absorption of drugs from the rectum has been studied, because it can be used, once again, as a method of drug delivery when another route for whatever reason cannot,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Esophageal motility disorders occur, so studies of esophageal function are common. But as the esophagus is &lt;em&gt;never&lt;/em&gt; normally the place for absorption of nutrients, there is no reason to study it except for the sake of satisfying pure curiosity. Studies take time, involve volunteers (or paid recipients), risk, and money. Pure curiosity &lt;em&gt;is&lt;/em&gt; a reason to study something. But to get the all the previously mentioned factors to come together and fund a study, the &lt;em&gt;reason&lt;/em&gt; usually outweighs pure curiosity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://europepmc.org/abstract/MED/1334135&quot;&gt;Esophageal scintigraphy: reproducibility and normal ranges&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1475-097X.1983.tb00700.x/abstract&quot;&gt;Oesophageal transit of a radionuclide solid bolus in normals&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://bja.oxfordjournals.org/content/56/1/69.extract&quot;&gt;DRUG ABSORPTION BY SUBLINGUAL AND RECTAL ROUTES&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-01-26T17:44:16.720" LastActivityDate="2015-01-26T17:44:16.720" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="28065" PostTypeId="2" ParentId="28063" CreationDate="2015-01-26T17:30:44.537" Score="2" Body="&lt;p&gt;This is &lt;a href=&quot;http://www.sarracenia.com/faq/faq5010.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;advice from a website on plants&lt;/a&gt;, but its advice is equally valid for plants or animals.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;For example, if you wish to discuss several Pinguicula species, do you&#xA;call them Pinguiculae or Pinguiculas? &lt;strong&gt;The answer is that you can do&#xA;neither!&lt;/strong&gt; Pinguicula is the name of the genus, a single group of plants&#xA;which was very carefully named. If you make up a word like&#xA;Pinguiculas, you are either implying that the genus has a letter &amp;quot;s&amp;quot;&#xA;at the end (which it does not), or you are saying that there is more&#xA;than one genus with the name Pinguicula---a logical absurdity.&lt;/p&gt;&#xA;&lt;p&gt;So it is just wrong&#xA;to fabricate a plural form of a genus name. If you find yourself&#xA;writing a sentence where you want to create a plural form of a genus&#xA;(suppose you wanted to say, &amp;quot;I saw several Pinguiculas&amp;quot;), reconstruct&#xA;the sentence slightly into something like &amp;quot;I saw many Pinguicula&#xA;plants&amp;quot; or &amp;quot;I saw many Pinguicula species,&amp;quot; whichever you meant. It is&#xA;not only correct, but also much clearer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;There is a caveat to this, which is when the genus is borrowed into English as a loanword, for example, a plant of the genus &lt;em&gt;Delphinium&lt;/em&gt; has the common English name &amp;quot;delphinium&amp;quot;, or an ape of the genus &lt;em&gt;Gorilla&lt;/em&gt; has the common English name &amp;quot;gorilla&amp;quot;. In this case, the English word is pluralised into &amp;quot;delphiniums&amp;quot; and &amp;quot;gorillas&amp;quot;. Note that it is still perfectly correct to say &amp;quot;I saw two apes belonging to the genus &lt;em&gt;Gorilla&lt;/em&gt;&amp;quot;, but it is just long-winded.&lt;/p&gt;&#xA;&lt;p&gt;In your case, the lizard does not fall into this category, so you should word your phrase as &amp;quot;several &lt;em&gt;Dibamus&lt;/em&gt; lizards&amp;quot; or a similar alternative phrasing.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-01-26T17:36:51.367" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28066" PostTypeId="1" AcceptedAnswerId="28067" CreationDate="2015-01-26T17:52:59.923" Score="6" ViewCount="2312" Body="&lt;p&gt;Many organisms have their common names identical to their scientific names. For example, there exist apes of the genus &lt;em&gt;Gorilla&lt;/em&gt; known commonly as gorillas, and plants of the genus &lt;em&gt;Delphinium&lt;/em&gt; known as delphiniums. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, are there any examples of the common name of an organism overlapping with the scientific name of another organism, therefore causing ambiguity when the organism's name is spoken aloud? If written with correct formatting, this should not cause a problem in any case, due to the formatting specifically describing a genus/species. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2019-07-13T13:30:36.527" Title="Is there an organism which has a common English name which overlaps with another organism's scientific name (or vice versa?)" Tags="&lt;nomenclature&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28067" PostTypeId="2" ParentId="28066" CreationDate="2015-01-26T18:09:51.827" Score="13" Body="&lt;p&gt;One great example I know of is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Platypus&quot;&gt;duck-billed platypus&lt;/a&gt; (&lt;em&gt;Ornithorhynchus anatinus&lt;/em&gt;),  often simply called a platypus, which shares its name with the &lt;a href=&quot;http://en.wikipedia.org/wiki/Platypus_(weevil)&quot;&gt;&lt;em&gt;Platypus&lt;/em&gt; genus&lt;/a&gt; of ambrosia beetle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia gives a brief history of the taxonomy of the duck-billed platypus:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The common name &quot;platypus&quot; is the latinisation of the Greek word πλατύπους (&lt;em&gt;platupous&lt;/em&gt;), &quot;flat-footed&quot;, from πλατύς (&lt;em&gt;platus&lt;/em&gt;), &quot;broad, wide, flat&quot; and πούς (&lt;em&gt;pous&lt;/em&gt;), &quot;foot&quot;. Shaw assigned it as a Linnaean genus name when he initially described it, but the term was quickly discovered to belong already to the wood-boring ambrosia beetle genus &lt;em&gt;Platypus&lt;/em&gt;. It was independently described as &lt;em&gt;Ornithorhynchus paradoxus&lt;/em&gt; by Johann Blumenbach in 1800 (from a specimen given to him by Sir Joseph Banks) and following the rules of priority of nomenclature, it was later officially recognised as &lt;em&gt;Ornithorhynchus anatinus&lt;/em&gt;. The scientific name &lt;em&gt;Ornithorhynchus anatinus&lt;/em&gt; is derived from ορνιθόρυνχος (&lt;em&gt;ornithorhynkhos&lt;/em&gt;), which literally means &quot;bird snout&quot; in Greek; and &lt;em&gt;anatinus&lt;/em&gt;, which means &quot;duck-like&quot; in Latin.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6703" LastEditorUserId="6703" LastEditDate="2015-01-26T19:34:28.320" LastActivityDate="2015-01-26T19:34:28.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28070" PostTypeId="2" ParentId="28059" CreationDate="2015-01-26T22:12:17.423" Score="2" Body="&lt;p&gt;Glycogen storage limitation is due to these additional facts also: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Glycogen is a hydrophilic molecule. This means an increase in glycogen concentration will cause a proportionate &lt;a href=&quot;http://www.humankinetics.com/excerpts/excerpts/the-bodyrsquos-fuel-sourcesin&quot; rel=&quot;nofollow&quot;&gt;increase&lt;/a&gt; cell weight due to water accumulation. As cells can contain only limited volume the amount of glycogen stores are limited. Lipids are hydrophobic hence can be accumulated without increasing the volume and weight of cell due to water accumulation. &lt;/li&gt;&#xA;&lt;li&gt;As a source of energy lipids are approximately 2.5 times more efficient than glucose. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-01-26T22:12:17.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28071" PostTypeId="2" ParentId="28025" CreationDate="2015-01-26T22:25:44.817" Score="1" Body="&lt;p&gt;You'll find the answer glucose best fits the definition of potential energy, as in it's standard state the glucose has all of it's energy stored in it's bonds (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21737/&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;). Every other answer is some sort of expenditure of energy (ATP in the case of firefly luciferase reaction, see (&lt;a href=&quot;http://www.piercenet.com/media/16174-Lucif-Firefly-rxn.jpg&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;)).&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-01-26T22:25:44.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28073" PostTypeId="2" ParentId="23549" CreationDate="2015-01-27T00:31:58.580" Score="2" Body="&lt;p&gt;The answers are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Yes, they know when to stop eating. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18316030&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Yes, &lt;a href=&quot;http://www.wormbook.org/chapters/www_obesity/obesity.html&quot; rel=&quot;nofollow&quot;&gt;they store extra energy as fat in the intestine&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;This one is a little more complicated. They can use extra energy, but not to move faster. Movement doesn't take much energy, and until they're close to death from starvation, they continue to move quite well. As for eggs, they do indeed slow down the rate of embryo production when nutrition is inadequate. But &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?Db=pubmed&amp;amp;Cmd=Retrieve&amp;amp;list_uids=11161565&amp;amp;dopt=abstractplus&quot; rel=&quot;nofollow&quot;&gt;the total number of eggs is limited by the supply of sperm&lt;/a&gt;, so there is an upper limit on how many they can produce, even in unlimited food. Probably the main benefit of stored nutrients is to allow them to survive longer if the food runs out. They are very, very good at dealing with a variable food supply -- much better than you, for instance -- and they do it partly by storing up extra energy. &lt;a href=&quot;http://www.pnas.org/content/102/38/13496.full&quot; rel=&quot;nofollow&quot;&gt;This paper and references therein describe some starvation responses&lt;/a&gt;. You can also look up &lt;a href=&quot;http://www.genetics.org/content/194/3/539.full.pdf&quot; rel=&quot;nofollow&quot;&gt;L1 diapause&lt;/a&gt;, &lt;a href=&quot;http://www.wormbook.org/chapters/www_dauer/dauer.html&quot; rel=&quot;nofollow&quot;&gt;the dauer larva&lt;/a&gt;, and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19713489&quot; rel=&quot;nofollow&quot;&gt;adult reproductive diapause&lt;/a&gt;. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="13219" LastEditorUserId="13219" LastEditDate="2015-01-27T13:03:05.723" LastActivityDate="2015-01-27T13:03:05.723" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28074" PostTypeId="2" ParentId="8946" CreationDate="2015-01-27T02:30:58.663" Score="0" Body="&lt;p&gt;If you get a higher resolution and closer image, it would be a little easier, but from what I can make out, I have two suggestions. To me, it appears to be tiny yellow eggs grouped together which leads me to believe it could be &lt;a href=&quot;http://en.wikipedia.org/wiki/Large_milkweed_bug&quot; rel=&quot;nofollow noreferrer&quot;&gt;milkweed bug&lt;/a&gt; or a &lt;a href=&quot;http://en.wikipedia.org/wiki/Coccinellidae&quot; rel=&quot;nofollow noreferrer&quot;&gt;lady bug&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The eggs of the milkweed bug look like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0Eu9L.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The eggs of a lady bug look like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FCV4C.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since these pictures are of a much higher quality, it easy to tell the eggs apart and they have height. If I stumble across any more viable options, I will post them.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastActivityDate="2015-01-27T02:30:58.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28075" PostTypeId="1" AcceptedAnswerId="28077" CreationDate="2015-01-27T04:11:28.750" Score="3" ViewCount="62" Body="&lt;p&gt;I'm an engineer who is looking to build a robotic hand for people without their upper forearm(from center of forearm in direction of hand), controlled by the &lt;a href=&quot;https://www.thalmic.com/en/myo/&quot; rel=&quot;nofollow&quot;&gt;Thalmic Myo&lt;/a&gt;(an EMG sensor). I am first checking for the idea's viability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering if one who does not have their upper forearm can still send the correct nerve impulses for a desired hand movement through their Median and Ulnar nerves? &lt;/p&gt;&#xA;" OwnerUserId="13224" LastEditorUserId="9943" LastEditDate="2015-01-27T11:00:49.393" LastActivityDate="2015-01-27T11:00:49.393" Title="Can an upper forearm amputee correctly control the Median and Ulnar nerves" Tags="&lt;human-anatomy&gt;&lt;neuroanatomy&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28076" PostTypeId="1" CreationDate="2015-01-27T04:50:39.567" Score="3" ViewCount="139" Body="&lt;p&gt;In taxonomy the term 'congener' refers to two species within the same genus. In more colloquial usage, it can refer to any two objects within the same category. Is there a way to refer to related species that is not specific to a particular taxonomic rank--as in, in the same order or family but not necessarily the same genus?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update: I guess the term 'relative' works, but I still wonder if there's a better term.&lt;/p&gt;&#xA;" OwnerUserId="43" LastActivityDate="2015-01-27T04:50:39.567" Title="More general usage of the term 'congener'" Tags="&lt;terminology&gt;&lt;taxonomy&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28077" PostTypeId="2" ParentId="28075" CreationDate="2015-01-27T05:26:37.927" Score="2" Body="&lt;p&gt;&lt;strong&gt;Yes, severed nerves still convey neural responses from the brain&lt;/strong&gt;.                &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, nerve potential recordings in the ulnar and median nerves of the stumps of arm amputees have already been successfully applied to control arm prosthetics (Jia et al. 2007; Kuiken et al., 2007. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-27T08:41:14.323" LastActivityDate="2015-01-27T08:41:14.323" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28078" PostTypeId="1" AcceptedAnswerId="29958" CreationDate="2015-01-27T09:55:05.643" Score="7" ViewCount="1022" Body="&lt;p&gt;I am wondering how much total RNA could be extracted from a single &lt;em&gt;D. melanogaster&lt;/em&gt; brain.&#xA;I could not find this information from the literature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The closest hit was &lt;a href=&quot;http://genomebiology.com/2001/2/3/research/0008&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;, that claims that 16-21.9µg of total RNA can be extracted from 100 brains, which translates to at least 160ng for a single brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also found in the supplementary material of &lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822%2814%2901273-1&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; that 1µg of total RNA was extracted from 5-10 fly brains, which would also make &gt; 100ng for a single brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am asking the question because I am envisioning to perform RNA-seq of single &lt;em&gt;Drosophila&lt;/em&gt; brains. The standard Illumina TruSeq library preparation protocol works with 100ng of total RNA. Thus I am wondering if this is realistic, or if I should rather target low input library preparation protocols.&lt;/p&gt;&#xA;" OwnerUserId="13226" LastEditorUserId="3340" LastEditDate="2015-02-26T06:37:39.120" LastActivityDate="2015-02-26T06:53:09.137" Title="How much total RNA can be extracted from Drosophila brain" Tags="&lt;brain&gt;&lt;rna&gt;&lt;rna-sequencing&gt;&lt;drosophila&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28080" PostTypeId="1" CreationDate="2015-01-27T10:42:39.837" Score="11" ViewCount="237" Body="&lt;p&gt;There are bacteria that can enter body cells as parasites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could it be that some of these are benign, such that the guest will not kill the host cell it lives in (&lt;strong&gt;especially in human&lt;/strong&gt;)?&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="10104" LastEditDate="2015-03-27T19:31:39.650" LastActivityDate="2015-04-18T10:09:28.573" Title="Non-harmful bacterial invasion of cells" Tags="&lt;microbiology&gt;" AnswerCount="3" CommentCount="15" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28081" PostTypeId="2" ParentId="28066" CreationDate="2015-01-27T10:54:19.527" Score="6" Body="&lt;p&gt;Plants known commonly as geraniums belong to the genus &lt;em&gt;Pelargonium&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, plants known commonly as cranesbills belong to the genus &lt;em&gt;Geranium&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="13229" LastEditorUserId="10456" LastEditDate="2015-01-27T11:29:51.897" LastActivityDate="2015-01-27T11:29:51.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28082" PostTypeId="2" ParentId="23623" CreationDate="2015-01-27T13:42:56.500" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Minimum_viable_population&quot; rel=&quot;nofollow&quot;&gt;Minimum viable population&lt;/a&gt; (MVP) can be &lt;a href=&quot;http://en.wikipedia.org/wiki/Minimum_viable_population#Estimation&quot; rel=&quot;nofollow&quot;&gt;predicted&lt;/a&gt; in two ways. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Computer simulations.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Population_viability_analysis&quot; rel=&quot;nofollow&quot;&gt;Population viability analyses&lt;/a&gt; (PVA)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;PVA is considered generally more common practice by ecologists and without a reference to the 1600 panda population you mention, my guess would be that this is what they did. PVAs work well for endangered species prediction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A typical example of PVA was carried out on an endangered species Fender's blue butterfly an endangered species (Schultz &lt;em&gt;et al.&lt;/em&gt;, 2003). However there is currently no scientific standard on how a PVA should be done.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Schultz, Cheryl B.; Hammond, Paul C. (October 2003). &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1523-1739.2003.02141.x/abstract&quot; rel=&quot;nofollow&quot;&gt;&quot;Using Population Viability Analysis to Develop Recovery Criteria for Endangered Insects: Case Study of the Fender's Blue Butterfly&quot;.&lt;/a&gt; Conservation Biology 17 (5): 1372–1385.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2015-11-30T16:20:26.527" LastActivityDate="2015-11-30T16:20:26.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28084" PostTypeId="1" AcceptedAnswerId="28086" CreationDate="2015-01-27T13:59:44.450" Score="8" ViewCount="1809" Body="&lt;p&gt;For the long time I am trying to find out if the following is truth: They say that some beverages dehydrates. I heard that about tea (sometimes green, sometimes black, sometimes both), coffee, beer and more (for example coke). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does hydration from these sorts of drinks compare to others (e.g. water)? Why do these drinks less efficiently hydrate?&lt;/p&gt;&#xA;" OwnerUserId="13230" LastEditorUserId="3553" LastEditDate="2016-07-09T03:40:47.823" LastActivityDate="2016-08-23T09:52:10.117" Title="How do tea, coffee, and beer dehydrate you?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;food&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28085" PostTypeId="2" ParentId="27975" CreationDate="2015-01-27T14:39:48.917" Score="2" Body="&lt;p&gt;Alberts et al, &lt;em&gt;Molecular Biology of the Cell&lt;/em&gt;, say that eukaryotic ribosomes add about 2 amino acids per second, and bacterial about 20 per second (5th edition, p 275). These should be taken only as ballpark estimates: the rate certainly will vary from species to species, from cell to cell, from protein to protein. Some cells (reticulocytes, for instance) are professional protein synthesizers. Others, for instance bacterial endospores, do almost no protein synthesis at all. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002755&quot; rel=&quot;nofollow&quot;&gt;These authors&lt;/a&gt; estimate the translation rate in mouse embryonic stem cells at around 5.5 amino acids/second. There is a lot of variation from gene to gene, even within this one cell type. They even see systematic variation depending on where you are in the gene. &lt;/p&gt;&#xA;" OwnerUserId="13219" LastEditorUserId="13219" LastEditDate="2015-01-27T14:53:37.993" LastActivityDate="2015-01-27T14:53:37.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28086" PostTypeId="2" ParentId="28084" CreationDate="2015-01-27T14:48:41.580" Score="8" Body="&lt;h1&gt;Diuretics&lt;/h1&gt;&#xA;&lt;p&gt;These drinks contain minor &lt;a href=&quot;http://en.wikipedia.org/wiki/Diuresis&quot; rel=&quot;nofollow noreferrer&quot;&gt;diuretics&lt;/a&gt;. Caffeine is the diuretic found in tea and coffee. Alcohol is the diuretic in beer. Diuretic substances increase the amount of urine produced i.e causes dehydration. This is often offset by the water content of mild diuretics like tea, coffee, and alcoholic drinks.&lt;/p&gt;&#xA;&lt;h1&gt;Tea, coffee, and coke&lt;/h1&gt;&#xA;&lt;p&gt;Caffeine belongs to the &lt;a href=&quot;https://en.wikipedia.org/wiki/Xanthine&quot; rel=&quot;nofollow noreferrer&quot;&gt;xanthines&lt;/a&gt;, and inhibits re-absorption of Na+ by cells, and increases flow rate of filtered fluid through the kidneys. This reduces water content in your body. In other words diuretics do dehydrate you, specifically caffeine will. Coffee, coke, and tea (very low doses of caffeine) are mild diuretics.&lt;/p&gt;&#xA;&lt;h1&gt;Beer&lt;/h1&gt;&#xA;&lt;p&gt;On the other hand &lt;a href=&quot;http://www.medicaldaily.com/science-breaking-seal-urge-urinate-comes-more-often-inhibition-anti-diuretic-hormone-316382&quot; rel=&quot;nofollow noreferrer&quot;&gt;alcohol is an anti-diuretic hormone inhibitor&lt;/a&gt; that inhibits arginine vasopressin.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2016-08-23T09:52:10.117" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="28087" PostTypeId="2" ParentId="28042" CreationDate="2015-01-27T15:18:27.167" Score="2" Body="&lt;p&gt;There is an interesting way to look at this question. By definition, two individuals are related only if they have a common ancestor. (If you mean something else by it, please correct me. For completeness, I include the trivial case in this: that is, I regard you as one of your own ancestors.) So your question can be inverted: it is really asking after how many generations &lt;strong&gt;everyone&lt;/strong&gt; in the ancestral population is your ancestor? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As indicated in the comments, the answer will depend on the specifics of the population structure, including its size. But a first stab can be taken in this way: you had 2 ancestors one generation back, 4 two generations back, ..., $2^n$ (not necessarily distinct) $n$ generations back. So you certainly cannot be descended from everyone in the ancestral population if less than $\log_2 N$ generations have passed. ($N$ = population size, which for simplicity I assume to be stable.) In a freely mixing population under the very simplest assumptions, you will eventually decay exponentially towards complete coverage with a half-time of one generation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is complicated by the fact that some lineages die out completely. For instance, some of the individuals in the ancestral population didn't have any children. Some had children, but no grandchildren, etc. Obviously none of them were your ancestors, so you will never be related to them (except through previous common ancestors), no matter how much time passes. In fact, as time passes, more lineages tend to die out. So, if you look back very far, you'll find that the entire current population has only a very small numbers of ancestors in the distant past. This is called coalescence, and is what people are talking about when they speak of &quot;mitochondrial Eve&quot;, for instance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in summary, it's complicated. It takes only a fairly small number of generations ($O(\log_2 N)$) before you're potentially related to most of the ancestral population. But over longer times ($O(N)$ generations) your relationship to the ancestral population actually goes down. &lt;/p&gt;&#xA;" OwnerUserId="13219" LastEditorUserId="13219" LastEditDate="2015-01-27T15:42:32.170" LastActivityDate="2015-01-27T15:42:32.170" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28088" PostTypeId="1" AcceptedAnswerId="28184" CreationDate="2015-01-27T15:33:36.300" Score="5" ViewCount="673" Body="&lt;p&gt;I'm simplifying things here:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;A.&lt;/strong&gt; Does a woman bleed &lt;strong&gt;constantly&lt;/strong&gt;, like a drop every 10 minutes? Two hours without pad or tampon and your underwear is dirty?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;or&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;B.&lt;/strong&gt; Does a woman bleed &lt;strong&gt;suddenly&lt;/strong&gt; a bigger amount of menstruation fluid? Then hours might pass before it happens again?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;or&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;C.&lt;/strong&gt; Both.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Might be a stupid question. I'm sorry. I read all the other information on the internet but no one answers this one for some reason. I read girls should change the pads and tampons a few times a day (like every 6 hours). Does that mean A is correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for any helpful information!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;(Well, I guess I'm male.)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt;&lt;br&gt;&#xA;What I want to know: If I was a woman, how would I experience the days of period bleedings? From what I read in the comments and answer(s), one should expect A (constant bleeding) and should wear pads/tampons all the time (for 2 to 7 days) and sometimes one could also experience an exceptional heavier bleeding (B)? Are there (healthy) women who would experience B most of the time? I visited Wikipedia and other random sites but they all have the other important information without answering my question. &lt;em&gt;(Also I will be glad to accept an answer, which satisfies my need for knowledge.)&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="13231" LastEditorUserId="13231" LastEditDate="2015-01-30T10:30:38.253" LastActivityDate="2019-07-15T12:07:31.440" Title="How does menstruation proceed during one period?" Tags="&lt;human-biology&gt;&lt;reproductive-biology&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28089" PostTypeId="1" CreationDate="2015-01-27T15:42:57.700" Score="1" ViewCount="171" Body="&lt;p&gt;How does a cell &quot;know&quot; the coding strand vs. the non-coding strand of DNA during transcription of mRNA?&lt;/p&gt;&#xA;" OwnerUserId="13232" LastActivityDate="2015-02-19T21:05:00.317" Title="mRNA Transcription from Nuclear DNA" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28090" PostTypeId="2" ParentId="28089" CreationDate="2015-01-27T15:48:57.177" Score="3" Body="&lt;p&gt;This is determined by the promoter -- the DNA sequence to which RNA polymerase binds. It's assymetric, and the polymerase binds in a specific orientation, that determines the strand and the direction it will go once elongation begins.  &lt;/p&gt;&#xA;" OwnerUserId="13219" LastEditorUserId="13219" LastEditDate="2015-01-27T16:05:36.913" LastActivityDate="2015-01-27T16:05:36.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28093" PostTypeId="1" CreationDate="2015-01-27T16:58:33.080" Score="2" ViewCount="389" Body="&lt;p&gt;Agrobacteria can deliver parts of their DNA to plant cells as T-DNA, transfer DNA. This DNA is delivered as a single strand and can be integrated into the plant genome or can be converted to a double stranded molecule by priming the T-DNA to make it a substrate for a DNA polymerase. &lt;a href=&quot;http://www.nature.com/ncomms/2013/130821/ncomms3253/full/ncomms3253.html&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; describes the process, but Nature makes getting to the article hard, sorry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm interested in is delivery of DNA to mammalian cells. I tried to find articles that used single stranded DNA in mammalian cells, but couldn't find much. Maybe I didn't spend enough time searching. I saw some suggestions that single stranded DNA could trigger apoptosis, or that single stranded DNA could be used to manipulate DNA repair mechanisms to cause integration into the genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, is there any way to deliver a single stranded DNA, and have it converted to a double stranded plasmid in situ? Would probably need an RNA or DNA primer, but I don't see why you couldn't pre-bind the primer and deliver the whole complex.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2017-11-14T00:22:26.160" Title="Transfect Mammalian Cells with Single Stranded DNA?" Tags="&lt;dna&gt;&lt;transformation&gt;&lt;transfection&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28094" PostTypeId="2" ParentId="28088" CreationDate="2015-01-27T17:30:25.633" Score="8" Body="&lt;p&gt;The answer is both. Different women experience menstruation differently depending on the levels of different hormones in their body, personal medical conditions, medications, on their age, and the activities they do in their lives. Bleeding is due to the sloughing off of the highly vascularized endometrial lining of uterus which is no longer receiving the appropriate levels of progesterone for its maintenance from the corpus luteum, in the absence of an implanted embryo in the uterus. You can imagine how different this common event would be if a woman was taking warfarin, had a bleeding or coagulation disorder, had polycystic ovarian syndrome, was a runner, or was a 13-year-old vs a 41-year-old. It varies!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Welt et al. Physiology of the Normal Menstrual Cycle. Last updated Feb 28, 2014. &lt;a href=&quot;http://www.uptodate.com/contents/physiology-of-the-normal-menstrual-cycle&quot;&gt;http://www.uptodate.com/contents/physiology-of-the-normal-menstrual-cycle&lt;/a&gt;. &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.womenshealth.gov/publications/our-publications/fact-sheet/menstruation.html&quot;&gt;http://www.womenshealth.gov/publications/our-publications/fact-sheet/menstruation.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11631" LastActivityDate="2015-01-27T17:30:25.633" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="28095" PostTypeId="1" AcceptedAnswerId="28096" CreationDate="2015-01-27T19:48:12.947" Score="-4" ViewCount="915" Body="&lt;p&gt;I'm becoming more interested in genetic engineering as I learn more about it, and it's becoming more and more apparent that there's very few resources on genetic engineering at home. A similar question was asked &lt;a href=&quot;https://biology.stackexchange.com/questions/19873/is-it-possible-to-genetically-modify-a-plant-at-home/19874#19874&quot;&gt;here&lt;/a&gt;, but the best answer linked to a failed indiegogo campaign. Is it feasible to genetically modify an organism without a laboratory setting? If so, what materials could be used to do this?&lt;/p&gt;&#xA;" OwnerUserId="13237" LastActivityDate="2015-01-28T01:22:08.007" Title="Can genetic engineering be performed without a laboratory setting?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;synthetic-biology&gt;&lt;diy-biology&gt;" AnswerCount="1" CommentCount="10" ClosedDate="2015-01-28T13:56:16.140" ContentLicense="CC BY-SA 3.0" />
  <row Id="28096" PostTypeId="2" ParentId="28095" CreationDate="2015-01-27T20:41:35.307" Score="-1" Body="&lt;p&gt;Thought I'd attempt to expand this into an answer, &lt;strong&gt;THOUGH THIS IS IN NO WAY MEANT TO SUGGEST YOU SHOULD ACTUALLY TRY THIS. THERE MAY BE LEGAL ISSUES INVOLVED IN CREATING A GENETICALLY MODIFIED ORGANISM, EVEN A HARMLESS ONE, DEPENDING ON YOUR LOCATION. SOME OF THE CHEMICALS REQUIRED TO HANDLE DNA ARE DANGEROUS, AND SHOULD ONLY BE HANDLED IN A FUME HOOD AND WITH PROPER PROTECTIVE EQUIPMENT. I &lt;em&gt;HIGHLY&lt;/em&gt; RECOMMEND THAT YOU DO NOT ATTEMPT THIS.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, you cannot do genetic engineering outside of a lab. You &lt;strong&gt;might&lt;/strong&gt; be able to set up a lab at home, but don't expect to do this using standard household chemicals. Lets assume you're only interested in adding DNA to bacteria, because that's &lt;strong&gt;relatively&lt;/strong&gt; simple.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first step you need to add DNA to bacteria is to get the DNA. Your major plasmid suppliers probably won't like selling to a non-lab, but if you're lucky you might get some from Invitrogen, Aldevron, or another supplier. If you know someone who works in a molecular biology lab, you might be able to get some from them, but that might violate rules with their university or employer. If possible, I'd get a green or red fluorescent protein gene, as those proteins are easy to detect using a UV lamp you might be able to build with UV LEDs, you might also be able to use a black light. Note that I do not know what promoter would be best to use on your gene. The lac operon is often used to express proteins in BL21 E. coli using the molecule IPTG as an inducer, but that requires you to have IPTG and BL21 bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Speaking of bacteria, you need competent bacteria. E. coli is the most often used species, but several strains are available. DH5a E. coli is most often used to grow up DNA plasmids, which is something you'll want to do because you probably won't be able to get much plasmid, so you have to make more or you'll run out. But DH5a usually isn't used to produce protein. BL21 E. coli is most often used to produce protein, but you'll probably need IPTG to induce the bacteria to make the protein. You might be able to get IPTG from Sigma Aldrich, but good luck getting them to sell anything to you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you have the bacteria, you'll need to grow them. You need bacterial media, which might be obtainable because it's relatively safe. LB media is a mixture of yeast extract, tryptone, and salt. If you want solid plates you'll need agar too. You can probably get the media sterile enough by boiling it. You'll need some ampicillin or kanamycin to make sure only bacteria with your desired gene is allowed to grow, again Sigma Aldrich &lt;strong&gt;might&lt;/strong&gt; sell it to you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course you can't just put DNA into bacteria, the bacteria must be competent. You can make chemically competent cells by carefully treating them with calcium chloride and magnesium chloride. You'll also need dry ice, these need to be kept very cold. So now you can add your plasmid your competent cells, heat shock them in water at precisely 37°C for precisely 60 seconds, and plate them on your agar media. Then you need to incubate them at 37°C overnight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you need to purify the DNA plasmid back from the bacteria, you need to pick a colony off that plate and put it in liquid LB media, also at 37°C overnight with antibiotic. Here you'll need a centrifuge to spin down the cells and remove the left over media. Then you'll need to lyse the cells to release the DNA. You might be able to do this with soap, but you'll probably need NaOH and SDS. Once the cells are lysed you need neutralize them with an acetic acid solution, vinegar &lt;strong&gt;might&lt;/strong&gt; be good enough. Then you have to centrifuge the cell debris to pull the insoluble crap out and leave the plasmid DNA and RNA in the supernatent. At this point you can extract the DNA and RNA with a phenol:chloroform:isoamyl alcohol mix. Good luck getting that, as the vapors from that solution &lt;strong&gt;are harmful to inhale, and really bad if you spill it on you, and should not be used outside a hood&lt;/strong&gt;. But if you manage to get the extraction to work, take the top layer and add an equal amount of isopropyl alcohol and put it in your freezer for a couple hours. Then spin it down, carefully remove the supernatent and you should have a pellet of DNA in the bottom. You might have to clean the pellet with a 70% ethanol solution (140 proof) and another centrifugation. Quantifying your DNA at home will be almost impossible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, this all assumes you just want to put a ready-made plasmid into bacteria. Trying to change the plasmid will require restriction enzymes, PCR, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes, you can do genetic engineering at home if your home has an incubator (preferably with shaking), a centrifuge, a water bath, a -80°C freezer, a fume hood, a variety of chemicals, and a decent set of pipettes. But if you have $10,000 you don't really need you might be ok.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2015-01-27T22:47:03.497" LastActivityDate="2015-01-27T22:47:03.497" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="28097" PostTypeId="2" ParentId="28048" CreationDate="2015-01-27T22:40:38.883" Score="1" Body="&lt;p&gt;Replicated from comment section:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Tumor,&quot; latin root Tumere is for swelling. If you're looking at a modern definition though, you have to consider the abnormal tissue growth. Yes, injuries may produce a thrombus, embolus, etc. however when you get injured and it swells, that isn't really a tumor. Injury swelling is just a biochemical response, but isn't characterized by cell proliferation.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-01-27T22:40:38.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28098" PostTypeId="1" AcceptedAnswerId="28099" CreationDate="2015-01-27T22:49:22.163" Score="3" ViewCount="151" Body="&lt;p&gt;Tea, Coffee, Beer, Coke etc…&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder if the benefit from amount of fluid we get from them is bigger or smaller then the handicap of dehydration. In other words it is worth to drink them if we want to have a good drinking regime?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Opening on the recommendation from &lt;a href=&quot;https://biology.stackexchange.com/questions/28084/dehydration-by-a-tea-coffee-beer-etc&quot;&gt;this question&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="13230" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2016-07-09T03:40:17.260" Title="Can drinking caffeine, alcohol and other diuretics be part of a good drinking regime?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;food&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28099" PostTypeId="2" ParentId="28098" CreationDate="2015-01-27T22:59:01.007" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084154&quot; rel=&quot;nofollow&quot;&gt;A PlOS One&lt;/a&gt; study notes drinking moderate amounts of coffee (aka moderate caffeine intake) doesn't necessarily lead to dehydration. They note coffee has hydrating qualities akin to water. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19774754&quot; rel=&quot;nofollow&quot;&gt;Further&lt;/a&gt; empirical studies found no substantial fluid loss in caffeinated beverages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Make note we're talking normal doses and moderate intake, though source 2 goes into diminishing effect of caffeine-mediated fluid loss in heavy/prolonged uptake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The issue therein is with alcohol, which tends to &lt;a href=&quot;http://pubs.niaaa.nih.gov/publications/arh21-1/84.pdf&quot; rel=&quot;nofollow&quot;&gt;inhibit vasopressin&lt;/a&gt; and the kidneys are constantly permeable to fluids.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="22956" LastEditDate="2016-07-08T13:39:45.277" LastActivityDate="2016-07-08T13:39:45.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28100" PostTypeId="1" CreationDate="2015-01-27T23:39:28.840" Score="5" ViewCount="319" Body="&lt;p&gt;In the Miller–Urey experiment they produced several amino acids.  I'm not sure if there were other similar experiments that got further.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jcvi.org/cms/press/press-releases/full-text/article/first-self-replicating-synthetic-bacterial-cell-constructed-by-j-craig-venter-institute-researcher/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.jcvi.org/cms/press/press-releases/full-text/article/first-self-replicating-synthetic-bacterial-cell-constructed-by-j-craig-venter-institute-researcher/&lt;/a&gt; is a reference to making a cell, but they really injected an engineered genome into an existing cell (which is pretty amazing!)  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I'm interested in work to make completely synthetic life with no preexisting biological components.&lt;/p&gt;&#xA;" OwnerUserId="13238" LastEditorUserId="64790" LastEditDate="2021-03-27T16:25:40.953" LastActivityDate="2021-03-27T16:25:40.953" Title="What is the most complex biological organism (or precursors) that we have been able to synthesize from raw materials?" Tags="&lt;molecular-genetics&gt;&lt;synthetic-biology&gt;&lt;abiogenesis&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="28101" PostTypeId="1" AcceptedAnswerId="28108" CreationDate="2015-01-27T23:49:50.100" Score="13" ViewCount="460" Body="&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_code&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;, in the section on the RNA codon table, I see a mapping between codons and amino acids. There, Valine is related to GUU, GUA, GUG, GUC.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it mean in the same context that these four codons are interchangeable? Could one replace GUU with GUG?&lt;/p&gt;&#xA;" OwnerUserId="13238" LastEditorUserId="6307" LastEditDate="2018-12-04T00:40:56.883" LastActivityDate="2018-12-04T00:40:56.883" Title="Are codons that map to the same amino acids interchangeable?" Tags="&lt;molecular-biology&gt;&lt;rna&gt;&lt;translation&gt;&lt;codon&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="28102" PostTypeId="2" ParentId="28048" CreationDate="2015-01-28T00:56:42.843" Score="3" Body="&lt;p&gt;The term tumor is used in the medical definition of inflammation. However it just denotes a temporary swelling that goes down once the inflammation subsides. This swelling is due to edema (accumulation of fluid). You have to understand that in practice no one uses the term tumor to denote an inflammatory swelling. So the term “tumor” denoting edematous swelling is of historical significance only. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In modern practice the term tumor is used only to indicate abnormal growth of any kind. Either benign or malignant. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;In pathology an inflammation is classically described as having the following features:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Tumor : Swelling&lt;/li&gt;&#xA;&lt;li&gt;Dolor : Pain&lt;/li&gt;&#xA;&lt;li&gt;Calor : Warmth&lt;/li&gt;&#xA;&lt;li&gt;Rubor : Redness&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-01-29T13:20:22.673" LastActivityDate="2015-01-29T13:20:22.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28104" PostTypeId="2" ParentId="28089" CreationDate="2015-01-28T01:23:47.093" Score="2" Body="&lt;p&gt;Strands in DNA double helix (and other nucleic acids) are anti-parallel: one strand in the helix is in 5'-&gt;3' direction while another is in 3'-&gt;5' direction. RNA polymerase can only synthesize RNA in 5'-&gt;3' direction, and so it uses the 3'-&gt;5' strand as the template (the second DNA strand is, I think, completely ignored by the polymerase during synthesis). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From one promoter transcription of both forward and reverse genomic strands can theoretically happen. However, the two possible nascent RNA strands are synthesized outward from the promoter and away from each other (i.e. they are not overlapping).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During evolution position of some promoters (but definitely not all of the promoters in the genome) have evolved to be in the place were at least one of the two theoretically possible RNA products can be translated. Transcription in the opposite direction (i.e. away from the gene) actually frequently happens in eukaryotes. These RNAs belong to a class of promoter associated RNA, but but they were not shown to be translated (their function is largely unknown). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt; (2015/02/19): New publication in &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1097276514010077&quot; rel=&quot;nofollow&quot;&gt;Molecular Cell by Duttke et al.&lt;/a&gt; is demonstrating that genic promoters are &lt;em&gt;&quot;intrinsically directional&quot;&lt;/em&gt; and, just as @Leon Avery commented here before, the divergent (i.e. bidirectional) promoters are actually two unidirectional promoters side-by-side, in reverse orientation relative to each other. So my above statement &lt;em&gt;&quot;From one promoter transcription of both forward and reverse genomic strand can theoretically happen&quot;&lt;/em&gt; is incorrect. However, the authors also say that approximately half of gene promoter regions in HeLa possess this bidirectional initiation property, so it is still an important feature to keep in mind when thinking of transcription of eukaryotic genes.  &lt;/p&gt;&#xA;" OwnerUserId="13239" LastEditorUserId="13239" LastEditDate="2015-02-19T21:05:00.317" LastActivityDate="2015-02-19T21:05:00.317" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28105" PostTypeId="1" AcceptedAnswerId="28106" CreationDate="2015-01-28T03:18:23.083" Score="1" ViewCount="178" Body="&lt;p&gt;Haloxyfop &lt;a href=&quot;http://www.dowagro.com/au/prod/verdict.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;(haloxyfop-P-methyl)&lt;/a&gt; is a selective herbicide used to control grassy weeds in young stages. The mode of action (iirc) is basically inhibition of acetyl CoA carboxylase (ACCase). Why does this affect the monocots, while not harming the dicots?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UPXss.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2015-01-28T09:07:26.733" Title="How does Haloxyfop control young grassy weeds in fields of broadleaved crops?" Tags="&lt;botany&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28106" PostTypeId="2" ParentId="28105" CreationDate="2015-01-28T03:44:13.767" Score="2" Body="&lt;p&gt;On the Botany department website of Purdue University (&lt;a href=&quot;http://www.btny.purdue.edu/weedscience/moa/ACCase_Inhibitors/text.html&quot; rel=&quot;nofollow&quot;&gt;http://www.btny.purdue.edu/weedscience/moa/ACCase_Inhibitors/text.html&lt;/a&gt;) I found the following information on Acetyl-CoA carboxylase (&lt;strong&gt;ACCase&lt;/strong&gt;) inhibitors:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] (ACCase inhibitors) inhibit the enzyme carboxyltransferase, an [...] Acetyl-CoAesterase which speeds the formation of malonyl-CoA from acetyl-CoA and CO2. &#xA;  Malonyl-CoA and acetyl-CoA are the building blocks of phospholipids and triacylglycerols [...] (that) combine to form lipid bilayers that serve as the cellular membranes. Affected plants cannot produce new cell membranes. This takes place in the grass’s meristematic tissue, which explains the mushy and disintegrated growing point. [...] &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Selectivity&lt;/strong&gt; [...] Monocots (grasses) [and] dicots (broadleaves) [...] both possess ACCase enzymes in their cytoplasm and chloroplasts. Dicots have a prokaryotic form of the enzyme in the chloroplast and the eukaryotic form in the cytoplasm. Monocots have the eukaryotic form in both their cytoplasm and chloroplasts. Only production of the eukaryotic form is inhibited. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So to sum up, ACCase inhibitors act on &lt;strong&gt;eukaryotic ACCase&lt;/strong&gt;, not the prokaryotic type. ACCase is &lt;strong&gt;essential for cell membrane&lt;/strong&gt; formation. Blocking ACCase results in a depletion of its product, namely malonyl-CoA. Malonyl-CoA is essential for the synthesis of long fatty acids used in the cell membrane. Without cell membranes, cells lose integrity and turn to mush. Tissue growth is impossible without ACCase activity. Since monocots only have the eukaryotic ACC in both cytoplasm and chloroplasts, they die. &lt;strong&gt;Dicots, on the other hand, express prokaryotic ACC in their chloroplasts, making them resistant to ACCase inhibitors&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After some literature search I also found that blocking (knocking out) acetyl-CoA carboxylase in &lt;em&gt;Arabidopsis&lt;/em&gt; (a dicotyledon) results in dead plant embryos and, hence, non-viable seeds (Baud et al., 2003). &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-28T09:07:26.733" LastActivityDate="2015-01-28T09:07:26.733" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28108" PostTypeId="2" ParentId="28101" CreationDate="2015-01-28T08:07:35.327" Score="12" Body="&lt;p&gt;I think given that you're just getting started with genetics, you can say that the codons are interchangeable. This is generally true, though not technically correct. Here are a few reasons for why this is the case, though there's probably more:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Specific organisms use specific codons with different frequencies. This is usually related to the tRNA abundance in the cell. Using a codon for which there is relatively less tRNA available would be expected to lead to a decreased protein synthesis rate. &lt;/li&gt;&#xA;&lt;li&gt;Using different codons can affect mRNA secondary structure, which could affect expression. &lt;/li&gt;&#xA;&lt;li&gt;Some codons, especially stop codons, can influence translation contextually through a process called recoding. This can include frame-shifting, read-throughs, cleavage or, perhaps most famously, coding for the amino acid selenocysteine and much more. See &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0378111902004237?via=ihub&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Different codons can also influence translation contextually through pausing. This affects the rate of protein synthesis as well as its folding. See &lt;a href=&quot;http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00140/full&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Changing codons can affect regulatory sequences such as miRNA binding sites. Though these are usually present in the UTRs, they can also occur in the CDS. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-02-26T21:36:53.913" LastActivityDate="2015-02-26T21:36:53.913" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28109" PostTypeId="1" AcceptedAnswerId="28116" CreationDate="2015-01-28T08:32:13.143" Score="4" ViewCount="5442" Body="&lt;p&gt;I have heard that our saliva contains cells. What cell types can be found in human saliva?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="16651" LastEditDate="2015-12-17T17:23:28.220" LastActivityDate="2015-12-17T17:23:28.220" Title="What kinds of cells does human saliva contain?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28110" PostTypeId="1" AcceptedAnswerId="28113" CreationDate="2015-01-28T09:07:59.590" Score="6" ViewCount="2488" Body="&lt;p&gt;I got streptavidin for surface reaction. The label says &quot;biotin binding: 16 units/mg&quot;. What does &lt;code&gt;units/mg&lt;/code&gt; mean? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it mean &quot;1 mg biotin can bind to 16 units SA&quot;? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much is the &lt;code&gt;unit&lt;/code&gt; here?&lt;/p&gt;&#xA;" OwnerUserId="10422" LastActivityDate="2015-01-28T21:36:06.383" Title="What does units/mg mean for Streptavidin" Tags="&lt;proteins&gt;&lt;protein-binding&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28112" PostTypeId="1" CreationDate="2015-01-28T10:30:27.613" Score="3" ViewCount="1071" Body="&lt;p&gt;How to retrieve full gene names and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any other software or language)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible vice versa: having full gene names or IDs get HUGO names or the other annotation data?&lt;/p&gt;&#xA;" OwnerUserId="12935" LastEditorUserId="3340" LastEditDate="2015-02-02T06:44:34.083" LastActivityDate="2015-02-02T06:44:34.083" Title="How to retrieve full gene names list and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any)?" Tags="&lt;bioinformatics&gt;&lt;software&gt;&lt;microarray&gt;&lt;data&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28113" PostTypeId="2" ParentId="28110" CreationDate="2015-01-28T10:30:44.883" Score="7" Body="&lt;p&gt;16 units/mg means 16 units per milligram of protein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many companies, including Invitrogen, define 1 unit streptavidin as &lt;strong&gt;the amount of streptavidin necessary to bind 1 microgram of biotin&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-28T11:21:57.737" LastActivityDate="2015-01-28T11:21:57.737" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28116" PostTypeId="2" ParentId="28109" CreationDate="2015-01-28T13:50:02.687" Score="6" Body="&lt;p&gt;It contains white blood cells (&lt;em&gt;leukocytes&lt;/em&gt;) and cells from the inner lining of the mouth (&lt;em&gt;buccal epithelial cells&lt;/em&gt;). The DNA obtained from these cells is the basis of DNA profiling based on saliva samples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.salimetrics.com/article/collecting-and-handling-saliva-for-dna-analysis&quot;&gt;Salimetrics&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-01-28T13:50:02.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28118" PostTypeId="1" CreationDate="2015-01-28T14:50:10.790" Score="2" ViewCount="34" Body="&lt;p&gt;I'm looking for a paper with gene expression data for mouse feeder cells, inactivated by gamma radiation or mitomycin C. Ideally I'd like RNA-seq data but I'll use microarray data if that's all there is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've spent quite a while looking (in GEO, Google Scholar, PubMed, etc) with no luck. Any leads would be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="13244" LastActivityDate="2015-01-28T14:50:10.790" Title="Gene expression for mouse feeder cells (inactivated MEFs)" Tags="&lt;molecular-biology&gt;&lt;rna-sequencing&gt;&lt;mrna&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28119" PostTypeId="2" ParentId="28112" CreationDate="2015-01-28T15:16:17.837" Score="5" Body="&lt;p&gt;I would recommend just downloading the database, which HUGO allows you to do free of charge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The HUGO website has a &quot;downloads&quot; tab at the top that takes you to the following page&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.genenames.org/cgi-bin/statistics&quot; rel=&quot;noreferrer&quot;&gt;http://www.genenames.org/cgi-bin/statistics&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will see a table of statistics relating to how many protein- or non-protein-coding genes there are catalogued, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under the tables is a section called &lt;strong&gt;Complete dataset download links&lt;/strong&gt; -- this is the section you want (unless you only want a subset of the data - but why not get it all!)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This plain text file (once uncompressed) can be loaded into R (or any other language) to be parsed and analysed as per your requirements.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is worth updating the version you download quite regularly, as they update the HUGO database with new/updated info quite regularly.&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2015-01-28T15:16:17.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28120" PostTypeId="1" CreationDate="2015-01-28T18:01:01.303" Score="2" ViewCount="5337" Body="&lt;p&gt;So, I'm doing some drosophila experiments with my high schoolers and I had really poor production of wild type individuals for doing the experiment resulting in not enough to cross with everyone... I am trying the following crosses and hoping the kids can still learn from it, but wanted input from any fly-herders on what I can expect with the first two  crosses....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sepia males x White Eye females&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sepia females x White Eye males&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dumpy males x Wild-type females&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dumpy females x Wild-type males&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think the gender separation will make any difference except in the white x sepia crosses since it is X-linked.&#xA;What should I get in the sepia x white crosses? Since they both control eye color and are both recessive I'm not sure. Am I correct that w is epistatic, thus should block sepia in an x-linked manner (same as if I had used wild-type instead of sepia)?&#xA;I assume the Dumpy x Wild-type will go by the books (F1 all wild-type with F2 3:1 ratio). Fingers crossed.&lt;/p&gt;&#xA;" OwnerUserId="1710" LastActivityDate="2015-06-28T16:45:40.533" Title="Crossing white eyed Drosophila with sepia eye" Tags="&lt;genetics&gt;&lt;drosophila&gt;&lt;sex-chromosome&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28121" PostTypeId="2" ParentId="28110" CreationDate="2015-01-28T21:36:06.383" Score="6" Body="&lt;p&gt;Just to add to Chris Stronk's answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1 U SAV can bind 1 ug biotin&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This tells you that in a 16 U/mg SAV sample, every mg of SAV will bind 16 ug of biotin. You can figure out the molar ratio from this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$16\mu g\ BIO\cdot\frac{1mol\ BIO}{244310000ug\ BIO}\cdot\frac{52800000mg\ SAV}{mol\ SAV}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which equals:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\frac{3.46mol\ BIO}{mol\ SAV}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Theoretically, each SAV tetramer can bind 4 biotins. This tells you that there is some heterogeneity in the sample and that, on average, each SAV tetramer can bind 3.46 biotins.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-01-28T21:36:06.383" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28122" PostTypeId="2" ParentId="28120" CreationDate="2015-01-28T22:16:11.190" Score="1" Body="&lt;p&gt;I posted this on &lt;a href=&quot;http://www.reddit.com/r/biology/comments/2tz4p3/potential_teaching_moment_in_a_drosophila/&quot; rel=&quot;nofollow&quot;&gt;Reddit&lt;/a&gt; as well, so credit to km1116 for working this out. Here is his response which follows my original logic (though I'm not sure if he is right):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;female x male:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;w x se&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;F1: wild-type females and white males&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;F2: 1/4 white-eyed males, 3/16 wild-type males, 1/16 sepia males, 1/4&#xA;  white-eyed females, 3/16 wild-type females, 1/16 sepia females&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;se x w&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;F1: all wild-type offspring&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;F2: 1/4 white-eyed males, 3/16 wild-type males, 1/16 sepia males; 3/8&#xA;  wild-type females, 1/8 sepia females&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;wt x dp (either direction)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;F1: all wild-type&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;F2: 3/4 wild-type, 1/4 dumpy&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My rationale for his answer is the genotype of the cross looks like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;X&lt;sup&gt;w&lt;/sup&gt;YNN with X&lt;sup&gt;W&lt;/sup&gt;X&lt;sup&gt;W&lt;/sup&gt; nn , where &quot;W&quot; is normal eyes, &quot;w&quot; is white&quot;, N is Wildtype and n is sepia. &lt;/p&gt;&#xA;" OwnerUserId="1710" LastEditorUserId="1710" LastEditDate="2015-01-29T14:21:47.303" LastActivityDate="2015-01-29T14:21:47.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28123" PostTypeId="1" CreationDate="2015-01-28T22:18:09.020" Score="5" ViewCount="542" Body="&lt;p&gt;Why do we wake up after 6-8 hours of sleep ? Why don't we sleep for lets say 20-30 hours ? What mechanism is it that controls when to wake us up and how does it determine the moment that we should wake up ?&lt;/p&gt;&#xA;" OwnerUserId="11869" LastActivityDate="2017-11-03T15:51:05.967" Title="Length of sleep time" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28124" PostTypeId="1" CreationDate="2015-01-28T23:17:14.843" Score="4" ViewCount="681" Body="&lt;p&gt;The boat-tailed grackle's deep-V tail would seem to cause a great deal of drag or even downward deflection (like an airplane's elevators). How much does this actually affect the bird's flight?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PpU4z.jpg&quot; alt=&quot;Boat tailed grackle&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="11628" LastEditorUserId="107" LastEditDate="2015-01-29T01:04:29.967" LastActivityDate="2015-01-29T01:41:52.440" Title="Are boat-tailed grackles efficient flyers?" Tags="&lt;ornithology&gt;&lt;flight&gt;" AnswerCount="1" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="28125" PostTypeId="2" ParentId="28055" CreationDate="2015-01-28T23:53:55.830" Score="2" Body="&lt;p&gt;Your answer to your titular question, &lt;em&gt;How was the origin of CTVT parasitic cancer determined?&lt;/em&gt; is that cytogenic studies were done on the tumors. It &lt;em&gt;arose in dogs&lt;/em&gt; and was logically assumed to be of dog origin, and was first characterized in 1876. The tumor cells were/are characterized by a rearranged karyotype, which is similar in tumors from in different parts of the world. (1969) Thus it was postulated that that the transmissible agent causing the CTVT is the tumor cell itself and that all worldwide CTVT have a clonal origin. (1985)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your later question states:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What percentage / degree of genetic similarity is needed to identify something as belonging to a specific species?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;When a tumor arises in an animal (say a dog), it is automatically assumed that the cancerous cells, regardless of their ploidy, arose from that animal (in this case, a dog), not a different animal. Not all animals have had their entire genome sequenced, so this question as stated isn't answerable (although the genome of the dog has been completely sequenced). And certainly, not all tumor cell lines have been completely sequenced. The assumption of origin is made by looking at certain genes (e.g. histocompatibility genes) and others known to be species specific.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since there are relatively few transmissible &lt;em&gt;cancers&lt;/em&gt; (that is, where the cancer itself acts as the infectious agent), this is still a safe assumption. While I'm fairly confident more transmissible cancers will be found, I'm also fairly confident that they will be species specific, because in order to escape detection, they will need to be recognized immunologically as &quot;self&quot;, as they must survive in the host at least long enough to be transmitted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the case with &lt;em&gt;canine transmissible venereal tumor&lt;/em&gt; (CTVT). It is also the case with the contagious tumor &lt;em&gt;Tasmanian Devil face tumor disease&lt;/em&gt; (DFTD). Just as with the canine infectious cancer, DFTD cells in different individuals have identical, complex chromosomal rearrangements and are &lt;em&gt;genetically identical to each other&lt;/em&gt; but &lt;em&gt;different to the host devil&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Spread of such an infectious cell line between unrelated individuals should be prevented by major histocompatibility complex (MHC) Class I antigens on the surface of the tumour cell, as Class I molecules play a key role in self/non-self-recognition. The recent emergence of the tumor (transmitted by biting) in the endangered marsupial Tasmanian devil (Sarcophilus harrisii) is an unfortunate exception. In the Tasmanian devil, the tumor is very aggressive and kills the host. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the case of canine transmissible venereal tumor (CTVT), it was shown about five decades ago to be the &lt;em&gt;same&lt;/em&gt; dog tumor being spread from dog to dog. The earliest studies were based on histological studies and karyotyping. Paraffin-embedded tumor samples still exist. More recently, with genetic analysis, it is possible to perform much more sophisticated testing on the tumor DNA.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The transmissible agent causing canine transmissible venereal tumor (CTVT) is thought to be the tumor cell itself. To test this hypothesis, we &lt;em&gt;analyzed genetic markers including major histocompatibility (MHC) genes, microsatellites, and mitochondrial DNA (mtDNA) in naturally occurring tumors and matched blood samples.&lt;/em&gt; In each case, the tumor is &lt;em&gt;genetically distinct from its host&lt;/em&gt;. Moreover, tumors collected from 40 dogs in 5 continents are derived from a single neoplastic clone that has diverged into two subclades. Phylogenetic analyses indicate that CTVT most likely originated from a wolf or an East Asian breed of dog between 200 and 2500 years ago. Although CTVT is highly aneuploid, it has a remarkably stable genotype.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Your quote &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;likely originated at least 250 years ago from a wolf or an &quot;old&quot; Asian dog breed such as a husky or Shih Tzu...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Has been disputed. Estimates vary widely, from 11,000 years to 250 years.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ivis.org/proceedings/acvp/2007/murgia.pdf?LA=1&quot; rel=&quot;nofollow&quot;&gt;Canine TVT: Evolution of Somatic Tumour Cell as Transmissible Parasites&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/277/1690/2001.short&quot; rel=&quot;nofollow&quot;&gt;MHC gene copy number variation in Tasmanian devils: implications for the spread of a contagious cancer&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593932/&quot; rel=&quot;nofollow&quot;&gt;Clonal Origin and Evolution of a Transmissible Cancer&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-01-28T23:59:00.123" LastActivityDate="2015-01-28T23:59:00.123" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28127" PostTypeId="2" ParentId="28124" CreationDate="2015-01-29T01:41:52.440" Score="7" Body="&lt;p&gt;I don't know of studies specifically of boat-tailed grackle flight, so I'll focus on elongated tails in general and come back to grackles at the end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Long tails in birds are obviously interesting from the standpoint of sexual selection. Going all the way back to Darwin, one hypothesis has been that females prefer males with long tails. There seems to be evidence for this, although experimental reduction or elongation of tail feathers is perhaps of questionable success. See this &lt;a href=&quot;http://beheco.oxfordjournals.org/content/10/1/112.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;back and forth in Behavioral Ecology&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Those interested in the study of flight have also studied elongate tail feathers to get at the questions you ask: are long tail feathers aerodynamically costly?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/340/1294/361&quot; rel=&quot;nofollow noreferrer&quot;&gt;Balmford (1993)&lt;/a&gt; compared the aerodynamic properties of different tail shapes. He found that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A forked tail that has a triangular planform when spread to just over 120° gives the best aerodynamic performance and this may be close to a universal optimum, in terms of aerodynamic efficiency, for a means to control pitch and yaw.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But the results were more complicated. Forked tails are only used in extreme maneuvers, they are more unstable, and suffer from greater loss of performance when damaged. He leaves open the possibility that natural selection, rather than or in addition to sexual selection, has played a role in shaping bird tails, possibly for increased aerodynamic performance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More relevant here, &lt;a href=&quot;http://www.nature.com/nature/journal/v361/n6413/abs/361628a0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Balmford et al. (1993)&lt;/a&gt; studied pairs of species, one with a long tail and one without, to assess the aerodynamic cost of long tail feathers. They studied ~600 specimens and used aerodynamic modeling to predict cost. Their results are summarized in this figure:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ki6tv.png&quot; alt=&quot;Tail Shape&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Graduated (rounded) tails are costliest over all lengths. Forked tails are notably less costly over all lengths, and shallow forks more efficient than deep forks (but there the difference is not great).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They conclude:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our model suggests that as long forked tails deepen, it becomes more likely that they are aerodynamically costly..., and therefore increasingly probable that sexual rather than natural selection explains their evolution.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And of the species pairs:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... then among species with long forked tails, sexual dimorphism in tail length should increase with fork depth. Pairwise comparisons of closely related species support this prediction.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;h2&gt;What of boat-tail grackles then?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;From what images I could find, it looks like boat-tailed grackles appear to have graduated tails when spread. If so, then these tails would be very inefficient and males with longer tails would incur a proportionately higher cost of flight than males with shorter tails.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Balmford, A., A. L. R. Thomas, and I. Jones. 1993. Aerodynamics and the evolution of long tails in birds. &lt;em&gt;Nature&lt;/em&gt; 361:628–631.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thomas, A. L. R. 1993. On the Aerodynamics of Birds' Tails. &lt;em&gt;Philosophical Transactions of the Royal Society of London B: Biological Sciences&lt;/em&gt; 340:361–380.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2015-01-29T01:41:52.440" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28128" PostTypeId="1" CreationDate="2015-01-29T04:23:45.483" Score="0" ViewCount="42284" Body="&lt;p&gt;Penis don't have bone like ears &amp;amp; nose, then why why male penis not considered as cartilage? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;en.wikipedia.org/wiki/Cartilage&lt;/p&gt;&#xA;" OwnerUserId="13251" LastEditorUserId="107" LastEditDate="2015-01-29T04:52:35.583" LastActivityDate="2015-01-29T09:04:05.550" Title="why male penis not considered as cartilage?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ClosedDate="2015-01-29T11:16:19.260" ContentLicense="CC BY-SA 3.0" />
  <row Id="28129" PostTypeId="1" AcceptedAnswerId="28135" CreationDate="2015-01-29T08:20:31.383" Score="7" ViewCount="78" Body="&lt;p&gt;What is a &lt;em&gt;positive epitope fragment&lt;/em&gt;? I found one paper on the subject: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19074155&quot; rel=&quot;nofollow&quot;&gt;COBEpro: a novel system for predicting continuous B-cell epitopes&lt;/a&gt; by&#xA;Michael J. Sweredoski and Pierre Baldi&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="6703" LastEditDate="2015-01-29T22:12:45.177" LastActivityDate="2015-01-29T22:12:45.177" Title="What is a positive epitope fragment" Tags="&lt;cell-biology&gt;&lt;bioinformatics&gt;&lt;immunology&gt;&lt;antigen&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28131" PostTypeId="1" CreationDate="2015-01-29T08:48:16.120" Score="1" ViewCount="175" Body="&lt;p&gt;What software to use to build a graph based on microarray gene expression mutual correlation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried Cytoscape`s Reactome FI and a recipe from R bioinformatics cookbook, however, need a more reliable robust software or R/Python tutorial on how to make a graph with gene-nodes and edges built on the rule of significant (p&amp;lt;0,05) positive and negative Pearson/Spearman correlations.&lt;/p&gt;&#xA;" OwnerUserId="12935" LastActivityDate="2015-01-29T08:48:16.120" Title="What software/approach to use to build a graph based on microarray gene expression correlation?" Tags="&lt;software&gt;&lt;microarray&gt;&lt;biological-networks&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28133" PostTypeId="2" ParentId="28128" CreationDate="2015-01-29T09:04:05.550" Score="8" Body="&lt;p&gt;feel the tip of your nose. Mush it around, It's got a certain stale gummy bear feeling to it. Now feel your ears, all over. The outer edge, the back, the hard part in the front where the ear meets the face. Feel your adam's apple. This is cartilege.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you feel your penis, does anything even feel close? Nope. It's just soft. Soft tissue, to be precise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When stimulated, there are comparmemts within the penis which engorge with blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wFyGm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When they fill up with blood, the penis gets hard. That's all there is to it. No bones, no cartelidge. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have any questions, noe's the time to ask.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-29T09:04:05.550" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28134" PostTypeId="1" CreationDate="2015-01-29T09:07:19.937" Score="6" ViewCount="160" Body="&lt;p&gt;What Websites Have Image Libraries for Bacteria and other Microorganisms?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With age of cell phone microscopes and hand held spectrometers it would be interesting and valuable to be able to compare in-home/at-work microbiology with data-banks. To be able to test for health or enjoy the visuals of tree of life seem relevant. What websites are out there?&lt;/p&gt;&#xA;" OwnerUserId="12875" LastActivityDate="2015-01-29T15:58:00.333" Title="What Websites Have Image Libraries for Bacteria and other Microorganisms" Tags="&lt;microbiology&gt;&lt;microscopy&gt;&lt;fluorescent-microscopy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28135" PostTypeId="2" ParentId="28129" CreationDate="2015-01-29T09:52:07.390" Score="5" Body="&lt;p&gt;The group tries to predict possible epitope sequences for the generation of antibodies. This includes also non-linear epitopes where not all amino acids of the epitope are line up behind each other, but come in close contact due to a 3D-structure. To train their algorithm, they use data, where the boundaries of the epitopes and the non-epitopes are known and clearly mapped.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;Dataset and Preparation&quot; section in this paper contains the following:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In this article, we used several different datasets to train and&#xA;  benchmark COBEpro. These datasets were derived from several different&#xA;  previously published sources: BciPep (Saha et al., 2005), Pellequer&#xA;  (Pellequer et al., 1993) and HIV (Korber et al., 2003). The BciPep&#xA;  datasets consist of epitope/non-epitope sequence fragments. The&#xA;  Pellequer and HIV datasets consist of whole antigen proteins annotated&#xA;  with precise epitope boundaries.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The &quot;positive epitope fragments&quot; are known and verified (&quot;positive&quot;) epitopes from these datasets in the training database. The fragment refers to restriction of length to 20 amino acids which they choose to apply. Shorter epitopes got amino acids added so they get 20 aa long, longer got truncated.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-01-29T15:58:35.777" LastActivityDate="2015-01-29T15:58:35.777" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28136" PostTypeId="1" CreationDate="2015-01-29T09:58:57.280" Score="1" ViewCount="70" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/7267/why-doesnt-recombination-occur-in-male-drosophila&quot;&gt;Following up from this question,&lt;/a&gt; I am wondering if the phenomenon of genome-wide suppressed male recombination is limited to &lt;em&gt;Drosophila melanogaster&lt;/em&gt; or is common to all &lt;em&gt;Drosophila&lt;/em&gt;? The answer to the aforementioned question hints that this may be the case but has no reference on that, and doesn't directly state it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an added bonus, is this recorded in any other species?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-01-29T10:04:40.660" Title="Is recombination suppressed in the males of all Drosophila species? Any other species?" Tags="&lt;recombination&gt;&lt;drosophila&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28137" PostTypeId="2" ParentId="28134" CreationDate="2015-01-29T10:05:03.043" Score="4" Body="&lt;p&gt;While I doubt that this might be possible in all cases (and I would be careful about classifications), there are indeed some great ressources, which contain a lot of images. Since there is a vast number of bacteria present on this planet, there is of course a limitation to bacteria available in photos, representing only the most common or important.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.bacteriainphotos.com/index.html&quot; rel=&quot;nofollow&quot;&gt;Bacteria in Photos&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.microbelibrary.org/home&quot; rel=&quot;nofollow&quot;&gt;American Society of Microbiologies Microbelibrary&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.microbiologyinpictures.com/&quot; rel=&quot;nofollow&quot;&gt;Microbiology in Photos&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Then there is an information page available from the CDC, which informs about parasitic diseases. These are non-bacterial, but probably also interesting. It can be found here:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cdc.gov/dpdx/az.html&quot; rel=&quot;nofollow&quot;&gt;Laboratory Identification of Parasitic Diseases of Public Health&#xA;Concern&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-01-29T15:58:00.333" LastActivityDate="2015-01-29T15:58:00.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28138" PostTypeId="1" AcceptedAnswerId="28140" CreationDate="2015-01-29T11:43:55.810" Score="10" ViewCount="30697" Body="&lt;p&gt;I'd like to know how much a person can see regarding the angles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it is a rectangle, I'd like to know it's height and width.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if is another shape, I'd like to know which kind of shape and the angles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suppose that we can see something like this and if this is true I am curious about 4 dimensions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&quot;vertical&quot; angle for both eyes&lt;/li&gt;&#xA;&lt;li&gt;&quot;horizontal&quot; angle for both eyes&lt;/li&gt;&#xA;&lt;li&gt;&quot;vertical&quot; angle for an eye&lt;/li&gt;&#xA;&lt;li&gt;&quot;horizontal&quot; angle for an eye&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MA8Lm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be also nice if there will be some &quot;areas&quot; with percentages. I mean, something related to &quot;central&quot; vs &quot;peripheral&quot; view, because we see better something that is in front of us than something that is near us.&lt;/p&gt;&#xA;" OwnerUserId="13252" LastActivityDate="2015-02-15T13:39:11.790" Title="What is the field of view for the human eyes?" Tags="&lt;vision&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28139" PostTypeId="1" AcceptedAnswerId="28141" CreationDate="2015-01-29T12:13:32.853" Score="1" ViewCount="399" Body="&lt;p&gt;Basic Gene, Chromosome, Genome, Protein - how are they ordered?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genes make up Chromosome, and Chromosomes make up a Genome...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, where does Protein come into play?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do you call Genes that are spliced together to form something new?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do you call a variable inside a Gene?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="13253" LastEditorUserId="16460" LastEditDate="2017-06-05T19:17:30.547" LastActivityDate="2017-06-05T19:17:30.547" Title="Molecular biology - fundamental questions" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-01-29T16:43:51.193" ContentLicense="CC BY-SA 3.0" />
  <row Id="28140" PostTypeId="2" ParentId="28138" CreationDate="2015-01-29T12:44:57.337" Score="13" Body="&lt;p&gt;The &lt;strong&gt;general shape&lt;/strong&gt; of the field of view has been answered in the related question &quot;&lt;a href=&quot;https://biology.stackexchange.com/questions/24046/if-human-eyes-watch-an-area-whats-the-shape-of-its-capturing-shape-rectangula/24048#24048&quot;&gt;If human eyes watch an area, what's the shape of its capturing shape? Rectangular? Half spherical?&lt;/a&gt;&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the central view: yes, &lt;strong&gt;foveal view has a higher acuity&lt;/strong&gt; than peripheral view.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the numerical dimensions of the monocular and binocular field of view: &lt;strong&gt;Monocular field of view  (measured from central fixation) is 160 deg (width w) x 175 deg (height h)&lt;/strong&gt;. The total &lt;strong&gt;binocular field of view is 200 deg (w) x 135 deg (h)&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The region of &lt;strong&gt;binocular overlap is 120 deg (w) x 135 deg (h)&lt;/strong&gt; (&lt;a href=&quot;http://webvision.med.utah.edu/book/part-xiii-facts-and-figures-concerning-the-human-retina/&quot; rel=&quot;nofollow noreferrer&quot;&gt;WebVision&lt;/a&gt;). The &lt;strong&gt;binocular foveal high-acuity part&lt;/strong&gt; (central view) is about &lt;strong&gt;&lt;a href=&quot;http://neuronresearch.net/vision/reading/foveola.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;6 degrees&lt;/a&gt; (5-15 degrees)&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-02-15T13:39:11.790" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="28141" PostTypeId="2" ParentId="28139" CreationDate="2015-01-29T13:17:54.050" Score="4" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;where does Protein come into play?&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;A Gene codes a protein.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;DNA is transcibed into messenger RNA (mRNA). mRNA is translated into protein.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;br&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;What do you call Genes that are spliced together to form something new?&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Genes are not spliced together. One single gene can consist of &lt;em&gt;introns&lt;/em&gt; (intervening sequences) and &lt;em&gt;exons&lt;/em&gt; (expressed sequences). Transcribed introns in the RNA are spliced out and the exons glued together to form a functional mRNA.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;br&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;What do you call a variable inside a Gene?&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Genes are made up of &lt;em&gt;DNA&lt;/em&gt;. DNA is made up of &lt;em&gt;nucleotides&lt;/em&gt;&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2017-06-05T19:12:19.980" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28142" PostTypeId="1" AcceptedAnswerId="28147" CreationDate="2015-01-29T13:39:23.150" Score="6" ViewCount="8917" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/27993/what-are-the-differences-between-cancer-and-tumour/28011?noredirect=1#comment45928_28011&quot;&gt;Comment&lt;/a&gt; by Anongoodnurse, has made me curious as to what a doctor means when (s)he says &quot;The cancer is cured&quot; to a patient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My idea up till this point (based on what I read and what I learned in my classes from my professors) was that the prognosis was declared based on the &lt;em&gt;survival rates&lt;/em&gt; and that cancers could never be declared cured as no one could be sure that every single malignant cell has been eradicated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However Anongoodnurse commented:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Curable cancers are &lt;em&gt;not&lt;/em&gt; few and far between.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So I would like to know what it means when it is said &quot;Cancer is cured&quot;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Though the answer by Anongoodnurse has been accepted, I would like to have other answers too, please feel free to contribute &lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2018-10-14T19:42:37.517" Title="What does it mean when a patient suffering from malignant tumor (cancer) has been declared cured?" Tags="&lt;cancer&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28143" PostTypeId="2" ParentId="23638" CreationDate="2015-01-29T16:50:05.550" Score="11" Body="&lt;p&gt;In my experience (in common with the experience of everyone I've talked to who could be considered an expert on the subject), taking old wood and using that as a scion when grafting new trees rejuvenates them, and they grow as new trees. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll take apple trees as an example. As you can see from the table &lt;a href=&quot;http://ag.arizona.edu/pubs/garden/mg/fruit/intro.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;, there is a distinct age after which the tree begins to decline. Now, that's not concrete (I've seen some apple trees last over 100 years (didn't plant those myself btw)), but generally, an apple tree will lose vigor and productivity before it reaches 50 years of age. This tree's 'immune system' also goes down, and it becomes susceptible to many diseases. You'll rarely see such a tree, as orchardists generally replace them rather fast.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But to the point of your question. When you will graft an apple tree, you will generally bud graft it, as described &lt;a href=&quot;http://www.garden.org/ediblelandscaping/?page=201008-how-to&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;. That article (which is spot-on) says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Select a healthy branch of this year's growth from your desired variety of tree. Look for a plump leaf bud about halfway down the branch. Leaf buds are close to the branch where fruiting buds tend to stand out more.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Note that it says nothing about the tree's age, simply stating that the wood must be healthy. That's because old wood/young wood produce the same result in the new trees. I was using a 40 year old &lt;a href=&quot;http://www.orangepippin.com/apples/razor-russet&quot; rel=&quot;noreferrer&quot;&gt;razor russet&lt;/a&gt; to graft onto all the &lt;a href=&quot;http://www.appleman.ca/korchard/rootstok.htm&quot; rel=&quot;noreferrer&quot;&gt;Malling V&lt;/a&gt; rootstocks I had for that variety. And of course they grew as expected, as a young sapling should. I've heard of a &lt;a href=&quot;https://plus.google.com/109880276393197709042/about?gl=us&amp;amp;hl=en&quot; rel=&quot;noreferrer&quot;&gt;nearby nursery&lt;/a&gt; taking budwood from a 100 year old tree that still looked good. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, you can use a rootstock taken from an old plant, and also a scion from an old plant, and the new plant created will grow as a young sapling. Here's how the rootstocks I use are created: You cut down a tree at ground level, and it sends out a lot of shoots. You pile soil over it, but allow the ends of the shoots to stick through. These shoots will root into the soil, and can be cut at the base, and planted out for grafting later. This way, you can have 1000's of identical (cloned) rootstocks. You can also get rootstocks from old trees. &lt;a href=&quot;https://i.stack.imgur.com/AaSuf.jpg&quot; rel=&quot;noreferrer&quot;&gt;Here's&lt;/a&gt; a diagram of the process. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;About herbaceous perennials, I've found (to some people's surprise) the same thing. The scion grows as a young plant again once grafted. I found this out because I graft heirloom tomatoes onto hybrid tomato rootstocks (the latter are seedlings). Usually, the scions will be from seedlings, but at times I take the scions from a large mature plant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just so you know, an indeterminate tomato plant will, once mature, flower and fruit until frost. A determinate tomato variety will produce a large crop all at once, and then die back (this is the kind preferred by owners of mechanised (machine harvested) fields). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my tests, you could take the scion from an old determinate plant that was through fruiting, right before it started dying back, and successfully use that for grafting the new plants. These new plants' growth was identical to the growth of grafted plants whose scions came from seedlings, and they began to flower and produce fruit at the same time. Of course, actual seedlings did not have the vigor of the grafted plants, and were behind in growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Off-topic for your question, but possibly still of interest, I've found that &lt;a href=&quot;http://www.wikihow.com/Grow-Cuttings-from-Established-Plants&quot; rel=&quot;noreferrer&quot;&gt;cuttings&lt;/a&gt; and &lt;a href=&quot;http://www.finegardening.com/making-more-shrubs&quot; rel=&quot;noreferrer&quot;&gt;layers&lt;/a&gt; (not scions) taken from old plants (both woody and herbaceous), and rooted, would grow as young plants again. &lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2015-01-31T01:14:21.533" LastActivityDate="2015-01-31T01:14:21.533" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28145" PostTypeId="1" AcceptedAnswerId="28152" CreationDate="2015-01-29T18:22:49.993" Score="2" ViewCount="107" Body="&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Glufosinate&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;, the mode of action of the non selective herbicide &lt;a href=&quot;http://en.wikipedia.org/wiki/Glufosinate&quot; rel=&quot;nofollow noreferrer&quot;&gt;Glufosinate&lt;/a&gt; is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Phosphinothricin is an &lt;a href=&quot;http://en.wikipedia.org/wiki/Glutamine_synthetase&quot; rel=&quot;nofollow noreferrer&quot;&gt;glutamine synthetase&lt;/a&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/Enzyme_inhibitor&quot; rel=&quot;nofollow noreferrer&quot;&gt;inhibitor&lt;/a&gt; that binds to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Glutamic_acid&quot; rel=&quot;nofollow noreferrer&quot;&gt;glutamate&lt;/a&gt; site. Glufosinate-treated plants die due to a buildup of &lt;a href=&quot;http://en.wikipedia.org/wiki/Ammonia&quot; rel=&quot;nofollow noreferrer&quot;&gt;ammonia&lt;/a&gt; and corresponding decrease in pH in the thylakoid lumen, leading to the uncoupling of &lt;a href=&quot;http://en.wikipedia.org/wiki/Photophosphorylation&quot; rel=&quot;nofollow noreferrer&quot;&gt;photophosphorylation&lt;/a&gt;. The uncoupling of photophosphorylation causes the production of &lt;a href=&quot;http://en.wikipedia.org/wiki/Reactive_oxygen_species&quot; rel=&quot;nofollow noreferrer&quot;&gt;reactive oxygen species&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipid_peroxidation&quot; rel=&quot;nofollow noreferrer&quot;&gt;lipid peroxidation&lt;/a&gt;, and membrane destruction.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/c6teb.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, in &lt;a href=&quot;http://ucanr.edu/blogs/blogcore/postdetail.cfm?postnum=4338&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt; from the University of California (Weed control, management, ecology, and minutia), it states:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Researchers in Malaysia reported a few years ago on a population of goosegrass resistant to glufosinate in vegetable and orchard systems (Lee L J &amp;amp; Ngim J (2000). A first report of glyphosate-resistant goosegrass (Eleusine indica (L) Gaertn) in Malaysia. Pest Management Science, 56, 336-339).  For a number of years this was the only reported case of resistance to this herbicide.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What would have to happen in the weed for it to become resistant to this chemical/mode of action, and what would initiate this process?&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2015-01-29T22:16:14.783" Title="How can a plant become resistant to glufosinate?" Tags="&lt;botany&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28147" PostTypeId="2" ParentId="28142" CreationDate="2015-01-29T19:03:48.530" Score="5" Body="&lt;p&gt;TL;DR - ask someone who has survived 45 years after treatment of their testicular cancer. The patient (and most doctors) would consider that a cure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe the kxcd cartoon explains &lt;strong&gt;prognosis&lt;/strong&gt; quite well. There is something that @Crags has overlooked, though, and that is the caveat &lt;em&gt;&quot;Once most cancers spread out into your body, they're incurable&quot;&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DMUNo.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would consider that sentence to be quite correct. A &lt;em&gt;good prognosis&lt;/em&gt; is very different from a &lt;em&gt;cure&lt;/em&gt;. Most of the surgeons, radiation therapists and oncologists I have worked with make that distinction. (Even surgeons, whose mottoes include &quot;A chance to cut is a chance to cure.&quot; and &quot;Nothing heals like cold hard steel.&quot; are careful not to use the word &lt;em&gt;cure&lt;/em&gt;, unless it &lt;em&gt;is&lt;/em&gt; a cure.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not an oncologist, but oncologists do write papers. From one of them:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;METHODS: We analysed postmenopausal women with localised invasive breast cancer. The primary endpoint &lt;strong&gt;disease-free survival (DFS)&lt;/strong&gt;, and the secondary endpoints &lt;strong&gt;time to recurrence (TTR)&lt;/strong&gt;, incidence of new contralateral breast cancer (CLBC), &lt;strong&gt;time to distant recurrence (TTDR)&lt;/strong&gt;, overall survival (OS), and death after recurrence were assessed... FINDINGS: &lt;strong&gt;At a median follow-up of &lt;em&gt;100 months&lt;/em&gt; (range 0-126), DFS, TTR, TTDR, and CLBC were improved significantly in the ITT and hormone-receptor-positive populations.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Although this study only followed patients for 100 months (8.3 years), some studies are much longer, and a cure is what you or I would think of as a cure: &lt;em&gt;disease-free survival&lt;/em&gt;, not of months, but for a lifetime, that is, non-recurrence of the cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your professors sound like they are using the standard approach to &lt;em&gt;cure&lt;/em&gt;, which is to hedge one's bets: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In medicine, a disease is considered cured when it’s been successfully treated and does not return. &lt;em&gt;The concept of “cure” is difficult to apply to cancer because undetected cancer cells can sometimes remain in the body after treatment, causing the cancer to return later (referred to as a recurrence or relapse).&lt;/em&gt; Many cancers are considered “cured” when there is no cancer detected five years after diagnosis. However, recurrence after five years is still possible.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the past, &lt;em&gt;cure&lt;/em&gt; was defined as 5-years cancer free. We now know that that is survival, not cure. The same can be said of 10 years (thought that one runs more true to &lt;em&gt;cure&lt;/em&gt;). The fact is, most studies don't follow patients indefinitely. That doesn't mean no cancer is &quot;cured&quot;. The patients (even many of those in the xkcd comic) without recurrence are &lt;em&gt;cured&lt;/em&gt;. Therefore it is a fallacy to say cancer can never be cured. Semantics and statistics are at play.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I said in my comments, there are &lt;em&gt;curable cancers&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Curable cancers: non-invasive basal cell carcinoma:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nearly every basal cell cancer can be cured, especially when the cancer is found early and treated.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(This is not a hedge. The authors are lumping aggressive BCCs in here with the less aggressive BCCs.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Certain early prostatic cancers:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These results suggest that a patient has a high likelihood of biochemical cure after treatment for prostate carcinoma with conventional doses of external beam RT if he has not demonstrated biochemical failure within 5 years of treatment. Patients with lower pretreatment PSA levels and lower Gleason scores may require longer follow-up than those with less favorable characteristics to achieve the same certainty of cure. Patients who achieve a PSA nadir ≤ 0.4 ng/mL and require ≥ 2.0 years to reach this nadir have the highest probability of cure. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Cervical cancer:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Early cervical cancer can be cured by removing or destroying the precancerous or cancerous tissue. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Colorectal cancer:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Conclusion: Patients who survive 10 years appear to be cured of their disease, whereas approximately one third of actual 5-year survivors succumb to a cancer-related death. In well-selected patients, there is at least a one in six chance of cure after hepatectomy for CLM. The presence of poor prognostic factors does not preclude the possibility of long-term survival and cure.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Childhood acute lymphocytic leukemia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Impressive improvements of survival rates in pediatric acute lymphoblastic leukemia (ALL) have been achieved during the last decades.1–21 Today, a long-term cure can be attained for approximately 75% of patients.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(Although good survival rates - defined by *event free survival - are defined at 6 years in this paper, there are papers which follow to 15 years with little change in the group. Like most studies, longer times mean more patients are &quot;lost to follow-up&quot;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It goes on and on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, my comment was an admonition to you to be wise with your words, not an absolute.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.cancer.net/navigating-cancer-care/cancer-basics/understanding-statistics-used-guide-prognosis-and-evaluate-treatment&quot; rel=&quot;noreferrer&quot;&gt;Understanding Statistics Used to Guide Prognosis and Evaluate Treatment&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ejcancer.com/article/S0959-8049%2808%2900918-0/abstract&quot; rel=&quot;noreferrer&quot;&gt;The cure of cancer: A European perspective&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;https://www.aad.org/dermatology-a-to-z/diseases-and-treatments/a---d/basal-cell-carcinoma/diagnosis-treatment&quot; rel=&quot;noreferrer&quot;&gt;Basal cell carcinoma: Diagnosis, treatment, and outcome&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000893.htm&quot; rel=&quot;noreferrer&quot;&gt;Cervical cancer&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.bloodjournal.org/content/111/9/4477.short&quot; rel=&quot;noreferrer&quot;&gt;Risk-adjusted therapy of acute lymphoblastic leukemia can decrease treatment burden and improve survival: treatment results of 2169 unselected pediatric and adolescent patients enrolled in the trial ALL-BFM 95&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-29T19:03:48.530" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="28149" PostTypeId="1" CreationDate="2015-01-29T19:57:13.347" Score="4" ViewCount="343" Body="&lt;p&gt;Many labs and many projects in biology institutes and university departments have been starting to study chromatin. Chromatin states, chromatin interactions, chromatin loopings, chromatin behaviours, etc. seem to have become the new priority of cancer scientists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm new to this field so there are many things that I still have to understand about chromatin and its relationship to cancer. These questions just flowed into my mind:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the relationship between &lt;strong&gt;chromatin&lt;/strong&gt; and &lt;strong&gt;cancer&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In cancer research, &lt;strong&gt;why is it so important to study chromatin and how chromatin loopings form?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What do scientists would like to find out about chromatin&lt;/strong&gt; when they investigate it?&lt;/p&gt;&#xA;" OwnerUserId="885" LastActivityDate="2015-05-25T19:58:09.677" Title="Why is it important to study chromatin to understand cancer?" Tags="&lt;cancer&gt;&lt;chromatin&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28150" PostTypeId="2" ParentId="21657" CreationDate="2015-01-29T20:34:11.257" Score="4" Body="&lt;p&gt;As far as I know there are 5 receptors for far-red and red light which are the phytochroms(phyA-phyE) Its all about the ratio between red and far-red light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each phytochrom has an inactive(PR) and an active(PFr) conformation. phyA is the only phytochrom which is activated by far-red light, so its active state is PR. (Only if the ratio between red and far-red light is low.) The other phytochroms, are activated by red light (high ratio between red and far-red).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An active phytochrom blocks the COP1/SPA complex. This complex is a E3 ubiquitin ligase which ubiquinates transcription factors for the light answer like HY5 or HFR1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Example:&lt;/strong&gt;&#xA;Under normal light conditions, phyB-phyE is active. They block the COP1/SPA complex so the transcription factors for the light answer are not getting ubiquinated. The plant can get a light phenotyp. &#xA;In the case that a plant grows under another plant, it gets less red light because the higher growing plant uses it for its photosynthesis. phyB-phyE become inactive. COP1/SPA can ubiquinate the transcriptions factors. The plant gets an low light phenotyp by trying to grow out of the shadow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The function of phyA is to produce a light phenotyp if there is a lot of far-red light but almost no red light. Than it is getting activated and blocks the COP1/SPA complex. Under red light phyA is not only inactivated it also gets degraded.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just found a paper for further reading: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828699/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828699/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="13257" LastEditorUserId="13257" LastEditDate="2015-02-04T12:59:10.110" LastActivityDate="2015-02-04T12:59:10.110" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28151" PostTypeId="1" CreationDate="2015-01-29T21:15:31.267" Score="3" ViewCount="362" Body="&lt;p&gt;Think about stored donated blood; What should we check before transfusing it to a patient, to see if blood is still viable?&lt;/p&gt;&#xA;&lt;p&gt;What methods to use?&#xA;What components should it have in what levels, to be counted as viable?&lt;/p&gt;&#xA;&lt;h3&gt;Detailed version of the question, including some background:&lt;/h3&gt;&#xA;&lt;p&gt;Since I'm a software engineer I'm not aware which kind of topics should I search to find answers that I need. Of course I have tried to find publications and books related directly to this topic. But I could not find any. What I need at the moment is some material to do &amp;quot;some reading/research&amp;quot;. And of course, if possible (which I don't know if there are too many possible answers or not) direct answers would be extremely helpful.&lt;/p&gt;&#xA;&lt;p&gt;Of course I have done some research on indirectly related topics. For example; I have read papers about results of blood storage on blood quality etc. But these papers just analyze the effects, while it is not clear for me if these analyzed materials represents viability of blood.&lt;/p&gt;&#xA;&lt;p&gt;For more detail, things those analyzed in few papers that I have read are;&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;CBC: The CBC consisted of 10 parameters: white blood cell (WBC) count, red blood cell (RBC) count, hemoglobin (HGB), hematocrit (HCT), mean cell volume (MCV), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), red cell distribution width (RDW), platelet (PLT) count, and mean platelet volume (MPV).&lt;/li&gt;&#xA;&lt;li&gt;Differantial: consisted of relative percentages (%) and absolute numbers (#) of neutrophils, lymphocytes, monocytes, eosinophils, and basophils.&lt;/li&gt;&#xA;&lt;li&gt;Reticulocyte: The reticulocyte enumeration consisted of relative percentage (retic %) and absolute number of reticulocytes (retic #), and immature reticulocyte fraction(IRF).&lt;/li&gt;&#xA;&lt;li&gt;The NRBC: enumeration consisted of NRBC per 100 WBC (NRBC %) and absolute number of NRBC.&lt;/li&gt;&#xA;&lt;li&gt;Others: Factors V, VII, VIII, X, and XI, protein S (PS), a2-antiplasmin (AP), and fibrinogen; and the activated partial thromboplastin (APTT) and prothrombin (PT) times. Factors VIII and factor IX.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;Still, I'm reading about each of these. What I'm in need is someone help and say; like:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&amp;quot;You are totally lost, these are not related to your case&amp;quot;&lt;/li&gt;&#xA;&lt;li&gt;&amp;quot;You should check this paper which is related to your case&amp;quot;&lt;/li&gt;&#xA;&lt;li&gt;&amp;quot;This, this and this ones in your list are what you are looking for. Focus on them.&amp;quot;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="13258" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-02T18:06:00.260" Title="How do you determine if donated, stored blood is viable?" Tags="&lt;hematology&gt;&lt;transfusion&gt;&lt;blood-transfusion&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28152" PostTypeId="2" ParentId="28145" CreationDate="2015-01-29T21:31:52.237" Score="3" Body="&lt;p&gt;Phosphinothricin is a metabolite from the bacteria &lt;em&gt;Streptomyces viridochromogenes&lt;/em&gt; which has a protein called phosphinothricin N-acetyltransferase (PAT). This Protein inactivates the phosphinothricin which is the reason why &lt;em&gt;S. viridochromogenes&lt;/em&gt; is not dying from it. If you want a plant to be resistant to phosphinothricin you can add the gen for the PAT protein to the plant genom. &#xA;This is also described in this paper about &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16547651&quot; rel=&quot;nofollow&quot;&gt;herbicide-tolerant crobs&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An explanation for the resistant goosegrass could be that somehow it got the gen for PAT, maybe by horizontal gen transfer from &lt;em&gt;S. viridochromogenes&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your case the publication which is cited in your &lt;a href=&quot;http://ucanr.edu/blogs/blogcore/postdetail.cfm?postnum=4338&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt; contains another possibility. &lt;a href=&quot;http://www.wssajournals.org/doi/full/10.1614/WS-D-11-00012.1&quot; rel=&quot;nofollow&quot;&gt;&quot;We hypothesize that reduced herbicide translocation is responsible for resistance to both glyphosate and glufosinate in these populations&quot;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="13257" LastEditorUserId="13257" LastEditDate="2015-01-29T22:16:14.783" LastActivityDate="2015-01-29T22:16:14.783" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28154" PostTypeId="1" CreationDate="2015-01-29T22:34:24.907" Score="2" ViewCount="42" Body="&lt;p&gt;I know that the isoprenoid, jasmonate, glucosinolate, fatty acids, chlorophyll, starch, and aromatic amino acid syntheses are located in the plastid. But I don't know if they are located in the thylakoidlumen or in the stroma. &lt;/p&gt;&#xA;" OwnerUserId="13257" LastActivityDate="2015-01-29T22:34:24.907" Title="Which biosynthetic pathways take place in the plastid and were are they located?" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;metabolism&gt;&lt;plant-physiology&gt;&lt;chloroplasts&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28157" PostTypeId="2" ParentId="21520" CreationDate="2015-01-29T23:41:18.837" Score="2" Body="&lt;p&gt;It is not possible, that a plant grows without any nutrients. Magnesium for example is needed in every chlorophyll, so there is no photosynthesis without magnesium. Another point is that plants can not get nitrogen from the air, so they have to get it from the soil and nitrogen is present in every amino acid, which build the plants proteins. Proteins are essential for every living organism. This are only two points and there are many many others why every plant needs nutrients like nitrogen phophorus, magnesium... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it seems that &lt;em&gt;Epipremnum aureum&lt;/em&gt; does only need water, maybe the plant gets its nutrients from a place you don't expect. Maybe the water is contaminated. Are there leafs falling into the water for example? Another possibility could be that &lt;em&gt;Epipremnum aureum&lt;/em&gt; stored a lot of nutrients before it got only water but this won't last for ever. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read your comment, thats why i think the nutrients have to come from the water. Additionally I found this publication about &lt;a href=&quot;http://hortsci.ashspublications.org/content265606.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Calcium Deficiency Symptoms of Epipremnum aureum&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think you know that tap water or rain water isn't pure H2O. We just measured the tap water in Cologne, by ICP-MS. This is no official measurement, and we measured only once but I think its nice to see whats else in tap water.     Unfortunately we couldn't measure nitrogen, because normally the machine is used for plant extracts and there would be to much nitrogen. &#xA;&lt;img src=&quot;https://i.stack.imgur.com/Bhz1V.jpg&quot; alt=&quot;barplot tap water cologne kalk&quot;&gt;&#xA;Maybe your Epipremnum aureum gets enough nutrients from the water, I don't know if this is possible and how often you change the water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your pot could also be a source for nutrients if its not sealed up. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion the answer is that in general it is not possible, that your plant grows without nutrients. So there is a source which can be only detected by yourself, because you know the exact conditions under which your plant grows. I hope I could give you some hints.&lt;/p&gt;&#xA;" OwnerUserId="13257" LastEditorUserId="13257" LastEditDate="2015-02-03T21:51:49.017" LastActivityDate="2015-02-03T21:51:49.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28158" PostTypeId="2" ParentId="28112" CreationDate="2015-01-30T00:01:50.870" Score="1" Body="&lt;p&gt;Install bioconductor and use this library: &lt;a href=&quot;http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html&quot; rel=&quot;nofollow&quot;&gt;http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can access BioMart which lets you translate between different ID types&lt;/p&gt;&#xA;" OwnerUserId="766" LastActivityDate="2015-01-30T00:01:50.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28159" PostTypeId="1" CreationDate="2015-01-30T00:24:09.270" Score="3" ViewCount="37" Body="&lt;p&gt;I assume that the key biological meaning of cytosine de-methylation during germline development in germline progenitor cells is to reset imprinted genes and then set methylation pattern on these genes according to the gender of the embryo. (this is simply my best guess, so if there is an alternative interpretation, please mention it in the answer)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This de-methylation procedure is dangerous, because DNA-demethylation affects a lot of different regions and some transpons get de-repressed. So there is a risk of novel transposon insertions. However, since it is important to set imprinting in your own gamets properly, the embryo takes this risk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I don't understand why does de-methylation in mammalian development happen twice. Well, the first round it is not as deep and, I am guessing, that the transposons are probably not affected very much during the first round, so the risk of novel transposon insertions is not as high. However, since the resetting of imprinting marks is happening in the second round anyway, why does the embryo bother the first time around at all?&lt;/p&gt;&#xA;" OwnerUserId="13239" LastEditorUserId="13239" LastEditDate="2015-01-30T03:20:07.927" LastActivityDate="2015-01-30T03:20:07.927" Title="Why there are two rounds of cytosine de-methylation in mammalian development?" Tags="&lt;genomics&gt;&lt;development&gt;&lt;mammals&gt;&lt;dna-methylation&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28163" PostTypeId="1" AcceptedAnswerId="28166" CreationDate="2015-01-30T04:03:14.690" Score="-2" ViewCount="11408" Body="&lt;p&gt;Why scientific names of animals &amp;amp; plants are made difficult to spell &amp;amp; remember? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mango: it is easy to spell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Corvus splendens: it is difficult to spell&lt;/p&gt;&#xA;" OwnerUserId="13251" LastActivityDate="2019-02-08T17:00:11.230" Title="Why scientific names of animals &amp; plants are made difficult to spell &amp; remember?" Tags="&lt;nomenclature&gt;" AnswerCount="4" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28164" PostTypeId="1" AcceptedAnswerId="28172" CreationDate="2015-01-30T04:10:16.287" Score="6" ViewCount="1145" Body="&lt;p&gt;Why do the white blood cells allow foreign bodies like sperm to exist inside body cavity without any reaction? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;White blood cells function is to fight against foreign bodies (from the text books). &lt;/p&gt;&#xA;" OwnerUserId="13251" LastEditorUserId="11841" LastEditDate="2015-01-30T05:33:59.027" LastActivityDate="2015-01-31T18:09:41.567" Title="Why White Blood Cells (WBCs) do not react to foreign bodies like sperm?" Tags="&lt;immunology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28165" PostTypeId="1" CreationDate="2015-01-30T04:11:30.717" Score="4" ViewCount="204" Body="&lt;p&gt;As larva, zebra fishes are transparent, at least up to 5-6 days. I wonder what would be the upper limit of the transparent period. This is of relevance considering purposes for imaging.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question primarily relates to normal zebra fish, and not especially to transgenic breeds.&lt;/p&gt;&#xA;" OwnerUserId="13261" LastEditorUserId="9943" LastEditDate="2015-01-30T08:25:28.453" LastActivityDate="2015-01-30T21:26:26.827" Title="How long do zebra fishes remain transparent?" Tags="&lt;development&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28166" PostTypeId="2" ParentId="28163" CreationDate="2015-01-30T04:15:47.970" Score="6" Body="&lt;p&gt;The reason scientific names are difficult to remember is because the scientific names are given in Latin. There are rules to be followed when naming a organism. That the name must be in the form of &lt;em&gt;Genus species&lt;/em&gt; is one of those rules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a person who knows latin, it would be just as easy as the English names are for a English speaking person.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In earlier days, Latin was considered the language of the scholars. That was the reason Latin was chosen for binomial nomenclature. As scholars of all languages learned Latin, just hearing the name would give the hearer an idea of what the organism is even if (s)he had not seen it in person.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;For more on scientific naming and rules while naming see:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Binomial_nomenclature&quot; rel=&quot;noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Binomial_nomenclature&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://education-portal.com/academy/lesson/binomial-nomenclature-definition-classification-system.html&quot; rel=&quot;noreferrer&quot;&gt;http://education-portal.com/academy/lesson/binomial-nomenclature-definition-classification-system.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.curioustaxonomy.net/rules.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.curioustaxonomy.net/rules.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-01-30T04:31:29.260" LastActivityDate="2015-01-30T04:31:29.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28167" PostTypeId="1" AcceptedAnswerId="28191" CreationDate="2015-01-30T04:16:04.713" Score="2" ViewCount="302" Body="&lt;p&gt;If it does occur during meiosis, are the alleles switched over from one sister chromatid to the other during the crossing over process in Prophase I?&lt;/p&gt;&#xA;" OwnerUserId="13143" LastActivityDate="2015-01-30T23:16:49.163" Title="Are alleles passed down and shuffled randomly to the offspring during meiosis or fertilization?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28168" PostTypeId="1" CreationDate="2015-01-30T04:22:28.667" Score="5" ViewCount="10833" Body="&lt;p&gt;I saw a video in which a decapitated snake head still tried to bite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also saw a video in which a man was hit by the moving tail of a dead crocodile.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why do reptiles move even after death? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Reptile&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Reptile&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="13251" LastEditorUserId="36209" LastEditDate="2017-10-19T12:01:42.177" LastActivityDate="2018-09-13T01:02:13.897" Title="Why do reptiles still move even after death?" Tags="&lt;herpetology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28169" PostTypeId="1" CreationDate="2015-01-30T04:26:14.873" Score="11" ViewCount="713" Body="&lt;p&gt;After researching why humans have white scleras when most primates have dark scleras, I stumbled upon the cooperative eye hypothesis. It proposed that white scleras may have evolved on behalf that it is an effective form of communication in that it makes the iris stand out and enables another to clearly see where the eye is looking so as to read expressions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I noticed that dogs, which also have white scleras, use eye direction periodically for expression. Does the cooperative eye hypothesis apply to canines as well? If not, then for what reason might dogs utilize eye movement as they seem to do? Might such a thing be learned behavior?&lt;/p&gt;&#xA;" OwnerUserId="12970" LastEditorUserId="5198" LastEditDate="2015-01-31T22:06:28.140" LastActivityDate="2015-02-01T18:43:52.917" Title="Can canines communicate with each other using gaze direction?" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;dogs&gt;&lt;anthropology&gt;&lt;behaviour&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28170" PostTypeId="2" ParentId="27981" CreationDate="2015-01-30T05:00:04.703" Score="1" Body="&lt;p&gt;The article at linked at the bottom says that the marine organisms keep the concentration of Ammonia under very strict control. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;pH of the ECF (Extra Cellular Fluid) is said to play a very important role. &lt;/li&gt;&#xA;&lt;li&gt;The concentration of ammonia in the environment (ambient ammonia levels) also plays an important role. &lt;/li&gt;&#xA;&lt;li&gt;Less importantly temperature also plays a role.&lt;/li&gt;&#xA;&lt;li&gt;Ionic strength of water also is involved.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The NH&lt;sup&gt;3&lt;/sup&gt;:NH&lt;sup&gt;4+&lt;/sup&gt; ratio seems to be more important than the abosolute value of ammonia.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Ammonia is more toxic than ammonium ion. The lipophilic (ammonia is amphiphilic - soluble in both water and lipid) nature of ammonia allows it to easily cross the cell membrane and the blood brain barrier (in organisms where BBB exist) and affect the physiologic functions. The ammonium ion on the other hand can't enter the cell as easily, as it is not as soluble in lipid as ammonia.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;For ammonia and marine organisms see &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1546509801200053&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S1546509801200053&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;For more on ammonium toxicity see: &lt;a href=&quot;http://www.ucl.ac.uk/~ucbcdab/urea/amtox.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.ucl.ac.uk/~ucbcdab/urea/amtox.htm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-01-30T05:00:04.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28171" PostTypeId="2" ParentId="26333" CreationDate="2015-01-30T05:15:02.303" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Do fruits/ vegetation contain compounds, which help the digestive&#xA;  system to regulate the absorption of fructose? If so, what are they?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, many polyphenols (e.g. resveratrol, curcumin, quercetin, anthocyanins, phloretin, etc.) do this and much more. Each fruit and vegetable has its polyphenol composition. There are other beneficial fruit and vegetable compounds as well, but I'll talk only about polyphenols in the current post.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sucrose is split by digestive enzymes (sucrase, glycoside hydrolase) in the small intestine into fructose and glucose. These enzymes are inhibited by polyphenols. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glucose is transported by SGLT1, while fructose is transported by GLUT5 into enterocytes in the intestines. After that the cells transport these sugars with GLUT2 into the blood. Polypheonls can inhibit these transporters and decrease their expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fructose and glucose is transported to the liver from the blood, with GLUT2, and they do nasty things in there. Fructose is more dangerous than glucose, because it is transformed without any regulation. It uses the same pathways as glucose and mostly fatty acids are created from it, which increase the blood VLDL, LDL, FFA level and cause insulin resistance. The byproducts are urate and free radicals, which cause hyperuricaemia and oxidative stress. Hyperuricaemia cause decreased NO levels (by counteracting with eNOS and reacting with NO directly), which cause increased blood pressure due to vasoconstriction. Hyperuricaemia damages the liver and the kidney too. Too high urate levels enhance LDL oxidation as well, which cause atherosclerosis. The free radicals deplete the antioxidants of the body and cause cancer. Polyphenols prevent atherosclerosis, restore NO levels, restore urate levels, scavenge free radicals, counteract with insulin resistance and prevent liver and kidney damage. So they can fix most of the problems fructose cause.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The interactions of gallic acid and tannic acid with purified brush&#xA;  border sucrase (EC 3.2.1.48) from mouse intestine have been studied.&#xA;  These findings indicate that both gallic acid and tannic acid inhibit&#xA;  sucrase activity, which is pH dependent.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1042/BSR20090012&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1042/BSR20090012&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The effects of tea polyphenols on the sucrase activity are shown in&#xA;  Table .1. Among 10 compounds, esterified (gallated) polyphenols (ECg,&#xA;  EGCg, TF2A, TF2B, and TF3) were potent inhibitors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1271/bbb.57.123&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1271/bbb.57.123&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Quercetin reduced the effect of sucrase and maltase in the in vivo and&#xA;  in vitro treatments.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.nut.2011.01.008&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1016/j.nut.2011.01.008&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In conclusion quercetin and its glycoside derivatives have alfa-glucosidase inhibitory activity and high peroxyl radical scavenging-linked antioxidant activity. The above benefits (anti-hyperglycemia and antioxidant activity) of quercetin and its glycoside derivatives taken together could support the evidence that diets rich in fruits and vegetables are associated with lower incidences of oxidation-linked diseases such as diabetes&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Comparison of Antioxidant Potential and Rat intestinal alfa-Glucosidases inhibitory Activities of Quercetin, Rutin, and Isoquercetin - &lt;a href=&quot;http://ijarnp.org/index.php/ijarnp/article/viewFile/41/41&quot; rel=&quot;nofollow&quot;&gt;http://ijarnp.org/index.php/ijarnp/article/viewFile/41/41&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Phloretin (Ph), which can be obtained from apples, apple juice, and cider, is a known inhibitor of the type II glucose transporter (GLUT2).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1002/mc.20480&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1002/mc.20480&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The ATPase inhibitor quercetin, which inhibits tumor glycolysis, was shown to be a glucose transport inhibitor like the chemically related compound phloretin.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Preferential inhibition by quercetin of mitogen-stimulated thymocyte glucose transport. - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/220448&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/220448&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Glucosides of some other flavonoid classes such as naringenin-7-O-glucoside, genistein-7-O-glucoside and cyanidin-3,5-O-diglucoside were ineffective as well. Thus, dietary quercetin monoglucosides, for example, Q3G and Q4G, have an impact on intestinal nutrient transporters such as SGLT1 and related systems.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1079/BJN20041128&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1079/BJN20041128&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Excessive post-prandial glucose excursions are a risk factor for developing diabetes, associated with impaired glucose tolerance. One way to limit the excursion is to inhibit the activity of digestive enzymes for glucose production and of the transporters responsible for glucose absorption. Flavonols, theaflavins, gallate esters, 5-caffeoylqunic acid and proanthocyanidins inhibit α-amylase activity. Anthocyanidins and catechin oxidation products, such as theaflavins and theasinsensins, inhibit maltase; sucrase is less strongly inhibited but anthocyanidins seem somewhat effective. Lactase is inhibited by green tea catechins. Once produced in the gut by digestion, glucose is absorbed by SGLT1 and GLUT2 transporters, inhibited by flavonols and flavonol glycosides, phlorizin and green tea catechins.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1002/mnfr.201200511&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1002/mnfr.201200511&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In addition, curcumin suppressed glut2 expression by stimulating the activity of peroxisome proliferator-activated receptor-gamma (PPARγ) and de novo synthesis of glutathione. In conclusion, hyperglycemia stimulated HSC activation in vitro by increasing intracellular glucose, which was eliminated by curcumin by blocking the membrane translocation of GLUT2 and suppressing glut2 expression. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.mce.2010.12.028&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1016/j.mce.2010.12.028&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This study investigated the effects of an anthocyanin-rich berry-extract on glucose uptake by human intestinal Caco-2 cells. Acute exposure (15 min) to berry extract (0.125%, w/v) significantly decreased both sodium-dependent (Total uptake) and sodium-independent (facilitated uptake) 3H-D-glucose uptake. In longer-term studies, SGLT1 mRNA and GLUT2 mRNA expression were reduced significantly. Polyphenols are known to interact directly with glucose transporters to regulate the rate of glucose absorption. Our in vitro data support this mechanism and also suggest that berry flavonoids may modulate post-prandial glycaemia by decreasing glucose transporter expression.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0078932&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1371/journal.pone.0078932&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;RES increased SIRT1 expression, but decreased the expression of GLUT5 and aldolase B in aortas from HFr-fed rats. These results suggest that RES contributes to the restoration of HFr-induced vascular dysfunction in rats, at least in part, by up-regulation of SIRT 1 and down-regulation of GLUT5 and aldolase B in the aorta. Moreover, RES may have a positive influence on vasculature by partly restoring the plasma arginine:ADMA ratio and leptin levels.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1139/cjpp-2014-0245&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1139/cjpp-2014-0245&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;High dietary fructose intake: Sweet or bitter life? - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158875/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158875/&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A causal role for uric acid in fructose-induced metabolic syndrome - &lt;a href=&quot;http://ajprenal.physiology.org/content/290/3/F625&quot; rel=&quot;nofollow&quot;&gt;http://ajprenal.physiology.org/content/290/3/F625&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Gut microbial adaptation to dietary consumption of fructose, artificial sweeteners and sugar alcohols: implications for host–microbe interactions contributing to obesity - &lt;a href=&quot;http://www.drperlmutter.com/wp-content/uploads/2014/04/Payne-et-al-2012-Obesity-reviews.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.drperlmutter.com/wp-content/uploads/2014/04/Payne-et-al-2012-Obesity-reviews.pdf&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Early Life Exposure to Fructose and Offspring Phenotype: Implications for Long Term Metabolic Homeostasis - &lt;a href=&quot;http://dx.doi.org/10.1155/2014/203474&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1155/2014/203474&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Dietary fructose, salt absorption and hypertension in metabolic syndrome: towards a new paradigm - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1748-1716.2010.02167.x/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1111/j.1748-1716.2010.02167.x/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Toward a Unifying Hypothesis of Metabolic Syndrome - &lt;a href=&quot;http://pediatrics.aappublications.org/content/129/3/557.short&quot; rel=&quot;nofollow&quot;&gt;http://pediatrics.aappublications.org/content/129/3/557.short&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Uric acid transport and disease - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877959/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877959/&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The present study demonstrates that resveratrol is more effective than metformin in improving insulin sensitivity, and attenuating metabolic syndrome and hepatic oxidative stress in fructose-fed rats.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.phrs.2012.05.003&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1016/j.phrs.2012.05.003&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Quercetin supplementation improved some risk factors of cardiovascular disease, yet exerted slightly pro-inflammatory effects. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.numecd.2011.08.010&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1016/j.numecd.2011.08.010&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In conclusion, dietary HFCS causes vascular insulin resistance and endothelial dysfunction through attenuating IRS-1 and eNOS expressions as well as increasing iNOS in rats. Resveratrol has capability to recover HFCS-induced disturbances.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.fct.2013.07.026&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1016/j.fct.2013.07.026&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The major flavonoid is Quercetin, which belongs to the class called flavonols and is mainly found in apples, tea, onions, nuts, berries, cauliflower, cabbage and many other foods. It exhibits a wide range of biological functions including anticarcenogenic, anti-inflammatory and antiviral; it also inhibits lipid peroxidation, platelet aggregation and capillary permeability. This review focuses on the main effects of Quercetin on obesity and diabetes. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Beneficial Effects of Quercetin on Obesity and Diabetes - &lt;a href=&quot;http://benthamopen.com/tonutraj/articles/V004/189TONUTRAJ.pdf&quot; rel=&quot;nofollow&quot;&gt;http://benthamopen.com/tonutraj/articles/V004/189TONUTRAJ.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These results indicate that resveratrol ameliorated FF A-induced insulin resistance by regulating mTOR and p70-S6K phosphorylation in skeletal muscle cells, through a mechanism involving sirtuins.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Attenuation of skeletal muscle FFA-induced insulin resistance by the polyphenol resveratrol. Elucidation of the mechanisms involved - &lt;a href=&quot;https://dr.library.brocku.ca/handle/10464/2832&quot; rel=&quot;nofollow&quot;&gt;https://dr.library.brocku.ca/handle/10464/2832&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Resveratrol, trans-4-hydroxystilbene, pterostilbene, polydatin, and mulberroside A were found to have antihyperuricemic activities. The uricosuric and nephroprotective actions of resveratrol and its analogues were mediated by regulating renal organic ion transporters in hyperuricemic mice, supporting their beneficial effects for the prevention of hyperuricemia.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1002/mnfr.201100828&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1002/mnfr.201100828&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Adult male Wistar rats were treated with a normal or high-fat/sucrose diet (HFS) with or without Res for 13 weeks. HFS and in vitro treatment with high glucose increased hyperpermeability in rat aorta, heart, liver and kidney and cultured bovine aortic endothelial cells (BAECs), respectively, which was attenuated by Res treatment. Application of Res reversed the changes in eNOS and Cav-1 expressions in aorta and heart of rats fed HFS and in BAECs incubated with high glucose. Res stimulated the formation of NO inhibited by high glucose in BAECs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1371/journal.pone.0113716&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1371/journal.pone.0113716&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In summary, all 3 tea polyphenol extracts induced weight loss and anti-inflammatory and angiogenic effects, although the tissue content of polyphenols differed significantly. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.3945/jn.114.191007&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.3945/jn.114.191007&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Blackcurrants and lingonberries, as either whole berries or nectars, optimize the postprandial metabolic responses to sucrose. The responses are consistent with delayed digestion of sucrose and consequent slower absorption of glucose.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.3945/ajcn.112.042184&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.3945/ajcn.112.042184&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Resveratrol prevented the HFS-induced arterial wall inflammation and the accompanying increase in PWV. Dietary resveratrol may hold promise as a therapy to ameliorate increases in PWV.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.cmet.2014.04.018&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1016/j.cmet.2014.04.018&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Taken together the data suggest that dietary flavonoids exhibit three distinct modes of action with regard to cancer prevention, based on their hydroxyl and methoxy decoration: (1) inhibitors of CYP1 enzymatic activity, (2) CYP1 substrates and (3) substrates and inhibitors of CYP1 enzymes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/j.bmc.2011.03.042&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1016/j.bmc.2011.03.042&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These data demonstrate that resveratrol inhibits CYP1A1 expression in vitro, and that it does this by preventing the binding of the AHR to promoter sequences that regulate CYP1A1 transcription. This activity may be an important part of the chemopreventive activity of resveratrol. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9865727&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/9865727&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As a chemoprevention agent, resveratrol has been shown to inhibit tumor initiation, promotion, and progression, as well as inhibit the growth of cancerous cells through increased apoptosis and/or cell cycle blockage. Inflammatory processes are associated in the pathogenesis of many chronic diseases including heart disease and cancer. Resveratrol has been shown to reduce inflammation via inhibition of prostaglandin production, cyclooxygenase-2 activity, and nuclear factor-кB activity. In addition, the estrogenic activity of resveratrol may help prevent post-menopausal bone loss. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1111/j.1541-4337.2006.00001.x&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1111/j.1541-4337.2006.00001.x&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These findings suggest that fructose-induced metabolic syndrome is attenuated by the polyphenol-rich fraction of amla.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1017/S0007114509991978&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1017/S0007114509991978&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2015-01-30T05:15:02.303" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28172" PostTypeId="2" ParentId="28164" CreationDate="2015-01-30T05:30:36.963" Score="6" Body="&lt;p&gt;Majority of white blood cells in general are present only within blood vessels, lymph vessels and lymph nodes. In addition various organs have locally adapted specialised immune cells. For example brain has microglia, Liver has kupfer cells, etc... Specialised immune cells are present along the mucosal linings which are named differently in different regions - Peyer's patch in the jejunum and ileum, tonsils in oral cavity, adenoids in the nasopharynx, etc...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As sperm &lt;strong&gt;do not enter&lt;/strong&gt; blood vessels, only local mucosal immunity will act on them. There is a local immune response to the sperm in the vaginal mucosa. However, the immune response to the sperm is transient. Several hypotheses have been put forth to explain this:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The seminal plasma suppresses the immune response. This is supported by the fact that sperm, if introduced without seminal plasma, do elicit an immune response--however this suppression seems to be inconsistent&lt;/li&gt;&#xA;&lt;li&gt;Insemination might activate a sequence that results in active immune tolerance to paternal antigens (antigens present in sperm)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;For details see here:&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1782486/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1782486/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="1306" LastEditDate="2015-01-31T18:09:41.567" LastActivityDate="2015-01-31T18:09:41.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28173" PostTypeId="1" AcceptedAnswerId="28174" CreationDate="2015-01-30T09:07:11.237" Score="8" ViewCount="2103" Body="&lt;p&gt;If we get stitches, we get marks left on the skin, but there are no marks for breast enlargements. I saw a YouTube video about a breast enlargement wherein a doctor makes a cut. Where does the cut mark go after surgery?&lt;/p&gt;&#xA;" OwnerUserId="13263" LastEditorUserId="-1" LastEditDate="2015-01-30T17:45:53.807" LastActivityDate="2015-01-31T17:25:09.787" Title="Why don't breast enlargements leave any marks of surgery on breasts?" Tags="&lt;human-biology&gt;&lt;surgery&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28174" PostTypeId="2" ParentId="28173" CreationDate="2015-01-30T11:14:49.347" Score="19" Body="&lt;p&gt;All cuts that go through the dermis (the full thickness of skin) will leave a scar, no matter what (and no matter what anyone tells you). The visibility of scar tissue has a lot to do with how a person heals, how much stress is put on the incision as it's healing, where the scar is, if it crosses the natural direction of skin (called &lt;a href=&quot;http://en.wikipedia.org/wiki/Langer%27s_lines&quot; rel=&quot;noreferrer&quot;&gt;Langer's lines&lt;/a&gt;) or goes along the lines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plastic surgeons have many years of training and experience in cosmetic skin surgery, and know how to minimize scar formation by their more fastidious closure methods and wound care, as well as hiding scars in ceases and along Langer's lines. But even the best plastic surgeons cannot prevent scars, only minimize them. If you still don't believe breast augmentation doesn't leave scars, you can &lt;a href=&quot;https://www.google.com/search?hl=en&amp;amp;authuser=0&amp;amp;site=imghp&amp;amp;tbm=isch&amp;amp;source=hp&amp;amp;biw=1239&amp;amp;bih=684&amp;amp;q=breast+implants&amp;amp;oq=breast&amp;amp;gs_l=img.1.5.0l10.2211.10625.0.15472.6.5.0.1.1.0.64.302.5.5.0.msedr...0...1ac.1.61.img..0.6.305.C53TAlenBRo#hl=en&amp;amp;authuser=0&amp;amp;tbm=isch&amp;amp;q=breast+implants+scars&quot; rel=&quot;noreferrer&quot;&gt;look at this page (NSFW)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-01-31T17:25:09.787" LastActivityDate="2015-01-31T17:25:09.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28175" PostTypeId="1" AcceptedAnswerId="28176" CreationDate="2015-01-30T11:41:26.410" Score="6" ViewCount="1062" Body="&lt;p&gt;If we insert a plasmid into a &lt;strong&gt;human nucleus&lt;/strong&gt; that contains exact copy of gene and all relevant promoters to produce &lt;strong&gt;some human protein&lt;/strong&gt;,  will the cell create functional protein from that plasmid &lt;strong&gt;only&lt;/strong&gt; when the cell needs it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not talking about inserting DNA to some chromosome. Inserting separate plasmid to the nucleus (transient transfection).&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="10104" LastEditDate="2015-01-30T12:37:21.093" LastActivityDate="2017-10-08T03:25:48.920" Title="Plasmid in the nucleus and gene expression" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;gene-expression&gt;&lt;plasmids&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28176" PostTypeId="2" ParentId="28175" CreationDate="2015-01-30T11:59:08.197" Score="8" Body="&lt;p&gt;If you transfect cells with plasmid then these plasmids need to go into the nucleus (otherwise they wouldn't be transcribed). Getting the plasmid either happens during cell division (when the nucleus is not present) or by adding a signal sequence to the plasmid which induces the import into the nucleus through nuclear pores. The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8956280&quot; rel=&quot;noreferrer&quot;&gt;SV40 sequence&lt;/a&gt; is an example of such a sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have the right promoter present on the plasmid, you can basically express any protein in the cell (unless it's toxic). The promoter either needs to come from the organism from which the cells are or has to be something universally activated like the CMV promoter (from the cytomegalo virus).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good example for this is the expression of green fluorescent protein (GFP) which originates from jellyfish and can be expressed in cells to make them glow green (from &lt;a href=&quot;http://www.thermoscientificbio.com/transfection/turbofect-transfection-reagent/&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/evBzT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Untransfected cells or cells transfected with an empty plasmid (without GFP) don't glow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Targeting specific cells or control the specific activation of genes only in one cell type is possible. For both you need sequence (and cell specific) promoter sequences which either allow the nuclear import (see reference 1-3) or the expression from a cell type specific promoter (see reference 4).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has been done in the liver of mice in which the ApoE has been knocked-out. The expression of the human ApoE gene with a specific promoter led to the correction of the hypercholesterolemia the mice were suffering from. This needs a lot of knowledge on the promoter as well as on the other transcriptional regulation elements in the specific gene (see reference 4).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10455402&quot; rel=&quot;noreferrer&quot;&gt;Cell-specific nuclear import of plasmid DNA.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19393704&quot; rel=&quot;noreferrer&quot;&gt;Tissue-specific and transcription factor-mediated nuclear entry of&#xA;DNA.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20200566&quot; rel=&quot;noreferrer&quot;&gt;Progress and prospects: nuclear import of nonviral vectors.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.filedropper.com/wooddell2008&quot; rel=&quot;noreferrer&quot;&gt;Sustained liver-specific transgene expression from the albumin&#xA;promoter in mice following hydrodynamic plasmid DNA delivery.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-01-30T15:05:53.087" LastActivityDate="2015-01-30T15:05:53.087" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="28177" PostTypeId="1" AcceptedAnswerId="28179" CreationDate="2015-01-30T13:18:55.490" Score="34" ViewCount="13265" Body="&lt;p&gt;Lately I have seen a number of unrelated &quot;scientific&quot; debates over whether certain substances should be outlawed because they are toxic to humans. My initial, informal reaction is usually to respond that anything is toxic to humans if you give them a sufficiently large dose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, formally I don't know if that's really true for &lt;em&gt;everything&lt;/em&gt; a human being could ingest in some way. I started to wonder if there were some substances that our body could handle unlimited amounts of without any negative consequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As this question has been (correctly) identified as a bit vague, I'll try to explain what i'm looking for. For the purposes of this question, I'm willing to ignore the limitations of actually ingesting a given substance in &quot;the usual way&quot;. For example, if you can't physically drink enough of some liquid fast enough to kill you without your stomach filling up and vomiting, but that same liquid injected intravenously &lt;em&gt;could&lt;/em&gt; be lethal, I could consider that toxic. I also recognize that the body can only physically contain a certain volume of stuff, after which sheer pressure would cause it to fail; I'm more interested in &quot;biochemical toxicity&quot; as opposed to any physical damage (I just don't know the term for what I'm looking for.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, one of my goals is to learn if, under laboratory conditions, a properly motivated researcher could &lt;em&gt;always&lt;/em&gt; find a dose that would be toxic, regardless of the impracticality of a real person ingesting that dose under normal circumstances.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, with that qualification, my ultimate question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any substance we know of that is completely non-toxic to humans at arbitrarily large doses ingested over an arbitrarily short period of time?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="6548" LastEditorUserId="6548" LastEditDate="2015-01-30T23:12:27.753" LastActivityDate="2017-04-26T05:55:42.550" Title="Is there anything that is completely non-toxic to humans at any dose?" Tags="&lt;toxicology&gt;" AnswerCount="8" CommentCount="10" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="28178" PostTypeId="2" ParentId="28177" CreationDate="2015-01-30T14:01:34.103" Score="10" Body="&lt;p&gt;There is a problem with definition of toxicity &amp;mdash; things that are dangerous in large amounts aren't usually called toxic. In spite of this, you're right: everything can be dangerous to a human in large enough amounts, or if delivered improperly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, &lt;a href=&quot;https://en.wikipedia.org/wiki/Water_intoxication&quot; rel=&quot;noreferrer&quot;&gt;even water can be toxic if drank too much&lt;/a&gt;. Also, when it gets into the lungs, it may cause drowning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, air, while necessary in lungs, is dangerous if present as a gas in the bloodstream.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW, even botox (being one of the strongest poisons) &lt;a href=&quot;https://en.wikipedia.org/wiki/Botulinum_toxin&quot; rel=&quot;noreferrer&quot;&gt;is used in medicine in very small doses&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="13094" LastEditorUserId="10062" LastEditDate="2015-02-02T00:41:19.943" LastActivityDate="2015-02-02T00:41:19.943" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28179" PostTypeId="2" ParentId="28177" CreationDate="2015-01-30T14:31:12.700" Score="33" Body="&lt;p&gt;I’ll answer this theoretically, since that’s how it has been posed. And if we’re ignoring practicalities, we may as well posit that the substance in question will be introduced directly into the bloodstream (This is, of course, simple to do in reality, but not how most people consume their non-toxic substances.) The easiest way to show that any unspecified substance can be toxic at an unlimited volume is to invoke the human body’s mechanisms for volume homeostasis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As mentioned in &lt;a href=&quot;https://biology.stackexchange.com/a/24406/9268&quot;&gt;this answer&lt;/a&gt;, the human kidneys functioning optimally can produce up to ~ 25 L/day of urine.&lt;sup&gt;1&lt;/sup&gt; This would require complete suppression of &lt;a href=&quot;http://en.wikipedia.org/wiki/Vasopressin&quot; rel=&quot;nofollow noreferrer&quot;&gt;ADH&lt;/a&gt; (anti-diuretic hormone, a.k.a. arginine vasopressin), which would occur only if the “toxin” load were markedly hypotonic (think water).&lt;sup&gt;2&lt;/sup&gt;  There is therefore a theoretical maximum &lt;strong&gt;volume&lt;/strong&gt; of any substance that can be dealt with by the body, which is something less than 25 L per day. (For any substance &lt;em&gt;other than&lt;/em&gt; water, the maximum will be lower because ADH will not be as fully suppressed by a less hypotonic load.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A volume of any substance introduced into the bloodstream (including a product precisely mimicking the constituents of the bloodstream itself!) will overwhelm the body’s homeostatic mechanism. This will result in edema which is unpleasant and, in the case of &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000140.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;pulmonary edema&lt;/a&gt;, certainly pathologic - a “toxidrome” in your scenario. In the case of hypotonic fluids, serum osmolality will also fall causing &lt;a href=&quot;http://en.wikipedia.org/wiki/Hyponatremia&quot; rel=&quot;nofollow noreferrer&quot;&gt;hyponatremia&lt;/a&gt; with all of its consequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Summary&lt;/strong&gt;: No, the human body can not tolerate an unlimited volume of anything, therefore there is no substance that is non-toxic &quot;at any dose.&quot; &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;1. Christopher Lote. (2012). Principles of Renal Physiology. Springer New York.&#xA;&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;2. No, you may not drink 25 liters of water per day. For one thing, urine can not be made with a tonicity of 0 to balance this (more like 60 mOsm/kg minimum). Additionally, ADH can rarely be completely suppressed, yielding a somewhat more concentrated urine and therefore lower tolerance for hypotonic intake before serum osmolality is compromised.&#xA;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-01-30T16:10:57.530" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="28180" PostTypeId="1" CreationDate="2015-01-30T15:12:58.977" Score="1" ViewCount="99" Body="&lt;p&gt;I have been trying to immobilize DNA by the bioconjugation of biotin and streptavidin, but I cannot get this work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I added EDC and streptavidin to &lt;code&gt;COOH&lt;/code&gt; functionalized resin, reacted for 3 hours in room temperature, and then washed with PBS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then I tried to anneal biotin-labeled primer and FAM-labeled complementary sequence. (Heated it up to 95 degree then let it cool down to room temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After I added SA-functionalized resin and FAM-Biotin strands together, the conjugation wouldn't work. The resins are not fluorescent after wash.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also tried to use &lt;code&gt;PCR&lt;/code&gt; products which are labeled on both side.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any problem with my assay? How long it takes for the conjugation of biotin and SA at very low concentration?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for any information.&lt;/p&gt;&#xA;" OwnerUserId="10422" LastActivityDate="2015-01-30T15:12:58.977" Title="Cannot conjugate Biotin-labeled DNA to Streptavidin-labeled solid surface" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;pcr&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28182" PostTypeId="2" ParentId="28177" CreationDate="2015-01-30T15:36:53.800" Score="11" Body="&lt;p&gt;It depends largely on the method of administration. If you are atomizing the substance and delivering it via water vapor, many, many substances have no known LDLo (lowest dose required to kill a member of the tested population). Almost any substance in existence has the potential to kill you if it is diluting your bloodstream via direct intravenous injection or oral consumption; however, when it comes to inhalants, many substances cannot kill you. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since your question was specific to intoxicants, here's a couple of examples: There is no LDLo level of Tetrahydrocannabinol (the active ingredient in marijuana) when delivered via atomization. There is also no known LD50 (a similar, albeit somewhat less reliable, metric) for lysergic acid diethylamide (commonly referred to as LSD). For psilocybin (the active ingredient in &quot;magic mushrooms&quot;), the LD50 is high enough that an average person would need to ingest around 6 pounds before cause for concern.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other far more dangerous substances that can kill with vastly lower amounts include anything that speeds or slows the heart rate: most specifically, cocaine (including crack), opiates (including morphine, heroin, and various pain pills), and any amphetamine, methamphetamine or derivative substance, or other stimulant (crystal meth, ADHD medication, and even caffeine or ephedrine). Of course, the most common killer categorically from a historical perspective is alcohol.&lt;/p&gt;&#xA;" OwnerUserId="615" LastEditorUserId="615" LastEditDate="2015-01-30T15:43:09.273" LastActivityDate="2015-01-30T15:43:09.273" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28183" PostTypeId="2" ParentId="28173" CreationDate="2015-01-30T15:54:51.663" Score="2" Body="&lt;p&gt;They don't always cut through the breast.  The armpit is a common alternative to slicing the breast tissue.  In these cases, there is absolutely no scarring on the breast of any kind.&lt;/p&gt;&#xA;" OwnerUserId="13266" LastActivityDate="2015-01-30T15:54:51.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28184" PostTypeId="2" ParentId="28088" CreationDate="2015-01-30T16:12:33.610" Score="0" Body="&lt;p&gt;This isn't much of an answer but here goes... Two things; it depends on which day of the period it is. There can be rather brief, heavy bleeding on the later part of the first day or sometime during the second. On most others days, the bleeding will be lighter with drop every now and again. I think most women would agree with me on the fact that when there is a rather heavy flow it can be felt. So, to boil things down, the correct answer is C.&#xA;Here are a couple of links to sites that will back me up on this: &lt;a href=&quot;http://advicefromannamarie.weebly.com/before-your-first-period.html&quot; rel=&quot;nofollow&quot;&gt;Advice From AnnaMarie&lt;/a&gt; and &lt;a href=&quot;http://youngwomenshealth.org/2010/04/21/menstrual-periods/&quot; rel=&quot;nofollow&quot;&gt;Center for Young Women's Health&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6289" LastEditorUserId="6289" LastEditDate="2015-02-04T02:39:40.807" LastActivityDate="2015-02-04T02:39:40.807" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28185" PostTypeId="2" ParentId="28101" CreationDate="2015-01-30T16:21:45.917" Score="5" Body="&lt;p&gt;A good answer is already provided by @canadianer, but as with many things in biology it is important to keep in mind what organism and/or cell type we are talking about. Because the nuances of the answer to a question about a seemingly universal process sometimes actually depend on whether we want to know about bacteria, or fungi, or mammalian stem cells, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I think the answer to your question is that synonymous codons are not always interchangeable because of what @canadianer described, but regulation of codon usage is probably more relevant in context of prokaryotes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, for sure availability of a particular synonymous tRNA can be rate limiting in protein synthesis in prokaryotes, but I actually haven't heard of this happening in a eukaryotic system. If there are demonstrated examples, please paste it in the comment..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, the secondary structure of the coding part of mRNA is probably less important in eukaryotes, since they have a multitude of ubiquitous RNA-binding proteins that practically coat mRNA (e.g. hnRNP in the nucleus, and probably something similar in the cytoplasm, too)&lt;/p&gt;&#xA;" OwnerUserId="13239" LastActivityDate="2015-01-30T16:21:45.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28189" PostTypeId="2" ParentId="28165" CreationDate="2015-01-30T21:26:26.827" Score="3" Body="&lt;p&gt;The upper limit of transparency time of zebrafishes is anywhere from two to three weeks for normal zebrafish for optimal high-resolution imaging. However, there is a modified species of Zebrafish called 'Casper' which is now the preferred zebrafish strain for studies in cancer and other research, because the length of transparency lasts into adulthood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://medicalphysicsweb.org/cws/article/research/51394&quot; rel=&quot;nofollow&quot;&gt;http://medicalphysicsweb.org/cws/article/research/51394&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.mit.edu/people/lisa_steiner#research_summary&quot; rel=&quot;nofollow&quot;&gt;https://biology.mit.edu/people/lisa_steiner#research_summary&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.the-scientist.com/?articles.view/articleNo/34834/title/Models-of-Transparency/&quot; rel=&quot;nofollow&quot;&gt;http://www.the-scientist.com/?articles.view/articleNo/34834/title/Models-of-Transparency/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11631" LastActivityDate="2015-01-30T21:26:26.827" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28190" PostTypeId="1" CreationDate="2015-01-30T21:36:15.907" Score="6" ViewCount="119" Body="&lt;p&gt;I am new to reading raw DNA. When comparing two people's raw data, why does one person have a different SNP than the other, at the same location, on specific chromosome? But on a different chromosome there will be the same SNP, at the same location, for both people. &lt;/p&gt;&#xA;" OwnerUserId="13270" LastEditorUserId="13094" LastEditDate="2015-01-31T03:50:03.060" LastActivityDate="2015-02-04T14:03:21.293" Title="SNPs and locations" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28191" PostTypeId="2" ParentId="28167" CreationDate="2015-01-30T22:04:47.970" Score="2" Body="&lt;p&gt;Crossing over/synapsis in Prophase I of Meiosis I is when alleles are switched over from one non-sister homologous chromatid to another non-sister homologous chromatid. This happens before fertilization ever happens. Meiosis occurs even before birth in females in order to make gametes in the form of oocytes. In contrast, this frequently occurs in men who continue to produce gametes in the form of spermatocytes throughout their lifetime. Fertilization simply refers to the fusion of two gametes-- a spermatocyte and oocyte combining together-- and does not involve meiosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a short and straightforward &lt;a href=&quot;https://www.youtube.com/watch?v=vA8aMpHwYh0&quot; rel=&quot;nofollow&quot;&gt;Youtube video about Meiosis&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="11631" LastEditorUserId="11631" LastEditDate="2015-01-30T23:16:49.163" LastActivityDate="2015-01-30T23:16:49.163" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28192" PostTypeId="2" ParentId="28169" CreationDate="2015-01-30T22:46:05.693" Score="3" Body="&lt;p&gt;It is hypothesized that the starkness of white sclera against darker colors of the pupil and iris is a unique mutation in primates that have become prevalent in human beings because it enhanced our ability to communicate with other humans and animals, including dogs, by more clearly communicating where we are looking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YiMRe.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it has not yet been established that dogs use this communication with each other, communicating more commonly with other means such as body language, head direction, vocalizations, etc. Some dogs, especially domesticated ones, do have white sclera and it is proposed that this is due to unintentional selection by humans who have a preference for such features. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NdO6h.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is extremely fascinating is that this 'mutation' occasionally occurs in chimpanzees and apes, too, but has not become prevalent in their respective populations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rd3MI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.dailymotion.com/video/x1e14ko_the-secret-life-of-dogs-documentary-in-hd_tech&quot; rel=&quot;nofollow noreferrer&quot;&gt;Secret Life of Dogs- BBC Film&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.academia.edu/3374272/Do_the_Eye_Have_It&quot; rel=&quot;nofollow noreferrer&quot;&gt;Do the Eye Have It?-Academia&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://carta.anthropogeny.org/moca/topics/visible-whites-eyes&quot; rel=&quot;nofollow noreferrer&quot;&gt;Common feature in domesticated dogs-CARTA&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3873274/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Juvenile features-NIH&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11631" LastEditorUserId="11631" LastEditDate="2015-02-01T18:43:52.917" LastActivityDate="2015-02-01T18:43:52.917" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28193" PostTypeId="2" ParentId="28177" CreationDate="2015-01-31T00:21:20.153" Score="4" Body="&lt;p&gt;The inert gasses Helium and Neon are non-toxic when administered through inhalation, so long as the patient's oxygen supply is sufficient.  They are also non-toxic when injected, so long as the injection is slow enough for them to be dissolved in the bloodstream.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can be killed by them through various means (asphyxiation through oxygen displacement, rapid injection causing an air embolism, rapid decompression causing decompression sickness, and so on), but since the cause of death is unrelated to the chemical properties of the substance involved, it's not accurate to call this &quot;toxicity&quot; (unless you're &lt;a href=&quot;http://xkcd.com/1260/&quot; rel=&quot;nofollow&quot;&gt;XKCD&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other inert gasses (Argon, Krypton, Xenon) may be toxic at high pressures: although I haven't found an LD50 for any of them, they can all induce &lt;a href=&quot;https://en.wikipedia.org/wiki/Nitrogen_narcosis&quot; rel=&quot;nofollow&quot;&gt;nitrogen narcosis&lt;/a&gt;, and Xenon is usable as a general anesthetic.&lt;/p&gt;&#xA;" OwnerUserId="5862" LastEditorUserId="5862" LastEditDate="2015-01-31T20:05:53.803" LastActivityDate="2015-01-31T20:05:53.803" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="28195" PostTypeId="2" ParentId="28177" CreationDate="2015-01-31T01:32:08.950" Score="-1" Body="&lt;p&gt;Vitamin C won't kill you no matter how much you get into your body as long as it is enough to help prevent arterial wounds and atherosclerosis(This happens in people with scurvy or vitamin C deficiency because of how cholesterol is used to help repair the wounds and this can lead to a complete blockage of the artery and thus an infarction of all the tissue that artery supplies. So if you don't want to have an MI, one of the things you have to do is get vitamin C into your system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example of this is chloride ions. While having high chloride ions might cause there to be a slower reaction time(since chloride acts as an inhibitor in neurons) it itself won't kill you. Yes it might affect the muscles by not having them contract as much as they are supposed to but this is naturally cured by urinating out more chloride and thus more sodium which can lead to a sodium deficiency which is bad because your body needs sodium in order to function. With a low amount of it it you wouldn't be able to think clearly or even have a normal heart rhythm which might lead to bradycardia from a higher pottasium concentration in the heart. &lt;/p&gt;&#xA;" OwnerUserId="5851" LastActivityDate="2015-01-31T01:32:08.950" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28196" PostTypeId="1" CreationDate="2015-01-31T02:43:18.217" Score="2" ViewCount="830" Body="&lt;p&gt;I did an experiment using nine different substrates (Lactose + lactase, corn, sugar cane, glucose control, wood, grass, no yeast control and yeast control) and observed their fermentation rates. Lactose + lactase had the highest fermentation rate. So now my question is: is there a usage of lactase in aiding the break down of lactose to make biofuels? I did a web search and all I could find was that lactase was used for helping lactose-intolerant people,etc.  And that the current whey-ethanol industry used special species of yeast that break down lactose directly instead of the enzyme lactase. There are other methods too, including the Carbery and the Bio-process Innovation (BPI) processes; all of which use yeast that can directly break down lactose. Does lactase play no role in the biofuel industry? And why don't people use lactase to aid them in making biofuels? &lt;/p&gt;&#xA;" OwnerUserId="13277" LastEditorUserId="6289" LastEditDate="2015-01-31T03:40:20.790" LastActivityDate="2015-01-31T03:40:20.790" Title="Why not use lactase to aid the break down of lactose when making biofuels?" Tags="&lt;yeast&gt;&lt;fermentation&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28198" PostTypeId="2" ParentId="28169" CreationDate="2015-01-31T03:44:09.090" Score="2" Body="&lt;p&gt;A new study published in the journal &lt;em&gt;PLoS One&lt;/em&gt; compared facial characteristics, gazing behaviors, and sociality of 26 different canid species (including wolves, bush dogs, and Arctic foxes). The researchers found that animals with eyes and facial features that are easier to discern are more likely to live and hunt socially. (One of the authors, S. Kohshima, has studied the morphology of the human eye, its adaptive meaning, and has done comparative studies on external morphology of the primate eye.)&lt;/p&gt;&#xA;&lt;p&gt;In this paper, the authors identified three face-eye types based on four contrast indices: the A-type, in which both pupil position in the eye outline &lt;em&gt;and&lt;/em&gt; eye position in the face were conspicuous (11 species, including wolves and coyotes); the B-type, in which only eye position on the face was conspicuous (9 species, including the Fennec fox and jackals); and the C-type, in which both the pupil and eye position were inconspicuous (6 species, including the bush dog and the African wild dog).&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yZj5N.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;They compared group living vs. solo/pair living, group hunting vs. solo hunting, gaze duration and other parameters. Citing supporting evidence from other authors as well, they found that in species engaging in group living, 8 of 10 study species exhibit A-type faces. African wild dogs (C-type) use their white-tipped tails as visual signals, and like dingos, use vocalization, suggesting a developed acoustic communication. In contrast, gray wolves made almost no sound even during play or fighting but had more gazing behavior in more postures. Therefore, species with B- or C-type faces that in engage group living may use acoustic and/or other visual signals instead of the gaze signal as their primary means of communication (as is true for wolves and dogs). The enhanced gaze-signal of the A-type face could be disadvantageous during hunting, as prey animals could use the gaze signal to realize that they have been targeted by the predator and then prepare to escape. A-type faces were more common, then, in group hunting, where solo hunters were more commonly B or C-type faces.&lt;/p&gt;&#xA;&lt;p&gt;In gray wolves, the gazing behavior (0.5s on average to humans, 3.32s average with up to 38s maximum with other wolves), termed &lt;em&gt;conspecific&lt;/em&gt; with others of the same species, suggest that the gaze signal of gray wolves is mainly used for communication among conspecifics.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;These results suggest that the facial color pattern of canid species is related to their gaze communication and that canids with A-type faces, especially gray wolves, use the gaze signal in conspecific communication... Our comparison of face morphology and gazing behavior among canid species highlighted the gaze-signal communication in species with A-type faces, especially gray wolves, and provided a novel perspective for studies on their communication and morphology.&lt;/p&gt;&#xA;&lt;p&gt;Could the cooperative eye hypothesis apply to dogs as well? If not, then for what reason might dogs utilize eye movement as they seem to do?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Yes. (By the way, many dogs have white sclera.) The difficulty is that dogs are usually raised alone with humans and can lose the ability to &amp;quot;read&amp;quot; other dogs. One study, however, examined the behavior of dogs with human social cues (such as gazing) and conspecific (other dog) social cues. (Primates have been found to respond to conspecific social cues more than human gaze/pointing.) When the informant in this study (the one giving the cues) was an unfamiliar human, dogs responded well to gaze and gaze/pointing. However, when the informant was an unfamiliar dog (tethered, standing still, no human around to look at), the dogs were also able to follow the &lt;em&gt;gaze&lt;/em&gt; of the informant dog, even when the body pointed elsewhere. Furthermore,&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;This skill with conspecifics is somewhat surprising because many of these domestic dogs had had only limited experience with other dogs. Indeed, the one intriguing developmental finding was that the 6-month old juvenile was &lt;em&gt;only able to use cues produced by conspecifics&lt;/em&gt;, whereas two 4-year olds (the oldest in the sample) were only able to use human cues. ...it does suggest the hypothesis that many dogs are able to use conspecific gaze cues from early in life without extensive experience with conspecifics, and then ontogenetically, they extend this ability to humans (to some degree on the basis of similarities in human and dog facial features) as they interact with them - perhaps in some cases to the point that they lose their ability with conspecifics.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;If more studies focused on conspcific cues among dogs instead of focusing on their interactions with humans, I think this behavior would be borne out and would be readily established.&lt;/p&gt;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098217&quot; rel=&quot;nofollow noreferrer&quot;&gt;A Comparison of Facial Color Pattern and Gazing Behavior in Canid Species Suggests Gaze Communication in Gray Wolves (Canis lupus)&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016888&quot; rel=&quot;nofollow noreferrer&quot;&gt;Development of Gaze Following Abilities in Wolves (Canis Lupus)&lt;/a&gt; (interesting video)&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://evolutionaryanthropology.duke.edu/uploads/assets/HareTomasello1999_DomesticDogsUseCues%20.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Domestic Dogs (Canis familiaris) Use Human and Conspecific Social Cues to Locate Hidden Food&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2251326/&quot; rel=&quot;nofollow noreferrer&quot;&gt;A Review of Domestic Dogs' (Canis Familiaris) Human-Like Behaviors: Or Why Behavior Analysts Should Stop Worrying and Love Their Dogs&lt;/a&gt; (just a cool paper)&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-01-31T22:27:39.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28199" PostTypeId="2" ParentId="28177" CreationDate="2015-01-31T04:37:57.527" Score="2" Body="&lt;p&gt;not even AIR, because if you force too much you will explode it depends on how extreme is the &quot;any dose&quot; statement&lt;/p&gt;&#xA;&#xA;&lt;p&gt;water is also toxic in large Ingestible amounts&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and since we go into theoretical application the answer would be dark matter &lt;/p&gt;&#xA;&#xA;&lt;p&gt;so the final answer is nothing , because the human body has evolved to exist in some equilibrium, so too much of one thing even if is harmless it itself ( like water, or proteins ) it causes an imbalance, and as a result it becomes &quot;toxic&quot;&lt;/p&gt;&#xA;" OwnerUserId="13280" LastActivityDate="2015-01-31T04:37:57.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28201" PostTypeId="2" ParentId="28163" CreationDate="2015-01-31T07:53:52.923" Score="1" Body="&lt;p&gt;The question bares a resentment to awkward sounding Latin names. It is unfortunate, since there is surely logic in Latin nomenclature.., but admittedly  it is also unfortunately a steep learning curve to learning some Latin. Anyway, having one gold standard nomenclature, no matter how stupid it sounds, is a blessing for scientist of the field (it's coming from a genomics-ist dealing with alternative gene names on a daily basis where there is no Latin-like-gold-standard and alternative databases compete for rightfulness of their logic and nomenclature). I work on a protein called Mili, and in dozens of papers it is called so, but I cannot guess without googling how it is called in RefSeq or Ensemble power houses of genomic annotations &lt;/p&gt;&#xA;" OwnerUserId="13239" LastActivityDate="2015-01-31T07:53:52.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28203" PostTypeId="2" ParentId="19938" CreationDate="2015-01-31T13:21:07.640" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Auxin&quot; rel=&quot;nofollow&quot;&gt;Auxins&lt;/a&gt; are a class of phytohormones involved in plant growth and behavior. Auxinic herbicides, such as clopyralid, induce an overinduction of the auxin response in susceptible plants (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0048357507000545&quot; rel=&quot;nofollow&quot;&gt;kelly &amp;amp; Riechers, 2007&lt;/a&gt;). From the Kelly &amp;amp; Riechers 2007 article I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[Auxinic herbicides] cause various growth abnormalities in sensitive dicots, ranging from leaf epinasty and/or cupping and stem twisting, to thickening of stems and roots, and ultimately chlorosis and necrosis [...]. Lack of phytotoxicity in grasses has been attributed to several factors, including &lt;strong&gt;anatomical differences in vascular structure and differences in ability to metabolize the herbicide&lt;/strong&gt; [...]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hence, grasses seem to be protected due to anatomical and metabolic differences. Specifically, auxinic herbicides seem to kill &lt;em&gt;dicots&lt;/em&gt; and spare &lt;em&gt;monocots&lt;/em&gt; (&lt;a href=&quot;http://210.72.92.31/bitstream/353005/4867/1/Insight%20into%20the%20mode%20of%20action%20of%202,4-dichlorophenoxyacetic%20acid%20(2,4-D)%20as%20an%20herbicide.pdf&quot; rel=&quot;nofollow&quot;&gt;Song, 2014&lt;/a&gt;). Song explains, and I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;However, &lt;strong&gt;the underlying molecular mechanism of how auxinic herbicides selectively kill dicots and spare monocots is not understood yet&lt;/strong&gt; [...]. Early research has&#xA;  proposed that the selectivity of auxinic herbicide is because of either &lt;strong&gt;limited translocation or rapid degradation of exogenous auxin, altered vascular anatomy, or altered perception of auxin in monocots&lt;/strong&gt; [...] The difference in vascular tissue structure between dicots and monocots may contribute to the selectivity of auxinic herbicides. In monocot stems, the vascular tissues (the phloem and xylem) are scattered in bundles, and lack a vascular cambium; in dicot stems, the vascular tissues are formed in rings and possess a cambium. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So in all, the exact mechanism of specificity between &lt;em&gt;monocots&lt;/em&gt; and &lt;em&gt;dicots&lt;/em&gt; is unclear, but may be related to structural and/or metabolical (pharmacokinetical) and/or different pharmacodynamical differences between &lt;em&gt;monocots&lt;/em&gt; and &lt;em&gt;dicots&lt;/em&gt; in general. &lt;em&gt;Dicots&lt;/em&gt; are susceptible to auxin herbicides, while grasses, being &lt;em&gt;monocots&lt;/em&gt;, are protected. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The complexity of the auxin hormonal system (&lt;a href=&quot;http://210.72.92.31/bitstream/353005/4867/1/Insight%20into%20the%20mode%20of%20action%20of%202,4-dichlorophenoxyacetic%20acid%20(2,4-D)%20as%20an%20herbicide.pdf&quot; rel=&quot;nofollow&quot;&gt;Song, 2014&lt;/a&gt;) may explain why differences exist between grass species, but this is speculative.     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/sup&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0048357507000545&quot; rel=&quot;nofollow&quot;&gt;Kelly &amp;amp; Riechers, &lt;em&gt;Pesticide Biochem Physiol&lt;/em&gt; 2007;&lt;strong&gt;89&lt;/strong&gt;:1–11&lt;/a&gt;&lt;/sup&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;a href=&quot;http://210.72.92.31/bitstream/353005/4867/1/Insight%20into%20the%20mode%20of%20action%20of%202,4-dichlorophenoxyacetic%20acid%20(2,4-D)%20as%20an%20herbicide.pdf&quot; rel=&quot;nofollow&quot;&gt;Song, &lt;em&gt;J Integr Plant Biol&lt;/em&gt; 2014; &lt;strong&gt;56&lt;/strong&gt;:106–13&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-01-31T22:48:25.033" LastActivityDate="2015-01-31T22:48:25.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28204" PostTypeId="2" ParentId="28190" CreationDate="2015-01-31T13:23:09.483" Score="4" Body="&lt;p&gt;Because that's how genetic variation works. SNPs are called single nucleotide &lt;em&gt;polymorphisms&lt;/em&gt; for a reason: they are &lt;a href=&quot;http://www.merriam-webster.com/dictionary/polymorphism&quot; rel=&quot;nofollow&quot;&gt;polymorphisms&lt;/a&gt;. This means that they are loci where different individuals will have a different nucleotide. This is precisely why they are studied and why we have databases of SNPs and the various genotypes they can manifest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remember that mutations can occur spontaneously in a single individual. In fact, they can appear spontaneously in a single cell. This means that if you sequence the genome of two different cells of the same individual it is actually possible that you will find small differences. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finding small differences between different individuals is certain. Our genomes are not identical and while most differences will be in non-coding regions, you will also have SNPs within genes. How much of our phenotypic variation depends on such small differences is an active topic of research but it is safe to assume that small, single nucleotide changes cause at least some of the variation you see in the people around you. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, what would be surprising is if two individuals were to share the exact same SNP forms for all SNPs in their genomes (I'm sure this happens, but I would expect it to be the case only for close relatives and probably not even then). This variation is the whole point of SNP and the only reason we analyze them. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2015-02-01T21:51:05.650" LastActivityDate="2015-02-01T21:51:05.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28205" PostTypeId="2" ParentId="19940" CreationDate="2015-01-31T13:49:40.033" Score="4" Body="&lt;p&gt;Halosulfuron-methyl is a member of the family of sulfonylurea herbicides. &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/ps.2780290304/abstract&quot; rel=&quot;nofollow&quot;&gt;Brown (2006)&lt;/a&gt; mentions in his abstract the following, and I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This class of herbicides acts through inhibition of acetolactate synthase [...], thereby blocking the biosynthesis of the branched-chain amino acids valine, leucine and isoleucine. This inhibition leads to the rapid cessation of plant cell division and growth. [...] &lt;strong&gt;Crop selectivity results from rapid metabolic inactivation of the herbicide in the tolerant crop.&lt;/strong&gt; Under growth-room conditions, metabolic half-lives in tolerant crop plants range from 1–5 h, while sensitive plant species metabolize these herbicides much more slowly, with half-lives &gt; 20 h. Pathways by which sulfonylurea herbicides are inactivated among these plants include aryl and aliphatic hydroxylation followed by glucose conjugation, sulfonylurea bridge hydrolysis and sulfonamide bond cleavage, oxidative O-demethylation and direct conjugation with (homo)glutathione.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hence, metabolic inactivation activity differs between susceptible and insusceptible species. To get to your question: this means that the &lt;strong&gt;enzymes in lawn grass are also inhibited&lt;/strong&gt;, but to a lesser extent, as the herbicide is metabolized and inactivated more rapidly in grasses.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;/sup&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/ps.2780290304/abstract&quot; rel=&quot;nofollow&quot;&gt;Brown, Pesticide Science 2006;29:241–378&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-01-31T13:49:40.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28206" PostTypeId="2" ParentId="28177" CreationDate="2015-01-31T14:00:09.897" Score="1" Body="&lt;p&gt;Even simple water is &quot;toxic in high amounts&quot; as kidneys can remove 25 l per day at most. All other substances are probably even more &quot;toxic&quot;.&lt;/p&gt;&#xA;" OwnerUserId="5924" LastActivityDate="2015-01-31T14:00:09.897" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28207" PostTypeId="1" AcceptedAnswerId="28217" CreationDate="2015-01-31T14:40:33.313" Score="3" ViewCount="6742" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;Which of the following shows the correct changes in thermodynamic properties for a chemical reaction in which amino acids are linked to form a protein?&lt;/p&gt;&#xA;&lt;p&gt;A) +ΔH, +ΔS, +ΔG&lt;br /&gt;&#xA;B) +ΔH, -ΔS, -ΔG&lt;br /&gt;&#xA;C) +ΔH, -ΔS, +ΔG&lt;br /&gt;&#xA;D) -ΔH, -ΔS, +ΔG&lt;br /&gt;&#xA;E) -ΔH, +ΔS, +ΔG&lt;br /&gt;&#xA;Answer:  C&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I know that dehydration is endergonic (+ΔG).&lt;/p&gt;&#xA;&lt;p&gt;I have two questions:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Why is entropy decreasing? In the beginning of the reaction, we have two amino acids. By dehydration, we have at the end two molecules: the two amino acids together and the H&lt;sub&gt;2&lt;/sub&gt;O molecule. The same number of particles before and after.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Why is enthalpy change positive? You made a bond between the two amino acids. That is exothermic.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8516" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-02T07:19:47.753" Title="Thermodynamics of Forming Peptide Bonds" Tags="&lt;proteins&gt;&lt;amino-acids&gt;&lt;thermodynamics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28210" PostTypeId="1" CreationDate="2015-01-31T15:15:41.613" Score="5" ViewCount="1764" Body="&lt;p&gt;In order for a woman to become pregnant, sperm is needed. Why is sperm count so important for pregnancy? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sperm&quot;&gt;http://en.wikipedia.org/wiki/Sperm&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="13285" LastEditorUserId="12909" LastEditDate="2015-01-31T17:43:39.747" LastActivityDate="2015-06-23T02:30:28.467" Title="Why sperm count matter for pregnancy?" Tags="&lt;sex&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28211" PostTypeId="1" CreationDate="2015-01-31T15:23:50.787" Score="3" ViewCount="2388" Body="&lt;p&gt;Whenever a foreign particle enters into someone's body, it is attacked by the white blood cells. I just want how it is that, when sperms enter the female body, they are not attacked by the the woman's immune system?&lt;/p&gt;&#xA;" OwnerUserId="13286" LastEditorUserId="11631" LastEditDate="2015-01-31T17:42:18.617" LastActivityDate="2015-01-31T17:42:18.617" Title="Why are sperm cells not attacked by the female immune system?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;reproductive-biology&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2015-01-31T17:20:11.593" ContentLicense="CC BY-SA 3.0" />
  <row Id="28212" PostTypeId="2" ParentId="28211" CreationDate="2015-01-31T16:44:41.307" Score="2" Body="&lt;p&gt;Studies show semen does mount a considerable immune response in the female mucosa, however:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Seminal plasma redirects the differentiation of human dendritic cells (DCs) toward a regulatory profile. By promoting a tolerogenic profile in DCs, seminal plasma might favor fertility, but might also compromise the capacity of the receptive partner to mount an effective immune response against sexually transmitted pathogens.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23066152&quot; rel=&quot;nofollow&quot;&gt;Semen promotes the differentiation of tolerogenic dendritic cells.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-01-31T16:44:41.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28213" PostTypeId="2" ParentId="28210" CreationDate="2015-01-31T16:53:41.573" Score="1" Body="&lt;p&gt;As sort of a generic textbook answer, there's a number of factors. The vagina tends to be acidic, much so it's within a range of intolerance for sperm. To counteract this, seminal fluid is often alkaline in nature &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC170534/pdf/040367.pdf&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt;. The cervix also tends to be covered in a mucus that sperm must penetrate to enter the uterus. On top of factors like sperm lifespan, tolerance to vaginal environment, etc. the necessary numbers to actually achieve fertilization is important. &lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-01-31T16:53:41.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28214" PostTypeId="1" AcceptedAnswerId="28231" CreationDate="2015-01-31T17:07:08.253" Score="2" ViewCount="111" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Isoxaben&quot; rel=&quot;nofollow noreferrer&quot;&gt;Isoxaben&lt;/a&gt; (N-[3-(1-ethyl-1-methylpropyl)-1,2-oxazol-5-yl]-2,6-dimethoxybenzamide) is a pre-emergent herbicide used in landscape beds before the application of mulch (my use for it, anyway). It kills the weeds as they germinate, while not harming most established plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/K0FOK.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the mode of action, as stated by &lt;a href=&quot;http://msdssearch.dow.com/PublishedLiteratureDAS/dh_0819/0901b80380819050.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dow AgroSciences&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Isoxaben belongs to the Benzamide family of herbicides and inhibits cellulose biosynthesis in the cell walls of susceptible&#xA;  weeds (WSSA group 21). This means that cells cannot divide during the reproductive cycle; therefore, they cannot grow,&#xA;  causing death. While cell division does not occur, this mode of action should not be confused with mitotic inhibition that&#xA;  occurs with dinitroaniline herbicides.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;How does this only affect germinating weeds, while not noticeably affecting weeds that have emerged from the soil (I have to hit those with another herbicide)?&lt;/p&gt;&#xA;" OwnerUserId="338" LastEditorUserId="338" LastEditDate="2015-02-01T01:05:55.687" LastActivityDate="2015-02-01T12:33:47.350" Title="How does Isoxaben kill newly germinating seeds, with almost no effects on established ones?" Tags="&lt;botany&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28215" PostTypeId="2" ParentId="28164" CreationDate="2015-01-31T17:22:12.260" Score="0" Body="&lt;p&gt;Studies show semen does mount a considerable immune response in the female mucosa, however:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Seminal plasma redirects the differentiation of human dendritic cells (DCs) toward a regulatory profile. By promoting a tolerogenic profile in DCs, seminal plasma might favor fertility, but might also compromise the capacity of the receptive partner to mount an effective immune response against sexually transmitted pathogens.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23066152&quot; rel=&quot;nofollow&quot;&gt;Semen promotes the differentiation of tolerogenic dendritic cells.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-01-31T17:22:12.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28216" PostTypeId="2" ParentId="28151" CreationDate="2015-01-31T17:23:50.143" Score="2" Body="&lt;p&gt;Blood can be stored as whole blood or packed red blood cells. The constituents of each are different. Which one will be used varies based on the patient, the availability and the situation. Whole blood (not necessarily warm) is used more often when there is massive blood loss, as it contains all the components of blood: clotting factors, platelets, plasma, etc. Packed red blood cells have had the white blood cells removed, most of the plasma, the platelets, etc. It is indicated for routine blood loss and to increase the oxygen carrying capacity of blood. The constituents of each are different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The primary problems of stored blood viability are red blood cell deformability (red cells are normally very flexible in order to pass through capillaries) and red blood cell fragility (this results in fewer RBCs actually active in the recipient, as RBCs will break apart.) The viability of RBCs in storage depend on factors such as adequate ADP (the energy substrate). When RBSs are less viable for any reason (less deformable, more fragile, or hemolysis has started in the stored blood), this is termed red cell (or red blood cell/rbc) storage lesion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though there are probably many questions you may have about storage methods and viability, this will give you an idea of search terms for your reading. Good luck in your research efforts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=8&amp;amp;sqi=2&amp;amp;ved=0CFAQFjAH&amp;amp;url=http%3A%2F%2Fwww.dmrti.army.mil%2Fdocuments%2F2008%252005%2520CPG%2520Fresh%2520Warm%2520Whole%2520Blood.doc&amp;amp;ei=7QDNVKeTHMewggTkkIHwBQ&amp;amp;usg=AFQjCNF8yntbhlFNWW11Sn9rie4TIBa7MA&amp;amp;sig2=a8hJHkB0zJXcg5oBpDoyFA&amp;amp;bvm=bv.85076809,d.eXY&quot; rel=&quot;nofollow&quot;&gt;Fresh Warm Whole Blood (FWB&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=8&amp;amp;ved=0CE4QFjAH&amp;amp;url=http%3A%2F%2Fwww.hematology.org%2FClinicians%2FGuidelines-Quality%2FQuick-Ref%2F527.aspx&amp;amp;ei=OATNVKiRDJPmgwSbo4K4CQ&amp;amp;usg=AFQjCNEsbPV_PSpZTXZmC5xqyZdTEPhyrA&amp;amp;sig2=Lb0JTeVynP22Y2DZlB-i0Q&amp;amp;bvm=bv.85076809,d.eXY&quot; rel=&quot;nofollow&quot;&gt;2012 Clinical Practice Guide on Red Blood Cell Transfusion&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://library.med.utah.edu/WebPath/TUTORIAL/BLDBANK/BBPROD.html&quot; rel=&quot;nofollow&quot;&gt;Blood Products&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1537-2995.1982.22282177134.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Deformability of stored red blood cells. Relationship to degree of packing&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.0041-1132.2004.04128.x/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;Microvascular perfusion upon exchange transfusion with stored red blood cells in normovolemic anemic conditions&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.translationalres.com/article/0022-2143%2867%2990086-8/abstract&quot; rel=&quot;nofollow&quot;&gt;Studies on the preservation of human blood. II. The relationship of erythrocyte adenosine triphosphate levels and other in vitro measures to red cell storageability&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://circ.ahajournals.org/content/124/4/465.short&quot; rel=&quot;nofollow&quot;&gt;Nitric Oxide Scavenging by Red Blood Cell Microparticles and Cell-Free Hemoglobin as a Mechanism for the Red Cell Storage Lesion&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3314461/&quot; rel=&quot;nofollow&quot;&gt;Hemoglobin-driven pathophysiology is an in vivo consequence of the red blood cell storage lesion that can be attenuated in guinea pigs by haptoglobin therapy&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-01-31T17:23:50.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28217" PostTypeId="2" ParentId="28207" CreationDate="2015-01-31T17:29:37.033" Score="5" Body="&lt;p&gt;The energy used to catalyze the peptidyl transferase reaction is from the breakage of the bond between the amino acid in question, and the aminoacyl-tRNA it's attached to. The two reactions are coupled by the ribosome. The ribosome can then lower the entropy by positioning of the molecules (including water) in the active site as described &lt;a href=&quot;http://www.cell.com/molecular-cell/abstract/S1097-2765(07)00185-2&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So we have our reaction ΔG = ΔH - TΔS&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your ΔG is positive because your reaction is &lt;strong&gt;endergonic&lt;/strong&gt;, and the ΔH is positive because the peptide bond is the system, and you're &lt;strong&gt;absorbing&lt;/strong&gt; energy to form it. The entropy is decreasing as such (removing enerygy = removing heat from outside the system), and the actual reaction for the formation of a peptide bond is unfavorable. As I mention above, this unfavorable reaction is coupled to a favorable reaction in the hydrolysis of an aminoacyl-tRNA to make it possible. What I forgot to mention above is that the ribosome is making this more favorable as well by decreasing the activation entropy for the reaction, and that's what they describe in the linked journal.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-01-31T19:50:41.327" LastActivityDate="2015-01-31T19:50:41.327" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28218" PostTypeId="2" ParentId="28210" CreationDate="2015-01-31T17:37:09.880" Score="5" Body="&lt;p&gt;It's more than just sperm count that matters for a pregnancy if you are considering normal methods of insemination such as intercourse or assisted methods such as artificial/intrauterine insemination or in vitro fertilization. For couples having trouble getting pregnant, most OB-GYNs and/or Reproductive Endocrinologists/Infertility physicians do a semen analysis. This involves checking several things:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Ejaculate Volume (&gt;1.5mL)&lt;/li&gt;&#xA;&lt;li&gt;Sperm Concentration (&gt;15million/mL)&lt;/li&gt;&#xA;&lt;li&gt;Motility (&gt;40%)&lt;/li&gt;&#xA;&lt;li&gt;Morphology (&gt;4%)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;(and a host of other factors including rapid progressive motility, pH, etc). Why? Because there is no point of there being high numbers of sperm, if their motility is poor, because they won't be able to reach the oocyte. There's no point if they can reach an oocyte, if they are poorly shaped and cannot penetrate it. There's also no point in there being a high concentration of sperm, if the ejaculate volume is so low that it thins out before reaching the cervix. All these factors matter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Total Motile Sperm Count (TMSC) is the most common way that physicians determine what route is best to increase chances for getting their patients pregnant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;TMSC = Concentration x Ejaculate Volume x % Motile (in decimals). Thus if, the value is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;greater than 10 million = normal male factor; check anatomy, check female causes&lt;/li&gt;&#xA;&lt;li&gt;less than 10 million = low male factor; consider intrauterine insemination (IUI)&lt;/li&gt;&#xA;&lt;li&gt;less than 5 million = severe male factor; consider in vitro fertilization (IVF) with intracytoplasmic sperm injection (ICSI)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Sources:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://applications.emro.who.int/imemrf/Int_J_Fertil_Steril/Int_J_Fertil_Steril_2011_5_3_168_173.pdf&quot; rel=&quot;noreferrer&quot;&gt;Paper 1&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.advancedfertility.com/iui-success-rates.htm&quot; rel=&quot;noreferrer&quot;&gt;Advanced Fertility&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11631" LastActivityDate="2015-01-31T17:37:09.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28219" PostTypeId="1" CreationDate="2015-01-31T22:13:43.613" Score="4" ViewCount="145" Body="&lt;p&gt;Is there a comprehensive list of dinosaurs synonyms with indications of which name is now considered correct? Something like &quot;there's no brontosaurus, there's only Apatosaurus&quot;, &quot;there's no Anatotitan, there's only Edmontosaurus&quot; and so on.&lt;/p&gt;&#xA;" OwnerUserId="11691" LastEditorUserId="3624" LastEditDate="2015-02-01T22:27:44.733" LastActivityDate="2015-02-02T09:06:30.900" Title="List of dinosaurs synonyms" Tags="&lt;taxonomy&gt;&lt;nomenclature&gt;&lt;palaeontology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28220" PostTypeId="1" CreationDate="2015-01-31T22:59:50.283" Score="3" ViewCount="281" Body="&lt;p&gt;When you surface from diving too quickly; you get &quot;bends&quot; - these are caused by gas bubbles forming in your lungs (especially nitrogen). This causes breathing problems if not treated since the bubbles are essentially blocking oxygen transport.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For treatment, you have to be in a hyperbaric chamber for several hours.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is it you don't get nitrogen and carbon dioxide bubbles in your bloodstream while being treated? I would think that in the machine the nitrogen, carbon dioxide and water concentrations would rise causing you to start having signs of low oxygen like loss of brain function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I stated previously, nitrogen bubbles block oxygen transport and thus carbon dioxide transport. Since there is nowhere else to go, it goes into the bloodstream where oxygenated blood is supposed to be. This is detected by the chemoreceptors in your arteries; this then tells the heart to beat faster in attempts to rid the body of CO2. Once again; however, this doesn't happen because now there are more nitrogen bubbles from breathing in more nitrogen and water. This leads to a progressively higher heart rate (Ventricular Tachycardia - V-tach) which is dangerous as it can lead to MI (Myocardial Infarction) symptoms - like chest pain. Ventricular tachycardia that lasts a maximum of a few minutes can then lead to V-fib (Ventricular Fibrillation) which, if not treated with epinephrine or defibrillation on time, will lead to asystole and death. &#xA;&lt;p&gt;&#xA;&lt;strong&gt;Summary:&lt;/strong&gt;&#xA;&lt;p&gt;&#xA;When someone has the bends and is being treated in a hyperbaric chamber; how do they not end up having an acute MI (due to accumulation of nitrogen gas in the bloodstream)?&lt;/p&gt;&#xA;" OwnerUserId="5851" LastEditorUserId="11841" LastEditDate="2015-02-01T06:29:57.793" LastActivityDate="2015-02-01T17:02:04.857" Title="Heart Rate being normal when under treatment for the bends" Tags="&lt;cardiology&gt;&lt;breathing&gt;&lt;lungs&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28221" PostTypeId="2" ParentId="27935" CreationDate="2015-01-31T23:19:29.483" Score="3" Body="&lt;p&gt;Increased cell turnover &lt;strong&gt;indirectly&lt;/strong&gt; leads to cancer. Below is a direct quote from Human Molecular Genetics, 2ed. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK7566/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chapter 9: Instability of the human genome: mutation and DNA repair&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Mutations can be induced in our DNA by exposure to a variety of mutagens occurring in our external environment or to mutagens generated in the intracellular environment. In the case of radiation-induced mutation, for example, Dubrova et al. 1996 reported that the normal germline mutation rate for hypervariable minisatellite loci was doubled as a consequence of heavy exposure to the radiaoctive fallout from the Chernobyl accident. However, under normal circumstances by far the greatest source of mutations is from endogenous mutation, notably spontaneous errors in DNA replication and repair. During an average human lifetime there are an estimated 10^17 cell divisions: about 2 × 10^14 divisions are required to generate the approximately 10^14 cells in the adult, and additional mitoses are required to permit cell renewal in the case of certain cell types, notably epithelial cells (see Cairns, 1975). As each cell division requires the incorporation of 6 × 10^9 new nucleotides, error-free DNA replication in an average lifetime would require a DNA replication-repair process with an accuracy great enough so that the correct nucleotide was inserted on the growing DNA strands on each of about 6 × 10^26 occasions.&lt;/p&gt;&#xA;&lt;p&gt;Such a level of DNA replication fidelity is impossible to sustain; indeed, the observed fidelity of replication of DNA polymerases is very much less than this and uncorrected replication errors occur with a frequency of about 10^-9 to 10^-11 per incorporated nucleotide (see Cooper et al., 1995). As the coding DNA of an average human gene is about 1.7 kb, coding DNA mutations will occur spontaneously with an average frequency of about 1.7 × 10^-6 -1.7 × 10^-8 per gene per cell division. &lt;strong&gt;Thus, during the approximately 10^16 mitoses undergone in an average human lifetime, each gene will be a locus for about 10^8-10^10 mutations (but for any one gene, only a tiny minority of cells will carry a mutation). In many cases, a deleterious gene mutation in a somatic cell will be inconsequential: the mutation may cause lethality for that single cell, but will not have consequences for other cells. However, in some cases, the mutation may lead to an inappropriate continuation of cell division, causing cancer&lt;/strong&gt; (see Chapter 18).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://cancerres.aacrjournals.org/content/50/23/7415.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here is another great paper&lt;/a&gt; that specifically addresses your question, linking increased cell division with the accumulation of both significant and insignificant mutations, which over time, lead to an accumulation of mutations needed for cancer to develop.&lt;/p&gt;&#xA;" OwnerUserId="11631" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-01-31T23:25:01.493" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28224" PostTypeId="1" AcceptedAnswerId="28230" CreationDate="2015-02-01T01:27:13.597" Score="3" ViewCount="376" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/trifluralin&quot; rel=&quot;nofollow noreferrer&quot;&gt;Trifluralin&lt;/a&gt; (2,6-Dinitro-N,N-dipropyl-4-(trifluoromethyl)aniline) is a pre-emergent herbicide used in landscape beds before the application of mulch (my use for it, anyway). It kills the weeds as they germinate, while not harming most established plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jEDdd.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://weedecology.css.cornell.edu/herbicide/herbicide.php?id=20&quot; rel=&quot;nofollow noreferrer&quot;&gt;From what I understand&lt;/a&gt;, the mode of action is as a &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitotic_inhibitor&quot; rel=&quot;nofollow noreferrer&quot;&gt;mitotic inhibitor&lt;/a&gt;, which disrupts the microtubules that pull the cell apart when it divides (stops cell division).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this only affect germinating weeds, while not noticeably affecting weeds that have emerged from the soil (I have to hit those with another herbicide)?&lt;/p&gt;&#xA;" OwnerUserId="338" LastActivityDate="2015-02-01T21:54:45.737" Title="How does Trifluralin kill newly germinating seeds, with almost no effects on established ones?" Tags="&lt;botany&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28226" PostTypeId="2" ParentId="28163" CreationDate="2015-02-01T06:04:11.900" Score="2" Body="&lt;p&gt;The thing is that there is such a language called Latin that is used to name species. During Linnaeus' times when he created the binomial naming system, Latin was the prevalent &lt;em&gt;lingua franca&lt;/em&gt; among international scholars. Therefore, all the species names actually make sense, though only hardly so in English.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Names that make a little sense in English include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Wolf: Canis lupus - Lupine canine&lt;/li&gt;&#xA;&lt;li&gt;Domestic cat: Felis domesticus - Domestic feline&lt;/li&gt;&#xA;&lt;li&gt;Wild horse: Equus ferus - Feral equine&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;These make sense because many English words originate from Latin, be it directly or through French.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the words used in binomial names are Latinization of Greek words (that there are not such words in Latin itself), or valid Latin words that originally came from Greek, so some names would also make sense in Greek. Besides some English words also trace back to Greek.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Lion: Panthera &lt;strong&gt;leo&lt;/strong&gt; - Latin word which originated from Greek&lt;/li&gt;&#xA;&lt;li&gt;Megalania - Latinization of Greek neologism &quot;mega&quot;+&quot;elaino&quot; = &quot;Great roamer&quot;&lt;/li&gt;&#xA;&lt;li&gt;Baker's yeast: &lt;strong&gt;Saccharomyces&lt;/strong&gt; cerevisiae - Latinization of Greek &quot;sacchar&quot; + &quot;myces&quot; = &quot;sugar fungus&quot;&lt;/li&gt;&#xA;&lt;li&gt;Penicillium &lt;strong&gt;chrysogenum&lt;/strong&gt; - Latinization of Greek &quot;chrysos&quot; + &quot;genos&quot; = &quot;Gold maker&quot; as it produces a yellow(golden) pigment&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Beyond those are names coined after locations and discoverers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Flores man/hobbit: Homo &lt;strong&gt;floresiensis&lt;/strong&gt; - Latinization of the location of discovery, Flores&lt;/li&gt;&#xA;&lt;li&gt;Common kingslayer: Malo &lt;strong&gt;kingi&lt;/strong&gt; - Latinization of the name of the victim, Robert King, whose death by the jellyfish's venom led to its discovery (note that the English common name also came from the name of the victim)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Some species are also named with Latinization of words in other &quot;native&quot; languages, such Panax &lt;strong&gt;ginseng&lt;/strong&gt;, named after the Chinese name 人参 (I'm not sure exactly what dialect/topolect it is).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Beyond species names, Latin is also used in other parts of biology such as anatomy:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Biceps femoris: Two-headed muscle of the femur&lt;/li&gt;&#xA;&lt;li&gt;Vena cava superior: Upper hollow vein&lt;/li&gt;&#xA;&lt;li&gt;Corpus luteum: Yellow body (body as in object)&lt;/li&gt;&#xA;&lt;li&gt;Ileum: Guts/intestines&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Beyond biology, Latin is used in meteorology to name clouds, astronomy as the common name of stars (Bayer designation), and remains an official language of the Holy See (the authority of the Vatican) as well as the motto of many organizations:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Cirrostratus fibratus - fibrous layered cirrus(curly hair) cloud&lt;/li&gt;&#xA;&lt;li&gt;Sirius: Alpha canis majoris - Alpha (number one) star of the constellation canis major&lt;/li&gt;&#xA;&lt;li&gt;Old motto of USA: E pluribus unum - &quot;Out of many, one&quot; (signifying unity among states)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="13067" LastActivityDate="2015-02-01T06:04:11.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28227" PostTypeId="1" AcceptedAnswerId="28236" CreationDate="2015-02-01T08:38:55.443" Score="3" ViewCount="1532" Body="&lt;p&gt;A closed wound is one where skin is intact and underlying tissue is not exposed to the environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abrasion is an erosion of skin usually due to sheering force. In most cases the dermis is intact and the injury is superficial limited to epidermis. Abrasions heal without scarring by epithelialization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are abrasions considered closed wounds? I would think they are open wounds as the underlying tissue (which would be dermis in this case) are exposed to the environment. Please state the reason why they are classified into whatever group.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-02-01T16:10:42.663" Title="Are abrasions considered closed wounds?" Tags="&lt;pathology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28228" PostTypeId="1" AcceptedAnswerId="28234" CreationDate="2015-02-01T11:13:55.347" Score="1" ViewCount="245" Body="&lt;p&gt;In addition to Linneaus-inspired taxonomies of the botanical world, I suppose there are some other proposals for different kinds of taxonomic accounts, perhaps for specific sub-domains of botany or perhaps historical. I'd be keen to learn about those.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, if any of you know there are some other alternative non-taxonomic approaches to botanic classification that are widely-used in sub-domains or in the early days of science, I'd be keen. I guess there are still some &quot;common sense&quot; classification to be made between use (ornamental/non-ornamental; medicinal/edible/poisonous), but perhaps there's more.&lt;/p&gt;&#xA;" OwnerUserId="13294" LastEditorUserId="13294" LastEditDate="2015-02-01T12:31:43.797" LastActivityDate="2015-02-01T15:19:14.377" Title="Alternative plant taxonomies to Linneaus" Tags="&lt;botany&gt;&lt;taxonomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28229" PostTypeId="2" ParentId="20004" CreationDate="2015-02-01T12:15:29.877" Score="2" Body="&lt;p&gt;A number of studies have been done that investigated resistance to Fenoxaprop-P-ethyl and related compounds. Most of these studies focused on resistance in crops (e.g., maize) or black grass. One of these studies (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0048357599924392&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kay et al., 1999&lt;/a&gt;) was particularly interesting as it focused on several possible mechanisms of herbicide resistance in &lt;em&gt;Alopecurus myosuroides&lt;/em&gt; (Black-Grass). I quote from the abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] Resistance at the whole-plant level correlated well with &lt;strong&gt;reduced acetyl Co-enzyme A carboxylase sensitivity (target site resistance)&lt;/strong&gt; in two of the populations (one from the United Kingdom and one from Germany) but &lt;strong&gt;enhanced metabolism&lt;/strong&gt; appeared to be the primary mechanism of resistance in the majority of the other populations. [...] We suggest that resistance in Lincs E1 may be explained by &lt;strong&gt;multiple resistance mechanisms&lt;/strong&gt;—the expression of both &lt;strong&gt;insensitive acetyl Co-enzyme A carboxylase&lt;/strong&gt; and an &lt;strong&gt;increased rate of detoxification&lt;/strong&gt;. However, resistance in the population Clay from the United Kingdom could be explained neither by target site insensitivity nor by an enhanced rate of metabolism. These results provide conclusive evidence that a single resistance mechanism alone cannot explain insensitivity to fenoxaprop-P-ethyl in European resistant black-grass populations and that additional, as yet uncharacterized, mechanisms must also be present.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So based on these data, I think several mechanisms may play a role in the cool season lawn grass resistance (a species name may help to specify my, admittedly, broad answer).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, Fenoxaprop-P-ethyl is an acetyl CoA carboxylase (ACC) inhibitor (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0048357599924392&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kay et al., 1999)&lt;/a&gt;. Note that Haloxyfop (as mentioned in your question &lt;a href=&quot;https://biology.stackexchange.com/questions/28105/how-does-haloxyfop-control-young-grassy-weeds-in-fields-of-broadleaved-crops/28106#28106&quot;&gt;&quot;How does Haloxyfop control young grassy weeds in fields of broadleaved crops?&quot;&lt;/a&gt;) is also an ACC inhibitor. From the answer on that question it appears that ACC inhibitors inhibit cell membrane formation and that &lt;em&gt;monocots&lt;/em&gt; (grasses) are most susceptible and &lt;em&gt;dicots&lt;/em&gt; less. &lt;em&gt;Dicots&lt;/em&gt; are less sensitive because they have two ACC types at their disposal, one being insensitive to ACC inhibitors. Not surprisingly then, Bermuda grass, being a &lt;em&gt;monocot&lt;/em&gt; is killed by this herbicide. Interestingly however, &lt;strong&gt;other &lt;em&gt;monocots&lt;/em&gt; seem to survive&lt;/strong&gt;, such as the cool-season lawns you mention. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was not able to find conclusive evidence as to why some &lt;em&gt;monocots&lt;/em&gt; survive ACC inhibitors. An &lt;strong&gt;educated guess&lt;/strong&gt; is that resistance can be conferred by &lt;strong&gt;mutations in the ACC enzyme&lt;/strong&gt; (&lt;a href=&quot;http://link.springer.com/article/10.1007/s001220100607&quot; rel=&quot;nofollow noreferrer&quot;&gt;Letouzé &amp;amp; Gasquez, 2001&lt;/a&gt;) that make the enzyme less sensitive to the herbicide. These mutations can be caused by repeated exposure to these herbicides, whereby strains become resistant to the material, much like the way in which (multi-) resistant bacterial strains emerge after repeated exposure to antibiotics.     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0048357599924392&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kay et al. Pesticide Biochem Physiol 1999; 65:169–80&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0048357599924392&quot; rel=&quot;nofollow noreferrer&quot;&gt;Letouzé &amp;amp; Gasquez, Theoretical Applied Genetics 2001; 103:288-96&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-02-01T12:21:41.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28230" PostTypeId="2" ParentId="28224" CreationDate="2015-02-01T12:29:15.360" Score="2" Body="&lt;p&gt;Mitotic (cell division) inhibitors in plants are pretty much what a chemo therapeuticum means for cancer, i.e., rapidly dividing tissues will be affected most. Germinating seeds depend on mitosis for growth. An established plant will also be affected (it will stop growing), but it will stand its ground. To push the analogy - chemotherapy is often commenced after surgical removal or irradiation therapy to remove the tumor, and then chemo is applied to make sure any surviving tumor cell will not start to divide. Your herbicide will prevent germination (cf. cancer re-growth), but will not grossly affect established plants (cf. existing tumor).    &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-02-01T21:54:45.737" LastActivityDate="2015-02-01T21:54:45.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28231" PostTypeId="2" ParentId="28214" CreationDate="2015-02-01T12:33:47.350" Score="2" Body="&lt;p&gt;As with your other question on mitotic inhibitors (&quot;&lt;a href=&quot;https://biology.stackexchange.com/questions/28224/how-does-trifluralin-kill-newly-germinating-seeds-with-almost-no-effects-on-est&quot;&gt;How does Trifluralin kill newly germinating seeds, with almost no effects on established ones&lt;/a&gt;?&quot;), inhibiting cellulose synthesis will inhibit growth. Hence, an established plant will stand its ground, but newly germinating plants cannot grow without cellulose synthesis and hence will fail to germinate.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-02-01T12:33:47.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28232" PostTypeId="1" CreationDate="2015-02-01T13:25:14.380" Score="8" ViewCount="217" Body="&lt;p&gt;I just finished reading the &lt;a href=&quot;http://en.wikipedia.org/wiki/Dinosaur&quot;&gt;Wikipedia page about dinosaurs&lt;/a&gt;, and I very much enjoyed it. I knew that much of what I learned in the 80's as a child is (and was) incorrect, and now that I am a parent, I am excited to finally make some time to learn about this stuff.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that a lot is known about ecosystems, socialization, and interactions between different species, herd behavior, and other interesting things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before I start reading books, I want to watch a good documentary.  A quick google search turned up some suggested documentaries, but in general they seem to be either old or focused on a particular dinosaur, and not on the era in particular.  All are short.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I watched &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Life_of_Mammals&quot;&gt;the 10 hour documentary &quot;The Life of Mammals&quot; by David Attenborough&lt;/a&gt; a few years ago, and developed a much better understanding of how we as humans evolved, and how we are related to other mammals. I'd love it if there was something as extensive about Triassic/Jurassic/Cretaceous era dinosaurs. Is there something recent, extensive, and mostly correct?&lt;/p&gt;&#xA;" OwnerUserId="13297" LastActivityDate="2019-02-17T05:27:49.760" Title="Up to date, extensive documentary about dinosaurs?" Tags="&lt;evolution&gt;&lt;palaeontology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ClosedDate="2019-02-21T16:23:59.677" ContentLicense="CC BY-SA 3.0" />
  <row Id="28233" PostTypeId="1" CreationDate="2015-02-01T14:24:45.503" Score="1" ViewCount="302" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Parasaurolophus#mediaviewer/File:Parasaurolophus_cyrtocristatus.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Parasaurolophus#mediaviewer/File:Parasaurolophus_cyrtocristatus.jpg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I cannot tell if the hands have fingers strung together to form a hove, or fingers to grab. I have seen so many pictures of Parasaurolophus standing up, suggesting possible other functions of the arms and hands. I think their arms are long enough to reach their mouth. Ironically, I have yet to find any literature talking about their hands, but lots of literature talking about their resonating chamber. Do Parasaurolophus have hands with fingers to grab?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/okOTz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9107" LastEditorUserId="9107" LastEditDate="2015-02-01T15:08:11.270" LastActivityDate="2015-02-01T15:08:11.270" Title="Do Parasaurolophus have hands with fingers to grab?" Tags="&lt;evolution&gt;&lt;extinction&gt;&lt;climate-change&gt;&lt;reptile&gt;&lt;global-warming&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28234" PostTypeId="2" ParentId="28228" CreationDate="2015-02-01T15:05:31.290" Score="3" Body="&lt;p&gt;The most common alternative to taxonomic classifications are functional classifications. Emphasizing ecological similarities rather than similarities in relatedness, they can be regarded as complementary approach to, but not as a replacement of taxonomy. Why do we need this? Because species often perform very similar tasks, exhibit very similar characteristics and, most importantly, are very, very numerous (there are ~ 300,000 vascular plants). Reducing this redundant complexity is crucial for decision-making in conservation politics or the projection of vegetation change under future climatic conditions (Woodward &amp;amp; Cramer, 1996).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea behind this is to use functional traits, such as seed size, height, photosynthetic pathway, root density, etc., as a surrogate of a species' ecological 'role' -- its response to environmental factors and its impact on ecosystems. Seed mass for example (functional trait), is a proxy for the dispersal ability of a plant (function, performance). You should have a look at Lavorel et al. (2007), there is a nice table (too big to include here) that links specific traits to the actual ecological functions they describe. But look at this figure from the same paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WcWDQ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By applying multivariate statistics like &lt;a href=&quot;http://en.wikipedia.org/wiki/Cluster_analysis&quot; rel=&quot;nofollow noreferrer&quot;&gt;cluster analyses&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/Ordination_%28statistics%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;ordination methods&lt;/a&gt;, species can then be classified into functional types. To make up one example, a functional type that might emerge from species with the following traits&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;height: &gt; 20 m&lt;/li&gt;&#xA;&lt;li&gt;seed size: &gt; 0.5 cm&lt;/li&gt;&#xA;&lt;li&gt;woody: yes&lt;/li&gt;&#xA;&lt;li&gt;Specific leaf area: low&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;would certainly represent climax forest trees. This classification does not distinguish between individual species, because, from an ecosystem perspective, they all are functionally roughly equivalent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For further research google 'Functional trait', 'Plant functional type' or have a look at refs 3 and 4. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Citations:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Woodward, F. I. and Cramer, W. (1996): Plant functional types and&#xA;climatic change: introduction. Journal of vegetation science, 7(3):&#xA;306–308.&lt;/li&gt;&#xA;&lt;li&gt;Lavorel, S., Díaz, S., Cornelissen, J. H. C., Garnier, E., Harrison, S. P., McIntyre, S., Pausas, J. G., Pérez-Harguindeguy, N., Roumet, C., and Urcelay, C. (2007): Plant&#xA;Functional Types: Are We Getting Any Closer to the Holy Grail? In: Canadell,&#xA;J. G., Pataki, D. E., and Pitelka, L. F. (editors): Terrestrial Ecosystems in a Changing&#xA;World, Global Change—The IGBP Series, pages 149–164. Springer Berlin Heidelberg.&lt;/li&gt;&#xA;&lt;li&gt;Halloy, S. (1990): A morphological classification of plants, with&#xA;special reference to the New Zealand alpine flora. Journal of&#xA;vegetation science, 1(3): 291–304.&lt;/li&gt;&#xA;&lt;li&gt;Leishman, M. R. and Westoby, M. (1992): Classifying plants into groups on the basis&#xA;of associations of individual traits–evidence from Australian semi-arid woodlands.&#xA;Journal of Ecology, 80: 417–424.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8015" LastEditorUserId="8015" LastEditDate="2015-02-01T15:19:14.377" LastActivityDate="2015-02-01T15:19:14.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28235" PostTypeId="2" ParentId="28220" CreationDate="2015-02-01T15:27:31.317" Score="1" Body="&lt;p&gt;You are wrong on several accounts:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Bends occur due to bubbles that form in muscles and joints and not lungs - They fall under Mild or Type 1 Decompression Sickness (Type 1 DCS).&lt;/li&gt;&#xA;&lt;li&gt;Formation of bubbles in blood stream do occur in the Decompression process - Hyperbaric chamber is used to treat this condition.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;h2&gt;What happens when diving:&lt;/h2&gt;&#xA;&lt;p&gt;During deep sea diving the pressure surrounding a person increases at the rate of 1 atm (atmospheric pressure) for every 10 m in sea water and 10.3 m in fresh water. This relation is linear.&lt;/p&gt;&#xA;&lt;p&gt;The pressure inside the body equalises with the pressure outside to prevent any deformation. The solid and liquid components of the body can withstand pressures upto 151 atm (depth of 1.5 km underwater) without undergoing any noticeable compression. But air, being extremely compressible undergoes compression.&lt;/p&gt;&#xA;&lt;p&gt;So at 2 atmospheric pressure the space occupied by the air in our body is halved. This would shrink the lungs to half the total volume. To circumvent this the divers breathe air compressed at the same pressure as the water pressure around them, so that the pressure gradient across the chest wall is normal.&lt;/p&gt;&#xA;&lt;h2&gt;Pressure Concentration relationship:&lt;/h2&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Dalton's Law:&lt;/p&gt;&#xA;&lt;p&gt;This law states that the Barometric Pressure is the sum of the partial pressures of the individual gases in the air mixture.&lt;/p&gt;&#xA;&lt;p&gt;Barometric Pressure - The total pressure measured&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;In air at 1 atmospheric pressure (760 mm Hg) the partial pressures of various gases are:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Nitrogen ~ 593 mm Hg&lt;/li&gt;&#xA;&lt;li&gt;Oxygen   ~ 159 mm Hg&lt;/li&gt;&#xA;&lt;li&gt;Co&lt;sub&gt;2&lt;/sub&gt; ~ 0.2 mm Hg&lt;/li&gt;&#xA;&lt;li&gt;Others   ~ 7 mm Hg&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;According to this Law, as the pressure inside the Lungs increase, the partial pressures of each gas increases. At 2 atm, the partial pressures of every gas doubles.&lt;/p&gt;&#xA;&lt;p&gt;The gas exchange in the lungs is based on &lt;strong&gt;partial pressure&lt;/strong&gt; of the gases. Thus due to increased partial pressure, the amount of gases dissolved in blood increases (This increase is proportionate to the pressure levels).&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0NUzB.jpg&quot; alt=&quot;Pressure at increasing depth of immersion&quot; /&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;During a extended dive (one lasting several hours) the body tissues gradually equilibriate with the high-pressure gases. At sea level our body contains 1 L of dissolved nitrogen, equally distributed between body's water and fat. As partial pressure of Nitrogen rises, the nitrogen equilibriates with the body's lipid stores because adipose tissue is relatively underperfused.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Once equilibrium is achieved the volume of nitrogen dissolved in tissues is proportional to the alveolar partial pressure of nitrogen. Thus at 4 atm the body will contain 4 L of nitrogen.&lt;/p&gt;&#xA;&lt;p&gt;The same principle applies to oxygen as well, though the solubility of oxygen and the speed at which equilibrium is attained are different.&lt;/p&gt;&#xA;&lt;h2&gt;Decompression&lt;/h2&gt;&#xA;&lt;p&gt;During ascent from the depths, the Barometric Pressure (surrounding pressure P&lt;sub&gt;b&lt;/sub&gt;) falls. As the P&lt;sub&gt;b&lt;/sub&gt; falls the pressure inside the alveoli fall as well. This causes a fall in the partial pressures of all gases in the lungs creating a gradient of gases from the tissues to the alveoli.&lt;/p&gt;&#xA;&lt;p&gt;So the diver has to ascend slowly to &lt;strong&gt;give enough time&lt;/strong&gt; for the gases to move into blood from the tissues and then get washed out. If the ascent is too rapid, gases dissolved in the tissues - due to high pressure - attains the gaseous form (due to pressure drop) and become bubbles. This is similar to opening a pressurised coke can where one can observe gas bubbles forming.&lt;/p&gt;&#xA;&lt;p&gt;The bubbles are the reason for the bends. Bubbles can also cause serious problems like arterial gas embolisation, CNS disorders (due to formation of bubbles in the myelin sheath of axons which compromise nerve conduction), pulmonary symptoms (due to pulmonary emboli), sometimes even Disseminated Intravascular Coagulation.&lt;/p&gt;&#xA;&lt;h2&gt;Solution&lt;/h2&gt;&#xA;&lt;p&gt;The decompression is done in stages - in which the divers spend various amount of time at various under water levels to allow complete diffusion of dissolved gases into blood and into the alveoli which is consequently breathed out.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/n5K1h.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;h2&gt;Hyperbaric Chamber&lt;/h2&gt;&#xA;&lt;p&gt;The hyperbaric chamber is used when the above solution is not applied i.e. the diver has surfaced rapidly without spending sufficient time at various levels to allow proper decompression.&lt;/p&gt;&#xA;&lt;p&gt;In a hyperbaric chamber the diver is recompressed to the pressures equal to the pressure experienced at the level to which the diver dived. Due to the increase in pressure, the bubbles get dissolved again. This instantly relieves many symptoms - like the nerve conduction delay, bends, niggles etc... Now the decompression is carried out by under controlled environment, simulating the various intervals the diver has to stay at various pressure levels under water.&lt;/p&gt;&#xA;&lt;p&gt;Hope this explains your doubt.&lt;/p&gt;&#xA;&lt;p&gt;So coming to myocardial infarction, the hyperbaric chamber redissolves the gas bubbles thus preventing myocardial infarction.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;For more info read chapter 61 of Medical Physiology, 2&lt;sup&gt;nd&lt;/sup&gt; edition, by Walter F. Boron and Emile L. Boulpaep.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-01T17:02:04.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28236" PostTypeId="2" ParentId="28227" CreationDate="2015-02-01T15:34:16.130" Score="5" Body="&lt;p&gt;The definition of closed and open wounds is variable. In histopathological terms (i.e. looking under a microscope) it is usually defined that a wound where the dermis is affected is open. In this case an abrasion is an open wound. This puts it in the same class as cuts (incisional/lacerations), tears and punctures. Closed wounds on the other hand are when the dermis isn't affected, such as in a haematoma (blood collection under the skin) or crush injury (extreme force typically for a long period of time) and contusions (i.e. bruises). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Medically they may be divided by management. Where open wounds are wounds which are likely to be contaminated and need thorough cleaning and may need antibiotic cover whereas closed wounds are ones that are very unlikely to be. In this case, abrasions may be considered a relatively closed wound as not all the protective layers of the skin have been breached (the dermis is not completely breached). Thus the physical barriers are relatively intact and continue to offer us defense against bacteria and organisms.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1757" LastEditDate="2015-02-01T16:10:42.663" LastActivityDate="2015-02-01T16:10:42.663" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28237" PostTypeId="1" CreationDate="2015-02-01T15:41:04.943" Score="0" ViewCount="91" Body="&lt;p&gt;I am a man in his mid thirties, but I already have a pretty bad memory. (I have always had a bad memory.) I can remember certain kinds of facts and music very well, but when it comes to words or even random  stuff like how did I fix a particular issue when I last encountered it, my mind goes blank. Lack of sleep aggravates it even more. Lack of sleep also severely retards my language skills because I can't recall any vocabulary. Other than the memory issues I am a healthy person. Is there anything I can do to improve my memory? &lt;/p&gt;&#xA;" OwnerUserId="13299" LastActivityDate="2016-01-31T09:15:13.337" Title="Can memory be improved with mental training?" Tags="&lt;memory&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2016-02-03T03:27:59.900" ContentLicense="CC BY-SA 3.0" />
  <row Id="28238" PostTypeId="1" CreationDate="2015-02-01T15:42:53.197" Score="5" ViewCount="77" Body="&lt;p&gt;I want to measure metabolism in tardigrades (a jar of 30 tardigrades). I know that an easy way to measure metabolism is heat loss; I can just measure the temperature of the water before and after a certain period of time and take the difference. I have a few questions: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Is this a viable way? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Do I need to put the tardigrades in a controlled system (or is the outside environment a constant)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Will the measurements be really really small (so I would need a very precise thermometer?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) How long should I wait between the two measurements?&lt;/p&gt;&#xA;" OwnerUserId="13132" LastEditorUserId="9943" LastEditDate="2015-02-02T13:10:26.683" LastActivityDate="2015-02-02T13:10:26.683" Title="How to measure heat loss in Tardigrades" Tags="&lt;metabolism&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28239" PostTypeId="2" ParentId="28088" CreationDate="2015-02-01T15:57:04.983" Score="3" Body="&lt;p&gt;Basically there is every variation under the sun possibly but I have structured my answer so that the more common variations are earlier. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On average a woman loses around 30-40 ml of fluid, this is a combination of mucous, secretions, endometrial tissue and around 50% blood. Because of this it is a slightly darker colour than just regular old blood. This of course varies with women with blood disorders or taking medication to &quot;thin&quot; the blood bleeding a lot more. The second day is typically the worst. On the worst day a woman may use 3-6 pads but this can be substantially more and changing every 2-3 hours is not uncommon. It is most typically more or less constant with some worse moments in the day, but there is a huge variation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clots are quite common but not all women get them. They're typically more common in older females and may look just like tissue. The size of these clots can very from the size of peas to grapes and even larger than 6-7cm in some women. This is a little more worrying as this may cause anaemia or iron deficiency unlike the regular bleeding above which typically doesn't. Women affected with blood clots are much more likely to have pain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pain itself is more common in younger women. However usually this settles down and usually it is not painful enough to affect daily activities. In some women however they get dysmennorrhea which basically means painful uterine cramps. This is because the blood flow to the uterus is restricted due to the hormone balance and the muscle is contracting really powerfully. The lack of blood flow causes the muscle to get starved of oxygen and the pain is said to be similar to angina or like a heart attack (both being caused by a similar mechanism). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Menorrhagia is the medical term for heavy periods. This is characterised by more than 80 ml of fluid each month and affects 1 in 10 women. Usually this is diagnosed by the number of pads and tampons used. Women affected by this may require to double protect, use both a tampon and pad. They may also take a number of extra underwear or trousers to work. The symptom affecting these women is termed flooding. Unexpectedly they get a &quot;flood&quot; which just basically goes everywhere and is uncontrollable and is usually quite a lot of volume. This is sometimes due to an underlying disease, of which, is most commonly fibroids but may also be contraceptive devices that go into the womb/uterus, blood thinners or polycystic ovary syndrome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is however much variation. Some women will have only 10ml or so of blood (light periods) and that's normal for them. Some women may have irregular bleeding lasting all month. Other women may have longer periods such as 10 or even 20 days per cycle. And then cycles themselves can vary from short (20 or so days) to very long with only a few cycles per year. Basically there is every variation possible under the sun. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2015-02-01T15:57:04.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28240" PostTypeId="1" AcceptedAnswerId="28242" CreationDate="2015-02-01T17:02:25.820" Score="15" ViewCount="3587" Body="&lt;p&gt;I realised that I have to pee more often in winter or simply the temperature is low. Is there any scientific explanation, or just simply psychology?&lt;/p&gt;&#xA;" OwnerUserId="13243" LastEditorUserId="13243" LastEditDate="2015-02-01T17:08:24.163" LastActivityDate="2015-02-04T06:47:19.560" Title="Why I have to pee more often in low temperature?" Tags="&lt;human-biology&gt;&lt;psychology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="3" ClosedDate="2015-02-04T11:53:59.300" ContentLicense="CC BY-SA 3.0" />
  <row Id="28242" PostTypeId="2" ParentId="28240" CreationDate="2015-02-01T17:15:03.883" Score="17" Body="&lt;p&gt;This phenomenon has been demonstrated in studies &lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00864230&quot;&gt;[1]&lt;/a&gt;&lt;a href=&quot;http://online.liebertpub.com/doi/abs/10.1089/ther.2013.0015&quot;&gt;[2]&lt;/a&gt; which show a significant increase in urine output in the cold. The latter study shows the biggest increase is when a person is initially exposed to the cold rather than when they continue to be exposed or rewarmed up. In the study, the average urine out was 157 mL/hour when a person was initially exposed to the cold, 103 mL/hour when they were being maintained at that cold temperature and 70 mL/hour when they were being rewarmed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanism however is unclear. &lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00864230&quot;&gt;This&lt;/a&gt; study showed that the mean arterial pressure increases. It is well known that the cold causes our blood vessels to constrict (in order to keep the blood and therefore heat inside our core body). The thought was therefore that our kidneys try to lower our blood pressure by taking more fluid out and emptying it into the bladder. This is called cold-induced diuresis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other thoughts include that we lose the water we ingest by sweating (perspiring), pooping (defaecation) and peeing (micturition/urination). In the winter, we don't typically sweat as much, which ISN'T counterbalanced with a lower water intake, so we need to pee more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another possibility is that aquaporins (the pores that water comes out from our kidneys) are inhibited by the cold. This means more fluid would be filtered out. However there isn't really much research in this area that I am able to find. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="1757" LastEditDate="2015-02-04T00:21:23.060" LastActivityDate="2015-02-04T00:21:23.060" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28243" PostTypeId="1" AcceptedAnswerId="28335" CreationDate="2015-02-01T18:16:24.653" Score="12" ViewCount="585" Body="&lt;p&gt;I'm wondering about a few technicalities of crossover in meiosis. The point of crossover is to create new chromosomes that don't have the same allele combinations as the original two chromosomes. Usually, the chromosomes are cut at the same place on both chromosomes, and each piece is then stitched to that place on the other. This is to avoid unequal recombination, a scenario in which one chromosome has several instances of a gene and the other no instance at all. I'm wondering how the molecular machinery knows where to cut. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So here's my question: How does the molecular machinery choose where to cut a chromosome for recombination?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question has two parts: At what type of place does it occur (does the machinery choose a completely random place, regardless of where genes start and end, does it just cut at the start of genes, or does it do something else)? Given that it happens at this type of place (e.g. start of a gene), how does it decide that it will cut here (the start of this gene) and not there (the start of that gene)?&lt;/p&gt;&#xA;" OwnerUserId="13300" LastEditorUserId="13300" LastEditDate="2015-02-03T20:57:28.280" LastActivityDate="2015-08-22T16:53:19.937" Title="How does the molecular machinery choose where to cut a chromosome for recombination?" Tags="&lt;chromosome&gt;&lt;meiosis&gt;&lt;allele&gt;&lt;crossover&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28244" PostTypeId="2" ParentId="27475" CreationDate="2015-02-01T18:29:51.820" Score="4" Body="&lt;p&gt;I doubt you are going to be satisfied with any answer since the authorities on the matter can't test the many hypothesis and don't all agree. Around the time of homo erectus (1.89 million years ago), hominids began walking upright on a more permanent basis but this wasn't the only evolutionary event. Additionally, hominids began growing taller now as well &lt;a href=&quot;http://www.smithsonianmag.com/science-nature/becoming-human-the-evolution-of-walking-upright-13837658/?no-ist&quot; rel=&quot;nofollow noreferrer&quot;&gt;[1]&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Charles Darwin hypothesized that upright walking was linked to tool use in 1871 &lt;a href=&quot;http://digitalcommons.iwu.edu/cgi/viewcontent.cgi?article=1013&amp;amp;context=socanth_honproj&quot; rel=&quot;nofollow noreferrer&quot;&gt;[2]&lt;/a&gt;. In 2009, Lovejoy reformalized Darwin's hypothesis and came to the conclusion that upright walking comes down to food and sex &lt;a href=&quot;http://news.nationalgeographic.com/news/2009/10/091001-ardipithecus-ramidus-ardi-oldest-human-fossils-sex.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;[3]&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;To be successful providers, males needed their arms and hands free to carry food, and thus bipedalism evolved. This scenario, as with all bipedalism hypotheses, is really hard to test. But earlier this year, researchers offered some support when they found that chimpanzees tend to walk bipedally when carrying rare or valuable foods.&lt;/p&gt;&#xA;&lt;p&gt;At this point, Lovejoy suggests, a mutually beneficial arrangement evolved: Males gathered food for females and their young and in return females mate exclusively with their providers. To be successful providers, males needed their arms and hands free to carry food, and thus bipedalism evolved. This scenario, as with all bipedalism hypotheses, is really hard to test. &lt;a href=&quot;http://www.smithsonianmag.com/science-nature/becoming-human-the-evolution-of-walking-upright-13837658/?no-ist&quot; rel=&quot;nofollow noreferrer&quot;&gt;[1]&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;In 1980, Peter Rodman and Henry McHenry claimed that bipedalism carries bioenergetic advantages &lt;a href=&quot;http://www.geology.upol.cz/Soubory/texty/Rodman_80.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;[4]&lt;/a&gt;. Then in 2007, another group of researchers validated the energy advantage of walking upright &lt;a href=&quot;http://www.nature.com/news/2007/070716/full/news070716-2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;[5]&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Raichlen notes that if the same variation existed in our early ape-like ancestors as does in today's chimps, with some finding it easier to walk than others, this could have helped to drive adaptation. &amp;quot;That's what natural selection would be able to work on,&amp;quot; he says &lt;a href=&quot;http://www.nature.com/news/2007/070716/full/news070716-2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;[5]&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Since there is no agreement and testing many of theses hypothesis are impossible since early hominids no longer exist, no one in their right mind can say, &amp;quot;Chris, this is why we evolved to walk.&amp;quot; Even if they were correct, it would take some time to cycle through the academic community before it gained enough support to be the consensus.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-01T19:03:32.530" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28245" PostTypeId="2" ParentId="27475" CreationDate="2015-02-01T19:46:48.037" Score="7" Body="&lt;p&gt;As already pointed it out, there is no scientific consensus on the answer to this question. This is because it is hard to test proposed explanations and it's likely that several factors interacted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of these have been claimed to be the explanation for the evolution of bipedalism:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Freed hands for increased tool use. (&lt;a href=&quot;http://www.britannica.com/EBchecked/topic/275670/human-evolution/250597/Theories-of-bipedalism&quot; rel=&quot;noreferrer&quot;&gt;Encyclopedia Britannica&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Freed hands for the use of weapons in hunting or the use of containers to transport plant foods obtained by gathering.&#xA;There are three variants: the “man the hunter” version which sees male hunting as the key stimulus (&lt;a href=&quot;https://books.google.ch/books?id=G1_Q3h5hPP0C&amp;amp;pg=PA332&amp;amp;lpg=PA332&amp;amp;dq=woman%20the%20gatherer%20man%20the%20hunter%20bipedalism&amp;amp;source=bl&amp;amp;ots=X1Yqewzs28&amp;amp;sig=_6slEN4pTbz3uInkvsYl5BlnA0w&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=R8nQVKLlO8zzUqDdgJgO&amp;amp;ved=0CDUQ6AEwBA#v=onepage&amp;amp;q=woman%20the%20gatherer%20man%20the%20hunter%20bipedalism&amp;amp;f=false&quot; rel=&quot;noreferrer&quot;&gt;Washburn 1967 in Haraway 2013)&lt;/a&gt;; the “woman the gatherer” version which sees women needing their hands free to carry gathered vegetable foods as the stimulus; and the “man the provisioner” version, which stresses males carrying food (either meat or plants) to provision females and offspring.&#xA;All of these explanations are probably flawed because they invoke present utility to explain the origins of bipedalism.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Bipedalism was created by female sexual selection of males with large, visible genitals.&#xA;Although unlikely, this may be correct, but it is impossible to test. (&lt;a href=&quot;http://www.britannica.com/EBchecked/topic/275670/human-evolution/250597/Theories-of-bipedalism&quot; rel=&quot;noreferrer&quot;&gt;Encyclopedia Britannica&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Bipedalism evolved to aid in avoiding predators. Higher head allows you to see longer distances over the grass. (&lt;a href=&quot;http://www.britannica.com/EBchecked/topic/275670/human-evolution/250597/Theories-of-bipedalism&quot; rel=&quot;noreferrer&quot;&gt;Encyclopedia Britannica&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Bipedalism evolves because it allows energy efficient locomotion between forest patches in an increasingly open environment. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;“Radiator theory”: Natural selection favored bipedalism in open environments because it decreases exposure to the sun and helps keep the brain cool. (&lt;a href=&quot;https://books.google.ch/books?id=LfYirloa_rUC&amp;amp;pg=PA144&amp;amp;lpg=PA144&amp;amp;dq=radiator%20theory%20reduced%20exposure%20to%20sun&amp;amp;source=bl&amp;amp;ots=ggp4i-2Z3V&amp;amp;sig=zoj5Ct2HX51r1u12CyaPDXAmDYk&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=Fb7QVLq5IOLgywP0_4L4DQ&amp;amp;ved=0CCAQ6AEwAA#v=onepage&amp;amp;q=radiator%20theory%20reduced%20exposure%20to%20sun&amp;amp;f=false&quot; rel=&quot;noreferrer&quot;&gt;Wheeler, discussed in Haviland 2007&lt;/a&gt; and &lt;a href=&quot;http://www.britannica.com/EBchecked/topic/275670/human-evolution/250597/Theories-of-bipedalism&quot; rel=&quot;noreferrer&quot;&gt;Encyclopedia Britannica&lt;/a&gt;)&#xA;Brain is highly sensitive to heat stress.&#xA;This allowed hominins to be active in mid-day, when competing predators are less active. (&lt;a href=&quot;https://books.google.ch/books?id=TSaSPza9LMYC&amp;amp;pg=PA165&amp;amp;lpg=PA165&amp;amp;dq=bipedalism%20midday%20activity&amp;amp;source=bl&amp;amp;ots=VemrzNRRZ8&amp;amp;sig=1utHjyovEuRqP6PbP6AvYUqt_8g&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=8MHQVOrZPKfXyQOstIGIAQ&amp;amp;ved=0CCYQ6AEwAQ#v=onepage&amp;amp;q=bipedalism%20midday%20activity&amp;amp;f=false&quot; rel=&quot;noreferrer&quot;&gt;Essentials of Physical Anthropology, p. 165&lt;/a&gt;). Since the same carnivorous animals with which hominins were in competition (both would scavenge dead game) could attack hominins, hominins were probably safer from predator attacks during midday as well.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Terrestrial bipedalism may be a continuation of an upright body posture inherent in a tree-climbing/brachiating adaptation.&#xA;Gibbons, the most arboreal of the apes and the best brachiators, walk bipedally on the rare occasions they come to the ground. (&lt;a href=&quot;http://www.britannica.com/EBchecked/topic/275670/human-evolution/250597/Theories-of-bipedalism&quot; rel=&quot;noreferrer&quot;&gt;Encyclopedia Britannica&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The earliest hominin fossils appear to have been bipedal, with no clear evidence of a transition through a knuckle-walking stage, the principal mode of locomotion of modern African ape. (&lt;a href=&quot;http://www.pnas.org/content/106/34/14241&quot; rel=&quot;noreferrer&quot;&gt;Kivell and Schmitt 2009&lt;/a&gt;, here's a &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evograms_07&quot; rel=&quot;noreferrer&quot;&gt;secondary source&lt;/a&gt;, and here's a primary source that disagrees, &lt;a href=&quot;http://www.nature.com/nature/journal/v404/n6776/abs/404382a0.html&quot; rel=&quot;noreferrer&quot;&gt;Richmond and Strait 2000&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is true, then the modern African ape mode of locomotion (knuckle-walking) is a derived trait, and vertical body posture may be the ancestral trait in the African hominoid evolutionary lineages. In other words, if this is true, the ancestor of all great apes including humans was already bipedal, and modern African apes have evolved to knuckle-walk since then.&#xA;Also if this is true, the previously mentioned factors would reinforce and refine bipedal locomotion in the hominin lineage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is likely that explanations 4, 5, 6 and 7 all interacted to select for bipedalism. They correspond best to the paleontological and ecological data. Numbers 1 and 2 are unlikely, because bipedalism appears long &lt;em&gt;before&lt;/em&gt; evidence of tool use.&lt;/p&gt;&#xA;" OwnerUserId="13300" LastEditorUserId="13300" LastEditDate="2015-02-03T13:14:46.357" LastActivityDate="2015-02-03T13:14:46.357" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28247" PostTypeId="1" AcceptedAnswerId="28249" CreationDate="2015-02-01T22:41:42.133" Score="4" ViewCount="670" Body="&lt;p&gt;Most species of salmon die after spawning. Are there any other types of fish that spawn once and then die after a multi-year life-cylce? Is this a rare life history strategy among our human exploited marine species? Googling this question only yields articles about Salmon.&lt;/p&gt;&#xA;" OwnerUserId="6893" LastEditorUserId="3624" LastEditDate="2015-02-01T23:26:13.033" LastActivityDate="2016-12-25T14:34:47.963" Title="What fish (and/or shellfish) species with a multi-year life-cycle, besides salmon, die after spawning?" Tags="&lt;ecology&gt;&lt;marine-biology&gt;&lt;ichthyology&gt;&lt;life-history&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28248" PostTypeId="2" ParentId="2073" CreationDate="2015-02-01T22:42:38.347" Score="4" Body="&lt;p&gt;Sorry to spoil the fun here, but male nipples are not completely useless. With stimulation and hormones, they can be used to make milk. I don't have a great peer reviewed source for this, because it is sort of &lt;a href=&quot;http://www.scientificamerican.com/article/strange-but-true-males-can-lactate/&quot; rel=&quot;nofollow&quot;&gt;common knowledge&lt;/a&gt;. I heard about it at a &lt;a href=&quot;http://www.llli.org/&quot; rel=&quot;nofollow&quot;&gt;Le Leche Leage&lt;/a&gt; meeting when my son was small. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's another &lt;a href=&quot;http://www.babymed.com/blogs/richard-banks/can-men-breastfeed&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="13297" LastEditorUserId="13297" LastEditDate="2016-07-29T03:48:14.780" LastActivityDate="2016-07-29T03:48:14.780" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28249" PostTypeId="2" ParentId="28247" CreationDate="2015-02-01T23:02:06.797" Score="5" Body="&lt;p&gt;Many species of &lt;a href=&quot;http://en.wikipedia.org/wiki/Eel&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eel&lt;/a&gt; (order Anguilliformes) have a semelparous life history (most species? all?), i.e. they only reproduce once and then die (as opposed to an &lt;a href=&quot;http://en.wikipedia.org/wiki/Semelparity_and_iteroparity&quot; rel=&quot;nofollow noreferrer&quot;&gt;iteroparous life history&lt;/a&gt;). Many species are now threatened by extinction (e.g. American eel and European eel), since they have been heavily exploited by fisheries and they are also vulnerable to habitat modifications (e.g. hydroelectric dams) and pollution. The nature of their life history was also unknown for a long time, since they migrate and spawn in the Sargasso Sea after living many years in fresh water (so the opposite migration path compared to Salmon), which is called a &lt;em&gt;catadromous&lt;/em&gt; life history. However, there are also many species of eel that are strictly marine, for instance the very large &lt;a href=&quot;http://en.wikipedia.org/wiki/European_conger&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Conger conger&lt;/em&gt;&lt;/a&gt;, but many of these species still migrate long distances before mating. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/11Tm1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;(American eel, &lt;em&gt;Anguilla rostrata&lt;/em&gt;, picture from Wikipedia in public domain)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a fun sidenote, captive eel can become very old, and earlier this year a more than 155-year-old European eel that was kept in a well died (see &lt;a href=&quot;http://www.thelocal.se/20140808/worlds-oldest-eel-dies-in-sweden&quot; rel=&quot;nofollow noreferrer&quot;&gt;newsstory&lt;/a&gt;) - the oldest known eel from what I know. Eels were often put in wells because they were believed to keep the well water clean.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Semelpary is also found in other fish species, for instance in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Smelt_%28fish%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;Smelt (Osmeridae)&lt;/a&gt; family, where many species are fished commercially. Some (most?) species in the family have multiyear life histories, but some, e.g. the &lt;a href=&quot;http://en.wikipedia.org/wiki/Delta_smelt&quot; rel=&quot;nofollow noreferrer&quot;&gt;Delta smelt (&lt;em&gt;Hypomesus transpacificus&lt;/em&gt;)&lt;/a&gt; only live for a single year. Similarly to Salmon, Smelt also migrate from sea to freshwater to spawn, i.e. an &lt;em&gt;anadromous&lt;/em&gt; life history.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall, less than 1% of teleost fish are semelparous according to &lt;a href=&quot;https://books.google.se/books?id=_JkMRundeNcC&amp;amp;pg=PA592#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Finch. 1994. Longevity, Senescence, and the Genome. University of Chicago Press&quot;&gt;Finch (1994)&lt;/a&gt; - see link for more examples of semelparous fish species and background. However, this figure is most likely uncertain, given that we know very little about the life history of many marine species. In some cases, you can also find a range of life-history strategies from semelparous to partially or totally iteroparous within the same species, depending on ecological context. Nevertheless, the low overall proportion of semelparous fish means that semelpary is generally a rare life history strategy in human exploited fish species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cLqzj.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;(Delta smelt, &lt;em&gt;Hypomesus transpacificus&lt;/em&gt;, picture from Wikipedia in public domain)&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-02-02T09:41:40.637" LastActivityDate="2015-02-02T09:41:40.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28251" PostTypeId="2" ParentId="17631" CreationDate="2015-02-01T23:30:15.950" Score="11" Body="&lt;p&gt;Flies see motion. When the monitor screen changes, the visible spectrum of the pixel is changing and nothing is moving.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Flies have limited color vision. Each color has its own wave frequency, but flies have only two kinds of color receptor cells. This means they have trouble distinguishing between colors, for instance discerning between yellow and white. Insects cannot see the color red, which is the lowest color frequency humans can see. However, houseflies have the ability to see polarized light, but humans cannot differentiate between polarized and unpolarized light. Polarized light is light in which the waves travel only in one plane. &lt;a href=&quot;http://animals.pawnation.com/flies-see-out-compound-eye-5361.html&quot;&gt;[1]&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Monitors have polarized film on them so you could test the color hypothesis by taking an old monitor you are willing to sacrifice and removing the polarized film. Then you could test if the flies jump when the screen changes. See &lt;a href=&quot;http://www.instructables.com/id/Privacy-monitor-made-from-an-old-LCD-Monitor/&quot;&gt;here&lt;/a&gt; for removing the polarized film on the monitor, or if you have access, this article on &lt;a href=&quot;http://link.springer.com/article/10.1007/BF00189764#page-1&quot;&gt;A behavioural study of polarization vision in the fly, Musca domestica&lt;/a&gt; may hold the answer without needing to ruining a monitor.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-02-01T23:35:31.500" LastActivityDate="2015-02-01T23:35:31.500" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="28252" PostTypeId="2" ParentId="28240" CreationDate="2015-02-02T02:05:26.080" Score="6" Body="&lt;p&gt;Cold-induced diuresis, where kidneys relieve blood pressure by increasing urine production.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cold-induced_diuresis&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Cold-induced_diuresis&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The blood pressure is thought to be increased by vasoconstriction due to the cold. One source that supports that theory: Sun, Z. American Journal of Physiology -- Regulatory, Integrative, and Comparative Physiology, February 2005; vol 288: pp R433-R439. American Heart Association: &quot;High Blood Pressure.&quot;&lt;/p&gt;&#xA;" OwnerUserId="13303" LastEditorUserId="13303" LastEditDate="2015-02-04T06:47:19.560" LastActivityDate="2015-02-04T06:47:19.560" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28254" PostTypeId="2" ParentId="28219" CreationDate="2015-02-02T09:06:30.900" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://eol.org/pages/4531260/names&quot; rel=&quot;nofollow&quot;&gt;Encyclopedia of Life&lt;/a&gt; includes information on synonyms (see link for Apatosaurus) - not a list but searchable and often with references and background info. After a quick google search I also found &lt;a href=&quot;http://www.dinosaurcentral.com/genera_list.php&quot; rel=&quot;nofollow&quot;&gt;this list from dinosaurcentral.com&lt;/a&gt;, but I don't know how credible and updated it is and it seems to lack references. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2015-02-02T09:06:30.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28256" PostTypeId="1" AcceptedAnswerId="28401" CreationDate="2015-02-02T11:17:47.997" Score="8" ViewCount="237" Body="&lt;p&gt;Under which keyword would you try to find out more about the grouping behaviour which looks like this? Does anybody recognizes such behaviour, or know an animal species which uses it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My tries: &lt;strong&gt;threshold group behaviour&lt;/strong&gt; (threshold here is the group size - if bigger than 5 individuals == stable), or &lt;strong&gt;gravitational group behaviour&lt;/strong&gt;? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZpQy2.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After &lt;strong&gt;step 6&lt;/strong&gt; the group disintegrates (for example due to foraging) and mechanism starts by &lt;strong&gt;step 1&lt;/strong&gt;. Important thing is that the location of forming stable group is &lt;strong&gt;always different&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8500" LastEditorUserId="8500" LastEditDate="2015-02-03T13:57:35.127" LastActivityDate="2015-02-07T13:23:49.617" Title="How to name such grouping behaviour?" Tags="&lt;behaviour&gt;&lt;sociality&gt;&lt;collective-behaviour&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28257" PostTypeId="1" CreationDate="2015-02-02T11:24:05.367" Score="9" ViewCount="2151" Body="&lt;p&gt;We know that some DNA binding proteins are site specific, that is they recognise and bind to a specific nucleotide sequence. My question is how can we precisely tell at which sites they bind? Is it the amino acid sequence of the protein? Or is it the repetitiveness factor in case they bind to multiple locations on the chromosome? &lt;/p&gt;&#xA;" OwnerUserId="13309" LastEditorUserId="9943" LastEditDate="2015-02-02T11:56:21.480" LastActivityDate="2015-02-04T14:05:32.047" Title="How are we able to find the specific sites at which DNA binding proteins bind?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28258" PostTypeId="1" CreationDate="2015-02-02T11:44:48.327" Score="4" ViewCount="31449" Body="&lt;p&gt;Do blood capillaries expand? If yes, through what means can it be done? And can warm water also be used to expand blood capillaries?&lt;/p&gt;&#xA;" OwnerUserId="13311" LastEditorUserId="9943" LastEditDate="2015-02-02T11:48:29.787" LastActivityDate="2015-02-03T08:17:32.800" Title="Blood circulation - How to expand blood capillaries?" Tags="&lt;blood-circulation&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28259" PostTypeId="2" ParentId="28238" CreationDate="2015-02-02T12:57:39.637" Score="4" Body="&lt;p&gt;1 and 2) You need to build/use a calorimeter : &lt;a href=&quot;http://en.wikipedia.org/wiki/Calorimeter&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Calorimeter&lt;/a&gt;&#xA;Different types exist, depending on your constraints.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3 and 4) It will depend on the size of your system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you decide to use an adiabatic calorimeter: First have an estimate of their metabolism (see e.g. [1]), then divide the energy spent over the duration you think you'll use by the heat capacity of the water volume you have, you get the temperature elevation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you use a flux calorimeter, then you don't multiply by the duration but check that the calorimeter will be sensitive enough.&lt;/p&gt;&#xA;" OwnerUserId="6224" LastActivityDate="2015-02-02T12:57:39.637" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28260" PostTypeId="1" CreationDate="2015-02-02T13:44:43.760" Score="1" ViewCount="138" Body="&lt;p&gt;I am interested to culture Wolbachia bacteria in cell line.&lt;/p&gt;&#xA;" OwnerUserId="13312" LastEditorUserId="3340" LastEditDate="2015-02-03T05:09:44.890" LastActivityDate="2015-02-03T09:47:23.007" Title="How can I isolate live Wolbachia endosymbionts from Drosophila" Tags="&lt;cell-biology&gt;&lt;zoology&gt;&lt;microbiology&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-02-03T15:18:06.393" ContentLicense="CC BY-SA 3.0" />
  <row Id="28261" PostTypeId="2" ParentId="28257" CreationDate="2015-02-02T14:21:06.013" Score="17" Body="&lt;p&gt;I will try to answer the question in the title: how can we know the sites where DNA binding proteins bind?&#xA;I'll explain two experimental methods to identify binding sites on DNA.&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;DNase footprinting&lt;/li&gt;&#xA;&lt;li&gt;ChIP-seq (&lt;strong&gt;Ch&lt;/strong&gt;romatin &lt;strong&gt;I&lt;/strong&gt;mmuno-&lt;strong&gt;P&lt;/strong&gt;recipitation with &lt;strong&gt;seq&lt;/strong&gt;uencing)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;h2&gt;DNase footprinting&lt;/h2&gt;&#xA;&lt;p&gt;We can locate proteins bound to DNA by their ability to protect DNA from some degradation. DNase I cleaves DNA in an &lt;em&gt;almost&lt;/em&gt;-random manner and is inhibited by proteins covering ('protecting') the DNA backbone.&lt;/p&gt;&#xA;&lt;p&gt;In order to locate a site which is protected from DNase I cleavage, we need to take some genomic DNA and treat it. We need separate, short lengths of DNA to examine - we can obtain these from genomic DNA by PCR amplification of different stretches. We need to label these amplicons at one end only, beta radiation is a good choice of label.&lt;/p&gt;&#xA;&lt;p&gt;Taking one labelled amplicon, exposing it to DNase I for a short time - not long enough for complete digestion - produces cleaved DNA of all possible lengths, which looks like a 'ladder' after separation by gel electrophoresis. Digestion time must be short, such that many DNA are only cleaved once, to have a complete ladder.&#xA;Repeating this digestion with your interesting protein present gives a ladder with a missing segment. This is because your protein protects a length of DNA from cleavage.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YzeGX.gif&quot; alt=&quot;DNase footprinting diagram&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Important points: DNA is labelled at one end only. Hence we only see the label-end-piece of DNA after cleavage: if DNA is labelled 5' and cleaved in half, we only see 5' halves. Thanks to this, we can estimate the position of the binding site: if our DNA is 100bp and our ladder has lengths 0 to 70bp, a gap, then more from 85 to 100bp, then our binding site is somewhere inside 70-85bp from the labelled end. We can sequence the piece of DNA and read the sequence of nucleotides 70-85.&lt;/p&gt;&#xA;&lt;h2&gt;ChIP-seq&lt;/h2&gt;&#xA;&lt;p&gt;This is a more recently-developed method, which is more suited to studying where a protein binds all over the genome or all over a chromosome. It requires an antibody which specifically binds your interesting protein.&lt;/p&gt;&#xA;&lt;p&gt;First, a 'snap-shot' of global protein-DNA binding is taken by irradiating cells with UV light, causing covalent cross-links between DNA and binding proteins. Chromatin (DNA with associated proteins) is isolated from cells and chopped up to smaller fragments; the cross-links preserve our 'snap-shot' of proteins and short lengths of their bound DNA.&lt;/p&gt;&#xA;&lt;p&gt;This mixture is incubated with an antibody (immobilised on beads) which binds our protein of interest. We can separate the antibody-covered beads and hence our protein along with it.&lt;/p&gt;&#xA;&lt;p&gt;Finally we can sequence the DNA fragments caught in this way. It's like &amp;quot;fishing for binding sequences&amp;quot;. The end result is a distribution of where our protein was bound across the genome at the time of our snap-shot.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1TrMz.png&quot; alt=&quot;ChIP-seq workflow diagram&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Ideally the DNA fragments should be long enough to place them uniquely in the genome. There are advanced PCR and sequencing methods which separate DNA fragments in to 'bubbles' in an emulsion containing one molecule of DNA each. In this way, we can sequence all the variants that are present and by counting the number of sequences ('reads') of each type, we have a measure of the abundance of each sequence. This abundance is interpreted as the occupancy of the protein at different binding sites.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jpCBN.jpg&quot; alt=&quot;Illustration of ChIP-seq output: distributions of a transcription complex and several histone modifications across a segment of a chromosome.&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Genome-wide studies of DNA binding have shown us that proteins are distributed around the genome. They have preferred binding sites but also have some affinity for similar sites, and spend some of their time bound to non-functional bits of the genome.&lt;/p&gt;&#xA;&lt;p&gt;Especially in mammals, a 'true' binding site isn't only (and isn't always) determined by having the highest affinity sequence, but also by being clustered with binding sites for other co-factors. This is because, in mammals, proteins often bind DNA, not solo, but as parts of large complexes which can interact with nucleosomes and which allow regulation of transcription or whatever else.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;My question is how can we precisely tell at which sites they bind? Is it the amino acid sequence of the protein? Or is it the repetitiveness factor in case they bind to multiple locations on the chromosome?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So, we can tell at which sequences (and where in the genome, even with what relative occupancy) proteins will bind to DNA by experiment. You could try to guess where they bind from their structure, but the way we precisely tell, is by experiment.&lt;/p&gt;&#xA;&lt;p&gt;The amino acid sequence of a protein ultimately determines its folded structure, and there are &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA-binding_domain&quot; rel=&quot;nofollow noreferrer&quot;&gt;many DNA-binding motifs&lt;/a&gt; or domains which appear in many different proteins. Some motifs bind the DNA backbone regardless of the sequence of bases, others bind specific sequences.&lt;/p&gt;&#xA;&lt;p&gt;Let's take zinc fingers as an example. The best-known class of zinc fingers basically inserts an alpha-helix in to the major groove of the DNA double helix, where certain amino acids on the appropriate side of the alpha-helix make contacts with the nucleotide bases. These contacts can be hydrogen bonds, or van-der-Waals contact. (E.g. Histidine and serine tend to hydrogen bond guanine; phenylalanine 'ring-stacks' between As and Ts; and threonine contacts the methyl group of thymine.)&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PKAv7m.png&quot; alt=&quot;Array of 3 zinc fingers with their 'reading helices' in the major groove.&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Zinc fingers are often found in arrays in proteins, as you might have been suggesting by &amp;quot;repetitiveness factor&amp;quot;. Meaning, a single finger might recognise a specific 3 or 4bp sequence, which isn't very unique. A protein will usually have 3 or more fingers held with regular spacing, so that this string of motifs: ZFa-ZFa-ZFb might recognise the DNA sequence: GCTAxxxGCTAxxxCCAA which is a much more unique site (this is imaginary.)&lt;/p&gt;&#xA;&lt;p&gt;So yes protein sequence and (thus) structure determines what sites a protein can bind (you can imagine a distribution of affinity for sequences, there will be a 'peak' sequence) - but again some proteins bind the DNA backbone non-specifically, and in mammals they often don't bind alone but within complexes.&lt;/p&gt;&#xA;&lt;p&gt;People have studied protein-DNA binding by engineering their own arrays of zinc fingers or TALENs, and also by &lt;a href=&quot;http://en.wikipedia.org/wiki/Systematic_evolution_of_ligands_by_exponential_enrichment&quot; rel=&quot;nofollow noreferrer&quot;&gt;engineering their own DNA binding sites&lt;/a&gt;, through a process of 'artificial evolution': selecting the strongest binders, mutating them, and repeat. These kinds of studies might come up with a sort of optimal 'binding code'.&lt;/p&gt;&#xA;" OwnerUserId="13310" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-04T14:05:32.047" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28263" PostTypeId="1" AcceptedAnswerId="28419" CreationDate="2015-02-02T15:04:12.653" Score="7" ViewCount="5531" Body="&lt;p&gt;Why do these circles form around the eyes if somebody is tired? And why does fatigue express itself around the eyes this way? Can I get eye bags very quickly in another way?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IGOeL.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tk5IM.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.todayifoundout.com/index.php/2014/06/causes-dark-circles-eyes-sleeping-people-really-tired/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.todayifoundout.com/index.php/2014/06/causes-dark-circles-eyes-sleeping-people-really-tired/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.top10homeremedies.com/how-to/how-to-get-rid-of-dark-circles-fast.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.top10homeremedies.com/how-to/how-to-get-rid-of-dark-circles-fast.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="13243" LastEditorUserId="6061" LastEditDate="2015-02-08T03:41:46.877" LastActivityDate="2016-02-10T11:55:41.627" Title="Why do we get 'bags under our eyes'?" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28264" PostTypeId="2" ParentId="7554" CreationDate="2015-02-02T15:13:40.200" Score="1" Body="&lt;p&gt;If your first question means: why is later-life ageing usually a long and painful process of degradation (rather than why do we have existential agony) with diseases of ageing like osteoporosis, heart disease, dementia - then I can offer one answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an absence &lt;em&gt;(almost)&lt;/em&gt; of any selection pressure after reproductive age. Once individuals are past reproductive age, any such diseases, unless they place a great survival burden on the immediate (related) community/family, do not influence fitness of the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, perhaps evolution has nothing to say about diseases of ageing, and no 'imperative' to purge our species of these afflictions. &lt;/p&gt;&#xA;" OwnerUserId="13310" LastActivityDate="2015-02-02T15:13:40.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28265" PostTypeId="1" AcceptedAnswerId="31185" CreationDate="2015-02-02T15:26:43.823" Score="3" ViewCount="1232" Body="&lt;p&gt;I have taken images from two different samples that have uptaken EdU during DNA synthesis (S-phase). The experiment setup is to find which condition had uptaken more EdU. Therefore I am detecting EdU with fluorescent to be able to quantify them in two conditions and compare them. The images are taken under same exposure. However in ImageJ when I want to adjust threshold I am not sure if I need to have the same threshold for both images or they can be different? Any tips are appreciated and let me know if I need to provide more info. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;cheers!&lt;/p&gt;&#xA;" OwnerUserId="13314" LastEditorUserId="5144" LastEditDate="2015-04-09T05:07:39.917" LastActivityDate="2015-04-09T05:07:39.917" Title="How to set threshold in ImageJ for quantifying relative fluorescence?" Tags="&lt;fluorescent-microscopy&gt;&lt;imaging&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28267" PostTypeId="2" ParentId="28258" CreationDate="2015-02-02T16:16:56.740" Score="3" Body="&lt;p&gt;Yes, some blood vessels change their diameter, they dilate or constrict. This is termed 'vasodilation' and 'vasoconstriction'. Large and mid-sized vessels contain smooth muscle in their walls. The walls of arteries tend to be stiffer than those of veins, to withstand high pressure coming from the heart.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/66uxm.jpg&quot; alt=&quot;Cross-sectional cartoon of the walls of arteries and veins.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Smooth muscle, when stimulated by the nervous system, can sustain contractions for long periods of time, and often with fine control. When smooth muscle in the walls of your blood vessels relaxes, those vessels will dilate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Small capillaries do not have smooth muscle in their walls, but the flow of blood through them can be controlled by the larger vessels that feed them. When arterioles constrict, the capillaries they feed can have reduced flow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oPGBy.jpg&quot; alt=&quot;Cartoon of a capillary bed.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our nervous system takes in a lot of signals relevant to controlling blood pressure and flow, and controls these smooth muscles. Flow can be increased or decreased to individual organs when needed, like the intestine (after a meal), the muscles (during exercise), the skin (for heat exchange).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question about warm water is actually quite interesting. Placing your arm in warm water will cause &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2342852/&quot; rel=&quot;nofollow noreferrer&quot;&gt;vasodilation in your other arm&lt;/a&gt; (the one not in the water), in order to lose some heat to the cold air and maintain your core temperature. Normally, the blood vessels in our 'extremities' (our hands and feet) are kept quite constricted to reduce heat loss with the cold air. &#xA;If we exercise or take a hot bath our core temperature will rise, some people will notice their skin gain a red hue after these activities, due to vasodilation.&lt;/p&gt;&#xA;" OwnerUserId="13310" LastActivityDate="2015-02-02T16:16:56.740" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28268" PostTypeId="1" AcceptedAnswerId="28277" CreationDate="2015-02-02T17:19:26.503" Score="1" ViewCount="129" Body="&lt;p&gt;The mass and size of the dinosaurs and prehistoric insects continues to amaze me. I read from an earlier post that oxygen was more abundant during the prehistoric era. However supporting the weight for me is still a mystery. Is it possible that the air was denser, allowing slight decrease in weight from greater buoyancy?&lt;/p&gt;&#xA;" OwnerUserId="9107" LastEditorUserId="3340" LastEditDate="2015-02-03T05:13:42.193" LastActivityDate="2015-02-03T06:18:24.280" Title="Was Earth's atmosphere more buoyant in the prehistoric era then today?" Tags="&lt;zoology&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="28269" PostTypeId="2" ParentId="27475" CreationDate="2015-02-02T17:26:19.940" Score="5" Body="&lt;p&gt;The thunder chimp's answer summarized the answer very well.  To try to pull things together a bit, if you have seven minutes, check out &lt;a href=&quot;https://www.youtube.com/watch?v=826HMLoiE_o&quot; rel=&quot;noreferrer&quot;&gt;this video&lt;/a&gt;.  It shows a man chasing down a &lt;a href=&quot;http://en.wikipedia.org/wiki/Kudu&quot; rel=&quot;noreferrer&quot;&gt;kudu&lt;/a&gt;. They both run for 8 hours, until the kudu literally collapses and the man calmly walks up to it and slays it.  The video shows the evolutionary adaptions that the man has - he sweats all over his body, cooling himself. The kudu needs shade to cool, and sweats only a little.  The man can carry water, to replenish himself.  The animal cannot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps more importantly, the man walks upright on two feet, thus shifting his center of gravity in a energetically favorable way.  The animal is restricted to galloping, which is faster for a sprint but not energetically favorable for long distance running.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are some articles for further reading:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://libgen.asia/283a81d4939d212ce1cec5a1a62eaa32/lieberman2007.pdf&quot; rel=&quot;noreferrer&quot;&gt;Evolution of Marathon Running&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://libgen.asia/789be3110ccaf48b7eff4ddffcb739c3/10.2307@2742907.pdf&quot; rel=&quot;noreferrer&quot;&gt;The Energetic Paradox of Human Running and Hominid Evolution&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://lib.gen.in/ocean/9843126ce104a99c5aeb7208568e9376/bramble2004.pdf&quot; rel=&quot;noreferrer&quot;&gt;Endurance running and the evolution of Homo&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They say similar things as the video: that we evolved for persistence hunting in an arid environment.  This is an activity that the other primates don't engage in. Our ability to hunt effectively allow us to eat more meat, and thus favored efficient long distance running.&lt;/p&gt;&#xA;" OwnerUserId="13297" LastActivityDate="2015-02-02T17:26:19.940" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28271" PostTypeId="1" CreationDate="2015-02-02T18:26:05.310" Score="3" ViewCount="96" Body="&lt;p&gt;I am trying to get a pdb file that contains a single atom, it doesn't matter if it's Hydrogen or another atom. How can I obtain this? Are there any pdb files with just a single atom available to download? Or do I have to take an existing molecule and remove the atoms manually?&lt;/p&gt;&#xA;" OwnerUserId="13315" LastEditorUserId="5144" LastEditDate="2015-02-02T19:09:06.680" LastActivityDate="2015-02-02T19:09:06.680" Title="How to get a pdb file of a single atom?" Tags="&lt;biophysics&gt;&lt;pdb&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28273" PostTypeId="1" CreationDate="2015-02-02T19:00:59.333" Score="1" ViewCount="189" Body="&lt;p&gt;I've been reading up on beneficial mutations, and am curious when we discovered and documented the first one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone point me to the first documented beneficial mutation?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Per request, let me try to clarify my answer a bit.&#xA;I know that we've been aware of mutations perhaps as long ago as the 1930s (I believe it was R.A Fisher who was one of the first to talk about them??).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read various documented beneficial mutations since then, such as lactase example in humans, or cit+ in E.Coli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm curious about is when it was that we first identified and documented (scientific paper or article) an observed beneficial mutation, in any organism (not just humans).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes, Remi.b, your wording would have been what I was looking for:&#xA;&quot;what is the first article that has documented a beneficial mutation, in any organism&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this clarify it enough?&lt;/p&gt;&#xA;" OwnerUserId="9772" LastEditorUserId="9458" LastEditDate="2015-02-04T02:52:51.510" LastActivityDate="2015-02-04T06:26:52.443" Title="First documented beneficial mutation?" Tags="&lt;evolution&gt;&lt;history&gt;" AnswerCount="0" CommentCount="11" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28274" PostTypeId="2" ParentId="7401" CreationDate="2015-02-02T20:10:40.057" Score="-1" Body="&lt;p&gt;Generally if one of the genes' biochemical functions becomes knocked out completely, the other copy will fill in for it, making the trait recessive - requiring both copies being knocked out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of such a recessive trait is Albinism - if both copies of the enzyme participating in melanin biosynthesis are ineffective, the result is someone with no pigment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dominant genes are often variant genes which convey a new ability (phenotype) and as such the trait can show up with just one copy has this variant. Phenylthiocarbamide tasting is an example of this dominance. If both copies of the gene were the variant, the original ability might disappear - making the original trait dominant as well. On the molecular level, genes most often encode proteins which perform some function for the cell: For example, they could be enzymes and catalyze chemical reactions. They could also have some structural function, such as make up the &quot;muscle&quot; part of your muscle cells... You get the idea. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the most simple case, the dominant allele encodes a protein that can perform its function. For example, the dominant allele for the CFTR gene encodes a channel that can let chloride into and out of the cells. The recessive allele, on the other hand encodes a protein that cannot do its job correctly (this also called a loss-of-function mutation). So if you inherit a functional copy from one parent and a non-functional copy from the other parent, you will still have one copy of the protein that can do its job. Only if you get a nonfunctional copy from both parents will you have a recessive condition called cystic fybrosis.&lt;/p&gt;&#xA;" OwnerUserId="13317" LastEditorUserId="5144" LastEditDate="2015-02-03T07:24:45.557" LastActivityDate="2015-02-03T07:24:45.557" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28275" PostTypeId="1" CreationDate="2015-02-03T01:55:25.157" Score="4" ViewCount="1446" Body="&lt;p&gt;I am told that beta branching interferes with alpha helix formation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Problem is that I don't see how beta branching has anything to do with alpha-helix formation. Beta-branches are on the outside of alpha helices and internal hydrogen bonding holds the helix together. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My book (Lehninger) also doesn't say anything about beta branching interfering with alpha helix formation. &lt;/p&gt;&#xA;" OwnerUserId="6759" LastEditorUserId="3340" LastEditDate="2015-02-03T05:30:20.757" LastActivityDate="2016-04-19T11:36:50.557" Title="How does beta branching stop alpha helices from forming?" Tags="&lt;biochemistry&gt;&lt;amino-acids&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28277" PostTypeId="2" ParentId="28268" CreationDate="2015-02-03T06:18:24.280" Score="3" Body="&lt;p&gt;While it seems difficult to me to imagine any mechanisms that would allow significant changes to the total amount of atmosphere (and therefore density) in geologically recent times (&amp;lt; 100M year), it's quite difficult to find direct evidence about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In 2012 Nature published a &lt;a href=&quot;http://www.nature.com/nature/journal/v484/n7394/full/nature11036.html&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; that calculated the air pressure (and therefore the air density) by noting the distribution of sizes of puddles formed by raindrops in 2.7 billion year old ash. The conclusion was that the air was no more than twice as great as it is today.  This amount would be quite a bit for flying creatures, but would be almost completely insignificant for  supporting the weight of large creatures.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an example, a large elephant has a volume of slightly more than $10m^3$, and a mass of over $5000kg$.  The buoyancy of the air only takes off the equivalent of about $12kg$ of that mass.  Even an atmosphere 10 times the modern density would be little help in supporting its weight.  &lt;/p&gt;&#xA;" OwnerUserId="11623" LastActivityDate="2015-02-03T06:18:24.280" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28278" PostTypeId="2" ParentId="28260" CreationDate="2015-02-03T07:17:31.477" Score="1" Body="&lt;p&gt;You can see &lt;a href=&quot;http://www.nature.com/protocolexchange/protocols/15#/main&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; protocol for &lt;em&gt;Wolbachia&lt;/em&gt; isolation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://ci.nii.ac.jp/els/110007004674.pdf?id=ART0008920957&amp;amp;type=pdf&amp;amp;lang=en&amp;amp;host=cinii&amp;amp;order_no=&amp;amp;ppv_type=0&amp;amp;lang_sw=&amp;amp;no=1422947612&amp;amp;cp=&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; protocol for infecting cell lines with &lt;em&gt;Wolbachia&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9013253&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; study the authors have established a cell line from a &lt;em&gt;Wolbachia&lt;/em&gt; infected tissue of &lt;em&gt;Aedes albopictus&lt;/em&gt;. You can have a look at that too. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-02-03T09:47:23.007" LastActivityDate="2015-02-03T09:47:23.007" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28281" PostTypeId="2" ParentId="28258" CreationDate="2015-02-03T08:17:32.800" Score="4" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Capillary&quot; rel=&quot;nofollow&quot;&gt;Capillaries&lt;/a&gt; are the smallest blood vessels. They are unique in that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;They don't have any muscular component like arterioles or venules do.&lt;/li&gt;&#xA;&lt;li&gt;They are lined by a single layer of endothelium  (cells lining blood vessels are called endothelial cells) overlying the basement membrane.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Due to these reasons the capillaries are very permeable facilitating nutrient and gas exchange.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The capillaries don't expand as they do not have muscular or elastic components. However exposure to heat do increase the circulation. This is due to the following facts:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Heat_therapy&quot; rel=&quot;nofollow&quot;&gt;Exposure to heat&lt;/a&gt; dilates the pre-capillary arterioles - this would inevitably cause improved capillary circulation in capillaries that are already open.&lt;/li&gt;&#xA;&lt;li&gt;Increase in pre-capillary flow opens up &lt;a href=&quot;http://faculty.clintoncc.suny.edu/faculty/michael.gregory/files/bio%20100/Bio%20100%20Lectures/Organ%20Systems/Circulatory%20System/Circulatory%20System.htm&quot; rel=&quot;nofollow&quot;&gt;collapsed capillaries&lt;/a&gt;. In the human body roughly only one-fourth of the capillaries are open during rest&lt;sup&gt;1&lt;/sup&gt;. As the pre-capillary arterioles dilate, the collapsed capillaries open up thus further improving circulation.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;To improve capillary perfusion:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Temporary improvement can be achieved by activity (exercise), exposure to warmth, emotions (flushing is due to vasodilation), even exposure to cold causes vasodilation after the initial vasoconstriction&lt;/li&gt;&#xA;&lt;li&gt;Permanent improvement of capillary circulation can be achieved by &lt;a href=&quot;http://healthyliving.azcentral.com/capillary-density-bodybuilding-19963.html&quot; rel=&quot;nofollow&quot;&gt;increasing capillary density&lt;/a&gt;. Capillary density refers to the number of capillaries present in 1 cm&lt;sup&gt;2&lt;/sup&gt; area. Capillary density can be increased by consistent anaerobic (isometric and to some extent isotonic) exercise.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;References:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;1: Boron and Boupaep text book of medical physiology, 2&lt;sup&gt;nd&lt;/sup&gt; Edition, p.467&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;For more:&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://corporate.dukemedicine.org/news_and_publications/news_office/news/6597&quot; rel=&quot;nofollow&quot;&gt;http://corporate.dukemedicine.org/news_and_publications/news_office/news/6597&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8852622&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/8852622&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-02-03T08:17:32.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28283" PostTypeId="1" CreationDate="2015-02-03T09:35:31.047" Score="3" ViewCount="360" Body="&lt;p&gt;Is there a standard, or most accepted, way to present a value for sexual dimorphism? For example, one could use &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{\text{Female value}}{\text{Male value}} -1$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This would give negative values when the female value is smaller than the males, and positive when male is smaller. My issue with this though is that when a female is twice the size of a male its value is -0.5, while when a male is twice the size of a female its value is 1.0, so they do not spread symmetrically around 0.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just playing around with some dummy data in R I came up with a possible solution&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$0.5 - \frac{\text{Female}}{\text{Female + Male}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This gives a zero centred value with equal distribution around the mean. For example, when Females are twice the size of males the value is -0.166, and when males are twice the size of females the value is 0.166, when they are the same size it is 0.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FFmPhl.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="3624" LastEditDate="2015-02-03T11:30:09.000" LastActivityDate="2015-02-03T11:30:09.000" Title="Is there a standard formula/calculation for sexual dimorphism?" Tags="&lt;mathematical-models&gt;&lt;biostatistics&gt;&lt;sexual-dimorphism&gt;&lt;methods&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28285" PostTypeId="1" CreationDate="2015-02-03T09:42:14.580" Score="4" ViewCount="454" Body="&lt;p&gt;Among mammals, cats are able to land safely when falling from great heights. For example, when compared to dogs or humans they can survive drops from relative large heights. How do they manage?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A 1987 study from the Journal of the American Veterinary Medical Association. Two vets examined 132 cases of cats that had fallen out of high-rise windows and were brought to the Animal Medical Center, a New York veterinary hospital, for treatment. On average the cats fell 5.5 stories, yet &lt;strong&gt;90 percent survived&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See wiki on &lt;a href=&quot;http://en.wikipedia.org/wiki/Cat&quot; rel=&quot;nofollow&quot;&gt;cats&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can cats do this?&lt;/p&gt;&#xA;" OwnerUserId="13324" LastEditorUserId="5198" LastEditDate="2015-02-05T06:22:31.677" LastActivityDate="2015-02-05T09:07:22.510" Title="How do cats survive falling from great heights?" Tags="&lt;zoology&gt;&lt;anatomy&gt;&lt;species&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28287" PostTypeId="5" CreationDate="2015-02-03T10:52:09.290" Score="0" Body="&lt;p&gt;Kinetics is the branch of chemistry/biochemistry that focuses on studying and measuring the rates of chemical reactions or physiological processes. Kinetic studies have been used to quantify the flux rates of a number of in vivo biochemical compounds including, but not limited to, amino acids, glucose, triglycerides/free fatty acids, bile acids, cholesterol, and hormones.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="16299" LastEditDate="2015-12-30T19:11:57.840" LastActivityDate="2015-12-30T19:11:57.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28288" PostTypeId="4" CreationDate="2015-02-03T10:52:09.290" Score="0" Body="Kinetics is the study of rates of chemical or biochemical reactions, as well as the metabolic flux rates of biochemical intermediates within the body (e.g. glucose, amino acids, lipids, bile acids). " OwnerUserId="9943" LastEditorUserId="16299" LastEditDate="2015-12-30T19:12:07.620" LastActivityDate="2015-12-30T19:12:07.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28289" PostTypeId="1" AcceptedAnswerId="28299" CreationDate="2015-02-03T10:54:02.093" Score="13" ViewCount="33236" Body="&lt;p&gt;During sleep, our body activity decreases. I am wondering on the extent of the lowering of this activity regarding our five senses. Clearly, the sense of touch is still very efficient since shaking a body is the most common way to awake someone, and hearing is also quite unaffacted (most, if not all, alarm clock, rely on this sense). Most deaths due to fire are due to intoxication rather than the burnt of the fire, so it suggests that smell and taste are pretty dimmed during sleep. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My main question: &lt;strong&gt;To which extent each sense is dimmed during sleep?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Can we smell during sleep? I don't remember having been awoken by the smell of something during my life...&lt;/li&gt;&#xA;&lt;li&gt;Similarly, can we taste? If someone gives me delicious food during my sleep, would I be able to feel its taste and remember this experience?&lt;/li&gt;&#xA;&lt;li&gt;Can we see? REM are well known but it is a mechanical feature of the sleep. Some people sleep with the eyes opened: what do they see?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note&lt;/strong&gt;: This &lt;a href=&quot;https://biology.stackexchange.com/questions/8361/how-are-our-senses-dimmed-during-sleep&quot;&gt;related question&lt;/a&gt; tries to explain &lt;em&gt;how&lt;/em&gt; senses are dimmed during sleep but not &lt;em&gt;how much&lt;/em&gt; they are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note 2&lt;/strong&gt;: I am aware this is person-dependant: any sound would awake my mother (a skill during my nightly escapades) whereas I would not notice a party around me when I am in deep sleep. But there should be some kind of average... It also depends on the phase of sleep; I am mostly interested in deep sleep and REM sleep, but an answer detailing every phase would be awesome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note 3&lt;/strong&gt;: This question is certainly naive in its current form. Please help me to improve it.&lt;/p&gt;&#xA;" OwnerUserId="13327" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2018-03-09T05:13:24.230" Title="What senses are active while sleeping?" Tags="&lt;human-biology&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28290" PostTypeId="1" AcceptedAnswerId="28301" CreationDate="2015-02-03T12:12:36.343" Score="5" ViewCount="627" Body="&lt;p&gt;I have given an input of this protein sequence:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;from &lt;a href=&quot;http://scratch.proteomics.ics.uci.edu/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; website  along with the option of COBEpro. Now the output sent by this site to my email is as follows:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;Name: temp_prot&#xA;&#xA;Amino Acids:&#xA;MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE&#xA;&#xA;Predicted Continuous B-cell Epitopes:&lt;br&gt;&#xA;MOST LIKELY EPITOPES:&lt;br&gt;&#xA;0.82848577 39 TKALGIS CCCCCEE eee-e-e&lt;br&gt;&#xA;0.82036375 39 TKALGI CCCCCE eee-e-&lt;br&gt;&#xA;0.76503265 38 TTKALGI ECCCCCE eeee-e-&lt;br&gt;&#xA;0.73178638 73 TSQPRGDP CCCCCCCC -eeeeeee&lt;br&gt;&#xA;…&#xA;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and a few more. Now can you tell me, if I consider the very first result, I was able to find &lt;code&gt;TKALGIS&lt;/code&gt; in the parent sequence but could not find &lt;code&gt;CCCCCEE&lt;/code&gt;. What is this &lt;code&gt;CCCCCEE&lt;/code&gt;?&#xA;And what does this &lt;code&gt;eee-e-e&lt;/code&gt; mean?&lt;br&gt;&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="3553" LastEditDate="2015-02-05T12:35:50.023" LastActivityDate="2017-03-23T04:49:35.290" Title="What do &quot;e&quot; &quot;-&quot; &quot;C&quot; and &quot;E&quot; mean in this output?" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;proteins&gt;&lt;database&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28292" PostTypeId="2" ParentId="28285" CreationDate="2015-02-03T12:40:50.387" Score="7" Body="&lt;p&gt;The reason why cats are superb jumpers has not received much attention, but one article in Nature was entirely devoted to just this (&lt;a href=&quot;http://adsabs.harvard.edu/abs/1988Natur.332..586D&quot; rel=&quot;nofollow noreferrer&quot;&gt;Diamond, 1988&lt;/a&gt;). Here follows a partly quoted and partly adapted text from this article:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First , because mass increases as the cube, but surface area as the square of linear dimensions, &lt;strong&gt;falling large animals are in general more injury-prone than small ones&lt;/strong&gt;, as they suffer greater impact stress, their bones experience greater stress, and they reach higher terminal velocities in free-fall because of a less favorable area/mass ratio. While a small drop breaks an elephant's leg, a falling mouse reaches terminal velocity in the atmosphere much sooner and at a much lower value than do falling elephants. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, falling cats have a &lt;strong&gt;superb vesti­bular system and make gyroscopic turns&#xA;such that all four feet are soon pointing downwards&lt;/strong&gt;, regardless of the cat's&#xA;orientation at the start of the fall. Hence cats dissipate the impact force over all four limbs. Falling human adults  tend to tumble uncontrollably but land most often&#xA;on two feet, next most often on their heads. These facts contribute to the low mortality of falling cats and to their low chance of breaking limbs after the fall.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Third, a &lt;strong&gt;cat&lt;/strong&gt; falling in the atmosphere reaches a terminal  velocity  of  about  &lt;strong&gt;60 m.p.h. (compared with 120 m.p.h. for adult humans&lt;/strong&gt;) after only  about  100 feet. As long as it experiences acceleration, the cat probably extends its limbs reflexively , but on reaching terminal velocity it may relax and extend the limbs more horizontally in &lt;strong&gt;flying-squirrel fashion&lt;/strong&gt;, thus not only &lt;strong&gt;reducing the velocity of fall&lt;/strong&gt; but also &lt;strong&gt;absorbing the  impact  over  a greater  area of its body&lt;/strong&gt;. This may explain the para­doxical decrease of mortality and injury in cats that fall more than 100 feet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, cats that land with their &lt;strong&gt;limbs flexed dissipate much of the impact force through soft tissue&lt;/strong&gt;. Parachutists are trained to dissipate impact forces by landing with knees and hips flexed, then rolling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://adsabs.harvard.edu/abs/1988Natur.332..586D&quot; rel=&quot;nofollow noreferrer&quot;&gt;Diamond. &lt;em&gt;Nature&lt;/em&gt; 1988; &lt;strong&gt;332&lt;/strong&gt;:586-7&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Further reading&lt;/strong&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.bbc.com/news/magazine-17492802&quot; rel=&quot;nofollow noreferrer&quot;&gt;BBC news&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YPjiX.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-02-05T01:16:18.070" LastActivityDate="2015-02-05T01:16:18.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28294" PostTypeId="1" AcceptedAnswerId="28412" CreationDate="2015-02-03T13:33:25.723" Score="5" ViewCount="354" Body="&lt;p&gt;Each DNA (RNA) sequence has 6 possible Open Reading Frames(ORF). My question is: What are the theoretical bases of &lt;em&gt;in vitro&lt;/em&gt; or &lt;em&gt;in silico&lt;/em&gt; tries to find correct reading frame of a sequence?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it just distance between Start and Stop codons, or are there some other factors with more important impacts in this subject?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="6" LastEditDate="2015-02-03T17:28:56.450" LastActivityDate="2015-02-07T18:04:22.577" Title="How do biologists infer correct ORF of a DNA sequence?" Tags="&lt;transcription&gt;&lt;sequence-analysis&gt;&lt;orf&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28299" PostTypeId="2" ParentId="28289" CreationDate="2015-02-03T20:16:01.060" Score="9" Body="&lt;p&gt;The answer is of interest not only in sleep but also the perceptions of patients under anesthesia, comatose states, etc.&lt;/p&gt;&#xA;&lt;p&gt;Our senses aren't 'dimmed' in sleep. There is no effective way to turn off our senses. The best way to explain what happens in sleep is that at some point (the last point, actually), our &lt;em&gt;cognitive processing&lt;/em&gt; of sensations changes. That is, our higher brain functions allow us to ignore certain sensory input. This effect has been most studied in sound perception.&lt;/p&gt;&#xA;&lt;p&gt;In a sleep study involving sound and EEG/fMRI during all phases of (drug-free) sleep,&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The first significant result of this study is that the pattern of brain activation associated with auditory stimulation was strikingly similar in wakefulness and sleep, suggesting that sensory processing occurred in both conditions. However, we found qualitative differences in brain activation associated with auditory processing during sleep compared to wakefulness. The reduced regional activity during sleep, compared to wakefulness, in the left parietal and, bilaterally, in the prefrontal cortex, thalamus, and cingulate gyrus (part of the limbic system) suggests that these areas may be involved in the further processing and perceptual integration of sensory inputs likely to occur during wakefulness only.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Supporting this is evidence that some sounds awaken someone no matter at what stage they are in sleep, for example, young mothers are woken up by their infants' lightest movements&lt;sup&gt;[2]&lt;/sup&gt;, and the fact that we respond to our own names in a similar fashion in sleep and in wakefulness, but such responses are not shown for presentation of other first names.&lt;sup&gt;[3]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;These results suggest that the sleeping brain, during SII and PS, elicits a differential cognitive response to the presentation of the subject's own name, comparable to that occurring during wakefulness, and therefore that the sleeping brain is able to detect and categorize some particular aspects of stimulus significance.&lt;sup&gt;[3]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;p&gt;Thus, the results suggest that when subjects were listening to their own name during sleep some brain regions were selectively more responsive than in any other condition. ...we have demonstrated that the sleeping brain is able to process auditory stimuli. In addition, we postulate the existence of a functional network capable of detecting and facilitating processing of emotionally relevant inputs during sleep.&lt;sup&gt;[1]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;p&gt;Our results support the view that PS is not a state of &amp;quot;sensory isolation&amp;quot;; failure to respond to external stimuli during this stage may depend upon mechanisms occurring only after the sensory input has undergone cognitive analysis.&lt;sup&gt;[4]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However, as you noted, odors are not good at waking people up.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Some suggest that the human olfactory system during sleep is sufficiently well tuned to ensure arousal to such threatening stimuli as odors associated with smoke from fire. Our results strongly suggest otherwise. The intensity, strength, and noxiousness of the pyridine stimulus elicited behavioral arousal or EEG activation on fewer than half of stage 2 trials, less than one third of REM-sleep trials, and virtually no stage-4- sleep trials. This is a nontrivial lack of response, since pyridine is a component of coal tar and is also used as a herbicide for firewood, and thus is a likely by-product of many real fires. In practical terms, therefore, olfactory awareness in humans is low to absent during sleep, and human olfaction appears insufficiently sensitive and reliable to act as a sentinel system. We further note that auditory arousal threshold is highest in young and sleep-deprived individuals, increasing the likelihood that olfactory processing is even worse for children and sleep-deprived adults.&lt;sup&gt;[5]&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The methodology in the olfactory study varies quite significantly from the auditory study. Better studies may shed more evidence on why olfactory stimuli are processed differently from other stimuli.&lt;/p&gt;&#xA;&lt;p&gt;As to what percent? That probably differs from person to person, and I did not search the literature for that.&lt;/p&gt;&#xA;&lt;p&gt;&lt;sub&gt;[1] &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0896627300001690&quot; rel=&quot;noreferrer&quot;&gt;Auditory Processing across the Sleep-Wake Cycle: Simultaneous EEG and fMRI Monitoring in Humans&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;[2] &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9885077&quot; rel=&quot;noreferrer&quot;&gt;Changes in sleep patterns of young women from late pregnancy to postpartum: relationships to their infants' movements&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;[3] &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1388245799001777&quot; rel=&quot;noreferrer&quot;&gt;A differential brain response to the subject's own name persist during sleep&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;[4] &lt;a href=&quot;http://journals.lww.com/clinicalneurophys/Abstract/1995/03000/Brain_Processing_of_Stimulus_Deviance_During.6.aspx&quot; rel=&quot;noreferrer&quot;&gt;Brain Processing of Stimulus Deviance During Slow-Wave and Paradoxical Sleep: A Study of Human Auditory Evoked Responses Using the Oddball Paradigm.&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;[5] &lt;a href=&quot;http://scholar.google.com/scholar?q=olfactory+sensory+processing+and+sleep+fMRI&amp;amp;btnG=&amp;amp;hl=en&amp;amp;as_sdt=0%2C39&quot; rel=&quot;noreferrer&quot;&gt;Minimal Olfactory Perception During Sleep: Why Odor Alarms Will Not Work for Humans&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-03T20:16:01.060" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28300" PostTypeId="1" CreationDate="2015-02-03T21:39:54.753" Score="10" ViewCount="1428" Body="&lt;p&gt;Predators at the top of a food chain, like lions, seem to have a relatively low fertility rate, which fits well to the ecosystem and avoids overpredation. But what is the mechanism that keeps the fertility rate at this level? A mutation that increases fertility among the predators should quickly spread in such a population, eventually leading to an increase of the predator fertility rate followed by overpredation. But it seems that this is usually not the case. What does keep the fertility rate of predators at the level they are?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S: Many explanations on population dynamics cite Lotka Volterra, including the existing question on Bio.SE &quot;&lt;a href=&quot;https://biology.stackexchange.com/questions/15514/what-prevents-predator-overpopulation&quot;&gt;What prevents predator overpopulation?&lt;/a&gt;&quot;. Population dynamics predict orbits for the population sizes of predator and prey. Still this does not explain why the &lt;strong&gt;fertility rate of predators&lt;/strong&gt; shouldn't go up.&lt;/p&gt;&#xA;" OwnerUserId="13332" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2016-09-30T05:21:10.613" Title="Why are the fertility rates of large predators kept low?" Tags="&lt;evolution&gt;&lt;ecology&gt;&lt;population-dynamics&gt;&lt;life-history&gt;&lt;predation&gt;" AnswerCount="4" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28301" PostTypeId="2" ParentId="28290" CreationDate="2015-02-03T21:40:28.863" Score="10" Body="&lt;p&gt;CCCEEE &lt;em&gt;etc.&lt;/em&gt; are the secondary structural elements. In this case, the &lt;code&gt;C&lt;/code&gt; refers to non-strand and non-helix regions &lt;em&gt;i.e&lt;/em&gt; loop regions rather than a coiled region. The &lt;code&gt;C&lt;/code&gt; or &lt;code&gt;E&lt;/code&gt; &lt;a href=&quot;http://biostat.jhsph.edu/~iruczins/teaching/260.841/notes/c9.6.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;usually&lt;/a&gt; refers to whether the residue is coiled (&lt;code&gt;C&lt;/code&gt;) or part of a strand (&lt;code&gt;E&lt;/code&gt;). &lt;code&gt;H&lt;/code&gt; would be used to denote a helix, however, in the question, it appears that there are no helices. These letters are often different in different software: it's merely a point of semantics between different software. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;e&lt;/code&gt; or &lt;code&gt;-&lt;/code&gt; refers to if the amino acid at that position is exposed or not (&lt;code&gt;-&lt;/code&gt; = buried).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the method, &lt;a href=&quot;http://peds.oxfordjournals.org/content/22/3/113.full?keytype=ref&amp;amp;ijkey=AnJNyFmdbTK9mDF&quot; rel=&quot;nofollow noreferrer&quot;&gt;here is the COBEpro paper&lt;/a&gt;, although it does seem very technical. The &lt;a href=&quot;http://www.ics.uci.edu/~baldig/scratch/explanation.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;help page&lt;/a&gt; has more easily accessible information on the output. &lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2017-03-23T04:49:35.290" LastActivityDate="2017-03-23T04:49:35.290" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28302" PostTypeId="2" ParentId="28300" CreationDate="2015-02-03T22:51:39.087" Score="3" Body="&lt;p&gt;In a given area there can be only a limited number of top predators due to resource limitations. Furthermore, as top predators are not hunted upon, a relatively high percentage of offspring will survive until adulthood. Hence, producing many offspring doesn't make sense as survival rates are high, while resources are limited. Producing many offspring is a huge investment of resources (must be raised and fed) and if in the end many offspring die of a lack of resources, then the invested effort and energy was for nothing. Hence, producing many offspring decreases fitness in top predators and this trait will have been selected against during evolution.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-02-03T22:58:04.340" LastActivityDate="2015-02-03T22:58:04.340" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28303" PostTypeId="2" ParentId="28190" CreationDate="2015-02-03T23:53:46.530" Score="1" Body="&lt;p&gt;It sounds to me as though you have misunderstood something about the &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_genome&quot; rel=&quot;nofollow&quot;&gt;chromosomes that make up a human genome&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;on a different chromosome [..] at the same location&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;is not the same location at all. There is no surprise in finding 2 genomes to differ in one place, and not at another unrelated place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;edit&lt;/strong&gt; If this is a mis-reading of your question, and you meant that the 2 persons' SNP was &quot;at the same location&quot; as the other person, then the rest of the answer is irrelevant. 'A SNP' refers to a location, given a name/identifier for the purpose of measuring variation with SNP-chips; necessarily the same location in any person, which may vary, but needn't always differ between everyone (come on, there are only 4 possible values). You should re-phrase your question &quot;why do they differ at SNP 1 and not at SNP2?&quot;.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Background&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;SNP means nothing more than 'a single basepair in the genome, that might vary in a population', so let's just talk of 'difference at a position'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A single haploid set of the human genome consists of 23 chromosomes, 22 of these are quite 'ordinary', while 1 is involved in sex determination. Of course, most of our cells are diploid and so we have 2 of these sets, with pairs of Chr1, Chr2, ...Chr22 and X/Y.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;What I think your problem &lt;em&gt;isn't&lt;/em&gt;, that you perhaps thought it was&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;I haven't analysed large bits of genomic data but I believe heterozygous positions (positions at which one individual's paired chromosomes differ) are represented in that individual's sequence data. For this reason, I do &lt;em&gt;not&lt;/em&gt; think your question is asking 'how can 2 persons have a difference at basepair &lt;em&gt;x&lt;/em&gt; on one copy of Chr1, and no difference on the other copy of Chr1' - because both copies of Chr1 are merged as one person's dataset. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact it's impossible to assign (meaning to group in to &lt;em&gt;haplotypes&lt;/em&gt;) heterozygous sequence to either one copy or the other without more information, i.e. sequences from parents &amp;amp; grandparents, to see which variants are inherited together (are linked).&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;What I think your problem really is&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;I think you are asking 'how can 2 persons have a difference at basepair &lt;em&gt;x&lt;/em&gt; on Chr1, and no difference at basepair &lt;em&gt;x&lt;/em&gt; on Chr6 (say)?'&#xA;This is easily answered. Basepair 100 of Chr1 is a completely different and unrelated position in the genome to basepair 100 of Chr6. There is no reason to expect that these positions should be related. &lt;/p&gt;&#xA;&#xA;&lt;h3&gt;A helpful thought experiment&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;We can concatenate the chromosomes rather than re-setting our count at the beginning of each, then bp 100 of Chr6 will instead be denoted (approximately) bp 1,080,000,100 of the genome - this makes the difference in these positions crystal clear.&lt;/p&gt;&#xA;" OwnerUserId="13310" LastEditorUserId="13310" LastEditDate="2015-02-04T14:03:21.293" LastActivityDate="2015-02-04T14:03:21.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28304" PostTypeId="1" AcceptedAnswerId="28315" CreationDate="2015-02-04T02:06:57.240" Score="8" ViewCount="80" Body="&lt;p&gt;I need to download all uniprotIDs of a cancer pathway, say the AKT Signaling. It may be super easy, but I don't know which resource to look at since it is a new field.&#xA;&lt;p&gt;&#xA;How/where do I find these?&lt;/p&gt;&#xA;" OwnerUserId="13334" LastEditorUserId="1306" LastEditDate="2015-02-04T14:27:32.750" LastActivityDate="2015-02-04T14:27:32.750" Title="All UniprotIDs of a cancer pathway" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;cancer&gt;&lt;signalling&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28305" PostTypeId="1" CreationDate="2015-02-04T02:25:19.873" Score="10" ViewCount="1404" Body="&lt;p&gt;I read that some sharks are ovoviviparous.  What advantages and disadvantages are provided by this type of reproduction as opposed to egg laying and live birth?&lt;/p&gt;&#xA;" OwnerUserId="8387" LastEditorUserId="9943" LastEditDate="2015-02-04T03:49:49.030" LastActivityDate="2015-02-04T10:41:44.837" Title="What evolutionary advantages are provided by ovoviviparity?" Tags="&lt;evolution&gt;&lt;ichthyology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28309" PostTypeId="1" CreationDate="2015-02-04T10:31:22.707" Score="8" ViewCount="3712" Body="&lt;p&gt;When it comes to &lt;a href=&quot;http://en.wikipedia.org/wiki/Eukaryote&quot; rel=&quot;nofollow&quot;&gt;eukaryotes&lt;/a&gt;, including ourselves, we have all different kinds of specialized cells and tissues that are so different, yet originally all came from the same single cell. And apparently the reason for that is differential gene expression, where different genes get to be expressed in different cells. But there are, however, a set of genes that gets to be expressed in almost all of the cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is not &lt;strong&gt;why&lt;/strong&gt;, but &lt;strong&gt;what&lt;/strong&gt; is it about these genes that in a way makes them above the laws of regulation? Is it in their sequence? Or are they located on a single chromosome or perhaps regions that are somehow non-regulatable?&lt;/p&gt;&#xA;" OwnerUserId="13309" LastEditorUserId="355" LastEditDate="2015-02-04T23:12:11.923" LastActivityDate="2015-02-04T23:12:11.923" Title="What is it about the housekeeping genes that makes them almost immune to gene regulation?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;gene-regulation&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28310" PostTypeId="2" ParentId="28305" CreationDate="2015-02-04T10:41:44.837" Score="1" Body="&lt;p&gt;Reading this website (&lt;a href=&quot;http://www.sharks-world.com/shark_reproduction/&quot; rel=&quot;nofollow&quot;&gt;www.sharks-world.com/shark_reproduction&lt;/a&gt;) it seems that for most sharks the eggs develop inside the mother (ovoviviparity), and the young sharks (&quot;pups&quot;) are born fully functional, but this is not true for all sharks (as you mention in your question).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This persons blog (&lt;a href=&quot;http://morgana249.blogspot.co.uk/2014/09/5-modern-reptiles-that-give-birth-to.html&quot; rel=&quot;nofollow&quot;&gt;morgana249/modern reptiles give birth to live young&lt;/a&gt;) discusses evolution of ovoviviparity in some reptiles, but not others. In some species this seems to have gone back and forth in their evolutionary history, which suggests that changing conditions favour one then the other at different times, possibly influenced by temperature, among other things. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The researchers stated, &quot;These results suggest that parity mode is a labile trait that shifts frequently in response to ecological conditions.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This could be similar for sharks, although I could not find an article postulating this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, this could be because the mother does no &quot;parenting&quot;; the pups are immediately independent. Because sharks do not have many eggs at a time (according to the sharks-world website) each individual egg/pup has a higher &quot;value&quot; than each individual offspring in other fish species, which often lay many hundreds of eggs at once outside their body (oviparity). Therefore sharks that evolved this trait may have been selected because the offspring are more likely to survive if they are protected until fully functional within the parent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No doubt there are other possible explanations, but as with all these questions along the lines of &quot;What are the evolutionary reasons...&quot; we cannot ever actually &lt;em&gt;know&lt;/em&gt;, only suggest.&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2015-02-04T10:41:44.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28311" PostTypeId="2" ParentId="28309" CreationDate="2015-02-04T10:53:16.297" Score="6" Body="&lt;p&gt;The problem with housekeeping genes is that they are often not stable and their expression depends on the cell types as well as the conditions. They can be stable under one condition, but are not under another. So this needs to be tested every time you have to choose a housekeeping gene - always use GAPDH or beta-Actin simply doesn't work or skews the results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reasons why the housekeeping genes are chosen is because they are thought to be independently expressed (more or less) in the cells and that the actual experiment has in influence on them. This is also the reason why genes involved in the energy metabolism or the structural integrity of the cell (like GAPDH or beta-Actin) are chosen. This idea is not wrong, but needs to be tested, since transcription regulation networks are complicated and often bear interesting, surprisinf (and unknown) relations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following articles should be interesting in this context:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.gene-quantification.de/Vandesompele-Kubista-Pfaffl-real-time-PCR-chapter-4.pdf&quot;&gt;Reference Gene Validation Software for Improved Normalization&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.biomedcentral.com/1471-2199/10/17&quot;&gt;Selection of suitable housekeeping genes for expression analysis in&#xA;glioblastoma using quantitative RT-PCR&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.gene-quantification.de/kozera-rapacz-ref-genes-2013.pdf&quot;&gt;Reference genes in real-time PCR&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;What also gives quite a lot of information including a large number of references on this topic is the website from &lt;a href=&quot;http://normalisation.gene-quantification.info/&quot;&gt;Gene Quantification&lt;/a&gt; (which sell products in this field).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-02-04T10:53:16.297" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28312" PostTypeId="2" ParentId="28304" CreationDate="2015-02-04T11:09:18.417" Score="2" Body="&lt;p&gt;The European Bioinformatics Institute (EBI) has a tool called &quot;Quick GO&quot;, which allows you to search the Gene Ontology (GO) database using specific pathways or terms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the &quot;Annotation Download&quot; section (&lt;a href=&quot;http://www.ebi.ac.uk/QuickGO/GAnnotation&quot; rel=&quot;nofollow&quot;&gt;http://www.ebi.ac.uk/QuickGO/GAnnotation&lt;/a&gt;) enter your search term (e.g. &quot;AKT signalling&quot;) and &quot;search&quot;. QuickGO will present you with the search results, which for this search include;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;protein kinase B signaling&lt;/li&gt;&#xA;&lt;li&gt;regulation of protein kinase B signaling&lt;/li&gt;&#xA;&lt;li&gt;positive regulation of protein kinase B signaling&lt;/li&gt;&#xA;&lt;li&gt;negative regulation of protein kinase B signaling&lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Select a pathway by clicking the GO ID (e.g. &quot;GO:0043491&quot; for &quot;protein kinase B signaling&quot;). This takes you to the information pages for this pathway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To download the UniProt information (amongst other things) navigate to the &quot;Protein Annotation&quot; table using the tabs. In the top right you are presented with a &quot;Download&quot; option for the whole table (for this pathway containing 1,337 proteins)!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps.&lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2015-02-04T11:09:18.417" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28313" PostTypeId="2" ParentId="28309" CreationDate="2015-02-04T13:29:42.180" Score="7" Body="&lt;p&gt;Housekeeping genes aren't clustered on a single chromosome. It is perhaps not that 'housekeeping' genes - broadly expressed genes - are 'above the laws of regulation'; rather that their regulation is merely more straight-forward than that of specialised genes.&lt;/p&gt;&#xA;&lt;p&gt;I can think of 2 factors that could be relevant:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Abundance of methylation sites (&lt;a href=&quot;http://en.wikipedia.org/wiki/CpG_site&quot; rel=&quot;noreferrer&quot;&gt;CpG sites&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Promoter sequences and hence the transcription factors regulating expression of housekeeping genes are distinct from those controlling specialisation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;I think the second (promoter sequences) is the better explanation, since housekeeping genes are abundant in CpG islands; but I'll explain a bit about both.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;tl;dr:&lt;/strong&gt; Housekeeping genes have simpler promoter and enhancer regions that are not bound by particular complexes which act to inactivate regions of the genome in a hierarchical manner during differentiation (according to the transcriptional program). &lt;a href=&quot;http://genomebiology.com/2007/8/7/R140&quot; rel=&quot;noreferrer&quot;&gt;http://genomebiology.com/2007/8/7/R140&lt;/a&gt;&lt;/p&gt;&#xA;&lt;h3&gt;Preamble&lt;/h3&gt;&#xA;&lt;p&gt;In forming tissues during development, cells must differentiate from &lt;a href=&quot;http://en.wikipedia.org/wiki/Embryonic_stem_cell&quot; rel=&quot;noreferrer&quot;&gt;embryonic stem cells&lt;/a&gt;, which have very wide potential to express many genes and give rise to all cell types; to partially specialised stem cells e.g. hematopoietic stem cells (&lt;a href=&quot;http://en.wikipedia.org/wiki/Hematopoietic_stem_cell&quot; rel=&quot;noreferrer&quot;&gt;HSCs&lt;/a&gt;) which are limited to give rise to all blood cells but not, say, neurons or pancreas or skin. Completely differentiated cells have a much more restricted domain of possible expression, and are more-or-less condemned to their fate.&lt;/p&gt;&#xA;&lt;p&gt;Waddington's developmental landscape is a nice metaphor for how cells specialise:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/lNEXk.jpg&quot; alt=&quot;Waddington's developmental landscape&quot; /&gt;&lt;/p&gt;&#xA;&lt;h3&gt;DNA Methylation&lt;/h3&gt;&#xA;&lt;p&gt;A major mechanism behind this one-way narrowing of potential is &lt;a href=&quot;http://www.nature.com/scitable/topicpage/the-role-of-methylation-in-gene-expression-1070&quot; rel=&quot;noreferrer&quot;&gt;methylation of DNA&lt;/a&gt;, which suppresses transcription. As the ball rolls down the landscape it acquires new stretches of methylation on its DNA, rendering it inactive which (for our purposes) is &lt;em&gt;permanent and irreversible.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;DNA methylation consolidates its chromatin inactivating function by acting as a signal for proteins which chemically modify &lt;a href=&quot;http://en.wikipedia.org/wiki/Histone&quot; rel=&quot;noreferrer&quot;&gt;histones&lt;/a&gt; (around which DNA is wrapped in chromatin) with further signals to condense chromatin, which occludes the transcriptional machinery from doing what it does best. (There are also activating histone modifications, and we imagine chromatin being, roughly, in OPEN and CLOSED states regarding the possibility of RNA polymerase gaining access to the DNA.) Since histones are ubiquitous &amp;amp; regularly spaced over the genome, there aren't &amp;quot;non-regulatable&amp;quot; regions - chromatin is opened or closed by the interactions of various DNA binding proteins, some reading and writing signals on to the chromatin.&lt;/p&gt;&#xA;&lt;p&gt;So one plausible hypothesis is that &lt;strong&gt;housekeeping genes are relatively devoid of CpG sites&lt;/strong&gt; (where methylation occurs). However I think this is &lt;strong&gt;not true&lt;/strong&gt;. Many human genes have regions abundant in CpG (called 'islands') around their promoters, &lt;a href=&quot;http://genesdev.cshlp.org/content/25/10/1010.full&quot; rel=&quot;noreferrer&quot;&gt;and in particular virtually all housekeeping genes&lt;/a&gt;. When genes are active, these CpG islands are unmethylated - hence in most tissues housekeeping genes have unmethylated CpG islands, something else is keeping them unmethylated.&lt;/p&gt;&#xA;&lt;p&gt;Specialised cells, through a hierarchical transcriptional program of 'master regulators', successively close unneeded regions of their chromatin during differentiation, and keep open regions containing housekeeping genes, and the 'specialised genes' that relate to its specialism - these regulators are transcription factors which recognise the regions they act upon by binding promotor or enhancer sequences.&lt;/p&gt;&#xA;&lt;h3&gt;Housekeeping promoters and transcription factors&lt;/h3&gt;&#xA;&lt;p&gt;Transcription factors bind to enhancer or promoter sequences and open or close the chromatin for RNA polymerase, usually as part of a co-operative complex of many factors, including proteins that modify the histones or methylate DNA.&lt;/p&gt;&#xA;&lt;p&gt;A good hypothesis is that the &lt;strong&gt;promoter/enhancer regions of housekeeping genes differ from those of specialised genes&lt;/strong&gt; which are inactivated in many tissues. The transcriptional programs in differentiation must call forth factors that bind and inactivate specialised genes but keep active things like actin, ribosomal genes, &lt;em&gt;etc.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://genomebiology.com/2007/8/7/R140&quot; rel=&quot;noreferrer&quot;&gt;This paper&lt;/a&gt; finds that upstream regions of housekeeping genes are less conserved, and a particular set of promoter motifs are over-represented. This suggests that housekeeping genes have relatively simple regulation by a few transcription factors; they lack binding sites for those transcription factors with important specialised roles in development.&lt;/p&gt;&#xA;&lt;p&gt;To summarise, I think the following is likely: Housekeeping genes' promoter and enhancer regions exempt them from the complex transcriptional programs of hierarchical inactivation responsible for cell differentiation that many other genes are subject to. Housekeeping genes simply lack the relevant binding sites for these specialised transcription factors; they have instead more simple 'core' promoter elements. All the DNA methylation and opening/closing of the chromatin is a consequence of the transcriptional program.&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/CpG_site&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/CpG_site&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Embryonic_stem_cell&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Embryonic_stem_cell&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hematopoietic_stem_cell&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Hematopoietic_stem_cell&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/scitable/topicpage/the-role-of-methylation-in-gene-expression-1070&quot; rel=&quot;noreferrer&quot;&gt;http://www.nature.com/scitable/topicpage/the-role-of-methylation-in-gene-expression-1070&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Histone&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Histone&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://genesdev.cshlp.org/content/25/10/1010.full&quot; rel=&quot;noreferrer&quot;&gt;http://genesdev.cshlp.org/content/25/10/1010.full&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://genomebiology.com/2007/8/7/R140&quot; rel=&quot;noreferrer&quot;&gt;http://genomebiology.com/2007/8/7/R140&lt;/a&gt;   &amp;lt; most relevant thing to read, and the basis of my own conclusion&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="13310" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-04T13:52:28.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28314" PostTypeId="1" CreationDate="2015-02-04T14:21:36.983" Score="1" ViewCount="31" Body="&lt;p&gt;Specific genetic engineering of chromosomal aberrations like deletions, inversions and translocations are doable by using the CRISPR/Cas system or the other programmable nuclease systems. Insertions are also possible but mostly limited by the size of the insert.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here two papers on the topic:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nrg/journal/v15/n5/full/nrg3686.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nrg/journal/v15/n5/full/nrg3686.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/ncomms/2014/140424/ncomms4728/full/ncomms4728.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/ncomms/2014/140424/ncomms4728/full/ncomms4728.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However these methods appear to be inadequate in case you want to insert a long DNA piece (&gt;1Mb) into a chromosome (in case you want to engineer a duplication).&#xA;As far I have understood, problems arise when 1) you want to make such long DNA in the first place and 2) --suppose you have the DNA-- you need to transfect it into the cell...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know how to tackle the genetic engineering of a large  chromosomal duplications? Is there any way to induce it without the need of supplementing the extra DNA?&lt;/p&gt;&#xA;" OwnerUserId="12923" LastEditorUserId="12923" LastEditDate="2015-02-04T14:47:59.407" LastActivityDate="2015-02-04T14:47:59.407" Title="How to engineer chromosomal duplications?" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;chromosome&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28315" PostTypeId="2" ParentId="28304" CreationDate="2015-02-04T14:26:43.447" Score="4" Body="&lt;p&gt;I would do this through the &lt;a href=&quot;http://www.reactome.org/&quot; rel=&quot;nofollow&quot;&gt;Reactome database&lt;/a&gt;. Searching for &lt;code&gt;&quot;AKT Signalling&quot;&lt;/code&gt; returns, among other things, an entry for &lt;a href=&quot;http://www.reactome.org/content/detail/REACT_147723&quot; rel=&quot;nofollow&quot;&gt;&lt;code&gt;PI3K/AKT Signaling in Cancer (Homo sapiens)&lt;/code&gt;&lt;/a&gt; (REACT_147723). Clicking on that link will take you to the pathway's page, and if you click on &quot;Disease&quot; (under &quot;Locations in the PathwayBrowser&quot;), you will be shown a link to the &lt;a href=&quot;http://www.reactome.org/PathwayBrowser/#DIAGRAM=2219528&amp;amp;PATH=1643685&quot; rel=&quot;nofollow&quot;&gt;pathway browser page&lt;/a&gt; of that particular pathway. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once there, click on the &quot;Molecules&quot; tab, select &quot;Proteins&quot; and you will get a list of the proteins involved in the pathway and their UniProt accessions. There, you can click on the &quot;Download&quot; link and retrieve this list:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;MoleculeType    Identifier  MoleculeName    &#xA;Proteins    P31751  UniProt:P31751 AKT2 &#xA;Proteins    P31749  UniProt:P31749 AKT1 &#xA;Proteins    Q9Y243  UniProt:Q9Y243 AKT3 &#xA;Proteins    P16220  UniProt:P16220 CREB1    &#xA;Proteins    Q12778  UniProt:Q12778 FOXO1    &#xA;Proteins    P98177  UniProt:P98177-2 FOXO4  &#xA;Proteins    O43524  UniProt:O43524 FOXO3    &#xA;Proteins    P98177  UniProt:P98177-1 FOXO4  &#xA;Proteins    O15530  UniProt:O15530 PDPK1    &#xA;Proteins    Q92934  UniProt:Q92934 BAD  &#xA;Proteins    P46527  UniProt:P46527 CDKN1B   &#xA;Proteins    P38936  UniProt:P38936 CDKN1A   &#xA;Proteins    Q00987  UniProt:Q00987 MDM2 &#xA;Proteins    P60484  UniProt:P60484 PTEN &#xA;Proteins    Q8WWG1  UniProt:Q8WWG1 NRG4 &#xA;Proteins    P10721  UniProt:P10721 KIT  &#xA;Proteins    Q9HCT0  UniProt:Q9HCT0 FGF22    &#xA;Proteins    P15498  UniProt:P15498 VAV1 &#xA;Proteins    P05230  UniProt:P05230 FGF1 &#xA;Proteins    Q15303  UniProt:Q15303-1 ERBB4  &#xA;Proteins    P08620  UniProt:P08620 FGF4 &#xA;Proteins    P42338  UniProt:P42338 PIK3CB   &#xA;Proteins    O14944  UniProt:O14944 EREG &#xA;Proteins    O15520  UniProt:O15520 FGF10    &#xA;Proteins    P21802  UniProt:P21802-3 FGFR2  &#xA;Proteins    Q13480  UniProt:Q13480 GAB1 &#xA;Proteins    P55075  UniProt:P55075-1 FGF8   &#xA;Proteins    O00459  UniProt:O00459 PIK3R2   &#xA;Proteins    Q9UEF7  UniProt:Q9UEF7-1 KL &#xA;Proteins    P09619  UniProt:P09619 PDGFRB   &#xA;Proteins    Q8WU20  UniProt:Q8WU20 FRS2 &#xA;Proteins    Q86Z14  UniProt:Q86Z14 KLB  &#xA;Proteins    O00329  UniProt:O00329 PIK3CD   &#xA;Proteins    P11487  UniProt:P11487 FGF3 &#xA;Proteins    Q9GZV9  UniProt:Q9GZV9 FGF23    &#xA;Proteins    P42336  UniProt:P42336 PIK3CA   &#xA;Proteins    P42081  UniProt:P42081 CD86 &#xA;Proteins    P35568  UniProt:P35568 IRS1 &#xA;Proteins    P04626  UniProt:P04626 ERBB2    &#xA;Proteins    Q02297  UniProt:Q02297 NRG1 &#xA;Proteins    P12034  UniProt:P12034-1 FGF5   &#xA;Proteins    P56975  UniProt:P56975 NRG3 &#xA;Proteins    Q9NP95  UniProt:Q9NP95 FGF20    &#xA;Proteins    Q02297  UniProt:Q02297-10 NRG1  &#xA;Proteins    P22607  UniProt:P22607-2 FGFR3  &#xA;Proteins    P21802  UniProt:P21802-1 FGFR2  &#xA;Proteins    Q15303  UniProt:Q15303-2 ERBB4  &#xA;Proteins    P62993  UniProt:P62993-1 GRB2   &#xA;Proteins    O60258  UniProt:O60258-1 FGF17  &#xA;Proteins    P11362  UniProt:P11362-1 FGFR1  &#xA;Proteins    P15391  UniProt:P15391 CD19 &#xA;Proteins    Q9Y4H2  UniProt:Q9Y4H2 IRS2 &#xA;Proteins    Q99075  UniProt:Q99075 HBEGF    &#xA;Proteins    P21583  UniProt:P21583-1 KITLG  &#xA;Proteins    P31371  UniProt:P31371 FGF9 &#xA;Proteins    P27986  UniProt:P27986 PIK3R1   &#xA;Proteins    P22455  UniProt:P22455 FGFR4    &#xA;Proteins    P04085  UniProt:P04085-2 PDGFA  &#xA;Proteins    P06241  UniProt:P06241 FYN  &#xA;Proteins    P01127  UniProt:P01127 PDGFB    &#xA;Proteins    P21802  UniProt:P21802-5 FGFR2  &#xA;Proteins    Q06124  UniProt:Q06124 PTPN11   &#xA;Proteins    P21781  UniProt:P21781 FGF7 &#xA;Proteins    O95750  UniProt:O95750 FGF19    &#xA;Proteins    P21860  UniProt:P21860-1 ERBB3  &#xA;Proteins    O14511  UniProt:O14511 NRG2 &#xA;Proteins    P01133  UniProt:P01133 EGF  &#xA;Proteins    O76093  UniProt:O76093 FGF18    &#xA;Proteins    P21802  UniProt:P21802-18 FGFR2 &#xA;Proteins    O43320  UniProt:O43320 FGF16    &#xA;Proteins    P04085  UniProt:P04085-1 PDGFA  &#xA;Proteins    P10767  UniProt:P10767 FGF6 &#xA;Proteins    P06239  UniProt:P06239 LCK  &#xA;Proteins    Q92569  UniProt:Q92569 PIK3R3   &#xA;Proteins    Q6PIZ9  UniProt:Q6PIZ9 TRAT1    &#xA;Proteins    Q9UEF7  UniProt:Q9UEF7-2 KL &#xA;Proteins    P35070  UniProt:P35070 BTC  &#xA;Proteins    P16234  UniProt:P16234 PDGFRA   &#xA;Proteins    P33681  UniProt:P33681 CD80 &#xA;Proteins    P22607  UniProt:P22607-1 FGFR3  &#xA;Proteins    P09038  UniProt:P09038 FGF2 &#xA;Proteins    P10747  UniProt:P10747 CD28 &#xA;Proteins    P00533  UniProt:P00533 EGFR &#xA;Proteins    P55211  UniProt:P55211 CASP9    &#xA;Proteins    P22736  UniProt:P22736 NR4A1    &#xA;Proteins    Q6ZVD8  UniProt:Q6ZVD8 PHLPP2   &#xA;Proteins    O60346  UniProt:O60346 PHLPP1   &#xA;Proteins    Q9UKV8  UniProt:Q9UKV8 AGO2 &#xA;Proteins    Q9HCE1  UniProt:Q9HCE1 MOV10    &#xA;Proteins    Q9UPQ9  UniProt:Q9UPQ9 TNRC6B   &#xA;Proteins    Q9HCJ0  UniProt:Q9HCJ0 TNRC6C   &#xA;Proteins    Q9UL18  UniProt:Q9UL18 AGO1 &#xA;Proteins    Q8NDV7  UniProt:Q8NDV7 TNRC6A   &#xA;Proteins    Q9H9G7  UniProt:Q9H9G7 AGO3 &#xA;Proteins    Q9HCK5  UniProt:Q9HCK5 AGO4 &#xA;Proteins    Q96RU7  UniProt:Q96RU7 TRIB3    &#xA;Proteins    Q5T1C6  UniProt:Q5T1C6 THEM4    &#xA;Proteins    Q96B36  UniProt:Q96B36 AKT1S1   &#xA;Proteins    P49841  UniProt:P49841 GSK3B    &#xA;Proteins    P49840  UniProt:P49840 GSK3A    &#xA;Proteins    O15111  UniProt:O15111 CHUK &#xA;Proteins    Q9BPZ7  UniProt:Q9BPZ7 MAPKAP1  &#xA;Proteins    Q6R327  UniProt:Q6R327 RICTOR   &#xA;Proteins    Q9BVC4  UniProt:Q9BVC4 MLST8    &#xA;Proteins    P42345  UniProt:P42345 MTOR &#xA;Proteins    Q9UBS0  UniProt:Q9UBS0 RPS6KB2  &#xA;Proteins    P49815  UniProt:P49815 TSC2 &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2015-02-04T14:26:43.447" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28316" PostTypeId="1" CreationDate="2015-02-04T15:28:23.760" Score="1" ViewCount="141" Body="&lt;p&gt;I've heard a statement in a talk that U-rich sequences cause transcriptional pausing. The intuitive explanation for this was that the UTP concentration is lower in the cell than the ATP concentration. Reducing the concentration of an educt obviously reduces the reaction rate, leading to pausing of the RNA polymerase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After reading up on transcriptional pausing, I haven't found any literature that shares this view. The recent papers I found don't show U-rich sequences and have completely different explanations on how pausing works. Those explanations mainly concern interactions at the edges of the transcription bubble.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I guess that there might be multiple mechanisms of transcriptional pausing. But I couldn't find any references in the literature to U-rich pause sites and how they could work. Is there any literature on this? Either on the fact that U-rich sequences tend to be pause sites, or that the concentration difference in NTPs leads to pausing at certain sites.&lt;/p&gt;&#xA;" OwnerUserId="13337" LastActivityDate="2015-02-04T17:52:10.007" Title="Are there U-rich transcriptional pause sites?" Tags="&lt;biochemistry&gt;&lt;transcription&gt;&lt;polymerase&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28317" PostTypeId="1" CreationDate="2015-02-04T16:40:54.090" Score="8" ViewCount="877" Body="&lt;p&gt;Most organisms exhibit circadian rhythms that have a periodicity of about, but not exactly 24 hours. Why is this? And to what extent can variation in periodicity in circadian rhythms among the individuals of the same species (if a variation does indeed exist) influence the level of competition they face in acquiring resources?&lt;/p&gt;&#xA;" OwnerDisplayName="user9950" LastActivityDate="2018-10-22T16:37:39.747" Title="Why aren't circadian rhythms exactly 24 hours long?" Tags="&lt;circadian-rhythms&gt;&lt;chronobiology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28318" PostTypeId="1" AcceptedAnswerId="28325" CreationDate="2015-02-04T16:43:28.483" Score="5" ViewCount="3405" Body="&lt;p&gt;I have been reading several articles explaining dizziness after eating (see &lt;a href=&quot;http://www.md-health.com/Dizziness-After-Eating.html&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.newhealthguide.org/Dizziness-After-Eating.html&quot;&gt;here&lt;/a&gt;), and both articles gloss over something that I found pretty remarkable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both articles claim that &quot;heart disease&quot; can cause one to experience dizziness after eating. For instance, as one article merely generalizes:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A healthy heart is needed to pump blood faster during digestion. Certain heart conditions can lead to its inability to send enough blood to the abdominal organs, which may lead to a drop in blood pressure, resulting in dizziness and sometimes, nausea.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To me, this is pretty &lt;em&gt;vague&lt;/em&gt; and uninformative. Making a blanket statement like &quot;&lt;em&gt;certain heart conditions can...lead to a drop in blood pressure&lt;/em&gt;&quot; is like saying &quot;&lt;em&gt;not eating or drinking water can cause death.&lt;/em&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested in are the &lt;strong&gt;hows&lt;/strong&gt; and the &lt;strong&gt;whats&lt;/strong&gt;: &lt;em&gt;How&lt;/em&gt; does/can heart disease cause dizziness after eating, &lt;em&gt;what&lt;/em&gt; are the reasons why this happens, and &lt;em&gt;what&lt;/em&gt; are some examples of heart disease (&quot;certain conditions&quot;) that cause this (as I'm sure there are many similarly-related diseases)?&lt;/p&gt;&#xA;" OwnerUserId="11581" LastActivityDate="2015-10-30T20:50:30.543" Title="How can heart disease cause dizziness after eating?" Tags="&lt;cardiology&gt;&lt;digestive-system&gt;&lt;blood-pressure&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28319" PostTypeId="2" ParentId="28316" CreationDate="2015-02-04T17:44:07.447" Score="1" Body="&lt;p&gt;Yes, there are: this is a feature of bacterial intrinsic termination. The mechanism of pausing is not as you describe, though.&#xA;In &lt;strong&gt;bacterial&lt;/strong&gt; transcription, two forms of termination are recognised (to my knowledge):&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Intrinsic termination, consisting of a hairpin and a stretch of Uridines.&lt;/li&gt;&#xA;&lt;li&gt;Rho-dependent termination, consisting of a 'loading' site for termination protein Rho, and a pausing site, &lt;em&gt;but not the stretch of Uridines you refer to.&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;If you were reading up on transcription in eukaryotes, or were reading about rho-dependent termination, that would explain why you found no mention of polyU tracts. When evolution provides many solutions to a problem, it can get tricky to keep on top of it all!&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21601/&quot; rel=&quot;nofollow noreferrer&quot;&gt;This lists a few types of termination&lt;/a&gt;, including &lt;a href=&quot;http://en.wikipedia.org/wiki/Trp_operon#Attenuation&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;attenuation&lt;/em&gt; which is fascinating&lt;/a&gt;, and &lt;em&gt;does&lt;/em&gt; involve regulation dependent on the concentration of a substrate.&lt;/p&gt;&#xA;&lt;h3&gt;Intrinsic Termination&lt;/h3&gt;&#xA;&lt;p&gt;A &lt;a href=&quot;http://en.wikipedia.org/wiki/Palindromic_sequence&quot; rel=&quot;nofollow noreferrer&quot;&gt;palindromic sequence&lt;/a&gt; situated just before the termination site causes a hairpin to form in the nascent RNA inside the exit channel of RNA polymerase, if given time (and if anti-termination factors do not bind the RNA to suppress hairpin formation). It appears that formation of this hairpin &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867401005827&quot; rel=&quot;nofollow noreferrer&quot;&gt;&amp;quot;destabilises the elongation complex [RNA polymerase + elongation factors]&amp;quot;&lt;/a&gt;, and is an irreversible step towards collapse of the transcription bubble and dissociation of the transcription machinery.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1097276500804773&quot; rel=&quot;nofollow noreferrer&quot;&gt;The polyU tract (~8nt long) proceeding the hairpin seems to have dual function&lt;/a&gt;: the A:U basepairing in the DNA:RNA hybrid is weak; the hybrid becomes less favourable. Since the hairpin (which is an RNA:RNA duplex) is adjacent to the RNA:DNA hybrid duplex in the bubble, they experience competition for formation. Weakening the hybrid duplex favours hairpin formation, which acts like a switch that separates most of the RNA:DNA duplex in the bubble - synthesis cannot proceed, and the unstable complex dissociates.&lt;/p&gt;&#xA;&lt;p&gt;Also, the ployU seems to be responsible for pausing which allows time for the hairpin to form, but not for the reason you suggest:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00928361&quot; rel=&quot;nofollow noreferrer&quot;&gt;The concentration of UTP in the cell is not unusually low&lt;/a&gt;. ATP concentrations are higher than other ribonucleotides since it is the cell's major 'energy currency', quite apart from nucleic acid synthesis. Hence I don't believe pausing can be explained as the polymerase waiting for UTP. The polyU tract probably acts as a 'back-tracking signal' to the polymerase, since the hybrid duplex in the catalytic site is weakened, and the repeated nature may be &amp;quot;slippery&amp;quot;(?). &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867412006940&quot; rel=&quot;nofollow noreferrer&quot;&gt;This back-tracking pauses the polymerase.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XqqUU.jpg&quot; alt=&quot;Intrinsic termination, paused &amp;amp; trapped states&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;To summarise:&lt;/strong&gt; The elongation complex passes the palindrome and reaches the polyU tract, where the hybrid duplex in the bubble is weak and tends to cause back-tracking/pausing. This allows time for the hairpin to form in the exit channel, which both unwinds the hybrid duplex further, and destabilises the elongation complex. The transcriptional machinery is now destined to dissociate and the bubble collapse: RNA is released from the DNA duplex.&lt;/p&gt;&#xA;&lt;p&gt;It is interesting to note that intrinsic termination can be suppressed by proteins that bind the hairpin. In bacterial operons, where sets of (almost) concatenated genes are separated by intrinsic termination signals, the amount of read-through at each termination site determines the relative expression levels of each gene.&lt;/p&gt;&#xA;&lt;h3&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1838574/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rho-dependent Termination&lt;/a&gt;&lt;/h3&gt;&#xA;&lt;p&gt;Rho is a hexameric protein complex that is loaded on to the nascent RNA at a loading sequence. It hydrolyses ATP to move along the emerging RNA - apparently it &amp;quot;races&amp;quot; with the polymerase, and when it catches up to the polymerase, it causes termination. There are pause sites in the RNA which allow rho to catch up - these sites tend to be rich in A and U, so perhaps polymerase is slowed by destabilisation of the hybrid duplex - but it is nothing like the intrinsic terminator, since it depends completely on rho for termination.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3bC1v.jpg&quot; alt=&quot;Rho-dependent termination process&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="13310" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-04T17:52:10.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28322" PostTypeId="1" AcceptedAnswerId="29965" CreationDate="2015-02-04T19:40:33.180" Score="5" ViewCount="19876" Body="&lt;p&gt;Is it because heterozygotes have a greater base pair length? (And if they do, why is that?) Or is it because recessive alleles are moving slower than the dominant alleles in the gel?&lt;/p&gt;&#xA;" OwnerUserId="13143" LastActivityDate="2017-02-15T16:50:17.243" Title="Why is it that heterozygous loci appear as two separate bands during gel electrophoresis while homozygous loci appear as one band?" Tags="&lt;dna&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28325" PostTypeId="2" ParentId="28318" CreationDate="2015-02-04T23:36:28.187" Score="10" Body="&lt;p&gt;Dizziness after eating, which can lead to falls and passing out, is called &lt;em&gt;postprandial hypotension&lt;/em&gt;, and as the heart is indeed responsible for responding to hypotension by increasing it's rate - which can be seen in any number of clinical scenarios from blood loss to standing up too suddenly - failure to do so, for any reason including heart disease, can result in continued hypotension, which is experienced by most of us as dizziness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Postprandial hypotension (PhTN) is defined as a fall in systolic blood pressure (SBP) of ≥ 20 mmHg occurring within 2 hours of a meal. This hypotension (hTN) can result not only in dizziness, but  may also cause syncope, falls, weakness, angina pectoris, and stroke. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because PhTN is particularly common in older hypertensive patients, and older patients tend to have higher incidences of heart disease, it was initially thought heart disease was the cause. However, that didn't explain why some young people without heart disease have PhTN.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In truth, the mechanism of PhTN is not fully understood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Normally after a meal, blood supply to the gastrointestinal (GI) tract increases, starting with increased flow through the left gastric and celiac arteries, followed by the mesenteric artery, which is more prolonged. Observations indicate that the postprandial hyperemia progresses along the GI tract in association with the movement of ingested food. The magnitude (25–200%) and the duration (3–7 h) of the hyperemia appear to depend somewhat on the composition of the meal. The increase in GI blood flow means there's less blood to circulate in the rest of the body (relative hTN). Normally this is corrected for in various ways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Baroreceptors (nerve cells within arteries near the heart and in the kidney) are sensitive to rises, falls, and the rates of change in BP, but are especially sensitive to sudden falls in BP, which results in decreased baroreceptor firing. Autonomic Nervous System responds by increasing sympathetic outflow and decreasing parasympathetic (vagal) outflow. Sympathetic outflow leads to vasoconstriction (increased systemic vascular resistance, or SVR), increased HR (tachycardia) and increased force of contraction on the heart (positive inotropy). This leads to a partial restoration of arterial pressure. In people with PhTN, any abnormality at any point in the system will result in an insufficient rise in SBP to overcome the fall.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore possible contributors to PhTN include inadequate sympathetic nervous system compensation for meal-induced GI blood pooling; impairments in baroreflex function; inadequate postprandial increases in cardiac output; impaired peripheral vasoconstriction, as well as abnormal responses to GI hormones released during digestion.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dysautonomic patients with postprandial hypotension fail to maintain systemic vascular resistance after a meal. This impairment in vascular response to meal ingestion may underlie the development of PhTN. Power spectral analysis suggests an impairment in the postprandial autonomic modulation of HR in healthy elderly and dysautonomic subjects, possibly predisposing to hTN when vascular compensation is inadequate. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Heart conditions that might result in an inadequate response to PhTN include low heart rate (bradycardia), heart valve problems (decreases cardiac output), heart failure (decreased ejection fraction equals cardiac output), patients with atrial fibrillation (decreases cardiac output because of inadequate filling of ventricles), heart attack (decreased ejection fraction), heart muscle disease (cardiomyopathy), severe left ventricular hypertrophy, people with HTN on medications which cause a lowered heart rate, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, Postprandial Hypotension is an important hemodynamic abnormality in patients with cardiac diseases as well as autonomic nervous system abnormalities such as can be seen in Parkinson's Disease, diabetes mellitus, and others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://annals.org/article.aspx?articleid=708429&quot;&gt;Postprandial Hypotension: Epidemiology, Pathophysiology, and Clinical Management&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://europepmc.org/abstract/med/9288010&quot;&gt;Association of postprandial hypotension with incidence of falls, syncope, coronary events, stroke, and total mortality at 29-month follow-up in 499 older nursing home residents.&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://hyper.ahajournals.org/content/18/5/694.short&quot;&gt;Postprandial hypotension. Pathophysiological mechanisms and clinical implications in different disorders.&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.2001.013442/full&quot;&gt;Postprandial hypotension in response to duodenal glucose delivery in healthy older subjects&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK53094/&quot;&gt;Postprandial Hyperemia&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://cvphysiology.com/Blood%20Pressure/BP012.htm&quot;&gt;Arterial Baroreceptors&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-02-04T23:36:28.187" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28326" PostTypeId="1" AcceptedAnswerId="30791" CreationDate="2015-02-05T00:37:57.480" Score="14" ViewCount="8370" Body="&lt;p&gt;I am wondering if anyone can point me to (a scientific source that provides) the estimates of the dimensions (length x width) of the human back? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am specifically interested in the dimensions (&lt;strong&gt;length * width&lt;/strong&gt;, or surface) of the &lt;strong&gt;lower back&lt;/strong&gt; of the average adult, and in specific the region between the 7&lt;sup&gt;th&lt;/sup&gt; thoracic and 4&lt;sup&gt;th&lt;/sup&gt; lumbar vertebra - i.e., the region between T7 - L4 in the image below:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ideally a distinction is made between males and females and perhaps kids as well. The area of research dealing with this matter is anthropometry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jygQs.jpg&quot; alt=&quot;back&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please mention the source to any information provided. I have access to some not-scientifically based sources (clothing companies for example). Although additional such sources are welcomed, scientifically-based answers are preferred.    &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-23T12:13:31.600" LastActivityDate="2015-03-26T09:41:50.640" Title="Average dimensions of the human back (anthropometry)" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28327" PostTypeId="2" ParentId="28300" CreationDate="2015-02-05T04:06:21.567" Score="3" Body="&lt;p&gt;The way you pose the question, as in what mechanisms limit the fertility of predators, together with your comment about the distinction to the population dynamic aspect, strongly that what you are thinking about an adaptional mechanism here and asking about its characteristics, right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In that case, this is very similar to the kind of scenarios you find in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Group_selection&quot; rel=&quot;nofollow&quot;&gt;group selection&lt;/a&gt; arguments: &lt;em&gt;It is better for the species to limit it's fertility rate, thus a limit on the fertility rate will evolve.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This simplified view on group selection is heavily criticized as it's not a &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionarily_stable_strategy&quot; rel=&quot;nofollow&quot;&gt;ESS&lt;/a&gt;: As you pointed our yourself, a mutation that would increase the fertility rate would quickly spread.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But this is &lt;strong&gt;assuming that an increased fertility rate actually would be beneficial&lt;/strong&gt;. And what we forget here is that we have an inherent balance of quality of offspring versus number of offspring: &lt;strong&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/R/K_selection_theory&quot; rel=&quot;nofollow&quot;&gt;r/K selection&lt;/a&gt;&lt;/strong&gt;. The view that evolution constantly strives to produce increasingly ferocious eating and breeding machines is obviously too simplified if we were to just take a look at the how the biosphere actually looks like and compare it to our imagination how it could be like.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So basically, we could assume that the local &quot;mechanism&quot; here is simply r/K selection, with the population dynamics providing a major influence of the overall dynamics behind the scenes.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;However, group selection &lt;em&gt;do&lt;/em&gt; have an influence in the general evolutionary dynamics, as even the otherwise avid opponent Richard Dawkins agrees upon, but this is under the condition that group selection really is active natural selection of distinctive groups, and not some omniscient mechanism that somehow makes groups inherently develop traits that is beneficial to the group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And the other conditions like ESS still have to be valid here as well: If a trait could be positively selected for by group selection, it has to 1. Be developed before any selection can act on it and 2. Stay a ESS for it to persist (unless the group selection pressure is very high, and I think it's generally assumed that it's many orders of magnitude less influential than selection within groups)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could imagine the possibility that group selection somehow &lt;strong&gt;has&lt;/strong&gt; had an influence in limiting the genetic pool of top predators to the kind that uses a this r/K strategy that we see today but here I digress, it's not needed to explain the fertility rate of the top predators we see today.&lt;/p&gt;&#xA;" OwnerUserId="9124" LastEditorUserId="9124" LastEditDate="2015-02-05T04:22:39.030" LastActivityDate="2015-02-05T04:22:39.030" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28328" PostTypeId="1" CreationDate="2015-02-05T04:20:20.407" Score="0" ViewCount="217" Body="&lt;p&gt;From what I understand, if the tetrads resulting from a cross exhibit the same number of parental ditypes as there are nonparental ditypes, then the genes under consideration are said to be unlinked.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, say I cross two gametes containing $ab^+$ and $a^+b$, respectively, and get 170 tetrads exhibiting parental ditype (all offspring are $ab^+$ or $a^+b$), 165 exhibiting nonparental ditype (offspring are $a^+b^+$ or $ab$), and 30 exhibiting tetratype (offspring one of $a^+b^+$, $a^+b$, $ab^+$ or $ab$).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure whether to classify these genes as linked or unlinked. I want to say yes, they are indeed linked, but 170 and 165 seem like close enough numbers to suggest they may be unlinked.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would think the ratio of parental to nonparental ditype has to be considered close enough to 1, but how do we decide a threshold for that?&lt;/p&gt;&#xA;" OwnerUserId="13127" LastActivityDate="2015-02-05T18:07:01.997" Title="How to decide if genes are linked in an unordered mapping problem?" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;genetic-linkage&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28329" PostTypeId="1" CreationDate="2015-02-05T06:11:39.627" Score="2" ViewCount="1690" Body="&lt;p&gt;I know this has something to do with the K&lt;sup&gt;+&lt;/sup&gt; leak channel. I just don't understand how. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that 3 Na&lt;sup&gt;+&lt;/sup&gt; are pumped out for every 2 K&lt;sup&gt;+&lt;/sup&gt; pumped in. This makes the cell interior net negative. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that K&lt;sup&gt;+&lt;/sup&gt; is allowed to leak out slowly via K&lt;sup&gt;+&lt;/sup&gt; leak channels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this place the resting potential of the cell so much closer to the equilibrium potential of K&lt;sup&gt;+&lt;/sup&gt; than Na&lt;sup&gt;+&lt;/sup&gt;?&lt;/p&gt;&#xA;" OwnerUserId="13343" LastEditorUserId="3340" LastEditDate="2015-02-05T06:31:09.427" LastActivityDate="2015-02-05T08:29:01.407" Title="Why is the resting potential of a neuron so close to the equilibrium potential of K⁺?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28330" PostTypeId="2" ParentId="28329" CreationDate="2015-02-05T06:49:05.433" Score="1" Body="&lt;p&gt;Lets just go with the basic Hodgkin-Huxley equation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$C_M \frac{\text{d}V}{\text{d}t}=-g_{Na}(V-E_{Na}) -g_K(V-E_K) -g_L(V-E_L)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At rest ${\large\frac{\text{d}V}{\text{d}t}}=0$ and therefore $V$ is dependent on the conductances ($g_X$) of different ions. &lt;br&gt;Since $g_K \sim 30\times g_{Na}$, the resting potential is closer to $E_K$ (Nernst equilibrium potential of K&lt;sup&gt;+&lt;/sup&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What it basically means is that since potassium has higher membrane conductance, it diffuses faster thereby attaining equilibrium faster than sodium (in isolated cases assuming only one ion at a time). When both ions are present the resting potential is because of both the ions but since K&lt;sup&gt;+&lt;/sup&gt; diffuses faster, it has a major contribution to the resting potential compared to Na&lt;sup&gt;+&lt;/sup&gt;. Leak current that is described in the above equation is a general leak (non-specific). Other channels like rectifiers and voltage gated channels are important when talking about action potential and all these channels contribute to the conductance; however you can group all that into a single metric called membrane conductance. Voltage gated channels can be considered separately when studying the dynamics (in this case the conductances themselves become a function of voltage).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-02-05T08:29:01.407" LastActivityDate="2015-02-05T08:29:01.407" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28331" PostTypeId="1" AcceptedAnswerId="28340" CreationDate="2015-02-05T07:58:06.417" Score="1" ViewCount="93" Body="&lt;p&gt;I read about &quot;topological crossover&quot; in &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1438422114001696#&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper&lt;/a&gt;, Table 1. What does this refer to?&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="16985" LastEditDate="2017-04-25T12:26:35.790" LastActivityDate="2017-04-25T12:26:35.790" Title="What is topological crossover?" Tags="&lt;topology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28332" PostTypeId="2" ParentId="26351" CreationDate="2015-02-05T08:35:22.610" Score="1" Body="&lt;p&gt;You will definitely get satellite colonies. Ampicillin breaks down after about a day, especially exposed to light. Kan, keeps pretty well at room temp, but that does you no good :)&lt;/p&gt;&#xA;" OwnerUserId="3887" LastActivityDate="2015-02-05T08:35:22.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28333" PostTypeId="2" ParentId="28300" CreationDate="2015-02-05T09:43:38.933" Score="4" Body="&lt;p&gt;This question can be tackled in several ways, and also seems to contain a couple of misconceptions about ecological processes (e.g. problematic group-selection ideas and how species 'fit' into the ecosystem). &#xA;However, I think it is most usefully answered from the perspective of &lt;strong&gt;life history theory&lt;/strong&gt; and the &lt;a href=&quot;http://www.nature.com/scitable/knowledge/library/life-history-evolution-68245673&quot; rel=&quot;nofollow&quot;&gt;evolution of life histories&lt;/a&gt; (see e.g. &lt;a href=&quot;https://books.google.co.in/books?id=M_ZzQgAACAAJ&amp;amp;dq=roff+2002+life+history&amp;amp;hl=sv&amp;amp;sa=X&amp;amp;ei=cjnTVP32HufiywPx7ICwCQ&amp;amp;ved=0CCkQ6AEwAA&quot; rel=&quot;nofollow&quot; title=&quot;Roff. 2002. Life History Evolution. Sinauer&quot;&gt;Roff, 2002&lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/scitable/knowledge/library/life-history-evolution-68245673&quot; rel=&quot;nofollow&quot; title=&quot;Fabian, D. &amp;amp; Flatt, T. (2012) Life History Evolution. Nature Education Knowledge 3(10):24&quot;&gt;Fabian &amp;amp; Flatt, 2012&lt;/a&gt; for background), and at its core this question is dealing with tradeoffs between e.g. fecundity and mortality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All organisms act under a limited energy budget, and when they spend energy on some activities that will limit what they can spend on other activities. &#xA;This lies at the core of life history tradeoffs.&#xA;If organisms use resources to produce or raise offspring, this can therefore have consequences on growth, maintenance (e.g. disease resistance), predator avoidance and many other traits and behaviours, which all affect fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regard to your question, there is a well-known tradeoff between survival and fecundity (an &lt;em&gt;intraindividual effect&lt;/em&gt;), which has been shown both between individuals within species and across species.&#xA;As with almost all species traits, there is also variability between individuals within populations, so that some have higher fecundity than others, but may then also suffer lower adult survival rates (maybe under certain environmental conditions). &#xA;Therefore, there are certainly already &quot;&lt;em&gt;mutation(s) that increases fertility among the predators&lt;/em&gt;&quot; within populations.&#xA;The reason that fertility is not continuously increasing over time, is that this would have negative fitness consequences overall.&#xA;So the reason that the (average) life history traits within a particular species are what they are, is that they are the result of the evolutionary pressures that the species have been experiencing over evolutionary timeframes, acting on the entire life history. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be sure, hypothetical mutations/changes in life history traits that would increase fecundity with no negative tradeoffs whatsoever for either parents or offspring (i.e. no negative fitness consequences) would definitely increase in frequency. &#xA;From the perspective of life history theory, everything else equal, selection will maximize the survival function, $l(x)$ (survival to age x) and the reproductive function, $m(x)$ (number of offspring at age x), while minimizing maturation age. &#xA;However, tradeoffs between these functions (directly or indirectly) and between generations will prevent these from being optimized one by one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Population growth in long-lived predator species is usually also very sensitive to changes in adult survival rate &lt;a href=&quot;http://books.google.co.in/books/about/Matrix_Population_Models.html?id=CPsTAQAAIAAJ&quot; rel=&quot;nofollow&quot; title=&quot;Caswell. 2001. Matrix Population Models: Construction, Analysis, and Interpretation. Sinauer&quot;&gt;(Caswell, 2001&lt;/a&gt;).&#xA;This result comes from analysing stage or age structured population models, and is the result of a life history strategy with high adult survival rates, fairly high age of maturation and relatively low fecundity. &#xA;To increase fecundity in this situation with negative effects on adult survival will risk adult death and therefore loss of many future years of reproduction.&#xA;These kinds of results and models are often used to identify which life history traits and stages to target in conservation actions, but can also be used to understand evolutionary processes, since population growth rate can be used as an overall measure of fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It should also be added that many other ecological processes must be considered.&#xA;For instance, large predators often care for their young for quite a long time, since their hunting/foraging behaviours are complex, and it takes a long time for young to learn how to hunt successfully by themselves. &#xA;This means that adults need to bear not only the direct cost of producing offspring, but also to support them until they are self-sufficient.&#xA;For an extreme case, look at the Orangutan (not a predator, but still) where the young stay with their mother and nurse for up to 5-6 years (sometimes more). &#xA;To increase fecundity in such a situation will put a large strain on adult mothers.&#xA;You also need to consider trade-offs between offspring number and offspring &quot;quality&quot;, which have been demonstrated in many species (an &lt;em&gt;intergenerational effect&lt;/em&gt;).&#xA;This means that an increase in fertility can result in lower offspring survival over longer timeframes, with overall negative effects on fitness. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, life history evolution is a large and complex field, and these are just a couple of examples and suggestions for why the situation isn't as simple as your question makes it out to be.&#xA;Environmental variability and the predictability of the environment are other factors that I haven't considered at all, but are both important processes when you try to understand life history evolution.&#xA;This question can also be approached from a more theoretical perspective, but without a background in life-history evolution I think it is more useful to start reading about different processes and tradeoffs, and then later if you are interested to go into the theory for a deeper understanding. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2016-02-26T10:25:32.167" LastActivityDate="2016-02-26T10:25:32.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28335" PostTypeId="2" ParentId="28243" CreationDate="2015-02-05T11:42:31.383" Score="5" Body="&lt;p&gt;The question is very broad and complicated, since the situation may differ in prokaryotes and eukaryotes. Nevertheless, I'm citing a good paper that is closely related to your question:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Studies in yeast show that initiation of recombination, which occurs by the formation of DNA double-strand breaks, determines the distribution of gene conversion and crossover events that take place in nearby intervals. Recent data in humans and mice also indicate the presence of highly localized initiation sites that promote crossovers clustered around the region of initiation and seem to share common features with sites in yeast. On a larger scale, chromosomal domains with various recombination rates have been identified from yeast to mammals. This indicates a higher level of regulation of recombination in the genome with potential consequences on genome structure...&#xA;  ...DSBs (Double Strand Breaks) occur in highly localized regions and spread over 70–250 bp. DNA sequence analysis reveals no unique conserved consensus sequences, although a degenerate 50-bp motif partly correlates with DSB sites. However, one common feature is that DSBs are located in accessible regions of the chromatin next to either promoters or binding sites for transcription factors. Based on two studies, DSB activity does not correlate with local transcriptional activity, but depends on transcription-factor binding (HIS4 in S. cerevisiae and ade6-M26 in S. pombe).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Bernard de Massy, Distribution of meiotic recombination sites. TRENDS in Genetics Vol.19 No.9 September 2003&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll sum that up into a more answer-like form. Seems like the process is not random, because the double strand breaking events are clearly not evenly distributed across a genome. As the paper says there are no specific consensus motifs found as of yet, though there clearly is something special before promoters and TF binding sites, which makes them more likely to be a breaking site. How the machinery choses the place? Once again, as the paper says the breaking event depends on TF binding. But that is for S. cerevisiae. There are 17 hot spots found in human and mice genomes some of which are intergenic (they occupy introns or 5'/ 3' flanking regions).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the distribution of recombination frequencies across one chromosome (the figure is taken from the paper).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fw48Q.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gFSwJ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a list of recombination sites in humans and mice&lt;/p&gt;&#xA;" OwnerUserId="13338" LastEditorUserId="13338" LastEditDate="2015-02-05T16:15:09.907" LastActivityDate="2015-02-05T16:15:09.907" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28336" PostTypeId="2" ParentId="28243" CreationDate="2015-02-05T14:44:01.223" Score="6" Body="&lt;p&gt;In humans and mice anyway ,a lot of it boils down to the recognition of a specific sequence that marks recombination hotspots by &lt;em&gt;PRDM9&lt;/em&gt;.&#xA;&lt;a href=&quot;http://www.sciencemag.org/content/327/5967/836&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.sciencemag.org/content/327/5967/836&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit - I'm expanding in response to the comment below...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Meiotic recombination occurs at vastly greater frequencies in some locations in the genome than others and these are called Recombination Hotspots. For example, the figure here, sourced from &lt;a href=&quot;http://www.sciencemag.org/content/327/5967/876/F1.large.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.sciencemag.org/content/327/5967/876/F1.large.jpg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Vjtf7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;shows the recombination rate at the hotspot and further away from it for Chimps and Humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These hotspots are recognised by the cutting machinery thanks to the binding of PRDM9, a zinc finger protein, to a DNA sequence that it specifically recognises and is present at hotspots. The DNA sequence varies from species to species (as does the sequence and the function of PRDM9) but in humans is a well-characterised motif 13 base pairs long and of the sequence CCNCCNTNNCCNC (where N is any one of the 4 bases in DNA) , and accounts for the activity of nearly 40% of known hotspots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first link I posted has evidence to suggest that variation in composition of PRDM9 is a determinant of which hotspots get used. PRDM9, it appears, stimulates the formation of a specific histone modification - H3k4me3 (DNA is wrapped around histones, there are five histones - H1, H2A, H2B, H3, H4, and each of them has a tail that can be chemically modified, and eight of these (2 of H2A, 2 of H2B, 2 of H3 and 2 of H4) form a nucleosome - in this case the fourth lysine residue of the tail of Histone H3 is trimethylated as regulated by PRDM9, and facilitates crossing over and recombination initiation.&#xA;Edit Summary&lt;/p&gt;&#xA;" OwnerUserId="6726" LastEditorUserId="6726" LastEditDate="2015-02-05T15:58:27.543" LastActivityDate="2015-02-05T15:58:27.543" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28337" PostTypeId="2" ParentId="28328" CreationDate="2015-02-05T18:07:01.997" Score="1" Body="&lt;p&gt;I'd use a chi-squared test.  You calculate what you expect to see if your hypothesis is true, and you take what you do see, and the chi-squared result tells you how likely it is that your results are different enough from what's expected to indicate that your hypothesis is incorrect.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2015-02-05T18:07:01.997" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28340" PostTypeId="2" ParentId="28331" CreationDate="2015-02-05T20:20:35.383" Score="0" Body="&lt;p&gt;You may not want to know. It really depends on how good your math background is. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A topological crossover is a class of representation independent operators that are well defined once a notion of distance over the solution space is defined &lt;a href=&quot;http://www.cs.bham.ac.uk/~moraglia/ppsn8tr.pdf&quot; rel=&quot;nofollow&quot;&gt;[1]&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Let's first start with the definition of Topology.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Topology is the mathematical study of shapes and topological spaces. It is an area of mathematics concerned with the properties of space that are preserved under continuous deformations including stretching and bending, but not tearing or gluing. This includes such properties as connectedness, continuity and boundary &lt;a href=&quot;http://en.wikipedia.org/wiki/Topology&quot; rel=&quot;nofollow&quot;&gt;[2]&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Later on in the paper they start to mention transverse topology which leads to Differential Geometry.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In mathematics, transversality is a notion that describes how spaces can intersect; transversality can be seen as the &quot;opposite&quot; of tangency, and plays a role in general position. It formalizes the idea of a generic intersection in differential topology. It is defined by considering the linearizations of the intersecting spaces at the points of intersection &lt;a href=&quot;http://en.wikipedia.org/wiki/Transversality_%28mathematics%29&quot; rel=&quot;nofollow&quot;&gt;[3]&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To understand the underlining math concepts of this paper, you may need a rigorous background in mathematics. I would check the authors backgrounds to see if they are Physicists or Mathematicians. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most students in mathematics generally take two courses in introductory real analysis and at least one course in abstract algebra before taking topology. The standard &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0131816292&quot; rel=&quot;nofollow&quot;&gt;book&lt;/a&gt; for a first course in topology is by Munkres.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A book you may want to look into is &lt;a href=&quot;http://www.springer.com/physics/biophysics+%26+biological+physics/book/978-3-540-23407-4&quot; rel=&quot;nofollow&quot;&gt;Topology in Molecular Biology&lt;/a&gt;. However, the author is a mathematician, so if you are not, you may need to start with courses in analysis, topology, differential geometry before you tackle this book. I have never seen the book so I don't know how difficult it will be but here is the about the author from amazon:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;M.Monastyrsky is a professor of mathematics and theoretical physics&#xA;  at the Institute of Theoretical and Experimental Physics, Moscow, Russia,&#xA;  graduated the mathematical department of Moscow state university(1967),&#xA;  author of numerous papers in diferent fields of mathematics and&#xA;  theoretical physics including the monograph :Topology in Gauge Fields&#xA;  and Condensed Matter (Plenum,1993 ) and two other books:Riemann,Topology&#xA;  Physics, Birkhauser, Boston, 1999, 2nd ed. and Modern mathematics in the&#xA;  light of Fields medals, AKPeters, 1997.I gave invited plenary talks on&#xA;  many conferences and was the visiting professor of many universities&#xA;  and institutes including IAS(Princeton), Harvard, Princeton and Yale&#xA;  Universities (USA), Cambridge and Oxford Universities (Great Britain),&#xA;  IHES and Universite de Paris (France).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-02-05T20:32:40.227" LastActivityDate="2015-02-05T20:32:40.227" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28341" PostTypeId="2" ParentId="21200" CreationDate="2015-02-05T21:48:32.780" Score="10" Body="&lt;p&gt;Many birds, especially &lt;a href=&quot;http://en.wikipedia.org/wiki/Bird_vision#Diurnal_birds_of_prey&quot;&gt;birds of prey and owls&lt;/a&gt;, have eyes that are proportionally much larger than that of similar-size mammals. Most birds &lt;a href=&quot;http://en.wikipedia.org/wiki/Bird#Anatomy_and_physiology&quot;&gt;cannot move&lt;/a&gt; their eyes, as with larger eyes there is little or no room for the required musculature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This, in addition to having two foveas as &lt;code&gt;@The Last Word&lt;/code&gt; mentioned, necessitates that a bird move its head to change viewing angle. The relatively rapid movement of a bird's head is analogous to that of the more subtle, but still rapid movement of your eye as you view different subjects within a frame of vision without moving your head.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Birds have &lt;a href=&quot;http://en.wikipedia.org/wiki/Bird_anatomy#Skeletal_system&quot;&gt;more vertebrae&lt;/a&gt; (13-25) in their neck to provide additional flexibility, which provides for their quick head movements. Some birds, such as owls, can &lt;a href=&quot;http://en.wikipedia.org/wiki/Owl#Anatomy&quot;&gt;turn their head 270 degrees&lt;/a&gt;. Other birds have a &lt;a href=&quot;http://en.wikipedia.org/wiki/Bird_vision#Extraocular_anatomy&quot;&gt;wide field of vision&lt;/a&gt; because their eyes are located on the sides of their head. This degree of flexibility or field of vision provides birds with good compensation for being unable to move their eyes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These characteristics, combined with the physiology of &lt;a href=&quot;http://en.wikipedia.org/wiki/Bird_vision#Anatomy_of_the_eye&quot;&gt;two fovea&lt;/a&gt;, make the abrupt, seemingly unusual movements of birds' heads more easily understood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For additional insight, consider the book &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1620401894&quot;&gt;&lt;strong&gt;Bird Sense: What It's Like To Be a Bird&lt;/strong&gt; by Tim Birkhead&lt;/a&gt; or &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0300076193&quot;&gt;&lt;strong&gt;Manual of Ornithology: Avian Structure and Function&lt;/strong&gt; by Noble S. Proctor and Patrick J. Lynch&lt;/a&gt;; both of which I own and can recommend.&lt;/p&gt;&#xA;" OwnerUserId="331" LastActivityDate="2015-02-05T21:48:32.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28343" PostTypeId="1" AcceptedAnswerId="28384" CreationDate="2015-02-05T22:26:07.387" Score="2" ViewCount="211" Body="&lt;p&gt;It is common for people to experience very moving situations (sad movies, etc) and have a physical reaction to it (such as crying). I am curious about how emotions can physically lead to the act of crying. Why/how does this happen? What is the mechanism?&lt;/p&gt;&#xA;" OwnerUserId="13243" LastEditorUserId="11631" LastEditDate="2015-02-06T04:07:19.830" LastActivityDate="2015-02-06T18:48:27.793" Title="Why do eyes water in response to particular emotions?" Tags="&lt;eyes&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28345" PostTypeId="5" CreationDate="2015-02-05T23:00:52.840" Score="0" Body="&lt;p&gt;SPAM is an unwanted entry on biology.stackexchange which has the only reason to either promote a product or cause attention for it. &lt;/p&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="5144" LastEditDate="2015-02-05T23:23:32.510" LastActivityDate="2015-02-05T23:23:32.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28346" PostTypeId="4" CreationDate="2015-02-05T23:00:52.840" Score="0" Body="SPAM is an unwanted entry on biology.stackexchange which has the only reason to either promote a product or cause attention for it. " OwnerUserId="-1" LastEditorUserId="5144" LastEditDate="2015-02-05T23:23:32.510" LastActivityDate="2015-02-05T23:23:32.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28347" PostTypeId="2" ParentId="28256" CreationDate="2015-02-05T23:22:02.677" Score="4" Body="&lt;p&gt;I believe it is a type of &lt;a href=&quot;http://en.wikipedia.org/wiki/Fission%E2%80%93fusion_society&quot; rel=&quot;nofollow&quot;&gt;fission-fusion society&lt;/a&gt; or even some hybrid with &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639936/&quot; rel=&quot;nofollow&quot;&gt;agent based&lt;/a&gt; modeling. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In ethology, a fission–fusion society is one in which the size and composition of the social group change as time passes and animals move throughout the environment; animals merge (fusion)—e.g. sleeping in one place—or split (fission)—e.g. foraging in small groups during the day. For species that live in fission–fusion societies, group composition is a dynamic property &lt;a href=&quot;http://en.wikipedia.org/wiki/Fission%E2%80%93fusion_society&quot; rel=&quot;nofollow&quot;&gt;[fission-fusion society]&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A classical example is the Bonobo or pigmy chimp.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.msu.edu/~bondemil/bonobo.htm&quot; rel=&quot;nofollow&quot;&gt;Bonobo - Pigmy Chimpanzee&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://books.google.com/books?id=FEsCBAAAQBAJ&amp;amp;pg=PA137&amp;amp;lpg=PA137&amp;amp;dq=animals%20that%20form%20groups%20break%20up%20to%20forage%20and%20then%20reform&amp;amp;source=bl&amp;amp;ots=1QNpl5ltNb&amp;amp;sig=EIYAZqT-aZU_LHD5zAiDs7Zr-AM&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=wPjTVITvDIvasATozYDYAQ&amp;amp;ved=0CCcQ6AEwAQ#v=onepage&amp;amp;q=animals%20that%20form%20groups%20break%20up%20to%20forage%20and%20then%20reform&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Sociobiology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://primate.uchicago.edu/Stanford.pdf&quot; rel=&quot;nofollow&quot;&gt;The Social Behavior of Chimpanzees and Bonobos&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="5144" LastEditDate="2015-02-05T23:27:34.080" LastActivityDate="2015-02-05T23:27:34.080" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28349" PostTypeId="1" AcceptedAnswerId="28351" CreationDate="2015-02-05T23:53:39.370" Score="1" ViewCount="13069" Body="&lt;p&gt;I came across these terms in Darwin's &quot;Origin of Species&quot; and I wasn't sure what the difference is.&lt;/p&gt;&#xA;" OwnerUserId="13143" LastActivityDate="2015-05-08T17:20:19.993" Title="What's the difference between stabilizing selection and balancing selection?" Tags="&lt;natural-selection&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28350" PostTypeId="1" AcceptedAnswerId="29743" CreationDate="2015-02-06T00:33:25.907" Score="7" ViewCount="107" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hidden_Markov_model&quot;&gt;HMM&lt;/a&gt; alignment tools like hhpred excel at finding subtle homologues of folded proteins that simpler scoring techniques (such those used in BLAST algorithms) would miss.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am only looking at a small (20AA) sequence and it is helical throughout. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is hhpred still likely to pick up on subtle similarities in the basic secondary structure as it would in a folded protein sequence, or would simpler alignment be just as appropriate?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2015-02-06T12:55:00.953" LastActivityDate="2015-06-20T17:21:44.920" Title="Is using Hidden Markov Models to find homologues sensible in abstract, short sequences?" Tags="&lt;biochemistry&gt;&lt;bioinformatics&gt;&lt;proteins&gt;&lt;protein-folding&gt;&lt;sequence-alignment&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28351" PostTypeId="2" ParentId="28349" CreationDate="2015-02-06T00:43:38.223" Score="1" Body="&lt;p&gt;&lt;strong&gt;Usual meaning&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually, Stabilizing selection is a concept that applies to a phenotypic trait while balancing selection is a concept that applies to a given locus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Balancing selection can either be due to negative-frequency dependence selection or due to overdominance (=heterozygous advantage at a single locus).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What Darwin may have meant&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because Darwin didn't know about genes, he was necessarily not using the term balancing selection as I am using it. I can think of several more or less related pattern of selection that might fall withing the definitions for &quot;stabilizing selection&quot; and/or &quot;balancing selection&quot;. Maybe he meant &quot;frequency-dependent selection&quot;, &quot;positive selection for an intermediate trait&quot;, &quot;varying selection through time (temporally heterogenous environment)&quot; and &quot;varying selection through space (spatially heterogenous environment)&quot;. Eventually again, that might mean &quot;positively correlated traits that undergo opposite selection pressure (or the opposite)&quot; but that would definitely be surprising.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-05-08T17:20:19.993" LastActivityDate="2015-05-08T17:20:19.993" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28352" PostTypeId="1" AcceptedAnswerId="28354" CreationDate="2015-02-06T01:22:15.090" Score="13" ViewCount="13725" Body="&lt;p&gt;&lt;strong&gt;Previous Research&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that cameras sometimes come with an anti &quot;red eye&quot; functionality that involves two flashes, presumably the second flash coincides with the shutter opening.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do camera flashes sometimes lead to photos of humans with red eyes? And why do dog's eyes appear green?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Related&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for the green dog's eyes has been answered quite shortly under the question &quot;&lt;a href=&quot;https://biology.stackexchange.com/questions/27621/why-do-dogs-eyes-glow-green-on-a-photo&quot;&gt;why-do-dogs-eyes-glow-green-on-a-photo&lt;/a&gt;&quot;, but that question does not answer my specific question: &lt;strong&gt;Why do humans have red eyes on flashed photos and why are dog's eyes  green?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uOHIe.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2019-05-14T04:31:21.257" Title="Why do human eyes glow red on a photo and dog's eyes green?" Tags="&lt;eyes&gt;&lt;human-eye&gt;&lt;light&gt;&lt;dogs&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28354" PostTypeId="2" ParentId="28352" CreationDate="2015-02-06T01:43:41.447" Score="17" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;In humans it is basically the red &lt;strong&gt;&lt;em&gt;choroid plexus&lt;/em&gt;&lt;/strong&gt; in the back of the eye you are seeing on a flashed photo, while it is the green-reflecting &lt;strong&gt;&lt;em&gt;tapetum lucidum&lt;/em&gt;&lt;/strong&gt; in dogs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The red-eye effect in humans was explained nicely by &lt;a href=&quot;http://www.yalescientific.org/2011/05/what-causes-the-red-eye-effect/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yale Scientific Magazine&lt;/a&gt;, and I adapted the following text from that source:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The human eye can effectively adjust to different light conditions, but this adaptation is also what leads to the red-eye effect. The eye regulates the amount of entering light by contracting or expanding the pupil. At night, your pupils will accordingly enlarge to extract more light from their surroundings. However, this dilation also leaves your eyes unprepared for the sudden burst of light from a camera flash.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When light from the flash enters your eyes under these conditions, &lt;strong&gt;your pupils are unable to contract fast enough&lt;/strong&gt; (full constriction takes a few seconds) to prevent the &lt;strong&gt;light from reflecting back&lt;/strong&gt;, off of the red blood vessels &lt;strong&gt;of the &lt;em&gt;choroid&lt;/em&gt;&lt;/strong&gt;. The choroid plexus nourishes the retina, and therefore contains ample blood supply. As a result, the camera will pick up the red reflection, resulting in the red-eye effect. Interestingly, due to their increased “dark adaptation,” children more commonly have red eyes in photographs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The amount of melanin, a light-absorbing pigment in the eye, also has a role in the red-eye effect. Individuals with &lt;strong&gt;lower levels of melanin&lt;/strong&gt; will absorb less and thus &lt;strong&gt;reflect more light&lt;/strong&gt;, explaining the high incidence of the red-eye effect in albinos.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though the cause of this effect is wired in the biology of the eye, some cameras can reduce red-eye by sending a few preliminary flashes before the final flash to give the &lt;strong&gt;pupils enough time to contract&lt;/strong&gt; and adapt to the increased-light conditions. Another way to reduce the effect is to avoid looking directly into the camera lens, which will reduce the reflection of light. Finally, if all else fails, modern image editing software, such as Photoshop, can remove the red discoloration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regard to why dogs and other animals may not have red-eyes but other colors, this was indeed answered in your &lt;a href=&quot;https://biology.stackexchange.com/questions/27621/why-do-dogs-eyes-glow-green-on-a-photo&quot;&gt;linked question&lt;/a&gt;: some animal species have a &lt;strong&gt;&lt;em&gt;tapetum lucidum&lt;/em&gt;, which is situated in front of the choroid and reflects light back&lt;/strong&gt; onto the retina thereby increasing light sensitivity. In dogs it is green, as aptly shown in the &lt;a href=&quot;https://biology.stackexchange.com/questions/27621/why-do-dogs-eyes-glow-green-on-a-photo&quot;&gt;linked question&lt;/a&gt;'s answer. The following figure shows the anatomy and the position of the &lt;em&gt;tapetum&lt;/em&gt; in front of the &lt;em&gt;choroid&lt;/em&gt;. It was adapted from Pets.SE with the related question &quot;&lt;a href=&quot;https://pets.stackexchange.com/questions/6450/should-i-be-concerned-that-my-dogs-right-eye-is-reflecting-green-in-the-dark-wh&quot;&gt;Should I be concerned that my dog's right eye is reflecting green in the dark when his left eye doesn't?&lt;/a&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/k7XmH.png&quot; alt=&quot;eye&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, the reason why animals with a &lt;em&gt;tapetum lucidum&lt;/em&gt; have another eye color is that light does not reach the &lt;strong&gt;&lt;em&gt;choroid&lt;/em&gt;&lt;/strong&gt; in these species, giving rise to green-eye effects in dogs and cats (picture taken from &lt;a href=&quot;http://www.asknature.org/strategy/2908eded592a0000549595ee148c904c#.VNQiRp2VLiE&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ask Nature&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GZfKW.jpg&quot; alt=&quot;cat&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:59:17.050" LastActivityDate="2015-02-13T13:58:42.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28357" PostTypeId="1" CreationDate="2015-02-06T02:23:21.730" Score="2" ViewCount="1334" Body="&lt;p&gt;I have seen &lt;a href=&quot;https://biology.stackexchange.com/questions/7541&quot;&gt;this question&lt;/a&gt; where the author is asking why people take drugs for fever. So my question is: Is fever is a disease or not? &lt;/p&gt;&#xA;" OwnerUserId="13354" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-02-06T16:12:44.557" Title="Is fever a disease or not?" Tags="&lt;pathology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28358" PostTypeId="1" CreationDate="2015-02-06T02:29:36.073" Score="11" ViewCount="3994" Body="&lt;p&gt;I read another question where the author is asking about the &lt;a href=&quot;https://biology.stackexchange.com/questions/3420/why-are-some-viruses-not-communicable-person-to-person&quot;&gt;infectivity of viruses&lt;/a&gt;. In the same vein, I am curious why cancer is not a communicable disease.&lt;/p&gt;&#xA;" OwnerUserId="13354" LastEditorUserId="166" LastEditDate="2020-04-29T16:50:36.170" LastActivityDate="2020-04-29T16:50:36.170" Title="Why is cancer not a communicable disease?" Tags="&lt;pathology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="28360" PostTypeId="2" ParentId="28358" CreationDate="2015-02-06T02:49:34.553" Score="12" Body="&lt;p&gt;&lt;strong&gt;A cancer is not a pathogen&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cancer is a group of cells that (because of several specific mutations) start to duplicate abnormally. This group of cancerous cells are the own cells of the sick patient. It is not another species infecting the individual carrying the disease. It is the individual itself who developed the disease. Cancer is not a pathogen (but see below) that infect hosts and get transmitted from one host to another. It is more correct to picture cancer as an internal mistake of the body rather than as an external attack on our body. You might want to have a look to the wiki page for &lt;a href=&quot;http://en.wikipedia.org/wiki/Cancer&quot; rel=&quot;nofollow noreferrer&quot;&gt;cancer&lt;/a&gt; for more information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Transmissible agents that can cause cancer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some cancers are caused by transmissible agents, such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Oncovirus&quot; rel=&quot;nofollow noreferrer&quot;&gt;oncoviruses&lt;/a&gt;. the transmissible agent may jump from one host to another and cause cancers giving the sensation that cancer is transmitted. It is just a sensation of course because in reality only the oncovirus gets transmitted and not cancer itself jumping from one host to another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Cancers that become transmissible&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note however that it is not impossible to imagine a tumour jumping from one individual to another in cases where the immune response cannot detect cancer as 'non-self'. Some cancers are transmissible. Those cancers are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Clonally_transmissible_cancer&quot; rel=&quot;nofollow noreferrer&quot;&gt;clonally transmissible cancer&lt;/a&gt; (As indicated by C Rags in the comments). Here is the list:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Devil_facial_tumour_disease&quot; rel=&quot;nofollow noreferrer&quot;&gt;Devil Facial Tumor Disease&lt;/a&gt; which occurs in &lt;a href=&quot;http://en.wikipedia.org/wiki/Tasmanian_devil&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tasmanian Devils&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;The &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867406009123&quot; rel=&quot;nofollow noreferrer&quot;&gt;canine transmissible venereal tumour&lt;/a&gt; (article from Chris Stronks in the comments)&lt;/li&gt;&#xA;&lt;li&gt;The Contagious reticulum cell sarcoma occurring in the hamster.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-29T14:39:48.933" LastActivityDate="2019-03-29T14:39:48.933" CommentCount="14" ContentLicense="CC BY-SA 4.0" />
  <row Id="28361" PostTypeId="2" ParentId="28357" CreationDate="2015-02-06T02:55:14.570" Score="3" Body="&lt;p&gt;I know pretty much nothing in medicine!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Fever#Signs_and_symptoms&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fever&lt;/a&gt; is an abnormally high body temperature. Fever is a symptom and not a disease &lt;em&gt;per se&lt;/em&gt;. Different medical conditions (incl. various infectious diseases) causes a patient to have fever.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that fever might be in some/most situations an adaptive response to a disease. In other words, for infectious disease causing fever, fever might be good for the host and not for the parasite. However this issue remains controversial (see &lt;a href=&quot;https://biology.stackexchange.com/questions/7541/if-fever-is-a-natural-immune-defense-why-do-people-take-drugs-to-lower-it&quot;&gt;the post linked in the OP's question&lt;/a&gt; for more info).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As GoodGravy said in the comments, many people get confused and consider fever as a disease instead of what it really is; a symptom. One likely reason for this confusion is that when one has fever, (s)he very often treat fever directly (taking drugs like &lt;a href=&quot;http://en.wikipedia.org/wiki/Aspirin&quot; rel=&quot;nofollow noreferrer&quot;&gt;Aspirin&lt;/a&gt; for example) rather than treating the underlying cause (the virus for example) of the fever.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-02-06T16:12:44.557" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28362" PostTypeId="1" CreationDate="2015-02-06T03:01:23.377" Score="2" ViewCount="172" Body="&lt;p&gt;How do butterflies defend themselves from other creatures when they don't have the ability to sting or some other offensive/defensive mechanism?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Butterflies are part of the class of Insects in the order Lepidoptera. Adult butterflies have large, often brightly coloured wings, and conspicuous, fluttering flight.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="13355" LastEditorUserId="12909" LastEditDate="2015-02-06T03:09:02.797" LastActivityDate="2015-02-06T14:06:48.043" Title="How do butterflies defend themselves from other creatures when they don't have the ability to sting or some other offensive/defensive mechanism?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28365" PostTypeId="2" ParentId="28357" CreationDate="2015-02-06T03:58:29.197" Score="0" Body="&lt;p&gt;Any malfunctioning in the body is the result of either external pathogens, environmental changes or it can be manifested by the body itself. Based on which we can call it a disease or a disorder.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some can be viewed with the help of its underlying symptoms. Fever is a natural response of the human body to any kind of imbalance, for example, temperature fluctuations, infections, etc., and that is why we can get fever by any number of reasons. What is important is that it shows us of some other underlying reason of change. Therefore I think it's more of a symptom than a disease.&lt;/p&gt;&#xA;" OwnerUserId="8026" LastEditorUserId="355" LastEditDate="2015-02-06T09:38:15.573" LastActivityDate="2015-02-06T09:38:15.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28368" PostTypeId="1" CreationDate="2015-02-06T04:46:24.150" Score="1" ViewCount="146" Body="&lt;p&gt;From &lt;a href=&quot;http://www.uwyo.edu/wjm/repro/spermat.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Effect of temperature. Sperm cells will not mature at core body temperature in most mammals (spermatogenic DNA polymerase b and recombinase activities exhibit unique temperature optima); to adapt, the testes assume an external position. Testicular descent from the abdomen normally transpires during fetal or neonatal life.&lt;/p&gt;&#xA;&lt;p&gt;If the testes fail to descend into the scrotum, a condition called cryptorchidism, the male will be sterile; gone uncorrected (by surgery or androgen treatment) spermatogonia will eventually degenerate.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;How many minutes of exposure to hot water is tolerable?&lt;/li&gt;&#xA;&lt;li&gt;Can regularly bathing in hot water lead to infertility?&lt;/li&gt;&#xA;&lt;li&gt;Up to what temperature (of bath water - assuming the maximum tolerable temperature would not hurt skin) is tolerable?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-06T04:46:24.150" Title="Hot water bath and Infertility" Tags="&lt;reproduction&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28370" PostTypeId="1" AcceptedAnswerId="28372" CreationDate="2015-02-06T08:56:47.370" Score="1" ViewCount="44" Body="&lt;p&gt;While having a conversation it happens to some peopl that clearly they know there exists a perfect word to be used but can not recall it during the conversation in real time and hence forced to use some other word which may not be so perfect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But after the conversation is done they will be able to recall it. This happens very frequently to some people. Is this some kind of medical condition. If yes what is the name of this condition called as. ?&lt;/p&gt;&#xA;" OwnerUserId="13360" LastEditorUserId="13360" LastEditDate="2015-02-06T09:45:40.140" LastActivityDate="2015-02-06T11:07:39.593" Title="Is it a medical condition to not able to recall the word in a language while having a conversation" Tags="&lt;neuroscience&gt;&lt;medicine&gt;&lt;memory&gt;&lt;neurophysiology&gt;&lt;cognition&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2015-02-06T14:33:28.060" ContentLicense="CC BY-SA 3.0" />
  <row Id="28371" PostTypeId="2" ParentId="28362" CreationDate="2015-02-06T09:50:57.930" Score="6" Body="&lt;p&gt;Butterflies have a number of defence mechanisms, even if they don't have the ability to sting (as adults - see spines in larvae below). Here is a non-comprehensive list of some defensive mechanisms:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Toxins or repellents, which can be present in both adults and larvae.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Aposematism&quot; rel=&quot;nofollow&quot;&gt;Aposematism&lt;/a&gt; (warning coloration)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Mimicry&quot; rel=&quot;nofollow&quot;&gt;Mimicry&lt;/a&gt;, both in the form of resembling other poisonous species and using features such as eyespots.&lt;/li&gt;&#xA;&lt;li&gt;Spines, bristles or long hairs, often in larvae (see &lt;a href=&quot;https://encrypted.google.com/search?q=caterpillar+spines&amp;amp;source=lnms&amp;amp;tbm=isch&amp;amp;sa=X&amp;amp;ei=aIzUVMjDHqOdygOf2YH4Bw&amp;amp;ved=0CAkQ_AUoAg&amp;amp;biw=1600&amp;amp;bih=773&quot; rel=&quot;nofollow&quot;&gt;google images&lt;/a&gt;), to make ingestion highly unpleasent or dangerous. See the &lt;a href=&quot;http://www.forestry.gov.uk/pineprocessionarymoth&quot; rel=&quot;nofollow&quot;&gt;Pine processionary moth (&lt;em&gt;Thaumetopoea pityocampa&lt;/em&gt;)&lt;/a&gt; for an nice example of defensive larval hairs.&lt;/li&gt;&#xA;&lt;li&gt;Camouflage/hiding&lt;/li&gt;&#xA;&lt;li&gt;Sound clicks used to startle or disorient predators. This is most often known from moths to prevent bat attacks (see e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Cycnia_tenera&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Cycnia tenera&lt;/em&gt;&lt;/a&gt; and &lt;a href=&quot;http://jeb.biologists.org/content/194/1/285.full.pdf&quot; rel=&quot;nofollow&quot; title=&quot;Fullard et al. 1994. J. exp. Biol. 194: 285–298&quot;&gt;Fullard et al, 1994&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;li&gt;Conspicuous features at the edge of wings to make them targets of attack, e.g. eyespots or appendages, which are used to lure predators to attack non-essential body parts (see &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/bij.12063/abstract&quot; rel=&quot;nofollow&quot; title=&quot;Olofsson et al. 2013. Bird attacks on a butterfly with marginal eyespots and the role of prey concealment against the background. Biological Journal of the Linnean Society 109(2): 290–297.&quot;&gt;Olofsson et al, 2013&lt;/a&gt; for an example). &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-02-06T14:06:48.043" LastActivityDate="2015-02-06T14:06:48.043" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28372" PostTypeId="2" ParentId="28370" CreationDate="2015-02-06T11:07:39.593" Score="3" Body="&lt;p&gt;The phenomenon you describe is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Tip_of_the_tongue&quot; rel=&quot;nofollow&quot;&gt;tip-of-the-tongue phenomenon&lt;/a&gt;, where you know there is a word, and you feel it's &quot;right on the tip of the tongue, but doesn't come out&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The phenomenon is normal and tends to worsen with age. Only in case it becomes so strong that it seriously interferes with daily life, it can be considered a medical condition (anomic aphasia) that may be indicative of damage to the brain, such as stroke, head trauma, dementia, or tumor. &lt;/p&gt;&#xA;" OwnerUserId="34" LastActivityDate="2015-02-06T11:07:39.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28374" PostTypeId="1" AcceptedAnswerId="30611" CreationDate="2015-02-06T14:26:06.410" Score="4" ViewCount="216" Body="&lt;p&gt;I'm looking for ways to set up a phase contrast microscope to reduce the brightness gradient that appears across the background of my images.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I use phase contrast to find the outlines of cells in my images. My problem is that the automated processing algorithms I use get confused by strong brightness gradients in some images. Post-processing of the images disrupts the continuous nature of the histogram, again throwing off the algorithms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know why these gradients appear and how to reduce their formation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oliver&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edited the question to clarify that I am interested in microscope usage, rather than image manipulation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sample image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/l6Gl9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The image background is darker at the left of the image than at the right&lt;/p&gt;&#xA;" OwnerUserId="13365" LastEditorUserId="3340" LastEditDate="2015-02-26T11:59:30.290" LastActivityDate="2015-03-20T17:45:01.310" Title="How can I reduce the background gradient in phase contrast microscopy?" Tags="&lt;microscopy&gt;&lt;methods&gt;" AnswerCount="1" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="28375" PostTypeId="1" CreationDate="2015-02-06T14:45:01.263" Score="1" ViewCount="22" Body="&lt;p&gt;Suppose I want to find out the number of herbivores in different kinds of trees, and also compare the numbers between day and night. How would this kind of study be run in practice? It easy to think of several possible confounding factors, such as the health of the trees, weather, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the trees are big, it is also difficult to find every living thing from that. One could of course then count the number of herbivores per defined area but again, picking the area should be carefully controlled.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a statistical perspective, I can just make an estimate of expected effect size, and calculate the sample size that is about enough for detecting possible differences in the above mentioned conditions. However, I find these other aspects very difficult to do... All help would be appreciated :)&lt;/p&gt;&#xA;" OwnerUserId="13367" LastActivityDate="2015-02-06T14:45:01.263" Title="How to study the number of herbivores per type of tree and time of day?" Tags="&lt;plant-physiology&gt;&lt;statistics&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28376" PostTypeId="1" CreationDate="2015-02-06T16:14:54.340" Score="2" ViewCount="492" Body="&lt;p&gt;Suppose I spend a day in a forest, collecting different kinds of leaves, which I would like to analyze under a compound microscope. Now, obviously, measures should be taken to preserve the leaves some how. What would be the appropriate procedure? It seems (based on browsing the web..) that refrigeration could be one option. Is it scientific (used in published papers)? &lt;/p&gt;&#xA;" OwnerUserId="13368" LastActivityDate="2015-02-07T21:58:36.100" Title="How to preserve leaves between sampling (collection) and analysis?" Tags="&lt;biochemistry&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28377" PostTypeId="1" AcceptedAnswerId="28387" CreationDate="2015-02-06T16:18:54.723" Score="12" ViewCount="128053" Body="&lt;p&gt;At the base of fingernail, there is a white semicircle (see on the first picture). But sometimes there isn't one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jabic.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/RWrOD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions are: what is this white semicircle on the fingernail, and what causes it? What is the explanation when there it isn't on all of the fingernails (see on the second picture)?&lt;/p&gt;&#xA;" OwnerUserId="13243" LastEditorUserId="5198" LastEditDate="2015-02-06T21:38:58.993" LastActivityDate="2016-05-03T03:09:01.443" Title="Name (and meaning of the absence) of the white semicircle at the base of the fingernail?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28378" PostTypeId="1" AcceptedAnswerId="34249" CreationDate="2015-02-06T16:39:09.800" Score="1" ViewCount="77" Body="&lt;p&gt;In the body we almost always assume that glutamate exists as glutamate rather than glutamic acid. It is so commonly glutamate yet glutamic acid and glutamate share the abbreviations of Glu and E. From the &lt;a href=&quot;http://en.wikipedia.org/wiki/Glutamic_acid&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia page&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The side chain carboxylic acid functional group has a pKa of 4.1 and therefore exists almost entirely in its negatively charged deprotonated carboxylate form at pH values greater than 4.1; therefore, it is negatively charged at physiological pH ranging from 7.35 to 7.45.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Glutamic acid:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FGrzF.png&quot; alt=&quot;glutamic acid (amino acid contains hydrogen)&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Glutamate:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dPZ03.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that the pKa of glutamate is 4.1, is their any biological situation (a cell type, organel etc.) that glutamic acid is preferred? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, does this have any large biochemical implications, or is that outweighed by the (relatively speaking) &quot;extreme&quot; acidic environment?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2015-02-07T15:48:53.073" LastActivityDate="2015-05-14T21:38:26.973" Title="Is there a biological environment that we can we assume glutamate exists as glutamic acid?" Tags="&lt;biochemistry&gt;&lt;amino-acids&gt;&lt;ph&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28379" PostTypeId="1" AcceptedAnswerId="28385" CreationDate="2015-02-06T17:24:21.337" Score="3" ViewCount="639" Body="&lt;p&gt;I've read about the overuse of antibiotics leading to antibiotic resistant strains of bacteria, so generally does long term use of antibiotics breed these strains in the bodies of antibiotic users and increase the risk of various bodily infections?&lt;/p&gt;&#xA;" OwnerUserId="9906" LastActivityDate="2015-02-07T00:06:14.860" Title="Does long term use of antibiotics in humans actually lead to a greater risk of infection?" Tags="&lt;infection&gt;&lt;antibiotics&gt;&lt;antibiotic-resistance&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28380" PostTypeId="1" AcceptedAnswerId="28382" CreationDate="2015-02-06T17:44:00.540" Score="1" ViewCount="543" Body="&lt;p&gt;I have a DNA sequence from a sequencer. How can I determine what protein is it? I tried some translator but it didn't help. What protein is this and how can I determine it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sequence: &lt;strong&gt;CGTTCTATAGATACGCGATGACGGTATACCATCCGCAAAGT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you very much!&lt;/p&gt;&#xA;" OwnerUserId="13369" LastEditorUserId="3553" LastEditDate="2015-02-06T18:03:20.377" LastActivityDate="2015-02-06T18:03:20.377" Title="How do I find a protein from this DNA sequence?" Tags="&lt;dna&gt;&lt;proteins&gt;&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28381" PostTypeId="2" ParentId="28380" CreationDate="2015-02-06T17:57:42.367" Score="1" Body="&lt;p&gt;You might want to try searching against NR/NT database using &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi&quot; rel=&quot;nofollow&quot;&gt;BLAST&lt;/a&gt;. This way you will get to know what this sequence might be similar too. The length of the sequence is too short to code for any meaningful protein.&lt;/p&gt;&#xA;" OwnerUserId="1648" LastActivityDate="2015-02-06T17:57:42.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28382" PostTypeId="2" ParentId="28380" CreationDate="2015-02-06T17:57:57.443" Score="1" Body="&lt;p&gt;Enter it in &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&amp;amp;PAGE_TYPE=BlastSearch&amp;amp;LINK_LOC=blasthome&quot; rel=&quot;nofollow&quot;&gt;BLASTX.&lt;/a&gt; This will give you any protein sequence matches as well as likely homologues given a nucleotide sequence.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastActivityDate="2015-02-06T17:57:57.443" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28383" PostTypeId="2" ParentId="28376" CreationDate="2015-02-06T18:33:12.653" Score="2" Body="&lt;p&gt;You may want to see:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mark W. Chase, Harold H. Hills; Taxon, Vol. 40, No. 2,  1991, pp. 215-220: 'Silica Gel: An Ideal Material for Field Preservation of Leaf Samples for DNA Studies'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Summarized, the process would be the following:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Place the leaves inside ziplock plastic bags;&lt;/li&gt;&#xA;&lt;li&gt;Add ten times (minium) the weight of the leaves in silica gel;&lt;/li&gt;&#xA;&lt;li&gt;After 12 hours (after which the degradation of the biological material is more likely), check the leaves by bending them: if they break cleanly, the leaf is dry;&lt;/li&gt;&#xA;&lt;li&gt;Store in the ziplock bag, inside a box with an hermetic lid;&lt;/li&gt;&#xA;&lt;li&gt;Refrigerate (if possible).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Note: Freezing by submersion in liquid nitrogen is also a viable approach, yet might be less practical&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="13370" LastActivityDate="2015-02-06T18:33:12.653" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28384" PostTypeId="2" ParentId="28343" CreationDate="2015-02-06T18:48:27.793" Score="3" Body="&lt;p&gt;When we are sad, our emotions are in an overdrive and the parasympathetic nervous system triggers lacrimation i.e. tears, and we cry.&lt;/p&gt;&#xA;" OwnerUserId="13362" LastActivityDate="2015-02-06T18:48:27.793" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28385" PostTypeId="2" ParentId="28379" CreationDate="2015-02-06T20:53:16.170" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;does long term use of antibiotics breed these strains in the bodies of antibiotic users[,] and increase the risk of various bodily infections?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Yes&lt;/em&gt; to the first question (although I would use the words &lt;em&gt;select for&lt;/em&gt;). &lt;em&gt;No, not usually&lt;/em&gt; for the second question in the individual(*), &lt;em&gt;yes&lt;/em&gt; in the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This should be looked at as a problem in &lt;em&gt;populations&lt;/em&gt; of both people/animals and bacterial populations in general. Given time, any living organism will be favored if a mutation involving a &lt;strong&gt;selective pressure&lt;/strong&gt; (like an antibiotic) is introduced, not only in those towards which the antibiotic is directed but also among the normal microbiota. The longer the selective pressure (antibiotic treatment), the greater the probability that a resistant strain of one bacteria or another will develop. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's why there's a push (in studies) to limit the number of days of antibiotic use necessary to the least number needed which still proves efficient in eradicating an infection. (The trend is towards kill 'em quick and kill 'em all - higher doses for shorter periods, or make it strong and only long enough to cause the extinction of the illness-causing bacteria and not long enough for selection of resistance mutations.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is quite normal to have potentially pathogenic bacteria as part of one's microbiome. Usually other beneficial bacteria and conditions keep these in check. But antibiotic resistance, once selected for, can persist for longer periods of time than previously recognized (up to four years in one study). This gives even a small population of resistant bacteria to genetically transfer resistance to others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Short-term use is less likely to select for resistance in one individual, but, in terms of populations of people, antibiotics are used so ubiquitously that resistant strains will be selected for in shorter treatment intervals by sheer numbers of people being treated.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When resistant and susceptible organisms compete to colonize or infect hosts, and use of an antibiotic has a greater impact on the transmission of susceptible bacteria than resistant ones, then increasing use of the antibiotic will result in an increase in frequency of organisms resistant to that drug in the population, even if the risk for treated patients is modest. Antimicrobial use and patient-to-patient transmission are not independent pathways for promoting of antimicrobial resistance, rather they are inextricably linked. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&quot;Long term use&quot; in one individual is relatively uncommon and unnecessary, but if necessary, usually does more good than harm &lt;em&gt;to that individual&lt;/em&gt;. Almost all (if not all) of the population of the bacteria you're trying to eliminate from one site will be susceptible to the antibiotic and will die, leaving, in a few cases, a few resistant ones that your body can handle naturally, or that can repopulate to &quot;normal&quot; levels without causing illness. But they are then there, the resistant ones, to spread within a population of the individual's microbiome, and the population of people. The next person with a problem, who might have picked up that resistant strain, will not respond well to the same antibiotic. Nor will the patient who was initially treated, if the problem recurs with an antibiotic resistant strain. So, as I said, yes and no.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's why people (doctors, vets, and - with help - patients) should consider a risk-to-benefit-ratio whenever using an antibiotic. From that standpoint, it is always unethical to use an antibiotic for what is probably a virus, because the benefit to a patient is very small, but the risk - to that patient, who might suffer complications from its use, and to the population if a resistant strain is selected for - is relatively high. Better to wait it out to see if it is bacterial (if one can't test for it directly), and treat it if it does turn out to be. Of course, the risk of not treating in certain populations must also be considered: the elderly, the immunosuppressed, infants, and people with other illnesses or predispositions to infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's not just use of antibiotics in patients/humans that causes problems; its use in &lt;em&gt;any situation&lt;/em&gt; can lead to selection for resistance. This is well documented to occur in the meat industry, where a grower often tries to minimize the effect of cost-efficient but insalubrious growing conditions by giving antibiotics to the entire population of meat-animals (beef or poultry) to cut the monetary losses associated with &lt;em&gt;potential&lt;/em&gt; illnesses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a multifactorial, and often monetarily driven, problem. Doctors share the blame, but so do patients who demand antibiotics thinking they know better than the doctor, and who will doctor-shop until they find one who will do their bidding, or make a stink for the doctor who refuses. Some doctors still refuse, but they pay a heavy (non-monetary and sometimes monetary) price for doing so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the meat industry, it's always a monetarily driven process.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This review focuses on agricultural antimicrobial drug use as a major driver of antimicrobial resistance worldwide for four reasons: It is the largest use of antimicrobials worldwide; much of the use of antimicrobials in agriculture results in subtherapeutic exposures of bacteria; drugs of every important clinical class are utilized in agriculture; and human populations are exposed to antimicrobial-resistant pathogens via consumption of animal products as well as through widespread release into the environment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;What YOU can do:&lt;/strong&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;Do not take an antibiotic for a viral infection like a cold or the flu.&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;Do not save some of your antibiotic for the next time you get sick.&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;Take an antibiotic exactly as the healthcare provider tells you. Complete the prescribed course of treatment even if you are feeling better. If treatment stops too soon, some bacteria may survive and re-infect.&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;Do not take antibiotics prescribed for someone else.&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;If your healthcare provider determines that you do not have a bacterial infection, ask about ways to help relieve your symptoms. Do not pressure your provider to prescribe an antibiotic.&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/medicine_03&quot; rel=&quot;nofollow&quot;&gt;Antibiotic resistance: delaying the inevitable&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.cdc.gov/getsmart/antibiotic-use/antibiotic-resistance-faqs.html#how-bacteria-resist&quot; rel=&quot;nofollow&quot;&gt;Get Smart: Know When Antibiotics Work&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009836&quot; rel=&quot;nofollow&quot;&gt;Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiome&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730242/pdf/01-0312_FinalP.pdf&quot; rel=&quot;nofollow&quot;&gt;Antimicrobial Use and Antimicrobial Resistance: A Population Perspective&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://jama.jamanetwork.com/article.aspx?articleid=197644&quot; rel=&quot;nofollow&quot;&gt;Comparison of 8 vs 15 Days of Antibiotic Therapy for Ventilator-Associated Pneumonia in AdultsA Randomized Trial&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1038/sj.bjp.0707607/pdf&quot; rel=&quot;nofollow&quot;&gt;Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://scholar.google.com/scholar_url?url=http://www.researchgate.net/profile/Jay_P_Graham/publication/5503183_Industrial_food_animal_production_antimicrobial_resistance_and_human_health/links/0deec5335f7b7a49fc000000.pdf&amp;amp;hl=en&amp;amp;sa=X&amp;amp;scisig=AAGBfm2WzW85xX7H8f6kTZ6ZkOWrxoYJuQ&amp;amp;nossl=1&amp;amp;oi=scholarr&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Industrial Food Animal Production, Antimicrobial Resistance, and Human Health&lt;/strong&gt;&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-02-07T00:06:14.860" LastActivityDate="2015-02-07T00:06:14.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28387" PostTypeId="2" ParentId="28377" CreationDate="2015-02-06T21:34:32.740" Score="11" Body="&lt;p&gt;The lighter crescent-shaped part at the base of the nail is called the lunula. It is a normal part of the nail matrix, and indicates nail growth. The faster your fingernails grow, the more obvious the lunula.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zUkw3.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Absence of the lunula without any other abnormalities of the nail is not uncommon, and while it can indicate anemia or malnutrition, it is often found normally, and with aging. In this case, careful inspection of all the nails will usually reveal a lunula on the thumbs and the fingers closest to the thumb, but a very small or absent lunula on the other fingers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your picture, there is clearly a lunula on the middle finger, and, I suspect, a larger one on the index finger, and a relatively normal one on the thumb. This is not a finding of great concern in the absence of other pathology.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The lunula: The small, whitish, half-moon shape that you sometime see at the bottom of your nails is called the lunula(pronounced loon-yoo-la). It's actually part of the matrix. You might be able to see it only on your thumbs, or maybe not at all. Don't worry if you can't see a lunula on any of your fingers. &lt;a href=&quot;https://www.aad.org/dermatology-a-to-z/for-kids/about-nails/how-nails-grow&quot; rel=&quot;noreferrer&quot;&gt;&lt;strong&gt;It's no big deal&lt;/strong&gt;&lt;/a&gt;. It's there, just under your skin.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.medscape.com/viewarticle/712251_3&quot; rel=&quot;noreferrer&quot;&gt;Examining the Fingernails When Evaluating Presenting Symptoms in Elderly Patients&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.medicine.virginia.edu/clinical/departments/medicine/grad-ed/geri/learning-materials/learning-modules/NailExamination.pdf&quot; rel=&quot;noreferrer&quot;&gt;Examining the Fingernails&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK211/&quot; rel=&quot;noreferrer&quot;&gt;Nails&lt;/a&gt;&lt;/sub&gt; &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-02-06T21:47:23.907" LastActivityDate="2015-02-06T21:47:23.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28388" PostTypeId="2" ParentId="28322" CreationDate="2015-02-07T00:27:40.397" Score="1" Body="&lt;p&gt;Heterozygous loci have both alleles present at a given time, for example Aa (considering diploid organism), where as homozygous have only one type (AA or aa). Generally, both alleles have different sequence lengths due to deletions, insertions etc. so if any locus is homozygous, it will produce only one length but heterozygous will produce two different lengths. That is why you will only see one band in case of homozygous and two in heterozygous.&lt;/p&gt;&#xA;" OwnerUserId="13351" LastActivityDate="2015-02-07T00:27:40.397" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28390" PostTypeId="1" AcceptedAnswerId="28391" CreationDate="2015-02-07T02:59:00.000" Score="-1" ViewCount="54" Body="&lt;p&gt;What is some computer science technology that can help the development of biology(eg. artificial intelligence, resolution technology) and  briefly talks about their potentials?&lt;/p&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="5479" LastEditDate="2015-02-07T03:31:44.807" LastActivityDate="2015-02-07T03:44:55.980" Title="What is some computer science technology that can help the development of biology?" Tags="&lt;computational-model&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ClosedDate="2015-02-07T06:30:04.263" ContentLicense="CC BY-SA 3.0" />
  <row Id="28391" PostTypeId="2" ParentId="28390" CreationDate="2015-02-07T03:44:55.980" Score="2" Body="&lt;p&gt;The question is very broad and it is impossible to correctly answer to it. I think you may not realize how much computation is everywhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a bunch of things for which I personally use modern computation power&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Population genetics simulations&lt;/li&gt;&#xA;&lt;li&gt;Simulations of developments (&lt;a href=&quot;http://en.wikipedia.org/wiki/Gillespie_algorithm&quot; rel=&quot;nofollow&quot;&gt;Gillespie algorithm&lt;/a&gt; and variants)&lt;/li&gt;&#xA;&lt;li&gt;Statistical analyses, incl. some analyses that are a bit demanding such as permutations test, bootstrap or maximum likelihood&lt;/li&gt;&#xA;&lt;li&gt;Numerical approximations to mathematical equations that can't be solved analytically.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Many people make good use of computation in biology for treating DNA sequence data (annotating sequences, aligning sequences, comparing sequences, building phylogenetic trees). Typically this kind of task can be extremely demanding. I know a lab who uses &lt;a href=&quot;http://en.wikipedia.org/wiki/Blue_Gene&quot; rel=&quot;nofollow&quot;&gt;Blue Gene&lt;/a&gt; in order to perform statistical analysis on sequence data. Some people simulate brain activities. Some people simulate the physics of molecules, some people simulate blood flow through the body while others simulate how a new substance injected in the body spread. and it goes on and on... This list is probably biased toward my field of expertise.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2015-02-07T03:44:55.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28394" PostTypeId="2" ParentId="28376" CreationDate="2015-02-07T04:45:19.647" Score="0" Body="&lt;p&gt;Placing the leaves in wax paper and under the pressure of several books would be beneficial (in terms of a short term preservation). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This method may not be suitable for field preservation, due to the bulky nature of books and other weights, although it might be suitable if using an alternate method of pressure. &lt;/p&gt;&#xA;" OwnerUserId="13023" LastEditorUserId="13370" LastEditDate="2015-02-07T21:58:36.100" LastActivityDate="2015-02-07T21:58:36.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28395" PostTypeId="1" CreationDate="2015-02-07T05:01:19.020" Score="3" ViewCount="4132" Body="&lt;p&gt;I am converting outputs in stockholm format to clustalw using &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Bio::AlignIO-&amp;gt;new(-file =&amp;gt; &quot;$ARGV[0]&quot;, -format =&amp;gt; &quot;stockholm&quot;); and&#xA;&#xA;Bio::AlignIO -&amp;gt;new (-format =&amp;gt;'clustalw');&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;I am also using &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;my $new=$aln-&amp;gt;remove_columns(['all_gaps_columns'],'.');&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and got an output like&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;head1  ----------------.GG-.-gggaguggugugguuacgaaugUGGCCUCUGC-----A&#xA;&#xA;head2  GGGGGUGUAGCUCAGU.GGU.A......................GAGCGGAUGCUUUGCA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;What is the meaning of dots and dashes? Is this natural in a clustalw output? Am I getting a bug?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was unable to find the sequences I used in the original message but these two pose a similar pattern. These are RNA sequences, including pseudogenes, so there are lots of palindromic sequences.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;# STOCKHOLM 1.0&#xA;#=GF AU Infernal 1.1.1&#xA;&#xA;head1          --------UGGAGAAU.G--.-ugggcguc.gaucccacUUCCUCUCGCAUGCUAA..............................................................GCGAGC-gcucuaccacuugagcuaauucccc-..-------------..................................&#xA; #=GR head1 PP ........89999988.4....6789****.********999**************..............................................................******.7999999866665555555554444..................................................&#xA;&#xA; head2         --------UGGAGAAU.---.-gcgggcaucgaucccgcUUCCUCUCGCAUGCUAA..............................................................GCGAGCG.........................-..-------------cucuaccauu........................&#xA; #=GR head2  PP ........89999887......46789************9999*************..............................................................*****86.........................................4555666666........................&#xA;&#xA;&#xA; CLUSTAL W (1.81) multiple sequence alignment&#xA;&#xA; head1  --------UGGAGAAU.G--.-ugggcguc.gaucccacUUCCUCUCGCAUGCUAA....&#xA; head2  --------UGGAGAAU.---.-gcgggcaucgaucccgcUUCCUCUCGCAUGCUAA....&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="13373" LastEditorUserId="13373" LastEditDate="2015-02-07T16:43:10.683" LastActivityDate="2015-12-14T08:36:29.663" Title="What is the meaning of dots and dashes in clustalw?" Tags="&lt;bioinformatics&gt;&lt;sequence-alignment&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28397" PostTypeId="1" AcceptedAnswerId="28399" CreationDate="2015-02-07T07:24:23.893" Score="2" ViewCount="75" Body="&lt;p&gt;Not sure if this is the correct stackexchange site - please migrate/advise as you see fit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm interested in the method by which ants &quot;break off&quot; a small amount of soil and then hold it in their jaws (?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To clarify I know ants break off soil in small quantities, so that a single ant carries very little soil; I'm interested to understand what exactly how this happens. For example does the ant literally pick the soil directly, or does it brush it loose first etc. Further to this I'd like to know how the ant holds the soil. Is it akin to the soil being atop a palm, or more like being held between two hands?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Broader context: I'm looking into making a model of this type of soil movement and I wanted a more detailed understanding.&lt;/p&gt;&#xA;" OwnerUserId="10515" LastEditorUserId="9943" LastEditDate="2015-02-07T12:12:10.537" LastActivityDate="2015-02-07T12:12:10.537" Title="By what method do ants dissect and hold soil" Tags="&lt;entomology&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28399" PostTypeId="2" ParentId="28397" CreationDate="2015-02-07T12:04:38.503" Score="2" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ants use specialized facial structures called &lt;strong&gt;&lt;em&gt;mandibles&lt;/em&gt;&lt;/strong&gt; to &lt;strong&gt;cut, shape and carry soil&lt;/strong&gt; and other matter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;you say &quot;&lt;code&gt;I know ants break off soil in small quantities, so that a single ant carries very little soil...&quot;&lt;/code&gt;. On the contrary I would say - Ants can carry relatively &lt;em&gt;a lot of soil&lt;/em&gt;, as they can lift up to about &lt;strong&gt;100 times their own body weight&lt;/strong&gt;. In absolute terms, however, the weight carried is about 500 mg (&lt;a href=&quot;http://www.theincredibleant.com/ant-how/how-much-weight-can-an-ant-lift&quot; rel=&quot;nofollow noreferrer&quot;&gt;Spectrum)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cZ01u.jpg&quot; alt=&quot;Ant lifting soil&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: &lt;a href=&quot;http://flickrhivemind.net/Tags/australia,bullant/Interesting&quot; rel=&quot;nofollow noreferrer&quot;&gt;The World's Best Photos&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The structure that ants use to break off and carry soil are their &lt;em&gt;mandibles&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GHPUK.jpg&quot; alt=&quot;Ant mandibles&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: &lt;a href=&quot;http://tolweb.org/treehouses/?treehouse_id=2482&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tree of Life Web Project&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mandibles are specialized bodily structures typical for insects, and I quote from the &lt;a href=&quot;http://bugs.bio.usyd.edu.au/learning/resources/Entomology/externalMorphology/imagePages/mouth_master.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;University of Sydney website&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The mandibles are the first pair of jaws in insects, moving laterally (i.e. from side to side) when in use. Mandible shape is strongly influenced by function and is therefore highly variable. For example a chewing insect will have strong tooth-shaped mandibles while in a sucking insect they will be thin and needle-shaped. Mandibles are used to &lt;strong&gt;cut, chew and tear food as well as to carry objects&lt;/strong&gt;, fight and mould materials such as wax or &lt;strong&gt;soil&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-02-07T12:09:41.590" LastActivityDate="2015-02-07T12:09:41.590" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28400" PostTypeId="2" ParentId="28358" CreationDate="2015-02-07T12:51:51.217" Score="6" Body="&lt;p&gt;Naïvely, there’s no reason why cancers wouldn’t be communicable. Tumours consist of abnormally multiplying cells which have switched off their response to repressive stimuli from other cells, which would otherwise cause them to stop growing (plus a few other properties which have first been collectively described in the seminal paper &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Hallmarks_of_Cancer&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;The hallmarks of cancer&lt;/em&gt;&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And tumour cells can absolutely split off and start growing elsewhere, thus effectively spreading the cancer. This happens in metastases, and it happens in the few types of communicable cancer that are known.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;So why does this normally &lt;/em&gt;not&lt;em&gt; happen between individuals?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason is our immune system. Our bodies are normally incredibly good at recognising and eliminating foreign bodies – so-called &lt;a href=&quot;https://en.wikipedia.org/wiki/Antigen&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;antigens&lt;/em&gt;&lt;/a&gt;. The problem with cancers is that they are &lt;em&gt;not&lt;/em&gt; foreign bodies: they are our own cells, only mutated. This makes it hard for our own immune system to recognise them as foreign. (It’s worth noting that at some point tumour cells have accumulated enough mutations to be recognised as foreign, but by this point the tumour is already mounting an effective resistance to the immune system.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It’s for this reason that most cancers are not transmissible: invading &lt;a href=&quot;https://en.wikipedia.org/wiki/Cancer_cell&quot; rel=&quot;nofollow&quot;&gt;cancer cells&lt;/a&gt; are immediately recognised as foreign bodies, and are efficiently eliminated by the immune system before they can multiply into a tumour. Unlike other antigens they have not &lt;a href=&quot;https://en.wikipedia.org/wiki/Evolutionary_arms_race&quot; rel=&quot;nofollow&quot;&gt;evolved&lt;/a&gt; effective ways of evading the host’s immune system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;— Let’s take a detour here and talk about organ transplantation: When a donor organ is transplanted into a new host, the host recognises this organ as foreign, and initiates an immune reaction against it (or &lt;a href=&quot;http://en.wikipedia.org/wiki/Graft-versus-host_disease&quot; rel=&quot;nofollow&quot;&gt;vice versa&lt;/a&gt;). This &lt;a href=&quot;http://en.wikipedia.org/wiki/Transplant_rejection&quot; rel=&quot;nofollow&quot;&gt;transplant rejection&lt;/a&gt; is a huge problem, and needs to be addressed by finding a closely related donor, and administering immunosuppressant drugs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which brings us back to transmissible cancers: all known types of transmissible cancer occur in species which have gone through a recent &lt;a href=&quot;http://en.wikipedia.org/wiki/Population_bottleneck&quot; rel=&quot;nofollow&quot;&gt;population bottleneck&lt;/a&gt;. All now-living individuals are very closely related. As a consequence, their immune systems don’t necessarily recognise another individual’s cells as foreign, or at least produces a reduced immune response.&lt;/p&gt;&#xA;" OwnerUserId="166" LastEditorUserId="166" LastEditDate="2015-09-23T09:03:31.527" LastActivityDate="2015-09-23T09:03:31.527" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="28401" PostTypeId="2" ParentId="28256" CreationDate="2015-02-07T13:23:49.617" Score="0" Body="&lt;p&gt;While I don't think it's precisely the behaviour you are asking about, you might also be interested in slime molds (e.g., Dictyostelium or Myxogastria). They start out as motile single cell organisms, have limited 'vision' (chemical cues), coalesce into a large multicellular structure when resources become limiting, and then disperse from (usually) a fruiting body.This is an example of &quot;emergent collective behaviour&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other searches you may want to try are &quot;Biased random walk models&quot; and &quot;Shoaling behaviour&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although pretty heavy, these papers may contain a formal mathematical description of the model you are after:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Akira Okubo, 1986, doi: 10.1016/0065-227X(86)90003-1&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Angela Stevens and Hans G. Othmer, 1997, doi: 10.1137/S0036139995288976 &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="13093" LastActivityDate="2015-02-07T13:23:49.617" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28404" PostTypeId="2" ParentId="28395" CreationDate="2015-02-07T14:42:44.733" Score="2" Body="&lt;p&gt;As WYSIWYG touches on in the comments, usually dashes mean that there are gaps in the alignment as the result of an &lt;a href=&quot;https://en.wikipedia.org/wiki/Indel&quot; rel=&quot;nofollow&quot;&gt;indel&lt;/a&gt; event. Dots are used to show specifically point mutations where the biochemical properties are mostly conserved, but the residue has changed.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;From original question, not relevant to question as it stands.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are right in that this isn't a proper alignment, however I'm not sure it is a bug. What you have appears to be the alignment of a nucleotide sequence that has gone horribly, horribly wrong. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a first guess without any more details I would say it doesn't look like you have installed clustalw correctly or pointed your bioperl to it. From &lt;a href=&quot;http://doc.bioperl.org/releases/bioperl-current/bioperl-run/Bio/Tools/Run/Alignment/Clustalw.html&quot; rel=&quot;nofollow&quot;&gt;the documentation&lt;/a&gt; here are common problems:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;&lt;p&gt;Make sure the clustalw executable is in your path so that&#xA;  which clustalw&#xA;  returns a clustalw executable on your system.&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Define an environmental variable CLUSTALDIR which is a &#xA;  directory which contains the 'clustalw' application:&#xA;  In bash:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;export CLUSTALDIR=/home/username/clustalw1.8&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In csh/tcsh:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;setenv CLUSTALDIR /home/username/clustalw1.8&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Include a definition of an environmental variable CLUSTALDIR in&#xA;  every script that will use this Clustalw wrapper module, e.g.:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;BEGIN { $ENV{CLUSTALDIR} = '/home/username/clustalw1.8/' }&#xA;  use Bio::Tools::Run::Alignment::Clustalw;&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Unless you are doing massive amounts of sequence alignment, the &lt;a href=&quot;http://www.ebi.ac.uk/Tools/msa/clustalw2/&quot; rel=&quot;nofollow&quot;&gt;clustalW2 webserver&lt;/a&gt; is quicker, more sensitive and way easier to use.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2015-12-14T08:36:29.663" LastActivityDate="2015-12-14T08:36:29.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28405" PostTypeId="1" AcceptedAnswerId="28415" CreationDate="2015-02-07T15:20:08.787" Score="2" ViewCount="105" Body="&lt;p&gt;I'm just curious why it has to happen every month when the uterus could have been prepared from the beginning and kept that way throughout life or till a certain point. But why make and break it every month? (The breaking of this preparation is the cause of menstrual pain, which is what I'm worried about).&lt;/p&gt;&#xA;" OwnerUserId="13377" LastEditorUserId="6289" LastEditDate="2015-02-07T16:23:33.220" LastActivityDate="2015-02-07T21:04:59.583" Title="Why does uterus have to be prepared every month for fertilization?" Tags="&lt;human-biology&gt;&lt;pain&gt;&lt;reproductive-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28406" PostTypeId="2" ParentId="1688" CreationDate="2015-02-07T17:17:05.607" Score="1" Body="&lt;p&gt;For the settling there's little you can do except agitation and using a taller thinner tube and larger suspending volume. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the clumping however if the analysis permits it, adding serum to a [final] of 5% will help slow the clumping (in the short term). You can also filter out initial clumps by pushing the cells through a nylon mesh filter (they make these especially for flow-commonly used with fixed cells). I've analyzed cells on ice in dark probably as long as 6 hours after harvesting with little change in viability, however this is of course bad practice.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2015-02-07T17:17:05.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28408" PostTypeId="1" CreationDate="2015-02-07T17:38:53.013" Score="3" ViewCount="8366" Body="&lt;p&gt;I have 10 samples of some food or other things and I need to know, if it contains amylase. I already ran an experiment with storch and iodine, but I have to make it right and my experiment must not be right. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;List of samples: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Saliva (I know this one)&lt;/li&gt;&#xA;&lt;li&gt;Banana peel (inner side)&lt;/li&gt;&#xA;&lt;li&gt;Corn&lt;/li&gt;&#xA;&lt;li&gt;Sponge biscuit&lt;br&gt;&#xA;(&lt;a href=&quot;http://www.kaloricketabulky.cz/fotografie-velka/f1136aba2e11082a/piskoty-detske-kulate.jpg&quot; rel=&quot;nofollow&quot;&gt;http://www.kaloricketabulky.cz/fotografie-velka/f1136aba2e11082a/piskoty-detske-kulate.jpg&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Tomato&lt;/li&gt;&#xA;&lt;li&gt;Banana (dried)&lt;/li&gt;&#xA;&lt;li&gt;Bread&lt;/li&gt;&#xA;&lt;li&gt;Potato peel&lt;/li&gt;&#xA;&lt;li&gt;Ketchup&lt;/li&gt;&#xA;&lt;li&gt;Milk&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Thank you very much!&lt;/p&gt;&#xA;" OwnerUserId="13369" LastActivityDate="2015-02-09T23:34:03.513" Title="Do these things contain amylase?" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2015-02-08T05:52:27.617" ContentLicense="CC BY-SA 3.0" />
  <row Id="28409" PostTypeId="2" ParentId="28265" CreationDate="2015-02-07T17:39:09.537" Score="2" Body="&lt;p&gt;You need to normalize both images to the background. This can be done in many softwares including photoshop.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I was learning this starting to do it with something more simple like SDS page protein bands helped me a lot. The principles are the same you are still subtracting background. Look at this tutorial:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://m.youtube.com/watch?v=JlR5v-DsTds&quot; rel=&quot;nofollow&quot;&gt;http://m.youtube.com/watch?v=JlR5v-DsTds&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, when analyzing intensity values in fluorescent microscopy the most important parameter is area of your analysis. This needs to be an objectively applied as much as possible, and that can be by increasing the number of replicates whose area you analyze. Your going to look at pixel intensities for many many cells and average those intensities. Using the imagej cell counter plug-in is helpful to see how to determine cell area.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2015-02-08T03:16:49.490" LastActivityDate="2015-02-08T03:16:49.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28410" PostTypeId="2" ParentId="28395" CreationDate="2015-02-07T17:43:03.777" Score="1" Body="&lt;p&gt;Based on the edit you made to your op, the dots are present in your initial stockholm alignment, and are simply being copied into the new clustal output. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the source of your alignment to begin with? I'm assuming you're selecting individual rows from a larger alignment, given the odd distribution of gaps. This could give you a clue as to the actual significance of the dots (dashes are pretty much always gaps).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, just fyi, if you want a command line tool to do the conversion for you, I have a python3 module called &lt;a href=&quot;https://github.com/biologyguy/BuddySuite&quot; rel=&quot;nofollow&quot;&gt;SeqBuddy&lt;/a&gt; that will work just fine. You'll need BioPython as a dependency though.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;$: python3 SeqBuddy.py input.stockholm -sf clustal &amp;gt; output.clustal&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="13093" LastActivityDate="2015-02-07T17:43:03.777" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28412" PostTypeId="2" ParentId="28294" CreationDate="2015-02-07T18:04:22.577" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://transdecoder.github.io/&quot; rel=&quot;nofollow&quot;&gt;TransDecoder&lt;/a&gt; is a commonly used program for extracting likely coding regions from transcriptome assemblies, which does the following to make a call:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;TransDecoder identifies likely coding sequences based on the following&#xA;  criteria:&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;a minimum length open reading frame (ORF) is found in a transcript&#xA;  sequence&lt;/li&gt;&#xA;  &lt;li&gt;a log-likelihood score similar to what is computed by the GeneID&#xA;  software is &gt; 0.&lt;/li&gt;&#xA;  &lt;li&gt;the above coding score is greatest when the ORF is scored in the 1st&#xA;  reading frame as compared to scores in the other 5 reading frames.&lt;/li&gt;&#xA;  &lt;li&gt;if a candidate ORF is found fully encapsulated by the coordinates of&#xA;  another candidate ORF, the longer one is reported. However, a single&#xA;  transcript can report multiple ORFs (allowing for operons, chimeras,&#xA;  etc).&lt;/li&gt;&#xA;  &lt;li&gt;optional the putative peptide has a match to a Pfam domain above the&#xA;  noise cutoff score.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So in essence, look for the longest ORF, and then use some secondary metric (hidden Markov model, position weight array, database query, etc) to refine your prediction. &lt;/p&gt;&#xA;" OwnerUserId="13093" LastActivityDate="2015-02-07T18:04:22.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28415" PostTypeId="2" ParentId="28405" CreationDate="2015-02-07T21:04:59.583" Score="2" Body="&lt;p&gt;A quick search through the Internet, as well as any textbook, will reveal that the lining of the uterus (endometrium) created thickened during every menstruation cycle is rich in nutrients, and requires a constant blood supply, in order to accommodate a fetus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, maintaining the lining would be more costly to the body than rebuilding it every month; in fact, as part of the lining is reabsorbed, rather than destroyed and expelled, thus conserving energy and nutrients. The reason a part of the endometrium is not reabsorbed is its thickness, which prevents its total reabsorption. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, the menstrual pain is, in fact, caused by the breaking down of the endometrium, although not directly, but by muscular contractions (cramps) and the contraction of blood vessels, which happen to prevent blood loss and help with the expelling of the endometrium.&lt;/p&gt;&#xA;" OwnerUserId="13370" LastActivityDate="2015-02-07T21:04:59.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28416" PostTypeId="1" CreationDate="2015-02-07T22:17:41.280" Score="1" ViewCount="470" Body="&lt;p&gt;What flower is this? &lt;img src=&quot;https://i.stack.imgur.com/3NuoE.jpg&quot; alt=&quot;some blue flower&quot;&gt; All help would be appreciated&lt;/p&gt;&#xA;" OwnerUserId="13380" LastActivityDate="2015-02-07T22:59:01.113" Title="What flower is this blue flower?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2015-02-17T08:59:48.783" ContentLicense="CC BY-SA 3.0" />
  <row Id="28417" PostTypeId="2" ParentId="28416" CreationDate="2015-02-07T22:51:32.233" Score="4" Body="&lt;p&gt;Without more detail about the whole plant (including leaves), where it came from, and about whether or not it was spray-painted, watered with dyed water, etc. it would be difficult to ID. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to be in the Asteraceae family, and in the pompon class, as seen in these vender's pictures. (Disclosure: I have no affiliation with the company.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.fiftyflowers.com/product/Blue-Cushion-Bulk-Flower_10.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.fiftyflowers.com/product/Blue-Cushion-Bulk-Flower_10.htm&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.fiftyflowers.com/product/Blue-Cremon-Bulk-Flowers_24307.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.fiftyflowers.com/product/Blue-Cremon-Bulk-Flowers_24307.htm&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.fiftyflowers.com/product/Electric-Blue-Flowers_10.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.fiftyflowers.com/product/Electric-Blue-Flowers_10.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is most similar to a blue chrysanthemum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mqjx8.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;a href=&quot;http://john-hallett.co.uk/2013/04/04/blue-crysanthemum/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://john-hallett.co.uk/2013/04/04/blue-crysanthemum/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2W2UH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;as listed above for images&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Chrysanthemum&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Chrysanthemum&lt;/a&gt; (pink image)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.mums.org/chrysanthemum-classes/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.mums.org/chrysanthemum-classes/&lt;/a&gt; &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11631" LastEditorUserId="11631" LastEditDate="2015-02-07T22:59:01.113" LastActivityDate="2015-02-07T22:59:01.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28418" PostTypeId="2" ParentId="28408" CreationDate="2015-02-07T23:55:16.307" Score="1" Body="&lt;p&gt;Amylase is an enzyme that breaks down starches to simpler sugars. Only living organisms can produce amylase. Animals produce only alpha-amylase. Plants, bacteria, and fungi produce both beta- and alpha- amylases. Like all proteins, the presence of amylase in food depends on if it is permanently denatured by high enough temperatures or extremes in pH. Interestingly, amylases can be classified into high/intermediate/low thermostability groups, depending on whether they become inactivated at a certain temperature. Taking this into consideration, saliva would definitely have alpha-amylase. Bread and biscuits may have alpha or beta amylase (depending on baking temperatures/pH, if amylase was added at all, and if it comes from a grain). Of the rest of your list, banana, corn, milk, and sweet potato would have amylase. Honey (not listed) would also have it. Tomato seems to amylase activity as well. For ketchup, it seems to be an added ingredient to speed processing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.gmo-compass.org/eng/database/enzymes/80.amylase.html&quot; rel=&quot;nofollow&quot;&gt;http://www.gmo-compass.org/eng/database/enzymes/80.amylase.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.lallemand.com/BakerYeastNA/eng/PDFs/LBU%20PDF%20FILES/2_7SOFT.PDF&quot; rel=&quot;nofollow&quot;&gt;http://www.lallemand.com/BakerYeastNA/eng/PDFs/LBU%20PDF%20FILES/2_7SOFT.PDF&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ehow.com/info_12013063_plants-contain-amylase.html&quot; rel=&quot;nofollow&quot;&gt;http://www.ehow.com/info_12013063_plants-contain-amylase.html&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ajofai.info/Abstract/Detection%20of%20amylase%20activity%20from%20vegetables%20and%20fruit%20in%20an%20undergraduate%20classroom.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.ajofai.info/Abstract/Detection%20of%20amylase%20activity%20from%20vegetables%20and%20fruit%20in%20an%20undergraduate%20classroom.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11631" LastEditorUserId="11631" LastEditDate="2015-02-09T23:34:03.513" LastActivityDate="2015-02-09T23:34:03.513" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28419" PostTypeId="2" ParentId="28263" CreationDate="2015-02-08T00:48:47.590" Score="4" Body="&lt;p&gt;According to the &lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/bags-under-eyes/basics/causes/con-20034185&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mayo Clinic website&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;As you age, the tissue structures and muscles supporting your eyelids weaken. The skin may start to sag, and fat that is normally confined to the area around the eye (orbit) can move into the area below your eyes. Also, the space below your eyes can accumulate fluid, making the under-eye area appear puffy or swollen. Several factors can lead to this, including:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Fluid retention due to changes in weather (for example, hot, humid days)&lt;/li&gt;&#xA;&lt;li&gt;hormone levels or eating salty foods&lt;/li&gt;&#xA;&lt;li&gt;Not getting enough sleep&lt;/li&gt;&#xA;&lt;li&gt;Allergies or dermatitis, especially if puffiness is accompanied by redness and itching&lt;/li&gt;&#xA;&lt;li&gt;Heredity — under-eye bags can run in families&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Of the list above, the most common reason is likely heredity.&lt;/p&gt;&#xA;&lt;p&gt;Sources:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mayo Clinic, as linked above&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.allaboutvision.com/cosmetic/puffy-eyes.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.allaboutvision.com/cosmetic/puffy-eyes.htm&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11631" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-08T00:48:47.590" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28420" PostTypeId="1" CreationDate="2015-02-08T02:08:40.043" Score="5" ViewCount="4838" Body="&lt;p&gt;I understand that an enzyme lowers the activation energy, allowing the reaction to run faster, however I am not sure, how it may be favorable during the addition of heat energy. Wouldn't that lower the activity of the enzyme since the enzyme is sensitive to heat?&lt;/p&gt;&#xA;" OwnerUserId="12876" LastActivityDate="2015-02-11T17:42:05.567" Title="What advantage does an enzyme serve over catalysis by the addition of heat energy?" Tags="&lt;cell-biology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28421" PostTypeId="1" CreationDate="2015-02-08T02:09:52.590" Score="6" ViewCount="12701" Body="&lt;p&gt;&lt;a href=&quot;http://mentalfloss.com/article/56805/16-fun-facts-about-tortoises&quot;&gt;This post at Mental Floss&lt;/a&gt; stated that a group of tortoises is called a 'Creep'. I had never heard of that before, and in trying to find the references for the name, I was surprised that I couldn't actually find anything.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia showed no results in either of their lists for animal names.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_animal_names&quot;&gt;http://en.wikipedia.org/wiki/List_of_animal_names&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_English_terms_of_venery,_by_animal&quot;&gt;http://en.wikipedia.org/wiki/List_of_English_terms_of_venery,_by_animal&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Neither did the Northern Prairie Wildlife Research Center: &lt;a href=&quot;http://www.npwrc.usgs.gov/about/faqs/animals/names.htm&quot;&gt;http://www.npwrc.usgs.gov/about/faqs/animals/names.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The closest I found was that a group of turtles is called a nest or a bale.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there an actual source for what a group of tortoises is called?&lt;/p&gt;&#xA;" OwnerUserId="13381" LastActivityDate="2017-01-09T11:19:16.040" Title="What is a group of tortoises called?" Tags="&lt;zoology&gt;&lt;classification&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28422" PostTypeId="1" AcceptedAnswerId="28425" CreationDate="2015-02-08T02:48:18.527" Score="3" ViewCount="95" Body="&lt;p&gt;My wife came across this youtube clip of a spider and a &lt;a href=&quot;http://youtu.be/4E5vUUtSWT4&quot; rel=&quot;nofollow&quot;&gt;worm&lt;/a&gt;. Can anyone identify at least the phylum? &lt;/p&gt;&#xA;" OwnerUserId="9906" LastActivityDate="2015-02-08T09:33:59.407" Title="Can anyone identify the worm in this video clip?" Tags="&lt;zoology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28423" PostTypeId="1" CreationDate="2015-02-08T02:51:55.583" Score="5" ViewCount="664" Body="&lt;p&gt;I'm confused on what a triglyceride is, from what my text book it says its a type of gylercide, then from a website it said &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Glycerides can be subdivided into two categories. The first group, the neutral glycerides are nonionic and nonpolar. The second group, the phosphoglycerides contain a polar region, the phosphoryl group. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Which makes triglyceride not a directly under a glyceride but under one of these groups. Then it says&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Esterification may occur at one, two or all three positions producing monoglycerides (monoacylglycerols), diglycerides (diacylglycerols), or triglycerides (triacylglycerols). The most prevalent and most important are the triglycerides.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So does that mean that triglyceride can be produced by either of the two groups &lt;strong&gt;phosphoglycerides&lt;/strong&gt; and &lt;strong&gt;neutral glycerides&lt;/strong&gt;. And if that's correct then how are monoglycerides and diglycerides produced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.chem.latech.edu/~deddy/chem121/Lipids.htm/&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="13071" LastActivityDate="2015-02-11T14:57:52.517" Title="What is a triglyceride?" Tags="&lt;biochemistry&gt;&lt;homework&gt;&lt;lipids&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28424" PostTypeId="1" AcceptedAnswerId="28427" CreationDate="2015-02-08T03:34:09.727" Score="11" ViewCount="5915" Body="&lt;p&gt;For most of the cell lines I've come across, ATCC recommends storing them in the vapor phase of liquid nitrogen. I'm taking that to mean any place above the level of liquid in the nitrogen storage tank. What is the reason for this? Under what conditions/requirements would one store cells/tissue submerged in liquid?&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2015-08-19T07:56:46.090" Title="Why are cell lines frozen in vapor phase?" Tags="&lt;lab-techniques&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28425" PostTypeId="2" ParentId="28422" CreationDate="2015-02-08T03:40:23.267" Score="3" Body="&lt;p&gt;I think it's a Gordian worm or more accurately known as &lt;em&gt;Spinochordodes tellinii&lt;/em&gt; . Good music for a parasitic event like that by the way. Nematomorpha is the phylum. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/f7hMq.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your a molecular guy, check out &lt;em&gt;Spinochordodes tellinii&lt;/em&gt; and the WNT pathway, pretty cool stuff.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2015-02-08T09:33:59.407" LastActivityDate="2015-02-08T09:33:59.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28426" PostTypeId="2" ParentId="28421" CreationDate="2015-02-08T05:47:56.837" Score="4" Body="&lt;p&gt;What I found was that creep is a collective noun. The professor &lt;a href=&quot;http://en.wikipedia.org/wiki/Peter_Trudgill&quot; rel=&quot;nofollow&quot;&gt;Peter Trudgill&lt;/a&gt; uses the word in a chapter about collective nouns and the example is of tortoises. I don't know what book to tell you to look in though. He is professor of sociolinguistics. From a search on &lt;a href=&quot;http://www.thealmightyguru.com/Pointless/AnimalGroups.html&quot; rel=&quot;nofollow&quot;&gt;collective nouns&lt;/a&gt; for animals, turtles, and reptiles, I only found turtles having the following collective nouns: bale, nest, turn, dole.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My guess is then that Peter Trudgill made up the word and some people have adopted it or it is primarily an English (England) word.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.collectivenouns.biz/list-of-collective-nouns/collective-nouns-animals/&quot; rel=&quot;nofollow&quot;&gt;collective noun list two&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I believe I found the source. In Geology, a creep is defined as a slow moving mass. By borrowing the word creep from Geology, one can accurately describe a group of tortoises.&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.onegeology.org/extra/kids/earthprocesses/creep.html&quot; rel=&quot;nofollow&quot;&gt;Creep&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-02-11T04:33:18.443" LastActivityDate="2015-02-11T04:33:18.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28427" PostTypeId="2" ParentId="28424" CreationDate="2015-02-08T10:21:36.570" Score="12" Body="&lt;p&gt;The storage itself can be done both in the liquid and also in the vapor phase in the liquid nitrogen. Both have their advantages and disadvantages. In my experience there are two main reasons why storage in the vapor phase (although there may be temperature fluctuations when the nitrogen gets low) is recommended. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, you avoid cross contaminations of your cells lines with mycoplasma (and possible other contaminants) which can get transferred into the liquid nitrogen phase and then into your other cultures. This is not a theoretical danger, but pretty real. See the papers in the reference below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then liquid nitrogen will enter your cryotubes (which is also the cause for contaminations). If you use tubes which are not explicitly made for this kind of storage (which is not a problem for the vapor phase storage) then the liquid nitrogen which made it into the tube will expand upon thawing and can cause your tube to explode. This can cause injuries. For more details see &lt;a href=&quot;http://www.sigmaaldrich.com/technical-documents/protocols/biology/cryopreservation-and.html&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://opsdiagnostics.com/notes/ranpri/rpcryoprescell.htm&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19561041/&quot;&gt;Risk of contamination of germplasm during cryopreservation and&#xA;cryobanking in IVF units.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0011224003000208&quot;&gt;Microbial contamination of embryos and semen during long term&#xA;banking in liquid nitrogen&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-02-08T10:21:36.570" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28429" PostTypeId="2" ParentId="28420" CreationDate="2015-02-08T10:28:15.520" Score="3" Body="&lt;p&gt;The enzyme does only one thing: It lowers the activation energy which is necessary for the specific reaction to happen. It does not change the speed of the reaction, nor does it change the rection enthalpy or the quilibrium of the reaction. See the figure for clarification (from &lt;a href=&quot;http://www.uic.edu/classes/bios/bios100/lectures/enzymes.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KQSgM.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Without the enzyme the Ea (activation energy) would be so high, that the reaction would be possible in the cell. Either because this high amount of energy is not available or because the amount of energy would destroy the cell or the reaction. So the lowering of Ea allows this specific reaction to take place.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-02-08T10:28:15.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28430" PostTypeId="1" AcceptedAnswerId="28438" CreationDate="2015-02-08T11:58:11.470" Score="4" ViewCount="568" Body="&lt;p&gt;I searched the web but cannot find an answer for my question. Has the genome size of &lt;em&gt;Crocus sativus&lt;/em&gt; been determined?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="6307" LastEditDate="2017-04-03T02:37:03.813" LastActivityDate="2017-04-03T02:37:03.813" Title="What is the genome size of Saffron (Crocus sativus)?" Tags="&lt;botany&gt;&lt;genomes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28431" PostTypeId="1" CreationDate="2015-02-08T12:24:52.827" Score="2" ViewCount="12199" Body="&lt;p&gt;I have a rough idea: endotherms need more food to keep their temperature stable whilst ectotherms use less of their food in respiration.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;but that's just me parroting the textbook I don't really understand it. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Could someone help out? Thank you.&lt;/p&gt;&#xA;" OwnerUserId="13384" LastEditorUserId="16866" LastEditDate="2017-04-03T17:38:34.230" LastActivityDate="2017-04-03T17:38:34.230" Title="Why do endotherms need more food than ectotherms?" Tags="&lt;food&gt;&lt;temperature&gt;&lt;homeostasis&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28433" PostTypeId="1" CreationDate="2015-02-08T13:42:11.660" Score="3" ViewCount="273" Body="&lt;p&gt;Through what mechanisms does estrogen interact with collagen synthesis? Especially in the context of elevated estrogen levels and genesis of purpura simplex .&lt;/p&gt;&#xA;" OwnerUserId="13387" LastEditorUserId="11841" LastEditDate="2015-02-08T15:25:54.190" LastActivityDate="2015-02-09T05:16:01.970" Title="How does estrogen influence collagen synthesis?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;endocrinology&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28434" PostTypeId="1" AcceptedAnswerId="28441" CreationDate="2015-02-08T13:45:50.447" Score="5" ViewCount="119" Body="&lt;p&gt;What is overdiagnosis ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have searched this &lt;a href=&quot;http://en.wikipedia.org/wiki/Overdiagnosis&quot; rel=&quot;noreferrer&quot;&gt;Wiki result&lt;/a&gt; but didn't understood at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you please explain the first two line of Wikipedia :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Overdiagnosis is the diagnosis of &quot;disease&quot; that will never cause symptoms or death during a patient's lifetime. Overdiagnosis is a side effect of screening for early forms of disease.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;What is over treatment ?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are overdiagnosis and over treatment same or different ?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="13366" LastActivityDate="2015-02-09T01:44:25.437" Title="What is overdiagnosis?" Tags="&lt;human-biology&gt;&lt;pathology&gt;&lt;medicine&gt;&lt;treatment&gt;&lt;clinical-trial&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28435" PostTypeId="2" ParentId="28434" CreationDate="2015-02-08T15:24:49.503" Score="2" Body="&lt;p&gt;Screening is the process of testing the population enmasse to check for the presence of risk factors for a disease or to detect the early form of a disease.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Usually the tests that are used in screening are not highly effective in excluding people who do not have the disease (low &lt;a href=&quot;http://en.wikipedia.org/wiki/Positive_and_negative_predictive_values&quot; rel=&quot;nofollow&quot;&gt;negative predictive value&lt;/a&gt;). Instead the goal of screening is to identify as many people as possible (high &lt;a href=&quot;http://en.wikipedia.org/wiki/Positive_and_negative_predictive_values&quot; rel=&quot;nofollow&quot;&gt;positive predictive value&lt;/a&gt;) who may have &quot;the disease&quot; which is being screened.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When screening for early form of disease, people who may never develop the disease in their lifetimes are also detected and they may be treated without the actual need. In such cases the treatment will result in more harm than the disease itself.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Usually after screening, people who are recognised to have the risk factors are subjected to further confirmatory tests which will then exclude the people who do not have the disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overdiagnosis is said to be done when a lot of people who don't have the disease at the present time are treated for the disease just because they have the risk factors for getting the disease or have the early form.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overtreatment is not the same as overdiagnosis. Overtreatment refers to treating a disease more vigorously than warranted. The main difference is that in overtreatment, the treatment is provided for even correctly diagnosed disease but excessively. This may include unneeded medical procedures, injections etc...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example getting antibiotics for a common cold (with just running nose) which has lasted for less than one week may be considered overtreatment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overdiagnosis may lead to overtreatment. However all overtreatment is not due to overdiagnosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&#xA;I have edited the answer thanks to anongoodnurse. &lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-02-09T01:44:25.437" LastActivityDate="2015-02-09T01:44:25.437" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28436" PostTypeId="2" ParentId="28431" CreationDate="2015-02-08T15:46:55.237" Score="2" Body="&lt;p&gt;Endotherms also called warm blooded animals have the ability to regulate their body temperature by themselves. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;If the endotherms are in a cold place their body increases the metabolism and generates more heat. This will compensate for the cold outside. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In a hot region the body metabolism is tuned down (this is not as efficient as the adaptation to cold region - as the metabolism can't be turned down below a certain limit - this will result in death) a little and heat generation is somewhat reduced. The second and more efficient mechanism is the heat dissipation by sweating and through skin (directly).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Ectotherms on the other hand, do not have efficient temperature regulation systems. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;In warm regions when the temperature is high, the ectotherms seek shade and low-temperature areas to prevent over-heating&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In cool regions they seek sunlight and expose themselves to the sunlight for warmth. For the same reason, they can also search out and stay near fire pits, campfires etc...&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So when we calculate the energy demands, the ectotherms need more energy as they regulate their own metabolisms to match the need. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The increase in need for energy in hot condition maybe due to:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The extra-processes that are regulated like sweating, increased peripheral vasodilation - thereby increasing circulatory rate (increased work for heart)&lt;/li&gt;&#xA;&lt;li&gt;This thermo-regulation inturn affects other processes and systems like electrolyte and water balance, excretory system, endocrine system, thrist, etc...&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;During the cold season increased metabolism itself is the main cause for increased need for energy.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-02-08T15:46:55.237" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28437" PostTypeId="2" ParentId="28423" CreationDate="2015-02-08T16:24:32.760" Score="4" Body="&lt;p&gt;The following answer was giving by &lt;a href=&quot;https://chemistry.stackexchange.com/users/7499/michael-d-m-dryden&quot;&gt;Michael D. Dryden&lt;/a&gt; from &lt;a href=&quot;https://chemistry.stackexchange.com/questions/24797/what-is-a-triglyceride/24799#24799&quot;&gt;https://chemistry.stackexchange.com/questions/24797/what-is-a-triglyceride/24799#24799&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is some minor argument as far as nomenclature goes for these lipids. Most sources I can find, including &lt;a href=&quot;http://goldbook.iupac.org/G02647.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;IUPAC&lt;/a&gt; have glycerides as only including esters of glycerol with fatty acids. Monoglycerides have a single fatty acid ester with two free OH groups, diglycerides have two fatty acid esters, and triglycerides have three. Phosphoglycerides are &lt;a href=&quot;http://goldbook.iupac.org/P04558.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;defined&lt;/a&gt; separately as esterified derivatives of phosphatidic acids, so you can think of them like glycerides where for one of the substituents, instead of a fatty acid, some derivative of phosphoric acid is present. However, the way the two terms are defined, they don't encompass any common molecules, i.e. there are no molecules that are both glycerides and phosphoglicerides and neither group is a subset of the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So: mono-, di-, and triglycerides are subsets of glycerides while phosphoglycerides are a different group altogether, though structurally similar.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="-1" LastEditDate="2017-04-13T12:57:01.693" LastActivityDate="2015-02-08T16:24:32.760" CommentCount="0" CommunityOwnedDate="2015-02-08T16:24:32.760" ContentLicense="CC BY-SA 3.0" />
  <row Id="28438" PostTypeId="2" ParentId="28430" CreationDate="2015-02-08T16:25:28.907" Score="6" Body="&lt;p&gt;Neither NCBI nor Ensembl have a genome project listed for any crocus species, although individual ethidium bromide stained nuclei have been analyzed by flow cytometry, &lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00985356&quot; rel=&quot;nofollow noreferrer&quot;&gt;revealing approximately 11.4 pg of DNA per nucleus&lt;/a&gt; (warning, pay wall). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;C. sativus&lt;/em&gt; is triploid, giving it a &lt;a href=&quot;http://en.wikipedia.org/wiki/C-value&quot; rel=&quot;nofollow noreferrer&quot;&gt;C-value&lt;/a&gt; of 3.8 pg which works out to a haploid genetic content of about 3.45 Gbp.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(full credit to &lt;a href=&quot;https://biology.stackexchange.com/users/6307/canadianer&quot;&gt;canadianer&lt;/a&gt; for finding the Brandizzi paper)&lt;/p&gt;&#xA;" OwnerUserId="13093" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-02-08T23:04:40.167" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28439" PostTypeId="1" CreationDate="2015-02-08T17:36:30.370" Score="3" ViewCount="55" Body="&lt;p&gt;Upon EGF binding, EGFR units dimerize and cross-phosphorylate. The phosphate groups are transfered to intracellular c-terminal tyrosine rich regions. Where do the phosphate units come from in this cross-reaction? Is it from bound GTP units?&lt;/p&gt;&#xA;" OwnerUserId="4971" LastEditorUserId="948" LastEditDate="2015-02-09T02:26:11.463" LastActivityDate="2015-02-09T02:26:11.463" Title="Where do the phosphate units come from when EGF units dimerize?" Tags="&lt;receptor&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28440" PostTypeId="2" ParentId="28420" CreationDate="2015-02-08T18:27:43.160" Score="5" Body="&lt;p&gt;Enzymes have two benefits over raising the temperature:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, reducing the activation energy by reusable enzymes is far more energy-efficient, apart from the fact that the required temperature would vary for different reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, enzymes are able to be controlled by allosteric mechanisms, which facilitates metabolic control by feedback loops, feedforward motivs and receptor-mediated processes. In the example of glycolysis this enables the cell to fine-control its supply with energy equivalents (see figure from &lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Glycolysis_regul_muscle.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikimedia Commons&lt;/a&gt; below). This mechanism may be the most important function of enzymes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7n6TQ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;William C. Plaxton: &lt;a href=&quot;http://media.johnwiley.com.au/product_data/excerpt/0X/04714109/047141090X.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Principles of Metabolic Control&lt;/a&gt;. In Kenneth B. Storey (ed.): Functional Metabolism: Regulation and Adaptation, John Wiley &amp;amp; Sons, Inc. 2004&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3865" LastActivityDate="2015-02-08T18:27:43.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28441" PostTypeId="2" ParentId="28434" CreationDate="2015-02-09T00:23:53.787" Score="7" Body="&lt;p&gt;Overdiagnosis and overtreatment are intertwined. There is debate about how to best describe the problem, but narrowly defined, &lt;em&gt;overdiagnosis&lt;/em&gt; occurs when increasingly sensitive tests - or changing definitions - identify abnormalities that are minor, non-progressive, or likely to resolve on their own, and that, if left untreated, will not cause symptoms or shorten an individual's life. Having a &lt;strong&gt;diagnosis&lt;/strong&gt; makes well-persons think &lt;em&gt;they're ill&lt;/em&gt; (overdiagnosis). If they are then treated for this &lt;strong&gt;diagnosis&lt;/strong&gt;, they are &lt;strong&gt;overtreated.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example involving changing definitions pertains to diabetes. When the official definition of &lt;em&gt;diabetes&lt;/em&gt; changed from having a fasting blood sugar (FBS) of &quot;X&quot; or greater to an FBS of &quot;X-y&quot; or greater, 1.6 million new diabetics were instantly &lt;em&gt;diagnosed&lt;/em&gt;, &lt;em&gt;some of whom&lt;/em&gt; are not likely to develop symptoms and complications and are not likely to benefit from treatment. This is &lt;em&gt;overdiagnosis&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If one goes on to put such a patient (let's say, on the lower end, &quot;X-y+1&quot; on a blood sugar (BS) lowering agent, and they pass out because their BS drops too low, then they are &lt;em&gt;overtreated&lt;/em&gt;. If they happened to be driving when they pass out, and get into a fatal accident, they literally die from overtreatment, &lt;em&gt;if it can't be shown that they would have suffered from a marginally elevated FBS.&lt;/em&gt; (If it can be shown to be dangerous to have an FBS of X-y+1, then this is a risk of &lt;em&gt;treatment&lt;/em&gt;, not &lt;em&gt;overtreatment&lt;/em&gt;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an example of increased sensitivity of tests, say a new test is available, a blood test called a &quot;D-dimer&quot;, which will reveal with 100% accuracy the presence of a dangerous pulmonary embolism (it's &lt;em&gt;very sensitive&lt;/em&gt;). However, it is also known to be positive when there is no pulmonary embolism as well, but it's not known how often (so it's &lt;em&gt;not specific&lt;/em&gt;). But it's an exciting new test! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A patient goes into the Emergency room for &lt;em&gt;one&lt;/em&gt; of the following: atypical chest pain, dizziness, shortness of breath, leg pain consistent with a blood clot in the calf, or loss of consciousness. In addition to an EKG, chest x-ray (CXR) and a few other tests, a &lt;em&gt;D-dimer&lt;/em&gt; is ordered. The EKG, CXR and other tests are negative, but the D-Dimer is positive. The tentative diagnosis is pulmonary embolism (PE).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the D-dimer indicates that a dangerous condition &lt;em&gt;may be present&lt;/em&gt;, a spiral CAT Scan with contrast is ordered on all those people. Some will have a life-threatening PE (appropriately diagnosed*). A large number will have a negative CAT Scan. (&lt;em&gt;diagnosis excluded&lt;/em&gt;) But a significant number will have a very small PE. Because this is relatively new and surprising, and it's not known whether they should be treated (maybe nothing will happen if they don't treat? Maybe this happens in normal people and we just never knew it?), the doctors, who are accustomed to treating &lt;strong&gt;all PE's&lt;/strong&gt; will put the patients on blood thinners. This is &lt;strong&gt;overdiagnosis&lt;/strong&gt; of PE, and treating it is &lt;strong&gt;overtreatment&lt;/strong&gt;, because some treated people will have &quot;bleeds&quot; - a stroke, GI bleeding, other. It is now known that these tiny PE's are often seen in patients who suffer &lt;em&gt;no harm at all&lt;/em&gt; from them, therefore in order to stem &lt;em&gt;overdiagnosis&lt;/em&gt; (and subsequent &lt;em&gt;overtreatment&lt;/em&gt;), the D-dimer test is ordered less frequently.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...[We] are in the midst of an &lt;strong&gt;epidemic of diagnosis&lt;/strong&gt;. Conventional wisdom tells us that finding problems early saves lives because we have the opportunity to fix the problems early. [Conventional wisdom tells us that} There is no risk in finding things early. The truth is that early diagnosis is a double-edged sword; while it has the potential to help some, it has a potential to harm us. Such &lt;strong&gt;overdiagnosis&lt;/strong&gt; leads to &lt;strong&gt;overtreatment&lt;/strong&gt; when these “pseudo-diseases” are conventionally managed and treated as if they were real abnormalities; because these findings have a benign prognosis, treatment can only do harm. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://books.google.com/books?hl=en&amp;amp;lr=&amp;amp;id=qe7XQxzAftEC&amp;amp;oi=fnd&amp;amp;pg=PT5&amp;amp;dq=Welch+G,+Schwartz+L,+Woloshin+S+%282011%29+Overdiagnosed:&amp;amp;ots=GONGUjZ8HY&amp;amp;sig=CQy031VkHIqGxgM8Sg0vnQOCB_A#v=onepage&amp;amp;q&amp;amp;f=false&quot;&gt;Overdiagnosed: Making People Sick in the Pursuit of Health&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.sciencebasedmedicine.org/overdiagnosis/&quot;&gt;Overdiagnosis&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1001655#pmed.1001655-Welch1&quot;&gt;Using Evidence to Combat Overdiagnosis and Overtreatment: Evaluating Treatments, Tests, and Disease Definitions in the Time of Too Much&lt;/a&gt;&lt;/sub&gt;   &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-02-09T00:23:53.787" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28444" PostTypeId="2" ParentId="28439" CreationDate="2015-02-09T01:20:28.420" Score="1" Body="&lt;p&gt;In protein &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphorylation&quot; rel=&quot;nofollow&quot;&gt;phosphorylation&lt;/a&gt;, the phosphate group transferred from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Kinase&quot; rel=&quot;nofollow&quot;&gt;kinase&lt;/a&gt; to the substrate comes almost universally from &lt;a href=&quot;http://en.wikipedia.org/wiki/Adenosine_triphosphate&quot; rel=&quot;nofollow&quot;&gt;ATP&lt;/a&gt;. However, there is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19857459&quot; rel=&quot;nofollow&quot;&gt;evidence&lt;/a&gt; of some protein kinases using GTP as their phosphate source, although they are few and far between.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-02-09T01:20:28.420" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28445" PostTypeId="1" CreationDate="2015-02-09T01:23:02.303" Score="4" ViewCount="108" Body="&lt;p&gt;I'm reading a paper that mentioned the elimination of senescent cells delays aging. I'd like to receive more information about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Baker study published in Nature demonstrates that targeted elimination of senescent cells in mice results in remarkable protection from several age-related pathologies, cancer, and makes cancer cells resistant to chemotherapy. I know that senescent cells drive aging, and induce cancer. Can we grow them in cell culture as a kind of stem cells ? How might they contribute to the aging process ?&lt;/p&gt;&#xA;" OwnerUserId="12990" LastEditorUserId="12877" LastEditDate="2015-02-09T19:46:03.210" LastActivityDate="2015-02-09T19:46:03.210" Title="What are senescent cells doing in our bodies?" Tags="&lt;genetics&gt;&lt;cell-biology&gt;&lt;senescence&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="2" ClosedDate="2015-02-09T04:49:33.947" ContentLicense="CC BY-SA 3.0" />
  <row Id="28446" PostTypeId="2" ParentId="28431" CreationDate="2015-02-09T01:28:48.737" Score="2" Body="&lt;p&gt;An ectotherm is an [cold-blooded] organism which is dependent on external sources of body heat. They do not need to regularly consume food to warm their bodies. As a result, they can subsist on lower metabolic rates and varying internal temperatures (poikilothermy). However, physical activity is restricted to certain hours (night) and or habitats; ectotherms tend to be rapidly exhausted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An endotherm is an [warm-blooded] organism which is dependent on the interal generation of heat. To maintain consistent temperatures (homeothermy), they must regularly consume food for metabolism. This also allows for a greater work capacity than ectotherms. Physical activity is not limited to certain hours and or habitats. &lt;/p&gt;&#xA;" OwnerUserId="10132" LastActivityDate="2015-02-09T01:28:48.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28447" PostTypeId="2" ParentId="28445" CreationDate="2015-02-09T01:36:36.387" Score="-2" Body="&lt;p&gt;Senescent cells are cells that go into permanent cell cycle arrest. Although they may be metabolically active, they are not actively dividing. This may occur when cells in our bodies undergo damage from an extraneous or endogenous source. I understand that its role in cancer and aging is a great topic of study. &lt;/p&gt;&#xA;" OwnerUserId="12876" LastActivityDate="2015-02-09T01:36:36.387" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28449" PostTypeId="1" CreationDate="2015-02-09T13:23:03.857" Score="2" ViewCount="80" Body="&lt;p&gt;We have sequenced the genome of 200 bacterial strains belonging to the same species, a swine bacterial pathogen. In a previous work, it was observed that a protein family of adhesins is present in some of these strains. Each strain has multiple copies separated in their genome. Genetic differences have been observed among the DNA sequence in the different strains. Since some mobile genetic elements are present near these genes, it is possible that they are playing a role in the molecular evolution of this protein family.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How could I add additional evidences that this is a putative genomic island?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some references would be also appreciated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE: For each strain, I thought about extracting the genomic region were these genes are located, maybe 8 Kb up- and down-stream of the gene. Then, running a miriad of tools to try to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20395967&quot; rel=&quot;nofollow&quot;&gt;predict&lt;/a&gt; some of these island-associated elements. However, assuming that these &quot;sequence-based&quot; tools need the entire genome sequence, is it possible that I run them using the whole genome sequence and then focus on certain selected genomic regions?&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="3340" LastEditDate="2015-02-10T05:12:03.997" LastActivityDate="2015-09-19T18:45:15.863" Title="How to characterise a protein family in a putative genome island?" Tags="&lt;bioinformatics&gt;&lt;bacteriology&gt;&lt;protein-evolution&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28450" PostTypeId="1" CreationDate="2015-02-09T14:07:09.087" Score="2" ViewCount="118" Body="&lt;p&gt;I am very new at this. I am wondering why fed batch cultures produce a lot of mycelia but no fruit. I thought the more mycelia you had, the greater chance of it forming a fruit body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am refering to this paper &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3768415/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3768415/&lt;/a&gt; but there are many others with the same methodology. It seems to oppose fruit  body production to submerged cultures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to be submerged in water and in sugar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also seems you can have fruit bodies with a single mating type :&#xA;- Coprinus sterquilinus (The Fungi by Sharma)&#xA;- A bisporus and V volvacea (Chang Chiu)&lt;/p&gt;&#xA;" OwnerUserId="13393" LastEditorUserId="13393" LastEditDate="2015-02-10T10:26:12.007" LastActivityDate="2015-02-10T10:26:12.007" Title="Why can't there be fructification of mycelium in submerged culture?" Tags="&lt;mycology&gt;&lt;sex&gt;&lt;fermentation&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28451" PostTypeId="1" AcceptedAnswerId="28458" CreationDate="2015-02-09T14:35:04.137" Score="10" ViewCount="1846" Body="&lt;p&gt;Why aren't green eyes more prevalent, given that the green allele is dominant over the blue one?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding is that human eye colour is determined by two genes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) HERC2, with alleles Bx, BB or xx,&lt;br&gt;&#xA;2) gey, with alleles GG, Gb or bb,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;B means brown&lt;/li&gt;&#xA;&lt;li&gt;x means not brown (this is less confusing than using b for blue here, because having no B allele in HERC2 doesn't necessarily give someone blue eyes; their eyes will be either blue or green depending on the gey gene)&lt;/li&gt;&#xA;&lt;li&gt;G means green&lt;/li&gt;&#xA;&lt;li&gt;b means blue.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Capital letters stand for alleles that are dominant; lower case, ones that are recessive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the 'algorithm' goes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1) look at HERC2; if it's anything other than xx, you've got BROWN eyes&lt;/li&gt;&#xA;&lt;li&gt;2) if HERC2 is xx, look at gey; if it's anything other than bb, you've got GREEN eyes&lt;/li&gt;&#xA;&lt;li&gt;3) still here? then you've got BLUE eyes&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My question is this: why is it that green eyes are so rare if the green allele is dominant over the blue one? When a blue-eyed person and a green-eyed person interbreed, their offspring will either be equally likely to have green eyes as blue (if the green-eyed parent is Gb) or always have green (if that parent is GG).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But many more people have blue eyes than green eyes, despite blue being recessive to green.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The obvious answer is that people with blue eyes (xx bb) and people with green eyes (other xx-ers) have tended to avoid breeding with each other to a large extent. Is any other explanation in the ring? Perhaps the greens are catching up?&lt;/p&gt;&#xA;" OwnerUserId="13394" LastEditorUserId="13394" LastEditDate="2015-02-09T15:10:52.387" LastActivityDate="2017-02-22T18:40:53.643" Title="Why aren't green eyes more prevalent?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28452" PostTypeId="1" AcceptedAnswerId="28480" CreationDate="2015-02-09T15:13:06.357" Score="17" ViewCount="58878" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Valonia_ventricosa&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Valonia ventricosa&lt;/em&gt;&lt;/a&gt; are single-celled algae that range between one and few centimetres. In rare cases, they can reach sizes exceeding 5cm. They range from grass-green to dark green, and some are even a blackish colour.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PRTcqm.jpg&quot; alt=&quot;Picture of large speherical Valonia ventricosa.&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Weirdly, a lot of the literature covering these organisms seems to be pre-1950. &lt;a href=&quot;http://www.leeds.ac.uk/heritage/Astbury/bibliography/Astbury_and_Preston_1937.pdf&quot; rel=&quot;noreferrer&quot;&gt;This X-ray crystallography project in 1937&lt;/a&gt; identified key structures in the cell wall of &lt;em&gt;V. ventricosa&lt;/em&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;It is found to consist of layers in which the cellulose chains in any&#xA;one layer are inclined to those in the preceding and subsequent layers&#xA;at an angle which is on the average rather less than a right angle.&lt;/p&gt;&#xA;&lt;p&gt;The two sets of striations on the layers of the wall correspond closely to the&#xA;meridian and spiral directions of cellulose chains, while the&#xA;extinction directions, being defined both by the directions and by the&#xA;relative proportions of the two sets of cellulose chains, lie in&#xA;variable positions between. The development of the rhizoids has been&#xA;investigated and found to be associated with regions of the wall&#xA;adjacent to the poles of the spiral.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Although the authors hesitate to speculate on their function, has any progress in the field suggested the fibres identified in this &lt;a href=&quot;http://www.nature.com/nature/journal/v162/n4121/abs/162665a0.html&quot; rel=&quot;noreferrer&quot;&gt;1948 Nature paper&lt;/a&gt; be involved in sustaining such a massive cell (Figure below)?&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/h3axTm.png&quot; alt=&quot;Fibrous surface of cell.&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;So it seems like the cell wall structure has been categorised long ago. But &lt;strong&gt;what allows these single-celled organisms to get so big?&lt;/strong&gt; Is it the plant-like cell wall, or something else? I was under the impression that cells would burst or collapse well before reaching this size.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-07-26T08:50:01.870" Title="How can Valonia ventricosa cells get so big?" Tags="&lt;cell-biology&gt;&lt;botany&gt;&lt;microbiology&gt;&lt;plant-physiology&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="28454" PostTypeId="2" ParentId="28421" CreationDate="2015-02-09T19:00:07.393" Score="7" Body="&lt;p&gt;Creep is correct. I sent an email asking this question to &lt;a href=&quot;http://www.tortoisegroup.org&quot; rel=&quot;noreferrer&quot;&gt;The Tortoise Group&lt;/a&gt;, which is a non-profit organization whose mission statement is:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Improving the lives of wild and desert tortoises through education.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The Executive Director replied:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;It's a bale for turtles and a creep for tortoises. I am sure they could have come up with a better name!&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;If you have additional questions, there's a wealth of scientific information on their website.&lt;/p&gt;&#xA;" OwnerUserId="13148" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-09T19:06:33.357" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28457" PostTypeId="1" CreationDate="2015-02-09T21:05:45.997" Score="2" ViewCount="204" Body="&lt;p&gt;I'm hoping for some information relating to yeast nutrition (specifically &lt;em&gt;Saccharomyces cerevisea&lt;/em&gt;) in beer fermentation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Zinc is &lt;a href=&quot;http://www.howtobrew.com/section1/chapter6-9-1.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;well-known&lt;/a&gt; to be necessary for yeast cultures to perform successful fermentations and since fermentable sugars derived from barley are often deficient in zinc, they are sometimes fortified with additions of zinc sulfate or zinc chloride. &lt;a href=&quot;http://braukaiser.com/blog/blog/2012/06/22/the-effect-of-zinc-on-fermentation-performance/&quot; rel=&quot;nofollow noreferrer&quot;&gt;This guy&lt;/a&gt; tried zinc gluconate, a readily available dietary supplement for the same purpose, and found it to have very little, if any, positive effect on fermentation performance. As he even suggests at the end of his paper, could this be because yeast can't assimilate Zn from this molecule the same way it does from the other two?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this question better directed towards &lt;a href=&quot;https://chemistry.stackexchange.com/&quot;&gt;Chemistry SE&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance for any help I can get on this.&lt;/p&gt;&#xA;" OwnerUserId="13396" LastEditorUserId="-1" LastEditDate="2017-04-13T12:57:01.693" LastActivityDate="2015-02-09T23:27:17.013" Title="Zinc and brewer's yeast" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;nutrition&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28458" PostTypeId="2" ParentId="28451" CreationDate="2015-02-09T22:03:53.257" Score="12" Body="&lt;p&gt;A gene being dominant does not necessarily imply the gene is also common. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An easy counterexample is &lt;a href=&quot;http://en.wikipedia.org/wiki/Huntington%27s_disease&quot; rel=&quot;nofollow noreferrer&quot;&gt;Huntington's disease&lt;/a&gt;. The gene is dominant, and only one mutant allele of huntingtin would result in development of the disease. However, the allele prevalence of the mutant is low in the general population. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the absence of a selective advantage of green eyes over blue eyes, the two alleles of the &lt;em&gt;gey&lt;/em&gt; gene should remain in &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_equilibrium&quot; rel=&quot;nofollow noreferrer&quot;&gt;genetic equilibrium&lt;/a&gt;, and therefore the number of people with green eyes will not increase. In fact, a similar misunderstanding applies to the &lt;a href=&quot;http://science.howstuffworks.com/life/genetic/redhead-extinction1.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;disappearance of blondes/redheads&lt;/a&gt;. In both cases, the allele frequencies will remain unchanged in the absence of selection pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The initial imbalance in the allele frequency could be due to many reasons. Population bottlenecks, genetic drift, and historical selection pressure could all be valid answers.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="6" LastEditDate="2017-02-22T18:40:53.643" LastActivityDate="2017-02-22T18:40:53.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28461" PostTypeId="1" CreationDate="2015-02-09T23:02:17.050" Score="1" ViewCount="121" Body="&lt;p&gt;I photographed a couple of birds and butterflies in Argentina and tried to identify them. I tried online species identification tools, looked in books, and just tried to find pictures on Google with similar animals. This worked for some of the pictures, but for others I couldn't find the correct species. So as a layman, what options do I have?&lt;/p&gt;&#xA;&lt;p&gt;Here are the ones that I couldn't identify so far&lt;/p&gt;&#xA;&lt;h1&gt;1 (There seems to be a bird and a beetle in this picture. The bird could be a Thraupis Episcopus)&lt;/h1&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4BQnv.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;h1&gt;2 (A hummingbird but which one?)&lt;/h1&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pxKgB.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;h1&gt;3 (Seems to be the same hummingbird)&lt;/h1&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QXEZV.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;h1&gt;4 (No idea)&lt;/h1&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PV3or.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;h1&gt;5 (No idea)&lt;/h1&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cTtmn.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;h1&gt;6 (No idea)&lt;/h1&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/d8kLJ.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;h1&gt;7 (No idea)&lt;/h1&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6KfYF.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;h1&gt;8 (No idea)&lt;/h1&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AmzKQ.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="608" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-10T12:18:15.073" Title="I photographed a couple of butterflies and birds in Argentina but can't identify them. What are my options?" Tags="&lt;entomology&gt;&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="2" CommentCount="3" ClosedDate="2015-02-14T03:08:00.833" ContentLicense="CC BY-SA 3.0" />
  <row Id="28462" PostTypeId="1" CreationDate="2015-02-09T23:17:25.767" Score="1" ViewCount="885" Body="&lt;p&gt;I am currently helping a PhD student in his research lab. We have been using Trypsin for the past couple of weeks but I am unsure of its purpose.&#xA;I was wondering how Trypsin functioned and what it was usually used for?&#xA;The Trypsin we had been using apparently had &quot;gone bad&quot; and therefore we have to start the experiment over again. What could have caused it to not function properly? &lt;/p&gt;&#xA;" OwnerUserId="12900" LastActivityDate="2015-02-09T23:21:11.457" Title="What is Trypsin?" Tags="&lt;cell-biology&gt;&lt;lab-reagents&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2015-02-13T07:15:48.680" ContentLicense="CC BY-SA 3.0" />
  <row Id="28463" PostTypeId="2" ParentId="28462" CreationDate="2015-02-09T23:21:11.457" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Trypsin&quot; rel=&quot;nofollow&quot;&gt;Trypsin&lt;/a&gt; is a protease, an enzyme that cuts other proteins. It is used in cell culture to help lift cells from a plate by cutting the proteins that hold the cells to the plate and to each other. Trypsin can go bad because a trypsin enzyme can cut other trypsins, eventually destroying the batch's enzyme activity. This is why trypsin must be kept frozen. Of course you have to thaw it out to use it, so it's best to split the trypsin stock into small aliquots, so you don't have to thaw out the whole bottle everytime you split your cells.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2015-02-09T23:21:11.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28464" PostTypeId="1" AcceptedAnswerId="30547" CreationDate="2015-02-10T01:42:20.023" Score="5" ViewCount="220" Body="&lt;p&gt;ROR1 is currently under investigation as a therapeutic target for cancer (1). A number of studies show different cancers may have their metastatic potential reduced, or become apoptotic through targeting or abrogation of ROR1 (1-3). ROR1 itself is show to have a number interactions (either through crosstalk or interaction) with some known tumorigenic markers; these include c-Met, PI3K, Akt, Wnt5a, EGF, c-Src (4-7). In terms of metastatic potential, interactions with vimentin, Snail/Slug, cadherins, ß-catenin, and CXCR4/CXCL12 were also identified (1, 8). Some of these are via expression of CREB. In terms of ROR1 is tissue, abnormalities that lead to death were noted in newborn mice that has ROR1 knocked down (9). A notable mechanism for ROR1 in development was in neuroprogenitor cells in which ROR1 regulation status determined whether these cells differentiated into neurons or not (10). It's also found that neural, heart, lung and kidney tissue in adults express some form or another of ROR1 (11). More recent studies suggest ROR1 downmodulation may present toxicity for some subsets of normal tissues (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20702778&quot; rel=&quot;noreferrer&quot;&gt;12&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question, now: Are there any empirical studies that illuminate the potential mechanism of ROR1 in healthy, adult tissues? This is from a treatment toxicity standpoint, since the subsets of affected cells seem to be rather slim. I can understand why the effect on metastatic potential can be significant from the fetal neural cortex development (the need to migrate the neurons into position). We also see a truncated version of ROR1 in some instances. If anyone can shed some light, thank you in advance!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Cui B. et al. Targeting ROR1 inhibits epithelial-mesenchymal transition and metastasis.      Cancer. Res. 73, 3649–3660 (2012).&lt;/li&gt;&#xA;&lt;li&gt;Hojjat-Farsangi, M., Ghaemimanesh, F., Daneshmanesh, A. H., Bayat, A. A., Mahmoudian, J., Jeddi-Tehrani, M., … Mellstedt, H. (2013). Inhibition of the Receptor Tyrosine Kinase ROR1 by Anti-ROR1 Monoclonal Antibodies and siRNA Induced Apoptosis of Melanoma Cells. PLoS ONE, 8. doi:10.1371/journal.pone.0061167&lt;/li&gt;&#xA;&lt;li&gt;Daneshmanesh AH, Hojjat-Farsangi M, Sandin A, Khan AS, Moshfegh A, et al.. (2012) Monoclonal Antibody Against ROR1 In Chronic Lymphocytic Leukemia Cells Induced Apoptosis Via PI3-kinase/AKT/CREB pathway. 54th American Society of hematology (ASH), Atlanta, USA, 8–11 December.&lt;/li&gt;&#xA;&lt;li&gt;T. Yamaguchi, K. Yanagisawa, R. Sugiyama, Y. Hosono, Y. Shimada, C. Arima, S. Kato, S. Tomida, M. Suzuki, H. Osada, T. Takahashi. NKX2-1/TITF1/TTF-1-induced ROR1 is required to sustain EGFR survival signaling in lung adenocarcinoma. Cancer Cell, 21 (2012), pp. 348–361&lt;/li&gt;&#xA;&lt;li&gt;Fukuda T, Chen L, Endo T, Tang L, Lu D, Castro JE, Widhopf GF, II, Rassenti LZ, Cantwell MJ, Prussak CE, et al. Antisera induced by infusions of autologous Ad-CD154-leukemia B cells identify ROR1 as an oncofetal antigen and receptor for Wnt5a. Proc Natl Acad Sci USA. 2008;105:3047–3052. doi: 10.1073/pnas.0712148105.&lt;/li&gt;&#xA;&lt;li&gt;Gentile A, Lazzari L, Benvenuti S, Trusolino L, Comoglio PM. Ror1 is a pseudokinase that is crucial for Met-driven tumorigenesis. Cancer Res 2011;71:3132–41.&lt;/li&gt;&#xA;&lt;li&gt;Zhang S, Chen L, Cui B, Chuang HY, Yu J, Wang-Rodriguez J, et al. ROR1 is expressed in human breast cancer and associated with enhanced tumor-cell growth. PLoS ONE 2012;7:e31127.&lt;/li&gt;&#xA;&lt;li&gt;Teicher BA, Fricker SP. CXCL12 (SDF-1)/CXCR4 pathway in cancer. Clin CancerRes. 2010;16(11):2927-31.&lt;/li&gt;&#xA;&lt;li&gt;Nomi M, Oishi I, Kani S, Suzuki H, Matsuda T, Yoda A, et al. Loss of mRor1 enhances the heart and skeletal abnormalities in mRor2-deficient mice: redundant and pleiotropic functions of mRor1 and mRor2 receptor tyrosine kinases. Mol Cell Biol 2001;21:8329–35.&lt;/li&gt;&#xA;&lt;li&gt;Endo M, Doi R, Nishita M, Minami Y. Ror family receptor tyrosine kinases regulate the maintenance of neural progenitor cells in the developing neocortex. J Cell Sci 2012;125:2017–29.&lt;/li&gt;&#xA;&lt;li&gt;Reddy UR, Phatak S, Pleasure D. Human neural tissues express a truncated Ror1 receptor tyrosine kinase, lacking both extracellular and transmembrane domains. Oncogene 1996;13:1555–9.&lt;/li&gt;&#xA;&lt;li&gt;Linked in text.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-03-18T22:46:18.993" Title="Expression/Mechanism of ROR1 in healthy tissue" Tags="&lt;cell-biology&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28465" PostTypeId="2" ParentId="28243" CreationDate="2015-02-10T01:58:19.940" Score="0" Body="&lt;p&gt;In meiosis, homologous recombination occurs. Two Spo11 proteins utilize tyrosines to induce a double-stranded break in the DNA. &lt;a href=&quot;http://genomebiology.com/2011/12/4/111&quot; rel=&quot;nofollow&quot;&gt;Spo11 has no specific cleavage site&lt;/a&gt;. However, cleavage by Spo11 lead to the discovery of Spo11-Oligonucleotide (Spo11 w/ attached oligonucleotide post-cleavage) complexes which could be mapped to 'hotspots' which the linked study finds a number of discriminating factors to Spo11 cleavage in meiosis:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;From the precise locations of the 2.2 million Spo11-oligonucleotide sequences, Pan et al. [1] showed that local DNA composition also influences Spo11 cleavage sites. As expected from previous studies, Spo11 does not have a specific recognition or cleavage site. However, sequence biases were detected: the 10 to 12 bp surrounding the cleavage site and predicted to be bound directly by Spo11 is relatively AT rich, predicting relatively narrow and deep helix grooves facing the bound Spo11 dimer. Cleavage favors sites immediately 3' of a C and disfavors G in the same position. Also, within a 32-bp core surrounding the Spo11 cleavage sites, a twofold rotational symmetry for complementary dinucleotide composition can be discerned, suggesting separate contributions of the flanking 'half sites' to Spo11 binding and/or cleavage. In addition, cleavage sites are negatively correlated with positioned nucleosomes. Similarly, Spo11 is generally occluded from cleaving sites where transcription factors are bound, even though the binding sites of several different transcription factors positively correlate with hotspot sites.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-02-10T01:58:19.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28467" PostTypeId="1" CreationDate="2015-02-10T04:43:51.187" Score="5" ViewCount="96" Body="&lt;p&gt;I was carrying a can of very cold liquid, had something heavy in my other hand so couldn't switch hands. After a few minutes, I started to feel very intense pain. I was very surprised. cold is just atoms moving slower. This makes more sense if you think about how heat, or burns can cause pain. But heat can cook tissue and disable it, it makes sense it would hurt. &lt;/p&gt;&#xA;" OwnerUserId="9356" LastActivityDate="2015-02-12T08:41:13.417" Title="How and why can cold inflict pain?" Tags="&lt;pain&gt;&lt;heat&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28468" PostTypeId="1" AcceptedAnswerId="40082" CreationDate="2015-02-10T07:04:50.273" Score="11" ViewCount="996" Body="&lt;p&gt;Iodine and related biological iodine-carrying hormones are phylogenetically very old, at least according to Wikipedia. Humans use iodine as a metabolic indicator, as do axolotls and apparently most multicellular life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why? Growth hormones, sex hormones, et cetera don't require strange heavy elements not used for anything else. It's not a requirement of transcription factors that they contain iodine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All I've got for hints is that selenium forms an essential part of deiodinases, as well as forming an essential part of thioredoxin reductase. Thioredoxin is a component used to reduce things around the cell, like thiols and RNA bits and so on and so forth, which I could see being worth the evolutionary cost of running down some selenium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the point of iodine? People have iodine deficiency 'all the time' (it's common enough to be named). Is that a product of agriculture somehow? Are there any advantages to using iodine for metabolic hormones? If there are, what are they? &lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-10-30T04:09:36.253" Title="Why is iodine used for metabolic hormones?" Tags="&lt;evolution&gt;&lt;metabolism&gt;" AnswerCount="3" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28469" PostTypeId="2" ParentId="28461" CreationDate="2015-02-10T07:52:13.130" Score="1" Body="&lt;p&gt;To answer your question as written, the best option I have for species ID is still to post to fora (such as this one), where experts (or interested amateurs like myself) can manually identify them. Computer identification, although much better nowadays, is still some way away from being able to recognise all species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;4 looks very much like a &lt;a href=&quot;http://en.wikipedia.org/wiki/Mourning_dove&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mourning Dove&lt;/a&gt;  &lt;em&gt;Zenaida macroura&lt;/em&gt;, although its range seems to be limited to North America. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Going up its taxonomy I found the &lt;a href=&quot;http://en.wikipedia.org/wiki/Eared_dove&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eared Dove&lt;/a&gt; &lt;em&gt;Zenaida auriculata&lt;/em&gt; which does live in Argentina. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4ubyQm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/sEA5lm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;8 looks like a collection of macaws, with the &lt;a href=&quot;http://en.wikipedia.org/wiki/Blue-and-yellow_macaw&quot; rel=&quot;nofollow noreferrer&quot;&gt;Blue and yellow macaw&lt;/a&gt; and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Scarlet_macaw&quot; rel=&quot;nofollow noreferrer&quot;&gt;Scarlet macaw&lt;/a&gt; being visible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WBeACm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Xz115m.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-02-10T08:06:35.457" LastActivityDate="2015-02-10T08:06:35.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28470" PostTypeId="1" AcceptedAnswerId="29675" CreationDate="2015-02-10T07:53:23.290" Score="4" ViewCount="268" Body="&lt;p&gt;I am currently attempting to grow a culture of P. Acnes bacteria.  Right now, my only hope in identifying colonies of the bacteria in the culture is to use a black light to find colonies that glow orange.  I am not sure whether or not this will work since nutrient agar may not provide them with something that helps them produce porphyrins.  It's also entirely possible that another form of bacteria contaminating the culture would produce the same effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to entertain the possibility of buying a microscope for this project.  I have never owned a quality microscope(just toy ones in the past), so I don't really know what type of microscope or what magnification I'll need in order to correctly identify and observe the P. Acnes bacteria.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would be interesting is if I could turn this into a pharmacological project; if I can verify that I have the correct bacteria(to a fair degree of certainty, anyway), I can see how the bacteria reacts to different chemicals and environments.&lt;/p&gt;&#xA;" OwnerUserId="13272" LastActivityDate="2015-02-18T16:55:04.767" Title="What microscope/magnification would I need to observe P. Acnes bacteria?" Tags="&lt;bacteriology&gt;&lt;pharmacology&gt;&lt;cell-culture&gt;&lt;microscopy&gt;&lt;experiment&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28471" PostTypeId="2" ParentId="28461" CreationDate="2015-02-10T08:58:24.753" Score="2" Body="&lt;p&gt;First, I think it is more useful to post separate questions, at least for each taxonomic group (birds, butterflies etc). To make a question a dumping ground for all sorts of species determination pictures is a bad idea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, the butterflies seem to belong to the families Nymphalidae,  (nr 5) and Papilionidae (Swallowtails) (nr 7), judged by overall apperance. I'm not directly familiar with South American butterflies, but two likely species are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Doxocopa_agathina&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Doxocopa agathina&lt;/em&gt;&lt;/a&gt; (Nr 5), or related species in the &lt;em&gt;Doxocopa&lt;/em&gt; genus.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/k7d1D.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;(from wikipedia commons)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Papilio_thoas&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Papilio thoas&lt;/em&gt;&lt;/a&gt; (Nr 7)&lt;br&gt;&#xA;This is the King Swallowtail, your specimen probably of the subspecies P. t. brasiliensis which is found in Argentina. Sometimes the name &lt;em&gt;Heraclides thoas&lt;/em&gt; is used. Pictures of subspecies can be found here: &lt;a href=&quot;http://en.butterflycorner.net/Papilio-thoas-King-Swallowtail.466.0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Butterflycorner.net&lt;/a&gt;. Your speciemen have lost the tail appendages (could be due to wear-and-tear or bird attacks). A related similar species is &lt;a href=&quot;http://en.butterflycorner.net/Papilio-astyalus-Broad-banded-Swallowtail-copy-1.1608.0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Papilio astyalus&lt;/em&gt;&lt;/a&gt;, which is also found in Argentina (&lt;a href=&quot;https://encrypted.google.com/search?q=Papilio+astyalus&amp;amp;biw=1600&amp;amp;bih=739&amp;amp;source=lnms&amp;amp;tbm=isch&amp;amp;sa=X&amp;amp;ei=kdLZVOeSCcHtUoeogqgC&amp;amp;ved=0CAYQ_AUoAQ&quot; rel=&quot;nofollow noreferrer&quot;&gt;pictures&lt;/a&gt;), but it usually has a broader yellow band.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Crqo6.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;(from wikipedia commons)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The bird in nr. 6 looks like a &lt;a href=&quot;http://en.wikipedia.org/wiki/Black_vulture&quot; rel=&quot;nofollow noreferrer&quot;&gt;Black vulture (&lt;em&gt;Coragyps atratus&lt;/em&gt;)&lt;/a&gt;.&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Dq8E4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-02-10T09:45:46.993" LastActivityDate="2015-02-10T09:45:46.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28472" PostTypeId="1" CreationDate="2015-02-10T09:56:59.090" Score="2" ViewCount="41" Body="&lt;p&gt;I have taken microscope pictures for proteins in HeLa cells, in order to quantify the intensity (immunofluorescence). The proteins are both at the nuclear envelope, and in order to quantify the intensity I draw a line that goes across the whole cell,through the nucleus, and measure the intensity on that line (ImageJ). Which value should I use as background?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="5144" LastEditDate="2015-02-10T10:00:41.437" LastActivityDate="2015-02-10T10:00:41.437" Title="background extraction in microscope analysis" Tags="&lt;microscopy&gt;&lt;fluorescent-microscopy&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28474" PostTypeId="2" ParentId="28467" CreationDate="2015-02-10T13:52:06.553" Score="3" Body="&lt;p&gt;I think your getting confused. Your assuming that it's actually the heat or cold that creates the feelings of pain. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I was very surprised. cold is just atoms moving slower.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Pain is a warning mechanism, &lt;code&gt;stop doing that or you'll hurt yourself&lt;/code&gt;. It is not caused by the atoms in your nerves moving faster or slower in response to heat. Your nerves are triggered by a stimulus that could cause harm to your body and react by passing a pain signal to your nervous system. The heat (or lack of it) does not transmit up your nerves.&lt;/p&gt;&#xA;" OwnerDisplayName="user9894" LastActivityDate="2015-02-10T13:52:06.553" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28476" PostTypeId="1" CreationDate="2015-02-10T15:25:52.743" Score="6" ViewCount="635" Body="&lt;p&gt;There are a few diseases that cause an &lt;a href=&quot;http://en.wikipedia.org/wiki/Congenital_insensitivity_to_pain&quot; rel=&quot;nofollow noreferrer&quot;&gt;insensitivity to pain&lt;/a&gt;. &lt;a href=&quot;https://biology.stackexchange.com/questions/28467/how-and-why-can-cold-inflict-pain&quot;&gt;This question&lt;/a&gt; asks about the relationship between the cold and pain, which got me thinking:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is shivering a response driven by the sensation of cold, &lt;em&gt;or&lt;/em&gt; a response to the pain associated caused by the cold? This is easy to work out by considering people that do not experience pain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key here is if people with congenital analgesia (AKA &lt;em&gt;CIPA, CIP&lt;/em&gt;) shiver then we may assume that it is the sensation of the cold, not the pain and the cold, that causes the shivering.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Do CIPA patients shiver in the cold?&lt;/strong&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Does this mean that the shivering is caused by sensation pathways or&#xA;pain pathways?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Disclaimer: I am not an anatomist and do not claim to have a working knowledge of the nervous system. Please point out any and all obvious errors in this question that might explain why this wouldn't be the case in the comments or as an answer if its a big error.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-08-24T06:01:12.627" Title="Do people with congenital analgesia feel cold?" Tags="&lt;physiology&gt;&lt;human-anatomy&gt;&lt;pathology&gt;&lt;neuroanatomy&gt;&lt;pain&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28477" PostTypeId="2" ParentId="28420" CreationDate="2015-02-10T15:41:58.923" Score="2" Body="&lt;p&gt;By reactions there is an energy barrier called &lt;a href=&quot;http://en.wikipedia.org/wiki/Activation_energy&quot; rel=&quot;nofollow noreferrer&quot;&gt;activation energy&lt;/a&gt;. Your substrate molecules have kinetic energy (they move, rotate, etc...), so when they collide properly, their kinetic energy can be used to overcome the activation energy and so the reaction takes place. According to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Arrhenius_equation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Arrhenius equation&lt;/a&gt; the &lt;a href=&quot;http://en.wikipedia.org/wiki/Reaction_rate&quot; rel=&quot;nofollow noreferrer&quot;&gt;reaction rate&lt;/a&gt; depends on the temperature, which is evident, because the kinetic energy of your molecules is higher by higher temperature. Enzymes lower the activation energy, because they help the substrates to collide with the proper orientation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Enzymes are mostly composed of amino acid chains. These chains must have proper &lt;a href=&quot;http://en.wikipedia.org/wiki/Protein_folding&quot; rel=&quot;nofollow noreferrer&quot;&gt;folding&lt;/a&gt;. Increasing (or decreasing) the temperature can disrupt this folding and make the enzyme useless. This inactivation can be reversible or irreversible depending on the enzyme type, the temperature and other environmental factors e.g. pressure, osmotic pressure, etc...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question, every enzyme have an optimum working temperature. At this temperature the inactivation is slow enough to be compensated by the increased reaction rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Dj9Pe.gif&quot; alt=&quot;optimum temperature&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;figure 1 -  optimum temperature of a single enzyme - &lt;a href=&quot;http://www.bbc.co.uk/bitesize/standard/biology/investigating_cells/enzymes_and_aerobic_respiration/revision/5/&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ca3VD.jpg&quot; alt=&quot;optimum temperatures of multiple enzymes&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;figure 2 - optimum temperatures of multiple enzymes - &lt;a href=&quot;http://classes.midlandstech.edu/carterp/courses/bio225/chap06/Microbial%20Growth%20ss1.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2015-02-11T17:42:05.567" LastActivityDate="2015-02-11T17:42:05.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28478" PostTypeId="1" AcceptedAnswerId="28492" CreationDate="2015-02-10T16:00:49.800" Score="8" ViewCount="922" Body="&lt;p&gt;In computer vision the color information is often discarded, as most object recognition tasks seem to work just as well on the greyscale image (even better, because there is less unnecessary information).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do animals exist which have good vision (e.g. see sharp, many details), but only see greyscale / very limited colors?&lt;/p&gt;&#xA;" OwnerUserId="8014" LastEditorUserId="22057" LastEditDate="2018-07-16T05:56:11.330" LastActivityDate="2018-07-16T05:56:11.330" Title="Do animals exist which have good vision, but see only grayscale?" Tags="&lt;zoology&gt;&lt;vision&gt;&lt;sensation&gt;" AnswerCount="2" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="28479" PostTypeId="1" CreationDate="2015-02-10T16:18:49.560" Score="21" ViewCount="2028" Body="&lt;p&gt;This creature was found on a bed. At first, I thought it was a piece of lint, but then it suddenly &lt;em&gt;moved&lt;/em&gt;. I picked it up in a paper towel and put it in an eye cream containers, which it is currently in. I believe this means that it is pretty strong, since it appeared to have pulled itself all the way up from the floor, to the top of the bed, then across to the other side of a King-sized mattress. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears to be a worm wrapped in a cocoon. It is pretty short, being small enough to fit inside an eye cream container.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The creature is a pale yellow-white/cream, with brownish-red tips on each end (unless it can somehow turn around without exiting its casing). It looks from the side as if it has a rather flat face, one that comes to a slight bump at the bottom, but is pretty much flat. The casing is light grey, with some small portions that appear to be almost the same color as the organism, just slightly darker. There is an opening at each end of the casing, which the organism uses to slide slightly out. It has never fully come out of the casing. The edges of the openings at each end are white. The casing seems to either be made out of or covered in dust.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It can create a substance that is sticky and strong enough to support its weight. I cannot tell if the substance is created by the 'worm', or the 'cocoon'. A thread at each end of the casing is connected to the side of the container by the substance. When I accidentally detached one end of the casing, the entire thing began to shake violently when held so that one end was hanging. It wouldn't stop until I had turned it so that both ends were touching the side of the container. Within minutes, though, it had reattached the broken end. &lt;em&gt;Minutes&lt;/em&gt;. Not hours, but &lt;em&gt;one minute&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The holes at each end of the cocoon can either grow or shrink closed. I believe this allows us to tell which opening is in use. If it is nearly shut, it will come out the other end.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears to be nocturnal, since it doesn't move during the day, but it is very active at night. It also appears to react to light. If some is put on it, it will poke out to look around.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has survived for four days straight without food, as far as we know. We put a small piece of lettuce in with it. However, there are two small, brownish things on the bottom of the container. This may be its excrement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The creature moves by reaching out with its 'tentacle/worm', grabbing onto something (including the ground), and pulling itself forward.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I cannot tell if the creature is attaching to the container's side to climb, or because it is morphing. If that is the case, then the outer shell may be a cocoon. It did detach itself from the side of the container, and first hid under a ledge of lettuce, but now has wrapped itself in lettuce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;To summarize: can someone please help me identify this creature?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eXbpL.jpg&quot; alt=&quot;Creature&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="13404" LastEditorUserId="16866" LastEditDate="2019-02-03T18:41:10.987" LastActivityDate="2019-02-03T18:41:10.987" Title="Identifying a creature that appears to be a worm wrapped in a cocoon" Tags="&lt;species-identification&gt;&lt;entomology&gt;&lt;lepidoptera&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="28480" PostTypeId="2" ParentId="28452" CreationDate="2015-02-10T17:34:26.817" Score="15" Body="&lt;p&gt;&lt;em&gt;Ventricaria ventricosa&lt;/em&gt; (previously called &lt;em&gt;Valonia ventricosa&lt;/em&gt;) is not exactly a single cell. It has a coenocytic structure with multiple nuclei and chloroplasts. As Jasand Pruski correctly guessed the organism possesses a large central vacuole which is multilobular in structure (lobules radiating from a central spheroid region). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The entire cell contains several &quot;cytoplasmic domains&quot; with each domain having a nucleus and a few chloroplasts (See the figure below). Cytoplasmic domains are interconnected by cytoplasmic &quot;bridges&quot; that are supported by microtubules (like in axons). The peripheral cytoplasm (whose membrane is overlaid by the cell wall), is only about 40nm thick.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/PrARe.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fluorescent confocal micrograph of a cytoplasmic domain. From &lt;em&gt;Shepherd et al. (2004) Protoplasma 223: 79–91&lt;/em&gt;. Here, &lt;strong&gt;n&lt;/strong&gt; is nucleus &lt;strong&gt;c&lt;/strong&gt; is chloroplast and &lt;strong&gt;v&lt;/strong&gt; is vacuole.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So these are not huge cellular balloons that can burst easily. Nonetheless a huge structure like this is susceptible to injuries by shearing forces of water currents and by other organisms like fish which may try to feed on them. These organisms have some mechanisms other than the cytoplasmic organization that allows them to cope up with injuries:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;When the outer membrane ruptures, then the cytoplasm contracts with the help of actin filaments that are attached to the former. Subsequently the membrane fuses, protoplasts form and then cell wall is regenerated. This movement is likely to be triggered by extracellular calcium.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A single cytoplasmic domain with nucleus and other essential organelles can regenerate an entire organism. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A muclilagenous layer made up of sulphated polysaccharides coats both the vacuolar and extracellular surfaces. During injury it impedes the movement of water and ions (by retaining them in the form of a gel) and therefore acts like a plug.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Other organisms like this (siphonous algae) also have similar mechanisms. Some even employ calcium carbonate to maintain rigidity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;REFERENCES:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://doi.org/10.1007/s00709-003-0032-4&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Shepherd et al. (2004) Protoplasma 223: 79–91&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://doi.org/10.1007/BF01637240&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Menzel (1988) Protoplasma 144: 73-91&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2019-07-26T08:50:01.870" LastActivityDate="2019-07-26T08:50:01.870" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="28481" PostTypeId="1" CreationDate="2015-02-10T18:21:00.870" Score="2" ViewCount="398" Body="&lt;p&gt;I need to convert all my sequences in a Stockholm format into this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;hg19_11_6_Ala          ----------------.GG--gggaguggugu....gguuacgaaugUGGCCUCUGC-----AA.............................................................GCAGACA.........................G..CCUGGGUUCAAUU...........................&#xA;#=GR hg19_11_6_Ala  PP .................22..45677788888....899999999996777899988.....56.............................................................8999999.........................9..*************...........................&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Into something like this: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; hg19_11_6_Ala         ................((..(((((((((((...)))))))))))))))))))))))....((................................)))))))))......)))).....................&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Obviously, being coherent with the stockholm format. Any hint?&lt;/p&gt;&#xA;" OwnerUserId="13373" LastEditorUserId="13373" LastEditDate="2015-02-10T20:13:33.613" LastActivityDate="2015-02-11T06:51:50.393" Title="Stockholm format to dot-brackets format?" Tags="&lt;bioinformatics&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28483" PostTypeId="1" AcceptedAnswerId="28496" CreationDate="2015-02-10T19:15:44.280" Score="3" ViewCount="94" Body="&lt;p&gt;Is there a term or any evidence of phage DNA integrating into chromosomes/ DNA but never being triggered? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, could a virus that affected Neanderthals still infect human cells today but is never expressed, triggered, or executed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How often is latent viral DNA ignored by the host?&lt;/p&gt;&#xA;" OwnerUserId="238" LastActivityDate="2015-02-11T19:18:50.217" Title="Are some virus loads introduced to human cell but never triggered?" Tags="&lt;pathology&gt;&lt;virology&gt;&lt;retrovirus&gt;&lt;lentivirus&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28484" PostTypeId="1" CreationDate="2015-02-10T19:36:16.967" Score="4" ViewCount="255" Body="&lt;p&gt;A drone bee is male and is the product of only a queen bee. How is it that the drone bee can be male. I know that a drone is produced by an unfertilized egg, but this does not explain where the two X chromosomes come from. To me, this means that the one X chromosome from the queen must some how be duplicated.&lt;/p&gt;&#xA;" OwnerUserId="13407" LastActivityDate="2015-02-11T22:58:25.883" Title="How can a drone be male?" Tags="&lt;zoology&gt;&lt;reproductive-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28487" PostTypeId="2" ParentId="28468" CreationDate="2015-02-10T21:49:21.200" Score="4" Body="&lt;p&gt;Classical thyroid hormones implement a very flexible signaling mechanism. Basically, they comprise two aromatic rings that are connected via an oxygen atom. Optionally, they may contain organic side chains and inorganic iodine atoms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of iodothyronines, which are represented e.g. by the well-known thyroid hormones T4, T3 and 3,5-T2, the side chain contains an amino group and a carboxylate group. Therefore, iodothyronines are amino acids. Up to four different hydrogen atoms (two at every ring) may be replaced by iodine atoms, and the resulting pattern of iodination determines their biological activity. Generally, iodination of the inner ring and deiodination of the outer ring results in high biological activity (e.g. in T3 and 3,5-T2), whereas iodination of the outer ring and deiodination of the inner ring delivers a receptor-blocking thyroid hormone (e.g. reverse-T3). There are three deiodinases encoded by the DIO1, DIO2 and DIO3 genes that catalyze the &quot;step-up&quot; and &quot;step-down&quot; reactions to active or inactive thyroid hormones, respectively. Multiple molecular processes are able to differentially upregulate and downregulate tissue deiodinases. Therefore, thyroid hormones are subject to both global and local control.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4VCWE.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Removal of the amino group results in iodothyroacetates. Their biological effects are similar to those of iodothyronines, but in addition to nuclear receptors they also have a strong effect on membrane-bound receptors, which are only weakly activated by iodothyronines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yeW9w.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thyronamines lack the carboxylate group. Their biological effect is different to that of iodothyronines and iodothyroacetates. By activating the membrane-bound TAAR1 receptor they have an effect that is in most respects antagonistic to that of classical thyroid hormones. Thyronamines seem to be most active in deiodinated state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3XZDB.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Summarizing, both organic and anorganic modifications are able to modulate the effect of thyroid hormones. This mechanism is a very effective way to encode a high  grade of information entropy in rather small molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gereben B, Zavacki AM, Ribich S, Kim BW, Huang SA, Simonides WS, Zeöld A, Bianco AC. Cellular and molecular basis of deiodinase-regulated thyroid hormone signaling. Endocr Rev. 2008 Dec;29(7):898-938. doi: 10.1210/er.2008-0019. PMID: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18815314&quot; rel=&quot;nofollow noreferrer&quot;&gt;18815314&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Engler D, Burger AG. The deiodination of the iodothyronines and of their derivatives in man. Endocr Rev. 1984 Spring;5(2):151-84. PMID &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6376077&quot; rel=&quot;nofollow noreferrer&quot;&gt;6376077&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Piehl S, Hoefig CS, Scanlan TS, Köhrle J. Thyronamines--past, present, and future. Endocr Rev. 2011 Feb;32(1):64-80. doi: 10.1210/er.2009-0040. PMID &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20880963&quot; rel=&quot;nofollow noreferrer&quot;&gt;20880963&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3865" LastActivityDate="2015-02-10T21:49:21.200" CommentCount="1" CommunityOwnedDate="2015-02-10T21:49:21.200" ContentLicense="CC BY-SA 3.0" />
  <row Id="28488" PostTypeId="2" ParentId="28478" CreationDate="2015-02-10T22:44:05.420" Score="3" Body="&lt;p&gt;Most marine mammals, some nocturnal mammals, and some fossorial mammals are &lt;em&gt;monochromats&lt;/em&gt; -- meaning they see in what is effectively greyscale. As previous commentators have mentioned, quantifying visual acuity is not a trivial matter. Still, I'd assume that under many measures a species such as the owl monkey--a monochromat--has quite good vision, at least at night. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="13072" LastEditDate="2015-02-11T00:02:14.300" LastActivityDate="2015-02-11T00:02:14.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28489" PostTypeId="2" ParentId="28479" CreationDate="2015-02-10T22:46:32.520" Score="6" Body="&lt;p&gt;That, I believe to be the larvae of an Indian Mealmoth &lt;em&gt;Plodia interpunctella&lt;/em&gt;, but it could also be &lt;em&gt;Tineola bisselliella&lt;/em&gt; or &lt;em&gt;Tinea pellionella&lt;/em&gt;. It's definitely emerging from a pupa, and it's definitely a moth larva, but I'd need more information for an accurate identification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.google.com/search?q=Plodia+interpunctella+larvae&amp;amp;safe=active&amp;amp;rlz=1C1CHFX_enUS540US540&amp;amp;es_sm=122&amp;amp;biw=970&amp;amp;bih=920&amp;amp;source=lnms&amp;amp;tbm=isch&amp;amp;sa=X&amp;amp;ei=DYzaVNbKCIK1ggS4v4TYCQ&amp;amp;ved=0CAYQ_AUoAQ&quot;&gt;To Google images&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-02-10T23:10:09.093" LastActivityDate="2015-02-10T23:10:09.093" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28492" PostTypeId="2" ParentId="28478" CreationDate="2015-02-11T00:21:34.733" Score="12" Body="&lt;h1&gt;Preamble &amp;amp; Overview.&lt;/h1&gt;&#xA;&lt;p&gt;This is a rather unsatisfying answer I'm afraid. I can't seem to find any animal that has &lt;em&gt;exceptional&lt;/em&gt; eyesight &lt;em&gt;&lt;strong&gt;and&lt;/strong&gt;&lt;/em&gt; sees in monochrome.&lt;/p&gt;&#xA;&lt;p&gt;Baring in mind the context of humans vs machines; machines cope better with shapes rather than colours however it generally appears that those animals which rely on exceptional eyesight to survive tend to see in colour and have other neurological systems to ease &amp;quot;data overload&amp;quot;.&lt;/p&gt;&#xA;&lt;h1&gt;Animals that see in grey-scale.&lt;/h1&gt;&#xA;&lt;p&gt;Some pinnipeds (seals) see in grey-scale, but note that their survival doesn't seem to depend on visibility, and it is generally regarded as poor even in a typically healthy animal. &lt;a href=&quot;https://seaworld.org/en/animal-info/animal-infobooks/harbor-seal/senses/&quot; rel=&quot;noreferrer&quot;&gt;According to SeaWorld&lt;/a&gt;, researchers have found blind seal mothers and pups that are otherwise perfectly healthy.&lt;/p&gt;&#xA;&lt;p&gt;Dolphins are a similar story. It is so murky that they rely on bio-sonar. Fresh water dolphins are almost completely blind.&lt;/p&gt;&#xA;&lt;p&gt;In fact, the more species that I have read about which have monochromatic vision, the more I see that these animals rely heavily on other senses.&lt;/p&gt;&#xA;&lt;p&gt;Some land animals with &amp;quot;decent&amp;quot; monochromatic vision:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Lorisiformes&lt;/li&gt;&#xA;&lt;li&gt;Bats&lt;/li&gt;&#xA;&lt;li&gt;Raccoons&lt;/li&gt;&#xA;&lt;li&gt;Nocturnal kinkajous&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Note that these often have another much more acute sense like smell or hearing.&lt;/p&gt;&#xA;&lt;p&gt;Surprisingly, there is also not necessarily a link between monochromatic vision and nocturnal state (there are some animals with dichromatic vision that are nocturnal, and some animals with monochromatic vision are crepuscular, or diurnal and &lt;em&gt;visa versa&lt;/em&gt;).&lt;/p&gt;&#xA;&lt;p&gt;From &lt;a href=&quot;http://en.wikipedia.org/wiki/Monochromacy&quot; rel=&quot;noreferrer&quot;&gt;wiki&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Many species, such as all marine mammals, the owl monkey, and the Australian sea lion have monochromatic vision under normal conditions...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;A trend I see is that animals that have exceptional eyesight tend to have also evolved some sort of colour differentiation.&lt;/p&gt;&#xA;&lt;h1&gt;Why not ditch the colour info to make it easier on the brain?&lt;/h1&gt;&#xA;&lt;p&gt;To bring this back to your context of machines I would say that identifying the difference between a ball, a chair, a human, and a car (the sort of things machines need to know about!) is much more dependent on shape than colour. A monochromatic person wouldn't struggle with that at all.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;However&lt;/em&gt; in a &amp;quot;wild&amp;quot; environment telling the difference between grass and tiger stripes means that an animal with trichromatic vision may get to live another day whereas the animal with monochromatic vision might not see the tiger in time. Or spotting berries and fruit in some distant trees might mean food that would have otherwise gone unnoticed.&lt;/p&gt;&#xA;&lt;p&gt;Those are obviously very narrow examples, but generally it seems animals always have one or more exceptional senses limited to smell, hearing, or colour vision (it would be great if someone could point out an exception to this in the comments, like touch or taste!).&lt;/p&gt;&#xA;&lt;p&gt;You are right to hint that there is a lot of information in colour vision. Like your example with loss of colour in machines, data needs to be dumped very quickly in the human brain.&lt;/p&gt;&#xA;&lt;p&gt;I'm not a neuroscientist, but I have read pop articles about how little we can remember with photo detail. Within seconds of looking at a scene all texture details are lost, most objects are forgotten about and all we can really recall are big shapes. But importantly, we would notice the tiger in the woods before forgetting and run for it! If we had no colour input, that wouldn't be the case.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h1&gt;Examples of &lt;em&gt;more&lt;/em&gt; colour being used.&lt;/h1&gt;&#xA;&lt;p&gt;Hopefully the above demonstrates that colours are important to many animals. If anything it seems that more colours even than our perception of the EM spectrum are preferable, particularly into the UV range.&lt;/p&gt;&#xA;&lt;p&gt;For prey identification reindeer rely on ultraviolet light to spot lichens that they eat. This same sight can spot the UV-absorbent urine of predators. &lt;a href=&quot;http://www.theatlantic.com/technology/archive/2011/08/6-animals-that-can-see-or-glow-in-ultraviolet-light/243634/&quot; rel=&quot;noreferrer&quot;&gt;This article&lt;/a&gt; has a few more examples.&lt;/p&gt;&#xA;&lt;p&gt;Some birds of paradise like &lt;a href=&quot;http://www.newscientist.com/article/dn1743-sunscreen-test-reveals-budgies-sexy-shine.html#.VNqfjVOsXlQ&quot; rel=&quot;noreferrer&quot;&gt;parrots&lt;/a&gt; have even more brilliant patters under UV light. &lt;a href=&quot;http://www.pnas.org/content/94/16/8618.full&quot; rel=&quot;noreferrer&quot;&gt;Even starlings&lt;/a&gt; look to have an identifying pattern under UV light. Both those examples are thought to be involved in mate selection.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ipsFy.jpg&quot; alt=&quot;parrots under UV&quot; /&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;White light does not reveal the feathers' yellow fluorescence in images (left), but short wavelength illumination does (right). Photo: Science&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This all hammers home that colour is more important to animals than machines and is involved in more than just camouflage.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2018-07-15T19:25:53.967" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="28494" PostTypeId="1" CreationDate="2015-02-11T02:03:09.387" Score="2" ViewCount="1432" Body="&lt;p&gt;For a DNA molecule, you can define directionality using the convention of a 5'-3' direction on the Sense strand. However, using an N to C convention for a protein doesn't work since the ends may be on the same side and if the protein is unstructured then the N to C direction will change. I'm asking the question from the perspective of addressing PPIs. If I have two proteins that interact with each other, how do you quantitatively describe the relationship of the two proteins with respect to one another. We have formal ways to describing this using domains and residues but not for quaternary structures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How would you mathematically define &quot;up&quot; for a protein structure?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would imagine that using RDCs would be able to make some progress into this problem. At the moment it doesn't seem as if there is any convention in the structural biophysics community.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2015-02-11T02:03:09.387" Title="How can the directionality of a protein structure be defined?" Tags="&lt;biophysics&gt;&lt;structural-biology&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28496" PostTypeId="2" ParentId="28483" CreationDate="2015-02-11T03:07:33.530" Score="6" Body="&lt;p&gt;There is viral DNA within our genomes. Embedded in the genomes of all vertebrates are the proviral remnants of previous retroviral infections. It is possible that some have conferred biological benefits.&lt;/p&gt;&#xA;&lt;p&gt;Human endogenous retroviruses (HERVs) represent the proviral phase of exogenous retroviruses that have integrated into the germ line of their host. They are transmitted vertically through the germline and are thus inherited by successive generations in a Mendelian manner.&lt;/p&gt;&#xA;&lt;p&gt;HERVs possess a similar genomic organisation to present day exogenous retroviruses such as human immunodeficiency virus (HIV) and human T cell leukaemia virus.&lt;/p&gt;&#xA;&lt;p&gt;Although many are defective through the accumulation of mutations, deletions, and termination signals, some HERVs have been implicated in certain autoimmune diseases and cancers and might have a role in the etiology and pathology of disease.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Within humans, the most recently active ERVs are members of the HERV-K (HML2) family. This family first integrated into the genome of the common ancestor of humans and Old World monkeys at least 30 million years ago, and it contains &amp;gt;12 elements that have integrated since the divergence of humans and chimpanzees, as well as at least two that are polymorphic among humans.&lt;/p&gt;&#xA;&lt;p&gt;Here we show that the HERV-K (HML2) family has increased in copy number predominantly via reinfection, and that the family has probably retained replication-competent and infectious members for &amp;gt;30 million years. We also present evidence for persistent reinfection by other ERV families within the human genome, and suggest &lt;em&gt;that endogenous retrovirus families are often capable of extremely long periods of smoldering infection&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC387345/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Long-term reinfection of the human genome by endogenous retroviruses&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8643549/&quot; rel=&quot;nofollow noreferrer&quot;&gt;The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1187282/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Demystified . . . Human endogenous retroviruses&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-11T19:18:50.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28497" PostTypeId="1" CreationDate="2015-02-11T04:31:21.997" Score="1" ViewCount="3470" Body="&lt;p&gt;For example, if I want to say something along the lines of &quot;this signaling pathway causes a cell to go through the process of apoptosis&quot;, but I want to shorten the phrase &quot;go through the process of apoptosis&quot; to one word, what would that word be? I've been saying &quot;apoptose&quot; so far but I'm not sure if that's correct.&lt;/p&gt;&#xA;" OwnerUserId="13411" LastActivityDate="2015-02-11T07:49:03.410" Title="What is the present tense verb form of apoptosis?" Tags="&lt;cell-biology&gt;&lt;apoptosis&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28498" PostTypeId="2" ParentId="28481" CreationDate="2015-02-11T06:51:50.393" Score="1" Body="&lt;p&gt;If what you want is to find a consensus structure for a group of alignments in stockholm format then you might try with &#xA;&lt;a href=&quot;http://rna.tbi.univie.ac.at/cgi-bin/RNAalifold.cgi&quot; rel=&quot;nofollow&quot; title=&quot;RNAalifold&quot;&gt;RNAalifold&lt;/a&gt;&#xA; and for single sequence folding check &lt;a href=&quot;http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi&quot; rel=&quot;nofollow&quot; title=&quot;RNAfold&quot;&gt;RNAfold&lt;/a&gt;. Both have online servers and can also be run offline.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After you get the consensus structure update the stockholm file by adding  a structure consensus line as: &lt;code&gt;#=GC SS_cons&lt;/code&gt; followed by the dot bracket notation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A nice RNA structure editor that will make your life easier is EMACS when complemented with &lt;a href=&quot;http://sgjlab.org/ralee/&quot; rel=&quot;nofollow&quot;&gt;RALEE&lt;/a&gt;. It allows you to view and manipulate RNA structures, predict structure folding and color the alignments based on basepairs relationships. It will be worth it to invest time into mastering RALEE.&lt;/p&gt;&#xA;" OwnerUserId="9647" LastActivityDate="2015-02-11T06:51:50.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28499" PostTypeId="2" ParentId="28497" CreationDate="2015-02-11T07:49:03.410" Score="5" Body="&lt;p&gt;According to Google Scholar, there were &lt;a href=&quot;http://scholar.google.co.uk/scholar?q=apoptose&amp;amp;btnG=&amp;amp;hl=en&amp;amp;as_sdt=0%2C5&quot; rel=&quot;noreferrer&quot;&gt;~40000 hits&lt;/a&gt; for &quot;apoptose&quot; and ~&lt;a href=&quot;http://scholar.google.co.uk/scholar?q=%22undergo%20apoptosis%22&amp;amp;btnG=&amp;amp;hl=en&amp;amp;as_sdt=0%2C5&quot; rel=&quot;noreferrer&quot;&gt;120k hits&lt;/a&gt; for &quot;undergo apoptosis&quot; in published literature, both of which had significant numbers of high-impact articles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, it is clear that both expressions are sufficiently used in literature for either to be used. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally, I would say &quot;undergo apoptosis&quot; being both shorter than your original phrase and not risking coining new word forms.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-02-11T07:49:03.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28500" PostTypeId="1" AcceptedAnswerId="28529" CreationDate="2015-02-11T09:30:28.340" Score="4" ViewCount="483" Body="&lt;p&gt;I understand that many curated trees of life already exist (eg &lt;a href=&quot;http://tolweb.org/tree/&quot; rel=&quot;nofollow&quot;&gt;http://tolweb.org/tree/&lt;/a&gt;) but is there any website that allows one to input a list of organisms, and then produce the current best guess at their evolutionary relationships?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best site I managed to find so far is &lt;a href=&quot;http://itol.embl.de/itol.cgi&quot; rel=&quot;nofollow&quot;&gt;http://itol.embl.de/itol.cgi&lt;/a&gt;, which allows you to select specific species from the main tree to plot into a sub-tree, but the tree itself is rather small, so more detailed comparisons cannot be made. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-02-12T12:11:22.657" Title="Visualising a subset of the tree of life" Tags="&lt;evolution&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28501" PostTypeId="1" CreationDate="2015-02-11T10:32:09.240" Score="4" ViewCount="171" Body="&lt;p&gt;I need some clarifications on the concept of &quot;orientation&quot; in case of chromosomal rearrangements.&#xA;Given a &lt;strong&gt;deletion&lt;/strong&gt; event on a chromosome for example, is the resulting DNA at the breakpoint always in TH (Tail to Head) orientation? Do all &lt;strong&gt;duplications&lt;/strong&gt; lead to HT orientation? And in case of &lt;strong&gt;translocations&lt;/strong&gt;, &lt;strong&gt;inversions&lt;/strong&gt;, etc..?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone give a clear definition of &quot;orientation&quot;, and make some examples?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here some specific examples found in the &lt;a href=&quot;http://cancer.sanger.ac.uk/cosmic&quot; rel=&quot;nofollow&quot;&gt;Cosmic database&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;CRC-3  large_intestine  NS  carcinoma  adenocarcinoma  intrachromosomal inversion  28066  0  2  53774826  53774826  +  2  53775947  53775947  +    21892161  &#xA;&#xA;CRC-3  large_intestine  NS  carcinoma  adenocarcinoma  intrachromosomal inversion  28072  0  2  60783417  60783417  -  2  60786447  60786447  -    21892161&#xA;&#xA;0006_CRUK_PC_0006_T1_DNA  prostate  NS  carcinoma  adenocarcinoma  intrachromosomal inversion  113193  0  18  60375963  60375963  +  18  77010169  77010169  -      538&#xA;&#xA;0006_CRUK_PC_0006_T1_DNA  prostate  NS  carcinoma  adenocarcinoma  intrachromosomal inversion  113314  0  7  153608258  153608258  -  7  153610727  153610727  +      538&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;As you can see, they have inversions having all of the possible strand orientations, '++','--','+-','-+'.&#xA;How is this even possible?! How to convert to H/T orientation in this case?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. This is the description of the header of the data:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;               HEADER[IDX] : IDX : DATA[IDX]&#xA;               Sample name :   0 : 0006_CRUK_PC_0006_T1_DNA&#xA;              Primary site :   1 : prostate&#xA;              Site subtype :   2 : NS&#xA;         Primary histology :   3 : carcinoma&#xA;         Histology subtype :   4 : adenocarcinoma&#xA;             Mutation Type :   5 : Interchromosomal unknown type&#xA;               Mutation ID :   6 : 113196&#xA;          Breakpoint Order :   7 : 0&#xA;         GRCh37 Chrom From :   8 : 6&#xA;  GRCh37 Location From min :   9 : 129148581&#xA;  GRCh37 Location From max :  10 : 129148581&#xA;        GRCh37 Strand From :  11 : -&#xA;           GRCh37 Chrom To :  12 : 7&#xA;    GRCh37 Location To min :  13 : 153610712&#xA;    GRCh37 Location To max :  14 : 153610712&#xA;          GRCh37 Strand To :  15 : -&#xA;     Non-templated ins seq :  16 : &#xA;                 Pubmed ID :  17 : &#xA;                  ID_STUDY :  18 : 538&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="12923" LastEditorUserId="19521" LastEditDate="2016-06-06T08:16:18.300" LastActivityDate="2016-06-06T08:16:18.300" Title="Clarification on the &quot;orientation&quot; of chromosomal rearrangements" Tags="&lt;dna&gt;&lt;chromosome&gt;&lt;3d-structure&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28502" PostTypeId="1" AcceptedAnswerId="28609" CreationDate="2015-02-11T11:22:52.447" Score="15" ViewCount="1893" Body="&lt;p&gt;The most famous example of a sealed bottle garden is David Latimer's bottle with a Spiderworth plant, pictured below, which has been sealed for 40 years. My own attempt at a bottle garden is failing and I'm looking to &quot;debug&quot; what's going on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My garden is a 2 litre glass jar filled with gravel, sand and soil, filling about a quarter of the jar. The soil is rather damp. I'm observing the following: When the bottle is sealed, plants such as moss, strawberry shoots and seeds thrive for a couple of weeks. They will then wilt and worms that had hitched a ride in the soil try to escape. When opening the bottle, there is a strong smell exactly like manure. The brief exchange of air when opening the bottle is enough to allow the plants to properly rot over the coming days, with mold only now spreading. (This proves that oxygen was depleted before I opened the jar) I removed the dead plants, sprinkled seeds on the soil and closed the jar. The seeds germinated and thrived for a couple of weeks until the process repeated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At first look, it appears that when oxygen has been depleted, anaerobic bacteria take over, producing H2S, which I assume kill the plants. Or are they killed by changes in pH under high CO2 concentrations? Why does this not occur for all bottle gardens? Is the problem that there's too few plants to keep up the oxygen level which keeps the anaerobic bacteria at bay, is it the waterlogged soil or some other factor I'm unaware of?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/8Sfrq.jpg&quot; alt=&quot;Latimer&amp;#39;s highly successful bottle garden&quot;&gt;&#xA;&lt;br&gt;Latimer did something right with his bottle garden, which started with a seedling and some compost. &lt;/p&gt;&#xA;" OwnerUserId="9583" LastEditorUserId="9583" LastEditDate="2015-02-12T10:13:42.773" LastActivityDate="2015-02-16T19:55:57.510" Title="What are the requirements for a stable carbon cycle in sealed &quot;bottle gardens&quot;`?" Tags="&lt;bacteriology&gt;&lt;plant-physiology&gt;&lt;ecosystem&gt;&lt;anaerobic-respiration&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28505" PostTypeId="2" ParentId="20757" CreationDate="2015-02-11T13:30:27.920" Score="2" Body="&lt;p&gt;I had a similar problem. In my case, I realized that it is absolutely essential to wash the membrane in TBS without Tween (TBS, not TBST) before you use ECL. If you have any amount of soap (Tween) on your membrane it reacts in some way with ECL and each time you should be getting a different pattern of these stains. Washing the membrane in TBS and then incubating with ECL made a difference for me and fixed the problem.&lt;/p&gt;&#xA;" OwnerUserId="13414" LastActivityDate="2015-02-11T13:30:27.920" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28507" PostTypeId="2" ParentId="28423" CreationDate="2015-02-11T14:57:52.517" Score="0" Body="&lt;p&gt;Triglyceride. It has 3 fatty acids, which are non polar (water-fearing). so they are hydrophobic. These 3 fatty acids are connected to a glycerol molecule. This molecule is polar and is hydrophilic (water-loving). The glycerol is attached to the 3 fatty acids via  a dehydration reaction. When they are connected, they loose a water molecule, and form an ester. &lt;/p&gt;&#xA;" OwnerUserId="12904" LastActivityDate="2015-02-11T14:57:52.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28508" PostTypeId="1" CreationDate="2015-02-11T16:19:28.677" Score="5" ViewCount="555" Body="&lt;p&gt;My lab has been using &lt;a href=&quot;https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp&quot; rel=&quot;nofollow&quot;&gt;TCGA&lt;/a&gt; data (somatic mutations and clinical data) to develop panels of genes and of mutations we expect to see in certain cancer populations. We'd like to validate our panels by checking how they hold up against other cancer datasets. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that one resource we can use is the &lt;a href=&quot;https://icgc.org/&quot; rel=&quot;nofollow&quot;&gt;International Cancer Genome Consortium&lt;/a&gt; but I'm wondering if members of this forum can suggest a few other places we can get both clinical and somatic mutations data for cohorts of cancer patients. &lt;/p&gt;&#xA;" OwnerUserId="8161" LastEditorUserId="3553" LastEditDate="2015-12-14T08:32:38.437" LastActivityDate="2015-12-16T01:44:23.317" Title="Where can I find mutation datasets for cancer?" Tags="&lt;bioinformatics&gt;&lt;cancer&gt;&lt;database&gt;&lt;tcga&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28509" PostTypeId="1" CreationDate="2015-02-11T17:00:55.240" Score="2" ViewCount="5093" Body="&lt;p&gt;I was reading about heat muscle contraction and I read:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The endocardium depolarization happens earlier than pericardium , but&#xA;  pericarduim repolarization happens earlier, therefore the T wave in&#xA;  healthy people is always positive.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I have two questions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What's the reason?&lt;/li&gt;&#xA;&lt;li&gt;Why doesn't it happen in atrium and atrial repolarization(T wave)?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerDisplayName="user12874" LastEditorUserId="11841" LastEditDate="2015-02-12T02:13:12.627" LastActivityDate="2015-02-14T16:03:52.627" Title="Why is pericardium muscle repolarizated earlier than endocardium?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ClosedDate="2015-03-02T06:59:27.653" ContentLicense="CC BY-SA 3.0" />
  <row Id="28510" PostTypeId="1" CreationDate="2015-02-11T17:59:46.927" Score="1" ViewCount="123" Body="&lt;p&gt;I'm come across this question and I'm somewhat confused:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the test for staphylococci, the clumping factor detects:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;staphylothrombin&lt;/li&gt;&#xA;&lt;li&gt;DNase&lt;/li&gt;&#xA;&lt;li&gt;mannitol fermentation&lt;/li&gt;&#xA;&lt;li&gt;Fimbriae&lt;/li&gt;&#xA;&lt;li&gt;fibrinogen-binding protein&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I know that bound coagulase can convert prothrombin into staphylothrombin and eventually fibrinogen into fibrin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm thinking it's staphylothrombin, but when it says ''detects'' does it mean that the test concludes whether staphylothrombin is produced or does it mean that the clumping factor actually ''detects'' a substance?&lt;/p&gt;&#xA;" OwnerUserId="13417" LastActivityDate="2015-02-11T17:59:46.927" Title="Clumping factor test" Tags="&lt;microbiology&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28511" PostTypeId="1" AcceptedAnswerId="28513" CreationDate="2015-02-11T18:27:32.010" Score="18" ViewCount="2906" Body="&lt;p&gt;When considering how organisms store energy for later use, I was wondering what substance known in Biology is best for compacting the most energy in the smallest space(volume-wise).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With my (limited) knowledge, I would &lt;em&gt;guess&lt;/em&gt; that it would be what we would normally call &quot;body fat&quot;. However, I know I am probably not aware of most forms of stored energy, and I considered that perhaps substances like egg-whites may potentially contain more energy in the same amount of volume.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the question as in the title: What is the most condensed form of (stored) energy used in biology?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, if there is no known &quot;best&quot;: What would the leading competitors be?&lt;/p&gt;&#xA;" OwnerUserId="9700" LastEditorUserId="5144" LastEditDate="2015-02-13T09:14:36.943" LastActivityDate="2015-02-13T16:09:18.723" Title="What is the most condensed form of (stored) energy used in biology?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28513" PostTypeId="2" ParentId="28511" CreationDate="2015-02-11T18:44:31.843" Score="24" Body="&lt;p&gt;The best ratio between weight and energy content (and of course also stability) has indeed fat. It's energy content is more than twice as high as for carbohydrates (sugars).&#xA;See this table from &lt;a href=&quot;http://www.ecoculturevillage.org/healthhappinesslongevity/calories-kilocalories-or-kcals/&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; on the energy contents:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KLpqR.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the reason why animals which hibernate or migrate fed up to build up fat resources before the winter or their journey. With carbohydrates they would need more than the double amount of stored carbohydrates to get the same energy. Proteins are approximately on the same level as carbohydrates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look on this problem not by energy per mass but volume per mass, fat still wins. For this we need the density of protein (muscles in this case) and fat. Paper 1 (see reference below) say that the human muscles have an average density of 1.06g/cm³. Paper 2 lists a density of 0.92g/cm³ for fat. So fats (this is practically only valid for the human body, but should be in the same range for other animals) are about 15% less dense than muscles. As the energy density per weight is about double as high for fat, this compensates for the lower density.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carbohydrates are better, but are still not as good as fat. It's a bit hard to find specific densities for carbohydrates in the human body, so let's use &lt;a href=&quot;http://en.wikipedia.org/wiki/Glycogen&quot; rel=&quot;noreferrer&quot;&gt;Glycogen&lt;/a&gt; (which is a widely found carbohydrate used for mid-term storage of energy) for this purpose. Paper 3 lists a density for Glycogen between 1.40–1.62 g/cm³, so fat has only 55-65% of it's density. Since the energy density of fat is about 2.25x that of carbohydrates, fat is still better.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Adenosine_triphosphate&quot; rel=&quot;noreferrer&quot;&gt;ATP&lt;/a&gt; in comparison, it has relatively little energy to provide. ATP delivers about 32.3 kJ/mole (with 507.18 g/mole this make around 64 J/gram) per phosphate released from the molecule, which is 128 J/gram if both phosphates are released. This is approximately 300x less energy per gram than fat. This makes sense, since fats are completely oxidized (down to water and carbon dioxide), while in ATP only the phosphate bonds are broken. ATP acts as an energy carrier in the body and not as an energy storage molecule.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://biomedgerontology.oxfordjournals.org/content/56/5/B191.full&quot; rel=&quot;noreferrer&quot;&gt;Specific Force Deficit in Skeletal Muscles of Old Rats Is Partially&#xA;Explained by the Existence of Denervated Muscle Fibers&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3896/w982ekoj_pdf.htm&quot; rel=&quot;noreferrer&quot;&gt;Association of adiponectin and resistin with adipose tissue&#xA;compartments, insulin resistance and dyslipidaemia&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069651&quot; rel=&quot;noreferrer&quot;&gt;Shifts in the Distribution of Mass Densities Is a Signature of&#xA;Caloric Restriction in Caenorhabditis elegans&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="-1" LastEditDate="2015-02-13T16:09:18.723" LastActivityDate="2015-02-13T16:09:18.723" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="28514" PostTypeId="2" ParentId="28468" CreationDate="2015-02-11T18:48:27.560" Score="0" Body="&lt;p&gt;here is an interesting article:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://plymsea.ac.uk/1701/1/The_accumulation_of_radioactive_iodine_by_Amphioxus.pdf&quot; rel=&quot;nofollow&quot;&gt;The accumulation of radioactive iodine by Amphioxus&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;summarizing the abstract: it's about cephalocordates that are not vertebrate, so they are close relatives (most related to the ancestors of) the vertebrate. The specific cephalocordate in question is amphioxus.The article talks about a specific gland called the &quot;endostyle&quot; of Amphioxus and it explored the homology with the subpharyngeal gland of the larval form of lampreys (an agnathan, the most primitive of vertebrate) called ammocoete. The sub pharyngeal gland is sort of the same thing as the thyroid. In fact this sub pharyngeal gland or thyroid is a defining characteristic  of vertebrate. The abstract describes an experiment where they took the endostyle from amphioxus and implanted it into a salamander (and amphibian) and it had effects similar to the thyroid gland. This means that this mucous producing gland in the cephalocordates produces compounds that have effects similar to the thyroid&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does the endostyle produce mucous? Because it is essential for their filter feeding (feeding by straining suspended matter and food particles from water). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why concentrate iodine in the mucous, I don't know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other answers explain the function of iodine. This answer was to explain the evolution of iodine concentrating glands at the very beginning of our vertebrate ancestors.&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2015-06-08T01:28:13.190" LastActivityDate="2015-06-08T01:28:13.190" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28515" PostTypeId="1" CreationDate="2015-02-11T21:26:08.943" Score="5" ViewCount="397" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Robert_Wadlow&quot; rel=&quot;nofollow&quot;&gt;Robert Pershing Wadlow&lt;/a&gt; was a man who lived in the first half of the twentieth century. He had hyperplasia of his pituitary gland, which caused him over-produce human growth hormone (HGH), and as a result, &lt;a href=&quot;https://upload.wikimedia.org/wikipedia/en/5/5c/Robert_Wadlow.jpg&quot; rel=&quot;nofollow&quot;&gt;he grew to nearly 9 feet (2.75m)&lt;/a&gt;. He had difficulty managing his body size and died at age 22, with no sign that this growth was slowing down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.webmd.com/fitness-exercise/human-growth-hormone-hgh&quot; rel=&quot;nofollow&quot;&gt;HGH can be used for medicinal purposes&lt;/a&gt;, and it seems that doctors prescribe it for conditions like chronic underdevelopment and HGH deficiencies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Putting aside ethical or government regulation issues, is it theoretically possible for someone (like a &quot;fully grown&quot; adult) to artificially grow beyond their genetic potential by providing them with regular doses of HGH? If not, what was different about Wadlow's case?&lt;/p&gt;&#xA;" OwnerUserId="13418" LastEditorUserId="16651" LastEditDate="2016-01-20T19:33:08.320" LastActivityDate="2018-09-11T10:50:44.997" Title="Can we artificially increase human growth using HGH?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;growth&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="28516" PostTypeId="2" ParentId="28484" CreationDate="2015-02-11T21:38:36.557" Score="7" Body="&lt;p&gt;The short answer, which has already been pointed out by user137, is that females are diploid while males are haploid. Bees do not have sex chromosomes per se; rather sex is determined by the &lt;em&gt;csd&lt;/em&gt; gene on chromosome III (&lt;em&gt;csd&lt;/em&gt; stands for complementary sex determination). Diploid bees that are heterozygous at the &lt;em&gt;csd&lt;/em&gt; locus (i.e. contain two different alleles (versions of a gene) for &lt;em&gt;csd&lt;/em&gt;) are female (workers).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bees that are haploid at the &lt;em&gt;csd&lt;/em&gt; are males. Interestingly, diploid bees that are homozygous at the &lt;em&gt;csd&lt;/em&gt; (i.e. contain two copies of the same &lt;em&gt;csd&lt;/em&gt; allele) are also males. But in the honey bee, these bees do not survive as they are killed by workers before they mature. In some other haplodiploid species, however, both haploid and diploid males are viable (&lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF01240420&quot; rel=&quot;nofollow&quot;&gt;the bumble bee &lt;em&gt;Bombus terrestris&lt;/em&gt; for example&lt;/a&gt;). Also note that diploid honey bee drones can be viable if they (somehow) make it to maturity without being killed by workers (e.g. &lt;a href=&quot;http://ncbi.nlm.nih.gov/pubmed/16475107&quot; rel=&quot;nofollow&quot;&gt;see here&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="13419" LastEditorUserId="13419" LastEditDate="2015-02-11T22:58:25.883" LastActivityDate="2015-02-11T22:58:25.883" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="28517" PostTypeId="1" AcceptedAnswerId="29718" CreationDate="2015-02-11T22:22:46.457" Score="3" ViewCount="268" Body="&lt;p&gt;In atherosclerosis, why macrophage store all the cholesterol from oxLDL inside, and turns to foam cell, and not just degrade it and going back to blood? (there are some amount that leave the plaque, but much more stay (&lt;em&gt;J Clin Invest. 2011 May;121(5):2025-36. doi: 10.1172/JCI43802. Epub 2011 Apr 18.&lt;/em&gt;))&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reading a lot about atherosclerosis, but no explanation about why macrophages stay there and form a plaque, instead leave or at least break the cholesterol.&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="10104" LastEditDate="2015-02-12T12:37:42.210" LastActivityDate="2015-02-19T23:09:34.100" Title="Why oxLDL accumulate to form foam cells?" Tags="&lt;hematology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28519" PostTypeId="2" ParentId="28509" CreationDate="2015-02-11T23:13:57.313" Score="2" Body="&lt;p&gt;I'm just going to link you to another post &lt;a href=&quot;https://biology.stackexchange.com/questions/27678/why-do-the-size-of-the-phase-1-notch-vary-among-cardiac-cells/27695#27695&quot;&gt;here&lt;/a&gt;, which I believe answers the same question. It's because the facilitation of the transient outward current if much more prominent in epicardial regions than in endocardial regions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And the following citation, &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.2005.086223/pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;Transient outward potassium current, ‘Ito’, phenotypes in the mammalian left ventricle: underlying molecular, cellular and biophysical mechanisms,&quot;&lt;/a&gt; provides some mechanistic insight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer the rest of the question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in an ECG you have leads that record whether a charge is moving toward, or away from the lead. These net charges are reflected on the ECG as either positive or negative deflections. You have a signal from the sinoatrial node that causes a depolarization in the right atrium, then the left atrium (biphasic p wave). In each case, however, we see the positive p wave because in this depolarization the net charge is moving toward the electrodes. Studies on atrial repolarization note that &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19149788&quot; rel=&quot;nofollow noreferrer&quot;&gt;yes&lt;/a&gt;, the atrial repolarization is generally obscured by the QRS complex &lt;em&gt;but&lt;/em&gt; &lt;strong&gt;occurs with polarity opposite that of the p wave&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With the ventricles, and the T wave you end up with a special case. The endocardial regions and the interventricular septum are the first to depolarize, and you get the QRS complex. These regions have a longer period of contraction than the epicardial regions, however. The outside of the ventricles begin to repolarize quickly (transient outward current, surface becomes more positive), and this repolarization begins at the apex and propagates toward the base of the heart. Where you'd get a negative T wave with the change in charge, &lt;strong&gt;the direction that the repolarization travels causes you to get a positive reading&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-02-14T16:03:52.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28520" PostTypeId="1" AcceptedAnswerId="28530" CreationDate="2015-02-12T00:30:51.050" Score="11" ViewCount="3974" Body="&lt;p&gt;The general understanding is that when I touch an object, I perceive its (relative) temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A metal object at room temperature, however, will often feel cool to the touch.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leads me to believe that the skin senses heat flux in addition to, or instead of temperature.&#xA;(The metal conducts heat well, and therefore creates a greater flux when touched than a more insulative material.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am unfamiliar with the chemical process by which temperature or flux is converted into meaningful signals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do humans perceive temperature or heat-flux? (or both?)&lt;/p&gt;&#xA;" OwnerUserId="13422" LastActivityDate="2015-02-13T13:23:59.913" Title="Do humans perceive temperature or heat-flux? (or both?)" Tags="&lt;skin&gt;&lt;perception&gt;&lt;temperature&gt;&lt;senses&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28521" PostTypeId="2" ParentId="28479" CreationDate="2015-02-12T02:04:26.313" Score="14" Body="&lt;p&gt;I think it's just a case bearing moth larva (Tinea pellionella).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AGw1U.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.hantsmoths.org.uk/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.hantsmoths.org.uk/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="1320" LastEditDate="2017-07-16T17:30:30.783" LastActivityDate="2017-07-16T17:30:30.783" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28522" PostTypeId="2" ParentId="28520" CreationDate="2015-02-12T02:06:21.937" Score="5" Body="&lt;p&gt;This is the modified answer in response to the discussion:&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Facts:&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;There are warmth and cold receptors in the body at two places: The Peripheral receptors and the Central Receptors&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The peripheral receptors are present in skin and the central receptors in the body core at multiple sites the notable site being the hypothalamus&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The Temperature receptors have two patterns of firing - The tonic response (sustained firing rate due to steady rise and maintainance in temperature over long time) and the phasic response (also called dynamic response - response to short changes in the temperature)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The Warmth receptors fire maximally at 44 - 46 degrees celcius. The firing stops almost completely at about 48-49 degrees celcius beyond which there is no effective thermoregulation&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The Cold receptors fire maximally ar 20 - 35 degrees celcius.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9QVfN.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;What is measured?&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The peripheral receptors sense the temperature of skin.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The central receptors measure the core body temperature.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Only the temperature is measured as WYSIWYG mentions&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However &lt;strong&gt;the frequency of stimulus&lt;/strong&gt; (How frequently the nerves fire - this depends on the temperature range in which the respective receptors fire) and &lt;strong&gt;the two types of receptors&lt;/strong&gt; present on the skin allows the brain to &lt;strong&gt;interpret the flux&lt;/strong&gt;. So &lt;strong&gt;Chris Stronks is correct&lt;/strong&gt; in telling the heat flux is &lt;strong&gt;perceived&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Mechanism of feeling cold:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;When you touch a cold object the heat is lost through conduction and radiation through the portion of skin that is in contact with the object. The cold will cause vasoconstriction of that part of skin - This means that the temperature of that part of skin rapidly equilibriates with that of the object. As there is rapid cooling (assuming that the object is cold) the rate of firing of the warmth receptors decrease and the rate of firing of the cold receptors increase. This allows the brain to interpret that the skin is losing heat (the flux).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The radiation part of heat loss is more appreciated when you pass a uncurtained window during the winter - the temperature difference is so great that very high loss of heat occurs through radiation that you shiver. You have to note that during these instances there is no decrease in the core body temperature. The actual decrease in core body heat needs a long exposure to such conditions. In the scenarios detailed above the heat loss is primarily from skin which reflects the ambient conditions (very quickly). Thus the peripheral receptors effect &lt;strong&gt;Anticipatory Control&lt;/strong&gt; which is effectively measuring the flux of heat through skin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The opposite occurs when you suddenly stand beneath the sun coming from a cold room - the radiant temperature of the sun being so great will cause the skin temperature to rapidly rise causing the body to feel very hot (though the core body temperature has not changed much).&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Interesting details that may increase your understanding (though not directly related to the question):&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The heat control effected through sensing the change in the skin temperature is called &lt;strong&gt;Anticipatory Control&lt;/strong&gt;. In this the brain &quot;anticipates&quot; what is going to happen - for example a sudden cold draught - and will respond to it - reponds by increasing the heat production (shivering).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heat control effected through sensing the core body temperature is &lt;strong&gt;Negative Feedback Control&lt;/strong&gt;. In this the brain &lt;strong&gt;responds&lt;/strong&gt; to increase in the core body temperature and takes steps to remedy this (the response will bring the temperature back to the set point).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;For more see:Boron &amp;amp; Boulpaep Textbook of Medical Physiology, 2nd Edition, Chapter 59.&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-02-12T16:18:19.230" LastActivityDate="2015-02-12T16:18:19.230" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="28523" PostTypeId="1" AcceptedAnswerId="28524" CreationDate="2015-02-12T03:40:58.313" Score="3" ViewCount="26578" Body="&lt;p&gt;I was always curious as to if or how much of the internal structure or workings of the umbilical cord are still in existence as we age.  What happens to it over time?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The wikipedia article &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Navel#Clinical_significance&quot; rel=&quot;nofollow&quot;&gt;naval&lt;/a&gt; almost exclusively describes physical appearance and only touches on some disorders that affect physical appearance.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then the wikipedia article on &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Umbilical_cord#Physiological_postnatal_occlusion&quot; rel=&quot;nofollow&quot;&gt;umbilical cord&lt;/a&gt; explains what happens briefly after birth, and only touches on it becoming part of the circulatory system.  What does it actually do in later life, as part of that system?&lt;/p&gt;&#xA;" OwnerUserId="13427" LastEditorUserId="9943" LastEditDate="2015-02-13T09:14:41.203" LastActivityDate="2015-02-13T09:14:41.203" Title="What happens to our umbilical cord internally as we age?" Tags="&lt;physiology&gt;&lt;human-anatomy&gt;&lt;development&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28524" PostTypeId="2" ParentId="28523" CreationDate="2015-02-12T05:37:22.223" Score="5" Body="&lt;p&gt;The umbilical cord, which contains the umbilical arteries and vein so important for nutrient, oxygen and waste transport before birth, becomes useless pretty much the moment the lungs start working (the kidneys already started before birth). As the baby breathes, the two arteries constrict to stop flow from the newborn to the placenta. The Wharton's Jelly, a structural element in the cord, causes collapse of the vein on cooling to outside temperature. Within a matter of a few minutes, the whole system is shut down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within the infant, the umbilical vein and ductus venosus (which carried blood to the liver and the inferior vena cava) close up and degenerate into fibrous remnants known as the round ligament of the liver and the ligamentum venosum respectively. The round ligament basically just divides the left part of the liver into medial and lateral sections. The ligamentum venosum does basically the same thing on the posterior surface of the liver. Both ligaments maintain their attachment to the umbilicus. (The small paraumbilical veins are unimportant except in the case of severe portal hypertension, where they act as a portacaval anastomosis.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The parts of the arteries closest to the navel degenerate into what are known as the medial umbilical ligaments (which basically serve no purpose whatsoever and are buried in the abdominal wall), while the more internal remaining sections are retained as part of the circulatory system as the umbilical artery. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The umbilical artery in adults is a branch of the anterior division of the internal iliac artery. The umbilical artery is found in the pelvis, and gives rise to the superior vesical arteries (supplying the superior part of the bladder, and parts of the ureters. In males, it also gives rise to the the deferential artery which supplies the ductus deferens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LHZ18.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-02-12T05:54:13.500" LastActivityDate="2015-02-12T05:54:13.500" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28526" PostTypeId="2" ParentId="28467" CreationDate="2015-02-12T08:41:13.417" Score="0" Body="&lt;p&gt;One mechanism through which low temperatures cause pain is through vasoconstriction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cold environment causes constriction of blood vessels in the periphery. This will cause decreased blood flow and the muscles will cramp due to lack of oxygen. The cramping is due to the accumulation of lactic acid (due to activation of anaerobic pathways of metabolism) and carbon dioxide. Both these chemicals will lower the pH which cause pain.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-02-12T08:41:13.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28527" PostTypeId="2" ParentId="28520" CreationDate="2015-02-12T09:04:36.577" Score="4" Body="&lt;p&gt;Flux is defined as amount of heat transferred per unit area per unit time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our body does not perceive heat flux. It perceives temperature and tries to adjust heat exchange mechanisms until thermal homeostasis is achieved (in all warm blooded animals). This is a feedback controlled process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it were to measure heat flux then the body cannot sense if it is at 47⁰C and the environment is at 60⁰C or if it is at 37⁰C and the environment is at 50⁰C. The heat sensors in our body have evolved to function at 37⁰C. Their conformation changes with increase/decrease in temperature thereby opening or closing the ion channels. The conformation is a function of temperature. If you put that channel in 45⁰C and try to measure a temperature higher that that then it wont work in the same way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Body function and metabolism are sensitive to absolute temperature. Also see &lt;a href=&quot;https://biology.stackexchange.com/questions/21258/how-does-temperature-influence-the-rate-of-protein-degradation/24218#24218&quot;&gt;this&lt;/a&gt; post. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So while temperature sensing is absolutely necessary even for cold-blooded animals, plants and other organisms, there is no mechanism to measure heat flux. You can just measure the effect of heat not the flow of heat. For e.g. you cannot say if a body is cooling more rapidly than the other just by perceiving it for a short duration. It is possible to consciously calculate heat flux but it is neither measured nor (afaik) is fed in as a parameter to any control systems that regulate body temperature.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-02-13T13:19:56.377" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="28528" PostTypeId="1" CreationDate="2015-02-12T09:47:26.927" Score="5" ViewCount="543" Body="&lt;p&gt;The human brain consists of neurons that transmit impulses like wires that conduct electricity.I am confused about where are our thoughts stored and what really are thoughts? For example if I think about space, what is actually happening in my brain, and in what form is my memory that there are black holes in space, stored?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After doing a little bit of research I somehow came to the conclusion that thoughts are nothing but the electro-chemical reactions that are triggered by external stimuli and Hippocampus is responsible for storing long term memory. But I was unable to understand what the following paragraph means:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The hippocampus helps to solidify the pattern of connections that form a memory but the memory itself depends on the solidification of connections between the individual brain cells&quot;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Please explain it. Am I correct so far? Please help. &lt;/p&gt;&#xA;" OwnerUserId="3881" LastEditorUserId="3881" LastEditDate="2015-02-14T08:59:03.530" LastActivityDate="2015-02-14T08:59:03.530" Title="What actually are thoughts?" Tags="&lt;human-biology&gt;&lt;brain&gt;&lt;memory&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="0" ClosedDate="2015-02-15T00:44:35.117" ContentLicense="CC BY-SA 3.0" />
  <row Id="28529" PostTypeId="2" ParentId="28500" CreationDate="2015-02-12T12:11:22.657" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://phylot.biobyte.de/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://phylot.biobyte.de/&lt;/a&gt; performs the requisite task (generating a phylogenetic tree based on the specific organisms provided, using the NCBI taxonomy tables). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, the input of tree elements&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Trichomonas vaginalis,Trypanosoma brucei,Homo sapiens,Fibroporia&#xA;  radiculosa,Paramecium tetraurelia,Tetrahymena&#xA;  thermophila,Cryptosporidium muris,Cryptosporidium hominis,Blastocystis&#xA;  hominis&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;generates the tree &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tvzgK.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-02-12T12:11:22.657" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28530" PostTypeId="2" ParentId="28520" CreationDate="2015-02-12T12:18:30.517" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans sense &lt;em&gt;temperature differences&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;&lt;sup&gt;(Including edits based upon comments)&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the question is &quot;Do humans &lt;strong&gt;&lt;em&gt;perceive&lt;/em&gt;&lt;/strong&gt; temperature or heat-flux?&quot;, I will answer the answer from a &lt;em&gt;psychophysical&lt;/em&gt; perspective, i.e., by dealing with sensory &lt;em&gt;awareness&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just as with many other sensory systems, temperature sensors in the human body &lt;strong&gt;&lt;em&gt;adapt&lt;/em&gt;&lt;/strong&gt; to ambient stimuli (i.e., constant absolute stimulus levels). In other words, after being exposed for a while to a certain temperature, one looses the perception of temperature &lt;em&gt;per se&lt;/em&gt; (assuming temperatures are within comfortable limits of course, otherwise general discomfort will arise such as shivering or sweating etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, temperature sensing in humans &lt;strong&gt;is not absolute, but differential&lt;/strong&gt;, and occurs when differences occur relative to the baseline.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.3758/BF03212769#page-1&quot; rel=&quot;nofollow&quot;&gt;Holmes and Wood (1968)&lt;/a&gt; mention in their Introduction the following, and I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...three variables of thermal stimulation [...] affect the sensitivity of human subjects to warm and cool stimuli. These are (1) the temperature to which the skin has been adapted, (2) the area of skin over which the thermal energy is applied, and (3) the rate at which the temperature of the skin is changed.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Variables (1) and (3) clearly emphasize the differential nature of temperature perception in humans. Variable (2) is a general psychophysical phenomenon, and basically shows that when a stimulus is sufficiently large, temperature differences will be more easily felt, while when the skin surface being stimulated is excessively small (say a needle with a small temperature difference is pressed against the skin) certain temperature differences may not be felt any longer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regard to your question on metal and whether heat-flux can be sensed: a metal surface will feel cool only when it is lower in temperature than your body. Suppose now you touch a metal object at room temperature, i.e. lower than your body temperature. In that case, as you already indicate, it will draw away heat quickly from your skin by conduction, creating a 'heat-flux' if you like. The extraction of heat thereby elicits a powerful stimulus, because a large temperature difference creeps into your skin as heat is drawn away from your skin and underlying tissues. As such, and contrary to other answers given elsewhere, I explicitly say &lt;strong&gt;yes, 'heat-flux' can be sensed&lt;/strong&gt; as it &lt;em&gt;per definition&lt;/em&gt; generates a &lt;strong&gt;temperature difference&lt;/strong&gt;. This in contrast to touching insulators like wood or plastic, which will quickly adopt the temperature of the skin very locally where you touch it. However, as has been pointed out by others - this &lt;strong&gt;does not mean&lt;/strong&gt; that temperature is measured by &lt;strong&gt;heat-flux sensors &lt;em&gt;per se&lt;/em&gt;&lt;/strong&gt;. In contrast, temperature is measured by temperature sensors that detect temperature differences (&lt;em&gt;differential stimuli&lt;/em&gt;) between skin and external media. Because a temperature change is also a differential stimulus, it will also be detected, and hence 'heat-flux' will therefore be detected as well.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;/sup&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;a href=&quot;http://link.springer.com/article/10.3758/BF03212769#page-1&quot; rel=&quot;nofollow&quot;&gt;Holmes &amp;amp; Wood, &lt;em&gt;Perception &amp;amp; Psychophysics&lt;/em&gt; 1968; &lt;strong&gt;3&lt;/strong&gt;:81-4&lt;/a&gt;&lt;/sup&gt;  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-02-13T13:23:59.913" LastActivityDate="2015-02-13T13:23:59.913" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="28534" PostTypeId="1" CreationDate="2015-02-12T18:40:18.287" Score="2" ViewCount="1277" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Digitalis is a drug that can be used during coronary insufficiency to&#xA;  increase the strength of cardiac muscle contraction. But when&#xA;  overdosages of digitalis are given, depolarization duration in one&#xA;  part of the ventricles may be increased out of proportion to that of&#xA;  other parts. As a result, nonspecific changes, such as T wave&#xA;  inversion or biphasic T waves, may occur in one or more of the&#xA;  electrocardiographic leads. A biphasic T wave caused by excessive&#xA;  administration of digitalis is shown in Figure.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BqqG1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, changes in the T wave during digitalis administration are often the earliest signs of digitalis toxicity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was reading about it in &lt;strong&gt;Guyton and Hall Physiology (volume 1, heart , chapter 12)&lt;/strong&gt; and there was nothing about this that answers my questions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And my questions are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why is &lt;strong&gt;T wave&lt;/strong&gt; more affected by digitalis toxicity?&lt;/li&gt;&#xA;&lt;li&gt;Why does it cause &lt;strong&gt;Biphasic&lt;/strong&gt; T wave?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerDisplayName="user12874" LastEditorUserId="11841" LastEditDate="2015-02-15T12:41:53.580" LastActivityDate="2015-02-16T11:53:51.810" Title="Biphasic T wave caused by digitalis toxicity" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;homework&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28535" PostTypeId="1" CreationDate="2015-02-12T19:43:51.297" Score="2" ViewCount="412" Body="&lt;p&gt;I recently read an article on how DNA barcoding was used to identify species present in health products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also read an article about how Real-Time PCR was used to identify meat species in meat products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm curious as to why one method is used over another. I know that DNA barcoding uses mitochondrial DNA to detect species, and Real-Time PCR uses species-specific primers to detect species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I correct in thinking that real-time PCR cannot identify unknown species, but can tell you if the DNA matches a specific species you're looking for? For example, if I test for &lt;em&gt;E. zebra&lt;/em&gt; but find something else, I cannot identify that unknown species and more testing is required?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whereas in DNA barcoding, all I do is match the results against a huge list of known species in a database, which means I can identify unknown species without providing any prior knowledge?&lt;/p&gt;&#xA;" OwnerUserId="13435" LastEditorUserId="3340" LastEditDate="2015-02-13T05:40:23.887" LastActivityDate="2015-02-13T05:40:23.887" Title="DNA barcoding and real-time PCR" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;species-identification&gt;&lt;pcr&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28536" PostTypeId="1" CreationDate="2015-02-12T20:49:44.283" Score="2" ViewCount="68" Body="&lt;p&gt;I'm curious about how protein structures are defined in general, but in particular, I'm wondering how a target structure can be specified without knowing the amino acid sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, in protein design (or from what I gather on the wikipedia page &lt;a href=&quot;http://en.wikipedia.org/wiki/Protein_design&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Protein_designs&lt;/a&gt;), scientists design a 3D structure that will perform a particular function.  They then try to come up with an amino acid sequence that will fold properly into that structure.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can a 3D structure be defined if no amino acid sequence (and hence no molecular geometry) has been determined?&lt;/p&gt;&#xA;" OwnerUserId="13436" LastActivityDate="2015-02-12T20:49:44.283" Title="Protein Design - Target Structure Specification" Tags="&lt;amino-acids&gt;&lt;protein-folding&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28538" PostTypeId="1" CreationDate="2015-02-12T22:37:31.710" Score="2" ViewCount="29" Body="&lt;p&gt;Regardless of the initial seed orientation, the root always grows/sprouts/germinates &quot;towards gravity&quot; (see &lt;a href=&quot;http://www.robsplants.com/images/seed/FilterSprouts2.jpg&quot; rel=&quot;nofollow&quot;&gt;picture&lt;/a&gt;), sometimes curving around in sharp 180&amp;deg;. What is the mechanism responsible for the &lt;strong&gt;gravity sensing&lt;/strong&gt; and for the &lt;strong&gt;growth adjustment&lt;/strong&gt;?&lt;/p&gt;&#xA;" OwnerUserId="13437" LastActivityDate="2015-02-12T22:37:31.710" Title="What mechanism is responsible for germinating in the right direction (root towards gravity)?" Tags="&lt;germination&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2015-02-13T09:07:02.910" ContentLicense="CC BY-SA 3.0" />
  <row Id="28539" PostTypeId="1" CreationDate="2015-02-12T23:16:33.420" Score="10" ViewCount="223" Body="&lt;p&gt;I'm looking for a cheap non-invasive ways to approximate the age of a tree (a birch). Measuring the radius pops up in the mind as the first alternative. How would one do that? Measure at multiple defined heights?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm hoping that I could get some kind of confidence interval for the approximation, so that the data could be used in a scientific publication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or is there any reliable DIY radiocarbon dating technique?&lt;/p&gt;&#xA;" OwnerUserId="13438" LastActivityDate="2015-06-05T17:36:28.220" Title="How well does the radius of a tree correlate with its age?" Tags="&lt;senescence&gt;&lt;plant-anatomy&gt;&lt;data&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28541" PostTypeId="2" ParentId="28535" CreationDate="2015-02-13T01:38:11.363" Score="3" Body="&lt;p&gt;You've done a pretty decent job of answering your own question, but there are a few things that can be elaborated on.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The general convention is to use the mitochondrial Cytochrome C Oxidase 1 (&lt;em&gt;COI&lt;/em&gt;) gene for barcoding animals and chloroplast genes (&lt;em&gt;rbcL&lt;/em&gt;, &lt;em&gt;matK&lt;/em&gt;, and &lt;em&gt;trnH-psbA&lt;/em&gt;) for plants. The three biggest reasons for selecting these genes are 1) their ubiquity; 2) the presence of many copies per cell, so it's easier to PCR amplify the sequences; and 3) mitochondrial and plastid DNA has a much higher mutation rate than nuclear DNA, making it possible to uniquely barcode very closely related organisms. This method is incredibly sensitive, reliable, and easy. The original DNA barcoding publication can be found at &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/270/1512/313&quot; rel=&quot;nofollow&quot;&gt;doi: 10.1098/rspb.2002.2218&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks to the efforts of consortia like &lt;a href=&quot;http://www.barcodeoflife.org/content/about/what-cbol&quot; rel=&quot;nofollow&quot;&gt;CBOL&lt;/a&gt;, &lt;a href=&quot;http://www.boldsystems.org/&quot; rel=&quot;nofollow&quot;&gt;BOLD&lt;/a&gt; and &lt;a href=&quot;http://ibol.org/&quot; rel=&quot;nofollow&quot;&gt;iBOL&lt;/a&gt;, there are now many millions of reference sequences databased, covering pretty much any multicellular organism you are ever likely to encounter (assuming you don't work on a deep-seq sub or something).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you say in your post, there are significant limitations to using qPCR to identify species. You have to know beforehand what it is you are looking for, and you are left with a simple yes-no. This is not to say there is no place at all for qPCR in the species identification game, however. The method is very fast, and in cases where you are only interested in detecting a single species or small number of species, it's much more convenient than getting the DNA sequenced (for example, during quality control in a meat processing plant, &lt;a href=&quot;http://www.tandfonline.com/doi/full/10.1080/02652030701584041&quot; rel=&quot;nofollow&quot;&gt;doi: 10.1080/02652030701584041&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="13093" LastActivityDate="2015-02-13T01:38:11.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28543" PostTypeId="1" AcceptedAnswerId="28551" CreationDate="2015-02-13T04:47:06.993" Score="3" ViewCount="2973" Body="&lt;p&gt;There are more than a few scenes in &lt;em&gt;Gravity&lt;/em&gt; that I find dubious. Specifically the ones where people are revolving very quickly, either about their own center of gravity or at the end of a rather long pole. I'd guess we'd need to know how long the pole was, but I'm more concerned with a person themselves, just flipping around out there (and I suppose we'd need their height, or does that cancel out?). How fast can they spin until it's night-night? Is it reasonable to assume they should've passed-out in at least one of those scenes?&lt;/p&gt;&#xA;" OwnerUserId="8559" LastActivityDate="2015-02-14T10:59:54.900" Title="Maximum RPM in zero-g before losing consciousness, spinning head-over-heels" Tags="&lt;blood-circulation&gt;&lt;circulatory-system&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28545" PostTypeId="2" ParentId="28535" CreationDate="2015-02-13T05:36:31.427" Score="2" Body="&lt;p&gt;DNA Barcoding is a method or a protocol which, as you have already mentioned, uses genetic markers to identify species. The barcodes can be &quot;scanned&quot; using PCR.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now Real-Time PCR is just a quantitative version of PCR. You don't need that to look for qualitative aspects. However in a mixed sample you may be able to calculate percentage constitution of the sample by each species, using Real-Time PCR.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-02-13T05:36:31.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28549" PostTypeId="2" ParentId="28528" CreationDate="2015-02-13T08:18:26.607" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;The hippocampus helps to solidify the pattern of connections that form a memory but the memory itself depends on the solidification of connections between the individual brain cells&quot;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This refers to the phenomenon called &lt;a href=&quot;http://en.wikipedia.org/wiki/Long-term_potentiation&quot; rel=&quot;nofollow&quot;&gt;Long Term Potentiation&lt;/a&gt; which regulates synaptic strength between neurons. Certain patterns of firing (high frequency) causes the post synaptic neuron to strengthen the synapses. One way of doing that is by increasing the number of receptors (Usually NMDA receptors). Due to this, the response would be stronger in the next firing event. You can imagine its effects- more number of times you read a passage better will you remember it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hippocampus is involved in this process (it is one region where a lot of synaptic dynamics happens) but consolidation and long term storage of memories is handled by the cortex. Essentially what happens when a memory is formed is strengthening of synapses.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-02-13T08:18:26.607" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28550" PostTypeId="1" CreationDate="2015-02-13T10:04:49.093" Score="2" ViewCount="47" Body="&lt;p&gt;Are there any known neural correlates of the function of the cardiovascular system? I'm looking for research results that use standard brain imaging techniques (e.g. electroencephalography, magnetoencephalography, or functional magnetic resonance imaging), and compare the brain signals to respiratory and/or electrocardiographic signals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually, ECG is frequently seen in EEG and MEG recordings. It is considered as an artefact, and typically removed in an early phase. Only the QRS complex is usually visible (or the R wave). If the ECG was recorded from the chest/limbs, proper signals would be gained. It would be interesting to compare the heart rate variability etc. to brain signals but has this for example been already done?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't have much background to respiratory signals, so I'm particularly interested about that.&lt;/p&gt;&#xA;" OwnerUserId="13444" LastEditorUserId="13444" LastEditDate="2015-02-13T12:30:52.860" LastActivityDate="2015-02-13T12:30:52.860" Title="Neural correlates of the function of the cardiovascular system?" Tags="&lt;human-biology&gt;&lt;cardiology&gt;&lt;electrophysiology&gt;&lt;electrocardiography&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28551" PostTypeId="2" ParentId="28543" CreationDate="2015-02-13T10:41:06.320" Score="7" Body="&lt;p&gt;I &lt;em&gt;think&lt;/em&gt; people can easily endure head-over-heel revolutions in space such as seen in &lt;em&gt;Gravity&lt;/em&gt;. I am no mathematician (let alone physicist, both of whom could answer this more accurately) but here is my reasoning (faulty though it may be).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are assuming that someone would pass out from lack of blood supply to the brain.  Given we have absolutely no problems normally at 1 g (the force of gravity on earth), the average non-couch-potato person can tolerate forces of up to 20 G for less than 10 seconds, to 10 G for 1 minute, and 6 G for 10 minutes before passing out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But g is very dependent on (as you stated) distance from center. It's also very dependent on revolutions per minute.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$g=\frac{R\left(\frac{\pi\times rpm}{30}\right)^2}{9.81}$$ &#xA;or &#xA;$$R=\frac{9.81 g}{\left(\pi\times rpm\over30 \right)^2}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;g = Decimal fraction of Earth gravity&lt;br&gt;&#xA;R = Radius from center of rotation in &lt;em&gt;meters&lt;/em&gt;&lt;br&gt;&#xA;π = 3.14159&lt;br&gt;&#xA;rpm = revolutions per minute&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The average North American male is 1.75m tall. That means the distance of the top of the head and bottom of the feet (if stretched out at full length) from center is under a meter (&lt;strong&gt;.875m&lt;/strong&gt;). At &lt;strong&gt;60 rpm's&lt;/strong&gt; (that's pretty fast), solving for the above, &lt;strong&gt;g = 3.52&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;g = [.875({3.14159x60}/30)^2]/9.81 = 3.521 (so just over 3.5G)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gravity at the top of the head and the bottom of the feet would be 3.5G, while the gravity at the center would be zero G. The heart can easily compensate for that for a while. An astronaut, trained for increased Gs, can do well for longer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Much worse than too little blood to the head is &lt;em&gt;too much&lt;/em&gt;, which is what I would be worried about. Eventually, slightly less than half the blood volume would end up below the waist with the feet feeling the most pressure, and the rest above, with the brain being engorged with blood, which can cause hemorrhage (not taking into account here precise fluid physics). I'm not sure how this would play out in space over longer periods of time, but survival would be the norm for the scenes we see in &lt;em&gt;Gravity&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;An Air Force physician named John Stapp was the first to determine just what humans could take in the way of G forces. On his final run, firing nine solid-fuel rockets, his &quot;sled&quot; accelerated to 632 miles per hour in five seconds, slamming him into two tons of wind pressure, then came to a stop in just over one second. A witness said it was &quot;absolutely inconceivable anybody could go that fast, then just stop, and survive.&quot; But Stapp did—in fact, he went on to live another 45 years, dying quietly at home in 1999 at the age of 89—and he experienced a record-breaking &lt;strong&gt;46.2 G's&lt;/strong&gt;. For an instant, his 168-pound body had weighed over 7,700 pounds.  Stapp's efforts put him on the cover of Time, and he was called &quot;The Fastest Man on Earth.&quot; More importantly, his work led to greatly improved safety in both planes and cars, and he gave us a much-improved understanding of human tolerance to G forces.&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.pbs.org/wgbh/nova/space/gravity-forces.html&quot; rel=&quot;nofollow&quot;&gt;All About G Forces&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-02-14T10:59:54.900" LastActivityDate="2015-02-14T10:59:54.900" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28553" PostTypeId="1" AcceptedAnswerId="28558" CreationDate="2015-02-13T17:50:11.037" Score="1" ViewCount="59" Body="&lt;p&gt;This in fact has bugged me for years, but now I finally remembered to ask.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suppose that if one variation is more frequent, it can be labeled as the default, but what about variations that are equally as common?&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19542902&quot; rel=&quot;nofollow noreferrer&quot;&gt;The example&lt;/a&gt; that I just saw, it seems that the frequency of both variants is the same, and yet somebody claims that G is the default and C is the polymorphism:&lt;br&gt;&#xA;&lt;a href=&quot;http://hell.org.pl/~kamyk/stackexchange/Zorena1.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Polymorphism with genotypes CC, CG and GG occuring in 30, 40 and 30% of the control group, respectively http://hell.org.pl/~kamyk/stackexchange/Zorena1.jpg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe it is possible to determine which one was first, but how? Is there ancient data about polymorphism frequencies?&lt;/p&gt;&#xA;" OwnerUserId="1427" LastActivityDate="2015-02-13T22:17:32.657" Title="How do scientists decide which version of a polymorphism is the main one?" Tags="&lt;human-genetics&gt;&lt;nomenclature&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28554" PostTypeId="2" ParentId="28553" CreationDate="2015-02-13T18:35:31.247" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;[..] G is the default and C is the polymorphism&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;An allele (or just a nucleotide variant) cannot be &quot;the polymorphism&quot;. There is polymorphism, if a given locus (or just a given nucleotide position) is polymorphic, that is, if as this position, there are different variants existing in the population. Therefore, an allele cannot be called &lt;code&gt;polymorphism&lt;/code&gt;, only a locus can be called to be polymorphic and if a locus is polymorphic, then there is some polymorphism in the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have never of people talking about the &lt;code&gt;main&lt;/code&gt; or &lt;code&gt;default&lt;/code&gt; variant. Do they use this word in the article you link? If yes, can you please indicate where?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Commonly, people talk about the wildtype versus the mutant variants. In this case, the wildtype variant is just the most common &lt;code&gt;variant&lt;/code&gt;. Rarely I have seen people referring to wildtype variant when talking about variants that are at low frequency because the mutant is increasing in frequency and slowly reaching fixation. In such case, the wildtype mutant would correspond to the original variant at an arbitrary time point in the past but would not depend on the frequencies observed today.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-02-13T19:00:31.793" LastActivityDate="2015-02-13T19:00:31.793" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28555" PostTypeId="1" CreationDate="2015-02-13T21:21:16.420" Score="6" ViewCount="157" Body="&lt;p&gt;Generally variant calling programs (such as GATK-UnifiedGenotyper) look for differences between reference genome and submitted sequence. However, we all know that reference genome consist rare variants in various positions. If submitted sequence has this rare form of that variant, variant call doesn't see it and doesn't report at all. However, that variant could be very precious for analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, how can I solve this problem? What should I do to not miss that rare variants even they are in reference genome?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/skzZV.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="13292" LastEditorUserId="5144" LastEditDate="2015-02-13T21:26:28.830" LastActivityDate="2016-05-31T09:30:07.237" Title="Do variant callers miss rare variants in reference?" Tags="&lt;bioinformatics&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28556" PostTypeId="2" ParentId="28555" CreationDate="2015-02-13T21:39:43.480" Score="1" Body="&lt;p&gt;If the reference sequence is associated with a disease or increased susceptibility to some phenotype, the the population you're using to compare against (with a variant) will show protection to it. So either way you're going to find an association, this will just change the sign of the coefficient.&lt;/p&gt;&#xA;" OwnerUserId="9523" LastActivityDate="2015-02-13T21:39:43.480" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28557" PostTypeId="2" ParentId="28553" CreationDate="2015-02-13T22:01:57.837" Score="2" Body="&lt;p&gt;In this case, G is the genotype used for comparison because that's what's in the reference sequence for humans. Of course, this raises the question of why that's the reference. The answer is that it's because that's the sequence from the sample used to create the BAC that was sequenced and used to create that portion of the reference sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, it's not always like that. For example, when we &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885139/&quot; rel=&quot;nofollow&quot;&gt;discovered KCNJ18&lt;/a&gt; and I submitted it for inclusion in the genome, I specifically submitted a sequence that represented the most likely haplotype given all of the samples we had sequenced. Of course, &quot;most likely&quot; may be population dependent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an aside, this is actually a bigger issue with some regions of the genome, where polymorphisms describe whole regions rather than just single bases. In the reference genome, these are the &lt;em&gt;_hap_&lt;/em&gt; chromosomes, which will often contain things like common structural rearrangements. These present a problem currently because they lead to biased mapping and variant calling. The first program known to make proper use of these was only released within the last month, in fact. One of the goals for the next human reference genome is to come up with a convenient graph representation of the genome that can include common polymorphic regions. This should lead to better quality genotyping of patients and study subjects.&lt;/p&gt;&#xA;" OwnerUserId="9523" LastActivityDate="2015-02-13T22:01:57.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28558" PostTypeId="2" ParentId="28553" CreationDate="2015-02-13T22:17:32.657" Score="2" Body="&lt;p&gt;A DNA locus may have two (or more) variants (alleles), but there isn't one termed a &lt;strong&gt;main&lt;/strong&gt; or &lt;strong&gt;default&lt;/strong&gt; variant.  In the example you cite, &lt;a href=&quot;http://www.nature.com/pr/journal/v66/n3/full/pr2009212a.html&quot; rel=&quot;nofollow&quot;&gt;Myśliwska 2009&lt;/a&gt;, the only asymmetric distinction between the G and C alleles that I could see was in this passage:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The polymorphic region −174G&gt;C of IL-6 encoding gene is implicated in&#xA;  transcription of this cytokine. The G&gt;C nucleotide substitution&#xA;  creates...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This passage uses &quot;substitution&quot; (and &quot;G&gt;C&quot; in −174G&gt;C), which suggests that &quot;G&quot; is what is termed the &lt;strong&gt;ancestral&lt;/strong&gt; variant, and &quot;C&quot; a later variant. The ancestral variant was the form that is believed to have been essentially the only form in some ancestral population; the later variant is a mutation (substitution in this example) which became established in part of a later occurring population.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all polymorphisms have their variants characterized in this way.  Those that do usually have DNA sequence evidence showing that species other than humans have a homologous gene, and those genes appear to have only the &quot;ancestral&quot; variant.  For the locus in the example you cite, the human IL6 -174 locus, a early paper by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC508984/&quot; rel=&quot;nofollow&quot;&gt;Fishman et al. (1998)&lt;/a&gt; says this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Considerable interethnic variation in the frequencies of these&#xA;  polymorphisms has been demonstrated (39), which is consistent with our&#xA;  data for the -174C allele, which is considerably rarer in Gujarati&#xA;  Indians and Afro-Caribbeans, compared with UK Caucasians. As all of&#xA;  the primates examined were GG homozygotes, it is likely that this&#xA;  allele is ancestral and that the C allele represents a relatively&#xA;  recent change in the IL-6 5' flanking sequence.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This assessment seems to have become &lt;a href=&quot;http://Considerable%20interethnic%20variation%20in%20the%20frequencies%20of%20these%20polymorphisms%20has%20been%20demonstrated%20(39),%20which%20is%20consistent%20with%20our%20data%20for%20the%202174C%20allele,%20which%20is%20considerably%20rarer%20in%20Gujarati%20Indians%20and%20Afro-Caribbeans,%20compared%20with%20UK%20Caucasians.%20As%20all%20of%20the%20primates%20examined%20were%20GG%20homozygotes,%20it%20is%20likely%20that%20this%20allele%20is%20ancestral%20and%20that%20the%20C%20allele%20represents%20a%20relatively%20recent%20change%20in%20the%20IL-6%2059%20flanking%20sequence.&quot; rel=&quot;nofollow&quot;&gt;generally accepted&lt;/a&gt;.  The rather even distribution of G and C variants in the table you show is likely due to the subjects being of European ancestry, as suggested by this from &lt;a href=&quot;http://www.snpedia.com/index.php/Rs1800795&quot; rel=&quot;nofollow&quot;&gt;SNPedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It [IL6 -174] tends to be quite polymorphic in Caucasians, but Asian&#xA;  and African populations are almost monomorphic (for the (G) allele).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="231" LastActivityDate="2015-02-13T22:17:32.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28559" PostTypeId="2" ParentId="28555" CreationDate="2015-02-13T22:52:09.030" Score="1" Body="&lt;p&gt;Well, you'd hope that the &quot;reference&quot; sequence is of a healthy individual, and won't be carrying a highly detrimental allele that you care about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or get a bunch of control data from the 1K genome project, and compare them to the reference as well; they won't carry the rare alleles that your reference does.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2015-02-13T22:52:09.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28560" PostTypeId="1" CreationDate="2015-02-14T00:12:04.833" Score="2" ViewCount="156" Body="&lt;p&gt;Learning about carbohydrates, I wonder what the differences there are in terms of metabolism, and overall health between the different types of saccharides. In other words, does the body use polysaccharides, such as starches the same, or similar to how it would use a disaccharide like table sugar, sucrose? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It piqued my interest because people seem to put sugars and other types of carbohydrates into totally different categories, and one is seen as &quot;healthy&quot;, the other &quot;unhealthy&quot;.&lt;/p&gt;&#xA;" OwnerUserId="13447" LastEditorUserId="6703" LastEditDate="2015-02-14T01:28:10.120" LastActivityDate="2015-02-14T12:47:34.467" Title="Metabolism of different saccharides" Tags="&lt;metabolism&gt;&lt;nutrition&gt;&lt;carbohydrates&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28562" PostTypeId="1" AcceptedAnswerId="28572" CreationDate="2015-02-14T03:04:59.137" Score="8" ViewCount="719" Body="&lt;p&gt;Many organs can be transplanted nowadays, including the liver, lungs and kidneys. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can the brain be transplanted?&lt;/strong&gt;   &lt;/p&gt;&#xA;" OwnerUserId="13450" LastEditorUserId="9943" LastEditDate="2015-02-14T10:25:34.693" LastActivityDate="2018-05-03T10:10:33.090" Title="Is brain transplantation possible?" Tags="&lt;neuroscience&gt;&lt;neurology&gt;&lt;transplantation&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28563" PostTypeId="1" CreationDate="2015-02-14T05:45:08.350" Score="3" ViewCount="217" Body="&lt;p&gt;Why are fingerprints different from person to person? It can't be genetics. Even identical twins has different sets of fingerprints. What is the deciding factor that form and shape our fingerprints?&lt;/p&gt;&#xA;" OwnerUserId="11855" LastEditorUserId="5198" LastEditDate="2015-02-14T08:05:20.007" LastActivityDate="2015-02-14T08:05:20.007" Title="Why are fingerprints different even in identical twins?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="0" ClosedDate="2015-02-14T16:43:27.617" ContentLicense="CC BY-SA 3.0" />
  <row Id="28564" PostTypeId="2" ParentId="20375" CreationDate="2015-02-14T06:58:18.733" Score="9" Body="&lt;p&gt;You might expect identical twins to have the same fingerprints as twins have virtually indistinguishable DNA. The distinguishing nature of physical characteristics of a person is due to both the inherent individual genetic diversity within the human population as well as the random processes affecting the development of the embryo. &lt;strong&gt;The same would then be true of clones of a person.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the case of fingerprints, the genes determine the general characteristics of the pattern. Fingerprint formation is similar to the growth of capillaries and blood vessels in angiogenesis. The general characteristics of the fingerprint emerge as the skin on the fingertip begins to differentiate. However, the flow of amniotic fluids around the fetus and its position in the uterus changes during the differentiation process. Thus, the cells on the fingertip grow in a microenvironment that is slightly different from hand to hand and finger to finger. The finer details of the fingerprints are determined by this changing microenvironment. A small difference in microenvironment is amplified by the differentiation process of the cells. There are so many variations during the formation of fingerprints that it would be virtually impossible for two fingerprints to be alike.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Therefore, fingerprints aren't entirely a genetic characteristic. They are a part of a ‘phenotype’ which means they are determined by the interaction of an individual’s genes and the intrauterine environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Overall, identical twins’ fingerprints tend to be similar&lt;/strong&gt;. Before genetic testing, the similarity of twins’ fingerprints was used to determine whether they were identical or fraternal. But there always will be subtle differences making even their fingerprints unique.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.cse.msu.edu/rgroups/biometrics/Publications/Fingerprint/JainetalTwinFp_PR02.pdf&quot;&gt;On the similarity of identical twin Fingerprints&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-02-14T07:10:06.120" LastActivityDate="2015-02-14T07:10:06.120" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28566" PostTypeId="2" ParentId="28560" CreationDate="2015-02-14T12:47:34.467" Score="1" Body="&lt;p&gt;If you can digest (break down) the polysaccharides to useable monosaccharides, then they can be incorporated into glycolysis (or some other metabolic pathway!). The metabolic pathways around glycolysis are complex, but here is a representation of some of them:&lt;img src=&quot;https://i.stack.imgur.com/QJcOb.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see in, in the top right corner, sucrose/starch, but also other sugars like nucleosides, can enter the overall simple sugar metabolic pathways. How and what exactly happens to the complex sugars will depend on how they are broken down (if they can be broken down at all) and they will have their own more or less complex metabolic pathways associated with that.&lt;/p&gt;&#xA;" OwnerUserId="5367" LastActivityDate="2015-02-14T12:47:34.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28567" PostTypeId="1" CreationDate="2015-02-14T15:11:59.403" Score="4" ViewCount="939" Body="&lt;p&gt;Do fingerprints change as we grow from child to adult? Most notably, what is the effect of the increase in surface area of palms and fingers on the finger print? Does the finger print simply increases in size, and/or does the pattern change?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And what about old age? As the connective tissue in dermis get lax, how is the fingerprint affected?&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="9943" LastEditDate="2015-02-15T13:20:09.050" LastActivityDate="2015-02-19T02:17:33.483" Title="How does aging affect fingerprint?" Tags="&lt;human-anatomy&gt;&lt;development&gt;&lt;growth&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28569" PostTypeId="1" CreationDate="2015-02-14T17:14:15.980" Score="6" ViewCount="18262" Body="&lt;p&gt;For investigative purposes, I'm searching for a tool that can be used as a quick visual assessment of the the length of time that blood has been exposed to air after the blood flow has stopped.. Let's say that you walk into a room and see someone unconscious. Where blood appears, it had already stopped any fresh flow &amp;amp; has already dried to a dark brown similar to mahogany wood.  That person has been there longer than how many minutes? Please understand that I'm not asking how long the person has been lying there but for &lt;em&gt;at least&lt;/em&gt; how long?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You come upon a dazed person unsteady on their feet with an injury to the face. The blood flow has stopped: the person may have smeared the blood when touching their face but you  see that the blood has not changed to a deep brown and still retains a bright red color..approximately how much time has likely elapsed between the injury occurring and your encounter with the injured person?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know there's no exact time estimate possible without testing but simply for quick field assessments, is anyone willing to hazard an opinion? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In summary: How can I tell the age of a blood stain?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="13456" LastEditorUserId="3340" LastEditDate="2015-03-04T12:27:00.047" LastActivityDate="2018-11-22T23:26:35.647" Title="Time lapse between fresh blood's exposure to air and that same blood turning darker red-brown" Tags="&lt;human-biology&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28570" PostTypeId="1" CreationDate="2015-02-14T23:31:26.197" Score="2" ViewCount="121" Body="&lt;p&gt;I quantified my protein using the standard Bradford method and the A280 methods and obtained values that were far off from the theoretical value of the protein of interest, and therefore was wondering if one method is better to use than the other. &lt;/p&gt;&#xA;" OwnerUserId="12876" LastEditorUserId="948" LastEditDate="2015-02-15T21:39:48.490" LastActivityDate="2015-02-15T21:39:48.490" Title="Which method would more accurately help to identify the unknown concentration of a protein sample between the A280 and the Bradford methods?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;protein-expression&gt;" AnswerCount="0" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="28571" PostTypeId="2" ParentId="28534" CreationDate="2015-02-15T09:09:10.990" Score="2" Body="&lt;p&gt;Digitalis (which was by the way originally synthesized from &lt;a href=&quot;http://en.wikipedia.org/wiki/Digitalis_purpurea&quot; rel=&quot;nofollow noreferrer&quot;&gt;Digitalis Purpurea&lt;/a&gt;) has two mechanisms of action:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The action by which digoxin improves contractility appears to be inhibition of the sarcolemmal Na&lt;span class=&quot;math-container&quot;&gt;$^+$&lt;/span&gt;K&lt;span class=&quot;math-container&quot;&gt;$^+$&lt;/span&gt;-ATPase &amp;quot;pump&amp;quot;, normally responsible for maintaining transmembrane Na&lt;span class=&quot;math-container&quot;&gt;$^+$&lt;/span&gt; and K&lt;span class=&quot;math-container&quot;&gt;$^+$&lt;/span&gt; gradients&lt;/p&gt;&#xA;&lt;p&gt;The major therapeutic electrical effect of digoxin occurs at the AV node, where it slows conduction velocity and increases refractoriness.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So it has a mechanical and an electrical mechanism. About the toxicity:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;For example, in atrial and ventricular Purkinje fibers, a high dixogin concentration has three important actions that may lead to dangerous arrhythmias:&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;less negative resting potential&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;decreased action potential duration&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;enhanced automaticity&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;All quotes are from the book &lt;em&gt;Pathophysiology of Heart Disease&lt;/em&gt; by Leonard S. Lilly, 5th edition.&lt;/p&gt;&#xA;&lt;p&gt;So, I would assume one of the three (or a combination of them) is the reason for the biphasic T-wave. I hope someone more experienced can improve upon this answer.&lt;/p&gt;&#xA;&lt;p&gt;This maybe has something to do with the relative &lt;a href=&quot;http://en.wikipedia.org/wiki/Refractory_period_%28physiology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;refractory period&lt;/a&gt; ending during the T-wave.&lt;/p&gt;&#xA;&lt;p&gt;Also, since the figure is from lead I, you can use that information for looking at where the net electrical axis is pointing at during the T-wave. Refer to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Hexaxial_reference_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;hexaxial system&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9300" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-16T11:53:51.810" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28572" PostTypeId="2" ParentId="28562" CreationDate="2015-02-15T12:25:34.310" Score="14" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, brain transplantation is technically possible, but only for short periods of time, and only in experimental settings.&#xA;&lt;br&gt;&#xA;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of a &lt;em&gt;full-brain transplant&lt;/em&gt; there has been only one group that have made serious attempts in doing this (according to &lt;a href=&quot;http://en.wikipedia.org/wiki/Brain_transplant&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt; and a literature search on my end). In the 1960's White and colleagues &lt;strong&gt;transplanted canine brains&lt;/strong&gt; from one animal to another (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/5844085&quot; rel=&quot;nofollow noreferrer&quot;&gt;White et al., 1965&lt;/a&gt;). In total 6 brains were transplanted. However, the recipients' brains were not removed and the &lt;strong&gt;brains were merely surgically transplanted into the neck region of the recipient animal&lt;/strong&gt;, and connected to the recipient's cervical vasculature (carotide arteries and jugular vein). Hence, the recipient canines ended up with &lt;strong&gt;two brains&lt;/strong&gt;. The authors, however showed with these experiments that the transplantation of brains was feasible, and that the transplants survived and remained functional, which was evidenced by EEG activity. The brains survived from 6 hours up to two days.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Later, White and colleagues worked out a way to keep an &lt;strong&gt;isolated&lt;/strong&gt; (but blood-perfused) monkey &lt;strong&gt;brain alive outside the skull&lt;/strong&gt;, potentially allowing for a primate brain to be transplanted (&lt;a href=&quot;http://www.resuscitationjournal.com/article/0300-9572%2875%2990043-X/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;White et al, 1975&lt;/a&gt;). The procedure could include longer-term 'storage' of the brain by cooling it, making the possibility of transplantation more feasible. However, White realized the difficulties with this approach, since, and I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] by definition the brain must be isolated before the transplantation, and thus requiring all nervous tissue connections to be severed (e.g. cranial nerves and spinal cord), the isolated transplanted monkey brain is without a mechanism to receive or transmit information. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To address this issue White et al. set out to &lt;strong&gt;transfer  the entire cephalon&lt;/strong&gt; (head) of a monkey to the body of a recipient whose own cephalon had been removed at a mid-cervical&#xA;level. Under these circumstances the brain, being within its own cephalon, still connects to the cranial nerves:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vFJZ9.png&quot; alt=&quot;CranialNerves&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;a href=&quot;https://faculty.washington.edu/chudler/cranial.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;source: University of washington&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;White et al. succeeded in transplanting a head, but the preparation rarely survived longer than three days&lt;/strong&gt; due to haemorrhagic shock (&lt;a href=&quot;http://www.resuscitationjournal.com/article/0300-9572%2875%2990043-X/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;White et al, 1975&lt;/a&gt;). Basically the recipient was quadriplegic, as the face was fully functional and White comments, and I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Observe the wakeful appearance of the cephalon and the obvious movement of the facial musculature with open mouth and eyes. This preparation gives every evidence of being in intelligent contact with its environment. [...] Cortical [EEG] activity in this preparation demonstrates awake recordings.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hence, with the current available technology it &lt;strong&gt;does not make much sense to perform a brain transplant, as the transplanted brain cannot be functionally (neurally) connected to recipient body&lt;/strong&gt;. However, strides are being made in re-connecting a severed spinal cord (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821155/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Canavero, 2013&lt;/a&gt;), endeavors that could bring head transplants a little closer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quadriplegic people obviously face extreme psychological challenges (&lt;a href=&quot;http://www.sane.org/information/factsheets-podcasts/848-staying-mentally-healthy-when-you-have-a-spinal-cord-injury&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sane Australia)&lt;/a&gt;. However, even when they have become quadriplegic due to an event later in life, they are not mentally changed, in that they are still 'themselves'. Therefore, although human transplants never have been done, I dare to say that the transplanted head will determine the psychological 'self' of the recipient body, which includes memory and personal traits. At least, assuming the brain can be transplanted without inflicting neuronal damage.&lt;br&gt;&#xA;&lt;br&gt;&#xA;&lt;br&gt;&#xA;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/5844085&quot; rel=&quot;nofollow noreferrer&quot;&gt;White et al. &lt;em&gt;Science&lt;/em&gt; 1965;&lt;strong&gt;150&lt;/strong&gt;:779-81&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.resuscitationjournal.com/article/0300-9572%2875%2990043-X/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;White et al. &lt;em&gt;Resuscitation&lt;/em&gt; 1975;&lt;strong&gt;4&lt;/strong&gt;,197-210&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.cbsnews.com/news/human-head-transplant-is-bad-science-says-neuroscientist/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Canavero et al. &lt;em&gt;Surg Neurol Int&lt;/em&gt; 2013;4:S335–S42&lt;/a&gt;&lt;/sub&gt;&#xA;&lt;br&gt;&#xA;&lt;br&gt;&#xA;&lt;sub&gt;&lt;strong&gt;Further reading&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.cbsnews.com/news/human-head-transplant-is-bad-science-says-neuroscientist/&quot; rel=&quot;nofollow noreferrer&quot;&gt;CBS News&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2018-05-03T10:10:33.090" LastActivityDate="2018-05-03T10:10:33.090" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="28576" PostTypeId="1" CreationDate="2015-02-15T16:40:37.520" Score="0" ViewCount="98" Body="&lt;p&gt;If a cell ,call it C1 has no functioning apoptosis mechanism could a stem cell somehow be 'induced' to be like C1 , at least have the same genome as C1. Then use this stem cell 'duplicate' to 'restart' the apoptosis mechanisms in C1 or even replace C1? ( forgive any broadness or vagueness, I'm trying to be specific)&lt;/p&gt;&#xA;" OwnerUserId="11605" LastActivityDate="2019-06-23T20:02:10.393" Title="Stem cells and if they can correct a lack of apoptosis" Tags="&lt;stem-cells&gt;&lt;apoptosis&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28577" PostTypeId="1" CreationDate="2015-02-15T16:45:27.407" Score="7" ViewCount="3111" Body="&lt;p&gt;In a given area A, we have two choices -&#xA;(i) we can plant maximum number of trees (which are larger in size) possible in A, say m&#xA;OR&#xA;(ii) we can plant maximum number of plants (which are smaller in size) possible in A, say n&#xA;(evidently m will be smaller than n)&#xA;Which choice will yield more amount of oxygen?&#xA;It can be assumed that the total number of leaves capable of Photosynthesis is N and is same for both the cases.&lt;/p&gt;&#xA;" OwnerUserId="6357" LastEditorUserId="22057" LastEditDate="2016-09-30T08:12:41.897" LastActivityDate="2016-12-20T22:34:44.120" Title="Which will produce more oxygen? A few large trees or a greater number of smaller plants?" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="10" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28578" PostTypeId="1" AcceptedAnswerId="29995" CreationDate="2015-02-15T18:21:39.173" Score="16" ViewCount="29854" Body="&lt;p&gt;This question is a result of my personal experience... But I guess that is common for many of us.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My school timing is 8:00 am to 1:30 pm (usually). During normal school days I typically urinate one time - at most. Last month when we were having our practical exams. There was a fair amount pressure to score high marks and on top of that we did not have any experience with such exams. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;On the day of the exam; I was a little nervous about it. The duration of the exam was 3 hours (from 9:00 am to noon) on this day I urinated 4 times.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several of my friends also experienced the same thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was nervous also because for two days before the exam I was afraid that I hadn't even touched any book. I was thinking that there was no way I could cover the whole book and so I didn't even touch them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now that I have final exams in about two weeks, I was revising my syllabus but for the last 4 days I'm not touching the books. Whenever I start solving problems from any chapter then I have to look back for the formulas. Questions in which reasoning is asked, I love to do that. I'm not very good at memorizing things and so when I compare myself to my classmates then I feel like I don't know anything and so I give up. &lt;strong&gt;I have never tried to memorize anything, but I understand the reasoning and the concepts.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kindly give me the answer of the question.&lt;/p&gt;&#xA;" OwnerUserId="5643" LastEditorUserId="6289" LastEditDate="2015-02-15T22:38:46.543" LastActivityDate="2015-09-30T20:09:00.167" Title="Why do we urinate more when we are nervous?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;psychology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28580" PostTypeId="1" CreationDate="2015-02-15T19:09:01.163" Score="3" ViewCount="102" Body="&lt;p&gt;This is unclear for me and I can not understand differences between complete and incomplete atrioventricular heart block.also I want an electrocardiograph of incomplete atrioventricular heart block. &lt;/p&gt;&#xA;" OwnerDisplayName="user13466" LastEditorDisplayName="user12874" LastEditDate="2015-02-15T21:26:44.350" LastActivityDate="2015-02-18T13:05:12.903" Title="What's Incomplete atrioventricular heart block (AV)?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;heart-failure&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="0" ClosedDate="2015-03-08T15:31:49.240" ContentLicense="CC BY-SA 3.0" />
  <row Id="28582" PostTypeId="1" CreationDate="2015-02-15T20:06:24.660" Score="8" ViewCount="259" Body="&lt;p&gt;I was wondering: why most, well, pretty much all organism with a brain have it right in front of their bodies or at the top.&lt;/p&gt;&#xA;" OwnerUserId="13467" LastEditorUserId="14552" LastEditDate="2015-04-19T17:20:38.300" LastActivityDate="2015-05-19T19:27:07.510" Title="Why did the Brain develop in the front in most organisms?" Tags="&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28584" PostTypeId="1" CreationDate="2015-02-15T21:16:02.547" Score="7" ViewCount="512" Body="&lt;p&gt;I am aware that each enzyme generate a certain amount of misproducts.&#xA;This is well documented, for example, for the DNA polymerase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested in enzyme involved in biochemical processes, so for example methytransferase, oxidoreductase, carboxylase and so on.&#xA;I have been looking for any reference that could report the error rate or the amount of misproduct for any of these enzymes, but I was not successful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know a reference reporting the error rate, or any other information about the misproduct generate by these enzymes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will try to clarify a bit better my question.&#xA;Let's assume that we are considering an enzyme that add a methyl group to a molecule, we can choose propionic acid for example.&#xA;In theory the correct product would derive from the addition of a methyl to the C3. &#xA;For the biochemistry study we know that the activation energy is decreased by an enzyme for example by orienting the molecules in the right way to react with the second molecule. &#xA;Therefore, if the enzyme in question will not be able to orient the molecule in the right way there is a certain probability that there will be a mis-product.&#xA;For example the methyl group could be added to the C2 and not the C3. Now. the probability for this process is quite low, but it cannot be excluded from happening.&#xA;My question is, if there is anything known about this type of error rates in the different type of enzymes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this make things a bit more clear&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT 2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lets consider the imagine below that was taken from &lt;a href=&quot;http://www.jbc.org/content/280/45/37742/F1.expansion&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sI5nh.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In B you can see the interaction of the active site of the enzyme with a substrate (for the example it does not matter if it is the real substrate or an inhibitor). I would say that among al possible interaction that this active site can make with substrates there are some much more likely than others. An hypothetical chart could be created considering the free energy of the complex enzyme-substrate, higher the free energy lower the stability.&#xA;Therefore among all possible enzyme-substrate combination we will have just few possibilities that have a low free energy. In the first place we will find the &quot;correct&quot; substrate, then we will find eventual competitors and other molecules that have similar chemical features as the substrate. Even though with low probability these interaction, enzyme-competitors, will happen.&#xA;This might led to the formation of &quot;unwanted product&quot; that I refereed to in my question as &quot;misproduct&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested in reading some paper that are considering thie phenomenon and also quantify its rate. I am also curious if this phenomenon can happen with different rates in different enzymes.&lt;/p&gt;&#xA;" OwnerUserId="12942" LastEditorUserId="12942" LastEditDate="2015-03-10T10:49:41.507" LastActivityDate="2015-03-10T10:49:41.507" Title="Enzymatic error rate" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;enzymes&gt;&lt;enzyme-kinetics&gt;" AnswerCount="4" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28587" PostTypeId="1" CreationDate="2015-02-16T03:14:16.847" Score="5" ViewCount="171" Body="&lt;p&gt;My understanding is that animal metabolism consists of exothermic reactions like&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\ce{C6H12O6 + 6 O2  -&amp;gt;6 CO2 + 6 H2O + energy}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This makes thermodynamic sense to me. Animals need an exothermic reaction to produce the energy we need to move around, etc. However, the other half of the picture, plants and other photosynthesizers producing oxygen, has never made complete sense to me. Are plants consuming $\ce{CO2}$, a &quot;low energy&quot; (I think) substance, and producing higher energy $\ce{O2}$ as a waste product? Is there so much energy available for photosynthesis that plants can afford to waste some of it producing $\ce{O2}$ simply to have enough carbon atoms to store energy via sugars?&lt;/p&gt;&#xA;" OwnerUserId="4697" LastEditorUserId="6" LastEditDate="2015-02-16T15:20:57.437" LastActivityDate="2015-02-17T12:41:06.190" Title="How does it make thermodynamic sense for photosynthesizers to turn CO₂ into O₂?" Tags="&lt;metabolism&gt;&lt;thermodynamics&gt;&lt;carbohydrates&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="28588" PostTypeId="1" CreationDate="2015-02-16T03:41:21.977" Score="2" ViewCount="85" Body="&lt;p&gt;By &quot;Alanine repeat&quot;, I am referring to the suppression of the formation of extra insect legs due to Ubx gene suppression through Distal-less repression.&lt;/p&gt;&#xA;" OwnerUserId="13143" LastActivityDate="2015-05-09T15:26:44.570" Title="In insects, does the Alanine repeat occur on the homeodomain sequence of the abdomen or does it occur on a different sequence?" Tags="&lt;genetics&gt;&lt;entomology&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28590" PostTypeId="1" CreationDate="2015-02-16T04:14:17.780" Score="5" ViewCount="2190" Body="&lt;p&gt;I remember reading this in a biology textbook, and decided to do a little digging. Redheads have a lower sensitivity to some pain and a higher sensitivity to other compared to people of other colored hair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sciencenordic.com and webmd.com note that redheads have a higher sensitivity of pain when it comes to dentistry, yet can tolerate more pain subcutaneously. According to the Journal of the American Dental Association, redheads require more anesthesia due to some mutation in the MC1R gene. What mutation could account for this difference, could this be a point mutation or nonsense mutation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.webmd.com/pain-management/features/whats-your-pain-tolerance?page=2&quot; rel=&quot;noreferrer&quot;&gt;http://www.webmd.com/pain-management/features/whats-your-pain-tolerance?page=2&lt;/a&gt;&#xA;&lt;a href=&quot;http://sciencenordic.com/redheads-feel-different-kind-pain&quot; rel=&quot;noreferrer&quot;&gt;http://sciencenordic.com/redheads-feel-different-kind-pain&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12891" LastActivityDate="2015-02-16T16:19:22.490" Title="Redheads and pain receptors" Tags="&lt;genetics&gt;&lt;human-genetics&gt;&lt;pain&gt;&lt;hair&gt;&lt;receptor&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28595" PostTypeId="1" CreationDate="2015-02-16T10:48:21.527" Score="5" ViewCount="4912" Body="&lt;p&gt;An awkward question. Bear with me...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of mass, what percentage of the food that we eat do we end up excreting? Of course, it depends on a whole host of factors so lets assume a healthy average build/height male with a balanced diet in his 30s who doesn't drink or smoke.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I ask this because I am quite intrigued by my own bowel movements (typically 2 or 3 days apart and average in size - I have no problem passing them btw they've just never been that regular). I know my bowels are not excercised like most other adult males but what's more intriguing is that when I do finally &quot;go&quot;, it looks like and feels like I've hardly eaten over the past few days! Take this weekend for example, it's fair to say I've been overdulging and overeaten but by the end of this week I will probably &quot;see&quot; only 10% of that in the toilet.&lt;/p&gt;&#xA;" OwnerUserId="13478" LastActivityDate="2015-02-16T18:17:33.080" Title="How much of what we eat ends up in the toilet?" Tags="&lt;food&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28597" PostTypeId="1" AcceptedAnswerId="28598" CreationDate="2015-02-16T11:20:38.723" Score="2" ViewCount="480" Body="&lt;p&gt;I am a physicist and trying to understand some protein chemistry for a small project. Basically, amino acids combine to form proteins and after forming the primary structure, some chemical modification may occur, such as phosphorylation or glycosylation (post translational modification). In case of the enzyme carbonic anhydrase a zinc ion is added post-translationally as a cofactor. (The amino acid sequence can be seen &lt;a href=&quot;http://www.uniprot.org/uniprot/P00915&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; (scroll down to 'sequence' title). &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Is the attachment of zinc regarded as a type of post-translational modification? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When carbonic anhydrase is denatured, is the zinc ion released in the medium? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Will the amino acid sequence (primary structure) be changed after denaturation? If yes, are amino acids removed after denaturation, if yes, which?   &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I guess Zinc will be removed after denaturation. Is the remaining structure the primary protein structure?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="13481" LastEditorUserId="3340" LastEditDate="2015-02-16T12:25:06.700" LastActivityDate="2015-02-16T15:42:31.177" Title="Proteins: Post translational modification" Tags="&lt;proteins&gt;&lt;protein-binding&gt;&lt;protein-folding&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28598" PostTypeId="2" ParentId="28597" CreationDate="2015-02-16T12:23:31.780" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;1) Is the attachment of zinc regarded as a type of post-translational&#xA;  modification?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is not really considered a post-translational modification because the zinc atom is not covalently bound to the protein. Binding to zinc is adsorption.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;2) When carbonic anhydrase is denatured, is the zinc ion released in&#xA;  the medium?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, but it depends on the extent of denaturation too. Metal ions can be removed using chelating ligands like EDTA, without actually denaturing the protein.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;3) Will the amino acid sequence (primary structure) be changed after&#xA;  denaturation? If yes, are amino acids removed after denaturation, if&#xA;  yes, which?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Denaturation does not include cleavage of covalent bonds. There won't be change in the amino acid sequence.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;4) I guess Zinc will be removed after denaturation. Is the remaining&#xA;  structure the primary protein structure?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes; just the polypeptide.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-02-16T15:42:31.177" LastActivityDate="2015-02-16T15:42:31.177" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28600" PostTypeId="2" ParentId="28595" CreationDate="2015-02-16T13:11:38.787" Score="1" Body="&lt;p&gt;It very much depends on what specific kind of food you are taking.&#xA;Say, if we eat more green vegetables then we are supposed to excrete more compared to a highly meat-rich diet.&lt;br&gt;&#xA;Also, it depends on the food-intervals, more the interval more the absorption by body so less amount going out(but giving extreme interval is not good either).&lt;br&gt;&#xA;All depends on the need of body, if body needs more than what you are giving to your body it gonna obviously excrete more.&lt;br&gt;&#xA;And always keep in mind to take sufficient water, because without it all things go malfunctioning in our body.&lt;/p&gt;&#xA;" OwnerUserId="8607" LastEditorUserId="3340" LastEditDate="2015-02-16T18:17:33.080" LastActivityDate="2015-02-16T18:17:33.080" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28603" PostTypeId="2" ParentId="28587" CreationDate="2015-02-16T15:06:32.190" Score="3" Body="&lt;p&gt;Oxygen in photosynthesis does not come from carbon dioxide. It comes from water and this is the step that actually requires light: Photolysis of water. &#xA;The proton produced in this process is used to synthesize ATP and NADPH by a chemiosmotic process similar to what happens in mitochondria. &#xA;These biochemical pathways are also referred to as Light reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carbon fixation (or Calvin-Benson Cycle) requires energy (in the from of NADPH) and is therefore dependent on light reactions. The light has no direct role in carbon fixation. Oxygen production also, is not directly coupled to carbon dioxide consumption. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-02-16T15:06:32.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28604" PostTypeId="2" ParentId="28590" CreationDate="2015-02-16T15:23:46.600" Score="3" Body="&lt;p&gt;I think it's best to break this question up in to two parts:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What mutations account for red hair and fair skin in humans&lt;/li&gt;&#xA;&lt;li&gt;How might these same mutations affect pain sensation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;h3&gt;MC1R variants &amp;amp; red hair&lt;/h3&gt;&#xA;&lt;p&gt;The MC1R gene encodes a transmembrane receptor protein (&lt;a href=&quot;http://en.wikipedia.org/wiki/G_protein-coupled_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;belonging to a very common family of receptors&lt;/a&gt;), called melanocortin 1 receptor. It also has another name describing its best known role in the body: 'alpha melanocyte stimulating hormone receptor'.&lt;/p&gt;&#xA;&lt;p&gt;This receptor binds ligands - &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanocortin_1_receptor#Ligands&quot; rel=&quot;nofollow noreferrer&quot;&gt;both agonists and an antagonist&lt;/a&gt; - outside the cell, and passes signals to the pigment-producing pathways in melanocytes; activation favours eumelanin (brown) production over pheomelanin (red).&lt;/p&gt;&#xA;&lt;p&gt;Common MC1R variants are all &lt;strong&gt;single point mutations&lt;/strong&gt; which cause an amino acid substitution and reduce/impair the normal function of the receptor - i.e. &lt;strong&gt;loss-of-function&lt;/strong&gt; mutations. E.g. Arg151Cys, Arg160Trp, Asp294His, the most common variants in european red-heads &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1288200/&quot; rel=&quot;nofollow noreferrer&quot;&gt;probably arose ~80,000ya in a eurasian population,&lt;/a&gt; and have a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10403794/&quot; rel=&quot;nofollow noreferrer&quot;&gt;reduced ability to activate adenylate cyclase&lt;/a&gt; inside the cell.&lt;/p&gt;&#xA;&lt;h3&gt;How &amp;amp; why could the same mutations affect pain sensation?&lt;/h3&gt;&#xA;&lt;p&gt;&lt;strong&gt;Genetic linkage, or dual role of MC1R?&lt;/strong&gt;&lt;br /&gt;&#xA;Firstly, it is possible that MC1R variants are &lt;em&gt;linked&lt;/em&gt; to a mutation at a separate nearby gene; the two making a &lt;a href=&quot;http://ghr.nlm.nih.gov/glossary=haplotype&quot; rel=&quot;nofollow noreferrer&quot;&gt;haplotype&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KCZ2e.png&quot; alt=&quot;haplogroup lineage diagram&quot; /&gt;&#xA;In this diagram, mutation A might be a red-hair MC1R mutant, and mutation B might be some other pain-sensitivity mutant. Through random effects on small populations, group Hg B might have 'seeded' the european population, say; meaning that the two mutations are inherited together in that population. If the two loci are very near, their linkage is less likely to be disturbed by recombination.&lt;/p&gt;&#xA;&lt;p&gt;This is an obvious possibility whenever two seemingly unrelated traits co-occur.&#xA;&lt;em&gt;However&lt;/em&gt;, there's good reason to believe that this case is due to a dual-role of MC1R...&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Arguments against linkage; for dual role of MC1R:&lt;/strong&gt; The existence of many different haplotypes in redheads argues against linkage, &lt;em&gt;if&lt;/em&gt; this pain sensitivity effect is found across all/many redhead haplotypes, and not in wildtype MC1R europeans.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BpTFa.gif&quot; alt=&quot;Redhead pain tolerance&quot; /&gt;&#xA;Indeed, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1736101/pdf/v042p00583.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this study&lt;/a&gt; shows that europeans with 2 MC1R mutant variants (homozygote or compound-heterozygote) have &lt;em&gt;increased pain tolerance&lt;/em&gt; to electric shocks compared to people with 1 or more functional copies of MC1R. The second panel shows that a mu-opiod analgesic (morphine) has greater effect on those with no functional MC1R. The effect coincides with presence of functional MC1R, &lt;em&gt;not&lt;/em&gt; a particular haplogroup.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;MC1R is &lt;em&gt;also&lt;/em&gt; expressed in a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed?cmd=Search&amp;amp;doptcmdl=Citation&amp;amp;defaultField=Title%20Word&amp;amp;term=Xia%5Bauthor%5D%20AND%20Expression%20of%20melanocortin%201%20receptor%20in%20periaqueductal%20gray%20matter.&quot; rel=&quot;nofollow noreferrer&quot;&gt;region of the midbrain&lt;/a&gt; responsible for pain modulation.&lt;/strong&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/Periaqueductal_gray&quot; rel=&quot;nofollow noreferrer&quot;&gt;This region produces endogenous opioids to control pain.&lt;/a&gt; As far as I can gather, researchers are trying to work out what exactly it does there.&lt;/p&gt;&#xA;&lt;p&gt;The study by Mogil et al suggests MC1R in the brain somehow counteracts pain inhibition by the opioid receptors, and so MC1R mutant redheads have more effective ex/endogenous opioid pain inhibition, which reduces noxious pain.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.scandinavianjournalpain.com/article/S1877-8860%2810%2900111-4/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;This study&lt;/a&gt; found that redheads are slightly less susceptible to pain-sensitisation by capsaicin.&lt;/p&gt;&#xA;&lt;p&gt;Whereas &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1692342/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this study&lt;/a&gt; found a contradictory result, that redheads are &lt;em&gt;more&lt;/em&gt; sensitive to thermal pain and that lidocaine is less effective for them. (This study didn't genotype the subjects, and red-hair may be caused by mutations in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene?Cmd=DetailsSearch&amp;amp;Term=3057&quot; rel=&quot;nofollow noreferrer&quot;&gt;other genes&lt;/a&gt;.)&lt;/p&gt;&#xA;&lt;p&gt;Overall, the number of subjects in these studies (both humans and mice) is fairly small; and the science of MCR pain modulation seems early-days.&lt;/p&gt;&#xA;&lt;p&gt;But at least we can answer your question: the mutations apparently responsible for red hair and altered pain sensitivity are amino acid substitutions in MC1R causing loss-of-function variants.&#xA;The fact that MC1R probably has totally different roles in the brain and in the skin is an interesting general point of biology.&lt;/p&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1288200/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1288200/&lt;/a&gt; &amp;lt; about the evolution of MC1R mutant variants.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10403794/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/10403794/&lt;/a&gt; &amp;lt; about the mechanism of loss-of-function&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1736101/pdf/v042p00583.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1736101/pdf/v042p00583.pdf&lt;/a&gt; &amp;lt; evidence of increased pain tolerance &amp;amp; greater morphine effectiveness&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.scandinavianjournalpain.com/article/S1877-8860%2810%2900111-4/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.scandinavianjournalpain.com/article/S1877-8860%2810%2900111-4/abstract&lt;/a&gt; &amp;lt; evidence of resistance to hyperalgesia&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1692342/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1692342/&lt;/a&gt; &amp;lt; evidence of decreased pain tolerance &amp;amp; lesser lidocaine effectiveness&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="13310" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-16T16:19:22.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28605" PostTypeId="2" ParentId="28587" CreationDate="2015-02-16T16:30:59.267" Score="3" Body="&lt;p&gt;This idea about photosynthesis is not correct.This reaction consists several reactions in between. O&lt;sub&gt;2&lt;/sub&gt; is produced by oxidation of H&lt;sub&gt;2&lt;/sub&gt;O to get electrons which are used to revive PQ(plastoquinone) to transport electrons. Chlorophyll can easily get an electron from a Revitalizing(H&lt;sub&gt;2&lt;/sub&gt;O) to transport the electron to cyt-bf and photosystem 1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lWm0z.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This reaction shows the conversion of H&lt;sub&gt;2&lt;/sub&gt;O to O&lt;sub&gt;2&lt;/sub&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\ce{2H2O -&amp;gt;O2 + 4H+ + 2e-}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you see in this reaction. Producing O&lt;sub&gt;2&lt;/sub&gt; is useful and the plant can receive  4 H&lt;sup&gt;+&lt;/sup&gt; for ATP synthase to produce ATP and e&lt;sup&gt;-&lt;/sup&gt; for producing hydrocarbons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CO&lt;sub&gt;2&lt;/sub&gt; is fixed in this reaction of Calvin cycle:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\ce{6Ribulose-1,5 bisphosphate + 6CO2 + 6 H2O -&amp;gt;12 phosphoglycyrate}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NGJZs.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user12874" LastEditorUserId="3340" LastEditDate="2015-02-17T12:41:06.190" LastActivityDate="2015-02-17T12:41:06.190" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28606" PostTypeId="1" AcceptedAnswerId="28612" CreationDate="2015-02-16T16:33:24.640" Score="2" ViewCount="118" Body="&lt;p&gt;When smelling, your nose detects the smells by absorbing them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this mean that, if you were in an enclosed space, you could smell so much all the smell goes, and there is none of that molecule left to smell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would it take so long it would never happen in reality, or does it happen?&lt;/p&gt;&#xA;" OwnerUserId="10304" LastEditorUserId="10304" LastEditDate="2015-02-16T16:39:23.727" LastActivityDate="2015-02-16T18:41:12.680" Title="Could someone entirely absorb smells by smelling?" Tags="&lt;senses&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28607" PostTypeId="1" CreationDate="2015-02-16T16:57:59.157" Score="3" ViewCount="169" Body="&lt;p&gt;I'm wondering about the minimal set of parameters necessary to define a protein's structure.  My understanding is that the backbone geometry is defined by the phi and psi angles (torsion angles), and then from this template the side-chain rotamers are defined.  Is this sufficient to yield a geometric structure, or are there other factors involved?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a related note, how exactly are two protein structures compared? I often see references to percent similarity, but what does this really mean?  In the Protein Data Bank, atomic coordinates are given, but my intuition is that coordinates are only important relative to all the other amino acids in the chain.  In other words, absolute coordinate comparison would seem to be uninformative.&lt;/p&gt;&#xA;" OwnerUserId="13436" LastEditorUserId="13094" LastEditDate="2015-02-16T22:29:33.020" LastActivityDate="2015-02-24T18:35:13.003" Title="Protein Structure Parameters" Tags="&lt;bioinformatics&gt;&lt;protein-structure&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28608" PostTypeId="2" ParentId="10632" CreationDate="2015-02-16T17:52:33.997" Score="0" Body="&lt;p&gt;My understanding of it got me to the point that non-allelic recessive means a single allele can show its effect in the complete absence of its partner; whether it is a dominant or recessive - as in the case if hemophilia. Because at the molecular level normally we define a recessive allele as that which cannot encode any enzyme. Help me to get through this. &lt;/p&gt;&#xA;" OwnerUserId="13488" LastEditorUserId="3340" LastEditDate="2015-02-16T20:19:38.487" LastActivityDate="2015-02-16T20:19:38.487" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28609" PostTypeId="2" ParentId="28502" CreationDate="2015-02-16T18:12:47.293" Score="6" Body="&lt;p&gt;The problem lies in soil bacteria. &#xA;There has been a project on a larger scale: &lt;a href=&quot;https://en.wikipedia.org/wiki/Biosphere_2&quot;&gt;Biosphere 2&lt;/a&gt;. After their initial trial they realised $O_2$ levels are getting much lower from what was predicted. The scientists team investigated the problem deeper and came to the conclusion that there was a lot of dead organic matter in the soil, which got consumed by aerobic bacteria. There were also other hypotheses: not enough sunlight and $O_2$ sequestration by concrete. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A solution for you would be to make sure there is little organic matter in your soil. Perhaps use inorganic &quot;soil&quot; like sand + some nutrients. And also make sure there is enough sunlight.&#xA;Start also with small plants - too large plants in the beginning might change $O_2/CO_2$ ratio to abruptly during day and night cycle. (remember that plants are also consuming oxygen at night).&lt;/p&gt;&#xA;" OwnerUserId="13489" LastEditorUserId="6289" LastEditDate="2015-02-16T19:55:57.510" LastActivityDate="2015-02-16T19:55:57.510" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28610" PostTypeId="2" ParentId="10632" CreationDate="2015-02-16T18:12:49.760" Score="1" Body="&lt;p&gt;The context of the term &quot;non-allelic&quot; is &lt;a href=&quot;http://en.wikipedia.org/wiki/Non-allelic_homologous_recombination&quot; rel=&quot;nofollow&quot;&gt;non-allelic recombinations&lt;/a&gt; which means recombinations between genes that are not exactly alleles but have enough sequence homology to permit recombination. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-02-16T18:12:49.760" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28612" PostTypeId="2" ParentId="28606" CreationDate="2015-02-16T18:41:12.680" Score="5" Body="&lt;p&gt;On the contrary, your olfactory epithelium - the bit that does the smelling up at the top of your nasal cavity - doesn't absorb smells. &lt;a href=&quot;https://books.google.co.uk/books?id=74Vv2LPE-xwC&amp;amp;pg=PA85&amp;amp;lpg=PA85&amp;amp;dq=olfaction%20reversible%20binding&amp;amp;source=bl&amp;amp;ots=StWDKgs8Fw&amp;amp;sig=-S23h-uMy7QZtRwnoGTHfTnVffc&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=ECziVNiXLYu2Uc-pgYAB&amp;amp;ved=0CFUQ6AEwCQ#v=onepage&amp;amp;q=olfaction%20reversible%20binding&amp;amp;f=false&quot; rel=&quot;noreferrer&quot;&gt;The olfactory receptors bind small molecules &lt;strong&gt;reversibly&lt;/strong&gt;.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;However, the olfactory epithelium has a coating of mucus, and so small molecules dissolve in the mucus in order to meet the receptors. Molecules will also evaporate off this mucus, but some &lt;em&gt;vanishingly&lt;/em&gt; small fraction of the odorant in a room may stay in the mucus of the nose and the upper respiratory tract long enough to be moved by cilia to the stomach.&lt;/p&gt;&#xA;&lt;p&gt;I think that for water-soluble molecules, the surface area of mucus lining the airways that odorant can reach is a more relevant factor than the number of a particular receptor (which is very low); but depleting a room of an odorant (which is concentrated enough for you to sense in the first place) by breathing would surely take an extremely long time; as the concentration dropped the remaining molecules would become 'harder to catch', and you'd suffocate first in this enclosed space.&lt;/p&gt;&#xA;&lt;p&gt;Interestingly, hydrophobic molecules that do not readily dissolve in mucus may be bound by soluble 'shuttle'-like proteins which bridge the gap to the receptors: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12044155&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/12044155&lt;/a&gt;&#xA;These odorant-binding-proteins probably contribute to the diversity of molecules we can smell, and presumably also bind odorants reversibly and may release them back in to the nasal cavity.&lt;/p&gt;&#xA;" OwnerUserId="13310" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-16T18:41:12.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28614" PostTypeId="1" AcceptedAnswerId="28627" CreationDate="2015-02-16T19:18:34.213" Score="0" ViewCount="69" Body="&lt;p&gt;This question came up as I work my way through the answers to &lt;a href=&quot;https://biology.stackexchange.com/questions/28587/how-does-it-make-thermodynamic-sense-for-photosynthesizers-to-turn-co%E2%82%82-into-o%E2%82%82/28605?iemail=1&amp;amp;noredirect=1#28605&quot;&gt;another question I just asked&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding is that plant photosynthesis looks something like this (though with lots more going on under the hood):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\ce{6 CO_2 + 6H_2O + light -&amp;gt; C_6 H_{12} O_6 (sugar) + 6 O_2}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(&lt;a href=&quot;https://en.wikipedia.org/wiki/Photosynthesis#mediaviewer/File:Photosynthesis_equation.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;)&#xA;and that the primary functions of the sugar are to store and transport energy. If that's true, then there's something fishy about the familiar view that plants need CO&lt;sub&gt;2&lt;/sub&gt; to breathe and produce O&lt;sub&gt;2&lt;/sub&gt;, while animals need O&lt;sub&gt;2&lt;/sub&gt; and produce CO&lt;sub&gt;2&lt;/sub&gt;. Doesn't a plant need just as much O&lt;sub&gt;2&lt;/sub&gt; as an animal would when it (the plant) gets around to consuming the sugar it has produced? Doesn't consumption of the sugar take you back to the original reactants?&lt;/p&gt;&#xA;" OwnerUserId="4697" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-02-17T06:44:20.720" Title="Do plants need O₂ to consume energy they've stored via sugar?" Tags="&lt;metabolism&gt;&lt;thermodynamics&gt;&lt;carbohydrates&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28615" PostTypeId="1" CreationDate="2015-02-16T19:45:50.910" Score="1" ViewCount="2202" Body="&lt;p&gt;I recently asked the question, &quot;Do plants need O&lt;sub&gt;2&lt;/sub&gt; to consume energy they've stored via sugar?&quot; to which &lt;a href=&quot;https://biology.stackexchange.com/questions/28614/do-plants-need-o2-to-consume-energy-theyve-stored-via-sugar?noredirect=1#comment47173_28614&quot;&gt;@canadianer responded&lt;/a&gt;, &quot;Yes, plants require oxygen to generate ATP from sugar. However, they generate far more sugar (and O&lt;sub&gt;2&lt;/sub&gt;) than they use.&quot; Why do plants produce all that extra sugar, especially given that sugar is thermodynamically expensive?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One reason, I believe, is to produce fruit and so recruit animals to help with reproduction. But are there others?&lt;/p&gt;&#xA;" OwnerUserId="4697" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-02-17T06:46:00.537" Title="Why do plants produce so much more sugar than they use?" Tags="&lt;botany&gt;&lt;metabolism&gt;&lt;fruit&gt;&lt;thermodynamics&gt;&lt;carbohydrates&gt;" AnswerCount="0" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="28616" PostTypeId="2" ParentId="5615" CreationDate="2015-02-16T20:55:57.150" Score="-1" Body="&lt;p&gt;I had this same question.  I believe the answer is this is a known effect caused by aberrations between your eyes and the way they perceive color.  This effect is called Chromostereopsis.  I know this is an old topic but hopefully this information will be useful to people like me who were also trying to learn more.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Chromostereopsis&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Chromostereopsis&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="13490" LastActivityDate="2015-02-16T20:55:57.150" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28617" PostTypeId="1" CreationDate="2015-02-16T21:17:39.393" Score="6" ViewCount="4064" Body="&lt;p&gt;Even simple vitamins seem to have this in the instruction. Why is is so? Is there some simple model of how do pills interact with food? Does it depend on the food type? (What about drinks?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Should not eating at all on some day be considered &quot;before food&quot; or &quot;after food&quot;?&lt;/p&gt;&#xA;" OwnerUserId="13491" LastEditorUserId="13491" LastEditDate="2015-02-17T21:36:06.470" LastActivityDate="2015-02-25T23:29:37.943" Title="How does food intake affect medicine? Why pill instructions recommends taking them before (after) meal?" Tags="&lt;food&gt;&lt;medicine&gt;&lt;pharmacokinetics&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28618" PostTypeId="1" AcceptedAnswerId="28620" CreationDate="2015-02-16T21:50:25.577" Score="6" ViewCount="1788" Body="&lt;p&gt;I just wanted to get a realistic viewpoint of our nervous system. I understand arteries and veins, but I wanted to know how similar our nervous system is to that? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand we have neurons (please correct me if I am wrong) all over the surface of body. Whenever we feel a touch a neuron fires a response, and that response travels through axons (myelin sheath). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My main question is what a nerve exactly is. Is it a long axon? How many axons (same thing as neuron body?) are in a nerve? I am sure it depends on different nerves.  &lt;/p&gt;&#xA;" OwnerUserId="13493" LastEditorUserId="9943" LastEditDate="2016-03-10T20:58:47.373" LastActivityDate="2016-03-10T20:58:47.373" Title="Relationship between nerves and axons" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;neurophysiology&gt;&lt;peripheral-nervous-system&gt;&lt;touch&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28619" PostTypeId="1" CreationDate="2015-02-16T23:32:06.437" Score="1" ViewCount="441" Body="&lt;p&gt;Can DNA ligase seal two non-complementary sticky ends if the reaction is incubated at the optimum conditions ? I do almost 100% double digestion in the lab. However, during ligation, when I do a control without the insert, I still get many circularized vector and they cause massive false positives during transformation. Can ligase sealing two non-complementary sticky ends be a possible reason behind this ? &lt;/p&gt;&#xA;" OwnerUserId="1843" LastActivityDate="2015-03-22T21:45:35.217" Title="Does DNA Ligase look for complementarity in sticky ends?" Tags="&lt;molecular-biology&gt;&lt;cloning&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28620" PostTypeId="2" ParentId="28618" CreationDate="2015-02-16T23:41:19.100" Score="8" Body="&lt;p&gt;I will go through your list of questions below:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;I wanted to know how similar is our nervous system to [the circulatory system]?&lt;/em&gt;&lt;br&gt;&#xA;&lt;strong&gt;They are very different, but as in every comparison of very complex systems, there is some overlap&lt;/strong&gt;. The circulatory system carries fluids, the nervous system electrical signals so they are functionally not alike. However, both systems run throughout the body and have a more or less central control unit (the brain and heart respectively). So there is a structural similarity. I reckon they are as much alike as a city's sewer system and electricity grid.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;I understand we have neurons (please correct me if I am wrong) all over the surface of body.&lt;/em&gt;&lt;br&gt;&#xA;&lt;strong&gt;That is correct&lt;/strong&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Whenever we feel a touch (stimulus arises) a neuron fires a response, and that response travels through axons (myelin sheath).&lt;/em&gt;&lt;br&gt;&#xA;&lt;strong&gt;Tactile stimulation may result in firing of one or more neurons&lt;/strong&gt;, dependent on the intensity of the stimulus. Larger stimuli will, obviously, recruit more fibers. Stronger stimuli will evoke stronger responses (increased firing). &lt;strong&gt;Axons indeed conduct the neuronal responses&lt;/strong&gt;, like an electrical wire conducts electrical current. Longer axons are often myelinated (insulated). Not all neurons related to touch are myelinated, however. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;So my main question is that what exactly is a nerve?&lt;/em&gt;&lt;br&gt;&#xA;&lt;strong&gt;A nerve is a bundle of axons&lt;/strong&gt; that carry related functional information. Typically, nerves conduct information originating from locations closely located together in the body, and generally they convey this information to a localized spot in the body as well. For example, the optic nerve carries information from the photoreceptors (related information) from the retina (localized source) to the brainstem (localized target).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Is [a nerve] a long axon?&lt;/em&gt;&lt;br&gt;&#xA;&lt;strong&gt;A nerve contains many axons&lt;/strong&gt;. 'Long' or 'short' is rather subjective.   &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;How many axons (same thing as neuron body?) are in a nerve? I am sure it depends on different nerves.&lt;/em&gt;&lt;br&gt;&#xA;&lt;strong&gt;Neuronal cell bodies are typically located outside a nerve&lt;/strong&gt;. &lt;strong&gt;Nerves contain varying numbers of fibers.&lt;/strong&gt; For example, the auditory nerve harbors the axons of the spiral ganglion cells that transmit auditory information from the inner ear to the brain. It contains between 31k - 32k (myelinated) fibers in normal-hearing humans (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2613564&quot; rel=&quot;nofollow&quot;&gt;Spoendlin &amp;amp; Schrott, 1989&lt;/a&gt;). In contrast, the optic nerve, which carries visual information from the retina to the brain, contains some 1.3 million (myelinated) fibers in young human adults (&lt;a href=&quot;http://www.iovs.org/content/33/6/2012.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Jonas et al., 1992&lt;/a&gt;)&#xA;&lt;br&gt;&#xA;&lt;br&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.iovs.org/content/33/6/2012.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Jonas et al., &lt;em&gt;IOVS&lt;/em&gt; 1992;&lt;strong&gt;33&lt;/strong&gt;:2012-8&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2613564&quot; rel=&quot;nofollow&quot;&gt;Spoendlin &amp;amp; Schrott, &lt;em&gt;Hear Res&lt;/em&gt; 1989;&lt;strong&gt;43&lt;/strong&gt;:25-38&lt;/a&gt;&lt;/sup&gt;  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-08-15T13:15:14.560" LastActivityDate="2015-08-15T13:15:14.560" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28621" PostTypeId="1" AcceptedAnswerId="67954" CreationDate="2015-02-17T00:55:28.907" Score="4" ViewCount="1565" Body="&lt;p&gt;We don't to know much about organisms living deep below the Earth's crust. Recently a team led by S. Giovanni discovered some microbes 300 m below the ocean floor. The microbes were found to be a completley new and exotic species and apparently they feed off hydrocarbons like methane and benzene. Scientists speculate that life may exist in our Solar System far below the surface of some planets or moons. This raises some questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;What is the theoretical minimum distance from Earth's core where life can still exist. Please explain how you came up with this number. For example, there are temperature-imposed limits on many biochemical processes.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is there the potential to discover some truly alien life forms in the Earth's mantle (by this I mean, life which is not carbon based, or life which gets its energy in ways we have not seen before, or non DNA-based life, or something along these lines)?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What is the greatest distance below the Earth's crust that life has been discovered? I believe it is the 300 m I cited above, but I am not 100% sure. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="13409" LastEditorUserId="13409" LastEditDate="2015-02-18T02:48:47.467" LastActivityDate="2017-11-16T21:12:31.987" Title="How close to Earth's core can organisms live?" Tags="&lt;life&gt;&lt;extremophiles&gt;" AnswerCount="2" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="28622" PostTypeId="1" AcceptedAnswerId="28633" CreationDate="2015-02-17T00:58:00.047" Score="6" ViewCount="149" Body="&lt;p&gt;I am interested in studying honey and other honeybee byproducts.  I have not been able to find sequence or structure records for any of the contents of honey.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, I want to study the protein sequence and structure and the amino acid compositions within honey.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has any of this data been produced and published in any databases or research papers?&lt;/p&gt;&#xA;" OwnerUserId="13495" LastEditorUserId="3340" LastEditDate="2015-02-17T04:44:28.727" LastActivityDate="2015-02-17T10:38:48.087" Title="Has the protein composition (with identification) in honey and other honeybee byproducts been studied?" Tags="&lt;proteins&gt;&lt;dna-sequencing&gt;&lt;3d-structure&gt;&lt;protein-structure&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28623" PostTypeId="1" CreationDate="2015-02-17T01:13:00.477" Score="1" ViewCount="407" Body="&lt;p&gt;What would happen if a human was injected with a rabies vaccine meant for dogs? I know vaccines can contain weak or dead strains of the virus, but is it possible that the human could become infected with rabies from a vaccine meant for dogs? My thinking is that maybe a dogs' immune system is more suited to deal with a weak strain of rabies that would otherwise infect a human.&lt;/p&gt;&#xA;" OwnerUserId="13473" LastActivityDate="2015-02-17T02:43:16.267" Title="Is it possible for a human to get rabies from a rabies vaccine meant for dogs?" Tags="&lt;medicine&gt;&lt;vaccination&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28624" PostTypeId="1" AcceptedAnswerId="28635" CreationDate="2015-02-17T01:55:14.260" Score="14" ViewCount="1746" Body="&lt;p&gt;I think I understand how a signal is transferred from neuron to neuron (from  &lt;a href=&quot;https://biology.stackexchange.com/questions/91/how-do-the-brain-and-nerves-create-electrical-pulses&quot;&gt;How do the brain and nerves create electrical pulses?&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question, however, is not about the standard textbook material on neuronal transduction. Instead, I am wondering how an electrical impulse starts in the first place in the brain. In other words, how can an action potential be generated &lt;em&gt;de novo&lt;/em&gt; from a conscious thought? I am wondering primarily about a signal like a movement of an appendage or something similar. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in short, my question is:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How is the 'first' action potential generated in the cortex when one consciously/voluntarily decides of moving a limb (or comparable action)?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-06-03T08:48:44.927" Title="How can action potentials be generated through thoughts?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="28625" PostTypeId="2" ParentId="28623" CreationDate="2015-02-17T02:43:16.267" Score="2" Body="&lt;p&gt;It would depend on which vaccine you're talking about, as there are &lt;a href=&quot;http://en.wikipedia.org/wiki/Rabies_vaccine&quot; rel=&quot;nofollow&quot;&gt;several&lt;/a&gt;. Some use attenuated strains of the Rabies virus, others use killed, and some are recombinant glycoprotein vaccines. &lt;a href=&quot;http://www.cdc.gov/mmwr/preview/mmwrhtml/rr6006a1.htm#table-1&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a list from the CDC of all the rabies vaccines available in the US in 2011 (I wasn't able to find anything newer). Generally speaking, through, one would expect the FDA in the US and the relevant authorities in other companies to require vaccine manufacturers show that their product is safe in other species, in case of accidental exposure, such as you are talking about here. This is especially true of something being given to an animal that is quite often a family pet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you think you've been exposed to any type of medication which has not been prescribed for you, including dog rabies vaccine, you should seek medical attention immediately, if not sooner, but based on my experience in the pharmaceutical industry and dealing with regulatory agencies, you should be pretty safe, as the regulations surrounding vaccines are quite stringent.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-02-17T02:43:16.267" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28627" PostTypeId="2" ParentId="28614" CreationDate="2015-02-17T04:37:41.283" Score="2" Body="&lt;p&gt;Plants need sugar not only for energy but also for synthesizing essential metabolites and building blocks including cellulose (used in cell wall), glycoproteins and 5-carbon sugars for nucleotides. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As already mentioned by canadianer, plants respire by oxidizing sugars. This happens mostly during the night. However photosynthesis also produces ATP and therefore plants are not strictly dependent on respiration for energy. Moreover the fixed carbon in the form of starch makes up an energy reserve (like fats and glycogen in animals).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-02-17T06:44:20.720" LastActivityDate="2015-02-17T06:44:20.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28628" PostTypeId="1" CreationDate="2015-02-17T05:16:16.037" Score="3" ViewCount="124" Body="&lt;p&gt;&quot;Weak memory&quot;, as used in this question, refers to the inability to retrieve a memory that a person otherwise knows he has memorized earlier. An example of this is some fact snippet that the individual memorized as part of a training exercise 2 weeks earlier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there scientific consensus for the cause of this type of weak memory? Or is the consensus that there are multiple causes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible that this type of weak memory is caused by interference between various signals in the brain, or what does the known evidence say (if anything)?&lt;/p&gt;&#xA;" OwnerUserId="12939" LastEditorUserId="11841" LastEditDate="2015-02-17T08:00:17.507" LastActivityDate="2015-02-17T08:00:17.507" Title="Is it possible that weak memory is due to interference between signals in the brain?" Tags="&lt;human-biology&gt;&lt;brain&gt;&lt;memory&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28629" PostTypeId="1" AcceptedAnswerId="28630" CreationDate="2015-02-17T09:02:16.227" Score="5" ViewCount="476" Body="&lt;p&gt;Considering the paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1171471/&quot;&gt;A single amino acid in E-cadherin responsible for&#xA;host specificity towards the human pathogen&#xA;Listeria monocytogenes&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;in the abstract portion, what does Pro→Glu mean? Does it mean that, in place of Glu(glucose), pro-16 is placed?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="5144" LastEditDate="2015-02-17T09:14:38.187" LastActivityDate="2015-02-17T16:00:04.427" Title="what does Pro→Glu substitution mean?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28630" PostTypeId="2" ParentId="28629" CreationDate="2015-02-17T09:13:04.127" Score="5" Body="&lt;p&gt;You are looking at a protein here, which is mutated in the higher host specificity, so glucose is not involved here. What is written here are the amino acids in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Amino_acid#Table_of_standard_amino_acid_abbreviations_and_properties&quot;&gt;three-letter-code&lt;/a&gt;, the notation Pro→Glu means that Proline (Pro) is replaced by Glutamic acid (Glu).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The notation Pro16 means the proline on amino acid position 16 in the protein. You often find this replacements noted as Pro16Glu or P16E (in the 1-letter-code)&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-02-17T09:13:04.127" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28632" PostTypeId="1" CreationDate="2015-02-17T09:32:11.380" Score="1" ViewCount="362" Body="&lt;p&gt;Complete molar pregnancy is one where an ovum devoid of nucleus is fertilized by a sperm after which the haploid set of chromosomes double to form a diploid set.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as my understanding extends if the sperm had &lt;code&gt;Y chromosome&lt;/code&gt; the embryo will not survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However if the sperm has &lt;code&gt;X chromosome&lt;/code&gt; the zygote will survive to have the 46 XX karyotype and will start to grow as molar pregnancy (which is basically trophoblastic tissue with no fetal parts, as answered by Anongoodnurse).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is there no proper fetus? Why can't a &quot;female clone&quot; of male parent form instead? Where is the defect as such?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The Question pointed out by WYSISYG contains data only from animal studies. Although it answers my question, I want more data obtained from study of human trophoblastic tissue (from the molar pregnancy).  Papers on imprinting which are linked in those questions have no mention of molar pregnancy although Prader-Willi and Angelman syndromes are mentioned (as cases seen in humans).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Oops, I corrected my question thanks to anongoodnurse. I mixed up complete and partial moles with each other.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-02-17T14:43:09.927" LastActivityDate="2015-02-17T14:43:09.927" Title="Why does an complete molar pregnancy not result in a clone?" Tags="&lt;pathology&gt;&lt;pregnancy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="28633" PostTypeId="2" ParentId="28622" CreationDate="2015-02-17T10:34:12.210" Score="3" Body="&lt;p&gt;First of all: Honey is not a byproduct of bees - it's their main and most important product which stores energy for the bee hive for the time when no flowers are available.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Honey itself consists (according to the USDA database) to about 99.5% of water and sugars (82.5% sugars, 17% water). The sugars are mostly fructose and glucose, but also some other mono- di and tri-saccherides in traces. See reference 1 for details. It also contains trace amounts of vitamins and minerals, see table from the Wikipedia on &lt;a href=&quot;http://en.wikipedia.org/wiki/Honey&quot; rel=&quot;nofollow noreferrer&quot;&gt;Honey&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SLS3b.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The protein content varies between honey sample but is somewhere in the range between 0.2 and 0.5% (see also reference 1). The proteins come from flowers (pollen incorporated into the honey) as well as from the bees (see reference 2). Paper 1 lists a number of enzymes as most common bee proteins in the honey, but doesn't go into much more details here. These are invertase, diastase, glucose oxidase and catalase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could now go into the sequence databases (&lt;em&gt;Apis mellifera&lt;/em&gt; has been complete sequenced) and look up the sequence information of the enzymes. Information can be found &lt;a href=&quot;http://hymenopteragenome.org/beebase/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome?term=apis%20mellifera&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3901/tt4jklhg_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;A review of the analytical methods to determine the geographical and&#xA;botanical origin of honey&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3901/rvokxgcy_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source of the honey protein responsible for apple juice&#xA;clarification&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-02-17T10:38:48.087" LastActivityDate="2015-02-17T10:38:48.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="28634" PostTypeId="1" AcceptedAnswerId="28636" CreationDate="2015-02-17T11:06:07.980" Score="9" ViewCount="14491" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many receptor types in the body, with various functions and various mechanisms of transduction. &lt;strong&gt;Receptor cells are considered to be part of the peripheral nervous system&lt;/strong&gt;, as they are the first step in conveying information from the periphery to the brain.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Many receptor cells do not fire action potentials. Action potentials are widely considered to be a key property of neurons&lt;/strong&gt;. Instead, receptors often operate by graded responses. For example, upon illumination photoreceptors gradually hyperpolarize. Cochlear hair cells gadually depolarize when the stereocilia are bent into one direction and hyperpolarize when they go in the opposite direction. Hence, many receptors are in fact analog sensors, whereas spiking neurons can be considered to be operating in binary (all-or-nothing) mode.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given their similarities and differences, &lt;strong&gt;are receptor cells classified as neurons?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;Credits: This question was formulated after a discussion with @OneFace on the question &quot;&lt;a href=&quot;https://biology.stackexchange.com/questions/28618/relationship-between-nerves-and-axons/28620#28620&quot;&gt;Relationship between nerves and axons&lt;/a&gt;&quot;&lt;/sup&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2018-09-03T08:45:08.033" LastActivityDate="2018-09-03T08:45:08.033" Title="Are sensory receptors neurons?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="28635" PostTypeId="2" ParentId="28624" CreationDate="2015-02-17T11:13:04.343" Score="9" Body="&lt;p&gt;&lt;a href=&quot;http://www.nature.com/neuro/journal/v17/n11/full/nn.3826.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;This paper&lt;/a&gt; addresses the question that you are asking. The study is based on conscious decision making in rats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Performance of rats were assessed in the following task:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rats have to poke their snout into a waiting port until a auditory signal (beep) is heard.&#xA;After first beep the rats can get a small reward (small amount of water) in the reward port. However if the rat waits for a second beep it gets to have a bigger reward. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there were three behavioral outcomes in the experiment done with 37 individuals:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Short-poke trials: Those that didn't wait for the signal (8.3 ± 4.6%)&lt;/li&gt;&#xA;&lt;li&gt;Impatient trials: Those that waited for the first beep but did not wait for the second beep (58.8 ± 3.9%)&lt;/li&gt;&#xA;&lt;li&gt;Patient trials: Those who successfully got the bigger reward. (32.9 ± 1.4%)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The impatient ones did not usually quit immediately after the first beep. This was not a lethargic response to signal but a moment of conflict between two decisions. There was a distribution of waiting times. The patient ones immediately responded to the second beep and took their reward.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neural activity was studied in the M2 (secondary motor) cortex of impatient rats during the tasks and two kinds of neural activity was observed:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Ramp-to-threshold: Firing rate kept increasing till the end of waiting time suggestive of a neural threshold to quit waiting. (Fig 1)&lt;/li&gt;&#xA;&lt;li&gt;Steady-transient activity: Firing rate correlated with waiting time i.e. higher firing rate higher the waiting time. This could constitute the neurons that are making the rat wait. (Fig 2)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/ktGd1.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Figure 1: Ramp-to-Threshold. &lt;br&gt; Reproduced from &lt;a href=&quot;http://www.nature.com/neuro/journal/v17/n11/full/nn.3826.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Murakami et al. (2014) Nature Neuroscience 17,1574–1582&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/lTTEe.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Figure 2: Transient activity. &lt;br&gt; Reproduced from &lt;a href=&quot;http://www.nature.com/neuro/journal/v17/n11/full/nn.3826.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Murakami et al. (2014) Nature Neuroscience 17,1574–1582&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It was also observed that this activity is task specific. The neurons that showed a certain activity in the above tasks did not behave the same way in the same rats performing a slightly different task.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So action potential is generated in the brain by &quot;thoughts&quot;. However these thoughts are not generated de-novo. Any conscious decision is based on memory of past events and similar events evoke those memories, which in cellular terms is generation of action potential. In this case the action potential is generated in response to the rats' sensory input in the form of a beep. Other kinds of responses are instinctive and the brain circuitry has evolved to generate these kinds of responses to certain stimuli such as fear. The above example is a study of conscious decision making based on an acquired memory.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-03T08:48:44.927" LastActivityDate="2015-06-03T08:48:44.927" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="28636" PostTypeId="2" ParentId="28634" CreationDate="2015-02-17T11:29:29.667" Score="12" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Receptor cells are specialized neurons&#xA;&lt;br&gt;&#xA;&lt;br&gt;&lt;br&gt;&#xA;&lt;strong&gt;Background&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are, globally, three types of neurons (&lt;a href=&quot;http://www.macmillanhighered.com/catalog/static/whf/animalphys5/&quot; rel=&quot;noreferrer&quot;&gt;Eckert's Animal Physiology&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Sensory neurons&lt;/strong&gt;: these cells transmit information from external stimuli (e.g., sound, light, pressure), or from internal stimuli (e.g., blood oxygen level or head orientation);&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Interneurons&lt;/strong&gt;: these cells connect other neurons &lt;em&gt;within&lt;/em&gt; the central nervous system;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Motor neurons&lt;/strong&gt;: these neurons carry effector signals to effector organs, causing contraction of muscles or secretion by gland cells.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;To illustrate these classes of neurons let's consider the visual peripheral system. Fig. 1 shows a schematized representation of the retinal circuitry, connecting the photoreceptors to the ganglion cells of the optic nerve (interneurons):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2EosJ.png&quot; alt=&quot;retina&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;Source: &lt;a href=&quot;http://www.ib.cnea.gov.ar/~redneu/2013/BOOKS/Principles%20of%20Neural%20Science%20-%20Kandel/gateway.ut.ovid.com/gw2/ovidweb.cgisidnjhkoalgmeho00dbookimagebookdb_7c_2fc~32.htm&quot; rel=&quot;noreferrer&quot;&gt;Instituto Balseiro&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;https://en.wikipedia.org/wiki/Photoreceptor_cell&quot; rel=&quot;noreferrer&quot;&gt;photoreceptor's response&lt;/a&gt; is graded. Notably, &lt;strong&gt;the &lt;a href=&quot;http://bipolar%20cell&quot; rel=&quot;noreferrer&quot;&gt;bipolar cell&lt;/a&gt;, being an interneuron has also a graded response&lt;/strong&gt;. The bipolar cells convey the signal, in turn, to the ganglion cells that translate the analog, graded signals into a binary, neural spiking code that enters the optic nerve.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Receptor cells are considered neurons, but they are &lt;strong&gt;highly specialized&lt;/strong&gt;. Although interneurons may come in various shapes and sizes, they are not so specialized as receptor cells. The photoreceptor, for example, has a &lt;strong&gt;highly specialized dendritic region&lt;/strong&gt; containing the photosensitive pigment and membrane stacks that capture light.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another receptor is the &lt;a href=&quot;http://medcell.med.yale.edu/histology/skin_lab/pacinian_corpuscle.php&quot; rel=&quot;noreferrer&quot;&gt;Pacinian corpuscle&lt;/a&gt;, a vibrotactile mechanoreceptor of the skin:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xjJWF.png&quot; alt=&quot;PC&quot;&gt;&lt;br&gt;&#xA;  &lt;sup&gt;Source: &lt;a href=&quot;http://pixgood.com/mechanoreceptor.html&quot; rel=&quot;noreferrer&quot;&gt;Pixgood&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case, the receptor cell is in fact a &lt;strong&gt;myelinized and spiking neuron&lt;/strong&gt; that functionally much resembles an interneuron. Just as the photoreceptor, the dendritic part does not connect to another neuron, but is highly specialized structure designed to sense a physical external stimulus. In case of the Painian corpuscle, it is an onion-like structure consisting of many lamina. These lamellar structures substantially change the receptor's response to mechanical stimuli. Specifically, it allows the corpuscle to respond rapidly to pressure changes and allow it to faithfully transmit vibratory stimuli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt; &#xA;&lt;br&gt;&#xA;&lt;br&gt; &#xA;&lt;strong&gt;&lt;a href=&quot;https://www.macmillanihe.com/page/detail/Eckert-Animal-Physiology/?K=9780716738633&quot; rel=&quot;noreferrer&quot;&gt;Eckert, Animal Phsyiology&lt;/a&gt;&lt;/strong&gt;:&lt;br&gt;&#xA; - Chapter 5 - The Physiological basis of Neuronal Function&lt;br&gt;&#xA; - Chapter 7 - Sensing the Environment&lt;/sub&gt;    &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2018-09-03T07:11:51.230" LastActivityDate="2018-09-03T07:11:51.230" CommentCount="13" ContentLicense="CC BY-SA 4.0" />
  <row Id="28637" PostTypeId="2" ParentId="28632" CreationDate="2015-02-17T12:07:46.183" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;However if the sperm has X chromosome the embryo will survive to have the 46 XX karyotype and will start to grow as molar pregnancy.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Complete molar pregnancy is diploid, and there is &lt;em&gt;no fetal tissue&lt;/em&gt; identifiable. It is a disease of the placenta, a uterine tumor (cancerous in some cases, non-cancerous in others); fetuses do not develop from such pregnancies, not haploid or diploid (though they are usually 46, XX). A male haploid 23,X replicates, but only trophoblastic (what should be the placenta) tissue results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Partial molar pregnancies are triploid, and a fetus can sometimes be identified. However, it is non-viable, as polyploidy is non-viable in humans. Even if it were, the abnormal placenta could not support it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMcp0900696&quot; rel=&quot;nofollow&quot;&gt;Molar Pregnancy&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0046817704006513&quot; rel=&quot;nofollow&quot;&gt;p57KIP2 immunohistochemistry in early molar pregnancies: emphasis on its complementary role in the differential diagnosis of hydropic abortuses&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-02-17T12:07:46.183" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="28638" PostTypeId="1" CreationDate="2015-02-17T13:09:14.930" Score="2" ViewCount="38" Body="&lt;p&gt;The question is simple: Why sudden stresses cause stuttering and/or other temporary or permanent impairs in children (and even adults)?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastActivityDate="2015-02-17T13:09:14.930" Title="Why sudden stresses cause stuttering and/or other impairs in children?" Tags="&lt;stress&gt;&lt;children&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29634" PostTypeId="2" ParentId="28607" CreationDate="2015-02-17T13:47:23.837" Score="1" Body="&lt;p&gt;It depends on how accurate you want the description to be. Ideal bond lengths are normally assumed, so the structure can be described using φ, ψ, ω (for the backbone) and χ1-χ5 (for the sidechain) angles. This is what is used in most cases. However, the positions of the hydrogens in the sidechains are not uniquely defined by this description. This also does not describe hydrogen bonds and disulfide bridges, but those could be deduced from the relative positions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can get more information here: &lt;a href=&quot;http://kinemage.biochem.duke.edu/teaching/anatax/html/anatax.1b.html&quot; rel=&quot;nofollow&quot;&gt;http://kinemage.biochem.duke.edu/teaching/anatax/html/anatax.1b.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This description should be enough for most applications, though. &lt;/p&gt;&#xA;" OwnerUserId="1307" LastActivityDate="2015-02-17T13:47:23.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29635" PostTypeId="1" CreationDate="2015-02-17T14:49:51.190" Score="2" ViewCount="938" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Sources include any exporting organs, typically mature leaves, that&#xA;  are capable of producing photosynthete in excess of their own needs.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Sinks include any nonphotosynthetic organs of the plant and organs&#xA;  that do not produce enough photosynthetic products to support their&#xA;  own growth or storage needs. Roots, tubers, developing fruits, and&#xA;  immature leaves, which must import carbohydrate for normal&#xA;  development, are all examples of sink tissues.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Sinks are always supplied by sources. Now, I want to know do all sources transport their photosythetic to all parts of plant or some sources just supply some especial sinks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a question for me:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do all sources supply all sinks on a plant?&lt;/p&gt;&#xA;" OwnerUserId="14499" LastEditorUserId="14499" LastEditDate="2015-02-17T15:28:05.263" LastActivityDate="2015-02-17T15:28:05.263" Title="Do all sources supply all sinks on a plant?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="29636" PostTypeId="2" ParentId="29635" CreationDate="2015-02-17T15:10:19.283" Score="3" Body="&lt;p&gt;What you think about phloem is not correct, actually there are a lot of phloem which transport the photosynthetic. Although the overall pattern of transport in the phloem can be stated simply as source-to-sink movement, the specific pathways involved are often more complex. Not all sources supply all sinks on a plant; rather, certain sources preferentially supply specific sinks. In the case of herbaceous plants, such as sugar beet and soybean, the following generalizations can be made.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Proximity&lt;/strong&gt;. The proximity of the source to the sink is a significant factor. The upper mature leaves on a plant usually provide photosynthetic to the growing shoot tip and young, immature leaves; the lower leaves supply predominantly the root system. Intermediate leaves export in both directions, bypassing the intervening mature leaves.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Development&lt;/strong&gt;. The importance of various sinks may shift during plant development. Whereas the root and shoot&#xA;apices are usually the major sinks during vegetative growth, fruits generally become the dominant sinks during&#xA;reproductive development, particularly for adjacent and other nearby leaves.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Vascular connections&lt;/strong&gt;. Source leaves preferentially supply sinks with which they have direct vascular connections. In the shoot system, for example, a given leaf is generally connected via the vascular system to other leaves directly above or below it on the stem. Such a vertical row of leaves is called an orthostichy. The number of internodes between leaves on the same orthostichy varies with the species.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Modification of translocation pathways&lt;/strong&gt;. Interference with a translocation pathway by wounding or pruning can alter the patterns established by proximity and vascular connections that have been outlined here. In the absence of direct connections between source and sink, vascular interconnections, called anastomoses (singular anastomosis), can provide an alternative pathway. In sugar beet, for example, removing source leaves from one side of the plant can bring about cross-transfer of photosynthetic to young leaves (sink leaves) on the pruned side. Removal of the lower source leaves on a plant can force the upper source leaves to translocate materials to the roots, and removal of the upper source leaves can force lower source leaves to translocate materials to the upper parts of the plant.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerDisplayName="user12874" LastActivityDate="2015-02-17T15:10:19.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29641" PostTypeId="2" ParentId="28539" CreationDate="2015-02-17T16:47:41.010" Score="1" Body="&lt;p&gt;A tried and true method is to measure the diameter of the tree (which plays into your radius idea). Measurements are taken at &quot;breast height&quot; (~4.3ft, 1.3m from the ground). You can purchase a 'diameter tape' or 'girth tape' which consists of pre-calculated measurements, this way you will not have to measure circumference and derive diameter from this measurement. Breast height has been a consistent standard measurement over time, despite where a tree may begin to buttress, or flare out at the base. Below is an image detailing atypical tree measurements. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5breg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="12972" LastActivityDate="2015-02-17T16:47:41.010" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29642" PostTypeId="1" AcceptedAnswerId="29657" CreationDate="2015-02-17T18:44:26.430" Score="5" ViewCount="2577" Body="&lt;p&gt;I recently stumbled upon the &lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_dark_matter&quot; rel=&quot;noreferrer&quot;&gt;Biological Dark Matter&lt;/a&gt; wiki page. Its pretty light on details, but it appears to be genetic material found in humans that doesn't fall into currently classifications. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what do we know about it? Is it really a big black box that we know nothing about? The article claims that it can make 40% of the genetic material in our gut, and I find it hard to believe that we really know nothing about it. &lt;/p&gt;&#xA;" OwnerUserId="9212" LastActivityDate="2018-09-09T13:46:56.353" Title="What is biological dark matter?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;human-genetics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29643" PostTypeId="1" AcceptedAnswerId="29742" CreationDate="2015-02-17T18:51:51.700" Score="9" ViewCount="1791" Body="&lt;p&gt;If I hang upside down, and feel blood rushing to my head, what structures are actually responsible for me &quot;feeling&quot; this excess flow of blood? Baroreceptors? Mechanoreceptors? Something else?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regardless, how does this process actually work? How do I &quot;feel&quot; excess blood pressure to a certain area of my body?&lt;/p&gt;&#xA;" OwnerUserId="11581" LastEditorUserId="9943" LastEditDate="2015-11-05T12:54:13.397" LastActivityDate="2015-11-05T12:54:13.397" Title="What creates the feeling of 'excess' blood pressure to an area of the body?" Tags="&lt;human-anatomy&gt;&lt;blood-circulation&gt;&lt;human-physiology&gt;&lt;blood-pressure&gt;&lt;sensory-systems&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29644" PostTypeId="2" ParentId="29642" CreationDate="2015-02-17T18:59:49.803" Score="0" Body="&lt;p&gt;Take a look at this article: &lt;a href=&quot;http://phys.org/news/2014-01-scientists-biological-dark.html&quot; rel=&quot;nofollow&quot;&gt;http://phys.org/news/2014-01-scientists-biological-dark.html&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this the same &quot;biological dark matter&quot; you're asking about? If so, it sounds like what used to be called &quot;junk DNA&quot; or &quot;non-coding DNA&quot;, which is what it was referred to as up until a few years ago when scientists discovered it is actually regulatory DNA, very interesting stuff, but basically it regulates gene expression, thus why it is usually in the form of RNA instead of a protein.&#xA;I hope this answers your question, I would strongly urge you to do some research on regulatory DNA, it's very intriguing.&lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-02-17T18:59:49.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29645" PostTypeId="1" CreationDate="2015-02-17T19:55:20.150" Score="4" ViewCount="210" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uuUpK.jpg&quot; alt=&quot;top and bottom of skull&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/T6IEV.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you help me identify these skulls I found in an old bottle in the woods?&lt;/p&gt;&#xA;" OwnerUserId="14502" LastEditorUserId="948" LastEditDate="2015-02-17T21:04:58.857" LastActivityDate="2015-02-18T04:58:26.540" Title="I found these skulls in a old bottle in the woods. Can you tell me what they are?" Tags="&lt;zoology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="29647" PostTypeId="1" AcceptedAnswerId="29649" CreationDate="2015-02-17T21:43:22.550" Score="10" ViewCount="5687" Body="&lt;p&gt;So, I am not sure I can reproduce it via images, but the steps are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) At night, open a window and have a look at the surface of the earth&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Suppose there's an object that reflects a tiny amount of light&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) When you actually try to focus your eyes at this object, you either don't see anything (depends on the amount of light it reflects) or you can hardly see it&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4) When you focus your eyes on something that is 3-10 metres away, you can easily see this object with your ambient vision. Not the details, but it seems that it reflects more light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does it happen?&lt;/p&gt;&#xA;" OwnerUserId="14503" LastEditorUserId="9943" LastEditDate="2015-02-18T03:32:39.400" LastActivityDate="2015-02-18T03:32:39.400" Title="Why does a light object appear lighter in your peripheral vision when it's dark?" Tags="&lt;vision&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29649" PostTypeId="2" ParentId="29647" CreationDate="2015-02-17T22:09:35.603" Score="19" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Peripheral vision is more light-sensitive than central vision.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;When you look directly at an object the image is projected onto the &lt;em&gt;fovea&lt;/em&gt;. The fovea has maximal visual acuity (high resolution) and a high density of cones, which are specialized photoreceptors to sense colors. However, cones are not very sensitive to light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a picture showing the foveal field of view:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xcRLD.jpg&quot; alt=&quot;foveal view&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;strong&gt;Source&lt;/strong&gt;: &lt;a href=&quot;http://cleareyesight-batesmethod.info/id114.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pinhole Eyeglasses&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at the same object using peripheral vision, the image is formed more eccentrically on the retina. Here, cones are sparse, but high densities of rods are present. Rods do not detect color, but are much more sensitive to light than cones. In fact, they can faithfully detect a single photon! (&lt;a href=&quot;http://webvision.umh.es/webvision/Evolution.%20PART%20III.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Webvision&lt;/a&gt;) Moreover, many rods converge onto a single ganglion cell, and rod responses are therefore summated. This spatial  summation further increases light sensitivity in the periphery, but degrades spatial resolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is an image on rod and cone distributions on the retina, showing a high cone-density in the fovea and a high rod density more eccentrically:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/E04Ue.gif&quot; alt=&quot;rods cones&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;strong&gt;Source&lt;/strong&gt;: &lt;a href=&quot;http://webvision.med.utah.edu/book/part-iii-retinal-circuits/circuitry-for-rod-cells-through-the-retina/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Webvision&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And here is an image showing the higher light sensitivity of rods over cones:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/69n8z.gif&quot; alt=&quot;Rod and cones&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;strong&gt;Source&lt;/strong&gt;: &lt;a href=&quot;http://webvision.umh.es/webvision/Evolution.%20PART%20III.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Webvision&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, &lt;strong&gt;peripheral vision is more light sensitive&lt;/strong&gt; because: (1) there are more rods in the peripheral retina; (2) rods are more light sensitive; and (3) eccentric retinal rod circuitry further amplifies the rod responses. However, color perception and spatial resolution are better developed in the central field of view.&#xA;&lt;br&gt;&#xA;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Further reading&lt;/strong&gt; (Cognitive Sciences.SE) &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Rod and cone distributions&lt;/strong&gt;: &lt;a href=&quot;https://cogsci.stackexchange.com/questions/6265/why-can-we-not-see-around-our-point-of-focus-of-our-eyes/8481#8481&quot;&gt;&quot;Why can we not see around our point of focus of our eyes?&quot;&lt;/a&gt;  &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Visual acuity as a function of retinal eccentricity&lt;/strong&gt;: &lt;a href=&quot;https://cogsci.stackexchange.com/questions/8928/visual-acuity-and-offset-stimuli/8997#8997&quot;&gt;&quot;Visual acuity and offset stimuli&quot;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:56:15.910" LastActivityDate="2015-02-18T01:32:25.877" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29652" PostTypeId="2" ParentId="29645" CreationDate="2015-02-18T03:33:05.473" Score="4" Body="&lt;p&gt;Its a Shrew skull.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/hPTzz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/hPTzz.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hainault Forest Website&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Photographs by © Brian Ecott&lt;/p&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="3340" LastEditDate="2015-02-18T04:58:26.540" LastActivityDate="2015-02-18T04:58:26.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29654" PostTypeId="1" AcceptedAnswerId="41712" CreationDate="2015-02-18T04:24:47.150" Score="7" ViewCount="12960" Body="&lt;p&gt;It's a well-established fact that blood group is decided by genotype. But, when a new child starts its journey in the womb, the mother's blood (along with it's agglutinins and agglutinogens) flows into the baby's heart. So, how does a baby (having a blood group different from that of the mother) retains it's own blood group (with it's own agglutinins and agglutinogens) instead of the mother's blood group, which moves in and out of the baby through the umbilical cord. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Do both kinds of blood flow in the baby's body constantly in such a case?&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Apart from that, I know of rhesus incompatibility. But there are also incompatible blood group types. How does a baby survive agglutination in those cases?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="14500" LastEditorUserId="19650" LastEditDate="2015-12-29T19:08:28.213" LastActivityDate="2020-08-04T18:54:26.690" Title="How does a fetus retain a blood group different from its mother?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;&lt;human-genetics&gt;&lt;reproductive-biology&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29655" PostTypeId="1" AcceptedAnswerId="29660" CreationDate="2015-02-18T04:50:24.077" Score="7" ViewCount="4946" Body="&lt;p&gt;I was under the impression that both ends of a muscle contract. For instance, the fibers of the biceps run parallel to the humerus so I thought they pulled toward the middle.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But now I'm confused because it sounds like the contraction of the fibers doesn't necessarily have to parallel the motion of the muscle itself. In other words, just because the fibers contract doesn't mean that the muscle lengthens or shortens in a particular direction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone clarify if muscles contract in both directions? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or perhaps a better question is do muscle contract in a particular direction and is this the same direction that the fibers contract or does the muscle as a whole move in a different direction in comparison to the direction the fibers are contracting? &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="3340" LastEditDate="2015-02-18T09:44:20.603" LastActivityDate="2015-02-21T22:32:19.623" Title="Do both ends of a muscle contract?" Tags="&lt;muscles&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29656" PostTypeId="1" CreationDate="2015-02-18T06:03:21.137" Score="5" ViewCount="53084" Body="&lt;p&gt;A diploid cell in G1 has 6 chromosomes. How many chromosomes and how many chromatids are present in each of the following stages?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is what I am guessing&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;G1: 6 chromosomes ; 6 chromatids &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;G2: 6 chromosomes ; 12 chromatids &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Prophase: 6 chromosomes; 12 chromatids &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Metaphase: 6 chromosomes; 12 chromatids &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Anaphase: 12 chromosomes; 12 chromatids &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Telophase: 12 chromosomes; 12 chromatids&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="14506" LastEditorUserId="16866" LastEditDate="2018-12-20T14:18:59.273" LastActivityDate="2018-12-20T14:18:59.273" Title="Chromosome and chromatid numbers during cell cycle phases" Tags="&lt;cell-biology&gt;&lt;dna&gt;&lt;homework&gt;&lt;chromosome&gt;&lt;mitosis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="29657" PostTypeId="2" ParentId="29642" CreationDate="2015-02-18T08:31:59.800" Score="5" Body="&lt;p&gt;There are multiple answers to this question depending on who you ask (meaning, what their field of expertise is).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biological dark matter from the wikipedia article in question seems to mean sequence from metagenomic samples which was not assigned to any of our commonly known domains of life. That might not necessarily mean that it does not belong to them. Sometimes it is hard to decide where a small particle of sequence informations belongs to, because it does not match anything we know. Still, it might be from a perfectly &quot;normal&quot; bacterium. Or it might be a result of sequencing errors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, depending on how you assign a taxonomy to the sequence, there might be cases where there are so many different possibilities for where this sequence came from (because it is very conserved in a lot of different organisms, even from different domains of life), that this sequence will not get any taxonomy assigned. Not because there is none, but because we cannot safely decide which it is.&#xA;Some people also speak of this information as &quot;dark matter&quot;.&#xA;There is for example &lt;a href=&quot;http://microbialdarkmatter.org&quot;&gt;this project&lt;/a&gt; which specifically is designed to study the dark matter we can (or at least for some reason do) assign to be microbes, but not more specifically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, any decision of where to place potential dark matter sequence is guided by our previous knowledge about the domains of life and the genomes of all those organisms. This knowledge is very incomplete. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am sorry this answer lacks some more nice sources. Most of the information is based on my knowledge as a person working with datasets that might include &quot;dark matter&quot;, if I would call it that. (I call it &quot;not assigned sequence&quot;.) I don't have the time right now to add more sources, but if needed I can maybe add some later.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&#xA;As a fast add-on after re-reading your question: How much of the sequence is unassigned for example if one would study your gut depends a lot on what is actually there in you gut that we know, how diverse the community in your gut is, what database is used for comparison and how old this database is, how the data is preprocessed and analysed, and so much more. But yes, there is still a lot of genomic information in nature that has not made it into any database.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastEditorUserId="3827" LastEditDate="2015-02-18T08:38:22.240" LastActivityDate="2015-02-18T08:38:22.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29658" PostTypeId="1" CreationDate="2015-02-18T08:41:07.977" Score="2" ViewCount="70" Body="&lt;p&gt;I'm reading The Perfect Health Diet, and in it the author says that the probability of a point mutation is (175/3*10^9) per new child. He then goes on to write:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In the Paleolithic, with 100000 children per generation, it would have taken 8000 generations, or 160000 years, for each possible mutation to occur once.&lt;/p&gt;&#xA;&lt;p&gt;Today, with more than a billion children per generation, every possible point mutation now appears about twenty times per generation, or almost yearly.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Using his probability, I get that you need 1 / (175 / (3 * 10^9)) (which is about 17 million children). But he writes that for the Paleolithic era, you need 10000 * 8000 = 80 million children! Can someone help me reason out how he got that number?&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&#xA;My math was wrong :-) leaving up the og calculation. Here's the reference that he cites:&lt;/p&gt;&#xA;&lt;p&gt;&amp;quot;Estimate of the Mutation Rate per Nucleotide in Humans&amp;quot; by Michael W. Nachman and Susan L. Crowell&#xA;In the abstract they write &amp;quot;The average mutation rate was estimated to be 2.5x10^-8 mutations per nucleotide&#xA;site or 175 mutations per diploid genome per generation.&amp;quot;&lt;/p&gt;&#xA;" OwnerUserId="6482" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-19T01:09:11.070" Title="What is the expected number of children that need to be born for every possible point mutation to occur once?" Tags="&lt;genetics&gt;&lt;mutations&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2015-02-18T15:43:35.233" ContentLicense="CC BY-SA 3.0" />
  <row Id="29659" PostTypeId="2" ParentId="29658" CreationDate="2015-02-18T09:32:08.587" Score="3" Body="&lt;p&gt;&lt;strong&gt;I don't think the book's reasoning is correct.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are about 3 billion base pairs in the human genome, but only ca 25.000 protein-coding genes. From the top of my head, I recall that each child has about 30 mutations. If that's in the total genome and if they were all point mutations and there's 4 options for the base pair, then we have $30$ mutations out of 12 billion options in each child. So that each possible point mutation has a probability of $30/12 \text{ billion} = 2.5 \times 10^{-9}$ or $1/(2.5 \times 10^{-9})$ if you like. The book's number is 23 times larger but in the same ballpark range. Lets call this probability $p$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the probability of a mutation occuring in n children &lt;em&gt;at least once&lt;/em&gt; is equal to one minus the probability of it never occuring in n children. In other words:&#xA;$$1 - (1 - p)^n =$$&#xA;$$1 - (1 - 2.5 \times 10^{-9})^n =$$&#xA;$$1 - (0.9999999975)^n$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we want the mutation to occur with probability 95%, we have to solve:&#xA;$1 - (0.9999999975)^n = 0.9$&#xA;This has the solution $n = 1 \times 10^9$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, with 1 billion children, each point mutation has a 95% probability of having occured at least once. Mathematically this is not the same as saying that every mutation will have occured. In fact, this implies that 5% of the mutations will not have occured. But perhaps surprisingly, we only need 4-5 billion to up the chance to 99.999%. That still leaves out thirty thousand point mutations, but is sufficiently close to &quot;everyone&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Compare this to the numbers you mentioned:&#xA;n = 17 million gives each gene a 4% chance of occuring&#xA;n = 80 million gives each gene an 18% chance of occurring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, a mandatory rant. :-) &quot;The Perfect Health Diet&quot; is written by Paul and Shou-Ching Jaminet, an astrophysicist and molecular biologist respectively. This has the potential to marry the physicist's penchance for oversimplification with the biologist's lack of mathematical prowess. We see both in the passage you ask about. A shoddy calculation about an oversimplification of what mutations and evolution is about. &#xA;Both the book's dustcover use of a word like &quot;detoxifying&quot; and mention of how diseases spontaneously resolve if you eat right, are both strong crackpot indicators. It's the kind of thinking that killed Steve Jobs because he didn't seek medical help soon enough but tried to eat his way out of his illness.&lt;/p&gt;&#xA;" OwnerUserId="9583" LastEditorUserId="9458" LastEditDate="2015-02-19T01:09:11.070" LastActivityDate="2015-02-19T01:09:11.070" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29660" PostTypeId="2" ParentId="29655" CreationDate="2015-02-18T10:01:34.907" Score="8" Body="&lt;p&gt;The muscular fibers (or more exactly the actin and myosin filaments) are contracted towards each other. This makes them &quot;move to the middle&quot; and you build up a force on both sides of the muscle. See this image (from the Wikipedia), which illustrates this process:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XpUMX.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also an animated picture available, which illustrates this process even better (from &lt;a href=&quot;http://163.178.103.176/Tema1G/Grupos1/GermanT1/GATP20/g2.htm&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DusNj.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The process of the contraction applies a equal force to both endpoints of the muscle.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-02-18T10:01:34.907" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="29661" PostTypeId="1" CreationDate="2015-02-18T11:57:45.357" Score="9" ViewCount="271" Body="&lt;p&gt;Listening to really good music right now, I was wondering why it raises goosebumps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any physiological reason for this reaction to specific wavelengths or something?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&#xA;Due sometimes strong vibration, roadwork for example,  raise goosebumps too I reckon it's about the wavelengths but if someone could explain what is happening and why, that would be great.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://cogsci.stackexchange.com/questions/9337/why-can-good-music-raise-goosebumps&quot;&gt;CROSS-POSTED&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9138" LastEditorUserId="-1" LastEditDate="2017-04-13T12:56:15.910" LastActivityDate="2015-04-27T05:41:34.703" Title="Why can good music raise goosebumps?" Tags="&lt;physiology&gt;&lt;skin&gt;&lt;hearing&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29662" PostTypeId="1" AcceptedAnswerId="29681" CreationDate="2015-02-18T12:16:11.130" Score="17" ViewCount="3551" Body="&lt;p&gt;My ten year old son was reading car number plates that were too fast, too far away and at the wrong angle for any of us to read or even believe that it was possible for him to read. We thought he was lying as he reeled off the whole number plate and not just some. My husband went across the road to prove him wrong and get him to admit he was making it up but he wasn't. We even asked people in the restaurant and waiting staff for their opinion and everyone was blown away. I'm totally astonished and slightly freaked out by his sight and I'm hoping someone can explain for me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Specifics&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I believe it was approx 20-25 metres away and I am under guessing.&lt;/li&gt;&#xA;&lt;li&gt;He had only 1 or 2 seconds as the cars drove left to right. &lt;/li&gt;&#xA;&lt;li&gt;Cars would be travelling 30/40 kmph along that road. &lt;/li&gt;&#xA;&lt;li&gt;We were sitting in the restaurant at night time so not in a car&#xA;ourselves&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="14507" LastEditorUserId="5005" LastEditDate="2015-02-18T22:11:36.070" LastActivityDate="2015-02-20T22:12:23.360" Title="Superhuman eyesight" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;vision&gt;&lt;human-eye&gt;" AnswerCount="3" CommentCount="12" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29663" PostTypeId="1" AcceptedAnswerId="30134" CreationDate="2015-02-18T12:48:15.870" Score="6" ViewCount="1236" Body="&lt;p&gt;The final frontier of Biological Sciences could be considered understanding the effects of variation in the DNA (and RNA). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If after fertilization the DNA of the zygote could be genetically engineered to prevent complications occurring later in the life of that human being, it could become the ultimate medicine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, we know that (in humans) only 2% of the genome encodes genes that are translated into proteins; is the rest required for function?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can DNA &amp;amp; RNA be considered the ultimate blueprint of all living organisms?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="14500" LastEditorUserId="740" LastEditDate="2015-02-27T14:05:13.630" LastActivityDate="2016-05-26T22:32:48.377" Title="Can DNA &amp; RNA be considered as nature's programming language?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;molecular-genetics&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="29664" PostTypeId="2" ParentId="29662" CreationDate="2015-02-18T13:01:44.500" Score="17" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Visual acuity decreases with age. Your son's age is within the age range that visual acuities are best. Acuity starts to decrease from about age 45. &#xA;&lt;br&gt;&#xA;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Visual acuity&lt;/strong&gt; (visual resolution) first &lt;strong&gt;increases from birth up until around 4-6 years&lt;/strong&gt;. Note that in the following graph better acuities are represented by lower numbers (logMAR scale): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XQn1X.jpg&quot; alt=&quot;acuity increase&quot;&gt;&lt;br&gt;&#xA;Source: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2742505/&quot;&gt;Pan et al, 2009&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Visual acuity starts to decrease after 45 years.&lt;/strong&gt; The acuity of a 6-year old is about 1 on the scale in the next figure, showing the decline in acuity in older folks. Note that the graph starts at 30 years and acuities are already less than that in the former study's end point (look at the lower set of lines, i.e., the uncorrected ones). Also note that better acuities are higher up in the scale as this graph expresses acuities in decimal Snellen equivalents &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GOcqo.png&quot; alt=&quot;old age&quot;&gt;&lt;br&gt;&#xA;Source: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3493168&quot;&gt;Gittings &amp;amp; Lozard, 1986&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, very likely, &lt;strong&gt;your 10-year old's vision is not superhuman&lt;/strong&gt; (sorry!), it's just a lot better than yours. However, if you are younger than 45, we might conclude your acuity should be comparable and your son may be a visual rock-star - statistical outliers do exist and a simple visit to the optometrist will tell you! However, if you are near-sighted and are not using corrective vision aids (glasses or the likes) then this may be the cause of your lesser visual acuity.&#xA;&lt;br&gt;&#xA;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2742505/&quot;&gt;Pan et al., &lt;em&gt;Optom Vis Sci&lt;/em&gt; 2009;&lt;strong&gt;86&lt;/strong&gt;:607–12&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3493168&quot;&gt;Gittings &amp;amp; Lozard, &lt;em&gt;exp gerontol&lt;/em&gt; 1986;&lt;strong&gt;21&lt;/strong&gt;:423-33&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-02-18T13:26:12.653" LastActivityDate="2015-02-18T13:26:12.653" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29666" PostTypeId="2" ParentId="29655" CreationDate="2015-02-18T13:11:25.913" Score="2" Body="&lt;p&gt;Muscles do contract in both directions. To understand this better you need to know few things:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The smallest unit of a muscle is called myofiber or a muscle fiber. It is basically a multinucleated elongated cell. Each muscle fiber is covered by a layer called endomysium&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A bunch of myofibers arranged linearly is called a fascicle. The fascicles are covered by a sheath called perimysium.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A muscle as you see in a cadaver or a picture is a group of fascicles surrounded by epimysium. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TzlGe.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;source: &lt;a href=&quot;https://classconnection.s3.amazonaws.com/536/flashcards/1808536/png/levels_of_muscle_structure1349648870863.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;classconnection&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A single muscle fiber is made up of &lt;strong&gt;numerous myofibrils&lt;/strong&gt; which are basically the sarcomere arranged side-by-side.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The junction between the neuron and muscle fiber is called &lt;strong&gt;motor end plate&lt;/strong&gt;. A single motor neuron innervates a group of muscle fibers. The whole assembly of muscle fibers innervated by the axon from one neuron is called a &lt;strong&gt;motor unit&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;The Key:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The key to understand muscle contraction on a macro level is in the fact:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Typically, an axon makes a single point of synaptic contact with a skeletal muscle fiber, midway along the length of the muscle fiber.&lt;sup&gt;1&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So when an action potential arrives at the neuromuscular junction (another name for end plate), the muscle starts depolarising and contracting from the center towards the periphery. In other words both the ends of the muscle contract toward the center. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RdBlw.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;source:&lt;a href=&quot;https://encrypted-tbn1.gstatic.com/images?q=tbn:ANd9GcQBBLIBFwuITkZlVi6E5OZ4wAaPh3b4KO7RNkhAcv6WUZI-YPzC5g&quot; rel=&quot;nofollow noreferrer&quot;&gt;encrypted-tbn1.gstatic.com&lt;/a&gt;. Image has been cropped and edited to illustrate the point&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;tl;dr:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Every skeletal muscle contracts toward its center, such that the proximal and distal ends act in opposite directions causing tension generation. The proximal end pulls the tendon down and the distal end pulls the tendon up thus generating tension.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1: Medical Physiology A Cellular and Molecular Approach, 2&lt;sup&gt;nd&lt;/sup&gt; Edition, Boron and Boulpaep p.217&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-02-18T14:55:55.367" LastActivityDate="2015-02-18T14:55:55.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29668" PostTypeId="1" AcceptedAnswerId="29760" CreationDate="2015-02-18T13:15:49.463" Score="3" ViewCount="147" Body="&lt;p&gt;My question is simple. If I wanted to make an exact twin of an individual, will genetically engineering the DNA of the zygote to match with the individual suffice?&lt;/p&gt;&#xA;" OwnerUserId="14500" LastEditorUserId="14500" LastEditDate="2015-02-18T13:31:49.250" LastActivityDate="2015-02-21T01:21:36.510" Title="Can genetically engineering the DNA of a human zygote, make it a twin of another human in entirety?" Tags="&lt;genetics&gt;&lt;reproduction&gt;&lt;human-genetics&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="29669" PostTypeId="1" AcceptedAnswerId="29688" CreationDate="2015-02-18T13:26:38.993" Score="7" ViewCount="536" Body="&lt;p&gt;If the conditions within the womb are mimicked, and proper amniotic fluid with constantly recycling nutrients is maintained, is it not possible to obtain an artificial womb? Is there anything missing? I think, artificial womb, if possible, could open new ways to study human anatomy and development and further the research studies. Starting with test tube fertilization, one could observe the entire process of growth of a zygote to a fetus.&lt;/p&gt;&#xA;" OwnerUserId="14500" LastEditorUserId="5144" LastEditDate="2015-02-20T19:36:50.400" LastActivityDate="2017-03-30T20:24:29.053" Title="Why are there no artificial wombs yet?" Tags="&lt;human-anatomy&gt;&lt;reproduction&gt;&lt;development&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29670" PostTypeId="2" ParentId="29656" CreationDate="2015-02-18T16:12:14.550" Score="5" Body="&lt;p&gt;The chromosomes copy at S phase. So S/G2 checkpoint up to early anaphase has 2n. You are on the right track to understanding the cell cycle, important to note the differences between homologous chromosomes (homologous pair) and sister chromatids, while understanding  ploidy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During S (synthesis) phase which occurs between G1 and G2 , all the somatic DNA replicates. So every chromosome gets copied and thus  has a sister chromatid. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Animals that undergo sexual reproduction have 2 sets of chromosomes, one from mom the other from dad. The chromosomes of each pair represents homologous chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your answer is almost correct. I believe it could be adjusted to:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;G1&lt;/strong&gt;: 6 chromosomes &#xA;&lt;strong&gt;G2&lt;/strong&gt;: 6 chromosomes /12 chromatids &lt;strong&gt;Prophase&lt;/strong&gt;: 12 chromatids &#xA;&lt;strong&gt;Metaphase&lt;/strong&gt;:  12 chromatids &#xA;&lt;strong&gt;Anaphase&lt;/strong&gt;: 12 separating chromatids &#xA;&lt;strong&gt;Telophase&lt;/strong&gt;: 12 chromosomes, 6 one each pole of the cell&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These very simple figures explain the principles I mentioned earlier&lt;img src=&quot;https://i.stack.imgur.com/FT2vx.jpg&quot; alt=&quot;homologous chromosomes&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FMAkv.jpg&quot; alt=&quot;ploidy in sexual reproduction&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2015-02-18T23:42:16.360" LastActivityDate="2015-02-18T23:42:16.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29672" PostTypeId="2" ParentId="28624" CreationDate="2015-02-18T16:19:56.080" Score="7" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;There's a philosophical issue here: if you believe &quot;thought&quot; originates outside of the physical brain, you are probably some sort of &lt;a href=&quot;http://en.wikipedia.org/wiki/Dualism_%28philosophy_of_mind%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;dualist&lt;/a&gt;. However, I believe it is more likely that the brain is the machine that enables (apparent) consciousness and thoughts. If you believe &quot;thought&quot; causes neurons to fire, you might not be able to find a scientific answer, unless you can measure that &quot;thought&quot; external to the brain...&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There are spontaneous activity in the brain. That is, neurons will fire by themselves with or without any external input at random times. See &lt;a href=&quot;https://biology.stackexchange.com/q/15252/460&quot;&gt;this question&lt;/a&gt; and &lt;a href=&quot;https://biology.stackexchange.com/a/15259/460&quot;&gt;my answer there in&lt;/a&gt;. Brain is surprisingly noisy. Perception and behavioral variability is often correlated with such noise, and studied in neuroscience. For example, see&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Nienborg, H. and Cumming, B. G. (2009). Decision-related activity in sensory neurons reflects more than a neuron’s causal effect. Nature, 459(7243):89-92.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="460" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-02-18T16:19:56.080" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29673" PostTypeId="1" CreationDate="2015-02-18T16:43:57.593" Score="9" ViewCount="342" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qckDq.png&quot; alt=&quot;speshell&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyone know exactly what species this is?  I gather it may be an auger (family) or cerith (family) of some sort.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This particular one is native to Indonesia's black beaches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know what is the genus and species of this specimen.&lt;/p&gt;&#xA;" OwnerUserId="14509" LastEditorUserId="6561" LastEditDate="2017-12-21T22:56:50.820" LastActivityDate="2017-12-21T22:56:50.820" Title="What species is this? Seashell from Indonesia" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29674" PostTypeId="1" AcceptedAnswerId="29676" CreationDate="2015-02-18T16:49:49.143" Score="3" ViewCount="672" Body="&lt;p&gt;I mean, Hemocytoblast is a stem cell which is constantly being differentiated into daughter cells and leads to formation of all the blood cells (having short and limited life spans), so how come those stem cells remain there and continue to function, even when we grow up and finally grow old (i.e for 70 years approx)? The no. of those stem cells gotta be limited.&lt;/p&gt;&#xA;" OwnerUserId="14500" LastActivityDate="2015-02-18T17:35:20.163" Title="How does Hemocytoblast constantly get formed into so many blood cells and yet remains there in the bone marrow throughout the lifetime?" Tags="&lt;hematology&gt;&lt;blood-circulation&gt;&lt;red-blood-cell&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29675" PostTypeId="2" ParentId="28470" CreationDate="2015-02-18T16:55:04.767" Score="2" Body="&lt;p&gt;I agree with canadianer that chemical tests are generally more useful for identification.  However, morphology does help and some staining techniques can be useful for identification (the Gram stain is the obvious one).  If you are looking for a microscope, look for a nice scope with a 100x oil-immersion objective and a 10x ocular lens (12x would be OK too). Zeiss, Nikon and Olympus are some old names that make good scopes - and there are more.  &lt;/p&gt;&#xA;" OwnerUserId="10430" LastActivityDate="2015-02-18T16:55:04.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29676" PostTypeId="2" ParentId="29674" CreationDate="2015-02-18T17:05:03.307" Score="4" Body="&lt;p&gt;The trick for the stem cells lies in the way the proliferate and differentiate. See the image (from the reference 1):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fDfVU.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stem cells have the problem that they need to differentiate and maintain their population at the same time (subfigure a). This can either be done by asymmetric cell division which leads to one daughter which is still a stem cell and one which has been differentiated (subfigure b). Then it is possible that the cells divide only symmetrical (as shown in subfigure c) so they will either deliver two stem cells or two differentiated cells. And then it is possible (shown in subfigure d) that both possibilities are mixed and that symmetrical and assymetrical division occurs. Either way you get both: Differentiated cells and you still manage to maintain the stem cell pool.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biochem.wisc.edu/sites/default/files/people/judith-kimble/pdfs/2000s/100s/134_Morrison_Kimble_2006.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Asymmetric and symmetric stem-cell divisions in development and&#xA;cancer&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs00018-013-1386-1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Asymmetric cell division of stem and progenitor cells during&#xA;homeostasis and cancer&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Asymmetric_cell_division&quot; rel=&quot;nofollow noreferrer&quot;&gt;Asymmetric cell division&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-02-18T17:35:20.163" LastActivityDate="2015-02-18T17:35:20.163" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="29677" PostTypeId="1" AcceptedAnswerId="29689" CreationDate="2015-02-18T17:16:00.907" Score="4" ViewCount="966" Body="&lt;p&gt;After giving birth to a child, the umblical cord is cut (and stored if they want). The end connected to the child's navel will fell off eventually but what happens to the end inside the mother? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Will it be removed right after birth by doctors or what happens?&lt;/p&gt;&#xA;" OwnerUserId="12957" LastActivityDate="2015-02-19T02:05:23.453" Title="What happens to the umblical cord inside the mother?" Tags="&lt;pregnancy&gt;&lt;children&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29678" PostTypeId="1" CreationDate="2015-02-18T17:59:23.807" Score="5" ViewCount="1150" Body="&lt;p&gt;Wikipedia has the following statement on its &lt;a href=&quot;http://en.wikipedia.org/wiki/Upper_respiratory_tract_infection&quot; rel=&quot;noreferrer&quot;&gt;Upper respiratory tract infection&lt;/a&gt; page:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In United States URIs are the most common infectious illness in the&#xA;  general population.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What is it about the upper respiratory tract that makes it so vulnerable to infections?&lt;/p&gt;&#xA;" OwnerUserId="13487" LastActivityDate="2015-02-27T01:17:01.830" Title="Why is the upper respiratory tract so vulnerable to infections?" Tags="&lt;pathology&gt;&lt;infection&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29679" PostTypeId="1" AcceptedAnswerId="29685" CreationDate="2015-02-18T18:46:48.903" Score="14" ViewCount="7276" Body="&lt;p&gt;Does the brain really function like a computer as in, ultimately every response is related to a binary sequence based on whether particular neurons fire or not?&lt;/p&gt;&#xA;" OwnerUserId="13448" LastActivityDate="2019-09-01T07:27:28.830" Title="Can the human brain be reduced to a binary system?" Tags="&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="6" CommentCount="0" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="29680" PostTypeId="2" ParentId="29678" CreationDate="2015-02-18T19:06:01.510" Score="1" Body="&lt;p&gt;Mostly because it is in almost constant contact with aerosols from the outside world (with regard, of course, to a thin layer of mucus), therefore any pathogens they might contain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You also have to remember what separates an airborne pathogen from any other pathogens- infection location. A pathogen is airborne when it infects and irritates the throat or nasal passage enough to make the organism's normal deterrence functions kick in. In most cases this would be coughing or sneezing, which produce contaminated aerosols for other organisms to inhale through their own upper respiratory tract.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this answers your question! &lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-02-18T19:06:01.510" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="29681" PostTypeId="2" ParentId="29662" CreationDate="2015-02-18T19:08:48.390" Score="20" Body="&lt;p&gt;The &quot;normal&quot; visual acuity in the Anglosphere is the 20/20 vision which means that on a &lt;a href=&quot;http://en.wikipedia.org/wiki/Snellen_chart&quot;&gt;Snellen chart&lt;/a&gt; characters with 8,86 mm height can be read conveniently from a distance of approximately 6 m.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now there are many known people who have very sharp eyes, having the doubled acuity of 20/10. This means they can discern characters of only 4,43 mm height from 6m.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The normal car signs in the EU (and I think it is not very different in size in other countries) is 75 mm. So a very good observer can discern number plates from a distance of&#xA;(75 mm / 4.46 mm) * 6 m = 100 meter or 109 yards, a normal observer from half the distance (50 m or 54 yards).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;People are mostly not aware how their sight is deteriorating. Chris already said that the acuity goes down with age, but the other problem is that the lens is less flexible with age and therefore not able to focus a fast approaching car. Your son has no problem with that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry, I don't think your son is superhuman.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;FOR THE CURIOUS: A rule of thumb is that normal sight has an acuity of 1 arcminute ('), the 60th part of a degree angle. This is a ratio of 0.000291 or 3 cm per 100 m (1 inch per 1 yard).&#xA;A character to read consists of parts, let's look for example at E. E has five vertical&#xA;sections and if you think about it, all other characters can be displayed if you have five&#xA;sections available. So Snellen set the height of the characters to 5 arcminutes and the stroke width to one arcminute. The patient looks from 20 ft (= 6.096 m) away. So the height&#xA;of the characters must be (5*0.000291)*6.096 = 8.866 mm&lt;/p&gt;&#xA;" OwnerDisplayName="user10094" LastEditorDisplayName="user10094" LastEditDate="2015-02-20T22:12:23.360" LastActivityDate="2015-02-20T22:12:23.360" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29683" PostTypeId="2" ParentId="29662" CreationDate="2015-02-18T19:58:59.093" Score="2" Body="&lt;p&gt;He may have extreme acuity, or he may even have an extra cone type that allows him to see extra colors (and more color attunement may allow easier reading of those particular plates). But, you won't know anything for sure by asking on here. Take him to an ophthalmologist and let us know what the doc says! If you aren't 40+ and have 20/20 vision and he's seeing things better than you, then yeah, he probably is special!&lt;/p&gt;&#xA;" OwnerUserId="14513" LastActivityDate="2015-02-18T19:58:59.093" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="29685" PostTypeId="2" ParentId="29679" CreationDate="2015-02-18T20:43:00.840" Score="20" Body="&lt;p&gt;First of all, I would like to point out that making analogy between digital computers and the brain is often very misleading.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, my answer is, some scientists believe so, some don't.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several things to consider:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Some neural systems are not spiking. C. elegans for example has a nervous system that is entirely analogue. Human nervous system also contains neurons with graded responses (mostly in the sensory front-end though).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Spiking neurons may be binary at each time point, but time itself is continuous. Firing at 0.003 seconds later can represent something different. (in contrast to the usual synchronous digital architecture of computers)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The neuron doctrine is sometimes challenged. Glial cells that do not fire may have important functions for information processing. See:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Bullock, T. H., Bennett, M. V. L., Johnston, D., Josephson, R., Marder, E., and Fields, R. D. (2005). The neuron doctrine, redux. Science, 310(5749):791-793.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="460" LastActivityDate="2015-02-18T20:43:00.840" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29686" PostTypeId="1" CreationDate="2015-02-18T22:30:55.557" Score="1" ViewCount="14959" Body="&lt;p&gt;If I'm loading a 3.5ul PCR onto an agarose gel, how do I calculate how much of the 6x loading dye to add? &lt;/p&gt;&#xA;" OwnerUserId="12899" LastEditorUserId="6061" LastEditDate="2015-02-18T23:50:23.750" LastActivityDate="2015-02-19T01:59:57.187" Title="How does one calculate how to dilute a solution to working strength?" Tags="&lt;pcr&gt;&lt;gel-electrophoresis&gt;" AnswerCount="2" CommentCount="0" ClosedDate="2015-02-19T15:04:16.593" ContentLicense="CC BY-SA 3.0" />
  <row Id="29687" PostTypeId="2" ParentId="29673" CreationDate="2015-02-18T22:35:53.283" Score="10" Body="&lt;p&gt;That is a piece broken off of a sea urchin shell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TR9Mv.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Without it's spines, it's not possible for me to say which species it is.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-02-18T22:42:49.993" LastActivityDate="2015-02-18T22:42:49.993" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29688" PostTypeId="2" ParentId="29669" CreationDate="2015-02-18T23:24:49.050" Score="7" Body="&lt;p&gt;It is impossible at present to reproduce all the conditions of a womb.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A womb is more than a warm fluid-filled home for nine months. A few days after fertilization, the trophoblast portion of the conceptus attaches itself to the uterine wall where it develops into a placenta and umbilical cord while the rest (the epiblast) becomes the baby.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Throughout the pregnancy, the mother delivers oxygen, nutrients and hormones through the her blood flow to the placenta, while carrying away waste. The womb also prevents infection of the placenta and amniotic fluid. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, the placenta contributes to amniotic fluid production. Production and reabsorption of amniotic fluid is a very dynamic process; it isn’t &lt;em&gt;just there.&lt;/em&gt; It is estimated that more than 95% of amniotic fluid turns over on daily basis, and the fluid composition changes throughout pregnancy.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While cell cultures of the womb's endometrium have been grown, there is nothing artificial which is close to this kind of environment yet, nor is there likely to be in the near future.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-02-18T23:53:34.000" LastActivityDate="2015-02-18T23:53:34.000" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="29689" PostTypeId="2" ParentId="29677" CreationDate="2015-02-18T23:25:27.040" Score="8" Body="&lt;p&gt;Labor is typically divided into 3 stages:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Stage 1: From the onset of contractions (true labor pains) to full dilatation of the cervix (which is about 10 cm) - this takes about 12 to 18 hours&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Stage 2: From full dilatation of cervix to expulsion of fetus - This takes about ~ 30 minutes&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Stage 3. From expulsion of fetus to expulsion of placenta - this takes about ~ 15 minutes. During the third stage, the umblical cord which is attached to placenta is expelled along with the placenta&lt;/strong&gt;. This would be the answer to your question.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/l4OuS.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;sub&gt;Source:&lt;a href=&quot;http://www.humpath.com/IMG/jpg_10143_normal_placenta_28w_1.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hympath.com&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-02-19T01:13:25.860" LastActivityDate="2015-02-19T01:13:25.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29690" PostTypeId="2" ParentId="29686" CreationDate="2015-02-18T23:45:55.930" Score="1" Body="&lt;p&gt;Since its 6x (6 times concentrated), you have to dilute it 1:6, so you add 1ul of 6x dye for every 5ul of reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5 +1=6ul final volume&lt;/p&gt;&#xA;&#xA;&lt;p&gt;6ul final volume / 6x concentrated = 1x working concentration&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the dye is diluted down to a 1x(working) strength.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2015-02-18T23:45:55.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29692" PostTypeId="1" AcceptedAnswerId="29770" CreationDate="2015-02-19T00:58:12.057" Score="4" ViewCount="892" Body="&lt;p&gt;Lyonization is the process in which there is inactivation of an X chromosome in females. This process is implicated in mosaic forms of turner's syndrome (in this case the altered &lt;code&gt;X chromosome&lt;/code&gt; is Lyonised, thus allowing the normal &lt;code&gt;X Chromosome&lt;/code&gt; to express itself).&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Is Lyonization considered as a form of genetic imprinting? What is the difference between the two (if no)?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Lyonization is a random process (according to the extent of my knowledge which &lt;code&gt;X chromosome&lt;/code&gt; is inactivated is not predicatable). Is genetic imprinting also random? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is there any known aberration of Lyonization in males? (meaning the single &lt;code&gt;X Chromosome&lt;/code&gt; or &lt;code&gt;Y Chromosome&lt;/code&gt; gets silenced)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-02-19T01:07:23.250" LastActivityDate="2015-02-21T20:44:29.407" Title="Lyonization vs Genetic Imprinting" Tags="&lt;genetics&gt;&lt;reproduction&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29695" PostTypeId="2" ParentId="28168" CreationDate="2015-02-19T01:52:38.273" Score="4" Body="&lt;p&gt;In warm-blooded animals, our high metabolisms are a significant disadvantage when being decapitated. Just a few minutes without oxygen and a mammal's brain is caput—the result of a massive cascading cellular die-off. Not so with cold-blooded reptiles. Their slow metabolism sustains their internal organs for far longer than a mammals causing them to completely die far more slowly. Essentially, cutting off their heads only makes them &quot;mostly dead&quot;.&lt;/p&gt;&#xA;" OwnerUserId="12972" LastActivityDate="2015-02-19T01:52:38.273" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29697" PostTypeId="2" ParentId="29686" CreationDate="2015-02-19T01:59:57.187" Score="0" Body="&lt;p&gt;You want to dilute concentrations to 1x, therefore a 1:6 ratio for dye:reaction.&lt;/p&gt;&#xA;" OwnerUserId="12972" LastActivityDate="2015-02-19T01:59:57.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29699" PostTypeId="2" ParentId="28567" CreationDate="2015-02-19T02:17:33.483" Score="1" Body="&lt;p&gt;Fingerprints form in the womb at 22 weeks and after that, all they will do is expand as you grow. Therefore, it is possible that a fingerprint 22 weeks after conception could be used to identify a 50-year-old criminal.&lt;/p&gt;&#xA;" OwnerUserId="12972" LastActivityDate="2015-02-19T02:17:33.483" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29700" PostTypeId="1" AcceptedAnswerId="29722" CreationDate="2015-02-19T04:23:11.730" Score="3" ViewCount="48" Body="&lt;p&gt;Is there an authority on definitions for molecular microbiology concepts, like an IUPAC book for chemical definitions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The particular definition I am debating is chromatin. Some say it encompasses DNA, RNA and protein, whilst others say that it contains DNA and only during the mitotic interphase can it transcribe to produce RNA and protein. &lt;/p&gt;&#xA;" OwnerUserId="14518" LastEditorUserId="14518" LastEditDate="2015-02-22T08:52:06.207" LastActivityDate="2015-02-22T08:52:06.207" Title="Authority on Microbiological Definitions" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29702" PostTypeId="1" AcceptedAnswerId="29715" CreationDate="2015-02-19T06:19:22.850" Score="1" ViewCount="230" Body="&lt;p&gt;I have come across some species of living organisms who are able to emit light at whim. Can that ability be incorporated into a portion of human skin (a specialized tissue)?&lt;/p&gt;&#xA;" OwnerUserId="14500" LastEditorUserId="14500" LastEditDate="2015-02-24T06:58:54.260" LastActivityDate="2015-02-24T06:58:54.260" Title="Can a portion of human skin cells be modified in some way to generate light?" Tags="&lt;skin&gt;&lt;cell&gt;&lt;tissue&gt;" AnswerCount="3" CommentCount="0" ClosedDate="2015-02-20T19:49:10.657" ContentLicense="CC BY-SA 3.0" />
  <row Id="29703" PostTypeId="1" CreationDate="2015-02-19T07:11:53.550" Score="4" ViewCount="100" Body="&lt;p&gt;One can easily find information on the topic of leukocytes trafficking between vessels and peripheral tissues during inflammation.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what happens during normal states when there is no pathology? Do all the subtypes of granulocytes, monocytes, and lymphocytes leave the blood vessels and enter healthy tissues in the same way they do under pathological (inflammatory) conditions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References and thoughts are very welcome.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="416" LastEditorUserId="11841" LastEditDate="2015-02-19T13:19:03.243" LastActivityDate="2015-02-19T13:19:03.243" Title="Human leukocytes (re)circulation/migration in homeostatic state" Tags="&lt;immunology&gt;&lt;blood-circulation&gt;&lt;homeostasis&gt;&lt;immunity&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29705" PostTypeId="2" ParentId="29702" CreationDate="2015-02-19T10:10:22.840" Score="2" Body="&lt;p&gt;Yes, the fibroblasts of skin cells can quite easily be Transfected with a fluorescent gene such as GFP. Fluorescence doesn't actually produce light, the fluorescent molecule just changes the wavelength of light shining on it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fibroblasts can also be made luminescent (light producing) by acquiring  genes for firefly luciferase or aquoren from jellyfish. This is a little more tricky since luminescent molecules typically require cofactors such as ATP, Calcium or other proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both methodologies are readily performed &lt;em&gt;in vitro&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2015-02-19T10:10:22.840" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29707" PostTypeId="2" ParentId="14164" CreationDate="2015-02-19T12:10:29.637" Score="9" Body="&lt;h2&gt;Short Answer:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;There was an &lt;a href=&quot;http://www.jbc.org/content/113/1/265.full.pdf&quot;&gt;interesting paper&lt;/a&gt; that dealt with the pH of urine when citric acid was consumed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The summary was: There was no increase in urinary pH or total nitrogen in 24 hours collection of urine&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;What This Means:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The food we take does not affect the blood pH directly. Acidic food will cause increased secretion of alkaline components into the digestive tract to neutralize the excess acid. This will cause a fall in the bicarbonate ions concentration (this being the major alkaline buffer) in the blood. This might cause acidosis (depending on how acidic the food is).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The body compensates the decrease in bicarbonate concentration by excreting H&lt;sup&gt;+&lt;/sup&gt; ions in the urine. Thus urine becomes more acidic when there is a relative state of metabolic acidity in the body. There is also hyperventilation and excretion of more CO&lt;sub&gt;2&lt;/sub&gt; as this will cause excretion of H&lt;sup&gt;+&lt;/sup&gt; ions.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; + H&lt;sup&gt;+&lt;/sup&gt; ----&gt; H&lt;sub&gt;2&lt;/sub&gt;O + CO&lt;sub&gt;2&lt;/sub&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Incase of alkaline foods, the stomach acid itself would be partly neutralized by the alkali present in food. Thus the body need spend only minimal bicarbonate ions to neutralize the remaining acid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is severe alkalosis body compensates by decreasing the respiratory drive (conserving more H&lt;sup&gt;+&lt;/sup&gt; ions) and excreting more bicarbonate ions through kidneys.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Compare this with the data obtained from experiment&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;If consuming citric acid would lower blood pH levels then the urinary pH should increase. As the data shows this is not so, that would mean the citric acid does not contribute to the acidity of food in any significant way even when consumed in large quantities.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-02-19T13:14:56.623" LastActivityDate="2015-02-19T13:14:56.623" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="29708" PostTypeId="1" CreationDate="2015-02-19T12:55:34.423" Score="0" ViewCount="81" Body="&lt;p&gt;I am looking for a mapping, list, ontology or graph that shows the connection between a diseases and its (currently known) causes and/or risk factors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example a well known risk factor for &lt;em&gt;acute kidney injury&lt;/em&gt; is &lt;em&gt;diabetes&lt;/em&gt;. There are other diseases whoms risk factor is &lt;em&gt;diabetes&lt;/em&gt;. This meanse &lt;em&gt;diabetes&lt;/em&gt; is a &lt;em&gt;risk factor&lt;/em&gt; for many &lt;em&gt;diseases&lt;/em&gt;. Maybe if one traverses trough this dependencies and builds a graph out of it, there will interesting clusters and lineages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I dont know if this is &lt;em&gt;inherent knowledge&lt;/em&gt; or formulated somewhere in a formal and explicit way (e.g. as ontology).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is &lt;a href=&quot;http://disease-ontology.org/&quot; rel=&quot;nofollow&quot;&gt;http://disease-ontology.org/&lt;/a&gt;, but it does not contain any causes, risk factors, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance!&lt;/p&gt;&#xA;" OwnerUserId="14527" LastActivityDate="2015-02-19T12:55:34.423" Title="Is there a graph or ontology that maps diseases to its possible causes or causing diseases?" Tags="&lt;pathology&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29710" PostTypeId="1" CreationDate="2015-02-19T13:14:44.770" Score="0" ViewCount="123" Body="&lt;p&gt;First of all, I am not a biology guy; I am in Computer Science. But, I have a strong interest in all the mysteries of nature, from universe to human body. So, I want to ask a question related to genetics.&lt;br&gt;&#xA;As I have read that all(both male's and female's) the biological traits of a person are passed genetically to the offspring(of course assuming the crossing). So if my mom's eye color is blue and my dad's eye color is also blue, I will get blue color too, but what about the core architecture of the body? I mean I have 2 legs at a certain location from my body(my waist but, not from my head!) and similarly other orientations.&lt;br&gt; Why they are that certain way? If they somehow got changed, would the resultant body be stable?Is the answer different in case change is artificially engineered or natural?&lt;br&gt;&#xA;Where is this core architectural information exactly stored(If the answer is DNA then how?) and in what form is it stored?How come that information is not changed in thousands of years or even millions of years? And is that information of such nature that it contains &quot;exact&quot; steps to develop a healthy say, brain structure(which is a really complex)?&lt;br&gt;&#xA;My another question is: If there is a community of mutated people, will their offsprings be mutated always with 100% certainty?&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know these are a lot of questions but you can see that, they basically revolve around the information that I am curious about. Can someone address my curiosity?&lt;/p&gt;&#xA;" OwnerUserId="14528" LastActivityDate="2015-02-19T17:28:23.017" Title="Core architecture of the body encoding" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;dna&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="6" ClosedDate="2015-02-19T16:57:36.167" ContentLicense="CC BY-SA 3.0" />
  <row Id="29711" PostTypeId="1" AcceptedAnswerId="29713" CreationDate="2015-02-19T14:17:17.363" Score="1" ViewCount="56" Body="&lt;p&gt;This is a more generalized question of my &lt;a href=&quot;https://biology.stackexchange.com/questions/29704/possibility-of-creating-a-non-invasive-biosensor-on-solid-non-homogenous-fish&quot;&gt;other question&lt;/a&gt; here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know if it is possible to determine a chemical compound in a non-homogeneous sample. I am asking this because we are aiming to create a device that will detect histamine level in fish without homogenizing the samples. In all the journals we've read (which are a lot), fish samples are homogenized (blended + chemically-treated) before histamine is determined.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am a computer engineering student with basic knowledge on biochemistry. I'm researching on this because this is our thesis topic (which our adviser has &lt;s&gt;forced&lt;/s&gt; recommended to us).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help/recommendation regarding this is appreciated. Thank you!&lt;/p&gt;&#xA;" OwnerUserId="14524" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-02-21T06:44:37.407" Title="Determination of a chemical compound in a non-homogeneous sample" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29712" PostTypeId="2" ParentId="29710" CreationDate="2015-02-19T15:11:23.140" Score="5" Body="&lt;p&gt;Welcome to Biology.SE!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question is very broad. Also, your post has the default of containing severals questions in it. Make sure in the future to restrict your post to only question, it will be much more likely that you receive a good answer then. I hope that I can give some indications about how to get some more knowledge in this answer. In this answer, I do not consider all your questions one by one to answer them (or guide you to the answer) but I think that all your questions will get an answer as you learn more about the subjects I cite. Hope that answer will help you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Very basics of molecular genetics&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should start to have a few ideas about genetics. Make sure you know what is a chromosome, a gene, an allele, a protein and a phenotype. Wikipedia will help you with that. Come back on Biology.SE if something seems unclear to you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Basics of genetics and evolution&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are definitely interested in concept of segregation. This is a very fundamental concept in genetics. The basis of the laws governing segregation has been first discovered by &lt;a href=&quot;http://en.wikipedia.org/wiki/Gregor_Mendel&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gregor Mendel&lt;/a&gt; and we still name these basics laws after Mendel. We talk about Mendelian segregation. You may want to google that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then you are interested in the concept of heritability. I have been talking about heritability in different posts. In the third sentence of my answer &lt;a href=&quot;https://biology.stackexchange.com/questions/16858/are-people-genetically-predisposed-to-being-interested-in-specific-fields-ideas/16862#16862&quot;&gt;here&lt;/a&gt;, there is a short list of posts that define the concept of heritability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Eye color you said?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You talked about the genetics of eye color inheritance. &lt;a href=&quot;https://biology.stackexchange.com/questions/728/how-is-eye-color-in-humans-inherited&quot;&gt;Here&lt;/a&gt; is a post that will interest you then.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The Genetics of Development&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question is not only about genetics but is about the genetic of development. You may want to have a look to the basics of &lt;a href=&quot;http://en.wikipedia.org/wiki/Developmental_biology&quot; rel=&quot;nofollow noreferrer&quot;&gt;developmental biology&lt;/a&gt;. The most famous DNA sequence  involved in determining the body plan of many different living things are the so-called &lt;a href=&quot;http://en.wikipedia.org/wiki/Homeobox&quot; rel=&quot;nofollow noreferrer&quot;&gt;homeobox&lt;/a&gt;. There is plenty of interested things about this homeobox. This &lt;a href=&quot;https://biology.stackexchange.com/questions/13808/how-does-the-colinearity-of-the-hox-genes-determine-the-body-plan-of-an-organism&quot;&gt;post&lt;/a&gt; may interest you btw.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Rough details about the evolution of development along the tree of life&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How come that information [architectural information] is not changed in thousands of years or even millions of years?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It really depends on what you call &lt;code&gt;architectural information&lt;/code&gt;. But in any case it does evolve. If you think of things such as like size of an animal. Then it may evolve fairly quickly. You may thing of more important change, such as evolving a new pair of legs or evolving wings or a head, then it tends to take more time. Below are just a bunch of examples of how animals differ in terms of body plan along the tree of life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might be interested to study a bit the development or early animals. Some have a radial symmetry while other (like us) have bilateral symmetry (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Symmetry_in_biology&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki&lt;/a&gt;). Some animals have a head, some don't. Some animals have two dermes while others have three dermes. The &lt;em&gt;Deuterostomata&lt;/em&gt; (vertebrates, tunicates, echinodermes, ...) have a development where the blastopore of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Gastrulation&quot; rel=&quot;nofollow noreferrer&quot;&gt;gastrula&lt;/a&gt; becomes the anus while in the &lt;em&gt;protestomata&lt;/em&gt; (now thought to not be monophyletic and divided into &lt;em&gt;ecdysozoa&lt;/em&gt; and &lt;em&gt;lophotrocozoa&lt;/em&gt; (see &lt;a href=&quot;http://tolweb.org/Bilateria/2459&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;)) the blastopore becomes the mouth. Among the &lt;em&gt;arthropoda&lt;/em&gt; (insects, spiders, millipedes, ...) the story is very interesting as well. Some have a highly segmented body with a pair of legs at each segment (millipedes) while other groups have fused those segments. Spiders have only two big body parts, while insects have three big body parts. In insects, the thorax (one of the 3 body parts with the head and the abdomen) contain three segments and each segment hold a pair of legs. The first flying insects also had three pairs of wings, now degenerated into two and even into one in &lt;em&gt;Diptera&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-02-19T17:28:23.017" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29713" PostTypeId="2" ParentId="29711" CreationDate="2015-02-19T16:20:21.573" Score="2" Body="&lt;p&gt;You should not actually homogenize samples because histamine works locally. If you know which region is releasing histamine then you can just study those regions. You can actually create a transgenic fish with GFP that is a target of histamine receptor signaling. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using mathematical models or statistical correlations you can obtain the level of histamine based on fluorescence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Activated histamine receptor H1 causes production of inositol triphosphate (IP3) which in turn causes release of calcium form ER. You can use &lt;a href=&quot;http://en.wikipedia.org/wiki/Cameleon_%28protein%29&quot; rel=&quot;nofollow&quot;&gt;Cameleon-GFP&lt;/a&gt; to sense the change in calcium levels. However, there are many events that may result in calcium release; you should carefully design your experiment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is another possibility (&lt;strong&gt;just a guess&lt;/strong&gt;)- a FRET based study using &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18638193&quot; rel=&quot;nofollow&quot;&gt;GFP-YFP FRET Pairs&lt;/a&gt; (or other variants). Since histamine receptors are G-protein coupled receptors you may fuse the GFP to alpha subunit and YFP to beta subunit. When upon signaling, the subunits dissociate, you would see a decrease in FRET. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-02-21T06:44:37.407" LastActivityDate="2015-02-21T06:44:37.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29715" PostTypeId="2" ParentId="29702" CreationDate="2015-02-19T17:40:17.437" Score="4" Body="&lt;p&gt;Genetic modification of any cell to overexpress a &lt;em&gt;fluorescent&lt;/em&gt; protein will &lt;strong&gt;not&lt;/strong&gt; 'generate' light, per-say: fluorophores absorb particular wavelengths and re-emit in less energetic wavelengths, dispersing some energy as heat. &lt;em&gt;(Perhaps there is some semantic choice here, but there is no transduction to light from another form of energy.)&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Bioluminescence&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Bio-luminescence&lt;/strong&gt;, on the other hand&lt;/a&gt;, can be considered generation of light. There are proteins commonly found in marine animals (which skin cells could be engineered to express) which convert chemical energy to emit light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regards to generation of &lt;em&gt;electricity&lt;/em&gt;, I think this gets a bit interesting...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Electron_transport_chain&quot; rel=&quot;nofollow&quot;&gt;The electron transport chain&lt;/a&gt; (ETC) in the inner membranes of our &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitochondrion&quot; rel=&quot;nofollow&quot;&gt;mitochondria&lt;/a&gt; carry out a series of &lt;a href=&quot;http://en.wikipedia.org/wiki/Redox&quot; rel=&quot;nofollow&quot;&gt;redox reactions&lt;/a&gt; which serve to oxidise food metabolites (thus freeing electrons). In order to maintain the free energy gradient that favours this directional cascade of reactions, electrons and protons are finally accepted by a continual supply of oxygen atoms, producing water. (You may be aware that aerobic respiration consumes oxygen and produces water.) In nature (in aerobes), oxygen acts as the &lt;em&gt;final electron acceptor&lt;/em&gt;, or an &lt;em&gt;electron sink&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria also have electron transport chains for their respiration (mitochondria were once bacteria, after all), and people have wondered whether these redox reactions could be used to produce a current instead of reducing oxygen to water as the final step. We normally use current in the form of electrons moving along a metal wire.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the idea of a &quot;microbial fuel cell&quot;. Just like a battery produces a current from a chemical redox reaction, the ETC might be recruited in to producing a current from its chemical redox reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this is a very difficult piece of bioengineering, since the ETC is integrated in to respiration and needs to be de- &amp;amp; re-coupled to some kind of inorganic mediator and ultimately a circuit; and also because the ETC produces very low voltages, I think.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Microbial_fuel_cell&quot; rel=&quot;nofollow&quot;&gt;nice wikipedia page on microbial fuel cells&lt;/a&gt; that you might find interesting, if you think this is relevant to your question.&lt;/p&gt;&#xA;" OwnerUserId="13310" LastActivityDate="2015-02-19T17:40:17.437" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29716" PostTypeId="1" AcceptedAnswerId="29894" CreationDate="2015-02-19T17:43:31.303" Score="5" ViewCount="17744" Body="&lt;p&gt;If there was crossing over in mitosis, then there would various nature of somatic cells. May be that's the logic, but what is the mechanism? Why are there no crossover events during mitosis?&lt;/p&gt;&#xA;" OwnerUserId="4806" LastEditorUserId="16299" LastEditDate="2017-01-19T22:44:56.527" LastActivityDate="2017-04-04T07:51:01.700" Title="Why doesn't crossing over happen in mitosis?" Tags="&lt;genetics&gt;&lt;mitosis&gt;&lt;cell-division&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29717" PostTypeId="1" AcceptedAnswerId="31364" CreationDate="2015-02-19T19:27:23.600" Score="10" ViewCount="1802" Body="&lt;p&gt;Cells and organelles are contained in &lt;a href=&quot;http://en.wikibooks.org/wiki/Structural_Biochemistry/Lipids/Lipid_Bilayer&quot; rel=&quot;nofollow&quot;&gt;lipid bilayers&lt;/a&gt;. I'm particularly interested in eukaryotic organelle bilayers and the biophysicochemical differences between them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many papers &lt;em&gt;assume&lt;/em&gt; a difference in membrane characteristics and some like &lt;a href=&quot;http://arjournals.annualreviews.org/doi/full/10.1146/annurev.biophys.36.040306.132643?url_ver=Z39.88-2003&amp;amp;rfr_id=ori:rid:crossref.org&amp;amp;rfr_dat=cr_pub%3dpubmed&quot; rel=&quot;nofollow&quot;&gt;Anderson &lt;em&gt;et al.,&lt;/em&gt; 2007&lt;/a&gt; have categorised the relationship between these characteristics and protein function in depth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do any reviews or comprehensive studies exist in the field that compare the thickness of the membrane, the rigidity of the surface, any differences in lipid entropy, or the overall charge inside and outside across &lt;strong&gt;different types of organelle membranes&lt;/strong&gt;?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2016-05-03T10:10:15.920" LastActivityDate="2016-05-03T10:10:15.920" Title="What is the difference between organelle membranes?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;biophysics&gt;&lt;cell-membrane&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29718" PostTypeId="2" ParentId="28517" CreationDate="2015-02-19T21:11:41.140" Score="3" Body="&lt;p&gt;In short, rate of expression of intracellular cholesterol removal proteins like ABCA1 in macrophages and cytokine waterfall molecules in T-lymphocytes beside other anti-inflammatory cytokines has an important role in AS and why oxLDLs accumulate in intima.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When there is high level of oxLDL, rate of removal mechanism must increase to take extra cholesterol out of macrophage and after that to the liver.&#xA;And it(increasing the rate of reverse mechanism) could be done by inhibitors or regulators(when natural way could not effort enough excretion). =&gt; drugs like TONSHINONE&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is huge amount of information about how regulation of adhesion molecules, costimulatory molecules, antigen presenting molecules and anti-inflammatory or inflammatory molecules could have effect on oxLDL accumulation in macrophages and T-lymphocytes which cause damage induced by hydrogen proxide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So accumulation of oxLDL molecules in Macrophages has genetic reason and why human being evolved in this way is a question for geneticists but how this happens could be explained by tracing adhesion and signaling molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1155/2014/267976&quot; rel=&quot;nofollow noreferrer&quot;&gt;This&lt;/a&gt; is one of the texts about oxLDL accumulation and AS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Macrophages take in, a large number of oxidized low density lipoproteins (oxLDL) under the intima and then become foam cells, which is one of the early signs of atherosclerotic lesions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ATP-binding cassette transporter A1 (ABCA1) is an integral membrane protein that transports lipid from the cells to the liver with subsequent lipid excretion by bile at last. This reversal transport inhibits the formation of lipid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This text shows how regulating cytokine waterfall and pro-inflammatory cytokines could have impact on creation or removal of foam cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They experimented that Tanshinone IIA (a molecule extracted from root of Salvia miltiorrhiza) significantly increased expression of ABCA1 in macrophage-derived foam cells, raised the outflow of intracellular cholesterol, and inhibited the formation of oxLDL induced foam cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HFurk.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, the liver X receptor (LXR) and peroxisome proliferator activated receptor (PPAR) which are members of nuclear receptor superfamily can increase expression of ABCA1 through coupling path. Tan IIA inhibited the formation of foam cells. The mechanism might be that Tan IIA increased expression of PPARa, LXRa, and ABCA1, facilitated reversal cholesterol transport, and ultimately promoted cholesterol efflux.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;T-lymphocytes in plaques are mostly CD4+ T-lymphocytes which belong to Th1 subtype. Most of CD4+ T-lymphocytes are active and can induce “cytokine waterfall” as well as secrete proinflammatory cytokines interferon-gamma (IFN-y), IL-12, and other cytokines, eventually leading to inflammation. Experiments showed that Tanshinone significantly inhibited production of Th1-derived IL-12 and IFN-y in a dose-dependent manner. T-lymphocytes play a role in the formation of AS, mainly because of proinflammatory cytokines secreted by T helper type (Th) 1 or Th2. Therefore, Tanshinone can inhibit the formation of AS and stabilize plaques via reducing the secretion of Th1 or Th2. Moreover, T-lymphocytes are activated to express CD40L, and the expression of tissue factor and matrix metalloproteinases (MMPs) is then promoted by interaction between CD40L and CD40. &#xA;TanIIA could improve the activity of superoxide dismutase (SOD), decrease the level of malondialdehyde (MDA), and reduce both the expression of CD40 and the activity of MMP-2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So normally macrophages could excrete cholesterols but problem occurs when your diet contains high level of cholesterol and oxLDL goes high in your blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evidence-Based Complementary and Alternative Medicine&#xA;Volume 2014 (2014), Article ID 267976, 6 pages&#xA;&lt;a href=&quot;http://dx.doi.org/10.1155/2014/267976&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://dx.doi.org/10.1155/2014/267976&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8540" LastEditorUserId="8540" LastEditDate="2015-02-19T23:09:34.100" LastActivityDate="2015-02-19T23:09:34.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29719" PostTypeId="2" ParentId="29716" CreationDate="2015-02-19T21:15:21.500" Score="2" Body="&lt;p&gt;The mechanism is straightforward: in Metaphase I of Meiosis, chromosomes line up in two lines, with homologous across from each other, which allows them to interact by crossing over. In Metaphase of Mitosis, the chromosomes are all lined up single file, so the homologous chromosomes cannot interact.&lt;/p&gt;&#xA;" OwnerUserId="14533" LastActivityDate="2015-02-19T21:15:21.500" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29720" PostTypeId="1" AcceptedAnswerId="29745" CreationDate="2015-02-19T21:37:01.397" Score="3" ViewCount="119" Body="&lt;p&gt;I was reading an article in nature communications, when I came across this sentence: &quot;The ‘match’ rule was indicated by either a blue circle or a auditory upward sweep&quot;.So I tried googling what was an upward sweep, and came across this: &quot;natural and complex vocalizations consist of basic elements such as upward sweeps, downward sweeps, constant frequency components, amplitude modulations...&quot; I don't understand this. Can someone explain what is an upward sweep? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the link to the article: &lt;a href=&quot;http://www.nature.com/ncomms/2013/131128/ncomms3878/abs/ncomms3878.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/ncomms/2013/131128/ncomms3878/abs/ncomms3878.html&lt;/a&gt;, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I think you have to pay to view the whole article, so here is another link that discusses the findings of the article:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.uni-tuebingen.de/en/landingpage/newsfullview-landingpage/article/von-wegen-spatzenhirn-wie-nervenzellen-schlaues-verhalten-bei-rabenvoegeln-ermoeglichen.html&quot; rel=&quot;nofollow&quot;&gt;http://www.uni-tuebingen.de/en/landingpage/newsfullview-landingpage/article/von-wegen-spatzenhirn-wie-nervenzellen-schlaues-verhalten-bei-rabenvoegeln-ermoeglichen.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="13277" LastEditorUserId="13277" LastEditDate="2015-02-20T15:00:30.897" LastActivityDate="2015-02-20T16:55:02.597" Title="What is an auditory upward sweep?" Tags="&lt;neuroscience&gt;&lt;neurology&gt;&lt;hearing&gt;&lt;human-ear&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29722" PostTypeId="2" ParentId="29700" CreationDate="2015-02-19T21:46:06.590" Score="2" Body="&lt;p&gt;So in a very broad definition, yes, &lt;a href=&quot;http://www.hhmi.org/content/chromatin-structure-and-function&quot; rel=&quot;nofollow noreferrer&quot;&gt;chromatin&lt;/a&gt; encompasses DNA, RNA and protein. The primary function of chromatin is to provide a method to effectively package all the DNA in a cell. This packaging is dynamic, and it's constantly regulated in a cell type-specific manner. We can see the broad interactions of protein and DNA in this cartoon representation from wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/izM8V.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Combined with histone-modifying complexes, and chromatin remodeling complexes, we obtain the aforementioned mode of regulation. Histone protein can be modified (acetylation, methylation, glycosylation, phosphorylation, etc.), they can also be moved, substituted in their subunits for specific pruposes (think H3.3 or H2A.X). We can also end up with varying regions of dsDNA, 10nm or 30nm fiber. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The RNA comes in as a &lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001182&quot; rel=&quot;nofollow noreferrer&quot;&gt;structural&lt;/a&gt; and &lt;a href=&quot;http://www.cell.com/molecular-cell/abstract/S1097-2765(11)00680-0&quot; rel=&quot;nofollow noreferrer&quot;&gt;functional&lt;/a&gt; components of the chromatin, participating in many controls as noncoding RNAs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe most of the method in defining chromatin comes in very much as the amassed literature on the subject to-date. You'd even consider it &quot;common knowledge&quot; entering the field (i.e. a quick google search can return you the right definition).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;only during the mitotic interphase can it transcribe to produce RNA and protein.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Transcription halts entering M phase or mitosis, transcription may occur during G1, S, G2, or &quot;interphase.&quot;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-02-19T21:46:06.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29723" PostTypeId="2" ParentId="29702" CreationDate="2015-02-19T22:18:06.023" Score="3" Body="&lt;p&gt;Sort of problematic is the &quot;at a whim&quot; part. Just a brief search to wikipedia on electric organs, &lt;a href=&quot;http://en.wikipedia.org/wiki/Electric_organ&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, we see that the electrocytes are controlled by a nucleus of pacemaker neurons. This is all unique to electric fish, and you'd have to express that whole system in a human being to elicit the same effect. You'd also have to consider how your organism is engineered to withstand the actual electric shock emitted by the electric organ.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can already tag molecules with &lt;a href=&quot;http://en.wikipedia.org/wiki/Luciferase&quot; rel=&quot;nofollow&quot;&gt;luciferase&lt;/a&gt; to emit light as a mode of bio-luminescence. To get an appreciable reaction, or rather an appreciably bright light, I can imagine we'd need a ridiculous amount of luciferin &lt;em&gt;in vivo&lt;/em&gt;, though. We also get stuck at the part about it being on a whim. The &lt;a href=&quot;http://ase.tufts.edu/biology/Firefly/&quot; rel=&quot;nofollow&quot;&gt;control mechanisms/structures&lt;/a&gt; for the light-emitting reaction simply aren't present.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-02-20T20:13:26.363" LastActivityDate="2015-02-20T20:13:26.363" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29724" PostTypeId="2" ParentId="3205" CreationDate="2015-02-19T23:19:53.033" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867411001279&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hallmarks of Cancer: The Next Generation&lt;/a&gt; is by far my favorite article at the moment explaining cancer in-depth. I'd recommend reading through it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cells replicate themselves, without regard for normal cellular restriction, due to a number of mutations that accumulate:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XU08f.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So our cancer cells are evading apoptosis. P53 might be knocked down, so cell cycle arrest cant occur, but what about when Akt is constitutively &quot;ON&quot;? Normally P53 can induce apoptosis &lt;em&gt;via&lt;/em&gt; the following mechanism:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GYkBc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And as it turns out, Akt inhibits apoptosis in the following manner:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ACbio.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the cells really aren't dying. What about replicative aging? We find cancer &lt;a href=&quot;http://hmg.oxfordjournals.org/content/10/7/677.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;cells have telomerase activity&lt;/a&gt; which essentially makes them immortal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's also evidence to support regulation of pathways which promote epithelial-mesenchymal transition in tumor cells, and promote invasiveness and cellular motility in most cases:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/U6xYH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the sake of a short response that isn't a wall of text/images, this is a broad survey of some relevant cancer pathways which essentially make cancer what it is. &lt;strong&gt;It's more complex than this&lt;/strong&gt;, but if you put in some research given these hallmarks of cancer, the answers are there.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-02-19T23:19:53.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29725" PostTypeId="1" AcceptedAnswerId="29739" CreationDate="2015-02-20T00:53:47.150" Score="6" ViewCount="210" Body="&lt;p&gt;First of all, I am not a biologist.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;Almost for a week, a question has come to my mind:&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;&amp;quot;Is it harmful ceaselessly exposing a plant to light?&amp;quot;&lt;/strong&gt;&lt;br&gt;&#xA;(I mean with natural &amp;amp; artificial light with proper spectrum)&lt;/p&gt;&#xA;&lt;p&gt;I have been searching for a week, and I stumble upon many weird and wonderful things, and by them, I have become able to consider this topic more deeply, and refine my original question. However I have still not found the answer.&lt;/p&gt;&#xA;&lt;p&gt;I am already familiar with these topics:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Light-dependent reactions&lt;/li&gt;&#xA;&lt;li&gt;Light-independent reactions&lt;/li&gt;&#xA;&lt;li&gt;Calvin cycle&lt;/li&gt;&#xA;&lt;li&gt;Photoperiodism&lt;/li&gt;&#xA;&lt;li&gt;Phytochrome&lt;/li&gt;&#xA;&lt;li&gt;Cryptochrome&lt;/li&gt;&#xA;&lt;li&gt;Long-day, Short-day, Day-neutral plants&lt;/li&gt;&#xA;&lt;li&gt;Grow light&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;So my &lt;strong&gt;main question:&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;h2&gt;Does ceaseless light exposure with proper spectrum adversely affect a day-neutral plant?&lt;/h2&gt;&#xA;&lt;p&gt;As a layman I have started to fumble towards light-independent reactions, but I have not found strong claim. I have learnt that there are processes which taking place during dark phase, but &lt;strong&gt;are these reactions impossible in presence of light?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;But probably there are other factors.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;My resources were: Google, Wikipedia, (a tons of) academic paper, many article from Botanical Gazette, many blog &amp;amp; webpages about botany &amp;amp; greenhouses etc.&lt;/p&gt;&#xA;" OwnerUserId="14536" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2016-05-09T17:19:58.340" Title="Total dark deprivation at day-neutral plants" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;photosynthesis&gt;&lt;growth&gt;&lt;photoperiod&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29727" PostTypeId="2" ParentId="29692" CreationDate="2015-02-20T06:55:08.493" Score="1" Body="&lt;p&gt;I guess, we are talking about mammals here (because in other organisms leveling up of expression on sex chromosomes happens differently: e.g. in flies females express both X chromosomes, while fly males express their single X at twice as high level).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In embryo proper the decision of whether to inactivate maternal or paternal X seems to be at random. This inactivation adjusts level of expression of genes on X to be in the same ball park as on autosomes and in the same ballpark between males and females. Neither farther nor mother cares about which copy of X gets inactivated in individual cells of an embryo.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When we say that a gene is imprinted, that means only one copy of the gene is expressed  but, to the contrary of what happens with X, maternal or paternal origin of the expressed copy is predetermined (so there is no randomness in which copy is inactive). Imprinting is usually a property of genes expressed during embryonic development and it is related to tug of war between farther and mother's interests: the farther &quot;wants&quot; embryo to take as much resources from the mother as possible (so paternal copies of some genes tend to be highly expressed), while mother wants not to give too much to one embryo, so that she can raise many more progeny (so maternal copies of some other genes tend to be highly expressed). This whole thing is interestingly described Matt Ridley book &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0060556579&quot; rel=&quot;nofollow&quot;&gt;The Red Queen: Sex and the Evolution of Human Nature&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note, that to confuse matters a little bit, in placenta of female embryos it is always the paternally inherted X that gets silenced, so the whole X chromosome is imprinted in extra-embryonic tissues of female embryos. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And in males X chromosomes do not get inactivated, since many genes are present solely on X chromosome and not on Y, so inactivating the only copy of X chromosome is lethal. &lt;/p&gt;&#xA;" OwnerUserId="13239" LastActivityDate="2015-02-20T06:55:08.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29729" PostTypeId="1" CreationDate="2015-02-20T08:43:30.967" Score="2" ViewCount="948" Body="&lt;p&gt;In the answers to &lt;a href=&quot;https://biology.stackexchange.com/questions/9993/is-there-any-use-of-co%E2%82%82-in-human-body&quot;&gt;this&lt;/a&gt; question, we've learnt that carbon dioxide is necessary for mammalian life, but is it necessary in the atmosphere/to breathe it in?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or does the act of respiration give a human (or other animal) enough carbon dioxide to fulfill all of the functions that carbon dioxide is needed for?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or, phrased another way, if you put an animal in a carbon-dioxide-free atmosphere, and continually removed the carbon-dioxide that they generate upon respiration/exhalation, would they get enough carbon dioxide to fulfill these requirements:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;fatty acid biosynthesis (FAS)&lt;/li&gt;&#xA;&lt;li&gt;mammalian/bacterial biotin-dependent carboxylation reactions. &lt;/li&gt;&#xA;&lt;li&gt;blood pH regulation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="14538" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-03-08T17:29:10.133" Title="Does the necessary Carbon Dioxide need to be in the atmosphere for mammals?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;physiology&gt;&lt;theoretical-biology&gt;&lt;respiration&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29730" PostTypeId="1" AcceptedAnswerId="29744" CreationDate="2015-02-20T09:14:50.743" Score="8" ViewCount="1704" Body="&lt;p&gt;What is called the &quot;area size that an animal usually lives in&quot; or &quot;needs for a normal life&quot;? Is there any specific term?&lt;/p&gt;&#xA;" OwnerUserId="14539" LastEditorUserId="3624" LastEditDate="2015-02-20T09:53:08.043" LastActivityDate="2016-12-26T07:01:55.360" Title="What is called the &quot;area size that an animal usually lives in&quot;?" Tags="&lt;zoology&gt;&lt;ecology&gt;&lt;population-biology&gt;&lt;nomenclature&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29731" PostTypeId="2" ParentId="29669" CreationDate="2015-02-20T09:17:29.340" Score="6" Body="&lt;p&gt;Artificial amniotic fluid has been used on goats, and for premature human babies.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;In the 1996 experiment, Thomas Shaffer, a scientist at Temple University, used an oxygenated liquid in a clinical trial with thirteen infants born at twenty-three to twenty-four weeks who were not expected to survive, and seven babies were discharged healthy. Jonathan Knight, An Out of Body Experience, 419 NATURE 106, 106-07 (2002); Partial Liquid Ventilation with Perflubron in Premature Infants with Severe Respiratory Distress Syndrome, 335 N. ENG. J. MED. 761, 761 (1996) &#xA;(documenting scientific results from Shaffer's experiment).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Also in 1996, Japanese professor Dr. Yoshinori Kuwabara of Juntendo University, successfully gestated goat embryos in a machine that holds amniotic fluid in tanks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dr. Helen Hung-Ching Liu, Director of the Reproductive Endocrine Laboratory at the Center for Reproductive Medicine and Infertility at Cornell University.  In 2003, her team was able to grow a mouse embryo, almost to full term, by adding engineered endometrium tissue to a bio-engineered, extra-uterine &quot;scaffold.&quot; Recently she grew a human embryo, for 10 days in an artificial womb. However, legislation imposes a 14-day limit on any research project of this nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if we do get a working artificial womb - we don't know how much we might be missing.  Something that appears to &lt;em&gt;work&lt;/em&gt;, may not be as good as the natural system.  And we will have some difficulty in testing it in non-animal applications.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm trying to find the laws, but I believe we're currently precluded from pursuing artificial wombs mostly because of legal measures, not particularly by engineering problems.  Also, allegedly, the US is one of the most &lt;strong&gt;un&lt;/strong&gt;-regulated first world nations for this type of research (while saying you can only research this for 14 days, smh).&lt;/p&gt;&#xA;" OwnerUserId="14538" LastEditorUserId="14538" LastEditDate="2015-02-20T10:31:31.950" LastActivityDate="2015-02-20T10:31:31.950" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29732" PostTypeId="2" ParentId="29730" CreationDate="2015-02-20T09:39:20.270" Score="9" Body="&lt;p&gt;Are you looking for '&lt;a href=&quot;http://en.wikipedia.org/wiki/Home_range&quot;&gt;Home range&lt;/a&gt;' (see also the definition in &lt;a href=&quot;http://global.britannica.com/EBchecked/topic/270112/home-range&quot;&gt;Encyclopaedia Britannica&lt;/a&gt;)? Generally, 'home range' is defined as the entire area an individual animal uses, while the '&lt;a href=&quot;http://en.wikipedia.org/wiki/Territory_%28animal%29&quot;&gt;territory&lt;/a&gt;' is the subset of the home range that is actually defended from conspecifics (in animals that show territoriality). 'Home range' is often delimited by the types of environments used and movement patterns of individuals.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-02-20T09:45:36.583" LastActivityDate="2015-02-20T09:45:36.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29734" PostTypeId="2" ParentId="29679" CreationDate="2015-02-20T10:16:37.620" Score="8" Body="&lt;p&gt;While action potentials are usually binary, you should note that &lt;a href=&quot;http://en.wikipedia.org/wiki/Synapse&quot;&gt;synaptic communication&lt;/a&gt; between neurons is generally not binary. Most synapses work by &lt;a href=&quot;http://en.wikipedia.org/wiki/Neurotransmitter&quot;&gt;neurotransmittors&lt;/a&gt;, and this is a chemically mediated &lt;a href=&quot;http://en.wikipedia.org/wiki/Postsynaptic_potential&quot;&gt;graded response&lt;/a&gt; that, for example, act on &lt;a href=&quot;http://en.wikipedia.org/wiki/Voltage-gated_ion_channel&quot;&gt;voltage-gated ion channels&lt;/a&gt;. So even though action potentials are often binary, communication between neurons are most often not, and action potential firing can involve the integration of synaptic information from many different neurons. Therefore, the brain as a whole cannot be reduced to a binary system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this as a complement to @Memmings answer.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="9943" LastEditDate="2015-02-20T13:10:45.940" LastActivityDate="2015-02-20T13:10:45.940" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29735" PostTypeId="1" CreationDate="2015-02-20T11:06:29.637" Score="4" ViewCount="337" Body="&lt;p&gt;I've been reading up a bit on the CRISPR-Cas9 system for gene manipulation. From what I read, it introduces double-strand breaks at specific points determined by the choice of sgRNA. But how do you get from double-strand breaks to editing genes in incredibly specific ways? As far as I read you can fix point mutations, insert whole genes or disable genes with CRISPR-Cas9. How do you specify which kind of repair mechanism is invoked?&lt;/p&gt;&#xA;" OwnerUserId="14541" LastEditorUserId="14541" LastEditDate="2015-02-20T15:20:12.030" LastActivityDate="2015-02-20T15:20:12.030" Title="How is the type of genetic manipulation determined in CRISPR-Cas9?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29736" PostTypeId="2" ParentId="29735" CreationDate="2015-02-20T11:30:02.223" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;But how do you get from double-strand breaks to editing genes in&#xA;  incredibly specific ways?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You should read the wikipedia page on CRISPR-Cas system. The target specificity is provided by the tracrRNA. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How do you specify which kind of repair mechanism is invoked?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The repair can be done either by Non Homologous End Joining (NHEJ) or Homologous Recombination (HR). If you provide excessive DNA template by transfection then it is likely to increase the chance of HR and this can be used for trangenesis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When no template is provided then DNA can be repaired by HR with sister chromatin or NHEJ. Depending on the stage of the cell cycle one of these mechanisms is preferred over the other. HR is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18769152&quot; rel=&quot;nofollow&quot;&gt;shown&lt;/a&gt; to be the most active in S-phase and starts declining in G2-phase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when you want to make transgenics or specific edits then co-transfect CRISPR-Cas with transgene DNA (with flanks homologous to target DNA sequence) or a homologous DNA with point mutation(s), preferably in cells at S-phase. It is possible to synchronize the cells using nocodazole or other molecules that arrest cell cycle.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-02-20T11:30:02.223" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="29737" PostTypeId="2" ParentId="21594" CreationDate="2015-02-20T11:55:45.510" Score="-1" Body="&lt;p&gt;Some people burn more calories than others, in the default mode.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just sitting in a chair, I warm the seat much more than some other members of my family.  That heat has to come from somewhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's a different metabolism.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, that's not something you can order and install.  It's not a pill.  Your doctor is &lt;strong&gt;right&lt;/strong&gt; to focus on what you &lt;em&gt;can&lt;/em&gt; control, and that's intake - along with your activity level; or outgo.  (But most people are unwilling to actually do the work to change their activity level to a higher one, which is why doctors don't even try anymore - patients just lie, and then doctors have to try to catch them at it, and nobody's got time for that).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you eat may also impact the number of calories that stick.  Not everything you eat gets digested, some passes through.  And digestion itself burns calories.  Things that are harder to digest take more energy, and leave less surplus behind.&#xA;Easy things are... easier to digest and get all the calories from.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, thinner people lose weight easier.  Not fair, right?  That's life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It &lt;em&gt;may&lt;/em&gt; have something to do with your microfauna, but that's not well studied.  And, we're not even sure if you can permanently change those populations.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mayoclinic.org/healthy-living/weight-loss/in-depth/metabolism/art-20046508&quot; rel=&quot;nofollow&quot;&gt;http://www.mayoclinic.org/healthy-living/weight-loss/in-depth/metabolism/art-20046508&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The warming of the seat is anecdotal speculation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So you're arguing that heat happens magically, and doesn't require caloric input? Do tell us more, I can't wait to hear about it.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;And why should thinner people loose weight easier? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If I had a handy cite, I'd give it to you.  Yeah, yeah, Abraham Lincoln said don't believe everything you read on the internutz&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;You say &quot;Not well studied&quot; - It is important to cite some material that is studied in your answer. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nytimes.com/2013/09/06/health/gut-bacteria-from-thin-humans-can-slim-mice-down.html?pagewanted=1&amp;amp;nl=todaysheadlines&amp;amp;emc=edit_th_20130906&amp;amp;_r=2&amp;amp;pagewanted=all&amp;amp;&quot; rel=&quot;nofollow&quot;&gt;http://www.nytimes.com/2013/09/06/health/gut-bacteria-from-thin-humans-can-slim-mice-down.html?pagewanted=1&amp;amp;nl=todaysheadlines&amp;amp;emc=edit_th_20130906&amp;amp;_r=2&amp;amp;pagewanted=all&amp;amp;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;And what are 'those populations'?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Populations of microfauna&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is more of a comment as it stands. Earn 9 more reputation and you can comment anywhere.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thanks for the upvote, to help me comment - oh wait.&lt;/p&gt;&#xA;" OwnerUserId="14538" LastEditorUserId="14538" LastEditDate="2015-02-20T23:09:22.567" LastActivityDate="2015-02-20T23:09:22.567" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29739" PostTypeId="2" ParentId="29725" CreationDate="2015-02-20T14:56:07.987" Score="4" Body="&lt;p&gt;I cannot say anything about the general case, or specifically for day-neutral plants. However, &lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038975&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Sforza et al. 2012. Adjusted Light and Dark Cycles Can Optimize Photosynthetic Efficiency in Algae Growing in Photobioreactors. *Plos One*&quot;&gt;Sforza et al. (2012)&lt;/a&gt; have studied the effects of light conditions on algae (used for biofuel production), and their results indicate several problems with continuous light. In continuous light conditions they find lower chlorophyll contents and higher carotenoid concentrations in cells, which leads to lower photosynthetic efficiency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/df7Dy.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;This figure shows chlorophyll contents (black) and chlorophyll/carotenoid ratio (red) under different conditions, with the two treatments to the left representing continuous light. (&lt;em&gt;graph from Plos One&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Results show that Nannochloropsis can efficiently exploit even very intense light, provided that dark cycles occur to allow for re-oxidation of the electron transporters of the photosynthetic apparatus. If alternation of light and dark is not optimal, algae undergo radiation damage and photosynthetic productivity is greatly reduced.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, they also experiment with pulsed light, which in some cases lead to even lower rates of photosynthesis:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;However, similar experiments, at different frequencies, also showed that alternating dark and light may be detrimental, as demonstrated by the growth inhibition observed in the 1200-1 and −5 Hz curves. These cells showed a decrease in Fv/Fm values similar to that observed under constant strong light, indicating that the inhibition of growth was due to photoinhibition.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They also find that light pulses can be very short, and still allow for the photosystem to reset:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The optimal duration of light pulses was found to be around 10 ms, which is consistent with the suggested PSII turnover rate in whole cells [4], [46]. Accordingly, after photon absorption by the photosystem, 1–15 ms are needed to reset the system, before it is ready to receive another photon [22]. If the illumination is this short, most photons are exploited for photosynthesis and do not lead to the formation of ROS which then causes photoinhibition. These results indicate that even strong light does not cause damage if it only lasts a short time. Conversely, longer exposure allows the generation of ROS and damage and, in this case, the abrupt changes in illumination undergone by the cells are as harmful to the photosynthetic apparatus as constant high light.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Different species of plants can have mechanisms to handle light stress in different ways, so the effects on different species and types of plants are likely to differ. However, their results should generalize to some extent/for some plant species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may also find &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs00425-013-1915-z&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Li et al. 2013. Light and abiotic stresses regulate the expression of GDP-l-galactose phosphorylase and levels of ascorbic acid in two kiwifruit genotypes via light-responsive and stress-inducible cis-elements in their promoters. *Planta* 238&quot;&gt;this&lt;/a&gt; paper by Li et al. (2013) interesting. &lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2015-02-20T14:56:07.987" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="29741" PostTypeId="2" ParentId="29729" CreationDate="2015-02-20T14:57:25.790" Score="4" Body="&lt;p&gt;No it isn't necessary to breathe in CO2 from the atmosphere. For the buffer system your brain detects the amount of CO2 (H+ which is an indicator of excess or too little CO2) and adjusts your breathing automatically to compensate so that your blood's pH stays normal. No outside CO2 is needed. Your kidneys also play a similar role but the lungs are what provide a rapid response.&lt;/p&gt;&#xA;" OwnerUserId="14544" LastActivityDate="2015-02-20T14:57:25.790" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29742" PostTypeId="2" ParentId="29643" CreationDate="2015-02-20T15:31:06.540" Score="8" Body="&lt;p&gt;Arterial Baroreceptors felling the pressure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0uHE8.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Arterial blood pressure is normally regulated within a narrow range, with a mean arterial pressure typically ranging from 85 to 100 mmHg in adults. &lt;strong&gt;It is important to tightly control this pressure to ensure adequate blood flow to organs throughout the body&lt;/strong&gt;. This is accomplished by negative feedback systems incorporating pressure sensors (i.e., baroreceptors) that sense the arterial pressure. The most important arterial baroreceptors are located in the carotid sinus (at the bifurcation of external and internal carotids) and in the aortic arch (Figure 1). These receptors respond to stretching of the arterial wall so that if arterial pressure suddenly rises, the walls of these vessels passively expand, which increases the firing frequency of receptor action potentials. If arterial blood pressure suddenly falls, decreased stretch of the arterial walls leads to a decrease in receptor firing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The carotid sinus baroreceptors are innervated by the sinus nerve of Hering, which is a branch of the glossopharyngeal nerve (IX cranial nerve). The glossopharyngeal nerve synapses in the nucleus tractus solitarius (NTS) located in the medulla of the brainstem. The aortic arch baroreceptors are innervated by the aortic nerve, which then combines with the vagus nerve (X cranial nerve) traveling to the NTS. The NTS modulates the activity of sympathetic and parasympathetic (vagal) neurons in the medulla, which in turn regulate the autonomic control of the heart and blood vessels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Pp9V6.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of these two sites for arterial baroreceptors, the carotid sinus is quantitatively the most important for regulating arterial pressure. The carotid sinus receptors respond to pressures ranging from 60-180 mmHg (Figure 2). Receptors within the aortic arch have a higher threshold pressure and are less sensitive than the carotid sinus receptors. Maximal carotid sinus sensitivity occurs near the normal mean arterial pressure; therefore, very small changes in arterial pressure around this &quot;set point&quot; dramatically alters receptor firing so that autonomic control can be reset in such a way that the arterial pressure remains very near to the set point. This set point changes during exercise, hypertension, and heart failure. The changing set point (response curve shifts to right) explains how arterial pressure can remain elevated during chronic hypertension.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Baroreceptors are sensitive to the rate of pressure change as well as to the steady or mean pressure. Therefore, at a given mean arterial pressure, decreasing the pulse pressure (systolic minus diastolic pressure) decreases the baroreceptor firing rate. This is important during conditions such as hemorrhagic shock in which pulse pressure as well as mean pressure decreases. The combination of reduced mean pressure and reduced pulse pressure amplifies the baroreceptor response. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1Kza8.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although the baroreceptors can respond to either an increase or decrease in systemic arterial pressure, their most important role is responding to sudden reductions in arterial pressure (Figure 3). This can occur, for example, when a person suddenly stands up or following blood loss (hemorrhage). A decrease in arterial pressure (mean, pulse or both) results in decreased baroreceptor firing. Autonomic neurons within the medulla respond by increasing sympathetic outflow and decreasing parasympathetic (vagal) outflow. Under normal physiological conditions, baroreceptor firing exerts a tonic inhibitory influence on sympathetic outflow from the medulla. Therefore, acute hypotension results in a disinhibition of sympathetic activity within the medulla, so that sympathetic activity originating within the rostral ventrolateral medulla increases. These autonomic changes cause vasoconstriction (increased systemic vascular resistance, SVR), tachycardia and positive inotropy. The latter two changes increase cardiac output. Increases in cardiac output and SVR lead to a partial restoration of arterial pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;It is important to note that baroreceptors adapt to sustained changes in arterial pressure. For example, if arterial pressure suddenly falls when a person stands, the baroreceptor firing rate will decrease; however, after a period of time, the firing returns to near normal levels as the receptors adapt to the lower pressure. Therefore, the long-term regulation of arterial pressure requires activation of other mechanisms (primarily hormonal and renal) to maintain normal blood pressure.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This information from &lt;strong&gt;PhD Richard E. Klabunde&lt;/strong&gt; lecture, that based on his book &lt;strong&gt;&lt;em&gt;Cardiovascular Physiology Concepts&lt;/em&gt;&lt;/strong&gt; (chapter 5, pages 93-123)&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="10104" LastEditDate="2015-02-20T20:37:32.193" LastActivityDate="2015-02-20T20:37:32.193" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29743" PostTypeId="2" ParentId="28350" CreationDate="2015-02-20T15:44:30.637" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.cbs.dtu.dk/services/TMHMM/&quot; rel=&quot;nofollow&quot;&gt;TMHMM&lt;/a&gt; is a very good standard on predicting the TMHs in the first place, so it stands to reason that predicting homologues using this approach is completely viable.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastActivityDate="2015-02-20T15:44:30.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29744" PostTypeId="2" ParentId="29730" CreationDate="2015-02-20T16:43:06.883" Score="5" Body="&lt;p&gt;To avoid confusion I just want to add to fileunderwater's answer the equivalent words we use to describe the &quot;area size a population/species lives in&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The spatial range a single individual occupies is generally called &lt;code&gt;home range&lt;/code&gt; or &lt;code&gt;territory&lt;/code&gt; (as fileunderwater said before me).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The spatial range a single species (or population) occupies is called &lt;code&gt;geographic range&lt;/code&gt; or &lt;code&gt;species range&lt;/code&gt; and we call the boundaries of this range the &lt;code&gt;geographic range limits&lt;/code&gt; or sometimes called &lt;code&gt;range limits&lt;/code&gt; only.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-02-20T16:56:33.127" LastActivityDate="2015-02-20T16:56:33.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29745" PostTypeId="2" ParentId="29720" CreationDate="2015-02-20T16:55:02.597" Score="2" Body="&lt;p&gt;Copied from my comment:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It just means a sound that starts at a low frequency and goes up to a higher frequency like a whistle sound. Perhaps someone can give you an example sound file and/or a spectrogram representation of it.&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2015-02-20T16:55:02.597" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29748" PostTypeId="2" ParentId="24371" CreationDate="2015-02-20T20:04:00.527" Score="3" Body="&lt;p&gt;&lt;em&gt;Preamble.&lt;/em&gt; There is a lot of misunderstood science here and you are more than right for questioning the lecturers interpretation of these energy values; something the other answers do not discuss. The problem arises from a &lt;strong&gt;dodgy reference&lt;/strong&gt; and &lt;strong&gt;a lot of conjecture&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;h3&gt;In summary.&lt;/h3&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Light and sound cannot be compared energetically in a biological context.&lt;/li&gt;&#xA;&lt;li&gt;Our ears probably don't hear lower energies than our eyes see to avoid prey.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;h3&gt;Let us ignore the reference...&lt;/h3&gt;&#xA;&lt;p&gt;The reference is from &lt;a href=&quot;http://de.wikipedia.org/wiki/Bundesamt_f%C3%BCr_Wehrtechnik_und_Beschaffung&quot; rel=&quot;nofollow noreferrer&quot;&gt;BWB&lt;/a&gt; which is as far as I can tell a non peer reviewed federal technical publisher and that this is a textbook about ergonomics. But given &lt;strong&gt;its obscurity, it having never undergone peer review, it being not biologically scientific,&lt;/strong&gt; it is safe to ignore from the context of a scientific biological topic. The fact it is in German doesn't help either.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;If anyone can provide an open link to this reference or correct me on this I would be grateful. Google scholar turned up no hits other than a citation.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;Let us give your lecturer the benefit of the doubt. This answer &lt;em&gt;assumes&lt;/em&gt; that there are derived energy values for sight and sound as your lecturer suggested and that eyes sense higher energy than ears.&lt;/p&gt;&#xA;&lt;h2&gt;Is hearing omnidirectional to detect predation?&lt;/h2&gt;&#xA;&lt;p&gt;&lt;em&gt;I'm going to use the term&lt;/em&gt; &lt;em&gt;&lt;strong&gt;sensory setup&lt;/strong&gt;&lt;/em&gt; &lt;em&gt;to describe that our senses use fixed ears that hear omnidirectionally and forward facing directional eyes.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;... hearing is much more important for this reason [omnidirectional] to detect predators, even if they are silent.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Let's flesh out this hypothesis so that it makes sense in practical terms.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;A small movement is made by the predator. This generates some sound and some change in light. In the case of forward sighted animals, the sound is much more difficult to detect than the light would be as it contains less energy. The ears must compensate by detecting lower energy signals than the eyes would need to in order to detect the predator.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Before we question the physics, this biological hypothesis is very tough to swallow. Without citation I would say it is unreasonable conjecture.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;Examples that contradict this hypothesis:&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Gorillas&lt;/strong&gt; have no natural predators or prey but have a very similar sensory setup to ours that helps social bonds.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Meerkats&lt;/strong&gt; on the other hand rely on sentries that broadcast a series of bleats after spotting prey by sight. Other meerkats immediately hide when hearing this signal (interestingly, this call is mimicked by &lt;a href=&quot;http://news.bbc.co.uk/earth/hi/earth_news/newsid_9149000/9149950.stm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Drongos&lt;/a&gt; who steal the meerkat food that is abandoned in the panic) before checking if a predator is present. Meerkats have a similar sensory setup to ours.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There are other megafauna like &lt;strong&gt;deer&lt;/strong&gt; that are prey for the big predators; predators that would have put ancestral humans on the menu. Deer-like prey animals rely heavily on near-omnidirectional eyesight and can angle their ears to focus on an area to hear stealthy predators. This is the &amp;quot;opposite&amp;quot; sensory setup that has the same conclusion of predator evasion.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Even those non-exhaustive examples makes the hypothesis &lt;strong&gt;questionable at best&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;...there is a range in which &amp;quot;interesting&amp;quot; signals occur. If the interesting signals have lower energy for sound than for visual signals the ear adapted to this range.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This answer too is based on pure conjecture it seems, however &lt;strong&gt;it more aligns with how biology might work&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;p&gt;It is sensible to say evolution selected for animals that could detect noises and lights that, if reacted to, saved the organisms life to continue propagating. This hypothesis bypasses the idea that sound and light are comparable energetic signals too, which is good (discussed below).&lt;/p&gt;&#xA;&lt;p&gt;This hypothesis also allows for various morphologies to have evolved depending on what an &amp;quot;interesting signal&amp;quot; is to that species.&lt;/p&gt;&#xA;&lt;h2&gt;Light vs Sound.&lt;/h2&gt;&#xA;&lt;p&gt;&lt;em&gt;These aren't the same thing.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;The elephant in the room of this question is that &lt;strong&gt;light and sound are non-comparable&lt;/strong&gt; energies. This is due to &lt;strong&gt;source, speed, distance, medium, mechanisms for receiving the energy&lt;/strong&gt; (eyes and ears) and most significantly in a biological context &lt;strong&gt;neural interpretation&lt;/strong&gt;. These values are so &lt;strong&gt;abstract&lt;/strong&gt; that even if an energy value is calculated, it is &lt;strong&gt;not in anyway quantitatively comparable in biological organisms&lt;/strong&gt;. For example a really loud subsonic whale call is not the same as a small change of grass parted by a wolf as it sneaks up on you. One is absolutely essential for survival, the other is undetectable. Both could theoretically have the same &amp;quot;energy&amp;quot;.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Note&lt;/em&gt; Frequencies are the biologically important part of the &amp;quot;energy&amp;quot; but must be considered as two different methods of acquiring sensory information. &lt;em&gt;The difference between a chimp mating call and a territorial threat are very similar but for their frequency, and eating the delicious red berries compared to the toxic blue berries is also down to the frequency reflected from them!&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;There is little to no biological literature that uses energy values as sensory input. This would just &lt;strong&gt;obscure the actual important physical aspects of the sensory input values&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;em&gt;I hope that helped clear things up and accurately discussed your dis-satisfaction with your lecturers' hypothesis despite being months too late!&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-03T17:21:06.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29749" PostTypeId="1" AcceptedAnswerId="29753" CreationDate="2015-02-20T20:53:49.690" Score="7" ViewCount="369" Body="&lt;p&gt;I am interested in learning about GMO. The topic is so wrapped in controversy, that it's hard to find a good book that introduces the basic concepts involved. I went through various university websites, but couldn't find any lecture notes on the topic. I don't know, is it too broad a topic? Is there even a book called Introduction to GMO? Maybe that's the problem. &#xA;I am interested in a book that tells you about how gene manipulation is done. How do biology students get introduced to this concept? I hope the question is not too general.&lt;/p&gt;&#xA;" OwnerUserId="14549" LastActivityDate="2015-02-21T08:28:28.397" Title="A good textbook on GMO" Tags="&lt;genetics&gt;&lt;book-recommendation&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29751" PostTypeId="1" AcceptedAnswerId="29752" CreationDate="2015-02-20T21:14:05.650" Score="3" ViewCount="260" Body="&lt;p&gt;We did an experiment were we have e coli with a plasmid with a gene from another bacteria in it, and we put in IPTG in for induction. Will after looking up more about IPTG online I see it's related to the lac operator, which from what I've found just deals with lactose. Is there some other function that has? How can this be related to or effect the thing we put in and what we're doing? I'm missing the connection here.&lt;/p&gt;&#xA;" OwnerUserId="13064" LastActivityDate="2015-02-20T21:41:52.410" Title="IPTG and lac operator with e coli for foreign gene question" Tags="&lt;proteins&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29752" PostTypeId="2" ParentId="29751" CreationDate="2015-02-20T21:41:52.410" Score="1" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Lac_operon&quot; rel=&quot;nofollow&quot;&gt;lac operon&lt;/a&gt; contains genes which are important for the metabolization of lactose as an energy source - normally glucose is used for this purpose. Usually the operon is tighly regulated and as long as there is another source of energy it is kept in an inhibited state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The presence of lactose removes the lac repressor from the lac operon and allows the expression of the genes and thus allowing the metabolization of lactose. The mechanism can be turned on and off depending on the presence of lactose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Isopropyl_%CE%B2-D-1-thiogalactopyranoside&quot; rel=&quot;nofollow&quot;&gt;IPTG&lt;/a&gt; is a substance which mimicks the presence of allolactose (a metabolite of lactose) and it can activate transcription from the lac operon. As IPTG (in contrast to allolactose) cannot be hydrolyzed by β-galactosidase, it's concentration in the cell stays the same. Using the lac operon and IPTG enables you to switch on the expression of the gene on your plasmid and to start the overexpression.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-02-20T21:41:52.410" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="29753" PostTypeId="2" ParentId="29749" CreationDate="2015-02-20T21:47:15.497" Score="4" Body="&lt;p&gt;I too had difficulty finding any textbooks or notes that focused solely on genetic engineering. However, after some rather intense looking, I did come across several textbooks that may be helpful. I wasn't sure how basic of a text you were looking for but I'm hoping college level is okay because that is all I have been able to find.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first book was &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0521615216&quot; rel=&quot;nofollow&quot;&gt;An Introduction to Genetic Engineering&lt;/a&gt; by Dr. Desmond S.T. Nicholl. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another was &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1405135441&quot; rel=&quot;nofollow&quot;&gt;Principals of Gene Manipulation and Genomics&lt;/a&gt; by Sandy B. Primrose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you need a more basic biology text for reference, I would recommend &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/013368718X&quot; rel=&quot;nofollow&quot;&gt;Miller &amp;amp; Levine Biology&lt;/a&gt; by Prentice Hall (&lt;a href=&quot;http://www.pearsoned.com/&quot; rel=&quot;nofollow&quot;&gt;Pearson Prentice Hall&lt;/a&gt;). Also, you could do a quick-study on genetics on &lt;a href=&quot;https://www.khanacademy.org/science/biology/crash-course-bio-ecology&quot; rel=&quot;nofollow&quot;&gt;Khan Academy - Crash Course: Biology and Ecology&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this information was helpful for you! &lt;/p&gt;&#xA;" OwnerUserId="6289" LastActivityDate="2015-02-20T21:47:15.497" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29754" PostTypeId="1" AcceptedAnswerId="29757" CreationDate="2015-02-20T21:57:54.190" Score="3" ViewCount="29016" Body="&lt;p&gt;I wasn't sure whether to ask this question on Biology or Chemistry Stack Exchange, since it is really biochemisty, but this is something that's been puzzling me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most pharmacists (all that I've encountered) tell you that antibiotics decrease the effectiveness of birth control. There are side-effect warnings on all Penicillin based antibiotics that say they decrease the effectiveness of birth control, and advise you to use a back-up method when taking antibiotics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, most health organization websites (Planned Parenthood, Mayo Clinic, NHS) explicitly state that ONLY two antibiotics have been shown to sometimes decrease the effectiveness of birth control-- Rifampicin and Rifabutin. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;NHS Website: &lt;a href=&quot;http://www.nhs.uk/conditions/contraception-guide/pages/antibiotics-contraception.aspx&quot; rel=&quot;nofollow&quot;&gt;http://www.nhs.uk/conditions/contraception-guide/pages/antibiotics-contraception.aspx&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Yet websites of Pharmacies like Walgreens or CVS say that to a lesser extent Penicillin based antibiotics can decrease birth control effectiveness, or in general remain vague about antibiotics affecting birth control :&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.walgreens.com/topic/faq/questionandanswer.jsp?questionTierId=600006&amp;amp;faqId=600022&quot; rel=&quot;nofollow&quot;&gt;http://www.walgreens.com/topic/faq/questionandanswer.jsp?questionTierId=600006&amp;amp;faqId=600022&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So--do Penicillin based antibiotics affect birth control?&lt;/p&gt;&#xA;" OwnerUserId="14550" LastActivityDate="2015-02-20T23:51:40.363" Title="Do Penicillin based antibiotics affect birth control?" Tags="&lt;pharmacology&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29757" PostTypeId="2" ParentId="29754" CreationDate="2015-02-20T23:51:40.363" Score="3" Body="&lt;p&gt;Evidence on the association between antibiotic use and combination oral contraceptive (COC) failure remains controversial, with recent studies reporting no evidence to support decreased effectiveness of birth control with the use of antibiotics except rifampin and rifabutin.&lt;/p&gt;&#xA;&lt;p&gt;The reasoning is antibiotics might interfere with the effectiveness of COCs by decreasing steroid hormone’s plasma concentrations by hepatic microsomal enzyme induction or inhibition, interference with enterohepatic circulation of&#xA;COC metabolites, interference with absorption from the GI tract, competition between two drugs for the same metabolizing enzyme, alterations in plasma protein binding, induction of an opposite physiologic effect, or increased urinary or fecal excretion of the contraceptive.&lt;/p&gt;&#xA;&lt;p&gt;As you stated, the strongest evidence is for rifabutin and rifampin: a significant decrease in the hormonal levels was noted in women taking rifampin even after &lt;em&gt;a single dose.&lt;/em&gt;  Dirithromycin slightly decreased plasma ethinyl estradiol levels, with questionable clinical importance. A recent study in the Netherlands &lt;em&gt;did&lt;/em&gt; find a relationship between the use of antibiotics and breakthrough pregnancy in a population-based &lt;em&gt;prescription&lt;/em&gt; database; also, individual patients do show large decreases in the plasma concentrations of ethinyl estradiol when they take certain antibiotics, notably tetracycline and penicillin derivatives.&lt;/p&gt;&#xA;&lt;p&gt;Because of earlier studies, anecdotal reports, and the above (it's not possible to identify whose levels will drop with antibiotic use), a cautious approach is advised. Physicians and pharmacists (80-90% of both) still lean towards believing that broad-spectrum antibiotics decrease the effectiveness of COCs, and continue to advise the use of back-up contraception.&lt;/p&gt;&#xA;&lt;p&gt;The tide is shifting, however, as new studies come out. Here are a few excerpts of recent studies:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Available scientific and pharmacokinetic data do not support the hypothesis that antibiotics (with the exception of rifampin) lower the contraceptive efficacy of oral contraceptives. (J Am Acad Dermatol 2002;46:917-23.)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Since dermatologists treat acne with antibiotics, and a significant percentage of these patients are young women of child-bearing age, they certainly have a vested interest in knowing if this is true.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Rifampicin and griseofulvin induce hepatic enzymes and do appear to have a genuine interaction with the COCP, leading to reduced efficacy. The situation with the broad-spectrum antibiotics is less clear. There are relatively few prospective studies of the pharmacokinetics of concurrent COCP and antibiotic use and few, if any, demonstrate a convincing basis for any reduced contraceptive efficacy.&lt;/p&gt;&#xA;&lt;p&gt;We did not find an association between concomitant antibiotic use and the risk of breakthrough pregnancy among COC users. However, due to limited power and potential carryover effects, findings from this study cannot rule out an elevated risk of COC failure among antibiotic users. (2011)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So, the answer is (except with your noted exceptions) the penicillin-class antibiotics &lt;em&gt;probably do not interfere with effectiveness of COCs.&lt;/em&gt; However, one unwanted pregnancy is one pregnancy too many, and the use of a back-up method is not a huge deal (just ~14 days).&lt;/p&gt;&#xA;&lt;p&gt;Until more and larger studies demonstrate a lack of interaction between most antibiotics and COCs, this will likely be the advice people continue to receive. When you look at the risk to benefit ratio of back-up, it's probably the wisest course for people prescribed a short course of antibiotics. It is more significantly problematic for people prescribed continuous antibiotic use for acne, Crohn's and other conditions/illnesses.&lt;/p&gt;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0190962202000373&quot; rel=&quot;nofollow noreferrer&quot;&gt;Oral contraceptive efficacy and antibiotic interaction: A myth debunked&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0010782499000098&quot; rel=&quot;nofollow noreferrer&quot;&gt;Interaction between broad-spectrum antibiotics and the combined oral contraceptive pill: A literature review&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0010782410005172&quot; rel=&quot;nofollow noreferrer&quot;&gt;Antibiotics and oral contraceptive failure — a case-crossover study&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/pds.3267/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Are antibiotics related to oral combination contraceptive failures in the Netherlands? A case-crossover study&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11704183/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Drug interactions between oral contraceptives and antibiotics.&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25143790&quot; rel=&quot;nofollow noreferrer&quot;&gt;Survey of pharmacists and physicians on drug interactions between combined oral contraceptives and broad-spectrum antibiotics.&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-20T23:51:40.363" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29758" PostTypeId="2" ParentId="29711" CreationDate="2015-02-20T23:51:56.057" Score="0" Body="&lt;p&gt;It is correct that imaging-based studies are super-awesome, but question seems to be about chemical. I don't know if there are antibodies available for histamine, if yes, then you can fix and label all sites of histamine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But imaging through fish tissues (say, more than 1 mm) is close to impossible with molecular resolution and sensitivity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My best guess would be following. If you are OK with blood level measurements, then try spectroscopic approach. That is measure Raman NIR scattering or fluorescence/absorption in UV-visible regions of light spectrum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fun option is to develop chemical-reaction based assay. Say, engineer reaction that will modify histamine using radioactive-labeled compound and then measure how fast/slow amount of the compound decreases&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-02-20T23:51:56.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29759" PostTypeId="1" AcceptedAnswerId="36761" CreationDate="2015-02-21T00:25:12.810" Score="8" ViewCount="4154" Body="&lt;p&gt;I've been reading a bit about the different layers of the cerebral cortex and its clear that certainly not &lt;em&gt;every&lt;/em&gt; region of the cortex has the same number of layers. Thus, the idea that every region has six-layers is clearly false.  And I think this fact is definitely well known. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do neuroscientists still view the six-layer model as an accurate model? If so, what aspects of it have changed over time that now incorporate the fact not every region has six layers? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Aside:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me clarify my question. If not every region has 6 layers, why don't we just say there is a layered cortex and not specify a number? But if we decide to do this, what distinguishes the mammalian &quot;6-layered&quot; cortex from non-mammalian species that have a so-called &quot;3-layer&quot; cortex &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102215/&quot; rel=&quot;nofollow&quot;&gt;The Microcircuit Concept Applied to Cortical Evolution: from Three-Layer to Six-Layer Cortex&lt;/a&gt; by Gordon Shepard for more. &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="11652" LastEditDate="2015-08-07T18:46:56.713" LastActivityDate="2015-08-24T13:38:49.967" Title="Is the six-layer cortex model of the mammalian cortex still the most accepted model?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29760" PostTypeId="2" ParentId="29668" CreationDate="2015-02-21T00:43:07.023" Score="3" Body="&lt;p&gt;The answer is no, and it is because sequence of the genome is not all information that is required for gene expression and development, there are also epigenetic factors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lot of patterns of epigenetic marks, such as most of DNA methylation and some histone modification patterns, are set during parental germline development, and these marks are transmitted to the zygote by gamets (except paternal histones, those are not transmitted because they are temporarily substituted for protamines in sperm for greater compaction). Therefore, the naked DNA inserted into zygotic nucleus will not have access to the machinery that established epigenome during development of the gametes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And even though nucleosomes may assemble in the zygote on the naked DNA and histones may acquire post-translational modifications, and cytosines may get methylated, but most definitely the zygote is going to have no means to correctly set distinct patterns of epigenetic marks at alleles that are normally imprinted, i.e. those alleles whose epigenetic state depends on the gender of the organism that produced the gamete.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, the twin created in this way will have the same DNA sequence, but it will be a  subject to &lt;a href=&quot;http://en.wikipedia.org/wiki/Genomic_imprinting#Disorders_associated_with_imprinting&quot; rel=&quot;nofollow&quot;&gt;disorders associated with imprinting&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="13239" LastActivityDate="2015-02-21T00:43:07.023" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29761" PostTypeId="2" ParentId="29668" CreationDate="2015-02-21T01:21:36.510" Score="0" Body="&lt;p&gt;DNA duplication (imagine, we PCR it) will net be enough. First of all, you also will have to duplicate and pack mitochondrial DNA into the cell. next, as been mentioned, epigenetic modification (methylation) and histone packing are crucial for proper development.&#xA;And these markers should essentially replicate state of the host cell.&#xA;My best guess is that all-synthetic replication atomic-resolution of zygote will be enough, but not just bare DNA code (750MB of information)&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-02-21T01:21:36.510" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29763" PostTypeId="1" CreationDate="2015-02-21T02:49:01.883" Score="1" ViewCount="114" Body="&lt;p&gt;I have constructed a PWM and want to test its accuracy. Scanning an entire chromosome (chr3, hg18) yields very high false positives (magnitudes higher than the true positives). Scanning the entire genome is much worse. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From some literature and biostars posts, its recommended that I only scan sections of the genome to get an understanding of the accuracy of my PWM. Some posts talked about just scanning the promoter regions with my PWM (or say, a 1000bp neighbourhood around the promoter region). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, &lt;em&gt;is there a database or some sort of annotation that tells me where the promoter regions are?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a feeling that this question may not be well formed because to get &quot;promoter&quot; regions, I need to be talking about genes. Since I am only working with the MEF2 family of transcription factors, is there a way to retrieve promoter regions in which these transcription factors bind?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My idea:&lt;/strong&gt; Since the TF binds upstream of the gene, usually in a promoter region, AND I know the true binding sites, would it be sufficient to just extract a 2000bp neighbourhood around the binding site? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is what my data (only the first couple of lines) looks like:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt;chr1:6585537-6585547(-)&#xA;------ctatttatag-------&#xA;&amp;gt;chr1:228916512-228916522(+)&#xA;------ctatttatag-------&#xA;&amp;gt;chr12:50731227-50731237(+)&#xA;------ctatttatag-------&#xA;&amp;gt;chr13:49597702-49597712(+)&#xA;------ctatttatag-------&#xA;&amp;gt;chr14:103058980-103058990(+)&#xA;------ctatttatag-------&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So again, is it sufficient to take &lt;code&gt;chr1:6585537-6585547(-)&lt;/code&gt;, extract a 2000bp neighbourhood around it, and scan this neighbourhood with my PWM. Clearly, I know there is one true binding site and I'll compare it with the number of false postives it gives me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;edit: Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have information (coordinates) for a total of 1875 binding sites. From these, only about 140 coordinates to binding sites on chromosome 3. These are my &quot;true binding sites&quot;. If I scan chromosome 3 with my PWM, it gets around 85,000 hits.. ie, 85000 sequences that have scored very high that could be potential binding sites. They are, for all intents and purposes, false positives unless they fall (or overlap) the true binding site. Out of 85000 hits, only a very overlap the true binding region.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, literature recommends that instead of scanning an entire chromosome (or the entire genome), its better just to scan promoter regions. I guess there is confusion here, because the question can be &quot;promoter regions for what gene?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I guess we have bonafide promoter regions if we take say 1000bp neighbourhoods about our true binding sites.&lt;/p&gt;&#xA;" OwnerUserId="6416" LastEditorUserId="6416" LastEditDate="2015-02-22T01:45:24.113" LastActivityDate="2015-02-22T01:45:24.113" Title="how to extract promoter regions given a TF binding site" Tags="&lt;bioinformatics&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29764" PostTypeId="1" AcceptedAnswerId="29768" CreationDate="2015-02-21T02:50:58.433" Score="3" ViewCount="4578" Body="&lt;p&gt;Why did Eukaryotes evolve to have linear DNA and not circular like Prokaryotes? What are the pros and/or cons?&lt;/p&gt;&#xA;" OwnerUserId="14551" LastActivityDate="2015-02-21T09:25:50.697" Title="Pros/cons: linear vs. circular DNA" Tags="&lt;evolution&gt;&lt;dna&gt;&lt;eukaryotic-cells&gt;&lt;prokaryotes&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2015-02-21T17:59:52.470" ContentLicense="CC BY-SA 3.0" />
  <row Id="29765" PostTypeId="1" AcceptedAnswerId="29771" CreationDate="2015-02-21T03:00:04.873" Score="3" ViewCount="50" Body="&lt;p&gt;This is a hypothetical question&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would happen if the DNA of a prokaryote was replaced with the one of a prokaryote of another species, would the cell structures change and adapt to the new DNA and would the cell survive? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Would the result be similar if we did the same with two eukaryotic zygotes of different species?)&lt;/p&gt;&#xA;" OwnerUserId="14551" LastActivityDate="2015-02-21T11:19:42.540" Title="DNA replacement: new species" Tags="&lt;dna&gt;&lt;animal-models&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29766" PostTypeId="1" CreationDate="2015-02-21T03:19:15.753" Score="2" ViewCount="1366" Body="&lt;p&gt;When performing genetic knockouts in yeast using homologous recombination to replace a target gene sequence via a vector DNA, does the region between the flanking regions in the vector have to be the same length as the site of recombination in the host cell's gene?&lt;/p&gt;&#xA;" OwnerUserId="14551" LastEditorUserId="3340" LastEditDate="2015-02-26T08:27:06.507" LastActivityDate="2015-02-26T11:10:03.450" Title="How does the size of insert affects the rate of Homologous Recombination in yeast?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;molecular-genetics&gt;&lt;dna-isolation&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29768" PostTypeId="2" ParentId="29764" CreationDate="2015-02-21T07:30:34.790" Score="6" Body="&lt;p&gt;This question has been asked before: &lt;a href=&quot;https://biology.stackexchange.com/questions/3455/is-there-an-advantage-to-linear-chromosomes&quot;&gt;Is there an advantage to linear chromosomes?&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, I should state that the generalisation that ALL prokaryotes have circular genomes is incorrect. A growing number of prokaryotes have been discovered which have linear chromosomes, such as &lt;em&gt;Borrelia burgdorferi&lt;/em&gt; ,which causes Lyme disease, members of the &lt;em&gt;Streptomyces&lt;/em&gt; family and &lt;em&gt;Agrobacterium tumafaciens&lt;/em&gt;, which has both a circular and a linear chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, on to the question being asked: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally, my feeling is that large circular chromosomes would have much greater supercoiling and related torsional problems, making it difficult to unwind them for transcription, replication or repair. This limitation on physical size limits the amount of genetic information that can be carried in a single chromosome, thereby limiting complexity of the organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could increase the number of circular chromosomes to compensate for their lack of size, but again, you end up having a physical limitation (size of the nucleus or size of the cell for anuclear organisms) on how many chromosomes you can pack into the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Linear chromosomes are just a more efficient shape when it comes to larger sizes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;=====================&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are a few good references to dig further, if you're interested:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution. Pubmed: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10802162&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/10802162&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Why do we have linear chromosomes? A matter of Adam and Eve. Pubmed: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10422538&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/10422538&lt;/a&gt; -- Proposes that meiosis was the driver for linear chromosomes.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="14553" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-02-21T09:25:50.697" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29769" PostTypeId="2" ParentId="29749" CreationDate="2015-02-21T08:23:18.690" Score="3" Body="&lt;p&gt;Before going into the trouble of reading a textbook on GMOs, ask yourself if you truly understand what the &quot;controversy&quot; is all about? I'll restrain the following comment to GMO crops (as I strongly feel it is in that area that the hysteria whipped up by a public that is poorly educated in science harms society the most).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The public perception often seems to be fall somewhere in between these two extremes: &quot;crazy scientists insert genes from jellyfish into [crop], making a jelly-[crop]-fish...which is just weird/wrong and must therefore be opposed&quot; or &quot;evil big corporation inserts bad genes into plants, which can then escape into the wild, transmit their bad genes into all other plants, and unleash...&quot;...err...zombie plants?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I would suggest that a lot of people are blissfully unaware that MOST of our cash crops have been heavily genetically modified, through millenia of domestication, hybridisation and selection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, durum wheat (commonly used in making semolina and pasta) is an artificial wheat crop, created sometime around 9000 years ago by farmers who crossed two different species of grass crops and selected for a hybrid polyploid plant that had favourable characteristics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The modern maize plant is another artificial organism created many millenia ago by mesoamericans through hybridization and artifical selection, two of the traditional genetic modification tools available to early farmers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The apple is a hybrid plant created through crossing of two different species of plants....again done at the dawn of civilization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect most people who are vehemently opposed to GMO technology are ignorant of the history of farming, let alone the science behind GMO.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;===============================&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, to answer your question, the &quot;concepts&quot; behind gene manipulation are very basic molecular biology techniques, applied in this context at improving the biochemistry of the organism. Therefore, a good place to start would be a basic textbook such as &quot;Molecular Biology of the Cell&quot; by Alberts or something akin. But a basic botanical textbook on crops would be just as beneficial, in my humble opinion.&lt;/p&gt;&#xA;" OwnerUserId="14553" LastEditorUserId="14553" LastEditDate="2015-02-21T08:28:28.397" LastActivityDate="2015-02-21T08:28:28.397" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29770" PostTypeId="2" ParentId="29692" CreationDate="2015-02-21T09:11:58.810" Score="3" Body="&lt;ol&gt;&#xA;&lt;li&gt;I use the term &quot;X-inactivation&quot; instead of &quot;lyonization&quot;. Anyway, X-inactivation is a very specific process by which an entire X chromosome (or equivalent sex chromosome) in a female mammal is completely silenced.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&quot;Imprinting&quot; is typically applied to single genes, wherein genes inherited from a specific parent are always epigenetically silenced. The genes are usually autosomal. Thus, we're talking about scales : entire sex chromosome composed of thousands of genes (x-inactivation) vs single genes (imprinting)&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;The choice for which X-chromosome is inactivated is sporadic and different in different cells within the body. It is controlled by opposing expression of different non-coding RNAs (XIST on the inactive X and TSIX on the active X).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Imprinting is very specific to the allele that is inherited from a specific parent (for example, some genes are paternally imprinted, while others can be maternally imprinted).&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;3&quot;&gt;&#xA;&lt;li&gt;Males with aberrant X-inactivation will lack any expression of genes carried on their single X-chromosome, a condition that will not result in a viable fetus. However, whether there are aberrant X-inactivations in single cells or tissues of ageing adult males....perhaps likely yes, given all the other aberrant somatic mutation events that occur over the course of life.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="14553" LastEditorUserId="14553" LastEditDate="2015-02-21T20:44:29.407" LastActivityDate="2015-02-21T20:44:29.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29771" PostTypeId="2" ParentId="29765" CreationDate="2015-02-21T11:19:42.540" Score="5" Body="&lt;p&gt;Such genome transplantation was performed between two Mycoplasma species in Craig Venter institute &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17600181&quot;&gt;Genome transplantation in bacteria: changing one species to another.&lt;/a&gt; They found that the donor genome completely changes the recipient cell to accept the identity of the original donor cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note of caution: the above experiment was conducted between two highly similar species, and as of yet it is unclear what is going to happen if the exchange is performed between two distantly related bacteria species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for eukaryotes -- the transplants may be not viable at all, because naked DNA is going to lack epigenetic information (histone modifications, DNA methylation) that is preset during gametogenesis.  &lt;/p&gt;&#xA;" OwnerUserId="13239" LastActivityDate="2015-02-21T11:19:42.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29774" PostTypeId="1" AcceptedAnswerId="29775" CreationDate="2015-02-21T16:57:48.820" Score="3" ViewCount="50" Body="&lt;p&gt;I've heard that narwals can grow their tusks up to 16 ft long. What do they need the tusk for? Hunting?  Comunication? &lt;/p&gt;&#xA;" OwnerUserId="14560" LastActivityDate="2015-02-21T17:51:45.380" Title="What is the purpose of narwals' tusks?" Tags="&lt;evolution&gt;&lt;animal-models&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29775" PostTypeId="2" ParentId="29774" CreationDate="2015-02-21T17:51:45.380" Score="2" Body="&lt;p&gt;The evidence shows that the tusk is innervated, and acts as a sensory organ to the outside environment, as well as a mating tool.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/ar.22886/abstract;jsessionid=C9F42D853D1319AAF960E61727E80456.f03t03&quot; rel=&quot;nofollow&quot;&gt;Sensory ability in the narwhal tooth organ system&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-02-21T17:51:45.380" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29776" PostTypeId="1" AcceptedAnswerId="29779" CreationDate="2015-02-21T18:45:34.960" Score="3" ViewCount="645" Body="&lt;p&gt;Is there any standard way to know how much pain an animal feels when it gets hurt like when a bird loses it's wing or hen when killed etc. All pain sensation points?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hey I'm new to biology. :)&lt;/p&gt;&#xA;" OwnerUserId="16367" LastEditorUserId="5198" LastEditDate="2015-02-21T20:30:46.647" LastActivityDate="2015-02-22T11:06:13.290" Title="How can we know or measure pain in animals?" Tags="&lt;zoology&gt;&lt;pain&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29777" PostTypeId="1" CreationDate="2015-02-21T19:19:49.360" Score="3" ViewCount="581" Body="&lt;p&gt;I'm looking at the gluconeogenic pathway:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pyruvate is shuttled into the mitochondria from the cytosol, converted to oxaloacetate by pyruvate carboxylase, converted to malate which is then shuttled out of the mitochondria, and then converted back to oxaloacetate in the cytosol.  Why is the mitochondrial step necessary?  Why can't pyruvate just be made into oxaloacetate in the cytosol?&lt;/p&gt;&#xA;" OwnerUserId="10470" LastActivityDate="2015-02-21T20:41:50.667" Title="Why is oxaloacetate made in the mitochondria?" Tags="&lt;mitochondria&gt;&lt;glucose&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29778" PostTypeId="1" CreationDate="2015-02-21T19:46:39.770" Score="0" ViewCount="51" Body="&lt;p&gt;My question is: If my microscope had a top entry specimen holder, instead of a side entry holder, what additional option(s) should I have to increase the contrast with the same constraint that I only have a single objective aperture? Why would this option work?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any ideas are welcome. Thanks in advance!&lt;/p&gt;&#xA;" OwnerUserId="14547" LastActivityDate="2015-02-21T19:46:39.770" Title="How to increase contrast with only a top entry specimen holder" Tags="&lt;microscopy&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29779" PostTypeId="2" ParentId="29776" CreationDate="2015-02-21T20:25:26.937" Score="10" Body="&lt;p&gt;&lt;strong&gt;Pain is subjective&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Pain&lt;/em&gt; is a subjective experience; you cannot even tell with certainty how much pain your fellow human is experiencing, which is why we &lt;em&gt;ask&lt;/em&gt; people; they then can tell us. Pain relief (both physical and emotional) is a significant part of medicine, yet we still have &quot;pain scales&quot; for self-reported pain, one of the more common ones being the Wong-Baker Faces Pain Rating Scale:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UEnH8.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, note well that even this scale must be interpreted for the patients. For instance, a patient might look like a 6, but be reporting a 10, in which case, a nurse must try to ascertain their actual level of pain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My point is evaluating &lt;em&gt;pain&lt;/em&gt; is contentious even in humans who can express themselves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Definition of pain&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The International Association for the Study of Pain (IASP; www.iasp-pain.org) defines pain &lt;em&gt;in humans&lt;/em&gt; as &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;an unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Pain usually involves a noxious stimulus that activates &lt;em&gt;nociceptors&lt;/em&gt; in the body that carry signals to the CNS where these signals are processed (and generate responses) including the “unpleasant sensory and emotional experience.”&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following are examples of common types of noxious stimuli for different tissues:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Skin: thermal (hot or cold), mechanical (cutting, pinching, crushing), and chemical (inflammatory and other mediators released from or synthesized by damaged skin, and exogenous chemical stimuli such as formalin, carrageenan, bee venom, capsaicin)&lt;/li&gt;&#xA;  &lt;li&gt;Joints: mechanical (rotation/torque beyond the joint’s normal range of motion) and chemical (inflammatory and other mediators released into or injected into the joint capsule)&lt;/li&gt;&#xA;  &lt;li&gt;Muscle: mechanical (blunt force, stretching, crushing, overuse) and chemical (inflammatory and other mediators released from or injected into muscle)&lt;/li&gt;&#xA;  &lt;li&gt;Viscera: mechanical (distension, traction on the mesentery) and chemical (inflammatory and other mediators released from inflamed or ischemic organs, inhaled irritants). &lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Animals need &lt;strong&gt;us&lt;/strong&gt; to interpret their pain into language. For political and emotional reasons, humans are ill-disposed to do so (how could we then justify eating, exploiting, experimenting on animals, etc.). Even into the late '80's, veterinarians were taught that animals didn't perceive pain &lt;em&gt;per se&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How we know animals understand pain&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To determine whether animals can experience actual pain (not simply nociception), it is necessary to show that they&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;can discriminate painful from nonpainful states; make decisions based on this discrimination in a way that cannot arise from evolved nonconscious nociceptive responses; demonstrate motivations to avoid pain; and display affective states of fear or anxiety if threatened with noxious stimuli. In addition, animals experiencing pain might be expected to exhibit spontaneous behavioral changes including sustained signals of distress and impairments in normal behaviors such as sleep.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Animals show all these behaviors. Additionally, there is ample evidence that emotional pain in animals is real. The mere threat of foot shock (electric) induces signs of stress in rats and mice that can be alleviated with anxiolytics (drugs that reduce anxiety).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even &lt;em&gt;fish&lt;/em&gt; show responses to a painful event: guarding behaviors, unresponsiveness to external stimuli and increased respiration, all of which improve with morphine. This is called analogous evidence: evidence that they are, mechanistically at least, directly analogous to pain responses in more complex animals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Humans are animals&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nervous system of mammals is fairly identical to our own (we are animals). A chimpanzee who is afraid of a pin after being stuck with one 20 times in a row clearly &lt;em&gt;feels physical pain and fear&lt;/em&gt;. That a chimp can mourn the death of a parent by not eating and not moving for days clearly indicates that they can experience &lt;em&gt;emotional pain.&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In summary:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pain is subjective. I cannot &lt;em&gt;really tell exactly what you feel&lt;/em&gt; if your arm is ripped off (your bird-wing example) or (don't read if queasy type)&lt;/p&gt;&#xA;&#xA;&lt;blockquote class=&quot;spoiler&quot;&gt;&#xA;  &lt;p&gt; if you are given an electric shock, your throat is slit and, while still bleeding, you are dipped in boiling water to remove your body hair in a whole body hair plucker (which is how most poultry - usually males, not hens, btw - meet their makers). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;By definition, only &lt;em&gt;you&lt;/em&gt; can tell us.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But common sense and experience tells us it would be painful. And, yes, animals feel pain pretty much exactly like we do. Because we are &lt;strong&gt;exceedingly&lt;/strong&gt; &quot;more alike&quot; than we are &quot;slightly different&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.wellcome.ac.uk/en/pain/microsite/culture2.html&quot; rel=&quot;noreferrer&quot;&gt;Can animals feel pain?&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK32655/&quot; rel=&quot;noreferrer&quot;&gt;Pain in Research Animals: General Principles and Considerations&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK32655/box/ch1.box4/?report=objectonly&quot; rel=&quot;noreferrer&quot;&gt;Which Responses Indicate Pain and Which Nonhuman Vertebrates Display Them?&lt;/a&gt;&lt;/sub&gt;&lt;sub&gt;&lt;strong&gt;&amp;lt;- read this if you really want to know&lt;/strong&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://vdt.ugent.be/sites/default/files/art70103.pdf&quot; rel=&quot;noreferrer&quot;&gt;Evolution of pain&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-02-22T06:36:27.000" LastActivityDate="2015-02-22T06:36:27.000" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="29781" PostTypeId="2" ParentId="29777" CreationDate="2015-02-21T20:41:50.667" Score="1" Body="&lt;p&gt;Got it.  The ratio of [NADH]/[NAD+] is about 100000 lower in the cytosol than it is in the mitochondria.  The conversion of malate to OAA reduces a molecule of NAD+ to NADH, and that NADH can be used for the later step in gluconeogenesis: the conversion of 1,3-bisphosphoglycerate to glyceraldehyde 3-phosphate requires a molecule of NADH.&lt;/p&gt;&#xA;" OwnerUserId="10470" LastActivityDate="2015-02-21T20:41:50.667" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29782" PostTypeId="1" CreationDate="2015-02-21T22:20:53.370" Score="1" ViewCount="267" Body="&lt;p&gt;I have PacBio CCS.h5 and the corresponding fasta and fastq files and I would like to demultiplex them. Does anyone know of how this can be done in the absence of bas.h5 files.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your help!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mandy&lt;/p&gt;&#xA;" OwnerUserId="14564" LastActivityDate="2015-02-21T22:20:53.370" Title="Demultiplexing symmetric PacBio reads" Tags="&lt;sequence-analysis&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29783" PostTypeId="2" ParentId="29655" CreationDate="2015-02-21T22:32:19.623" Score="2" Body="&lt;p&gt;The above answers are correct, I just want to add a distinction between the different muscle types.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are 3 types of muscle tissues:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Skeletal muscle (locomotion)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Striated&lt;/li&gt;&#xA;&lt;li&gt;Voluntary&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The skeletal muscle has visible striations under the microscope, because the myofilaments are aligned: they are all parallel. During contraction, the thin filaments slide over the thick filaments - at the end of the contraction the Z lines will be closer together. The filaments stay the same length, they just slide over one another, shortening the muscle. The muscle doesn’t contract by “going” in a particular direction, it shorts everywhere and the alignment of the filaments enables the muscle to shorten in only one dimension. The muscle is connected to the bone by tendons. When it shortens, it pulls on the tendons which pull on the bone, bringing it closer. A skeletal muscle cell can be up to 30cm long (Sartorius muscle).&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;&lt;p&gt;Cardiac muscle (in the heart)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Striated&lt;/li&gt;&#xA;&lt;li&gt;Involuntary&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Cardiac muscle cells are very similar to skeletal muscle cells, however the fibers are interconnected via intercalated discs, which enables them to work in an even more synchronized way.&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;3&quot;&gt;&#xA;&lt;li&gt;&lt;p&gt;Smooth muscle (in the vascular system, the gastrointestinal tract, etc.)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Not striated&lt;/li&gt;&#xA;&lt;li&gt;Involuntary&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Smooth muscle filaments aren’t as organized as the ones in skeletal muscle. Therefore, the shortening can occur in all directions within the cell. It results in the shortening of the cell in more than 1 dimension.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/aUfQ0.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, many organs such as the stomach have more than one layer of smooth muscle, providing constriction in many different “directions” (longitudinal layer, circular layer and oblique layer).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/S10X6.gif&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14551" LastActivityDate="2015-02-21T22:32:19.623" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29785" PostTypeId="1" AcceptedAnswerId="29786" CreationDate="2015-02-21T23:26:52.540" Score="20" ViewCount="2556" Body="&lt;p&gt;Is there a plant (not a microscopic type but one that is visible to the naked eye) that has so much iron (or magnetite), cobalt, or nickel in its body that it can attract a magnet?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case &quot;attract&quot; would mean that a person holding a small magnet next to the plant can feel a small attraction between the magnet and the plant.&lt;/p&gt;&#xA;" OwnerUserId="12939" LastActivityDate="2015-02-22T11:42:57.377" Title="Is any known plant magnetic?" Tags="&lt;botany&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29786" PostTypeId="2" ParentId="29785" CreationDate="2015-02-21T23:48:24.767" Score="20" Body="&lt;p&gt;There was a 2011 &lt;a href=&quot;http://authors.library.caltech.edu/23694/1/Corsini2011p13835J_Appl_Phys.pdf&quot;&gt;study&lt;/a&gt; where they used a sensitive atomic magnetometer to try to detect a plant's magnetic field. They stated that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To our knowledge, no one has yet detected the magnetic&#xA;  field from a plant. Biochemical processes, in the form of ionic&#xA;  flows and time varying ionic distributions, generate electrical&#xA;  currents and time-varying electric fields, both of which produce&#xA;  a magnetic field. However, contrasted to muscle contraction&#xA;  and brain processes, which have a characteristic time&#xA;  scale shorter than one second, plant bioprocesses span several&#xA;  minutes to several days and the expected magnetic field from&#xA;  such processes is correspondingly smaller. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Measurements with a sensitive atomic magnetometer were performed on the Titan arum&#xA;  (Amorphophallus titanum) inflorescence, known for its fast biochemical processes while blooming.&#xA;  We find that the magnetic field from these processes, projected along the Earth’s magnetic field,&#xA;  and measured at the surface of the plant, is &amp;lt;&#xA;   0.6 lG. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So according to this, no, you wouldn't be able to sense the magnetic field from a plant with a magnet. &lt;/p&gt;&#xA;" OwnerUserId="14551" LastActivityDate="2015-02-21T23:48:24.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29787" PostTypeId="1" AcceptedAnswerId="29789" CreationDate="2015-02-22T00:02:09.990" Score="0" ViewCount="7281" Body="&lt;p&gt;What would happen if I drink lactic acid?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I use lactic acid to clean an espresso coffee machine and I wonder what injuries could occour drinking it.&lt;/p&gt;&#xA;" OwnerUserId="14565" LastActivityDate="2015-02-22T04:12:25.037" Title="Effects of lactic acid ingestion" Tags="&lt;injury&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2015-02-22T08:26:47.737" ContentLicense="CC BY-SA 3.0" />
  <row Id="29788" PostTypeId="1" CreationDate="2015-02-22T03:09:59.637" Score="15" ViewCount="1479" Body="&lt;p&gt;Plants must have nitrogen to grow. According to the answer to &lt;a href=&quot;https://biology.stackexchange.com/questions/686/are-there-any-plants-that-fix-their-own-nitrogen&quot;&gt;this question&lt;/a&gt;, there are no plants that can fix their own nitrogen (without the help of bacteria).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants get their nitrogen in the form of nitrates (NO&lt;sub&gt;3&lt;/sub&gt;-) or ammonia (NH&lt;sub&gt;4&lt;/sub&gt;+). Nitrates and ammonia get into the soil through &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;lightning (causing N&lt;sub&gt;2&lt;/sub&gt; and O&lt;sub&gt;2&lt;/sub&gt; to combine to form NO which then reacts with atmospheric water and is brought to earth by rain)&lt;/li&gt;&#xA;&lt;li&gt;nitrogen-fixing bacteria associated with leguminous plants&lt;/li&gt;&#xA;&lt;li&gt;fixed nitrogen from dead plants/animals (ammonification), urine, etc.&lt;/li&gt;&#xA;&lt;li&gt;ammonifying and other bacteria&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The answer also states that it seems to be possible to engineer plants to be able to fix nitrogen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So one could think plants &lt;em&gt;could have evolved&lt;/em&gt; to be able to fix nitrogen, but did not.  Maybe it just did not happen based on it's probability to happen.&lt;br&gt;&#xA;Is there any other explanation?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe the ability to fix nitrogen would have a harmful effect on plants? Or fixation requires a complex set of related mutations? Are there enough areas with soil depleted of nitrates to exert a selection pressure for nitrogen-fixing plants?&lt;/p&gt;&#xA;" OwnerUserId="6194" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2017-04-13T04:22:59.510" Title="Is there a fundamental reason that plants cannot fix their own nitrogen?" Tags="&lt;evolution&gt;&lt;biochemistry&gt;&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29789" PostTypeId="2" ParentId="29787" CreationDate="2015-02-22T04:12:25.037" Score="-2" Body="&lt;p&gt;No, don't drink it... And here's why.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ingesting lactic acid or for some reason having too much of it in your body can cause a variety of health problems ranging from mild to deadly. There are two types of lactic acidosis; the first is called metabolic acidosis and the second is known as respiratory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Metabolic acidosis - which is what would be caused by ingestion - occurs when the fluids in your body build up too much of the acid and your kidneys can no longer keep up with the demand placed on them. Or they over respond and remove too much base from your body, leaving you acidic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Respiratory acidosis is caused when your lungs cannot effectively remove CO2 from the blood. A buildup of CO2 leads to a more acidic body chemistry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regardless of what the cause of the acidosis was, you can expect some of the following.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Symptoms of metabolic acidosis:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;~Rapid and shallow breathing&lt;/p&gt;&#xA;&#xA;&lt;p&gt;~Confusion&lt;/p&gt;&#xA;&#xA;&lt;p&gt;~Fatigue&lt;/p&gt;&#xA;&#xA;&lt;p&gt;~Headache &lt;/p&gt;&#xA;&#xA;&lt;p&gt;~Sleeplessness &lt;/p&gt;&#xA;&#xA;&lt;p&gt;~Lack of appetite&lt;/p&gt;&#xA;&#xA;&lt;p&gt;~Severe acidosis can cause shock, organ failure and even death&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Diagnosis of acidosis:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A series of blood tests will check calcium, sugar and electrolyte concentrations in your blood.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My sources for this information:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.healthline.com/health/acidosis#Prognosis6&quot; rel=&quot;nofollow&quot;&gt;Healthline&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Lactic_acidosis&quot; rel=&quot;nofollow&quot;&gt;WikiPedia on Lactic Acidosis&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6289" LastActivityDate="2015-02-22T04:12:25.037" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29790" PostTypeId="2" ParentId="28584" CreationDate="2015-02-22T05:46:00.653" Score="0" Body="&lt;p&gt;Chris is right here, polymerases are generating sequences,  the enzymes your asking about do a single type of reaction, so you would be assessing its activity not its fidelity. A good resource I've found for looking at qc data for enzymes like these are just the product inserts from the manufacturer. NEB for example generally seems to provide sufficient qc data in my opinion. For example:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.neb.com/~/media/Catalog/All-Products/B2D1E3A4F480489EAD7A1CD43E164DA0/Datacards%20or%20Manuals/M0233Datasheet-Lot0031209-1.pdf&quot; rel=&quot;nofollow&quot;&gt;https://www.neb.com/~/media/Catalog/All-Products/B2D1E3A4F480489EAD7A1CD43E164DA0/Datacards%20or%20Manuals/M0233Datasheet-Lot0031209-1.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2015-02-22T05:46:00.653" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29791" PostTypeId="1" CreationDate="2015-02-22T05:59:18.090" Score="1" ViewCount="87" Body="&lt;p&gt;I have a mold problem in my bathroom.  There is a narrow groove between the top of my tub and the wall it is attached to where a black gunk repeatedly grows.  I can shoot the material out with a spray bottle but it grows back.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been taught many times that a bacterial film can prevent the growth of other bacteria, because the film created by one prevents another from colonizing that spot.  I have the inclination to think yogurt has bacteria.  If I were to clear the groove of the material, then spray the groove with a mixture of yogurt and water, would the bacteria in the yogurt colonize the freshly cleared groove and prevent the growth of what I assume to be mold?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I assume this is on topic as I am looking for a sort of corroboration/rejection of this scenario rooted in the biological workings of bacteria.&lt;/p&gt;&#xA;" OwnerUserId="14570" LastEditorUserId="14570" LastEditDate="2015-02-22T06:49:59.253" LastActivityDate="2015-02-22T06:49:59.253" Title="Can I use yogurt to prevent the growth of black mold?" Tags="&lt;bacteriology&gt;" AnswerCount="0" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="29795" PostTypeId="1" AcceptedAnswerId="29960" CreationDate="2015-02-22T07:32:42.023" Score="2" ViewCount="7299" Body="&lt;p&gt;How does a virus like HIV mutate into so many strains, and yet all of them are  harmful to our immune system? What gives this virus the ability to mutate so efficiently?&lt;/p&gt;&#xA;" OwnerUserId="14500" LastEditorUserId="6061" LastEditDate="2015-02-22T10:25:17.297" LastActivityDate="2016-09-26T18:59:06.430" Title="How does HIV mutate into other strains while keeping their virulent phenotype?" Tags="&lt;mutations&gt;&lt;virus&gt;&lt;hiv&gt;&lt;retrovirus&gt;&lt;aids&gt;" AnswerCount="5" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29796" PostTypeId="2" ParentId="29795" CreationDate="2015-02-22T08:03:36.613" Score="2" Body="&lt;p&gt;Viral recombination produces genetic variation that contributes mostly to the evolution of the HIV-1 virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HIV being an RNA Virus utilizes  an enzyme called reverse transcriptase, which produces DNA from RNA. HIV also has &lt;strong&gt;two&lt;/strong&gt; RNA genomes. After infection and then replication, which is catalyzed by reverse transcriptase, recombination between the two genomes can occur. specifically the single-strand (+)RNA genomes are reverse transcribed to form DNA. Then during this reverse transcription the nascent DNA can switch multiple times between the two copies of the viral RNA and multiple recombination occur throughout the genome. Furthermore, multiple events per genome may occur during each replication cycle, thus compounding the mutation. &lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2015-02-22T08:03:36.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29797" PostTypeId="1" CreationDate="2015-02-22T09:22:58.993" Score="3" ViewCount="68" Body="&lt;p&gt;In a comment to &lt;a href=&quot;https://biology.stackexchange.com/questions/28539/how-well-does-the-radius-of-a-tree-correlate-with-its-age&quot;&gt;this question&lt;/a&gt;, it was said that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Radiocarbon dating won't work. For a start the tree needs to be dead, which since you're not using the rings I'm assuming it isn't. Also the atomic testing in the 20th century completely messed up the level of C14 in the atmosphere, so radiocarbon dating can't be used for anything that didn't die 70 years ago or more.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I did not know this. So, what kind of dating techniques biologists use today? :-)&lt;/p&gt;&#xA;" OwnerUserId="14572" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-02-25T14:50:57.110" Title="About modern dating techniques" Tags="&lt;senescence&gt;&lt;radiation&gt;&lt;data&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29798" PostTypeId="1" CreationDate="2015-02-22T09:51:57.383" Score="3" ViewCount="427" Body="&lt;p&gt;Why do only corpses of species rot and be eaten by bacteria? What is keeping us from rotting? &#xA;Just like fruits, and foods we eat; meat and vegetables rot when left uneaten. Like food, corpses rot and get eaten by maggots. Why? &#xA;Why don't these apply to living species?&lt;/p&gt;&#xA;" OwnerUserId="14573" LastEditorUserId="14573" LastEditDate="2015-02-22T10:00:19.263" LastActivityDate="2015-02-22T10:58:04.647" Title="What's keeping living species from rotting?" Tags="&lt;health&gt;&lt;species&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29799" PostTypeId="2" ParentId="29795" CreationDate="2015-02-22T10:42:45.177" Score="1" Body="&lt;p&gt;Simple answer is that those mutations that create inactive virus, will never show up on screen, since it  will be asymptomatic. In same fashion if virus loses its ability to infect new target (via sexual contact or blood directly) it will show up only in first victim, so that effectively be a non-problem for society.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Addendum: I think I answered portion, starting with &quot;and yet...&quot;, which seems to be most important in the question. I think that exact mechanism of mutagenesis must be covered in literature, if known. Also, it seems that since there are no vaccine for HIV, it's mutagenesis cannot be really &quot;efficient&quot;, since it is not actively fighting anything.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-02-22T10:42:45.177" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29800" PostTypeId="2" ParentId="29795" CreationDate="2015-02-22T10:48:53.657" Score="3" Body="&lt;p&gt;&lt;strong&gt;What gives HIV the ability to mutate?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HIV is a single standed RNA virus. DNA is much more stable than RNA as it has a stronger backbone and it is typically double stranded. But HIV mutates at a rate far higher than just being a RNA virus. That's because it uses an enzyme called reverse transcriptase (RT) to build it's RNA genome from RNA bases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RT is meant to copy the old HIV and make a new one but it does a rubbish job. Most the time it copies it well but every now and then (3 x 10&lt;sup&gt;−5&lt;/sup&gt; per nucleotide base) it puts in a random base. That might seem like a small rate but that's HUGE if that was coding our genome we would die (if we ever even lived). And since HIV's replication rate is enormously high, there's always going to be a range of good and junk HIV (but it's mostly just junk - next answer for why that's not a bad thing).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But that's not all, RT doesn't just use one old HIV to make a new one. It can use several different old HIVs to make a new one that's not only a combination of all the other ones but then add in the mutations from above, completely different. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So I get that there's lots of mutated strains all over the place. Surely that'd make them useless because the mutations are random?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yeah they are random and yes that does mean some virus particles are useless. But it's very variable. There's ones which are greatly infectious, partly infectious, slightly infectious and basically junk. The body doesn't really know which ones are which and that's the beauty of it all. The body tries to fight all of them and has no clue which one to get. If it happens to target the greatly infectious one, the numbers of this go down but then the partly infectious one will become the most infectious one and the cycle continues. The junk HIV is basically just a sticky pool of most of the HIV particles that just gets the immune system going crazy and diverts it from the real threat.&lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="3340" LastEditDate="2015-02-26T08:04:54.103" LastActivityDate="2015-02-26T08:04:54.103" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29801" PostTypeId="2" ParentId="29798" CreationDate="2015-02-22T10:53:25.197" Score="3" Body="&lt;p&gt;One can calculate that there are more non-human cells (mainly bacteria) inside human body than there are actual human cells. Why those bacteria don't eat us from within? Epithelium is pretty good barrier between outer world and internal systems. It is essentially one-cell thick layer that protects internal organs and infrastructure. In cases when epithelium breaks, bacteria can get into blood stream and start very bad infection, which can cause necrosis (effectively, rotting, tissue decay). Natural cell death is fought by natural cell proliferation so that there are no gaps in defense layers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also one should not forget about immune system that is looking for invaders or anything that should be where it is. In healthy person immune response will close gaps in epithelium and kill bacterial infections pretty quick.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dead people, as well as dead plants, have their skin and epithelium, immune system destroyed by cell death or infection. Then bugs start to eat vessels, tasty nerve tissues, muscle and cartilages, blood cells filled with proteins and everything eatable.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-02-22T10:53:25.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29802" PostTypeId="2" ParentId="29798" CreationDate="2015-02-22T10:58:04.647" Score="0" Body="&lt;p&gt;&lt;strong&gt;What's rotting mean?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The stages of rotting or decomposition are Fresh, Bloat, Active decay, Advanced decay and Dry/remains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fresh decomposition is first and is typically required before the other stages. It is caused by failure to remove carbon dioxide (which makes things acidic) and provide oxygen to tissues (because the hearts stopped for example). There's lots of bacteria in us but they're kept in check by our immune system and also the presence of oxygen (a lot of them are anaerobes which dislike too much oxygen). They start eating are carbohydrates, fats, protein and making chemicals such as acids, gases like methane and ammonia. Multiplication of these bacteria and continued production is called putrefaction and leads to the next stages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in summary it's the cell barriers, the oxygen and the immune system stopping this first stage from happening (which let's the next insect stages occur). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Rotting in living organisms&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes this can happen in living organisms such as in gangrene where parts of the body (typically the toes or fingers) aren't getting oxygen and then rotting can occur in a living organism. It's a great idea to then chop off the affected part before these bacteria eat into a blood vessel and spread throughout the body. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2015-02-22T10:58:04.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29803" PostTypeId="2" ParentId="29776" CreationDate="2015-02-22T11:00:34.147" Score="0" Body="&lt;p&gt;We work a bit with pain and memory. My understanding is that you can measure what in behavioral field is called &quot;pain&quot; by detecting aversive response of an animal. That is there is always something unpleasant and attractive in nature. Only difference is that pungent smell will not kill subject. Evolution taught animals that bad smells and loud sounds might bring danger and thus pain, so they try to escape. But pain per se is something that is definitely tissue-damage inducing at some point of intensity. Pain is only signal that tissue damaging influence has approached.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ADD: I re-read your question. There is no way to tell whether or not bird feels pain when wings are cut without anesthesia. Nice experiment would be to rip off human's arms and bird's wings while both are in fMRI scanners or other functional brain imager. If same areas of brain light up, it means that feeling might be similar.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-02-22T11:06:13.290" LastActivityDate="2015-02-22T11:06:13.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29804" PostTypeId="1" CreationDate="2015-02-22T11:13:09.273" Score="7" ViewCount="3878" Body="&lt;p&gt;Blood is removed from meat before it is consumed. Below is, for example, how chickens are processed from Wikipedia. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Removed from transport cages&lt;/li&gt;&#xA;&lt;li&gt;Hung by the legs on a shackle, mounted on a conveyor chain.&lt;/li&gt;&#xA;&lt;li&gt;Stunned using an electrically charged water bath&lt;/li&gt;&#xA;&lt;li&gt;Killed by cutting the blood vessels in the neck&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Bled so that most blood has left the carcass&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;li&gt;Scalded to soften the attachment of the feathers&lt;/li&gt;&#xA;&lt;li&gt;Plucked to remove the feathers&lt;/li&gt;&#xA;&lt;li&gt;Head removed&lt;/li&gt;&#xA;&lt;li&gt;Hock cutting to remove the feet&lt;/li&gt;&#xA;&lt;li&gt;Rehung in the evisceration room&lt;/li&gt;&#xA;&lt;li&gt;Gutted or eviscerated to remove the internal organs&lt;/li&gt;&#xA;&lt;li&gt;Washed to &lt;strong&gt;remove blood&lt;/strong&gt; and soiling from the carcass&lt;/li&gt;&#xA;&lt;li&gt;Chilled to prevent bacterial spoiling&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Why is the blood removed? Does it just simply taste bad? This might be a stupid question but being vegetarian, I may not know. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="16866" LastEditDate="2017-06-02T18:39:23.850" LastActivityDate="2017-06-02T18:39:23.850" Title="Why is blood removed from meat?" Tags="&lt;zoology&gt;&lt;food&gt;&lt;safety&gt;" AnswerCount="2" CommentCount="3" ClosedDate="2015-02-26T10:19:35.693" ContentLicense="CC BY-SA 3.0" />
  <row Id="29805" PostTypeId="2" ParentId="29788" CreationDate="2015-02-22T11:20:39.370" Score="6" Body="&lt;p&gt;That is an interesting question. But rises some line of thought by analogy, e.g. why people won't evolve to produce their own ATP without mitochondria? (I mean of course Eukaryotas in general). I don't see any reason why multicellular organism cannot incorporate bacterial functionality either as happened with mitochondria, or as just separate cell type, that will provide desirable enzymatic reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer, no matter how unsatisfactory, might be simple: because it so happened. We definitely can create experimental conditions lacking N-fixing bacteria as well as varying amounts of nitrates, nitrites etc. And then produce and screen line of mutants for ability to fix nitrogen without symbiotic partners.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-02-22T11:20:39.370" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="29806" PostTypeId="2" ParentId="29804" CreationDate="2015-02-22T11:28:22.787" Score="0" Body="&lt;p&gt;Blood finds use in many different dishes as well as biotechnological applications. Research-grade BSA (bovine serum albumin) is derived from cow's blood, there are not special facilities, same cows go for steaks and car seats. So part answer is economical: blood can be processed further. Also it is just easier not trying to preserve liquid inside vessel already opened by slitting the throat. It also seems that blood can rot faster than other tissues, maybe, because in dead animal immune responses are deteriorated and every infection in blood will activate.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-02-22T11:28:22.787" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="29808" PostTypeId="2" ParentId="29785" CreationDate="2015-02-22T11:42:57.377" Score="6" Body="&lt;p&gt;I would like to add from my random-seminar experience that there are magnetic bacteria, that orient along magnetic field due to magnetosomes, e.g. &lt;em&gt;Magnetospirillum magnetotacticum&lt;/em&gt;. Please look into &lt;a href=&quot;http://en.wikipedia.org/wiki/Magnetotactic_bacteria&quot;&gt;Wiki article&lt;/a&gt;. So one can imagine symbiotic association between plant and such bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More to OP's question, remember that any electric current (aka moving charges) creates magnetic field around it. If net charge of plant's xylem sap is non-zero than there will be magnetic field created when current flows. But it will be minuscule.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-02-22T11:42:57.377" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29809" PostTypeId="1" CreationDate="2015-02-22T12:23:17.073" Score="1" ViewCount="336" Body="&lt;p&gt;In an imaginary sense, If you alone were replicated into 2 so that there should now be 2 of &quot;you&quot; (meaning you both have the same DNA). Then let's say one of you shrunk to the size of a bacteria, and was placed inside the other you (normal human size. Let's call this the actual you). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is how would your immune system affect the bacterial sized you in your own body? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would white blood/T cells try to get rid of the smaller you?&#xA;If so, how? And could the smaller you die from this?&lt;/p&gt;&#xA;" OwnerUserId="14573" LastActivityDate="2015-02-24T16:46:02.957" Title="Can your immune system's cells destroy you? (Critical thinking and Fictional sense)" Tags="&lt;cell-signaling&gt;&lt;replication&gt;&lt;systems-biology&gt;&lt;autoimmune&gt;&lt;dna-replication&gt;" AnswerCount="5" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29810" PostTypeId="2" ParentId="29809" CreationDate="2015-02-22T12:31:34.050" Score="0" Body="&lt;p&gt;When your body develops, immune system learns which tissues are foreign and which are innate. So usually immune system does not attack host's cells. Opposite case is autoimmune diseases. Immune system does that by addressing surface proteins of cells. Only foreign cells, never presented before, cause response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you think that large-you immune system will not attack large-you cells, then you should agree that large-you immune system will not attack small-you. Except, maybe, for bacteria that are on the skin on small-you and now sitting in blood stream of large-you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question boils down to: why my cells are not attacked by my immune system? Answer: because in healthy animals it discriminates host vs invaders due to memory of immune system.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-02-22T12:31:34.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29812" PostTypeId="1" AcceptedAnswerId="29824" CreationDate="2015-02-22T13:49:06.760" Score="1" ViewCount="507" Body="&lt;p&gt;I am trying to find out how these networks can be linked together. I know that Protein-protein interaction networks and metabolic networks both fall under the Intra-cellular type of biological networks that describe the cellular functioning. But what is the relationship between them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you very much.&lt;/p&gt;&#xA;" OwnerUserId="14578" LastActivityDate="2015-03-03T15:45:23.093" Title="What is the relationship between protein-protein interaction networks and metabolic networks?" Tags="&lt;proteins&gt;&lt;metabolism&gt;" AnswerCount="3" CommentCount="2" ClosedDate="2015-02-23T23:20:16.360" ContentLicense="CC BY-SA 3.0" />
  <row Id="29813" PostTypeId="1" AcceptedAnswerId="29814" CreationDate="2015-02-22T14:13:11.983" Score="3" ViewCount="28146" Body="&lt;p&gt;How come that one's arm has to be at heart level so that the blood pressure can be measured accurately. I've tried researching this question, but most answers to it were just &quot;if the arm is above the heart level the blood pressure is too high and vise versa,&quot; but I want to know why this is so.&lt;/p&gt;&#xA;" OwnerUserId="12958" LastActivityDate="2019-03-01T15:39:16.197" Title="Arm at Heart Level when Measuring Blood Pressure" Tags="&lt;cardiology&gt;&lt;blood-pressure&gt;&lt;measurement&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29814" PostTypeId="2" ParentId="29813" CreationDate="2015-02-22T14:35:16.780" Score="7" Body="&lt;p&gt;&lt;a href=&quot;http://electron6.phys.utk.edu/101/CH5/pumps.htm&quot; rel=&quot;noreferrer&quot;&gt;This page&lt;/a&gt; (and many others) explain the idea rather well. This is more of a physics than a biology question, but the fundamental concepts are the same. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, contrary to what you wrote in the question, the measured blood pressure should be lower than expected if the arm is elevated above heart level. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XhO3W.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you reduce the pressure on the bent pipe, the water level on the side where the pressure is reduced rises. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, When the arm is elevated, it is equivalent to the right hand side of the image, where the right hand tube's water level is higher than the left hand side. Raising the arm above heart level, with the pressure of blood at the heart level remaining constant, will result in a lower pressure being measured, due to the heart effectively having to pump the blood up the distance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the same reason, &lt;a href=&quot;http://www.giraffeconservation.org/giraffe_facts.php?pgid=4&quot; rel=&quot;noreferrer&quot;&gt;giraffes have very high blood pressures&lt;/a&gt; (double that of humans) due to their long necks. If their blood pressure was at the level of humans, they would faint when raising their necks, due to the blood pressure falling to zero at their brains. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-02-22T14:35:16.780" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29815" PostTypeId="1" CreationDate="2015-02-22T10:28:03.777" Score="5" ViewCount="158" Body="&lt;p&gt;Please help me identify these fish. I looked around but wasn't able to determine its species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NhDeL.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DGCSt.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="David" LastEditorUserId="11841" LastEditDate="2015-02-25T16:06:03.140" LastActivityDate="2015-03-10T13:47:34.043" Title="Help needed in fish identification" Tags="&lt;species-identification&gt;&lt;ichthyology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="29816" PostTypeId="2" ParentId="29812" CreationDate="2015-02-22T16:09:10.803" Score="1" Body="&lt;p&gt;In short, proteins in Protein-protein interaction networks perform a function by directly interacting with one another.  They may for instance bind to one another forming permanent or momentary complexes (e.g. insulin binding to insulin receptor or the pieces of F0-F1 ATPase combining), or they may chemically modify one another (e.g. protein kinases adding a phosphate to the residue of another protein). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/R8hIm.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Proteins in a Metabolic network might never be in physical contact one another. They effect one another by producing chemical compounds which are utilized by other enzymes, forming a &lt;a href=&quot;http://www.genome.jp/kegg-bin/show_pathway?ko01200&quot; rel=&quot;nofollow noreferrer&quot;&gt;network of chemical transformations&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course an enzyme in a metabolic network might also have its activity modulated through interacting with other proteins in a protein-protein network.  The two terms are of course not mutually exclusive, but describe different sorts of relationships between proteins. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3624" LastEditDate="2015-03-03T09:54:39.420" LastActivityDate="2015-03-03T09:54:39.420" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29817" PostTypeId="1" AcceptedAnswerId="29819" CreationDate="2015-02-22T17:08:45.127" Score="1" ViewCount="5885" Body="&lt;p&gt;Disclaimer, I'm not a biology undergrad and I only know the basics about muscle movement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that doing a bench press works the chest, and specifically the Pectoralis Major because, well, I feel muscle soreness. However, it is not obvious to me what the Pectoralis Major has to do with extending the arm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thinking about muscle contraction, I see clearly how, for example, the Bicep flexes the elbow when it contracts. In a similar way, when the Pectoralis Major contracts you get horizontal shoulder adduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what about the bench press? The majority of the movement consists of raising the arms upwards from a tucked position, and the is little shoulder adduction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="14581" LastActivityDate="2018-03-26T20:55:09.233" Title="How does the Pectoralis Major work when doing a bench press?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29818" PostTypeId="1" CreationDate="2015-02-22T17:12:27.233" Score="0" ViewCount="536" Body="&lt;p&gt;After recently seeing Christopher Nolan's &lt;em&gt;Interstellar&lt;/em&gt; and reading Kip Thorne's &lt;em&gt;The Science of Interstellar&lt;/em&gt;, I've seriously been reflecting on the challenges mankind faces in becoming space pioneers, which in my belief will be a necessity to survive as a species. Not just the technological challenges, but the biological ones as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Technology can only go so far to aid and protect an organism against the brutal environment of space travel. And so the day may come where we have to make a choice on engineering our own evolution to become a hardier species that can better cope with that environment. The two immediate attributes that come to mind are resistance to radiation and extended life spans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And this brings me to my question. Putting aside for the time being the question &lt;em&gt;Should we make this choice ?&lt;/em&gt;, my question is &lt;em&gt;How far could we go towards engineering a space-durable human species&lt;/em&gt;?&lt;/p&gt;&#xA;" OwnerUserId="9906" LastActivityDate="2015-02-22T19:00:35.043" Title="How far can we go in engineering our own evolution?" Tags="&lt;human-genetics&gt;&lt;radiation&gt;&lt;human-evolution&gt;&lt;lifespan&gt;&lt;protein-engineering&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2015-02-22T19:17:48.930" ContentLicense="CC BY-SA 3.0" />
  <row Id="29819" PostTypeId="2" ParentId="29817" CreationDate="2015-02-22T17:18:12.797" Score="5" Body="&lt;p&gt;The pectoralis muscle attaches to the top to the inner half of the clavicle, just underneath the biceps on the inner part of your arm and the breastbone (a.k.a the sternum) which is found in the middle of your ribs. See below: &lt;img src=&quot;https://i.stack.imgur.com/i6GfZ.jpg&quot; alt=&quot;Pectoralis major muscle attachments&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So taking that in account the pectoralis muscle helps bring your arm closer to your body (adducts your arm), pulling it forward in front of you (flexes the humerus) to push up like you would when you bench press. This action can be seen below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/z6H9K.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2015-02-22T17:18:12.797" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29820" PostTypeId="2" ParentId="29809" CreationDate="2015-02-22T17:25:58.790" Score="0" Body="&lt;p&gt;&lt;strong&gt;How does the body know you is you?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's two forms of immunity: innate and adaptive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Innate&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The innate immune system is the first line of defence that basically works on pattern recognition. &quot;If I see these chemicals, they're usually bacteria/fungi/viruses, so I'm going to kill anything with these chemicals.&quot; Little you wouldn't have any of these chemicals unless of course the fact is our body is covered in bacteria which might be recognised (were the chemicals big enough to be recognised). Then they also try to kill things when they're worried somethings causing damage. So if they see that the area is inflamed because little you accidentally broke something, they might come and gobble you up because they're extra activated by the inflammation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Adaptive&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the adaptive immune system, this looks for certain markers and can identify specific bacteria and things that aren't us. There's these proteins on cells called MHC (a.k.a HLA). Our body cells are covered in OUR ones and everyone has different ones (unless you're an identical twin). So in little you's case as long as those proteins were there, the body would think you're okay. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2015-02-22T17:25:58.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29821" PostTypeId="2" ParentId="29818" CreationDate="2015-02-22T17:55:11.057" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;How far could we go towards engineering a space-durable human species?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think this question is likely to get closed as off-topic. It is extremely hypothetical and would be a better fit on &lt;a href=&quot;http://worldbuilding.stackexchange.com&quot;&gt;WorldBuilding.SE&lt;/a&gt;. But here is my messy attempt to answer this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Assumptions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I guess in your question, you assume that we know everything about how our genotype (≈the genes of an individual) make up the phenotype (≈how we look basically). So, I will try to give a short answer to this question by assuming that we were to know exactly what would happen if we were to add the sequence &lt;code&gt;ATTTAG&lt;/code&gt; in the somewhere in the alpha-globulin gene or the sequence &lt;code&gt;CCTATA&lt;/code&gt; somewhere in the regulatory sequence of the lactase gene. It is important to understand that today we are very far from having such knowledge. I also assume that we are able to recreate the environments we need to develop the new thing (human2.0 if you want) that we would have engineered. For example if we make up humans that need to grow in a different environment than the womb. By the end of the answer, I will pretty much assume that we know everything that can be known about organic chemistry and how chemicals process genetic information. Note that to the point we're doing the drastic modifications I will be talking about, it will be a philosophical issue to decide whether the new species we created is a human or not (it may even come to the discussion whether the new thing we created is a living thing or not).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Resistant to evolution as a species or only resistance as an individual?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are talking about a species that would definitely be resistant to survive in these extreme environments or are you talking about a bunch of individuals surviving in this extreme environments. The difference is &quot;evolution&quot;. Species evolve and not necessarily in the right way. High radiation may yield to high mutation rate and therefore to mutational meltdown (decrease in mean fecundity of the population through time yielding to extinction of the species).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;General Limitation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With these very extreme assumptions, then we are only limited by physics. We could not add wings of the size of the wings of a warbler to a big animal like human and hope that it is going to fly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Resistance to radiation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know little about this subject but will try to say some things that may eventually help you. We cannot really make our DNA insensitive to radiation (although we may eventually make our DNA slightly more stable) because radiation will alter matter. It is a physical process that cannot be altered. We may create a lot more of tumour suppressor genes to protect ourselves from developing cancer. Eventually we could create a species that would be able to synthesize (and carry) a concrete shield around its body to protect itself from radiation. But it might eventually be easier to code genetic information with something else than DNA! Eventually made up of quartz because quartz is relatively insensitive to radiation. We could indeed create a whole new form of life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;High radiation yield to high mutation rate and high mutation rate may likely lead a species to extinction (mutational meltdown) but not necessary directly kill the first generations of this made-up species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Extending lifespan&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This sounds &quot;easier&quot;. We may &quot;just&quot; target the alleles (=variant of a gene) that are known to diminish the human lifespan, to slightly (but probably considerably) increase human lifespan. Again, I assume that we can know these alleles and can replace them with better variants. However, evolutionary processes will just recreate those genes, just because there always has an equilibrium between the rate at which new deleterious mutations appear and selection purging the genome from these mutations. Moreover, at an age where reproduction has already occurred selection is less important and it allows for deleterious allele that are expressed late in the age of the individual to eventually spread in the population. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-02-22T19:00:35.043" LastActivityDate="2015-02-22T19:00:35.043" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29823" PostTypeId="1" CreationDate="2015-02-22T19:49:24.650" Score="1" ViewCount="5043" Body="&lt;p&gt;When I was a kid, my parents taught me to apply hydrogen peroxide on my nose whenever it bled. It's a rare event, but my nose bleeds from time to time, and when it does, I always go through the same procedure of dipping a cotton bud in hydrogen peroxide, and applying it to the inside of the bleeding nostril. It always stops the bleeding immediately and I get on with my day.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It happened right now, and since I always just go through the motions without thinking about it, today I was curious about the principles at stake here. In looking for an answer about why it does what it does, I found only references to the effects of drinking hydrogen peroxide, which looks like a controversial subject whose benefits may be non-existent; but I didn't find a single mention about the application of hydrogen peroxide directly on a bleeding nose, which made me worried if what I'm doing is even recommended or if I'm doing something potentially dangerous. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is: is this practice beneficial, and why?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update:&lt;/strong&gt; This question mentioned oxygenated water, which is the literal translation of &quot;água oxigenada&quot; (PT), but apparently that's only the commercial name for &quot;peróxido de hidrogénio&quot; where I live, which translates to hydrogen peroxide (H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt;); and since that returns many more hits on google, I've renamed all instances of oxygenated water to hydrogen peroxide in this question.&lt;/p&gt;&#xA;" OwnerUserId="13487" LastEditorUserId="3624" LastEditDate="2015-02-23T08:54:25.127" LastActivityDate="2015-02-23T08:54:25.127" Title="Should hydrogen peroxide be applied on a bloody nose?" Tags="&lt;hematology&gt;&lt;medicine&gt;" AnswerCount="2" CommentCount="6" ClosedDate="2015-02-23T07:08:37.993" ContentLicense="CC BY-SA 3.0" />
  <row Id="29824" PostTypeId="2" ParentId="29812" CreationDate="2015-02-22T21:08:40.420" Score="1" Body="&lt;p&gt;Proteins interact with each other often for regulation purposes and for localization of several enzymatic reactions for increased efficiency. For example, some proteins inhibit their binding partners. Or DNA replication complex is made of bunch of proteins, many of which do different jobs, but they are in physical complex (e.g. helicase with DNA polymerase).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Metabolic networks are sets of chemical reactions, they might even happen in different compartments inside the cell. While you can try to investigate protein interaction network by cross-linking proteins and then analyzing complexes you extract, metabolic networks are constructed by deciphering sequences of chemical reactions (e.g. metabolic cycles) and finding appropriate enzymes for each reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Metabolic process (e.g. DNA replication) can be run by interacting proteins, but also might include proteins that don't directly interact with each other. For example, DNA polymerase complex does not produce nucleotides, but they are necessary for it's function.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-03-03T15:45:23.093" LastActivityDate="2015-03-03T15:45:23.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29825" PostTypeId="2" ParentId="29823" CreationDate="2015-02-22T21:26:56.417" Score="4" Body="&lt;p&gt;No, I don't think oxygenated water does anything to stop bloody noses. But holding a wet cotton swab with pressure to the inside of the nose might.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The vast majority of bloody noses in healthy individuals arise from one specific area in the nose (on either side):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tDxYJ.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the mucosa of the nasal septum (the cartilagenous structure separating the nose into two sides), there is an area where several arteries &quot;meet&quot;, giving it an exceptionally rich vascular supply, called Kiesselbach's plexus. It is on the anterior surface, and exposed to dry air and trauma (even such as might be sustained by a bad cold). Bleeding typically occurs when the mucosa erodes for any reason, and the capillaries and venules (and sometimes arterioles) become exposed and subsequently break. The result is the familiar bloody dripping of a nosebleed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most common treatment is &lt;em&gt;direct pressure&lt;/em&gt; (squeezing the sides of the nose together) for 5-10 minutes. This works because putting direct pressure on any bleed stops the blood flow long enough for a clot to form and the arteriole to close down.&#xA;If needed, more aggressive control can be achieved by a professional.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you happen to apply pressure with the wet cotton swab to a large enough part of the plexus (or somewhere near the spot from which your nose is bleeding), your nosebleed will stop. But it really doesn't matter what you use to wet the cotton swab (plain water, oxygenated water, carbonated water (ouch!), or other. (&lt;em&gt;Noted: OP added that the liquid is hydrogen peroxide. This is not a good idea as it is an irritant and actually can cause mucosal damage.&lt;/em&gt;) Sufficient pressure and clot formation (and subsequent tenderness with the nose) is all that is needed.*&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What doesn't work: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;icepacks to the neck&lt;/li&gt;&#xA;&lt;li&gt;leaning your head forward (increases blood flow) or back (may cause the blood to flow into your throat)&lt;/li&gt;&#xA;&lt;li&gt;lying down (increases blood flow)&lt;/li&gt;&#xA;&lt;li&gt;frequent 'peeking' to see if bleeding has stopped&lt;/li&gt;&#xA;&lt;li&gt;a dry object placed against the area of bleeding (it will break up the clot when pulled away from the septum)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Aftercare and prevention is another subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: The safest way to end a common nosebleed is by squeezing as much of the 'rubbery' portion of the nose together for up to 30 minutes if necessary. Putting something into your nose poses the risk of infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*more serious or recurrent bleeding needs medical attention&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-02-22T22:13:45.133" LastActivityDate="2015-02-22T22:13:45.133" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29826" PostTypeId="2" ParentId="29823" CreationDate="2015-02-22T22:11:30.447" Score="1" Body="&lt;p&gt;Hydrogen peroxide, very potent oxidant, is used in case of skin cutting, small wounds etc. I think, firstly, It helps by killing bacteria that might otherwise cause infection. I couldn't find evidence of hydrogen peroxide promoting clot formation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, being an oxidative agent, H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; might be very harmful to gentle epithelium of nose. Theoretically, it can destroy it by chemical burns. Imagine pouring acid into your throat or intestines, it will definitely not be good.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You don't find information on applicating of H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; to bleeding noses because it is very harmful in first place.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="3340" LastEditDate="2015-02-23T08:46:55.687" LastActivityDate="2015-02-23T08:46:55.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29827" PostTypeId="2" ParentId="28584" CreationDate="2015-02-22T23:45:38.117" Score="-1" Body="&lt;p&gt;Since chemical reactions are governed by quantum physics, there is a whole lot of products that can come out of mixing together several multi-atom molecules. And all of those will have non-zero probability of occurrence. But this probability is extremely low at normal temperatures, so you don't see those products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Enzymes lower activation energy and so increase chance of reaction, but only for certain substances and products (spatial position of reagents can influence outcome). In case of DNA replication, when wrong nucleotide is inserted, it happens because enzyme/template nucleotide complex has not enough specificity. All 4 nucleotides have rather high chance of participating in the reaction (but errors are still on order of $10^{-6}$ and lower).&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-02-22T23:45:38.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29828" PostTypeId="1" CreationDate="2015-02-22T23:57:03.697" Score="6" ViewCount="476" Body="&lt;p&gt;I'm getting started using ECG using a 3 lead system by iWorx. I have place the leads on my two wrists and the ground on my ankle and have recorded some data into the provided LabScribe 3 software using the ECG template. Can anyone help me interpret what I'm seeing?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6pyJa.png&quot; alt=&quot;ECG Recording&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It doesn't look like the standard QRS I see in my textbook, but it's so regular (this is just a snippet) that I don't believe I'm seeing artifacts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any insight would be greatly appreciated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="14589" LastEditorDisplayName="user14640" LastEditDate="2015-02-28T18:58:25.577" LastActivityDate="2017-06-06T18:42:44.050" Title="Normal ECG/EKG Measurement?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;lab-techniques&gt;&lt;electrocardiography&gt;&lt;human-physiology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="29832" PostTypeId="1" CreationDate="2015-02-23T03:23:22.453" Score="3" ViewCount="1635" Body="&lt;p&gt;The wikipedia definition of Absolute fitness is &quot;the ratio between the number of individuals with that genotype after selection to those before selection. It is calculated for a single generation and must be calculated from absolute numbers.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But in one generation there are no reproductive events so it should be theoretically impossible for the population to be larger after the selection event than before it (since no reproduction is taking place).&lt;/p&gt;&#xA;" OwnerUserId="14591" LastEditorUserId="3624" LastEditDate="2015-02-23T10:20:20.840" LastActivityDate="2017-08-16T15:43:12.033" Title="How is it possible for the absolute fitness to be more than 1?" Tags="&lt;evolution&gt;&lt;population-genetics&gt;&lt;quantitative-genetics&gt;&lt;fitness&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29833" PostTypeId="1" CreationDate="2015-02-23T03:30:49.447" Score="3" ViewCount="4912" Body="&lt;p&gt;My whole family tree up to my grandparents have brown eyes,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have blue eyes, how come?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know if it matters but I have not received enough oxygen at birth, doctors said it's probably the reason I'm left handed while my most of my family is right handed&lt;/p&gt;&#xA;" OwnerUserId="14592" LastEditorUserId="14592" LastEditDate="2015-02-23T03:36:24.217" LastActivityDate="2020-05-14T07:22:13.853" Title="How come all my family have brown eyes and I have blue eyes?" Tags="&lt;eyes&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29834" PostTypeId="2" ParentId="29812" CreationDate="2015-02-23T03:40:27.643" Score="0" Body="&lt;p&gt;The basic struture of the metabolic networks  (MN) is like this:&#xA;molecule1 -&gt; molecule2, where the edges are enzymes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And the basic structure of the PPIN is like this:&#xA;Protein1 - Protein2, where the edges are van der Waals forces between proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some diferences, PPIN isnt directional and  MN is directional in the way of the spontaneous reaction. PPIN has two modes of interaction date interactions (1-1) and party interactions (many-many).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One easy way to combine both is to invert the MN so the enzymes are now the nodes and the metabolites are now the edges, like this: enzyme1 -&gt; enzyme2, and then add the proteins in the PPIN, like this: enzyme1(protein1) -&gt; enzyme(protein2). But in this way you need to demostrate that some properties of the network are conserved.&lt;/p&gt;&#xA;" OwnerUserId="14591" LastActivityDate="2015-02-23T03:40:27.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29836" PostTypeId="2" ParentId="29809" CreationDate="2015-02-23T03:51:11.793" Score="0" Body="&lt;p&gt;Its impossible to happend, why worried about it? Maybe you`re writing a fiction book. I cant answered using biological arguments because this is fiction.&lt;/p&gt;&#xA;" OwnerUserId="14591" LastActivityDate="2015-02-23T03:51:11.793" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29837" PostTypeId="1" AcceptedAnswerId="29840" CreationDate="2015-02-23T03:51:14.903" Score="4" ViewCount="10119" Body="&lt;p&gt;I know that point mutations can change the base sequence of a gene by altering a specific codon that codes for a particular amino acid. Are these mutations purely random events that occur when DNA is being copied into a cell? Furthermore, can environmental factors play a role in the amount of mutations that occur?&lt;/p&gt;&#xA;" OwnerUserId="14574" LastActivityDate="2016-11-21T17:09:50.947" Title="What are the major causes of mutations in DNA?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29838" PostTypeId="2" ParentId="29832" CreationDate="2015-02-23T03:52:55.513" Score="3" Body="&lt;p&gt;That &lt;a href=&quot;http://en.wikipedia.org/wiki/Fitness_%28biology%29#Absolute_fitness&quot; rel=&quot;nofollow&quot;&gt;definition&lt;/a&gt; in the wikipedia is misleading at best. Contrary to what it seems to suggest there, absolute fitness is computed &lt;em&gt;across&lt;/em&gt; a single generation, not &lt;em&gt;within&lt;/em&gt; a single generation. For simplicity, let's look at an example using asexual haploids with discrete non-overlapping generations. If individuals with the A genotype produce an average of 3 offspring, each of which survive with probability 0.5, the A genotype has an absolute fitness of 1.5. The key is that we've multiplied fecundity (3) by viability (0.5) and this allows us to obtain a value greater than 1. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Things get more complicated if we look at diploid sexuals. The absolute fitness of the Aa genotype is &lt;strong&gt;not&lt;/strong&gt; the ratio of the number of individuals with the Aa genotype at time t+1 to the number of Aa at time t. An easy way to see this: in a population of AA and aa parents only, e.g. as produced by a cross, the ratio of Aa at t+1 to Aa at t is infinite, which would imply infinite fitness if we went this with definition. Rather, the absolute fitness of the Aa genotype is one-half the number of surviving offspring at time t+1 produced by Aa parents at time t. The one-half comes from the fact that a parent individual contributes only one-half of the genetic material of each surviving offspring. For some traits, e.g. those involved in sex ratio determination or parental care, it will not be sufficient to count surviving offspring; in these cases we apply comparable logic to counting grand-offspring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The wikipedia seems to suggest we are to look only at viability because we are comparing before-selection numbers to after-selection numbers, within a single generation and thus without an opportunity for fecundity to come into play. That is not consistent with the common usage of the term. To be fair, I have on rare occasion seen &quot;absolute fitness&quot; used as a synonym for &quot;viability&quot;--though I cannot think of any good justification for this usage. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="13072" LastEditDate="2015-02-23T04:05:10.423" LastActivityDate="2015-02-23T04:05:10.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29839" PostTypeId="2" ParentId="29832" CreationDate="2015-02-23T03:58:33.880" Score="0" Body="&lt;p&gt;Welcome to Biology.SE!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Definition of Absolute Fitness&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's forget about the wikipedia definition for a little while. There exists different definitions of fitness. They vary only slightly and usually it does not really matter. Let's talk only about absolute fitness at first. Absolute fitness can be calculated&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;for a genotype&lt;/li&gt;&#xA;&lt;li&gt;for a haplotype&lt;/li&gt;&#xA;&lt;li&gt;for an individual&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;fitness can be calculated for&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;for a given period of the lifetime of an individual&lt;/li&gt;&#xA;&lt;li&gt;for the whole life of an individual.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Also, absolute fitness can be calculated in function of &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the number of offsprings&lt;/li&gt;&#xA;&lt;li&gt;the number of offsprings that survive at a given age (typically age of sexual maturity), that is the number of offsrping after selection on survival.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Very often, when talking about theoretical concepts, we consider exclusively for semelparous species (species that have only one reproductive event and then die like some salmon species for example). In such case, when talking about one generation, we think of a population of adults that gets entirely replaced by a new population of offspring. Thinking about semelparous species has the advantage (among other advantages) to avoid confusion about lifetime reproductive success versus rate at which offsprings are produced. So, yes in one generation there is reproductive events. Even if selection on survival hasn't yet occurred on the offsrpings of the parents in a given generation, the fitness of these parents during this generation is calculated in function of the number of offspring that will survive later. Hope that makes sense. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Relating the above definition to your question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, let's relate the above to the wikipedia definition. Absolute fitness is NOT &quot;the ratio between the number of individuals with that genotype after selection to those before selection&quot;. It is only the number of offsrpings produced by an individual for a given period (often the whole life of the individual. It can eventually be the number of offsprings that survive to a given age (selection on survival). Wikipedia seems to be wrong unless it has been misquoted. You should indicate where you read that so that one can correct wiki if there is indeed an error.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Relative Fitness&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, relative fitness of a genotype/haplotype/individual for a given period of time (eventually the whole life of the individuals of interest) is just the absolute fitness of the individuals of interest divided by a standard absolute fitness. This standard absolute fitness is either the maximal absolute fitness observed in the population (or metapopulation) of interest or the maximum theoretical fitness based on some assumptions. For example we may calculate the relative fitness of an individual by dividing the absolute fitness of this individual by the fitness of a theoretical individual that would carry only the best possible mutations even though this individual doesn't exist in the population.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-02-24T16:44:20.380" LastActivityDate="2015-02-24T16:44:20.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29840" PostTypeId="2" ParentId="29837" CreationDate="2015-02-23T05:42:03.237" Score="8" Body="&lt;p&gt;Welcome to Biology.SE!&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;can environmental factors play a role in the amount of mutations that occur?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes! The environmental factors that increase the mutation rate are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Mutagen&quot; rel=&quot;nofollow noreferrer&quot;&gt;mutagens&lt;/a&gt;. You will definitely want to have a look in the wikipedia article. You may also want to read the wikipedia page on &lt;a href=&quot;http://en.wikipedia.org/wiki/Mutagenesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;mutagenesis&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some chemicals increase the mutation rate, physical agents such as radiation also increase the mutation rate. There are viruses that are mutagens as well. Also, the number of mutations that an organism produce can also be phenotypically plastic. For example, plants have been shown to increase thee number of mutations they produced in response to stressing environment. The reason (or at least the commonly stated reason) is that they produce many mutations, &quot;hoping&quot; that at least one of the offsprings will carry a beneficial mutation and will be very fit even in this environment that is stressing for the parents. Many viruses and some bacteria also act as mutagens.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Are these mutations purely random events that occur when DNA is being copied into a cell?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Mutations are random in the sense that it is impossible to predict with certitude that a given mutation will occur at a given locus (locus=position in the genome). As a consequence, it is also true that mutations are random in the sense that it is impossible to predict the effect on the phenotype (and on the fitness) of a future mutation. Mutation rate varies throughout the genome. Typically, repeated DNA sequence tend to have higher mutation rate. Also, transposons causes many mutations and regions in the vicinity of transposons have higher mutation rate. But again, you should have a close look to the wikipedia pages I linked above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that a full answer would require going into the terminology of the term &quot;random&quot; which itself is a question of philosophy. When using the term random, it is always important to specify what is meant exactly (which is not done in the question) as one may argue that since the Big Bang happened everything has been deterministic.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2016-11-21T17:09:50.947" LastActivityDate="2016-11-21T17:09:50.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29842" PostTypeId="1" CreationDate="2015-02-23T10:05:08.907" Score="2" ViewCount="164" Body="&lt;p&gt;I would like to know why the recombinant protein with his tag at c terminus is not being detected neither in western blot or dot blot. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm trying to validate protein expression of four proteins. Three of the four proteins have no assigned protein family or domain (PFAM). The size of the proteins is small: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Locus   Nucleotide length   Protein size    Membrane features   Cloned  WB  Dot blot    Dot blot urea   COG&#xA;HPNK_06205  360 120 signal peptide  yes no  no  -   -&#xA;HPNK_09829  129 43  signal peptide  yes low low -   -&#xA;HPNK_10446  756 252 transmembrane   yes no  no  -   COG1175 ABC-type sugar transport systems, permease components&#xA;HPNK_11461  264 88  signal peptide  yes yes yes -   -&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Next steps:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-Discard possible his tag hidding by adding urea to dot blot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-Revise annotation for the proteins. Since all are annotated as hypothetical proteins, maybe there is an alternative annotation that could lead to longer proteins and maybe more stable products.&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="4717" LastEditDate="2015-02-23T10:11:12.493" LastActivityDate="2015-02-23T10:11:12.493" Title="Why HIS tag is not detected in WB or dot blot?" Tags="&lt;western-blot&gt;&lt;protein-expression&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29843" PostTypeId="2" ParentId="29832" CreationDate="2015-02-23T10:12:05.813" Score="1" Body="&lt;p&gt;That definition is problematic and incomplete. &lt;em&gt;Absolute fitness&lt;/em&gt; can be used in different ways, and can be calculated at different levels of organisation (individuals, genes etc). However, &lt;em&gt;absolute fitness&lt;/em&gt; always relate to actual growth rate, actual numbers of offspring or other measures of fitness (so an absolute measure), while &lt;em&gt;relative fitness&lt;/em&gt; is calculated as a fitness ratio in relation to a specific genotype (so a relative measure).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Absolute fitness&lt;/em&gt; is often defined in terms of the per capita growth rate of a genotype (or the intrinsic rate of increase (&lt;em&gt;r&lt;/em&gt;) for e.g. bacterial clones), which can clearly be above or below one. However, how to measure this is another thing, and this is where many different metrics are used. In quantitative genetics and life history evolution it is common to use the net reproductive rate (R&lt;sub&gt;0&lt;/sub&gt;) derived from the &lt;a href=&quot;https://books.google.se/books?id=N3JPEm5g7oQC&amp;amp;pg=PA99#v=onepage&amp;amp;q&amp;amp;f=falsehttp://en.wikipedia.org/wiki/Euler%E2%80%93Lotka_equation&quot; rel=&quot;nofollow&quot;&gt;characteristic equation&lt;/a&gt; as a measure of fitness. However, sometimes the number of offspring or other measures are used as proxies for absolute fitness (as fitness components). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The definition of fitness is a tricky subject, and what to use depends on exactly what type of organism you are studying. The Wikipedia definition is clearly inadequate, and I feel that the formulation &quot;&lt;em&gt;...is calculated for a single generation...&lt;/em&gt;&quot; is a direct mistake. The section &quot;Measures of fitness&quot; in &lt;a href=&quot;https://books.google.se/books?id=N3JPEm5g7oQC&amp;amp;pg=PA36#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot; title=&quot;Roff. 1992. Evolution Of Life Histories: Theory and Analysis. Springer&quot;&gt;Roff (1992)&lt;/a&gt; and &lt;a href=&quot;http://www.zoology.ubc.ca/~otto/reprints/Day2001.pdf&quot; rel=&quot;nofollow&quot; title=&quot;Day &amp;amp; Otto. 2001. Fitness. In: Encylopedia of Life Sciences. MacMillan Publishing&quot;&gt;Day &amp;amp; Otto (2001)&lt;/a&gt; (chapter on fitness from the Encylopedia of Life Sciences) are both very useful to read to better understand different measures of fitness.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-02-25T08:15:56.977" LastActivityDate="2015-02-25T08:15:56.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29844" PostTypeId="2" ParentId="29766" CreationDate="2015-02-23T11:51:29.713" Score="1" Body="&lt;p&gt;In my view there is direct link between probability of recombination and size of the insert. Smaller inserts with larger flanks get incorporated easier. That I understand from reviewing studies based on Cas9/CRISPRs system. Same should stand for HR-mutagenesis in yeast.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, short answer will be: shorter inserts are more efficient. However, I couldn't find any studies of relation between recombination efficiency and using smaller than target inserts, or relation between sizes of target and insert. Cas9/CRISPR system &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25263330&quot; rel=&quot;nofollow&quot;&gt;was used&lt;/a&gt; to insert loxP site (34nt) instead of ~10 bp in mice ES cells. People usually try to insert GFP or something similar in size instead of shorter genomic sequences.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-02-23T11:51:29.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29846" PostTypeId="1" CreationDate="2015-02-23T14:23:04.470" Score="9" ViewCount="11465" Body="&lt;p&gt;It seems at first glance that it would be an evolutionary disadvantage for a sea creature to have to come up to the surface on a regular basis in order to breathe, so why are there animals (e.g. whales and dolphins) which still need to do so?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is some advantage to breathing from the air instead of using gills, why haven't animals such as sharks (or indeed fish in general) evolved to do this instead?&lt;/p&gt;&#xA;" OwnerUserId="14562" LastActivityDate="2018-04-20T03:27:33.333" Title="Why have whales and dolphins not evolved to have gills?" Tags="&lt;evolution&gt;&lt;mammals&gt;&lt;ichthyology&gt;&lt;breathing&gt;" AnswerCount="3" CommentCount="12" ClosedDate="2018-04-20T20:17:31.847" ContentLicense="CC BY-SA 3.0" />
  <row Id="29847" PostTypeId="1" CreationDate="2015-02-23T15:03:01.300" Score="1" ViewCount="78" Body="&lt;p&gt;I am trying to align a sequence to the mouse genome. I know a priori that &lt;em&gt;part&lt;/em&gt; of my sequence should align to chromosome 9, but not all of it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I gathered that EMBOSS' &lt;code&gt;matcher&lt;/code&gt; and &lt;code&gt;supermatcher&lt;/code&gt; would be adequate tools to do this locally on my machine - with supermatcher being (a lot!) faster and matcher being (allegedly) more accurate. Strangely enough, the two functions give me very similar fits (quality-wise) which are however at non-identical but very close positions. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;How can I explain this? &lt;/li&gt;&#xA;&lt;li&gt;What are the odds that an ~800-bp sequence has multiple equally good fits right next to each other (how can I test if I hit a repeat-heavy area?)?&lt;/li&gt;&#xA;&lt;li&gt;Why do &lt;code&gt;match&lt;/code&gt; and &lt;code&gt;supermatch&lt;/code&gt; not give me both fits then?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My current alignments:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;#=======================================&#xA;#&#xA;# Aligned_sequences: 2&#xA;# 1: &#xA;# 2: CM001002.2&#xA;# Matrix: EDNAFULL&#xA;# Gap_penalty: 16.0&#xA;# Extend_penalty: 4.0&#xA;#&#xA;# Length: 357&#xA;# Identity:     322/357 (90.2%)&#xA;# Similarity:   322/357 (90.2%)&#xA;# Gaps:           2/357 ( 0.6%)&#xA;# Score: 1458.0&#xA;# &#xA;#&#xA;#=======================================&#xA;&#xA;                   1 AAAAACGTGAAAAATGAGAAATGCACACTGTAGGACCTGAAATATGGCAA     50&#xA;                     ||||.|..|.||||||||||||.||||||.||||||.|||||.|||||.|&#xA;CM001002.2    35305253 AAAATCACGGAAAATGAGAAATACACACTTTAGGACGTGAAAAATGGCGA 35305302&#xA;&#xA;                  51 GGAAAACTGAAAAAGGTGGAAAATTTAGAAATGTCCACTATAGGACGTGG    100&#xA;                     ||||||||||||||||||||||||||||||||||||.||.||||||.|||&#xA;CM001002.2    35305303 GGAAAACTGAAAAAGGTGGAAAATTTAGAAATGTCCTCTGTAGGACATGG 35305352&#xA;&#xA;                 101 AATATGGCAAGAAAAATGAAAATCATTGAAAATGAGAAACATACAGTTGA    150&#xA;                     |||||||||||||||.||||||||||.|||||||||||||||.||.||||&#xA;CM001002.2    35305353 AATATGGCAAGAAAACTGAAAATCATGGAAAATGAGAAACATCCACTTGA 35305402&#xA;&#xA;                 151 CGACTTGAAAAATGATGAAATCACTGAAAAACGTGAAAAATGAGAAATGC    200&#xA;                     .||||||||||||||.|||||||.|.||||||||||||||||||||||||&#xA;CM001002.2    35305403 TGACTTGAAAAATGACGAAATCATTAAAAAACGTGAAAAATGAGAAATGC 35305452&#xA;&#xA;                 201 ACCCTGTAAGACCTGGAATATGTCGAGAAAACTGAAAATCACGGAAAATG    250&#xA;                     .|.|||.|.|||||||||||||..||||||||||||||||||||||||||&#xA;CM001002.2    35305453 CCACTGAAGGACCTGGAATATGGGGAGAAAACTGAAAATCACGGAAAATG 35305502&#xA;&#xA;                 251 AGAAATACACACTTTAGGACGTGAAATATGGCGAGGAAAACTGAAAAAGG    300&#xA;                     ||||||||||||||||||||||||||||||||||||||||||||||||||&#xA;CM001002.2    35305503 AGAAATACACACTTTAGGACGTGAAATATGGCGAGGAAAACTGAAAAAGG 35305552&#xA;&#xA;                 301 TGGAAAATTTAGAAATGTCCACTGTAGGACATGGAATAT--GGCAAGAAA    348&#xA;                     |||||.||||||||||||||||||||||||.||||||||  |.|.|||||&#xA;CM001002.2    35305553 TGGAATATTTAGAAATGTCCACTGTAGGACGTGGAATATAAGTCCAGAAA 35305602&#xA;&#xA;                 349 ACTGAAA    355&#xA;                     .||.|.|&#xA;CM001002.2    35305603 CCTAAGA 35305609&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;and:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;#=======================================&#xA;#&#xA;# Aligned_sequences: 2&#xA;# 1: &#xA;# 2: CM001002.2&#xA;# Matrix: EDNAFULL&#xA;# Gap_penalty: 16&#xA;# Extend_penalty: 4&#xA;#&#xA;# Length: 417&#xA;# Identity:     377/417 (90.4%)&#xA;# Similarity:   377/417 (90.4%)&#xA;# Gaps:           2/417 ( 0.5%)&#xA;# Score: 1713&#xA;# &#xA;#&#xA;#=======================================&#xA;&#xA;          180       190       200       210       220    &#xA;       TGAAAAACGTGAAAAATGAGAAATGCACCCTGTAAGACCTGGAATATGTC&#xA;       ::  : ::   : :: :  ::  ::::: ::: : ::::::::::    :&#xA;CM0010 TGTCACACACTATAATTTTGAGGTGCACACTGAAGGACCTGGAATTATGC&#xA;       35305200  35305210  35305220  35305230  35305240  &#xA;&#xA;          230       240       250       260       270    &#xA;       GAGAAAACTGAAAATCACGGAAAATGAGAAATACACACTTTAGGACGTGA&#xA;       ::::::::::::::::::::::::::::::::::::::::::::::::::&#xA;CM0010 GAGAAAACTGAAAATCACGGAAAATGAGAAATACACACTTTAGGACGTGA&#xA;       35305250  35305260  35305270  35305280  35305290  &#xA;&#xA;          280       290       300       310       320    &#xA;       AATATGGCGAGGAAAACTGAAAAAGGTGGAAAATTTAGAAATGTCCACTG&#xA;       :: ::::::::::::::::::::::::::::::::::::::::::: :::&#xA;CM0010 AAAATGGCGAGGAAAACTGAAAAAGGTGGAAAATTTAGAAATGTCCTCTG&#xA;       35305300  35305310  35305320  35305330  35305340  &#xA;&#xA;          330       340       350       360       370    &#xA;       TAGGACATGGAATATGGCAAGAAAACTGAAAATCATGGAAAATGAGAAAC&#xA;       ::::::::::::::::::::::::::::::::::::::::::::::::::&#xA;CM0010 TAGGACATGGAATATGGCAAGAAAACTGAAAATCATGGAAAATGAGAAAC&#xA;       35305350  35305360  35305370  35305380  35305390  &#xA;&#xA;          380       390       400       410       420    &#xA;       ATCCACTTGACGACGTGAAAAATGACGAAATCACTGAAAAACGTGAAAAA&#xA;       :::::::::: ::: :::::::::::::::::: : ::::::::::::::&#xA;CM0010 ATCCACTTGATGACTTGAAAAATGACGAAATCATTAAAAAACGTGAAAAA&#xA;       35305400  35305410  35305420  35305430  35305440  &#xA;&#xA;          430       440       450       460       470    &#xA;       TGAGAAATGCACACTGTAGGACCTGGAATATGTCGAGAAAACTGAAAATC&#xA;       :::::::::: ::::: :::::::::::::::  ::::::::::::::::&#xA;CM0010 TGAGAAATGCCCACTGAAGGACCTGGAATATGGGGAGAAAACTGAAAATC&#xA;       35305450  35305460  35305470  35305480  35305490  &#xA;&#xA;          480       490       500       510       520    &#xA;       ACGGAAAATGAGAAATACACACTTTAGGACGTGAAATATGGCGAGGAAAA&#xA;       ::::::::::::::::::::::::::::::::::::::::::::::::::&#xA;CM0010 ACGGAAAATGAGAAATACACACTTTAGGACGTGAAATATGGCGAGGAAAA&#xA;       35305500  35305510  35305520  35305530  35305540  &#xA;&#xA;          530       540       550       560       570    &#xA;       CTGAAAAAGTTGGAAAATTTAGAAATGTCCATTGTAGGACATGGAATAT-&#xA;       ::::::::: ::::: ::::::::::::::: :::::::: :::::::: &#xA;CM0010 CTGAAAAAGGTGGAATATTTAGAAATGTCCACTGTAGGACGTGGAATATA&#xA;       35305550  35305560  35305570  35305580  35305590  &#xA;&#xA;            580         &#xA;       -GGCAAGAAAACTGAAA&#xA;        : : ::::: :: : :&#xA;CM0010 AGTCCAGAAACCTAAGA&#xA;       35305600  &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="4795" LastActivityDate="2015-02-23T15:03:01.300" Title="EMBOSS matcher and supermatcher - incongruent results?" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;genomics&gt;&lt;sequence-alignment&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29848" PostTypeId="1" AcceptedAnswerId="29856" CreationDate="2015-02-23T15:40:59.403" Score="1" ViewCount="51" Body="&lt;p&gt;This question is about substances such as insulin and some vitamins that the human body is able to produce on its own.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some substances that are produced by the body are also present in various body building supplements.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I wanted to ask is, is there evidence that ingesting these types of substances for prolonged period leads to (permanent?) withering of the organs that produce the substance?&lt;/p&gt;&#xA;" OwnerUserId="12939" LastActivityDate="2015-02-23T20:03:01.153" Title="Can ingesting substances that are produced by the body cause a permanent withering of the organs that produce the substance?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29850" PostTypeId="2" ParentId="29804" CreationDate="2015-02-23T15:54:03.250" Score="-1" Body="&lt;p&gt;I found a &lt;a href=&quot;http://www.forensicpathologyonline.com/e-book/post-mortem-changes/putrefaction&quot; rel=&quot;nofollow&quot;&gt;forensic article&lt;/a&gt; that states the following:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because the protective agencies of the body are absent, the bacteria spread through the blood vessels using the proteins and carbohydrates of the blood as culture media.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I was unable to find anything more on this with my limited searching skill, though I plied it to the best.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There was &lt;a href=&quot;https://www.google.co.in/url?sa=t&amp;amp;source=web&amp;amp;rct=j&amp;amp;ei=zkXrVNbaGdOHuASxgoKgCg&amp;amp;url=http://ajph.aphapublications.org/doi/pdf/10.2105/AJPH.14.11.946&amp;amp;ved=0CCQQFjAC&amp;amp;usg=AFQjCNFRYw_gxU6w83Gxg1jZRMTFQ53c4g&quot; rel=&quot;nofollow&quot;&gt;an interesting study&lt;/a&gt; on the relation between decompostion of animal meat and the bacterial load though. It was a good read!&lt;/p&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-02-23T15:54:03.250" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29851" PostTypeId="1" AcceptedAnswerId="29858" CreationDate="2015-02-23T16:35:17.180" Score="1" ViewCount="4000" Body="&lt;p&gt;What percentage of human body's cells are contained in blood vs. the rest of the body?&lt;/p&gt;&#xA;" OwnerUserId="185" LastActivityDate="2015-07-30T04:25:56.193" Title="What percentage of human body's cells are contained in blood?" Tags="&lt;human-biology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29852" PostTypeId="2" ParentId="29833" CreationDate="2015-02-23T17:47:46.883" Score="2" Body="&lt;p&gt;The eye color follow quite well mendelian inheritance rules...&#xA;Probably your parents are heterozygote recessive for the blue color, hence the children have 25% of probability of having blue eyes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say color of the eyes has 2 alleles &quot;BLACK&quot; for the dark eyes and &quot;blue&quot; for the light eyes. Your parents are probably both BLACK-blue, BLACK-blue. They show the dark eyes because that allele is dominant over the blue one.&#xA;During recombination all the possible combination can come out:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;BLACK x BLACK=25% resulting color=dark &lt;/li&gt;&#xA;&lt;li&gt;BLACK x blue=25% resulting color=dark&lt;/li&gt;&#xA;&lt;li&gt;blue x BLACK=25% resulting color=dark &lt;/li&gt;&#xA;&lt;li&gt;blue x blue=25% resulting color=light&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Check out the wiki page about mendelian rules of inheritance if you wanna know more!!&#xA;Of course in realty the situation is much more complicated, however you can still approximate the results to mendelian rules...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;have fun!!&lt;/p&gt;&#xA;" OwnerUserId="9333" LastActivityDate="2015-02-23T17:47:46.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29853" PostTypeId="1" AcceptedAnswerId="29892" CreationDate="2015-02-23T19:13:31.143" Score="4" ViewCount="224" Body="&lt;p&gt;Is there any one DNA sequence shared by all or most viruses? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I highly doubt there is mainly because of how different all of them are, but it's still worth a try.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-02-24T16:48:34.307" Title="Are there any DNA sequences shared by all/most Viruses?" Tags="&lt;virology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="29854" PostTypeId="1" AcceptedAnswerId="29873" CreationDate="2015-02-23T19:47:05.727" Score="3" ViewCount="1691" Body="&lt;p&gt;I have recently completed a study on Brent Goose. I found that Brent Geese occupy high quality habitat first then once this is full of geese, they fill up low quality habitat. However, there were always fewer geese in the low quality habitat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This pattern therefore seems like a good match for the ideal free distribution…but is it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under the ideal free distribution, do birds fill up high quality first, then low quality habitat second?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or do birds fill up both high and low quality habitats simultaneously, but fill up high quality at a faster rate?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or does the ideal free distribution not make explicit the order/rate at which birds fill up high and low quality habitats?&lt;/p&gt;&#xA;" OwnerUserId="1216" LastActivityDate="2016-01-20T13:52:56.803" Title="How does the ideal free distribution work?" Tags="&lt;ecology&gt;&lt;ornithology&gt;&lt;behaviour&gt;&lt;species-distribution&gt;&lt;habitat&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29855" PostTypeId="2" ParentId="29848" CreationDate="2015-02-23T19:49:45.213" Score="2" Body="&lt;p&gt;Mostly no. For example, if a non-diabetic person were to be injected with a small amount of insulin, the pancreas would halt its own production of insulin and, if the dose was too large, begin producing glucagon, which stimulates the liver to produce more glucose to match the dose of insulin. If these periodic doses continue, the size of the islets in the pancreas may decrease, but it is always reversible and the beta cell count may return to normal if the doses cease, although it should be noted that a short period of &quot;withdrawal&quot; may occur. The intensity of this withdrawal will depend on how long the supplement was used and what the supplement is.&lt;/p&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="13496" LastEditDate="2015-02-23T19:58:52.047" LastActivityDate="2015-02-23T19:58:52.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29856" PostTypeId="2" ParentId="29848" CreationDate="2015-02-23T20:03:01.153" Score="3" Body="&lt;p&gt;Yes it is possible but in most cases it will not occur as the body simply halts production. The most infamous manifestation of this is in adrenal insufficiency. That's where when we take glucocorticoids (e.g. prednisolone used in management of lots of inflammatory diseases like asthma and autoimmune diseases) for a prolonged period at high dose. This causes the adrenal glands to atrophy (physically shrink) and following this sudden withdrawal can be dangerous for a patient. That's why we always slowly withdraw steroids when a patient has been on them for a long period of time. &lt;/p&gt;&#xA;" OwnerUserId="1757" LastActivityDate="2015-02-23T20:03:01.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29857" PostTypeId="1" AcceptedAnswerId="29864" CreationDate="2015-02-23T20:44:38.373" Score="6" ViewCount="22506" Body="&lt;p&gt;Since as long as I have been doing cell culture, the word confluency has been used to describe the percentage growth of cells or area covered by them. However, no dictionary that I have found uses this word. I was wondering if anyone could reliably state where the meaning comes from or how the association began, and truly what it means. I don't believe I can post this on another Stack Exchange  because the word doesn't have even a resembling meaning in the dictionary. Cell culture is such an integral part of cell biology, medical research and biological manufacturing. And this term is an integral part of cell culture. I was surprised to be unable to reliably verify its meaning.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="22057" LastEditDate="2020-04-19T18:06:20.613" LastActivityDate="2020-05-06T22:34:06.570" Title="Origin of term ‘confluency’ in cell culture" Tags="&lt;terminology&gt;&lt;cell-culture&gt;&lt;etymology&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="29858" PostTypeId="2" ParentId="29851" CreationDate="2015-02-23T20:58:57.397" Score="3" Body="&lt;p&gt;The human body has about $3.72 × 10^{13}$ cells according to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23829164&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bianconi et al. 2013&lt;/a&gt;, although this &lt;a href=&quot;https://biology.stackexchange.com/questions/3327/how-many-human-cells-are-there-in-our-body-on-average&quot;&gt;is disputed&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also has about 5 liters of blood, which is made approximately 40-45% of erythrocytes. Let's assume 2.5 liters = 2500 $cm^3$ of red blood cells (RBC). Assuming a mean value of 5 millions RBC per $mm^3$ there should be in total $5 \cdot 10^6 \cdot 10^3 \cdot 2500 = 7.5 \cdot 10^{12}$ RBC.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By completely taking out white blood cells and thrombocytes out of the equation, a number of ${7.5 \over {3.72 \cdot 10}} \cdot 100 = 20 \%$ of &lt;strong&gt;number of cells&lt;/strong&gt; are contained in the blood (approximately).&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-02-23T21:09:41.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29859" PostTypeId="2" ParentId="29851" CreationDate="2015-02-23T20:59:55.030" Score="1" Body="&lt;p&gt;Given the hypothetical 70 kg man, let him be separated into components:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Blood&lt;/strong&gt;: 7% (70 kg x .07 = 4.9 kg)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of that, 60% is plasma, so (4.9 kg x .4 = 1.96 kg blood cell weight.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore of a 70 kg male, ~ 2 kg is blood cells&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Tissue and bone&lt;/strong&gt;: 93% of body weight (70 kg x .93 = 65kg)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of that, 27% is extracellular fluid, so (65 kg x .73 = ~ 47.5 kg cell weight)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But we need to subtract the weight of bones:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dry bone weight = ~6.5% total body weight, (70 kg x .065 = 4.55 kg bone weight)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, cell weight minus extracellular fluid:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Blood cells: 2 kg&#xA;Body cells (minus bone weight): 43 kg&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2kg/(43kg + 2 kg) = 4.4% of the weight of cells in the body are the blood cells.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-02-23T20:59:55.030" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29860" PostTypeId="2" ParentId="29853" CreationDate="2015-02-23T21:15:12.617" Score="4" Body="&lt;p&gt;No, virus are polyphyletic and there are no genes that are common to all viruses. There may be similarities in capsid structure due to convergent evolution, but these are not universal. See &lt;a href=&quot;http://www.nature.com/nrmicro/journal/v7/n4/full/nrmicro2108.html&quot; rel=&quot;nofollow&quot;&gt;Moreira and López-García (2009)&lt;/a&gt; for further detail. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-02-23T21:15:12.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29861" PostTypeId="2" ParentId="29846" CreationDate="2015-02-23T21:19:52.940" Score="3" Body="&lt;p&gt;I think you're looking at this the wrong way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Animals evolve to fill &lt;a href=&quot;http://evolution.about.com/od/Evolution-Glossary/a/What-Is-A-Niche.htm&quot; rel=&quot;nofollow&quot;&gt;niches&lt;/a&gt;. Many, many land animals returned to the water as a place to live, including:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;whales, dolphins, porpoises, seals, sea lions, walruses, manatees, dugongs, otters, hippos, pygmy hippos, crocodiles, sea snakes, sea turtles, river turtles, river snakes, etc. etc. etc.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Their success in this environment points to no need whatsoever to &quot;evolve&quot; gills to be better suited. Without the interference of man, there would be yet many more of them.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-02-23T21:19:52.940" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29863" PostTypeId="2" ParentId="29857" CreationDate="2015-02-23T21:40:50.223" Score="3" Body="&lt;p&gt;con- (com-) is prefix that usually means &quot;togetherness&quot;, joining. Root fluency/fluent comes from latin &lt;em&gt;fluere&lt;/em&gt;, to flow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: Google's definitions for &lt;a href=&quot;https://www.google.com/search?q=con-%20definition&amp;amp;oq=con-%20definition&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;con-&lt;/em&gt;&lt;/a&gt; and &lt;a href=&quot;https://www.google.com/search?q=con-%20definition&amp;amp;oq=fluency%20definition&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;fluency&lt;/em&gt;&lt;/a&gt; (information scraped from &lt;a href=&quot;https://www.lexico.com/about&quot; rel=&quot;nofollow noreferrer&quot;&gt;OUP&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="42780" LastEditDate="2020-04-19T23:21:52.920" LastActivityDate="2020-04-19T23:21:52.920" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="29864" PostTypeId="2" ParentId="29857" CreationDate="2015-02-23T22:03:50.913" Score="8" Body="&lt;p&gt;Besides the etymologic explanation that @aandreev gave, in cell culture this term is commonly used to describe the density of adherent cells and it is used as a measure of their proliferation. It is usually combined with an estimated (or counted) percentage, so 10% confluency means that 10% of the surface the dish or flask used is covered with cells, 100% means that it is entirely covered. The cells grow twodimensional on the surface of the flask in this case. The picture below (from &lt;a href=&quot;https://www.mirusbio.com/transfectopedia/methods&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;) illustrates different levels of confluency:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qUvoI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The level of confluency is important as the cells change their growth with changing densities. Low density cells (10-20%) usually grow slower than 50% confluent cells. If the plate is complete grown by cells, they tend to grow much slower again. This influences their genetic program, behaviour in experiments and transfections.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As @Roland pointed out it is important to say that confluency is not a hard measure, but rather an estimate of the cell density. Different people will get different estimations, but the trend should be the same.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2016-04-04T10:14:00.783" LastActivityDate="2016-04-04T10:14:00.783" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="29865" PostTypeId="1" AcceptedAnswerId="29874" CreationDate="2015-02-23T23:45:59.980" Score="4" ViewCount="3474" Body="&lt;p&gt;If the brain uses extremely low voltage signals to communicate (from what I understand around 100 mV), what sort of breakthroughs would be necessary to intercept these signals and interpret them as exact thoughts? I know we interface with the brain's electrical field through already at a much higher level, but what is stopping us from being able to interpret it more precisely?&lt;/p&gt;&#xA;" OwnerUserId="13448" LastActivityDate="2016-12-24T16:28:19.320" Title="Is it possible to process electrical signals from the brain and interpret the results as exact thoughts?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;neurology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29867" PostTypeId="1" CreationDate="2015-02-24T03:10:32.613" Score="5" ViewCount="59" Body="&lt;p&gt;Can an oncoming stroke/seizure, be stopped by a setup consisting of a brain-computer-interface (BCI) that immediately detects the variation in wave-form, and then another machine that neutralizes the anomaly by sending a measured voltage to select areas of the brain OR by Transcranial Magnetic Stimulation?&lt;/p&gt;&#xA;" OwnerUserId="14608" LastEditorUserId="9943" LastEditDate="2015-02-24T09:59:37.643" LastActivityDate="2015-05-22T14:58:00.727" Title="Immediate stroke/seizure Therapy" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29868" PostTypeId="1" CreationDate="2015-02-24T04:49:26.370" Score="1" ViewCount="139" Body="&lt;p&gt;In order to determine whether a particular segment of the genome is a mutation, there must first be a baseline code on which that code looks somehow different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How has the baseline genome been determined? Did someone dig up a _very_old_ human skeleton which was subsequently DNA-analyzed to be used as the baseline?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or do mutations contain some kind of fingerprint that tells researchers that &quot;it is not the original genome&quot;? If so, how does that fingerprint look like?&lt;/p&gt;&#xA;" OwnerUserId="12939" LastEditorUserId="22057" LastEditDate="2016-03-23T01:46:41.693" LastActivityDate="2016-03-23T01:46:41.693" Title="What do we use as baseline to determine what genetic segments are &quot;mutations&quot; (and what are not)" Tags="&lt;human-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29869" PostTypeId="2" ParentId="28578" CreationDate="2015-02-24T05:41:03.077" Score="6" Body="&lt;p&gt;I found an interesting article that dealt with anxiety and micturition. There are no proven or accepted view on this. There are a few theories as to how this happens. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am quoting it:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There are several beliefs for what causes frequent urination from anxiety, and the likelihood is that all of these factors play a role:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Muscle Tension – This is one of the most likely causes of frequent urination. When you have anxiety, your muscles get very tense. This tension puts pressure on your bladder, which in turn makes you feel like you need to urinate more than you would otherwise.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Evolutionary Adaptation – Another theory is that there is an evolutionary reason that frequent urination would be advantageous. Remember, anxiety is the misfiring of your healthy fight/flight system. In times of fear, urination may keep the body lighter by losing extra weight, making it easier to flee.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Light Overload – It's also possible that, because anxiety is a misfiring of the fight/flight system, your body may simply be lightly overloaded. The fear is not intense enough to cause immediate urination, but it may make it harder for you to feel like you can hold it back.&#xA;  Also, those with anxiety are more prone to focusing on different sensations unintentionally. There are often times when you may feel the need to urinate slightly but your body has no problem ignoring the feeling and holding it back. With anxiety, it's possible that your brain is focused on the sensation, potentially causing you to feel like you need to urinate more than you do.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Finally, anxiety can also change your body chemistry, altering your digestion and changing the way you process nutrients. That may cause more water to pass through your body.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source:&lt;a href=&quot;http://www.calmclinic.com/anxiety/signs/urination-problems&quot; rel=&quot;nofollow&quot;&gt;http://www.calmclinic.com/anxiety/signs/urination-problems&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-02-24T15:26:05.167" LastActivityDate="2015-02-24T15:26:05.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29870" PostTypeId="2" ParentId="29868" CreationDate="2015-02-24T05:53:46.123" Score="1" Body="&lt;p&gt;It may help to think about the genealogy of the sequences in question. In general, we suppose that all DNA sequences from organisms are related by a set of processes. A particularly important process relating DNA sequences is &lt;strong&gt;replication&lt;/strong&gt;. This establishes a parent-child relationship between DNA sequences in one round of &lt;strong&gt;replication&lt;/strong&gt; or an ancestor-descendent relationship when we view more than one round of replication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For simplicity, consider a single bacterial cell, which replicates its genome and divides, yielding a descendent cell. This process continues for each cell and produces a population of cells over time. This population of cells (and their genomes) are related to each other by this process of replication and division. The structure of this relationship is a tree (in the mathematical sense). The vertices of the tree are the DNA sequences (or cells) and a directed edge from &lt;code&gt;vertex i&lt;/code&gt; to &lt;code&gt;vertex j&lt;/code&gt; exists if and only if the sequence represented by &lt;code&gt;vertex j&lt;/code&gt; is the result of a replication of the sequence represented by &lt;code&gt;vertex i&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to the replication process which makes this tree structure relating sequences, there are mutational processes that lead to sequence differences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many ways for mutations to arise before or during DNA replication. The important thing to note is that these mutations are passed on to descendants. So, a cell is either genetically identical to its parent cell, or it contains some number of mutations (insertions, deletions, or polymorphisms in the DNA) with respect to its parent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These mutations (sequence differences) are inherited during replication, and you can think of them as &quot;occurring&quot; along a given edge in the tree from a parent cell to a child cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, if you consider any two DNA sequences, as well as the model just given, these two sequences are related through the replication-mutation process (the tree). If the DNA sequences are not identical, you have many ways to interpret this question of what is a mutation. It is useful to consider the most recent common ancestor of the two DNA sequences in making sense of the differences observed in the DNA. If you think of the genealogy as a tree, and you're considering two vertices in the tree, then tracing backwards towards the root of the tree from each vertex, these traces will eventually meet at another vertex. The first vertex at which they meet is the most recent common ancestor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible that mutations have occurred along both paths from the (most recent) common ancestor to the descendent sequences you're investigating. If you're investigating N sequences, there are N paths from the common ancestor on which mutations may have occurred.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of this is to say that mutations occur with respect to this genealogical process. If you just consider 2, or N, sequences without regard to the process that generated them, then it can be meaningless or confusing to consider a particular sequence difference as a &lt;em&gt;mutation&lt;/em&gt; with respect to another sequence under consideration. For example, if you observe a single nucleotide polymorphism between two sequences, how would you know which sequence was the result of the mutation? It is possible that one or both sequences carries a mutation event in its genealogical history since the common ancestor of both sequences.&lt;/p&gt;&#xA;" OwnerUserId="14609" LastEditorUserId="14609" LastEditDate="2015-02-24T06:04:48.267" LastActivityDate="2015-02-24T06:04:48.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29871" PostTypeId="1" CreationDate="2015-02-24T06:03:05.750" Score="5" ViewCount="84" Body="&lt;p&gt;There are some carps which differ in colour, or has some easily noticeable morphological differences. But apart from that, most of the carps look &quot;almost&quot; the same. How does one differentiate one species from another?&#xA;Citing behavioral differences, differences in morphological characteristics (maybe subtle) and the likes which addresses this problem would be helpful. The characteristics with broader scope would be better.&lt;/p&gt;&#xA;" OwnerUserId="14500" LastEditorUserId="14500" LastEditDate="2017-05-01T21:04:02.663" LastActivityDate="2017-05-01T21:04:02.663" Title="How do similar looking carps, but belonging to different species, differ from each other?" Tags="&lt;species-identification&gt;&lt;ichthyology&gt;&lt;species&gt;" AnswerCount="0" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="29872" PostTypeId="1" CreationDate="2015-02-24T07:59:29.457" Score="1" ViewCount="50" Body="&lt;p&gt;Thiazide diuretics are on the World Anti Doping Agency's, as well as the International Olympic Committee, list of banned substances due to it ability to mask illegal substances in urine. The rapid expulsion of water from the body helps to achieve this. Additionally, with Thiazide diuretics blood levels decrease. The hair follicle is fed by blood, sweat, and sebum. Will the body's inability to retain or reabsorb water and decreased blood level prevent substances from being deposited into the hair cortex?&lt;/p&gt;&#xA;" OwnerUserId="14610" LastActivityDate="2015-02-24T07:59:29.457" Title="Does the use of a Thiazide diuretic affect the ability of a hair follicle to absorb substances?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;hair&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29873" PostTypeId="2" ParentId="29854" CreationDate="2015-02-24T09:20:51.760" Score="3" Body="&lt;p&gt;The order of settling depends on the resource availability in different patches (in your case the difference between high and low quality habitat), but generally speaking, the pattern you observe conforms to the &lt;em&gt;ideal free distribution&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key factor in the &lt;em&gt;ideal free distribution&lt;/em&gt; is that habitat patches are filled according to the current resource availablity (~per capita resource access), given the current density of individuals in the patch (so the marginal resource availability). If the high quality patch has much higher resource levels than the low quality patch, this means that many individuals can settle in the high quality patch before the marginal resource availability becomes equal to the resource availability in the low quality patch, at which point individuals will start settling in both patches. Therefore, the two observations you make; 1) lower overall density in low quality habitat and 2) the high quality patch being settled first, both agree with the &lt;em&gt;ideal free distribution&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This graph (from wikipedia.org) illustrates this pattern nicely, for the standard version of the &lt;em&gt;ideal free distribution&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7f7MH.jpg&quot; alt=&quot;Ideal free dist, from Wikipedia&quot;&gt;&lt;br&gt;&#xA;Here, the marginal, apparent value of a patch is shown on the y-axis and the number of individuals in the patch on the x-axis, and the numbers refer to the order that individuals will settle in the two patches (so the first 6 settle in the high-quality Patch B, ind. 7-9 in Patch A, ind. 10 in Patch B etc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I encourage you to read about other theories on habitat choice, and the pattern you describe can probably be explained by other processes as well. The &lt;em&gt;ideal free distribution&lt;/em&gt; also has some rather restrictive assumptions (e.g. equal quality of individuals and no dominance/territorial/interference behaviours among individuals), which you have have to consider.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2016-01-20T13:52:56.803" LastActivityDate="2016-01-20T13:52:56.803" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29874" PostTypeId="2" ParentId="29865" CreationDate="2015-02-24T10:15:38.820" Score="8" Body="&lt;p&gt;The brain activity is electric and chemical. The male adult human brain contains about 86 billion neurons (Azevedo et al). There is about 100 trillion connections between them. Solving a puzzle like that is not easy..&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;what sort of breakthroughs would be necessary to intercept these signals and interpret them as exact thoughts?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What you are referring to would be called &lt;em&gt;solving the neural code&lt;/em&gt; in neuroscience. With today's methods, it is probably not possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider electroencephalography (EEG). It records the electrical activity of the brain. Ag/AgCl sensors are placed along the scalp (typically 64-256 in research settings). When about 50,000 &lt;em&gt;parallel&lt;/em&gt; neurons fire &lt;em&gt;simultaneously&lt;/em&gt;, a change in a recorded signal can be seen. While the time resolution is about 1 ms for EEG, the spatial resolution is several centimeters (it is not easy to find which areas produced the recorded signals; it is an &lt;em&gt;inverse problem&lt;/em&gt;). A newer technique, called magnetoencephalography (MEG), is becoming more and more used but is expensive. It records the magnetic fields related to the electrical activity and allows better localization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there other complications? Well... lot's of them. Blink your eyes during the recording and there will be a major artefact masking the brain signals in most channels (10-100x greater in amplitude than the brain signals).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, you would probably be interested in the new research involving the use of machine learning techniques: it has been possible to decode the contents of dreams, reconstruct what a subject is seeing, etc. The best papers have been published by &lt;em&gt;Science&lt;/em&gt;, &lt;em&gt;Nature&lt;/em&gt;, and &lt;em&gt;PNAS&lt;/em&gt;, so using their search engines with the keywords &lt;em&gt;decoding&lt;/em&gt; and &lt;em&gt;brain&lt;/em&gt; should allow you to explore the topic easily.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS. I did not have time discuss fMRI; someone else can may be do that..&lt;/p&gt;&#xA;" OwnerUserId="14612" LastActivityDate="2015-02-24T10:15:38.820" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29875" PostTypeId="1" CreationDate="2015-02-24T10:36:00.450" Score="3" ViewCount="312" Body="&lt;p&gt;My main question is can we map what a fruit is made of? For instance apples are made of 0.0002% of protein X, 0.00001 of protein Y, 0.001% of amino acid Z... etc...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we can, then my next question would be why do people fear eating GMOs?&#xA;I understand the argument that if you introduce a new compound to your body you don't know its effect on you, but if for instance you insert a new gene into the plant where it is resistant to drought- can we not simply analyze its product and if its composition haven't changed than everything is alright?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you very much!&lt;/p&gt;&#xA;" OwnerUserId="14614" LastActivityDate="2015-02-24T11:44:40.277" Title="Why people fear GMOs? Can't we map a plant composition?" Tags="&lt;molecular-biology&gt;&lt;gene-expression&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29876" PostTypeId="2" ParentId="29875" CreationDate="2015-02-24T10:53:26.650" Score="1" Body="&lt;p&gt;People are not always rational when it comes to what they eat, especially when the compounds that make up the food have long, arcane-sounding names. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is indeed possible to analyse the amino acid composition of a food substance. However, this has no bearing whatsoever on the safety of the food product. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, the following are two truncated protein sequences. One of them is a fragment constituent of cobra venom, the other is a fragment of harmless DNA polymerase. Without looking up or otherwise referring to the PDB IDs, it is not obvious which is which, even to an experienced molecular biologist. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;3HRZ:A|PDBID|CHAIN|SEQUENCE&#xA;  ALYTLITPAVLRTDTEEQILVEAHGDSTPKQLDIFVHDFPRKQKTLFQTRVDMNPAGGMLVTPTIEIPAKEVSTDSRQNQ&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;1KLN:A|PDBID|CHAIN|SEQUENCE&#xA;  VISYDNYVTILDEETLKAWIAKLEKAPVFAFATETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALE&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Furthermore, even if scientists can prove beyond reasonable doubt that the two products are chemically identical, people will still irrationally purchase them. A clear example is the different prices commanded by &quot;natural&quot; versus &quot;artificial&quot; flavourings, as seen in &lt;a href=&quot;http://www.scientificamerican.com/article/what-is-the-difference-be-2002-07-29/&quot; rel=&quot;nofollow&quot;&gt;this Scientific American article&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Consumers pay a lot for natural flavorings. But these are in fact no better in quality, nor are they safer, than their cost-effective artificial counterparts. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-02-24T10:53:26.650" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="29877" PostTypeId="2" ParentId="29875" CreationDate="2015-02-24T11:36:34.240" Score="1" Body="&lt;p&gt;I agree with March Ho in general: people are not rational about food. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said there are two fairly different kinds of GMO, with different implications on the fears to have about them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) GMO embedding genes from the same species&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are not supposed to be any different from plants obtained using classical breeding techniques. The process in brief is for example: you see a wheat individual with short stems, an other with big grains. You want both. In classical selection you have to breed the two, select the descendants, breed again, select etc... until all descendants have both characters. Using GMO you can simply pick the gene you want and put it in the strain of your liking. It is much, much faster and the changes in the genome are much less than what you get by breeding two strains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) GMO embedding genes from other species&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can be more problematic as the gene you brought in could be from an organism nobody did ever eat, such as the Bt toxin in &lt;a href=&quot;http://en.wikipedia.org/wiki/MON_810&quot; rel=&quot;nofollow&quot; title=&quot;MON 810&quot;&gt;MON 810&lt;/a&gt;, hence the questions about toxicity. It doesn't mean it's toxic and the controls are very stringent about that but I can understand better why such GMO should be carefully checked.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) The false problem of GMOs and environment&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A Last problem is the indirect effect of the GMO, for example, if it's designed to be herbicide tolerant it might allow more herbicide to be poured on the plants and hence cause more herbicide residuals to be in the food, or in the environment, people then not liking GMO for environmental related reasons. But that should be addressed by checks on herbicides in food or in the environment, not by banning GMOs!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, GMOs have been around now for 20 years and people against GMO have a very hard time showing any kind of negative effects (see links posted previously), and some studies &quot;proving&quot; the toxicity have been shown to be statistically weak, not to say fraudulent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conclusion &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no good reason to reject type 1) GMOs based on food safety and very little reasons to reject type 2) GMOs. I would personally push hard for a general adoption of GMOs bearing genes from the same species or other edible plants. It would already make a lot of things easier! &lt;/p&gt;&#xA;" OwnerUserId="14615" LastEditorUserId="14615" LastEditDate="2015-02-24T11:44:40.277" LastActivityDate="2015-02-24T11:44:40.277" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="29878" PostTypeId="1" AcceptedAnswerId="30045" CreationDate="2015-02-24T14:00:36.387" Score="0" ViewCount="560" Body="&lt;p&gt;I want to transform a TCGA mRNA expression matrix (in linear data format) to log&lt;sub&gt;2&lt;/sub&gt;-ratios and then run a feature (gene) selection, selecting the 1000 most variant genes (genes with higher standard deviation across samples). The workflow is the following:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Select &quot;good&quot; genes before log&lt;sub&gt;2&lt;/sub&gt; ratio (genes each with median signal at least &lt;strong&gt;t&lt;/strong&gt; in &lt;strong&gt;p&lt;/strong&gt;% of samples);&lt;/li&gt;&#xA;&lt;li&gt;On selected genes, run log&lt;sub&gt;2&lt;/sub&gt; ratio, dividing each gene by its median signal and then log&lt;sub&gt;2&lt;/sub&gt;-transforming the result matrix;&lt;/li&gt;&#xA;&lt;li&gt;Select the 1000 most variant genes along all samples.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;How do I select &lt;strong&gt;t&lt;/strong&gt; and &lt;strong&gt;p&lt;/strong&gt;?&lt;/p&gt;&#xA;" OwnerUserId="3466" LastEditorUserId="14852" LastEditDate="2015-04-24T04:47:54.637" LastActivityDate="2015-04-24T04:47:54.637" Title="How to select genes before log2 ratio on a RNASeq gene expression matrix, based on signal median" Tags="&lt;bioinformatics&gt;&lt;gene-expression&gt;&lt;statistics&gt;&lt;tcga&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29879" PostTypeId="1" AcceptedAnswerId="29880" CreationDate="2015-02-24T14:22:08.073" Score="3" ViewCount="11435" Body="&lt;p&gt;Last night I came across a question that goes as follows:-&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cells cannot exist without&#xA;a) cell wall&#xA;b) cell membrane&#xA;c) mitochondria&#xA;d) ribosomes&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am getting confused with option B and option D&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;If RBC is lacking ribosomes then where the antigen proteins on RBC are coming from ?&lt;/p&gt;&#xA;" OwnerUserId="14616" LastEditorUserId="6" LastEditDate="2015-02-24T19:49:47.847" LastActivityDate="2015-02-24T19:49:47.847" Title="Can cell exist without Ribosomes?" Tags="&lt;cell-biology&gt;" AnswerCount="2" CommentCount="0" ClosedDate="2015-02-24T20:51:29.900" ContentLicense="CC BY-SA 3.0" />
  <row Id="29880" PostTypeId="2" ParentId="29879" CreationDate="2015-02-24T14:27:37.740" Score="6" Body="&lt;p&gt;The most essential thing for a cell to survive is a membrane. Without a membrane there is no boundary between cell and its surroundings. A selectively permeable membrane is needed for cells (from single celled organisms to elephants and giraffes and whales) to survive. Cells will die quickly on removal of cell membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The RBCs are good example of cells without mitochondria or ribosomes which survive for 120 days.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Please read the article on &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Erythropoiesis&quot; rel=&quot;nofollow&quot;&gt;Erythropoiesis&lt;/a&gt; for detailed information on how RBCs form and how they have proteins in their surface.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, the RBCs acquire the surface proteins during their formation period in the bone marrow. Inside the bone marrow the premature RBCs have nucleus, ribosomes, mitochondria, etc... and produce all the required structural and functional proteins. On maturing they loose the nucleus and cell organelles and contain only hemoglobin in their cytoplasm.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-02-24T16:56:02.933" LastActivityDate="2015-02-24T16:56:02.933" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="29881" PostTypeId="2" ParentId="29837" CreationDate="2015-02-24T14:29:30.677" Score="3" Body="&lt;p&gt;There are many different types ('scales', you might say, and mechanisms) of mutation in the genome.&lt;/p&gt;&#xA;&lt;p&gt;Maybe your question was really about base mutations, but I want to add one interesting tangential thing (which also points out the importance of clarifying the term 'mutation'):&lt;/p&gt;&#xA;&lt;h3&gt;Segmental Duplications - non-random genomic mutation&lt;/h3&gt;&#xA;&lt;p&gt;There are mutations that you would not call random; that occur again and again in patients of some disorders. By studying patients with Charcot-Marie-Tooth 1A (and other diseases), geneticists identified structures in the genome which act as 'platforms' for large-scale mutations i.e. chromosomal rearrangements.&lt;/p&gt;&#xA;&lt;p&gt;Certain places in the genome are rich in &lt;strong&gt;segmental duplications&lt;/strong&gt;, paralogous segments of the genome which can be reasonably large (1-400kb), may contain genes, and have very high identity (&amp;gt;90%) making them prone to recombine.&lt;/p&gt;&#xA;&lt;p&gt;The presence of segmental duplications (SDs) creates local genomic instability; a propensity for recombination, causing rearrangements - the term &lt;strong&gt;&amp;quot;genomic disorder&amp;quot;&lt;/strong&gt; was coined for diseases arising from these rearrangements.&lt;/p&gt;&#xA;&lt;p&gt;These genomic disorders are typically gene dosage imbalances. In the case of Charcot-Marie-Tooth 1A, duplication of a region between 2 SDs contains a gene involved in myelination. Deletion of that region causes another neuropathy. Haemophilia A can be caused by the inversion of a region between 2 SDs which lies partially within a long gene encoding a clotting factor. Inversion totally disrupts the exons.&lt;/p&gt;&#xA;&lt;p&gt;Read more here: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1226196/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1226196/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="13310" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-24T14:38:02.023" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29884" PostTypeId="2" ParentId="29809" CreationDate="2015-02-24T15:58:26.467" Score="1" Body="&lt;p&gt;This is a very interesting question. As others have alluded to, the body generally recognises self and non-self. However, as with any biology it's not that simple. Even leaving aside autoimmune disorders, the body doesn't always attack non-self and doesn't always leave self alone. Think of a pregnancy - the foetus is non-self, and yet the body doesn't reject it. The same can be said for a whole host of molecules that enter the body, such as food or things breathed in (e.g. pollen).  For this reason, Charles Janeway put forward the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1739426&quot; rel=&quot;nofollow noreferrer&quot;&gt;infectious non-self theory&lt;/a&gt;. This postulated that the body had a degree of leniency towards non-self, and would only attack if the macrophages became activated. This is done through recognition of Pathogen Associated Molecular Patterns, or &lt;a href=&quot;http://en.wikipedia.org/wiki/Pathogen-associated_molecular_pattern&quot; rel=&quot;nofollow noreferrer&quot;&gt;PAMPs&lt;/a&gt;, binding to Pattern Recognition Receptors, &lt;a href=&quot;http://en.wikipedia.org/wiki/Pattern_recognition_receptor&quot; rel=&quot;nofollow noreferrer&quot;&gt;PRR&lt;/a&gt;s. These PRRs are receptors present on immune cell surfaces, though most relevantly on macrophage surfaces, and when they bind to PAMPs it sends a message to the cell that it's likely in contact with a pathogen (or at least there is likely a pathogen in the area somewhere). This causes activation, and starts an immune response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it's also too simplistic to suggest that the immune system always leaves self alone, and in fact one of the key jobs of macrophages is to clean up self cells that are damaged, and undergoing apoptosis - programmed cell death. (You can read more on macrophages &lt;a href=&quot;http://education-portal.com/academy/lesson/macrophages-definition-function-types.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and more on apoptosis/other methods of cell death &lt;a href=&quot;https://biology.stackexchange.com/questions/27980/why-do-some-cells-in-the-body-prefer-necrosis-to-apoptosis-as-a-means-of-cell-de/28004#28004&quot;&gt;here&lt;/a&gt;). Therefore Polly Matzinger put forward what is known as the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Danger_model&quot; rel=&quot;nofollow noreferrer&quot;&gt;Danger Model&lt;/a&gt;&quot;. This basically speculates that in order for an immune response to occur, the body has to recognise certian molecules that are evolutionarily associated with danger. PAMPs would indeed count, but there could also be endogenous molecules such as HSPs - proteins produced when a cell is under duress through heat, pH, cold, irradiation, viral infection etc. This tells the immune cell that detects it that the body is in danger, and allows activation and mobilisation of an immune response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the question here is, would the body respond to a miniature version of yourself? That would depend on a number of factors:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Where in the body would you go?&lt;/strong&gt; If you were to stay in the digestive tract, so get swallowed and 'passed through' the body, I would say it's very unlikely you would be attacked. The body has a high tolerance for places such as the gut, because it's constantly exposed to external and non-self molecules. If it were in the blood stream, it's more likely because you're more likely to come across immune cells.&#xA;&lt;br&gt;&lt;strong&gt;How is this 'shrinkage' achieved?&lt;/strong&gt; Growth comes in two ways, through increase in cell size and increase in cell number. Which of these are you reducing? Are the cells the same size, but there are many fewer of them (unlikely, especially given that the opening question specifies to bacterium size, which are many times smaller than human cells already) or do you have the same number of cells but each cell is shrunk to a much smaller size (given that the entire body is the size of a bacterium, each cell would have to be many times smaller than a bacterium). If the cells were the same size, or even a bacterium-sized each, then an immune response is much more likely. If the whole organism is the size of a bacterium, the cells are going to be far too small to elicit an immune response.&#xA;&lt;br&gt;&lt;strong&gt;Are you causing danger signals&lt;/strong&gt;? As mentioned above, if no danger signals are present then it's unlikely an immune response will be launched regardless of anything else. Provided you're not killing or injuring cells, the body will pretty much ignore you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would say you wouldn't be attacked if you shrunk down as far as you've suggested. Everything would be too small for the body to recognise. However, if you didn't shrink down nearly as far, so your cells remained a size the body could recognise, and then started blundering about causing all manner of danger signals around you, the body may pick up some of your antigen and launch a response against you. On the other hand, the body is likely to have become tolerant to your antigens so even if this was the case, a full immune response is unlikely.&lt;/p&gt;&#xA;" OwnerUserId="10067" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-02-24T15:58:26.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29886" PostTypeId="2" ParentId="29879" CreationDate="2015-02-24T16:21:16.077" Score="1" Body="&lt;p&gt;Cells can survive without ribosomes, but they would accumulate damage and be unable to restore worn out or exhausted supplies of any proteins they may require. The ribosome is necessary to be able to perform protein translation from RNA. Thus, if the cell can survive without protein, then it would be able to survive without ribosomes. No known organism that exists today meets that definition, if I am not mistaken. However, at some point, it is theorized that the earliest cells were able to perform replication and metabolism without the use of protein. So, it is likely, but not something that is seen in life today.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nicholas H. Barton Derek E.G. Briggs Jonathan A. Eisen , David B. Goldstein and Nipam H. Patel.(2010). Evolution. Cold Stone Harbor Laboratory Press.&lt;/p&gt;&#xA;" OwnerUserId="12946" LastEditorUserId="12946" LastEditDate="2015-02-24T17:22:30.627" LastActivityDate="2015-02-24T17:22:30.627" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29887" PostTypeId="1" CreationDate="2015-02-24T16:22:38.273" Score="1" ViewCount="46" Body="&lt;p&gt;When using mass spectrometry analysis software we use carbonylation as a fixed modification. What is the significance of this modification and why doesn't it change?  &lt;/p&gt;&#xA;" OwnerUserId="12880" LastActivityDate="2015-02-24T16:22:38.273" Title="Why is carbonylation added as a fixed modification in mass spectrometry peptide analysis?" Tags="&lt;molecular-biology&gt;&lt;biochemistry&gt;&lt;mass-spectrometry&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29891" PostTypeId="2" ParentId="29809" CreationDate="2015-02-24T16:46:02.957" Score="1" Body="&lt;p&gt;The immune system recognizes patterns - incase of innate immunity and shapes - incase of active immunity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am making a few assumptions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The Shrinking would result in a smaller version of &quot;the person&quot; - meaning he/she is a bacteria sized person capable of executing all actions that a human can do.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The shrunk person is placed inside the blood vessel or some place where the immune cells will have easy access.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now, the answer would basically depend on two factors:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The pattern recognition: It is higly unlikely that the innate immunity would recognize anything that is so small - As the person himself is the size of bacteria, the pattern recognition would be unable to find the patterns.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The Shape recognition  - This might be able to identify a specific structure. The structure in question may be a whole cell or a cluster of cells or a hair follicle, etc... The epitopes on foreign organisms which are recognized by the active immunity are much smaller than the organism itself. Infact a single bacteria may have thousands of epitopes. The epitopes are usually proteins and what is recognized may be as small as 3 to 4 amino acid cluster. Thus this system has the potential to identify and eliminate the shrunk person.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The shrunk person will not be considered as &quot;self&quot; because on shrinking, the &quot;self-shapes&quot; don't apply anymore. Think of it as a glove specifically made for the hand of an adult. A child's hand will not fit into it. Likewise any change in size of proteins will eliminate all question of self and everything in that &quot;new size&quot; is considered foreign.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-02-24T16:46:02.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29892" PostTypeId="2" ParentId="29853" CreationDate="2015-02-24T16:48:34.307" Score="2" Body="&lt;p&gt;There are commonalities within certain related viral families. But no, there are no universal viral genes, there are many reasons for this:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Viral genomes in general are much smaller than the average cell genome and the pressure for selection against extraneous genes is high due to the need to be able to replicate as fast as possible within the host cell. This also allows for rapid evolutionary rates due to the sheer mass of  viruses creates and spread through a given host.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There are viruses that infect wildly different hosts and thus require highly divergent entrance mechanisms and strategies. Due to this difference, there would be no need for the bacteriophage for instance to share the same proteins or genes with those of HIV or another human virus.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It is possible that viruses have evolved multiple times throughout the history of life, this is however not confirmed as of this time. If it is true however, then it would preclude the possibility of universal viral genes as they would not share a common homology.(Though viruses may be able to mix their genetic material by sheer chance, if they share a common host.)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Viruses, by definition lack the common replication, translation and generally, transcription machinery that is shared by their cellular hosts. Thus, they do not have this source of common genes, as living organisms do.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="12946" LastActivityDate="2015-02-24T16:48:34.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29893" PostTypeId="1" CreationDate="2015-02-24T17:00:01.240" Score="9" ViewCount="231" Body="&lt;p&gt;I have been reading about the echolocation system in bats. papers state that bats tend to produce a sonar beam that has a beam angle (-3db) of about 30-40 degrees. This would be considered a wide beam given the fact the sonar sensors used by robots have beams 15-20 degrees or down to 10 degrees with multi-sonar. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the beam width increases, the azimuth resolution decreases. Yet, bats have good navigational capabilities and good object discrimination in azimuth. How is that achieved? what is the technique used?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I searched hard but what I found is that they rely on the timing between two ears. however, given the complexity of the environment and the multiple echos that return, how is it possible to correlate which echo in the left ear belongs to which in the right ear?&lt;/p&gt;&#xA;" OwnerUserId="14624" LastEditorUserId="9943" LastEditDate="2015-05-31T13:06:25.153" LastActivityDate="2015-05-31T14:09:25.710" Title="How can bats achieve good resolution with wide beams?" Tags="&lt;mammals&gt;&lt;perception&gt;&lt;echolocation&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29894" PostTypeId="2" ParentId="29716" CreationDate="2015-02-24T17:33:29.200" Score="3" Body="&lt;p&gt;It can actually on very rare occasions however, it is also highly problematic and generally creates deleterious mutations and can inactivate genes. Depending on the location of the cell and the cross-over within the genome, it can also contribute to the formation of cancer. For instance, in the case of retinoblastoma, if there is one mutated copy of RAS on one chromosome and a normal copy on the other and mitotic crossing over occurs, then you can potentially remove the protective nonmutant copy of RAS from one of the daughter cells. This cell is then one step closer to becoming tumorgenic. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, one reason this may not occur ordinarily is to reduce the chance of causing such a cancer. As for why it does occur on the rare times it does, I am not certain as of the time of writing this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference: The Biology of Cancer, by Robert A. Weinberg&lt;/p&gt;&#xA;" OwnerUserId="12946" LastActivityDate="2015-02-24T17:33:29.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29895" PostTypeId="2" ParentId="29788" CreationDate="2015-02-24T18:14:30.253" Score="1" Body="&lt;p&gt;I believe that evolution is driven by the needs of the organism to adapt not by the need to adapt for human beings consumption. meaning that some nitrogen gets back to the soil through the effect of nature e.g. fixation of nitrogen during storms  and when fecal matter decomposes in soil and these I assume provide enough nitrogen for normal plant growth and so the plant is not &quot;forced&quot; to adapt to say a deficiency in nitrogen but for humans I assume because of agriculture the land gets &quot;exhausted&quot; and so we need fertilisers but plants have not evolved becuase I assume there was no pressing need for it. That is my own thinking assuming I understood your question&lt;/p&gt;&#xA;" OwnerUserId="14624" LastActivityDate="2015-02-24T18:14:30.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29896" PostTypeId="1" CreationDate="2015-02-24T18:18:51.033" Score="1" ViewCount="87" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;What are these white spots? It's like Braille writing or something. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How is the appearance encoded in the plant? (which I think is a Pine, though I am not sure).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lm6Bk.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14625" LastEditorUserId="11841" LastEditDate="2015-02-25T15:59:19.440" LastActivityDate="2015-02-25T15:59:19.440" Title="What are the white spots?" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29897" PostTypeId="2" ParentId="29679" CreationDate="2015-02-24T18:29:38.653" Score="0" Body="&lt;p&gt;as far as I know the brain processes data in stages the neurons themselves are not purely binary as in a computer in that every action has a predetermined output. the neuron response tends to be goverened by sigmoid function output and hence the use of this function in artificial neural networks. further, the synapses have strengths that is depended on the amount of neurotransmitter in there which obviously varies from cell to cell and even in the same cell and hence one speaks of the probability of a neuron firing given a certain stimulus. additionally the neurons from sensory organs fire pulses at a frequency that increases with the strength of the stimulus. furthermore, the data from sensors is processed in layers of neurons lower layers have rapidly firing neurons whule higher layers fire at much lower rates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;you also have to consider the fact that the brain is actually a complicated network of &quot;recurrent&quot; neurons meaning that the output is fedback as an input and this is different from simple computer gates such as AND gates or XOR gates it is similar to counters may be but obviously on a very bigger scale. one more point is that recurrent neural networks have built in memory that enables the pattern recall and recognition and so the study of the brain as a binary system is very complicated and will fail to explain how the brain works.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;on the macro scale the human brain operates as a bayesian inference engine more or less I mean when it comes to thinking and inference i.e. it relies on probabilities and knowledge gained from past experiences to deal with current problems and new data&lt;/p&gt;&#xA;" OwnerUserId="14624" LastActivityDate="2015-02-24T18:29:38.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29898" PostTypeId="2" ParentId="28607" CreationDate="2015-02-24T18:35:13.003" Score="1" Body="&lt;p&gt;&lt;strong&gt;Comparing Protein Structures&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a number of things you can look at such as root mean square deviation. This method compares the co-ordinates of two structures by superposing them on top of each other. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions&quot; rel=&quot;nofollow&quot;&gt;RMSD&lt;/a&gt;: This is implemented in the modelling &lt;a href=&quot;https://salilab.org/modeller/&quot; rel=&quot;nofollow&quot;&gt;Modeller&lt;/a&gt; or can be used in &lt;a href=&quot;http://www.cgl.ucsf.edu/chimera/&quot; rel=&quot;nofollow&quot;&gt;USCF Chimera&lt;/a&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;RMSD will provide a number in angstroms squared, with higher values indicating structural differences. A RMSD of 0.0 would indicate the structures are identical. There are different types of RMSD calculations such C-alpha, backbone and all-atom. C-alpha RMSD will only look at the C-alpha atoms to calculate the RMSD. Backbone RMSD will look at the backbone only and all-atom will take into account all the atoms to calculate the RMSD.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other Things to Look at&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Assuming the structure was created yourself, was the structure minimised? To remove clashes?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In addition phi, psi angles and mentioned above have you checked for clashes in your structure? Clashes can be checked in USCF chimera which checks for clashes with a default value of 0.6 Angstrom van der Wall radii overlap.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="158" LastActivityDate="2015-02-24T18:35:13.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29899" PostTypeId="1" CreationDate="2015-02-24T18:44:54.740" Score="0" ViewCount="337" Body="&lt;p&gt;I can imagine several specialized unicellular beings collaborating. But how does life get from that point to a unique pluricelular being that reproduces into another pluricelular being?&lt;/p&gt;&#xA;" OwnerUserId="14626" LastEditorUserId="9943" LastEditDate="2015-02-24T20:31:43.060" LastActivityDate="2015-02-24T20:31:43.060" Title="How did multicellular life evolve?" Tags="&lt;cell-biology&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2015-02-24T22:21:23.517" ContentLicense="CC BY-SA 3.0" />
  <row Id="29901" PostTypeId="2" ParentId="24426" CreationDate="2015-02-24T19:06:44.883" Score="0" Body="&lt;p&gt;This is a test cross - a cross with a recessive pair of alleles and either a heterozygous or homozygous pair of dominant alleles( eg- Tt X tt or TT x tt respectively). These crosses are carried out to check the if genes are homozygous or not. In this the ratio is always 1:1.&#xA;So don't worry. :)&#xA;Be confident about your answer, because it is obvious that the answer cannot be half if you work it out using the Punnett square. &lt;/p&gt;&#xA;" OwnerUserId="14627" LastActivityDate="2015-02-24T19:06:44.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29903" PostTypeId="1" AcceptedAnswerId="29905" CreationDate="2015-02-24T19:16:29.863" Score="4" ViewCount="382" Body="&lt;p&gt;If plasmids are important for bacteria to express specific genes under stressful conditions, why are these genes not already incorporated into their chromosome to begin with? What is the evolutionary significance for this?&lt;/p&gt;&#xA;" OwnerUserId="12959" LastActivityDate="2015-02-24T19:29:03.313" Title="Why are plasmid genes not already incorporated into bacterial chromosomes if necessary for stressful situations?" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;plasmids&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29904" PostTypeId="1" CreationDate="2015-02-24T19:22:30.687" Score="3" ViewCount="88" Body="&lt;p&gt;Is it possible to tell or rule out (potentially a priori) whether any given substance or compound is likely and how likely to cause allergies with high confidence, without the need to conduct experiments, e.g. by looking at its properties, e.g. solubility, molecular structure or reactivity?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I've heard is that generally speaking, things that we come in contact with in early years tend to be less likely to cause problems later on, but still, there seem to be differences even with food and substances that do not quite appear to be exotic, e.g. peanuts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question is related to these, though I'd consider it more generic.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/8566/meat-and-mushroom-allergies-why-are-they-so-rare&quot;&gt;Meat and mushroom allergies, why are they so rare?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/7905/what-is-the-smallest-molecule-that-can-present-as-an-antigen-to-the-immune-syste&quot;&gt;What is the smallest molecule that can present as an antigen to the immune system in the context of allergies?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11664" LastActivityDate="2015-03-03T17:25:04.860" Title="What makes substances allergenic?" Tags="&lt;immunology&gt;&lt;allergies&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29905" PostTypeId="2" ParentId="29903" CreationDate="2015-02-24T19:29:03.313" Score="2" Body="&lt;p&gt;Plasmids do have the advantage that they replicate independently of the cells chromosome and that they can be transferred between different bacteria. This spreads the gene encoded by the plasmid to other bacteria, which then can also survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think about antibiotic resistance. Bacteria which have a plasmid which allows protection against the antibiotic will survive. They can transfer this protection to other bacteria which then also become resistant. This can either happen through &lt;a href=&quot;http://en.wikipedia.org/wiki/Pilus&quot; rel=&quot;nofollow&quot;&gt;pili&lt;/a&gt; which develop between bacteria or also via the uptake of plasmid DNA from the environment in a process called &lt;a href=&quot;http://en.wikipedia.org/wiki/Horizontal_gene_transfer&quot; rel=&quot;nofollow&quot;&gt;horizontal gene transfer&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally mutations on the plasmids are not as dangerous on the plasmids than on the chromosomal DNA, where essential genes might be damaged. Plasmids can also get lost, if they are not needed by the bacteria due to a missing selection pressure, which is also much harder for genes encoded on the chromosome.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-02-24T19:29:03.313" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29906" PostTypeId="2" ParentId="29899" CreationDate="2015-02-24T19:46:51.190" Score="1" Body="&lt;p&gt;The key is specialization: e.g. some cells specializing in getting food, others in producing something sticky to keep them together. Which cell does what is usually determined by chemical signals: depending on their specialization they produce particular chemical compounds. So if a non-specialized cell notes that one compound is rather low because the specialized type of cell producing it is in low supply then it specializes that way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While initially all cells are capable of reproduction, at some point there also will be cells specialized for reproduction, whereas the others lose the ability to reproduce to better concentrate on their specialized duty. Hence the other cells do not have an independent existence anymore but exist only as part of the larger organism. When such an organism is then to be considered a separate pluricellular entity is a matter of definition: if it is an entity independent of the original (e.g. capable of moving away)? if sexual reproduction happens?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Multicellular_organism#Evolutionary_history&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; also has some things to say.&lt;/p&gt;&#xA;" OwnerUserId="14628" LastEditorUserId="14628" LastEditDate="2015-02-24T20:13:47.843" LastActivityDate="2015-02-24T20:13:47.843" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29907" PostTypeId="1" AcceptedAnswerId="29917" CreationDate="2015-02-24T20:09:00.237" Score="1" ViewCount="1305" Body="&lt;p&gt;ANF as we know reduce the Na+ uptake and K+ removal in the distal tubules and it also functions as a Vasodialator (?) But again it says that ANF increases the Glomerular filtrate ? But if it is acting has a Vasoldialator (&lt;em&gt;ie, antagonistic to Vasopressin&lt;/em&gt;) how is it increasing the GFR ? Shouldnt it lower the GFR ?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;ANF - Atrial Natriuretic Factor also called Atrial Natriuretic Peptide&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GFR - Glomerular Filtration Rate&lt;/p&gt;&#xA;" OwnerUserId="14616" LastEditorUserId="11841" LastEditDate="2015-02-25T01:42:52.783" LastActivityDate="2015-02-26T09:06:54.313" Title="How does ANF increase GFR?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;kidney&gt;&lt;human-physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29908" PostTypeId="1" CreationDate="2015-02-24T20:09:31.830" Score="2" ViewCount="938" Body="&lt;p&gt;Are there animals (or plants) that are parasitic on both animals and plants?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Especially such that they rely on their plant host being eaten by their animal host?&lt;/p&gt;&#xA;" OwnerUserId="14628" LastActivityDate="2015-02-25T17:05:31.443" Title="Parasites with both plant and animal hosts?" Tags="&lt;parasitology&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29913" PostTypeId="1" CreationDate="2015-02-24T20:51:59.617" Score="4" ViewCount="624" Body="&lt;p&gt;I have a conceptual question that I was hoping someone could answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can I say that microRNA A is expressed x-fold greater than microRNA B directly from the TCGA miRseq data?  Can I do this after normalizing the data?  Does it matter if I use RSEM or RPKM values.  It seems to me that it should be legitimate in any case since microRNAs are approximately the same length, but maybe I am overlooking something.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, I am following a paper published in Nature Communications entitled &quot;Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif&quot;.  The authors download the data and collapse isoform reads to a single read count using the reads.  They say they used the reads per million microRNAs mapped, which establishes each microRNA read count as a fraction of the total microRNA population.  The authors then do upper quartile normalization which they say is important because a subset of microRNAs (miR-143 in particular) contributes so significantly to the total read count.  In the text, the authors appear to use the resulting values to do a direct comparison between microRNAs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I definitely want the collapsed isoforms, and I think it makes sense to do the normalization.  However, I would like to say that a particular microRNA is expressed x-fold higher than another.  Can I do this from the collapsed and normalized data? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this has already been answered, I apologize.  I could not find it.  Thanks.  &lt;/p&gt;&#xA;" OwnerUserId="14631" LastEditorUserId="14852" LastEditDate="2015-04-24T04:47:35.303" LastActivityDate="2015-04-24T04:47:35.303" Title="Relative microRNA comparison from from TCGA data?" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;microrna&gt;&lt;tcga&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29914" PostTypeId="1" AcceptedAnswerId="29928" CreationDate="2015-02-24T21:13:02.747" Score="1" ViewCount="966" Body="&lt;p&gt;I know, for instance, that RNA is much more succetible to alkaline hydrolysis than DNA and this difference is determined by the presence of 2'-hydroxyl group in ribose.&#xA;I have also heard that &quot;DNA is more stable&quot; and thus was selected as the repository of genetic information. Though, I still haven't understood why the lack of just one hydroxyl would lead to more stability...&lt;/p&gt;&#xA;" OwnerUserId="14630" LastActivityDate="2015-02-25T06:52:50.200" Title="Examples of how the presence or absence 2'-hydroxyl groups influence physicochemical properties of DNA and RNA" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;nucleic-acids&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29915" PostTypeId="2" ParentId="29913" CreationDate="2015-02-24T21:20:22.500" Score="1" Body="&lt;p&gt;I would be very careful in making such a claim from sequencing data. There are well known biases in sequencing due to things like GC composition and hexamer composition. Because of this, it's possible to compare relative levels of some species across treatments but tricky to do so within a given sample or samples. One way around this is to perform qPCR using absolute quantification on a few samples and then compare that to sequencing results. Granted, you're not going to have the same samples as TCGA or exactly identical library prep, but it'll be a reasonable starting point. You could then use that to calibrate how reliable the relative levels might be within the TCGA dataset.&lt;/p&gt;&#xA;" OwnerUserId="9523" LastActivityDate="2015-02-24T21:20:22.500" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29917" PostTypeId="2" ParentId="29907" CreationDate="2015-02-24T22:25:09.830" Score="4" Body="&lt;p&gt;ANF (Atrial Natriuretic Factor more commonly known as ANP - atrial natriuretic peptide) squeezes (vasoconstricts) the efferent arteriole. This means the pressure in the glomerulus is higher (like if you squeeze the end of a hose) and so more fluid is squeezed out i.e. the glomerular filtration rate (GFR) is higher. It also dilates the afferent which means more fluid is going in, further increasing GFR &lt;a href=&quot;http://www.nature.com/nature/journal/v324/n6096/abs/324473a0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;(&lt;em&gt;Marin-Grez et al.&lt;/em&gt;)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lrwM4.jpg&quot; alt=&quot;Glomerulus&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1757" LastEditorUserId="3340" LastEditDate="2015-02-26T09:06:54.313" LastActivityDate="2015-02-26T09:06:54.313" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="29918" PostTypeId="1" CreationDate="2015-02-24T22:56:33.973" Score="7" ViewCount="3909" Body="&lt;p&gt;It has been observed that in nature most organisms have negative supercoiled DNA and that few organisms have positive supercoiled DNA. Some of the organisms that have the positive supercoiled DNA live in strong acidic environments but are very rare compared to negative supercoiled DNA. Why wouldn't all organisms have the same DNA supercoiling? Does it affect their survival in any way? &lt;/p&gt;&#xA;" OwnerUserId="12900" LastEditorUserId="16460" LastEditDate="2017-04-01T08:16:47.983" LastActivityDate="2019-11-06T20:16:56.287" Title="Why do most organisms have negative supercoiled DNA?" Tags="&lt;molecular-biology&gt;&lt;biophysics&gt;&lt;supercoiling&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29919" PostTypeId="1" CreationDate="2015-02-25T00:25:40.827" Score="1" ViewCount="326" Body="&lt;p&gt;If you were to use an older sphygmomanometer and a stethoscope to record blood pressure, why would you hear no sound when the cuff was inflated to 160mmHg&lt;/p&gt;&#xA;" OwnerUserId="14633" LastActivityDate="2015-02-25T01:29:13.567" Title="Using a Sphygmomanometer" Tags="&lt;homework&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-02-25T06:07:32.917" ContentLicense="CC BY-SA 3.0" />
  <row Id="29920" PostTypeId="1" CreationDate="2015-02-25T00:40:07.987" Score="4" ViewCount="787" Body="&lt;p&gt;Chicks (baby of chickens) and ducklings seem to have fine hairs, at least something that look like hairs to me. Most mammals have hairs, but reptiles, fish, or other animal groups do not have hairs as far as I know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have looked up the tree of evolution, and it looks like this.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/1RLR4.gif&quot; alt=&quot;http://www.talkorigins.org/faqs/wells/images/richardson_fig9.gif&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the tortoises, crocodiles (I do not know what lepidosauria means but I guess it is reptiles other than the aforementioned), and birds diverged after their common ancestor was split from the common ancestor of mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since none of the tortoises, lepidosauria, or crocodiles have hairs now, does this mean that the hair of birds and mammalian hair is an example of convergent evolution? Or did these other taxa lose hair during evolution?&lt;/p&gt;&#xA;" OwnerUserId="8091" LastEditorUserId="16866" LastEditDate="2017-02-13T18:24:15.867" LastActivityDate="2017-03-15T19:30:10.983" Title="Did baby bird hair and mammalian hair convergently evolve?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;ornithology&gt;&lt;hair&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="29921" PostTypeId="2" ParentId="29919" CreationDate="2015-02-25T01:29:13.567" Score="3" Body="&lt;p&gt;The measured blood pressure is the radial pressure exerted by the blood column againt the arterial wall.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a normal patient, this pressure varies between 120 mm of Hg and 80 mm of Hg.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cdc.gov/bloodpressure/about.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/S8BWV.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;click on the image to go to the source&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a cuff is inflated to 160 mm of Hg, the arteries collapse and circulation is temporarily suspended. As blood flow does not occur, no sound is audible.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.m.wikipedia.org/wiki/Korotkoff_sounds&quot; rel=&quot;nofollow noreferrer&quot;&gt;The korotkoff sounds&lt;/a&gt; that are heard while measuring BP are due to disturbance in the streamlined flow of blood. When auscultating an artery without applying pressure no sounds should be heard in a normal person. Generally they are heard when blood flow occurs in spurts. This occurs when the cuff pressure is lesser than the systolic pressure but more than the diastolic pressure. &lt;/p&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-02-25T01:29:13.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29925" PostTypeId="1" AcceptedAnswerId="29942" CreationDate="2015-02-25T03:24:40.373" Score="5" ViewCount="22247" Body="&lt;p&gt;In the Southern blot method, for example, a solution of NaOH is used to denature the DNA in the sample. &#xA;I find this counterintuitive since I expected that $\text{Na}^+$  cations would neutralize the negative charges of phosphate groups, hence stabilizing the double helix.&lt;/p&gt;&#xA;" OwnerUserId="14630" LastEditorUserId="10456" LastEditDate="2015-02-27T21:28:18.830" LastActivityDate="2015-02-27T21:28:18.830" Title="Why does high pH result in the denaturation of DNA?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;nucleic-acids&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29926" PostTypeId="1" CreationDate="2015-02-25T03:47:36.040" Score="1" ViewCount="193" Body="&lt;p&gt;In humans, is being transgender something that is innate, or is it caused (or made more likely) by social factors such as their political beliefs, their religious views or their social environment?&lt;/p&gt;&#xA;" OwnerUserId="576" LastActivityDate="2015-02-25T03:47:36.040" Title="With humans, is being transgender innate, or caused by social factors?" Tags="&lt;human-biology&gt;&lt;gender&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29928" PostTypeId="2" ParentId="29914" CreationDate="2015-02-25T06:04:08.860" Score="3" Body="&lt;p&gt;As user137 said, the general base abstracts a proton from the 2'OH and subsequently the 2'O&lt;sup&gt;-&lt;/sup&gt; renders a nucleophilic attack on the δ&lt;sup&gt;+&lt;/sup&gt; Phosphorous, leading to the hydrolysis of the phosphodiester bond. There can be slight variations in the mechanism and the intermediates; for details see &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/anie.199704321/pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; review.&lt;/p&gt;&#xA;&lt;p&gt;             &lt;img src=&quot;https://i.stack.imgur.com/95YC0.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;After hydrolysis both 2'- and 3'- phosphates can form.&lt;/p&gt;&#xA;&lt;p&gt;RNA is not thermodynamically unstable; apart from being unstable in the presence of a strong base RNA is biochemically unstable too. This is because there are several RNAses and most of them degrade RNA by a mechanism similar to alkaline hydrolysis (they cannot act on DNA). Also see &lt;a href=&quot;https://biology.stackexchange.com/questions/24786/why-deoxyribose-for-dna-and-ribose-for-rna/25792#25792&quot;&gt;this&lt;/a&gt; post.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-25T06:52:50.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29929" PostTypeId="1" AcceptedAnswerId="29931" CreationDate="2015-02-25T09:28:27.657" Score="3" ViewCount="3248" Body="&lt;p&gt;I have a bunch of sequence files fetched from the EBI ENA and I'm trying to find the end of the 5' UTR for specific genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The UTR itself doesn't seem to be annotated in most sequence files I have. My original idea was to simply use the CDS annotations, as the start of those should clearly identify the end of the 5' UTR. But I also noticed gene annotations in many of the sequences, most of them starting and ending at exactly the same locations as the corresponding CDS annotation. But there are also cases where there are small differences between the gene and the CDS annotation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I'm wondering how exactly the gene annotation is defined (if there is actually an agreed definition) and how the gene and CDS annotations are used in practice. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which annotation would be the most reliable to identify the end of the 5' UTR?&lt;/p&gt;&#xA;" OwnerUserId="14541" LastActivityDate="2015-02-26T09:08:04.270" Title="What is the difference between gene and CDS annotations?" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29931" PostTypeId="2" ParentId="29929" CreationDate="2015-02-25T12:14:44.753" Score="2" Body="&lt;p&gt;CDS is based on ORF prediction and unless the protein product is known it is classified as an mRNA for a hypothetical protein (Refseq id: XM_*). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As Devon Ryan said sometimes UTR ends are not accurately annotated. If you are interested in finding the 3' end of 5'UTR then the problem is basically to find the translation start site. You can have a look at ribosome profiling experiments or try doing eIF2 CLIP-RNAseq (I don't think it has been done); peptide sequences may not be of help because N-terminal region in many cases, gets clipped.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in finding the 5' end of 5'UTR then the problem is relatively simple. You just need to do a &lt;a href=&quot;http://www.nature.com/nmeth/journal/v2/n8/full/nmeth0805-629.html&quot; rel=&quot;nofollow&quot;&gt;5'-RACE&lt;/a&gt; followed by Sanger sequencing (this would work in most cases or you can do a deep-RNAseq). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are official GTF files that provide the most reliable annotations. For human I would recommend &lt;a href=&quot;http://www.gencodegenes.org/&quot; rel=&quot;nofollow&quot;&gt;GENCODE&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the annotations the term &lt;code&gt;Gene&lt;/code&gt; denotes the entire DNA region that is responsible for all of its RNA products (splice variants, alternate start/termination etc). Other features include &lt;code&gt;Transcript&lt;/code&gt;, &lt;code&gt;Exon&lt;/code&gt;, &lt;code&gt;CDS&lt;/code&gt;, &lt;code&gt;UTR&lt;/code&gt; and in some cases translation start site is separately annotated. &lt;code&gt;CDS&lt;/code&gt; comprises of just the protein coding region. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should read more about the &lt;a href=&quot;http://asia.ensembl.org/info/website/upload/gff.html&quot; rel=&quot;nofollow&quot;&gt;GTF/GFF annotation format&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-02-26T09:08:04.270" LastActivityDate="2015-02-26T09:08:04.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29932" PostTypeId="2" ParentId="29913" CreationDate="2015-02-25T12:55:14.177" Score="1" Body="&lt;p&gt;Small RNA sequencing is good for a preliminary screen because as with most high throughput experiments, the sample size is less and therefore inter-sample comparisons may not be accurate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For miRNA expression calculation, I use &lt;a href=&quot;https://www.mdc-berlin.de/8551903/en/&quot; rel=&quot;nofollow&quot;&gt;mirdeep2's&lt;/a&gt; quantifier script with a slight modification. The script basically aligns the reads to known pre-miRNAs and finds if they are aligning to the annotated mature miRNA region (some window of partial mapping into non-mature region is allowed and can be set to zero as well). It uses bowtie for alignment. &#xA;What I generally do is, instead of running bowtie in the &lt;code&gt;-v&lt;/code&gt; mode (as set in mirdeep), I run it in the &lt;code&gt;-n&lt;/code&gt; alignment mode by making a small modification in the script. The &lt;code&gt;-n&lt;/code&gt; mode lets you define a &lt;em&gt;seed region&lt;/em&gt;, and number of mismatches in seed and non-seed regions. I set seed length to &lt;code&gt;10&lt;/code&gt; with &lt;code&gt;0&lt;/code&gt; seed mismatches and around &lt;code&gt;2&lt;/code&gt; non-seed mismatches. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To calculate reads per million (RPM) I normalize it with number of unique mappings to genome, with same alignment parameters (except &lt;code&gt;--norc&lt;/code&gt;). As per &lt;a href=&quot;http://www.nature.com/nmeth/journal/v9/n8/full/nmeth.2078.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; study an RPM of 100 is biologically relevant. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Can I say that microRNA A is expressed x-fold greater than microRNA B?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, if the read counts are clearly different. EM and other likelihood models calculate a confidence interval for read counts or RP(K)M and if two RNAs do not have overlapping intervals then they can be said to be expressed in different levels. I haven't used likelihood models for miRNAs though, but I guess it is fine because:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The search space is highly reduced. &lt;/li&gt;&#xA;&lt;li&gt;Search is stringent.&lt;/li&gt;&#xA;&lt;li&gt;Isoforms are collapsed.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This effectively eliminates the possibility of dubious reads. You can set an RPM difference of 100 to call two miRNAs as differentially expressed, as 100 is the lower limit of biological significance (as previously mentioned).&#xA;Most relevant miRNAs have comparable GC content; so there may not be such a great sequencing bias (moreover the read itself is quite small). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-02-25T16:57:41.593" LastActivityDate="2015-02-25T16:57:41.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29933" PostTypeId="2" ParentId="29797" CreationDate="2015-02-25T14:50:57.110" Score="2" Body="&lt;p&gt;In order to date the age of a tree, you have &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_oldest_trees&quot; rel=&quot;nofollow&quot;&gt;three solutions&lt;/a&gt; :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you can cut the tree then you can simply count the number of rings. Note that for very old trees the central rings will have rotted and you will only have a lower bound on its age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If some parts of the tree are dead, you can use radiocarbon dating to estimate &lt;em&gt;the time of death&lt;/em&gt; with a relatively bad precision (the error is about 100 years which can be a lot for a tree)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can estimate its growth rate (either using the width of the rings, or by doing multiple measurements for several years), and deduce the age from its size.&lt;/p&gt;&#xA;" OwnerUserId="6042" LastActivityDate="2015-02-25T14:50:57.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29935" PostTypeId="1" CreationDate="2015-02-25T16:00:30.320" Score="2" ViewCount="45" Body="&lt;p&gt;I was wondering: What is the protein with the highest affinity to lactose? Are there some databases with values for affinity?&lt;/p&gt;&#xA;" OwnerUserId="4746" LastEditorUserId="28834" LastEditDate="2017-03-27T11:36:53.470" LastActivityDate="2017-03-27T11:36:53.470" Title="What is the protein with the highest affinity to lactose?" Tags="&lt;protein-interaction&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="29936" PostTypeId="1" CreationDate="2015-02-25T16:10:14.223" Score="2" ViewCount="69" Body="&lt;p&gt;I was wondering if anybody knows some publication about macro lncRNA (very long unspliced RNAs) or more generally a transcribed RNA that may lead to cis-DNA looping of genomic regions overlapped by the (macro) lncRNA transcript ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="359" LastEditorUserId="3340" LastEditDate="2015-02-25T17:14:03.777" LastActivityDate="2015-02-25T17:14:03.777" Title="Link between macro lncRNA and DNA looping" Tags="&lt;dna&gt;&lt;rna&gt;&lt;transcription&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="29937" PostTypeId="1" CreationDate="2015-02-25T17:02:29.050" Score="2" ViewCount="60" Body="&lt;p&gt;Why is rabies incurable after onset of symptoms? Although we administer HRIG (lyssa virus antibody) to the patient, why doesn't it work after onset of symptoms? And are there any other successful treatments for rabies like that of Milwaukee protocol which are under research? I also want to know how successful  is Milwaukee protocol so far?&lt;/p&gt;&#xA;" OwnerUserId="14641" LastEditorUserId="14641" LastEditDate="2015-02-26T17:51:44.180" LastActivityDate="2015-02-26T17:51:44.180" Title="Are there anyother method under research for curing rabies?" Tags="&lt;pathology&gt;&lt;antibody&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2015-02-26T06:39:23.167" ContentLicense="CC BY-SA 3.0" />
  <row Id="29939" PostTypeId="2" ParentId="29729" CreationDate="2015-02-25T17:10:16.237" Score="2" Body="&lt;p&gt;No, mammals need not take in CO2 from atmosphere. The body's homeostatic function will maintain its composition by checking the amount of CO2 released out by lungs. So certainly animals would survive if put in a CO2 free atmosphere.&lt;/p&gt;&#xA;" OwnerUserId="14641" LastActivityDate="2015-02-25T17:10:16.237" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29942" PostTypeId="2" ParentId="29925" CreationDate="2015-02-25T17:20:52.610" Score="9" Body="&lt;p&gt;The pKas of (neutral) guanine and thymine are 9-10 (&lt;a href=&quot;http://chem.wayne.edu/schlegel/Pub_folder/322.pdf&quot; rel=&quot;noreferrer&quot;&gt;ref&lt;/a&gt;). At high pH (&gt;~10), those bases will be deprotonated and exist as negatively charged conjugate bases. As the deprotonated species, part of the G/C and A/T hydrogen bonding networks are eliminated. In the figure below, green dotted lines represent the hydrogen bonds that explain the observed base pairing. Red dotted lines represent disrupted interactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0kokm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10143" LastEditorUserId="10143" LastEditDate="2015-02-26T00:19:01.857" LastActivityDate="2015-02-26T00:19:01.857" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29943" PostTypeId="1" AcceptedAnswerId="59784" CreationDate="2015-02-25T17:34:09.680" Score="8" ViewCount="9139" Body="&lt;p&gt;We currently have a problem of increasing $\ce{CO2}$ in the atmosphere.  But assuming we find a way to carbon sink it, what is the minimum $\ce{CO2}$ we need to leave in the atmosphere to provide a source for plants to photosynthesize?  I'm assuming this may vary per plant, and that we could choke plants so they're less productive - but at some point they will starve to death if we remove too much $\ce{CO2}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Where does this point lie?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Approximations, or a specific data point (say for one plant, or one type of plant) would be an adequate place to start.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Current atmosphere composition is $\pu{0.035\%}$ carbon dioxide.  In the past it has been higher (has it ever been lower?), which &lt;em&gt;in theory&lt;/em&gt; has resulted in higher plant growth - but I've seen some contradictory statements about higher Carbon Dioxide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(related: &lt;a href=&quot;https://biology.stackexchange.com/questions/3043/what-is-the-effect-of-a-pure-oxygen-environment-on-a-plant?rq=1&quot;&gt;What is the effect of a pure-oxygen environment on a plant?&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="14538" LastEditorUserId="30245" LastEditDate="2017-04-18T21:14:12.400" LastActivityDate="2019-10-26T00:18:49.557" Title="What's the (or some of the) minimum(s) amount of atmospheric carbon dioxide needed by plants?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;respiration&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29950" PostTypeId="2" ParentId="29729" CreationDate="2015-02-25T21:56:17.850" Score="0" Body="&lt;p&gt;It is unneccessary for a mammal to breath in CO2, though our bodies are able to expel unneeded gasses easily. However, if there were no CO2 in the atmosphere, animals would all die, as no oxygen could be produced by plants. In other words, we don't need to breath in CO2, but we need it to be plentiful.&lt;/p&gt;&#xA;" OwnerUserId="14649" LastActivityDate="2015-02-25T21:56:17.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29951" PostTypeId="2" ParentId="28617" CreationDate="2015-02-25T23:29:37.943" Score="1" Body="&lt;p&gt;From the &lt;a href=&quot;http://www.merckmanuals.com/home/drugs/administration_and_kinetics_of_drugs/drug_absorption.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Merck website&lt;/a&gt; :&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Drug absorption is the movement of a drug into the bloodstream after administration.&lt;/p&gt;&#xA;&lt;p&gt;Absorption affects bioavailability—how quickly and how much of a drug reaches its &amp;gt;intended target (site) of action. Factors that affect absorption (and therefore &amp;gt;bioavailability) include&lt;/p&gt;&#xA;&lt;p&gt;1.The way a drug product is designed and manufactured&lt;/p&gt;&#xA;&lt;p&gt;2.Its physical and chemical properties&lt;/p&gt;&#xA;&lt;p&gt;3.Other ingredients it contains&lt;/p&gt;&#xA;&lt;p&gt;4.The physiologic characteristics of the person taking the drug&lt;/p&gt;&#xA;&lt;p&gt;5.How the drug is stored&lt;/p&gt;&#xA;&lt;p&gt;If a tablet releases the drug too quickly, the blood level of the drug may become too high, causing an excessive response. If the tablet does not release the drug quickly enough, much of the drug may be eliminated in the feces without being absorbed, and blood levels may be too low. Drug manufacturers formulate the tablet to release the drug at the desired speed.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Essentially, most drug's absorption rates are slowed down by food in the digestive tract, which is beneficial for various reasons depending on the drug.&#xA;Some pills are irritants to the stomach, in which case they usually have a coating that may need an acidic environment to break down. Food would assist in this, as well as serving as a sort of diluting agent and even a physical barrier for the stomach.&#xA;Conversely, some nutrients (and certain pharmaceuticals) are absorbed by the stomach lining and small intestine much more efficiently when the body is actively digesting food, which is why vitamins and other supplements have the food recommendation.&lt;/p&gt;&#xA;&lt;p&gt;I think that 'before or after' food should be read as '&lt;strong&gt;shortly&lt;/strong&gt; before or after', i.e., so food and pill are digested simultaneously. Otherwise, I believe they just don't mention it. Of course, this is a simplistic rendering of pharmacological absorption vis a vis food (there are some very specific interactions; grapefruit and various blood pressure medications come to mind), but this is the general answer to your general question, I believe.&lt;/p&gt;&#xA;" OwnerUserId="14650" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-25T23:29:37.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29954" PostTypeId="1" CreationDate="2015-02-26T03:39:40.447" Score="4" ViewCount="216" Body="&lt;p&gt;Earth's atmosphere constitutes 78% of Nitrogen, then why do plants need to absorb Nitrogen from the soil. Why couldn't it possible for them to absorb the atmospheric Nitrogen like they do in the case of CO2. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of the plants relies on other sources to fix their Nitrogen, why couldn't be there a single plant which can absorb atmospheric Nitrogen ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any ancient plant which is considered to be using atmospheric Nitrogen ?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I have done a simple research, I could only find that previously&#xA;  atmosphere is not so abundant with Nitrogen and plants developed&#xA;  mechanisms to use Nitrogen fixed in soil. So now they are following&#xA;  the same mechanism when Nitrogen is abundant in the atmosphere. Is&#xA;  this a valid answer ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastActivityDate="2015-02-26T12:33:03.777" Title="why plants cannot use atmospheric nitrogen?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ClosedDate="2015-02-26T09:31:18.507" ContentLicense="CC BY-SA 3.0" />
  <row Id="29956" PostTypeId="1" CreationDate="2015-02-26T04:27:23.380" Score="2" ViewCount="1128" Body="&lt;p&gt;I came across a question which somewhat goes like&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In which of the following kingdom, &lt;strong&gt;most&lt;/strong&gt; of the members have a cell wall made of &lt;strong&gt;polysaccharide&lt;/strong&gt; and &lt;strong&gt;amino acids&lt;/strong&gt; ? - &lt;strong&gt;Monera&lt;/strong&gt; or &lt;strong&gt;Fungi&lt;/strong&gt;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To me it looks like both are correct answers because both are having hetero polymers of glucose and amine. Please enlighten me if I am wrong.&lt;/p&gt;&#xA;" OwnerUserId="14616" LastEditorUserId="19099" LastEditDate="2016-05-03T10:13:38.437" LastActivityDate="2016-07-02T10:44:59.983" Title="Which organisms have their cell wall made of polysaccharides and amino acids?" Tags="&lt;biochemistry&gt;&lt;homework&gt;&lt;classification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29957" PostTypeId="1" AcceptedAnswerId="29959" CreationDate="2015-02-26T05:37:52.497" Score="5" ViewCount="497" Body="&lt;p&gt;In the past few weeks, after the rain started up I noticed these mushrooms around my local area. I'd never seen them previously out of the 20 years I've lived here (a town in Queensland, Australia).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes they have a net-like section, and they sometimes have 10+ flies around a mushroom cluster.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are these mushrooms? Are they common in Australia?&lt;img src=&quot;https://i.stack.imgur.com/bzR5r.jpg&quot; alt=&quot;Netted Mushroom&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8177" LastEditorUserId="6703" LastEditDate="2015-02-26T23:51:42.547" LastActivityDate="2016-04-02T18:25:26.500" Title="Strange Cordeyceps-looking Mushroom in Australia" Tags="&lt;species-identification&gt;&lt;mycology&gt;&lt;mushroom&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29958" PostTypeId="2" ParentId="28078" CreationDate="2015-02-26T06:53:09.137" Score="2" Body="&lt;p&gt;In my opinion you should try &lt;a href=&quot;http://www.illumina.com/products/truseq-rna-access-kit.html&quot; rel=&quot;nofollow&quot;&gt;low input library prep protocols&lt;/a&gt; because in my experience even with a decent quantity of RNA, standardizing the sequencing is not an easy job. The manual says that this kit works with 10-20ng of RNA; always assume the higher limit to be true. There is a higher chance of loss (relative) during extraction also. Try doing precipitation with 5M LiCl and a little glycogen along with alcohol; but assuming your yield is 80ng you can still run replicates for statistical comparisons. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-02-26T06:53:09.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29959" PostTypeId="2" ParentId="29957" CreationDate="2015-02-26T07:27:50.987" Score="5" Body="&lt;p&gt;You found a member of the stinkhorn family, The Phallales (in the family Phallacea), probably a Veiled Lady (&lt;a href=&quot;http://www.inaturalist.org/taxa/hongo_velo_de_novia&quot; rel=&quot;nofollow noreferrer&quot;&gt;Phallus indusiatus&lt;/a&gt;) or a Phallus multicolor (they have other names as well.) They are common in Asia, Africa, the Americas, and Australia. Don't eat them; they're attractive to dogs (lovely aroma!) and there have been dog deaths.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zbbiK.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These fungi produce a spore slime which has an intense smell of rotting meat or sewage, which is why flies are attracted to them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are commonly found in rotted woody material.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2016-04-02T18:25:26.500" LastActivityDate="2016-04-02T18:25:26.500" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29960" PostTypeId="2" ParentId="29795" CreationDate="2015-02-26T08:02:37.727" Score="4" Body="&lt;p&gt;Others have already touched the important points. Consider this as a summary.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What gives HIV the ability to mutate?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;All organisms mutate by two mechanisms:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Replication errors&lt;/li&gt;&#xA;&lt;li&gt;Mutagenesis by physical/chemical agents that cause a chemical change&#xA;(lesion) on DNA&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The main enzyme responsible for HIV replication is &lt;strong&gt;reverse transcriptase&lt;/strong&gt; which makes a DNA copy of its RNA genome. All RNA and DNA polymerases make some amount of error but the error rate of reverse transcriptase is much higher than usual DNA-dependent DNA polymerases because it does not have a proofreading mechanism. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How does a virus like HIV mutate into so many strains, and yet all of&#xA;  them are harmful to our immune system?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As indicated in previous answers, the mutations will produce a virions with a spectrum of infectivity/pathogenicity (some can even be non-infective).&#xA;However, the immune system acts as a selective barrier which selects only those mutants that can survive (similar to what happens in evolutionary process of natural selection). The selected strains expand their population and that is how these strains get established.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-02-26T08:02:37.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29961" PostTypeId="2" ParentId="29766" CreationDate="2015-02-26T08:44:17.310" Score="3" Body="&lt;p&gt;As pointed out by aandreev, the greater the size of the insert relative to the flanks lower will be the recombination rate. This is because the donor DNA essentially becomes non-homologous. See the figures below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/Yy11X.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Figure1: Effect of insert size on recombination efficiency. &lt;a href=&quot;http://aem.asm.org/content/79/5/1712.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Kung et al. (2013) Appl Environ Microbiol. Mar;79(5):1712-7&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/2i41A.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Figure2: Effect of flank size on recombination efficiency. &lt;a href=&quot;http://aem.asm.org/content/79/5/1712.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Kung et al. (2013) Appl Environ Microbiol. Mar;79(5):1712-7&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, you mentioned that you want to make gene knockouts. In this case you just need to make a small mutation (for example introducing a premature stop codon). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Use of genome editing tools such as Crispr-Cas, ZFN and TALEN increase the rate of transgenesis by introducing DNA double strand break.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These can also be used for making knockouts when NHEJ dominates over HR as the DNA repair mechanism. NHEJ is error-prone and can cause indels that can disrupt gene function. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-02-26T11:10:03.450" LastActivityDate="2015-02-26T11:10:03.450" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29962" PostTypeId="2" ParentId="20989" CreationDate="2015-02-26T09:51:15.787" Score="2" Body="&lt;p&gt;I don't think bleach can denature RNA. Bleach is an oxidizing agent and it will damage the RNA. Also, the protocol mentions addition of hypochlorite before heating which I think is illogical because heat will decompose it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For testing RNA integrity you need not make a denaturing gel. What you can instead do is to heat the RNA with the 2xRNA loading buffer that contains 95% formamide and run it in a normal TBE/TAE agarose gel. Heating with formamide denatures the RNA permanently. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Denaturing gels are only essential for Northern Blots. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also run your sample in a bioanalyzer to check for RNA integrity and this is always recommended for RNAseq experiments (even for microarrays but I cannot comment much on that because I have never done it and am not aware of the usual practice).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-02-26T12:05:52.560" LastActivityDate="2015-02-26T12:05:52.560" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29963" PostTypeId="2" ParentId="27474" CreationDate="2015-02-26T10:23:18.480" Score="-1" Body="&lt;h2&gt;Winter swimming and infarcts&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The publication &lt;a href=&quot;http://www.internationaljournalofcardiology.com/article/S0167-5273(14)01865-8/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Long-term risks of cardiac and cerebral vascular diseases increased following winter swimming in the cold seawater&lt;/a&gt; which came out just some weeks ago shows a link between long-term winter swimming and CVD. &#xA;I think this is the best evidence so far about the possible link. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;WYSIWYG's comment has some good general idea:&lt;/h2&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many processes are affected by temperature including metabolism and&#xA;  growth rates. Reaction rates increase with temperature but not in case&#xA;  of catalysed reactions where the catalyst can operate at only an&#xA;  optimum temperature.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Some related topics&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/21258/how-does-temperature-influence-the-rate-of-protein-degradation&quot;&gt;temperature effect on the rate of protein degradation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So further studies&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;protein degradation in the heart in persistent hypothermia&lt;/li&gt;&#xA;&lt;li&gt;...&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Effect of persistent hypothermia on processes of cAF&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;[1]&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's have cAF (chronic atrial fibrillation) here as an target. &#xA;Electrophysiological study shows that cAF-related remodeling is typically divided into three categories: 1) electrical, 2) contractile and 3) structural. &#xA;They cause respectively&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;1) shortening of both the action potential (AP) duration and effective refractory period (ERP)&lt;/li&gt;&#xA;&lt;li&gt;2) possibly a result of impaired Ca2+ intracellular handling&lt;/li&gt;&#xA;&lt;li&gt;3) changes of cellular level (hypertrophy, glycogen accumulation and modified mitochondrial morphology) and tissue fibrosis&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;cAF's processes in persistent hypothermia&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I cannot say now more anything about persistent hypothermia and cAF by confidence. &#xA;Those mechanisms of Koivumäki et al are cellular processes, while the representation of the heart requires integrative analysis in the cellular, tissue and organ levels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In cellular level &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Only some catalyzed reactions can work in persistent hypothermia. TODO consider which enzymes of the heart and body work in low temperature in short-term and long-term cases. Depletion cases too. &lt;/li&gt;&#xA;&lt;li&gt;Effect of persistent hypothermia on the outflux of Calcium (probably, slows down). &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In tissue level&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I can say without rigor that electrical coordination is uncoordinated in tissue fibrosis. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In organ level &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I say say without rigor that the mean electrical axis should be determined and fixed in the study. &lt;/li&gt;&#xA;&lt;li&gt;Effect of Arterial hypertension must be fixed. Sokolew-Lyon index can a starting point for the indicator but better indicator is required with higher specificity. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Persistent hypothermia from the extreme side (Sauna)&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;[2] Regular Sauna is with better hemodynamic function; however, the association of sauna bathing with cardiovascular and all-cause mortality is not known.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;so possible effect of persistent hypothermia can be &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;lower hemodynamic function if no compensation mechanism&lt;/li&gt;&#xA;&lt;li&gt;better hemodynamic function if some compensation mechanism (genetics; unknown)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Some research topics&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Effect of Persistent Hypothermia on the Arterial Hypertension. This may be associated with coagulopathy, especially in the lower limb. &lt;/li&gt;&#xA;&lt;li&gt;Effect of Persistent Hypothermia on Atherosclerosis. It would be very nice to see long-term study about the effect of regular 4-7 winter swimming on the cardiovascular risk score, SCORE and others.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h2&gt;Sources&lt;/h2&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;In Silico Screening of the Key Cellular Remodeling Targets in Chronic Atrial Fibrillation. Koivumäki et al. Computational Biology. &lt;/li&gt;&#xA;&lt;li&gt;Association Between Sauna Bathing and Fatal Cardiovascular and All-Cause Mortality Events, &lt;a href=&quot;http://archinte.jamanetwork.com/article.aspx?articleid=2130724&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Please, see the reference of the publication for more better view. &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2016-02-16T05:48:55.080" CommentCount="0" CommunityOwnedDate="2015-02-26T10:23:18.480" ContentLicense="CC BY-SA 3.0" />
  <row Id="29965" PostTypeId="2" ParentId="28322" CreationDate="2015-02-26T10:24:04.983" Score="3" Body="&lt;p&gt;A heterozygous locus has two different alleles and therefore it is possible that their DNA sequence lengths are different. However, it is unlikely that they are so different so as to be clearly resolved in a gel electrophoresis. Agarose gels can at best resolve 20bp; polyacrylamide gels can resolve smaller differences but it is only done for small DNA fragments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I think upto 50bp difference is possible between alleles. But such huge insertions/deletions are rare and the difference between the alleles is usually a point mutation or small insertions/deletions(indels). Big indels are possible when a transgene is inserted specifically in one chromosome; these cases are mostly experimental.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you consider paralogs as alleles then they can be of different lengths and can be resolved in agarose gels— usually the difference is in the untranslated regions. If you are doing Southern blot and using a probe that can bind to both paralogs then you will end up getting two bands. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having said that, it is possible to see a difference in gel bands even if there is no size difference. This is possible by a technique called &lt;a href=&quot;http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism&quot; rel=&quot;nofollow&quot;&gt;RFLP&lt;/a&gt;. In this technique the DNA is digested using a restriction enzyme which basically cuts the DNA at a specific sequence (usually a hexamer). If a point mutation abolishes or creates a restriction site then the fragment length would be different between the alleles. This is detectable on the gel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A similar technique is &lt;a href=&quot;http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism&quot; rel=&quot;nofollow&quot;&gt;AFLP&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-02-26T11:12:47.637" LastActivityDate="2015-02-26T11:12:47.637" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29968" PostTypeId="2" ParentId="28577" CreationDate="2015-02-26T11:54:45.943" Score="2" Body="&lt;p&gt;Ignoring parameters such as:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Leaf shapes&lt;/li&gt;&#xA;&lt;li&gt;Difference in photosynthetic efficiency due to other metabolic factors&lt;/li&gt;&#xA;&lt;li&gt;Unequal illumination of leaves&lt;/li&gt;&#xA;&lt;li&gt;Nutrient content of the soil&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Photosynthesis rate of a plant&lt;sup&gt;&lt;strong&gt;1&lt;/strong&gt;&lt;/sup&gt; depends on the [total number of leaves] × [surface area of a leaf].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that a tree occupies same ground area as a shrub, there will be same number of trees as shrubs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A tree is taller and can bear more number of leaves and if we assume that the surface area of the leaves are similar between trees and shrubs then the tree would carry out more photosynthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However you say that the number of leaves is the same; in this case both will carry out same amount of photosynthesis (the shrub may outlive the tree though, as the latter won't be able to support its huge size with same level of photosynthesis as the shrub).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A note on phtoplanktons and algae: One reason amongst a few for why they are efficient at photosynthesis is because the number of photosynthetic cells per volume is higher in them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;em&gt;&lt;sup&gt;&lt;strong&gt;1&lt;/strong&gt;&lt;/sup&gt; I am using the term plant to denote all plants. Big trees are called trees and small plants are called shrubs, for convenience.&lt;/em&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-02-27T04:50:42.113" LastActivityDate="2015-02-27T04:50:42.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29969" PostTypeId="1" AcceptedAnswerId="29973" CreationDate="2015-02-26T13:28:25.940" Score="2" ViewCount="87" Body="&lt;p&gt;My mother has told that if your organism needs a vitamin, you want fruits include that vitamin. For example you have lack of C-vitamin you would like to eat lemon. Is there any explanation for it, or just it is a myth? The human organism knows that what we have to eat?&lt;/p&gt;&#xA;" OwnerUserId="13243" LastEditorUserId="13243" LastEditDate="2015-02-26T22:44:41.860" LastActivityDate="2015-02-26T22:44:41.860" Title="The human organism knows what we have to eat?" Tags="&lt;human-biology&gt;&lt;vitamins&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-02-26T18:13:19.517" ContentLicense="CC BY-SA 3.0" />
  <row Id="29972" PostTypeId="1" CreationDate="2015-02-26T15:02:43.223" Score="5" ViewCount="2143" Body="&lt;p&gt;The gram positive have negative components in the peptidoglycan layer in the form of teichoic acid phosphodiester bonds, and the gram negative have negative components in their outer membrane in the form of lipopolysaccharide. Is that where the crystal violet binds?&lt;/p&gt;&#xA;" OwnerUserId="14656" LastEditorUserId="3340" LastEditDate="2015-02-27T05:02:00.933" LastActivityDate="2015-02-28T21:45:20.547" Title="To which negatively charged components of the cell envelopes do the crystal violet complexes bind in gram staining?" Tags="&lt;biochemistry&gt;&lt;microbiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29973" PostTypeId="2" ParentId="29969" CreationDate="2015-02-26T16:22:24.443" Score="1" Body="&lt;p&gt;Assuming you mean organism, not organisation, it's not entirely false that cravings can be driven by deficiencies. In the case of the eating disorder pica, where a person eats non-food items like dirt and clay, can be caused by iron deficiency (&lt;a href=&quot;http://www.academia.edu/202338/Pica_An_Update&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;). However, that article also suggests the possibility that pica &lt;em&gt;causes&lt;/em&gt; iron deficiency by causing the person to eat items that lower iron absorption. So, my answer to your question is, maybe.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-02-26T16:22:24.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29974" PostTypeId="1" AcceptedAnswerId="29988" CreationDate="2015-02-26T17:25:25.057" Score="2" ViewCount="161" Body="&lt;p&gt;I have read in some texts that diabetes mellitus type 1 is caused by degeneration of beta cells due to our body's own immune reaction.Is it true? Can you explain further how are such types of immune reactions are induced? And are there any other causative factors known?&lt;/p&gt;&#xA;" OwnerUserId="14641" LastEditorDisplayName="user14640" LastEditDate="2015-02-28T18:58:33.743" LastActivityDate="2015-02-28T18:58:33.743" Title="Detailed mechanism of the cause of diabetes mellitus type 1?" Tags="&lt;cell-biology&gt;&lt;physiology&gt;&lt;zoology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29975" PostTypeId="1" CreationDate="2015-02-26T17:32:23.250" Score="2" ViewCount="2392" Body="&lt;p&gt;If a person is a chimera and has two different blood types in his veins, how does he not die? Shouldn't the immune system attack one of the blood types?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In 1953 a human chimera was reported in the British Medical Journal. A&#xA;  woman was found to have blood containing two different blood types.&#xA;  Apparently this resulted from her twin brother's cells living in her&#xA;  body. More recently, a study found that such blood group chimerism&#xA;  is not rare.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="14657" LastEditorUserId="15051" LastEditDate="2015-04-09T19:06:35.707" LastActivityDate="2018-06-27T23:54:21.167" Title="How do genetic chimeras with different blood types not die?" Tags="&lt;dna&gt;&lt;hematology&gt;&lt;autoimmune&gt;&lt;chimerism&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="29979" PostTypeId="1" AcceptedAnswerId="29981" CreationDate="2015-02-26T21:01:07.567" Score="0" ViewCount="3631" Body="&lt;p&gt;I just know that Acetyl-CoA is a positive allosteric modulator for pyruvate carboxylase, but I cannot find anything else.&lt;/p&gt;&#xA;" OwnerUserId="10470" LastActivityDate="2015-02-26T22:58:46.150" Title="What is the role pyruvate carboxylase in lipogenesis?" Tags="&lt;lipids&gt;&lt;biosynthesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29980" PostTypeId="1" AcceptedAnswerId="29983" CreationDate="2015-02-26T22:05:00.930" Score="8" ViewCount="1374" Body="&lt;p&gt;Bacteria are essential to life in that they are responsible for breakdown of organic substances, etc. but are bacteria necessary for an &lt;em&gt;individual's&lt;/em&gt; life?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, how long would a human survive if they took a super-antibiotic which killed &lt;em&gt;all&lt;/em&gt; the bacteria in their body, with the current state of medical technology? If they died what would be the most likely cause of death?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume bacteria don't recolonize your body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Background: I call bacteria the &quot;Lords of the Earth&quot; both to remind myself to be humble and (rather more) as a conversation-starter. I'd like to be able to underline their importance in the ensuing discussions.&lt;/p&gt;&#xA;" OwnerUserId="14660" LastEditorUserId="14660" LastEditDate="2015-02-28T23:16:06.707" LastActivityDate="2015-02-28T23:16:06.707" Title="Are bacteria necessary for an individual's life, or, how long could a person live without bacteria?" Tags="&lt;human-biology&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-02-27T08:46:01.977" ContentLicense="CC BY-SA 3.0" />
  <row Id="29981" PostTypeId="2" ParentId="29979" CreationDate="2015-02-26T22:58:46.150" Score="3" Body="&lt;p&gt;Okay so pyruvate carboxylase is a ligase-class enzyme, meaning it forms covalent bonds. What we see is that pyruvate is carboxylated into oxaloacetate by pyruvate carboxylase, here's our proposed reaction,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AduZ3.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What this does is replenish mitochondrial oxaloacetate levels, because when we switch into lipogenesis, TCA intermediates must be shuttled into the cytoplasm for forming triglycerides, like so,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8i1kx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1220216/pdf/10229653.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;, page 2, they go into how the production of NADPH is coupled to acetyl group export and how PC must perform the aforementioned function to keep substantial flow maintained. Block quoted them for ease of access,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As shown in Scheme 1, the&#xA;  generation of NADPH is coupled to the transport of mitochondrial&#xA;  acetyl groups into the cytosol for fatty acid synthesis.&#xA;  Acetyl-CoA is generated in the mitochondria by the oxidative&#xA;  decarboxylation of pyruvate, and, after condensation with oxaloacetate,&#xA;  acetyl groups are transported to the cytoplasm as citrate,&#xA;  which undergoes ATP-dependent cleavage to yield acetyl-CoA&#xA;  and oxaloacetate. This pathway requires a continuous supply of&#xA;  oxaloacetate, which is produced by the activity of PC. AcetylCoA,&#xA;  a building block for the synthesis of long-chain fatty acids,&#xA;  is then converted into malonyl-CoA by acetyl-CoA carboxylase&#xA;  (ACC). Meanwhile, the oxaloacetate generated in the cytosol&#xA;  from citrate is reduced with NADH to malate, which in turn is&#xA;  oxidatively decarboxylated in a reaction catalysed by NADP+-&#xA;  dependent malate dehydrogenase (‘malic enzyme’; EC 1.1.1.40).&#xA;  The pyruvate thereby produced is taken up by the mitochondria&#xA;  and carboxylated to give oxaloacetate, while the NADPH&#xA;  generated is used in the pathway of fatty acid synthesis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-02-26T22:58:46.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29983" PostTypeId="2" ParentId="29980" CreationDate="2015-02-27T00:58:34.473" Score="11" Body="&lt;p&gt;You might need to demote your single-celled 'lords' to 'squires'. They're not essential to an individual's life. You wouldn't die (dispensing with the &quot;how&quot; right off the bat.) You'd be just fine if no bacteria reentered your body. Your fecal output would be greater; you would derive somewhat less nutrition from your food, you would need to take vitamin K, and there would be an adjustment period, but theoretically, you'd be just fine. You might even be healthier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your hypothetical is impossible, of course, because experimentation on humans is unethical. However, it might surprise you to learn that there are colonies of germ-free animals (also called &lt;em&gt;gnotobiotic&lt;/em&gt;) used to study the effect of certain bacteria on animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The derivation of such subjects was initially fairly gruesome.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The process of engineering biology and machine began by removing intact uteruses from near- to full-term pregnant animals within a purpose-built germ-free &quot;surgical isolator.&quot; The uterus was subsequently passed through various disinfection procedures, involving total immersion in germicide-filled &quot;dunk tanks,&quot; before the progeny were surgically released and hand reared within a second microbially sterile isolator.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These animals are costly to keep, as you can imagine. The originals must be delivered by Cesarean section, and housed and raised in sterile conditions. But once you can do that, they can multiply. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To start a germ-free colony, one must remove a young animal from its mother’s womb through a careful surgical procedure to avoid exposing it to the microorganisms in the mother’s vagina and skin. Then, the animal is raised in a sterile cage and only exposed to food, water, and other equipment that has also been sterilized. On a weekly basis—or more often—a technician swabs cages and animal feces to ensure that no bacteria have contaminated the sterile housing. Once the colony has been created, it becomes easier to rear new germ-free animals; a germ-free mother can give birth naturally without exposing her newborns to any bacteria.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;By the 1950s, researchers were rearing germ-free mice, rats, guinea pigs, and chicks inside sterile stainless steel (and later, plastic) housings. Germ-free animals are especially useful in researching, among other things, diabetes, auto-immune diseases, obesity, genetic engineering, cancer, immunology, nutrition, and the effects of normal intestinal flora on health.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vitamin K must be added to their diets, and it is important to sterilize their food without destroying nutrients, but otherwise they do well in their environments. Their feces, of course, are sterile. Everything is microbe-free. They also have no &quot;normal&quot; antibodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since generations of germ-free animals can exist and multiply, it is not only possible but quite likely that germ-free humans can exist as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which is not to say that gut (and skin, etc.) microbiomes are unimportant. If you release a germ-free animal into a normal environment, it can die if it picks up pathogenic bacteria before more normal gut flora. To do this safely, a germ-free animal is first given a cocktail of bacteria to colonize the gut. After a while, they can be in a normal environment without problems. But your hypothetical human wouldn't even have this problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://irp.nih.gov/catalyst/v19i4/germ-free-mice&quot;&gt;Germ-Free Mice&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3918800/&quot;&gt;Gnotobiotics&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.narlabs.org.tw/en/pressroom/topic/topic.php?group_id=3&amp;amp;topic_id=1&quot;&gt;Technology Highlights：ESTABLISHMENT OF THE FIRST GERMFREE MOUSE AND RAT COLONIES IN TAIWAN&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477854/&quot;&gt;&quot;Life in a Germ-Free World&quot;:&#xA;Isolating Life from the Laboratory Animal to the Bubble Boy&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-02-27T04:17:19.567" LastActivityDate="2015-02-27T04:17:19.567" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="29985" PostTypeId="1" AcceptedAnswerId="29986" CreationDate="2015-02-27T01:33:10.380" Score="1" ViewCount="158" Body="&lt;p&gt;I'm trying to get my head around what a pseudoknot is and how I can identify them given some RNA string. For example, suppose I have a string s = CGUUGUGUACACGAUAGUACAU. Suppose the two longest substring inversions are identified in bold &lt;strong&gt;CGU&lt;/strong&gt;UGUGUAC&lt;strong&gt;ACG&lt;/strong&gt;AUAGUACAU, which form the stack of the hairpin and everything after the first substring and before the start of the last substring make up the hairpin as illustrated below.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;                                  U G U&#xA;                                G       A&#xA;                                 U     C&#xA;                                  C - A&#xA;                                  G - C&#xA;                                  U - G A U A G U A C A U&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;By definition, a pseudoknot is defined as a secondary structure formed by pairing between a loop and a region located outside of the stem flanking the loop. In this example, we would start the pairing using some substring of the outer tail and start matching bases around the hairpin. My question: is the pseduoknot the alignment of these base pairs, and what is the significance of this alignment?&lt;/p&gt;&#xA;" OwnerUserId="14574" LastActivityDate="2015-02-27T03:11:28.967" Title="What are pseudoknots?" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29986" PostTypeId="2" ParentId="29985" CreationDate="2015-02-27T03:11:28.967" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;is the pseduoknot the alignment of these base pairs&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I'm not exactly sure what is meant by &lt;em&gt;alignment&lt;/em&gt;, but if you mean base pairing from the flanking RNA to the loop of the hairpin you have depicted, then you would have an H-type pseudoknot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since you are interested in predicting these structures, it's important to note that a nucleic acid sequence capable of forming the necessary base-pairs for a pseudoknot structure does &lt;em&gt;not&lt;/em&gt; imply that the sequence indeed forms a pseudoknot. It's likely that the sequence has a minimum free energy (MFE) structure that is &lt;em&gt;not&lt;/em&gt; pseudoknotted. So the base-pairing capability is necessary but not sufficient for predicting these structures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take a look at the following (full-text) articles on pseudoknot prediction for additional information:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472101/&quot; rel=&quot;nofollow&quot;&gt;Computational Analysis of Noncoding RNAs&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853144/&quot; rel=&quot;nofollow&quot;&gt;DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064103/&quot; rel=&quot;nofollow&quot;&gt;A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2271355/&quot; rel=&quot;nofollow&quot;&gt;KnotSeeker: Heuristic pseudoknot detection in long RNA sequences&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="14609" LastActivityDate="2015-02-27T03:11:28.967" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29987" PostTypeId="1" CreationDate="2015-02-27T03:20:27.883" Score="4" ViewCount="83" Body="&lt;p&gt;I am writing a step by step guide for doing a western blot for a class.  It is intended for any  one with basic Biology lab skills.  I am hoping people will review my draft and give feedback on how to improve it.  Be as critical as you like about any aspect of it, I need it to be clear and concise as well as accurate.  Any tips appreciated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://docs.google.com/document/d/1Lpprwn4s127cb0D5TQezpurbjdF9hqJZQC0H7PIovE0/edit?usp=sharing&quot; rel=&quot;nofollow&quot;&gt;https://docs.google.com/document/d/1Lpprwn4s127cb0D5TQezpurbjdF9hqJZQC0H7PIovE0/edit?usp=sharing&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14664" LastActivityDate="2015-02-27T03:20:27.883" Title="Procedure for doing western blot" Tags="&lt;lab-techniques&gt;&lt;cell&gt;&lt;western-blot&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2015-02-28T00:07:05.723" ContentLicense="CC BY-SA 3.0" />
  <row Id="29988" PostTypeId="2" ParentId="29974" CreationDate="2015-02-27T03:28:32.067" Score="2" Body="&lt;p&gt;Diabetes mellitus is divided into four  type 1, type 2, gestational diabetes, and specific type of diabetes. Type 1 diabetes is commonly called as Juvenile diabetes or Brittle diabetes.&#xA;It is also called as &quot;Insulin-dependent diabetes mellitus (IDDM)&quot;. For our bad-luck the causes of Type 1 diabetes remains obscure, and scientists believes its mostly related to genetics and other environmental factors like mutations or virus attacks. I found some articles that may help.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But it&#xA;  is believed that genetic and environmental factors (possibly viruses)&#xA;  may be involved. The aetiology ('cause') of type 1 diabetes is&#xA;  unknown, but a good deal is known about its pathogenesis (the way in&#xA;  which it develops). As with other complex diseases, the outcome is&#xA;  determined by the interplay of multiple genes and (most likely)&#xA;  multiple environmental determinants, together with an element of&#xA;  happenstance. The risk of developing diabetes is strongly influenced&#xA;  by genes affecting immune function, particularly the &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_leukocyte_antigen&quot; rel=&quot;nofollow noreferrer&quot;&gt;HLA system&lt;/a&gt;,&#xA;  but other factors are involved. The best evidence for this comes from&#xA;  the study of identical twins: if one twin develops diabetes in&#xA;  childhood, the other (who has identical genes) has no more than a one&#xA;  in three chance of developing the disease. Prospective studies in&#xA;  human populations reveal that circulating auto antibodies directed&#xA;  against the &lt;a href=&quot;http://en.wikipedia.org/wiki/Islets_of_Langerhans&quot; rel=&quot;nofollow noreferrer&quot;&gt;islets&lt;/a&gt; typically appear in the first 5 years of life, and&#xA;  may be present for many years (sometimes 20 years or more) before the&#xA;  disease develops. A similar latent period is seen with coeliac&#xA;  disease, and implies that some sort of regulatory balance has been&#xA;  achieved within the immune system, and subsequently lost. This opens&#xA;  the door to the possibility of 're-education' of the immune system by&#xA;  various forms of immune intervention.&#xA;  &lt;a href=&quot;http://webcache.googleusercontent.com/search?q=cache:8SahffUIrC0J:www.diapedia.org/type-1-diabetes-mellitus/pathogenesis%20&amp;amp;cd=4&amp;amp;hl=en&amp;amp;ct=clnk&amp;amp;gl=in&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The pathogenesis of Diabetes mellitus type 1 shows a strong tendency towards genetic related factors,&#xA;  &lt;img src=&quot;https://i.stack.imgur.com/y4YcK.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;  &lt;a href=&quot;http://link.springer.com/article/10.2165/00063030-200115050-00002#page-1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastActivityDate="2015-02-27T03:28:32.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29989" PostTypeId="1" CreationDate="2015-02-27T04:37:06.937" Score="2" ViewCount="402" Body="&lt;p&gt;Recently came across Wiki article about anaphrodisiac herbs and other products.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;An anaphrodisiac (also antaphrodisiac or antiaphrodisiac) is something&#xA;that quells or blunts the libido. It is the opposite of an&#xA;aphrodisiac, something that enhances sexual appetite. The word&#xA;anaphrodisiac comes from the Greek privative prefix ἀν-, denoting&#xA;negation, and aphrodisiac, from the Greek goddess of love, Aphrodite.&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Anaphrodisiac&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The article mentioned some of the herbs and plant related putative anaphrodisiacs like,&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Marjoram (Origanum majorana) (Family: Lamiaceae)&lt;/li&gt;&#xA;&lt;li&gt;Humulus lupulus (Family: Cannabaceae)&lt;/li&gt;&#xA;&lt;li&gt;Heracleum mantegazzianum  (Family: Apiaceae)&lt;/li&gt;&#xA;&lt;li&gt;Morton Arboretum  (Family: Salicaceae)&lt;/li&gt;&#xA;&lt;li&gt;Vitex agnus-castus (Family: Lamiaceae)&lt;/li&gt;&#xA;&lt;li&gt;Ruta graveolens (Family: Rutaceae)&lt;/li&gt;&#xA;&lt;li&gt;Coriandrum sativum (Family:  Apiaceae)&lt;/li&gt;&#xA;&lt;li&gt;Tropaeolum tuberosum(Family:  Tropaeolaceae)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;&lt;strong&gt;I am not sure that is there any relevance in these claims that these herbs triggers anaphrodisiac effect.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;The question is,&lt;/p&gt;&#xA;&lt;p&gt;Is there any common alkaloid, aromatic hydrocarbons or any other chemicals present in these herbs which triggers the anaphrodisiac effects ?&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-27T05:41:57.897" Title="Common properties of herbs in creating anaphrodisiac effect?" Tags="&lt;botany&gt;&lt;sexuality&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="29990" PostTypeId="1" AcceptedAnswerId="29992" CreationDate="2015-02-27T04:41:45.130" Score="1" ViewCount="887" Body="&lt;p&gt;I know that oxaloacetate cannot cross the mitochondrial membrane, but can instead be converted to aspartate, shuttled out, and then re-converted back to oxaloacetate.  What does this have to do with gluconeogenesis?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The traditional route is to convert pyruvate to OAA to malate in the mitochondria, shuttle the malate out, and then convert malate back to OAA in the cytosol.  If lactate is the precursor, then the conversion of lactate to pyruvate in the cytosol can generate an NADH, making the conversion to malate in the mitochondria unnecessary.  Thus, OAA is converted directly to PEP in the mitochondria by mitochondrial PEPCK and shuttled out to the cytosol to begin gluconeogenesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we have these two pathways, what is the point of using aspartate?&lt;/p&gt;&#xA;" OwnerUserId="10470" LastEditorUserId="3340" LastEditDate="2015-06-04T11:38:27.550" LastActivityDate="2015-06-04T11:38:27.550" Title="What is the role of Aspartate Transaminase in gluconeogenesis?" Tags="&lt;glucose&gt;&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29991" PostTypeId="1" CreationDate="2015-02-27T05:47:24.550" Score="2" ViewCount="243" Body="&lt;p&gt;So I'm sure you've all seen the dress photo where people see the dress as either White and Gold or Blue and Black.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has essentially 'split' the internet because some people see the dress and they think that it is coloured blue and black, whereas the other half think that it is white and gold. It is trending on most social media sites as people fight about what the colour difference is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is why do different peoples eyes perceive different colours in this picture specifically?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For reference the photo with a color breakdown can be found &lt;a href=&quot;http://www.wired.com/wp-content/uploads/2015/02/Unknown.png&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9198" LastEditorUserId="9198" LastEditDate="2015-02-27T08:43:33.567" LastActivityDate="2015-03-10T23:16:33.557" Title="White/Gold vs Blue/Black dress" Tags="&lt;eyes&gt;&lt;perception&gt;" AnswerCount="0" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29992" PostTypeId="2" ParentId="29990" CreationDate="2015-02-27T06:13:38.737" Score="1" Body="&lt;p&gt;I may have approached this problem from the wrong direction, so here's my attempt at an answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For gluconeogenesis to function, glycolysis needs to be shut off.  Glycolysis feeds the TCA cycle with Acetyl-CoA through the decarboxylation of pyruvate, and without glucose as a source, we need to look to other methods of generating OAA to make into PEP.  We can make OAA through Aspartate Transaminase by reacting Aspartate with α-ketoglutarate.&lt;/p&gt;&#xA;" OwnerUserId="10470" LastActivityDate="2015-02-27T06:13:38.737" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29994" PostTypeId="1" CreationDate="2015-02-27T07:42:11.313" Score="2" ViewCount="523" Body="&lt;p&gt;We have been raising mealworms for some time and while mealworm frass has proven very useful as a plant fertilizer, I started wondering about other potential uses of this leftover waste.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone please explain what kind of compounds make up the frass from mealworms as percentages of overall makeup?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular I would like to understand how mealworm waste compares to other commonly used animal wastes used as fertilizer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bonus points if you can suggest &lt;strong&gt;&lt;em&gt;other&lt;/em&gt;&lt;/strong&gt; applications (than just fertilizer) for mealworm frass! &lt;/p&gt;&#xA;" OwnerUserId="14667" LastActivityDate="2015-02-27T07:42:11.313" Title="What is the chemical makeup of mealworm frass?" Tags="&lt;entomology&gt;&lt;organic-chemistry&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="29995" PostTypeId="2" ParentId="28578" CreationDate="2015-02-27T07:47:11.510" Score="6" Body="&lt;p&gt;It's all about chemical reactions in your body triggered by your brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lot's of researches and documents confirmed this is what happens when you face a stressful situation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Stress -&gt; hypothalamus -&gt; sympathetic nerves -&gt; Epinephrine (Adrenaline) -&gt; more urine flow&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Domino neural connectivity (Thinking) =&gt; Domino Chemistry (Body reaction = stress and anxiety)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Situations like thinking about exam and how hard it would be or how it could change opportunities and feelings in your life you are triggering a chain of neural and chemical responses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your thoughts (Activated neurons) end with unsolved vital problem, it activates parts of your brain that is related to anxiety and stress and these neurons activate hypothalamus.&#xA;Hypothalamus turns sympathetic nerves on.&#xA;The sympathetic nerves release adrenaline (epinephrine).&#xA;And adrenaline cause more urine flow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://www.adrenaladvice.com/adrenal-fatigue-urination.shtml&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt;&lt;/strong&gt; example shows two more kinds of polyuria&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in how increasing level of adrenaline results in more urine flow read &lt;strong&gt;&lt;a href=&quot;http://fblt.cz/en/skripta/vii-vylucovaci-soustava-a-acidobazicka-rovnovaha/3-tvorba-moci/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;&lt;/strong&gt; and &lt;strong&gt;&lt;a href=&quot;http://www.thestudentroom.co.uk/showthread.php?t=1206413&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;&lt;/strong&gt; and &lt;a href=&quot;http://ajplegacy.physiology.org/content/192/1/131&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8540" LastEditorUserId="8540" LastEditDate="2015-09-30T20:09:00.167" LastActivityDate="2015-09-30T20:09:00.167" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="29996" PostTypeId="1" CreationDate="2015-02-27T09:00:29.493" Score="3" ViewCount="189" Body="&lt;p&gt;I'm currently sick because of scarlet fever but I got treated with antibiotics. I know that after 1.5 day using antibiotics the streptococci I release at home are dangerous anymore. But my question is, what about the streptococci I've spread before? I've read that &lt;em&gt;Streptococcus pyogenes&lt;/em&gt; can survive 3 days to 6.5 months outside the host, does that mean, I have to disinfect the whole house? And if so, with what should I desinfect? I worked heavily on the laptop, how do I desinfect that? Thank you.&lt;/p&gt;&#xA;" OwnerUserId="14669" LastEditorUserId="11841" LastEditDate="2015-02-27T20:05:56.243" LastActivityDate="2015-02-28T14:31:40.757" Title="Survival of streptococcus after my scarlet fever" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;epidemiology&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="29997" PostTypeId="1" CreationDate="2015-02-27T10:08:51.723" Score="1" ViewCount="249" Body="&lt;p&gt;I am interested in using BEAST to find the divergence time estimates of species separations within a genus of frogs. The genus separated from a outgroup taxon I have chosen around 80 million years ago. That is all the information I have. Is it possible for me to do a divergence analysis using BEAST and set an informative prior based on the information I have ?&lt;/p&gt;&#xA;" OwnerUserId="18932" LastActivityDate="2015-02-27T10:08:51.723" Title="How do I use BEAST for divergence time estimation in this case?" Tags="&lt;bioinformatics&gt;&lt;phylogenetics&gt;&lt;speciation&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="29999" PostTypeId="1" CreationDate="2015-02-27T13:51:09.733" Score="5" ViewCount="124" Body="&lt;p&gt;Is there any reliable open-source software for simulating the behaviour of human cortical neurons? I am looking for serious software, so let's assume I have access to a computer with more than 10,000 computing cores.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I would like to do is to scan a subject's brain with MRI, record EEG during a simple task (e.g. listening to tone pips), project the EEG data to the cortical surface calculated from the MRI (solve the so-called electromagnetic inverse problem), and once that is done try to simulate the behavior of the cortical neurons at the &quot;active&quot; regions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This simulation part is new to me, the rest I know quite well. All hints and ideas are welcome!&lt;/p&gt;&#xA;" OwnerUserId="14672" LastActivityDate="2015-02-28T11:22:34.563" Title="What (open) software there are for simulating behaviour of human (cortical) neurons?" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;&lt;software&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30000" PostTypeId="2" ParentId="29999" CreationDate="2015-02-27T14:16:53.813" Score="3" Body="&lt;ol&gt;&#xA;&lt;li&gt;No, not in the neuronal level. Because IMHO this is an ill-posed problem.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;EEG combined with MRI won't have the resolution to do solve the inverse problem of neuronal network simulation. There are at least hundreds of thousands of neurons that would be involved in your specific behavioral task, and you have at most a few hundred electrodes. You'll have to make &lt;em&gt;grossly simplifying assumptions about how the brain works&lt;/em&gt; to start any inference. You might learn something, but the claim would be somewhat weak.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally, I wouldn't work with EEG if you are interested in the mechanistic details of the brain. It is a very useful signal for some cognitive investigations (especially for humans), but the current technology lacks the spatial resolution.&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;Yes, in the coarse scale network level. (response to @sets' feedback)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;If you don't care about micro-scale dynamics of the neural network, and want to model some population-wide activation that changes EEG, as @sets commented, there are various source localization &amp;amp; dynamical system models that you can use. I am not an expert on this, so see @sets' answer, or hopefully someone else will answer in detail.&lt;/p&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2015-02-28T11:22:34.563" LastActivityDate="2015-02-28T11:22:34.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30001" PostTypeId="1" CreationDate="2015-02-27T14:39:28.197" Score="3" ViewCount="426" Body="&lt;p&gt;Creating an action potential needs at least tens of mV potential difference across the membrane to occur.&#xA;But the membrane is really thin, surely less then 0.01µm (some reference give 25A).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then the potential gradient, that is to say the electric field E, must be very strong :&#xA;The order of magnitude of the needed electric field is much greater than 10mV/0.01µm = $10^{6}$ V/m&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But TMS produces E of the order of 200 V/m on the scalp, which is even less inside the brain. Then how can TMS induces neurons depolarization ? &lt;/p&gt;&#xA;" OwnerUserId="5484" LastEditorUserId="5484" LastEditDate="2015-02-28T22:42:24.243" LastActivityDate="2015-03-05T13:57:08.093" Title="How can TMS induce enough depolarization to cause an action potential?" Tags="&lt;neuroscience&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30002" PostTypeId="1" CreationDate="2015-02-27T15:42:22.617" Score="3" ViewCount="381" Body="&lt;p&gt;I am wondering what the exact definition of biochemical coupling between two enzymatic reactions is. I know that these two enzymatic reactions have to&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;share the same intermediate(s) &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;one is thermodynamically favorable and the other is not. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So  the thermodynamically unfavorable reaction can happen when it coupled with the  thermodynamically favorable reaction. I just want to confirm that : &lt;strong&gt;Do these two enzymes have to be physically associated with each other&lt;/strong&gt;? Since I do not have any evidence to support the physically interactions between these two enzymes, can I still use the term &quot;biochemical coupling&quot;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many thanks.&lt;/p&gt;&#xA;" OwnerUserId="14673" LastEditorUserId="11607" LastEditDate="2015-02-27T18:36:08.820" LastActivityDate="2015-03-02T08:16:46.127" Title="Biochemical coupling between two enzymatic reactions - Enzymes physically associated?" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30003" PostTypeId="1" AcceptedAnswerId="30010" CreationDate="2015-02-27T15:44:09.190" Score="3" ViewCount="4150" Body="&lt;p&gt;I'm not biologist and I have just a basic knowledge. I've been thinking for a long time about the following question: How does the body choose which 23 chromosomes should be active in human sperm and female eggs? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance for helping me with this!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&#xA;Each egg cell or sperm contains 23 chromosome whereas a normal cell has 46 chromosomes. So How is it that those specific 23 chromosomes are the chosen ones. Are a random collection of chromosomes selected at the end of meiosis or is it more specific than that?&lt;/p&gt;&#xA;" OwnerUserId="14674" LastEditorUserId="5144" LastEditDate="2015-02-28T08:04:35.483" LastActivityDate="2016-01-15T21:05:58.183" Title="How are 23 chromosomes in human sperm chosen?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30005" PostTypeId="1" AcceptedAnswerId="30018" CreationDate="2015-02-27T17:17:47.880" Score="17" ViewCount="9895" Body="&lt;p&gt;Some mammals can have a black, pink or spotted skin, depending on race - see for example humans or pigs. But I recently learned that this is not the case with mice. Even black furred mice have pink skin, and there is a rare mutation which produces black skinned mice. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was talking with a friend about cats and we got to wonder if (domestic) cats are the type of animal which can have dark skin, like pigs, or the type which doesn't, like mice. The tons of cat related sites on the Internet seem to all talk about black furred cats only, or about diseases presenting with skin discoloration, but they don't mention the skin color. So, which type of animal are cats?&lt;/p&gt;&#xA;" OwnerUserId="1578" LastActivityDate="2020-01-27T02:57:22.333" Title="Are there cats with black skin?" Tags="&lt;zoology&gt;&lt;pigmentation&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30007" PostTypeId="2" ParentId="29996" CreationDate="2015-02-27T19:50:51.800" Score="2" Body="&lt;p&gt;The Streptococci are a part of the normal human flora.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The streptococci are widely distributed in nature and frequently form part of the normal human flora (seeTable 29-1). Approximately 5-15% of humans carry S pyogenes or S agalactiae in the nasopharynx. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Please see:&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK7611/#!po=51.4706&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK7611/#!po=51.4706&lt;/a&gt; for more details on epidemiology of streptococci.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As 5-15% humans have it in their nasopharynx, it is not really possible to maintain streptococci free environment. It will get repopulated quickly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually the reason you get infected is because of some alteration in your normal flora.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;S pneumoniae and, to a lesser extent, S pyogenes are part of the normal human nasopharyngeal flora. Their numbers are usually limited by competition from the nasopharyngeal microbial ecosystem and by nonspecific host defense mechanisms, but failure of these mechanisms can result in disease. More often disease results from the acquisition of a new strain following alteration of the normal flora. (From the same article, under pathogenesis)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So basically disinfecting wont help much as humans have the streptococci as a part of their normal flora. And it is very likely that the people you live with or come in contact with regularly have the streptococci already in their flora (either they got it from you or they originally had it themselves).&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-02-28T14:31:40.757" LastActivityDate="2015-02-28T14:31:40.757" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="30008" PostTypeId="2" ParentId="30005" CreationDate="2015-02-27T21:22:57.153" Score="9" Body="&lt;p&gt;&lt;a href=&quot;http://pets.thenest.com/skin-pigmentation-cats-11322.html&quot; rel=&quot;noreferrer&quot;&gt;This source&lt;/a&gt; seems to suggest that cats' skin colour is determined by their fur colour, as the same genes expressed in the fur which produce the colours (melanins) are also expressed in the skin.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The density of melanin can vary from one part of the body to another, down to patterns within individual hairs or gradients across skin, thus accounting for a wide variety of cat colors. Cats' skin appears strongly tied to fur pigmentation.&lt;/p&gt;&#xA;&lt;p&gt;A cat who has darker fur probably has darker skin and vice versa on account of the melanin content of his skin and fur. Tortoiseshell cats and their white-stricken siblings, calico cats, have patches of both dark and light skin.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-02-27T21:22:57.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30009" PostTypeId="2" ParentId="30002" CreationDate="2015-02-27T22:20:44.063" Score="3" Body="&lt;p&gt;The enzymes don't need physical interactions to couple reactions. Some enzymes do share subunits which are physically associated, but this is a special case. The following &lt;a href=&quot;http://www.wiley.com/college/boyer/0470003790/reviews/thermo/thermo_coupled.htm&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt; gives a sort of general example during glycolysis, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For example, in the biochemical pathway that breaks down glucose for energy, two enzymes work one after the other to create a high-energy ATP molecule:&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;We can also look at the peptidyltransferase reaction during the elongation step in translation. Earlier, an aminoacyl tRNA synthetase catalyzed the covalent addition of an amino acid to it's associated tRNA. The energy from breaking this bond in the ribosome provides energy for the peptidyltransferase to link the two amino acids together. This isn't assuming the ATP/GTP needed by elongation factors, etc.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-02-27T22:20:44.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30010" PostTypeId="2" ParentId="30003" CreationDate="2015-02-27T22:44:54.323" Score="5" Body="&lt;p&gt;They are not chosen, they represent an even half, a complete set of chromosomes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The entirity of a cells genes (found on the chromosomes) is called a genome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Somatic cells are the cells in our bodies that exclude sperm and egg. Sperm and egg are called germline cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The billions of somatic cells in a &lt;em&gt;homo&lt;/em&gt; &lt;em&gt;sapien&lt;/em&gt; have the same 46 chromosomes. 23 ( half) of them came from dad and 23 from mom. Thus we say somatic cells have two copies of each chromosome and it is abbreviated 2n. The germline cells are 1n or just n.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So your sperm has 23 chromosomes and after sexy time one of them can combine with an egg (which also has 23) to produce a cell(called a zygote) that has an entire complete genome (46). Then that zygote splits, and splits and splits.... And each time before it splits, &lt;strong&gt;all&lt;/strong&gt; 46 &lt;strong&gt;chromosomes are copied&lt;/strong&gt; (the copies are called sisters, or sister chromatids, respective to each other). The cells split into two new cells called  daughter cell and each daughter has an entire genome. This form of cell splitting is called mitosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probably the most important event in the cell cycle is the duplication of every DNA stand. This is called a Synthesis (S) phase. This is not a component of mitosis! It's a required event that happens before mitosis. So all 46 chromosomes get copied and then during mitosis each copy (an identical copy) is attached to each other at a region called the kinetachor. A kinetachor attaches sister chromatids (each sister is a copy of each other).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the beginning of mitosis a web forms in the cell and you can think of the strands that make the web as sliding chains that can pull stuff from the center of the cell to 1 of two perimeter locations (poles) of the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The chain like web attaches to the kinetachor and it rips apart the pair of chromosomes, rips apart the sisters. So that one sister goes to one side of the cell and the other sister chromosome goes to the other side of the cell. So now at opposite sides of the cell you have a complete genome (which will become the new daughter cells).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An identical process occurs in meiosis (specifically meiosis II) which is part of the  process that forms the sperm and the egg. During meiosis however there's additional separation (separation of homologs which occurs in meiosis I) that occurs but it's really not pertinent to your question.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/iTd5c.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2015-03-03T01:31:30.517" LastActivityDate="2015-03-03T01:31:30.517" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30011" PostTypeId="2" ParentId="30005" CreationDate="2015-02-27T23:23:59.090" Score="8" Body="&lt;p&gt;The color of mammals is determined by the pigment melanin. More specifically it is the mixture of the dark brown to black &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanin#Eumelanin&quot; rel=&quot;nofollow&quot;&gt;Eumelanin&lt;/a&gt; and the red to yellow &lt;a href=&quot;http://en.wikipedia.org/wiki/Melanin#Pheomelanin&quot; rel=&quot;nofollow&quot;&gt;Pheomelanin&lt;/a&gt;. These pigments are made a specialized cell type called melanocytes, which are located in the hair follicles (when they pigment the hairs) and in the skin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some animals (like mice) almost completely lack melanocytes in their skin (except for their ears, nose, parts of their feet and sometimes the tip of the tail), so they can only be pigmented when their fur is pigmented. For cats there is only very little data available and more, I haven't really found a good scientific article yet. From the descriptions (like &lt;a href=&quot;http://www.pethealthnetwork.com/cat-health/cat-diseases-conditions-a-z/depigmentation-disorders-cats-changing-skin-color&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) I would say that the skin of cats is pigmented. Additionally they can get cutaneous melanoma which have their origin in skin melanocytes which would be possible if they weren't be there (this is the reason why mice cannot get cutaneous melanoma if they are not engineered).&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-02-28T15:29:22.330" LastActivityDate="2015-02-28T15:29:22.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30012" PostTypeId="1" AcceptedAnswerId="30022" CreationDate="2015-02-27T23:41:41.527" Score="0" ViewCount="634" Body="&lt;p&gt;Geometrically speaking, a muscle contraction should exert a force between the two attachment sites. However, the actual effect of the force on the overall geometry of the body near the point of attachment may not match the direction the force pulls. For example, although the bicep contraction in principle would pull the forearm closer to the humerus, instead during eccentric lengthening the arm is actually extending due to how the rest of the system is configured. This is an example of where the direction of force exerted by the muscle doesn't coincide with the movement of the&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My Question:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can a muscle's net effect on the geometry of the system it acts on change mid-way through contraction? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, if my arm is eccentrically extending due to too heavy a weight in my hand and suddenly I drop the weight and now the bicep can contract. That's a simple example but I'm wondering how common it is for a the effect of a muscle's action to change midway through. &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="11652" LastEditDate="2015-03-02T03:49:14.173" LastActivityDate="2015-03-02T03:49:14.173" Title="if the load is removed from an eccentrically contracting muscle, will it start contracting concentrically?" Tags="&lt;muscles&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30015" PostTypeId="2" ParentId="13690" CreationDate="2015-02-28T07:16:23.850" Score="6" Body="&lt;p&gt;I think you are misunderstanding &quot;color&quot; here. When applied to cats, it doesn't literally mean a color shade as used in color theory, but &quot;coat color&quot; which can in fact also be a &quot;coat pattern&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cats above are two-colored, not three-colored. One color is white. The other color is what is called &quot;tabby&quot; in English and is a pattern of dark spots arranged in regular stripes on a lighter background. These spots are &lt;em&gt;not&lt;/em&gt; considered a third color in cats. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hsRKa.jpg&quot; alt=&quot;calico picture&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a calico cat. Her three coat colors are white, orange, and grey tabby. See how the orange and grey are irregularly interspersed, this is the pattern of paternal and maternal chromosome expression on her body. Again, the grey and black patches within the tabby part are regularly placed. They don't make two separate colors, grey and black, but a single coat coloring, grey tabby. There are also other color combinations in calico cats, for example white-orange-black, and they are more straightforward to recognize. &lt;/p&gt;&#xA;" OwnerUserId="1578" LastEditorUserId="10401" LastEditDate="2019-04-19T04:56:16.993" LastActivityDate="2019-04-19T04:56:16.993" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="30017" PostTypeId="2" ParentId="30002" CreationDate="2015-02-28T08:51:43.463" Score="0" Body="&lt;p&gt;In any coupled system the activity of one component is dependent on the other. For example translation and transcription are coupled; here translation is dependent on transcription but not vice versa. Coupling need not be bidirectional.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no question of unfavourable thermodynamics. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For coupled biochemical reactions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;One of the reactions should be dependent on the other. In multicomponent systems there should be at least a pairwise unidirectional dependency (A→B, B→C, C→D). In other words there should be a pathway that connects all the components.&lt;/li&gt;&#xA;&lt;li&gt;There need not be any physical interaction&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-02T08:16:46.127" LastActivityDate="2015-03-02T08:16:46.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30018" PostTypeId="2" ParentId="30005" CreationDate="2015-02-28T09:40:01.243" Score="22" Body="&lt;p&gt;Easy: look at images of hairless cats. You will see they can be not only all black, but also grey, spotted, pink, and a few other rarer colors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3bT7ym.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, take an average cat - and shave for surgery:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZCvUx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note pigmented skin matching dark stripes.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-07-10T01:36:55.950" LastActivityDate="2015-07-10T01:36:55.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30020" PostTypeId="1" CreationDate="2015-02-28T11:58:54.187" Score="3" ViewCount="104" Body="&lt;p&gt;Kwashiorkor is characterised by decreased serum protein (including serum albumin) due to poor dietary protein intake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the effect of this lowered serum protein on highly-protein-bound drugs? Is it substantial enough that administering such drugs (such as warfarin, though it's hard to imagine a situation in which a patient with kwashiorkor would need anticoagulant therapy) is potentially dangerous, and if so, can this be compensated for?&lt;/p&gt;&#xA;" OwnerUserId="13187" LastActivityDate="2015-02-28T11:58:54.187" Title="Protein-Bound Drugs in Kwashiorkor" Tags="&lt;pharmacokinetics&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30022" PostTypeId="2" ParentId="30012" CreationDate="2015-02-28T15:19:40.740" Score="3" Body="&lt;p&gt;Yes, because net force is the only thing that matters. To address @Chris's comment, in an eccentric contraction and a concentric contraction, the muscle is applying force in the &lt;em&gt;same&lt;/em&gt; direction. However, in an eccentric contraction, the muscle is not applying enough force to actually lift the load. A biceps curl is a good model:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Qjb46.jpg&quot; alt=&quot;sportscience.com&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sportsscience.co/strength/concentric-versus-eccentric-contraction-for-hypertrophy/&quot; rel=&quot;nofollow noreferrer&quot;&gt;SportScience&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the second image, the muscle is contracting but not exerting enough force to lift the weight--the net force causes a slow lowering of the weight.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Rather than working to pull a joint in the direction of the muscle contraction, the muscle acts to decelerate the joint at the end of a movement or otherwise control the repositioning of a load. - &lt;a href=&quot;http://en.wikipedia.org/wiki/Muscle_contraction#Eccentric_contraction&quot; rel=&quot;nofollow noreferrer&quot;&gt;Muscle contraction&lt;/a&gt; (Wikipedia)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It may be clearer with an actual force diagram:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pqvtX.jpg&quot; alt=&quot;force diagram&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.soe.uoguelph.ca/webfiles/mleuniss/Biomechanics/biomechanics_page_3.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;University of Guelph&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only factor influencing which way the lever (your arm) moves is the net force. So yes, if you change the load (force F in the above image), the muscle could begin pulling your arm in the opposite direction. The muscle isn't really &quot;changing action&quot;, it's exerting the same force, but now there's less force resisting it and the overall movement changes direction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question in the title and in the body are not really the same question, but the force is still exerted in the same direction as the muscle. You don't &quot;see&quot; movement in that direction because the forearm on which the force is being exerted is fixed at the elbow joint.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-02-28T15:19:40.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30023" PostTypeId="1" CreationDate="2015-02-28T15:19:59.197" Score="1" ViewCount="29" Body="&lt;p&gt;This is a very very basic question, and I am looking at it more from point of view of physics. The small intestine is a highly coiled structure, which means it has horizontal coils as well. I can understand the vertical downward movement of food (when the person is in standing position) due to gravity, but how come the food can move in horizontal direction?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any insights will be highly appreciated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="14689" LastActivityDate="2015-02-28T15:19:59.197" Title="how food moves in horizontal coils of small intestines" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;human-anatomy&gt;&lt;digestive-system&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2015-03-01T15:35:58.747" ContentLicense="CC BY-SA 3.0" />
  <row Id="30024" PostTypeId="2" ParentId="29975" CreationDate="2015-02-28T17:10:15.213" Score="3" Body="&lt;p&gt;Since these cells are there by the development of the immune system, the immune cells recognize them as self. By blood transfusion with incompatible blood type, the immune system recognizes the blood cells with different histocompatibility antigens (A,B,Rh etc...) as non-self, that's why it attacks them.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2015-02-28T17:10:15.213" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30026" PostTypeId="1" CreationDate="2015-02-28T19:51:15.390" Score="2" ViewCount="113" Body="&lt;p&gt;I am reading a paper which talks about promoter/enhancer regions of certain protein coding genes. These genes are for which evidence points to having strong MEF2 transcription factor binding sites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper says&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sequence data were taken mainly from the international nucleotide&#xA;  sequence database. Accession numbers and approximate locations of the&#xA;  MEF2 site centers are as follows: human adolase A, X06351 and&#xA;  1985/1986, rat adolase A, X04260 and 450/451...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now, I looked up accession number &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/X06351&quot; rel=&quot;nofollow&quot;&gt;X06351&lt;/a&gt; but I find no evidence of a enhancer region on that page.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone explain to me how I should be looking for these sites?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper is available for free and can be found here: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8524326&quot; rel=&quot;nofollow&quot;&gt;Link to paper&lt;/a&gt;&#xA;My interest is in the first and third paragraphs of &lt;code&gt;Materials and Methods&lt;/code&gt; where the first paragraphs gives a general description of the MEF2 sites and the third paragraphs gives specific accession numbers.&lt;/p&gt;&#xA;" OwnerUserId="6416" LastEditorUserId="6416" LastEditDate="2015-02-28T20:48:14.777" LastActivityDate="2015-02-28T21:03:10.180" Title="interpreting enhancer and promoter regions of a target gene" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30027" PostTypeId="2" ParentId="30026" CreationDate="2015-02-28T21:03:10.180" Score="1" Body="&lt;p&gt;The NCBI nucleotide page does not have information on regulatory regions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UCSC browser also displays regulatory regions mostly based on the ENCODE ChIP-Seq data. ENCODE project has &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/sra/SRX100465&quot; rel=&quot;nofollow&quot;&gt;MEF2 ChIP-Seq&lt;/a&gt; experiment for human cell lines. You can have a look at that. There is a MEF2 ChIP-seq experiment for &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Traces/sra/?study=SRP046328&quot; rel=&quot;nofollow&quot;&gt;mouse&lt;/a&gt; too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can analyse these data for a more detailed information. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-02-28T21:03:10.180" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30028" PostTypeId="1" CreationDate="2015-02-28T21:09:02.067" Score="0" ViewCount="54" Body="&lt;p&gt;Two heterozygote mice for skin color are reproduced. Black is dominant to white color. Find the probability that in 3 children 2 will be dark and one white. How did you do the ordering. Well I found it that in F1: 1/4 are AA, 1/2 Aa, 1/4 aa or 3/4 black and 1/4 white.Now nI think I should multiply the chances: 3/4*1/4*3/4, but it would be according to an order. What should I do? Is my answer correct?&lt;/p&gt;&#xA;" OwnerUserId="14697" LastActivityDate="2015-03-01T02:28:47.940" Title="Two heterozygote mice for skin color are reproduced. Find the probability that in 3 children 2 will be dark and one white" Tags="&lt;genetics&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30029" PostTypeId="1" AcceptedAnswerId="30041" CreationDate="2015-02-28T21:09:14.237" Score="3" ViewCount="13913" Body="&lt;p&gt;Based on my understanding from &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_code#RNA_codon_table&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;, there is the (RNA) start codon AUG and the stop codons UAA, UGA, UAG.  AUG can also encode Methionine, I'm assuming if it appears in the middle of a mRNA sequence.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But is there a chemical reason there are both start and stop codons?  Eg, if I only had a stop codon, would that also imply the next codon was start? Are there cases where there is a stop codon and the next codon isn't start?&lt;/p&gt;&#xA;" OwnerUserId="13238" LastEditorUserId="3340" LastEditDate="2015-03-01T07:39:35.373" LastActivityDate="2015-03-01T12:41:58.423" Title="Why are there both stop and start codons?" Tags="&lt;molecular-biology&gt;&lt;rna&gt;&lt;molecular-evolution&gt;&lt;codon-usage&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30030" PostTypeId="2" ParentId="30029" CreationDate="2015-02-28T21:40:41.207" Score="3" Body="&lt;p&gt;Not all the RNA is to be translated into proteins. Actually most of it is for regulation and sometimes unknown use. There are non coding regions before the start codon and after the stop codon. Hence the need for both.&lt;/p&gt;&#xA;" OwnerUserId="14615" LastActivityDate="2015-02-28T21:40:41.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30031" PostTypeId="2" ParentId="29972" CreationDate="2015-02-28T21:45:20.547" Score="3" Body="&lt;p&gt;The gram staining relies on the differences in the bacterial membranes. The gram positive bacteria have a thick peptidoglycan layer on top of the cell membrane, the gram negative bacteria have a lipid layer on the outside followed by a thin peptidoglycan layer and then the cell membrane. See the image for clarification (from &lt;a href=&quot;http://inside107and109.blogspot.de/2014/11/the-gram-stain.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lKWeM.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Crytall violet dissociates into a positively charged dye molecule (CV&lt;sup&gt;+&lt;/sup&gt;) and chloride (Cl&lt;sup&gt;-&lt;/sup&gt;). The CV&lt;sup&gt;+&lt;/sup&gt; travels between the membrane layers (outer and inner membrane) and is trapped there by the addition of iodine. This is used to form large crytal violet-iodine complexes which are retained during the destaining process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the destaining process, the peptidoglycan layer of gram positive bacteria is dehydrated and therefore shrinks which prevents the staining from being washed out. In the gram negative bacteria, the outer lipid layer is removed and the peptidoglycan layer (which is much thinner) exposed which allows the removal of the stain. The teichoic acid is important for the rigidity of the membrane but not for the binding itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Gram_staining&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gram staining&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3912/35u93yff_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Gram Stain after More than a Century&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3912/jcy2obo9_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Use of the Gram stain in microbiology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-02-28T21:45:20.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30032" PostTypeId="2" ParentId="30029" CreationDate="2015-02-28T23:01:51.447" Score="3" Body="&lt;p&gt;It is important to have start and stop codons so that the molecular machinery of the cell (ribosome etc.) &quot;know&quot; where the actual transcript starts and ends. This is especially important, since mature mRNA contains untranslated regions which are of regulatory importance. These regions occur on both sides of the coding sequence called 5' and 3'UTR (untranslated region), then you also have the CAP-region and the poly-A tail, see the illustration below (from &lt;a href=&quot;http://en.wikiversity.org/wiki/Transcription_start_sites&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9l9tN.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You only want the coding sequence between the start and stop translated into a protein and to recognize these borders you need a specific marker. Behind the stop codon is untranslated sequence, not directly the next gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally there is a large number of &lt;a href=&quot;https://en.wikipedia.org/wiki/Non-coding_RNA&quot; rel=&quot;nofollow noreferrer&quot;&gt;non-coding RNA&lt;/a&gt; species, like miRNA, siRNA, lnRNA and so on which fulfill regulatory purposes, play a role in splicing, replication etc. These shall not be translated into a protein (this would probably block the ribosomes and would also cost immense amounts of energy) as they wouldn't give useful proteins.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-02-28T23:01:51.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30033" PostTypeId="2" ParentId="30029" CreationDate="2015-02-28T23:40:32.807" Score="2" Body="&lt;p&gt;Next to helping to define the region for translation on the mRNA, the stop codon also prevents transcripts that have been frame-shifted by a mutation from translating into big proteins, and also helps flagging the mRNA for destruction (nonsense-mediated RNA decay). This is because in random sequence, a codon has 3/64 chance of being a stop codon, so in a frame-shifted gene sequence there suddenly are many. The premature stop codon will prematurely end the first round of translation, but if any machinery for the splicing of the mRNA is still present (it is not at the normal stop codon), the mRNA will be destroyed so it can not generate additional mutated proteins.&lt;/p&gt;&#xA;" OwnerUserId="14698" LastActivityDate="2015-02-28T23:40:32.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30035" PostTypeId="2" ParentId="27766" CreationDate="2015-03-01T00:33:17.513" Score="0" Body="&lt;p&gt;If Y can be seen as the inverse or absence of X function, it sounds to me like an incoherent type 3 feed-forward loop, where&#xA;A activates B&#xA;B activates C&#xA;A inhibits/reverses C&lt;/p&gt;&#xA;&#xA;&lt;p&gt;example from literature, E.coli: fnr as A, and arcA as B, cydAB as C&#xA;source: &lt;a href=&quot;http://www.pnas.org/content/100/21/11980.long&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/100/21/11980.long&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14698" LastActivityDate="2015-03-01T00:33:17.513" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30037" PostTypeId="2" ParentId="30028" CreationDate="2015-03-01T02:28:47.940" Score="1" Body="&lt;p&gt;You are on the right track, but you have to keep in mind there are multiple ways to have two dark and one child in a group of three. You have to add the probabilities of each unique outcome that results in two dark and one light child. So, the probability is (1/4) x (3/4) x (3/4) PLUS (3/4) x (1/4) x (3/4) PLUS (3/4) x (3/4) x (1/4)&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-03-01T02:28:47.940" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30040" PostTypeId="1" CreationDate="2015-03-01T06:35:58.710" Score="3" ViewCount="1368" Body="&lt;p&gt;I know two examples: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1-The binding of hemoglobin to oxygen (binding of oxygen to one site of hemoglobin induces conformational changes which increase the affinity of the other sites for oxygen - the curve could be interpreted as transition from a low affinity T sate to a high affinity R state). The plot can be seen &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Talk:Hemocyanin#/media/File:Hb_saturation_curve.png/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2-The denaturation of DNA by temperature (when one segment of the double helix opens, base stacking is disrupted, making the denaturation of the rest of the molecule easier); Another &lt;a href=&quot;http://www.lpt.ups-tlse.fr/local/cache-vignettes/L570xH327/fig_web-1647a.jpg&quot; rel=&quot;nofollow&quot;&gt;plot&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two examples I gave were actually of positive cooperative phenomena, that is, the occurence of a first event favours the next events. There is also the titration curve, which is a sigmoid, but I don't think it's correlated.&#xA;I'm asking that because I found it amazing that the same sort of curve appeared in the study of such different subjects.&#xA;&lt;strong&gt;Are these examples somehow correlated, that is, for which sort of phenomena sigmoid curves are expected?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="14630" LastEditorUserId="14630" LastEditDate="2015-03-01T19:12:12.860" LastActivityDate="2015-03-01T19:12:12.860" Title="Why sigmoid curves appear in quantitative analysis of many biological phenomena?" Tags="&lt;biochemistry&gt;&lt;mathematical-models&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="1" ClosedDate="2015-03-01T15:36:34.363" ContentLicense="CC BY-SA 3.0" />
  <row Id="30041" PostTypeId="2" ParentId="30029" CreationDate="2015-03-01T06:55:02.683" Score="6" Body="&lt;p&gt;Start and stop codons are instructions for the ribosome to start and stop protein synthesis, respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The region between the start and stop codon (inclusive of them) is called ORF (open reading frame) or sometimes CDS (Coding sequence). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why does ribosome need explicit instructions for start and stop?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ribosome recognizes an RNA as a mRNA if it has certain features. In bacteria and other prokaryotes there is a region on the mRNA called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Ribosomal_binding_site&quot; rel=&quot;nofollow&quot;&gt;Ribosome Binding Site&lt;/a&gt; (RBS) that helps in initial recruitment of the ribosome. In eukaryotes there are &lt;a href=&quot;http://en.wikipedia.org/wiki/Kozak_consensus_sequence&quot; rel=&quot;nofollow&quot;&gt;Kozak consensus&lt;/a&gt; sequences that help in identification of a start site. When the ribosome encounters an &lt;code&gt;AUG&lt;/code&gt; codon then the initiation reactions take place (there are some proteins called &lt;a href=&quot;http://en.wikipedia.org/wiki/Initiation_factor&quot; rel=&quot;nofollow&quot;&gt;initiation factors&lt;/a&gt; that help in this process). The ribosome just keeps moving along the mRNA and producing a polypeptide unless it encounters a stop codon. When it does other proteins called &lt;a href=&quot;http://en.wikipedia.org/wiki/Release_factor&quot; rel=&quot;nofollow&quot;&gt;release factors&lt;/a&gt; come into play and they dislodge the ribosome from the mRNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What about a second &lt;code&gt;AUG&lt;/code&gt; codon?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the ribosome encounters another &lt;code&gt;AUG&lt;/code&gt; codon after the start then it would consider it as a codon for methionine. However there are situations when the second &lt;code&gt;AUG&lt;/code&gt; can act as an alternative start site. You can see this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025576/&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; for details. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why is stop codon essential?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can imagine a situation where ribosome just goes till the end of mRNA — why stop it? The reason for this is that the mRNA 3' terminus usually has regulatory regions and most importantly poly-A tails (in eukaryotes) that should not be translated. Moreover stop codon also signals the ribosome to dislodge from the mRNA. If such processes didn't exist then ribosome will remain attached to the RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;If I only had a stop codon, would that also imply the next codon was start?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No. Because stop codon works only when translation has already started. However it is not essential that the stop codon should be followed by the 3'UTR. Usually in bacteria a single mRNA codes for multiple proteins. There are many ORFs that are lined one after the other; such mRNAs are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Messenger_RNA#Monocistronic_versus_polycistronic_mRNA&quot; rel=&quot;nofollow&quot;&gt;polycistronic mRNAs&lt;/a&gt;. In these cases there is another start codon a few distance ahead of a previous stop codon. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-01T12:41:58.423" LastActivityDate="2015-03-01T12:41:58.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30043" PostTypeId="2" ParentId="90" CreationDate="2015-03-01T08:51:01.640" Score="3" Body="&lt;p&gt;This recent &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1074552113004262&quot; rel=&quot;nofollow&quot;&gt;Cell paper&lt;/a&gt; mentions a ribozyme (RNA enzyme) that ligates two oligonucleotides into itself. Given a sufficient source of input oligonucleotides and the correct conditions, it can catalyse its own replication and undergo Darwinian evolution, and can be thought of as a rudimentary form of RNA-based life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors hypothesise that ligase-based RNA replicators could have been the first RNA replicators, which were later replaced by the now-standard polymerisation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A somewhat different approach relies on RNA enzymes with RNA-templated&#xA;  RNA ligase activity to join oligonucleotide substrates to form&#xA;  complementary RNA products. It has been proposed that the first&#xA;  replicating, evolving systems on Earth operated by this mechanism and&#xA;  only later came to depend upon residue-by-residue polymerization&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It should be noted that RNA ribozyme polymerases already exist, but many of them require proteins in addition to the RNA structure. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-03-02T06:54:48.113" LastActivityDate="2015-03-02T06:54:48.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30044" PostTypeId="2" ParentId="28584" CreationDate="2015-03-01T09:19:09.240" Score="1" Body="&lt;p&gt;First it is important to define what actually an error is. What you call misproduct is actually a right product for a different substrate. The enzyme has a low specificity; but you won't say hexokinase is error prone because it has wide substrate specificity. The question is — is specificity critical?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coming to the example of DNA polymerase, you should note that DNA polymerase only adds a nucleotide to the DNA strand. Here the template DNA strand acts like a co-enzyme and it is the template DNA that provides specificity to the reaction. In this case the specificity is really critical and there are mechanisms that help in ensuring that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other enzymes also make errors and the probability of making errors depends on different parameters. Take the example of restriction enzymes that are supposed to cut at a specific site. When this specificity is lost we say that the enzyme is showing a &quot;star activity&quot; i.e. non-specific cleavage. This depends on different parameters such as buffer composition, enzyme concentration etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general specificity is provided because of high affinity of binding towards one molecule compared to the other. These binding reactions are second order — a high affinity substrate will bind to the enzyme even at a low concentration, however if you increase the concentration of the low affinity substrate or the enzyme, then at some point the rate of binding may be significant enough to create a &quot;wrong&quot; product.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes there are cases where the enzyme can bind to a wrong substrate but cannot create a product. This is the typical case of a competitive inhibitor. It is also possible that a certain molecule is good at binding but the conversion rate is slower.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To conclude, these kinds of &quot;errors&quot; happen with many enzymes but it is very critical in case of DNA polymerization. You can get information on star activity of restriction enzymes (just google it). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-01T09:29:17.703" LastActivityDate="2015-03-01T09:29:17.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30045" PostTypeId="2" ParentId="29878" CreationDate="2015-03-01T10:14:59.487" Score="3" Body="&lt;p&gt;There is no rule for fixing &lt;strong&gt;t&lt;/strong&gt; and &lt;strong&gt;p&lt;/strong&gt;. It depends on the level of stringency you expect. Value of &lt;strong&gt;t&lt;/strong&gt; depends on what is considered to be an active concentration; this need not be same for all genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is an RNAseq data; I don't understand what is the &quot;median&quot; signal you are talking about. For each sample a gene would have a normalized expression value which is typically RPKM (Reads Per Kilobase per Million mapped reads). If you have replicates for each sample then take the mean not the median. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Regarding calculation of log-ratios:&lt;/em&gt; Always be careful with this especially in case of zeros. Instead of log ratios you may use some sort of a gain metric: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;if &#xA;ratio = x/y &#xA;then&#xA;gain = (x-y)/y&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;You can also do a principal component analysis on the data and select first &lt;code&gt;n&lt;/code&gt; principal components.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-03-01T10:14:59.487" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30047" PostTypeId="2" ParentId="30040" CreationDate="2015-03-01T13:25:10.953" Score="1" Body="&lt;p&gt;I would suggest following: take any one-dimensional process that is described by gaussian function. If you integrate such process along variable, you will get a sigmoidal curve. For details see &lt;a href=&quot;http://en.wikipedia.org/wiki/Normal_distribution&quot; rel=&quot;nofollow noreferrer&quot;&gt;normal and cumulative distribution&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the question is: how many biological processes are described/modeled by Gaussian distribution and dependencies? A lot!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's take a look at dinosaur growth from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864909/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Revisiting the Estimation of Dinosaur Growth Rates&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NkAdW.jpg&quot; alt=&quot;Dinosaur growth rate&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This figure describes how size of dinosaur changes with some time (model, I assume). Remember link between gaussian and sigmoidal functions? If you differentiate, that is find how fast aforementioned sigmoidal function changes, you will get gaussian bell-curve! Which tells you: dinosaur grows faster during middle age, and slower before and after that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA denaturation curve is sigmoidal because efficiency of denaturation is again gaussian. At low temperatures very limited amount of molecules will denature, but at high temperature there are no more molecules to denaturate left, so the bell-curve. Anothe explanation goes like that: at low temperature additional heat doesn't change much because it is still too &quot;cold&quot;, at higher temperature same amount of heat is just a drop in a bucket, barely noticeable.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-03-01T13:25:10.953" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30048" PostTypeId="1" CreationDate="2015-03-01T13:25:31.183" Score="2" ViewCount="51" Body="&lt;p&gt;I would like to compare rennet capability under various conditions. The issue is, I don't want to use calf rennet, but I can't figure out if nettle and syconium, which also coagulate milk, contain regular rennet or other enzyme? If so, what is its name? It's quite important.&#xA;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="14705" LastEditorUserId="10456" LastEditDate="2015-03-01T14:27:09.107" LastActivityDate="2015-03-01T14:27:09.107" Title="Are the proteolytic enzymes in syconiums and nettles identical to those in rennet?" Tags="&lt;enzymes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30049" PostTypeId="1" AcceptedAnswerId="30052" CreationDate="2015-03-01T13:36:48.113" Score="4" ViewCount="475" Body="&lt;p&gt;Assuming the cell membrane to have a spherical shape, geometry tells us that the area of the inner leaflet is smaller than the area of the outer due to the difference in radius between them. Does this mean that the inner layer has fewer phosholipids? And, if so, how does it affect the fluidity relation between the layers?&lt;/p&gt;&#xA;" OwnerUserId="14706" LastActivityDate="2015-03-01T17:25:07.983" Title="Do cell membranes have more phospholipids in one layer than in the other?" Tags="&lt;cell-membrane&gt;&lt;cell&gt;&lt;membrane&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30050" PostTypeId="2" ParentId="30048" CreationDate="2015-03-01T14:22:29.217" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Rennet&quot; rel=&quot;nofollow&quot;&gt;Rennet&lt;/a&gt; is not an enzyme, but &lt;a href=&quot;http://en.wikipedia.org/wiki/Chymosin&quot; rel=&quot;nofollow&quot;&gt;rennin&lt;/a&gt; is. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any protease enzyme should be capable of causing milk to coagulate, or prevent gelatin from setting. Examples such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Papain&quot; rel=&quot;nofollow&quot;&gt;papain&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Bromelain&quot; rel=&quot;nofollow&quot;&gt;bromelain&lt;/a&gt; are all &lt;a href=&quot;http://en.wikipedia.org/wiki/Cysteine_protease&quot; rel=&quot;nofollow&quot;&gt;cysteine proteases&lt;/a&gt;, and all of them will cause milk to coagulate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The example of fig protease that you mentioned is a cysteine protease (no specific name found, referred to in scientific literature as &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20163660&quot; rel=&quot;nofollow&quot;&gt;fig protease&lt;/a&gt;). &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_plants_known_as_nettle&quot; rel=&quot;nofollow&quot;&gt;Nettles are a highly polyphyletic group&lt;/a&gt;, and the specific enzyme cannot be named without a more specific phylogenetic group being identified. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-03-01T14:22:29.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30051" PostTypeId="2" ParentId="28584" CreationDate="2015-03-01T14:50:31.563" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/RuBisCO#Substrates&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rubisco&lt;/a&gt; is an enzyme that is involved in the biochemical process of carbon fixation in photosynthesis, but also has an economically important error (&lt;a href=&quot;http://en.wikipedia.org/wiki/Photorespiration&quot; rel=&quot;nofollow noreferrer&quot;&gt;photorespiration&lt;/a&gt;) which incorporates the wrong molecule (oxygen) into RuBP, therefore wasting the energy captured by the plant and producing toxic downstream products. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rubisco's error rate in carbon fixation &lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.arplant.53.100301.135233&quot; rel=&quot;nofollow noreferrer&quot;&gt;ranges from approximately 1:10 to 1:80&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MO5UX.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-03-01T14:50:31.563" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30052" PostTypeId="2" ParentId="30049" CreationDate="2015-03-01T15:13:15.033" Score="3" Body="&lt;p&gt;Yes there is a difference in the number of phospholipid molecules because of the curvature. This is very evident when there is a lot of bending as in case of exocytosis (see &lt;a href=&quot;http://www.annualreviews.org/doi/pdf/10.1146/annurev-biochem-051710-094912&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) but otherwise I do not think there would be an enormous difference in the number of phospholipids between inner and outer surface of the bilayer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assumptions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Cell is spherical&lt;/li&gt;&#xA;&lt;li&gt;Cell diameter = 1µm (overall)&lt;/li&gt;&#xA;&lt;li&gt;Thickness of bilayer = 6nm&lt;/li&gt;&#xA;&lt;li&gt;Width of a phospholipid molecule = 1nm &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Difference in circumference of outer and inner layers = 2π(6nm) ≅ 37.7nm&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So approximately 37 more phospholipid molecules in the outer layer in this cross section of the cell. This is just 0.6% of total number of phospholipids in the outer membrane. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think fluidity will be compromised because of this - only if a layer is overpacked will the fluidity be affected.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-01T17:25:07.983" LastActivityDate="2015-03-01T17:25:07.983" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30053" PostTypeId="1" AcceptedAnswerId="30057" CreationDate="2015-03-01T19:07:10.397" Score="7" ViewCount="4650" Body="&lt;p&gt;I've found &lt;a href=&quot;http://www.pnas.org/content/71/12/4980.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt;, which is a very old one (from the time when nucleoside analogs where researched as a possible way to prevent replication of virus genetic material, before the HIV epidemics).&#xA;In the last page, the authors suggest that cellular repair enzymes could remove azidothymidine (AZT, zidovudine) from cellular DNA if it's incorporated, but viruses' polymerases lack this ability.&#xA;As it's an old article, I would like to know if this hypothesis was confirmed. As both azidothymidine and thymidine can form normal base pairings, how could human enzymes detect an azidothymidine was incorporated?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If someone is not familiar with AZT mechanism: basically, it's an analog of thymidine which has an azide group instead of 3'-OH&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dKoGi.jpg&quot; alt=&quot;(picture)&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It can be phosphorylated by cell kinases and incorporated to the growing DNA chain; however, this will stop the polymerization because it depends on free 3'-OH. The natural question which follows is: why wouldn't AZT also block the replication of human cells' DNA?&lt;/p&gt;&#xA;" OwnerUserId="14630" LastEditorUserId="15950" LastEditDate="2019-02-11T13:55:06.577" LastActivityDate="2019-02-11T13:55:06.577" Title="Why AZT is selective towards HIV and doesn't impair human DNA replication?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;hiv&gt;&lt;dna-damage&gt;&lt;retrovirus&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 4.0" />
  <row Id="30054" PostTypeId="1" AcceptedAnswerId="61142" CreationDate="2015-03-01T19:53:31.013" Score="5" ViewCount="153" Body="&lt;p&gt;When somebody else tells me about his or her itching or pain in some specific body part, I sometimes begin to feel similar feelings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can think of about three explanations:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;I feel pain all over my body all the time for many different reasons but my entrance neural pathways stop it as unimportant of these signals but when I focus on a single signal, it begins to be important for me.&lt;/li&gt;&#xA;&lt;li&gt;Mirror neurons are doing their job.&lt;/li&gt;&#xA;&lt;li&gt;For an unknown reason, I psychosomatically induce my friend's feelings.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Which of these theories is at least partially engaged in said phenomenon?&lt;/p&gt;&#xA;" OwnerUserId="6124" LastEditorUserId="6124" LastEditDate="2018-12-28T17:33:07.650" LastActivityDate="2018-12-28T17:33:07.650" Title="How do we share pain?" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;&lt;pain&gt;&lt;psychology&gt;&lt;cognition&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="30055" PostTypeId="1" AcceptedAnswerId="30063" CreationDate="2015-03-01T20:53:29.210" Score="1" ViewCount="2753" Body="&lt;p&gt;I have this paragraph that i have halfway finished, but i do not know what to put in the spaces.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;A Cladogram is a branching diagram that represents the proposed phylogeny or evolution of a species or a group. The groups used in Cladograms are called clades.. To &lt;em&gt;construct&lt;/em&gt; a cladogram, &lt;em&gt;two&lt;/em&gt; characters are defined. Then the &lt;em&gt;outgroup&lt;/em&gt; of various species are identified based on the &lt;em&gt;sequencing&lt;/em&gt; or &lt;em&gt;closeness&lt;/em&gt; of the derived characters in the &lt;em&gt;clades&lt;/em&gt;. In making a cladogram, ______ assume that groups that _____ more derived characters have a more &lt;em&gt;close&lt;/em&gt; common ancestor.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The letters that are italicized are words that i think are correct. This paragraph is needed for part of a recite that i have to do in front of my class. The prof. gave me a page like this. And  I don't know what those spaces are. Can someone help me.. &lt;strong&gt;please&lt;/strong&gt;?&lt;/p&gt;&#xA;" OwnerUserId="14710" LastEditorUserId="14710" LastEditDate="2015-03-01T21:07:40.790" LastActivityDate="2015-03-02T05:19:04.547" Title="How would i describe a Cladogram as paragraph?" Tags="&lt;homework&gt;&lt;cladistics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ClosedDate="2015-03-02T09:41:36.473" ContentLicense="CC BY-SA 3.0" />
  <row Id="30056" PostTypeId="1" CreationDate="2015-03-01T21:35:21.530" Score="1" ViewCount="2767" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;What gives the nucleus&#xA;  its shape is a mesh of intermediate filaments called the nuclear&#xA;  lamina. It forms an interface between the chromosomes and the inside&#xA;  of the nuclear envelope. If these large protein fibres were to be&#xA;  temporarily separated into their component nuclear lamina, the nuclear&#xA;  envelope would pull away from the chromosomes and withdraw into the&#xA;  endoplasmic reticulum. Problem solved.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am confused by the last sentence starting with &quot;If these large proteins...&quot; Could someone explain this in another way? I would appreciate any response. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="14711" LastEditorUserId="6061" LastEditDate="2015-03-02T07:16:52.073" LastActivityDate="2015-03-03T00:37:19.927" Title="What is the basic structure of the nuclear lamina" Tags="&lt;cell-biology&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30057" PostTypeId="2" ParentId="30053" CreationDate="2015-03-01T21:46:04.093" Score="9" Body="&lt;p&gt;Retroviruses depend on being able to convert their RNA genome into a DNA copy, and have a reverse transcriptase enzyme to do that. This unique activity is not found in human cells, allowing for potential antiviral therapy if a drug can be used to inhibit the reverse transcriptase while not affecting the human enzymes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;AZT is one such drug, by mimicking the nucleotide thymidine, it can it can act as a substrate for nucleotide kinases and become 5' phosphorylated. AZT is phosphorylated by host cell enzymes, specifically thymidine kinase, this means that the levels of AZT phosphates are similar between HIV infected and non-infected cells. Once the 5' triphosphate is formed, the drug is a substrate for the viral reverse transcriptase. If an AZT is incorporated into the DNA backbone, it terminates the DNA because the 3' OH is not available for further polymerization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, at &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2430286&quot;&gt;high enough doses&lt;/a&gt; AZT can be toxic to healthy cells. One mechanism for toxicity is the depletion of thymidine, because AZT competes with thymidine for the kinase enzymes, but is phosphorylated at a slower rate. At high doses, &gt;1mM, AZT can act as a substrate for human DNA polymerases. Thankfully, AZT is about 100 fold more selective for HIV reverse transcriptase than human DNA polymerase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mitochondrial DNA polymerase seems to be a little more sensitive to AZT than other human DNA polymerases. This can lead to toxicity in the heart, skeletal muscles, hepatocytes, or other cells that use a lot of mitochondria. This toxicity is generally reversible if doses are reduced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information, read about other nucleotide analogs, such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Aciclovir&quot;&gt;acyclovir&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Ganciclovir&quot;&gt;ganciclovir&lt;/a&gt;, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Reverse-transcriptase_inhibitor&quot;&gt;others&lt;/a&gt; which work through similar mechanisms.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2015-03-01T21:46:04.093" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30059" PostTypeId="2" ParentId="30056" CreationDate="2015-03-01T22:54:56.043" Score="1" Body="&lt;p&gt;Watch this animation and you'll understand the general process of mitosis:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sumanasinc.com/webcontent/animations/content/mitosis.html&quot; rel=&quot;nofollow&quot;&gt;http://www.sumanasinc.com/webcontent/animations/content/mitosis.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="13143" LastEditorUserId="6061" LastEditDate="2015-03-02T04:20:48.607" LastActivityDate="2015-03-02T04:20:48.607" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30060" PostTypeId="1" CreationDate="2015-03-02T04:07:45.223" Score="1" ViewCount="70" Body="&lt;p&gt;I am not a bio or science major, but we have a subject, like an elective on biotechnology and we were tasked to think of a product that hasn't been invented yet. My groupmates and I thought of a vitamin enhanced crop to help fight against malnutrition. As for the crop we thought of using sweet potatoes and altering its DNA to produce a more nutritious one. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our plan is to use agrobacterium tumefaciens, cut its plasmid and insert a foreign DNA to it. Now we are stuck with what foreign DNA can we add to it so that we will produce a more nutritious sweet potato. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our teacher gave us a hint that whatever we will add to the organism should be a protein because the DNA only codes for protein. So if we plan to add vitamins to the sweet potato then it should be protein-based.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sorry but I am very confused with biotech terms because I am not a bio major. But any help would be very much appreciated! thank you in advance!&lt;/p&gt;&#xA;" OwnerUserId="14713" LastEditorUserId="14713" LastEditDate="2015-03-02T09:20:23.063" LastActivityDate="2015-03-02T19:28:52.410" Title="Nutritious protein substance for vitamin enhanced crop?" Tags="&lt;dna&gt;&lt;proteins&gt;&lt;biotechnology&gt;&lt;vitamins&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30061" PostTypeId="2" ParentId="30056" CreationDate="2015-03-02T04:09:36.140" Score="1" Body="&lt;p&gt;This is a fair question, his text or source words it funny.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To keep it simple, the nuclear lamina is a network of filaments inside the nucleus and it includes the proteins associated with the nuclear membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's connected to the inner face of the nuclear lipid bilayer that makes up the nuclear envelope whereas the &lt;strong&gt;outer face is continuous with the endoplasmic reticulum.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look at most any cartoon of a cell, it shows the nuc envelope attached to the ER, which it is. Makes up a big part of the cells endomembrane system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5rSpP.jpg&quot; alt=&quot;cell showing nuc membrane connected to ER &quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think in other words the author is trying to say if the lamina came apart, the envelope would essentially just be a continuation of the ER, as it's the lamina that essentially folds up that &quot;portion of the ER membrane&quot; up to create the nuc envelope.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2015-03-02T04:19:49.373" LastActivityDate="2015-03-02T04:19:49.373" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30062" PostTypeId="1" CreationDate="2015-03-02T04:37:18.227" Score="0" ViewCount="164" Body="&lt;p&gt;i have designed primers for HLA locus DPA1(exon 2 region) based on Real-Time PCR (qPCR) Primer Design guidelines. primer will start from intron regions to cover full exonic region.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;F-CAGCAACAGAGAATGTCAGC&lt;/p&gt;&#xA;&#xA;&lt;p&gt;R-CCCTGAAGCAGCAATTGATG&lt;/p&gt;&#xA;&#xA;&lt;p&gt;to check for amplification of only a single region  i have used in silico PCR UCSC but it shows multiple region from chr6. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;pls kindly help me with solving this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks&lt;/p&gt;&#xA;" OwnerUserId="14714" LastActivityDate="2015-03-02T07:15:58.150" Title="Primer design for HLA locus" Tags="&lt;primer&gt;&lt;hla&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30063" PostTypeId="2" ParentId="30055" CreationDate="2015-03-02T05:19:04.547" Score="1" Body="&lt;p&gt;I provided some edits in my comment -- hope the following clarifies things for you a little bit.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To construct a cladogram, two characters are defined.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You may be confusing &lt;em&gt;character&lt;/em&gt; and &lt;em&gt;character state&lt;/em&gt;. It's valid to have a cladogram with a single character (e.g. the single character, &quot;warm-blooded&quot;), but you will need at least two character states to infer a non-trivial cladogram. The states for the character warm-blooded would be Yes or No.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A molecular example would be a cladogram inferred from a column of a sequence alignment. That &lt;em&gt;column&lt;/em&gt; is the character, and for, say, DNA, the character states are the set {A,C,G,T}.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Then the outgroup of various species are identified based on the sequencing or closeness of the derived characters in the clades.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The outgroup is specified by you, the investigator. It's typically a hypothesis (viz. model parameter), which is either a guess or is based on some external evidence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, the analysis starts from character-state data for some number of taxa (&quot;species&quot; in your paragraph). From this data you are selecting (constructing) a tree-topology that best fits this data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E.g. for four taxa, labeled A,B,C,D, with D the outgroup, the process is like:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; start  --&amp;gt; cladogram&#xA; ABC(D)     A  B C (D)&#xA;             \/ / /&#xA;              \/ /&#xA;               \/&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;There are many different methods to construct the cladogram. One popular method is  maximum parsimony, but the assumptions of that model are severe. However, &lt;em&gt;any&lt;/em&gt; method is effectively selecting a tree topology out of all the finitely-many possible tree topologies over N leaves, where N is the number of taxa (species) in your investigation.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In making a cladogram, ______ assume that groups that _____ more derived characters have a more close common ancestor.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In this sentence, you seem to be expressing a relationship between the number of shared derived characters (synapomorphies) for a given clade, and the common ancestor of that clade.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can be very confusing, maybe an example will help. Let me annotate the above tree with a binary character, having states + and -. &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;            +   +  -   - &#xA;            A   B  C  (D)&#xA;             \ /  /   /&#xA;              +  /   /&#xA;               \/   /&#xA;                -  /                   &#xA;                 \/&#xA;                  -&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The idea is that the ancestral state for the entire group is -, as was the state for the ancestor of {A,B,C}. However, the + state was derived after the ancestor of {A,B,C} but before (or &quot;in&quot;) the ancestor of {A,B}. Then it was passed to the terminal units, A and B. (Note: typically you don't have this ancestral-state information, only the information at the tips of the tree. You're actually inferring the ancestral states and topology &lt;strong&gt;from&lt;/strong&gt; the data at the tips.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would claim that, in general, taxa that share more derived character (states) have a more recent common ancestor than taxa that do not. Although, this can be confounded by homoplasy.&lt;/p&gt;&#xA;" OwnerUserId="14609" LastActivityDate="2015-03-02T05:19:04.547" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30064" PostTypeId="2" ParentId="30062" CreationDate="2015-03-02T07:15:58.150" Score="1" Body="&lt;p&gt;When designing rtPCR primers always check the extensive and well validated  taqman library for the ABI system, the primers for the region you want are already well characterized:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.lifetechnologies.com/order/genome-database/details/gene-expression/Hs01072897_m1#more-information-section&quot; rel=&quot;nofollow&quot;&gt;http://www.lifetechnologies.com/order/genome-database/details/gene-expression/Hs01072897_m1#more-information-section&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2015-03-02T07:15:58.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30067" PostTypeId="1" CreationDate="2015-03-02T11:18:32.520" Score="2" ViewCount="116" Body="&lt;p&gt;I want to list all proteins in the protein database and list them by the ratio of number of disulphide bonds per peptide bond. &#xA;I am not particular about the reliability of identification of disulphide bond.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;--EDIT 1&#xA;I've been doing some research on this topic, and heres what i've found. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The PDB structure file lists all the Disulphide bonds in each structure.(SSBOND)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The PBD structure file does not list the number of peptide bonds, however it does &#xA;mention the number of amino acids. And number of peptide bonds = [no. of amino acids - 1].&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;We can generate a list of all PDB structure IDs with atleast 1 disulphide bond, using PDB.org's advanced search feature. This gives a list of 22543 structures. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Downloading all the 22543 structures and then parsing them using any programming language would be easy, except for the difficulty of downloading all the 22543 sturctures.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So the question now is: &#xA; How do I parse all the 22543 structures to output only the number of disulphide bonds and the number of amino acids in each chain, without downloading the PDB structure files?&lt;/p&gt;&#xA;" OwnerUserId="6897" LastEditorUserId="6897" LastEditDate="2015-03-03T05:23:39.720" LastActivityDate="2015-03-03T05:23:39.720" Title="How do I identify the protein with the highest Disulfide bond density? i.e protein with highest ratio of Disulphide bonds per Peptide bond?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;protein-folding&gt;&lt;protein-structure&gt;" AnswerCount="0" CommentCount="11" FavoriteCount="1" ClosedDate="2015-03-03T13:32:06.917" ContentLicense="CC BY-SA 3.0" />
  <row Id="30069" PostTypeId="1" AcceptedAnswerId="30073" CreationDate="2015-03-02T14:33:48.077" Score="7" ViewCount="1238" Body="&lt;p&gt;I just came across a statement in my book , while reading genetics, that haemophiliac females do not survive till birth (the reason not mentioned here why) . Before posting this question here I conducted quite a bit searching on the net but couldnt find any document on this. Can anyone tell me the reason why don't haemophiliac foetus make till birth ? I mean where is the problem, when a haemophiliac male having &lt;strong&gt;&lt;em&gt;X&lt;sup&gt;h&lt;/sup&gt;Y&lt;/em&gt;&lt;/strong&gt; can survive why not an &lt;strong&gt;&lt;em&gt;X&lt;sup&gt;h&lt;/sup&gt;X&lt;sup&gt;h&lt;/sup&gt;&lt;/em&gt;&lt;/strong&gt;  female ? &lt;img src=&quot;https://i.stack.imgur.com/uwrc7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14616" LastEditorUserId="3340" LastEditDate="2015-03-02T17:55:22.363" LastActivityDate="2018-05-23T02:21:26.717" Title="Why do haemophillic females $X^hX^h$ die before birth?" Tags="&lt;human-biology&gt;&lt;human-genetics&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="13" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30070" PostTypeId="1" CreationDate="2015-03-02T15:48:16.890" Score="0" ViewCount="554" Body="&lt;p&gt;The colorimetric assays by &lt;a href=&quot;http://www.biovision.com/manuals/K789.pdf?osCsid=4dh8peelaulm53p8dr9qhgoj11&quot; rel=&quot;nofollow&quot;&gt;Biovision&lt;/a&gt; and &lt;a href=&quot;http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Bulletin/1/mak082bul.pdf&quot; rel=&quot;nofollow&quot;&gt;Sigma Aldrich&lt;/a&gt; seem to utilise a probe that binds to or reacts with NADH in order to cause absorbance at 450nm which can then be quantified by a spectrophotometer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the chemical basis of this reaction?&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-03-02T15:48:16.890" Title="What is the probe that absorbs at 450nm in the presence of NADH in this assay?" Tags="&lt;biochemistry&gt;&lt;assay-development&gt;" AnswerCount="0" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30072" PostTypeId="1" CreationDate="2015-03-02T17:13:43.770" Score="6" ViewCount="80" Body="&lt;p&gt;Beverages of any type generally contain some measure of water. However, in the case of some liquids, the non-water components take more water from the human body to filter out than the water contained in the beverage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most-known example of this is salt-water from the ocean - there is too much salt so the body tries to use water from the body to &quot;water down&quot; the salt water.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strike&gt;Given a beverage with unknown additives, how would one determine if the beverage would actually hydrate or dehydrate a person?&lt;/strike&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strike&gt;If you knew the ingredients (and the amounts), could you tell that way?&lt;/strike&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&lt;br&gt;comments seem to indicate that it depends on the solutes and tonicity of the solution: are there any other factors to be aware of?&#xA;What (common) solutes will have the largest affect on whether the human body will be hydrated and why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;if you need &quot;common&quot; to be defined, consider it defined as: &lt;em&gt;contained in many[more than 3] store-bought beverages&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="9700" LastEditorUserId="9700" LastEditDate="2015-03-03T16:54:12.937" LastActivityDate="2015-03-03T16:54:12.937" Title="How to tell if a beverage will hydrate or dehydrate?" Tags="&lt;human-biology&gt;&lt;hydration&gt;" AnswerCount="0" CommentCount="7" ClosedDate="2015-07-16T07:57:20.127" ContentLicense="CC BY-SA 3.0" />
  <row Id="30073" PostTypeId="2" ParentId="30069" CreationDate="2015-03-02T17:44:38.373" Score="3" Body="&lt;p&gt;Haemophiliac females are rare but they can survive just like affected males do. However, the case is slightly more complicated in women because of menstruation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could not find an article from any medical journal but &lt;a href=&quot;https://www.hemophilia.org/Community-Resources/Women-with-Bleeding-Disorders/Women-also-Bleed&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; site seems authentic enough for a reference. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-03-02T17:44:38.373" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30074" PostTypeId="1" AcceptedAnswerId="30077" CreationDate="2015-03-02T18:47:06.080" Score="3" ViewCount="36" Body="&lt;p&gt;If I have a squash plant that has a mosaic virus of some kind, and I breed its descendants (via seed) for generations, each with exposure to the same virus, will future generations be likely to eventually obtain resistance to the virus, and if so, how long would this typically take?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to me that this might be how the resistant plants would have first developed resistance, but I could be wrong.&lt;/p&gt;&#xA;" OwnerUserId="9601" LastActivityDate="2015-03-02T20:48:52.587" Title="Can virus resistance be acquired through generational exposure?" Tags="&lt;botany&gt;&lt;virus&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30075" PostTypeId="1" AcceptedAnswerId="30081" CreationDate="2015-03-02T19:06:26.807" Score="8" ViewCount="15635" Body="&lt;p&gt;I watching some TV program some time ago and a guy in it mentioned that when-ever museums display real dinosaur bones (as opposed to a replica) the bones are painted over with a lead paint, because they are radioactive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sentence was not qualified (so he did not e.g. say that just some bones found somewhere are radioactive).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So is this true of most or all dinosaur bones, or just some of them? If I ever find a huge dino fossil somewhere, should I be concerned?&lt;/p&gt;&#xA;" OwnerUserId="12939" LastActivityDate="2015-05-21T19:23:59.627" Title="Are all dinosaur bones radioactive?" Tags="&lt;palaeontology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30077" PostTypeId="2" ParentId="30074" CreationDate="2015-03-02T20:48:52.587" Score="1" Body="&lt;p&gt;Perhaps the answer is in natural selection. Over many generations, if these plants are constantly exposed to the same virus, one of them may obtain a mutation or something similar that allows it to be resistant, thus that plant will have higher survival and growth rate and thus more seeds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The current plant itself may also adapt to the presence of this virus (perhaps in growth patterns, etc.) over a long period of time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the time for the genetic resistance to take place, it is almost impossible to say as it is almost completely random (and would also depend on what other plants you may pollinate it with as an already resistant plant would, of course, cancel the need for a mutation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-03-02T20:48:52.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30079" PostTypeId="1" CreationDate="2015-03-02T21:29:19.810" Score="2" ViewCount="50" Body="&lt;p&gt;I originally thought that cloning a gene meant to put it into bacteria and have them express it. But sometimes I see it used and it seems like it's just a synonym for &quot;identify the sequence and/or location of&quot;. So what does &quot;clone a gene&quot; really mean&quot;&lt;/p&gt;&#xA;" OwnerUserId="14727" LastActivityDate="2015-03-02T22:18:38.323" Title="Are there multiple meanings to &quot;clone&quot; as in &quot;clone a gene&quot;?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30080" PostTypeId="1" AcceptedAnswerId="30246" CreationDate="2015-03-02T21:29:32.927" Score="8" ViewCount="2711" Body="&lt;p&gt;The E. coli has a genome with approximately &lt;strong&gt;5×10&lt;sup&gt;6&lt;/sup&gt;&lt;/strong&gt; bp. The main DNA polymerase involved in its chromosome duplication (DNA pol III , the one with highest processivity) can polymerize ~&lt;strong&gt;10&lt;sup&gt;3&lt;/sup&gt;&lt;/strong&gt; nucleotides per second.&#xA;By a simple calculation, we would conclude that the whole chromosome duplication would take ~ 5000 seconds ( about 80 minutes, so &lt;em&gt;more than an hour&lt;/em&gt;). The whole cell duplication would probably take much more than that, considering not only DNA Pol III is involved.&#xA;However, in optimal conditions, E. coli can actually duplicate in ~&lt;strong&gt;30 minutes&lt;/strong&gt;.&#xA;How could that be possible?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;OBS.: all the numbers used here are aproximate, but sufficient to account for the correct orders of magnitude.&lt;/p&gt;&#xA;" OwnerUserId="14630" LastEditorUserId="3340" LastEditDate="2015-03-03T05:17:54.660" LastActivityDate="2017-12-15T22:52:44.033" Title="How can E. coli proliferate so rapidly?" Tags="&lt;molecular-biology&gt;&lt;bacteriology&gt;&lt;replication&gt;&lt;polymerase&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30081" PostTypeId="2" ParentId="30075" CreationDate="2015-03-02T21:39:44.443" Score="11" Body="&lt;p&gt;While it is true that some fossils can be radioactive, not all of them are. According to the ressources I have found, it depends on the place where these minerals are found and also the other minerals present at this place. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When there are uranium and or potassium rich ores available, the fossils seem to enrich these radioactive isotopes in the calcium matrix of the bone during fossilation. See the reference for some more details on this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The isotopes which are occurring there are Uranium (U&lt;sup&gt;235&lt;/sup&gt; and U&lt;sup&gt;238&lt;/sup&gt;), Potassium (K&lt;sup&gt;40)&lt;/sup&gt;) and Rubidium (Rb&lt;sup&gt;87&lt;/sup&gt;), all of them with half lives in the billion years. Carbon does not play a role in these very old fossils (millions of years old), as the half life of the relevant carbon isotope is to short. These elements are also used for radiodating these fossils, see the table below (from &lt;a href=&quot;http://www.agiweb.org/news/evolution/datingfossilrecord.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VhZs5.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the radioactive safety I think there are some fossils where you should be cautious and carry them around all day long in your pocket. Most of these isotopes release $\alpha$ and $\beta$ radiation, some $\gamma$. While the $\alpha$ radiation is relatively easy to shield, lead can have detrimental effects due to the occurance of retardation radiation of the slowed down particles. In the lab we use thick acrylic glass shields to protect us from $\beta$ radiation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally I have found some secondary sources for painting the dinosaur bones with lead paint, but no real first hand source from a museum or so. Additionally the rules for radiation safety are pretty strict. If the bones would be so radioactive that a short visit would endanger you (how long are you looking at such pieces, a few minutes at maximum I would say) than they couldn't be shown anyway. Let alone the dangers for the scientists which analyze them. So I would think this is an urban legend.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3914/wya8dz6p_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Radioactivity in fossils at the Hagerman Fossil Beds National&#xA;Monument&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-03-03T07:28:45.423" LastActivityDate="2015-03-03T07:28:45.423" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30082" PostTypeId="2" ParentId="30079" CreationDate="2015-03-02T22:18:38.323" Score="1" Body="&lt;p&gt;&quot;Cloning a gene&quot; also just means making tons of copies of it, like in PCR, so you can sequence it&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-03-02T22:18:38.323" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30084" PostTypeId="1" AcceptedAnswerId="30086" CreationDate="2015-03-03T00:26:34.247" Score="1" ViewCount="575" Body="&lt;p&gt;Why exactly were bacteria and archaea kingdoms separated from the now unused kingdom of Monera? Aren't they the same? They are both prokaryotes, so what is the difference?&lt;/p&gt;&#xA;" OwnerUserId="14710" LastActivityDate="2015-03-04T04:23:14.160" Title="The Ancient Kingdom of Monera" Tags="&lt;cell-biology&gt;&lt;cell&gt;&lt;prokaryotes&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30085" PostTypeId="2" ParentId="30056" CreationDate="2015-03-03T00:37:19.927" Score="0" Body="&lt;p&gt;Okay, so your nuclear lamina is composed like so,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ltsj4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;Source: Wikipedia&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When cdc25 is upregulated between G2 and M, we see dephosphorylation of Cdk1 and it's subsequent association with cyclinB. Cdk1-Cyclin B activates the &lt;a href=&quot;http://en.wikipedia.org/wiki/Maturation_promoting_factor&quot; rel=&quot;nofollow noreferrer&quot;&gt;MPF&lt;/a&gt;, and the MPF initiates phosphorylation of the proteins called lamins. As the nuclear lamina depolymerizes, it's resorbed into the ER,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xXZsq.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;Source: &lt;a href=&quot;http://www.jbiomedsci.com/content/16/1/96&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.jbiomedsci.com/content/16/1/96&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What we find is that lamins actually help anchor heterochromatin (tightly packed) to the nuclear lamina, so when we phosphorylate the lamins, the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23374351&quot; rel=&quot;nofollow noreferrer&quot;&gt;heterochromatin is shown&lt;/a&gt; to move from the periphery to the more central areas of the nucleus. So we couple this uprooting of the chromatin from the lamins, and the resorption of the lamina to the ER through phosphorylation of the lamins during mitosis to broadly answer the question.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-03-03T00:37:19.927" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30086" PostTypeId="2" ParentId="30084" CreationDate="2015-03-03T00:56:37.357" Score="1" Body="&lt;p&gt;I'm surprised this term shows up much anymore. Though it's a part of history now, the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2112744&quot; rel=&quot;nofollow noreferrer&quot;&gt;following&lt;/a&gt; paper by Woese demonstrated the three domain system long ago.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This, however, is the net result of the sequenced genomes of eukaryotes, archaea and bacteria:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iIoy3.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16513982&quot; rel=&quot;nofollow noreferrer&quot;&gt;Toward automatic reconstruction of a highly resolved tree of life.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The phylogenetic differences between these organisms shed light that bacteria and archaebacteria were not as closely related as was initially though, hence the abolishment of Monera.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-03-03T00:56:37.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30087" PostTypeId="2" ParentId="30084" CreationDate="2015-03-03T01:02:37.287" Score="1" Body="&lt;p&gt;As you note, &quot;Monera&quot; includes both Bacteria and Archaea -- but genetic analysis and molecular comparisons reveal without a shadow of a doubt that Archaea share a more recent common ancestor with Eukaryota than they do with Bacteria. Consequently, &quot;Monera&quot; is a paraphyletic group, not a proper taxonomic category.  Thus the term has been abandoned in favor of the three domain model. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt; You'll find quite a nice explanation of this at the &lt;a href=&quot;https://en.wikipedia.org/wiki/Monera&quot; rel=&quot;nofollow&quot;&gt;Wikipedia page for Monera&lt;/a&gt;.&#xA;While modern evolutionary biology textbooks tend not to discuss the now outdated term &quot;Monera&quot;, each of the following textbooks lays out the relation among the three domains and discusses the reasons that we avoid paraphyletic groups: Futuyma &lt;em&gt;Evolution&lt;/em&gt; 2nd Edition, Herron and Freeman &lt;em&gt;Evolutionary Analysis&lt;/em&gt; 5th edition, Bergstrom and Dugatkin &lt;em&gt;Evolution&lt;/em&gt; 1st Edition, Zimmer and Emlen &lt;em&gt;Evolution&lt;/em&gt; 1st edition, Barton et al Evolution 1st Edition. (Presumably other texts and other editions would cover the same ground).&lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="13072" LastEditDate="2015-03-04T04:23:14.160" LastActivityDate="2015-03-04T04:23:14.160" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30088" PostTypeId="1" AcceptedAnswerId="30090" CreationDate="2015-03-03T02:05:32.360" Score="2" ViewCount="86" Body="&lt;p&gt;Would electroporation be successful on a one/two-celled mouse embryo? If it would, what buffer could be used and what percentage of cells would be viable?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-03-03T05:15:43.833" Title="Electroporation of one-cell embryo?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30089" PostTypeId="1" AcceptedAnswerId="30345" CreationDate="2015-03-03T04:30:34.367" Score="7" ViewCount="420" Body="&lt;p&gt;The Labrador Sea is between Greenland, Labrador, and Qikiqtaaluk:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IRSBL.jpg&quot; alt=&quot;Map of Labrador sea&quot; /&gt;&#xA;&lt;br /&gt;&lt;a href=&quot;http://www.animalbase.uni-goettingen.de/mapimage/map-labrador-sea.jpg&quot; rel=&quot;noreferrer&quot;&gt;Map source&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;A &lt;a href=&quot;http://www.greenland.com/en/about-greenland/nature-climate/fauna-of-greenland/the-polar-bear/&quot; rel=&quot;noreferrer&quot;&gt;Greenlandic source on polar bears&lt;/a&gt; states:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In Greenland the polar bear lives and breeds in the northernmost parts of West Greenland and in Northeast Greenland, but is also occasionally seen elsewhere in Greenland, as it moves with the drifting ice.&lt;/p&gt;&#xA;&lt;p&gt;However, it is extremely rare for either local inhabitants or tourists to see a living polar bear. The chances of seeing a polar bear are greatest when sailing by ship along the coast.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;On the other hand, &lt;a href=&quot;http://www.pc.gc.ca/eng/pn-np/nl/torngats/visit/secur.aspx&quot; rel=&quot;noreferrer&quot;&gt;Parks Canada for Torngat Mountains National Park&lt;/a&gt; (northern Labrador) states:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Polar bears are true carnivores and can be a significant risk to human beings. Visitors travelling and camping in the park are in polar bear country and are at high risk of encounters. Polar bears are almost always present along the north Labrador coast.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The observation that polar bears are more common in Labrador than in southern Greenland is supported by &lt;a href=&quot;http://www.nature.com/nature/journal/v468/n7326/full/468905a.html&quot; rel=&quot;noreferrer&quot;&gt;Derocher (2010), Nature&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/phW19.png&quot; alt=&quot;Polar bear distribution, Derocher (2010), Nature&quot; /&gt;&#xA;&lt;br /&gt;Derocher (2010), Nature&lt;/p&gt;&#xA;&lt;p&gt;Polar bears like the sea ice edge, but this is very far from either Labrador or Greenland when at its fall minimum.  When sea ice is at its spring maximum, both Labrador and almost all of Greenland are packed deeply in ice (see maps below).&lt;/p&gt;&#xA;&lt;p&gt;Then why are polar bears so much more common in Labrador than they are in southern Greenland?  Arey they really?  And how do they survive all summer long, when the sea ice is very, very far away?  &lt;a href=&quot;http://www.cbc.ca/news/canada/newfoundland-labrador/hikers-woken-by-screams-during-labrador-polar-bear-attack-1.1413645&quot; rel=&quot;noreferrer&quot;&gt;The occasional tourist&lt;/a&gt; might not be enough, I guess.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nAQ3s.jpg&quot; alt=&quot;Arctic minimum sea ice&quot; /&gt;&#xA;&lt;br /&gt;Arctic minimum sea ice from &lt;a href=&quot;http://nsidc.org/arcticseaicenews/files/2012/09/N_20120916_doy_extn_hires.png&quot; rel=&quot;noreferrer&quot;&gt;NSIDC&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uvd9c.png&quot; alt=&quot;Arctic maximum sea ice&quot; /&gt;&#xA;&lt;br /&gt;Arctic maximum sea ice from &lt;a href=&quot;http://nsidc.org/images/arcticseaicenews/200804_Figure1.png&quot; rel=&quot;noreferrer&quot;&gt;NSIDC&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1384" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-11T17:32:04.057" Title="(Why) are polar bears more common in Labrador than in southern Greenland?" Tags="&lt;zoology&gt;&lt;ecology&gt;&lt;species-distribution&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30090" PostTypeId="2" ParentId="30088" CreationDate="2015-03-03T05:15:43.833" Score="4" Body="&lt;p&gt;The buffers are usually supplied with the electroporation instrument; at least Lonza provides buffers for different types of cells. Single cell electroporation techniques exist, but they have been mostly done on neurons.&lt;sup&gt;[&lt;a href=&quot;http://www.nature.com/nprot/journal/v4/n6/abs/nprot.2009.56.html&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;,&lt;a href=&quot;http://www.jove.com/video/705/single-cell-electroporation-in-vivo-within-the-intact-developing-brain&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also try microinjection but it requires some practice. &lt;a href=&quot;http://www.nature.com/srep/2014/140624/srep05417/full/srep05417.html&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; study reports a transfection agent called VisuFect which can be used for zygotes as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not very sure about the success rate (AFAIK it is not that good) but I think it is anyway risky with organisms which do not produce a lot of embryos. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-03-03T05:15:43.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30093" PostTypeId="1" CreationDate="2015-03-03T10:59:34.007" Score="4" ViewCount="77" Body="&lt;p&gt;In &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674252/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper&lt;/a&gt; the authors state that the dosage compensation seen in &lt;em&gt;Drosophila&lt;/em&gt; is approximately twofold, but they do not provide any source or numbers (as far as I can see) for this. What is the mean degree of dosage compensation in &lt;em&gt;Drosophila (melanogaster)&lt;/em&gt;? For example, if X linked genes are, on average, perfectly upregulated the X:AA ratio in males would be 1, while if they are nearly perfectly (but slightly under) upregulated it will be ~0.9.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/23760/imperfect-dosage-compensation&quot;&gt;Here&lt;/a&gt; is a similar (but different) question RE perfection in DC in general (here I am specific to &lt;em&gt;Drosophila melanogaster&lt;/em&gt;).&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-05-25T10:30:07.360" Title="Degree of dosage compensation in Drosophila melanogaster" Tags="&lt;genomics&gt;&lt;genomes&gt;&lt;drosophila&gt;&lt;dosage-compensation&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30098" PostTypeId="1" CreationDate="2015-03-03T17:25:32.623" Score="0" ViewCount="24" Body="&lt;p&gt;Two mice are crossed and both are dark and heterozygote. Find the probability of their filium(children) dark (and) heterozygote in F1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's what our teacher explained:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PhlNM.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't understand. I thought it would be 1/2.&lt;/p&gt;&#xA;" OwnerUserId="14702" LastActivityDate="2015-03-03T17:25:32.623" Title="Find the probability of Filium (child) that are dark (and) heterozygote" Tags="&lt;genetics&gt;" AnswerCount="0" CommentCount="5" ClosedDate="2015-03-11T23:22:23.123" ContentLicense="CC BY-SA 3.0" />
  <row Id="30099" PostTypeId="1" CreationDate="2015-03-03T17:47:15.680" Score="1" ViewCount="1672" Body="&lt;p&gt;Can warm blooded vertebrates other than humans act as reservoir hosts for malaria parasites? I'm mainly interested in &lt;em&gt;Plasmodium vivax&lt;/em&gt; and possible reservoir hosts in the wider area of Europe/ Eurasia. &lt;/p&gt;&#xA;" OwnerUserId="3382" LastEditorUserId="3382" LastEditDate="2015-05-09T22:42:45.510" LastActivityDate="2017-11-20T19:40:06.253" Title="Does malaria have a reservoir host?" Tags="&lt;parasitology&gt;&lt;malaria&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30101" PostTypeId="1" AcceptedAnswerId="30137" CreationDate="2015-03-03T19:13:12.303" Score="6" ViewCount="1161" Body="&lt;p&gt;Having lived in various places all over the world for the past 9 years of my life, one thing stood out to me throughout this time, and now in particular. From a quiet place on the countryside in Sweden, I moved to Manchester for my studies. When I first arrived there, I felt the city was very noisy, a feeling which gradually reduced as I presumably got used to the noise levels there. From Manchester I moved over to Saitama in Japan, an enormous city right next to Tokyo with a considerable amount of noise during the day, and buildings that have little to no sound insulation. With the exception of particularly loud noises, I again adapted to the sound levels in the country, which at the time, I felt was no more than a natural response in terms of how much attention we pay to the noise. If I'm distracted by work or other activities, I have little reason to dwell on the sounds of driving cars and talking people. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thing I couldn't explain purely by the 'paying attention' argument however was when I moved back to the Netherlands, to an apartment with excellent sound insulation. My apartment is located in front of a somewhat larger road, and cars pass by almost consistently. However, when I moved in I could barely hear these cars driving past, something that stood out to me as fairly pleasant. I thought a little bit of ambient music would kill the sound of these vehicles driving past altogether. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now skip ahead one month, and I can hear the cars almost as if I'm standing next to them, an exaggeration of course, but the sound is much clearer than it was when I moved in. I know that nothing has changed in terms of insulation and I know that no windows are open. Strangely the only thing that appears to have changed is the clarity in which I perceive this noise, as none of the other people whom I've asked seem to share the same opinion (that is, that the noise has grown louder). This made me wonder - does our hearing adapt to noise pollution, and if so, how does it work?&lt;/p&gt;&#xA;" OwnerUserId="14738" LastActivityDate="2019-09-03T14:55:33.510" Title="Do our ears or brains gradually adapt to noise pollution?" Tags="&lt;hearing&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30102" PostTypeId="1" AcceptedAnswerId="30103" CreationDate="2015-03-03T19:50:33.320" Score="18" ViewCount="1636" Body="&lt;p&gt;So I get the concept that a vaccine is a weakened form of a virus so that the body can &quot;learn&quot; to fight it and make a person immune to that disease, but how exactly does this learning take place? What learns? The white blood cells? Do they have their own database or something and do they go from cell to cell informing them of what they learned? I read that they only last around 5 to 7 days so that means there's constantly new white blood cells that also need this information for all diseases ever encountered. How does this work? Thanks!&lt;/p&gt;&#xA;" OwnerUserId="14739" LastActivityDate="2015-03-04T00:52:32.337" Title="How Do White Blood Cells Learn? Or Do They?" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30103" PostTypeId="2" ParentId="30102" CreationDate="2015-03-03T20:36:24.253" Score="18" Body="&lt;p&gt;So while some kind of a biological database might have been an evolutionary option, the way we evolved is different from this. Rather than 'planning' what diseases could be recognized in the environment and recording this, our bone marrow constantly pumps out naive B and T cells that have a randomized receptor on them. The effect of this is that every new B and T cell that your bone marrow makes will recognize a unique, random protein sequence, and you will have billions of these cells floating around in your blood circulation at any given time. These cells however will only float around in circulation for a short period of time before dying and being replaced by other cells with new random sequence receptors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you get a vaccination, you are injecting in specific protein sequences from a specific pathogen. As these injected protein sequences circulate through your blood they will eventually bump into a B or T cell that has a receptor that recognizes them. When this happens, the B or T cell will now start to divide and give rise to long lasting memory cells that express the exact same receptor and will therefore recognize the exact same protein sequence again in the future. These cells will float around in your blood for most of your life and make you 'immune' to the recognized pathogen. When you get reinfected with the same pathogen or the pathogen to which you were vaccinated these memory cells will rapidly divide upon recognition of the pathogen and give rise to a large number of effector cells that eliminate the pathogen before it can 'make you sick'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is really cool about this is that because each T or B cell carries on it a receptor that recognizes a random protein sequence, you currently have in you B and T cells that would recognize a protein that does not even exist on Earth, but might exist on Mars or somewhere else in the Universe. This makes our immune system quite valuable because any protein that nature creates for all of time anywhere in the universe will still be recognizable by our immune systems. &lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-03-03T20:36:24.253" CommentCount="17" ContentLicense="CC BY-SA 3.0" />
  <row Id="30104" PostTypeId="1" AcceptedAnswerId="30105" CreationDate="2015-03-03T20:57:16.573" Score="5" ViewCount="561" Body="&lt;p&gt;Is there an approximate figure of the total number of action potentials in the human brain? It's my understanding that there are ~ 60 billion neurons in the brain with ~ 100 trillion connections between them. Plus there are graded responses between those connections. Is there an estimated figure for what the total might be?&lt;/p&gt;&#xA;" OwnerUserId="13448" LastActivityDate="2015-03-03T21:02:17.423" Title="What are the total number of action potentials in the human brain?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;synapses&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30105" PostTypeId="2" ParentId="30104" CreationDate="2015-03-03T21:02:17.423" Score="6" Body="&lt;p&gt;If firing rate is from 1 Hz to 200 Hz, 100 trillion to 20 quadrillion synaptic firings. Neuronal (say, measured from soma) firings  will add up to 86 billion to 17.2 trillion action potentials per second.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It important to remember, that synaptic firings &quot;sum up&quot; in soma or interfere between each other, so the are more of those.&#xA;Read more: &lt;a href=&quot;http://neuroblog.stanford.edu/?p=4541&quot;&gt;http://neuroblog.stanford.edu/?p=4541&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-03-03T21:02:17.423" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30106" PostTypeId="1" AcceptedAnswerId="30121" CreationDate="2015-03-03T21:25:11.010" Score="4" ViewCount="441" Body="&lt;p&gt;It is a classical result that the expected time for a neutral mutation to occur and to get fixed is $2 N \mu \frac{1}{2N} = \mu$, where $N$ is the population size and $\mu$ is the neutral mutation rate (&lt;a href=&quot;http://en.wikipedia.org/wiki/Fixation_(population_genetics)&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not sure I understand what this actually mean. What is the probability of (at least) one fixation event to occur in $\frac{1}{\mu}$ generations? Is it 0.5? Could we calculate the probability that (at least) one fixation event occurs in $n$ generations? For example after $n=\frac{\mu}{10}$ generations, is the probability of observing (at least) one fixation event equal to $0.1$ or is it more complicated?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;UPDATE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following @DanielWeissman comments:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's consider we are starting with an initially monomorphic population (population of clones). In addition to that, let's consider that the population is relatively small $N\mu &amp;lt; 1$&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-03-12T18:55:41.907" LastActivityDate="2015-03-12T18:55:41.907" Title="Fixation rate at neutral loci" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30107" PostTypeId="1" CreationDate="2015-03-03T22:32:47.863" Score="1" ViewCount="105" Body="&lt;p&gt;I understand that all life forms on the planet are made from adenine, gauatine, cytosine and thymine, which chemically joined together to form RNA or DNA (correct me if I'm wrong). This goes on to form all complex life as we know it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering if it was possible- even studied theoretically- that other life forms could exist made of different elements and compounds, perhaps let's say iron, cobalt or tungsten? Or are the 4 bases the only possible way of life as we currently know it?&lt;/p&gt;&#xA;" OwnerUserId="6968" LastActivityDate="2015-03-07T15:31:06.053" Title="Can life forms exist from simple structures not made of the four bases?" Tags="&lt;evolution&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ClosedDate="2015-03-04T06:00:43.977" ContentLicense="CC BY-SA 3.0" />
  <row Id="30108" PostTypeId="1" CreationDate="2015-03-03T23:17:24.397" Score="3" ViewCount="46" Body="&lt;p&gt;I already know about recombinases (specifically excisionases), but was wondering if there were other mechanisms present.&lt;/p&gt;&#xA;" OwnerUserId="14741" LastActivityDate="2015-03-04T11:52:23.417" Title="What mechanisms exist for the excision of specific sequences from DNA?" Tags="&lt;dna&gt;&lt;recombination&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30110" PostTypeId="2" ParentId="8195" CreationDate="2015-03-04T01:17:59.337" Score="2" Body="&lt;p&gt;It depends what you mean by &quot;predict&quot;. Consider that the faces on genetically identical individuals, such as identical twins, are very similar, even in old age. If you look at the processes of development over the life of an individual as a more-or-less deterministic and predictable phenomenon, then you might argue that faces are predictable from DNA info. The fact that no one has ever done this from first principles is another issue - in principle it is possible.&lt;/p&gt;&#xA;" OwnerUserId="14742" LastActivityDate="2015-03-04T01:17:59.337" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30111" PostTypeId="2" ParentId="30107" CreationDate="2015-03-04T01:41:34.000" Score="3" Body="&lt;p&gt;So this question is difficult to answer because it has some errors in it, in that lifeforms being dependent on rarely used elements is a different question than lifeforms using different DNA bases, but I will answer both.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for the question about whether or not organisms could exist that use DNA bases not found in organisms on earth, the answer is certainly yes.&lt;sup&gt;[&lt;a href=&quot;http://www.nature.com/nature/journal/v509/n7500/full/nature13314.html&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;,&lt;a href=&quot;http://www.nature.com/nature/journal/v509/n7500/full/nature13335.html&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above reference shows a very elegant example of completely synthetic DNA bases being incorporated into E Coli and propagated in culture without providing any noticeable negative effects. This provides strong support that life on Earth developed around the same 5 bases (CTGAU) by chance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for whether or not organisms could rely heavily on elements other than H,C,N,O, and P, this is certainly possible and evident already here on Earth. Extremophiles are a general class of organisms that have some pretty interesting properties to them. Some metabolize sulfur or metals, others live in really extreme temperatures or in areas of high radiation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So really yes in both cases, life can really take numerous shapes and forms even when it seems completely impossible for them to do so.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastEditorUserId="3340" LastEditDate="2015-03-07T15:31:06.053" LastActivityDate="2015-03-07T15:31:06.053" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30112" PostTypeId="1" CreationDate="2015-03-04T02:33:05.217" Score="4" ViewCount="5946" Body="&lt;p&gt;As said in the title I am a little confused on the idea of traits located on the sex chromosomes. The example we worked on in class was haemophilia, a recessive trait located on the X chromosome. Does this mean males only have one allele to choose from while females have two? Does this mean that only females have the ability to be heterozygous in sex linked traits? &lt;/p&gt;&#xA;" OwnerUserId="14744" LastEditorUserId="1590" LastEditDate="2015-12-31T08:44:09.450" LastActivityDate="2015-12-31T08:46:08.260" Title="If a gene is located on the X chromosome, does that mean males are never heterozygous for these genes?" Tags="&lt;genetics&gt;" AnswerCount="5" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30113" PostTypeId="1" AcceptedAnswerId="30122" CreationDate="2015-03-04T02:47:50.317" Score="4" ViewCount="537" Body="&lt;p&gt;&lt;strong&gt;Previous Research&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I stumbled across a trending reddit post &quot;&lt;a href=&quot;http://www.reddit.com/r/pics/comments/2xtis9/lapidaria_margaretae_looks_like_stones/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lapidaria margaretae looks like stones&lt;/a&gt;&quot; (as of 3rd Februrary 2015); but I could not find discussions as to reasons behind why.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question/s&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why do Lapidaria margaretae look like stones? I am interested in both the morphological/physiological reasons, as well as possible evolutionary mechanisms.&lt;/li&gt;&#xA;&lt;li&gt;Or perhaps I am asking the wrong question, then what should it be?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xGpYH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="5005" LastEditDate="2015-03-04T03:07:45.217" LastActivityDate="2015-03-04T06:28:27.633" Title="Why do Lapidaria margaretae look like stones?" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30114" PostTypeId="2" ParentId="30112" CreationDate="2015-03-04T02:59:52.967" Score="0" Body="&lt;p&gt;Because males only have one X chromosome, they can only have one copy of any gene found on the X chromosome, and therefore only have one allele. This means that in the case of a recessive disorder like hemophilia, should they happen to inherit a recessive allele from their mothers, they will have the recessive (disordered) phenotype because there is no other allele present to give them the dominant phenotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Homozygous recessive&quot; and &quot;homozygous dominant&quot; are perhaps a little misleading here because male individuals aren't homozygous at all, having only one copy of genes present only on the X-chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But yes, this means only women can be heterozygous for sex-linked traits. Men will have either the dominant or the recessive phenotype, and cannot be carriers.&lt;/p&gt;&#xA;" OwnerUserId="13430" LastActivityDate="2015-03-04T02:59:52.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30115" PostTypeId="2" ParentId="30112" CreationDate="2015-03-04T03:02:30.307" Score="0" Body="&lt;p&gt;It sounds like you pretty much have it. Hemophilia is recessive, meaning that a single function copy of the necessary clotting genes will be sufficient to function. So a female can inherit defective genes on one X chromosome and functional genes on the other and be perfectly fine. However, if a male inherits defective genes on one X chromosome he will have the disorder because he does not have another X chromosome to provide the functional genes to compensate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize that you also said you are confused about traits located on sex chromosomes. They are essentially just like any other chromosome and carry genes just like other chromosomes. It just so happens that they also carry genes that are important in gender determination.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-03-04T03:02:30.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30116" PostTypeId="1" AcceptedAnswerId="30120" CreationDate="2015-03-04T03:10:39.550" Score="159" ViewCount="17224" Body="&lt;p&gt;Does DNA have anything like IF-statements, GOTO-jumps, or WHILE loops?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In software development, these constructs have the following functions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;IF-statements:&lt;/strong&gt; An IF statement executes the code in a subsequent code block if some specific condition is met.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;WHILE-loops:&lt;/strong&gt; The code in a subsequent code block is executes as many times as specified, or as long as a specific condition is met.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Function calls:&lt;/strong&gt; The code temporarily bypasses the subsequent code block, executing instead some other code block. After execution of the other code block the code returns (sometimes with some value) and continues the execution of the subsequent block.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;GOTO-statements:&lt;/strong&gt; The code bypasses the subsequent code block, jumping instead directly to some other block.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Are constructs similar to these present in DNA? If yes, how are they implemented and what are they called?&lt;/p&gt;&#xA;" OwnerUserId="12939" LastEditorUserId="3340" LastEditDate="2015-03-04T12:28:28.437" LastActivityDate="2019-03-13T04:22:13.660" Title="Does DNA have the equivalent of IF-statements, WHILE loops, or function calls? How about GOTO?" Tags="&lt;dna&gt;&lt;bioinformatics&gt;&lt;systems-biology&gt;" AnswerCount="7" CommentCount="18" FavoriteCount="72" ContentLicense="CC BY-SA 3.0" />
  <row Id="30117" PostTypeId="2" ParentId="30116" CreationDate="2015-03-04T03:39:41.073" Score="19" Body="&lt;p&gt;There are certainly some comparisons that could be made between the way genes are expressed from DNA and logic functions, but they aren't great.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But synthetic Biology is really a blossoming new field that is attempting to integrate logic functions into biology, see e.g. &lt;a href=&quot;http://www.nature.com/nbt/journal/v31/n5/abs/nbt.2510.html&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;Siuti et al. 2013. Synthetic circuits integrating logic and memory in living cells. Nature Biotechnology 31, 448–452. doi:10.1038/nbt.2510&quot;&gt;Siuti et al (2013)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above paper is a brilliant example of a group using bacteria to store information and assembling into biological circuits that can then be used to process logic functions. So its being done but not exactly in the way that you propose.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastEditorUserId="16921" LastEditDate="2018-04-24T05:38:39.563" LastActivityDate="2018-04-24T05:38:39.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30118" PostTypeId="1" CreationDate="2015-03-04T04:05:06.347" Score="2" ViewCount="2159" Body="&lt;p&gt;What is the name of the machine used to measure optical density? We used it in a lab but I can't remember what they called it.&lt;/p&gt;&#xA;" OwnerUserId="14746" LastActivityDate="2015-03-04T17:03:47.430" Title="Optical density machine name" Tags="&lt;terminology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30120" PostTypeId="2" ParentId="30116" CreationDate="2015-03-04T04:42:57.097" Score="122" Body="&lt;p&gt;Biological examples similar to programming statements:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;code&gt;IF&lt;/code&gt; : Transcriptional activator; when present a gene will be transcribed. In general there is no termination of events unless the signal is gone; the program ends only with the death of the cell. So the &lt;code&gt;IF&lt;/code&gt; statement is always a part of a loop.&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;WHILE&lt;/code&gt; : Transcriptional repressor; gene will be transcribed until repressor is not present.&lt;/li&gt;&#xA;&lt;li&gt;There are no equivalents of &lt;code&gt;function&lt;/code&gt; calls. All events happen is the&#xA;same space and there is always a likelihood of interference. One can&#xA;argue that organelles can act as a compartment that may have a&#xA;&lt;code&gt;function&lt;/code&gt; like properties but they are highly complex and are&#xA;not just some kind of input-output devices.&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;GOTO&lt;/code&gt; is always dependent on a condition. This can happen in case of certain network connections such as feedforward loops and branched pathways. For example if there is a signalling pathway like this: &lt;br&gt; &lt;strong&gt;A → B → C&lt;/strong&gt; and there is another connection &lt;strong&gt;D → C&lt;/strong&gt; then if somehow &lt;strong&gt;D&lt;/strong&gt; is activated it will directly affect &lt;strong&gt;C&lt;/strong&gt;, making &lt;strong&gt;A&lt;/strong&gt; and &lt;strong&gt;B&lt;/strong&gt; dispensable. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Logic gates have been constructed using synthetic biological circuits. See &lt;a href=&quot;http://www.nature.com/nrg/journal/v16/n3/abs/nrg3885.html&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; review for more information. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Note&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Molecular biological processes cannot be directly compared to a computer code. It is the underlying logic that is important and not the statement construct itself and these examples should not be taken as absolute analogies. It is also to be noted that DNA is just a set of instructions and not really a fully functional entity (it is functional to some extent). However, even being just a code it is comparable to a HLL code that has to be compiled to execute its functions. See &lt;a href=&quot;https://biology.stackexchange.com/questions/29663/can-dna-rna-be-considered-as-natures-programming-language&quot;&gt;this&lt;/a&gt; post too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also important to note that the cell, like many other physical systems, is analog in nature. Therefore, in most situations there is no 0/1 (binary) value of variables. Consider gene expression. If a transcriptional activator is present, the gene will be transcribed. However, if you keep increasing the concentration of the activator, the expression of that gene will increase until it reaches a saturation point. So there is no digital logic here. Having said that, I would add that switching behaviour is possible in biological systems (including gene expression) and is also used in many cases. Certain kinds of regulatory network structures can give rise to such dynamics. Co-operativity with or without positive feedback is one of the mechanisms that can implement switching behaviour. For more details read about &lt;a href=&quot;https://en.wikipedia.org/wiki/Ultrasensitivity&quot; rel=&quot;noreferrer&quot;&gt;ultrasensitivity&lt;/a&gt;. Also check out &quot;&lt;a href=&quot;https://biology.stackexchange.com/q/30588/3340&quot;&gt;Can molecular genetics make a boolean variable from a continuous variable?&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2016-11-29T05:26:59.620" CommentCount="20" ContentLicense="CC BY-SA 3.0" />
  <row Id="30121" PostTypeId="2" ParentId="30106" CreationDate="2015-03-04T04:49:22.720" Score="4" Body="&lt;p&gt;First of all, the $\mu$ is not expected time for a mutation to occur and get fixed; it is the rate at which mutations are fixed in the population. The basic result states that if neutral mutations arise at a locus at rate $\mu$ &lt;em&gt;within individuals&lt;/em&gt;, mutations at this locus will be fixed &lt;em&gt;in the population&lt;/em&gt; at rate $\mu$ as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The expected time for a given neutral mutation to fix after arising, given that it is not lost from the population, is approximately $4N_e$, where $N_e$ is the effective population size. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1212239/&quot; rel=&quot;nofollow&quot;&gt;Kimura and Ohta (1969)&lt;/a&gt; derive this result using a diffusion approximation; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0304414982900114&quot; rel=&quot;nofollow&quot;&gt;Kingman (1982)&lt;/a&gt; develops coalescent theory and in the process obtains what in my opinion is a more elegant derivation of the same approximation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now what is the probability that &lt;em&gt;some&lt;/em&gt; mutation goes to fixation in the population as a function of time? Even though the fixation rate in the population is $\mu$, this does not mean that with probability 0.5 some mutation fixes within $1/\mu$ time units. That probability will depend on the distribution of fixation events in the population. Here's a good way to think about it. If fixation events were evenly spaced and occurred at rate $\mu$, then with probability 1 you would have a mutation within an interval of length $1/\mu$. If fixation events were highly clumped, then you would have a very low probability of having a fixation event within an interval of length $1/\mu$ -- but if you did have one event, you would probably have many. If fixation events are distributed as a Poisson process--which I suspect they would be in a purely neutral model--the probability of having a fixation event within a time interval $1/\mu$ would be given by a &lt;a href=&quot;https://en.wikipedia.org/wiki/Exponential_distribution&quot; rel=&quot;nofollow&quot;&gt;(negative) exponential distribution&lt;/a&gt; and thus the probability of having at least one fixation event in a time interval of length $1/\mu$ would be $1-\frac{1}{e}$.&lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-03-04T04:49:22.720" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30122" PostTypeId="2" ParentId="30113" CreationDate="2015-03-04T06:28:27.633" Score="5" Body="&lt;p&gt;&quot;Teleology is like a mistress to a biologist: he cannot live without her but he's unwilling to be seen with her in public.&quot; - J.B.S. Haldane (1892 - 1964)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't tell you why Lapidaria &lt;em&gt;margaretae&lt;/em&gt; looks like 'stones'. But I can deduce something from the way this plant looks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First and foremost, I can say this plant probably evolved in an arid region, possibly a desert (less than 10 inches of water per year), because it is a succulent, with a shape that comes pretty close to minimizing it's surface to volume area (decreased evaporation, decreased transpiration). Seeing as it's a dwarf and shaped as it is, I might hazard that it's windy and sandy where this plant evolved, also because of it's shape - low to the ground, sturdy, low surface area, able to resist the wind. Finally, the light color of the plant suggests a lot of bright sun (reflects sunlight more than some darker colors).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;None of that is foolproof, but in this case, it turns out to be right; the plant comes from southern Namibia, and is commonly called the &quot;Karoo rose&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is one image of the Karoo region:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1O8su.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stones come in all kinds of shapes and sizes, also influenced by water, wind and other environmental influences. That this plant looks like stones is mostly coincidental.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-03-04T06:28:27.633" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30123" PostTypeId="2" ParentId="30118" CreationDate="2015-03-04T08:48:18.180" Score="6" Body="&lt;p&gt;Optical Density is synonymous with &lt;strong&gt;absorbance&lt;/strong&gt; which is based on the principle of absorption of light. The machine that is used to measure absorbance is called a &lt;strong&gt;spectrophotometer&lt;/strong&gt;. Spectrometer does not indicate that light absorbance is being measured. A spectrometer can measure any spectrum; for e.g. Mass Spectrometer measures the spectrum of molecular mass (to be precice mass per charge).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cell density can be also measured by the level of light scattering; turbidimeters or nephelometers are used for these kind of measurements. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;PS: You should pay more attention in your class&lt;/em&gt; :P&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-04T14:04:58.933" LastActivityDate="2015-03-04T14:04:58.933" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30124" PostTypeId="2" ParentId="30116" CreationDate="2015-03-04T09:27:25.980" Score="10" Body="&lt;p&gt;As WYSIWYG said there is no equivalent for function calls, as there will always be some interference. However one could argue that some modular pathways (eg. apoptosis signalling) can be seen as a &quot;code block&quot; where a certain input will (almost) certainly lead to a certain effect. The analogy with function calls is that, in describing many different mechanisms, it makes for shorter and more efficient &quot;code&quot; to consider everything between eg. caspase activation and cytochrome leakage as one block. Also, marking a protein with ubiquitin can maybe be seen as a function call for degradation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in the building blocks for programming with biology, check out the biobricks.org program, which aims to define modular parts (bricks) which can be sensors, logic functions, effectors,...&lt;/p&gt;&#xA;" OwnerUserId="14698" LastActivityDate="2015-03-04T09:27:25.980" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30125" PostTypeId="1" CreationDate="2015-03-04T09:33:19.543" Score="2" ViewCount="904" Body="&lt;p&gt;My eyes are very sensitive to flashing lights - for example I'm always the first person to notice that a fluorescent tube is about to fail because I see it flickering when other people can't.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I'm driving at night, I perceive LED rear lights on cars as being a series of unconnected dots when I scan my eyes quickly across the scene. Evidently, many, if not all, LEDs are actually flashing at a high rate which most people don't perceive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It almost seems as though I have a higher &quot;refresh rate&quot; than most people. How unusual am I? What is the physiology of it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I suppose what I find most fascinating is that at times when I see a trail of flashes, the spacing between them is remarkably consistent. This implies to me that there is an incredibly accurate timing mechanism somewhere in my visual system that is taking &quot;snapshots&quot; with clockwork regularity - probably between 50 and 100 samples per second. I'd like an insight into this &quot;clock&quot; and why mine seems to be faster than anyone I've ever met.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This similar to what I perceive:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XPpyT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14750" LastEditorUserId="14750" LastEditDate="2015-03-04T22:59:17.457" LastActivityDate="2015-03-04T22:59:17.457" Title="Sensitivity of eyes to flashing lights" Tags="&lt;eyes&gt;&lt;vision&gt;&lt;human-eye&gt;" AnswerCount="0" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="30126" PostTypeId="2" ParentId="30116" CreationDate="2015-03-04T09:47:08.220" Score="14" Body="&lt;p&gt;Just to add to previous answers, but &lt;strong&gt;transcriptional interference&lt;/strong&gt; (see e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2941638/&quot;&gt;Shearwin et al., 2005&lt;/a&gt;) can be seen as a form of IF-statement (or WHILE) in the sense that:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;if(x transcribed){not y transcribed}&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The interference does not have to be binary though, and more common are graded responses. Transcriptional interference can also take place at the RNA stage (see e.g. &lt;a href=&quot;http://www.nature.com/nature/journal/v514/n7524/full/nature13671.html&quot;&gt;Xue et al, 2014&lt;/a&gt;), using &lt;a href=&quot;http://en.wikipedia.org/wiki/Antisense_RNA&quot;&gt;&lt;em&gt;antisense RNA&lt;/em&gt;&lt;/a&gt; and often providing a negative feedback loop, but the interference is then removed from the DNA, and does not represent a direct IF-statement analog at the DNA stage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To me, GOTO mainly makes sense for sequential code execution, and this is not the case for DNA (lots of transcription is happening all the time in parallel). More generally, the parallel &quot;execution&quot; of DNA along with the continuous interactions and feedback loops between DNA, transcripts and proteins (among other things) also means that cellular processes are far less clear-cut and traceable than computer code, which means that computer code is a very poor metaphor for cellular processes and the functioning of DNA.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-03-04T22:29:55.833" LastActivityDate="2015-03-04T22:29:55.833" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30127" PostTypeId="1" AcceptedAnswerId="30130" CreationDate="2015-03-04T10:52:10.217" Score="2" ViewCount="52" Body="&lt;p&gt;Next to double positive feedback loops and chromatin modification, which other mechanisms can make a gene susceptible to a certain environment in one cell-type but not in another?&lt;/p&gt;&#xA;" OwnerUserId="14698" LastActivityDate="2015-03-05T04:34:19.160" Title="What network motifs or other mechanisms can make the expression of a gene invariable to the environment?" Tags="&lt;gene-expression&gt;&lt;systems-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30128" PostTypeId="2" ParentId="21400" CreationDate="2015-03-04T11:02:20.570" Score="3" Body="&lt;p&gt;There are two antipodes: The molecular (or makromolecular) biology, which has the concept of large macromolecules which fulfill one task. This can for example be an enzyme which breaks down its subtrate. The properties and the structure of all molecules of the enzyme are the same and the factor determining the function of the enzyme.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The coloidal biology assumes that the function is granted by adding small amounts of an enzyme to water to form a colloid, which thenchanges the properties of the water in the way that it does break down the subtrate. Life was also explained as the sum of the functions of the colloids building the body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This theory came up in a time when macromolecules and their functions where not very well understood. The better understanding of macromolecules rendered this theory irrelevant. This is also neatly sumarized in the conclusions section of the article you cite.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-03-04T11:02:20.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30129" PostTypeId="2" ParentId="30108" CreationDate="2015-03-04T11:52:23.417" Score="1" Body="&lt;p&gt;Genome editing techniques like CRISPR-Cas and TALEN use non-specific recombinases coupled to a DNA-recognizing part that can be designed to be specific for any stretch of sequence, as it is constructed out of single zinc-finger 'modules' that each specifically bind a couple of nucleotides (one nucleotide each in the case of TALEN).&lt;/p&gt;&#xA;" OwnerUserId="14698" LastActivityDate="2015-03-04T11:52:23.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30130" PostTypeId="2" ParentId="30127" CreationDate="2015-03-04T12:13:04.897" Score="4" Body="&lt;p&gt;This phenomenon of being insensitive to certain fluctuations is called robustness. The fluctuations can be of two kinds for an input-output device such as a gene that is activated by a signal:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Fluctuations in the signal&lt;/li&gt;&#xA;&lt;li&gt;Fluctuations in the intrinsic parameters&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Signal fluctuations can be temporal but parameter fluctuations are not (parameters are supposed to be time invariant). Parameter fluctuation can exist in a genotypic space or a population of cells because of variation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some motifs are robust to signal perturbations whereas some are robust to parameter fluctuations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Negative feedbacks and incoherent feed-forward can confer robustness by correcting the output fluctuations because of fluctuations in the input. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When an all or none sort of (binary: one state need not be smaller in magnitude than the other) behaviour is important, then positive feedbacks confer robustness to such systems because of their property of bistability. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I cannot recall any particular motif that is robust to parameters. There are certain cases though (&lt;em&gt;I am still working on that!! :P&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case environment can be thought of as an input. &lt;br&gt; For your question &lt;strong&gt;&quot;what mechanisms can make a gene susceptible to a certain environment in one cell-type but not in another&quot;&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There can be a heterogeneous population of cells which can arise because of bistability or even otherwise, due to stochastic effects. If the gene that is in one of the two states (expression levels) in these two sub-population of cells, and this gene is responsible for the expression control (the controller gene in feedback), then one sub-population will be sensitive to the environment while the other will not be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information on biological robustness read this &lt;a href=&quot;http://www.nature.com/nrg/journal/v5/n11/abs/nrg1471.html&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-05T04:34:19.160" LastActivityDate="2015-03-05T04:34:19.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30131" PostTypeId="1" CreationDate="2015-03-04T12:29:18.440" Score="6" ViewCount="14568" Body="&lt;p&gt;Again, it is a basic question. What is our skin made up of? is it made up of many cells arranged in a systematic way or is it just like any layer say of a book?? what is the difference? where is the living and dead thing coming into picture? is it the fact that skin can self-heal makes it living and in turn made up of cells??&lt;/p&gt;&#xA;" OwnerUserId="14689" LastActivityDate="2017-05-17T17:14:51.940" Title="What is our skin made up of?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;skin&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30132" PostTypeId="2" ParentId="30131" CreationDate="2015-03-04T12:49:48.917" Score="8" Body="&lt;p&gt;The human skin is indeed made off a number of different layers, the three most important are epidermis, dermis and hypodermis (also called subcutaneous fat), see the figure (from &lt;a href=&quot;http://www.beautyskinexpert.com/your-skin-layers-part-2/&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;) for details:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8LT1y.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All three layers can be subcategorized further, I'll only give a few details here. More can be found for example in the Wikipedia article on &lt;a href=&quot;https://en.wikipedia.org/wiki/Skin&quot; rel=&quot;noreferrer&quot;&gt;skin&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Epidermis:&lt;/strong&gt; Top layer of our skin, is covered with the stratum corneum, which consists of several layers of dead cells, which protect the layers below. New cells of the epidermis are made at the border between dermis and epidermis and travel upwards (actually the top layers are worn off). The epidermis is the place where the pigmentation takes place due to melanocytes embedded in the keratinocytes of the epidermis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Dermis:&lt;/strong&gt; The next layer is the dermis where a lot of important functions on the skin happen. Sweat and oil are produced in the dermis. The feeling of the skin is also mediated in the dermis where the ends of the nerves are embedded. The hair roots of the hairs of the skin are also located here as well as the blood capillaries which supply the skin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Hypodermis or Subcutaneous fat:&lt;/strong&gt; The last layer is the hypodermis. It attaches the dermis to the underlaying muscles and bones and houses bigger blood vessels and nerves which go up into the dermis. The fat layer is also important for controlling the body temperature and storing fat reserves.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-03-04T12:49:48.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30133" PostTypeId="2" ParentId="30116" CreationDate="2015-03-04T13:10:32.617" Score="17" Body="&lt;p&gt;DNA is not analogous to computer code which renders your search for similar constructs in it meaningless. To give a couple of simple examples why this is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Computer code has a sequential order of execution; DNA acts in&#xA;parallel and out of sequence, it is not &quot;executed&quot;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Computer code has a strict and consistent meaning so the line &lt;code&gt;if x==4 : x=7&lt;/code&gt; always does the same thing; coding DNA&#xA;translates to amino acids and it's the complex chemical interactions&#xA;between these acids which give proteins their function thus no piece&#xA;of coding DNA can be understood outside of its protein.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Biological systems do have some pathways that operate in a similar way to computers, but you should be looking for these at the protein level not the DNA level and, even then, you need to be extremely careful that your analogy does not impair your understanding of what is really happening.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastEditorUserId="2938" LastEditDate="2016-11-25T09:11:31.100" LastActivityDate="2016-11-25T09:11:31.100" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30134" PostTypeId="2" ParentId="29663" CreationDate="2015-03-04T13:35:39.520" Score="12" Body="&lt;p&gt;This question can't be answered with a simple yes/no, but I would say that the analogy of DNA being the &quot;code&quot; used by cells is a reasonable one, if taken with a number of other considerations.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;DNA function&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;When Watson and Crick first described the structure of DNA (being a double-stranded sequence  of the nucleotides &lt;strong&gt;A&lt;/strong&gt;denine, &lt;strong&gt;C&lt;/strong&gt;ytosine, &lt;strong&gt;G&lt;/strong&gt;uanine and &lt;strong&gt;T&lt;/strong&gt;hymine) this led to what is known as the &lt;em&gt;Central Dogma of Molecular Biology&lt;/em&gt; [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/central_dogma.html&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt;], which posits that DNA makes RNA makes Protein (figure from [&lt;a href=&quot;http://sandwalk.blogspot.co.uk/2007/01/central-dogma-of-molecular-biology.html&quot; rel=&quot;noreferrer&quot;&gt;2&lt;/a&gt;], as originally produced by Watson).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lYd8A.jpg&quot; alt=&quot;http://sandwalk.blogspot.co.uk/2007/01/central-dogma-of-molecular-biology.html&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you correctly point out, less than 2% of the genome is protein-coding, however our understanding of the rest of the genome is increasing manifold due to projects like ENCODE [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15499007&quot; rel=&quot;noreferrer&quot;&gt;3&lt;/a&gt;], which are discovering not only the &quot;regulatory&quot; regions that control the expression of protein-coding genes, but also the discovery of non-coding RNA's, many of which are totally uncharacterised [&lt;a href=&quot;http://www.nature.com/encode/threads/non-coding-rna-characterization&quot; rel=&quot;noreferrer&quot;&gt;4&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The point of this section is to clarify that although only 2% of the genome codes for protein, it is incorrect to say the rest is &quot;junk&quot; or non-functional. The &lt;em&gt;Central Dogma&lt;/em&gt; described above is now an outdated model - certainly some DNA makes RNA makes Protein, but not all; many RNA molecules are functional in their own right.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could argue that proteins and non-coding RNA molecules are the product of &quot;scripts&quot; in the DNA that are run or performed by cells, although you are unlikely to find any genomic scientists talking in these terms.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Epigenetic control&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Where the analogy breaks down is that all* the cells in an organism have the same genome, yet they are vastly different to one another. These differences are due to &lt;em&gt;epigenetic&lt;/em&gt; processes, which are described as non-coding modifications to the DNA that affect expression of transcripts. A basic overview can be found here [&lt;a href=&quot;http://www.whatisepigenetics.com/fundamentals/&quot; rel=&quot;noreferrer&quot;&gt;5&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These modifications come in several forms and include:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;DNA methylation &#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the addition of a methyl-group to cytosine nucleotides that can affect binding of transcription factors etc,&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Histone modifications&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;DNA is actually a 3-dimensional structure, and is wrapped around proteins called histones, which wrap together to form chromatin and the characteristic chromosomal structure.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The availability of DNA to transcription factors is completely dependent on these modifications to the DNA, which are specific to individual cell types and prevent retinal cells, for instance, expressing liver enzymes. (Below figure from [&lt;a href=&quot;http://www.eusem.com/main/CH/epi&quot; rel=&quot;noreferrer&quot;&gt;6&lt;/a&gt;])&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/idOb5.jpg&quot; alt=&quot;http://www.eusem.com/main/CH/epi&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Overview&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;In short, genetics and the DNA sequence can certainly be thought of as the blueprint for an organism - changes to this sequence can profoundly affect phenotype - however it is too simplistic to imagine that the sequence alone provides all the information needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not only are there many non-coding molecules essential for functioning in cells, there is exquisite control over expression by DNA modifications that do &lt;strong&gt;not&lt;/strong&gt; affect the sequence of nucleotides and are essential for cellular differentiation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ENCODE (Encyclopedia of DNA elements) project [&lt;a href=&quot;http://www.genome.gov/encode/&quot; rel=&quot;noreferrer&quot;&gt;7&lt;/a&gt;] is making headway into the interpretation of the non-protein-coding elements of the DNA, but there is still a long way to go.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;* not quite all, for instance B-cells have a hypervariable region to enrich antibodies for variation [&lt;a href=&quot;http://www.anaptysbio.com/technology/somatic-hypermutation/&quot; rel=&quot;noreferrer&quot;&gt;8&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/central_dogma.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/central_dogma.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://sandwalk.blogspot.co.uk/2007/01/central-dogma-of-molecular-biology.html&quot; rel=&quot;noreferrer&quot;&gt;http://sandwalk.blogspot.co.uk/2007/01/central-dogma-of-molecular-biology.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;ENCODE Project Consortium, “The ENCODE (ENCyclopedia Of DNA Elements) Project.,” Science, vol. 306, pp. 636–640, 2004. PMID: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15499007&quot; rel=&quot;noreferrer&quot;&gt;15499007&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/encode/threads/non-coding-rna-characterization&quot; rel=&quot;noreferrer&quot;&gt;http://www.nature.com/encode/threads/non-coding-rna-characterization&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.whatisepigenetics.com/fundamentals/&quot; rel=&quot;noreferrer&quot;&gt;http://www.whatisepigenetics.com/fundamentals/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.eusem.com/main/CH/epi&quot; rel=&quot;noreferrer&quot;&gt;http://www.eusem.com/main/CH/epi&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.genome.gov/encode/&quot; rel=&quot;noreferrer&quot;&gt;http://www.genome.gov/encode/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.anaptysbio.com/technology/somatic-hypermutation/&quot; rel=&quot;noreferrer&quot;&gt;http://www.anaptysbio.com/technology/somatic-hypermutation/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastEditorUserId="740" LastEditDate="2015-03-04T13:41:07.140" LastActivityDate="2015-03-04T13:41:07.140" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30135" PostTypeId="1" CreationDate="2015-03-04T13:35:45.327" Score="7" ViewCount="151" Body="&lt;p&gt;&lt;strong&gt;BACKGROUND&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;NK&lt;/strong&gt; model of fitness landscape considers &lt;strong&gt;N&lt;/strong&gt; states which can interact with &lt;strong&gt;K&lt;/strong&gt; other states. For example &lt;strong&gt;N&lt;/strong&gt; is the total number of genes in a haploid genome and &lt;strong&gt;K&lt;/strong&gt; is the number of other genes that each gene may interact with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022519389800190&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article Kaufman says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The fully connected NK model yields a completely random fitness&#xA;  landscape. For &lt;strong&gt;K = N - 1&lt;/strong&gt;, the fitness contribution of each site&#xA;  depends on all of the other sites in the sequence and therefore&#xA;  altering any site from one to the other value, 0-1, alters the fitness&#xA;  contribution of each site to a new random value. Thus the fitness of&#xA;  any 1-mutant neighboring sequence is completely random with respect to&#xA;  the initial sequence. The landscape is fully random. As was shown in&#xA;  Kauffman &amp;amp; Levin (1987), Weinberger (1988), and Macken &amp;amp; Pereison&#xA;  (1989), such random landscapes have very many local optima, on&#xA;  average, &lt;strong&gt;2&lt;sup&gt;N&lt;/sup&gt;/(N +1)&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I did not read the references mentioned in the text but I read the related section in Kaufman's book: &lt;em&gt;Origins of Order: Self-Organization and Selection in Evolution&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the book he says that the fitness of a genotype can be ordered and given ranks; the probability that a genotype is fitter than its neighbours (local optima) is same as its probability of ranking higher than its &lt;strong&gt;N&lt;/strong&gt; neighbours. So this probability:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$P_m=\frac{1}{N+1}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and if each gene can have only two states lets say &lt;em&gt;on&lt;/em&gt; or &lt;em&gt;off&lt;/em&gt; then the expected number of optima with respect to one-mutants (i.e. the difference between a gene and its neighbour is just one mutation) would be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$M_1=\frac{2^N}{N+1}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I don't understand is the role of &lt;strong&gt;K&lt;/strong&gt; in this expression. This reason should be valid for any number of &lt;strong&gt;K&lt;/strong&gt; (See the quote above). Even in the book this explanation is given in the case where &lt;strong&gt;K&lt;/strong&gt; is maximum i.e. &lt;strong&gt;N-1&lt;/strong&gt;. I can understand that &lt;strong&gt;K&lt;/strong&gt; can affect the ruggedness of the landscape but can anyone explain how &lt;strong&gt;K&lt;/strong&gt; affects the number of optima? (&lt;em&gt;or are they just two separate statements written together, which is confusing me&lt;/em&gt;)&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-05T07:46:21.233" LastActivityDate="2016-01-15T07:01:46.410" Title="How does the value of K determine number of local optima in NK model?" Tags="&lt;evolution&gt;&lt;theoretical-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30136" PostTypeId="2" ParentId="30112" CreationDate="2015-03-04T14:46:29.717" Score="8" Body="&lt;p&gt;There is a specific term for this called hemizygous / hemizygote - meaning that only one allele of the gene is present. Therefore males cannot be heterozygous for genes on the X or Y chromosome (not counting for gene duplication or other chromosome disorders) since they naturally carry only one copy of these chromosomes.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="1590" LastEditDate="2015-12-31T08:46:08.260" LastActivityDate="2015-12-31T08:46:08.260" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30137" PostTypeId="2" ParentId="30101" CreationDate="2015-03-04T16:29:06.653" Score="6" Body="&lt;p&gt;This is a fascinating case of sensory adaptation and neural adaptation. Another example of this would be when you stop smelling something after being exposed to it for long periods of time (as you probably know, this &quot;long period of time&quot; happens to only be a few minutes). A great representation of this happening with the nerves in the skin was done by Georg Meissner:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/5kK8l.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This image is from &lt;a href=&quot;https://www.boundless.com/psychology/textbooks/boundless-psychology-textbook/sensation-and-perception-5/sensation-37/sensory-adaptation-160-12695/&quot; rel=&quot;noreferrer&quot;&gt;https://www.boundless.com/psychology/textbooks/boundless-psychology-textbook/sensation-and-perception-5/sensation-37/sensory-adaptation-160-12695/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When stimulus is applied, these nerves begin rapidly sending messages to the brain in the alarm period. The rate of these signals slowly start to decrease over time in the resistance period until they finally reach exhaustion and stop completely in, of course, the exhaustion period. Keep in mind that the time it takes for all this to happen varies greatly upon what type of cell it is (obviously olfactory cells have a much shorter exhaustion time than, say, hair cells (hearing cells)). After these cells have had a chance to recover (more like recalibrate actually), we can begin to hear/smell/feel/taste again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-03-04T16:29:06.653" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30138" PostTypeId="1" CreationDate="2015-03-04T16:49:40.793" Score="2" ViewCount="61" Body="&lt;p&gt;I would like to insert a 6 kbp construct, which I have on a plasmid into the genome of S. cerevisiae. This plasmid was originally constructed to integrate at the HIS locus via homologous recombination after transformation with the plasmid. The problem is that the strain I would like to use is HIS-Δ0, so the complete HIS-ORF has been deleted so that the plasmid will not insert via homologous recombination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is now whether I can still insert my construct into the genome via PCR based homologous recombination, by amplifying the region of interest on the plasmid with primers which have a homology to the genomic sequence where I would like to insert my construct. I am afraid that 6 kbp are too much to transform yeast cells efficiently. Does anyone have experience with such long inserts?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks for your help,&#xA;Jannis&lt;/p&gt;&#xA;" OwnerUserId="14756" LastActivityDate="2015-03-04T16:49:40.793" Title="What is the maximal insert length for PCR based homologous recombination in S. cerevisae" Tags="&lt;pcr&gt;&lt;yeast&gt;&lt;transformation&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30139" PostTypeId="1" CreationDate="2015-03-04T16:56:41.887" Score="3" ViewCount="75" Body="&lt;p&gt;The cloned sheep, Dolly, was said to have died very soon because the cells used to create it were taken from an adult sheep with an aged telomere. Why doesn't this happen with humans? Why aren't we born with 25 years less lifespan?&lt;/p&gt;&#xA;" OwnerUserId="14757" LastEditorUserId="1306" LastEditDate="2015-03-04T16:59:34.890" LastActivityDate="2015-03-04T17:27:22.397" Title="Telomere and its effect on aging" Tags="&lt;molecular-genetics&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30141" PostTypeId="2" ParentId="30139" CreationDate="2015-03-04T17:15:47.377" Score="4" Body="&lt;p&gt;Broadly speaking there are two classes of cell in an organism:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Somatic cells&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;These are by far the most numerous in your body, and are the differentiated cells including everything from retinal cells to liver cells to neurons.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Stem cells and germ cells&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Stem cells reside in tissues and replenish the somatic cells as they are damaged or removed, or as the organ grows,&lt;/li&gt;&#xA;&lt;li&gt;Germ cells - in particular oocytes in women's ovaries - are pools of immature eggs that are generated when a women is still a foetus in her own mothers womb!&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The difference between these two types that relates to your question is that somatic cells have a limited replicative lifespan - a limit to the number of times they can divide - because their telomeres (caps to the ends of chromosomes) erode during cell division, whereas stem cells are able express the enzyme &lt;strong&gt;telomerase&lt;/strong&gt; which extends the telomeres and allows cells limitless replicative potential (excluding other factors). Replenishing telomeres is a major step in cancer progression [&lt;a href=&quot;http://hmg.oxfordjournals.org/content/10/7/677.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Embryonic cells have 'complete' telomeres when they are fertilised and begin to proliferate into a new organism. Interestingly the telomere length of the germ cells is not at all related to fertility [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23519357&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;], suggesting to me that telomerase is expressed for a while post-fertilisation, so the length prior to fertilisation is not important.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dolly was produced by a process called Somatic Cell Nuclear Transferase, where the nucleus from a somatic cell from an adult organism is transplated into an embryo with its nucleus removed [&lt;a href=&quot;http://learn.genetics.utah.edu/content/cloning/whatiscloning/&quot; rel=&quot;nofollow noreferrer&quot;&gt;3&lt;/a&gt;]. A study found that she had consistently shorter telomeres corresponding to the fact that the original donor was 6-years old already [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16218837&quot; rel=&quot;nofollow noreferrer&quot;&gt;4&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;You might also be interested in my answers to these questions&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/2879&quot;&gt;Are human bodies programmed to die?&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/2984/&quot;&gt;Cell proliferation limit and senescence of embryonic stem cells and fibroblasts&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/2055&quot;&gt;Do trees age on a microscopic level?&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/5589&quot;&gt;Difference In Telomeres Between A Thale Cress Plant And A Methuselah Tree&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Shay, 2001, &lt;em&gt;Human Molecular Genetics&lt;/em&gt;. &lt;strong&gt;Telomerase and cancer&lt;/strong&gt;. &lt;a href=&quot;http://hmg.oxfordjournals.org/content/10/7/677.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://hmg.oxfordjournals.org/content/10/7/677.full&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Turner, 2013, &lt;em&gt;Mol Hum reprod&lt;/em&gt;. &lt;strong&gt;Telomere lengths in human pronuclei, oocytes and spermatozoa&lt;/strong&gt;. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23519357&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/23519357&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://learn.genetics.utah.edu/content/cloning/whatiscloning/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://learn.genetics.utah.edu/content/cloning/whatiscloning/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Shiels, 1999. &lt;em&gt;Cloning&lt;/em&gt;. &lt;strong&gt;Analysis of telomere length in Dolly, a sheep derived by nuclear transfer&lt;/strong&gt;. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16218837&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/16218837&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-03-04T17:27:22.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30142" PostTypeId="1" AcceptedAnswerId="30150" CreationDate="2015-03-04T17:46:58.027" Score="6" ViewCount="16232" Body="&lt;p&gt;I'm an undergraduate student at computer science and currently, I'm interested in bioinformatics. Today, I've started to read a paper about clustering and classification of non-coding RNAs &lt;a href=&quot;http://bioinformatics.oxfordjournals.org/content/30/12/i274.long&quot;&gt;can be found here&lt;/a&gt; and I've seen a word &lt;strong&gt;&lt;em&gt;RNA-seq read&lt;/em&gt;&lt;/strong&gt;. Altough I searched a lot to learn about, I can not find the definition of it, the thingsI found was about performance issues of techniques rather than explanation of the word. So, is there anyone who can simply explain me what is the meaning of this word as well as RNA-seq technique? &lt;/p&gt;&#xA;" OwnerUserId="14759" LastActivityDate="2015-03-04T20:35:00.170" Title="meaning of the &quot;reads&quot; keyword in terms of RNA-seq or next generation sequencing" Tags="&lt;bioinformatics&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30143" PostTypeId="1" AcceptedAnswerId="30144" CreationDate="2015-03-04T18:01:11.360" Score="4" ViewCount="66" Body="&lt;p&gt;&lt;a href=&quot;https://worldbuilding.stackexchange.com/questions/11277/how-could-i-scientifically-explain-ice-breath&quot;&gt;This question&lt;/a&gt; got me wondering about the pressure inside a &lt;a href=&quot;http://en.wikipedia.org/wiki/Bombardier_beetle&quot; rel=&quot;nofollow noreferrer&quot;&gt;bombardier beetle&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lots of articles mention &lt;a href=&quot;http://creation.com/preliminary-observations-of-the-pygidial-gland-of-the-bombardier-beetle-brachinus-sp&quot; rel=&quot;nofollow noreferrer&quot;&gt;pressure&lt;/a&gt;, but don't specify the amount of it:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One study records the velocity of the spray to be within a range of 325 to a stunning 1950 cm/s.&#xA;  [...]&#xA;  Once the muscles around the reservoir squeeze the first amount of&#xA;  reactants through the valve into the reaction chamber, the resulting&#xA;  explosion causes the pressure to rise rapidly in the reaction chamber,&#xA;  forcing shut the one-way valve. The products of the reaction then exit&#xA;  the chamber with a pop and a puff, and the pressure inside the&#xA;  reaction chamber lowers again, falling below the pressure of the&#xA;  collection reservoir, which is still being squeezed by the reservoir&#xA;  muscles.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Calculating from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Spray_characteristics&quot; rel=&quot;nofollow noreferrer&quot;&gt;spray characteristics&lt;/a&gt; is beyond me.&lt;/p&gt;&#xA;" OwnerUserId="6001" LastEditorUserId="-1" LastEditDate="2017-04-13T12:52:23.867" LastActivityDate="2015-03-04T18:01:11.360" Title="What's the maximum pressure inside a bombardier beetle?" Tags="&lt;entomology&gt;&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30144" PostTypeId="2" ParentId="30143" CreationDate="2015-03-04T18:01:11.360" Score="4" Body="&lt;p&gt;According to &lt;a href=&quot;http://europepmc.org/articles/PMC3565695&quot; rel=&quot;nofollow noreferrer&quot;&gt;this study&lt;/a&gt;, model data shows a maximum pressure of &lt;strong&gt;110 kPa&lt;/strong&gt;, that's 16 psi and only 1.086 atm:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kLiM3.jpg&quot; alt=&quot;Model data shows a maximum pressure of 110 kPa&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The three-phase process involved in the beetles explosive secretory&#xA;  discharge (ESD) process. The inlet size is shown as a proportion of&#xA;  the inlet radius. During the first phase of refill and heating (blue),&#xA;  only the inlet valve is open. During the second phase (red), the&#xA;  chamber is closed. Finally, the third phase (marked by an arrow) is&#xA;  the exhaust phase, when only the outlet valve is open. This phase is&#xA;  significantly shorter than the first two phases. This cycle then&#xA;  repeats with phase 1 starting at approximately 5.1 and again at 7.8&#xA;  ms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6001" LastActivityDate="2015-03-04T18:01:11.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30145" PostTypeId="1" AcceptedAnswerId="30146" CreationDate="2015-03-04T18:15:16.557" Score="5" ViewCount="16004" Body="&lt;p&gt;Almost all of the papers about bioinformatics, I faced with the high-throughput word, but I could not find any explanation about it (I think it is so easy to understand and that's why anyone explains it but I could not do it ) . Is there anyone who can explain me what do they mean by high-throughput ? Thanks in advance. &lt;/p&gt;&#xA;" OwnerUserId="14759" LastEditorUserId="16460" LastEditDate="2017-04-03T14:17:02.920" LastActivityDate="2017-04-23T15:59:05.777" Title="Explanation of the meaning of high-throughput" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30146" PostTypeId="2" ParentId="30145" CreationDate="2015-03-04T18:26:49.380" Score="5" Body="&lt;p&gt;High-throughput sequencing specifically refers to sequencing techniques like Illumina that allow you to sequence massive amounts of DNA at once (hundreds of thousands of strands), as opposed to older techniques such as cloning the cDNA in plasmids, followed by sequencing.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastEditorUserId="3340" LastEditDate="2015-03-05T14:29:41.510" LastActivityDate="2015-03-05T14:29:41.510" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30149" PostTypeId="2" ParentId="30145" CreationDate="2015-03-04T20:15:20.467" Score="5" Body="&lt;p&gt;High-throughput, as indicated by canadianer in their comments refers to amount of data that is processed by the system. Though the answer by CactusWoman would be correct for the case of DNA sequencing, high-throughput is not really confined to that domain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any high-throughput technique tries to measure several variables simultaneously. The examples include, other than the Next Gen DNA sequencing, RNA sequencing, protein identification and quantification by mass spectrometry (LC-MS), lipid profiling by GC-MS etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also medium-throughput techniques that can measure several variables but much less than high-throughput techniques. Many low-throughput techniques can be converted to medium-throughput by some level of automation and experimental planning. Example would include real-time PCR.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-04T20:40:26.950" LastActivityDate="2015-03-04T20:40:26.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30150" PostTypeId="2" ParentId="30142" CreationDate="2015-03-04T20:35:00.170" Score="6" Body="&lt;p&gt;In RNA sequencing, the RNA is fragmented, DNA is synthesized complementary to the RNA fragments, which is  followed by a complementary strand synthesis. Fragmentation can be done after the cDNA synthesis too.&#xA;This DNA is then amplified to form a cluster that is sequenced. Most Next-Gen sequencing approaches sequence a short segment of the DNA (it has improved with experimental and technical optimization).&lt;/p&gt;&#xA;&lt;p&gt;A read refers to the sequence of a cluster that is obtained after the end of the sequencing process which is ultimately the sequence of a section of a unique fragment. If an RNA is expressed in high copies then there will be more reads coming from it; reads can be redundant as well.&#xA;&lt;br&gt; &lt;br&gt;&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zdRql.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://home.cc.umanitoba.ca/%7Ezhangx39/PLNT7690/presentation/presentation.html&quot; rel=&quot;noreferrer&quot;&gt;Courtesy&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-04T20:35:00.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30151" PostTypeId="1" CreationDate="2015-03-04T21:46:16.513" Score="0" ViewCount="338" Body="&lt;p&gt;I am reading an article about Genetic Polymorphism and there are lines in the article about genetic polymophism that I don't quite understand like.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/110/8/2893.full&quot; rel=&quot;nofollow&quot;&gt;In this area, there are six different chemotypes that are the expression of a genetically controlled polymorphism in T.vulgaris(24).&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Can someone explain genetic polymorphism and morphic distribution in layman terms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="8279" LastEditorUserId="16651" LastEditDate="2015-09-19T05:56:21.363" LastActivityDate="2015-09-19T05:56:21.363" Title="Layman definition of genetic polymorphism?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30153" PostTypeId="2" ParentId="7245" CreationDate="2015-03-05T01:28:39.927" Score="1" Body="&lt;p&gt;My society finch love to eat moist grass particularly orchard grass. Nibbling the whole strand they have chosen back and forth until they are satisfied with the texture and then proceeds to swallow it. They brake most grass into no bigger than an inch in length. I buy the orchard grass from most pet stores. problem with that is the grass has been dried. not very suitable for eating but Fantastic Four nesting. I grab a handful of dry grass and mist it with water then place it in a plastic sandwich bag, put it in the microwave for 30 seconds.&#xA;Do not completely seal the bag. &#xA;When i place it in the enclosure its like bird ice cream. fantastic treat!&lt;/p&gt;&#xA;" OwnerUserId="14769" LastActivityDate="2015-03-05T01:28:39.927" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30154" PostTypeId="1" AcceptedAnswerId="30156" CreationDate="2015-03-05T02:36:41.093" Score="4" ViewCount="6979" Body="&lt;p&gt;A young animal has never had much energy. He is brought to a veterinarian for help and is sent to the animal hospital for some tests. There they discover his mitochondria can use only fatty acids and amino acids for respiration, and his cells produce more lactate than normal. Of the following, which is the best explanation of his condition?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A) His mitochondria lack the transport protein that moves pyruvate across the outer mitochondrial membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B) His cells cannot move NADH from glycolysis into the mitochondria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C) His cells contain something that inhibits oxygen use in his mitochondria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D) His cells lack the enzyme in glycolysis that forms pyruvate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E) His cells have a defective electron transport chain, so glucose goes to lactate instead of to acetyl CoA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Answer:  A&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A) So, from this assumption, pyruvate would build up in the cytosol of cell. However, I do not see why lactate would be formed. Lactate forms when there is a lack of NAD+. In this case, there is no problem with NAD+. All NADH will be recycled into NAD+ by the Electron Transport Chain in the mitochondria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B) I do not know what will happen in this case. Too many contradicting factors. Can anyone explain?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C) This is clearly not correct. If there were no O2,then there would only be lactic acid fermentation; the protein and fatty acids would not be used.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D) If lactate is formed, pyruvate must have been formed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E) The electron transport chain needs to work. See C). Same explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I am debating between A and B. Can anyone explain why the textbook says A?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT :&lt;/strong&gt;&#xA;&lt;strong&gt;If anyone could give me a step-by-step approach to solving this problem, I would really appreciate it. This is supposed to be a challenge problem not representative of test questions, but I still want to fully get it.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="8516" LastEditorUserId="22057" LastEditDate="2017-04-13T16:21:40.193" LastActivityDate="2017-04-13T16:21:40.193" Title="Cellular Respiration/Fermentation Problem Leading to Lack of Energy" Tags="&lt;biochemistry&gt;&lt;homework&gt;&lt;cellular-respiration&gt;&lt;fermentation&gt;&lt;energy-metabolism&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30155" PostTypeId="1" AcceptedAnswerId="30171" CreationDate="2015-03-05T02:50:28.790" Score="5" ViewCount="172" Body="&lt;p&gt;For example, mutation in MHS2, which encodes a protein involved in the repair of mismatches that occur during DNA replication, dramatically increases the risk of developing colon cancer.&#xA;(There are many other examples, like the RB gene which encodes a tumor supressor protein and is correlated to retinoblastoma, thus its name)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: how a gene like MHS2 which participates in a general mechanism of DNA repair increases the risk of a specific type of cancer? Why doesn't it increase the risk of developing cancer in other tissues as well?&lt;/p&gt;&#xA;" OwnerUserId="14630" LastEditorUserId="14630" LastEditDate="2015-03-05T03:01:22.367" LastActivityDate="2016-03-25T08:39:28.660" Title="Why mutations in genes involved in general processes like DNA repair increase the risk of developing specific types of cancer?" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;cancer&gt;&lt;mutations&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30156" PostTypeId="2" ParentId="30154" CreationDate="2015-03-05T02:55:14.927" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;(A) is a possible answer and is indeed cause for fatigue, as pyruvate is needed for the Krebs cycle to run. The krebs cycle is an essential step in the generation of ATP in aerobic organisms. (B) is incorrect because NADH is never transported into the mitochondria in any organism (it is a nonsense answer). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;NADH is not transported into mitochondria. Instead, its electrons are transported into mitochondria, and I quote from &lt;a href=&quot;https://i.stack.imgur.com/A4uwf.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Berg et al. (2002)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;NADH cannot simply pass into mitochondria for oxidation by the respiratory chain, because the inner mitochondrial membrane is impermeable to NADH and NAD+. The solution is that electrons from NADH, rather than NADH itself, are carried across the mitochondrial membrane. One of several means of introducing electrons from NADH into the electron transport chain is the glycerol 3-phosphate shuttle (Figure 18.37).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/A4uwf.jpg&quot; alt=&quot;e- shuttle&quot;&gt;  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Electrons from NADH can enter the mitochondrial electron transport chain by being used to reduce dihydroxyacetone phosphate to glycerol 3-phosphate. Glycerol 3-phosphate is reoxidized by electron transfer to an FAD prosthetic group in a membrane-bound glycerol 3-phosphate dehydrogenase. Subsequent electron transfer to Q to form QH2 allows these electrons to enter the electron-transport chain.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hence, (B) is incorrect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;: Now why would lactate be formed in (A)? Pyruvate builds up in the cell, as it cannot be transported into the mitochondria. Since lactate dehydrogenase has pyruvate as a substrate, the equilibrium of this reaction will be pushed to the right and lactate will be formed:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QEnu5.png&quot; alt=&quot;LDH&quot;&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Lactate_dehydrogenase&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;sup&gt;Source: wikipedia page on lactate dehydrogenase&lt;/sup&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lack of glucose oxidation takes away the main power supply of aerobic organisms, causing fatigue. Lactate buildup may also induce fatigue.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK22470/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Berg et al. Biochemistry 2002, Freeman, New York&lt;/a&gt;  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-05T13:44:10.903" LastActivityDate="2015-03-05T13:44:10.903" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30157" PostTypeId="1" CreationDate="2015-03-05T03:35:42.630" Score="1" ViewCount="158" Body="&lt;p&gt;I'm fascinated by evolutionary theory and the predictive aspect of it-the notion of an animal entering a strongly divergent state of evolution whereby it is evolving into a new form yet remains suboptimal, and is therefore undergoing rapid morphological change, and the idea that this allows us to project onto possible new variants of life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To give a past example, the praying mantis is believed to have split from the cockroach around 250M years ago. During this period the mantis developed its upright stance, large range of vision and pronounced raptorial claws, and has seemingly stabilised into this optimal new form over the past 50M+ years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The interesting thing is that this change could actually have been predicted by analysis of the animals evolutionary history, niche and further available advantageous adaptive forms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone give a good example of a current animal in this volatile state that we could make accurate projections for?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And please, no trivial answers like &quot;everything is constantly in a state of evolution&quot;, I already know that and thats not I'm referring to.&lt;/p&gt;&#xA;" OwnerUserId="14770" LastActivityDate="2015-03-05T20:58:26.577" Title="Examples of extant animals in a submature morphologically unstable evolutionary state?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30158" PostTypeId="1" CreationDate="2015-03-05T04:07:02.153" Score="0" ViewCount="27" Body="&lt;p&gt;I need to achieve stable transfection of a pCI-Neo plasmid into the genome of a mouse embryo. The most common way to achieve stable transfection is through positive selection, however positive selection would not work with embryos. How can I ensure stable transfection of this plasmid in a mouse embryo without damaging the embryo? Would this plasmid integrate itself when the cell divided? I plan to use effectene as the transfection agent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="13496" LastEditDate="2015-03-05T04:15:50.287" LastActivityDate="2015-03-05T04:15:50.287" Title="Stable transfection" Tags="&lt;molecular-genetics&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30159" PostTypeId="1" CreationDate="2015-03-05T05:20:51.650" Score="1" ViewCount="67" Body="&lt;p&gt;By mutator phenotype, I mean being more prone to mutations, for example due to mutations in genes involved in DNA repair.&#xA;I was thinking about exposing the cells to agents that damage DNA (uv light, for example). Compared to normal cells, mutators would be less likely to survive, because they lack the ability to repair damages in the genetic material. To a certain extent, that's the principle of radiotherapy (cancer cells are more suscetible towards radiation).&#xA;Are there other options? Moreover, is it possible to select the mutators (instead of killing them)?&lt;/p&gt;&#xA;" OwnerUserId="14630" LastEditorUserId="14630" LastEditDate="2015-03-05T11:53:13.113" LastActivityDate="2015-03-05T11:53:13.113" Title="What sort of assay could be used to identify mutants with mutator phenotype?" Tags="&lt;molecular-biology&gt;&lt;cancer&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-03-09T12:54:23.280" ContentLicense="CC BY-SA 3.0" />
  <row Id="30160" PostTypeId="2" ParentId="30155" CreationDate="2015-03-05T05:41:58.383" Score="2" Body="&lt;p&gt;You should have a look at &lt;a href=&quot;http://www.sciencemag.org/content/347/6217/78.abstract&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; interesting article published earlier this year in Science. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two mechanisms by which cells can accumulate mutations in DNA:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Replication errors&lt;/li&gt;&#xA;&lt;li&gt;External physicochemical agents such as UV, carcinogens etc&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In the abovementioned paper, the authors classify cancers into two types:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;That arise predominantly because of environmental agents (D-type)&lt;/li&gt;&#xA;&lt;li&gt;That arise predominantly because of replicative errors (R-type)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Moreover in the same article, the authors point out that the lifetime risk of a cancer is positively correlated with the number of stem cell divisions in the associated tissue. FAP colorectal carcinoma features highest with respect to, number of stem cell divisions and consequently lifetime risk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since these cells divide more, they are likely to accumulate more mutations and a defective DNA repair process will worsen the situation. I cannot find a great amount of study on MHS2 gene and its connection with different types of cancers but in general, the above explanation would be applicable to most genes that are involved in DNA repair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;&lt;em&gt;NOTE: As mentioned in the other answer, the abovementioned paper has received some &lt;a href=&quot;https://www.theguardian.com/science/grrlscientist/2015/jan/02/bad-luck-bad-journalism-and-cancer-rates&quot; rel=&quot;nofollow&quot;&gt;criticism&lt;/a&gt; from the scientific community for making far-fetched claims which apparently fits so beautifully with the theory that it seems quite correct. The article however is not retracted. Therefore, it is important to not completely believe in this hypothesis but at the same time keep it in mind considering it as a possibility that needs further verification.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-03-25T08:39:28.660" LastActivityDate="2016-03-25T08:39:28.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30161" PostTypeId="2" ParentId="30159" CreationDate="2015-03-05T06:08:41.770" Score="1" Body="&lt;p&gt;There are a number of ways to screen for mutator genes. One straightforward approach in bacteria is to take an antibiotic sensitive non-mutator strain, grow it up, and expose to different antibiotics. Cells that survive in the presence of multiple antibiotics have acquired multiple de novo resistance mutations and thus are highly enriched for mutator alleles. Here is one example: &lt;a href=&quot;http://aac.asm.org/content/52/10/3810.full&quot; rel=&quot;nofollow&quot;&gt;Wiegand et al (2008) AAC&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-03-05T06:08:41.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30163" PostTypeId="1" CreationDate="2015-03-05T11:33:36.093" Score="1" ViewCount="1275" Body="&lt;p&gt;I'm using urea-containing growth medium for experiments with bacteria (1-2 l/day). After the experiment, the growth medium has to be sterilized and disposed. I did this so far by autoclaving, but our technician complained about the ammonia smell that develops (urea breaks down when heated, releasing ammonia). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm pretty sure the amount released into the air is not dangerous (I've emptied the autoclave several times), especially if you don't purposefully breathe in the first gust of air that comes out after opening, but I think it's useful to look into alternatives. Also I'm not sure if the autoclave might get damaged on the long run.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have experience with this? Do you see a way to sterilize larger amounts of growth medium reliably without heating?&lt;/p&gt;&#xA;" OwnerUserId="5682" LastActivityDate="2015-03-07T07:51:35.327" Title="How to safely sterilize urea-containing growth medium?" Tags="&lt;lab-techniques&gt;&lt;lab-reagents&gt;&lt;safety&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30166" PostTypeId="1" AcceptedAnswerId="30172" CreationDate="2015-03-05T13:09:18.730" Score="12" ViewCount="1570" Body="&lt;p&gt;Since bacteria can evolve to overcome antibiotic use, why wouldn't they be able to evolve to overcome antibody or cell-mediated immunity?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(One possible explanation: antibiotics have only one target while vaccines elicit antibodies against multiple targets and multiple T-cell epitopes. Even more targets arise when comparing sub-unit vs inactivated vaccines, where the number of targets are extremely higher using inactivated vaccines, containing whole bacterial cell.)&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="13405" LastEditDate="2019-02-23T17:23:22.550" LastActivityDate="2019-02-23T17:23:22.550" Title="Why don't vaccines cause bacterial resistance?" Tags="&lt;bacteriology&gt;&lt;vaccination&gt;&lt;antibiotic-resistance&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="30167" PostTypeId="1" AcceptedAnswerId="30330" CreationDate="2015-03-05T13:48:32.277" Score="10" ViewCount="5696" Body="&lt;p&gt;How long can cholera bacterium survive inside a dead host? Can they remain dormant in such conditions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;BACKGROUND&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a hill not far from where I live, there was a hospital operating since 16th until 19th century, for cholera patients, and a cemetery for those, who didn't make it. It was closed in 1st half of 19th century and until 20th century not even ruins of the hospital remained; the gravestones got lost under a layer of soil.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Currently, the area is being built over. Large amounts of soil are being excavated for foundations and basements of new houses. Rainwater falling on the piles of excavated soil floats down through driveways, backyards and gardens of houses down the hill, including my own.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Should I worry?&lt;/p&gt;&#xA;" OwnerUserId="6512" LastEditorUserId="3340" LastEditDate="2015-03-05T14:54:27.083" LastActivityDate="2017-07-26T03:45:00.220" Title="How long can Cholera bacteria survive in a dead host?" Tags="&lt;bacteriology&gt;&lt;epidemiology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30168" PostTypeId="2" ParentId="30001" CreationDate="2015-03-05T13:51:59.813" Score="2" Body="&lt;p&gt;I think my mistake was to believe that the electric field has to be somewhat perpendicular to the membrane, so that it can directly apply a voltage difference across the membrane, and that the resistance inside and outside the axon was the same, so that a tangential field was useless.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact these are false : depolarization and action potential creation happen where the axon is parallel to the electric field and where the gradient of the tangent field is the bigger.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here you have a complete explanation but I think we can make a simplified one :&#xA;&lt;a href=&quot;http://stbb.nichd.nih.gov/pdf/Nerve_Fiber_Stimulation_Model.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://stbb.nichd.nih.gov/pdf/Nerve_Fiber_Stimulation_Model.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's look at a membrane model (Hodgkin-Huxley) : &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dzyx1.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As we said if we try to apply an electric field $\vec{E}$ along $\vec{y}$ , it should be incredibly strong to produce a trans-membrane potential $V$ strong enough to create an action potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In between the inside an the outside of the membrane you have all the channels and the capacitance of the membrane. but I think the crux of the matter here are the resistances inside and outside : the small surface of a section of axon limits the conductivity, whereas the outside is supposed to be bigger so that its resistance is negligible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a result if you apply a gradient $\frac{dE_{x}}{dx}$ you can create trans-membrane current and potential:&#xA;because of the gradient, the fields $E_{1} = E(x)$ and $E_{2} = E(x+\Delta x)$ are different : $E_{2} = E_{1} + \frac{dE_{x}}{dx}\Delta x$.&#xA;Then using electricity laws : &#xA;$$i_{m} = I_{1} - I_{2}$$&#xA;$$i_{1} = -\frac{ E_{1} \Delta x}{R}$$&#xA;$$i_{2} = -\frac{ E_{2} \Delta x}{R}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;then :&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$i_{m} = \frac{\Delta x}{R} (E_{2}-E_{1}) = \frac{\Delta^{2} x}{R} \frac{dE_{x}}{dx}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This trans-membrane current will produce a potential across the membrane which will be proportional to $\frac{dE_{x}}{dx}$, electromagnetic stimulations shows that TMS can easily produce gradients strong enough to create actions potential.&lt;/p&gt;&#xA;" OwnerUserId="5484" LastEditorUserId="5484" LastEditDate="2015-03-05T13:57:08.093" LastActivityDate="2015-03-05T13:57:08.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30171" PostTypeId="2" ParentId="30155" CreationDate="2015-03-05T16:30:10.733" Score="3" Body="&lt;p&gt;I can't fault @WYSIWYG for mentioning the cited Vogelstein article in providing an answer. You point to what seems like a great explanation for why certain cancers arise in some tissues but not others. However, for those who look closely this paper has some serious errors in its derivation of the model, and for good reason it has come under strong fire in the last couple of months.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this for a really important rebuttal:&#xA;&lt;a href=&quot;http://ameyer.me/science/2015/01/02/vogel.html&quot; rel=&quot;nofollow&quot;&gt;http://ameyer.me/science/2015/01/02/vogel.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, the paper provides an elegantly specious explanation for, in part, the longstanding paradox of why cancers more readily arise in some tissues like the intestines and from seemingly identical mechanisms, but do not seem to arise in other tissues. My favorite example, though @El Cid you do list some good ones, are inactivating BRCA1 mutations which normally play a role in repairing double stranded DNA breaks. And yet even when mutated in the germline this only seems to increase cancer risk in the breast, and really only in one gender (females).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So the answer is still quite certainly that the field does not understand this paradox&lt;/strong&gt;, and the cited Vogelstein paper was a total tragedy of a publication. There have been a number of officially submitted critiques of the paper and the Vogelstein lab has been trying to defend it as best they can. This is however a great example of how big name labs can seem to get anything published in Cell/Nature/Science.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another thing to consider and @El Cid points to a good example, is the pRb mutations (in a very central tumor suppressor pathway for all cells) cause retinoblastoma and not for instance intestinal or blood cancers very readily, and the retina is not a rapidly dividing tissue. So the Vogelstein paper cannot explain this.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastEditorUserId="16299" LastEditDate="2015-12-25T00:23:43.993" LastActivityDate="2015-12-25T00:23:43.993" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="30172" PostTypeId="2" ParentId="30166" CreationDate="2015-03-05T16:35:36.113" Score="14" Body="&lt;p&gt;Unfortunately, we do see examples of bacteria and viruses evolving vaccine resistance. For instance, vaccine resistant strains of &lt;a href=&quot;http://www.sciencedaily.com/releases/2014/11/141104111408.htm&quot;&gt;polio&lt;/a&gt; and &lt;a href=&quot;http://www.cidrap.umn.edu/news-perspective/2013/02/researchers-find-first-us-evidence-vaccine-resistant-pertussis&quot;&gt;pertussis&lt;/a&gt; have recently been identified. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet these seem like the exception rather than the rule. One thing that makes it harder for pathogens to evolve resistance is that vaccines usually generate antibodies to multiple antigens, all of which the pathogen would have to alter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another reason vaccines tend not to drive vaccine resistance is that the diseases for which we vaccinate are typically those that are not antigenically variable. (Haemophilus influenza is a notable exception; there we use a conjugate vaccine). This may have something to do with how we view vaccine efficacy. For example, we don't say that the influenza virus evolves vaccine resistance--yet we need a new vaccination each year due to antigenic shift. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in learning more, Angela McLean has a &lt;a href=&quot;http://bmb.oxfordjournals.org/content/54/3/545.short&quot;&gt;nice article&lt;/a&gt; looking into this question. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-03-05T16:35:36.113" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30173" PostTypeId="1" AcceptedAnswerId="30188" CreationDate="2015-03-05T17:30:05.087" Score="3" ViewCount="767" Body="&lt;p&gt;The options provided are-&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Chronic blood loss&lt;/li&gt;&#xA;&lt;li&gt;Sickle cell anaemia&lt;/li&gt;&#xA;&lt;li&gt;Haemolytic anaemia&lt;/li&gt;&#xA;&lt;li&gt;Thallasaemia&lt;/li&gt;&#xA;&lt;li&gt;Transfusion reactions&#xA;               -&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;*Q-15: pg-785; **Review of Medical Physiology&lt;/strong&gt; - William F. Ganong;    International 22nd Edition***&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here, the answer provided is (4), i.e Thallasaemia...&#xA;My point is that, &lt;a href=&quot;http://en.wikipedia.org/wiki/Thalassemia&quot; rel=&quot;nofollow&quot;&gt;Thallasaemia&lt;/a&gt; is essentially a genetic defect resulting in &lt;strong&gt;mutation&lt;/strong&gt; of &lt;strong&gt;either alpha or beta or both the chains&lt;/strong&gt;, thus rendering the structure of haemoglobin fragile....the disease as far as I know don't cause any reduction in blood volume...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to me option (1) i.e chronic blood loss is more feasible as in case of diseases resulting from nematodes like Hookworm (&lt;a href=&quot;http://en.wikipedia.org/wiki/Ancylostoma_duodenale&quot; rel=&quot;nofollow&quot;&gt;Ancylostoma duodenale&lt;/a&gt;)....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, where am I wrong???&lt;/p&gt;&#xA;" OwnerUserId="10045" LastActivityDate="2015-03-06T02:19:03.353" Title="In which of the following diseases structure of haemoglobin produced is normal but their amount reduced?" Tags="&lt;homework&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30176" PostTypeId="1" AcceptedAnswerId="30561" CreationDate="2015-03-05T18:20:24.683" Score="9" ViewCount="7813" Body="&lt;p&gt;If a scorpion pierces itself, will it die or immune to its poison? If it produces the venom its blood should be immune to itself poison.&lt;/p&gt;&#xA;" OwnerUserId="13243" LastEditorUserId="13243" LastEditDate="2015-03-05T21:28:42.680" LastActivityDate="2019-12-19T14:05:40.463" Title="What will happen if a scorpion pierces itself?" Tags="&lt;zoology&gt;&lt;poison&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30177" PostTypeId="1" CreationDate="2015-03-05T19:13:14.173" Score="0" ViewCount="71" Body="&lt;p&gt;I would like to know whether someone could tell me &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) some of the online programs that will &lt;strong&gt;predict the top microRNAs that bind to 3`UTR of a specific gene (for eg-GAPDH).&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am relatively new to the field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks&lt;/p&gt;&#xA;" OwnerUserId="14786" LastActivityDate="2015-03-05T20:30:47.070" Title="How to predict the top microRNAs that bind to 3`UTR of a specific gene" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2015-03-07T01:24:25.107" ContentLicense="CC BY-SA 3.0" />
  <row Id="30179" PostTypeId="2" ParentId="30177" CreationDate="2015-03-05T20:30:47.070" Score="0" Body="&lt;p&gt;You'll find &lt;a href=&quot;http://www.targetscan.org/&quot; rel=&quot;nofollow&quot;&gt;TargetScan&lt;/a&gt; quite useful. You can pick from a number of species and simply enter a gene name. It will then get the 3' UTR, show its conservation across species (binding sites in a conserved area are more likely to be active), find miRNAs that can bind to the 3'UTR, and then split those up by whether they bind to highly or poorly conserved regions. It also categorizes the hits according to various properties, like proximity to the open reading frame, in case you want to perform any sort of filtering by that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;: BTW, you may want to take the target miRNAs and look at their expression in your tissue of interest. That's a good way to further narrow down their relevance.&lt;/p&gt;&#xA;" OwnerUserId="9523" LastActivityDate="2015-03-05T20:30:47.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30180" PostTypeId="2" ParentId="30157" CreationDate="2015-03-05T20:58:26.577" Score="1" Body="&lt;p&gt;Not sure exactly what you're looking for, but maybe the Giant Panda is of interest to you. The Giant Panda is an herbivore, but it has evolved from a meat-eating animal (the most recent common ancestor of Pandas and the other bears). It made the switch from omnivore to herbivore just ~2 MYA. According to wikipedia, pandas still have the digestive system of a carnivore. They can still eat meat and do not actually get much protein/energy from bamboo. Thus, you could consider them to be in a state of evolving from an omnivore into a more efficient herbivore&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-03-05T20:58:26.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30181" PostTypeId="1" CreationDate="2015-03-05T21:05:18.830" Score="3" ViewCount="237" Body="&lt;p&gt;I excerpt from &lt;a href=&quot;http://www.webmd.com/skin-problems-and-treatments/acne/understanding-acne-treatment?page=2&quot; rel=&quot;nofollow noreferrer&quot;&gt;p 2 of 4&lt;/a&gt;, but &lt;a href=&quot;http://www.webmd.com/skin-problems-and-treatments/acne/understanding-acne-treatment?page=2&quot; rel=&quot;nofollow noreferrer&quot;&gt;p 4 of 4&lt;/a&gt; reviews the entire article by &lt;a href=&quot;http://www.webmd.com/h-debra-jaliman&quot; rel=&quot;nofollow noreferrer&quot;&gt;Debra Jaliman, MD&lt;/a&gt; on Apr 17 2014.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Usually, topical antibiotics aren't recommended alone as an acne treatment, as they can increase the risk for antibiotic resistance in skin bacteria. However, using benzoyl peroxide with a topical antibiotic may reduce the chances of developing antibiotic resistance.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.facingacne.com/acne-antibiotics/&quot; rel=&quot;nofollow noreferrer&quot;&gt;[Source:]&lt;/a&gt; Substances that kill acne bacteria by inflammation, such as benzoyl peroxide, oil of cloves, and chlorhexidine gluconate. Bacteria don’t develop resistance to these treatments, but they don’t kill as many bacteria, either.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;If topical antibiotics can cause antibiotic resistance, why can't compounds like benzyl peroxide? I ask in general about other bactericide, not just benzyl peroxide.&lt;/p&gt;&#xA;" OwnerUserId="4466" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2020-04-05T19:29:59.000" Title="Why can bacteria resist topical antibiotics, but not compounds like Benzoyl Peroxide?" Tags="&lt;antibiotic-resistance&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="30182" PostTypeId="1" AcceptedAnswerId="30186" CreationDate="2015-03-05T21:22:58.330" Score="5" ViewCount="1389" Body="&lt;p&gt;I was reading &lt;a href=&quot;http://www.webmd.com/skin-problems-and-treatments/acne/adult-10/slideshow-adult-acne&quot; rel=&quot;nofollow noreferrer&quot;&gt;this site&lt;/a&gt; which broached &lt;strong&gt;comedones&lt;/strong&gt;, an esoteric word to me; so I thought to look up its etymology which I find exceptionally singular and peculiar (I would have never guessed that the word originated from &lt;em&gt;&lt;code&gt;to eat up&lt;/code&gt;&lt;/em&gt; !) :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.etymonline.com/index.php?allowed_in_frame=0&amp;amp;search=comedo&amp;amp;searchmode=none&quot; rel=&quot;nofollow noreferrer&quot;&gt;Etmyonline&lt;/a&gt;: &quot;blackhead,&quot; etc., 1866, from Latin comedo &quot;glutton,&quot; from comedere &lt;code&gt;&quot;to eat up&quot;&lt;/code&gt; (see &lt;a href=&quot;http://www.etymonline.com/index.php?term=comestible&amp;amp;allowed_in_frame=0&quot; rel=&quot;nofollow noreferrer&quot;&gt;comestible&lt;/a&gt;). &lt;strong&gt;A name formerly given to worms that devour the body&lt;/strong&gt;; transferred in medical use to secretions that resemble them.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Footnote: &lt;a href=&quot;http://www.oxforddictionaries.com/definition/english/comedo?q=comedones&quot; rel=&quot;nofollow noreferrer&quot;&gt;ODO&lt;/a&gt; also offers an etymology. &lt;/p&gt;&#xA;" OwnerUserId="4466" LastEditorUserId="16866" LastEditDate="2017-04-26T19:17:40.383" LastActivityDate="2017-10-18T17:01:59.667" Title="What worms devour the body?" Tags="&lt;entomology&gt;&lt;etymology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30183" PostTypeId="1" AcceptedAnswerId="30184" CreationDate="2015-03-05T22:49:58.267" Score="1" ViewCount="6417" Body="&lt;p&gt;Are the irises an exact match in a human's set of eyes? Assuming the eyes are healthy with 20/20 vision.&lt;/p&gt;&#xA;" OwnerUserId="11855" LastActivityDate="2015-03-06T01:58:59.860" Title="Are the irises an exact match in a human's set of eyes?" Tags="&lt;eyes&gt;&lt;human-eye&gt;&lt;iris&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30184" PostTypeId="2" ParentId="30183" CreationDate="2015-03-05T23:27:42.923" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;&lt;em&gt;No&lt;/em&gt;&lt;/strong&gt;. Not two irises are alike, including the irises of identical twins and even the two irises of one and the same person. This uniqueness of the human iris is used in &lt;a href=&quot;http://www.explainthatstuff.com/how-iris-scans-work.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;iris scans&lt;/a&gt;. The variety of the iris is caused by its complex structure and coloring pattern. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/k5ZVA.jpg&quot; alt=&quot;iris&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: &lt;a href=&quot;http://fingerchip.pagesperso-orange.fr/biometrics/types/iris.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Jean-François Mainguet&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt; &#xA;The iris is explained on &lt;a href=&quot;http://blog.m2sys.com/biometric-hardware/iris-recognition-vs-retina-scanning-what-are-the-differences/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Biometric Technology's&lt;/a&gt; website, and I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The iris [...] is a thin, circular structure in the eye, responsible for controlling the diameter [...] of the pupil [...]. “Eye color” is the color of the iris, which can be green, blue, or brown. In some cases it can be hazel (a combination of light brown, green and gold), grey, violet, or even pink. In response to the amount of light entering the eye, muscles attached to the iris expand or contract the aperture at the center of the iris, known as the pupil.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A striking example of the dissimilarity of the iris in one person are people with &lt;em&gt;heterochromia&lt;/em&gt;. Heterochromia can result in both eyes having a different color. Examples are given in the figure below: On the left is Demi Moore (if you look closely her right eye is hazel, while her left eye is green). On the right-hand side a more striking example is shown (taken from the &lt;a href=&quot;http://en.kllproject.lv/the-unique-phenomenonheterochromia.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kliproject&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1l4Bu.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/soSQq.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Heterochromia iridium&lt;/em&gt; (differing iris colors) and &lt;em&gt;heterochromia iridis&lt;/em&gt; (a variety of color within a single iris) are relatively rare in humans and result from increased or decreased pigmentation of the iris. Most cases are the result of an alteration in the expression of the &lt;strong&gt;EYCL3&lt;/strong&gt; gene (which codes for brown/blue eye color) and &lt;strong&gt;EYCL1&lt;/strong&gt; (which codes for green/blue eye color), among other genes within the cells of the entire iris or even a particular section. Other potential causes include trauma around the time of birth or later in life, congenital pigmented nevi or even medications such as those used in the treatment of glaucoma. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fun fact&lt;/strong&gt;&lt;br&gt;&#xA;David Bowie's eyes are in fact of the same color - his pupils are of a different size:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/TXHsk.jpg&quot; alt=&quot;Bowie&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;em&gt;Scientific American&lt;/em&gt; (&lt;a href=&quot;http://www.scientificamerican.com/article/how-does-someone-get-two/&quot; rel=&quot;nofollow noreferrer&quot;&gt;November issue, 2001&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-06T01:58:59.860" LastActivityDate="2015-03-06T01:58:59.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30186" PostTypeId="2" ParentId="30182" CreationDate="2015-03-06T01:26:46.017" Score="4" Body="&lt;p&gt;A maggot typically feeds on carrion. A maggot is the larva of a fly and usually  particular to the larvae of &lt;em&gt;Brachyceran&lt;/em&gt; flies, such as houseflies, cheese flies, and blowflies.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/KznV6.jpg&quot; alt=&quot;maggot&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly decomposition from maggots has a lot of use in forensic science as the presence or development of maggots on a corpse can be useful to a forensic entomologists to determine the approximate time of death. Depending on the species and the conditions, maggots may be observed on a body within 24 hours. The eggs are laid on the body and when the eggs hatch, the maggots move towards their preferred conditions and begin to feed. Insects are usually useful  25–80 hours post mortem and is contingent on temp humidity and oxygen availability. After 80 hours, this method becomes less reliable.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="10456" LastEditDate="2015-03-06T20:19:36.587" LastActivityDate="2015-03-06T20:19:36.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30188" PostTypeId="2" ParentId="30173" CreationDate="2015-03-06T02:19:03.353" Score="4" Body="&lt;p&gt;You are correct, Thalassemia is the wrong answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Thalassemia and Sickle Cell Anemia, the structure of Hemoglobin is altered.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Chronic Blood Loss: Here the hemoglobin and packed cell values will be low, however there is no alteration in structure of either RBC or Hemoglobin&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Hemolytic Anemia: This is a host of conditions which can cause hemolytic anemia. Some mechanisms where Hemoglobin structure remain normal would be:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The structure of RBC membrane is altered, this will make RBCs less maleable and cause early destruction - Example: &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Spherocytosis&quot; rel=&quot;nofollow&quot;&gt;Spherocytosis&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.g6pd.org/g6pddeficiency.aspx&quot; rel=&quot;nofollow&quot;&gt;G6PD Deficieny&lt;/a&gt; - In this the deficiency of G6PD will decrease the ability of Red Blood Cells to handle oxidative stress and when subjected to sudden oxidative stress, hemolysis will occur. Here the structure of both RBC membrane and Hemoglobin are normal.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Transfusion reaction (I am talking about only hemolytic transfusion reaction, there are other &lt;a href=&quot;http://emedicine.medscape.com/article/206885-overview&quot; rel=&quot;nofollow&quot;&gt;transfusion reactions&lt;/a&gt; too): Here the problem is the host reaction to transfused Red Cells. The host was initially severly anemic (Therefore low Hb) for which transfusion was done, now the host immunity is reacting against transfused RBCs which have normal Hemoglobin, resulting in reduced RBC counts and Hemoglobin. So this too can be taken as a correct answer as the end-result will be severe normochromic normocytic anemia.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-03-06T02:19:03.353" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30189" PostTypeId="1" AcceptedAnswerId="30190" CreationDate="2015-03-06T02:35:02.047" Score="2" ViewCount="116" Body="&lt;p&gt;The research journals Ive published in require significant financial cost to publish. On top of that many require a membership to the society the journal is associated with, in addition to publication fees. I was wondering if anyone is familiar with any journals (reputable hopefully) that do not require fees like this to publish a research article?&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2015-03-06T02:42:30.203" Title="Are any biology research journals free to publish in?" Tags="&lt;research-process&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2015-03-07T08:18:40.880" ContentLicense="CC BY-SA 3.0" />
  <row Id="30190" PostTypeId="2" ParentId="30189" CreationDate="2015-03-06T02:42:30.203" Score="5" Body="&lt;p&gt;Many biology journals are free to publish in. As a rule of thumb:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Most journals from for-profit publishers such as Elsevier, Wiley, etc. charge nothing to the author (but of course bill the libraries handsomely).&lt;/li&gt;&#xA;&lt;li&gt;Many but by no means all society journals charge page charges even if they are not open access.&lt;/li&gt;&#xA;&lt;li&gt;Most but not all open access journals charge substantial publication fees. You could try &lt;a href=&quot;http://www.eigenfactor.org/openaccess/&quot;&gt;this website&lt;/a&gt; to search for open access journals that do not charge publication fees.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-03-06T02:42:30.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30191" PostTypeId="1" AcceptedAnswerId="30202" CreationDate="2015-03-06T02:50:04.423" Score="12" ViewCount="403" Body="&lt;p&gt;I'm coming across some conflicting information regarding the correlation between cancer incidents and trisomy 21. I read a report from nature that discusses how Downs are only a tenth as likely to develop cancers, but at the same time are 20x more likely to develop certain B cell malignancies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the more prominent findings show that a regulator of angiogenesis, &lt;em&gt;DSRC1&lt;/em&gt; plays a significant role.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm trying to find out is what gene(s) on 21 contribute to the associated risk for lymphoma?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And does there exist a good list of those genes on 21 that suppress or enhance tumor genesis.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="14709" LastEditDate="2015-03-07T19:31:54.250" LastActivityDate="2015-03-07T19:31:54.250" Title="Why do people with Down syndrome get fewer cancers?" Tags="&lt;genetics&gt;&lt;pathology&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30193" PostTypeId="1" AcceptedAnswerId="30395" CreationDate="2015-03-06T04:41:24.803" Score="3" ViewCount="2499" Body="&lt;p&gt;Assuming 100% of the pollen gets delivered to exactly the locations it needs to pollinate a female flower, how much pollen is needed to pollinate a flower? If it's more than one unit of pollen, what, if anything, prevents more than one plant's pollen from pollinating the flower?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we need an example plant to answer this question, let's assume zucchini. For instance, if you plant a zucchini in the middle of a spaghetti squash and an orange-fleshed squash, is there any likelihood at all that you'll get a single zucchini pollinated by both in one generation (such that the next generation of cross-pollinated zucchini would be both stringy and orange-fleshed instead of just one or the other)?&lt;/p&gt;&#xA;" OwnerUserId="9601" LastEditorUserId="9601" LastEditDate="2015-03-07T01:52:19.310" LastActivityDate="2018-04-04T23:48:06.907" Title="How much pollen is needed to pollinate a flower?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30195" PostTypeId="1" CreationDate="2015-03-06T06:14:37.740" Score="14" ViewCount="3024" Body="&lt;p&gt;After reading &lt;a href=&quot;https://biology.stackexchange.com/a/30103/13418&quot;&gt;an answer&lt;/a&gt; to the question of &lt;a href=&quot;https://biology.stackexchange.com/q/30102/13418&quot;&gt;How Do White Blood Cells Learn? Or Do They?&lt;/a&gt;, I came to wonder something. Specifically,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The effect of this is that every new B and T cell that your bone marrow makes will recognize a unique, random protein sequence, and you will have billions of these cells floating around in your blood circulation at any given time. These cells however will only float around in circulation for a short period of time before dying and being replaced by other cells with new random sequence receptors.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Assumption:&lt;/strong&gt; What I gather from this (and the remainder of the answer) is that basically, a vaccine &quot;teaches&quot; the &lt;em&gt;existing&lt;/em&gt; white blood cells in your body; eventually, these cells will  be purged, so you will no longer be immune.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, many vaccines seem to only be once-in-a-lifetime, or at least require a vaccine only once per decade (or less).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some examples would be the &lt;a href=&quot;https://en.wikipedia.org/wiki/Varicella_vaccine&quot; rel=&quot;noreferrer&quot;&gt;Varicella vaccine&lt;/a&gt;, which can last up to 20 years, the &lt;a href=&quot;https://en.wikipedia.org/wiki/Tetanus_vaccine&quot; rel=&quot;noreferrer&quot;&gt;Tetanus vaccine&lt;/a&gt;, which recommends a booster every 10 years, and the &lt;a href=&quot;https://en.wikipedia.org/wiki/HPV_vaccines&quot; rel=&quot;noreferrer&quot;&gt;HPV vaccine&lt;/a&gt;, which lasts 5-6 years. Durations also vary with Hepatitis, Influenza, Polio, and numerous other common vaccines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would assume that, regardless of what a cell has &quot;learned,&quot; it is purged with the same likelihood as any other cell; yet, it seems that some &quot;learned&quot; defenses can be retained longer than others. In essence, my question is: &lt;strong&gt;Why do some vaccines take longer to &quot;wear off&quot; than others?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;(&lt;em&gt;Note: This question is &lt;strong&gt;not&lt;/strong&gt; a duplicate of &lt;a href=&quot;https://biology.stackexchange.com/q/15637/13418&quot;&gt;Why do I need a flu shot every year, while many other vaccinations last years or even a lifetime?&lt;/a&gt;; I understand that some pathogens can mutate, so immune cells are of no use against mutated strains since they were not vaccinated against the mutation.&lt;/em&gt;)&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="13418" LastEditorUserId="1320" LastEditDate="2017-07-07T07:06:58.237" LastActivityDate="2018-05-09T13:37:03.983" Title="Why does the protection afforded by some vaccines last longer than for others?" Tags="&lt;immunology&gt;&lt;vaccination&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30196" PostTypeId="1" AcceptedAnswerId="30197" CreationDate="2015-03-06T07:20:39.590" Score="2" ViewCount="38" Body="&lt;p&gt;With respect to this paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18854154&quot; rel=&quot;nofollow&quot;&gt;Global Analysis of Host-Pathogen&#xA;Interactions that Regulate&#xA;Early-Stage HIV-1 Replication&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does the term &quot;host cellular factors&quot; mean??&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="5144" LastEditDate="2015-03-06T07:31:24.517" LastActivityDate="2015-03-06T07:39:48.030" Title="What are host cellular factors?" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30197" PostTypeId="2" ParentId="30196" CreationDate="2015-03-06T07:39:48.030" Score="3" Body="&lt;p&gt;Generally spoken, &quot;host cellular factors&quot; are proteins, receptors etc. of the host cell. In this case, they are important for the HIV infection. The authors write:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Recently, a genome-wide siRNA analysis revealed over 250 host cellular&#xA;  factors that influence HIV-1 infection.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This means gene silencing techniques where used to identify the host cellular factors which are important for the infection, you can find these results here: &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18187620&quot; rel=&quot;nofollow&quot;&gt;Identification of host proteins required for HIV infection through a functional genomic screen.&lt;/a&gt;&quot;&#xA;The overall goal is to identify proteins which are important for the function and infection of HIV to understand the interaction between virus and host cell better.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-03-06T07:39:48.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30200" PostTypeId="1" CreationDate="2015-03-06T14:01:17.387" Score="3" ViewCount="102" Body="&lt;p&gt;I have a presentation to do where non-biologist are attending. In order to introduce a little bit my work I have to do a quick summary on genomes. So what is a genome, a gene, an mRNA and a protein. And the best would be to have that in one figure, an easy to understand. I found this : &lt;a href=&quot;http://dnamismatch.com/Test/wp-content/uploads/2013/07/Genes-and-genomes.png&quot; rel=&quot;nofollow&quot;&gt;http://dnamismatch.com/Test/wp-content/uploads/2013/07/Genes-and-genomes.png&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyone knows other resources ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="359" LastEditorUserId="1590" LastEditDate="2015-03-06T14:08:36.283" LastActivityDate="2015-03-06T14:08:36.283" Title="How to explain Genome, Genes, RNA and protein in one figure to non-biologist?" Tags="&lt;genomes&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30202" PostTypeId="2" ParentId="30191" CreationDate="2015-03-06T17:17:59.477" Score="12" Body="&lt;p&gt;This is a great question. Just to make it clear people with DS do have a reduced risk of solid cancers and an increased risk of blood cancers, (B-ALL and AML).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are correct in picking out DSRC1 because of its angiogenic implications. The current hypothesis centers around people with DS being less capable of driving angiogenesis, and therefore having an internal environment that is less nurturing to metastasized or even developing solid cancers. Current unpublished work I have recently seen shows this very clearly in the eye, where the vasculature in DS is far less branched than in the wild-type population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why however they show an increased risk of leukemias is a largely unanswered question, with one exception being AMKL (Acute Megakaryocytic Leukemia). People with DS are at a ~500X increased risk of AMKL over the unafected population, and it appears to be entirely driven by the in-utero introduction of a stop mutation in codon 2 the transcription factor GATA1. This transcription factor is important in driving differentiation of progenitor cells in the bone marrow to become erythrocytes and megakaryocytes. Thus inactivating this transcription factor plays a large role in disrupting normal hematopoiesis such that megakaryocytes are overproduced and become a leukemia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All that being said, and as you mentioned people with DS have around a 20-50X increased risk of AML and B-ALL. There are certainly some chromosome 21 genes that have been implicated in this like Bach1 (important in DNA repair) Ifngr2 (plays a role in cell death) Usp16 (epigenetic regulator &lt;a href=&quot;http://www.nature.com/nature/journal/v501/n7467/full/nature12530.html&quot;&gt;Really important recent Nature Paper&lt;/a&gt;) and Runx1 (important in stress response) but the field is entirely unsure why this directly leads to increased risk of leukemias. Many current cancer biologists favor the direct gene-dosage problem that people with DS face in that a some ~120 genes are overexpressed when they shouldn't be, and assume that these gene level cocktail directly leads to this increased risk of leukemogenesis, and this very well may be in part the answer. There is however a great 'contrarian' view, in that hematopoietic stem and progenitor cells will become pro-apoptotic and pro-differentiative when faced with certain stresses like aneuploidy. The effect of this on a global scale would be that many of the stem and progenitor cells in the bone marrow would die or differentiate prematurely. This would then result in teenagers with DS having far fewer blood stem cells then they should, and these cells would then be tasked with pumping out more blood per cell than originally meant for them quite possibly leading to an exhaustive phenotype. In this way the blood systems of people with DS will 'prematurely age', and might thus rapidly increase the risk of cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Make sense?&lt;/p&gt;&#xA;" OwnerUserId="14587" LastEditorUserId="14587" LastEditDate="2015-03-06T20:32:03.670" LastActivityDate="2015-03-06T20:32:03.670" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30203" PostTypeId="1" AcceptedAnswerId="30232" CreationDate="2015-03-06T21:07:16.607" Score="5" ViewCount="2666" Body="&lt;p&gt;I am aware of the post here '&lt;a href=&quot;https://biology.stackexchange.com/questions/8612/optogenetics-how-do-microbial-opsins-work&quot;&gt;Optogenetics - How do microbial opsins work?&lt;/a&gt;'&#xA;however it is a bit too technical for me. I am struggling to understand how the neurons can be genetically engineered to produce these light-sensitive molecules in optogenetics, and how genetically engineering the neurones is even a usable method considering it seems you would have to genetically engineer the neurons one by one. So I suppose my question is: in the trials run of optogenetics so far (with mice), how where the neurons made to respond to the light stimulus?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I was wondering whether the principle behind optogenetics- controlling calls with light- could be used for other treatments e.g. to kill cancer cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My biology knowledge is limited to A-Level (final year of high school), however I really want to understand this topic thoroughly, so detailed but not too technical answers would be much appreciated! Thank you!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I just wanted to add two more quick questions...&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Are the light-sensitive molecules (which I now have read are channelrhodopsins) present all along the axolemma, or just the membrane of the soma of the neuron? (I hope I used those terms correctly!)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Wikipedia says that these channelrhodopsins are non-specific (with some exceptions: The L132C mutation (CatCh) increases the permeability for calcium and generates very large currents.[17] Mutating E90 to the positively charged amino acid arginine turns channelrhodopsin from an unspecific cation channel into an anion channel. This chloride-conducting channelrhodopsin (ChloC) inhibits neuronal spiking when illuminated with blue light.[18]). How then can these channels work, if any cation can diffuse any way through the channel?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6136" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-03-09T13:41:15.760" Title="How does optogenetics work?" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30204" PostTypeId="2" ParentId="30163" CreationDate="2015-03-06T21:48:08.417" Score="3" Body="&lt;p&gt;Autoclaving is the best way for sterilization. If your growth medium is large, how much chemical disinfectant do you think you would need to bring up to its working concentration?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Add some acid to your waste medium (so that it's only weakly acidic), not as disinfectant, but to suppress ammonia formation. Urea will still break down during autoclave, but ammonium ion (pKa~9) will generally stay in solution.&lt;/p&gt;&#xA;" OwnerUserId="9731" LastActivityDate="2015-03-06T21:48:08.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30205" PostTypeId="2" ParentId="30181" CreationDate="2015-03-06T23:43:58.970" Score="3" Body="&lt;p&gt;Antibiotics ARE compounds, and they kill or inhibit the growth of bacteria by specific mechanisms. Each class of antibiotics has specific mechanism of actions. Given enough exposure to these antibiotics compounds, bacteria can develop specific molecular mechanism to nullify their effect, and hence antibiotics resistance. Antibiotics resistance will eventually develop with enough exposure to drive the organism's evolution . Whereas there are combination therapy, there are multi-drug resistance; whereas there are wonder drug, there are super bug.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;General disinfectant compounds such as benzoyl peroxide or sodium dodecyl sulfate (in soap and detergent) have no specific molecular target that would differentiate host and intruders and hence can harm bacteria as much as the host cells. They are safe to use only because you have skin to prevent their intake. Since there is no molecular target to mutate to develop resistance, the resistance to general disinfectant will simply take a very long time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is to say, who could ensure bacteria cannot develop resistance to benzoyl peroxide? Resistance to phenyl derivative has long been reported [1], and bacterial catalase can easily break down the damaging effect of peroxide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] Heinz Berger and Orville Wyss. J of Bacteriology (1953) vol. 65 p.103  &lt;/p&gt;&#xA;" OwnerUserId="9731" LastActivityDate="2015-03-06T23:43:58.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30207" PostTypeId="2" ParentId="30163" CreationDate="2015-03-07T07:51:35.327" Score="0" Body="&lt;p&gt;You should check with your institutions guidelines as different facilities have different regulations but generally it is acceptable to:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a fume hood and in a ventilated (unsealed) container:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1.add liquid bleach to a final concentration of 20% (add 1 part bleach to 3 parts culture)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2.Let sit overnight&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3.Dispose down drain with copious amounts of water&lt;/p&gt;&#xA;" OwnerUserId="6061" LastActivityDate="2015-03-07T07:51:35.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30208" PostTypeId="1" AcceptedAnswerId="30210" CreationDate="2015-03-07T09:51:42.503" Score="1" ViewCount="63" Body="&lt;p&gt;Well, here's what I did: P: Aa*Aa&lt;/p&gt;&#xA;&#xA;&lt;p&gt;F1: 1/4 AA, 1/2 Aa, 1/4 aa, SO the answer is 1/2, but out teacher did this:&#xA;AA(1)    Aa(2)    aa(1) and she said we divide the number of filium for the phenotypes number and get 2/3. This is the probability. I don't get it.&lt;/p&gt;&#xA;" OwnerUserId="14702" LastEditorUserId="11841" LastEditDate="2015-03-07T13:43:12.547" LastActivityDate="2015-03-07T16:35:43.517" Title="Two mice heterozygote and black are reproduced. Find the probability of getting the filium dark and heterozygote" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2015-03-07T14:28:58.230" ContentLicense="CC BY-SA 3.0" />
  <row Id="30210" PostTypeId="2" ParentId="30208" CreationDate="2015-03-07T10:48:03.853" Score="2" Body="&lt;p&gt;Okay so in your teachers answer there are four offsprings. . You used all offsprings when you made the division so 2/4 = 1/2.Your teachers 2/3 comes from the fact that 3 out of four is black, but only 2 out of that 3 black is heterozygote so 2/3 is good by this logic. I think that your teacher's logic faulty because you have to take into consideration all the offsprings. Basic genetics and Mendel's law tells us that crossing two heterozygotes with independent alleles result in a 3:1 ratio in phenotype separation in the next generation with 1:2:1 genotype separation -- that is what basically both of you have wrote. The fault is in the getting the probability - basic maths tells us that in an independent experiment, the probability variables have to sum up to one. In your teacher's logic this basic rule is not kept, because finding homozygous non-dark offspring would be one (there is only one non-dark filium and that one is homozygous). So by this logic all filium are non dark-homozygous, but then what about the others. I hope you see the problem with that logic.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-03-07T16:35:43.517" LastActivityDate="2015-03-07T16:35:43.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30212" PostTypeId="1" AcceptedAnswerId="30279" CreationDate="2015-03-07T14:23:01.740" Score="10" ViewCount="14695" Body="&lt;p&gt;I recently read that cucumber skin is an effective repellent for some ants:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Set out cucumber peels or slices in the kitchen or at the ants' point of entry. Many ants have a natural aversion to cucumber. Bitter cucumbers work best.&lt;/p&gt;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://eartheasy.com/live_natpest_control.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Natural Insect Pest Control&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;See also: &lt;a href=&quot;http://www.wikihow.com/Use-Cucumbers-to-Prevent-Ants-from-Entering-the-Home&quot; rel=&quot;nofollow noreferrer&quot;&gt;How to Use Cucumbers to Prevent Ants from Entering the Home&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;But when I tried it out they died instead. What made this happen?&lt;/p&gt;&#xA;" OwnerUserId="14817" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-08-05T08:34:47.580" Title="Why does cucumber skin kill ants?" Tags="&lt;biochemistry&gt;&lt;zoology&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30214" PostTypeId="1" CreationDate="2015-03-07T18:14:00.750" Score="3" ViewCount="289" Body="&lt;p&gt;What is the minimum eye which confers some evolutionary advantage?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By minimum I mean anything less than this has no advantage whatsoever and therefore is not favored by natural selection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By eye, I mean not just a light sensor but also infrastructure which converts the light stimulus into an advantageous response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ideally would like a clear unambiguous before/after case especially on the infrastructure between the mutated protein and the cell's response mechanism which translates this into a survival advantage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I assume Opsin proteins floating around the cytoplasm by themselves confers no advantage without some kind of other infrastructure)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;please also provide an estimate of the number of coordinated DNA base pairs which needed to change to confer this advantage so that a proper probability estimate can be done.&lt;/p&gt;&#xA;" OwnerUserId="8290" LastEditorUserId="14709" LastEditDate="2015-03-08T15:29:49.650" LastActivityDate="2015-03-09T13:34:38.163" Title="What is the minimum eye?" Tags="&lt;evolution&gt;&lt;eyes&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="10" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30215" PostTypeId="1" CreationDate="2015-03-07T18:37:39.827" Score="3" ViewCount="371" Body="&lt;p&gt;I have carried out a native PAGE with 4 reaction mixtures. To each I had added an equal volume of EDTA (1 µl/1mM) to sequester any divalent ions and an equal volume of calmodulin (5 µl/0.5 mg/ml). I added 2 µl of calcium (2 mM), magnesium (2 mM) and manganese (2 mM) ions respectively to three reaction mixtures and had a control that was made up to an equal volume with Tris-HCl. All reaction mixtures were made up to 10 µl with Tris-HCl. Here I ran into a problem with the waterbaths and the reactions couldn't be incubated at 37 degrees Celsius.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After I added the loading buffer to each, I added the 4 reaction mixtures to the polyacrylamide gel and electrophoresed for 45 minutes at 150 V. After this I placed the gel in Coomassie Blue stain for 20 minutes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After the destaining process, I reviewed the gel to find that the calmodulin in the 4 lanes had migrated the same distance. I had expected the EDTA control to have migrated the furthest on the gel, with Ca2+ and Mn2+ migrating similar distances due to their similar ionic radii; making it a good substitute for the binding to the calmodulin. I was unsure of how far the Mg2+ would travel as I thought it would have a lower affinity to the calmodulin due to its binding to the N-terminus rather than the C-terminus. However, I was wondering if this was negligible in the absence of Ca2+, although now I can't be sure due to the results of the gel. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering what errors in the experimental design or process could have resulted in this? And if the experiment was run correctly, what results would be expected?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first image is the result I was expecting. The second is the results from my gel electrophoresis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EXnc5.png&quot; alt=&quot;This was the result I was expecting&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0KfR4.png&quot; alt=&quot;This is the result I got&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14821" LastEditorUserId="14821" LastEditDate="2015-03-07T22:03:24.253" LastActivityDate="2015-03-08T07:33:34.613" Title="Divalent cation binding to calmodulin" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;gel-electrophoresis&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="30216" PostTypeId="1" AcceptedAnswerId="43563" CreationDate="2015-03-07T20:36:47.287" Score="2" ViewCount="94" Body="&lt;p&gt;I have a few different fluorescent microscopes, the two that use Mercury  lamps are older than 7 years. I notice on those that the thin film filters in the filter cubes (green, red, blue) have accumulated this haziness. Both the excitation and barrier filters seem to have this, more so on the ex filter and it's not present on the dichroic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've always referred to this as the filter being &quot;burned&quot; and my rational is that it's from the heat &amp;amp; intensity &amp;amp; low wavelengths from the Mercury lamp.  But in all honesty I don't know what it is or if it's removable and if so how? I would like to see if removing it improves my image clarity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know a picture would help here and I'm having trouble showing it but will keep attempting and add it to an edit for this question. However I have seen this on many microscopes if you have one with a merc arc lamp and it's getting up there in age take a look at the filters on it. Let me know if you see this too.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="9943" LastEditDate="2016-02-22T21:07:02.173" LastActivityDate="2016-02-22T21:07:02.173" Title="Possible to remove accumulated haze on fluorescence interference filters?" Tags="&lt;fluorescent-microscopy&gt;&lt;signal-processing&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30217" PostTypeId="2" ParentId="30214" CreationDate="2015-03-07T20:39:32.897" Score="6" Body="&lt;p&gt;I think that you are expecting for some complicated system while such things are not necessarily involved. You basically just need a protein that is light-sensitive and some cascade of signal transduction. A light-sensitive protein is just a protein which conformation is changed in the presence of photons of a given wavelength. This cascade of signal transduction can be very standard. It doesn't need to be anything extraordinary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider a mutation that turns a given protein into a light-sensitive protein. Such mutant protein could easily still activate the same cascade (and eventually regulate the expression of the same gene) and may eventually be beneficial. A visual signal (presence/absence of photons of a given wavelength) directly affect the conformation of the protein which in result can activate a whole cascade. The cascade doesn't need to have evolved after the protein had acquired the ability to response to photons. You may want to dive into the details of how the &lt;a href=&quot;http://en.wikipedia.org/wiki/Opsin#Structure_and_function&quot; rel=&quot;noreferrer&quot;&gt;structure and function of the opsin proteins&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880087/&quot; rel=&quot;noreferrer&quot;&gt;This article&lt;/a&gt; describes how an ancestral non-light sensitive protein (coded in GPCR gene. The proteins are also called serpentine) evolved into a light-sensitive protein (opsin). The article also link to other articles that discuss this transition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several types of light-senstive proteins in different kingdom, including plants and bacteria that don't have nerves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can learn more about the cascade of transduction on wikipedia (&lt;a href=&quot;http://en.wikipedia.org/wiki/Biochemical_cascade&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/Signal_transduction&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; for example). You may want to learn more about &lt;a href=&quot;http://en.wikipedia.org/wiki/Opsin&quot; rel=&quot;noreferrer&quot;&gt;opsin proteins&lt;/a&gt; and learn more about &lt;a href=&quot;http://en.wikipedia.org/wiki/Photoreceptor_protein&quot; rel=&quot;noreferrer&quot;&gt;light-sensitive proteins&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia page: &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_the_eye#Early_eyes&quot; rel=&quot;noreferrer&quot;&gt;Evolution of eyes &gt; Early Eyes&lt;/a&gt; will probably interest you as well. Depending on the definition you use for &quot;eye&quot; (note, &quot;eyes&quot; have evolved independently 50 to 100 times), &lt;a href=&quot;http://en.wikipedia.org/wiki/Planarian&quot; rel=&quot;noreferrer&quot;&gt;Planarian&lt;/a&gt; might be a good example of a species that have a primitive eye.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-03-07T21:33:48.233" LastActivityDate="2015-03-07T21:33:48.233" CommentCount="21" ContentLicense="CC BY-SA 3.0" />
  <row Id="30218" PostTypeId="1" AcceptedAnswerId="30268" CreationDate="2015-03-07T20:50:30.267" Score="5" ViewCount="535" Body="&lt;p&gt;many papers I read mentioned &quot;RNA-seq data&quot;. While searching for the meaning of this word, I could not find any layman's definition. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I understand, &lt;strong&gt;RNA-seq data&lt;/strong&gt; is the complete RNA information in a cell (or all of the cells) of a species that is extracted at a certain time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I correct with this definition? If yes, does this mean that by extracting all the RNA information ones knows all the RNA sequences in that species (like AUGGUCAUCAG....)? Or does it mean I have the RNA, but not the sequence? &lt;/p&gt;&#xA;" OwnerUserId="14759" LastEditorUserId="9943" LastEditDate="2015-03-09T13:31:54.653" LastActivityDate="2015-03-09T14:24:09.643" Title="The meaning of RNA-seq data" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;rna-sequencing&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30219" PostTypeId="1" CreationDate="2015-03-07T23:42:27.087" Score="2" ViewCount="97" Body="&lt;p&gt;I know that being heterozygous or homozygous recessive for the MTHFR gene prevents that person from being able to process and use folate and B-12. It causes an unhealthy level of homocysteine to accumulate in the bloodstream which can cause more serious problems. Taking methylated B-vitamins, specifically Methylfolate and Methylcobalamine will prevent homocysteine from building up, but I am not sure why. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone explain how this process works? I am wondering how the body uses folate and B-12 (cobalamine) normally and how the recessive MTHFR genes interfere with this process. &lt;/p&gt;&#xA;" OwnerUserId="14824" LastActivityDate="2015-06-15T10:22:44.607" Title="MTHFR recessive alleles and B-vitamins" Tags="&lt;metabolism&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30220" PostTypeId="1" CreationDate="2015-03-08T06:35:29.213" Score="4" ViewCount="277" Body="&lt;p&gt;I can only think of one reason, which is because different codons can specify the same amino acids. However I am having trouble thinking of another reason. &lt;/p&gt;&#xA;" OwnerUserId="12876" LastEditorUserId="948" LastEditDate="2015-03-08T07:02:27.703" LastActivityDate="2015-03-12T04:43:36.200" Title="Name two reasons why it is impossible to determine a gene's nucleotide sequence from the amino acid sequence of the polypeptide" Tags="&lt;cell-biology&gt;&lt;gene-expression&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30221" PostTypeId="2" ParentId="30220" CreationDate="2015-03-08T07:14:23.500" Score="8" Body="&lt;p&gt;I can think of at least 3 reasons in addition to the one you gave:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1: As mentioned in the comments, &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA_splicing&quot;&gt;RNA splicing&lt;/a&gt; takes place on most messenger RNA encoding proteins in eukaryotes. Sections of the mRNA may be spliced out, therefore multiple mRNAs with different codon sequence can encode the same gene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2: Translation is a &lt;a href=&quot;http://en.wikipedia.org/wiki/State_%28computer_science%29&quot;&gt;stateful process&lt;/a&gt;, since it depends on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Reading_frame&quot;&gt;frame&lt;/a&gt; of the codon. Therefore, a gene with the sequence GGATGATGATGTAA will encode the same protein as a gene with the sequence ATGATGATGTAA, due to the start codon shifting the frame of translation downwards. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3: Genes contain &lt;a href=&quot;http://en.wikipedia.org/wiki/Untranslated_region&quot;&gt;untranslated regions&lt;/a&gt; in regions before the start and after the stop codon. These nucleotides cannot be predicted from protein sequence, but are generally important in regulating protein expression. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-03-08T07:14:23.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30222" PostTypeId="1" AcceptedAnswerId="30228" CreationDate="2015-03-08T07:17:37.773" Score="3" ViewCount="2878" Body="&lt;p&gt;Why is retina transplant not as easy as the normal eye donation and transplant (I think the latter involves the cornea ) ?&lt;br&gt;&#xA;&lt;a href=&quot;http://www.theglobeandmail.com/life/health-and-fitness/health/successful-retina-transplant-sparks-hope/article21270294/&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; says that a new method has come up but why isnt the process similar and simple as the normal transplant ?&lt;br&gt;&#xA;What are the difficulties in retina transplant ?&lt;/p&gt;&#xA;" OwnerUserId="14817" LastActivityDate="2015-03-08T22:33:53.297" Title="Retina Transplant Difficulties" Tags="&lt;vision&gt;&lt;human-eye&gt;&lt;transplantation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30223" PostTypeId="2" ParentId="30215" CreationDate="2015-03-08T07:33:34.613" Score="1" Body="&lt;p&gt;The change in gel migration distance is due to the conformational changes due to the binding of the ion, and have nothing (detectable) to do with the ionic radius of the ion. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The left image shows calmodulin with no ligand bound, and the right image shows it with calcium and peptide bound to it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UCjFAm.gif&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/KV2spm.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can clearly see, the unbound calmodulin is significantly thinner, and therefore can migrate faster through the gel. The change in charge on the protein due to cation binding in native PAGE may also affect the result. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the calmodulin conformational change is enhanced by &lt;a href=&quot;http://www.jbc.org/content/273/28/17579.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;both a peptide and calcium cations&lt;/a&gt;, as well as its phosphorylation state, it would be reasonable to investigate the contributions of these factors to your result. Reading the original paper again to see what you missed the first time may also be helpful. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-03-08T07:33:34.613" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30224" PostTypeId="2" ParentId="30218" CreationDate="2015-03-08T07:38:29.970" Score="2" Body="&lt;p&gt;RNA sequencing occurs when you perform an RNA extraction and then sequence them, which usually involves fragmenting them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You do in fact know all of the sequences for all of the RNA molecules that are being sequenced. I can't see an interpretation that does not result in you having the sequences of the molecules, what with it being called &quot;sequencing&quot; and all. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-03-08T07:38:29.970" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30225" PostTypeId="1" CreationDate="2015-03-08T08:08:09.547" Score="1" ViewCount="225" Body="&lt;p&gt;I would like to know the distribution of mitochondrial content per tissue type in humans. I understand the simple metric that energetically active or energy requiring tissues will have more mitochondrial content, however is there any study/link for a more quantitative estimate ? &lt;/p&gt;&#xA;" OwnerUserId="14827" LastActivityDate="2015-03-08T08:22:00.427" Title="Mitochondria variability per tissue in humans?" Tags="&lt;metabolism&gt;&lt;cancer&gt;&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30226" PostTypeId="2" ParentId="30225" CreationDate="2015-03-08T08:22:00.427" Score="2" Body="&lt;p&gt;BioNumbers is a great site to answer this kind of question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bionumbers.hms.harvard.edu/search.aspx?log=y&amp;amp;task=searchbytrmorg&amp;amp;trm=mitochondria%20per%20cell&amp;amp;time=2015/03/08%2004:18:16.577&amp;amp;rpp=100&quot; rel=&quot;nofollow noreferrer&quot;&gt;This search&lt;/a&gt; produced a link to &lt;a href=&quot;http://kirschner.med.harvard.edu/files/bionumbers/A%20comparison%20of%20mtDNA%20per%20mt,%20virtual%20mt%20number%20per%20cell,%20mt%20DNA%20per%20cell,%20Cyaa3%20per%20mt,%20and%20Cyaa3%20per%20cell%20in%20five%20cell%20types%20from%20four%20mammalian%20species.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper&lt;/a&gt; , which has measurements for mitochondria per cell for multiple species and cell type.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jQQ2T.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-03-08T08:22:00.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30227" PostTypeId="1" CreationDate="2015-03-08T09:19:31.897" Score="2" ViewCount="199" Body="&lt;p&gt;Can we understand a cell as an organic computational device? In that case the whole organism can be considered an ensemble of a large number of interacting computational devices? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is the case, biology can be studied using methods of graph theory, network theory, computation theory and complex systems theory. &lt;/p&gt;&#xA;" OwnerUserId="14828" LastEditorUserId="6703" LastEditDate="2015-03-08T17:29:22.690" LastActivityDate="2015-03-08T20:37:05.187" Title="Can all biological processes be understood as computations and studied as such?" Tags="&lt;bioinformatics&gt;&lt;computational-model&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="2" ClosedDate="2015-03-08T15:29:08.473" ContentLicense="CC BY-SA 3.0" />
  <row Id="30228" PostTypeId="2" ParentId="30222" CreationDate="2015-03-08T10:17:42.050" Score="4" Body="&lt;p&gt;&lt;em&gt;This is a diagram of a cross-section of the cornea&lt;/em&gt;:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0NGWI.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;It is an amazing but relatively simple structure, the shape of which is responsible for about 60% of our focusing power, and the clarity of which allows light to enter. It is avascular (no blood vessels), and the non-mylenated nerve endings are very tiny and present in the epithelium.&lt;/p&gt;&#xA;&lt;p&gt;Transplanting this relatively simple tissue is easy (well, not do-it-at-home easy, but easy.) The only problem with cutting all those nerve endings is that the new cornea will feel nothing if there's dust in the eye, etc. This is a problem, but nothing compared to blindness.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;This is a diagram of a cross section of the retina&lt;/em&gt;:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KBYrq.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;As you can see, it is not nearly as simple as the cornea. The nerves (to the left: yellow, light blue, medium blue and darker blue), which collect information from the rods and cones (pink and purple) are very numerous, and absolutely vital to the ability of the brain to interpreting information from these photoreceptors. Therefore, a cut piece of retina immediately loses the ability to send any information to the brain. To transplant it into an eye with a damaged retina would do nothing to improve vision. Also, it is not easy surgery. It's &lt;em&gt;very&lt;/em&gt; difficult.&lt;/p&gt;&#xA;&lt;p&gt;What has been called &amp;quot;retinal transplants&amp;quot; in the recent past have been tiny pieces of embryonic retina, about...&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;4 millimetre square of retinal tissue, complete with retinal progenitor cells and the retinal pigment epithelium that nourishes them. The tissues were placed in the sub-retinal space beneath the fovea, the area of the retina responsible for sharp central vision.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Note, they didn't try to connect nerves or blood vessels. And, it came from &lt;em&gt;an embyro&lt;/em&gt; (so the supply is a problem.) The improvement in vision - which was significant in 7 out of 8 recipients (one patient going from 20/800 to 20/160) - is not long lasting, and believed to have been not from the transplanted retina connecting to the existing retina, but from the release of growth factors from the embryonic tissue improving the health of the degenerating retina.&lt;/p&gt;&#xA;&lt;p&gt;The newest in &amp;quot;retinal transplants&amp;quot; (which might be better called stem-cell-supplied growth factors implanted in the retina) actually derives from the patient's own stem cells:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;A Japanese woman in her 70s is the first person to receive tissue derived from induced pluripotent stem cells, a technology that has created great expectations since it could offer the same regenerative potential as embryo-derived cells but without some of the ethical and safety concerns. [No news yet on whether it worked.]&lt;/p&gt;&#xA;&lt;p&gt;In a two-hour procedure... a team of three eye specialists lead by Yasuo Kurimoto of the Kobe City Medical Center General Hospital implanted a 1.3 by 3.0 millimetre sheet of retinal pigment epithelium cells into an eye of the Hyogo prefecture resident, who suffers from age-related macular degeneration, a common eye condition that can lead to blindness.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;TL;DR: It's not as easy as taking cadaver retina and replacing a patients retina (that would result in immediate and permanent blindness). Whereas corneal transplantation is very easy.&lt;/p&gt;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.iovs.org/content/48/2/621.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;Corneal Innervation and Cellular Changes after Corneal Transplantation: An In Vivo Confocal Microscopy Study&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.nature.com/news/2008/080908/full/news.2008.1088.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Retinal transplants see fleeting success&lt;/a&gt;&lt;/sub&gt;&lt;br /&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.nature.com/news/japanese-woman-is-first-recipient-of-next-generation-stem-cells-1.15915&quot; rel=&quot;nofollow noreferrer&quot;&gt;Japanese woman is first recipient of next-generation stem cells&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-08T22:33:53.297" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30229" PostTypeId="1" AcceptedAnswerId="30235" CreationDate="2015-03-08T10:48:53.220" Score="10" ViewCount="1107" Body="&lt;p&gt;I seem to have come across two contrasting explanations for tinnitus induced by loud noises- i.e. damage to the hair cells in the cochlea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the one hand, I have read that damage to the hair cells results in them releasing excess glutamate, the neurotransmitter that carries the impulse from the hair cells to the neurones in the auditory nerve. This would result in the neurones constantly being excited, which I can understand would lead to constantly perceiving sound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand I have read that when the hair cells are damaged, the auditory cortex is no longer receiving electrical impulses from the hair cells that detect those frequencies, and so the neurones start to fire (although I am not sure why no input would lead to neurones going off by themselves! Surely there must be some input to cause the initial depolarisation to cause an action potential?) and so you perceive a constant sound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These seem to me to be two contrasting explanations. My only other guess on how these explanations overlap is that the excess glutamate being released causes death of the neurone, and therefore the neurones after that one do not receive and input and they start firing spontaneously (although again I would appreciate if someone could explain how lack of input results in neurones firing by themselves).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance! &lt;/p&gt;&#xA;" OwnerUserId="6136" LastEditorUserId="9943" LastEditDate="2015-03-22T12:14:55.303" LastActivityDate="2015-08-19T06:26:50.037" Title="What is the mechanism behind tinnitus?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;hearing&gt;&lt;neurophysiology&gt;&lt;neurodegenerative-disorders&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30230" PostTypeId="2" ParentId="30227" CreationDate="2015-03-08T10:54:09.383" Score="4" Body="&lt;p&gt;If you abstract enough, anything cam be considered as a computational device. The issue with doing this with cells is the sheer number of variables.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For any given cell, the following &lt;em&gt;internal&lt;/em&gt; variables exist:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Internal ion concentrations for dozens of ions of importance importance&lt;/li&gt;&#xA;&lt;li&gt;Internal concentrations of hundreds or thousands of various simple organic molecules, including &quot;raw&quot; internalised molecules, various steps in dozens or even hundreds of metabolic processes, and metabolic end-products and by-products.&lt;/li&gt;&#xA;&lt;li&gt;Internal concentrations of hundreds or thousands of different proteins and other complex biological &quot;mechanical parts&quot;, as well as the states of these &quot;parts&quot;.&lt;/li&gt;&#xA;&lt;li&gt;The physical state of the cell - stretched, contracted, relaxed, hot, cold, etc.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This list is not exhaustive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also worth noting that the above variables may also exist for multiple separate &quot;compartments&quot; within the cell; vesicles, the endoplasmic reticulum and the golgi apparatus being three which come to mind immediately.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other issue is that cells do not exist in a vacuum; the external environment plays an important role in their functioning. The human body is at any one moment existing in direct contact and interaction with the following extracellular environments:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The atmosphere (Mainly, but not only, temperature exchange)&lt;/li&gt;&#xA;&lt;li&gt;The air within the respiratory system, including nose and mouth&lt;/li&gt;&#xA;&lt;li&gt;Stomach contents&lt;/li&gt;&#xA;&lt;li&gt;Small intestine contents (which would need to be considered in several segements, since the nature of the interaction changes along the path of the small intestine.&lt;/li&gt;&#xA;&lt;li&gt;Large intestine contents&lt;/li&gt;&#xA;&lt;li&gt;Blood&lt;/li&gt;&#xA;&lt;li&gt;Cerebrospinal fluid (Fluid found &quot;inside&quot; the brain)&lt;/li&gt;&#xA;&lt;li&gt;Extracellular fluid, or &quot;tissue fluid&quot; (A separate compartment for each small swatch of tissue in the body)&lt;/li&gt;&#xA;&lt;li&gt;Lymph&lt;/li&gt;&#xA;&lt;li&gt;Pleural fluid (Fluid surrounding the lungs; a separate compartment for each lung)&lt;/li&gt;&#xA;&lt;li&gt;Pericardial fluid (A small amount of fluid surrounding the heart)&lt;/li&gt;&#xA;&lt;li&gt;Joint capsule contents (A separate compartment for each joint)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;...and the list goes on. Each of these compartments requires tracking of the same variables as individual cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is yet further complicated by the fact that some of these compartments can't easily be considered as one big compartment, because of the importance of spatial relations. For example, the oxygen and carbon dioxide concentrations of blood (as well as the concentrations of other substances like alcohol) change centimeter-to-centimeter. Yet another issue is the fact that cells are not static in terms of their relations to each other; red blood cells move with blood flow, and experience turbulence and other effects, and other cells (like macrophages) are capable of &quot;deliberate&quot; movement in the blood and in tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You would also have to account for physical disturbances - things like a stab wound or even a pinprick are ludicrously complex at a cellular level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, human beings are very complex organisms, and there exist much simpler organisms. You might be interested in &lt;a href=&quot;http://en.wikipedia.org/wiki/OpenWorm&quot; rel=&quot;nofollow&quot; title=&quot;OpenWorm&quot;&gt;OpenWorm&lt;/a&gt;, which is an attempt to computationally simulate &lt;em&gt;Caenorhabditis elegans&lt;/em&gt;, a species of roundworm, at a cellular level. Doing so even for an organism as simple as &lt;em&gt;C. elegans&lt;/em&gt; is a massive undertaking, as evidenced by the fact that even with the contributions of dozens of experts in their fields the project has been ongoing for some time and is yet to reach stage one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The short version: Is it &lt;strong&gt;possible&lt;/strong&gt;? Perhaps. Is it &lt;strong&gt;easy&lt;/strong&gt;? Definitely not.&lt;/p&gt;&#xA;" OwnerUserId="13187" LastEditorUserId="13187" LastEditDate="2015-03-08T20:37:05.187" LastActivityDate="2015-03-08T20:37:05.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30231" PostTypeId="2" ParentId="30227" CreationDate="2015-03-08T10:56:55.703" Score="1" Body="&lt;p&gt;As a mathematician interested in biology I am very curious about informed answers, here I add mine, with the understanding that it is in no way complete and it might be very biased or ignorant as concerns biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We may understand a cell as a chemical and physics based program which runs itself. The cell is a computational device in the sense that the outcomes of its activity are computable functions of its inputs (a reasonable hypothesis), but more than that: at the cell level there is no distinction between the computer, the program which runs on the computer, input and output data AND the execution of the program. All is at the same level, i.e. every abstraction is embodied in a concrete chemical or physical thing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This concreteness part adds, I believe to the difficulty, because the usual thinking in computer science is all about structuring abstractions, while in biology everything is ultimately at only one level: real, physics and chemistry embodied.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a claim which needs strong supporting evidence. Being a matter of principle, it cannot be proved rigorously, but it might be given a rigorous support by constructing simple proofs of principle models. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many computing models which are inspired by chemistry, therefore in return they can be seen as such proof of principles. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemical_reaction_network_theory&quot; rel=&quot;nofollow&quot;&gt;Chemical Reaction Networks and Petri Nets models&lt;/a&gt; which are more like structuring tools than real embodied models of computation, because they don't consider the structure of molecules (they are just nodes in a graph), nor the way chemical reactions happen (they are edges in a graph). They are very useful tools though and the description given here is very much simplified. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is the CHAM (chemical abstract machine), &lt;a href=&quot;http://hal-institut-mines-telecom.archives-ouvertes.fr/file/index/docid/75426/filename/RR-1133.pdf&quot; rel=&quot;nofollow&quot;&gt;G. Berry and G. Boudol. The chemical abstract machine. Theoretical Computer Science, 96(1):217–248, 1992&lt;/a&gt;. In this model states of the machine (imagine: a cell) &quot;are chemical solutions where floating molecules can interact according to reaction rules&quot; (cite from the abstract). In this model &quot;solution&quot; means a multiset of molecules, reaction rules are between molecules and they do not apply inside molecules. This is a limitation of the model because the structure of the molecule is not as important as the number of molecules in a species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another very interesting model is the &lt;a href=&quot;http://fontana.med.harvard.edu/www/Documents/WF/Papers/alchemy.pdf&quot; rel=&quot;nofollow&quot;&gt;Algorithmic Chemistry of Fontana and Buss&lt;/a&gt;. The main idea is that chemistry and computation are basically the same. The reasoning goes as following. There are two pillars of the rigorous notion of computation: the Turing Machine (well known) and Church's lambda calculus. Lambda calculus is less known outside computer science, but is a formalism which may be more helpful to chemists, or biologists even, than the Turing machine.  Fontana and Buss propose that lambda calculus is a kind of chemistry, in the sense that the its basic operations, namely abstraction and application, can be given chemical analogies. Molecules are like mathematical functions, abstractions are like reaction sites and applications are like chemical reactions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Algorithmic Chemistry is almost as closer as possible to be (proof of principle) answer to the question. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally I mention &lt;a href=&quot;https://chorasimilarity.github.io/chemlambda-gui/dynamic/demos.html&quot; rel=&quot;nofollow&quot;&gt;chemlambda&lt;/a&gt;, or the &lt;a href=&quot;http://mitpress.mit.edu/sites/default/files/titles/content/alife14/ch079.html&quot; rel=&quot;nofollow&quot;&gt;Chemical concrete machine&lt;/a&gt;, which is like Algorithmic Chemistry, but it is far more concrete. Molecules are graphs, applications and abstractions are molecules, chemical reactions are graph rewrites. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is very interesting in all these models, in my opinion, is that they suggest that answering to the question &quot;Can we understand a cell as an organic computational device?&quot; is somehow relevant to the Computer Science question &quot;How to design an asynchronous, decentralized Internet?&quot;.&lt;/p&gt;&#xA;" OwnerUserId="14830" LastEditorUserId="14830" LastEditDate="2015-03-08T11:24:16.383" LastActivityDate="2015-03-08T11:24:16.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30232" PostTypeId="2" ParentId="30203" CreationDate="2015-03-08T11:24:04.790" Score="3" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt; &#xA;&lt;br&gt;&lt;br&gt;&#xA;Optogenetics can be used to make cells responsive to light. One striking use of this technology is to restore vision in the blind by making the surviving neurons in the retina light-sensitive. This can be done by transfecting the retina with genetically engineered viruses that induce the expression of bacterial &lt;em&gt;channelrhodopsin&lt;/em&gt; proteins in retinal neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt; &#xA;&lt;strong&gt;Background&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will explain optogenetics by focusing on one of the most striking applications: to make the blind see. In humans light is sensed by &lt;strong&gt;photoreceptors&lt;/strong&gt; in the retina (&lt;a href=&quot;https://biology.stackexchange.com/questions/27833/parallels-between-pixelized-image-and-the-human-retina/27854#27854&quot;&gt;see further reading #2&lt;/a&gt;). Rods infer grey-scale vision (i.e., night vision), while cones provide color vision when there is enough light available. Rods and cones contain light-sensitive proteins: the &lt;strong&gt;photopigments&lt;/strong&gt;. The pigment in rod photoreceptors is called &lt;em&gt;rhodopsin&lt;/em&gt;, in cones they are referred to as cone pigments, which are used for color vision. When light hits the rods and cones, the photopigments catch the light and activate a cascade of second messenger reactions, eventually causing hyperpolarization of the membrane. This hyperpolarization in turn activates secondary neurons in the retina, which eventually carry the receptor signal to the brain, where it is processed and used to generate a visual percept. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Light sensing&lt;/strong&gt; across single-celled and multicellelar animals is mediated by two large families of proteins: the &lt;em&gt;opsins&lt;/em&gt;. Opsin genes are divided into two distinct superfamilies: microbial opsins (type I) and animal opsins (type II). The rohodpsin and cone pigments found in humans belong to type II. Among other differences, type I opsins are bound to ion channels, while type II is not. Type II opsins therefore need a battery of intracellular &lt;em&gt;second messenger&lt;/em&gt; molecules to operate. In contrast, the type I opsins, being channel proteins, directly cause intracellular changes by changing the membrane potential upon activation due to ion flow. Type I opsins, being channel proteins are referred to as &lt;strong&gt;channelrhodopsins&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In retinal degenerative diseases such as &lt;em&gt;retinitis pigmentosa&lt;/em&gt; (RP) the photoreceptors degenerate and patients eventually loose their vision. The secondary neurons in the retina, however, partly survive. As explained above, these secondary neurons are responsible for processing the photoreceptor signal and sending it to the optic nerve. Hence, although RP patients miss the photoreceptors, the rest of the visual pathway is ready to rock! Hence, somehow these neurons should be activated. There are a battery of approaches to do just this. Retinal implants activate the neurons directly by electrical activation (&lt;a href=&quot;https://cogsci.stackexchange.com/questions/9272/does-the-retina-encode-visual-information-like-a-bitmap-or-an-svg&quot;&gt;see further reading #3&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Optogenetics&lt;/strong&gt; (&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev-neuro-061010-113817&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fenno et al., 2013&lt;/a&gt;) is another approach where the secondary &lt;strong&gt;surviving neurons are made photosensitive&lt;/strong&gt;, thereby bypassing the photoreceptors by turning the secondary neurons into photoreceptors. The neurons are made photosensitive by making them express channelrhodospins. This is done by injecting a viral vector into the eye such that the virus infects the retinal cells. Instead of a viable virus, however, it is tinkered aound with and the only thing the virus does is incorporate the channelrhodopsin into the genome of the neurons, which start to express it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Channelrhodopsins&lt;/strong&gt; are cation channels, and therefore, upon light activation, they allow positively charged ions (notably Na&lt;sup&gt;+&lt;/sup&gt;, but also Ca&lt;sup&gt;+&lt;/sup&gt;) into the cell. This &lt;em&gt;depolarizes&lt;/em&gt; the neuron and can induce action potential firing (&lt;a href=&quot;https://biology.stackexchange.com/questions/91/how-do-the-brain-and-nerves-create-electrical-pulses/110#110&quot;&gt;see further reading #1&lt;/a&gt;). Action potentials is the neuron way of transmitting signals to the brain. Hence, by activating the secondary neurons through channelrhodopsin transformation, they start sending light-induced neural activity to the brain. The brain will handle this input as if evoked by photoreceptors and hence will interpret it as light-evoked visual stimuli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regard to cancer: It has been shown that expression of channelrhodopsin and illumination of whole-mice resulted in diminished subcutaneous cancer cell counts &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev-neuro-061010-113817&quot; rel=&quot;nofollow noreferrer&quot;&gt;(yang et al., 2013)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regard to your first added question: dependent on the exact peptide regulatory sequences added to the protein, or by using viral vectors specifically targeting axons, &lt;strong&gt;expression of channelrhodopsins can occur wherever one likes&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your second added question: Cation channels activate neurons, anion channels inhibit them. This means you can play around with different variants to control neurons at will. &#xA;&lt;br&gt;&#xA;&lt;br&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev-neuro-061010-113817&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fenno et al. &lt;em&gt;Annu Rev Neurosci&lt;/em&gt; 2011;34:389–412&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev-neuro-061010-113817&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yang et al. &lt;em&gt;Cell death and disease&lt;/em&gt; 2013;&lt;strong&gt;4&lt;/strong&gt;:e893&lt;/a&gt;&#xA;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Further reading&lt;/strong&gt;&lt;br&gt;&#xA; 1. Action potentials and neurons: &lt;a href=&quot;https://biology.stackexchange.com/questions/91/how-do-the-brain-and-nerves-create-electrical-pulses/110#110&quot;&gt;how-do-the-brain-and-nerves-create-electrical-pulses&lt;/a&gt;&lt;br&gt;&#xA; 2. Photoreceptors: &lt;a href=&quot;https://biology.stackexchange.com/questions/27833/parallels-between-pixelized-image-and-the-human-retina/27854#27854&quot;&gt;parallels-between-pixelized-image-and-the-human-retina&lt;/a&gt;&lt;br&gt;&#xA; 3. Retina and retinal implants: &lt;a href=&quot;https://cogsci.stackexchange.com/questions/9272/does-the-retina-encode-visual-information-like-a-bitmap-or-an-svg&quot;&gt;does-the-retina-encode-visual-information-like-a-bitmap-or-an-svg&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:56:15.910" LastActivityDate="2015-03-09T12:17:01.150" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30235" PostTypeId="2" ParentId="30229" CreationDate="2015-03-08T12:44:30.390" Score="12" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt; &#xA;&lt;br&gt;&lt;br&gt;&#xA;The exact mechanism behind tinnitus (ringing in the ear) is unknown. &#xA;&lt;br&gt;&lt;br&gt;&#xA;&lt;br&gt; &#xA;&lt;strong&gt;Background&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of the two theories you pose here, to the best of my knowledge the second one is the most widely accepted. It is a generally accepted phenomenon that whenever neural systems are being deprived of input, they start seeking new input, or even generate it themselves. For example, blind folks rarely have no visual perceptions at all. In contrast, they often perceive spontaneous visual sensations. For example, many blind folks report perceiving a persistent grayish background hue. In other words, it is never black in the eyes of a blind person. They also often see spontaneous spots of light. The most striking example, however, being &lt;em&gt;Charles Bonnet&lt;/em&gt; syndrome, where the blind person may perceive complex scenes with faces and objects &lt;a href=&quot;http://medind.nic.in/daa/t12/i2/daat12i2p423.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Bhatia et al., 2013)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of tinnitus, the perceived sounds are mostly not complex, but repetitive and simple in nature ('ringing', beeps etc.). It is thought that the deafferented auditory cortex actively starts generating sound perceptions. However, many other explanations have been brought forward, such as spontaneous activity in the hair cells in the cochlea and spontaneous activity in the auditory nerve fibers &lt;a href=&quot;http://synapse.koreamed.org/DOIx.php?id=10.3988/jcn.2009.5.1.11&amp;amp;vmode=FULL&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Luxon, 1993)&lt;/a&gt;. I will sum up a list of potential causes mentioned in &lt;a href=&quot;http://synapse.koreamed.org/DOIx.php?id=10.3988/jcn.2009.5.1.11&amp;amp;vmode=FULL&quot; rel=&quot;nofollow noreferrer&quot;&gt;Han et al. (2009)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Peripheral mechanisms&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(1) Spontaneous otoacoustic emissions&lt;/strong&gt;&lt;br&gt;&#xA;Spontaneous otoacoustic emissions (SOAEs) are small acoustic signals generated by the electromotile activity of outer hair cells (OHCs) in the cochlea. While normally inaudible, SOAEs may be perceived as tinnitus. Tinnitus due to SOAEs is mild and is more common in subjects with functional hearing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(2) Discordant theory&lt;/strong&gt;&lt;br&gt;&#xA;Tinnitus may be induced by the dysfunction of damaged OHCs while inner hair cells (IHCs) are still intact. For example, intense noise and ototoxic agents initially damage OHCs in the basal turn of the cochlea, and subsequently, if continued or repeated, affect IHCs, because IHCs are generally more resistant to such damage. IHCs are the receptor cells for sound transduction. In contrast, OHCs work as mechanical amplifiers, enhancing weak sounds by providing up to 50 dB, which can be evaluated by measuring OAEs. When OHCs die, cells in the dorsal cochlear nuclei (DCNs) show increased spontaneous activity due to the fact that IHC input is relatively normal, but OHCs input is decreased due to damage to the OHCs. This spontaneous activity is perceived as tinnitus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Spontaneous activity&lt;/em&gt; in neurons can occur through a host of mechanisms. Basically, a depolarization beyond a certain thresholds sets the neuron off to fire. In case of the disinhbited DCN neurons, the input from the OHCs is taken away. OHC input to the DCN is inhibitory,m as it is believed OHCs activate inhibitory interneurons. The exact mechanism is unknown, but a central inhibitory neurotransmitter is GABA. GABA can activate GABA-A receptors, that open up a Cl&lt;sup&gt;-&lt;/sup&gt; channel, which in turn leads to Cl&lt;sup&gt;-&lt;/sup&gt; influx into DCN neurons and hyperpolarization. When this input is taken away, you can imagine that DCN neurons depolarize and when this depolarization reaches threshold, the DCN neuron may increase firing &lt;a href=&quot;http://jn.physiology.org/content/88/2/699.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kaltenbach et al. &lt;em&gt;J Neurophys&lt;/em&gt; 2002;&lt;strong&gt;88&lt;/strong&gt;:699-714&lt;/a&gt;. Hence, as you question whether, in the absence of neurotransmitters, cells can fire action potentials, I say: **yes*. In fact, many neurons have spontaneous spiking activity, often with very regular frequency. These oscillating behaviors are often mediated by cation channels that gradually depolarize the cell up until its spiking threshold.     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(3) Crosstalk theory&lt;/strong&gt;&lt;br&gt;&#xA;Nerve compression (e.g., due to a tumor) may cause artificial synapses to be formed between nerve fibers of the cochlear and vestibular nerve  (crosstalk). The breakdown of the myelin insulation of the nerve fibers may further enhance coupling. Hence, spontaneous activity in the auditory nerve may be generated through vestibular activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Central mechanisms&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some patients may &lt;strong&gt;still perceive tinnitus after the auditory nerve is transected&lt;/strong&gt;. Hence, tinnitus in this subgroup must be caused by mechanisms located more centrally from the auditory nerve. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(4) Auditory plasticity theory&lt;/strong&gt;&lt;br&gt;&#xA;Damage to the cochlea enhances neural activity in the central auditory pathway, specifically in the temporal lobe in the auditory association cortex and inferior colliculus. This theory was touched upon further above in the first paragraph. Basically, when neural tissue is deafferented, it tends to look for new input or even generate activity &lt;em&gt;de novo&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(5) Somatosensory system&lt;/strong&gt;&lt;br&gt;&#xA;The activity of the DCN is also influenced by stimulation of nonauditory structures and the somatosensory system has been implicated in development of tinnitus. Somatic tinnitus can develop as somtaosensory input may disinhibit the DCN.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;(6) Limbic and autonomic nervous systems&lt;/strong&gt;&lt;br&gt;&#xA;The aforementioned theories cannot explain why some people suffer from tinnitus while others do not. More than 80% of those perceiving tinnitus for the first time do not associate the sound with any negative meaning and experience spontaneous habituation. However, if the first perception of tinnitus induces high levels of annoyance or anxiety by association with unpleasant stimuli or with periods of stress and anxiety, tinnitus might develop into a problem. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&#xA;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://medind.nic.in/daa/t12/i2/daat12i2p423.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bhatia et al. &lt;em&gt;Delhi Psych&lt;/em&gt; J 2012;&lt;strong&gt;15&lt;/strong&gt;:423-4&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://synapse.koreamed.org/DOIx.php?id=10.3988/jcn.2009.5.1.11&amp;amp;vmode=FULL&quot; rel=&quot;nofollow noreferrer&quot;&gt;Han et al. &lt;em&gt;J Clin Neurol&lt;/em&gt; 2009;&lt;strong&gt;5&lt;/strong&gt;:11-9&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://jn.physiology.org/content/88/2/699.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kaltenbach et al. &lt;em&gt;J Neurophys&lt;/em&gt; 2002;&lt;strong&gt;88&lt;/strong&gt;:699-714&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.bmj.com/content/bmj/306/6891/1490.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Luxon, &lt;em&gt;BMJ&lt;/em&gt; 1993; &lt;strong&gt;306&lt;/strong&gt;:1490-1&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;Further reading&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; Action potentials in the absence of neurotransmitters: &lt;a href=&quot;https://biology.stackexchange.com/questions/30203/how-does-optogenetics-work&quot;&gt;how-does-optogenetics-work&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-08-19T06:26:50.037" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30237" PostTypeId="1" CreationDate="2015-03-08T14:33:35.453" Score="1" ViewCount="52" Body="&lt;p&gt;I am running &lt;a href=&quot;https://dna.five3genomics.com/paradigm/&quot; rel=&quot;nofollow&quot; title=&quot;Paradigm&quot;&gt;Paradigm&lt;/a&gt; on a matrix of mRNA expression. I read &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Vaske, Charles J., et al. &quot;Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.&quot; Bioinformatics 26.12 (2010): i237-i245.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and also the help section in the web application. However it is not defined which format is best-suited for mRNA expression. Using log$_2$-ratios instead of log$_2$ data format gave me different results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="3466" LastEditorUserId="3466" LastEditDate="2015-03-10T14:18:56.877" LastActivityDate="2015-03-10T14:18:56.877" Title="Which data format for mRNA expression matrix is necessary to run pathway analysis with Paradigm?" Tags="&lt;gene-expression&gt;&lt;mrna&gt;&lt;data&gt;&lt;pathway&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30238" PostTypeId="1" CreationDate="2015-03-08T16:01:18.580" Score="2" ViewCount="71" Body="&lt;p&gt;Based on my search online, I have found some theories which try to validate the activity of some birds (like pigeons) which involves moving their heads and neck while walking. These theories include - Assistance with balance, Providing depth perception, Sharpening their vision. Also, most of the studies state that similar to our eye movement, they need to move their heads along with their eyes to stabilize their surroundings visually.&#xA;If the above mentioned hypothesis is true, then how do some birds which do not move their heads while walking, manage to visually stabilize their surroundings and balance themselves?&lt;/p&gt;&#xA;" OwnerUserId="14500" LastEditorUserId="9943" LastEditDate="2015-03-09T10:48:27.940" LastActivityDate="2015-03-09T22:59:17.417" Title="How do parrots stabilize their field of view without moving their necks while walking?" Tags="&lt;vision&gt;&lt;ornithology&gt;" AnswerCount="0" CommentCount="5" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30239" PostTypeId="1" AcceptedAnswerId="30248" CreationDate="2015-03-08T16:09:56.270" Score="2" ViewCount="139" Body="&lt;p&gt;Is there any in silico analysis method to predict post-translational modification sites on a given protein? &lt;/p&gt;&#xA;" OwnerUserId="3657" LastActivityDate="2015-03-08T20:53:24.927" Title="Protein PTM site prediction" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30240" PostTypeId="1" CreationDate="2015-03-08T16:32:54.677" Score="10" ViewCount="535" Body="&lt;p&gt;Some of us are involved in the &lt;a href=&quot;https://folding.stanford.edu/&quot; rel=&quot;nofollow noreferrer&quot;&gt;folding@home&lt;/a&gt; project, spending time, money, and resources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know the answer to two main questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;How do we know we fold it right? I mean, these models used in folding calculations. Is it probable that in a decade we will find that all these results are nil and void?&lt;/li&gt;&#xA;&lt;li&gt;Do we have any example that these calculations were practically applied anywhere?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="14833" LastEditorUserId="3553" LastEditDate="2017-02-27T04:43:19.553" LastActivityDate="2017-02-27T04:43:19.553" Title="How do we know if the folding@home project results are right?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;protein-binding&gt;&lt;protein-folding&gt;&lt;protein-engineering&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30241" PostTypeId="1" AcceptedAnswerId="30280" CreationDate="2015-03-08T16:39:13.897" Score="3" ViewCount="100" Body="&lt;p&gt;I was reading an article in nature : &lt;a href=&quot;http://www.nature.com/nature/journal/v518/n7539/full/518314a.html&quot; rel=&quot;nofollow&quot;&gt;Epigenomics: Roadmap for regulation&lt;/a&gt; and was confused by the definition or/and interpretation of enhancers.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Enhancers are activated through interactions with transcription&#xA;  factors, which recognize and bind to specific DNA sequences within the&#xA;  enhancer region. Bound transcription factors recruit co-regulators,&#xA;  many of which deposit or remove modifications on histones. […]&#xA;  Enhancers that are active in cell-type-specific epigenomic signatures&#xA;  are typically highly enriched in DNA sequences to which&#xA;  lineage-determining and signal-dependent transcription factors bind.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As far as I know enhancers are the DNA sequences to which TFs bind, and then everything including co-activators complexes bind to basal TFs on the promoter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am confused by the last line:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Enhancers that are active in cell-type-specific epigenomic signatures&#xA;  are typically highly enriched in DNA sequences to which&#xA;  lineage-determining and signal-dependent transcription factors bind.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They state, that in DNA sequences to which TFs bind the active enhancers are highly enriched. For me it sounds strange because the definition of enhancers says that these are the DNA sequences to which TFs bind. &lt;em&gt;And of course enhancers are enriched there because otherwise they would not be called enhancers.&lt;/em&gt; As for me they are trying to say that active enhancers (by definition TFs bind to them) are highly enriched in enhancers region to which TFs bind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it make sense or not?&lt;/p&gt;&#xA;" OwnerUserId="14834" LastEditorUserId="3340" LastEditDate="2015-03-09T04:14:10.250" LastActivityDate="2015-03-10T05:16:32.503" Title="enhancers in cell-type-specific signatures" Tags="&lt;gene-regulation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30242" PostTypeId="1" AcceptedAnswerId="30988" CreationDate="2015-03-08T16:46:49.563" Score="5" ViewCount="176" Body="&lt;p&gt;From what I understand, only the oligodendrocytes are affected in multiple sclerosis, and they are attacked by T cells which cross the blood-brain barrier. This leads me to two questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;How is the blood-brain barrier affected in MS that allows T lymphocytes to cross the barrier?&lt;/li&gt;&#xA;&lt;li&gt;Why do the T lymphocytes attack the oligodendroccytes? And when they do, what is the mechanism for de-myelination?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance!&lt;/p&gt;&#xA;" OwnerUserId="6136" LastActivityDate="2015-04-02T10:25:18.367" Title="How does de-myelination occur in multiple sclerosis?" Tags="&lt;genetics&gt;&lt;brain&gt;&lt;autoimmune&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30243" PostTypeId="2" ParentId="30241" CreationDate="2015-03-08T17:16:18.993" Score="2" Body="&lt;p&gt;Enhancer is a just a term for a regulatory region distant from a gene that contains specific sites where transcription factors bind. As it happens, a single enhancer can contain DNA binding sites for multiple transcription factors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, an enhancer called TESCO, which regulates a gene called &lt;em&gt;SOX9&lt;/em&gt; (involved in sex determination) has binding sites for many different proteins (confirmed or putative): SRY, SF1, SOX9, ESR1, FOXL2 and likely many more that I haven't heard of. This allows complex regulation of &lt;em&gt;SOX9&lt;/em&gt; through protein-protein interactions. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-03-09T05:39:42.083" LastActivityDate="2015-03-09T05:39:42.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30244" PostTypeId="2" ParentId="30240" CreationDate="2015-03-08T17:41:05.540" Score="6" Body="&lt;p&gt;&lt;em&gt;in silico&lt;/em&gt; modelling of anything in biology is an active field of research. It's very useful for making predictions and developing hypotheses, but any findings need to be confirmed experimentally.&lt;/p&gt;&#xA;&lt;p&gt;From the &lt;a href=&quot;http://folding.stanford.edu/home/the-science%23ntoc7&quot; rel=&quot;nofollow noreferrer&quot;&gt;Folding@Home&lt;/a&gt; website:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Folding@home has been a success. In 2000-2001, we folded several small and fast folding proteins with experimental validation of our method. We are now working to further develop our method, and to apply it to more complex and interesting proteins and protein folding and misfolding questions. Since then (2002-2006), Folding@home has studied more complex proteins, reporting on the folding of many proteins on the microsecond timescale, including BBA5, the villin headpiece, Trp Cage, among others. In 2007, we crossed the millisecond milestone by simulating a protein called NTL9, and the 10 millisecond barrier in 2010 with ACBP.&lt;/p&gt;&#xA;&lt;p&gt;More recently (2006-present), we have been putting a great deal of effort into studying proteins relevant for diseases, such as Alzheimer’s and Hunntington’s Disease. You can learn more about our results and peer-reviewed scientific achievements on our Papers Page.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;As they say, you should check out their &lt;a href=&quot;http://folding.stanford.edu/home/papers&quot; rel=&quot;nofollow noreferrer&quot;&gt;research contributions&lt;/a&gt; for how it's being practically applied.&lt;/p&gt;&#xA;&lt;p&gt;You may also be interest in this article for the science behind and prospects of protein folding prediction: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042729/pdf/nihms-249590.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bowman GR, Voelz VA, Pande VS. 2011. Taming the complexity of protein folding. Curr Opin Struct Biol 21(1):4-11&lt;/a&gt;. At least try reading the conclusion for a less technical overview.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-08T23:28:27.147" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30246" PostTypeId="2" ParentId="30080" CreationDate="2015-03-08T19:04:00.040" Score="3" Body="&lt;p&gt;Though &lt;em&gt;Escherichia coli&lt;/em&gt; has only one &lt;a href=&quot;https://en.wikipedia.org/wiki/Origin_of_replication&quot; rel=&quot;nofollow noreferrer&quot;&gt;origin of replication&lt;/a&gt; (oriC), replication proceeds in both directions from it. Thus, based on your calculations, DNA replication takes 40 minutes (which is still too long if the doubling time is 30 minutes). The solution is to start replication again before the previous round has completed, and here's some research which shows just that:&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC300381/pdf/pnas00184-0111.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yoshikawa H, O'Sulliven A, Sueoka N. 1964. Sequential replication of the &lt;em&gt;Bacillus subtilis&lt;/em&gt; chromosome. Prod Nat Acad Sci 52:973-980&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Obviously, dichotomous replication is advantageous for bacterial growth because the bacteria can replicate chromosomes faster than by having one replication point. With one replication point, the replication time, and consequently the cell generation time, would be limited by the maximal rate of DNA polymerase.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/4866337/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cooper S, Helmstetter CE. 1968. Chromosome replication and the division cycle of Escherichia coli B/r. J Mol Bio 31(3):519-540&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;…cells growing faster than 40 minutes per doubling must initiate new replication points prior to the completion of DNA synthesis at the previous points; in other words, there should be multiple forks.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1166998/pdf/emboj00170-0290.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Skarstad K, Boye E, Steen HB. 1986. Timing of initiation of chromosome replication in individual Escherichia coli cells. EMBO J 5(7):1711-1717 &lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In rapidly growing cultures, with parallel replication of several chromosomes, cells will end up with 2n (n = 1, 2, 3) chromosomes if initiation occurs simultaneously at all origins. A culture with asynchronous initiation may in addition contain cells with irregular numbers (not equal to 2n) of chromosomes. The frequency of cells with irregular numbers of chromosomes is a measure of the degree of asynchrony of initiation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2063475/pdf/7601871a.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fossum S, Crooke E, Skarstad K. 2007. Organization of sister origins and replisomes during multifork DNA replication in Escherichia coli. EMBO J 26(21):4514-4522&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;…initiation occurs at two origins in the ‘mother' cell. It can even occur in the ‘grandmother' cell at four origins if the time it takes to replicate and segregate the chromosome exceeds two generations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kCc8e.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gSILA.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This last image is interesting because you actually see the multiple replication origins in single cells by fluorescence microscopy. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2017-12-15T22:52:44.033" LastActivityDate="2017-12-15T22:52:44.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30248" PostTypeId="2" ParentId="30239" CreationDate="2015-03-08T20:53:24.927" Score="3" Body="&lt;p&gt;There are actually a lot of these sites available, I have used some of the one listed below. Additionally there are some huge list of other services available in this field from ExPASy, you can find it &lt;a href=&quot;http://www.expasy.org/proteomics&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and the Center for Biological Sequence Analysis, which can be found &lt;a href=&quot;http://www.cbs.dtu.dk/researchgroups/PTM.php&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://web.expasy.org/findmod/&quot; rel=&quot;nofollow&quot;&gt;ExPASy - FindMod&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://elm.eu.org/&quot; rel=&quot;nofollow&quot;&gt;The Eukaryote Linear Motif resource for Functional Sites in Proteins&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.phosida.com/&quot; rel=&quot;nofollow&quot;&gt;Phosida&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-03-08T20:53:24.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30251" PostTypeId="2" ParentId="30240" CreationDate="2015-03-08T23:07:22.163" Score="1" Body="&lt;p&gt;A certain fold of a peptide string can be validated or ruled out if other experimental data is available. Some other techniques to infer protein structure are &lt;a href=&quot;http://en.wikipedia.org/wiki/X-ray_crystallography&quot; rel=&quot;nofollow&quot;&gt;X-ray crystallography&lt;/a&gt; (requires pure protein that will crystallize) and &lt;a href=&quot;http://en.wikipedia.org/wiki/Single_particle_analysis&quot; rel=&quot;nofollow&quot;&gt;single particle analysis&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="14698" LastActivityDate="2015-03-08T23:07:22.163" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30252" PostTypeId="1" CreationDate="2015-03-09T00:14:01.000" Score="2" ViewCount="651" Body="&lt;p&gt;For example I know it is produced in Potato's and fruits and its purpose is to synthesize glucose in to starch through polymerization. But why is it only present in some cells? Is it only present in cells with higher glucose content?  &lt;/p&gt;&#xA;" OwnerUserId="14745" LastActivityDate="2017-02-20T08:04:46.257" Title="Why is amyloplast produced by some plant cells but not other cells?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30253" PostTypeId="2" ParentId="9419" CreationDate="2015-03-09T03:22:37.077" Score="12" Body="&lt;p&gt;Well there is the common Bloodworm (Glycera dibranchiata)which people use for fishing bait. The animals are unique in that they contain a lot of copper without being poisoned. Their jaws are unusually strong since they too contain the metal in the form of a copper-based chloride biomineral, known as atacamite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencemag.org/content/298/5592/389.long&quot;&gt;http://www.sciencemag.org/content/298/5592/389.long&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And unlike the clamworm (Nereis limbata), whose jaws contain the metal zinc, the copper in the mineral in the jaws of Glycera is actually present in its crystalline form.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/cgi/pmidlookup?view=long&amp;amp;pmid=12886017&quot;&gt;http://www.pnas.org/cgi/pmidlookup?view=long&amp;amp;pmid=12886017&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is theorized that this copper is used as a catalyst for its poisonous bite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I got this from Wikipedia)&lt;/p&gt;&#xA;" OwnerUserId="14839" LastActivityDate="2015-03-09T03:22:37.077" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30254" PostTypeId="1" CreationDate="2015-03-09T03:49:37.190" Score="3" ViewCount="236" Body="&lt;p&gt;I have been asked this questions by many biology students and even non-biologist without a pretty straightforward answer to give. We are quite accustomed to phylogenetic trees where a common ancestor becomes two different species and these new species become, each one, two more. But, Why is not possible that a species might divide in three different species? Or four? Or more?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What arguments support this conception of the evolutionary process? Also, if somebody has a good article explaining this, please provide me with the link or citation so I can refer my fellow biology students to it.&lt;/p&gt;&#xA;" OwnerUserId="13373" LastEditorUserId="3340" LastEditDate="2015-03-09T04:15:25.963" LastActivityDate="2015-03-09T08:10:02.793" Title="What proves that speciation is a pairwise process?" Tags="&lt;evolution&gt;&lt;phylogenetics&gt;&lt;speciation&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ClosedDate="2015-03-10T13:49:10.060" ContentLicense="CC BY-SA 3.0" />
  <row Id="30255" PostTypeId="2" ParentId="30254" CreationDate="2015-03-09T04:37:15.430" Score="2" Body="&lt;p&gt;It is not impossible that a species can give rise to more than two lineages simultaneously, but it is just highly unlikely in certain cases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you assume that a point mutation in the DNA gives rise to a lineage then the number of two different mutations happening simultaneously (in two different individuals from the population) and also getting fixed, would be low for a small population. In any case a single DNA won't give rise to two different mutants. However this number would increase with increase in population size. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In such cases (small population) two separate events can be assumed rather than a single event that gives rise to two mutants. However, if the time difference between the occurrence of these two events cannot be determined (or it is too small compared to other timescales) then a single event can be assumed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phylogenetic trees can have nodes with multiple branches if the distance between all of them is the same (as in the abovementioned example; the distance between all of them is 1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I think it can be said that the likelihood of simultaneous formation of multiple lineage increases with population size. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-09T08:10:02.793" LastActivityDate="2015-03-09T08:10:02.793" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30256" PostTypeId="1" CreationDate="2015-03-09T05:36:39.523" Score="2" ViewCount="78" Body="&lt;p&gt;with respect to the paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23552990&quot; rel=&quot;nofollow&quot;&gt;Adaptive reconfiguration of the human NK-cell compartment in response to cytomegalovirus: A different perspective of the host-pathogen interaction&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is meant by NK-cells compartment?&lt;br&gt; I searched Google but couldn't find a proper text that would help me understand what it means.. Google search shows papers which has this term, but I need to understand what it means before reading the paper. Please help.&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="3340" LastEditDate="2015-03-09T05:42:48.923" LastActivityDate="2015-03-09T05:42:48.923" Title="What is NK-cell compartments?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;immunology&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30257" PostTypeId="2" ParentId="30254" CreationDate="2015-03-09T06:33:37.767" Score="4" Body="&lt;p&gt;I offer this perspective in addition to what WYSIWYG has provided.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phylogenetic trees are tools to &lt;em&gt;model&lt;/em&gt; what has actually happened, or what some evidence &lt;em&gt;implies&lt;/em&gt; has happened, to a population of entities that exchange genetic material. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These models fail, for instance, when describing the phenomenon of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842723/&quot; rel=&quot;nofollow&quot;&gt;horizontal gene transfer&lt;/a&gt; since a tree is acyclic by &lt;a href=&quot;http://en.wikipedia.org/wiki/Tree_(graph_theory)&quot; rel=&quot;nofollow&quot;&gt;definition&lt;/a&gt;. Consider a viral genome that has integrated into a host genome. The host now contains DNA from its ancestral lineage and the viral lineage. This process cannot be modeled by a tree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some founder population that is susceptible to exogenous genetic transformation may give rise to many distinct lineages, some of which your species concept may qualify as &quot;new&quot; species.&lt;/p&gt;&#xA;" OwnerUserId="14609" LastActivityDate="2015-03-09T06:33:37.767" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30258" PostTypeId="1" AcceptedAnswerId="30287" CreationDate="2015-03-09T08:20:23.963" Score="8" ViewCount="2380" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;A &lt;a href=&quot;http://en.wikipedia.org/wiki/Living_fossil&quot;&gt;living fossil&lt;/a&gt; is a living species (or clade) that&#xA;  appears to be similar to another species otherwise known only from fossils,&#xA;  typically with no close living relatives.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A living fossil is considered as a successful organism, which has made its way through many  major &lt;a href=&quot;http://en.wikipedia.org/wiki/Extinction_event&quot;&gt;extinction events&lt;/a&gt;. Also, the morphology of living fossils resemble some species of organisms which we know only through their fossil remains.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;What is the reason for a particular type of species to become a living fossil; is the engineering of this particular species extraordinary, in that it can survive any selection process encountered thus far?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is there not enough selection pressure exerted on this species in order to force it to change morphologically?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Have these organisms modified themselves, so that currently their morphology seems to be similar to a fossil organism?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="3340" LastEditDate="2015-03-09T14:01:27.477" LastActivityDate="2015-03-10T08:54:33.900" Title="Reasons why living fossils exist?" Tags="&lt;evolution&gt;&lt;species&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30259" PostTypeId="1" CreationDate="2015-03-09T09:43:49.247" Score="4" ViewCount="1001" Body="&lt;p&gt;Trans fats cause health problems, especially to the heart.  &lt;a href=&quot;https://en.wikipedia.org/wiki/Trans_fat#Health_risks&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Trans_fat#Health_risks&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My guess is that all effects happen because trans-fats are inherently toxic as the body never evolved to process them. But then L-glucose has no harmful effects, even if it cannot be digested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how are trans-fats processed in the body differently, and where does all the harm happen?&lt;/p&gt;&#xA;" OwnerUserId="9418" LastEditorUserId="9943" LastEditDate="2015-03-09T12:34:45.507" LastActivityDate="2015-03-09T12:34:45.507" Title="What do trans-fats do when in human body?" Tags="&lt;human-biology&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30260" PostTypeId="1" CreationDate="2015-03-09T10:25:01.867" Score="2" ViewCount="82" Body="&lt;p&gt;I have followed the David Attenborough series on 'First life' and heard, that an increase in the amount of oxygen in the atmosphere, as it took place just before the Cambrium, is generally favorable for life and also enables the evolution of larger organisms. &#xA;Why is that so? Is it because aerobic respiration had a better conversion rate to energy?&lt;/p&gt;&#xA;" OwnerUserId="14841" LastEditorUserId="14709" LastEditDate="2015-03-09T12:05:22.530" LastActivityDate="2015-06-08T00:42:40.150" Title="Why is an increase in the amount of oxygen in the atmosphere favorable for life?" Tags="&lt;evolution&gt;&lt;respiration&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30262" PostTypeId="1" CreationDate="2015-03-09T11:14:15.187" Score="20" ViewCount="6242" Body="&lt;p&gt;Humans have the ABO and Rhesus blood typing systems. I have two questions about it:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why have we evolved these blood types?&lt;/li&gt;&#xA;&lt;li&gt;Do other animals have different blood types as well?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="14843" LastEditorUserId="22057" LastEditDate="2018-01-05T13:09:40.443" LastActivityDate="2018-01-05T13:09:40.443" Title="Do animals other than humans have different blood types?" Tags="&lt;zoology&gt;&lt;molecular-genetics&gt;&lt;hematology&gt;&lt;molecular-evolution&gt;&lt;red-blood-cell&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30263" PostTypeId="2" ParentId="30259" CreationDate="2015-03-09T12:01:09.767" Score="4" Body="&lt;p&gt;In Ascherio &amp;amp; Willen (1997) it is mentioned that, and I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] Trans fatty acids increase plasma concentrations of low-density lipoprotein (LDL)&#xA;  cholesterol and reduce concentrations of high-density lipoprotein (HDL) cholesterol relative to the parent natural fat. [...] &lt;strong&gt;[T]rans fatty acids increased the plasma ratio of total to HDL cholesterol nearly twofold compared with saturated fats&lt;/strong&gt;. On the basis of these metabolic effects and the known relation of blood lipid concentrations to risk of coronary artery disease, we estimate conservatively that 30 000 premature deaths/y in the United States are attributable to consumption of trans fatty acids. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The US &lt;a href=&quot;http://www.heartfoundation.org.au/healthy-eating/fats/Pages/trans-fats.aspx&quot; rel=&quot;nofollow&quot;&gt;Heart Foundation&lt;/a&gt; explains in more layman's terms the same principles:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Trans fat is a type of unsaturated fat that behaves like a saturated fat because of its chemical structure. It increases our risk of heart disease by increasing the “bad” LDL cholesterol, while also lowering the “good” HDL cholesterol in our blood.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And from the &lt;a href=&quot;http://www.betterhealth.vic.gov.au/bhcv2/bhcarticles.nsf/pages/Cholesterol_explained?open&quot; rel=&quot;nofollow&quot;&gt;Better Health Channel Australia&lt;/a&gt; we learn why LDL is 'bad':&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Too much cholesterol circulating within LDL in our bloodstream leads to fatty deposits developing in the arteries. This causes the vessels to narrow and they can eventually become blocked. This can lead to heart disease and stroke.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;Ascherio &amp;amp; Willen, &lt;em&gt;Am J Clin Nutr&lt;/em&gt; 1997;&lt;strong&gt;66&lt;/strong&gt;(suppl):1006S-lOS.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-09T12:07:35.010" LastActivityDate="2015-03-09T12:07:35.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30264" PostTypeId="1" CreationDate="2015-03-09T12:58:00.333" Score="2" ViewCount="693" Body="&lt;p&gt;What could be the reason for a difference in color perception between the two eyes of an adult individual without any known eye conditions? In particular, a difference in the perceived color temperature in each individual eye and an average of the two when looking through both eyes.&lt;/p&gt;&#xA;" OwnerUserId="14846" LastEditorUserId="14846" LastEditDate="2015-03-09T15:29:29.237" LastActivityDate="2015-03-09T15:29:29.237" Title="Reason for different color perception in left/right eyes?" Tags="&lt;human-eye&gt;&lt;perception&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30265" PostTypeId="2" ParentId="30214" CreationDate="2015-03-09T13:00:08.267" Score="2" Body="&lt;p&gt;A relatively simple proto-eye is the &lt;strong&gt;pineal gland&lt;/strong&gt;. It has been considered to be the third eye and it is involved in circadian rhythms in man, it is involved in thermo regulation, and in reptiles and amfibians it is in fact directly light-sensitive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it is not an eye as such, because the pineal does not convey topographical information about the environment to the brain. It is more of a light sensor in reptiles and amfibians. However, it is a sensor &lt;strong&gt;embedded in the central nervous system&lt;/strong&gt; of higher organisms including humans. As such, it is &lt;em&gt;not just a light sensor&lt;/em&gt;, but an &lt;strong&gt;endocrinic organ involved in the light-based entrain of endogenous circadian clocks&lt;/strong&gt; present in various organs. It has been implicated to be an integral part of the visual system in early life:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cnytl.png&quot; alt=&quot;pineal&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;hypothetic four-eyed protovertebrate. Source: &lt;a href=&quot;http://www.hh.um.es/Abstracts/Vol_17/17_2/17_2_555.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Vigh et al., 2002&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hypothetical system in the picture is not so much different from the lancet fish today, a 'living fossil'. In early life, and reptiles and amfibians today, the pineal is directly light-sensitive and thereby entrains the circadian clock directly via endocrinic functions. Synchronizing the circadian clock helps organisms to adapt to the environmental light periods, in other words prepare diurnal creatures to wake up in the morning and get ready to hunt etc. Hence it aids survival of various species in different biotopes (&lt;a href=&quot;http://www.hh.um.es/Abstracts/Vol_17/17_2/17_2_555.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Vigh et al., 2002&lt;/a&gt;). In humans and other mammals with a dense, solid skull light-sensng is taken over by the retina, as the skull prevents admission of light. Here the pineal has only an endocrinic function receiving afferent input from the eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;Vigh et al., &lt;em&gt;Histol Histopathol&lt;/em&gt; 2002;&lt;strong&gt;17&lt;/strong&gt;:555-90&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-09T13:34:38.163" LastActivityDate="2015-03-09T13:34:38.163" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30266" PostTypeId="2" ParentId="30203" CreationDate="2015-03-09T13:34:33.593" Score="2" Body="&lt;p&gt;Addition to the previous answer.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How to express channelrhodopsins in neurons?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Other than the method involving direct viral injection, as described in the previous answer, these proteins can be expressed in specific cells by making transgenics (by using promoters that will express the downstream gene in only specific cells).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How does it work?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;When a neuron is made light sensitive by ectopic expression of channel-rhodopsins, then they can be made to &quot;fire&quot; (generate &lt;a href=&quot;http://en.wikipedia.org/wiki/Action_potential&quot; rel=&quot;nofollow noreferrer&quot;&gt;action potential&lt;/a&gt;) by simple illumination. Fibre optics are used to illuminate specific neurons in the brain. See the image below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/xYUhO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Are the light-sensitive molecules (which I now have read are&#xA;  channelrhodopsins) present all along the axolemma…&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They would be expressed everywhere but their expression on the axons can be limited because of myelination. It is possible to make certain proteins express in the dendritic region. This requires localization signals called zipcodes (this process is still not understood very well).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How then can these channels work, if any cation can diffuse any way through the channel?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Chr2 can conduct Na&lt;sup&gt;+&lt;/sup&gt;, Ca&lt;sup&gt;2+&lt;/sup&gt; and K&lt;sup&gt;+&lt;/sup&gt;. Its conductivity for sodium is higher than that for potassium. When the channels open the higher inward flow of sodium would trigger action potential (AP). Moreover Calcium also helps in strengthening the AP. Though the channel can conduct Li&lt;sup&gt;+&lt;/sup&gt;, the ion is not present in the extracellular fluid. Usually the nonspecific channels are not used.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Also, I was wondering whether the principle behind optogenetics-&#xA;  controlling calls with light- could be used for other treatments e.g.&#xA;  to kill cancer cells?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Light (as lasers) is used for killing cancer cells but it does not involve optogenetic techniques. You would need to genetically modify the cancer cell first. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-09T13:41:15.760" LastActivityDate="2015-03-09T13:41:15.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30267" PostTypeId="1" CreationDate="2015-03-09T13:41:40.120" Score="9" ViewCount="350" Body="&lt;p&gt;Suppose I have a genotype-phenotype map defined by the matrix $\mathbf{Z}$:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/nRMGc.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The scalars $G,P$ represent the number of genotypes and traits, respectively. The map assigns a set of phenotypic traits (the columns) to a set of genotypes (the rows), where $z_{ij}$ is the quantitative measure of an individual of genotype $i$ with respect to a trait $j$. I want to know how the average value of each of the phenotypic traits changes over time, suggesting I should use quantitative genetics theory and formulate the equation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\Delta \bar{\boldsymbol{z}} = \mathbf{G}\mathbf{P}^{-1}\mathbf{s}$,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where, $\mathbf{G}$ is the additive genetic variance covariance matrix, $\mathbf{P}$ is the phenotypic variance covariance matrix, and $\mathbf{s}$ is a vector of covariances of each trait with fitness. Assume that I know the frequencies of the different genotypes in the population. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question 1&lt;/strong&gt; Can I formulate the additive genetic variance-covariance matrix from the genotype-phenotype map alone (and pop freq)? Note, I don't know anything about the underlying genetic model - number of loci representing each genotype, dominance structure, epistatic interactions, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question 2&lt;/strong&gt; If I assume the genotypes represent haploid individuals, does this change things? Is the additive genetic variance always equal to the phenotypic variance (assuming no environmental effects) in a haploid model? In other words does $\mathbf{G}\mathbf{P}^{-1} = \mathbf{I}$? What I'm thinking is that epistatic variance might affect things, but it shouldn't affect heritability in a haploid model, which is what $\mathbf{G}\mathbf{P}^{-1}$ is a measure of. &lt;/p&gt;&#xA;" OwnerUserId="14849" LastEditorUserId="3340" LastEditDate="2015-03-09T13:51:53.317" LastActivityDate="2015-04-13T15:12:06.577" Title="Genotype to phenotype map and the G-matrix" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30268" PostTypeId="2" ParentId="30218" CreationDate="2015-03-09T14:24:09.643" Score="6" Body="&lt;p&gt;RNA-seq data usually provides a snapshot in time of the transcriptome of that which is being sequenced. Single-cell sequencing is possible, but less common than RNA-seq on a sample (containing many cells). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are correct that RNA-seq provides one with knowledge of RNA sequences, like AUGGUCAUCAG and so on. However, one will not necessarily have information about &lt;em&gt;all possible&lt;/em&gt; RNA sequences from a particular species. Performing RNA-seq on the same cell type of a species at two different time points, or two different cell types at the same time point, may result in different profiles for the RNA sequences you get back. It depends on which parts of the genome are being &lt;em&gt;expressed&lt;/em&gt; by the cells in a sample at the time of RNA extraction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The data one gets back from RNA sequencing depends on the technology and company used. Typically, RNA-seq involves using a reverse transcription step so that the sequence data you get back is actually reported as the cDNA version of your original mRNA transcripts. Usually one gets a (very large) file of sequencing 'reads'. One can either then 'assemble' these directly to form a snapshot of the transcriptome or one can map them to a known reference genome. One of the main benefits of RNA-seq is that we learn not just what the sequences of the RNA molecules are, but also their relative abundances within the sample. Knowledge of this can be particularly useful in testing or developing a large range of biological hypotheses. &lt;/p&gt;&#xA;" OwnerUserId="14849" LastActivityDate="2015-03-09T14:24:09.643" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30269" PostTypeId="2" ParentId="30258" CreationDate="2015-03-09T14:30:21.933" Score="7" Body="&lt;p&gt;&lt;strong&gt;TL;DR:&lt;/strong&gt; Living fossils are the children of long-dead fossilised creatures that were good at being alike, other animals are the children that were good at being different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The boring answer is that living fossils are around because nothing has happened to make them go extinct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The more exciting answer is a tale of intrigue and lies stretching back hundreds of millions of years:&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;The lie that is the 'species'&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The notion of a species is, of course, a lie. It's a useful lie, and one without which the equally useful field of taxonomy would be impossible, but a lie all the same. Every living thing is ultimately a unique individual unto itself. We group these individuals up and call them things, according to things that are more or less arbitrary, and we arrange these groups into bigger groups and fill books upon books with this method, because it makes it super easy to get a good overview of how life developed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if we want to understand the details, we have to see past species, and look at the lineages.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;The shark, our ancestor&lt;sup&gt;1&lt;/sup&gt;&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;One such lineage that is of interest is that of the shark. Sharks are &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Shark#Evolution&quot;&gt;ancient&lt;/a&gt;&lt;/em&gt;: They are roughly as old as plants, and older than almost all land fauna. They are vicious, unrelenting killing machines, and all but perfectly suited for being this, with their sleek shape, their conveyor belts of teeth, and rough skin. At some point way back when, however, the lineage of sharks split in two: One branch that leads to fish, amphibians and eventually dinosaurs, squirrels and dolphins, and one that leads to sharks. The forebear to all these things were the &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_fish#Jawed_fish&quot;&gt;early cartilaginous fish of the Cambrian ocean&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer the question as posed, we have to compare the success factors of the two lineages.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Why sharks are still around as living fossils&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The real answer here is that, in a very real sense, they aren't. Modern sharks are no more alike their long-dead forebears than squirrels are. However, the biological niche inhabited by sharks (apex predator) is a successful one, and sharks, already existing in this niche, have had successful children, made more successful by being superficially and behaviourally &lt;em&gt;alike&lt;/em&gt; to their parents, and so, the modern shark presents as a living fossil.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Why shark contemporaries are &lt;em&gt;not&lt;/em&gt; still around as living fossils&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The real answer here is that, in a very real sense, they are. Morphological differences aside, squirrels are no more different from their long-dead forebears than sharks. Rather, crowded niches have made generation upon generation of increasingly squirrely animals more successful by being superficially and behaviourally &lt;em&gt;different&lt;/em&gt; from their parents, and so, modern squirrels have arisen.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt; Footnotes:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The shark is not in fact our ancestor, rather &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_fish#Jawed_fish&quot;&gt;Cambrian early jawed fish&lt;/a&gt; are. The image of a shark is however far more evocative and easier to talk about.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1095" LastEditorUserId="1095" LastEditDate="2015-03-10T08:34:27.787" LastActivityDate="2015-03-10T08:34:27.787" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30271" PostTypeId="2" ParentId="30262" CreationDate="2015-03-09T16:04:37.130" Score="1" Body="&lt;p&gt;To answer your first question; it is not necessary that every trait have an evolutionary advantage. Neutral traits can persist in the population without having any adaptive value, or they can persist as a byproduct of another trait that does have adaptive value. Even a slightly detrimental trait can become fixed due to genetic drift. Take a look at this rather famous paper critiquing the &quot;&lt;a href=&quot;http://www.jstor.org/stable/77447?seq=1#page_scan_tab_contents&quot; rel=&quot;nofollow&quot;&gt;adaptionist programme&lt;/a&gt;&quot; if you're interested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, I personally don't know for sure whether or not different blood groups have an adaptive advantage. Someone else can probably provide a better answer to this portion of your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, to answer your second question: &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood_type_%28non-human%29&quot; rel=&quot;nofollow&quot;&gt;yes, yes they do&lt;/a&gt;. Indeed the Rhesus blood typing system was named after the rhesus monkey.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-03-09T16:04:37.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30272" PostTypeId="2" ParentId="30262" CreationDate="2015-03-09T16:06:33.937" Score="4" Body="&lt;p&gt;The answer to this question can be found by searching the Internet.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For some blood types, evolution and environmental selective pressures&#xA;  are clearly important for their persistence. For example, the Duffy&#xA;  blood type includes a receptor that allows certain types of malarial&#xA;  parasites to enter the red cell. Thus, in some malarial areas of&#xA;  Africa, populations with Duffy-negative blood types have a distinct&#xA;  survival advantage because absence of the Duffy antigen provides a&#xA;  measure of protection against malaria. The percentage of people&#xA;  lacking the Duffy antigen is much higher in these locations than in&#xA;  areas not endemic for malaria.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;more here &lt;a href=&quot;http://www.scientificamerican.com/article/why-do-people-have-differ/&quot; rel=&quot;nofollow&quot;&gt;http://www.scientificamerican.com/article/why-do-people-have-differ/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Animals and bacteria have cell surface antigens referred to as a blood&#xA;  type. Antigens from the human ABO blood group system are also found in&#xA;  apes and old world monkeys, which have inherited the same system.&#xA;  Other animal blood sometimes agglutinates (to varying levels of&#xA;  intensity) with human blood group reagents, but the structure of the&#xA;  blood group antigens in animals is not always identical to those&#xA;  typically found in humans. The classification of most animal blood&#xA;  groups therefore uses different blood typing systems to those used for&#xA;  classification of human blood.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;more here  &lt;a href=&quot;http://en.wikipedia.org/wiki/Blood_type_%28non-human%29&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Blood_type_%28non-human%29&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="22057" LastEditDate="2016-03-21T20:03:07.920" LastActivityDate="2016-03-21T20:03:07.920" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30273" PostTypeId="1" CreationDate="2015-03-09T17:26:40.840" Score="2" ViewCount="76" Body="&lt;p&gt;Some RM systems (restriction-modification systems) are plasmid-borne and are transferred through bacterial conjugation. As you all know, there are two genes in an RM system, the gene that codes for the restriction enzyme that restricts a certain nucleotide sequence and the other that codes for the methyltransferase that methylate the sequence to protect the cell from its own restriction enzymes. If these genes are both being expressed at the same rate after the bacteria receives this plasmid, how is the bacteria's DNA protected from the restriction enzymes for the first few hours of expression if the methyltransferase have not yet methylated the entire host genome yet?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CDB&lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-03-09T17:26:40.840" Title="Why do restriction-modification systems work?" Tags="&lt;genetics&gt;&lt;cell-biology&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30274" PostTypeId="1" CreationDate="2015-03-10T01:53:44.500" Score="1" ViewCount="995" Body="&lt;p&gt;I have noticed that when insects are placed on their backs, they tend to turn themselves over quickly or else appear to be in distress. Is there a physiologic, anatomic, or adaptive reason why supine positioning might be unfavorable in insects? &lt;/p&gt;&#xA;" OwnerUserId="14851" LastEditorUserId="9268" LastEditDate="2015-03-10T03:57:06.843" LastActivityDate="2019-01-23T01:43:19.657" Title="Why do insects avoid being on their back?" Tags="&lt;zoology&gt;&lt;entomology&gt;" AnswerCount="2" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="30276" PostTypeId="1" AcceptedAnswerId="30278" CreationDate="2015-03-10T03:37:55.403" Score="6" ViewCount="1348" Body="&lt;p&gt;Genes in the (+) strand are black and genes in the (-)strand are red.&#xA;The gene distribution in E. coli genome is somewhat expected: transcribed regions would tend to alternate with non transcribed regions, as a consequence of (random) evolutionary process. Also, genes don't overlap (it would be highly  unlikely that two complementary strands both carried useful information).&#xA;In B. subtilis, on the other hand, there seems to be a preference for one of the strands in each side of the chromosome. &lt;strong&gt;What sort of evolutionary pressure could give raise to such a pattern?&lt;/strong&gt;&#xA;I have a guess, but I'm not sure, that this may be related to bacterial transformation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/40dCk.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14630" LastEditorUserId="13072" LastEditDate="2015-03-11T03:34:26.483" LastActivityDate="2017-01-04T04:05:52.663" Title="Why do some bacteria have most genes on the leading strand of the genome?" Tags="&lt;molecular-biology&gt;&lt;bacteriology&gt;&lt;molecular-genetics&gt;&lt;genomes&gt;&lt;polymerase&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30277" PostTypeId="1" CreationDate="2015-03-10T03:47:08.410" Score="7" ViewCount="106" Body="&lt;p&gt;I would like to know if there is an assay which could allow us to analyse a protein before it has assumed its 3D functional form.&#xA;While studying structural biology, I only came to know the forces that stabilize the structure, but not the gap between the original random coil and the protein in its native form.&lt;/p&gt;&#xA;" OwnerUserId="14630" LastActivityDate="2017-12-04T13:18:07.350" Title="Is it possible to isolate and analyse intermediates of protein folding?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;protein-folding&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30278" PostTypeId="2" ParentId="30276" CreationDate="2015-03-10T04:27:29.417" Score="8" Body="&lt;p&gt;The pattern we see in &lt;em&gt;B. subtilis&lt;/em&gt; is quite common in prokaryotes. The origin of replication is shown at the top of the genome diagram. DNA replication proceeds bidirectionally from this point. In the &lt;em&gt;B. subtilis&lt;/em&gt; diagram, most genes are located along the leading strand in each direction. Even in E. coli, by the way, important genes, including all rRNAs, tend to appear on the leading strand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is that? Rapidly growing bacteria are &lt;a href=&quot;https://biology.stackexchange.com/questions/30080/how-can-e-coli-proliferate-so-rapidly&quot;&gt;replicating their genomes most or all of the time&lt;/a&gt;, so you've got replication and transcription happening at the same time.  If genes are on the lagging strand, RNA transcription proceeds in the opposite direction from DNA replication, and the DNA polymerase will often collide with the RNA polymerase. If the genes are on the leading strand, however, RNA transcription proceeds in the same direction as replication and collisions are minimized. Hence the selective advantage to positioning most genes along the leading strand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some genes may also be on the lagging strand in order to target them for mutagenesis (Paul et al. 2013, Million-Weaver et al 2015). This goes back to the concept of transcription-replication collisions where the head-on collisions are worse than co-directional collisions. Head-on genes actually have a higher mutation rate and incidence of convergent mutations which suggests that they are mutated and evolve faster than leading strand genes. This is a controlled process in that it only occurs in lagging strand genes, and only when the gene is transcribed (i.e. when it is needed). It was argued that this is a way bacteria can control and ratchet up or down the rate of evolution in a controlled way. This was argued against by Chen and Zhang based upon computer based modelling. It is an interesting concept that has been hotly debated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT for additional clarification and references:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This diagram from &lt;a href=&quot;http://gbe.oxfordjournals.org/content/5/12/2436.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chen and Zhang (2013)&lt;/a&gt; helps show what is going on:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0x5uf.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Caption:&lt;/strong&gt; &quot;&lt;em&gt;Schematic drawing of a collision between a working DNA polymerase and a working RNA polymerase in bacteria. (a) Codirectional collision when a gene is encoded on the leading strand. (b) Head-on collision when a gene is encoded on the lagging strand. Arrows show the directions of movement.&lt;/em&gt;&quot; (Chen and Zhang 2013)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A few references&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The original idea goes back almost 40 years to Nomura M. and Morgan,E.A. (1977) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/339818&quot; rel=&quot;nofollow noreferrer&quot;&gt;Genetics of bacterial ribosomes&lt;/a&gt;. &lt;em&gt;Annu. Rev. Genet.&lt;/em&gt;, 11, 297–347.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;An early paper about highly transcribed rRNA on the leading strand: Ellwood M. and Nomura,M. (1982) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC216529/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chromosomal locations of the genes for rRNA in Escherichia coli K-12. &lt;em&gt;J. Bacteriol.&lt;/em&gt;&lt;/a&gt;, 149, 458–468.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A recent overview: Rocha, E. P. (2004). &lt;a href=&quot;http://mic.sgmjournals.org/content/150/6/1609.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;The replication-related organization of bacterial genomes&lt;/a&gt;. &lt;em&gt;Microbiology&lt;/em&gt;, 150(6), 1609-1627.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Why some genes remain on the lagging strand: Chen, X., &amp;amp; Zhang, J. (2013). &lt;a href=&quot;http://gbe.oxfordjournals.org/content/5/12/2436.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Why are genes encoded on the lagging strand of the bacterial genome?&lt;/a&gt;. &lt;em&gt;Genome biology and evolution&lt;/em&gt;, 5(12), 2436-2439.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Paul, S., Million-Weaver, S., Chattopadhyay, S., Sokurenko, E., and Merrikh, H. (2013). Accelerated gene evolution through replication-transcription conflicts. Nature 495, 512-515.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Million-Weaver, S., Samadpour, A.N., Moreno-Habel, D.A., Nugent, P., Brittnacher, M.J., Weiss, E., Hayden, H.S., Miller, S.I., Liachko, I., and Merrikh, H. (2015b). An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis. Proc Natl Acad Sci U S A 112, E1096-1105.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2017-01-04T04:05:52.663" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30279" PostTypeId="2" ParentId="30212" CreationDate="2015-03-10T05:13:04.523" Score="13" Body="&lt;p&gt;Cucumber contains a compound called &lt;strong&gt;trans-2-nonenal&lt;/strong&gt; (&lt;a href=&quot;http://www.ghorganics.com/page11.html&quot;&gt;reference 1&lt;/a&gt; and &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0005276076901612&quot;&gt;reference 2&lt;/a&gt;) that repels insects. This particular compound (&lt;a href=&quot;http://en.wikipedia.org/wiki/2-Nonenal&quot;&gt;reference&lt;/a&gt;) has can also be used in insecticide foams for repelling ants (&lt;a href=&quot;https://www.google.com/patents/US20100140368&quot;&gt;reference&lt;/a&gt;) &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2015-03-10T05:13:04.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30280" PostTypeId="2" ParentId="30241" CreationDate="2015-03-10T05:16:32.503" Score="2" Body="&lt;p&gt;You nailed down what enhancers are (canadianer give a good explanation too, while not answering the question in my opinion).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For understanding the authors statement you first need to know that:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Lineage-specific and signal-dependent transcription factors are specific classes of transcription factors. Those are TFs that require external signals for activation.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;All enhancers are not always accessible. This depends on the epigenetic marks, and subsequently histones binding, around those regions. If, for example, an enhancer is in a region of tightly packed DNA (i.e. heterochromatin) it will not bind any TFs and is therefore not active. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;What the authors where trying to convey is, in my opinion, that active enhancers are highly enriched in DNA sequences specific for signal-dependent TFs. In other terms, the cell's identity is given by a combination of 1) epigenetic regulation of gene expression via a) a certain pattern of active enhancers and b) chromatin state of genes in conjunction with 2) signal-dependent transcription factors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In summary this means that the cell identity is not only described by signal-dependent TFs but also by the active enhancer pattern&lt;/strong&gt;. And this therefore implies that one might be able &lt;strong&gt;to predict TFs necessary to determine a specific cell's identity&lt;/strong&gt; as stated in their next sentence:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Therefore, the delineation of a particular cell's active enhancer repertoire provides a powerful means of predicting the transcription factors required for that cell's identity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastActivityDate="2015-03-10T05:16:32.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30281" PostTypeId="2" ParentId="28476" CreationDate="2015-03-10T05:55:45.963" Score="3" Body="&lt;p&gt;Interesting question. Here what I think (I am not an expert in congenital analgesia so take it with a grain of salt).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pain provoked by an high temperature is mainly transmitted via the receptor TRPV1 (a Ca2+-channel nocireceptor) while cold sensation is driven by TRPM8 and possibly, for noxious cold, via TRPA1 (two similar types of Ca2+-channels). Those receptors are known as the temperature sensors. As an anecdote, TRPV1 is what give you a pungency sensation when eating spices while TRPM8/TRPA1 give you the cooling sensation from mint.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mechanical pain is transmitted via other receptors, including TRP channels, but this is not fully understood at the molecular level.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I know, the encoding of pain, and more generally physiological sensations, in the brain are also not yet fully understood but it is very likely that the pathways taken by TRPV1 differs from the one taken by TRPM8/A1 which would suggest that it is possible that CIPA individuals experience high-temperature pain and cold differently at the molecular level and therefore might respond, to some degree, to one but not the other. This also probably applies to mechanical pain vs temperature-driven pain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would actually not be too surprised if CIVA people shiver even if not feeling any temperature sensations. Would be interesting to have the opinion or even better the observations of experts in this field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. I know this is not a definitive answer but I have not enough reputation to comment.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-10T06:04:51.920" LastActivityDate="2015-03-10T06:04:51.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30282" PostTypeId="1" CreationDate="2015-03-10T06:08:28.687" Score="1" ViewCount="155" Body="&lt;p&gt;As a follow up to this &lt;a href=&quot;https://biology.stackexchange.com/questions/30214/what-is-the-minimum-eye&quot;&gt;question&lt;/a&gt; regarding the evolution of the eye, it was suggested that primitive eyes only needed to evolve a light sensor and could perhaps use the existing biochemical cascade infrastructure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the minimum of this biological light sensor? Please provide a &lt;em&gt;detailed&lt;/em&gt; biochemical description of how many proteins are involved and their interactions which can be &quot;hooked up&quot; to the existing biochemical cascade infrastructure. (to the best of our knowledge)&lt;/p&gt;&#xA;" OwnerUserId="8290" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-03-10T12:56:19.423" Title="What is the minimum functional biological light sensor?" Tags="&lt;evolution&gt;&lt;eyes&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-03-10T23:13:12.833" ContentLicense="CC BY-SA 3.0" />
  <row Id="30285" PostTypeId="1" AcceptedAnswerId="30307" CreationDate="2015-03-10T07:05:09.033" Score="2" ViewCount="278" Body="&lt;p&gt;I'd like to ask why are there no fluorescence microscopes that use a monochromator instead of filters?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there are any, then I should change my question as, which ones use it and why are they so rare?&lt;/p&gt;&#xA;" OwnerUserId="1458" LastActivityDate="2015-03-10T19:04:57.890" Title="Monochromator in fluorescence microscopy" Tags="&lt;fluorescent-microscopy&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-03-10T23:13:04.133" ContentLicense="CC BY-SA 3.0" />
  <row Id="30287" PostTypeId="2" ParentId="30258" CreationDate="2015-03-10T08:54:33.900" Score="6" Body="&lt;p&gt;One part of your question betrays a serious error:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;Is there not enough selection pressure exerted on this species in order to force it to change morphologically?&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Actually the reverse is true; constancy of form can only be maintained in the presence of continuous selective pressure. It's just that this is stabilising selection that acts to maintain the existing form rather than push the organism to new morphologies. In fact, &lt;em&gt;most&lt;/em&gt; selection acts in this manner. This shouldn't surprise you: organisms are typically well adapted to their environments so changes are more likely to reduce fitness than increase fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also worth noting that although living fossils show little morphological change they can continue to show change at the molecular level at rates as high as, or higher than, other organisms - e.g. (&lt;a href=&quot;http://www.cell.com/trends/genetics/abstract/S0168-9525%2808%2900003-6&quot;&gt;May et al 2007&lt;/a&gt;; &lt;a href=&quot;http://www.nature.com/ncomms/2013/131015/ncomms3602/full/ncomms3602.html&quot;&gt;Cao et al 2013&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2015-03-10T08:54:33.900" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30288" PostTypeId="2" ParentId="30282" CreationDate="2015-03-10T11:25:32.323" Score="2" Body="&lt;p&gt;The minimum biological light sensor is just an existing signaling molecule that, by chance, also has some change in its activity due to light.  There are several ways this could happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One extremely simple example would be based on a G-protein coupled receptor (GPCR).  GPCRs are a family of related signal transduction proteins (the largest family) that sit on the surface of a cell's membrane.   Each one is sensitive to a molecule or small group of related molecules.  When exposed to the molecule it is sensitive to, the GPCR sets of a series of chemical cascades that trigger some activity in the cell.  For example, it can serve as a signal for the cell to move towards the place where the chemical was detected, or move away.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, imagine that, just by chance, the molecule the GPCR is sensitive to has some sensitivity to light, in that when exposed to light the molecule either has a larger or smaller chance (even slightly) of binding to the GPCR.  This is not improbable, a ton of biological molecules have this characteristic, in fact many have substantial responses to light even though they are not involved in light-sensing pathways.  A good example is called &quot;photoisomerization&quot;, where the same molecule can have more than one shape, and switches between two shapes when exposed to light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This would be a biological light sensor.  Not necessarily a very sensitive one, but once you have such a basic light sensor, natural selection would take over and lead to stronger and stronger effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, this is pretty much how our eyes work today.  It uses a GPCR whose target is a molecule that changes its shape when exposed to light, which makes it no longer able to bind to the receptor, shutting of the signaling cascade.  What is more, this molecule is not only used in sensing light, it is a precursor to a molecule needed for gene transcription and signaling.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, you can splice light-sensitive GPCRs from bacteria (which are different than those in animals) into non-light-sensitive animal cells, and those molecules will automatically integrate with existing GPCR signaling cascades, rendering the cell light sensitive.&lt;/p&gt;&#xA;" OwnerUserId="13345" LastEditorUserId="13345" LastEditDate="2015-03-10T12:56:19.423" LastActivityDate="2015-03-10T12:56:19.423" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30291" PostTypeId="1" CreationDate="2015-03-10T12:23:38.920" Score="6" ViewCount="3721" Body="&lt;p&gt;I think the title says it. I always read that alleles are gene variants at a given locus, which confuses me. Thanks!&lt;/p&gt;&#xA;" OwnerUserId="14860" LastActivityDate="2015-03-11T14:58:35.570" Title="Are gene variants at different loci also called alleles?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30292" PostTypeId="2" ParentId="30291" CreationDate="2015-03-10T12:43:47.277" Score="3" Body="&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;:&#xA;&lt;strong&gt;Short answer&lt;/strong&gt; : Yes: &quot;allele&quot; is a synonym for &quot;gene variant&quot;, irrespective of location (locus).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Original answer: &lt;em&gt;From &lt;a href=&quot;http://biology.about.com/od/geneticsglossary/g/alleles.htm&quot; rel=&quot;nofollow&quot;&gt;About Education&lt;/a&gt; I found this definition for an allele:&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;An &lt;strong&gt;allele&lt;/strong&gt; is an alternative form of a &lt;strong&gt;gene&lt;/strong&gt; (one member of a pair) that is located at a &lt;strong&gt;specific position&lt;/strong&gt; on a &lt;strong&gt;specific chromosome&lt;/strong&gt;.&lt;/em&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt; &#xA;&lt;strike&gt;&lt;em&gt;Hence, two alleles are located at the &lt;strong&gt;same locus&lt;/strong&gt;, but are situated on a &lt;strong&gt;different chromosome&lt;/em&gt;&lt;/strong&gt;.&lt;/strike&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;ADDITION EDIT&lt;/strong&gt;: Given the many high-quality comments (and the downvote) I erased the concluding sentence of my first attempt and I will elaborate below: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Feero et al. (&lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMra0907175&quot; rel=&quot;nofollow&quot;&gt;2010&lt;/a&gt;) gives the following more elaborate definition of &quot;allele&quot; (text relevant to the question is bolded out):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Specific locations&lt;/strong&gt; in the human genome where differences between individual people&#xA;  are found are generally referred to as &lt;strong&gt;variations&lt;/strong&gt;, and the term “normal” or “wild type” is often used to refer to the most common variant at a location in a given population group. In its &lt;strong&gt;simplest form&lt;/strong&gt;, the &lt;strong&gt;variation&lt;/strong&gt; has two different spellings, referred to as &lt;strong&gt;“alleles.”&lt;/strong&gt; If the frequency of the minor allele is greater than 1%, such variants are called &lt;strong&gt;polymorphisms&lt;/strong&gt;. The word &lt;strong&gt;“mutation”&lt;/strong&gt; is generally reserved for changes in DNA that are believed or known to be pathologic [...] or for changes that are [very] recent (e.g., not inherited DNA changes). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hence, from my understanding, the original quoted definition from &lt;a href=&quot;http://biology.about.com/od/geneticsglossary/g/alleles.htm&quot; rel=&quot;nofollow&quot;&gt;About Education&lt;/a&gt; still stands. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the critical comments placed by the PO, @fileunderwater and @WYSIWYG:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) &lt;code&gt;[...] what is a copy or a variant of a gene at a different locus on the same chromosome?&lt;/code&gt; - That is a very interesting question, and I think Feero et al. (&lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMra0907175&quot; rel=&quot;nofollow&quot;&gt;2010&lt;/a&gt;) deals with that simply by saying &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In its &lt;strong&gt;simplest form&lt;/strong&gt;, the variation has two different spellings, referred to as “alleles.” &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In other words - perhaps the gene duplication is a step too far for this terminology. And in fact, although I regret having to cite &lt;a href=&quot;http://en.wikipedia.org/wiki/Allele&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; here, it does provide a very enlightening sentence:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] [A]t the gene locus for the ABO blood type [...] classical genetics recognizes three alleles, IA, IB, and i, that determine compatibility of blood transfusions. Any individual has one of six possible genotypes (IAIA, IAi, IBIB, IBi, IAIB, and ii) that produce one of four possible phenotypes [...].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hence, what this implicitly tells us is that an &lt;strong&gt;allele is&lt;/strong&gt;, as Feero et al. (&lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMra0907175&quot; rel=&quot;nofollow&quot;&gt;2010&lt;/a&gt;) also says, simply a &lt;strong&gt;gene variation&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that it basically boils down to what is a &lt;strong&gt;&quot;chromosome locus&quot;&lt;/strong&gt;? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An article by &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2006.tb01168.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Proulx &amp;amp; Phillips, 2006&lt;/a&gt; entitled &quot;ALLELIC DIVERGENCE PRECEDES AND PROMOTES GENE DUPLICATION&quot; mentions: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] [H]eterozygotes at a single locus are broken up by segregation, whereas for duplicate loci an individual can carry copies of alternative alleles at separate&#xA;  loci.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hence, what the authors implicitly say is that an allele is a &lt;strong&gt;gene variation&lt;/strong&gt; and that a &lt;strong&gt;locus is a fixed position&lt;/strong&gt; on a chromosome. Hence, a gene duplication means 2 loci that can carry &lt;strong&gt;the same or a different allele&lt;/strong&gt;. This should answer &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) &lt;code&gt;Are the alleles at the two duplicated loci then named differently, even if their DNA sequences are identical (as well as the protein they might be coding for)&lt;/code&gt;, namely &lt;strong&gt;no&lt;/strong&gt;, an allele has a name (e.g. IA) that remains unchanged when duplicated. The locus is then different for the duplicate, but the name of the allele stays the same (as an allele is, by definition, simply a gene variant wherever on the chromosome).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3a) &lt;code&gt;[...] two versions of a gene at two different loci are alleles (not paralogs)?&lt;/code&gt;: &lt;strong&gt;yes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3b) &lt;code&gt;What about the same identical version at two different loci: same allele or not?&lt;/code&gt; &lt;strong&gt;yes, same allele&lt;/strong&gt;, allele has nothing to do with locus. Just a gene variant. Where ever.&#xA;&lt;br&gt;&lt;br&gt;&#xA;&lt;br&gt;&#xA;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMra0907175&quot; rel=&quot;nofollow&quot;&gt;Feero et al. &lt;em&gt;N Engl J Med&lt;/em&gt; 2010;&lt;strong&gt;362&lt;/strong&gt;:2001-11&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2006.tb01168.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Proulx &amp;amp; Phillips. &lt;em&gt;Evolution&lt;/em&gt; 2006;&lt;strong&gt;60&lt;/strong&gt;:881-892&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-11T14:58:35.570" LastActivityDate="2015-03-11T14:58:35.570" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30293" PostTypeId="2" ParentId="29815" CreationDate="2015-03-10T13:47:34.043" Score="6" Body="&lt;p&gt;It looks like southern platyfish (Xiphophorus maculatus) to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IubrR.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Courtesy: &lt;a href=&quot;http://aquaticszone.blogspot.in/2011_04_01_archive.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://aquaticszone.blogspot.in/2011_04_01_archive.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2015-03-10T13:47:34.043" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30294" PostTypeId="1" AcceptedAnswerId="30321" CreationDate="2015-03-10T13:54:51.197" Score="2" ViewCount="218" Body="&lt;p&gt;Question from a thesis defense list ask me this. But I can't find the exact answer on the internet or in books. In my thesis, I described isohydric plants, for example maize, lupin, pea, poplar. This plants response to a decrease in soil water in same way. How Norway spruce response to decrease in soil water? As a isohydric plant or anisohydric?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your time and help. &lt;/p&gt;&#xA;" OwnerUserId="14856" LastEditorUserId="14856" LastEditDate="2015-03-10T14:25:57.357" LastActivityDate="2015-03-11T05:00:42.777" Title="Is Norway spruce (Picea abies (L.) Karst.) isohydric or anisohydric species?" Tags="&lt;physiology&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30296" PostTypeId="2" ParentId="30220" CreationDate="2015-03-10T14:09:41.217" Score="1" Body="&lt;p&gt;Introns are not included in the polypeptide sequence.&lt;/p&gt;&#xA;" OwnerUserId="13346" LastEditorUserId="13346" LastEditDate="2015-03-12T04:43:36.200" LastActivityDate="2015-03-12T04:43:36.200" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30298" PostTypeId="1" AcceptedAnswerId="30299" CreationDate="2015-03-10T14:25:26.350" Score="25" ViewCount="4570" Body="&lt;p&gt;I understand (a little) that there are biological clocks and reason that after a certain amount of time organisms die. I'm wondering if that is something inherent in our DNA or in biology/chemistry in general. EG, is it possible that there could be a complex organism that would not die and would just regenerate it's cells In Perpetuam? I'm specifically interested in mammals and even more specifically interested in humans. But, I would be interested in hearing about other organisms like bugs, fish, plant, algae, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not asking if this practical, do we know how to do this, etc.. I just want to know theoretically if living forever is biologically possible, as far as we know. If not, is there an estimated upper limit?&lt;/p&gt;&#xA;" OwnerUserId="13238" LastEditorUserId="13238" LastEditDate="2015-03-11T10:52:25.207" LastActivityDate="2015-11-29T04:58:16.170" Title="Do all organisms have to die?" Tags="&lt;senescence&gt;&lt;death&gt;" AnswerCount="3" CommentCount="15" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30299" PostTypeId="2" ParentId="30298" CreationDate="2015-03-10T15:07:30.597" Score="20" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Turritopsis_dohrnii&quot;&gt;immortal jellyfish&lt;/a&gt; can revert back to its immature polyp stage after reaching maturity, then mature again, over and over. You can read more on the wikipedia page, but this ability means it can potentially avoid senescence altogether.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-03-10T15:07:30.597" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30300" PostTypeId="2" ParentId="30274" CreationDate="2015-03-10T15:48:03.480" Score="6" Body="&lt;p&gt;Welcome to Biology.SE&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Insects don't &quot;like&quot; being on their back because they can't get back on their legs and they therefore get stuck somewhere where they can gently wait for death to come.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all insects are unable to switch back on their legs but some can't do that (or can hardly do that). The reasons for which many insects are not able to get back on their legs (while mammals for example usually can do that) is that they have a exoskeleton. Their exoskeleton limits drastically their movements. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-06-05T00:32:44.150" LastActivityDate="2015-06-05T00:32:44.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30301" PostTypeId="1" AcceptedAnswerId="30303" CreationDate="2015-03-10T15:48:41.433" Score="3" ViewCount="4087" Body="&lt;p&gt;My hypothesis is that one can decrease the allergic reactions over time by continuously exposing yourself to slowly increasing doses of allergens.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any scientific evidence pointing this right or wrong?&lt;/p&gt;&#xA;" OwnerUserId="11675" LastActivityDate="2019-04-24T08:33:04.517" Title="Is it possible to train allergic resistance by exposing yourself to allergens?" Tags="&lt;immunology&gt;&lt;allergies&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30303" PostTypeId="2" ParentId="30301" CreationDate="2015-03-10T16:10:01.077" Score="1" Body="&lt;p&gt;This is exactly the point of allergy shots. The continuous exposure to an allergen causes tolerization. Maybe instead of me writing a bunch of stuff up check out this simple Wikipedia article:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;http://en.wikipedia.org/wiki/Immune_tolerance&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Then if you have specific questions you can ask them here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-03-10T16:10:01.077" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30305" PostTypeId="2" ParentId="30298" CreationDate="2015-03-10T16:32:30.483" Score="6" Body="&lt;p&gt;You have a very interesting question there! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to answer, however, we must examine the most widely accepted &quot;reason&quot; for why we age and eventually die. Most scientists agree that it is because of mass cell death. Normally you and I would be able to deal quite well with mass cell death (such as a very large injury), the problem comes in when we are older because we &lt;em&gt;cannot&lt;/em&gt; replenish them because we have physically exhausted our own supply of something called stem cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most cells in our bodies actually cannot divide, so they rely on these stem cells (which can divide into any cell; think of them as a wild card) to replenish whatever cells die. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sounds perfect, right? Not quite, each of us only have a given number of stem cells in our body (even though stem cells can divide into more stem cells, they usually don't). So the reason we age and die is because we &quot;run out&quot;, if you will, of these stem cells and our supply of cellular replenishment is slowly cut off. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Back to your question, is it possible to stop this? Well you've probably already come to this conclusion by now, but &lt;em&gt;theoretically&lt;/em&gt; if you could somehow supply the body with a constant number of stem cells, theoretically, you could live forever (or at least a &lt;em&gt;really&lt;/em&gt; long time). This is evident, as you are aware, in flatworms, who have stem cells constantly circulating their bodies and are practically immortal.&lt;/p&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="231" LastEditDate="2015-11-29T03:19:43.347" LastActivityDate="2015-11-29T03:19:43.347" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="30306" PostTypeId="2" ParentId="30301" CreationDate="2015-03-10T16:41:28.930" Score="3" Body="&lt;p&gt;The phenomenon called oral tolerance is quite a common way to reduce allergic reactions. Basically patients have to eat a lot of the antigen with their daily diet under the supervision of doctors, so in time allergic reactions can be alleviated. The idea behind this is that our immune system is much more tolerant to things that get in our digestive system (in most cases). Here is a good &lt;a href=&quot;http://www.nature.com/mi/journal/v5/n3/full/mi20124a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;article&lt;/a&gt; on oral tolerance from Nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Citation: Pabst, O; Mowat, A M - Oral tolerance to food protein Mucosal Immunology 2012 &lt;a href=&quot;https://doi.org/10.1038/mi.2012.4&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://doi.org/10.1038/mi.2012.4&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2019-04-24T08:33:04.517" LastActivityDate="2019-04-24T08:33:04.517" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="30307" PostTypeId="2" ParentId="30285" CreationDate="2015-03-10T19:04:57.890" Score="2" Body="&lt;p&gt;Zeiss LSM780 uses essentially monochromator to spread all fluorescence across 34 detectors for multi-spectral acquisition. It is used to detect autofluorescence, unmix closely positioned emission spectra (unmix GFP and YFP for example) and to measure precise spectral peaks with ~1nm resolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Monochromator is useful when you need to transform frequency domain information into spatial domain. In fluorescence microscopy we usually collect light from wide bands of well-separated GFP-like proteins, so that filters make more sense. We usually don't detect 1-nm wide lines or plot spectra. LSM780 does allow all that, if you need to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can use spectral imaging, but for that you will have to either scan for very long time, or spread signal onto array of detectors.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-03-10T19:04:57.890" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30308" PostTypeId="1" CreationDate="2015-03-10T20:34:04.750" Score="9" ViewCount="3956" Body="&lt;p&gt;I'm taking a microbial physiology course and we noted that, while some archaea are phototrophic, there are no known photosynethetic archaea.  Are there any physiological characteristics that make archaea less suited for photosynthesis?  Or is it simply a matter of there likely being photosynthetic archaea, but they have not yet been found (which seems like it could easily be the case, given that there are many extremophilic archaea)?&lt;/p&gt;&#xA;" OwnerUserId="12886" LastActivityDate="2015-03-14T06:06:04.950" Title="Why are there no known photosynthetic archaea?" Tags="&lt;microbiology&gt;&lt;photosynthesis&gt;&lt;archaea&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30310" PostTypeId="1" AcceptedAnswerId="30325" CreationDate="2015-03-10T21:35:02.177" Score="1" ViewCount="44" Body="&lt;p&gt;I am searching for source, that providing information about enzymes\proteins, in different types of cancers, that their amount in cell is significantly higher - comparing to normal, healthy cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some pathways that exist in cancer in much more higher amounts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example - Telomerase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there some sort of database for this information?&lt;/p&gt;&#xA;" OwnerUserId="10104" LastActivityDate="2015-03-11T05:52:58.700" Title="Enzyme\Protein amounts in cancer" Tags="&lt;cancer&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30311" PostTypeId="1" AcceptedAnswerId="30312" CreationDate="2015-03-10T22:43:12.493" Score="2" ViewCount="105" Body="&lt;p&gt;I found this caterpillar in in El Cerrito, CA and was wondering what kind it is?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://cl.ly/image/0P1O3R0V3X0g/caterpillar.jpg&quot; alt=&quot;mystery caterpillar&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14873" LastEditorUserId="9686" LastEditDate="2018-06-11T08:06:28.647" LastActivityDate="2018-06-11T08:06:28.647" Title="Can anyone identify this mystery caterpillar?" Tags="&lt;species-identification&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30312" PostTypeId="2" ParentId="30311" CreationDate="2015-03-10T22:54:11.870" Score="2" Body="&lt;p&gt;Best assumption, &lt;a href=&quot;http://en.wikipedia.org/wiki/Gulf_fritillary&quot; rel=&quot;nofollow&quot;&gt;Gulf Fritillary Caterpillar&lt;/a&gt; (&lt;em&gt;Agraulis vanillae&lt;/em&gt;). I could be wrong though.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The larva is a caterpillar which grows to approximately 4 cm (1.6 in) in length. It is bright orange in color and covered in rows of black spines. The spines are soft to the touch and do not sting, but the larva is poisonous if eaten. Source: Wikipedia.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-03-10T22:59:19.133" LastActivityDate="2015-03-10T22:59:19.133" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30313" PostTypeId="1" AcceptedAnswerId="30314" CreationDate="2015-03-11T01:02:01.990" Score="1" ViewCount="796" Body="&lt;p&gt;I found one of these beetles on my bed as I was attempting to get in. I'm 80% sure my cat carried it in (I found it in the exact same space he had been sitting ten minutes previously).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is what, if any, diseases do these bugs carry? It did not bite me, though it may have bitten my cat. I'm more worried about bacteria etc that it may have carried around my bed/room. Can they transmit salmonella? Should I break out the disinfectant, or is it no big deal?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have researched them as best I can, and I found someone noting that they &lt;em&gt;can&lt;/em&gt; spread bacteria, but found nothing on how severe it is. For example, my cat obviously spreads bacteria, but I let him on my bed without worry. I have never see one of these beetles before.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a secondary question, if that's allowed - what are the chances it laid eggs on my bed? It was there for possibly 4-5 hours if my cat indeed carried it in. I have rodents (pets) in my room and am peripherally worried about an infestation happening. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For context, I live in the center of the UK.&lt;/p&gt;&#xA;" OwnerUserId="14874" LastEditorUserId="14874" LastEditDate="2015-03-11T01:11:19.580" LastActivityDate="2015-03-11T01:25:33.140" Title="What, if any, diseases do larder beetles carry?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30314" PostTypeId="2" ParentId="30313" CreationDate="2015-03-11T01:25:33.140" Score="2" Body="&lt;p&gt;I have never heard of larder beetles carrying any serious diseases and chances are slim that it could have laid any eggs, so you probably have nothing to worry about. If you want you can spray the area down with a cleaner, but as I said earlier, it's probably fine.&lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-03-11T01:25:33.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30315" PostTypeId="1" AcceptedAnswerId="30324" CreationDate="2015-03-11T01:38:34.073" Score="3" ViewCount="178" Body="&lt;p&gt;Is it possible to introduce a novel gene into the genome of every cell (or at least most cells) of an adult multicellular organism? How would this be done?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CDB&lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-03-11T05:31:50.920" Title="Introducing novel genes to an adult multicellular organism?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30316" PostTypeId="2" ParentId="1093" CreationDate="2015-03-11T02:07:42.627" Score="0" Body="&lt;p&gt;Cows only produce milk after a calf is born and their lactation period lasts approximately 10 months. In many instances, farmers have given growth hormone (GH)&lt;a href=&quot;http://jn.nutrition.org/content/111/9/1662.full.pdf&quot; rel=&quot;nofollow&quot;&gt;¹&lt;/a&gt; to cows in order for them to produce more milk. It must be noted that there are many side effects associated with this, not to mention the residual effects it may have on us humans as consumers. Primarily though, the cows would have decreased immune efficiency and this would leave them vulnerable to all types of parasitic infections or disease.   &lt;/p&gt;&#xA;" OwnerUserId="14875" LastEditorUserId="14875" LastEditDate="2015-03-15T19:12:13.663" LastActivityDate="2015-03-15T19:12:13.663" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30318" PostTypeId="1" AcceptedAnswerId="30322" CreationDate="2015-03-11T03:57:44.503" Score="4" ViewCount="1043" Body="&lt;p&gt;With respect to this paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18187620&quot; rel=&quot;nofollow&quot;&gt;Identification of Host Proteins Required&#xA;for HIV Infection Through a Functional&#xA;Genomic Screen&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the abstract, I found names such as Rab6 and Vps35 and TNPO3. So Rab6 and Vps35 are proteins and TNPO3 is a gene? So the strings written in full caps are the genes and those strings whose just first letter is capital and the rest of the letters are small is a protein?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="5144" LastEditDate="2015-03-21T18:33:23.573" LastActivityDate="2015-03-21T18:33:23.573" Title="Nomenclature of genes and proteins" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30319" PostTypeId="1" AcceptedAnswerId="30343" CreationDate="2015-03-11T04:28:31.153" Score="2" ViewCount="1184" Body="&lt;p&gt;We can see numerous leaf structures in plant kingdom. As the leaves are designed for photosynthesis, their structure must be a factor for any optimization in photosynthesis or chlorophyll distribution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.ext.colostate.edu/mg/gardennotes/134.html&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt; describes many leaf structures but I cannot find what I am looking for in anywhere.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;I think taxonomy of plants deals with the flower structure but is their any relationship among plant species that we can describe with leaf structure ?&lt;/li&gt;&#xA;&lt;li&gt;Do the leaf structure is optimized for maximum photosynthesis rate if so then why these different structures ?&lt;/li&gt;&#xA;&lt;li&gt;Any other advantage for these diverse leaf structures ?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="10294" LastEditDate="2015-03-11T09:10:26.797" LastActivityDate="2015-03-11T15:51:33.473" Title="Relationship between leaf structure and Photosynthesis rate" Tags="&lt;botany&gt;&lt;taxonomy&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30320" PostTypeId="1" CreationDate="2015-03-11T04:31:01.997" Score="1" ViewCount="126" Body="&lt;p&gt;I know that cadherins control the expression of cancer cells involved in the epithelial-mesenchymal transitions, but I was wondering exactly how the process worked.&lt;/p&gt;&#xA;" OwnerUserId="12900" LastEditorUserId="14709" LastEditDate="2015-03-11T05:54:16.033" LastActivityDate="2015-03-11T05:54:16.033" Title="What are the roles of cadherins in epithelial mesenchymal transitions?" Tags="&lt;human-biology&gt;&lt;molecular-biology&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-03-11T18:17:22.933" ContentLicense="CC BY-SA 3.0" />
  <row Id="30321" PostTypeId="2" ParentId="30294" CreationDate="2015-03-11T05:00:42.777" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1007/s00468-014-1035-9&quot; rel=&quot;nofollow&quot;&gt;This review paper&lt;/a&gt; states that spruce is isohydric, citing &lt;em&gt;Physiologie und Ökologie der Gehölze&lt;/em&gt; by Lyr, Fiedler, &amp;amp; Tranquillini:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Spruce appears to reﬂect an isohydric strategy (Lyr et al. 1992), reducing stomatal conductance at early stages of soil drought.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's important to note that this is not a binary distinction, isohydric and anisohydric are two extremes in a spectrum of how plants respond to drought.&lt;/p&gt;&#xA;" OwnerUserId="11657" LastActivityDate="2015-03-11T05:00:42.777" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30322" PostTypeId="2" ParentId="30318" CreationDate="2015-03-11T05:03:16.737" Score="5" Body="&lt;p&gt;Genes, conventionally, are always written in italic (e.g. &lt;em&gt;SHH&lt;/em&gt;) which is not the case for proteins (in the former example SHH). That should allow you to tell apart gene and protein symbols (&lt;em&gt;SHH&lt;/em&gt; vs SHH).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The capitalization of gene/protein names is a bit more in the grey area. Usually one will use capitalized gene and protein symbols for human and primates (e.g. &lt;em&gt;SHH&lt;/em&gt; and SHH) and use non-capitalized symbols for mice and rat genes (e.g. &lt;em&gt;Shh&lt;/em&gt; but still SHH for the protein). This is dependent on the organism and journals usually have specific guidelines on how to exactly write gene and protein symbols.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your case the article refers to Rab6, Vps53 (not 35) and TNPO3 as proteins, if not clearly stated differently, such as the Rab6 siRNA, not only in the abstract alone but over the entire article. They use italic names for genes as shown in one of the sentence:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... and 48 hours later staining for p24, produced from the HIV &lt;em&gt;gag&lt;/em&gt; gene...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Just as a footnote, full gene names (e.g. the sonic hedgehog gene) are not italicized.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-21T18:27:37.267" LastActivityDate="2015-03-21T18:27:37.267" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30323" PostTypeId="2" ParentId="30320" CreationDate="2015-03-11T05:22:37.937" Score="0" Body="&lt;p&gt;So let's just quickly define what cadherins are, using general information from wikipedia,&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/A6PwQ.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Source: Wikipedia&lt;/p&gt;&#xA;&lt;p&gt;Cells express E-cadherin (epithelial), N-cadherin (neuronal, or P-cadherin (placental). These generally interact with ß-catenins to modulate cell adhesion. There are pathways intrinsic to cancer which downregulate the expression of cadherins,&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ufsZF.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.nature.com/onc/journal/v24/n50/full/1209091a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Epithelial–mesenchymal transition in development and cancer: role of phosphatidylinositol 3' kinase/AKT pathways&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;We see in the above pathway described in a study of PI3K/Akt signaling in cancer, some of the ways E-cadherin (encoded by CDH1) becomes downregulated. We also see that &lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023899&quot; rel=&quot;nofollow noreferrer&quot;&gt;ß-catenin may be sequestered by E-cadherin&lt;/a&gt; at the plasma membrane, and cytosolic ß-catenin actually interacts within the nucleus as a transcription factor for SLUG (or snail2) where &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21199805&quot; rel=&quot;nofollow noreferrer&quot;&gt;Snail2 is an essential mediator of Twist1-induced epithelial mesenchymal transition and metastasis&lt;/a&gt;. In the above figure this modulates reduced cell-cell adhesion, but we also see there's a number of other pathways which modulate the entirety of the EMT process.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;What I found interesting, maybe unrelated&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;An interesting concept currently being investigated involves many of the shown membrane receptors, most of which are involved in some sort of crosstalk in aggressive cancer types. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23771907&quot; rel=&quot;nofollow noreferrer&quot;&gt;ROR1 was identified as a critical component for modulating EMT&lt;/a&gt;, and was shown to participate in Wnt signaling through it's frizzled domain, as well as crosstalk with Met tyrosine kinase, EGFR, and TGFß in some way. These interactions were able to increase expression of snail1/2, vimentin, etc. &lt;em&gt;i.e.&lt;/em&gt; characteristics of EMT in breast adenocarcinoma (The linked article provides most of this background, but some may be missing, I'm unsure), and decrease expression of epithelial biomarkers like E-cadherin. When they used a ROR1 Ab to target ROR1, they found cadherin levels could be rescued, and morphological components returned to a more epithelial phenotype. Other articles showed this targeting could induce &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22289919&quot; rel=&quot;nofollow noreferrer&quot;&gt;apoptosis in CLL&lt;/a&gt; and this &lt;a href=&quot;http://meetinglibrary.asco.org/content/116631-132&quot; rel=&quot;nofollow noreferrer&quot;&gt;occurs through interaction with PI3K/Akt&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-11T05:34:12.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30324" PostTypeId="2" ParentId="30315" CreationDate="2015-03-11T05:23:27.537" Score="4" Body="&lt;p&gt;Short answer, in theory yes, in reality, at the current state of the art, no.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess you are speaking about higher organisms (such as mice or humans), if you are referring to small non-complex multicellular organisms then the answer is yes as far as you can transfect every cells with the system described hereafter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most promising technique is using the &lt;a href=&quot;http://en.wikipedia.org/wiki/CRISPR&quot; rel=&quot;nofollow&quot;&gt;CRISPR/Cas9&lt;/a&gt; system which has already been used to create all types of modified organisms but starting from the embryo. Here a good Nature reference &lt;a href=&quot;http://www.nature.com/nbt/journal/v32/n4/full/nbt.2842.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nbt/journal/v32/n4/full/nbt.2842.html&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are no ways, at the moment, to transfect an entire organism with the full system. The most recent attempts I heard off is to target specific cells using an encapsulation techniques that only merges with the membrane of specific cells therefore delivering the CRISPR/Cas9 system in a targeted manner. This was in an attempt to knock-out a defined genomic regions in those specific cells, not to introduce a new gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe in the near future that this will be possible. Not necessarily every cells of an organism but at least some specific cell types.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-11T05:31:50.920" LastActivityDate="2015-03-11T05:31:50.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30325" PostTypeId="2" ParentId="30310" CreationDate="2015-03-11T05:44:25.120" Score="2" Body="&lt;p&gt;Yes. The &lt;a href=&quot;http://lifecenter.sgst.cn/dbdepc/index.do&quot; rel=&quot;nofollow&quot;&gt;dbDEPC 2.0&lt;/a&gt; database for example.&#xA;If you want to extend your search to pathways the best database I know of is the &lt;a href=&quot;http://www.genome.jp/kegg/pathway.html&quot; rel=&quot;nofollow&quot;&gt;KEGG&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are multiple databases out there. You might want to look at this &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_biological_databases&quot; rel=&quot;nofollow&quot;&gt;wikipedia page&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way what you are looking for is called a &lt;strong&gt;cancer proteomic signature&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-11T05:52:58.700" LastActivityDate="2015-03-11T05:52:58.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30326" PostTypeId="1" CreationDate="2015-03-11T05:54:48.910" Score="5" ViewCount="5201" Body="&lt;p&gt;I'm reading a &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1931312811004033&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; and the authors mention a &quot;protein pulldown&quot; assay. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've never done this before, and googling doesn't bring up much. Could I get a rundown of the basic theory behind it? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also does % coverage have anything to do with this assay?&lt;/p&gt;&#xA;" OwnerUserId="13344" LastEditorUserId="3340" LastEditDate="2015-03-11T06:58:09.837" LastActivityDate="2015-03-11T06:59:07.357" Title="What's a protein pulldown assay?" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30327" PostTypeId="2" ParentId="30326" CreationDate="2015-03-11T06:10:16.787" Score="2" Body="&lt;p&gt;From &lt;a href=&quot;http://www.lifetechnologies.com/us/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/pull-down-assays.html&quot; rel=&quot;nofollow&quot;&gt;Life Technologies&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The pull-down assay is an in vitro method used to determine a physical interaction between two or more proteins. Pull-down assays are useful for both confirming the existence of a protein-protein interaction predicted by other research techniques (e.g., co-immunoprecipitation) and as an initial screening assay for identifying previously unknown protein-protein interactions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is essentially the same as an &lt;a href=&quot;http://en.wikipedia.org/wiki/Immunoprecipitation&quot; rel=&quot;nofollow&quot;&gt;immunoprecipitation&lt;/a&gt; experiment but using proteins instead of antibodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coverage comes into play for identifying the pulled-down proteins as they used an &lt;a href=&quot;http://en.wikipedia.org/wiki/Liquid_chromatography%E2%80%93mass_spectrometry&quot; rel=&quot;nofollow&quot;&gt;LC-MS/MS&lt;/a&gt; analysis. You essentially have to map back the short peptide reads you get from the MS to the actual pulled-down proteins which gives you a coverage score, i.e. how much of the full protein sequence you covered with short peptides.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="5144" LastEditDate="2015-03-11T06:43:11.317" LastActivityDate="2015-03-11T06:43:11.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30328" PostTypeId="2" ParentId="30326" CreationDate="2015-03-11T06:42:22.350" Score="6" Body="&lt;p&gt;Pull down mostly refers to immunoprecipitation, however pulling down can be done using other interactions such as streptavidin-biotin or His-tag-Nickel. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a protein pull-down a protein is enriched along with the molecules bound to it. When the DNA that is bound to a protein is studied, the experiment is called ChIP (Chromatin ImmunoPrecipitation). When other proteins that are bound to a given protein are studied then the experiment is called Co-IP. &#xA;Similarly RNA bound to protein can also be studied. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also possible to pull-down an RNA or a DNA fragment using complementary oligonucleotide, streptavidin, antibodies etc and study their interacting partners.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the linked paper, they have immunoprecipitated a HA (haemagglutinin) tagged protein using an anti-HA-tag antibody (Note that this is just a small tag of 9-10 amino acids and not the entire HA protein. Such tags are useful when you don't have the antibody for a given protein).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They have done both co-IP and ChIP:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;HA-tagged, full-length PfSET10 protein and interacting proteins from&#xA;  3D7/PfSET10HA and control line 3D7 were purified using anti-HA beads&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Chromatin Immunoprecipitation (ChIP) and Transcriptional Profiling&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;ChIP analysis was performed as described (Flueck et al., 2009).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Coverage is a term used in sequencing experiments which usually refers to average number of reads that map to any locus; this is also called &lt;strong&gt;depth&lt;/strong&gt;. This is commonly used in RNA/DNA sequencing studies (See &lt;a href=&quot;https://biology.stackexchange.com/questions/8048/results-of-a-complete-dna-sequencing-are-they-100-reusable/8050#8050&quot;&gt;this&lt;/a&gt; post too). In this paper, as mentioned in the other answer, the term coverage is used for peptide reads (analyzed by mass spectrometry) and it is the &lt;strong&gt;horizontal coverage&lt;/strong&gt; not a vertical coverage. Horizontal coverage refers to the fraction of actual molecule (DNA/RNA/protein) covered by the assembly of reads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coverage has got nothing to do with the pull-down assay; it is used in the context of the downstream experiment. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-03-11T06:59:07.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30329" PostTypeId="1" AcceptedAnswerId="30334" CreationDate="2015-03-11T10:18:14.130" Score="1" ViewCount="49" Body="&lt;p&gt;I have a list of differentially regulated genes from a high-throughput experiment of the human genome. I would like to find out which of these genes are transcribed by a RNA polymerase III and which of them (probably most) are transcribed by the RNA polymerase II.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have downloaded some Chip-Seq tracks for polymerase II and III and some GO categories which apply for the RNA polymerase III transcription.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have also tried the biomaRt repository to search for these mentioned GO categories, but I can't really find substantial results.&#xA;For example I have the gene RN7SL1 which according to the literature is transcribed by PolIII, but I'm not able to find any repository which also says so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any (better) way to search for this kind of data/annotations?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;thanks a lot &#xA;Assa&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS.&#xA;I am not sure, if I have found the correct GO categories (e.g. GO:0006383 - transcription from RNA polymerase III promoter). So are there any better one?&lt;/p&gt;&#xA;" OwnerUserId="14879" LastEditorUserId="3340" LastEditDate="2015-03-11T12:47:22.020" LastActivityDate="2015-03-11T14:00:55.420" Title="RNA-Polymerase III transcribed genes" Tags="&lt;bioinformatics&gt;&lt;gene-annotation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30330" PostTypeId="2" ParentId="30167" CreationDate="2015-03-11T10:22:54.430" Score="4" Body="&lt;p&gt;No, I don't think so. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mostly estuaries (brackish water) and marine biofilms on submerged surfaces are a reservoir for &lt;em&gt;Vibrio cholerae&lt;/em&gt;. Vibrio cholerae is isolated from rivers, creeks, washes, irrigation ditches, hulls of ships, etc. (Indeed, cholera spread rapidly throughout the world after the 1817 epidemic, largely due to the inadvertent transport of contaminated bilge water, mainly from British ships.)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Transmission is by the fecal–oral route. Infections are particularly common after ingesting contaminated water or food. Cases are occasionally seen in people who have eaten raw or undercooked shellfish, particularly oysters, from contaminated waters. V. cholerae is excreted in the feces and vomitus. Viable organisms can be found in feces for up to 50 days, on glass for up to a month, on coins for a week, in soil or dust for up to 16 days and on fingertips for 1 to 2 hours. Bacteria survive well in water and may remain viable in shellfish, algae or plankton in coastal regions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In 1855, a wave of cholera hit London. Thousands became ill and died before John Snow identified the Broad Street &lt;em&gt;water pump&lt;/em&gt; as the single point source of that outbreak. Today, patrons of the John Snow Pub (built on the site) can enjoy local ale, and more importantly, a glass of crystal clear, &lt;em&gt;pathogen-free water&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;V. cholerae&lt;/em&gt; [is] an autochthonous aquatic bacterium rather than a human pathogen that is a transient resident of the aquatic environment. &lt;em&gt;V. cholerae&lt;/em&gt; has over 200 serogroups, with O1 and O139 being the causative agents of cholera, due to their carriage of the genes encoding cholera toxin (CT) and the toxin co-regulated pilus. ...[A]ssociations with the human host is only one small aspect of the V. cholerae life cycle and is not necessary for environmental persistence. ...[T]his bacterium is a &lt;strong&gt;cosmopolitan aquatic species&lt;/strong&gt; that is capable of causing illness in humans.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Vibrio cholerae&lt;/em&gt; attachment is mediated by pili, which promote surface attachment and subsequent &lt;em&gt;biofilm&lt;/em&gt; formation. It is rather difficult to believe that an aquatic biofilm was preserved on the hill for all those years, even in a dormant stage.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...they could transform into a unique dormant stage that was able to survive for months &lt;em&gt;in the sediment of the estuary&lt;/em&gt;. ...These exciting new data enabled investigators to now integrate information regarding the seasonal nature of events surrounding an outbreak in populations living near estuaries.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I have found nowhere that the dormant stage can occur outside of water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3863721/&quot; rel=&quot;nofollow&quot;&gt;Environmental reservoirs and mechanisms of persistence of Vibrio cholerae&lt;/a&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.medicalecology.org/water/cholera/cholera.htm&quot; rel=&quot;nofollow&quot;&gt;Medical Ecology Main Page&lt;/a&gt;&lt;/sub&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.cfsph.iastate.edu/Factsheets/pdfs/cholera.pdf&quot; rel=&quot;nofollow&quot;&gt;Cholera&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt; Something goofy going on with these, sorry.&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-03-11T10:22:54.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30332" PostTypeId="2" ParentId="23635" CreationDate="2015-03-11T10:29:34.033" Score="0" Body="&lt;p&gt;The other day I was reading &quot;Sleep soundly every night,feeling fantastic everyday&quot; by Robert S. Rosenberg.&lt;br&gt;&#xA;Somewhere in the books it was written as:&#xA;&quot;Sound: You need your bedroom to not only be cool and dark, but also quiet. If a &lt;strong&gt;dripping faucet or the barking of a neighbor’s dog is interfering with your sleep, try earplugs, earphones, or generating white or pink noise to even the sound field so your ears won’t focus on the background contrast of environmental sounds&lt;/strong&gt;. There are machines available to do so, but for some the sound of a fan will do the trick. If your partner’s snoring is keeping you awake, you should encourage him or her to be checked by a doctor for sleep apnea. Treatment can improve your sleep and also might save his or her life.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;by searching more I found out that the difference between the range of frequencies from moment to moment is a more important factor than a sudden loud noise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea behind white or pink noise or the natural ones like the sound of fan is that they produce a broad range of frequencies at the same level.And by doing so they can reduce or at least mask the disruption.&lt;/p&gt;&#xA;" OwnerUserId="6927" LastActivityDate="2015-03-11T10:29:34.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30334" PostTypeId="2" ParentId="30329" CreationDate="2015-03-11T13:04:08.287" Score="1" Body="&lt;p&gt;GO is based on experimental evidences; biomart is quite good. GO:0006383 seems to be the right tag.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to use the ChIPseq data then you can do this:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Map the ChIPseq reads to the genome. If you already have the tracks&#xA;then you need not do the mapping. You would have the position of the&#xA;reads in the genome.&lt;/li&gt;&#xA;&lt;li&gt;Now count the number of reads mapping to each geneic region. The gene boundaries can be obtained from a GTF file.&lt;/li&gt;&#xA;&lt;li&gt;Optional: Normalize the reads with the length of the gene.&lt;/li&gt;&#xA;&lt;li&gt;Find the difference between the number of Pol-II and Pol-III reads for each gene. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;By doing this you still won't be able to say that &quot;&lt;em&gt;gene-x is transcribed by pol-III&lt;/em&gt;&quot;. All you can say is that &quot;&lt;em&gt;pol-III binds to that geneic region&lt;/em&gt;&quot;. If there is an even distribution of the ChIPseq reads along the gene then you can assume that there is an active transcription and the polymerase is not merely stalled. You can also do a CLIP (Crosslink-Immunoprecipitation) of Pol-III followed by a RNAseq. This will enable you to find RNAs transcribed by pol-III (this is a better way than ChIPseq but I don't think anyone has done it yet; so no ready data). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-11T14:00:55.420" LastActivityDate="2015-03-11T14:00:55.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30335" PostTypeId="1" AcceptedAnswerId="30341" CreationDate="2015-03-11T14:10:48.127" Score="2" ViewCount="5048" Body="&lt;p&gt;From what I understand, microRNA binds to proteins which can cut certain mRNA strands do that this protein is not synthesised. This seems like gene silencing to me, however I have also come across the term siRNA and antisense RNA...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would be grateful if someone could explain what these are and how they work, and perhaps how they can be applied to treating diseases... Thank you in advance :)&lt;/p&gt;&#xA;" OwnerUserId="6136" LastEditorUserId="4747" LastEditDate="2015-03-11T14:50:00.753" LastActivityDate="2015-03-11T15:07:44.350" Title="What are microRNA, siRNA and antisense RNA?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30336" PostTypeId="1" AcceptedAnswerId="30339" CreationDate="2015-03-11T14:16:17.603" Score="2" ViewCount="375" Body="&lt;p&gt;I am trying to find out what controls what exons are spliced out, and I keep coming across the term cis regulator, but I cannot seem to find a clear explanation of what happens...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: to clarify, I have tried to read the Wikipedia article on alternative splicing and I get the main idea (some exons being cut out of the mRNA with the introns to produce the mature mRNA, I think...) but I don't understand the 'mechanism' section, I.e. What controls which exons will be cut out? And what enzymes 'splice' the mRNA- how do they do it in the right place, and stick the mRNA together again?&lt;/p&gt;&#xA;" OwnerUserId="6136" LastEditorUserId="6136" LastEditDate="2015-03-11T14:50:50.870" LastActivityDate="2017-11-05T21:36:16.180" Title="How does alternative splicing work?" Tags="&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;rna&gt;&lt;transcription&gt;&lt;dna-methylation&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30337" PostTypeId="1" AcceptedAnswerId="30338" CreationDate="2015-03-11T14:26:23.250" Score="6" ViewCount="300" Body="&lt;p&gt;As the genetic code is universal, can mRNA from a human cell be correctly translated by a prokaryote in a in vitro translation system?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-03-11T14:38:03.790" Title="Can human mRNA be translated in vitro by prokaryotes?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;rna&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30338" PostTypeId="2" ParentId="30337" CreationDate="2015-03-11T14:38:03.790" Score="5" Body="&lt;p&gt;Short answer: Yes, you can. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually these are coupled systems for transcription and translation. For these you clone the gene of interest into a vector which contains a prokaryotic promoter which is then used to generate the mRNA in the tube. This mRNA is then translated in the second step into a protein. This works very well, but the protein is missing the typical post-translational modifications of eukaryotic cells like glycosylations, as these are not existant in the bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These kits can be purchased of the shelf from the usual biotech companies. Mostly these are based on &lt;em&gt;E.coli&lt;/em&gt; cell lysates. They work like shown in the figure (from &lt;a href=&quot;http://www.5prime.com/applications/protein-technologies/rts/technologies.aspx&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mW02O.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-03-11T14:38:03.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30339" PostTypeId="2" ParentId="30336" CreationDate="2015-03-11T14:48:21.947" Score="3" Body="&lt;p&gt;21joanna12, look into snRNPs.  These are parts of the splicosomal apparatus and some of them (the U1 and U2, U11 and U12 snRNPs) are also the guideposts that bind near the splice junctions at the end of introns.  These help guide the splicing apparatus to the splice sites. There are also proteins that bind RNA and interact with the splicing apparatus to switch alternative splicing, such as SP proteins.&lt;br&gt;&#xA;&lt;a href=&quot;https://en.wikipedia.org/wiki/SnRNP&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/SnRNP&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;https://en.wikipedia.org/wiki/SR_protein&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/SR_protein&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;https://en.wikipedia.org/wiki/Exonic_splicing_enhancer&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Exonic_splicing_enhancer&lt;/a&gt;     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a recent review that might serve as an entry into the literature: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4232567/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4232567/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10430" LastEditorUserId="10430" LastEditDate="2015-03-11T15:15:44.500" LastActivityDate="2015-03-11T15:15:44.500" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30340" PostTypeId="1" AcceptedAnswerId="30348" CreationDate="2015-03-11T14:53:41.267" Score="4" ViewCount="498" Body="&lt;p&gt;First off, let me start by outlining the problem:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your laboratory has established a technique for examining DNA replication in a cellular extract. To the cellular protein extract, you add nucleotides, a small amount of radiolabeled 32P-dGTP to aid visualization of the synthesized DNA, and a 4000-base-pair linear double-stranded DNA molecule that contains an origin of replication in the middle. After allowing the reaction to proceed for 30 minutes at 30°C, you boil the mixture to denature the proteins and the DNA strands, separate the components on an acrylamide gel, and detect the radiolabeled DNA products. This complete reaction is shown in lane 2 on the gel in the Figure below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/q0jJs.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Problem A:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;You perform the assay by yourself for the first time with no one else is in lab. The tube labeled “nucleotide mixture” has only enough for a single reaction, but you find a tube with a label that reads “dATP, dTTP, dGTP, dCTP” and you use this in a second reaction. You find the first reaction looks like lane 2 and the second reaction looks like lane 3. Why was no DNA synthesized in the second reaction?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because deoxyribose triphosphates do not have a –OH group to attach. You essentially can’t build with them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Problem B:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Your lab partner has recently isolated a mutant strain that can replicate its DNA normally at 30°C but exhibit no DNA replication at 40°C. He calls the mutant tsr1, for Temperature Sensitive Replication. The wild-type strain replicates efficiently at both temperatures. You believe that you can use the biochemical assay of cell extracts to identify which genes are defective in the mutant. You grow wild-type cells and tsr1 cells at 40°C, make the extracts, incubate the DNA replication reaction at 40°C, and detect the products on a gel. You observe the pattern shown in lanes 4 and 5. You are so excited by the results that you run to your lab partner and tell him that you know what enzyme is defective. He is delighted by your results but says that there are three different enzymes that can account for your results. What are they?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am 100% lost on this one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand from the figure that the wild-type at 40 degrees has 4000 nucleotides so it's not being cut off. The mutant, trs1 is being cut off one into two slices of 2000 and one of these slices has been cut off into slices of 500? Am I understanding this correctly?&#xA;I also don't understand why the 500 line is so thick compared to the others?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyhow I feel really confused on this. I've been learning about Sanger sequencing and it makes 100% sense with ddXTP added into the mix to view the length of each sequence and therefore be able to read the sequence, but I'm not even sure if that's what's happening here.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="5144" LastEditDate="2015-03-11T14:55:56.087" LastActivityDate="2015-03-11T18:41:19.120" Title="DNA sequencing problem" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;homework&gt;&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30341" PostTypeId="2" ParentId="30335" CreationDate="2015-03-11T15:07:44.350" Score="3" Body="&lt;p&gt;MicroRNA (miRNA) are gene-regulatory RNAs that are loaded onto the RNA-induced silencing complex (RISC) and interact with partially-complementary targets on mRNA to suppress protein expression.  The miRNA is originally double-stranded and composed of strands about 21 nucleotides long; on loading onto RISC, one strand is degraded and the other, the &quot;guide&quot; strand, is held on the surface of RISC where it can interact with mRNA. The targets recognized by the guide strand are most commonly on the 3'-untranslated region (UTR) of an RNA.  Binding can suppress assembly of an initiation complex on the 5' cap of an mRNA because the mRNA is bound into a circular shape at the initiation of translation, bringing the 3'-UTR and 5'-UTR close together.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the RISC loads an RNA than then finds a perfectly complementary target, RISC cleaves the target RNA using the activity of one of the protein components of RISC called Argonaute.  This property is exploited experimentally by manufacturing small interfering RNAs (siRNA) intentionally targeted to particular target sequences.  Once loaded into RISC these siRNA might recognize and cleave their perfectly complementary target sequence within an mRNA (though there is a significant failure rate, so several sequences are often tried).  The siRNA will also have miRNA-like effects on some partially-complementary targets on various mRNAs, leading to the observation that a single siRNA sequence can modulate expression of hundreds of off-target genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antisense is a nucleic acid strand (or nucleic acid analog) that is complementary to an mRNA sequence.  Antisense occurs naturally and can trigger RNA degradation by the action of the enzyme RNase H.  Originally natural antisense RNA was tried as a method for silencing a gene, but the poor stability of RNA in cells led to development of nucleic acid analogs that are more nuclease resistant and still activate RNase H (such as phosphorothioate RNA) and other nucleic acid analogs that bind to RNA and sterically inhibit processes without activating RNase H (such as 2'-O-methyl phosphorothioate RNA, Morpholino oligos, locked nucleic acids, or peptide nucleic acids).  These latter RNase-H independent oligos do not trigger degradation of mRNA but they can be used like molecular masking tape to block translation, alter splicing of pre-mRNA, inhibit activity of miRNA, block ribozyme activity, and interfere with various other processes that require some other factor to bind to a particular sequence on an RNA molecule.&lt;/p&gt;&#xA;" OwnerUserId="10430" LastActivityDate="2015-03-11T15:07:44.350" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30342" PostTypeId="1" AcceptedAnswerId="30344" CreationDate="2015-03-11T15:51:31.190" Score="5" ViewCount="146" Body="&lt;p&gt;I was reading &quot;&lt;a href=&quot;http://www.wisdom.weizmann.ac.il/~/eran/NucleosomeModel.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;A genomic code for nucleosome positioning&lt;/a&gt;&quot; (by Eran Segal et al). And I am having 2 doubts.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/7eyzE.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The figure(b) in this image from the paper shows the graph of fraction (3-bp moving average) of AA/TA/TT dinucleotides of nucleosome dna sequence they analysed statistically as far as I understand.&#xA;What is 3-bp moving average here?&#xA;I also don't understand how they chose 0th position (the so called dyad). &#xA;Also what does it mean to have oscillations (correlation?) in this graph?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;UPDATE : I am adding some supplementary information related to finding the dinucleotide fractions. Still I don't understand why is the fraction found so?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Lbb33.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5669" LastEditorUserId="5669" LastEditDate="2015-03-12T08:23:50.513" LastActivityDate="2015-03-12T09:13:03.527" Title="Doubt on genomic code for nucleosome positioning?" Tags="&lt;genetics&gt;&lt;epigenetics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30343" PostTypeId="2" ParentId="30319" CreationDate="2015-03-11T15:51:33.473" Score="2" Body="&lt;p&gt;1) Your understanding of taxonomy is outdated by a few hundred years. Linneaus' original system was based on flower morphology, but we since realized that the most effective taxonomy takes into account many different traits. In today's times, we mainly use DNA sequencing to determine relationships between organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The leaf structure is not necessarily only optimized for maximum photosynthesis rate. For instance, the leaves of cacti are spines: thin and pointy to minimize water loss and defend the plant. In fact in cacti the stem is the photosynthetic part of the plant, not the leaves. More generally, leaves may be thicker or thinner to cope with drought. You can check out the wikipedia page for &lt;a href=&quot;http://en.wikipedia.org/wiki/Specific_leaf_area&quot; rel=&quot;nofollow&quot;&gt;Specific Leaf Area&lt;/a&gt; for more information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Long story short: different plants grow in different environmental conditions, so the optimal leaf shape for any one plant depends on conditions like drought and shade.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) There are many advantages that can be conferred by leaf shape. One example is how leaf shape can affect what is known as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Boundary_layer&quot; rel=&quot;nofollow&quot;&gt;boundary layer&lt;/a&gt; of the leaf. The boundary layer is thicker in larger, uniformly-shaped leaves and thinner in dissected or compound leaves. The intro on &lt;a href=&quot;http://employees.csbsju.edu/ssaupe/biol327/Lab/Leaf_Lab/leaf_lab.htm&quot; rel=&quot;nofollow&quot;&gt;this webpage&lt;/a&gt; seems like a good resource&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall, good question. You have to keep in mind that any trait is going to be the product of many different factors; no one factor can entirely determine a trait's morphology. For leaves, it's many different factors including photosynthetic rate, drought, shade tolerance, defense against predators, etc. that determine the shape of the leaf.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-03-11T15:51:33.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30344" PostTypeId="2" ParentId="30342" CreationDate="2015-03-11T17:31:08.987" Score="4" Body="&lt;p&gt;Dyad is the centre of the DNA that is wrapped around the nucleosome core (It basically is the centre of symmetry of the nucleosome). It is a common practice to set it at 0 thereby making incoming DNA half, negative and outgoing DNA half, positive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By oscillations the authors mean that there is a periodic repeat of A/T dinucleotide. IMO it is actually not correct to call it oscillation which is mostly used in a time course dynamical sense. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess this is what is meant by the &lt;strong&gt;3-nt moving average&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You have conditional dinucleotide probabilities for each position (As shown in the figure). Now you calculate the A/T dinucleotide probability which is: &lt;pre&gt; P&lt;sub&gt;[A/T]&lt;/sub&gt; = P&lt;sub&gt;AA&lt;/sub&gt; + P&lt;sub&gt;AT&lt;/sub&gt; + P&lt;sub&gt;TT&lt;/sub&gt; + P&lt;sub&gt;TA&lt;/sub&gt;&lt;/pre&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now you find the moving average for 3 steps:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;MA&lt;sub&gt;(n)&lt;/sub&gt; = (1/3)×(P&lt;sub&gt;[A/T](n)&lt;/sub&gt; + P&lt;sub&gt;[A/T](n-1)&lt;/sub&gt; + P&lt;sub&gt;[A/T](n-2)&lt;/sub&gt;)&#xA;&#xA;&lt;i&gt;where &lt;b&gt;n&lt;/b&gt; is the n&lt;sup&gt;th&lt;/sup&gt; position of the DNA&lt;/i&gt;&lt;/pre&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-12T09:13:03.527" LastActivityDate="2015-03-12T09:13:03.527" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="30345" PostTypeId="2" ParentId="30089" CreationDate="2015-03-11T17:32:04.057" Score="5" Body="&lt;p&gt;I think the lack of sea ice coverage would point you somewhere- even with the maximum sea ice coverage picture, the SW corner of Greenland has next to none, which may impact the carrying capacity for both bears and prey animals on that narrow strip of land between the ice cap and the sea- less space and less things to hunt, less ways to get around, etc. And then there's not much continental shelf over there, either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Labrador is surrounded by more continental shelf, which might contribute to higher levels of sea ice at high levels and greater seasonality. Might lead to more prey?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This article might get you somewhere:&lt;a href=&quot;http://icb.oxfordjournals.org/content/44/2/163.abstract&quot; rel=&quot;noreferrer&quot;&gt;Polar Bears in a Warming Climate&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14886" LastActivityDate="2015-03-11T17:32:04.057" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30346" PostTypeId="2" ParentId="30308" CreationDate="2015-03-11T17:40:22.213" Score="8" Body="&lt;p&gt;There are photosynthetic archaea (such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Haloarchaea&quot; rel=&quot;noreferrer&quot;&gt;Halobacterium&lt;/a&gt;) but the mechanism is different. They use rhodopsin-like ion pumps (bacteriorhodopsin and halorhodopsin) to move ions against the gradient and produce ATP via chemiosmosis (like mitochondria). &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-14T06:06:04.950" LastActivityDate="2015-03-14T06:06:04.950" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30347" PostTypeId="1" CreationDate="2015-03-11T18:04:15.993" Score="3" ViewCount="121" Body="&lt;p&gt;We are looking for a way to insert DNA into a genome, but we would like to do it in a way that the recognition site stay intact to be able to add again DNA at the same location. Do you know if it is possible or if it is already the way CRISPR/Cas9 does it? Apparently multiple systems were already engineered but the few papers we read weren't about our problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sincerely,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Emilie &lt;/p&gt;&#xA;" OwnerUserId="14887" LastEditorUserId="14709" LastEditDate="2015-03-11T18:43:11.587" LastActivityDate="2015-04-11T02:27:20.077" Title="Is it possible to insert DNA without cutting the recognition site with CRISPR/Cas9?" Tags="&lt;dna&gt;&lt;synthetic-biology&gt;" AnswerCount="1" CommentCount="12" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30348" PostTypeId="2" ParentId="30340" CreationDate="2015-03-11T18:18:17.497" Score="5" Body="&lt;p&gt;Even though you - or the problem did not clarify, I assume in my answer that you work with eukaryote system, even though the principle of the replication is the same.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;dNTPs do have an OH group on their 3rd carbon atom (for eg. check this &lt;a href=&quot;http://en.wikipedia.org/wiki/Deoxycytidine_triphosphate&quot; rel=&quot;nofollow&quot;&gt;wiki-page&lt;/a&gt; for dCTP) so I don't think that's the issue here. My guess is that the first tube contains the radio labeled GTP and the second does not, so even the DNA is there, you cannot see it - even though the question specifically asked why DNA was not synthesized, my opinion is that it's a tricky question to confuse you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the second problem we need to dig into the replication process a little bit:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the replication fork the two strands are synthesized differently. The so called leading strand is made continuously, without interruptions, however the other strand - the so called lagging strand is synthesized by ligating small fragments - aka Okazaki fragments. These small fragments require their own RNA primers that need to be removed after synthesis is done.&#xA;Now since the origin of replication is in the middle and replication can proceed both ways, on a linear fragment such as yours you can get two 2000bp fragment from the two leading strands. Would it be a circular DNA, then you could still get 4kbp fragments since the replication could go around the DNA circle.&#xA;The smaller 500bp fragments that are quite abundant in the tsr1 lane, are the fragments that cannot be ligated. That being said I must admit that 500bp Okazaki-fragments would by atypical for eukaryotes (usual is around 100-200bp). So the enzymes responsible for this could be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA Ligase - the one responsible for ligating (joining ) the lagging strand's fragments.&#xA;Polymerase delta (Pol δ): That is responsible for lagging strand synthesis and primer removal - in this case the primer removal function might be defective, this causes that the primers stay on the DNA and complete synthesis and ligation cannot occur.&#xA;The last protein although it is not quite an enzyme is the DNA clamp complex (PCNA). This complex stabilizes the polymerase to DNA, but when reaching a previous fragment the polymerase should dissociate. But if the clamp is dysfunctional than the polymerase gets stuck on the end of the fragment thus no primer removal and ligation can occur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If need more info read this &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_replication&quot; rel=&quot;nofollow&quot;&gt;wiki-page&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-03-11T18:41:19.120" LastActivityDate="2015-03-11T18:41:19.120" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30349" PostTypeId="1" AcceptedAnswerId="30361" CreationDate="2015-03-11T19:08:22.893" Score="3" ViewCount="158" Body="&lt;p&gt;Why is knowledge of pathogenesis increased more and more for common bacterial pathogens? Most of these studies lack a near application in disease control such as vaccines or antibiotics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0882401008001381&quot; rel=&quot;nofollow&quot;&gt;Studies on the interactions of Haemophilus parasuis with porcine&#xA;epithelial tracheal cells: Limited role of LOS in apoptosis and&#xA;pro-inflammatory cytokine release&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10447878&quot; rel=&quot;nofollow&quot;&gt;Sialic acid in the lipopolysaccharide of Haemophilus influenzae:&#xA;strain distribution, influence on serum resistance and structural&#xA;characterization&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="5144" LastEditDate="2015-03-11T22:33:59.677" LastActivityDate="2015-03-11T22:33:59.677" Title="Why is knowledge of bacterial pathogenesis important?" Tags="&lt;bacteriology&gt;&lt;pathogenesis&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-03-12T07:25:38.093" ContentLicense="CC BY-SA 3.0" />
  <row Id="30351" PostTypeId="1" AcceptedAnswerId="30658" CreationDate="2015-03-11T19:23:25.413" Score="9" ViewCount="1398" Body="&lt;p&gt;So I ran into an interesting problem.  I'm getting a linear DNA band that is twice as long (4x bases, but as denatured probably only 2x) as an RNA band running at the same size in a formaldehyde gel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both sequences have been isolated an 100% confirmed.  The gel was run in MOPS buffer.  My experience, and all the publications I've found, show that if anything RNA should run faster.  Can anyone think of a reason why the DNA band and RNA band would be running the distance despite the DNA being twice as long?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've read a lot of fun papers on drag factors in gel matrices now, but none of it leads to this confusing and repeated result.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Edit: Gel and Conditions&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Gel was 1M formaldehyde, 1% agarose.  Run at 100V for 1.5h.  RNA was mixed in a RNA loading dye which contained 15.3% v/v formaldehyde, 41.3% v/v di formamide, 4.6mM EDTA, MOPS, and bromophenol blue.  We believe our RNA loading dye to be denaturing, and it ran at expected size with RNA ladder.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;................(1)........................(2)............................(3)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oYVA7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lane 1 is a DNA template plasmid, cut 1 location.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lane 2 is the Template + DNase from in vitro transcription reaction w/o polymerase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lane 3 is the RNA + DNase from in vitro transcription reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are no other bands in the DNA lane, and it looks like if anything, the DNA is migrating much faster than expected, despite being sequence confirmed (both before the process, and gel purified out and confirmed again).&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2015-03-13T13:51:32.427" LastActivityDate="2015-03-22T21:26:28.470" Title="RNA migrating slower than DNA on Formaldehyde Gel?" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="17" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30355" PostTypeId="1" AcceptedAnswerId="30356" CreationDate="2015-03-11T19:42:34.233" Score="6" ViewCount="892" Body="&lt;p&gt;I am reading the paper &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12499247&quot;&gt;Activity of the bcr-abl kinase inhibitor PD180970&lt;/a&gt;&quot; but I don't understand how IC50 works on table 1. Can you tell with simple words and give me an easy example?&lt;/p&gt;&#xA;" OwnerUserId="14888" LastEditorUserId="5144" LastEditDate="2015-03-11T20:10:24.107" LastActivityDate="2015-03-11T20:29:38.143" Title="What is the IC50 exactly?" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30356" PostTypeId="2" ParentId="30355" CreationDate="2015-03-11T20:06:12.520" Score="4" Body="&lt;p&gt;The IC&lt;sub&gt;50&lt;/sub&gt; is the concentration of an inhibitor at which you observe the half maximal inhibition. See the figure from the Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HnwOm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The IC&lt;sub&gt;50&lt;/sub&gt; can be seen as a way to measure the effectiveness of an inhibitor on a biological function as an enzyme. In the case of PD180970 you have an inhibitor which inhibits the p210 Bcr-Abl tyrosine kinase. The IC&lt;sub&gt;50&lt;/sub&gt; is the concentration at which 50% of the kinase is inhibited. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In table 1 different mutations of the tyrosine kinase are tested against the inhibitor to see, if the mutations have an influence on the IC&lt;sub&gt;50&lt;/sub&gt;. This is important as PD180970 is considered as an anti-cancer drug and possible mutations would make it less effective here.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-03-11T20:12:36.440" LastActivityDate="2015-03-11T20:12:36.440" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30357" PostTypeId="2" ParentId="30355" CreationDate="2015-03-11T20:08:44.283" Score="4" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/IC50&quot; rel=&quot;nofollow noreferrer&quot;&gt;IC50&lt;/a&gt; is the concentration of inhibitor required to reduce the activity of a molecule/protein by one-half. It is the inverse of &lt;a href=&quot;http://en.wikipedia.org/wiki/EC50&quot; rel=&quot;nofollow noreferrer&quot;&gt;EC50&lt;/a&gt;. Usually inhibition curves looks sigmoidal so the IC50 is the middle point of the S curve. Here an example. (Note that the Y-axis can be pretty much anything, like enzyme activity and the X-axis is the concentration in a logarithmic scale).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/68HEc.gif&quot; alt=&quot;Illustration&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-11T20:29:38.143" LastActivityDate="2015-03-11T20:29:38.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30361" PostTypeId="2" ParentId="30349" CreationDate="2015-03-11T20:49:09.930" Score="3" Body="&lt;p&gt;Because it is first important to understand a mechanism before you can think about using it for drugs. Take melanoma for example: A large subset of melanoma has a mutated and constitutive active BRAF kinase which permanently signals towards the nucleus and thus deregulates gene expression. Once this mutation was found it was possible to design inhibitors which only work on this specific mutation, which are available in the clinic today.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same is true for example for activity of antibiotic on bacteria and the fight against resistance. Once it was known that the enzyme beta lactamase inhibits beta lactam antibiotice (penicillin or ampicillin for example) it was possible to find an inhibitor of the enzyme. The clavulanic acid works as a specific inhibitor and has been added to beta lactam antibiotics subsequently to overcome resistance. The same is true for changing antibiotic molecules chemically so they evade the established resistance mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The contributions of basic research is the basis for applied research and drug design. Without them, this wouldn't work. Besides that it is also the curiosity of humans which drives science - without having any particular application in mind. These often come much later.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-03-11T20:49:09.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30362" PostTypeId="1" AcceptedAnswerId="30586" CreationDate="2015-03-11T21:52:20.930" Score="10" ViewCount="574" Body="&lt;p&gt;I live in central Massachusetts, and have begun seeing robins, as we generally do in early March. The temperature is well below normal, though, and three feet of snow are covering the still-frozen ground from which they usually feed. We were expecting them to arrive late, when conditions would seem more conducive to survival. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What triggers their migration process?&lt;/p&gt;&#xA;" OwnerUserId="13148" LastEditorUserId="3624" LastEditDate="2015-03-12T13:21:32.503" LastActivityDate="2017-03-01T01:59:04.883" Title="What triggers the migration of robins?" Tags="&lt;ecology&gt;&lt;ornithology&gt;&lt;ethology&gt;&lt;phenology&gt;&lt;migration&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30363" PostTypeId="1" CreationDate="2015-03-11T21:56:10.997" Score="2" ViewCount="1000" Body="&lt;p&gt;Surfactant is a protein lipid mixture produced by alveolar pneumocytes composed of Dipalmitoyl Phosphatidyl Choline lipid, apoproteins and calcium ions.&#xA;This surface lines the alveolar epithelium thereby reducing surface tension preventing lungs from collapse.&#xA;Atelectasis is collapse of lung mainly due to lack of surfactant.&#xA;Moreover it may also be due to obstruction of the airway tract.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is why is this surfactant found to be lowered in patients who have undergone cardiac surgery under pump oxygentor? Why does long term exposure to 100% Oxygen affect the surfactant.&#xA;Is it due to its chemical composition or is it something to do with pulmonary circulation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This Wikipedia article states alveolar collapse due to Oxygen Toxicity &#xA;&lt;a href=&quot;http://en.m.wikipedia.org/wiki/Oxygen_toxicity&quot; rel=&quot;nofollow&quot;&gt;http://en.m.wikipedia.org/wiki/Oxygen_toxicity&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9919" LastEditorUserId="15136" LastEditDate="2015-04-07T10:33:30.907" LastActivityDate="2015-04-07T10:33:30.907" Title="Atelectasis due to decreased surfactant in lungs" Tags="&lt;human-biology&gt;&lt;respiration&gt;&lt;lungs&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30364" PostTypeId="2" ParentId="30362" CreationDate="2015-03-11T22:01:55.240" Score="2" Body="&lt;p&gt;I'm not a specialist in this area, but I would guess that the length of day-light periods compared to night time could be a good trigger. This is quite independent of the weather, is quite constant (even though length of days is known to have changed through over the millions of years past since the formation of earth).&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-03-11T22:01:55.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30365" PostTypeId="1" AcceptedAnswerId="30382" CreationDate="2015-03-11T22:07:10.410" Score="8" ViewCount="23164" Body="&lt;p&gt;Yesterday I had a discussion with a friend. He said that consuming proteins and amino-acids is different. He said that those who grow muscles would agree on that. I wanted to argue against that statement, but I lacked arguments... As far as I know, amino-acids are part of proteins. So, when proteins go to our body with food, we digest it and make amino-acids. Then they can form any kind of proteins we need. The same would happen when consuming amino-acids directly, not in protein form. Maybe then the process would be faster. But from my point of view, there is no much of a difference. Could anyone please give me a more sound opinion on why is consuming proteins and amino-acids different, if it is?&lt;/p&gt;&#xA;" OwnerUserId="14891" LastActivityDate="2015-08-14T22:32:31.493" Title="Is consuming proteins different vs. consuming amino-acids and how?" Tags="&lt;proteins&gt;&lt;amino-acids&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30366" PostTypeId="1" CreationDate="2015-03-11T22:32:38.740" Score="0" ViewCount="178" Body="&lt;p&gt;Antarctic Phosphatase is used to catalyze the removal of 5' phosphate from DNA. If I'm using it in the lab on a sample of 1-5 micrograms of digested DNA, how would I figure out how long to incubate the sample at 37 degrees Celsius?  &lt;/p&gt;&#xA;" OwnerUserId="12899" LastActivityDate="2015-03-12T04:45:01.833" Title="Incubation time of Antarctic Phosphatase in lab" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ClosedDate="2015-03-12T13:19:13.360" ContentLicense="CC BY-SA 3.0" />
  <row Id="30370" PostTypeId="1" AcceptedAnswerId="30373" CreationDate="2015-03-11T23:55:35.823" Score="7" ViewCount="859" Body="&lt;p&gt;Jacob-Monod model for the lac Operon was based on experiments using two strands of bacteria which constitutively expressed $\beta$-gal: $I^{c}$(mutation in the gene lacI , which encodes the repressor) and $O^{c}$(mutation in the operator, the site where the repressor binds).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$I^{c}$ mutants are usually recessive: the Lac Repressor cannot bind to the operator, however, if a wild-copy of the gene is present in a merodiploid, the inducible pattern of expression is restored, because the Lac Repressor acts in trans (that is, it will inhibit expression of both operons when lactose is not present).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I've &lt;a href=&quot;http://ocw.mit.edu/courses/biology/7-03-genetics-fall-2004/lecture-notes/lecture16.pdf&quot;&gt;read&lt;/a&gt; that there's a strain ($lacI^{d}$) which is dominant, so the expression is constitutive even in the presence of the normal repressor. According to the article linked, abnormal subunits may mix with normal subunits, resulting in a disfunctional tetramer, even if a wild type lacI is also present.&#xA;In terms of protein structure, why some mutations may have this effect and be dominant while other mutations do not interfere with normal copies of the protein and are recessive?&lt;/p&gt;&#xA;" OwnerUserId="14630" LastEditorUserId="14630" LastEditDate="2015-03-12T01:07:58.433" LastActivityDate="2015-03-17T18:36:35.627" Title="Mechanism by which $lacI^{d}$ is a dominant mutation, impairing the function of normal copies of the Lac Repressor" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;gene-expression&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30371" PostTypeId="1" CreationDate="2015-03-12T00:21:56.310" Score="6" ViewCount="220" Body="&lt;p&gt;Let's imagine  that we understood DNA programming and our genome very well and realized that there were some significant flaws (we die, we need sleep, etc.) And let's imagine that we understand how to make our genome do what we want, but it's a major refactor.  We're going to have adjust 10-15% of our DNA. (Note this is just a contrived example to suggest why we would want to make such a drastic change - our ability to actually know what changes to make is unimportant for the question.)  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How would we replace/or modify this much of our DNA?  It seems the problem is very similar to &lt;a href=&quot;http://en.wikipedia.org/wiki/Gene_therapy&quot; rel=&quot;nofollow noreferrer&quot;&gt;gene therapy&lt;/a&gt;, but on a larger scale.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few possibilities come to mind.  We could make a virus that would modify our DNA.  Or perhaps we could generate the new genome and inject it into some cells which would then just outlive the others (eg because these cells won't have a &lt;a href=&quot;http://en.wikipedia.org/wiki/Hayflick_limit&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hayflick limit&lt;/a&gt;) or will be able to generate lots of new adult stems cells with the &quot;refactored&quot; DNA?  &lt;/p&gt;&#xA;" OwnerUserId="13238" LastEditorUserId="6307" LastEditDate="2017-08-04T18:08:22.860" LastActivityDate="2017-08-04T18:08:22.860" Title="How would you effect bulk DNA gene therapy for a human?" Tags="&lt;dna&gt;&lt;synthetic-biology&gt;&lt;human-genome&gt;&lt;gene-therapy&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30372" PostTypeId="1" CreationDate="2015-03-12T01:01:25.233" Score="1" ViewCount="390" Body="&lt;p&gt;I am trying to figure out the details of the homolougous recombination in order to be able to insert a certain piece of DNA in the host genome after double strand break.. Does anybody know how long the homology arms of the repair template must be ? Can the left arm be longer than the right one? I have read several papers which have different sizes 90 bp vs kb..&#xA;In my case, i am not so much preoccupied by off target but the insertion should occur also on the desired site possibly at high frequency and as fast as possible.&#xA;Thank you,&#xA;Paola&lt;/p&gt;&#xA;" OwnerUserId="4746" LastActivityDate="2015-03-12T01:37:22.320" Title="How long the homologous arms of the &quot;repair&quot; sequence must be to do homologous recombination?" Tags="&lt;recombination&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2015-03-13T13:59:09.307" ContentLicense="CC BY-SA 3.0" />
  <row Id="30373" PostTypeId="2" ParentId="30370" CreationDate="2015-03-12T01:07:41.067" Score="4" Body="&lt;p&gt;The lac repressor act as a tetramere molecule and requires &lt;strong&gt;all 4&lt;/strong&gt; of the subunit to be able to bind DNA to act on the operon and repress β-galactosidase expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;all 4&quot; is the key here, if &lt;strong&gt;any of the 4 subunits is unable&lt;/strong&gt; to bind DNA then the whole complex cannot attach to the operon. The &lt;em&gt;lacI&lt;sup&gt;d&lt;/sup&gt;&lt;/em&gt; mutation produces a repressor subunit that cannot attach DNA, &lt;strong&gt;yet can tetramerize with other lac repressor subunits&lt;/strong&gt;, therefore impeding WT subunits to bind the operon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For your question on the protein structure. Mutations can occur at different locations in a gene and therefore impact different proteins domains. Proteins contain different type of domains, such as an active site for an enzyme or a binding sites for attaching to the DNA. A mutation might act on one of the domain while leaving others fully functional.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your case this is exactly what happens, the mutation is in the protein region involved in binding DNA but does not affect the region involved in the protein-protein binding with other subunits.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-12T01:14:11.690" LastActivityDate="2015-03-12T01:14:11.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30374" PostTypeId="1" AcceptedAnswerId="30375" CreationDate="2015-03-12T01:11:34.957" Score="4" ViewCount="191" Body="&lt;p&gt;If not, is it impossible for DNA to have enzymatic activity?&lt;/p&gt;&#xA;" OwnerUserId="14741" LastActivityDate="2015-03-12T09:37:19.120" Title="Is there a DNA analogue to ribozymes?" Tags="&lt;dna&gt;&lt;rna&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ClosedDate="2015-03-12T09:28:42.987" ContentLicense="CC BY-SA 3.0" />
  <row Id="30375" PostTypeId="2" ParentId="30374" CreationDate="2015-03-12T01:31:02.257" Score="5" Body="&lt;p&gt;Not very common, and &lt;strong&gt;not found so far in nature&lt;/strong&gt;, but they exist and are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Deoxyribozyme&quot; rel=&quot;nofollow&quot;&gt;deoxyribozymes&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additional information:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Deoxyribozymes are the equivalent of ribozymes in the DNA world and can function as catalysts for different biochemical reactions, such as DNA cleavage. While DNAzymes (short name) were synthesized in a laboratory context (&lt;em&gt;In-vitro&lt;/em&gt;) and proved to be active, no observations were made of DNA molecules having an enzymatic activity &lt;em&gt;In-vivo&lt;/em&gt; which is of course not a definitive proof they don't exist in nature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The latter point is a major difference compared to ribozymes which were proved to be active and functional in living cells.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-12T09:37:19.120" LastActivityDate="2015-03-12T09:37:19.120" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30376" PostTypeId="2" ParentId="30372" CreationDate="2015-03-12T01:37:22.320" Score="2" Body="&lt;p&gt;As little as 14bp of homology can work. See this &lt;a href=&quot;http://mcb.asm.org/content/4/11/2253&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would recommend at least a length of 90bp but 1kb is probably overkilled. Yes both arms can have different length (staying in the same order of magnitude).&lt;/p&gt;&#xA;" OwnerUserId="14826" LastActivityDate="2015-03-12T01:37:22.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30377" PostTypeId="2" ParentId="30347" CreationDate="2015-03-12T02:14:52.777" Score="1" Body="&lt;p&gt;Look into &lt;a href=&quot;http://en.wikipedia.org/wiki/Site-specific_recombination&quot; rel=&quot;nofollow noreferrer&quot;&gt;site-specific recombination&lt;/a&gt;.  You can use a site-specific recombinase, specifically an integrase, that can insert a sequence of DNA at a certain attachment site.  You can add an identical attachment site into the DNA sequence to insert, allowing for the reintegration of a new attachment site.  Note however that you might get SSR onto the insertion plasmid itself, so don't do this if you need a specific amount of integration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sES0K.png&quot; alt=&quot;Look at the bottom subfigure of A for an example of integration.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look at the bottom subfigure of A for an example of integration.  Recombinases can also do other things, such as excision and inversion, based on the orientation of the attachment sites.&lt;/p&gt;&#xA;" OwnerUserId="14741" LastActivityDate="2015-03-12T02:14:52.777" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30379" PostTypeId="1" CreationDate="2015-03-12T03:06:17.390" Score="3" ViewCount="288" Body="&lt;p&gt;For example, when one takes aspirin or ibuprofen does the chemical get dispersed to all pain receptor? My question really is, how does the chemical know where to target in the body? I figure wherever there is pain in the body that a certain signal is being produced; which possibly acts as a chaperone to direct the medication chemical where to bind and inhibit.&lt;/p&gt;&#xA;" OwnerUserId="12891" LastEditorUserId="6" LastEditDate="2015-03-12T11:11:56.020" LastActivityDate="2015-03-12T14:15:49.780" Title="Is there a specific mechanism for the delivery of pain medication?" Tags="&lt;pharmacology&gt;&lt;pain&gt;&lt;receptor&gt;&lt;pharmacokinetics&gt;&lt;pharmacodynamics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30380" PostTypeId="1" CreationDate="2015-03-12T03:22:13.583" Score="4" ViewCount="3017" Body="&lt;p&gt;The line patterns on the hand are unique to each individual, but what causes these lines and re they advantageous in anyway?&lt;/p&gt;&#xA;" OwnerUserId="12891" LastActivityDate="2015-04-26T14:44:56.080" Title="What causes the line patterns in the palm of the hand?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;skin&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30381" PostTypeId="1" AcceptedAnswerId="30393" CreationDate="2015-03-12T03:36:35.007" Score="1" ViewCount="62" Body="&lt;p&gt;The catabolite activator protein (CAP) activates the expression of more than 100 genes involved in secondary sugar metabolism in E.coli.&#xA;Apparently, it always binds in sites that are away from -10 and -35 elements of the promoter by &lt;strong&gt;multiples of 10 base pairs (-70 or -60, for example)&lt;/strong&gt;. How could this be related to its mechanism of action?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've searched about this particular activator and I found that it acts mainly by recruiting RNAP to weak promoters, although it does alter the architecture of the DNA, introducing an abrupt bend (for some CAP-dependent genes, this favours conformational changes in RNAP involved in the initialization of transcription): &lt;a href=&quot;http://www.sciencemag.org/content/253/5023/1001&quot; rel=&quot;nofollow&quot;&gt;here's the crystallographic data&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I did not find anything conclusive about the pattern of binding to distances which are usually multiple of 10 base pairs (which is close to the number of base pair in a complete turn of the double helix).&lt;/p&gt;&#xA;" OwnerUserId="14630" LastEditorUserId="14630" LastEditDate="2015-03-12T03:47:05.970" LastActivityDate="2015-03-12T14:16:45.790" Title="How to correlate the pattern by which CAP activator from E.coli binds to DNA and its mechanism of action?" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30382" PostTypeId="2" ParentId="30365" CreationDate="2015-03-12T03:37:52.810" Score="5" Body="&lt;p&gt;To put it shortly: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Proteins have properties that individual amino acids that make up the protein does not have. &lt;/li&gt;&#xA;&lt;li&gt;Similarly the individual amino acids have properties that the protein does not have. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This is analogous to elements vs compounds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The site referenced below quotes 3 experiments done to examine this phenomena. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All experiments compared effectiveness of whey protein with that of essential amino acid (EAA) supplements. Experiments 1 and 2 involved old people while experiment 3 involved young people. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conclusion of experiments is as follows: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Both EAA and whey protein (15 g of EAA and 15 g whey was taken by the respective groups) induced muscle growth, however EAA had better anabolic effect as compared to whey. &lt;/li&gt;&#xA;&lt;li&gt;In this 3 groups were compared. 15 g of whey vs 6.72 g of EAA vs. 7.57 g of non-essential amino acids. &lt;strong&gt;Whey had higher anabolic effect as compared to EAA while the third group showed no improvement&lt;/strong&gt;. This additional anabolic effect is attributed to unknown mechanisms. The anabolic effect was measured using a different method add compared to the first experiment. So results may not be comparable. &lt;/li&gt;&#xA;&lt;li&gt;In this 3 groups of young men were compared. The first group was given carbohydrate (30 g) and EAA (15 g) drink, the second group liquid meal containing same quantity of EAA and total 850 calories while the third group was given both. The conclusion: &#xA;&lt;ul&gt;&#xA;&lt;li&gt;The third group, as expected had the highest anabolic rate &lt;/li&gt;&#xA;&lt;li&gt;The first group (protein and carbohydrate drink) had better anabolic rate when compared with the liquid meal group though they both took the same amount of EAA. The difference was in carbohydrate content. The liquid meal had higher carbohydrates content when compared with the first group. &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Whey has insulinogenic effect invitro. Whey also has the same effect whether taken before or after exercise while the protein drink has better effect when taken before exercise. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Among amino acids leucine, when taken alone has anabolic effect comparable to a mixture of EAA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;However, whey contains various bioactive peptides that act to enhance recovery and potentially in other ways that positively effect the adaptive process to exercise (12). These bioactive peptides are not found in EAA, BCAA, or Leucine, and appear to be a unique quality to dairy proteins. So what we can't say is that these aminos are the deciding factor in whey's effects...or that we can use one in place of the other (interchangeably) in all cases.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.vpxsports.com/article-detail/supplements/whey-protein-versus-amino-acids-whats-the-difference&quot; rel=&quot;nofollow&quot;&gt;http://www.vpxsports.com/article-detail/supplements/whey-protein-versus-amino-acids-whats-the-difference&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please read the article which has more details and graphs and references for further study. &lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-03-12T08:38:23.313" LastActivityDate="2015-03-12T08:38:23.313" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30383" PostTypeId="1" AcceptedAnswerId="30385" CreationDate="2015-03-12T03:42:08.690" Score="5" ViewCount="326" Body="&lt;p&gt;Is there a reason for the choice of E.coli as a model for many bacterial systems? Other bacteria such as B.subtilis are also used, but why is E. coli preferred?&lt;/p&gt;&#xA;" OwnerUserId="14630" LastActivityDate="2015-03-12T05:58:07.770" Title="Why is E.coli used as a model?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;bacteriology&gt;&lt;history&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30384" PostTypeId="2" ParentId="30379" CreationDate="2015-03-12T03:46:01.047" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;No, orally taken painkillers act systemically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Taking a painkiller orally results in the drug being taken up into the bloodstream by the digestive system. From there it can potentially reach all tissues.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, a pain response does not act as a chaperone. A hypothetical drug that would home in on tissues with a pain response, while avoiding unaffected tissues would be the ultimate painkiller, if it existed.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT:&lt;/strong&gt; To emphasize that painkillers act systemically I will elaborate on aspirine's pharmacokinetics. Notably, aspirine's actions are &lt;em&gt;not&lt;/em&gt; restricted to the pain centers in the brain, and I quote the following excerpt from Wiley's interactive Concepts in Biochemistry]&lt;a href=&quot;http://www.wiley.com/legacy/college/boyer/0471661791/cutting_edge/aspirin/aspirin.htm&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Aspirin's analgesic and anti-inflammatory effects are due to the drug's ability to stop the production of prostaglandins that cause &lt;strong&gt;tissue swelling and pain&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Aspirin's antipyretic (fever-reducing) effect is due to its direct action on the &lt;strong&gt;hypothalamus gland&lt;/strong&gt;, which results in vasodilation of peripheral blood vessels and sweating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prostaglandins are also the key mediators of &lt;strong&gt;platelet aggregation&lt;/strong&gt;. By modifying the COX enzymes within platelets, aspirin causes platelets to lose the &quot;stickiness&quot; that is needed to stimulate blood clotting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, by these examples it can be seen that aspirine works in the &lt;strong&gt;periphery (wound swelling and pain)&lt;/strong&gt;, &lt;strong&gt;centrally (brain's hypothalamus)&lt;/strong&gt; as well as in the &lt;strong&gt;bloodstream&lt;/strong&gt;. Hence, aspirine (and other orally administered painkillers) do &lt;em&gt;not&lt;/em&gt; target specific areas in the body, and most certainly not only the brain.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are such targeted drugs, however. An interesting one is carbamezipine, an anti-epileptic that blocks Na&lt;sup&gt;+&lt;/sup&gt; channels. It blocks Na&lt;sup&gt;+&lt;/sup&gt; channels only when they are in an active conformation, however (i.e., engaged in action potential firing). Epileptic activity is basically paroxysmal (massive), synchronous over-activity in the brain that is accompanied by massive Na&lt;sup&gt;+&lt;/sup&gt; channel activity. Hence, epileptic activity will in effect trigger the drug into action.  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-12T14:15:49.780" LastActivityDate="2015-03-12T14:15:49.780" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="30385" PostTypeId="2" ParentId="30383" CreationDate="2015-03-12T04:11:06.727" Score="4" Body="&lt;p&gt;Short answer. It was discovered pretty early (late 1800's). It is easy to get (you probably know where it comes from), purify, grow and is not virulent. &lt;em&gt;E.coli&lt;/em&gt; spreads very rapidly (30 minutes division rate).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why this one in particular and not another similar bacteria? Well you have to choose something at some stage and usually the more an organism is used the most valuable it becomes which means that more and more scientists will start to use it creating a loop which favors certain organisms, like it happened with &lt;em&gt;E.coli&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;E.coli&lt;/em&gt; started to be studied because Theodor Escherich wanted to prove the &lt;a href=&quot;http://en.wikipedia.org/wiki/Germ_theory_of_disease&quot; rel=&quot;nofollow&quot;&gt;&quot;germ theory of disease&quot;&lt;/a&gt; which led him and later other scientists to work with &lt;em&gt;E.coli&lt;/em&gt; and everybody uses it today.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, the mouse model is actually quite interesting. Started by breeding huge amount of mice for selling them as pets.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-12T05:58:07.770" LastActivityDate="2015-03-12T05:58:07.770" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30386" PostTypeId="2" ParentId="30366" CreationDate="2015-03-12T04:45:01.833" Score="1" Body="&lt;p&gt;For 5' extensions or blunt ends, incubate the sample for 15 minutes at 37 degrees Celsius.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For 3' extensions, incubate the sample for an hour.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.neb.com/protocols/1/01/01/vector-dephosphorylation-protocol&quot; rel=&quot;nofollow&quot;&gt;https://www.neb.com/protocols/1/01/01/vector-dephosphorylation-protocol&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="11855" LastActivityDate="2015-03-12T04:45:01.833" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30387" PostTypeId="2" ParentId="30379" CreationDate="2015-03-12T05:02:57.063" Score="2" Body="&lt;p&gt;Most &lt;a href=&quot;https://en.wikipedia.org/wiki/Nonsteroidal_anti-inflammatory_drug&quot; rel=&quot;nofollow&quot;&gt;NSAIDs&lt;/a&gt; derive their analgesic effects from inhibit the cyclooxygenase (COX) enzymes that produce the prostaglandin-H2 precursor to the prostaglandins that sensitize neurons to pain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;: With respect to where this takes place, the COX enzymes are expressed in inflamed tissues as well as constitutively in the stomach and kidney. The prostaglandins whose production they block act on the spinal nerves and can diffuse across the blood-brain barrier. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="13072" LastEditDate="2015-03-12T10:26:12.597" LastActivityDate="2015-03-12T10:26:12.597" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30389" PostTypeId="2" ParentId="30380" CreationDate="2015-03-12T07:36:32.463" Score="3" Body="&lt;p&gt;The lines on the hand are known as &lt;a href=&quot;http://medical-dictionary.thefreedictionary.com/flexion+crease&quot; rel=&quot;nofollow noreferrer&quot;&gt;flexion creases&lt;/a&gt;, and they exist because in their absence, the skin will stretch outwards when the palm is closed due to the decreased surface area of the closed palm, causing problems with gripping. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Developmental disorders such as Down Syndrome often cause there to be only one palm line, known as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Single_transverse_palmar_crease&quot; rel=&quot;nofollow noreferrer&quot;&gt;simian crease&lt;/a&gt;, as shown on the left. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Bgvxcm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/a6NDYm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-03-12T07:36:32.463" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30392" PostTypeId="2" ParentId="25913" CreationDate="2015-03-12T13:48:30.420" Score="1" Body="&lt;p&gt;In a side-by-side comparison of 3 viral proteins (2 from paramyxoviridae, 1 from caliciviridae) each with both a &quot;maximizing&quot; and &quot;matched&quot; codon bias, we found the &quot;maximized&quot; version produced more protein the &quot;matched&quot; version in each instance.  Protein levels were quantified via Western and flow, cell lines tested were 293T, HEp2 (HeLa contaminate), and Vero.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is certainly not wide enough testing for any kind of general statement, it's just what we found.  I think this will take a cell bio or pure micro-bio lab to fully study.  We're in infectious diseases, and this question would be off grant and off topic for the paper.  If we can find a way to squeeze it into a publication we will.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm going to accept Jan's answer because it contains more information on optimization, but with this answer in place to:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Address what we observed.&lt;/li&gt;&#xA;&lt;li&gt;Note that Jan's doesn't offer any information on &quot;matching&quot; the codon bias of the target host (other than perhaps noting optimization is heuristic).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2015-03-12T14:27:47.977" LastActivityDate="2015-03-12T14:27:47.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30393" PostTypeId="2" ParentId="30381" CreationDate="2015-03-12T14:16:45.790" Score="0" Body="&lt;p&gt;I found a great &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765107/&quot; rel=&quot;nofollow noreferrer&quot;&gt;article&lt;/a&gt; that might help. To summarize the contents of the article, there are two classes of CAP dependent promoters/genes, and the distance of the CAP bindings site in these classes are different. Also the actions in which CAP is involved are different in the two classes of promoters. In the first class it does not overlap with the promoter region and is only involved in RNAP recruitment. In the second class it overlaps with -35 element of the core promoter and is involved in multiple interactions. &#xA;So the binding distance of the CAP is determines what interactions is it involved. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see the difference between the two classes on the picture below (taken from the article i linked). And I think this answers your question on why the patterns are multiples of ten - because this is the space needed for alpha-CTD to make a bridge between the protein complexes, or the CAP to interact with the RANP complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/r2sGn.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I only took a glance at the paper I linked and quickly extracted the info, but I hope it still helps&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-03-12T14:16:45.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30394" PostTypeId="2" ParentId="30371" CreationDate="2015-03-12T15:35:03.937" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Let's imagine that we understood DNA programming and our genome very well and &gt;realized that there were some significant flaws (we die, we need sleep, etc.) And &gt;let's imagine that we understand how to make our genome do what we want, but it's a &gt;major refactor. We're going to have adjust 10-15% of our DNA.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think we both recognise that this is a very naive view of biology and the nature of how organismal properties emerge (through multiple levels of systems) ultimately from the genetic code, the information in the genome, and the developmental process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is more pertinent and promising to think about treating genetic diseases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some genetic diseases are caused by mutations to single basepairs (e.g. the HgbS variant of the haemoglobin beta chain, which causes sickle-cell anaemia).&#xA;Other genetic diseases are caused by rearrangements of large segments of chromosomes, and the gene dosage imbalances that arise from this (e.g. Charcot-Marie-Tooth syndrome 1A). Finally, some genetic diseases are caused by a major gene-dosage imbalance caused by having an unusual set of chromosomes, &quot;aneuploidy&quot; (e.g. down syndrome, where chromosome 21 is present in 3 copies).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;'Large-scale' gene therapy could be something useful for aneuploidy. &lt;a href=&quot;http://www.nature.com/nature/journal/v500/n7462/full/nature12394.html&quot; rel=&quot;nofollow&quot;&gt;Recently, the mechanism for inactivating one X-chromosome in female somatic cells has been applied to silencing the surplus chromosome 21 of Down Syndrome.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencemag.org/content/344/6179/55&quot; rel=&quot;nofollow&quot;&gt;In yeast, a 'designer chromosome' has been chemically synthesised, and has been used to replace the corresponding native chromosome in yeast cells.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So although I think the &lt;em&gt;premise&lt;/em&gt; of your question is basically science-fiction and naive, it is becoming possible to silence or replace whole chromosomes. More realistically than making our species immortal and ever-awake, this technology could possibly translate to therapies for some genetic diseases. But of course, the problem of retrospectively getting your therapy in to many somatic cells is still there. Engineering zygotes is feasible but has ethical problems - also, where pre-implantation screening is permitted, IVF can simply include genetic selection rather than genetic engineering!&lt;/p&gt;&#xA;" OwnerUserId="13310" LastActivityDate="2015-03-12T15:35:03.937" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30395" PostTypeId="2" ParentId="30193" CreationDate="2015-03-12T15:48:07.070" Score="3" Body="&lt;p&gt;A single ovule in a fruit is pollinated by a single grain of pollen. So, in theory, a fruit with n seeds can be pollinated by n grains of pollen. In reality, of course, not every pollen grain makes it to the ovules, but if we treat your assumption as true, then a flower can be fully pollinated by as many pollen grains as there are ovules in the flower. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you plant your zucchini and cross your zucchini flower with pollen from spaghetti squash and orange-fleshed squash, you will end up with a zucchini fruit filled with seeds that are either half spaghetti squash or half orange-fleshed squash. If you planted the seeds from that zucchini, you would end up with some individual plants that have spaghetti-squash traits and some with orange-fleshed squash traits. You would not end up with any plants with both stringy and orange-fleshed fruit.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-03-12T15:48:07.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30396" PostTypeId="1" AcceptedAnswerId="30399" CreationDate="2015-03-12T16:08:12.413" Score="16" ViewCount="15452" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Translation, or decoding, of the four-nucleotide language of DNA and&#xA;  mRNA into the 20–amino acid language of proteins requires tRNAs and&#xA;  enzymes called aminoacyl-tRNA synthetases. To participate in protein&#xA;  synthesis, a tRNA molecule must become chemically linked to a&#xA;  particular amino acid via a high-energy bond, forming an&#xA;  aminoacyl-tRNA; the anticodon in the tRNA then base-pairs with a codon&#xA;  in mRNA so that the activated amino acid can be added to the growing&#xA;  polypeptide chain.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Some 30–40 different tRNAs have been identified in bacterial cells&#xA;  and as many as 50–100 in animal and plant cells. Thus the number of&#xA;  tRNAs in most cells is more than the number of amino acids used in&#xA;  protein synthesis (20) and also differs from the number of amino acid&#xA;  codons in the genetic code (61). Consequently, many amino acids have&#xA;  more than one tRNA to which they can attach ; in addition, many tRNAs&#xA;  can pair with more than one codon.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If perfect Watson-Crick base pairing were demanded between codons and anticodons, cells would have to contain exactly 61 different tRNA species, one for each codon that specifies an amino acid. As noted above, however, many cells contain fewer than 61 tRNAs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the explanation for the smaller number of tRNA than  codons codons?&lt;/p&gt;&#xA;" OwnerUserId="14709" LastEditorUserId="14709" LastEditDate="2015-05-04T13:59:26.247" LastActivityDate="2018-05-03T07:52:27.767" Title="What is the explanation for the smaller number of tRNA than codons?" Tags="&lt;biochemistry&gt;&lt;rna&gt;&lt;amino-acids&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30397" PostTypeId="2" ParentId="30396" CreationDate="2015-03-12T16:32:17.147" Score="4" Body="&lt;p&gt;Watson-Crick base pairing can be violated by &lt;a href=&quot;http://en.wikipedia.org/wiki/Wobble_base_pair&quot; rel=&quot;nofollow&quot;&gt;wobble base pairing&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The 5' of the anticodon has more freedom in binding, that is why, for many amino acids, the last part of the codon has more possible characters.&lt;/p&gt;&#xA;" OwnerUserId="14698" LastEditorUserId="14698" LastEditDate="2015-03-12T16:38:10.997" LastActivityDate="2015-03-12T16:38:10.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30399" PostTypeId="2" ParentId="30396" CreationDate="2015-03-12T16:55:21.957" Score="17" Body="&lt;p&gt;Th reason for this is that for the third base of the tRNA non-Watson-Crick pairing is allowed. This phenomenon is called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Wobble_base_pair&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wobble base pairing&lt;/a&gt;&quot;. See the figure (from here) for illustration (from &lt;a href=&quot;http://www.mun.ca/biology/scarr/iGen3_06-08.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/43ars.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have a look at the codon table for amino acids, than the variation in the code for one amino acid mostly happens on the third position (from &lt;a href=&quot;http://weloveteaching.com/0bio105/lectures/organics/proteinsynthesis.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PmCFm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This allows a smaller number of tRNA than 64, as there is some flexibility. The third base can be represented like this (taken from &lt;a href=&quot;https://biology.stackexchange.com/questions/23508/redundancy-of-the-genetic-code/46640#46640&quot;&gt;this&lt;/a&gt; answer):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/1BndE.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/1BndE.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the table Cricks predictions are compared to the pairings found in experiments.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2018-05-03T07:52:27.767" LastActivityDate="2018-05-03T07:52:27.767" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="30400" PostTypeId="1" AcceptedAnswerId="30402" CreationDate="2015-03-12T19:38:51.403" Score="7" ViewCount="3789" Body="&lt;p&gt;I’ve found many sources about the positive effects of kefir for the digestive system. However I haven’t found any information about the fermenting process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the exact biology (chemistry?) behind the process of milk becoming kefir?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do the kefir grains exactly consume from the milk? And what do they defecate?  What happens inside the microbes? &lt;/p&gt;&#xA;" OwnerUserId="14901" LastActivityDate="2015-03-12T20:08:21.573" Title="What happens during kefir fermentation process?" Tags="&lt;microbiology&gt;&lt;ecology&gt;&lt;food&gt;&lt;milk&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30401" PostTypeId="2" ParentId="30400" CreationDate="2015-03-12T20:04:34.450" Score="5" Body="&lt;p&gt;Well essentially the added Lactobacillus species ferment lactose and other sugars to lactic acid, thus lowering the pH of the product (they take up lactose use it as an energy source under anaerobic conditions and secrete lactic acid). This gives the kefir and other fermented milk products their sourness. Also the lower pH prevents many other bacteria from growing in the product so this is also serves as a natural preservation method. Further more the low pH can denature some of the protein in the milk/kefir resulting in a more solid form. Many of these Lactobacillus species or their relatives are natural part of our gut flora.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-03-12T20:04:34.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30402" PostTypeId="2" ParentId="30400" CreationDate="2015-03-12T20:08:21.573" Score="5" Body="&lt;p&gt;The fermentation is relatively complex, as quite a number of different bacterial species and yeast live in the Kefir grains. These are made of of the polysaccheride &lt;a href=&quot;http://en.wikipedia.org/wiki/Kefiran&quot;&gt;kefiran&lt;/a&gt; which immobilizes the bacteria (in contrast for example to yoghurt). The microbes live symbiotic on this matrix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the references a number of different microorganisms has been found, these include mainly Lactic acid bacteria, followed by yeasts and acetic acid bacteria. The species include: &lt;em&gt;Lactobacillus paracasei, Lactobacillus parabuchneri, Lactobacillus casei, Lactobacillus kefiri, Lactococcus lactis, Acetobacter lovaniensis, Kluyveromyces lactis, Kazachstania aerobia, Saccharomyces cerevisiae&lt;/em&gt; and &lt;em&gt;Lachancea meyersii&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In brief the lactobacilli break down lactose to produce lactic acid, while the yeasts make alcohol and carbon dioxide while the acetobacter species make acetic acid. This consumes the lactose and the fat content of the milk making it suitable for lactose intollerant people. It also lowers the pH of the kefir. The exact mixture is hard to identify as this contains strongly on the exact composition of the kefir grains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested further, I recommend you have a look into the references, I find both articles relatively good to understand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24031681/&quot;&gt;Brazilian kefir: structure, microbial communities and chemical&#xA;composition.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24294220&quot;&gt;Microbiological, technological and therapeutic properties of kefir: a&#xA;natural probiotic beverage.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-03-12T20:08:21.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30403" PostTypeId="1" AcceptedAnswerId="30961" CreationDate="2015-03-12T21:20:12.023" Score="5" ViewCount="258" Body="&lt;p&gt;I'm working with data downloaded from STRING database (string-db.org) for protein-protein interactions.&#xA;My idea is to compare the topology of connections of the same protein on different organisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I noticed that the same protein can receive different ID on each organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I would like to know if there is any way to convert all ID's into just one pattern.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="14902" LastActivityDate="2015-04-01T07:45:12.940" Title="Help with STRING database data" Tags="&lt;bioinformatics&gt;&lt;protein-interaction&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30404" PostTypeId="1" AcceptedAnswerId="30509" CreationDate="2015-03-12T21:29:12.107" Score="8" ViewCount="566" Body="&lt;p&gt;I am interested in creating Bayesian Skyline Plots to look at demographic changes in certain population groups. However, these populations have very little within population variation. Around 5 polymorphic sites within each population and one dominating haplotype that comprises almost 90% of the population (the rest being rare haplotypes). Because, BSP uses Coalescent processes for the calculations, the sample sizes would have a effect on the results. I wanted to know if sample sizes of around 30 (for DNA alignments of 700bp) would be ideal for carrying out the analysis and expect reasonably good results ?&lt;/p&gt;&#xA;" OwnerUserId="18932" LastEditorUserId="3340" LastEditDate="2015-03-17T12:45:22.237" LastActivityDate="2015-03-17T13:24:11.837" Title="What sample sizes are ideal for carrying out Bayesian Skyline Plots?" Tags="&lt;bioinformatics&gt;&lt;population-biology&gt;&lt;demography&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30405" PostTypeId="1" CreationDate="2015-03-12T23:47:53.063" Score="2" ViewCount="185" Body="&lt;p&gt;By bullying, I mean individuals harassing others with name-calling or violence but not for the purpose of gaining resources such as with extortion or theft. The only explanation I've thought of is that bullying offers practice for types of extortion that do result in increased resources.&lt;/p&gt;&#xA;" OwnerUserId="14904" LastEditorUserId="9943" LastEditDate="2015-03-12T23:59:28.767" LastActivityDate="2019-07-22T19:48:47.820" Title="How did bullying arise evolutionarily?" Tags="&lt;evolution&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30406" PostTypeId="1" CreationDate="2015-03-12T23:52:10.347" Score="5" ViewCount="154" Body="&lt;p&gt;I'm not strong in biology, so bear with me on this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been reading that as we age, our DNA is damaged by internal (e.g. errors during replication) and external (e.g. sun damage or radiation) factors.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;If you take, say, an 80 year old, can you find DNA in their body that's the same as when they were a newborn? What kind of cells would have undamaged DNA?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is DNA damage distributed evenly across the body or will some parts have more damage than others?   &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is there any published data on how much DNA damage an average person accumulates over their lifetime? I'm not sure how this can be quantified, but I'm wondering if there has been any study on gauging damage.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="14903" LastActivityDate="2015-03-13T00:24:20.280" Title="Questions on DNA damage" Tags="&lt;dna&gt;&lt;dna-damage&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30407" PostTypeId="2" ParentId="30406" CreationDate="2015-03-13T00:04:07.713" Score="1" Body="&lt;p&gt;You've asked a number of questions here, but yes -- mutation rates have been studied extensively in humans as well as in model organisms. And as you suggest, they vary substantially across tissues. One starting point to read about how mutation rates are measured and how they vary across species, tissues, etc., is a 2010 &lt;a href=&quot;http://www.indiana.edu/~lynchlab/PDF/Lynch183.pdf&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Trends in Genetics&lt;/em&gt; review&lt;/a&gt; by Mike Lynch. See particularly Table 1. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-03-13T00:04:07.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30408" PostTypeId="2" ParentId="30406" CreationDate="2015-03-13T00:24:20.280" Score="2" Body="&lt;p&gt;Excellent question! &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;You would definitely be able to find quite a few &lt;em&gt;sequences&lt;/em&gt; of DNA that are undamaged (in fact most of them would be undamaged), but it is very unlikely that any cells in his/her body would have a perfect copy of the entire original genome.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I'm sure that cells closer to the skin (exposed to more radiation) would have more mutations, but beyond that most everything depends on where you live, your habits, etc. (if you're a smoker you will obviously have more mutations in your lung cells).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Under regular circumstances (low levels of mutagens), about 3 nucleotide mutations occur in the human genome per cell per division (DNA replication) (from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26881/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK26881/&lt;/a&gt;). The rest of the math would be a very rough estimate, seeing as you'd need to make a lot of assumptions (cell division rate average, other mutagens an organism may encounter, life span, the list goes on), but however you want to do it, there's the number you need to start with.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I hope this helps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CDB&lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-03-13T00:24:20.280" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30409" PostTypeId="2" ParentId="30405" CreationDate="2015-03-13T02:42:54.917" Score="2" Body="&lt;p&gt;I think bullying is really more of an emergent behavior that manifests itself because of natural aggression built in for survival, as well as our complex social-based psychology leading to insecurity when dealing with other:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;People who are highly aggressive, and or apathetic to the suffering of others are more likely to control a majority of resources if they don't face significant opposition. This leads to their favored propagation obviously. Then, in their free-time, with all resources under control, they simply continue to do what comes naturally to them: dominating others. It can also work even in those without the ability to actually control resources, due to lack of intelligence for instance. I have met far more non-intelligent bullies than the reverse. The reason for their behavior is still explained by an attempt to control their territory and social status, however ineffective.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Again, due to our complex psychology centered around social interaction, we can develop insecurities about our self-perceived 'fitness', and therefore acceptance by mates and peers. This low self-esteem can lead to bullying others to boost one's ego. Chemically, this can result in a release of endorphins because they feel they have achieved something, which supports bullying behavior as an emergent behavior. Also, those with lower intelligence are likely to have trouble with reasoning skills, and therefore find it difficult to self-analyze and realize their behavior is negative. This leads to bad interactions with others, which can make those individuals feel even more insecure, which in turn fuels their drive to assert themselves through bullying.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Many studies have been conducted on sociopaths/psychopaths. Just like any other evolved trait, whether or not their &quot;personality disorder&quot; is beneficial to the propagation of their genes depends on environmental factors. If they face only opposition from entities that are relatively weak, physically and mentally, then they have an advantage over those peers. But if their peers are sufficiently strong and organized, then the personality disorder becomes a disadvantage if they can't adapt, because they will be attacked by those seeking cooperation from others when they misbehave. Obviously, when our species' numbers were few, high-aggression and a willingness to kill for resources needed for survival aided in survival. In these modern times, its less acceptable for socio/psychopaths to display their innate behavior, due to modern laws, but obviously society can take turns that allow them to express themselves without worry...see the holocaust or any other genocide for an example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://link.springer.com/article/10.1007/s40806-017-0097-5&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://link.springer.com/article/10.1007/s40806-017-0097-5&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=2ahUKEwj5vKjk88bjAhUfJTQIHaFDA9wQFjABegQIARAC&amp;amp;url=https%3A%2F%2Fwww.apa.org%2Fpubs%2Fjournals%2Freleases%2Famp-a0038929.pdf&amp;amp;usg=AOvVaw1fUJiPHl8rSKMm6Gc9VEeA&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=2ahUKEwj5vKjk88bjAhUfJTQIHaFDA9wQFjABegQIARAC&amp;amp;url=https%3A%2F%2Fwww.apa.org%2Fpubs%2Fjournals%2Freleases%2Famp-a0038929.pdf&amp;amp;usg=AOvVaw1fUJiPHl8rSKMm6Gc9VEeA&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8619" LastEditorUserId="8619" LastEditDate="2019-07-22T19:48:47.820" LastActivityDate="2019-07-22T19:48:47.820" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="30410" PostTypeId="1" CreationDate="2015-03-13T03:05:05.740" Score="1" ViewCount="1090" Body="&lt;p&gt;I am a M.SC(mathematics) student. I have no subject like mathematically modelling.But  i'm interesting in research in mathematical biology.Initially which book i should study.&#xA;Please guide me.THANKS...&lt;/p&gt;&#xA;" OwnerUserId="14906" LastActivityDate="2015-03-13T03:32:47.247" Title="books for beginners in research in mathematical biology" Tags="&lt;book-recommendation&gt;" AnswerCount="2" CommentCount="3" ClosedDate="2015-03-13T06:00:42.807" ContentLicense="CC BY-SA 3.0" />
  <row Id="30411" PostTypeId="2" ParentId="30410" CreationDate="2015-03-13T03:12:53.393" Score="2" Body="&lt;p&gt;Probably the best contemporary book taking a broad view of mathematical biology modeling is &lt;a href=&quot;http://press.princeton.edu/titles/8458.html&quot; rel=&quot;nofollow&quot;&gt;Otto and Day's&lt;/a&gt; 2007 book &lt;em&gt;A Biologist's Guide to Mathematical Modeling in Ecology and Evolution&lt;/em&gt; published by Princeton University Press.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also a number of books that focus on more specific areas e.g. mathematical population genetics, ecological modeling, infectious disease epidemiology, etc. But without knowing which areas of modeling interest you it is difficult to recommend at this level.&lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="13072" LastEditDate="2015-03-13T03:32:41.630" LastActivityDate="2015-03-13T03:32:41.630" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30412" PostTypeId="2" ParentId="30410" CreationDate="2015-03-13T03:32:47.247" Score="0" Body="&lt;p&gt;The post is too broad. Mathematics is used in tons of different fields of biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Population genetics is one of the main field of biology that is contains quite a lot of mathematical formulations. &lt;a href=&quot;https://biology.stackexchange.com/questions/16470/book-recommendation-on-population-evolutionary-genetics&quot;&gt;This post&lt;/a&gt; gives a list of references for books in population genetics.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-03-13T03:32:47.247" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30413" PostTypeId="1" CreationDate="2015-03-13T03:37:56.693" Score="7" ViewCount="24319" Body="&lt;p&gt;This is a lab question I cant find the answer in the lab manual or in the text book.&#xA;What physiological processes in a muscle cause the latent period in a muscle fiber?&#xA;Please help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&#xA;The latent period is the short delay between the muscle action potential and the beginning of muscle tension development. This is what I'm talking about. I'm sorry I didn't make that clear.&lt;/p&gt;&#xA;" OwnerUserId="14907" LastEditorUserId="14615" LastEditDate="2015-03-15T10:22:30.697" LastActivityDate="2015-03-26T04:40:45.363" Title="What physiological processes within a muscle cause the latent period in a muscle fiber?" Tags="&lt;physiology&gt;&lt;muscles&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30414" PostTypeId="2" ParentId="20028" CreationDate="2015-03-13T03:53:13.997" Score="2" Body="&lt;p&gt;Like with the rat monogamous pair bond study a similar experiment was done with monogamous Prarie voles where they found similar results. Women naturally Have more neurological receptors in their brains for oxytocin. The rise in oxytocin comes from blood level measurements so when people say oxytocin rises through orgasm they mean it rises in the blood stream. So oxytocin the neurotransmitter or hormone? When Looking at oxytocin in the brain we only see it under an MRI scan highlighted in a certain area. As far as men men's bodies excrete record high levels of a hormone called Vasopressin which they call the (monogamy) hormone during orgasm and after sex. Testosterone mutes oxytocin in the bloodstream but testosterone increases vasopressin meaning for a man vasopressin is like Oxytocin. Estrogen increases oxytocin but progesterone mutes it. To answer your question women are not wired to bond to something that doesn't have biological capability to bond with her back. The mass media is trying to make it seem that way. Humans and many other mammals release bonding hormones during sex and mating. Oxytocin and Vasopressin are key and both men and women release them. &lt;/p&gt;&#xA;" OwnerUserId="14908" LastActivityDate="2015-03-13T03:53:13.997" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30416" PostTypeId="1" CreationDate="2015-03-13T04:17:04.827" Score="6" ViewCount="101" Body="&lt;p&gt;I am looking for examples (if any) of genomic regions which regulates the activity of enhancers, either augmenting or reducing it. Essentially some kind of enhancers (or repressors) of enhancers to make a Russian doll analogy. I know about epigenetic markings but I am really looking at an example of a DNA region directly acting on a enhancer similar to an enhancer acting directly onto a promoter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am asking that because I couldn't find any examples and was wondering if I missed such a report/paper.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-13T04:42:17.690" LastActivityDate="2015-04-15T21:02:52.703" Title="&quot;Enhancers&quot; of enhancers?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30417" PostTypeId="1" AcceptedAnswerId="30423" CreationDate="2015-03-13T04:30:38.400" Score="7" ViewCount="123" Body="&lt;p&gt;I know about enhancers and the mechanism that lead them to increase the gene expression of their targets but I was wondering if similarly DNA repressors exist. I know about protein repressors but I am looking for some kind of anti(or reversed)-enhancer equivalent in the genome which would act like an enhancer but reduce gene expression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am aware of repressed/poised enhancers which would kind of be that process, even if not really a pure repression of the target gene but rather a &quot;non-overexpression&quot;. I also know about insulators but again this would be a different mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some intergenic region binding protein repressors which by a folding mechanism similar to enhancers would repress a gene perhaps?&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-13T05:33:40.317" LastActivityDate="2015-03-13T09:43:03.740" Title="Do DNA repressors exist?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30418" PostTypeId="1" AcceptedAnswerId="30425" CreationDate="2015-03-13T05:04:25.400" Score="14" ViewCount="3200" Body="&lt;p&gt;Do transcription factors (or generally proteins) bind to only single strand of DNA or both strands? Since it can have non covalent bonds to both strands in theory. I would like to know the mechanism. Any reference books, papers or links will be helpful.&lt;/p&gt;&#xA;" OwnerUserId="5669" LastEditorUserId="948" LastEditDate="2015-03-16T17:25:03.437" LastActivityDate="2015-03-17T12:43:56.343" Title="Do transcription factors bind to both strands of DNA?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;protein-binding&gt;&lt;transcription-factor&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30420" PostTypeId="2" ParentId="29918" CreationDate="2015-03-13T07:52:20.273" Score="3" Body="&lt;p&gt;One important notion in DNA topology is the linking number ($Lk$) which is the sum of right-handed twisting # and left-handed writhing # ($Tw+Wr$). Say the $Lk = x$ for relaxed DNA. If $Lk&amp;lt;x$ then you have negative supercoiling while positive supercoiling happens when $Lk&amp;gt;x$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The higher the $Lk$ value the higher the helical energy of the DNA and the harder it is to separate it meaning the DNA is now more stable. In so-called &quot;extreme&quot; conditions (e.g. high acidity or high T˚) the organism must protect his DNA from degradation. Therefore those organisms require a more stable form of their DNA which can be achieve by positive-supercoiling and/or high GC content.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now why do the vast majority of the organisms have negatively-supercoiled DNAs? If you let the DNA by itself, it will adopt an $Lk=x$, i.e. it will be in his &quot;relaxed&quot;-form. Negative supercoiling arose because of the presence of Topoisomerases (type I and II), which are proteins that cleave the DNA and release the helical tensions and which cumulatively provokes the DNA to be slightly underwinded compared to it's relax-form. Is this good for the organism, if living in non aggressive conditions? Yes it is because a decrease of the $Lk$ will make the DNA easier to separate. This means replication and transcription can occur more easily or in proper terms, they now require less energy to perform their functions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here an excellent &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK22498/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt; on this subject as well as a &lt;a href=&quot;https://www.youtube.com/watch?v=BKSiCSfEuF0&quot; rel=&quot;nofollow&quot;&gt;Youtube video&lt;/a&gt; that explains those concepts using strings. The latter is really helpful as those concepts are easier to understand visually than in writing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-13T08:38:22.227" LastActivityDate="2015-03-13T08:38:22.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30421" PostTypeId="2" ParentId="30413" CreationDate="2015-03-13T08:42:41.257" Score="4" Body="&lt;p&gt;The action potential causes Ca2+ ions to be released in the cells, that is needed for muscle fiber contraction. There is a small time delay from the arrival of the action-potential until the Ca-ions are released and reach the required concentration in the cell for contraction. On the molecular level there is a protein called troponin (this is bacically located on the actin filament along with tropomyosin and obscures the myosin binding site(s)), that bind calcium and then undergoes conformational change - this also adds up to the delay. After this - the conformational change of troponin - myosin and actin can bind together and contraction can occur through conformational changes. All these binding and conformation changes take a small time to be completed, and thus causes a small delay. Below is a picture about the molecular mechanism ofof muscle contraction taken from this &lt;a href=&quot;http://en.wikipedia.org/wiki/Muscle_contraction&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki&lt;/a&gt; page. The linked wiki page has real good detailed information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tBEft.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4274888/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; article and where they exactly measured things. To clarify my answer (taken from the linked article):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Electromechanical delay (EMD) was described as a time elapse between the onset of muscle electrical activation and onset of force production, reflecting both electrochemical processes [i.e., synaptic transmission, propagation of the action potential, excitation-contraction (EC) coupling] and mechanical processes [i.e., force transmission along the active and passive parts of the series elastic components (SECs)] &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So as for the whole muscle, not for just one cell the delay is caused by the things listed in the above quote - although excitation-contraction (EC) coupling and force transmission (things I have described earlier) take place in every single muscle cell that is in a specific muscle fiber. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit 2: I found a good and simple ppt/pdf about AP propagation and muscle contraction &lt;a href=&quot;http://www.kean.edu/~jfasick/docs/Fall%20Semester%20Lectures%20Chapt.%201-15%20%20%2707/Chapter%209B.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-03-13T18:38:11.667" LastActivityDate="2015-03-13T18:38:11.667" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30422" PostTypeId="1" AcceptedAnswerId="30501" CreationDate="2015-03-13T09:38:04.587" Score="1" ViewCount="174" Body="&lt;p&gt;There are two types of interaction classifications used to describe Protein-protein interactions, namely physical and functional. Whilst physical interactions are obvious in nature and methodological determination, I was wondering what a functional interaction/linkage refers to, such as the one cited in the below paper, and is it purely inferred from genomic data?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14654685&quot; rel=&quot;nofollow&quot;&gt;Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps.&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="6289" LastEditDate="2015-03-14T22:25:39.883" LastActivityDate="2015-03-17T15:29:20.280" Title="What are genome wide functional linkages?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30423" PostTypeId="2" ParentId="30417" CreationDate="2015-03-13T09:43:03.740" Score="9" Body="&lt;p&gt;Yes, these sequences exist and they are called &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Silencer_%28DNA%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;silencers&lt;/a&gt;&quot; (surprising, right?). There are different mechanisms by which this silencing of genes can happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the &quot;classical&quot; way the silencer is bound by a  transcription factor which either passively suppress the gene by hindering the binding of specific transcription factors or by actively preventing the assembly of the general transcription factors. See the figure from paper 1:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UyanS.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally there are non-classical negative regulatory element (NRE), which are usually elements upstream of the promoter which inhibit the binding regulatory proteins. NRE can also be enhancers depending on the proteins bound on them. Some NRE can induce a bend of the DNA, inhibiting the access to enhancer or promoter elements.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9512455&quot; rel=&quot;nofollow noreferrer&quot;&gt;Transcriptional control and the role of silencers in transcriptional&#xA;regulation in eukaryotes.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bejerano.stanford.edu/readings/public/10_Intro_TxRegReview.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Transcriptional Regulatory Elements in the Human Genome&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-03-13T09:43:03.740" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30425" PostTypeId="2" ParentId="30418" CreationDate="2015-03-13T17:20:22.530" Score="14" Body="&lt;p&gt;The short summary is that typical TFs bind and read &lt;strong&gt;both&lt;/strong&gt; strands together, &lt;strong&gt;as a basepair sequence&lt;/strong&gt;. Some proteins instead recognise a site on the helix by its &lt;strong&gt;shape and flexibility&lt;/strong&gt;. ssDNA-binding proteins obviously bind one strand but they do this in a &lt;strong&gt;non-specific&lt;/strong&gt; manner.&#xA;RNA-binding proteins recognise the sequence on a single strand by inserting intercalating planar residues between bases! All of this binding is &lt;strong&gt;non-covalent&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Transcription factors recognise sites in dsDNA, with &lt;em&gt;DNA-binding domains&lt;/em&gt;. The rest of the protein might surround (partially, to varying degree) the negative outer surface of the dsDNA double helix with positively-charged surface, in order to hold it on to DNA as it scans (perhaps) along its length.&lt;/p&gt;&#xA;&lt;h3&gt;DNA-binding domains: major groove&lt;/h3&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bhP4s.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The following domains are found in many transcription factors, and they all recognise &lt;strong&gt;both&lt;/strong&gt; strands. More correctly, they recognise &lt;strong&gt;basepairs&lt;/strong&gt; and their orientation. &lt;a href=&quot;http://voh.chem.ucla.edu/vohtar/spring05/classes/153B-1/pdf/lecture20.pdf&quot; rel=&quot;noreferrer&quot;&gt;The first 5 pages of this lecture slideshow&lt;/a&gt; demonstrate that the chemical groups on the side of basepairs, accessible in the major groove, allow proteins to distinguish A:T, T:A, C:G &amp;amp; G:C &lt;em&gt;by the order of hydrogen-bond donors, acceptors, and a methyl group&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Hence, TFs recognise a sequence of basepairs - &lt;em&gt;oriented&lt;/em&gt; such that one strand is (e.g.) p&lt;strong&gt;T&lt;/strong&gt;p&lt;strong&gt;C&lt;/strong&gt;p&lt;strong&gt;A&lt;/strong&gt;p&lt;strong&gt;G&lt;/strong&gt;, and the complementary strand is p&lt;strong&gt;C&lt;/strong&gt;p&lt;strong&gt;T&lt;/strong&gt;p&lt;strong&gt;G&lt;/strong&gt;p&lt;strong&gt;A&lt;/strong&gt;; and the bulk of the protein may 'sit' on one strand or the other - or a nearby gene may locally define one strand or the other as the coding strand &lt;strong&gt;but this does not mean that this one strand is read.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Zinc_finger&quot; rel=&quot;noreferrer&quot;&gt;Zinc fingers&lt;/a&gt; probe the major groove with reading helices.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Helix-turn-helix&quot; rel=&quot;noreferrer&quot;&gt;Helix-turn-helix motifs&lt;/a&gt; do much the same.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Leucine_zipper&quot; rel=&quot;noreferrer&quot;&gt;Leucine zippers&lt;/a&gt; also do much the same.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;These are common domains that all recognise basepairs in the major groove by interactions with residues on a probing aplha-helix.&lt;/p&gt;&#xA;&lt;h3&gt;TATA-binding protein: minor groove&lt;/h3&gt;&#xA;&lt;p&gt;TATA-binding protein (TBP) is a different, interesting case. It binds the 'TATA-box' via the minor groove, where the exposed chemical groups only distinguish [A/T] from [C/G], but not their orientation. This means that the sequences on each strand cannot be easily read from the minor groove. TBP instead recognises the shape and flexibility of the double-helix at the TATA-box, 'grips' it by the minor groove and bends the DNA, which aids the melting of the strands to the transcription 'bubble'.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ZzUnX.gif&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The TATA-box sequence is usually p&lt;strong&gt;T&lt;/strong&gt;p&lt;strong&gt;A&lt;/strong&gt;p&lt;strong&gt;T&lt;/strong&gt;p&lt;strong&gt;A&lt;/strong&gt;p&lt;strong&gt;A&lt;/strong&gt;p&lt;strong&gt;A&lt;/strong&gt; &lt;em&gt;on the coding strand upstream of the transcriptional start.&lt;/em&gt; This is the &lt;strong&gt;convention&lt;/strong&gt; when giving the sequence of a TF-binding site, &lt;em&gt;but you couldn't say that TBP actually reads TATAAA - it doesn't!&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://classes.biology.ucsd.edu/old.web.classes/bibc100.SS03.1/pdf/ch32_transcription.pdf&quot; rel=&quot;noreferrer&quot;&gt;Here is another, similar set of lecture slides.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26806/&quot; rel=&quot;noreferrer&quot;&gt;Even better, here is the same material covered in a popular textbook.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="13310" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-16T16:53:41.380" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30429" PostTypeId="1" CreationDate="2015-03-13T19:53:11.020" Score="4" ViewCount="238" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Deinococcus_radiodurans&quot; rel=&quot;nofollow&quot;&gt;Deinococcus radiodurans&lt;/a&gt; has a remarkable ability to resist damage to its DNA due to radiation, dehydration or (to my knowledge) any other source. It keeps multiple copies of its genome and has a repair mechanism as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: how could this thing evolve to be so sophisticated at preventing the processes behind evolution? It seems that a mechanism to prevent errors would also prevent changes, so that as soon as the organism got OK at preventing changes it wouldn't be able to evolve to get better at it. Were genes for these processes borrowed from other extremophiles? Is the assumption that it was in such extreme environments that the damaging influences were keeping up with the repair mechanisms? That's my guess, but I'd love to hear from others with more knowledge of evolutionary processes.&lt;/p&gt;&#xA;" OwnerUserId="14920" LastActivityDate="2015-04-14T22:33:15.430" Title="How can (or did) Deinococcus radiodurans continue to evolve after developing resistance to mutation?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;molecular-biology&gt;&lt;molecular-evolution&gt;&lt;extremophiles&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30430" PostTypeId="2" ParentId="30429" CreationDate="2015-03-13T21:56:31.193" Score="2" Body="&lt;p&gt;According to the &quot;Functional adaptation&quot; section of this &lt;a href=&quot;http://eol.org/pages/974108/details&quot; rel=&quot;nofollow&quot;&gt;webpage&lt;/a&gt;, Deinococcus radiodurans uses repair proteins to stitch up DNA after radiation damage. Meaning, after a burst of radiation, the DNA will be in pieces and the repair proteins put it back together. It seems like this mechanism would not come into play during other forms of DNA mutation that happen during replication, such as point mutations or inversions. &lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-03-13T21:56:31.193" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30432" PostTypeId="1" CreationDate="2015-03-14T08:51:28.127" Score="2" ViewCount="1084" Body="&lt;p&gt;I'd like to monitor the growth of a yeast population by shining light through it and monitoring the change in light that gets through as it grows. I'm not sure if I should use IR, or any particular colour of light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any charts that show the light absorption of brewers yeast to different spectra of light?&lt;/p&gt;&#xA;" OwnerUserId="14923" LastActivityDate="2020-02-13T03:14:28.833" Title="Yeast absorption of different spectra of light" Tags="&lt;yeast&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30434" PostTypeId="1" CreationDate="2015-03-14T15:34:27.840" Score="5" ViewCount="1928" Body="&lt;p&gt;Is hands-only CPR as effective as traditional CPR ? Wouldn't 30 chest compressions + 2 rescue breaths be more effective if the person doesn't have a pulse AND not breathing?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From my understanding (correct me if I'm wrong) by doing chest compression you manually make the blood continue to circulate the body in order to deliver oxygen to the organs (and most importantly, to the brain), but after some time (several minutes?) all the oxygen from the blood will be used up, and if the person is not breathing, that means that no new oxygen is entering the bloodstream, so that would mean that chest compressions alone won't provide oxygen to the brain anymore, so they would be useless... am I wrong?&lt;/p&gt;&#xA;" OwnerUserId="14928" LastEditorUserId="9943" LastEditDate="2015-03-16T10:44:50.613" LastActivityDate="2018-03-14T09:31:08.803" Title="Is hands-only CPR as effective as traditional CPR?" Tags="&lt;physiology&gt;&lt;cardiology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30437" PostTypeId="1" AcceptedAnswerId="30574" CreationDate="2015-03-14T17:31:29.833" Score="2" ViewCount="15934" Body="&lt;p&gt;When does the second polar body gets expelled from the egg nucleus during oogenesis ? I know that it occurs after the entry of the sperm into the secondary oocyte but does it occur before the fertilization or in the period between the entry of the sperm and fertilization ? &lt;/p&gt;&#xA;" OwnerUserId="14616" LastActivityDate="2019-05-08T12:42:26.907" Title="When is the second polar body extruded from the egg nucleus?" Tags="&lt;reproduction&gt;&lt;oogenesis&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30438" PostTypeId="1" AcceptedAnswerId="30441" CreationDate="2015-03-14T17:54:26.023" Score="3" ViewCount="150" Body="&lt;p&gt;I'm just starting my MSc research and I am in the process of making a list of equipments/consumables to order. Is there a specific flask in which I can culture NTERA2 (NTERA2/D1) cell line? &lt;/p&gt;&#xA;" OwnerUserId="14932" LastEditorUserId="6511" LastEditDate="2015-03-14T18:23:25.047" LastActivityDate="2015-03-14T18:32:18.863" Title="What type of flask should I use to culture NTERA2 embryonic cancer stem cells?" Tags="&lt;molecular-biology&gt;&lt;cancer&gt;&lt;cell-culture&gt;&lt;stem-cells&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30439" PostTypeId="1" CreationDate="2015-03-14T18:09:15.350" Score="2" ViewCount="47" Body="&lt;p&gt;I am interested in qualitative (flowers of some plants have petal or sepal, but some plants have not) and quantitative (number of flowers of plants) differences between flowers of different plants.&#xA;Formation of flower in flowering plants is under control of which genes?&#xA;Which genes are the most important ones in flower development, for example which gene tell the flower that you should have for example 2 stigmas. or which genes tell the plant that you should have 4 flowers or your flowers will not have sepal...&#xA;Thank you&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="1916" LastEditDate="2015-03-14T18:18:00.523" LastActivityDate="2015-03-14T18:18:00.523" Title="Is (are) there any crucial gene(s) for the formation of flower in flowering plants?" Tags="&lt;genetics&gt;&lt;botany&gt;&lt;flowering&gt;&lt;flowers&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2015-03-15T17:23:44.737" ContentLicense="CC BY-SA 3.0" />
  <row Id="30440" PostTypeId="2" ParentId="30437" CreationDate="2015-03-14T18:09:59.360" Score="0" Body="&lt;p&gt;Polar bodies will usually undergo apoptosis in about 17 to 24 hours after the egg forms (the final stages of telophase II (cytokinesis)) because they have relatively little cytoplasm and shunted organelle development (&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3164815/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Schmerler &amp;amp; Wessel, 2011&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="3340" LastEditDate="2019-05-08T12:37:14.853" LastActivityDate="2019-05-08T12:37:14.853" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="30441" PostTypeId="2" ParentId="30438" CreationDate="2015-03-14T18:32:18.863" Score="5" Body="&lt;p&gt;I found a &lt;a href=&quot;http://www.uwencode.org/media/protocols/cell_culture/human/NT2-D1_protocol.pdf&quot;&gt;protocol&lt;/a&gt; by ATCC for NTERM2 cells, and it didn't mention any specific flask, so any cell culture flask would do. Since ATCC is basically a cell culture bank I trust that their protocol is valid.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-03-14T18:32:18.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30442" PostTypeId="2" ParentId="30434" CreationDate="2015-03-14T18:40:03.387" Score="3" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Cardiopulmonary_resuscitation#Compression_only&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia page&lt;/a&gt; for CPR actually goes into some detail on this, going to block quote the section here for ease of access,&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Compression-only (hands-only or cardiocerebral resuscitation) CPR is a technique that involves chest compressions without artificial respiration. It is recommended as the method of choice for the untrained rescuer or those who are not proficient because it is easier to perform and instructions are easier to give over a phone. In adults with out-of-hospital cardiac arrest, compression-only CPR by the lay public has a higher success rate than standard CPR. The exceptions are cases of drownings, drug overdose and arrest in children. Children who receive compression-only CPR have the same outcomes as those having received no CPR. The method of delivering chest compressions remains the same, as does the rate (at least 100 per minute). It is hoped that the use of compression-only delivery will increase the chances of the lay public delivering CPR. As per the American Heart Association, the beat of the Bee Gees song &amp;quot;Stayin' Alive&amp;quot; provides an ideal rhythm in terms of beats per minute to use for hands-only CPR. One can also hum Queen's &amp;quot;Another One Bites The Dust&amp;quot;, which is exactly 100 beats-per-minute and contains a memorable repeating drum pattern. For those with non cardiac arrest and people less than 20 years of age, standard CPR is superior to compression-only CPR.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The American Heart Association has assembled some efficacy testing studies in the following review article, &lt;a href=&quot;http://circ.ahajournals.org/content/117/16/2162.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hands-Only (Compression-Only) Cardiopulmonary Resuscitation: A Call to Action for Bystander Response to Adults Who Experience Out-of-Hospital Sudden Cardiac Arrest&lt;/a&gt;. Importantly, the human clinical studies reported no significant difference between those who received conventional cpr and those who received compression-only CPR. Some animal efficacy studies are noted, and with respect conventional CPR, the animals that didn't receive &amp;quot;rescue breaths&amp;quot; experienced a lower survival rate. In the end they note some limitations to hands-only CPR:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&amp;quot;...raised concerns about the possibility that recommending hands-only CPR for witnessed sudden cardiac arrest will, in fact, increase the complexity of decision-making for bystanders or that unresponsive victims of noncardiac medical emergencies (eg, drowning, drug overdose) will not receive rescue breathing.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;&amp;quot;There may be situations in which ventilation alone could be life-saving but is not provided. There may be an interval after cardiac arrest when ventilations become absolutely critical for survival.&amp;quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;And as to the content in the second paragraph of the original post,&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&amp;quot;It is important to acknowledge that during cardiac arrest without lung inflation and ventilation, there is a continuous decrement of blood oxygen saturation. At some point in time, the possible hemodynamic advantage conferred by continuous chest compressions (without ventilations) will be offset by this reduction in oxygen saturation, and the ultimate result will be a compromise in oxygen delivery. One porcine cardiac arrest study (3 minutes of untreated ventricular fibrillation, then 12 minutes of CPR) suggests that after 4 minutes of continuous chest compressions without rescue breathing, the delivery of 2 rescue breaths every 100 compressions provides a survival advantage over chest compressions alone.&amp;quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The paradigm, again, is that hand-only CPR provides opportunity to get some help, other than no help at all, but the review also notes that more clinical data is needed on all fronts.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-16T20:41:16.420" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30444" PostTypeId="1" AcceptedAnswerId="30482" CreationDate="2015-03-14T19:27:20.113" Score="8" ViewCount="1593" Body="&lt;p&gt;Butterflies, like many other insects, understand that I am getting near from behind. How do they feel this - through vision, hearing, or some other sense?&lt;/p&gt;&#xA;" OwnerDisplayName="user11667" LastEditorUserId="9943" LastEditDate="2015-03-16T00:23:55.380" LastActivityDate="2017-07-30T14:55:07.037" Title="Do butterflies see behind?" Tags="&lt;entomology&gt;&lt;sensation&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30447" PostTypeId="1" CreationDate="2015-03-14T22:42:38.400" Score="2" ViewCount="45" Body="&lt;p&gt;According to articles I read, AGEs (advanced glycation end products) activate RAGEs (receptors for AGEs). This activation increases the ROS (reactive oxygen species) levels in the cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CnVk4.gif&quot; alt=&quot;Reactive Oxygen Species-Regulated Signaling Pathways in Diabetic Nephropathy&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://jasn.asnjournals.org/content/14/suppl_3/S241/F3.expansion&quot; rel=&quot;nofollow noreferrer&quot;&gt;2003 - Reactive Oxygen Species-Regulated Signaling Pathways in Diabetic Nephropathy&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Free radicals can cause damage in cells, which is definitely not good. What do you think, what is the role of RAGEs, which is more important than cellular damage?&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2015-03-14T22:42:38.400" Title="What is the role of RAGEs?" Tags="&lt;senescence&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30448" PostTypeId="1" AcceptedAnswerId="30528" CreationDate="2015-03-14T23:12:18.537" Score="9" ViewCount="3709" Body="&lt;p&gt;According to &lt;a href=&quot;https://www.youtube.com/watch?v=Dq2H8tNyk4Q&quot;&gt;this&lt;/a&gt; video, butterflies sometimes drink blood. Do they have the organs necessary to digest blood? I thought they eat only salts and nectar, which are easy to digest compared to proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;@aandreev&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;100mg/dL&lt;/strong&gt; is the human blood sugar content (I assume it is similar in other animals). Afaik. sugar energy density is about &lt;strong&gt;4kcal/g&lt;/strong&gt;. A butterfly is about &lt;strong&gt;1g&lt;/strong&gt; of weight, which means &lt;strong&gt;1mL&lt;/strong&gt; if we count with water. So it can drink around &lt;strong&gt;0.5mL&lt;/strong&gt; of blood. That means &lt;strong&gt;0.5mL×100mg/dL×4kcal/g = 0.002kcal = 8.4J&lt;/strong&gt;. The top butterfly speed is about &lt;strong&gt;12 mph&lt;/strong&gt;, so I think we can count with &lt;strong&gt;6mph&lt;/strong&gt; by an average butterfly, which is about &lt;strong&gt;2.7m/s&lt;/strong&gt;. So it needs &lt;strong&gt;1/2×1g×(2.7m/s)&lt;sup&gt;2&lt;/sup&gt; = 0.0036J&lt;/strong&gt; kinetic energy to move and &lt;strong&gt;1g×9.81m/s&lt;sup&gt;2&lt;/sup&gt;×1m = 0.0098J&lt;/strong&gt; potential energy to keep the 1m height of flight. I think we can guess that it loses this kind of energy in &lt;strong&gt;2secs&lt;/strong&gt;, which means it needs &lt;strong&gt;0.0134J/2s = 0.0067W&lt;/strong&gt; power to fly. So the &lt;strong&gt;0.5mL&lt;/strong&gt; blood means &lt;strong&gt;8.4J/0.0067W = 24925s = 21min&lt;/strong&gt; of flight time, which is not much compared to nectar (&lt;strong&gt;30g/dL$, $2500J$, $100h&lt;/strong&gt;). Ofc. this is just a very rough estimation (the real flight time is probably much lower) based on data coming from non-scientific sources, but I think you can see the difference.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3340" LastEditDate="2015-03-16T09:00:38.170" LastActivityDate="2015-03-18T05:09:49.393" Title="Why are butterflies drinking blood?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30449" PostTypeId="1" CreationDate="2015-03-15T01:21:41.407" Score="4" ViewCount="163" Body="&lt;p&gt;I have access to a small (approx 20 nodes) cluster that has HADOOP running on it, and I need to do some de-novo genome assembly. I'd like to ask is anyone knows of any program that can do this on a HADOOP cluster. Cloud based stuff is not an option right now, unfortunately, so I need something that I can deploy on our cluster locally. Thx in advance.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="9943" LastEditDate="2015-03-20T13:38:28.270" LastActivityDate="2015-11-02T14:55:29.627" Title="Are there any de-novo genome assembly programs for HADOOP?" Tags="&lt;bioinformatics&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30450" PostTypeId="1" CreationDate="2015-03-15T07:43:35.983" Score="9" ViewCount="1110" Body="&lt;p&gt;ClustalW and Omega of EBI and Blast of NCBI, both globally align sequences. Smith waterman of EBI aligns sequences locally, but works with just two sequences. How can I align more than 2 sequences locally?&lt;/p&gt;&#xA;" OwnerDisplayName="user11667" LastEditorUserId="3340" LastEditDate="2015-03-18T09:20:44.573" LastActivityDate="2015-03-18T11:19:11.617" Title="How can I align more than 2 sequences locally?" Tags="&lt;bioinformatics&gt;&lt;sequence-alignment&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30451" PostTypeId="2" ParentId="30450" CreationDate="2015-03-15T08:44:12.577" Score="1" Body="&lt;p&gt;Even Water (in EBI itself) is Local alignment tool for multiple sequence alignment. Also in BLAST you get bla2seq which is also used for pairwise alignment. In any of these tools  you just have to enter FASTA sequences (any number you want) or any sequence with &gt; sign and run it against the subject (database or your required sequence). &#xA;If you want to see the results for all the alignment in one screen, a tool like BioEdit would be ideal. &#xA;I hope this is helpful, I'm not an expert in bioinformatics so feel free to correct me :)&lt;/p&gt;&#xA;" OwnerUserId="14932" LastActivityDate="2015-03-15T08:44:12.577" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30453" PostTypeId="2" ParentId="30450" CreationDate="2015-03-15T09:42:54.570" Score="1" Body="&lt;p&gt;I use Jalview, that is a small program written in Java. It is simple to use and can do many many things. It's web-service based and it has 7 different services built in just for sequence alignment. You can load your sequences from many file formats, or get them by reference id. It's really a small swiss-army-knife. I really recommend to take a look at it. It's available on &lt;a href=&quot;http://www.jalview.org/&quot; rel=&quot;nofollow&quot;&gt;http://www.jalview.org/&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I might have missed the local alignment part earlier, but I did some research and found that MULAN (MUltiple sequence Local AligNment and conservation visualization tool&#xA;) may be what you're looking for. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;PMC &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288/&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; of Mulan, and the &lt;a href=&quot;http://mulan.dcode.org/mulanInstructions.php&quot; rel=&quot;nofollow&quot;&gt;manual&lt;/a&gt; for Mulan.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-03-15T10:18:05.563" LastActivityDate="2015-03-15T10:18:05.563" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30456" PostTypeId="1" AcceptedAnswerId="30472" CreationDate="2015-03-15T13:27:28.207" Score="4" ViewCount="203" Body="&lt;p&gt;There has been much talk of the anti-psychotic drug Rispeirdone causing un-natural breast tissue growth as well as galactorhea (milk production). Especially in young men and boys.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the mechanism of this drug that is causing this? Is it actually introducing some amount of female hormones into the male's body or is just causing increased production of them?&lt;/p&gt;&#xA;" OwnerUserId="14937" LastEditorUserId="6289" LastEditDate="2015-03-15T21:04:42.433" LastActivityDate="2015-03-16T17:40:50.533" Title="By what mechanism does Risperidone swell breast tissue?" Tags="&lt;human-biology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30459" PostTypeId="1" CreationDate="2015-03-15T14:38:01.950" Score="1" ViewCount="609" Body="&lt;p&gt;All google searches have simply returned more info on catalase. I'm looking for a catalyst that isn't found inside living organisms which  can break down H2O2. Looking for any resources to look at, or just examples of other catalysts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Side question since I don't want to clutter with a new thread.&#xA;Can catalase be used for anything other than the decomposition of h2o2?&lt;/p&gt;&#xA;" OwnerUserId="14940" LastEditorUserId="14940" LastEditDate="2015-03-15T14:58:01.773" LastActivityDate="2015-03-15T20:27:03.393" Title="Hydrogen peroxide decomposition and catalase uses" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-03-16T04:45:04.097" ContentLicense="CC BY-SA 3.0" />
  <row Id="30460" PostTypeId="1" CreationDate="2015-03-15T14:50:02.697" Score="2" ViewCount="102" Body="&lt;p&gt;Using the CRISPR/Cas9 technology, it is possible that after inducing a DSB with the Cas9 endonuclease guided with an RNA designed by the user and using a template DNA, get a desired Knock-In (KI) by homologous recombination.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have read that for desired KI-s that are less than 200 bp, a olygonucleatide should be enough as template. On the contrary, if the desired KI is bigger than that, a plasmid vector should be used.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is that information accurate and correct? and, where is the upper limit for the KI length?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="20449" LastEditDate="2016-12-30T13:41:43.203" LastActivityDate="2016-12-30T13:41:43.203" Title="CRISPR Knock in" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;gene&gt;&lt;transformation&gt;&lt;crispr&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30462" PostTypeId="2" ParentId="30370" CreationDate="2015-03-15T17:10:54.260" Score="2" Body="&lt;p&gt;Concerning the difference between dominant vs. recessive mutations, in general, recessive, or loss-of-function mutations, are much more frequent than dominant, or gain-of-function, mutations, because there are many different ways to &quot;break&quot; or inactivate a protein.  For example, not every amino acid site has the potential to mutate to a residue with dominant phenotype, but most sites can mutate to a side chain that might destabilize, disrupt, etc. &#xA;The lacId allele is a dominant loss-of-function (and so somewhat more complex than the simple explanation I just gave). It makes a so-called &quot;poison product&quot;&lt;/p&gt;&#xA;" OwnerUserId="14942" LastActivityDate="2015-03-15T17:10:54.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30463" PostTypeId="1" AcceptedAnswerId="30464" CreationDate="2015-03-15T18:22:02.317" Score="6" ViewCount="171" Body="&lt;p&gt;There are a lot of publications, starting from 2000, about using telomerase for targeting cancer cells (it is upregulated in more than 80-90% of tumor cells). Specifically using its promoter (hTERT). In all publications, researches talking about the success of this approach. &#xA;So my questions,  why there is no use of this? What is the problem? I read a lot of articles - and didn't find an answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://scholar.google.com/scholar?q=telomerase+suicide-gene+promoter&quot; rel=&quot;nofollow&quot;&gt;http://scholar.google.com/scholar?q=telomerase+suicide-gene+promoter&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.spandidos-publications.com/ijo/21/3/661&quot; rel=&quot;nofollow&quot;&gt;http://www.spandidos-publications.com/ijo/21/3/661&lt;/a&gt;  (one of the newest) &lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="10104" LastEditDate="2015-03-15T21:40:00.310" LastActivityDate="2015-03-15T21:40:00.310" Title="Telomerase as cancer target" Tags="&lt;cancer&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30464" PostTypeId="2" ParentId="30463" CreationDate="2015-03-15T19:33:39.563" Score="3" Body="&lt;p&gt;With help of &lt;strong&gt;canadianer&lt;/strong&gt; (thank you) I think I found the right article, so just want to share.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This study not talking specifically about telomerase, but about the same approach of using promoters that are upregulated in tumors - exactly what I looked for. Published in 2014.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://symbiosisonlinepublishing.com/genetic-science/genetic-science03.pdf&quot; rel=&quot;nofollow&quot;&gt;http://symbiosisonlinepublishing.com/genetic-science/genetic-science03.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;However, the therapeutic approach in humans is limited by&#xA;  low efficiency of delivering the suicide genes and concerns regarding&#xA;  safety. Thus the number of clinical trials in human patients has been&#xA;  limited and treatment benefits observed modest. An intensive research&#xA;  effort is necessary to overcome these obstacles and turn suicide gene&#xA;  therapy into real benefit for our patients.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10104" LastActivityDate="2015-03-15T19:33:39.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30466" PostTypeId="2" ParentId="30459" CreationDate="2015-03-15T20:27:03.393" Score="-1" Body="&lt;p&gt;Manganese(IV)oxide can be used as a catalyst to speed up the decomposition of hydrogen peroxide&lt;/p&gt;&#xA;" OwnerUserId="14937" LastActivityDate="2015-03-15T20:27:03.393" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30467" PostTypeId="1" CreationDate="2015-03-15T20:44:43.503" Score="0" ViewCount="718" Body="&lt;p&gt;A relative of mine is a driving instructor and he regularly likes to bring up that the field of view narrows noticeably when driving at higher speeds.&lt;br&gt;&#xA;Is this true, why is this so and does this apply for other species as well (for example, leopards, who are widely known for their fast speed)?&lt;/p&gt;&#xA;" OwnerUserId="6433" LastEditorUserId="9943" LastEditDate="2015-03-16T12:48:08.467" LastActivityDate="2015-03-16T12:48:08.467" Title="Why does a human's field of view narrow when moving faster?" Tags="&lt;eyes&gt;&lt;vision&gt;&lt;anecdotal-evidence&gt;" AnswerCount="0" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="30468" PostTypeId="1" AcceptedAnswerId="30470" CreationDate="2015-03-15T21:19:35.013" Score="13" ViewCount="18272" Body="&lt;p&gt;Why is the action of flexing the foot so that the toes move anteriorly/superiorly (i.e. in the direction opposite that which they move during plantar flexion) described as &quot;dorsiflexion?&quot; In the same vein, why is the top surface of the foot called the &quot;dorsal surface?&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If anything, the action opposite to plantar flexion moves the foot in the ventral direction, doesn't it? And surely if you've ever seen a human in the anatomical position, you can see that there's nothing dorsal about the top surface of the foot - it's superior, perhaps, but by no means dorsal.&lt;/p&gt;&#xA;" OwnerUserId="3128" LastEditorUserId="16866" LastEditDate="2017-04-26T19:38:26.173" LastActivityDate="2020-07-24T03:08:53.723" Title="Why is the opposite of plantar flexion called &quot;dorsiflexion&quot;?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;terminology&gt;&lt;anatomy&gt;&lt;etymology&gt;" AnswerCount="5" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30469" PostTypeId="2" ParentId="30468" CreationDate="2015-03-15T22:00:40.867" Score="4" Body="&lt;p&gt;&lt;em&gt;Dors/dorsum&lt;/em&gt; in Latin simply means &quot;back&quot;, and it is rather normal and reasonable to use the equivalent term in English with regard to the extremities (hands and feet), see &quot;&lt;a href=&quot;http://dictionary.cambridge.org/dictionary/british/know-sth-like-the-back-of-your-hand&quot; rel=&quot;nofollow&quot;&gt;back of my hand&lt;/a&gt;&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is medical convention to refer to the &lt;a href=&quot;http://medical-dictionary.thefreedictionary.com/dorsal&quot; rel=&quot;nofollow&quot;&gt;non-gripping surfaces of the feet and hands&lt;/a&gt;, as well as the upper (towards the brain) &lt;a href=&quot;http://dictionary.reference.com/browse/dorsal&quot; rel=&quot;nofollow&quot;&gt;surface of the tongue&lt;/a&gt; as &quot;dorsal&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My best guess for the etymology sequence is that all the terms were borrowed from Latin anatomical books written by Roman and Greek doctors (Dioscorides, Galen) which named the anatomical structures in normal language (back/dorsum, stomach/venter, sole/plantarum) and these terms were then fixed into modern medical terminology as jargon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Caveat: I could not find any citation for the etymological sequence, but it seems a rather reasonable explanation to me. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-03-15T22:22:12.893" LastActivityDate="2015-03-15T22:22:12.893" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30470" PostTypeId="2" ParentId="30468" CreationDate="2015-03-15T22:10:34.037" Score="17" Body="&lt;p&gt;Anatomical terms must be able to fit a wide variety of organisms, from insects to fish, dogs, horses, chimpanzees to humans. That's why the terms are sometimes confusing to people who are thinking only of bipedal humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In anatomy, the dorsum is the &lt;strong&gt;upper side of animals that typically run fly, swim or crawl in a horizontal position&lt;/strong&gt;. In vertebrates the dorsum contains the backbone. In such an animal the &quot;ground side&quot; is the ventrum. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Due to varied orientation on quadrupedal mammals (where the term is more appropriately used) the &quot;back&quot;-side of the hand, the &quot;top&quot;-side of the foot and the upper surface of the tongue are referred to by the term dorsum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/edn2U.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this picture help? Note the dorsal surfaces of the body, muzzle, feet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In anatomy, the sole of the foot is called the &lt;em&gt;plantar&lt;/em&gt; surface. The top of the foot is called the &lt;em&gt;dorsum&lt;/em&gt; of the foot. (Imagine us walking on all fours like apes.) Therefore when you extend your foot, it's called plantar flexion; when you flex your foot upwards towards your head, it's called dorsiflexion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, the arteries feeding the bottom of your foot form the plantar arch. Those feeding the top are the dorsal artery (or the dorsalis pedis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because anatomy must describe other animals than ourselves with other orientations, it must be consistent. In a quadruped, the dorsum of the tongue and the feet &lt;em&gt;do&lt;/em&gt; actually point to it's &quot;back&quot; surface. See the picture below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/U3aAg.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/U3aAg.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lynxes have big paws, so it's more obvious that the surface facing the backbone is appropriately called the dorsum of the paw/foot. This picture is particularly interesting because it shows three degrees of dorsiflexion and one paw in full plantar flexion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In humans, the &quot;back&quot; is actually the posterior surface, because we are not primarily in a horizontal orientation. The ventral surface is called &quot;anterior&quot;. Thus we speak of the anterior chest wall and the posterior chest wall, not the dorsal and ventral surfaces, although those designations would still be entirely correct.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2018-05-23T15:33:06.497" LastActivityDate="2018-05-23T15:33:06.497" CommentCount="10" ContentLicense="CC BY-SA 4.0" />
  <row Id="30471" PostTypeId="1" AcceptedAnswerId="30473" CreationDate="2015-03-15T22:29:39.527" Score="4" ViewCount="1316" Body="&lt;p&gt;Where does this signal sequence &quot;go&quot; after it has been cleaved by signal peptidase and what is its next function? &lt;/p&gt;&#xA;" OwnerUserId="12959" LastEditorUserId="6307" LastEditDate="2015-03-16T00:44:39.933" LastActivityDate="2015-03-16T00:56:18.097" Title="What happens to the precursor protein's signal sequence after it is cleaved?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;proteins&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30472" PostTypeId="2" ParentId="30456" CreationDate="2015-03-15T23:33:00.030" Score="9" Body="&lt;p&gt;Risperidone prevents dopamine from acting on the pituitary gland by blocking dopamine type 2 receptors. One of dopamine's effects on the pituitary is to suppress prolactin production. In patients taking risperidone, prolactin production thus increases and prolactin levels in the body are higher than normal. In younger males, this can result in abnormal growth of breast tissue and even milk production. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See e.g. Melkersson, K. I. (2006). Prolactin elevation of the antipsychotic risperidone is predominantly related to its 9‐hydroxy metabolite. &lt;em&gt;Human Psychopharmacology: Clinical and Experimental&lt;/em&gt;, 21(8), 529-532.&lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="13072" LastEditDate="2015-03-16T17:40:50.533" LastActivityDate="2015-03-16T17:40:50.533" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30473" PostTypeId="2" ParentId="30471" CreationDate="2015-03-16T00:33:52.437" Score="10" Body="&lt;p&gt;After cleavage, the signal sequence is generally thought to be degraded by intramembrane proteases (since it is embedded in the endoplasmic reticulum membrane). For at least some proteins, the signal sequence is further processed and released into the cytoplasm or ER lumen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14641034&quot;&gt;Martoglio B. 2003. Intramembrane proteolysis and post-targeting functions of signal peptides. Biochem Soc Trans 31:1243-1247&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When translocation continues, the signal sequence’s c-region appears in the ER lumen and becomes accessible to signal peptidase, which cleaves the signal sequence from the pre-protein. The latter is further translocated into the ER lumen, while the liberated signal peptide is usually not detected in assay systems, implying rapid degradation. In a cell-free in vitro system with ER membranes from canine pancreas, we reported several years ago that after cleavage by signal peptidase, the liberated signal peptide is transiently embedded in the lipid bilayer and undergoes further processing to be released from the membrane. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The activity of released signal sequences is not entirely known and only partially characterized for some proteins. The following review discusses some functions of signal peptides after cleavage:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9789330&quot;&gt;Martoglio B, Dobberstein B. 1998. Signal sequences: more than just greasy peptides. Trends Cell Bio 8(10):410-415&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The signal peptide of bovine preprolactin and HIV gp160 can bind calmodulin.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;…the signal sequence of bovine preprolactin, which consists of 30 amino acid residues, is cleaved by signal peptidase and then further processed by an unknown signal peptide peptidase (SPPase; Fig. 4) … This signal peptide fragment resides initially in the membrane and, after a chase period, is released into the cytosol. Once in the cytosol, the signal peptide fragment binds to calmodulin in a Ca2+-dependent manner. A signal peptide fragment derived from HIV-1 gp160 also binds to calmodulin when it is released into the cytosol … With their n-regions having the potential to form a basic amphiphilic α-helix and their hydrophobic C-terminal region, they are similar to other calmodulin-binding domains. Calmodulin is a small, acidic protein involved in the regulation of many cellular processes controlled by Ca2+-dependent signalling pathways. It is possible that binding of signal peptide fragments to calmodulin influences Ca2+/calmodulin-dependent cellular signal-transduction pathways. Further studies are required to elucidate the physiological consequences of interactions between signal peptide fragments and calmodulin.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The signal peptides of MHC class I proteins are presented to NK cells by MHC-I (with HLA-E alpha chain). This allows monitoring of MHC-I expression, which is often disrupted in virally infected or cancerous cells.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Peptides presented by classical MHC class I molecules represent the broad spectrum of peptides generated by the proteasome. In contrast to this general use of peptides, only a very specific signal peptide fragment is presented by so-called nonclassical MHC class I molecules (HLA-E in human). These molecules monitor the presence of classical MHC class I molecules by presenting a signal peptide fragment derived from HLA-A, -B or -C to natural killer (NK) cells (Fig. 5b). NK cells destroy cells unable to activate inhibitory receptors specific for MHC class I molecules. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;This book section discusses the function of signal peptides in some viruses:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK6322/&quot;&gt;Kapp K, Schrempf S, Lemberg MK, Dobberstein B. 2009. Post-targeting functions of signal peptides. In: Protein Transport into the Endoplasmic Reticulum, Zimmermann R.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-03-16T00:56:18.097" LastActivityDate="2015-03-16T00:56:18.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30474" PostTypeId="1" CreationDate="2015-03-16T02:43:53.017" Score="0" ViewCount="108" Body="&lt;p&gt;One interesting thing I recently learned is that venom has medical uses that can actually save lives! But from what I see so far this either applies to venoms from creatures that are not fatal to humans or that only proteins or enzymes from these venoms are what is being used medically. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these proteins or enzymes themselves fatal to humans or is this just a misrepresentation of the fact that venoms can save human lives?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: To clarfiy, while I realize venom is harmless in lower doses, I also read the following : &#xA;Enzymes from cobra venom may be instrumental to finding cures for Parkinson's disease and Alzheimer's disease.&#xA;An enzyme derived from copperhead venom could be used to treatment for breast cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I was not sure of was whether the enzyme by itself was toxic or they were just extracting a non-lethal element of the venom to use medically. Can this enzyme alone of venom administered in large enough doses be fatal?&lt;/p&gt;&#xA;" OwnerUserId="14949" LastEditorUserId="14949" LastEditDate="2015-03-16T07:07:31.313" LastActivityDate="2015-03-22T18:28:36.673" Title="Medical Uses of toxic venom" Tags="&lt;proteins&gt;&lt;enzymes&gt;&lt;toxicology&gt;&lt;reptile&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30477" PostTypeId="1" AcceptedAnswerId="30479" CreationDate="2015-03-16T06:22:31.240" Score="3" ViewCount="108" Body="&lt;p&gt;&lt;em&gt;cross-posted to &lt;a href=&quot;https://dsp.stackexchange.com/questions/22103/reconstruction-of-distributions-of-multiple-unevenly-sampled-species-in-a-2d-spa&quot;&gt;Signal Processing&lt;/a&gt;, &lt;a href=&quot;https://stats.stackexchange.com/questions/141900/reconstruction-of-species-distribution-based-on-poorly-sampled-data&quot;&gt;Cross Validated&lt;/a&gt;, and &lt;a href=&quot;https://worldbuilding.stackexchange.com/questions/12009/ideas-for-reconstruction-of-a-biosphere-based-on-poorly-sampled-references&quot;&gt;World Building&lt;/a&gt; Stack Exchange&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Hi, I thought I'd also put this here in case there are any field biologists with ideas on the matter.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Problem:&lt;/em&gt;&lt;/strong&gt; After reading a series of fantasy novels, I noticed that the biosphere in that world made no sense. To clarify, this is a world where despite magical occurrences, the world itself is almost entirely non-magical. 'Alternate history magical realism,' perhaps. i.e., unlike, for example, Harry Potter, in which almost all plant and animal species mentioned are fictitious and magical, this series uses real flora and fauna. This allows me to extract information about the fictional world's environment based on the distribution of these animals, by assuming that similar animals will live in similar climates on Earth and in the fictional world.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ignoring the likelihood that the original author did not put enough thought into worldbuilding to make this a necessarily reasonable endeavor, my idea for how to proceed was as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As maps exist of the fictional world, and the path of the characters can be plotted, I hoped to mark every mention of a specific plant or animal in the text, along with the location of the characters when it occurred, and from this reconstruct a plausible distribution for each species. I've created a theoretical example (in photoshop), for illustration:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/40E5V.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where the red dotted line represents the paths of various characters, the orange, green, and blue splotches represent the true distribution of the species; the stars, triangles, and circles represent the locations at which a species is mentioned; and the brown, green, and blue lines represent the reconstructed contours of the distribution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a method to do such a reconstruction? It sounds a bit like a Monte Carlo analysis, but I figured I should check... (It also sounds rather like the magical programs detective shows use to plot serial killers' locations)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Note:&lt;/em&gt;&lt;/strong&gt; It should be clear from the problem statement that just because a species is not mentioned at a specific location does not mean that it does not exist there. i.e., a sample at a specific location returning only 'A' - 'Bill and Jeff saw a lemur.' - does not exclude the possibility of 'B' and 'C' also at that location, but not sampled. Just because the text may specifically say that Bill and Jeff saw a lemur, and doesn't mention any other flora or fauna doesn't mean we should assume that they are in a universe devoid of anything but the occasional lemur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Final Thoughts:&lt;/em&gt;&lt;/strong&gt; Ideally, the analysis method would further:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;take into account the coverage of the paths, and not assume that (in&#xA;the example above) nothing exists in Mexico or northern Canada, just&#xA;because there are no samples taken there. Remember that samples can&#xA;only be taken along paths.&lt;/li&gt;&#xA;&lt;li&gt;take into account edges, in this case coastlines. If A, B, and C are&#xA;land animals, it does not make sense that a reconstruction of their&#xA;distribution would include water, even if their range surrounds a&#xA;lake or something.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Sorry for the long-winded explanation. Any thoughts?&lt;/p&gt;&#xA;" OwnerUserId="14951" LastEditorUserId="-1" LastEditDate="2017-04-13T12:52:23.867" LastActivityDate="2015-03-16T12:47:17.063" Title="Reconstruction of wildlife distribution based on poorly-sampled data" Tags="&lt;ecology&gt;&lt;measurement&gt;&lt;visualization&gt;&lt;species-distribution&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ClosedDate="2015-03-16T10:27:18.300" ContentLicense="CC BY-SA 3.0" />
  <row Id="30478" PostTypeId="2" ParentId="30450" CreationDate="2015-03-16T08:38:38.190" Score="3" Body="&lt;p&gt;You have to do it pairwise (there is no other option).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can do that with &lt;code&gt;BLAST&lt;/code&gt; or even &lt;code&gt;SSEARCH&lt;/code&gt; (Smith-Watermann). If you have a &lt;code&gt;fasta&lt;/code&gt; file of your sequences then do this:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;make index of your sequences using &lt;code&gt;makeblastdb -dbtype nucl -in &amp;lt;yourfastafile&amp;gt; -out &amp;lt;yourdbindex&amp;gt;&lt;/code&gt;&lt;/li&gt;&#xA;&lt;li&gt;Run &lt;code&gt;BLAST&lt;/code&gt; with your &lt;code&gt;&amp;lt;yourfastafile&amp;gt;&lt;/code&gt; as input and &lt;code&gt;&amp;lt;yourdbindex&amp;gt;&lt;/code&gt; as database with desired parameters. This will do a pairwise alignment between all sequences&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Similar strategy can be used for &lt;code&gt;SSEARCH&lt;/code&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-03-16T08:38:38.190" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30479" PostTypeId="2" ParentId="30477" CreationDate="2015-03-16T08:45:56.930" Score="2" Body="&lt;p&gt;The problem of how to infer species distributions from scattered species occurrences is common in ecology, and there exists a number of methods to construct distribution maps. As a start, you should have a look at &lt;em&gt;Species Distribution Models&lt;/em&gt; (SDMs) using regressions models or Maxent, and the paper by &lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev.ecolsys.110308.120159&quot; rel=&quot;nofollow&quot; title=&quot;Elith et al. 2009. Species Distribution Models: Ecological Explanation and Prediction Across Space and Time. Annual Review of Ecology, Evolution, and Systematics Vol. 40: 677-697&quot;&gt;Elith et al (2009)&lt;/a&gt; is a good starting point and a standard reference. SDMs using maxent is now a common approach, which integrates species occurrences as point data along with environmental layers (e.g. temperature, moisture and topography) to predict species distribution maps, and this can also include absence data or &quot;pseudo-absence&quot; data (randomly sampled data from a region of interest). The maxent software is described and can be downloaded here: &lt;a href=&quot;http://www.cs.princeton.edu/~schapire/maxent/&quot; rel=&quot;nofollow&quot;&gt;http://www.cs.princeton.edu/~schapire/maxent/&lt;/a&gt;&#xA;A common criticism against distributions produced by Maxent is however that they ignore e.g. species interactions, and they only considers the species occurences and the environmental variables that has been included in the model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your &quot;&lt;em&gt;Note&lt;/em&gt;&quot;, you touch upon the issue of detectability, which is an important issue that has received much attention recently. The problem is largest when you only have presence data, and to have real presence/absence data is preferable. Even if you don't have real absenses (the species has been searched for but not found), an estimate of sampling effort in different areas is still very useful, since this means that you can at least evaluate whether absenses is due to &quot;real&quot; absense or lack of sampling. In your case, the movement paths of characters could be used as a measure of spatial &quot;sampling effort&quot;. The main issue with detectability in studies of distribution of species trends is if there is trends or bias in detectability, which means that apparent changes over time or patterns in distribution might be due to differences in detectability and not real differences between areas or over time. This could for instance be the case if observers are more likely to spot a species in one type of habitat (open savannah) then in another type of habitat (closed forest). Useful starting points for issues of detectability are &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/geb.12216/abstract&quot; rel=&quot;nofollow&quot; title=&quot;Dorazio. 2014. Accounting for imperfect detection and survey bias in statistical analysis of presence-only data. Global Ecology and Biogeography 23(12)&quot;&gt;Dorazio (2014)&lt;/a&gt; (technical though) and &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2010.02345.x/abstract&quot; rel=&quot;nofollow&quot; title=&quot;Kery et al. 2010. Predicting species distributions from checklist data using site-occupancy models. Journal of Biogeography 37(10)&quot;&gt;Kery et al (2010)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-03-16T12:47:17.063" LastActivityDate="2015-03-16T12:47:17.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30480" PostTypeId="2" ParentId="30418" CreationDate="2015-03-16T09:13:48.663" Score="2" Body="&lt;p&gt;Addition to the answer provided by Teige.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Transcription factors bind to both the strands however your question also included proteins in general.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA remains double stranded and twisted as helix most of the times; most proteins bind to both the strands as mentioned in the previous answer. However some proteins such as SSB (Single-strand binding protein) and Rad52 bind to ssDNA during replication and recombination respectively (there are more examples). These are not transcription factors though. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-17T12:43:56.343" LastActivityDate="2015-03-17T12:43:56.343" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30481" PostTypeId="2" ParentId="30444" CreationDate="2015-03-16T10:06:58.297" Score="4" Body="&lt;p&gt;Butterflies have nearly 360 degree field of vision (see e.g. &lt;a href=&quot;https://books.google.se/books?id=c9B4x7j6cJEC&amp;amp;pg=PA217&amp;amp;lpg=PA217#v=onepage&amp;amp;q&amp;amp;f=false&quot;&gt;Belth. &lt;em&gt;Butterflies of Indiana&lt;/em&gt;&lt;/a&gt;), so they can see you or other predators approaching from behind at the same time as they examine the flower they are feeding from. A large field of vision is common in many animals that are preyed upon, and for instance many birds (e.g. waders) have 360 vision, some even with overlapping, binocular vision behind their heads.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2015-03-16T10:06:58.297" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30482" PostTypeId="2" ParentId="30444" CreationDate="2015-03-16T10:07:18.817" Score="10" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Butterflies can see behind them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022191005002404&quot; rel=&quot;nofollow noreferrer&quot;&gt;Merry et al. (2006)&lt;/a&gt; have estimated the field of view of the butterfly, by investigating the Orange Sulphur butterfly (&lt;em&gt;Colias eurytheme&lt;/em&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qg0nV.jpg&quot; alt=&quot;Orange Suplhur&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;em&gt;Colias eurytheme&lt;/em&gt;. Source: &lt;a href=&quot;http://www.naba.org/chapters/nabambc/construct-species-page.asp?sp=orange-sulphur&quot; rel=&quot;nofollow noreferrer&quot;&gt;Massachusetts Butterfly Club&lt;/a&gt;&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors found that this butterfly has a very &lt;strong&gt;large visual field&lt;/strong&gt;, encompassing&#xA;&lt;strong&gt;93% of the spherical space&lt;/strong&gt; around the animal. There was a small blind spot behind the head not seen by either eye. Another study by the same group showed similar results in another species of butterfly, the Empress Leilia (&lt;em&gt;Asterocampa leilia&lt;/em&gt;). Here is a picture of the estimated binocular field of view of the Orange Sulphur, revealing that the animals' vision is virtually spherical, with only a small blind spot at the back (the white area):&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/QQcAE.png&quot; alt=&quot;FieldofView&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022191005002404&quot; rel=&quot;nofollow noreferrer&quot;&gt;Merry et al., 2006&lt;/a&gt;. Grey is the field of view, white the blind spot posteriorly. Cardinal directions are indicated (Dorsal, Ventral, Posterior, Left and Right).&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are a few pictures of other species of butterfly that show the protruding compound eyes covering a large field of view: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4E5Rq.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/pGCCO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Sources: &lt;a href=&quot;http://alexsukonkin.com/album/Macro/slides/buttrefly-closeup-portrait_en.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Alex Sukonkin&lt;/a&gt; and &lt;a href=&quot;http://www.photographersdirect.com/buyers/stockphoto.asp?imageid=2905843&quot; rel=&quot;nofollow noreferrer&quot;&gt;PhotographersDirect&lt;/a&gt;&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The feature of large visual fields in insects is, however, not restricted to butterflies &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs00359-001-0273-7&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Lutowski &amp;amp; Warrant, 2002)&lt;/a&gt;. Another insect I often try sneak upon to take pictures are dragon flies, and more often than not they fly away regardless of the angle I approach them. They too have these large compound eyes with a field of view extending to the back:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/m8qJc.jpg&quot; alt=&quot;dragon fly&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: &lt;a href=&quot;http://www.naturenorth.com/dragonfly/DOM/Page08_Flight.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nature North&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&#xA;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs00359-001-0273-7&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lutowski &amp;amp; Warrant, &lt;em&gt;J Comp Physiol&lt;/em&gt; 2002;&lt;strong&gt;188&lt;/strong&gt;:1-12&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022191005002404&quot; rel=&quot;nofollow noreferrer&quot;&gt;Merry et al., &lt;em&gt;J Insect Physiol&lt;/em&gt; 2006;&lt;strong&gt;52&lt;/strong&gt;:240–8&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2017-07-30T14:55:07.037" LastActivityDate="2017-07-30T14:55:07.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30484" PostTypeId="5" CreationDate="2015-03-16T12:50:37.557" Score="0" Body="" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-16T12:50:37.557" LastActivityDate="2015-03-16T12:50:37.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30485" PostTypeId="4" CreationDate="2015-03-16T12:50:37.557" Score="0" Body="Anecdotal evidence refers to findings, hypotheses, speculations or ideas based on observations in a subject group typically consisting of a single individual, or consisting of a few, often related, individuals. " OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-16T12:50:37.557" LastActivityDate="2015-03-16T12:50:37.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30488" PostTypeId="1" CreationDate="2015-03-16T14:50:15.330" Score="0" ViewCount="67" Body="&lt;p&gt;I really would like to know if sticky end ligation could potentially be performed with very high efficiency, and which factors influence that.  However, I can't find any papers on the subject, even though I'm sure they exist.  I was hoping someone would know of some literature.&lt;/p&gt;&#xA;" OwnerUserId="14741" LastEditorUserId="14709" LastEditDate="2015-03-16T17:13:28.107" LastActivityDate="2015-03-16T22:23:51.497" Title="Can someone link me to resources on the efficiency of sticky end ligation?" Tags="&lt;dna&gt;&lt;literature&gt;&lt;ligation&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30489" PostTypeId="1" AcceptedAnswerId="30492" CreationDate="2015-03-16T18:46:25.873" Score="4" ViewCount="313" Body="&lt;p&gt;I have read that there are proteins in oat which are similar to those in soy, milk and eggs. I know nothing about biochemistry, and I'm struggling to decipher the info i find.. &#xA;the closest Ive got to an answer is albumin - which i believe to be a group of proteins, all present in the above? &#xA;Can you be intolerant to albumin? or a derivative of?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a simpilar version of the question - what is the name of the protein(s) found in milk/oat/eggs and soy, if any?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;the reason for my question, my daughter has a milk/egg/oat (protein) intolerance and I'm just interested to find out if its a particular protein (or group of), or if its an intolerance to random things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many thanks!&lt;/p&gt;&#xA;" OwnerUserId="14962" LastActivityDate="2015-03-16T20:52:51.517" Title="Proteins in Milk, Oat , Eggs and Soy" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;food&gt;&lt;allergies&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30490" PostTypeId="2" ParentId="30488" CreationDate="2015-03-16T19:17:50.097" Score="3" Body="&lt;p&gt;The best resource for troubleshooting ligations I found (and use frequently) is &lt;a href=&quot;https://www.neb.com/tools-and-resources/usage-guidelines/tips-for-maximizing-ligation-efficiencies&quot; rel=&quot;nofollow&quot;&gt;this NEB page&lt;/a&gt;.  That is assuming you've already referred to the instructions provided with the enzyme you're using.   In my case it's &lt;a href=&quot;https://www.neb.com/products/m0202-t4-dna-ligase&quot; rel=&quot;nofollow&quot;&gt;T4 Ligase&lt;/a&gt;, again from NEB.   It's helpful to check the FAQs and the references listed on that page.    Also, you can make use of their Molar Calculator tool on Ligation setting (see more from first link).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Good luck with high efficiency!&lt;/p&gt;&#xA;" OwnerUserId="14963" LastActivityDate="2015-03-16T19:17:50.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30492" PostTypeId="2" ParentId="30489" CreationDate="2015-03-16T20:52:51.517" Score="2" Body="&lt;p&gt;Allergies are often caused by the immune system reacting to &lt;a href=&quot;http://en.wikipedia.org/wiki/Epitope&quot; rel=&quot;nofollow&quot;&gt;a part of a specific protein&lt;/a&gt;, therefore it is in fact a specific protein in the food that is causing the allergic reaction to occur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Milk allergies are caused by casein and whey (&lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/milk-allergy/basics/causes/con-20032147&quot; rel=&quot;nofollow&quot;&gt;Source: Mayo Clinic&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oat allergies can be caused by avenin (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2362.2000.00684.x/abstract;jsessionid=EDDD28A3A4B53E6620A96673DCDFF59E.f01t02&quot; rel=&quot;nofollow&quot;&gt;Source: EJCI&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Soy and egg allergies are caused by their respective albumin proteins. Additionally, egg lysozyme can also cause allergy. (Source: &lt;a href=&quot;https://my.clevelandclinic.org/health/diseases_conditions/hic_Allergy_Overview/hic_Food_Allergies/hic_Soy_Allergy&quot; rel=&quot;nofollow&quot;&gt;Cleveland Clinic&lt;/a&gt;, &lt;a href=&quot;http://www.foodallergy.org/allergens/egg-allergy&quot; rel=&quot;nofollow&quot;&gt;Food Allergy&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-03-16T20:52:51.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30494" PostTypeId="1" AcceptedAnswerId="30495" CreationDate="2015-03-16T21:18:30.330" Score="8" ViewCount="3275" Body="&lt;p&gt;What causes an animal sperm cell to die? Does it die somehow from being outside its original environment?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've studied the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sperm&quot;&gt;Wikipedia page&lt;/a&gt;&#xA; on sperm and I see a lot of information on what makes up a sperm cell, but can't quite figure out its lifecycle and exactly how it dies.&lt;/p&gt;&#xA;" OwnerUserId="14968" LastEditorUserId="5144" LastEditDate="2015-03-16T21:55:48.397" LastActivityDate="2015-03-16T22:16:56.800" Title="How does a sperm cell die?" Tags="&lt;reproduction&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30495" PostTypeId="2" ParentId="30494" CreationDate="2015-03-16T21:54:26.360" Score="14" Body="&lt;p&gt;So most cells require growth factors and survival factors to stay alive in an organism. Cells which stop receiving survival factors, such as sperm, undergo a process of programmed cell death (PCD) called apoptosis. Some cells will also undergo necrosis, or autophagy, among other types of PCD. &lt;a href=&quot;http://hera.ugr.es/doi/15059200.pdf&quot; rel=&quot;noreferrer&quot;&gt;Lachaud &lt;em&gt;et al.&lt;/em&gt;&lt;/a&gt; performed a study in 2004 on the contribution of apoptosis and necrosis in ejaculated sperm. They make note in the intro that from other literature that we see some hallmarks of apoptosis like externalized phosphatidylserine, fragmented DNA, etc. despite inactivated nuclei and a small cytoplasm. Their data notes that ejaculate sperm cell death mainly occurs from necrosis, however, because sperm themselves lack the ability to initiate apoptosis. However, in the testes, there's data to note that &lt;a href=&quot;https://www.bioscience.org/2012/v4e/af/415/fulltext.htm&quot; rel=&quot;noreferrer&quot;&gt;apoptosis plays a role&lt;/a&gt;, and the presence of apoptotic spermatozoa in the ejactulate may be result of the inititation of apoptosis by factors which still inside the body. Apoptosis of spermatozoa in the testes is currently under investigation in male infertility, and damage in cryopreservation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just to give you an idea of the difference, necrosis is a much messier outcome derived from physical factors, or those factors external to the cell. Apoptosis is organized, controlled, and modulated by cellular signals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/u7rZ4.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-03-16T22:16:56.800" LastActivityDate="2015-03-16T22:16:56.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30496" PostTypeId="2" ParentId="30488" CreationDate="2015-03-16T22:23:51.497" Score="1" Body="&lt;p&gt;To measure the frequency of indels at the ligation site you can use a vector with a unique restriction site in the lacZ gene. With a colorimetric assay you can count the number of white cfu. Perfect ligation in-frame yields blue cfu&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-03-16T22:23:51.497" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30498" PostTypeId="1" AcceptedAnswerId="30500" CreationDate="2015-03-17T03:21:01.833" Score="5" ViewCount="620" Body="&lt;p&gt;The Young's modulus of elasticity when a bone is stretched is : 16×10&lt;sup&gt;9&lt;/sup&gt; and when it is compressed, it is 9×10&lt;sup&gt;9&lt;/sup&gt; N/m&lt;sup&gt;2&lt;/sup&gt;. That means, change in length will be more if you compress a bone as compared to stretching it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the biomechanical reason behind this ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3340" LastEditDate="2015-03-18T05:17:52.527" LastActivityDate="2015-03-18T05:17:52.527" Title="Stretching and compressing bones" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;biophysics&gt;&lt;anatomy&gt;&lt;bone-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30499" PostTypeId="2" ParentId="1977" CreationDate="2015-03-17T03:24:17.810" Score="0" Body="&lt;p&gt;I am not a chemist and unfortunately I will have to refer to &lt;a href=&quot;http://en.wikipedia.org/wiki/Homoassociation&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;, but the ionization constant for HF (10&lt;sup&gt;−3.15&lt;/sup&gt;, according to wikipedia) does not take &lt;strong&gt;homo-association&lt;/strong&gt; into account. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Homo-association is an association between a base and its conjugate acid through a hydrogen bond. This process stabilizes the conjugate base, thereby increasing ionization. Often this behavior increases acidity, especially at high concentrations. In case of HF (double arrows indicate equilibria):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2HF &amp;lt;- -&gt; H&lt;sub&gt;2&lt;/sub&gt;F&lt;sup&gt;+&lt;/sup&gt; + F&lt;sup&gt;−&lt;/sup&gt; (autoionization of HF)&lt;br&gt;&#xA;HF + F&lt;sup&gt;−&lt;/sup&gt; &amp;lt;- -&gt; HF&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;−&lt;/sup&gt; (homoassociation)  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The formation of the bifluoride anion (HF&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;−&lt;/sup&gt;) encourages the ionization of HF by stabilizing and removing F&lt;sup&gt;−&lt;/sup&gt; from solution hence pulling the dissociation equilibrium of HF (HF + H&lt;sub&gt;2&lt;/sub&gt;O &amp;lt;- -&gt; H&lt;sub&gt;3&lt;/sub&gt;O&lt;sup&gt;+&lt;/sup&gt; + F&lt;sup&gt;-&lt;/sup&gt;) to the right. Thus, the usual ionization constant for hydrofluoric acid (10&lt;sup&gt;−3.15&lt;/sup&gt;) understates the acidity of concentrated solutions of HF.   &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-03-17T03:24:17.810" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30500" PostTypeId="2" ParentId="30498" CreationDate="2015-03-17T08:14:20.023" Score="8" Body="&lt;p&gt;Citing your source would help to answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to test an elastic modulus, you need to apply some non-zero strain. If the strain is infinitesimal, then compression and stretch modulus will be equal. But if it is finite, then there can be a difference due to the structure of the material.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In bone, I believe porosity will provide most of the dissymetry between compression and extension: at small scales, the material can rearrange using the pores without much deformation. Whereas in extension, there has to be some deformation of the osteons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other living tissue, the difference can be due to filamentous proteins: if you compress them, they buckle (form loops) without much resistance. If you exert extensive stress, once they are stretched tight they will resist any further extension. (Think of what a piece of string would do, it's very similar)&lt;/p&gt;&#xA;" OwnerUserId="6224" LastActivityDate="2015-03-17T08:14:20.023" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30501" PostTypeId="2" ParentId="30422" CreationDate="2015-03-17T09:14:56.217" Score="3" Body="&lt;p&gt;Genome wide functional linkages refers to protein in a biochemical or signalling pathway. Inferences of functional interactions can be obtained from methods such as coexpression data from microarray analysis. Since experimental detection of genome-wide protein–protein interactions is costly and time-consuming a computational scope for essentially predictive genome-wide protein–protein interactions is created &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1832100/&quot; rel=&quot;nofollow&quot;&gt; [1]&lt;/a&gt;, which is what the above paper is referring to. As obvious from the abstract of the paper, there are many ways of obtaining the linkages, which are often inferred by the Rosetta Stone, Phylogenetic Profile, Operon and Conserved Gene Neighbor computational methods&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14654685&quot; rel=&quot;nofollow&quot;&gt; [2]&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Algorithms that identify genome-wide interactions between proteins mainly focus on coregulation of interacting proteins. These methods assume that the genes that are coregulated often occur close to each other on the genomes and show conserved gene order. Thus the genes, which are part of an operon, could be functionally linked.&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2015-03-17T15:29:20.280" LastActivityDate="2015-03-17T15:29:20.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30502" PostTypeId="1" CreationDate="2015-03-17T09:47:44.527" Score="5" ViewCount="168" Body="&lt;p&gt;I have a friend who told me that anti-aging cream cannot work to reduce wrinkles as it only penetrates x amount of skin layers and can never make a long term effect. Me not knowing much about how penetrative skin actually is, I was wondering if anyone knows if this is true and if anti-aging products are only working like a temporary moisturiser?&lt;/p&gt;&#xA;" OwnerUserId="14973" LastEditorUserId="14973" LastEditDate="2015-03-17T14:55:47.223" LastActivityDate="2015-03-17T15:30:08.147" Title="Can anti-aging cream work?" Tags="&lt;skin&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30503" PostTypeId="1" CreationDate="2015-03-17T09:59:13.180" Score="3" ViewCount="335" Body="&lt;p&gt;I'm looking for sequences and annotations of known riboswitches, but so far I haven't found a resource that actually fulfills my requirements. The best database I found so far is Rfam, which has entries for many riboswitch classes. The biggest drawbacks of Rfam for my case are that it doesn't contain any information about the expression platform, only about the aptamer. I'd like to know if a riboswitch is translational or transcriptional, and where the terminator/Shine-Dalgarno sequences that are regulated by the switch are. Another limitation of Rfam is that I can't easily see which sequences are validated biologically in some way, and which are just predicted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a database of riboswitches that also contains information about the expression platform? &lt;/p&gt;&#xA;" OwnerUserId="14541" LastActivityDate="2015-03-17T09:59:13.180" Title="Is there a database of known riboswitches?" Tags="&lt;rna&gt;&lt;database&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30504" PostTypeId="1" AcceptedAnswerId="30506" CreationDate="2015-03-17T11:23:29.210" Score="2" ViewCount="2919" Body="&lt;p&gt;In &lt;em&gt;myopia&lt;/em&gt; the lens is bending the light too much even in the most relaxed state. Thus the image is produced in front of the retina. If the object comes closer  the lens just adjusts a bit less than a healthy eye and the myopic subject is able to see clearly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is the &lt;em&gt;hyperopic&lt;/em&gt; eye not able to do that? If the object is far away, could the lens not just bend a bit more to elicit normal vision? So, why is the Myopic eye able to adjust its focus, but the Hyperopic not?&lt;/p&gt;&#xA;" OwnerUserId="8196" LastEditorUserId="9943" LastEditDate="2015-03-22T12:54:35.523" LastActivityDate="2016-03-29T16:22:43.997" Title="What is the difference between myopia and hyperopia?" Tags="&lt;vision&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30506" PostTypeId="2" ParentId="30504" CreationDate="2015-03-17T12:07:05.183" Score="1" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Myopic eyes can still focus on nearby images as the lens needs to relax a bit more than in a normally-sighted person. However, objects far away cannot be focused, because in a complete relaxed state (for distant objects), the lens focuses the image in front of the retina. Hyperopic eyes cannot focus on nearby objects as, at a certain close distance, the lens reaches maximum accomodation (maximum roundness) and objects cannot be focused any longer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;&lt;em&gt;Myopia&lt;/em&gt; or near-sightedness is a condition of the eye where the light that comes in does not directly focus on the retina but in front of it, causing the image that one sees when looking at a distant object to be out of focus, but in focus when looking at a close object. Often the eye ball is too long, or the cornea has too much curvature (&lt;a href=&quot;http://www.webmd.com/eye-health/nearsightedness-myopia&quot; rel=&quot;nofollow noreferrer&quot;&gt;Web MD&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Hyperopia&lt;/em&gt; (&quot;over-measured sight&quot;) or farsightedness, is a defect of vision caused typically by the eyeball being too short, or a lens that cannot accomodate/become round enough. It causes difficulty focusing on near objects (&lt;a href=&quot;http://en.wikipedia.org/wiki/Hyperopia&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PuGHw.jpg&quot; alt=&quot;Far and nearsightedness&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source:&lt;a href=&quot;http://www.monroepublishing.com/feature/kidshealth/sight3.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Monroe Publishing&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-17T13:21:49.523" LastActivityDate="2015-03-17T13:21:49.523" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30508" PostTypeId="1" AcceptedAnswerId="30513" CreationDate="2015-03-17T13:03:35.290" Score="2" ViewCount="176" Body="&lt;p&gt;From my understanding C. elegans are mainly hermaphrodites but are occasionally males to increase genetic variation. Why is it that random females aren't born instead to achieve he same goal (genetic diversity)?&lt;/p&gt;&#xA;" OwnerUserId="13023" LastActivityDate="2015-03-17T15:59:05.027" Title="C. elegans are either male or hermaphrodites, but why aren't there any females?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30509" PostTypeId="2" ParentId="30404" CreationDate="2015-03-17T13:24:11.837" Score="1" Body="&lt;p&gt;I found a PLOS one &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646956/&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; that might help. In this they used similar numbers you're planning to use (if i get your question and the article's data right). &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The influence of the sampling scheme was investigated by drawing 40 samples in three different ways: 1) all 40 samples from a single deme, 2) 4 samples from each of 10 demes and 3) one sample from each of the 40 demes in the structured population. These correspond respectively to the local, pooled and scattered &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(taken from the above linked article)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So depending on your sampling scenario your 30 samples seems to okay.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also this is a &lt;a href=&quot;http://beast.bio.ed.ac.uk/FAQ#Effective_Sample_Size_.28ESS.29_of_parameters&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt; for the BEAST FAQ that might be helpful. &lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-03-17T13:24:11.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30510" PostTypeId="1" CreationDate="2015-03-17T13:35:02.870" Score="1" ViewCount="38" Body="&lt;p&gt;In &lt;em&gt;Neuroscience&lt;/em&gt; 3rd ed by Bear et al. on page 607, immediate early genes are described as related to changing synaptic strength, yet have decreased expression during sleep. The explanation given is that &quot;learning and memory formation are largely absent in [sleep].&quot; But that seems somewhat counterintuitive as LTP occurs during sleep.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is really going on here?&lt;/p&gt;&#xA;" OwnerUserId="14975" LastActivityDate="2015-03-17T13:35:02.870" Title="Immediate Early Genes during sleep" Tags="&lt;neuroscience&gt;&lt;sleep&gt;&lt;learning&gt;&lt;gene&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30511" PostTypeId="2" ParentId="30508" CreationDate="2015-03-17T14:58:15.727" Score="0" Body="&lt;p&gt;C.elegans makes use of an &lt;a href=&quot;http://en.wikipedia.org/wiki/X0_sex-determination_system&quot; rel=&quot;nofollow&quot;&gt;X0 sex determination system&lt;/a&gt;, so there is only one sex chromosome (X), which only allows for two sexes (XX and X0) as 00 is not viable.&lt;/p&gt;&#xA;" OwnerUserId="14698" LastActivityDate="2015-03-17T14:58:15.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30512" PostTypeId="2" ParentId="30502" CreationDate="2015-03-17T15:30:08.147" Score="5" Body="&lt;p&gt;Since there are different formulations for anti-aging creams, it would be helpful to focus on the specific compound or combination of compounds.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to a comprehensive literature review done in 2007, certain compounds (Vitamin C, alpha-hydroxy acids, Vitamin A, Vitamin B derivatives, and botanicals) have had varied success in literature demonstrating anti-aging efficacy with Vitamin C and alpha-hydroxy acids being the better candidates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vitamin A/retinols have been shown to reduce wrinkles in some studies but no large studies have been conducted to show efficacy, Vitamin C has been shown to be the most effective (statistically significant improvement in texture, wrinkling, etc.) and alpha-hydroxy acids have been shown to increase collagen density, for example among other improvements.  A lot of these and other compounds have had positive or encouraging results replicated in literature, on mostly animal and human cell models so whether they actually have a significant effect on a large group of people needs to be looked at but to assess whether or not they actually &quot;work&quot; depends on what issues of skin damage as a result of aging one is targetting, the severity, the age at &quot;treatment&quot; and whether you're referring to over the counter or prescription-strength.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Huang, C. K. and T. A. Miller (2007). &quot;The truth about over-the-counter topical anti-aging products: a comprehensive review.&quot; Aesthet Surg J 27(4): 402-412; quiz 413-405.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="14916" LastActivityDate="2015-03-17T15:30:08.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30513" PostTypeId="2" ParentId="30508" CreationDate="2015-03-17T15:59:05.027" Score="4" Body="&lt;p&gt;The evolution of self-fertile hermaphrodites is thought to be a specialization that occurred several times in the nematoda. For example, most of small, free-living soil nematode species related to C. elegans are male/female. C. briggsae, which last shared a common ancestor 80 myr ago is also male/hermaphrodite, but I believe their ancestor is thought to have been male/female. &#xA;At the developmental level, the first germ cells to mature in the somatic gonad develop as sperm and then the Germline switches over to make oocytes.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-03-17T15:59:05.027" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30514" PostTypeId="1" CreationDate="2015-03-17T16:54:37.467" Score="5" ViewCount="1547" Body="&lt;p&gt;As a caretaker of a turtle, I sometimes struggle understanding the logic behind the inclusion of corn, soybean, and wheat meals in reptile food, such ingredients seem truly aberrant from what a reptile would naturally be exposed to. Nevertheless I am aware of the biological and chemical similarity between most organisms, so I wonder whether that will help reptiles, especially omnivores with an eclectic digestive ability, to digest these compounds. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking for legitimate studies on reptile digestibility; anecdotal experience or advice is supplementary if present. &lt;/p&gt;&#xA;" OwnerUserId="14976" LastEditorUserId="14976" LastEditDate="2015-03-17T18:41:25.610" LastActivityDate="2015-03-17T20:41:31.490" Title="Can reptiles digest grains?" Tags="&lt;digestive-system&gt;&lt;diet&gt;&lt;reptile&gt;&lt;digestion&gt;&lt;herpetology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30515" PostTypeId="2" ParentId="23993" CreationDate="2015-03-17T17:21:39.193" Score="5" Body="&lt;p&gt;I have only ever heard of one case where RP caused blindness in a newborn. Unfortunately, I am unable to release the name or any details of the patient because of privacy issues and so forth. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually blindness from RP comes after a few years of life (as you said), making blindness from birth (or even early infancy) very rare. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can tell you, however, that the formerly stated patient suffered from type I Usher Syndrome, if I remember correctly. I apologize for my inability to provide you with more specific details on this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know how much this will help in your search, but I sincerely hope that it does.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CDB&lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-03-17T17:21:39.193" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30516" PostTypeId="2" ParentId="30370" CreationDate="2015-03-17T18:29:34.260" Score="0" Body="&lt;p&gt;lacID is an example of a dominant-negative allele (or mutation) so the phenotype is visible in m/+ (the bacterial merodiploids are the prokaryotic version of heterozygotes), and therefore, by definition, dominant, however the phenotype (in this case constitutive expression of the lac operon) is the same as the loss-of-function phenotype (a complete knock-out, or deletion of the lac Repressor gene).&#xA;If m/+ has the same phenotype as m/m it could be dose-sensitive, or the protein could be a multimer, or the mutant protein could titrate (or sequester) an interacting protein.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-03-17T18:29:34.260" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30518" PostTypeId="2" ParentId="30432" CreationDate="2015-03-17T19:09:23.997" Score="2" Body="&lt;p&gt;Most of the loss of light being transmitted through individual cells is not absorbed, rather it is scattered (redirected from its original direction to a new one without loss of energy).  There is actually not very much in cells that can absorb visible light, and virtually nothing at all that can absorb many red or near-infrared wavelengths.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scattering does depend on wavelength, but the relationship is very complex.  For scattering from small cellular components (mitochondria for example), Rayleigh scattering dominates, which will decrease with the 4th power of wavelength, so that green light will scatter much more strongly than red.  For larger components that are comparable or larger than a wavelength (nuclei or whole cells), scattering will increase much more slowly.  The relationship between the direction of scattering and the size/wavelength is even more complex, but is very useful in applications like label-free cytometry where cells can be sorted based on scattered light.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;600-800 nm light is a reasonable choice because it will not damage the cells unless the power level is very high, although using shorter wavelengths may give you more sensitive measurements.  &lt;/p&gt;&#xA;" OwnerUserId="9561" LastActivityDate="2015-03-17T19:09:23.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30519" PostTypeId="1" CreationDate="2015-03-17T20:00:14.310" Score="8" ViewCount="2415" Body="&lt;p&gt;I was listening lectures from Mark Saltzman via &lt;a href=&quot;http://oyc.yale.edu&quot; rel=&quot;noreferrer&quot;&gt;Open Yale Courses&lt;/a&gt;. Now, if I did not understand him wrong, he said that the amount of blood that travels through every vein and artery in our bodies per minute is a constant. Five liters of blood go through the aorta every minute, and since the blood circulation is a closed system, also every other vein/artery must pass that amount of blood per minute. Is this true? How could I (mathematically) show that it is true?&lt;/p&gt;&#xA;" OwnerUserId="14978" LastEditorUserId="14709" LastEditDate="2015-03-17T21:55:46.363" LastActivityDate="2018-11-03T22:08:23.390" Title="Is the amount of blood that flows through every vein and artery per minute really a constant?" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;blood-circulation&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30520" PostTypeId="2" ParentId="30514" CreationDate="2015-03-17T20:09:13.473" Score="4" Body="&lt;p&gt;This is not a yes / no question. Many tortoise eat plants (veggies and fruits) while some turtles eat fish too. Snakes are basically predators and do not dwell on plants neither do most of the lizards. I think if a reptile is capable of digesting plant food in general, then it should be able to digest preprocessed grains as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:  As for whole intact grains I'm unsure, as canadianer pointed out in comments section, intact grains are hard(er) to digest. /end of edit/&#xA;I found &lt;a href=&quot;http://jn.nutrition.org/content/120/7/775.long&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article where scientist fed alligators with a mixed diet in various setup. The diet included corn too and the 'gators responded well in terms that they could use carbon-hydrates.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Recently, we (3) have demonstrated that hatchling alligators benefit from and apparently do utilize some dietary carbohydrate. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-03-17T20:41:31.490" LastActivityDate="2015-03-17T20:41:31.490" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30522" PostTypeId="2" ParentId="30519" CreationDate="2015-03-17T21:28:40.423" Score="0" Body="&lt;p&gt;The amount of blood flow is not constant in general.  As you exert yourself, your heart rate and therefore blood flow increases.  Furthermore, individual vessels dilate or constrict to increase or decrease flow by modulating their resistance to flow.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your circulatory system is closed however, so all of the blood leaving the heart must eventually come back to it.  &lt;/p&gt;&#xA;" OwnerUserId="9561" LastActivityDate="2015-03-17T21:28:40.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30523" PostTypeId="1" CreationDate="2015-03-17T22:59:09.010" Score="2" ViewCount="197" Body="&lt;p&gt;For a little less than half the cell cycle, a significant number of genes are represented twice (just before dividing).  Does the cell differentiate between these DNA in any way or are transcription rates limited by the amount of polymerase anyway?&lt;/p&gt;&#xA;" OwnerUserId="14980" LastEditorUserId="14735" LastEditDate="2015-03-18T01:52:38.540" LastActivityDate="2015-03-18T04:03:26.387" Title="Are both (partial) copies of DNA transcribed in S and G2 phases of cell cycle?" Tags="&lt;dna&gt;&lt;transcription&gt;&lt;mrna&gt;&lt;cell-cycle&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30524" PostTypeId="1" AcceptedAnswerId="30532" CreationDate="2015-03-18T01:42:18.037" Score="6" ViewCount="204" Body="&lt;p&gt;What level of radiation at the frequencies used by the cellular network(1-2 Ghz) is harmful for human health?&lt;/p&gt;&#xA;" OwnerUserId="14983" LastEditorUserId="4109" LastEditDate="2015-03-18T03:52:26.953" LastActivityDate="2015-03-18T11:18:56.167" Title="What level of cellular radiation is harmful for humans?" Tags="&lt;human-biology&gt;&lt;radiation&gt;&lt;health&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30525" PostTypeId="2" ParentId="30519" CreationDate="2015-03-18T03:48:37.383" Score="1" Body="&lt;p&gt;Nope. All blood flows in the body can change at any time(more or less).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the heart rate and blood pressure, etc, is constant the amount of blood that travels through the aorta is constant, yes. But there is far more capacity in the arterial and venous systems for the actual amount of blood flow there normally is. Veins and arteries contract and expand to route blood flow to different parts of the body, so the amount of blood flowing through any particular artery can change without changing the aortic flow. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good example of this: &lt;a href=&quot;http://en.wikipedia.org/wiki/Vasomotion&quot; rel=&quot;nofollow&quot;&gt;Vasomotion&lt;/a&gt;. It happens all the time in your hands (sometimes it's even visible as patches of red/white skin. On my hands they're a little smaller than the head of a thumbtack) on the order of minutes. &lt;a href=&quot;http://en.wikipedia.org/wiki/Functional_magnetic_resonance_imaging&quot; rel=&quot;nofollow&quot;&gt;fMRI&lt;/a&gt; is a neat technology based around watching brain blood vessel changes in flow as a proxy for activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All the flows through all your arteries don't even have to sum to the aortic flow, due to compliance(a fluid dynamics term. essentially, the aorta or other arteries/veins can 'inflate' so more blood is flowing in than is flowing out. Then later they 'deflate' and more blood flows out than in. Arteries tend to be more compliant because they have to be springier to deal with heartbeat). There are also osmotic effects where fluid leaves the arteries and becomes lymph, which then later drains back into veins. It's not a huge effect but it's there. If you measure total blood flow through the aorta and then total blood flow through all the capillaries, there will be less total blood flowing through the capillaries. Not much less( 10% at the most) depending on blood salt and blood vessel position and whether you count the kidneys, etcetera etcetera.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So: the amount of blood that passes through a given artery given the aortic blood flow is not fixed. The amount of blood that passes through all arteries given the aortic blood flow is much closer to fixed, but even that can be different(even if you're not bleeding). And if you were asking if the amount of blood that flows through the aorta is constant, that's absolutely not true. That can vary through the heart rate, the contractility of the heart, the venous return pressure, the overall blood pressure, and a bunch of other things that very slightly affect flow rates.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-03-18T03:48:37.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30527" PostTypeId="2" ParentId="30523" CreationDate="2015-03-18T04:03:26.387" Score="1" Body="&lt;p&gt;I can't unequivocally say, at least without further literature review, that both sister chromatids are transcribed equally everywhere, especially since the cell does have mechanisms to differentiate between the old and new DNA strands (such as methylation state). It would be conceivable to expect, however, that the same regulatory factors that were present before replication have the same effect on newly synthesized DNA as they did on the old. Here are some electron micrographs showing transcription from both chromatids at some locus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cell.com/cell/references/0092-8674%2879%2990263-0&quot; rel=&quot;nofollow noreferrer&quot;&gt;McKnight SL, Miller, OL Jr. 1979. Post-replicative nonribosomal transcription units in D. melanogaster embryos. Cell 17:551-563&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here you can see RNA (solid line in schematic, b) of increasing length branching from both sister chromatids (dotted line):&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Abujm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A similar image but this time showing the replication fork (arrow):&#xA;&lt;img src=&quot;https://i.stack.imgur.com/68R0o.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This image shows RNA free gaps (arrows) in a single transcription unit, which are symmetrical between the two chromatids:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/EzzCC.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From which they conclude:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The observation that fiber-free gaps often occur at symmetrical positions on sister chromatid transcription units suggests that the two identical transcription units respond similarly to the mechanisms that control RNA polymerase chain initiation. These cannot now be specified, but could include the local supply of RNA polymerase or other controlling molecules. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-03-18T04:03:26.387" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30528" PostTypeId="2" ParentId="30448" CreationDate="2015-03-18T05:09:49.393" Score="5" Body="&lt;p&gt;I didn't watch the video so I don't know if this was mentioned. Butterflies will exhibit a behavior called &lt;a href=&quot;http://en.wikipedia.org/wiki/Mud-puddling&quot;&gt;mud puddling&lt;/a&gt; which occurs mainly with male butterflies &lt;a href=&quot;http://www.stanford.edu/group/CCB/Pubs/Boggs_pdfs/1991%20Boggs%20&amp;amp;%20Jackson%20puddling.pdf&quot;&gt;[1]&lt;/a&gt;. Puddling is when butterflies seek out moist surfaces in order to consume the fluid. Butterflies will puddle in soil, dung, carrion (rotting flesh/meat), etc. Boggs and Jackson claim that puddling falls into two categories which aren't mutually exclusive &lt;a href=&quot;http://www.stanford.edu/group/CCB/Pubs/Boggs_pdfs/1991%20Boggs%20&amp;amp;%20Jackson%20puddling.pdf&quot;&gt;[1]&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;scarce nutrients for example sodium&lt;/li&gt;&#xA;&lt;li&gt;competitive exclusion of males or young individuals from flowers &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;But we can see blood isn't the only option for puddling. Basically anything that provides moisture and nutrients will do.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastActivityDate="2015-03-18T05:09:49.393" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30529" PostTypeId="2" ParentId="21440" CreationDate="2015-03-18T08:17:55.227" Score="3" Body="&lt;p&gt;I think you should start with immortalized cell lines and so in vitro division rates by perfect conditions. This is easier to measure than in vivo division rates. E.g. HeLa has a division time of 23 hours. MDA-MB-231 and A549 division times are around 28 hours.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://staff.science.nus.edu.sg/~syao/Resources/5.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Growth of HeLa Cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0046536&quot; rel=&quot;nofollow noreferrer&quot;&gt;Comparative Analysis of Dynamic Cell Viability, Migration and Invasion Assessments by Novel Real-Time Technology and Classic Endpoint Assays&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So I assume there is a physical barrier somewhere around one division per day or so, and it simply cannot grow faster. While bacterial division times are much lower (down to 20min), they also depend on special mechanisms (see &lt;a href=&quot;https://biology.stackexchange.com/questions/39641/bacteria-replication&quot;&gt;this&lt;/a&gt; question/answer) and are orders of magnitude smaller than mammalian cells, so they don't count as a counter argument to this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you check zygote division times (10-12h, 14-16h, 22-24h, ...), you can see that they highly depend on the cell size. After some divisions the zygote depleted the reserves necessary to divide at higher rates, so after that it is limited by the ~24h barrier too.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.biomed.cas.cz/physiolres/pdf/61/61_513.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Time-Lapse Cleavage Rating Pr&#xA;edicts Human Embryo Viability&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Same 24h data here by rapidly proliferating cells.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK9876/&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Cell: A Molecular Approach. 2nd edition.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So we can assume that 1/24h is the maximum rate of cell division by cancer. Let's read more about cancer in vivo, because it behaves completely different than immortalized cell lines in in vitro tests.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Originally tumours were thought to grow because they consisted of&#xA;  cells that multiplied more rapidly than cells in the surrounding&#xA;  tissue. In fact the average cell cycle of 48 hours for human tumour&#xA;  cells is slightly longer than the cycle of non-malignant cells. ...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;When a normal cell divides, it does os only to replace a cell that has&#xA;  been lost and in this way a constant cell population is maintained. In&#xA;  tumour cells the control mechanism appears to have been lost: as the&#xA;  cell divides it adds to existing numbers of cells and increases the&#xA;  total population. ...&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;A measure of the rate of tumour growth is the time taken for a given&#xA;  population of malignant cells to double in size (doubling time). If&#xA;  the cell cycle takes between 15 and 120 hours, the doubling time can&#xA;  be between 96 hours and 500 days, depending on the histological type&#xA;  of the tumour, its age and whether it is a primary or metastatic&#xA;  growth. A shorter doubling time (less than 30 days) can be between is&#xA;  seen with teratomas, non-Hodgkin's lymphomas, and acute leukaemias;&#xA;  common solid tumours such as squamous cell carcinoma of the bronchus&#xA;  and adenocarcinoma of the breast and bowel have doubling times in&#xA;  excess of 70 days. In the patient the growth of a cacncer is only&#xA;  detectable and observable during the last 10-14 of its 35-40 doubling&#xA;  times.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://books.google.hu/books?id=RI7eS2Z8DHMC&amp;amp;pg=PA270&amp;amp;lpg=PA270&amp;amp;dq=cancer+division+time+hours&amp;amp;source=bl&amp;amp;ots=pl6wRJXhvq&amp;amp;sig=Lt7-cupUnyOS0XzP0Lg8Z6x6Cm4&amp;amp;hl=hu&amp;amp;sa=X&amp;amp;ei=Ni4JVZyTEcz9UqTngsAD&amp;amp;ved=0CGkQ6AEwCQ#v=onepage&amp;amp;q=cancer%20division%20time%20hours&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cancer Nursing: Care in Context (page 270)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So according to this book the division rate of cancer cells are similar to healthy cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to another book this statement is from Dougherty &amp;amp; Bailey 2001, but I wasn't able to find the scientific article. :S&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Tumour cells appear to have lost control mechanisms which prevent cells from growing until replacement is required. Human tumour cells are thought to have an average cycle time of 48 hours. This is not more rapid than the cycle of most normal cells. The reason tumours become larger is because their cell division creates additional cells rather than replacements (Dougherty &amp;amp; Bailey 2001).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://books.google.hu/books?id=F7NE_iXpEvgC&amp;amp;pg=PA236&amp;amp;lpg=PA236&amp;amp;dq=average+cell+cycle+for+human+tumour+cells+time&amp;amp;source=bl&amp;amp;ots=CPn0dnG5gh&amp;amp;sig=PMDoeLSg-HMJ_WVSGeDqz2m5Dtk&amp;amp;hl=hu&amp;amp;sa=X&amp;amp;ei=OjQJVaLQMYXWU7LmgvAB&amp;amp;ved=0CEYQ6AEwAw#v=onepage&amp;amp;q=average%20cell%20cycle%20for%20human%20tumour%20cells%20time&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Stoma Care and Rehabilitation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="32671" LastEditDate="2017-06-29T10:50:10.713" LastActivityDate="2017-06-29T10:50:10.713" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30530" PostTypeId="2" ParentId="30524" CreationDate="2015-03-18T09:02:48.310" Score="2" Body="&lt;p&gt;Afaik. &lt;a href=&quot;http://en.wikipedia.org/wiki/Electromagnetic_spectrum&quot; rel=&quot;nofollow&quot;&gt;radio waves&lt;/a&gt; don't have enough energy to cause anything similar to the damage ionizing radiation (gamma rays) does.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What it can cause is probably heat damage similar to microwave ovens.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;According to the United States Food and Drug Administration's Center for Devices and Radiological Health, a U.S. Federal Standard limits the amount of microwaves that can leak from an oven throughout its lifetime to 5 milliwatts of microwave radiation per square centimeter at approximately 5 cm (2 in) from the surface of the oven.[52] This is far below the exposure level currently considered to be harmful to human health.[53]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Microwave_oven&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Microwave_oven&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Advanced Measurements of Microwave Oven Leakage - &lt;a href=&quot;http://www.arpansa.gov.au/pubs/emr/microwave.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.arpansa.gov.au/pubs/emr/microwave.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;According to the article referenced by wikipedia a 35 W/kg SAR level (caused by a 30 mW/cm2 leakage) can raise the tissue temperature with 1.5°C, which probably does not any serious damage. I guess from this you can count the radiation intensities - you are interested in - to any frequencies.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2015-03-18T09:12:47.963" LastActivityDate="2015-03-18T09:12:47.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30531" PostTypeId="2" ParentId="30519" CreationDate="2015-03-18T09:11:39.260" Score="3" Body="&lt;p&gt;It is ofc. not true, because it is not a closed system. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Renal_function&quot; rel=&quot;nofollow&quot;&gt;kidneys filter blood and excrete water and other compounds&lt;/a&gt; (which are reabsorbed or go to urine), the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sweat_gland&quot; rel=&quot;nofollow&quot;&gt;sweat glands remove water and salts&lt;/a&gt;. By drinking daily 2 liters (the total blood volume is about 5 liters) of fresh water and salts are &lt;a href=&quot;http://en.wikipedia.org/wiki/Digestion&quot; rel=&quot;nofollow&quot;&gt;absorbed from the intestines&lt;/a&gt; to the circulation, by eating just the opposite happens. Every cell has &lt;a href=&quot;http://en.wikipedia.org/wiki/Aquaporin&quot; rel=&quot;nofollow&quot;&gt;aquaporins&lt;/a&gt; which are responsible for water transport, so they can dilute the blood for a while, if necessary. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Spleen&quot; rel=&quot;nofollow&quot;&gt;spleen can withhold red blood cells&lt;/a&gt; (before injury) which reduces the blood volume. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Leukocyte_extravasation&quot; rel=&quot;nofollow&quot;&gt;white blood cells can leave the circulation&lt;/a&gt;. By &lt;a href=&quot;http://en.wikipedia.org/wiki/Inflammation#Vasodilation_and_Increased_Permeability&quot; rel=&quot;nofollow&quot;&gt;inflammation water leaves the vessels because of increased permeability&lt;/a&gt;, and so on...&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2015-03-18T17:14:29.920" LastActivityDate="2015-03-18T17:14:29.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30532" PostTypeId="2" ParentId="30524" CreationDate="2015-03-18T11:13:37.047" Score="4" Body="&lt;p&gt;Addition to the previous answer&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;First you need to understand how radiation causes cellular &lt;strong&gt;damage&lt;/strong&gt;.&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EM waves like γ-rays, X-rays and high-energy UV (in certain molecules even visible light) can knock out the electrons from the atom and create an ion and free radicals by breaking chemical bonds. This term — ionizing radiation is not used for low energy UV and visible light because these waves can only ionize a few types of molecules and are not ionizing in general. Moreover X-rays and γ-rays can dislodge even inner electrons which UV and visible light cannot (High energy γ-rays can also lead to the nuclear reaction of &lt;a href=&quot;http://en.wikipedia.org/wiki/Pair_production&quot; rel=&quot;nofollow noreferrer&quot;&gt;pair production&lt;/a&gt;). These ions that are formed are reactive and can attack other molecules (DNA/proteins etc) around them. DNA absorbs UV and this can cause DNA lesions such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Pyrimidine_dimer&quot; rel=&quot;nofollow noreferrer&quot;&gt;dimerization of adjacent pyrimidines&lt;/a&gt; (via a cyclobutane bridge). Both reactive ions and pyrimidine dimers can cause cancer; the former is most frequent in melanomas which happen because of solar UV. Since UV cannot penetrate very deep, they affect mostly the skin (See &lt;a href=&quot;https://biology.stackexchange.com/questions/8788/what-is-the-relationship-between-uv-wavelength-and-penetration-depth-into-human/8789#8789&quot;&gt;here&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;IR, with energy lower than visible light does not have sufficient energy to cause electronic transitions. But it can cause vibrational transitions such as bond stretching and bending. Microwaves have even lower energy and can only cause molecular rotation. Both IR and microwaves because of their property to make molecules move, generate heat. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Continuous usage of mobile phones can cause discomfort but only because of their heating effect. They can by no means cause cancer and even though mobile phone radiation is classified as a potential carcinogen (IARC Group 2B) perhaps because of the pressing allegations of certain factions, they &lt;strong&gt;do not&lt;/strong&gt; have sufficient energy to cause DNA damage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you ask me if mobile phone radiation can be harmful to human health, then I would say yes, they can be potentially harmful with prolonged usage but in no way as harmful as to be causing cancer. &lt;em&gt;I would say that it is as harmful as wine :P&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-03-18T11:18:56.167" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30535" PostTypeId="1" CreationDate="2015-03-18T12:08:25.800" Score="2" ViewCount="2932" Body="&lt;p&gt;There is always a certain amount of &lt;a href=&quot;http://www.ansto.gov.au/NuclearFacts/AboutNuclearScience/NaturalBackgroundRadiation/index.htm&quot; rel=&quot;nofollow&quot;&gt;background radiation&lt;/a&gt; present, for example due to ionizing radiation from the sun and other stars. Also certain materials like granite may emit relatively large amounts of radiation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ionizing radiation may cause mutations in the DNA (&lt;a href=&quot;http://www.pnas.org/content/82/24/8602.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Gevertz et al, PNAS 1985&lt;/a&gt;). Mutations, in turn, may lead to altered phenotypes. Altered phenotypes and survival of the fittest are key to evolution and formation of new species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the (relative) contribution of background radiation on the formation of new species?&lt;/strong&gt;. In other words, is background radiation a critical component in evolution and would the course of evolution have changed substantially when there would be no such background radiation?   &lt;/p&gt;&#xA;" OwnerUserId="14979" LastEditorUserId="9943" LastEditDate="2015-03-18T22:45:38.290" LastActivityDate="2021-03-09T10:18:23.463" Title="What is the relationship between radiation and evolution?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;molecular-evolution&gt;&lt;radiation&gt;" AnswerCount="2" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30536" PostTypeId="1" AcceptedAnswerId="30537" CreationDate="2015-03-18T12:13:48.700" Score="2" ViewCount="176" Body="&lt;p&gt;I have a data set with expression levels of a list of genes, measured in replicate at two different time points between two groups; a control group and a disease group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to identify the changes in expression between the two groups, however I'm having some trouble on formulating how best to do this. For example, if I have $[C_0]$ and $[C_1]$ as the control group measured at $t=0$ and $t=1$ respectively, and $[D_0]$ and $[D_1]$ as the disease group, I had tried to do:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{([D_1] - [D_0]) - ([C_1] - [C_0])}{[C_1] - [C_0]}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I feel like a fold change would be appropriate, however it doesn't seem to make any sense logically for the genes where $[C_0] = [C_1]$ or $[D_0] = [D_1]$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could anyone suggest an appropriate ratio or measurement? This is straightforward enough when it's simply comparing between C and D, (e.g. you just find $\frac{D}{C}$), however I'm not sure how to treat the different time points.&lt;/p&gt;&#xA;" OwnerUserId="4622" LastEditorUserId="1590" LastEditDate="2015-03-19T17:11:59.147" LastActivityDate="2015-03-19T17:11:59.147" Title="Comparing gene expression levels between control and disease at different time points" Tags="&lt;gene-expression&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30537" PostTypeId="2" ParentId="30536" CreationDate="2015-03-18T12:52:11.677" Score="2" Body="&lt;p&gt;The gene expression profile may change at different time points between the two groups; you should decide what you actually want to measure. If you want to see if the diseased group is different from the control then you should compare them at every time point. For most situations you would need to compare just their steady state behaviour.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Imagine a diseased individual who shows some physiological differences at certain developmental stages compared to the control but in the end turns out to be perfectly normal. So what matters in most cases is the steady state and not the transients.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However if you are interested in the &lt;strong&gt;change in expression&lt;/strong&gt; then you should compare &lt;strong&gt;([D&lt;sub&gt;1&lt;/sub&gt;] - [D&lt;sub&gt;0&lt;/sub&gt;])&lt;/strong&gt; with &lt;strong&gt;([C&lt;sub&gt;1&lt;/sub&gt;] - [C&lt;sub&gt;0&lt;/sub&gt;])&lt;/strong&gt;. This will tell you if the dynamics of the diseased and the control samples are similar or not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are issues with fold changes. Though they are decent measures, you cannot really apply a t-test with fold changes (normalizing to 1 is a different thing).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can do another t-test between &lt;strong&gt;[C&lt;sub&gt;1&lt;/sub&gt;]&lt;/strong&gt; and &lt;strong&gt;[C&lt;sub&gt;0&lt;/sub&gt;]&lt;/strong&gt; (similarly for &lt;strong&gt;D&lt;/strong&gt;). This would tell you if the diseased or control population changes its expression at time &lt;strong&gt;t=1&lt;/strong&gt; or not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AFAIK you cannot compare the dynamics and the values simulatenously. What you should test depends on what you are interested in.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-03-18T12:52:11.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30538" PostTypeId="2" ParentId="14040" CreationDate="2015-03-18T13:29:33.323" Score="9" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Color vision is mediated by &lt;em&gt;spike rate modulation&lt;/em&gt; (frequency modulation if you like), as well as ganglion-cell specific stimulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Ganglion cells exist that transmit opponent colors. The &lt;strong&gt;&lt;em&gt;&lt;a href=&quot;http://fourier.eng.hmc.edu/e180/lectures/color2/node1.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;color opponency&lt;/a&gt; model&lt;/em&gt;&lt;/strong&gt; predicts that we cannot perceive a greenish-red or yellowish blue, which is quite right. We can, however, see mixtures of the two channels, such as red and yellow (orange), and red and blue (purple). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then opponent model predicts the existence of ganglion cells that are sensitive to red/green opponency and blue/yellow opponency (in trichromats like humans):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nzp71.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed, it has been shown that these ganglion cells exist, i.e. cells that &lt;strong&gt;increase their firing&lt;/strong&gt; in response to short-wavelength-sensitive (S+) and decrease their firing to middle-wavelength-sensitive (M-) and vice versa &lt;a href=&quot;http://www.jneurosci.org/content/29/9/2706.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Yin et al., 2009)&lt;/a&gt;. Hence, it is not so that the frequency of light is represented in firing rate &lt;em&gt;per se&lt;/em&gt;, but the frequencies of light are translated in spike rates, because spike rate is the only means in which neurons can transmit graded responses. In other words, &lt;em&gt;every&lt;/em&gt; type of graded information is translated into spike rate eventually, including pressure differences, acoustic loudness etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, as ganglion cells are sensitive to opponent pairs of colors, &lt;strong&gt;they do respond to particular colors&lt;/strong&gt;. However, a &quot;purple ganglion cell&quot; does not exist, it is the combination of red and blue activations that lets us see colors due to synthetic processes in higher neural centers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;One ganglion cell can send different signals to the brain&lt;/strong&gt; as it is basically an analogue converter of the red/green and yellow/blue opponent colors.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These inputs are sent to the &lt;strong&gt;thalamus&lt;/strong&gt; (&lt;em&gt;lateral geniculate nucleus&lt;/em&gt;) and higher &lt;strong&gt;visual cortices&lt;/strong&gt;, where color-selective cells pick up the signals and integrate them for further processing. Here color mixtures are made to present the full gamut of colors as we know it:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dFsM1.jpg&quot; alt=&quot;color spectrum&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;a href=&quot;http://dot-color.com/category/color-gamut-standards/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source: Dot-Color&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.jneurosci.org/content/29/9/2706.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yin et al. &lt;em&gt;J Neurosci 2009&lt;/em&gt;;&lt;strong&gt;29&lt;/strong&gt;:2706-24&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Further reading&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;https://biology.stackexchange.com/questions/26216/advantage-of-opponent-color/27486#27486&quot;&gt;Advantage of opponent color?&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2016-02-21T22:39:45.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30540" PostTypeId="1" CreationDate="2015-03-18T15:44:55.463" Score="-2" ViewCount="1604" Body="&lt;p&gt;Not all the female cheek cells show Barr Bodies when stained with Giemsa stain? Only 30 to 40% female cells show Barr Bodies. Why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Our Experiment:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We washed mouth twice with listerine to reduce bacteria count, then scraped cheek cells with moistened ear bud then smeared that on clean glass slide. then air drying the smear we fixated it with methanol, then after air drying we applied thin layer of giemsa stain and after 15 minutes drained and washed off extra stain. the cells were stained and we could see the nucleus but nobody could see barr bodies. it was an experiment in our undergraduate lab and nobody could identify barr bodies in female cells. very few samples had barr bodies.&lt;/p&gt;&#xA;" OwnerUserId="14855" LastEditorUserId="16866" LastEditDate="2017-06-02T18:22:31.447" LastActivityDate="2021-04-13T23:43:29.677" Title="Barr body Giemsa staining" Tags="&lt;genetics&gt;&lt;chromosome&gt;&lt;staining&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30541" PostTypeId="1" AcceptedAnswerId="30544" CreationDate="2015-03-18T17:31:30.653" Score="7" ViewCount="588" Body="&lt;p&gt;I categorically accept that bacteria differ from viruses; so antibiotics DON'T help in viral infections. I also read &lt;a href=&quot;https://biology.stackexchange.com/a/930/4466&quot;&gt;this&lt;/a&gt; and &lt;a href=&quot;https://biology.stackexchange.com/a/3693/4466&quot;&gt;this&lt;/a&gt;; so no need to explain this. I've read about the negative effects (eg exacerbation of antibiotic resistance); I ask only about the positive effects here, and NOT for reasons to exploit antibiotics for infections not due bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet I myself have witnessed that &lt;a href=&quot;https://cogsci.stackexchange.com/q/9532/64790&quot;&gt;some people with viral infections feel better after wrongly taking antibiotics?&lt;/a&gt; and so asked about this first on Cognitive Sciences SE. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Initially, I suspected only some placebo effect, but &lt;a href=&quot;https://cogsci.stackexchange.com/a/9546/6479&quot;&gt;this&lt;/a&gt; enlightened me on the side benefits of antibiotic consumption for a viral infection and motivated this question, now that my original question on psychology has revealed the relevance of biology. &lt;/p&gt;&#xA;" OwnerUserId="4466" LastEditorUserId="-1" LastEditDate="2017-04-13T12:56:15.910" LastActivityDate="2015-03-18T20:04:53.617" Title="What are the positive effects of wrongful antibiotic use on a viral infection?" Tags="&lt;virus&gt;&lt;antibiotics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30542" PostTypeId="1" AcceptedAnswerId="30543" CreationDate="2015-03-18T18:18:05.290" Score="6" ViewCount="10010" Body="&lt;p&gt;Are Whales smarter than Humans? &#xA;Their brain size leads me to think so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vgcxI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14994" LastActivityDate="2019-12-08T17:45:23.160" Title="Are Whales More Intelligent Than Humans?" Tags="&lt;brain&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30543" PostTypeId="2" ParentId="30542" CreationDate="2015-03-18T18:31:34.250" Score="12" Body="&lt;p&gt;The &quot;wiring&quot; of the brain is more important than the actual size. If only size would matter that basically humans would be rather unintelligent beings ( many many animals have larger head and brain than us). Intelligence is more related to the complexity of the brain (number and size of different brain components) and the number of connections between neurons. We humans are intelligent because we have high complexity compared to our brain size, our brain has more grooves therefore higher surface than a whale brain. So even though whales are quite smart they're not as smart as us.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: After getting a few comments I felt I need to clarify my answer, so here it comes: as pointed out by user137 humans have much higher brain-to-body size ration than whales and this is very important. What I was trying to explain (yet failed for the first time it seems), that mere physical size / volume is not that important. The level of development and complexity is that matters the most. Many parts of the human brain is found in lower order animals as shown in the image below: &lt;img src=&quot;https://i.stack.imgur.com/sPhTI.png&quot; alt=&quot;brain areas&quot;&gt; (taken from &lt;a href=&quot;http://en.wikipedia.org/wiki/Brain&quot;&gt;http://en.wikipedia.org/wiki/Brain&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The surface to volume ratio matters because the higher ratio implies a more complex brain structure. So while whales have a higher surface in absolute value (approx 2-3 times) yet their brain is larger by approx 5-6 times ( lots of comparison data &lt;a href=&quot;https://faculty.washington.edu/chudler/facts.html&quot;&gt;here&lt;/a&gt;), thus we have higher surface/volume ratio (i left the ratio part out on my original answer). In the accepted answer on the question linked by Bez it is said that more grey matter in frontal lobe correlates with IQ. Now since grey matter is made of neuron bodies and (fewer)axons, this is quite straightfoward --&gt; more neurons = more connections = higher complexity. But all that comparison was made between humans. So brain size differences between different individuals of the same species may contribute to individual qualities. Comparing mere physical brain sizes of different species is not straightforward because of different brain development levels and brain structure.  &lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-03-19T00:24:08.480" LastActivityDate="2015-03-19T00:24:08.480" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30544" PostTypeId="2" ParentId="30541" CreationDate="2015-03-18T20:04:53.617" Score="7" Body="&lt;p&gt;There are indeed antibiotics which have immunomodulatory side-effects, these are mostly from the class of &lt;a href=&quot;http://en.wikipedia.org/wiki/Macrolide&quot;&gt;macrolide antibiotics&lt;/a&gt; (erythromycin, clarithromycin, roxithromycin, azithromycin) and to some degree from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Tetracycline&quot;&gt;tetracyclines&lt;/a&gt;. Beta-lactam antibiotics (as Penicillin or Ampicillin) have not been shown to be immunomodulatory, but they are among the most commonly used. See reference 1 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biggest effect has been shown on pulmonary diseases such as cystic fibrosis or diffuse panbrochiolitis (see reference 2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although the exact mechanism of action is not known, Macrolides are know to downregulate the inflammatory cascade and that the reduce the strong cytokine expression of some viral infections. However, these regulatory effects are relatively weak if you compare them to the anti-inflammatory properties of corticosteroids. So the question here is if the advantages are really sufficient compared to the problems, which an unnecessary use of antibiotics may cause. See reference 3 and the references in the paper for more details here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antibiotics may be useful to fight bacterial secondary or superinfections which accompany a virus infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.medicinabiomolecular.com.br/biblioteca/pdfs/Biomolecular/mb-0467.pdf&quot;&gt;Immunomodulatory Properties of Antibiotics&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://jac.oxfordjournals.org/content/54/1/21.full.pdf&quot;&gt;Macrolide activities beyond their antimicrobial effects: macrolides&#xA;in diffuse panbronchiolitis and cystic fibrosis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.hindawi.com/journals/mi/2012/649570/&quot;&gt;Macrolide Therapy in Respiratory Viral Infections&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-03-18T20:04:53.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30547" PostTypeId="2" ParentId="28464" CreationDate="2015-03-18T22:46:18.993" Score="1" Body="&lt;p&gt;Examining the literature it'd seem that the ROR pathways incl. ROR1 and ROR2 are critical for developing tissues in the majority of cases. We also see relevance in the expression of ROR1/2, more specifically ROR2, in cases where taxic cell types are required to migrate, branch, etc. Most of the literature determines much of this occurs through a noncanonical Wnt signaling pathway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/109/11/4044.abstract&quot; rel=&quot;nofollow&quot;&gt;Wnt5a–Ror–Dishevelled signaling constitutes a core developmental pathway that controls tissue morphogenesis&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jbc.org/content/289/30/20664.abstract&quot; rel=&quot;nofollow&quot;&gt;Ror2 Receptor Mediates Wnt11 Ligand Signaling and Affects Convergence and Extension Movements in Zebrafish&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jcb.rupress.org/content/208/3/351.abstract&quot; rel=&quot;nofollow&quot;&gt;Ror2 regulates branching, differentiation, and actin-cytoskeletal dynamics within the mammary epithelium&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notwithstanding the abnormalities we see in neonates with knocked down ROR, is it wrong to assume we'd see developmental defects of branching tissues in developing (or juvenile) organisms such as lung, mammary, neural, glandular tissue, etc.? Some data in that respect would be interesting, but it's also illuminating given the presence of ROR in cancer metastasis and EMT events.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-03-18T22:46:18.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30548" PostTypeId="1" CreationDate="2015-03-19T01:54:43.913" Score="17" ViewCount="619" Body="&lt;p&gt;this is my first time posting here. I was in my Zoology lab doing a dissection on a Crayfish when I noticed these hairlike structures within the gills. They were very &quot;snappy&quot; and fine, and would break off if I pulled hard enough. I put some on a wet mount under a dissecting microscope, but my Lab prof and the parasitologist could not identify it. We put it under a compound microscope and thought maybe it is an animal but we couldn't definitively say it had no cell well. My profs thought it was an animal, with setae, but I would really like to know what it is &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit here are the images:&lt;img src=&quot;https://i.stack.imgur.com/Ve6qv.jpg&quot; alt=&quot;microscope image&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/2OmVe.jpg&quot; alt=&quot;microscope image 2&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14997" LastEditorUserId="14735" LastEditDate="2015-03-19T02:07:25.117" LastActivityDate="2020-02-13T05:46:34.433" Title="Help identifying what this is in Crayfish gills?" Tags="&lt;zoology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30549" PostTypeId="1" CreationDate="2015-03-19T02:00:10.073" Score="4" ViewCount="1974" Body="&lt;p&gt;I am looking for the loudness limits, expressed in decibels, for the human ear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Google and Wikipedia is only giving me the frequency limit that the &lt;a href=&quot;http://en.wikipedia.org/wiki/Ear&quot; rel=&quot;nofollow noreferrer&quot;&gt;human ear&lt;/a&gt; can receive, but I cannot find mention about the decibel limits. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Related question on acoustic frequency: &lt;a href=&quot;https://biology.stackexchange.com/questions/26067/why-do-humans-hear-better-between-2khz-and-5khz&quot;&gt;why-do-humans-hear-better-between-2khz-and-5khz&lt;/a&gt;  &lt;/p&gt;&#xA;" OwnerUserId="14998" LastEditorUserId="49570" LastEditDate="2019-02-08T10:57:19.473" LastActivityDate="2019-02-08T10:57:19.473" Title="What are the lower and upper hearing limits of the human ear?" Tags="&lt;hearing&gt;&lt;human-ear&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="30551" PostTypeId="1" CreationDate="2015-03-19T02:12:28.960" Score="7" ViewCount="658" Body="&lt;p&gt;Deer ran away from tiger or cheetah, but not from giraffe or zebra.&#xA;where did deer learn this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How animals know which is carnivorous and herbivorous?&lt;/p&gt;&#xA;" OwnerUserId="14998" LastActivityDate="2015-05-05T23:39:08.320" Title="How animals know which is carnivorous and herbivorous?" Tags="&lt;zoology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30552" PostTypeId="2" ParentId="30549" CreationDate="2015-03-19T02:25:06.947" Score="3" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Hearing threshold is 0 dB SPL at 1 kHz, and pain threshold is around 125 dB SPL at that frequency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Loudness thresholds depend on acoustic frequency (pitch), as depicted in the following figure:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4wbqm.gif&quot; alt=&quot;Contours&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Loudness contours in human. Source: &lt;a href=&quot;http://adg.stanford.edu/aa241/noise/noise.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Stanford Uni&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When expressed in dB sound pressure level (dB SPL) the threshold of pain is approximately 125 dB SPL. The lower bound peaks at a hearing threshold of about -5 dB SPL at 4 kHz (maximum sensitivity). Outside that frequency, hearing sensitivity declines (and threshold hence increases).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that dB SPL references to a sound pressure of 20 µPa = 2 × 10&lt;sup&gt;−5&lt;/sup&gt; Pa. This sound pressure corresponds to the hearing threshold at 1 kHz and is hence defined as 0 dB SPL. (&lt;a href=&quot;http://adg.stanford.edu/aa241/noise/noise.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Stanford Uni&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&#xA;&lt;strong&gt;Further reading&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;https://biology.stackexchange.com/questions/26067/why-do-humans-hear-better-between-2khz-and-5khz&quot;&gt;Why do humans hear better between 2kHz and 5 kHz&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-03-19T06:03:04.430" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30553" PostTypeId="2" ParentId="30551" CreationDate="2015-03-19T02:26:48.490" Score="1" Body="&lt;p&gt;They probably don't know and probably don't need to. They tend to run away from potential danger and predators in the same evolution environment because those who don't run away will have fewer offsprings that exhibit similar behaviors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If an animal suddenly sees a predator that his ancestor has never seen before, then it may not run away from it, to its own detriment. Dodo Bird thought humans were harmless.&lt;/p&gt;&#xA;" OwnerUserId="9731" LastActivityDate="2015-03-19T02:26:48.490" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30554" PostTypeId="1" CreationDate="2015-03-19T02:30:50.967" Score="3" ViewCount="101" Body="&lt;p&gt;I have seen a Discovery Channel video of a bird throwing stones in a pot to raise the water level so it is able to reach and drink it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A similar experiment &lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822%2809%2901455-9&quot; rel=&quot;nofollow&quot;&gt;in this paper from &lt;em&gt;Current Biology&lt;/em&gt;&lt;/a&gt; shows the same phenomenon under controlled conditions, and is documented in &lt;a href=&quot;https://www.youtube.com/watch?v=B7cw_9AT5hg&quot; rel=&quot;nofollow&quot;&gt;this video&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This clearly illustrates how intelligent these animals are may well be more intelligent than many mammals. For example, the regular domestic dog will definitely not push stones in a bucket of water to quench his thirst. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How did crows, and perhaps birds in general, became so intelligent, and even more intelligent than many mammalian species?&lt;/p&gt;&#xA;" OwnerUserId="14998" LastEditorUserId="13072" LastEditDate="2015-03-20T09:45:41.193" LastActivityDate="2015-03-20T21:14:44.630" Title="How did birds become so intelligent?" Tags="&lt;zoology&gt;&lt;learning&gt;" AnswerCount="0" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="30555" PostTypeId="2" ParentId="1977" CreationDate="2015-03-19T04:40:42.157" Score="6" Body="&lt;p&gt;This question appears to have a revived interest? I would like to clarify this Q&amp;amp;A you don't mind.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;HF(aq), like other hydrogen halides, &lt;b&gt;does&lt;/b&gt; completely give up its proton to $\ce{H2O}$ but since F is the most eletronegative element on earth, it will pair up with hydronium ion in the aqueous environment, making the proton &quot;less available&quot;, at least to a pH electrode. This is one of strongest hydrogen bond known.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;$\ce{HF(aq) -&amp;gt; F^-.... H3O+}$&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thus HF(aq) has a depressed pKa in water whilst its &quot;real acidity&quot; can be much higher.&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;&lt;p&gt;Homo-association of HF only occurs in very high concentration (close to unity). You can estimate the extent of homo-association of anhydrous HF by measuring its conductivity. Anhydrous HF has lower conductivity (&amp;lt;1.6 $\mu$S/cm) than deionized water (~5 $\mu$S/cm) &lt;a href=&quot;http://www.solvaychemicals.com/Chemicals%20Literature%20Documents/Fluor/HF_Inorg_Fluoride/HF_Physical_Properties.pdf&quot;&gt;[1]&lt;/a&gt; so it's probably not terribly important in driving disassociation of HF, esp in water.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;HF causes deep burn, often with a delayed onset because while the skin prevents charged raw hydronium ion from penetrating too deeply, HF or the hydronium-flouride ion pair can be absorbed and releases the hydronium ion (by exchanging with water abundant in tissue) at deeper level. (Thus it's often reported as more painful than other acid burn)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Although fluoride in ppm level is anti-microbial and prevents cavity (by reacting with calcium mineral in tooth), high concentration of fluoride is toxic because, as cited in previous answer, fluoride interferes with calcium metabolism in forming insoluble calcium fluoride. It causes skeletal fluorosis and suppresses some essential metabolic enzymes.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;HF is corrosive because of its proton; it's corrosive to bones because of its fluoride. HF corrodes glass and HCl doesn't because silicon tetrafluoride is a more stable complex than the highly reactive silicon tetrachloride. It has little to do with whether the acid is weak or strong. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9731" LastActivityDate="2015-03-19T04:40:42.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30557" PostTypeId="1" CreationDate="2015-03-19T06:11:41.497" Score="3" ViewCount="15726" Body="&lt;p&gt;Autosomal trisomy syndromes are usually lethal but sex chromosome number related abnormalities do not lead to that much fatality. why?&lt;/p&gt;&#xA;" OwnerUserId="14855" LastEditorUserId="6307" LastEditDate="2018-06-25T19:27:44.343" LastActivityDate="2018-06-26T05:29:32.047" Title="Why does autosomal trisomy have more adverse effects than sex choromosome monosomy or trisomy?" Tags="&lt;genetics&gt;&lt;chromosome&gt;" AnswerCount="4" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="30558" PostTypeId="2" ParentId="30240" CreationDate="2015-03-19T06:20:11.510" Score="2" Body="&lt;p&gt;I will try answer your question directly.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;How do we know if we fold it right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A. If you're interested in only the end product pf folding -- the 3D structure, then this is the subset of the folding problem called the structure prediction (from sequence alone). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;a. We can verify the structure experimentally by determining the 3D structures by NMR or crystallography. In fact, the &lt;a href=&quot;http://en.wikipedia.org/wiki/CASP&quot; rel=&quot;nofollow&quot;&gt;CASP&lt;/a&gt; competition withholds newly solved structures and see which algorithm comes out the closest to the experimental structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b. Based on &lt;a href=&quot;http://en.wikipedia.org/wiki/Anfinsen%27s_dogma&quot; rel=&quot;nofollow&quot;&gt;Anfinsen's hypothesi&lt;/a&gt;s, we can calculate the free energy of folding, and the structure that has the lowest energy among the assembles is probably (but not necessarily) the folded state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B. If you're also interested in how exactly the protein folds, including its folding rate, plausible intermediates etc.:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a. You can experimentally determine the folding rate although the computed folding rate is often off by several order of magnitude.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b. Some interactions, esp non-native interactions (aka. interactions between amino acids that are only observed during folding but not in the final folded structure) can be verified by carefully designed NMR experiment.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;1b. Yes it is possible. Adjusting the force constants and force field in molecular dynamics (MD) (the core engine of Folding@Home) so that the calculations converge to consistent and sensible results is not trivial. &lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;If you mean the method of calculation, then yes, MD has a wide range of application outside the field of protein folding. Besides the improvement in MD algorithm and necessary approximation, it also facilitates some advances on calculation on more specialized hardwares e.g. GPU and programmable array.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;2b. If you mean the end of product of computation model, then probably no, but &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17934447&quot; rel=&quot;nofollow&quot;&gt;one example came close&lt;/a&gt;. A model determined purely computationally (aka. ab initio), although still not as useful as an experimental structure, was close enough to facilitate the experimental determination of that structure (by a method called molecular replacement in X-ray crystallography)&lt;/p&gt;&#xA;" OwnerUserId="9731" LastActivityDate="2015-03-19T06:20:11.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30559" PostTypeId="1" CreationDate="2015-03-19T07:45:24.753" Score="3" ViewCount="4852" Body="&lt;p&gt;I've learnt in chemistry that gaining electrons means reduction, while losing electrons means oxidation. But why is it in Biology textbooks I sometimes come across the term gaining hydrogen??&lt;/p&gt;&#xA;" OwnerUserId="15002" LastActivityDate="2015-03-19T18:58:34.007" Title="Why does gaining a hydrogen in biology considered reducing a molecule?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ClosedDate="2015-03-20T16:24:59.610" ContentLicense="CC BY-SA 3.0" />
  <row Id="30560" PostTypeId="1" AcceptedAnswerId="30562" CreationDate="2015-03-19T07:59:44.893" Score="32" ViewCount="4852" Body="&lt;p&gt;As long as we only look at humans the differences are clear: males have chromosomes XY, produce sperm and don't get pregnant. Females have chromosomes XX, produce egg cells and bear babies. But when you consider other species, things are more complicated: in birds, it's females who carry the Y chromosomes. In pipefish and sea horses, it's the males who get pregnant. So maybe the only reliable criterion to tell if an animal is a male or a female is looking at its reproductive cells, and decide if they look like spermatozoa or egg cells. But then there are male and female plants, where none of the methods above applies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how do you tell, in general, who's male and who's female in a species? Or is the distinction arbitrary?&lt;/p&gt;&#xA;" OwnerUserId="15004" LastEditorUserId="3624" LastEditDate="2016-01-21T15:50:02.803" LastActivityDate="2019-08-13T09:03:15.860" Title="What's the difference between male and female?" Tags="&lt;reproduction&gt;&lt;nomenclature&gt;&lt;sex&gt;&lt;sexual-dimorphism&gt;&lt;sexual-reproduction&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30561" PostTypeId="2" ParentId="30176" CreationDate="2015-03-19T08:40:31.073" Score="5" Body="&lt;p&gt;Scorpions are immune to their own venom (&lt;a href=&quot;http://animals.sandiegozoo.org/animals/scorpion&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;) as has been said in some studies as well (&lt;a href=&quot;http://jeb.biologists.org/content/201/18/2625.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;) But some other studies and eye witness accounts have referred to the contrary.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;in an experiment a scorpion, Bulteus australis, was killed by an&#xA;  injection of the same venom as its own (&lt;a href=&quot;http://www.mocavo.com/Nature-a-Weekly-Illustrated-Journal-of-Science-July-Dec-1922-Volume-110/696683/328&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, it should be safe to say that there is a very low chance for a scorpion to be affected by its own venom. It is said that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mutations in the scorpion’s own membrane protein genes make the&#xA;  arachnid immune to its own venom (&lt;a href=&quot;https://www.sciencenews.org/article/scorpion-genome-decoded&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A scorpion could die quickly if venom is injected into its brain (nerve ganglion). Larger species inject a higher amount of venom to overcome the smaller ones and should have specific neurotoxins if smaller scorpions are their prey to disable them (&lt;a href=&quot;https://books.google.co.in/books?id=vQFEeohchVQC&amp;amp;pg=PA35&amp;amp;lpg=PA35&amp;amp;dq=scorpion%20immune%20to%20its%20own%20venom&amp;amp;source=bl&amp;amp;ots=pMdK7YvbMj&amp;amp;sig=fngLmrllpfxg56LHkbrVRA5YaT0&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=e3AKVaWQCpDluQT234DgAg&amp;amp;ved=0CC8Q6AEwAw#v=onepage&amp;amp;q=scorpion%20immune%20to%20its%20own%20venom&amp;amp;f=false&quot; rel=&quot;noreferrer&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="5762" LastActivityDate="2015-03-19T08:40:31.073" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30562" PostTypeId="2" ParentId="30560" CreationDate="2015-03-19T09:34:51.083" Score="41" Body="&lt;p&gt;Sexes (male and female) are generally defined in terms of &lt;a href=&quot;http://en.wikipedia.org/wiki/Anisogamy&quot; rel=&quot;noreferrer&quot;&gt;&lt;strong&gt;&lt;em&gt;Anisogamy&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt;, which means that there are size differences between the &lt;a href=&quot;http://en.wikipedia.org/wiki/Gamete&quot; rel=&quot;noreferrer&quot;&gt;gametes&lt;/a&gt; (i.e. the reproductive cells that fuse at fertilization). The sex with smaller gametes is defined as male and the sex with larger gametes is defined as female, and individuals that can produce both types of gametes are called hermaphrodites. This is the case in both animals and plants (plants have pollen vs. ovules and microsporangia vs. megasporangia), and the definition of sexes is therefore not dependent on chromosomal makeup as such or which sex that carries the young. Actual sex determiniation in a particular species is often based on chromosomal inheritance though, but other systems also exists (e.g. environmental cues or sequential hermaphroditism). &lt;em&gt;Anisogamy&lt;/em&gt; also comes in several different types, where animals generally have &lt;a href=&quot;http://en.wikipedia.org/wiki/Oogamy&quot; rel=&quot;noreferrer&quot;&gt;Oogamy&lt;/a&gt;, where males have small mobile spermatozoa and females large stationary egg cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More generally, &lt;em&gt;Anisogamy&lt;/em&gt; is a special case of &lt;a href=&quot;http://en.wikipedia.org/wiki/Mating_type&quot; rel=&quot;noreferrer&quot;&gt;&lt;strong&gt;&lt;em&gt;mating types&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt; in sexually reproducing organisms, where fertilization (on syngamy) generally can only occur between gametes of different mating types. In for instance fungi, gametes of different mating types are of the same size (&lt;em&gt;isogamous&lt;/em&gt;) and they are therefore only labelled as mating types (e.g +/-) and not different sexes. Functionally, if we are simplifying the issue, male gametes can be viewed only as carriers of genetic information, while female gametes also contain the nutrients necessary for the early development of a newly formed embryo.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2019-08-13T09:03:15.860" LastActivityDate="2019-08-13T09:03:15.860" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="30563" PostTypeId="2" ParentId="30559" CreationDate="2015-03-19T10:13:12.727" Score="4" Body="&lt;p&gt;Hydrogen can accept electrons or donate them, so it can get a bit confusing. For instance, hydrogen donates electrons &lt;strong&gt;from a reducing agent&lt;/strong&gt;. For example, in biology, consider cellular respiration. A co-factor will carry electrons often by reducing an atom with a nitrogen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide_phosphate&quot; rel=&quot;nofollow noreferrer&quot;&gt;Consider NADP+ to NADPH.&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YMv4A.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nitrogen atom on the Pyridine group has an oxidation state of +1. When it picks up a hydrogen, to become NADPH, the oxidation state will go to 0 by gaining electrons brought by the hydrogen. Although the hydrogen doesn't bond to the nitrogen directly, it breaks the double bond on the para carbon (The carbon on which the new hydrogen is attached) at the top of the ring, and thus distributes the electrons to the nitrogen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT -&#xA;Hydrogen comes from some reducing agent, not a free hydride I'm sure.&lt;/p&gt;&#xA;" OwnerUserId="3887" LastEditorUserId="3887" LastEditDate="2015-03-19T17:00:42.957" LastActivityDate="2015-03-19T17:00:42.957" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30564" PostTypeId="2" ParentId="30519" CreationDate="2015-03-19T10:15:40.250" Score="4" Body="&lt;p&gt;I think the question is not whether the blood flux is constant &lt;em&gt;in time&lt;/em&gt;, but rather &lt;em&gt;in space&lt;/em&gt;: if 5L/min is the flux through aorta (in given physiological conditions), then at the same moment 5L/min will cross the capillaries. This is volume conservation, for a closed system filled with an incompressible fluid, see this sketch:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7Lq23.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If 5L are pushed through the main pipe, the same volume needs to be pushed through the system downstream of it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then comes the fact that the system is not perfeclty closed, and some water (and solutes) will &quot;leak&quot; in and out, as @inf3rno points, so this is only approximatively true. Another limitation is that vessel walls are actually elastic, so a change in vessel radius does occur during blood flow. However I believe it is a fair approximation.&lt;/p&gt;&#xA;" OwnerUserId="6224" LastEditorUserId="6224" LastEditDate="2015-03-19T10:23:23.143" LastActivityDate="2015-03-19T10:23:23.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30565" PostTypeId="2" ParentId="7506" CreationDate="2015-03-19T11:32:09.523" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Perceived tinnitus pitch tends to resemble the frequency content of the loud sound that induced the tinnitus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Solid, laboratory-controlled studies to the perceived pitch of temporary, noise-induced tinnitus (&quot;ringing in the ears&quot;) are ethically questionable, because researchers have to deliberately expose study subjects to potentially damaging loud sounds. Therefore, data on temporary noise-induced tinnitus are scarce and confined to a small handful of studies done in the 1960's (&lt;a href=&quot;http://www.audiologynow.com/sites/default/files/journal/JAAA_11_03_03.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Henry &amp;amp; Meikle, 2000&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In one of these studies (&lt;a href=&quot;http://journals.lww.com/joem/Citation/1969/12000/Study_of_Tinnitus_Induced_Temporarily_by_Noise_.44.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;Atherly et al., 1968&lt;/a&gt;) the authors exposed the study subjects to loud acoustic stimuli of various pure tones. The subjects reported to experience tinnitus pitched within a certain frequency band around the tonal stimuli received. The stimulus frequency and perceived pitch approached a 1:1 relationship, such that the tinnitus pitch was e.g. 4 kHz when the noise frequency was 4 kHz. Between-subject variability was, however, considerable. For example, at a stimulus of 6 kHz, the range of perceived pitch was 4-9 kHz.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other study I found based on the review by Henry &amp;amp; Meikle (&lt;a href=&quot;http://www.audiologynow.com/sites/default/files/journal/JAAA_11_03_03.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;2000&lt;/a&gt;) showed that the perceived &lt;strong&gt;tinnitus pitch increased&lt;/strong&gt; when the frequency of the loud &lt;strong&gt;tonal stimulus or frequency content of broadband noise increased&lt;/strong&gt; &lt;a href=&quot;http://scitation.aip.org/content/asa/journal/jasa/42/2/10.1121/1.1910600&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Loeb &amp;amp; Smith, 1967)&lt;/a&gt;. Basically this confirms the data from Atherly et al. (&lt;a href=&quot;http://journals.lww.com/joem/Citation/1969/12000/Study_of_Tinnitus_Induced_Temporarily_by_Noise_.44.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;1968&lt;/a&gt;). However, the perceived pitch did not coincide with the stimulus frequencies, and there was considerable variability between subjects. For example, some subjects reported multiple frequencies in their tinnitus, some reported a hissing tinnitus, while others did not develop any tinnitus at all &lt;a href=&quot;http://scitation.aip.org/content/asa/journal/jasa/42/2/10.1121/1.1910600&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Loeb &amp;amp; Smith, 1967)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In all, &lt;strong&gt;your suggested perceived tinnitus pitch of 17 kHz is unexpected&lt;/strong&gt;, given that noise-induced hearing loss (by loud music exposure etc.) typically results in a &lt;a href=&quot;http://www.aafp.org/afp/2000/0501/p2749.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;4-kHz notch&lt;/a&gt; in the audiogram where hearing loss is greatest. Hence, tinnitus would be expected to occur around this frequency as well. But again, variability is very high and it may well be possible it is higher pitched in your case. Also note that 17 kHz is very high and near the upper audible frequency limit for humans (e.g., the sound an old CRT screen makes, i.e., hardly perceivable for many adults).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most research on tinnitus has been done regarding patients with chronic tinnitus complaints that suffer from sensorineural hearing loss (i.e., damage to the hair cells in the cochlea). Typically, the perceived tinnitus pitch in this group is associated with their hearing loss. In other words, the pitch of the tinnitus generally matches a frequency range within the region of frequency loss &lt;a href=&quot;https://biology.stackexchange.com/questions/27898/can-humans-perceive-sounds-above-20-kHz?&quot;&gt;(Eggermont &amp;amp; Roberts, 2004)&lt;/a&gt;.     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://journals.lww.com/joem/Citation/1969/12000/Study_of_Tinnitus_Induced_Temporarily_by_Noise_.44.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;Atherly et al., &lt;em&gt;JASA&lt;/em&gt; 1968;&lt;strong&gt;44&lt;/strong&gt;:1503-6&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.psychology.mcmaster.ca/hnplab/publications/TINS2004.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eggermont &amp;amp; Roberts, &lt;em&gt;Trends Neurosci 2004&lt;/em&gt;;&lt;strong&gt;27&lt;/strong&gt;:676-82&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.audiologynow.com/sites/default/files/journal/JAAA_11_03_03.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Henry &amp;amp; Meikle, &lt;em&gt;J Am Acad Audiol 2000&lt;/em&gt;;&lt;strong&gt;11&lt;/strong&gt;:138-55&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://scitation.aip.org/content/asa/journal/jasa/42/2/10.1121/1.1910600&quot; rel=&quot;nofollow noreferrer&quot;&gt;Loeb &amp;amp; Smith, &lt;em&gt;JASA&lt;/em&gt; 1967;&lt;strong&gt;42&lt;/strong&gt;:453-5&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Further reading&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;https://cogsci.stackexchange.com/q/3100/55&quot;&gt;What's the Frequency of the ringing in my ear?&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;https://biology.stackexchange.com/questions/27898/can-humans-perceive-sounds-above-20-kHz?&quot;&gt;Can humans perceive sounds above 20 kHz?&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2018-06-21T07:39:44.840" LastActivityDate="2018-06-21T07:39:44.840" CommentCount="7" ContentLicense="CC BY-SA 4.0" />
  <row Id="30566" PostTypeId="1" AcceptedAnswerId="30627" CreationDate="2015-03-19T11:58:49.177" Score="3" ViewCount="76" Body="&lt;p&gt;In humans, are there phenotypic markers that prove parenthood? For example, if mother and father have &lt;code&gt;&amp;lt;trait characteristic&amp;gt;&lt;/code&gt; (let's say, specific ear lobe form), then any child will have &lt;code&gt;&amp;lt;trait characteristic&amp;gt;&lt;/code&gt;. If the child does not exhibit that characteristic, than either father or mother or both are only alleged, not actual. &lt;/p&gt;&#xA;" OwnerUserId="15005" LastActivityDate="2015-03-21T13:33:35.050" Title="Obvious phenotypic inheritance markers in humans" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30567" PostTypeId="5" CreationDate="2015-03-19T12:24:28.170" Score="0" Body="" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-19T12:24:28.170" LastActivityDate="2015-03-19T12:24:28.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30568" PostTypeId="4" CreationDate="2015-03-19T12:24:28.170" Score="0" Body="Psychophysics is the scientific study of the relationship between physical stimuli and the subjective sensations and perceptions evoked by these stimuli. The term psychophysics is used to denote both the substantive study of stimulus-response relationships and the methodologies used for this study. " OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-19T12:24:28.170" LastActivityDate="2015-03-19T12:24:28.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30569" PostTypeId="1" AcceptedAnswerId="30581" CreationDate="2015-03-19T13:10:56.860" Score="2" ViewCount="245" Body="&lt;p&gt;We all know that in this method the PTH reacts with the first amino acid (aa) from the N-terminal to the peptide and separates from it giving PTH-aa so that we can know the amino acids sequence in the peptide.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is what prevents the PTH from reacting with the second amino acid after it separates with the first amino acid in the same time and phase? Because if it does we can't distinguish between the first and second amino acid residue in the sequence. &lt;/p&gt;&#xA;" OwnerUserId="15007" LastEditorUserId="10143" LastEditDate="2015-03-19T20:29:45.270" LastActivityDate="2015-03-19T20:29:45.270" Title="Edman method to identify peptides with Phenylisothiocyanate (PTH)" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;amino-acids&gt;&lt;protein-binding&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30571" PostTypeId="1" CreationDate="2015-03-19T14:02:22.770" Score="9" ViewCount="1475" Body="&lt;p&gt;My question is on people deafened in one ear, but normal hearing in the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Time and level differences between the two ears are only part of how the human body can localize the source of the sound. So what other factors are there and are they enough to help accurately determine the location of the sound for unilaterally deaf people ?&lt;/p&gt;&#xA;" OwnerUserId="15010" OwnerDisplayName="Fofole" LastEditorUserId="9943" LastEditDate="2016-04-15T20:14:14.783" LastActivityDate="2016-04-15T20:14:14.783" Title="Are unilaterally deaf people able to determine where sound comes from?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;neurophysiology&gt;&lt;hearing&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30572" PostTypeId="2" ParentId="30560" CreationDate="2015-03-19T14:38:55.853" Score="2" Body="&lt;p&gt;In general, It's pretty much the reproductive cells with plants and animals.  The male's unique cells (sperm, pollen) fertilizes the female's unique cells (egg, ovule).  The resulting offspring develops and hatches from within the female's egg/ovule.  Now whether that egg/ovule stays put, gets ejected, hides in a flower, or transferred to the male (like your seahorses)... that's just rearranging the furniture after it's been designed.&lt;/p&gt;&#xA;" OwnerUserId="15011" LastActivityDate="2015-03-19T14:38:55.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30573" PostTypeId="1" AcceptedAnswerId="30576" CreationDate="2015-03-19T15:00:14.973" Score="1" ViewCount="253" Body="&lt;p&gt;Industrial melanism is an example of natural selection. Can it be considered as a evolution due to anthropogenic action?&lt;/p&gt;&#xA;" OwnerUserId="14933" LastActivityDate="2015-03-19T16:28:40.590" Title="Explaining natural selection in moth" Tags="&lt;natural-selection&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ClosedDate="2015-03-19T21:28:47.960" ContentLicense="CC BY-SA 3.0" />
  <row Id="30574" PostTypeId="2" ParentId="30437" CreationDate="2015-03-19T15:30:52.707" Score="1" Body="&lt;p&gt;As stated in the &lt;a href=&quot;https://biology.stackexchange.com/a/30440/3340&quot;&gt;answer by @CDB&lt;/a&gt;, these polar bodies don't last too long, and the second polar body which forms as the result of meiosis II, extrude only &lt;strong&gt;after&lt;/strong&gt; fertilisation. The secondary oocyte is arrested in metaphase II until it becomes fertilised, so meiosis II can only by completed after ovulation and fertilisation (see e.g. &lt;a href=&quot;https://embryology.med.unsw.edu.au/embryology/index.php/Oocyte_Development#Meiosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;UNSW Embryology: Meiosis&lt;/a&gt; at &lt;a href=&quot;https://embryology.med.unsw.edu.au&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://embryology.med.unsw.edu.au&lt;/a&gt;). This means that meiosis II, which actually forms the second polar body, occurs as a result of fertilisation. The secondary oocyte becomes a mature oocyte (ovum) by the expulsion of second polar body into perivitelline space. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The metaphase arrest is caused by the presence of two types of cytoplasmic activity &#xA;1. MPF - maturation promoting factor&#xA;2. CSF - Cytostatic factor that inhibits APC/C &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Only when MPF is present, stabilized by CSF, and active will the M phase persist. However, this complex is very sensitive to calcium, such that a rise in calcium tilts the equilibrium away from complex synthesis towards destruction. &#xA;  &lt;img src=&quot;https://i.stack.imgur.com/vo8ER.png&quot; alt=&quot;Johnson and Everitts Essential Reproduction chapter 9&quot;&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Capcitated spermatozoa that have undergone an acrosome reaction is capable of fusion and Calcium mediated calmodulin is required for this process. When fusion happens spermatozoon ceases to move and the nuclear with parts of mid piece and tail passes to the ooplasm. So sperm initiate Calcium release at fertilisation this helps in the completion of the 2nd meiotic division.&#xA;For further detail on these processes you could read the article &lt;a href=&quot;http://www.sciencemag.org/content/296/5576/2183.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Penetration, Adhesion, and Fusion in Mammalian Sperm-Egg Interaction&lt;/a&gt;&#xA;Increased Calcium activated Calpain (calcium dependent cysteine protease which causes CSF to disappear thereby activating APC/C which in turn causes dissociation of MPF. This results in completion of 2nd meiotic division.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For further details I recommend you to read Johnson and Everitts Essential Reproduction (6th edition), cell cycle chapter in The cell by Bruce Albert (5th edition)  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/S0HCW.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;During oocyte–sperm fusion and second polar body expulsion, the cytoplasmic contents of the sperm cell membrane (now fused with the oocyte membrane) pass into the oocyte cytoplasm. Between 4 and 7h after fusion, the two sets of haploid chromosomes each become surrounded by distinct mem- branes and are now known as pronuclei (see Fig. d). The male is usually the larger of the two. Both pronuclei contain several nucleoli. During the next few hours, each pronucleus gradually moves from its subcortical position to a more central and adjacent cytoplasmic position. During this period, the haploid chromosomes synthesize DNA in preparation for the first mitotic division, which occursabout 18–24h after gamete fusion. The pronuclear membranes around the reduplicated sets of parental chromo- somes break down (see Fig. e), the mitotic metaphase spindle forms and the chromosomes assume their positions at its equator. The final phase of fertilization has been achieved: syngamy (or coming together of the gametic chromosomes) has occurred. Immediately the first mitotic anaphase and telophase are completed, the cleavage furrow forms, and the one-cell zygote becomes a two-cell conceptus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="14932" LastEditorUserId="3340" LastEditDate="2019-05-08T12:42:26.907" LastActivityDate="2019-05-08T12:42:26.907" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="30575" PostTypeId="2" ParentId="30571" CreationDate="2015-03-19T15:39:13.077" Score="6" Body="&lt;p&gt;From what I could gather, there is a decent amount of variability in the ability to detect which direction sound is coming from in unilateral hearing impaired people. It would appear that some people have severely impaired localization skills, akin to someone with an earplug in one ear, but others can use their monaural hearing cues to better locate sound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Monaural cues seem to be based on the structure of the outer ear as well as how the sound bounces off of the head and shoulders.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0378595594900531&quot;&gt;http://www.sciencedirect.com/science/article/pii/0378595594900531&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Sound_localization#Monaural_cues&quot;&gt;http://en.wikipedia.org/wiki/Sound_localization#Monaural_cues&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-03-19T15:39:13.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30576" PostTypeId="2" ParentId="30573" CreationDate="2015-03-19T16:28:40.590" Score="2" Body="&lt;p&gt;Evolution is a change in &lt;a href=&quot;http://en.wikipedia.org/wiki/Allele&quot; rel=&quot;nofollow noreferrer&quot;&gt;allele&lt;/a&gt; frequency through time. Alleles underlying moth melanism are changing through time in response to environment change, so indeed moths are evolving.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The environmental change is induced by human activities indeed. But the question of what is the cause of the environmental change causing the selection pressure is totally irrelevant to the question of whether there is such selection pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Artificial selection is in essence the exact same thing than natural selection except that there is a goal (increasing milk production or making smaller dogs for example) that is decided by humans. In the moth example, the environmental changed is caused by human activities, but it has never been a goal for human to put selection pressure on moths to force them to change color. As a consequence, change in color melanism is an evolutionary process that is induced by natural selection, selection toward a new environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution is not just the same thing as natural selection. The reason is that other mechanism than natural selection yield to change in allele frequency. One of them is genetic drift. You can have a look to &lt;a href=&quot;https://biology.stackexchange.com/questions/14543/why-is-the-strength-of-genetic-drift-inversely-proportional-to-the-population-si&quot;&gt;this post&lt;/a&gt; to have a better understanding of what genetic drift is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-03-19T16:28:40.590" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30579" PostTypeId="1" AcceptedAnswerId="30580" CreationDate="2015-03-19T19:40:59.270" Score="19" ViewCount="4941" Body="&lt;p&gt;My eyes tear up when cycling at 15 mph, which is nothing compared to bird airspeeds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do birds continuously produce lots of tears and blink a lot, or do the eyes self-moisturize from the inside without need of blinking, or are their eye surfaces just dry most of the time and they don't mind?&lt;/p&gt;&#xA;" OwnerUserId="10055" LastEditorUserId="14709" LastEditDate="2015-03-19T22:03:46.627" LastActivityDate="2015-03-24T20:52:20.143" Title="How do birds deal with their eyes drying out at high speeds?" Tags="&lt;zoology&gt;&lt;eyes&gt;&lt;ornithology&gt;&lt;biophysics&gt;&lt;flight&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30580" PostTypeId="2" ParentId="30579" CreationDate="2015-03-19T19:57:13.610" Score="21" Body="&lt;p&gt;Birds have a body part known as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nictitating_membrane&quot; rel=&quot;noreferrer&quot;&gt;nicitating membrane&lt;/a&gt; otherwise known as the &quot;third eyelid&quot;. This part has become vestigial in humans, where it remains as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Plica_semilunaris_of_conjunctiva&quot; rel=&quot;noreferrer&quot;&gt;plica semilunaris&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/n2jnQ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This image of a &lt;a href=&quot;http://en.wikipedia.org/wiki/Masked_Lapwing&quot; rel=&quot;noreferrer&quot;&gt;masked lapwing&lt;/a&gt; clearly shows its nicitating membrane in action, where it covers the eye in a horizontal motion. This is analogous to blinking in humans, and the membrane moisturises the eye and removes debris while the bird is in flight. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pg1wA.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1771963/&quot; rel=&quot;noreferrer&quot;&gt;This paper&lt;/a&gt; explains in detail how the peregrine falcon (the world's fastest bird) clears and moisturises its eyes when diving at speeds of over 300km/h. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-03-19T19:57:13.610" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30581" PostTypeId="2" ParentId="30569" CreationDate="2015-03-19T20:17:02.563" Score="3" Body="&lt;p&gt;The short answer is that the Edman degradation is a multi-step process. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Edman_degradation&quot; rel=&quot;nofollow&quot;&gt;Wikipedia page&lt;/a&gt; has a decent picture of the mechanism. In practice, the peptide is reacted with phenylisothiocyanate (PTH) under mildly basic conditions to give a thiourea, which is stable. The excess PTH is separated from the thiourea intermediate. The thiourea is then treated with acid to cleave the &lt;em&gt;N&lt;/em&gt;-terminal residue from the peptide. The PTH is no longer present, so there's no concern about reacting with the second residue.&lt;/p&gt;&#xA;" OwnerUserId="10143" LastActivityDate="2015-03-19T20:17:02.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30583" PostTypeId="1" CreationDate="2015-03-19T22:49:32.263" Score="3" ViewCount="89" Body="&lt;p&gt;I have digested my DNA with NotI enzyme and put it in the −20 °C freezer without heat inactivating it. Can restriction enzymes work at −20 °C? Should I expect STAR activity?&lt;/p&gt;&#xA;" OwnerUserId="1843" LastEditorDisplayName="user9516" LastEditDate="2015-03-20T12:09:55.113" LastActivityDate="2015-03-20T12:10:01.813" Title="Are restriction enzymes active at −20 °C?" Tags="&lt;molecular-biology&gt;&lt;restriction-enzymes&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30584" PostTypeId="2" ParentId="30583" CreationDate="2015-03-19T23:01:12.677" Score="3" Body="&lt;p&gt;Enzymes have temperature optima based on the organism they were isolated from. So I would predict the there is virtually no activity at −20 °C. Another consideration is that the reactions are likely to be frozen solid, so that would limit diffusion, and also slow it down. But the real question is: what are you afraid of? Just the star activity? Even if there were star activity, would that adversely affect your experiments?&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorDisplayName="user9516" LastEditDate="2015-03-20T12:10:01.813" LastActivityDate="2015-03-20T12:10:01.813" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30585" PostTypeId="2" ParentId="30557" CreationDate="2015-03-19T23:12:40.900" Score="0" Body="&lt;p&gt;First it depends on the species in question. I assume that you are referring to humans and/or mice. In diploid organisms the toxicity of losing or gaining a chromosome is related in part to the size of the chromosome, but also determined by which genes are on the chromosome in question. Some genes could be lethal if their copy number is increased or decreased (dose sensitive). The longer the chromosome the more genes it is likely to have and therefore the greater the chance of a problem. In humans viable trisomics usually involve the shortest chromosomes. Human X is very large but it is dosage compensated.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-03-19T23:12:40.900" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30586" PostTypeId="2" ParentId="30362" CreationDate="2015-03-19T23:20:49.737" Score="4" Body="&lt;p&gt;I don't know about the specific cues that American robins use for migration. This species is also both a short range (e.g. between states or to lower altitudes) and long range migrant (e.g. Florida &amp;amp; Mexico), so the cues that they use can probably differ between overwintering populations. There are also year-round populations of robins in the US, but probably not many (if any) in Massachusetts. There are however at least two papers that show that American robins are arriving earlier and earlier, at least in Wisconsin and Colorado (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC26486/&quot; rel=&quot;nofollow&quot; title=&quot;Inouye et al. 2000. Climate change is affecting altitudinal migrants and hibernating species. PNAS  97(4): 1630–1633.&quot;&gt;Inouye et al, 2000&lt;/a&gt; and &lt;a href=&quot;http://labs.russell.wisc.edu/peery/files/2013/08/Jones-Zuckerberg-Paulios-2012.pdf&quot; rel=&quot;nofollow&quot; title=&quot;Jones, G.M., B. Zuckerberg, and A. Paulios. 2012. The early bird gets earlier: a phenological shift in migration timing of the American Robin (Turdus migratorius) in the state of Wisconsin. Passenger Pigeon 74(2): 131-142.&quot;&gt;Jones et al, 2012&lt;/a&gt;). The studies find that arrivals dates have shifted ~13 days earlier between 1990 and 2010 in Wisconsin and 14 days earlier between 1981 and 2000 in Colorado. The study from Colorado also shows that the first date of bare ground has not changed, so snow melt has not changed over the time period. As a consequence, the interval between arrival and bare ground has grown by 18 days. This could indicate a phenological mismatch between spring arrival and the resources used by robins, and your observations seems to agree with this pattern.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This are at least some comments and a couple of papers that could be useful for your question. Sorry I cannot say more about the actual cues used for their migration.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2015-03-19T23:20:49.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30587" PostTypeId="2" ParentId="30571" CreationDate="2015-03-19T23:37:46.123" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Sound localization in the vertical plane should not be affected too much, while localization in the horizontal plane is impaired in unilateral deafness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The two most important mechanisms used to localize sounds can be grossly divided into localizing sounds in the horizontal (&lt;em&gt;azimuth&lt;/em&gt;) and vertical plane (&lt;em&gt;elevation&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the horizontal plane it is the exquisite capability of the auditory system to distinguish between slight &lt;strong&gt;intensity&lt;/strong&gt;, &lt;strong&gt;latency&lt;/strong&gt; and &lt;strong&gt;phase&lt;/strong&gt; differences between the two ears that allow the brain to deduce where a sound is coming from. For low frequencies it is mainly the inter-aural time and phase differences that play a role. For high frequencies, the difference in sound level between the ears becomes more important (head-shadow effect). For example, if a sound is coming from the left, the left ear will receive the highest sound level. The sound stimulus will also have a shorter latency because of the intervening head tissue, and a phase difference due to the time lag &lt;a href=&quot;http://jn.physiology.org/content/97/1/715.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Van Wanrooij &amp;amp; Opstal, 2007)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9FPyC.jpg&quot; alt=&quot;head shadow&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Head shadow effect at high, but not at low frequencies. Source: &lt;a href=&quot;http://www.ssc.education.ed.ac.uk/courses/deaf/dnov10i.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;University of Edinborough&lt;/a&gt;&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the vertical plane and front-back discrimination it is the analysis of spectral shape cues that lie at the basis of directional hearing. The spectral cues arise from direction-dependent reflections within the pinna (described by so-called head-related transfer functions, see below figure graphs). The pinna provide a monaural localization cue for sound frequencies exceeding about 3–4 kHz &lt;a href=&quot;http://jn.physiology.org/content/97/1/715.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Van Wanrooij &amp;amp; Opstal, 2007)&lt;/a&gt;.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cvbRh.gif&quot; alt=&quot;Pinna&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Head-related transfer function due to the pinna. Source: &lt;a href=&quot;http://interface.cipic.ucdavis.edu/sound/tutorial/psych.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;University of California&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this hard distinction between elevation and azimuth directional analysis is somewhat simplified, as it appears that elevation is also analyzed in terms of binaural cues, and azimuth is also identified using monaural cues. Hence, all available cues seem to be &lt;em&gt;integrated&lt;/em&gt; for both vertical and horizontal localization. Nonetheless, the two distinct pathways are the primary and preferred ways of the auditory system to determine elevation and azimuth. However, when one ear is plugged, or in unilateral deaf people, the textbook binaural hearing in the horizontal plane may be substituted by monaural cues, and I quote from &lt;a href=&quot;http://jn.physiology.org/content/97/1/715.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Van Wanrooij &amp;amp; Opstal, 2007)&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[L]isteners rely on monaural spectral cues for sound-source azimuth localization as soon as the binaural difference cues break down.  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Therefore, to wrap up, unilateral deafness degrades directional hearing and in particular in the horizontal plane. However, the use of monaural cues may still allow localization of sounds in the horizontal plane in unilaterally deaf subjects, albeit less effectively than normal-hearing subjects using binaural hearing &lt;a href=&quot;http://jn.physiology.org/content/97/1/715.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Van Wanrooij &amp;amp; Opstal, 2007)&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;https://i.stack.imgur.com/9FPyC.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Van Wanrooij &amp;amp; Opstal, &lt;em&gt;J Neurophysiol&lt;/em&gt; 2007;&lt;strong&gt;97&lt;/strong&gt;:715-26&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-04-15T19:57:32.783" LastActivityDate="2016-04-15T19:57:32.783" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30588" PostTypeId="1" AcceptedAnswerId="30592" CreationDate="2015-03-20T00:58:27.657" Score="6" ViewCount="197" Body="&lt;p&gt;In the same kind of idea than &lt;a href=&quot;https://biology.stackexchange.com/questions/30116/does-dna-have-the-equivalent-of-if-statements-while-loops-or-function-calls-h&quot;&gt;this question&lt;/a&gt;. Gene expression are regulated through complex interactions. The concentration of enhancers and repressors is an important aspect that dictate the level of expression of a given gene. These concentrations can take different value on a continuous scale.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine a case where fitness is maximized when a given gene produce &lt;code&gt;n&lt;/code&gt; proteins per minute if the concentration of a given protein is greater than &lt;code&gt;x&lt;/code&gt;. If the concentration of the protein was to be lower than &lt;code&gt;x&lt;/code&gt;, then the gene should not be expressed (0 proteins per minute are produced). In such case, it would be great if a bunch of reactants were to be able to simulate a &quot;switch function&quot; that would switch from &quot;NO EXPRESSION&quot; to &quot;EXPRESSION&quot; at &lt;code&gt;x&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to me that such switch function should be very complicated to evolve. I would suspect that all chemical reactions, including the binding of enhancer to promoter region should follow the law of Michaelis-Menten and the Michaelis-Menten function is not at all switch function. So, I have been thinking about cooperative binding. &lt;a href=&quot;http://en.wikipedia.org/wiki/Hill_equation_(biochemistry)&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hill's equation&lt;/a&gt; describes a function that is effectively a switch function given that the hill coefficient is high enough. However, seeking a bit in the literature, it's seems that the Hill coefficient never really overpass 3 (or 5 for extreme estimates). A Hill coefficient of within this range gives a logistic function but still looks quite suboptimal compared to what a perfect switch function could do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are there switch functions in molecular genetics that could translate a concentration into a TRUE/FALSE signal?&#xA;How well do they simulate the perfect switch function?&#xA;Are they based on cooperative binding or on some other mechanism?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;References for estimate of Hill coefficients:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1435008/pdf/biophysj00200-0109.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1435008/pdf/biophysj00200-0109.pdf&lt;/a&gt;&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;sub&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1537-2995.1983.23283172857.x/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1046/j.1537-2995.1983.23283172857.x/abstract&lt;/a&gt;&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;sub&gt;&lt;a href=&quot;http://www.pnas.org/content/93/19/10078.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.pnas.org/content/93/19/10078.short&lt;/a&gt; &lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8816754&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/8816754&lt;/a&gt; &lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;sub&gt;&lt;a href=&quot;http://www.fasebj.org/content/11/11/835.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.fasebj.org/content/11/11/835.short&lt;/a&gt; &lt;/sub&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2816740/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2816740/&lt;/a&gt;&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-03-20T11:33:40.067" Title="Can molecular genetics make a boolean variable from a continuous variable?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30589" PostTypeId="2" ParentId="30557" CreationDate="2015-03-20T01:11:23.743" Score="-5" Body="&lt;p&gt;Assuming you are discussing our species, sex chromossomes abnormalities do not lead to such fatality because of it's purpose, i.e a gene in these chromossomes mainly affects sexual related hormone producing which do not play any role (there are exceptions like steroid hormones) in general metabolism or imune responses so a mutation in those genes or a duplication of chromossomes does not cause the death of the individual and it survives during the embryonic and fetal stages becoming later a healthy individual but with serious sexual problems like infertility and sterility . In the other hand, a mutation or duplication in autosomal chromossomes is likely dangerous to survival of the organism and many times it cannot survive in the early stages. Those who survive many times face serious health problems in their life because unlike sexual activity, autosomal gene functions are necessary for cells to survive. Sexual activity is just a way to pass genes between generations not to survive in one generation !  &lt;/p&gt;&#xA;" OwnerUserId="15017" LastActivityDate="2015-03-20T01:11:23.743" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30590" PostTypeId="2" ParentId="8991" CreationDate="2015-03-20T01:36:25.020" Score="-3" Body="&lt;p&gt;Below are responses generated using the isolated guinea-pig ileum preparation to determine a pA2 value for a sample of the cholinergic antagonist homatropine.&#xA;Responses are expressed in millimetres +/- SDM (n =4). Plot the data and then determine by Schild analysis the pA2 value and Schild slope. What conclusions can you draw; does the experiment/data fulfil the criteria for a valid Schild analysis?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Acetylcholine      ACH Alone    ACH +Homotropine       ACH +Homotropine   ACH +Homotrop&#xA;Concentration                     3x10^-9 M              1x10^8M            3x10^-8M&#xA;[Molar]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3 x 10^-9            3+/-1&lt;br&gt;&#xA;6 x 10^-9            8+/-3            Not Response&#xA;3 x 10^-8            28+/-6             10+/-4             No response&#xA;6 x 10^-8            38+/-8             21+/-9           5+/-2                                                    No response&#xA;3 x 10^-7            55+/-5             43+/-7                27+/-9             10+/-4&#xA;6 x 10^-7            56+/-5             52+/-3              38+/-7             20+/-7&#xA;3 x 10^-6              -                55+/-4              53+/-6             43+/-6&#xA;6 x 10^-6              -                   -                56+/-2             54+/-5&lt;/p&gt;&#xA;" OwnerUserId="15018" LastActivityDate="2015-03-20T01:36:25.020" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30591" PostTypeId="2" ParentId="30195" CreationDate="2015-03-20T01:38:41.220" Score="-1" Body="&lt;p&gt;This issue is deep but one answer is bacteria/virus genetic variability. Some organisms have the ability to change their DNA in just a few generations (for example the influenza virus which requires a new vaccine every year). When you take a vaccine for influenza virus you expect that will protect you in a short period of time (winter season) because this virus is a nasty one, i.e it has the ability to present antigen variability due to mutation/constitution of its DNA and antigen is the source of power of vaccine (a vaccine assumes the organism has a antigen that could be a protein or other biomolecule that is relatively fixed between generations and is specific to that organism) so the vaccine loses its effect because the organisms are no longer susceptible which causes immune response to be weak (no longer recognizes the organism as it recognized) and you get sick. If the organism has slow mutation/variability the vaccine will last longer because the antigens are present for a longer period of time but eventually you will need to get another vaccine years later (for example tetanus).&lt;/p&gt;&#xA;" OwnerUserId="15017" LastEditorUserId="13405" LastEditDate="2017-07-07T04:15:15.787" LastActivityDate="2017-07-07T04:15:15.787" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30592" PostTypeId="2" ParentId="30588" CreationDate="2015-03-20T06:09:14.320" Score="5" Body="&lt;p&gt;Positive feedbacks can be one alternative. Positive feedbacks exhibit bistability and can therefore adopt one of the two stable states depending on the initial condition. A famous example of a positive feedback switch would be that between &lt;em&gt;cI&lt;/em&gt; and &lt;em&gt;Cro&lt;/em&gt; in &lt;em&gt;λ&lt;/em&gt;-phage, which repress each other. Positive feedbacks also display hysteresis: if the state of the system is dependent on an inducing ligand &lt;code&gt;X&lt;/code&gt; such that system attains state &lt;code&gt;S2&lt;/code&gt; at high levels of the ligand, then to switch from &lt;code&gt;S2&lt;/code&gt; to &lt;code&gt;S1&lt;/code&gt; the concentration of &lt;code&gt;X&lt;/code&gt; would have to be reduced below the level that was required for the &lt;code&gt;S1&lt;/code&gt; to &lt;code&gt;S2&lt;/code&gt; switch; and vice-versa. In other words, the system tries to remain in its current state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the transcription factors that constitute the genetic positive feedback have a co-operative behaviour then you can expect a steep switching curve. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For details see &lt;a href=&quot;http://dx.doi.org/10.1002%2Fbies.20769&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; review. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-20T11:33:40.067" LastActivityDate="2015-03-20T11:33:40.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30593" PostTypeId="2" ParentId="30583" CreationDate="2015-03-20T06:18:06.017" Score="1" Body="&lt;p&gt;While there is unlikely to be any activity when the enzyme is frozen, there are better methods to prevent star activity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1: If you are running the reaction in a PCR machine, you can program the machine prior to the digest to heat up to 65 degrees for 10 minutes after the intended digestion timeframe to heat inactivate NotI. &lt;a href=&quot;https://www.neb.com/products/r0189-noti&quot; rel=&quot;nofollow&quot;&gt;Since NotI is a heat-labile enzyme&lt;/a&gt;, this prevents star activity by denaturing it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2: You can use &lt;a href=&quot;https://www.neb.com/products/r3189-noti-hf&quot; rel=&quot;nofollow&quot;&gt;NotI-HF&lt;/a&gt;, which has been engineered by NEB to greatly reduce the amount of star activity and can therefore be left incubating at 37°C overnight. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3: You can gel purify or perform a &quot;PCR purification&quot; on your digested DNA samples, this also removes any protein present and therefore prevents star activity.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-03-20T06:33:07.817" LastActivityDate="2015-03-20T06:33:07.817" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30594" PostTypeId="2" ParentId="23682" CreationDate="2015-03-20T06:28:33.933" Score="0" Body="&lt;p&gt;BLAST is not the correct program to use in metagenomics analyses for determining the number of reads that map to a certain region of the genome, as it is optimised for single hits instead of a large number of different hits. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sheer number of hits within a metagenomics database (which contains a large amount of redundant data) is likely to cause inefficient scaling and high memory usage when the detection of all possible hits is required. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the number of hits required is low, it is possible to have it return those hits, but if you are looking at &gt;1000 hits, it is probably recommended to use a mapper program such as &lt;a href=&quot;http://bio-bwa.sourceforge.net/&quot; rel=&quot;nofollow&quot;&gt;BWA&lt;/a&gt; or &lt;a href=&quot;http://bowtie-bio.sourceforge.net/index.shtml&quot; rel=&quot;nofollow&quot;&gt;Bowtie&lt;/a&gt;. They are designed for the express purpose of mapping reads (such as from an RNASeq experiment) onto genomes.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-03-20T06:35:40.180" LastActivityDate="2015-03-20T06:35:40.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30595" PostTypeId="2" ParentId="30588" CreationDate="2015-03-20T07:33:17.003" Score="2" Body="&lt;p&gt;Transcription interference can also be a good mechanism to provide such switches. Transcription interference occurs between genes in close adjacency to each other. This is basically, as the term suggest, that the neighbouring genes can interfere with each others transcription (by overlapping promoters blocking transcription initiation, collision of transcription machinery on 3' ends etc). In &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22783276&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; article all of this is well explained along with a theoretical model called Transcription Interference network.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So a switch mentioned in the question can be carried out by this mechanism. Let's take two genes (A and B) that exhibit this transcrigption interference phenomena. Also let's imagine a gene orientation where the tow genes face each other with their 3' ends like in the picture below ( part B3 but with smaller overlap at the 3' ends). The setup is that gene A is 'stronger' than gene B ( has higher transcription initiation rate), thus at the 3' prime ends it can suppress gene by knockin off the polymerase (there are many possible scenarios when two RNAP-s collide or meet one knocking off the other is just one of them). Now if gene A's activity were to be lowered then gene B could over take and nullify gene A with the same mechanism seen before. In this case transcription initiation would still occur on gene A but it could not produce viable RNA because transcription would terminate early. This results in complete shut down in gene A's expression. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8UQyx.jpg&quot; alt=&quot;antiparallel overlaps&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(source the linked article above)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since gene expression and transcription are 'leaky', some minimal activity is basically always present, the above mentioned mechanism can be taken care of. In the article I linked there are many other examples how such switch could be carried out by transcription interference I just took one of them. Also you'll notice that the Transcription Interference Network model is based on such switches.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-03-20T10:11:54.027" LastActivityDate="2015-03-20T10:11:54.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30596" PostTypeId="1" CreationDate="2015-03-20T10:04:45.420" Score="2" ViewCount="650" Body="&lt;p&gt;Context:&#xA;Most countries require milk to be sterilised through radiation or heat to remove possible harmful bacteria. Both of these processes denature the proteins in the milk (&lt;a href=&quot;http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there methods of sterilisation that will not denature proteins?&lt;/p&gt;&#xA;" OwnerUserId="5387" LastEditorUserId="5387" LastEditDate="2015-03-21T09:13:47.760" LastActivityDate="2015-03-22T11:31:18.010" Title="Are there sterilisation methods that do not denature proteins as heat does?" Tags="&lt;proteins&gt;&lt;sterilisation&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30597" PostTypeId="1" CreationDate="2015-03-20T10:27:00.163" Score="1" ViewCount="932" Body="&lt;p&gt;I have to use the old version of Blast (not Blast+) to compare DNA sequences and I have to know the number of all hits. They are not given in the header and I have to know them for many many of blast outputs and its nearly impossible to count them (or to export them in excel). I think I probably have to write a 'Perl Script' and I did my best but I am not familiar with programming and it is not working. Furthermore I had a look on the internet and they are always comparing it to BIO Search. I have e code, which for me looks pretty good,but it also done a comparison with BIO Search, what I don't need/want. &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;use strict;&#xA;use warnings;&#xA;use Bio::SearchIO;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;h1&gt;Usage information&lt;/h1&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;die &quot;Usage: $0 &amp;lt;BLAST-report-file&amp;gt; &amp;lt;number-of-top-hits&amp;gt; &amp;lt;output-file&amp;gt;\n&quot;, if (@ARGV != 3);&#xA;&#xA;my ($infile,$numHits,$outfile) = @ARGV;&#xA;    print &quot;Parsing the BLAST result ...&quot;;&#xA;    my $in = Bio::SearchIO-&amp;gt;new(-format =&amp;gt; 'blast', -file =&amp;gt; $infile);&#xA;    open (OUT,&quot;&amp;gt;$outfile&quot;) or die &quot;Cannot open $outfile: $!&quot;;&#xA;&#xA;# print the header info for tab-deliminated columns&#xA;print OUT &quot;query_name\tquery_length\taccession_number\tlength\tdescription\tE value\tbit score\tframe\tquery_start\t&quot;;&#xA;print OUT &quot;query_end\thit_start\thit_end\tpositives\tidentical\n&quot;;&#xA;&#xA;# extraction of information for each result recursively&#xA;while ( my $result = $in-&amp;gt;next_result ) {&#xA;    # the name of the query sequence&#xA;    print OUT $result-&amp;gt;query_name . &quot;\t&quot;;&#xA;&#xA;        # the length of the query sequence&#xA;        print OUT $result-&amp;gt;query_length;&#xA;&#xA;        # output &quot;no hits found&quot; if there is no hits&#xA;        if ( $result-&amp;gt;num_hits == 0 ) {&#xA;    		print OUT &quot;\tNo hits found\n&quot;;&#xA;        	} else {&#xA;    		my $count = 0;&#xA;&#xA;                # process each hit recursively&#xA;        while (my $hit = $result-&amp;gt;next_hit) {&#xA;            print OUT &quot;\t&quot; if ($count &amp;gt; 0);&#xA;                            # get the accession numbers of the hits&#xA;    			print OUT &quot;\t&quot; . $hit-&amp;gt;accession . &quot;\t&quot;;&#xA;                        # get the lengths of the hit sequences&#xA;                        print OUT $hit-&amp;gt;length . &quot;\t&quot;;&#xA;                            # get the description of the hit sequences&#xA;    			print OUT $hit-&amp;gt;description . &quot;\t&quot;;&#xA;                        # get the E value of the hit&#xA;            print OUT $hit-&amp;gt;significance . &quot;\t&quot;;&#xA;                            #get the bit score of the hit&#xA;    			print OUT $hit-&amp;gt;bits . &quot;\t&quot;;&#xA;&#xA;                        my $hspcount = 0;&#xA;&#xA;                        # process the top HSP for the top hit&#xA;            while (my $hsp = $hit-&amp;gt;next_hsp) {&#xA;                            print OUT &quot;\t\t\t\t\t\t\t&quot;, if ($hspcount &amp;gt; 0);&#xA;                            	# get the frame of the query sequence&#xA;    				print OUT $hsp-&amp;gt;query-&amp;gt;frame . &quot;\t&quot;;&#xA;                                # get the start and the end of the query sequence in the alignment&#xA;                print OUT $hsp-&amp;gt;start('query') . &quot;\t&quot; . $hsp-&amp;gt;end('query'). &quot;\t&quot;;&#xA;                                # get the start and the end of the hit sequence in the alignment&#xA;                print OUT $hsp-&amp;gt;start('hit') . &quot;\t&quot; . $hsp-&amp;gt;end('hit') . &quot;\t&quot;;&#xA;                                # get the similarity value&#xA;                printf OUT &quot;%.1f&quot; , ($hsp-&amp;gt;frac_conserved * 100);&#xA;    				print OUT &quot;%\t&quot;;&#xA;                                    # get the identity value&#xA;    				printf OUT &quot;%.1f&quot; , ($hsp-&amp;gt;frac_identical * 100);&#xA;                    print OUT &quot;%\n&quot;;&#xA;                                $hspcount++;&#xA;                            }&#xA;    			$count++;&#xA;&#xA;                        # flow control for the number of hits needed&#xA;            last if ($count == $numHits);&#xA;        }&#xA;        }&#xA;}&#xA;close OUT;&#xA;print &quot; DONE!!!\n&quot;;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;May someone help me, please. I need a program, which first tells me the header and then the number of hits. I am a little bit desperate and would be so happy if someone can help me. That would be so nice. Greetings Tina &lt;/p&gt;&#xA;" OwnerUserId="15015" LastEditorUserId="3340" LastEditDate="2015-03-20T12:16:28.303" LastActivityDate="2015-03-21T01:03:53.223" Title="Blast output - program to count the number of hits" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="8" ClosedDate="2015-03-21T01:11:08.850" ContentLicense="CC BY-SA 3.0" />
  <row Id="30598" PostTypeId="1" CreationDate="2015-03-20T11:45:17.173" Score="5" ViewCount="2022" Body="&lt;p&gt;Can someone who has a damaged larynx, which does not allow them to talk, still create a tune when they whistle?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that the larynx is what allows a person to manipulate their pitch and volume, but whistling sounds are just air making a noise as they are through the lips.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would a person with a damaged larynx be able to whistle physically, but it would just be a toneless noise?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is so, is there any situation where a human would not be able to talk, but could still whistle with a tune and understand the speech of others perfectly? (i.e. having not suffered brain damage or are deaf)&lt;/p&gt;&#xA;" OwnerUserId="15022" LastEditorUserId="15022" LastEditDate="2015-03-23T10:23:33.627" LastActivityDate="2015-03-24T20:45:44.190" Title="Can someone who cannot talk still whistle?" Tags="&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30599" PostTypeId="2" ParentId="30598" CreationDate="2015-03-20T11:55:53.023" Score="5" Body="&lt;p&gt;Sounds such as certain phonemes are made merely with the use of air flow and movement of the lips or tongue, without the need for action of the vocal chords. Think of '&lt;em&gt;f&lt;/em&gt;', '&lt;em&gt;s&lt;/em&gt;', '&lt;em&gt;t&lt;/em&gt;', &lt;em&gt;k&lt;/em&gt; in the English language. These are called &lt;em&gt;unvoiced phonemes&lt;/em&gt; in phoniatrics (&lt;a href=&quot;http://phonemicchart.com/what/index3.html&quot; rel=&quot;nofollow&quot;&gt;see the phonemic chart&lt;/a&gt;). Also, clicking sounds and whistling can be made without use of the vocal chords. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-20T13:40:32.957" LastActivityDate="2015-03-20T13:40:32.957" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30600" PostTypeId="1" AcceptedAnswerId="30602" CreationDate="2015-03-20T11:59:14.153" Score="14" ViewCount="35590" Body="&lt;p&gt;I recently noticed that it is hard to focus on blue light sources, especially at night. When observing a blue light source, e.g. a neon sign, it looks somewhat blurry. A sign with a different colour right beside it looks sharp.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I already know about the three kinds of cone cells in the human eye (I'm not a biologist) with their spectral sensitivity peaks in in short (S, 420–440 nm), middle (M, 530–540 nm), and long (L, 560–580 nm) light wavelengths [1]. But does the spectral sensitivity correlate with focus? Or does our eye lens refract blue light in a different way?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I screw up my eyes looking at a blue light, it becomes less blurry, but then all the other colours are blurred.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] &lt;a href=&quot;http://en.wikipedia.org/wiki/Cone_cell#/media/File:Cones_SMJ2_E.svg&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Cone_cell#/media/File:Cones_SMJ2_E.svg&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15024" LastEditorUserId="15024" LastEditDate="2015-03-20T13:40:53.673" LastActivityDate="2017-09-21T17:48:00.500" Title="Why can't the human eye focus blue light?" Tags="&lt;vision&gt;&lt;human-eye&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30601" PostTypeId="2" ParentId="30600" CreationDate="2015-03-20T12:35:53.787" Score="3" Body="&lt;p&gt;Light is scattered by gas molecules in air. The shorter the wavelength of light, the more it is scattered by the atmosphere. Because it has a shorter wavelength, blue light is scattered ten times more than red light. One reason is that&#xA;blue light has a frequency that is closer to the resonant frequency of atoms than e.g. red light (&lt;a href=&quot;http://www.exploratorium.edu/snacks/blue_sky/&quot; rel=&quot;nofollow&quot;&gt;Exploratorum&lt;/a&gt;). Due to this scattering the eye has difficulty focussing as object edges get fuzzy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The scattering of blue light degrades vision in normal day light, especially in foggy conditions when light scattering is at its worst due to the droplets of water in the air. Yellow filters (for example yellow sports sunglasses) improve visual acuity by filtering out the aberrant blue light (&lt;a href=&quot;http://www.laramyk.com/resources/education/dispensing/the-dangers-of-night-driving-glasses/&quot; rel=&quot;nofollow&quot;&gt;Laramy-K Optical&lt;/a&gt;).     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fun fact&lt;/strong&gt;&lt;br&gt;&#xA;The predominant scattering of blue light makes that the sun is clear in the sky as a yellowish circle, while the sky is blue due to the fact that it is the blue light predominantly being scattered away from the sunlight. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-20T13:04:38.550" LastActivityDate="2015-03-20T13:04:38.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30602" PostTypeId="2" ParentId="30600" CreationDate="2015-03-20T12:39:28.807" Score="8" Body="&lt;p&gt;The same thing happens in photography when you see an image with colorful shadows of objects on it - this is called chromatic aberration. Check &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromatic_aberration&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; wiki page if you're not familiar with. Now this happens because the lens in the objective has different refractive properties for different wavelengths or if go the other way around different wavelengths refract differently within the same material. This is why the famous triangular rainbow prism is capable of separating the sunlight to rainbow. So back to the question: in our eye there is the eye lens that is responsible for focusing. Let's assume that it is homogenous enough. So when light enters into our lens it refracts to separate colours and our lens is not complex enough to fully compensate for this. The second picture is a good approximation of the human eye lens in shape.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: so when you focus one color perfectly the others will be blurry a bit since those will be out of focus due to different refraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VDuRr.png&quot; alt=&quot;rainbow prism&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;taken from: &lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Prism-rainbow-black.svg&quot; rel=&quot;noreferrer&quot;&gt;http://commons.wikimedia.org/wiki/File:Prism-rainbow-black.svg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pI8rS.png&quot; alt=&quot;lens&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;taken from:&lt;a href=&quot;http://en.wikipedia.org/wiki/Chromatic_aberration#/media/File:Chromatic_aberration_lens_diagram.svg&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Chromatic_aberration#/media/File:Chromatic_aberration_lens_diagram.svg&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-03-20T12:53:14.123" LastActivityDate="2015-03-20T12:53:14.123" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30603" PostTypeId="1" CreationDate="2015-03-20T13:39:36.427" Score="4" ViewCount="2192" Body="&lt;p&gt;I have seen biologists use mouse grown primary antibodies in mouse tissue, and they've told me that if the blood is perfused well then there is no problem with this method. How does the secondary antibody (anti mouse) not stick everywhere on all the mouse antigens in the tissue? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clarification: I  understand that the secondary antibody is very specific to all mouse &quot;class&quot; primary antibodies. Can I ask then why using a secondary mouse antibody does not recognize background antibodies in the tissue, the ones that the mouse produced for itself naturally before I added any of my primary antibody? Are the existing primary antibody levels already present in the mouse much lower than the levels of the primary antibody I am adding?   &lt;/p&gt;&#xA;" OwnerUserId="15027" LastEditorUserId="-1" LastEditDate="2015-03-22T11:33:19.597" LastActivityDate="2015-07-02T13:15:35.713" Title="Why can we use mouse-produced antibodies on mice tissues?" Tags="&lt;immunology&gt;&lt;antibody&gt;&lt;histology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30604" PostTypeId="2" ParentId="30603" CreationDate="2015-03-20T13:52:24.860" Score="0" Body="&lt;p&gt;Antibodies are very specific on what they recognize (this is called epitope that is the small part of the antigen that is recognized by a specific antibody), and secondary antibodies are made to attach to a specific part of the primary antibody - you can achieve this with monoclonal ABs. Antigens can be recognized by many antibodies (because they can have many epitopes for different antibodies), but usually a single antibody recognizes only a few or more likely a single antigen at max (since the specific epitope it attaches to is only present on a few or a single antigen(s)).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Antibody&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt; page for antibodies has plenty of detail on how ABs work.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-03-20T13:52:24.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30605" PostTypeId="2" ParentId="30603" CreationDate="2015-03-20T14:14:03.857" Score="2" Body="&lt;p&gt;The reason why the secondary antibody only recognizes the primary antibody is relatively simple: It is directed against the Fc-part of the primary antibody. As this part is species specific (but constant between all antibodies from one species, hence the name constant) a secondary anti-mouse antibody is directed against all mouse antibodies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The general principle can be seen in the figure (although this is from immunolabelling, the principle stays the same, Image from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Primary_and_secondary_antibodies&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Fb7zB.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The anti-mouse secondary does recognize the antibodies which are present in the tissue. These are usually present at low levels (unless you work with immune tissues as spleens) and only cause a relatively low background. If it causes a problem, you can treat your sample before you add the primary with an Fc block which blocks the antibodies present in the tissue so that the secondary antibody will not recognize anymore later.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-03-22T11:45:27.480" LastActivityDate="2015-03-22T11:45:27.480" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30606" PostTypeId="1" CreationDate="2015-03-20T16:32:47.253" Score="10" ViewCount="1384" Body="&lt;p&gt;Contrary to all of the textbook images of mitochondria that I have seen over the years, I had just learned that the mitochondria within a cell form a dynamic branching network along microtubule scaffolding by fusing with each other. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why would they need to fuse together?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When they fuse, would this involve only the outer mitochondrial membrane? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would it not behoove a mitochondrion to remain distinct from others both physically and genetically? &lt;/p&gt;&#xA;" OwnerUserId="12970" LastEditorUserId="1306" LastEditDate="2015-03-20T16:43:43.830" LastActivityDate="2016-04-30T14:36:34.820" Title="Why do mitochondria fuse together?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30607" PostTypeId="2" ParentId="30606" CreationDate="2015-03-20T16:43:37.193" Score="7" Body="&lt;p&gt;Mitochondria produce a large quantity of reactive oxygen species (ROS) that damage the mitochondrial genetic material. These cell organelles do have a  DNA repair mechanism similar to that of the nucleus to some extent &lt;a href=&quot;http://cshperspectives.cshlp.org/content/5/5/a012641.full&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt; which is not entirely understood however they have multiple copies and so the fusion and fission of mitochondria work together to maintain as many viable/healthy mitochondria as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When two mitochondria fuse, their genetic material can recombine and thus exchange their damaged DNA. In this way, one of them repairs its DNA at the expense of the other accumulating more damaged DNA. Mitochondria that accumulate too much damaged DNA will 'die' - get eliminated, but they can be replaced by fission of healthy ones. Take a look at &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitochondrial_fusion&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; wiki page, it has useful info.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: This &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768568/&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; may also be useful. (Mitochondrial fusion and division: regulation and role in cell viability&#xA;Giovanni BENARD and Mariusz KARBOWSKI, Semin Cell Dev Biol. 2009 May;20(3):365-74.)&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="-1" LastEditDate="2016-04-30T14:36:34.820" LastActivityDate="2016-04-30T14:36:34.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30608" PostTypeId="1" AcceptedAnswerId="30613" CreationDate="2015-03-20T16:49:46.607" Score="2" ViewCount="347" Body="&lt;p&gt;I'm looking to create blunt ends from sticky ends with mung bean nuclease for subsequent ligation.  Does anyone know full mechanism by which mung bean nuclease will do this?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular after the reaction, will the ends of resulting dsDNA have phosphate groups or will I need to phosphorylate the ends with an extra step for successful ligation?&lt;/p&gt;&#xA;" OwnerUserId="14963" LastActivityDate="2015-03-20T18:01:55.637" Title="Does mung bean nuclease cleave a phosphate group when it's chewing off 5' or 3' ssDNA ends?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;restriction-enzymes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30609" PostTypeId="1" CreationDate="2015-03-20T16:57:39.977" Score="0" ViewCount="431" Body="&lt;p&gt;When someone is having a heart attack, could it be considered , in some situations, a spasm? Below, I have written how I believe the process may work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heart is basically a muscle working constantly to create a sinus rhythm. As I understand it, one can get muscle spasms in any muscle (correct me if I'm wrong). If so, then couldn't someone get a muscle spasm in a part of the heart muscle that disrupts the sinus rhythm and causes chaotic signals? Thus causing a spasm throughout the muscle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When one is having a heart attack, does the electric shock used cause a dramatic and fast 'stretching' of the heart muscles allowing the heart to get over the spasm and back to normal rhythm? Could something else, like an ElectroMagnetic Pulse be used to 'stretch' the heart muscles away from the spasms?&lt;/p&gt;&#xA;" OwnerUserId="11605" LastEditorUserId="11605" LastEditDate="2015-03-24T04:16:20.170" LastActivityDate="2015-04-27T20:05:11.643" Title="Similarity between a heart attack and a spasm" Tags="&lt;physiology&gt;&lt;cardiology&gt;&lt;muscles&gt;&lt;electrophysiology&gt;&lt;pathophysiology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30610" PostTypeId="1" AcceptedAnswerId="30626" CreationDate="2015-03-20T17:43:41.797" Score="7" ViewCount="348" Body="&lt;p&gt;As some background I've been building Electrophysiological models of neurons, and in the process stumbled upon a model, that in all respects is biologically plausible, but has a bizarre property I didn't think happened in nature. It spikes in response to hyper polarized currents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My particular model has only one ion channel which is has similar properties to Hodgkin-Huxley's transient sodium channel. It has one activation gate and one inactivation gate.  The reason I only use a single Ion Channel was I was exploring If I could create a minimal spiking neuron with just a single channel. The answer is yes, but has different properties then I expected. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically when I inject a hyper-polarizing current it spikes and depolarizing current causes it to stop spiking. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that Depolarization block can occur, my current isn't that High, in fact its no current produces no spikes. It has a normal rest potential around -55 mV and Fires upward to about +40 mV.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also note that If I change the parameters around I get a more normal neuron that spikes in response to depolarizing currents. So the property must be somehow related to the ion channel kinetics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is: Are there biological neurons that spike when hyper-polarizing currents are injected? &lt;/p&gt;&#xA;" OwnerUserId="13388" LastEditorUserId="13388" LastEditDate="2015-03-21T12:28:53.323" LastActivityDate="2015-03-24T00:59:26.960" Title="Is there a biological neuron that spikes in response to hyperpolarizing currents?" Tags="&lt;neuroscience&gt;&lt;mathematical-models&gt;&lt;electrophysiology&gt;&lt;neurophysiology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30611" PostTypeId="2" ParentId="28374" CreationDate="2015-03-20T17:45:01.310" Score="4" Body="&lt;p&gt;If you're not already doing so, make sure you set up Kohler illumination every time you use the microscope -- see this &lt;a href=&quot;http://microscopy.berkeley.edu/courses/TLM/condenser/kohler.html&quot; rel=&quot;nofollow&quot;&gt;tutorial&lt;/a&gt; by Steven Ruzin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The lamp or the phase ring may be misaligned. There are usually small hexagonal set screws on the lamp housing and the condenser, respectively, to adjust these.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imaging near the edge of a dish or well can lead to uneven illumination as the light is bent by the walls of the culture vessel. If this might be the cause, try re-doing the Kohler illumination before you take each image.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you can't find the cause of the problem, there are several ways to correct for uneven background described &lt;a href=&quot;http://fiji.sc/Image_Intensity_Processing#Background_correction&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. Maybe one of them will work with your analysis.&lt;/p&gt;&#xA;" OwnerUserId="15033" LastActivityDate="2015-03-20T17:45:01.310" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30612" PostTypeId="2" ParentId="30609" CreationDate="2015-03-20T18:01:52.000" Score="5" Body="&lt;p&gt;I was able to do some reading and research and I found some interesting information that was a). news to me. And b). the answer is yes... And no.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A spasm can be the cause of a heart attack by causing the coronary artery to contract. When that artery contracts, it causes a dramatic decrease in blood flow to the heart. When the heart looses access to oxygenated blood it can cause chest pain (angina) or even an MI (Myocardial Infarction a.k.a. a heart attack). This spasm is can be caused by exposure to extreme cold, smoking and the use of certain recreational drugs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this type of spasm cannot be stopped with defibrillation. Treatment for these involves administering Nitroglycerin and then later treatment involving Statin drugs and such.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the terms you are speaking of, I don't see that that would be quite accurate. The most common cause of sudden cardiac death is VF (Ventricular Fibrillation) which is essentially an uncontrollable quivering of the heart muscle. I've never heard this described as a spasm though. Google searches of spasm and heart spasm have all lead to definitions of the word spasm and the coronary artery spasm mentioned above. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, within that, I think you have a valid point and a decent understanding of how things work, just perhaps not fitting under the definition of a spasm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a defibrillator is used, it delivers a measured electrical shock to the person's heart and hopefully stops the chaotic electrical rhythm. I'm not sure if this part is correct however, I do not think you should look at that as a stretching of the muscle though. It is an electrical intervention that interrupts the former rhythm and hopefully the heart &quot;forgets&quot; what it was doing and returns to a sinus rhythm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So, to summarize:&lt;/strong&gt; A heart attack can be caused by a spasm; however, defibrillation does not help that type of attack. A defibrillator does not 'stretch' the heart but rather interrupts it's former rhythm. Because an irregular heart beat is not considered a spasm, I find it difficult to believe that any form of EMP would help it; however, I would love to hear that it has!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information on Ventricular Fibrillation, CAS (Coronary Artery Spasm) and AED's (Automated External Defibrillator(s)). Please see the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/007200.htm&quot; rel=&quot;nofollow&quot;&gt;MedlinePlus - on V-fib&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/angina/expert-answers/coronary-artery-spasm/faq-20058316&quot; rel=&quot;nofollow&quot;&gt;The Mayo Clinic - on CAS&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://heartsine.com/2012/12/how-does-an-automated-external-defibrillator-work/&quot; rel=&quot;nofollow&quot;&gt;HeartSine - on AED's&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this was helpful for you!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edits:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the comments, we had discussed a variety of possible causes and treatments for spasms, as well as what - if any - connection there is between how a spasm in perhaps a leg would be caused as compared to how one in your heart could be caused. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the reading and research I did, I was fairly inconclusive about the safety or desirability of a device to prevent heart attacks using an EMP device implanted in your brain or on your brain stem. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as how similar a spasm in your heart is to a spasm in any other muscle, they are not very similar. As seen &lt;a href=&quot;http://www.webmd.com/pain-management/muscle-spasms-cramps-charley-horse&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, a muscle spasm in most parts of the body can be caused by numerous things, such as dehydration, poor blood circulation, mineral deficiencies etc. Whereas a heart spasm (know as a CAS) can be caused by alcohol withdrawal, stimulant use, extreme cold... As seen &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000159.htm&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6289" LastEditorUserId="6289" LastEditDate="2015-04-27T20:05:11.643" LastActivityDate="2015-04-27T20:05:11.643" CommentCount="19" ContentLicense="CC BY-SA 3.0" />
  <row Id="30613" PostTypeId="2" ParentId="30608" CreationDate="2015-03-20T18:01:55.637" Score="3" Body="&lt;p&gt;According to &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/bi00665a020&quot; rel=&quot;nofollow&quot;&gt;Kroeker WD, Kowalski W, Laskowski M. 1976. Mung Bean Nuclease I. Terminally Directed Hydrolysis of Native DNA. Biochemistry 15(20):4463-4467&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It was concluded that the products of the terminally directed hydrolysis of native DNA possess 5’-phosphoryl groups because: (1) greater than 99% of acid-soluble activity applied to the column was recovered in products which coeluted with 5’-terminated standards and (2) the w-monophosphatase activity of mung bean nuclease would have dephosphorylated 3’-phosphoryl-terminated products. The endonucleolytic activity of mung bean nuclease on denatured DNA also results in the production of 5’-phosphoryl-terminated products. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Also, from &lt;a href=&quot;https://www.promega.ca/products/cloning-and-dna-markers/cloning-tools-and-competent-cells/mung-bean-nuclease/&quot; rel=&quot;nofollow&quot;&gt;Promega&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mung Bean Nuclease catalyzes the degradation of single-stranded DNA and RNA endonucleolytically to yield 5´-phosphoryl-terminated products&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-03-20T18:01:55.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30615" PostTypeId="1" CreationDate="2015-03-20T18:35:35.263" Score="3" ViewCount="46" Body="&lt;p&gt;I know that colonial Cnidaria enlarge their colony by the means of asexual reproduction and sexual and asexual reproduction can originate individuals that will be part of other colonies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nevertheless, I cannot find any precise information about whether the individuals of a certain colony are all descendants of one founder or not. I thank you anybody for any answer!&lt;/p&gt;&#xA;" OwnerUserId="8124" LastActivityDate="2015-03-20T18:35:35.263" Title="Founders of Cnidarian colony" Tags="&lt;zoology&gt;&lt;reproduction&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30616" PostTypeId="1" AcceptedAnswerId="30619" CreationDate="2015-03-20T15:51:01.473" Score="4" ViewCount="3437" Body="&lt;p&gt;I was reading a &lt;a href=&quot;https://www.researchgate.net/profile/Mikael_Kubista/publication/12969838_Sequence_motifs_and_free_energies_of_selected_natural_and_non-natural_nucleosome_positioning_DNA_sequences/links/0912f511140f11590c000000.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper&lt;/a&gt; and came across this table showing  $ \Delta \Delta G$ numbers of different nucleotide sequences in DNA/RNA. I know that $\Delta G$ is free energy and $ \Delta \Delta G$ is relative free energy with respect to L. variegatus 5 S RNA gene. What does this numbers signify actually?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qM1l9.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5669" OwnerDisplayName="dexterdev" LastEditorUserId="6307" LastEditDate="2015-03-21T00:57:11.143" LastActivityDate="2015-03-21T01:22:05.293" Title="What does these $\Delta \Delta G$ numbers signify?" Tags="&lt;thermodynamics&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30617" PostTypeId="1" AcceptedAnswerId="30620" CreationDate="2015-03-21T00:44:41.887" Score="2" ViewCount="23938" Body="&lt;p&gt;I want to know the correct definitions for the terms &lt;em&gt;apomorphy&lt;/em&gt; and &lt;em&gt;plesiomorphy&lt;/em&gt;. Unfortunately, there seems to be a variety of ways to define these terms depending on the language one uses. Thus, it has been hard to determine the correct definitions. I have settled on definitions that seem correct to me and also have examples. I would like confirmation from someone if I am understanding the definitions correctly.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Apomorphy&lt;/strong&gt; -- any character state or trait novel to a species and its descendants. An apomorphy occurs when a taxon is selected to have a particular trait. &lt;strong&gt;Example:&lt;/strong&gt; within the class reptilia, the suborder serpentes (snakes) has an apomorphy because its members have no legs. &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Plesiomorphy&lt;/strong&gt; -- an evolutionary trait or character state that is homologous within a particular taxon but is not unique to members of that group and therefore cannot be used as a diagnostic character for the group. &lt;strong&gt;Example:&lt;/strong&gt; within the class reptilia, legs are a plesiomorphy for its members. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My Question:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these definitions and examples accurate? &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="11652" LastEditDate="2015-03-21T01:23:17.970" LastActivityDate="2017-10-15T15:25:40.887" Title="What is an apomorphy? What is a plesiomorphy? Can someone confirm these definitions?" Tags="&lt;cladistics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30618" PostTypeId="2" ParentId="30597" CreationDate="2015-03-21T01:03:53.223" Score="0" Body="&lt;p&gt;This script, named blast2table.pl is from the code accompanying the Blast book by Korf &amp;amp; Yandell (there is a 3rd author whom I haven't met).&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;#!/usr/bin/perl -w&#xA;use strict;&#xA;use Getopt::Std;&#xA;use vars qw($opt_p $opt_b $opt_e $opt_m $opt_n);&#xA;    getopts('p:b:e:m:n:');&#xA;    my $PERCENT = $opt_p ? $opt_p : 0;&#xA;my $BITS    = $opt_b ? $opt_b : 0;&#xA;    my $EXPECT  = $opt_e ? $opt_e : 1e30;&#xA;my $START   = $opt_m ? $opt_m : 0;&#xA;    my $END     = $opt_n ? $opt_n : 1e30;&#xA;&#xA;my ($Query, $Sbjct);&#xA;my $HSP = &quot;&quot;;&#xA;    while (&amp;lt;&amp;gt;) {&#xA;        if    (/^Query=\s+(\S+)/) {outputHSP(); $Query = $1}&#xA;        elsif (/^&amp;gt;(\S+)/)         {outputHSP(); $Sbjct = $1}&#xA;        elsif (/^ Score = /) {&#xA;            outputHSP();&#xA;            my @stat = ($_);&#xA;            while (&amp;lt;&amp;gt;) {&#xA;                last unless /\S/;&#xA;                push @stat, $_&#xA;            }&#xA;            my $stats = join(&quot;&quot;, @stat);&#xA;            my ($bits) = $stats =~ /(\d\S+) bits/;&#xA;            my ($expect) = $stats =~ /Expect\S* = ([\d\.\+\-e]+)/;&#xA;	     	$expect = &quot;1$expect&quot; if $expect =~ /^e/;&#xA;            my ($match, $total, $percent) = $stats =~ /Identities = (\d+)\/(\d+) \((\d+)%\)/;&#xA;            my $mismatch = $total - $match;&#xA;&#xA;        $HSP = {bits =&amp;gt; $bits, &#xA;                    expect =&amp;gt; $expect, &#xA;                    mismatch =&amp;gt; $mismatch, &#xA;                    percent =&amp;gt; $percent, &#xA;                    q_begin =&amp;gt; 0, &#xA;                    q_end =&amp;gt; 0, &#xA;                    q_align =&amp;gt; 0, &#xA;                    s_begin =&amp;gt; 0, &#xA;                    s_end =&amp;gt; 0, &#xA;                    s_align =&amp;gt; &quot;&quot;};&#xA;        }&#xA;        elsif (/^Query:\s+(\d+)\s+(\S+)\s+(\d+)/) {&#xA;            $HSP-&amp;gt;{q_begin}  = $1 unless $HSP-&amp;gt;{q_begin};&#xA;            $HSP-&amp;gt;{q_end}    = $3;&#xA;            $HSP-&amp;gt;{q_align} .= $2;&#xA;        }&#xA;        elsif (/^Sbjct:\s+(\d+)\s+(\S+)\s+(\d+)/) {&#xA;            $HSP-&amp;gt;{s_begin}  = $1 unless $HSP-&amp;gt;{s_begin};&#xA;            $HSP-&amp;gt;{s_end}    = $3;&#xA;            $HSP-&amp;gt;{s_align} .= $2;&#xA;    }&#xA;}&#xA;outputHSP();&#xA;&#xA;sub outputHSP {&#xA;    return unless $HSP;&#xA;        return if $HSP-&amp;gt;{percent}  &amp;lt; $PERCENT;&#xA;        return if $HSP-&amp;gt;{bits}     &amp;lt; $BITS;&#xA;        return if $HSP-&amp;gt;{expect}   &amp;gt; $EXPECT;&#xA;        return if ($HSP-&amp;gt;{q_begin} &amp;lt; $START or $HSP-&amp;gt;{q_end} &amp;lt; $START);&#xA;        return if ($HSP-&amp;gt;{q_begin} &amp;gt; $END   or $HSP-&amp;gt;{q_end} &amp;gt; $END);&#xA;        foreach my $field ('percent', 'q_align', 'mismatch', 's_align', 'q_begin', 'q_end', 's_begin', 's_end', 'expect', 'bits'){&#xA;        print &quot;$field not defined\n&quot; if not defined $HSP-&amp;gt;{$field};&#xA;        }&#xA;        print join(&quot;\t&quot;, $Query, $Sbjct, $HSP-&amp;gt;{percent}, length($HSP-&amp;gt;{q_align}), $HSP-&amp;gt;{mismatch}, countGaps($HSP-&amp;gt;{q_align}) + countGaps($HSP-&amp;gt;{s_align}), $HSP-&amp;gt;{q_begin}, $HSP-&amp;gt;{q_end}, $HSP-&amp;gt;{s_begin}, $HSP-&amp;gt;{s_end}, $HSP-&amp;gt;{expect}, $HSP-&amp;gt;{bits}), &quot;\n&quot;;&#xA;    $HSP = &quot;&quot;;&#xA;}&#xA;&#xA;sub countGaps {&#xA;    my ($string) = @_;&#xA;        my $count = 0;&#xA;    while ($string =~ /\-+/g) {$count++}&#xA;        return $count;&#xA;}&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-03-21T01:03:53.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30619" PostTypeId="2" ParentId="30616" CreationDate="2015-03-21T01:14:08.860" Score="4" Body="&lt;p&gt;Very basically, what they've done in the paper was incubate different DNA sequences with histone octamers which were then separated on a gel. From this they could measure the ratio between nucleosomal and free DNA, which represents an equilibrium constant. This can then be expressed as a change in free energy ($\Delta G=-RTln(K)$), which is what the table shows. A lower (more negative) free energy change corresponds to a higher equilibrium constant which represents a greater proportion of DNA bound to histones. In other words, the free energy change quantifies the propensity of these different DNA sequences to form nucleosomes. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-03-21T01:22:05.293" LastActivityDate="2015-03-21T01:22:05.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30620" PostTypeId="2" ParentId="30617" CreationDate="2015-03-21T01:24:45.487" Score="0" Body="&lt;p&gt;That sounds pretty good. On this kind of things wikipaedia is very reliable.&#xA;You can also look at this very synthetic page: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.enotes.com/homework-help/distinguish-between-synapomorphy-apomorphy-304128&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.enotes.com/homework-help/distinguish-between-synapomorphy-apomorphy-304128&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="14615" LastEditorUserId="14615" LastEditDate="2017-05-17T12:34:21.477" LastActivityDate="2017-05-17T12:34:21.477" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30622" PostTypeId="1" AcceptedAnswerId="46061" CreationDate="2015-03-21T04:14:51.720" Score="7" ViewCount="741" Body="&lt;p&gt;The 3C (chromosome conformation capture) technology for studying chromatin 3D organization starts by a cross-linking step using formaldehyde to find segments of DNA interacting. In my understanding the cross-linking happens &lt;strong&gt;only&lt;/strong&gt; between the DNA and proteins forming a DNA-protein-DNA complex. The &quot;only&quot; is from a DNA stand-point as of course protein-protein cross-links will also occur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can formaldehyde cross-link two double stranded DNA molecules? Is the 3C approach also capturing direct DNA-DNA interactions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I looked at the literature, especially &lt;a href=&quot;http://www.sciencemag.org/content/295/5558/1306.long&quot;&gt;Dekker et al.&lt;/a&gt; description of the method, but couldn't find this information. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-21T05:10:37.277" LastActivityDate="2016-05-11T15:26:51.350" Title="DNA-DNA cross-linking with formaldehyde?" Tags="&lt;dna&gt;&lt;structural-biology&gt;&lt;chromatin&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30623" PostTypeId="1" CreationDate="2015-03-21T05:36:22.900" Score="3" ViewCount="60" Body="&lt;p&gt;In the case of a gene therapy trial where viral vectors are used to deliver genes into mammalian cells, including humans, should biosafety and ethical protocols include isolation of the patient as a precaution post administration that the viral vector may recover its ability to cause disease and harm the environment (more so the patient as the animals tested can be destroyed by incineration)? And how long should that isolation stay be to ensure safe disarmament of the viral vector?&lt;/p&gt;&#xA;" OwnerUserId="9748" LastActivityDate="2015-05-02T06:10:16.450" Title="Should gene therapy safety protocol include isolation?" Tags="&lt;molecular-genetics&gt;&lt;pathology&gt;&lt;virology&gt;&lt;lentivirus&gt;" AnswerCount="0" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="30625" PostTypeId="1" CreationDate="2015-03-21T12:36:10.420" Score="3" ViewCount="64" Body="&lt;p&gt;I'm an undergraduate computer engineering student, and I have a project about bioinformatics. In this manner, I need to find prediction( or association I'm not sure the correct terminology) confidence of miRNA disease relationships. Let me make more clear my question with an example. For instance, in one of the bioinformatics related databases( HMDD) it is said that, miRNA X is related with disease Y. I want to find that what is the confidence. I mean  you're 100% sure about such releationship? Do you know any database for that purpose? In HMDD I can only find miRNA - disease name couples it does not give any statistics. &lt;/p&gt;&#xA;" OwnerUserId="14759" LastEditorUserId="14709" LastEditDate="2015-03-22T13:29:30.980" LastActivityDate="2016-04-26T06:32:57.247" Title="Finding confidence level of miRNA disease associations" Tags="&lt;bioinformatics&gt;&lt;pathology&gt;&lt;rna&gt;&lt;genomics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30626" PostTypeId="2" ParentId="30610" CreationDate="2015-03-21T12:51:05.190" Score="1" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Action potentials are always generated after a depolarization step.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Action potentials are generated by prior depolarization of a neuron, typically by the action of an excitatory neurotransmitter. An action potential is per definition a sharp depolarization, followed by a somewhat slower re-polarization step. The most important step in an action potential is the activation of voltage-gated sodium channels (VGSCs). VGSCs open when the membrane potential exceeds a certain voltage upon depolarization (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23095258&quot; rel=&quot;nofollow noreferrer&quot;&gt;Liu et al. 2012&lt;/a&gt;), in turn initiating the depolarization step of the action potential. Hence, action potentials are always generated through depolarization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only ion channel I am aware of that may mediate a hyperpolarization-induced cation influx resembling that seen in VOSCs is the hyperpolarization-activated cyclic nucleotide-gated (HCN) class of channels. The associated current (I&lt;sub&gt;h&lt;/sub&gt;) is a non-specific cation flux (Na&lt;sup&gt;+&lt;/sup&gt;, Ca&lt;sup&gt;2+&lt;/sup&gt;). The HCN channel opens when the membrane potential hyperpolarizes. Thereby it generates a relatively small positive, depolarizing influx current. it is mainly involved in setting the frequency of pacemaker activity in, e.g., thalamic relay neurons that are involved in the oscillatory cortical activity characteristic of slow-wave sleep. However, I&lt;sub&gt;h&lt;/sub&gt; itself does not elicit spikes, it generates excitatory postsynaptic currents (EPSCs) associated with excitatory postsynaptic potentials (EPSPs), but not full blown spikes &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181775/&quot; rel=&quot;nofollow noreferrer&quot;&gt;(McCormick &amp;amp; Pape, 1990)&lt;/a&gt;.&lt;br&gt;&#xA;&lt;br&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Model evaluation and recommendations&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Perhaps you identified EPSPs as action potentials? They are not.  &lt;/li&gt;&#xA;&lt;li&gt;Your resting membrane potential is very high (depolarized) - a more typical value is &lt;a href=&quot;http://www.columbia.edu/cu/psychology/courses/1010/mangels/neuro/neurosignaling/neurosignaling.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;-70 mV&lt;/strong&gt;&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;VOSCs are opened at around &lt;a href=&quot;http://www.columbia.edu/cu/psychology/courses/1010/mangels/neuro/neurosignaling/neurosignaling.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;-50 mV&lt;/strong&gt;&lt;/a&gt;, hence your resting membrane potential is awfully close to action potential threshold. Any small perturbation leading to a bit cation influx will trigger action potentials. With a bit of stochastic leak currents included, a spontaneous spiking neuron is what you get. I&lt;sub&gt;h&lt;/sub&gt; (-like) activity may also set the stage for your out-of-the-ordinary observation.&lt;/li&gt;&#xA;&lt;li&gt;Suggestion - lower your resting membrane potential to a more conservative value (-70 mV) and check the difference between EPSPs and action potentials. If you look at the following figure you can see that at your chosen resting membrane potential you are hovering between EPSP / actin potential threshold. A bi-stable situation results.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SyXci.jpg&quot; alt=&quot;AP vs EPSP&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Action potential versus EPSP. &lt;a href=&quot;http://what-when-how.com/neuroscience/synaptic-transmission-the-neuron-part-1/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source: What when and how&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23095258&quot; rel=&quot;nofollow noreferrer&quot;&gt;Liu et al. &lt;em&gt;BMC Neurosci&lt;/em&gt; 2012;&lt;strong&gt;25&lt;/strong&gt;:2-9&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1181775/&quot; rel=&quot;nofollow noreferrer&quot;&gt;McCormick &amp;amp; Pape. &lt;em&gt;J Physiol&lt;/em&gt; 1990;&lt;strong&gt;431&lt;/strong&gt;:291-318&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-21T13:17:47.930" LastActivityDate="2015-03-21T13:17:47.930" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30627" PostTypeId="2" ParentId="30566" CreationDate="2015-03-21T13:33:35.050" Score="2" Body="&lt;p&gt;No. To determine the genetic relationship (if any) between two individuals requires molecular evidence based on genetic markers in their somatic DNA. Using phenotypes &lt;em&gt;could&lt;/em&gt; be misleading because a genetic marker (an allele) can have variable penetrance (the percentage of carriers who actually have the phenotype) &lt;em&gt;and&lt;/em&gt; variable expressivity (the severity or degree of the phenotype). Some of this variability can come from gene-environment interactions, and some could come from epigenetic effects (ie non-heritable).&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-03-21T13:33:35.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30628" PostTypeId="1" AcceptedAnswerId="30633" CreationDate="2015-03-21T15:27:08.780" Score="12" ViewCount="1428" Body="&lt;p&gt;Why do many plants produce such large fruits(apples and strawberries,for example) if those contain only relatively small seeds? &lt;/p&gt;&#xA;" OwnerUserId="15039" LastEditorUserId="24354" LastEditDate="2020-05-09T13:33:59.433" LastActivityDate="2020-05-09T13:33:59.433" Title="Why are fruits so large compared to their seeds?" Tags="&lt;botany&gt;&lt;fruit&gt;&lt;agriculture&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30630" PostTypeId="1" AcceptedAnswerId="34205" CreationDate="2015-03-21T16:58:16.627" Score="4" ViewCount="1403" Body="&lt;p&gt;The (human) genetic code encodes 20 amino acids. They form a protein using peptide bonds. Each amino acid has a carboxyl group (COOH) and an amino group (NH&lt;sub&gt;2&lt;/sub&gt;) that can potentially form a peptide bond. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/O2Vp5.jpg&quot; alt=&quot;enter image description here&quot;&gt;  &lt;br&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: &lt;a href=&quot;http://cultureofchemistry.fieldofscience.com/2010/12/calm-amino-acids.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Culture of Chemistry&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this property of amino acids means that each amino acid can form a peptide bond in any combination? In other words, are there certain amino acid doublets in existence that never pair up? &lt;/p&gt;&#xA;" OwnerUserId="14586" LastEditorUserId="3340" LastEditDate="2015-03-25T07:04:26.333" LastActivityDate="2015-05-13T04:21:37.947" Title="Amino acid compatibility" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;amino-acids&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30632" PostTypeId="2" ParentId="30628" CreationDate="2015-03-21T18:50:50.207" Score="2" Body="&lt;p&gt;Because seeds are not appealing to animals and they can only be carried by animals if they are made appealing - there are exceptions of course such as &lt;a href=&quot;http://antranik.org/wp-content/uploads/2011/06/cockleburs-fruits-1024x957.jpg?9873a6&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt; -. Seeds are covered with juicy layers that can be nutrient to animals in order to be made appealing and to be dispersed. Animals eat those juicy layers along with seeds, seeds resist digestion and fall on the ground where animals defecate. If the layer was thin and provided only protection to seeds, animals would not eat them and the seeds would have to be dispersed by other means. Therefore we would not call them fruits. The reason why seeds are not as large as their fruits is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;They have to be dry to resist climate changes while staying dormant below ground. And dry is generally small.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Seeds' task is to be dispersed, not to be nutritious to animals. And they usually do not taste very  well compared to fruits - some do taste well as we know but I do not know why -. So why make them large and irritate the animal? Make them small so they will be overlooked by the animal and be dispersed happily&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1843" LastActivityDate="2015-03-21T18:50:50.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30633" PostTypeId="2" ParentId="30628" CreationDate="2015-03-21T19:00:08.863" Score="14" Body="&lt;p&gt;The short answer: Fruits are large compared to seeds because humans have made them large. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the natural environment, there is a different set of evolutionary pressures. A fruit has to be able to successfully propagate itself using its seeds, while commercially farmed fruit is usually cloned via vegetative propagation. Therefore, the commercial farmed fruits do not need large seeds to propagate, since they are cloned by the farmers. In many cases, their seeds are actually nonviable (i.e. they will not grow when planted). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, this is a wild banana, before being selectively bred by humans. As you can see here, the seeds are enormous compared to those in commercial Cavendish bananas. &#xA;&lt;img src=&quot;https://i.stack.imgur.com/SpTOJm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/UtYurm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, this is a wild strawberry compared to its commercial farmed variant. &#xA;&lt;img src=&quot;https://i.stack.imgur.com/OjBLfm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/wwuKRm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fruits with large seeds don't appeal to consumers, and therefore farmers who sell fruits with large seeds will get a poorer return on investment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, farmers who plant the fruits which appeal the best to consumers by being the easiest to eat (small seeds) will reap the greatest profits. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-03-22T11:43:45.757" LastActivityDate="2015-03-22T11:43:45.757" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30634" PostTypeId="2" ParentId="6915" CreationDate="2015-03-21T19:24:34.987" Score="3" Body="&lt;p&gt;In addition to cultural preferences and psychological factors, there may be some evolutionary basis in this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cooking food is a relatively new development and unique to the &lt;em&gt;Homo spp.&lt;/em&gt; line. It makes sense that the tongue/mouth may be more sensitive to cooler temperatures than warm temperatures, given the amount of actual exposure it is given to sunlight and/or objects (across all species).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is perhaps supported by the concentration of various receptor channels, TRPV1-4, TRPA1 and TRPM8, which are each sensitive/activated across various temperature ranges. TRPV3 operates through a range close to body temp. and has been associated with taste perception. One could hypothesise that in the mouth there is a greater concentration of cold-sensitive channels (such as TRPA1 and TRPM8) than warm ones, thus cold is perceived more readily and the addition of 'taste' channels (TPRV3) may contribute to the preference for cool water over say luke warm/room temp. water. This thinking falls down when we think of the amount of hot food we eat and can of course taste, in addition to the many studies conducted on taste perception, however this entire answer is very rudimentary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't found literature detailing the relative proportions of said channels, however, this makes for an interesting read: &lt;a href=&quot;http://www.mnf.uni-greifswald.de/fileadmin/Zoologisches_Museum/Hildebrandt/Dokumente/schepers10.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.mnf.uni-greifswald.de/fileadmin/Zoologisches_Museum/Hildebrandt/Dokumente/schepers10.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user15037" LastEditorDisplayName="user15037" LastEditDate="2015-03-22T17:09:41.140" LastActivityDate="2015-03-22T17:09:41.140" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30637" PostTypeId="1" CreationDate="2015-03-21T22:46:54.070" Score="4" ViewCount="89" Body="&lt;p&gt;I have ordered 36bp oligonucleotides that anneal to each other and create sticky ends to be cloned in a vector afterwards. I have tried cloning many times with different methods and I failed. Now I started to think that my oligos are actually shorter than 36 nt since desalting is not an effective method and most of my oligos do not create complete sticky ends when they anneal to each other. I believe I have also found &lt;a href=&quot;http://www.sigmaaldrich.com/technical-documents/articles/biology/best-purification.html&quot; rel=&quot;nofollow&quot;&gt;support for this&lt;/a&gt;. So, how much is it possible that most of my oligos are actually shorter than 36 nt ? Is this a good troubleshooting or 36 nt oligos not being purified with more efficient method should not really create a problem? &lt;/p&gt;&#xA;" OwnerUserId="1843" LastActivityDate="2015-03-22T00:45:20.093" Title="Oligonucleotide purification with desalting" Tags="&lt;molecular-biology&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30638" PostTypeId="1" CreationDate="2015-03-21T23:06:39.670" Score="0" ViewCount="63" Body="&lt;p&gt;I was doing an initial search on google but couldn't come up with anything I'm looking for. I know were stem cells come from and a bit about their levels of differentiation. For example, embryonic stem still becoming mesenchymal stem cells and what not. I also understand that epithelial tissue cells can be converted to a pluripotent stem cell state but at very low efficiency. So, all that aside how are stem cells obtained in the volumes necessary for stem cell based therapies without causing them to start differentiating during production?&lt;/p&gt;&#xA;" OwnerUserId="10026" LastActivityDate="2015-10-15T03:36:43.193" Title="How are Stem Cells Produced for Stem Cell Based Therapies?" Tags="&lt;biotechnology&gt;&lt;stem-cells&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30639" PostTypeId="2" ParentId="30637" CreationDate="2015-03-22T00:45:20.093" Score="2" Body="&lt;p&gt;Oligos from well-known companies are pretty good to my knowledge. Problems begin after 100-300bp oligos/dsDNA fragments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I suggest is PCRing your vector like that:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;          Primer F: ---------------------__________&#xA;vector: ======|v site for 36 bp insert v|==========...&#xA;        Upstream                        Downstream&#xA;        ______----------------- : primer R&#xA;&#xA;Legend:     &#xA;__ portion of primer annealing to vector&#xA;-- portion that is your insert of interest&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Then you can actually just transform that PCR into e. coli, which will seal two nicks together and propagate your vector. Treating your PCR reaction with Dpn enzyme will ensure that all template DNA is removed.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-03-22T00:45:20.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30641" PostTypeId="2" ParentId="30628" CreationDate="2015-03-22T03:32:16.883" Score="0" Body="&lt;p&gt;Most fruit/seed evolution is probably a reflection of the plants propagation strategy and any existing symbiotic forager relationship. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The strawberry expands its range by creeping with feeder shoots. It is also heavily foraged by small birds , thus the exterior small seeds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nut trees i.e. walnuts , are on the other end of the spectrum. The seed is nearly the size of the &quot;fruit&quot;. All they want is some little squirrel to shake them loose and fall to the ground, then try to outgrow everything else.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;cherries....&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just making all this up.&lt;/p&gt;&#xA;" OwnerUserId="15048" LastActivityDate="2015-03-22T03:32:16.883" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30642" PostTypeId="1" CreationDate="2015-03-22T03:49:15.750" Score="3" ViewCount="1764" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TBvzw.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a native gel. Let's call the left 2 lanes protein A and the right 2 lanes protein B. B is the same as A except it has a FLAG tag. They are both homotetramers of about 65 kDa. After purification, both appeared as single bands on SDS-PAGE. However, these are relatively old samples and I expect multiple bands due to degradation (which I've observed with previous samples). Either way, I cannot for the life of me resolve them with native PAGE. B is somewhat workable, though still atrocious. For each of A and B, I've loaded 5 and 15 uL (hence why there are two lanes for each) with 5 uL of 5X loading buffer. Yes, I know that's not the correct ratio; I can't imagine that being my problem but I'm running it again with the correct ratio. The rest of the conditions are pretty standard:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The protein was in PBS (50 mM dibasic sodium phosphate, 75 mM NaCl, pH~7.3) prior to adding loading buffer; I've also used TBS (50 mM Tris, 7.5 mM NaCl, pH~7.4) with similar results &lt;/li&gt;&#xA;&lt;li&gt;4% stacking gel, pH=6.8&lt;/li&gt;&#xA;&lt;li&gt;6% resolving, pH=8.8&lt;/li&gt;&#xA;&lt;li&gt;Tris-glycine running buffer, pH~8.3, ran at 4°C with 23 mA constant current. I've also ran at 30 mA with similar results. &lt;/li&gt;&#xA;&lt;li&gt;Stained with Coomassie&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Let me know if any other info is needed. Any advice will be greatly appreciated. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-03-22T03:49:15.750" Title="Can't resolve protein with native PAGE" Tags="&lt;proteins&gt;&lt;gel-electrophoresis&gt;&lt;experimental-design&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30643" PostTypeId="2" ParentId="30630" CreationDate="2015-03-22T06:22:15.747" Score="9" Body="&lt;p&gt;It seems like you may be thinking along the lines of DNA, where adenine pairs only with thymine and guanine with cytosine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unlike DNA, amino acid chains are single-stranded...&lt;img src=&quot;https://i.stack.imgur.com/awhY7.jpg&quot; alt=&quot;example chain of amino acids, aka a polypeptide chain&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;...so there is no pairing of compatible types like there is in DNA. &lt;em&gt;Neighboring&lt;/em&gt; amino acids in the chain can be in any combination (as you say, because each has a carboxyl group and an amino acid group), just as neighboring nucleotides in DNA (ie those next to, not across from, each other) can come in any order.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practical terms, the functional groups of amino acids have different chemical properties (hydrophobic, hydrophilic, aromatic), therefore some pairings are probably more commonly found than others. But in principle there is no restriction on who is next to who.&lt;/p&gt;&#xA;" OwnerDisplayName="user15049" LastActivityDate="2015-03-22T06:22:15.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30645" PostTypeId="1" AcceptedAnswerId="30646" CreationDate="2015-03-22T07:46:58.267" Score="5" ViewCount="551" Body="&lt;p&gt;What I'm actually interested about is whether a modification in one cell during the life of an &lt;strong&gt;asexually&lt;/strong&gt; reproducing organism affects its genetic information? Which cell's genetic information is used during reproduction like budding, for example in the case of &lt;em&gt;Hydra&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or does the incidental advantage it could have given rise to disappear with the death of the organism? &lt;/p&gt;&#xA;" OwnerUserId="15051" LastEditorUserId="15051" LastEditDate="2015-03-22T22:10:34.410" LastActivityDate="2015-03-23T20:06:15.613" Title="Do changes in an organism's cell modify the genetic information it uses for reproduction?" Tags="&lt;dna&gt;&lt;reproduction&gt;&lt;cell&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30646" PostTypeId="2" ParentId="30645" CreationDate="2015-03-22T08:23:50.953" Score="6" Body="&lt;p&gt;In multicellular organisms there are specialised cells called gametes that are responsible for sexual reproduction (sperm/ egg cells). Mutations occurring in these cells can be passed on to offspring (germ line mutations). Mutations occurring in others cells affect only the given individual (somatic mutations).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&#xA;For unicellular organisms it is pretty straight forward, the daughter cells formed through fission are identical. As for multicellular organisms here are many forms of asexual reproduction, and even these may involve the formation of specialized cells (eg. spores). So my answer is: it depends on the type of asexual reproduction and the actual cell(s) that accumulate mutation(s). For example in parthenogenesis - where the unfertilized egg cell develops into a new individual - , a mutation can be inherited if it occurs in the germ line cells generating the egg cell, but any somatic mutation would stay in the parent. You can find detailed info on asexual reproduction with details on each form on &lt;a href=&quot;http://en.wikipedia.org/wiki/Asexual_reproduction&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; wiki page&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-03-23T20:06:15.613" LastActivityDate="2015-03-23T20:06:15.613" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30648" PostTypeId="2" ParentId="9075" CreationDate="2015-03-22T13:22:16.497" Score="2" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Adverse stimuli in general are accompanied by contraction of facial muscles. It is part of our repertoire of emotional expressions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;A &lt;strong&gt;disgusted&lt;/strong&gt; expression and the expression of &lt;strong&gt;pain&lt;/strong&gt; are both accompanied by &lt;strong&gt;squinting&lt;/strong&gt;. Disgusting stimuli include your example of a sour taste, but also include other adverse tastes (bitter) or visual stimuli such as a gross-looking objects. In other words, squinting is likely a common way of expressing &lt;strong&gt;adverse stimuli&lt;/strong&gt;. So the &quot;&lt;strong&gt;sour look&lt;/strong&gt;&quot; may not be easily explained on its own. Instead, it is part of a huge emotional expressive repertoire that makes us human beings. To be able to read these expressions allows us to be empathetic towards others. People with autism and Asperger's syndrome may not be able to do so and are disadvantaged in their social behaviors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To illustrate the commonalities between sour (#1), disgust (#2) and pain (#3) I would like to share the following web finds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3KRDY.jpg&quot; alt=&quot;Sour&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;strong&gt;Sour taste&lt;/strong&gt;. Source: &lt;a href=&quot;http://www.gettyimages.com.au/detail/photo/young-girl-making-sour-face-royalty-free-image/83822898&quot; rel=&quot;nofollow noreferrer&quot;&gt;Getty Images&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kMmAY.jpg&quot; alt=&quot;disgust&quot;&gt;!&lt;br&gt;&#xA;&lt;sup&gt;&lt;strong&gt;Disgust&lt;/strong&gt;. Source: &lt;a href=&quot;http://greatergood.berkeley.edu/ei_quiz/#10&quot; rel=&quot;nofollow noreferrer&quot;&gt;Berkeley Emotional IQ test&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WVSRu.jpg&quot; alt=&quot;pain&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;strong&gt;Pain&lt;/strong&gt;. Source: &lt;a href=&quot;http://greatergood.berkeley.edu/ei_quiz/#10&quot; rel=&quot;nofollow noreferrer&quot;&gt;Berkeley Emotional IQ test&lt;/a&gt;&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;PS&lt;/strong&gt;: I am not a psychologist - Consider my contribution as an educated guess.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-23T12:56:37.577" LastActivityDate="2015-03-23T12:56:37.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30649" PostTypeId="1" AcceptedAnswerId="30650" CreationDate="2015-03-22T15:00:10.980" Score="2" ViewCount="5207" Body="&lt;p&gt;When you contract your muscle, will your muscle spindle stretch or contract? And why? I was always under the impression that it was contracting your muscle spindle, but now I am not sure.&lt;/p&gt;&#xA;" OwnerUserId="15055" LastEditorUserId="6289" LastEditDate="2015-03-22T16:10:26.557" LastActivityDate="2015-03-22T16:10:26.557" Title="When contracting a muscle will the muscle spindle stretch or contract?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30650" PostTypeId="2" ParentId="30649" CreationDate="2015-03-22T15:16:13.610" Score="7" Body="&lt;p&gt;The muscle spindle normally stretches/contracts in concert with the muscle fibres in order to maintain detection of changes in length.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This image should demonstrate it clearly:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/avbcF.jpg&quot; alt=&quot;Alpha-gamma coactivation&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When the muscle spindle is stretched and excited it sends impulses to the spinal cord more rapidly (increased frequency). The sensory neurons synapse with alpha motor neurons in the spinal cord, which stimulate the extrafusal muscle fibers of the stretched muscle to contract and resist further stretching.&#xA;  Contraction of the muscle (extrafusal fibers) would cause the muscle spindle to become slack and stop transmitting impulses, however descending fibers of motor pathways synapse with both alpha and gamma motor neurons (alpha - gamma coactivation) so the ends of the intrafusal fibers contract and maintain muscle spindle sensitivity when the muscle contracts.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Further reading: &lt;a href=&quot;http://classes.midlandstech.edu/carterp/Courses/bio210/chap13/lecture1.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerDisplayName="user15037" LastEditorDisplayName="user15037" LastEditDate="2015-03-22T15:26:14.247" LastActivityDate="2015-03-22T15:26:14.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30651" PostTypeId="1" AcceptedAnswerId="30673" CreationDate="2015-03-22T15:19:39.330" Score="7" ViewCount="429" Body="&lt;p&gt;I'm trying to understand naming convention of miRNAs. I've found the wikipedia article about it &lt;a href=&quot;http://en.wikipedia.org/wiki/MicroRNA#Nomenclature/&quot;&gt;nomenclature&lt;/a&gt; Based on it, I try to figure out what is &lt;strong&gt;hsa-let-7a&lt;/strong&gt;. As far as I understood, hsa refers to human but I expected a &quot;&lt;em&gt;mir&lt;/em&gt;&quot; or &quot;&lt;em&gt;miR&lt;/em&gt;&quot; after hsa but there is a word &quot;&lt;em&gt;let&lt;/em&gt;&quot; .So my question is that hsa-let-7a is a name for a single mature miRNA or is it a name of a miRNA family(if there exists such a thing) ?  &lt;/p&gt;&#xA;" OwnerUserId="14759" LastEditorUserId="14759" LastEditDate="2015-03-22T15:24:53.460" LastActivityDate="2015-03-30T04:51:56.077" Title="Naming convention of miRNAs" Tags="&lt;rna&gt;&lt;microrna&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30652" PostTypeId="1" AcceptedAnswerId="48047" CreationDate="2015-03-22T16:36:40.957" Score="8" ViewCount="312" Body="&lt;p&gt;What does a genomic code for nucleosome positioning in eukaryotes actually mean? By the code is it right to think that specific DNA sequences favour nucleosomes and others don't? I see that there for and against arguments on this topic. What is the current view on this topic? &lt;/p&gt;&#xA;" OwnerUserId="5669" LastEditorUserId="5669" LastEditDate="2015-03-22T16:44:33.820" LastActivityDate="2016-06-14T16:03:00.767" Title="Is there a genomic code for nucleosome positioning?" Tags="&lt;genetics&gt;&lt;epigenetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30653" PostTypeId="1" CreationDate="2015-03-22T16:44:47.243" Score="2" ViewCount="69" Body="&lt;p&gt;What I'm interested about is whether environmental changes' effects are coded into the genome, like metamorphosis, deciduous plants. Can it be explained by morphogens, or it's something completely different?&lt;/p&gt;&#xA;" OwnerUserId="15051" LastEditorUserId="15051" LastEditDate="2015-03-22T20:36:46.347" LastActivityDate="2015-03-22T20:36:46.347" Title="Is the &quot;concept of time&quot; coded into the genome?" Tags="&lt;genomes&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2015-03-22T19:15:16.577" ContentLicense="CC BY-SA 3.0" />
  <row Id="30655" PostTypeId="2" ParentId="30652" CreationDate="2015-03-22T18:30:58.607" Score="4" Body="&lt;p&gt;There are definitely genomic DNA sequences that nucleosomes preferentially package in vitro. They are A/T rich and have a periodic structure that facilitates bending.  However such sequences would typically not be found on exons in vivo (because their protein-coding potential is reduced). Based on the accumulating literature, active promoters (and regions that will soon be activated) are usually Nucleosome-free, but I have yet to see evidence that this correlates with sequences that do not favour nucleosomes binding. These open areas are sensitive to DNase I, and the first nucleosomes downstream are phased.&#xA;For Epigenetic codes, people focus on the many post-translational modifications on the Histone tails.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-03-22T18:30:58.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30656" PostTypeId="1" CreationDate="2015-03-22T19:28:03.083" Score="2" ViewCount="74" Body="&lt;p&gt;&lt;strong&gt;How does one decide whether the presence of certain cell types is clinically important or negligible? Would the presence of certain cells in conjunction with other symptoms be enough, or should it be judged on relative proportions?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have arrived at a diagnosis for a case study (and I know it is correct) and am just reviewing what I have included and am beginning to question myself. I fear that I am making unnecessary tenuous connections to further support my conclusions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example, to put this into context:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A peripheral blood film has all the hallmarks of acute myeloid&#xA;leukaemia (AML), however, the film alone is not enough to confirm.&lt;/li&gt;&#xA;&lt;li&gt;In addition, have spotted &lt;em&gt;definitely one&lt;/em&gt;, &lt;em&gt;maybe two&lt;/em&gt;, dacrocytes (teardrop cell) on the film, these are not typically associated with AML as far as I am aware.&lt;/li&gt;&#xA;&lt;li&gt;Dacryocytes are not diagnostically indicative of any specific&#xA;condition.&lt;/li&gt;&#xA;&lt;li&gt;Dacrocytes are however present in several conditions that can&#xA;transform to AML.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, in this scenario, I feel it would be worth mentioning considering the clinical setting but the numbers just seem so insignificant that I am concerned it would appear as grasping, or a bit &lt;em&gt;through the grapevine&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any guidance in general is appreciated, I'm not looking for an answer to the provided example per se. &lt;/p&gt;&#xA;" OwnerDisplayName="user15037" LastActivityDate="2015-03-22T19:28:03.083" Title="How to gauge the clinical significance of specific cell type presence?" Tags="&lt;homework&gt;&lt;hematology&gt;&lt;pathophysiology&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30657" PostTypeId="2" ParentId="6915" CreationDate="2015-03-22T19:40:17.747" Score="14" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;: Cold is pleasant only when your are not already freezing and cold might satiate thirst better because it acts as enhancer of the &quot;water intake flow meter&quot;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is cold water more tasty than warm water?&lt;/strong&gt; No, it is actually the reverse as detailed in my footnote.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cold is pleasant when your body is over-heating and definitely not if you live naked in the North Pole. Over-heating means sweating which means you loose water and therefore feel thirsty faster. Yet drinking cold water will not rehydrate the body more than warm water and drinking water has only a very small impact on the body temperature. So why do we like it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A study was actually conducted on the subject and answers most of your questions. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0195666313003930#&quot; rel=&quot;noreferrer&quot;&gt;Here the reference&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The temperature of the body will indeed not change&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;cold stimuli applied to the mouth&#xA;  (internal surface of the body) do not appear to impact on body&#xA;  temperature and are not reported to cause any reflex shivering&#xA;  or skin vasoconstriction that influence body temperature.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As you pointed out, the temperature of the ingested water will &lt;strong&gt;not affect the overall hydration of the body&lt;/strong&gt; as cells are rehydrated mostly via the blood  stream and the blood temperature will not be affected. Someone could argue that, at identical volumes, cold water (above 4C) contains more molecules (i.e. is denser) than warm water but this difference is likely very slim.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this paper they also define &quot;thirst&quot;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Thirst is a homeostatic mechanism that regulates blood osmolarity&#xA;  by initiating water intake when blood osmolarity increases&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The problem is that it takes some time before the water reaches the blood stream, and therefore you need a feedback mechanism that tells you to stop drinking independently of the blood's osmolarity. This is where cold might play a role.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The cold stimulus to the mouth from ingestion of water may act&#xA;  as a satiety signal to meter water intake and prevent excessive&#xA;  ingestion of water&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The picture would then be the following&#xA;&lt;img src=&quot;https://i.stack.imgur.com/BgAON.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In essence, a cold sensation is pleasant in warm weather, both on the skin and in the mouth, and it apparently helps in reducing thirst by being some kind of an  enhancer of the &quot;water intake flow meter&quot;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Footnote&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reading the comments I just want to clarify some points.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The 5 basic tastes (sweet, salty, bitter, sour and umami) are very distinct from taste sensations (pungency, smoothness, cooling to name a few). The main difference is that taste and &quot;sensation&quot; signals use completely different paths to reach the brain - namely, the facial and glossopharyngeal nerves for the former and the trigeminal nerve for the latter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the temperature affecting basic taste perceptions? The answer is &lt;a href=&quot;http://www.nature.com/nature/journal/v438/n7070/full/nature04248.html&quot; rel=&quot;noreferrer&quot;&gt;yes&lt;/a&gt;. How this happens is quite simple if you understand the fundamental concepts of molecular taste perception. Essentially the temperature affects the response of the receptor TRPM5 which is the main player in depolarizing taste receptor cells in the papillae. To put it simply, higher temperatures provoke a greater perception for taste, and this is not only in term of perceived taste but really modifies the amplitude of the response at the molecular level. As an example this is why ice cream does not taste sweet when frozen but only after it melted in the mouth or on the tongue.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="20317" LastEditDate="2016-03-19T23:34:57.027" LastActivityDate="2016-03-19T23:34:57.027" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30658" PostTypeId="2" ParentId="30351" CreationDate="2015-03-22T21:26:28.470" Score="3" Body="&lt;p&gt;The inclusion of formaldehyde in the gel and buffer is to keep the RNA denatured (ie after heating the sample to melt the double-stranded stem-loops, just prior to loading the gel), in the hope that the RNA will migrate through the gel with an Rf proportional to its molecular weight (approximated here by its length). Therefore the correct size markers would also be made of RNA (and prepared the same way, by heating).&#xA;It is difficult to predict, a priori, how a double-stranded DNA fragment would migrate under similar conditions, without also including a lane of ds DNA size markers.&#xA;In other words I would only use DNA markers for DNA and RNA markers for RNA. By repeating this experiment (1 lane of DNA MW vs 1 lane of RNA MW) at different voltage gradients and different concentrations of agarose, you might be able to plot two standard curves that would let you predict where your DNA fragment is expected to migrate relative to the RNA transcript, but without that data I would not assume that a larger DNA fragment would run slower than its RNA transcript.&#xA;Even if the dsDNA was exactly the same length as the ssRNA (and pretending that the MW of the dNTPs and NTPs are identical), the DNA's MW would be &lt;em&gt;twice&lt;/em&gt; as much as the RNA, but the negative charge on the DNA would also be &lt;em&gt;twice&lt;/em&gt; as much.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-03-22T21:26:28.470" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30659" PostTypeId="2" ParentId="28619" CreationDate="2015-03-22T21:39:32.853" Score="1" Body="&lt;p&gt;If I understand correctly you are preparing your cloning vector by digesting it with two enzymes that are 31 bp apart. If you have a high background of recircularized vector see if there is a unique restriction enzyme site within that 31 bp.  If there is, and if the fragment you are trying to insert also lacks that site, then a simple approach would be to inactivate the ligase, and digest the reaction with the third enzyme.  That should drastically reduce the background of recircularized vector.&#xA;If after gel purifying the vector backbone after the double-digestion, you get a  significant background of recircularization, then you can easily test your hypothesis about ligase ligating mismatched sticky ends: both of the starting sites should be gone and any sites in-between them should be gone.  Have you tested this?&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="14946" LastEditDate="2015-03-22T21:45:35.217" LastActivityDate="2015-03-22T21:45:35.217" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30660" PostTypeId="2" ParentId="6915" CreationDate="2015-03-22T22:45:32.417" Score="0" Body="&lt;p&gt;The organism as a thermodynamic machine does need a coolant. The more difference in temperature the more efficiently thermal machine can use energy. Also in all processes in organism it is produced excessive thermal energy, which should be removed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus colder water and air are pleasant.&lt;/p&gt;&#xA;" OwnerUserId="408" LastActivityDate="2015-03-22T22:45:32.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30661" PostTypeId="1" AcceptedAnswerId="30680" CreationDate="2015-03-23T00:28:44.907" Score="1" ViewCount="42" Body="&lt;p&gt;If humans were to discover organisms on another planet, it is supposed that (unless both we and they were seeded by the same source) we would have nothing to fear from alien pathogens, as they would likely be totally incompatible with our &quot;brand&quot; of life here on Earth. This is due to a set of fundamental particulars not inherent in all possible biologies (as apposed to physics, where characteristics are more omni-present). I know, for example, that the left-handed chirality of amino acids marks one such trait. There appears to be no reason why life could not arise with the opposite orientation. My question is, what other particulars make up this set? &lt;/p&gt;&#xA;" OwnerUserId="15063" LastActivityDate="2015-03-23T09:23:26.900" Title="What factors, other than its homochirality, make our &quot;brand&quot; of biology unique?" Tags="&lt;evolution&gt;&lt;molecular-biology&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2015-03-23T10:02:09.127" ContentLicense="CC BY-SA 3.0" />
  <row Id="30662" PostTypeId="1" AcceptedAnswerId="30663" CreationDate="2015-03-23T01:09:05.747" Score="10" ViewCount="949" Body="&lt;p&gt;I'm a curious person, I've never had any medical training, but I wish to know some more about aneurysms. &lt;em&gt;Aneurysms&lt;/em&gt; are basically weakened spots in the elastic artery wall. This can eventually result in a blood-filled balloon bulging from the artery wall due to the high blood pressure in these vessels. Aneurysms can rupture and this can lead to brain damage when it occurs in the brain. Aneurysms can be detected by injecting contrast material into the bloodstream and making an X-ray (called an &lt;em&gt;angiogram&lt;/em&gt;). Now I was reading a wikipedia article about &lt;a href=&quot;http://en.wikipedia.org/wiki/Aneurysm&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;aneurysms&lt;/strong&gt;&lt;/a&gt; where I saw the following picture of an angiogram where reportedly an aneurysm should be visble:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UC5t7.jpg&quot; alt=&quot;aneurysm&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, as I said, I know nothing about biology so I would really appreciate it if someone could download the picture and reupload it with the aneurysm circled.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it the really dark spot or the big soft spot to the right? Thanks!&lt;/p&gt;&#xA;" OwnerUserId="15064" LastEditorUserId="9943" LastEditDate="2015-03-23T03:57:14.753" LastActivityDate="2015-03-23T12:38:24.613" Title="Where is the aneurysm in this picture?" Tags="&lt;hematology&gt;&lt;neuroanatomy&gt;&lt;circulatory-system&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30663" PostTypeId="2" ParentId="30662" CreationDate="2015-03-23T01:45:22.087" Score="9" Body="&lt;p&gt;Your image comes from the wiki page &lt;a href=&quot;http://en.wikipedia.org/wiki/Aneurysm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Aneurysm&lt;/a&gt;. The figure legend on the wiki page identifies it as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Angiography of an aneurysm in a cerebral artery&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am not an MD so I chose to first dig up a similar appearing cerebral angiography with the aneurysm identified (dark protruding spot indicated by the arrow):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lDuEI.png&quot; alt=&quot;aneurysm&quot;&gt;&lt;sup&gt;Source: &lt;a href=&quot;http://westjem.com/articles/posterior-communicating-artery-aneurysm-in-20-year-old-female-with-noonans-syndrome.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;WestJEM, UC Irvine&lt;/a&gt;&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taking into account the normal vasculature as seen on this graph from UC Irvine, and given the similarity between the identified aneurysm in this angiopgraph and your wiki angiograph, I tentatively have identified the red-encircled structure in your original image as an aneurysm:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JCWyp.png&quot; alt=&quot;wiki + identification&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-23T04:03:38.780" LastActivityDate="2015-03-23T04:03:38.780" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30664" PostTypeId="1" AcceptedAnswerId="30666" CreationDate="2015-03-23T02:47:13.240" Score="2" ViewCount="252" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lEHKN.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know some scientific rigorous way to look at a slice of meat. I am not asking what kind of meat it is or which part of the animal it came from. I wonder what is the different lining on the meat, what is that huge white spot in the middle and what do the cells of that red part look like and what they are called. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If someone can provide a reference on that it would be great.&lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="3624" LastEditDate="2015-03-23T10:04:49.463" LastActivityDate="2015-03-23T10:04:49.463" Title="Serious question about a piece of meat" Tags="&lt;anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30665" PostTypeId="1" CreationDate="2015-03-23T03:35:29.220" Score="4" ViewCount="908" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;In humans, the ability or inability to roll the tongue is a single&#xA;  gene trait.  The allele for tongue rolling (R) is dominant to the&#xA;  allele for not being able to roll the tongue (r).  Whether or not an&#xA;  individual can taste PTC is also an single gene trait.  The allele for&#xA;  being a taster (T) is dominants to the allele for not being able to&#xA;  taste PTC (t).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Claudia cannot roll her tongue but can taste PTC. Her mom also can taste PTC but her dad is not a taster. Claudia's grandparents were all unable to roll tongues.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1)  Based on the Info, what is Claudia's GENOTYPE?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know she is &quot;rr&quot; because she cannot roll her tongue and it is recessive. However; I do not know the complete genotype for the PTC taster.  I know it for sure is a &quot;T,&quot; but is it &quot;TT&quot; or &quot;Tt?&quot; How do we know? Do we have enough info to figure it out?&lt;/p&gt;&#xA;" OwnerUserId="14506" LastEditorUserId="14709" LastEditDate="2015-03-23T14:13:39.480" LastActivityDate="2015-03-23T14:13:39.480" Title="How to determine genotype?" Tags="&lt;genetics&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30666" PostTypeId="2" ParentId="30664" CreationDate="2015-03-23T03:48:08.737" Score="6" Body="&lt;p&gt;The white circle in the center is a bone, probably the femur. The muscles are covered with an external later of fascia, the epimysium (&lt;a href=&quot;https://biology.stackexchange.com/questions/19215/is-epimysium-same-as-fascia&quot;&gt;here's a question with some information&lt;/a&gt;). These layers separate muscles from each other, and often fat will also deposit in the spaces between muscles, which is what the white lines between muscle bellies are. There is also some cutaneous fat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is probably a section through the thigh, possibly a pig (though it looks a little too red). Regardless, the muscle will have the same basic layout as the &lt;a href=&quot;http://porcine.unl.edu/pages/index.jsp?what=crossectionD&amp;amp;sectionName=k&quot; rel=&quot;nofollow noreferrer&quot;&gt;image below of a pig thigh from pork.org&lt;/a&gt;, even if your image is from some other mammal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AGKgR.jpg&quot; alt=&quot;pork&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You have to rotate your image clockwise about 45 degrees to get them to match up. The back of the thigh is at the top of the image.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-03-23T03:48:08.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30667" PostTypeId="2" ParentId="30665" CreationDate="2015-03-23T03:48:17.023" Score="4" Body="&lt;p&gt;Claudia's dad is not a taster, so he is tt. He passes one allele on to his daughter. Since he is homozygous, he can only pass t. Claudia is a taster, so she must have the dominant allele from her mother, who is also a taster. Thus, Claudia is Tt. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-03-23T03:48:17.023" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30669" PostTypeId="1" AcceptedAnswerId="30671" CreationDate="2015-03-23T04:21:14.113" Score="3" ViewCount="1003" Body="&lt;p&gt;A phasic receptor by definition is one that quickly adapts to change. In terms of neuron firing, this means that it does not trigger another firing because the receptors are used to the stimulus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But when I place my fingers on my arm, I continuously feel pressure. Does this mean that skin receptors are only phasic in the sense that it will fire as soon as it is touched and does not prolong this touching sensation?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="9943" LastEditDate="2015-03-23T04:40:11.207" LastActivityDate="2015-03-23T04:41:48.157" Title="Why are skin tactile receptors considered to be phasic receptors?" Tags="&lt;neuroscience&gt;&lt;skin&gt;&lt;neurophysiology&gt;&lt;receptor&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30670" PostTypeId="1" CreationDate="2015-03-23T04:29:03.723" Score="-2" ViewCount="833" Body="&lt;p&gt;Male: Blood type O   (Genotype written as: i^o i^o since O allele is recessive to the A and B alleles).&#xA;Female: Blood type AB&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Draw a punnett square to show all of the possible offspring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I got Ai^o,  Ai^o,  Bi^o,  Bi^o)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the possible phenotypes for the children?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I got...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phenotypes: Blood type A&#xA;            Blood type B&lt;/p&gt;&#xA;" OwnerUserId="14506" LastActivityDate="2015-03-23T11:15:53.793" Title="Blood Type/Punnett Square" Tags="&lt;general-biology&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-03-23T14:03:36.433" ContentLicense="CC BY-SA 3.0" />
  <row Id="30671" PostTypeId="2" ParentId="30669" CreationDate="2015-03-23T04:36:04.917" Score="3" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Slowly adapting mechanoreceptors in the skin mediate the perception of static pressure stimuli, while rapidly adapting skin receptors mediate swiftly changing (e.g., vibratory) stimuli. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;There are various skin receptors. Hairy skin, such as that encountered on the arm, contains at least four specialized mechanoreceptors, namely Pacinian corpuscles, hair follicle receptors, Ruffini endings and tactile discs. They can be roughly distinguished by their adaptation rates, namely fast adapting (Pacinian corpuscles and hair follicle receptors) and slowly adapting (Ruffini endings and tactile discs). Rapidly adapting receptors generate robust responses to vibratory stimuli, but respond weakly to static pressures. The opposite is true for slowly adapting receptors &lt;a href=&quot;https://minds.wisconsin.edu/bitstream/handle/1793/9626/file_1.pdf?sequence=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Kaczmarek et al., 1991)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, the static pressure is faithfully registered by static pressure receptors, while the phasic receptors are specialized in vibratory perceptions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Static receptors fire a continuous train upon a continuous pressure stimulus, phasic receptors do so only at the start and the end of a static pressure stimulus. Hence, when there is a fast vibrating stimulus (say 200 Hz), then the phasic receptors will &lt;em&gt;also&lt;/em&gt; fire action potentials each time at onset and offset of a pressure phase, thereby faithfully representing the stimulus. Here follows a picture of various skin receptors and their responses to a static pressure stimulus. Note that only the slowly adapting receptros show a rocust response: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/StkPK.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;a href=&quot;http://michaeldmann.net/mann5.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source: Michael Mann&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;https://minds.wisconsin.edu/bitstream/handle/1793/9626/file_1.pdf?sequence=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kaczmareck et al., &lt;em&gt;IEEE Trans Biomed Eng&lt;/em&gt; 1991;&lt;strong&gt;38&lt;/strong&gt;:1-16&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-23T04:41:48.157" LastActivityDate="2015-03-23T04:41:48.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30673" PostTypeId="2" ParentId="30651" CreationDate="2015-03-23T04:47:56.123" Score="1" Body="&lt;p&gt;let-7 is a miRNA family (let stands for lethal) and, in fact, was one of the first to be discovered (in &lt;em&gt;Caenorhabditis elegans&lt;/em&gt;). let-7a is but one of &lt;a href=&quot;http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=MIPF0000002&quot; rel=&quot;nofollow noreferrer&quot;&gt;many members of the family&lt;/a&gt;, with orthologs in many species. It seems rare in biology that established names are changed to match &lt;a href=&quot;http://rnajournal.cshlp.org/content/9/3/277.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;newer nomenclature&lt;/a&gt;, though I can't say for sure if that is why many (but not all) of the let-7 family members don't follow the standard.&lt;/p&gt;&#xA;&lt;p&gt;Edit: Coincidentally, I was just reading a review about miRNA and came cross this informative excerpt which should at least give some sense of legitimacy to my above speculation.&lt;/p&gt;&#xA;&lt;p&gt;Ha M, Kim VN. 2014. Regulation of microRNA biogenesis. Nat Rev Mol Cell Bio 15(8):509-524&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The nomenclature of miRNA genes is somewhat inconsistent. The genes found in early genetic studies were named after their phenotypes (for example, &lt;em&gt;lin-4&lt;/em&gt;, &lt;em&gt;let-7&lt;/em&gt; and &lt;em&gt;lsy-6&lt;/em&gt;), whereas most miRNAs found from cloning or sequencing received numerical names (for example, the &lt;em&gt;lin-4&lt;/em&gt; homologues in other species are called &lt;em&gt;mir-125&lt;/em&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cell.com/trends/cell-biology/abstract/S0962-8924(08)00210-9?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0962892408002109%3Fshowall%3Dtrue&quot; rel=&quot;nofollow noreferrer&quot;&gt;Roush S, Slack FJ. 2008. The let-7 family of microRNAs. Trends Cell Biol 18(10):505-516&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The lethal-7 (let-7) gene was initially discovered as an essential developmental gene in C. elegans and, later, as one of the first miRNAs (Figure 1). Soon afterwards, a simple BLAST (basic local alignment search tool) search revealed exact matches to the mature let-7 miRNA sequence in the emerging Drosophila melanogaster and human genomes. It is now known that mature let-7 is highly conserved across animal species.&lt;/p&gt;&#xA;&lt;p&gt;The let-7 family of miRNAs is often present in multiple copies in a genome (Table 1). To distinguish between multiple isoforms, a letter is placed after let-7 to indicate a let-7 with a slightly different sequence, and a number at the end denotes that the same sequence is present in multiple genomic locations. For example, humans have ten mature let-7-family sequences (Figure 3) that are produced from 13 precursor sequences (Figure 4). Three separate precursors produce the mature let-7a sequence (let-7a-1, let-7a-2 and let-7a-3) and precursors from two different genomic locations produce the let-7f (let-7f-1 and let-7f-2) sequence. However, the size of the family can differ between organisms. Drosophila (fly) has only one let-7, whereas the zebrafish Danio rerio has 11 mature sequences in 19 loci throughout its genome…&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;Early characterization of let-7:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v403/n6772/abs/403901a0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G. 2000. The 21-nucleotide &lt;em&gt;let-7&lt;/em&gt; RNA regulates developmental timing in &lt;em&gt;Caenorhabditis elegans&lt;/em&gt;. Nature 403:901-906&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-23T07:57:28.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30675" PostTypeId="1" CreationDate="2015-03-23T05:49:28.493" Score="0" ViewCount="184" Body="&lt;p&gt;What can you conclude about the risk (with each pregnancy) that a couple could have a child affected with an autosomal dominant disorder if...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One parent is affected (heterozygous) and the other parent is unaffected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did a punnet square and concluded it was 50 percent because half were Aa and half were aa.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But a classmate told me to line up Aa and aa and conclude that there is only a 25 percent chance that a child is affected because there is only one capital or dominant A and three are &quot;a&quot;.  Which do I do?&lt;/p&gt;&#xA;" OwnerUserId="14506" LastEditorUserId="3624" LastEditDate="2015-03-23T14:14:22.250" LastActivityDate="2015-03-24T15:54:28.297" Title="Risk of autosomal dominant disorder" Tags="&lt;homework&gt;&lt;general-biology&gt;" AnswerCount="2" CommentCount="0" ClosedDate="2015-03-24T17:12:18.870" ContentLicense="CC BY-SA 3.0" />
  <row Id="30680" PostTypeId="2" ParentId="30661" CreationDate="2015-03-23T09:23:25.737" Score="2" Body="&lt;p&gt;I think the opposite list---what features of life might be reasonably expected to be the &lt;em&gt;same&lt;/em&gt; elsewhere---would be much shorter. Nearly every feature of life on earth as I can think of it is arbitrary in the particular molecules.&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;DNA. Why only 4 bases? Why the bases that we have (ACTG)? Researchers are able to create organisms with expanded DNA alphabets even here on earth &lt;a href=&quot;http://www.nature.com/nature/journal/v509/n7500/full/nature13314.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;(1)&lt;/a&gt;. Even if you believe that some form of molecular mechanism of heredity is a requirement for life, there is no reason it need be DNA. And while there has been plenty of controversy about arsenic-based life here on Earth, I don't see why there couldn't be arsenic-based life elsewhere.&lt;/li&gt;&#xA;&lt;li&gt;Ribosomes. Why a combination of RNA and protein? There is a lot in the overall architecture of ribosomes that is locked in due to historical/evolutionary contingency, not any necessary feature of life.&lt;/li&gt;&#xA;&lt;li&gt;The Central Dogma. Biology as we know it has certainly made great use of the ability to make temporary copies of messages, but I don't see why life orbiting Alpha Centauri would have to have arrived at a similar solution.&lt;/li&gt;&#xA;&lt;li&gt;Phospholipid membranes. You could make the argument that some degree of compartmentalization is necessary for life to occur (to reduce complexity and allow evolution via drift and small-number effects to generate change), but I don't think they need to be phospholipids. I can also imagine all life on another planet contained within viral-like particles with purely protein (or some other alien polymer) coats.&lt;/li&gt;&#xA;&lt;li&gt;Genes. Depending on the level one is arguing I can see this going either way. If a gene is just a modular set of instructions for a limited number of components, then perhaps this will show up everywhere---life on our planet is surprisingly modular, and it is hard to imagine life on another planet being able to get by without some modularity (though of course it is possible in principle). But certainly nothing is inevitable about the details of gene organization into promoters, coding regions (why a 3-base code?), introns and exons (I'm still surprised these exist on our &lt;em&gt;own&lt;/em&gt; planet), operons, etc.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;I think you get the idea. In fact, it's really hard to envision any feature of life on earth that doesn't smack of contingency in some way or other. Astrobiologists have held on to water as an essential ingredient for life as we know it, but still, that's &amp;quot;as we know it.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;I am really tempted to make some sweeping speculative statement about what features I might expect to be &amp;quot;inherent in all possible biologies&amp;quot; (a fascinating idea to think about), but that is way out of my depth. Right now I find it hard to come up with good candidates.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v509/n7500/full/nature13314.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;(1): Malyshev D &lt;em&gt;et al.&lt;/em&gt; (2014). A semi-synthetic organism with an expanded genetic alphabet. &lt;em&gt;Nature&lt;/em&gt; 509: 385-8.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4840" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-23T09:23:25.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30682" PostTypeId="2" ParentId="30675" CreationDate="2015-03-23T09:30:27.677" Score="2" Body="&lt;p&gt;Your classmate is forgetting that the child will have to inherit one allele (A or a) from each parent. Suppose the dad is affected---so his genotype is Aa. He has a 50% chance of passing the A on to his kid. That means the kid has a 50% chance of being affected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your classmate was right, then it would be possible for both the kid's alleles to come from just one parent. You have to pick one allele from each parent.&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2015-03-23T09:30:27.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30683" PostTypeId="2" ParentId="30645" CreationDate="2015-03-23T10:01:11.087" Score="3" Body="&lt;p&gt;Would something like &lt;a href=&quot;http://en.wikipedia.org/wiki/CRISPR&quot; rel=&quot;nofollow&quot;&gt;CRISPR&lt;/a&gt; fit your criteria? CRISPR is essentially an adaptive immune system for bacteria. When a bacteria encounters foreign DNA (usually from an invading bacteriophage), it can cut it up and insert part of it in between palindromic repeats called CRISPRs. This small piece of DNA can be transcribed and then used as a template to recognize other copies of the foreign DNA. When a match is found, the foreign DNA is degraded, impairing the invading virus. Because a record of this foreign DNA is stored in the bacterial chromosome, it is transmitted to daughter cells, which will now have some protection against the offending virus in the future.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the same vein, when certain bacteriophages invade bacteria, they integrate their viral genomes into the host bacterial genome---phage lambda is the classic example. At this juncture, the phage can choose between &lt;a href=&quot;http://en.wikipedia.org/wiki/Lysogenic_cycle&quot; rel=&quot;nofollow&quot;&gt;two lifestyles&lt;/a&gt;: lysis, in which the virus replicates like crazy, killing the host cell and spreading to other cells; or lysogeny, in which the virus lies dormant, allowing its genome to hitch a ride in the host genome, getting replicated and passed on to daughter cells just like any other piece of chromosomal DNA. When the time is right, the virus can switch back to lysis, proliferate, and infect new cells. Thus viral invasion of an asexually reproducing organism can lead to heritable changes in the host genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm sure you've heard of &lt;a href=&quot;http://en.wikipedia.org/wiki/Epigenetics&quot; rel=&quot;nofollow&quot;&gt;epigenetics&lt;/a&gt;, in which environmental factors can cause heritable changes to an organism without specifically mutating genes. While typically appreciated in eukaryotic organisms, asexually reproducing bacteria also have epigenetic mechanisms &lt;a href=&quot;http://mmbr.asm.org/content/70/3/830.full&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://mmbr.asm.org/content/70/3/830.full&quot; rel=&quot;nofollow&quot;&gt;(1): Casadesus J and Low D. (2006). Epigenetic gene regulation in the bacterial world. &lt;em&gt;Microbiol. Mol. Biol. Rev.&lt;/em&gt; 70(3): 830-56.&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2015-03-23T10:01:11.087" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30684" PostTypeId="2" ParentId="30651" CreationDate="2015-03-23T10:08:31.767" Score="2" Body="&lt;p&gt;Some general aspects about miRNA nomenclature in addition to canadianer's answer:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;code&gt;mir&lt;/code&gt; refers to the pre-miRNA whereas &lt;code&gt;miR&lt;/code&gt; refers to the mature form&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;mir-x-y&lt;/code&gt; &lt;code&gt;mir-x-z&lt;/code&gt; for example &lt;code&gt;mir-1-1&lt;/code&gt; and &lt;code&gt;mir-1-2&lt;/code&gt; refer to different precursors that give rise to same mature miRNA (i.e. &lt;code&gt;miR-1&lt;/code&gt;). These different precursors can be regulated differently. &lt;/li&gt;&#xA;&lt;li&gt;The mature miRNA resulting from the 5' arm of the precursor hairpin has a suffix of &lt;code&gt;-5p&lt;/code&gt;; similarly the product from the 3' arm has the suffix of &lt;code&gt;-3p&lt;/code&gt;. Previously, the lesser expressed/abundant (or unexpressed) of the two products was designated with an asterisk. For e.g. &lt;code&gt;miR-124*&lt;/code&gt;. This convention is obsolete now. Any miRNA by default has the &lt;code&gt;-5p/3p&lt;/code&gt; suffix. This is useful especially in case of &lt;code&gt;let-7&lt;/code&gt; because there is no uppercase notation to differentiate precursor from the mature miRNA. For example, the mature form is always denoted as &lt;code&gt;hsa-let-7b-5p&lt;/code&gt; even though the &lt;code&gt;-3p&lt;/code&gt; is never expressed. &lt;/li&gt;&#xA;&lt;li&gt;A &quot;family&quot; consists of miRNAs with the same seed sequence (usually 2&lt;sup&gt;nd&lt;/sup&gt;-9&lt;sup&gt;th&lt;/sup&gt; residue). Sometimes it can be observed that one of the arms is less conserved than the other between different precursors. For example in the case of &lt;code&gt;let-7&lt;/code&gt; the &lt;code&gt;-3p(s)&lt;/code&gt; do not have a conserved seed sequence, however, all &lt;code&gt;-5p(s)&lt;/code&gt; have the same seed sequence. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;And as mentioned in the other answer, the name &lt;code&gt;let-7&lt;/code&gt; just sticks around because of historical reasons.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-03-30T04:51:56.077" LastActivityDate="2015-03-30T04:51:56.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30685" PostTypeId="1" AcceptedAnswerId="30687" CreationDate="2015-03-23T10:31:10.527" Score="9" ViewCount="2051" Body="&lt;p&gt;Is there any situation anatomically, where a human could understand the speech of others perfectly, without any capabilities of speech themselves, but would retain the ability to whistle with a tune?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was led to believe that the larynx is the most important thing for creating the sounds in speech, however I don't know if a damaged larynx would necessarily &lt;a href=&quot;https://biology.stackexchange.com/questions/30598/can-someone-who-cannot-talk-still-whistle&quot;&gt;not allow someone to speak&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would suggest someone who has no tongue cannot speak coherently, however I would imagine that the tongue is instrumental (pardon the pun) in creating a range of sounds whilst whistling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there perhaps a part of the brain that could be affected in order to stop someone speaking? Or would this also mean the person could not understand speech either?&lt;/p&gt;&#xA;" OwnerUserId="15022" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-03-23T22:52:33.687" Title="Is there any way a human could whistle and be unable to speak?" Tags="&lt;neuroscience&gt;&lt;human-anatomy&gt;&lt;neuroanatomy&gt;&lt;neurology&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30686" PostTypeId="2" ParentId="30670" CreationDate="2015-03-23T11:15:53.793" Score="4" Body="&lt;p&gt;as far as simple punnet square is concerned your answer is correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZQXdw.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14932" LastActivityDate="2015-03-23T11:15:53.793" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30687" PostTypeId="2" ParentId="30685" CreationDate="2015-03-23T12:07:23.650" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer(s)&lt;/strong&gt;&lt;br&gt;&#xA;Someone with a damaged larynx may still speak with the use of a speech aid (electronic larynx). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ability to understand speech does not necessarily mean one can speak normally. There are neurological disorders where folks can understand speech, but have difficulty producing it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;A full removal of the larynx (&lt;em&gt;laryngectomy&lt;/em&gt;) prevents the patient to produce speech because the vocal chords are removed. However, with the use of a voice prosthesis this can be solved (&lt;a href=&quot;http://www.cancerresearchuk.org/about-cancer/type/larynx-cancer/living/speaking-after-laryngectomy&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cancer Research UK&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are neurological disorders where one can still understand speech, but has impaired ability to generate it, called &lt;em&gt;apraxia&lt;/em&gt;. Apraxia can be acquired or congenital (developmental) (&lt;a href=&quot;http://www.nidcd.nih.gov/health/voice/pages/apraxia.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;NIH&lt;/a&gt;). The developmental type is not well understood a the neural level (&lt;a href=&quot;http://www.dyspraxiafoundation.org.uk/wp-content/uploads/2013/10/Developmental_Verbal_Dyspraxia.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dyspraxia Foundation UK&lt;/a&gt;). The acquired type is known to occur through damage to specific brain areas, for example due to trauma or stroke. One of these areas associated with acquired apraxia is &lt;em&gt;Broca's area&lt;/em&gt; (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0093934X14000091&quot; rel=&quot;nofollow noreferrer&quot;&gt;Graff-Radford et al., 2014&lt;/a&gt;), which is a brain area intimately associated with the production of speech . &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kjjN8.jpg&quot; alt=&quot;Broca&amp;#39;s area&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Broca's area. Source: &lt;a href=&quot;http://www-rohan.sdsu.edu/~gawron/intro/course_core/lectures/aphasia_cases_slides.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;UC Irvine&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, although damage to this area can result in &lt;em&gt;pure&lt;/em&gt; apraxia (i.e., impaired speech but normal speech understanding), it can also result in &lt;em&gt;Broca's aphasia&lt;/em&gt;, which means that language understanding is also impaired (&lt;a href=&quot;http://www.strokeassociation.org/STROKEORG/LifeAfterStroke/RegainingIndependence/CommunicationChallenges/Types-of-Aphasia_UCM_310096_Article.jsp&quot; rel=&quot;nofollow noreferrer&quot;&gt;American Heart Association&lt;/a&gt;). Moreover, regarding your specific question, apraxia is characterized by impaired speech, but not a total lack of speech production.     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0093934X14000091&quot; rel=&quot;nofollow noreferrer&quot;&gt;Graff-Radford et al. &lt;em&gt;Brain &amp;amp; Language&lt;/em&gt; 2014;&lt;strong&gt;129&lt;/strong&gt;:43–6&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-23T12:44:15.110" LastActivityDate="2015-03-23T12:44:15.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30688" PostTypeId="1" CreationDate="2015-03-23T12:20:39.793" Score="5" ViewCount="93" Body="&lt;p&gt;I am interested in identifying the differential expression between several genes-of-interest of different organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am trying to assess the benefits of RNA sequencing over microarrays. Both techniques are a means to an end. With both of these two methods one can &quot;count&quot; the differences between two conditions, e.g. cell types, time points etc. They do use different technology to achieve it, but they both give a certain number 't' in the end, which can be looked at as the strength of the expression of a specific gene under a certain cellular condition. One can than compare the two (or more) conditions to get a picture of what is different in the cell due to the changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I am new to this field, can someone tell me what the advantages are of RNA sequencing over micro arrays? Alternatively, information on comparisons between microarrays and RNA sequencing methods are welcome.&lt;/p&gt;&#xA;" OwnerUserId="15074" LastEditorUserId="107" LastEditDate="2015-03-23T13:58:07.427" LastActivityDate="2015-03-23T13:58:07.427" Title="Genes-of-interest analysis between organisms" Tags="&lt;rna-sequencing&gt;&lt;microarray&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30690" PostTypeId="2" ParentId="30688" CreationDate="2015-03-23T13:06:06.123" Score="4" Body="&lt;p&gt;In RNA sequencing, total RNA is extracted, then mRNAs are purified out from the sample using polyT columns (since mRNAs have a polyA tail, this will attach to a polyT DNA chunk that is attached to some solid surface). This step is necessary because ribosomal RNAs are much more abundant than mRNAs, and for sequencing you only want to use mRNAs. Then the purified mRNA is transcribed to DNA using reverse-transcriptase and finally the cDNA is sequenced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for microarray a set of single stranded oligonucleotids (short DNA sequences) (aka. probes) are attached to a solid (usually glass) surface as small dots. This the so called DNA/RNA-chip. Then the chip is washed with the fluorescently labelled singlestranded sample, and the complementary strands attach to each other, the rest is washed away - this is a so called hybridization technique. The signal is then detected by reading the fluorescence signals at each spot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The microarray technique is quite old and is less sensible and the number of probes are limited / array, while with RNA sequencing you can sequence the total mRNA population of each organism and examine anything you want. Also since most sequencing techniques include a PCR step less starting material is sufficient, and has higher sensitivity and specificity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These wiki pages on &lt;a href=&quot;http://en.wikipedia.org/wiki/RNA-Seq&quot; rel=&quot;nofollow&quot;&gt;RNA-seq&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_microarray&quot; rel=&quot;nofollow&quot;&gt;microarray&lt;/a&gt; technique provide detailed info on both.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-03-23T13:06:06.123" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30693" PostTypeId="1" AcceptedAnswerId="30700" CreationDate="2015-03-23T14:45:51.253" Score="23" ViewCount="13123" Body="&lt;p&gt;&lt;a href=&quot;http://www.livescience.com/16015-oldest-viruses-insects.html&quot;&gt;The oldest known virus&lt;/a&gt; is known to have infected prehistoric insects 300 million years ago. A virus is basically a parasitic strand if DNA or RNA encapsulated in a protein coat. It enters cells by &quot;wearing&quot; a protein coat made out of proteins needed by a certain cell (e.g. Lung cells and flu virus).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, my question:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Do we know how viruses naturally formed? To simplify the question, if we went back to the first virus, how would it form?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Note that I am looking for a scientific answer, and not wild-ass speculation. While I can accept some degree of speculation the accepted answer will &lt;strong&gt;NOT&lt;/strong&gt; be based entirely on speculation if it is avoidable.&lt;/p&gt;&#xA;" OwnerUserId="11674" LastActivityDate="2016-10-02T19:13:08.877" Title="Is it known how the first viruses formed?" Tags="&lt;evolution&gt;&lt;biochemistry&gt;&lt;virus&gt;&lt;protein-evolution&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="30694" PostTypeId="2" ParentId="30685" CreationDate="2015-03-23T15:07:23.443" Score="2" Body="&lt;p&gt;Speech is generated by generating a frequency spectrum with the vocal folds, and then filtering it with the upper vocal tract.  Whistling is done by blowing air over shaped tongue and lips.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, give someone a &lt;a href=&quot;http://en.wikipedia.org/wiki/Laryngectomy&quot; rel=&quot;nofollow&quot;&gt;laryngectomy&lt;/a&gt;.  They still retain the upper vocal tract (and so can still whistle), but they cannot generate the source vibrations to speak.  Do it as an adult and they probably understand the speech of others.&lt;/p&gt;&#xA;" OwnerUserId="9804" LastActivityDate="2015-03-23T15:07:23.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30696" PostTypeId="1" CreationDate="2015-03-23T15:27:21.880" Score="3" ViewCount="1302" Body="&lt;p&gt;I have &lt;a href=&quot;http://www.blopig.com/blog/2014/04/quick-standalone-blast-setup-for-ubuntu-linux/&quot; rel=&quot;nofollow&quot;&gt;installed Blast locally&lt;/a&gt; and I've configured the nucleotide database to use. I want to search some sequences (from a &lt;kbd&gt;.fasta&lt;/kbd&gt;file) in this genome. So I used blastn:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;blastn -db NewDb -query input.fasta -out blast.txt&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Then I added some options to require a 100% identity and no gaps:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;blastn -db NewDb -query input.fasta -perc_identity 100 -ungapped -out blast.txt&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;But I still have some results where only a subpart of the string is matching the genome:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;BLASTN 2.2.29+&#xA;&#xA;[…]&#xA;&#xA;Database: […].fasta&#xA;           20 sequences; N total letters&#xA;&#xA;Query= Mutant M :&#xA;&#xA;Length=226&#xA;                                                                      Score     E&#xA;Sequences producing significant alignments:                          (Bits)  Value&#xA;&#xA;  chrom19                                                               435   3e-122&#xA;  chrom2                                                                429   1e-120&#xA;&#xA;&amp;gt; chrom19&#xA;Length=W&#xA;&#xA; Score =   435 bits (226),  Expect = 3e-122&#xA; Identities = 226/226 (100%), Gaps = 0/226 (0%)&#xA; Strand=Plus/Plus&#xA;&#xA;[…]&#xA;&#xA;&amp;gt; chrom2&#xA;Length=Y&#xA;&#xA; Score =   429 bits (223),  Expect = 1e-120&#xA; Identities = 223/223 (100%), Gaps = 0/223 (0%)&#xA; Strand=Plus/Plus&#xA;&#xA;[…]&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Both results have an identity score of 100%, but the second result only use 223 of the 226 bases from the input sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What parameters can I use with &lt;code&gt;blastn&lt;/code&gt; to get only perfect matches, with 100% identity and all the nucleotide bases from the input sequence used?&lt;/p&gt;&#xA;" OwnerUserId="5857" LastActivityDate="2015-03-23T15:27:21.880" Title="How to get only perfect matches with blastn?" Tags="&lt;bioinformatics&gt;&lt;sequence-alignment&gt;&lt;blast&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="1" ClosedDate="2016-03-22T09:40:13.740" ContentLicense="CC BY-SA 3.0" />
  <row Id="30697" PostTypeId="2" ParentId="30693" CreationDate="2015-03-23T16:07:15.350" Score="10" Body="&lt;p&gt;Great question. There are several hypotheses, but in reality no one really &quot;knows&quot; because this is incredibly difficult to prove. We may never know for certain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, on to the three main hypotheses, I got this from &lt;a href=&quot;http://en.wikipedia.org/wiki/Viral_evolution&quot;&gt;http://en.wikipedia.org/wiki/Viral_evolution&lt;/a&gt;, I think you'll find it to be helpful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;There are three classical hypotheses on the origins of viruses: Viruses may have once been small cells that parasitized larger cells (the degeneracy hypothesis or reduction hypothesis); some viruses may have evolved from bits of DNA or RNA that &quot;escaped&quot; from the genes of a larger organism (the vagrancy hypothesis or escape hypothesis); or viruses could have evolved from complex molecules of protein and nucleic acid at the same time as cells first appeared on earth (the virus-first hypothesis).&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, as you may have guessed, there are plenty of questions that these theories do not answer. The next paragraph:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;None of these hypotheses was fully accepted: the regressive hypothesis did not explain why even the smallest of cellular parasites do not resemble viruses in any way. The escape hypothesis did not explain the complex capsids and other structures on virus particles. The virus-first hypothesis was quickly dismissed because it contravened the definition of viruses, in that they require host cells. Virologists are, however, beginning to reconsider and re-evaluate all three hypotheses.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a little more information on the Wikipedia page, I would recommend that you read that and do a little research on the different theories if you would like to know more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CDB&lt;/p&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="13496" LastEditDate="2015-03-23T16:13:08.733" LastActivityDate="2015-03-23T16:13:08.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30698" PostTypeId="1" AcceptedAnswerId="30713" CreationDate="2015-03-23T16:27:35.757" Score="4" ViewCount="1936" Body="&lt;p&gt;I'm trying to find out why a prompt, severe, short pain is causing a stimulation of the vagus nerve. What could the physiological explanation be?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is that because the pain is triggering the sympathetic system (Huge stress because of the pain), and directly after that the parasympathetic system is trying to balance it, but it's overreacting? and then the sympathetic system is going back to normal when parasympathetic stays high ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a physiologic explanation ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="15082" LastActivityDate="2018-04-09T09:22:45.180" Title="How pain can stimulate the vagus nerve" Tags="&lt;neuroscience&gt;&lt;human-anatomy&gt;&lt;neurophysiology&gt;&lt;central-nervous-system&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30699" PostTypeId="2" ParentId="30685" CreationDate="2015-03-23T17:07:28.863" Score="4" Body="&lt;p&gt;You can whisper without a larynx. &lt;em&gt;&quot;Patients who have undergone partial or full laryngectomy are typically unable to speak anything more than hoarse whispers, without the aid of prostheses or specialized speaking techniques.&quot;&lt;/em&gt; (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20570761&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the remainder of the vocal tract is capable of enough modulation to present typical human speech in many languages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I expect, however, that the tongue, throat, jaw, and facial muscles figure very heavily into this modulation.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If these muscles become paralyzed or otherwise unusable, it's reasonable to assume that they may still be able to whistle with the use of the lungs and hands or fingers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hands free whistling, however, would require at least teeth and lips, or teeth and tongue, or lips and tongue - one surface to control the flow of air over the other surface that produces the whistle.  With control over just these few things, one could likely communicate to a reasonable degree in many languages.&lt;/p&gt;&#xA;" OwnerUserId="5940" LastActivityDate="2015-03-23T17:07:28.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30700" PostTypeId="2" ParentId="30693" CreationDate="2015-03-23T17:55:43.800" Score="24" Body="&lt;p&gt;One of the main points of contention in the study of virus evolution is whether or not they appear before the last universal cellular ancestor (LUCA) or afterwards (commonly accepted: genes that &quot;escaped&quot; from host organisms aka the escape hypothesis or vagrancy hypothesis).  Basically though, the LUCA is the most recent ancestor that all organisms living on Earth are derived from. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Increasing evidence support that ancestry of viruses may predate the LUCA, for example an idea is that there &quot;was an 'ancient virus world' of primordial replicators that existed before any cellular organisms and that both RNA (first) and DNA (later) viruses originated at this time, donating some features to the first cellular organisms.  However, &quot;a competing theory is that RNA cells existed before the LUCA and that RNA viruses were parasites on these RNA cells that later evolved DNA as a way of escaping host cell responses.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So basically, some theories support the pre-LUCA ancient virus origin and some support post-LUCA.  Because it's impossible to replicate conditions from billions of years ago, several approaches using evolutionary genetics and probability models are recommended by the author of the paper, referenced below.  He also discusses the specific supporting criteria for the theories that you can read in greater detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Holmes, E. C. (2011). &quot;What does virus evolution tell us about virus origins?&quot; J Virol 85(11): 5247-5251.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="14916" LastActivityDate="2015-03-23T17:55:43.800" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30701" PostTypeId="1" CreationDate="2015-03-23T17:58:48.147" Score="5" ViewCount="506" Body="&lt;p&gt;When a multicellular organism is under its development how does the current outermost layer of cells &quot;know&quot; that they should not divide furthermore, as their bodyplan coded into DNA is already achieved. Is it because of morphogens or something else's work is in the background?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it is entirely controlled by morpogens, than it would mean, that injecting a given morphogen to the outermost cells, would result in further increase in the organism's size? &lt;/p&gt;&#xA;" OwnerUserId="15051" LastEditorUserId="15051" LastEditDate="2015-07-03T21:01:57.003" LastActivityDate="2015-07-03T21:01:57.003" Title="How does an organism know when to stop growing, whether it is already on the outermost layer?" Tags="&lt;development&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="2" ClosedDate="2015-03-24T19:32:44.690" ContentLicense="CC BY-SA 3.0" />
  <row Id="30702" PostTypeId="1" AcceptedAnswerId="30835" CreationDate="2015-03-23T19:08:09.323" Score="4" ViewCount="14180" Body="&lt;p&gt;When we make yogurt at home and do not refrigerate it, it will become sour because of conversion of lactose into lactic acid by Lactobacillus bacteria, but this does not happen in case of Nestle's yogurt or any other brand until it remains air tight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder though bacteria is still present in it and continue to convert lactose into lactic acid then why does not packed yogurt becomes sour? How these companies increase the shelf life of yogurt..?&lt;/p&gt;&#xA;" OwnerUserId="5729" LastEditorUserId="14826" LastEditDate="2015-03-29T07:39:51.710" LastActivityDate="2019-07-09T03:08:24.790" Title="How to increase the shelf life of yogurt without refrigeration?" Tags="&lt;food&gt;&lt;biotechnology&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30704" PostTypeId="2" ParentId="30685" CreationDate="2015-03-23T19:41:14.177" Score="0" Body="&lt;p&gt;It seems that speech can be recovered after total &lt;a href=&quot;http://en.wikipedia.org/wiki/Glossectomy&quot; rel=&quot;nofollow&quot;&gt;glossectomy&lt;/a&gt;, although it's not a short or an easy process. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's one case:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a case study, reporting the evaluation and evolution findings of the speech-language pathology rehabilitation of the swallowing and speech functions of a 58-year-old man submitted to total glossectomy in June 2009. After evaluation, the subject was diagnosed with severe mechanical oropharyngeal dysphagia and alteration in speech articulation. Speech rehabilitation used direct and indirect therapies. Indirect therapy focused on oral motor control, sensitivity, mobility, motricity, tonus and posture of the structures adjacent to the resected tongue. Direct therapy used the head back posture maneuver to help the ejection of food into the pharynx. The patient started exclusive oral feeding, except for solid foods, after ten months in treatment. Over-articulation, speed and rhythm exercises were used to improve speech intelligibility. Thus, the results of speech-language pathology intervention were considered positive, and the patient was discharged after a year in treatment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.scielo.br/scielo.php?pid=S1516-80342011000400019&amp;amp;script=sci_arttext&amp;amp;tlng=en&quot; rel=&quot;nofollow&quot;&gt;Speech therapy in total glossectomy - case study&lt;/a&gt;, Vieira 2011&lt;/p&gt;&#xA;" OwnerUserId="10061" LastEditorUserId="10061" LastEditDate="2015-03-23T19:46:56.453" LastActivityDate="2015-03-23T19:46:56.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30705" PostTypeId="1" AcceptedAnswerId="30709" CreationDate="2015-03-23T21:14:47.917" Score="1" ViewCount="92" Body="&lt;p&gt;It might be a strange question, but I'm interested in the mechanics of separation/detachment during asexual reproduction, for example when an organism reproduces by budding &lt;em&gt;(I don't mean cellular budding like baker's yeast)&lt;/em&gt;. When the newly formed body is fully matured it detaches itself from the parent / original body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It might not be caused by a specific tissue, as animals with not so differentiated bodies are (also) capable of such, but I could easily be wrong. Is this (the detachment) triggered by changes in the cell membrane? I can't really think of other explanations.&lt;/p&gt;&#xA;" OwnerUserId="15051" LastEditorUserId="15051" LastEditDate="2015-03-24T11:54:18.100" LastActivityDate="2015-03-24T11:54:18.100" Title="How detachment/separation works in biology?" Tags="&lt;development&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30707" PostTypeId="1" AcceptedAnswerId="85337" CreationDate="2015-03-23T23:26:53.290" Score="15" ViewCount="1239" Body="&lt;p&gt;The following article refers to contact inhibition of cell division in epithelial cells, specifically MDCK cells: &lt;a href=&quot;http://www.pnas.org/content/109/3/739.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Collective and single cell behavior in epithelial contact inhibition&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In their review of the literature, there are a number of possible signalling pathways implicated in contact inhibition of cell division. These pathways are outlined in the following quotes:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is widely accepted that contact inhibition requires establishment of E-cadherin-mediated cell-cell contacts and subsequent maturation of the adherens junctions (AJs) that link E-cadherin and F-actin in a synapse-like complex involving numerous other proteins&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;One possible pathway involves β-catenin, a mediator of Wnt signalling, that, in addition to its function as a transcriptional cofactor, is associated with the AJs at the cell surface&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;A contact inhibition role has been reported for NF2/Merlin, a tumor suppressor gene that encodes a membrane-cytoskeletal scaffolding protein, which most likely acts via the Hippo kinase pathway, controlling nuclear localization of the transcriptional activator YAP—itself a known regulator of cell proliferation.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Contact inhibition is known to involve the MAPK pathway, which, in turn, promotes cell cycle entry by regulating the expression of cyclinD1. Also implicated are Nectins—a family of cell adhesion molecules that are involved, together with integrins and other proteins, in the regulation of cell motility and proliferation. &lt;strong&gt;Yet, this accumulated knowledge falls far short of a comprehensive picture of contact inhibition.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the article, the findings were as follows:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our findings show that contact between cells is not sufficient for inhibition of mitosis in MDCK cells. Instead, inhibition of cell proliferation is a consequence of mechanical constraint that causes successive cell divisions to reduce cell area.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Where, in the discussion, they note the following:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Our measurements also suggest that inhibition of cell division is a distinct single cell state rather than a global state induced by cell-cell signalling across the layer, as illustrated in Fig. 4E. In fact, confluent MDCK cell cultures with an average cell density corresponding to the morphological transition are often sufficiently heterogeneous in local cell density that highly motile cells and completely arrested cells coexist in the same colony. Thus contact inhibition is a local phenomenon...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Published later, the article &lt;a href=&quot;http://www.pnas.org/content/111/15/5586.full.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Spatial constraints control cell proliferation in tissues&lt;/a&gt; showed that reducing the amount of space in a tissue prevented entry into S-phase. Actually stretching the tissue quickly reactivated the cell cycle, and compression leads quickly to arrest. More so, they found that cells had no memory of past constraint, and were able to suggest a model of growth in relation to the spatial constraint. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm editing my question because the way I posted it initially, to me, was unanswerable. Being said, I suspect that at this point cell volume and extracellular contacts are synergistic. This is probably going to need two separate questions, but:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) How does the mitotic entry machinery roughly respond to cell volume? I'm currently reading into Cdc25/Wee1 regulation in addition to some stuff about &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736675/&quot; rel=&quot;nofollow noreferrer&quot;&gt;internal fluidics&lt;/a&gt; that are influenced by water, ion channels, etc. but I still don't fully understand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) What's a relatively straightforward downstream pathway (core elements), starting at the adherens junctions, that illustrates how cell-cell signalling gets the STOP signal to the mitotic entry machinery (based on what we know)? This might require some much more in-depth knowledge about the field, however, but articles with some good figures are appreciated, too.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="3553" LastEditDate="2017-03-27T11:19:42.377" LastActivityDate="2021-05-24T11:35:33.400" Title="Contact Inhibition of Cell Division: Signaling Pathway" Tags="&lt;cell-biology&gt;&lt;cancer&gt;&lt;cell-division&gt;&lt;cell-cycle&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="30708" PostTypeId="2" ParentId="30610" CreationDate="2015-03-24T00:59:26.960" Score="2" Body="&lt;p&gt;I was doing some more research and stumbled upon this paper &lt;a href=&quot;https://www.somasimple.com/pdf_files/resfire.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; by Dr. Izhikevich that describe neurons as a system that can exhibit resonance. The author built a model that he calls the resonate and fire, which is a linear piece-wise model of a neuron. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The interesting thing, and why I bring it up, is it can respond to a &quot;two inhibitory pulses, that if timed correctly will cause the neuron to fire. but neither inhibitory pulse alone can cause the neuron to fire. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following some of the citations in the article (found &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-7793.2000.00205.x/full&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;), apparently thalumus neurons can exhibit resonance and thus theoretically can fire in response to the right frequency of input. However it is important to note that they thalamic neurons are close to threshold, and are not receiving the double inhibitory input that Izhekivich talks about in his paper. The second paper uses a ZAP protocol. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A Zap protocol is injecting a Sine wave into a neuron and slowly change the frequency linearly in time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$I_{ZAP}(t) = \sin((\omega_0+\omega t) t) $$ where $\omega_0$ and $\omega_1$ are constants.    &lt;/p&gt;&#xA;" OwnerUserId="13388" LastActivityDate="2015-03-24T00:59:26.960" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30709" PostTypeId="2" ParentId="30705" CreationDate="2015-03-24T03:10:34.917" Score="1" Body="&lt;p&gt;Reproductive budding and what you call 'cellular budding' are really highly related processes. Budding as a form of reproduction essentially partitions protein aggregates and damaged cellular components into the host or mother and builds fresh or 'young' cells on the opposite side of a partition. To begin understanding this look at &lt;em&gt;Saccharomyces cerevisiae&lt;/em&gt; (budding yeast) which forms protein rings (from the septin proteins) at the membrane, around the bud neck which separates the mother and daughter cells &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0014482771902230&quot; rel=&quot;nofollow&quot; title=&quot;Hartwell 1971&quot;&gt;Hartwell 1971&lt;/a&gt;. This ring acts a partition that in part, withholds protein aggregates and certain proteins from diffusing from the mother to the daughter. This protein ring is an example of how cells limit diffusion of proteins and cellular components to the daughter cell. Another good example that comes to mind is &lt;a href=&quot;http://www.pnas.org/content/105/8/3076.full&quot; rel=&quot;nofollow&quot;&gt;Linder 2007&lt;/a&gt;, though it is done in E Coli, not budding yeast, where mother cells maintain protein aggregates and age, while the daughter cells are given fresh components and are therefore more fresh and 'young'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now like you mention, imagine this process in a multicellular organism to be fundamentally the same. At some point the multicellular organism will start an outgrowth of cells, while restricting what materials are given to the daughter cells to maintain their youth. And eventually a new organism will have been created. Some of the details will be different, but the fundamental process is is quite similar. In that you start with an old cell that creates a new cell from scratch, but rather than splitting all cellular components equally between mother and daughter, the daughter cells is made in peak condition while the mother cell retains much of the cell 'junk' like protein aggregates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully that starts to answer your question.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-03-24T03:10:34.917" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30710" PostTypeId="1" AcceptedAnswerId="35184" CreationDate="2015-03-24T04:22:23.423" Score="3" ViewCount="972" Body="&lt;p&gt;I consider the existence of a broken GULO gene in humans to be the clearest evidence for human evolution - just what else is it doing there otherwise?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any other examples of vestigial genes in the Human genome? Or perhaps vestigial proteins?&lt;/p&gt;&#xA;" OwnerUserId="2987" LastActivityDate="2016-04-27T14:16:52.017" Title="Examples of Vestigial Genes" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30711" PostTypeId="2" ParentId="5416" CreationDate="2015-03-24T08:24:19.350" Score="1" Body="&lt;p&gt;The two main chemical processes in the human body that generate carbon dioxide (CO&lt;sub&gt;2&lt;/sub&gt;) are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Basal metabolic process of CO&lt;sub&gt;2&lt;/sub&gt; (CO&lt;sub&gt;2m&lt;/sub&gt;) produced by the &lt;strong&gt;combustion of sugar&lt;/strong&gt; in organs and tissues of the body.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Bacterial decay&lt;/strong&gt; processes occurring as a result of activity of the microbial fauna in the colon. This forms CO&lt;sub&gt;2&lt;/sub&gt; (CO&lt;sub&gt;2c&lt;/sub&gt;), H&lt;sub&gt;2&lt;/sub&gt;, CH&lt;sub&gt;4&lt;/sub&gt; and higher hydrocarbons, NH&lt;sub&gt;3&lt;/sub&gt;, H&lt;sub&gt;2&lt;/sub&gt;S and other mercaptans.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The total level of carbon dioxide in the blood (CO&lt;sub&gt;2b&lt;/sub&gt;) is therefore the sum of the metabolic (CO&lt;sub&gt;2m&lt;/sub&gt;) and carbon dioxide arising in the large bowel (CO&lt;sub&gt;2c&lt;/sub&gt;). In certain circumstances CO&lt;sub&gt;2c&lt;/sub&gt; arising in the colon may be resorb into the bloodstream. &lt;/p&gt;&#xA;" OwnerUserId="15092" LastEditorUserId="9943" LastEditDate="2015-03-24T11:31:21.490" LastActivityDate="2015-03-24T11:31:21.490" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30712" PostTypeId="1" CreationDate="2015-03-24T12:37:23.713" Score="3" ViewCount="869" Body="&lt;p&gt;I am equally disgusted and fascinated by the &quot;Silverfish&quot; (&lt;em&gt;Lepisma saccharina&lt;/em&gt;) that we regularly find in our UK home. I tried searching for information on the internet but they seem poorly understood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We only ever find them on the work surface in the kitchen when we switch on a light at night. They are presumably feeding off food residues - but they never seem to be found in the most obvious place, among the crumbs under the toaster.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When caught by the lights, they run for cover but never, ever climb. You would think them unable to climb at all but then how have they reached the work surface?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other day there appeared a new twist; 2 &quot;husks&quot; hanging from silk threads between 2 containers, maybe 8cm from the surface. If they were caught and eaten by a spider, why did it take them to a rudimentary web when it (presumably) caught them on the surface? There was no sign of a spider around. The only other possibility I can see is that they somehow suspended THEMSELVES from the silk and this was a moulting behaviour. Thus they now CAN climb - and very well - and also produce silk!&#xA;Can anyone explain the mystery?&lt;/p&gt;&#xA;" OwnerUserId="14750" LastEditorUserId="3624" LastEditDate="2015-03-24T15:16:54.867" LastActivityDate="2015-03-24T21:51:24.337" Title="Can silverfish climb and produce silk?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30713" PostTypeId="2" ParentId="30698" CreationDate="2015-03-24T12:59:30.077" Score="3" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Given your comments you are referring to the cause of fainting after being triggered by certain stressors. The reason is a sudden drop in blood pressure due to parasympathetic nervous system activation (&lt;em&gt;vagus nerve activity&lt;/em&gt;). This leads to reduced blood flow to your brain, which results in a brief loss of consciousness (&lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/vasovagal-syncope/basics/definition/con-20026900&quot; rel=&quot;nofollow&quot;&gt;Mayo Clinic&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;There are various types of fainting (syncope) with various causes. The type you are referring to is &lt;em&gt;neurally mediated syncope&lt;/em&gt; &lt;a href=&quot;http://pmj.bmj.com/content/76/902/750.full&quot; rel=&quot;nofollow&quot;&gt;(Arthur &amp;amp; kaye, 2000)&lt;/a&gt;. It is evoked by emotional activation due to stressors (pain, fear etc.) Stress responses are accompanied by the release of stress hormonses, most notably Adrenaline (epinephrine). Epinephrine release results in sympathetic nervous system arousal, resulting in increased blood pressure, increased pulse and sweating. It also increases amounts of blood being funneled to peripheral organs. These mechanisms aids in the &lt;a href=&quot;http://www.simplypsychology.org/stress-biology.html&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;fight,fright and flight response&lt;/em&gt;&lt;/a&gt;, as more blood in the periphery allows more glucose to be transported to the muscles &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2600095/&quot; rel=&quot;nofollow&quot;&gt;(Agarwal, 2007)&lt;/a&gt;. The funneling of blood in the periphery (venous pooling), however, can reach a point in which venous return of blood to the heart falls too sharply. This in turn can lead to a substantial increase in the muscle activity in the ventricles, as they are likely struggling to pump the small available amounts of venous blood into the heart chambers. The increased muscular activity in the ventricles is believed to activate mechanoreceptors that would normally fire only during stretch. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stretch of heart muscle is normally associated with a high blood pressure. The warning message of a high blood pressure by the mechanoreceptors is sent to the medulla in the brainstem, which in turn leads to parasympathetic nervous arousal. As a part of the parasympathetic response, the vagus nerve is stimulated which reduces heart activity to reduce blood pressure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, when the mechanoreceptors are stimulated due to the overt contractility of the ventricles due to a low blood volume, they sent the same neural input to the medulla which normally signals hypertension, thus causing vagus nerve stimulation and hence a paradoxic parasympathetic arousal that results in low blood pressure (&lt;em&gt;hypotension&lt;/em&gt;), low heart rate (&lt;em&gt;bradycardia&lt;/em&gt;), and ultimately fainting (&lt;em&gt;syncope&lt;/em&gt;) &lt;a href=&quot;http://circ.ahajournals.org/content/111/22/2997.full&quot; rel=&quot;nofollow&quot;&gt;(Grubb, 2005)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2600095/&quot; rel=&quot;nofollow&quot;&gt;Agarwal et al., &lt;em&gt;Postgrad Med J&lt;/em&gt; 2007;&lt;strong&gt;83&lt;/strong&gt;:478–80&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://pmj.bmj.com/content/76/902/750.full&quot; rel=&quot;nofollow&quot;&gt;Arthus &amp;amp; Kaye, &lt;em&gt;Postgrad Med J&lt;/em&gt; 2000;&lt;strong&gt;76&lt;/strong&gt;:750-75&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://circ.ahajournals.org/content/111/22/2997.full&quot; rel=&quot;nofollow&quot;&gt;Grubb, &lt;em&gt;Circulation&lt;/em&gt; 2005;&lt;strong&gt;111&lt;/strong&gt;:2997-3006&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-25T02:05:04.673" LastActivityDate="2015-03-25T02:05:04.673" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30716" PostTypeId="2" ParentId="30712" CreationDate="2015-03-24T14:19:59.270" Score="2" Body="&lt;p&gt;According to a paper by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23578395&quot; rel=&quot;nofollow&quot; title=&quot;Walker et al. 2013. Silverfish silk is formed by entanglement of randomly coiled protein chains. Insect Biochem Mol Biol. 43(7):572-9. doi: 10.1016/j.ibmb.2013.03.014.&quot;&gt;Walker et al. (2013)&lt;/a&gt; (found by googling &quot;&lt;a href=&quot;https://www.google.se/search?q=silverfish+silk&amp;amp;ie=utf-8&amp;amp;oe=utf-8&amp;amp;gws_rd=cr&amp;amp;ei=wHARVZ_9L4j4ywP71oDYDA&quot; rel=&quot;nofollow&quot;&gt;silverfish + silk&lt;/a&gt;&quot;, so not very hard to come by), silverfish can indeed produce silk. The paper also mentions that silverfish (Thysanura) and bristletails (Archaeognatha) use silk to transfer their sperm, and they also use it for &quot;&lt;em&gt;...tactile cue during courtship (Sturm, 1956)&lt;/em&gt;&quot;. &lt;a href=&quot;http://www.cals.ncsu.edu/course/ent425/library/compendium/thysanura.html&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; webpage (from NY State University) explains that male silverfish will deposit a spermatophore on a silk thread that is vertically suspended, and the spermatophore is later picked up by a female. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Abstract:&lt;/strong&gt;&lt;br&gt;&#xA;  Silks are semi-crystalline solids in which protein chains are associated by intermolecular hydrogen bonding within ordered crystallites, and by entanglement within unordered regions. By varying the type of protein secondary structure within crystallites and the overall degree of molecular order within fibers, arthropods produce fibers with a variety of physical properties suited to many purposes. We characterized silk produced as a tactile stimulus during mating by the grey silverfish (Ctenolepisma longicaudata) using Fourier transform infrared spectroscopy, polarized Raman spectroscopy, gel electrophoresis and amino acid analysis. Fibers were proteinaceous-the main component being a 220 kDa protein-and were rich in Gln/Glu, Leu, and Lys. The protein structure present was predominantly random coil, with a lesser amount of beta-structure. Silk fibers could readily be solubilized in aqueous solutions of a mild chaotrope, sodium dodecyl sulfate, indicating protein chains were not cross-linked by disulfide or other covalent bonds. We conclude that entanglement is the major mechanism by which these silk proteins cohere into a solid material. We propose silks used as short-term tactile cues are subject to less stringent requirements for molecular order relative to other silks, allowing the random coil structure to be favored as an adaptation promoting maximal entanglement and adhesion.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The linked paper contains several references that should be useful if you want to look deeper into how silverfish use silk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I've seen, they don't use silk for climbing. Silverfish can usually climb rough surfaces, but not smooth surfaces, which is why they are often found trapped in sinks, bathtubs etc.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-03-24T21:51:24.337" LastActivityDate="2015-03-24T21:51:24.337" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="30717" PostTypeId="1" AcceptedAnswerId="30723" CreationDate="2015-03-24T14:46:58.013" Score="2" ViewCount="1672" Body="&lt;p&gt;I am not quite seeing how the T-tubule and sarcolemma is connected. It says that the T-tubule is an &quot;invagination&quot; of the sarcolemma, which is sarcolemma folded from the inside to form a T-tubule&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone verify whether the following picture is a good presentation of this relationship?&#xA;&lt;img src=&quot;https://i.stack.imgur.com/csFX0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="9020" LastEditDate="2015-03-24T16:45:33.290" LastActivityDate="2015-03-24T20:41:42.237" Title="Is the Klein's bottle a good analogy to the relation between T-tubule and sarcolemma?" Tags="&lt;muscles&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ClosedDate="2015-03-24T22:33:59.947" ContentLicense="CC BY-SA 3.0" />
  <row Id="30718" PostTypeId="2" ParentId="30675" CreationDate="2015-03-24T15:54:28.297" Score="0" Body="&lt;p&gt;Agree with the answer by @A.Kennard. Here's a punnet square to clarify your answer further. &#xA;&lt;img src=&quot;https://i.stack.imgur.com/hFIAO.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14932" LastActivityDate="2015-03-24T15:54:28.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30720" PostTypeId="1" CreationDate="2015-03-24T16:12:44.380" Score="5" ViewCount="5037" Body="&lt;p&gt;I was looking at one of David Goodsell's illustrations of a cell:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/r9V3y.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And it seems to suggest a very crowded picture of the intracellular environment. Just how crowded are cytoplasms? What percentage of the volume is typically taken up by protein, water, and other major species?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2015-03-24T21:46:44.277" Title="What percentage of a cell's volume is occupied by protein?" Tags="&lt;cell-biology&gt;&lt;proteins&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30721" PostTypeId="1" AcceptedAnswerId="30722" CreationDate="2015-03-24T18:41:18.863" Score="-1" ViewCount="8120" Body="&lt;p&gt;&lt;strong&gt;&lt;em&gt;How does one prepare concentrations in the mass/volume (weight/volume) form, for substances like nucleic acids or in this case, proteinase? A detailed example would be helpful.&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I need to prepare squishing buffer for a DNA extraction /PCR exercise to help me learn the materials better for a in class &quot;internship&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The squishing buffer recipe I found from a laboratory class manual describes it as: 10 mM of Tris-Cl, pH 8.2, 1 mM of EDTA, 25 mM of NaCl , and 200 µg/ml of proteinse K (freshly diulted).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand molarity concentrations well enough. One only has to determine the total molar mass of a substance, in this case NaCl, and with that molar mass (g/mol) then use the given desired molarity (in this case 25 mM of NaCl, which equals 0.025 mol /one liters) to get the number of grams of the substance needed. In this case, since we need 0.025 moles / 1 Liter, we would need to multiply that by the molar mass to get: (g/mol) X (mol/l) = g/l of NaCl.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand percent solutions (to a degree) as well. If I  needed 1% agrose gel, I would take 1 gram of agarose solid powder and bring that to 100 ml total to obtain a 1%, either using water or buffer?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am having trouble understanding the concepts of concentration, in reference to mg/ml. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I understand, µg/ml is a weight (mass)/volume type of concentration. Therefore, should it be the case that if I wanted to prepare&#xA;200 µg/ml of proteinase (freshly diluted), how would I go about it? Would I add 5 ml of deionized water to get a working volume of 1000 µg of proteinase per 5 ml of water, which would be equivalent to 1 mg of proteinase per 5 ml of water. From that 1mg of proteinase to 5ml of water, should I then draw 0.2 µl (or 200 ml) of solution to then have the 200 µg/ml? Or am I totally wrong? I tried googling for more information, but I became more and more confused.&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="3340" LastEditDate="2015-03-25T09:13:45.107" LastActivityDate="2015-03-25T18:15:28.093" Title="How to make µg/ml concentrations of proteinase-K?" Tags="&lt;lab-techniques&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30722" PostTypeId="2" ParentId="30721" CreationDate="2015-03-24T18:53:21.583" Score="2" Body="&lt;p&gt;It depends on what form your proteinase K is in.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;You may have a stock solution of some concentration, in which case you just add a specific volume according to $C_1V_1=C_2V_2$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Example:&lt;/strong&gt; Let's say you want to prepare 5 mL ($V_2$) of 200 µg/mL ($C_2$) proteinase K from a stock of 1000 µg/mL ($C_1$). You're looking for the volume of stock solution to add ($V_1$).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$V_1=\frac{5\ mL\ \cdot \ 200\ \mu g/mL}{1000\ \mu g/mL}=1\ mL$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you take 1 mL of the stock and bring it up to 5 mL.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Or you may have a lyophilized powder. In this case, you have two options:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) You can make a stock solution from the powder and, again, use $C_1V_1=C_2V_2$. This has the advantage of not having to weigh the powder every time you need to use it. This may not be a viable option, however, as I'm not sure of the stability of proteinase K in solution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) You can just weigh out the amount that will give you the desired concentration (which depends on the volume of buffer you're making).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Example:&lt;/strong&gt; Again, you want to prepare 5 mL of 200 µg/mL proteinase K. The total mass you need is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$200\ \mu g / mL\ \cdot \ 5\ mL=1000\ \mu g$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So weigh out a milligram and bring it up to 5 mL.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;There's nothing special about mass concentration; you can convert it to molarity given the molecular weight of proteinase K. &lt;a href=&quot;http://en.wikipedia.org/wiki/Proteinase_K&quot; rel=&quot;nofollow&quot;&gt;According to Wikipedia&lt;/a&gt;, proteinase K is 28.9 kDa or 28900 g/mol. If you are making this conversion, however, make sure you find the actual molecular weight of the protein you're using. 200 µg/mL is equal to:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{0.2\ g/L}{28900\ g/mol}=6.92\ \mu M$$&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-03-25T18:15:28.093" LastActivityDate="2015-03-25T18:15:28.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30723" PostTypeId="2" ParentId="30717" CreationDate="2015-03-24T19:47:42.780" Score="1" Body="&lt;p&gt;If we're looking at diagrams for the t-tubule with respect to the sarcolemma, we see the two are actually fused:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CcEWe.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6wTBx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The function therein is to allow depolarization to penetrate the interior of the cell quickly. The surface isn't transected anywhere, it simply folds inward. You can visualize this by sort of pushing a hole through some putty with a finger, and making a hole to the other side. Really no need to upvote me here, just easier to paste images in answers.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-03-24T20:41:42.237" LastActivityDate="2015-03-24T20:41:42.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30724" PostTypeId="2" ParentId="21337" CreationDate="2015-03-24T20:20:04.010" Score="5" Body="&lt;p&gt;First of all MHC stands for major histocompatibility complex. There are two types of MHC.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MHC type one is present on all of our cells with a nucleus. The purpose of these protein complexes is called antigen presentation. T-cells cannot recognize free antigens on their own, it has to be presented to them in the proper way. This is what these proteins do. In every cell there are lots and lots of proteins, that get digested to small polypeptides (short aminoacid sequences) by proteases during the natural recycling process. The cell takes a small portion of these polypeptides and presents them on its surface through MHC I complexes, that the immune system can read. This is like the cell saying to the immune syytem that &quot;hey I got these proteins in me&quot;. Now if the cell is infected (by a virus most likely) then the &quot;attacker's&quot; proteins get digested and presented as well and its like saying &quot; hey I'm infected and the attacker has these proteins&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;MHC II serves similar function but it is only present on professional antigen presenting cells (APCs). These complexes present peptides derived from proteins consumed and digested through phagocytosis or receptor mediated endocytosis. It's like saying &quot;hey we got a larger attacker and it has these proteins&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, long story short T-cells cannot recognise antigens on their own it needs to be presented to them on MHC complexes and then and only then can they be activated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: A list of useful articles in the topic of antigen processing / presentation for further details:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.annualreviews.org/doi/pdf/10.1146/annurev.immunol.16.1.323&quot; rel=&quot;nofollow&quot;&gt;January 14, 1998 14:59 Annual Reviews AR052-12&#xA;Annu. Rev. Immunol. 1998. 16:323–58&#xA;MECHANISMS OF MHC CLASS I–RESTRICTED ANTIGEN&#xA;PROCESSING Eric Pamer and Peter Cresswell&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://ac.els-cdn.com/0092867494903360/1-s2.0-0092867494903360-main.pdf?_tid=45c8f9b6-d6de-11e4-a641-00000aab0f27&amp;amp;acdnat=1427721267_90e23d9105d617574963766458f2b4ac&quot; rel=&quot;nofollow&quot;&gt;Cell, Vol. 76, 287-299, January 28, 1994. &#xA;MHC-Dependent Antigen Processing and Peptide Presentation: Providing&#xA;Ligands for T Lymphocyte Activation&lt;/a&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1600-065X.1999.tb01361.x/pdf&quot; rel=&quot;nofollow&quot;&gt;Terry Y Nakagawa, Alexaiider Y Kudensky&#xA;The role of lysosomal proteinases in MHC class Il-mediated antigen processing&#xA;and presentation&lt;/a&gt;&lt;br&gt;&#xA;This one may require subscription.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Antigen_processing&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt; page :)&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14826" LastEditDate="2015-03-30T16:24:45.130" LastActivityDate="2015-03-30T16:24:45.130" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30726" PostTypeId="2" ParentId="29661" CreationDate="2015-03-24T20:34:33.057" Score="0" Body="&lt;p&gt;This is an emotional response which elicits a physical response. All emotions stimulate the hypothalamus, a part of the brain, which controls responses such as goose bumps, increased heart rate, and sweating. With goose bumps, the hypothalamus is sending messages through the nerves to contract muscles in the skin, in effect creating 'goose bumps'. More chemical research needs to be done to further understand the pathways of emotional responses to music.&lt;/p&gt;&#xA;" OwnerUserId="12972" LastActivityDate="2015-03-24T20:34:33.057" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30728" PostTypeId="2" ParentId="30598" CreationDate="2015-03-24T20:45:44.190" Score="-1" Body="&lt;p&gt;Yes, as long as the person is able to blow air and 'shape' it using their tongue+lips, a person can whistle; even if it means this person lacks the ability to create the vibrational patterns necessary to talk. &lt;/p&gt;&#xA;" OwnerUserId="12972" LastActivityDate="2015-03-24T20:45:44.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30729" PostTypeId="2" ParentId="30579" CreationDate="2015-03-24T20:52:20.143" Score="1" Body="&lt;p&gt;Birds, like amphibians, have a third eyelid (the nicitating membrane) that helps them keeps their eyes moistened and allows them to better visualize at high speeds (or, for amphibians, underwater). The glands in birds' eyes allow them to secrete a fluid that is more resistant to evaporation than tears. The membrane also acts as a 'windshield wiper,' with each blink a birds' eyes are wiped free of excess fluid and debris.&lt;/p&gt;&#xA;" OwnerUserId="12972" LastActivityDate="2015-03-24T20:52:20.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30730" PostTypeId="1" CreationDate="2015-03-24T21:39:14.473" Score="3" ViewCount="186" Body="&lt;p&gt;As someone working with sequencing data and sequence files I was wondering whether is there a compression method / format for sequence / read files? Of course one can use general compressors like rar or zip to compress a fasta file, which is suitable for transferring data, but reading the sequence out of it is infeasible. Also I'm aware of BAM file format which is a block copressed gzip file of a SAM file, but as far as I know it is mainly used in alignments. But is there a compression for plain fastq(-like) files for storing millions of reads or a collection of sequences while being able to get sequence and quality info directly from the file?&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-03-24T22:55:52.640" LastActivityDate="2015-03-26T05:25:04.323" Title="Sequence compression method / format" Tags="&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30731" PostTypeId="2" ParentId="30720" CreationDate="2015-03-24T21:45:03.240" Score="1" Body="&lt;p&gt;According to the Molecular Biology of the Cell, (4th Ed), the cell is ~70% water, the remaining 30% of which is composed of macromolecules (proteins, nucleic acids, and carbohydrates). While this is just a single citation, there are lots of other sources in the literature that cite similar values. &lt;/p&gt;&#xA;" OwnerUserId="15098" LastActivityDate="2015-03-24T21:45:03.240" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30732" PostTypeId="2" ParentId="30720" CreationDate="2015-03-24T21:46:44.277" Score="2" Body="&lt;p&gt;The tricky part is to define what is the volume of a biomolecule as it is a folded chain full of bumps and holes. Water is all around and in the folded structure and is actually important to keep the conformation of at least some of the proteins/RNA/DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the same time we know that 60% of your body in mass is water. Let's visualize that. Bio molecules have roughly the same weight per volume than water. Now add into the equation that a good third of the filled actually is water due to the structure holes, adsorption etc. You now have roughly:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;% empty space = 60%-(40%/3)= 47%&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To help think about it imagine a grid with roughly one cell out of two being filled. That looks pretty crowded to me. Then you of course have variations with blood and secretions on one side and bones on the other but you have the big picture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For an example look at an electron microscopy picture of a striated muscle cell: &lt;a href=&quot;http://histology.med.umich.edu/sites/default/files/muscleQ4.jpg&quot; rel=&quot;nofollow&quot;&gt;http://histology.med.umich.edu/sites/default/files/muscleQ4.jpg&lt;/a&gt;. It looks pretty much like the half filled grid isn't it? Of course seeing individual molecules is hard but the white space correspond to mostly empty space with a couple of actine fibers. The dark corresponds to actine+myosine fibers: an extremely tight space. And we have roughly half of each :-)&lt;/p&gt;&#xA;" OwnerUserId="14615" LastActivityDate="2015-03-24T21:46:44.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30733" PostTypeId="2" ParentId="30730" CreationDate="2015-03-24T22:08:12.593" Score="3" Body="&lt;p&gt;BAM is the current standard for sequence alignments, and can be used to store unaligned reads/sequences, but when used for unaligned sequences also contains unused alignment data that would bloat the file. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An alternative way to compress a DNA sequence file is via 2-bit (or 4-bit encoding) which can compress the sequence content by 75% (in 2-bit encoding, each nucleotide can be represented by 2-bits in the file eg A: 00, G: 01, C: 10, T: 11). I do not know of a generalizable tool that will compress/decompress aside from rolling your own. Further, the data must be de-compressed prior to streaming it into any alignment/sequence software. For general purpose compression algorithms, bzip2 can outperform (at least in compression) other algorithms (eg zip, gzip)&lt;/p&gt;&#xA;" OwnerUserId="15098" LastActivityDate="2015-03-24T22:08:12.593" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30734" PostTypeId="2" ParentId="16150" CreationDate="2015-03-24T22:16:03.067" Score="4" Body="&lt;p&gt;Richard Dawkins discusses this in his book &lt;em&gt;The Greatest Show on Earth: The Evidence for Evolution&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The birds, in the aforementioned example Starlings, 'know' which direction to fly and where to be by obeying simple local rules concerning the distance and spacing of other members of the flock in their immediate vicinity, without any global knowledge of the size or shape of the flock in its entirety.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key to this behavior is that there is no choreographer and no leader.  Order, organization and structure all emerge as by-products of rules obeyed locally, many times over.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dawkins equates this to 'bottom-up' design or 'self-assembly'.  This is also how embryology works.  Beautifully 'designed' bodies emerge as a result of single cells obeying local rules.  The idea of a blueprint is a misconception.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dawkins mentions a man in the book named Craig Reynolds who wrote a program in 1986 called 'Boids' which models the flocking behavior of thousands of birds - &lt;a href=&quot;http://en.wikipedia.org/wiki/Boids&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Boids&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15097" LastActivityDate="2015-03-24T22:16:03.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30735" PostTypeId="1" CreationDate="2015-03-24T22:44:57.133" Score="1" ViewCount="33" Body="&lt;p&gt;I can't quite make out this teratoma:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/neu2F.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3900981/figure/F3/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;sup&gt;[Source: FIG 3B]&lt;/sup&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can kind of guess at ectoderm, mesoderm and endoderm structures based on generalized textbook developmental biology references but it looks like the stain was messed up. Shouldn't a hematoxylin-eosin stain be blue and red? Is this a legitimate confirmation of germ cell development from human pluripotent stem cells?&lt;/p&gt;&#xA;" OwnerUserId="10026" LastEditorUserId="3340" LastEditDate="2015-03-25T05:29:52.130" LastActivityDate="2015-03-25T05:29:52.130" Title="Is this a legitimate teratoma for a human pluripotent stem cell assay?" Tags="&lt;development&gt;&lt;histology&gt;&lt;stem-cells&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30736" PostTypeId="1" CreationDate="2015-03-24T23:09:42.713" Score="4" ViewCount="4321" Body="&lt;p&gt;If i needed to prepare 200µg/ml of proteinase K, and the proteinase K  was in a solid powder form, would I  have to weight out 200 µg using an analytical balance, and if so, is it possible with a balance that only goes up to four decimal places? (i.e. 0.0000) I assumed 1 microgram is 1×10&lt;sup&gt;-6&lt;/sup&gt; gram and therefore 0.000001 gram.&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="3340" LastEditDate="2015-03-25T05:21:20.740" LastActivityDate="2015-03-25T05:21:20.740" Title="Using an analytical balance (0.0000 precision) to measure µg (micrograms)?" Tags="&lt;lab-techniques&gt;&lt;measurement&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30738" PostTypeId="2" ParentId="30736" CreationDate="2015-03-24T23:17:31.153" Score="4" Body="&lt;p&gt;In this case make a large quantity and store it as stock - this is a general lab practice. Preparing 10 ml of your protK solurion would you need 2000ug (=2mg) of protK powder.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-03-24T23:17:31.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30739" PostTypeId="2" ParentId="30736" CreationDate="2015-03-24T23:32:53.800" Score="6" Body="&lt;p&gt;As others have said, that mass is too small to measure with a standard analytical scale. There are two options you could use:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Make a larger volume of your 200 ug/mL solution. &lt;/li&gt;&#xA;&lt;li&gt;Make a concentrated stock such as 20 mg/mL. This a 100X stock; you can make 1 mL of 200 ug/mL proteinase K with 10 uL of stock and 990 uL of buffer. Small volumes are easier to measure than small masses (with a micropipette). &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-03-24T23:32:53.800" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30740" PostTypeId="5" CreationDate="2015-03-25T00:11:29.903" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2015-03-25T00:11:29.903" LastActivityDate="2015-03-25T00:11:29.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30741" PostTypeId="4" CreationDate="2015-03-25T00:11:29.903" Score="0" Body="A toxin. Poison is defined by http://dictionary.reference.com/browse/poison as: a substance with an inherent property that tends to destroy life or impair health." OwnerUserId="6289" LastEditorUserId="6289" LastEditDate="2015-03-25T04:11:39.607" LastActivityDate="2015-03-25T04:11:39.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30742" PostTypeId="1" AcceptedAnswerId="30751" CreationDate="2015-03-25T00:12:44.363" Score="3" ViewCount="302" Body="&lt;p&gt;Was the most recent common ancestor of all swans black, or white, or some other color? How do we know, and how certain can we be?&lt;/p&gt;&#xA;" OwnerUserId="10184" LastEditorUserId="10184" LastEditDate="2015-03-25T06:06:11.657" LastActivityDate="2015-03-25T07:38:36.107" Title="What color was the most recent common ancestor of all swans?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30743" PostTypeId="1" AcceptedAnswerId="30749" CreationDate="2015-03-25T01:52:30.107" Score="2" ViewCount="68" Body="&lt;p&gt;I have not been able to find much information beyond what tests are normally done with Capillary puncture sampling, as opposed to what tests are possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could we test for a single micronutrient, or maybe some subset of nutrients with the blood drawn in this way? Is the issue purely volume, or are there other factors?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="15099" LastActivityDate="2015-03-25T05:37:26.027" Title="Is it possible to accurately measure micronutrient levels with the blood volume from a Dermal / Capillary puncture?" Tags="&lt;nutrition&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30745" PostTypeId="1" CreationDate="2015-03-25T02:44:22.967" Score="7" ViewCount="242" Body="&lt;p&gt;I'm interested in the concept of lineage selection &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0306987791902606&quot;&gt;(Aboitiz, 1991)&lt;/a&gt; as an explanation for why traits would be selected for that enhance the rate at which evolution can occur, rather than directly enhancing an individual's fitness. (Such traits could include gene duplication; body plans that can easily be adapted to new niches; learning (which enhances evolution due to the Baldwin effect) and so on. Questions about the evolution of such traits are collectively termed &quot;evolution of evolvability.&quot;) The term &quot;lineage selection&quot; does not refer to group selection or kin selection, but simply to selection between distinct genetic lineages in a mixed population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I would like to know is whether a mathematical theory has been developed along the lines of the Price equation that can capture the concept of lineage selection and make predictions about it. Lineage selection does not appear to be modelled by the Price equation itself, at least not in a straightforward and obvious way, because on the face of it the Price equation only directly accounts for the relation between a trait and the number of offspring in the &lt;em&gt;next&lt;/em&gt; generation, rather than the number of surviving descendants several generations later, which is what is required for lineage selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason I'm looking for a mathematical model is that there are a number of intuitions that many people seem to share about lineage selection and I'd like to understand what assumptions are needed in order for them to be true. In particular, it seems clear that large populations are needed for lineage selection to be effective, and I'd like to understand precisely the relationship between population size and the effectiveness of lineage selection. (My intuition is that with a population size of around a million, lineage selection can select for traits that have a beneficial effect around 20 generations later, since $1,000,000\approx 2^{20}$, but this intuition lacks a formal basis.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A literature search did not turn up anything along the lines of what I'm looking for, but this is not my main field and I may simply not know the most appropriate search terms to use.&lt;/p&gt;&#xA;" OwnerUserId="3347" LastActivityDate="2019-03-28T09:58:38.540" Title="Mathematical models of lineage selection" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;population-genetics&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="2" CommentCount="11" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30746" PostTypeId="1" AcceptedAnswerId="30750" CreationDate="2015-03-25T02:48:52.143" Score="3" ViewCount="399" Body="&lt;p&gt;What diagnostic applications, if any, are there in using bioluminescence to detect cancer or tumors (in vivo)?&lt;/p&gt;&#xA;" OwnerUserId="13023" LastEditorUserId="13023" LastEditDate="2015-03-27T17:03:01.267" LastActivityDate="2015-03-27T17:03:01.267" Title="Can bioluminescence be used for cancer or tumor detection?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;health&gt;&lt;cancer&gt;" AnswerCount="3" CommentCount="2" ClosedDate="2015-03-25T14:33:56.530" ContentLicense="CC BY-SA 3.0" />
  <row Id="30747" PostTypeId="2" ParentId="30702" CreationDate="2015-03-25T03:08:27.303" Score="1" Body="&lt;p&gt;Commercial yoghurt usually contains alive Lactobacillus, as exemplified by the fact that you can use them to &quot;seed&quot; your yoghurt at home. I actually don't think they &lt;em&gt;add&lt;/em&gt; anything. In France at least it is just pasteurized milk and lactobacillus (ex from &lt;a href=&quot;http://fr.openfoodfacts.org/produit/3596710047826/yaourt-nature-auchan&quot; rel=&quot;nofollow&quot;&gt;Auchan yogurt list of ingredients&lt;/a&gt;: Semi-skimmed milk, lactose and milk protein, lactic ferments). Some preparations that are not yoghurt &lt;em&gt;stricto-sensu&lt;/em&gt; might have &lt;a href=&quot;http://en.wikipedia.org/wiki/Yogurt#Sweetened_and_flavored_yogurt&quot; rel=&quot;nofollow&quot;&gt;added sugar, starch, pectin or gelatin&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think they just do yoghurt in an aseptic environment (&lt;a href=&quot;http://www.packworld.com/machinery/conveying-amp-material-handling/opa-greek-yogurt-company-celebrates-state-art-filling&quot; rel=&quot;nofollow&quot;&gt;ex&lt;/a&gt;) preventing bacteria other than Lactobacillus to chime in and further mess up the mix. That would go well with your own observation that opening the &quot;brand&quot; yoghurt make them &quot;spoil&quot; faster. &lt;/p&gt;&#xA;" OwnerUserId="14615" LastEditorUserId="14615" LastEditDate="2015-03-25T10:56:54.017" LastActivityDate="2015-03-25T10:56:54.017" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30748" PostTypeId="2" ParentId="30746" CreationDate="2015-03-25T05:15:45.843" Score="0" Body="&lt;p&gt;&lt;em&gt;In vivo&lt;/em&gt;, none.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bioluminescence is cool, but it's not a powerful light source. Even if you could tag a cancer cell (all of them), unless it were on your skin or in your eye, you wouldn't be able to see it, even with some kind of scope. &lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-03-25T05:15:45.843" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30749" PostTypeId="2" ParentId="30743" CreationDate="2015-03-25T05:37:26.027" Score="3" Body="&lt;p&gt;Detection methods are constantly getting better, requiring lesser amounts of blood to make a determination. In newborns, a heel blood sample (of capillary blood) is used to detect up to 40 (sometimes more) disorders from maple-sugar urine disease and hypothyroidism to hemoglobinopathies and organic acid conditions. If such large molecules can be detected in capillary blood, smaller molecules should as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are differences in central venous sampling and capillary blood sampling, but it could be argued that since the capillaries are the site of exchange of nutrients, this is the most accurate site to determine availability of micronutrients in blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One reason labs take more blood than required for the test is to run a second analysis if the first is abnormal. Although it's not done for every abnormal, clinicians often want to confirm significant abnormals before treating a possible lab error.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/007257.htm&quot; rel=&quot;nofollow&quot;&gt;Newborn screening tests&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.cdc.gov/ncbddd/newbornscreening/&quot; rel=&quot;nofollow&quot;&gt;Newborn Screening&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.babysfirsttest.org/newborn-screening/states/pennsylvania&quot; rel=&quot;nofollow&quot;&gt;Conditions Screened By State&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://masspec.scripps.edu/metabo_science/Tandem%20Mass%20Spectrometry%20Chace.pdf&quot; rel=&quot;nofollow&quot;&gt;A Layperson's Guide to Tandem Mass Spectrometry&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-03-25T05:37:26.027" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30750" PostTypeId="2" ParentId="30746" CreationDate="2015-03-25T06:06:52.403" Score="3" Body="&lt;p&gt;Not in human but you can use this technique with genetically modified model organisms as described &lt;a href=&quot;http://www.ingentaconnect.com/content/aalas/cm/2004/00000054/00000006/art00005?token=004a10c8405847447b49762f7b7342425e2079475833757e6f4f2858592f3f3b579225a506&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The procedure is quite simple, you express the luciferase enzyme under the control of a specific promoter (specific for your cell type, like cancer) and provide luciferin via intravascular or intraperitoneal injection. The targeted cell type (for example cancer) will light up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to use that as a &lt;strong&gt;diagnostic tool in human you can't&lt;/strong&gt; as the organism must express an enzyme catalyzing a bioluminescent reaction. Actually with the advance of genome engineering tools you might be able to do that even in humans (e.g. using &lt;a href=&quot;http://en.wikipedia.org/wiki/CRISPR&quot; rel=&quot;nofollow&quot;&gt;CRISP/Cas9&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the advantage of bioluminescence over fluorescence? I might be wrong but I don't think there are any. I would rather express a fluorophore rather than an enzyme that requires a substrat.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-25T06:12:22.453" LastActivityDate="2015-03-25T06:12:22.453" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="30751" PostTypeId="2" ParentId="30742" CreationDate="2015-03-25T07:38:36.107" Score="4" Body="&lt;p&gt;According to the known phylogeny of Anserinae &lt;a href=&quot;http://sysbio.oxfordjournals.org/content/45/4/415.full.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;in this paper&lt;/a&gt;, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/USXfl.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Cygnus atratus&lt;/em&gt; (the black swan) is most closely related to &lt;em&gt;Cygnus melanocoryphus&lt;/em&gt; (the black-necked swan). All of the other swans in the genus &lt;em&gt;Cygnus&lt;/em&gt; are white, or close to white. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, it is reasonable to assume via &lt;a href=&quot;http://en.wikipedia.org/wiki/Maximum_parsimony_%28phylogenetics%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;maximum parsimony&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Maximum_likelihood&quot; rel=&quot;nofollow noreferrer&quot;&gt;maximum likelihood&lt;/a&gt; that the two genera evolved their blackness from a white ancestor, and not that all of the swans independently turned white from a black ancestor. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-03-25T07:38:36.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30753" PostTypeId="2" ParentId="30745" CreationDate="2015-03-25T10:25:33.510" Score="3" Body="&lt;p&gt;The writings by Samir Okasha (philosopher of biology/science) could be a good starting point. In his book &lt;a href=&quot;http://www.oxfordscholarship.com/view/10.1093/acprof:oso/9780199267972.001.0001/acprof-9780199267972&quot; rel=&quot;nofollow&quot; title=&quot;Okasha. 2006. Evolution and the Levels of Selection. Oxford University Press&quot;&gt;Evolution and the Levels of Selection&lt;/a&gt;, he explicitly uses the Price equation to discuss selection at multiple levels (e.g. chapter 2.3: Price's equation in a hierarchical setting), and also derives a multi-level version of the Price equation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\bar{w}\Delta\bar{z} = Cov(W,Z) + E(Cov_k(w,z))$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where the first part on the right hand side represents collective-level selection and the second part particle-level selection. This is mostly aimed at aspects of group-level selection though. There is also a chapter on &quot;&lt;em&gt;Species Selection, Clade Selection, and Macroecolution&lt;/em&gt;&quot; (ch. 7), but this is not directly tied to the Price equation. A note though; I own the book and have read parts of it casually, but I haven't worked with the Price equation myself, and I haven't checked exactly how the extended version of the Price equation is developed and used in the book.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A couple of references that might be useful are &lt;a href=&quot;http://press.princeton.edu/titles/6360.html&quot; rel=&quot;nofollow&quot; title=&quot;Frank. 1998. *Foundations of Social Evolution*. Princeton UP&quot;&gt;Frank (1998)&lt;/a&gt; (and other papers by him) and papers by Vrba. The work presented in &lt;a href=&quot;https://gsa.confex.com/gsa/2014AM/webprogram/Paper247086.html&quot; rel=&quot;nofollow&quot; title=&quot;Rankin et al. 2014. Using the extended price equation to analyze species selection in mammalian body size evolution across the paleocene/eocene thermal maximum. Conference abstract for GSA 2014&quot;&gt;this&lt;/a&gt; recent conference abstract by Rankin, Fox et al (2014), &quot;&lt;em&gt;Using the Extended Price Equation to Analyze Species Selection in Mammalian Body Size Evolution Across the Paleocene/eocene Thermal Maximum&lt;/em&gt;&quot;, seems to describe exactly the type of theoretical developments that you are looking for (I didn't attend the conference, and haven't heard the talk though).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-03-25T14:25:07.683" LastActivityDate="2015-03-25T14:25:07.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30755" PostTypeId="2" ParentId="6869" CreationDate="2015-03-25T12:20:07.373" Score="0" Body="&lt;p&gt;Yawning increases pressure in eustachian tube because it takes place during inspiratory phase of respiration, so pushes Ear drum on the outer side&lt;/p&gt;&#xA;" OwnerUserId="15103" LastActivityDate="2015-03-25T12:20:07.373" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30758" PostTypeId="1" CreationDate="2015-03-25T13:03:10.747" Score="5" ViewCount="280" Body="&lt;p&gt;I am not sure if this is the right place for this question, but this is a debate that has been going on between two colleagues for days and I need a resolution because it's driving me crazy. So any help would be appreciated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is a common philosophical argument that it is impossible for one person to know if another person is at the same place on the colour wheel (e.g. how I see blue and how you see blue could be different, and we will never know). By that reasoning, it is possible that some species see colours differently to us. However, black and white are not the colour wheel because they are not colours. So essentially, the question is, &lt;strong&gt;could another species that &quot;sees&quot; by sensing light with their eyes as humans do ever see an &quot;absence of light&quot; as a colour OTHER than black&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not quite sure what these two imbeciles are debating, but I believe they are arguing as follows:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Party 1: Black and white are shades not colours, and therefore, even if another species saw colours differently, they would always see black as black, white as white, and all shades of grey relative as usual to the colours they see.&lt;/li&gt;&#xA;&lt;li&gt;Party 2: Black is only inserted into our vision by our brain to resolve the &quot;problem&quot; of not receiving any light. So, therefore, it is equally possible that another species could deal with this problem&quot; differently, and they will see something other than black.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="15107" LastEditorUserId="5144" LastEditDate="2015-03-25T13:07:09.107" LastActivityDate="2015-03-25T13:55:06.973" Title="Can other animals see black differently?" Tags="&lt;vision&gt;&lt;light&gt;&lt;senses&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30759" PostTypeId="1" CreationDate="2015-03-25T13:36:47.310" Score="1" ViewCount="124" Body="&lt;p&gt;I found the following homology ratio:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;protein coding genes of the organism with an homolog in mouse / all protein coding genes in the organism&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have done this for all protein coding genes between several organisms and mouse using a phylogenetic-based approach. I have noticed that the ratio found between an organism and mouse is greater than the ratio between another organism and mouse! On the other hand the second is evolutionary closer to mouse than the first.So:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1.Is such an approach trying to quantify homology? Which i know is not correct as homology is qualitive measure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2.Can we compare the ratio of homology between the above 2 couples od species or such a comparison is biased?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3.Shouldn't the ratio of homology be proportional to the evolutionary distance of the organisms (according to conservation)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can understand, in the way i calculate the above ratio, i don't take into account the one-to-many or many-to many relationships! I just take into account the genes that have at least one homolog in mouse..is that the bias of my calculation?&lt;/p&gt;&#xA;" OwnerUserId="15108" LastActivityDate="2015-04-14T22:25:51.390" Title="Homology ratio comparison between different species" Tags="&lt;evolution&gt;&lt;homology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30760" PostTypeId="2" ParentId="30746" CreationDate="2015-03-25T13:47:28.903" Score="0" Body="&lt;p&gt;Bioluminescence could not be used but it is possible to 'tag' with fluorescence to better view pathways within the body. Tagging is often used in research, a simple google search should produce a plethora of results. &lt;/p&gt;&#xA;" OwnerUserId="12972" LastActivityDate="2015-03-25T13:47:28.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30761" PostTypeId="2" ParentId="30758" CreationDate="2015-03-25T13:55:06.973" Score="1" Body="&lt;p&gt;Yes, animals can see 'black' differently, in terms of different shades, similar to what you stated about humans perceiving different hues of 'blue'. It is all relative to the cones in the eye of the referenced animal. Animals that see in black-and-white see several different hues of both, black and white. Animals that depend on color to judge the ripeness of a food also see in several different hues of black. For example, a parrot differentiating between seeds that humans may perceive as both being 'black'. Here is a color chart showing the colors that bees can perceive in juxtaposition to humans; it indicates high differentiation between hues of black, as opposed to humans' low differentiation.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/z7siJ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="12972" LastActivityDate="2015-03-25T13:55:06.973" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30762" PostTypeId="1" AcceptedAnswerId="30763" CreationDate="2015-03-25T14:01:19.223" Score="4" ViewCount="3080" Body="&lt;p&gt;As far as I understood it, both are cases of karyokinesis, not followed by cytokinesis. &lt;/p&gt;&#xA;" OwnerUserId="15109" LastEditorUserId="15109" LastEditDate="2015-03-25T15:11:43.467" LastActivityDate="2018-01-18T00:20:08.553" Title="Are free-nuclear division and endomitosis the same?" Tags="&lt;cell-division&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30763" PostTypeId="2" ParentId="30762" CreationDate="2015-03-25T14:58:16.287" Score="1" Body="&lt;p&gt;No. If you google the terms you'll get a lot of sites with definitions. For example:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Nuclear division&lt;/p&gt;&#xA;&lt;p&gt;Definition&lt;/p&gt;&#xA;&lt;p&gt;noun&lt;/p&gt;&#xA;&lt;p&gt;The process by which a nucleus divides, resulting in the segregation of the genome to opposite poles of a dividing cell.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;source: &lt;a href=&quot;http://www.biology-online.org/dictionary/Nuclear_division&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.biology-online.org/dictionary/Nuclear_division&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Edit:&lt;/p&gt;&#xA;&lt;p&gt;or&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;free nuclear division    mitotic division of nuclei without accompanying cytokinesis, i.e. nuclei divide in a common cytoplasm, the cells walls only forming around each later&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;source: &lt;a href=&quot;http://ecflora.cavehill.uwi.edu/bio_courses/bl14apl/Gloss.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://ecflora.cavehill.uwi.edu/bio_courses/bl14apl/Gloss.htm&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;versus&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;endomitosis&#xA;mitosis taking place without dissolution of the nuclear membrane, and not followed by cytoplasmic division, resulting in doubling of the number of chromosomes within the nucleus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;source: &lt;a href=&quot;http://medical-dictionary.thefreedictionary.com/endomitosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://medical-dictionary.thefreedictionary.com/endomitosis&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;or a bit more revealing:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Duplicated chromosomes produced by endomitosis exist as discrete units&#xA;in a single polyploid nucleus or may be packaged into separate nuclei,&#xA;depending on the phase at which mitosis is aborted&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;source: &lt;a href=&quot;http://en.wikipedia.org/wiki/Endoreduplication&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Endoreduplication&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;So as you see by definition nuclear division is part of a bigger process (cell division), and accoriding to the first source karyokinesis is a synonim for nuclear division (karyo = nucleus kinesis = moving, both come form greek language).&lt;/p&gt;&#xA;&lt;p&gt;Edit:&lt;/p&gt;&#xA;&lt;p&gt;If you check the definition above, you can see that free-nuclear division is a mitosis without cytokinesis, thus chromosome separation still occurs.&lt;/p&gt;&#xA;&lt;p&gt;In endomitosis the can end up with a polyploid nucleus, in contrast to the other two aforementioned mechanism where no polyploidy occurs.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-03-25T15:32:39.713" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30764" PostTypeId="1" CreationDate="2015-03-25T17:22:04.117" Score="6" ViewCount="245" Body="&lt;p&gt;Women possess two X chromosomes. However, during development, when the embryo has about 32 - 64 cells, one of these chromosomes is randomly inactivated (in each cell) by an lncRNA named Xist. As a consequence, females are mosaics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was interested if this might affect phenotypes of X-linked genetic diseases, for example...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Is it possible for a woman who is heterozygote to color vision deficiency be &quot;partially&quot; color blind, considering that some of her cones will only possess the mutated allele?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Is it possible that a heterozygote female who carries a dominant allele for a X-linked disease be asymptomatic?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any references on these issues are welcome.&lt;/p&gt;&#xA;" OwnerUserId="14630" LastEditorUserId="9943" LastEditDate="2015-06-12T12:18:47.600" LastActivityDate="2015-07-12T14:34:07.170" Title="Can a woman possessing 1 mutated allele show attenuated color-vision deficiency?" Tags="&lt;genetics&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30765" PostTypeId="1" CreationDate="2015-03-25T17:29:48.987" Score="2" ViewCount="32" Body="&lt;p&gt;For example, consider a gene X which has an intron which encodes a miRNA that downregulates expression of another gene Y.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the gene X is translated, this miRNA will appear as a byproduct of splicing, then expression of gene X will inhibit expression of gene Y, which could be deleterious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How did the mechanisms of gene expression evolve to avoid possible unplanned interference in gene expression?&lt;/p&gt;&#xA;" OwnerUserId="14630" LastEditorUserId="3340" LastEditDate="2015-03-25T17:53:42.707" LastActivityDate="2015-03-25T17:53:42.707" Title="Can encoding of miRNAs in introns not cause dysregulation of gene expression?" Tags="&lt;molecular-biology&gt;&lt;rna-interference&gt;" AnswerCount="0" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30766" PostTypeId="1" AcceptedAnswerId="30768" CreationDate="2015-03-25T17:48:25.310" Score="4" ViewCount="18129" Body="&lt;p&gt;If I am blood type B, what are all the possible genotypes that could be expressed by my parents?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think it might be 16 but I was reading online and saw this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Similarly, someone who is blood type B could have a genotype of either&#xA;  BB or BO.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So if someone can help me answer this, that would be great.&lt;/p&gt;&#xA;" OwnerUserId="15110" LastEditorUserId="14826" LastEditDate="2015-03-29T18:45:58.060" LastActivityDate="2015-10-30T09:13:10.743" Title="Possible genotypes for blood types?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;hematology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30768" PostTypeId="2" ParentId="30766" CreationDate="2015-03-25T18:39:06.537" Score="9" Body="&lt;p&gt;&lt;strong&gt;Parent 1 and 2 have each 5 possible genotypes&lt;/strong&gt; (OO, AO, BB, BO and AB).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here a &lt;a href=&quot;http://www.moveeatlivewell.com/2012/02/blood-type-genetics.html&quot; rel=&quot;noreferrer&quot;&gt;Punnett square&lt;/a&gt; with each possibilities. I highlighted the possible parent genotypes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Mp8NG.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The total number of possible crosses is exactly 21&lt;/strong&gt;. Note that here A = Ia, B = Ib and O = i.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;OOxBB,OOxBO,OOxAB&lt;/li&gt;&#xA;&lt;li&gt;AOxBB,AOxBO,AOxAB&lt;/li&gt;&#xA;&lt;li&gt;BBxOO,BBxAO,BBxBB,BBxBO,BBxAB&lt;/li&gt;&#xA;&lt;li&gt;BOxOO,BOxBB,BOxAO,BOxBO,BOxAB&lt;/li&gt;&#xA;&lt;li&gt;ABxOO,ABxAO,ABxBB,ABxBO,ABxAB&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This is starting from the information based on your blood type only (i.e. no information about your genotype).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some background information. Antigen expressing alleles (here referred as Ia or A and Ib or B) are dominant. Not expressing an allele is notated i or O. Being of blood type O is when you don't express both alleles so it is a recessive trait (only possible genotype is ii or OO genotype).&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-25T19:02:40.447" LastActivityDate="2015-03-25T19:02:40.447" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30770" PostTypeId="1" CreationDate="2015-03-25T19:47:00.553" Score="4" ViewCount="503" Body="&lt;p&gt;Does the membrane potential usually quoted for Gram negative bacteria (&lt;em&gt;e.g.&lt;/em&gt;, &lt;em&gt;E. coli&lt;/em&gt;) refer to the potential across both membranes? - If yes, then does the potential fall more over the inner or outer membrane? Are there any studies that estimate/measure the relative fraction for each membrane?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume that the measurements of potential are usually carried out by inserting an electrode inside the cell and measuring the difference with the outside, this would make the answer to the first question yes.&lt;/p&gt;&#xA;" OwnerUserId="15113" LastEditorUserId="9943" LastEditDate="2016-05-03T12:43:23.317" LastActivityDate="2016-05-03T22:10:24.443" Title="Are Gram negative bacteria classified as such because of their negative membrane potential?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;terminology&gt;&lt;cell-membrane&gt;&lt;electrophysiology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30771" PostTypeId="1" AcceptedAnswerId="30774" CreationDate="2015-03-25T20:06:27.207" Score="2" ViewCount="154" Body="&lt;p&gt;Can the DNA polymerase in PCR (polymerase chain reaction) recognize both DNA and RNA for use as a template?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know is it possible if my primers bind to contaminant RNA and then any DNA polymerase like Taq DNA polymerase use this strand as the template for elongation?&lt;/p&gt;&#xA;" OwnerUserId="9101" LastEditorUserId="6307" LastEditDate="2017-05-20T05:29:10.973" LastActivityDate="2017-05-20T05:29:10.973" Title="DNA polymerase in PCR (polymerase chain reaction)" Tags="&lt;molecular-biology&gt;&lt;pcr&gt;&lt;polymerase&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30772" PostTypeId="1" CreationDate="2015-03-25T20:26:56.317" Score="1" ViewCount="154" Body="&lt;p&gt;I am aware that ingesting Branched chain amino acids (BCAA's) prior, during, and after workouts has an effect on muscle recovery due to their difficulty of metabolism. However, how much more efficiently do they speed up recovery versus whey proteins for example? &lt;/p&gt;&#xA;" OwnerUserId="12959" LastEditorUserId="14826" LastEditDate="2015-03-29T07:39:46.660" LastActivityDate="2015-03-29T07:39:46.660" Title="How do BCAA's promote faster muscle recovery?" Tags="&lt;proteins&gt;&lt;muscles&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30774" PostTypeId="2" ParentId="30771" CreationDate="2015-03-25T22:04:15.767" Score="5" Body="&lt;p&gt;No, this does not happen, as the DNA polymerases used for PCR are DNA dependent. This means that they only synthesize DNA when it is bound to DNA. Even if your primers bind to the RNA, the polymerase will not starting new strands here. To use RNA as a template for PCR you first need to reverse transcribe it.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-03-25T22:04:15.767" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30775" PostTypeId="1" AcceptedAnswerId="30913" CreationDate="2015-03-25T23:02:38.653" Score="3" ViewCount="2966" Body="&lt;p&gt;I need to optimize a transfection protocol to transiently express a plasmid encoding a chimera of  eyfp attached to the c term of a Golgi apparatus signaling molecule) in hela cells and hepg2 cells and get as high expression as I can get.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I need enough protein for about 100 wb's. I've seeded hela cells to 12 150mm dishes. And the same with the hepg2. I've prepped mg's of plasmid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm using invitrogens &lt;strong&gt;original&lt;/strong&gt; lipofectamine reagent; not the 2000, or ltx or any of that stuff.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any suggestions on a protocol here for hela and hepg2 plasmid dna and lipofectamine mediated transfection on such a large plate size. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I figure just scaling up should work but there's some pitfalls here. Look at this table for example when you go from 60 to 100 mm you about double the area, so you also about double the culture volume. However when you go from 100 to 150mm you triple the area, but only increase the culture volume two fold about. This is making my scale-up calculations for transfection look really off:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xRetR.jpg&quot; alt=&quot;culture volumes and areas&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2015-03-26T00:21:25.163" LastActivityDate="2015-03-30T16:41:53.753" Title="Cationic lipid mediated transfection optimization for 150mm dishes" Tags="&lt;cell-culture&gt;&lt;transfection&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30776" PostTypeId="1" AcceptedAnswerId="30789" CreationDate="2015-03-25T23:12:14.153" Score="6" ViewCount="437" Body="&lt;p&gt;Are food additives like vitamins better absorbed when you mix them among fruits? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I heard that secondary substances in fruit promote the absorption. &lt;/p&gt;&#xA;" OwnerUserId="5344" LastEditorUserId="14826" LastEditDate="2015-03-26T03:14:01.103" LastActivityDate="2015-03-26T04:56:54.967" Title="Can the absorption of vitamins be enhanced?" Tags="&lt;vitamins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30778" PostTypeId="1" CreationDate="2015-03-25T23:45:13.380" Score="2" ViewCount="177" Body="&lt;p&gt;It is often heard that home-grown fruits and veggies are a lot tastier than the produce found in the supermarket. Although this question may contain a skeptics element in it, it is so often heard there must be at least some biological ground behind it.   &lt;/p&gt;&#xA;" OwnerUserId="15115" LastEditorUserId="9943" LastEditDate="2015-03-26T02:14:30.013" LastActivityDate="2015-03-26T02:14:30.013" Title="Why do home-grown fruits tend to taste better than mass-produced consumer fruits?" Tags="&lt;fruit&gt;&lt;taste&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2015-03-26T05:58:58.887" ContentLicense="CC BY-SA 3.0" />
  <row Id="30780" PostTypeId="2" ParentId="30778" CreationDate="2015-03-26T00:31:18.110" Score="3" Body="&lt;p&gt;&quot;Industrial&quot; fruits and vegetables are not grown as much for flavor as for convenience, pest resistance, appearance, resistance to peel problems, resistance to bruising, etc. etc. Profitability is the main consideration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many varieties of apple grown in orchards that taste &lt;em&gt;wonderful&lt;/em&gt; (better than my grandmother's gnarly green apples) but don't hold up to shipping and storage well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, please don't get your information from fantasy tales. There are so many good sites for attaining information.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-03-26T00:31:18.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30781" PostTypeId="1" AcceptedAnswerId="30784" CreationDate="2015-03-26T00:59:52.640" Score="4" ViewCount="152" Body="&lt;p&gt;A simple daily event has amazed me and triggered this question. I have read and heard about hand-eye coordination. It quite straightforward when you e.g. want to open a door or play Xbox. In this case either your hand is in your view or your hand will feel the buttons of your Xbox.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But when it comes to catching a ball or try to catch a falling object, our hand is totally out of our view since we are closely following the trajectory of the moving object. But meanwhile our hands moves in a 3D space and align it self perfectly in the path of trajectory correctly. This is what amazed me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you can see your hand and the object/ball simultaneously, its just a matter of moving our hand in the path of that ball/object. But having hands totally out of sight but catching the ball/object perfectly every time is amazing piece of nature's engineering.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How humans have achieved such a amazing piece of coordination in a 3D space without seeing where the hands are located?&lt;/p&gt;&#xA;" OwnerUserId="15117" LastEditorUserId="14735" LastEditDate="2015-03-26T13:33:24.910" LastActivityDate="2015-03-26T13:33:24.910" Title="Hand-eye coordination in 3D space" Tags="&lt;muscles&gt;&lt;sensation&gt;&lt;neurophysiology&gt;&lt;movement&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30782" PostTypeId="1" CreationDate="2015-03-26T01:13:41.427" Score="1" ViewCount="90" Body="&lt;p&gt;What floral organ does the development of the embryos of angiosperms occurs in? Is it the ovary? The pollen tube grows down through the style and double fertilization occurs and the embryo begins to develop in the megasporangium.&lt;/p&gt;&#xA;" OwnerUserId="15116" LastEditorUserId="14826" LastEditDate="2015-03-29T07:40:05.053" LastActivityDate="2017-10-24T03:48:32.140" Title="Location of embryo development in angiosperms" Tags="&lt;botany&gt;&lt;reproduction&gt;&lt;plant-anatomy&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30783" PostTypeId="1" CreationDate="2015-03-26T02:50:10.567" Score="3" ViewCount="93" Body="&lt;p&gt;RNAi became famous after Fire and Mello experiment in C.elegans; however, it had been observed before. In the 80's, Jorgensen was trying to increase pigmentation of Petunia flowers by introducing extra copies of chalcone synthetase gene, which encodes an enzyme involved in anthocyanin synthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, this experiment lead to post transcriptional gene silencing (PTGS) by a mechanism that was not understood at that time, called RNA interference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sbs.utexas.edu/bio350m/lecnotes/Lec15_RNAi%20%28PTGS%29.ppt&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt;&#xA;you might find more information about the experiment (including the vector used to introduce the gene).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know how RNAi works by the classical pathway; however, I didn't understand how an extra copy of the gene could generate gene silencing. Introducing of DNA sequences has been used to knock downs target genes, however, generally these sequences are planned so that they will form a hairpin which is recognised by Dicer; probably, the researcher did not use such a sequence. Moreover, exogenenic genes are widely used without resulting in unplanned RNAi.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does someone know more information about what possibly happened in the experiment to produce RNAi?&lt;/p&gt;&#xA;" OwnerUserId="14630" LastActivityDate="2015-04-04T19:00:00.567" Title="Why introduction of an extra copy of a gene related to pigmentation causes RNA interference in Petunia?" Tags="&lt;molecular-biology&gt;&lt;gene-expression&gt;&lt;rna-interference&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30784" PostTypeId="2" ParentId="30781" CreationDate="2015-03-26T02:54:02.037" Score="6" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;&lt;em&gt;Proprioceptic&lt;/em&gt; receptors provide a feedback mechanism from the body to the brain, telling the brain what our limbs are doing and where they are with respect to the body without visual feedback being needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Muscles, skin and joints contain &lt;em&gt;proprioceptic receptors&lt;/em&gt;. They &lt;em&gt;sense position and movement of our limbs&lt;/em&gt; and trunk, they register force as well as heaviness. Examples of such receptors are limb tendon organs and possibly also muscle spindles, which contribute to the senses of force and heaviness. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Proprioceptive sensations are influenced by visual input, but operate without it. The proprioceptive system is responsible for the ability to touch your nose with your eyes closed and the examples you have given related to catching a ball while not paying visual attention to the position of your hands.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Afferent signals from these receptors are combined and processed in the brain. Together they form information about limb position and movement. This information is mapped relative to a central body map to determine the location of the limbs in space.  The proprioceptive senses, particularly of limb position and movement, deteriorate with age and are associated with an increased risk of falls in the elderly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://physrev.physiology.org/content/92/4/1651&quot;&gt;Proske &amp;amp; Gandevia, &lt;em&gt;Phys Rev&lt;/em&gt; 2012; &lt;strong&gt;92&lt;/strong&gt;:1651-97&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-26T12:14:37.287" LastActivityDate="2015-03-26T12:14:37.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30786" PostTypeId="2" ParentId="30413" CreationDate="2015-03-26T04:40:45.363" Score="0" Body="&lt;p&gt;The Latent period is caused by:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Time taken for the stimulus to travel along the nerve to the neuromuscular junction&lt;/li&gt;&#xA;&lt;li&gt;Time taken for the impulse to cross the neuromuscular junction and to stimulate the muscle&lt;/li&gt;&#xA;&lt;li&gt;Time taken for the excitation-contraction coupling to occur&lt;/li&gt;&#xA;&lt;li&gt;Time taken by the lever to overcome the inertia of rest&lt;/li&gt;&#xA;&lt;li&gt;Time taken to overcome the vicous resistance of the muscle.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The latent period is usually about 10 ms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xPBAo.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Taken from Textbook of Practical Physiology Edition 2, by GK Pal &amp;amp; Pravati Pal&lt;/p&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-03-26T04:40:45.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30787" PostTypeId="1" AcceptedAnswerId="30826" CreationDate="2015-03-26T04:42:54.523" Score="4" ViewCount="330" Body="&lt;p&gt;This may be a bit abrupt/vague question, but I didn't know how to proceed the search to get the answer.&lt;br&gt;&#xA;What are the properties of a 3D biomolecule which gets ignored when a 3D biomolecule is converted to 1D representation in SMILES(Simplified molecular-input line-entry system)? two properties I found that gets neglected are linkages,interaction properties. By properties I meant isomeric count,isomeric threshold etc. Are there anymore properties that gets neglected?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="14826" LastEditDate="2015-03-26T17:26:53.100" LastActivityDate="2016-11-11T15:00:50.670" Title="Simplified molecular-input line-entry system" Tags="&lt;bioinformatics&gt;&lt;structural-biology&gt;&lt;3d-structure&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30788" PostTypeId="2" ParentId="8897" CreationDate="2015-03-26T04:46:38.097" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dream&quot; rel=&quot;nofollow&quot;&gt;Dreams&lt;/a&gt; are simulations created by the brain in order to train us to cope with challenging situations. Most of the dreams present situations where the individual is confronted with challenges or risks he/she might face during the life. Evolutionary concept of dream suggests that its a way by which brain try to notify some risks and train us to invade through it. The evolutionary acceptance of dreams is due to the &quot;threat simulation&quot; feature it possess. By which an individual can gain advantage of several situations he/she confronts in life.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Finnish psychologist Antti Revonsuo posits that dreams have evolved&#xA;  for &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dream#Evolutionary_psychology_theories_of_dreams&quot; rel=&quot;nofollow&quot;&gt;threat simulation&lt;/a&gt;&quot; exclusively. According to the Threat&#xA;  Simulation Theory he proposes, during much of human evolution physical&#xA;  and interpersonal threats were serious, giving reproductive advantage&#xA;  to those who survived them. Therefore dreaming evolved to replicate&#xA;  these threats and continually practice dealing with them. In support&#xA;  of this theory, Revonsuo shows that contemporary dreams comprise much&#xA;  more threatening events than people meet in daily non-dream life, and&#xA;  the dreamer usually engages appropriately with them. It is suggested&#xA;  by this theory that dreams serve the purpose of allowing for the&#xA;  rehearsal of threatening scenarios in order to better prepare an&#xA;  individual for real-life threats.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Question 1&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Yes they do. Studies suggests that animals can dream while sleeping, entire  human dreams occur during the &lt;a href=&quot;http://en.wikipedia.org/wiki/Rapid_eye_movement_sleep&quot; rel=&quot;nofollow&quot;&gt;REM&lt;/a&gt; sleep period. Most of the mammals do have the REM sleep period and it suggests that they do dream in this time of sleep.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dreams occur during REM sleep. We typically have 3 to 5 periods of REM&#xA;  sleep per night. They occur at intervals of 1-2 hours and are quite&#xA;  variable in length. An episode of REM sleep may last 5 minutes or over&#xA;  an hour. About 20% of sleep is REM sleep. If you sleep 7-8 hours a&#xA;  night, perhaps an hour and half of that time, 90 minutes, is REM&#xA;  sleep.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;REM sleep is characterized by a number of other features including&#xA;  rapid, low-voltage brain waves detectable on the&#xA;  electroencephalographic (EEG) recording, irregular breathing and heart&#xA;  rate and involuntary muscle jerks.&#xA;  &lt;a href=&quot;http://www.medicinenet.com/script/main/art.asp%3Farticlekey%3D8677+&amp;amp;cd=15&amp;amp;hl=en&amp;amp;ct=clnk&amp;amp;gl=in&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://animals.io9.com/what-do-animals-dream-about-1625103575&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt; provides much more examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the studies of MIT,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Wilson, associate professor of brain and cognitive sciences at MIT,&#xA;  and biology graduate student Kenway Louie trained rats to run along a&#xA;  circular track for a food reward.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;They monitored the animals' brain activity during the task and while&#xA;  they were asleep. While the animal ran, its brain created a&#xA;  distinctive pattern of neurons firing in the hippocampus, a brain area&#xA;  known to be involved in memory.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Like us, rats go through multiple stages of sleep, from slow-wave&#xA;  sleep to REM sleep. In humans, it is during REM sleep that most&#xA;  dreaming occurs.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The researchers then examined more than 40 REM episodes recorded while&#xA;  the rats slept. About half repeated the unique signature of brain&#xA;  activity that was created as the animal ran. The correlation was so&#xA;  close that the researchers found that as the animal dreamed, they&#xA;  could reconstruct where it would be in the maze if it were awake and&#xA;  whether the animal was dreaming of running or standing still.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;These memories were replayed at about the same speed that the animal&#xA;  had experienced them while awake.&#xA;  &lt;a href=&quot;http://newsoffice.mit.edu/2001/dreaming&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Question 2&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Dreaming about their future life while being awake, good question. If they do so then it will be a contradiction to our long held view of animal thought process. Most of the animal thought process that we try to reveal is through the firing of particular areas in their brain with the association of certain hormones. By this process we can find that which all neural pathways are used while dreaming and which are not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As we can find that animals also have dreams, then it is obvious that they could recollect it (some what vague) and can prepare mentally to face those particular situations. This doesn't mean that they do have plans about events coming for them in future, but researchers states that dreams are their only offline experience with those events. The memory of those dreams help them to ensure little advantage over those future events. While in the case of humans, we have a highly complex brain which is so good at simulating events by which we can plan our future, but other animals lack this complex structure(complex but not as much as ours), so they entirely rely on dreams for that purpose.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why do animals dream about one experience and not another? &quot;This work&#xA;  allows us to evaluate the content of dreams and create tests to see&#xA;  which awake patterns create patterns when the animal is asleep,&quot;&#xA;  Wilson said. &quot;If we are able to evaluate the content of the dreaming&#xA;  state, we may be able to find out why certain events get replayed and&#xA;  others don't.&quot;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This work also raises questions about long-held assumptions about&#xA;  animals' thought processes. Only a handful of species — among them&#xA;  chimps and dolphins — were thought to have any ability at all to&#xA;  recall and evaluate detailed sequences of events after they occurred.&#xA;  Wilson points out that &quot;dreams are the ultimate off-line experience.&#xA;  This work demonstrates that animals are capable of re-evaluating their&#xA;  experiences when they are not in the midst of them.&quot;&#xA;  &lt;a href=&quot;http://newsoffice.mit.edu/2001/dreaming&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastActivityDate="2015-03-26T04:46:38.097" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30789" PostTypeId="2" ParentId="30776" CreationDate="2015-03-26T04:56:54.967" Score="6" Body="&lt;p&gt;There are two types of vitamins:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Fat soluble vitamins - Vitamins A, D, E, K&lt;/li&gt;&#xA;&lt;li&gt;Water soluble vitamins - B complex Vitamins and Vitamin C&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Fat soluble vitamins get better abosorbed when fat content of food is good. The bile secretion is also very important. These vitamins form miscelles with the fat molecules and get absorbed as such. The absorption of these vitamins can be enhanced by taking fatty diet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The water soluble vitamins are absorbed freely and they are also excreted freely - Excess are expelled through urine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are inter-vitamin competition and some food biomolecules can inhibit vitamin absorption. For example avidin in the egg would bind to biotin and prevent its absorption. The articles below deal a little with such inhibitions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more see:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://healthyeating.sfgate.com/improve-bodys-absorption-vitamins-2898.html&quot;&gt;http://healthyeating.sfgate.com/improve-bodys-absorption-vitamins-2898.html&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17023940&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/17023940&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://health.howstuffworks.com/wellness/food-nutrition/vitamin-supplements/body-absorb-vitamins.htm&quot;&gt;http://health.howstuffworks.com/wellness/food-nutrition/vitamin-supplements/body-absorb-vitamins.htm&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2015-03-26T04:56:54.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30790" PostTypeId="2" ParentId="30730" CreationDate="2015-03-26T05:25:04.323" Score="1" Body="&lt;p&gt;BFQ = binary fastq&#xA;Described here:&#xA;&lt;a href=&quot;http://ngsutils.org/modules/fastqutils/&quot; rel=&quot;nofollow&quot;&gt;http://ngsutils.org/modules/fastqutils/&lt;/a&gt;&#xA;I have not used it myself, but I gather that the maq aligner package can use (or generate) these files.&#xA;Even though the bam format already incorporates the block compression (described by yourself and others), we routinely deal with gripped bam files and my sense is that there is some additional compression that takes place (I haven't calculated a percentage)&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-03-26T05:25:04.323" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30791" PostTypeId="2" ParentId="28326" CreationDate="2015-03-26T09:41:50.640" Score="6" Body="&lt;p&gt;This doesn't really answer the question and I only post it at the asker's request. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://msis.jsc.nasa.gov/sections/section03.htm%23_3.3_ANTHROPOMETRIC_AND&quot; rel=&quot;noreferrer&quot;&gt;NASA has measured the dimensions of the back in 40 year old American males and 40 year old Japanese females in the year 2000 at 1G.&lt;/a&gt; Of course gravity matters to NASA…&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WnAHI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From figure 3.3.1.3-1 (American male). All data in centimetres:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;921 Waist back&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;5th percentile: 43.7&lt;/li&gt;&#xA;&lt;li&gt;50th percentile: 47.6&lt;/li&gt;&#xA;&lt;li&gt;95th percentile: 51.6&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;506 Interscye&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;5th percentile: 32.9&lt;/li&gt;&#xA;&lt;li&gt;50th percentile: 39.2&lt;/li&gt;&#xA;&lt;li&gt;95th percentile: 45.4&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-03-26T09:41:50.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30792" PostTypeId="1" AcceptedAnswerId="30795" CreationDate="2015-03-26T09:55:32.580" Score="1" ViewCount="3684" Body="&lt;p&gt;Are there any carnivores with horns (whether extinct or currently alive)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do any flying creatures have horns?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By horns I mean horn like structure.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-03-26T14:32:24.067" LastActivityDate="2019-03-20T15:01:08.793" Title="Horns in animals and birds" Tags="&lt;zoology&gt;&lt;anatomy&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ClosedDate="2015-03-26T16:56:06.627" ContentLicense="CC BY-SA 3.0" />
  <row Id="30793" PostTypeId="2" ParentId="30792" CreationDate="2015-03-26T11:09:23.837" Score="2" Body="&lt;p&gt;As far as alive carnivorous land animals go, there are non. But let's search in the sea:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Narwhal (&lt;a href=&quot;http://en.wikipedia.org/wiki/Narwhal&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;&lt;em&gt;Monodon monoceros&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/O7Jbt.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/O7Jbt.jpg&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt; courtesy: &lt;a href=&quot;http://i.huffpost.com/gen/1625488/images/o-NARWHAL-facebook.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://i.huffpost.com/gen/1625488/images/o-NARWHAL-facebook.jpg&lt;/a&gt; &lt;/sup&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Longhorn cowfish (&lt;a href=&quot;http://en.wikipedia.org/wiki/Longhorn_cowfish&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;&lt;em&gt;Lactoria cornuta&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/e/e1/Lactoria_cornuta.002_-_Aquarium_Finisterrae.JPG/800px-Lactoria_cornuta.002_-_Aquarium_Finisterrae.JPG&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt; courtesy: Wikipedia &lt;/sup&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;They are omnivourus and feed mainly on microorganism. There are loads of sites claiming them horned puffer fish.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Extinct&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Carnotaurus (&lt;a href=&quot;http://en.wikipedia.org/wiki/Carnotaurus&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;&lt;em&gt;Carnotaurus sastrei&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://img1.wikia.nocookie.net/__cb20141130153854/dinosaurs/images/e/ed/084d14_0ce4968fba228be913b757cc8ba15f88.gif&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt; courtesy: &lt;a href=&quot;https://img1.wikia.nocookie.net/__cb20141130153854/dinosaurs/images/e/ed/084d14_0ce4968fba228be913b757cc8ba15f88.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://img1.wikia.nocookie.net/__cb20141130153854/dinosaurs/images/e/ed/084d14_0ce4968fba228be913b757cc8ba15f88.gif&lt;/a&gt; &lt;/sup&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Horned Flying Bird&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Gread hornbill (&lt;a href=&quot;http://en.wikipedia.org/wiki/Great_hornbill&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;&lt;em&gt;Buceros bicornis&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt;)&#xA;&lt;a href=&quot;https://i.stack.imgur.com/8jyiq.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/8jyiq.jpg&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt; courtesy: &lt;a href=&quot;http://www.livepterosaur.com/LP_Blog/wp-content/uploads/2011/05/Lip-Kee-Malaysia-Hornbill-5110157612_e1e078296f_z.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.livepterosaur.com/LP_Blog/wp-content/uploads/2011/05/Lip-Kee-Malaysia-Hornbill-5110157612_e1e078296f_z.jpg&lt;/a&gt; &lt;/sup&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8186" LastEditorUserId="16866" LastEditDate="2019-03-20T15:01:08.793" LastActivityDate="2019-03-20T15:01:08.793" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="30794" PostTypeId="2" ParentId="30764" CreationDate="2015-03-26T11:40:04.890" Score="-1" Body="&lt;p&gt;Your theoretical understanding of the ramifications of X-chromosome inactivation is excellent (e.g., the two situations you described).  However, it is important to consider the size of the resulting clones. At that early stage of embryogenesis only ~ half (or less) of those cells will go on to contribute to the fetus, the rest will form the placenta. Also at this stage each cell is likely totipotent, and capable of contributing to all of the different tissues, but eventually the daughters of these cells will become committed, or determined in their developmental lineage. Depending on how much mixing of cells occurs prior to determination, I think it unlikely that within one retina the cone cells would originate from more than a single clone--so I would think that either they all are + or the all are mutant. Since there is L-R symmetry between the two optic cups that will give rise to the developing eyes, I think it is more likely that one female could have one eye that is mutant and one eye that is +.  Given that the prevalence of red-green color-blindness in males approaches 7 % of the population, we can infer that heterozygous females are very common, yet to the best of my knowledge there are not millions of females with partial color-blindness--they either have it (m/m), or they don't (+/+ &amp;amp; m/+). So I think a mosaic female with one eye color-blind and one eye normal must be exceedingly rare.&#xA;Re: autosomal dominant diseases, it all depends on the tissue(s) and the affected developmental stage. The OMIM, Mendelian inheritance in Man database may have some discussion of this interesting point(?).&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-03-26T11:40:04.890" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30795" PostTypeId="2" ParentId="30792" CreationDate="2015-03-26T11:43:41.500" Score="9" Body="&lt;p&gt;Males of the carnivorous &lt;a href=&quot;http://en.wikipedia.org/wiki/Jackson%27s_chameleon&quot; rel=&quot;nofollow noreferrer&quot;&gt;Jackson's chameleon&lt;/a&gt; (&lt;em&gt;Trioceros jacksonii&lt;/em&gt;) have three hornlike structures on their heads (also found in a couple of related species). From what I know, these are true horns, which means that they are pointed keratin-covered protrusions that have a core of living bone, see e.g. &lt;a href=&quot;http://www.torontozoo.com/ExploretheZoo/AnimalDetails.asp?pg=794&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; website from Toronto Zoo (&lt;a href=&quot;http://reptilis.net/lacertilia/chamaeleonidae/bodyplan.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; page also claims that their horns show annual growth rings). However, there are many definitions of horns (some only consider the horns in Artiodactyla to be &quot;true&quot; horns), so you need to be specific in what you are asking for. Used casually, the &lt;a href=&quot;https://en.wikipedia.org/wiki/Antler&quot; rel=&quot;nofollow noreferrer&quot;&gt;antlers&lt;/a&gt; of Cervids or other similar structures, are often considered as horns.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DHTkH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for birds, the closest thing to a horned bird I can think of are species of the Australian &lt;a href=&quot;http://en.wikipedia.org/wiki/Cassowary&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cassowary&lt;/a&gt; (&lt;em&gt;Casuarius&lt;/em&gt;). They have a bony crest on the top of their heads, which is covered by keratinous skin. However, the bony crest is supposed to be relatively soft and spongy, and can hardly be counted as a horn is the strict sense of the word.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8ILGv.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;(Southern cassowary, &lt;em&gt;Casuarius casuarius&lt;/em&gt;, from Wikipedia)&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-03-26T18:43:00.400" LastActivityDate="2015-03-26T18:43:00.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30796" PostTypeId="1" AcceptedAnswerId="30800" CreationDate="2015-03-26T12:55:00.313" Score="5" ViewCount="2935" Body="&lt;p&gt;I have a problem in western blot that I can't resolve by myself.&#xA;When I am use to add 100 microgram of proteins for each sample but after running and transfer its impossible to me to see bands of protein.&#xA;What can be the reason of that? &#xA;Thank you for your help&lt;img src=&quot;https://i.stack.imgur.com/teR0k.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="15123" LastEditorUserId="15123" LastEditDate="2015-03-27T13:18:36.887" LastActivityDate="2015-03-31T04:15:08.530" Title="Why proteins are not visible on my membrane after ponceau staining?" Tags="&lt;proteins&gt;&lt;western-blot&gt;" AnswerCount="2" CommentCount="10" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30797" PostTypeId="1" AcceptedAnswerId="30799" CreationDate="2015-03-26T13:16:05.633" Score="3" ViewCount="102" Body="&lt;p&gt;I have to perform an RNA extraction that should start with 900 uL of 2%SDS bacterial solution. The problem is that the sample is in 900 uL of PBS. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought about centrifugation of the sample at 5ºC, remove PBS and then add the 2%SDS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DO you think bacterial RNA quantities will vary?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="14735" LastEditDate="2015-03-26T13:18:24.613" LastActivityDate="2015-03-26T13:27:27.987" Title="Change solvent of bacterial solution" Tags="&lt;rna&gt;&lt;protocol&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30798" PostTypeId="2" ParentId="30797" CreationDate="2015-03-26T13:22:16.270" Score="3" Body="&lt;p&gt;I'm assuming that you have a solution of bacteria in your buffer directly after growing them for some time, and without performing a lysis step yet. The 2% SDS step looks like it is for lysis of your cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In that case, centrifuging the bacteria and resuspending them in lysis buffer is a very common step in many protocols. Separating whole bacteria from medium or buffer by centrifugation is pretty easy and should just work. But if at any of your previous steps you already lysed your bacteria, this won't work because the cells aren't intact anymore.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2015-03-26T13:27:27.987" LastActivityDate="2015-03-26T13:27:27.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30799" PostTypeId="2" ParentId="30797" CreationDate="2015-03-26T13:23:17.660" Score="2" Body="&lt;p&gt;PBS is isotonic to most cells, so in this buffer your bacterial cells are intact. Centrifuging them to remove PBS won't harm them it is quite standard procedure. You have to be careful after adding 2% SDS because it will lyse your cells and then the RNA contained within them will become &quot;free&quot; and RNAs are fragile molecules.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-03-26T13:23:17.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30800" PostTypeId="2" ParentId="30796" CreationDate="2015-03-26T13:58:17.763" Score="5" Body="&lt;p&gt;From what you say, I can only give a few advices:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;For the quantification, make sure your sample does not contain any substances which disturb the assay. The Bradford assay is for example sensitive against SDS or DTT. See &lt;a href=&quot;http://www.bio-rad.com/LifeScience/pdf/Bulletin_9004.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for more details. This prevents you from loading a sample without enough protein.&lt;/li&gt;&#xA;&lt;li&gt;Make sure that you really have protein on your gel. Run a gel as normal and then stain it with Coomassie Blue (it cannot be used for western afterwards).&lt;/li&gt;&#xA;&lt;li&gt;Don't loose your sample - this happens easier than most people think.&lt;/li&gt;&#xA;&lt;li&gt;Make sure your transfer works. This can either be done by using pre-stained ladders (which are helpful anyway) or by doing Ponceau Red staining. This can be washed off with water and doesn't disturb downstream applications.&lt;/li&gt;&#xA;&lt;li&gt;Depending on the type of membrane you are using, they might need pre-treatment. PVDF membranes are extremely hydrophobic and need to be activated in methanol.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-03-27T21:35:18.033" LastActivityDate="2015-03-27T21:35:18.033" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="30801" PostTypeId="1" CreationDate="2015-03-26T14:26:32.713" Score="3" ViewCount="41" Body="&lt;p&gt;For 16s rDNA metagenomic analysis, do I need to do the following steps?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;DNA extraction-&gt; Purification-&gt; PCR amplification-&gt; Clone -&gt; Pick every single&#xA;  colony-&gt; PCR amplify -&gt; Sequence -&gt; Phylogenetic Analysis&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For the abundance of a particular gene abundance, what steps do I need to follow? Is it necessary to clone?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;`&lt;/p&gt;&#xA;" OwnerUserId="15125" LastEditorUserId="6289" LastEditDate="2015-03-26T17:26:49.850" LastActivityDate="2015-03-26T17:26:49.850" Title="How to quantify the Abundance of a particular gene in Bacteria and Archaea?" Tags="&lt;phylogenetics&gt;&lt;experiment&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30804" PostTypeId="1" CreationDate="2015-03-26T15:45:54.283" Score="2" ViewCount="32" Body="&lt;p&gt;When a protein solution is heated above the denaturation temperature, it seems that denaturation does not happen at the time the temperature is reached, but it takes some time.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assumed that Brownian motion degrades the protein structure more and more. But I noticed that, in practice, one has a mixture of proteins, and I wonder whether they may behave differently, causing some macroscopic effect?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an example, taking the clear part of a chicken egg:&lt;br&gt;&#xA;No doubt it contains multiple proteins. When heating it slightly above the denaturation point, it coagulates slowly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to understand in which way that is caused:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;by proteins that denature at some temperature dependent rate - where all proteins behave very similar&lt;/li&gt;&#xA;&lt;li&gt;by different proteins denaturing at different temperatures at a much higher rate than others, so that partial coagulation means some proteins are coagulated, and some are not&lt;/li&gt;&#xA;&lt;li&gt;of course, it could be both combined, or a completely different way.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6194" LastEditorUserId="4840" LastEditDate="2015-03-29T06:41:00.407" LastActivityDate="2015-03-29T06:41:00.407" Title="Incremental denaturation of protein mixtures" Tags="&lt;proteins&gt;&lt;protein-folding&gt;&lt;kinetics&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30805" PostTypeId="1" CreationDate="2015-03-26T16:47:54.323" Score="7" ViewCount="88" Body="&lt;p&gt;It is known that dolphins never sleep in the sense that we do, instead they have one hemisphere of the brain sleeping while the other one is awake. I wonder, do they show observable changes in behavior in regard to this, depending on which hemisphere is active? Do their hemispheres even have a specification similar to ours (logic and emotion)?&lt;/p&gt;&#xA;" OwnerUserId="10490" LastEditorUserId="13148" LastEditDate="2015-03-26T18:21:59.997" LastActivityDate="2015-03-27T05:02:28.097" Title="Behavioral change in dolphins during different hemispheres activity periods?" Tags="&lt;neuroscience&gt;&lt;sleep&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30808" PostTypeId="2" ParentId="28149" CreationDate="2015-03-26T19:07:27.047" Score="2" Body="&lt;p&gt;Most cancers involve, in addition to genetic changes, a whole suite of epigenetic changes that orchestrate changes in transcriptional profiles. Additionally, multiple epigenetic modifiers (Eg - EZH2) are associated with worse prognoses. &#xA;There is also the fact that chromatin modification machinery is very highly mutated in cancers; examples include EP300 - a histone acetyltransferase, and members of the SWI/SNF nucleosome remodelling complex. The study of epigenetic factors needed for the continued transcription of oncogenes like Myc has also led to the formulation of potential therapeutic strategies (Check out some of the literature on inhibiting Brd4 to silence Myc in certain settings). &lt;/p&gt;&#xA;" OwnerUserId="6726" LastActivityDate="2015-03-26T19:07:27.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30809" PostTypeId="2" ParentId="27788" CreationDate="2015-03-26T19:16:30.880" Score="3" Body="&lt;p&gt;Two things...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rapidly proliferating tissues (esp tumours) rewire their energy metabolism anyway to aerobic glycolysis where you have energy being produced by lactic acid fermentation even if oxygen is present. This is called the Warburg effect.Here's the thing about &quot;low yield&quot; though - glycolysis chucks out less ATP per reaction at the end, but you can crunch through a lot more ATP by just having more of it going on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, hypoxia in a tumour is generally rate limiting, and therefore the shunting away of alpha-KG with the consequence of increased angiogenesis is good for the tumour.  &lt;/p&gt;&#xA;" OwnerUserId="6726" LastActivityDate="2015-03-26T19:16:30.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30810" PostTypeId="1" AcceptedAnswerId="30814" CreationDate="2015-03-26T19:19:57.407" Score="5" ViewCount="1602" Body="&lt;p&gt;I'm looking for a good, understandable and simple explanation about protein folding, mechanisms and function, and their relationship with enzymes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that the protein is a polypeptidic chain, I know its composition, but the part that I really can't figure out is &quot;the folding of proteins&quot;, I mean &quot;How a straight polypeptid chain turns into a complex folded structure?&quot;&lt;/p&gt;&#xA;" OwnerUserId="6114" LastEditorUserId="14735" LastEditDate="2015-03-26T20:45:25.517" LastActivityDate="2015-05-15T19:47:07.173" Title="Any good website/book to understand protein folding and enzymes?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="4" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30811" PostTypeId="1" CreationDate="2015-03-26T20:19:08.587" Score="4" ViewCount="49" Body="&lt;p&gt;About 4 days ago I found a large amount of caterpillars (Pieris brassicae) in my radishes, I took them aside for seeing how they grow and I am out of radishes to give them. I bought a cabbage in the supermarket to give them as food but I am concerned it could be GMO anti pests which to my understanding could kill the caterpillars.&#xA;I took one of them aside and it is happily eating the cabbage, if this cabbage is designed to resist pests how long would it take for the caterpillar to die since she started eating?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you so much for the info :)&lt;/p&gt;&#xA;" OwnerUserId="15128" LastActivityDate="2015-03-26T20:19:08.587" Title="Will a store bought cabbage kill my Pieris brassicaes?" Tags="&lt;entomology&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30812" PostTypeId="1" CreationDate="2015-03-26T21:00:50.163" Score="10" ViewCount="468" Body="&lt;p&gt;&lt;a href=&quot;http://www.genetics.org/content/61/3/763.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Kimura and Ohta (1968)&lt;/a&gt; showed that the expected time for a neutral allele to reach fixation (given that it will reach fixation) is &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\bar t(p_0)=-4N\left(\frac{1-p_0}{p_0}\right)\ln(1-p_0),$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $p_0$ is the initial frequency and $N$ is the population size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From their work, can we generalize this result to calculate the expected time to reach a frequency of $p_1$ (given that this frequency will be reached at some point), where $p_1$ is not necessarily equal to $1$?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="12909" LastEditDate="2015-05-12T18:23:48.873" LastActivityDate="2015-11-04T09:02:49.750" Title="Expected time for a neutral allele to reach a frequency of $p_1$ when starting at frequency $p_0$" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;mathematical-models&gt;&lt;population-dynamics&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30813" PostTypeId="2" ParentId="28080" CreationDate="2015-03-26T21:21:16.443" Score="3" Body="&lt;p&gt;Survival of the host cell is in many cases dependent on the egress strategy of the pathogen. There are &lt;a href=&quot;http://mmbr.asm.org/content/76/4/707.full&quot; rel=&quot;nofollow&quot;&gt;many&lt;/a&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21949650&quot; rel=&quot;nofollow&quot;&gt;examples&lt;/a&gt; documented in various species. The only &lt;a href=&quot;http://iai.asm.org/content/68/11/6431.abstract?ijkey=fcf036f7f2a66aae63295955edc0aa405a3bbe15&amp;amp;keytype2=tf_ipsecsha&quot; rel=&quot;nofollow&quot;&gt;case&lt;/a&gt; I found that's somewhat relevant to human cells was were mutant Legionella pneumophila, defective in the lytic pore complex, did not produce necrosis of the host cell. However, the cells did release the bacteria after a while, probably apoptosis due to accumulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I found an &lt;a href=&quot;http://mbio.asm.org/content/2/4/e00167-11.abstract&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; documenting Cryptococcus neoformans infection. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cryptococcus neoformans causes disease in people with immune deficiencies such as AIDS. Upon infection, C. neoformans cells are ingested by macrophage immune cells, which provide a niche for survival and replication. After ingestion, macrophages can expel the fungi without causing harm to either cell type, a process named nonlytic exocytosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="14698" LastEditorUserId="14698" LastEditDate="2015-04-07T14:13:15.390" LastActivityDate="2015-04-07T14:13:15.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30814" PostTypeId="2" ParentId="30810" CreationDate="2015-03-26T21:36:18.550" Score="6" Body="&lt;p&gt;Okay, so for introduction the 4 levels of protein structure (each level influences the levels after it):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;primary (1st): the order of amino acids.&lt;/li&gt;&#xA;&lt;li&gt;secondary (2nd): alpha-helicies and beta-sheets&lt;/li&gt;&#xA;&lt;li&gt;tertiary (3rd): complex 3d structure&lt;/li&gt;&#xA;&lt;li&gt;quaternary (4th) : 3rd+ non-protein elements (ions, co-factors etc)&lt;br&gt;&#xA;and / or multple subunits interact. Not every protein has this kind&lt;br&gt;&#xA;of structure.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I think the first does not need any explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The secondary structure is where amino acids form 2D structures: alpha-helices or beta sheets. From wikipedia on &lt;a href=&quot;http://en.wikipedia.org/wiki/Alpha_helix&quot; rel=&quot;nofollow noreferrer&quot;&gt;a-helix&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Beta_sheet&quot; rel=&quot;nofollow noreferrer&quot;&gt;b-sheet&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The alpha helix (α-helix) is a common secondary structure of proteins and is a righthand-coiled or spiral conformation (helix) in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier (i+4 \rightarrow i hydrogen bonding)&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The β sheet (also β-pleated sheet) is the second form of regular secondary structure in proteins. It is less common than the alpha helix. Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Pictures are from &lt;a href=&quot;http://www.nslc.wustl.edu/courses/bio2960/labs/02Protein_Structure/PS2011.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;, that is a great site that explains basic protein strucutre in a quite understandable way.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/sS4TT.gif&quot; alt=&quot;a-helix&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/2omiz.jpg&quot; alt=&quot;beta sheet&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These secondary structures are important because they can from motifs with specific functions like DNA binding, interaction surface with other proteins. The aforementioned wiki sites have detailed info. These secondary structures and motifs serve as building block for higher order functions. Between motifs &quot;loose&quot; non-structured parts can be found to allow for flexibility.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tertiary structure:&#xA;This is the level where complex 3D geometric structure is defined. The aforementioned 2D structures are packed into domains - a single functional element of a protein. A single protein can have multiple domains and the relative position of these domains result in the tertiary structure. The domains themselves are connected with loose regions that do not show any high order structure and provide flexibility between the domains. Flexibility is necessary for conformational changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The quaternary structure is where non protein elements and / or multple subunits are involved. For example the positioning of the heme group in hemoglobin. Or when monomers from dimers, trimers etc. so in general when mature proteins get together to form a larger complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a great image about the different structure levels:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/5ER3t.gif&quot; alt=&quot;prot structure&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;source: &lt;a href=&quot;https://dopeahmeanbio.files.wordpress.com/2013/03/333.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://dopeahmeanbio.files.wordpress.com/2013/03/333.gif&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So now onto the &quot;how&quot; part :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I mentioned in the beginning all levels influence the levels after it. So the amino acid sequence predestines the 2D structures to be formed. The secondary structures themselves are formed by amino acid forming hydrogen bonds with each other. This process occurs &quot;naturrally&quot;, so by the inherent properties of the amino acids. At the third level &lt;a href=&quot;http://en.wikipedia.org/wiki/Disulfide_bond&quot; rel=&quot;nofollow noreferrer&quot;&gt;disulfide bonds&lt;/a&gt; stabilize the structure. This is also a naturally occuring event. Also binding ions, co-factors, etc also stabilizes the protein strucutre. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The folding process can also be supported by &lt;a href=&quot;http://en.wikipedia.org/wiki/Chaperone&quot; rel=&quot;nofollow noreferrer&quot;&gt;chaperon&lt;/a&gt; proteins, These proteins can actively &quot;twist&quot; the polypetide chain using ATP as energy source. They can &quot;sense&quot; if there are hidrophobic amino acid chains facing the outer surface of the protein, a thing usually avoided because these amino acids need to face inner surface of the protein where they can avoid water - this is energetically better. This signal (outward facing hidofobic AAs) indicate that either the protein is un/misfolded or it is damaged because of for example heat - that denatures (&quot;unwinds&quot;) proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally the &lt;a href=&quot;http://en.wikipedia.org/wiki/Protein_folding&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki&lt;/a&gt; page on protein folding if you need more. I hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-03-26T21:44:23.037" LastActivityDate="2015-03-26T21:44:23.037" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30815" PostTypeId="2" ParentId="10836" CreationDate="2015-03-26T22:04:25.860" Score="1" Body="&lt;p&gt;The two distinct types you have mentioned in your question (determinate/indeterminate cleavage) are actually called &lt;strong&gt;autonomous specification&lt;/strong&gt; and &lt;strong&gt;conditional specification&lt;/strong&gt;, respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of the former one, if we were to remove a &lt;a href=&quot;https://en.wikipedia.org/wiki/Blastomere&quot; rel=&quot;nofollow noreferrer&quot;&gt;blastomere&lt;/a&gt;, it would still produce the previously determined type of cells, while in the case of &lt;em&gt;conditional specification&lt;/em&gt; the cells, which are going to be produced, depend entirely on the neighbouring ones. The latter's ability to alter their fate is called &lt;strong&gt;regulation&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for answering your questions, cytoplasmic determinants are spread unevenly in deuterostomes as well, as otherwise no axis could be developed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might be interested about &lt;a href=&quot;https://biology.stackexchange.com/questions/2739/impact-of-alan-turings-approach-to-morphogenesis/3352#3352&quot;&gt;this&lt;/a&gt; answer as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I've used the following book as source: Gilbert, S. (2000). Developmental Biology [ &lt;a href=&quot;https://docs.google.com/file/d/0B8TV5dZFQHEHaDNIQVliYVozamM/edit&quot; rel=&quot;nofollow noreferrer&quot;&gt;online version&lt;/a&gt; ]&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="15051" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-03-26T22:04:25.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30816" PostTypeId="1" AcceptedAnswerId="30819" CreationDate="2015-03-26T22:36:27.633" Score="4" ViewCount="169" Body="&lt;p&gt;Consider &lt;a href=&quot;https://worldbuilding.stackexchange.com/a/12395/7999&quot;&gt;this answer&lt;/a&gt; to an interesting question. It's not possible to prove completely that someone is the descendant of someone else, there's always a nonzero probability that the results are a coincidence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How confident can you get that genome T is the descendant of four unrelated grandparents? How would you tell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Restrictions: You're not allowed to sequence all other humans and rule out other possible parents. Time traveller is has the normal number of chromosomes. You can test people's parents if that would help.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The maternal grandmother would share mitochondrial DNA, and the paternal grandfather would share the Y-chromosome, or the paternal grandparents would have one X chromosome between them. I'm not an expert on SNP accumulation but would there be enough information to conclude this person was from the future? Would there be too much mutation in two generations to pick out the relationships under it?&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="-1" LastEditDate="2017-04-13T12:52:23.867" LastActivityDate="2015-04-26T04:39:00.947" Title="Proving time travel" Tags="&lt;human-genetics&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30817" PostTypeId="1" AcceptedAnswerId="30869" CreationDate="2015-03-27T00:29:18.583" Score="2" ViewCount="74" Body="&lt;p&gt;I am reading in notes for a comparative annotation lecture that :&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;all DNA is subject to mutations&lt;/li&gt;&#xA;&lt;li&gt;most functional regions are under negative selection (ie., mutations are often deleterious)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The conclusion was: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;that pieces of DNA with specific functions (especially genes) tend to be conserved against mutation more strongly than a DNA region with no specific function.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So if i understand it properly, since all DNA can accumulate mutations, the regions of genes that provide some fitness benefits avoid the negative selection of random mutations and are preserved (conserved?).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, the author placed in parentheses, (especially genes), therefore are there non coding regions that can provide benefits? Is he referring to &quot;Selfish DNA&quot; like Transposable elements that can have regulatory functions (or so i have heard).&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="14826" LastEditDate="2015-03-29T07:40:01.260" LastActivityDate="2015-03-29T07:40:01.260" Title="Understanding conclusions that functional regions are under negative selection?" Tags="&lt;genetics&gt;&lt;genomics&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30818" PostTypeId="1" CreationDate="2015-03-27T00:48:02.630" Score="1" ViewCount="721" Body="&lt;p&gt;I was learning about allele linkage in Biology class and I got confused by the resultant phenotypic ratios.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Say you have a dihybrid cross BbGg x BbGg.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Punnett square would look like the following (sorry for bad formatting):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;     BG...... | Bg.... |  bG.... |  bg&#xA;&#xA;&#xA;BG   BBGG       BBGg      BbGG      BbGg&#xA;---  -----------------------------------&#xA;Bg   BBGg       BBgg      BbGg      Bbgg&#xA;---  -----------------------------------&#xA;bG   BbGG       BbGg      bbGG      bbGg&#xA;---  -----------------------------------&#xA;bg   BbGg       Bbgg      bbGg      bbgg&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;h2&gt;So:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;This would result in a a 9:3:3:1 phenotypic ratio. &lt;i&gt;(Dom/Dom : Dom/Rec : Rec/Dom : Rec/Rec)&lt;/i&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if the alleles B/b and G/g were on the same chromosome, the ratios turned out to be around 4:1:1:4 in an example &lt;i&gt;(still Dom/Dom : Dom/Rec : Rec/Dom : Rec/Rec)&lt;/i&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The stated reason was that there would only be Dom/Dom and Rec/Rec, and the Dom/Rec and Rec/Dom only showed up due to crossing over. However, this begs the question: Why could Dom/Rec and Rec/Dom not have occurred prior to recombination? My reasoning is that &lt;i&gt;just because the alleles are on the same chromosome does not mean that they must both the autosomal chromosomes for the allele must have either a dominant genotype or recesssive phenotype.&lt;/i&gt; That is, before crossover, there should still be a 9:3:3:1 random distribution between phenotypes represented by genotype sets (BbGg/BBGg/BbGG/BBGG):(Bbgg/BBgg):(bbGg/bbGG):(bbgg).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: when I say dom/rec for example, I mean that for the first allele the character represented by BB or Bb was expressed, and the &quot;rec&quot; means that for the second allele the character represented by gg was expressed. I am assuming autosomal dominance for simplicity.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;If anything is unclear, don't hesitate to comment. I'm pretty tapped out right now. Thanks, hob&lt;/h2&gt;&#xA;" OwnerUserId="15131" LastEditorUserId="231" LastEditDate="2015-03-27T06:40:52.417" LastActivityDate="2015-03-28T01:43:06.260" Title="Why does allele linkage cause disproportionate phenotypic ratios?" Tags="&lt;genetics&gt;&lt;allele&gt;&lt;genetic-linkage&gt;&lt;crossover&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ClosedDate="2015-03-29T07:38:27.063" ContentLicense="CC BY-SA 3.0" />
  <row Id="30819" PostTypeId="2" ParentId="30816" CreationDate="2015-03-27T04:03:21.303" Score="3" Body="&lt;p&gt;This should be pretty easy to demonstrate. Over the two generations, there would be 200-300 mutations in the entire genome of 3.3*10&lt;sup&gt;9&lt;/sup&gt; base pairs, i.e. about 1*10&lt;sup&gt;-7&lt;/sup&gt; of the base pairs should be altered. If Time Traveler is male, for example, imply sequencing the Y chromosome and mitochrondrial DNA and comparing to the paternal grandfather and maternal grandmother should be adequate to decisively validate the claim.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this isn't sufficiently satisflying could then move on to the autosomes and note that only about 200-300 base pairs max should be different from the union of the four grandparental genomes. The chances of this occurring given random set of four unrelated genomes will be vanishingly small.&lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-03-27T04:03:21.303" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30820" PostTypeId="2" ParentId="30810" CreationDate="2015-03-27T04:37:25.690" Score="0" Body="&lt;p&gt;All the information can be found here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21054/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK21054/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The whole book is there, you simply have to search whichever part interests you or you can also find the paper version in a library. The part on protein structure is Chapter 3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a textbook used in some biochemistry and cell biology introductory courses at my university, so it will cover the basics as well as some more detailed things.&lt;/p&gt;&#xA;" OwnerUserId="14551" LastActivityDate="2015-03-27T04:37:25.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30821" PostTypeId="2" ParentId="30805" CreationDate="2015-03-27T05:02:28.097" Score="2" Body="&lt;p&gt;Sleeping is a biological stage which we presume as a relaxation period but its really a highly functional stage for brain. Most of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sleep#Memory_processing&quot; rel=&quot;nofollow&quot;&gt;memory related processing&lt;/a&gt; such as management of working memory and cognitive functions such as decision making, reasoning, and episodic memory are closely related with sleep. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dolphins never sleep in the sense that we do, CORRECT, because we close our both eyes and enter into a stage of decreased ability to react to a stimuli. But in the case of dolphins they need to breath, so by fully entering into a sleep stage like us is suicidal in their case. &#xA;Dolphins have a specialised way of dealing with this problem, they do a &quot;&lt;a href=&quot;http://www.livescience.com/44822-how-do-dolphins-sleep.html&quot; rel=&quot;nofollow&quot;&gt;unihemispheric slow-wave sleep&lt;/a&gt;&quot;. They only sleep with one hemisphere of the brain while the other being active, when the right hemisphere is sleeping the left eye is closed and vice-verse, as the right hemisphere controls the left part of the body. The observable change in their behavior is &lt;a href=&quot;http://www.livescience.com/44822-how-do-dolphins-sleep.html&quot; rel=&quot;nofollow&quot;&gt;visible&lt;/a&gt; from the closed single eye. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans and dolphins had a common ancestor that lived 95 million years ago. During the last 50 million years dolphins have been evolving in water and their brain evolution had taken a different route. The &lt;a href=&quot;http://en.wikipedia.org/wiki/Neocortex&quot; rel=&quot;nofollow&quot;&gt;neocortex&lt;/a&gt;, the outer most layer of brain which is considered as the recent evolved part of brain. The neocortex is actively developing in both humans and dolphins, one of the most striking features among them is that human neocortex is having large thickness and dolphins are having thin one with more folds than ours. The folding in neocortex is a technique to increase its surface area. This substantial difference is due to the evolutionary divergent way both the species took. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dolphins have a complex echolocation system and binocular eyes, they need to create the visual and sonar image of their surroundings and studies shown that their increased brain size is due to the tremendous volume of data they need to process for these purposes. Also being a social animal their neocortex consists of connections like us but as we both are evolutionary separated for about 95 million years ago most of the brain areas are diversified and evolved. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dolphins showed that they can understand a symbolic, human-based&#xA;  language, where the words are either whistles or hand gestures. And&#xA;  the dolphins could easily understand that we use different word orders&#xA;  to mean different things. So they understand syntax. The dolphin brain&#xA;  is arranged in a completely different way from ours, and yet they can&#xA;  still understand what we are trying to teach them. Lou Herman also&#xA;  showed that dolphins are right up there with humans and chimpanzees in&#xA;  being able to understand that when we point at something or look at&#xA;  something, we’re meaning “Don’t look at me; look at what I’m looking&#xA;  at.” He’s done all kinds of really fascinating things, and his work&#xA;  has contributed the most to our understanding of what these animals&#xA;  can do.&lt;a href=&quot;http://webcache.googleusercontent.com/search?q=cache:aLwZGGfACqsJ:www.earthintransition.org/2010/05/dolphins-how-smart/%20&amp;amp;cd=3&amp;amp;hl=en&amp;amp;ct=clnk&amp;amp;gl=in&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10294" LastActivityDate="2015-03-27T05:02:28.097" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30822" PostTypeId="1" AcceptedAnswerId="30849" CreationDate="2015-03-27T06:19:35.030" Score="1" ViewCount="1763" Body="&lt;p&gt;Can blood donation cause any harm to the donor? I have been told so, but cannot find any references supporting this claim. I have also learned that our body will replace the lost fluids within 24 hours and the RBCs within weeks. Can blood donation still cause health issues for our body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not a personal medication question, and I mainly want to know how the body responds to blood loss and what mechanisms that monitor the altered levels of blood volume? To me, it would also be unethical by medical doctors to withhold the possible risks of blood donation to prospective donors, but it might also be seen as unethical to discourage a person willing to donate blood from doing so, so there might be a conflict of interest here.&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="10294" LastEditDate="2015-03-27T09:02:39.180" LastActivityDate="2015-03-29T07:34:25.563" Title="How does the body respond to blood donation; are there any possible risks?" Tags="&lt;human-biology&gt;&lt;hematology&gt;&lt;medicine&gt;&lt;blood-circulation&gt;" AnswerCount="1" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="30823" PostTypeId="2" ParentId="30810" CreationDate="2015-03-27T06:24:39.307" Score="0" Body="&lt;p&gt;For basic knowledge I would recommend the 5th edition of &quot;the cell&quot; and &quot;Lehninger Principles of Biochemistry&quot; 6th edition (3rd and 4th chapter). Even Lippincott's Biochemistry (chapter 2) and Biochemistry by Stryer (6th edition, chapter 2) is good. You can find the 5th edition of Stryer here &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21154/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK21154/&lt;/a&gt;&#xA;If you have access to a library you could try out the latest editions. If not older editions are available online. Protein folding should be among the first few chapters. &lt;/p&gt;&#xA;" OwnerUserId="14932" LastActivityDate="2015-03-27T06:24:39.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30824" PostTypeId="1" CreationDate="2015-03-27T07:04:56.710" Score="13" ViewCount="7293" Body="&lt;p&gt;I am currently reading &quot;The Fundamentals of Anatomy Physiology&quot; 10th edition, and have found it an incredibly interesting book. I have just been reading about the lymphatic system, and the various Leukocytes and their roles. When it mentioned fever as an immune response, I was familiar with the concept: Bacteria and viruses operate very nicely at our usual body temperature, but not so well at around 39 degrees Celsius.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I wasn't aware of was &quot;For each 1 degree Celsius rise in body temperature, metabolic rate increases by 10 percent. Cells can move faster, and enzymatic reactions take place quicker.&quot; (Quoted from page 828 of that book).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now that seems like a massive benefit (though I believe you could only really push 1 or 2 degrees before you start getting into dangerous territory), but I notice that fever is not present in all illnesses. Inflammation seems to induce fever through the wounded area, which makes sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So now for my question: Could it be beneficial to artificially induce fever in a person who has an illness if they are not already experiencing fever? I believe a few things would need to be considered (more than likely a lot more than I can think to list):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Increased metabolic activity would surely need a higher energy intake would it not?&lt;/li&gt;&#xA;&lt;li&gt;Are there cells that are actually going to suffer from the temperature increase?&lt;/li&gt;&#xA;&lt;li&gt;I'm assuming this would actually be a rather poor technique to deal with cancer as from my currently limited knowledge, it is simply a cell that is producing abnormal proteins. If this is the case, the metabolic increase would likely apply to these abnormal cells, resulting in faster proliferation. Are there other such cells/infections that will benefit from temperature increase?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Finally, what are possible downsides of long term fever if energy intake is sufficient to maintain an increased metabolic rate at these higher temperatures?&lt;/p&gt;&#xA;" OwnerUserId="15133" LastEditorUserId="15133" LastEditDate="2015-03-27T07:11:54.783" LastActivityDate="2020-02-23T17:54:36.347" Title="Should we induce fever to assist healing?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;metabolism&gt;&lt;cell&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30825" PostTypeId="1" AcceptedAnswerId="30827" CreationDate="2015-03-27T08:10:13.643" Score="5" ViewCount="1970" Body="&lt;p&gt;Some bacteria can undergo gene transfer by conjugation. Conjugation is a form of horizontal gene transfer, meaning from one (unrelated) bacterium to another (in contrast to vertical gene transfer, which is from predecessor bacterial cell to successor (daughter) cells). Conjugation is initiated when one bacterium has an F-plasmid (Fertility plasmid) and forms an F-pilus, connecting the F+ bacterium with an F- bacterium, initiating transfer of the F-plasmid. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is it that during evolution not all bacteria have acquired this F-plasmid?&lt;/p&gt;&#xA;" OwnerUserId="15136" LastEditorUserId="14735" LastEditDate="2015-03-27T11:17:20.297" LastActivityDate="2015-03-27T11:17:20.297" Title="Why don't all bacteria have F-plasmids by now?" Tags="&lt;genetics&gt;&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30826" PostTypeId="2" ParentId="30787" CreationDate="2015-03-27T09:14:24.093" Score="5" Body="&lt;p&gt;A &lt;i&gt;3D&lt;/i&gt; model of a (bio)moelcule represents a physical 3-dimensions. For an experimental structure, each atom has a 3D coordinate (x, y, z) and, if determined by crystallography, an additional isotropic or aniosotropic B-factor (that models atom fluctuations).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A '1D' SMILES is not a &lt;i&gt;physical&lt;/i&gt; 1-dimensional representation, and can be converted to a &lt;a href=&quot;http://en.wikipedia.org/wiki/Graph_(mathematics)&quot; rel=&quot;nofollow noreferrer&quot;&gt;graph (mathematics)&lt;/a&gt; representing the chemical structure. The specification of SMILES &lt;i&gt;CAN&lt;/i&gt; retain information about structural isomers, stereoisomers (cis/trans; D/L), but not conformers/rotomers, which, unlike smaller chemical structures, &lt;i&gt;IS&lt;/i&gt; restricted to certain favorable regions for larger biomolecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By &quot;linkage&quot; if you mean chemical linkage such as a disulfide bond, then SMILES can retain such information. By &quot;interactions&quot;, if you mean hydrogen-bonding, salt-bridges and even hydrophobic interactions etc., then SMILES does not code in such information, but neither does a 3D model explicitly -- they are implied from the 3D coordinates for each atom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, converting from a 3D model to SMILES, you would lose&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Unusual bond length and bond angle: they are necessarily specified from the 3D coordinates, but in SMILES (or the subsequent graph), they are taken as 'ideal'.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Debye%E2%80%93Waller_factor&quot; rel=&quot;nofollow noreferrer&quot;&gt;B-factor or temperature factor&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Rotomers: e.g. Proteins have favored dihedral angles in both &lt;a href=&quot;http://en.wikipedia.org/wiki/Ramachandran_plot&quot; rel=&quot;nofollow noreferrer&quot;&gt;backbone&lt;/a&gt; and side chains, which is not specified in SMILES.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&quot;Interactions&quot;: certain intramolecular interaction that is inevitable (e.g. salicylaldehyde) is implied in both SMILES and a 3D model. Most others can only be inferred in the 3D model.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9731" LastEditorUserId="10456" LastEditDate="2016-11-11T15:00:50.670" LastActivityDate="2016-11-11T15:00:50.670" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30827" PostTypeId="2" ParentId="30825" CreationDate="2015-03-27T09:45:46.133" Score="4" Body="&lt;p&gt;Conjugation occurs between cells of the same species too. For this to occur cell have to be close to each other. Now, if you have an isolated population of bacteria that never gets in contact with an F+ bacteria then this population would stay F-. Also not all conjugation events are successful, mechanical perturbations can disrupt the pilus through which genetic material is transferred. &#xA;This old article can give you good details: &#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC440990/pdf/bactrev00192-0002.pdf&quot; rel=&quot;nofollow&quot;&gt;THE ORIGIN OF BACTERIAL SPECIES - GENETIC RECOMBINATION AND FACTORS LIMITING &#xA;IT BETWEEN BACTERIAL POPULATIONS ARNOLD by W.RAVIN&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;F+ shares, however, an important property of bacteriophage: after infection&#xA;  it behaves as though it were an addition to the bacterial genome. As an addition, it can furthermore exist in one of two forms: in one form, it&#xA;  is an unintegrated part of the bacterial genome, and may be  replicated either more or less rapidly than the &quot;chromosomal&quot; or linked genes (being&#xA;  infectious or lost through dilution, respectively); in its other form, it&#xA;  is integrated in the sense that its replication is coordinated with the&#xA;  replication of the host's genes, as though attached to them. In this latter form, found in Hfr bacteria, the F+ factor is incapable of infecting other bacteria (while permitting conjugation with them) and also prevents &#xA;  superinfection of its host bacterium by a nonintegrated F+ factor.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Taken from the linked paper. So you can see that are situations where conjugation occurs yet the F- won't become F+.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What is particularly interesting about the F+ factor is the fact that there&#xA;  seem to be a number of different  kinds. An F+ factor making a bacterium&#xA;  fertile with some  F- cultures does not necessarily  make it capable  of conjugating with others (49).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So not every F+ cell can conjugate with another F- cell.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-03-27T09:45:46.133" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30830" PostTypeId="1" AcceptedAnswerId="30834" CreationDate="2015-03-27T12:10:31.133" Score="5" ViewCount="2027" Body="&lt;p&gt;I need to detect a FLAG tagged protein on a western blot and have to order an antibody. I'm not expecting to see a massive amount of my protein. To keep analysis time to a minimum  I am considering a HRP-conjugated anti-FLAG. Are there any disadvantages to it (e.g. sensitivity)? First hand experiences/problems?&lt;/p&gt;&#xA;" OwnerUserId="15138" LastEditorUserId="15138" LastEditDate="2015-03-27T12:29:44.360" LastActivityDate="2015-03-27T13:16:05.963" Title="Are there any disadvantages to HRP conjugated PRIMARY antibodies" Tags="&lt;antibody&gt;&lt;western-blot&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30831" PostTypeId="1" AcceptedAnswerId="30833" CreationDate="2015-03-27T12:42:26.603" Score="5" ViewCount="224" Body="&lt;p&gt;I would like to know if bacterial RNA in a 1.5 mL 2%SDS solution can be degraded.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Comes from a pellet of pure liquid culture.&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="49230" LastEditDate="2019-03-12T04:31:13.620" LastActivityDate="2019-03-12T04:31:13.620" Title="Can bacterial RNA be degraded at -80⁰C in a SDS solution?" Tags="&lt;rna&gt;&lt;protocol&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="30833" PostTypeId="2" ParentId="30831" CreationDate="2015-03-27T12:57:46.320" Score="6" Body="&lt;p&gt;I think it is relatively unlikely that the RNA will degrade under these conditions. For the future, I would handle this differently:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;You can centrifuge the cells and snap freeze them in an appropriate&#xA;buffer in liquid nitrogen and then store them at -80°C. I would not freeze the dry pellet, as these are often hard to re-dissolve after freezing.&lt;/li&gt;&#xA;&lt;li&gt;Alternatively, you centrifuge them, break them up with Trizol (or whatever you use for this purpose) and freeze them in this solution. This will be&#xA;safer as it completely denatures all proteins including all nucleases.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I would choose (and have done this already several times with cell samples that I couldn't process without problems) the second method.  &lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="49230" LastEditDate="2019-03-12T04:31:05.227" LastActivityDate="2019-03-12T04:31:05.227" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="30834" PostTypeId="2" ParentId="30830" CreationDate="2015-03-27T13:16:05.963" Score="4" Body="&lt;p&gt;You can compare directly coupled antibodies to the classical indirect primary-secondary systems:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Directly coupled antibodies&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Advantages:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;quicker workflow as only one antibody is used&lt;/li&gt;&#xA;&lt;li&gt;eliminates the chance of a cross-reacting secondary antibody (possibly less background)&lt;/li&gt;&#xA;&lt;li&gt;possibility to use differently labelled antibodies on the same blot&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Disadvantages:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;lower sensitivity because the signal is not amplified&lt;/li&gt;&#xA;&lt;li&gt;only few labels are available&lt;/li&gt;&#xA;&lt;li&gt;directly labelled primary antibodies tend to be expensive and you need relatively high amounts of them&lt;/li&gt;&#xA;&lt;li&gt;the labelling can damage or reduce the immunoreactivity of the&#xA;antibody&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Indirect Primary-Secondary Antibody systems&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Advantages:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the secondary antibody amplifies the signal (which is especially&#xA;interesting for weakly expressed proteins)&lt;/li&gt;&#xA;&lt;li&gt;differently labelled secondary antibodies can be used on the same&#xA;primary&lt;/li&gt;&#xA;&lt;li&gt;primary antibodies from different species can be used simultaneously&lt;/li&gt;&#xA;&lt;li&gt;one secondary antibody can be used with different primary antibodies&#xA;(for example for the protein of interest and the loading control)&lt;/li&gt;&#xA;&lt;li&gt;the labelling reaction does not affect the primary antibody&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Disadvantages:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;cross-reactivity of the secondary antibody can lead to non-specific&#xA;bands&lt;/li&gt;&#xA;&lt;li&gt;the method takes longer, as more steps in the process are necessary&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;For me the most important point is the higher sensitivity of the indirect method, for comparision see these images (from &lt;a href=&quot;https://www.lifetechnologies.com/de/de/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-western-blotting.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Life technologies&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1I5ZP.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/BaH5k.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-03-27T13:16:05.963" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30835" PostTypeId="2" ParentId="30702" CreationDate="2015-03-27T14:04:56.603" Score="6" Body="&lt;p&gt;This article gives an excellent review on yogurt manufacturing, but to summarize:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-Raw milk goes through centrifugation to remove somatic cells and other solid impurities.&#xA;-Thermalization is conducted at &quot;60–69 °C for 20–30 s, aiming at the killing of many vegetative microorganisms and the partial inactivation of some enzymes.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After this point, the milk may be inoculated with lactic acid bacteria or other microfloras.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-Then, standardization occurs which for milk refers to the standardization of fat and solid-non-fat content (SNF).  This in short affects the fermentation process (&quot;an increase of SNF increases the duration of the fermentation process&quot;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-The next step is homogenization, which prevents milk fat from rising to the top of the liquid.  This has an effect on the stability of the emulsion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-I think this step is where &quot;sterility&quot; comes into play, &quot;heat treatment of milk reduces the number of pathogenic microorganisms to safe limits for the consumer’s health. Various heat treatments can be applied, which are classified based on the duration and the temperature. The most common are known as thermalization, low and high pasteurization, sterilization and UHT (Ultra Heat Treatment).&quot;  The review goes into more detail about each type and what they eliminate or don't eliminate (spores, vegetative bacteria, etc.).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;-The fermentation process is the most important one for developing flavor and texture.  The two live bacterial strains of &lt;em&gt;Streptococcus salivarius&lt;/em&gt; subsp. &lt;em&gt;thermophilus&lt;/em&gt; (ST) and &lt;em&gt;Lactobacillus delbrueckii&lt;/em&gt; subsp. &lt;em&gt;bulgaricus&lt;/em&gt; (LB) are the two most basic strains used in yogurt.  LB is what metabolizes lactose into lactic acid and LB and ST acting in synergy is what causes a decrease in milk pH.  &quot;When the pH of the yogurt approaches 5.0, activity of ST subsides and LB gradually dominates the overall fermentation process until the target value of pH is reached and the fermentation process ceases. Normally, the fermentation period is terminated by lowering the temperature to 4 °C. At this temperature, the culture is still alive, but its activity is drastically limited to allow controlled flavor during storage and distribution.&quot;  I think to answer your question, yogurt manufacturers probably have a very sensitive gauge for pH and can control temperature fluctuations finely to maintain yogurt pH and flavor (not too sour).  &quot;After the pH of yogurt reaches the value of 4.7–4.3, the yogurt is cooled to around 5 °C. This inhibits the growth and metabolic reaction of the starter culture and prevents the rise in acidity. Cooling of yogurt can be in one or two phases. One-phase cooling involves the rapid decrease of the coagulum temperature to less than 10 °C, where the fermentation process is inhibited leading to yogurt with low viscosity. Two-phase cooling is initiated by rapidly decreasing the temperature to less than 20 °C and then gradually reaching the storage temperature of 5 °C leading to yogurt with an increased viscosity and limited syneresis. This is quite common in the yogurt manufacture process, especially when fruits are to be added.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read about the other innovative methods involved in yogurt making such as: Ultra High Pressure (UHP) which inactivates pathogens and microorganisms that cause milk to spoil, High Intensity Ultrasonication and Pulsed Electric Field (PEF) which all can reduce microbial content.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: Forgot to mention that some DIY yogurt instructions mention that if you ferment longer and/or in warm temperatre the more sour it will be so to reduce how sour it is, either ferment it less and/or start fermentation at a lower temperature &lt;a href=&quot;http://nourishedkitchen.com/troubleshooting-homemade-yogurt-questions/&quot;&gt;(source)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Sfakianakis P, Tzia C. Conventional and Innovative Processing of Milk for Yogurt Manufacture; Development of Texture and Flavor: A Review. Foods. 2014; 3(1):176-193.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="14916" LastEditorUserId="14916" LastEditDate="2015-03-27T20:14:49.457" LastActivityDate="2015-03-27T20:14:49.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30836" PostTypeId="1" AcceptedAnswerId="30882" CreationDate="2015-03-27T14:31:02.617" Score="11" ViewCount="1111" Body="&lt;p&gt;I would like to know what advantages polyploidy holds. I have come across a few examples during my research of polyploidy, for example human adults' hearts contain 27% diploid, 71% tetraploid and 2% octaploid nuclei, &lt;em&gt;Deinococcus radiodurans&lt;/em&gt; can have up to 10 copies of genome, and most of the plants consumed by humans have more than 2 copies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have no source of any sort for these, but I think they could be advantages:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;One of the most obvious one would be resistance to more physical effects.&lt;/li&gt;&#xA;&lt;li&gt;In the case of plants it might be the increased need for protein construction during the development of the seed.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;What I would like to ask is whether the ones I wrote &lt;strong&gt;are correct&lt;/strong&gt;, and if there are &lt;strong&gt;any other&lt;/strong&gt; possible advantage.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I have read similar questions but could not find what I was looking for.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="15051" LastEditorUserId="15136" LastEditDate="2015-03-29T17:18:58.773" LastActivityDate="2015-03-29T17:18:58.773" Title="Why does polyploidy give an evolutionary advantage?" Tags="&lt;genetics&gt;&lt;genomes&gt;&lt;polyploidy&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30839" PostTypeId="1" AcceptedAnswerId="30983" CreationDate="2015-03-27T21:33:56.837" Score="9" ViewCount="480" Body="&lt;p&gt;I need to splice a gene into a human cell genome, with highest rate possible. I mean, doesn't really matter where the gene enters, nor does it matter if some cells die as a result of this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CRISPR know to knock-in genes with very high specifically, this reduce the success rate if we have a low amount of gRNA and/or of the protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I need to insert the gene, without the need of targeting some specific place.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this possible in some way with CRISPR?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that there may be better technique to do this, but I can only use CRISPR.&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="20449" LastEditDate="2016-12-30T13:41:55.513" LastActivityDate="2016-12-30T13:41:55.513" Title="Splice in with CRISPR/Cas" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;crispr&gt;" AnswerCount="3" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30840" PostTypeId="2" ParentId="30824" CreationDate="2015-03-27T21:41:55.553" Score="1" Body="&lt;p&gt;Actually, &lt;a href=&quot;http://en.wikipedia.org/wiki/Hyperthermia_therapy&quot; rel=&quot;nofollow&quot;&gt;hyperthermia&lt;/a&gt; is a known treatment for a range of diseases, including cancer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Induced hyperthermia can be whole-body as well as local/regional and is under investigation in multiple studies (&lt;a href=&quot;http://www.cancer.gov/cancertopics/treatment/types/surgery/hyperthermia-fact-sheet&quot; rel=&quot;nofollow&quot;&gt;for example&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-03-27T21:41:55.553" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30841" PostTypeId="1" CreationDate="2015-03-27T22:06:30.033" Score="3" ViewCount="77" Body="&lt;p&gt;I have found the following pictures representing cysticercoids of Eucestoda.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I correctly understand the right part of the picture, I would say that the development of the scolex is portrayed on the right, as the formation of what I think to be two acetabula shows. Nevertheless, with respect to the images on the left, it is totally unclear to me, since the text says nothing about it, what the structure that seems to be encapsulating the animal is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BJVtn.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that cysticercoids develops from an oncosphere, but I do not know whether that sort of capsule that seems to be enveloping the animal is a part of what was the oncosphere's tegument -the embrionophore- that it can have gone out of and is entering again...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anybody reading this question know more about it? I thank you very much for any answer!&lt;/p&gt;&#xA;" OwnerUserId="8124" LastActivityDate="2015-03-27T22:42:34.613" Title="Cysticercoids of Eucestoda" Tags="&lt;zoology&gt;&lt;development&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30842" PostTypeId="2" ParentId="30841" CreationDate="2015-03-27T22:42:34.613" Score="1" Body="&lt;p&gt;I would say that the left part of the picture depicts 2 stages of the development of cysticercoid, while the right part shows the consecutive stages in the development of cysticercus. These two parts represent different species of tapeworms in the same stage of their developments.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-03-27T22:42:34.613" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30843" PostTypeId="1" AcceptedAnswerId="30850" CreationDate="2015-03-28T00:14:47.390" Score="3" ViewCount="484" Body="&lt;h1&gt;Introduction&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;I've recently stumbled upon David Eagleman's TED talk on the concept of sensory substitution and addition. Being the most inspiring thing I've seen on the internet for the last few months I've decided to give it a try and mix it with some of my coding/electronics projects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've settled on using electrical impulses over electrode pads to feed sensory data onto a patch of skin, instead of vibro-motors as it is more energy efficient. That being said, when planning on running electrical current through me 24/7, safety obviously comes first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;[edit]&lt;/strong&gt;&lt;br&gt;&#xA;I am targeting the lower back or the side of the hips as these parts have the least contact with the environment and won't make you look goofy. In the long run this would probably have to run on dry skin to avoid the &quot;wrinkling effect&quot;, caused when staying in water for too long.&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Questions&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;Main unknowns I want to sort out are:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;What is the range of perceivable voltage and current that can be safely  fed through the skin without causing any damage to the nerves or any other part of the body?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is there a risk of permanent damage or reduction of sensitivity of nerves when exposed to an electrical current for a prolonged time? Any way to circumvent this problem?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What &quot;resolution&quot; or input density can I hope to achieve, before signal becomes &quot;blurry&quot; because of cross-talk?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="15143" LastEditorUserId="15143" LastEditDate="2015-03-28T10:58:15.063" LastActivityDate="2015-03-28T12:32:18.283" Title="Safe parameters for external nerve stimulation using electrical impulses" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30844" PostTypeId="1" CreationDate="2015-03-28T01:11:44.783" Score="0" ViewCount="115" Body="&lt;p&gt;Hypothetically speaking, suppose there is a device that produces a limitless supply of oxygen. The device is inhaled by a human and is resting inside the (a) lung.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would hypothetically happen if this were possible? &lt;/p&gt;&#xA;" OwnerUserId="15144" LastEditorUserId="4840" LastEditDate="2015-03-28T03:28:07.613" LastActivityDate="2015-03-28T07:54:17.370" Title="What would happen if we had a device that produced oxygen inside of our lungs?" Tags="&lt;human-biology&gt;&lt;breathing&gt;&lt;human-physiology&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2015-03-28T08:06:40.767" ContentLicense="CC BY-SA 3.0" />
  <row Id="30845" PostTypeId="2" ParentId="30818" CreationDate="2015-03-28T01:43:06.260" Score="0" Body="&lt;p&gt;I found the explanation at this site helpful:&#xA;&lt;a href=&quot;http://www.ndsu.edu/pubweb/~mcclean/plsc431/linkage/linkage1.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.ndsu.edu/pubweb/~mcclean/plsc431/linkage/linkage1.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't have a clear sense of what you mean when you ask about assorted phenotypes occurring before recombination (&quot;crossover&quot;). All of your examples deal with diploid organisms. If they are multicellular then the cells that can undergo meiosis are highly specialized, and eventually become haploid. As the chromosomes are prepared they tend to become compact, and are often not expressed. So it is difficult to assess the phenotype of those haploid cells. The rest of the cells in the organism are diploid  and at least some of them can express the alleles that give rise to the phenotypes that you are scoring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the moment of fertilization there is no further recombination, as the zygotic cells undergo mitosis.  There is no segregation, no independent assortment, no linkage (that you can measure--the genes are still arrayed along their chromosomes). Each mother cell divides to give two perfect copies of itself. Then the daughters divide, etc. Even in the cells that are going to become germ cells, they divide by carbon copy mitosis right up until they enter meiosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So there is no mechanism that would lead to genotypes different from the genotype of the zygote (until meiosis).&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-03-28T01:43:06.260" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30846" PostTypeId="1" AcceptedAnswerId="30861" CreationDate="2015-03-28T02:07:01.723" Score="3" ViewCount="120" Body="&lt;p&gt;I recently found out that there are killer whales that live in the Gulf of Mexico, but they are smaller than killer whales that are commonly found in the Pacific Ocean. Why is it they are smaller in size?&lt;/p&gt;&#xA;" OwnerUserId="13023" LastActivityDate="2015-03-28T22:41:37.257" Title="Why are killer whales found in the Gulf of Mexico smaller than ones found in the Pacific?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30848" PostTypeId="2" ParentId="30844" CreationDate="2015-03-28T07:54:17.370" Score="5" Body="&lt;p&gt;You might need to narrow your parameters a bit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just things to consider:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Our lungs are not hollow organs that can accommodate an oxygen producing machine. They are basically narrow tubes that get smaller and smaller until they end in a tiny balloon-like structure - about 700 million of them. Where would the machine go?&lt;/li&gt;&#xA;&lt;li&gt;100% oxygen is toxic to the lungs, as it is to many other things as well.  &lt;/li&gt;&#xA;&lt;li&gt;How would the oxygen diffuse to all the other areas of the lung that need oxygen? Diffusion is a complicated process in a structure like the lungs.&lt;/li&gt;&#xA;&lt;li&gt;from what would it produce oxygen? For example, would it extract it from water? How would the body deal with the loss of moisture from the air in out lungs? Where would the excess hydrogen go?&lt;/li&gt;&#xA;&lt;li&gt;Hydrogen is highly flammable around 29%. Would we become fire-breathing?&lt;/li&gt;&#xA;&lt;li&gt;How would the machine not hyperinflate and thus injure the lung?  &lt;/li&gt;&#xA;&lt;li&gt;How would we get rid of CO&lt;sub&gt;2&lt;/sub&gt;? We would still have to breathe in and out.&lt;/li&gt;&#xA;&lt;li&gt;Etc.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-03-28T07:54:17.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30849" PostTypeId="2" ParentId="30822" CreationDate="2015-03-28T11:34:35.317" Score="2" Body="&lt;p&gt;My answer below directly (and solely) addresses what I think is the main gist of the question: Are there any adverse effects on one's physiology as a direct result of donating blood? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Blood donation, at the amounts typically taken (200~500mls), will not harm you. A healthy human being produces approximately 100,000,000,000 (one hundred billion) NEW hematopoietic cells DAILY to replenish short-lived blood cells and platelets. All of these ultimately derive from the hematopoietic stem cells residing in the bone marrow within one's long bones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can appreciate, with such a huge amount of turnover daily, the body is constantly churning out new blood cells. Thus, any depletion in blood cells one will experience as a result of blood donation is a fraction of what will be lost normally in daily homeostasis anyway and thus will not affect a healthy individual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And then there are the knock-on benefits suggested by epidemiological studies, some of which are alluded in this layman article: &lt;a href=&quot;http://news.health.com/2014/06/13/4-unexpected-benefits-of-donating-blood/&quot; rel=&quot;nofollow&quot;&gt;http://news.health.com/2014/06/13/4-unexpected-benefits-of-donating-blood/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[source: I'm a hematologist]&lt;/p&gt;&#xA;" OwnerUserId="14553" LastEditorUserId="14553" LastEditDate="2015-03-28T12:00:14.413" LastActivityDate="2015-03-28T12:00:14.413" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30850" PostTypeId="2" ParentId="30843" CreationDate="2015-03-28T12:26:30.230" Score="2" Body="&lt;p&gt;Nice question(s). I will go through them in sequence.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Safe current limits&lt;/em&gt;&lt;/strong&gt;. With regard to electrical stimuli it is &lt;strong&gt;current density&lt;/strong&gt; that determines safety limits. Therefore, in medical devices, it is not a matter of what is a safe maximum &lt;em&gt;current level&lt;/em&gt;, but what is the maximum safe current level given the surface of the electrode? And in terms of skin stimulation, it is not the safety limit that is the bottle neck, but the &lt;strong&gt;maximum tolerable current density&lt;/strong&gt;, which is around 0.5 mA/cm&lt;sup&gt;2&lt;/sup&gt; (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0169409X9500081H&quot; rel=&quot;nofollow noreferrer&quot;&gt;Prausnitz, 1996&lt;/a&gt;). Higher stimuli result in pain sensations. This is one of the reasons why the &lt;a href=&quot;http://www.wicab.com/en_us/&quot; rel=&quot;nofollow noreferrer&quot;&gt;BrainPort&lt;/a&gt; device is used on the tongue; the moist surface reduces impedance and hence the currrent needed to elicit a tactile response.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Permanent damage&lt;/em&gt;&lt;/strong&gt;. As said, the tolerable sensation limit is more of an issue (a must-read in this regard is &lt;a href=&quot;https://minds.wisconsin.edu/bitstream/handle/1793/9626/file_1.pdf?sequence=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kaczmareck et al., 1991&lt;/a&gt;). &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Acuity&lt;/em&gt;&lt;/strong&gt;. The best-possible tactile &quot;resolution&quot; is generally expressed in terms of &lt;strong&gt;tactile acuity&lt;/strong&gt;. Tactile acuity varies across body sites, and unfortunately it is about the worst on the thigh (45 mm) and the back (40 mm). A much cited picture on tactile acuities is the following from Weinstein (&lt;a href=&quot;http://www.psypress.com/books/details/9780805829419/&quot; rel=&quot;nofollow noreferrer&quot;&gt;1968&lt;/a&gt;):&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Wnkvd.png&quot; alt=&quot;2-point discrimination thresholds&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These acuities represent the distance in which 2 simultaneously presented, static pressure points need to be spaced to be &lt;em&gt;just noticeable&lt;/em&gt; (the so called two-point discrimination threshold). Although your proposed electric stimuli are different from pressure stimuli, these reported values in the figure (40 - 45 mm) give an impression on the inter-electrode distance needed. From my own work I can confirm the ~40 mm using vibratory stimuli. The unfavorable acuity of the back and external bodily skin in general was also one of the rasons to put the electrode grid of the BrainPort on the tongue, which has excellent tactile acuity.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA; - &lt;a href=&quot;https://minds.wisconsin.edu/bitstream/handle/1793/9626/file_1.pdf?sequence=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kaczmareck et al. &lt;em&gt;IEEE Trans Biomed Eng&lt;/em&gt; 1991;&lt;strong&gt;38&lt;/strong&gt;:1-16&lt;/a&gt;&lt;br&gt;&#xA; - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0169409X9500081H&quot; rel=&quot;nofollow noreferrer&quot;&gt;Prausnitz, &lt;em&gt;Adv Drug Delivery Rev 1996&lt;/em&gt;;&lt;strong&gt;18&lt;/strong&gt;:395-425&lt;/a&gt;&lt;br&gt;&#xA; - &lt;a href=&quot;http://www.psypress.com/books/details/9780805829419/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Weinstein S. 1968. In: Kenshalo. The Skin Senses:195-222. Springfield, IL: Thomas&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-28T12:32:18.283" LastActivityDate="2015-03-28T12:32:18.283" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30851" PostTypeId="1" AcceptedAnswerId="30853" CreationDate="2015-03-28T15:52:37.750" Score="5" ViewCount="5837" Body="&lt;p&gt;I've found various results online and I was recently marked in on an important test as wrong when I made the assumption they were not found in the cell membrane. Does anyone know what the correct answer is in this case?  Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="14940" LastActivityDate="2020-06-14T05:22:26.607" Title="Are nucleic acids found in cell membranes?" Tags="&lt;cell-biology&gt;&lt;cell-membrane&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30852" PostTypeId="1" CreationDate="2015-03-28T16:05:01.593" Score="4" ViewCount="354" Body="&lt;p&gt;I've seen spike, huge spike. And I thought that development of such spikes could be contrary to the evolution theory. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lQPXB.jpg&quot; alt=&quot;Spikes&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Being „little more” spiky doesn’t give you any advantage... So those individuals having one won't have smaller mortality rate than those with smooth stem. &#xA;Even more, the individuals with bulgy (more spiky) waste resources their ruggedness and have more things to feed, which should mean that they would have higher mortality rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I can see no way to develop spikes on the stems of roses according to the evolution theory which embrace &quot;small improvement&quot;. Spike is only efficient (to deter aggressor) when it's very sharp, it's either sharp or it isn't - there is little in between. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could anybody tell me that this is bullshit (and why it is bullshit), and that I should us believe in Darwin competence?;) &lt;/p&gt;&#xA;" OwnerUserId="8618" LastActivityDate="2015-03-30T15:45:29.860" Title="Evolution theory - roses spikes - being more bulgy doesn't give you advantage" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;plant-anatomy&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30853" PostTypeId="2" ParentId="30851" CreationDate="2015-03-28T16:18:25.797" Score="2" Body="&lt;p&gt;Nucleic acids are not structural components of cell membranes (ribosomes and nucleus are the main places where they are found).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, being open system, cell exchanges chemicals with its surrounding and cellular membrane can transport nucleic acids as well. This is why these acids can potentially be detected in the cell membranes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have the exact question expression it can help with more precise answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/URvB6.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-03-28T16:18:25.797" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30854" PostTypeId="2" ParentId="30852" CreationDate="2015-03-28T16:32:42.123" Score="4" Body="&lt;p&gt;Just because you cannot forsee a use for more &quot;bulgy&quot; spikes doesn't mean there isn't a use for them. Furthermore, natural selection isn't about producing perfect organisms, it's about selecting for traits that are &quot;good enough&quot;. There is also more to evolution than natural selection. The phenomenon of genetic drift can cause a neutral or slightly maladaptive trait to become fixed in the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, not every single trait is adaptive. Check out the famous paper &lt;a href=&quot;http://www.jstor.org/discover/10.2307/77447?sid=21106272514503&amp;amp;uid=2129&amp;amp;uid=3739656&amp;amp;uid=2&amp;amp;uid=4&amp;amp;uid=3739256&amp;amp;uid=70&quot; rel=&quot;nofollow&quot;&gt;The Spandrels of San Marco&lt;/a&gt; if you want to read more. It talks about how we shouldn't focus on trying to come up with an adaptionist theory for every trait and instead consider that other agents of evolutionary change, such as genetic drift, can generate non-adaptive traits.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-03-28T16:32:42.123" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30856" PostTypeId="1" AcceptedAnswerId="30859" CreationDate="2015-03-28T19:48:51.793" Score="11" ViewCount="512" Body="&lt;p&gt;I've read that, on average, a sedentary female burns between 1,600 - 2,000 calories and a sedentary male burns between 2,000 and 2,500 calories. I've also read that the brain itself burns quite a few of these.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say two people are exactly the same, and have the exact same (sedentary) lifestyle—except one of them often does intense mathematics. Is there a significant difference in calorie burn? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so, how much is it?&lt;/p&gt;&#xA;" OwnerUserId="15146" LastEditorUserId="3340" LastEditDate="2015-06-04T11:38:07.720" LastActivityDate="2015-06-04T11:38:07.720" Title="Is there a significant difference in sedentary calorie-burn between a thinker and non-thinker?" Tags="&lt;brain&gt;&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30857" PostTypeId="1" AcceptedAnswerId="39022" CreationDate="2015-03-28T20:05:45.277" Score="6" ViewCount="20324" Body="&lt;p&gt;I have counted the degrees of freedom in my hand over and over and I keep getting the number 19.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose each finger has 3 degrees of freedom. Then 5 * 3 = 15. The wrist can rotate around or back and forth so that contributes to 4 degrees of freedom. In total the hand has 19 degrees of freedom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a cursory &lt;a href=&quot;https://www.google.com/search?q=human+hand+has+27+degrees+of+freedom&quot; rel=&quot;nofollow&quot;&gt;google search&lt;/a&gt;, I can notice that it is commonly agreed upon that human hand has 27 degrees of freedom. Can someone provide a good reference and explanation for this?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="3340" LastEditDate="2015-09-23T14:49:47.783" LastActivityDate="2015-09-24T04:08:10.480" Title="Does the human hand have 27 degrees of freedom?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30858" PostTypeId="1" AcceptedAnswerId="34748" CreationDate="2015-03-28T20:09:44.607" Score="6" ViewCount="492" Body="&lt;p&gt;When I press my finger, even with relatively little force, into beef or chicken (say, at a grocery store), the indentation remains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I poke a cow with my finger, the indentation does not remain. When I squeeze my own arm, even with the same (or greater) amount of force used to alter the shape of meat with my finger, my arm remains the same shape afterwards.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the difference between dead and living muscle tissue, with respect to mechanisms that allow it to maintain its shape? Does living muscle tissue somehow actively maintain its shape while dead tissue cannot? Is it something more passive, such as a breakdown of something in dead muscle tissue that makes it more malleable (and if so, what)? &lt;/p&gt;&#xA;" OwnerUserId="8218" LastEditorUserId="8218" LastEditDate="2015-05-31T04:04:23.590" LastActivityDate="2015-05-31T13:10:12.693" Title="Why is living muscle tissue seemingly able to restore its shape under force, while dead tissue is not?" Tags="&lt;muscles&gt;&lt;death&gt;" AnswerCount="2" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30859" PostTypeId="2" ParentId="30856" CreationDate="2015-03-28T20:47:34.230" Score="13" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there a significant difference in calorie burn? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The brain, while only making up 2% of our body weight, accounts for ~20% of our energy use at rest. That's because the brain, being critical for survival, is a very high-maintenance organ. At rest, the membrane potentials of all neurons - firing or at &quot;rest&quot; - need to be controlled/maintained.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of all the energy used by the brain, about 25% of it is needed for signal-independent function (protein synthesis, phospholipid turnover, etc.) Furthermore, there are two types of cells in the brain: neurons and glial cells. The glial cells (about 30%) use from 17 to 40% of the energy depending on whose estimates you use. The rest is needed (by neurons) for signal-related processes - maintaining/restoring cell membrane potential, etc. - only a fraction of which is used for &lt;em&gt;thinking&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The brain never rests - it is highly active even in sleep, with both excitatory and inhibitory activities needing energy. Higher mental functions (e.g. doing math problems) only shifts the areas of highest activity a little bit compared to all the activity that occurs without our awareness of it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, if we could measure glucose consumption of &lt;em&gt;the entire brain&lt;/em&gt; while daydreaming vs. doing math, we might be able to answer that question, but the truth is, brain activity doesn't occur in isolation. Someone doing challenging math problems is using more energy in other areas of the body as well; respiration rate, heart rate, muscle tension, etc. varies with the stress of the challenge, so glucose levels alone can't be relied upon (in fact, stress would increase our body's production of glucose) to indicate energy expenditure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The end result is that in isolation, rigorous mental activity (which can be maintained only for a relatively short duration without fatigue, so it occurs in bursts) expends very little of the total energy the brain uses.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A common view equates concentrated mental effort with mental work, and it is fashionable to attribute a high demand for mental effort to the process of problem solving in mathematics. Nevertheless, there appears to be no increased energy utilization by the brain during such processes. From resting levels, total cerebral blood flow and oxygen consumption remain unchanged during the exertion of the mental effort required to solve complex arithmetical problems.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK27977/&quot; rel=&quot;noreferrer&quot;&gt;Cerebral Metabolic Rate in Various Physiological States&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.scientificamerican.com/article/thinking-hard-calories/&quot; rel=&quot;noreferrer&quot;&gt;Does Thinking Really Hard Burn More Calories?&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="15051" LastEditDate="2015-03-29T21:51:26.487" LastActivityDate="2015-03-29T21:51:26.487" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30861" PostTypeId="2" ParentId="30846" CreationDate="2015-03-28T22:41:37.257" Score="2" Body="&lt;p&gt;Animals living in colder climate / environment are larger because this way they have better body surface / volume (mass) ration thus they're more resistant to cold. Animals living in warmer areas are smaller thus they have larger body surface compared to their volume(mass) to dissipate heat easier.&#xA;Check &lt;a href=&quot;http://en.wikipedia.org/wiki/Bergmann%27s_rule&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; wiki page for more details.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-03-28T22:41:37.257" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30862" PostTypeId="1" AcceptedAnswerId="30877" CreationDate="2015-03-28T22:54:48.517" Score="6" ViewCount="3810" Body="&lt;p&gt;When a ligand and receptor interact with a given kd, one can easily determine % of ligand bound to the receptor when the kd, total concentration of ligand, and total concentration of receptor are known. When there is a mixture of multiple ligands and receptors where each ligand and each receptor can interact with eachother, this is not so simple. For example, lets say you have the following set of information:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$K_{11} = \frac{[R_1][L_1]}{[R_1L_1]}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$K_{12} = \frac{[R_1][L_2]}{[R_1L_2]}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$K_{21} = \frac{[R_2][L_1]}{[R_2L_1]}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$K_{22} = \frac{[R_2][L_2]}{[R_2L_2]}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;along with the $K_d$'s ($K_{ij}$) and the total concentrations of $R_1$, $R_2$, $L_1$, and $L_2$. I have not managed to find any publications where this has been demonstrated but I would be surprised if it hasn't been figured out by someone.&lt;/p&gt;&#xA;" OwnerUserId="15149" LastEditorUserId="4840" LastEditDate="2015-03-29T08:03:32.720" LastActivityDate="2015-03-29T10:15:36.897" Title="Is there a formula for determining the % of ligand bound to a given receptor in a mixture with multiple ligands and receptors?" Tags="&lt;protein-binding&gt;&lt;enzyme-kinetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30863" PostTypeId="1" CreationDate="2015-03-28T22:55:00.863" Score="2" ViewCount="570" Body="&lt;p&gt;As far as I know, &lt;em&gt;neuroplasticity&lt;/em&gt; is about restoring brain functions by moving some functions to other still functional. Neuroplasticity is more prominent in children than in adults.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are other examples of neuroplasticity that are unrelated to pathologies? Can it be demonstrated by a simple experiment outside the laboratory? Are learning, or simply the getting used to new things examples of neuroplasticity?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, after wearing red-cyan goggles, I see a color mismatch for some time after I take off the goggles. Is it related to neuroplasticity or some other thing?&lt;/p&gt;&#xA;" OwnerUserId="15148" LastEditorUserId="9943" LastEditDate="2015-03-29T09:25:50.857" LastActivityDate="2015-03-30T13:41:54.680" Title="What exactly is neuroplasticity, and can it be demonstrated with a simple experiment?" Tags="&lt;brain&gt;&lt;experimental-design&gt;&lt;neurophysiology&gt;&lt;neuroplasticity&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30865" PostTypeId="1" AcceptedAnswerId="30866" CreationDate="2015-03-29T01:11:39.950" Score="3" ViewCount="170" Body="&lt;p&gt;&lt;strong&gt;In this question we are examining a bacterial RNA polymerase that elongates at 20 codons per second.&#xA;Question 1: How long will this RNA polymerase take to transcribe the Lac Z gene at 3510 base pairs?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;My answer: A codon is 3 base pairs so I start by dividing 3510 by 3 and then by 20 to get 58,5 seconds.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question 2: Your bacteria can produce a Lac Z mRNA about every other second. How can you explain this?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;My answer: I am very lost on this one. I thought that the mRNA would be as long as the gene so wouldn't this be 58,5 seconds not roughly 2 seconds??&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-03-29T12:02:34.433" Title="RNA polymerase question" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;dna&gt;&lt;transcription&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30866" PostTypeId="2" ParentId="30865" CreationDate="2015-03-29T01:38:05.657" Score="6" Body="&lt;p&gt;Multiple RNA Polymerase transcription complexes engaged on the &lt;em&gt;lacZ&lt;/em&gt; gene at the same time, staggered along the gene.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-03-29T01:38:05.657" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30867" PostTypeId="2" ParentId="30863" CreationDate="2015-03-29T01:54:16.330" Score="3" Body="&lt;p&gt;Your question is basically a matter of defining &lt;em&gt;brain plasticity&lt;/em&gt; or more broader, &lt;em&gt;neuroplasticity&lt;/em&gt;. According to a well-cited paper in &lt;em&gt;Brain&lt;/em&gt; &lt;a href=&quot;http://brain.oxfordjournals.org/content/134/6/1591.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Cramer et al., 2011)&lt;/a&gt; neuroplasticity is defined as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] the ability of the nervous system to respond to intrinsic or extrinsic stimuli by reorganizing its structure, function and connections.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hence, the term can be, and indeed is used very broadly. A more elaborate definition in the same article should answer you question as to whether &lt;em&gt;learning&lt;/em&gt; and &lt;em&gt;habituation&lt;/em&gt; can be considered to be associated with neuroplasticity:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Neuroplasticity can be broadly defined as the ability of the nervous system to respond to intrinsic and extrinsic stimuli by reorganizing its structure, function and connections; can be described at many levels, from molecular to cellular to systems to behaviour; and can occur during development, &lt;strong&gt;in response to the environment&lt;/strong&gt;, &lt;strong&gt;in support of learning&lt;/strong&gt;, in response to disease, or in relation to therapy. Such plasticity can be viewed as adaptive when associated&#xA;  with a gain in function [...] or as maladaptive when associated with negative consequences [...]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Your vision example, however, is more appropriately referred to as &lt;em&gt;adaptation&lt;/em&gt;. Although it strictly spoken falls under the above definition of plasticity (...reorganizing its... function,  color adaptation is (at least in my opinion) too short-lived (minutes) to be associated with plasticity.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, as to experiments - Although learning a chunk of material from a textbook as a homework assignment is definitely related to plasticity, it cannot be seen as proof; it is the result of neuroplasticity. Experiments showing plasticity can and have been done with imaging (most notably fMRI) or with electrophysiological approaches (patch clamp studies showing long-term potentiation reflecting learning). These techniques cannot be applied outside the laboratory, as they require advanced and pricey equipment, careful experimental design, and not least importantly ethical clearance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA; - &lt;a href=&quot;http://brain.oxfordjournals.org/content/134/6/1591.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cramer et al., &lt;em&gt;Brain&lt;/em&gt; 2011;&lt;strong&gt;134&lt;/strong&gt;:1591–609&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Further reading&lt;/strong&gt;&lt;br&gt;&#xA; - Color adaptation: &lt;strong&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/26014/what-is-the-science-behind-the-inaccurate-perception-of-colors&quot;&gt;What is the science behind the   inaccurate perception of colors&lt;/a&gt;?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-03-29T09:34:55.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30869" PostTypeId="2" ParentId="30817" CreationDate="2015-03-29T05:33:19.033" Score="2" Body="&lt;p&gt;Lets assume for simplicity that DNA is globally subjected to the same mutation rate (which is probably not a fully correct assumption).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now let take a DNA region which is functional (what you meant by giving a fitness benefit), mutations in this region will occur as anywhere else in the genome. Some mutations will be deleterious and reduce the fitness of (or kill) the cell therefore, on the long run, cells that do not carry those deleterious mutations will propagate. This means that now if you look at the genome in the cell that propagated, certain genomic regions will contain less mutations than other because of the negative selection. They were &quot;protected&quot; against deleterious mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, In multicellular organisms any mutations that reduces the fitness of the germline cells will be negatively selected (again functional regions will be more conserved).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The author was likely referring to regulatory regions. These are regions that do not encode proteins but are very important for gene regulations. Regulatory regions include enhancers, silencers, insulators and locus control regions (&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.genom.7.080505.115623?url_ver=Z39.88-2003&amp;amp;rfr_dat=cr_pub%3Dpubmed&amp;amp;rfr_id=ori%3Arid%3Acrossref.org&amp;amp;journalCode=genom&quot; rel=&quot;nofollow&quot;&gt;Maston GA, 2006&lt;/a&gt;). These regions will also be more conserved as deleterious mutations in regulatory elements could reduce the fitness of the cell/germline.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-29T05:59:11.667" LastActivityDate="2015-03-29T05:59:11.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30871" PostTypeId="1" CreationDate="2015-03-29T07:13:50.913" Score="0" ViewCount="283" Body="&lt;p&gt;I also searched it on internet, and just basically know it's related to the Stem Cells, but there are too many resources, can anyone help me find out more about them, like their applications? They really interest me.   &lt;/p&gt;&#xA;" OwnerUserId="14913" LastEditorUserId="15136" LastEditDate="2015-03-29T10:02:48.790" LastActivityDate="2015-03-29T10:06:24.810" Title="What are iPSC cells, and what are their applications?" Tags="&lt;cell-biology&gt;&lt;cell&gt;&lt;stem-cells&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2015-03-29T22:44:52.330" ContentLicense="CC BY-SA 3.0" />
  <row Id="30872" PostTypeId="2" ParentId="28080" CreationDate="2015-03-29T07:24:58.707" Score="2" Body="&lt;p&gt;I couldn't find any examples in humans (aside from &lt;a href=&quot;https://en.wikipedia.org/wiki/Mitochondrion#Origin&quot; rel=&quot;nofollow&quot;&gt;mitochondria&lt;/a&gt;, if those count), but there are examples of varying degrees of intracellular endosymbiosis in insects, plants, and single-celled organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example is &lt;em&gt;Ca.&lt;/em&gt; Carsonella ruddii, an endosymbiontic bacterium of psyllids (a family of plant-feeding insects).  The bacterium lives within specialized host cells called &lt;a href=&quot;https://en.wikipedia.org/wiki/Bacteriocyte&quot; rel=&quot;nofollow&quot;&gt;bacteriocytes&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Many insects harbor intracellular bacteria that produce and excrete essential amino acids into the host cytosol. Although, in some cases, ‘dead-end’ bacterial cells with incomplete genomes are replaced by new endosymbionts, this is not the case for the bacteriocyte &lt;em&gt;Carsonella ruddii&lt;/em&gt;. The genome of &lt;em&gt;Carsonella&lt;/em&gt; is reduced to a mere 160 kb (within the range for organelles), has lost all genes for many essential functions, and no other bacterial endosymbionts are present to offer potential compensation. Thus, &lt;em&gt;Carsonella&lt;/em&gt; seems to be at the end of an endosymbiotic continuum in sap-feeding psyllid insects and represents the recent acquisition of a new type of organelle for biosynthesis of amino acids.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;Source: &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0966842X0700087X&quot; rel=&quot;nofollow&quot;&gt;The intracellular cyanobacteria of Paulinella chromatophora: endosymbionts or organelles?&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia's article on &lt;a href=&quot;https://en.wikipedia.org/wiki/Endosymbiont&quot; rel=&quot;nofollow&quot;&gt;endosymbionts&lt;/a&gt; has some other interesting examples.&lt;/p&gt;&#xA;" OwnerUserId="11657" LastActivityDate="2015-03-29T07:24:58.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30874" PostTypeId="2" ParentId="30871" CreationDate="2015-03-29T09:18:17.327" Score="4" Body="&lt;p&gt;From &lt;a href=&quot;http://www.nature.com/nature/journal/v516/n7530/full/nature14047.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article: iPSC's or induced pluripotent stem cells are somatic cells that have been driven to acquire an induced pluripotent cell state.  Somatic cells can be any cell of the body except sperm cells, egg cells and undifferentiated stem cells. Investigators can induce these cells to 'return' to a stem cell like state by forcing the expression of key transcription factors, and by genome-wide remodeling of epigenetic marks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an entire spectrum of different iPSC's that can be generated, but much is not yet known. Future applications include using them for regenerative medicine, drug discovery, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recently there were several articles published in nature:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v516/n7530/full/516172a.html&quot; rel=&quot;nofollow&quot;&gt;Stem cells: A designer's guide to pluripotency&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v516/n7530/full/nature14046.html&quot; rel=&quot;nofollow&quot;&gt;Genome-wide characterization of the routes to pluripotency&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;amongst others. Also you can check out &lt;a href=&quot;http://www.stemformatics.org/&quot; rel=&quot;nofollow&quot;&gt;http://www.stemformatics.org/&lt;/a&gt; for more information on stem cells and research being done. &lt;/p&gt;&#xA;" OwnerUserId="15136" LastEditorUserId="5144" LastEditDate="2015-03-29T10:06:24.810" LastActivityDate="2015-03-29T10:06:24.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30875" PostTypeId="1" CreationDate="2015-03-29T09:34:05.343" Score="7" ViewCount="115" Body="&lt;p&gt;Not all bacteria have acquired F-plasmids through conjugation. Some of the mechanisms for this are unsuccesful conjugation events (mechanical disruption), no transfer due to integration in bacterial chromosome, etc (See previous question and answer). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now I am wondering if there are also mechanisms that self-limit the conjugation and transfer of F-plasmids. For instance that a bacterium can only transfer its F-plasmid once during its lifetime. &lt;/p&gt;&#xA;" OwnerUserId="15136" LastActivityDate="2015-06-22T18:50:42.747" Title="Are there mechanisms that limit the amounts of time conjugation and F-plasmid transfer can happen? If yes, what are they?" Tags="&lt;genetics&gt;&lt;microbiology&gt;&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30877" PostTypeId="2" ParentId="30862" CreationDate="2015-03-29T10:09:01.257" Score="6" Body="&lt;p&gt;The answer is here, but depending on your level of comfort with the math I'm not sure how enlightening it will be. I think that the reason people tend to stick to one ligand/one receptor models is that they capture all the intuition without the tedious algebra. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's interesting that you are asking for the fraction of &lt;em&gt;ligand&lt;/em&gt; bound to receptors ($[RL]/[L]_{tot}$). Typically one is interested in the fraction of &lt;em&gt;receptors&lt;/em&gt; that have ligand bound ($[RL]/[R]_{tot}$). This is for two reasons:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Typically the fraction of bound receptor is the physiologically relevant variable for a cell, determining the response of the cells to the ligand stimulus. Since the cell can only sense the concentration of ligand when it binds to the receptor, the fraction of bound receptor is the natural variable to study.&lt;/li&gt;&#xA;&lt;li&gt;In most contexts, the number of receptors is much smaller than the number of ligands. This motivates the approximation found in pretty much all treatments of receptor-ligand equilibrium that &lt;em&gt;the concentration of receptor-ligand complex is negligible compared to the total concentration of ligand&lt;/em&gt;. For cells, this is a fairly reasonable assumption. In this limit, the fraction of ligands bound to receptors ($[RL]/[L]_{tot}$) is always negligible. It's the fraction $[RL]/[R]_{tot}$ that is  interesting. Another reason this assumption might be adopted is that in practice, ligands tend to be soluble while receptors are insoluble. In this case, it is easier to control the concentration of ligand, adding it in excess to a pellet of receptors, and then measure the amount of bound receptors (maybe by radioactivity): in this experiment the total concentration of receptors is &lt;em&gt;measured,&lt;/em&gt; not controlled, so you want your equation to be a function of your controlled variable, the concentration of ligand. This requires adopting the approximation above.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The situation in which there are two ligands binding to one receptor has been solved (in the limit that $[RL]\ll[L]_{tot}$): this case is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Competitive_inhibition&quot;&gt;competitive inhibition&lt;/a&gt;. In your notation, the fraction of receptor 1 bound to ligand 1 (ligand 2 is the &quot;competitive inhibitor,&quot; i.e. rival ligand):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{[RL]}{[R]_{tot}} = \frac{[L_1]}{[L_1]+K_{11}(1+\frac{[L_2]}{K_{12}})}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I'm going to generalize to the case that there are $N$ ligands and I am interested in the fraction of a given receptor $R_i$ bound to ligand $L_j$. The equilibrium constant for this reaction is $K_{ij}\equiv [R_i][L_j]/[R_iL_j]$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The receptor is also binding to all the other ligands, so that the free concentration of receptor $[R_i]$ is equal to the difference between the total receptor concentration $[R_i]_{tot}$ and the concentration of each bound complex $[R_iL_k]$ for $k$ from 1 to $N$. And the ligand is also binding to all the other receptors. In order to get a reasonable equation, we have to invoke an approximation very similar in spirit to the one mentioned above, namely, that &lt;em&gt;the concentration of all ligand-receptor complexes is small compared to the total concentration of each ligand individually.&lt;/em&gt; Thus I can ignore the difference between $[L_j]_{free}$ and $[L_j]_{tot}$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this approximation, I expand out the expression for the equilibrium constant (using $[L_j]$ as shorthand to stand for $[L_j]_{tot}$).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$K_{ij} = \frac{([R_i]_{tot}-[R_iL_j]-\sum_{k\neq j}^{N}[R_iL_k])[L_j]}{[R_iL_j]}=\frac{[R_i]_{tot}[L_j]}{[R_iL_j]}-[L_j]-\sum_{k\neq j}^N\frac{L_kK_{ij}}{K_{ik}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the sum is over $k$ from 1 to $N$ &lt;em&gt;except&lt;/em&gt; $k=j$, which I pulled out of the sum early. I also used the definition of each dissociation constant to write the sum in terms of dissociation constants instead of $[R_iL_k]$, which makes the algebra a lot simpler.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This can then be simplified to solve for the fraction of bound receptors:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{[R_iL_j]}{[R_i]_{tot}} = \frac{[L_j]}{[L_j]+K_{ij}(1+\sum_{k\neq j}^N\frac{[L_k]}{K_{ik}})}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose instead of being interested in the fraction of receptor $i$ bound to a particular ligand $j$, one is interested in the fraction of receptor $i$ bound to &lt;em&gt;any&lt;/em&gt; ligand. I'll call this quantity $[R_i\mathbf{L}]/[R_i]_{tot}$. We can figure this out by noting that &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$[R_i\mathbf{L}]\equiv \sum_{k=1}^N[R_iL_k] = [R_i]_{tot} - [R_i]_{free}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We obtain $[R_i]_{free}$ from the formula for each $K_d$:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$[R_i]_{free}\equiv[R_i] = \frac{K_{ij}[R_iL_j]}{[L]_j}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And so using our equation for $[R_iL_j]$, we obtain (I'll spare you some of the gory algebra details)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{[R_i\mathbf{L}]}{[R_i]_{tot}} = \frac{\sum_{k=1}^N\frac{[L]_k}{K_{ik}}}{1+\sum_{k=1}^N\frac{[L]_k}{K_{ik}}}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(these sums are again unrestricted, from $k=1$ to $N$ including $k=j$). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Happily, if there is only one ligand, these formula reduce to the regular result, namely $[L_1]/([L_1]+K_{i1})$. As another check, if all the $K_d$s are equal, then the fraction of receptors bound to &lt;em&gt;any&lt;/em&gt; type of ligand is the same as the bound fraction for the same amount of a &lt;em&gt;single&lt;/em&gt; type of ligand with the same concentration as the whole pool of different ligands ($\sum_{k=1}^N[L_k]$), and the fraction of receptor bound to a particular ligand $L_j$ is smaller by the fraction of the total ligand pool that is species $j$, $[L_j]/\sum_{k=1}^N[L_k]$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are really interested in the fraction of &lt;em&gt;ligands&lt;/em&gt; bound to receptors---that is, you are working in the limit in which there are tons of receptors compared to ligands, so that the number of receptor-ligand complexes is tiny compared to the number of receptors---then you can use the above equations just by switching $L$'s and $R$'s. In this case you would obtain&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{[R_iL_j]}{[L_j]_{tot}} = \frac{[R_i]}{[R_i]+K_{ij}(1+\sum_{k\neq i}^{N}\frac{[R_k]}{K_{kj}})}\qquad [R_i]\equiv[R_i]_{free}\approx[R_i]_{tot}$$&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;A caveat&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;To derive these equations, I made a pretty strong assumption that the total concentration of &lt;em&gt;all&lt;/em&gt; receptor-ligand complexes (for different receptors as well as different ligands) is small compared to the total concentration of each ligand individually. In this limit, we can assume that the pools of free ligands of each species are so large that each receptor equilibrates with this pool independently of each other receptor (there's plenty of ligands to go around). You might be interested in the limit in which ligand binding and unbinding to one receptor affects the binding and unbinding to another receptors, so that receptors are not independent. I am not sure how to approach this problem. I'm skeptical that there will be any sort of closed form solution; in my preliminary thinking about this limit, I think I can imagine situations in which stationary equilibria are not possible: depending on rates, receptor A might partially equilibrate, depleting the pool of ligands, affecting the equilibration of receptor B, which would cause receptor B to &quot;pull&quot; more ligands away from A, in some sort of oscillation. However, that is just speculation, and I'd be very curious if someone could provide more insight to this case, in which receptors are able to &quot;interact&quot; through the pool of free ligand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the take-aways of this whole analysis is that it is very helpful to be aware of the assumptions made in standard derivations that lead to the nice results we learn in biochemistry class, and how those assumptions might have to change if we generalize the system somewhat. &lt;/p&gt;&#xA;" OwnerUserId="4840" LastEditorUserId="4840" LastEditDate="2015-03-29T10:15:36.897" LastActivityDate="2015-03-29T10:15:36.897" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30879" PostTypeId="2" ParentId="30865" CreationDate="2015-03-29T12:02:34.433" Score="4" Body="&lt;p&gt;Either the gene is present in multiple copies (especially possible if it is in a plasmid) or multiple RNA polymerases are transcribing it, each beginning from the start site one after the other with some amount of time delay, much like multiple ribosomes translate the same mRNA to increase rate of protein production.&lt;/p&gt;&#xA;" OwnerUserId="11716" LastActivityDate="2015-03-29T12:02:34.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30882" PostTypeId="2" ParentId="30836" CreationDate="2015-03-29T16:50:42.813" Score="5" Body="&lt;p&gt;First of all I am not sure if your examples are per se correct. But they might also be an additional bonus. Secondly, I would like to refer to two articles: &quot;&lt;a href=&quot;http://www.nature.com/scitable/topicpage/polyploidy-1552814&quot; rel=&quot;noreferrer&quot;&gt;Polyploidy&lt;/a&gt;&quot; and &quot;&lt;a href=&quot;http://www.nature.com/scitable/content/The-advantages-and-disadvantages-of-being-polyploid-1554633&quot; rel=&quot;noreferrer&quot;&gt;The advantages and disadvantages of being polyploid&lt;/a&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the main benefits could be allowing organisms long-term evolutionary flexibility. Often adapted polyploids can undergo a proces that is called diploidization, during which genomic redundancy is removed. This means extra copies of genes will undergo less negative selection. Meaning alleles containing deleterious mutations at functionally important nucleotides are selected against. This allows more mutational freedom, leading to what is called subfunctionalization and neofunctionalization: new genes are created with slightly different or new functions. Other redundant genes are lost or become inactivated (pseudogenes). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example of benefits from polyploidy, this time not in an evolutionary, but in a more individual context, is the fenomenon called hybrid vigor or heterosis. Heterosis is a phenomenon in which a polyploid offspring of two diploid parents is more healthy and vigorous than its progenitors. One of the factors explaining this could be due to a protection against recessive characters, as being homozygous as a polyploid is even more 'uncommon'.&lt;/p&gt;&#xA;" OwnerUserId="15136" LastActivityDate="2015-03-29T16:50:42.813" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30883" PostTypeId="1" AcceptedAnswerId="31020" CreationDate="2015-03-29T17:34:42.307" Score="8" ViewCount="4388" Body="&lt;p&gt;So when dietary fats are in the small intestine, they are emulsified by bile salts in order for action by lipases to occur.  Lipases degrade the triacylglycerols into monoacylglycerols, diacylglycerols, free fatty acids, and glycerol, and these are taken up by intestinal epithelial cells.  Once taken up, these are reformed into triacylglycerols.  &lt;br&gt;&#xA;My question: why do these have to be broken down in order to be absorbed, and what is the driving force for reformation of triacylglycerols once absorbed?&lt;/p&gt;&#xA;" OwnerUserId="10470" LastActivityDate="2019-01-09T07:09:31.683" Title="Why are triacylglycerols broken down before being absorbed?" Tags="&lt;lipids&gt;&lt;digestion&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30884" PostTypeId="1" AcceptedAnswerId="30890" CreationDate="2015-03-29T18:32:42.623" Score="5" ViewCount="195" Body="&lt;p&gt;I have an annotated set of SNPs and I would like to explore the difference in the binding affinity of the transcription factor (TF) if I have a SNP in my locus. As my SNPs are annotated (I know wether it is in an intron variant, downstream gene variant, missions variant, etc...) I might explore the binding affinity of those SNPs that are categorized as intron variant, downstream variant,upstream_gene_variant, non_coding_transcript_variant, 5_prime_UTR_variant and not take into consideration SNPs that are &quot;missense variants&quot;. The reason why I want to do so is that transcription factor binding sites (TFBS) might be located before gene and after it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do you think about it? Can a TFBS be located in the exon of a gene? What are the locations of the TFBS regarding the exons,introns, 5' UTR etc?&lt;/p&gt;&#xA;" OwnerUserId="14834" LastEditorUserId="14826" LastEditDate="2015-03-29T22:45:10.140" LastActivityDate="2015-03-30T01:15:52.700" Title="Location of TFBS in genome" Tags="&lt;transcription&gt;&lt;snp&gt;&lt;binding-sites&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30885" PostTypeId="1" AcceptedAnswerId="30887" CreationDate="2015-03-29T18:48:15.637" Score="6" ViewCount="2399" Body="&lt;p&gt;I am having some problems understanding recombination, and I am not sure what element I am missing here. This figure is an example from my text book. The pedigree belongs to a family with an &lt;strong&gt;autosomal&lt;/strong&gt; &lt;strong&gt;dominant&lt;/strong&gt; disease, typed for a marker with alleles A1-A6. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Aqsfb.png&quot; alt=&quot;Figure 14.9 Human Molecular Genetics, 4ed. (© Garland Science)&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, all meioses are &lt;strong&gt;phase-known&lt;/strong&gt;, meaning we know which combination of alleles was inherited from each parent. Apparently this leads us to be able to &lt;strong&gt;unambiguously&lt;/strong&gt; score III1-III5 as non-recombinant (N) and III6 as recombinant (R). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is were I get lost, I don't understand how it is possible to unambiguously score each individual as N or R. Also, if the disease is dominant, how is it possible that III6 is affected, as both alleles originate from the both unaffected I1 and II2?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Blue colour in the pedigree means the person is affected by disease, white symbolizes unaffected individuals. I believe the red stars symbolizes that the person carries the disease gene. That would mean blue corresponds to not carrying the disease gene. If this is the case The red colour of III2 is a fault in the figure.&lt;/p&gt;&#xA;" OwnerUserId="15136" LastEditorUserId="15136" LastEditDate="2015-03-30T17:37:19.840" LastActivityDate="2018-11-26T16:02:28.910" Title="Understanding recombination scoring in family pedigrees" Tags="&lt;genetics&gt;&lt;human-genetics&gt;&lt;recombination&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30887" PostTypeId="2" ParentId="30885" CreationDate="2015-03-29T19:31:00.337" Score="6" Body="&lt;p&gt;Ns are not non-recombinant at the genomic level. What you know is that they do not show recombination events at the risk allele locus as subjects carrying the marker A1 show signs of the disease and similarly healthy subject do not carry the marker A1. Hence they are called non-recombinant. On top of that 3rd generation subjects (excepted III6) show combinations of alleles reflecting inheritance of one allele from each parent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is very important is that A1 is not the allele, it is the &lt;strong&gt;marker for the risk allele&lt;/strong&gt;. This means that A1 is not directly the allele but a region of DNA close to the allele provoking the disease, sufficiently close to be co-inherited most of the time with the disease allele.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For III6 you actually know that a recombination must have happened as this subject obviously carry the risk allele (shows the disease) yet not the marker associated with it, therefore a recombination event happened between the marker and the disease allele.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-30T02:37:15.117" LastActivityDate="2015-03-30T02:37:15.117" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30889" PostTypeId="2" ParentId="23135" CreationDate="2015-03-29T21:54:00.133" Score="2" Body="&lt;p&gt;As stated &lt;a href=&quot;http://books.google.com.br/books?id=d4cLBAAAQBAJ&amp;amp;lpg=PP1&amp;amp;hl=hu&amp;amp;pg=PA6#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; the first sexual reproduction seems to be isogamy, which's purpose was likely to repair the DNA, as a damaged cell could repair its' (DNA) strands via recombination with a &quot;healthy&quot; one. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for lineages, the only thing I could find was also in this book at the very beginning, but there doesn't seem to be a difference as for which is the most ancestral.&lt;/p&gt;&#xA;" OwnerUserId="15051" LastActivityDate="2015-03-29T21:54:00.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30890" PostTypeId="2" ParentId="30884" CreationDate="2015-03-29T21:56:11.787" Score="3" Body="&lt;p&gt;I would link your data with the &lt;a href=&quot;https://www.encodeproject.org/&quot; rel=&quot;nofollow&quot;&gt;ENCODE&lt;/a&gt; dataset. This dataset provides locations of TFBS. It is also accessible via the &lt;a href=&quot;https://genome.ucsc.edu/&quot; rel=&quot;nofollow&quot;&gt;UCSC genome browser&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the actual question TFBS are located pretty much everywhere, including exons (as described &lt;a href=&quot;http://www.sciencemag.org/content/342/6164/1325.summary&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;), introns and of course intergenic regions (e.g. enhancers, silencers, control locus regions - &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.genom.7.080505.115623?url_ver=Z39.88-2003&amp;amp;rfr_dat=cr_pub%3Dpubmed&amp;amp;rfr_id=ori%3Arid%3Acrossref.org&amp;amp;journalCode=genom&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; a reference).&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-30T01:15:52.700" LastActivityDate="2015-03-30T01:15:52.700" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30891" PostTypeId="1" AcceptedAnswerId="30892" CreationDate="2015-03-29T22:00:23.917" Score="5" ViewCount="1044" Body="&lt;p&gt;As bacteria are involved in the production of ethanol through fermentation and ethanol is also used as antiseptic that kills bacteria, so &lt;strong&gt;how&lt;/strong&gt; and &lt;strong&gt;why&lt;/strong&gt; bacteria are involved in the synthesis of such alcohol which is lethal for itself(bacteria)?&lt;/p&gt;&#xA;" OwnerUserId="5729" LastEditorUserId="14735" LastEditDate="2015-03-29T23:41:06.753" LastActivityDate="2015-03-30T01:23:00.740" Title="Ethanol production by fermentation?" Tags="&lt;microbiology&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30892" PostTypeId="2" ParentId="30891" CreationDate="2015-03-29T22:27:44.637" Score="4" Body="&lt;p&gt;Yeast can produce up to 16-17 v/v% ethanol without dying according to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3533426&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article. Yeast is a primary industrial ethanol producer, it produces ethanol even under aerobic conditions, in contrast to bacteria that usually ferment sugar to ethanol under anaerobic conditions. Bacteria can also withstand up to several percent v/v concentration ethanol in their media. Check &lt;a href=&quot;https://ispub.com/IJMB/7/1/5909&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper for details. They produce ethanol because it is a natural byproduct of their cellular metabolism. Under anaerobic conditions sugar as the primary energy source cannot be oxidized and utilized as well as in aerobic conditions. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Alcoholic fermentation converts one mole of sucrose into two moles of ethanol and two moles of carbon dioxide, producing two moles of ATP in the process.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;from: &lt;a href=&quot;http://en.wikipedia.org/wiki/Ethanol_fermentation&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Ethanol_fermentation&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anaerobic bacteria follow this path because fermentation of ethanol does not require oxygen. This byproduct is secreted from the cells. In natural environments ethanol either dilutes in the media bacteria live in or can be taken up by &lt;a href=&quot;http://en.wikipedia.org/wiki/Acetic_acid_bacteria&quot; rel=&quot;nofollow&quot;&gt;acetic acid bacteria&lt;/a&gt; and used as an energy source.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-03-29T22:27:44.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30894" PostTypeId="1" AcceptedAnswerId="30999" CreationDate="2015-03-30T01:10:53.817" Score="11" ViewCount="492" Body="&lt;p&gt;There's an old folk saying that goes like &quot;He got out of bed on a wrong foot&quot; - to indicate that the person's day is going poorly because of the way that person woke up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is it is possible for a human to disrupt the awakening process, causing negative cognitive side effects for the rest of the day?&lt;/strong&gt; If so, how long does it take to restore normal cognition?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's this related question that I asked - &lt;a href=&quot;https://biology.stackexchange.com/questions/8995/can-parts-of-a-human-brain-be-asleep-independently-of-each-other-or-vary-in-the&quot;&gt;if different parts of a human brain can be asleep independently of each other&lt;/a&gt;? This question is a variation on that one, and specifically deals with the process of awakening or activating brain regions in the morning. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm aware of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Sleep_inertia&quot; rel=&quot;nofollow noreferrer&quot;&gt;concept of &quot;Sleep inertia&lt;/a&gt;&quot;. However, it does not seem to be the phenomenon in question, as sleep inertia is frequently mentioned in the context of napping. (where napping over a certain time leads to sleep inertia). Additionally, sleep inertia has been described in terms of decline of motor activity, and not as cognitive side effects lasting for a whole day. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From personal experience, it seems that I'm doing best if I get out of bed immediately following a natural awakening, even if it is rather early, as opposed to snoozing for another 30-40 minutes. &lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-04-03T07:31:47.493" Title="Is it possible for a human to wake up in a wrong way?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;brain&gt;&lt;endocrinology&gt;&lt;sleep&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="30895" PostTypeId="1" AcceptedAnswerId="30898" CreationDate="2015-03-30T01:16:23.587" Score="6" ViewCount="485" Body="&lt;p&gt;I was reading a section from my textbook about tautomeric shifts, and it seems to suggest that there are some mutagens that can be directly responsible for the phenomenon. The section is mainly describing spontaneous mutations as opposed to induced mutations, and examples of mutagens are mentioned. However, the author explicitly states that the sort of changes made to DNA due to spontaneous mutations also occur at a higher rate during induced mutagenesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a tautomeric shift can occur due to mutagenic activity, is it possible for the mutagen to undo and &quot;correct&quot; the mutation by reversing the shift? If so, what kind of chemicals or physical mutagens (e.g. radiation) would be involved?&lt;/p&gt;&#xA;" OwnerUserId="13127" LastActivityDate="2015-03-30T01:52:12.407" Title="Are there any mutagens that can undo the mutations they cause?" Tags="&lt;genetics&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30897" PostTypeId="2" ParentId="21875" CreationDate="2015-03-30T01:49:54.770" Score="0" Body="&lt;p&gt;Since no one else decide to post anything that was put in the comments as an answer I decided to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an excellent article from Wikipedia on the subject, found &lt;a href=&quot;https://en.wikipedia.org/wiki/Template:Eukaryota&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt;. It was also recommended in the comments that you should read the sources provided. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also found this PDF to be quite helpful, &lt;a href=&quot;http://www.nebraskamed.com/app_files/pdf/careers/education-programs/asp/guidebook.pdf&quot; rel=&quot;nofollow&quot;&gt;Nebraska Med&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps! &lt;/p&gt;&#xA;" OwnerUserId="6289" LastActivityDate="2015-03-30T01:49:54.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30898" PostTypeId="2" ParentId="30895" CreationDate="2015-03-30T01:52:12.407" Score="3" Body="&lt;p&gt;It is possible but extremely unlikely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a base undergoes tautomeric shift the DNA does not contain a mutation yet, just an unmatched pair. The mutation will only becomes inscribed into the DNA permanently after the DNA is replicated or wrongly repaired.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to reverse the mutation you would need to provoke a chemical change to that specific base using the same or another mutagen and as most of them are unspecific the likelihood of obtaining both the correct mutation to reverse the effect AND at that specific location is extremely low. Just for the location itself (i.e. that base pair), &lt;strong&gt;in human you have ~0.000000033%  chances&lt;/strong&gt; (1/3 billions) to mutate that base. This is assuming equal probabilities across the genome and a single modification event which is of course not true but shouldn't modify much the conclusion. I am not even speaking about provoking the chemical modification that will reverse it which will even further reduce that probability.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such induced or natural mutations will actually only rarely appear in the genome permanently as the cell has multiple DNA repair mechanisms (see this &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_repair&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;). So in this case the modified base does not need to be reverse as the cell will make sure to repair it directly but using mechanisms not based on mutagenesis.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastActivityDate="2015-03-30T01:52:12.407" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30899" PostTypeId="2" ParentId="23664" CreationDate="2015-03-30T03:54:10.693" Score="4" Body="&lt;p&gt;B-form DNA is wrapped around histones in a &lt;strong&gt;left-handed manner resulting in a left-handed solenoidal superhelix&lt;/strong&gt; (see &lt;a href=&quot;http://homepages.rpi.edu/~bellos/new_page_1.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;that&lt;/a&gt;, &lt;a href=&quot;http://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/DNA/Supercoiling_and_Nucleosomes&quot; rel=&quot;nofollow noreferrer&quot;&gt;that&lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/nature/journal/v436/n7047/full/nature03686.html?free=2&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt;). The reason for this wrapping is that it reduces the helical tension. This &lt;a href=&quot;https://biology.stackexchange.com/questions/29918/why-do-most-organisms-have-negative-supercoiled-dna/30420#30420&quot;&gt;post&lt;/a&gt; has more information about DNA helical tension. Also note that exceptions exist (i.e. right-ended direction) especially for histone at the centromere as described in this &lt;a href=&quot;http://jcb.rupress.org/content/186/4/453.full#ref-16&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For your second question, the exact way nucleosomes are then arranged to produce the chromatin fiber is, as far as I know, still not fully understood but the most accepted model is a zigzag arrangement (&lt;a href=&quot;http://cshperspectives.cshlp.org/content/2/5/a000596.full.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Woodcock CL &amp;amp; Ghosh RP, 2010&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=22394510&quot; rel=&quot;nofollow noreferrer&quot;&gt;Grigoryev SA &amp;amp; Woodcock CL&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-03-30T03:54:10.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30900" PostTypeId="1" AcceptedAnswerId="30908" CreationDate="2015-03-30T04:24:33.273" Score="3" ViewCount="1860" Body="&lt;p&gt;As with anything that is taking place within a cell, the metabolic waste too must be proportional to the size of the cell. In particular the surface area to volume ratio. But how is the waste excretion related to the concept of above ratio and how to determine it?&lt;/p&gt;&#xA;" OwnerUserId="8709" LastEditorUserId="3624" LastEditDate="2015-03-30T16:15:41.543" LastActivityDate="2015-03-30T16:15:41.543" Title="How is excretion of metabolic wastes from a cell related to its size?" Tags="&lt;cell-biology&gt;&lt;homework&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30902" PostTypeId="1" AcceptedAnswerId="30904" CreationDate="2015-03-30T06:26:17.200" Score="10" ViewCount="858" Body="&lt;p&gt;This plant appears to have fleshy protrusions resembling flowers growing out of its stem (although I am unable to identify them as such). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know the identity of these plants?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WRasu.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="13148" LastEditDate="2015-04-01T03:52:53.540" LastActivityDate="2015-04-01T03:52:53.540" Title="What is this pink-flowering plant found in Shanghai, China in March?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30903" PostTypeId="2" ParentId="21875" CreationDate="2015-03-30T06:33:30.290" Score="1" Body="&lt;p&gt;While not comprehensive, the &lt;a href=&quot;http://protozoa.uga.edu/portal/reference.html&quot; rel=&quot;nofollow&quot;&gt;Portal to Protistology&lt;/a&gt; has many resources for exploring the diversity of protozoa. I especially recommend their &lt;a href=&quot;http://protozoa.uga.edu/portal/images_sartiano.html&quot; rel=&quot;nofollow&quot;&gt;videos&lt;/a&gt; that are really fascinating, focus on distinguishing features of different protists, and may be helpful for identification to some degree. But given your interest you should just explore all the pages on the site, check out the books they recommend (e.g. the Illustrated Guide to Protozoa), and see what is useful for you!&lt;/p&gt;&#xA;" OwnerUserId="4840" LastActivityDate="2015-03-30T06:33:30.290" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30904" PostTypeId="2" ParentId="30902" CreationDate="2015-03-30T07:05:07.773" Score="13" Body="&lt;p&gt;I think this is the Chinese Redbud (&lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cercis_chinensis&quot; rel=&quot;noreferrer&quot;&gt;Cercis chinensis&lt;/a&gt;&lt;/em&gt;), see this image (from here):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IuzZ7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-03-30T07:05:07.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30905" PostTypeId="1" CreationDate="2015-03-30T08:06:37.730" Score="2" ViewCount="70" Body="&lt;p&gt;I know about fission, an unicellular asexual reproduction method, where the mother cell splits into two daughter cells. Does this kind of asexual reproductions let mutations happen, leading to much needed evolutionary process? Is it same for all unicellular asexual reproductions?&lt;/p&gt;&#xA;" OwnerUserId="15159" LastEditorUserId="15159" LastEditDate="2015-03-31T03:14:48.640" LastActivityDate="2015-03-31T08:55:10.270" Title="Do all kind of unicellular asexual reproductions let mutations happen, resulting in evolution?" Tags="&lt;evolution&gt;&lt;reproduction&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30906" PostTypeId="1" CreationDate="2015-03-30T09:55:21.983" Score="8" ViewCount="4829" Body="&lt;p&gt;Sometimes when eating an apple, I notice that the bottom (blossom) end of the apple has a lot more sweetness and flavour to it, whereas the top half (stem) is often more watery, crispier and feels less dense than the bottom part.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A quick search on the internet revealed that I'm not the only one asking this question, but answers seemed to be mainly opinions. The largest discussion I stumbled upon can be found &lt;a href=&quot;http://boards.straightdope.com/sdmb/archive/index.php/t-461111.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;, but comes to no satisfying conclusion.&#xA;Apparently, this phenomenon seems to occur in &lt;a href=&quot;http://www.reddit.com/r/NoStupidQuestions/comments/300ipt/why_do_some_fruits_like_apples_and_pears_taste/&quot; rel=&quot;noreferrer&quot;&gt;pears&lt;/a&gt; (supposedly even mentioned in a &lt;a href=&quot;http://www.soshiok.com/print/content/bottom-pear-sweeter-top&quot; rel=&quot;noreferrer&quot;&gt;japanese saying&lt;/a&gt;, but the article does not provide a solution to the question) and &lt;a href=&quot;https://answers.yahoo.com/question/index?qid=20070530163645AAv1Gyw&quot; rel=&quot;noreferrer&quot;&gt;pineapples&lt;/a&gt; as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for a more scientific explanation, as I believe that the biology of apples might be more complex than to allow a simple &quot;sugar is denser than water and gathers at the bottom&quot;-solution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do apples ripen unevenly (the blossom-end growing first, allowing it to ripen for a longer time)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Might this phenomenon be the result of how apples meant for long-term controlled atmosphere storage are picked slightly less mature?&lt;/p&gt;&#xA;" OwnerUserId="15121" LastEditorUserId="15121" LastEditDate="2015-03-30T10:42:23.073" LastActivityDate="2020-05-06T20:24:52.143" Title="Why do apples taste sweeter at the bottom?" Tags="&lt;botany&gt;&lt;food&gt;&lt;fruit&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30907" PostTypeId="2" ParentId="30905" CreationDate="2015-03-30T10:05:32.890" Score="1" Body="&lt;p&gt;It is not essentially asexual reproduction that causes mutations. Mutations can be caused because of errors in DNA replication which can happen during both &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;mitosis&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Meiosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;meiosis&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations can also be caused because of error-prone &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_repair&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNA repair&lt;/a&gt; mechanism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other than these intrinsic factors there are physical and chemical mutagens that alter the DNA or accelerate the intrinsic mutagenesis mechanisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These mechanisms are universally common for all living organisms (&lt;em&gt;that we know of :P&lt;/em&gt; ), however, their tolerance to mutagens and rates of intrinsic mutagenesis may vary. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have a look at &lt;a href=&quot;https://biology.stackexchange.com/questions/29795/how-does-hiv-mutate-into-other-strains-while-keeping-their-virulent-phenotype/29960#29960&quot;&gt;this post&lt;/a&gt; too.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-03-31T08:55:10.270" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30908" PostTypeId="2" ParentId="30900" CreationDate="2015-03-30T13:07:31.040" Score="3" Body="&lt;p&gt;The critical element here is that building materials that need to be absorbed, or waste materials that need excretion have to cross the cell membrane. The larger the surface of the cell's membrane relative to its volume, the faster the exchange rate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;https://www.pearsonschoolsandfecolleges.co.uk/Secondary/BusinessAndEconomics/IBResources/PearsonBaccalaureate/Samples/SampleMaterialBiology/Heinemann-Baccalaureate_Biology-HL_chapter2dis.pdf&quot; rel=&quot;nofollow&quot;&gt;book section&lt;/a&gt; you linked in the comments mentions the following on p.14:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The volume [of a spherical cell] increases by a factor calculated by cubing the radius, [...] the surface area increases by a factor calculated by squaring the radius. [...] This means that a large cell has relatively less surface area to bring in needed materials and to rid the cell of waste [...]. Cells are limited as to the size they can attain [...]. Cells that are larger [...] have modifications that allow them to function efficiently. This is accomplished by shape changes such as from spherical to long and thin, [or] have infoldings or outfolding to increase their surface relative to their volume.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-03-30T13:13:57.637" LastActivityDate="2015-03-30T13:13:57.637" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30909" PostTypeId="2" ParentId="30548" CreationDate="2015-03-30T14:21:29.363" Score="5" Body="&lt;p&gt;My best guess would be &lt;a href=&quot;http://en.wikipedia.org/wiki/Trematoda&quot; rel=&quot;noreferrer&quot;&gt;Trematoda&lt;/a&gt; which is a fluke worm that infects mollusk. I would think this is the larval stage of &lt;a href=&quot;http://www.merriam-webster.com/dictionary/cercaria&quot; rel=&quot;noreferrer&quot;&gt;cercaria&lt;/a&gt; which is free swimming and develops in the mollusk and then moves on to infect others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are some different images of a cercaria:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/anvGh.png&quot; alt=&quot;http://bogleech.com/flatworms.html&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2PZsM.png&quot; alt=&quot;http://www.otago.ac.nz/parasitegroup/downloads.html&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;https://www.youtube.com/watch?v=bvxtCyprfIA&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; YouTube video you will see what is known as a &quot;Rat King&quot; which is just a ball essential of Trematoda. Here is a screenshot &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4Yi19.png&quot; alt=&quot;https://www.youtube.com/watch?v=bvxtCyprfIA&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="12909" LastActivityDate="2015-03-30T14:21:29.363" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30911" PostTypeId="2" ParentId="30852" CreationDate="2015-03-30T15:45:29.860" Score="6" Body="&lt;p&gt;I think that the most important point has been given by CactusWoman, when (s)he says &quot;Just because you cannot forsee a use for more &quot;bulgy&quot; spikes doesn't mean there isn't a use for them.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to that, I would like to say that several plants evolved traits that were beneficial at a time where other herbivores existed and that are now useless. Those lineages did not lose their traits (yet?) just because there is a relatively low cost to making the trait in question.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Your post shows several of the very common misconception about evolutionary processes. Evolution is not all about Natural Selection. It is more interesting than that.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;small improvement&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The conception that evolution proceed through &quot;small improvements&quot; is either partially wrong or totally wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, because of the loaded term &quot;improvement&quot;. Evolution can yield a population to have a lower mean reproductive success or a lower complexity, things that you could eventually see as deterioration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, because changes not need to necessarily be small. Some mutations have a very big effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Third, because even small deleterious mutations can spread in the population and reach fixation (=and all individuals carry this mutation), just because of the joint effect of other evolutionary processes such as genetic drift. This post may help you to get a quick grasp of what &lt;a href=&quot;https://biology.stackexchange.com/questions/14543/why-is-the-strength-of-genetic-drift-inversely-proportional-to-the-population-si&quot;&gt;genetic drift&lt;/a&gt; is. There are already multiple posts that emphasize the importance of other processes than natural selection in evolution to layman. &lt;a href=&quot;https://biology.stackexchange.com/questions/21772/why-dont-mammals-have-more-than-4-limbs&quot;&gt;Here&lt;/a&gt; is one of them.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;believe in Darwin competence&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Evolutionary biology is not anymore &lt;code&gt;Darwin's evolution theory&lt;/code&gt;. It is way more than that. We've been working on the subject a lot since Darwin and today we have a much much better understanding of evolutionary processes than Darwin at its time. Everything is not fully understood yet and therefore there are still many people researching to better understand evolution. Of course, not to better test if evolution is true as this has been known for a long time now.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-03-30T15:45:29.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30913" PostTypeId="2" ParentId="30775" CreationDate="2015-03-30T16:41:53.753" Score="2" Body="&lt;p&gt;So, for every row on the dish protocol, the entire process is scaled up a discrete value. In the case of 100mm to 150mm, the values are scaled up by about 2.76 across all values:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(a) 152/55 = 2.76, (b) 1.52e7/5.5e6 = 2.76, (c) |avg(30.4-45.6)/avg(11-16.5)| = 2.76&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(as answered in comments)&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-03-30T16:41:53.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30914" PostTypeId="2" ParentId="14238" CreationDate="2015-03-30T16:51:48.273" Score="3" Body="&lt;p&gt;At the molecular level this is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Homologous_desensitization&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;receptor desensitization&lt;/strong&gt;&lt;/a&gt;. This is the reason why for example spices (like red hot chili paper) taste more pungent the first time you put them in your mouth and less and less subsequent times (in this case the receptor is called TRPV1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mechanosensory perception is mediated, at least in part, by similar transient receptor potential (&lt;a href=&quot;http://en.wikipedia.org/wiki/Transient_receptor_potential_channel&quot; rel=&quot;nofollow&quot;&gt;TRP&lt;/a&gt;) channels therefore mechanosensory perception is also subjected to desensitization at the molecular level. In this particular case it is specifically called homologous desensitization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is, in my opinion, the primarily reason why a constant stimulus will stop producing action potentials, in essence the receptor will be desensitized and does not provoke a membrane-potential change that mediates the transmission of a neuronal signal.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Footnote&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Desensitization in TRP channels happens because those channels open to let $Ca^{2+}$ ions to enter the cell and after prolongated stimulation the intracellular $Ca^{2+}$ concentration will reach the same $Ca^{2+}$ level of the extracellular medium preventing more $Ca^{2+}$ ions to enter the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$Ca^{2+}$ influx into the cell is what provokes a difference in membrane-potential (i.e. the cell is now electrically charged) which mediates a signal that is then transmitted to the neuronal circuitry.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-03-30T17:53:55.397" LastActivityDate="2015-03-30T17:53:55.397" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30916" PostTypeId="2" ParentId="13863" CreationDate="2015-03-30T17:52:46.273" Score="3" Body="&lt;p&gt;First off this is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Mosaic_%28genetics%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;genetic mosaicism&lt;/a&gt; and indeed mitotic recombination is a contribution factor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mitotic crossover events involve the exchange, by homologous recombination, of regions of chromosomes. 60% of homologous recombination events might occur during G1 and 40% of those event occurs after chromosomes are replicated (see this &lt;a href=&quot;http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1000410&amp;amp;representation=PDF&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper&lt;/a&gt;). For twin spotting to occur, you need the homologous recombination to happen on replicated chromosomes (i.e. you need 4 chromatids).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For you question on twin spotting. The following &lt;a href=&quot;http://www.utexas.edu/courses/zoo325/6-18.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;picture&lt;/a&gt; illustrates well what are the outcomes of homologous recombination involving two alleles and replicated chromosomes (each line being a chromatid).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9fjJ4.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the cell is heterozygous (normal phenotype) for the two recessive alleles, here called &lt;em&gt;y&lt;/em&gt; and &lt;em&gt;sn&lt;/em&gt; (respectively the &quot;yellow&quot; and &quot;singed bristles&quot; alleles), then two recombination scenarios are possible and differs based on where the recombination occurred. Note that &lt;em&gt;y+&lt;/em&gt; and &lt;em&gt;sn+&lt;/em&gt; are the wild-type alleles and carrying those alleles do not provoke a particular phenotype. The phenotype of the resulting daughter cells are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Twin spots&lt;/strong&gt;: Yellow but not singed spots (y/sn+) and singed but not yellow spots (y+/sn) for recombination after the &lt;em&gt;y/sn&lt;/em&gt; locus&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Single yellow spots&lt;/strong&gt;: Yellow but not singed spots (y/sn+) and no spots (y+/sn+) for recombination between &lt;em&gt;y&lt;/em&gt; and &lt;em&gt;sn&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Here the actual &lt;a href=&quot;http://biology200.gsu.edu/houghton&amp;#39;04//4564%20&amp;#39;14/figures/lecture%202/Singed_spots2.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;picture&lt;/a&gt; of what happens:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/StVZZ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore this should make clear why daughter cells can show phenotypes that differ from the original parent cell, i.e. the combination of alleles (especially for recessive ones) changes after mitotic crossover events. The twin spot phenotype in &lt;em&gt;Drosophila melanogaster&lt;/em&gt; is an excellent example for illustrating that.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-04-03T04:37:56.393" LastActivityDate="2015-04-03T04:37:56.393" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30917" PostTypeId="1" CreationDate="2015-03-30T18:36:20.587" Score="4" ViewCount="8600" Body="&lt;p&gt;From what I understand, gradualism is the idea that small changes affect species over time. Uniformitarianism argues that the same processes that occurred in the past are the same as those in the present.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does gradualism state that these small changes are constant over time? In that case, it isn't much different from uniformitarianism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm thinking that the difference that uniformitarianism allows for catastrophes and supports Aristotle's scala naturae, while gradualism makes a point for evolution due to its theory of slow processes. &lt;/p&gt;&#xA;" OwnerUserId="5179" LastEditorUserId="3624" LastEditDate="2015-04-01T08:33:37.220" LastActivityDate="2019-01-07T20:29:56.773" Title="Differences between Gradualism and Uniformitarianism" Tags="&lt;evolution&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30918" PostTypeId="1" CreationDate="2015-03-30T18:40:25.013" Score="3" ViewCount="165" Body="&lt;p&gt;I refer with this question to those among you who have a strong background and work in fields like: botanics, horticulture, dendrology, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to start building a solid preparation, both practical and theoretical, in horticulture, with a strong scientific background.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am a physicist at the moment, but I am trying to lay the basis for a career switch. In September I will attend the RHS courses, but in the meanwhile I would like to start studying something on my own.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any introductory, basic, read that you would suggest? Also, if any of you have in mind a sort of &quot;curriculum&quot; (in terms of subjects, books, etc.) or would like to play with it, this would be of great help! Thanks a lot :)&lt;/p&gt;&#xA;" OwnerUserId="1620" LastEditorUserId="3952" LastEditDate="2015-05-24T16:19:42.177" LastActivityDate="2016-05-09T17:14:15.323" Title="Which sources can I use to study botany and horticulture?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30919" PostTypeId="2" ParentId="30839" CreationDate="2015-03-30T18:46:35.390" Score="0" Body="&lt;p&gt;I'm going to preface this answer with the disclaimer that I have never used CRISPR/Cas, and there is a fair amount of speculation here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I think that efficient CRISPR mediated knock-in probably has three parts, targeting, integration, and selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The targeting is accomplished by the guide RNA, which is often introduced as DNA on the same plasmid that codes for the Cas9, or can be in vitro transcribed or synthesized as delivered as RNA. However, a &lt;a href=&quot;http://www.idtdna.com/pages/docs/default-source/synthetic-biology/2015-01-05-crispr-methods-poster.pdf?sfvrsn=8&quot; rel=&quot;nofollow&quot;&gt;poster&lt;/a&gt; suggests that a properly designed DNA fragment can be delivered and produce sufficient amounts of guide RNA in situ to produce efficient cutting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The integration step is where the template DNA is inserted into the double strand break by homologous repair. Homologous repair efficiencies vary greatly from cell to cell, and is often less efficient than non-homologous end joining. However, using a &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/?term=nat.+methods+8+2011+753+-+755&quot; rel=&quot;nofollow&quot;&gt;single-stranded DNA&lt;/a&gt; might increase the efficiency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, even if only a small percentage of cells is correctly edited, it may be possible to select those cells and grow them. &lt;a href=&quot;https://www.neb.com/~/media/NebUs/Files/Brochures/Expressions_IssueI_2014.pdf&quot; rel=&quot;nofollow&quot;&gt;NEB&lt;/a&gt; describes a Cas9-GFP fusion (page 4) that can be used to bind GFP to a certain DNA sequence. It may be possible to produce CFP and YFP variants of this construct and use FRET to detect cells with the knock in. (This is where the speculation comes in) With the two fusion proteins and two guide RNAs for adjacent sequences in the knock-in gene, you might be able to detect cells where a CFP and YFP cas9 are close enough that you get FRET. This might allow you to sort cells by FACS, and then grow those cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course if your knock-in is making a membrane bound protein exposed to the surface, you could just use labeled antibodies to detect that protein.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2015-03-30T18:46:35.390" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30920" PostTypeId="2" ParentId="30917" CreationDate="2015-03-30T19:46:23.087" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Gradualism&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;&lt;em&gt;Gradualism&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt; is the view that large-scale changes occurs by the accumulated effects of small changes over long periods of time, rather than by rare cataclysmic events of massive effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Uniformitarianism&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;&lt;em&gt;Uniformitarianism&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt; is the view that the same forces that shaped the world in the past continue to operate today. Historically, uniformitarianism has often included aspects of gradualism (i.e. definitions by Lyell), e.g. by assuming &lt;em&gt;uniformity of rates&lt;/em&gt;. Uniformitarianism was also originally proposed as the opposite of &lt;a href=&quot;http://en.wikipedia.org/wiki/Catastrophism&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Catastrophism&lt;/em&gt;&lt;/a&gt;. However, in modern use, the focus lies on uniformity of processes, and rapid catastrophic changes are allowed under uniformitarianism. Also note that the term &lt;a href=&quot;http://en.wikibooks.org/wiki/Historical_Geology/Actualism&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Actualism&lt;/em&gt;&lt;/a&gt; is sometimes used for modern interpretations of uniformitarianism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we posited that early evolution occurred by small Lamarckian changes and current evolution occurs by small Darwinian changes, we have a model that is gradualist but not uniformitarian. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we posited that the earth's topography was formed by meteor impacts and massive tsunamis, in sharp sudden strokes of massive effect, but acknowledged that these same processes occur today, we would have a theory that is uniformitarian but not gradualist. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I don't understand what you are asking in your last paragraph, or how this relates to your main question.)&lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="3624" LastEditDate="2015-04-01T08:27:43.240" LastActivityDate="2015-04-01T08:27:43.240" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30921" PostTypeId="2" ParentId="30824" CreationDate="2015-03-30T23:26:40.840" Score="10" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Could it be beneficial to artificially induce fever in a person who has an illness if they are not already experiencing fever?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No, not really. Pretty much the only use of hyperthermia in medicine is in the treatment of cancer. If you google &quot;use of hyperthermia in medical treatment&quot;, you'll likely only find two kinds of hits: those for cancer treatment and those for malignant hyperthermia (a side effect of some psychotropic drugs.) The hyperthermia used to kill resistant cancer cells is high enough to destroy proteins (~113°-114°) and very localized; your entire body raised to this temperature would result in death very quickly. Lower (i.e. physiological) levers of &quot;hyperthermia&quot; (or hyperpyrexia) would not kill the cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the turn of the century, there were many who believed in the therapeutic use of hyperthermia in the form of hot baths, hot springs, and even injection of infectious agents to produce fever(!), but the practice has fallen into disuse, probably because there were no studies which supported it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, hyperthermia isn't good for you; it is something to treat seriously. When the cause isn't known, the efforts used to treat it can amount to many unnecessary tests and treatments (as seen in the accident victim in the fourth reference. When it's present in a moderate amount, it can still be dangerous:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When fever occurs, many physiological stresses take place. Some of these include increased oxygen consumption as a response to increased cell metabolism, increased heart rate, increased cardiac output, increased leukocyte count, and an increased level of C-reactive protein. Oxygen consumption increases by 13% for every 1°C increase in body temperature, provided no shivering occurs. If shivering is present, oxygen consumption may increase by 100% to 200%. Some cytokines released during fever states also induce physiological stress. These cytokines can trigger accelerated muscle catabolism by causing weight loss, loss of strength, and negative nitrogen balance. Physiological stress can be manifested by decreased mental acuity, delirium, and seizures, which are more frequent in children.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is likely beneficial &lt;strong&gt;in the presence of infection&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Heat shock proteins are one of the more recently studied fever-responsive proteins. These proteins are produced during fever states and are critical for cellular survival during stress. Studies suggest that these proteins may have anti-inflammatory effects by decreasing the levels of proinflammatory cytokines. Fever also triggers other beneficial effects, including an increase in the phagocytic and bacteriocidal activity of neutrophils and enhanced cytotoxic effects of lymphocytes. Some bacteria become less virulent and grow slower at the higher temperatures associated with fever. Increased levels of C-reactive protein promote phagocytic adherence to invading organisms, modulate inflammations, and encourage tissue repair.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In the absence of infection, there is no benefit to systemic elevation of temperature. For the disadvantages of continued elevated metabolic rate, one need only look at hyperthyroidism to see the deleterious effects, the worst being cardiotoxicity, even in subclinical hyperthyroidism, as well as dementia, atrial fibrillation, ventricular hypertrophy, miscarriage, perinatal morbidity and mortality, decreased exercise tolerance, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;Years ago, one of the most common self-inflicted illnesses was hyperthyroidism - people taking thyroid hormone replacement unnecessarily - usually because of the weight loss that occurs with elevated metabolic states. Interestingly, efforts are underway to isolste and manufacture a thyroid-hormone like substance which will cause decreased weight without cardiotoxic effects.&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.cancer.gov/cancertopics/treatment/types/surgery/hyperthermia-fact-sheet&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hyperthermia in Cancer Treatment&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://archneurpsyc.jamanetwork.com/article.aspx?articleid=644349&quot; rel=&quot;nofollow noreferrer&quot;&gt;HYPERPYREXIA PRODUCED BY BATHS&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://jama.jamanetwork.com/article.aspx?articleid=1156478&quot; rel=&quot;nofollow noreferrer&quot;&gt;ARTIFICIAL FEVER IN THE TREATMENT OF GONORRHEAL OPHTHALMIA&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2352308/?page=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Thyrotoxicosis in a patient with multiple trauma&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://online.liebertpub.com/doi/abs/10.1089/thy.2007.0248&quot; rel=&quot;nofollow noreferrer&quot;&gt;Metabolic Effects of Thyroid Hormone Derivatives&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2020-02-23T17:54:36.347" LastActivityDate="2020-02-23T17:54:36.347" CommentCount="17" ContentLicense="CC BY-SA 4.0" />
  <row Id="30922" PostTypeId="1" CreationDate="2015-03-30T23:33:23.780" Score="2" ViewCount="40" Body="&lt;p&gt;There are some molecular targets to identify vertebrate hosts from arthropod bloodmeals including the Cyt b gene and the COI gene. Which are the standards or characteristics that I have to bear in mind to choose a molecular target to identify host blood from mosquitoes? I would appreciate your help.&lt;/p&gt;&#xA;" OwnerUserId="9128" LastActivityDate="2015-05-09T17:47:28.907" Title="Which is the guideline to choose a molecular target to identify vertebrate hosts from arthropod bloodmeals?" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;invertebrates&gt;&lt;vertebrates&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30923" PostTypeId="2" ParentId="10520" CreationDate="2015-03-31T00:10:11.537" Score="-1" Body="&lt;p&gt;Cocaine is cardiotoxic. After chronic exposure to high doses I would assume that primary damage would attack the cardiovascular system before levels of dopamine would be able to cause damage. Cocaine intoxication deaths have mostly been caused by this cardiotoxicity. Primarily, myocardial infarction, arrhythmia, heart failure, and sudden cardiac death are a result of overdose. Cocaine is a vasoconstrictor, which may be a leading cause to myocardial infarctions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19463023&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/19463023&lt;/a&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="12959" LastActivityDate="2015-03-31T00:10:11.537" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30924" PostTypeId="2" ParentId="14238" CreationDate="2015-03-31T00:14:26.987" Score="3" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;In case of Pacinian corpusles, the adaptation is generally ascribed to the mechanical characteristics of the &lt;strong&gt;outer capsule&lt;/strong&gt; of the receptor. The capsule's onion-like structure quickly molds itself to pressure stimuli, thereby rapidly desensitizing the receptor. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;There are two classes of mechanoreceptors in the skin based on their rates of adaptation, namely rapidly adapting and slowly adapting receptors. The Pacinian corpuscles (and hair follicle receptors) are of the rapidly adapting type. These receptors swiftly become unresponsive (they adapt) when a pressure stimulus is applied, but faithfully transmit rapidly changing stimuli (such as vibrations).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pacinian corpuscles are specialized vibration receptors. Their dendritic region is shaped as an onion-like structure with layers of stacked lamellae:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wTtJg.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Specialized dendritic capsule of the Pacinian corpuscle. Source: &lt;a href=&quot;http://www.biologymad.com/nervoussystem/nerveimpulses.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Biologymad&lt;/a&gt;&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These lamellae act as high-pass filters that result in a sharp drop in sensitivity below 150 Hz (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11502392&quot; rel=&quot;nofollow noreferrer&quot;&gt;Johnson, 2001&lt;/a&gt;). If this capsule is dissected from the receptor and a pressure stimulus is directly applied to the sensor element underneat the capsule, the receptor response to a sustained stimulus substantially increases &lt;a href=&quot;http://www.jstor.org/stable/1713151&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Mendelson &amp;amp; Loewenstein, 1964)&lt;/a&gt;. Basically, these elastic lamellae mold their shape to the stimulus and pressure stimuli are only transmitted for a few milliseconds, after which the lamellae absorb the pressure. So only a one or a few spikes are generated at the start of a pressure stimulus. Upon release of the pressure stimulus another spike or two are generated. Hence, a continued pressure stimulus is not faithfully reproduced. However, vibratory stimuli generate spikes on the pressure onset as well as offset as well, and this happens on every phase of the vibration. Hence, vibratory stimuli are faithfully transmitted.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ei1tn.jpg&quot; alt=&quot;PC response&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Response of Pacinian corpuscle to a sustained pressure stimulus (indentation of the skin) and superimposed vibratory stimuli. Note the vigorous response to vibrations, but the rapid adaptation to the static pressure stimulus. Source: &lt;a href=&quot;http://zavantag.com/docs/1632/index-2968.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Zavantag&lt;/a&gt;&lt;/sup&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although the adaptation of the Pacinian corpuscle is generally ascribed to the mechanical properties of its capsule, further high-pass filtering may be accommodated by neurophysiological properties that limit spike initiation, as described by Cagliari2005.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11502392&quot; rel=&quot;nofollow noreferrer&quot;&gt;Johnson, &lt;em&gt;Curr Opin Neuobiol&lt;/em&gt; 2001;&lt;strong&gt;11&lt;/strong&gt;:455–461&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.jstor.org/stable/1713151&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mendelson &amp;amp; Loewenstein, &lt;em&gt;Science&lt;/em&gt; 1964;&lt;strong&gt;3618&lt;/strong&gt;:554-5&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Further reading&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;https://biology.stackexchange.com/questions/30669/why-are-skin-tactile-receptors-considered-to-be-phasic-receptors&quot;&gt;Why are skin tactile receptors considered to be phasic receptors?&lt;/a&gt;      &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-07-08T14:14:22.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30926" PostTypeId="2" ParentId="30796" CreationDate="2015-03-31T04:15:08.530" Score="2" Body="&lt;p&gt;After I had check so many possibilities I finally resolve the problem. It turns out that ph of the tris 1,5M for gel preparation was too many basic...which explain a smear of the proteins into the gel&lt;/p&gt;&#xA;" OwnerUserId="15123" LastActivityDate="2015-03-31T04:15:08.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30927" PostTypeId="2" ParentId="30918" CreationDate="2015-03-31T04:58:45.017" Score="3" Body="&lt;p&gt;This book could be a good start: &lt;a href=&quot;http://books.google.com.co/books/about/Botany.html?id=0BGEs95p5EsC&amp;amp;redir_esc=y&quot; rel=&quot;nofollow&quot;&gt;Botany by Mauseth&lt;/a&gt;. However if you don't have any knowledge about biology I suggest you to get starting with the basics of cellular biology. A good book could be &quot;The cell&quot; by Cooper, you can find it in electronic version.  There are many books about cellular biology but I recommended this because it is complete and detailed without being too long compared with others. &lt;/p&gt;&#xA;" OwnerUserId="9128" LastEditorUserId="9128" LastEditDate="2015-03-31T22:01:48.307" LastActivityDate="2015-03-31T22:01:48.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30928" PostTypeId="1" CreationDate="2015-03-31T05:20:00.663" Score="15" ViewCount="17103" Body="&lt;p&gt;When playing sports, coaches and trainers are always very clear that it is necessary to warm up and stretch. But sometimes athletes sometimes want to get an extra stretch in and don't want to go through the hassle of warming up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Will taking a hot shower warm up muscles or does an athlete sctually have to do physical exercises like jogging in order to be ready to stretch? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know this sounds like a question I could go on the physical fitness SE, but I'm really hoping for an answer involving thermodynamics and I doubt I'll get that there. &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="11652" LastEditDate="2015-03-31T13:30:22.500" LastActivityDate="2015-04-02T02:29:12.367" Title="Does taking a shower have the same effect on muscles as warming up?" Tags="&lt;muscles&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30933" PostTypeId="2" ParentId="30928" CreationDate="2015-03-31T09:15:27.947" Score="6" Body="&lt;p&gt;Hot shower will definitely affect your muscles health. Hot water shower results in &lt;a href=&quot;http://en.wikipedia.org/wiki/Vasodilation&quot;&gt;Vasodilation&lt;/a&gt;,which will decrease the vascular resistance and allows blood to flow easily through the blood vessels. As the vasodilation (increase in diameter of blood vessels) allows blood to move without resistance and which in turn nourish the tissues with sufficient oxygen and nutrients. Also it affects in the removal of metabolic wastes from cells. There is another process called  &lt;a href=&quot;http://en.wikipedia.org/wiki/Vasoconstriction&quot;&gt;Vasoconstriction&lt;/a&gt; (decrease in blood vessel diameter) which makes the blood vessels to contract and may lead to increased blood pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a technique called as Heat therapy which will be effective in muscle and body health.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Heat therapy, also called thermotherapy, is the use of heat in&#xA;  therapy, such as for pain relief and health. It can take the form of a&#xA;  hot cloth, hot water, ultrasound, heating pad, hydrocollator packs,&#xA;  whirlpool baths, cordless FIR heat therapy wraps, and others. It can&#xA;  be beneficial to those with arthritis and stiff muscles and injuries&#xA;  to the deep tissue of the skin. Heat may be an effective self-care&#xA;  treatment for conditions like rheumatoid arthritis.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Heat therapy is most commonly used for rehabilitation purposes. The&#xA;  therapeutic effects of heat include increasing the extensibility of&#xA;  collagen tissues; decreasing joint stiffness; reducing pain; relieving&#xA;  muscle spasms; reducing inflammation, edema, and aids in the post&#xA;  acute phase of healing; and increasing blood flow. The increased blood&#xA;  flow to the affected area provides proteins, nutrients, and oxygen for&#xA;  better healing.&lt;a href=&quot;http://en.wikipedia.org/wiki/Heat_therapy&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;While taking a hot water bath we are just making our muscles and tissues nourished, which means the muscles will be in a healthy state for expansion and contraction. So it is recommendable to take a hot bath before exercising. &lt;/p&gt;&#xA;" OwnerUserId="10294" LastActivityDate="2015-03-31T09:15:27.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30934" PostTypeId="1" AcceptedAnswerId="30935" CreationDate="2015-03-31T09:25:43.310" Score="1" ViewCount="42" Body="&lt;p&gt;I am researching a way to monitor the membrane damage of cells. To do that I fist have to have reference points, namely, cells with damaged membranes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am working with Dunalliela, Hematococcus (both microalgae), and common yeast. I have been using mostly ethanol to damage the membranes so far.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What other ways are there to cause the most possible damage to microalgae (or yeast) membranes?. The idea is not total cell obliteration, but rather membrane damage (death is expected).&lt;/p&gt;&#xA;" OwnerUserId="15170" LastActivityDate="2015-03-31T10:15:11.243" Title="Ways to cause membrane damage to microalgae and yeast?" Tags="&lt;biochemistry&gt;&lt;microbiology&gt;&lt;membrane&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30935" PostTypeId="2" ParentId="30934" CreationDate="2015-03-31T10:15:11.243" Score="1" Body="&lt;p&gt;To get to the membrane of these species you first need to get past a formidable cell wall. The methods listed below are therefore more aimed at making cells permeable but the membranes must sustain some damage in the process.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;At our lab we regularly use glass bead transformation for microalgae&#xA;transformation. The microabrasion allows DNA to go in so I imagine&#xA;the membranes must be damaged somehow.&lt;/li&gt;&#xA;&lt;li&gt;I've also used hypotonic media (depending on the strain) to swell&#xA;cells close to their bursting point. I imagine they become rather&#xA;permeable at this point since they let several dyes in that are&#xA;otherwise excluded.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="15138" LastActivityDate="2015-03-31T10:15:11.243" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30936" PostTypeId="2" ParentId="1995" CreationDate="2015-03-31T10:23:49.297" Score="1" Body="&lt;p&gt;I assume it has an analogous function in ligation buffers. There it apparently takes up a large proportion of the volume and thereby increases the chance of interaction between bits of DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a transformation buffer it should increase the chance of DNA getting into a cell. Unfortunately the only reference I found for this was at Bitesizebio: &lt;a href=&quot;http://bitesizebio.com/20/5-dna-ligation-tips/&quot; rel=&quot;nofollow&quot;&gt;http://bitesizebio.com/20/5-dna-ligation-tips/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15138" LastActivityDate="2015-03-31T10:23:49.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30937" PostTypeId="1" CreationDate="2015-03-31T11:00:35.897" Score="2" ViewCount="3223" Body="&lt;p&gt;Humans grow most quickly when young, and to a lesser extent in preadolescence and early adolescence. However an equilibrium is then reached in adulthood, typically at around 1.6/1.7 meters tall.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found the age at which people &quot;stop growing&quot;, meaning that they are at their tallest hight, is around the age of 21-25.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Why is it beneficial for humans to grow to 1.6/1.7 meters?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is there so so much variation in this, with some reaching there full height in there early teenage years?&lt;/p&gt;&#xA;" OwnerUserId="15171" LastEditorUserId="843" LastEditDate="2016-02-06T14:00:54.853" LastActivityDate="2016-02-06T14:00:54.853" Title="Why do humans stop growing?" Tags="&lt;health&gt;&lt;growth&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2015-05-13T22:22:16.863" ContentLicense="CC BY-SA 3.0" />
  <row Id="30938" PostTypeId="1" CreationDate="2015-03-31T11:53:24.850" Score="1" ViewCount="806" Body="&lt;p&gt;I would like to measure a plant's electric activity / voltage, I've looked online to find out where to place the electrodes and what type of electrodes to use but they seem to very wildly.  Any ideas?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At the moment &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;I plan on wiring one end of a needle to the stalk and one end to the soil.&lt;/li&gt;&#xA;&lt;li&gt;The connections from the plant would go to a laptop mic input to record the signal then I would normalize the signal.&lt;/li&gt;&#xA;&lt;li&gt;I would then process the signal in MATLAB/Octave using FFT.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Any thoughts or videos on connecting the electrodes to the plants or trees? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did find this &lt;a href=&quot;http://www.hindawi.com/journals/jr/2011/124314/&quot; rel=&quot;nofollow&quot;&gt;Development of Bio-Machine Based on the Plant Response to External Stimuli&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15139" LastEditorUserId="15139" LastEditDate="2015-05-04T18:52:10.327" LastActivityDate="2015-06-28T08:34:38.430" Title="Measuring a plant's electric activity any instructions where to place electrodes?" Tags="&lt;plant-physiology&gt;&lt;plant-anatomy&gt;&lt;electrophysiology&gt;" AnswerCount="0" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="30939" PostTypeId="2" ParentId="30928" CreationDate="2015-03-31T12:19:12.550" Score="4" Body="&lt;p&gt;I am not an expert but I would definitely say &lt;em&gt;never&lt;/em&gt; replace a warming-up by a hot bath. However, this depends on the activity to be undertaken. When you go for a round of chess or a stroll through the forest on a Sunday afternoon, sure, take a bath. When you're getting ready for a bout of sparring in a martial arts tournament, a hot bath is the perfect recipe to get injured (and beaten).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.ausport.gov.au/participating/coaches/tools/the_training_session/Warmup-Cooldown&quot; rel=&quot;nofollow&quot;&gt;Australia Sports Commission&lt;/a&gt; says that a warming-up aims to: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;prepare the body and mind for the activity&lt;/li&gt;&#xA;&lt;li&gt;increase the body's core temperature&lt;/li&gt;&#xA;&lt;li&gt;increase heart rate&lt;/li&gt;&#xA;&lt;li&gt;increase breathing rate.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;None of these are targeted with a shower, on the contrary even I would say. The only thing that a hot bath can do is superficially increase temperature, flexibility and blood flow in the muscles. But this can never replace a warming up. I would save the bath for after exercise, as everyone does :) &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-03-31T12:19:12.550" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30940" PostTypeId="1" AcceptedAnswerId="30972" CreationDate="2015-03-31T13:50:26.370" Score="4" ViewCount="318" Body="&lt;p&gt;I am investigating a role of SNPs in DNase hypersensitive sites and in the DNA regions of histone marks and have some questions about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;SNPs in DNase hypersensitive sites&lt;/strong&gt; might mean that those SNPs are in enhancer regions and might influence TF binding affinity what can influence a transcriptional output. Is it correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;SNPs in histone marks sites&lt;/strong&gt;&#xA;I have the number of SNPs that fall in the peaks (chip-seq) for the following histone modifications of healthy patients:&#xA;H3K27ac,H3K4me1,H3K4me3 (represent the active chromosome)&#xA;H3K27me3, H3K9me3 (represent the repressed chromosome)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Histone modifications represent if the chromosome is active or repressed. A SNP might change the binding affinity of a histone. It means that if I have a SNP in data for active chromosome (H3K27ac,H3K4me1,H3K4me3), it might change the status of a chromosome, namely turn it into a repressed one or it might induce a histone not to bind at all(it means that this region is still active,no?) Is it right? I am not sure I understand the possible influences of a SNP histone marks sites.&lt;/p&gt;&#xA;" OwnerUserId="14834" LastActivityDate="2015-04-03T01:31:09.620" Title="SNPs in DNase hypersensitive and histone marks sites" Tags="&lt;snp&gt;&lt;histone&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30943" PostTypeId="1" CreationDate="2015-03-31T16:42:41.850" Score="4" ViewCount="192" Body="&lt;p&gt;Can stress trigger any changes in the human body? I'd like to know more about things less commonly known than, for example: sweating and tiredness. What are the long term risks of chronic stress? Do stressful people have higher chance of having heart-diseases or affected by hair-loss, for example?&#xA;I'm also interested in how can an emotion induce physiological changes in our body?&lt;/p&gt;&#xA;" OwnerUserId="15175" LastEditorUserId="14826" LastEditDate="2015-03-31T20:33:20.410" LastActivityDate="2016-05-13T11:45:10.263" Title="What is the impact of stress on the human body?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;stress&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30944" PostTypeId="2" ParentId="30535" CreationDate="2015-03-31T16:58:47.637" Score="3" Body="&lt;p&gt;Is background radiation a critical component of evolution? No, it most certainly is not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The DNA replication and DNA repair mechanisms aren't perfect and errors happen without any external cause or catalyst. You could say mutations happen on their own. There are mutagens that also cause DNA damage or mutations, but they're merely affecting the DNA replication in a negative way, causing it to err more often.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the effect of background radiation isn't the key here, the key is that the biological processes of DNA replication and repair are not infallible, although radiation does increase the error rate (the rate of mutation) just like many other mutagens do.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2015-03-31T16:58:47.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30945" PostTypeId="2" ParentId="30940" CreationDate="2015-03-31T17:39:23.337" Score="1" Body="&lt;p&gt;Keep in mind that it is not individual histones that are binding, there are 8 histone proteins forming a compact nucleoside particle, and the particle has 146 bp of DNA tightly wrapped around it.  Since the interaction between the histones and the DNA are not sequence-specific, it is unlikely that a single nucleotide polymorphism would have a measurable affect on the occupancy of the nucleosome at that site.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-03-31T17:39:23.337" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30947" PostTypeId="2" ParentId="7932" CreationDate="2015-03-31T18:08:11.587" Score="5" Body="&lt;p&gt;There's a basic philosophical problem with asking why there aren't such-and-such.  We could as easily ask why there are no six-limbed vertebrates, or creatures that use hydrogen to fly like balloons.  It's not (necessarily) that they're mechanically or biologically impossible, it's just that evolution started down another pathway first, and (by changing the nature of the &quot;adjacent possible&quot;) that closed off the paths that led to such creatures.&lt;/p&gt;&#xA;" OwnerUserId="11736" LastActivityDate="2015-03-31T18:08:11.587" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30948" PostTypeId="2" ParentId="30403" CreationDate="2015-03-31T18:35:39.403" Score="0" Body="&lt;p&gt;If I understand it correctly you have downloaded for example 1000 protein sequences with 1000 IDs, but there are duplicates in sequences so in reality it is like having 600 unique sequences with 1000 ID's? If so it should be fairly easy to write a script which would create a set of unique sequences with all corresponding IDs so you could choose which one to use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In python it could be done using the sequence as dictionary key with the ID as a value. While looping over each sequence check if the sequence is already in dictionary. If yes, append the new ID as a value.&#xA;Finally you would get &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;seqs = {&#xA;'DFABIODFAFDIOAF....':['ID001', 'ID007'],&#xA;'ANOTHERUNIQUESEQUENCE':['ID50'],&#xA;...&#xA;}&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;from which it should be easy to choose&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TBH not sure about efficiency of this but this depends on the size of dataset? How large is it? Just give me a sample dataset and I can write it.&lt;/p&gt;&#xA;" OwnerUserId="15176" LastActivityDate="2015-03-31T18:35:39.403" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30949" PostTypeId="1" AcceptedAnswerId="30953" CreationDate="2015-03-31T20:48:51.210" Score="2" ViewCount="2392" Body="&lt;p&gt;What are the effects of pasteurization on the antioxidants found in beet juice ? Does the process render most of the beneficial nutrients (betaine) useless and make them unable for the body to process as efficiently as it would with raw beet juice? Also, does the pasteurization process do this to most fruit and vegetable juices ? I appreciate any insight, I've seen a lot of conflicting reports and am curious of anyones thoughts. Thank you&lt;/p&gt;&#xA;" OwnerUserId="8059" LastEditorUserId="8059" LastEditDate="2015-03-31T20:57:53.073" LastActivityDate="2015-03-31T22:51:55.097" Title="Pasteurization and Bioavailability of Antioxidants in Beet Juice" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30950" PostTypeId="1" CreationDate="2015-03-31T21:02:35.337" Score="12" ViewCount="3612" Body="&lt;p&gt;I've been wondering about this for some time, and I can't come to an answer...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Everybody keeps telling me that scratching one's own skin is bad. It damages the epidermis, creates the hazard of malicious bacteria getting past the skin barrier, and creates the vicious circle of scratching increasing the itching, and itching increasing the scratching (I think I recall reading that this vicious circle also happens even without any special skin diseases, like &lt;em&gt;atopic dermatitis&lt;/em&gt; - I might be mistaken here, however)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, it seems there are hardly any benefits for the body from the scratch reflex. However, if this was true, then &quot;grandma Evolution&quot; wouldn't have given this to us!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the benefits of scratching? Are there any benefits of it from the evolutionary point of view? I can come up with just one such benefit, namely fending off insects such as ticks, mosquitoes, fleas or lice. Would this be the evolutionary benefit of scratching?  &lt;/p&gt;&#xA;" OwnerUserId="15177" LastEditorUserId="9943" LastEditDate="2015-04-01T22:35:20.500" LastActivityDate="2015-09-28T14:35:38.460" Title="Why did humans evolved the scratch reflex?" Tags="&lt;skin&gt;&lt;human-evolution&gt;&lt;reflexes&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30951" PostTypeId="2" ParentId="23637" CreationDate="2015-03-31T21:30:16.877" Score="2" Body="&lt;p&gt;Answer &lt;strong&gt;version1&lt;/strong&gt; (read the comments, I leave v1 for the those who can make the same assumptions in the future)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer the question we should clarify some general concepts and processes mentioned it the clause:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;EMG is performed by means of direct placement of the electrode (the are two types here - surface-EMG and needle-EMG) on/into the skeletal muscles, this is why there is no such thing  &quot;iris-sphincter-related EMG&quot;: the sphincter is inside the eye and there is no way to contact it without eyewall penetration somewhere. Thus, this part of the question is hypothetical. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;ERG is performed after pharmacological mydriasis (pupil dilation to ensure retinal mass response or to perform multifocal ERG), so in the standard settings there is no substantial pupils reaction during the test. Thus, this part of the question is hypothetical too.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;ERG measures electrical changes when one of the electrodes is directly attached to the cornea - here we should stress &quot;to one cornea&quot;, and &quot;reads&quot; the current from only one side. This is why, the reaction of contralateral pupil, skeletal muscles, heart/defibrillator activity are irrelevant since they are out of the electrical loop existing between the electrodes (the second electrode is on the forehead).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;ERG measures electrical activity only - there is no muscle contractions in the process, while EMG involves the time needed to acetylcholine to be released and muscle contraction to begin. This means that the time scopes of these tests are different. In addition, as stated, pupils react as an efferent organ (III nerve, mediator related), while retinal photoreceptors react directly to the light stimulation, so there is a clear delay between these two processes. Theoretically, one can perform full cut of the optic nerve with the resultant loss of afferent signal and consequent loss of efferent pupil reaction, but the ERG will still detect the normal curves if the photoreceptors are intact.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Back to question itself: according to the mentioned facts we should state that the question is more hypothetical and theoretical, thus answering it directly is problematic and the answer should not be assessed without facts mentioned above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the final answer - 1+2: No, pupil reaction does not affect the ERG in the real and standard settings and should not be counted as an interfering factor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Version2&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've found an interesting patent claiming that pupillary responses can contribute to eERG (electrical stimulus instead of light). These influences stated to be artifacts, thus the authors raise the question how to diminish/filter them out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They say &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Eye movements and pupil responses may contribute to the eERG; &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Pharmacologic dilation abolished these pupil responses;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Bilateral artifacts, such as pupil responses, in the corneal eERG&#xA;  cannot be sufficiently reduced by using dilation drops; Even after&#xA;  dilation, a residual, but substantial electrical response persisted in&#xA;  the contralateral eye.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, I should convert my answer to yes/yes. Taking into account the obscure nature of the subject, I hope you will agree that by making mistakes we can learn something new. I personally learnt a lot trying to answer this excellent question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Patent application number: 20120143080 (if the link will be broken in future, one can find the patent by this number).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Direct link&#xA;&lt;a href=&quot;http://www.faqs.org/patents/app/20120143080&quot; rel=&quot;nofollow&quot;&gt;http://www.faqs.org/patents/app/20120143080&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-04-01T06:34:17.670" LastActivityDate="2015-04-01T06:34:17.670" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30952" PostTypeId="1" AcceptedAnswerId="30958" CreationDate="2015-03-31T21:35:48.227" Score="8" ViewCount="12122" Body="&lt;p&gt;We have thermoreceptors, thus we can sense temperature (both warm and cold).  I'm interested in the sensitivity of our thermoreceptors - &lt;br&gt;&lt;br&gt;What is the smallest temperature difference that we can sense?&lt;br&gt;&lt;br&gt; I assume that different parts / organs may have different sensitivity (eg. lips vs fingers), thus I'd like to narrow my focus on the palms / fingers. But if someone has comparative data, that is welcomed too.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="9943" LastEditDate="2015-04-01T03:00:13.743" LastActivityDate="2020-01-19T19:57:03.643" Title="How precisely can we sense temperature differences?" Tags="&lt;neuroscience&gt;&lt;sensation&gt;&lt;perception&gt;&lt;neurophysiology&gt;&lt;receptor&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30953" PostTypeId="2" ParentId="30949" CreationDate="2015-03-31T22:51:55.097" Score="3" Body="&lt;p&gt;So, when they subjected &quot;ready to drink&quot; beetroot juice to thermal pasteurization, they found the betacyanin and betaxanthin (our major antioxidants, and pigment molecules) content to be 39.9 and 42.28% degraded, respectively &lt;a href=&quot;http://www.ifrj.upm.edu.my/21%20(04)%202014/6%20IFRJ%2021%20(04)%202014%20Karthivaran%20420.pdf&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt;. Their conclusion was as follows:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Standardization of process condition and&#xA;  quality degradation of beetroot juice due to thermal&#xA;  pasteurization was studied. The standardized T2&#xA;   batch&#xA;  with total heating time (fh) of 720 s thermal in-pack&#xA;  pasteurization leads to the minimal degradation of&#xA;  color, betalain content (Betacyanin and Betaxanthin),&#xA;  antioxidant activity and complete inactivation of&#xA;  micro flora of beetroot juice. The color, betalain&#xA;  content (Betacyanin and Betaxanthin) antioxidant&#xA;  activity and sensory of the beetroot juice was&#xA;  significantly (p &amp;lt; 0.05) reduced during 180 days&#xA;  ambient (27-30°C) storage, but still the quality of the&#xA;  juice was adequate upto 180 days. We concluded that&#xA;  thermal pasteurization of 96 °C for a total heating time&#xA;  (fh) of 720 seconds with P-values of 11.16 would be&#xA;  a good method to produce microbiologically stable&#xA;  beetroot juice with the retention of quality attributes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So our goal is to get a juice that retains as many &quot;good&quot; attributes as possible, while producing a product that isn't going to get anyone a foodborne illness. As for the net effect of pasteurization on fruit juice in general, im still coming to a conclusion there. The process shouldn't render too much of the fruit/vegetable ineffective, though I'd still expect &lt;em&gt;some&lt;/em&gt; degradation either in storage or processing.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-03-31T22:51:55.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30954" PostTypeId="2" ParentId="30937" CreationDate="2015-04-01T01:21:11.310" Score="3" Body="&lt;p&gt;Human bones grow in length due to the effects of human growth hormone on the epiphyseal plates near the ends of the bone. Over time these two growing margins decrease in size, or width, until those special cells are either gone, or can no longer respond to hGH. At that point the body has no mechanism to increase the size of the skeleton, and growth stops. In females this tends to happen earlier than in males; approximately 2 years after the onset of puberty for females.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-04-01T01:21:11.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30956" PostTypeId="1" AcceptedAnswerId="30960" CreationDate="2015-04-01T01:25:45.693" Score="3" ViewCount="458" Body="&lt;p&gt;I am wondering for someone to discuss the phenomena that newborn babies (humans) are able to submerge underwater up until a few months where that ability is lost again? What is the explanation for this? &lt;/p&gt;&#xA;" OwnerUserId="15066" LastActivityDate="2015-04-02T16:20:19.417" Title="Why can newborns swim?" Tags="&lt;physiology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30957" PostTypeId="2" ParentId="30928" CreationDate="2015-04-01T01:53:21.003" Score="3" Body="&lt;p&gt;I am going to address only the stretching portion of the question since some misinformation is out there. When you say stretching, I hope you mean dynamic as opposed to static stretching especially if you are about to compete in a sport. If you are referring to static stretching, taking a shower may be a better option then, but if you mean dynamic stretching, a shower will not provide a greater benefit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For peak performance, athletes or weekend warriors should use dynamic stretching prior to an event.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In previous research it has been recommended to use dynamic stretching as the primary method of stretching pre-event warm-up before high speed, and power activities (Little &amp;amp; Williams, 2004). The findings of this study agree with that recommendation for agility activities as well. This study supported the use of dynamic stretching in eliciting the greatest performance in agility movements by decreased T-Drill time. The findings&#xA;  of the current study are consistent with those of Fletcher and Jones (2004), and Young and Behm (2003) who determined that dynamic stretching elicits the best performance in power and high-speed activities &lt;a href=&quot;http://digitalcommons.usu.edu/cgi/viewcontent.cgi?article=1691&amp;amp;context=etd&quot; rel=&quot;nofollow&quot;&gt;[1]&lt;/a&gt;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, static stretching does not improve performance and can actually lead to injury.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The current study found static stretching to have a negative effect on agility, and acceleration (Fletcher &amp;amp; Jones, 2004; Nelson et al., 2005). As acceleration is a component of agility, these findings support those of Fletcher and Jones (2004) and Nelson et al. (2005). Agility also involves components of braking, and change of direction. Static stretching prior to agility activities was found to have a negative effect on agility performance &lt;a href=&quot;http://digitalcommons.usu.edu/cgi/viewcontent.cgi?article=1691&amp;amp;context=etd&quot; rel=&quot;nofollow&quot;&gt;[1]&lt;/a&gt;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To read up on dynamic and static stretching as well as other types of stretching, I would recommend MIT's &lt;a href=&quot;http://web.mit.edu/tkd/stretch/stretching_4.html&quot; rel=&quot;nofollow&quot;&gt;Types of Stretching&lt;/a&gt; page.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, the references to my reference one provides many more useful articles to look into.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://digitalcommons.usu.edu/cgi/viewcontent.cgi?article=1691&amp;amp;context=etd&quot; rel=&quot;nofollow&quot;&gt;Static versus dynamic stretching effect on agility and performance&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-04-02T02:29:12.367" LastActivityDate="2015-04-02T02:29:12.367" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="30958" PostTypeId="2" ParentId="30952" CreationDate="2015-04-01T02:12:05.713" Score="8" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br /&gt;&#xA;Temperature differences of 0.02 degrees Celcius can be distinguished, dependent on various factors including experimental conditions and bodily location.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br /&gt;&#xA;The ability to discriminate temperature differences depends on whether it is a cooling or heating pulse, the skin temperature, the duration of the temperature stimulus, age, bodily location among other factors. Unfortunately I cannot access the primary literature other than a few isolated smaller studies. However, &lt;a href=&quot;http://www.scholarpedia.org/article/Thermal_touch&quot; rel=&quot;nofollow noreferrer&quot;&gt;Scholarpedia&lt;/a&gt; has a very nice entry and associated references, and I quote:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The thermal sensory system is extremely sensitive to very small changes in temperature and on the hairless skin at the base of the thumb, people can perceive a difference of &lt;strong&gt;0.02-0.07 °C&lt;/strong&gt; in the amplitudes of two cooling pulses or &lt;strong&gt;0.03-0.09 °C&lt;/strong&gt; of two warming pulses delivered to the hand. The threshold for detecting a change in skin temperature is larger than the threshold for discriminating between two cooling or warming pulses delivered to the skin. When the skin at the base of the thumb is at 33 °C, the threshold for detecting an increase in temperature is &lt;strong&gt;0.20 °C&lt;/strong&gt; and is &lt;strong&gt;0.11 °C&lt;/strong&gt; for detecting a decrease in temperature.&lt;/p&gt;&#xA;&lt;p&gt;The rate that skin temperature changes influences how readily people can detect the change in temperature. If the temperature changes very slowly, for example at a rate of less than 0.5 °C per minute, then a person can be unaware of a 4-5 °C change in temperature, provided that the temperature of the skin remains within the neutral thermal region of 30-36 °C. If the temperature changes more rapidly, such as at 0.1 °C/s, then small decreases and increases in skin temperature are detected. [...]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;You also were interested in the palmar skin: here average difference limens are 0.02 - 0.06 °C, dependent on the temperature step used. These values were obtained using cooling pulses. In other words, differences in two cooling pulses of 0.02 - 0.06 °C were discernible, with higher limens needed for higher pulses. Baseline temperatures (29 - 39 °C) had little effect (&lt;a href=&quot;http://www.nature.com/jid/journal/v69/n1/abs/5616722a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Darian-Smith et al., 1977&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br /&gt;&#xA;&lt;a href=&quot;http://www.nature.com/jid/journal/v69/n1/abs/5616722a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Darian-Smith et al., &lt;em&gt;J Invest Dermat 1977&lt;/em&gt;;&lt;strong&gt;69&lt;/strong&gt;:146-53&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Note&lt;/strong&gt;&lt;br /&gt;&#xA;The &lt;strong&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9583574&quot; rel=&quot;nofollow noreferrer&quot;&gt;Stevens, J. C., &amp;amp; Choo, K. K. (1998). Temperature sensitivity of the body surface over the life span. Somatosensory &amp;amp; motor research, 15(1), 13-28&lt;/a&gt;&lt;/strong&gt; article as commented on by Corvus is indeed a must-read, but my uni library does not have access to it unfortunately&lt;/sub&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2020-01-19T19:57:03.643" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="30959" PostTypeId="2" ParentId="30950" CreationDate="2015-04-01T02:12:13.767" Score="10" Body="&lt;p&gt;With about 20 square feet of skin constantly exposed to potential irritation, itching must serve an important protective/defensive function. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;scratch reflex&quot; (I'm not sure I would call it that) is necessary to life and limb. Itch is a major somatic sensation, along with (and different from) pain, temperature, and touch. Itch can be an acute sensation, e.g. a mosquito bite, or a chronic condition (peripheral or internal disease). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Research on itch signaling is still at its infancy, and basic mechanisms by which the itch sensation is transmitted and regulated have yet to be fully understood. It is meant to give us information about how we are interacting with our environment. Loss of such fine sensation, such as occurs with Hansen's Disease - aka leprosy, where patches of skin become painless and do not itch, so are ignored by the patient - leads to festering wounds and resultant problems. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As @MattDMo stated in a comment, sensation allows us to respond appropriately to irritants which, if ignored, might lead to festering wounds: thorns and other foreign bodies, sucking or biting insects (parasites or other, which can act as disease vectors as well), etc. It allows us to learn how to avoid and treat such irritants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Various types of itch can be classified by the origin of the itch, which could be skin-related, neuropathic, systemic, or psychogenic. The most common cause of itching is dry skin; tiny cracks in the skin cause an inflammatory response, which (within reason) is not a problem in and of itself. The response to the itch, though, can be beneficial or damaging. One can treat dry skin, wash off irritants, treat infections, avoid causes, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scratching can be benign if done sensibly, or it can injure the skin, allowing infection, etc. However, the benefit of having such sensation under normal circumstances certainly outweighs the inconvenience.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is not to say that pathological conditions that cause itching are not problematic. They are, and one might reasonably curse the sensation under those circumstances.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edited to add&lt;/strong&gt;: Itching, or pruritus, is defined as an unpleasant cutaneous sensation that serves as a physiological self-protective mechanism to prevent the body from being hurt by harmful external agents. (&lt;a href=&quot;http://www.nature.com/nature/journal/v448/n7154/full/nature06029.html&quot;&gt;Nature, 2007&lt;/a&gt;) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Scratching is simply a reasonable response to itching from any source and is not necessarily harmful.&lt;/strong&gt; It's not a reflex &lt;em&gt;per se&lt;/em&gt;. You can avoid scratching. Some animals must actively seek out a way to scratch. This takes it well outside of the terminology of &lt;em&gt;reflex&lt;/em&gt; as neurologically understood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://physiologyonline.physiology.org/content/26/4/286&quot;&gt;Itch Signaling in the Nervous System&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.clevelandclinicmeded.com/medicalpubs/diseasemanagement/dermatology/pruritus-itch/Default.htm&quot;&gt;Pruritus&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://health.howstuffworks.com/skin-care/information/anatomy/question600.htm&quot;&gt;When you have an itch, what is happening under your skin?&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-04-02T22:51:47.763" LastActivityDate="2015-04-02T22:51:47.763" CommentCount="16" ContentLicense="CC BY-SA 3.0" />
  <row Id="30960" PostTypeId="2" ParentId="30956" CreationDate="2015-04-01T02:39:43.230" Score="3" Body="&lt;p&gt;It's called the Diving reflex, also known as the bradycardic response. It goes away around six months.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;https://www.breatheology.com/articles/mammalian-dive-response/&quot; rel=&quot;nofollow&quot;&gt;https://www.breatheology.com/articles/mammalian-dive-response/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Another action of the diving response can be observed in infants when they are under water. The windpipe by the vocal chords sponta­neously closes to prevent water from entering the lungs. This reflex is initiated as soon as there is contact with water. However, it disappears when the child reaches the age of roughly six months.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="11855" LastActivityDate="2015-04-01T02:39:43.230" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30961" PostTypeId="2" ParentId="30403" CreationDate="2015-04-01T07:45:12.940" Score="1" Body="&lt;p&gt;Proteins evolve and have different sequences between species, so you would have to define what you mean with &quot;same protein&quot;. One option would be to use an orthology database like &lt;a href=&quot;http://eggnog.embl.de/version_3.0/&quot; rel=&quot;nofollow&quot;&gt;eggNOG&lt;/a&gt;. (eggNOG has the same protein identifiers as STRING.) Then you could figure out 1:1 correspondences between proteins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You probably also want to read up on &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=Roded%20Sharan&quot; rel=&quot;nofollow&quot;&gt;Roded Sharan's work&lt;/a&gt;, e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23192538&quot; rel=&quot;nofollow&quot;&gt;Global alignment of protein-protein interaction networks.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2015-04-01T07:45:12.940" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30964" PostTypeId="2" ParentId="30943" CreationDate="2015-04-01T12:00:48.573" Score="1" Body="&lt;p&gt;Stress is the reaction, which our body reacts against the pressure or tension. There are many impact of stress on the human body, which includes&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Emotional:  Moodiness, short temper, agitation, inability to relax, feeling lonely and always depressed.&lt;/li&gt;&#xA;&lt;li&gt;Cognitive:  Memory problems, unable to concentrate, very poor judgment, negative thoughts, always anxious and worrying&lt;/li&gt;&#xA;&lt;li&gt;Physical: Frequently suffering from pains and aches&lt;/li&gt;&#xA;&lt;li&gt;Behavior: Addiction toward drugs, alcohol or cigarettes for relief, nervous, being alone, insomnia.&lt;/li&gt;&#xA;&lt;li&gt;Other problems like headache, muscle pain, chest pain, fatigue, etc.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="15182" LastActivityDate="2015-04-01T12:00:48.573" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30965" PostTypeId="2" ParentId="775" CreationDate="2015-04-01T12:03:08.863" Score="0" Body="&lt;p&gt;Memories are not stored in just one part of the brain. They are widely distributed throughout the cortex and neurons. The long-term memories are stored throughout the brain as groups of neurons, the brain stores memories in three ways--Short-term memories,   Sensory memory and Long-term memory the human brain cell can hold 5 times as much of information as the Encyclopedia Britannica.&lt;/p&gt;&#xA;" OwnerUserId="15182" LastActivityDate="2015-04-01T12:03:08.863" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30966" PostTypeId="1" AcceptedAnswerId="30981" CreationDate="2015-04-01T13:07:46.193" Score="4" ViewCount="824" Body="&lt;p&gt;After baby teeth go, secondary teeth grow, is there a scientific reason why they are just 2 sets not more? &lt;/p&gt;&#xA;" OwnerUserId="15122" LastEditorUserId="15122" LastEditDate="2015-04-01T21:49:23.987" LastActivityDate="2015-04-02T04:52:28.740" Title="Why we have just 2 teeth cycles, primary and secondary not more?" Tags="&lt;teeth&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30967" PostTypeId="2" ParentId="30950" CreationDate="2015-04-01T13:13:38.133" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;People scratch to alleviate the itchiness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Itch (&lt;em&gt;&lt;a href=&quot;http://dermnetnz.org/systemic/itch.html&quot; rel=&quot;nofollow&quot;&gt;pruritis&lt;/a&gt;&lt;/em&gt;) is caused by a moderate stimulation of pain receptors. There is not such a thing as an itch receptor. Due to the neural circuitry involved, rubbing a painful bruise actually dulls the pain due to stimulation of the tactile sense (&lt;a href=&quot;http://jnnp.bmj.com/content/55/4/282.short&quot; rel=&quot;nofollow&quot;&gt;Kakigi &amp;amp; Shibasaki, 1992&lt;/a&gt;). This may explain the familiar first action one does when injured - grabbing the injured spot and rub it (cats lick their wounds, likely dulling the pain and cleaning it up at the same time). Given the similarity with the neural processing of pain, it is not surprising that a very similar mechanism applies to scratching - scratching relieves the itchy sensation (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1468-3083.2004.00724.x/abstract;jsessionid=721384A9AEBE306763A93B9693A550EE.f02t03?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;Nillson et al., 2003&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So while evolutionary explanations may be valid, they can never be proven. And in fact, too much scratching can be harmful, and I quote from &lt;a href=&quot;http://dermnetnz.org/systemic/itch.html&quot; rel=&quot;nofollow&quot;&gt;Dermnet&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Itch [...] provokes the desire to rub or scratch the area to obtain relief. [...] Constant scratching to obtain relief can damage the skin (excoriation, lichenification) and reduce its effectiveness as a major protective barrier.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Hence, from a behavioral and neurophysiological point of view, we simply want to get rid of itchiness and we scratch. Whether this is evolutionary advantageous other than to provide a means to temporarily reduce debilitating itchiness, is questionable.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA; - &lt;a href=&quot;http://jnnp.bmj.com/content/55/4/282.short&quot; rel=&quot;nofollow&quot;&gt;Kakigi &amp;amp; Shibasaki &lt;em&gt;J Neurol Neurosurg Psychiatry&lt;/em&gt; 1992;&lt;strong&gt;55&lt;/strong&gt;:282-6&lt;/a&gt;&lt;br&gt;&#xA; - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1468-3083.2004.00724.x/abstract;jsessionid=721384A9AEBE306763A93B9693A550EE.f02t03?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;Nillson et al. &lt;em&gt;J Eur Acad Dermatol Venereol&lt;/em&gt; 2004;&lt;strong&gt;18&lt;/strong&gt;:37–43&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-04-01T13:33:33.590" LastActivityDate="2015-04-01T13:33:33.590" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="30968" PostTypeId="1" CreationDate="2015-04-01T16:31:39.647" Score="2" ViewCount="244" Body="&lt;p&gt;Lets say I only have a list of gene names. I know they are up regulated and I know they are related to cancer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What information can I obtain from having only the names of genes? For example is there any way to find a gene-gene interaction, or anything else? Is it possible to retrieve any information by having only the name of the genes?&lt;/p&gt;&#xA;" OwnerUserId="13359" LastEditorUserId="14826" LastEditDate="2015-04-01T18:21:45.177" LastActivityDate="2015-05-25T05:49:34.800" Title="Which information can be obtained from a list of gene names?" Tags="&lt;bioinformatics&gt;&lt;human-genetics&gt;&lt;gene&gt;" AnswerCount="6" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="30969" PostTypeId="2" ParentId="29788" CreationDate="2015-04-01T16:59:59.283" Score="5" Body="&lt;p&gt;The most obvious answer to your question is that the enzyme responsible for nitrogen fixation is inactivated by oxygen. So photosynthesis, which produces oxygen, rules out nitrogen fixation, and, as you know, plants photosynthesise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, they could have evolved specialized cells for nitrogen fixation, which do not photosynthesise. In fact, some colonial cyanobacteria, which photosynthesise, form such specialized cells called heterocysts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why haven't plants evolved such specialized cells? I think a fundamental answer to this question would invoke the evolutionary theory of specialization which says that specialization in one thing at the cost of the ability to do something else is selected for when the trade-off is convex, i.e. when you can be really good at only one thing, and being able to do both implies you are actually quite bad at both.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this sets you off to find the fundamental reason you are looking for.&lt;/p&gt;&#xA;" OwnerUserId="8552" LastEditorUserId="8552" LastEditDate="2015-04-02T15:14:57.653" LastActivityDate="2015-04-02T15:14:57.653" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="30970" PostTypeId="1" AcceptedAnswerId="30976" CreationDate="2015-04-01T17:07:25.253" Score="0" ViewCount="489" Body="&lt;p&gt;I am not a biologist and I would love to understand what is going on with &lt;strong&gt;&lt;a href=&quot;http://www.genome.jp/kegg-bin/show_pathway?hsa05210&quot; rel=&quot;nofollow&quot;&gt;this pathway&lt;/a&gt;&lt;/strong&gt;.&lt;br&gt;&#xA;I went to the description but it's still complicated, and I couldn't follow. Can someone please help me with it? Is this a comprehensive pathway or is it based on specific details? How do i read this pathway? &lt;/p&gt;&#xA;" OwnerUserId="13359" LastEditorUserId="12877" LastEditDate="2015-04-01T23:25:01.393" LastActivityDate="2015-04-01T23:25:01.393" Title="Difficulties understanding a pathway" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;cancer&gt;&lt;database&gt;&lt;pathway&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ClosedDate="2015-04-02T02:21:41.213" ContentLicense="CC BY-SA 3.0" />
  <row Id="30971" PostTypeId="2" ParentId="30968" CreationDate="2015-04-01T17:19:25.420" Score="7" Body="&lt;p&gt;I would suggest searching the name in any trusted genetics database such as NCBI's GenBank (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genbank/&quot;&gt;http://www.ncbi.nlm.nih.gov/genbank/&lt;/a&gt;). You can just Google search it, but it may take a little longer to find useful information that way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps and good luck with your research,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CDB&lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-04-01T17:19:25.420" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30972" PostTypeId="2" ParentId="30940" CreationDate="2015-04-01T17:46:35.000" Score="2" Body="&lt;p&gt;First off let's define some concepts.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;DNAse hypersensitive regions are DNA regions which are in an open chromatin conformation (i.e. euchromatin). This means that those regions are more active at the genomic level (i.e. higher gene expression, gene regulation and higher TF binding) and are less prone to form nucleosomes.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Histone mark sites are DNA regions known to bind certain type of histones and therefore also influences the chromatin conformation leading to the same effects described previously. &lt;strong&gt;The critical point is that the histones you are listing do not primarily bind a specific DNA sequence (as described by @mdperry) but rather DNA sequence marked by epigenetic modifications such as methylation and acetylation&lt;/strong&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now for your first questions, SNPs in DNAse hypersensitive regions might influence the chromatin state and therefore yes might influence gene expression and gene regulation. Will those SNPs also influence TF binding? Well they might indirectly via chromatin modifications. They will not directly act on TF binding if not located in a sequence known to bind TFs (TFBS). DNAse hypersensitivity is not a synonym for transcription factor binding regions/sequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For your second question, SNPs in histone mark sites are a little bit more difficult to interpret. They might, or might not, provoke chromatin changes by influencing the binding of histones but not in a direct way. &lt;a href=&quot;http://en.wikipedia.org/wiki/CpG_site&quot; rel=&quot;nofollow&quot;&gt;CpG islands&lt;/a&gt; are, for example, DNA regions known to be greatly under the influence of epigenetic marks and therefore mutations in those specific regions (e.g. a C -&gt; T mutation) might influence the relative methylation/acetylation state and therefore the binding of histones. SNPs might therefore influence gene expression via chromatin changes which leads to higher/lower TF binding but again not in a direct way. Here again a SNP would influence TF binding directly only if the mutation is located in a TFBS. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see my answer is full of &quot;might&quot; and the reason is that it is very difficult, at the current state-of-the-art, to determine the exact impact of a SNP on the 3D conformation of the chromatin and therefore predict the effect on specific gene expressions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An advice would be to try to co-localize your SNPs with known TFBS either predicted &lt;em&gt;In-silico&lt;/em&gt; or measured via CHiP-SEQ experiments and merge that with the information about DNAse hyperactivity and histone marks you already gathered. For example a SNP in a TFBS in a DNAse hyperactive region is very likely to have a greater impact than a SNP in a TFBS in a non active region.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am sorry I cannot be more specific but this is a very active research area in genetics and there is still a lot to understand, especially for the interactions between all the players influencing the chromatin conformation.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-04-03T01:31:09.620" LastActivityDate="2015-04-03T01:31:09.620" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30973" PostTypeId="2" ParentId="30970" CreationDate="2015-04-01T18:03:48.697" Score="3" Body="&lt;p&gt;Pathways in biology are very hard to interpret without being an expert in the subject. Here a link to &lt;a href=&quot;http://sbml.org/images/f/f3/20021212-kitano-stdgraphicalnotation.pdf&quot; rel=&quot;nofollow&quot;&gt;The Standard Graphical Notation for Biological Networks&lt;/a&gt; that might help you understanding the notation used.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pathway are generally based on evidences of links between the players. These links do not require to be found using one particular technique. Those evidences could come from genome-wide association studies (GWAS), RNA-seq, functional assays, receptor based assays, clinical data etc.. just to cite a few.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example The MAPK pathway was linked to colorectal cancer via gene expression experiments as shown &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15863380&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. The MAPK pathway is known to influence cell proliferation and therefore contributes to colorectal cancer development but if you don't know what the MAPK pathway is doing at first it is hard to comprehend the full picture.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastActivityDate="2015-04-01T18:03:48.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30974" PostTypeId="2" ParentId="30968" CreationDate="2015-04-01T18:26:34.067" Score="3" Body="&lt;p&gt;It depends; what species are the genes from? Some organisms have extensively annotated genomes, and actively curated species-specific databases, while other species may not even have a reference genome sequence available.  By itself, a priori, if you were lucky, about all you list would tell you was how to spell the names of those genes--if you're lucky. But to a skilled Bioinformatician said list could be a gateway to a discovery, or a patent, or a publication, or a grant, although none of these is very likely.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-04-01T18:26:34.067" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30976" PostTypeId="2" ParentId="30970" CreationDate="2015-04-01T18:47:24.680" Score="6" Body="&lt;p&gt;So if you're reading the flowchart, understanding the notation of the arrows is important:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;We have rectangles around the gene products&lt;/li&gt;&#xA;&lt;li&gt;There's a circle, denoted by DNA, noting that the proteins are expressing the product that follows through interaction with DNA&lt;/li&gt;&#xA;&lt;li&gt;The solid line with an arrowhead means there's some sort of interaction&lt;/li&gt;&#xA;&lt;li&gt;The solid line with the blunted or T head means this pathway or interaction has been abrogated somehow&lt;/li&gt;&#xA;&lt;li&gt;The solid line with the slash through it means there's some missing interaction that we don't see&lt;/li&gt;&#xA;&lt;li&gt;The +p means phosphorylation&lt;/li&gt;&#xA;&lt;li&gt;The double solid line to the left is the plasma membrane, whereas the dotted line central to the figure is the nuclear envelope&lt;/li&gt;&#xA;&lt;li&gt;The dotted line means an indirect effect&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.genome.jp/kegg/document/help_pathway.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.genome.jp/kegg/document/help_pathway.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pathway is kind of broad but it provides some mechanisms for tumorigenesis from two standpoints: &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosome_instability&quot; rel=&quot;nofollow noreferrer&quot;&gt;chromosomal instability&lt;/a&gt;, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Microsatellite_instability&quot; rel=&quot;nofollow noreferrer&quot;&gt;microsatellite instability&lt;/a&gt;. The pathways we're seeing promotes the tumor development by upregulating proliferation signals, and downregulating &lt;a href=&quot;http://en.wikipedia.org/wiki/Apoptosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;apoptosis&lt;/a&gt; pathways. There's bound to be more to it, especially since we see other players involved when we get into cases like metastasis like snail1/2, Met, Src, etc. Below is a survey of apoptotic pathways from Nature, with pro-apoptotic in red, and pro-survival in green:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Gc4QX.gif&quot; alt=&quot;enter image description here&quot;&gt;&#xA;Source: &lt;a href=&quot;http://www.nature.com/reviews/poster/apoptosis/index.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.nature.com/reviews/poster/apoptosis/index.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ignoring the therapeutic targeting jargon, you can see that when growth factors bind, the cell generally pushes towards a survival state. When death factors bind or something goes wrong, the cell pushes toward an apoptotic state. &lt;a href=&quot;http://www.cell.com/abstract/S0092-8674%2811%2900127-9&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cancers, however, are intrinsically disregulated&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WKpXp.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They have methods of overstepping their boundaries as cells, which is what makes them problematic. The general conclusion I'd draw from that KEGG pathway, though, is that many pathways need to be disregulated to end up with colorectal tumors, and the method of disregulation is (a) downmodulated mismatch repair, and (b) chromosomal aberrations due to duplication, etc. Andkeeping in mind the box of oncogenes vs tumor suppressors in the corner: &quot;&lt;a href=&quot;http://www.cancer.org/acs/groups/cid/documents/webcontent/002550-pdf.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;An important difference between oncogenes and tumor suppressor genes is that oncogenes result&#xA;from the activation (turning on) of proto-oncogenes, but tumor suppressor genes cause cancer when they are inactivated (turned off)&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-04-01T19:06:53.150" LastActivityDate="2015-04-01T19:06:53.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30977" PostTypeId="1" AcceptedAnswerId="31043" CreationDate="2015-04-01T20:32:20.837" Score="1" ViewCount="2389" Body="&lt;p&gt;I am not sure... Most textbooks just state &quot;they line up&quot; but I don't know how... Something to do with the cytoskeleton or microtubules? Thanks for any help &lt;/p&gt;&#xA;" OwnerUserId="15187" LastActivityDate="2015-04-03T18:50:28.910" Title="How do the homologous chromosomes pair up and position themselves along the center of the cell?" Tags="&lt;meiosis&gt;&lt;cytoskeleton&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ClosedDate="2015-04-07T05:31:02.103" ContentLicense="CC BY-SA 3.0" />
  <row Id="30981" PostTypeId="2" ParentId="30966" CreationDate="2015-04-02T04:52:28.740" Score="4" Body="&lt;p&gt;Humans are &lt;a href=&quot;http://en.wikipedia.org/wiki/Diphyodont&quot; rel=&quot;nofollow noreferrer&quot;&gt;diphyodont&lt;/a&gt; animals, which means we are having two sets of teeth cycles, on contrast, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Polyphyodont&quot; rel=&quot;nofollow noreferrer&quot;&gt;polyphyodont&lt;/a&gt; animals which are having multiple tooth cycles. The first &lt;a href=&quot;http://en.wikipedia.org/wiki/Deciduous_teeth&quot; rel=&quot;nofollow noreferrer&quot;&gt;deciduous teeth&lt;/a&gt;(milk teeth,baby teeth or primary teeth) then followed by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Permanent_teeth&quot; rel=&quot;nofollow noreferrer&quot;&gt;permanent teeth&lt;/a&gt;. Milk teeth develop from the embryonic stage and continue to develop for 6-7 years and gradually erupts forming the permanent teeth. The permanent teeth is developed and it pushes the milk teeth from the bottom which result in the shredding of milk teeth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most of these polyphyodont animals uses their teeth for more severe purposes like grabbing and slashing. Due to these massive work load, their tooth are considered as their main advantage for survival. Also their tooth are subjected to heavy flaws while they grab or slash, so having multiple tooth cycles help them ensure healthy teeth all over their life time. On the other hand considering the diphyodonts, their tooth have been using for chewing and grinding and they will having low flaws compared to the others. So from the evolutionary standpoint increasing the number of tooth cycles are not so economic for them.&#xA;&lt;a href=&quot;http://www.herebeanswers.com/2010/02/why-have-deciduous-permanent-teeth.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10294" LastActivityDate="2015-04-02T04:52:28.740" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30983" PostTypeId="2" ParentId="30839" CreationDate="2015-04-02T05:50:50.237" Score="6" Body="&lt;p&gt;A paper was published about a week ago in Nature Biotechnology and adresses your question, &lt;a href=&quot;http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3190.html&quot; rel=&quot;nofollow&quot;&gt;Maruyama T et al., 2015&lt;/a&gt;. I must say I found the authors' strategy extremely clever.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not about increasing efficiency by reducing specificity, but simply increasing efficiency (which is your ultimate goal anyway). What the authors did was to inhibit nonhomologous end joining (NHEJ) to promote homology-directed repair (HDR), two DNA repair mechanisms that compete in cells and of course HDR is the mechanism needed for the CRISPR/Cas9 system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They achieve NHEJ inhibition using the molecule Scr7, a DNA ligase IV inhibitor which in turns perturbes NHEJ.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Using Scr7 they boosted by 3 to 19 fold&lt;/strong&gt; (depending on the cell line) the insertion of the target gene. Here the graph showing these results&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;See paper figures&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover using 1μM of Scr7 over 24h on DC2.4 cells increased the % of transfected cells from &lt;strong&gt;4.58% to 58.3%&lt;/strong&gt;, a neat ~13-fold increase. Here their results:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;See paper figures&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully this should give you some ideas.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-09-23T19:48:26.377" LastActivityDate="2015-09-23T19:48:26.377" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="30984" PostTypeId="1" AcceptedAnswerId="31005" CreationDate="2015-04-02T06:28:04.833" Score="4" ViewCount="982" Body="&lt;p&gt;In &lt;a href=&quot;http://www.cholinergicurticaria.net/cholinergic-urticaria-causes-what-causes-cholinergic-urticaria-to-develop/&quot; rel=&quot;nofollow&quot;&gt;Cholinergic Urticaria&lt;/a&gt;, some people believe that the itching which is generally more in winters might be because that the diameter of sweat pores is less due to less activity(less sweat production) and in summers the diameter is usually more due to high activity (more sweat production). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question:&lt;/strong&gt; Hence the question in general, &lt;strong&gt;Do sweat pores change diameter?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="16367" LastEditorUserId="5144" LastEditDate="2015-04-02T19:15:39.293" LastActivityDate="2015-04-02T19:15:39.293" Title="Do sweat pores change diameter?" Tags="&lt;skin&gt;&lt;allergies&gt;&lt;heat&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="30985" PostTypeId="2" ParentId="26368" CreationDate="2015-04-02T08:57:47.043" Score="1" Body="&lt;p&gt;Centi-Morgan (cM) is based on observation not precise measurements. Now since double crossing-overs (and actually any arbitrary even number of crossing-overs) revert gene combination to the parental type, resulting lower recombinant frequency. So in your case since the chance (or the frequency if you wish) for double COs is 0.6%, you have to subtract this from parental genotypes and add it to the recombinants.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-04-02T08:57:47.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30986" PostTypeId="1" AcceptedAnswerId="30990" CreationDate="2015-04-02T09:51:41.600" Score="6" ViewCount="1211" Body="&lt;p&gt;I am searching &lt;em&gt;E.coli&lt;/em&gt; whole genome expression data with different conditions, any suggestion is appreciated. Condition could be for example different growth temperature, different medias, etc. &#xA;I have tried GEO but it only gives a list and one should read all pages and samples one by one to see which conditions were used. &lt;/p&gt;&#xA;" OwnerUserId="13359" LastEditorUserId="14826" LastEditDate="2015-04-02T21:24:51.780" LastActivityDate="2015-04-02T21:24:51.780" Title="Where to find E.coli gene expression data?" Tags="&lt;bioinformatics&gt;&lt;gene-expression&gt;&lt;rna-sequencing&gt;&lt;ecoli&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30988" PostTypeId="2" ParentId="30242" CreationDate="2015-04-02T10:25:18.367" Score="4" Body="&lt;p&gt;T-cell migration to the brain is very limited and occurs at a very low level in healthy conditions, however during diseases the number of T cells passing through the blood-brain barrier is elevate due to increased expression of traffic signals and adhesive molecules. &#xA;I've found two good articles on how T-cells migrate through blood-brain barrier:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://download-v2.springer.com/static/pdf/451/art%253A10.1007%252Fs00702-005-0409-y.pdf?token2=exp=1427967013~acl=%2Fstatic%2Fpdf%2F451%2Fart%25253A10.1007%25252Fs00702-005-0409-y.pdf*~hmac=ce8eb39c0a3ab7c37129d8978921d993895e1a635ddcf7a9d760c05eb0e7e4fb&quot; rel=&quot;nofollow&quot;&gt;J Neural Transm (2006) 113: 477–485&#xA;Molecular mechanisms involved in T cell migration across&#xA;the blood–brain barrier, B. Engelhardt&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and &#xA; &lt;a href=&quot;http://jneurovirol.com/pdf/5%286%29/570-578.pdf&quot; rel=&quot;nofollow&quot;&gt;D. W. Miller, “Immunobiology of the blood-brain barrier.,” J. Neurovirol., vol. 5, no. 6, pp. 570–578, 1999.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During T-cell maturation, those that react too heavily to antigens of the body are killed to avoid having T-cells that would kill the body's own cells. But in rare cases this process fails and auto-reactive T-cell get released from the thymus (&lt;a href=&quot;http://www.nature.com/nature/journal/v372/n6501/pdf/372100a0.pdf&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; short paper is good for starters). So the (simplified) reason why T-cells attack oligodendrocytes is that they falsely recognize them as pathogens, and therefore kill them. The loss of oligodendrocytes results in loss of myelin sheats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also in &lt;a href=&quot;http://brain.oxfordjournals.org/content/122/7/1283&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper (it holds many info on demyelination and multiple sclerosis) it is shown that even non-specicfic T-cells can open the way for antibodies through the blood-brain barried, and this results in extended demyelination. &lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-04-02T10:25:18.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="30990" PostTypeId="2" ParentId="30986" CreationDate="2015-04-02T10:42:49.047" Score="7" Body="&lt;p&gt;There are some databases in which you can search for &lt;em&gt;E.coli&lt;/em&gt; gene expression data:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://genexpdb.ou.edu/main/&quot;&gt;GenExpDB&lt;/a&gt;: &lt;em&gt;E. coli&lt;/em&gt; Gene Expression Database&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://m3d.mssm.edu/&quot;&gt;Many Microbe Microarrays Database (M3D)&lt;/a&gt;: A resource of microbial&#xA;gene expression data&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://smd.princeton.edu/index.shtml&quot;&gt;Stanford MicroArray Database&lt;/a&gt; (use the search tool to find relevant organisms)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.colombos.net/&quot;&gt;Colombos&lt;/a&gt; (COLlection Of Microarrays for Bacterial OrganismS)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ebi.ac.uk/arrayexpress/&quot;&gt;ArrayExpress&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;To find out about the purpose and the conditions of the experiments behind this data sets you will have to read the respective publications.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-04-02T11:20:36.940" LastActivityDate="2015-04-02T11:20:36.940" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30992" PostTypeId="2" ParentId="30606" CreationDate="2015-04-02T11:27:09.507" Score="0" Body="&lt;p&gt;Mitochondria are granular or filamentous organelle, which are present in the cytoplasm of a cell. They are ovoid in shape, with the presence of double membranes.&#xA;Mitochondrial fusion is required to distribute mitochondrial DNA to the mitochondrial population and to maintain its respiratory competent and energized organelles. Mitochondrial division is required to efficiently distribute organelles to distal parts of cells.&lt;/p&gt;&#xA;" OwnerUserId="15182" LastActivityDate="2015-04-02T11:27:09.507" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30993" PostTypeId="2" ParentId="30851" CreationDate="2015-04-02T11:46:49.833" Score="0" Body="&lt;p&gt;No, plasma membrane does not contain any nucleic acids – DNA and RNA. The main components of plasma membrane are lipids, glycol- lipids, phospho lipid bilayer and cholesterol.&lt;/p&gt;&#xA;" OwnerUserId="15182" LastActivityDate="2015-04-02T11:46:49.833" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30994" PostTypeId="1" CreationDate="2015-04-02T12:45:49.503" Score="0" ViewCount="3174" Body="&lt;p&gt;I'm interested in how dendritic cells present antigens to  helper T-cells? I'm also interested in the molecular actions between a dendritic cell and a helper T-cell during the activation of the helper T-cell?  What function does the homing receptor on a T-cell have?&lt;/p&gt;&#xA;" OwnerUserId="15162" LastEditorUserId="14735" LastEditDate="2015-04-03T11:01:35.403" LastActivityDate="2015-04-03T19:31:51.833" Title="What is the function of dendritic cell in immunity?" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30995" PostTypeId="1" CreationDate="2015-04-02T13:29:17.300" Score="2" ViewCount="190" Body="&lt;p&gt;I've seen a lot of articles claiming that alcohol has a very bad impact on athletic performance. Examples include, but are by far not limited to: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://oade.nd.edu/educate-yourself-alcohol/alcohol-and-athletes/&quot; rel=&quot;nofollow&quot;&gt;http://oade.nd.edu/educate-yourself-alcohol/alcohol-and-athletes/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.theguardian.com/lifeandstyle/the-running-blog/2014/apr/23/how-does-alcohol-affect-athletic-performance&quot; rel=&quot;nofollow&quot;&gt;http://www.theguardian.com/lifeandstyle/the-running-blog/2014/apr/23/how-does-alcohol-affect-athletic-performance&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.acsm.org/docs/current-comments/alcoholandathleticperformance.pdf&quot; rel=&quot;nofollow&quot;&gt;https://www.acsm.org/docs/current-comments/alcoholandathleticperformance.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.athletestore.co.uk/wordpress/wp-content/uploads/2013/01/The_Effect_of_Alcohol_on_Athletic_Performance.7.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.athletestore.co.uk/wordpress/wp-content/uploads/2013/01/The_Effect_of_Alcohol_on_Athletic_Performance.7.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I'm of course not in position to doubt those articles, as I'm a no expert in biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However. There is one thing I find odd.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Namely. These articles themselves claim that alcohol is widely consumed even by the highest ranking athletes. I mean, if alcohol has that bad effects... then it couldn't have been consumed by highest-ranking athletes, as alcohol-consuming athletes could never rich the heights of the tops of proffessional sports?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also. AFAIK mediaval knights were not abstinents by any means, they were drinking beer and wine and mead to excess; yet they were able to bring their strength, stamina, etc, to an extreme.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not something I wish to argue about; rather, this is something I fail to understand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW. This question is not personal; I don't do sports and I very rarely drink. And I regret the former, not the latter.&lt;/p&gt;&#xA;" OwnerUserId="15177" LastActivityDate="2015-04-03T01:36:28.060" Title="Alcohol and athletes?" Tags="&lt;alcohol&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ClosedDate="2015-04-03T10:50:32.790" ContentLicense="CC BY-SA 3.0" />
  <row Id="30997" PostTypeId="1" CreationDate="2015-04-02T15:07:25.190" Score="10" ViewCount="733" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Life_expectancy#Gender_differences&quot;&gt;Wikipedia&lt;/a&gt; and many other sources, women live substancially longer than men (over 5 years in the U.S.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Men can reproduce for much longer than women.  So longer living men would have the most offspring, while the longevity of the women would be more or less irrelevant in reproducing.  These offspring would be the product, on average, of men and women where the men are older than the women.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why do women live longer than men?  Am I misinformed, or what don't I get?&lt;/p&gt;&#xA;" OwnerUserId="11742" LastActivityDate="2016-02-26T14:25:42.160" Title="Why do women live longer than men?" Tags="&lt;evolution&gt;&lt;reproduction&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="30998" PostTypeId="2" ParentId="30894" CreationDate="2015-04-02T15:20:30.253" Score="1" Body="&lt;p&gt;Sleep occurs in &lt;a href=&quot;http://en.wikipedia.org/wiki/Sleep#Stages&quot; rel=&quot;nofollow&quot;&gt;stages&lt;/a&gt;. There are three stages of non-REM sleep followed by REM sleep. Natural waking occurs during the &lt;a href=&quot;http://sleepsync.com/images/sleep-cycle.gif&quot; rel=&quot;nofollow&quot;&gt;REM stage&lt;/a&gt;. If your alarm goes off while you are in the middle of deep sleep, you are going to feel different from if you had woken up naturally. That's why there's a market for &lt;a href=&quot;http://www.reuters.com/article/2007/08/29/us-sleep-alarms-tech-idUSL0878172320070829&quot; rel=&quot;nofollow&quot;&gt;alarm clocks&lt;/a&gt; designed to wake you up during light sleep.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-04-02T15:20:30.253" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="30999" PostTypeId="2" ParentId="30894" CreationDate="2015-04-02T15:45:39.050" Score="6" Body="&lt;p&gt;I did a quick search and found some research in this area. &lt;strong&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Sleep_inertia&quot; rel=&quot;nofollow&quot;&gt;Sleep inertia&lt;/a&gt;&lt;/strong&gt; is the technical term for feeling groggy for a while after waking up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a review article by Patricia Tassi, Alain Muzet (&lt;a href=&quot;http://dx.doi.org/10.1053/smrv.2000.0098&quot; rel=&quot;nofollow&quot;&gt;Sleep inertia&lt;/a&gt;. Sleep Medicine Reviews. Volume 4, Issue 4, August 2000, Pages 341–353), they define sleep inertia as&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sleep inertia is a transitional state of lowered arousal occurring immediately after awakening from sleep and producing a temporary decrement in subsequent performance.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and also says,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Depending on the studies, it [sleep inertia] can last from 1 min to 4 h. However, in the absence of major sleep deprivation, the duration of sleep inertia rarely exceeds 30 min. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Same article reviews several studies (first report in 1964) on sleep inertia relating to sleep stages:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Abrupt awakening during a slow wave sleep (SWS) episode produces more sleep inertia than awakening in stage 1 or 2, REM sleep being intermediate.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So yes, sleep stage seems to correlate with &quot;waking up in the wrong way&quot; as @CactusWoman suggested.&lt;/p&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2015-04-02T23:06:02.843" LastActivityDate="2015-04-02T23:06:02.843" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31000" PostTypeId="1" CreationDate="2015-04-02T15:53:51.837" Score="5" ViewCount="4651" Body="&lt;p&gt;Keep reading both terms quite frequently while studying plant physiology. I did some research trying to establish their differences and I learnt that meristems are undifferentiated cells that can generate more cells that eventually could grow to form any part of the plant. But I really mess up both concepts, so I would really appreciate a comprehensive explanation of both of them separately. Thank you in advance for your help!&lt;/p&gt;&#xA;" OwnerUserId="15044" LastEditorUserId="14709" LastEditDate="2015-04-02T22:04:01.977" LastActivityDate="2015-09-05T12:41:23.350" Title="What is the difference between meristem and bud?" Tags="&lt;physiology&gt;&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31001" PostTypeId="1" CreationDate="2015-04-02T16:12:33.640" Score="0" ViewCount="389" Body="&lt;p&gt;I don't see any possible evolutionary disadvantage in &lt;a href=&quot;http://en.wikipedia.org/wiki/Situs_inversus&quot; rel=&quot;nofollow&quot;&gt;situs inversus&lt;/a&gt;(the condition where major organs are mirrored from their normal positions) when people with situs inversus can have a normal healthy life.&lt;/p&gt;&#xA;" OwnerUserId="15635" LastEditorUserId="14629" LastEditDate="2015-04-02T17:02:53.477" LastActivityDate="2015-08-20T05:52:37.397" Title="Why don't half of us have situs inversus?" Tags="&lt;human-evolution&gt;" AnswerCount="3" CommentCount="11" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31002" PostTypeId="2" ParentId="31000" CreationDate="2015-04-02T16:14:08.923" Score="0" Body="&lt;p&gt;A bud is capable of developing into a new individual while meristem can develop into any part of the individual. Buds can produce shoots, flowers, etc. while meristems have more variability - capable of developing into the tissues within the stem, a new individual, etc.&lt;/p&gt;&#xA;" OwnerUserId="12972" LastActivityDate="2015-04-02T16:14:08.923" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31003" PostTypeId="2" ParentId="30956" CreationDate="2015-04-02T16:20:19.417" Score="1" Body="&lt;p&gt;When the face of an infant is exposed to cold water, the heart slows down and blood is shifted away from the peripheral muscles to conserve oxygen for the brain and heart, and they typically hold their breath. The reflex is the same one that protects babies from getting milk in their lungs. The reflex kind of reroutes the entire circulatory system to save blood for the heart and brain, and not pump it through the rest of the body.&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12022304&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/12022304&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12972" LastActivityDate="2015-04-02T16:20:19.417" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31004" PostTypeId="2" ParentId="31001" CreationDate="2015-04-02T16:41:25.617" Score="6" Body="&lt;p&gt;If a polymorphism is neutral and has no effect on reproduction, it will not necessarily present itself to the population in a 1:1 ratio. For instance, for a single-gene polymorphism with two alleles in the absence of evolutionary forces like selection and gene flow, the trait will be at &lt;a href=&quot;http://en.wikipedia.org/wiki/Hardy%E2%80%93Weinberg_principle&quot;&gt;Hardy-Weinberg&lt;/a&gt; equilibrium, meaning the two different alleles will be present in some ratio (not necessarily 1:1) and will stay in that ratio from generation to generation. Of course, I'm not an expert on animal physiology and I don't know the genetic basis for situs inversus, but either way two equally fit traits may still be present in the population at very different ratios as there is no force pushing them to be present at equal ratios.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Traits undergoing &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18429672&quot;&gt;density-dependent selection&lt;/a&gt;, on the other hand, such as sex, are under selective pressure to exist in a 1:1 ratio. There are unlikely to be any such forces acting on situs inversus vs situs solitus&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-04-02T16:41:25.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31005" PostTypeId="2" ParentId="30984" CreationDate="2015-04-02T16:57:06.097" Score="5" Body="&lt;p&gt;Pores don't change size; that is, the diameter of pore does not increase or decrease in hot or cold environments. Your skin, where pores are located, is not muscle but an organ so the pores don't contract or expand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UVtB7.png&quot; alt=&quot;http://en.wikipedia.org/wiki/Skin#/media/File:Skin.png&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pores can become clogged with dirt, oil, and debris (make up). When pores are clogged, you are more inclined to notice which would cause the illusion that the pore is bigger.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It's important to know that you can't actually &quot;shrink&quot; your pores. They're nothing but small openings in the skin -- because they don't have muscles, they can't open or close. So although you can't physically change the structure of your pores by making them smaller, there are things that you can do to minimize their appearance&lt;a href=&quot;http://health.howstuffworks.com/skin-care/problems/treating/shrink-large-pores.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;$^1$&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="12909" LastActivityDate="2015-04-02T16:57:06.097" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31006" PostTypeId="1" AcceptedAnswerId="31010" CreationDate="2015-04-02T17:10:29.653" Score="3" ViewCount="551" Body="&lt;p&gt;I am wondering if Leptospirosis can be spread via the urine of an infected human individual. All of the sources I have been able to find on the web have stated that the disease is primarily spread through infected animal urine, however, none of them mention human urine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, Wikipedia states:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After 7 to 10 days the microorganism can be found in fresh urine&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Which would imply that it could be spread via the urine of an infected individual?&lt;/p&gt;&#xA;" OwnerUserId="1081" LastActivityDate="2015-04-02T20:42:36.113" Title="Can Leptospirosis be spread through human urine" Tags="&lt;human-biology&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31007" PostTypeId="2" ParentId="28501" CreationDate="2015-04-02T17:45:22.437" Score="8" Body="&lt;p&gt;I think the picture will help you. In fact, to determine which kind of rearrangement for the chromosomal, we need to define an &quot;orientation&quot;. However, this orientation is not fixed. It is a definition compared with the two chromosomes before and after the rearrangement. As the picture shows, the duplicated sequence after rearrangement should be in the same orientation, if one of them not, it should be described as &quot;inversion after duplication&quot;. For deletion, there is no difference in the orientation if the remain parts still in their previous pattern. The key point to understand,  is to check the sequence before and after the rearrangement and find difference(s) between them, then compare to this picture(which is the definition of rearrangement) to find if the chromosome has one or multiple rearrangements.&#xA;Hope this could help you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zVCwq.png&quot; alt=&quot;DNA rearrangement&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="12879" LastEditorUserId="14735" LastEditDate="2015-04-02T18:03:58.370" LastActivityDate="2015-04-02T18:03:58.370" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31009" PostTypeId="2" ParentId="31001" CreationDate="2015-04-02T18:29:27.230" Score="7" Body="&lt;p&gt;In the Wikipedia article linked to in the question, one will note that there are several medical conditions associated with situs inversus, including congenital heart disease, primary ciliary dyskinesia, and Kartagener Syndrome. These can easily lead to reduced fitness for reproduction, especially PCD/Kartagener Syndrome, as one effect is male infertility due to lack of functional cilia on sperm. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, there likely &lt;em&gt;is&lt;/em&gt; a negative pressure on the alleles responsible for this condition, explaining why it is so rare.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-04-02T18:29:27.230" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31010" PostTypeId="2" ParentId="31006" CreationDate="2015-04-02T20:20:46.357" Score="4" Body="&lt;p&gt;It can be spread from human to human through urine but it is very rare seeing as we are relatively clean creatures (most of the time) and our excrement hardly ever comes into contact with other individuals without first being purified. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cfsph.iastate.edu/Factsheets/pdfs/leptospirosis.pdf&quot; rel=&quot;nofollow&quot;&gt;Leptospirosis&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cdc.gov/leptospirosis/infection/&quot; rel=&quot;nofollow&quot;&gt;CDC: Leptospirosis infection&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="5144" LastEditDate="2015-04-02T20:42:36.113" LastActivityDate="2015-04-02T20:42:36.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31012" PostTypeId="2" ParentId="30968" CreationDate="2015-04-02T21:20:54.497" Score="5" Body="&lt;p&gt;Was getting long in the comments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In light of your comments, you might be interested in &lt;a href=&quot;http://www.broadinstitute.org/gsea/index.jsp&quot;&gt;Gene-set enrichment analysis&lt;/a&gt; (GSEA). You can do a GSEA using your set, the other one coming from reference databases such as MSigDB (see &lt;a href=&quot;http://www.broadinstitute.org/gsea/msigdb/index.jsp&quot;&gt;here&lt;/a&gt;). You can categorize your list by gene families using this technique for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can get an idea of what cellular process is the most impacted by the genes in your list and from there try to reach some conclusions but just as a warning, what you are attempting is not trivial at all. It will be hard to reach valid conclusions from a simple list of genes as correlation does not mean causation (i.e. is the gene up regulated because of cancer or is it provoking the cancer?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To visualize pathways you might want to look at &lt;a href=&quot;https://www.biostars.org/p/4805/&quot;&gt;this post&lt;/a&gt; on Biostars. Several software are available for this purpose.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastActivityDate="2015-04-02T21:20:54.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31013" PostTypeId="1" AcceptedAnswerId="31016" CreationDate="2015-04-02T21:26:22.373" Score="0" ViewCount="102" Body="&lt;p&gt;Our bodies digest food using enzymes that have evolved to convert food here on Earth. Could we even possibly get nutrients from something we haven't evolved alongside? - Is it possible for humans to digest and live on food that isn't based on DNA or RNA?&lt;/p&gt;&#xA;" OwnerUserId="15195" LastEditorUserId="15195" LastEditDate="2015-04-03T10:28:37.593" LastActivityDate="2015-04-03T10:28:37.593" Title="Is it possible for humans to digest and live on food that isn't based on DNA or RNA?" Tags="&lt;astrobiology&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="1" ClosedDate="2015-04-03T08:33:08.410" ContentLicense="CC BY-SA 3.0" />
  <row Id="31014" PostTypeId="2" ParentId="5202" CreationDate="2015-04-02T21:29:55.740" Score="-3" Body="&lt;p&gt;Well , Ime sorry but sometimes a question have to be rephrased in order to reach the ''elefant in the room''  : The important question is if the existence of contraceptives in itself wil change the direction  of human evolution . After the invention of contraceptives the meaning of ''survival of the fittest'' is something very different , from now on the RESISTANCE to the effect of contraceptives becomes the dominant factor in determining fitness for suvival .&#xA; This resistance can be compared to the resistance develped by a population of insects being subjected to a targeted poison :  before or later the population will develop some kind of resistance , even in cases where this can only be achieved by a complicated and indirect mecanism .&#xA;  Humans can achieve such resistance in several ways easy to imagine , and probably also in others very hard to imagine .&#xA; The most obvious is by cultural adabtion , by developing a culture that prevents the efects of contraceptives . This can already be seen in the demografic growth of several population groups dominated by strict compliance with a beliefsystem damning contraceptives... . Many would argue that this has nothing to do with genetics , but actually a very strong case can be made for the opposite position .&lt;br&gt;&#xA; A less obvious way to devellop resistance is selection for a maternal or parental instinct , operating seperately from the sexual drive which has been ''poisoned'' .  In any population , even with an extemely low birthrate , there will always be a few individuals who will have lots of children , no matter what .  Given time enough ,and especially in a low-bithrate population , this behavour will be selected again and again until the underlying genetic mecanism  will cause it to be come  truely hereditary .  Such is the lessons of  selective breeding towards a derirable quality in  everything from horses to tomatoes , and there are  no reason to believe  humans to be different .  The million dollar question is how many generations this proces wil take ....  &lt;/p&gt;&#xA;" OwnerUserId="15194" LastActivityDate="2015-04-02T21:29:55.740" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31015" PostTypeId="2" ParentId="30997" CreationDate="2015-04-02T21:31:26.287" Score="3" Body="&lt;p&gt;&lt;strong&gt;Behaviour&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would think that the most important causal factor between this difference is behaviour. Men probably smoke more than women, probably eat more junk food and are eventually more stressed. Men also probably take more risks and have more accidents. This last point might have been very important at an earlier time when men were hunting outside while the females would work inside the cave. Depression is more prevalent in men as well and it is possible that might affect health. These differences in behaviour might be caused by genetic (and epi-genetics) differences (sexual chromosomes) or by culture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Oestrogen&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There was a time where some doctors thought that the different was due to oestrogen but I think that this hypothesis has been ruled out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The Y chromosome is short&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Men have a Y chromosome while women have two X chromosomes. At each mitosis, the chromosomes get shortened (telomere are shortened). It is possible that the presence of the Y chromosome may explain some of the observed difference due to its small size. However, according to @cantona'sCollar the Y chromosome is often lost in somatic cells and therefore the difference of length between the X and the Y chromosome doesn't seem to be a good explanation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Grandmother hypothesis&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While women stop reproducing earlier than males, women often provide more care to their grandchildren than men do. As a result of this behaviour, genes coding for longer lifespan are beneficial by the fact that they help other copies of themselves (found in the grandchildren) to thrive (kin selection).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-04-06T00:02:15.040" LastActivityDate="2015-04-06T00:02:15.040" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="31016" PostTypeId="2" ParentId="31013" CreationDate="2015-04-02T21:44:13.083" Score="1" Body="&lt;p&gt;This might be flagged for being somewhat of a subjective question, but to survey human diet:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mnemonic SPONCH can be used to sum up the necessary building blocks of life, in the elements &lt;strong&gt;S&lt;/strong&gt;ulfur, &lt;strong&gt;P&lt;/strong&gt;hosphorus, &lt;strong&gt;O&lt;/strong&gt;xygen, &lt;strong&gt;N&lt;/strong&gt;itrogen, &lt;strong&gt;C&lt;/strong&gt;arbon, &lt;strong&gt;H&lt;/strong&gt;ydrogen. There are others, trace elements, which are necessary and come from diet (selenium, for example). These elements are used in building our biological macromolecules: Carbohydrates, lipids, nucleic acids, and proteins. The molecular interactions between these macromolecules, their cofactors, etc. are essential for life. Some of these compounds, however, can't be made in the human body from scratch; hence essential amino acids, and the necessity to consume foods which provide metals, carbohydrates, fats/triglycerides, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, at this point our body is optimized to incorporate &lt;em&gt;terrestrial&lt;/em&gt; foods. Sometimes, though, we can see that the body will sometimes accept analogs to normal compounds, although this is often to disastrous effect (like chemotherapy in cancer). The real question, then, would be: does said extraterrestrial food compose of necessary biological elements or analogs in a way our body can actually use this food for sustenance? That, however, is 100% speculation as we have no reference in even a single case to base our assumptions.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-04-02T21:44:13.083" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31019" PostTypeId="1" AcceptedAnswerId="31029" CreationDate="2015-04-03T00:49:24.510" Score="7" ViewCount="418" Body="&lt;p&gt;In eukaryotic transcription will the nucleosomes ever completely unwind the DNA and the histone complex disassemble? If an operon is more 160 base pairs it seems it must.&lt;/p&gt;&#xA;" OwnerUserId="10026" LastEditorUserId="10026" LastEditDate="2015-04-03T02:06:46.433" LastActivityDate="2018-10-18T22:33:29.950" Title="Do nucleosomes ever completely unwrap during transcription?" Tags="&lt;molecular-genetics&gt;&lt;gene-regulation&gt;&lt;chromatin&gt;&lt;3d-structure&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31020" PostTypeId="2" ParentId="30883" CreationDate="2015-04-03T01:09:27.863" Score="7" Body="&lt;p&gt;Your question does not have a clear answer yet, as stated in &lt;em&gt;Metabolic regulation: a human perspective / Keith N. Frayn. – 3rd ed (2010)&lt;/em&gt; on page 39.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There is still debate about how fatty acids cross cell membranes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;On that page they claim that a simple diffusion transport is possible through a 'flip-flop' mechanism, where the fatty acid inserts itself in the membrane and then experiences a reversal movement. The kinetics of the process seem to be in agreement with the observed utilization rates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, it is claimed that there is growing evidence specific fatty acid transporters like FAT and FATP (fatty acid translocase and transport protein) play a key role in the process. They might join forces with the fatty acyl-CoA synthase, consuming ATP. ATP consumption activates them, i. e provides energy, for the acyl-CoA formation (not in order to move against gradient). The activated state would enable them to both move into the cell and regenerate a triacylglycerol.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cLzE4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Why do these (triacylglycerols) have to be broken down in order to be absorbed?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I would say that the hydrolyzed products (fatty acid and glycerol) are more readily internalized because their structure is simpler. Fatty acids can perform the flip flop mechanism, but whole triacylglycerols might not (I am not sure). There is a fatty acid binding protein that may help maintain the fatty acid importation gradient too.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;What is the driving force for reformation once absorbed?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;It is the secretion of chylomicrons loaded with regenerated triacylglycerols. Since they are secreted, they don't pile up inside the enterocyte (intestine cell) and the equilibrium in the synthesis route (the &lt;em&gt;monoacylglycerol esterification pathway&lt;/em&gt;) favors the production of triacylglycerols.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remarkably, not all fatty acids are reesterified, those of short length (&amp;lt; 14 carbons) are not compatible with the acyl-CoA synthase and enter the plasma in a free state. That happens when digesting dairy products.&lt;/p&gt;&#xA;" OwnerUserId="15044" LastActivityDate="2015-04-03T01:09:27.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31022" PostTypeId="2" ParentId="30995" CreationDate="2015-04-03T01:31:03.627" Score="0" Body="&lt;p&gt;Whenever you look at any parameter in a population, you will have a spread. Let's take I.Q., for instance (and lets not quibble about how it's measured; it's irrelevant for our purposes):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yyoVF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the famous &quot;bell shaped curve&quot;. You can see how few people are significantly above normal. Now, that line continues to include people with an I.Q. of 200+. That's not immediately obvious from the graph. It also continues the other way - people with an I.Q. so low that they cannot participate in their own testing. That's because the vast majority of people fall between 70 and 130.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same principle applies to physical skill, bravery in battle, etc. The curve may be flattened or sharper depending on what parameter is being measured, but rest assured, paid professional athletes fall in the upper 1 percentile.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lets go back to intelligence for a moment. Take someone like Bobby Fischer (Chess Player), I.Q.: 187&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guarantee you that &lt;strong&gt;even falling-down drunk, Bobby Fischer would have beaten me easily in a game of chess&lt;/strong&gt; (and it's not because my I.Q. is average or below). It's because he was so very much, unimaginably better at chess than I am.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guarantee you that &lt;strong&gt;even falling-down drunk, Albert Einstein could solve mathematical equations I can't even write&lt;/strong&gt;. It's because he was so very much, unimaginably more intelligent than I am.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's the same with great athletes. &lt;em&gt;Even if they drink every night, a great athlete will outperform you or me on any given day.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's why you are just dead wrong when you state &quot;&lt;em&gt;then it couldn't have been consumed by highest-ranking athletes, as alcohol-consuming athletes could never rich the heights of the tops of proffessional sports&lt;/em&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are just laboring under a completely false premise. These people are so much better than people only 1 percentile below them that drinking doesn't necessitate that they fall in the ranks. &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-04-03T01:36:28.060" LastActivityDate="2015-04-03T01:36:28.060" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31023" PostTypeId="1" AcceptedAnswerId="31024" CreationDate="2015-04-03T03:12:24.510" Score="4" ViewCount="700" Body="&lt;p&gt;Apologies for any failures in nomenclature. I'm a mathematician who is making a foray into genetics for a masters thesis. Specifically, I'm generating artificial diploid genetic sequence data and phenotype data based on known epistatic interactions.&lt;/p&gt;&#xA;&lt;h1&gt;Primary Question&lt;/h1&gt;&#xA;&lt;p&gt;I am familiar with the concept that having multiple copies of a single allele (e.g. one from each parent) can actually increase expression and thereby change the quantitative phenotype (at least in some cases?). &lt;em&gt;Can this also happen with epistatic effects?&lt;/em&gt; For example, consider the case that locus 1 (&lt;span class=&quot;math-container&quot;&gt;$L_1$&lt;/span&gt;) and locus 2 (&lt;span class=&quot;math-container&quot;&gt;$L_2$&lt;/span&gt;) exhibit some positive interaction (&lt;span class=&quot;math-container&quot;&gt;$\beta$&lt;/span&gt;) on the trait (&lt;span class=&quot;math-container&quot;&gt;$Y$&lt;/span&gt;).&#xA;&lt;span class=&quot;math-container&quot;&gt;$$E[Y]=\mu+\beta(L_1L_2)$$&lt;/span&gt;&#xA;If both chromosomes contain the allele in question at both loci, then does this individual exhibit &lt;em&gt;more&lt;/em&gt; of a trait increase than if he only had one chromosome with the epistatic alleles?&lt;/p&gt;&#xA;&lt;h1&gt;Secondary question&lt;/h1&gt;&#xA;&lt;p&gt;Can alleles interact epistatically even when they are present on different chromosomes? e.g. assume allele &lt;em&gt;A&lt;/em&gt; at locus 1 interacts with allele &lt;em&gt;B&lt;/em&gt; at locus 2. Individual has &lt;em&gt;A&lt;/em&gt; at locus 1 and &lt;em&gt;b&lt;/em&gt; at locus 2 on chromosome 1. He also has &lt;em&gt;a&lt;/em&gt; at locus 1 and &lt;em&gt;B&lt;/em&gt; at locus 2 on chromosome 2. Do &lt;em&gt;A&lt;/em&gt; and &lt;em&gt;B&lt;/em&gt; from the different chromosomes interact? My intuition is yes but I want verification.&lt;/p&gt;&#xA;&lt;p&gt;Many thanks!!!&lt;/p&gt;&#xA;" OwnerUserId="15199" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-03T03:48:24.790" Title="Epistasis Across Chromosomes and Individuals 'Homozygous for Interactions'" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;gene-expression&gt;&lt;chromosome&gt;&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31024" PostTypeId="2" ParentId="31023" CreationDate="2015-04-03T03:48:24.790" Score="2" Body="&lt;p&gt;&lt;strong&gt;Question 1:&lt;/strong&gt; The phenomena you describe in which it matters whether you have one or two copies of an allele (e.g., the AA phenotype being different than the Aa phenotype) are known as &lt;em&gt;dominance effects&lt;/em&gt;. Dominance effects can interact with epistatic effects (in which the phenotypic effect of one locus depends on the genotype at the another locus). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One good example is the interaction between the &lt;em&gt;Agouti&lt;/em&gt; locus and the &lt;em&gt;Mc1R&lt;/em&gt; locus in the oldfield mouse (&lt;em&gt;Peromyscus polionotus&lt;/em&gt;) in determining coat color. Dark-color homozygotes for the &lt;em&gt;Agouti&lt;/em&gt; locus have dark coats irrespective of the allele at the &lt;em&gt;Mc1R&lt;/em&gt; locus, whereas color in &lt;em&gt;Agouti&lt;/em&gt; heterozygotes or light color homozygotes depends on genotype at the &lt;em&gt;Mc1R&lt;/em&gt; locus. The figure below, from &lt;a href=&quot;http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050219&quot; rel=&quot;nofollow noreferrer&quot;&gt;Steiner et al (2007)&lt;/a&gt;, illustrates:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fZxMb.png&quot; alt=&quot;Dominance and epistasic effects in coat coloration&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question 2&lt;/strong&gt;: Epistatically interacting loci need not be on the same chromosome. The loci discussed above provide a perfectly good example. &lt;em&gt;Mc1R&lt;/em&gt; is on chromosome 1, where as &lt;em&gt;Agouti&lt;/em&gt; is on chromosome 7, yet they interact epistatically. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-04-03T03:48:24.790" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31025" PostTypeId="1" AcceptedAnswerId="42577" CreationDate="2015-04-03T05:08:00.353" Score="6" ViewCount="646" Body="&lt;p&gt;What is the proposed selection pressure that leads to the distinctive coloration of Orca whales? I can find nothing in the literature.&lt;/p&gt;&#xA;" OwnerUserId="15199" LastActivityDate="2017-05-17T13:16:41.683" Title="Selection Pressure on Orca Whale Coloration" Tags="&lt;evolution&gt;&lt;ecology&gt;&lt;natural-selection&gt;&lt;marine-biology&gt;&lt;sexual-selection&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31026" PostTypeId="1" AcceptedAnswerId="31068" CreationDate="2015-04-03T05:42:20.663" Score="4" ViewCount="61" Body="&lt;p&gt;This question tries to narrow down the scope of &lt;a href=&quot;https://biology.stackexchange.com/questions/30535/what-is-the-relationship-between-radiation-and-evolution&quot;&gt;that question&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the statistical relationship between radioactivity and mutation rate? By how much would the mutation rate be lowered in a idealized world were radioactivity is absent?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-04-04T17:05:08.417" Title="What is the statistical relationship between radioactivity and mutation rate?" Tags="&lt;molecular-genetics&gt;&lt;mutations&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31027" PostTypeId="1" CreationDate="2015-04-03T06:31:28.847" Score="6" ViewCount="585" Body="&lt;p&gt;Is it possible that the use of contraceptives will produce evolution humans? Contraceptives can reduce reproductive success, so shouldn't selection favour resistance to them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case it might be useful to think of evolution as a &quot;black box&quot;, an information processing mechanism  where only input and output is relevant. From this point of view, we would expect the box to produce an output comparable to the resistance that evolution will produce in a population experiencing a poisoning effect which seriously damages its reproduction mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The evolutionary &quot;output&quot; from such poisoning  has been studied in great detail. Are there any lessons relevant to future human evolution in these studies?&lt;/p&gt;&#xA;" OwnerUserId="15194" LastEditorUserId="1590" LastEditDate="2016-08-19T07:50:56.857" LastActivityDate="2016-10-15T11:41:57.970" Title="The selective pressure of contraceptives" Tags="&lt;evolution&gt;&lt;reproduction&gt;" AnswerCount="5" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="31028" PostTypeId="2" ParentId="15576" CreationDate="2015-04-03T07:17:43.127" Score="0" Body="&lt;p&gt;Frequency of allele for Haemophilia (q) = 0.4 &lt;br&gt;&#xA;Frequency of normal allele (p) = 0.6 &lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cross between Heterozygote female and hemophiliac male&#xA;by punnett square:&lt;br&gt;&#xA;Probability of hemophiliac daughter = 0.5 &lt;br&gt;&#xA;P(hemophiliac male) = 0.4&lt;br&gt;&#xA;P(heterozygote female) = 2pq = 2 × 0.4 × 0.6 = 0.48 &lt;br&gt;&#xA;P(hetero female+hemophiliac male+hemophiliac daughter) = 0.5 × 0.4 × 0.48 = 0.096&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence 9.6% &lt;/p&gt;&#xA;" OwnerUserId="15201" LastEditorUserId="3340" LastEditDate="2015-04-03T08:45:23.620" LastActivityDate="2015-04-03T08:45:23.620" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31029" PostTypeId="2" ParentId="31019" CreationDate="2015-04-03T10:00:33.843" Score="10" Body="&lt;p&gt;Yes, nucleosomes are completely unwound. Histone chaperones such as FACT (for H2A/H2B) and ASF1, CAF-1, HIRA, Nucleophosmin etc (for H3/H4), associate with RNA Pol II and handle the displaced nucleosomes. As you surmised, the histone octamer complex is disassembled, into the H3/H4 tetramer and two H2A/H2B dimers. Right behind the elongating Pol II, the chaperones reassemble nucleosomes. During the process of reassembly, it has been shown that &quot;new&quot; H2A/H2B dimers (and possibly H3/H4 tetramers too) can get incorporated into an &quot;old&quot; histone octamer. Finally, nucleosome remodelling complexes such as SWI/SNF re-space the nucleosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a decent review of the process (by one of the discoverers of the FACT complex, incidentally): &quot;New chaps in the histone chaperone arena&quot;. Campos &amp;amp; Reinberg. Genes &amp;amp; Development (2010): 24: 1334-1338&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a comprehensive review of histone chaperones and nucleosome dynamics during various DNA-dependent processes (such as transcription, replication and repair). There is an entire section on their role in gene transcription, which is the main thrust of this question: &quot;Histone Chaperones: Assisting Histone Traffic and Nucleosome Dynamics&quot;. Gurard-Levin, Z.A., Quivy, J., and Almouzni, G. Annual Review of Biochemistry (2014): 83: 487-517&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And finally, a good overview on histone dynamics and chromatin structure during transcription: &quot;Histone exchange, chromatin structure and the regulation of transcription&quot;. Venkatesh &amp;amp; Workman. Nature Reviews Mol. Cell. Biol. (2015): 16:178–189 &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I should add that an inability to disassemble nucleosomes (or displace any other factor bound very tightly to DNA) can actually pause an elongating Pol II complex.&lt;/p&gt;&#xA;" OwnerUserId="14553" LastEditorUserId="14553" LastEditDate="2015-04-07T01:39:34.887" LastActivityDate="2015-04-07T01:39:34.887" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31031" PostTypeId="1" AcceptedAnswerId="31052" CreationDate="2015-04-03T12:57:34.807" Score="2" ViewCount="399" Body="&lt;p&gt;I'm physicist by training, so please excuse me if I don't use the proper terminology. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think there is a way to make a sensor that detects if a single antibody has caught something from the flow. So I'm trying to figure out if this would be a useful sensor, but this depends on how specific the antibodies really are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I ask biologists &quot;How specific are antibodies?&quot;, they reply: &quot;Very-very specific&quot;, but provide no values that I understand on microscopic level. But I am trying to make a quantitative estimation, e.g. for the following thought experiment:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose I have attached an antibody to inorganic surface. It's an antibody for catching object &lt;strong&gt;X&lt;/strong&gt;. And I flow blood over the surface, slowly. Suppose there's no &lt;strong&gt;X&lt;/strong&gt; in this blood at all. But there are lots (maybe &lt;strong&gt;10&lt;sup&gt;17&lt;/sup&gt;&lt;/strong&gt;, or some crazy number like that) of other stray particles flowing by this antibody every second, right? So, when one of these particles bumps into this one antibody, what is the probability that it would stick to this antibody? Is it really &lt;strong&gt;10&lt;sup&gt;-17&lt;/sup&gt;&lt;/strong&gt; ? Is it really so small? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And, in any case, how do I estimate this probability at least to 1-2 orders of magnitude? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, how do I estimate the &quot;collision cross section area&quot; through which an object has to fly to make an attempt to bind to an antibody? In other words, does it only have to touch it slightly, or bump into antibody in a hard and messy collision?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the probability of successful bind depend on the flow speed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How would the values change if I take serum instead of blood?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could you please point to some relevant papers, books or just keywords? I would very much appreciate any help.&lt;/p&gt;&#xA;" OwnerUserId="15205" LastEditorUserId="6307" LastEditDate="2015-04-04T06:33:32.413" LastActivityDate="2015-04-04T14:19:27.297" Title="What are the typical values of probabilities for nonspecific binding to an antibody?" Tags="&lt;biochemistry&gt;&lt;antibody&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31032" PostTypeId="2" ParentId="30883" CreationDate="2015-04-03T14:16:35.043" Score="2" Body="&lt;p&gt;I'd like to just add on with some more detail.  According to &lt;a href=&quot;http://advan.physiology.org/content/34/2/44&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;, gastric lipase cleaves 15-20% of fatty acids in the stomach.  The rest is completed in the duodenum by lipases secreted by the pancreas.  Bile salts, phospholipids and cholesterol coat these lipid particles to prevent them from coalescing.  The reason is because lipases have adapted to oil-water interfaces.  Therefore breaking down dietary fact into &quot;into an emulsion of fine oil droplets enhances the action of lipases.  The smaller fat globules have an increased surface area and are more easily accessible to active pancreatic enzymes for further breakdown.&quot;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your question on the driving force of why they are reassembled, &quot;several enzymes reassemble the fatty acids and monoacylglycerides to reconstitute triglycerides.  Subsequently, the enterocytes package the reconstituted triglycerides with proteins and phospholipids into chylomicrons.&quot;  These chylomicrons travel into the blood stream through the lymph system where they go to adipose tissue and muscle cells for further breakdown. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Barbara E. Goodman &#xA;Advances in Physiology Education Jun 2010, 34 (2) 44-53; DOI: 10.1152/advan.00094.2009&lt;/em&gt; &lt;/p&gt;&#xA;" OwnerUserId="14916" LastActivityDate="2015-04-03T14:16:35.043" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31033" PostTypeId="1" CreationDate="2015-04-03T14:43:45.813" Score="11" ViewCount="210" Body="&lt;p&gt;I am interested in knowing how our Circadian Clock responds (and if there are resultant changes) when we travel across Time Zones?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;UPDATE 24th April&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am reopening this question as the statement in the answer &quot;&lt;em&gt;When you travel to different time zones, your circadian clock will be off&lt;/em&gt;&quot; has further confused me. If it's the case, then I am looking to get a better explanation than that (&lt;em&gt;with solid references&lt;/em&gt;). Thanks&lt;/p&gt;&#xA;" OwnerUserId="14852" LastEditorUserId="32234" LastEditDate="2017-08-27T09:29:36.640" LastActivityDate="2017-08-27T09:29:36.640" Title="Circadian Clock During a Flight" Tags="&lt;human-biology&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31034" PostTypeId="2" ParentId="31033" CreationDate="2015-04-03T15:08:36.903" Score="8" Body="&lt;p&gt;When you travel to different time zones, your circadian clock will be off (incorrect). The reason your circadian clock will be off is because your body has adapted to the time zone you are from. When you enter a new time zone, your circadian clock will still be functioning on the old the time zone. If the time zone difference is $\pm 12$ hours, this is a huge adjustment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, your body takes inputs from the environment. That is, you may see it is day light when your body is under the impression it is evening. Your circadian clock is controlled by your master clock located in the hypothalamus. As you take in these external inputs that counter your circadian clock, a group of nerve cells called the suprachiasmagic nucleus will slowly make the master clock adjustment &lt;a href=&quot;http://www.nigms.nih.gov/Education/Pages/Factsheet_CircadianRhythms.aspx&quot; rel=&quot;nofollow&quot;&gt;[1]&lt;/a&gt;. This resetting can take a few days. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/002110.htm&quot; rel=&quot;nofollow&quot;&gt;NIH Jet Lag Prevention Guideline&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Additionally, there has been a bit of research on exercise reducing jet lag. In a study, researchers test outdoor exercise with flight crew members and found that the group that exercised outdoors had a hastened re synchronization of their circadian clock &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8968481&quot; rel=&quot;nofollow&quot;&gt;[2]&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another interesting article is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435929/&quot; rel=&quot;nofollow&quot;&gt;Jet Lag in Athletes&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="3952" LastEditDate="2015-04-19T13:55:02.723" LastActivityDate="2015-04-19T13:55:02.723" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31035" PostTypeId="2" ParentId="30968" CreationDate="2015-04-03T15:24:28.797" Score="2" Body="&lt;p&gt;Also try putting the list through Reactome or String DB to see if you see mapping to certain pathways. &lt;a href=&quot;http://string-db.org/&quot; rel=&quot;nofollow&quot;&gt;http://string-db.org/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also put lists through ConceptGen to carry out ontology based analyses&#xA;&lt;a href=&quot;http://portal.ncibi.org/gateway/conceptgen.html&quot; rel=&quot;nofollow&quot;&gt;http://portal.ncibi.org/gateway/conceptgen.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6726" LastActivityDate="2015-04-03T15:24:28.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31036" PostTypeId="2" ParentId="30839" CreationDate="2015-04-03T15:35:53.533" Score="0" Body="&lt;p&gt;If you want to have random integration you need to find gRNA sequences that are nonspecific ; everything built for CRISPR so far has been geared towards precise integration, not random integration. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Talk to an informatician about pulling out non-unique sequences from the human genome. You will then need to clone out a library of 20nt sequences that end with a PAM sequence (NGG) and chuck them into cells with another construct encoding a Cas9 and the insert. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, if you simply need integration you don't need CRISPR either - you can use any bog standard lentiviral vector and you will get a stable cell line made with the gene inserted in random places. Using CRISPR for this overcomplicates things greatly. &lt;/p&gt;&#xA;" OwnerUserId="6726" LastActivityDate="2015-04-03T15:35:53.533" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31040" PostTypeId="1" AcceptedAnswerId="31041" CreationDate="2015-04-03T18:14:08.990" Score="5" ViewCount="1006" Body="&lt;p&gt;I've been watching some videos on signal transduction and it says that because there are enzymes being activated by the signal, then there is a &quot;cascade&quot; which happens afterwards...I don't understand why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-04-03T18:33:35.530" Title="Why does a &quot;cascade&quot; of events happen during signal transduction?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;cell-membrane&gt;&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31041" PostTypeId="2" ParentId="31040" CreationDate="2015-04-03T18:33:35.530" Score="6" Body="&lt;p&gt;There is one main reason: Amplification of the signal. You can start a signal downwards the cascade with relatively few receptors which need to be activated which allows even for weak signals to be translated into the nucleus. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This figure shows this for G protein coupled receptors (from &lt;a href=&quot;http://www.mun.ca/biology/desmid/brian/BIOL2060/BIOL2060-14/CB14.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cGZvO.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example one molecule of cAMP can activate many molecules of pKA until it's hydrolysed which in turn can phosphorylate many other protein molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information you can read the references articles (at least the introduction) and follow the references in them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pnas.org/content/93/19/10078.abstract?ijkey=304d92ae30b6d034918e9a14b1d7d0064b4052b6&amp;amp;keytype2=tf_ipsecsha&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ultrasensitivity in the mitogen-activated protein kinase cascade&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pnas.org/content/102/2/331.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Noisy signal amplification in ultrasensitive signal transduction&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-04-03T18:33:35.530" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31042" PostTypeId="1" AcceptedAnswerId="31105" CreationDate="2015-04-03T18:35:22.697" Score="3" ViewCount="159" Body="&lt;p&gt;&lt;strong&gt;[TLDR] I dont understand the fault people had/have with Richard Goldscmidt's concept of systemic mutations [/TLDR]&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a preface, I am a undergrad biology student, so sorry if this is a &quot;Stupid question&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does Richard Goldschmidt's concept of systemic mutations, reject the classical gene concept, why were biologists so against it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I  understand he used the concept of systemic mutations and developmental macromutations in his lectures to explain how macromutations could cause speciation(macroevolution?). The results of the developmental macromutations, if I understand him correctly would be then the Hopeful Monsters? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And from what I have read on a timeline of his work, systemic mutations describe the &quot;large rearrangments of the chromosome&quot;, with a new arrangement meaning a new phenotype?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is that wrong though? Do chromosomes not have rearrangements via cross over events during meiosis or via transposable elements? Or is he referring to something else, since I understand at the time, meiosis and TE's were not understood well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The source i was reading from was:&#xA;(Richard Goldschmidt: hopeful monsters and other 'heresies' by Michael R. Dietrich) Available from &lt;a href=&quot;http://www.dartmouth.edu/~dietrich/NRG2003.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.dartmouth.edu/~dietrich/NRG2003.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="6307" LastEditDate="2015-04-03T20:03:03.423" LastActivityDate="2015-04-06T17:34:59.587" Title="Richard Goldschmidt's “systemic mutations”?" Tags="&lt;evolution&gt;&lt;mutations&gt;&lt;theoretical-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31043" PostTypeId="2" ParentId="30977" CreationDate="2015-04-03T18:50:28.910" Score="1" Body="&lt;p&gt;There are many things involved in the pairing of homologue chromosomes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Before mitosis can occur an important prerequisite must happen: the division of centrosome. This small complex is the principal microtubule-organizing center in the (animal and therefore human) cells. During interphase the microtubules originating from the centrosome, project to the cell perimiter with their + ends (this where they grow). At the beginning of mitosis the duplicated centrosomes separate and migrate to oppsite sites of the nucleus to form the poles of the mitotic spindle. As the nuclear envelope disintegrates the spindle captures the chromosomes at the cetromeres. Since the microtubules are growing from the centrosomes this capture eventually pushes the choromosomes to center. Source: The Molecular Biology of the cell. Fourth Edition. ISBN: 0-8153-3218-1 (hardbound) 0-8153-4072-9 - (pbk).&#xA;A searchable online version: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21054/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK21054/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've found a few good articles with many details:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0960982202010904&quot; rel=&quot;nofollow&quot;&gt;Current Biology, Volume 12, Issue 17, 3 September 2002, Pages 1473–1483&#xA;The Dynamics of Homologous Chromosome Pairing during Male Drosophila Meiosis&#xA;Julio Vazquez, Andrew S Belmont, John W Sedat&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and &#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0167478103003075#&quot; rel=&quot;nofollow&quot;&gt;Homologous pairing and chromosome dynamics in meiosis and mitosis&#xA;Bruce D. McKee&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I took a quick glance at the above mentioned articles, and it seems that homologous chromosomes tend to be close together (paired if you wish) during interphase most of the time.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-04-03T18:50:28.910" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31044" PostTypeId="2" ParentId="31000" CreationDate="2015-04-03T19:23:20.730" Score="1" Body="&lt;p&gt;I looked in &lt;em&gt;Taiz and Zeiger. Plant Physiology 5th ed&lt;/em&gt; and this is what I found:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Plant growth is concentrated in localized regions of cell division called&#xA;meristems. Nearly all nuclear divisions (mitosis) and cell divisions&#xA;(cytokinesis) occur in these meristematic regions. In a young plant, the&#xA;most active meristems are called apical meristems; they are located at the&#xA;tips of the stem and the root (see Figure 1.1). At the nodes, axillary buds&#xA;contain the apical meristems for branch shoots.&lt;/p&gt;&#xA;&lt;p&gt;The root and shoot apical meristems formed during embryogenesis are called&#xA;primary meristems. After germination, the activity of these primary&#xA;meristems generates the primary tissues and organs that constitute the&#xA;primary plant body.&lt;/p&gt;&#xA;&lt;p&gt;Most plants also develop a variety of secondary meristems during&#xA;postembryonic development. Secondary meristems can have a structure similar&#xA;to that of primary meristems, but some secondary meristems have a quite&#xA;different structure. These include axillary meristems, inflorescence&#xA;meristems, floral meristems, intercalary meristems, and lateral meristems.&lt;/p&gt;&#xA;&lt;p&gt;Axillary buds are secondary meristems; if they are also vegetative meristems, they will have a structure and developmental potential similar to that of the apical meristem.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So, briefly, I could say that meristems are localized regions where undifferentiated cells reproduce themselves and originate new plant tissue. Axillary buds contain secondary (formed after embryogenesis) meristems. This meristem can behave like an apical meristem if it becomes vegetative i.e. either apical dominance disappears or it is excised and subcultured elsewhere.&lt;/p&gt;&#xA;" OwnerUserId="15044" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-03T19:23:20.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31045" PostTypeId="2" ParentId="30994" CreationDate="2015-04-03T19:31:51.833" Score="4" Body="&lt;p&gt;Dendritic cells are so called professional antigen-presenting cells (APCs) as pointed out by Sleepes in comment section. They express both MHC-I and MHC-II receptors on their cell surface on which they present small peptides. These small peptides come from digested proteins of their own (MHC-I) or antigens that were phagocited or taken up by receptor mediated endocytosis (MHC-II). They also express costimulatory molecules necessary for the activation of T-cells (eg. CD80/CD86).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ReTbP.gif&quot; alt=&quot;T-cell activation&quot;&gt;&#xA;source: &lt;a href=&quot;http://journals.cambridge.org/fulltext_content/ERM/ERM2_09/S1462399400002143sup004.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://journals.cambridge.org/fulltext_content/ERM/ERM2_09/S1462399400002143sup004.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see in image above, activation of a T-cell requires two distinct signals: the recognition of an antigen and a co-stimulatory signal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xHmi1.gif&quot; alt=&quot;diversification of t-cells&quot;&gt;&#xA;source: &lt;a href=&quot;http://www.mhhe.com/biosci/ap/dynamichuman2/content/gifs/0158.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.mhhe.com/biosci/ap/dynamichuman2/content/gifs/0158.gif&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After activation T-cells undergo rapid division and diversification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Details of T-cell activation by dendritic cells can be found in this article for example:&#xA;&lt;a href=&quot;http://www.nature.com/icb/journal/v75/n3/pdf/icb199735a.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Immunol Cell Biol. 1997 Jun;75(3):223-30.&#xA;The role of dendritic cells in T cell activation.&#xA;Ni K1, O'Neill HC.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-04-03T19:31:51.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31046" PostTypeId="1" AcceptedAnswerId="31047" CreationDate="2015-04-03T20:19:09.540" Score="4" ViewCount="3387" Body="&lt;p&gt;I believe I may have misunderstood water solubility this entire time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assumed that water soluble meant that it would literally dissolve in water. It would break down into atoms. A sugar molecule would break its bonds and become something else...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However I must be mistaken because I'm reading about why DNA is spiral shaped and it says that it is to keep the hydrophobic bases inside the spiral to protect them from the water, but keeping the hydrophilic phosphate and sugar molecules on the outside.&#xA;I would assume that because these molecules are hydrophilic they would disassociate from each other but this has to be incorrect. What am I misunderstanding about water solubility and what would happen if the bases were exposed to water?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="948" LastEditDate="2015-04-03T20:39:53.847" LastActivityDate="2015-04-03T20:39:53.847" Title="Water soluble molecules" Tags="&lt;biochemistry&gt;&lt;organic-chemistry&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31047" PostTypeId="2" ParentId="31046" CreationDate="2015-04-03T20:29:22.377" Score="7" Body="&lt;p&gt;This question really belongs at &lt;a href=&quot;http://chemistry.stackexchange.com&quot;&gt;Chemistry.SE&lt;/a&gt;, but I'll give you a quick answer. A substance is soluble in water when its solid form (such as a sugar cube) completely dissolves in water to become a sugar solution. The sugar molecules themselves are unaffected, essentially - instead of all being bound to one another in a crystal, they are now floating around in the water. The proof is in the taste - solid sugar and sugar solutions taste pretty much the same. If the sugar had been broken down into component hydrogen, oxygen, and carbon, it would taste &lt;em&gt;much&lt;/em&gt; different!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, hydrolysis is what happens when water actually participates in a chemical reaction to break one or more molecular bonds within a certain molecule, breaking it down to two new molecules (or one molecule and an atom, or whatever). While sugar can be hydrolyzed, it requires either very high heat, or the presence of a catalyst such as an enzyme.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-04-03T20:29:22.377" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31048" PostTypeId="1" CreationDate="2015-04-03T20:33:03.237" Score="2" ViewCount="145" Body="&lt;p&gt;I am a computer scientist delving into Bioinformatics and I need to gain insight in biological phenomena. How would you explain three core concepts as:&#xA;Evolution, Selection and Variation, to a Computer Scientist? I am looking for something in the middle. I read Futuyma's book and was very useful, but I would like an explanation I can relate with my background, something to start building &quot;bridges&quot;... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bibliography suggestions are welcome.&lt;/p&gt;&#xA;" OwnerUserId="13373" LastActivityDate="2015-04-04T12:08:53.823" Title="Core Biological concepts explained to a Computer Scientist?" Tags="&lt;bioinformatics&gt;&lt;mathematical-models&gt;&lt;computational-model&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31049" PostTypeId="2" ParentId="31048" CreationDate="2015-04-03T21:12:39.460" Score="1" Body="&lt;p&gt;Please note that these are just analogies not exact definitions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Okay so let's imagine DNA as string of 4 letters that is the program code of an organism. Also the running environment is a good analogue to the biological environment (RAM, CPU time, disk space - as resources like food, water etc.) Genes of organism could be imagined as methods of an object like in object oriented programing. Let's define some functions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reproduction: copies the string and creates a new instance of the organism (like a new instance of the program) - cell or an offspring - this stands for asexual reproduction. Sexual reproduction takes two instances of the program and randomly exchange their functions and create a new instance with this shuffled code (recombination).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutation: induces random changes to the string at random times. This ensures that different &quot;versions&quot; are present of the code. You need mutation for evolution to work. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also you need Selection - or rather selective pressure -  that is like changing the environment - more efficient codes will survive, the rest die of (aka crash, run out of memory (food)) etc.) Selection drives evolution forward. Also programs can interact with each other and function as a selective pressure - think of anti-virus programs and trojans or viruses - you need better and better AV programs because new viruses come out, and bad guys need new viruses because AV virus programs keep getting better and better - they both put selective pressure on the other and drive each other's evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Genetic) Variation: think of a group of softwares with similar function: like text editing. These are like different individuals of a species because they can do the same thing but they are all a bit different. These &quot;species&quot; evolve by gaining new functions by mutations (the programmer adds new code sections - mutation), and after they gain enough new function they turn into a new software - new species. Evolution takes a lot of time to produce new species - as does coding a new software :).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-04T12:08:53.823" LastActivityDate="2015-04-04T12:08:53.823" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31050" PostTypeId="2" ParentId="31048" CreationDate="2015-04-03T23:46:55.483" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Evolution&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Evolution&lt;/em&gt;&lt;/strong&gt; is the accumulation of genetic mutations that results in phenotypic variation (physical characteristics) where surviving variations are more suited to the environment the organism lives in, thus allowing it to survive better and -- &lt;strong&gt;critically&lt;/strong&gt; -- reproduce as-good-as or better-than its competing organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of computer science this would be like a starting with basic CPU design with all the absolute necessities. Now, let's pretend every generation of CPU after your first is going to be randomly designed by something called &quot;Pressure OS&quot;. Pressure OS doesn't care if the CPUs it designs match the needs of the consumer. PrOS is unfeeling. An OS of pure logic. &lt;strong&gt;ALL&lt;/strong&gt; it will do is make a bunch of random ones, note which ones sell the best, and make the best-selling ones to be the template for its next round of random designs.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Selection and Variation&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Selection&lt;/em&gt;&lt;/strong&gt; is the process by which environmental pressures (low moisture, high heat, high altitude, available food, extreme pressures at the bottom of oceanic trenches, etc.) dictate how well each successive generation of organisms survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In our analogy, the Pressure OS is the cause of Selection. Some CPU designs aren't going to meet the needs of consumers (first-gen Atoms which could barely operate a toaster). Those ones won't be produced again. Others will be very successful (like the Pentium-4 Series which lasted for years) and will quickly outnumber the inferior ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some designs, as odd as they are, will find success in areas outside enthusiast desktops or workstations. Like ARM designs which were never part of the desktop market, but found lots of success in phones and business devices.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Market requirements/environments, as met by the random variations produced by Pressure OS, created &lt;strong&gt;&lt;em&gt;Variation&lt;/em&gt;&lt;/strong&gt; in the types of CPUs available.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ARM Snapdragons could never, &lt;em&gt;ever&lt;/em&gt; compete in the desktop enthusiast market. That's the realm of Sandy Bridges, Haswells, Semprons, and Phenoms. Then again, they're dramatically different designs -- which stem from common designs decades ago that have been heavily modified over the years -- that don't need to compete. Snapdragons and Semprons can co-exist because they fill different niches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, when consumer needs change again -- if everybody gets tired of mobile phones, tablets, and desktops in favor of cone-shaped personal assistants which go in your ear -- then designs will change again under that new pressure. Eventually CPU one design will become the standard for that particular piece of hardware, and you could say that CPU &lt;strong&gt;variation&lt;/strong&gt; had &lt;strong&gt;evolved&lt;/strong&gt; to get there via &lt;strong&gt;selective pressure&lt;/strong&gt; from consumers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biology operates in the exact same way, except the selection process is instigated by environmental pressures to produce organism variations that can successfully reproduce. It's also been going on for &gt;3 Billion Years.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="1231" LastEditDate="2015-04-04T02:50:50.263" LastActivityDate="2015-04-04T02:50:50.263" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31052" PostTypeId="2" ParentId="31031" CreationDate="2015-04-04T01:02:02.967" Score="0" Body="&lt;p&gt;&lt;strong&gt;TL;DR&lt;/strong&gt; Specificity of antibody can be not superb. It can give false-positive results in up to 90% of experiments. However, some essay are 90% specific.&lt;/p&gt;&#xA;&lt;p&gt;That is an interesting question and there sure a lot of research done to understand specificity and strength of binding of antibody to its target.&lt;/p&gt;&#xA;&lt;p&gt;First of all, let me say that antibody-epitope interaction is, as many biological processes, probabilistic process, which means it can go either way, however, after binding antibody need a lot more energy or time to &amp;quot;fall off&amp;quot;. Direct contact is always required for establishment of non-covalent bond between antibody and epitope, because characteristic length of that interaction is very low (order or angstroms, 0.1nm and less). Point here is that you don't need to run antibody in stream, rather let is sit in solution with your sample or mix gently, random thermal motion will take care of them finding each other. In flow you will waste a lot of antibody, which is expensive.&lt;/p&gt;&#xA;&lt;p&gt;I think that you can estimate probability of given antibody binding given molecule from their 3D structures, but this is extremely burdensome calculation. What you can do experimentally, I suppose, is label &amp;quot;right&amp;quot; epitope with red fluorescent tag, and every other molecule in your solution with green tag. Then run solution through column with antibody sitting on beads (as in chromatography), elute everything and compare green to red signal. Measuring accurately, this will tell you how much &amp;quot;junk&amp;quot; antibody picked out of solution.&lt;/p&gt;&#xA;&lt;p&gt;Now, to numbers. &lt;a href=&quot;http://www.abcam.com/primary-antibodies/high-specificity-the-fifth-rabmab-advantage&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here Abcam talks&lt;/a&gt; about its antibody for progesterone. Molecules, closely related to progesterone, are recognized with 40-90% efficiency, compared to true-positive target (progesterone). But this is absolute-worst case scenario, because those molecules are so closely related.&lt;/p&gt;&#xA;&lt;p&gt;On other note, antibody specificity is very important when essay is used, e.g. for HIV diagnosis. &lt;a href=&quot;http://www.uphs.upenn.edu/bugdrug/antibiotic_manual/HIVtesting.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here is nice page&lt;/a&gt; from U Penn, that discusses issues with specificity:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;For example, in one study of 290,000 asymptomatic Minnesota blood donors donating 630,000 blood units, the false positive rate when both the screening and confirmatory assays were positive was was 0% per donation (95% confidence interval 0% to 0.0006%).&lt;/p&gt;&#xA;&lt;p&gt;...&lt;/p&gt;&#xA;&lt;p&gt;For example, in one study of asymptomatic Italian blood donors, only about 13% of donors with repeatedly-reactive EIA tests were confirmed to be HIV-infected on the basis of positive immunoblot. However, in a high risk population the false-positive rate can be much lower, as low as 1-3%.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I couldn't find any more precise data or studies. In biological imaging (my field) antibodies are split into &amp;quot;works&amp;quot; and &amp;quot;don't work, drop it&amp;quot; (aka high background) groups.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-04T06:07:22.243" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31053" PostTypeId="1" CreationDate="2015-04-04T02:02:02.067" Score="5" ViewCount="104" Body="&lt;p&gt;What was the evolutionary advantage in having queens? Is it because the ones that had queen like tendencies in the new environment had kids that cooperated better giving higher chance of survival of the colony? Do the worker naked mole rats have an evolutionary advantage in not reproducing because it allows them to devote more energy to the long journey to make one of their siblings the new queen?&lt;/p&gt;&#xA;" OwnerUserId="15635" LastActivityDate="2015-04-04T02:02:02.067" Title="Why do naked mole rats live in colonies with a queen?" Tags="&lt;evolution&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31054" PostTypeId="1" CreationDate="2015-04-04T05:14:11.113" Score="4" ViewCount="847" Body="&lt;p&gt;A few years back my Physics professor made a joke that his myopia (i.e., nearsightedness) gave him a &quot;superpower&quot; that allowed him to see close objects much more clearly than someone with typical eyesight. For example, reading small fine print or tiny details on a surface. The physics made sense, as a person with myopia should have a closer near focus point. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recently, this belief was challenged by a normal-sighted friend. I did some Google-ing and couldn't find any evidence or articles confirming or refuting this belief. All I found was &lt;strong&gt;a lot&lt;/strong&gt; of anecdotal evidence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: Is this belief correct? Are there any scholarly articles or similarly trustworthy sources confirming this?&lt;/p&gt;&#xA;" OwnerUserId="15210" LastEditorUserId="9943" LastEditDate="2015-05-30T14:16:08.083" LastActivityDate="2015-05-30T14:35:38.423" Title="Myopia as a microscopic superpower?" Tags="&lt;human-biology&gt;&lt;vision&gt;&lt;human-eye&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31055" PostTypeId="1" AcceptedAnswerId="31056" CreationDate="2015-04-04T10:27:24.583" Score="15" ViewCount="1898" Body="&lt;p&gt;I have heard that a reference genome such as humans is generated by randomly choosing samples from a group of donors. But why do we call the DNA sequence generated as a reference? Why should we believe those few samples can represent all humans, from which we need to align with?&lt;/p&gt;&#xA;" OwnerUserId="14905" LastActivityDate="2015-05-01T03:20:47.507" Title="Why reference genome is a reference?" Tags="&lt;bioinformatics&gt;&lt;genomes&gt;&lt;human-genome&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31056" PostTypeId="2" ParentId="31055" CreationDate="2015-04-04T11:23:36.127" Score="13" Body="&lt;p&gt;The main reason is because the genetic differences between individuals of the same species are &lt;em&gt;tiny&lt;/em&gt;. For the vast majority of studies, they can simply be ignored. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Differences between individuals are usually (not always, but mostly) differences in SNP genotypes. These are single nucleotide differences which, while they can have phenotypic effect, don't really affect the ability of sequences to align. Sequence alignment software is designed to be able to deal with such small differences. For example, consider these two random sequences:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt;seq1&#xA;ACCTTGCATCGGATCGAATTCGCGTTAGCGATCG&#xA;&amp;gt;seq2&#xA;GCCTAGCATCGGACCGAATTCCCGTTAGCAATCG&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;If we align them, we will get:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;seq1            ACCTTGCATCGGATCGAATTCGCGTTAGCGATCG&#xA;seq2            GCCTAGCATCGGACCGAATTCCCGTTAGCAATCG&#xA;                 *** ******** ******* ******* ****&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;As you can see, despite the small differences in sequence, the two can be aligned very well. The same is true when you look at real data. My haemoglobin gene, for example, will align perfectly well against both yours and the one in the reference genome. In fact, they will almost certainly be identical or, at best, have a couple of different residues. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, when doing work that is not about studying specific polymorphisms, we need a representative genome. Anyone's will do, unless they have a particularly serious mutation such as a chromosomal translocation. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2015-04-04T11:23:36.127" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31059" PostTypeId="1" AcceptedAnswerId="31171" CreationDate="2015-04-04T12:35:15.830" Score="5" ViewCount="3056" Body="&lt;p&gt;I was thinking about audio compression (namely mp3), that &quot;filters&quot; out sound that we would not likely hear.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The MP3 lossy audio data compression algorithm takes advantage of a perceptual limitation of human hearing called auditory masking.&#xA;  from: &lt;a href=&quot;http://en.wikipedia.org/wiki/MP3&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/MP3&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I've also checked the wiki entry for &lt;a href=&quot;http://en.wikipedia.org/wiki/Auditory_masking&quot; rel=&quot;nofollow&quot;&gt;auditory masking&lt;/a&gt;, and found this: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If two sounds of two different frequencies are played at the same time, two separate sounds can often be heard rather than a combination tone. The ability to hear frequencies separately is known as frequency resolution or frequency selectivity. When signals are perceived as a combination tone, they are said to reside in the same critical bandwidth.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My question is how much is this critical bandwidth or what's the smallest frequency difference we can perceive as two different tones, if you wish. Let's assume that both tones are equally loud, are coming from the same direction and distance and we are in a quiet room - so basically we eliminate as much noise and affecting phenomenons as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As @ sanchises pointed out (thank you again!) in the comment section the frequency resolution is 3.6Hz between 1 and 2kHz. But since perception threshold is a function of the pitch of the sound I'd assume that the ability to resolve two tones would change with pitch too. Does anybody have any data on that? For example resolution X pitch graph.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="5144" LastEditDate="2015-04-08T15:06:06.427" LastActivityDate="2018-02-05T19:50:00.967" Title="What's the frequency resolution of the human ear?" Tags="&lt;sensation&gt;&lt;perception&gt;&lt;hearing&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31060" PostTypeId="1" CreationDate="2015-04-04T14:09:26.577" Score="0" ViewCount="124" Body="&lt;p&gt;I know how to do a 80-mer window search against a single protein&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;fasta35 -k 0 -w 80 -a -m 9 -C 20 -Q -3 -E10 -d20 -B tempQuery:0-80 &#xA;&#xA;FASTAbyGI15/378405189 &#xA;fasta35 -k 0 -w 80 -a -m 9 -C 20 -Q -3 -E10 -d20 -B tempQuery:1-81 FASTAbyGI15/378405189 &#xA;fasta35 -k 0 -w 80 -a -m 9 -C 20 -Q -3 -E10 -d20 -B tempQuery:2-82 FASTAbyGI15/378405189 &#xA;&#xA;....&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This will give me the detailed results but I want to do the search against a database in Fasta like this website:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.allermatch.org/allermatch.py/form&quot; rel=&quot;nofollow&quot;&gt;http://www.allermatch.org/allermatch.py/form&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone help me?&lt;/p&gt;&#xA;" OwnerUserId="15217" LastEditorUserId="14826" LastEditDate="2015-04-06T17:36:47.370" LastActivityDate="2015-04-06T17:36:47.370" Title="How to do Sliding 80mer Window search against a database with fasta" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;software&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31061" PostTypeId="2" ParentId="31031" CreationDate="2015-04-04T14:19:27.297" Score="0" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Clarify, when you say &quot;antibody&quot; do you mean a monoclonal antibody (where every antibody is identical, and therefore a pure population), or do you mean a polyclonal antibody (which is a mixture of antibodies that all recognize the same antigen, but may each be recognizing different epitopes on the antigen)? A monoclonal Ab (mAb) recognizes a single epitope.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Textbooks and supplier catalogs often act like Ab binding is absolute, as if you could not measure the three quantities: molar concentration of free antigen, molar concentration of free mAb, and molar concentration of bound antibody antigen complex. In other words, as if every antibody is fully occupied all the time, once the Ab encounters a molecule of free antigen.  But I think you can discern from the discussions and answers above that not all Ab are created equally.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In cases where people have measured this Kd (the dissociation constant) for a &quot;tight&quot; binding antibody the value is in the order of 10EE-14 or smaller (as I recall).  When we say tight binding we usually mean that the so-called off-rate is very slow, with a t1/2 on the order of hours. In a typical reaction the on-rate is usually limited by the rate of diffusion, and cannot be faster (but search for discussions of lac Repressor DNA binding protein finding its targets with kinetics that are faster than the rate of diffusion!)&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;3&quot;&gt;&#xA;&lt;li&gt;&lt;p&gt;The device you are describing (that detects binding events using fixed proteins on a surface and target proteins in solution) measures surface plasmon resonance, and at one point was available for purchase under then brand name BIAcore. It was developed by Mel Simon, at CalTech.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Finally, if your goal is an automated way to use antibody reagents to detect vanishingly small quantities of antigen in a complex mixture of fluid, you would do well to familiarize yourself with the radioimmunoassay (RIA), it can be exquisitely sensitive.  Keep in mind that all of these different techniques will have a lower limit of detection such that a negative result (&quot;We could not measure any of protein X in the sample from this patient&quot;) always has to be considered with the proviso of &quot;using this particular detection assay&quot;. So it is a type of confidence level.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-04-04T14:19:27.297" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31062" PostTypeId="2" ParentId="31054" CreationDate="2015-04-04T14:43:33.373" Score="0" Body="&lt;p&gt;The changes in image size in myopic eyes are not as large as one would imagine. In fact, they are pretty close and the myops are probably not aware of them until the proper correction is placed which affect the image size in a much greater degree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see on the image that the sizes of retinal images are very similar - the uncorrected image size is shown in Y' row:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Y'' is an image size with a proper corrective lense)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/e5OYj.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is true the near point of accommodation of myopic eye is closer that of emmetropic eye, but it is war away from &quot;superpower&quot; mentioned by the professor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, the discrimination ability in myopic subjects are greater than of emmetropes, because they able to see smaller points, but at the same time the image quality is affected as well, thus overall image quality is more compromised compared to emmetropic eye.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-04-04T15:00:03.007" LastActivityDate="2015-04-04T15:00:03.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31063" PostTypeId="1" AcceptedAnswerId="31065" CreationDate="2015-04-04T16:05:17.213" Score="9" ViewCount="11614" Body="&lt;p&gt;I know you could divide the female fertility period (~40 years, right?) by 9 months which would give something like ~50 kids (with no multiple kids per pregnancy). The limiting factor in this calculation is time but is there a biological upper limit as well?&lt;/p&gt;&#xA;" OwnerUserId="15219" LastActivityDate="2016-09-01T17:06:18.010" Title="What is the maximum number of babies a human woman can have?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;&lt;pregnancy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31064" PostTypeId="1" AcceptedAnswerId="31080" CreationDate="2015-04-04T16:15:41.553" Score="2" ViewCount="55" Body="&lt;p&gt;I'm currently in high school biology (final year) and am currently working on an assignment. I need to create some sort of interactive model, so I've decided to make a simulation-type program. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've looked a bunch at lots of papers and journals and I was wondering how I could take the data and make a function out of it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is one example (Pleasants &amp;amp; Oberhauser, 2012):&#xA;&lt;img src=&quot;https://i.stack.imgur.com/2qiPA.png&quot; alt=&quot;Monarch Egg Production (Pleasants &amp;amp; Oberhauser, 2012)&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, I want to know how to make sense of the values F_1,11; r^2; and P. I am finding a lot of these values in the papers I'm looking at so it would be awesome if one of you guys could point me in the right direction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="15220" LastEditorUserId="15220" LastEditDate="2015-04-04T16:24:42.920" LastActivityDate="2015-04-05T07:00:45.927" Title="How can I use this data to make a function?" Tags="&lt;data&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2015-04-05T07:59:47.357" ContentLicense="CC BY-SA 3.0" />
  <row Id="31065" PostTypeId="2" ParentId="31063" CreationDate="2015-04-04T16:32:56.357" Score="7" Body="&lt;p&gt;&lt;strong&gt;How do you define the biological limit?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It very much depends on how you define a biological limit. If you prefer, it very much depends on how you define a human! Some women are completely sterile while others are highly fertile and there is genetic predisposition to that.  How much &quot;perfect&quot; should the genotype of an individual be so that it is still considered as a human? There is genetic variance underlying fecundity that is important to consider. For example, in your calculation you took lifespan as a constant but it obviously is not a constant. Fecundity is reduced by all these small mutations segregating in the human populations that reduce the fecundity of any single human. There exist no human that is free from all deleterious alleles. Imagine a giant woman with 10 independent reproductive system! Would she still be a human? That was probably kind of a too extreme thought experiment. Imagine a woman that can have a reproductive lifespan of 100 years. Would it still be a human? The issue behind this question reminds me an old post (now closed, I can't find it anymore) that asked whether a leopard would run faster if it had more legs. Well... one can imagine something running faster than a leopard, but it would not be a leopard anymore. So how many changes from a leopard are we allowed to make to answer the question. So I had to chose a definition of what a &quot;perfect woman&quot; is. Or a definition of a woman that would set this so called biological limit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;The definition I am using to answer this question&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the below answer, I will assume that by biological limit you mean the expected fitness of a female that would live in the same environment than we live in today but would not carry any single of the deleterious locus that are segregating in the human population. In other words I assume that you accept that the &quot;perfect woman&quot;, that is a woman that would not carry any single of the deleterious mutations that segregate in the populations will set this biological limit to woman maximal fecundity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Mutation load Theory&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The decrease in the mean fitness of an idealized population where no deleterious mutations would exist compared to the realized mean fitness of a population is called the mutation load. The mutation (in an infinite population) is a function of the genome-wide mutation rate only. Let the genome-wide mutation rate in human be $U=2.2$, the mutation load $L$ in the human population is equal to $L=1-e^{-2.2}=0.89$. The estimates are taken from &lt;a href=&quot;https://www.youtube.com/watch?v=jctvV5xrWw4&amp;amp;spfreload=10&quot; rel=&quot;nofollow&quot;&gt;this video&lt;/a&gt;. You may want to have a look to the video in order to have a better understanding of why $L=1-e^{-U}$ and what are the assumptions of these calculations. The main assumptions are 1) infinite population size, 2) multiplicity of fitness effects at different loci and 3) additivity of fitness effect between alleles at the same locus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So what does mutation load theory predicts?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above calculation means that segregating deleterious allele reduce the fitness of the average woman by 89%! If we assume that an average woman can have 10 babies (this number is just a random guess) if she wants to, then the maximum biological limit of a &quot;perfect woman&quot; (in a world where there is no more competition than the one in which we are living) is $\frac{10}{1-0.89}≈91$  babies!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_people_with_the_most_children&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;, the world record is 69 and is owned by Mrs. Vassilyev. It is reasuring to see that the observed world record (69) is lower than the the biological limit we just calculated (91). If we were to know the distribution of maximal number of babies per woman (not to be confused with the realized number of babies), we could calculate the probability to have 69 or more babies and compare this probability to the total number of females that has ever lived (or the total number of females that would have never had the idea to have so many babies). Always according to wikipedia, the world record for men would be 867 and is owned by &lt;a href=&quot;http://en.wikipedia.org/wiki/Ismail_Ibn_Sharif&quot; rel=&quot;nofollow&quot;&gt;Ismail Ibn Sharif&lt;/a&gt;. However, sounds possible to me (but I really have no idea) that some sperm donor may have overshoot this number today.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-04-05T14:52:51.353" LastActivityDate="2015-04-05T14:52:51.353" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31066" PostTypeId="1" AcceptedAnswerId="31131" CreationDate="2015-04-04T16:37:38.227" Score="3" ViewCount="4038" Body="&lt;p&gt;On Wikipedia, the entire microelectrode page states only the following: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A microelectrode is an electrode of very small size, used in electrophysiology for either recording of neural signals or electrical stimulation of nervous tissue. Initially, pulled glass pipette microelectrode was used with later introduction of insulated metal wires. These microelectrodes are made from inert metals with high Young modulus such as tungsten, stainless steel, platinum and iridium oxide and coated with glass or polymer insulator with exposed conductive tips. More recent advances in lithography yielded to silicon based microelectrodes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can someone provide a more elaborate explanation of how it works?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Like ideally, I would like something as specific as the usual descriptions you see in introductory chemistry books for how emf works in a battery.&lt;/strong&gt; In other words, I know how electric potential works, but I am not understanding the exact mechanism of the microelectrode works. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there are many types of microelectrodes, just give me the properties of one involving small shafts of hollow glass filled with a conductive salt solution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pictures would be great. &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="9943" LastEditDate="2015-04-07T12:59:00.820" LastActivityDate="2020-02-03T08:54:07.963" Title="How does a microelectrode work?" Tags="&lt;neuroscience&gt;&lt;electrophysiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31067" PostTypeId="1" AcceptedAnswerId="31088" CreationDate="2015-04-04T16:48:31.970" Score="4" ViewCount="14400" Body="&lt;p&gt;The most common visualization of an action potential is a graph of the difference in membrane potential (y axis) at a particular time (x axis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to my textbook &lt;em&gt;Cognitive Psychology&lt;/em&gt; by E. Bruce Goldstein, an action potential sent from neuron down the axon remains the same. That is, if we plot the action potential as described above, then at each as it is propagated down it will have the same shape on the graph (within some range of error obviously, but he is saying the error is trivial). &#xA;But he then says on page 34 &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One way to answer the question of how action potentials determine different qualities [(e.g. taste of something sweet)] is to propose that the action potentials for each quality might look different. However, [Edgar] Adrian rules out that possibility by determining that all action potentials have basically the same height and shape. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone confirm these two facts: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Once an action potential is sent from a given neuron down the axon, does the shape and amplitude remain constant as it is propagated? &lt;/li&gt;&#xA;&lt;li&gt;Do all action potentials have the same amplitude and shape? &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11652" LastActivityDate="2019-07-27T22:35:59.930" Title="Are all action potentials the same shape and amplitude when graphed with respect to time?" Tags="&lt;neuroscience&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31068" PostTypeId="2" ParentId="31026" CreationDate="2015-04-04T17:05:08.417" Score="4" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Background_radiation&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; wiki page , the average background radiation is 3.01 milli-Sievert per year (including natural and artificial sources). This equals 0.301 rad.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found a short &lt;a href=&quot;https://www.researchgate.net/publication/18894543_Uniformity_of_radiation-induced_mutation_rates_among_different_species&quot; rel=&quot;nofollow&quot;&gt;letter&lt;/a&gt; to nature that says the average forward mutation rate in human is 2.6 * 10^-7 per locus per rad = 2.6 mutations per ten million bases. Also it say that this mutation rate is quite uniform among species. The size of the human genome is approximately 3.2 gigabases.&#xA;So doing a quick maths: (2.6*3.2*100)*0.301 = 250.432 mutations per year per human. This is an approximation because I rounded the size of the human genome to 3.2 gigabases. Also this doesn't mean that we actually acquire this amount of mutations because we have repair mechanisms.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-04-04T17:05:08.417" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31069" PostTypeId="1" AcceptedAnswerId="31076" CreationDate="2015-04-04T17:05:48.207" Score="5" ViewCount="528" Body="&lt;p&gt;I understand &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;How a signal is propagated down the axon.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How the membrane potential of a neuron changes during the course of it's &quot;firing&quot;. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;But I don't understand how physically the change in the membrane potential actual starts the signal down the axon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A stimulus causes the voltage gated sodium channels to open and sodium ions rush in. This creates a positive charge density inside the cell and negative charge density outside. This difference is by definition a potential difference.  Potassium gates sensitive to this difference then open, the potassium ions to rush out, which again flips the polarity of the inside and outside such that positive charge density outside the cell and negative charge density inside.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;But how does that actually lead to the signal that is propagated down the axon? Can someone explain?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="9943" LastEditDate="2015-04-07T23:44:44.483" LastActivityDate="2015-04-07T23:44:44.483" Title="How does a change in the potential across a neuron's membrane get turned into a signal that is sent down the axon?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31070" PostTypeId="1" AcceptedAnswerId="58412" CreationDate="2015-04-04T17:39:52.330" Score="0" ViewCount="91" Body="&lt;p&gt;I am trying to get a good pair (or better yet, library of pairs) of primers that give me one band in WT mice (C57BL/6). Do you know where I could find such a thing?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, I thought of just designing a few sets of primers myself for highly-conserved regions. But that's quite a bit of guessing work (what regions, what pairs from what &lt;code&gt;eprimer3&lt;/code&gt; will calculate for me etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Do you know where such a database could be found?&lt;/li&gt;&#xA;&lt;li&gt;If not, could you help me get started with creating it myself? What specific regions would in your opinion be particularly good for this purpose?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4795" LastActivityDate="2017-04-14T17:21:05.140" Title="Solid mouse (C57BL/6) WT primers" Tags="&lt;genetics&gt;&lt;genomics&gt;&lt;pcr&gt;&lt;mouse&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31072" PostTypeId="2" ParentId="30783" CreationDate="2015-04-04T19:00:00.567" Score="1" Body="&lt;p&gt;The answer is in the slides you provided a link to. The key fact is that Craig &amp;amp; Andy did careful controls to show that it was the presence of dsRNA in both the sense control, and in the anti-sense experimental sample that was responsible for the RNAi-mediated knock-down.  Actually, Ken Kemphues showed this earlier in a Nature paper (the control also knocked down gene expression) but did not pursue the mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, I infer that the transgenic gene expression construct introduced into the petunias must also give rise to dsRNA. I am less familiar with the consequences of introducing foreign DNA into a plant cell (e.g., does a single copy become integrated, multiple copies?, is it maintained extrachromosomally?)&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-04-04T19:00:00.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31073" PostTypeId="1" AcceptedAnswerId="31074" CreationDate="2015-04-04T20:05:28.603" Score="5" ViewCount="5783" Body="&lt;p&gt;Some very basic parts of transcription/translation seem to be left out in various literature. I can't find the answer to this anywhere:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How exactly is tRNA synthesized? I realize that mRNA is synthesized through transcription and I know a lot about that. However tRNA is supposedly synthesized the same way but every time you read about transcription they just talk about how the mRNA then gets this and that...?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where do the amino acids get attached? Is it in the nucleus or outside the nucleus?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-04-04T21:28:00.700" Title="Where do amino acids get attached to tRNA and where is it synthesized?" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;proteins&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31074" PostTypeId="2" ParentId="31073" CreationDate="2015-04-04T20:48:45.977" Score="9" Body="&lt;p&gt;A pre-tRNA is transcribed from tRNA genes in DNA by RNA polymerase III. Processing occurs in the nucleus, where a 5' sequence is cleaved by RNase P, the 3's CCA motif is added, and ~10% of the nucleotides are substituted. The tRNA are transported out via the pore complexes. Aminoacyl-tRNA synthetase enzymes attach amino acids in the cytoplasm in a 2-step reaction that requires ATP. You'll find there's a unique splicing mechanism in tRNA that additionally splices out an anticodon intron which is abesnt in mature tRNA's:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The wikipedia article notes RNA Pol III generally recognizes internal control elements rather than upstream control elements as in a normal gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YfqFK.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;https://www.qiagen.com/us/products/genes%20and%20pathways/pathway%20details/?pwid=44&quot; rel=&quot;noreferrer&quot;&gt;Qiagen&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MoA9l.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eTbpd.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21729/&quot; rel=&quot;noreferrer&quot;&gt;Molecular Cell Biology. 4th edition.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Addendum: I said in my post that tRNA is charged in the cytoplasm, this is somewhat true. In mammalian cells, we also see that tRNA are charged in the nucleus as well, and it might aid in the export of some of these charged tRNAs. &lt;a href=&quot;http://www.jbc.org/content/275/41/31559.full&quot; rel=&quot;noreferrer&quot;&gt;(Source)&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-04-04T21:28:00.700" LastActivityDate="2015-04-04T21:28:00.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31075" PostTypeId="1" AcceptedAnswerId="31078" CreationDate="2015-04-04T20:53:16.703" Score="2" ViewCount="740" Body="&lt;p&gt;Hi I am little confused in one of my classes; because the teacher will say that &quot; the actin is nucleated by the ARP 2/3 complex&quot; or &quot;microtubles are nucleated by the centrosome&quot;. Unless I am misunderstanding, I don't take this as having anything to do with the nucleus as in the nucleus inside a cell. ( or does it). so what does this really mean than?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you&lt;/p&gt;&#xA;" OwnerUserId="15066" LastActivityDate="2015-04-04T21:17:53.557" Title="What is meant by nucleated in this context?" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31076" PostTypeId="2" ParentId="31069" CreationDate="2015-04-04T20:55:17.013" Score="6" Body="&lt;p&gt;As you pointed out sodium as sodium enters the cell depolarizes (becomes more positive). Recall the sodium gates open the more positive the voltage is, which in turn opens more sodium gates. If a patch of neural membrane is depolarized, the charge  diffuses into the nearby patches of neural membrane. This will open the sodium channels of the nearby membrane patch. Now once enough sodium channels open, the neuron will fire a action potential, at this point potassium channels open and potassium rushes out of the cell repolarizing it(making it more negative). Furthermore the sodium gates close at positive voltages which further repolarizes the neuron and prevents back propagation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the key is the influx of the sodium ions diffusing down the axon and causing a downstream depolarization of the axon.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I find &lt;a href=&quot;http://neuroscience.uth.tmc.edu/s1/chapter03.html&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; website instructive, as well as this &lt;a href=&quot;https://sites.google.com/site/ch12nervesaudrat/home/propagation-of-an-action-potential&quot; rel=&quot;noreferrer&quot;&gt;picture&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UlgeT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Update:&#xA;As the voltage builds up in the soma the charge spills over into the &lt;a href=&quot;http://en.wikipedia.org/wiki/Axon_hillock&quot; rel=&quot;noreferrer&quot;&gt;Axon Hillock&lt;/a&gt; (an area of high concentration of sodium and potassium gates) If enough sodium ions diffuse into the axon hillock and passes a (somewhat ill defined) voltage threshold then the sodium gates will open and start the action potential. Then the action potential proceeds down the axon as described above &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A useful metaphor is the soma, and by extension the Axon Hillock, sums up the synaptic input from the dendrites, and again, if its over the threshold then the sodium gates open, if not, they slowly return to rest. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The synaptic input can be excitatory (cause depolarization) or inhibitory(hyper polarization) depending on the type of receptors and channels in the dendrites, but in general these voltage changes in the dendrite diffuse down into the soma and are eventually reach the axon hillock. &lt;/p&gt;&#xA;" OwnerUserId="13388" LastEditorUserId="13388" LastEditDate="2015-04-04T21:24:59.817" LastActivityDate="2015-04-04T21:24:59.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31077" PostTypeId="2" ParentId="31075" CreationDate="2015-04-04T21:07:11.593" Score="0" Body="&lt;p&gt;In this context, i feel nucleated means being a &quot;core structure&quot;, a substrate for the organization of one or multiple polymer chains.&lt;/p&gt;&#xA;" OwnerUserId="14698" LastActivityDate="2015-04-04T21:07:11.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31078" PostTypeId="2" ParentId="31075" CreationDate="2015-04-04T21:17:53.557" Score="5" Body="&lt;p&gt;Cytoskeletal nucleation refers to the &lt;em&gt;de novo&lt;/em&gt; formation of cytoskeleton filaments. If microtubules are nucleating, that means microtubules are being polymerized from lit. &quot;From the beginning&quot; by α/ß-tubulin dimers. So literally, and we see in the image below, Arp2/3 complexes act as progenitor sites so to say for new actin filaments by the &quot;nucleation&quot; of actin:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PmSro.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From wikipedia for &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nucleation&lt;/a&gt;: &quot;Nucleation is the first step in the formation of either a new thermodynamic phase &lt;strong&gt;or a new structure via self-assembly or self-organisation&lt;/strong&gt;.&quot;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-04-04T21:17:53.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31080" PostTypeId="2" ParentId="31064" CreationDate="2015-04-05T00:47:32.147" Score="2" Body="&lt;p&gt;I will not go too deep into the details but here some information to facilitate your understanding of these ubiquitous statistics in biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The F, $r^2$ and p-value are all equivalent statistics to measures the &lt;a href=&quot;http://en.wikipedia.org/wiki/Goodness_of_fit&quot; rel=&quot;nofollow&quot;&gt;goodness-of-fit&lt;/a&gt; of a model against the data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The F is the ratio of the $unexplained~variance~/~explained~variance$. I let you look out what the &lt;a href=&quot;http://en.wikipedia.org/wiki/Variance&quot; rel=&quot;nofollow&quot;&gt;variance&lt;/a&gt; is. The F (originating from a &lt;a href=&quot;http://en.wikipedia.org/wiki/F-test&quot; rel=&quot;nofollow&quot;&gt;F-test&lt;/a&gt;) allows, using the proper &lt;a href=&quot;http://en.wikipedia.org/wiki/F-distribution&quot; rel=&quot;nofollow&quot;&gt;F-distribution&lt;/a&gt; cumulative density function (cdf) for the number of observation you have, to compute a p-value.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/P-value&quot; rel=&quot;nofollow&quot;&gt;p-value&lt;/a&gt; gives you the probability of obtaining the observed fit with your model (here a linear one) by random chance only. For example in your case a p-value=0.01 means that you have a 1% chance to observe this correlation just by chance. Usually the p-value threshold used to claim statistical significance is 0.05 (i.e. 5% chances to observe that fitting by random chance). In linear regression, the lowest the p-value the closest the distance (called variance) of the observed data point to the line.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Coefficient_of_determination&quot; rel=&quot;nofollow&quot;&gt;$r^2$&lt;/a&gt; is the coefficient of determination (or the square of the correlation coefficient). This measure is very interesting as it give you an estimate of the &quot;proportion of the data&quot; explained by your model. For example a $r^2$=1 means that 100% of the variance of the data is explained by your model, in other terms your model perfectly fits the data. A $r^2$=0 in the other hand means that your model does not at all explain the data (no fits between your model and the data).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The $r^2$ and the p-value can be computed for any type of fitting, like trying to fit an exponential curve instead of a linear one. What you usually look for when modeling data is the highest $r^2$ possible. As all of this statistics are linked a higher $r^2$ means a lower p-value for an identical number of observations.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-04-05T07:00:45.927" LastActivityDate="2015-04-05T07:00:45.927" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31081" PostTypeId="1" AcceptedAnswerId="46696" CreationDate="2015-04-05T01:26:22.850" Score="1" ViewCount="119" Body="&lt;p&gt;&lt;strong&gt;How is the maxillary bone split in the Bolyerine Snakes described in T.H Frazzetta's &quot;From Hopeful Monsters to Bolyerine Snakes?&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In T. H. Frazzetta, &quot;From Hopeful Monsters to Bolyerine Snakes?&quot; He describes boid snakes on the island of Mauritius as being unique among snakes in that they had a split jaw, connected by a joint. This was said to be an example of how continuous evolution could not be true for all cases, as what is the point of 1/2 of jaw, according to Stephen J Gould. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I dont seem to understand the pictures illustrated in the aritcle though, and how the maxillary bone is split and where it is connected to a joint. I could not find a legible picture of a  Bolyerine Snake described like this, if anyone could help with understanding it with a picture that would be appreciated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would provide the pictures, but I am not sure if that counts as plagiarism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Citation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Published by: The University of Chicago Press for The American Society of Naturalists,&#xA;Available from: &lt;a href=&quot;http://www.jstor.org/stable/2459073&quot; rel=&quot;nofollow&quot;&gt;http://www.jstor.org/stable/2459073&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14815" LastActivityDate="2020-09-27T08:19:58.333" Title="Bolyerine Snakes maxillary bone, split?" Tags="&lt;anatomy&gt;&lt;bone-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31082" PostTypeId="1" CreationDate="2015-04-05T05:21:28.480" Score="1" ViewCount="142" Body="&lt;p&gt;I'm going over some of my notes, and I have written down that motor proteins with + cytoskeletal directionality have a reversed schematic representation relative to - directed motor proteins. Then I have this sort of image drawn. I just want to clarify it, since I don't remember this part of lecture at all. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Schematic representations&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Kinesin: N terminal - |Head||Coils||Tail| - C terminal&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Dynein: N terminal - |Tail||Coils||Head|| - C terminal&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Does this look right?&lt;/p&gt;&#xA;" OwnerUserId="13344" LastEditorUserId="12877" LastEditDate="2015-04-07T21:14:44.530" LastActivityDate="2015-04-07T21:14:44.530" Title="How does the placement of it's motor domain affect the directionality of a motor protein?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31083" PostTypeId="2" ParentId="31082" CreationDate="2015-04-05T05:34:12.597" Score="2" Body="&lt;p&gt;No. DNA, and RNA have a polarity in the orientation of their sugar-phosphate backbones, based on the numbering of the carbon atoms in the sugar rings. So, for example, we say that the sequence of this RNA is being read from the 5' to the 3' end, which indicates that the first nucleotide is exposing the hydroxyl at the 5’ carbon on its sugar ring.  At the other end of the linear polynucleotide the sugar is exposing the hydroxyl on its 3’ carbon of the sugar ring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All mRNAs are translated in the 5’ to 3’ direction and all proteins are synthesized from the amino terminus to the carboxylate terminus, because the peptide bonds in the protein also have a directional polarity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You appear to have mislabeled the N and C termini of Dynein in your diagram. Perhaps the  lecture was about the domain structure of these two motor proteins? And the point might have been that they each have three equivalent domains but in one case the part we call the head is synthesized first and in the other case the tail is synthesized first(?).&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-04-05T05:34:12.597" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31088" PostTypeId="2" ParentId="31067" CreationDate="2015-04-05T21:33:26.127" Score="4" Body="&lt;ol&gt;&#xA;&lt;li&gt;Generally speaking, yes. For reference see &lt;a href=&quot;http://www.nature.com/ncomms/2013/130719/ncomms3181/full/ncomms3181.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper in Nature&lt;/a&gt;&#xA;This is Fig. 7 from it with comment:&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IoSje.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;Reason is that most axons are not passive tubes of electrolyte with leakage (in which case AP would be attenuated along it) but rather active media with membrane potential across that have ion channels that reproduce initial action potential along the axon. However, in more passive tubes, like in dendrites, action potentials might be attenuated.&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;Generally, no. Amplitude of action potential depends on properties of ion channels, at what potential, for example, $K^+$ channels will open to start repolarization (peak of AP). Duration also depends on properties of ion channels. But since there are not a lot of variability in ion channels and extracellular ion composition is mainly same in animals, most of APs will have same shape/duration/amplitude.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-04-06T08:18:55.537" LastActivityDate="2015-04-06T08:18:55.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31091" PostTypeId="1" AcceptedAnswerId="31120" CreationDate="2015-04-05T21:41:13.423" Score="3" ViewCount="214" Body="&lt;p&gt;I understand the different ways bacteria can undergo horizontal gene transfer (transformation, transduction (phages), conjugation (plasmids)). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there an experimental method to tell how a specific gene got into the host (during evolution)? For example if a gene A got into host X from species Y, is it possible to know how gene A was transmitted?&lt;/p&gt;&#xA;" OwnerUserId="11626" LastEditorUserId="11626" LastEditDate="2015-04-06T03:24:02.143" LastActivityDate="2015-04-07T03:06:20.490" Title="Horizontal Gene Transfer" Tags="&lt;genetics&gt;&lt;microbiology&gt;&lt;bacteriology&gt;&lt;horizontal-gene-transfer&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31093" PostTypeId="1" CreationDate="2015-04-06T00:04:01.790" Score="1" ViewCount="38" Body="&lt;p&gt;I'm stuck between two ideas. Not sure which one of them would be best.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Do a FRAP on the middle of a MT. If it grows from the + end, that section will remain dark. If it grows from the - end, existing fluorescent tubulin will be pushed into the photobleached area. However, how would I be able to tell if the middle region is dynamic using a FRAP?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Introduce GFP-Tubulin into a cell. See where existing microtubules begin to fluoresce as new subunits are added. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Do either of these sound reasonable? Any better ideas? &lt;/p&gt;&#xA;" OwnerUserId="13344" LastActivityDate="2015-04-06T00:04:01.790" Title="What kind of experiments could you do to see which end of a microtubule is most dynamic?" Tags="&lt;cell-biology&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31094" PostTypeId="1" CreationDate="2015-04-06T03:18:41.277" Score="3" ViewCount="1213" Body="&lt;p&gt;What physical force attracts the anti-codon on tRNA to the codon on mRNA during translation? I know that these two bond together, but what actually makes the tRNA move through the cytoplasm to the mRNA on the ribosome?&lt;/p&gt;&#xA;" OwnerUserId="15228" LastActivityDate="2015-06-06T09:22:48.113" Title="What physical force attracts the anti-codon on tRNA to the codon on mRNA during translation?" Tags="&lt;molecular-biology&gt;&lt;rna&gt;&lt;translation&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31097" PostTypeId="2" ParentId="31094" CreationDate="2015-04-06T06:19:15.247" Score="1" Body="&lt;p&gt;As with many processes in cellular biology, nothing really moves anywhere, attracted by specific force. What that means, is that any molecule has a chance to interact with any other molecule, say, bind to it. Only force that is acted is electrical force of attraction of negative charges to positive ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Due to diffusion and temperature fluctuations, molecules wander around, bumping in each other. Sometimes, two complimentary molecules will bump into each other in a very desirable, energy-efficient orientation. Their atomic-scale interfaces (with tiny charges on it) will find each other as neat as hand finds glove of the right size/orientation neat and comfy. That is the way, for example, tRNA finds slot on ribosome/mRNA complex to plug into. just simple key-and-lock, or hand-and-glove model, that's all there is. And beauty is that you can try computationally calculate probability and energy of different interactions from molecular 3D structures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, there are many tRNAs, but Glycine-tRNA will bind tightest to glycine-codon/ribosome complex. There is a chance that Alanine-tRNA will get in that spot, but that chance is very little compared to chance of proper interaction. Also, because interfaces of Ala-tRNA and Ala-codone don't match exactly, molecular vibration due to heat (temperature) will destroy this complex quickly. This allows specificity.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-06T06:19:15.247" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31098" PostTypeId="2" ParentId="24305" CreationDate="2015-04-06T06:42:15.757" Score="-2" Body="&lt;p&gt;Thank you for the query, I would have search would have shown that, we are the pioneers to first use Turmeric against snake venom.  Be it, Cobra, Krait or Viper. It is the universal truth that, all the snake venom is 90% protein and out of that, 60% is the lethal inflammatory toxic enzyme called Phospholipase A2 (PLA2).  PLA2 is an enzyme that breaks down the cellular plasma membrane containing phospholipid and allows the entry of toxic enzyme.  The toxic enzyme let loose a cascade of events that goes through cyclo-oxygenase and lipoxygenase pathway with release of arachidonic acid - 20 carbon fatty acid which forms the precursor of pain causing inflammatory by-products.  Since, Turmeric can destroy the activity of phospholipase A2,the inflammation and accompanying inflammation reduced considerably and the life of the patient extended by two to three hours giving time for the anti-venom antibody treatment. The attractive feature of the above &quot;On the spot&quot; treatment by Turmeric is that, the snake can be any species because PLA2 is the key toxic enzyme in all the venoms. The way to administer Turmeric on the field is to take two to three fist full of Turmeric powder and dissolve it in warm water, then it is filtered through a clean cloth and the clear extract without any residue about a glass is given to drink by the patient when it is warm.  The rest of the water is used to continuously washed the bitten spot so that, the local inflammation is subsidized. You may refer the to the following publications where it is shown that Turmerin, a water soluble antioxidant protein from Turmeric binds to PLA2 distal to the active site and changes the conformation of Phospholipase A2 in such a way that, it is no more hypertoxic.  Thus extending the life of the patient and reducing pain and inflammation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;br&gt;&#xA;&lt;a href=&quot;http://www.degruyter.com/view/j/bchm.2008.389.issue-3/bc.2008.024/bc.2008.024.xml;jsessionid=BA4284943310CD38D2BD7E782A7CF511&quot; rel=&quot;nofollow&quot;&gt;New biological activity against phospholipase A2 by Turmerin, a protein from Curcuma longa L.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15230" LastEditorUserId="3340" LastEditDate="2015-04-07T04:22:14.150" LastActivityDate="2015-04-07T04:22:14.150" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31099" PostTypeId="1" AcceptedAnswerId="31104" CreationDate="2015-04-06T09:17:26.583" Score="3" ViewCount="156" Body="&lt;p&gt;For human genetic mapping several different types of markers are used:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;RFLPs (Restriction Fragment Length Polymorphisms)&lt;/li&gt;&#xA;&lt;li&gt;VNTRs (Variable Number of Tandem Repeats) such as mini- and microsatellites&lt;/li&gt;&#xA;&lt;li&gt;SNPs (Single Nucleotide Polymorphisms)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;What are the pro's and con's of using each type?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do any of these markers have a specific functionality in human genetic mapping, or can they all be used for the same purposes?&lt;/p&gt;&#xA;" OwnerUserId="15136" LastEditorUserId="6307" LastEditDate="2015-04-06T17:08:30.533" LastActivityDate="2015-04-06T17:17:50.167" Title="Markers for human genetic mapping" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;human-genetics&gt;&lt;human-genome&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31100" PostTypeId="1" CreationDate="2015-04-06T11:15:25.767" Score="1" ViewCount="164" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4pzxw.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;em&gt;Crocus sativus&lt;/em&gt;, or saffron crocus, the most commercially important part is the stigma of flowers. Each plant produces one flower (so there is more than one plant in this picture) and each flower has three stigmas (stigmas are red in this picture). What are the possible mechanisms to produce more stigma in a plant for commercial cultivation?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="6307" LastEditDate="2017-04-03T02:34:44.217" LastActivityDate="2020-05-31T12:26:41.047" Title="Do you know of ways that help a plant to produce more flowers?" Tags="&lt;botany&gt;&lt;agriculture&gt;&lt;flowering&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31101" PostTypeId="1" CreationDate="2015-04-06T12:07:12.007" Score="4" ViewCount="56" Body="&lt;p&gt;I'm studying the digestion of fats and I understand that our dietary fats mostly consist of triglycerides. We absorb the fats and eventually they end up in a muscle/adipose cell for storage (as triglycerides) or for oxidation for energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However I don't understand exactly where cholesterol plays in? I read about lipids being synthesized by the liver being exported by VLDL and then taken up by cells. We're moving closer to cholesterol here but I still don't see the connection.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-04-06T12:07:12.007" Title="Cholesterol's role in lipid uptake" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;metabolism&gt;&lt;fat-metabolism&gt;" AnswerCount="0" CommentCount="1" ClosedDate="2015-06-22T19:09:43.950" ContentLicense="CC BY-SA 3.0" />
  <row Id="31103" PostTypeId="2" ParentId="31100" CreationDate="2015-04-06T16:08:00.200" Score="3" Body="&lt;p&gt;Each species of flowering plant produces a set number of floral parts, more or less. Having three styles and three stigmas per flower is a trait that is determined genetically. Mutations can cause floral parts to be duplicated. &lt;a href=&quot;http://www.plantcell.org/content/16/suppl_1/S181.short&quot; rel=&quot;nofollow&quot;&gt;Heirloom tomatoes&lt;/a&gt; have mutations in the &lt;em&gt;fascicated&lt;/em&gt; and &lt;em&gt;locule-number&lt;/em&gt; genes, resulting in more &lt;a href=&quot;http://en.wikipedia.org/wiki/Locule&quot; rel=&quot;nofollow&quot;&gt;locules&lt;/a&gt; being produced per fruit. Mutations in the &lt;em&gt;fascicated&lt;/em&gt; gene also cause increases in other floral parts, such as petals, sepals, and stamens. If you compare a regular tomato to an heirloom, you'll notice that heirlooms tend to have around 10 petals and sepals compared to a regular tomato's 5.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the question is, do such mutations exist for &lt;em&gt;Crocus sativus&lt;/em&gt;? A quick Google search didn't turn up anything other than the normal three-stigma flowers, so it doesn't look like such a mutation is common, if it exists at all. My answer to your question is: there is no easy way to get a saffron flower to produce more stigmas, for if such a method existed, everyone would be using it. I don't doubt that a dedicated botanist could come up with something (crossing with a &lt;a href=&quot;http://en.wikipedia.org/wiki/Crocus_speciosus&quot; rel=&quot;nofollow&quot;&gt;related species&lt;/a&gt;, perhaps), but it's not something you can likely accomplish in your home garden.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: &#xA;User Sleepses found an article where a high-yielding mutant with 5 stigmas was obtained through gamma radiation mutagenesis. I'm not sure whether or not this mutant is for sale commercially, though. &lt;/p&gt;&#xA;" OwnerUserId="14629" LastEditorUserId="14629" LastEditDate="2015-04-07T15:25:42.500" LastActivityDate="2015-04-07T15:25:42.500" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31104" PostTypeId="2" ParentId="31099" CreationDate="2015-04-06T16:28:01.663" Score="3" Body="&lt;p&gt;SNPs are much denser than RFLPs and VNTRs therefore the DNA resolution is much greater with SNPs. VNTRs were historically used for &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_linkage&quot; rel=&quot;nofollow&quot;&gt;linkage mapping&lt;/a&gt; while SNPs allowed for association studies (e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Genome-wide_association_study&quot; rel=&quot;nofollow&quot;&gt;GWA studies&lt;/a&gt;). Therefore your question goes down to what are the differences between linkage mapping and association studies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are both forward genetic methods which aim to identify a genetic modification provoking a trait.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two major differences between both approaches are 1) linkage mapping requires a pedigree but can be performed using a fairly small sample size while 2) association studies can be performed at the population level but usually require a much larger sample size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both approaches require markers but for different reasons. For linkage mapping, markers, such as microsatellites, are used to delimit the genomic region associated with the trait and take advantage of recombination events in the genome to pin down that region. This, of course, requires both 1) recombinant individuals in the pedigree and 2) at least one marker that is co-inherited with the trait. Linkage mapping allows to find virtually any genetic modifications, such as a genomic deletion, but only in the case of a genetic modification showing high penetrance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For association studies, markers are the actual genomic modification themselves (usually SNPs) and are used directly in statistical tests (often a logistic or linear regression) for association with the trait. This means that either 1) the causal marker is available or 2) at least one marker is highly co-inherited with the causal mutation (i.e. in linkage disequilibrium). Association studies allows to find both low- or high-penetrance mutations, given a sufficiently big sample size. Also an association study can be conducted in the presence of a non-discrete (i.e. linear) phenotype which one cannot use in linkage mapping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another difference is that linkage mapping does not require any a priori knowledge of the genomic modification causing the trait while association studies do (as markers are statistically associated with the phenotype).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually both methods will highlight, with varying resolution based on the phenotype and markers used, the genomic region causing a trait but rarely the actual causal mutation will be found with 100% certainty.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-04-06T17:17:50.167" LastActivityDate="2015-04-06T17:17:50.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31105" PostTypeId="2" ParentId="31042" CreationDate="2015-04-06T17:34:59.587" Score="2" Body="&lt;p&gt;His notion of systemic mutations involved the postulation of massive chromosomal rearrangements (not mere recombination/crossing-over) as mediators of speciation in one-step. While whole genome duplications have been shown to induce speciation (see, for example, cryptic speciation in &lt;em&gt;Hyla versicolor&lt;/em&gt;) they are not large scale rearrangements as he suggested. Additionally, while there is evidence for multiple large scale chromosomal arrangements at once in cancers (Chromothripsis) , there is no evidence of a similar process resulting in immediate reproductive isolation.  &lt;/p&gt;&#xA;" OwnerUserId="6726" LastActivityDate="2015-04-06T17:34:59.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31106" PostTypeId="2" ParentId="23062" CreationDate="2015-04-06T17:48:58.043" Score="6" Body="&lt;p&gt;It might be due to livor mortis, also called postmortem lividity, which is the settling of the blood in the lower parts of the body which in your case might have been the limbs. By time the color can be interpreted as either blue or purple, but given, that not much time has passed it can very well be the reddish color you might have asked, as stated &lt;a href=&quot;https://books.google.hu/books?id=yHHABAAAQBAJ&amp;amp;pg=PA23&amp;amp;lpg=PA23&amp;amp;source=bl&amp;amp;ots=Z1Dnt36iMe&amp;amp;sig=I_9Y7KxhsJBDlJvuTeNRyjdf4aY&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=6-oiVf_4H4bYsAWqwoCQCA&amp;amp;redir_esc=y#v=onepage&amp;amp;q=bright%20red&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; on page 39:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first manifestation of livor mortis can be expected 20-30 min following the irreversible cardiovascular arrest, initially as bright-red spots that subsequently become confluent and turn bluish-violet.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Which might better describe your case is the fact, that cold conditions can cause bright red color in livor mortis, as it can also be found on page 39:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cold conditions, such as keeping a body in cold storage, cause ... bright-red livor mortis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can read more about it &lt;a href=&quot;http://en.wikipedia.org/wiki/Livor_mortis&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; or &lt;a href=&quot;http://medical-dictionary.thefreedictionary.com/livor+mortis&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have added references thanks to @Kendall, who provided them.&lt;/p&gt;&#xA;" OwnerUserId="15051" LastEditorUserId="9943" LastEditDate="2015-04-07T03:05:56.680" LastActivityDate="2015-04-07T03:05:56.680" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31107" PostTypeId="1" AcceptedAnswerId="31115" CreationDate="2015-04-06T18:18:15.977" Score="3" ViewCount="212" Body="&lt;p&gt;I assume most people either experienced or have seen people with the following phenomenon: in the early phases of sleep sometimes involuntary twitches occur that usually accompany the pause of breathing (I'm aware that there's a  chronic sleeping disorder called sleeping apnea but I think it's different because what I'm asking about now is acute). I wonder if the twitching is some sort of emergency signal, so that the person would wake up (to some level not necessarily full awake) and start breathing. Is there any data that these (the pause in breathing and the twitches) are connected or they are independent? Also I'm also interested why this acute pause of breathing occurs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've researched myself on this topic and it seems that what I've described is more likely a form of Obstructive sleep apnea.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="9943" LastEditDate="2015-04-25T12:53:17.920" LastActivityDate="2015-04-25T12:53:17.920" Title="Involuntary twitches and apnoea during early phases of sleep" Tags="&lt;sleep&gt;&lt;muscles&gt;&lt;breathing&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31108" PostTypeId="1" AcceptedAnswerId="31127" CreationDate="2015-04-06T18:35:01.530" Score="3" ViewCount="555" Body="&lt;p&gt;So I know that several different environmental signals, such as pH, bile, and temperature, regulate virulence gene expression in V. cholerae. Specifically, they control expression of the genes encoding the toxin co- regulated pilus (TCP) and cholera toxin (CT). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what are the two key (main) transcriptional regulatory proteins that control TCP and CT expression, and where is each localized in the bacterial cell? Also, what does each protein do?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that the proteins involved are ToxR/S, ToxP/H, and ToxT, but I don't know which are the MAIN ones and why...&lt;/p&gt;&#xA;" OwnerUserId="11626" LastActivityDate="2015-04-11T21:52:11.630" Title="Regulation of V. cholerae virulence factors" Tags="&lt;microbiology&gt;&lt;bacteriology&gt;&lt;gene-regulation&gt;&lt;pathogenesis&gt;&lt;bacterial-toxins&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31109" PostTypeId="2" ParentId="6933" CreationDate="2015-04-06T19:05:32.550" Score="1" Body="&lt;p&gt;Might I suggest you go directly to the source? Here is a link to a paper published by Francis Crick (et al) in 1957 entitled: 'Codes Without Commas' &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528468/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528468/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15235" LastActivityDate="2015-04-06T19:05:32.550" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31112" PostTypeId="2" ParentId="10326" CreationDate="2015-04-06T22:10:35.403" Score="2" Body="&lt;p&gt;Kinetochore (KT) is a multilayer protein complex. It's main function is to link chromosomes to the positive ends of the spindle microtubules. Also it plays role in the formation of heterogenic region at and around the centromer. The attachment of the KT is not uniform among living species. According to this paper on KT assembly in yeast:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;.  ...  KTs  remain attached to the MTs throughout the cell cycle in this organism. However, a temporary detachment of chromosomes  from  MTs  occurs  (for  1–2 min)  at  the  time of CEN DNA replication in S phase in S.cerevisiae (Kitamura et al. , 2007). After completion of CEN replication, a KT reassembles and reestablishes its attachment with  MTs.  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;source:&lt;a href=&quot;http://femsle.oxfordjournals.org/content/femsle/338/2/107.full.pdf&quot; rel=&quot;nofollow&quot;&gt;http://femsle.oxfordjournals.org/content/femsle/338/2/107.full.pdf&lt;/a&gt;&#xA;(CEN - centromere, MT- (spindle)microtubules)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus the exact time of kinetochore attachment depends on the organism, though I must note that S. cerevisiae has somewhat different mitosis than us.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-11T21:21:51.400" LastActivityDate="2015-04-11T21:21:51.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31113" PostTypeId="2" ParentId="31094" CreationDate="2015-04-06T22:31:27.647" Score="0" Body="&lt;p&gt;I wanted to illustrate the process I explained in a comment on aandreev's answer with some images, I just copy/pasted the actual text sections, however.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From comments:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The tRNA is bound to an elongation EF-Tu (which is also bound to GTP). The Ef-Tu has an affinity for a factor binding site in the A-site of the large ribosomal subunit. You have an anticodon triplet on the tRNA, and a bend in the 3D structure of the anticodon loop gives you wobble base pairing on the last nitrogenous base. When the anticodon of the tRNA binds tightly enough to the mRNA, two adjacent adenines in the 16s rRNA of the A site crosslink (via hydrogen bonding) the minor grooves formed by the correctly paired tRNA. These adenines don't differentiate between G:C or A:T pairs, just the tightness/correctness of the tRNA binding.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8jK6A.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-04-06T22:31:27.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31115" PostTypeId="2" ParentId="31107" CreationDate="2015-04-07T00:10:32.040" Score="4" Body="&lt;p&gt;Jerk-like muscle contractions occurring while drifting off to sleep are normal and are referred to as &quot;sleep starts&quot; or &lt;em&gt;sleep myoclonus&lt;/em&gt; (&lt;a href=&quot;http://www.ninds.nih.gov/disorders/myoclonus/detail_myoclonus.htm&quot; rel=&quot;nofollow&quot;&gt;National Institute of Health - NINDS&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sleep Education explains the symptoms:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sleep starts usually consist of one strong jerk that affects much of the body. The arms and legs are most likely to be affected.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So sleep starts may be quite vigorous, but may consist just of small lip movements too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;https://www.sleepassociation.org/patients-general-public/sleep-myoclonus/&quot; rel=&quot;nofollow&quot;&gt;American Sleep Association&lt;/a&gt; mentions that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sleep myoclonus will rarely disturb the subject or any bed partner to the point of waking and disrupting sleep [...]. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In fact, sleep starts are associated with &lt;em&gt;tachypnea&lt;/em&gt;, i.e., an increased in breath rate (&lt;a href=&quot;http://www.sleep-journal.com/article/S1389-9457%2811%2900316-9/abstract&quot; rel=&quot;nofollow&quot;&gt;Vetrugno &amp;amp; Montagna, 2011&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, your hypothesis that a myoclonus is a mechanism to wake a person up (for whatever reason) seems unsupported.&lt;br&gt;&#xA;&lt;br&gt;&lt;br&gt;&#xA;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;- Vetrugno &amp;amp; Montagna, &lt;em&gt;Sleep Medicine&lt;/em&gt; 2011; &lt;strong&gt;12&lt;/strong&gt;: S11–S16    &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-04-25T12:49:14.880" LastActivityDate="2015-04-25T12:49:14.880" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31117" PostTypeId="1" CreationDate="2015-04-07T01:13:32.507" Score="2" ViewCount="3046" Body="&lt;p&gt;Viruses such as polio are so well documented that a search for &quot;empirical formula polio&quot; gives you something like&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; C332,652  &#xA; H492,388  &#xA; N98,245  &#xA; O131,196  &#xA; P7,501  &#xA; S2,340&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;We know that the virus consists of 70% protein, 22% phospholipid, 6.5% DNA, 1.5% carbohydrate (from the book &lt;em&gt;Herpes Simplex and Pseudorabies Viruses&lt;/em&gt; by Kaplan)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any information on the actual chemical composition of HSV1 and varieties?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="15239" LastEditorUserId="15239" LastEditDate="2015-04-07T06:12:24.387" LastActivityDate="2019-01-18T03:25:59.937" Title="What is the chemical composition / empirical formula of Herpes Simplex 1?" Tags="&lt;virus&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31118" PostTypeId="1" CreationDate="2015-04-07T02:03:22.253" Score="5" ViewCount="210" Body="&lt;p&gt;I understand that this would be a very rough estimate, but approximately how many cells in the human body are infected during an average non-fatal viral infection before the infection is eliminated by the immune system? It doesn't matter what virus you use as an example, I'm just looking for a general case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CDB&lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-04-07T02:03:22.253" Title="What percentage of cells in the human body are infected during a non-fatal viral infection?" Tags="&lt;virology&gt;" AnswerCount="0" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31120" PostTypeId="2" ParentId="31091" CreationDate="2015-04-07T03:06:20.490" Score="1" Body="&lt;p&gt;If you're looking at evolutionary timescales, then the only available source of information is the target organism's genome sequence. At least some of the methods of horizontal gene transfer you mention leave a distinctive signature in the genome. For example, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC387345/&quot; rel=&quot;nofollow&quot;&gt;retrovirus particles that have become incorporated into the human genome are easily identified by their local DNA sequence&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in terms of an experiment, you would sequence your specific gene of interest as well as the surrounding local sequence (say, 10,000 base pairs downstream and upstream of your gene). In at least some cases you would be able to say for sure &quot;this gene arose from retroviral incorporation&quot;, whereas in others it would be more ambiguous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;br&gt;&#xA;Belshaw, R. et al. &lt;em&gt;Long-term reinfection of the human genome by endogenous retroviruses.&lt;/em&gt; PNAS (2004)&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2015-04-07T03:06:20.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31121" PostTypeId="2" ParentId="31117" CreationDate="2015-04-07T03:24:26.080" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;The Herpes viruses have a unique four-layered structure: a core containing the large, double-stranded DNA genome is enclosed by an icosapentahedral capsid which is composed of capsomers. The capsid is surrounded by an amorphous protein coat called the tegument. It is encased in a glycoprotein-bearing lipid bilayer envelope &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK8157/&quot; rel=&quot;noreferrer&quot;&gt;&lt;a href=&quot;https://i.stack.imgur.com/kmllL.png&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kmllL.png&quot; alt=&quot;http://en.wikipedia.org/wiki/Herpes_simplex_virus&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can watch an animation of infection and steps of replication &lt;a href=&quot;http://darwin.bio.uci.edu/~faculty/wagner/hsvstructure.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;, and below the video, they say that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;HSV is a nuclear replicating, icosahedral, enveloped DNA virus. The HSV envelope contains at least 8 glycoproteins. The matrix or tegument which contacts both the envelope and the capsid contains at least 15-20 proteins&lt;a href=&quot;http://darwin.bio.uci.edu/~faculty/wagner/hsvstructure.html&quot; rel=&quot;noreferrer&quot;&gt;[2]&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In this definition of the structure, they at least assigned some values to the makeup. Additionally, in wikipedia, the viral genome is listed which I would recommend you take a look at as well. It can be found &lt;a href=&quot;http://en.wikipedia.org/wiki/Herpes_simplex_virus&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; but here is the synopsis of the table &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;UL1 through UL56&#xA;US1 through US12&#xA;RS1, ICP0, LRP1, LRP2&#xA;RL1, LAT&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Additional resources:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://darwin.bio.uci.edu/~faculty/wagner/hsv3f.html&quot; rel=&quot;noreferrer&quot;&gt;HSV Genome 2nd link&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://darwin.bio.uci.edu/~faculty/wagner/hsv9fnew.html&quot; rel=&quot;noreferrer&quot;&gt;The use of microarrays to analyze gene expression&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://darwin.bio.uci.edu/~faculty/wagner/hsv6f.html&quot; rel=&quot;noreferrer&quot;&gt;Structural properties of HSV promoters&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://darwin.bio.uci.edu/~faculty/wagner/array2.html&quot; rel=&quot;noreferrer&quot;&gt;Animation of the Construction of a HSV-1 DNA Microarray for Global Analysis of Transcript Abundance&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://darwin.bio.uci.edu/~faculty/wagner/rnatime.html&quot; rel=&quot;noreferrer&quot;&gt;Animation of the Time-dependant Changes in HSV-1 Transcript Abundance During Productive Infection&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://darwin.bio.uci.edu/~faculty/wagner/table.html&quot; rel=&quot;noreferrer&quot;&gt;Some Genetic Functions Encoded by Herpes Simplex Virus type 1&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://darwin.bio.uci.edu/~faculty/wagner/probetable.html&quot; rel=&quot;noreferrer&quot;&gt;Herpes Simplex Virus Oligonucleotide Probes used in the DNA-microarray&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="9943" LastEditDate="2015-04-07T04:26:03.007" LastActivityDate="2015-04-07T04:26:03.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31122" PostTypeId="2" ParentId="31067" CreationDate="2015-04-07T05:23:26.323" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Action potentials differ in shape between neuronal cell types, and action potentials may even change shapes during action potential propagation within one and the same axon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;blockquote&gt;&#xA;  &lt;p&gt;Once an action potential is sent from a given neuron down the axon, does the shape and amplitude remain constant as it is propagated?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Although the textbooks will typically say action potentials are transmitted without their &lt;strong&gt;amplitude&lt;/strong&gt; being changed this claim is theoretically virtually impossible due to the many variables encountered in and around the axon. For example, axons in the sciatic nerve may extend to &lt;a href=&quot;http://www.sciencedaily.com/articles/a/axon.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;a meter&lt;/a&gt; and it is virtually impossible to keep the exact conditions along that length exactly identical. The &lt;strong&gt;amplitude&lt;/strong&gt; of the action potential is mainly dependent on the influx of Na&lt;sup&gt;+&lt;/sup&gt;. Slight variations in membrane potential, concentration of sodium, or channel (subtype) densities may therefore change the amplitude. In addition, temperature affects action potential amplitude (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.1949.sp004388/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hodgkin &amp;amp; Katz, 1949&lt;/a&gt;) and slight temperature differences along long axons may therefore be expected to alter amplitude. Likewise, &lt;strong&gt;shape&lt;/strong&gt; may alter as well. For example, glutamate released alongside axons of hippocampal pyramidal neurons results in &lt;strong&gt;widening&lt;/strong&gt; of action potentials (&lt;a href=&quot;http://www.sciencemag.org/content/331/6017/599.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sasaki et al., 2011&lt;/a&gt;).   &lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;&lt;blockquote&gt;&#xA;  &lt;p&gt;Do all action potentials have the same amplitude and shape? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Therefore, given the answer under question 1 &lt;strong&gt;no&lt;/strong&gt;, they do not have to. Even a propagated action potential in a given axon may change amplitude and shape, as said. Most notably, different neuronal types may in fact be classified according to their action potential morphology, such as the various neuronal types in the dorsal root ganglia of the spine that can be differentiated based on their duration (&lt;a href=&quot;http://jn.physiology.org/cgi/pmidlookup?view=long&amp;amp;pmid=8890304&quot; rel=&quot;nofollow noreferrer&quot;&gt;Villiere &amp;amp; McLachlan, 1996&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA; - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.1949.sp004388/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hodgkin &amp;amp; Katz, &lt;em&gt;J Physiol&lt;/em&gt;; &lt;strong&gt;109&lt;/strong&gt;: 240–9&lt;/a&gt;&lt;br&gt;&#xA; - &lt;a href=&quot;http://www.sciencemag.org/content/331/6017/599.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sasaki et al., &lt;em&gt;Science&lt;/em&gt; 2011; &lt;strong&gt;331&lt;/strong&gt;: 599-601&lt;/a&gt;&lt;br&gt;&#xA; - &lt;a href=&quot;http://jn.physiology.org/cgi/pmidlookup?view=long&amp;amp;pmid=8890304&quot; rel=&quot;nofollow noreferrer&quot;&gt;Villiere &amp;amp; McLachlan, &lt;em&gt;J Physiol&lt;/em&gt; 1996; &lt;strong&gt;76&lt;/strong&gt;: 1924-41&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2019-07-27T22:35:59.930" LastActivityDate="2019-07-27T22:35:59.930" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="31124" PostTypeId="1" AcceptedAnswerId="31152" CreationDate="2015-04-07T08:13:20.760" Score="3" ViewCount="1130" Body="&lt;p&gt;Gastric acid secretion shows a circadian rhythm where acid production in the morning is minimal and it reaches a maximum towards the evening. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is this process regulated?&lt;/p&gt;&#xA;" OwnerUserId="15136" LastEditorUserId="5144" LastEditDate="2015-04-07T08:20:31.620" LastActivityDate="2015-04-08T03:38:22.590" Title="How is circadian rhythm of gastric acid secretion regulated?" Tags="&lt;physiology&gt;&lt;human-physiology&gt;&lt;gastroenterology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31125" PostTypeId="2" ParentId="24378" CreationDate="2015-04-07T08:37:50.083" Score="2" Body="&lt;p&gt;I've found a great &lt;a href=&quot;http://www.pasteur.fr/recherche/unites/tcruzi/minoprio/Int_parasitol.pdf&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; that says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mitogens   and   superantigens   have   been   described   to&#xA;  explain the strategy used by microorganisms to avoid the&#xA;  host specifc immune responses and to ensure persistence.&#xA;  These  moieties  are  responsible  for  the  initiation  of  non-&#xA;  specifc  (polyclonal)  immune  responses. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Mitogens are chemicals (usually proteins) that promote mitosis. Superantigens (sAg) form a subclass of antigens and are capable of inducing massive polyclonal T-cell activation and cytokine release (Cytokines crucial role in immune system mediation). Their ability to inflict massive T-cell activation comes from the fact that they bind directly to MHC-II without any pre-processing, and stimulate T-cell activation.&#xA;Source: &lt;a href=&quot;https://escholarship.org/uc/item/47g8w51m&quot; rel=&quot;nofollow&quot;&gt;https://escholarship.org/uc/item/47g8w51m&lt;/a&gt;&#xA;Also there are B-cell sAgs that stimulate B-cells, and their activation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These altogether (mitogens cytokines, sAgs) result in rapid expansion of B-cells and T-cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also &lt;a href=&quot;http://www.hindawi.com/journals/jpr/2012/362131/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper might help to understand why parasites trigger polyclonal T and B-cell activation. Namely to avoid host specific immune system, dilute the pathogen specific anti-bodies. It is important to note that chronic infections could lead to several auto-immune diseases.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-12T19:33:13.993" LastActivityDate="2015-04-12T19:33:13.993" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31126" PostTypeId="2" ParentId="30363" CreationDate="2015-04-07T08:42:30.520" Score="2" Body="&lt;p&gt;Long-term exposure to excessive oxygen will lead to damage in pulmonary tissue. This damage resembles the same damage which is seen in patients with Acute Respiratory Distress Syndrome (ARDS). In these patients &lt;a href=&quot;http://www.thelancet.com/pdfs/journals/lancet/PIIS0140673698094495.pdf&quot; rel=&quot;nofollow&quot;&gt;surfactant specific proteins are damaged by proteolysis&lt;/a&gt;. This proteolysis is caused by the neutrophil elastase enzyme, after a massive influx of activated neutrophils. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The damage done by exposure to excessive oxygen is thought to be done by &lt;a href=&quot;http://en.wikipedia.org/wiki/Reactive_oxygen_species&quot; rel=&quot;nofollow&quot;&gt;Reactive Oxygen Species (ROS)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Reactive oxygen species (ROS) are chemically reactive molecules containing oxygen. Examples include oxygen ions and peroxides. ROS are formed as a natural byproduct of the normal metabolism of oxygen...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;These ROS can cause oxidative damage to DNA, RNA and proteins. They can form covalent bonds between molecules in the surfactant, thus inactivating them. Damaging of molecules can lead to cellular damage, causing ROS-mediated necrosis or apoptosis. Therefore there will be less surfactant production possible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also &lt;a href=&quot;http://www.medscape.com/viewarticle/778505_3&quot; rel=&quot;nofollow&quot;&gt;interestingly&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An important feature of pulmonary oxygen toxicity is that it is almost impossible to distinguish from damage caused by other lung injury processes. Consequently, it is unclear whether deterioration of lung function during high concentration oxygen therapy is due to worsening of the primary disease process or to oxygen-free radical-induced damage; the administration of high concentration oxygen may be perpetuating lung injury in some patients.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So in patients who undergo long-term 100% oxygen exposure, for example due to lung problems, the problems could be perpetuated or even worsened due to oxygen therapy and the oxidative stress caused by it.&lt;/p&gt;&#xA;" OwnerUserId="15136" LastActivityDate="2015-04-07T08:42:30.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31127" PostTypeId="2" ParentId="31108" CreationDate="2015-04-07T09:04:17.043" Score="1" Body="&lt;p&gt;Virulence factors of V cholerae is regulated by a hierarchical regulatory system. The proteins you listed in your question are part of this system. In &lt;a href=&quot;http://mbio.asm.org/content/4/5/e00366-13.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; paper it is said that the actual activation of TCP and CT is done by ToxT- thus this could be your &quot;key&quot; protein. I'd also like to note that just because these are two different genes does not necessarily mean that there has to be two key factors - this assumption of yours if a bit faulty. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also because the activation of the virulence factors are regulated by a chain of events, each link is can be considered equally important, because if one of them fails the whole chain is dysfunctional.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The short description of the regulatory chain taken from the article linked above:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The ToxR regulon is a hierarchical regulatory system that activates virulence gene expression in response to environmental stimuli (2). Induction of the ToxR regulon starts with activation of tcpPH expression by AphA and AphB (4, 5). AphA and AphB are cytoplasmic regulatory proteins that cooperatively bind to the tcpPH promoter and activate its expression. Once TcpP is produced, it functions in conjunction with ToxR to activate toxT expression. TcpP and ToxR are structurally similar membrane-bound DNA binding proteins that are thought to modulate gene expression in response to external stimuli (6, 7). When stimulated, TcpP and ToxR bind to the toxT promoter and activate its expression. ToxT then directly activates the expression of the genes that encode for CT and TCP production (8).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This paper might also be helpful. Unfortunately I could only access the full text this way (through researchgate):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.researchgate.net/publication/6176851_Regulation_of_virulence_in_Vibrio_cholerae_the_ToxR_regulon&quot; rel=&quot;nofollow noreferrer&quot;&gt;Regulation of virulence in Vibrio cholerae: the ToxR regulon.&lt;/a&gt;&#xA;Brandon Childers, Karl E Klose&#xA;Future Microbiology (Impact Factor: 4.02). 07/2007; 2(3):335-44. &#xA;DOI: 10.2217/17460913.2.3.335 &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://iai.asm.org/content/75/12/5542.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;This&lt;/a&gt; paper provides details of regulation and mechanism of ToxT.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ifo9x.gif&quot; alt=&quot;ToxT regulation&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taken from the third linked paper. As you can see the final activator of CT (termed CTX in the picture) and TCP is indeed the ToxT, but as I wrote it earlier each link in the chain is important.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-11T21:52:11.630" LastActivityDate="2015-04-11T21:52:11.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31128" PostTypeId="1" CreationDate="2015-04-07T09:53:52.040" Score="5" ViewCount="407" Body="&lt;p&gt;While transcription of rRNAs happens in nucleolus mediated by RNA Polymerase-I, we see that 5S-rRNA is transcribed elsewhere by RNA Polymerase-III. What is the cause and why?&lt;/p&gt;&#xA;" OwnerDisplayName="user11667" LastEditorUserId="3340" LastEditDate="2015-04-07T10:36:02.200" LastActivityDate="2015-04-11T15:36:32.307" Title="Why is 5S-rRNA is different from other rRNAs in place of transcription and usage of RNA polymerase?" Tags="&lt;molecular-genetics&gt;&lt;rna&gt;&lt;transcription&gt;&lt;rrna&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31129" PostTypeId="2" ParentId="31128" CreationDate="2015-04-07T12:12:21.370" Score="2" Body="&lt;p&gt;The three RNA polymerases (RNAPs) are very similar to each other, yet not identical. As described in &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0888754309002043&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; article, there are subunits that are specific for each type of polymerases. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In addition to providing unique substrates that polymerase-specific subunits bind to give each of the RNAPs their specific functionality, the two largest subunits also shape the active site cleft of the enzymes where the transcription reaction occurs. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The results of the linked article also claim that even though the cleft loops are conserved regions, there are significant length differences between the three polymerases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also rRNA gene is similar to the tRNA genes and they differ from other genes in the recruitment of the polymerases. &quot;Traditional' promoters are located upstream the start site, while 5s rRNA gene and tRNA genes have one and two boxes respectively that recruits RNAPIII.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The 5s rRNA and tRNA genes have promoters within the coding region of the gene. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;source: &lt;a href=&quot;http://mol-biol4masters.masters.grkraj.org/html/Gene_Structure5C-Eukaryotic_Promoter_Structure_for_RNA_Polymerase_III.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://mol-biol4masters.masters.grkraj.org/html/Gene_Structure5C-Eukaryotic_Promoter_Structure_for_RNA_Polymerase_III.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are two images form the linked page:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/asQpD.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6a6IS.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://mbe.oxfordjournals.org/content/12/3/481.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; article it is described that 5s RNA genes have translocated severeal times throughout evolution, and on of the mechanisms for this could be analogous of the second class of SINE elements, that contain internal RNAP III promoters, and are derived form tRNA (this could also indicate the similar structure to tRNA genes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this good review &lt;a href=&quot;http://www.google.hu/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=7&amp;amp;ved=0CFAQFjAG&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fprofile%2FDina_Grohmann%2Fpublication%2F49754339_Evolution_of_multisubunit_RNA_polymerases_in_the_three_domains_of_life%2Flinks%2F0fcfd5087ed0867962000000.pdf&amp;amp;ei=8l4lVY3FEuu_ygOe64DwCg&amp;amp;usg=AFQjCNEyoTVu_8m3TjUxNGKQJ5B0r85PUQ&amp;amp;bvm=bv.90237346,d.bGQ&amp;amp;cad=rja&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evolution of multisubunit RNA polymerases in the three domains of life&lt;/a&gt;&#xA; I'd like to take one short quote that might help:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...The structure and function of some of these factors are conserved across the three domains, whereas some non-homologous factors show an intriguing level of structural and functional similarity, suggesting that convergent evolution has led to alternative means of facilitating the same process.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-11T09:34:23.027" LastActivityDate="2015-04-11T09:34:23.027" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31130" PostTypeId="1" AcceptedAnswerId="31132" CreationDate="2015-04-07T12:20:59.640" Score="3" ViewCount="233" Body="&lt;p&gt;Why is the malate-aspartate and the glycerol-3-phosphate shuttles located in the cytosol and intermembrane space?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The krebs cycle happens in the matrix so why wouldn't they push electrons from the matrix and into the intermembrane complex for oxidative phosphorylation??&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="3340" LastEditDate="2015-06-04T11:37:32.143" LastActivityDate="2015-06-04T11:37:32.143" Title="NADH shuttles - Why cytosol?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31131" PostTypeId="2" ParentId="31066" CreationDate="2015-04-07T13:33:38.940" Score="3" Body="&lt;p&gt;A &lt;strong&gt;microelectrode&lt;/strong&gt; is quite literally a &lt;strong&gt;small electrode&lt;/strong&gt; and they come in a variety of shapes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;glass pipette electrode&lt;/strong&gt; you are specifically referring to is mostly used for patch clamp experiments. Patch clamp experiments are performed using various configurations: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Yo6CL.gif&quot; alt=&quot;patch clamp configurations&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: &lt;a href=&quot;https://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Leica&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So basically there is the &lt;strong&gt;cell-attached&lt;/strong&gt; configuration, where a patch of cell membrane is sucked slightly into the pipette. Upon stronger suction the membrane is ruptured and the &lt;strong&gt;whole-cell&lt;/strong&gt; patch clamp configuration is obtained. Here, access is gained to the cell, but a high-impedance seal is maintained between pipette and cell membrane. Lastly, there is a configuration where the patch is broken off the cell to exclude effects of the entire cell. This patch configuration is often used to obtain single-channel recordings. Dependent on the exact technique an &lt;strong&gt;inside-out&lt;/strong&gt; or &lt;strong&gt;outside-out&lt;/strong&gt; patch configuration is reached (see the picture above).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, the glass pipette is basically only there to obtain a proper seal (cell-attached), to gain access to the cell (whole-cell), or to break off a piece of membrane. Notably, in whole-cell mode the pipette provides a means to &lt;strong&gt;administer compounds&lt;/strong&gt; into the cell (think ions or drugs).   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;recording electrode&lt;/strong&gt; is situated inside the pipette and is a simple metal wire (platinum or platinum/iridium) and nothing different from any microelectrode as you rightfully state in your question. The electrode wire simply picks up a voltage difference (or current flow) between the interior of the cell (in whole-cell mode) and the exterior. The exterior is measured using a reference electrode outside the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, current can be injected to stimulate the cell, or to current-clamp the cell at a specific current. Likewise, voltage can be applied to voltage-clamp the cell. Therefore, an inert material is often chosen such as platinum or platinum/iridium to maintain integrity and prevent electrolytic breakdown. Electrodes are made out of &lt;strong&gt;metal&lt;/strong&gt; to provide a low-resistance means to pick up currents or voltage-differences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Voltage differences or currents can be amplified with an amplifier, registered and analyzed. See the following picture for the basic recording setup: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ariaA.jpg&quot; alt=&quot;PatchClamp&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: Robinson et al. (2013)&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA; - &lt;a href=&quot;http://journal.frontiersin.org/article/10.3389/fncir.2013.00038/full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Robinson et al. &lt;em&gt;Front Neur Circuits&lt;/em&gt; 2013; &lt;strong&gt;7&lt;/strong&gt;: 1-7&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2020-02-03T08:54:07.963" LastActivityDate="2020-02-03T08:54:07.963" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="31132" PostTypeId="2" ParentId="31130" CreationDate="2015-04-07T14:27:00.310" Score="3" Body="&lt;p&gt;The electrons for shuttling are mainly generated in the cytosol from glycolysis. NADH can easily pass the outer membrane, but must be shuttled over the inner membrane. It is important to consider that the electrons must be fed to oxidative phosphorylation from the matrix of the mitochondrion, and not the intermembrane space.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/8/84/Malate-aspartate_shuttle.png/1280px-Malate-aspartate_shuttle.png&quot; alt=&quot;image&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14698" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.910" LastActivityDate="2015-04-07T14:32:36.880" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31133" PostTypeId="1" AcceptedAnswerId="31134" CreationDate="2015-04-01T15:24:32.063" Score="7" ViewCount="10731" Body="&lt;p&gt;I wonder what the difference between sinew and tendon is. I searched for it but didn't get any clear answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.quora.com/Whats-the-difference-between-sinew-and-tendon&quot; rel=&quot;noreferrer&quot;&gt;https://www.quora.com/Whats-the-difference-between-sinew-and-tendon&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;They are often used interchangably but to be technical, a tendon&#xA;  connects a muscle to a bone. The term sinew also seems to include&#xA;  ligaments which connect bones to bones. It is however, not a medical&#xA;  term.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://answers.yahoo.com/question/index?qid=20070410182936AA2Kcnk&quot; rel=&quot;noreferrer&quot;&gt;https://answers.yahoo.com/question/index?qid=20070410182936AA2Kcnk&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sinew is another word for muscle which is the functional unit of&#xA;  movement. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Tendons connect bone to muscle to make movement possible: The muscle&#xA;  contracts and pulls the bone that it's connected to Source(s)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://the-difference-between.com/tendon/sinew&quot; rel=&quot;noreferrer&quot;&gt;http://the-difference-between.com/tendon/sinew&lt;/a&gt; :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sinew is a synonym of tendon. As nouns the difference between sinew&#xA;  and tendon is that sinew is (anatomy) a cord or tendon of the body&#xA;  while tendon is (anatomy) a tough band of inelastic fibrous tissue&#xA;  that connects a muscle with its bony attachment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.thefreedictionary.com/sinew&quot; rel=&quot;noreferrer&quot;&gt;http://www.thefreedictionary.com/sinew&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;sinew = tendon&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Tendon&quot; rel=&quot;noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Tendon&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A tendon (or sinew) is a [...]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is sinew a synonym for tendon, and if not what is the difference?&lt;/p&gt;&#xA;" OwnerUserId="630" OwnerDisplayName="Franck Dernoncourt" LastEditorUserId="630" LastEditDate="2019-06-17T23:29:59.760" LastActivityDate="2019-06-17T23:29:59.760" Title="What is the difference between sinew and tendon?" Tags="&lt;terminology&gt;&lt;tendons&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31134" PostTypeId="2" ParentId="31133" CreationDate="2015-04-01T15:29:57.423" Score="9" Body="&lt;p&gt;They get used somewhat interchangeably, which blurs the lines on the definitions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I had my anatomy classes, sinews were regarded as an inclusive class, which included both ligaments and tendons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the breakdown:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Tendon: Fibrous tissue that connects muscle to bone.&lt;/li&gt;&#xA;&lt;li&gt;Ligament: Fibrous tissue that connects bone to bone.&lt;/li&gt;&#xA;&lt;li&gt;Sinew: Includes both of the above.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="15243" OwnerDisplayName="JohnP" LastActivityDate="2015-04-01T15:29:57.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31135" PostTypeId="1" AcceptedAnswerId="31136" CreationDate="2015-04-07T16:40:32.117" Score="12" ViewCount="21245" Body="&lt;p&gt;The gluconeogenesis pathway seems quite pointless to me. I don't understand why an organism would want to spend energy to create a molecule that can then be metabolized again for less energy? The pathway seems only to serve as a complete waste of energy?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone explain why we have gluconeogenesis and when it is used?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="22057" LastEditDate="2016-03-13T15:05:38.133" LastActivityDate="2016-03-13T15:05:38.133" Title="What is the purpose of gluconeogenesis?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;metabolism&gt;&lt;glucose&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31136" PostTypeId="2" ParentId="31135" CreationDate="2015-04-07T16:48:23.390" Score="12" Body="&lt;p&gt;Gluconeogenesis is not the reversal of the glycolysis, but the generation of glucose from non-carbohydrate precursors (like odd chain fatty acids and proteins). The reason why we have this process is because some organs and tissues can only use glucose as their energy source. These include the brain (although ketone bodies can be used here as well), erythrocytes, testes and the kidney medulla.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually the glucose for the supply of these tissues comes directly from carbohydrates in food or storage carbohydrates as glycogen or starch, but when these are not available, the body has another way to get around this problem and to avoid the starvation of these tissues. See for example &lt;a href=&quot;http://chemwiki.ucdavis.edu/Biological_Chemistry/Metabolism/Gluconeogenisis&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21150/&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-04-08T10:38:21.973" LastActivityDate="2015-04-08T10:38:21.973" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31137" PostTypeId="1" AcceptedAnswerId="31138" CreationDate="2015-04-07T16:58:12.757" Score="3" ViewCount="143" Body="&lt;p&gt;While searching for literature on ketone bodies, I can only seem to find how they are synthesized, but not how they are broken down.&#xA;I'm looking for the series of events with enzyme names and intermediates. Does anyone have this?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-04-08T05:29:15.430" Title="How are ketone bodies used?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;metabolism&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31138" PostTypeId="2" ParentId="31137" CreationDate="2015-04-07T17:06:40.837" Score="4" Body="&lt;p&gt;First, there are three ketone bodies: Acetone (top), acetoacetic acid (middle), and beta-hydroxybutyric acid (bottom), see the illustration from the &lt;a href=&quot;http://en.wikipedia.org/wiki/Ketone_bodies&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ARuuo.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second and the third are taken up by heart and brain cells and then converted into Acetyl-CoA which is fed into the &lt;a href=&quot;http://en.wikipedia.org/wiki/Citric_acid_cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;citric acid cycle&lt;/a&gt; where it is further metabolized. Acetone is mostly excreted. See &lt;a href=&quot;http://en.wikipedia.org/wiki/Ketone_bodies&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for some more information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aceto acetic acid is either converted into acetone and removed from the body or enzymatically converted into beta-hydroxybutyric acid by the beta-hydroxybutyrate dehydrogenase.&#xA;The third possibility is that it is converted into Acetyl-CoA. See the figure for the scheme:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/F1iJx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a more detailed explanation of this process (both, the generation and the metabolization of the ketone bodies) see &lt;a href=&quot;http://www.derangedphysiology.com/php/Acid-Base-Disturbance/ketoacidosis.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-04-08T05:29:15.430" LastActivityDate="2015-04-08T05:29:15.430" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31139" PostTypeId="1" AcceptedAnswerId="31146" CreationDate="2015-04-07T17:07:17.473" Score="5" ViewCount="2675" Body="&lt;p&gt;I precipitated bacterial RNA during 1 hour at -80ºC after depleting rRNA with Ribo-Zero kit. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does more time lead to better results?&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="4717" LastEditDate="2015-04-07T17:41:39.303" LastActivityDate="2015-04-07T23:14:17.653" Title="Time required for RNA precipitation in ethanol" Tags="&lt;rna&gt;&lt;protocol&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31140" PostTypeId="1" CreationDate="2015-04-07T17:13:39.780" Score="2" ViewCount="121" Body="&lt;p&gt;Ketone bodies are produced due to an excess of fatty acids being burned (accumulation of acetyl-CoA) so my question is: Why doesn't the body simply regulate how many fats it burns so it doesn't have to produce ketone bodies?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-04-07T17:13:39.780" Title="Why doesn't the body optimize how many fatty acids it burns?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;metabolism&gt;&lt;fat-metabolism&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31141" PostTypeId="2" ParentId="30906" CreationDate="2015-04-07T17:31:02.630" Score="1" Body="&lt;p&gt;For whether or not your assumption is correct, I have found the following (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jsfa.2740690309/abstract&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;), which states that sweetness indeed differs, as well as pH level:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The bottom sections of ‘McIntosh’ apples were sweeter; whereas the bottom sections of ‘Jonagold’ were less crisp and more fruity.&#xA;  The bottom sections of both the ‘McIntosh’ and ‘Jonagold’ apples had significantly lower pH than the top. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Fruits consist of two main parts, the pericarp and the seeds. The pericarp can be further divided into the followings: exocarp, mesocarp and endocarp. In the case of apples, the one responsible for composing most part of the fruit flesh is the mesocarp, so I would like to disregard the other two. The mesocarp consists of ground tissue almost exclusively&lt;sup&gt;[&lt;a href=&quot;http://www.degruyter.com/view/j/intag.2013.27.issue-1/v10247-012-0073-z/v10247-012-0073-z.xml&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]&lt;/sup&gt; and no vascular system, thus the only way for sugars to travel inside the flesh of fruit is diffusion, which is mostly determined by gravitation, hence the result.&lt;/p&gt;&#xA;" OwnerUserId="15051" LastEditorUserId="15051" LastEditDate="2015-04-07T17:44:32.220" LastActivityDate="2015-04-07T17:44:32.220" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31142" PostTypeId="1" AcceptedAnswerId="31150" CreationDate="2015-04-07T17:33:07.570" Score="1" ViewCount="944" Body="&lt;p&gt;We use creatine phosphate as an energy storage to resupply ADP with a phosphate group as our muscle cells only contain about 2-5 mM ATP. But why doesn't the muscle cells just keep 20-30 mM ATP instead of 20-30 mM creatine phosphate?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-04-07T23:24:17.240" Title="Why use creatine phosphate?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;metabolism&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31144" PostTypeId="1" CreationDate="2015-04-07T20:23:01.563" Score="5" ViewCount="140" Body="&lt;p&gt;I am currently working on a project where I study the change of a continuous morphological variable with body size (measured as body weight) across diverse taxa (insects, spiders, lizards, frogs). In order to account for the non-independence of the data, I built an approximate tree based on published phylogenies. I have a reasonable branching pattern down to family or genus level for most taxa, but lack statistically supported branch length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I find a strong change of the scaling coefficient when using phylogenetic least squares (with a covariance matrix based on my tree) vs a non-corrected least-squares approach, suggesting that most of the change observed in my continuous variable is explained by evolutionary history, rather than by body mass as such. I would now like to investigate how early on in the tree these shifts occur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intuitively, I could start collapsing my tree into polytomies down to arbitrary taxonomic levels, eg genus, family, order etc, and re-do my phylogenetic least squares. I would expect a stepwise approximation of the pgls to the uncorrected result (in the extreme case, I would end up with a star phylogeny, which should give an identical result to my uncorrected regression). Such an approach may allow to say something about whether most of the change occurs between genera, families etc, but it requires the use of somewhat arbitrary (and controversial) taxonomic levels. I would be grateful if someone would have an alternative suggestions on how to perform such an analysis, with arbitrary branch length and non-ultrametric trees.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&#xA;Thriceguy&lt;/p&gt;&#xA;" OwnerUserId="15247" LastActivityDate="2015-04-10T15:19:52.333" Title="Phylogenetic method to detect shift in mean of continuous variable" Tags="&lt;phylogenetics&gt;&lt;morphology&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31145" PostTypeId="2" ParentId="31082" CreationDate="2015-04-07T20:50:14.923" Score="0" Body="&lt;p&gt;So, as I pointed out in comments, and requoting:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The direction in which cargo is transported is dependent in part upon the position of the motor domain, which can be located N-terminally (N-kinesins), C-terminally (C-kinesins) or internally (M-kinesins). In general, kinesins with N-terminal motor domains move their cargo towards the plus ends of microtubules located at the cell periphery, while kinesins with C-terminal motor domains move cargo towards the minus ends of microtubules located at the nucleus.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And that was a &lt;a href=&quot;http://www.ebi.ac.uk/interpro/potm/2005_4/Page1.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;short excerpt from Jennifer McDowall on Interpro&lt;/a&gt;. And then just surveying kinesins from the mouse genome, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/l3dTs.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.nature.com/nrm/journal/v10/n10/fig_tab/nrm2774_F1.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kinesin superfamily motor proteins and intracellular transport&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of dyneins, however, I believe they're all (-)-directed motor proteins with the following general structure,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/acSai.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.nature.com/nature/journal/v484/n7394/full/nature10955.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;The 2.8 Å crystal structure of the dynein motor domain&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Keep in mind these representations are always expressed N-terminal (left) to C-terminal (right). So while your model for dyneins is correct, for kinesins this depends on the location of the motor domain.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-04-07T20:50:14.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31146" PostTypeId="2" ParentId="31139" CreationDate="2015-04-07T21:09:03.863" Score="5" Body="&lt;p&gt;As far as I know this has never been thoroughly analyzed for RNA, but there is an excellent paper on the precipitation of DNA and the usual conditions in BRL Focus by Zeugin (see below for the paper). Since DNA and RNA are pretty much the same (except for one OH-Group) and the conditions used for precipitation are also similar, I think we can use this for a very close estimate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly neither the time nor the temperature of a precipitation have a great influence on the outcome - they change the yield only by a few percent. If you look on figure 2 from the paper mentioned, you see the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TXB1S.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This subfigure shows that the recovery is almost not influenced by the temperature, but only by the conconcentration of the DNA (or RNA). Depending on how much RNA you expect (how much cells did you use for the isolation) I would add a co-precipitation agent when you have only very small amounts on RNA. Glycogen works very well here. Otherwise I wouldn't worry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NK8eh.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This figure shows that the incubation time has only an influence on the percentage of the recovery when then time is too short. If you incubate for an hour, you are on the safe side.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.lifetechnologies.com/content/dam/LifeTech/migration/en/filelibrary/pdf/focus.par.56415.file.dat/focus%20volume%207%20issue%204.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ethanol Precipitation of DNA.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-04-07T21:09:03.863" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31148" PostTypeId="2" ParentId="31139" CreationDate="2015-04-07T23:14:17.653" Score="0" Body="&lt;p&gt;As many kits suggest, RNA concentration has the most profound influence on precipitation efficiency / recovery fraction. Time, temperature and precipitation agent concentration has lesser effect. See for example instruction by Life Technologies on LiCl precipitation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.lifetechnologies.com/us/en/home/references/ambion-tech-support/rna-isolation/general-articles/the-use-of-licl-precipitation-for-rna-purification.html&quot; rel=&quot;nofollow&quot;&gt;The Use of LiCl Precipitation for RNA Purification&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-07T23:14:17.653" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31149" PostTypeId="1" AcceptedAnswerId="36775" CreationDate="2015-04-07T23:16:47.470" Score="10" ViewCount="165" Body="&lt;p&gt;So, the HIV-1 jump to humans occurred as early as the 1920s, but the AIDS epidemic didn't start until the early 1980s.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some things I don't understand about this:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why the delay?&lt;/li&gt;&#xA;&lt;li&gt;What is needed for a successful zoonosis transmission in the first place?&lt;/li&gt;&#xA;&lt;li&gt;If Bushmeat practices (eating meat from non-domesticated animals, in this case HIV-infected fruit bats) have been the same for centuries, why has HIV only really spread in THIS century?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11626" LastActivityDate="2015-09-11T14:38:54.163" Title="Reasons for the HIV-1 epidemic" Tags="&lt;microbiology&gt;&lt;epidemiology&gt;&lt;hiv&gt;&lt;aids&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31150" PostTypeId="2" ParentId="31142" CreationDate="2015-04-07T23:24:17.240" Score="2" Body="&lt;p&gt;Because all available ATP will likely be quickly spent by various cellular machinery.&#xA;If there was 20-30mM of ATP, what would stop muscle from contraction and how could you keep ATP level constant at rest, be ready for rapid movement? By blocking all myosin? This creates enormous regulatory problems for the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phosphocreatine buffers energy for a period of time when it will be actually needed. Having buffer allows for more robust control of energy spending, for example via regulation creatine kinases and other enzymes. Just by activating single enzyme you then start rapid conversion of ADT into ATP via phosphocreatine.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-07T23:24:17.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31152" PostTypeId="2" ParentId="31124" CreationDate="2015-04-08T03:22:33.953" Score="1" Body="&lt;p&gt;I'd suggest reading &lt;a href=&quot;http://en.wikipedia.org/wiki/Gastric_acid#Regulation_of_secretion&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt; first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Autonomic nervous system, the one that regulates breathing rate, heart rate and other physiological processes as a function of circadian time, regulates secretion of gastric acid. Vagus nerve, part of parasympathetic nervous system (the one responsible for &quot;rest and digest&quot; part of behavior, opposite to sympathetic &quot;fight or flight&quot;) stimulates secretion of gastric acid and regulated through circadian mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also here, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24305819&quot; rel=&quot;nofollow&quot;&gt;Circadian variation in gastric vagal afferent mechanosensitivity&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Thus, gastric vagal mechanoreceptors display circadian rhythm, which may act to control food intake differentially at different times of the day.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is another interesting review: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21673361&quot; rel=&quot;nofollow&quot;&gt;Gut clock: implication of circadian rhythms in the gastrointestinal tract&lt;/a&gt;. It states that GI tract has its segments set their own circadian clocks, different for various segments. But all of them are operating and adjusted by main clock, regulated by, as I know, melatonin and orexin hormones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Surprisingly, not much seems to be known about this connection. Pineal gland seems to be very important in this process, because it produces melatonin.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-04-08T03:38:22.590" LastActivityDate="2015-04-08T03:38:22.590" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31153" PostTypeId="1" CreationDate="2015-04-08T06:27:54.203" Score="1" ViewCount="116" Body="&lt;p&gt;I am trying to study for a biology and I am having some confusion over the following topic. Can anyone help explain/ shed some light on the concepts of Rho family GTPases. Is it true that we have Rho activates forimins to relieve  auto inhibition of actin filaments while Rac promotes lamellopodia and Cdc42 works on the leading edge and fillipodia?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, how are the microtubules involved in cytoskeleton coordination? Do they simply affect Rho and Rac concentrations. How else is the concentrations of these spread throughout the cell as to maintain distinct concentration gradients?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you all for any help!&lt;/p&gt;&#xA;" OwnerUserId="15066" LastEditorUserId="15066" LastEditDate="2015-04-08T15:04:29.480" LastActivityDate="2015-04-08T15:04:29.480" Title="Question about cytoskeleton coordination" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;proteins&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31155" PostTypeId="1" CreationDate="2015-04-08T06:43:44.563" Score="2" ViewCount="1249" Body="&lt;p&gt;&lt;em&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Pilobolus&quot; rel=&quot;nofollow&quot;&gt;Pilobolus&lt;/a&gt;&lt;/em&gt; is a fungal genus whose fruiting bodies consist of a stalk ending in a spore mass that is launched via turgor pressure to disperse the spores.  The fruiting bodies grow towards light, which ultimately influences the direction in which the spores are launched.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that gravity-directed growth would be sufficient to ensure an upward trajectory, so I'm wondering what the value is of phototropism.  Has this been studied at all?&lt;/p&gt;&#xA;" OwnerUserId="11657" LastActivityDate="2016-02-15T22:20:59.133" Title="Why is Pilobolus phototropic?" Tags="&lt;mycology&gt;&lt;adaptation&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31156" PostTypeId="1" CreationDate="2015-04-08T07:17:21.910" Score="0" ViewCount="129" Body="&lt;p&gt;Adults and elder children can use HIV rapid test to test HIV infection. Can we use the HIV antibody test to detect HIV in newborns too?&lt;/p&gt;&#xA;" OwnerUserId="15251" LastActivityDate="2015-04-08T10:43:57.380" Title="Can we use the HIV antibody test to detect HIV in newborns?" Tags="&lt;antibody&gt;&lt;hiv&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-04-09T00:39:36.037" ContentLicense="CC BY-SA 3.0" />
  <row Id="31159" PostTypeId="2" ParentId="31156" CreationDate="2015-04-08T07:40:43.810" Score="3" Body="&lt;p&gt;The rapid screen usually tests the oral mucosa by swabing the inside of the cheek and checking for the presence of anti-HIV envelope antibodies. Although the precise target of these antibodies seems to be kept propriatary, my guess would be the detection of either p24 antibodies or envelope antibodies that bind the V3 region. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regardless, the point is they test for the presence of antibodies, which a child does not start making until they are born. &lt;a href=&quot;https://biology.stackexchange.com/questions/5782/at-what-age-do-babies-begin-to-synthesize-their-own-antibodies&quot;&gt;See this post for a great explanation&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since a child has mostly maternal antibodies, the presence of anti-HIV antibodies would only mean that the mother has started producing antibodies to HIV (&lt;a href=&quot;http://en.wikipedia.org/wiki/Seroconversion&quot; rel=&quot;nofollow noreferrer&quot;&gt;Seroconversion&lt;/a&gt;). This means that although the child has been exposed, they may themselves not be infected. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mucosa, particularly in the oral region has a very low titer of anti-HIV antibodies, so I think this test would probably be best to direct the physician to conduct additional tests that are more indicative of HIV infection like &lt;a href=&quot;http://www.cdc.gov/mmwr/preview/mmwrhtml/00001431.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;p24 western blot&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3887" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-04-08T10:43:57.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31161" PostTypeId="1" AcceptedAnswerId="31163" CreationDate="2015-04-08T08:24:07.373" Score="0" ViewCount="211" Body="&lt;p&gt;I now have some data on the RNA seq counts and related Hi-C matrix of gene segment on a chromosome. My concern is, basically, what can we do with these data so as to establish the connection between the two types of data such as the level of expression of gene segment and the interaction of the gene segment, since it seems that they are correlated. Thanks&lt;/p&gt;&#xA;" OwnerUserId="15252" LastActivityDate="2015-04-08T18:08:28.823" Title="What pattern can be learned from the data of RNA seq counts and HiC matrix?" Tags="&lt;gene-expression&gt;&lt;chromosome&gt;&lt;rna-sequencing&gt;&lt;network&gt;&lt;biological-networks&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ClosedDate="2015-04-08T14:54:34.037" ContentLicense="CC BY-SA 3.0" />
  <row Id="31162" PostTypeId="1" AcceptedAnswerId="31173" CreationDate="2015-04-08T08:45:42.527" Score="3" ViewCount="5386" Body="&lt;p&gt;In a city, 4% of male population have color blindness. How many of the female are (a) color blind carrier, (b) color blind? Suppose the city holds Hardy Weinberg equilibrium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My progress: 4% of male have color blind =&gt; $p=F(cb~allele)=0.04$ and therefore $q=F(not~cb)=0.96$. Since HW equilibrium stand, we get the allele frequency among female is the same as among male. Then (a) $2pq=2*0.04*0.96=0.0768=7.68\%$ and (b) $q^2=0.9216=92.16\%$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I correct?&lt;/p&gt;&#xA;" OwnerUserId="15254" LastEditorUserId="14826" LastEditDate="2015-04-08T17:55:29.647" LastActivityDate="2015-04-08T17:55:29.647" Title="Hardy-Weinberg Color-blind" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;hardy-weinberg&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31163" PostTypeId="2" ParentId="31161" CreationDate="2015-04-08T09:38:14.290" Score="1" Body="&lt;p&gt;This seems to me to be two independent pieces of data. mRNA seq allows one (in case of linear amplification) to quantify message RNA transcripts of genes of interest. that is, how many copies of mRNA for given gene are in the cell at the moment. It is ultimately, how active this gene is. In neurons different genes will be more active, than in epithelial cells, and vice versa. Genetic expression pattern provides identity of the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hi-C method, closely related to &lt;a href=&quot;http://en.wikipedia.org/wiki/Chromosome_conformation_capture&quot; rel=&quot;nofollow&quot;&gt;chromosome conformation capture&lt;/a&gt; answers question: what genes are physically interact in the nucleus via stabilizing proteins (e.g. enhcancers). There is more &lt;a href=&quot;http://www.jove.com/video/1869/hi-c-a-method-to-study-the-three-dimensional-architecture-of-genomes&quot; rel=&quot;nofollow&quot;&gt;in the video&lt;/a&gt;, but general idea is that it allows you to see how genes positioned inside intricate chromatin. Since many genetic elements might physically interact via, for example, enhancers, 3C/Hi-C allows detection of such interactions. Or, at least, quantification of correlation between physical positions of two genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the only direct connection between mRNA seq and Hi-C that I can draw is following logic: actively transcribed genes are located in expanded, less tense regions of chromatin. Hence, it will be hard to crosslink genes in such regions and correlation going to be low. Silent genes, &lt;em&gt;if they are located closely in nucleus&lt;/em&gt; will be cross-linked with high probability, because chromatin is denser around non-transcribed genes.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-04-08T18:08:28.823" LastActivityDate="2015-04-08T18:08:28.823" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31164" PostTypeId="2" ParentId="31055" CreationDate="2015-04-08T10:08:53.063" Score="0" Body="&lt;p&gt;Reference genomes do not accurately represent the set of genes of any single person.it is created by fragments of various donors, which when built,is used as a template for creating the real genome. Though we will find All humans are 99.9 per cent identical and, of that tiny 0.1 per cent difference the reference genome might not be 100% identical to the real genome.Every reference genome con be sequenced again and the gaps can be reduced each time. We can reach a point where we can say that the accuracy is high enough to be used as a reference platform for constructing the real genome   &lt;/p&gt;&#xA;" OwnerUserId="8026" LastActivityDate="2015-04-08T10:08:53.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31165" PostTypeId="2" ParentId="30968" CreationDate="2015-04-08T10:21:50.980" Score="0" Body="&lt;p&gt;take the gene names and copy all of them, next open an online tool called gene mania. paste all your genes on the window. you will get their interaction and other related genes.&#xA;Now go to a database called gene cards and type in all the gene you got from gene mania and paste it one after the other to get useful information about the individual genes. some of which are restriction site information's, transcription factors etc.&lt;/p&gt;&#xA;" OwnerUserId="8026" LastActivityDate="2015-04-08T10:21:50.980" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31167" PostTypeId="1" AcceptedAnswerId="31181" CreationDate="2015-04-08T12:25:05.487" Score="2" ViewCount="657" Body="&lt;p&gt;I am looking at the following question&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If $m$ alleles may occur at a given locus, how many distinct diploid genotypes are possible at that locus?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The obvious answer is that there their is $m$ possible paternal alleles and $m$ possible maternal alleles so the solution is $m^2$. However this considers inheriting allele $a$ maternally and allele $A$ paternally as the same as inheriting $a$ paternally and $A$ maternally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If they are considered distinct we have double counted all matchings apart from matchings where the same allele is inherited maternally and paternally so I think the answer to the question if $Aa$ is the same as $aA$ would be $\frac{m(m-1)}{2}+m$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is which if any of my interpretations is correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance&lt;/p&gt;&#xA;" OwnerUserId="9482" LastEditorUserId="3624" LastEditDate="2015-04-08T22:51:59.077" LastActivityDate="2015-04-09T17:11:59.510" Title="Are genotypes with the same two alleles equivalent even if the alleles come from different parents?" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31170" PostTypeId="1" AcceptedAnswerId="31180" CreationDate="2015-04-08T14:37:33.983" Score="1" ViewCount="5526" Body="&lt;p&gt;As far as I understand, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Primary_motor_cortex&quot; rel=&quot;nofollow&quot;&gt;primary motor cortex&lt;/a&gt; (M1) and primary sensorimotor (SM1) are notations for the same cortical area in the brain. Am I right that there &lt;em&gt;is no&lt;/em&gt; dedicated motor cortex, and that M1 actually processes both sensation and movement functions? &lt;/p&gt;&#xA;" OwnerUserId="4206" LastEditorUserId="9943" LastEditDate="2015-04-09T04:25:48.323" LastActivityDate="2015-04-09T12:35:27.960" Title="Is the motor cortex identical to the sensorimotor cortex?" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;terminology&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31171" PostTypeId="2" ParentId="31059" CreationDate="2015-04-08T15:03:18.837" Score="2" Body="&lt;p&gt;The &lt;strong&gt;frequency limen&lt;/strong&gt;, or &lt;strong&gt;frequency resolution&lt;/strong&gt; can be determined in various ways using &lt;em&gt;psychophysical measures&lt;/em&gt;. You refer to a simultaneous method, in which two (or more) frequencies are presented at the same time. This has consequences for the test as different frequencies are perceived with different perceived loudness under constant sound pressure levels, meaning that additional cues are present besides pitch cues. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One carefully controlled study &lt;a href=&quot;http://www.ee.columbia.edu/~dpwe/e6820/papers/ZwicFS57-crband.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Zwicker et al (1957)&lt;/a&gt; in this regard defined the &lt;strong&gt;critical band&lt;/strong&gt; basically as &quot;&lt;em&gt;those frequencies where no intensity summation occurs&lt;/em&gt;&quot;, meaning that adding those frequencies (below or above the center frequency) do not result in differences in loudness perception (as expressed in &lt;em&gt;acoustic threshold&lt;/em&gt; of the center frequency). This method nicely prevents loudness summation cues by deploying them in the criterion. This article shows the following picture (after &lt;a href=&quot;http://www.ee.columbia.edu/~dpwe/e6820/papers/ZwicFS57-crband.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Zwicker et al. (1957)&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IVYT8.png&quot; alt=&quot;Difference limen&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;critical band&lt;/strong&gt; (upper graph) is dependent on frequency, and ranges from 0.1 kHz to &gt;2 kHz. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The markedly lower difference limen of 3.6 Hz as touched upon in the comments may have been obtained using an alternative psychophysical test where the test frequency is &lt;strong&gt;modulated&lt;/strong&gt; by another frequency (bottom graph). This procedure is based on adding a frequency to a certain sinusoidal stimulus, basically resulting in a single stimulus instead of two (or more). This procedure is technically not defined as a critical band and indeed results in a difference limen of ~3.5 hz and up. The other graph plotted in the figure is a &lt;strong&gt;masking procedure&lt;/strong&gt; (middle plot), which basically determines the physiological overlap between frequencies in the cochlea in the intensity domain by determining the amount of masking from one frequency by another. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;NB: The authors worked with headphones so no effects of direction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ee.columbia.edu/~dpwe/e6820/papers/ZwicFS57-crband.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Zwicker et al. &lt;em&gt;JASA&lt;/em&gt; 1957; &lt;strong&gt;29&lt;/strong&gt;: 548-57&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-04-09T00:19:24.593" LastActivityDate="2015-04-09T00:19:24.593" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31173" PostTypeId="2" ParentId="31162" CreationDate="2015-04-08T16:48:14.283" Score="3" Body="&lt;p&gt;A: wild-type allele / a: color blind allele&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because color blindness is recessive and X-linked your assumption $p=F(a)=4\%$ is correct as men do only have one copy of the allele. Subsequently $F(A)=q=1-p=0.96$ is also correct. Therefore:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) $F(Aa)=2pq=7.68\%$ is correct and b) is wrong, a is the color blind allele and $F(a)=0.04$ therefore it's $p^2=0.04^2=0.0016=0.16\%$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;92% color blind among females seems a bit high :).&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-04-08T16:54:34.343" LastActivityDate="2015-04-08T16:54:34.343" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31177" PostTypeId="1" CreationDate="2015-04-08T18:40:03.063" Score="-1" ViewCount="416" Body="&lt;p&gt;It's been a while since my last class in genetics, so I've forgot most of it. However, I found myself studying human reproduction and I've the following doubt concerning spermatogenesis: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;the process begins with a spermatogonium, a diploid cell (i.e. it contains 23 chromosomes and the corresponding homologous), which, through mitosis, generates the primary spermatocytes. The latter undergoes meiosis generating the two secondary spermatocytes; these are haploid, one of them contains 23 chromosomes and the other the corresponding homologous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since a chromosome A and its homologous B contain the same genes but with (generally) different alleles, the two secondary spermatocites have different genomes. Now, each of them splits into two equal cells (spermatids), through mitosis. My textbook says that the four spermatids have all different genomes, but shouldn't there be only two genomes?&lt;/p&gt;&#xA;" OwnerUserId="15264" LastActivityDate="2019-09-02T11:02:15.310" Title="Why do four spermatids have different genomes?" Tags="&lt;reproduction&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31178" PostTypeId="1" AcceptedAnswerId="31183" CreationDate="2015-04-08T23:01:57.337" Score="1" ViewCount="48" Body="&lt;p&gt;In my text book there is an example of a 18 carbon long fat and it says that it can run 8 laps of oxidation. I don't understand why it doesn't run 9? 2 are removed each cycle?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="3340" LastEditDate="2015-06-04T11:36:44.183" LastActivityDate="2015-06-04T11:36:44.183" Title="Beta oxidation of saturated fats" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;metabolism&gt;&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31179" PostTypeId="2" ParentId="1375" CreationDate="2015-04-08T23:06:41.610" Score="5" Body="&lt;p&gt;Following your answer to my comment, I deduced the “yellow” color to be more brownish as there is not big bird with really bright yellow color (like the golden oriole). &#xA; With these parameters I search as well in the ornitho.ch database (all observations given by ornithologist professionals and amateurs) : there was no observation of vulture or eagle in that area (could be possible sometime when they migrate).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then the more possible answer was a &lt;a href=&quot;http://www.vogelwarte.ch/en/birds/birds-of-switzerland/red-kite.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;red kite&lt;/a&gt; which is quite common summer time in this area (mainly on the north part of Switzerland). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/qEdy4.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/qEdy4.jpg&quot; alt=&quot;RedKite&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next time you see a bird of prey, try to take notice of the tail form (forked or flat or round) that can help more for determining the bird.&lt;/p&gt;&#xA;" OwnerUserId="6561" LastEditorUserId="6561" LastEditDate="2020-01-27T23:44:47.923" LastActivityDate="2020-01-27T23:44:47.923" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="31180" PostTypeId="2" ParentId="31170" CreationDate="2015-04-08T23:57:52.363" Score="1" Body="&lt;p&gt;The &lt;strong&gt;primary somatosensory&lt;/strong&gt; and &lt;strong&gt;primary motor cortices&lt;/strong&gt; are &lt;em&gt;distinct&lt;/em&gt; cortical areas. According to the structural classification of Brodmann, the primary somatosensory cortex is referred to as Brodmann's areas 1,2 and 3 (BA1, BA2 and BA3). The primary motor cortex is referred to as Brodmann's area 4 (BA4). The primary sensory cortex is sometimes denoted by S1, and primary motor cortex by M1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FMr9p.jpg&quot; alt=&quot;Cortex&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: &lt;a href=&quot;http://mybrainnotes.com/memory-language-brain.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;My Brain Notes&lt;/a&gt;&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The primary somatosensory cortex is concerned with the processing of somatosensory &lt;strong&gt;input&lt;/strong&gt;, such as tactile stimuli coming from the skin. The motor cortex is concerned with executing movements and hence with motor &lt;strong&gt;output&lt;/strong&gt;. As such, there is a functional as well as structural distinction between the two areas.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within the primary somatosensory cortex, basic processing of somatosensory information takes place in BA3, while more advanced processing takes place in BA1 and 2. Neurons in the somatosensory cortex project to adjacent regions, including the motor cortex &lt;a href=&quot;http://www.mhprofessional.com/product.php?isbn=0071390111&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Kendal et al., 2000)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the primary sensory and motor cortices are four strips of cortex closely situated together, and because they are functionally coupled at the physiological level, they are sometimes collectively referred to as the sensorimotor cortex. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.mhprofessional.com/product.php?isbn=0071390111&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kendal et al. 2000. Principles of Neural Science&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-04-09T12:35:27.960" LastActivityDate="2015-04-09T12:35:27.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31181" PostTypeId="2" ParentId="31167" CreationDate="2015-04-09T00:11:17.013" Score="2" Body="&lt;p&gt;If you have &lt;a href=&quot;http://en.wikipedia.org/wiki/Genomic_imprinting&quot; rel=&quot;nofollow&quot;&gt;genomic imprinting&lt;/a&gt; then $k^n=m^2$ (with k=m and n=2 because of diploidy) is correct as inheriting a from the father and b from the mother (i.e. ab) is not equivalent to inheriting b from the father and a from the mother (i.e. ba). For 3 alleles (a,b,c) you have 9 possible genotypes (aa,ab,ac,ba,bb,bc,ca,cb,cc).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under no genomic imprinting, ab and ba are equivalent. This is equivalent of calculating the number of elements of a triangular matrix which is $\frac{(m+1)*m}{2}$. So for m=3, you have 6 possible genotypes (aa,ab,ac,bb,bc,cc), for m=4 you have 10 possibilities (aa,ab,ac,ad,bb,bc,bd,cc,cd,dd) etc...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps. Your formula is actually equivalent.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-04-09T17:11:59.510" LastActivityDate="2015-04-09T17:11:59.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31182" PostTypeId="1" AcceptedAnswerId="31184" CreationDate="2015-04-09T02:12:33.107" Score="7" ViewCount="4500" Body="&lt;p&gt;Are there specific chemicals responsible for producing the strong, putrid odor that is present after an animal deceases? Also, how long does this odor last? &lt;/p&gt;&#xA;" OwnerUserId="12959" LastEditorUserId="9943" LastEditDate="2016-03-15T14:12:34.983" LastActivityDate="2016-03-15T14:12:34.983" Title="What produces the strong odor of decaying dead animals?" Tags="&lt;zoology&gt;&lt;death&gt;&lt;biochemistry&gt;&lt;olfaction&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31183" PostTypeId="2" ParentId="31178" CreationDate="2015-04-09T02:38:14.837" Score="1" Body="&lt;p&gt;I believe your textbook is referring to the fact that you only perform the &lt;em&gt;complete&lt;/em&gt; beta oxidation eight times.  Because there's a carboxylic acid at the terminus of a fatty acid chain, the cell takes a slightly different route and reacts it with ATP, which generates a fatty acyl adenylate and pyrophosphate (PPi).  This AMP can subsequently be displaced in an attack by CoASH, at which point the beta oxidation process can proceed in full to begin cleaving off acetyl-CoA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a &lt;a href=&quot;http://oregonstate.edu/dept/biochem/hhmi/hhmiclasses/biochem/figsch18/fig18p14.html&quot; rel=&quot;nofollow&quot;&gt;visual representation&lt;/a&gt; of this activation process, too.&lt;/p&gt;&#xA;" OwnerUserId="12886" LastActivityDate="2015-04-09T02:38:14.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31184" PostTypeId="2" ParentId="31182" CreationDate="2015-04-09T02:51:43.603" Score="11" Body="&lt;p&gt;Two compounds are specifically associated with the smell of decaying cadavers (&lt;a href=&quot;http://www.pawsoflife.org/Library/HRD/Hoffman_2009.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hoffman et al., 2009&lt;/a&gt;), namely: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;1,5-pentanediamine&lt;/em&gt; (&lt;strong&gt;cadaverine&lt;/strong&gt;), and &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;1,4-butanediamine&lt;/em&gt; (&lt;strong&gt;putrescine&lt;/strong&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Cadaverine is produced by breakdown of lysin and putrescine by the breakdown of ornithine (&lt;a href=&quot;http://ciencia.me/quimica-dos-fedores-mal-cheiro-quimica/?lang=en&quot; rel=&quot;nofollow noreferrer&quot;&gt;Science ME&lt;/a&gt;). Both are nitrogen-rich compounds and particularly pungent-smelling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IplDp.png&quot; alt=&quot;structures&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: &lt;a href=&quot;http://ciencia.me/quimica-dos-fedores-mal-cheiro-quimica/?lang=en&quot; rel=&quot;nofollow noreferrer&quot;&gt;Science ME&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both compounds are also responsible, in part, for the smell of bodily fluids such as urine and semen, smell of rancid butter, bad breath and stinky cheeses (&lt;a href=&quot;http://ciencia.me/quimica-dos-fedores-mal-cheiro-quimica/?lang=en&quot; rel=&quot;nofollow noreferrer&quot;&gt;Science ME&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://forensicsciencecentral.co.uk/decomposition.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;Forensic Science Central UK&lt;/a&gt; mentions that after death, the body begins to decay after about 5-11 days (after an initial phase of bloating). The putrid smells subside mostly after 10-24 days, although a rancid cheesy smell might persist due to butyric acid. Note that many factors will affect decomposition rates and will affect this time course. Moreover, trained police dogs may be able to sniff out minute amounts of putrescine and cadaverine long after humans cannot detect it anymore. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that, given the complex composition of animals and the complexity of the decomposition process, a host of volatile organic components are released during decomposition besides putrescine and cadaverine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.pawsoflife.org/Library/HRD/Hoffman_2009.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hoffman et al. &lt;em&gt;Forensic Science International&lt;/em&gt; 2009; &lt;strong&gt;186&lt;/strong&gt;: 6-13&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-03-15T14:12:18.850" LastActivityDate="2016-03-15T14:12:18.850" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31185" PostTypeId="2" ParentId="28265" CreationDate="2015-04-09T02:53:59.587" Score="2" Body="&lt;p&gt;You definitely need to have the same threshold for both images because you want to make comparison between them. Do you have a control condition (the condition which is not supposed to uptake EdU)? if yes, then use it to set your threshold and keep the same threshold for the tests conditions. If not, you can either make a experiment control, or select a region of interest (ROI) in one of your 2 tests where there is no coloration (no uptaking of EdU) and set the threshold in this ROI. &#xA;Cheers&lt;/p&gt;&#xA;" OwnerUserId="15266" LastActivityDate="2015-04-09T02:53:59.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31186" PostTypeId="1" CreationDate="2015-04-09T03:35:21.313" Score="4" ViewCount="226" Body="&lt;p&gt;It does not seem possible that these two processes can coexist: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Genetic imprinting is the phenomenon where genes are expressed differently depending on the parent of origin: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1a. Methylated stretches of DNA are not transcribed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1b. If the gene copy originating with mom is methylated but dad's copy is not, then only dad's copy will be expressed (e.g. Prader Willi syndrome).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1c. Methylation is preserved during cell divisions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1d. Methylation is wiped at gametogenesis, when females will erase dad's imprints and re-imprint according to maternal imprint before meiosis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But now I'm reading about the role of epigenetics in cell differentiation, and I discover:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Cell differentiation occurs with lineage-specific patterns of methylation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2a. Immediately after fertilization (prior to the first cell division), the paternal genome undergoes demethylation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2b. The maternal genome undergoes demethylation during the first few cell divisions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2c. Cell differentiation is accompanied and perhaps even accomplished by progressive re-methylation following these &quot;wipes.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source for 2): &lt;a href=&quot;http://labs.genetics.ucla.edu/fan/papers/HuangK_RM2010.pdf&quot; rel=&quot;nofollow&quot;&gt;http://labs.genetics.ucla.edu/fan/papers/HuangK_RM2010.pdf&lt;/a&gt; &#xA;&quot;DNA methylation in cell differentiation and reprogramming: an emerging systematic view&quot; Huang &amp;amp; Fan (2010). Regen Med. 5(4):531-44.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect that there is no conflict and I merely misunderstand one, the other, or both. Otherwise, how can a pattern of methylation be wiped both during gametogenesis and early embryonic stages and still be inherited? &lt;/p&gt;&#xA;" OwnerUserId="15268" LastEditorUserId="5144" LastEditDate="2015-05-09T11:59:39.860" LastActivityDate="2015-08-07T17:39:40.447" Title="Genetic Imprinting and Cell differentiation" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;epigenetics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31188" PostTypeId="2" ParentId="10466" CreationDate="2015-04-09T06:12:05.183" Score="1" Body="&lt;p&gt;The most common IV drip that would be sent home with a pet owner is Ringer's solution. This fluid is also commonly injected as a subcutaneous (between muscle and skin) bolus into both cats and dogs. Although IV administration is more efficient, this fluid is completely harmless if an IV catheter were dislodged allowing it to accumulate in the surrounding tissue. &lt;/p&gt;&#xA;" OwnerUserId="15271" LastActivityDate="2015-04-09T06:12:05.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31189" PostTypeId="1" CreationDate="2015-04-09T06:13:32.940" Score="2" ViewCount="1525" Body="&lt;p&gt;I have got the IC50 data for a drug on different cell lines. How to define if the cell line is sensitive or resistant towards this drug?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could anyone tell me how to define this?&lt;/p&gt;&#xA;" OwnerUserId="15265" LastEditorUserId="14826" LastEditDate="2015-04-09T20:28:59.273" LastActivityDate="2015-04-09T20:38:17.607" Title="How to define drug-resistant or -sensitive cell line when knowing the IC50 values?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31190" PostTypeId="1" CreationDate="2015-04-09T08:42:38.950" Score="3" ViewCount="62" Body="&lt;p&gt;For a prep exam: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A healtly pacient has a carotid with the following characteristics:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;intern ratio: = 2.8 mm, &#xA;2 = 89 , &#xA;1 = 90 ,&#xA; blood = 3.5 cp,&#xA;=10.0 cm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using the following equations calculate:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$V(r)=\frac{P_1 - P_2}{4 \mu L}R^2 [1-(\frac{r}{R})^2]$$&#xA;$$V_{max}= V(r=0)$$&#xA;$$\overline{V} = \frac{Q}{A}=\frac{1}{2}V_{max}$$&#xA;$$Q=\frac{\pi(P_1 - P_2)}{8 \mu L}R^4$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where P_1 and P_2 are the mean pressure to in and out the vase, R is ve vase radius, L is the length of the vase segment and $\mu$ is the viscosity of the fluid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A healthy patient has a carotid withe the following characteristics: intern radius R = 2.8 mm, $P_2$ = 89 mmHg, $P_1$ = 90 mmHg, $\mu_{blood}$=3.5cp, L = 10cm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using the previous equations calculate:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) Mean velocity on the carotid artery Rta: 0.372 m/s&#xA;b) Maximum velocity Rta: 0.744 m/s&#xA;c) caudal on the carotid artery Rta: $9.16x10^{-6} m^{-6}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried to solve this problem but when i try to replace changing the units to the adecuate I have not the correct answer&lt;/p&gt;&#xA;" OwnerUserId="15274" LastEditorUserId="3624" LastEditDate="2015-04-09T20:50:39.593" LastActivityDate="2015-04-09T20:50:39.593" Title="Blood as newtonian flow and Poiseuille law" Tags="&lt;physiology&gt;&lt;homework&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2015-04-10T07:33:36.880" ContentLicense="CC BY-SA 3.0" />
  <row Id="31191" PostTypeId="1" AcceptedAnswerId="31193" CreationDate="2015-04-09T09:42:12.540" Score="8" ViewCount="1310" Body="&lt;p&gt;Recently a little insect crawled over the carpet. First I did not notice, as its appearance is quite similar to the coloring of the carpet. Then I understood that it is not a rolling crumble, as the window and the door were closed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I took it on an ordinary sheet of DIN A4 paper, but have not the slightest idea, what kind of insect it is. It makes the impression to have taken a shower of water and dust in a row.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What's that insect called?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second photo gives an idea of the size, as it shows a drinking glass turned upside down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Note:&lt;/em&gt; The place this insect was encountered is in eastern Germany&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/n0zF7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MGkYs.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user15275" LastEditorDisplayName="user15275" LastEditDate="2015-04-09T09:54:36.020" LastActivityDate="2015-04-09T13:02:51.247" Title="Identifying an insect looking like a crumle" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2017-06-20T09:02:08.367" ContentLicense="CC BY-SA 3.0" />
  <row Id="31192" PostTypeId="1" AcceptedAnswerId="31195" CreationDate="2015-04-09T09:44:02.520" Score="6" ViewCount="75" Body="&lt;p&gt;In light-harvesting complexes, how is the energy of a photon transferred from one pigment molecule to another? And in reaction-center complexes, how does the primary electron acceptor capture an electron from the chlorophyll &lt;em&gt;a&lt;/em&gt;? It’d be best if any of you could explain this to me in terms of what’s happening at the molecular or atomic level, say with electrons.&lt;/p&gt;&#xA;" OwnerUserId="15272" LastEditorUserId="5144" LastEditDate="2015-04-09T09:46:06.083" LastActivityDate="2015-04-09T10:12:32.950" Title="What Goes on in Photosystems at the Molecular/Atomic Level?" Tags="&lt;biochemistry&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31193" PostTypeId="2" ParentId="31191" CreationDate="2015-04-09T09:54:14.657" Score="13" Body="&lt;p&gt;Looks like the nymph of a &lt;a href=&quot;http://en.wikipedia.org/wiki/Reduvius_personatus&quot; rel=&quot;noreferrer&quot;&gt;masked hunter&lt;/a&gt;.&#xA;They carmouflage in dust and sand.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/7/75/Reduvius_personatus,_Masked_Hunter_Bug_nymph_camouflaged_with_sand_grains.JPG&quot; alt=&quot;&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="15257" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-09T13:02:51.247" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31194" PostTypeId="1" CreationDate="2015-04-09T10:11:30.080" Score="2" ViewCount="55" Body="&lt;p&gt;I know that there are certain diseases that are predominant on genes. But, is there any sort of surety that if parents are suffering from a disorder then their offspring has to suffer from the same. Like my dad is schizophrenic so will I become the victim of the same mental disorder?  &lt;/p&gt;&#xA;" OwnerUserId="15270" LastActivityDate="2015-04-09T11:05:55.990" Title="Do The Traces Genetic Diseases Remain in families?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;molecular-evolution&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31195" PostTypeId="2" ParentId="31192" CreationDate="2015-04-09T10:12:32.950" Score="5" Body="&lt;p&gt;The energy transfer is achieved by a process called &quot;resonance energy transfer&quot;. It needs the positioning of the donor and the acceptor in very close proximity to each other - the light harvesting complexes are optimized for this. This allows the collection of small amounts of light energy and still enables photosynthesis. The figure shows how this works schematically:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iSzPt.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The figure is from this &lt;a href=&quot;http://employees.csbsju.edu/hjakubowski/classes/ch331/oxphos/olphotsynthesis.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;webpage&lt;/a&gt;, which gives a good introduction.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-04-09T10:12:32.950" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31197" PostTypeId="2" ParentId="31186" CreationDate="2015-04-09T10:53:26.173" Score="1" Body="&lt;p&gt;What if imprinted regions are immune to being wiped? Also, you may be confusing DNA methylation, and histone methylation (?). Classical biochemistry posits that DNA methylation states can be transmitted from a dividing mother cell to both daughter cells because after DNA replication the two daughter chromosomes will each be hemi-methylated, and a DNA methylase that finds a hemi-methylated site will methylate the other strand (like a corrective editing mechanism).&#xA;The third thing to consider in your question is that parental imprinting is established in the germ line. In terms of wiping other epigenetic marks during early embryogenesis, the only ones present would be the ones involved in gametogenesis.  In other words, as far as we know, genes activated in muscle development are never expressed after fertilization in the zygotic cells that will give rise to the primordial germ cells, so those muscle-specific epigenetic marks don't need to be wiped off in the embryo. Neither the sperm nor the egg ever expressed muscle myosin, etc.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-04-09T10:53:26.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31199" PostTypeId="1" CreationDate="2015-04-09T16:12:42.757" Score="0" ViewCount="177" Body="&lt;p&gt;I have been having trouble with what should be a fairly simple ligation. I had a plasmid that I needed to cut part out of, so I designed a couple PCR primers to do that. The plasmid already had a BamHI site on 1 side of the region I wanted to remove, so I made the other PCR primer with a BamHI site on its 5' end with 3 extra Cs so the restriction enzyme would bind better. Here is a crude diagram of what I tried to do:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ChPPj.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I did the PCR and BamHI digest, it looked good on gel, so I purified it from the gel, got the concentration on the Nanodrop, and set up a ligation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I keep getting zero colonies. I have tried a 24 hour reaction at 4 degrees, and 10 minute reaction at room temp. I am currently trying a reaction where I supplement the buffer with fresh ATP, because the buffers are a little old. If that works, problem solved, if not, I am asking how to troubleshoot this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This seems like it should be relatively simple, because I have no insert, just trying to close an empty vector, which seems to happen on its own when I don't want it to and dephosphorylate the vector.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reaction with extra ATP did not produce colonies. I will keep trying. One idea I had was to do the PCR and then try blunt end ligation, since the Pfu polymerase should make blunt ends. Also got a new sample of ligase.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2015-04-14T15:36:05.937" LastActivityDate="2015-04-14T15:36:05.937" Title="Closing a Plasmid by Ligation" Tags="&lt;pcr&gt;&lt;cloning&gt;&lt;ligation&gt;" AnswerCount="0" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="31200" PostTypeId="1" CreationDate="2015-04-09T17:06:50.257" Score="6" ViewCount="133" Body="&lt;p&gt;In a process called differentiation, the cells of the developing organism undergo huge changes, which result in cells, functioning &quot;completely&quot; differently. Two cells are considered to be of different types if they are having different sets of template-competent genes, though most of the genes in the human genome are common even in highly differentiated cells. Being able to produce specific proteins from the same genome is achieved by something called open chromatin state of the DNA. What I would like to ask is why can't this specific conformation of the DNA be reversed as this would likely answer the title of this question? I would also like to have some tips on further reading in the topic of DNA conformations and about DNA generally.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I used Gabor Forgacs's and Stuart A. Newman's book called Biological Physics of the Developing Embryo&lt;/em&gt; &lt;/p&gt;&#xA;" OwnerUserId="15051" LastActivityDate="2015-04-09T21:07:06.440" Title="Why differentiated cells can't &quot;undifferentiate&quot; (under normal conditions)?" Tags="&lt;dna&gt;&lt;development&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31202" PostTypeId="2" ParentId="30922" CreationDate="2015-04-09T17:34:20.637" Score="1" Body="&lt;p&gt;I have looked about the topic and I have asked experts and the best aproximation to know the vertebrate host from arthropod blood meals is targeting mitochondrial genes because you can get clean sequence data due the fact that only one allele is present rather than two. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Within the mitochondrial genome, you should select a gene which has been widely sequenced for most vertebrate species you are likely to detect in your region, other wise you will have many unknown identities among your bloodmeals. Really, there are just two choices that match these criteria: cytochrome oxidase I (COI) gene, which has been used by the Database of Life project; and cytochrome b, for which sequences are widely available (i.e. for many vertebrate species) in GenBank. If you get a negative result for one, you can try the other. Primer sequences are widely available in the literature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion, you must be target COI and Cytb genes to assure the host identification and prevent a unidentified match in Database of Life project or GenBank.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I give you a paper example to review the metodology: &lt;a href=&quot;https://www.researchgate.net/publication/231740032_Host_preference_of_the_arbovirus_vector_Culex_erraticus_%28Diptera_Culicidae%29_at_Sonso_Lake_Cauca_Valley_Department_Colombia&quot; rel=&quot;nofollow&quot;&gt;Host Preference of the Arbovirus Vector Culex erraticus (Diptera: Culicidae) at Sonso Lake, Cauca Valley Department, Colombia&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9128" LastActivityDate="2015-04-09T17:34:20.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31204" PostTypeId="5" CreationDate="2015-04-09T19:26:47.433" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2015-04-09T19:26:47.433" LastActivityDate="2015-04-09T19:26:47.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31205" PostTypeId="4" CreationDate="2015-04-09T19:26:47.433" Score="0" Body="Autophagy is an intracellular degradation system that delivers cytoplasmic constituents to the lysosome." OwnerUserId="15051" LastEditorUserId="15051" LastEditDate="2015-04-09T20:53:24.793" LastActivityDate="2015-04-09T20:53:24.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31206" PostTypeId="2" ParentId="31189" CreationDate="2015-04-09T20:33:07.180" Score="1" Body="&lt;p&gt;From this &lt;a href=&quot;https://biology.stackexchange.com/questions/30355/what-is-the-ic50-exactly/30357#30357&quot;&gt;post&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/IC50&quot; rel=&quot;nofollow noreferrer&quot;&gt;IC50&lt;/a&gt; is the concentration of inhibitor required to reduce the activity of a molecule/protein by one-half. It is the inverse of &lt;a href=&quot;http://en.wikipedia.org/wiki/EC50&quot; rel=&quot;nofollow noreferrer&quot;&gt;EC50&lt;/a&gt;. Usually inhibition curves looks sigmoidal so the IC50 is the middle point of the S curve. Here an example. (Note that the Y-axis can be pretty much anything, like enzyme activity and the X-axis is the concentration in a logarithmic scale).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/68HEc.gif&quot; alt=&quot;Illustration&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now for your actual question. The IC50 you got is by plotting a measure of the cell death rate vs the concentration of the drug. IC50 is expressed as a concentration so the higher the concentration of drug needed to kill the cell line the more resistant that cell line is. If the IC50 is very low then the concentration (or amount) of drug needed to kill the cell line is also very low which means the cell line is more sensitive.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-04-09T20:38:17.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31209" PostTypeId="2" ParentId="31200" CreationDate="2015-04-09T21:07:06.440" Score="5" Body="&lt;p&gt;This &quot;undifferentiation&quot; is actually possible and it is known as induced pluripotent stem cell (iPSC). The first &quot;undifferentiation&quot; cells i.e. iPSCs were mouse fibroblasts created in 2006 by researchers in Shina Yamanaka's lab who got the Nobel prize in 2012 for this work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find further reading on this topic on the &lt;a href=&quot;http://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell&quot;&gt;according Wikipedia-Page&lt;/a&gt; or more scientific details on the according &lt;a href=&quot;http://www.nature.com/subjects/induced-pluripotent-stem-cells&quot;&gt;nature.com topic&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8791" LastActivityDate="2015-04-09T21:07:06.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31211" PostTypeId="1" CreationDate="2015-04-09T22:02:44.070" Score="1" ViewCount="96" Body="&lt;p&gt;Consider the Robin boundary condition for the diffusion/heat equation $\mathrm{u_t=a(t)u_{xx}+f(x,t)}$: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\mathrm{-k(t)u_x(0,t)=h(t)u(0,t)}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\mathrm{u_x(0,t)+\frac{h(t)}{k(t)}u(0,t)=0}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $\mathrm{k(t)}$ thermal conductivity and $\mathrm{h(t)}$ heat tranfer coefficient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My Question: Is it possible that the ratio $\mathrm{h(t)/k(t)}$ to be constant? Could anyone please help me? I have really no idea. &lt;/p&gt;&#xA;" OwnerUserId="9781" LastActivityDate="2015-04-10T01:57:59.997" Title="ratio between heat transfer coefficient and thermal conductivity" Tags="&lt;biochemistry&gt;&lt;mathematical-models&gt;&lt;heat&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-04-10T02:11:42.933" ContentLicense="CC BY-SA 3.0" />
  <row Id="31212" PostTypeId="2" ParentId="31211" CreationDate="2015-04-09T22:45:09.513" Score="2" Body="&lt;p&gt;Most likely, you can't assume that $h/k$ might be constant. Reason is that those parameters are characteristics of two very separate systems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thermal conductivity shows how fast heat can be propagated through &lt;strong&gt;material&lt;/strong&gt;. That is, it answers question: if block of metal has $T_0$ temperature on its surface A, and you apply temperature $T_1$ (higher) to opposite surface B, how long it will take for whole block to get to temperature $T_1$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heat transfer coefficient is a characteristic of a &lt;strong&gt;system&lt;/strong&gt;. For example, when you have coolant on one side of metal plate, and heated air on the other. Question is how efficiently heat will be transferred from one side to the other. For more you can check &lt;a href=&quot;http://www.engineeringtoolbox.com/overall-heat-transfer-coefficient-d_434.html&quot; rel=&quot;nofollow&quot;&gt;this link&lt;/a&gt;. As you can see, transfer coefficient $U$ is a function of conductivity of the metal plate $k$. Hence, generally, relationship is non-linear.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-04-10T01:57:59.997" LastActivityDate="2015-04-10T01:57:59.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31214" PostTypeId="1" AcceptedAnswerId="31217" CreationDate="2015-04-10T00:12:09.750" Score="4" ViewCount="287" Body="&lt;p&gt;I read on the Wikipedia article about Chymosin &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Chymosin&quot; rel=&quot;nofollow&quot;&gt;http://en.m.wikipedia.org/wiki/Chymosin&lt;/a&gt;&#xA;It stated that chymosin is produced by gastric chief cell in human infants.&#xA;But it also stated that human only has a pseudogene for chymosin that does not actually encode the enzyme. On the other hand, another article show that gastric chief cell only secret chymosin in ruminant &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Gastric_chief_cell&quot; rel=&quot;nofollow&quot;&gt;http://en.m.wikipedia.org/wiki/Gastric_chief_cell&lt;/a&gt;&#xA;How can infants express chymosin without a functional gene?&lt;/p&gt;&#xA;" OwnerUserId="8834" LastEditorUserId="9943" LastEditDate="2015-04-10T02:40:11.260" LastActivityDate="2015-04-10T05:52:12.787" Title="How can human infants express chymosin with only a pseudogene at their disposal?" Tags="&lt;human-biology&gt;&lt;proteins&gt;&lt;enzymes&gt;&lt;gene&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31216" PostTypeId="1" CreationDate="2015-04-10T02:55:02.287" Score="6" ViewCount="1350" Body="&lt;p&gt;I am very interested in the case of the man named &lt;a href=&quot;http://en.wikipedia.org/wiki/Edward_Mordake&quot; rel=&quot;nofollow&quot;&gt;Edward Mordake&lt;/a&gt; who lived in the 19th century. In particular, he had two faces. If you have not heard of this man, please, search this up as there are a very few amount of photos, but it is something very, very strange.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, all the information on him seems to be speculation, so I am looking for a scientific look at this. I am unsure if it will even be possible seeing as how the years have passed and records may not have been accurate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be specific, has this condition been noted before? There seems to possibly be differing opinions onto wether the face was indeed its own individual inside, or a low functioning other half of the same man.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed I am looking for any info on the biology of his brain, possibly the neuroscience and or physiology, and of course any comments and discussion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you&lt;/p&gt;&#xA;" OwnerUserId="15066" LastEditorUserId="9943" LastEditDate="2015-08-27T14:08:17.370" LastActivityDate="2015-08-28T04:53:30.200" Title="Case study and speculations on the brain of Edward Mordake" Tags="&lt;neuroscience&gt;&lt;physiology&gt;&lt;brain&gt;&lt;pathology&gt;&lt;teratology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31217" PostTypeId="2" ParentId="31214" CreationDate="2015-04-10T05:52:12.787" Score="5" Body="&lt;p&gt;&lt;strong&gt;TL;DR:&lt;/strong&gt; Chymosin is similar to pepsin and I couldn't find any evidence of functional/expressed chymosin gene in human genome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems like a common misconception that chymosin is functional in humans. Already in 1940s it &lt;a href=&quot;http://ajplegacy.physiology.org/content/ajplegacy/138/3/557.full.pdf&quot; rel=&quot;noreferrer&quot;&gt;has been shown&lt;/a&gt; that rennin (aka chymosin) is absent from &quot;gastric juice&quot; in adult humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genetically there is only &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/643160&quot; rel=&quot;noreferrer&quot;&gt;pseudo-gene for chymosin&lt;/a&gt;, as wiki and other sources state. At the same link that leads to chymosin gene page you can find some literature on cloning and structural analysis of chymosin pseudo-gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you use BLAST for finding homologous proteins to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/102277564&quot; rel=&quot;noreferrer&quot;&gt;chymosin from, say &lt;em&gt;Bos  mutus&lt;/em&gt;&lt;/a&gt; (aka yak), you &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;amp;RID=JESS77S2016&quot; rel=&quot;noreferrer&quot;&gt;can find&lt;/a&gt; that in humans closes sequence can be attributed to pepsinogen and similar proteins. Which very much might mean that what is called chymosin in other animals is pepsin in humans, or there is some convergence/divergence which eliminated chymosin in humans. But this is only a speculation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can try to scan &lt;a href=&quot;https://scholar.google.com/scholar?hl=en&amp;amp;q=human%20chymosin&amp;amp;btnG=&amp;amp;as_sdt=1%2C5&amp;amp;as_sdtp=&quot; rel=&quot;noreferrer&quot;&gt;Google scholar for more sources&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;NB&lt;/strong&gt; link to BLAST search will expire in ~24 hrs.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-10T05:52:12.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31218" PostTypeId="1" AcceptedAnswerId="31244" CreationDate="2015-04-10T06:30:48.910" Score="1" ViewCount="202" Body="&lt;p&gt;What response of cellular immunity would appear after complementary protein activation to keep pathogenic bacteria away from our body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notes: I do appreciate your explanation. Though I am facing multiple choices:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(a) wrapping the bacteria cell (b) immobilize the bacteria cell (c)    destroying the bacteria cell by enzyme (d) creating pores on the bacteria cell&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key answer is (c) but then I do not know what enzymes make this happens. Any Idea?&lt;/p&gt;&#xA;" OwnerUserId="15254" LastEditorUserId="15254" LastEditDate="2015-04-10T13:27:43.670" LastActivityDate="2015-04-12T00:10:01.220" Title="Cellular Immunity Response" Tags="&lt;homework&gt;&lt;immunity&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31220" PostTypeId="1" CreationDate="2015-04-10T09:34:47.213" Score="5" ViewCount="913" Body="&lt;p&gt;Why does the DNA content of a cell get doubled in interphase? Why doesn't it become tripled or quadrupled? What's stopping it from doing so? &lt;/p&gt;&#xA;" OwnerUserId="4806" LastEditorUserId="12877" LastEditDate="2015-04-10T20:03:34.730" LastActivityDate="2017-01-25T02:39:17.703" Title="DNA content doubling in interphase" Tags="&lt;mitosis&gt;&lt;cell-division&gt;&lt;dna-replication&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31222" PostTypeId="1" CreationDate="2015-04-10T11:49:07.390" Score="3" ViewCount="405" Body="&lt;p&gt;So, gene therapy is to take out a gene, correct its mutation, and put the corrected one back into the organism, right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it also possible to take out a gene from an organism and put in a totally different one?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read about this study where a scientist found four genes seemingly responsible for creating high, medium, low pan sensitivities.&#xA;Genes: COMT, DRD2, DRD1 and OPRK1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DRD1 - more common among people with low pain perception.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;COMT and OPRK genes were seen more, for those with moderate pain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DRD2 gene variant was more common among those with a high pain perception.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for example, can we take out a DRD2 gene from a person who has high pain sensitivity and put DRD1 in him/her so that he/she can have low pain sensitivity?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is that technically possible?&lt;/p&gt;&#xA;" OwnerUserId="15288" LastEditorUserId="14826" LastEditDate="2015-04-10T16:43:30.707" LastActivityDate="2016-04-30T04:20:02.007" Title="Swapping genes?" Tags="&lt;genetics&gt;&lt;human-genetics&gt;&lt;pain&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31223" PostTypeId="1" AcceptedAnswerId="31856" CreationDate="2015-04-10T12:31:45.797" Score="4" ViewCount="443" Body="&lt;p&gt;Liver is the most resilient of the human organ (on par with or next to skin). A very interesting experiment on liver regeneration is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701258/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. Even if two-thirds of the liver is removed, the remaining liver would regenerate to recover the full volume and function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cirrhosis of liver is a condition where excessive fibrosis occurs shattering the architecture of the liver. The blood vessels and the parenchymal cells of the liver get constricted into narrow spaces causing portal hypertension and fall in the Liver Function Test parameters (albumin level falls, clotting factors fall leading to spontaneous bleeding, bilirubin level rises causing jaundice, etc...). It can be either congenital or acquired. Cirrhosis is considered an end stage liver disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the end stages of cirrhosis the only treatment option available is liver transplantation. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Question:&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why is partial hepatectomy (removal of part of liver) not a treatment option for end stage liver disease (cirrhosis of the acquired variety)?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="11841" LastActivityDate="2017-01-23T12:04:33.597" Title="Liver - Regeneration in Cirrhosis" Tags="&lt;physiology&gt;&lt;pathology&gt;&lt;liver&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31225" PostTypeId="1" CreationDate="2015-04-10T12:37:20.143" Score="4" ViewCount="74" Body="&lt;p&gt;I accidentally spun down the cells after heat shock treatment before adding the media into the tubes while doing transformation? will the transformation work?&lt;/p&gt;&#xA;" OwnerUserId="15290" LastActivityDate="2015-04-10T14:52:45.667" Title="Transformation efficiency" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31226" PostTypeId="2" ParentId="31225" CreationDate="2015-04-10T13:47:10.777" Score="2" Body="&lt;p&gt;This is hard to answer since we don't know the exact conditions you chose, as these are rotation speed (or better g), how long you spun them down and also if you used a cooled centrifuge or not. It's also important how gentle you resuspended the pellet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I would plate these cells, no matter what happened since you are at the last step of the procedure and have nothing to loose. Do the usual dilutions you use for plating your cells and then add another plate with undiluted transformation mix. If you have only very few surviving cells after your mistake you might get your clones on this plate. If it doesn't work, you will have to repeat the transformation.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-04-10T13:47:10.777" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31227" PostTypeId="2" ParentId="31225" CreationDate="2015-04-10T14:52:45.667" Score="2" Body="&lt;p&gt;The question is following: did you incubate cells on ice before spinning? Protocol, for example &lt;a href=&quot;https://www.neb.com/protocols/1/01/01/high-efficiency-transformation-protocol-c2987&quot; rel=&quot;nofollow&quot;&gt;this one for $DH5\alpha$&lt;/a&gt;, calls for just 10 minute incubation after heat shock:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Heat shock at exactly 42°C for exactly 30 seconds. Do not mix.&#xA;  &lt;strong&gt;Place on ice for 5 minutes. Do not mix.&lt;/strong&gt;&#xA;  Pipette 950 µl of room temperature SOC into the mixture.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Did you centrifuge your tubes after step in bold?&#xA;My bet is that spinning cells down (taking into account what @chris wrote about centrifugation parameters) will not dramatically decrease efficiency of transformation. DNA should be already in cells after step, highlighted in the quote.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-10T14:52:45.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31229" PostTypeId="1" CreationDate="2015-04-10T15:49:34.740" Score="2" ViewCount="66" Body="&lt;p&gt;I hope Im not asking a dumb question!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where can i find video of gene manipulation in action under microscope?&#xA;Like extracting a gene from a cell, fixing gene mutations, putting the gene in a vector, that kinda stuff. Is this too small to show in video or photos?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If i look up youtube all I find is scientists using lab machines and equipments except for under miscroscope!!!&lt;/p&gt;&#xA;" OwnerUserId="15288" LastActivityDate="2015-06-08T04:27:29.967" Title="Where to find gene manipulation video (or photos)" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;microscopy&gt;&lt;gene&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31230" PostTypeId="1" CreationDate="2015-04-10T17:45:31.400" Score="2" ViewCount="66" Body="&lt;p&gt;Our bronchus and uterus has beta adrenoreceptors, but they have no active sympathetic nervous system innervation in these organs. Was there a sympathetic innervation in trachea and uterus, earlier, that we lost it during the course of evolution, if no, why did nature gives us only adrenergic receptors and no adrenergic nerves in trachea and uterus?&lt;/p&gt;&#xA;" OwnerUserId="11580" LastEditorUserId="11580" LastEditDate="2015-04-10T17:50:39.683" LastActivityDate="2015-04-10T17:50:39.683" Title="Why is there only adrenoreceptors and no active adrenergic innervation in bronchus and uterus?" Tags="&lt;pharmacology&gt;&lt;receptor&gt;&lt;pharmacodynamics&gt;&lt;autonomic-nervous-system&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31231" PostTypeId="1" AcceptedAnswerId="31271" CreationDate="2015-04-10T18:37:46.173" Score="3" ViewCount="664" Body="&lt;p&gt;If a person has developed leukopenia as a side-effect of long-term use of anti-convulsant medications and his/her immune system appears normal otherwise (does not get infections any more often than a healthy person, and bone marrow biopsy &lt;strong&gt;&lt;em&gt;did not&lt;/em&gt;&lt;/strong&gt; indicate anything abnormal), does the condition need to be treated? Is it even possible to treat leukopenia effectively as long as the person is on anti-convulsant medication?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does leukopenia increase a person's chances of getting some &lt;em&gt;non-infectious&lt;/em&gt; diseases too? I know WBC is primarily responsible for fighting infectious micro-organisms, but does it have any significant role in cleaning up body's own malfunctioning or ageing cells?&lt;/p&gt;&#xA;" OwnerUserId="9524" LastEditorUserId="9524" LastEditDate="2015-04-10T18:49:40.683" LastActivityDate="2015-04-12T06:17:16.800" Title="Can leukopenia in a person with an otherwise normal immune system lead to non-infectious diseases in the long-term?" Tags="&lt;human-biology&gt;&lt;immunology&gt;&lt;pathology&gt;&lt;hematology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31232" PostTypeId="2" ParentId="31220" CreationDate="2015-04-10T19:04:35.057" Score="7" Body="&lt;p&gt;So in mitosis, the cell has to split itself into two cells; each daughter cell has a functional genome that may again split into more daughter cells. The cell replicates the DNA before dividing, so the error in replicating 3x or 4x is that upon division, the daughter cells will have more DNA than the initial cell, and every generation will have more DNA than the last. One replication ensures both daughter cells receive one functional genome. We can see the result of extra DNA in cases like Down Syndrome (trisomy of chromosome 21).&lt;/p&gt;&#xA;&lt;p&gt;The cell controls this process by controlling the cyclins present in the cell temporally, namely cyclin-A and cyclin-E when we talk about DNA replication in S-phase,&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/y6wtD.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;From wikipedia,&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Cyclin A resides in the nucleus during S phase where it is involved in the initiation and completion of DNA replication. As the cell passes from G1 into S phase, cyclin A associates with CDK2, replacing cyclin E. Cyclin E is responsible for initiating the assembly of the pre-replication complex. This complex makes chromatin capable of replication. When the amount of cyclin A/CDK2 complex reaches a threshold level, it terminates the assembly of the pre-replication complex made by cyclin E/CDK2. As the amount of Cyclin A/CDK2 complex increases, the complex initiates DNA replication.&lt;/p&gt;&#xA;&lt;p&gt;Cyclin A has a second function in S phase, in addition to initiating DNA synthesis, Cyclin A ensures that DNA is replicated once per cell cycle by preventing the assembly of additional replication complexes. This is thought to occur through the phosphorylation of particular DNA replication machinery components, such as CDC6, by the cyclin A/CDK2 complex. Since the action of cyclin A/CDK2 inhibits that of cyclin E/CDK2, the sequential activation of cyclin E followed by the activation of cyclin A is important and tightly regulated in S phase.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://en.wikipedia.org/wiki/Cyclin_A&quot; rel=&quot;noreferrer&quot;&gt;Cyclin A&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-10T19:04:35.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31234" PostTypeId="1" AcceptedAnswerId="31236" CreationDate="2015-04-10T22:57:14.563" Score="2" ViewCount="367" Body="&lt;p&gt;All-trans retinoic acid (atRA) is a potent ligand for a nuclear receptor called retinoic acid receptor alpha (RARa). The concentration of atRA at which RARa is half maximal is 19nM. The dose-response curve is sigmoidal, with concentration (log scale) on the x-axis and percentage of maximal activity on the y.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How would I use this information to reproduce the dose-response curve? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="13212" LastEditorUserId="14826" LastEditDate="2015-04-11T04:09:58.743" LastActivityDate="2015-04-11T04:09:58.743" Title="Given an EC50 value, how do I reproduce the sigmoidal curve from which this was calculated?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;pharmacology&gt;&lt;pharmacokinetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31235" PostTypeId="1" CreationDate="2015-04-10T23:50:07.607" Score="0" ViewCount="250" Body="&lt;p&gt;How long can the average, healthy adult human survive with only water? &lt;/p&gt;&#xA;" OwnerUserId="15292" LastEditorUserId="9943" LastEditDate="2015-04-11T02:46:52.397" LastActivityDate="2015-04-12T08:26:34.790" Title="Survival with only water but no food" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-04-12T08:54:54.133" ContentLicense="CC BY-SA 3.0" />
  <row Id="31236" PostTypeId="2" ParentId="31234" CreationDate="2015-04-11T00:08:12.020" Score="1" Body="&lt;p&gt;Basic sigmoidal curve looks like that: zero at $-\inf$ and one at $+\inf$. All in between should look like an integral of gaussian distribution. Take a look on &lt;a href=&quot;http://en.wikipedia.org/wiki/Normal_distribution&quot; rel=&quot;nofollow noreferrer&quot;&gt;this wiki page&lt;/a&gt; for more information. Now, the question, why sigmoidal curve is integral of gaussian function, I will leave out for now. My understanding is that gaussian distribution tells you how much system response will increase (say, efficiency of treatment) if you increase stimulus by $dx$. E.g., how much response changes when you go from $5$ to $5+dx$ versus from $10$ to $10+dt$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem, as you might realize, that gaussian distribution has two parameters: mean value and width of the function. When you construct your fit, frist one will be 19nM, but second, $\sigma$, is unknown from your question. What you don't know is how rapidly response changes when you increase concentration by little around your EC50. So all your sigmoidal plots will go through same point but with different slope, like that:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PKL9P.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Without knowing second parameter, $\sigma$, it makes little sense to plot your sigmoidal curve. However, if you want to, this is MATLAB code. See that &lt;em&gt;cumsum()&lt;/em&gt; function effectively integrates gaussian distribution rendering sigmoidal curve.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;c = 0:100; % range of concentrations you test&#xA;sigma = 1; % unknown parameter&#xA;m = 19; % your EC50 19 nM&#xA;g = 1/(sigma*sqrt(2*pi))*exp(-((c - m).^2)/(2*sigma^2)); % gaussian&#xA;gs = cumsum(g);&#xA;plot(c, gs)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;If you want, you can plot it with log-scale of X, using semilogx() instead of plot().&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;NB&lt;/strong&gt; here I started with Gaussian function and its integral just as a wild guess. You real function &lt;a href=&quot;http://en.wikipedia.org/wiki/Sigmoid_function&quot; rel=&quot;nofollow noreferrer&quot;&gt;might very well be&lt;/a&gt; something like $f(x)=\frac{1}{1+e^{-x}}$. &quot;Sigmoid&quot; function is just description of general shape, not mathematical definition.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-04-11T01:04:07.320" LastActivityDate="2015-04-11T01:04:07.320" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31237" PostTypeId="1" AcceptedAnswerId="31243" CreationDate="2015-04-11T03:01:02.177" Score="2" ViewCount="7668" Body="&lt;p&gt;I came across this term in my readings but I do not understand how this works. Can someone direct me to some reference as to what this &quot;hepatic&quot; glucose production is all about?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastActivityDate="2015-04-11T09:52:50.170" Title="What is the so called &quot;hepatic glucose production&quot;" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31238" PostTypeId="1" AcceptedAnswerId="31239" CreationDate="2015-04-11T03:03:46.847" Score="9" ViewCount="4409" Body="&lt;p&gt;Can someone very generally describe how the brain consumes ketoacids/ketone bodies when blood glucose has been completely depleted?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="16299" LastEditDate="2015-11-27T06:03:59.330" LastActivityDate="2015-11-27T06:03:59.330" Title="When glucose production is low, the brain begins using ketoacids as energy... how does that work?" Tags="&lt;physiology&gt;&lt;brain&gt;&lt;metabolism&gt;&lt;endocrinology&gt;&lt;glucose&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31239" PostTypeId="2" ParentId="31238" CreationDate="2015-04-11T05:03:29.263" Score="7" Body="&lt;p&gt;Human body is a glucose driven machine which intake carbohydrates and converts to glucose. Energy is yielded from the glucose and glucose is stored as glycogen. When the carbohydrate intake is somehow reduced then body will shift its mechanism and uses the fatty acids to produce energy. Liver synthesis &lt;a href=&quot;http://en.wikipedia.org/wiki/Ketone_bodies&quot; rel=&quot;noreferrer&quot;&gt;ketones&lt;/a&gt; from fatty acids in our diet or from body fat. Ketones(acetoacetate and acetone) are released into the blood, which is absorbed by the brain and synthesis energy from it through their mitochondria.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The brain gets a portion of its energy from ketone bodies when glucose&#xA;  is less available (e.g., during fasting, strenuous exercise, low&#xA;  carbohydrate, ketogenic diet and in neonates). In the event of low&#xA;  blood glucose, most other tissues have additional energy sources&#xA;  besides ketone bodies (such as fatty acids), but the brain has an&#xA;  obligatory requirement for some glucose. After the diet has been&#xA;  changed to lower blood glucose for 3 days, the brain gets 25% of its&#xA;  energy from ketone bodies.After about 4 days, this goes up to 70%&#xA;  (during the initial stages the brain does not burn ketones, since they&#xA;  are an important substrate for lipid synthesis in the brain).&#xA;  Furthermore, ketones produced from omega-3 fatty acids may reduce&#xA;  cognitive deterioration in old age.&#xA;  &lt;a href=&quot;http://en.wikipedia.org/wiki/Ketone_bodies&quot; rel=&quot;noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;When the body starts using the fatty acids for energy production, one problem arises in the brain and that is the blood-brain barrier( barrier that separates the circulating blood from the brain extracellular fluid in the central nervous system )Brain cannot use long chain fatty acids because they cannot cross the blood-brain barrier due to their bondage with albumin. As ketones are medium chain fatty acids which can effectively cross the barrier. So brain uses the ketones for energy production by a process called as &lt;a href=&quot;http://en.wikipedia.org/wiki/Ketosis&quot; rel=&quot;noreferrer&quot;&gt;ketosis&lt;/a&gt;. The ketone bodies are then incorporated into acetyl-CoA and used in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Citric_acid_cycle&quot; rel=&quot;noreferrer&quot;&gt;citric acid cycle&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The citric acid cycle – also known as the tricarboxylic acid (TCA)&#xA;  cycle or the Krebs cycle – is a series of chemical reactions used by&#xA;  all aerobic organisms to generate energy through the oxidation of&#xA;  acetate derived from carbohydrates, fats and proteins into carbon&#xA;  dioxide and chemical energy in the form of adenosine triphosphate&#xA;  (ATP).&#xA;  &lt;a href=&quot;http://en.wikipedia.org/wiki/Citric_acid_cycle&quot; rel=&quot;noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Metabolic pathways to produce energy&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6qnex.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10294" LastActivityDate="2015-04-11T05:03:29.263" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31240" PostTypeId="1" AcceptedAnswerId="55065" CreationDate="2015-04-11T05:29:11.113" Score="3" ViewCount="261" Body="&lt;p&gt;What are commonly accepted metrics for assessing DNA sequence quality (platform-specific answers are fine)? I am relatively new to this topic, and I want to either find or code (in Python or C++) algorithms for checking sequencing data quality before getting into analysis.&lt;/p&gt;&#xA;" OwnerUserId="11538" LastEditorUserId="6307" LastEditDate="2015-04-11T07:35:55.967" LastActivityDate="2017-01-09T17:18:30.973" Title="Common Metrics of Assessing DNA Sequence Quality" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31241" PostTypeId="1" AcceptedAnswerId="31242" CreationDate="2015-04-11T06:15:50.960" Score="1" ViewCount="760" Body="&lt;p&gt;I see that the genome contains large regions of repeating sequences called interspersed or dispersed elements. The long dispersed elements (LINES) such as LINE-1, can reach up to 6-8 kb in length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm wondering, given the amount of repetition that takes place in these regions, wouldn't a system where a pointer (such as in computer programming) existed  be more efficient? For example, instead of including a LINE, include a unique 5 base pair sequence acting as a pointer to that LINE. A separate chromosome (containing one copy of each LINE) would then be read at the correct position once the pointer was read.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you think that given enough time in evolution, such a system would be more sustainable? Sort of like using a proper functional language instead of Assembler in computer programming, where f(x) can be defined once, and accessed via pointers, instead of being repeated many times?&lt;/p&gt;&#xA;" OwnerUserId="15295" LastActivityDate="2015-04-11T06:32:46.307" Title="Why didn't a concept like &quot;pointers&quot; in Computer Science evolve in the genome?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31242" PostTypeId="2" ParentId="31241" CreationDate="2015-04-11T06:32:46.307" Score="8" Body="&lt;p&gt;Short answer: Pointers already exist within the genome, in terms of transcription elements (such as repressor/&lt;a href=&quot;http://en.wikipedia.org/wiki/Activator_%28genetics%29&quot;&gt;activator systems&lt;/a&gt;). These systems can remotely activate a specific gene for transcription based on concentrations of specific chemicals within the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem with LINEs are that they are &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2249.2004.02592.x/full#ss3&quot;&gt;thought to be ancient retroviruses which lost their capacity to infect other cells&lt;/a&gt;, instead jumping around within the genome. They are therefore parasitic in nature, and they reproduce by inserting multiple copies of themselves into the genome. It makes more sense to think of LINEs as nearly inactivated retroviruses instead.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-04-11T06:32:46.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31243" PostTypeId="2" ParentId="31237" CreationDate="2015-04-11T09:52:50.170" Score="5" Body="&lt;p&gt;&quot;Hepatic glucose production&quot; is the gluconeogenesis process (the opposite of the gycolysis process), that is the formation of glucose primarily from lactate and amino acids. This process takes place in the liver's cells and it is regulated by hormones (insulin and glucagon). &#xA;Look &lt;a href=&quot;http://classes.biology.ucsd.edu/old.web.classes/bibc102.SU04.1/pdf/ch02-glycolysis.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://spectrum.diabetesjournals.org/content/17/3/183.full&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for a better explanation! &lt;/p&gt;&#xA;" OwnerUserId="3645" LastActivityDate="2015-04-11T09:52:50.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31244" PostTypeId="2" ParentId="31218" CreationDate="2015-04-11T10:10:18.583" Score="1" Body="&lt;p&gt;As you can simply find on Wikipedia, the cellular immunity, or Cell-mediated immunity, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;is an immune response that does not involve antibodies, but rather&#xA;  involves the activation of phagocytes, antigen-specific cytotoxic&#xA;  T-lymphocytes, and the release of various cytokines in response to an&#xA;  antigen.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The answer (c) (destroying the bacteria cell by enzyme) refers to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Phagocyte&quot; rel=&quot;nofollow&quot;&gt;phagocytes&lt;/a&gt;, cells that contain many enzymes, like lysozymes. Those funny enzyme can destroy the bacteria cell's wall.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually, I think that the answer (d) could be right, but it's not complete. In fact not every enzymes works on the cell's wall! &lt;/p&gt;&#xA;" OwnerUserId="3645" LastActivityDate="2015-04-11T10:10:18.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31245" PostTypeId="1" AcceptedAnswerId="31263" CreationDate="2015-04-11T10:10:42.223" Score="0" ViewCount="5494" Body="&lt;p&gt;I can't find a definition for 'refractile' (not 'refractory', and not explicitly in an optical context).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As in:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A tumour cell phenotype features increased proliferation, anchorage- and growth factor-independenth growth and ‘refractile’ cell morphology&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's not in any of the dictionaries I can access online, nor in the Oxford Dictionary of Biochemistry and Molecular Biology. Any help would be appreciated, thanks.&lt;/p&gt;&#xA;" OwnerUserId="4202" LastActivityDate="2018-05-27T23:23:30.507" Title="What is 'refractile' cell morphology?" Tags="&lt;cell-biology&gt;&lt;terminology&gt;&lt;morphology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31246" PostTypeId="1" CreationDate="2015-04-11T11:15:00.900" Score="2" ViewCount="194" Body="&lt;p&gt;I have a question I could not get an understandable reply from Google and I am no expert in the matter, so my plead to you is if you could give me practical and relatively easy to follow advice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With the view of the breakthroughs in DNA research and all the anticipated applications to medicine in the near-future, I am willing to build a storage of the DNAs in my family (eg 20-30 people, some at a very old age). The use may not be for cloning :) but rather, for eg to map and trace specific hereditary genes when such services become more available to the wide public; and thus, probably help with a personalized medicine for someone, or find genome problems, and probably be able to 'turn them off' at some point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a way I can extract cells (ie from inside the cheek, or hairs), and store them for a few decades while preserving the DNA (eg put them in a freezer at -18C or in some solution)?&#xA;I have only common knowledge in this area so apologies if the examples are silly, but I assume you can understand my point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be grateful if you provide practical instructions as: &quot;you buy 500ml of the chemical xx&quot;; or &quot;mix 150ml of xx and 200ml of zz&quot;, so me and anyone who finds the idea appealing, can follow.&#xA;Ps-the lower the costs of the procedures, the better (I found some personal &quot;dna vaults&quot; costing several '000$).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you for your consideration!&lt;/p&gt;&#xA;" OwnerUserId="15298" LastActivityDate="2016-11-19T14:02:46.003" Title="DIY storing family DNAs' samples for future uses (eg medical)" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;dna&gt;&lt;human-genetics&gt;&lt;dna-sequencing&gt;" AnswerCount="5" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31247" PostTypeId="2" ParentId="31246" CreationDate="2015-04-11T13:20:42.340" Score="0" Body="&lt;p&gt;So cryopreservation would be the long-term mode of storage, and you'd do something like store your sample in a cryonic freezer supplied w/ liquid nitrogen at -196C. Cellgro provides some recommendations for cryopreservation &lt;a href=&quot;http://cellgro.com/media/upload/file/techinfosheets/new/Cryopreservation-freezing%20cells.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. Keep in mind, cryonic freezers are typically pricey, but broady, the idea is you need to keep your cells at the right temperature, in the right media. The source I gave you provides suggestions for media, DMSO as a cryoprotectant, and a protein source to protect the cells during the process. Also, keep in mind there are recovery issues with cryopreservation. There's some data to suggest reactive oxygen species, and apoptosis mechanisms damage/fragment the DNA in cells that have undergone that sort of freezing(&lt;a href=&quot;http://www.vetmed.ucdavis.edu/apc/meyerslab/labsite%2003/PDF&amp;#39;s/Baumber-DNA%20fragmentation.pdf&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20077485&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;, &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs10561-005-0275-8&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;). These articles mainly refer to sperm storage.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-04-11T13:20:42.340" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31248" PostTypeId="2" ParentId="31128" CreationDate="2015-04-11T15:36:32.307" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://nar.oxfordjournals.org/content/34/13/3615.long&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; article suggests RNA Pol III formed early in eukaryote evolution, and while there's a lot of conservation, the enzyme-specific subunits result from divergent evolution. &lt;a href=&quot;http://mbe.oxfordjournals.org/content/27/5/1035.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;Another&lt;/a&gt; article suggests the actual increase of subunits, however, is a result of the permanent recruitment of transcription factors to the core RNAP by studying homology of subunits to existing TF's. So if you were to ask why another polymerase? The article suggests gene duplication events. There are homologs for every RNAPII subunit in archaea, and and the subunits unique to RNAPI and III are homologous to transcription factors for RNAPII (TF's denoted TFII...). They further conclude that,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first RNAP duplication event(s) likely resulted in&#xA;  two RNAPs: RNAPI and the ancestral RNAPII/RNAPIII. This&#xA;  is supported by the existence of three homologous proteins&#xA;  that are found in the RNAPII and RNAPIII transcriptional&#xA;  systems but with no homologs in RNAPI. The first two proteins&#xA;  are TFIIE a and b that are found in RNAPII and that&#xA;  are homologous to RPC82 and RPC34 in RNAPIII, respectively.&#xA;  In contrast, RNAPI lacks a homolog of either subunit&#xA;  of TFIIE, indicating a loss of TFE in this RNAP. Thus, the&#xA;  ancestral TFE was likely lost along the RNAPI lineage&#xA;  but maintained in both RNAPII and RNAPIII following&#xA;  duplication of the RNAPII/RNAPIII ancestor. The third&#xA;  such protein is the archaeal TFB, which is common to both&#xA;  RNAPII (where it is named TFIIB) and RNAPIII (where it is&#xA;  named TFIIIB-BRF) but absent from RNAPI (fig. 4). These&#xA;  recruitment events resulted in the expansion of the number&#xA;  of RNAP subunits from 12 in the ancestral eukaryotic&#xA;  RNAP to 14 in RNAPI (Kuhn et al. 2007) and 16 in RNAPIII&#xA;  (17 if we include the unikont- and plant-specific RPC31&#xA;  protein; Proshkina et al. 2006).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So in speculation, if you had to ask why a different polymerase, the evolution of the two lineages of RNAP's dictated a different binding/initiation motif for what are perhaps (retro)viral or (retro)transposable elements [the tRNA and 5s rRNA genes]. This is still under investigation, however.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-04-11T15:36:32.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31249" PostTypeId="1" AcceptedAnswerId="35016" CreationDate="2015-04-11T16:15:02.787" Score="2" ViewCount="159" Body="&lt;p&gt;I did some quick google searches for how a cellular organism generates or acquires its first ribosomes, but I found nothing. For instance, do the organisms initiating replication form extra Ribosomes to pass on to the created organism? &lt;/p&gt;&#xA;" OwnerUserId="8619" LastEditorUserId="948" LastEditDate="2015-04-11T23:59:05.940" LastActivityDate="2015-06-08T05:38:36.900" Title="How does a cell create/gain its initial ribosomes for protein synthesis?" Tags="&lt;proteins&gt;&lt;ribosome&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31250" PostTypeId="1" AcceptedAnswerId="35015" CreationDate="2015-04-11T16:44:34.577" Score="2" ViewCount="219" Body="&lt;p&gt;What steps should be taken in a molecular lab environment to help ensure that DNA samples/stocks are not contaminated, or contaminate other objects in the lab?&lt;/p&gt;&#xA;" OwnerUserId="11538" LastActivityDate="2015-06-08T04:30:18.723" Title="Workspace preparation and cleanup for DNA work" Tags="&lt;molecular-biology&gt;&lt;lab-techniques&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2015-06-08T11:17:45.393" ContentLicense="CC BY-SA 3.0" />
  <row Id="31251" PostTypeId="1" CreationDate="2015-04-11T17:15:01.890" Score="6" ViewCount="141" Body="&lt;p&gt;I'd appreciate a suggestion for software to compare models of two proteins in an alternating electric field. The more detail, or perhaps direction towards an existing and similar paper, the better. Right now I'm particularly interested in comparing rotation of the proteins as a result of the field. The first protein, tubulin (1TUB), will be modeled as a dimer while the second, septin (2QAG), will be modeled as a trimer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The electric field will consist of a 200Khz field at 1.5V/m with a spatial resolution of 300Ax300Ax300A. I believe that I will only need a temporal resolution of 1.5 milliseconds for 10 solutions(?) per cycle for 3 cycles in the 200Khz field (particularly unsure of this part). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of computational power I have access to two 7870 Radeon GPUs, but am also interested in cloud computing if that's not enough. &lt;/p&gt;&#xA;" OwnerUserId="15299" LastEditorUserId="15299" LastEditDate="2016-03-25T15:44:01.180" LastActivityDate="2016-03-25T15:44:01.180" Title="Software recommendation for protein in electric field modeling?" Tags="&lt;bioinformatics&gt;&lt;biophysics&gt;&lt;electrophysiology&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2016-03-23T09:15:32.413" ContentLicense="CC BY-SA 3.0" />
  <row Id="31254" PostTypeId="1" AcceptedAnswerId="31395" CreationDate="2015-04-11T19:34:34.873" Score="7" ViewCount="202" Body="&lt;p&gt;Are there differences between &lt;em&gt;renal, hepatic, cardiac&lt;/em&gt; and &lt;em&gt;kidney, liver and heart&lt;/em&gt;? Is the &quot;jargon&quot; used more commonly because of tradition, or is there some definitive biological basis to it?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="3553" LastEditDate="2015-11-23T10:00:45.737" LastActivityDate="2015-11-23T10:00:45.737" Title="Why do people in the scientific community use terminology such as renal, hepatic, cardiac instead of kidney, liver and heart?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;medicine&gt;&lt;nomenclature&gt;&lt;general-biology&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ClosedDate="2015-04-15T22:50:19.950" ContentLicense="CC BY-SA 3.0" />
  <row Id="31256" PostTypeId="1" CreationDate="2015-04-11T20:54:15.023" Score="2" ViewCount="93" Body="&lt;p&gt;I'm going to teach a c ollege-level introductory entomology course soon, and I'm looking for free online entomology resources. Does anyone have any recommendations?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular I'm looking for phylogenetic resources, experiment ideas, images, topics, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ideally, I'd love to find a discussion forum consisting of other entomology instructors sharing their ideas.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="1906" LastEditorUserId="3952" LastEditDate="2015-04-19T14:48:59.397" LastActivityDate="2015-04-19T14:48:59.397" Title="Online resources for entomology?" Tags="&lt;entomology&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31258" PostTypeId="1" CreationDate="2015-04-11T22:48:30.117" Score="6" ViewCount="236" Body="&lt;p&gt;I came across a photo on Wikipedia depicting an &lt;em&gt;Oreocereus celsianus&lt;/em&gt; with what looks to me like some kind of harvestman on it. The photo was taken at the San Francisco Botanical Garden.  Can anyone identify the arachnid in the photo?  (See link below for full-size image.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Oreocereus_celsianus_1.jpg/414px-Oreocereus_celsianus_1.jpg&quot; alt=&quot;Oreocereus celsianus with unidentified arachnid&quot;&gt;&lt;br /&gt;&#xA;&lt;sub&gt;Source: &lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Oreocereus_celsianus_1.jpg&quot;&gt;https://commons.wikimedia.org/wiki/File:Oreocereus_celsianus_1.jpg&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="11657" LastActivityDate="2015-06-04T11:31:09.407" Title="What is this arachnid?" Tags="&lt;species-identification&gt;&lt;arachnology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31259" PostTypeId="1" AcceptedAnswerId="31264" CreationDate="2015-04-11T23:05:52.353" Score="9" ViewCount="9604" Body="&lt;p&gt;The feeling when using an amusement park unit is usually a pleasure. Why is it not a pain instead?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there advantages, from an evolutionary point of view, in loving this potentially dangerous activity? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it related to the liking for extreme sports?&lt;/p&gt;&#xA;" OwnerUserId="15148" LastEditorUserId="8619" LastEditDate="2015-04-12T02:31:00.963" LastActivityDate="2018-04-16T18:51:04.840" Title="Why do people feel pleasure when using roller coasters / centrifuges?" Tags="&lt;human-biology&gt;&lt;human-evolution&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31260" PostTypeId="2" ParentId="31238" CreationDate="2015-04-11T23:56:27.973" Score="2" Body="&lt;p&gt;Actually there is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21395585&quot; rel=&quot;nofollow noreferrer&quot;&gt;fatty acid transport through the BBB&lt;/a&gt;. Maybe the rate of this transport is not enough, I don't know, I think it does not really matter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What really happens here, that the liver prepares the fatty acids, so the brain can use them more easily in the form of ketoacids to produce energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/J1ITj.jpg&quot; alt=&quot;fatty acid catabolism shared between the liver and the brain&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;fatty acid catabolism shared between the liver and the brain - &lt;a href=&quot;https://thestrangeandspectacularworldofbiochemistry.wordpress.com/tag/ketoacidosis/&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2015-04-11T23:56:27.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31262" PostTypeId="2" ParentId="31218" CreationDate="2015-04-12T00:10:01.220" Score="1" Body="&lt;p&gt;After opsonization the antigen goes through phagocytosis or the complement system destroys it. The complement is a cascade of reactions, which at the end creates a hole (many holes) on the membrane of bacteria which causes lysis. &lt;a href=&quot;http://en.wikipedia.org/wiki/Complement_membrane_attack_complex&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Complement_membrane_attack_complex&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the right answer is d.) in your case.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2015-04-12T00:10:01.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31263" PostTypeId="2" ParentId="31245" CreationDate="2015-04-12T00:13:58.417" Score="1" Body="&lt;p&gt;From the &lt;a href=&quot;http://www.biology-online.org/dictionary/Refractile&quot; rel=&quot;nofollow&quot;&gt;Biology Online Dictionary&lt;/a&gt;, &lt;em&gt;refractile&lt;/em&gt; refers to:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... the ability of cellular granules to refract or scatter light.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Tumor cells can be more &quot;dense&quot;, as they are usually rapidly dividing, and so need extra ribosomes to maintain protein production, may have a higher DNA/RNA content reflecting increased transcription and duplication, more mitochondria to power the cells, etc. This can alter the refractive index of a suspension of tumor cells as compared to organ-matched normal cells, for example.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-04-12T00:13:58.417" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31264" PostTypeId="2" ParentId="31259" CreationDate="2015-04-12T00:18:17.477" Score="7" Body="&lt;p&gt;Riding roller-coasters usually (unless you are psycho) induces a release of adrenaline and other chemicals, like endorphin (your bodies pre-emptive effort to combat any possible pain and stress you may be about to experience), into your body. Endorphin is a strong chemical, specifically released to make you feel relaxed and confident. Obviously this explains the natural high you may get from riding a coaster. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, every now and then you get that person who ruins it for everyone by having a heart-attack. This person's body was not conditioned for this type of stress, and clearly they did not enjoy their ride much. Elevated blood pressure,&#xA;erratic heartbeat and palpitations...they should have instead taken a ride on the log flume. For the rest of us thrill-seekers, this type of gung-ho, take-all-comers attitude gives us a confidence boost by wiring our brains to not be overly stressed in actual emergencies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine the people out there who have grown up in small towns. You may have heard how such people can have a difficult time adjusting to the hustle and bustle of city life, especially in larger cities. This has to do with everything from their metabolism and diet, to their sleep cycle. Their body simply needs to get used to the new environment. The same goes for new combatants. Military's try their best to simulate combat for new trainees. The better the simulation, the better prepared people will be for combat. The first few combat situations for people are obviously going to be the most dangerous, being a truly foreign experience for most peoples bodies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Physiologically it's going to push your body to the limit. After all, you sense your life is in serious danger. But as many people deal with this stress, they can start to acclimate until they ideally stay fearful, but become extremely focused on the fight. The adrenaline rush (and again, other chems) is part of what you need to get used to. If your body has a naturally stable system when exposed to these chemicals, or you have trained it to be so, then you are at an advantage compared to your peers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.psychologytoday.com/blog/threat-management/201001/adrenaline-rushes-can-they-help-us-deal-real-crisis&quot; rel=&quot;nofollow&quot;&gt;https://www.psychologytoday.com/blog/threat-management/201001/adrenaline-rushes-can-they-help-us-deal-real-crisis&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.faqs.org/health/topics/15/Risk-taking-behaviors.html&quot; rel=&quot;nofollow&quot;&gt;http://www.faqs.org/health/topics/15/Risk-taking-behaviors.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8619" LastEditorUserId="-1" LastEditDate="2015-07-21T08:11:21.633" LastActivityDate="2015-07-21T08:11:21.633" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31265" PostTypeId="1" CreationDate="2015-04-12T00:25:04.777" Score="3" ViewCount="71" Body="&lt;p&gt;What kinds of options, if any, do cells (Eukary and Prokary) have for detecting, and repairing damage in Ribosomes (of all types)? I am curious as to &#xA;what happens when a cell sustains damage of some form, such as radiation, and the Ribosomes are damaged. &lt;/p&gt;&#xA;" OwnerUserId="8619" LastActivityDate="2015-04-12T00:25:04.777" Title="Is there a cellular mechanism that detects Ribosomal damage?" Tags="&lt;proteins&gt;&lt;rna&gt;&lt;amino-acids&gt;&lt;ribosome&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31266" PostTypeId="2" ParentId="31231" CreationDate="2015-04-12T01:17:39.553" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I know WBC is primarily responsible for fighting infectious&#xA;  micro-organisms, but does it have any significant role in cleaning up&#xA;  body's own malfunctioning or ageing cells?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They kill the pathogens, infected, senescent, mutated or unnecessary cells, clean up the cell fragments, clean up the oxidized LDL from the surface or arteries, etc... So I think the shortage of leukocytes can cause for example cancer, cardiovascular diseases (dependent on the nutrient composition of the food), etc... in severe cases, but it is hard to find any evidence, since these people die because of infections caused by normally harmless (or well controlled) pathogens, for example HHV8 - causes a cancer type called &lt;a href=&quot;http://en.wikipedia.org/wiki/Kaposi%27s_sarcoma&quot; rel=&quot;nofollow&quot;&gt;Kaposi's sarcoma&lt;/a&gt; in immunodeficient patients, saccharomycosis (S. cerevisiae, S. boulardii, etc... members of the normal flora), aspergillosis (A. niger - it is everywhere in the air), etc... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess there are experiments with NOD/SCID mice (which lack T-cells, B-cells, and NK cells, so a huge part of their immune system is defective), but I cannot find anything about cancer or cardiovascular diseases by them. They are usually engrafted with human cancer, etc... in the experiments, which is not the same as naturally developing cancer. Maybe if you have time to google a day or two, you can find more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Be aware that there are many different types of leukocytes (WBCs), which have their own role in the immune system. Some of the people with leukopenia have lack only of a single type of leukocytes and not all of them. For example HIV patients have helper T-cell deficiency, people with neutropenia have neutrophil granulocyte deficiency, and so on...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know anything of the treatment, I guess bone marrow transplant is involved in the severe cases. If it is caused by medication as a side effect, or you are seeking for medical advice, I think you should consult a doctor.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2015-04-12T01:17:39.553" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31268" PostTypeId="1" AcceptedAnswerId="31270" CreationDate="2015-04-12T03:38:08.663" Score="4" ViewCount="638" Body="&lt;p&gt;In my class we were told that adrenaline (or epinephrine) causes vasoconstriction.&#xA;My question was I had always thought that people took this via an EpiPen when they were having an allergic reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I thought it would make sense, that it would dilate vessels, because this will allow more air through. Or does the constriction help because it tightens the vessels in the throat allowing a reduction of swelling?&lt;/p&gt;&#xA;" OwnerUserId="15066" LastEditorUserId="14552" LastEditDate="2015-04-12T05:25:44.317" LastActivityDate="2015-04-12T05:25:44.317" Title="Question about epinephrine" Tags="&lt;physiology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31270" PostTypeId="2" ParentId="31268" CreationDate="2015-04-12T04:49:34.527" Score="6" Body="&lt;p&gt;An allergic reaction requiring an epipen can be caused by swelling in the throat and/or bronchoconstriction (spasms decreasing the diameter of bronchioles). Bronchoconstriction can occur in the absence of soft tissue swelling in the lips, tongue and throat, and vs. versa.&lt;/p&gt;&#xA;&lt;p&gt;Epinephrine reduces pharyngeal edema (swelling) because it is a potent vasoconstrictor in small arterioles and precapillary sphincters in most body organ systems. This is effected through alpha-1 adrenergic receptor activation. While the blood pressure and heart rate increase (due to beta-1 adrenergic effects), the permeability at the capillary level is decreased, relieving swelling.&lt;/p&gt;&#xA;&lt;p&gt;At the same time, epinephrine relaxes bronchial muscle. It has a powerful bronchodilator action when bronchial muscle is contracted because it is a powerful beta2 adrenergic agonist.&lt;/p&gt;&#xA;&lt;p&gt;Finally, epinephrine inhibits antigen-induced release of inflammatory mediators from mast cells, and to a lesser extent from diminution of bronchial secretions and congestion within the mucosa. Inhibition of mast cell secretion is mediated by beta2 adrenergic receptors.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Uu2Oh.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;sup&gt;Adapted from Simons. Kemp et al. World Allergy Organization Journal 2008 1(Suppl 2):S18-S26   doi:10.1186/1939-4551-1-S2-S18 &lt;/sup&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.waojournal.org/content/1/S2/S18/#B39&quot; rel=&quot;noreferrer&quot;&gt;Epinephrine: The Drug of Choice for Anaphylaxis--A Statement of the World Allergy Organization&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-12T04:49:34.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31271" PostTypeId="2" ParentId="31231" CreationDate="2015-04-12T06:06:42.307" Score="2" Body="&lt;p&gt;Leukopenia is just a definition. In medicine, there's a saying:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Treat the patient, not the numbers.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Numbers can mislead people, sometimes quite seriously. Definitions of leukopenia vary: some define it as less than 5,000 WBCs per µL of blood; others define it as less than 4,000.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Decreases in &lt;em&gt;specific&lt;/em&gt; WBCs is usually described as neutropenia, lymphocytopenia, monocytopenia, etc. This, too, is important information, as each cell has a different function, and thus different results are possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In leukopenia, bone marrow biopsies are very informative. They reveal if the cause is a decreased production of WBCs due to destruction of precursor cells, replacement of marrow by other tissue, invasion of marrow by cancer, etc. If a bone marrow biopsy is normal, that is very comforting.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;does the condition need to be treated?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Most people with anti-epileptic drug (AED) induced leukopenia are just fine. Some common-sense precautions (such as avoiding other drugs which might also cause leukopenia, and checking a white count if you fall significantly ill) should be heeded. If your doctor is a neurologist, they should be thoroughly versed in the side effects of AEDs, as this constitutes a very large patient population for them. Some of the newer AEDs have a lower incidence of leukopenia. Talk to your doctor about the potential benefits and drawbacks of switching.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Does leukopenia increase a person's chances of getting some non-infectious diseases too?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Theoretically possible, but not particularly likely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are truly concerned, ask if you can get a referral to see a hematologist. They should be able to give you a real picture of the problems with long-term AED-induced leukopenia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remember: treat the patient, not the numbers. If you're healthy now, you're likely to continue to be so. Maybe you'll need more blood tests than others, but that doesn't mean you're not healthy. Talk to your doctors, not the internet.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-04-12T06:17:16.800" LastActivityDate="2015-04-12T06:17:16.800" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31272" PostTypeId="2" ParentId="31235" CreationDate="2015-04-12T08:26:34.790" Score="0" Body="&lt;p&gt;On average, it has been stated to be about five weeks however it differs from person to person based primarily on physical stats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The process that would occur :&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;First food that remains in your stomach is digested&lt;/li&gt;&#xA;&lt;li&gt;Readily available energy is then absorbed (This includes glucose, carbohydrates, anything that generally doesn't mean fat)&lt;/li&gt;&#xA;&lt;li&gt;Your body then begins to convert fat into a source of energy. Your body would then begin to lose the resources to make protein and you would experience various effects such as night time blindness due to vitamin deficiencies&lt;/li&gt;&#xA;&lt;li&gt;As you lose salt and other minerals the water you consume begins to build up in your cells via diffusion&lt;/li&gt;&#xA;&lt;li&gt;You can either die of not enough energy or lack of protein or too many cells disintegrate from too much water&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Source(s) : Biology book, Internet, Knowledge.&lt;/p&gt;&#xA;" OwnerUserId="15301" LastActivityDate="2015-04-12T08:26:34.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31274" PostTypeId="1" CreationDate="2015-04-12T10:34:55.027" Score="1" ViewCount="2520" Body="&lt;p&gt;I'm not sure what 'resolution' means in the context of phylogenies.&lt;/p&gt;&#xA;" OwnerUserId="15303" LastActivityDate="2015-04-12T10:48:36.437" Title="What does saying a phylogenetic tree is 'well resolved' mean?" Tags="&lt;bioinformatics&gt;&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2015-04-12T21:34:08.403" ContentLicense="CC BY-SA 3.0" />
  <row Id="31275" PostTypeId="1" AcceptedAnswerId="31316" CreationDate="2015-04-12T10:41:00.867" Score="2" ViewCount="1529" Body="&lt;p&gt;How can one improve a phylogenetic tree? If one was to make the 'golden standard' of phylogenetic trees, what features would it have? Would it be highly reliable, well resolved etc? What other features are important to aim to maximise when it comes to improving phylogenetic trees? &lt;/p&gt;&#xA;" OwnerUserId="15303" LastEditorDisplayName="user24284" LastEditDate="2017-05-30T04:21:48.363" LastActivityDate="2017-12-01T19:34:28.983" Title="What makes a good phylogenetic tree?" Tags="&lt;evolution&gt;&lt;bioinformatics&gt;&lt;homework&gt;&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31276" PostTypeId="2" ParentId="31274" CreationDate="2015-04-12T10:43:18.517" Score="1" Body="&lt;p&gt;It means incomplete separation or a failure to split into two groups unambiguously. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are multiple ways to estimate the resolution of a phylogenetic tree; involving an index to measure the likelihood of observing the phylogenetic tree that you derive relative to those produced by drawing species at random, for instance, or permuting species to produce a null distribution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A badly resolved tree should show up in sets of randomly generated trees far more often than well resolved ones. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2012.00196.x/abstract&quot; rel=&quot;nofollow&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2012.00196.x/abstract&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="6726" LastEditorUserId="6726" LastEditDate="2015-04-12T10:48:36.437" LastActivityDate="2015-04-12T10:48:36.437" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31277" PostTypeId="1" CreationDate="2015-04-12T12:54:42.860" Score="2" ViewCount="52" Body="&lt;p&gt;Cryonics is very popular in science fiction today, as a method of preserving animals, including humans, for long time storage and thawing the tissue later in the future. What is the difficulties with this method? Why can't we simply freeze living persons and expect them to be fully functional again later?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've heard that the membrane potentials get lost in the process and thus all neural activity stops. I've also heard that freezing cells leads to cells imploding, due to the formation of ice crystals, leading to rapid necrosis. Is any of this true or just myths?&lt;/p&gt;&#xA;" OwnerUserId="15304" LastActivityDate="2015-04-12T12:54:42.860" Title="Regarding cryonics, why can't you freeze a living body and then thaw it later, fully functional?" Tags="&lt;neuroscience&gt;&lt;tissue&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31278" PostTypeId="1" CreationDate="2015-04-12T13:29:31.563" Score="3" ViewCount="804" Body="&lt;p&gt;Just before I fall asleep I sometimes experience an itchy and stinging feeling in my body parts. It can be that the nose or neck suddenly start to itch or a tingling stinging feeling in the legs. Sometimes my fingers also start to do small uncontrolled movements.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is this about?&lt;/p&gt;&#xA;" OwnerUserId="15304" LastEditorUserId="5144" LastEditDate="2015-04-12T14:46:36.540" LastActivityDate="2017-08-10T20:07:45.630" Title="Why do body parts sometimes get a itching and tingling feeling when falling asleep?" Tags="&lt;sleep&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31280" PostTypeId="1" CreationDate="2015-04-12T14:47:42.247" Score="2" ViewCount="382" Body="&lt;p&gt;What are the environmental limitations of mosquitos I should know of if I want to avoid getting bitten?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;How fast should I walk in order to be moving too fast for one to bite&#xA;me?&lt;/li&gt;&#xA;&lt;li&gt;Can a fan work to blow mosquitos away from me?&lt;/li&gt;&#xA;&lt;li&gt;If I'm looking to&#xA;buy an apartment, is there a minimum height in which mosquitos will&#xA;no longer reach?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="15308" LastActivityDate="2015-05-14T20:07:53.107" Title="Mosquito physics" Tags="&lt;zoology&gt;&lt;entomology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31281" PostTypeId="1" AcceptedAnswerId="31282" CreationDate="2015-04-12T15:36:28.623" Score="16" ViewCount="2211" Body="&lt;p&gt;Mushrooms disperse their spore in all direction. Then why is there a formation of fairy rings? &lt;strong&gt;Why do they grow in one shape and not randomly?&lt;/strong&gt;  &lt;/p&gt;&#xA;" OwnerUserId="4503" LastEditorUserId="10061" LastEditDate="2015-04-12T17:20:17.387" LastActivityDate="2019-02-13T11:32:58.303" Title="Why do mushrooms grow in rings (sometimes called &quot;Fairy Rings&quot;)?" Tags="&lt;mycology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31282" PostTypeId="2" ParentId="31281" CreationDate="2015-04-12T15:44:46.310" Score="17" Body="&lt;p&gt;When spores germinate, they do not generate mushrooms directly, but haploid &lt;a href=&quot;http://en.wikipedia.org/wiki/Mycelium&quot; rel=&quot;nofollow noreferrer&quot;&gt;mycelium&lt;/a&gt; starts to grow. Only when the mycelium from spores with the other mating type is met, cells fuse and generate diploid mycelium, from which mushrooms can grow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wqZDi.jpg&quot; alt=&quot;basidiocycle&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fairy rings are caused by a radial outgrowth pattern of the diploid mycelium, followed by resource depletion in the oldest part (middle).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4tapJ.gif&quot; alt=&quot;image&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cpbr.gov.au/fungi/mycelium.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;This&lt;/a&gt; page seems to have good additional information about hyphal growth.&lt;/p&gt;&#xA;" OwnerUserId="14698" LastEditorUserId="15950" LastEditDate="2019-02-13T11:32:58.303" LastActivityDate="2019-02-13T11:32:58.303" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="31283" PostTypeId="2" ParentId="31280" CreationDate="2015-04-12T15:48:58.223" Score="3" Body="&lt;p&gt;Speed of mosquitoes vary from place to place and their current health status.But if there is any such problem, maybe you can run a short distance (some yards) and then they won't harass you for some time till they cope up with you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yeah, a fan usually at comfortable speed will be enough to blow the mosquito away. If this doesn't work then set speed at full speed and wrap yourself in a blanket&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think there is some height where mosquitoes can't reach but my friend who lives on 12th floor in his apartment hardly has 4-5 mosquitoes bugging him.&lt;/p&gt;&#xA;" OwnerUserId="4503" LastActivityDate="2015-04-12T15:48:58.223" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31284" PostTypeId="1" CreationDate="2015-04-12T15:56:48.983" Score="2" ViewCount="742" Body="&lt;p&gt;A retrovirus with RNA genome infected a host cell. You would like to isolate the host cell’s RNA (rRNA, tRNA, and mRNA) from the virus RNA. What properties can you rely on to determine the three types of host cell RNA- for example, in terms of their size, complexity, GC content, or abundance in the cell? The undetermined RNA can be identified as the virus RNA.&lt;/p&gt;&#xA;" OwnerUserId="15310" LastEditorUserId="948" LastEditDate="2015-04-12T19:50:36.153" LastActivityDate="2015-04-13T20:29:12.793" Title="How to isolate host cell RNA (tRNA,mRNA,rRNA) from viral RNA?" Tags="&lt;molecular-biology&gt;&lt;homework&gt;&lt;rna&gt;&lt;retrovirus&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31285" PostTypeId="1" CreationDate="2015-04-12T16:10:23.063" Score="4" ViewCount="5279" Body="&lt;p&gt;In Texas, there is lot of grassland and many cotton fields, which need a great deal of water. However, I have not seen any forests or areas with many trees.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why are there no forests or heavily-treed areas in Texas?&lt;/p&gt;&#xA;" OwnerUserId="5688" LastEditorUserId="948" LastEditDate="2015-04-15T01:24:51.580" LastActivityDate="2017-06-01T01:04:29.667" Title="Why are there no trees in Texas?" Tags="&lt;botany&gt;" AnswerCount="5" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31286" PostTypeId="1" AcceptedAnswerId="31288" CreationDate="2015-04-12T16:22:31.960" Score="0" ViewCount="904" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2JdXQ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my book there is a plot of the arterial pressure against time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the plot, during heart contraction, there is greater pressure on the artery and during heart relaxation, there is lower amount of pressure on the arteries. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This makes sense because P = F/A, the surface area of the heart is smaller when it is contracted versus when it is relaxed, hence greater pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But why is there a small bump while the pressure is decreasing from systolic pressure to diastolic pressure?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastActivityDate="2015-04-12T17:29:12.140" Title="What causes a small bump in the arterial pressure plot?" Tags="&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31287" PostTypeId="1" AcceptedAnswerId="31290" CreationDate="2015-04-12T17:13:11.523" Score="0" ViewCount="224" Body="&lt;p&gt;For example, when you are sick but don't feel thirsty, this could be due to baroreceptor reflex that is attempting to readjust salt and water balancing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why shouldn't a patient be left thirsty and let the body to adjust until he or she feels thirsty again?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastActivityDate="2015-04-12T21:55:07.400" Title="Why should or shouldn't we allow the human body to take its natural course?" Tags="&lt;human-biology&gt;&lt;physiology&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-04-13T07:32:31.697" ContentLicense="CC BY-SA 3.0" />
  <row Id="31288" PostTypeId="2" ParentId="31286" CreationDate="2015-04-12T17:23:15.540" Score="1" Body="&lt;p&gt;This bump is related to the closure of the aortic valve as a reaction to the retrograde blood flow which in turn gives small change in blood pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GRXnC.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-04-12T17:29:12.140" LastActivityDate="2015-04-12T17:29:12.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31290" PostTypeId="2" ParentId="31287" CreationDate="2015-04-12T18:08:19.433" Score="2" Body="&lt;p&gt;I am assuming that your question is: &quot;why can a human intervention improve health?&quot;. Let me know if I misunderstood your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why can a human intervention improve health?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's first avoid going into the details of your example. It is quite obvious that human intervention can often improve health in a way that your body alone cannot. To me, an intuitive way to classify the reasons why human intervention are important to improve health into two categories.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The body does not always react in an adaptive manner.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Example: &lt;a href=&quot;http://en.wikipedia.org/wiki/Anaphylaxis&quot; rel=&quot;nofollow&quot;&gt;Anaphylaxis&lt;/a&gt; is a serious and sudden allergic reaction that may cause death. An allergic reaction is what is happening when your immune system recognize a chemical as a infectious element while it is not. The reaction of the body is not adaptive and taking medication such as an anti-histaminic can force the body to stop this &quot;stupid&quot; reaction.&lt;/li&gt;&#xA;&lt;li&gt;Note: There are reasons why the body cannot be always perfect but it is a bit long to make an overview here. There is stochasticity in the developmental processes, there is genetic variation for example due to always occurring deleterious mutations, there is also an arms race between parasites and host. This arm race leads parasites to take advantage of normal host physiological pathways. There are tons of other reasons that relate to the stochasticity and to the physic and physiological constraints of evolutionary processes.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The body sometimes cannot (physical constraint) produce the action that is required to be performed to improve health.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Example:  If you have an important wound, then a human-made compression can by far improve your chance of the survival. The body is not able by itself to simulate this external compression to prevent blood to exit the body through the wound.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;You might easily find semantic issues with these categories though such as the question of cancer and its removal for example and some may argue against this categorization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Dehydration and thirst&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your example would fall into the first category. It is not so uncommon that the body needs water while not causing thirst. Because after 50 years old, the sensation of thirst start to diminished, dehydration without the sensation of thirst is common among old people. Dehydration along with hyperthermia is a relatively important cause of death during hot weather in summer. It is especially true in old people as the sensation of thirst diminishes with age. Dehydration following diarrhea is also a common and important issue in old people sometimes leading to death.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-04-12T21:55:07.400" LastActivityDate="2015-04-12T21:55:07.400" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31292" PostTypeId="2" ParentId="31285" CreationDate="2015-04-12T20:14:38.707" Score="19" Body="&lt;p&gt;A quick &lt;a href=&quot;https://www.google.com/search?q=texas+forests&amp;amp;tbm=isch&quot; rel=&quot;noreferrer&quot;&gt;google image search&lt;/a&gt; reveals that, indeed, Texas has quite lush forests. Remember that the state is extremely large (as compared to the Northeastern states, for example), and encompasses a huge variety of terrain, climates, rainfall amounts, etc. While the stereotypical view of Texas is rugged, dusty terrain:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KaUlc.jpg&quot; alt=&quot;Rugged Texas!&quot;&gt;&#xA;&lt;sup&gt;From: &lt;a href=&quot;http://texasmountaintrail.blogspot.com/2013/12/big-bend-landscape.html&quot; rel=&quot;noreferrer&quot;&gt;http://texasmountaintrail.blogspot.com/2013/12/big-bend-landscape.html&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The eastern part of the state borders Louisiana, and is definitely &lt;em&gt;not&lt;/em&gt; dusty and dry:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DvbtF.jpg&quot; alt=&quot;Northeast Texas&quot;&gt;&#xA;&lt;sup&gt;From: &lt;a href=&quot;https://www.flickr.com/photos/horwath/2488138213/&quot; rel=&quot;noreferrer&quot;&gt;https://www.flickr.com/photos/horwath/2488138213/&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rainfall varies across the state from east to west:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XyTp1.gif&quot; alt=&quot;Texas rainfall 1961-1990&quot;&gt;&#xA;&lt;sup&gt;From: &lt;a href=&quot;http://www.worldatlas.com/webimage/countrys/namerica/usstates/weathermaps/txprecip.htm&quot; rel=&quot;noreferrer&quot;&gt;http://www.worldatlas.com/webimage/countrys/namerica/usstates/weathermaps/txprecip.htm&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;There are many different reasons why trees are not very likely to grow in certain regions, and these may vary from place to place. There may not be enough precipitation to support trees that are not adapted to a drier environment, while some species of grass could survive just fine. Temperature changes could be too severe between summer and winter (grasses just go dormant or die during harsh winters, and regrow in the spring). Fire is a big issue, as well - prairies often burn, and while grasses can regrow quite quickly, a tree that doesn't mature for 20 years may not make it between fires. Grasslands also have very deep, tightly-intertwined root networks, with some reaching 15 feet (~5m) or more below the surface:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.conservationresearchinstitute.org/assets/rootsposter.enlarge.pdf&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/yyyzl.gif&quot; alt=&quot;prairie root network&quot;&gt;&lt;/a&gt;&#xA;&lt;sup&gt;(Click image for higher-resolution PDF)&lt;br /&gt;From: &lt;a href=&quot;http://www.conservationresearchinstitute.org/educational-offerings.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.conservationresearchinstitute.org/educational-offerings.html&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Tree species that survive the other challenges may not be able to penetrate deeply enough to adequately take root, sustain itself, and not fall over. Also, speaking of which, grasslands tend to be susceptible to tornadoes as well, and while grasses just bend before the wind, trees get uprooted or break. So, while any one or two of these issues may be overcome by a particular tree species, when added together it translates into a very inhospitable environment for trees.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2015-04-15T14:50:47.957" LastActivityDate="2015-04-15T14:50:47.957" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="31293" PostTypeId="1" CreationDate="2015-04-12T20:36:02.597" Score="3" ViewCount="379" Body="&lt;p&gt;Afaik skeletal muscles take glucose from the blood to store it localy as glycogen, to be used in the case of intensive exercise. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this still happen&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;if the calorie input is exclusively made up of fats and proteins?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;while fasting / starving?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I know that muscles can run on fatty acids and ketone bodies.&#xA;And that the liver can create glucose by gluconeogenesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But is this &quot;backup&quot;-glucose still used to refill the glycogen stores in the skeletal muscles in those two respective cases? (while resting)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, how would the performance of exercises like sprinting, that normally make use of those stores, be affected?&lt;/p&gt;&#xA;" OwnerUserId="15313" LastActivityDate="2015-05-31T20:44:31.943" Title="Do muscles still hold glycogen reserves if there is no carbohydrate input" Tags="&lt;metabolism&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31294" PostTypeId="2" ParentId="21728" CreationDate="2015-04-12T22:05:38.773" Score="1" Body="&lt;p&gt;There are several subconcepts within the concept of robustness. Several definitions exist for all of these concepts and I am just suggesting one variant of the possible definitions below.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mutational robustness&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Might be defined as a function of the mean and variance of the distribution of mutational effects.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Environmental robustness&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Might be defined as the opposite of phenotypic plasticity. Here, plasticity is not only defined as adaptive plasticity. Plasticity is any phenotypic change induced by an environmental change. Environmental robustness might therefore eventually be defined as the inverse of the slope of the reaction norm.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;Developmental robustness&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Might be defined as the variance of phenotypes that a given genotype produces in a given environment.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.amazon.ca/Ecological-Developmental-Biology-Integrating-Epigenetics/dp/0878932992/ref=sr_1_1?ie=UTF8&amp;amp;qid=1428875955&amp;amp;sr=8-1&amp;amp;keywords=ecological+developmental+biology&quot; rel=&quot;nofollow&quot;&gt;Gilbert and Epel (2009), page 384&lt;/a&gt;, Canalization is developmental robustness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Biology, those concepts almost always refers to genotypes. Rarely do they apply to populations or ecosystems and when they do the definitions are often quite different.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-04-12T22:11:13.010" LastActivityDate="2015-04-12T22:11:13.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31295" PostTypeId="1" AcceptedAnswerId="31297" CreationDate="2015-04-12T22:23:55.940" Score="3" ViewCount="257" Body="&lt;p&gt;Outside of evolution, what were the leading scientific schools of thought that Charles Darwin contented with when he published his evolution theory as way of natural selection in 1859? &lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="238" LastEditDate="2015-04-17T23:26:12.860" LastActivityDate="2015-04-17T23:26:12.860" Title="Before Evolution was proposed by Charles Darwin, what were the leading secular theories to explain how life developed?" Tags="&lt;evolution&gt;&lt;history&gt;" AnswerCount="1" CommentCount="10" ClosedDate="2015-04-13T19:23:43.297" ContentLicense="CC BY-SA 3.0" />
  <row Id="31296" PostTypeId="1" AcceptedAnswerId="31298" CreationDate="2015-04-12T22:24:45.537" Score="1" ViewCount="736" Body="&lt;p&gt;This is a problem taken from &quot;Concepts of Genetics&quot;, Klug et al, 10e. I'm given the following table about the mutations in the &lt;em&gt;BRCA1&lt;/em&gt; gene:&#xA;$$\begin{array}{c|c|c|c|c}&#xA;\text{Kindred}&amp;amp;\text{Codon}&amp;amp;\text{Nucleotide}&amp;amp;\text{Coding}&amp;amp;\text{Frequency in}\\&#xA;&amp;amp;&amp;amp;\text{change}&amp;amp;\text{effect}&amp;amp;\text{control chromosomes}\\&#xA;\hline&#xA;1&amp;amp;24&amp;amp;-11\text{ bp}&amp;amp;\text{Frameshift or splice}&amp;amp;0/180\\&#xA;2&amp;amp;1313&amp;amp;\text{C}\to\text{T}&amp;amp;\text{gln}\to\text{stop}&amp;amp;0/170\\&#xA;3&amp;amp;1756&amp;amp;\text{Extra C}&amp;amp;\text{Frameshift}&amp;amp;0/162\\&#xA;4&amp;amp;1775&amp;amp;\text{T}\to\text{G}&amp;amp;\text{met}\to\text{arg}&amp;amp;0/120\\&#xA;5&amp;amp;\text{N/A}&amp;amp;?&amp;amp;\text{Loss of transcript}&amp;amp;\text{N/A}\end{array}$$&#xA;Footnote: &quot;*N/A indicates not applicable, as the regulatory gene is inferred, and the position has not been identified.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using this information, how can I decide whether the gene is a tumor suppressor or an oncogene?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I already know that &lt;em&gt;BRCA1&lt;/em&gt; is a tumor suppressor, so put another way, how can I arrive at this conclusion given the data above?&lt;/p&gt;&#xA;" OwnerUserId="13127" LastActivityDate="2015-04-13T00:27:32.527" Title="How to tell if a given gene is a tumor suppressor or oncogene?" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31297" PostTypeId="2" ParentId="31295" CreationDate="2015-04-12T22:46:21.513" Score="9" Body="&lt;p&gt;There were many (more or less) non-theological theories of how life had developed before Darwin, starting at the ancient greeks. Many theories included &lt;a href=&quot;http://en.wikipedia.org/wiki/Spontaneous_generation&quot; rel=&quot;nofollow&quot;&gt;spontaneous generation&lt;/a&gt; but also aspects of modification by descent of existing species (i.e. evolutionary change), but most were not that well developed and complete thought. However, one of the more complete evolutionary theories that pre-dated Darwin was &lt;a href=&quot;http://en.wikipedia.org/wiki/Lamarckism&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Lamarckism&lt;/strong&gt;&lt;/a&gt;, which claimed that individuals pass on traits that they have acquired during their life time. So the basic idea was that individuals respond and adapt to the environmental conditions they experience, and that these traits are then transferred to their offspring. This is one example of a non-theological theory that pre-dated Darwin, but I cannot really say if it was the leading one. I do know that Lamarck's ideas were relatively ignored during his own lifetime.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Darwin included some aspects of these ideas in his &quot;&lt;em&gt;Origin of Species&lt;/em&gt;&quot;, but challanged Lamarckism when it came to the main processes of evolution. A weak interpretation of Lamarckism has actually seen a revival after the discovery that epigenetics can be transferred from parents to offspring, see e.g. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867414002864&quot; rel=&quot;nofollow&quot;&gt;Heard &amp;amp; Martienssen (2014)&lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/neuro/journal/v17/n1/abs/nn.3603.html&quot; rel=&quot;nofollow&quot;&gt;Szyf (2014)&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-04-15T22:56:17.587" LastActivityDate="2015-04-15T22:56:17.587" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31298" PostTypeId="2" ParentId="31296" CreationDate="2015-04-12T22:56:33.103" Score="1" Body="&lt;p&gt;I assume these are all carcinogenic mutations. Because some them are clearly recessive loss-of-function mutations (like loss of transcript), you can conclude that the function of the gene consists of &quot;holding back cancer&quot;. When these mutations occur, they can generally be complemented by a healthy allele on the sister chromosome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oncogenes on the other hand, require gain-of-function mutations, like translocation to a more active promotor or dominant negative mutations (like a loss-of-function mutation in a protein which forms multimers, which get &quot;polluted&quot; by the mutant and thus can not be complemented by the other allele). In most cases this &quot;increases&quot; their stimulation of cell division and thus cancerous growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Loss of transcript of an oncogene would not cause cancer.&lt;/p&gt;&#xA;" OwnerUserId="14698" LastEditorUserId="948" LastEditDate="2015-04-13T00:27:32.527" LastActivityDate="2015-04-13T00:27:32.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31299" PostTypeId="1" AcceptedAnswerId="31300" CreationDate="2015-04-12T23:45:04.847" Score="3" ViewCount="337" Body="&lt;p&gt;So if I were to pitch bread yeast, and get to primary fermentation, which as I understand it, is the point at which regular cellular respiration can no longer continue due to a lack of oxygen , which is needed for the electron transport chain. Therefore the yeast switch to fermentation, which produces my desired product, ethanol. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But as I understand it, at this state the yeast are no longer reproducing and are in a survival mode.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore if I were to cut a 2$L$ bottle of my primary ferment in half, and then add more sugar and water to the now separate 1$L$ bottles, and oxygen (if possible), up to 2$L$, would I be able to have the same amount of ethanol produced/would fermentation even occur?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I feel there would be diminishing returns even if it was possible, since yeast can only reproduce asexually so many times, which happens during stressful times, which this process might induce?&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="948" LastEditDate="2015-04-13T01:00:10.047" LastActivityDate="2015-11-26T00:10:47.583" Title="Can yeast in a primary fermentation of wine be used as a source of yeast for new fermentation?" Tags="&lt;reproduction&gt;&lt;yeast&gt;&lt;fermentation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31300" PostTypeId="2" ParentId="31299" CreationDate="2015-04-13T00:44:04.830" Score="3" Body="&lt;p&gt;Yes, it is possible to reuse yeast in both beer and wine fermentation - commercial brewers do it all the time for cost savings and batch reproducibility, and although I'm not as familiar with making wine, many sites including &lt;a href=&quot;http://homedistiller.org/wash/ferment/reuse&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt; say it's perfectly fine, as long as the viability of the cells is high enough. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The yeast aren't necessarily in stress-induced survival mode during fermentation, they're just living (and metabolizing) anaerobically. They may no longer be reproducing, or doing it very infrequently, but they'll remain perfectly happy little buggers (that's a technical term) for quite a while. Give them more food (sugar), and they'll keep fermenting. What eventually stops the process with wine is the level of ethanol rising too high for their comfort. If you were to dilute the ethanol out with water, they'd keep going.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I wouldn't recommend doing this indefinitely (some strains may exhibit genomic instability, etc.), but new batches can certainly be produced with existing pitches.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-04-13T00:44:04.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31301" PostTypeId="1" AcceptedAnswerId="34883" CreationDate="2015-04-13T01:06:01.373" Score="8" ViewCount="758" Body="&lt;p&gt;I found a singular mushroom in my back yard,  It is jet black, seems to have gills and looks somewhat like a flower do to it's upturned-ness. Sorry for not having spore colors, but I didn't want to disturb it. I will post a picture soon. I found this mushroom at 4/11/15 and it disappeared the next day. I'm just south of San Antonio.&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/s6fmD.jpg&quot; alt=&quot;mushroom&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="15317" LastEditorUserId="15317" LastEditDate="2015-04-14T20:53:06.037" LastActivityDate="2015-06-03T17:08:01.710" Title="What is this mushroom?" Tags="&lt;species-identification&gt;&lt;mycology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31302" PostTypeId="1" CreationDate="2015-04-13T01:48:55.133" Score="6" ViewCount="77" Body="&lt;p&gt;I've been reading a little about the &quot;two-hit&quot; hypothesis for tumor suppressor genes &lt;a href=&quot;http://en.wikipedia.org/wiki/Tumor_suppressor_gene#Two-hit_hypothesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;, which mentions that some genes exhibiting haploinsufficiency are exceptions to the hypothesis. I've read elsewhere on this site (namely the answer to &lt;a href=&quot;https://biology.stackexchange.com/a/20404/13127&quot;&gt;this question&lt;/a&gt;) that suggests haplosufficiency as a means of &quot;silencing&quot; the mutation of the tumor suppressor gene such that the expression of the wild-type allele compensates for the mutant allele.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any other mechanisms that contribute to incomplete penetrance of tumor suppressor mutations?&lt;/p&gt;&#xA;" OwnerUserId="13127" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-06-03T17:41:55.497" Title="How can the phenotypic effects of a tumor suppressor mutation be silenced?" Tags="&lt;genetics&gt;&lt;cancer&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31303" PostTypeId="2" ParentId="30267" CreationDate="2015-04-13T03:12:35.573" Score="2" Body="&lt;p&gt;From the pheno-geno map and the genotypes frequencies, you have the whole distribution of phenotypes in your population. The mean of the phenoype $n$, $P_n$ is the &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\bar P_n = \sum f_{G_i} P_{G_i}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $f_{G_i}$ is the proportions of individuals having genotype $G_i$ and $P_{G_i}$ is the phenotype of the individuals with genotype $G_i$. Therefore, the variance of $P_n$ is &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$var(P_n) = \sum f_{G_i} (P_{G_i} - \bar P_n)^2$$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The covariance between the phenotypic traits $n$ and $m$ is &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$cov(P_n,P_m) = \sum f_{G_i} (P_{G_i} - \bar P_n)(P_{G_i} - \bar P_m)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only assumptions you need is that there is no environmental variance. I don't think the above calculations required any other assumption. $G$ can be defined at the haploid or diploid stage, it doesn't change anything.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above calculations however give you the genetic variance and covariance but not the additive genetic variance covariance. I think (but I might be mistaken) that the additive genetic variance would be equal to &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma_D^2 = \sum_i f_i^2(1-f_i)^2(2 \cdot P_{n,i,12} - P_{n,i,11} - P_{n,i,22})^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\sigma_A^2 = \sum_i 2f_i(1-f_i)(f_iP_{n,i,11}+(1-2f_i)P_{n,i,12} - (1-f_i)P_{n,i,22})^2$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;, where $f_i$ is the frequency of the allele $A$ at the locus $i$ (you should get those data by reformatting your geno-pheno map matrix) and $P_{n,i,11}$, $P_{n,i,12}$ and &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$P_{n,i,22} =\frac{1}{l-1} \sum_j P_{n,i,j,22}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;is the $n^{th}$ phenotypic trait for the genotype $22$ and locus $i$ averaged over all other genotypes. There are $l$ genotypes in total. Of course, this works only for biallelic loci. I don't know what it would look like for more alleles.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-04-13T15:12:06.577" LastActivityDate="2015-04-13T15:12:06.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31304" PostTypeId="2" ParentId="19767" CreationDate="2015-04-13T03:57:24.960" Score="15" Body="&lt;p&gt;There's a very big difference between doing the calculations needed to simulate the human brain (or any animal brain - we can do a fairly decent job on &lt;em&gt;C. elegans&lt;/em&gt;), and doing computations.  While a basic leaky integrate &amp;amp; fire model is fairly simple, to &lt;em&gt;accurately&lt;/em&gt; simulate a single neuron in real time takes a pretty fast computer.  See e.g. these links for more, &lt;a href=&quot;http://www.neuron.yale.edu/neuron/&quot; rel=&quot;noreferrer&quot;&gt;http://www.neuron.yale.edu/neuron/&lt;/a&gt;,  &lt;a href=&quot;http://bluebrain.epfl.ch/&quot; rel=&quot;noreferrer&quot;&gt;http://bluebrain.epfl.ch/&lt;/a&gt;  &lt;a href=&quot;http://www.artificialbrains.com/darpa-synapse-program&quot; rel=&quot;noreferrer&quot;&gt;http://www.artificialbrains.com/darpa-synapse-program&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brains do well what computers do poorly, and vice versa.  The HP12C calculator on my desk, made in the early '80s, can do many sorts of mathematical calculations faster than I can, because brains aren't really optimized for doing, for example, compound interest calculations.  But my brain, or my dog's brain for that matter, can do all the 'calculations' needed to process a stream of images, recognize that they show a ball, predict its path, and catch it - while simultaneously processing visual, auditory, olfactory, and kinesthetic inputs for obstacle avoidance and threat recognition, and (in my case, anyway) perhaps thinking about how to solve complex programming problems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe I should add that there are basically three different things that a computer can do in this context:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Complex calculations, whether compound interest, weather modeling, seismic tomography or whatever.&lt;/li&gt;&#xA;&lt;li&gt;Simulating the actual behavior of a brain, or some subset of one, starting from a single neuron.  &lt;/li&gt;&#xA;&lt;li&gt;Trying to replicate what a brain does through algorithms, or Artificial Intelligence.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;(1) is what we mostly use computers for, and they're way better at it than human brains.  (2) is a special case of (1), which we do because we don't have much of an idea how to do (3), and having a simulated brain we can alter at will might help in learning how real brains do what they do.&lt;/p&gt;&#xA;" OwnerUserId="11736" LastEditorUserId="107" LastEditDate="2016-08-18T14:28:53.953" LastActivityDate="2016-08-18T14:28:53.953" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31305" PostTypeId="2" ParentId="28123" CreationDate="2015-04-13T09:02:49.010" Score="4" Body="&lt;p&gt;Think this &lt;a href=&quot;http://staging.aesnet.org/files/dmfile/Saper1.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;review&lt;/a&gt; from Nature can answer your question. A brief summary  ( with slight simplification):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ascending activating system (that is responsible for wakefulness) has two branches:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first one ascends to the thalamus and activates the thalamic relay neurons - these transmit information to the cortex. They get their main input form two acetylcholine producing group of cells:  the pedunculo-&#xA;pontine and laterodorsal tegmental nuclei (PPT/LDT). These two group of cells are also the source of main input for reticular nucleus of the thalamus.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The neurons in the PPT/LDT fire most rapidly during wakefulness and rapid eye movement (REM) sleep, which is the stage accompanied by cortical&#xA;  activation, loss of muscle tone in the body and active dreams&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The second branch, directly activates neurons in the hypothalamus, basal forebrain (BF) and cortex, bypassing the thalamus. This pathway has origins in monoaminergic neurons in the upper brainstem, caudal hypothalamus, as well as the noradrenergic locus coeruleus (LC), serotoninergic dorsal (DR) and median raphe nuclei, dopaminergic ventral periaqueductal grey matter and histaminergic tuberomammillary neurons. Input from this pathway to the cortex is extended /augmented by the lateral hypothalamic peptidergic neurons (that contain melanin-concentrating hormone (MCH) or orexin/hypocretin), and BF neurons(that produce acetylcholine or GABA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sleep is promoted by the so called VLPO (ventrolateral preoptic nucleus).&#xA;The VLPO send outputs to major group of cells of the arousal system in the hypothalamus and brainstem. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The VLPO neurons are primarily active during sleep, and contain the inhibitory neurotransmitters, galanin and GABA.&#xA;  The VLPO also receives afferents from each of the major&#xA;  monoaminergic systems. Both noradrenaline and serotonin inhibit&#xA;  VLPO neurons. The latter do not have histamine receptors, but the&#xA;  tuberomammillary neurons also contain GABA, which is inhibitory&#xA;  to VLPO neurons, as well as several other potentially inhibitory pep&#xA;  tides, such as galanin and endomorphin. Therefore, the VLPO can&#xA;  be inhibited by the very arousal systems that it inhibits during sleep.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2Da0A.png&quot; alt=&quot;sleep-wake pathways&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see in the quote from the paper these two systems can mutually inhibit each other and basically work as a seesaw or 'flip-flop switch'. In this system activity in one  subsystem shuts down the inhibition from the other subsystem and disinhibits its own action (selfreinforcing loop). The transition from one state to the other is relatively fast. Orexin plays important role in stabilizing the switch in one position or the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1YO0h.png&quot; alt=&quot;flip-flop switch&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regulation pf sleep:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Homeostatic:&#xA;It is unclear how homeaostatic regulation of sleep work, yet it has been proposed, that adenosine accumulation in the brain may signal for 'need for sleep'. The extended wakefulness causes the exhaustion of brain glycogen reserves and depletion of ATP levels. As ATP is degraded to ADP, AMP and eventually adenosine, extracellular adenosine levels rise in some parts of the brain including the BF. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In addition, adenosine might disinhibit the  VLPO via presynaptic A1 receptors by reducing inhibitory GABAergic inputs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This implies that during sleep ATP and energy sources are regenerated and free adenosine levels drop, thus inhibition of VLPO might take place again. &#xA;Also it is important to note that the amount of sleep we need is proportional to the time we spend awake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Circadian regulation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is known that humans have quite precise :circadian rhythm:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The suprachiasmatic nucleus (SCN) serves as the brain’s ‘master&#xA;  clock’. Neurons in the SCN fire in a 24-hour cycle that is driven by a&#xA;  transcriptional–translational loop, which persists even when the neurons are dissociated in cell culture.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The SCN has moderate output to the VLPO or orexin neurons, but it has more important projections to the adjacent subparaventricular zone (SPZ) and the dorsomedial nucleus of the hypothalamus (DMH).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The SPZ also has relatively limited projections to the VLPO, orexin&#xA;  neurons and other components of the wake-sleep-regulatory system. However, a major target is the DMH. This region receives inputs from many more neurons in the SPZ than the SCN, so the SPZ is in a position to amplify the output of the SCN. (...) The DMH is one of the largest sources of input to the VLPO and orexin neurons and is crucial for conveying SCN influence to the wake–sleep-regulatory system. The DMH projection to the VLPO comes largely from GABA-containing neurons (that is, those that promote wakefulness by inhibiting sleep), and the projection to the LHA originates from neurons containing glutamate and thyrotropin-releasing hormone (which should presumably be excitatory and promote wakefulness).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So as you can see our circadian rhythm as direct control over our sleep-wake cycle, and that the SCN can heavily promote awakening through SPZ and DMH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thorough review and details can be found in the article I linked at the beginning, I only tried to select key information to provide a (not so ) brief summary. We only sleep about 7-8 hours normally because this is enough for homeostatic regeneration and our circadian rhythm promotes wakefulness in the morning (this is quite simplified).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on their abstract these limited access papers might also be useful (unfortunately I do not have full access to them right now):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.eurekaselect.com/87813/article&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.eurekaselect.com/87813/article&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0074774210930018&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0074774210930018&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0896627315001312&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0896627315001312&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-15T15:55:51.810" LastActivityDate="2015-04-15T15:55:51.810" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31306" PostTypeId="1" CreationDate="2015-04-13T10:11:59.010" Score="2" ViewCount="772" Body="&lt;p&gt;Whenever someone is sick, doctor places 2 fingers on wrist &amp;amp; observes the heart-beat-rate by feeling pulses of a certain artery.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To me it seems the distribution of blood vessels are pretty standard across all variations of humans (I mean identical blood vessel positioning seen across Caucasians, Africans, etc. members)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when someone is born with extra finger or joined skull - which rule/gene/algorithm decides the distribution of network-of-blood-vessels in those special parts?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;em&gt;PS&lt;/em&gt;: I am definitely / apparently not a biology student, so pardon my ignorance&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;Is positioning of blood capillaries random or they too are identically positioned among all humans, although we can't see them.&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="15318" LastActivityDate="2016-07-29T16:39:12.230" Title="What governs the distribution of blood vessels?" Tags="&lt;genetics&gt;&lt;mathematical-models&gt;&lt;biophysics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31307" PostTypeId="1" CreationDate="2015-04-13T11:53:06.217" Score="4" ViewCount="743" Body="&lt;p&gt;I reckon that if you would be able to widen the AP width, it would produce more neurotransmitters in that larger time interval. Is that correct? Or does the neuron have a standard amount of neurotransmitters it releases in order to pass the signal post-synaptically?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(bonus: could it NOT result in neurotransmitter release, or does the definition of an AP include the release of neurotransmitters?)&lt;/p&gt;&#xA;" OwnerUserId="6016" LastActivityDate="2019-02-19T09:36:21.197" Title="Could an action potential produce few or more neurotransmitters based on the stimulus received?" Tags="&lt;neuroscience&gt;&lt;neurotransmitter&gt;&lt;neurophysiology&gt;&lt;action-potential&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31308" PostTypeId="2" ParentId="31307" CreationDate="2015-04-13T12:06:02.033" Score="5" Body="&lt;p&gt;Neurons encode the &quot;largness&quot; of the stimulus in firing frequency. Neurotransmitters are stored in vesicules near the end of the axon. It has been shown that neurotransmitter release follows Poisson-distribution and that usually a single &quot;packet&quot; (quantum) is released - this is known as quantal release. Although the actual number of molecules in a single vesicle vary a bit, and ocasionally multiple vesicles may be emptied, it is accepted that for a single AP a neuron releases a single vesicle. &#xA;These two pages can give you more info and details:&#xA;&lt;a href=&quot;http://neuroscience.uth.tmc.edu/s1/chapter04.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://neuroscience.uth.tmc.edu/s1/chapter04.html&lt;/a&gt;&#xA;&lt;a href=&quot;http://neuroscience.uth.tmc.edu/s1/chapter05.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://neuroscience.uth.tmc.edu/s1/chapter05.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also this &lt;a href=&quot;http://advan.physiology.org/content/37/1/112&quot; rel=&quot;nofollow noreferrer&quot;&gt;link&lt;/a&gt; provides introductionary info on the topic&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A great image from :&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.2006.123224/full&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.2006.123224/full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/03FgN.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-13T13:04:39.213" LastActivityDate="2015-04-13T13:04:39.213" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31309" PostTypeId="2" ParentId="31306" CreationDate="2015-04-13T12:23:57.040" Score="4" Body="&lt;p&gt;The growth of blood vessels is called angiogenesis. This process occures during embrional development, tissue repair, and even tumor formation (in fact this is a crucial step for tumors to survive). This Nature review (&quot;&lt;a href=&quot;ftp://ftp.mpib-tuebingen.mpg.de/kyb/bweber/papers_db/2007/Adams/Nat%20Rev%20Mol%20Cell%20Biol%202007%20Adams.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Molecular regulation of angiogenesis and lymphangiogenesis&lt;/a&gt;&quot;)provides great overview of the process, I'll try and briefly summarize things:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general large arteries grow circumferential  to keep up with increased blood transfer, while capillaries branch to a more complex network in order to be able to supply blood to every cell. The circulation system starts as a &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;primitive &#xA;  and uniform vascular structures, known as primary capil-&#xA;  lary plexi,&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;that later develop into a hiearchical system of arteries, capillaries and veins. Main regulator of the morphogenesis of blood-vessels is the &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;vascular endothelial growth factor A (VEGFA; also known as vascular&#xA;  permeability factor (VPF)).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This needed for the chemotaxis (the movement of an organism in response to a chemical stimulus. from: &lt;a href=&quot;http://en.wikipedia.org/wiki/Chemotaxis&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Chemotaxis&lt;/a&gt;) and differentiation of endothelial precursor cells (EPCs; angioblasts), endothelial cells (ECs) and the assembly of ECs to vascular structures (termed vasculogenesis), as shown in the figure taken from the article I linked. EPCs themselves differentiate from mesodermal cells during early embryo development and aggregate to form blood islands that later form the  vasculogenic formation of honeycomb-shaped primary capillary plexi.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PUmGp.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also it is important to note that :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;alternative splicing of VEGFA can generate several variants of the growth factor, including the so-called b isoforms that differ in the last six C-terminal amino-acid residues and have anti-angiogenic properties. The balance between the different VEGFA isoforms can regulate blood-vessel &#xA;  growth and patterning. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also local composition of extracellular matrix (ECM) and the interaction between ECM and cells can affect angiogenesis. For example release of matrix bound VEGF is important in the regulation of the level of available VEGF. Also: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Furthermore, the physical contact between ECs and pericytes is thought to induce a quiescent, non-sprouting phenotype.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Sprouting itself carried out by the selection of some ECs in the capillary wall to lead the growth of the new sprout. See next figure also from the linked article:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eVeRK.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notch receptors and Delta-like 4 (DLL4) ligands play key role in this process. In tip cell(s) DLL4 expression is induced (in response to VEGFA), while the Notch signaling in neighboring cells (activated by the DLL4) represses sprouting (by down regulating VEGFR2 - VEGF receptor 2) . This is important, because otherwise excess sprouting would lead to a dense network of capillaries and blood would just spread out too thin and would be unable to supply the organs with oxygen and nutrients.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to tip ECs be able to grow new capillaries they ahve to undergo some changes. Mobility is most likely gained by activated secreted or cell-surface bound proteases, to locally degrade the basal membrane. Interaction with other ECs have to be changed, without completely disrputing cell-cell junctions and the integrity of the vessel-wall. Also the apical-basal (apical side - faces the lumen of the vessel) polarity of the cells have to be reversed in order to be able to grow outwards (from the basal side of the endothelium. In order for the new capillary vessel to grow, the elongation of the new sprout has to be polarized and directional. This is achieved by spatial concentration gradient of ECM bound VEGFA isoforms along with prominent expression of VEGFR2 in the tips of sprouts.&#xA;For blood functional blood vessels to be formed the tips must cease growing and exploratory phenotype when they find their target, and string EC-EC junctions need to be formed. Also the generation of the lumen of the newly formed vessel is required.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see forming of new blood vessels is a complex process that is controlled by local signals, yet it is part of a bigger process - the development of the embryo and organs that is regulated by many many genes and processes. Since our general architecture is the same it is logical that or circulatory system is similar. As for the abnormal structure of a body I think perfusion of that extra body part depends on the local environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The review linked at the beginning of this post has extra info on arterio-venosus differention and many other things.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="5144" LastEditDate="2016-07-29T16:39:12.230" LastActivityDate="2016-07-29T16:39:12.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31310" PostTypeId="2" ParentId="31307" CreationDate="2015-04-13T12:37:58.500" Score="6" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Widening of the action potential increases neurotransmitter release;&lt;/li&gt;&#xA;&lt;li&gt;Generally, an action potential results in the release of about one vesicle of  neurotranmitters; &lt;/li&gt;&#xA;&lt;li&gt;An action potential does not have to lead to neurotransmitter release - the chance being anywhere between 9 - 100%, depending on the synapse under investigation.&#xA;&lt;br&gt;&#xA;&lt;br&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Neurotransmitters are released in packets, called neurotransmitter &lt;strong&gt;vesicles&lt;/strong&gt;: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rYYII.gif&quot; alt=&quot;synaptic vesicles&quot;&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://scienceblogs.com/purepedantry/2007/03/06/neuron-to-glia-synapse-on-axon/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;sup&gt;Source: Science blogs&lt;/sup&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vesicles are released via a mechanism involving Ca&lt;sup&gt;2+&lt;/sup&gt;. When an action potential reaches the synaptic terminal, voltage-gated Ca&lt;sup&gt;2+&lt;/sup&gt; channels open, which leads to Ca&lt;sup&gt;2+&lt;/sup&gt; influx. The increased Ca&lt;sup&gt;2+&lt;/sup&gt; in the terminal leads to release of vesicles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A study by &lt;a href=&quot;http://www.jneurosci.org/content/17/10/3425.full.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sabatini &amp;amp; Regehr (1997)&lt;/a&gt; showed that widening of the presynaptic action potential in rat cerebellar cells resulted in enhanced Ca&lt;sup&gt;2+&lt;/sup&gt; influx, which in turn greatly enhanced neurotranmitter release.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to a study in rat hippocampal cells it was shown that, on average, a single action potential releases approximately 0.5% of the vesicle pool from the presynaptic terminal. The presynaptic vesicle pool was estimated to be 100 - 200 vesicles, which hence &lt;strong&gt;added up to 0.5 - 1 vesicle released per action potential&lt;/strong&gt; &lt;a href=&quot;http://www.cell.com/neuron/abstract/0896-6273(95)90336-4?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2F0896627395903364%3Fshowall%3Dtrue&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Ryan &amp;amp; Smith, 1995)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An earlier study of &lt;a href=&quot;http://www.sciencemag.org/content/262/5134/754.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rosenmund et al. (1993)&lt;/a&gt; confirms these findings in hippocampal neurons, and investigated the variability between different synapses in greater detail. They found that the chance that a single action potential released neurotranmitters was &lt;strong&gt;9 - 54%&lt;/strong&gt;. They reasoned that larger synaptic terminals, or terminals triggered by long-term potentiation have a higher chance of releasing neurotransmitter. Moreover, such terminals with enhanced release probability may also have a higher chance of releasing &lt;strong&gt;multiple vesicles per action potential&lt;/strong&gt;. They predicted that 54% of release events from such enhanced terminals may release multiple vesicles per action potentials, whereas just 9% of normal terminals may do this.&lt;br&gt;&#xA;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA; &lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.sciencemag.org/content/262/5134/754.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rosenmund et al. &lt;em&gt;Science&lt;/em&gt; 1993; &lt;strong&gt;262&lt;/strong&gt;: 754-6&lt;/a&gt;&lt;br&gt;&#xA; &lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.cell.com/neuron/abstract/0896-6273(95)90336-4?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2F0896627395903364%3Fshowall%3Dtrue&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ryan &amp;amp; Smith, &lt;em&gt;Neuron&lt;/em&gt; 1995; &lt;strong&gt;14&lt;/strong&gt;: 983-9&lt;/a&gt;&lt;br&gt;&#xA; &lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.jneurosci.org/content/17/10/3425.full.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sabatini &amp;amp; Regehr, &lt;em&gt;J Neurosci&lt;/em&gt; 1997; &lt;strong&gt;17&lt;/strong&gt;: 3425-35&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2019-02-19T09:36:21.197" LastActivityDate="2019-02-19T09:36:21.197" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="31311" PostTypeId="1" AcceptedAnswerId="31312" CreationDate="2015-04-13T14:56:12.797" Score="7" ViewCount="5362" Body="&lt;p&gt;Having muscle tissue in our bronchioles that can constrict seems like a poor choice for tissue. Why would our airway want to ever close up? Wouldn't it be more beneficial for our bronchioles to just remain open? &lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6307" LastEditDate="2015-04-13T15:32:51.353" LastActivityDate="2021-04-23T11:30:35.947" Title="Why is there smooth muscle in our bronchioles?" Tags="&lt;muscles&gt;&lt;lungs&gt;&lt;human-physiology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31312" PostTypeId="2" ParentId="31311" CreationDate="2015-04-13T15:19:40.107" Score="6" Body="&lt;p&gt;There are at least two things to consider.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, ability to limit airflow is a &lt;a href=&quot;http://www.disabled-world.com/health/respiratory/asthma/&quot; rel=&quot;nofollow noreferrer&quot;&gt;defense mechanism&lt;/a&gt; for animal. Imagine getting into area of some sort of toxic evaporation, e.g. CO2 cloud near volcano , then it makes sense to decrease delivery of toxin via lungs to minimum. As I understand, that is what an allergic asthma attack. (Sorry for not providing good enough source of that)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, you are incorrect in assuming that normal state is &quot;dilated&quot;. Dilation of branchioles is &lt;a href=&quot;http://en.wikipedia.org/wiki/Sympathetic_nervous_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;sympathetic&lt;/a&gt; (&quot;fight-and-fly&quot;) response of the nervous system to something like danger, that requires short-term boost in energy production. That is, by default, your airflow is limited. Probably, to limit amount of energy you effectively burn via oxygenation. But most importantly, you leave yourself a reserve in terms of oxygen supply for critical moments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some more information you might &lt;a href=&quot;http://hsc.uwe.ac.uk/rcp/rs-rt-bronchioles.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;find here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="20758" LastEditDate="2017-07-25T05:58:52.133" LastActivityDate="2017-07-25T05:58:52.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31313" PostTypeId="1" CreationDate="2015-04-13T15:39:42.063" Score="2" ViewCount="479" Body="&lt;p&gt;Let's suppose the concentration of a 20-nt DNA strand is $10^{-4}$M and the solution does not contain any salt ions. In a solution with pH 7, $[H^+]=10^{-7}$M, on average each DNA has only 0.001 protons. But the DNA phosphate groups become charged through de-protonation so each DNA should effectively release 20 protons thus we would expect $[H^+]=20\times 10^{-4}$M. How does the system maintain chemical equilibrium while keeping charge neutrality? If $[H^+]=10^{-7}$M because pH=7, where do other protons go?&lt;/p&gt;&#xA;" OwnerUserId="15307" LastActivityDate="2015-04-15T02:20:55.407" Title="What's the proton concentration around a DNA helix?" Tags="&lt;dna&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31314" PostTypeId="1" CreationDate="2015-04-13T15:43:09.490" Score="2" ViewCount="238" Body="&lt;p&gt;I have been having difficulties with low transduction efficiencies of my retrovirus production. I expand my plasmid of interest (on MiG-GFP plasmid) in DH5α E Coli for ~24 hours, purify with Qiagen midi prep kits, then put on ~90% confluent 293FT cells with either retronectin or polybrene for 24 hours. I then change media and harvest supernatant at 48 and 72 hours of incubation with the 293FT cells. I then expose 3T3 cells to varying volumes of the virus containing 293FT media and am able to transduce about 10% of the 3T3 cells, which is really low. That being said, here and there I am able to get very high transduction efficiencies on the 3T3 cells, but for unknown reasons. I have tried concentrating the virus but transduction efficiencies don't increase all that much. And I have tried growing up the plasmid in Stbl3 cells, which if anything gives me worse virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anything here jump out as being responsible for low transduction efficiencies. Or is there another way somebody does this that works really well?&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-04-13T18:36:45.683" Title="Retrovirus Production" Tags="&lt;molecular-biology&gt;&lt;virus&gt;&lt;retrovirus&gt;&lt;transfection&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31315" PostTypeId="2" ParentId="31313" CreationDate="2015-04-13T16:50:59.760" Score="4" Body="&lt;p&gt; DNA stands for &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA&quot; rel=&quot;nofollow&quot;&gt;deoxyribonucleic &lt;strong&gt;acid&lt;/strong&gt;&lt;/a&gt;. Acid, by definition and mechanism in aqueous environment, is something that donates proton ($H^+$). HCl dissolved in water will donate proton to solution, thus bringing pH down, since $pH=-log_{10}[H^+]$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA, being an acid, donates protons to water and brings pH down a notch. Just like in case with HCl, it has nothing to do with keeping charge neutrality. Water is not a buffer, that is able to tolerate or smooth change in pH. What happens when you add DNA to buffered solution, say phosphate buffer, is completely different story from biochemistry.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-04-14T06:32:07.770" LastActivityDate="2015-04-14T06:32:07.770" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31316" PostTypeId="2" ParentId="31275" CreationDate="2015-04-13T17:39:12.643" Score="4" Body="&lt;p&gt;A 'good' phylogenetic tree would be completely refined, properly binary, have high bootstrap support for all its branches, and reconstruct clades we think exist with high support values.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally high support values(there are other methods besides bootstrapping but that is a question for another time) is a measure of a good tree. There are other concerns, for example a tree that has no &lt;a href=&quot;http://www.dbbm.fiocruz.br/james/GlossaryF.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;felsenstein zones&lt;/a&gt; is probably better than one that has lots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can know a lot more about trees than you suppose, though. Through simulation studies we can create datasets with a known phylogenetic history and then see how well the methods reconstruct the history. There are still problems(errors in the model used, just random error, ILS, HGT, other things) but mostly that kind of study tells us what good phylogenies look like.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's very easy to generate a lot of different phylogenies. Using different methods, different models or approximation schemes, different genes or sequences from each species, or simply bootstrapping &quot;new&quot; samples from your existing dataset. A phylogeneticist usually has dozens of trees to choose from, which is a sort of crude bootstrap method itself. If trees look similar, they're probably pretty good. If they don't, you have a problem.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="4109" LastEditDate="2017-12-01T19:34:28.983" LastActivityDate="2017-12-01T19:34:28.983" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31319" PostTypeId="2" ParentId="31314" CreationDate="2015-04-13T18:36:45.683" Score="2" Body="&lt;p&gt;In my experience, transduction efficiencies skyrocketed when I applied a spin-infection procedure. A 30 min low speed centrifuge with the virus changed a lot. Here is the TRC protocol for this: &lt;a href=&quot;http://www.broadinstitute.org/rnai/public/dir/download?dirpath=protocols/production&amp;amp;filename=TRC%20viral%20infection%20200909.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.broadinstitute.org/rnai/public/dir/download?dirpath=protocols/production&amp;amp;filename=TRC%20viral%20infection%20200909.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15321" LastActivityDate="2015-04-13T18:36:45.683" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31320" PostTypeId="2" ParentId="31284" CreationDate="2015-04-13T20:19:19.320" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.lifetechnologies.com/us/en/home/references/ambion-tech-support/rna-isolation/tech-notes/bacterial-rna-isolation-from-infected-eukaryotic-hosts.html&quot; rel=&quot;nofollow&quot;&gt;Thermo Fisher has a protocol&lt;/a&gt; for the separation of host mammalian RNA from prokaryotic RNA, optimized for E. coli vs human, mouse or rat sequences. Capture oligonucleotides bind portions of the mammalian RNA and hybridize. These hybridized oligo/RNA are then removed from solution via &quot;oligonucleotide-derivatized magnetic beads,&quot; after which the remaining RNA assumed to be from whatever prokaryote can be precipitated out w/ ethanol. If you know enough about your virus and your host, I don't see why a similar assay can't be created. Otherwise, Thermo Fisher has additional links to RNA isolation protocol.. most of the viral assays, however, utilize serum, plasma, etc. because host DNA/RNA will elute along with the viral RNA if they're present, as in samples containing cells. &lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-04-13T20:29:12.793" LastActivityDate="2015-04-13T20:29:12.793" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31321" PostTypeId="1" AcceptedAnswerId="31322" CreationDate="2015-04-13T21:19:39.780" Score="1" ViewCount="2992" Body="&lt;p&gt;In my text book it says that &quot;Troponin&quot; is a complex of Troponin C, I and T. In this sense, what is the relation between Troponin complex and C, I, T?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastActivityDate="2017-11-16T16:09:57.763" Title="What is a complex?" Tags="&lt;proteins&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="8" ClosedDate="2017-11-26T19:37:02.130" ContentLicense="CC BY-SA 3.0" />
  <row Id="31322" PostTypeId="2" ParentId="31321" CreationDate="2015-04-13T21:44:52.513" Score="5" Body="&lt;p&gt;The word complex in your sentence designate a &lt;code&gt;protein complex&lt;/code&gt;, also called &lt;code&gt;multiprotein complex&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A protein complex is a group of two or more polypeptide chains that bind together to make up a functional unit. A complex can be made up of similar polypeptide chains or totally different polypeptide chains. Proteasome, Metabolon or hemoglobins are examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more info, have a look at &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Multiprotein_complex&quot;&gt;wiki&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2015-04-13T21:44:52.513" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31323" PostTypeId="1" AcceptedAnswerId="34123" CreationDate="2015-04-13T21:52:00.810" Score="3" ViewCount="25801" Body="&lt;p&gt;The sliding filament mechanism as explained by my text does not elaborate on how ATP is involved in the cross bridge binding and contraction process. How does muscle contraction utilize ATP?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my text explains this is the procedure for a contraction:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Ach released by motor neuron cross cleft and binds to motor end&#xA;plate&lt;/li&gt;&#xA;&lt;li&gt;AP generated in response to binding of Ach gated channels and propagates down T tuble&lt;/li&gt;&#xA;&lt;li&gt;T tuble triggers Ca2+ from sarcoplasmic reticulum&lt;/li&gt;&#xA;&lt;li&gt;Ca2+ binds onto tropinin on actin filament and removes tropomyosin&lt;/li&gt;&#xA;&lt;li&gt;This opens up sites for myosin to attach to actin using protein heads&lt;/li&gt;&#xA;&lt;li&gt;Actin filament is pulled toward the center of sarcomere, causing contraction&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I see that the action potential definitely needs ATP in order to be generated, aside from that I am surprised that the actual contraction via cross bridge binding does not seem to need ATP. &lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="9943" LastEditDate="2015-04-14T04:02:58.223" LastActivityDate="2015-05-09T12:08:28.917" Title="How is ATP involved in muscle contraction?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31324" PostTypeId="1" CreationDate="2015-04-14T00:58:39.397" Score="2" ViewCount="1560" Body="&lt;p&gt;I know of someone who cannot seem to wear watches without the battery dying or something else about the watch going haywire. this person was told it is because their body is producing too much electricity and that by putting nail polish on the reverse of the watch to block the current the watch would work.&#xA;This was tried and it actually worked. My question is, is this a real thing? I couldn't find a legit discussion of this online.&lt;/p&gt;&#xA;" OwnerUserId="15323" LastActivityDate="2015-04-14T00:58:39.397" Title="Can a person's body produce enough electricity to break a wristwatch?" Tags="&lt;energy&gt;" AnswerCount="0" CommentCount="4" ClosedDate="2015-04-14T07:54:32.267" ContentLicense="CC BY-SA 3.0" />
  <row Id="31326" PostTypeId="1" AcceptedAnswerId="31362" CreationDate="2015-04-14T01:48:04.793" Score="13" ViewCount="1257" Body="&lt;p&gt;Infection with many viruses will result in decades-long if not lifetime immunity, for example chicken pox.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of the large number of viruses responsible for the common cold, lifelong immunity to the common cold isn't possible; we will still be susceptible to those we haven't encountered before. But we do develop immunity to those we've been exposed to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Influenza virus mutates quickly enough that there will nearly always be strains which will be new to us. Immunity to HIV is difficult because of the particular cells the virus attacks (as well as mutations).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, Norovirus, while there are many strains, is particularly problematic because immunity to a strain lasts less than a year, making reinfection with the same strain repeatedly possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the reason Norovirus infection doesn't confer longer-lasting immunity known?&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-04-15T02:49:52.063" Title="Why are people unable to develop lasting immunity against Norovirus?" Tags="&lt;immunology&gt;&lt;virus&gt;&lt;immunity&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31327" PostTypeId="1" AcceptedAnswerId="31331" CreationDate="2015-04-14T06:22:19.897" Score="2" ViewCount="484" Body="&lt;p&gt;The Frank Starling law appears to be a trivial observation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;stroke volume is directly related to the end diastolic volume&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In everyday language, as more blood fills the heart, the heart pumps more blood out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone point out whether there are some inaccuracies in the above description because I don't understand why every article on FS law requires upward 20 pages. Even youtube video on this topic is 8 minutes long. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the big idea here that I am missing?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastActivityDate="2015-04-14T12:08:04.123" Title="What is the insight of Frank Starling law of the heart?" Tags="&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31329" PostTypeId="2" ParentId="27536" CreationDate="2015-04-14T09:55:06.863" Score="8" Body="&lt;p&gt;I found a nice &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0268960X14000046&quot;&gt;article&lt;/a&gt; that has insights to this matter. As posted before me it is true that only adults, but not juvenile individuals show this difference. Direct and indirect effects of sex hormones on bone marrow erythropoiesis and renal erythropoietin production has been proven, but it works in both sexes the same way. Females are capable to elevate their haemoglobin / red blood cell levels to external stimuli, yet at same conditions (same altitude etc) the difference remains. Also:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Men, premenopausal women and postmenopausal women have similar plasma erythropoietin levels&lt;/strong&gt;, indicating that women do not attempt to compensate for their lower haemoglobin levels by increasing erythropoietic drive. These observations show that the prevailing lower haemoglobin level in females cannot be ascribed to a lack of bone marrow or renal erythropoietic capability: they indicate that &lt;strong&gt;adult females maintain their venous haemoglobin levels at a lower level than adult males as a physiological steady state&lt;/strong&gt; — they do not try under physiological conditions to maintain the same levels as adult males. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This could be achieved by modulation of the juxtaglomerular apparatus signal (JGA) of the kidney. The JGA has important role in the regulation of the haemoglobin level - it is the main input for erythropoietic red blood cell production by regulating renal filtration and thus regulating the amount of oxygen that gets to the EPO producing peritubular cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is noteworthy to say that similar difference exist in mammals and even there are examples among birds and reptiles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is described in the linked paper that both men and women achieve the same or very similar microcirculatory haematocrit level inspite the different mean venous haemoglobin levels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This implies the very interesting theory / reasoning in the article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(...) that both sexes set their mean optimum level separately and to some degree independently.(...) the red cell mass is an enormous resource in animals — one third of the body's cells by number in adult humans, and demands enormous effort to establish and maintain.(...)This price must be paid for by increased fitness.(...)The excess red cells over the critical minimum that circulate in the large vessels (and slowly through in the spleen in some species) and that constitute half or more of the venous haemoglobin level probably provide a storage function for the reserve red cell mass for use when the need arises for increased work — fight, flight, food and reproduction. They may also act as reserves for heat exchange and iron storage. It is likely that the return in fitness from this reserve differs between the sexes, and therefore that the optimal size for maximal cost benefit also differs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-15T15:54:26.197" LastActivityDate="2015-04-15T15:54:26.197" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31330" PostTypeId="1" AcceptedAnswerId="31437" CreationDate="2015-04-14T11:57:57.027" Score="4" ViewCount="616" Body="&lt;p&gt;Most microalgae have rigid cell walls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Dunaliella Salina&lt;/em&gt; is a pretty famous example of an algae with no cell wall, but just a plasma membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any other microalgae without a cell wall?. I have researched but I can only find Dunaliella being mentioned.&lt;/p&gt;&#xA;" OwnerUserId="15170" LastActivityDate="2015-04-17T04:40:10.360" Title="Microalgae without cell walls?" Tags="&lt;microbiology&gt;&lt;cell-membrane&gt;&lt;cell&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31331" PostTypeId="2" ParentId="31327" CreationDate="2015-04-14T12:08:04.123" Score="0" Body="&lt;p&gt;This is the short answer from &lt;a href=&quot;http://en.wikipedia.org/wiki/Frank%E2%80%93Starling_law#Physiology&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; :) :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As the heart fills with more blood than usual, the force of cardiac&#xA;  muscular contractions increases.[2] This is a result of an increase in&#xA;  the load experienced by each muscle fiber due to the extra blood load&#xA;  entering the heart. The stretching of the muscle fibers augments&#xA;  cardiac muscle contraction by increasing the calcium sensitivity of&#xA;  the myofibrils, [3] causing a greater number of actin-myosin&#xA;  cross-bridges to form within the muscle fibers. The force that any&#xA;  single cardiac muscle fiber generates is proportional to the initial&#xA;  sarcomere length (known as preload), and the stretch on the individual&#xA;  fibers is related to the end-diastolic volume of the left and right&#xA;  ventricles.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In the human heart, maximal force is generated with an initial&#xA;  sarcomere length of 2.2 micrometers, a length which is rarely exceeded&#xA;  in the normal heart. Initial lengths larger or smaller than this&#xA;  optimal value will decrease the force the muscle can achieve. For&#xA;  larger sarcomere lengths, this is the result of less overlap of the&#xA;  thin and thick filaments; for smaller sarcomere lengths, the cause is&#xA;  the decreased sensitivity for calcium by the myofilaments.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;in one sentence, it is a response to tension.&lt;/p&gt;&#xA;" OwnerUserId="1916" LastActivityDate="2015-04-14T12:08:04.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31332" PostTypeId="2" ParentId="13618" CreationDate="2015-04-14T12:13:45.783" Score="3" Body="&lt;p&gt;Yes, transcription of a polyA sequence will be unreliable: for a repetition of 15 times the same nucleotide, the rate of transcription errors will be huge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example in E. coli, this paper &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC331007/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC331007/&lt;/a&gt; gives some order of magnitude of transcription errors caused by repeats of nucleotides. According to their data, for a run of 11 A (so shorter than yours), their are more than one third of transcripts with a frame-shift (deletion or insertion of one nucleotide).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition you may have bigger problems than transcription errors: your construct will also be extremely prone to frame-shift mutations. For example according to the data on figure 3 of &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22991466&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/22991466&lt;/a&gt; by extrapolating to a run of 15 A, you can expect an indel rate higher than 10^-2 per base pair per generations. Because you have 15 target nucleotides it means that more than 10% of the cells will have a frameshift mutation leading to your gene not being functional.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not have data for 'A consecutive sequence of two nucleotides'.&lt;/p&gt;&#xA;" OwnerUserId="15330" LastEditorUserId="15330" LastEditDate="2015-04-14T14:20:10.420" LastActivityDate="2015-04-14T14:20:10.420" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31333" PostTypeId="2" ParentId="19767" CreationDate="2015-04-14T12:23:31.913" Score="3" Body="&lt;p&gt;A simple calculator (which is a computer) calculates 298465+46547 much faster than us. a PC forecast possible events faster than us. But even the fastest computer can't recognize a new pattern faster than us (the computer may never do that). So each one has its relative advantages.&lt;/p&gt;&#xA;" OwnerDisplayName="user11667" LastActivityDate="2015-04-14T12:23:31.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31334" PostTypeId="1" AcceptedAnswerId="31436" CreationDate="2015-04-14T13:51:56.473" Score="5" ViewCount="1234" Body="&lt;p&gt;In my textbook it is stated that the T3 hormone produced at the thyroid gland is 3-5 times more biologically active than T4.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is being active defined and how can this effect be measured?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="14735" LastEditDate="2015-04-14T13:53:38.603" LastActivityDate="2015-04-17T02:56:09.837" Title="What does it mean for a hormone to be &quot;active&quot;" Tags="&lt;endocrinology&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31335" PostTypeId="1" CreationDate="2015-04-14T14:11:39.650" Score="1" ViewCount="68" Body="&lt;p&gt;On the one hand, somatic cells's DNA age as life goes on, mitosis after mitosis, and that is reflected into reduced telomeres.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, during life, reproductive stem cells must age too. However one half of the DNA of some random old reproductive stem cell is eventually transferred through reproduction, and the ageing cycle begins again, with new somatic cells with long telomeres.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What mechanisms can explain reproductive stem cells DNA do not age as somatic cells' DNA ? Or do we know how telomeres are growing back from old reproductive stem cells to gamete during meiosis ? Put another way, how is it possible that we are born with long telomeres ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am sorry for the formulation of my question. I think it is understandable but not really well written. However I don't know how to formulate it another way yet. Do not hesitate to reformulate it if you feel like it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="9796" LastActivityDate="2015-04-14T14:11:39.650" Title="from an ageing reproductive stem cell's DNA to baby's &quot;brand new&quot; somatic cells' DNA" Tags="&lt;stem-cells&gt;&lt;reproductive-biology&gt;" AnswerCount="0" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31336" PostTypeId="1" CreationDate="2015-04-14T16:01:52.490" Score="0" ViewCount="7910" Body="&lt;p&gt;1.What is the function of heterocyst?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2.Where it is present?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A heterocyst I think may be a protecting organ in cells!&lt;/p&gt;&#xA;" OwnerUserId="15331" LastEditorUserId="14735" LastEditDate="2015-04-14T21:36:44.450" LastActivityDate="2017-08-05T06:07:58.037" Title="Heterocyst function in cyanobacteria and its localization" Tags="&lt;bacteriology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31337" PostTypeId="2" ParentId="31336" CreationDate="2015-04-14T16:44:59.470" Score="3" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Heterocyst&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt; :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Heterocysts are specialized, pale-yellow,thick-walled cells with disputed function nitrogen-fixing formed during nitrogen starvation by some filamentous cyanobacteria, such as Nostoc punctiforme...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Thus by definition these are not within the cells, but differentiated cells themselves.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a good &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC94876/&quot; rel=&quot;nofollow noreferrer&quot;&gt;paper&lt;/a&gt; that can give you details on nitrogen fixation in the cyanobacterium Anabaena variabilis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general: cyanobacteria are photosynthetic prokaryotes, and many of them are capable of fixing nitrogen (that is the ability to use and incorporate nitrogen from the air as N2 gas). The enzyme called nitrogenase is oxygen sensitive thus either temporal or spatial separation of nitrogen fixing must be done to avoid damage to the enzmye from oxygen produced by photosynthesis.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In Anabaena spp., aerobic nitrogen fixation is confined to differentiated cells called heterocysts that form in a semiregular pattern in a filament in response to nitrogen starvation. Fixed nitrogen in the heterocysts is transported to vegetative cells in the filament, while vegetative cells supply carbon and reductant to heterocysts&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So as you can see spearate cells work together to supply each other with necessary nutrients. It is important to note that when sufficient fixed nitrogen source is available the number of such specialized formations is low due there is no need for extra nitrogen to be fixed&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are plenty of details on heterocysts and nitrogen fixation in the linked article. Also &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1360138598012904&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; paper hold details of regulation of nitrogen fixation and also has a thorough image of the process:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bXN27.jpg&quot; alt=&quot;nitrogen fixation&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-14T20:50:14.013" LastActivityDate="2015-04-14T20:50:14.013" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31338" PostTypeId="1" AcceptedAnswerId="31385" CreationDate="2015-04-14T16:51:41.177" Score="4" ViewCount="441" Body="&lt;p&gt;We have the hypothalamus-anterior pituitary-endocrine axis, but is there a similar chain of command for posterior pituitary gland such that oxycotin and vasopressin are regulated by some tropic hormones?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="14735" LastEditDate="2015-04-15T17:31:24.150" LastActivityDate="2015-04-16T05:09:01.337" Title="Does hypothalamus regulate posterior pituitary gland?" Tags="&lt;brain&gt;&lt;endocrinology&gt;&lt;hypothalamus&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31343" PostTypeId="1" AcceptedAnswerId="31380" CreationDate="2015-04-14T19:05:51.197" Score="4" ViewCount="2136" Body="&lt;p&gt;I searched sac1 in uniprot to know more about this gene. in &lt;a href=&quot;http://www.uniprot.org/uniprot/P30619#interaction&quot; rel=&quot;nofollow&quot;&gt;interaction&lt;/a&gt; I selected &lt;a href=&quot;http://thebiogrid.org/32215&quot; rel=&quot;nofollow&quot;&gt;this link&lt;/a&gt; and there I see that this gene has some &quot;physical interactions&quot; and &quot;genetic interactions&quot;. I am wondering that what is the difference between &quot;physical interaction&quot; and &quot;genetic interaction&quot;?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastActivityDate="2015-04-15T15:44:29.030" Title="What is the difference between &quot;physical interaction&quot; and &quot;genetic interaction&quot;?" Tags="&lt;database&gt;&lt;gene&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31346" PostTypeId="2" ParentId="31334" CreationDate="2015-04-14T19:49:47.493" Score="1" Body="&lt;p&gt;Biological activity has a range of definitions, but in this case I believe it to mean that the T3 hormone is produced at a rate 3-5x that of T4. This can be measured with fluorescent tags. Typically, fluorescent tagging uses a reactive derivative of a fluorescent molecule, called a fluorophore. The fluorophore selectively binds to a specific region or functional group on the target molecule and can be attached chemically or biologically. Using technologies, such as microscopes, fluorescence can be viewed/imaged; this allows scientists to count, track, and/or monitor molecules over time. &lt;/p&gt;&#xA;" OwnerUserId="12972" LastActivityDate="2015-04-14T19:49:47.493" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31347" PostTypeId="1" CreationDate="2015-04-14T20:16:46.793" Score="5" ViewCount="338" Body="&lt;p&gt;I am trying to design a wet lab experiment with no wet lab experience to name.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Right now, in my dream land, it would be excellent if it were possible to create a Caspase-9 knockout mouse (damage to the Caspase-9 gene is associated with the development of breast cancer), and somehow be able to control the development of the breast cancer phenotype, so I can create a Caspase-9 KO control as well as a non Caspase-9 control group. In total, I would love to have the following control groups:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;1. Normal mouse - normal Caspase9 gene, no breast cancer phenotype&#xA;2. Caspase9 KO mouse - no breast cancer phenotype&#xA;3. Caspase9 KO mouse - breast cancer phenotype&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Can anyone help me answer whether or not group 2 above is possible? Can you direct me to any papers, any experiments, where this has been done before, or has been tried below and failed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a paper that talks about the association of Caspase-9 with breast cancer development: &lt;a href=&quot;http://breast-cancer-research.com/content/pdf/s13058-014-0443-5.pdf&quot; rel=&quot;nofollow&quot;&gt;http://breast-cancer-research.com/content/pdf/s13058-014-0443-5.pdf&lt;/a&gt;. Caspase-9 is a type 2 member of the Caspase protein family. When I talk of the &quot;Caspase-9 gene&quot;, I'm talking about the DNA which codes for these cellular apoptosis susceptibility 9 (Caspase-9) proteins. This isn't my area of expertise, but this is what I currently understand.&lt;/p&gt;&#xA;" OwnerUserId="15336" LastEditorUserId="948" LastEditDate="2015-04-15T15:26:46.417" LastActivityDate="2015-06-15T21:08:14.037" Title="Can we knock out Caspase-9 *and* avoid breast cancer phenotype in our mouse model?" Tags="&lt;molecular-genetics&gt;&lt;cancer&gt;&lt;experimental-design&gt;" AnswerCount="3" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="31348" PostTypeId="1" CreationDate="2015-04-14T20:42:04.223" Score="2" ViewCount="93" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Phenetics&quot; rel=&quot;nofollow&quot;&gt;Phenetics&lt;/a&gt; (grouping of organisms based on similarity) used to be claimed to be an alternative to &lt;a href=&quot;http://en.wikipedia.org/wiki/Cladistics&quot; rel=&quot;nofollow&quot;&gt;cladistics&lt;/a&gt;, but now it is widely accepted that phenetic analyses cannot be used to infer evolutionary relationships. However, phenetic methods like neighbor-joining trees are still being developed today. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are phenetic analyses still valid today for purposes other than determining evolutionary relationships, or are they completely obsolete? Does anyone have an example of a recent paper that uses phenetic analyses in a valid way?&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2020-08-21T03:47:58.497" Title="What are phenetic analyses used for?" Tags="&lt;phylogenetics&gt;&lt;history&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31349" PostTypeId="1" AcceptedAnswerId="31351" CreationDate="2015-04-14T21:39:12.933" Score="2" ViewCount="43" Body="&lt;p&gt;Imagine a family pedigree.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematically it is a graph, which consists of nodes and edges.&#xA;Nodes being family members, and edges - their relationships.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a clinical setting, what is the proper term for the nodes? Would they be called 'leafs'?&lt;/p&gt;&#xA;" OwnerUserId="15338" LastActivityDate="2015-04-14T21:49:33.687" Title="Term for a leaf in a family tree" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31350" PostTypeId="2" ParentId="31027" CreationDate="2015-04-14T21:44:05.953" Score="-2" Body="&lt;p&gt;Do you mean that &lt;strong&gt;(A)&lt;/strong&gt; the choice of using contraception is part of the human phenotype and we can study the selection pressures that apply to it or that &lt;strong&gt;(B)&lt;/strong&gt; you consider the absorption of a contraceptive as an external selection pressure and are wondering what evolutionary answer this selection pressure will cause?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If &lt;strong&gt;(A)&lt;/strong&gt;:&#xA;One can only study the evolutionary pressures applying on the use of contraception under the following conditions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The choice of using contraceptive is inheritable&lt;/li&gt;&#xA;&lt;li&gt;People who do use contraceptive have significantly less (or more) kids over their entire life than people who do not&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am not sure any of these conditions is fullfilled. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If &lt;strong&gt;(B)&lt;/strong&gt;:&#xA;If it was as simple as a &quot;poisoning effect which seriously damages its reproduction mechanism&quot;, you could expect the emergence of a resistance allele (for example that would make females insensitive to oestrogens in oral contraceptives).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However I guess that persons who use contraception are likely to choose abortion if pregnant, decreasing the fitness effect of such a potential resistance allele.&lt;/p&gt;&#xA;" OwnerUserId="15330" LastActivityDate="2015-04-14T21:44:05.953" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31351" PostTypeId="2" ParentId="31349" CreationDate="2015-04-14T21:49:33.687" Score="2" Body="&lt;p&gt;So in a pedigree, &lt;em&gt;&lt;a href=&quot;http://geneticcounselingtoolkit.com/cases/pedigree/Bennett%20JGC%202008%20-%20Standardized%20Human%20Pedigree%20Nomenclature%20-%20Update%20and%20Assessment%20of%20the%20Recommendations%20of%20the%20National%20Society%20of%20Genetic%20Counselors.pdf&quot; rel=&quot;nofollow&quot;&gt;Standardized Human Pedigree Nomenclature: Update and Assessment of the Recommendations of the National Society of Genetic Counselors&lt;/a&gt;&lt;/em&gt; notes that these &quot;nodes&quot; in the pedigree are the &quot;individual symbol&quot; denoting individuals. Although, when you read it, you'd read &quot;Male,&quot; &quot;Female,&quot; &quot;Gender Unspecified,&quot; etc. instead of individual symbol.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-04-14T21:49:33.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31352" PostTypeId="1" AcceptedAnswerId="39749" CreationDate="2015-04-14T22:25:37.687" Score="8" ViewCount="195" Body="&lt;p&gt;There's increasing public discussion about the health risks of chronic insulin resistance* (IR). In many cases there's a focus on high glycemic index foods that &quot;spike&quot; your blood sugar, which implies that a rapid increase in blood glucose is by itself sufficient to contribute to IR. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, I've heard the claim that if a person is 1) moderately active, 2) not in caloric surplus, and 3) not already insulin resistant, then they will will quickly clear excess blood glucose by replenishing glycogen or through general energy expenditure. This is claimed to have no effect on IR, even though the individual was temporarily exposed to elevated glucose / insulin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leads me to two questions:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Is it true that high blood glucose is normalized substantially more rapidly in people who have depleted their glycogen, or who have higher energy needs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Does repeated exposure to high levels of blood glucose contribute to IR by itself, or are high &lt;em&gt;and prolonged&lt;/em&gt; levels of blood glucose required?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has public health implications -- If the &quot;spikes&quot; theory is inaccurate, then glycemic index may not be very important to sufficiently active people**, and low glycemic index meals may not be as helpful as expected for people at risk of developing IR if total glucose exposure is high.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;*&quot;chronic insulin resistance&quot; would exclude gestational diabetes and the reversible insulin resistance seen on ketogenic diets.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;**For this discussion, let's ignore effects of blood sugar swings on hunger, mood, behavior, etc, since my interest is in the specific physiological triggers for IR. &lt;/p&gt;&#xA;" OwnerUserId="827" LastActivityDate="2015-10-19T04:30:01.567" Title="Do blood glucose &quot;spikes&quot; contribute to insulin resistance, or is prolonged elevation required?" Tags="&lt;human-biology&gt;&lt;nutrition&gt;&lt;diabetes-mellitus&gt;&lt;insulin&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31353" PostTypeId="2" ParentId="30759" CreationDate="2015-04-14T22:25:51.390" Score="1" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;1.Is such an approach trying to quantify homology? Which i know is not correct as homology is qualitive measure.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;A common approach to identify orthologs (homology between two genes resulting from a speciation event) it 'best bidirectional match': if you blast gene A (in species 1) against all genes of species 2 the best match is gene B, &lt;strong&gt;and&lt;/strong&gt; if you blast gene B against all genes of species 1 the best match is gene A.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;2.Can we compare the ratio of homology between the above 2 couples od species or such a comparison is biased?&lt;/p&gt;&#xA;&lt;p&gt;3.Shouldn't the ratio of homology be proportional to the evolutionary distance of the organisms (according to conservation)?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Not necessarly. The fact that two genes diverged a very long time ago does not prevent them from being homologous. Homology is about shared ancestry (here of two genes) and not about evolutionary distance.&lt;/p&gt;&#xA;&lt;p&gt;Could you clarify how you get the homologies? Did you compute them yourself (if so how) or did you use a specific database?&lt;/p&gt;&#xA;" OwnerUserId="15330" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-14T22:25:51.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31354" PostTypeId="2" ParentId="30429" CreationDate="2015-04-14T22:33:15.430" Score="1" Body="&lt;p&gt;Deinococcus radiodurans did not &quot;develop resistance to mutations&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is able to repair its chromosome when scatered in pieces by radiations or desiccation, while other bacteria would die in such conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So this is adaptive in extreme environments, such as deserts (where it has evolved) or canned corned beef (where it was discovered).&lt;/p&gt;&#xA;" OwnerUserId="15330" LastActivityDate="2015-04-14T22:33:15.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31355" PostTypeId="2" ParentId="23078" CreationDate="2015-04-14T22:42:34.177" Score="1" Body="&lt;p&gt;Noting that the right hand side can also be written $\mathbf{G}\mathbf{P}^{-1}\mathbf{s}$, we see that the only theoretical limitation of the multivariate breeders equation is the invertibility of the matrix $\mathbf{P}$. This happens when the measures of two traits are the same for all individuals, making two columns of the matrix the same I.e. It becomes singular. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This theoretical concern can become a practical concern quite quickly when multiple traits are measured. The solution is to effectively consider two traits as one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The 'power' of the equation, by which I assume you mean something like 'accuracy of prediction', actually improves with the number of traits measured. Indeed, a big concern with measuring only a few traits is that the response to selection on those traits is actually 'caused' by selection on some other correlated but unmeasured trait. &lt;/p&gt;&#xA;" OwnerUserId="14849" LastActivityDate="2015-04-14T22:42:34.177" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31357" PostTypeId="2" ParentId="27478" CreationDate="2015-04-15T00:28:26.067" Score="2" Body="&lt;p&gt;It is not a regression (not at this stage of the paper, a regression will be done latter)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only complicated thing to understand is $b_i$, which is the 'base relatedness', ie how $i$ is related to a random individual (to be compared to how related it is to individuals with whom it interacts). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To simplify let's first consider the situation where $b_i = 0$:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$E(qj) = b_{i,j} q_i + (1-b_{i,j}) q$ is just the translation of 'the gene frequency of the replica part is q_i' and 'the gene frequency of the non replica part is $q$'; because $b_{i,j}$ is the fraction of the replica part, ie the chances that our locus of interest belongs to the replica part of individual $i$ in individual $j$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now let's re-introduce $b_i$. The idea is to compare relatedness of the two individuals $i$ and $j$ to the average relatedness of $i$ with a randomly picked individual in the population (this random relatedness is exactly $bi$). This is important because $q$ already accounts for this 'random relatedness'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So instead of giving probability $b_{i,j}$ to $q_i$, we give it probability $b_{i,j}-b_i$, which is the chance that the allele of interest is present because of the replica fraction being higher than random. And because now the quantity varies between 0 and $1-b_i$ we normalize it by $1-b_i$&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The underlying intuition of Hamilton's model of inclusive fitness is that we should study social behaviors from the point of view of actors -- rather than the recipients&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Not exactly, it is saying that we should study social behaviors from the point of view of the alleles causing it, that may be shared between the actors and the recipients. But this paper &lt;strong&gt;is not the paper that introduces inclusive fitness&lt;/strong&gt;, quite the opposite it is the paper that tries to reconciliate kin selection with Price equation.&lt;/p&gt;&#xA;" OwnerUserId="15330" LastActivityDate="2015-04-15T00:28:26.067" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31358" PostTypeId="2" ParentId="24556" CreationDate="2015-04-15T00:49:13.847" Score="0" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;From what I understand, over time random mutations occur which in some cases provide an advantage allowing that animal to survive and reproduce. Its children will have that mutation allowing them to survive and so on over many many years until it evolves into a new species and / or the old ones become extinct.&lt;/p&gt;&#xA;&lt;p&gt;The part I'm getting stuck on is that unless these mutations happen instantly and in a large number, given its over such a big time scale how do animals who are not well adapted get enough time to evolve to survive?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;You are quite confused about what is evolution!&#xA;The idea &lt;strong&gt;is not at all&lt;/strong&gt; that all the individuals of a population will acquire the same change and become another species.&lt;/p&gt;&#xA;&lt;p&gt;One individual gets a beneficial mutation and thus reproduces faster than others. So this mutation spreads little by little in the population &lt;strong&gt;because eventually only descendants of the first individual bearing the mutation will remain&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;p&gt;This is what is called a selective sweep. But it has nothing to do with the concept of species, which involves much more complex processes.&lt;/p&gt;&#xA;" OwnerUserId="15330" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-15T00:49:13.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31359" PostTypeId="2" ParentId="24398" CreationDate="2015-04-15T00:56:29.367" Score="0" Body="&lt;p&gt;The key to rapid evolution of viruses is high mutation rate, as pointed by @Chris, and high population size.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;But can it occur due to internal urge of an organism, say virus?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If your question is whether in the case of Ebola the vaccination caused the mutations the answer is no. The vaccination lead to the fixation of some mutations that would have happened anyway (but the would not have fixed without the vaccination).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are however a few exceptions, for example stress-induced mutagenesis.&lt;/p&gt;&#xA;" OwnerUserId="15330" LastActivityDate="2015-04-15T00:56:29.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31360" PostTypeId="1" AcceptedAnswerId="31363" CreationDate="2015-04-15T01:29:41.560" Score="5" ViewCount="8882" Body="&lt;p&gt;So I have this Large Water Jug that I fill only water with. &#xA;And this is the 2nd time there has been a layer of green film that builds up at the bottom of the bottle. I don't have any way of getting to the bottom to clean this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wanted to know.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;What does this green film consist of?&lt;/li&gt;&#xA;&lt;li&gt;What Chemicals or methods can I use to remove the film without having to manually scrub the bottle?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/D2BTG.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ps. not sure if this was the correct place to ask this question.&lt;/p&gt;&#xA;" OwnerUserId="15340" LastActivityDate="2019-07-23T15:51:48.323" Title="Green Film Build up in Glass Water Bottle" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31361" PostTypeId="2" ParentId="31313" CreationDate="2015-04-15T02:20:55.407" Score="2" Body="&lt;p&gt;Since DNA is an acid it is reasonable to ask: what is the pKa of the phosphate residues located all along the polynucleotide's sugar-phosphate backbone? Apparently that number is at a pH between 1 and 2 (&lt;a href=&quot;http://www.bio.brandeis.edu/classes/biochem104/DNA_lecture.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.bio.brandeis.edu/classes/biochem104/DNA_lecture.pdf&lt;/a&gt;). That  means at physiological pH ranges (for example, the pH found inside the nucleus or cytoplasm of a cell, around 7 or so) 100 % of these phosphates would be ionized (unprotonated), and therefore strongly negatively charged.  The counter ions would be any suitable mono- or divalent cations handy. When you purchase intact DNA the fibres are typically the sodium salt--I believe this is similar to the material Wilkins &amp;amp; Franklin used to obtain the images Watson &amp;amp; Crick used to solve the structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So strictly speaking, the experimental situation described in the question does not exist. You could never obtain a pure sample of protonated DNA that you could then add to pure water. At the pH the DNA would be protonated the DNA would depurinate leading to strand scission at the abasic sites.  This is the whole principle of soaking your agarose gel in HCl in preparation for a Southern Blot, to fragment the high molecular weight fragments so they will migrate more efficiently out of the gel and onto the blotting membrane.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-04-15T02:20:55.407" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31362" PostTypeId="2" ParentId="31326" CreationDate="2015-04-15T02:49:52.063" Score="11" Body="&lt;p&gt;So the direct mechanisms of norovirus immunity aren't well understood - the shortage of straightforward animal models, and the &lt;em&gt;extreme&lt;/em&gt; difficulty in culturing the virus make mechanistic studies really rather hard.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;http://wwwnc.cdc.gov/eid/article/19/8/13-0472_article&quot;&gt;modeling study&lt;/a&gt; pegged the duration of immunity at 4.1 to 8.7 years when talking about symptomatic disease, which is much higher than many of the estimate's you've encountered, and isn't actually all that fast. The older estimates were built off human challenge studies, which involved &lt;em&gt;massive&lt;/em&gt; doses of norovirus, rather than the normal exposure you'd have. Now that is for a single strain, but immune cross-reactivity for strains isn't well understood. There's also several efforts to develop norovirus vaccines, which suggests some duration of immunity is at least possible. It's also possible that a proportion of the population (~20%) is simply immune due to the absence of the FUT2 gene, which acts as a receptor for the virus in the intestines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, there's definitely some antigenic drift, where mutations in the primary antigens negate previous immunity to the disease (the same mechanism that causes you to eventually lose immunity to a particular strain of influenza).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1002921&quot;&gt;This paper&lt;/a&gt; is a pretty brief review of all these factors, written by some norovirus experts.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2015-04-15T02:49:52.063" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31363" PostTypeId="2" ParentId="31360" CreationDate="2015-04-15T04:19:04.283" Score="8" Body="&lt;p&gt;What seems to be forming in reusable water bottles and water coolers is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Biofilm&quot; rel=&quot;nofollow noreferrer&quot;&gt;biofilm&lt;/a&gt;. Since it is a complicated system, after maturation biofilm might be very hard to remove without scrubbing. There is a &lt;a href=&quot;http://www.allaboutwateridaho.com/WC&amp;amp;P%20Water%20Cooler%20Sanitizing%20Article.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;nice article about cleaning water coolers&lt;/a&gt;, which might give you some information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look closer on the &lt;a href=&quot;https://scholar.google.com/scholar?hl=en&amp;amp;q=biofilm%20in%20water%20coolers%20&amp;amp;btnG=&amp;amp;as_sdt=1%2C5&amp;amp;as_sdtp=&quot; rel=&quot;nofollow noreferrer&quot;&gt;Google Scholar search results&lt;/a&gt;, you'll find that quite a bit of research has been conducted in the area of sanitation of water coolers and study of their flora. For example, consider the following paper from 1996: &lt;a href=&quot;http://www.microbecolhealthdis.net/index.php/mehd/article/viewFile/8354/9759&quot; rel=&quot;nofollow noreferrer&quot;&gt;Analysis of the Virulence Characteristics of Bacteria Isolated from Bottled, Water Cooler, and Tap Water&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a very nice list (Table 1) of different bacteria isolated from water. But I would like to point your attention to following table from the paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AJI6g.png&quot; alt=&quot;Table 3. Antibiotic resistance of water bacteria&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quote from methods section listing tested antibiotics:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The&#xA;  natural and first generation antibiotics included:&#xA;  penicillin, ampicillin, erythromycin, kanamycin,&#xA;  streptomycin, tetracycline, chloramphenicol, and&#xA;  sulphonamide. The synthetic and later generation&#xA;  antibiotics included: gentamicin, cefoxitin,&#xA;  cefoperazone, oxacillin, piperacillin, imipenem,&#xA;  ciprofloxacin, and sulphonamideftrimethoprim&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The green slime you observe, I think, is a combination of all those bacteria, plus some that were brought after the water was poured into the container. And it seems that all commercial sources that you didn't purify yourself, will have a variety of microorganisms growing. And around 5% of the total bacterial cell mass is resistant to common antibiotics.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2019-07-23T15:51:48.323" LastActivityDate="2019-07-23T15:51:48.323" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="31364" PostTypeId="2" ParentId="29717" CreationDate="2015-04-15T04:44:03.447" Score="3" Body="&lt;p&gt;Great question. Turns out, there is some information about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, consider following resource: &lt;a href=&quot;http://opm.phar.umich.edu/atlas.php?membrane=Mitochondrial%20outer%20membrane&quot; rel=&quot;nofollow noreferrer&quot;&gt;Membrane Protein Lipid Composition Atlas&lt;/a&gt;. Published by University of Michigan, it provides information on, primarily, protein content of different membranes from different species, but also has a list of lipid content.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just as an example, consider following difference between membranes of mitochondria in yeast:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EbteG.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/KoFGg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, concerning your interest in biophysics. To my taste, starting with just bulk lipid composition is a good first approximation. Although you also want to know about lipid raft formation and density/distribution of proteins. Next step, probably, will be symmetry considerations, that is, difference between sides of same membrane. You can imagine membranes with same bulk composition, but because of different lipid position (in/out) properties will be different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems you can assess &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022283604015967&quot; rel=&quot;nofollow noreferrer&quot;&gt;raft composition based on membrane lipid composition&lt;/a&gt;. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0005273676900432#&quot; rel=&quot;nofollow noreferrer&quot;&gt;Membrane capacity also&lt;/a&gt; is a property of membrane content.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Following quick walk through &lt;a href=&quot;https://scholar.google.com/scholar?q=membrane%20composition&amp;amp;btnG=&amp;amp;hl=en&amp;amp;as_sdt=0%2C5&amp;amp;as_vis=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;this Google Scholar search&lt;/a&gt; provides even more links between biophysical properties and lipid bilayer composition. However, it might be challenging to find exactly what you are looking for.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-15T04:44:03.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31365" PostTypeId="2" ParentId="28569" CreationDate="2015-04-15T05:03:43.133" Score="1" Body="&lt;p&gt;In comments it been discussed that clotting is partial answer to OP. I would say, that is is somewhat tangential to the original question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I may re-phrase, OP asks: how one can estimate age of blood that has been exposed to air? Problem is that you will have to have a starting point to solve that backwards, like having an initial condition for solving differential equation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One example that can be used is measurement of $pCO_2$ content in blood serum. If it is available, someone &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0009898103002420&quot; rel=&quot;nofollow&quot;&gt;already collected this data&lt;/a&gt;. In 2 hours $pCO_2$drops 30% and total $CO_2$ drops about 6%.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, it seems that &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11386620&quot; rel=&quot;nofollow&quot;&gt;during hemorrhagic shock RBC shape changes&lt;/a&gt;, which means that sampling patient you will be able to approximate time since bleeding started. However, you will need an electron microscope at your disposal...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, and I'll leave it like that, cellular death is a powerful process that leaves a lot of traces. Apoptotic cells have mitochondria bursting (except in RBC there are no mitochondria) and releasing, for example, cytochrome C. In case of bleeding probable cause of cellular death is necrosis, so different biochemical changes will occur. Point is that you can measure time since necrosis/apoptosis started by careful measurement.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-04-15T05:10:21.727" LastActivityDate="2015-04-15T05:10:21.727" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31366" PostTypeId="2" ParentId="31347" CreationDate="2015-04-15T06:01:17.843" Score="3" Body="&lt;p&gt;This seems to be a standard procedure knockout and complementation rescue experiment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Breed 2 can be produced from Breed 3 (assuming the Caspase 9 gene indeed causes cancer when it is not expressed). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, knockout Caspase 9 from a wild type, creating Breed 3. Verify that the cancer phenotype is shown and is statistically significant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, transform Breed 3 with an artificial copy of the Caspase 9 gene in an alternative chromosomal location. This breed (Breed 2) will act as a positive control for the gene, and should behave identically to the wild type. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, you can then produce multiple breeds of mice transformed with different versions of the gene (for example serine/threonine mutagenesis to detect the kinase specificity) in order to determine mutations that cause the Caspase 9 protein to become non-functional. Alternatively, the same gene but with a stronger/weaker promoter can be used to determine the dose-dependent effects of the gene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cell.com/cell/abstract/S0092-8674%2800%2980246-9?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867400802469%3Fshowall%3Dtrue&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; regarding a circadian clock gene shows the general procedure required to carry out such a complementation rescue experiment.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-04-15T06:01:17.843" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31368" PostTypeId="1" AcceptedAnswerId="34220" CreationDate="2015-04-15T09:38:57.290" Score="8" ViewCount="245" Body="&lt;p&gt;In some (perhaps small) human communities people may starve because they have no income. This could be interpreted as a consequence of them not participating in the community, hence they don't get any income and are left to their fate of starvation. Also, we can imagine that important members of the community are less likely to starve, as they are given priority treatment (e.g. a royal family will less likely starve to death during a given famine). &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Do ants in a given colony allow members to starve when they don't serve the colony, even if there is no scarcity of food? &lt;/li&gt;&#xA;&lt;li&gt;Secondly, do ants follow a chain of importance and are members of least importance allowed to starve first in times of shortage?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerDisplayName="user15342" LastEditorUserId="3624" LastEditDate="2015-05-19T08:40:17.933" LastActivityDate="2015-05-19T08:40:17.933" Title="Do ant colonies prioritize survival of particular members above others?" Tags="&lt;ethology&gt;&lt;behaviour&gt;&lt;sociality&gt;&lt;ant&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31369" PostTypeId="1" AcceptedAnswerId="31382" CreationDate="2015-04-15T10:05:10.567" Score="4" ViewCount="122" Body="&lt;p&gt;I am a med student, and as far as I see from our pharmacology lectures, pharmacologists work almost completely experimental. Quite typically they take a substance (e.g., from nature), they add, change or remove some chemical groups, and then they test it (either with high throughput screening or on animals), for example to see whether the new drug is active or not. To me, this sounds a bit indirect. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ideally, we should know exactly what we are targeting, and then custom-make a new drug. For example, if we know which receptor (the 'lock') we wish to activate or inhibit, why do pharmacologists not simply design a fitting key (a plug to block, or a substrate-resembling activator) to the specific lock? &lt;/p&gt;&#xA;" OwnerDisplayName="user13196" LastEditorDisplayName="user13196" LastEditDate="2015-09-26T13:34:52.730" LastActivityDate="2015-09-26T13:34:52.730" Title="Why are pharmacology studies so experimental?" Tags="&lt;pharmacology&gt;&lt;medicine&gt;&lt;experimental&gt;&lt;clinical-trial&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31370" PostTypeId="1" AcceptedAnswerId="31374" CreationDate="2015-04-15T10:16:58.343" Score="2" ViewCount="31" Body="&lt;p&gt;I read that &lt;strong&gt;Sciomyzidae&lt;/strong&gt; are also called &lt;em&gt;snail-killing flies&lt;/em&gt;, which immediateley made me think: &quot;I need those&quot;!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Questions: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Are they really fit to control snail over-population in my garden? and&lt;/li&gt;&#xA;&lt;li&gt;if so where do i get them?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="15257" LastEditorUserId="15257" LastEditDate="2015-04-15T10:53:27.433" LastActivityDate="2015-04-15T13:03:17.853" Title="Are Sciomyzidae fit to combat snails?" Tags="&lt;parasitology&gt;&lt;pest-control&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31371" PostTypeId="1" AcceptedAnswerId="31381" CreationDate="2015-04-15T10:18:22.660" Score="6" ViewCount="2260" Body="&lt;p&gt;Do plants that lose their leaves (i.e., &lt;em&gt;deciduous&lt;/em&gt; plants) do so because of external conditions (e.g., drought, cold), or because of an internal process?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way of looking at it: if you take a deciduous plant that loses its leaves during cold winters with long nights (e.g., Canada), and plant it in an environment where it is always warm and sunny (i.e., at the equator), would this plant continue to shed its leaves and re-grow them according to the seasons in Canada, or would it behave as an evergreen instead?&lt;/p&gt;&#xA;" OwnerUserId="15344" LastEditorUserId="107" LastEditDate="2015-04-15T14:25:58.210" LastActivityDate="2015-04-16T04:34:04.753" Title="What is the mechanism behind plants losing their leaves?" Tags="&lt;botany&gt;&lt;ecology&gt;" AnswerCount="2" CommentCount="2" ClosedDate="2015-04-16T08:56:14.653" ContentLicense="CC BY-SA 3.0" />
  <row Id="31374" PostTypeId="2" ParentId="31370" CreationDate="2015-04-15T13:03:17.853" Score="2" Body="&lt;p&gt;Short answers:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These insects live near water or marsh areas so that's where you can get them from. This is because many species of this group has larvae that are aquatic or semi-aquatic.  According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Sciomyzidae&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The adults drink dew and nectar.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And it is their larvae that either prey on or become parasites of gastropods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0764446900001268&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article the following is stated:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;(...) Sciomyzidae is of interest from practical viewpoints because of their potential as biocontrol agents of aquatic snails carrying diseases (e.g. schistosomiasis and fascioliasis) and terrestrial, pestiferous snails..&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So the answer is yes, they might be fit to use as biological pest control, yet they may not be suitable against all species. Details of their life cycle and their biology can be found in the linked article or in this book:&#xA;&lt;a href=&quot;https://books.google.hu/books?id=vqE1AMIj-HUC&amp;amp;pg=PR16&amp;amp;lpg=PR16&amp;amp;dq=Sciomyzidae&amp;amp;source=bl&amp;amp;ots=pCVJJUu2cb&amp;amp;sig=M1F8GhR51VI1Y62htF7eX0kNpfo&amp;amp;hl=hu&amp;amp;sa=X&amp;amp;ei=AF0uVf_tKI3taNLhgIAL&amp;amp;ved=0CFgQ6AEwBzgK#v=onepage&amp;amp;q=Sciomyzidae&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;https://books.google.hu/books?id=vqE1AMIj-HUC&amp;amp;pg=PR16&amp;amp;lpg=PR16&amp;amp;dq=Sciomyzidae&amp;amp;source=bl&amp;amp;ots=pCVJJUu2cb&amp;amp;sig=M1F8GhR51VI1Y62htF7eX0kNpfo&amp;amp;hl=hu&amp;amp;sa=X&amp;amp;ei=AF0uVf_tKI3taNLhgIAL&amp;amp;ved=0CFgQ6AEwBzgK#v=onepage&amp;amp;q=Sciomyzidae&amp;amp;f=false&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-04-15T13:03:17.853" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31376" PostTypeId="1" CreationDate="2015-04-15T13:56:01.200" Score="7" ViewCount="221" Body="&lt;p&gt;Is there a list of neural coordinates for &lt;em&gt;C.elegans&lt;/em&gt;? I need it to build a 3D model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update:&lt;/strong&gt;&#xA;What is available at the moment is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;full connectome for example, at &lt;a href=&quot;http://openconnectomeproject.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;openconnectome&lt;/a&gt;;&lt;/li&gt;&#xA;&lt;li&gt;neuron description with images of relative position at &lt;a href=&quot;http://wormatlas.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;wormatlas&lt;/a&gt;;&lt;/li&gt;&#xA;&lt;li&gt;2d position data at &lt;a href=&quot;http://www.dynamic-connectome.org/?page_id=25&quot; rel=&quot;nofollow noreferrer&quot;&gt;dynamic-connectome&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update 2:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've created very simple 3d model that consists of three layers (left, right and center) based on neuron labels. This shouldn't be considered as a real biological, but better than nothing. Code and data is on &lt;a href=&quot;https://github.com/bbrh/celegans_neuron_spatial_coordinates&quot; rel=&quot;nofollow noreferrer&quot;&gt;github&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tClip.gif&quot; alt=&quot;celegans neurons in 3d&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Clarification:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is still there, I've provided very basic model and everyone are welcome to use it. But it still would be interesting to get experimental results. I'll keep the question open in case someone could share the data.&lt;/p&gt;&#xA;" OwnerUserId="15347" LastEditorUserId="15347" LastEditDate="2015-04-16T12:14:53.750" LastActivityDate="2015-05-20T12:29:55.890" Title="Neuronal coordinates of C.elegans" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31377" PostTypeId="1" CreationDate="2015-04-15T15:15:55.907" Score="5" ViewCount="222" Body="&lt;p&gt;In my lab class this week my partner and I were making a SDS-PAGE Laemmli Gel. We made the resolving gel solution which was made of 30% Acrylamide, DI water, 1.5 M Tris-HCL pH8.8, and 20% SDS. We mixed the measured amounts into a conical vial. We then added 10% APS and TEMED and mixed carefully. We then immediately pipetted the solution into the casting stand so the gel could solidify. We then pipetted DI water onto the top of the gel so it would not dehydrate. We left some solution in the conical vial so we knew when the solution would be solidified completely. After waiting 45 minutes the gel in the conical vial was solidified but the gel in the casting stand was still liquid. How come the gel did not solidify in the casting stand but solidified in the conical vial? &lt;/p&gt;&#xA;" OwnerUserId="12899" LastEditorUserId="948" LastEditDate="2015-04-15T15:30:42.733" LastActivityDate="2015-04-15T19:24:04.670" Title="SDS Laemmli Gel that did not solidify" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;" AnswerCount="0" CommentCount="10" FavoriteCount="1" ClosedDate="2015-07-16T08:01:08.637" ContentLicense="CC BY-SA 3.0" />
  <row Id="31378" PostTypeId="2" ParentId="19692" CreationDate="2015-04-15T15:20:25.640" Score="6" Body="&lt;p&gt;First of all, there is a very heated debate about this in the field of social evolution at present, and you aren't likely to get a conclusive answer. One theorist may give you one answer, but another will vehemently disagree. I'll start by logically answering your questions in reverse order!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question 2:&lt;/strong&gt; &lt;em&gt;Can you please provide an intuitive explanation of why kin- and group-selection are the same thing?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first formal 'proof' that they are the same came from a paper by &lt;a href=&quot;http://www.jstor.org/stable/2462497?seq=1#page_scan_tab_contents&quot;&gt;Queller&lt;/a&gt; in 1992. Let me give you the gist of what he found without being ultra rigorous. I won't focus on relatedness, since that was answered nicely by @falsum, &quot;Price's equation tells us that this happens when the genetic variance between-groups is higher than the genetic variance within-groups. This is equivalent to saying that altruists tend to interact with other altruists and, accordingly, that the coefficient of relatedness increases.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Queller explored the change in mean additive genetic (breeding) value for a trait over a single generation using Price's equation &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$&#xA;\Delta \bar{G} = \mathrm{Cov}(W,G)&#xA;$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $G$ is the additive genetic value, and $W$ is relative fitness. Now, the key question is, how should we define fitness? If we treat it as a random variable, we can do a linear regression of fitness on a set of explanatory variables. What should we choose for the explanatory variables? One natural choice might be to predict the fitness of a focal individual based on the phenotype of the focal individual itself, &lt;em&gt;and&lt;/em&gt; the phenotype of the individuals the individual interacts with socially:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$&#xA;W_{i} = w_{0} + \beta_{direct} P_{i} + \beta_{social} P_{j}&#xA;$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $w_{0}$ is baseline fitness, $P_{i}$ is the phenotype of the focal individual, and $P_{j}$ is the phenotype of the focal individual's social partner. However, another way to predict the fitness of a focal individual might be to focus on the average phenotype of individuals in the focal individual's group, and the deviation of the focal individual's phenotype from the mean phenotype of individuals in the group&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$&#xA;W_{i} = w_{0} + \beta_{deviation} (\bar{P}_{group} - P_{i}) + \beta_{group} \bar{P}_{group}&#xA;$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These regression equations for fitness hold exactly (only for a single generation), independent of the 'true' form of the fitness functions (they can be as non-linear as you like). What these allow us to do, however, is partition fitness effects into those that are due to benefits of a behaviour, those that are due to costs of a behaviour (and unmodelled residuals or 'noise'). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a kin-selection perspective, it turns out that the benefit in Hamilton's rule is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$&#xA;\beta_{social} = B&#xA;$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and the cost in Hamilton's rule is&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$&#xA;\beta_{direct} = C&#xA;$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a group-selection perspective, it turns out that the benefits and costs in Hamilton's rule are distributed over deivation and group effects&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$&#xA;\beta_{deviation} = C - B&#xA;$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$&#xA;\beta_{group} = C + (N-1)B&#xA;$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, we find that it possible to write fitness equivalently in two different ways that relate the change in frequency of individuals to benefits and costs associated with a social phenotype. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question 1&lt;/strong&gt; &lt;em&gt;Is group selection equivalent to kin selection for any evolutionary game or exclusively for the prisoner's dilemna?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are always equivalent no matter what game is being played or how the population is structured &lt;em&gt;if&lt;/em&gt; you are happy use the regression methods described to define fitness, benefits, costs, and relatedness. Many people have issues with the regression methods though. See &lt;a href=&quot;http://www.pnas.org/content/110/50/20135.abstract&quot;&gt;Allen et al&lt;/a&gt; for a discussion of this. Others argue that kin-selection holds in every case and that the problems with kin-selection stem from a misunderstanding of the methodology. See &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2011.02236.x/pdf&quot;&gt;Gardner et al&lt;/a&gt; for a discussion of this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many biologists find the debates in social evolution about kin/multi-level selection unhelpful (at best), and choose either framework to work in based on the question at hand. A few are very partisan on either side. There is a great deal of misrepresentation floating around about both, so read papers making strong claims with skepticism and caution.  &lt;/p&gt;&#xA;" OwnerUserId="14849" LastActivityDate="2015-04-15T15:20:25.640" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31379" PostTypeId="2" ParentId="31285" CreationDate="2015-04-15T15:39:39.593" Score="1" Body="&lt;p&gt;Each part of the Earth is divided into temperate zones depending on their latitude. Texas happens to be considered a Temperate Grassland. Temperate Grasslands are usually dominated by herbaceous vegetation. Because of where Texas is located on the Earth it has high summer temperatures which encourages fires. These fires help exclude woody vegetation such as trees and usually limits trees and shrubs to margins of streams and rivers. These grassland vegetation vary from about 5 cm in dry, short grass prairies to over 200 cm in the wetter, tall grass prairies. Of course there are still going to be trees in Texas but there will not be forests like along the coasts of the Atlantic Ocean. Those are considered to be in a different temperate zone called Temperate Forest. These areas usually have more rain and temperatures are not as extreme as Texas.  &lt;/p&gt;&#xA;" OwnerUserId="12899" LastActivityDate="2015-04-15T15:39:39.593" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31380" PostTypeId="2" ParentId="31343" CreationDate="2015-04-15T15:44:29.030" Score="4" Body="&lt;p&gt;Physical and genetic interactions are described in the &lt;a href=&quot;http://wiki.thebiogrid.org/doku.php/experimental_systems&quot; rel=&quot;nofollow&quot;&gt;help wiki&lt;/a&gt;, accessed via the top menu bar on the page you linked to. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Physical interactions&lt;/em&gt; refer to experiments where the gene product (protein) has been shown to physically interact with another protein, such as by co-immunoprecipitation, fluorescent staining, yeast two-hybrid system, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Genetic interactions&lt;/em&gt; refer to experiments where changes in a certain gene reflect in changes to your gene of interest (or vice-versa) - dosage lethality, dosage rescue, synthetic haploinsufficiency, etc.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-04-15T15:44:29.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31381" PostTypeId="2" ParentId="31371" CreationDate="2015-04-15T15:57:00.913" Score="5" Body="&lt;p&gt;The process of a deciduous plant losing its leaves seasonally is known as &lt;a href=&quot;http://en.wikipedia.org/wiki/Abscission&quot; rel=&quot;nofollow&quot;&gt;abscission&lt;/a&gt;. It occurs when a layer of cells known as the abscission zone elongate and weaken, causing the leaf to fall off. It is mediated mainly by the hormones auxin and ethylene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The functional purpose of abscission is to remove leaves when they are no longer producing a net gain of biomass. Leaves decrease in productivity during &lt;a href=&quot;http://www.publish.csiro.au/?paper=FP03236&quot; rel=&quot;nofollow&quot;&gt;drought&lt;/a&gt;, decreased &lt;a href=&quot;http://www.annualreviews.org/doi/pdf/10.1146/annurev.pp.07.060156.001203&quot; rel=&quot;nofollow&quot;&gt;day length&lt;/a&gt;, and when under the effect of &lt;a href=&quot;http://link.springer.com/article/10.1007/s004420000576&quot; rel=&quot;nofollow&quot;&gt;herbivory&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In some species (according to the day-length source), &quot;When the daylength exceeds a certain 'critical' duration, growth may be&#xA;maintained continuously for at least 18 months under favourable tempera­ture conditions, e.g., in &lt;em&gt;Liriodendron tulipifera, Robinia pseudacacia&lt;/em&gt;&quot;. So, to answer your final question, some deciduous species (but not all) may indeed retain their leaves if they are grown in favorable conditions. One reason why not all deciduous trees retain their leaves even in favorable conditions is that internal ageing can also induce abscission: &quot;In such species, growth is determined primarily by the endogenous ageing process and is only modified by environmental factors, including daylength&quot;&lt;/p&gt;&#xA;" OwnerUserId="14629" LastEditorUserId="14629" LastEditDate="2015-04-15T16:09:21.377" LastActivityDate="2015-04-15T16:09:21.377" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31382" PostTypeId="2" ParentId="31369" CreationDate="2015-04-15T17:35:40.140" Score="3" Body="&lt;p&gt;The First thing is that that you can't study any process until it happens. So even if you know the structure of receptor molecule, you can't always be sure that it is completely safe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It does seem a bit random in beginning but this is how it works. You can't just derive a medicine or drug and send it for mass production. You never know what are the side effects of the drug. For this reason, the drugs are tested on other animals (usually rats because they are quite in number, having short lifespan and not many oppose experiments on rats ethically.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the side effects are severe, then the drug is banned from mass production.&#xA;But if such drug is produced,more harm will be done than good. Also you can't give it to humans first. If all tests are successful, then only the drug is tested on humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So Screening and Testing are indirect but essential steps for studying the effects of it.&lt;/p&gt;&#xA;" OwnerUserId="4503" LastActivityDate="2015-04-15T17:35:40.140" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31383" PostTypeId="1" AcceptedAnswerId="31408" CreationDate="2015-04-15T17:43:22.973" Score="9" ViewCount="986" Body="&lt;p&gt;I recorded a video of this bug:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xVfkC.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://youtu.be/0eoWfHLEo7A&quot;&gt;https://youtu.be/0eoWfHLEo7A&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I counted 8 legs, the front legs are a little curved. The drawing on the flat back is dark and looks like the image of Jesus with some light from behind, hahahaha. I found it on the curtain of my bedroom. I believe it belongs to some tree where it can use its camouflage. Can anyone identify it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Location: Valencia, Spain.&lt;/p&gt;&#xA;" OwnerUserId="15349" LastEditorUserId="10456" LastEditDate="2015-04-15T18:57:02.117" LastActivityDate="2015-07-09T14:02:07.777" Title="What is this bug?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;&lt;arachnology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31384" PostTypeId="2" ParentId="31334" CreationDate="2015-04-15T18:17:44.697" Score="0" Body="&lt;p&gt;In my opinion, activeness of a hormone is more about its effect than its production rate. Cortisol and Aldosterone are both adrenal hormones, yet as a mineralocorticid, aldosterone is the active one by great margin (due to intracellular degradation of the glucocorticoids).&lt;/p&gt;&#xA;" OwnerUserId="15321" LastActivityDate="2015-04-15T18:17:44.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31385" PostTypeId="2" ParentId="31338" CreationDate="2015-04-15T18:26:23.557" Score="1" Body="&lt;p&gt;The difference between secretion of ACTH  and neurohypophysial hormones is that the prior is a two step process, with CRF from hypothalamus stimulating the anterior pituitary. The latter is produced and secreted from the same cell, only in different organs! Magnocellular neurons stretch from the hypothalamus to the posterior pituitary, where they have their neurosecretory endings packed with hormone storing large dense-core vesicles. The same neurons are osmosensitive, regulating their secretion themselves as physiological need arises. Also, they apparently do dendritic secretion as autocrine signalling. Some reading about this: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24265070&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/24265070&lt;/a&gt;&#xA;and &#xA;&lt;a href=&quot;http://www.nature.com/nrn/journal/v7/n2/full/nrn1845.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nrn/journal/v7/n2/full/nrn1845.html&lt;/a&gt;&#xA;Hope it helps.&lt;/p&gt;&#xA;" OwnerUserId="15321" LastEditorUserId="15321" LastEditDate="2015-04-16T05:09:01.337" LastActivityDate="2015-04-16T05:09:01.337" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31386" PostTypeId="2" ParentId="31383" CreationDate="2015-04-15T18:26:50.623" Score="6" Body="&lt;p&gt;My best guess is a soft-bodied tick, perhaps of the &lt;em&gt;Ornithodoros&lt;/em&gt; genus, although the determination of the species is a little more difficult. Though, if it's &lt;em&gt;O. erraticus&lt;/em&gt; they're known for causing african swine fever in Spain and Portugal &lt;a href=&quot;http://en.wikipedia.org/wiki/Ornithodoros_erraticus&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Ornithodoros&quot; rel=&quot;nofollow&quot;&gt;Ornithodoros&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In response to the comments, here's a &lt;a href=&quot;http://tickapp.tamu.edu/tickbiology.php&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt; from Texas A&amp;amp;M which notes the ticks pump waste+water back out into the host, and this is why they transmit so many infections.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-04-15T19:26:26.037" LastActivityDate="2015-04-15T19:26:26.037" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31388" PostTypeId="1" CreationDate="2015-04-15T18:39:06.540" Score="6" ViewCount="139" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WzDeC.png&quot; alt=&quot;biologists&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know the third one in the front row is James Watson. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone recognize the others?&lt;/p&gt;&#xA;" OwnerUserId="15350" LastEditorUserId="6561" LastEditDate="2015-10-12T23:49:43.273" LastActivityDate="2015-10-12T23:49:43.273" Title="Who are these biologists?" Tags="&lt;history&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="31389" PostTypeId="1" AcceptedAnswerId="31392" CreationDate="2015-04-15T18:51:43.983" Score="0" ViewCount="121" Body="&lt;p&gt;Does anyone know of any research/examples on Hopeful Monsters in Plants? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I define Hopeful Monsters as organisms of a species that have macroevolutions to prompt new speciations. These macroevolutions being themselves, prompted by smaller gradual microevolutions in the species. See &lt;a href=&quot;http://www.evolocus.com/publications/Theissen2006.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper for more details. I'm interested in a plant based example, or any good recent example, if plants can not suffice. Ideally research that is easily read and recent, and useful for arguing the existence of themselves?&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="14735" LastEditDate="2015-04-15T19:11:59.283" LastActivityDate="2015-04-15T20:26:02.287" Title="Hopeful Monsters in Plants?" Tags="&lt;botany&gt;&lt;theoretical-biology&gt;" AnswerCount="2" CommentCount="11" ClosedDate="2015-04-16T08:50:22.070" ContentLicense="CC BY-SA 3.0" />
  <row Id="31390" PostTypeId="2" ParentId="30416" CreationDate="2015-04-15T19:14:10.780" Score="1" Body="&lt;p&gt;If you're looking for a strictly and directly DNA-DNA mediated effect (no histones, no transcription involved) I'd look for sequence effects on chromatin remodelling, modulating access of transcription factors (TFs) to their elements. Something about this might be in this paper: &#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21326360&quot; rel=&quot;nofollow&quot;&gt;Szerlong, H. J., &amp;amp; Hansen, J. C. (2011)&lt;/a&gt;. Nucleosome distribution and linker DNA: connecting nuclear function to dynamic chromatin structure. Biochemistry and Cell Biology = Biochimie et Biologie Cellulaire, 89(1), 24–34. doi:10.1139/O10-139&lt;/p&gt;&#xA;" OwnerUserId="15321" LastEditorUserId="14552" LastEditDate="2015-04-15T21:02:52.703" LastActivityDate="2015-04-15T21:02:52.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31391" PostTypeId="2" ParentId="31389" CreationDate="2015-04-15T19:15:23.337" Score="2" Body="&lt;p&gt;One example of what you may consider to be a macroevolutionary change is a whole-genome-duplication, or polyploidy event. These are not uncommon in plants, and can promote speciation due to a reproductive barrier arising between the polyploid progeny and the diploid parents. You can find many papers about this topic, here is one from 2009: &lt;a href=&quot;http://www.pnas.org/content/106/33/13875.short&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/106/33/13875.short&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-04-15T19:15:23.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31392" PostTypeId="2" ParentId="31389" CreationDate="2015-04-15T19:23:49.593" Score="1" Body="&lt;p&gt;I am not sure what your question is but here is an example that may interest you.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The three sunflower species &lt;em&gt;Helianthus anomalus&lt;/em&gt;, &lt;em&gt;H. deserticola&lt;/em&gt;, and &lt;em&gt;H. paradoxus&lt;/em&gt; are all of hybrid origin of the same two &quot;parent species&quot; (&lt;em&gt;H. annuus&lt;/em&gt; and &lt;em&gt;H. petiolaris&lt;/em&gt;).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12907807&quot; rel=&quot;nofollow&quot;&gt;Major ecological transitions in wild sunflowers facilitated by hybridization&lt;/a&gt; is a paper that will likely interest you. This paper has been written by L. Riesberg and colleagues. You may want to read through some of the work of L. Rieseberg (CactusWoman already linked one of his articles). &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-04-15T20:26:02.287" LastActivityDate="2015-04-15T20:26:02.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31394" PostTypeId="1" AcceptedAnswerId="31405" CreationDate="2015-04-15T20:40:55.363" Score="18" ViewCount="827" Body="&lt;p&gt;I'm reading this paper about transmissible cancer cells in clams (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867415002433&quot; rel=&quot;nofollow noreferrer&quot;&gt;Metzger et al. 2015&lt;/a&gt;) and I was wondering if there are any single-cellular organisms that are around today that are suspected as having descended from a multicellular organism&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is different from &lt;a href=&quot;https://biology.stackexchange.com/questions/8894/could-cancer-be-in-itself-a-evolutionary-process/8900#8900&quot;&gt;this&lt;/a&gt; question as I'm not asking about cancer specifically but rather single-celled organisms evolving from multicellular organisms in general.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-04-17T11:26:05.773" Title="Are there single-celled organisms that have evolved from multi-cellular ones?" Tags="&lt;evolution&gt;&lt;microbiology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31395" PostTypeId="2" ParentId="31254" CreationDate="2015-04-15T22:34:37.513" Score="14" Body="&lt;p&gt;Medicine is not my field, but I want to point out two things:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The former words have latin (or greek) roots, and historically latin was the international language of science. Therefore, nomenclature in different scientific fields are often based on latin. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The former words describe tissues and the related functions/processes (e.g. renal = kidney + related tissues + processes carried out by the renal system), while the latter are names of organs. Therefore, the former words are more suitable and precise when you want to describe these processes. For instance (as far as I know), &lt;em&gt;Hepatic disease&lt;/em&gt; can be be caused by problems outside of the liver as such, e.g. blockage in the hepatic vein.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Users more knowledgeable in medicine are welcome to fill in or correct me if I'm mistaken.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-11-23T09:33:42.013" LastActivityDate="2015-11-23T09:33:42.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31399" PostTypeId="1" AcceptedAnswerId="31404" CreationDate="2015-04-16T03:52:17.417" Score="7" ViewCount="1353" Body="&lt;p&gt;When an action potential is transmitted along the axon, the membrane reaches its depolarized state by opening Na&lt;sup&gt;+&lt;/sup&gt; channels. Both K&lt;sup&gt;+&lt;/sup&gt; (potassium) and Na&lt;sup&gt;+&lt;/sup&gt; (sodium) are now on both sides with close to equal concentration-ratios. It is the next step that confuses me: the K&lt;sup&gt;+&lt;/sup&gt; rushing out of the cell, thus repolarizing the membrane. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wouldn't the two substances balance themselves out according to the Electric-/Substance-Concentration-Gradient once the Na&lt;sup&gt;+&lt;/sup&gt;/K&lt;sup&gt;+&lt;/sup&gt; channels are open? I don't understand where that energy comes from, the energy that not only mediates polarization, but also the subsequent re-polarization.&lt;/p&gt;&#xA;" OwnerUserId="15359" LastEditorUserId="9943" LastEditDate="2015-04-16T05:24:30.967" LastActivityDate="2018-10-08T12:52:38.267" Title="Why does the membrane of a neuron not stay at its depolarized state?" Tags="&lt;biophysics&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31400" PostTypeId="2" ParentId="31371" CreationDate="2015-04-16T04:34:04.753" Score="2" Body="&lt;p&gt;The shedding of leaves has more to do with the condition of the leaf itself. When leaves become inefficient and unable to produce food and&#xA;growth regulators, a process of abscission starts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Abscission a step in the planned senescence process within tree leaves. Senescence is a series of events that allow trees to conserve resources, prepare for a dormant period, and shed inefficient tissues. Senescence is not disruptive and not always caused by climatic factors.&#xA;Senescence is a highly ordered and carefully controlled set of steps initiated in preparation for a resting period of a tree (winter).&lt;/p&gt;&#xA;" OwnerUserId="12898" LastActivityDate="2015-04-16T04:34:04.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31401" PostTypeId="1" AcceptedAnswerId="31407" CreationDate="2015-04-16T04:39:17.833" Score="6" ViewCount="1129" Body="&lt;p&gt;Plants seem to be less complex organisms than animals, but despite that there are less plant genomes sequenced. Is that because plant genomes are more complex, for example in terms of regulatory regions and transposons that make sequencing more difficult, or are there other reasons why the number of sequenced plant genomes is smaller than animals?&lt;/p&gt;&#xA;" OwnerUserId="12898" LastEditorUserId="9943" LastEditDate="2015-04-16T05:06:35.870" LastActivityDate="2015-04-16T07:05:00.910" Title="Why is it harder to sequence plant genomes than animal genomes?" Tags="&lt;plant-physiology&gt;&lt;dna-sequencing&gt;&lt;chromosome&gt;&lt;genomes&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31402" PostTypeId="1" AcceptedAnswerId="31403" CreationDate="2015-04-16T05:09:26.297" Score="2" ViewCount="61" Body="&lt;p&gt;My university's -80 freezer just broke down and the repair will take 4 months according to the vendor. Is there any other way to preserve cells? Maintaining lot of flasks until the freezer is repaired is not viable option. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any alternative to cryopreserve cell lines without -80 freezer?. &lt;/p&gt;&#xA;" OwnerUserId="12898" LastActivityDate="2015-04-16T05:13:01.730" Title="Is there any alternative to cryopreserve cell lines without -80 freezer?" Tags="&lt;cell-culture&gt;&lt;cell&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31403" PostTypeId="2" ParentId="31402" CreationDate="2015-04-16T05:13:01.730" Score="2" Body="&lt;p&gt;A tank of liquid nitrogen is not just an alternative, but a much better substitute, IMHO. The problem of gradually cooling inside a isopropanol container can be overcome by using a box full of dry ice (-79°C as I recall).&lt;/p&gt;&#xA;" OwnerUserId="15321" LastActivityDate="2015-04-16T05:13:01.730" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31404" PostTypeId="2" ParentId="31399" CreationDate="2015-04-16T05:58:26.697" Score="9" Body="&lt;h2&gt;Three facts:&lt;/h2&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The K&lt;sup&gt;+&lt;/sup&gt; ions are heavily concentrated on the inside while the Na&lt;sup&gt;+&lt;/sup&gt; ions are heavily concentrated on the outside&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The Na&lt;sup&gt;+&lt;/sup&gt;/K&lt;sup&gt;+&lt;/sup&gt; ion pump is unidirectional. It can only pump K&lt;sup&gt;+&lt;/sup&gt; ions inside the cell while expelling the Na&lt;sup&gt;+&lt;/sup&gt; ions.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Finally only the Na&lt;sup&gt;+&lt;/sup&gt;/K&lt;sup&gt;+&lt;/sup&gt; ion pumps can restore the ionic equilibrium.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QYqnU.gif&quot; alt=&quot;ionic concentration inside neurons&quot; /&gt;&lt;/p&gt;&#xA;&lt;h2&gt;The full scene:&lt;/h2&gt;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Once the threshold is reached the Na&lt;sup&gt;+&lt;/sup&gt; voltage gated channels open up. So Na&lt;sup&gt;+&lt;/sup&gt; ions rush in, causing depolarisation.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Then the Na&lt;sup&gt;+&lt;/sup&gt; channels close while the K&lt;sup&gt;+&lt;/sup&gt; channels open. This causes rushing of K&lt;sup&gt;+&lt;/sup&gt; ions outside, thus slowly reducing the potential difference starting the process of repolarisation&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Now the Na&lt;sup&gt;+&lt;/sup&gt;/K&lt;sup&gt;+&lt;/sup&gt; ion pumps are geared up as the extracellular concentration of K&lt;sup&gt;+&lt;/sup&gt; and intracellular concentration of Na&lt;sup&gt;+&lt;/sup&gt; ions are high (which is the ideal environment for the pump to work.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Iv5Pe.gif&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;h2&gt;PS:&lt;/h2&gt;&#xA;&lt;p&gt;Without the high extracellular concentration of the K&lt;sup&gt;+&lt;/sup&gt; ions the pump can't function any faster than the basal rate even though the intracellular concentration of Na&lt;sup&gt;+&lt;/sup&gt; ions exceed the normal value by many times. High concentration of K&lt;sup&gt;+&lt;/sup&gt; ions in the extracellular environment is essential for restoration of the ionic equilibrium.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;Edit:&lt;/p&gt;&#xA;&lt;p&gt;I meant unidirectional in the sense that when actively pumping sodium is always pushed out while potassium is always pushed in.&lt;/p&gt;&#xA;&lt;p&gt;Thanks to AliceD for pointing out that when the gradient is reversed, the pump synthesizes ATP due to forced movement of ions in the opposite direction.&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-16T15:02:33.200" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31405" PostTypeId="2" ParentId="31394" CreationDate="2015-04-16T06:20:54.130" Score="11" Body="&lt;p&gt;I would consider &lt;a href=&quot;http://en.wikipedia.org/wiki/HeLa&quot;&gt;HeLa cells&lt;/a&gt; to be an example of a unicellular eukaryotic organism that evolved from humans. It can survive independently and replicate within cell culture plates, but cannot survive in the wild, however. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/H9fHX.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HeLa cells are, like in your example, cancer cells, in this specific case human cervical cancer cells. They were propagated as an immortal cell line, and completely match the replication characteristics of eukaryotic cell lines when propagated in the laboratory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It can be even considered the case that HeLa cells are actually a kind of unicellular eukaryotic model organism not unlike &lt;em&gt;S. cerevisiae&lt;/em&gt;, since they are widely used in experiments involving human-like cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As WYSIWYG has said in the comments, some biologists have even assigned the binomial name &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/HeLa#New_species_proposal&quot;&gt;Helacyton gartleri&lt;/a&gt;&lt;/em&gt; to the cells (albeit with some controversy). &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-04-16T16:39:16.340" LastActivityDate="2015-04-16T16:39:16.340" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31406" PostTypeId="2" ParentId="31388" CreationDate="2015-04-16T06:46:05.530" Score="14" Body="&lt;p&gt;Front row, left to right; &lt;a href=&quot;http://en.wikipedia.org/wiki/Victor_A._McKusick&quot;&gt;Victor McKusick&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Maurice_Wilkins&quot;&gt;Maurice Wilkins&lt;/a&gt;, James Watson, &lt;a href=&quot;http://en.wikipedia.org/wiki/Walter_Gilbert&quot;&gt;Walter Gilbert&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/John_Kendrew&quot;&gt;John Kendrew&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="3624" LastEditDate="2015-04-16T12:12:51.993" LastActivityDate="2015-04-16T12:12:51.993" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31407" PostTypeId="2" ParentId="31401" CreationDate="2015-04-16T07:05:00.910" Score="10" Body="&lt;p&gt;The authors of &lt;a href=&quot;http://genomebiology.com/2012/13/4/243&quot;&gt;this&lt;/a&gt; 2012 review article summarize the problem well in their introduction:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In contrast to the tremendous advances in throughput, assembling sequencing reads remains a substantial endeavor, much greater than the sequencing efforts alone would suggest [22-24]. Large complex plant genomes remain a particularly difficult challenge for de novo assembly for a variety of biological, computational and biomolecular reasons. Plant genomes can be nearly 100 times larger [25] than the currently sequenced bird [26], fish [27] or mammalian genomes [28]. In addition they can have much higher ploidy, which is estimated to occur in up to 80% of all plant species [29], and higher rates of heterozygosity and repeats [30] than their counterparts in other kingdoms. Furthermore, the gene content in plants can be very complex, as shown by the presence of large gene families and abundant pseudogenes with nearly identical sequences derived from recent whole genome duplication events and transposon activity [13]. Plants tend to have high copy chloroplasts and mitochondria organelles, which complicate assembly of their remnants in the nuclear genome and skew coverage levels [12]. Finally, it is often very difficult to extract large quantities of high-quality DNA from plant material, making it difficult to prepare proper libraries for sequencing.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From: Schatz, Witkowski and McCombie. &quot;&lt;strong&gt;Current challenges in de novo plant genome sequencing and assembly&lt;/strong&gt;&quot;. Genome Biology (2012). &lt;strong&gt;13&lt;/strong&gt;:243&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see, all of the key reasons have been touched on by the various people who have commented below your question.&lt;/p&gt;&#xA;" OwnerUserId="14553" LastActivityDate="2015-04-16T07:05:00.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31408" PostTypeId="2" ParentId="31383" CreationDate="2015-04-16T08:41:20.297" Score="14" Body="&lt;p&gt;I think it looks a lot like a European Pigeon Tick (&lt;em&gt;Argas reflexus&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XA5ir.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They infest pigeons and they die when infesting humans, which they only do if they are very hungry (yours looks hungry though).&#xA;May also transmit diseases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt;&lt;br&gt;&#xA;It could also be an Blyborough Tick (&lt;em&gt;Argas vespertilionis&lt;/em&gt;). They infest bats and are a little rounder in shape but look otherwise similar.&lt;/p&gt;&#xA;" OwnerUserId="15257" LastEditorUserId="15257" LastEditDate="2015-07-09T14:02:07.777" LastActivityDate="2015-07-09T14:02:07.777" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31411" PostTypeId="1" AcceptedAnswerId="31418" CreationDate="2015-04-16T12:38:01.830" Score="3" ViewCount="163" Body="&lt;p&gt;Why is (in forensic genetics) in some cases more appropriate comparison of nuclear DNA but in some other cases comparison of mitochondrial DNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it because geneticists are sometimes unable to find nDNA or if nDNA is too damaged? Also could it be because of the structure of mtDNA (it's more protected against degradation, which is good for identifying old biological material)? I can't see any other advantages, since mitochondrial DNA mutations occur frequently, due to the lack of the error checking, but are there any that I am missing?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you in advance.&lt;/p&gt;&#xA;" OwnerUserId="6950" LastEditorUserId="6950" LastEditDate="2015-04-16T15:29:26.240" LastActivityDate="2017-10-18T16:59:31.920" Title="Forensic genetics- why is mtDNA comparison sometimes better than nDNA comparison?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;human-genetics&gt;&lt;mitochondria&gt;&lt;forensics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31413" PostTypeId="1" AcceptedAnswerId="31415" CreationDate="2015-04-16T14:40:53.277" Score="3" ViewCount="1297" Body="&lt;p&gt;I'm writing up a report and I see conflicts everywhere on the internet. Should it be Murine Minute Virus (MMV) or Minute Virus of Mice (MVM).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The followup question is does it really matter.&lt;/p&gt;&#xA;" OwnerUserId="389" LastActivityDate="2015-04-16T16:11:47.090" Title="What is correct MVM vs. MMV?" Tags="&lt;terminology&gt;&lt;virology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31414" PostTypeId="2" ParentId="31413" CreationDate="2015-04-16T15:50:18.590" Score="0" Body="&lt;p&gt;Given the wide variety of academic sources using each abbreviation, it's fairly clear that there is no standardised usage; as such, as long as you state the full phrase the first time you use it and use whichever form you pick consistently throughout your report, it doesn't really matter which you use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To avoid confusion, I would recommend mentioning that both are used to refer to the same thing the first time you introduce the term.&lt;/p&gt;&#xA;" OwnerUserId="13187" LastActivityDate="2015-04-16T15:50:18.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31415" PostTypeId="2" ParentId="31413" CreationDate="2015-04-16T15:51:36.497" Score="4" Body="&lt;p&gt;According to the &lt;a href=&quot;http://ictvonline.org/taxonomyHistory.asp?taxnode_id=20142982&quot; rel=&quot;nofollow&quot;&gt;International Committee on Taxonomy of Viruses&lt;/a&gt;, it has had several official variations of that name over the years:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Minute mouse virus&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Minute of mice virus&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;MVM Virus&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Minute virus of mice&lt;/em&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Mice minute virus&lt;/em&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The current (2014) accepted name is: &lt;em&gt;Rodent protoparvovirus 1&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Does it really matter?&quot; As long as you write in full the name you're using the first time you use it, people will know what you're talking about. However, for consistency amongst current literature, perhaps we should all strive to keep up with current taxonomy.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-04-16T16:11:47.090" LastActivityDate="2015-04-16T16:11:47.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31418" PostTypeId="2" ParentId="31411" CreationDate="2015-04-16T16:37:05.117" Score="1" Body="&lt;p&gt;mtDNA is present in a much higher copy number per cell than nuclear DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://nar.oxfordjournals.org/content/31/11/e61.full&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;, there are approximately 4000 or so mitochondrial DNA copies per human muscle cell. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;copy number of mtDNA per diploid nuclear genome in myocardium was 6970 ± 920, significantly higher than that in skeletal muscle, 3650 ± 620 (P = 0.006).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This makes it far more likely that a non-degraded copy of mtDNA exists, considering that there are normally only 2 or 4 copies of nuclear DNA per cell per locus for almost all kinds of cells.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-04-16T21:34:01.700" LastActivityDate="2015-04-16T21:34:01.700" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31419" PostTypeId="1" AcceptedAnswerId="31422" CreationDate="2015-04-16T16:55:20.383" Score="11" ViewCount="36117" Body="&lt;p&gt;I just made a SDS-PAGE with a top layer of stacking gel and a bottom layer of separating gel with different pH values of 0.5M Tris-HCl. The stacking was 6.8 and the separating gel was 8.8. What about this pH change makes the gels different? What effect does this have on the proteins that I ran? &lt;/p&gt;&#xA;" OwnerUserId="12898" LastEditorUserId="4747" LastEditDate="2015-04-16T18:00:57.290" LastActivityDate="2015-04-16T18:20:25.973" Title="What is the purpose of using two layers of gel in SDS- PAGE?" Tags="&lt;proteins&gt;&lt;protocol&gt;&lt;sds-page&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31420" PostTypeId="1" AcceptedAnswerId="31423" CreationDate="2015-04-16T17:04:29.420" Score="5" ViewCount="130" Body="&lt;p&gt;My daughter, while reading a book about dinosaurs, asked me if prosauropods are ancestors of all sauropods. Are they? From the name (&quot;pro-sauropods&quot;), I guess that they are, but am I right?&lt;/p&gt;&#xA;" OwnerUserId="15365" LastEditorUserId="1306" LastEditDate="2015-04-16T18:32:19.153" LastActivityDate="2015-04-16T18:53:31.693" Title="Are prosauropods ancestors of all sauropods?" Tags="&lt;taxonomy&gt;&lt;palaeontology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31421" PostTypeId="2" ParentId="31419" CreationDate="2015-04-16T17:22:10.747" Score="6" Body="&lt;p&gt;The other major difference between the two is the amount of acrylamide in the upper (stacking) gel - it's generally around 4%, while the lower (resolving) gel can vary from 6 or 8% to 20%, depending on the size of the protein(s) you're looking for. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you load your samples in the wells at the top of the gel, then start the current, not all of the sample enters the gel at the same time. The purpose of the stacking gel, with its lower pH and low acrylamide percentage, is to &quot;stack&quot; all of the proteins in your sample into as narrow of a band as possible, so that they all enter the resolving gel at essentially the same time. If you didn't have that stacking gel, your band(s) of interest could be very diffuse, and may not match up with your molecular weight marker.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-04-16T17:22:10.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31422" PostTypeId="2" ParentId="31419" CreationDate="2015-04-16T18:20:25.973" Score="9" Body="&lt;p&gt;The stacking gel concentrates proteins loaded into the sample wells so that they are resolved as a unified &quot;line&quot; once they enter the stacking gel.  The reason for the lower pH is that this &quot;lower ionic strength implies higher electrical resistance and consequently a higher electric field, provoking the faster movement of the proteins and of every other charged particle in the gel. Such a high electric field coupled with the glycine in the running buffer (that will not go into the resolving gel due to the pH), helps to clean the sample from the Cl- ions from the Tris-HCl buffer. That concludes in a stack of clean, denatured, and equally charged proteins in the boundary with the resolving gel; this will account for a good quality PAGE.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bassically, in the stacking gel the pore size is larger so it gives a chance for the larger proteins and smaller proteins to equalize with each other.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;As the proteins are denatured and linearized by heating, SDS and dithiothreitol (if there is any di-sulfide bond), the proteins are loaded onto the wells on the stacking gel. The denatured proteins have a uniform mass to negative charge ratio. Since the current run from negative (top) to positive (bottom), the proteins move toward the bottom. When the electricity is turned on, the proteins and Tris-glycine enter the stacking gel. In stacking gel with pH 6.8, the N-terminal amino group of the proteins and amino acids are protonated at equilibrium which makes them less negative. The average electrophoretic mobility is very slow. A Gly-chloride ion boundary is formed since glycine moves slower than chloride ion. However, glycine still runs slightly faster than other proteins. As a result, the glycine keeps pushing the protein towards the chloride ion. In other words, the proteins are trapped between glycine and chloride ion. The proteins form a very tight band inside the stacking gel. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once the protein reaches the resolving gel, the pH changes from 6.8 to 8.8 and the pores are smaller. As pH increases, the N-terminal amino groups are deprotonated. Amino acids and proteins are more negatively charged at equilibrium than in stacking gel. As a result, glycine moves faster than proteins. Glycine and chloride ions move ahead of the proteins. As the pores are smaller in the resolving gel, the size of the protein determines the mobility (speed). So the smaller the protein is, the faster it will reach the bottom.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;a href=&quot;https://sites.google.com/a/tamu.edu/bich608-602/bich608---announcements-and-more/sds-pagestackinggel&quot;&gt;SDS-PAGE stacking gel&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="14916" LastActivityDate="2015-04-16T18:20:25.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31423" PostTypeId="2" ParentId="31420" CreationDate="2015-04-16T18:53:31.693" Score="6" Body="&lt;p&gt;Welcome to Biology.SE! Your daughter asks interesting questions!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is debated. It is currently mostly thought that &lt;em&gt;sauropods&lt;/em&gt; and &lt;em&gt;pro-sauropods&lt;/em&gt; are sister lineages and therefore, one does not contain the other. In other words, the &lt;em&gt;pro-sauropods&lt;/em&gt; are no more the ancestors of the &lt;em&gt;sauropods&lt;/em&gt; than were the mammals are the dogs are the ancestors to the cats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the most updated source of information for phylogenetic questions of the kind is &lt;a href=&quot;http://www.tolweb.org&quot;&gt;tolweb.org&lt;/a&gt;. You should have a look. Here is the page for the &lt;a href=&quot;http://tolweb.org/Sauropodomorpha/15725&quot;&gt;Sauropodomorpha&lt;/a&gt; (which contains the &lt;em&gt;sauropods&lt;/em&gt; and the &lt;em&gt;pro-sauropods&lt;/em&gt;). You have a nice list of reference on this page including some from Sereno, who is the author who first defined the &lt;em&gt;pro-sauropods&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I quickly sought through the literature. It seems indeed that all phylogenetic analysis were based on phenotypic comparisons and not on genetic comparisons. Citing from &lt;a href=&quot;http://en.wikipedia.org/wiki/Sauropodomorpha&quot;&gt;wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Evidence against sauropod ancestry within Prosauropoda comes from the fact that prosauropods had a smaller outer toe on their hind feet than the sauropods. Many maintain that it is easier for digits to be reduced or lost during evolution than the reverse, however there is no evidence for this. The lengthening, or gaining of extra digits is common in marine reptiles, and within the theropods digit lengthening occurred at least once. Therefore, using this as evidence against ancestral prosauropods is questionable.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2015-04-16T18:53:31.693" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31424" PostTypeId="1" CreationDate="2015-04-16T20:19:31.717" Score="0" ViewCount="516" Body="&lt;p&gt;The classical definition of the Genetic Matrix &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;G = ZZ'/2p(1-p)&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where Z = M - P&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where P = 2(p-0.5)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't have a background in biology but understand Maths and Computer Science very well. I am trying to wrap my head around&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Why do we define P the way we do?&#xA;2) Why do we subtract  P from M&#xA;3) How to interpret a negative entry in G?&#xA;4) Does the j,k element of G give me the genetic distance between j and k individuals?&lt;/p&gt;&#xA;" OwnerUserId="15367" LastActivityDate="2015-04-16T20:19:31.717" Title="Genetic Relationship Matrix" Tags="&lt;genetics&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31425" PostTypeId="1" AcceptedAnswerId="31564" CreationDate="2015-04-16T20:54:13.367" Score="4" ViewCount="96" Body="&lt;p&gt;Why do plants produce so many hybrids? I have read that they are the largest kingdom of organisms to do so. Does this have something to do with polyploidy events? &lt;/p&gt;&#xA;" OwnerUserId="14815" LastActivityDate="2015-04-21T15:24:10.030" Title="Why do plants produce so many hybrids as a kingdom?" Tags="&lt;evolution&gt;&lt;botany&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31426" PostTypeId="1" CreationDate="2015-04-16T20:55:34.243" Score="10" ViewCount="558" Body="&lt;p&gt;X-posted on reddit AskScience &lt;a href=&quot;http://www.reddit.com/r/askscience/comments/32qc00/do_macrophages_get_nutritional_value_from_the/&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that macrophages engulf foreign bodies and transport them to various waste excretion pathways (sorry if the terminology is wrong), and if the foreign bodies are cellular in nature, they get trapped in phagolysosomes and get digested by enzymes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the macrophage get any &quot;nutrition&quot; by destroying the cells, the same way that a person would if those same cells were to pass through their digestive system? Is there any chemical energy produced by the catalysis that the macrophage then uses, e.g. pyruvate for its mitochondria? Or scavenged cellular components that it can use to build its own cytoskeleton?&lt;/p&gt;&#xA;" OwnerUserId="10288" LastActivityDate="2015-04-17T15:28:42.553" Title="Do macrophages get nutritional value from the pathogens that they eat?" Tags="&lt;molecular-biology&gt;&lt;nutrition&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31427" PostTypeId="1" CreationDate="2015-04-16T21:04:49.933" Score="10" ViewCount="49864" Body="&lt;p&gt;Does freezing microorganisms such as probiotics kill them?  If not, what is the process that allows them to &quot;come back to life&quot; after the temperatures are increased?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an example, lets say you freeze a yogurt (whether it be Greek, Australian, Turkish, Indian, Russian, European, or Western) and &lt;strong&gt;eat it while frozen&lt;/strong&gt;.  Would the probiotics in the yogurt &quot;come back to life&quot; and be beneficial?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, I am referring to freezing refrigerated yogurts, and not products that are sold as &quot;frozen yogurts&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the biological basis for this?&lt;/p&gt;&#xA;" OwnerUserId="15368" LastEditorUserId="15368" LastEditDate="2015-04-16T22:31:54.873" LastActivityDate="2018-08-02T16:43:34.653" Title="Does freezing microorganisms such as probiotics kill them?" Tags="&lt;microbiology&gt;&lt;digestive-system&gt;&lt;health&gt;&lt;digestion&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31429" PostTypeId="2" ParentId="31427" CreationDate="2015-04-16T22:12:30.803" Score="10" Body="&lt;p&gt;Yes, they do. For a look at survival of &lt;em&gt;Lactobacillus&lt;/em&gt; and other bacterial species after multiple freeze/thaw cycles, check out &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC386276/?page=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Harrison 1955&lt;/a&gt; (below).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The awesome hand-drawn graphs show that many bacteria survive after being frozen for 11 weeks. There's also a figure on the following page showing that many bacteria also survive after multiple freeze-thaw cycles, but I won't include that page here for brevity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prof. Don Schaffner of Rutgers also &lt;a href=&quot;http://www.madsci.org/posts/archives/2004-10/1098383406.Gb.r.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;supports&lt;/a&gt; this conclusion:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;So it's possible, even likely, that frozen and thawed yogurt will contain &#xA;  living lactic acid bacteria, although it may only be 10% or 1% of the &#xA;  total number of bacteria that were there before the yogurt was frozen.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I couldn't find a great deal of official resources on the topic, hence the paper from 1955 and random quote from a food science professor. However, in a lab setting, scientists regularly freeze bacteria and even eukaryotic human cell lines. Usually scientists use a cryoprotectant like glycerol, but many foods (like yogurt and ice cream) may contain an FDA-approved cryoprotectant (&lt;a href=&quot;http://en.wikipedia.org/wiki/Antifreeze_protein#Recent_news&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One recent, successful business endeavor has been the introduction of [anti-freeze proteins] AFPs into ice cream and yogurt products. This ingredient, labelled ice-structuring protein, has been approved by the Food and Drug Administration.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, yes, at least some of the bacteria in your frozen yogurt are still alive, and will have whatever beneficial/harmful/lack of effect when you ingest them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KtcRF.gif&quot; alt=&quot;journal page&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Judging from figures 1-3 above, bacterial survival depends on how long and how many times you freeze the bacteria. My rough estimates of the graph above say &lt;a href=&quot;http://www.wolframalpha.com/input/?i=100-%288*10%5E8-3*10%5E8%29%2F8*10%5E8*100&quot; rel=&quot;nofollow noreferrer&quot;&gt;40%&lt;/a&gt;-&lt;a href=&quot;http://www.wolframalpha.com/input/?i=100-%288*10%5E8-7*10%5E7%29%2F8*10%5E8*100&quot; rel=&quot;nofollow noreferrer&quot;&gt;10%&lt;/a&gt; after a single freeze, and after multiple freeze-thaws getting into the &lt;a href=&quot;http://www.wolframalpha.com/input/?i=100-%288*10%5E8-9*10%5E6%29%2F8*10%5E8*100&quot; rel=&quot;nofollow noreferrer&quot;&gt;1%&lt;/a&gt; range. Also, it doesn't matter whether you thaw it first or eat it frozen as far as bacterial content is concerned, the bacteria will be unfrozen either way when they reach your digestive tract.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="9829" LastEditDate="2015-04-19T13:55:45.247" LastActivityDate="2015-04-19T13:55:45.247" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31430" PostTypeId="1" AcceptedAnswerId="31583" CreationDate="2015-04-16T22:36:23.637" Score="7" ViewCount="3798" Body="&lt;p&gt;Almost all the landmark GWAS (Genome-Wide Association Studies) reviews agree that, for a GWAS finding to be valid, it needs to be replicated in an independent cohort. What exactly is the rationale behind this? Is this criterion still valid even when the objective is looking for genes to do functional studies, instead of a clinical perspective of searching for susceptibility loci? Considering the difficulty in replicating some phenotypical characterizations in a large numbers of subjects, for a biologist this whole thing seems irrelevant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider the following scenario: Suppose I have 5000 phenotyped individuals with a budget to genome-wide genotype them all. The phenotyping requires state-of-the art methodology with immense costs, and the cohort was phenotyped through another grant. What would be the point of dividing my cohort to two as a discovery and replication groups, other than to save money in exchange for stat power. To this, add the subsequent functional studies on the associated loci, what would the point in genotyping a few SNPs in 500 more people be? If one can indeed find that additional cohort, wouldn't it be a better option to combine any available cohorts in a meta-analysis, rather than using them for replication?  &lt;/p&gt;&#xA;" OwnerUserId="15321" LastEditorUserId="15321" LastEditDate="2015-04-16T23:27:21.450" LastActivityDate="2015-04-21T23:38:36.360" Title="GWAS: why is replication in another cohort so crucial?" Tags="&lt;genetics&gt;&lt;human-genetics&gt;&lt;experimental-design&gt;&lt;epidemiology&gt;&lt;gwas&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31431" PostTypeId="2" ParentId="31430" CreationDate="2015-04-16T22:54:30.927" Score="1" Body="&lt;p&gt;As with all serious scientific result GWAS results need to validated by others. In this case it think is extremely important because these studies link mutations to diseases or in more general given genotypes to phenotypes, thus pointing out possible causes. So validating these results with the use of independent &quot;samples&quot; is indeed crucial. But as I said all serious (noteworthy) scientific finding should be reproducible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: the point in it is randomness and sub sampling. Such large cohort should not come from a small sub-population but many regions of the world, and by randomly dividing your individuals to two or even more groups you ensure that other background effects such as local gene allele variation frequencies, life-style differences etc average out. Imagine a scenario where you have 90 individuals in 60 of them you can link the genotype to the phenotype. that is 2/3 of the individuals. But if you take 3 sub samples of 30 individuals and get 7/23 , 17/13 and  6/24 (not linked / linked), that is 76.6% (23/30) , 43.3% (13/30) and 80% (24/30). From these you can get tbe same average of 66.6% but with standard deviation (15,5), and confidence interval not just a number. &lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-17T00:25:26.017" LastActivityDate="2015-04-17T00:25:26.017" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31432" PostTypeId="1" AcceptedAnswerId="52626" CreationDate="2015-04-17T00:11:27.707" Score="4" ViewCount="405" Body="&lt;p&gt;Up front, I am specifically not interested in philosophical or ethical considerations re Eugenics and related concepts. In an effort to receive a concise answer I'll post a narrowly defined question following this preamble to set the stage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Preamble:&lt;br&gt;&#xA;In the movie &lt;em&gt;Idiocracy&lt;/em&gt; there is a montage at the beginning &quot;explaining&quot; how the human population degrades, vis-à-vis intelligence, to an alarming (and absurd?) extent due to unplanned differential breeding resulting from several generations of the intellectually &quot;more capable&quot; people limiting their number of progeny, through active and passive family planning, while the bulk of humanity leaves caution to the wind. This exponential social differentiation eventually makes for a global imbalance that degrades our species' overall intellectual fitness to a debilitation level. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Question:&lt;br&gt;&#xA;Is the premise of this movie merely a gag or is our species already doing something very much like this?&lt;br&gt;&#xA;If yes or no, how might one measure the impact of differential procreation of this sort? Since testing results are always relative to the population as a whole and computers along with the &lt;em&gt;Internet of Things&lt;/em&gt; would tend to obfuscate the initial degradation of mental capacity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;EDIT&lt;/em&gt;:&lt;br&gt;&#xA;Based on the brief discussion in the comments - a summary of fecundity and IQ would potentially answer my question but only if it accounted for the current selection process we see going on in modern technophile societies. That is, it must account for the effect of our most educated couples generally choosing &lt;em&gt;not&lt;/em&gt; to procreate and here I'm &lt;em&gt;assuming&lt;/em&gt; there is in fact an effect (cf. &lt;em&gt;Idiocracy&lt;/em&gt; for the (absurd?) degree to which the present-day trend may work itself out). &lt;/p&gt;&#xA;" OwnerUserId="15370" LastEditorUserId="15370" LastEditDate="2015-04-21T15:05:16.063" LastActivityDate="2016-11-23T09:38:38.167" Title="Current Trend in Evolution of Human Intelligence" Tags="&lt;human-genetics&gt;&lt;natural-selection&gt;&lt;intelligence&gt;&lt;human-evolution&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="31433" PostTypeId="1" AcceptedAnswerId="31446" CreationDate="2015-04-17T00:31:20.273" Score="2" ViewCount="364" Body="&lt;p&gt;In papers reporting a relative quantification of gene expression by RTPCR, I often see a bar chart with mean ± standard error or deviation, with the deviation belonging to biological replicates. This ignores all the previous layers of technical replicates. In the regular $2^{\Delta(\Delta Ct)}$ estimation with 3 reactions per primer/template, we have the standard deviation (SD) from each technical replicate, then the SD from normalization, end finally the SD from quantification. If the end results are fold changes, add one more layer to this. I'm not even including normalization with the geometric mean of 3 housekeeping genes (the better method)  How can I  correctly calculate / depict the statistical variations in this case?&lt;/p&gt;&#xA;" OwnerUserId="15321" LastEditorUserId="3340" LastEditDate="2015-04-17T11:26:41.940" LastActivityDate="2015-04-18T04:51:51.513" Title="Correct/complete representation of RTPCR statistics" Tags="&lt;gene-expression&gt;&lt;pcr&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31434" PostTypeId="2" ParentId="31426" CreationDate="2015-04-17T00:51:34.733" Score="5" Body="&lt;p&gt;In &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1742-4658.2009.06951.x/pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article it is described that starved macrophages 'consume' heat inactivated bacteria through phagocytosis with enhanced ability. Starving can also induce (macro)autophagy and the pathways are connected with phagocytosis,in the macrophages under investigation it was shown that autophagy did not play role in the enhanced ability of phagocytosis. The paper however does not mention anything about macrophages utilizing the resources obtained by the digestion of the bacteria. although it would seem logical. I'll keep looking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found a text book that says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;in general cells of the macrophage series have two major functions. On f their functions ,as their name (&quot;large eater&quot;) implies, is to &lt;strong&gt;engulf&lt;/strong&gt; and, with the aid of all the degradative enzymes in their lysosomal granules, &lt;strong&gt;break down&lt;/strong&gt; trapped materials int ismple amino acids, sugars and other substances, for excretion and reutilization.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source : IMMUNOLOGY A Short course 3rd edition by Eli Benjamini, Geoffrey Sunshine and Sidney Leskowitz 1996 pages 23-24. ISBN 0-471-59791-0. I only have printed copy, but I'll try to find online version.&#xA;The other function is antigen presenting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus I can say that yes macrophages and other cells do utilize resources from digested pathogens.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-17T11:13:01.973" LastActivityDate="2015-04-17T11:13:01.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31436" PostTypeId="2" ParentId="31334" CreationDate="2015-04-17T02:26:55.890" Score="1" Body="&lt;p&gt;Activity of a hormone represents the efficacy of the hormone in causing the intended effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case of T3 vs T4, though T4 is the majority fraction, T3 is more active, meaning it is much more efficacious in effecting the results. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concentration of T4 is 30 - 50 times higher than T3&lt;sup&gt;1&lt;/sup&gt;. Though T3 is produced by thyroid it is in minority. The majority of T3 is produced by peripheral conversion of T4 into T3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thyroid hormones are transported in the blood vessels by albumin, thyroxine binding prealbumin (also called transthyretin). T4 binds more tightly to these transport proteins than T3. In other words T3 constitutes the majority of the free fraction (unbound to carrier/transport proteins). Only the free form of the hormone is metabolically active. So T3 is 3 to 5 times more active than T4.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;T3 - triiodothyroxine&lt;/p&gt;&#xA;&#xA;&lt;p&gt;T4 - tetraiodothyroxine&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1: pg. 312, Essentials of surgery, Sanjay Azad&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-04-17T02:56:09.837" LastActivityDate="2015-04-17T02:56:09.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31437" PostTypeId="2" ParentId="31330" CreationDate="2015-04-17T04:40:10.360" Score="4" Body="&lt;p&gt;&lt;em&gt;Cyanidioschyzon merolae&lt;/em&gt; &lt;a href=&quot;http://www.nature.com/nature/journal/v428/n6983/full/nature02398.html&quot; rel=&quot;nofollow&quot;&gt;seems to be an example&lt;/a&gt; of such algae. Cryptomonad, aka &lt;em&gt;Cryptophyceae&lt;/em&gt; also &lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF01666391#page-1&quot; rel=&quot;nofollow&quot;&gt;lacks cell wall&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think, problem you encounter is that most studies are concerned with structure and function of cell walls, as such knowledge can be used in biotech industry. Hence, you will not find answer by looking for &quot;algae without cell wall&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a suggestion, I would point to this evolutionary study on development of plants: &lt;a href=&quot;http://www.annualreviews.org/doi/full/10.1146/annurev-arplant-042110-103809?url_ver=Z39.88-2003&amp;amp;rfr_id=ori:rid:crossref.org&amp;amp;rfr_dat=cr_pub%3Dpubmed&quot; rel=&quot;nofollow&quot;&gt;Evolution and Diversity of Plant Cell Walls: From Algae to Flowering Plants&lt;/a&gt;. Seems like trying to look through evolutionary trees might give you more examples.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-17T04:40:10.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31439" PostTypeId="1" CreationDate="2015-04-17T08:56:54.920" Score="2" ViewCount="266" Body="&lt;p&gt;We performed 36h biofilm cultures and would like to know if this time is enough to planktonic bacteria to precipitate. &#xA;Since we observed biofilm formation one the surface of the microtiter plate. Were  biofilm bacteria derived from precipitation of suspended bacteria or rather replicated from some initial attached bacteria cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specie: Haemophilus parasuis. A facultative anaerobe.&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="4717" LastEditDate="2015-04-17T19:39:49.127" LastActivityDate="2015-04-17T19:39:49.127" Title="Do bacteria precipitate in static liquid culture media?" Tags="&lt;biofilms&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31440" PostTypeId="1" AcceptedAnswerId="31445" CreationDate="2015-04-17T09:01:52.637" Score="1" ViewCount="797" Body="&lt;p&gt;By accident, I found a &lt;a href=&quot;http://www.google.pl/imgres?imgurl=http://images.slideplayer.pl/8/2423760/slides/slide_2.jpg&amp;amp;imgrefurl=http://slideplayer.pl/slide/2423760/&amp;amp;h=720&amp;amp;w=960&amp;amp;tbnid=NOICclwr0la57M:&amp;amp;zoom=1&amp;amp;docid=rrtd517gCuWmWM&amp;amp;hl=pl&amp;amp;ei=f8UwVZ3aEcHjaKyQgKgO&amp;amp;tbm=isch&amp;amp;ved=0CGEQMyg4MDg&quot; rel=&quot;nofollow&quot;&gt;slide from a Polish chemical presentation&lt;/a&gt;, that talks about a small group of biological organisms which contain chemical elements not found in the human body, like:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;B (&lt;a href=&quot;http://en.wikipedia.org/wiki/Boron&quot; rel=&quot;nofollow&quot;&gt;boron&lt;/a&gt;),&lt;/li&gt;&#xA;&lt;li&gt;F (&lt;a href=&quot;http://en.wikipedia.org/wiki/Fluorine&quot; rel=&quot;nofollow&quot;&gt;fluorine&lt;/a&gt;),&lt;/li&gt;&#xA;&lt;li&gt;Si (&lt;a href=&quot;http://en.wikipedia.org/wiki/Silicon&quot; rel=&quot;nofollow&quot;&gt;silicon&lt;/a&gt;),&lt;/li&gt;&#xA;&lt;li&gt;V (&lt;a href=&quot;http://en.wikipedia.org/wiki/Vanadium&quot; rel=&quot;nofollow&quot;&gt;vanadium&lt;/a&gt;),&lt;/li&gt;&#xA;&lt;li&gt;Cr (&lt;a href=&quot;http://en.wikipedia.org/wiki/Chromium&quot; rel=&quot;nofollow&quot;&gt;chromium&lt;/a&gt;),&lt;/li&gt;&#xA;&lt;li&gt;Se (&lt;a href=&quot;http://en.wikipedia.org/wiki/Selenium&quot; rel=&quot;nofollow&quot;&gt;selenium&lt;/a&gt;) and&lt;/li&gt;&#xA;&lt;li&gt;Sn (&lt;a href=&quot;http://en.wikipedia.org/wiki/Tin&quot; rel=&quot;nofollow&quot;&gt;tin&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Can someone provide a list of examples of organisms containing these chemical elements?&lt;/p&gt;&#xA;" OwnerUserId="8986" LastEditorUserId="9943" LastEditDate="2015-04-17T11:54:59.177" LastActivityDate="2015-04-18T06:21:59.703" Title="Organisms that contain rare chemical elements" Tags="&lt;nutrition&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31441" PostTypeId="2" ParentId="31440" CreationDate="2015-04-17T09:35:10.933" Score="2" Body="&lt;p&gt;Silicon is not rare at all. Silicon Dioxide is Sand and Sand is content of every soil. Even just rice hull and grass blade contain silicon&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you just read in wiki page of silicon there you would see this&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Silicon is an essential element in biology, although only tiny traces&#xA;  of it appear to be required by animals.[10] However, various sea&#xA;  sponges as well as microorganisms like diatoms and radiolaria secrete&#xA;  skeletal structures made of silica. Silica is often deposited in plant&#xA;  tissues, such as in the bark and wood of Chrysobalanaceae and the&#xA;  silica cells and silicified trichomes of Cannabis sativa, horsetails&#xA;  and many grasses&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also in each wiki page you place about each element. Some of them have content about biology/organism chemical component. Such as Boron and Fluoride. You can search their page with {organ} or {bio}&lt;/p&gt;&#xA;" OwnerUserId="9910" LastEditorUserId="9910" LastEditDate="2015-04-17T15:41:21.470" LastActivityDate="2015-04-17T15:41:21.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31443" PostTypeId="2" ParentId="31256" CreationDate="2015-04-17T10:57:37.377" Score="2" Body="&lt;p&gt;The &lt;a href=&quot;http://www.entsoc.org/&quot; rel=&quot;nofollow&quot;&gt;Entomological Society of America&lt;/a&gt; has dedicated page called &lt;a href=&quot;http://www.entsoc.org/teachers&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Entomology Resources for Teachers&lt;/strong&gt;&lt;/a&gt;, which might answer many of your questions. It compiles curated links to resources, universities, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are a couple of other entomological links/resources that I have saved from before:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bugguide.net&quot; rel=&quot;nofollow&quot;&gt;Bugguide.net&lt;/a&gt;&lt;br&gt;&#xA;Pictures, simple keys and taxonomical info. Also has a forum.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.entfdn.org/education_links.php&quot; rel=&quot;nofollow&quot;&gt;The Entomological Foundation: Education&lt;/a&gt;&lt;br&gt;&#xA;Links, project ideas etc.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.kerbtier.de/enindex.html&quot; rel=&quot;nofollow&quot;&gt;Kerbtier.de&lt;/a&gt;&lt;br&gt;&#xA;Webpage on beetles found in Germny, but relevant for many European countries. Also has general pages on e.g. beetle morphology and a glossary that might be useful.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2015-04-17T10:57:37.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31444" PostTypeId="2" ParentId="31394" CreationDate="2015-04-17T11:15:29.917" Score="5" Body="&lt;p&gt;Inspired by the answer by @MarchHo, I came to think of the contagious cancer that attacks Tasmanian Devils - &lt;a href=&quot;http://en.wikipedia.org/wiki/Devil_facial_tumour_disease&quot;&gt;Devil facial tumour disease&lt;/a&gt; - which should provide a very similar example to the clams in your question. I don't think it has been given a species name though, but for most purposes it functions as an independent species. This &quot;organism&quot; lives as a parasite on Tasmanian devils, but has originated from a cancer tumour in an individual Tasmanian devil. You could maybe argue that it is not single-celled, since it develops into tumours, but it most likely spreads as single cells and I suspect that the cells functions as independent entities. However, I don't know enought about the disease to really say if e.g. cells in the tumours differentiate into different types. The cancer is spread by bites, and only affects Tasmanian devils (see &lt;a href=&quot;http://www.tassiedevil.com.au/tasdevil.nsf/TheDisease/BD2717C762779EE8CA2576F1001D0110&quot;&gt;http://www.tassiedevil.com: The Disease&lt;/a&gt;). This disease is apparently one of only three known cases of contagious cancers (also in dogs and hamsters), but this is maybe 4 now if the clams are a similar case).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Iq61T.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;(picture from Wikipedia)&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-04-17T11:26:05.773" LastActivityDate="2015-04-17T11:26:05.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31445" PostTypeId="2" ParentId="31440" CreationDate="2015-04-17T11:50:00.130" Score="4" Body="&lt;p&gt;All the elements you mention (B, Fl, Si, V, Cr, Se and Ti) are listed as (probable) essential trace elements in humans by the &lt;a href=&quot;http://apps.who.int/iris/bitstream/10665/37931/1/9241561734_eng.pdf&quot; rel=&quot;nofollow&quot;&gt;World Health Organization&lt;/a&gt;. The WHO document &quot;&lt;a href=&quot;http://apps.who.int/iris/bitstream/10665/37931/1/9241561734_eng.pdf&quot; rel=&quot;nofollow&quot;&gt;Trace elements in human nutrition and health&lt;/a&gt;&quot; mentions a host of studies addressing the functions of these elements in species ranging from &lt;strong&gt;bacteria and plants to primates&lt;/strong&gt;. The following list provides some of the functions these trace elements have in humans:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Boron&lt;/strong&gt; - essential for cell membrane characteristics and transmembrane signaling (&lt;a href=&quot;http://www.fasebj.org/content/5/12/2661.short&quot; rel=&quot;nofollow&quot;&gt;Nielsen, 1991&lt;/a&gt;);&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Fluoride&lt;/strong&gt; - necessary for the prevention of caries and it is associated with bone health (&lt;a href=&quot;http://apps.who.int/iris/bitstream/10665/37931/1/9241561734_eng.pdf&quot; rel=&quot;nofollow&quot;&gt;WHO&lt;/a&gt;);&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Silicium&lt;/strong&gt; - probably essential for healthy connective tissue and bone (&lt;a href=&quot;http://apps.who.int/iris/bitstream/10665/37931/1/9241561734_eng.pdf&quot; rel=&quot;nofollow&quot;&gt;WHO&lt;/a&gt;);&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Vanadium&lt;/strong&gt; - possible role as an enzyme cofactor and in hormone, glucose, lipid, bone and tooth metabolism (&lt;a href=&quot;http://apps.who.int/iris/bitstream/10665/37931/1/9241561734_eng.pdf&quot; rel=&quot;nofollow&quot;&gt;WHO&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Chromium&lt;/strong&gt; - essential trace element that potentiates insulin action and thus&#xA;influences carbohydrate, lipid and protein metabolism (&lt;a href=&quot;http://apps.who.int/iris/bitstream/10665/37931/1/9241561734_eng.pdf&quot; rel=&quot;nofollow&quot;&gt;WHO&lt;/a&gt;);&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Selenium&lt;/strong&gt; - essential component of one of the antioxidant defense systems of the body (&lt;a href=&quot;http://apps.who.int/iris/bitstream/10665/37931/1/9241561734_eng.pdf&quot; rel=&quot;nofollow&quot;&gt;WHO&lt;/a&gt;);&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Tin&lt;/strong&gt; - expected to have a function in the tertiary structure of proteins (&lt;a href=&quot;http://apps.who.int/iris/bitstream/10665/37931/1/9241561734_eng.pdf&quot; rel=&quot;nofollow&quot;&gt;WHO&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.fasebj.org/content/5/12/2661.short&quot; rel=&quot;nofollow&quot;&gt;Nielsen, &lt;em&gt;FASEB&lt;/em&gt; 1991; &lt;strong&gt;5&lt;/strong&gt;: 2661-7&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://apps.who.int/iris/bitstream/10665/37931/1/9241561734_eng.pdf&quot; rel=&quot;nofollow&quot;&gt;WHO, Trace elements in human nutrition and health 1991&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-04-18T06:21:59.703" LastActivityDate="2015-04-18T06:21:59.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31446" PostTypeId="2" ParentId="31433" CreationDate="2015-04-17T11:51:00.980" Score="3" Body="&lt;p&gt;I think you can follow this method:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Test the statistical significance of a single experiment by comparing technical replicates (lets say Tests: T&lt;sub&gt;1&lt;/sub&gt;, T&lt;sub&gt;2&lt;/sub&gt;, T&lt;sub&gt;3&lt;/sub&gt; and Controls: C&lt;sub&gt;1&lt;/sub&gt;, C&lt;sub&gt;2&lt;/sub&gt;, C&lt;sub&gt;3&lt;/sub&gt;). This will tell you if the instrument can reliably detect difference or not. Note that you should compare the relative expression (i.e. wrt your reference gene) and not the CT values. The ΔΔCt method is fine but you should note that it is not necessarily a power of 2; 2 denotes perfect PCR efficiency. See these posts: &#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/16228/real-time-pcr-normalization-algorithm/16247#16247&quot;&gt;Real time PCR normalization algorithm&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/16035/real-time-pcr-standard-curve/16038#16038&quot;&gt;Real time PCR standard curve&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;If the difference is found significant in all technical replicates then test the difference between biological replicates by using the means of the technical replicates in each experiment; for example mean of T&lt;sub&gt;1&lt;/sub&gt;, T&lt;sub&gt;2&lt;/sub&gt; and T&lt;sub&gt;3&lt;/sub&gt; in biological replicate-&lt;strong&gt;&lt;em&gt;a&lt;/em&gt;&lt;/strong&gt; ($\bar{T_a}$) used as the sample value for that replicate. You can proceed with t-test for computing statistical significance which will tell you if the difference in expression is because of a random cellular behaviour or not. You can also do an ANOVA to compare the variance between technical replicates (within an experiment) and biological replicates (mean of the technical replicates between experiments). ANOVA lets you know some aspects of reproducibility of a measurement technique.&lt;/li&gt;&#xA;&lt;li&gt;Fold changes (FC) are a problematic issue because many biologists seem to mess up with the interpretation of the data. First of all a t-test cannot be applied to FC directly (especially if FC is calculated pairwise for each replicate). Now all you have is a single random variable i.e fold change that you cannot statistically compare with anything. Fold changes are not really bad but I would recommend that a t-test be done between the control and the test samples and if the difference is found statistically relevant then report the FC. I personally know many people who do the other way round and set variance of the control sample as zero (because pairwise FC would be = 1 in all cases): This is a blunder.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-04-18T04:51:51.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31450" PostTypeId="2" ParentId="31426" CreationDate="2015-04-17T14:11:42.953" Score="5" Body="&lt;p&gt;I've found an &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14022146?dopt=Abstract&quot;&gt;old paper&lt;/a&gt; using radioactively labeled bacteria to track their fate in macrophages. According to the data, both $^{14}$C and $^{32}$P are reutilized in the host cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14022146?dopt=Abstract&quot;&gt;COHN ZA. (1963)&lt;/a&gt;. The fate of bacteria within phagocytic cells. I. The degradation of isotopically labeled bacteria by polymorphonuclear leucocytes and macrophages. J Exp Med. Jan 1;117:27-42.&lt;/p&gt;&#xA;" OwnerUserId="15321" LastEditorUserId="15321" LastEditDate="2015-04-17T15:28:42.553" LastActivityDate="2015-04-17T15:28:42.553" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31452" PostTypeId="1" AcceptedAnswerId="31456" CreationDate="2015-04-17T19:24:21.717" Score="3" ViewCount="524" Body="&lt;p&gt;I'm new to the Bio/Medical field so kindly bear with me. I am doing studies on volunteers to formulate algorithms for evaluating Respiration rate from ECG and accelerometer data. I learned about this device when I read &lt;a href=&quot;http://cardiovascres.oxfordjournals.org/content/38/2/332&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper. I'd like to know how exactly the metronome device helps in controlling the breathing rate, how is it to be used and precautions to be taken?&lt;/p&gt;&#xA;" OwnerUserId="15376" LastActivityDate="2015-04-17T22:58:53.693" Title="How does a metronome help in controlling breathing rate?" Tags="&lt;respiration&gt;&lt;breathing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31453" PostTypeId="1" AcceptedAnswerId="31506" CreationDate="2015-04-17T19:36:09.553" Score="5" ViewCount="922" Body="&lt;p&gt;As we know that the preferred source of energy for our body (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK22436/&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;) are carbohydrates but heart muscle is an exception and need some explanation for this exception, that why the preferred source of energy for  or cardiac muscle are FATS?&lt;/p&gt;&#xA;" OwnerUserId="5729" LastEditorUserId="14735" LastEditDate="2015-04-19T19:18:52.103" LastActivityDate="2015-04-19T20:48:34.987" Title="Fats as energy source" Tags="&lt;biochemistry&gt;&lt;nutrition&gt;&lt;human-physiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31454" PostTypeId="1" CreationDate="2015-04-17T19:36:52.150" Score="3" ViewCount="26" Body="&lt;p&gt;We sequenced RNA using RNA-seq from biofilm (attached to bottom) and planktonic growing bacteria (supernatant) in 3 mL microtiter plates. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure how is possible to obtain planktonic cells since they may have precipitated. For bacteria growing on the bottom I'm convinced these were derived from initial attached cells and then formed biofilms growing anaerobically (this is a facultative bacteria). However, since this bacteria is not motile, how is possible I obtained planktonic bacterial cells RNA? Maybe was a suttle layer on the surface growing aerobically. Wouldn't them have precipitated after the 36h of the assay?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specie: Haemophilus parasuis. A facultative anaerobe.&lt;/p&gt;&#xA;" OwnerUserId="4717" LastActivityDate="2015-04-17T19:36:52.150" Title="Biofilm microtiter experimental design" Tags="&lt;biofilms&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31455" PostTypeId="2" ParentId="30135" CreationDate="2015-04-17T21:45:26.577" Score="2" Body="&lt;p&gt;Let's take the opposite extreme, $K=0$, so that each site has an independent effect on fitness. Without loss of generality, we can say that at each locus $n$, the $1$ allele confers an advantage $s_n$ over the $0$ allele. Then there is just one local optimum, the global optimum, at $\vec{1}$, so $M_1=1$ (and $P_m=2^{-N}$).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key difference is that in the $K=0$ case each fitness comparison of a focal genotype with a neighbor is independent of the rest: the fact that mutating the first gene decreases fitness, for instance, doesn't make it any more likely that mutating the second gene will decrease fitness. For any $K$, it is necessarily true that the focal genotype has a probability $1/(N+1)$ of being fitter than all of a set of $N$ other &lt;em&gt;randomly chosen&lt;/em&gt; genotypes, but we're interested in comparing it to its neighbors, which are not a random selection, and are only equivalent to a random selection when $K=N-1$.&lt;/p&gt;&#xA;" OwnerUserId="6313" LastActivityDate="2015-04-17T21:45:26.577" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31456" PostTypeId="2" ParentId="31452" CreationDate="2015-04-17T22:58:53.693" Score="1" Body="&lt;p&gt;The paper in question used metronome to aid test subjects control their breathing rate. This seems like a good approach, much better, than asking &quot;please, breath with 0.1Hz frequency&quot;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The subjects were asked to remain at rest in a supine position for 10 min, and then to &lt;strong&gt;control their respiratory rate with the help of a metronome&lt;/strong&gt; at different breathing rates: 6 (near 0.10 Hz), 10 (near 0.16 Hz) and 16 (near 0.27 Hz) breaths/min.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Metronome&quot; rel=&quot;nofollow&quot;&gt;Metronome&lt;/a&gt; is a device that produces any perceivable ticks (sound clicks or, maybe, light flashes can be used) with given and constant frequency. So patients were asked to synchronize their breathing with metronome clicks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Only precaution in mentioned experiment is that high frequency of breathing can cause voluntary &lt;a href=&quot;http://en.wikipedia.org/wiki/Hyperventilation&quot; rel=&quot;nofollow&quot;&gt;hyperventilation&lt;/a&gt;. Or if preset frequency is low and patient is trying to follow it, hypoventilation might occur. Fainting seems among the worst of consequences in both conditions (if person is relatively healthy).&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-17T22:58:53.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31457" PostTypeId="1" CreationDate="2015-04-17T23:48:49.690" Score="1" ViewCount="245" Body="&lt;p&gt;Is there any adaptive behaviour in non humans which, when it is functioning as it was selected to do, creates a spandrel behaviour?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In evolutionary biology, a spandrel is a phenotypic characteristic&#xA;  that is a byproduct of the evolution of some other characteristic,&#xA;  rather than a direct product of adaptive selection&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="15379" LastEditorUserId="15379" LastEditDate="2015-04-18T01:12:14.830" LastActivityDate="2016-01-07T00:01:29.040" Title="A non human adaptive behaviour with a spandrel" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31458" PostTypeId="1" CreationDate="2015-04-18T00:26:38.587" Score="22" ViewCount="7074" Body="&lt;p&gt;Some plants and vines spiral clockwise as they go along (right direction) and some spiral anticlockwise (left direction). What determines which direction they spiral along? At first, I believed it to be determined by which hemisphere you are in (influenced by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Coriolis_effect&quot; rel=&quot;noreferrer&quot;&gt;Coriolis Effect&lt;/a&gt;), and this result could be tested by finding spirals in both northern and southern hemispheres and comparing their directions. However, the very first spiral I found seemed to cripple that idea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.imgur.com/Sb81oIO.jpg?1&quot; alt=&quot;here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The spiral I found spirals first in the right direction, then suddenly decides to spiral in the left direction, and then further along in the right direction again. Since the Earth does not arbitrarily change its rotational direction, this phenomenon must be explained by some other explanation. The change in rotational direction seems to be abrupt, almost like a catastrophic event. A few that I thought of:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1: Arbitrary. The spiral seeks merely to latch onto something, and will try both directions to see if either work out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2: The spiral is somehow influenced by the night day cycles. Since the spiral switches from right to left back to right having been subjected to two sudden changes, the only large changes I can think of is the day night cycle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;-I live in Australia by the way&lt;/p&gt;&#xA;" OwnerUserId="10302" LastEditorUserId="16866" LastEditDate="2017-04-13T04:28:29.043" LastActivityDate="2020-08-04T09:40:54.110" Title="What determines the spiral direction of plants?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;&lt;chirality&gt;" AnswerCount="6" CommentCount="9" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31459" PostTypeId="1" AcceptedAnswerId="31493" CreationDate="2015-04-18T00:47:13.470" Score="4" ViewCount="167" Body="&lt;p&gt;How can non-structural information, specifically instinct (a fixed pattern of behavior that an organism reverts to as a response to certain stimuli), be passed on from generation to generation (such as an unborn baby's instinct to begin inhaling and exhaling amniotic fluid while still in the mother's womb to &quot;practice&quot; breathing, a sea turtle's inclination to enter the sea after hatching, etc.)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does DNA have anything to do with it? I can't imagine what else it could be, considering that the genome is the only thing an organism passes on to it's progeny.&lt;/p&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="1306" LastEditDate="2015-11-24T13:24:54.937" LastActivityDate="2015-11-24T13:24:54.937" Title="How is instinct carried from one generation to another?" Tags="&lt;behaviour&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31460" PostTypeId="1" CreationDate="2015-04-18T01:46:45.417" Score="2" ViewCount="31" Body="&lt;p&gt;I found this review on the Maternal-to-Zygotic transition (MZT), describing how developmental control switches from maternally deposited RNAs to zygotic expression. I was struck by figure 1, and the apparent difference between viviparous and oviparous life histories. &#xA;My maybe naive question is, Could the sharp increase of zygotic expression reflect conflict between the maternal and zygotic genomes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wbYFA.gif&quot; alt=&quot;waves of zygotic gene expression&quot;&gt;&#xA;&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev-cellbio-100913-013027&quot; rel=&quot;nofollow noreferrer&quot;&gt;MZT review&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6134" LastActivityDate="2015-04-18T01:46:45.417" Title="variance in zygotic gene expression across species" Tags="&lt;development&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31461" PostTypeId="1" AcceptedAnswerId="31465" CreationDate="2015-04-18T02:05:20.047" Score="5" ViewCount="599" Body="&lt;p&gt;Found this in my garden today in Sydney, Australia (specifically Lane Cove). Can you tell me what it is?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Bh01j.jpg&quot; alt=&quot;spider from above&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Mbiwv.jpg&quot; alt=&quot;spider from below&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="15380" LastActivityDate="2015-04-18T08:35:46.267" Title="Help me identify this spider from my garden" Tags="&lt;arachnology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31462" PostTypeId="1" CreationDate="2015-04-18T02:19:46.507" Score="7" ViewCount="19579" Body="&lt;p&gt;Specifically, what is the difference between facilitated diffusion carrier processes (passive transport) and secondary active transport co-transport processes (active transport)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They seem to be the same thing - doesn't the passive process with the carrier transports substance $x$ against its gradient together with substance $y$ that is moving down its electrochemical gradient? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, in the active process, substance $x$ is transported against the gradient, and substance $y$ down its electrochemical gradient? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't see how energy differentiates the active transport in this case from the passive transport.&lt;/p&gt;&#xA;" OwnerUserId="15382" LastEditorUserId="9943" LastEditDate="2015-04-19T01:44:02.160" LastActivityDate="2017-08-11T18:52:18.010" Title="Difference between facilitated diffusion and secondary active transport in cells" Tags="&lt;physiology&gt;&lt;cell-membrane&gt;&lt;glucose&gt;&lt;membrane-transport&gt;" AnswerCount="4" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31463" PostTypeId="1" CreationDate="2015-04-18T03:04:23.217" Score="5" ViewCount="70" Body="&lt;p&gt;Are orthologs and paralogs examples of conserved genes? Orthologs are the genes or DNA that is present in 2 different species, having once been present in a common ancestor. It comes about by a speciation event. Paralogs come about by gene duplication events. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, would we characterize these genes as conserved genes? &lt;/p&gt;&#xA;" OwnerUserId="15383" LastEditorUserId="1306" LastEditDate="2015-04-19T12:36:40.420" LastActivityDate="2015-04-19T12:36:40.420" Title="Comparative Genomics" Tags="&lt;evolution&gt;&lt;genomics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31464" PostTypeId="2" ParentId="31461" CreationDate="2015-04-18T03:17:43.123" Score="1" Body="&lt;p&gt;It looks like Neoscona Crucifera to me, but I could be wrong.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a picture of her: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/231qp.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another one, only this is more of the web: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/w5rh1.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="15386" LastEditDate="2015-04-18T08:35:46.267" LastActivityDate="2015-04-18T08:35:46.267" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31465" PostTypeId="2" ParentId="31461" CreationDate="2015-04-18T03:27:06.240" Score="7" Body="&lt;p&gt;I believe it is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Orb-weaver_spider&quot; rel=&quot;nofollow noreferrer&quot;&gt;Garden Orb Weaver&lt;/a&gt; spider. The Australian garden orb weaver, &lt;a href=&quot;http://en.wikipedia.org/wiki/Australian_garden_orb_weaver_spider&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eriophora transmarina&lt;/a&gt;, has a strikingly similar body &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/72KyU.jpg&quot; alt=&quot;http://en.wikipedia.org/wiki/Australian_garden_orb_weaver_spider#/media/File:Eriophora_transmarina.jpg&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jdeVn.jpg&quot; alt=&quot;http://en.wikipedia.org/wiki/Australian_garden_orb_weaver_spider#/media/File:Orb_weaver_black_bckgrnd03_crop.jpg&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="12909" LastActivityDate="2015-04-18T03:27:06.240" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31466" PostTypeId="2" ParentId="31462" CreationDate="2015-04-18T05:07:25.933" Score="1" Body="&lt;p&gt;&quot;Specifically, what is the difference between facilitated diffusion carrier processes (passive) and secondary active transport co-transport processes (active)?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Facilitated diffusion creates alternative paths for polar/charged substances to move down their electrochemical gradients across the hydrophobic interior of the membrane, thus greatly speeding up their movement into the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondary active transport is a form of active transport where the transport of a substance AGAINST its electrochemical gradient (endergonic) is coupled to the movement of another substance DOWN its electrochemical gradient (exergonic), thus providing energy to transport the first substance against its electrochemical gradient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key difference is really that passive transport does not require energy whereas active transport does.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to wikipedia the GLUT1 you mention is a uniporter that facilitates the diffusion of glucose into the cell, so it is a passive transporter. It does not require energy as it simply helps glucose move down its concentration gradient.&lt;/p&gt;&#xA;" OwnerUserId="15385" LastEditorUserId="15385" LastEditDate="2015-04-18T13:15:12.413" LastActivityDate="2015-04-18T13:15:12.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31467" PostTypeId="2" ParentId="31457" CreationDate="2015-04-18T07:34:29.347" Score="1" Body="&lt;p&gt;One of the first example of spandrel that has been suggested by Gould was the &lt;a href=&quot;http://en.wikipedia.org/wiki/Spotted_hyena#Female_genitalia&quot; rel=&quot;nofollow&quot;&gt;genitalia of hyenas&lt;/a&gt;. At the time the term was created, behavioural consequences of having a big brain was a common example and of course, this does not concern only humans but many other animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The riddles on the knuckles is another example (that is not specific to humans only either). Those riddles are a by-product of the need the make movement with your fingers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am personally not a big fan of the term &lt;code&gt;spandrel&lt;/code&gt; as used in evolutionary biology. This term easily leads to limit cases and it depends on how you define the phenotypic traits and the functions they serve. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2016-01-07T00:01:29.040" LastActivityDate="2016-01-07T00:01:29.040" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31468" PostTypeId="1" AcceptedAnswerId="31474" CreationDate="2015-04-18T08:00:01.603" Score="2" ViewCount="804" Body="&lt;p&gt;Here's another question taken from &quot;Concepts of Genetics,&quot; Klug et al (10ed), revolving around a paternity test. PCR and a Southern blot were carried out in order to determine whether 3 chimpanzees (lanes 3, 4, 5 in the blot below) were the &quot;legitimate&quot; offspring of 2 potential parents (lanes 1 and 2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question makes a point of saying that the primers used to bind to the chimp DNA originates from humans, and that they &quot;flank highly polymorphic sites in human DNA that result from variable numbers of tandem nucleotide repeats.&quot; My first question is &lt;strong&gt;what exactly does &quot;flanking&quot; mean in this context?&lt;/strong&gt; It sounds to me like the human DNA &quot;mirrors&quot; the chimp DNA, and so makes it good enough to use as a primer, but I'm not sure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've come across a few other examples not in the text about how to infer whether a potential parent is indeed a parent based on whether the offspring's lane contains bands found in both the maternal and paternal lanes, which leads me to believe I can rule out the chimp in lane 5.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm given five answers to choose from to decide which of the offspring, if any, are legitimate:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;None&lt;/li&gt;&#xA;&lt;li&gt;A only&lt;/li&gt;&#xA;&lt;li&gt;A and B only&lt;/li&gt;&#xA;&lt;li&gt;Not enough data; more polymorphic sites should be examined&lt;/li&gt;&#xA;&lt;li&gt;No conclusion can be made because &quot;human&quot; primers  were used&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Main questions: &lt;strong&gt;Does that fact that we're using human DNA as primers cause any problems? Do we know enough from this blot to determine paternity?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OCTFo.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="13127" LastActivityDate="2015-04-18T12:06:23.400" Title="How do I make conclusions from the autoradiograph of a Southern blot?" Tags="&lt;genetics&gt;&lt;homework&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31469" PostTypeId="1" CreationDate="2015-04-18T08:36:11.637" Score="2" ViewCount="199" Body="&lt;p&gt;As far as I know, breathing air containing relatively high levels of CO&lt;sub&gt;2&lt;/sub&gt; may get you a headache. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also know that CO&lt;sub&gt;2&lt;/sub&gt; level in the fruit bodies of peppers can reach levels as high as 3% at certain stages in development (&lt;a href=&quot;http://journal.ashspublications.org/content/131/1/164.short&quot; rel=&quot;nofollow&quot;&gt;Blasiak, 2006&lt;/a&gt;). So clearly it is possible in a natural setting to achieve these high level of CO&lt;sub&gt;2&lt;/sub&gt;, at least in a micro-environment like around the locules of pepper seeds developing in its fruit. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I was wondering, if we would have to breath air containing 3% CO&lt;sub&gt;2&lt;/sub&gt;, would get a headache if we breath it in?&lt;/p&gt;&#xA;" OwnerUserId="15387" LastEditorUserId="9943" LastEditDate="2015-04-18T23:55:52.830" LastActivityDate="2015-04-18T23:55:52.830" Title="Does breathing air containing 3% carbon dioxide gives you a headache?" Tags="&lt;physiology&gt;&lt;neuroscience&gt;&lt;botany&gt;&lt;breathing&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31470" PostTypeId="2" ParentId="31469" CreationDate="2015-04-18T09:01:24.047" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Carbon_dioxide#Toxicity&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Carbon_dioxide#Toxicity&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;In concentrations up to 1% (10,000 ppm), it will make some people feel drowsy.[83] Concentrations of 7% to 10% may cause suffocation, even in the presence of sufficient oxygen, manifesting as dizziness, headache, visual and hearing dysfunction, and unconsciousness within a few minutes to an hour.&#xA;...&#xA;Occupational CO2 exposure limits have been set in the United States at 0.5% (5000 ppm) for an 8-hour period.[90] At this level of CO2, International Space Station crew experienced headaches, lethargy, mental slowness, emotional irritation, and sleep disruption.&quot;&#xA;So according to this, yes you could breathe it, and yes, you would get a headache.&quot;&lt;/p&gt;&#xA;" OwnerUserId="15385" LastActivityDate="2015-04-18T09:01:24.047" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31471" PostTypeId="2" ParentId="31427" CreationDate="2015-04-18T09:25:02.693" Score="3" Body="&lt;p&gt;usually the growth of bacteria is slowed down as they are in freezing temperature and they almost carry out no metabolic reaction at this stage.but another problem occurs that is ice crystals formation which disrupts or pierce the bacterial cell wall causing the death of bacterial cells,this problem can be solved by adding  glycerol or any other cryoprotectant into it which will make the concentration equal,inside and out side the bacteria,thus bacteria will not be harmed.&#xA;in case of lactobacillus,they are psychrophile and also facultatively anaerobic so yes,they can survive in freezing condition&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10843056&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/10843056&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15216" LastActivityDate="2015-04-18T09:25:02.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31472" PostTypeId="2" ParentId="28080" CreationDate="2015-04-18T10:09:28.573" Score="0" Body="&lt;p&gt;there is a word symbiosis which means interaction between two different organisms living in close physical association, typically to the advantage of both.Often, especially with microbes, one organism lives inside another — the host.&#xA;&lt;a href=&quot;http://microbes.org/microscopic-worlds/symbiotic-microbes&quot; rel=&quot;nofollow&quot;&gt;symbiotic microbes&lt;/a&gt;When both organisms benefit from the relationship, it is called mutualism. When only one organism benefits, but the other one is not harmed, it is called commensalism. &#xA;and yes,bacteria can have symbiotic relationship with human.&lt;a href=&quot;http://www.scientificamerican.com/article/human-microbiome-change/&quot; rel=&quot;nofollow&quot;&gt;bugs inside&#xA;&lt;/a&gt;One example is the bacteria that live inside the human digestive system. These microbes break down food and produce vitamins that humans need. In return, the bacteria benefit from the stable environment inside the intestines. Bacteria also colonize human skin. The bacteria obtain nutrients from the surface of the skin, while providing people with protection against more dangerous microbes.&#xA;moreover Your body is made up of around ten trillion cells, but you harbour a hundred trillion bacteria. For every gene in your genome, there are 100 bacterial ones. This is your ‘microbiome’ and it has a huge impact on your health, your ability to digest food and more. &lt;a href=&quot;http://discovermagazine.com/galleries/zen-photo/m/microbiome&quot; rel=&quot;nofollow&quot;&gt;microbiome&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15216" LastActivityDate="2015-04-18T10:09:28.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31473" PostTypeId="2" ParentId="31458" CreationDate="2015-04-18T11:42:25.827" Score="12" Body="&lt;p&gt;First of all, you assumption &lt;a href=&quot;http://www.namethatplant.net/article_asthevinetwines.shtml&quot;&gt;seems to be incorrect&lt;/a&gt;. Plants in same part of the world can twine in opposite directions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Little seems to be known exactly. Gravity &lt;a href=&quot;http://www.madsci.org/posts/archives/1998-08/903280279.Bt.r.html&quot;&gt;has nothing to do&lt;/a&gt; with plant's chirality (or &quot;handedness&quot;) or spiraling:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How plants do this is still unknown. Darwin proposed that it was &quot;autonomously induced.&quot; This came to be known as the internal oscillator theory. In the 1960's the gravitropic overshoot theory explained mathematically how circumnutation could spontaneously occur as a result of forces related to gravity and growth. Recent experiments on the Space Shuttle have demonstrated that gravity is not necessary for circumnutation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here is another &lt;a href=&quot;http://www.granny-miller.com/do-you-know-which-way-vines-grow/&quot;&gt;link to a blog&lt;/a&gt;, but it does contain reference to original paper on observation of chirality. Main conclusion, taken from &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1466-8238.2007.00326.x/abstract&quot;&gt;the abstract&lt;/a&gt;, is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The predominance of right-handed helical growth in climbing plants cannot be explained by hypotheses attempting to link plant growth behaviour and global location. One alternative hypothesis for our findings is that the widespread phenomenon of anticlockwise twining arises as a function of microtubule orientation operating at a subcellular level.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To elaborate a little on that, remember that actin filaments as well as microtubules are all chiral polymers. That is, they form spiral structures with defined orientation. Even more, microtubules all start roughly from the nucleus away to membrane, so this might suggest cellular mechanism for preference toward twining chirality. However, this does not address your observation that given plant changes direction of growth twice.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-18T11:42:25.827" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31474" PostTypeId="2" ParentId="31468" CreationDate="2015-04-18T12:06:23.400" Score="2" Body="&lt;p&gt;As @canadianer pointed out in the comments section flanking sequence is a sequence that is immediately near the target on either side. Since chimps and humans are closely related and the sequence different is minimal (according to &lt;a href=&quot;http://genome.cshlp.org/content/15/12/1746.full&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper its approx 4% for the entire genome)  so using human primers is totally fine.  Now if take a look at the picture of the gel:&#xA; The answer is 2. only A because only this offspring has a variant in large amount (that can be determined from the width of the band) that can be acquired from both parents and in this case chimp A actually did inherit the 136bp variant from both parents. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For chimp 4 either parent can be the same (as for chimp A) from the two because it has the 136bp variant as well ( that can be inherited either chimp one or two), but has a different one that cannot come from chimps 1 and 2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you said chimp 5 can be ruled out instantly because it has a large band that cannot be found in either of the two parents.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-04-18T12:06:23.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31475" PostTypeId="2" ParentId="31462" CreationDate="2015-04-18T12:29:38.690" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;&lt;em&gt;Facilitated diffusion&lt;/em&gt; is a &lt;strong&gt;passive&lt;/strong&gt; process in which membrane channels mediate the transport of polar, or big molecules that are not solvable in the cell membrane. &lt;em&gt;Co-transport&lt;/em&gt;, on the other hand, is &lt;strong&gt;active transport&lt;/strong&gt;, as it depends on the electrochemical gradient of ions across the cell's membrane, particularly Na&lt;sup&gt;+&lt;/sup&gt;. Because ATP or other energetic compounds are not directly involved in co-transport, it is referred to as secondary active transport. The electrochemical ion gradient is mainly established by the Na&lt;sup&gt;+&lt;/sup&gt;,K&lt;sup&gt;+&lt;/sup&gt;-ATPase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;As commented upon by others, your question is not entirely clear and the best way to approach this question is by defining the various terminologies and physiological mechanisms used in your question:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;Active transport&lt;/strong&gt; needs an energy source such as ATP. For example, the Na&lt;sup&gt;+&lt;/sup&gt;,K&lt;sup&gt;+&lt;/sup&gt;-ATPase is an enzyme that pumps Na&lt;sup&gt;+&lt;/sup&gt; and K&lt;sup&gt;+&lt;/sup&gt; ions against their concentration gradients into the cytosol (K&lt;sup&gt;+&lt;/sup&gt;) or out of the cell (Na&lt;sup&gt;+&lt;/sup&gt;). Note that both Na&lt;sup&gt;+&lt;/sup&gt; and K&lt;sup&gt;+&lt;/sup&gt; are transported against their chemical gradients (and Na&lt;sup&gt;+&lt;/sup&gt; also against its electrical gradient as the cell is negative). Therefore your statement that &lt;code&gt;[...] in the active process, substance x is transported against the gradient, and substance y down its electrochemical gradient&lt;/code&gt; is untrue, and likely the cause of your confusion. &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Passive transport&lt;/strong&gt; is mediated by &lt;strong&gt;diffusion&lt;/strong&gt;, which typically occurs through a concentration gradient. Only small, relatively hydrophobic molecules are able to diffuse across a phospholipid bilayer at significant rates. Examples are gases (such as O&lt;sub&gt;2&lt;/sub&gt; and CO&lt;sub&gt;2&lt;/sub&gt;) in the lungs, and small polar but uncharged molecules (such as H&lt;sub&gt;2&lt;/sub&gt;O and ethanol) (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.2040-1124.2012.00227.x/full&quot; rel=&quot;nofollow&quot;&gt;Cooper, 2000)&lt;/a&gt;.  &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Facilitated diffusion&lt;/strong&gt; is an example of &lt;strong&gt;passive diffusion&lt;/strong&gt;, but aided by membrane-spanning channel proteins that span the lipid bilayer. Therefore the particles (molecules or ions) do not have to dissolve in the cell membrane's hydrophobic lipid bilayer, allowing hydrophylic and larger molecules (carbohydrates, ions) to be transported into the cell. No external source of energy is needed and  travel across the membrane in the direction determined by their concentration gradients and, in the case of charged molecules, by the electric potential across the membrane (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.2040-1124.2012.00227.x/full&quot; rel=&quot;nofollow&quot;&gt;Cooper, 2000)&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Co-transport&lt;/strong&gt; is &lt;strong&gt;active transport&lt;/strong&gt;, where the &lt;strong&gt;energetically unfavorable transport&lt;/strong&gt; of a particle &lt;em&gt;against&lt;/em&gt; its electrochemical gradient is facilitated by the co-transport of a &lt;strong&gt;favorable one&lt;/strong&gt; &lt;em&gt;down&lt;/em&gt; its gradient. In other words, multiple particles are transported so as to neutralize the sum of the transport. For example, sodium-dependent glucose tranporters transport glucose into the cell against the concentration gradient (unfavorable) and Na&lt;sup&gt;+&lt;/sup&gt; is transported along with it into the cell which is a favorable transport (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.2040-1124.2012.00227.x/full&quot; rel=&quot;nofollow&quot;&gt;Haraki &amp;amp; Inagaki, 2012&lt;/a&gt;). This is an example of a &lt;em&gt;symporter&lt;/em&gt;. An example of an &lt;em&gt;antiporter&lt;/em&gt; is the Na&lt;sup&gt;+&lt;/sup&gt;/Ca&lt;sup&gt;2+&lt;/sup&gt; antiporter found in the heart to transport Ca&lt;sup&gt;2+&lt;/sup&gt; out of the cell against a steep concentration gradient and electrical gradient, while 3 Na&lt;sup&gt;+&lt;/sup&gt; is imported into the cell to balance the unfavorable Ca&lt;sup&gt;2+&lt;/sup&gt; transport. Note that all these mentioned co-transporters and many others are dependent on the Na,K-ATPase that ultimately generates the Na&lt;sup&gt;+&lt;/sup&gt; and K&lt;sup&gt;+&lt;/sup&gt; gradients by pumping Na&lt;sup&gt;+&lt;/sup&gt; out of the cell and K&lt;sup&gt;+&lt;/sup&gt; into the cell using ATP (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21687/&quot; rel=&quot;nofollow&quot;&gt;Freeman, 2000&lt;/a&gt;). This generated membrane potential works like a battery being charged, and co-transporters discharge it by using the energy stored by importing Na&lt;sup&gt;+&lt;/sup&gt;. Hence, it is referred to as &lt;strong&gt;secondary active transport&lt;/strong&gt;, as no direct energy input from ATP is needed, but instead it utilizes the electrochemical gradient created by the Na&lt;sup&gt;+&lt;/sup&gt;,K&lt;sup&gt;+&lt;/sup&gt;-ATPase.  &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;These considerations should clarify your issues and answer your question on what co-transport exactly is. Specifically, the glucose transporter mentioned, &lt;strong&gt;GLUT1&lt;/strong&gt; as you refer to, is a symporter that mediates secondary active transport. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK9847/&quot; rel=&quot;nofollow&quot;&gt;Cooper, &lt;em&gt;The Cell&lt;/em&gt;, 2000&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.2040-1124.2012.00227.x/full&quot; rel=&quot;nofollow&quot;&gt;Haraki &amp;amp; Inagaki, &lt;em&gt;J Diabetes Invest&lt;/em&gt; 2012; &lt;strong&gt;3&lt;/strong&gt;: 352-3&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21687/&quot; rel=&quot;nofollow&quot;&gt;Molecular Cell Biology, 2000&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-09-05T19:16:44.687" LastActivityDate="2016-09-05T19:16:44.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31476" PostTypeId="1" CreationDate="2015-04-18T12:58:35.947" Score="1" ViewCount="821" Body="&lt;p&gt;I got into an argument surrounding beer type and hangover. Apparently there is a &lt;a href=&quot;https://alcohol.stackexchange.com/questions/983/does-drinking-mainstream-mass-produced-lagers-give-you-a-worse-hangover-than-re&quot;&gt;opinion that ales give you less hangover than lagers&lt;/a&gt; do (considering same alcohol content consumed). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding is that a hangover is &lt;a href=&quot;https://biology.stackexchange.com/questions/5087/what-is-the-molecular-basis-of-hangovers&quot;&gt;nothing more than dehydration caused by alcohol&lt;/a&gt;. More alcohol per unit of mass - more dehydration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there any biological evidence to show that the same amount of alcohol consumed (with a different type of yeast) per same body mass would have different effects?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="8129" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-04-19T14:42:57.017" Title="Does ale give less of a hangover than a lager?" Tags="&lt;human-anatomy&gt;&lt;metabolism&gt;&lt;alcohol&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31477" PostTypeId="1" AcceptedAnswerId="31478" CreationDate="2015-04-18T13:25:24.297" Score="3" ViewCount="91" Body="&lt;p&gt;In paper chromatography, as the mobile phase (I used 1:9 acetone/petroleum ether) climbs higher and higher, will the solubility of the solutes decrease as the solvent moves higher? I speak mostly about the beginning, when the solvent just begins to climb up the paper. Will the solutes travel right at the solvent front at the beginning, and then start to lag behind (and separate) as the solvent front moves higher?&lt;/p&gt;&#xA;" OwnerUserId="15272" LastEditorUserId="9829" LastEditDate="2015-04-20T15:52:50.757" LastActivityDate="2015-04-20T15:52:50.757" Title="Decreasing Solubility as Solvent Moves Higher in Paper Chromatography" Tags="&lt;lab-techniques&gt;&lt;photosynthesis&gt;&lt;chromatography&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31478" PostTypeId="2" ParentId="31477" CreationDate="2015-04-18T15:32:21.067" Score="5" Body="&lt;p&gt;The solubility of the solutes is the same at all points in the chromatography process. The solutes are clustered together at the beginning (at the solvent front) because none of them has moved very far yet. The reason for the separation of the solutes isn't that they become less soluble, it's that the solutes are moving at different speeds, like cars in an auto race:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;  _______&#xA; /____/SF\___&#xA; |_,._____,._)&#xA;---`'-----`'--     &#xA;  _______&#xA; /____/S1\___&#xA; |_,._____,._)&#xA;---`'-----`'--&#xA;  _______&#xA; /____/S2\___&#xA; |_,._____,._)&#xA;---`'-----`'--&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;At the beginning, both cars (solutes) S1 and S2 are even with the solute front car (SF) because the race (chromatography) has just begun. However, over time, the SF car outpaces S1 and S2 because it is moving faster.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;                     _______&#xA;                    /____/SF\___&#xA;                    |_,._____,._)&#xA;                   ---`'-----`'--     &#xA;         _______&#xA;        /____/S1\___&#xA;        |_,._____,._)&#xA;       ---`'-----`'--&#xA;              _______&#xA;             /____/S2\___&#xA;             |_,._____,._)&#xA;             ---`'-----`'--&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;And at the end, you get great separation:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;                                                                _______&#xA;                                                               /____/SF\___&#xA;                                                               |_,._____,._)&#xA;                                                              ---`'-----`'--     &#xA;                        _______&#xA;                       /____/S1\___&#xA;                       |_,._____,._)&#xA;                      ---`'-----`'--&#xA;                                           _______&#xA;                                          /____/S2\___&#xA;                                          |_,._____,._)&#xA;                                         ---`'-----`'--&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;(Thanks to &lt;a href=&quot;http://www.retrojunkie.com/asciiart/vehicles/cars.htm&quot;&gt;retrojunkies.com&lt;/a&gt; for the ASCII car)&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-04-18T15:32:21.067" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31479" PostTypeId="1" CreationDate="2015-04-18T15:46:53.570" Score="0" ViewCount="109" Body="&lt;p&gt;I don't think &quot;non-human&quot; animal like cat, dog, bird or fish think about future while sleeping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think when sleeping, the &quot;non-human&quot; animal will &lt;strong&gt;feel&lt;/strong&gt; rather &lt;strong&gt;think&lt;/strong&gt; about anything. I think when sleeping, the &quot;non-human&quot; animal will &lt;strong&gt;feel&lt;/strong&gt;  their breath just like when we are meditating. So, when we meditate we will feel our breath like &quot;non-human&quot; animal that are sleeping.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do &quot;non-human&quot; animal like cat, dog, bird or fish think about future while sleeping?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="15115" LastActivityDate="2015-04-18T16:38:46.713" Title="Do &quot;non-human&quot; animal like cat, dog, bird or fish think about future while sleeping?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2015-04-18T18:55:58.853" ContentLicense="CC BY-SA 3.0" />
  <row Id="31480" PostTypeId="2" ParentId="31479" CreationDate="2015-04-18T16:33:43.427" Score="1" Body="&lt;p&gt;&lt;strong&gt;Issue with your question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question is full of terms that don't have a proper definition in Biology. I don't think there is any clear definition in the verbs &quot;feel&quot; and &quot;think&quot;. Also, I don't fully understand what the differences between feeling or thinking (whatever that means) when sleeping matter for the question of whether some animals &quot;think&quot; (and its variants) about future while sleeping. I am not sure either what &quot;thinking about future&quot; really means. One doesn't know the future, he can imagine it and in some cases it is kinda complicated to really know whether a set of thoughts are encompassed within the concept of &quot;thinking about the future&quot;. I vote to close for primarily-opinion based. Finally, your question might eventually be a better fit on &lt;a href=&quot;http://cogsci.stackexchange.com&quot;&gt;CognitiveScience.SE&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Theory of Mind&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might be interested in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Theory_of_mind&quot; rel=&quot;nofollow&quot;&gt;Theory of Mind&lt;/a&gt; (ToM). Having the ToM (I know it is weird formulation, ToM is not a theory per se) means having the ability to 1) be aware (might have various definitions for &quot;aware&quot;) of its own existence and 2) be aware that others also think and have intentions and 3) more importantly be aware that others might be aware that you think and have intentions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is pretty hard to investigate whether an animal has the ToM. Here is a list of species (and lineages) where ToM has been found (or thought to exist at some level). The list is probably not exhaustive and the difficulty to accurately define ToM and awareness make those pretty arbitrary.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Chimpanzee&lt;/li&gt;&#xA;&lt;li&gt;Orang-outan&lt;/li&gt;&#xA;&lt;li&gt;elephants&lt;/li&gt;&#xA;&lt;li&gt;dolphins&lt;/li&gt;&#xA;&lt;li&gt;corvids&lt;/li&gt;&#xA;&lt;li&gt;some parrots&lt;/li&gt;&#xA;&lt;li&gt;bee-eater&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Btw, your list of lineages is funny by the fact that you seem to weight equally two relatively closely related domestic species (cat and dogs) and two gigantic taxa that are fishes (fishes do not represent a monophyletic group) and birds&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-04-18T16:38:46.713" LastActivityDate="2015-04-18T16:38:46.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31481" PostTypeId="1" AcceptedAnswerId="31485" CreationDate="2015-04-18T16:35:07.637" Score="2" ViewCount="137" Body="&lt;p&gt;Is there a drastic difference between top and bottom of the tube, with no stirring?&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="10456" LastEditDate="2015-04-18T18:24:08.513" LastActivityDate="2015-04-18T18:24:08.513" Title="Is [O2] different in a 5 mL liquid media?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31482" PostTypeId="1" AcceptedAnswerId="31490" CreationDate="2015-04-18T16:35:12.043" Score="7" ViewCount="6537" Body="&lt;p&gt;When sorting cell populations it is possible to use either magnetic-activated cell sorting or fluorescence-activated cell-sorting (FACS). I am wondering when you would choose either technique and what the pro's and con's of each technique are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As FACS sorts cells one by one, I can imagine magnetic-activated cell sorting is a faster process. So I guess if time is an important factor this could be used to base your decision on. Also by sorting cells one at a time I assume FACS is a lot more precise, and will lead to less 'contamination'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, are there &lt;strong&gt;other factors&lt;/strong&gt; at play here that can influence the choice of magnetic-activated cell sorting over FACS, and what are the &lt;strong&gt;pro's and con's&lt;/strong&gt; of these techniques respectively?&lt;/p&gt;&#xA;" OwnerUserId="15136" LastEditorUserId="948" LastEditDate="2015-04-18T23:39:50.477" LastActivityDate="2015-04-21T15:19:25.200" Title="Magnetic-activated cell sorting vs. FACS" Tags="&lt;immunology&gt;&lt;lab-techniques&gt;&lt;flow-cytometry&gt;&lt;cell-sorting&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31484" PostTypeId="2" ParentId="31463" CreationDate="2015-04-18T16:47:21.077" Score="3" Body="&lt;p&gt;Could not fit in a comment...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To my understanding, paralogs and orthologs refers, as you said, to the relative isolation of gene copy to the isolation of populations (and eventually species). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gene conservation on the other hand refers to the variability of a given gene along many species. If a gene does not show any variance along many species, than we say that it is a conserved gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eventually, gene duplication may allow for neo-functionalisation, sub-functionalisation or loss yielding to variance among this gene copy. Aside the philosophical problem of what is the identity of the gene, there is no relationships between the concepts of orthologs versus paralogs and gene duplication. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2015-04-18T16:47:21.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31485" PostTypeId="2" ParentId="31481" CreationDate="2015-04-18T16:56:11.477" Score="4" Body="&lt;p&gt;I believe there is. As you can see in the image below, strictly anaerobic bacteria can survive in liquid medium in test tubes, herefore they will migrate to the bodem of the medium to avoid Oxygen. Also you can see that microaerophiles, which require an oxygen percentage of approximately 2-10% (versus approximately 20% in normal air), will be able to survive below the surface of the medium. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yes, there is a drastic change, seeing as obligate aerobic bacteria can surive at the surface of the medium, and obligate anaerobic bacteria can survive at the bodem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/t1dDp.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To this I have one caveat to add. Namely that these tests are normally done in standard test tubes (approximately 9, 22 or 28mL depending on size), which would most likely contain more medium. So I am not absolutely sure, nor have I found any specific information on oxygen gradients in 5mL tubes. You could test this by performing the experiment in described in the figure in your tubes with 5mL medium and see what happens. Then you will definitely know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps!&lt;/p&gt;&#xA;" OwnerUserId="15136" LastActivityDate="2015-04-18T16:56:11.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31487" PostTypeId="1" AcceptedAnswerId="31489" CreationDate="2015-04-18T19:47:30.673" Score="0" ViewCount="97" Body="&lt;p&gt;What is the energy penalty of maintaining rarely used synapse?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm wondering if forgetting is cheaper than remembering unnecessary details.&lt;/p&gt;&#xA;" OwnerUserId="6156" LastEditorUserId="3340" LastEditDate="2015-06-04T11:36:15.243" LastActivityDate="2015-06-04T11:36:15.243" Title="Energy consumption of a resting synapse" Tags="&lt;brain&gt;&lt;memory&gt;&lt;synapses&gt;&lt;bioenergetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31488" PostTypeId="2" ParentId="892" CreationDate="2015-04-18T20:34:58.070" Score="0" Body="&lt;p&gt;As you know &lt;a href=&quot;http://en.wikipedia.org/wiki/CD3_%28immunology%29&quot; rel=&quot;nofollow&quot;&gt;CD3 is&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a protein complex and is composed of four distinct chains. In mammals, the complex contains a CD3γ chain, a CD3δ chain, and two CD3ε chains.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Natural_killer_cell&quot; rel=&quot;nofollow&quot;&gt;Natural Killer (NK) cells&lt;/a&gt; have been &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1387664&quot; rel=&quot;nofollow&quot;&gt;shown&lt;/a&gt; to express CD3 epsilon proteins, but not CD3 delta or gamma. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also on a side note, there are several other non peripheral mononucleated cells besides Purkinje cells that can express CD3, but mostly in pathological circumstances. For instance &lt;a href=&quot;http://en.wikipedia.org/wiki/Warthin%E2%80%93Finkeldey_cell&quot; rel=&quot;nofollow&quot;&gt;Warthin-Finkeldey cells&lt;/a&gt;, also known as polykaryocyes, &lt;a href=&quot;http://www.pathologyoutlines.com/topic/lymphnodespolykaryocytes.html&quot; rel=&quot;nofollow&quot;&gt;display&lt;/a&gt; CD3, although the origin of these cells is not certain (they &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1312298&quot; rel=&quot;nofollow&quot;&gt;might be&lt;/a&gt; multinucleated T-cells). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(PS: If you want more information on CD3, I found &lt;a href=&quot;http://www.pathologyoutlines.com/topic/cdmarkerscd3.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; site very interesting.)&lt;/p&gt;&#xA;" OwnerUserId="15136" LastActivityDate="2015-04-18T20:34:58.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31489" PostTypeId="2" ParentId="31487" CreationDate="2015-04-18T20:50:48.403" Score="2" Body="&lt;p&gt;Short answer is yes, of course. Maintaining a healthy synapse is very energy-consuming process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me first note that forgetting as we know it is more complicated than just pruning of synapses. It might involve rearrangement of proteins in pre/post-synaptic membrane and near it, local de-regulation of local protein synthesis, decrease in synaptic mRNA content and epigenetic change of transcription.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, average energy spending on a synapse, if it is not being used too often, includes mainly maintaining of membrane potential at resting -80mV level. Cellular membrane is a leaky barrier, so that without ion pumps, such as $K^+/Na^+$-ATPase, potential will quickly go to zero. Maintaining and recycling neurotransmitter pool also require energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Action potentials itself are passive processes, its generating does not require energy. ATPase will have to maintain potential at rest and keep it from fluctuating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read this review for more: &lt;a href=&quot;http://www.cell.com/neuron/fulltext/S0896-6273(12)00756-8&quot; rel=&quot;nofollow&quot;&gt;Synaptic Energy Use and Supply&lt;/a&gt; (Neuron, 2012). It generally describes where energy comes from and how it is being used.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-18T20:50:48.403" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31490" PostTypeId="2" ParentId="31482" CreationDate="2015-04-18T21:19:11.077" Score="8" Body="&lt;p&gt;&lt;a href=&quot;http://www.miltenyibiotec.com/~/media/Files/Navigation/Cell%20Separation/macs-technology-cell-isolation-brochure.ashx&quot; rel=&quot;nofollow noreferrer&quot;&gt;Magnetic-activated cell sorting&lt;/a&gt; (PDF download), or MACS, is a procedure developed by &lt;a href=&quot;http://www.miltenyibiotec.com/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Miltenyi Biotec&lt;/a&gt; to separate cells from complex mixtures using antibody-coated magnetic nanoparticles. The antibodies are specific for certain cell surface markers, either expressed on your population of interest (positive selection), or expressed on undesired cell types (negative selection). After adding the antibody-coated beads to the cell mixture and incubating, the suspension is added to a special single-use separation column affixed to a magnet, to which the beads stick, while unlabeled cells flow through. If performing a negative selection, the flow-through is your population of interest and the bound beads and cells are discarded. If your cells of interest are bound to the beads (positive selection), the column is washed several times to make sure unbound or weakly-bound cells are washed through, then the column is removed from the magnet and the cell-bead complexes are eluted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://en.wikipedia.org/wiki/Flow_cytometry#Fluorescence-activated_cell_sorting_.28FACS.29&quot; rel=&quot;nofollow noreferrer&quot;&gt;fluorescence-activated cell sorting&lt;/a&gt; or FACS, the initial complex cell mixture is first labeled with one or more cell surface marker-specific antibodies that have been conjugated to fluorescent dyes. Cells can also be analyzed that express one or more recombinant &lt;a href=&quot;http://en.wikipedia.org/wiki/Green_fluorescent_protein&quot; rel=&quot;nofollow noreferrer&quot;&gt;fluorescent proteins&lt;/a&gt; in conjunction with a gene of interest, allowing for selection of cells without using antibodies. After incubation and wash steps, red blood cells are lysed, if analyzing whole blood. The reason for RBC lysis is shown below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WZm0j.png&quot; alt=&quot;whole blood FACS&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Without lysis, the RBCs overwhelm the cytometer, as they make up around 95% of the cells in human whole blood. White blood cells (leukocytes), on the other hand, only make up 0.1-0.2% of cells, and lymphocytes between about 15 to 50% of leukocytes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cell mixture is then analyzed on a cell sorter such as a &lt;a href=&quot;http://www.bdbiosciences.com/us/instruments/research/cell-sorters/bd-facsaria-iii/m/744763&quot; rel=&quot;nofollow noreferrer&quot;&gt;BD FACSAria&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Tg1dL.jpg&quot; alt=&quot;FACS&quot;&gt;&#xA;&lt;sup&gt;From: &lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Fluorescence_Assisted_Cell_Sorting_%28FACS%29_B.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://commons.wikimedia.org/wiki/File:Fluorescence_Assisted_Cell_Sorting_%28FACS%29_B.jpg&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cells pass in single file past one or more laser beams, which excite the dyes and cause them to fluoresce at a certain wavelength. The user can then use gating to select the combination and intensity of colors they are interested in, and when a cell meets the criteria, it is given an electrical charge, and electro magnets direct it into a collection container.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;So what are the pros and cons of each technology? MACS separation generally is quicker than FACS staining, and a greater number of cells can be processed at one time (sometimes orders of magnitude more, depending on instrument and protocol). If you are, for example, looking to purify large numbers of CD4+ T cells from whole blood, MACS may be the better choice of the two (although I prefer the &lt;a href=&quot;http://www.stemcell.com/en/Products/Popular-Product-Lines/RosetteSep.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;RosetteSep&lt;/a&gt; system for that particular requirement). MACS doesn't require a rather expensive dedicated instrument, although automatic platforms are available if needed. On the downside, most MACS-qualified beads are mostly only available from Miltenyi, so if they do not have beads with your particular marker of interest available, you will need to do the conjugation yourself, at the expense of time and possibly precious antibody while you optimize conditions. Fluorescent-conjugated antibodies are extremely common, and available from practically innumerable companies, so unless you are working with a self-generated antibody it's much more likely that you'll be able to find one for FACS quite easily. There &lt;em&gt;are&lt;/em&gt; MACS beads that contain antibodies directed at certain fluorophores, so you can use flow antibodies for MACS, although optimization is likely still necessary. Finally, MACS separation is only an option for cells that have your marker of interest expressed on the cell surface.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the major advantages of FACS is multicolor staining (depending on the instrument you're using). This makes it much more straightforward to purify potentially rare populations that are only differentiated by their combined expression of a number of surface markers, necessitating multiple gating steps. If this were to be accomplished by MACS, you would need to go through multiple rounds of purification, something that could take longer than FACS, and not necessarily be feasible, as a certain number of cells are required for each MACS run. With FACS, these rare populations (which may only be tens or hundreds of cells per million) can be collected just as easily as more common ones. Also, as mentioned above, there are more antibodies available for flow/FACS than for direct MACS. Additionally, FACS allows for sorting of cells expressing GFP and relatives, letting you collect populations based on internal markers.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2015-04-21T15:19:25.200" LastActivityDate="2015-04-21T15:19:25.200" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31493" PostTypeId="2" ParentId="31459" CreationDate="2015-04-19T01:47:25.917" Score="5" Body="&lt;p&gt;This stuff is hard-wired into either the organism's nervous system, or endocrine signalling pathways (e.g., hormones), or possibly a combination of those two mechanisms.  In that sense, yes it is encoded in the genome, but not in a language that we can understand or interpret yet. Also, don't overlook all of the macromolecules that the female provides to the developing egg during oogenesis, your mother gave you lots of things besides a copy of her genome--you just don't have any of those macromolecules left now--but you wouldn't be here without them.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="14946" LastEditDate="2015-04-19T09:09:36.237" LastActivityDate="2015-04-19T09:09:36.237" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31494" PostTypeId="1" CreationDate="2015-04-19T05:37:37.713" Score="2" ViewCount="17" Body="&lt;p&gt;I am looking to find out what is the ballpark power density of a fluorescing PCR reaction using a SYBR Green or Taq Man dye might be. Is it on the order of $E_e=1mW/cm^2$, less or more? Any help of data would be useful.&lt;/p&gt;&#xA;" OwnerUserId="12985" LastEditorUserId="14552" LastEditDate="2015-04-19T06:17:43.170" LastActivityDate="2015-04-19T06:17:43.170" Title="Surface Power Density of Fluorescing Reaction" Tags="&lt;pcr&gt;&lt;light&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31495" PostTypeId="2" ParentId="306" CreationDate="2015-04-19T05:53:54.600" Score="0" Body="&lt;p&gt;PDBe's new search system is designed to answer just such questions&#xA;&lt;a href=&quot;http://www.ebi.ac.uk/pdbe/entry/search/index?organism_synonyms:HUMAN&amp;amp;view=macromolecules&quot; rel=&quot;nofollow&quot;&gt;http://www.ebi.ac.uk/pdbe/entry/search/index?organism_synonyms:HUMAN&amp;amp;view=macromolecules&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;shows there are 6964 unique human macromolecules with structure data in the PDB.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, many will be fragments of proteins rather than the whole molecule. &lt;/p&gt;&#xA;" OwnerUserId="15395" LastActivityDate="2015-04-19T05:53:54.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31496" PostTypeId="1" CreationDate="2015-04-19T06:15:35.690" Score="5" ViewCount="2332" Body="&lt;p&gt;I know ringworm is caused by a fungus on the skin, nails or scalp but what causes the rash to form as a ring instead of like a normal spread out rash? &lt;/p&gt;&#xA;" OwnerUserId="12899" LastActivityDate="2016-08-21T04:21:36.937" Title="The ring formation of ringworm" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;mycology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31497" PostTypeId="1" AcceptedAnswerId="31549" CreationDate="2015-04-19T07:53:21.753" Score="7" ViewCount="3760" Body="&lt;p&gt;Can a person live with this alternative nutrition? Of course, assuming that eating pleasure is assumed the same.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The nutrients that contain are far better than average meal a person eats the majority of times, al least me. However, since is not solid food, do our digestive system need to work harder?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scientific reports would be appreciated, comparing these two modes of feeding.&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="4717" LastEditDate="2015-04-19T10:58:48.830" LastActivityDate="2015-09-14T14:55:35.780" Title="Powdered meal replacement vs regular meal" Tags="&lt;food&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31499" PostTypeId="1" CreationDate="2015-04-19T10:31:50.773" Score="4" ViewCount="4851" Body="&lt;p&gt;In chemistry, I studied the decomposition of water as being $2H_2O_{(l)} \rightarrow 2H_{2(g)} + O_{2(g)}$. However, when water is split, the equation is $2H_2O_{(l)} \rightarrow 4H^+ + 4e^- +O_{2(g)}$. Why is that? How does $H_2$ just ionize?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, what &lt;em&gt;is&lt;/em&gt; the mechanism for photolysis? I would have thought that splitting water molecules requires a ton of energy; yet it can be accomplished simply with light energy during photosynthesis?&lt;/p&gt;&#xA;" OwnerUserId="15272" LastEditorUserId="9943" LastEditDate="2015-04-24T02:11:23.193" LastActivityDate="2018-02-01T20:34:34.953" Title="Photolysis of Water?" Tags="&lt;biochemistry&gt;&lt;photosynthesis&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31500" PostTypeId="2" ParentId="31463" CreationDate="2015-04-19T12:35:58.453" Score="1" Body="&lt;p&gt;Yes, of course they are conserved. Conservation is basically a measure of sequence identity. It can be used to describe the relationship between both paralogs (genes created by a duplication event) and orthologs (genes created by a speciaton event). Any type of homology relationship can be described in terms of the conservation (sequence similarity) between the genes investigated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even entire genomes can be described as more or less conserved. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2015-04-19T12:35:58.453" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31502" PostTypeId="2" ParentId="23706" CreationDate="2015-04-19T17:11:44.313" Score="3" Body="&lt;p&gt;Yes, there is a lot of evidence for self-awareness in animals. The gold standard test for self-awareness is the mirror self-recognition test (MSR)--we can tell from the behavior of an animal exposed to a mirror whether or not it can tell itself apart from other animals of the same species:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Animals that possess MSR typically progress through four stages of behavior when facing a mirror: (i) social responses, (ii) physical inspection (e.g., looking behind the mirror), (iii) repetitive mirror-testing behavior, and (iv) realization of seeing themselves. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17075063&quot; rel=&quot;nofollow&quot;&gt;Plotnik &lt;em&gt;et al.&lt;/em&gt; 2006&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That quote was taken from the abstract of a paper showing self-recognition in a single African elephant, but there is evidence for self-awareness in magpies (&lt;a href=&quot;http://www.plosbiology.org/article/fetchObject.action?representation=PDF&amp;amp;uri=info:doi/10.1371/journal.pbio.0060202&quot; rel=&quot;nofollow&quot;&gt;Prior &lt;em&gt;et al.&lt;/em&gt; 2008&lt;/a&gt;), dolphins (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23649907&quot; rel=&quot;nofollow&quot;&gt;Harley 2013)&lt;/a&gt;, chimpanzees (&lt;a href=&quot;http://psycnet.apa.org/journals/com/107/4/347.html&quot; rel=&quot;nofollow&quot;&gt;Povinelli &lt;em&gt;et al.&lt;/em&gt; 2006&lt;/a&gt;) and orangutans (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0047248481800164&quot; rel=&quot;nofollow&quot;&gt;Suarez and Gallup 1981&lt;/a&gt;). Many of these studies use the Gallup mark test (&lt;a href=&quot;http://en.wikipedia.org/wiki/Mirror_test&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Gallup anaesthetised the chimpanzees and then painted a red alcohol-soluble dye on the eyebrow ridge and on the top half of the opposite ear. When the dye dried, it had virtually no olfactory or tactile cues. Gallup then returned the chimpanzees to the cage (with the mirror removed) and allowed them to regain full consciousness. He then recorded the frequency which the chimpanzees spontaneously touched the marked areas of skin. After 30 minutes, the mirror was re-introduced into the room and the frequency of touching the marked areas again determined. The frequency of touching increased to 4-10 with the mirror present compared to only 1 when the mirror had been removed. The chimpanzees sometimes inspected their fingers visually or olfactorily after touching the marks.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Basically, an animal which has seen and recognized itself in a mirror recognizes the mark as being new, so it touches &lt;em&gt;its own body&lt;/em&gt; on the marked area, which shows that the animal recognizes the image in the mirror as itself.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-04-19T17:11:44.313" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31503" PostTypeId="2" ParentId="28582" CreationDate="2015-04-19T17:46:32.007" Score="1" Body="&lt;p&gt;&lt;strong&gt;TL;DR&lt;/strong&gt; Visual and auditory systems are crucial for survival, especially in higher animals. Also, visual/auditory systems have great number of cells. For processing to be effective, it should be performed closer to data acquisition (eyes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, for example, in mouse or human, &lt;a href=&quot;http://en.wikipedia.org/wiki/Central_nervous_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;central nervous system&lt;/a&gt; includes brain &lt;em&gt;and spinal cord&lt;/em&gt;. Since spinal cord is extremely important at regulating different physiological processes as well as in performing complicated motor tasks, it would be unjust to not think about CNS as a whole.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you talk only about brain part of CNS, it makes sense to locate important processing pathways near sensitive organs for two reasons. First, it saves material on running long axons from many sensory cells. Secondly, longer axons deliver information slower. If there is a sense that is important for survival, than information in that modality must be delivered and processes as quick as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In comments to the question @anongoodnurse &lt;a href=&quot;https://biology.stackexchange.com/questions/28582/why-did-the-brain-develop-in-the-front-in-most-organisms#comment47118_28582&quot;&gt;mentioned&lt;/a&gt; that &quot;&lt;em&gt;butterflies 'taste' with their feet&lt;/em&gt;&quot;. I would argue that a) taste in butterflies is not vital for immediate survival and b) number of taste buds is very limited, whereas retinal cells are count up to &lt;a href=&quot;http://jeb.biologists.org/content/201/9/1255.full.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;more than thousand&lt;/a&gt; per eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what about humans? We also able to &quot;taste with our feet&quot;, e.g. feel temperature. For survival it is crucial to be able to escape hot surface as fast as we can. And we do, thanks to a direct reflex arc going from sensory cells to &lt;em&gt;spinal cord&lt;/em&gt; and motor neurons. Which brings back point about CNS as a whole system. Crucial information and immediate decisions are made closer to sensitive organs.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-04-19T17:46:32.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31504" PostTypeId="2" ParentId="28582" CreationDate="2015-04-19T18:32:54.543" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I was wondering: why most, well, pretty much all organism with a brain have it right in front of their bodies or at the top.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I believe you're confounding origins. Complex brains -- like those in us and other mammals -- are situated in the position that has been the best-protected over millions of years of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution did not decide where the front of the animal should be and then put the brain there. Rather, evolutionary pressures resulted in the brain being an excellent survival tool, and the species that could protect it best kept its benefits. It just so happened that, since complex brains require an enormous amount of resources and are quite fragile, wherever the organism could best protect the brain became its &quot;front&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In mammals that became a skull. In some insects it's in the thorax or abdomen. In sea slugs... well, there really isn't a complex brain in sea-slugs... so the difference between their front-end and back-end is pretty minimal. Same with worms and other very simple creatures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So think of it like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Brain = Good for Survival, but Fragile&lt;/em&gt; &lt;strong&gt;--&gt;&lt;/strong&gt; &lt;em&gt;Brain Needs Protection&lt;/em&gt; &lt;strong&gt;--&gt;&lt;/strong&gt; &lt;em&gt;Wherever Protection is Best = Where the &quot;head&quot;/&quot;front&quot; has evolved&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2015-04-19T18:32:54.543" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31505" PostTypeId="1" AcceptedAnswerId="31666" CreationDate="2015-04-19T19:53:16.210" Score="7" ViewCount="1702" Body="&lt;p&gt;I would be interested in knowing how long it takes between the moment something touches our skin and the moment something is activated in the brain. Also how long does it take in total until we subjectively perceive something? And I would like to know whether this is dependent on which part of the body was stimulated (same latency for foot and neck?), or if it is dependent on the nature of stimuli (heat or mechanical). I would also be interested in that latency in the auditory and visual system. I tried searching for that but could not find what I needed due to the lack of the correct terminology.  &lt;/p&gt;&#xA;" OwnerUserId="6213" LastEditorUserId="9943" LastEditDate="2021-03-25T10:00:01.113" LastActivityDate="2021-03-25T10:00:01.113" Title="Latency differences between our senses" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;&lt;senses&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31506" PostTypeId="2" ParentId="31453" CreationDate="2015-04-19T20:05:05.650" Score="4" Body="&lt;p&gt;Nice question! I've found a great &lt;a href=&quot;http://physrev.physiology.org/content/90/1/207?ijkey=dfcf5a02627f79fccee51b656dfc8d8611bcdfbe&amp;amp;keytype2=tf_ipsecsha&quot; rel=&quot;nofollow noreferrer&quot;&gt;article&lt;/a&gt; about fatty acid metabolism in heart muscle in healthy and disease conditions. As it is stated in this paper long chain fatty acids are utilized through beta-oxidation to meet the high energy need of continuous contraction. Beta-oxidation of long chain fatty acids produce far more ATPs than glucose. According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Beta_oxidation&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;For an even-numbered saturated fat (C2n), n - 1 oxidations are necessary, and the final process yields an additional acetyl CoA. In addition, two equivalents of ATP are lost during the activation of the fatty acid. Therefore, the total ATP yield can be stated as:&#xA;(n - 1) * 14 + 10 - 2 = total ATP or 14n-6 (alternatively)&#xA;For instance, the ATP yield of palmitate (C16, n = 8) is:&#xA;(8 - 1) * 14 + 10 - 2 = 106 ATP&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;While a single molecule of glucose produces 36 ATPs (under aerobic conditions)&lt;/p&gt;&#xA;&lt;p&gt;Thus use of fatty acids (fats) in cardiac muscle is beneficial because of their higher energy concentration. Also it is noteworthy that this does not occur in isolation, so this is a response to contractile work and other competing energy sources (such as glucose, lactose etc). Also excessive uptake and beta-oxidation in disease conditions can even endanger cardiac functions. See details in the linked paper.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-19T20:48:34.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31507" PostTypeId="1" CreationDate="2015-04-19T20:42:25.197" Score="7" ViewCount="23566" Body="&lt;p&gt;Mouth ulcers are red/white rings with a crater. They are sore and last for 7-10 days.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I want to know is what they are 'made of' - i.e., what is the ring filled with, and why is the centre crater so sore? And why do these relatively benign and short-lasting ulcers have to hurt so much when they simply heal in a couple of days&lt;/p&gt;&#xA;" OwnerUserId="15404" LastEditorUserId="9943" LastEditDate="2015-04-20T23:24:25.397" LastActivityDate="2018-10-22T16:48:31.190" Title="What's a mouth ulcer/canker sore &quot;made of&quot;, and why do they develop?" Tags="&lt;human-biology&gt;&lt;pathology&gt;&lt;pain&gt;&lt;injury&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31508" PostTypeId="1" CreationDate="2015-04-19T20:42:53.550" Score="0" ViewCount="81" Body="&lt;p&gt;At the present time it looks as if there is no other life in the Universe other than here on Earth . If this is true then why didn't it occur anywhere else ? Is it possible for something to happen only once ? Hundreds of Billions of  other Planets have formed so whatever happened here why wouldn't it have happened again elsewhere ? It is very , very strange indeed .     &lt;/p&gt;&#xA;" OwnerUserId="11869" LastActivityDate="2015-04-20T06:12:38.503" Title="Formation of life on other Planets" Tags="&lt;life&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2015-04-20T00:53:52.480" ContentLicense="CC BY-SA 3.0" />
  <row Id="31509" PostTypeId="2" ParentId="31508" CreationDate="2015-04-19T21:41:30.287" Score="1" Body="&lt;p&gt;&lt;strong&gt;Issues with the post&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I agree that the question is &lt;em&gt;too broad&lt;/em&gt;. It is not the only issue, it is also &lt;em&gt;primarily opinion-based&lt;/em&gt; (see below for explanations). The post is also somehow &lt;em&gt;unclear&lt;/em&gt; (see below for explanations). But here is some kind of an answer that may help you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you google your question you will get tons and tons of hits. There is a whole lot of videos on youtube that address this question. You may want to have a look at those and come on StackExchange to ask a more accurate question because for the moment the question is &lt;em&gt;too broad&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;As a first short answer to the questions...&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At the present time it looks as if there is no other life in the Universe other than here on Earth&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It sounds wrong (as a consequence your question would be &lt;em&gt;primarily opinion based&lt;/em&gt;). We haven't found life. This doesn't mean that life doesn't exist elsewhere. Actually most people think that life exist elsewhere. Part of the issue behind this question is the definition of life. Often, people refers to &lt;a href=&quot;http://en.wikipedia.org/wiki/Drake_equation&quot; rel=&quot;nofollow&quot;&gt;Drake equation&lt;/a&gt; (you might want to read about it) which gives you the number of planets where life should exist. However, Drake equation is a speculation that has no solid grounds. It is actually pretty complicated (or impossible because we need to assume things about what the original conditions are) to calculate a probability that life occurs on a given planet. While it sounds pretty intuitive to many people (me, including) that life should exist somewhere else, there is really not much certainty.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is it possible for something to happen only once?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well....yes, the death of Napoleon occurred only once.... I am not quite sure what you mean with this question, it is &lt;em&gt;unclear&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-04-20T06:12:38.503" LastActivityDate="2015-04-20T06:12:38.503" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="31511" PostTypeId="1" CreationDate="2015-04-20T02:09:17.787" Score="2" ViewCount="278" Body="&lt;p&gt;I recently found out that alder trees have root nodules which contain nitrogen-fixing bacteria and that alders are primary colonizers in primary succession. That leads me to this question: since there are really no fungi in the soil and since the alder is a colonizing species, where does the fungi come from? Or is my assumption that there are no fungi in the soil incorrect?&lt;/p&gt;&#xA;" OwnerUserId="11615" LastEditorUserId="14552" LastEditDate="2015-04-20T03:18:49.987" LastActivityDate="2016-11-05T21:27:26.780" Title="Alder Tree Root Nodule Origins?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31512" PostTypeId="1" CreationDate="2015-04-20T06:48:12.137" Score="5" ViewCount="646" Body="&lt;p&gt;I had a discussion with a friend of mine; from his understanding, bacteria and other small organisms have higher amounts of &quot;coding&quot; DNA and, as such, are able to evolve much faster than organisms like us.  His argument was that if bacteria are able to evolve so much faster than us, then they should have become the Apex Predators on Earth instead of humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I argued that the 2% of the &quot;coding&quot; DNA is probably as long as the 90% of a bacterium (I'm guessing at this point) and that it is the bacterium's small life span that makes it evolve so fast.  Was hoping to get clarification from someone with more experience in the field.&lt;/p&gt;&#xA;" OwnerUserId="15407" LastEditorUserId="1306" LastEditDate="2015-04-20T12:14:11.900" LastActivityDate="2015-05-20T22:42:03.277" Title="Non Coding DNA and its effect on evolution" Tags="&lt;genetics&gt;&lt;mutations&gt;&lt;molecular-evolution&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31513" PostTypeId="2" ParentId="31512" CreationDate="2015-04-20T10:53:33.163" Score="-1" Body="&lt;p&gt;&lt;a href=&quot;http://www.livescience.com/46986-human-genome-junk-dna.html&quot; rel=&quot;nofollow&quot;&gt;http://www.livescience.com/46986-human-genome-junk-dna.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Microorganisms are often able to adapt to new environments quickly, but they lack the specialized functions of macro-organisms. Consider that the micro-organisms of macro-organisms have developed to form machinery that builds solutions to problems, rather than being retrofitted themselves to counteract new threats. Each time a bacteria needs to adapt itself to attack, whereas the specialized cells of our body can manufacture a solution on the fly rather than waiting around for a random beneficial strait to show up in the population. It would be like a small manufacturer quickly retrofitting it's production system to produce a new product. Sure, it can produce a new product, but it takes time for setup, and the company can only produce a limited number of varied products at a time, whereas a giant production company may have a huge amount of preset equipment for manufacturing a enormous variety of products with no need for retrofitting (evolution). The larger factory could have the advantage when it comes to efficient production, with quicker turnaround. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, the specialization of micro-organisms leads to nature allowing the evolution of macro-organisms as the major factories of nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Excess, unused (or at least non-critical) DNA is useful because it allows evolution some wiggle room. If a bacteria suffers a deleterious mutation in a vital gene, then it's obviously not fit. But, that same bacterium with can accumulate potentially useful codes in the previously unused portion of it's genome, without needing to deal with risky mutations in vital genes. And again, as microorganisms specialize, they can fabricate new proteins and such, with lower risk, and less time, compared to micro-organisms which use evolution of their genome as the sole/primary means of short term adaption.&lt;/p&gt;&#xA;" OwnerUserId="8619" LastEditorUserId="8619" LastEditDate="2015-04-20T20:44:27.783" LastActivityDate="2015-04-20T20:44:27.783" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="31515" PostTypeId="2" ParentId="31376" CreationDate="2015-04-20T11:36:02.347" Score="2" Body="&lt;p&gt;The Worm Atlas you cited is &lt;em&gt;NOT&lt;/em&gt; just a &quot;model.&quot; The neuronal cell coordinates were determined from an actual 3-D reconstruction of a worm based on serial thin section electron micrographs.  The serial sections were manually digitized to permit annotation and analysis using computer graphics. The annotation (over a period of years) established the synaptic connectivity, published by John White et al. in 1986 in the Proceedings of the Royal Society of London.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-04-20T11:36:02.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31516" PostTypeId="1" AcceptedAnswerId="31521" CreationDate="2015-04-20T11:53:57.060" Score="1" ViewCount="63" Body="&lt;p&gt;I remember coming across a popular science article years ago about a monkey species which featured two male genotypes: the first were good looking males who acquired social status (as alphas or betas) within the group and could thus achieve reproductive succes. The alternative (less frequent) phenotype achieved similar fitness by adopting an outgroup (omega) lurking rapist kind of reproductive strategy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anybody know which species and whose observervations I could be referring to? I'm curious to find out if this was a valid observation and if any further research has been done on this phenomenon.&lt;/p&gt;&#xA;" OwnerUserId="4470" LastActivityDate="2015-04-20T15:18:12.193" Title="Which monkey species features two distinct male phenotypes?" Tags="&lt;reproduction&gt;&lt;sociality&gt;&lt;fitness&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31517" PostTypeId="2" ParentId="31505" CreationDate="2015-04-20T12:02:10.987" Score="8" Body="&lt;p&gt;This is a really interesting set of questions and I'll try to answer all yet keep it compact. So first of all let's see the nerve classes and conduction speed from this and this wikipedia pages:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Peripherial nerves can be classified into three groups A, B, and C (based on their diameter).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Group A are the thickest (largest in diameter), are myelinated and have high conduction velocity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Group A can be divided to subclasses:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;'A' alpha nerves are 13-20um (micrometer) thick and have 80-120m/s&#xA;conduction velocity (this equals 288-432km/h (meter/s * 3,6) or&#xA;180-270mph (khm/h / 1,6)). These are associated with proprioception (this &#xA;subconscious sensation is responsible for us knowing how our body is positioned in 3D and where are our limbs compared to our body)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This means that in a fairly average 180 cm (approx 6 feet) tall human a stimulus on such nerve can travel the whole body of the person in 0,018s (with an average of 100m/s conduction velocity) How ever this is not the real case, I'll discuss that later.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;'A' beta nerves are about half as thick as 'A' alpha (6-12um) and&#xA;conduct stimulus with 33-75m/s. Among others these are linked to cutaneous mechano receptors&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Alpha and beta fibers can be both afferent (sensory) or efferent (motor)&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;'A' delta nerves are thinly myelinated and far slower than the&#xA;previous nerves with 3-30m/s velocity. These type of nerves are linked to nociception, cold thermoreceptors and make up the free nerve endings for touch and pressure.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;'A' gamma fibers are efferent fibers and with 4-34m/s velocity.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Group B nerves are preganglionic fibers (ganglions are hubs of neurons of the autonomic nervous system) and conduct stimuli with 3-15m/s velocity. Thes are 1-5um thick and myelinated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Group C are post ganglionic fibers (leading to the organs) and belong to nociceptors and warmth receptors They're thin (0.2 - 1.5um) and non myelinated. Their conduction speed is 0.5-2m/s.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So different sensory types have different nerves associated to them, and this results in different conduction velocity of that stimuli. Thus the answer is yes there is difference in sensation lag times to different types of stimuli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &lt;a href=&quot;http://ac.els-cdn.com/0006899383906509/1-s2.0-0006899383906509-main.pdf?_tid=8e6ea386-e747-11e4-89d0-00000aab0f26&amp;amp;acdnat=1429525704_33bb151952bb761424b4e017bbb9712b&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; paper scientist tested reaction lag time to heat caused pain and found the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DBDKU.png&quot; alt=&quot;lag time differences&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Researchers stimulated two different parts of the hand of test subjects, the thenar eminence - that is the base of the thumb, and the volar forearm - that is the same side of the forearm as the palm ( the lower part of your forearm if you imagine your hands palms down). As you can see on the graph the volar forearm has lower lag times that the base of the thumb after a certain level of stimulus.&#xA;These authors also made a control experiment to:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;estimate the sum total of time necessary for central sensory processing, the decision making plus motor execution times were measured in one subject for responses to suprathreshold auditory stimuli. Auditory stimuli were chosen because primary afferent conduction time is negligible. Latencies were measured in the same way as with the thermal stimuli. The tenth percentile (point at which 10 ~ of the latencies were faster and 90 ~ were &#xA;  slower) was near 0.19 s. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So response to sound is pretty fast, but this as with the heat experiment includes the measurable response of the test subject, thus the value is higher than the actual sensation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the heat-pain experiment the authors concluded :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The conduction distance from the area stimulated to the spinal cord was 0.78 m in this subject. If receptor utilization time, rise time, and conduction time in the cervical spinal cord are ignored, then primary afferents that signal first pain must have a conduction velocity of at &#xA;  least 0.78 m/ (0.33 --0.19) s, or 6 m/s.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The 6/ms velocity correlates well with the A-delta nerve's conduction speed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also here's another diagram on the distribution of lag times to different level of stimulus:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/p8mQV.png&quot; alt=&quot;latency to stimulus level&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The difference of lag times can result from the activation of differrent receptors. Temperatures around 40 degrees Celsius are more likely to activate warmth receptors only that have lower conduction velocity. The high numbers of slow (1-1,5s) response to these stimuli correlate well with the group C fibers for warmth reception. On the other hand, responses to higher and potentially more damaging temperatures, nociceptors are more likely to be activated and faster conduction of these stimuli result in lower latencies. Also the transition from high latency to low is quite smooth with increase of the temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Difference in nerve conduction values are not the only thing that occurs lag in sensation. These stimuli do not travel directly to the brain from receptors, but have to be transmitted to a sensory neuron, then these have connections in the spinal cord before stimulus can be transmitted to the adequate part of the brain, and then these neurons of the brain still have to process the signal. It is important to note that lag times are different from individual to individual. Authors of &lt;a href=&quot;http://deepblue.lib.umich.edu/bitstream/handle/2027.42/50152/880151007_ftp.pdf?sequence=1&amp;amp;isAllowed=y&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; paper conducted a great series of measurements to find out effects of age, sex and height on nerve conduction velocity and it turns out that for example:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Controlling for age and temperature, the 0.17 m/s decrease in sural  conduction velocity per centimeter increase in height (0.44 m/s per inch) &#xA;  was somewhat larger than previously reported.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also this last article has many good comparison tables of different nerves and conditions.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-20T15:14:12.227" LastActivityDate="2015-04-20T15:14:12.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31518" PostTypeId="1" CreationDate="2015-04-20T13:28:13.220" Score="3" ViewCount="57" Body="&lt;p&gt;A fractal algorithm like Mandelbrot is self-similar in all size scales. This is not the case in nature. A tree is fractal in the sense that each branch is similar to the tree as a whole. But that is only true at a certain range of scales, about 0.1 - 10 meter. The forest does not look like one tree, nor does the texture at millimeter scale or the cellular structure at microscopic scale. At those scales the tree may or not be fractal, but at least it is not fractal in the same way as on the 1 meter size. Nature breaks the fractal regime after only a couple or so self-similar scales.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these transitions between fractal regimes studied by biology?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any ideas around about how different fractal regimes might be connected with &lt;a href=&quot;https://en.wikipedia.org/wiki/Emergence&quot; rel=&quot;nofollow&quot;&gt;emergent phenomena&lt;/a&gt;? At very small scales there exists no tree, but only elementary quantum particles/waves. Macromolecules and cells and the tree and the forest each emerge as a phenomena on different size scales. I wonder if this emergence is matched by the different fractal regimes at those scales?&lt;/p&gt;&#xA;" OwnerUserId="8025" LastActivityDate="2015-04-20T13:28:13.220" Title="Is emergence connected to nature's transition between fractal regimes at different size scales?" Tags="&lt;theoretical-biology&gt;&lt;information-theory&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31519" PostTypeId="1" CreationDate="2015-04-20T14:11:49.133" Score="7" ViewCount="1386" Body="&lt;p&gt;I wonder why life uses the particular proteins that it does, about 10^6 different proteins, I think? Evolution cannot explain it because the number of possible proteins is far far too large to ever come into existence anywhere in the visible universe, let alone on Earth. And evolutionary selection only works on stuff that exists.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there some chemical or other explanation, or is this an unresolved paradox in biology?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The median number of amino acids in a human protein is 375. Most are longer than 200 and maybe all are longer than 100. The 20 different kinds of amino acids can be combined to 20^375 = 10^487 different proteins which have the length 375.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the entire crust of the Earth consisted of proteins which all were 375 long and each protein mutated once every nanosecond during 5 billion years and each mutation resulted in a protein which is unique in time and space, and there exists 100 such &quot;protein Earths&quot; around every star and 1000 billion stars in each of 1000 billion galaxies in the visible universe, it still only adds up to something like 10^100 proteins. Adding 10^37 years until the last star remnant has cooled down to less than 1 Kelvin, doesn't change this picture, almost all of the possible proteins will literally never exist anywhere. Even if I'm off by a factor a million on each of those numbers, only one in 10^300 of all possible median length proteins could ever exist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since our mind-bendingly small subset of possible proteins supports life, shouldn't we expect that many many (as in 10^300) other potential subsets of different proteins would do so too? And can we conclude that if DNA/protein based life has originated somewhere else, it will not have even one single protein in common with us or with any other independent origin of life? Or is this focus on proteins somehow invalid?&lt;/p&gt;&#xA;" OwnerUserId="8025" LastEditorUserId="8025" LastEditDate="2015-04-20T15:15:10.623" LastActivityDate="2018-06-10T02:24:39.587" Title="What has caused life to choose this unfathomably tiny subset of all possible proteins?" Tags="&lt;evolution&gt;&lt;proteins&gt;&lt;mutations&gt;&lt;theoretical-biology&gt;&lt;information-theory&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31521" PostTypeId="2" ParentId="31516" CreationDate="2015-04-20T15:18:12.193" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/BF02382664&quot; rel=&quot;nofollow&quot;&gt;Patas monkeys&lt;/a&gt; exhibit &quot;sneak mating&quot; where a male other than the resident male sires offspring. Resident males do sire more offspring than sneaker males, but both strategies do co-occur. I'm pretty sure there are other species that have a similar mating strategy as well. &lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-04-20T15:18:12.193" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31522" PostTypeId="1" AcceptedAnswerId="34642" CreationDate="2015-04-20T15:22:32.357" Score="2" ViewCount="70" Body="&lt;p&gt;I was looking at some tumour suppressing genes that can be helpful in diagnosing lung cancer (particularly NSCLC - Non-small-cell lung carcinoma) at an early stage. I came across a few such as p53, etc. However, as a beginner (and someone who has never pursued higher studies in biology), I do not have much knowledge as to which is the most reliable and the most extensively documented tumour suppressing gene for NSCLC.&lt;/p&gt;&#xA;" OwnerUserId="15415" LastEditorUserId="14735" LastEditDate="2015-04-20T15:25:15.397" LastActivityDate="2018-07-15T19:26:14.057" Title="What is the most reliable tumour suppressing gene for NSCLC?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31523" PostTypeId="2" ParentId="31519" CreationDate="2015-04-20T15:37:51.363" Score="14" Body="&lt;p&gt;&lt;strong&gt;The answer is &lt;em&gt;chance&lt;/em&gt; or, even better, &lt;em&gt;contingency&lt;/em&gt;.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About your calculations, it is true that the theoretical sequences are almost unlimited, but the basic scaffolds are not. Very different sequences can fold into the same basic scaffold and have a similar reactivity/function. So, even if not all the sequences have been explored on this planet, most of the scaffolds and functionalities have been. It is true that protein-based life could be evolved somewhere else, and it is true that the overall sequence space evolved somewhere else would be different from the one evolved on this planet. However, I would expect to find almost the same palette of biochemical reactions that we have discovered on our proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would suggest reading the work of P.L. Luisi &lt;a href=&quot;http://www.plluisi.org/emergence.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;. He makes really good points on this issue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/vaop/ncurrent/full/nature23902.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;A new paper just came out&lt;/a&gt;, I think it is a nice addendum to this answer.&lt;/p&gt;&#xA;" OwnerUserId="12923" LastEditorUserId="12923" LastEditDate="2017-09-15T18:00:26.107" LastActivityDate="2017-09-15T18:00:26.107" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31524" PostTypeId="2" ParentId="31507" CreationDate="2015-04-20T15:54:18.713" Score="5" Body="&lt;p&gt;The redden area around the grayish-white indentation of the canker sore isn't filled with anything. This circular area is simply inflamed. The grayish-white area in the center is not filled with puss or anything else as well. This is an area of dead cells but underneath this layer of dead cells the tissue red [&lt;a href=&quot;http://www.mckinley.illinois.edu/handouts/canker_sore.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;],[&lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/canker-sore/basics/causes/con-20021262&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;],[&lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000998.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;3&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Canker sores, &lt;a href=&quot;http://en.wikipedia.org/wiki/Aphthous_stomatitis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Aphthous stomatitis&lt;/a&gt;, is an ulcer. An ulcer is a break in the membrane. That is, you have an open sore in your mouth. As with any open wound, pain and discomfort will occur but the mouth is how we consume our food. Since we intake our daily bread in this manner, what we consume can cause the pain to increase; for instance, &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;acidic foods&lt;/li&gt;&#xA;&lt;li&gt;spicy foods&lt;/li&gt;&#xA;&lt;li&gt;abrasive foods&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The cause of canker sores is not entirely known, but according to the Mayo clinic [&lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/canker-sore/basics/causes/con-20021262&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;], possible triggers are&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;A minor injury to your mouth from dental work, overzealous brushing, sports mishaps or an accidental cheek bite&lt;/li&gt;&#xA;&lt;li&gt;Toothpastes and mouth rinses containing sodium lauryl sulfate&lt;/li&gt;&#xA;&lt;li&gt;Food sensitivities, particularly to chocolate, coffee, strawberries, eggs, nuts, cheese, and spicy or acidic foods&lt;/li&gt;&#xA;&lt;li&gt;A diet lacking in vitamin B-12, zinc, folate (folic acid) or iron&lt;/li&gt;&#xA;&lt;li&gt;An allergic response to certain bacteria in your mouth&lt;/li&gt;&#xA;&lt;li&gt;Helicobacter pylori, the same bacteria that cause peptic ulcers&lt;/li&gt;&#xA;&lt;li&gt;Hormonal shifts during menstruation&lt;/li&gt;&#xA;&lt;li&gt;Emotional stress&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Canker sores may also be caused by the following diseases as well [&lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/canker-sore/basics/causes/con-20021262&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Celiac disease, a serious intestinal disorder caused by a sensitivity to gluten, a protein found in most grains&lt;/li&gt;&#xA;&lt;li&gt;Inflammatory bowel diseases, such as Crohn's disease and ulcerative colitis&lt;/li&gt;&#xA;&lt;li&gt;Behcet's disease, a rare disorder that causes inflammation throughout the body, including the mouth&lt;/li&gt;&#xA;&lt;li&gt;A faulty immune system that attacks healthy cells in your mouth instead of pathogens, such as viruses and bacteria&lt;/li&gt;&#xA;&lt;li&gt;HIV/AIDS, which suppresses the immune system&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="46826" LastEditDate="2018-10-22T16:48:31.190" LastActivityDate="2018-10-22T16:48:31.190" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="31525" PostTypeId="1" CreationDate="2015-04-20T16:09:40.623" Score="0" ViewCount="54" Body="&lt;p&gt;I'm studying two bird populations that are competing against each other for a resource: Population A and Population B. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Population A is present in much higher numbers than Population B, and as a consequence, I think that Population A has a competitive advantage over Population B.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking for literature that demonstrates that when one population is present in higher numbers than the other population, the population present in higher numbers has a competitive advantage. Can anyone point me in the direction of literature that demonstrates this?&lt;/p&gt;&#xA;" OwnerUserId="1216" LastEditorUserId="3952" LastEditDate="2015-04-20T20:02:32.990" LastActivityDate="2015-04-20T20:02:32.990" Title="Literature that demonstrates organisms have a competitive advantage in numbers" Tags="&lt;ecology&gt;&lt;ornithology&gt;&lt;population-biology&gt;&lt;literature&gt;&lt;community-ecology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31526" PostTypeId="1" CreationDate="2015-04-20T17:25:59.203" Score="1" ViewCount="362" Body="&lt;p&gt;gene knockout is mainly used in creating newborn animals... right? Well can you do it to already-adult animals or humans so that they themselves would experience change in their body and not just their off springs?&lt;/p&gt;&#xA;" OwnerUserId="15416" LastActivityDate="2015-04-21T03:52:07.993" Title="Is it possible to knock out a gene in adults?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="31527" PostTypeId="2" ParentId="31525" CreationDate="2015-04-20T17:27:58.510" Score="1" Body="&lt;p&gt;I have found these papers:&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0169534713002322&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0169534713002322&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0040580912001360&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0040580912001360&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19416834&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/19416834&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21930936&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/21930936&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The last two argue that larger groups have better &quot;problem solving&quot; capability, and this is a clear advantage in competition.&lt;/p&gt;&#xA;" OwnerUserId="12923" LastActivityDate="2015-04-20T17:27:58.510" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31528" PostTypeId="2" ParentId="31519" CreationDate="2015-04-20T17:33:13.333" Score="2" Body="&lt;p&gt;I'm not sure I understand the question. You've elegantly demonstrated that only a tiny fraction of all protein sequences could possibly exist, but then asked why only a tiny fraction of all protein sequences do exist. Your conclusions about independent origins of life having no proteins in common are accurate, but also consider that you as a human being have not even a single protein in common with the bacteria in your yogurt (I mean you do, but they have slightly different sequences).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as which protein subsets make life, there are demonstrably thousands of sets of proteins that support life. Each genetically distinct individual has a slightly different set of proteins, most of which support life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as how many of these subsets exist, that's unknown. Maybe aliens use only ribozymes based on RNA molecules. Maybe they have a different set of amino acids, or a silicon backbone to their proteins, or what have you. Until we find alien life(or perfect abiogenesis in the lab) the total diversity of life-like things is unknowable.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="4109" LastEditDate="2015-04-21T10:33:55.553" LastActivityDate="2015-04-21T10:33:55.553" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31530" PostTypeId="1" CreationDate="2015-04-20T18:46:26.500" Score="4" ViewCount="77" Body="&lt;p&gt;I'm a high school student whose interested in bioinformatics. Therefore I chose a project which I study Sequence Assembly. My main goal is to compare different paradigms (&lt;em&gt;Greedy&lt;/em&gt;, &lt;em&gt;OLC&lt;/em&gt;, &lt;em&gt;De Bruijn&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have done my initial research but &lt;strong&gt;I don't know which assembler to use for comparing paradigms&lt;/strong&gt;. Most of them are designed for real world usage, where there are many different factors to consider, but &lt;strong&gt;in my case the problem is more like a Computer Science problem&lt;/strong&gt;: &lt;em&gt;Reconstructing an array of symbols from it's fragments.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is no hope, I will try to implement them myself but I want to avoid that since it will very likely to be error-prone and slower than real world implementations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="15399" LastActivityDate="2015-04-20T18:46:26.500" Title="Which sequence assemblers I can use to compare different paradigms?" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;sequence-assembly&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31533" PostTypeId="1" CreationDate="2015-04-20T21:11:02.687" Score="0" ViewCount="57" Body="&lt;p&gt;genes make alpha beta gamma subunits (proteins) to be used in making sodium channels... If I understand correctly? And so, since the genes keep making those subunits, does that mean new sodium channels are continuously being made with those proteins till you die? &#xA;In other words, if those genes suddenly stop making the subunits in your 50's or something, your sodium channels will disappear or stop working? (Probably unrealistic, but theoretically...)&lt;/p&gt;&#xA;" OwnerUserId="15416" LastActivityDate="2015-05-22T08:19:04.357" Title="Do sodium channels keep renewing themselves with new subunits made by genes?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31535" PostTypeId="2" ParentId="31533" CreationDate="2015-04-20T21:37:51.090" Score="1" Body="&lt;p&gt;You are asking about two different processes: turnover (degradation) of mRNA and turnover of proteins.  In a typical mammalian cell the mRNA half-lives of stable messages approach the length of the cell cycle (e.g. 24 hr). One mRNA could be translated around the clock if needed. The resulting proteins will also have a measurable half-life, and that will vary with the protein and the cellular conditions. If a cell ran out of protein and its mRNA there is often a feedback loop that activates transcription of the structural gene back in the nucleus.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-04-20T21:37:51.090" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31536" PostTypeId="1" AcceptedAnswerId="31537" CreationDate="2015-04-20T21:08:13.760" Score="11" ViewCount="7535" Body="&lt;p&gt;When I'm looking at an old CRT monitor or a worn fluorescent lamp, but not directly in the center of my gaze, the light from it seems to flicker. When I focus my gaze onto the monitor or lamp, the flickering stops.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why can I see a light flicker &lt;em&gt;only&lt;/em&gt; when it's in my peripheral vision?&lt;/p&gt;&#xA;" OwnerUserId="15433" OwnerDisplayName="Marc Dingena" LastEditorUserId="15433" LastEditDate="2015-04-21T10:53:46.837" LastActivityDate="2015-04-21T10:53:46.837" Title="Why can I see a light flicker when it's in my peripheral vision?" Tags="&lt;eyes&gt;&lt;vision&gt;&lt;light&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31537" PostTypeId="2" ParentId="31536" CreationDate="2015-04-20T21:15:10.843" Score="14" Body="&lt;p&gt;Your retina contains both rods and cones. Cones are color sensitive, slow, and concentrated near the center of your field of vision. Rods are &quot;light&quot; sensitive, fast, and concentrated near the periphery. You want to be able to respond quickly to a threat &quot;in the corner of your eye&quot; without needing to see the color of the threat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is nicely explained by this diagram (source: &lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/vision/imgvis/retina.gif&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://hyperphysics.phy-astr.gsu.edu/hbase/vision/imgvis/retina.gif&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gBWH5.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when you see a CRT in the corner of your eye, your rods respond quickly enough that you can tell the light of the CRT is flickering. As you turn your gaze towards it, you get the higher resolution, color rendition of the cones - and lose the temporal resolution.&lt;/p&gt;&#xA;" OwnerUserId="8668" OwnerDisplayName="Floris" LastEditorUserId="8668" LastEditDate="2015-04-21T00:30:43.867" LastActivityDate="2015-04-21T00:30:43.867" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31538" PostTypeId="2" ParentId="31512" CreationDate="2015-04-20T22:17:06.663" Score="1" Body="&lt;p&gt;Richard Dawkins discusses this in his book &lt;em&gt;The Greatest Show on Earth: The Evidence for Evolution&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bacteria and other microorganisms, specifically Archaea, are able to exchange in a sort of 'copy and paste' genetic exchange that differs wildly from sexual reproduction.  They can even exchange genes with other distantly related species.  This, coupled with their short (compared to Humans) lifecycle, accounts for much of the difference in evolutionary rates.  Often, it makes sense to speak in terms of evolution in terms of specific genes themselves (in the case of bacteria), as opposed to evolution of the species as a whole, due to the 'copy and paste' exchange that can take place.  For Bacteria, there is something to be said for compiling a 'true' family tree for each gene separately, regardless of which kind of bacteria in which it resides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dawkins remarks, &quot;The philosopher Dan Dennett has put it, 'Where the tree of life for animals is a majestically spreading oak, that for bacteria is more like a banyan.'&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, evolution by Natural Selection and random mutation does act on 'non-coding' DNA, just to be clear.  &lt;/p&gt;&#xA;" OwnerUserId="15097" LastActivityDate="2015-04-20T22:17:06.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31540" PostTypeId="1" CreationDate="2015-04-20T22:36:38.287" Score="-2" ViewCount="6688" Body="&lt;p&gt;Did cats evolve from monkeys? or vice versa?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How similar are the genes of cats and monkeys?&lt;br&gt;&#xA;What is the proof that they are related or that they are not related?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most monkeys climb in trees and there are other similarities but I could not find any evidence on the internet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do cats and monkeys have a common ancestor?&lt;/p&gt;&#xA;" OwnerUserId="15423" LastEditorUserId="49230" LastEditDate="2019-03-29T19:39:50.070" LastActivityDate="2019-03-30T21:57:21.690" Title="Did cats evolve from monkeys ? or vice versa?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;zoology&gt;&lt;phylogenetics&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="31541" PostTypeId="2" ParentId="31540" CreationDate="2015-04-20T22:47:29.540" Score="14" Body="&lt;p&gt;Cats and monkeys have a common ancestor, both are &lt;a href=&quot;https://en.wikipedia.org/wiki/Placentalia&quot;&gt;placental mammals&lt;/a&gt;, so at the very least they must have both evolved from the first placental mammal. Cats are members of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Laurasiatheria&quot;&gt;Laurasiatheria group&lt;/a&gt; and primates are members of &lt;a href=&quot;https://en.wikipedia.org/wiki/Euarchontoglires&quot;&gt;Euarchontoglires&lt;/a&gt;. These groups of mammals probably split off from each other about 100 millionish years ago. For more information about mammalian phylogeny, look &lt;a href=&quot;https://en.wikipedia.org/wiki/Mammal#Molecular_classification_of_placentals&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2015-04-20T22:47:29.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31542" PostTypeId="1" CreationDate="2015-04-21T00:07:31.867" Score="2" ViewCount="455" Body="&lt;p&gt;I have the following facts:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;It is possible to convert ATP &amp;lt;-&gt; creatine vice-versa. (&lt;a href=&quot;http://image.slidesharecdn.com/tang05-efficiencyregulationandalternatives-131016190320-phpapp02/95/tang-05-efficiency-regulation-and-alternatives-8-638.jpg?cb=1381968250&quot; rel=&quot;nofollow&quot;&gt;ref - non scientific&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;CP supplementation protects against metabolic syndrome. &lt;a href=&quot;http://jn.nutrition.org/content/141/10/1799.short&quot; rel=&quot;nofollow&quot;&gt;ref1&lt;/a&gt; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1388198114001735&quot; rel=&quot;nofollow&quot;&gt;ref2&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Fructose digestion depletes NADH via TG synthesis. &lt;a href=&quot;http://joe.endocrinology-journals.org/content/208/3/273.full&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I assume that CP supplementation regenerates not just ATP, but NADH, if it is depleted, and so it restores the redox balance in the liver. Both ATP and NADH are similar energy storing molecules, so I guess there is a biochemical pathway which converts ATP to NADH, or there is a pathway, which regenerates NADH using CP. Am I right, if so, which pathway is it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;note: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I might be wrong. From one of the references:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Taken together, this study provides direct evidence that creatine reduces lipid accumulation in hepatocytes by the stimulation of fatty acid oxidation and TG secretion.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So maybe ATP is enough to prevent TG accumulation in the liver.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2015-05-10T11:55:38.307" Title="Does creatine-phosphate (CP) supplementation regenerate NADH?" Tags="&lt;biochemistry&gt;&lt;physiology&gt;&lt;metabolism&gt;&lt;human-physiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31543" PostTypeId="1" CreationDate="2015-04-21T00:29:16.300" Score="3" ViewCount="3244" Body="&lt;p&gt;My PT teachers professes &lt;em&gt;working-out/training&lt;/em&gt; in early morning hours is the best time to do so. A quick search on &lt;a href=&quot;https://www.google.com/?gws_rd=ssl#q=benefits%20of%20morning%20walk&quot; rel=&quot;nofollow noreferrer&quot;&gt;benefits of morning walk&lt;/a&gt; (or similar phrases) reveals a lot of information which seem to be backed by sound scientific evidence. In fact it is common wisdom around the world, across all cultures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Okay - accepted. But why is it beneficial in first place? Because there is plenty of oxygen in the morning; &lt;em&gt;or is it?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After long hours of darkness (plants respirating at night) when first light comes plants would have just started photosynthesis, that too at a pretty slower rate (owing to lower intensity of light at dawn). In fact I remember having read something about compensation point&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The &lt;strong&gt;(light) compensation point&lt;/strong&gt; is the amount of light intensity on the light curve where the rate of photosynthesis exactly matches the rate of respiration. At this point, the uptake of CO2 through photosynthetic pathways is exactly matched to the respiratory release of carbon dioxide, and the uptake of O2 by respiration is exactly matched to the photosynthetic release of oxygen. &lt;sup&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Compensation_point&quot; rel=&quot;nofollow noreferrer&quot;&gt;SRC&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So now, obviously, we can establish the fact that concentration of oxygen &lt;em&gt;should be/is&lt;/em&gt; much lower than carbon-dioxide in early morning hours.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;So why morning walk or early morning exercises?&lt;/li&gt;&#xA;&lt;li&gt;If oxygen content is important why not exercise in early evening hours &lt;sub&gt;because not all people would like an endurance drill at &lt;em&gt;theoretically perfect&lt;/em&gt; time of noon :)&lt;/sub&gt;?&lt;/li&gt;&#xA;&lt;li&gt;Is there some other mechanism makes oxygen content more than carbon-dioxide content in the morning?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Personally - I do feel more fresh in the morning hours but maybe that is because of my internal biology, correct me if I am wrong.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;em&gt;P.S. I am not a biology student, so pardon my ignorance.&lt;/em&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="15318" LastEditorUserId="15318" LastEditDate="2017-04-25T06:44:49.267" LastActivityDate="2017-04-25T11:18:05.337" Title="Why *morning walk*?" Tags="&lt;photosynthesis&gt;&lt;respiration&gt;&lt;health&gt;" AnswerCount="5" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31544" PostTypeId="2" ParentId="31543" CreationDate="2015-04-21T01:32:27.613" Score="1" Body="&lt;p&gt;I am going to play the devil's advocate here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know if working out within the first three hours of waking is necessarily the &lt;em&gt;best&lt;/em&gt; time to do so. In the morning, we have what is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Cortisol_awakening_response&quot; rel=&quot;nofollow&quot;&gt;cortisol awakening response&lt;/a&gt; which is where the body releases cortisol. Cortisol is a by product of the sympathetic nervous nervous system. Dr.s James E. Muller, Geoffrey H. Tofler, and Richard L. Verrier in their article &lt;em&gt;Sympathetic Activity as the Cause of the Morning Increase in Cardiac Events&lt;/em&gt; said that early morning activity is a likely culprit but only circumstantial in sudden cardiac infarction [&lt;a href=&quot;http://circ.ahajournals.org/content/91/10/2508.full&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]. However, Dr.s Douglas P. Zipes and Hein J. J. Wellens in their article &lt;em&gt;Clinical Cardiology: New Frontiers Sudden Cardiac Death&lt;/em&gt; found that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Time of day is also important, with more sudden cardiac deaths, strokes, and myocardial infarctions occurring in the morning on arising from bed, perhaps related to increased sympathetic discharge in response to venous pooling that then triggers increased blood viscosity and platelet aggregation [&lt;a href=&quot;http://circ.ahajournals.org/content/98/21/2334.full&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In &lt;em&gt;Exercise and Acute Cardiovascular Events&lt;/em&gt; in Collaboration With the American College of Sports Medicine and Dr.s Paul D. Thompson, FAHA, Co-Chair; Barry A. Franklin, FAHA, Co-Chair; Gary J. Balady, FAHA, Steven N. Blair, PED, FAHA; Domenico Corrado, N.A. Mark Estes III, FAHA; Janet E. Fulton, Neil F. Gordon, William L. Haskell, FAHA, Mark S. Link, Barry J. Maron, Murray A. Mittleman, FAHA, Antonio Pelliccia, Nanette K. Wenger, FAHA, Stefan N. Willich, FAHA, and Fernando Costa, FAHA, felt they that didn't have enough data on claiming early morning exercises and sudden cardiac death (SCD); however, early morning SCD occurred in adults whereas for teens it SCD occurred in the afternoon [&lt;a href=&quot;http://circ.ahajournals.org/content/115/17/2358.full&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;] but &quot;vigorous exercise, however, transiently increases the risk of acute myocardial infarction (AMI) and SCD, even in exercise-conditioned individuals, and several strategies are recommended to potentially reduce this risk&quot;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Active individuals should know the nature of cardiac prodromal symptoms and seek prompt medical care if such symptoms develop.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That is, I wouldn't claim victory for working out as soon as you rise the best choice. However, I am not suggesting that you don't work out in the morning either but just be carefully about it. The best time to workout is the time that will allow you to be consistent, get in at least 30mins, and keep you motivated. If that time is the morning, just be aware of what is going on in the body.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Additional article found in support of afternoon/evening training&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Serendipitously, I stumbled across an article on swim performance and time. The article found that the best performance was afternoon to evening and not in the morning [&lt;a href=&quot;http://jap.physiology.org/content/102/2/641&quot; rel=&quot;nofollow&quot;&gt;4&lt;/a&gt;]. This was published in 2007 in the &lt;em&gt;Journal of Applied Physiology&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-05-09T17:34:56.430" LastActivityDate="2015-05-09T17:34:56.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31545" PostTypeId="2" ParentId="31540" CreationDate="2015-04-21T01:40:06.510" Score="13" Body="&lt;p&gt;&lt;strong&gt;&quot;Evolving from another species&quot; versus &quot;Most Recent Common Ancestor (MRCA)&quot;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One cannot say about two extant species that one evolved from the other. It just doesn't make any sense. It is not only true for cats and chimpanzees (just to pick one species of monkey) but it is true for any pair of extant species. One extant species has never evolved from another extant species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, one can say from any pair of species (Eventual exception with viruses but don't pay attention to them now) that they have a common ancestor. Again, it is not only true for cats and chimpanzees but also for yeasts and ants or for chestnut trees and reticulated pythons. The interesting question is always, &quot;when did the MRCA live?&quot; or if you prefer &quot;when was the time when the lineage that will one day yield to cat and chimpanzee was living?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do cats and monkeys have a common ancestor?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes! All life on earth shares a common ancestor. The question of interest is when did the Most Recent Common Ancestor lived between cats and monkeys lived?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please consider having a quick look to &lt;a href=&quot;https://biology.stackexchange.com/questions/52700/why-do-the-ancestors-of-birds-still-exist/52729#52729&quot;&gt;this post for an introduction to phylogenetics&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Chimpanzee and cats evolutionary relationships&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question has been answered by @user137. Cats and chimpanzee are both mammals. Their most recent common ancestor was therefore also a mammal and this most recent common ancestor lived about 100 million years ago. This is the kind of information you can get with DNA comparison.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How do we know that?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;@user137 already linked to an article that shows when the most common ancestor of cats and chimpanzee has lived. If you want, you can learn more about how such inferences can be made. As you like mathematics (I read from your profile), you might be not too scared (although it will take some time) of statistics and algorithmic to have a look at those Wikipedia articles:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Phylogenetics&quot; rel=&quot;nofollow noreferrer&quot;&gt;Phylogenetics&lt;/a&gt; - generality about phylogenetics (=the study of the evolutionary relationship between organisms)&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Computational_phylogenetics&quot; rel=&quot;nofollow noreferrer&quot;&gt;Computational phylogenetics&lt;/a&gt; - How to build a phylogenetic tree&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Molecular_clock&quot; rel=&quot;nofollow noreferrer&quot;&gt;Molecular clock&lt;/a&gt; - One method to estimate the length of the branches in a phylogenetic tree. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;To understand the stats, you may need first to follow a stats course, such as &lt;a href=&quot;https://www.khanacademy.org/math/probability&quot; rel=&quot;nofollow noreferrer&quot;&gt;this one&lt;/a&gt; from Khan Academy but again it will take some time. Of course, aside from the multitude of tools that one can use to infer time to MRCA from genetic data, one can also make an inference from phenotypic comparison although this method is generally much less accurate.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-29T18:02:41.490" LastActivityDate="2019-03-29T18:02:41.490" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="31546" PostTypeId="1" AcceptedAnswerId="31558" CreationDate="2015-04-21T02:18:50.787" Score="8" ViewCount="1068" Body="&lt;p&gt;Does anyone know of sources for learning bioinformatics, focused on genomics? I would like to learn alot of skills I could apply potently in the workforce if I ever became adept at the fields. My computer science knowledge is weak, and my biology knowledge is mediocre, but i find the topics to be interesting. I have read &quot;The dynamic Genome, A Darwinian Approach, by Fontdevila, and it was a bit rough for me. I have also read some of a introduction to genomics textbook, by Arthur M Lesk, and found it to be very &quot;Academic&quot;.&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="12909" LastEditDate="2015-04-21T03:36:14.813" LastActivityDate="2015-04-25T18:01:11.127" Title="Book/source for learning bioinformatics, focused on genomics?" Tags="&lt;bioinformatics&gt;&lt;book-recommendation&gt;&lt;literature&gt;" AnswerCount="5" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31547" PostTypeId="2" ParentId="31543" CreationDate="2015-04-21T02:31:55.717" Score="0" Body="&lt;p&gt;I would offer the counter point that this has to do with energy availability. (I'm on my phone so I can't put in references just yet). But there was just a great recent study published in Science (I'll go find it), in which a group looked at plaque deposition as a proxy of overall cardiovascular health of groups of mice exercised before and after food intake. They find that exercise under fasting conditions, which would be akin to morning running, appears to be significantly more protective against cadiovascular disease than exercise after feeding. This is also consistent with some human data suggestive of fasting exercise benefits as well. In a separate experiment the mice were fed the same number of calories per day, but those that were exercises after sleep and before eating were significantly leaner and had less plaque deposition in their vasculature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In part the idea is that after a period of fasting exercise will promote scavenging of residual cholesterols in the vasculature as well as cellular autophagy (which promotes &quot;fixing&quot; of current cells rather than just replacing them). To the layman, Resveratrol from red wine is probably the most commonly known way in which autophagy might be promoted. But in general think of periodic fasting and feasting as protective because it can help maintain metabolic homeostasis and prevent unnecessary cell turnover. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopeful that helps lead you in the right direction. Metabolics and aging is a huge and exciting field and this question could be answered with a small textbook. But you should at least understand that this field is far from being well understood. And that your PT teachers may end up being right, but this field still quite primitive, and this is not accepted yet or really understood by the scientific community.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastEditorUserId="14587" LastEditDate="2015-04-21T03:07:39.687" LastActivityDate="2015-04-21T03:07:39.687" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31549" PostTypeId="2" ParentId="31497" CreationDate="2015-04-21T03:31:12.387" Score="4" Body="&lt;p&gt;Yes you could live off a protein shake type supplement if it had the vitamins, minerals, protein, carbohydrates, and fats you would need. Would you want to? Probably not. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First thing we must determine is the protein whey or soy? If a male is consuming this meal replacement and the only protein is from soy, their estrogen levels will be elevated. In &lt;em&gt;Soy Protein Isolate Increases Urinary Estrogens and the Ratio of 2:16α-Hydroxyestrone in Men at High Risk of Prostate Cancer&lt;/em&gt;, Dr.s Jill M. Hamilton-Reeves, Salome A. Rebello, William Thomas, Joel W. Slaton, and Mindy S. Kurzer concluded that soy does elevated estrogen in men which helped with the reduction of prostate cancer [&lt;a href=&quot;http://jn.nutrition.org/content/137/10/2258.long&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;], but as a male, you wouldn't want to have a lifetime of increased estrogen [&lt;a href=&quot;http://www.healthline.com/health/high-estrogen&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Infertility. Estrogen is partly responsible for creating healthy&#xA;sperm. When estrogen levels are high, sperm levels in semen may fall.&#xA;This can lead to fertility issues.&lt;/li&gt;&#xA;&lt;li&gt;Gynecomastia. Estrogen may stimulate breast tissue growth. Men with&#xA;too much estrogen may start developing larger breasts.&lt;/li&gt;&#xA;&lt;li&gt;Erectile dysfunction. A balance of both testosterone and estrogen is&#xA;important for healthy sexual growth and development. Sexual function&#xA;may be impacted when these hormones become imbalanced. Men with high&#xA;levels of estrogen may have difficulty getting or maintaining an&#xA;erection.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So to be on the safe side, let's assume that the protein is from whey and we have one less thing to worry about. Now as for the vitamins and minerals, the Mayo Clinic states that [&lt;a href=&quot;http://www.mayoclinic.org/healthy-lifestyle/nutrition-and-healthy-eating/in-depth/supplements/art-20044894&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;]:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Supplements aren't intended to be a food substitute because they can't replicate all of the nutrients and benefits of whole foods, such as fruits and vegetables.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and there are three main differences:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Greater nutrition. Whole foods are complex, containing a variety of&#xA;the micronutrients your body needs — not just one. An orange, for&#xA;example, provides vitamin C plus some beta carotene, calcium and&#xA;other nutrients. It's likely these compounds work together to produce&#xA;their beneficial effect.&lt;/li&gt;&#xA;&lt;li&gt;Essential fiber. Whole foods, such as whole grains, fruits,&#xA;vegetables and legumes, provide dietary fiber. Most high-fiber foods&#xA;are also packed with other essential nutrients. Fiber, as part of a&#xA;healthy diet, can help prevent certain diseases, such as type 2&#xA;diabetes and heart disease, and it can also help manage constipation.&lt;/li&gt;&#xA;&lt;li&gt;Protective substances. Whole foods contain other substances important&#xA;for good health. Fruits and vegetables, for example, contain&#xA;naturally occurring substances called phytochemicals, which may help&#xA;protect you against cancer, heart disease, diabetes and high blood&#xA;pressure. Many are also good sources of antioxidants — substances&#xA;that slow down oxidation, a natural process that leads to cell and&#xA;tissue damage.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So you could live off of some meal replacement shake for the rest of your life but should you? Probably not.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="374" LastEditDate="2015-09-14T14:55:35.780" LastActivityDate="2015-09-14T14:55:35.780" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31551" PostTypeId="2" ParentId="31526" CreationDate="2015-04-21T03:52:07.993" Score="1" Body="&lt;p&gt;Actually, Cas9 system might be a possible method to achieve your aim in the future, research teams are trying to utilize cas9 in vivo, which means maybe someday we can doing some genetic modification in body cell precisely. However, this is only a future direction and we still can not say its fit for a knockout.(Patrick D. Hsu, Eric S. Lander, and Feng Zhang, (2014) Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell 14(6): 1262-1278)&#xA;And for editing some cell gene in a limited area, some research are on going for therapeutic purpose (Liqun Zhang et al.CFTR Delivery to 25% of Surface Epithelial Cells Restores Normal Rates of Mucus Transport to Human Cystic Fibrosis Airway Epithelium), but haven't seen research are trying to built KO cell in vivo.&lt;/p&gt;&#xA;" OwnerUserId="12879" LastActivityDate="2015-04-21T03:52:07.993" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31552" PostTypeId="2" ParentId="31546" CreationDate="2015-04-21T05:07:20.910" Score="5" Body="&lt;p&gt;Beginning Perl for Bioinformatics by Jim Tisdall &lt;a href=&quot;http://shop.oreilly.com&quot;&gt;http://shop.oreilly.com&lt;/a&gt; is quite good, in my opinion, and his sequel, Mastering Perl for Bioinformatics is also great. The focus is largely, but not exclusively genomics.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-04-21T05:07:20.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31553" PostTypeId="1" CreationDate="2015-04-21T06:02:34.900" Score="0" ViewCount="84" Body="&lt;p&gt;I am wondering if each cell in human body starts consuming ten percent more energy, how much food one has to consume compared to normal intake?&lt;/p&gt;&#xA;" OwnerUserId="6228" LastEditorUserId="3340" LastEditDate="2015-06-04T11:35:51.870" LastActivityDate="2015-06-04T11:35:51.870" Title="Cell energy consumption and food intake" Tags="&lt;metabolism&gt;&lt;food&gt;&lt;nutrition&gt;&lt;bioenergetics&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31554" PostTypeId="1" AcceptedAnswerId="31561" CreationDate="2015-04-21T06:33:02.907" Score="5" ViewCount="954" Body="&lt;p&gt;This may be trivia to many of you. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Textbook says the oxygen deficiency, even for a short while can injure our cells. Then why do people go for sports like swimming? (where rhythmic breathing is required yet, there's a practical possibility of holding the breath longer than usual inhale exhale process) I am looking for a reasoning from cellular biology/patho-physiology/respiration &lt;strong&gt;aspect.&lt;/strong&gt; And not because swimming or any other such exercise is anyone's choice/preference. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is: during sport like swimming, does the oxygen level in our blood drop below a critical level, that cells might suffer from lack of oxygen? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/q/755/8709&quot;&gt;Also found some relevant information here.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Currently referring to this online text : &lt;a href=&quot;http://www.amazon.com/gp/search?index=books&amp;amp;linkCode=qs&amp;amp;keywords=9780736031806&quot; rel=&quot;nofollow noreferrer&quot;&gt;Swimming Fastest: Physiological Responses to Exercise.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8709" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-04-21T10:32:57.870" Title="If oxygen deficiency is bad even for a short while, why do people swim?" Tags="&lt;cellular-respiration&gt;&lt;injury&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31555" PostTypeId="1" AcceptedAnswerId="31556" CreationDate="2015-04-21T06:39:39.483" Score="3" ViewCount="414" Body="&lt;p&gt;I have a mixture plasmids and undesired short linear fragments that share the same sequences. During denaturation and annealing, I would like the plasmids to 'find each other' before annealing to the shorter linear fragments. Assuming the concentration of shorter fragments is significant, is there a temperature profile to bias towards re-annealing of longer DNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More specifically, this is for a variation of the Surveyor Mutation detection assay, where re-annealed DNA with mismatches are digested, leaving non-mutant DNA intact. I would like to keep non-mutant plasmids for E. coli transformation. However, some linear fragments  ~10-50% of the length of the plasmid have escaped exonuclease treatment and would compete with the plasmids during annealing.&lt;/p&gt;&#xA;" OwnerUserId="15429" LastEditorUserId="15136" LastEditDate="2015-04-21T06:59:16.040" LastActivityDate="2015-04-21T06:59:16.040" Title="DNA length and annealing kinetics" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;pcr&gt;&lt;experimental-design&gt;&lt;enzyme-kinetics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31556" PostTypeId="2" ParentId="31555" CreationDate="2015-04-21T06:59:04.190" Score="1" Body="&lt;p&gt;Short answer is that higher temperature favors annealing of longer sequences. There are &lt;a href=&quot;http://www.entelechon.com/2008/08/dna-melting-temperature/&quot; rel=&quot;nofollow&quot;&gt;number of ways&lt;/a&gt; to calculate melting temperature, but all of them produce similar results: longer polymers require more thermal energy to melt. Hence, &lt;strong&gt;quick&lt;/strong&gt; cooling from higher (say, from 95C thermocycler can cool in &lt;a href=&quot;http://www.eppendorf.com/int/index.php?sitemap=2.1&amp;amp;action=products&amp;amp;contentid=1&amp;amp;catalognode=65631&quot; rel=&quot;nofollow&quot;&gt;10-12 sec&lt;/a&gt;) to RT/4C will favor re-annealing of circular strands. Slower cooling should allow more ssDNAs to bind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But again, if end goal is to select for circular dsDNA, simple transformation should take care of that.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-21T06:59:04.190" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31557" PostTypeId="1" AcceptedAnswerId="31584" CreationDate="2015-04-21T07:28:08.623" Score="1" ViewCount="175" Body="&lt;p&gt;Does protein-protein interaction only happens when one of them is basic and the other acidic? Do protein interactions also depend on the protein structure? Are there more factors?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="9943" LastEditDate="2015-04-22T02:08:14.520" LastActivityDate="2015-04-22T02:08:14.520" Title="What are the factors on which protein-protein interaction depend?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="0" ClosedDate="2015-04-23T05:27:33.567" ContentLicense="CC BY-SA 3.0" />
  <row Id="31558" PostTypeId="2" ParentId="31546" CreationDate="2015-04-21T07:33:33.250" Score="6" Body="&lt;p&gt;&lt;a href=&quot;http://unixandperl.com/&quot; rel=&quot;nofollow&quot;&gt;Unix and Perl to the Rescue&lt;/a&gt; by Keith Bradnam and Ian Korf is an excellent introductory book and guide for bioinformatics (Linux and Perl) in genomics. It includes exercises and starts with the very fundamentals. You will still need some basic understanding of genetics and biology though.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-04-21T20:29:56.880" LastActivityDate="2015-04-21T20:29:56.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31559" PostTypeId="2" ParentId="31546" CreationDate="2015-04-21T09:30:42.567" Score="3" Body="&lt;p&gt;Elementary Sequence Analysis by Brian Golding and Dick Morton is a good starter. Online resources can be found here:&lt;a href=&quot;http://helix.biology.mcmaster.ca/courses.html&quot; rel=&quot;nofollow&quot;&gt;http://helix.biology.mcmaster.ca/courses.html&lt;/a&gt; &#xA;Here's a great online tutorial for sequencing techniques, with introduction, examples and everything.&#xA;&lt;a href=&quot;http://bioinf.comav.upv.es/courses/sequence_analysis/sequencing_technologies.html&quot; rel=&quot;nofollow&quot;&gt;http://bioinf.comav.upv.es/courses/sequence_analysis/sequencing_technologies.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-21T13:17:35.767" LastActivityDate="2015-04-21T13:17:35.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31560" PostTypeId="1" CreationDate="2015-04-21T10:31:17.783" Score="6" ViewCount="1493" Body="&lt;p&gt;At the end of a day full of work, it is general for people that their eyelids start to feel heavy. Laziness takes over and  we begin to yawn. We all know that we're tired at that time, but why people get tired?&lt;/p&gt;&#xA;" OwnerUserId="8424" LastEditorUserId="14735" LastEditDate="2015-04-21T10:40:10.053" LastActivityDate="2015-05-28T21:21:10.987" Title="Why do we get tired" Tags="&lt;human-biology&gt;&lt;energy&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-05-29T13:53:02.907" ContentLicense="CC BY-SA 3.0" />
  <row Id="31561" PostTypeId="2" ParentId="31554" CreationDate="2015-04-21T10:32:57.870" Score="3" Body="&lt;p&gt;In &lt;a href=&quot;http://journal.publications.chestnet.org/data/Journals/CHEST/21396/181.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; paper the authors measured decrease of arterial blood oxygen saturation in healthy and patients with sleep apnae (this latter part is not really relevant only the measurements in healthy individuals). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RVxqY.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They found that fall of oxygen saturation depends on the initial saturation rate, but is not affected by the breath-holding time. As you can see on the graph at high initial saturation the fall rate per second is quite low. Here is the info in a table format:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/uCPDF.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At high initial saturation only mean 0.16% saturation drop occurs per second, thus in average a healthy individual looses 1% oxygen saturation approx every 5 seconds (I'd also like to note that the urge to breathe does not come from the lack of oxygen when holding breath, but from the accumulation of CO2). According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Oxygen_saturation_%28medicine%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt; normal oxygen saturation is between 100-95%, and only below 90% is considered hypoxemia /hypoxia (a medical condition where blood oxygen level is low). So if we look at the data in the table, it is safe to say that it takes approx 20s until the blood saturation level drops from 97% to 93% and another 5-6 seconds until it drops to 90% (with approx 0.5% saturation loss per sec at 93% initial saturation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;People who are conditioned by exercise have larger vital-capacity (they can breathe more air in for a single breath), thus have means to acquire more oxygen can compensate for the excess use of oxygen. During heavy sport activity like swimming it is unlikely that anybody will hold his/her breath for several tens of seconds.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-04-21T10:32:57.870" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31562" PostTypeId="2" ParentId="31546" CreationDate="2015-04-21T13:47:41.000" Score="3" Body="&lt;p&gt;While not a book per se, the edX Lifesciences course has been really useful for me, it does a great job of covering the entire pipeline of genome analysis that one would need to use. The link containing all 8 classes is here, scroll down a bit and you can see links to all of the classes in this module:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://courses.edx.org/courses/HarvardX/PH525.3x/1T2015/dffde833663e4f71ab64246ebe5598d1/&quot; rel=&quot;nofollow&quot;&gt;https://courses.edx.org/courses/HarvardX/PH525.3x/1T2015/dffde833663e4f71ab64246ebe5598d1/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-04-21T13:47:41.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31563" PostTypeId="2" ParentId="31543" CreationDate="2015-04-21T15:04:07.037" Score="0" Body="&lt;p&gt;If walking in the morning is truly more beneficial than walking at a different, it certainly wouldn't be related to atmospheric oxygen content. The oxygen content of the atmosphere fluctuates on the timescale of &lt;a href=&quot;http://scrippso2.ucsd.edu/&quot; rel=&quot;nofollow&quot;&gt;years&lt;/a&gt;, not hours. And keep in mind that when it's morning where you are currently, it's going to be noon somewhere else, and dusk somewhere else. &lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-04-21T15:04:07.037" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31564" PostTypeId="2" ParentId="31425" CreationDate="2015-04-21T15:24:10.030" Score="1" Body="&lt;p&gt;Yes, it has very much to do with the poliploidy events. Specifically if you look at the grasses, most grasses that are diploid (eg., AA, BB), cannot hybridize, but in some rare events when they form polyploid (AAAA, BBBB), they can readily hybridize to form fertile progenies (AABB). &lt;/p&gt;&#xA;" OwnerUserId="1648" LastActivityDate="2015-04-21T15:24:10.030" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31565" PostTypeId="1" AcceptedAnswerId="31571" CreationDate="2015-04-21T15:57:01.533" Score="2" ViewCount="644" Body="&lt;p&gt;Thomas Hunt Morgan was a pioneer in genetics and proposed the now false model of genes being &quot;beads&quot; on a string. These beads being indivisible and responsible for a single phenotype, if I understand correctly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know of a good, reputable source of information on this theory that would be sufficient to use as a citation? I would use wikipedia, but it is disallowed. &lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="5144" LastEditDate="2015-04-21T16:00:22.310" LastActivityDate="2015-04-21T16:56:56.607" Title="&quot;bead&quot; on a string theory of genetics, source?" Tags="&lt;genetics&gt;&lt;gene&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31566" PostTypeId="1" AcceptedAnswerId="31673" CreationDate="2015-04-21T16:01:27.720" Score="6" ViewCount="4889" Body="&lt;p&gt;Thoughout life everyone tells you that brain is essentially a computer but just like computers your brain would create immense amounts of heat by being in use, so if that's the case how does it cool down.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is like liquid cooling where the blood transfers the heat away? and if so what is the critical temperature when your blood can no longer cool your brain? Also at what temperature are you at risk of brain damage?&lt;/p&gt;&#xA;" OwnerUserId="15436" LastEditorUserId="14826" LastEditDate="2015-04-21T20:40:43.880" LastActivityDate="2015-04-24T04:16:21.600" Title="How does the brain cool itself?" Tags="&lt;brain&gt;&lt;blood-circulation&gt;&lt;temperature&gt;&lt;homeostasis&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31567" PostTypeId="1" AcceptedAnswerId="31569" CreationDate="2015-04-21T16:29:52.453" Score="2" ViewCount="2219" Body="&lt;p&gt;In my experience, clementines have been significantly easier to peel by hand than and orange.  The skin of the orange seems to cling to the rest of the orange much more so than the skin of the clementine does.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What causes this?  &lt;a href=&quot;http://en.wikipedia.org/wiki/Clementine&quot; rel=&quot;nofollow&quot;&gt;Wikipedia (Clementine)&lt;/a&gt; merely mentions that they are easy to peel, but leaves it there. What is different between the way the skins are attached?&lt;/p&gt;&#xA;" OwnerUserId="15437" LastEditorUserId="15437" LastEditDate="2015-04-22T12:29:35.817" LastActivityDate="2015-04-22T12:29:35.817" Title="Why are clementines easier to peel than oranges?" Tags="&lt;fruit&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31569" PostTypeId="2" ParentId="31567" CreationDate="2015-04-21T16:45:15.663" Score="1" Body="&lt;p&gt;I think it all comes down to the thickness of the skin and how it's attached to the fruit itself.  For me, it depends on the variety of oranges and/or clementines, mandarins, etc. that I'm peeling.  Usually fruits with thick, hard skin are easier to peel whereas fruits with softer more delicate skin are harder to peel off in one piece.  Factors like growth climate and ripeness effect the skin quality. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you roll the fruit on a hard surface under your palm before peeling, it makes the skin easier to peel off in one piece. &lt;/p&gt;&#xA;" OwnerUserId="15097" LastActivityDate="2015-04-21T16:45:15.663" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31571" PostTypeId="2" ParentId="31565" CreationDate="2015-04-21T16:56:56.607" Score="3" Body="&lt;p&gt;If the Cold Spring Harbor Laboratory is considered a reputable source (it should be), you can check out their &lt;a href=&quot;http://www.dnalc.org/view/15881-Defining-the-gene.html&quot; rel=&quot;nofollow&quot;&gt;Defining the gene&lt;/a&gt; page which has an overview of the beads-on-a-string theory, and how it was disproved by Seymour Benzer. You could also try to find &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/13293416&quot; rel=&quot;nofollow&quot;&gt;Benzer's original paper&lt;/a&gt;, although it doesnt seem to be available online.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Related and possibly helpful:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.dnalc.org/view/16023-Seymour-Benzer-1954.html&quot; rel=&quot;nofollow&quot;&gt;Benzer's page&lt;/a&gt; on Cold Spring Harbor website&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://symposium.cshlp.org/content/24/15.extract&quot; rel=&quot;nofollow&quot;&gt;Evolution of Genes and Genes in Evolution&lt;/a&gt; - very interesting paper from 1959 on genes/genetics, look on the fourth page (marked 18) for the bead-on-string theory&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-04-21T16:56:56.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31572" PostTypeId="1" CreationDate="2015-04-21T17:24:32.767" Score="5" ViewCount="584" Body="&lt;p&gt;Over the last week or so as warmer weather has arrived, I've noticed small insects crawling around in the bathroom. I'm located in western Europe. They are perhaps 1mm in length, quite difficult to see without a magnifying glass. I used a macro lens to capture these pictures. What might they be? Ticks? Aren't ticks larger? Why are there so many?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: these pictures are &lt;strong&gt;heavily magnified&lt;/strong&gt; (they are on an old wooden door with cracking paint), and I've applied lighting auto correction. Actual size of each insect is 1mm or less.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OSECZ.jpg&quot; alt=&quot;Macro lens on highest magnification&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/O31zo.jpg&quot; alt=&quot;Lower magnification, group of insects&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0qTe4.jpg&quot; alt=&quot;Sheet of toilet paper for reference&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lV56U.jpg&quot; alt=&quot;With natural lighting&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="15440" LastEditorUserId="15440" LastEditDate="2015-04-21T19:46:21.307" LastActivityDate="2015-04-21T22:05:29.480" Title="Help me identify this insect" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31573" PostTypeId="2" ParentId="16854" CreationDate="2015-04-21T18:41:19.433" Score="6" Body="&lt;p&gt;Nitrogen is much less reactive than oxygen.  Indeed, if I haven't totally forgotten my long-ago chemistry courses, most chemical reactions involving N2 are energy-consuming.  Thus you get nitrogen compounds produced by lightning, in auto engines, and other places where there's a lot of energy to spare.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oxygen reactions, OTOH, are energy-producing.  You might think instead of fire: most organic stuff will burn (if dried), but it only combines with the oxygen in the air, not the nitrogen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: Indeed, many nitrogen compounds take so much energy to create that they are explosives.  Ammonium nitrate, nitroglycerin, trinitrotolulene (TNT), even the potassium nitrate (saltpeter) used to make gunpowder.&lt;/p&gt;&#xA;" OwnerUserId="11736" LastEditorUserId="11736" LastEditDate="2015-04-22T05:02:49.140" LastActivityDate="2015-04-22T05:02:49.140" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31574" PostTypeId="1" AcceptedAnswerId="31579" CreationDate="2015-04-21T19:20:40.823" Score="3" ViewCount="1042" Body="&lt;p&gt;Kiwis have the enzyme actinidain. This enzyme will break the peptide bonds from the gelatin. Making gelatin with raw kiwis will not work, because the peptide bonds in the gelatin will be broken down. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what if you would make plain gelatin, and apply raw kiwis to it? Do the enzymes break down the gelatin when the gelatin already has set?&lt;/p&gt;&#xA;" OwnerUserId="15055" LastEditorUserId="15055" LastEditDate="2015-04-21T19:32:16.487" LastActivityDate="2015-04-21T22:10:04.593" Title="Applying kiwis on gelatin" Tags="&lt;biochemistry&gt;&lt;enzymes&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31575" PostTypeId="1" AcceptedAnswerId="31608" CreationDate="2015-04-21T19:37:11.587" Score="4" ViewCount="666" Body="&lt;p&gt;Why do spiders make their webs near the ceiling and near light sources ? &#xA;Is their an advantage for spiders in doing that? For example do they catch more insects when their web is near a light source because prey insects are drawn to it, hence giving those spiders with a well-lit web a better chance of survival? &lt;/p&gt;&#xA;" OwnerUserId="15442" LastEditorUserId="9943" LastEditDate="2015-04-22T03:55:11.777" LastActivityDate="2015-04-22T17:10:04.793" Title="Why do spiders make their web near the ceiling and near a light source?" Tags="&lt;evolution&gt;&lt;predation&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31576" PostTypeId="1" AcceptedAnswerId="31577" CreationDate="2015-04-21T20:28:44.683" Score="5" ViewCount="120" Body="&lt;p&gt;I was outside today thinking how nice it was to hear the birds back from winter when I started thinking about the fact that we like bird song.  It makes us happy in a very basic level, the sort of level that usually implies subtle evolved instincts.  Thus I started wondering, &lt;em&gt;why&lt;/em&gt; do humans all over the world naturally love the sound of birds?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The simplest explanation that came to my mind was because birds supposedly will flee or be quite when predators are around.  Thus the presence of birds singing may indirectly mean a lower chance of predation.  In other words it's less that were happy when birds are singing, as that were a little more on edge when they aren't singing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, that seems almost too easy an explanation.  Has anyone more intelligent then a random computer geek who's just happy to be away from the computer for a few hours put any more effort into considering this?  What is the generally accepted hypothesis?&lt;/p&gt;&#xA;" OwnerUserId="9788" LastEditorUserId="6061" LastEditDate="2015-04-21T22:55:48.017" LastActivityDate="2015-04-22T16:59:44.000" Title="Do we instinctially interpret birdsongs as a sign that there are no predators present?" Tags="&lt;evolution&gt;&lt;instinct&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31577" PostTypeId="2" ParentId="31576" CreationDate="2015-04-21T20:43:29.193" Score="2" Body="&lt;p&gt;Crows and gulls would probably also flee predators but their songs are definitely not really pleasant to listen to! I know it, they woke me up last week-end $\ddot \smile$. The canadian goose or the common starling (see &lt;a href=&quot;https://www.youtube.com/watch?v=Y2pjUlp2Cy0&amp;amp;spfreload=10&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;) are other examples of not really pleasant songs.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Too a selectionist view of evolutionary processes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important not to make the mistake to see anything as an adaptation (a result of natural selection only). Evolution is way more than natural selection and it encompasses tons of stochastic processes. &lt;a href=&quot;https://biology.stackexchange.com/questions/21772/why-dont-mammals-have-more-than-4-limbs/21776#21776&quot;&gt;This answer&lt;/a&gt; has a paragraph on the subject of not thinking of anything as a result of natural selection. This kind of over-consideration of adaptive processes in evolution is a common mistake especially when thinking about how human behaviour evolved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Evolutionary psychology and evolution of appreciation of bird songs&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The field of &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionary_psychology&quot; rel=&quot;nofollow noreferrer&quot;&gt;evolutionary psychology&lt;/a&gt; may interest you but note that it is a field that is sometimes still at the limit between psychology, philosophy and biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Appreciation of art as a by-product&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Appreciation of art (like birds songs) and beauty is a pretty poorly understood subject yet. The first hypotheses came from Darwin and Gould. They pretty much argued that we enjoy sex, grasp facial expressions (&lt;a href=&quot;http://en.wikipedia.org/wiki/Kin_recognition&quot; rel=&quot;nofollow noreferrer&quot;&gt;kin recognition&lt;/a&gt;), have to like logical proof to appreciate learning and acquire language, efficient communication (&lt;a href=&quot;http://en.wikipedia.org/wiki/Cooperative_hunting&quot; rel=&quot;nofollow noreferrer&quot;&gt;cooperative hunting&lt;/a&gt;), appreciate put oneself into others thoughts (&lt;a href=&quot;http://en.wikipedia.org/wiki/Machiavellian_intelligence&quot; rel=&quot;nofollow noreferrer&quot;&gt;Machiavellian intelligence&lt;/a&gt;),  etc... As a result of those selection pressure, we may have evolved, so-called by-products. A by-product is a phenotypic trait that hasn't been directly selected for but that has been  selected via its correlation to some other phenotypic trait that is under positive selection and that is correlated. If this is true, then there would have a correlation between cognitive abilities and art appreciation and therefore a correlation between art appreciation and fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Appreciation of art due to sexual selection&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some have argued that looking at the importance of art appreciation and intelligence in today's mate choice, it is likely that art appreciation may have been reinforced by sexual selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Either sexual selection may have reinforced a trait that was correlated to fitness (&quot;evolution of appreciation of art as a by-product&quot; hypothesis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also possible that sexual selection may have selected for art appreciation without art appreciation being correlated with fitness but just because it asks for a big brain and lots of energy (brains consumes lots of energy) and being able to appreciate arts means that the individual has extra-energy to spare and is therefore very fit (&lt;a href=&quot;http://en.wikipedia.org/wiki/Handicap_principle&quot; rel=&quot;nofollow noreferrer&quot;&gt;handicap principle&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-04-22T16:59:44.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31578" PostTypeId="2" ParentId="31572" CreationDate="2015-04-21T20:59:41.277" Score="6" Body="&lt;p&gt;After a long hunt it seems they are Dermanyssus gallinae. It appears I have a pigeon's nest somewhere near my building.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Dermanyssus_gallinae&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Dermanyssus_gallinae&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gzRjo.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="15440" LastEditorUserId="10456" LastEditDate="2015-04-21T22:05:29.480" LastActivityDate="2015-04-21T22:05:29.480" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31579" PostTypeId="2" ParentId="31574" CreationDate="2015-04-21T22:10:04.593" Score="2" Body="&lt;p&gt;According to the (non peer reviewed) scientific experiment &lt;a href=&quot;https://spa-chemistry.wikispaces.com/Proteolytic+Enzymes?responseToken=03967f85382a80e22a6873fdd182d2463&quot; rel=&quot;nofollow&quot;&gt;found here&lt;/a&gt;, simply placing a piece of kiwi onto gelatin that has set will cause the gelatin to be hydrolysed by actinidain. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This experiment aims to show the effects of Proteolytic enzymes on proteins and, subsequently, the effects of extreme temperatures on the proteins themselves. Petri dishes filled with gelatin, a derivative of collagen, were acted upon by kiwifruit samples overnight. Some samples were fresh and used as controls; others had been frozen or boiled for two, four, six, eight or ten minutes. The mass of digested gelatin was taken the next day. The results ultimately reflect the effectiveness of the actinidin, the kiwi’s Proteolytic enzyme, under normal conditions and after exposure to extreme temperatures. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-04-21T22:10:04.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31582" PostTypeId="2" ParentId="19850" CreationDate="2015-04-21T23:32:50.940" Score="8" Body="&lt;p&gt;A paper was just published that explains this phenomenon in PLOS One, found &lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119470&quot;&gt;here&lt;/a&gt;. It looks like the sound is caused by the formation of a gas cavity in synovial fluid of the joints. They do mention that contrary to what is stated in the most upvoted answer here, the sound does not come from the collapse of the bubble, but rather its formation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And in response to the comments, as mentioned in the paper, this does not seem to cause any harm to the meniscus or surrounding tissue. &lt;/p&gt;&#xA;" OwnerUserId="14587" LastEditorUserId="14587" LastEditDate="2015-04-21T23:38:01.937" LastActivityDate="2015-04-21T23:38:01.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31583" PostTypeId="2" ParentId="31430" CreationDate="2015-04-21T23:38:36.360" Score="4" Body="&lt;p&gt;As an elaboration of my comment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Summary: &lt;strong&gt;Replication is required in GWAS studies to account for non-random technical biases.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of such bias is, for example, a chip used for genotyping giving consistently incorrect genotypes for a locus. In this situation adding more subjects will not correct for this effect and therefore the only solution is to genotype additional subjects with another method (e.g. another chip or experimental protocol). Another source of non-random technical bias is at the phenotype measurement level. You might want, if possible, to measure the phenotype using other techniques to make sure that bias will be corrected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A replication cohort does not need to be huge and the actual size needed will largely depend on the effect size of the SNP seen in the discovery cohort. A &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Statistical_power&quot; rel=&quot;nofollow&quot;&gt;power-to-detect&lt;/a&gt;&quot; calculation would help in predicting the cohort size needed. For a SNP to be significant, it must pass Bonferroni correction but as you can run a statistical test at the candidate site only the correction will be usually not very astringent (i.e. you might run association tests on &quot;only&quot; a few dozens or hundreds SNPs).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Historically GWAS replication was also required to correct for population structure but as the tools evolved substantially (e.g. the use of principal component analysis) and the cohort sizes are now substantially bigger compared to the first GWA-studies, this is less a concern. What was required is to sample independently other subjects from either the same or a different population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For your situation what you could do is to split your cohort into a discovery and a replication panel, genotype your subject in the replication panel using an independent technique, eventually do the same with the phenotyping and replicate you candidate SNPs. The replication panel needed is usually must smaller than the discovery cohort for the reasons stated in the previous paragraph.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For your last question about the meta-analysis. Yes this could also be a way to go but be careful that you will still need a replication cohort to validate SNPs found this way therefore resulting in the exact same problematic you described. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this help!&lt;/p&gt;&#xA;" OwnerUserId="14826" LastActivityDate="2015-04-21T23:38:36.360" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31584" PostTypeId="2" ParentId="31557" CreationDate="2015-04-21T23:51:22.330" Score="2" Body="&lt;p&gt;It depends both on structure and charge. Binding sites of proteins are essentially formed by amino acids placed in a particular conformations such that it will match the binding site of their counterpart protein or substrate. This is commonly referred to as the lock and key model of protein binding. This is similar to how two puzzle pieces fit together, the pieces are exactly the same shape at the point at which the puzzle pieces connect. At a protein binding site amino acids are clustered together to form the matching shape to the appropriate binding partner. This however is not just dictated by 'physical shape' of each amino acid but also their charges. This is important because negatively charged amino acids will repel other negatively charged amino acids, and attract to positive amino acids, thereby modulating the exact 'shape' of the protein binding site. &lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-04-21T23:51:22.330" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31585" PostTypeId="1" CreationDate="2015-04-22T00:54:35.430" Score="4" ViewCount="7624" Body="&lt;p&gt;I read that mutations are more likely to occur on &quot;the strand that DNA polymerase replicates discontinuously&quot;. Does DNA polymerase always replicate the same strand discontinuously and, if so, how/why?&lt;/p&gt;&#xA;" OwnerUserId="15448" LastEditorUserId="6307" LastEditDate="2017-05-20T05:29:58.850" LastActivityDate="2017-05-20T05:29:58.850" Title="Does DNA polymerase always go the same direction?" Tags="&lt;dna&gt;&lt;dna-replication&gt;&lt;polymerase&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31588" PostTypeId="1" CreationDate="2015-04-22T02:48:48.907" Score="2" ViewCount="96" Body="&lt;p&gt;We have a GFP mutant that displays a different excitation spectra with emission at 510nm than the WT. However, their emission profiles with excitation at 490nm are the same, and we do not observe the same trend. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We're confused as to what might be happening.&lt;/p&gt;&#xA;" OwnerUserId="15449" LastActivityDate="2015-04-22T05:36:15.327" Title="What does it mean when a protein has a different excitation spectra than wildtype, but the same emission spectra?" Tags="&lt;biochemistry&gt;&lt;green-fluorescent-protein&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31589" PostTypeId="2" ParentId="31588" CreationDate="2015-04-22T05:36:15.327" Score="1" Body="&lt;p&gt;Let me start from short description of fluorescence (since we talk about it here).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fluorescence is &lt;em&gt;one&lt;/em&gt; of the processes through which excited molecule can relax, lose its excessive energy. That is, quantum interaction between atoms in molecule (organic dye or complex GFP) create permitted energy levels. There is &quot;ground state&quot; $S_0$, for example, and excited state $S_1$. You &quot;pump&quot; your molecule with excitation light from $S_0$ to $S_1$. All this can be nicely illustrated as absorption in Jablonski diagram (look at &lt;em&gt;a&lt;/em&gt; for now):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ltULk.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;via &lt;a href=&quot;http://micro.magnet.fsu.edu/primer/java/jablonski/lightandcolor/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://micro.magnet.fsu.edu/&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Loss of energy&quot; here is some process via which molecule returns to ground state. In case of GFP energy is released as an emission photon. Nature of fluorophores is that they tend to return to ground state as the state of less energy, and almost all systems tends to go to state with lesser energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, to your question. Why GFP can has different excitation profile but same emission? Notice, how in (a) molecule get pumped to highest state, then relaxes a bit to lowest of $S_1$ states and then go all the way to $S_0$? That initial relaxation is thermal relaxation. Some energy is lost, essentially, to water molecules around GFP. That is why emission is always &quot;more red&quot;, i.e. has lower energy than excitation. Initial relaxation is why your GFP spectra also broad. There are many levels GFP can emit from, as well as be excited to. In crystals of GFP transitions will be very narrow, because much less of excitation energy will go not into fluorescence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, my point is following. Nobody prevents one from engineering a mutant molecule of GFP that could be pumped to some even higher level $S_2$, which then relaxes to $S_1$ via non-irradiative process (e.g. gives energy to water, but not into fluorescence!). Only requirement is that for mutant direct pathway from $S_0$ to $S_1$ would be forbidden (see &lt;em&gt;b&lt;/em&gt; and &lt;em&gt;c&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another point is that whether your spectra are different in shape or only intensity. Different shape of spectra means there are differences in those levels and transitions.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-22T05:36:15.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31590" PostTypeId="2" ParentId="31585" CreationDate="2015-04-22T05:41:08.987" Score="5" Body="&lt;h3&gt;Summary:&lt;/h3&gt;&#xA;&lt;p&gt;In bacteria or organisms with only one well defined replication origin and a circular chromosome, yes for a given DNA region the same strand is replicated discontinuously.&lt;/p&gt;&#xA;&lt;p&gt;In high order animals, which replicate chromosomes using several origins of replication (&lt;em&gt;ori&lt;/em&gt;), this is less clear as the way &lt;em&gt;ori&lt;/em&gt; are recognized is still not fully understood but seems to involve DNA structure. Chromatin structure is dynamic which means &lt;em&gt;ori&lt;/em&gt; are also likely dynamic which results in defined regions of the DNA not likely to always be replicated discontinuously from a well defined strand (i.e. DNA replication might not always start at the exact same sites).&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;First off, as you probably know, DNA is always transcribed in a 5' to 3' direction. The why is nicely answered in this &lt;a href=&quot;https://biology.stackexchange.com/questions/477/why-is-dna-replication-performed-in-the-5-to-3-direction&quot;&gt;post&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;DNA replication forks start at replication origins. &lt;a href=&quot;http://en.wikipedia.org/wiki/Origin_of_replication&quot; rel=&quot;nofollow noreferrer&quot;&gt;Replication origins&lt;/a&gt; are recognized by &lt;a href=&quot;http://en.wikipedia.org/wiki/Origin_recognition_complex&quot; rel=&quot;nofollow noreferrer&quot;&gt;origin recognition complexes&lt;/a&gt;. The way DNA replication occurs is by having two DNA polymerase complexes traveling in opposite direction (i.e. two bidirectional replication forks) from the origin as shown in the following &lt;a href=&quot;http://www.mun.ca/biology/scarr/iGen3_03-09.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;schema&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8DCKu.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;This means that given constant origins of replication in an organism (like bacteria which usually only have only a single origin of replication) and given the DNA is replicated in a 5'-3' direction, same strands will be replicated discontinuously from the origin (i.e. in the schema, the bottom one on the left and the top one on the right). A global view of the replication at the chromosome level in bacteria is shown &lt;a href=&quot;http://oregonstate.edu/instruction/bi314/summer09/Fig-06-12.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;here below&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Iq2dj.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Now for more complex organisms&lt;/strong&gt;, the origin of replication is not a single site but rather multiple ones across chromosomes (30'000-50'000 &lt;em&gt;ori&lt;/em&gt; in humans). Where does DNA replication starts exactly, this is still not fully understood. DNA sequence is likely to play a role but no highly conserved consensus sequences were found and it is believed that origins of replication are linked to the structure of the DNA instead. In essence the chromatin structure is what seems to dictate where DNA replication starts and as the chromatin structure is dynamic within a cell, it is likely that origins of replication are also dynamic therefore making the identification of the discontinuously replicated strands very difficult &lt;a href=&quot;http://www.nature.com/nrm/journal/v11/n10/full/nrm2976.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Méchali M, 2010)&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Finally if you wonder what happens when two replication forks collide, well the answer is simple, replication stops and the two DNA polymerase complexes leave the DNA.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-22T05:46:39.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31591" PostTypeId="1" AcceptedAnswerId="31592" CreationDate="2015-04-22T06:18:44.067" Score="18" ViewCount="4015" Body="&lt;p&gt;My daughter is 5 and wants to learn about Biology. I thought a great start is to see life from pond water through a USB microscope. It would be great if she could see organisms like &lt;a href=&quot;http://www.microscope-microscope.org/applications/pond-critters/pond-critters.htm&quot;&gt;amoebas, flagellates and ciliates&lt;/a&gt; with her own eyes. The microscopes I have seen typically have a zoom range of about 40 to 400x. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would this range be sufficient to see microscopic pond life? &lt;/p&gt;&#xA;" OwnerUserId="15450" LastEditorUserId="9943" LastEditDate="2015-04-22T06:32:07.317" LastActivityDate="2020-11-20T05:51:02.050" Title="What is the magnification necessary to see pond life" Tags="&lt;microscopy&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31592" PostTypeId="2" ParentId="31591" CreationDate="2015-04-22T06:30:23.870" Score="13" Body="&lt;p&gt;&lt;strong&gt;2019-05-01 Edited: Updated dead links&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the comment section:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would go with a cheap one with a magnification of ~40X. According to &lt;a href=&quot;https://www.ebiomedia.com/protozoans-and-algae.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this source&lt;/a&gt;, 10-20X is already sufficient to see large protozoans and algae in a pond. &lt;a href=&quot;https://www.toptenreviews.com/home/articles/top-10-things-to-see-with-your-first-microscope/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; some suggestions on what you could look at.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2019-05-02T06:14:23.413" LastActivityDate="2019-05-02T06:14:23.413" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="31594" PostTypeId="2" ParentId="29867" CreationDate="2015-04-22T08:49:23.210" Score="2" Body="&lt;p&gt;Yes, these devices and treatment programs are being actively developed. General idea is that epileptic episode follows certain path within the brain. It can start in thalamus, after which sporadic activity spreads into cortical areas, for example motor cortex. There is a number of papers on prediction of epileptic seizure, e.g. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3237404/&quot; rel=&quot;nofollow&quot;&gt;Seizure Prediction and its Applications&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The device then will detect initiation of seizure before evident symptoms and provide inhibition via cortical electrodes, microelectrode array (MEA). It seems that currently MEAs are used more for research (&lt;a href=&quot;http://www.hopkinsmedicine.org/news/publications/neuronow/neuronow_spring_2012/for_epilepsy_a_microelectrode_array_with_big_promise&quot; rel=&quot;nofollow&quot;&gt;recording from tens of neurons&lt;/a&gt;), but single electrodes are useful for actual control of epilepsy. Also one can control vagus nerve, which causes parasympathetic response (general inhibition, aka &quot;rest-and-digest&quot;). More you can read &lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/epilepsy/diagnosis-treatment/treatment/txc-20117241&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Transcranial magnetic stimulation, as I understand, is not portable enough to be useful. &lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14735" LastEditDate="2015-04-22T08:55:09.583" LastActivityDate="2015-04-22T08:55:09.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31597" PostTypeId="1" CreationDate="2015-04-22T09:22:49.293" Score="4" ViewCount="1304" Body="&lt;p&gt;We inserted GFP-gene into plasmid Bluescript SK+, transformed E. coli with this construct, and then plated on an agar plate with Ampicillin and X-gal to do a blue/white screening. We got blue colonies and white colonies, and normally the white colonies are considered positive for the insert and the blue ones are negative for the insert.&#xA;The problem is that the results we got are actually the opposite. If we look at the plate under UV-light, we see that ALL the blue colonies are fluorescent, which means they actually produce the GFP, and ALL the white ones are not!! How would you explain this??&#xA;Thank you&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: i thought that maybe the insert could be in frame with lacz', so we get fusion proteins. However this doesn't explain why we got white colonies which are not fluorescent&lt;/p&gt;&#xA;" OwnerUserId="5686" LastEditorUserId="5686" LastEditDate="2015-04-22T12:07:31.173" LastActivityDate="2015-04-22T12:07:31.173" Title="blue/white screening - results are opposite as expected" Tags="&lt;molecular-biology&gt;&lt;plasmids&gt;&lt;transformation&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31598" PostTypeId="2" ParentId="31597" CreationDate="2015-04-22T11:35:08.520" Score="1" Body="&lt;p&gt;Given the fact that the negative control uncut plasmids are producing white colonies, it seems that there have been significant mutations within the lacZ gene in the plasmid, causing the uncut plasmids to become white due to inactivation of the gene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would suggest purchasing a new batch of pBluescript, or if that is not possible for whatever reason, perform a miniprep on one of the blue colonies and sequence its multiple cloning site to verify that the MCS is present and not mutated before continuing. If you are not going to buy a new batch of plasmids, it would also be prudent to verify the plasmid's length using gel electrophoresis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most likely explanation is that the plasmids are mutated, and therefore you are getting bad results in the blue/white screen.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-04-22T11:35:08.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31599" PostTypeId="1" CreationDate="2015-04-22T13:57:45.863" Score="5" ViewCount="112" Body="&lt;p&gt;Can their be a kind of chemical reaction pathway in a cell, that is catalyzed or regulated but NOT necessarily by enzymes? I could not find anything on Google.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have almost no background in biology, and am only studying certain topics from a mathematical perspective.&lt;/p&gt;&#xA;" OwnerUserId="15454" LastEditorUserId="14552" LastEditDate="2015-04-22T15:03:51.983" LastActivityDate="2015-04-23T14:08:42.353" Title="Do non-enzyme catalysed reaction pathways exist?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;enzymes&gt;&lt;pathway&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31600" PostTypeId="2" ParentId="29867" CreationDate="2015-04-22T14:05:02.107" Score="2" Body="&lt;p&gt;This is more of a long comment than an answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been active research in this area for several decades now. The problem is that once you detect seizure (which is relatively easy), it's usually too late. Therefore, a lot of effort has been to &lt;strong&gt;predict&lt;/strong&gt; epileptic seizures some time before it happens. This has proven quite difficult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this review article for the state-of-the-art in 2007:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mormann, F., Andrzejak, R. G., Elger, C. E., and Lehnertz, K. (2007). Seizure prediction: the long and winding road. Brain, 130(2):314-333.&#xA;&lt;a href=&quot;http://ntsa.upf.edu/system/files/biblio/Mormann-Brain2007.pdf&quot; rel=&quot;nofollow&quot;&gt;http://ntsa.upf.edu/system/files/biblio/Mormann-Brain2007.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2015-04-22T14:15:37.723" LastActivityDate="2015-04-22T14:15:37.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31602" PostTypeId="2" ParentId="31599" CreationDate="2015-04-22T15:03:11.033" Score="2" Body="&lt;p&gt;If by enzyme you mean &quot;protein&quot; &lt;em&gt;aka&lt;/em&gt; polypeptide, than there are such things as &lt;a href=&quot;http://en.wikipedia.org/wiki/Ribozyme&quot; rel=&quot;nofollow&quot;&gt;catalitic RNAs&lt;/a&gt;. Those are molecules of RNA that facilitate chemical reactions but don't change themselves (definition of catalyst). I think that, based on the discovery of such RNAs, it is now believed that life might have started from or with the help of catalytic RNAs (please forgive the speculative tone, see &lt;a href=&quot;https://scholar.google.com/scholar?q=self-replicating%20rna&amp;amp;hl=en&amp;amp;as_sdt=0&amp;amp;as_vis=1&amp;amp;oi=scholart&amp;amp;sa=X&amp;amp;ei=ILk3VbDMEMzaoAS4joHYBQ&amp;amp;ved=0CBwQgQMwAA&quot; rel=&quot;nofollow&quot;&gt;self-replicating RNAs&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might find this article interesting: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18613152&quot; rel=&quot;nofollow&quot;&gt;The Road to Non-Enzymatic Molecular Networks&lt;/a&gt;, which describes non-enzymatic networks. The problem with searching this topic is that &lt;a href=&quot;https://scholar.google.com/scholar?hl=en&amp;amp;q=non-enzymatic%20catalysis&amp;amp;btnG=&amp;amp;as_sdt=1%2C5&amp;amp;as_sdtp=&quot; rel=&quot;nofollow&quot;&gt;most current publications&lt;/a&gt;, seem to me, to concentrate on way to transfer enzymatic reactions into inorganic catalysis systems--because those systems can be more clean and easy to expand--than purifying enzymes for biotech.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="1306" LastEditDate="2015-04-23T14:08:42.353" LastActivityDate="2015-04-23T14:08:42.353" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="31603" PostTypeId="1" AcceptedAnswerId="31610" CreationDate="2015-04-22T15:09:21.963" Score="3" ViewCount="333" Body="&lt;p&gt;Does biomass represent all of the resources of the biosphere and therefore it would be theoretically infinitely renewable (as long as we have the sun) since all the biomass is part of the carbon cycle?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, should I consider resources like gold to be part of the biosphere and therefore all the resources would not be infinite nor infinitely renewable?&lt;/p&gt;&#xA;" OwnerUserId="15456" LastEditorUserId="3340" LastEditDate="2015-06-04T11:35:09.627" LastActivityDate="2016-05-18T06:56:22.653" Title="Does the biosphere have infinite resources and are they infinitely renewable?" Tags="&lt;ecology&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31604" PostTypeId="1" AcceptedAnswerId="31606" CreationDate="2015-04-22T15:25:22.187" Score="2" ViewCount="910" Body="&lt;p&gt;A genetic variation is found in this chromatogram:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/7TODa.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It says that the &quot;reference sequence&quot; is the top line and that I can use the general genetic code to find the reading frame.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can see that there are two N's instead of a G and a C. However I don't know what this means. I'm also not sure how I'd find the reading frame? I suppose I could look for a start and stop codon but I could read them both ways?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Last question: Is this change likely pathogenic? I'm not sure how to classify a variation as pathogenic or not.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="948" LastEditDate="2015-04-22T15:40:29.557" LastActivityDate="2015-04-22T16:49:04.183" Title="Help reading chromatogram" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;&lt;homework&gt;&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31605" PostTypeId="1" AcceptedAnswerId="31622" CreationDate="2015-04-22T15:31:46.013" Score="2" ViewCount="80" Body="&lt;p&gt;I'm sorry if &quot;gene markers&quot; is not the correct word. An edit could be appreciated but I don't study in an English speaking country unfortunately.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Question overview:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a family, there is a genetic, dominant disease. The father and a son is sick.&#xA;A gene marker analysis is performed with markers close to the assumed mutated gene on chromosome 11.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kSHjv.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Marker D11S4088&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6NEG5.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Marker D11S1344&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ge7c0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How do I read these and &quot;What sort of markers are these&quot;? I'm not sure what is going on here and I'm not sure what to search either due to language problems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-05-22T23:03:51.307" Title="Help reading gene markers" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31606" PostTypeId="2" ParentId="31604" CreationDate="2015-04-22T16:09:33.013" Score="1" Body="&lt;p&gt;So the two Ns that you see are not necessarily variants, but rather likely just poor quality reads. Essentially when you sequence DNA and the sequencer can't make a call as to what the base is, it will just designate it N meaning that the base could be any of the four DNA bases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for finding the reading from, if you know this sequence contains a stop codon, that helps, and just look for any of the stop sequences. If not, look for bases that match codon sequences and if you get a full strand of sequence that codes for amino acids you will likely be correct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For reference &lt;a href=&quot;http://jacksonstrickland.weebly.com/uploads/1/3/5/8/13584186/4324322.jpg?437&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; is a link to a codon chart that will help you decipher the reading frame.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does that help?&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-04-22T16:09:33.013" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31607" PostTypeId="2" ParentId="31604" CreationDate="2015-04-22T16:21:48.620" Score="2" Body="&lt;p&gt;The traces you have come from &lt;a href=&quot;http://en.wikipedia.org/wiki/Sanger_sequencing&quot; rel=&quot;nofollow&quot;&gt;Sanger sequencing&lt;/a&gt;. N in genetics means nucleotide (surprising right?). N is used when the base at a given location is unknown (or could be any base pairs).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your case you have Ns because the base-calling software is unable to determine the nucleotide. The first N is due to two peaks overlapping (G and A signals) and the second one should be a C rather than a N.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I can see, you have no apparent mutations so no those changes are unlikely to be pathogenic. A mutation can be called when you know a base in the reference is modified in your sample, which is not the case here (simply N -&gt; G and a N -&gt; C). The signals for your Ns look very similar between your reference and your sample therefore not suggesting a mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the reading frame, you have to look for a start (ATG) and a stop codon (TAG,TAA or TGA) to identify the &lt;a href=&quot;http://en.wikipedia.org/wiki/Open_reading_frame&quot; rel=&quot;nofollow&quot;&gt;open reading frame&lt;/a&gt; (ORF). Multiple software do that and here a link to an online NCBI tool called &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gorf/gorf.html&quot; rel=&quot;nofollow&quot;&gt;ORF Finder&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you pointed out the ORF can also be in the reverse strand. You don't want to look at the reverse sequence but at the &lt;strong&gt;reverse complementary&lt;/strong&gt; sequence. Usually tools to detect ORFs have the option to look at both strands.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-04-22T16:49:04.183" LastActivityDate="2015-04-22T16:49:04.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31608" PostTypeId="2" ParentId="31575" CreationDate="2015-04-22T17:10:04.793" Score="1" Body="&lt;p&gt;Because many insects (their food) are attracted to light. This attraction is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Phototaxis&quot; rel=&quot;nofollow noreferrer&quot;&gt;phototaxis&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Hypotheses for why insects are attracted to light&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The leading hypothesis for why so many insects are attracted to light is that before artificial existed, insects were using the light from the moon in order to navigate. They would keep themselves at a given angle relative to the light source in order to navigate straight.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Another hypothesis is the presence of light indicates that the pathway is clear.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A third hypothesis is that some insects may confuse artificial light source with the other sex. This appeared to be true for moths for example&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;These three hypotheses are not mutually exclusive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How do spiders chose their habitats&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information about the abilities of spiders to find a good habitat, have a look at &lt;a href=&quot;https://biology.stackexchange.com/questions/21295/did-spiders-respond-to-light-for-building-webs-before-artificial-light-was-inven?rq=1&quot;&gt;this very interesting answer&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-04-22T17:10:04.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31609" PostTypeId="2" ParentId="31603" CreationDate="2015-04-22T18:01:24.980" Score="1" Body="&lt;p&gt;Obviously not infinite, since the Earth has a finite mass, and the sun has a finite lifetime.  Also the Earth continually loses some (very small) fraction of its atmosphere &amp;amp; water to space, so eventually it would wind up like Mars (which was warmer, wetter, and probably habitable a billion years or so ago).&lt;/p&gt;&#xA;" OwnerUserId="11736" LastActivityDate="2015-04-22T18:01:24.980" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31610" PostTypeId="2" ParentId="31603" CreationDate="2015-04-22T18:07:33.483" Score="3" Body="&lt;p&gt;No, it is not infinite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sun has not an infinite mass neither does the earth. So energy is not infinite. But we probably don't really care about that as it applies at a scale we're not really concerned with. What is important at our scale is the rate at which is the rate at which the biomass we're destroying (eating, building houses with) is produced. The rate at which we consume this biomass has to not overpass the rate at which this biomass is produced. Than, practically speaking, biomass will be produced infinitely. Of course, ecosystem stability is not that easy but it is not within the scope of the post to talk about that.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2015-04-22T18:07:33.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31611" PostTypeId="1" AcceptedAnswerId="31683" CreationDate="2015-04-22T18:26:01.470" Score="2" ViewCount="120" Body="&lt;p&gt;Consider a population of two altruist with coefficient of relatedness&#xA;$r$. The average inclusive fitness of this population will be&#xA;$w_{0} + br -c$. Like in this example, assignment of inclusive fitness&#xA;I've seen in books and articles follow the rule that you should&#xA;&lt;strong&gt;not&lt;/strong&gt; count changes in inclusive fitness that result from the&#xA;action of your neighbor. For instance, in our example, the calculation&#xA;of average inclusive fitness include the increase in indirect fitness&#xA;to the actor (i.e., $br$), the costs (i.e., $c$), but do not include&#xA;the effects of the altruist behavior of the neighbor (i.e., $b$). That&#xA;is, the average inclusive fitness is not $(w_{0} + br -c) + b$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: why is it that, in inclusive fitness models, you do&#xA;&lt;strong&gt;not&lt;/strong&gt; count changes in inclusive fitness that result from the&#xA;action of your neighbor? Wouldn't it make the model more accurate to&#xA;take into account the effects of your neighbor's behavior? In other&#xA;words, in our example, why isn't $(w_{0} + br -c) + b$ a better value&#xA;for the average inclusive fitness than simply $(w_{0} + br -c)$?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As @Corvus pointed out, if we include changes in inclusive fitness that result from the action of your neighbor, we will double-count benefits. Consider the example mentioned above once again of a population of two altruists with a coefficient of relatedness $r$:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8fdHI.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we write $w_1 = w_2= (w_{0} + br -c) + b$, the help of 1 on 2 appears as $rb$ in $w_1$ and as $b$ in $w_2$. If we write the fitness in the right way, $w_1 = w_2= (w_{0} + br -c)$, the help of 1 on 2 is only counted once (i.e., $br$ in $w_1$). However, I cannot help but ask &quot;Why not count the help of 1 on 2 twice?&quot; We are counting the help of 1 on 2 twice, but each time we are assigning it to different individuals, 1 and 2. &lt;/p&gt;&#xA;" OwnerUserId="11829" LastEditorUserId="11829" LastEditDate="2015-04-24T16:47:14.213" LastActivityDate="2015-04-25T00:14:04.560" Title="Modeling inclusive fitness" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;mathematical-models&gt;&lt;population-genetics&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31612" PostTypeId="1" AcceptedAnswerId="31886" CreationDate="2015-04-22T18:55:26.383" Score="4" ViewCount="231" Body="&lt;p&gt;I understand it is not the most accurate source but I recall a House episode where he claimed the body had a control mechanism for pain in which only the most painful thing was felt. Is that true? and if so how does the body control which injury we feel and could we use this to our advantage?&lt;/p&gt;&#xA;" OwnerUserId="15436" LastEditorUserId="3340" LastEditDate="2015-06-24T08:56:07.653" LastActivityDate="2015-06-24T08:56:07.653" Title="Does the body have a gate control for pain" Tags="&lt;brain&gt;&lt;pain&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31613" PostTypeId="1" AcceptedAnswerId="31614" CreationDate="2015-04-22T19:23:39.233" Score="2" ViewCount="1520" Body="&lt;p&gt;Is there such a thing as cysteine deficiency in humans or other mammals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What effects would such a deficiency have?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I understand it, most cysteine for humans comes from dietary sources, though it can be biosynthesized in humans.&lt;/p&gt;&#xA;" OwnerUserId="8821" LastActivityDate="2015-04-23T13:52:56.580" Title="Is cysteine deficiency possible?" Tags="&lt;amino-acids&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31614" PostTypeId="2" ParentId="31613" CreationDate="2015-04-22T19:32:06.473" Score="6" Body="&lt;p&gt;Cysteine deficiencies are possible, and one cause is the genetic disorder &lt;a href=&quot;http://en.wikipedia.org/wiki/Homocystinuria&quot; rel=&quot;nofollow&quot;&gt;homocystinuria&lt;/a&gt;. Cysteine can be produced from methionine through a homocysteine intermediate, and defective genes for the enzymes involved can prevent proper cysteine production and cause a buildup of homocysteine. Patients have to eat a very carefully controlled diet with very low amounts of protein. This prevents homocysteine buildup by avoiding methionine exposure, but also requires that the patient take vitamin B6 and  B12 supplements and betaine. They might need to take cysteine supplements as well. The symptoms affect many organ systems, including the brain, nerves, and blood vessels, with about 25% of patients dying due to blood clots by age 30.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2015-04-23T13:52:56.580" LastActivityDate="2015-04-23T13:52:56.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31615" PostTypeId="1" AcceptedAnswerId="31811" CreationDate="2015-04-22T19:39:57.393" Score="12" ViewCount="183" Body="&lt;p&gt;&lt;strong&gt;What Information am I looking for?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Think about a tree that is sending pollen all over the place. Because of wind, most pollen grain will go toward one direction. Imagine, we split the 2D area around the tree where pollen grains fall into two half disks of equal size. We chose the disks so that the number of pollen grains falling into one half-disk is minimized and the quantity of pollen falling in the other half-disk is maximized.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The information I need&lt;/strong&gt; &lt;em&gt;is what proportion of pollen grain falls into each disk? Is it $\frac{0.5}{0.5}$ (in which case the wind would have no effect) or is it something like $\frac{0.8}{0.2}$?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Where to get the information from?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was reading &lt;a href=&quot;http://www.nature.com/hdy/journal/v77/n3/pdf/hdy1996139a.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; paper about pollen dispersal directionality and was trying to extract the info I need.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On pages 4 and 5 they explain their analysis under the section &lt;code&gt;statistical procedure&lt;/code&gt;. More specifically, in the first paragraph of the 5th page, they seem to describe the meaning of the parameters that are trying to estimate. One of them is the so-called &lt;code&gt;directionality parameter&lt;/code&gt; $\delta$. I don't understand how to interpret this parameter $\delta$.  This parameter is part of a logistic regression I think (although the authors do not characterize it as such) of &quot;mating success&quot; $y$ against variables $d$ (&quot;distance&quot;) and $h$ (&quot;height&quot;) and an angular variable $a = \cos(\alpha_0 - \alpha)$.  ($\alpha_0$ is the &quot;presumed prevailing direction of effective pollen dispersal,&quot; which apparently is not estimated from these data.)  The corresponding parameters of the model are $\beta$, $\gamma$, and $\delta$, respectively, hence&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\phi_j = \Pr(y_j = 1) = \frac{\exp\left(\beta d_j + \gamma h_j + \delta a_j\right)}{\sum_{k=1}^r \exp\left(\beta d_k + \gamma h_k + \delta a_k\right)}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where the index $j$ ranges over all $r$ &quot;male(s) in the neighborhood.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Their Results&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using maximum likelihood, they found that the &lt;code&gt;directionality parameter&lt;/code&gt;, $\hat\delta = 0.56$ (SE = $ 0.15$; bottom of page 6). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can I relate their finding to the information I need (even if it is just a rough approximation)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think I have to understand the so-called &lt;code&gt;directionality paramter&lt;/code&gt; $\delta$ Can you help me to interpret the meaning of this parameter $\delta$?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Burczyk, Adams, &amp;amp; Shimizu, &lt;em&gt;Mating patterns and pollen dispersal in a natural knobcone pine ... stand&lt;/em&gt;.  Heredity &lt;strong&gt;77&lt;/strong&gt; (1996) pp 251-260.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Not receiving any answer on Biology.SE, I asked the same question here on &lt;a href=&quot;https://math.stackexchange.com/questions/1253329/mathematical-statistics-pollen-dispersal-directionality&quot;&gt;Mathematics.SE&lt;/a&gt; but sadly, the question doesn't receive any attention!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:19:22.807" LastActivityDate="2015-04-28T02:07:28.640" Title="Biostatistics: Pollen dispersal directionality" Tags="&lt;botany&gt;&lt;mathematical-models&gt;&lt;statistics&gt;&lt;biostatistics&gt;&lt;migration&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31616" PostTypeId="1" AcceptedAnswerId="34741" CreationDate="2015-04-22T19:44:49.113" Score="12" ViewCount="418" Body="&lt;p&gt;This question was inspired by watching one of the Pirates of the Caribbean movies; particularly where Jack Sparrow allegedly survives on a desert island by finding an unlimited supply of rum. I've heard alcoholic drinks dehydrate you more than hydrate you, so this seems like an unsustainable strategy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is threefold. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;How long can a human survive by drinking hard liquor (40%&#xA;alcohol by volume) for their sole water intake (ignoring food)?&lt;/li&gt;&#xA;&lt;li&gt;If it's unsustainable, what will finally take you down?&lt;/li&gt;&#xA;&lt;li&gt;If the hard-liquor approach isn't viable, what % alcohol can&#xA;keep you hydrated (beer, wine, etc.)?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Related:&lt;br&gt;&#xA;1. &lt;a href=&quot;https://biology.stackexchange.com/questions/28098/dehydration-from-caffeine-alcohol-and-other&quot;&gt;Question on dehydration studies&lt;/a&gt;&lt;br&gt;&#xA;2. &lt;a href=&quot;https://biology.stackexchange.com/questions/28084/dehydration-by-a-tea-coffee-beer-etc/28086#28086&quot;&gt;Question on what dehydrates&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9130" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2017-08-15T20:30:25.953" Title="What are the survival limitations of alcohol?" Tags="&lt;nutrition&gt;&lt;health&gt;&lt;alcohol&gt;&lt;hydration&gt;&lt;dehydration&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31618" PostTypeId="1" CreationDate="2015-04-22T20:59:45.387" Score="5" ViewCount="141" Body="&lt;p&gt;During reading about genetics I came across with the term of linkage disequilibrium, and I do not really understand what it supposed to mean. What is linkage disequilibrium? My current understanding that it is &quot;deviation from independent assortment&quot;,&lt;/p&gt;&#xA;" OwnerUserId="15459" LastEditorUserId="14735" LastEditDate="2015-04-22T21:34:49.557" LastActivityDate="2015-04-22T21:34:49.557" Title="what is linkage disequilibrium supposed to measure?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31619" PostTypeId="2" ParentId="31618" CreationDate="2015-04-22T21:21:38.020" Score="3" Body="&lt;p&gt;Linkage disequilibrium refers to a situation whereby two or more alleles, from different loci, segregate non-randomly. Therefore we have a statistical association between this two alleles.&#xA;The linkage disequilibrium can be used in gene mapping, because we assume that these loci are in the same region on the chromosome. The more often they appear together, the more they segregate non-randomly, the closer they should be on the chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.researchgate.net/post/What_is_the_difference_between_Linkage_Equilibrium_and_Linkage_Disequilibrium&quot; rel=&quot;nofollow&quot;&gt;http://www.researchgate.net/post/What_is_the_difference_between_Linkage_Equilibrium_and_Linkage_Disequilibrium&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5686" LastActivityDate="2015-04-22T21:21:38.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31622" PostTypeId="2" ParentId="31605" CreationDate="2015-04-22T22:12:44.073" Score="1" Body="&lt;p&gt;Just googling, they are SSLPs.  You do PCR, and the different alleles make different length amplicons.  Looks like there is some kind of artifact that causes some of the amplicons to have peaks that look 2, or 4, or 6 letters shorter than the true length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for the top marker, the 211 bp long allele is linked to the disease, and for the other one, the 118 bp allele is linked to the disease.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2015-04-22T22:12:44.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31623" PostTypeId="1" CreationDate="2015-04-22T23:10:13.013" Score="3" ViewCount="320" Body="&lt;p&gt;So for Google Earth Day's quiz I ended up being a &quot;Pangolin.&quot; Turns out I had no idea what it was so I looked into it and honestly it reminded me a lot of an Armadillo. So I decided to find out the difference between the two, and I stumbled across &lt;a href=&quot;http://www.differencebetween.com/difference-between-pangolin-and-vs-armadillo/&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was all making sense until I got to the &quot;bullet points&quot; at the bottom where I saw this&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pangolin is a mammal while armadillo is a placental mammal.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And I'm now very confused. I thought placental mammal was just a subset of mammals. And I look up Pangolin's taxonomy and now I'm seeing all kinds of stuff I have no idea how to interpret. Back in my day, it was &quot;Kings Play Cards On Fat Green Stools&quot; for &quot;Kingdom Phylum Class Order Family Genus Species&quot;. And now I'm seeing things like clade, infraclass, subcohort, superorder and all kinds of things I just don't get.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I guess I have many questions, but I'm going to boil it down to &quot;If the Pangolin isn't considered a placental mammal, then what kind of mammal is it, and where does it diverge in taxonomy from the Armadillo?&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;Oh, and if someone could point me to a primer on the changes to taxonomy in the last 20 years, that'd be cool too.&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="8474" LastEditorUserId="12909" LastEditDate="2015-04-22T23:22:48.940" LastActivityDate="2015-04-23T00:11:41.573" Title="Mammal vs Placental Mammal" Tags="&lt;taxonomy&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31624" PostTypeId="2" ParentId="31623" CreationDate="2015-04-23T00:11:41.573" Score="4" Body="&lt;p&gt;From the Tree of Life page for &lt;a href=&quot;http://tolweb.org/Mammalia&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mammalia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cpdvx.jpg&quot; alt=&quot;Mammalia&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;All of these groups of animals are mammals, including extinct &lt;a href=&quot;http://palaeos.com/vertebrates/mammalia/triconodonta.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;triconodonts&lt;/a&gt; and &lt;a href=&quot;http://www.ucmp.berkeley.edu/mammal/multis/multis.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;multituberculates&lt;/a&gt;. Among living mammals are monotremes (most notably the platypus), marsupials (kangaroos and opossums), and eutherians. Eutherians are placental mammals, so all eutherians are placental mammals, but not all mammals are eutherians.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both armadillos and pangolins are eutherian mammals, so both are mammals and both are placentals. &quot;Difference Between&quot; is quite incorrect.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2015-04-23T00:11:41.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31625" PostTypeId="1" AcceptedAnswerId="31640" CreationDate="2015-04-23T00:52:46.203" Score="9" ViewCount="770" Body="&lt;p&gt;For plasmids is so much shorter than their host cell's genome (about 1/1000 in my case), it will take only 1/1000 time for it to replicate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With respect to cell cycle, when will that replication occur?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Description of the situation I'm facing: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a low copy number plasmids (pSC101) in E.coli, and I'm measuring a fluorescence protein expression level. The problem is, even if the plasmid copy number is known (N), depending on when it is replicated, the number of plasmid in my cell can vary. Therefore, I cannot directly infer expression level per plasmid. Higher expression level might just result from higher number of plasmids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, if it is replicated right after cell division, I will have 2N plasmids for the most of my cell cycle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If on the other hand, it gets replicated right before cell division (and partitioning machinery delivers exactly half the number to each daughter cell), I will have N plasmids per cell for the most my my cell cycle.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, when do plasmids get replicated?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could not find a similar question here with search.&#xA;Thank you very much in advance.&lt;/p&gt;&#xA;" OwnerUserId="15462" LastActivityDate="2015-04-24T16:13:31.580" Title="When do plasmids replicate relative to its host cell cycle?" Tags="&lt;microbiology&gt;&lt;ecoli&gt;&lt;plasmids&gt;&lt;replication&gt;&lt;copy-number-variation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31626" PostTypeId="1" CreationDate="2015-04-23T01:00:43.827" Score="6" ViewCount="129" Body="&lt;p&gt;I have been analyzing TCGA Ovary Cancer data. In &lt;strong&gt;&lt;em&gt;Somatic Mutation&lt;/em&gt;&lt;/strong&gt; data, there is data of mutations in all the chromosomes (&lt;em&gt;1-22 and X&lt;/em&gt;), but amazingly, I have found one (&lt;em&gt;just one&lt;/em&gt;) row of &lt;strong&gt;&lt;em&gt;Y Chromosome&lt;/em&gt;&lt;/strong&gt; mutation as well. What can it mean?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For Reference, I have pasted that row below:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;icgc_mutation_id icgc_donor_id project_code chromosome chromosome_start &#xA;MU42454          DO28056       OV-US        Y          13500742         &#xA;&#xA;chromosome_end chromosome_strand mutation_type            &#xA;13500742       1                 single base substitution &#xA;&#xA;reference_genome_allele mutated_from_allele mutated_to_allele &#xA;G                       G                   A                 &#xA;&#xA;consequence_type aa_mutation cds_mutation gene_affected   transcript_affected &#xA;stop_gained      R194*       580C&amp;gt;T       ENSG00000183704 ENST00000331172&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="14852" LastEditorUserId="14852" LastEditDate="2015-04-23T23:53:19.897" LastActivityDate="2015-04-23T23:53:19.897" Title="Y Chromosome in Ovary Cancer Data" Tags="&lt;genetics&gt;&lt;cancer&gt;&lt;human-genetics&gt;&lt;tcga&gt;&lt;icgc&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31627" PostTypeId="2" ParentId="10376" CreationDate="2015-04-23T02:19:42.140" Score="5" Body="&lt;p&gt;You should check out Richard Dawkins' book The &lt;em&gt;Greatest Show on Earth: The Evidence for Evolution&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It does focus heavily on evolution but it is an amazing book on biology in general.  He covers a wide rage of other topics, from how birds flock so elegantly to dating fossils using dendrochronology.  The chapter on embryology is fascinating.  &lt;/p&gt;&#xA;" OwnerUserId="15097" LastActivityDate="2015-04-23T02:19:42.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31628" PostTypeId="1" CreationDate="2015-04-23T03:57:16.120" Score="3" ViewCount="57" Body="&lt;p&gt;I am designing a synthetic gene construct to express genes in &lt;em&gt;E. coli&lt;/em&gt; driven by either Ptet or PLacO. The construct would look like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;-Ptet-(Gene1)-PLacO-(Gene2)-&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to express each gene using either aTc or IPTG, but I want to make sure that the transcription of each gene can be controlled independently. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let say I only add aTc and transcription is initiated at the Ptet location, would RNA polymerase bump into LacI bound to the PLacO promoter and stop transcribing? Or would it knock-off LacI transcribe (Gene 2)? I am not sure whether or not need to include terminator sequence to make sure the expression of each gene is decoupled.&lt;/p&gt;&#xA;" OwnerUserId="15463" LastActivityDate="2015-05-23T16:11:37.217" Title="Is RNA polymerase affected by proteins bound to the coding sequence of a gene?" Tags="&lt;transcription&gt;&lt;gene-regulation&gt;&lt;transcription-factor&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31629" PostTypeId="1" CreationDate="2015-04-23T04:46:15.057" Score="10" ViewCount="206" Body="&lt;p&gt;I recently learned from &lt;a href=&quot;https://health.stackexchange.com/a/613/165&quot;&gt;an answer at health.SE&lt;/a&gt;* that influenza B tends to occur later in the season compared to influenza A. According to the graph in that answer, during this year’s flu season the peak for influenza B was mid-March, compared to late December for influenza A. I’m wondering why this is. What are the virological factors that account for this difference?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;*Now public!&lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="-1" LastEditDate="2017-04-13T12:53:19.983" LastActivityDate="2015-06-02T14:36:14.220" Title="What is the difference between influenza A and B viruses that causes their distinct seasonal patterns?" Tags="&lt;pathology&gt;&lt;virus&gt;&lt;infection&gt;&lt;influenza&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31630" PostTypeId="2" ParentId="31629" CreationDate="2015-04-23T04:59:51.273" Score="5" Body="&lt;p&gt;Regrettably, I don't believe we know - we don't actually know why influenza is a seasonal disease in the first place. There are a number of possible theories, discussed in &lt;a href=&quot;http://jvi.asm.org/content/81/11/5429.full&quot; rel=&quot;noreferrer&quot;&gt;this review&lt;/a&gt;, but none of them are compelling enough to be a definitive causal explanation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of the difference between Influenza A and B, B mutates at a much lower rate, which may explain the slower rate of dramatic antigenic shifts, but that isn't enough to disrupt the seasonal cycle by a few months at most.&lt;/p&gt;&#xA;" OwnerUserId="67" LastActivityDate="2015-04-23T04:59:51.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31631" PostTypeId="1" AcceptedAnswerId="31634" CreationDate="2015-04-23T07:02:47.810" Score="4" ViewCount="454" Body="&lt;p&gt;Do the following compounds have any charge? If not, then why? If yes, is there any database that would give me this information if the compound is negatively or positively charged?&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The compounds are as follows:&lt;br&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.genome.jp/dbget-bin/www_bget?cpd:C00024&quot; rel=&quot;nofollow&quot;&gt;Acetyl-CoA&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.genome.jp/dbget-bin/www_bget?cpd:C01139&quot; rel=&quot;nofollow&quot;&gt;Acetyl-CoA carboxylase&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.genome.jp/dbget-bin/www_bget?cpd:C00624&quot; rel=&quot;nofollow&quot;&gt;Acetyl-glutamate&lt;/a&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have searched and somehow I am getting more confused. &lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="9943" LastEditDate="2015-04-23T10:33:26.110" LastActivityDate="2015-04-23T10:34:33.900" Title="Do acetyl-CoA, acetyl-CoA carboxylase and acetyl-glutamate carry any charge?" Tags="&lt;organic-chemistry&gt;&lt;biochemistry&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31632" PostTypeId="2" ParentId="31628" CreationDate="2015-04-23T07:34:03.227" Score="1" Body="&lt;p&gt;Nice question!&#xA;First of all make sure that you have multiple transcription stop / terminator sequences at the end of your first gene . This is quite standard procedure. Also in your case the phenomenon called transcription interference (TI) comes handy. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0168952505001125&quot; rel=&quot;nofollow&quot;&gt;Here's&lt;/a&gt; a review on TI. In short:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the term TI usually refers to the direct negative impact of one transcriptional activity on a second transcriptional activity in cis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Although TI is mostly defined as two transcription events affecting each other, at the low level the basis of it is that two proteins bound to the DNA affect each other's activity. Now since LacI's function is to inhibit transcription, thus it is strongly bound to the DNA and I'd say even if a polymerase somehow slips through the polyA signals at the end of the first gene it is likely to be stopped by the LacI already bound at the second promoter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively you could put a weak promoter opposing the first gene and drive its expression, so it would collide with the oncoming polymerase from the first gene thus stopping it before reaching the second gene. Also &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389743/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; is another article on TI, that proposes a gene regulation network based on TI.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-23T15:24:05.327" LastActivityDate="2015-04-23T15:24:05.327" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31633" PostTypeId="2" ParentId="31631" CreationDate="2015-04-23T07:35:26.180" Score="4" Body="&lt;p&gt;The first compound you mention is acetyl-co-enzyme A (&lt;a href=&quot;http://www.genome.jp/dbget-bin/www_bget?cpd:C00024&quot; rel=&quot;nofollow noreferrer&quot;&gt;acetyl-CoA&lt;/a&gt;) (first picture, left panel). The acetyl group is uncharged, but the &lt;a href=&quot;http://en.wikipedia.org/wiki/Coenzyme_A&quot; rel=&quot;nofollow noreferrer&quot;&gt;co-enzyme A (CoA)&lt;/a&gt; group (Fig. 1, right panel) does carry charge through its phosphate groups. In normal physiologic environments these phosphate groups will donate one or more protons, leaving the molecule negatively charged, as shown in Fig. 1, right panel below: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yDNjb.gif&quot; alt=&quot;acCoA&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/cCK5B.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1 &lt;a href=&quot;http://www.genome.jp/dbget-bin/www_bget?cpd:C00024&quot; rel=&quot;nofollow noreferrer&quot;&gt;Acetyl-CoA&lt;/a&gt; (left) and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Coenzyme_A&quot; rel=&quot;nofollow noreferrer&quot;&gt;co-enzyme A group&lt;/a&gt; (right).&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second compound is an enzyme, namely &lt;a href=&quot;http://www.genome.jp/dbget-bin/www_bget?cpd:C01139&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;acetyl-CoA carboxylase&lt;/em&gt;&lt;/a&gt;. Consisting of many, many amino-acids it will carry many, many charges under physiological conditions. Some of these will be negative, some positive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The third compound you mention is &lt;a href=&quot;http://www.genome.jp/dbget-bin/www_bget?cpd:C00624&quot; rel=&quot;nofollow noreferrer&quot;&gt;acetyl-glutamate&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jzSyk.gif&quot; alt=&quot;ac-Glu&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;a href=&quot;http://www.genome.jp/dbget-bin/www_bget?cpd:C00624&quot; rel=&quot;nofollow noreferrer&quot;&gt;Acetyl-Glutamate&lt;/a&gt;&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This compound carries two carboxyl groups, which makes the compound acidic and negatively charged under physiological conditions, as it will donate one or two protons to the environment, dependent on the pH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;sup&gt;PS: For an in-depth answer on the basic chemistry and pKa values I would ask this at Chemistry.SE :)&lt;/sup&gt;&lt;/em&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-04-23T10:34:33.900" LastActivityDate="2015-04-23T10:34:33.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31634" PostTypeId="2" ParentId="31631" CreationDate="2015-04-23T08:00:55.913" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://www.chemicalize.org&quot; rel=&quot;nofollow&quot;&gt;chemicalize.org&lt;/a&gt; is a good utility for predicting many molecular properties such as pKa, pI and charge. The &lt;a href=&quot;http://www.hmdb.ca&quot; rel=&quot;nofollow&quot;&gt;Human Metabolome Database&lt;/a&gt; uses the same underlying software but tabulates some of the data (eg charge is explicitly stated). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Acetyl-CoA, for example, has a pI of 1.32 and charge of -4 at pH=7.4. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Your second link is to a portion of an enzyme (a serine residue that gets phosphorylated). Prediction of protein properties can be done with &lt;a href=&quot;http://web.expasy.org/protparam/&quot; rel=&quot;nofollow&quot;&gt;ProtParam&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Human Acetyl-CoA Carboxylase 1, for example, has a pI of 5.95 and charge of -39. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-04-23T08:00:55.913" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31635" PostTypeId="1" AcceptedAnswerId="31639" CreationDate="2015-04-23T09:26:46.077" Score="5" ViewCount="1864" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;In human females one X chromosome is inactivated forming a Barr Body. Then how is it that haemophilia is dominant?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Suppose a female has one normal X chromosome and one chromosome with the haemophilia gene. Now suppose that the normal X chromosome is inactivated — will the female show haemophilia?&lt;/p&gt;&#xA;" OwnerUserId="14855" LastEditorUserId="22057" LastEditDate="2018-02-27T13:39:01.467" LastActivityDate="2018-02-27T13:39:01.467" Title="How is haemophilia dominant in human females?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31637" PostTypeId="1" CreationDate="2015-04-23T10:18:50.403" Score="4" ViewCount="148" Body="&lt;p&gt;There are HeLa cells, which were taken from sick cancer patient and now is growing worldwide in different laboratories for experiments. HeLa cells can be kept because they are immortal and so they are an instance of &lt;a href=&quot;https://en.wikipedia.org/wiki/Immortalised_cell_line&quot; rel=&quot;nofollow&quot;&gt;immortal cell line&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about stem cells? They are also immortal. Such cells can be taken from normal healthy person and also kept forever. Do scientists do this? Why don't we hear about it then? For example, they are distinguished in Wikipedia article, referred above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there some special properties of stem cell lines, making them different? For example, being low differentiated they may be useless for experiments.&lt;/p&gt;&#xA;" OwnerUserId="5720" LastEditorUserId="6061" LastEditDate="2015-05-09T04:45:10.957" LastActivityDate="2015-05-09T04:45:10.957" Title="Are stem cell lines cryogenically preserved or commercially available like HeLa cells are?" Tags="&lt;cell-biology&gt;&lt;cell-culture&gt;&lt;stem-cells&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31638" PostTypeId="2" ParentId="14611" CreationDate="2015-04-23T10:25:22.803" Score="5" Body="&lt;p&gt;I think HELA cells are edible, although from moral point of view this would be cannibalism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite they are cancer cells, they are safe for foreign organism, because any ate matter is destroyed. Even if these cells were implanted into another being by surgery, they will be safe since immunity will recognize them as foreign and kill. They are much less cancerous for recipient than just foreign.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remember, then when we are eating meat, we don't care if cow or pig had cancer. Even if we avoid eating explicit tumors, we can still eat metastatic cells from sick animals. I think this happening all the time and has no consequences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Simultaneously HELA cells are dangerous for other cell cultures in laboratory. There were several cases, when other cultures were infected by HELA cells and crowd out. HELA cells were traveled by air and on objects unexpectedly. Scientists were not ready for this phenomenon.&lt;/p&gt;&#xA;" OwnerUserId="5720" LastActivityDate="2015-04-23T10:25:22.803" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31639" PostTypeId="2" ParentId="31635" CreationDate="2015-04-23T10:29:09.517" Score="6" Body="&lt;p&gt;X-linked Hemophilia &lt;a href=&quot;http://en.wikipedia.org/wiki/Haemophilia#Genetics&quot; rel=&quot;noreferrer&quot;&gt;is caused by&lt;/a&gt; the lack of production of the clotting factors VIII or IX. It is not inherited dominantly, but instead inherited in an X-linked recessive manner.&lt;/p&gt;&#xA;&lt;p&gt;These proteins are produced in multiple regions around the body. In a female heterozygous for the gene coding for Factor VIII or IX, X-inactivation would randomly prevent one of the chromosomes from expressing its allele. Therefore, the production of active Factor VIII or IX would only occur in half the cells which have the faulty allele inactivated.&lt;/p&gt;&#xA;&lt;p&gt;However, half the production of the relevant factor results in a close to normal phenotype, as the hemophilic phenotype would not manifest unless the clotting factor activity levels are very low.&lt;/p&gt;&#xA;&lt;p&gt;This &lt;a href=&quot;http://emedicine.medscape.com/article/779322-overview&quot; rel=&quot;noreferrer&quot;&gt;Medscape article on hemophilia&lt;/a&gt; states that:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Normal values for FVIII assays are 50-150%. Values in hemophilia are as follows:&lt;/p&gt;&#xA;&lt;p&gt;Mild: &amp;gt;5%&lt;/p&gt;&#xA;&lt;p&gt;Moderate: 1-5%&lt;/p&gt;&#xA;&lt;p&gt;Severe: &amp;lt; 1%&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Therefore, despite X-inactivation reducing the production of clotting factors by 50%, the heterozygous female still displays the healthy, non-hemophilic phenotype.&lt;/p&gt;&#xA;&lt;p&gt;While the clotting factor concentration can only be reduced to approximately 50% of normal, it is still possible for heterozygotes to suffer from mild hemophilia. This is because &lt;a href=&quot;http://emedicine.medscape.com/article/779322-overview#aw2aab6b2b2&quot; rel=&quot;noreferrer&quot;&gt;other genetic factors&lt;/a&gt; may also affect the hemophilia phenotype.&lt;/p&gt;&#xA;&lt;p&gt;For example, the gene encoding FVIII may have point mutations which reduce the effectiveness of the protease, therefore reducing activity levels below the expected 50%. Mutations in regulatory elements or interacting proteins may also result in hemophilia due to the regulatory elements downregulating the expression or activity of the protein.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Approximately 40% of cases of severe FVIII deficiency arise from a large inversion that disrupts the FVIII gene. Deletions, insertions, and point mutations account for the remaining 50-60% of the F8C defects that cause hemophilia A.&lt;/p&gt;&#xA;&lt;p&gt;Low FVIII levels may arise from defects outside the FVIII gene, as in type IIN von Willebrand disease, in which the molecular defect resides in the FVIII-binding domain of von Willebrand factor.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-23T11:50:13.450" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31640" PostTypeId="2" ParentId="31625" CreationDate="2015-04-23T10:43:28.133" Score="7" Body="&lt;p&gt;I've found a nice &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC98921/&quot; rel=&quot;nofollow noreferrer&quot;&gt;review&lt;/a&gt; that has many details on plasmid replication in general, and several papers about pSC101 in detail, and I'll try to extract the key information from these papers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all your plasmid as an ori region that contains so called iteron:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In many cases, the origin of replication contains directly repeated sequences, termed iterons, which are the binding sites for the plasmid-encoded Rep proteins and which have control properties. (...)iterons have been described for several replicons like P1, F, pSC101 (...).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;pSC101 plasmid has three of these iterons present, along with a protein called rep that is necessary for replication. Besides these there are sequences that provide binding sites for host proteins such as DnaA and integration host factor (IHF).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Details of these can be found in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC206681/pdf/jbacter00060-0257.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; and &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.1991.tb02103.x/pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; paper, both provides details on replication and the function of ori region in your plasmid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As stated in &lt;a href=&quot;http://ac.els-cdn.com/0092867490904054/1-s2.0-0092867490904054-main.pdf?_tid=1f400f92-e99d-11e4-9070-00000aab0f26&amp;amp;acdnat=1429782357_c54181f96ff892855b53355b20628bd1&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; other paper, plasmid copy number is controlled by the plasmids themselves, that may vary on host type and growth conditions but:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;At steady state, the 1 number of replications per plasmid copy is exactly &#xA;  one per cell generation. This defines the steady state as shown in Figure 1. It should be stressed that while this is true for the population, it is not for individual plasmids-these are selected randomly for replication. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dRlr0.png&quot; alt=&quot;fig1&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So not all plasmid copies are replicated once per cell cycle rather random ones are selected and they replicate to maintain the desired number.&#xA;When your plasmid has reached its target copy number it will adjust its replication frequency to maintain this number. This is achieved by negative control loops. There are many ways to do this (repressor proteins, anti-sense RNA) or in your case iterons. These sequence along with the rep protein may inhibit replication if too much plasmid is present by a phenomenon called  “steric hindrance&quot; or “handcuffing”. This happens because the rep protein is capable to bind two iteron, simultaneously. &#xA;At low copy numbers saturation of iteron sequences by rep proteins initiate replication, but at high copy number rep proteins tend to interact with each other and plasmids pair up through rep-rep interactions therefore cannot replicate. See figure below:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/RhIuI.png&quot; alt=&quot;rep handcuffing&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, long story short: plasmid replication in part depends on host factors but plasmids have means to control their copy number, and once target has been reached they maintain this number in a stable form. I know this answer does not provide solution to the when part of your question, but it provides an answer to the practical part of your problem namely: plasmid numbers are quite stable after the target number has been reached. I hope this helps&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I've found this article &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC210920/pdf/jbacter00181-0364.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC210920/pdf/jbacter00181-0364.pdf&lt;/a&gt; that says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In all experiments, plasmids pSG21 (oriS only), F'lac (oriS oriV),pBR322,&#xA;  and pSC101 were capable of replicating at all stages of the division cycle,&#xA;  with no detectable differences in the patterns.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So bad news for you, because according to the paper above you cannot tell when your plasmid actually replicates. Yet still as the average copy number is quite stable due to reasons described above this may not pose a big problem. Keep in mind even if you have an extra plasmid for a short time that may still not cause problem, because transcription of your riporter gene, folding, etc takes time under which previously synthesized proteins might degrade.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC207836/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; paper says the F+ plasmid replication is cell-cycle specific, you may wan to give it a try.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-24T16:13:31.580" LastActivityDate="2015-04-24T16:13:31.580" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31641" PostTypeId="1" AcceptedAnswerId="31642" CreationDate="2015-04-23T10:49:45.227" Score="3" ViewCount="1766" Body="&lt;p&gt;Most proteins are fixed in the membrane by alpha helices. But some use beta barrels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Beta_barrel&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; describes beta barrels as used for porins, preprotein translocases, and lipocalins. To me, a coiled coil alpha helix structure could surely perform the same functions and given the &lt;a href=&quot;http://www.uniprot.org/uniprot/?query=annotation%3A%28type%3Atransmem%29&amp;amp;sort=score&quot; rel=&quot;nofollow&quot;&gt;vast number of proteins using alpha helices&lt;/a&gt; there might be some out there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is twofold:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Are these functions &lt;strong&gt;exclusive&lt;/strong&gt; to beta barrels?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If so, what about alpha helices makes them unsuitable for those functions?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3553" LastActivityDate="2015-04-24T05:33:35.977" Title="Why do some proteins &quot;use&quot; a beta barrel structure instead of alpha helices in transmembrane space?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31642" PostTypeId="2" ParentId="31641" CreationDate="2015-04-23T11:37:29.660" Score="2" Body="&lt;p&gt;As you can see on the wikipedia page you linked yourself that beta barrels have far larger diameters (in some cases up to 40 angstroms as stated in &lt;a href=&quot;http://users.sdsc.edu/~youkha/duplication/_B_BARRELS/VIRUSES+BARRELS/Beta_barrels_membrane_proteins_review2000.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper) depending on the numbers of beta sheets that make up the barrel, compared to the diameter of an alpha helix (that is fixed) of 6 angstroms. (source &lt;a href=&quot;http://www.chem.uwec.edu/Modeling/GGProteinStructures/Pages/alpha_helix/helix.html&quot; rel=&quot;nofollow&quot;&gt;http://www.chem.uwec.edu/Modeling/GGProteinStructures/Pages/alpha_helix/helix.html&lt;/a&gt;). Alpha helices are good to anchor proteins into the membrane, or forming small holes that is suitable for compounds like ions, while with beta barrels larger compounds such as sugars, or various drugs can be transported. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's a good list of proteins with different functions for both types on &lt;a href=&quot;http://en.wikipedia.org/wiki/Transmembrane_protein&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="231" LastEditDate="2015-04-24T05:33:35.977" LastActivityDate="2015-04-24T05:33:35.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31643" PostTypeId="2" ParentId="31637" CreationDate="2015-04-23T11:39:21.277" Score="2" Body="&lt;p&gt;This is too long for a comment, so I have to write it in here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mostly this is because other cell lines are more practical in the lab.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stem cells are much more tricky to maintain - especially if you want to keep their stem cell properties. They only grow very slow, tend to differentiate when they get too much stress, cellular signals and so on and need special media (these need to be defined, so that they are not containing factors which promote differentiation for example). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For everyday experiments (like expression profiles, experiments on the effects of certain substances on the growth, gene expression or whatever of cells) &quot;normal&quot; cell lines are much more suited as these are much easier to keep in the lab using standard media. Additionally,experiments can be more easily repeated and reproduced, since these cells should behave always the same.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-04-23T11:39:21.277" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31644" PostTypeId="1" AcceptedAnswerId="31651" CreationDate="2015-04-23T12:23:39.617" Score="5" ViewCount="79" Body="&lt;p&gt;I have a question about amino acid composition of proteins: Are there proteins in animals that are made up only from a small subset of amino acids? So instead of all 20 amino acids let's say only 6-14 ( or any arbitrarily small subset) amino acids are used in a particular protein. Could you give me an example (or maybe a few examples) of such protein(s).&lt;/p&gt;&#xA;" OwnerUserId="15470" LastEditorUserId="14735" LastEditDate="2015-04-23T13:11:50.257" LastActivityDate="2015-04-23T15:56:24.583" Title="Are all protein composed of all the amino acid (in animal) or are there less diverse protein?" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31645" PostTypeId="1" CreationDate="2015-04-23T13:11:27.180" Score="1" ViewCount="277" Body="&lt;p&gt;How do I assess the quality of a cDNA library?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to clone CDS copies of genes from a library, but I don't know what's a typical expectation of getting a full length clone even for a shorter gene (~1000 bp).  I know it doesn't have to be composed of full length cDNA for sequencing, but I'd imagine quality of starting materials is important there too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there some common transcripts I can try to obtain from PCR that will tell me how fragmented the sequences are in there?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's a typical result from a commercial cDNA library - are there any QC tests that are quick to run in the lab? &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2015-04-24T04:34:07.527" LastActivityDate="2015-04-24T04:34:07.527" Title="What's a good simple test for cDNA library quality?" Tags="&lt;pcr&gt;&lt;cdna&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31646" PostTypeId="1" AcceptedAnswerId="31647" CreationDate="2015-04-23T13:25:13.657" Score="4" ViewCount="28754" Body="&lt;p&gt;Hello my Professor has been teaching about apoptosis and sometimes makes the distinction between extrinsic and intrinsic. I am not sure if I know for sure what this means. Does this just refer to intrinsic is a cell doing itself while extrinsic refers to Fas ligand? Thanks.&lt;/p&gt;&#xA;" OwnerUserId="15066" LastEditorUserId="14735" LastEditDate="2015-04-23T13:27:07.240" LastActivityDate="2015-04-23T17:10:47.103" Title="What is the difference between intrinsic and extrinsic apoptosis?" Tags="&lt;apoptosis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31647" PostTypeId="2" ParentId="31646" CreationDate="2015-04-23T13:56:30.697" Score="2" Body="&lt;p&gt;In both pathways 'the cell does itself' the difference is in the reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short:&#xA;Intrinsic apoptosis is a response to 'internal damage' eg. damaged DNA, chromosom rearrangement, hang ups in division, hypoxia, etc. that the cell senses itself and 'decides to commit suicide'. This is done by the mitochondrial pathway - release of cytochrome C from the mitochondria activates the caspase cascade that results in programmed cell death. This is like &quot;I'm too damaged, I must die&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the extrinsic pathway as you have mentioned is indeed related to the FAS ligand (and Fas/FasL being the main pathway for apoptosis), but that is not the only external signal as TNF (also known as TNA-alpha) binding to TNF-R1 (tumor necrosis factor receptor 1) may also lead to apoptosis. These pathways are usually activated by the immune system for example in cellular immune response. This is like &quot;You're abnormal / dangerous / infected, you must die&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both pathways activates the caspase cascade at some point that results in apoptosis. Either way the actual process of apoptosis is carried out by the cell itself in a programmed, regulated manner.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://en.wikipedia.org/wiki/Apoptosis&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Apoptosis&lt;/a&gt;&#xA;This papaer offers a great review on the topic, including both pathways:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2117903/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2117903/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like to quote few  important parts to support my answer:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The extrinsic, intrinsic, and granzyme B pathways converge on the same terminal, or execution pathway. This pathway is initiated by the cleavage of caspase-3 and results in DNA fragmentation, degradation of cytoskeletal and nuclear proteins, cross-linking of proteins, formation of apoptotic bodies, expression of ligands for phagocytic cell receptors and finally uptake by phagocytic cells. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(...)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The extrinsic signaling pathways that initiate apoptosis involve transmembrane receptor-mediated interactions. These involve death receptors that are members of the tumor necrosis factor (TNF) receptor gene superfamily&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(...)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The intrinsic signaling pathways that initiate apoptosis involve a diverse array of non-receptor-mediated stimuli that produce intracellular signals that act directly on targets within the cell and are mitochondrial-initiated events. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-23T17:10:47.103" LastActivityDate="2015-04-23T17:10:47.103" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31648" PostTypeId="1" AcceptedAnswerId="31758" CreationDate="2015-04-05T16:22:58.297" Score="22" ViewCount="7983" Body="&lt;p&gt;When putting (japanese) mintoil on the skin it produces a cool feeling. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can experience this, when adding it to your bath or using a spray with mint oil on your skin. The cool feeling occures even if the actual temperature of the spray or bath is quite warm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where does this sensoric impression come from?&lt;/p&gt;&#xA;" OwnerUserId="9313" OwnerDisplayName="Kaadzia" LastEditorUserId="9313" LastEditDate="2015-05-04T15:53:35.790" LastActivityDate="2015-05-04T15:53:35.790" Title="Why does mint oil feel cold on the skin?" Tags="&lt;human-biology&gt;&lt;senses&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31649" PostTypeId="1" AcceptedAnswerId="31661" CreationDate="2015-04-23T14:46:44.367" Score="2" ViewCount="413" Body="&lt;p&gt;I only know that electrons are captured by the primary electron acceptor and then go through the electron transport chain, ultimately ending up at photosystem I. But why do 2 leave photosystem II in the first place? I thought the oxygen-evolving complex only replenishes the electron hole one-by-one?&lt;/p&gt;&#xA;" OwnerUserId="15272" LastActivityDate="2015-04-23T23:27:16.797" Title="Why are 2 electrons transported from photosystem II at the same time?" Tags="&lt;biochemistry&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31651" PostTypeId="2" ParentId="31644" CreationDate="2015-04-23T15:56:24.583" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.rcsb.org/pdb/explore/explore.do?structureId=1L2Y&quot; rel=&quot;nofollow&quot;&gt;Trp-Cage&lt;/a&gt; is a protein found in Gila monsters, and it is only 20 amino acids long and there are plenty of repeated amino acids so this does not use all 20. But there must be plenty of other examples, there is no reason why physically a protein must use all available amino acids.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-04-23T15:56:24.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31652" PostTypeId="1" AcceptedAnswerId="31653" CreationDate="2015-04-23T16:32:42.557" Score="15" ViewCount="31719" Body="&lt;p&gt;It consist approximately 7 percent of body weight.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By definition organ is composed of multiple tissues. Blood is a fluid, a circulating tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore can we call this fluid system a liquid organ? &lt;/p&gt;&#xA;" OwnerUserId="1195" LastEditorUserId="22057" LastEditDate="2017-11-05T15:22:09.430" LastActivityDate="2017-11-05T15:22:09.430" Title="Is blood regarded as an organ?" Tags="&lt;hematology&gt;&lt;definitions&gt;&lt;organs&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31653" PostTypeId="2" ParentId="31652" CreationDate="2015-04-23T16:38:05.990" Score="18" Body="&lt;p&gt;Blood is considered a type of &lt;a href=&quot;http://en.wikipedia.org/wiki/Connective_tissue&quot;&gt;connective tissue&lt;/a&gt; (sometimes). However, an organ is formed of multiple &lt;em&gt;different&lt;/em&gt; tissues. Thus, blood is a tissue, not an organ.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-04-23T16:38:05.990" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31654" PostTypeId="2" ParentId="31652" CreationDate="2015-04-23T17:16:28.430" Score="5" Body="&lt;p&gt;While organs are generally considered to have a single, specified function (or perhaps a group of closely-related functions), blood (the fluid inside the vessels, not the vessels themselves) has many different functions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;deliver $O_2$ from lungs to cells&lt;/li&gt;&#xA;&lt;li&gt;remove waste $CO_2$ from cells to lungs&lt;/li&gt;&#xA;&lt;li&gt;respond to injury by clotting&lt;/li&gt;&#xA;&lt;li&gt;carry multiple different types of nutrients by multiple different means (free-floating, carrier protein-associated, lipid particles, etc.)&lt;/li&gt;&#xA;&lt;li&gt;provide transport for the immune system, which in itself has diverse functions&lt;/li&gt;&#xA;&lt;li&gt;transport waste products to liver and kidneys&lt;/li&gt;&#xA;&lt;li&gt;move regulatory molecules around the body (hormones, chemokines, cytokines, antibodies, etc.)&lt;/li&gt;&#xA;&lt;li&gt;regulate heat in the body&lt;/li&gt;&#xA;&lt;li&gt;maintain $pH$ and $H_2O$ balance&lt;/li&gt;&#xA;&lt;li&gt;and probably more I haven't thought of&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So, I don't think blood should be classified as an organ, just because of its multitude of uses. Instead, it is vital for the proper functioning of pretty much all the organs in the body, and allows for connections among them.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-04-23T17:16:28.430" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31655" PostTypeId="1" AcceptedAnswerId="31658" CreationDate="2015-04-23T18:31:14.533" Score="3" ViewCount="277" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://public.wsu.edu/~brians/errors/palate.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source:&lt;/a&gt; Your “palate” is the roof of your mouth, and by extension, your sense of taste. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I was reading Etymonline's entry for &lt;a href=&quot;http://www.etymonline.com/index.php?allowed_in_frame=0&amp;amp;search=palatable&amp;amp;searchmode=none&quot; rel=&quot;nofollow noreferrer&quot;&gt;palatable {adj.}&lt;/a&gt;, which cites and derives from &lt;a href=&quot;http://www.etymonline.com/index.php?term=palate&amp;amp;allowed_in_frame=0&quot; rel=&quot;nofollow noreferrer&quot;&gt;palate {noun}&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... Popularly considered the seat of taste, hence transferred meaning &quot;sense of taste&quot; (late 14c.), which also was in classical Latin. ...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Are the quotes above factually right about mouth anatomy (I ask NOT about language here)? Or was this an outdated wrong idea? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Footnote: Did the etymology become corrupt? I heed the Etymological Fallacy.&lt;/p&gt;&#xA;" OwnerUserId="4466" LastEditorUserId="16866" LastEditDate="2017-04-26T19:13:14.763" LastActivityDate="2017-04-26T19:13:14.763" Title="Does the palate truly house the sense of taste?" Tags="&lt;human-anatomy&gt;&lt;organs&gt;&lt;etymology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31658" PostTypeId="2" ParentId="31655" CreationDate="2015-04-23T19:52:01.383" Score="5" Body="&lt;p&gt;Anatomically speaking, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Palate&quot;&gt;palate&lt;/a&gt; is the roof of the mouth, separating the oral cavity (mouth) from the nasal cavity (inner nose). While the palate may be sensitive to heat and spiciness (via the &lt;a href=&quot;http://en.wikipedia.org/wiki/TRPV1&quot;&gt;capsaicin receptor&lt;/a&gt;, for example), it does not contain any &lt;a href=&quot;http://en.wikipedia.org/wiki/Taste_bud&quot;&gt;taste buds&lt;/a&gt;, which are located on the tongue, and are part of the taste-sensing system. The other part of this system, &lt;a href=&quot;http://en.wikipedia.org/wiki/Olfactory_receptor&quot;&gt;olfactory receptors&lt;/a&gt;, are responsible for sensing odors, and are mainly located in the nasal cavity, as well as partway down the back of the throat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, unfortunately, while your palate is figuratively the center of your sense of taste, in reality it has almost nothing to do with it.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-04-23T19:52:01.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31659" PostTypeId="1" CreationDate="2015-04-23T20:31:25.883" Score="1" ViewCount="211" Body="&lt;p&gt;I'm trying to predict the protein secondary and 3-D structure for the sequence [Q1NN20] and need some help getting the ball rolling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm getting confused with how and when to use Jpred, swiss-mod, and PDB. So far, I got the sequence from scanprosite, put it into swiss-mod, but what next? When does jpred come in? &lt;/p&gt;&#xA;" OwnerUserId="15223" LastEditorUserId="3553" LastEditDate="2015-12-02T09:08:14.107" LastActivityDate="2015-12-02T09:08:14.107" Title="How to use swiss-mod to predict the secondary structure and 3D structure of a protein?" Tags="&lt;bioinformatics&gt;&lt;homework&gt;&lt;protein-folding&gt;&lt;structure-prediction&gt;&lt;3d-structure&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31660" PostTypeId="1" AcceptedAnswerId="31790" CreationDate="2015-04-23T20:33:23.517" Score="8" ViewCount="34921" Body="&lt;p&gt;This bug is crawling all around the house it stays within the shadows and moves very very slow, i have never seen it jump or run, it just moves very slowly&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NYA4x.jpg&quot; alt=&quot;DSC_108&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. those bugs as u can see are smaller than 1mm so it's hard to take better pictures but i will get better ones tomorrow&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. the hairs are not hairs they are wool from the carpets, i just got married in october 2014 and everything in the house is new, including the flat, it was built in january 2014.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.dropbox.com/sh/knxjw6psd793anb/AADuYjPZAmTRHmZjgKy4_Wdza?dl=0&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bug pictures with a 1 mm thick pencil refill&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;it is very similar to what's in this picture, but i couldn't take a picture of it because it's tooo tiny&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I really need to know what it is so I can deal with it :(&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: once i found a very little few under the carpet but it generally stays away from the carpets and stays on the tiles and I don't think it is a termite because I don't find any piles of eaten wood&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT 2:&#xA;More pictures:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;-- Stage 1 --&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fV4tb.jpg&quot; alt=&quot;Insect 1 of 2 Stage 1 of 2 Pic 1 of 4&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/a7Qdj.jpg&quot; alt=&quot;Insect 1 of 2 Stage 1 of 2 Pic 2 of 4&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/aCxLf.jpg&quot; alt=&quot;Insect 1 of 2 Stage 1 of 2 Pic 3 of 4&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/dvXlc.jpg&quot; alt=&quot;Insect 1 of 2 Stage 1 of 2 Pic 4 of 4&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;-- Stage 2 --&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cQlzd.jpg&quot; alt=&quot;Insect 1 of 2 Stage 2 of 2 Pic 1 of 2&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/L8ZmH.jpg&quot; alt=&quot;Insect 1 of 2 Stage 2 of 2 Pic 2 of 2&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://youtu.be/qR7s6LbbdOM&quot; rel=&quot;nofollow noreferrer&quot;&gt;-- Video for stage 2 --&lt;/a&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know what it is but I know that there is ones young in age i call them stage 1 they are unable to move&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and there are ones I call stage 2 older in age and bigger in size and they can move and I think they can bite too&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;-- Insect 2 --&lt;/strong&gt; 5mm by 5mm&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FyS8k.jpg&quot; alt=&quot;Insect 2 of 2 Pic 1 of 2&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/5U7mk.jpg&quot; alt=&quot;Insect 2 of 2 Pic 2 of 2&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this one across the hall from the others and I do't know if it's related, i found it dead but I haven't sprayed that side with insecticides i sprayed the other side so it's possible that it was with the others but ran and died far from them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: More photos&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P.S. I found those moving in daylight (now)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Zm85H.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/pzxSz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/VKDCc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/8C2r1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/azAPx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/3zIsy.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/mdhrd.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/j6UFL.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/2XgAm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/cp397.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/BbydD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;when i blew a little air i think i turned it&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jTDFq.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="15476" LastEditorUserId="15476" LastEditDate="2015-04-24T16:07:08.757" LastActivityDate="2019-07-03T16:46:35.493" Title="I have a black tiny bug crawling all over the house" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="3" CommentCount="11" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31661" PostTypeId="2" ParentId="31649" CreationDate="2015-04-23T23:27:16.797" Score="1" Body="&lt;p&gt;So refer to the following diagram,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SPx7j.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the photosystem II complex, water is decomposed into oxygen and protons. That's two electrons liberated from each water molecule. Plastoquinone accepts two protons from the stroma by coupling it to the two electrons it receives from the photosystem complex. In this manner, the protons are transported to the lumen, and the electrons are sent into the electron transport chain. So PQ binds in a QB site in the D1 protein, and it's not released until it's double reduced/protonated. Another PQ binds in it's place when PQH2 leaves the binding site. &lt;a href=&quot;http://www.jbc.org/content/266/31/21293.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Short answer: Two electrons are liberated in splitting water, and that mechanism feeds into asymmetric lumen/stroma H+ concentrations and movement of electrons through the ETC.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-04-23T23:27:16.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31662" PostTypeId="1" AcceptedAnswerId="31670" CreationDate="2015-04-23T23:52:53.113" Score="8" ViewCount="20942" Body="&lt;p&gt;I know that blood platelets and &lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCAQFjAB&amp;amp;url=http%3A%2F%2Fbiology.stackexchange.com%2Fquestions%2F1037%2Fwhy-do-mammalian-red-blood-cells-lack-a-nucleus&amp;amp;ei=_pA5VfDABMa2mwWPxICwDA&amp;amp;usg=AFQjCNHX1uOKpqi4bxpPZqOoi_d1lmO0Tg&amp;amp;sig2=zq-aLiZexnTMbAe9z2yafw&amp;amp;bvm=bv.91427555,d.dGY&quot;&gt;erythrocytes&lt;/a&gt; do not have a nucleus. Are there more cells in the human body without a nucleus, such as pancreas, cartilage, or lung cells? &lt;/p&gt;&#xA;" OwnerUserId="15480" LastEditorUserId="9943" LastEditDate="2015-04-24T02:09:34.553" LastActivityDate="2017-06-02T17:03:10.270" Title="Are there human cells, apart from red blood cells and platelets, without a nucleus?" Tags="&lt;cell-biology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31663" PostTypeId="5" CreationDate="2015-04-23T23:55:28.783" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2015-04-23T23:55:28.783" LastActivityDate="2015-04-23T23:55:28.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31664" PostTypeId="4" CreationDate="2015-04-23T23:55:28.783" Score="0" Body="TCGA (The Cancer Genome Atlas) is a biology-oriented project for understanding the genomics of different types of cancers. " OwnerUserId="14852" LastEditorUserId="9943" LastEditDate="2015-04-24T00:39:10.813" LastActivityDate="2015-04-24T00:39:10.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31665" PostTypeId="1" CreationDate="2015-04-24T00:03:00.383" Score="3" ViewCount="395" Body="&lt;p&gt;I'm wondering what would we need to do to create a living dinosaur using DNA technology? If it is not possible with current technology, will it ever be feasible?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the movie Jurassic Park, scientists extract dinosaur DNA from a mosquito which was preserved in amber, and which has sucked blood from a dinosaur. The DNA is incomplete, so the scientists splice it with frog DNA. The DNA is then inserted into a crocodile ova and an embryo is created, and so on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Jurrassic park method is dubious. Although dinosaur DNA has been found and isolated, it was too damaged to restore it to its original form using current technology. It's not clear that splicing with frog DNA would work. Let's for the moment forget about how you would get the dinosaur embryo to develop and the eggs to incubate and hatch. I want to know how would we fully sequence the genome of some dinosaur?&lt;/p&gt;&#xA;" OwnerUserId="13409" LastActivityDate="2015-09-08T16:08:03.470" Title="How can we create a living dinosaur using DNA technology?" Tags="&lt;dna-sequencing&gt;&lt;cloning&gt;&lt;dna-damage&gt;&lt;extinction&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31666" PostTypeId="2" ParentId="31505" CreationDate="2015-04-24T00:30:20.147" Score="10" Body="&lt;p&gt;Given your questions taken together and your comment &lt;code&gt;It would be interesting to know how much delay the brain can handle in understanding causality and associating events&lt;/code&gt; I think you are interested in &lt;em&gt;&lt;strong&gt;intersensory asynchrony&lt;/strong&gt;&lt;/em&gt;. A well-known example where two stimulus modalities are perceived as separate while they are in fact coming from the same event is a thunder heard &lt;em&gt;after&lt;/em&gt; lightning. This is caused by the fact that sound travels at a speed much slower than light, and hence a thunder can lag lightning by seconds.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/P4Q3J.png&quot; alt=&quot;Thunder lightning&quot; /&gt;&lt;br /&gt;&#xA;&lt;sup&gt;source: &lt;a href=&quot;http://www.grc.nasa.gov/WWW/k-12/airplane/sound2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;NASA&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;p&gt;In many instances, however, one event generating perceptions across stimulus modalities are actually perceived as synchronous while they are in fact offset in time due to differences in physical characteristics of the stimuli. Taking the storm as an example - when it is far away, the thunder is perceived as separate because the thunder lags by seconds. But when the thunderstorm is close enough, the auditory crack and visual lightning are actually perceived as synchronous, while in fact they are still offset because of the sound travelling so much slower than light.&lt;/p&gt;&#xA;&lt;p&gt;So the question becomes, as you rightfully ask, what are the &lt;em&gt;margins&lt;/em&gt; in which stimuli across modalities can be asynchronous while perceived as one event? In other words, what is the &lt;em&gt;window of integration&lt;/em&gt;?&lt;/p&gt;&#xA;&lt;p&gt;A review by &lt;a href=&quot;http://www.researchgate.net/profile/Jean_Vroomen/publication/43535149_Perception_of_intersensory_synchrony_a_tutorial_review/links/0fcfd506d6effbeaa1000000.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Vroomen and Keetels (2010)&lt;/a&gt; describes various psychophysical studies that have examined what the &lt;em&gt;minimal asynchrony&lt;/em&gt; is between two stimuli of different modality that lead to a synchronized percept. The following values are for simple stimuli, such as tactile taps, auditory beeps and visual flashes.&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Auditory and tactile stimuli: &lt;strong&gt;80&lt;/strong&gt; ms&lt;/li&gt;&#xA;&lt;li&gt;Auditory beeps and visual flashes: &lt;strong&gt;25 - 50&lt;/strong&gt; ms&lt;/li&gt;&#xA;&lt;li&gt;Visual and tactile stimili: &lt;strong&gt;35 - 65&lt;/strong&gt; ms&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Note that these lag differences are relatively large, given the speed of peripheral neural transduction (see the other answer of Nandor Poka below). Moreover, the window of integration between more complex stimuli can be much greater. For example, the window for &lt;strong&gt;speech and visual information&lt;/strong&gt; can be as large as &lt;strong&gt;203 ms&lt;/strong&gt;.  Such large windows of integration point toward higher processes playing a role in the brain.&#xA;Note that only temporal lags &lt;strong&gt;below 20 msec&lt;/strong&gt; are expected to go &lt;strong&gt;unnoticed because of hard-wired limitations&lt;/strong&gt; on the resolution power of the individual senses,&lt;/p&gt;&#xA;&lt;p&gt;Hence, &lt;a href=&quot;http://www.researchgate.net/profile/Jean_Vroomen/publication/43535149_Perception_of_intersensory_synchrony_a_tutorial_review/links/0fcfd506d6effbeaa1000000.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Vroomen and Keetels (2010)&lt;/a&gt; argue there must be &lt;strong&gt;higher processes&lt;/strong&gt; at work in the brain that actively synchronize percepts that are offset in time, but seem to belong to one and the same event. One such mechanism is referred to as &lt;em&gt;temporal ventriloquism&lt;/em&gt;, which means that one perceptual modality is actively shifted in time to match it with another. This effect is most pronounced in visual stimuli, in that a visual percept is actively adjusted in time to match a sound or tactile stimulus. Likely visual percepts are shifted preferably by the brain, because the visual system is the slowest of all the senses.&lt;/p&gt;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br /&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.researchgate.net/profile/Jean_Vroomen/publication/43535149_Perception_of_intersensory_synchrony_a_tutorial_review/links/0fcfd506d6effbeaa1000000.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Vroomen &amp;amp; Keetels, &lt;em&gt;Att Percept Psychophys&lt;/em&gt; 2010; &lt;strong&gt;72&lt;/strong&gt;(4): 871-84&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2021-03-25T08:07:42.133" LastActivityDate="2021-03-25T08:07:42.133" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="31669" PostTypeId="2" ParentId="31499" CreationDate="2015-04-24T01:57:27.447" Score="3" Body="&lt;p&gt;Water is split in chloroplasts in the &lt;strong&gt;&lt;a href=&quot;http://www.uic.edu/classes/bios/bios100/lectures/ps01.htm&quot; rel=&quot;nofollow&quot;&gt;light reaction of photosynthesis&lt;/a&gt;&lt;/strong&gt;. Chlorophyll, acting as a photopigment, captures sunlight and transfers that energy to an electron pair of a water molecule. Under the influence of a water-splitting enzyme (George et al, 1989) it is separated into 2 protons, molecular oxygen and a free electron pair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2916124&quot; rel=&quot;nofollow&quot;&gt;George et al. &lt;em&gt;Science&lt;/em&gt; 1989; &lt;strong&gt;243&lt;/strong&gt;(4892): 789-91&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-04-29T13:39:59.510" LastActivityDate="2015-04-29T13:39:59.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31670" PostTypeId="2" ParentId="31662" CreationDate="2015-04-24T02:05:10.040" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;As far as I know, red blood cells and blood platelets are the only &lt;em&gt;human&lt;/em&gt; cells in our body without a nucleus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Erythrocytes and thrombocytes are the &lt;strong&gt;only &lt;em&gt;human&lt;/em&gt; cells&lt;/strong&gt; without a nucleus, as far as I know. However, if you count the gut as being part of the human body (in essence it is a continuation of the skin and as such it can be considered to be on our &lt;em&gt;outside&lt;/em&gt;), then we are &lt;em&gt;loaded&lt;/em&gt; with cells lacking a nucleus, namely all the bacteria that live in our intestines such as &lt;em&gt;E. coli&lt;/em&gt;. Bacteria, being prokaryotes, lack a nucleus. In fact, there are ten times more bacteria than human cells in our gut &lt;a href=&quot;http://www.scientificamerican.com/article/strange-but-true-humans-carry-more-bacterial-cells-than-human-ones/&quot; rel=&quot;nofollow&quot;&gt;(Wenner, 2007)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.scientificamerican.com/article/strange-but-true-humans-carry-more-bacterial-cells-than-human-ones/&quot; rel=&quot;nofollow&quot;&gt;Wenner, &lt;em&gt;Sci Am&lt;/em&gt; 2007&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="3340" LastEditDate="2015-04-25T09:48:57.813" LastActivityDate="2015-04-25T09:48:57.813" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31671" PostTypeId="5" CreationDate="2015-04-24T02:12:08.913" Score="0" Body="&lt;p&gt;International Cancer Genome Consortium (&lt;a href=&quot;http://icgc.org&quot; rel=&quot;nofollow&quot;&gt;ICGC&lt;/a&gt;) is a consortium of different countries for understanding the Cancer Genomics. ICGC Data Portal is unified and easier to use.&lt;/p&gt;&#xA;" OwnerUserId="14852" LastEditorUserId="14852" LastEditDate="2015-04-24T04:00:08.287" LastActivityDate="2015-04-24T04:00:08.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31672" PostTypeId="4" CreationDate="2015-04-24T02:12:08.913" Score="0" Body="ICGC is International Cancer Genome Consortium. Use this tag if your question is relevant (just relevant, mainly about Biology) If you have FAQ about any ICGC data, etc. contact them at https://icgc.org/icgc/contacts" OwnerUserId="14852" LastEditorUserId="14852" LastEditDate="2015-04-24T04:09:01.133" LastActivityDate="2015-04-24T04:09:01.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31673" PostTypeId="2" ParentId="31566" CreationDate="2015-04-24T04:16:21.600" Score="0" Body="&lt;p&gt;Computers rely on cooling mechanisms like &lt;a href=&quot;http://en.wikipedia.org/wiki/Heat_sink&quot; rel=&quot;nofollow noreferrer&quot;&gt;heat sinks&lt;/a&gt;( an aluminum alloy mounted over the micro integrated chip) and fan. So far none of these mechanisms are utilized by nature, but analogies like cooling mechanisms in elephants which are in turn considered to be a model quite like the fan.&lt;/p&gt;&#xA;&lt;p&gt;As the largest land animal, elephant's ears have crucial role in regulating &lt;a href=&quot;http://en.wikipedia.org/wiki/Homeostasis&quot; rel=&quot;nofollow noreferrer&quot;&gt;homeostasis&lt;/a&gt;. When we see an elephant, it always wave its ears in order to reduce the brain temperature. On the other hand humming birds which are very smaller in size reduces its temperature by flowing blood to its wings. Humming birds wings flutter 90 times a second and it allows them to exchange much of its heat to the environment and the cooled blood is driven back to the brain.&lt;/p&gt;&#xA;&lt;p&gt;The  carotid rete or &lt;a href=&quot;http://en.wikipedia.org/wiki/Rete_mirabile&quot; rel=&quot;nofollow noreferrer&quot;&gt;rete mirabile&lt;/a&gt; in birds have been developed for heat exchange. In mammals, a pool of the cool venous&#xA;blood  returns from the nose or&#xA;head skin, exchanges the heat with&#xA;warm arterial blood of the carotid artery.&#xA;These arteries are sub divided into hundreds of&#xA;small arteries forming a net like structure which significantly improve the&#xA;heat transfer in brain.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Vascular retia mirabilia are also found in the limbs of a range of&#xA;mammals. These reduce the temperature in the extremities. Some of&#xA;these probably function to prevent heat loss in cold conditions by&#xA;reducing the temperature gradient between the limb and the&#xA;environment. Others reduce the temperature of the testes increasing&#xA;their productivity. In the neck of the dog, a rete mirabile protects&#xA;the brain when the body overheats during hunting; the venous blood is&#xA;cooled down by panting before entering the net.&lt;a href=&quot;http://en.wikipedia.org/wiki/Rete_mirabile&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;In Humans,&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The net effect of heat production in the brain and brain cooling&#xA;keeps the brain cooler than the rest of the body and is achieved by&#xA;surrounding and bathing the brain with venous blood that has been&#xA;cooled outside the cranial vault, by bone and fat acting as&#xA;insulation, by the veins of the face and scalp through conduction,&#xA;convection, sweat and evaporation and by cooled venous blood flowing&#xA;through the cavernous and suboccipital cavernous sinuses cooling&#xA;incoming blood in the internal carotid and vertebral arteries before&#xA;it enters the brain. The combined effect of the brain cooling system&#xA;keeps the temperature inside the vault and brain about two to three&#xA;degrees cooler than the rest of the body. The effect is important&#xA;enough that some physical anthropologists attribute the extra-large&#xA;size of the human brain more to its exceptional cooling capacity than&#xA;to the increase in arterial blood flow that comes with upright&#xA;posture. Anthropologists refer to human encephalization due to&#xA;enhanced brain cooling capacity as the &amp;quot;radiator theory&amp;quot;.&#xA;&lt;a href=&quot;http://www.upright-health.com/brain-cooling.html+&amp;amp;cd=6&amp;amp;hl=en&amp;amp;ct=clnk&amp;amp;gl=in&quot; rel=&quot;nofollow noreferrer&quot;&gt;Reference&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Also yawning and panting are considered to be mechanisms to reduce brain temperature.&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-24T04:16:21.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31674" PostTypeId="1" AcceptedAnswerId="31700" CreationDate="2015-04-24T05:18:31.163" Score="3" ViewCount="171" Body="&lt;p&gt;I do not seem to understand the concept of Quantitative Trait Loci(QTL's), can anyone explain it to me in detail? Reading the wikipedia article helped somewhat, but I do not understand it well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I understand:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-quantitative traits = a number(quantity) of phenotypes(traits) that vary&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-To &quot;make&quot; a QTL, one must &quot;map&quot; the phenotypical traits to the genes that they are believed to propagate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-This is done by AFLP-PCR, or Amplified fragment length polymorphism, according to wikipedia at least. This process cuts the genomic DNA into pieces and then amplifies the target region with primers via PCR. Then it is visualized using some type of gel technique? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;-I am not sure how this gel data then allows the mapping of phenotypes to genes. I know gel electrophoresis can help to identify the length of a gene or region of a gene if using a ladder to compare.&lt;/p&gt;&#xA;" OwnerUserId="14815" LastActivityDate="2015-04-25T01:01:04.643" Title="Quantitative Trait Locus process?" Tags="&lt;genetics&gt;&lt;pcr&gt;&lt;gel-electrophoresis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31676" PostTypeId="2" ParentId="31660" CreationDate="2015-04-24T08:06:52.517" Score="4" Body="&lt;p&gt;&lt;strong&gt;Update:&lt;/strong&gt; This is an &lt;em&gt;incorrect&lt;/em&gt; answer. From the poster's &lt;a href=&quot;https://biology.stackexchange.com/questions/31660/i-have-a-black-tiny-bug-crawling-all-over-the-house#comment53444_31790&quot;&gt;comment&lt;/a&gt; above: &quot;&lt;code&gt;Clearer pictures would have eliminated my termite guess at a much earlier stage&lt;/code&gt;.&quot;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The organism you call 'stage 2' looks like a &lt;a href=&quot;http://en.wikipedia.org/wiki/Termite&quot; rel=&quot;nofollow noreferrer&quot;&gt;termite&lt;/a&gt; to me, and the movement pattern shown in the video also fits well. They are mostly nocturnal, which also fits your observations. Your 'insect 2' is some sort of &lt;a href=&quot;http://en.wikipedia.org/wiki/Isopoda&quot; rel=&quot;nofollow noreferrer&quot;&gt;Isopod&lt;/a&gt; (an anthropod but not an insect), and unrelated to other organism. However, 1 mm is really small for a termite from what I know, but there are many different species and some can probably be that small. You should try to see if they have strait, beaded antennas and no narrow waist (which ants have) - both these characters are used to separate termites from ants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is another &lt;a href=&quot;https://insects.tamu.edu/extension/publications/epubs/e-368.cfm&quot; rel=&quot;nofollow noreferrer&quot;&gt;useful page on termites&lt;/a&gt; from Texas A&amp;amp;M university, which includes more pictures and information on how to deal with infestations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This picture shows soldiers (large jaws) and workers (pale heads) of the Formosan subterranean termite (&lt;em&gt;Coptotermes formosanus&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/P0Kn5.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;(public domain picture from wikipedia)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another possibility would be springtails (which are generally smaller than termites), but they are mostly found in moist soil, wood and similar environments, and they can jump.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="16866" LastEditDate="2019-07-03T16:46:35.493" LastActivityDate="2019-07-03T16:46:35.493" CommentCount="7" ContentLicense="CC BY-SA 4.0" />
  <row Id="31677" PostTypeId="2" ParentId="13884" CreationDate="2015-04-24T11:59:45.240" Score="2" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;I can be &lt;strong&gt;75%&lt;/strong&gt; sure that the lights are synchronized within &lt;strong&gt;0.02 - 0.2&lt;/strong&gt; seconds of one another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Interesting question, but hard to answer! Because it has been unanswered for quite a while I will try to formulate an answer that may provide an approximate value for the minimal asynchrony perceivable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The temporal resolution of the visual system can be quantified in a number of ways. As you are referring to relatively simple stimuli, the &lt;strong&gt;&lt;em&gt;critical flicker fusion frequency&lt;/em&gt;&lt;/strong&gt; is probably the most relevant. At a certain critical frequency, a flickering stimulus will appear as a continuous stimulus &lt;a href=&quot;http://www.psych.usyd.edu.au/staff/alexh/research/papers/Holcombe2009SeeingSlowSeeingFast.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Holcomb, 2009)&lt;/a&gt;. For example, the good old CRT screens can sometimes seem to be flickering. The mains is 50 Hz (US) or 60 Hz (Europe, Australia), and indeed the critical flicker fusion frequency is &lt;strong&gt;5 - 50 Hz&lt;/strong&gt;, dependent on the lighting conditions (&lt;a href=&quot;http://webvision.med.utah.edu/book/part-viii-gabac-receptors/temporal-resolution/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kalloniatis &amp;amp; Luu&lt;/a&gt;). Hence, stimuli separated by &lt;strong&gt;200 ms&lt;/strong&gt; (low lighting) to &lt;strong&gt;20 ms&lt;/strong&gt; (high lighting conditions) can be temporally resolved. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am aware that your question is different, as you ask whether two stimuli on the retina can be perceived as being asycnchronous. Flicker fusion testing is mainly done with flash stimuli, i.e., a single stimulus per image, not two. However, from the various measures of temporal resolution of the visual system that have been used to date, the critical flicker fusion has the most conservative value, in that it provides the top-value of temporal resolution. Higher-level processing is much slower and values of around 4 Hz are obtained. For example, when subjects are tested on a stimulus of dots that are white when moving right and black when moving left, and they change directions/colors at a certain frequency, it becomes hard to tell whether the color change and direction change are synchronized at alteration rates of ~5 Hz and higher (&lt;a href=&quot;http://webvision.med.utah.edu/book/part-viii-gabac-receptors/temporal-resolution/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kalloniatis &amp;amp; Luu&lt;/a&gt;).    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to your question what the &lt;strong&gt;percentage chance&lt;/strong&gt; is that stimuli separate by 20 -200 ms are separable, I can say that in general, psychophysical procedures determine the &lt;em&gt;threshold&lt;/em&gt; defined as &lt;em&gt;halfway between chance and 100% correct&lt;/em&gt;. Assuming a typical yes/no tasK (&lt;em&gt;are the traffic lights synchronous yes/no?&lt;/em&gt;), chance would be 50% (guessing), and threshold would thus be defined as halfway between 50% and 100%, i.e., &lt;strong&gt;75% correct&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.psych.usyd.edu.au/staff/alexh/research/papers/Holcombe2009SeeingSlowSeeingFast.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Holcomb, &lt;em&gt;Trends Cog Sci 2009&lt;/em&gt;; &lt;strong&gt;13&lt;/strong&gt;(5): 216-21&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://webvision.med.utah.edu/book/part-viii-gabac-receptors/temporal-resolution/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kalloniatis &amp;amp; Luu, WebVision, chapter &quot;Temporal Resolution&quot; 2007&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2018-08-19T18:44:37.320" LastActivityDate="2018-08-19T18:44:37.320" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="31678" PostTypeId="1" CreationDate="2015-04-24T13:10:12.007" Score="6" ViewCount="397" Body="&lt;p&gt;(Man, there's a &lt;em&gt;lot&lt;/em&gt; of 'What is this X?' questions here...)&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mL3It.jpg&quot; alt=&quot;mysterious frog&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;I saw this while walking in Cyprus in early April. It was at about 100m altitude, in woodlands, sitting in the sun on a concrete step beside a muddy ditch; it's about 3cm long.&lt;/p&gt;&#xA;&lt;p&gt;There appear to be &lt;strike&gt;three&lt;/strike&gt; four types of frog in Cyprus, one of which is actually a toad, and this doesn't really look like any of them --- the closest is the Middle Eastern tree frog (&lt;a href=&quot;http://en.wikipedia.org/wiki/Middle_East_tree_frog&quot; rel=&quot;noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Middle_East_tree_frog&lt;/a&gt;) but the colouring doesn't match and my frog is much more wrinkly and chunky-looking.&lt;/p&gt;&#xA;&lt;p&gt;So what &lt;em&gt;is&lt;/em&gt; it?&lt;/p&gt;&#xA;" OwnerUserId="15486" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-11-04T14:47:43.387" Title="What is this frog?" Tags="&lt;species-identification&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31681" PostTypeId="1" AcceptedAnswerId="31703" CreationDate="2015-04-24T14:12:44.853" Score="4" ViewCount="19467" Body="&lt;p&gt;The background to this is i'm doing some work using ECGs for an animation of the heart and i'm having trouble defining the end points of these periods, particularly diastole. Currently, the only information the animation uses is the time (in seconds) when a R peak was detected in an ECG. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So i was wondering what the normal lengths of these periods are and what could affect the lengths of these periods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume that the lengths of the periods is mainly affected by pressure/blood volume and not electrical activity so an ECG won't tell you how long these periods are (unless a heart beat is interrupted by another?). Is that assumption correct? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On a side note: what would happens to the heart physically if there is a large gap between beats. Does it sit relatively still during that period?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My original post could have worded better, so: I want to know specifically about long it takes for the ventricles to physical contract and relax. How would i determine the length of these two periods in seconds and where could i find the &quot;normal&quot; lengths of these periods? in the cause of relaxation, i'm wondering about what to do when there is a substantial gap between heart beats.&lt;/p&gt;&#xA;" OwnerUserId="15489" LastEditorUserId="15489" LastEditDate="2015-04-25T13:15:29.940" LastActivityDate="2017-07-14T02:19:27.617" Title="How long do the periods of systole and diastole last?" Tags="&lt;cardiology&gt;&lt;electrocardiography&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31682" PostTypeId="2" ParentId="31662" CreationDate="2015-04-24T14:44:26.937" Score="14" Body="&lt;p&gt;&lt;em&gt;Wanted to give a one line answer some day!!&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903674/&quot;&gt;Lens fiber cells&lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/cdd/journal/v7/n12/full/4400785a.html&quot;&gt;keratinocytes&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-04-24T14:44:26.937" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31683" PostTypeId="2" ParentId="31611" CreationDate="2015-04-24T15:04:53.970" Score="1" Body="&lt;p&gt;&lt;strong&gt;Generalities&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are plenty of ways at looking at phenotypes that affect the fitness of the carrier and of other individuals. One of them is group selection and another one is kin selection. Those two concepts are just two different ways of looking at the same processes. Now let's consider only the kin selection way of looking at these processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can either consider the impact of the phenotype of a focus individual to neighbour individuals or the impact of neighbour individuals to the focus individual. Looking at it both ways, would yield to count the effect of your phenotype on twice. It doesn't make much sense to talk about the mean inclusive fitness of a population. You can only talk about the mean fitness of a population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The confusion&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for all these confusion boils down to what $B$ and $C$ really mean. One of the issue is that you confuse $B$ and $b$, $C$ and $c$. The formulation $rB&amp;gt;C$ is a oversimplification of the reality. Hamilton did not use this formulation at first and interpreting $b$ as the benefit for the carrier might be misleading. It is important to understand Hamilton's rule in its original formulation and it is important to understand the evolutionary game theory that underlies the evolution of social traits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is Hamilton's rule&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One cannot study the evolution of social traits under the kin selection framework if (s)he doesn't understand the underlying game theory. $rB&amp;gt;C$ assumes that the game we're playing is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Prisoner&amp;#39;s_dilemma&quot; rel=&quot;nofollow&quot;&gt;Prisoner's dilemna&lt;/a&gt;. You can learn more about game theory. You can learn more about evolutionary game theory on &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolutionary_game_theory&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt; or in &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0262731215&quot; rel=&quot;nofollow&quot;&gt;this book&lt;/a&gt;. &lt;a href=&quot;https://www.khanacademy.org/economics-finance-domain/microeconomics/nash-equilibrium-tutorial/nash-eq-tutorial/v/prisoners-dilemma-and-nash-equilibrium&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a Khan academy video on Prisoner's dilemna&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Let's assume we are playing prisoner's dilemna&lt;/strong&gt;. The fitness of an individual which cooperate is by definition $w_o + b - c$ (note the letters are not capitalized). If you cooperate and the other don't, your fitness is $w_o - c$. If you don't cooperate and the other does cooperate, you fitness is $w_o + b$. If nobody cooperates, your fitness if $w_o$. And by definition , $b&amp;gt;c$. Knowing the frequency of people that cooperate in the population $y$ and knowing and your probability of cooperating is $x$. Then, the level of altruism (frequency of cooperations) increases in the population if and only if &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$R\cdot\frac{dw(x,y)}{dx}&amp;gt;\frac{dw(x,y)}{dy}$$, where $R$ is the coefficient of relatedness which can itself be expressed as a correlation between the variables $x$ and $y$. $w(x,y)$ is the fitness of the the individual being altruistic with probability $x$ in a population where individuals cooperate with probability $y$ and $\frac{dw(x,y)}{dx}$ is the partial derivative of the fitness function with respect to $x$. By definition, $\frac{dw(x,y)}{dx} = B$ and $\frac{dw(x,y)}{dy}=C$ (capital letters).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mean fitness of the population therefore depends on the frequency of cooperation $y$. Let's assume for simplicity that $y=1$ (equilibrium), then the mean fitness of the population is $w_o + b - c$ (note that the letters, $b$ and $c$ are not capital letter), and the variance in fitness is null. All individuals has a fitness of $w_o + b -c$ as all individuals are altruistic and perform action that has a negative impact on the fitness $-c$ and a positive impact on their fitness $b$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In short&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$b$ and $c$ in your question, correspond to $b$ and $c$ in my answer and not to $B$ and $C$. If you're playing prisoner's dilemna, then by definition, if everybody cooperate (no variance in the population), then everybody has a fitness of $w_o + b - c$ and the mean fitness is $w_0 + b - c$ (as there is no variance). Now the question of whether everybody ends up cooperating depends on $B$, $C$ and $R$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your edit, you write $rb$ and $c$ but you get confused about the meaning of $b$ and $c$. If you are playing prisoner's dilemna, when you cooperate with someone that is also cooperating, you inclusive fitness is $b-c + r(b-c)$ and if you cooperate with someone that is not cooperating, your inclusive fitness is $b-c + r(b)$.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-04-25T00:14:04.560" LastActivityDate="2015-04-25T00:14:04.560" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31684" PostTypeId="1" CreationDate="2015-04-24T15:17:44.017" Score="3" ViewCount="658" Body="&lt;p&gt;If NADPH returns to being NADP+, then that means one proton and two electrons have been incorporated into 1,3-BPG. If only one proton and one electron were attached to the carbon in 1,3-BPG (removing phosphate), I’d understand, since there’s a single covalent bond between carbon and hydrogen which establishes stable octets. But there’s another electron hanging around. What happens to this one? Or am I totally mistaken about the whole process?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the chemical formula for G3P:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FiVRX.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Lewis diagram below shows the top part:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TFcjD.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As stated, NADPH gave off 2 electrons, yet only one is needed to bond with carbon (orange). Where did the other electron disappear to?&lt;/p&gt;&#xA;" OwnerUserId="15272" LastEditorUserId="15272" LastEditDate="2015-04-25T02:33:37.243" LastActivityDate="2015-04-25T02:33:37.243" Title="How Does NADPH Reduce 1,3-BPG?" Tags="&lt;biochemistry&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31686" PostTypeId="2" ParentId="10376" CreationDate="2015-04-24T16:00:37.827" Score="1" Body="&lt;p&gt;The Bible of biology is the Alberts' Molecular Biology of the Cell:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21054/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK21054/&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The Campbell is also pretty good and maybe easier to read..&lt;/p&gt;&#xA;" OwnerUserId="4746" LastActivityDate="2015-04-24T16:00:37.827" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31688" PostTypeId="1" CreationDate="2015-04-24T16:25:02.933" Score="8" ViewCount="1140" Body="&lt;p&gt;I have a project about extracting features from a homemade ECG. I need the PQRST points from the signal of the heart beat. The ECG I'm using has 3 electrodes that attach to the chest. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem is I don't know where I should define the PQRST points because the result does not look much like an ECG. I want to try to create a program later that can find those points.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are the raw ECG traces data taken from 3 subjects that were alcohol-intoxicated (0.2 to 0.3 promille):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vj6ri.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/chRpM.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm guessing the red and orange points here. And I'm pretty sure the green points are accurate located:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QAE39.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Green points is easy to locate but the orange is a little harder and the red ones are really hard to pin point out. Those points can be used to define the length of different complexes, intervals and segments of PQRST.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which points is safe to extract? Where exactly are those points located in the graph?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the data too inaccurate for finding abnormalities?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any other useful feature, beside heart rate, I can extract from my graph?&lt;/p&gt;&#xA;" OwnerUserId="10301" LastEditorUserId="16866" LastEditDate="2017-04-13T03:59:10.967" LastActivityDate="2017-05-24T14:24:32.243" Title="How to analyse an ECG?" Tags="&lt;cardiology&gt;&lt;electrophysiology&gt;&lt;electrocardiography&gt;" AnswerCount="4" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31689" PostTypeId="1" AcceptedAnswerId="31699" CreationDate="2015-04-24T16:50:33.413" Score="11" ViewCount="24208" Body="&lt;p&gt;The formula for photosynthesis is: $$6CO_2+12H_2O \rightarrow C_6H_{12}O_6+6O_2+6H_2O$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can count the carbons, the waters on the reactant side, the oxygens, and the glucose, but I cannot seem to locate where in either light or dark reaction 6 water molecules were produced again. Where and when were they produced?&lt;/p&gt;&#xA;" OwnerUserId="15272" LastActivityDate="2018-02-16T09:39:33.643" Title="When is Water Produced During Photosynthesis?" Tags="&lt;biochemistry&gt;&lt;photosynthesis&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31690" PostTypeId="2" ParentId="31688" CreationDate="2015-04-24T17:23:42.850" Score="5" Body="&lt;p&gt;First bump is called P point, middle is QRS &lt;em&gt;wave&lt;/em&gt; (as in Q-down, R-up, S-down), and last bump is T. Every feature is representation of electrical activity in certain region of heart. &lt;em&gt;E.g.&lt;/em&gt; P bump is contraction of atrium. See &lt;a href=&quot;http://www.cyberphysics.co.uk/topics/medical/heart/PQRST.html&quot; rel=&quot;noreferrer&quot;&gt;more here&lt;/a&gt;. Bumps are P/QRS/T.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason why you see so many different recordings is that it was taken with many-lead ECG. Heart has very distinct shape, its atrium is on top of ventricle, it is a bit tilted to the right, &lt;em&gt;etc&lt;/em&gt;. Your recording is a &lt;strong&gt;projection&lt;/strong&gt; of electrical activity vector onto vector that connects two leads used for given recording. Pick two other electrodes and you will have different picture just because axis of projection changed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gM3Yf.png&quot; alt=&quot;heart ECG vectors&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://openi.nlm.nih.gov/detailedresult.php?img=3044884_TOBEJ-4-217_F2&amp;amp;req=4&quot; rel=&quot;noreferrer&quot;&gt;via NIH&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to me that recording you show are from different pairs of electrodes, but it shouldn't matter. As you can see, different pairs of electrodes will &quot;pick up&quot; some processes better that the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, because ECG is electrical activity recording, heart rate is least useful information to extract from it. Measuring pulse will be less of a hassle and as accurate. But what you can do is estimate biophysicals properties of given heart. For example, distance between P and QRS (PR interval) complexes is time that it takes for heart to contract ventricle after atrial contraction. Any abnormalities will cause lengthening of PR or other change. Lengthening of PR interval often indicates 1st degree AV block (AV node is not conducting as usual).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is bunch of information out there on ECG and abnormalities, you can find useful &lt;a href=&quot;http://ecg.utah.edu/lesson/6&quot; rel=&quot;noreferrer&quot;&gt;this page from U Utah&lt;/a&gt; with examples of many severe conduction abnormalities.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-24T17:23:42.850" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31691" PostTypeId="2" ParentId="31684" CreationDate="2015-04-24T17:32:23.537" Score="1" Body="&lt;p&gt;Single covalent bond is a &lt;strong&gt;shared pair&lt;/strong&gt; of electrons. For stable bond there should be 2 atoms with unfilled higher orbitals and at least a pair of electrons that is &quot;distributed&quot; among those slots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UC Davis have hilarious &lt;a href=&quot;http://chemwiki.ucdavis.edu/Theoretical_Chemistry/Chemical_Bonding/General_Principles/Covalent_Bonds&quot; rel=&quot;nofollow&quot;&gt;page on that&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-24T17:32:23.537" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31692" PostTypeId="1" AcceptedAnswerId="31693" CreationDate="2015-04-24T18:10:29.063" Score="1" ViewCount="1313" Body="&lt;p&gt;I see on &lt;a href=&quot;http://en.wikipedia.org/wiki/Upper_limb&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Upper_limb&lt;/a&gt; that the term &quot;upper extremity&quot; seem to include hands. However, in many hospitals, there is a &quot;Hand &amp;amp; Upper Extremity Service&quot;, which would tend to indicate that the term &quot;upper extremity&quot; does not include hands. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the term &quot;upper extremity&quot; include hands?&lt;/p&gt;&#xA;" OwnerUserId="630" LastEditorUserId="630" LastEditDate="2015-04-24T18:26:45.977" LastActivityDate="2015-04-24T18:44:24.147" Title="Does the term &quot;upper extremity&quot; include hands?" Tags="&lt;human-anatomy&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31693" PostTypeId="2" ParentId="31692" CreationDate="2015-04-24T18:44:24.147" Score="2" Body="&lt;p&gt;As far as I know, and the same is written on &lt;a href=&quot;http://medical-dictionary.thefreedictionary.com/upper+extremity&quot; rel=&quot;nofollow&quot;&gt;Farlex Free Dictionary&lt;/a&gt;, the &lt;em&gt;upper extremity&lt;/em&gt; or &lt;em&gt;superior limb&lt;/em&gt; includes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the shoulder girdle&lt;/li&gt;&#xA;&lt;li&gt;the arm&lt;/li&gt;&#xA;&lt;li&gt;the forearm&lt;/li&gt;&#xA;&lt;li&gt;the hand&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Again, on this &lt;a href=&quot;https://www.dartmouth.edu/~humananatomy/part_2/chapter_6.html&quot; rel=&quot;nofollow&quot;&gt;Dartmouth Medical School&lt;/a&gt; page, the upper limb bones are described and the article includes the bones of the hand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, &lt;strong&gt;anatomically speaking&lt;/strong&gt;, the upper limb includes the hand.&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2015-04-24T18:44:24.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31697" PostTypeId="2" ParentId="31665" CreationDate="2015-04-24T19:12:55.263" Score="0" Body="&lt;p&gt;Comparing back to related DNA is how it has been done in the &lt;a href=&quot;http://www.nature.com/nature/journal/v456/n7220/full/nature07446.html&quot; rel=&quot;nofollow&quot;&gt;past&lt;/a&gt; with the woolly mammoth. So it might be a mater of extracting enough and finding close enough relatives to do this. But from what I have read, the DNA is so heavily fragmented that is is relatively impossible to map even to close relatives. You can understand this as the more heavily fragmented the DNA the smaller the pieces. So if you have a strand like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ACTGATCGTACGTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTACTACTAGCT&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;It is long and may map to only one or two locations on a relative's genome. But if you have heavily fragmented strands that are much shorter like this:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;AGTC&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;You can imagine that would map to millions of different locations. So putting these in order would essentially be impossible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We have to also put these things on a timeline to really understand the difficulty, Woolly Mammoths lived 500,000 years ago, dinosaurs were like 60 million years ago.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-04-24T19:12:55.263" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31698" PostTypeId="1" CreationDate="2015-04-24T20:53:20.773" Score="5" ViewCount="107" Body="&lt;p&gt;During Chemotaxis in bacteria with flagella, the flagellar rotation dictates how the cell moves. If the flagella rotate counterclockwise, then they form a bundle at one end of the cell (---O) and propel it forward in a coordinated fashion. However, if the flagella rotate clockwise, then each flagella acts independently to push the cell in many different directions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, why doesn't clockwise flagellar rotation simply cause the bundle to form on the opposite end of the cell? (O---)&lt;/p&gt;&#xA;" OwnerUserId="12970" LastActivityDate="2017-03-29T09:06:48.763" Title="Why do flagella form a bundle only when they rotate counterclockwise during chemotaxis?" Tags="&lt;cell-biology&gt;&lt;microbiology&gt;&lt;bio-mechanics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31699" PostTypeId="2" ParentId="31689" CreationDate="2015-04-24T22:05:48.903" Score="5" Body="&lt;p&gt;Some of the water that's split is regenerated when the hydroxyl radicals (reactive oxygen species) are converted to hydrogen peroxide, water, etc. by superoxide dismutases and antioxidative mechanisms in the chloroplast (peroxisomes/catalases, etc. take care of this). There's also some evidence that the presence of mannitol, ascorbate and glutathione protect against ROS produced in chloroplasts as well. So you input water, and in an effort to avoid oxidative damage, you do get some water generated. However, the balanced equation doesn't reflect this because it's not an actual product of photosynthesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC158511/pdf/1150527.pdf&quot; rel=&quot;noreferrer&quot;&gt;About ROS and protective elements&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sebiology.org/publications/Bulletin/October06/Reactive_Oxygen.html&quot; rel=&quot;noreferrer&quot;&gt;Extra Reading on ROS in photosynthetic systems&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that's a very obscure fact, and despite the reality of things, it's actually difficult to query the literature. Good question.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-04-24T22:11:21.877" LastActivityDate="2015-04-24T22:11:21.877" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31700" PostTypeId="2" ParentId="31674" CreationDate="2015-04-25T01:01:04.643" Score="1" Body="&lt;p&gt;When we say that something is a genetic marker we mean that we can establish its linkage to a chromosome AND that we have some way of discerning, or detecting, how the marker has segregated after meiotic recombination (this definition is only valid for diploid species that undergo sexual reproduction).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, for example, in the fruit fly, Drosphila melanogaster, the &lt;em&gt;white&lt;/em&gt; gene is linked to the X chromosome. Wild-type flies have red eyes, a mutation in the &lt;em&gt;white&lt;/em&gt; gene yields flies with white eyes.  You can use genetic crosses (matings) to (a) show that the &lt;em&gt;white&lt;/em&gt; gene is linked to only one of the four fly chromosomes, and (b) if you have other genetic markers on that chromosome you might be able to construct a genetic map showing the order and distance of the linked genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also use a DNA fragment from a chromosome as a genetic marker--if you have an assay that lets you track the fragment after meiotic recombination.  A Southern blot, using a labeled probe is one way to accomplish this (e.g. a Restriction Fragment Length Polymorphism or RFLP).  PCR that lets you detect a RFLP or a SNP serves the same function, and is much quicker than a Southern Blot (and requires less DNA starting material).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A QTL is just one of these &quot;molecular&quot; genetic markers that shows linkage to the trait you are assaying. So, for example, if you had RFLPs or SNPs sprinkled all along the human chromosomes, and if you had a way to detect the segregation of all those markers after meiotic recombination, then you could use DNA from a family with lots of kids of varying heights, where one parent was tall, and the other parent was short, to see if any of your genetic markers were segregating, or linked to the phenotype of height in the children (this example assumes that height in humans is a quantitative trait).&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-04-25T01:01:04.643" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31701" PostTypeId="1" AcceptedAnswerId="31711" CreationDate="2015-04-25T02:08:42.103" Score="4" ViewCount="312" Body="&lt;p&gt;From a physiological perspective, all that is done during exercise is the expending of energy in the form of ATP to fuel muscle contraction and extension.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I looked up why muscle grow due to exercise, there is the claim that recovery of micro lesions formed during exercise enables slight growth of muscle. I am not sure how micro lesions are formed and intuitively, these micro lesions should cause atrophy of the muscle rather than strengthening of the muscle fibers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further there is no logical connection as to why muscle fibers would be strengthened rather than just restored to its previous form during rest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone help me make the mental leap from the consumption of ATP through exercise to muscle growth? &lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="3340" LastEditDate="2019-04-17T11:23:00.290" LastActivityDate="2019-04-17T11:23:00.290" Title="What is the connection between exercise and muscle growth" Tags="&lt;physiology&gt;&lt;muscles&gt;&lt;growth&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31702" PostTypeId="1" CreationDate="2015-04-25T03:33:46.883" Score="2" ViewCount="292" Body="&lt;p&gt;During the dark reaction, 9 molecules of ATP are consumed for every 3 carbon dioxide molecules, yet only 6 molecules of inorganic phosphate ultimately leave the cycle. Does that mean that there is a greater concentration of ADP than inorganic phosphate returning to the light reactions?&lt;/p&gt;&#xA;" OwnerUserId="15272" LastEditorUserId="9943" LastEditDate="2015-04-25T13:05:13.000" LastActivityDate="2015-04-25T13:05:13.000" Title="Are more molecules of ADP than inorganic phosphate returned to the light reaction in photosynthesis?" Tags="&lt;biochemistry&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31703" PostTypeId="2" ParentId="31681" CreationDate="2015-04-25T07:20:43.980" Score="3" Body="&lt;p&gt;The following image from &lt;a href=&quot;http://en.wikipedia.org/wiki/Cardiac_cycle#/media/File:Wiggers_Diagram.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt; answer what you need. You can check corresponding &lt;a href=&quot;http://en.wikipedia.org/wiki/Cardiac_cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;page&lt;/a&gt; for details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SDdHw.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The top part shows the details of the different processes during a heart beat. Corresponding to these events the ECG reads are marked. As you can see the distance between the T wave ( the small bump after the QRS complex) and the next P wave corresponds to the diastole. As you can see the pressure changes correlate well with the electric reads from the heart. &lt;a href=&quot;http://en.wikipedia.org/wiki/Electrocardiography&quot; rel=&quot;nofollow noreferrer&quot;&gt;This&lt;/a&gt; wiki page has great descriptions of the features of the ECG and the corresponding events.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example P to QRS corresponds to the conduction of stimulus from the sine node to AV node, or QRS depicts the rapid depolarization and repoliarization of the ventricles. This latter leads to strong muscle contraction and this causes intaventicular pressure rise, that is followed by aortic pressure change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: Sorry, for missing the key point, I totally misunderstood what you needed. I'll try to correct my mistake (I'll leave the previous info as it may be useful for others) The authors of this paper did a really nice work on modeling and measuring left ventricle contraction time and other things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reference: (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1434992/pdf/biophysj00204-0121.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Beyar and Sidman 1984&lt;/a&gt;)&lt;br&gt;&#xA;Long story short: the contraction of the ventricle depends on the initial amount of blood (preload), aortic blood pressure at the end (afterload), and intial contractility. The results are summarized in three tables:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/yOMW9.png&quot; alt=&quot;preload&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Le7kR.png&quot; alt=&quot;afterload&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/nxCNE.png&quot; alt=&quot;contractility&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see in the last columns, the ejection time varies with the parameters. The ejection time that is required for the ventricle to push the blood out to the aorta. Under normal circumstances a complete heart cycle is about 0.8s (or 800ms) this pie char shows the time ratio of main events. (Image taken from: &lt;a href=&quot;http://www.tutorvista.com/content/biology/biology-iv/circulation-animals/heart-cardiac-cycle.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;tutorvista.com&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SrPtw.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that complete cardiac diastole is when all the heart muscles are relaxed (this can be shortened if higher heart rate is required).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Isovolumic_relaxation_time&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Isovolumic relaxation time (IVRT) is an interval in the cardiac cycle, from the aortic component of the second heart sound, that is, closure of the aortic valve, to onset of filling by opening of the mitral valve. A normal IVRT is about 70 ± 12 ms, and approximately 10 ms longer in people over forty years. In abnormal relaxation, IVRT is usually in excess of 110 ms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Isovolumic relaxation is when the muscle relaxes, yet the volume of the ventricle remains the same, thus only the internal pressure changes (it is analogue to isovolumic contraction - when the volume is unchanged, but pressure is built up, this happens at early ventricle contraction).&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="4833" LastEditDate="2015-11-12T07:41:42.340" LastActivityDate="2015-11-12T07:41:42.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31704" PostTypeId="1" AcceptedAnswerId="31706" CreationDate="2015-04-25T07:44:32.570" Score="5" ViewCount="487" Body="&lt;p&gt;What is the biological origin of the following behavior:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes, during the early, formative phase of sleep (when you have a gradually dimming consciousness of what all is happening around), you feel some kind of a tremor of sorts - a feeling as if you are about to fall off. The body responds by twitching the limbs, so as to &quot;balance&quot;, and you end up waking up for a second or two, where you realize that you aren't about to fall and all is fine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since &lt;a href=&quot;http://en.wikipedia.org/wiki/Cerebellum&quot;&gt;Cerebellum is involved with maintaining equilibrium and balance&lt;/a&gt;, I have the intuition that this is related to some transient behavior where the Cerebellum is dimming down. When you are in deep sleep, you do not have a sense of balance, so I guess Cerebellum does dim down the sense of equilibrium. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the apparent flaw in my reasoning is - if this was indeed the origin, one would have experienced these tremors every time one slept. That doesn't happen, it is only occasional (AFAIK).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, biologically, what is the true origin of this behavior? &lt;/p&gt;&#xA;" OwnerUserId="15494" LastActivityDate="2015-04-25T08:50:55.107" Title="Biological origin of shuddering during sleep" Tags="&lt;sleep&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31706" PostTypeId="2" ParentId="31704" CreationDate="2015-04-25T08:09:26.183" Score="7" Body="&lt;p&gt;These are called hypnic jerks, also known as hypnagogic jerks or sleep starts. They are normal part of the wake-to-sleep transition. Hypic jerks consist of non-periodic myoclonic movements, generally involving an isolated limb.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exact physiologic origin of hypic jerks is unknown. We can say that they correlate with a particular waveform on the EEG known as a &lt;a href=&quot;http://www.journalsleep.org/ViewAbstract.aspx?pid=26115&quot; rel=&quot;nofollow noreferrer&quot;&gt;K-complex&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.imgur.com/s15jDK6.png&quot; alt=&quot;enter image description here&quot;&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;Picture from &lt;a href=&quot;http://en.wikipedia.org/wiki/K-complex&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/K-complex&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;K-complexes are a normal part of Stage II sleep and can evoked using auditory stimuli, even if sleep is not interrupted. In the case of hypnic jerks, the K-complex is usually followed by alpha (wake) activity. To my knowledge, there is no evidence that hypnic jerks originate in or are routed through the cerebellum. &lt;a href=&quot;http://www.journalsleep.org/ViewAbstract.aspx?pid=26115&quot; rel=&quot;nofollow noreferrer&quot;&gt;K-complexes themselves&lt;/a&gt; are related to cross-talk between the cortex and the thalamus, a circuit that doesn’t involve the cerebellum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition to the EEG findings, it has also been shown that the jerks are accompanied by autonomic activation &amp;mdash; transiently increased heart rate and respiratory rate. There is also an (unexplained) subjective aspect. You described it as feeling &quot;as if you are about to fall off,” which seems to be consistent with the published literature on this. As mentioned in the review cited below, some people report a sensation of &quot;falling into the void.”&lt;sup&gt;1&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The clinical implications, in case you were wondering, are summarized well by Vertugno et al.:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sleep starts are common physiological phenomenon affecting up to 70% of the adult population and their course is benign, resolving without any neurological sequel. Therefore, reassurance and counselling are all that is needed to treat the patient. Though an adequate explanation and reassurance may be sufficient, some patients may require a small dose of clonazepam (0.5–1 mg at bedtime) to ameliorate the symptoms on a short-term basis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;1. Vetrugno R, Montagna P. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22136891&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Sleep-to-wake transition movement disorders.&lt;/em&gt;&lt;/a&gt; Sleep Med. 2011 Dec;12 Suppl 2:S11-6.&#xA;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&#xA;You requested in a comment a reference to introductory material on the topic. What we know about the neuro-physiology of sleep is mostly based on the analysis of EEG (brain-wave) tracings. I therefore refer you to &lt;a href=&quot;http://com-peds-neurodynamicslab.sites.medinfo.ufl.edu/files/2012/02/Chap11.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;this introduction to sleep polysomnography&lt;/a&gt; if you would like to get a better handle on how scientists think about sleep.&#xA;&lt;/sub&gt; &lt;/p&gt;&#xA;" OwnerUserId="9268" LastEditorUserId="9268" LastEditDate="2015-04-25T08:50:55.107" LastActivityDate="2015-04-25T08:50:55.107" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="31708" PostTypeId="1" CreationDate="2015-04-25T11:45:08.377" Score="2" ViewCount="64" Body="&lt;p&gt;I saw some documents which were trying to say that they can prove via sweat smell selected by women that humans are developed to find a partner with similar genes. At the first glance, I refused it as absurd for many examples of organisms behaving in reverse but then I realized that I don't know any satisfying evolutionary explanation for this (and more: I could even explain the contrary: If less developed and more developed human had a baby, the better genes could be maybe annulled by the worse genes, on the contrary two very developed partners would have not only a lot of descendants, but their descendants would have also lot of descendants and so on.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And more thing: if genetic diversity is truly evolutionary practical, could for example even people with genetically transmitted disease help our gene pool?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks a lot.&lt;/p&gt;&#xA;" OwnerUserId="6124" LastEditorUserId="3340" LastEditDate="2015-04-25T14:24:45.737" LastActivityDate="2015-04-25T17:54:47.587" Title="What is genodiversity good for?" Tags="&lt;genetics&gt;&lt;sexual-selection&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31709" PostTypeId="2" ParentId="31702" CreationDate="2015-04-25T13:02:37.867" Score="1" Body="&lt;p&gt;Not 6, but &lt;strong&gt;9 molecules of P&lt;sub&gt;i&lt;/sub&gt;&lt;/strong&gt; are formed in the Calvin cycle, from the conversion of 9 ATP to 9 ADP: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/N34LK.gif&quot; alt=&quot;Calvin Cycle&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: &lt;a href=&quot;http://eesc.columbia.edu/courses/ees/life/lectures/lect19.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Columbia University&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-04-25T13:02:37.867" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31710" PostTypeId="1" CreationDate="2015-04-25T14:12:41.260" Score="2" ViewCount="2833" Body="&lt;p&gt;We have learned that the same information is saved in the DNA in the same place. So when DNA splits and then connects again (during reproduction); how does it maintain the integrity of the information? In other words, do they split and come back like a zipper, or does something else happen?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DTtkU.gif&quot; alt=&quot;DNA reproduction&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6124" LastEditorUserId="9943" LastEditDate="2015-04-28T12:30:20.947" LastActivityDate="2015-04-28T13:14:41.310" Title="How accurate does the alignment of molecules in DNA have to be?" Tags="&lt;dna&gt;&lt;replication&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31711" PostTypeId="2" ParentId="31701" CreationDate="2015-04-25T14:28:56.463" Score="3" Body="&lt;p&gt;Muscle growth and development is mediated by &quot;trophic factors&quot; not biochemical reactions (ATP) or muscle contraction directly. The best method of releasing tropic factors is exercise and not electrical stimulation or biochemical reactions (ATP) or biomechanical contraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nerve ending release growth or tropic factors which stimulate muscle growth and for example if the nerves die off either due to injury or disease (ALS) the muscles will atrophy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not all of the tropic factors are as of yet known, but it is these tropic factors that stimulate muscle growth, not the biochemical or biomechanical reaction of the muscle (contraction). One can not as of yet stimulate muscle growth by delivering electrical energy to the muscle, for example (it has been tried to in an effort to maintain muscle mass in critically ill patients).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a review of the trophic factors here - &lt;a href=&quot;http://neuromuscular.wustl.edu/lab/trophic.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://neuromuscular.wustl.edu/lab/trophic.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And a review of electrical stimulation - &lt;a href=&quot;http://www.medword.com/MedwordStore/PCP/EMS_truth.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.medword.com/MedwordStore/PCP/EMS_truth.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many claims of benefit for electrical stimulation, such as regeneration of the facial nerve in facial paralysis, such as Bell's palsy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;problem&quot; is that the prognosis in Bell's palsy is very good, even without electrical stimulation, and so it is difficult to &quot;prove&quot; benefit with electrical stimulation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;With or without treatment, most individuals begin to get better within 2 weeks after the initial onset of symptoms and most recover completely, returning to normal function within 3 to 6 months.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ninds.nih.gov/disorders/bells/detail_bells.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ninds.nih.gov/disorders/bells/detail_bells.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Statistically, the natural history without treatment was described in a study of 1011 patients in 1982 [8]. One-third had an incomplete paralysis, and two-thirds had complete paralysis. Overall, 85 percent showed signs of recovery within three weeks, 71 percent had complete recovery, 13 percent had slight sequelae, and 16 percent had residual weakness, synkinesis and/or contracture. Patients with incomplete lesions had a 94 percent rate of return to normal function, while only 60 percent of those with clinically complete lesions returned to normal function. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="15499" LastEditorUserId="22537" LastEditDate="2017-09-21T22:22:02.513" LastActivityDate="2017-09-21T22:22:02.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31712" PostTypeId="1" AcceptedAnswerId="31713" CreationDate="2015-04-25T15:57:55.063" Score="-2" ViewCount="145" Body="&lt;p&gt;I'm looking for any new biotechnology issue related to Biochemistry, Metabolic processes, molecular Genetics, or other relevant fields. If anyone knows of an issue that has solid resources around I'd love to hear all about it.&lt;/p&gt;&#xA;" OwnerUserId="14940" LastEditorUserId="14940" LastEditDate="2015-04-25T16:32:50.357" LastActivityDate="2015-04-25T16:49:57.170" Title="What is a new biotechnology issue?" Tags="&lt;biochemistry&gt;&lt;biotechnology&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-04-25T18:37:52.980" ContentLicense="CC BY-SA 3.0" />
  <row Id="31713" PostTypeId="2" ParentId="31712" CreationDate="2015-04-25T16:39:21.653" Score="5" Body="&lt;p&gt;Biotechnology is a &lt;strong&gt;gigantic field&lt;/strong&gt;. You should have a look at the wikipedia entry for &lt;a href=&quot;http://en.wikipedia.org/wiki/Biotechnology&quot; rel=&quot;nofollow&quot;&gt;biotechnology&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of the size of the field &quot;biotechnology&quot;, because the word biotechnology accept different definitions and because the word interesting is extremely arbitrary it is pretty much impossible to give a good answer to this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am using below wikipedia's definiton of biotechnology that encompass...pretty much everything! The wiki definition include fields such as:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;chemical and bioprocess engineering&lt;/li&gt;&#xA;&lt;li&gt;bioinformatics and biostatistics&lt;/li&gt;&#xA;&lt;li&gt;biorobotics&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;From @poka.nando's comment, the UN definition is &#xA;Hoping it will help you, below are few random examples of research in biotechnology: &quot;Biotechnology is the use of living systems and organisms to develop or make products, or &quot;any technological application that uses biological systems, living organisms or derivatives thereof, to make or modify products or processes for specific use&quot; (UN Convention on Biological Diversity, Art. 2)&quot; Under this definition fields such as bioinformatics would probably not really fit within the field of biotechnology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using wiki's definition of biotechnology below are few examples of s^hitngs you might be looking for. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Improve the statistical tools to detect differential selection pressure in a phylogeny (methods such as &lt;a href=&quot;http://abacus.gene.ucl.ac.uk/software/paml.html&quot; rel=&quot;nofollow&quot;&gt;PAML&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Improving &lt;a href=&quot;http://en.wikipedia.org/wiki/Fungiculture&quot; rel=&quot;nofollow&quot;&gt;fungiculture&lt;/a&gt; by improving our understanding of the mushroom life cycle variation in response to temperature.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Track down genes of resistance to drought in tomato (&lt;a href=&quot;http://en.wikipedia.org/wiki/Genome-wide_association_study&quot; rel=&quot;nofollow&quot;&gt;GWAS&lt;/a&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Design better &lt;a href=&quot;http://en.wikipedia.org/wiki/Artificial_heart&quot; rel=&quot;nofollow&quot;&gt;artificial hearts&lt;/a&gt; or get a better understanding of &lt;a href=&quot;http://en.wikipedia.org/wiki/Cellular_differentiation&quot; rel=&quot;nofollow&quot;&gt;cell differentiation&lt;/a&gt; in order to be able to rebuild lost tissues or even organs (see &lt;a href=&quot;http://en.wikipedia.org/wiki/Regenerative_medicine&quot; rel=&quot;nofollow&quot;&gt;regenerative medicine&lt;/a&gt;).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Improve understanding of the transmission of the &lt;a href=&quot;http://en.wikipedia.org/wiki/African_swine_fever_virus&quot; rel=&quot;nofollow&quot;&gt;African swine fever&lt;/a&gt; in order to improve its use as a &lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_warfare&quot; rel=&quot;nofollow&quot;&gt;biological warfare&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-04-25T16:49:57.170" LastActivityDate="2015-04-25T16:49:57.170" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31714" PostTypeId="2" ParentId="31708" CreationDate="2015-04-25T17:54:47.587" Score="2" Body="&lt;p&gt;Genetic diversity is indeed very important for many reasons, most notably resistance to diseases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Gros_Michel_banana&quot; rel=&quot;nofollow&quot;&gt;Gros Michel&lt;/a&gt; banana used to be the most cultivated banana, until it was almost completely wiped out by a fungal disease due to lack of resistance in the genetically homogenous cultivars grown in plantations. As a result, it had to be replaced by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Cavendish_bananas&quot; rel=&quot;nofollow&quot;&gt;Cavendish banana&lt;/a&gt; across most of its former range by banana growers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, the answer is a definite &quot;yes&quot; to people with genetically transmitted diseases helping the gene pool. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, the case of &lt;a href=&quot;http://en.wikipedia.org/wiki/Sickle-cell_disease&quot; rel=&quot;nofollow&quot;&gt;sickle cell anemia&lt;/a&gt; clearly shows why even people with genetic diseases can help the gene pool by providing useful alleles. Heterozygotes for the sickle cell allele are &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0952791509000788&quot; rel=&quot;nofollow&quot;&gt;resistant to malaria&lt;/a&gt;. This has led to the allele having a high propensity in subsaharan Africa, where malaria is endemic.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first example of genetically controlled innate resistance to human malaria was the demonstration in 1954 that sickle-cell heterozygotes have less severe Plasmodium falciparum infections than do children with normal adult hemoglobin. This observation has been repeatedly confirmed, most recently by independent studies of genome-wide associations in severe falciparum malaria, which have identified the HBB locus as the major signal of association. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Additional examples are the &lt;a href=&quot;http://serendip.brynmawr.edu/biology/b103/f02/web1/emyers.html&quot; rel=&quot;nofollow&quot;&gt;cystic fibrosis gene&lt;/a&gt;, which confers resistance to cholera, and &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1196/annals.1345.068/abstract&quot; rel=&quot;nofollow&quot;&gt;thalassemia&lt;/a&gt;, which confers resistance to heart attacks. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-04-25T17:54:47.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31715" PostTypeId="2" ParentId="31546" CreationDate="2015-04-25T18:01:11.127" Score="0" Body="&lt;p&gt;I strongly suggest you to take a free course on &lt;a href=&quot;http://coursera.org&quot; rel=&quot;nofollow&quot;&gt;coursera&lt;/a&gt;There are many valid courses focused on bioinformatics for beginners and they offers slides, notes and everything is necessary to start. If you are looking for a nice book to get started, then I suggest you &lt;a href=&quot;http://www.onlamp.com/pub/a/python/2002/10/17/biopython.html&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12923" LastActivityDate="2015-04-25T18:01:11.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31716" PostTypeId="1" CreationDate="2015-04-25T18:05:37.243" Score="4" ViewCount="691" Body="&lt;p&gt;I never suffocated myself so not entirely sure, but when you suffocate, it's painful, right? But of course different kind of pain than being injured or sick. What I'm wondering is, if the &quot;painful&quot; (or suffering) experience of suffocation involves the standard pain pathway mediated by nociceptors? Or is it some other kind of pain pathway due to a lack of oxygen? I don't mean psychological pain.&lt;/p&gt;&#xA;" OwnerUserId="15416" LastEditorUserId="9943" LastEditDate="2015-06-22T12:59:12.437" LastActivityDate="2015-06-22T13:04:11.937" Title="Does suffocation pain involve nociceptors?" Tags="&lt;molecular-biology&gt;&lt;sensation&gt;&lt;pain&gt;&lt;receptor&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31717" PostTypeId="1" CreationDate="2015-04-25T18:32:53.563" Score="2" ViewCount="148" Body="&lt;p&gt;Why are some protein complexes composed of many different types of proteins? How many different types are they composed of? In particular, which protein complex has the greater number of different types of proteins in it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, I've read that the ribosome consists of 70-80 different types of proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How many different types of proteins are in the spliceosome for example?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm using the phrasing &quot;types of proteins&quot; to distinguish aggregates/complexes composed of many different copies of the same protein (i.e. some viral capsids) from those composed of many different kinds (i.e. ribosome, exosome complex, spliceosome).&lt;/p&gt;&#xA;" OwnerUserId="160" LastEditorUserId="160" LastEditDate="2015-04-25T23:03:00.120" LastActivityDate="2015-04-26T11:22:48.227" Title="Which protein complex is composed of the greatest number of different kinds of proteins, and how many types are involved?" Tags="&lt;proteins&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31718" PostTypeId="1" CreationDate="2015-04-25T19:07:53.163" Score="5" ViewCount="79" Body="&lt;p&gt;Is it, in principle, possible to revive an extinct species having no living close relatives but whose DNA and other tissues have been preserved?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about the case where there are no living individuals of a species but there are some living somatic cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about the case where only individuals of only one sex are alive?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="14735" LastEditDate="2015-04-25T19:39:56.267" LastActivityDate="2015-04-25T20:41:24.927" Title="Is it in principle possible to revive an extinct species having no living relatives?" Tags="&lt;extinction&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31719" PostTypeId="2" ParentId="31717" CreationDate="2015-04-25T19:37:46.730" Score="4" Body="&lt;p&gt;In this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119917/&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; detailed analysis has been made on spliceosome (U2-type) composition. It should be noted that this complex has dynamic composition. In the paper authors state that up to 170 proteins may associate to a metozoan spliceosome during its course of action. Individual assemblies contain approx 110 proteins (human). Similar complex of the yeast contains approx 60 proteins (precatalytic B complex), while C complexes have 50 proteins, altogether 90 different were identified in yeast. See the linked paper for details.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-04-26T11:22:48.227" LastActivityDate="2015-04-26T11:22:48.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31720" PostTypeId="2" ParentId="11230" CreationDate="2015-04-25T20:37:04.047" Score="0" Body="&lt;p&gt;According to a theory proposed by Amotz Zahavi (formulator of the so called Handicap Principle), and others, sexual selection can be seen as a subtype of signal selection, which in it's turn is a subtype of natural selection.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The well known example of a signal that is selected for is the tail of the peacock, which signals the high quality of it's owner.  The interesting thing is that to maximise fitness it would be better for the peacock to have a smaller and less colorfull tail.  Signal selection and efficiency selection (for want of a better word) hence often work in opposite directions! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some quotes from the &lt;a href=&quot;http://www.descil.ethz.ch/icsd2013/mobile/details.aspx?sid=7&quot; rel=&quot;nofollow&quot;&gt;abstract&lt;/a&gt; of the article &quot;The Logic of Analog Signaling and the Theory of Signal Selection&quot; by Amotz Zahavi &amp;amp; Avishag Zahavi:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... evolution by natural selection is a consequence of two selection mechanisms: the selection for efficiency on the one hand, and signal selection that reduces efficiency in order to provide reliability on the other hand.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The fundamental difference between signal selection and efficiency selection is that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;when the investment required for signalling is reduced to the extent that everyone can signal alike, the trait loses its value as a signal. This loss of value is unique to biological analog signals&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For example, lace used to be a signal of wealth, but it's effect as a signal diminished once lace machines took over manual production.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exciting thing about this approach is that it could explain the evolution of features that would be hard to explain by efficiency selection only:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We further suggest that the interaction between the selection of signals and the selection of other traits enabled the evolution of new traits that require the accumulation of many mutations that reduce efficiency before they can start contributing to new efficient adaptations e.g. antlers and feathers.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="15396" LastActivityDate="2015-04-25T20:37:04.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31721" PostTypeId="2" ParentId="31718" CreationDate="2015-04-25T20:41:24.927" Score="2" Body="&lt;p&gt;This may absolutely be possible. Check &lt;a href=&quot;http://www.sciencemag.org/content/340/6128/32.short&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; for some info. But really it appears that using somatic nuclear transfer, using the same principle used to generate Dolly, we may be able to recreate an extinct species by swapping in the genetic material into a new cell. One current problem that we face with this is that while the genetics should be fine in nuclear transfer, controlling proper epigenetic programming is difficult.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-04-25T20:41:24.927" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31722" PostTypeId="2" ParentId="31660" CreationDate="2015-04-25T21:47:30.547" Score="3" Body="&lt;p&gt;Insect #2 is not an insect, it seems to be a &lt;a href=&quot;https://en.wikipedia.org/wiki/Woodlouse&quot; rel=&quot;nofollow&quot;&gt;woodlouse&lt;/a&gt; species. It's a small harmless detritivorous crustacean that likes dark and damp places. They are not uncommon in houses, but though they usually live outside. They probably died from waterloss after entering your house.&lt;/p&gt;&#xA;" OwnerUserId="3394" LastActivityDate="2015-04-25T21:47:30.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31724" PostTypeId="1" AcceptedAnswerId="34891" CreationDate="2015-04-25T22:41:08.543" Score="6" ViewCount="96" Body="&lt;p&gt;Plants in urbanized areas are constantly exposed to artificial light after sunset. In their natural habitat there is a more distinct day and night cycle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since light is an important factor in a plant life cycle, I wonder if the introduction of the artificial light forces any changes in the life cycle of plants in urbanized areas?&lt;/p&gt;&#xA;" OwnerUserId="15502" LastEditorUserId="9943" LastEditDate="2015-04-25T23:21:23.257" LastActivityDate="2015-06-03T20:16:46.967" Title="How did the introduction of artificial light changed the life cycle of a plant?" Tags="&lt;plant-physiology&gt;&lt;circadian-rhythms&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31725" PostTypeId="1" AcceptedAnswerId="31726" CreationDate="2015-04-25T23:05:02.817" Score="15" ViewCount="927" Body="&lt;p&gt;I took the pictures today in Cusco Peru. It is the third insect of its class in a month. I never see it before. I thought that it is a wasp, but I think it's really thin to be a wasp. It's about 4 or 5cm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know what kind of insect is and if it's dangerous. Thanks!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/11m82.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Hj6JQ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/upCMh.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2Geo8.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="15503" LastEditorUserId="15503" LastEditDate="2015-04-25T23:10:35.877" LastActivityDate="2015-09-02T19:06:20.947" Title="What is this insect? Found in Peru" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31726" PostTypeId="2" ParentId="31725" CreationDate="2015-04-25T23:36:09.693" Score="12" Body="&lt;p&gt;So that looks to me like the &lt;em&gt;Ophioninae&lt;/em&gt; family of wasps, genus &lt;em&gt;Ophion&lt;/em&gt;. I'll query the list of known species to try to find a more direct match.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/0iBWz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some evidence exists which notes &lt;em&gt;Ophion&lt;/em&gt; may &lt;a href=&quot;http://www.uksafari.com/yellow_ophion.htm&quot; rel=&quot;noreferrer&quot;&gt;sting when threatened&lt;/a&gt;, but at the same time (and I don't have the reference ready) it's believed that the sting contains no toxin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for a positive identification, it's difficult without examining the the features of the wasp extremely close up. Identification keys exist &lt;a href=&quot;http://www.waspweb.org/Ichneumonoidea/Ichneumonidae/Ophioninae/Keys/index.htm&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-09-02T19:06:20.947" LastActivityDate="2015-09-02T19:06:20.947" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31727" PostTypeId="1" AcceptedAnswerId="31813" CreationDate="2015-04-26T01:41:06.280" Score="5" ViewCount="531" Body="&lt;p&gt;I've tried to google this but everything that comes up are things like &quot;mathematical neuroscience&quot; rather than the other way around.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, I'm interested in the workings of a mathematician's brain that sets her apart from others. For example, is there evidence to be found in MRI scans or EEG recordings of mathematicians as to why they excel in math?&lt;/p&gt;&#xA;" OwnerUserId="14975" LastEditorUserId="9943" LastEditDate="2015-04-28T11:15:17.050" LastActivityDate="2015-04-30T05:25:36.413" Title="Neuroscience of mathematicians" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="10" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31728" PostTypeId="1" AcceptedAnswerId="31736" CreationDate="2015-04-26T01:55:01.297" Score="4" ViewCount="17381" Body="&lt;p&gt;If we had a hypotheical gene called gene &lt;strong&gt;&lt;em&gt;exampleGene&lt;/em&gt;&lt;/strong&gt; and this gene had 5 exons, labeled &lt;strong&gt;&lt;em&gt;A, B, C, D, and E&lt;/em&gt;&lt;/strong&gt; in that order on the chromosome, could it be the case that the stop codon for this gene be on exon &lt;strong&gt;&lt;em&gt;D&lt;/em&gt;&lt;/strong&gt; and the exon &lt;strong&gt;&lt;em&gt;E&lt;/em&gt;&lt;/strong&gt; still being a exon that would be transcribed in? I can not see this to be true, since If I  remember correctly, transcription stops BEFORE the stop codon, and when stopped, the pre-mRNA is then further processed, but everything after that stop would not be a part of the &lt;strong&gt;&lt;em&gt;exampleGene&lt;/em&gt;&lt;/strong&gt; ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My lazy diagram of how I think of the supposed &lt;strong&gt;&lt;em&gt;exampleGene&lt;/em&gt;&lt;/strong&gt; to be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;---A-----B---C---------D(stop codon)-------E---&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After transcription via RNA polymerase:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A-----B---C---------D&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="14552" LastEditDate="2015-04-26T02:38:02.613" LastActivityDate="2015-04-26T19:00:25.463" Title="Stop codons and exons?" Tags="&lt;transcription&gt;&lt;translation&gt;&lt;polymerase&gt;&lt;gene&gt;&lt;codon&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31729" PostTypeId="2" ParentId="31728" CreationDate="2015-04-26T02:36:52.983" Score="5" Body="&lt;p&gt;You mix up &lt;a href=&quot;http://www.genome.gov/27552603&quot; rel=&quot;nofollow&quot;&gt;translation and transcription&lt;/a&gt;. &lt;strong&gt;Transcription&lt;/strong&gt; creates mRNA from DNA template. Transcription also includes splicing, that is excision of introns so that mature mRNA contains only exons. In your example it goes like that:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA (chromosome): ---A----B--...--D&lt;strong&gt;stop&lt;/strong&gt;---E---&lt;/p&gt;&#xA;&#xA;&lt;p&gt;premature mRNA: A----B---...---D&lt;strong&gt;stop&lt;/strong&gt;--E---polyA&lt;/p&gt;&#xA;&#xA;&lt;p&gt;mature mRNA: AB..D&lt;strong&gt;stop&lt;/strong&gt;E-polyA&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Translation&lt;/strong&gt; is the creation of polypeptide from template mature mRNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If codons in exon A correspond to polypeptide sequence &lt;em&gt;a&lt;/em&gt; and so on for other exons, your polypeptide translated from mature mRNA will look something like that:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$NH_2$-&lt;em&gt;ab..d&lt;/em&gt;-$COOH$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stop codon stops translation. mRNA might still contain a lot of information after the stop codon, for example, for targeting mRNA to compartment of the cell (e.g. presynaptic site).&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="948" LastEditDate="2015-04-26T07:03:09.787" LastActivityDate="2015-04-26T07:03:09.787" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31730" PostTypeId="1" AcceptedAnswerId="31738" CreationDate="2015-04-26T03:35:11.207" Score="2" ViewCount="500" Body="&lt;p&gt;Hailed as the &quot;gold standard&quot; of sequencing, I was wondering to what Sanger sequencing owes its incredible accuracy to. If possible, I would like a quantification of the accuracy (because I doubt it is 100%, though possibly very close). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand ddNTP chain termination and the strategies involved in Sanger sequencing but I lack the connection to accuracy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="15504" LastActivityDate="2015-04-26T07:57:11.710" Title="Reliability of Sanger sequencing" Tags="&lt;molecular-biology&gt;&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31731" PostTypeId="2" ParentId="31716" CreationDate="2015-04-26T03:53:11.420" Score="0" Body="&lt;p&gt;Being no expert on pain, I will share some thoughts on the issue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the following site(&lt;a href=&quot;http://www.helpforpain.com/arch2000dec.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.helpforpain.com/arch2000dec.htm&lt;/a&gt;), there are two types of pain: nociceptive and neuropathic pain. Neuropathic pain involves the central and peripheral nervous system, a possibility I would discount due to no apparent link to suffocation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, it is likely that, if &quot;traditional pain&quot; is felt, nociceptors are involved. A possible pathway is the decrease in oxygen, possibly detected by certain nociceptors which respond to lead to pain. However, I have not suffocated either, not met anyone suffocating so this is only a possibility. &lt;/p&gt;&#xA;" OwnerUserId="15504" LastActivityDate="2015-04-26T03:53:11.420" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31733" PostTypeId="1" CreationDate="2015-04-26T05:16:15.700" Score="1" ViewCount="254" Body="&lt;p&gt;Have we ever observed a new functional biological structure arising spontaneously such as a new functional organ (sensory or otherwise. such as tracing some creature in the past few hundred years which had no electroreception organ and now has evolved this organ)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or has what we observed been limited to changes in existing structures. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Lenski's &lt;em&gt;E. coli&lt;/em&gt; bacteria is not what i am looking for since it is a change in an existing metabolic system (not a new functional structure) and furthermore e-coli already had some &lt;a href=&quot;http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment#Evolution_of_aerobic_citrate_usage_in_one_population&quot; rel=&quot;nofollow&quot;&gt;ability&lt;/a&gt; to use citrate as an energy source )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking for a completely new functional organ (such as a new sensory organ) that we have actually observed - not deduced from fossil record.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also not looking for something trivial such as a new/modified enzyme or protein molecule but rather a new organ in a species at least the size of an insect.&lt;/p&gt;&#xA;" OwnerUserId="8290" LastEditorUserId="8290" LastEditDate="2015-04-26T11:15:54.083" LastActivityDate="2018-03-18T19:16:50.083" Title="Has a new functional structure ever been observed arising spontaneously?" Tags="&lt;evolution&gt;" AnswerCount="4" CommentCount="17" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31735" PostTypeId="1" AcceptedAnswerId="31868" CreationDate="2015-04-26T06:46:08.613" Score="4" ViewCount="15119" Body="&lt;p&gt;If you have more calcium in the cell, wouldn’t more attach to troponin and initiate muscle contraction? Why does hypercalcemia cause muscle weakness instead of spasms?&lt;/p&gt;&#xA;" OwnerUserId="15272" LastEditorUserId="9943" LastEditDate="2015-04-27T02:25:50.980" LastActivityDate="2017-06-19T01:05:20.040" Title="Why Doesn’t Hypercalcemia Cause Muscle Spasms?" Tags="&lt;physiology&gt;&lt;muscles&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31736" PostTypeId="2" ParentId="31728" CreationDate="2015-04-26T07:08:54.543" Score="8" Body="&lt;p&gt;Take a look at this schematic of a mature mRNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IsISE.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;a href=&quot;http://en.m.wikipedia.org/wiki/File:Mature_mRNA.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;[source]&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The coding region (ie the part that is translated) is between the start and stop codons, but the 5' and 3' untranslated regions (UTRs) are also transcribed by RNA polymerase; these are part of the first and last exons, respectively. The transcription start site is labelled right in front of the 5' UTR. For the purpose of this answer, transcription termination can be said to occur at the poly(A) signal (the poly(A) tail is added post-transcriptionally, as is the 5' cap). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be clear, the point I'm hopefully making is that transcription does not involve codons. RNA polymerase does not stop at the stop codon nor does it start at the start codon. In fact, it doesn't even &quot;know&quot; what codons are. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-04-26T19:00:25.463" LastActivityDate="2015-04-26T19:00:25.463" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31737" PostTypeId="1" AcceptedAnswerId="31742" CreationDate="2015-04-26T07:33:54.557" Score="10" ViewCount="822" Body="&lt;p&gt;There are sometimes people names in taxonomy, like &lt;em&gt;Myotis keenii&lt;/em&gt; was names after Mr. Keen who contributed to discover the species. So, if you discover a species and someone else is constructing the scientific name and names you, it's clear. But when &lt;em&gt;you&lt;/em&gt; discover a species and &lt;em&gt;you&lt;/em&gt; publish it in a paper, can you propose a scientific name that contains your name? Has it ever happened, or is it considered an unhealthy practice?&lt;/p&gt;&#xA;" OwnerUserId="409" LastEditorUserId="409" LastEditDate="2015-04-26T07:55:44.797" LastActivityDate="2015-06-20T20:42:13.797" Title="Can scientists name themselves in the scientific name when they discover a new taxon?" Tags="&lt;taxonomy&gt;&lt;species&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31738" PostTypeId="2" ParentId="31730" CreationDate="2015-04-26T07:57:11.710" Score="2" Body="&lt;p&gt;Reliability comes from the fact that in Sanger sequencing (AFAIK) the synthesis of the new strand to the template and the actual reading of the sequence is separated. As you may know Sanger seq uses capillary gel elfo. thus separating the newly produced DNA fragments on a single nucleotide difference, and the reading is done by fluorescence detectors (then base calling etc.) Now compared to this the other sequencing methods like Illumina and 454 detect each nucleotide incorporation that may produce less reliable signals. For eg. in Illumina colonies may overlap on the plate, or in 454 incorporation of multiple nucleotides at homopolymer regions cause a hard time deciding how many nucleotides have actually incorporated. Also it must be noted that quality of the singals / reads is not constant through out Sanger sequencing. The beginning and the end of the reads tend to have noisy and low quality signals, thus actually only the 100-500(-600)bp segment of the whole fragment can be read reliably. Also ABI's SOLID uses a 2 color color-space and each base is read twice and is extremely reliable (99.96% is said by the inventors). Also clever base calling and error correction algorithms may improve accuracy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is noteworthy to say that next gen sequencers also achieve high accuracy by taking advantage of their immerse throughput / output - due to clonal amplification of template sequences each original fragment is sequenced multiple times and errors in a single read can be corrected by the use of others.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-04-26T07:57:11.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31740" PostTypeId="1" AcceptedAnswerId="31759" CreationDate="2015-04-26T09:29:32.850" Score="16" ViewCount="54264" Body="&lt;p&gt;I am a student of 10th grade, and I eagerly want to learn biology. What is the difference between respiration and breathing?&lt;/p&gt;&#xA;" OwnerUserId="15510" LastEditorUserId="9943" LastEditDate="2015-04-27T02:24:50.717" LastActivityDate="2018-02-11T05:01:03.153" Title="How can we differentiate between respiration and breathing?" Tags="&lt;physiology&gt;&lt;respiration&gt;&lt;breathing&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31741" PostTypeId="1" CreationDate="2015-04-26T09:32:20.500" Score="4" ViewCount="187" Body="&lt;p&gt;I have a insertion fragment that I wish to express from pUC19 in Escherichia coli. The insertion fragment is a sub-section from a larger operon sequence and contains just the last two cistrons from this operon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I plan to insert this fragment into pUC19 under the control of its single lac promoter. Therefore, there will be two cistrons under the control of a single promoter (which is of course, very similar to how it would be expressed in the WT operon). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my mind, expressing both the cistrons under the control of the single pUC19 lac promoter should allow both genes to be translated; once the mRNA is transcribed, both cistrons have their respective Ribosome Binding Sites upstream of their ORFs, and should be translated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, has anyone ever had experience expressing poly-cistronic fragments from plasmids using just a single promoter for the entire fragment? I cannot see any glaring issues with this in theory, but I thought i'd ask before I went ahead. Ultimately, I'd rather express both cistrons from a single plasmid, rather than express each cistron on a separate plasmid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cheers!&#xA;Izaak &lt;/p&gt;&#xA;" OwnerUserId="15509" LastActivityDate="2015-04-26T09:59:00.887" Title="Is it possible to express the cistrons from a polycistronic insertion fragment in a single plasmid?" Tags="&lt;bacteriology&gt;&lt;gene-expression&gt;&lt;translation&gt;&lt;plasmids&gt;&lt;protein-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31742" PostTypeId="2" ParentId="31737" CreationDate="2015-04-26T09:45:50.287" Score="20" Body="&lt;p&gt;The answer is that in general, self-naming is severely frowned upon in the scientific community, but the act itself is not disallowed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been at least two instances of self-naming recorded in literature, as stated in John Wright's book &lt;a href=&quot;https://books.google.co.uk/books?id=yphEBQAAQBAJ&amp;amp;lpg=PA295&amp;amp;ots=vDsDAzjbI1&amp;amp;dq=taxonomy%20%22self%20naming%22&amp;amp;pg=PA34#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;The Naming of the Shrew&lt;/em&gt;&lt;/a&gt;, page 34, where &lt;a href=&quot;http://en.wikipedia.org/wiki/Jules_Ren%C3%A9_Bourguignat&quot; rel=&quot;nofollow noreferrer&quot;&gt;Jules Bourguignat&lt;/a&gt; named a species of snail after himself as &lt;em&gt;Ferussacia bourguignatiana&lt;/em&gt;. The naming was apparently very poorly received (being referred to as taxonomic &lt;a href=&quot;http://en.wikipedia.org/wiki/Masturbation&quot; rel=&quot;nofollow noreferrer&quot;&gt;onanism&lt;/a&gt;), although I was unable to confirm this by locating the original citation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another example was given in the book on &lt;a href=&quot;https://en.wikipedia.org/wiki/Sigismund_Ernst_Hohenwart&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sigismund Hochenwarth&lt;/a&gt; who named a species of moth (now &lt;a href=&quot;http://en.wikipedia.org/wiki/Syngrapha_hochenwarthi&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Syngrapha hochenwarthi&lt;/em&gt;&lt;/a&gt;) after himself (original citation &lt;a href=&quot;http://www.jstor.org/stable/pdf/25003342.pdf?acceptTC=true&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/E7ewE.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/hiC3W.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-06-12T05:40:17.720" LastActivityDate="2015-06-12T05:40:17.720" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31743" PostTypeId="2" ParentId="31740" CreationDate="2015-04-26T09:50:02.147" Score="3" Body="&lt;p&gt;To my limited knowledge, I believe respiration is the chemical process of the body converting glucose and oxygen into energy, whereas breathing is the physical process of inhaling oxygen and exhaling carbon dioxide. Breathing is somewhat like an &quot;external&quot; respiration.&lt;/p&gt;&#xA;" OwnerUserId="15511" LastActivityDate="2015-04-26T09:50:02.147" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31744" PostTypeId="2" ParentId="31741" CreationDate="2015-04-26T09:59:00.887" Score="1" Body="&lt;p&gt;If I understand correctly, you are seeking option for polycistronic expression. Have you considered using T2A or P2A sequences? These come &lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018556&quot; rel=&quot;nofollow&quot;&gt;from virus and essentially break polypeptide&lt;/a&gt; into two parts, so-called &lt;em&gt;self-cleaving&lt;/em&gt; peptide T2A. Real mechanism of its work is that ribosome stalls on the sequence and unable to create peptide bond, effectively re-starting translation with next after T2A amino acid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, you lose independent control over expression, both products will be expressed at same level (but degradation might be different).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, you should consider creating construct that looks something like that:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;strong&gt;lac&lt;/strong&gt;:gene1-T2A-gene2-stop&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thing is that a) it might not work in &lt;em&gt;E.coli&lt;/em&gt; and b) it might not be necessary, because primary purpose of T2A is &lt;strong&gt;equal&lt;/strong&gt; expression level of two polypeptides. And, if your 2 genes are big, for bacteria it is easier to handle two separate plasmids, rather than one but much larger.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-26T09:59:00.887" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31745" PostTypeId="2" ParentId="31740" CreationDate="2015-04-26T10:51:38.973" Score="11" Body="&lt;p&gt;Breathing is a part of respiration but respiration is not a part of breathing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Breathing is a process through which oxygen is taken into the body for use in respiration. This involves physical movement to take oxygen (into the lungs) and also chemical action (haemoglobin-carries oxygen from lungs to blood and carbon dioxide from blood to lungs).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But respiration is a chemical process that involves the break down of the glucose that was formed during digestion to form energy (chemically, energy is Adenosine Triphosphate) for our everyday or metabolic processes.&lt;/p&gt;&#xA;" OwnerUserId="15513" LastEditorUserId="5940" LastEditDate="2015-04-27T15:37:24.990" LastActivityDate="2015-04-27T15:37:24.990" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31747" PostTypeId="1" CreationDate="2015-04-26T11:54:29.603" Score="5" ViewCount="963" Body="&lt;p&gt;In terms of energy, how does chemiosmosis drive ATP synthase? How does electrical energy turn into mechanical energy and then into chemical energy? Would the movement of $H^+$ be considered passive diffusion or secondary active transport?&lt;/p&gt;&#xA;" OwnerUserId="15272" LastEditorUserId="3340" LastEditDate="2015-06-04T11:34:10.163" LastActivityDate="2015-07-10T09:21:41.507" Title="Energy transformations in chemiosmosis and ATP synthase" Tags="&lt;biochemistry&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31748" PostTypeId="1" AcceptedAnswerId="31750" CreationDate="2015-04-26T12:29:30.000" Score="3" ViewCount="297" Body="&lt;p&gt;I am looking for a encyclopedia or biochemical pathway atlas of all known or reported pathways. I am very much interested in network and systems biology. Also the references can be open databases, books or whatever. I came to know about a site called &lt;a href=&quot;http://www.wikipathways.org&quot; rel=&quot;nofollow&quot;&gt;wikipathways&lt;/a&gt; , but it is not opening for me.&lt;/p&gt;&#xA;" OwnerUserId="5669" LastActivityDate="2015-04-26T14:50:28.757" Title="Resources of all known biochemical pathways?" Tags="&lt;database&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31750" PostTypeId="2" ParentId="31748" CreationDate="2015-04-26T14:50:28.757" Score="7" Body="&lt;p&gt;You can find biochemical pathways on &lt;a href=&quot;http://www.genome.jp/kegg/pathway.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;KEGG pathway&lt;/a&gt; for example. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks for:&#xA;  1. Metabolism &#xA;      Global/overview   Carbohydrate   Energy   Lipid   Nucleotide   Amino acid   Other amino   Glycan &#xA;      Cofactor/vitamin   Terpenoid/PK   Other secondary metabolite   Xenobiotics   Chemical structure &#xA;  2. Genetic Information Processing &#xA;  3. Environmental Information Processing &#xA;  4. Cellular Processes &#xA;  5. Organismal Systems &#xA;  6. Human Diseases&#xA;  and also on the structure relationships (KEGG drug structure maps) in:&#xA;  7. Drug Development&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To illustrate the information you can find there, here is a screenshot: &lt;img src=&quot;https://i.stack.imgur.com/0nYsI.png&quot; alt=&quot;kegg pathway main page&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you click on kegg atlas, you get an atlas with all metabolic pathways. You can zoom in to great detail en click for further links.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eZUqf.png&quot; alt=&quot;kegg atlas&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you click on glycolysis or oxidative phosphorylation for example, you will get linked to the following page (see picture). In these detailed schemes of the metabolic pathway, each intermediate can be clicked on, leading to a more detailed page.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Q7AP4.png&quot; alt=&quot;kegg glycolysis detail&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cU2rG.png&quot; alt=&quot;kegg oxfos&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="15136" LastActivityDate="2015-04-26T14:50:28.757" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31751" PostTypeId="1" AcceptedAnswerId="31756" CreationDate="2015-04-26T15:20:26.410" Score="2" ViewCount="138" Body="&lt;p&gt;Reading this study&#xA;&lt;a href=&quot;http://www.nature.com/cr/journal/v23/n10/full/cr2013122a.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/cr/journal/v23/n10/full/cr2013122a.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They writing&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Multiple &lt;strong&gt;exogenous&lt;/strong&gt; and endogenous genes can be simultaneously activated&#xA;  by CRISPR-on&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;We tested single, double and triple activation of a TetO::tdTomato&#xA;  transgene and the endogenous SOX2 and IL1RN genes (Figure 3A) in&#xA;  HEK293T cells carrying the stably integrated TetO::tdTomato transgene&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Could you please help me to understand: They talking about exogenous gene. But saying &quot;carrying the stably integrated&quot;. Does that mean that this gene (TetO::tdTomato) is in the cell genome (integrated to genome)? If so, what is the meaning of exogenous here?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="10104" LastActivityDate="2015-04-26T16:17:06.843" Title="What does it mean: carrying the stably integrated gene" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31752" PostTypeId="1" AcceptedAnswerId="31753" CreationDate="2015-04-26T15:45:49.417" Score="2" ViewCount="1358" Body="&lt;p&gt;Comparing the families &lt;em&gt;Canidae&lt;/em&gt; and &lt;em&gt;Felidae&lt;/em&gt;, which have the shorter evolutionary distance to the order &lt;em&gt;Rodentia&lt;/em&gt;? Less sophisticatedly put, are cats or dogs more related to rodents?&lt;/p&gt;&#xA;" OwnerUserId="11538" LastActivityDate="2015-04-26T19:55:21.910" Title="Evolutionary distance between Canidae, Felidae, and Rodentia" Tags="&lt;taxonomy&gt;&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31753" PostTypeId="2" ParentId="31752" CreationDate="2015-04-26T15:53:04.967" Score="6" Body="&lt;p&gt;&lt;strong&gt;Online Ressources&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is exactly the kind of question where &lt;a href=&quot;http://tolweb.org&quot; rel=&quot;nofollow&quot;&gt;tolweb.org&lt;/a&gt; is your best friend. tolweb.org is one of the most updated phylogenetic tree online. It also contains tons of reference, very useful to understand controversy over some nodes. &lt;a href=&quot;http://www.onezoom.org&quot; rel=&quot;nofollow&quot;&gt;onezoom.org&lt;/a&gt; is another online source that offer you to seek through the tree of life. Also, onezoom shows only the tetrapods (incl. mammals, birds, amphibians, lizards, snakes, turtles). However, onezoom has an awesome display and is a great tool for displaying diversity (they use the total length (in years) of all branches within a clade) within a clade and the threaten index (IUCN (red list) categories).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Dogs, Cats and Rodents&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will find the placental mammals &lt;a href=&quot;http://tolweb.org/Eutheria/15997&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; (tolweb). As you can see, the cats and dogs are both &lt;em&gt;carnivora&lt;/em&gt;, while a rodent is a &lt;em&gt;Rodentia&lt;/em&gt; (as you said). This means that cats and dogs have a more recent common ancestor than does either the cat or the dog with any rodent. Stated differently again, cats are not closer or further to rodents than dogs are. There is exactly the same distance between cats and rodents than between dogs and rodents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One onezoom, the carnivorans is presented as a sister group to the ungulates. I have no idea what representation is the most correct but in any case, cats and dogs are carnivorans and share a common ancestor that is more recent than the common ancestor shared by carnivorans and rodents. So again, there is exactly the same distance between cats and rodents than between dogs and rodents.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-04-26T19:55:21.910" LastActivityDate="2015-04-26T19:55:21.910" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31754" PostTypeId="2" ParentId="10376" CreationDate="2015-04-26T15:58:52.197" Score="2" Body="&lt;p&gt;@xuanji offers a good choice with &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0321775651&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Campbell&lt;/em&gt; Biology&lt;/a&gt;  if you want a text solid biology textbook. I've got a copy in my library. I would suggest buying a previous edition if you're trying to save money. However, the book could be a bit dry. Reading semi-popular books on topics you are interested about would probably be better approach. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both @ebrohman and @Remi.b provide good suggestions with Dawkins. I also like Ernst Mayr's &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0465044263&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;What is evolution&lt;/em&gt;&lt;/a&gt; on the topic of evolution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For ecology, check out books by &lt;a href=&quot;http://www.amazon.com/Edward-O.-Wilson/e/B000AQ4776/ref=sr_ntt_srch_lnk_1?qid=1430063182&amp;amp;sr=1-1&quot; rel=&quot;nofollow&quot;&gt;E.O. Wilson&lt;/a&gt; or &lt;a href=&quot;http://www.amazon.com/Jared-Diamond/e/B000AQ01ZS/ref=sr_tc_2_0?qid=1430063228&amp;amp;sr=1-2-ent&quot; rel=&quot;nofollow&quot;&gt;Jared Diamond&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to learn more about environmental toxicology, Rachel Carson's &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0618249060&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Silent Spring&lt;/em&gt;&lt;/a&gt; is a good book to start off with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're looking for a mathematical biology book, Linda Allen has two biomath text books, one on &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0130352160&quot; rel=&quot;nofollow&quot;&gt;deterministic models&lt;/a&gt; the other on &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1439818827&quot; rel=&quot;nofollow&quot;&gt;stochastic models&lt;/a&gt;. Murry's also produced some classical mathematical biology &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0387952233&quot; rel=&quot;nofollow&quot;&gt;books&lt;/a&gt;. Most people would consider these books dry, but as a mathematician, you might like them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;James Watson can be controversial but he's written some interesting books. His &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/074321630X&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Double Helix&lt;/em&gt;&lt;/a&gt; is a good read. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you provide what specific type of biology and mathematics you are interested in, I will provide more suggestions. &lt;/p&gt;&#xA;" OwnerUserId="15516" LastActivityDate="2015-04-26T15:58:52.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31755" PostTypeId="1" CreationDate="2015-04-26T16:13:55.850" Score="3" ViewCount="95" Body="&lt;p&gt;I am working on a past exam problem where the first bit is as follows&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A plant is repeatably selfed to generate inbred lines. Let $\mathbb{P}(He|He)$ denote the probability that a heterozygous parent gives rise to a heterozygous offspring, and let $\mathbb{P}(Ho|He)$ denote the probability that a heterozygous parent gives rise to homozygous offspring.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am asked to work out the two probabilities as well as an interpretation and state the value of $\mathbb{P}(Ho|Ho)$. The interpretation is obvious and I calculate the conditional probabilities to be &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\mathbb{P}(He|He)=\frac12, \quad \mathbb{P}(Ho|He)=\frac12, \quad \mathbb{P}(Ho|Ho)=1$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next I am given the following &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The inbreeding protocol is carried out $i$ times in an effort to obtain representatives of all alleles that can occur at a locus of interest. Suppose that there are 3 alleles, equally prevalent in the population at large and not under selective pressure during the inbreeding experiment. Let $p_j(i)$ denote the probability that, after $i$ repetitions the lines share $j$ distinct alleles between them. Let $p(i) \in [0,1]^3$ be a vector whose $j$th element is $p_j(i)$. Consider the following equation: $$p(i+1) = M p(i)$$&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would like to calculate the transition matrix $M$ and explain the boundary condition $p(1) = [ 1, 0 ,0 ]^T$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am lost on how to do this, I'm given the answer for $M$ to be $$\begin{pmatrix} \frac13 &amp;amp; 0 &amp;amp; 0 \\ \frac23 &amp;amp; \frac23 &amp;amp; 0 \\ 0 &amp;amp; \frac13 &amp;amp; 1  \end{pmatrix}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But for example looking along the first line I would interpret this as $$\mathbb{P}(\text{There is 1 distinct allele between all lines at time t}) = \frac{1}{3} \mathbb{P}(\text{There is 1 distinct allele between all lines at time t-1})$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However if there is a single allele between the lines at time $t-1$ then this means every line is homozygous for a single allele so why would that change at the next time step?!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the boundary condition, I would of thought it would be $[0, 0, 1]^T$ since is the alleles occur with equal chance and you select a large enough number of lines, you should find all $3$ alleles between them. I was thinking perhaps there is a mistake in the question/solution and the vectors are defined the wrong way round, but even then I would be confused. Surely the number of lines we have makes a large difference, if every line is of genotype $\alpha_1 \alpha_2$ and we would like the probability that there is a single allele between lines at the next selfing step, then every single line would need to become homozygous for the same allele, which seems unlikely if we have a massive number of lines.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone help me work out what is going on here? &lt;/p&gt;&#xA;" OwnerUserId="9482" LastEditorUserId="3624" LastEditDate="2015-04-26T21:38:13.177" LastActivityDate="2015-04-26T21:38:13.177" Title="Problem involving selfing (inbreeding it with itself) a plant to generate purebred lines" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31756" PostTypeId="2" ParentId="31751" CreationDate="2015-04-26T16:17:06.843" Score="2" Body="&lt;p&gt;According to Merriam Webster, an exogeneous gene is defined as &quot; introduced from or produced outside the organism or system; specifically :  not synthesized within the organism or system—compare endogenous&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe they refer to the tetO::tdTomato transgene as an exogeneous, or not originating from the species of study&lt;/p&gt;&#xA;" OwnerUserId="15504" LastActivityDate="2015-04-26T16:17:06.843" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31757" PostTypeId="2" ParentId="30362" CreationDate="2015-04-26T18:43:18.207" Score="1" Body="&lt;p&gt;Thank you for these answers. My robin sightings decreased over the first few weeks since I wrote this, however they're back in full force now. This made me curious enough to do further research, and I happened upon two fact sheets about American Robins, whose scientific name is Turdis Migratorius, meaning Migrating Thrush.&lt;/p&gt;&#xA;&lt;p&gt;I've extrapolated data from a series published by Learner.org entitled Journey North, and will be referring to and quoting sections of &lt;a href=&quot;http://www.learner.org/jnorth/tm/robin/facts_migration&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; and &lt;a href=&quot;http://www.learner.org/jnorth/search/RobinNotes3.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;As indicated by the thorough sources referenced in @fileunderwater's excellent answer, it's clear that not all robins migrate, and among those that do, there are a number of variables, many of which are not fully understood. Robins are considered nomadic, meaning they travel in many different directions, and, unlike other species, they don't necessarily come and go from the same location, further complicating the study of migration.&lt;/p&gt;&#xA;&lt;p&gt;In general, food supply is the robin's most important consideration, and weather controls the availability of that food, so a complex combination of the two appears to be the main migration trigger.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Migrators rely heavily on earthworms, caterpillars and other insects for the bulk of their diet.&lt;/p&gt;&#xA;&lt;p&gt;In the fall, they fly south because the ground freezes, locking them out from their favorite food, earthworms, and because winter weather makes it impossible to find juicy caterpillars and other insect food.&lt;/p&gt;&#xA;&lt;p&gt;The same theory applies in their motivation to return from the south. Soils in the south can get so warm and dry that worms retreat deeper into their burrows during hot, dry spells, making them harder for robins to find.&lt;/p&gt;&#xA;&lt;p&gt;Robins are easily overheated, so they become stressed and restless when the southern temperatures remain high for an extended period of time.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The south to north migrators are programmed to follow something called a 37-degree isotope. They move ahead of warm fronts, the intention being to settle down where the temperature averages 37 degrees or more. That weather pattern also brings spring rains, causing the ground thaw that triggers the end of earthworm hibernation.&lt;/p&gt;&#xA;&lt;p&gt;The male robin migrates first. He bulks up by eating more than usual to sustain him through the arduous journey, which is why the first robins we see are generally chubby! (The male also has a much darker head than the female.) As @fileunderwater pointed out, in some areas robins have begun to arrive significantly earlier, while the ground is still frozen, so that extra preparation helps them survive for a time by eating berries and insects found in trees. If all else fails, some will re-join a flock and fly to a warmer area for a few days or weeks, which supports my recent observation.&lt;/p&gt;&#xA;&lt;p&gt;Upon arrival, the male's job is to stake out a territory conducive to good breeding conditions. Once he finds an area that has a good feeding source, a safe place for breeding, and the right materials for the female to create a nest, he spends most of his time in a nearby tree singing. It's a unique sound rarely used at any other time, and it lets other males in the area know to stay away.&lt;/p&gt;&#xA;&lt;p&gt;A few weeks later, the female arrives. Her trigger seems to be related to  ideal nesting conditions.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;She has no urgent need to return early, since there is nothing important for her to do until there is a good mud supply for building her nest. As a matter of fact, if she builds too early, hard frosts at night can weaken her nest. And if she runs out of food too soon before the nesting season, it can make it hard for her body to produce eggs. So she waits until conditions are more favorable and she can continue to get a reliable winter diet as long as necessary.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;A few other fun facts about migration:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Robins migrate mostly at night.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;They fly at speeds of 30-36 mph, traveling between 100 and 200 miles per day.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;To keep from getting lost, they figure out their location on the planet in much the way sailors on the high seas once did--using the angle of the sun in relation to the time of day. If blown off course, they fly to where the sun will be at the proper angle.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Flock sizes during migration vary greatly. Although groups of 10-50 are the most commonly seen, they'll fly in groups as few as three or four, and I (the author of one of these articles) once counted 60,000 robins flying along Lake Superior in just 5 hours!&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;For various reasons, many robins don't survive migration. Scientists estimate that only 25% of fledglings born in the summer survive until November, and even many experienced adults die during migration.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="13148" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-26T18:43:18.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31758" PostTypeId="2" ParentId="31648" CreationDate="2015-04-26T18:44:28.180" Score="18" Body="&lt;p&gt;Anything related to mint usually contains menthol. What does it do? It triggers the TRPM8 ion channels, causing your skin's cold receptor to become sensitive, and causing it to overfire.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This causes the brain (receiving cold signals from skin) to feel cold, and that's why you feel cold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have summarised it in a few sentences, but as with any scientific discovery, it took quite a few years to fully understand what was going on. NCBI have summarised this quite nicely over here (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK5238/&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK5238/&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-04-27T15:44:12.310" LastActivityDate="2015-04-27T15:44:12.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31759" PostTypeId="2" ParentId="31740" CreationDate="2015-04-26T19:30:09.410" Score="18" Body="&lt;p&gt;There are two uses of the term respiration: &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Respiration_%28physiology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;physiological respiration&lt;/a&gt; and &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Cellular_respiration&quot; rel=&quot;nofollow noreferrer&quot;&gt;cellular respiration&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Physiological respiration involves the intake of outside oxygen and its distribution to the tissues of the body. Breathing is a part of physiological respiration and functions to bring oxygen into the lungs and expel carbon dioxide. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cellular respiration is a chemical process by which energy is obtained within individual cells from biomolecules like glucose. In aerobic respiration, oxygen is used. Cells can also use fermentation and, for some, anaerobic respiration to obtain energy. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2018-02-11T05:01:03.153" LastActivityDate="2018-02-11T05:01:03.153" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31762" PostTypeId="1" AcceptedAnswerId="31782" CreationDate="2015-04-26T23:31:08.690" Score="3" ViewCount="2139" Body="&lt;p&gt;It is stated on &lt;a href=&quot;http://www.lairweb.org.nz/tiger/conflict13.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; website that the density of a Grizzly bear bone is ten times our own. And since I am not into biology at all, I am confused as I don't understand the meaning of bone density here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know what the &quot;bone mineral density&quot; term means, and I know it is measured in $g/cm^2$, but there is also the &quot;physical&quot; density term which is the mass by volume and it's measured in $g/cm^3$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, what does it mean when we say that an animal has a bone that is 10 times more dense than ours ? Does it mean that the bone weighs 10 times more for the same size (or volume) ? Or does it mean that it has 10 times the amount of minerals and so it is somehow stronger ?&lt;/p&gt;&#xA;" OwnerUserId="15520" LastActivityDate="2015-04-27T18:17:28.503" Title="Human bone density and Brown Bear bone density?" Tags="&lt;human-biology&gt;&lt;zoology&gt;&lt;bone-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31766" PostTypeId="1" CreationDate="2015-04-27T01:27:35.650" Score="4" ViewCount="1857" Body="&lt;p&gt;From this image &lt;img src=&quot;https://i.stack.imgur.com/TQ8kV.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can see several exons that are actually introns in other genes. It's not a really a different gene, it's an alternative splicing of a gene. My background is not biology so is it possible for alternative splicing to behave like this? I only know that alternative splicing is just exon skipping and introns will just stay introns and not become exons. Can someone explain this to me and give any suggestions on which part of biology (or genetics) I need to learn. Thank you. &lt;/p&gt;&#xA;" OwnerUserId="15496" LastEditorUserId="6307" LastEditDate="2015-07-09T18:30:30.447" LastActivityDate="2015-12-06T23:12:23.113" Title="Can intron become exon in alternative splicing?" Tags="&lt;gene-expression&gt;&lt;exons&gt;&lt;isoforms&gt;" AnswerCount="2" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="31768" PostTypeId="2" ParentId="31735" CreationDate="2015-04-27T02:40:23.513" Score="1" Body="&lt;p&gt;Lets think about sodium channels for a moment. Empirical studies show that calcium has the ability to transiently &lt;strong&gt;block&lt;/strong&gt; sodium channels &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10097179&quot; rel=&quot;nofollow&quot;&gt;(1)&lt;/a&gt;. So if you have a high amount of calcium floating around, what you're doing is blocking the flux of sodium through the neural membranes. Neurons aren't going to fire if there's little or no flux through these sodium ion channels, so if the neurons decrease in their firing rate, yo end up with muscle weakness.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-04-27T02:40:23.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31769" PostTypeId="2" ParentId="31710" CreationDate="2015-04-27T03:02:46.967" Score="2" Body="&lt;p&gt;In the case of replication the &lt;strong&gt;parent strands do not pair up back into the original helix&lt;/strong&gt;. Instead, as your picture and the one below show, the complementary bases are paired up on one of the parent strands, resulting in two copies, each with one parent strand and one new one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PrKtc.jpg&quot; alt=&quot;replication&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: &lt;a href=&quot;http://www.ch.ic.ac.uk/local/projects/burgoine/origins.txt.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kathy's webpage on DNA&lt;/a&gt;&lt;/sup&gt;  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-04-28T13:14:41.310" LastActivityDate="2015-04-28T13:14:41.310" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31770" PostTypeId="1" AcceptedAnswerId="31779" CreationDate="2015-04-27T03:08:43.177" Score="1" ViewCount="285" Body="&lt;p&gt;Could anyone please explain to be in very basic terms how Fig 2, and the associated text(located above the figure) is done? The jargon is too much for me to understand and I really need a simplified, step by step, version of the process to aid my understanding.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a copy and paste of the text, the figure, and the figure description in that order from the paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Fine mapping of pelvic regulatory region. To further localize the position of the cis-acting changes, we looked for the smallest chromosome region co-segregating with bilateral absence of pelvic structures in a cross between pelvic-complete [Japanese marine (JAMA) and pelvic-reduced (PAXB) fish (13)]. High-resolution mapping identified a 124-kb minimal interval, containing only the Pitx1 and Histone 2A (H2AFY) genes, which showed perfect concordance between PAXB alleles and absence of the pelvis (fig. S1A).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recombination in natural populations can also be used to narrow the size of regions controlling polymorphic traits in sticklebacks (18). We therefore tested whether markers in the Pitx1 region were associated with the presence or absence of pelvic structures in lakes with dimorphic stickleback forms: benthic and limnetic sticklebacks from Paxton Lake, British Columbia (PAXB/PAXL), and pelvic-complete and pelvic-reduced sticklebacks from Wallace Lake, Alaska (WALR/WALC) (fig. S2) (13, 14). Microsatellite markers located in an intergenic region approximately 30 kb upstream of Pitx1 showed highly significant allele frequency differences in fish with contrasting pelvic phenoytpes (P &amp;lt; 10−35) (Fig. S1B and table S2). In contrast, markers around thePitx1 and H2AFY coding regions showed little or no differentiation above background levels. These results suggest that an approximately 23-kb intergenic region upstream of Pitx1 controls pelvic development. This region is conserved among zebrafish and other teleosts (Fig. 2A), suggesting that it may contain ancestrally conserved regulatory enhancers.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://scienceintheclassroom.org/sites/default/files/stickleback_2.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://scienceintheclassroom.org/sites/default/files/stickleback_2.jpg&lt;/a&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/SbFhp.jpg&quot; alt=&quot;Fig2&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Fig. 2.  (A) VISTA/mLAGAN (&lt;a href=&quot;http://genome.lbl.gov/vista/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://genome.lbl.gov/vista/&lt;/a&gt;) alignment ofPitx1 candidate region from pelvic-complete stickleback (SALR), medaka, and zebrafish. Red peaks indicate &gt;40% sequence identity in 20-bp sliding windows; grey bars at topindicate repetitive sequences; and circles indicate microsatellite markers used in association mapping in fig. S1. (B) Reporter gene expression in transgenic animals. (C) Pel-2.5-kbSALR from a marine population drives tissue-specific EGFP (green) expression in the developing pelvic bud ofSwarup stage-32 larvae (36). (F) Detail of (C). (D and G)Altered Pel-Δ2.5-kbPAXB sequence from pelvic-reduced PAXB stickleback fails to drive pelvic EGFP expression. (E and H) A smaller fragment from marine fish, Pel-501-bpSALR, also drives EGFP expression in the developing pelvic bud of multiple stage-30 larvae. This region is completely missing in PAXB.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source :&lt;a href=&quot;http://scienceintheclassroom.org/research-papers/what-pelvis-can-teach-us-about-evolution/university&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://scienceintheclassroom.org/research-papers/what-pelvis-can-teach-us-about-evolution/university&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Paper:Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer.  Chan et al. &lt;/p&gt;&#xA;" OwnerUserId="14815" LastActivityDate="2015-04-27T17:28:14.617" Title="How is the &quot;fine mapping of pelvic regulatory region&quot; done in this paper?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31771" PostTypeId="1" AcceptedAnswerId="31815" CreationDate="2015-04-27T03:18:09.240" Score="7" ViewCount="1282" Body="&lt;p&gt;I see that cyanocobalamin is not naturally occurring, and is synthesized in vivo to methylcobalamin. As part of the synthetic pathway, cyanide is broken off. All opinions I can find are that this isn't a problem as cyanide is naturally occurring in many foods anyway, and is safely detoxified via the the Rhodenase pathway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, given its synthetic creation and vast prevalence as the primary B12 source in nearly all supplements, I was curious if any actual studies did exist to rule out potential (albeit minor) long term cyanide toxicity for this synthetic form of B12. I'm unable to find a single study where cyanide toxicity  was directly tested for, only studies stating that RDA in excess of 1000 times the daily dosage isn't lethal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand no evidence currently exists for cyanocobalamin toxicity, but this wouldn't be surprising if there aren't any studies done in the first place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would anyone be able to reference an actual study that directly measured levels of potential cyanide toxicity for cyanocobalamin in any animal or humans?&lt;/p&gt;&#xA;" OwnerUserId="15295" LastEditorUserId="3340" LastEditDate="2015-04-27T10:26:47.573" LastActivityDate="2015-04-28T12:37:31.223" Title="Is cyanocobalamin toxic?" Tags="&lt;biochemistry&gt;&lt;nutrition&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31772" PostTypeId="2" ParentId="31710" CreationDate="2015-04-27T03:47:39.860" Score="0" Body="&lt;p&gt;When I was reading the question, I had a flash of insight into what I presume the question the OP is asking: how do we maintain &quot;integrity&quot; of DNA when we get a set of DNA from mother, and the other set from father (ignoring mitochondrial DNA and other neat things). I would assume this is the question due to the key word reproduction, but anyway,I am here to provide an answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe the OP has a misconception. DNA of the parents do not pair up in the progeny. Rather, we have 23 pairs of chromosomes, or 46 total chromosomes. What does this mean? The set from the mother and the father do not come together, like a zipper, and have certain bases that just happen to be different (due to single nucleotide polymorphisms and whatnot). Instead, there are two sets of DNA, each with a double helix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think this may be what AliceD is also conveying, but I wished to add some more points such as bringing to numbers to help clarify. If I misunderstood, please clarify!&lt;/p&gt;&#xA;" OwnerUserId="15504" LastActivityDate="2015-04-27T03:47:39.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31773" PostTypeId="2" ParentId="31770" CreationDate="2015-04-27T04:05:17.843" Score="1" Body="&lt;p&gt;I'll try to help clarify the picture, but given that I have not read the paper, I am not too clear on the context.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A. IT compares the DNA of the stickleback (the SALR), medaka, and zebrafish. If there is a red peak, there is relatively high sequence identity (or similarity), indicating similarity (in evolutionary ancestry in this context?). Gray is repeating sequence, perhaps due to duplication or some kind of evolutionary history. For microsatellite markers, I believe that the paper is referring to the use of microsatellites (small tandem nucleotide repeats) as markers to compare the three.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B. Reporter genes are expressed and help the researcher identify something (by giving information, such as fluorescence etc.) (eGFP indicates green fluorescent protein e= enhanced)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C-H. These are just pictures of the fishes. Note the fluorescence (green). It indicates some expression (of the gene of interest). The absence or presence of the fluorescence indicates something, based on what the eGFP was attached to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helped! But you need to do the analysis yourself, or at least I can't :P&lt;/p&gt;&#xA;" OwnerUserId="15504" LastActivityDate="2015-04-27T04:05:17.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31774" PostTypeId="2" ParentId="29661" CreationDate="2015-04-27T05:41:34.703" Score="5" Body="&lt;p&gt;It's a phenomenon called Frisson.  From the wikipedia page.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Frisson (French for 'shiver') is a sensation somewhat like shivering, usually caused by stimuli. It is typically expressed as an overwhelming emotional response combined with piloerection (goosebumps). Stimuli that produce a response are specific to the individual.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Frisson is of short duration, usually no more than 4–5 seconds, usually pleasurable.&lt;a href=&quot;http://www.npr.org/2012/02/13/146818461/the-ballad-of-the-tearful-why-some-songs-make-you-cry&quot;&gt;1&lt;/a&gt; Typical stimuli include loud passages of music and passages that violate some level of musical expectation.[2]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There is some interesting research that shows it occurs when a sound contains certain chords or has certain notes because of how our biological setup reacts to those specific notes.  See the &quot;crying chords&quot; that were supposedly present in Adele's song &quot;Someone Like You&quot;. &lt;a href=&quot;http://www.npr.org/2012/02/13/146818461/the-ballad-of-the-tearful-why-some-songs-make-you-cry&quot;&gt;npr article about crying chords&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15524" LastActivityDate="2015-04-27T05:41:34.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31775" PostTypeId="2" ParentId="31740" CreationDate="2015-04-27T06:31:50.110" Score="6" Body="&lt;p&gt;&lt;strong&gt;An addition to previous answers plus some clarification&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term respiration originally meant breathing i.e inhaling and exhaling (See &lt;a href=&quot;http://www.etymonline.com/index.php?term=respire&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;). It was believed that it is the oxygen and in turn the act of breathing is what lets an organism survive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After substantial research it had been found that, in individual cells it is the &lt;a href=&quot;http://en.wikipedia.org/wiki/Adenosine_triphosphate&quot; rel=&quot;nofollow&quot;&gt;ATP&lt;/a&gt; production by &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitochondrion&quot; rel=&quot;nofollow&quot;&gt;mitochondria&lt;/a&gt; that requires oxygen (as a terminal electron acceptor) and therefore for a cell, respiration is basically the &lt;a href=&quot;http://en.wikipedia.org/wiki/Electron_transport_chain#Electron_transport_chains_in_mitochondria&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;electron transport chain&lt;/strong&gt;&lt;/a&gt; (ETC).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that glucose or any other food molecule or its breakdown has got nothing to do with respiration. The process of glucose breakdown i.e glycolysis is not a part of respiration. &lt;a href=&quot;http://en.wikipedia.org/wiki/Citric_acid_cycle&quot; rel=&quot;nofollow&quot;&gt;TCA cycle&lt;/a&gt; is however considered a part of respiration because it is coupled with the ETC.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Later it had been found out that molecules/ions other than oxygen such as Fe&lt;sup&gt;3+&lt;/sup&gt;, Fumarate etc, can also serve as the terminal electron acceptor. So cellular respiration expanded to include these cases as well;  these fall in the subcategory of &lt;strong&gt;anaerobic respiration&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that &lt;strong&gt;fermentation&lt;/strong&gt; also is a pathway that generates energy in the absence of oxygen but it is not considered respiration. It was previously classified as anaerobic respiration (if I am not wrong) but not any more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So you can see that respiration which was originally synonymous with breathing now denotes a very specialized process. However, respiration is still used to mean breathing and distribution of oxygen in the body when cellular physiology is not in discussion. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-04-27T14:14:35.403" LastActivityDate="2015-04-27T14:14:35.403" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31776" PostTypeId="1" CreationDate="2015-04-27T08:48:34.200" Score="-2" ViewCount="51601" Body="&lt;p&gt;When exercising, tissue in the hands may swell. This may be caused by the muscles generating heat, which leads to blood being pushed to the vessels closest to the surface of your body to dissipate the heat. This response triggers perspiration and may contribute to hand swelling (&lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/edema/expert-answers/hand-swelling/faq-20058255&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mayo Clinic&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This all makes sense. But why do fingers swell during the winter in freezing temperatures? It is referred to as &lt;em&gt;&lt;a href=&quot;https://indswift.wordpress.com/2014/11/14/swollen-toes-and-fingers-during-winter/&quot; rel=&quot;nofollow noreferrer&quot;&gt;chillbains&lt;/a&gt;&lt;/em&gt; and may affect the toes as well. See the following &lt;a href=&quot;http://www.dermnetnz.org/reactions/chilblains.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;picture of chillbains&lt;/a&gt; affecting the fingers:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/18td3.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="15487" LastEditorUserId="9943" LastEditDate="2015-04-27T12:50:47.423" LastActivityDate="2015-04-30T16:20:06.133" Title="Why do fingers swell during cold winters?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;blood-circulation&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="31777" PostTypeId="1" AcceptedAnswerId="31785" CreationDate="2015-04-27T09:25:15.747" Score="1" ViewCount="772" Body="&lt;p&gt;How can green algae be both multicellular and unicellular? What are the cases in which it can be both uni and multi cellular?&lt;/p&gt;&#xA;" OwnerUserId="15487" LastEditorUserId="9943" LastEditDate="2015-04-27T13:23:43.957" LastActivityDate="2015-05-03T05:37:58.767" Title="How can green algae be both multicellular and unicellular?" Tags="&lt;taxonomy&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31778" PostTypeId="2" ParentId="31771" CreationDate="2015-04-27T10:21:53.077" Score="5" Body="&lt;p&gt;Potassium cyanide is added to the cobalamins produced by bacteria to give rise to cyanocobalamin. &lt;strong&gt;CN&lt;/strong&gt; is strongly bonded to &lt;strong&gt;Co&lt;/strong&gt; and will not easily dissociate, thereby making this form of B12 inactive. Therefore, it has been argued that cyanocobalamin is not a good vitamin supplement and other variants such as hydroxycobalamin or methylcobalamin should be used. Displacement of &lt;strong&gt;CN&lt;/strong&gt; from the complex would be energy expensive and even if the reaction is efficient the amount of cyanide released would not be in the toxic concentration. The &lt;strong&gt;CN-Co&lt;/strong&gt; bond is so strong that hydroxycobalamin is used as an antidote for cyanide poisoning; it forms cyanocobalamin by displacing &lt;strong&gt;OH&lt;/strong&gt; with &lt;strong&gt;CN&lt;/strong&gt;. &#xA;&lt;hr&gt;&#xA;&lt;sup&gt; Source: &lt;a href=&quot;http://en.wikipedia.org/wiki/Cyanocobalamin&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; and the cross references.&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-04-28T12:37:31.223" LastActivityDate="2015-04-28T12:37:31.223" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="31779" PostTypeId="2" ParentId="31770" CreationDate="2015-04-27T10:48:45.857" Score="1" Body="&lt;p&gt;This is conceptually similar to our discussion about QTLs, except that I believe that in this example the authors had already narrowed down (which means crudely mapped, as opposed to finely mapped) the actual genetic region by some previous experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on that prior work they may have already deduced that they were seeking a single gene (or a Mendelian factor). Note that this is different than a QTL. QTLs are used when the phenotype of interest is polygenic, and cannot be mapped to just one single Mendelian locus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other important thing to realize is that the genetic map (derived from meiotic recombination between genetic markers), is an abstract concept, and on its own cannot be aligned to the physical map. The physical map is built by either creating a DNA library and making a restriction map of the clones to form contigs, or more likely by sequencing all of the clones in a library--or just using an NGS shotgun approach.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is the RFLPs (the small DNA sequences that can be used as genetic markers)  that tie, or pin, or link the physical map of DNA to the genetic map. Once this alignment has been achieved in the region of interest you just need to establish the left and right boundaries of your region of interest. That should yield one, or more, candidate genes. Rough mapping, or gross mapping, might narrow the genetic interval to a segment containing dozens, or scores of genes, while fine-mapping lets you zoom in to perhaps just a handful of genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the authors do a cross between a wild-type and a mutant, and then figure out some way to homozygose the recombinant chromosomes (I am assuming that the phenotype is recessive). Then they do two things. For each recombinant chromosome the score the phenotype (in this case that involves an anatomical structure for the pelvis). Then they also isolate genomic DNA from those scored animals and use their RFLPs to establish the molecular markers that map genetically the closest to the segregating phenotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With both a genetic and a physical map in hand they can establish the left and right boundaries.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="12909" LastEditDate="2015-04-27T17:28:14.617" LastActivityDate="2015-04-27T17:28:14.617" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31782" PostTypeId="2" ParentId="31762" CreationDate="2015-04-27T11:28:41.873" Score="4" Body="&lt;p&gt;The word &lt;em&gt;density&lt;/em&gt; in the medical term &lt;em&gt;bone density&lt;/em&gt; is used to quantify only the mineral content of the bone (&lt;a href=&quot;http://en.wikipedia.org/wiki/Bone_mineral&quot; rel=&quot;nofollow noreferrer&quot;&gt;bone mineral&lt;/a&gt;). It's not intended to describe the total mass density of the bone like we are used to from physics.&lt;/p&gt;&#xA;&lt;p&gt;This is all on wikipedia: &lt;a href=&quot;http://en.wikipedia.org/wiki/Bone_density&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Bone_density&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Thus, when one say that a Grizzly bear have 10 times the bone density, it implies that its bones have 10 times the mineral content compared to humans, and this is indeed seen as a proxy indicator for bone strength. However, this claim does seem unsupported and unrealistic as &lt;strong&gt;kmm&lt;/strong&gt; points out.&lt;/p&gt;&#xA;" OwnerUserId="9124" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-27T18:17:28.503" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31783" PostTypeId="2" ParentId="31776" CreationDate="2015-04-27T12:49:35.933" Score="4" Body="&lt;p&gt;From the website of &lt;a href=&quot;http://www.dermnetnz.org/reactions/chilblains.html&quot; rel=&quot;nofollow&quot;&gt;Dermatology New Zealand&lt;/a&gt; I learned the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chilblains are due to the constriction of blood vessels in cold conditions. Cold causes constriction of the small arteries and veins in the skin to reduce heat dissipation. This is normal and temporary in nature. However, rewarming after cold exposure may result in leakage of blood into the tissues and swelling of the skin. This can occur several hours after exposure to the cold in temperate humid climates. It can be aggravated by sun exposure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chilblains are less common in countries where the cold is more extreme because the air is drier and people have specially designed living conditions and clothing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chilblains are more likely to develop in people with poor peripheral circulation. Other contributing factors include genetic predisposition, diabetes, smoking and connective tissue disease such as &lt;em&gt;lupus erythematosus&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-04-27T12:58:36.863" LastActivityDate="2015-04-27T12:58:36.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31785" PostTypeId="2" ParentId="31777" CreationDate="2015-04-27T13:23:12.820" Score="5" Body="&lt;p&gt;Because &lt;em&gt;Algae&lt;/em&gt; are represented across four kingdoms, namely &lt;em&gt;Bacteria&lt;/em&gt; (&lt;a href=&quot;http://www.encyclopedia.com/topic/bacteria.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;unicellular prokaryotes&lt;/a&gt;), &lt;em&gt;Plantae&lt;/em&gt; (&lt;a href=&quot;http://en.wikipedia.org/wiki/Plant&quot; rel=&quot;nofollow noreferrer&quot;&gt;multicellular eukaryotes&lt;/a&gt;), Chromista (&lt;a href=&quot;http://www.ucmp.berkeley.edu/chromista/chromista.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;multicellular eukaryotes&lt;/a&gt;), and Protozoa (&lt;a href=&quot;http://www.encyclopedia.com/topic/Protozoa.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;single-celled eukaryotes&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, &lt;em&gt;I. Chlorophyta&lt;/em&gt; is unicellular: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tHUF6.jpg&quot; alt=&quot;Unicellular&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;em&gt;I. Chlorophyta&lt;/em&gt;. Source: &lt;a href=&quot;http://www4.uwsp.edu/biology/courses/botlab/Lab20a.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;University of Wisconsin&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While kelp can become huge and can form underwater forests:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8E6nM.jpg&quot; alt=&quot;Kelp&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Kelp. Source: &lt;a href=&quot;http://www.nature.com/nature/journal/v461/n7267/full/4611066a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nature&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://seaweed.ie/guiry/pdfs/How_Many_Published.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Guiry, &lt;em&gt;J Phycol&lt;/em&gt; 2012; &lt;strong&gt;48&lt;/strong&gt;, 1057–63&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-03T05:37:58.767" LastActivityDate="2015-05-03T05:37:58.767" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31787" PostTypeId="2" ParentId="24185" CreationDate="2015-04-27T17:06:26.777" Score="0" Body="&lt;p&gt;You may inherit a gene, which is actually detrimental to your (most efficient) functioning and hence has a cost (eg. gene for being small when food is available from tall trees). On the other hand, you may inherit a gene which has a benefit for you (gene for being tall with food available from tall trees).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sexual Antagonism:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What’s good for the goose may not be good for the gander. Thistwist on&#xA;  an old proverb captures the notion of sexual antagonism.Traits that&#xA;  confer high fitness on geese (females) may confer lowfitness on&#xA;  ganders (males), and vice versa.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In sexually dimorphic species (like all common complex life), the evolution of males is usually decoupled from females. This is not as bad as it seems, as females and males may have different patterns of selection, different phenotypes of mutations all at the same time dodging pleiotropic effects. Hence mutations benefiting one sex will sometimes be deleterious to the other (i.e. their fitness effects are ‘sexually antagonistic’)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sexual Conflict:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Males and females have divergent interests in reproduction that are rooted in anisogamy and lead to distinct roles, due to sexual antagonism. Sexual conflict occurs between the same or different genes,  when there are different optima for a trait expressed in both sexes (intralocus conflict) or when there is conflict over the outcome of a male–female interaction (interlocus conflict).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intralocus sexual conflicts are potentially very common. Researchers have found a strong positive genetic correlation between male and female fitness at the larval stage in the fruit fly (when interests of the males and females are essentially the same -&gt; survive and grow), but a strong negative genetic correlation between adult male and female reproductive success (when the sexes are expected to have different genetic interests). This is possibly due to sexual antagonism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interlocus conflicts occur when there is conflict over the outcome of male–female interactions, so that the optimal outcome is different for the two sexes,as occurs in yellow dung fly mating behaviour. In a rare instance, wikipedia does a good job of explaining the example: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In the yellow dung fly &lt;em&gt;Scathophaga stercoraria&lt;/em&gt;, females can be injured&#xA;  in the battles between males suitors. Males are selected to evolve&#xA;  traits for competitive ability that would increase their reproductive&#xA;  success, but females would evolve a set of antagonistic adaptations to&#xA;  reduce their chances of being injured in battles between the males.&#xA;  Therefore, there is an interlocus sexual conflict in males and females&#xA;  that could possibly lead to an &quot;unresolvable evolutionary chase&quot; when&#xA;  a novel trait in males increases their competitive ability while&#xA;  harming the females&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;[5,6]&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Parental Antagonism:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An allele in a gene is said to be parentally antagonistic if it has an inclusive fitness benefit when derived from one parent (say the mother), but an fitness cost when derived from the other parent (in this case the father) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many different theories out there, but the gist of it is essentially some process creating an asymmetry between the genes that you inherit from your father and mother (patriGENIC and matriGENIC), that causes differential expression of alleles (silencing the other copy) &lt;strong&gt;[2]&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Parental Conflict:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When parent-offspring relations in sexually reproducing species are&#xA;  viewed from the standpoint of the offspring as well as the parent,&#xA;  conflict is seen to be an expected feature of such relations. In&#xA;  particular, parent and offspring are expected to disagree over how&#xA;  long the period of parental investment should last, over the amount of&#xA;  parental investment that should be given, and over the altruistic and&#xA;  egoistic tendencies of the offspring as these tendencies affect other&#xA;  relatives. In addition, under certain conditions parents and offspring&#xA;  are expected to disagree over the preferred sex of the potential&#xA;  offspring. In general, parent-offspring conflict is expected to&#xA;  increase during the period of parental care, and offspring are&#xA;  expected to employ psychological weapons in order to compete with&#xA;  their parents. &lt;strong&gt;[7]&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reading:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1] Haig, David. &quot;Parental antagonism, relatedness asymmetries, and genomic imprinting.&quot; Proceedings of the Royal Society of London. Series B: Biological Sciences 264.1388 (1997): 1657-1662.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[2] Patten, M. M., et al. &quot;The evolution of genomic imprinting: theories, predictions and empirical tests.&quot; Heredity 113.2 (2014): 119-128.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[3] Patten, Manus M., and David Haig. &quot;Maintenance or loss of genetic variation under sexual and parental antagonism at a sex‐linked locus.&quot; Evolution 63.11 (2009): 2888-2895.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[4] Normark, Benjamin B. &quot;Perspective: maternal kin groups and the origins of asymmetric genetic systems—genomic imprinting, haplodiploidy, and parthenogenesis.&quot; Evolution 60.4 (2006): 631-642.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[5] Connallon, Tim, and Andrew G. Clark. &quot;Evolutionary inevitability of sexual antagonism.&quot; Proceedings of the Royal Society of London B: Biological Sciences 281.1776 (2014): 20132123.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[6] Chapman, Tracey, et al. &quot;Sexual conflict.&quot; Trends in Ecology &amp;amp; Evolution 18.1 (2003): 41-47.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[7] Trivers, Robert L. &quot;Parent-offspring conflict.&quot; American zoologist 14.1 (1974): 249-264.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-04-27T17:36:40.557" LastActivityDate="2015-04-27T17:36:40.557" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31788" PostTypeId="1" AcceptedAnswerId="31809" CreationDate="2015-04-27T17:10:21.290" Score="6" ViewCount="371" Body="&lt;p&gt;I'm a high school student who's currently in AP Biology, so my background in biology is quite limited. I'm interested in mathematically modelling action potentials.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Doing a quick google search, I discovered the Fitzhugh-Nagumo model, a simplified case modelling the voltage of the cell during an action potential as a second order differential equation $ C \frac{d^2V}{dt^2} + \epsilon(V^2-1) + \frac{V}{L} = 0$. I want to solve this equation numerically, but I can't find the numerical values of $\epsilon$, $L$, or $C$ online. What are some reasonable parameters for this model for a human neuron?&lt;/p&gt;&#xA;" OwnerUserId="15536" LastActivityDate="2015-04-28T16:20:07.203" Title="Parameters for Fitzhugh-Nagumo model of Action Potential" Tags="&lt;mathematical-models&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31789" PostTypeId="1" AcceptedAnswerId="31791" CreationDate="2015-04-27T17:23:40.070" Score="6" ViewCount="187" Body="&lt;p&gt;I am a high school student. I'm doing a project where I need to find a planet in our galaxy that might be habitable. Then I need to create an organism that could live on that planet and justify everything about it Ex: Sight, whether or not it can see and why or why not / Touch / Smell / Respiration / Central Nervous System / Cell Count... My final outcome must have these and a lot more. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just need to justify and explain where it lives on the planet I have chosen. I found a planet (Kepler-422b) which was described as being one of the most Earth-like planets, in terms of size and temperature, yet found. Since it is very Earth-like, it made my job a bit easier. But the planet orbits a red dwarf star that is cooler than our star, and this planet is -40 degrees Fahrenheit (80 degrees cooler than earth) so my organism will have to live in the ground of the planet and rely on the core for warmth. But I do not know how deep organisms can go into the Earth. Can someone please help me? I have done a lot of research and spent a lot of time trying to find this but extremophiles are the only organisms listed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you so much for helping me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An extremophile is defined as a microorganism, especially an archaean, that lives in conditions of extreme temperature, acidity, alkalinity, or chemical concentration. Like the Tardigrade. Im sorry I did not make this clear initialy&lt;/p&gt;&#xA;" OwnerUserId="15537" LastEditorUserId="15537" LastEditDate="2015-04-29T15:56:17.807" LastActivityDate="2015-11-17T01:11:21.080" Title="How far in can non-extremophiles live, in Earth?" Tags="&lt;ecology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31790" PostTypeId="2" ParentId="31660" CreationDate="2015-04-27T18:26:16.120" Score="8" Body="&lt;p&gt;Insect 1 is a:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Booklice&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Introduction&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Booklice, also called psocids, are not true lice. While they resemble lice in size and shape, booklice feed only on fungi or mold. If you find them in grain or other stored food products, it is an indication of high humidity which encourages mold growth. In addition to food products, psocids may be found under wallpaper, in furniture, along the sides of windows or on window sills around potted plants. Booklice do not bite, transmit disease, or damage food or fabric, but they can be very annoying when present in large numbers.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Biology&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/w9xt6.jpg&quot; alt=&quot;Booklice&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Booklice found inside homes are wingless and very tiny: less than 1/16 of an inch long. While their back legs are thicker than the other four, and resemble the legs found in jumping insects, booklice do not jump, but run about rather quickly.&lt;/p&gt;&#xA;&lt;p&gt;Adult booklice range in color from translucent white to gray or brown. Females can produce about 60 eggs during the warm summer months and their life cycle (from egg to adult) can be completed in less than one month. When cool temperatures prevail, female booklice produce fewer eggs and the time required to complete their life cycle is over three months. Females deposit their eggs singly and often conceal them by covering with debris. Booklice undergo simple metamorphosis, that is their nymphs look just like adults except that they are much smaller and sexually immature. The common house-infesting booklice normally have four nymphal stages.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Injury&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Booklice feed on molds and will overrun cereals and similar materials that support mold growth. Their presence, therefore, is a nuisance and can render some foods unfit. The starchy paste of wallpaper and books also can support mold growth or may be attacked directly by booklice. Outside of annoyance, their damage is insignificant.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Management&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;The best way to control booklice is to eliminate moist environmental conditions. Reducing the humidity in your home will eliminate the mold on which the booklice feed. Lowering the relative humidity to less than 50% will prevent their development. An air space under potted plants on windowsills will help keep the humidity down and reduce mold growth. Throw away any infested food material and make sure other foods are kept dry. Pesticides are not normally necessary to control booklice in homes.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Warning&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Pesticides are poisonous. Read and follow directions and safety precautions on labels. Handle carefully and store in original labeled containers out of the reach of children, pets, and livestock. Dispose of empty containers right away, in a safe manner and place. Do not contaminate forage, streams, or ponds.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://ento.psu.edu/extension/factsheets/booklice&quot; rel=&quot;noreferrer&quot;&gt;Penn State, Entomology: Booklice&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15476" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-27T19:59:25.447" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31791" PostTypeId="2" ParentId="31789" CreationDate="2015-04-27T19:07:04.447" Score="6" Body="&lt;p&gt;Welcome to Biology.SE and what a great project, it sounds fascinating!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A few years back there was an expedition that drilled down to the deepest layer of the ocean's crust. Down there they found hundreds of different species of bacteria (mostly Proteobacteria) surviving largely on hydrocarbons and other minerals found in the rock. The deepest (that was sequenced) was found 1391.01 mbsf (meters below sea floor) and survived at a temperature of about 102°C (215°F). Like I said, there were several species sequenced, so you could really use any of them that match your needs as at least a start to your organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the deepest point I know of that we have found life, and, considering your project, I don't think you have need to go much deeper. I assume Kepler-422b has liquid water (obviously not at the surface, but perhaps a few miles down)? If so, there is a chance that the water goes relatively close to that depth already.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this helps and good luck!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CDB&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2974637/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2974637/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: If you are looking for a multicellular organism that survives deep enough underground to rely on core warmth, I suggest Halicephalobus mephisto, a nematode living about 1.3 km underground at about 32°C (90°F). This is still considered an extremophile, however it is multicellular with a digestive tract, nervous system, etc. I apologize for the confusion in my initial answer and thanks to jamesqf for noticing my mistake. If you are not content with any extremophiles (even multicellular) please let me know and I will do my best to find something else. Again, I am very sorry for my error.&lt;/p&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="13496" LastEditDate="2015-11-17T01:11:21.080" LastActivityDate="2015-11-17T01:11:21.080" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="31792" PostTypeId="1" AcceptedAnswerId="31794" CreationDate="2015-04-27T19:11:19.117" Score="1" ViewCount="334" Body="&lt;p&gt;I am trying to design primers for sanger sequencing snp detection. In the past I have used &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/tools/primer-blast/&quot; rel=&quot;nofollow&quot;&gt;Primer-BLAST&lt;/a&gt;, but I'm trying to pick up KRAS codon 12 mutations. The problem is that in Primer-BLAST you specify refseq gene ID and so it doesn't seem to design primers outside of the gene locus. This means that my primers will sit on the SNP. Is there a way to tell Primer-BLAST the exact locus I am trying to sequence? Or is there a better way of doing this? Thanks.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-04-29T09:40:03.580" Title="Primer Design With Primer-BLAST" Tags="&lt;dna-sequencing&gt;&lt;blast&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31793" PostTypeId="1" CreationDate="2015-04-27T19:22:39.603" Score="2" ViewCount="179" Body="&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/9920/model-for-fluctuating-selection/27808#27808&quot;&gt;Here&lt;/a&gt; is an answer which explains how one can model the frequency of an allele that is under fluctuating selection (the selection that varies through time).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not, thinking about fluctuating selection, there exist several derivations of the probability of fixation of an allele present at frequency &lt;span class=&quot;math-container&quot;&gt;$p$&lt;/span&gt; with selection coefficient &lt;span class=&quot;math-container&quot;&gt;$s$&lt;/span&gt; in a finite population of size &lt;span class=&quot;math-container&quot;&gt;$N$&lt;/span&gt;. For example, Kimura (using diffusion equations) approximated the probability of fixation &lt;span class=&quot;math-container&quot;&gt;$P_{fix}$&lt;/span&gt; to be&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$P_{fix}≈\frac{1-e^{-4Ns} }{1-e^{-4Nsp}}$$&lt;/span&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How to model the probability of fixation (in a finite population) of an allele that undergoes fluctuating selection?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I welcome one to answer by using whatever type of fluctuating selection. It might be an alternate of &lt;span class=&quot;math-container&quot;&gt;$s_1$&lt;/span&gt; (uneven generation) and &lt;span class=&quot;math-container&quot;&gt;$s_2$&lt;/span&gt; (even generation) or &lt;span class=&quot;math-container&quot;&gt;$s(t)$&lt;/span&gt; might be a sinusoidal function of the time &lt;span class=&quot;math-container&quot;&gt;$t$&lt;/span&gt; (in generations). Or &lt;span class=&quot;math-container&quot;&gt;$s$&lt;/span&gt; might be drawn randomly from some distribution.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-05-01T14:25:46.280" LastActivityDate="2019-05-01T14:25:46.280" Title="What is the probability of fixation for a mutant under fluctuating selection?" Tags="&lt;evolution&gt;&lt;population-genetics&gt;&lt;theoretical-biology&gt;&lt;natural-selection&gt;&lt;population-dynamics&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="31794" PostTypeId="2" ParentId="31792" CreationDate="2015-04-27T20:38:12.207" Score="2" Body="&lt;p&gt;&lt;strong&gt;You can manually restrict the design ranges in Primer-BLAST screen.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0tYuv.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;First of all you should enter the targeted sequence. In this case, it will be &lt;em&gt;NC_000012.12&lt;/em&gt; which corresponds to chromosome 12 that has KRAS gene.&lt;/li&gt;&#xA;&lt;li&gt;You should determine the position of variant that you interested in that chromosome. The &lt;em&gt;KRAS G12D&lt;/em&gt; -or &lt;em&gt;rs121913529&lt;/em&gt;- variant is in 25245350. position. You can find the position of specific variant on &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?searchType=adhoc_search&amp;amp;type=rs&amp;amp;rs=rs121913529&quot; rel=&quot;nofollow noreferrer&quot;&gt;dbSNP&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;For Sanger sequencing, the recommended size is 600-1000 bp. So, we should select ranges +/- 300-500 bp apart from the variant position.&lt;/li&gt;&#xA;&lt;li&gt;For the left primer we choose From:25244850 To:25245050; for the right primer we choose From:25245650 To:25245850. And then submit.&lt;/li&gt;&#xA;&lt;li&gt;Here are the primer-sets that you are looking for. :)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BvQah.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="13292" LastActivityDate="2015-04-27T20:38:12.207" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31795" PostTypeId="1" AcceptedAnswerId="31799" CreationDate="2015-04-27T20:45:47.367" Score="0" ViewCount="505" Body="&lt;p&gt;I'm a very naive and biologically illiterate person, and from what I've read on the internet I'm not really sure I understand the difference between &lt;code&gt;pulse&lt;/code&gt; and &lt;code&gt;blood pressure&lt;/code&gt;. I'm guessing for most of you this is trivial so I'm hoping for something clear for someone of my &amp;quot;level&amp;quot;.&lt;/p&gt;&#xA;&lt;p&gt;On a side note, I speak french, and we have two words: &lt;code&gt;pression&lt;/code&gt; / &lt;code&gt;tension&lt;/code&gt; (artérielle). One of them must be wrong since they mean totally different things and makes things even more confusing.&lt;/p&gt;&#xA;&lt;p&gt;But from what I could gather, are the next statements correct/accurate or am I completely off?&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The blood pressure is the fluid's movement &amp;quot;strength&amp;quot; in the veins (or &amp;quot;&lt;strong&gt;arteries&lt;/strong&gt;&amp;quot;, please edit my post with the correct english word)&lt;/li&gt;&#xA;&lt;li&gt;The &amp;quot;tension&amp;quot; is the force applied on the veins itself, kind of like when you're pulling a rubber band&lt;/li&gt;&#xA;&lt;li&gt;The pulse is just the wave of blood moving, which creates different tensions over the vein and whose movement is created by the pressure.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="12892" LastEditorUserId="-1" LastEditDate="2021-03-04T13:33:59.317" LastActivityDate="2021-03-04T14:15:27.640" Title="Difference between pulse and blood pressure" Tags="&lt;human-biology&gt;&lt;blood-circulation&gt;&lt;blood-pressure&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="31796" PostTypeId="1" CreationDate="2015-04-27T20:46:31.983" Score="3" ViewCount="120" Body="&lt;p&gt;illumina instruments have built-in -or online- analysis software for variant analysis (CASAVA). This software can filter out the false positive variants near the homopolymer repeats (AAAAAAAA) and filter them with &quot;R8&quot; tag. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to make homopolymer repeat filter without using illumina's own pipeline? (with another software?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;P.S&lt;/strong&gt; I noticed that, GATK have HomopolymerRun script that makes similar job. But it is no longer supported and recommended.&lt;/p&gt;&#xA;" OwnerUserId="13292" LastActivityDate="2015-04-27T20:46:31.983" Title="How can I create R8 (homopolymer repeat) filter without using illumina pipeline?" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;sequence-analysis&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31797" PostTypeId="1" CreationDate="2015-04-27T21:40:49.670" Score="0" ViewCount="5386" Body="&lt;p&gt;I have a strange question, but let me tell you something first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you think of this carefully, then you realize something, please try this right now:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Contract your muscles only so that your arms move without you doing it. You can't.&#xA;The way it happens is that you move your arm (or you do something or whatever you call it), then your muscles contract.&#xA;If our muscles weren't there, then we wouldn't be able to move our arms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;We don't contract our muscles, we move our arms, then our muscles contract automatically. So the muscles contract themselves, but what gives us the ability to make our arms move after deciding when we want to move our arm?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can't contract our muscles so that our arm moves, we make that movement, then our muscles contract, but you can't even feel it because it's so light. &#xA;This is hard to explain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So what gives us the ability to make our arms move, but not the muscles?&lt;/strong&gt; I'm telling you, some people won't even understand, but this is real.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="15540" LastEditorUserId="4747" LastEditDate="2015-04-27T22:36:27.420" LastActivityDate="2015-04-27T23:01:53.557" Title="Our muscles give us the ability to move our arms but....?" Tags="&lt;human-biology&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2015-04-28T00:21:37.387" ContentLicense="CC BY-SA 3.0" />
  <row Id="31799" PostTypeId="2" ParentId="31795" CreationDate="2015-04-27T22:13:18.507" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;The blood pressure is the fluid's movement &quot;strength&quot; in the&#xA;  &lt;em&gt;arteries&lt;/em&gt; (or &quot;artères&quot;, please edit my post with the correct english word)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Blood pressure is a measurement of the strength of flow through the arteries. (I.e., the force per unit area exerted by the blood on arterial walls.) So replace vein with artery and your definition is correct.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The &quot;tension&quot; is the force applied on the veins itself, kind of like&#xA;  when you're pulling a rubber band&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In cardiovascular terminology, hypertension and hypotension are used interchangeably with high and low blood pressure (even though technically tension uses force units and pressure uses force/unit area units). Your definition sounds more like arterial tensile strength, which is the ability of the artery to withstand pulling forces without breaking (which decreases with age).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The pulse is just the wave of blood moving, which creates different&#xA;  tensions over the vein and whose movement is created by the pressure.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Pulse is an indirect measurement of heart rate. So, yes, it's the rate of the &quot;wave of blood moving.&quot; It creates different &quot;pressures&quot; measured by systolic (the &quot;wave&quot; in your terms) and diastolic (the &quot;trough&quot;) whose movement is created by the force (of the heart walls contracting).&lt;/p&gt;&#xA;" OwnerUserId="15539" LastActivityDate="2015-04-27T22:13:18.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31801" PostTypeId="2" ParentId="31797" CreationDate="2015-04-27T22:30:28.033" Score="2" Body="&lt;p&gt;I am a bit confused as to what you are asking. You don't move your arm, like your suggesting, ever. No one does, and no one can. You contract your muscles which happen to move your arm. The movement of the arm is the result of your muscles contracting, not the cause.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How it happens is that your brain sends a signal to your muscles (which you cant feel). The muscles get excited and they contract. The instant your muscle contracts your hand begins to move. In the end your bones are like sticks, and your muscles are the ones that pull the stick in different directions, in order to achieve flexion and extension.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Might i suggest you read up on the musculoskeletal system (&lt;a href=&quot;http://kidshealth.org/teen/your_body/body_basics/bones_muscles_joints.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://kidshealth.org/teen/your_body/body_basics/bones_muscles_joints.html&lt;/a&gt;) ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/z0Xwc.jpg&quot; alt=&quot;Motor pathway&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-04-27T22:37:46.193" LastActivityDate="2015-04-27T22:37:46.193" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31804" PostTypeId="1" AcceptedAnswerId="31805" CreationDate="2015-04-27T23:19:24.707" Score="0" ViewCount="50" Body="&lt;p&gt;I'm having a bit of trouble with searching for this piece of information. I'm doing a study related to phylogenetic susceptibility of hosts to pathogens (based on a recent Nature publication), specifically to flu. This requires knowing the &lt;strong&gt;reference&lt;/strong&gt; 18S ribosomal DNA sequence for chickens, wild ducks, horses, pigs and humans (amongst others). Is there a resource that enables us to easily download these?&lt;/p&gt;&#xA;" OwnerUserId="1536" LastActivityDate="2015-04-27T23:39:06.607" Title="Ribosomal DNA references sequences" Tags="&lt;bioinformatics&gt;&lt;sequence-analysis&gt;&lt;ribosome&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31805" PostTypeId="2" ParentId="31804" CreationDate="2015-04-27T23:29:21.807" Score="2" Body="&lt;p&gt;For birds you can start by searching &lt;em&gt;18s&lt;/em&gt; in &lt;a href=&quot;http://birdgenenames.org/cgnc/&quot; rel=&quot;nofollow&quot;&gt;http://birdgenenames.org/cgnc/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But generally NCBI Nucleotide database, should provide you with all information and accession numbers. See this broad search: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/?term=18S+ribosomal+RNA+gene&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/nuccore/?term=18S+ribosomal+RNA+gene&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adding species specification and other parameters, you might find what you are looking for. For example, see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/66270902&quot; rel=&quot;nofollow&quot;&gt;chicken 18S ribosomal RNA gene&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-27T23:29:21.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31806" PostTypeId="2" ParentId="31804" CreationDate="2015-04-27T23:33:56.167" Score="2" Body="&lt;p&gt;I may be jumping the gun here, but assuming that you haven't searched NCBI or ensembl, I'd do that first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially all genomic information is maintained by a collaboration between US NIH, EU EBI and Japan. All databases are synced to each other, and hence the data should (theoretically) be the same (in practice it never is). I'd suggest you pick one server and stick to it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my lab we prefer to use NCBI, but that differs from lab to lab.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can search NCBI by following the tutorial here (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/guide/howto/find-published-info-gene-sequence/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/guide/howto/find-published-info-gene-sequence/&lt;/a&gt;) or ensembl bu following the tutorial here (&lt;a href=&quot;http://www.ebi.ac.uk/training/online/course/ensembl-browsing-chordate-genomes/how-search-ensembl&quot; rel=&quot;nofollow&quot;&gt;http://www.ebi.ac.uk/training/online/course/ensembl-browsing-chordate-genomes/how-search-ensembl&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A sample search for chicken gives you this (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/100861561&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/gene/100861561&lt;/a&gt;) with three entries for genomic dna and one for mRNA. I'd choose a complete sequence over a partial sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might also want to look up in their help the meaning of cds (coding sequence; you'll encounter it)&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-04-27T23:39:06.607" LastActivityDate="2015-04-27T23:39:06.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31807" PostTypeId="1" CreationDate="2015-04-27T23:38:21.260" Score="2" ViewCount="261" Body="&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question is about human physiology and gametogenesis. A spermatozoid is not necessarily the direct &quot;offspring&quot; of a diploid cell. Stated differently, a spermatozoid cell can be the offspring cell of another haploid cell. I am saying &quot;can be&quot; and &quot;is not necessarily&quot;, but the correct formulation might be &quot;always is&quot;. A given spermatozoid might eventually be the descendent of 1000 generations of haploid cells before (going back in time) finding the diploid ancestor (the one who underwent meiosis II). I'd expect the same to be true for ovules although I'd expect that a given ovule have fewer haploid descendent before (going back in time) finding the diploid cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;How many haploid generations preceded a typical &lt;em&gt;spermatozoid/ovule&lt;/em&gt; that could eventually fertilize an egg?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;How does this answer vary with age and sex?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In its most beautiful form, the question is:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What is the distribution of the number of mitotic divisions that happened in the father/mother of a given individual?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Any answer that would offer a step toward answering these questions are welcome!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="10401" LastEditDate="2019-05-01T19:56:23.490" LastActivityDate="2019-05-01T19:56:23.490" Title="How many mitotic divisions do haploid cells undergo before fertilization?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;reproduction&gt;&lt;sex&gt;&lt;mitosis&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="31808" PostTypeId="1" AcceptedAnswerId="31810" CreationDate="2015-04-27T23:56:07.727" Score="0" ViewCount="122" Body="&lt;p&gt;I was sitting out on my balcony earlier and saw a woodpecker land on a tree nearby. It began pecking at the tree, and did so about five times, in intervals of about four pecks each time, before finally giving up and flying away. My question is quite simple, were woodpeckers gifted(did probability glean favorably upon) with a positive form of evolution? Does the reward justify the amount of energy they have to exert for food? Were they given an improper and doomed form of evolution?&lt;/p&gt;&#xA;" OwnerUserId="13353" LastEditorUserId="13353" LastEditDate="2015-04-28T05:19:07.193" LastActivityDate="2015-04-28T05:33:51.880" Title="Woodpecker pecking, an effective evolution?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="10" ClosedDate="2015-05-03T04:40:12.057" ContentLicense="CC BY-SA 3.0" />
  <row Id="31809" PostTypeId="2" ParentId="31788" CreationDate="2015-04-28T00:15:03.943" Score="5" Body="&lt;p&gt;This is actually not the Fitzhugh-Nagumo model of the a neuron, however it is highly related to it. I believe the the Equation you have there, is capable of oscilations for any positive values of $\epsilon$, $C$, $L$. I generated this graph with the parameter values all set to 1.  Note how it is very similar to a sine wave.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Bf12R.png&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I believe you where trying to write Van der Pol's equation &lt;a href=&quot;http://en.wikipedia.org/wiki/Van_der_Pol_oscillator&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;:&#xA;$$C\frac{d^2V}{dt^2} +\epsilon (V^2-1) \frac{dV}{dt}+ \frac{V}{L}$$ &#xA;Note the subtle difference of multiplying by the first derivative. &#xA;Here is again a image with all parameters set to 1&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ufBe6.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Fitzhugh-Nagumo equation can be found on wikipedia &lt;a href=&quot;http://en.wikipedia.org/wiki/FitzHugh%E2%80%93Nagumo_model&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and on peer reviewed  scholarpedia &lt;a href=&quot;http://scholarpedia.org/article/FitzHugh-Nagumo_model&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;. For reference it is a two state model described by the equation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ \frac{dV}{dt}=V-V^3/3-W+I$$&#xA;$$ \tau \frac{dW}{dt}= V + a -bW$$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A common value for the parameters are $a=.7$,$b=.8$,$\tau=12.5$ $I$ can be anything really, I used $I=.5$ to generate the graph below. Also note that the model wont spike if I below a certain value. The Fitzhugh Equation is is slightly more general, but does simplify to the Van der pol under the assumption $a=b=0$. Here is the graph of it with the constants I described. &lt;img src=&quot;https://i.stack.imgur.com/q0aeu.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="13388" LastEditorUserId="13388" LastEditDate="2015-04-28T16:20:07.203" LastActivityDate="2015-04-28T16:20:07.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31810" PostTypeId="2" ParentId="31808" CreationDate="2015-04-28T01:34:07.580" Score="7" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;My question is quite simple, were woodpeckers gifted with a positive form of evolution?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Though this has been addressed in comments, it's an opportunity to address a popular mind frame about evolution, that is &lt;a href=&quot;http://www.thefreedictionary.com/anthropomorphize&quot; rel=&quot;nofollow&quot;&gt;anthropormorphizing&lt;/a&gt; it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution does not think or bestow in the sense that a philanthropist might. Evolution does not doom or treat unfairly as a dictator might. Evolution is &lt;strong&gt;merely&lt;/strong&gt; the process of predominantly random changes in genetic material that result in a change in the expression of that genetic material. If it is a change that radically affects expression of a critical gene (say, that encodes the structure of hemoglobin), the organism experiences a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK22011/&quot; rel=&quot;nofollow&quot;&gt;lethal point mutation&lt;/a&gt; and ceases to exist. Evolution for that organism stops there; if death occurs before reproduction, the mutation is lost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution &lt;em&gt;seems&lt;/em&gt; beneficial because the environment exerts selective pressures on life: if two animals (say, birds) in the same habitat (say, woodlands) eat the same food (say, larval insects), competition for resources exists, decreasing the numbers of both animals. However, if a mutation (say, a marginally different beak shape) allows even a slight chance that the animal will have a competitive advantage, it is kept in the population. A staggering number of mutations similarly either harmless or advantageous may eventually allow two animals to inhabit the same habitat without competition - a net gain for both animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But there's no gift involved. Just a mind-numbing number of non-lethal mutations over a mind-numbing number of years, under the influence of the selective pressures of the environment. You don't see all the mutations that were deleterious, resulting in countless deaths and dead ends because you are standing in one point in time, seeing what exists around you &lt;em&gt;now&lt;/em&gt;. The woodpecker seems almost fantastical.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Were [woodpeckers] given an improper and doomed form of evolution?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Evolution follows the same principles for all species: predominantly random mutations without rhyme or reason or form. If you want to speak of doomed animals, look to mankind's effects on the environment in the last 2000 years, or the last 20. When ecological niches are wiped out, that, not evolution, dooms an animal. The Monarch Butterfly is a poignant example of dooming a species by destroying it's habitat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A great way the understand selective pressures of habitat is to read about marsupial evolution in Australia. The effect of ecological niches on evolution is very clear.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-04-28T05:33:51.880" LastActivityDate="2015-04-28T05:33:51.880" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31811" PostTypeId="2" ParentId="31615" CreationDate="2015-04-28T02:07:28.640" Score="5" Body="&lt;p&gt;(This isn't an answer, but hopefully it will help get it past the experimental design into just solving the equation.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where did you get that α0 was not determined from their data? On p. 10 (256), they state, &quot;The prevailing direction of effective pollen dispersal within neighbourhoods (a0) that gave the best ﬁt of the model was 91 degrees from north (nearly due east).&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best-fit δ parameter value of 0.56 (which determines the size of the effect of the angle between the male tree and the wind) is also determined by their model (table 1, model 9) based on their sample set.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This math is too much for me to solve, but here is how I would go about getting through the experimental setup to just solving the math equation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since you're only looking for the effect of wind/directionality, you would set the tree height and distance between trees to be equal. So βd and γh would remain constant and cancel out when you solve for a. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then you want to determine what angles would give you the highest and lowest pollen counts. Set a0 to wind direction and aj to the angle between a0 and the half disk. The highest pollen count would happen at aj = a0. The lowest pollen counts would happen at aj = (a0-180) or (a0-π or whatever unit of angle is appropriate. Stupid trig.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With those settings, it should be possible to determine the values of ϕ where aj = a0 and where aj = a0-180. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then you can get the proportion of pollen grain falls into each disk by finding the ratio of ϕj(a0-180) / ϕj(a0).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assumptions:&#xA;1) There's a linear correlation between ϕ, &quot;the mating success (i.e. fertility) of each outcross male in the neighbourhood&quot; and the distribution of pollen grain dispersal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) That a0 (&quot;The prevailing direction of effective pollen dispersal within neighbourhoods&quot;) is entirely due to wind. Here I could see terrain being a factor, which would make the effect of wind xδ, such that x&amp;lt;1. If this were the case, the calculated ratio of high pollen / low pollen would be higher than actual.&lt;/p&gt;&#xA;" OwnerUserId="15539" LastActivityDate="2015-04-28T02:07:28.640" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31813" PostTypeId="2" ParentId="31727" CreationDate="2015-04-28T05:47:28.973" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;People competent in mathematics have been shown to have higher activation of the left &lt;em&gt;angular gyrus&lt;/em&gt; according to fMRI. EEG recordings have shown larger activity in the &lt;em&gt;posterior parietal cortex&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;I think you are interested in &lt;strong&gt;what makes a good mathematician&lt;/strong&gt;. A brain imaging study by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3208209/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Grabner et al. (2011)&lt;/a&gt;. showed that the left anterior gyrus was more activated in individuals more competent in math. Specifically, the authors argue that the stronger left AG activity in the more competent subjects reflects a higher proficiency in processing mathematical symbols. The anterior gyrus is involved in mathematical symbol processing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pKSzz.jpg&quot; alt=&quot;left angular gyrus&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Left angular gyrus, lateral view. Source: &lt;a href=&quot;https://www.kenhub.com/en/atlas/gyrus-angularis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kenhub Neuroanatomy Atlas&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ERP studies (event-related potentials deduced from the EEG) have shown higher activity in posterior parietal cortex in subjects excelling in math &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs10763-014-9513-5#page-1&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Waisman et al., 2014)&lt;/a&gt;. This region is associated with algebra and handling mathematical functions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IXUMw.jpg&quot; alt=&quot;Posterior parietal cortex&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Posterior parietal cortex among other regions not relevant to the question answer. Source: &lt;a href=&quot;http://www.livescience.com/7110-store.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Live Science&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3208209/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Grabner et al. &lt;em&gt;Front Hum Neurosci&lt;/em&gt; 2011; &lt;strong&gt;5&lt;/strong&gt;: 130&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs10763-014-9513-5#page-1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Waisman et al., &lt;em&gt;Int J Sci Math Edu&lt;/em&gt; 2014; &lt;strong&gt;12&lt;/strong&gt;(3): 669-96&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="15579" LastEditDate="2015-04-30T05:25:36.413" LastActivityDate="2015-04-30T05:25:36.413" CommentCount="15" ContentLicense="CC BY-SA 3.0" />
  <row Id="31814" PostTypeId="1" AcceptedAnswerId="31818" CreationDate="2015-04-28T06:33:05.133" Score="7" ViewCount="1286" Body="&lt;p&gt;Pacemaker cells have high resting membrane potentials of -50 to -40 mV, whereas normal cells have their resting membrane potential around -70 mV. Which ions, and what kind of channels are responsible for the high resting potential of pacemaker cells?&lt;/p&gt;&#xA;" OwnerUserId="15543" LastEditorUserId="9943" LastEditDate="2015-04-28T11:40:49.577" LastActivityDate="2015-04-28T11:40:49.577" Title="What is the reason behind high resting membrane potential of pacemaker cells?" Tags="&lt;biophysics&gt;&lt;electrophysiology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31815" PostTypeId="2" ParentId="31771" CreationDate="2015-04-28T06:52:03.693" Score="3" Body="&lt;p&gt;The &lt;a href=&quot;http://ods.od.nih.gov/factsheets/vitaminb12&quot; rel=&quot;nofollow&quot;&gt;NIH RDA&lt;/a&gt; for vitamin B12 is 2-3µg/day. Cyanocobalamin has an $M_r$ of 1355, of which 26, or less than 2% ($CN^-$) is cyanide. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the &lt;a href=&quot;http://www.atsdr.cdc.gov/toxprofiles/tp8-a.pdf&quot; rel=&quot;nofollow&quot;&gt;Minimal Risk Level&lt;/a&gt; for cyanide is &lt;a href=&quot;http://www.atsdr.cdc.gov/toxprofiles/tp8-c8.pdf&quot; rel=&quot;nofollow&quot;&gt;50µg/kg/day&lt;/a&gt;, your studies are correct in that 1000x the RDA of vitamin B12 in the form of cyanocobalamin is not lethal, and furthermore is expected to not cause any negative effects even in the most sensitive of individuals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This holds true even if 100% of the cyanide ligands dissociate from cyanocobalamin, which is unlikely to be the case in practice due to cyanide being a very strong binding ligand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cyanocobalamin contains too little cyanide, and is consumed in too low an amount, to cause cyanide toxicity. &lt;a href=&quot;http://en.wikipedia.org/wiki/The_dose_makes_the_poison&quot; rel=&quot;nofollow&quot;&gt;The dose makes the poison&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-04-28T07:56:24.180" LastActivityDate="2015-04-28T07:56:24.180" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31816" PostTypeId="2" ParentId="31543" CreationDate="2015-04-28T06:54:30.357" Score="-4" Body="&lt;p&gt;Morning walks are preferred because the sunlight that falls on the earth in the morning is good for your skin for producing Vitamin D.&#xA;and also it is said that morning walks are good for:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Strengthening Bones and Joints&lt;/p&gt;&#xA;&lt;p&gt;Weight control&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;and also independent of the time of the day, due to exercise and walking you keep moving your joints an this improves your Blood circulation.&lt;/p&gt;&#xA;&lt;p&gt;And also as you keep moving your muscles too which improves Muscle Strength &lt;strong&gt;.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;this was from my knowledge.If you want to know more &lt;strong&gt;:&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://healthnbodytips.com/4-great-advantages-and-health-benefits-of-early-morning-walk.html/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Click Here(link 1) &lt;/a&gt;&lt;strong&gt;||&lt;/strong&gt;&#xA;&lt;a href=&quot;http://listdose.com/10-reasons-why-morning-walks-are-important-for-your-health/&quot; rel=&quot;nofollow noreferrer&quot;&gt;and here(link 2)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Share your thoughts with comments,&lt;/p&gt;&#xA;&lt;p&gt;Any suggestions and questions welcomed,&lt;/p&gt;&#xA;&lt;p&gt;Anurag &lt;strong&gt;.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="15513" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-28T06:54:30.357" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31817" PostTypeId="1" CreationDate="2015-04-28T07:54:49.133" Score="4" ViewCount="129" Body="&lt;p&gt;Many daily activities that we perform are result of inbuilt oscillatory circuits in our body. For example walking, breathing, heart beat, blinking, etc. The coding and decoding of stored memory also happen via controlled oscillations. The link &lt;a href=&quot;http://en.wikipedia.org/wiki/Neural_oscillation&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Neural_oscillation&lt;/a&gt; contains information about neural oscillations. It says in here that a single neuron, an ensemble of neurons and activity of brain may exhibit synchronised oscillations. It is also said that these oscillatory circuits can control all the parameters of oscillations i.e. frequency, phase and amplitude.While above are true for neurons as a part of bigger systems, my question is related to study of isolated neurons.&lt;br&gt;&lt;br&gt;&#xA;There are many instances of studies of artificial neural circuitary created on a customized substrate(Micro Electrode Array) by masking techniques. Also there are loads of ongoing research to study the simple neural circuits in temporal and spatial domain by electrical interfacing of semiconductor and nerve cells using Field Effect Transistor(FET).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know if these kind of oscillations are unique to some special kinds of neuron? Is the control of oscillation parameter possible in every neurons and isolated neurons? Can a neuron or any other cell exhibit change in action potential independently? Do other cells except neuron and pacemaker cells exhibit oscillation? Can a single neuron exhibit memory?&lt;br&gt;&#xA;Can a simple circuit like below generate oscillations?&lt;br&gt;&#xA;Suppose I culture the neurons on a substrate in a controlled way such that one neuron is connected to only one other neuron in a linear fashion and the last neuron is connected to first. Assuming we supply the ions if there is loss, can a clock pulse of varying frequencies be generated, where the frequency is the function of the no. of intermediate neurons and their length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be a great help if somebody can provide information about softwares to simulate simple neural circuits (If available).&lt;/p&gt;&#xA;" OwnerUserId="15543" LastEditorUserId="15543" LastEditDate="2015-04-29T06:38:15.003" LastActivityDate="2015-05-25T12:42:12.073" Title="Oscillatory electrical system using a chain of neurons" Tags="&lt;neuroscience&gt;&lt;neurotransmitter&gt;&lt;memory&gt;&lt;action-potential&gt;&lt;microarray&gt;" AnswerCount="1" CommentCount="15" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31818" PostTypeId="2" ParentId="31814" CreationDate="2015-04-28T08:08:38.657" Score="6" Body="&lt;p&gt;The pacemaker potential is interesting (to a biologist) as it involves your typical Na/K channels, Ca channel, as well as a funny current (If) or alternatively called hyperpolarization-activated current.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The funny current is a mixed sodium-potassium current that activates&#xA;  upon hyperpolarization at voltages in the diastolic range (normally&#xA;  from -60/-70 mV to -40 mV). When at the end of a SA potential the&#xA;  membrane repolarizes below the If threshold (about -40/-50 mV), the&#xA;  funny current is activated and supplies inward current, which is&#xA;  responsible for starting the diastolic depolarization phase (DD); by&#xA;  this mechanism, the funny current controls the rate of spontaneous&#xA;  activity of sinoatrial myocytes, hence the cardiac rate.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SMOws.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pacemaker activity (or spontaneous electrical activity) of the&#xA;  sino-atrial node is based on the presence of a special phase called&#xA;  the diastolic depolarization during the action potential, in which&#xA;  cells depolarize spontaneously towards the AP threshold. Animal&#xA;  studies (mostly conducted on rabbit heart) have identified that this&#xA;  net inward current during the diastolic depolarization phase is the&#xA;  result of a complex interaction of multiple inwardly and outwardly&#xA;  directed ion currents....&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Verkerk, Arie O., Antoni CG van Ginneken, and Ronald Wilders. &quot;Pacemaker activity of the human sinoatrial node: role of the hyperpolarization-activated current, I f.&quot; International journal of cardiology 132.3 (2009): 318-336.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also this&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The SAN is a complex tissue with regional differences in morphological&#xA;  and electrical properties.Animal studies have revealed that&#xA;  pacemaking in SAN cells follows from diastolic depolarization driven&#xA;  by a net inward current, which results from an interaction of multiple&#xA;  ion currents. Inward currents are activated during diastole:&#xA;  hyperpolarization-activated pacemaker current (If), background Na+&#xA;  current (Ib,Na), sustained inward current (Ist), T- and L-type Ca2+&#xA;  currents (ICa,T and ICa,L, respectively), and Ca2+-release activated&#xA;  Na+–Ca2+ exchange current (INCX). Conversely, outward currents are&#xA;  deactivated: rapid delayed rectifier K+ current (IKr) and slow delayed&#xA;  rectifier K+ current (IKs). The relative contributions of these&#xA;  currents to diastolic depolarization are a matter of debate.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Verkerk, Arie O., et al. &quot;Pacemaker current (If) in the human sinoatrial node.&quot; European heart journal 28.20 (2007): 2472-2478.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Might I suggest you read up on the papers mentioned above?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might also be interested in this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Noma, Akinori. &quot;Ionic mechanisms of the cardiac pacemaker potential.&quot; Japanese heart journal 37.5 (1996): 673-682.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastActivityDate="2015-04-28T08:08:38.657" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31819" PostTypeId="1" CreationDate="2015-04-28T09:43:26.063" Score="2" ViewCount="271" Body="&lt;p&gt;The theory of evolution states that random variations in organisms occur to better suit their surroundings. We take for example a bacteria's flagella. There's a bacteria who has a tube kind of structure that it uses to inject toxins in other cells. Structure of flagella and this tubular structure is very similar. So biologists state that this is clear evidence for evolutionary process wherein this tubular structure underwent gradual changes that resulted into a flagella.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now my question is, minute changes did occur to this tubular structure, but how do those changes get carried over to the next generation? Almost all components of a cell are created as per the instructions coded into DNA. So does it mean that every minute changes that occur to an organism get recorded into DNA so that they can be carried over? In above example, assume, that a few proteins got accidentally attached to the tubular structure that will help the structure to rotate. Now when this temporarily changed bacteria gets divided into a new one it will have lost that change. So to actually carry over this &quot;beneficial&quot; change would the bacteria have changed its genome? How does this happen? What is the basal mechanism that supports evolutionary changes?&lt;/p&gt;&#xA;" OwnerUserId="15546" LastEditorUserId="22057" LastEditDate="2016-03-23T01:46:57.193" LastActivityDate="2016-03-23T01:46:57.193" Title="How do minute changes in an organism, as a result of evolution, get carried over to next generation" Tags="&lt;evolution&gt;&lt;bacteriology&gt;&lt;molecular-evolution&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31820" PostTypeId="2" ParentId="31819" CreationDate="2015-04-28T09:55:30.763" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;As populations expand, generation by generation, they will inevitably&#xA;  run into limits on resources. Not all individuals in a population are&#xA;  exactly alike as some will have traits that give them an advantage in&#xA;  survival. A change in any aspect of the environment can suddenly turn&#xA;  what had been just another variation or variant into either an&#xA;  advantage or a disadvantage  If a selective pressure (i.e. change in&#xA;  the environment), acts against or upon the differences between the&#xA;  individuals in a population, you get natural selection, which, through&#xA;  time, can cause a population to evolve&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rmitchellbioanthro.weebly.com/uploads/2/3/7/6/23767919/natselinanutshell.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://rmitchellbioanthro.weebly.com/uploads/2/3/7/6/23767919/natselinanutshell.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution consists of two essential things:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Random mutagenesis (in this case a slight change that occurs in the DNA, that causes a slight change in the protein to show up)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second stage of evolution is natural selection. After the mutagenesis event, nature rigorously selects for the mutation. If the mutation has a fitness cost to the organism, it gets removed (the organism doesn't survive). By removing all things that are more costly than beneficial, nature selects for the fittest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qVofK.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take the examples of beetels here (&lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evo_25&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://evolution.berkeley.edu/evolibrary/article/evo_25&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Very rarely does the external environment directly change the DNA code (you can argue about epigenetics, but that's a different can of worms). Changes in the environment usually dictate the survival of organisms with different traits. In fact what usually happens is a change in the DNA code occurs naturally due to mutagenesis and that change undergoes the rigours of natural selection.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in you case what might have happened is (I am postulating here, I would recommend a literature search to verify this), your bacteria had a tubular structure that it used to inject toxins in other cells. Some bacteria (due to genetic variation in sexual reproduction) had mutations that allowed it to move this tubular structure. This allowed it to survive more efficiently, and hence reproduce more. Eventually this population of bacteria, slowly replaced the bacteria who had no locomotor control on their &quot;tube&quot;, and hence one stage of natural selection has occurred. Now this happens again and again, till the efficiency of the locomotion is optimal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Might I suggest you read this book ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bonner, John Tyler. The evolution of complexity by means of natural selection. Princeton University Press, 1988.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-04-28T10:08:06.463" LastActivityDate="2015-04-28T10:08:06.463" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31821" PostTypeId="1" CreationDate="2015-04-28T10:03:21.583" Score="2" ViewCount="1175" Body="&lt;p&gt;Even though we cannot survive for more than few minutes if we stop breathing or if our heart stops, why is it so that our heart beat is controlled involuntarily while breathing can be voluntarily controlled to a certain extent. I just noticed that blinking of eyes also falls in this category; though we involuntarily blink and our eyelids close involuntarily in bright light, there is still voluntary modulation. What kind of evolutionary changes and natural selection could have led to these kind of voluntary modulations i.e. cortical control over these processes?&lt;/p&gt;&#xA;" OwnerUserId="15543" LastEditorUserId="3340" LastEditDate="2015-04-28T13:33:34.273" LastActivityDate="2015-04-28T13:33:34.273" Title="Why can we control our breath rate but not our heart rate?" Tags="&lt;evolution&gt;&lt;physiology&gt;&lt;neuroscience&gt;&lt;cardiology&gt;" AnswerCount="0" CommentCount="12" ClosedDate="2015-04-28T14:36:39.480" ContentLicense="CC BY-SA 3.0" />
  <row Id="31822" PostTypeId="1" CreationDate="2015-04-28T10:39:16.770" Score="0" ViewCount="93" Body="&lt;p&gt;I want to believe that eating vegetables is necessary even when one takes&#xA;vitamins, but I can't find any medical evidence for this.  To make my question&#xA;specific, suppose a study on twins were done in which one ate anything they&#xA;wanted and the other was limited to just potatoes, chicken, vanilla ice cream,&#xA;and water, but both took vitamins (with 100% RDA from the 2015 guidelines).&#xA;What statistically measurable difference will you see?  Will the twin with the&#xA;free diet live much longer on average?  Is there a published medical study&#xA;(perhaps on mice) showing this benefit?&lt;/p&gt;&#xA;" OwnerUserId="1339" LastActivityDate="2015-10-05T05:23:22.523" Title="Are vegetables really needed in our diet?" Tags="&lt;health&gt;&lt;vitamins&gt;&lt;diet&gt;&lt;vegetable&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31823" PostTypeId="2" ParentId="31688" CreationDate="2015-04-28T10:44:48.457" Score="2" Body="&lt;p&gt;The only abnormality which can be seen on the ECG curve is a prolonged PR Interval but only when acute alcohol poisoning has been done. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the referenced paper the patient had consumed 3.7 g/l (3.7 per mille) which resulted in a PR prolongation of 200-300 ms. The normal PR interval is different for everybody but it normally is 0.12 to 0.20 seconds. A long PR interval will result in a first degree heart block. In your case (0.2 per mille) I doubt that you are going to see any abnormalities. But if the ECG sensor has a good sampling rate then maybe there is a chance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The PR interval reference 1 is defined as shown here: &#xA;&lt;img src=&quot;https://i.stack.imgur.com/imMeP.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PR interval reference 2:&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/vCRwp.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further reading: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ecglibrary.com/norm.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;Normal ECG&lt;/a&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22679160&quot; rel=&quot;nofollow noreferrer&quot;&gt;Third-degree atrioventricular block in an&#xA;adolescent following acute alcohol intoxication. van Cleef AN1,&#xA;Schuurman MJ, Busari JO.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8097" LastActivityDate="2015-04-28T10:44:48.457" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31824" PostTypeId="1" CreationDate="2015-04-28T13:35:28.717" Score="1" ViewCount="60" Body="&lt;p&gt;I currently take tertiary-high school biology and I am taught that translocation of food in the phloem occurs by the pressure flow hypothesis.&#xA;I would like to ask why it is still a hypothesis, and what are arguments against it. If possible are there any scientific literature or journals for me to chew on? Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="15002" LastActivityDate="2015-04-28T13:35:28.717" Title="Why is translocation of food in the phloem still a debate?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31825" PostTypeId="1" CreationDate="2015-04-28T14:14:41.577" Score="0" ViewCount="651" Body="&lt;p&gt;Does the DNA of a tadpole change after it becomes a frog? In other words what changes take place as a tadpole becomes a frog, and does this metamorphosis affect the DNA in any way?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would appreciate your help. I am doing research for a book I'm in the process of writing. If you can refer me to research material, I would appreciate that also. &lt;/p&gt;&#xA;" OwnerUserId="15548" LastEditorUserId="8105" LastEditDate="2015-04-28T18:54:16.970" LastActivityDate="2015-04-29T11:29:28.740" Title="Does the DNA of a tadpole change after it becomes a frog?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;&lt;zoology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31826" PostTypeId="2" ParentId="31825" CreationDate="2015-04-28T14:28:56.947" Score="4" Body="&lt;p&gt;Your germline DNA remains the same no matter what you do in the growth process (The DNA of a child is the same as the DNA of the adult). What does change is the expression of the DNA (transcriptomic profile), other regulatory factors (Epigenetic modifications), alternative forms of the same DNA expressed differently (splice site variations and alternative promoters) things like that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your somatic DNA does undergo small changes, caused by (retro) transposons, and in a few cells, like the mature B and T cells, they contain only a small subset of a few essential genes (that give them their specificity to an antigen), and other small changes like that (credit: mdperry, see comments). &lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-04-29T11:29:28.740" LastActivityDate="2015-04-29T11:29:28.740" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31828" PostTypeId="1" AcceptedAnswerId="31835" CreationDate="2015-04-28T15:35:31.673" Score="2" ViewCount="56" Body="&lt;p&gt;With respect to this link&lt;br&gt;&#xA;&lt;a href=&quot;http://www.biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&amp;amp;object=RXN-14479&quot; rel=&quot;nofollow&quot;&gt;http://www.biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&amp;amp;object=RXN-14479&lt;/a&gt; &lt;br&gt;&#xA;Here the enzyme is mentioned and the two reacting compounds. Now , my question is &lt;br&gt; &#xA;1. When these two compounds react, do they initially get attached to the enzyme before reaction?&lt;br&gt;&#xA;2.If they Do both these compounds get attached to the enzyme, what is such an interaction called? Protein compound interaction?? &lt;br&gt;&lt;/p&gt;&#xA;" OwnerUserId="8835" LastActivityDate="2015-04-28T21:56:46.227" Title="Question regarding an Escherichia coli reaction" Tags="&lt;organic-chemistry&gt;&lt;biochemistry&gt;&lt;bioinorganic-chemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31830" PostTypeId="1" CreationDate="2015-04-28T16:28:40.453" Score="3" ViewCount="365" Body="&lt;p&gt;&lt;strong&gt;Is there any support in modern biology for the &lt;a href=&quot;http://en.wikipedia.org/wiki/Chakra&quot; rel=&quot;nofollow&quot;&gt;ancient concept of &quot;Chakras&quot;&lt;/a&gt;?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've seen the concept of 7 chakras &lt;a href=&quot;http://en.wikipedia.org/wiki/Chakra#Endocrine_system&quot; rel=&quot;nofollow&quot;&gt;linked to the major endocrine glands in the human body&lt;/a&gt; (pineal,thyroid, adrenal, testes, etc). This makes some sense, however, I've seen other numbering start to talk about 14, 21, etc number of chakras, which makes me skeptical.  Are chakras real?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2015-04-28T16:28:40.453" Title="Is there any biological support for the concept of &quot;chakras&quot;?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;" AnswerCount="0" CommentCount="11" FavoriteCount="1" ClosedDate="2015-04-29T03:54:15.327" ContentLicense="CC BY-SA 3.0" />
  <row Id="31831" PostTypeId="1" CreationDate="2015-04-28T17:24:11.640" Score="7" ViewCount="2711" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Petroleum#Formation&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; by the formation of oil there are a lot of organic materials present including DNA. Is it possible that this DNA is conserved somehow for millions of years?&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2015-04-29T03:11:32.293" LastActivityDate="2018-04-16T11:33:45.343" Title="Does crude oil or kerogen contain ancient DNA?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="31832" PostTypeId="1" CreationDate="2015-04-28T17:57:16.957" Score="5" ViewCount="761" Body="&lt;p&gt;We know that the adaptive immune system recognizes foreign particles when their proteins are expessed of the the surface of T-cells, complexed with MHCs. But MHCs present only short peptides of length 8-11 amino acids long. How is it that every antigen has one characteristic 8-11 residues long stretch in some protein of its which none of the host's protein has. Conversely, how is it that this 8-11 amino acid long peptide, which the body is recognizing as foreign is not found in any protein of any cell of our body?&lt;/p&gt;&#xA;" OwnerUserId="11716" LastActivityDate="2015-04-28T18:47:11.963" Title="Specificity of the immune system" Tags="&lt;immunology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31833" PostTypeId="2" ParentId="31832" CreationDate="2015-04-28T18:07:34.063" Score="3" Body="&lt;p&gt;For starters, your conception of antigen presentation seems a bit off, but that's not the crux of your question. There's around 10^15 different sequence permutations for a peptide 11-mer. Despite that, it's actually likely that highly conserved regions of some proteins will be present in both the pathogen and the host. T cells will not recognize them, however, as they are negatively selected in the thymus. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-04-28T18:16:41.143" LastActivityDate="2015-04-28T18:16:41.143" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="31834" PostTypeId="2" ParentId="31832" CreationDate="2015-04-28T18:08:39.413" Score="2" Body="&lt;p&gt;The immune system is the most beautiful, complex biological process that operates on a scale that it can be termed as engineering.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;MHC polymorphism:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MHC's have two particular properties that give it flexibility in the face of the antigen: Its polygenicitcy (it contains several different MHC class I and MHC class II genes with different ranges of peptide-binding specificities) and secondly, MHCs are polymorphic (having multiple variants of each gene within the population).&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Note: MHCs are also called HLA (Human Leukocyte Antigen)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mofCL.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So as you can see, there is a lot of possible variation possible. I'd recommend reading through this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK27156/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK27156/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the source above:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The outstanding feature of the MHC molecules is their extensive&#xA;  polymorphism. This polymorphism is of critical importance in antigen&#xA;  recognition by T cells. A T cell recognizes antigen as a peptide bound&#xA;  by a particular allelic variant of an MHC molecule, and will not&#xA;  recognize the same peptide bound to other MHC molecules. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This behavior of T cells is called MHC restriction. Most MHC alleles&#xA;  differ from one another by multiple amino acid substitutions, and&#xA;  these differences are focused on the peptide-binding site and adjacent&#xA;  regions that make direct contact with the T-cell receptor.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;At least three properties of MHC molecules are affected by MHC&#xA;  polymorphism: the range of peptides bound; the conformation of the&#xA;  bound peptide; and the direct interaction of the MHC molecule with the&#xA;  T-cell receptor. Thus the highly polymorphic nature of the MHC has&#xA;  functional consequences, and the evolutionary selection for this&#xA;  polymorphism suggests that it is critical to the role of the MHC&#xA;  molecules in the immune response.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-04-28T18:47:11.963" LastActivityDate="2015-04-28T18:47:11.963" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31835" PostTypeId="2" ParentId="31828" CreationDate="2015-04-28T21:50:36.937" Score="1" Body="&lt;p&gt;As far as I can tell, enterochelin esterase (Fes) utilizes an &lt;a href=&quot;http://www.ebi.ac.uk/interpro/entry/IPR029058&quot; rel=&quot;nofollow noreferrer&quot;&gt;Alpha/Beta hydrolase&lt;/a&gt; fold to catalyze it's reactions, which means there's a triad of catalytic amino acid side chains. Where Fes differs from other proteins in the pathway is an amino terminal lid domain which confers specificity to the substrates of Fes (&lt;a href=&quot;https://walsh.med.harvard.edu/pubs/PDFs_2/IroE_structure.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(1)&lt;/a&gt; dictates this forms a deep pocket in the protein). I'm having trouble finding the exact catalytic amino acids, but homology modeling between IroE and Fes from the same source shows this may be a triad of Glu, His and Ser. If we kind of visualize what a catalytic triad's mechanism looks like, and the following image is a generic lipase/esterase catalytic site,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YR32C.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A sort of &lt;strong&gt;transition state&lt;/strong&gt; is formed between the target molecule and the serine, where the water reacts with help from the asp/glu and histidine to catalyze the hydrolysis. You'd just call it protein-ligand interactions.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-04-28T21:56:46.227" LastActivityDate="2015-04-28T21:56:46.227" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31836" PostTypeId="1" CreationDate="2015-04-28T23:51:36.063" Score="4" ViewCount="1188" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Please tell me what causes the brain to send signals, how does the brain send signals?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;can you tell me what happens between the point when you make an intention to pick up a glass of water, and before the brains sends signals to the body which excites the muscles. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So what happens at the moment when you make the intention to pick up a glass of water but before the brains sends signals after you reach to pick up a glass of water.&lt;/p&gt;&#xA;" OwnerUserId="15540" LastEditorUserId="15540" LastEditDate="2015-04-29T21:13:12.650" LastActivityDate="2015-04-30T01:49:13.900" Title="Before I move my arm the brain sends signals - what causes the brain to send signals?" Tags="&lt;brain&gt;&lt;muscles&gt;&lt;central-nervous-system&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="0" ClosedDate="2015-04-30T04:14:40.947" ContentLicense="CC BY-SA 3.0" />
  <row Id="31837" PostTypeId="1" AcceptedAnswerId="31900" CreationDate="2015-04-29T01:20:21.360" Score="3" ViewCount="174" Body="&lt;p&gt;Why do genes with closely related products are so often positioned on different chromosomes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To illustrate what I mean, here is an &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK27156/&quot; rel=&quot;nofollow&quot;&gt;example&lt;/a&gt; from immunology:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the invariant region of MHC is on chromosome 5&lt;/li&gt;&#xA;&lt;li&gt;the variant region of MHC is on chromosome 6&lt;/li&gt;&#xA;&lt;li&gt;β2-microglobulin is on chromosome 15&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;These three gene products associate into a single protein-complex to present antigens. Why are these genes situated on different chromosomes? Wouldn't it make more sense to keep them associated into a localized region onto a single chromosome so that their transcription can be jointly regulated? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is just an example; I get the impression that many multiprotein complexes are formed with products from different chromosomes.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="14552" LastEditDate="2015-04-30T16:36:06.053" LastActivityDate="2015-04-30T16:36:06.053" Title="Why do genes with closely related functions often reside on different chromosomes?" Tags="&lt;molecular-genetics&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31838" PostTypeId="1" CreationDate="2015-04-29T01:42:27.127" Score="5" ViewCount="739" Body="&lt;p&gt;Since humans and apes share up to 99% of their DNA, can they interbreed? For example, a horse and a donkey seem to be just as distantly related and produce offspring. Mules, however, are sterile. Would ape-human interbreds be sterile? &lt;/p&gt;&#xA;" OwnerUserId="15554" LastEditorUserId="9943" LastEditDate="2015-04-29T05:02:00.817" LastActivityDate="2018-08-27T16:51:36.367" Title="Do human-ape hybrids exist?" Tags="&lt;human-biology&gt;&lt;hybridization&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31839" PostTypeId="1" CreationDate="2015-04-29T03:01:43.917" Score="2" ViewCount="1682" Body="&lt;p&gt;I've run into a question that I disagree with others on but I would like to receive the input of others. The question is: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a population is at Hardy-Weinberg equilibrium, which of the following can be predicted for the recessive alleles in the population? 1) They will eventually disappear, 2) They will be selected against, 3) They will be maintained at the same frequency, 4) They will be expressed in the heterozygous condition, and 5) They will become dominant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some people said that the answer to this question was that the recessive alleles would be selected against, but I interpreted the question as having the answer that the allele frequency of the recessive alleles would not change and instead would be maintained at the same frequency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My rationale for this was that Hardy-Weinberg equilibrium means there is random mating and basically no radical shifts in allele frequencies from outside sources, such as gene flow, natural selection, etc. I would think that the allele frequency would not change, but I may be incorrect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is my methodology correct? &lt;/p&gt;&#xA;" OwnerUserId="15556" LastActivityDate="2015-04-29T04:02:54.093" Title="Recessive alleles at Hardy-Weinberg equilibrium" Tags="&lt;population-biology&gt;&lt;allele&gt;&lt;gene&gt;&lt;hardy-weinberg&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31840" PostTypeId="2" ParentId="31839" CreationDate="2015-04-29T04:02:54.093" Score="2" Body="&lt;p&gt;Let's go through the possible answers. Which of the following could be predicted? Not (1), because we don't know whether selection favors or disfavors the recessive alleles. Not (2) for the same reason. Not (4) by definition. Not (5) because recessive alleles don't magically become dominant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This leaves us with (3), which also seems correct: not only do we know that frequencies don't change under the Hardy-Weinberg assumptions, but also an equilibrium is by definition a state at which frequencies remain the same. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An aside: this question fairly clearly recalls G. Udny Yule's confusion about the fate of recessive alleles, which lead Punnett to enlist G. H. Hardy's help in deriving Hardy-Weinberg equilibrium. Yule expected recessive alleles to decline in frequency by virtue of their recessiveness; Hardy showed otherwise. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-04-29T04:02:54.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31841" PostTypeId="2" ParentId="31836" CreationDate="2015-04-29T04:37:01.217" Score="2" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Action_potential&quot; rel=&quot;nofollow&quot;&gt;Action potential&lt;/a&gt; - I haven't read through the entire Wikipedia article so I can't vouch for its accuracy (not that my neurophysiology is good enough to critique it), but it's probably a good start.&lt;/li&gt;&#xA;&lt;li&gt;Broadly speaking: the brain contains different regions that are each responsible for fairly specific tasks. In the case of picking up a glass of water we can, at a high level, describe the mechanism behind thirst. Your blood contains electrolytes in water; you can consider the electrolytes as being like cordial (reduce the water and you have a higher &lt;a href=&quot;https://en.wikipedia.org/wiki/Plasma_osmolality&quot; rel=&quot;nofollow&quot;&gt;concentration&lt;/a&gt; of cordial / electrolytes). A sensing mechanism (beyond the scope of this answer) will trigger action potentials between the relevant areas of the brain (motor, memory, etc.) to result in the final movement.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="15557" LastActivityDate="2015-04-29T04:37:01.217" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31843" PostTypeId="1" AcceptedAnswerId="31853" CreationDate="2015-04-29T05:37:56.963" Score="0" ViewCount="13932" Body="&lt;p&gt;GPCR = G-protein coupled receptor&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gi = G inhibitory alpha subunit&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gs = G stimulatory alpha subunit&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there structural differences between Gi and Gs subunits (secondary structure)? Or is it just categorization by effect on cAMP level? (Gi inhibits cAMP production, while Gs stimulates cAMP production)&lt;/p&gt;&#xA;" OwnerUserId="15558" LastEditorUserId="15558" LastEditDate="2015-04-29T06:05:33.027" LastActivityDate="2015-04-29T12:12:17.317" Title="GPCRs: Gi and Gs" Tags="&lt;cell-biology&gt;&lt;receptor&gt;&lt;pathway&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="31844" PostTypeId="2" ParentId="31659" CreationDate="2015-04-29T05:45:02.093" Score="2" Body="&lt;p&gt;Swiss model is an online tool for modelling protein tertiary and Quaternary structure using evolutionary information. J-pred and Swiss model both are pretty straight forward tools which requires only the sequence. Swiss model requires searching for a template and based on which the protein will be modeled further.J=pred is exclusively used for secondary structure prediction.&lt;/p&gt;&#xA;" OwnerUserId="8026" LastActivityDate="2015-04-29T05:45:02.093" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31845" PostTypeId="1" CreationDate="2015-04-29T07:05:06.367" Score="6" ViewCount="372" Body="&lt;p&gt;I had an idea come to me during Biology class and I immediately asked my teacher, but she couldn't really answer the question, so I'll ask it here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the limiting factors in the production of synthetic red blood cells with no antigens? I mean, we do have the human genome mapped, but am I naive to think that we have genetic technology capable of doing this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If red blood cells are too complex to manufacture, is it feasible to manufacture much smaller particles of just hemoglobin inside small spheres of cell membrane and use that as a temporary replacement for red blood cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I was at a medical research talk a while ago and one professor was explaining that there are many other proteins bound onto a red blood cell that aren't of the ABO or RH system. Normally this isn't a problem for recipients who only occasionally received transfusions but for people who need a long-term supply of blood, their bodies do get sensitized to the foreign proteins and will eventually start attacking the foreign red blood cells).&lt;/p&gt;&#xA;" OwnerUserId="15559" LastEditorUserId="9943" LastEditDate="2015-04-29T13:47:11.150" LastActivityDate="2018-10-16T13:07:03.390" Title="Can we produce synthetic red blood cells lacking antigens?" Tags="&lt;human-genetics&gt;&lt;red-blood-cell&gt;&lt;antigen&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31846" PostTypeId="1" AcceptedAnswerId="31852" CreationDate="2015-04-29T07:28:16.970" Score="0" ViewCount="206" Body="&lt;p&gt;I am reading this &lt;a href=&quot;https://homepages.warwick.ac.uk/~masfz/Pop_Dyn/PAPERS/KeelingFMD2001.pdf&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; related to FMD (foot and mouth disease) epidemics which occurred in UK. It mentioned about terms like IP (infected premise culling), CP (contiguous premise) and DC (dangerous contact cull). IP is the mandatory slaughter of all livestock on an infected premise. But what is CP and DC?&lt;/p&gt;&#xA;" OwnerUserId="5669" LastActivityDate="2015-04-29T11:50:24.200" Title="What is contiguous premise culling and dangerous contact culling?" Tags="&lt;pathology&gt;&lt;epidemiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31847" PostTypeId="1" AcceptedAnswerId="31861" CreationDate="2015-04-29T08:42:58.297" Score="7" ViewCount="271" Body="&lt;p&gt;As saying &quot;fundamental conflict&quot;, I mean something like two (or more) widely accepted results from &lt;strong&gt;different&lt;/strong&gt; areas (or scales) can not exist logically together. In physics, there have been three conflicts&lt;sup&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/sup&gt;. I wonder if in biology, do we have such conflicts? And how biologists resolved that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;sup&gt;1&lt;/sup&gt;  One of them is the conflict between Einstein's general relativism and quantum mechanics. String theory, if it is proved to be true, will reconcile this (&lt;a href=&quot;http://www.physics-astronomy.com/2014/02/the-three-major-conflicts-in-history-of.html#.VUCWJvAufIU&quot; rel=&quot;nofollow&quot;&gt;read more&lt;/a&gt;). But it can also be like the controversy of the property of light. Some said it was particle, some said it was wave. Modern physics says it is both.&lt;/sup&gt; &lt;/p&gt;&#xA;" OwnerUserId="6786" LastEditorUserId="6786" LastEditDate="2015-04-29T17:44:19.167" LastActivityDate="2015-05-01T18:54:09.340" Title="Do we have fundamental conflict in biology?" Tags="&lt;history&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31848" PostTypeId="2" ParentId="31792" CreationDate="2015-04-29T09:40:03.580" Score="1" Body="&lt;p&gt;For sequencing primers, I've always used this tool to great effect. You can set up how many bases you want to include before your target, and define how to divide large exons and set up no. of overlapping bases. I think this is what you ask for in your comment to the previous answer.&#xA;&lt;a href=&quot;http://ihg.gsf.de/ihg/ExonPrimer.html&quot; rel=&quot;nofollow&quot;&gt;http://ihg.gsf.de/ihg/ExonPrimer.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15321" LastActivityDate="2015-04-29T09:40:03.580" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31849" PostTypeId="2" ParentId="31838" CreationDate="2015-04-29T09:48:09.033" Score="15" Body="&lt;p&gt;Although this question sounds easy to answer in the first place, it is not. The main problem between humans and the apes we are most closely related to is that we have 46 chromosomes, while the apes all have 48. At some point in the evolution of the humans the ancestral chromosomes 2 and 4 fused together to form our chromosome 2, leaving us with only 46 chromosomes (see reference 1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This makes offsprings much more complicated, but not completely impossible. A good example for this are crosses between donkey and horses (donkeys have 64 chromosomes, horses 62) to get &lt;a href=&quot;http://en.wikipedia.org/wiki/Mule&quot;&gt;mules&lt;/a&gt; (male donkey crossed with a female horse) or &lt;a href=&quot;http://en.wikipedia.org/wiki/Hinny&quot;&gt;hinnys&lt;/a&gt; (male horse crossed with a female donkey) which subsequently have 63 chromosomes and are infertile. There are even crosses possible between horses and zebras which even differ wider. &lt;a href=&quot;http://en.wikipedia.org/wiki/Zebra&quot;&gt;Zebras&lt;/a&gt; have between 32 and 46 chromosomes (depending on the species) but still &lt;a href=&quot;http://en.wikipedia.org/wiki/Zebroid&quot;&gt;zebroids&lt;/a&gt; are possible. See reference 2 for some more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far there has been no successfull attempt to produce such hybrids, although there have been some attempts to make them. Some information can be found in reference 3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides this problems (which are also due to ethical restrictions), there is a study available that at least humans and chimpanzees interbred for at least 1.2 million years after diverging and still produced fertile off-springs. See references 4 (for a summary) and 5 (original paper) for details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on this evidence, I would say it is possible for humans and apes to produces off-springs, however, this is relatively unlikely and they will probably be infertile.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1924367&quot;&gt;Origin of human chromosome 2: an ancestral telomere-telomere fusion.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1601-5223.1991.tb03552.x/pdf&quot;&gt;The chromosomes of two horse x zebra hybrids; E. cahallus x E.&#xA;grevyi and E. hurchelli&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.newscientist.com/article/mg19926701.000-the-forgotten-scandal-of-the-soviet-apeman.html#.VUCm9vAQWzg&quot;&gt;Blasts from the past: The Soviet ape-man scandal&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.washingtonpost.com/wp-dyn/content/article/2006/05/17/AR2006051702158.html&quot;&gt;Human Ancestors May Have Interbred With Chimpanzees&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://genepath.med.harvard.edu/~reich/Patterson%20et%20al.2.pdf&quot;&gt;Genetic evidence for complex speciation of humans and chimpanzees&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="4108" LastEditDate="2015-04-29T15:54:56.203" LastActivityDate="2015-04-29T15:54:56.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31850" PostTypeId="1" CreationDate="2015-04-29T10:03:35.993" Score="2" ViewCount="127" Body="&lt;p&gt;During inflammation transudate and exudate is formed by vessels. I would like to make sure if it comes from arterioles, venules, or both, and the reason why.&lt;/p&gt;&#xA;" OwnerUserId="15561" LastEditorUserId="9943" LastEditDate="2015-04-29T14:02:01.900" LastActivityDate="2015-04-30T14:48:47.160" Title="Where does the exudate comes from during inflammation?" Tags="&lt;physiology&gt;&lt;blood-circulation&gt;&lt;pathophysiology&gt;&lt;injury&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31851" PostTypeId="2" ParentId="31850" CreationDate="2015-04-29T11:28:45.910" Score="1" Body="&lt;p&gt;exsudates almost exclusively come from the capillary compartment. If you think about the structure of the vessels, this appears logical. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The capillary compartment :&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;has vessels only several microns thick&lt;/li&gt;&#xA;&lt;li&gt;has only the endothelial and basal lamina layers&lt;/li&gt;&#xA;&lt;li&gt;spans an enormous surface, far greater than arterioles or venules&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So when the fenestrations and tight junctions of the capillaries are impaired, serum directly passes into the extracellular medium.&#xA;A good example of that would be advanced anaphylactic shock. In this situation, the general inflammatory state causes a loss of endothelial integrity. Adrenaline given in such a state will have an inotropic and chronotropic effect on the heart, will cause vasoconstriction, but will also act to restore endothelial integrity. This last element is the main reason why allergic people carry an epinephrine syringe at all times.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2015-04-30T14:48:47.160" LastActivityDate="2015-04-30T14:48:47.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31852" PostTypeId="2" ParentId="31846" CreationDate="2015-04-29T11:50:24.200" Score="1" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;Dangerous Contacts were defined as premises where animals have been in direct contact with infected animals or have, in any way, become exposed to infection&lt;/p&gt;&#xA;&lt;p&gt;Contigous Premises are defined as a category of dangerous contacts where animals may have been exposed to infection on neighbouring infected premises&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Tildesley, Michael J., et al. &amp;quot;The role of pre-emptive culling in the control of foot-and-mouth disease.&amp;quot; Proceedings of the Royal Society B: Biological Sciences (2009): rspb20090427.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-04-29T11:50:24.200" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31853" PostTypeId="2" ParentId="31843" CreationDate="2015-04-29T12:04:41.547" Score="1" Body="&lt;p&gt;Gi and Gs have a structurally different sub unit in their alpha chain.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The receptors for PGE1 and adenosine interact with inhibitory Gi,&#xA;  which contains the same β and γ subunits as stimulatory Gs but a&#xA;  different α subunit (Giα). In response to binding of an inhibitory&#xA;  ligand to its receptor, the associated Gi protein releases its bound&#xA;  GDP and binds GTP; the active Giα · GTP complex then dissociates from&#xA;  Gβγ and inhibits (rather than stimulates) adenylyl cyclase. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6zcuk.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Both β1- and β2-adrenergic receptors are coupled to G proteins (Gs), which activate adenylyl cyclase. In contrast, α1 and α2 receptors are coupled to two other G proteins, Gq and Gi, respectively. Gi inhibits adenylyl cyclase, and Gq stimulates phospholipase C to generate IP3 and DAG as second messengers.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also this, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A comparison of chimeric receptor 1, which interacts with Gs, and&#xA;  chimeric receptor 3, which interacts with Gi, shows that the G protein&#xA;  specificity is determined primarily by the source of the&#xA;  cytosol-facing loop between α helices 5 and 6. A comparison of&#xA;  chimeras 1 and 2 indicates that α helix 7 plays a role in determining&#xA;  the ligand-binding . B. Kobilka et al., 1988, Science 240:1310; W. A.&#xA;  Catterall, 1989, Science 243:236.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nc08h.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd recommend reading through this:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21718/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK21718/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-04-29T12:12:17.317" LastActivityDate="2015-04-29T12:12:17.317" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31855" PostTypeId="1" CreationDate="2015-04-29T12:29:18.477" Score="5" ViewCount="1553" Body="&lt;p&gt;Where is the pollenkitt material secreted? I think the &lt;em&gt;tapetum&lt;/em&gt; would be a good candidate, since it provides nutrition to the pollen grains.&lt;/p&gt;&#xA;" OwnerUserId="15562" LastEditorDisplayName="user24284" LastEditDate="2017-12-10T00:11:11.740" LastActivityDate="2018-01-09T07:14:35.757" Title="Where is pollenkitt secreted?" Tags="&lt;plant-physiology&gt;&lt;plant-anatomy&gt;&lt;flowering&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31856" PostTypeId="2" ParentId="31223" CreationDate="2015-04-29T12:47:49.377" Score="3" Body="&lt;p&gt;The answer lies in the question. Liver cirrhosis constrains hepatocytes into small fibrous spaces limiting regeneration, hence the nodular pattern.&#xA;However,fibrous degeneration occurs in specific patterns. It can be located mostly around portal regions (centrolobular pattern) or diffusely through the whole lobule.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So basically, it is all good that hepatocytes can regenerate, but the limiting factor is not that. It is the structural impairment of the liver lobules and drainage system that will impair regeneration. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, most cirrhotic patients could not tolerate halving of their residual hepatic function. Not to mention the extensive surgery required. It would kill them swiftly.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2015-04-29T12:47:49.377" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31857" PostTypeId="2" ParentId="31845" CreationDate="2015-04-29T14:02:28.860" Score="4" Body="&lt;p&gt;Actually there are such particles. It is estimated that about 20% of the hemoglobin (HGB hereafter) is in HGB vesicles (HbV hereafter) formed by RBCs. So sure, it is possible to use small particles instead of RBCs, but these vesicles have major and minor antigens on their surface. According to some of the articles they cause other complications too by blood transfusions and they are destroyed by the immune system within 3 to 7 days. So they don't solve the problem.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003839&quot; rel=&quot;nofollow&quot;&gt;In Vivo Volume and Hemoglobin Dynamics of Human Red Blood Cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/chapter/10.1007%2F978-3-642-21729-6_206&quot; rel=&quot;nofollow&quot;&gt;Artificial Oxygen Carriers (Hemoglobin-Vesicles) as a Transfusion Alternative and for Oxygen Therapeutics&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://journal.frontiersin.org/article/10.3389/fphys.2013.00365/full&quot; rel=&quot;nofollow&quot;&gt;Red blood cell vesiculation in hereditary hemolytic anemia&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15095784&quot; rel=&quot;nofollow&quot;&gt;The red cell revisited--matters of life and death.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418626/&quot; rel=&quot;nofollow&quot;&gt;Red blood cell microparticles and blood group antigens: an analysis by flow cytometry&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1850444/&quot; rel=&quot;nofollow&quot;&gt;Hemoglobin-Vesicles as Oxygen Carriers&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://jpet.aspetjournals.org/content/311/3/874.full&quot; rel=&quot;nofollow&quot;&gt;Physiological Capacity of the Reticuloendothelial System for the Degradation of Hemoglobin Vesicles (Artificial Oxygen Carriers) after Massive Intravenous Doses by Daily Repeated Infusions for 14 Days&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;HGB vesicles without major and minor antigens are not a perfect solution either (I think), because the immune system tends to attack such things. For example by viral infections the MHC1 levels are low (in cells with nucleus) to avoid T cell response and the NK cells does not like that, so they destroy such cells. I am almost sure something similar would happen with this kind of vesicles as well. At least afaik. the immune system checks not just the presence of these antigens, but their composition as well. So if a RBC is under stress, then it changes the antigen composition on its surface and the leukocytes destroy it if necessary. According to some of the experiments PEG can cover HbV antigens and increase immune compatibility, so having less surface antigens seems to be a better choice than having more.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.researchgate.net/publication/235117141_Development_of_a_Synthetic_Blood_Substitute_Utilizing_Hemoglobin_Vesicles&quot; rel=&quot;nofollow&quot;&gt;Development of a Synthetic Blood Substitute Utilizing Hemoglobin Vesicles&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/chapter/10.1007/978-3-642-40717-8_22&quot; rel=&quot;nofollow&quot;&gt;Biocompatibility of Hemoglobin Vesicles, a Cellular-Type Artificial Oxygen Carrier, on Blood Cells and Plasma Proteins In Vitro and In Vivo&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/bc800431d&quot; rel=&quot;nofollow&quot;&gt;Artificial Oxygen Carriers, Hemoglobin Vesicles and Albumin−Hemes, Based on Bioconjugate Chemistry&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.researchgate.net/publication/26740970_Hemoglobin_Vesicles_Polyethylene_Glycol_%28PEG%29ylated_Liposomes_Developed_as_a_Red_Blood_Cell_Substitute_Do_Not_Induce_the_Accelerated_Blood_Clearance_Phenomenon_in_Mice&quot; rel=&quot;nofollow&quot;&gt;Hemoglobin Vesicles, Polyethylene Glycol (PEG)ylated Liposomes Developed as a Red Blood Cell Substitute, Do Not Induce the Accelerated Blood Clearance Phenomenon in Mice&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;HGB vesicles have another problem. The HGB inactivates in them without reduction (metHb formation). Only Fe2+ HGB can carry oxygen. This can be solved with methylene blue according to this study.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/bc500153x&quot; rel=&quot;nofollow&quot;&gt;Red Blood Cells Donate Electrons to Methylene Blue Mediated Chemical Reduction of Methemoglobin Compartmentalized in Liposomes in Blood&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0141813013006600&quot; rel=&quot;nofollow&quot;&gt;Inhibition of methemoglobin formation in aqueous solutions under aerobic conditions by the addition of amino acids&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;We cannot use free HGB either, because it would decrease the NO levels and lead to endothelial dysfunction. I think to small particles would have the same effect because of increased surface.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.jbc.org/content/286/38/33567.short&quot; rel=&quot;nofollow&quot;&gt;Mechanisms of Slower Nitric Oxide Uptake by Red Blood Cells and Other Hemoglobin-containing Vesicles&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1537-2995.2011.03099.x/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;Microparticles in stored red blood cells as potential mediators of transfusion complications&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1525-1594.2011.01236.x/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;Removal of Cellular-Type Hemoglobin-Based Oxygen Carrier (Hemoglobin-Vesicles) From Blood Using Centrifugation and Ultrafiltration&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;According to other studies RHSA-heme (serum albumin bound to synthetic heme) is another option. It seems to be safe if you replace only 20% of blood volume (of rats). I think a complete transfusion is not safe, because it would reduce the NO levels as we already discussed. I have not found an experiment which does complete transfusion.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15672783&quot; rel=&quot;nofollow&quot;&gt;Safety evaluation of an artificial O2 carrier as a red blood cell substitute by blood biochemical tests and histopathology observations.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/jbm.a.30200/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow&quot;&gt;Exchange transfusion with synthetic oxygen-carrying plasma protein “albumin-heme” into an acute anemia rat model after seventy-percent hemodilution&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So there is ongoing research in the topic. There is progress, but none of the current solutions is perfect I think.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2015-04-29T14:59:10.757" LastActivityDate="2015-04-29T14:59:10.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31860" PostTypeId="1" CreationDate="2015-04-29T16:15:26.873" Score="3" ViewCount="60" Body="&lt;p&gt;I would like to generate T2/T1 phage resistant Stbl3 E Coli to use in virus production. Is there a plasmid somebody has used that confers resistance, or is this done another way?&lt;/p&gt;&#xA;" OwnerUserId="14587" LastEditorUserId="14587" LastEditDate="2015-04-29T20:50:23.897" LastActivityDate="2015-04-29T20:50:23.897" Title="Generate T2/T1 Phage Resistant E Coli" Tags="&lt;bacteriology&gt;&lt;transformation&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31861" PostTypeId="2" ParentId="31847" CreationDate="2015-04-29T16:27:40.167" Score="4" Body="&lt;p&gt;Peto's Paradox is a great one. This addresses the disconnect in cancer incidence with cell number in an organism. It goes something like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume current oncogenesis theory to be correct in that mutation acquisition is the rate limiting step in creating a cancer, such that you need ~5 specific mutations in a single cell for that cell to be fully transformed into a cancerous cell. This then being the case, it is so rare that any cell can acquire all necessary mutations that in humans we don't see cancer incidence appreciably increase until the 5th decade of life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, let's assume man has an average weight of 50kg and a blue whale has an average weight of 130000kg, with roughly equivalent lifespans. Assuming average cell weights are the same in both organisms, there are 2500X more cells in a blue whale than a human.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If linear mutation rate is the rate limiting step in cancer then increasing cell numbers is akin to increasing the number of times you flip a coin to try and get heads, which means there is a 2500X greater chance of getting all ~5 necessary mutations in a single blue whale cell than in a single human cell. If human cancer incidence starts to spike at 50 years, this means blue whale cancer incidence should spike after 7 days and blue whales should largely be eliminated by cancers within the first month of life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully makes you question a bit what is causing cancer.&#xA;Make sense?&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-04-29T16:27:40.167" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31862" PostTypeId="2" ParentId="31847" CreationDate="2015-04-29T16:44:41.690" Score="2" Body="&lt;p&gt;Could not fit in a comment...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question very much depend on what you mean by &lt;code&gt;fundamental conflict&lt;/code&gt; (to the point that I am surprised to see nobody complaining that the question is &lt;em&gt;primarily-opinion based&lt;/em&gt;). My first reaction is to think that there is no such fundamental conflict in biology just because biology is not really a &quot;fundamental science&quot;. I am not sure what I mean by fundamental but I hope the comic will help understanding my point!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QT6R5.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, it is not true that biology is just applied chemistry (as I would expect the other relations to be wrong as well). Personally, I know nothing about chemistry and in my field of research (theoretical population genetics), we use math, statistics (which is just applied math) and algorithmic (which I guess is just applied math as well). Math is just applied logic by the way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are things we don't understand, but I don't think there are many fundamental conflict or paradox. There are many things that we have hypothesis (sometimes vague hypothesis) for it and have no idea how to test them. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2015-04-29T16:44:41.690" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="31863" PostTypeId="1" CreationDate="2015-04-29T16:50:27.467" Score="0" ViewCount="375" Body="&lt;p&gt;I'm trying to explain why birds (specifically wildfowl) are gregarious during the winter and solitary during the summer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that in winter, birds are gregarious to reduce the risk of predation and to share foraging information. But gregariousness also brings with it competition, and because birds have offspring to feed in the summer, they trade-off increased predation/loss of information with reduced competition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this sound correct?&lt;/p&gt;&#xA;" OwnerUserId="1216" LastEditorUserId="1216" LastEditDate="2015-04-30T21:04:07.713" LastActivityDate="2015-06-01T04:08:55.690" Title="Advantages of gregarious vs solitary behaviour?" Tags="&lt;ecology&gt;&lt;ornithology&gt;&lt;ethology&gt;&lt;behaviour&gt;&lt;sociality&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31866" PostTypeId="1" CreationDate="2015-04-29T17:05:05.693" Score="1" ViewCount="285" Body="&lt;p&gt;The placental sac is the organ that provides nutrients to the embryo from the mother. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is that, since this obviously involves a lot of complexity, where does the sac originate from  (maternal / embryonic) ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, what is the genetic basis of the above? do the genes intercommunicate between the embryo and the mother ?&lt;/p&gt;&#xA;" OwnerUserId="15564" LastEditorUserId="8105" LastEditDate="2015-04-29T18:18:10.293" LastActivityDate="2015-04-29T18:18:10.293" Title="What is the developmental basis of the placental sac?" Tags="&lt;reproduction&gt;&lt;reproductive-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31867" PostTypeId="2" ParentId="31866" CreationDate="2015-04-29T17:17:16.830" Score="2" Body="&lt;p&gt;We used to spend a few days studying the placenta in our embryology course. The short answer is, both. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Organ level embryogenesis:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The placenta connects the fetus to the uterine wall, and is the organ by means of which the nutritive, respiratory, and excretory functions of the fetus are carried on. It is composed of both fetal and maternal portions. The placenta can be traced right from the moment when the blastocyst is implanted into the uterine wall, though it takes a good portion of 12 weeks to develop.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NXHhY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After this adhesion, the invasion process starts, during which the cytotrophoblast cells from the trophoblast layer migrate deeper into the decidual layer. The formed vacuoles of the embryo become confluent to the uterus with the formation of the lacunar space 13 days after fertilization. The lacunar space will develop into the intervillous space for blood circulation a few weeks later. The placental progenitor stem cell is the cytotrophoblast cell. These cells are responsible for the cellular growth of the placenta, and they have the ability to proliferate and differentiate throughout gestation. The proliferating cytotrophoblast cells provide, after differentiation, the villous syncytiotrophoblasts as the outer cellular layer of the placenta.  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I took the above paragraph from here (&lt;a href=&quot;http://www.medscape.com/viewarticle/780615_2).You&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.medscape.com/viewarticle/780615_2).You&lt;/a&gt; can read more about it here (&lt;a href=&quot;https://embryology.med.unsw.edu.au/embryology/index.php?title=Placenta_Development&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://embryology.med.unsw.edu.au/embryology/index.php?title=Placenta_Development&lt;/a&gt;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But for a serious scholarly study, you might be better off using textbooks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Genetic basis of placental development:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the second part of your question, that is the genetic basis of development for a placenta, allow me to lift a paragraph from a book. You must remember that the embryo as it were, is not a distinct entity genetically, in that it contains half of the genes of the mother, and half of the genes from the father. And this is where biology becomes more complex, beautiful and truly mind boggling. It involves intricate interactions between evolution, organogenesis and developmental biology.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These results [in mice] led to an extraordinary conclusion. Paternal genes, inherited from the father, are responsible for making the placenta – maternal genes, inherited from the mother, are responsible for making the greater part of the embryo, especially its head and brain… &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;David Haig had begun to reinterpret the mammalian placenta, not as a maternal organ designed to give sustenance to the foetus, but more as a foetal organ designed to parasitise the maternal blood supply and brook no opposition in the process. He noted that the placenta literally bores its way into the mother’s vessels, forcing them to dilate, and then proceeds to produce hormones which raise the mother’s blood pressure and blood sugar. The mother responds by raising her insulin levels to combat this invasion, yet, if for some reason the foetal hormone is missing, the mother does not need to raise her insulin levels and a normal pregnancy ensues. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In other words, although mother and foetus have a common purpose, they argue fiercely about the details of how much of the mother’s resources the foetus may have - exactly as they will later during weaning. But the foetus is built partly with maternal genes, so it would not be surprising  if these genes found themselves with, as it were, a conflict of interest. The father’s genes in the foetus have no such worries. They do not have the mother’s interest at heart, except insofar as she provides a home for them. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The father’s genes do not trust the mother’s genes to make a sufficiently invasive placenta; so they do the job themselves…. Modern evolutionary theorists, led by David Haig, now think of the placenta as more like a parasitic takeover of the mother’s body by paternal genes in the foetus. The placenta tries, against maternal resistance, to control her blood-sugar levels and blood pressure to the benefit of the foetus.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Taken from: Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters, Fourth Estate, 2000 &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a more scientific explanation, I'd suggest reading the following papers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wang, Xu, et al. &quot;Paternally expressed genes predominate in the placenta.&quot; Proceedings of the National Academy of Sciences 110.26 (2013): 10705-10710.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hemberger, Myriam, and James C. Cross. &quot;Genes governing placental development.&quot; Trends in Endocrinology &amp;amp; Metabolism 12.4 (2001): 162-168.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-04-29T17:44:30.570" LastActivityDate="2015-04-29T17:44:30.570" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31868" PostTypeId="2" ParentId="31735" CreationDate="2015-04-29T18:08:56.743" Score="3" Body="&lt;p&gt;Hypercalcemia does indeed cause muscle spasm, but as someone else wrote, hypercalcemia indicates the calcium levels in blood and not in the sarcoplasmic reticuli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One example where you can observe that increased calcium leads to increased contraction is when you take the cardiac glycoside, digoxin. Digoxin inhibits the Na+/K+ ATPase causing an increased concentration of intracellular sodium ions. Indirectly, the increased levels of sodium will disturb the sodium gradient (because of the accumulation of sodium ions inside the cell) and stop the Na+/Ca2+ exchanger. The consequence of the disturbance of the sodium/calcium exchanger will lead to the increased levels of calcium and the increased storage of calcium in the sarcoplasmic reticulum and thus cause positive inotropy of the myocytes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read more about it here:&#xA;Gheorghiade, Mihai, Kirkwood F. Adams, and Wilson S. Colucci. &quot;Digoxin in the management of cardiovascular disorders.&quot; Circulation 109.24 (2004): 2959-2964.&lt;/p&gt;&#xA;" OwnerUserId="15566" LastEditorUserId="8105" LastEditDate="2015-04-29T18:23:45.533" LastActivityDate="2015-04-29T18:23:45.533" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31870" PostTypeId="1" CreationDate="2015-04-29T11:29:45.863" Score="2" ViewCount="84" Body="&lt;p&gt;Are there any differences when a surgeon takes tissue from secondary place (for example from metastasis) rather then from primary place (from an organ where cancer is) for morphological research?&lt;/p&gt;&#xA;" OwnerUserId="15569" OwnerDisplayName="Aleko Gharibashvili" LastActivityDate="2015-04-29T22:39:22.280" Title="Difference between taking tissue of cancer from secondary place or primary place" Tags="&lt;cancer&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31871" PostTypeId="2" ParentId="31870" CreationDate="2015-04-29T18:00:09.927" Score="0" Body="&lt;p&gt;By definition, a cancer which has spread to another site via the circulatory or the lymphatic system (called metastasis) is malignant. If a surgeon takes it from a secondary site, it is malignant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the past, there were times that a cancer was so undifferentiated that to determine it's source was not possible. As science (particularly genetics) and technology continue to advance, tissue of origin is more easily determined.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Are there any differences when a surgeon takes tissue from secondary place rather then from primary place for morphological research?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Theoretically, it seems as it shouldn't, but it can happen at times, because, for example, a carcinoma may contain a mixed population of cancer cells, while the metastatic tumor may be of only one type. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For research purposes - which is different from diagnostics - it depends on the features most desired for research purposes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the past, there were times that a cancer was so undifferentiated that to determine it's source was not possible. As science (particularly genetics) and technology continue to advance, tissue of origin &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.cancer.gov/dictionary?cdrid=45771&quot; rel=&quot;nofollow&quot;&gt;NCI Dictionary of Cancer Terms&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://jco.ascopubs.org/content/27/15/2503.short&quot; rel=&quot;nofollow&quot;&gt;Multicenter Validation of a 1,550-Gene Expression Profile for Identification of Tumor Tissue of Origin&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" OwnerDisplayName="anongoodnurse" LastActivityDate="2015-04-29T18:00:09.927" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31872" PostTypeId="1" AcceptedAnswerId="31873" CreationDate="2015-04-29T21:13:15.410" Score="4" ViewCount="328" Body="&lt;p&gt;I have in my flat a plant which sometime make strange flowers. When the start it looks like plastic stars: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TldQW.jpg&quot; alt=&quot;Before Maturity&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then the flowers are opening after few days and looks like this: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/55E9U.jpg&quot; alt=&quot;Opened&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The smell is a bit strange (I cannot say bad but definitively not good as other flowers). In general this plant does not need many watering and even I am in Switzerland, I guess it is living normally somewhere else. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the size, mine is quite small (30 cm high but many wires) but my mother have a very long one along the wall (few meters).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many picture with higher resolution are in my &lt;a href=&quot;https://www.flickr.com/photos/44724926@N03/sets/72157652252868365&quot; rel=&quot;nofollow noreferrer&quot;&gt;flikr gallery&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anybody can tell me what is the name of this plant and where it lives normally?&lt;/p&gt;&#xA;" OwnerUserId="6561" LastActivityDate="2015-04-29T21:50:34.613" Title="Identification of a plant (in a pot)" Tags="&lt;botany&gt;&lt;species-identification&gt;&lt;flowers&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31873" PostTypeId="2" ParentId="31872" CreationDate="2015-04-29T21:34:51.720" Score="3" Body="&lt;p&gt;It is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Hoya_carnosa&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hoya Carnosa&lt;/a&gt; &lt;a href=&quot;http://www.plantsrescue.com/tag/hoya-carnosa-krinkle-kurl/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Krinkle Kurl flower&lt;/a&gt;. It is native to Australia and East Asia. Hoya Carnosa links to wikipedia and Krinkle Kurl links to plant rescue in case you want to read more on it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZG94u.jpg&quot; alt=&quot;http://livingsoganofla.blogspot.com/2011/01/hoya-carnosa-krinkle-curl.html&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LD4ad.jpg&quot; alt=&quot;http://www.plantsrescue.com/tag/hoya-carnosa-krinkle-kurl/&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-04-29T21:50:34.613" LastActivityDate="2015-04-29T21:50:34.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31874" PostTypeId="1" AcceptedAnswerId="31877" CreationDate="2015-04-29T21:41:46.407" Score="6" ViewCount="402" Body="&lt;p&gt;Just recently started learning about gene therapy, many websites explain that the corrected DNA can be added to the genome using a vector and all that. I just don't understand what happens to the other sequence of nitrogenous bases that codes for the incorrect protein.&#xA;Thanks in advance for any answers :)&lt;/p&gt;&#xA;" OwnerUserId="14940" LastActivityDate="2016-03-12T01:15:42.167" Title="During the process of correcting mutations via gene therapy, is the defective gene removed?" Tags="&lt;cell-biology&gt;&lt;dna&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31875" PostTypeId="1" AcceptedAnswerId="31876" CreationDate="2015-04-29T21:50:16.100" Score="2" ViewCount="445" Body="&lt;p&gt;Last week-end I was working in my parent's garden and when I dig a bit the ground, I found few larvas I never seen before. My father told me there are there every time when he's doing the garden springtime.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I took some pictures (I just put it on leaves for the picture to see better than on the ground). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One low-res: &#xA;&lt;img src=&quot;https://i.stack.imgur.com/npggK.jpg&quot; alt=&quot;Larva-Unknown&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And the gallery &lt;a href=&quot;https://flic.kr/s/aHska4Tgts&quot; rel=&quot;nofollow noreferrer&quot;&gt;hi-resolution pictures&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The location is in northern of Switzerland (Jura) at around 700 meters above the sea and the larvas were inside the ground in around 3-5 centimeters (1-2 inches) deep.&lt;/p&gt;&#xA;" OwnerUserId="6561" LastActivityDate="2015-04-29T22:14:44.543" Title="Identification of a larva" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31876" PostTypeId="2" ParentId="31875" CreationDate="2015-04-29T22:03:49.767" Score="3" Body="&lt;p&gt;What you are seeing is a cocoon for a &lt;a href=&quot;http://www.waldeneffect.org/blog/Moth_pupa_in_the_soil/&quot; rel=&quot;nofollow noreferrer&quot;&gt;moth pupa&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IZMTV.jpg&quot; alt=&quot;http://www.waldeneffect.org/blog/Moth_pupa_in_the_soil/&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=arAUDaQhW5E&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; is a link to a YouTube video of one hatching that is normal found in the soil.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-04-29T22:14:44.543" LastActivityDate="2015-04-29T22:14:44.543" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31877" PostTypeId="2" ParentId="31874" CreationDate="2015-04-29T22:29:26.427" Score="8" Body="&lt;p&gt;&lt;strong&gt;To be specific&lt;/strong&gt;: &lt;em&gt;I am talking about adult, somatic gene therapy here, and germline gene therapy experiments is still a landmine when considering ethical reasons.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The defective gene codes for a defective protein, that usually plays a part in pathways. Since the protein is also defective, that pathway is also rendered defective because of this protein, and usually when pathways go defective, bad things happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are three target approaches to gene therapy:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Gene silencing by Antisense Oligonucleotide Therapy&lt;/li&gt;&#xA;&lt;li&gt;Genome Surgery by ZFN, Crispr/Cas9 etc..&lt;/li&gt;&#xA;&lt;li&gt;Gene Replacement by viral vectors&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The only method that corrects the defective gene here is the genome surgery method. By using Zinc Finger Nucleases, or Crispr/Cas9s, TALENS or other methods like that, the defective protein is corrected at the genome level, which automatically corrects the mRNA and protein, and everything works as it should.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4v9uY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other methods like Antisense, just prevent the incorrect protein from forming. This is really useful if the defective protein is itself toxic to the body, and a replacement protein can be achieved by masking the defective region to produce a truncated but functional protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qT2xs.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gene replacement usually puts in a healthy copy of the gene in, that functions along with the defective copy, and this solves majority of the problems as the affected pathway is no longer rendered inactive, as the healthy protein takes over the defective pathway. The defective protein is still produced, but doesnt do anything (or rather, is rendered moot as the healthy protein takes over) and gets removed during regular maintenance of the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nhhP3.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now depending on the type of disease the individual has, gene replacement may also take place along with gene knockout (depending on if the defective gene is toxic), but obviously many considerations have to be thought about before the combinatorial therapy can be used (toxicity of treatment itself being the primary concern, followed closely by efficacy).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now obvious question with gene replacement, antisense or any other form of gene therapy is how we get the therapeutic agent to all cells, and yes that is a major challenge, and that's why gene therapy is expensive. And no, the therapy doesn't correct all the cells in your affected tissue, but it aims to correct majority of the cells, and that should restore function (atleast in myopathies like the muscular dystrophies)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can see here, in DMD, dystrophin gets muated due to a mutation We can either mask the mutation by Antisense therapy at the level of the RNA (which leads to a functional protein forming), put in an alternative form of dystrophin (mini or micro dystrophin) that takes over the function of dystrophin in majority (if we are so lucky) of the cells, and the overall phenotype of the individual improves. Recent advances in genome surgery are also being investigated for ameliorating disease symptoms. The reason I concentrated on DMD is that, gene therapy for DMD is my PhD. So apologies for the bias.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="1306" LastEditDate="2015-05-02T09:05:00.577" LastActivityDate="2015-05-02T09:05:00.577" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31878" PostTypeId="2" ParentId="31870" CreationDate="2015-04-29T22:39:22.280" Score="1" Body="&lt;p&gt;I would disagree a bit with the previous answer. There are absolutely differences between the metastasis and the primary tumor. One result of this is that people very rarely die of primary tumors, but rather from the metastases of those tumors. The primary tumors will be quite heterogeneous and contain largely cells that have not undergone steps necessary for migration like epithelial to mesenchymal transition. After cells have metastasized they will be separate from the original primary tumor, and contain unique genomes. Because this is the more 'progressed' group of cancer cells, these are often the cells that need to be targeted. So, determination of the proper treatment strategy should be done on the metastasized cells.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-04-29T22:39:22.280" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31879" PostTypeId="1" CreationDate="2015-04-29T23:30:55.903" Score="12" ViewCount="3939" Body="&lt;p&gt;According to what we've learnt :&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;we can approximate the number of generations since the first human pretty much like us (depending what / who we talk about).&lt;/li&gt;&#xA;&lt;li&gt;we have an idea of the series of life forms we come from.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So is it possible to give it a &lt;em&gt;very rough&lt;/em&gt; number ? Or it's not, because of some issues - but which ones ? (I only think about the many, short generations of the first forms, which moreover we don't really know about, as a limit to counting)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What if we stop counting at &quot;unicellular&quot; (or else) ?&lt;/p&gt;&#xA;" OwnerUserId="15574" LastActivityDate="2019-12-02T09:57:24.227" Title="Can we make a rough estimate of the number of generations since the origin of life?" Tags="&lt;evolution&gt;&lt;abiogenesis&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31880" PostTypeId="1" CreationDate="2015-04-30T01:36:41.917" Score="6" ViewCount="423" Body="&lt;p&gt;Imagine that someone tries to develop a knockout mouse for a gene, but this result in lethality for the homozygous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to express that mutant gene only in a specific tissue of interest to get a idea of which phenotype it produces? Does someone know an experiment which used this idea or something similar?&lt;/p&gt;&#xA;" OwnerUserId="14630" LastEditorUserId="14826" LastEditDate="2015-05-01T04:11:19.627" LastActivityDate="2015-05-01T05:23:30.027" Title="Is it possible to express a mutant gene only in a specific tissue?" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;mutations&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31881" PostTypeId="2" ParentId="31836" CreationDate="2015-04-30T01:49:13.900" Score="1" Body="&lt;p&gt;1) There is always a persistent sodium current which is slowly inactivating in comparison with the fast transient sodium current that occurs when a neuron is depolarized. The effects of this persistent sodium current brings the resting membrane potential near the threshold. Furthermore, neurons do indeed fire and reach depolarization state due to these fluctuations in membrane potential, but those action potentials will not always cause a depolarization of the post-synaptic neurons, since those neurons have inputs of convergence from inhibitory neurons that produce inhibitory post-synaptic potentials. There is no moment or situations where all of your neurons are quiet.&#xA;Further information about persistent sodium current can be read in French et al.,1990., &quot;A Voltage-dependent Persistent Sodium Current in Mammalian Hippocampal Neurons&quot;., J. Gen. Physiol., Vol 95;1139-1157 &lt;a href=&quot;http://jgp.rupress.org/content/95/6/1139.full.pdf&quot; rel=&quot;nofollow&quot;&gt;http://jgp.rupress.org/content/95/6/1139.full.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The brain center which is thought to play an important role, not only in decision making, but also in behavioral control of the decision making dependent on the reward and outcome, is the prefrontal cortex. Except for its associative learning capabilities prefrontal cortex is thought to have neuronal connections with many part of other brain structures and it must first gather information and integrate the information before deciding what to do. In your question the reward is the glass of water, the emotional response you would get to drink that cold water would aid to the decision making, and the motoric movement is initiated by the subsequent firing of neurons when you see the glass of water and when you recall/remember the feeling to drink it. Prefrontal cortex is therefore activated and can thereafter send action potentials to motor cortex and then to your peripheral nervous system and muscles, so you can pick up the glass of water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More about this here: &lt;a href=&quot;http://ac.els-cdn.com/S0959438800001926/1-s2.0-S0959438800001926-main.pdf?_tid=83268f2a-eed1-11e4-ae1f-00000aab0f6c&amp;amp;acdnat=1430354614_ddc06d6aeae4543af28ebe02e29486cc&quot; rel=&quot;nofollow&quot;&gt;http://ac.els-cdn.com/S0959438800001926/1-s2.0-S0959438800001926-main.pdf?_tid=83268f2a-eed1-11e4-ae1f-00000aab0f6c&amp;amp;acdnat=1430354614_ddc06d6aeae4543af28ebe02e29486cc&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15566" LastActivityDate="2015-04-30T01:49:13.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31882" PostTypeId="2" ParentId="31880" CreationDate="2015-04-30T01:53:13.217" Score="7" Body="&lt;p&gt;It is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Conditional_gene_knockout&quot; rel=&quot;nofollow noreferrer&quot;&gt;conditional mutation&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You &lt;a href=&quot;http://en.wikipedia.org/wiki/Cre-Lox_recombination&quot; rel=&quot;nofollow noreferrer&quot;&gt;flox&lt;/a&gt; (put &lt;em&gt;lox&lt;/em&gt; sites around) gene of interest and express Cre recombinase driven by tissue-of-interest-specific promoter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Illustration &lt;a href=&quot;https://wiki.brown.edu/confluence/display/BN0193S04/Cre-lox+system&quot; rel=&quot;nofollow noreferrer&quot;&gt;from here&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GMav4.png&quot; alt=&quot;This image shows how the Cre-lox system can be used to produce tissue-specific, GFP-marked knockout mice&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using chemically-activatable variant of Cre recombinase (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19266339&quot; rel=&quot;nofollow noreferrer&quot;&gt;cre-ER&lt;/a&gt;) you can create knock-out &lt;em&gt;in some&lt;/em&gt; cells of tissue of interest, not every.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Addition&lt;/strong&gt;: a bit weird but still useful method is to produce KO by means of CRISPR/Cas9 system. Tissue-specific expression of Cas9 protein together with gene-specific sgRNA will likely produce KO in mosaic fashion. One of positive sides is that such approach requires only one transgenic line, e.g. Tg(&lt;em&gt;promoter&lt;/em&gt;:Cas9;sgRNA)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Addition&lt;/strong&gt;: (via WYSIWYG's suggestion) you can express shRNA or other gene transcription-interfering product from promoter that only active in specific tissue/specific period of time. And beauty of genetic/bioengineering is that you can combine several methods for additional control, robustness, efficiency etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taken &lt;a href=&quot;http://journal.frontiersin.org/article/10.3389/fncel.2014.00062/full&quot; rel=&quot;nofollow noreferrer&quot;&gt;from here&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lqsxo.jpg&quot; alt=&quot;Inducible and sell-specific gene KO with shRNA&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Inducible and sell-specific gene KO with shRNA&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For further reading:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://cre.jax.org/introduction.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://cre.jax.org/introduction.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/protocol/10.1385/1-59259-065-9:477#page-1&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://link.springer.com/protocol/10.1385/1-59259-065-9:477#page-1&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I re-read OP question and, as commented to it, feel some confusion. So I would like to mention as well way to express mutated gene in specific tissue that, when expressed constitutively (all the time, everywhere), is lethal. Imagine some very strong oncogene. Or something like cell-toxic protein, e.g. chemically-activatable &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18536643&quot; rel=&quot;nofollow noreferrer&quot;&gt;nitroreductase&lt;/a&gt; or light-activatable &lt;a href=&quot;http://www.evrogen.com/products/KillerRed/KillerRed.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;Killer-red&lt;/a&gt;. Or it might be mutated version of your favourite synaptic protein that, when expressed in all neurons, causes severe lethal phenotype.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you do, is create transgenic animal with transgene-GFP fusion (nitroreductase, KillerRed, &lt;em&gt;etc&lt;/em&gt;) that has &lt;em&gt;floxed&lt;/em&gt; stop-codons in front, and cross that animal with transgenic with tissue-specific CreER (for example). What you get is animal that, when injected with tamoxifen, start to express mutated gene/toxic protein in tissue of interest. Then you are sure that only GFP-positive cells express that gene. That is how you &quot;express that mutant gene only in a specific tissue of interest to get a idea of which phenotype it produces&quot;.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-05-01T05:23:30.027" LastActivityDate="2015-05-01T05:23:30.027" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31883" PostTypeId="2" ParentId="14888" CreationDate="2015-04-30T03:23:04.443" Score="6" Body="&lt;p&gt;The Plant List has 642 families listed: &lt;a href=&quot;http://www.theplantlist.org/1.1/about/#changes&quot; rel=&quot;noreferrer&quot;&gt;http://www.theplantlist.org/1.1/about/#changes&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a quick comparison, Wikipedia lists &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;522 fish families:&#xA;en.wikipedia.org/wiki/List_of_fish_families&lt;/li&gt;&#xA;&lt;li&gt;136 mammal families:&#xA;en.wikipedia.org/wiki/Mammal_classification&lt;/li&gt;&#xA;&lt;li&gt;61 amphibian&#xA;families: en.wikipedia.org/wiki/List_of_amphibians&lt;/li&gt;&#xA;&lt;li&gt;57 reptile families: en.wikipedia.org/wiki/List_of_reptiles.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This only covers a subset of the total, however (see &lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_animal_classes&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt; for other animal classes). It is relatively difficult to find a good, and relatively complete answer to this, though. &lt;/p&gt;&#xA;" OwnerUserId="15577" LastActivityDate="2015-04-30T03:23:04.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31885" PostTypeId="1" CreationDate="2015-04-30T05:51:22.377" Score="3" ViewCount="255" Body="&lt;p&gt;I asked a &lt;a href=&quot;https://worldbuilding.stackexchange.com/questions/15314/are-diamond-berries-possible/15447#15447&quot;&gt;question on WorldBuilding.SE&lt;/a&gt;, &quot;Are diamond berries possible?&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This led to asking a &lt;a href=&quot;https://chemistry.stackexchange.com/a/29585/15880&quot;&gt;question on Chemistry.SE&lt;/a&gt; about the amount of energy required to burn a 1 ct. diamond (−6.527kJ).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The helpful commenter on WB.SE said that a plant would roughly require &lt;a href=&quot;https://worldbuilding.stackexchange.com/a/15324/844&quot;&gt;three times this amount of energy&lt;/a&gt; to essentially reverse the process through some biological means to create the diamond berry.  And that I would need to know the &quot;wattage input&quot; of various plants to compare with my hypothetical plant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a way to arrive at how much energy various plants take in?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also any other related information from a biological perspective would be helpful.&lt;/p&gt;&#xA;" OwnerUserId="15580" LastEditorUserId="-1" LastEditDate="2017-04-13T12:57:01.693" LastActivityDate="2015-06-04T11:33:44.353" Title="Determining how much energy a plant takes in?" Tags="&lt;physiology&gt;&lt;plant-physiology&gt;&lt;biophysics&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31886" PostTypeId="2" ParentId="31612" CreationDate="2015-04-30T08:57:46.697" Score="1" Body="&lt;p&gt;Pain receptors, more precisely pain signal propagation, can be inhibited in several ways. One is, for example, fine touch receptors (mechanoreceptor in illustration) inhibit propagation of pain signal in spinal cord (a lot of pain processing happens in spinal cord):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jOXNe.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is why humans often rub skin around or nearby injury, whether it is in joints or something more superficial. You should find more information about such control in any textbook on pain. See &lt;a href=&quot;http://courses.washington.edu/conj/sensory/pain.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;this page&lt;/a&gt; for short primer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Next, pain propagation is modulated -- still in spinal cord -- by descending pathway from brain and brain stem. See &lt;a href=&quot;http://neuroscience.uth.tmc.edu/s2/chapter08.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this page&lt;/a&gt; for more, or address Kandel's textbook.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I don't know whether or not it is identified how/where brain &quot;selects&quot; to what pain pay attention. My hypothesis is that it happens by competition, e.g. several signals compete by inhibiting each other &lt;em&gt;via&lt;/em&gt; some mechanism, probably, related to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2876446&quot; rel=&quot;nofollow noreferrer&quot;&gt;stress-induced analgesia&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-04-30T08:57:46.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31887" PostTypeId="2" ParentId="31885" CreationDate="2015-04-30T09:52:00.277" Score="3" Body="&lt;p&gt;&lt;em&gt;Just a speculation for whether diamond berries could exist or not. This is not an answer for &quot;what is the energy uptake rate of plants&quot; because the actual question tends to be &quot;whether a plant can gather enough energy to form diamonds&quot;. For energy uptake rate of plants please see &lt;a href=&quot;https://biology.stackexchange.com/a/31898/3340&quot;&gt;MCM's answer&lt;/a&gt;.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even though enthalpy of formation is same as heat required for destruction, burning a diamond is much easier than creating it (I presume it is easier to generate high temperature compared to high pressure). Natural diamond requires both high pressure and temperature to form. Synthetic diamonds are made by chemical vapour deposition; that also requires high temperature. Such high energies cannot be produced by any known organism (requires devices like arc furnace), and moreover at these temperatures the biological structure will disintegrate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However there is one possibility of diamond berries; the berries would not be solid diamond though. A plant could be growing in an area where there are a lot of nanodiamonds (meteorite rocks) which could be bioaccumulated in the berries. Living organisms do accumulate nanoparticles &lt;sup&gt;[&lt;a href=&quot;http://informahealthcare.com/doi/abs/10.3109/17435390.2013.778346&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;,&lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/es202864r&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;]&lt;/sup&gt;. There have been studies on biological application and effects of nanodiamonds too &lt;sup&gt;[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20633617&quot; rel=&quot;nofollow noreferrer&quot;&gt;3&lt;/a&gt;,&lt;a href=&quot;http://www.nano2014.org/thesis/view/4686&quot; rel=&quot;nofollow noreferrer&quot;&gt;4&lt;/a&gt;]&lt;/sup&gt;. However these would not look lustrous like bigger diamonds. Xylem vessels in trees have a mean diameter of 30-40µm; it may be possible that the plant can take up bigger sized diamond particles. Density of diamond is ~3g/cm&lt;sup&gt;3&lt;/sup&gt; — three times that of water and it would require thrice the force required for water to get diamond to the destination. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a spherical diamond of diameter 20µm:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;Cross sectional Area = 314.15 µm&lt;sup&gt;2&lt;/sup&gt;&#xA;Volume = 3351 µm&lt;sup&gt;3&lt;/sup&gt;&#xA;Mass = 3×3351×10&lt;sup&gt;-12&lt;/sup&gt; ≅ 10&lt;sup&gt;-8&lt;/sup&gt; g&#xA;Gravitational force on the diamond = 9.8×10&lt;sup&gt;-8&lt;/sup&gt; ≅ 10&lt;sup&gt;-7&lt;/sup&gt; N&#xA;Pressure required to counteract gravity = 10&lt;sup&gt;-7&lt;/sup&gt;/314.15×10&lt;sup&gt;-12&lt;/sup&gt; ≅ 3.18×10&lt;sup&gt;2&lt;/sup&gt; Pa&#xA;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;However, I am not sure if that much of pressure can be generated within a vessel and whether small particles can be lifted like this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is another possibility that bigger diamonds are encapsulated by living tissue (not the fruits of course).  &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-04-30T18:35:38.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31890" PostTypeId="2" ParentId="31612" CreationDate="2015-04-30T11:40:19.183" Score="1" Body="&lt;p&gt;Firstly you have to take into consideration that nociceptors do not adapt to stimulus. This means that a nociceptor will not only fire at the beginning of the stimulus, as seen in mechanoreceptors that have phasic responses, but will fire as long as the stimulus lasts. This type of response is called tonic response (see figure). Figure A shows the tonic response whereas figure B shows the phasic response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/knMhU.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So by this, we can conclude that, peripherally, every noxious stimuli, will induce action potentials as long as that noxious stimulus lasts. During the ascending propagation of the action potentials induced by the noxious stimuli, other neurons will have the &quot;opportunity&quot; to inhibit the response. Some ways that the pain transmission can be inhibited is by the release of endogenous opioids by descending neurons from brain parts in mid-brain and medulla.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other mechanism is the one explained above by aandreev. And as you mention in your title, this mechanism is called the gate control theory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ref: Purves et al (2012).,Neuroscience 5th ed.,Sinauer associates.&#xA;&lt;a href=&quot;http://www.ucl.ac.uk/anaesthesia/StudentsandTrainees/PainPathwaysIntroduction&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ucl.ac.uk/anaesthesia/StudentsandTrainees/PainPathwaysIntroduction&lt;/a&gt; [2015-04-30]&lt;/p&gt;&#xA;" OwnerUserId="15566" LastActivityDate="2015-04-30T11:40:19.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31891" PostTypeId="1" AcceptedAnswerId="31892" CreationDate="2015-04-30T12:17:41.787" Score="0" ViewCount="619" Body="&lt;p&gt;Could anyone explain the concept of Synteny relating to genetics? A picture would help. I tried read the wikipedia source along with another PDF &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://gep.wustl.edu/repository/course_materials_WU/annotation/About_Synteny_Analysis.pdf&quot; rel=&quot;nofollow&quot;&gt;http://gep.wustl.edu/repository/course_materials_WU/annotation/About_Synteny_Analysis.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And I feel it only somewhat helped. From what I gather synteny is about the order of genes, relative to their homologous genes? Or their location in general?&lt;/p&gt;&#xA;" OwnerUserId="14815" LastActivityDate="2015-04-30T13:15:32.187" Title="Synteny, genetics?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31892" PostTypeId="2" ParentId="31891" CreationDate="2015-04-30T13:15:32.187" Score="2" Body="&lt;p&gt;Syntenic blocks contain the same genes of order between chromosomes of different species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZwBC1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The figure above shows (left to right) syntenic block shared between human chromosome 17 and corresponding chromosomes in three other mammals (horse, pig and chimpanzee). And as expected, the more distinct the species (such as pig and horse) the more disarranged the order of genes are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ref: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758187/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758187/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15566" LastActivityDate="2015-04-30T13:15:32.187" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31898" PostTypeId="2" ParentId="31885" CreationDate="2015-04-30T14:22:12.410" Score="0" Body="&lt;p&gt;What I think would be a rough estimate (ignoring the physical/thermal requirements for diamond creation) &lt;strong&gt;TL;DR -- It's about 68W/m&lt;sup&gt;2&lt;/sup&gt;&lt;/strong&gt; given the caveats below. Also: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Disclaimer: This is the best way I could think of to figure it out. It is a rough estimate only, and your level of desired precision will introduce more complicated calculations than the ones I've done. Not all of the calculations I performed are explicitly necessary, but were simply the best way for me to wrap my head around it at the time and &lt;em&gt;may&lt;/em&gt; be incorrect!&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since plants are mostly glucose and water you could find the net glucose content of the plant (which will vary greatly -- but let's give a rough estimate of 90% as an average). So if you have a 10kg plant, ~1kg of the mass will be a mixture of cellulose, starch, and other stuff.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the sake of ease, let's ignore the other stuff and focus on the cellulose and starch which we'll say makes up the 1kg. Both Cellulose and Starch are Glucose configurations, so what we have is 1kg of Glucose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to Wikipedia the net amount of energy a plant devotes to biomass construction/CO&lt;sub&gt;2&lt;/sub&gt; fixation is &lt;a href=&quot;http://en.wikipedia.org/wiki/Photosynthetic_efficiency&quot; rel=&quot;nofollow&quot;&gt;3-6%&lt;/a&gt;, and the Gibbs Free Energy conversion of CO&lt;sub&gt;2&lt;/sub&gt; to Glucose is 114kcal. If I've done my math correctly that means a mole of CO&lt;sub&gt;2&lt;/sub&gt; to Glucose for a typical plant takes 2280kcal (or about what I burn in a day as a 6'4&quot; man). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, how many moles of Glucose is in our 1kg Glucose plant mass? The molecular mass of Glucose is 180.16g/mol. 1kg/180.16g/mol = 5.55 moles of Glucose. We don't need to know how many moles of CO&lt;sub&gt;2&lt;/sub&gt; we started with because we're not limited there; the atmosphere provides all the CO&lt;sub&gt;2&lt;/sub&gt; we could ask for. We just know that we have 5.55 moles of Glucose, and it took 12654kcal of energy to convert however many moles of CO&lt;sub&gt;2&lt;/sub&gt; into that many moles of Glucose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That 12654kcal is also equivalent to 52944.34kJ of energy. Now, the solar constant is ~1.36kW/m&lt;sup&gt;2&lt;/sup&gt; ... or (1360J/s)/m&lt;sup&gt;2&lt;/sup&gt;. So, how much area of your hypothetical plant is exposed to the Sun? A square-meter isn't an unreasonable amount for larger houseplants, so let's just work with that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;52944.34kJ / 1.36kW = 38929.66s = 648.82min = 10.8 hours' worth of Sun exposure to produce 1kg of plant mass. Some species of Bamboo can grow 91cm/day, but I couldn't find a source for density... but nearly 3-feet of bamboo could definitely weigh 1kg.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sooooooo... Plants &quot;take-in&quot; 1.36kW/m&lt;sup&gt;2&lt;/sup&gt; when exposed to sunlight. How large the plant's area is will determine how much energy it takes in overall. How much energy a plant devotes to producing its mass is about 3-6%... or about 68 Joules every second &lt;strong&gt;&lt;em&gt;(68 Watts using 5%)&lt;/em&gt;&lt;/strong&gt; for a large plant with 1m&lt;sup&gt;2&lt;/sup&gt; exposed area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your 1ct diamond would take just over a minute and a half if 100% of the plant's mass-growing resources went into it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, that seems really fast. The important assumptions are that the plant is in &lt;em&gt;direct&lt;/em&gt; sunlight, is not limited by other factors (Nitrogen is actually a major rate-of-growth limiter, as-is Phosphorous), halts all other growth-oriented metabolic activity to do so, and the metabolic processes for the conversion other carbon forms to Diamond was 100% efficient with the energy the plant demarcated for growth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In reality about the only potentially &quot;true&quot; assumption from that list is that it's completely possible to have a plant with 1m&lt;sup&gt;2&lt;/sup&gt; of surface area exposed to sunlight. Everything else will be a fraction of what the working assumptions are. &lt;/p&gt;&#xA;" OwnerUserId="1231" LastEditorUserId="3340" LastEditDate="2015-04-30T18:37:46.323" LastActivityDate="2015-04-30T18:37:46.323" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31899" PostTypeId="2" ParentId="14888" CreationDate="2015-04-30T14:51:11.450" Score="8" Body="&lt;p&gt;The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=statistics&amp;amp;uncultured=hide&amp;amp;unspecified=hide&amp;amp;m=0&quot;&gt;NCBI Taxonomy statistics page&lt;/a&gt; displays the following information:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are currently 73540 genera, 331418 species, and 23127 taxa of higher order. Since the number of taxa decreases with the genericity of the taxon, there are probably around 20000 families, give or take a few thousand. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-04-30T14:51:11.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31900" PostTypeId="2" ParentId="31837" CreationDate="2015-04-30T14:51:31.863" Score="1" Body="&lt;p&gt;The thing we must remember is that during evolution, there occurs many events that may result in genomic reshuffling. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering your example of MHC, when we look into the evolution of the complexes&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The classical human MHC contains 224 genes, .... Antibody and T cell mediated immune responses against invading pathogens are initiated through MHC class I and class II molecules. &lt;strong&gt;These main components are not only missing from invertebrates, but are also not present in primitive jawless fish, such as hagfish and lamprey. MHC class I and II molecules do, however, exist in all jawed vertebrates, including the cartilaginous fish.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now that tells us something in itself. If you observe the universal evolutionary tree, we can conclude that the hagfish and lamprey are most ancestral, especially compared to telostii. This is crucial when speaking in terms of evolution, as &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;this demonstrates that the separation of the MHC class I and class II loci is characteristic of teleost fish, which represent half of all vertebrates. Since the genes of the immune system were present in the common ancestor of tetrapods and teleosts, t&lt;strong&gt;he differences in their genomic organisation may be the result of lineage-specific chromosomal events such as duplications, inversions, deletions and translocations.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can read more about the MHCs here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Sambrook, Jennifer G., Felipe Figueroa, and Stephan Beck. &quot;A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish.&quot; BMC genomics 6.1 (2005): 152.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And thats usually the reason for the major changes you see. Often other changes occur, due to transposons, which cause pseudogenes to form and/or neofunctionaliation to occur. You can read about them here: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Feschotte, Cédric, and Ellen J. Pritham. &quot;DNA transposons and the evolution of eukaryotic genomes.&quot; Annual review of genetics 41 (2007): 331.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am fairly certain, that this applies practically to majority of the genes, that are not linked strongly genetically (&lt;a href=&quot;http://learn.genetics.utah.edu/content/pigeons/geneticlinkage/&quot; rel=&quot;nofollow&quot;&gt;http://learn.genetics.utah.edu/content/pigeons/geneticlinkage/&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-04-30T14:56:55.040" LastActivityDate="2015-04-30T14:56:55.040" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="31903" PostTypeId="1" AcceptedAnswerId="31906" CreationDate="2015-04-30T15:13:48.040" Score="1" ViewCount="21674" Body="&lt;p&gt;I often walk around my house at night with the lights turned off and one night I noticed that looking straight at an object with very little light available made the object disappear from sight but if I directed my visual else where I could clearly see the object in my peripheral&lt;/p&gt;&#xA;" OwnerUserId="15436" LastActivityDate="2015-04-30T15:49:11.297" Title="Why is my peripheral vision better for seeing in the dark?" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;vision&gt;" AnswerCount="2" CommentCount="1" ClosedDate="2015-04-30T16:23:18.483" ContentLicense="CC BY-SA 3.0" />
  <row Id="31905" PostTypeId="2" ParentId="31903" CreationDate="2015-04-30T15:48:30.333" Score="0" Body="&lt;p&gt;Because peripheral vision uses the peripheral retina,which has mostly rods as photoreceptor,while central vision uses the foveola,a central part of the retina which mostly has cones as photoreceptors.&#xA;Rods are more sensitive to light. That is why they are more efficient in the dark.&lt;/p&gt;&#xA;" OwnerUserId="8804" LastActivityDate="2015-04-30T15:48:30.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31906" PostTypeId="2" ParentId="31903" CreationDate="2015-04-30T15:49:11.297" Score="3" Body="&lt;p&gt;Its down to the structure of your eyes. The eyes are made of rods and cones, which have difefrences in detecting light. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, compare the images below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hJNgk.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hIiuT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you can probably see, the peripherl vision is predominatlty due to your rods, and your central vision made of cones.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Measured density curves for the rods and cones on the retina show an enormous density of cones in the fovea centralis. To them is attributed both color vision and the highest visual acuity. Visual examination of small detail involves focusing light from that detail onto the fovea centralis. On the other hand, the rods are absent from the fovea. At a few degrees away from it their density rises to a high value and spreads over a large area of the retina. These rods are responsible for night vision, our most sensitive motion detection, and our peripheral vision.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(Taken from: &lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/vision/rodcone.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://hyperphysics.phy-astr.gsu.edu/hbase/vision/rodcone.html&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read about the photorecptors of the eyes here:&#xA;&lt;a href=&quot;http://webvision.med.utah.edu/book/part-ii-anatomy-and-physiology-of-the-retina/photoreceptors/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://webvision.med.utah.edu/book/part-ii-anatomy-and-physiology-of-the-retina/photoreceptors/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastActivityDate="2015-04-30T15:49:11.297" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31907" PostTypeId="1" CreationDate="2015-04-30T17:11:19.370" Score="0" ViewCount="343" Body="&lt;p&gt;Wikipedia definition of symbiosis: &quot;Symbiosis (from Greek σύν &quot;together&quot; and βίωσις &quot;living&quot;)[2] is close and often long-term interaction between two or more different biological species.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wikipedia definition of mutualism: &quot;Mutualism is the way two organisms of different species exist in a relationship in which each individual benefits from the activity of the other.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In intro biology class, I (and many other people, I'm sure) was taught that mutualism is a type of symbiosis. However, now that I think more about it, it seems like some relationships that are mutualistic don't appear to fit the definition of symbiotic. Some relationships are clearly mutualistic and symbiotic (humans and gut flora, for example) but other relationships (like bees pollinating flowers) are mutualistic but don't appear to fit the definition of &quot;close and often long-term interaction&quot;. The same of course goes for parasitic, ammensalistic, etc. relationships as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thoughts, anyone?&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-04-30T17:34:32.717" Title="Can a relationship exist that is mutualistic/parasitic/etc. but not considered symbiotic?" Tags="&lt;definitions&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31908" PostTypeId="2" ParentId="31907" CreationDate="2015-04-30T17:28:56.297" Score="1" Body="&lt;p&gt;&lt;strong&gt;TL;DR:&lt;/strong&gt; mutualistic/parasitic relationships are members of symbiotic relationships class&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, first of all, there is a way to &lt;a href=&quot;https://www.google.com/search?q=is%20parasitism%20a%20form%20of%20symbiosis&amp;amp;oq=is%20parasitism%20%20symbiosis%20&amp;amp;aqs=chrome.1.69i57j0l5.11808j0j7&amp;amp;sourceid=chrome&amp;amp;es_sm=122&amp;amp;ie=UTF-8&quot; rel=&quot;nofollow&quot;&gt;look it up&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, the very same article in wiki has &lt;a href=&quot;http://en.wikipedia.org/wiki/Symbiosis#Parasitism&quot; rel=&quot;nofollow&quot;&gt;subsection on parasitism&lt;/a&gt;. Reading it would be useful:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This is also known as antagonistic or antipathetic symbiosis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also, &lt;a href=&quot;https://scholar.google.com/scholar?hl=en&amp;amp;q=symbiosis%20parasitism&amp;amp;btnG=&amp;amp;as_sdt=1%2C5&amp;amp;as_sdtp=&quot; rel=&quot;nofollow&quot;&gt;brief search&lt;/a&gt; through Google Scholar will show how these words are used in context. papers include such as:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Fungal symbiosis from mutualism to parasitism: who controls the outcome, host or invader?&lt;/li&gt;&#xA;&lt;li&gt;Mutualism and parasitism: the yin and yang of plant symbioses&lt;/li&gt;&#xA;&lt;li&gt;Mutualism or parasitism? The variable outcome of cleaning symbioses&lt;/li&gt;&#xA;&lt;li&gt;Enhanced growth as a manifestation of parasitism and shell deposition in parasitized mollusks. Aspects of the biology of symbiosis.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-04-30T17:34:32.717" LastActivityDate="2015-04-30T17:34:32.717" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31909" PostTypeId="1" CreationDate="2015-04-30T17:48:02.793" Score="8" ViewCount="1699" Body="&lt;p&gt;Homo sapiens have menopause - as some other mammals (e.g. some Cetacea) - a phenomenon where older females live for decades after the end of their own reproduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps homosexuality, that looks to hold at 10% levels in any population, may be just the same sort of adaptation?&lt;/p&gt;&#xA;" OwnerUserId="4821" LastActivityDate="2015-05-31T22:09:23.887" Title="Is homosexuality an adaptation in humans?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;ethology&gt;&lt;sex&gt;&lt;homosexuality&gt;" AnswerCount="3" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="31910" PostTypeId="1" CreationDate="2015-04-30T18:08:42.527" Score="1" ViewCount="56" Body="&lt;p&gt;I was wondering if it could be possible to engineer a virus, that when it comes into contact with human hair follicles, it could alter someones natural hair color. &#xA;Naturally blue hair anyone?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Doubtless there are loads of problems, but i was hoping they could be identified and potentially worked around.&lt;/p&gt;&#xA;" OwnerUserId="15589" LastEditorUserId="22057" LastEditDate="2016-03-23T01:47:09.867" LastActivityDate="2016-03-23T01:47:09.867" Title="Would it be possible to create a gel, holding viruses, that could alter the human genome when rubbed in?" Tags="&lt;gene-expression&gt;&lt;human-genetics&gt;&lt;hair&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31911" PostTypeId="2" ParentId="31909" CreationDate="2015-04-30T18:15:50.867" Score="1" Body="&lt;p&gt;Genetic view of adaptation:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Do note that this is looking at the view from the POV of a gene. Please read the comments below this answer, for a small discussion on the kin selection hypothesis. Do note that I do not study evolutionary psychology, or work on the level of the population.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is a bit of a misconception, as nature really doesn't work like that. Nature works by allowing people to pass on genes, and then selecting those genes which are the best. Now the issue with homosexuality when viewing from an evolutionary angle is that, homosexuality by definition doesn't allow for genes to be passed on. I would also quote Richard Dawkins in this issue&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;“That’s a very tempting error,” Dawkins replied, “not with respect to&#xA;  homosexuality, but with respect to the idea that nature does&#xA;  population control. That’s not the way nature works.”&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;“It’s so tempting to think that things will be best for the species,&#xA;  so nature will do whatever it takes to keep the species going. But&#xA;  that’s just not the way evolution works.”&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;“Natural selection,” he continued, “works at the level of the&#xA;  individual gene. So in order for natural selection to favor population&#xA;  control, [it] would have to favor a gene or genes within an individual&#xA;  that limited that individual’s reproduction.”&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;“Homosexuality would do that, but of course, it wouldn’t actually be&#xA;  naturally selected because the individual [who] doesn’t have children&#xA;  doesn’t pass on the genes for not having children.”&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;“In order for natural selection to favor population control,” Dawkins&#xA;  said, “it would have to be the case that an individual who has too&#xA;  many children ends up rearing fewer” successfully.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;He noted that this is exactly what ornithologist David Lack found when&#xA;  he studied avian clutch size — those birds that laid too many eggs&#xA;  were not able to care for all their hatchlings, whereas as those who&#xA;  laid too few were not selected for the obvious reason — they didn’t&#xA;  produce enough progeny.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Taken from: &lt;a href=&quot;http://www.rawstory.com/2015/03/richard-dawkins-explains-homosexuality-didnt-evolve-as-natural-population-control/&quot; rel=&quot;nofollow&quot;&gt;http://www.rawstory.com/2015/03/richard-dawkins-explains-homosexuality-didnt-evolve-as-natural-population-control/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="10456" LastEditDate="2015-05-31T07:45:50.443" LastActivityDate="2015-05-31T07:45:50.443" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="31916" PostTypeId="2" ParentId="31499" CreationDate="2015-05-01T03:09:41.313" Score="1" Body="&lt;p&gt;The splitting of water in chloroplasts is catalysed by the Oxygen Evolving Complex. It's all about redox reactions but in general hydrogen is the less electronegative of biological elements so it is easily ionised in many life reactions.&lt;/p&gt;&#xA;" OwnerUserId="15002" LastActivityDate="2015-05-01T03:09:41.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31917" PostTypeId="2" ParentId="31055" CreationDate="2015-05-01T03:20:47.507" Score="0" Body="&lt;p&gt;The same question sticked in my mind a month ago. Even &lt;strong&gt;@terdon&lt;/strong&gt; gave an explanatory answer, I want to make a small contribution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I asked similar question on seqanswers &lt;a href=&quot;http://seqanswers.com/forums/showthread.php?t=50289&quot; rel=&quot;nofollow&quot;&gt;*&lt;/a&gt;, one of users gave the link of the study &lt;a href=&quot;http://ashleylab.stanford.edu/tools/synthetic_reference.html&quot; rel=&quot;nofollow&quot;&gt;Ashley Lab&lt;/a&gt; in Stanford. They generated the &quot;&lt;strong&gt;Synthetic major allele human reference genomes&lt;/strong&gt;&quot;.  (1)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They combined the current reference sequence (in that time it was hg19), with the 1000Genomes data of variants with high allele frequencies. This combination creates three different reference genome of three human population (YRI, CEU and CHBJPT). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This synthetic reference sequences represents the variants that are highly seen in these population. It is possible to download these genomes from &lt;a href=&quot;http://datadryad.org/handle/10255/dryad.34659&quot; rel=&quot;nofollow&quot;&gt;their page&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Dewey FE, et. al. (2011) Phased whole-genome genetic risk in a family&#xA;  quartet using a major allele reference sequence. PLoS Genetics 7(9):&#xA;  e1002280. &lt;a href=&quot;http://dx.doi.org/10.1371/journal.pgen.1002280&quot; rel=&quot;nofollow&quot;&gt;http://dx.doi.org/10.1371/journal.pgen.1002280&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="13292" LastActivityDate="2015-05-01T03:20:47.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31918" PostTypeId="1" AcceptedAnswerId="31931" CreationDate="2015-05-01T03:37:10.647" Score="2" ViewCount="104" Body="&lt;p&gt;I am confused and I have the following questions:&lt;br&gt;&lt;br&gt;&#xA;1. What are (in the context of article below) protein cavity centres?&lt;br&gt;&#xA;2. How are they related to binding?&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(&lt;a href=&quot;http://www.biomedcentral.com/1471-2105/13/162&quot; rel=&quot;nofollow&quot;&gt;Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study&lt;/a&gt;, Santos et a. 2012) &lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="13094" LastEditDate="2015-05-07T00:19:28.717" LastActivityDate="2015-05-07T00:19:28.717" Title="How is protein cavity centre related to binding?" Tags="&lt;bioinformatics&gt;&lt;protein-binding&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31920" PostTypeId="1" AcceptedAnswerId="31922" CreationDate="2015-05-01T04:06:17.573" Score="5" ViewCount="231" Body="&lt;p&gt;What is the explanation of people having blood types from an evolutionary perspective?&lt;/p&gt;&#xA;" OwnerUserId="238" LastEditorUserId="3624" LastEditDate="2015-05-19T08:42:30.200" LastActivityDate="2015-05-19T08:42:30.200" Title="Any evolutionary explanation for human blood groups?" Tags="&lt;evolution&gt;&lt;hematology&gt;&lt;blood-group&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31922" PostTypeId="2" ParentId="31920" CreationDate="2015-05-01T07:28:48.543" Score="5" Body="&lt;p&gt;Researchers have puzzled over the selective explanation for the ABO polymorphism at least back to the 1950s. Multiple lines of more recent evidence, including the &lt;em&gt;very&lt;/em&gt; old age of the ABO polymorphism and (perhaps) multiple convergent evolution events, suggest that the ABO polymorphism is maintained by balancing selection (E.g. &lt;a href=&quot;http://mbe.oxfordjournals.org/content/14/4/399.short&quot; rel=&quot;noreferrer&quot;&gt;Saitou and Yamamoto 1997&lt;/a&gt;, &lt;a href=&quot;http://www.pnas.org/content/109/45/18493.abstract&quot; rel=&quot;noreferrer&quot;&gt;Segurel et al 2012&lt;/a&gt;). As best as I know, is no general consensus on what is driving balancing selection, though some researchers have argued that the selective agent is Plasmodium falciparum (e.g. &lt;a href=&quot;http://www.bloodjournal.org/content/110/7/2250?sso-checked=true&quot; rel=&quot;noreferrer&quot;&gt;Cserti and Dzik 2007&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="3340" LastEditDate="2015-05-01T08:28:25.330" LastActivityDate="2015-05-01T08:28:25.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31923" PostTypeId="1" AcceptedAnswerId="31926" CreationDate="2015-05-01T08:51:55.447" Score="5" ViewCount="1009" Body="&lt;p&gt;Yesterday I went to a hospital and heard a doctor say that one of the heart valves of a patient is not working. However, the patient was still alive and was healthy; the patient could walk and talk too. I could not understand it because I have read that all valves of heart are extremely important. I have tried searching on google but all I could find was heart attack problems.  &lt;/p&gt;&#xA;" OwnerUserId="15510" LastEditorUserId="3340" LastEditDate="2015-05-01T13:47:12.397" LastActivityDate="2018-07-11T01:03:40.163" Title="How can a heart of human work if one of its valve is not working?" Tags="&lt;human-biology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31924" PostTypeId="1" AcceptedAnswerId="31929" CreationDate="2015-05-01T10:25:05.337" Score="0" ViewCount="350" Body="&lt;p&gt;I want to find a RNA-Seq dataset for C. Elegans to use it in RNA-Skim software. For those who does not know RNA-Skim let me explain it a bit. It is a tool which is used to quantify RNA-Seq data using &lt;em&gt;sig-mers&lt;/em&gt;(special kind of k-mer). Firstly RNA-Skim clusters protein coding genes and find substrings that are special to cluster of that gene. After this preperation stage, it takes an RNA-seq data as an input and tries to quantify transcripts in it. So, I need to find a dataset in &lt;strong&gt;fasta file format&lt;/strong&gt; for this step. Since I'm pretty new in this area, is there anyone who could provide me information about how could I find it? &#xA;Complete information about RNA-skim can be found here : &lt;a href=&quot;https://github.com/zzj/RNASkim&quot; rel=&quot;nofollow&quot;&gt;RNA_SKIM&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&#xA;The type of a dataset I'm looking for is something like that: &lt;a href=&quot;http://codepad.org/n3ioT3nj&quot; rel=&quot;nofollow&quot;&gt;http://codepad.org/n3ioT3nj&lt;/a&gt; .This dataset is for mouse, I need to find such a dataset for C. elegans as I said before&lt;/p&gt;&#xA;" OwnerUserId="14759" LastEditorUserId="14759" LastEditDate="2015-05-01T11:02:35.390" LastActivityDate="2015-05-01T16:18:48.357" Title="Finding Rna-Seq dataset for C. Elegans (Caenorhabditis elegans)" Tags="&lt;rna&gt;&lt;rna-sequencing&gt;&lt;database&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31926" PostTypeId="2" ParentId="31923" CreationDate="2015-05-01T12:11:05.110" Score="2" Body="&lt;p&gt;It is not possible that one of the valve is completely closed and the person is still alive without being in ICU. I think what the doctor was trying to communicate to the patient was that one of the valves is in the process of complete closure. There are three main types of diseases associated with heart valves :-&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1- Blood flows backwards&#xA;2- Heart valve opening becomes narrow&#xA;3- upper condition may lead to complete closure&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For details see the following link:-&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nhlbi.nih.gov/health/health-topics/topics/hvd&quot; rel=&quot;nofollow&quot;&gt;http://www.nhlbi.nih.gov/health/health-topics/topics/hvd&lt;/a&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Pulmonary_atresia&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Pulmonary_atresia&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope you understand. :)&lt;/p&gt;&#xA;" OwnerUserId="15596" LastActivityDate="2015-05-01T12:11:05.110" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31927" PostTypeId="2" ParentId="26174" CreationDate="2015-05-01T12:17:33.677" Score="0" Body="&lt;p&gt;The optimization done by service providers like IDT should be fine because they weigh in multiple factors like avoiding mRNA secondary structures and specified restriction endonucleases. Even I was considering manual editing but then some research on the internet revealed that codon usage is not the only factor involved :)&lt;/p&gt;&#xA;" OwnerUserId="15597" LastActivityDate="2015-05-01T12:17:33.677" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31928" PostTypeId="1" AcceptedAnswerId="31930" CreationDate="2015-05-01T12:36:22.740" Score="0" ViewCount="241" Body="&lt;p&gt;I need to stop some protein from being active and searching for some universal way to do so. In mammalians. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With CRISPR it is possible to knock-out the entire gene. But it's a little complicate (need two gRNA for eg.). There are also another reasons, so I need to do this with only one gRNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I am thinking about inserting some mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My question&lt;/strong&gt;: Is there way to make some mutation that will prevent creation of functional protein, with high efficiently - with one gRNA. And without need to know the active site of protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, frame-shift or mutation around start codon? Is it possible? If so, how can I do this? To where I need to send the gRNA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks. &lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="20449" LastEditDate="2016-12-30T13:39:00.240" LastActivityDate="2016-12-30T13:39:00.240" Title="Mutations/deletions with CRISPR" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;crispr&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31929" PostTypeId="2" ParentId="31924" CreationDate="2015-05-01T13:15:47.273" Score="1" Body="&lt;p&gt;Go to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/sra&quot; rel=&quot;nofollow&quot;&gt;NCBI-SRA&lt;/a&gt; or &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/&quot; rel=&quot;nofollow&quot;&gt;GEO&lt;/a&gt; and search for RNAseq data. Set organism as &lt;em&gt;C. elegans&lt;/em&gt; and optionally any other keywords that you are interested in. This search term will give you all RNAseq data in SRA from &lt;em&gt;C. elegans&lt;/em&gt;: &lt;br&gt;&lt;code&gt;(&quot;caenorhabditis elegans&quot;[Organism]) AND &quot;strategy rna seq&quot;[Properties]&lt;/code&gt; &#xA;&lt;br&gt;&#xA;You will generally find files in &lt;strong&gt;fastq&lt;/strong&gt; format which you can easily convert to fasta. There are many tools that do that; you can also do it with your own script. Following awk command will do the job:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;awk 'NR%4==1{print &quot;&amp;gt;&quot;substr($0,2)} NR%4==2{print}' data.fastq &amp;gt; data.fasta&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from SRA you can also look at ENA (&lt;a href=&quot;http://www.ebi.ac.uk/ena&quot; rel=&quot;nofollow&quot;&gt;European Nucleotide Archive&lt;/a&gt;) and &lt;a href=&quot;http://trace.ddbj.nig.ac.jp/dra/index_e.html&quot; rel=&quot;nofollow&quot;&gt;DDBJ&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-05-01T16:18:48.357" LastActivityDate="2015-05-01T16:18:48.357" CommentCount="19" ContentLicense="CC BY-SA 3.0" />
  <row Id="31930" PostTypeId="2" ParentId="31928" CreationDate="2015-05-01T13:40:42.887" Score="3" Body="&lt;p&gt;You can do with a single gRNA. All that CRISPR-Cas, ZFN or TALEN systems do is to introduce a double strand break at a specific site. The DNA gets repaired via two mechanisms — non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is error prone and it may introduce indels that can compromise with gene function (frameshifts etc). While HR can be used to integrate a transgene or repair a mutation, NHEJ can be used to create mutations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I haven't really knocked out a gene using CRISPR-Cas but it is good to target the initial part of the ORF. There will be many other factors too that will determine what site should be chosen for targeting and an important factor would be the uniqueness of the target sequence. See &lt;a href=&quot;https://labnodes.vanderbilt.edu/resource/view/id/5265&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; site for guidelines on selecting a good target sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You would have to do rigorous screening nonetheless; the advantage of insertional knock out is that screening can much be easier (for e.g. by inserting GFP or puromycin-resistance gene).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can have a look at &lt;a href=&quot;http://www.sciencemag.org/content/343/6166/84&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; and the supplemental information; they have targeted 18080 genes with a CRISPR-Cas library.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-05-07T06:42:21.637" LastActivityDate="2015-05-07T06:42:21.637" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="31931" PostTypeId="2" ParentId="31918" CreationDate="2015-05-01T13:42:06.260" Score="2" Body="&lt;p&gt;As you can find under the table with cavity centers in &lt;a href=&quot;http://www.biomedcentral.com/content/pdf/1471-2105-13-162.pdf&quot; rel=&quot;nofollow&quot;&gt;pdf version of this article&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The table lists the protein’s PDB ID, the ligand considered and the specified cavity center. 22 ligands are similar to hexoses in shape and/or size. &lt;strong&gt;The cavity center is the centroid of the reported PDB atom numbers.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And a little later:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The binding-site center is computed as the&#xA;  hexose pyranose ring centroid for the positive examples,&#xA;  and as the ligand or empty pocket centroid for the negative&#xA;  ones. The hexose pyranose-ring atoms are located up to&#xA;  2.9&#xA;   ̊&#xA;  A away from the ring’s centroid. Since some atomic&#xA;  interactions can be important up to 7&#xA;   ̊&#xA;  A [22], we consider&#xA;  the binding-site as all protein atoms present within a 10&#xA;   ̊&#xA;  A radius sphere around the binding center. All other atoms&#xA;  are discarded.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So basically @aandreev is right. You can read about centroids &lt;a href=&quot;https://en.wikipedia.org/wiki/Centroid&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="13094" LastActivityDate="2015-05-01T13:42:06.260" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="31933" PostTypeId="1" AcceptedAnswerId="31936" CreationDate="2015-05-01T14:36:49.490" Score="4" ViewCount="3229" Body="&lt;p&gt;Why would this be &quot;L-cysteine&quot;? This is taken from the answer key for my biochem final. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wFpFM.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I understand if the -NH3(+) is on the left then the alpha-amino acid is in the L-configuration. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I wrong, or is my prof wrong? &lt;/p&gt;&#xA;" OwnerUserId="6759" LastEditorUserId="14709" LastEditDate="2015-05-01T18:58:02.847" LastActivityDate="2018-11-09T02:33:18.127" Title="D/L configuration for amino acids" Tags="&lt;biochemistry&gt;&lt;amino-acids&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31934" PostTypeId="1" AcceptedAnswerId="31957" CreationDate="2015-05-01T14:44:47.683" Score="4" ViewCount="214" Body="&lt;p&gt;MEN 2A is a dominant inherited disease caused by a mutation in the RET proto-oncogene.&#xA;The probability of being sick when you have the mutation of the RET proto-oncogene varies with age and is assumed to be 40% at 40 years of age.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With autosomal dominant inherited diseases, this formula can be used, where p indicated penetration and D is the sick allele:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;P(II inherits D given that II is healthy) = $\frac{1-p}{2-p}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The uncle of the son III1 in the tree has the disease so he assumes it comes from I1 or I2. The father of the son II2 is 40 years old with no symptoms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the odds of the father having the mutation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the odds of the son having the mutation knowing the % in the first question?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/VQp2B.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just used the formula above as so for the first question: $$\frac{1-0.4}{2-0.4} = 37.5\%$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm having problems with the second though and I assume to use Bayes formula.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've tried as so:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$P(\text{son mut given dad mut}) = \frac{P(\text{Dad mut given son mut}) \cdot P(\text{son mut)}}{P(\text{Dad mut})}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know the probability of the dad having the mutation is 37,5% and the probability of the dad having the mutation given that his son has the mutation is 100%. However I can't seem to know what to put in the probability of the son having the mutation? Any help appreciated, thanks! Sorry for a long question.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="3340" LastEditDate="2015-05-02T06:52:13.723" LastActivityDate="2015-06-05T14:37:31.413" Title="Bayes theorem for mutations" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;&lt;homework&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31935" PostTypeId="1" CreationDate="2015-05-01T15:05:43.897" Score="5" ViewCount="564" Body="&lt;p&gt;Is there a pattern/tactics of behavior in any birds species that consists of &lt;strong&gt;attacking a predator's eyes with its beak&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking for established tactics, not 1 or 2 anecdotal examples.&lt;/p&gt;&#xA;" OwnerUserId="185" LastEditorUserId="3624" LastEditDate="2015-05-19T08:41:31.013" LastActivityDate="2015-06-19T19:58:03.720" Title="Do any birds have established &quot;poke a predator's eyes out&quot; behavior?" Tags="&lt;ornithology&gt;&lt;ethology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31936" PostTypeId="2" ParentId="31933" CreationDate="2015-05-01T15:18:11.987" Score="7" Body="&lt;p&gt;We can look at the list of amino acids on &lt;a href=&quot;http://en.wikipedia.org/wiki/Proteinogenic_amino_acid&quot; rel=&quot;noreferrer&quot;&gt;wikipedia&lt;/a&gt; for a start. And we can look at this L-alanine:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/sVns1.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What makes your image confusing is that it's a &lt;a href=&quot;http://en.wikipedia.org/wiki/Fischer_projection&quot; rel=&quot;noreferrer&quot;&gt;Fischer Projection&lt;/a&gt;, and I hate those because you have to remember what way the stereochemistry goes. In Fischer Projections, vertical lines face away from you, while horizontal lines face towards you. So if we convert the L-alanine I provided to a Fischer Projection, first we have to rotate the alpha carbon to put the methyl side chain in line with the rest of the carbon backbone. Now we look at the alpha carbon with the NH2 and H looking at us to create the Fischer projection. Here, the amine is on the left, not the right. You drew the amine on the right, which would give you the opposite orientation. If your professor had the amine on the right, I think he was wrong.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/DKE8s.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, the D vs L nomenclature is confusing. I prefer the S vs R nomenclature because that's what I was taught for molecules in general. Most amino acids fall into the S configuration, but cysteine is an R, because the sulfur atom has higher priority. However, cysteine is still an L, and the amine would still appear on the left in the Fischer Projection. This is why biologists stick to D and L for amino acids.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="4747" LastEditDate="2015-05-01T15:24:58.543" LastActivityDate="2015-05-01T15:24:58.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31937" PostTypeId="1" CreationDate="2015-05-01T16:32:36.810" Score="3" ViewCount="3951" Body="&lt;p&gt;From the &lt;a href=&quot;http://en.wikipedia.org/wiki/Stretching&quot; rel=&quot;nofollow&quot;&gt;wikipedia page&lt;/a&gt; on stretching:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Stretching is a form of physical exercise in which a specific muscle or tendon (or muscle group) is deliberately flexed or stretched in order to improve the muscle's felt elasticity and achieve comfortable muscle tone.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;How is this improvement of elasticity achieved, at the physiological level?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Searching around on this topic brings a lot of articles about the types of stretches (e.g. again, &lt;a href=&quot;http://en.wikipedia.org/w/index.php?title=Stretching&amp;amp;oldid=657351643#Types_of_stretches&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;) and what are their benefits and disadvantages.&#xA;But how do they differ at the biological level?&lt;/p&gt;&#xA;" OwnerUserId="10198" LastEditorUserId="8105" LastEditDate="2015-05-02T16:28:40.513" LastActivityDate="2018-02-18T10:45:33.637" Title="What happens when we stretch?" Tags="&lt;human-biology&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31939" PostTypeId="2" ParentId="31935" CreationDate="2015-05-01T18:06:32.863" Score="3" Body="&lt;p&gt;From this paper about &lt;a href=&quot;http://www.jstor.org.proxy.cc.uic.edu/stable/30039149?seq=7#page_scan_tab_contents&quot; rel=&quot;nofollow&quot;&gt;black-headed gulls&lt;/a&gt; responding to a hedgehog:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The gull might peck the intruder, or strike it with its feet. Pecks were&#xA;  mostly directed at the hedgehog's head and might be delivered after a&#xA;  horizontal approach with the wings partly lifted.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Although not directed at the eyes specifically, they observed the birds directing attacks to the predator's head. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's another paper (&lt;a href=&quot;http://link.springer.com/chapter/10.1007/978-1-4684-2835-3_8#page-1&quot; rel=&quot;nofollow&quot;&gt;Ratner 1975&lt;/a&gt;) that also looks promising, but I'm on my home computer and can't access it right now&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-05-01T18:06:32.863" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31944" PostTypeId="1" AcceptedAnswerId="32965" CreationDate="2015-05-01T20:37:17.380" Score="0" ViewCount="93" Body="&lt;p&gt;I'm trying to find some reference that shows what percentage of the human genome is similar to some organism from the domain Archea that lives  near or on deep sea hydrothermal vents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone points me out in the right direction?&lt;/p&gt;&#xA;" OwnerUserId="15601" LastActivityDate="2015-05-02T23:58:00.173" Title="Similarity between the human genome and archea genome in deep sea hydrothermal vents?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;human-genome&gt;&lt;archaea&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="31945" PostTypeId="1" CreationDate="2015-05-01T21:48:00.623" Score="7" ViewCount="1908" Body="&lt;p&gt;Has anybody had any success in extracting cell free DNA from plasma without using expensive kits? I've already spent a lot of my own blood trying to use standard phenol/chloroform methods with very minimal yield. I know it's possible that since I am not pregnant and don't have cancer (I hope) my blood may not have a large quantity of cell free DNA to begin with but I'm afraid to start using precious experimental samples until I'm confident I have a technique that will work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For some background, cell free DNA is DNA that is circulating in the plasma (as opposed to the majority of DNA which is cellular). This has become an exciting new way to analyze fetal DNA from a mother's blood without doing a dangerous amniocentesis. There's also strong evidence that tumour DNA can also be found in some abundance this way (most studies seem to be with prostate cancer).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Qiagen has a kit for sale to extract this DNA but it is pretty expensive and I would still think that phenol/chloroform would give me a high (if less pure) yield. There is a paper in Cancer Biomarkers 2013 by Mazurek et al that claims that compares methods and shows a reasonable yield with this method but I haven't reproduced it. Has anybody here had success and if so what modifications did you use? Is it just time to move on to using samples that are more likely to have larger amounts of cell free DNA?&lt;/p&gt;&#xA;" OwnerUserId="15594" LastEditorUserId="9943" LastEditDate="2015-05-01T22:32:17.380" LastActivityDate="2016-05-19T16:08:36.313" Title="Extracting cell-free DNA" Tags="&lt;lab-techniques&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="31946" PostTypeId="2" ParentId="31945" CreationDate="2015-05-01T23:45:07.660" Score="2" Body="&lt;p&gt;&lt;strong&gt;To note:&lt;/strong&gt; &lt;em&gt;I have no personal experience with this protocol. I am forwarding this paper, passed on to me by a colleague&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many kits and methods available that don't rely on Qiagen. Or alternatively, if you ask them nicely, they do heavily discount their first kit you buy off them as a sort of trial (as they dont do samples).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, to answer your primary question, are you adding a detergent and heat denaturing your samples first before phenol-chloroform (Triton/Heat/&#xA;Phenol)?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Blood samples for CFDNA&#xA;  analysis are collected into EDTA tubes and held at/or below RT&#xA;  (18 °C–22 °C) for no more than 2 h before separation of plasma.&#xA;  Plasma should be separated from whole blood samples by double&#xA;  centrifugation (800 g and 1600 g for 10 min, separately), avoiding&#xA;  leukocyte lysis. We prefer to isolate CFDNA immediately after plasma&#xA;  separation to minimize the effect of prolonged storage. Otherwise,&#xA;  samples should be aliquoted into small portions and stored at −70 °C&#xA;  before extraction because fragmentation of CFDNA might be caused by&#xA;  repeated freeze–thaw cycles&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;For the THP method, 500 μl of plasma/serum was mixed with 5 μl Triton X-100&#xA;  (Sigma-Aldrich, UK) and heat denatured at 98 °C for 5 min. Samples were placed on ice&#xA;  for 5 min, then extracted with an equal volume of phenol–chloroform–isoamyl alcohol&#xA;  (25:24:1, v:v:v) (Sigma-Aldrich, UK) and centrifuged for 10 min at 14,000 g. The&#xA;  aqueous phase was precipitated overnight with 1/10 volume of 3 M NaOAc and 2.5&#xA;  volume of 100% ethanol at −20 °C. The DNA pellet was washed with ethanol, air-dried&#xA;  and resuspended in 50 μl of ddH2O.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In the THP protocol, 98 °C incubation was used to inactivate&#xA;  PCR inhibitors and denature proteins in plasma/serum samples.&#xA;  Different times and temperatures were tested before choosing this.&#xA;  Since we had noticed substantial DNA contamination in SDS, Triton&#xA;  X-100 was used in the protein solubilization step. Direct conventional&#xA;  PCR was performed successfully on heat-denatured samples&#xA;  and able to detect 25 ng/ml DNA, indicating that this simple&#xA;  procedure offered sufficient protein digestion and inhibitor elimination&#xA;  for PCR analysis. The THP protocol gave a significantly&#xA;  higher yield of pure DNA solution for qPCR analysis than the&#xA;  QIAamp kit. The THP protocol showed high efficiency even with&#xA;  small DNA fragments as low as 100 bp. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You might want to read this: &#xA;&lt;em&gt;Xue, Xiaoyan, et al. &quot;Optimizing the yield and utility of circulating cell-free DNA from plasma and serum.&quot; Clinica Chimica Acta 404.2 (2009): 100-104.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A quick search of google scholar also revealed a few other papers you might be interested in:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fleischhacker, Michael, et al. &quot;Methods for isolation of cell-free plasma DNA strongly affect DNA yield.&quot; Clinica Chimica Acta 412.23 (2011): 2085-2088.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After reading this (&lt;em&gt;Fong, Siew Lee, et al. &quot;Comparison of 7 methods for extracting cell-free DNA from serum samples of colorectal cancer patients.&quot; Clinical chemistry 55.3 (2009): 587-589.&lt;/em&gt;) which gives about 7 protocols (sadly without any references for some reason) I went hunting for  came up with this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;DNA was extracted from 1.0 ml plasma by phenol-chloroform method with slight modifications.&#xA;  One ml of plasma was treated with 1x SDS/Proteinase K solution (0.5 mg/ml) (1:1), incubated&#xA;  overnight at 56 °C followed by phenol-chloroform (4:1) treatment and centrifuged at 7 000 rpm.&#xA;  The upper layer was transferred into fresh 15 ml centrifuge tubes and the same step was repeated&#xA;  again; DNA was precipitated by adding glycogen (0.1 µg/µl), ammonium acetate (7.5 M) and&#xA;  absolute alcohol. DNA pellet was obtained by centrifuging at 7 000 rpm; was washed with 70%&#xA;  alcohol at 10 000 rpm, dried and finally dissolved in TE buffer at 56 °C and stored at -20 °C until&#xA;  further use.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can read about the above method here: &lt;em&gt;Singh, Deepika Misra1 Renu, and Monisha Banerjee. &quot;A simple and reliable method of obtaining fetal DNA from maternal circulation; its accuracy and sensitivity.&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, if its available to you, it might be worth it:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Gahan, Peter B., ed. Circulating Nucleic Acids in Early Diagnosis, Prognosis and Treatment Monitoring: An Introduction. Vol. 5. Springer, 2014.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-02T12:32:36.193" LastActivityDate="2015-05-02T12:32:36.193" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31947" PostTypeId="2" ParentId="29893" CreationDate="2015-05-01T23:45:56.813" Score="1" Body="&lt;p&gt;I think you are forgetting bats can see as well. Bat's that use echo location are referred to as &lt;a href=&quot;http://en.wikipedia.org/wiki/Microbat&quot; rel=&quot;nofollow&quot;&gt;Microchiroptera&lt;/a&gt;. Since we are speaking about echolocation, we can disregard the megachiropteral class since there most prominent sense is their eyes. This doesn't mean though that Micro's don't use their eyes in conjunction with echolocation. In &lt;a href=&quot;http://books.google.com/books/about/Handbuch_Der_Zoologie.html?id=ydgibUf07t0C&quot; rel=&quot;nofollow&quot;&gt;Handbuch Der Zoologie: Eine Naturgeschichte Der Stämme Des Tierreiches, Volume 2; Volume 5&lt;/a&gt;, the authors state&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In experimental situations, when visual information and echolocation were competing, the bats relied on vision and ignored the acoustical cues [&lt;a href=&quot;https://books.google.com/books?id=ydgibUf07t0C&amp;amp;pg=PA29&amp;amp;lpg=PA29&amp;amp;dq=Microchiroptera+vision+ability&amp;amp;source=bl&amp;amp;ots=TX6WKZNs62&amp;amp;sig=odl_zwKN9hpU_YPNXRbdewKkCww&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=uQlEVaKHMpPIsQSp8oHICw&amp;amp;ved=0CDMQ6AEwAw#v=onepage&amp;amp;q=Microchiroptera%20vision%20ability&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From this we can surmise that even with echolocating bats, they still fall back on vision in ambiguous situations. Moreover, researchers have determined that bats have ultraviolet cone receptors [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712075/&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your question, Micro bats have good object discrimination because they use both their eyes and echolocation to discern objects in their environment instead of solely relying on echolocation.&lt;/p&gt;&#xA;" OwnerUserId="12909" LastActivityDate="2015-05-01T23:45:56.813" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31949" PostTypeId="1" CreationDate="2015-05-02T00:53:45.847" Score="0" ViewCount="45" Body="&lt;p&gt;I want to know what is the minimum percentage of the shortest isoform/transcript to the longest one that derived from the same parent gene? Does it have organism specificity? What is the function of the shortest isoform?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because I want to filter the gtf file from cuffmerge. One consideration is that the very short isoform maybe artificial or random transcripts that should be filtered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this page &lt;a href=&quot;https://i.stack.imgur.com/zQPgm.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;, the CREB gene has been manually annotated and included a processed transcripts only 84bp, while the longest transcript of this gene is 8532bp. So the ratio is &amp;lt; 0.01; However, this transcript is not coding sequences. I also plot the minimum ratio distribution in human GENCODE v22 data. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zQPgm.png&quot; alt=&quot;minimum ratio distribution in human&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/zQPgm.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt; vega.sanger.ac.uk/Homo_sapiens/Transcript/Summary?g=OTTHUMG00000097081;r=7:28724300-28726731;t=OTTHUMT00000327948&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Best,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pengcheng&lt;/p&gt;&#xA;" OwnerUserId="15604" LastEditorUserId="15604" LastEditDate="2015-05-02T03:14:15.177" LastActivityDate="2015-05-02T03:14:15.177" Title="minimum ratio of the shortest isoform to the longest one derived from one same parent gene" Tags="&lt;gene&gt;&lt;isoforms&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="31950" PostTypeId="2" ParentId="31863" CreationDate="2015-05-02T03:14:45.870" Score="1" Body="&lt;p&gt;I will assume that you are talking about Mallards, although other wildfowl are likely to exhibit similar behaviors.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mallards aren't actually solitary during the summer, instead they form breeding pairs.  They form groups (sords) in the winter to migrate and for protection while moulting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://sta.uwi.edu/fst/lifesciences/documents/Anas_platyrhynchos.pdf&quot; rel=&quot;nofollow&quot;&gt;https://sta.uwi.edu/fst/lifesciences/documents/Anas_platyrhynchos.pdf&lt;/a&gt;&#xA;&lt;a href=&quot;http://thefarmatwalnutcreek.com/Ducks_Swans_Mallard-Duck.html&quot; rel=&quot;nofollow&quot;&gt;http://thefarmatwalnutcreek.com/Ducks_Swans_Mallard-Duck.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9487" LastActivityDate="2015-05-02T03:14:45.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31953" PostTypeId="1" AcceptedAnswerId="31954" CreationDate="2015-05-02T07:47:14.417" Score="0" ViewCount="111" Body="&lt;p&gt;Imagine a gene with  $n$ exons and $m$ introns. How many proteins are possible from that gene? Would all the proteins be isoforms?&lt;/p&gt;&#xA;" OwnerUserId="5892" LastEditorUserId="1306" LastEditDate="2015-05-02T09:07:37.857" LastActivityDate="2015-05-02T09:07:37.857" Title="One Gene and many proteins" Tags="&lt;proteins&gt;&lt;gene&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-05-02T15:53:39.187" ContentLicense="CC BY-SA 3.0" />
  <row Id="31954" PostTypeId="2" ParentId="31953" CreationDate="2015-05-02T08:12:35.723" Score="1" Body="&lt;p&gt;I might be wrong, but aren't numbers $n$ and $m$ are connected as $n=m+1$?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Answer seems to be combinatorial: how many combinations of $n$ objects can be assembled under certain restrictions? Namely, how many isoforms certain gene can have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Restrictions include: how many exon-intron junctions on codon (or precisely between codons), how many exons are actually contain protein-coding sequence of mRNA (some exons are coding untranslated region, 3'- or 5'-UTR, for example), how certain gene processes alternative splicing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, as you can see, answer will highly depend on sequence of given gene. As far as I know, maximum number of isoforms is limited by 5, even though there are genes with &lt;a href=&quot;http://www.cshlp.org/ghg5_all/section/gene.shtml&quot; rel=&quot;nofollow&quot;&gt;hundreds of exons&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-05-02T08:12:35.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31955" PostTypeId="2" ParentId="31937" CreationDate="2015-05-02T13:01:38.453" Score="2" Body="&lt;p&gt;Short answer: Due to habituation. You do something enough number of times, then that event ceases to be something new, and your body adapts to it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case, you train your body to accept more risks allowing greater lengthening, before it begins to internally signal the muscles that an injury is incoming. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Read below for the slightly longer version:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The stretching of a muscle fiber begins with the sarcomere, the basic unit of contraction in the muscle fiber. As the sarcomere contracts, the area of overlap between the thick and thin myofilaments increases. As it stretches, this area of overlap decreases, allowing the muscle fiber to elongate. Once the muscle fiber is at its maximum resting length (all the sarcomeres are fully stretched), additional stretching places force on the surrounding connective tissue. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;There are two kinds of muscle fibers: intrafusal muscle fibers and extrafusal muscle fibers. Extrafusil fibers are the ones that contain myofibrils. Intrafusal fibers are also called muscle spindles and lie parallel to the extrafusal fibers and are the primary proprioceptors in the muscle.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;When the muscle is stretched, so is the muscle spindle. The muscle spindle records the change in length (and how fast) and sends signals to the spine which convey this information. This triggers the stretch reflex (also called the myotatic reflex) which attempts to resist the change in muscle length by causing the stretched muscle to contract. The more sudden the change in muscle length, the stronger the muscle contractions will be (plyometric, or &quot;jump&quot;, training is based on this fact). This basic function of the muscle spindle helps to maintain muscle tone and to protect the body from injury.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;One of the reasons for holding a stretch for a prolonged period of time is that as you hold the muscle in a stretched position, the muscle spindle habituates (becomes accustomed to the new length) and reduces its signaling. Gradually, you can train your stretch receptors to allow greater lengthening of the muscles.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can read more about it (including the role of the lengthening reaction by the gogli tendon organs) here: &lt;a href=&quot;http://people.bath.ac.uk/masrjb/Stretch/stretching_2.html#SEC13&quot; rel=&quot;nofollow&quot;&gt;http://people.bath.ac.uk/masrjb/Stretch/stretching_2.html#SEC13&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has also been published in a short section in this paper. I am sure you can follow the reference chain if you need to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Smith, Craig A. &quot;The warm-up procedure: to stretch or not to stretch. A brief review.&quot; Journal of Orthopaedic &amp;amp; Sports Physical Therapy 19.1 (1994): 12-17.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-02T13:15:31.990" LastActivityDate="2015-05-02T13:15:31.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31956" PostTypeId="1" AcceptedAnswerId="31960" CreationDate="2015-05-02T13:28:15.597" Score="0" ViewCount="175" Body="&lt;p&gt;I am having confusing about treatment of phorpyria . I read it somewhere that for treating phopyria hemin and glucose is given IV . Please give me an easy explanation of it&lt;/p&gt;&#xA;" OwnerUserId="15561" LastActivityDate="2015-05-02T17:29:46.630" Title="Why in acute phorpyria?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2015-05-02T19:12:43.163" ContentLicense="CC BY-SA 3.0" />
  <row Id="31957" PostTypeId="2" ParentId="31934" CreationDate="2015-05-02T14:48:51.870" Score="5" Body="&lt;p&gt;I don't understand your calculations and I don't understand why you're trying to use Bayes formula. I don't know the $\frac{1-p}{2-p}$ formula and I don't understand what it is supposed to calculate. It seems to me that you're overthinking a simple problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We don't have all the information and need to make a bunch of assumptions but if I understand the question correctly then..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Probability that the father carries the mutant allele&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I neglect the probability that a new mutation occurred and that the son is the first carrier of the mutant in the lineage. I assume that we have a probability of 0 of being sick if we don't carry the disease. Because MEN is a pretty bad disease, the autosomal dominant alelle causing the disease is probably kept at pretty low frequency. From &lt;a href=&quot;http://en.wikipedia.org/wiki/Multiple_endocrine_neoplasia#The_MEN1_gene&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;, I read that MEN 2A has a frequency of 1/40000. This means that the probability of being homozygous mutant is $\left(\frac{1}{40000}\right)^2 ≈ 10^{-9}$. I think we can safely assume that the sick kid is heterozygous. Given that the kid is heterozygous, the mutant allele comes either from the mother or from the father with equal probability. So the probability it comes from the father is $0.5$ and the odds are $\frac{p}{1-p}=\frac{0.5}{1-0.5}=\frac{0.5}{0.5}=1$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Knowing that the father is heterozygous, what is the probability that a given kids receives this mutant&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the law of segregation, the probability is 0.5 and the odds are 1.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-06-05T14:37:31.413" LastActivityDate="2015-06-05T14:37:31.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="31958" PostTypeId="1" CreationDate="2015-05-02T15:11:25.173" Score="1" ViewCount="623" Body="&lt;p&gt;I'm sure this is a basic question, but I couldn't find an answer anywhere. Let's say I'm provided with the location of an amino acid or a nucleotide (&lt;a href=&quot;http://en.wikipedia.org/wiki/Medium-chain_acyl-coenzyme_A_dehydrogenase_deficiency#Genetics&quot; rel=&quot;nofollow&quot;&gt;for example&lt;/a&gt;, which lists the location as the ACADM gene, 985A&gt;G (the nucleotide polymorphism) and 304 as the amino acid mutation (from Lys&gt;Glu)). How would I go about now identifying the exact position of this on the chromosome? Eg: Chromosome 1, location 76123456?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Currently the only way I can think is to manually count 304 amino acids, or 985 nucleobases, from the start of the gene where the start location is listed. However this isn't practical. I downloaded some software (IGV &amp;amp; GenomeViewer) and can't see a way I can view the actual amino acid or nucleobase number from the start of the gene.&lt;/p&gt;&#xA;" OwnerUserId="15295" LastActivityDate="2015-05-02T16:55:48.080" Title="Identify chromosome location from gene nucleotide or amino acid number" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31959" PostTypeId="2" ParentId="31958" CreationDate="2015-05-02T15:58:53.630" Score="3" Body="&lt;p&gt;&lt;strong&gt;Option 1:&lt;/strong&gt; You can use the SNP database, to see if it has (and it usually is) characterised before: The tutorial is here (&lt;a href=&quot;http://www.sciencebuddies.org/science-fair-projects/project_ideas/BioMed_Bioinformatics_NCBIGene_SNP.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.sciencebuddies.org/science-fair-projects/project_ideas/BioMed_Bioinformatics_NCBIGene_SNP.shtml&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Option 2:&lt;/strong&gt; is to use a go to character function in a few text editors. If you are on windows, You can do it in Notepad++ (&lt;a href=&quot;https://superuser.com/questions/487507/how-can-i-find-nth-character-in-notepad&quot;&gt;https://superuser.com/questions/487507/how-can-i-find-nth-character-in-notepad&lt;/a&gt;); if in Linux/mac, you probably know how to do it in vim (&lt;a href=&quot;https://stackoverflow.com/questions/22862558/go-to-a-specific-offset-in-a-document&quot;&gt;https://stackoverflow.com/questions/22862558/go-to-a-specific-offset-in-a-document&lt;/a&gt;). If using other text editors in Linux, ask around that community, and they'll tell you how to go about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Option 3:&lt;/strong&gt; One another labour intensive but easy way to do it is to use the tools available online. I personally use NCBI for this, and play around with the region shown. This prevents you from counting. Once you get the local region, select a  few nucleotides  to the left and right, and use that as a search term in your sequence (find text and replace text)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2mTqP.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Option 4:&lt;/strong&gt; And my personal favourite, get the computer to do it for you like this: &lt;a href=&quot;https://stackoverflow.com/questions/23662748/replace-a-nucleotide-at-a-certain-position-in-a-dna-sequence-file&quot;&gt;https://stackoverflow.com/questions/23662748/replace-a-nucleotide-at-a-certain-position-in-a-dna-sequence-file&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are using IGV, it is said in the documentation here (&lt;a href=&quot;https://www.broadinstitute.org/igv/Navigate&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.broadinstitute.org/igv/Navigate&lt;/a&gt;) on how to search for regions and even insert mutations. Were you not able to make this work ?&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="-1" LastEditDate="2017-05-23T12:35:01.883" LastActivityDate="2015-05-02T16:55:48.080" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="31960" PostTypeId="2" ParentId="31956" CreationDate="2015-05-02T17:29:46.630" Score="2" Body="&lt;p&gt;Since porphyria is not one disease but many, I suppose that with &quot;acute porphyria&quot; you mean acute intermittent porphyria. The reason of the disease is an autosomal dominant mutation on the enzyme porphobilinogen deaminase, an enzyme that converts porphobilinogen to hydroxymethylbilane by a deamination reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now the heme is produced in many steps, and the enzyme above is important in the early steps of heme synthesis. In persons with porphyria, these heme precursors accumulate, causing toxicity. In acute porphyria the symptoms are mostly from the central nervous system. The figure under shows the steps of the biosynthesis of heme, and as you see at the upper right corner, defect in the enzyme porphobilinogen deaminase (PBG-deaminase) results in accumulation of porphobilinogen.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Mbrxg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Glucose and other carbohydrates can help suppress disease activity, are given by vein or by mouth, and are part of initial treatment. Intravenous heme, however, is both more specific and effective than glucose and should be started if the patient’s symptoms fail to improve within 36 hours.&lt;/em&gt;&lt;a href=&quot;http://www.porphyriafoundation.com/about-porphyria/types-of-porphyria/AIP&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.porphyriafoundation.com/about-porphyria/types-of-porphyria/AIP&lt;/a&gt; [2015-05-02]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More about carbohydrates and the suppression of symptoms in porphyria &lt;a href=&quot;http://www.porphyriafoundation.com/about-porphyria/diet-and-nutrition/the-glucose-effect-in-acute-porphyria&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.porphyriafoundation.com/about-porphyria/diet-and-nutrition/the-glucose-effect-in-acute-porphyria&lt;/a&gt; [2015-05-02].&lt;/p&gt;&#xA;" OwnerUserId="15566" LastActivityDate="2015-05-02T17:29:46.630" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="31962" PostTypeId="1" AcceptedAnswerId="32970" CreationDate="2015-05-02T18:26:17.053" Score="6" ViewCount="6110" Body="&lt;p&gt;According to the book &quot;&lt;a href=&quot;https://books.google.se/books?id=WM7rvNUcrdsC&amp;amp;pg=PA22&amp;amp;lpg=PA22&amp;amp;dq=non%20competitive%20antagonist%20bind%20on%20active%20site%20dose%20response%20curve&amp;amp;source=bl&amp;amp;ots=P9zbJtvXIl&amp;amp;sig=IGA6bMtoBGwyN8fukyBl5E_aWHA&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=ghNFVYK1EMaksAGg6IGIBA&amp;amp;ved=0CCwQ6AEwAg#v=onepage&amp;amp;q&amp;amp;f=false%20[2015-05.02].&quot; rel=&quot;nofollow noreferrer&quot;&gt;Principles of Pharmacology: The Pathophysiologic Basis of Drug Therapy&quot; by Golan et al&lt;/a&gt;, non-competetive antagonists can bind to both the allosteric site and the active site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that a non-competetive antagonist that binds to the allosteric site causes a decrease in efficacy, but no decrease in potency (see figure below). Figure A shows the agonist alone and the agonist together with a competetive antagonist. This causes the dose response curve to shift to the right, thus increasing the EC50 and decreasing the potency of the agonist. Figure B shows the dose-response curve for the agonist alone and agonist together with a non-competetive antagonist that binds to an allosteric site. As you see this type of antagonist causes a decrease in efficacy, but no decrease in potency is observed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rEqrE.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But how does a non-competetive antagonist that binds to the active site affect the dose-response curve? Does it lead to both a decrease in efficacy and potency? Unfortunately, there is no figure in the book to answer my question.&lt;/p&gt;&#xA;" OwnerUserId="15566" LastEditorUserId="9943" LastEditDate="2015-05-04T17:56:28.237" LastActivityDate="2015-05-13T05:11:53.607" Title="The effect on the efficacy and potency of a non-competetive antagonist binding to the active site of the receptor (dose-response curve)" Tags="&lt;biochemistry&gt;&lt;pharmacology&gt;&lt;enzymes&gt;&lt;enzyme-kinetics&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32961" PostTypeId="1" AcceptedAnswerId="32962" CreationDate="2015-05-02T21:50:58.710" Score="8" ViewCount="360" Body="&lt;p&gt;Can someone tell me where can I find detailed text about mechanisms of evolution of dominance? Or, if it is possible, I would be grateful if someone will tell me about them here.&lt;/p&gt;&#xA;" OwnerUserId="15609" LastEditorUserId="12909" LastEditDate="2015-05-03T19:02:13.503" LastActivityDate="2020-10-11T17:06:33.453" Title="Evolution of dominance of alleles" Tags="&lt;evolution&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="32962" PostTypeId="2" ParentId="32961" CreationDate="2015-05-02T22:01:19.153" Score="8" Body="&lt;p&gt;Welcome to Biology.SE!&lt;/p&gt;&#xA;&lt;p&gt;I am not aware of any book that talks extensively about the evolution of dominance. It is a very interesting field of research. You can probably search for papers on the subject that will go much further than my below answer. For example, you may want to read &lt;a href=&quot;http://journals.cambridge.org/action/displayAbstract?fromPage=online&amp;amp;aid=637&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mayo and  Burger (1996)&lt;/a&gt;, &lt;a href=&quot;https://www.nature.com/articles/6885600/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bourguet (1999)&lt;/a&gt; and &lt;a href=&quot;http://www.cell.com/trends/genetics/abstract/S0168-9525(11)00096-5?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0168952511000965%3Fshowall%3Dtrue&quot; rel=&quot;nofollow noreferrer&quot;&gt;Billiard and Castric (2011)&lt;/a&gt; I hope that my answer below can provide the ground for more searching by presenting the two main (and of historical importance) hypotheses.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;There are several hypotheses about the evolution of dominance. It is important first of all, to note that empirical observations show that &lt;em&gt;beneficial alleles tend to be more dominant than detrimental alleles&lt;/em&gt;. There are a number of hypotheses and I won't be able to make a complete review. Among the two main hypotheses to explain the evolution of dominance, one has been formulated by &lt;a href=&quot;http://en.wikipedia.org/wiki/Ronald_Fisher&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ronald Fisher&lt;/a&gt; and one by &lt;a href=&quot;http://en.wikipedia.org/wiki/Sewall_Wright&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sewall Wright (and J.B.S Haldane)&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Fisher's hypothesis&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;According to Fisher's hypothesis, between two equally beneficial alleles, if one is more dominant than the other than it's heterozygote carrier will have higher fitness. In consequence, beneficial alleles evolve to become more dominant while detrimental alleles evolve to be recessive (so that they can hide from selection in heterozygotes). The main criticism to this model is that selection for dominance is possible only when the locus is polymorphic. This means that the strength of selection for dominance is of the level of the mutation rate, seemingly way too weak to explain the observed pattern of dominance.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Wright's hypothesis&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;According to Wright's hypothesis, beneficial alleles are more dominant because of the kinetic of biochemical reactions. The rate of a biochemical reaction is a function of the concentration in the substrates of interest. The function is called &amp;quot;Michaelis-Menten function&amp;quot; after the name of the authors. The Michaelis-Menten function looks like this:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rFgql.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;Think about a knock-out mutation. Such mutation will decrease by half the concentration of protein the gene in question produce in heterozygotes. Imagine, the concentration of proteins in the wildtype homozygote was 3 (see above graph). The rate of reaction of this homozygote is therefore about 3. The heterozygote would have a concentration of 1.5 and the rate of the reaction is therefore about 2.5-2.75. Assuming that the rate of this biochemical reaction is directly related to fitness, then a the locus of interest, benefical alleles are necessarily dominant and detrimental alleles are necessarily recessive. Selection for dominance is not involved in Wirght's model.&lt;/p&gt;&#xA;&lt;p&gt;In addition to that, if you have a series of biochemical reactions, you will likely have one reaction that is causing a bottleneck. One reaction that is the limiting factor of the speed of some biochemical pathway. Let's call this reaction &lt;code&gt;process A&lt;/code&gt;. If a mutation occurs on a gene coding for any other reaction &lt;code&gt;process B&lt;/code&gt; that is not the limiting factor (&lt;code&gt;process A&lt;/code&gt;), then this mutation will have no effect on fitness as long as it is not important enough to make &lt;code&gt;process B&lt;/code&gt; slower than process &lt;code&gt;A&lt;/code&gt;. This may lead to pattern of dominance. I am not quite sure by how much of this has been formulated by Wright and Haldane though.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Is Fisher's or Wright's hypothesis correct?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;To my understanding&lt;/em&gt;, current state of the art is to consider Wright's model to be correct and Fisher's model to be wrong. In reality, the truth probably lies somewhere in between these two extremes. There exists more detailed (and more mechanistic) models of the evolution of dominance that and the above dichotomy might not be very representative of the current debate on the subject. For example, I (vaguely) remember that during my undergrad, Sylvain Billiard gave a talk at my university in which he reported that some alleles actually have some domain that are directly responsible for decreasing the expression of the other allele on the sister chromosome suggesting that Fisher's hypothesis might sometime be quite a good explanation as well.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;This answer was recycled from what I wrote &lt;a href=&quot;https://biology.stackexchange.com/questions/1294/why-are-some-genes-dominant-over-others-what-is-the-mechanism-behind-it/27594#27594&quot;&gt;here&lt;/a&gt;. But it is a much better fit to your question than to where it was originally posted.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2020-10-11T17:06:33.453" LastActivityDate="2020-10-11T17:06:33.453" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="32963" PostTypeId="2" ParentId="31962" CreationDate="2015-05-02T22:20:36.960" Score="4" Body="&lt;p&gt;This is a tough question. I was reading this paper &lt;em&gt;Patrono, C., et al. &quot;Clinical pharmacology of platelet cyclooxygenase inhibition.&quot; Circulation 72.6 (1985): 1177-1184.&lt;/em&gt; and they seemed t mention this paragraph in the introduction.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Platelet Cycloxygenase or prostaglandin (PG) H synthase (i.e., the&#xA;  enzyme that converts arachidonate released from membrane phospholipids&#xA;  into PG endoperoxides) is the target of several antiplatelet agents&#xA;  that can reversibly or irreversibly block the activity of the enzyme&#xA;  by competing with the substrate or permanently altering the active&#xA;  site, respectively.Such drugs belong to the class of so-called&#xA;  nonsteroidal anti-inflammatory agents (e.g., indomethacin, aspirin),&#xA;  but also include a uricosuric agent, i.e., sulfinpyrazone.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So we have to look for  DRC of a NSAID to say COX. Now I was unable to find a good DRC for aspirin (If you find it, let me know in the comments below. I would love to take a look at it). But I did find DRC for other drugs that inhibit COX.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It led me to this paper &lt;em&gt;Walker, M., et al. &quot;A three-step kinetic mechanism for selective inhibition of cyclo-oxygenase-2 by diarylheterocyclic inhibitors.&quot; Biochem. J 357 (2001): 709-718.&lt;/em&gt; which described the inhibiton of COX2 by a NSAID called celecoxib.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The inhibition of COX isoenzymes by NSAIDs generally conforms to one of three inhibitory mechanisms: simple reversible inhibition, as demonstrated by ibuprofen ; time-dependent reversible inhibition, which includes both weaker binding inhibitors, such as naproxen , and tight binding inhibitors, such as indomethacin and meclofenamic acid ; and irreversible covalent inhibition, as demonstrated by aspirin  and o-(acetoxy-phenyl)hept-2-ynyl sulphide ('APHS') . Most of the traditional NSAIDs display similar inhibitory mechanisms against both COX-1 and COX-2 , and are relatively non-selective. However, COX-2-selective diarylheterocyclic inhibitors demonstrate distinct inhibitory mechanisms for the two isoforms . &lt;strong&gt;For example, celecoxib  has been reported to be a reversible competitive inhibitor of COX-1 while demonstrating time-dependent irreversible inhibition of COX-2.&lt;/strong&gt; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Considering the highlighted statement, I think you can consider the COX1 curve as a standard competitive inhibition and COX2 as non competitive inhibition. The resulting change is essentially the curve shape itself (being shifted to the right). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The DRCs were reported here: &lt;em&gt;Tacconelli, Stefania, et al. &quot;The biochemical selectivity of novel COX-2 inhibitors in whole blood assays of COX-isozyme activity.&quot; Current Medical Research and Opinion® 18.8 (2002): 503-511.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5DkIT.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly the second paper (By Walker) also described how (the authors proposed) the binding occurs. A very interesting read.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-02T23:29:10.360" LastActivityDate="2015-05-02T23:29:10.360" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="32964" PostTypeId="1" AcceptedAnswerId="52730" CreationDate="2015-05-02T23:12:57.280" Score="7" ViewCount="1024" Body="&lt;p&gt;I'm an engineer by training and teaching myself the basics of cell and developmental biology. I'm using Scott F. Gilbert's Developmental Biology and Alberts' Essential Cell Biology right now, and they are both great resources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you recommend good books on similar topics that are written in a non-textbook format?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: For example, I found books like The Greatest Show on Earth, Extended Phenotype, and Nature via Nurture really useful to learn about the basics of evolution while I was reading Watson's Molecular Biology of the Gene. Are there similarly well-written books for cell biology, developmental biology, or biochemistry? I know this sounds broad, but I'm not asking for textbook recommendations. I'd like to read something that isn't a textbook alongside my current studies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;SECOND EDIT: I'd be like to extend this question to recommendations of broad review articles in Cell and Developmental Biology too. For example 'How do cells know where they are?' is an excellent article on different strategies cells may use to assess distance in a developing embryo.&lt;/p&gt;&#xA;" OwnerUserId="15610" LastEditorUserId="15610" LastEditDate="2015-05-04T20:23:44.760" LastActivityDate="2017-03-03T05:57:32.120" Title="Recommend good conversational books to learn about cell and developmental biology or biochemisty?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;development&gt;&lt;book-recommendation&gt;" AnswerCount="6" CommentCount="5" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="32965" PostTypeId="2" ParentId="31944" CreationDate="2015-05-02T23:48:57.960" Score="0" Body="&lt;p&gt;To achieve whole genome alignment between a genome as large as a human, and as small as an archea organism, is possible, but in the end, you'll have to strain your eyes to see patterns. The archea genome is about 1-5 million bp long, whereas the human genome is about 3.3 billion bp long (that's a thousand times too large).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In practice what this means is that you may or may not have small islands of similarity, in vast regions of emptiness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nevertheless, you can align whole genomes using the MUMer tool (&lt;a href=&quot;http://mummer.sourceforge.net/&quot; rel=&quot;nofollow&quot;&gt;http://mummer.sourceforge.net/&lt;/a&gt;). The white paper is here &#xA;&lt;em&gt;Delcher, Arthur L., et al. &quot;Alignment of whole genomes.&quot; Nucleic acids research 27.11 (1999): 2369-2376.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might also be interested in reading this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Wei, Liping, et al. &quot;Comparative genomics approaches to study organism similarities and differences.&quot; Journal of biomedical informatics 35.2 (2002): 142-150.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-02T23:58:00.173" LastActivityDate="2015-05-02T23:58:00.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32966" PostTypeId="1" AcceptedAnswerId="32967" CreationDate="2015-05-02T23:54:16.643" Score="7" ViewCount="1357" Body="&lt;p&gt;In this guide i was reading for annotations, there is a diagram of chromosomes of &lt;em&gt;D.mel&lt;/em&gt;, I am confused as to why the chromosomes are all attached to one another, is this picture taken in a certain stage of mitosis in which they are all condensed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://gep.wustl.edu/repository/course_materials_GEP_partners/Saville_McNeil_Annotation_Walkthrough.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Original source&lt;/a&gt;&#xA; (page 2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2raaO.png&quot; alt=&quot;enter image description here&quot;&gt; &lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="3340" LastEditDate="2015-05-06T06:48:44.617" LastActivityDate="2015-05-06T06:48:44.617" Title="Chromosome picture, how to interpret?" Tags="&lt;chromosome&gt;&lt;drosophila&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="32967" PostTypeId="2" ParentId="32966" CreationDate="2015-05-03T00:12:03.017" Score="3" Body="&lt;p&gt;You need to look up polytene (giant) chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Polytene chromosomes are over-sized chromosomes which have developed from standard chromosomes and are commonly found in the salivary glands of Drosophila melanogaster. Specialized cells undergo repeated rounds of DNA replication without cell division (endomitosis), to increase cell volume, forming a giant polytene chromosome. Polytene chromosomes form when multiple rounds of replication produce many sister chromatids that remain synapsed together.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can read more about it at wikipedia (&lt;a href=&quot;http://en.wikipedia.org/wiki/Polytene_chromosome&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Polytene_chromosome&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="8105" LastActivityDate="2015-05-03T00:12:03.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32968" PostTypeId="2" ParentId="15165" CreationDate="2015-05-03T02:44:26.973" Score="5" Body="&lt;p&gt;I think the Wikipedia entry on &lt;a href=&quot;http://en.wikipedia.org/wiki/Colony_%28biology%29&quot; rel=&quot;noreferrer&quot;&gt;Colonies&lt;/a&gt; in biology is helpful. It writes:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...a colonial organism can be distinguished from a conventional&#xA;  multicellular organism by the looser association and repeating nature&#xA;  of its component subunits—perhaps with specializations, but still&#xA;  visibly similar. The components can also be recognized as organisms in&#xA;  their own right by comparison with evolutionarily related free-living&#xA;  species. For example, the Portuguese man o' war is a colony of four&#xA;  different types of polyp or related forms. These four types can be&#xA;  readily seen to be analogs of one another (or of immature stages), and&#xA;  also of related free-living cnidarians such as jellyfish.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If I interpret this correctly, the Portuguese man o' war seems to be descended from colonies of less specialized organisms, in a way that, say, jellyfish are not. Of course, we are all descended from colonies of single-celled organisms, but I think it's clear that being a colony on the level of the man o' war is an unusual thing and worth getting a special label.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also like the label &quot;colonial organism&quot;. I don't know how standard that is, but it seems to recognize a man o' war is a single organism in a real sense, even though it is structured as a group of specialized parts that maybe were more obviously separate organisms in the evolutionary past.&lt;/p&gt;&#xA;" OwnerUserId="15605" LastActivityDate="2015-05-03T02:44:26.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32969" PostTypeId="1" AcceptedAnswerId="32975" CreationDate="2015-05-03T03:42:53.583" Score="0" ViewCount="401" Body="&lt;p&gt;I'm trying to use Jpred to predict secondary structure for a protein sequence. When I run J-pred, I get a bunch of hits from PDB. I've also noticed these 'hits' are the same name as the templates i use when using Swiss mod. How do i interpret these hits, do I just ignore them and force jpred to predict structure anyway?&lt;/p&gt;&#xA;" OwnerUserId="15223" LastEditorUserId="14826" LastEditDate="2015-05-03T10:16:56.530" LastActivityDate="2015-05-03T10:16:56.530" Title="Using Jpred to predict secondary structure" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;structural-biology&gt;&lt;protein-folding&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32970" PostTypeId="2" ParentId="31962" CreationDate="2015-05-03T05:30:09.493" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short anwer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;'Non-competitive active site–binding inhibitors' are called &lt;strong&gt;mixed-type inhibitors&lt;/strong&gt;. These inhibitors exhibit features of both competitive and non-competitive inhibitors, as they increase K&lt;sub&gt;m&lt;/sub&gt; (like a competitive inhibitor) and decrease V&lt;sub&gt;max&lt;/sub&gt; (like a non-competitive inhibitor).&#xA;&lt;br&gt;&lt;br&gt;&lt;br&gt;&#xA;&lt;strong&gt;Background&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What an interesting question! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In theory, a reversible inhibitor binding to the active site of an enzyme is per definition competitive. In a review by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20374252&quot; rel=&quot;nofollow noreferrer&quot;&gt;Blat (2010)&lt;/a&gt; the author mentions that active site–binding inhibitors that display non-competitive inhibition are indeed unusual. Such inhibitors are referred to as &lt;strong&gt;mixed-type inhibitors&lt;/strong&gt;. In many cases the unusual behavior is observed with (1) enzymes utilizing &lt;strong&gt;an exosite&lt;/strong&gt; for substrate binding, or (2) &lt;strong&gt;isomechanism enzymes&lt;/strong&gt;, (3) enzymes with &lt;strong&gt;multiple substrates/products&lt;/strong&gt; and⁄or (4) &lt;strong&gt;products and two-step binding inhibitors&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) &lt;strong&gt;Enzymes with an exosite&lt;/strong&gt; have a substrate recognition site that is different from the active site. For example, some proteases bind their target on the exosite and then catalyze proteolysis in the active site. Mixed-type inhibitors then bind to the exosite, thereby inducing non-competitive behavior, as the active site is not bound.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) &lt;strong&gt;isomechanism enzymes&lt;/strong&gt; are enzymes that undergo several structural transitional changes during catalysis. When one of these conformations is rate limiting and binds the mixed-type inhibitor, it may non-competitively inhibit the enzyme when another conformational form binds the substrate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3) &lt;strong&gt;Enzymes with multiple substrates or products&lt;/strong&gt; sometimes follow a sequential binding and release of two substrates (or products). Suppose substrate A and cofactor B (e.g. NADPH). The enzyme converts substrate A into A' and cofactor B to B'. Now suppose that the enzyme obligatory has to release A' before B' can be released and that the B' bound state is unable to bind substrate A in the active site, but is able to bind the mixed-type inhibitor. In this case, again, a non-competitive inhibition pattern is observed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(4) &lt;strong&gt;Two-step binding inhibitors&lt;/strong&gt; refer to inhibitors that cause a conformational change of the enzyme after binding its inhibitor, that very slowly reverts back. In the conformationally changed state, the enzyme cannot bind the substrate and competition with substrate is lost. The most extreme case are inhibitors that covalently bind to the active site (note this is the mechanism addressed by @RoverEye).   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You ask what the dose-response graphs are of mixed-type inhibitors. A more common way of displaying inhibitor behavior is using Lineweaver-Burk plots. Many enzymes follow Michaelis-Menten kinetics (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK22430/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Berg et al., 2002&lt;/a&gt;) and by plotting the enzyme kinetics as Lineweaver-Burk plots more insight is gained into the affinity (&lt;em&gt;K&lt;sub&gt;m&lt;/sub&gt;&lt;/em&gt;, you call this 'potency') and maximum rate of the enzyme (&lt;em&gt;V&lt;sub&gt;max&lt;/sub&gt;&lt;/em&gt;, you call this 'efficacy') compared to dose-response graphs. In Lineweaver-Burk plots the &lt;em&gt;reciprocal velocity&lt;/em&gt; of the enzyme is plotted against the &lt;em&gt;reciprocal of the substrate concentration&lt;/em&gt;, resulting in a straight line out of which affinity an maximum velocity can be easily obtained via linear regression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following graphs obtained from &lt;a href=&quot;http://csrri.iit.edu/~howard/biochem/lectures/enzymeinhibition.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Illinois Institute of Technology&lt;/a&gt; show the three different modes of inhibition discussed, starting with the two common types:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gW5T4.jpg&quot; alt=&quot;Competitive&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Competitive inhibitors increase &lt;em&gt;K&lt;sub&gt;m&lt;sub&gt;&lt;/em&gt; (i.e., decrease substrate affinity)&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cnOVg.jpg&quot; alt=&quot;Non-competitive&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Non-competitive inhibitors decrease &lt;em&gt;Vmax&lt;/sub&gt;&lt;/em&gt; (i.e., decrease substrate turnover)&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PQdDz.jpg&quot; alt=&quot;Mixed-type&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Mixed-type inhibitors increase &lt;em&gt;Km&lt;/em&gt; and decrease &lt;em&gt;Vmax&lt;/sub&gt;&lt;/sup&gt;&lt;/em&gt;&#xA;&lt;br&gt;&lt;br&gt;&lt;br&gt; &#xA;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK22430/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Berg et al. (2002). &lt;em&gt;Biochemistry&lt;/em&gt;, 5&lt;sup&gt;th&lt;/sup&gt; edition&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20374252&quot; rel=&quot;nofollow noreferrer&quot;&gt;Blat, &lt;em&gt;Chem Biol Drug Des&lt;/em&gt; 2010;&lt;strong&gt;75&lt;/strong&gt;(6):535-40&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-13T05:11:53.607" LastActivityDate="2015-05-13T05:11:53.607" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="32971" PostTypeId="1" CreationDate="2015-05-03T06:09:13.850" Score="0" ViewCount="104" Body="&lt;p&gt;i don't understand if some thing bites or hurt we feel pain, but its differ for &lt;a href=&quot;https://www.google.co.in/search?q=insect%20bites&amp;amp;oq=insect%20bites&amp;amp;aqs=chrome..69i57&amp;amp;sourceid=chrome&amp;amp;ie=UTF-8&quot; rel=&quot;nofollow&quot;&gt;insect bites&lt;/a&gt;, why so? &lt;/p&gt;&#xA;" OwnerUserId="15612" LastActivityDate="2015-05-03T07:54:24.103" Title="Why Insect bites are itchy rather than pain?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-05-03T10:20:13.347" ContentLicense="CC BY-SA 3.0" />
  <row Id="32973" PostTypeId="2" ParentId="32971" CreationDate="2015-05-03T07:38:44.347" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;You're more likely to have an allergic reaction if you're stung by an insect. The reaction can be classed as:&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Minor localised reaction&lt;/strong&gt; – this is normal and doesn't require allergy testing, although the affected area will often be painful for&#xA;  a few days&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;large localised reaction (LLR)&lt;/strong&gt; – this can cause other symptoms, such as swelling, itching and a rash&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;systemic reaction (SR)&lt;/strong&gt; – this often requires immediate medical attention because it can cause a potentially life-threatening allergic&#xA;  reaction (anaphylaxis)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Taken from : &lt;a href=&quot;http://www.nhs.uk/Conditions/Bites-insect/Pages/Symptoms.aspx&quot; rel=&quot;nofollow&quot;&gt;http://www.nhs.uk/Conditions/Bites-insect/Pages/Symptoms.aspx&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read up on this here: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Inflammation&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Inflammation&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://primer.crohn.ie/the-inflammatory-response&quot; rel=&quot;nofollow&quot;&gt;http://primer.crohn.ie/the-inflammatory-response&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a more detailed look, I would suggest papers like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Loza, Matthew J., et al. &quot;Assembly of inflammation-related genes for pathway-focused genetic analysis.&quot; PLoS One 2.10 (2007): e1035.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or a good immunology textbook.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-03T07:54:24.103" LastActivityDate="2015-05-03T07:54:24.103" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32974" PostTypeId="1" AcceptedAnswerId="32976" CreationDate="2015-05-03T09:47:58.113" Score="3" ViewCount="357" Body="&lt;p&gt;I have done a survey on my friend&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When everytime they eat something spicy, They will eat ice or drink icy water. First, Mostly they feel nothing but a cool sensation. However when they finished, they feel spicy again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes, they will drink warm mill or hot coco. Now everybody feel extremely spicy at first and less spicy afterwards&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Why don't I feel spicy when drinking icy water or eat ice?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Why do I feel spicy after the action at 1) ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Why do I feel extremely spicy when drinking warm milk or hot coco but less spicy afterwards?&lt;/p&gt;&#xA;" OwnerUserId="10274" LastEditorUserId="10274" LastEditDate="2015-05-03T10:48:41.843" LastActivityDate="2015-07-30T12:51:21.887" Title="Feeling of spicy" Tags="&lt;human-biology&gt;&lt;taste&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32975" PostTypeId="2" ParentId="32969" CreationDate="2015-05-03T10:16:33.660" Score="0" Body="&lt;p&gt;That depends on what your are trying to do. Apparently your query sequence is similar to that of proteins with a known 3D-structure. As it says on Jpred's result page (and &lt;a href=&quot;http://www.compbio.dundee.ac.uk/jpred4/help.shtml&quot; rel=&quot;nofollow&quot;&gt;help&lt;/a&gt;), in this case it might be worth looking at these homologues with experimentally determined structures for information on secondary structure. Most likely it will be more accurate than Jpred's prediction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much of the secondary structure you can use from the 3D-structure also depends on which parts align between your sequence and the ones in the PDB. You can show the alignments on Jpred's result page by clicking the button below 'Alignment of PDB hits to your sequence'. However, if you are going with annotations from the 3D-structure, it would probably be better to use SWISS-MODEL directly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you don't want to see those hits and just force a Jpred prediction, you can tick 'Skip searching PDB before prediction' in the advanced options before submitting your prediction. The hits are shown merely as a convenience, ignoring them doesn't change anything about Jpred's prediction.&lt;/p&gt;&#xA;" OwnerUserId="754" LastActivityDate="2015-05-03T10:16:33.660" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="32976" PostTypeId="2" ParentId="32974" CreationDate="2015-05-03T11:54:27.623" Score="6" Body="&lt;p&gt;The spicy feeling essentially is the feeling of heat and pain. It is caused by the molecule Capsaicin (&lt;a href=&quot;https://en.wikipedia.org/wiki/Capsaicin&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Capsaicin&lt;/a&gt;) binding to the ion channel TRPV1 (&lt;a href=&quot;https://en.wikipedia.org/wiki/TRPV1&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/TRPV1&lt;/a&gt;), activating it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can temporarily get rid of the pain by cooling (as you would with any other injury) - hence the effect of ice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately, this does not get rid of the cause of the pain, i.e. the molecule bound to the ion channel. Capsaicin is not very water soluble, but only fat soluble. This is why drinking milk helps: it contains microdroplets of fat, which can solvate the Capsaicin, which then can get washed away from the &quot;pain receptor&quot;.&lt;/p&gt;&#xA;" OwnerUserId="14970" LastEditorUserId="10456" LastEditDate="2015-07-30T12:51:21.887" LastActivityDate="2015-07-30T12:51:21.887" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="32977" PostTypeId="2" ParentId="27459" CreationDate="2015-05-03T12:51:37.393" Score="5" Body="&lt;p&gt;I think that the OP was asking about relevance of using urea with respect to the FASP method. In the FASP method, the primary denaturant is SDS . Protein are denatured with a ~4% SDS solution (buffered to pH 7.5 - 8.0). Then 8 M urea solution is used to replace the SDS. Urea serves two purposes here, first it keeps the protein denatured and in solutions as SDS is replaced/washed off. Second, because urea is a chaotropic agent, it reduces the size of SDS micelles which otherwise would block the pores of the membrane filter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Read the original article here: &lt;a href=&quot;http://www.nature.com/nmeth/journal/v6/n5/abs/nmeth.1322.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nmeth/journal/v6/n5/abs/nmeth.1322.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15615" LastEditorUserId="15615" LastEditDate="2016-05-20T10:12:29.173" LastActivityDate="2016-05-20T10:12:29.173" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="32978" PostTypeId="1" AcceptedAnswerId="32979" CreationDate="2015-05-03T12:53:45.190" Score="4" ViewCount="214" Body="&lt;p&gt;From what I recall, mitochondrial DNA is very susceptible to damage from oxidative stress because it is a site where free radicals are generated and their DNA isn't packed into chromatin like nucleic DNA is. How then is it possible that mitochondria can stay in-tact when it is repeatedly passed on to offspring?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would have thought that an accumulation of errors would cause them to malfunction over time.&lt;/p&gt;&#xA;" OwnerUserId="368" LastActivityDate="2015-05-03T13:07:48.287" Title="Why doesn't mitochondrial DNA accumulate damage over successive generations?" Tags="&lt;dna&gt;&lt;mitochondria&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32979" PostTypeId="2" ParentId="32978" CreationDate="2015-05-03T13:07:48.287" Score="3" Body="&lt;p&gt;If it was the case that we were inheriting damaged mtDNA, we would be inheriting ageing from our parents which in itself is not advantageous in terms of evolution.Considering that the germline mitochondria is purely maternal, nature has evolved a way to switch off the mitochondria of oocytes, and keep it in a simple state, mainly to serve as a template. This template is essentially error free, as the levels of ROS generated, is very low.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Mutations in DNA (mitochondrial or nuclear) in most cells in the body can be harmful to the health of the individual, but will have no influence on the next generation. The genes which we pass onto the next generation are separated off during early development into special ‘germ line’ cells which form sperm and eggs. Great care is taken to minimise the risk of mutation to these genes – genes in germline cells act as a blue print for the next generation. This is essentially why aging is not heritable, and it is a system that works pretty well.&lt;/p&gt;&#xA;&lt;p&gt;Research has uncovered a rather elegant solution to this problem – those mitochondria that will be passed to the next generation are maintained in an inactive state.Mitochondria are only inherited through the maternal line – every mitochondria in your body came from your mother, and this is true for most animal species. The mitochondria in sperm are generally discarded at some point prior to fertilisation.&lt;/p&gt;&#xA;&lt;p&gt;Membrane electrical potential, a measure of the activity of the electron transport chain, was reduced in oocytes compared to both sperm and the surrounding tissue. Further, ROS production was 50- and 100-fold lower in the eggs of fruit flies and zebrafish respectively. Finally, they confirmed that oocyte mitochodria in both species exhibit a simpler structure, indicative of reduced activity. So, it seems that in both fish and flies, the mitochondria in egg cells represent little more than a blueprint, ready to be passed on to the next generation error-free. By deactivating ovarian mitochondria, the fidelity of information is ensured across generations, and aging is not heritable.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Taken from: &lt;a href=&quot;http://blogs.ucl.ac.uk/gee-research/2013/11/11/damage-and-fidelity-the-role-of-the-female-germline-in-mtdna-inheritance/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://blogs.ucl.ac.uk/gee-research/2013/11/11/damage-and-fidelity-the-role-of-the-female-germline-in-mtdna-inheritance/&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;You can read the article here: &lt;em&gt;de Paula, Wilson BM, et al. &amp;quot;Female and male gamete mitochondria are distinct and complementary in transcription, structure, and genome function.&amp;quot; Genome biology and evolution 5.10 (2013): 1969-1977.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-05-03T13:07:48.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32980" PostTypeId="1" AcceptedAnswerId="32987" CreationDate="2015-05-03T15:04:23.597" Score="0" ViewCount="239" Body="&lt;p&gt;The larynx is part of the respiratory system and is responsible for producing sound (our voices). My question is how cancer in the larynx (voice box) affect the respiratory system overall? I appreciate any answer, but if it's not too inconvenient, please don't use too complex terminology (I'm in grade 10 Canada). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="15616" LastActivityDate="2015-05-04T00:50:07.740" Title="How does cancer of the larynx (laryngeal cancer) affect the respiratory system?" Tags="&lt;human-biology&gt;&lt;cancer&gt;&lt;systems-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="32981" PostTypeId="1" AcceptedAnswerId="32995" CreationDate="2015-05-03T19:23:31.593" Score="1" ViewCount="112" Body="&lt;p&gt;Out of curiosity, I'd like play around with data of human global demography.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where can I find data that describe the &quot;per region (per continent for example) population size&quot; versus time since the &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Recent_African_origin_of_modern_humans#Movement_out_of_Africa&quot; rel=&quot;nofollow noreferrer&quot;&gt;Out-of-Africa Event&lt;/a&gt;&quot; or earlier?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is for example the kind of graph I'd like to reproduce but if possible in a region per region basis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/F7Gl7.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-05-04T12:54:29.863" LastActivityDate="2015-09-30T16:15:12.450" Title="Human population growth - where can I find the data?" Tags="&lt;human-biology&gt;&lt;population-biology&gt;&lt;database&gt;&lt;demography&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="32982" PostTypeId="1" CreationDate="2015-05-03T19:39:31.797" Score="0" ViewCount="190" Body="&lt;p&gt;What do we know about the forces/mechanisms which lead to this seemingly &quot;fast forward&quot; evolution stages of the embryo? What are the theories dealing with this idea?&lt;/p&gt;&#xA;" OwnerUserId="578" LastEditorUserId="578" LastEditDate="2015-05-04T08:04:52.007" LastActivityDate="2015-05-04T18:06:22.383" Title="Does embryonic development mimic (partly at least) the evolution of organisms on earth?" Tags="&lt;evolution&gt;&lt;embryology&gt;" AnswerCount="0" CommentCount="12" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="32983" PostTypeId="1" CreationDate="2015-05-03T23:52:42.710" Score="1" ViewCount="102" Body="&lt;p&gt;When doing an annotation of a contig31 of &lt;em&gt;Drosophila biarmipes&lt;/em&gt; genome, the gene predictions(in orange, red, green, tan, blue, brown, and gray) picked up numerous possible genes in the area circled in blue below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5gTRE.png&quot; alt=&quot;GEP genome browser on *D.biarmipes*, dot chromosome, contig 31&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So according to the GEP(genomic education partnership) guide I was reading, I was to then BLASTP the amino acid sequence from these predicted genes to a non-redundant protein database. Using NCBI BLAST I did just that, and observed alot of results of significance (E value &amp;lt; 1 X 10^-5). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many of the BLASTP results were somthing like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/chGw4.png&quot; alt=&quot;First BLASTP result, possible TE?&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reading up on gag proteins I found they were related to transposable element activity, specifically reverse transcriptase activity. So then should I conclude that these regoins are showing a gene because they are a Transposable element, or the remenats of one?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also found:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6IZjk.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And reading on &lt;em&gt;Wolbachia&lt;/em&gt; I found that there is Horizontal gene transfer with its genome and &lt;em&gt;Drosophila&lt;/em&gt; in general, according to wikipedia:&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Wolbachia#Horizontal_gene_transfer_and_genomics&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Wolbachia#Horizontal_gene_transfer_and_genomics&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So then, can I conclude the area circled in blue is a result of Transposable element, and not an actual gene belonging to &lt;em&gt;D. biarmipes&lt;/em&gt;?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="3340" LastEditDate="2015-05-07T10:06:52.993" LastActivityDate="2015-05-07T10:06:52.993" Title="Drosophila biarmipes gene annotation, transposable element?" Tags="&lt;bioinformatics&gt;&lt;drosophila&gt;&lt;gene-annotation&gt;&lt;horizontal-gene-transfer&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="32984" PostTypeId="1" AcceptedAnswerId="32998" CreationDate="2015-05-04T00:08:52.160" Score="6" ViewCount="1591" Body="&lt;p&gt;The answer is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The doctor is assuming that the rapid breathing is the body’s response to low blood pH.&#xA;(Source: Campbell Biology)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But this answer doesn't make sense. Why would the doctor give the patient even more CO&lt;sub&gt;2&lt;/sub&gt; if the patient is already suffering from an excess of CO&lt;sub&gt;2&lt;/sub&gt; that is causing the low body pH?&lt;/p&gt;&#xA;" OwnerUserId="13143" LastEditorUserId="3615" LastEditDate="2015-05-04T14:55:56.443" LastActivityDate="2015-05-04T14:55:56.443" Title="A doctor might give bicarbonate (HCO₃¯) to a patient who is breathing very rapidly. What is the doctor assuming about the patient’s blood chemistry?" Tags="&lt;biochemistry&gt;&lt;respiration&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="32985" PostTypeId="1" AcceptedAnswerId="58411" CreationDate="2015-05-04T00:18:34.510" Score="4" ViewCount="119" Body="&lt;p&gt;I want to run multiplex PCRs for my genotyping, with a primer pair targeting my construct and a primer pair targeting some housekeeping gene (sort of a built-in control). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I designed the control amplicon to be very short (I tested 3 primer pairs with ~120, 85, and ~50bp amplicons respectively). The main rationale behind this being that usually my amplicons are ~200-400bp, and I want something clearly distinguishable, but shorter rather than longer (I want to keep my options open for longer target amplicons).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In any case, regardless which control primer pair I use, whenever I try to multiplex I only end up seeing the shorter amplicon. See the gel picture below for an example (lanes: 1-ladder, 2,3-target+control, 4,5-control, 5,6- target).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/W0UUl.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see that lanes 2,3 have a very faint additional smear compared to 4,5, but I want a band for my target amplicon. Also, my shorter bands are quite blurred.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, just for reference, my amplicons do not overlap at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I guess my questions are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Why is the longer band disappearing?&lt;/li&gt;&#xA;&lt;li&gt;Why is the shorter band so blurred? &lt;/li&gt;&#xA;&lt;li&gt;What can I do to prevent this form happening?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4795" LastEditorUserId="4795" LastEditDate="2015-05-04T09:11:13.927" LastActivityDate="2017-04-14T16:57:19.913" Title="Multiplex PCR, shorter amplicon inhibiting longer amplicon?" Tags="&lt;genetics&gt;&lt;pcr&gt;&lt;primer&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="32986" PostTypeId="2" ParentId="32984" CreationDate="2015-05-04T00:30:12.047" Score="5" Body="&lt;p&gt;if a person is both (1) hyperventilating and (2) has a low blood pH then this is a case of &lt;strong&gt;metabolic acidosis&lt;/strong&gt;... in metabolic acidosis the patient compensates by breathing heavy... why? because hydrogen ions are captured by bicarbonate (the conjugate base of carbonic acid) which is then exhaled as carbon dioxide... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;metabolic acidosis is not caused by excess carbon dioxide... this is the case of respiratory acidosis... but under respiratory acidosis the breathing is supressed, however tachypnea with frequent shallow breaths could lead to poor removal of carbon dioxide...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;here are some causes of metabolic acidosis:&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Metabolic_acidosis#Causes&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Metabolic_acidosis#Causes&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2015-05-04T01:39:49.490" LastActivityDate="2015-05-04T01:39:49.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32987" PostTypeId="2" ParentId="32980" CreationDate="2015-05-04T00:42:36.777" Score="0" Body="&lt;p&gt;According to this website:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.spirometry.guru/fvc.html&quot; rel=&quot;nofollow&quot;&gt;http://www.spirometry.guru/fvc.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;it causes difficulty with inhalation but exhalation is normal...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Typically the expiratory part of the F/V-loop is normal: the&#xA;  obstruction is pushed outwards by the force of the expiration.&quot;&lt;br&gt;&#xA;  &quot;During inspiration the obstruction is sucked into the trachea with&#xA;  partial obstruction and flattening of the inspiratory part of the&#xA;  flow-volume loop.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;the exact symptoms of a laryngeal tumor depends on where it is located on the larynx... above the vocal cords, on the vocal cords, or below the vocal cords...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;but more generally:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;anatomy:&lt;/strong&gt; &#xA;&lt;em&gt;mouth/nose--&gt;pharynx--&gt;larynx--&gt;trachea--&gt;bronchi--&gt;lungs&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a tracheostomy may be necessary... basically the surgeon makes a connection between the skin outside the throat and the trachea... this bypasses the larynx (as well as pharynx and nose/mouth)...&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2015-05-04T00:50:07.740" LastActivityDate="2015-05-04T00:50:07.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32988" PostTypeId="1" CreationDate="2015-05-04T01:03:56.813" Score="8" ViewCount="168" Body="&lt;p&gt;I am pretty bad in thinking quantitative genetics models. I am trying to get some basic understanding of modelling the evolution of a quantitative trait. I am therefore asking for help to analyze a very simple model. I welcome any explanation of some other classic model of the evolution of quantitative traits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Scenario&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider a haploid population of constant size $N$. The fitness of the individuals is determined exclusively by a single quantitative trait $z$. $l$ loci codes for this trait. The genetic value at each locus adds up to give the quantitative trait $z$. The mutation rate at each locus is $\mu$. A mutation changes the genetic value at any given locus by $+ \Delta z$ with probability $\frac{1}{2}$ and by $- \Delta z$ with probability $\frac{1}{2}$. If you prefer to consider the effects of a mutation to be drawn from a normal distribution with mean $=0$ and variance $= \sigma^2$, please feel free to do so. The fitness $w(z)$ of an individual is given as a gaussian function of its quantitative trait $z$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$w(z)=\exp\bigl(-Vz^2\bigr),$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $V$ is the strength of selection. The optimal phenotype is $0$, that is $w(0)=1$. The larger is $V$, the more severe it is to be at a given distance to the optimal phenotype. If you want to assume that the fitness $w(z)$ is some other function of the trait $z$, such as the even more simple $w(z)=z$, please feel free to do so. For simplicity, we assume no environmental variance on the quantitative trait.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the equilibrium mean fitness $\bar w$ of the population?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the equilibrium genetic variance (=phenotypic variance) for fitness $w$ and for phenotype $z$?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-05-04T15:25:28.227" LastActivityDate="2015-05-30T15:37:20.403" Title="Basic Modelling in Quantitative Genetics" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;theoretical-biology&gt;&lt;population-biology&gt;&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="32989" PostTypeId="1" CreationDate="2015-05-04T03:25:15.710" Score="4" ViewCount="2057" Body="&lt;p&gt;The midbrain is a centre for certain visual and auditory reflexes. But what are those reflexes exactly? My study book says that these reflexes are, e.g., responsible for moving the eyes to view something as the head turns. But I don't quite get it. What is the difference between those reflexes controlled by the midbrain and those mediated by the spinal cord?&lt;/p&gt;&#xA;" OwnerUserId="15621" LastEditorUserId="9943" LastEditDate="2015-05-04T05:35:30.707" LastActivityDate="2015-05-04T05:35:30.707" Title="What are those visual and auditory reflex controlled by the midbrain?" Tags="&lt;physiology&gt;&lt;brain&gt;&lt;vision&gt;&lt;brain-stem&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="0" ClosedDate="2015-05-26T14:16:50.063" ContentLicense="CC BY-SA 3.0" />
  <row Id="32990" PostTypeId="1" AcceptedAnswerId="32994" CreationDate="2015-05-04T07:18:21.440" Score="1" ViewCount="1114" Body="&lt;p&gt;What causes muscle spasms with muscles that are not in the heart  ? Could it be some sort of stimulus overload that causes a massive contraction?&lt;/p&gt;&#xA;" OwnerUserId="11605" LastEditorUserId="14735" LastEditDate="2015-05-04T09:33:05.640" LastActivityDate="2015-05-04T10:02:57.783" Title="What causes muscle spasms?" Tags="&lt;human-biology&gt;&lt;muscles&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32991" PostTypeId="1" CreationDate="2015-05-04T09:06:08.803" Score="0" ViewCount="53" Body="&lt;p&gt;There are various software for simulating reads for Next Generation Sequencing. Can anyone tell what exactly is done by a read simulator software&lt;/p&gt;&#xA;" OwnerUserId="14579" LastEditorUserId="14735" LastEditDate="2015-05-04T09:25:25.207" LastActivityDate="2015-05-04T09:25:25.207" Title="What does a read simulator do?" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;genomics&gt;&lt;sequence-analysis&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="32992" PostTypeId="2" ParentId="32991" CreationDate="2015-05-04T09:16:30.173" Score="1" Body="&lt;p&gt;In general, a read simulator does the following:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Selects regions from a reference sequence with some sort of predefined or user-specified size distribution.&lt;/li&gt;&#xA;&lt;li&gt;Converts the sequence from those regions into single or paired end reads with quality scores. The quality scores and read lengths are typically user defined.&lt;/li&gt;&#xA;&lt;li&gt;Introduces errors into the aforementioned sequences, typically with more at the 3' end, which matches what comes from a sequencer.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;A simulator may also try to reproduce the uneven coverage that you'd see in real data. In any case, most simulators will place the original coordinates of the simulated reads in the read names so that the quality of the resulting alignments of the reads can be assessed.&lt;/p&gt;&#xA;" OwnerUserId="9523" LastActivityDate="2015-05-04T09:16:30.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32993" PostTypeId="1" AcceptedAnswerId="34175" CreationDate="2015-05-04T09:55:09.857" Score="2" ViewCount="794" Body="&lt;p&gt;An example can be seen in this &lt;a href=&quot;https://www.youtube.com/watch?v=B79Z56vl02A&quot; rel=&quot;nofollow&quot;&gt;Youtube video&lt;/a&gt;, where the slime mold pulsates as it engulfs a rock in order to form its fruiting body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does this pulsing happen? &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="3553" LastEditDate="2015-05-13T16:46:02.210" LastActivityDate="2015-05-13T16:46:02.210" Title="Why do slime molds pulsate when growing into their fruiting body?" Tags="&lt;microbiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32994" PostTypeId="2" ParentId="32990" CreationDate="2015-05-04T10:02:57.783" Score="0" Body="&lt;p&gt;According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Spasm&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; and &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/003193.htm&quot; rel=&quot;nofollow&quot;&gt;MedlinePlus&lt;/a&gt; muscle cramps can be caused by muscle overuse or injury or dehydration and lack of minerals (eg. potassium or calcium). In this &lt;a href=&quot;http://en.wikipedia.org/wiki/Muscle_contraction&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; page you can read about the mechanism of muscle contraction. I'd emphasize and quote the most important parts here:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;ATP binds to myosin, allowing it to release actin and be in the weak binding state (a lack of ATP makes this step impossible, resulting in the rigor state characteristic of rigor mortis). The myosin then hydrolyzes the ATP and uses the energy to move into the &quot;cocked back&quot; conformation. In general, evidence (predicted and in vivo) indicates that each skeletal muscle myosin head moves 10–12 nm each power stroke, however there is also evidence (in vitro) of variations (smaller and larger) that appear specific to the myosin isoform.&#xA;  Steps 9 and 10 repeat as long as ATP is available and calcium is freely bound within the thin filaments.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As you can see ATP is essential in the release of myosin from actin. In case of muscle overuse and dehydration ATP is depleted from the muscle cells and may cause the muscle to cramp.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also according to &lt;a href=&quot;http://bestpractice.bmj.com/best-practice/monograph/569/basics/pathophysiology.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; site it is said that repetitive firing of motor units with high frequency is associated with muscle cramps, although tehe origin of this is yet not clear. It can be either from the central nervous system or the peripherial.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastActivityDate="2015-05-04T10:02:57.783" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="32995" PostTypeId="2" ParentId="32981" CreationDate="2015-05-04T13:20:49.760" Score="1" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;National censuses are collected, published and disseminated primarily by each country's census or national statistical office (NSO) or its equivalent. Census data are published in each country's vernacular, and as appropriate, many offer English as well as other language versions.&lt;/p&gt;&#xA;&lt;p&gt;Statistical offices of international agencies (e.g. United Nations, statistical organizations for member states like the ASEAN, Eurostat, and OECD), also publish statistical data including population figures. The most consistent data in terms of format and frequency, whether online or in print are usually generated from them.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The US Library of congress provides some interesting links here:&#xA;&lt;a href=&quot;http://www.loc.gov/rr/business/census/intlcensus.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.loc.gov/rr/business/census/intlcensus.html&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;Also Cornell provides a few resources also:&#xA;&lt;a href=&quot;https://www.ciser.cornell.edu/ASPs/datasource.asp&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.ciser.cornell.edu/ASPs/datasource.asp&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;If you still need some information, your best bet is to then contact social scientists and ask for their opinion.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-05-04T13:20:49.760" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32996" PostTypeId="1" CreationDate="2015-05-04T13:36:20.140" Score="0" ViewCount="63" Body="&lt;p&gt;One of the users on the chemistry s.e. mentioned that when benzoic acid forms in the body in response to other chemicals it might have a mutating effect on one's DNA. Is this true?&lt;/p&gt;&#xA;" OwnerUserId="11605" LastActivityDate="2015-05-04T13:36:20.140" Title="Regarding benzoic acid and its effects" Tags="&lt;human-biology&gt;&lt;gene-expression&gt;&lt;food&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="32997" PostTypeId="1" CreationDate="2015-05-04T14:15:30.873" Score="4" ViewCount="3213" Body="&lt;p&gt;Is there &lt;strong&gt;proteins&lt;/strong&gt; that have strong color, that could be seen without the need of UV and with naked eyes (with white light) - in mammalian cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Searching for reporter, something like GFP, but that we could see it without UV (not fluorescence).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like chromoprotein - but it is problematic in mammalian cells because most chromoproteins need a prosthetic group.&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="10104" LastEditDate="2015-05-05T19:40:14.977" LastActivityDate="2017-11-22T10:20:28.797" Title="Proteins that give color (without fluorescence)" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;biophysics&gt;" AnswerCount="2" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="32998" PostTypeId="2" ParentId="32984" CreationDate="2015-05-04T14:42:17.137" Score="4" Body="&lt;p&gt;Bicarbonate is not carbon dioxide. In acidic conditions, bicarbonate will be protonated to form carbonic acid which in turn decomposes into carbon dioxide and water. The overall result is the removal of a proton (ie increase in pH) and formation of carbon dioxide (which accounts for the rapid breathing). The idea behind giving bicarbonate is that it will replenish the buffer. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-05-04T14:42:17.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="32999" PostTypeId="1" AcceptedAnswerId="33000" CreationDate="2015-05-04T14:47:31.207" Score="4" ViewCount="68" Body="&lt;p&gt;Reading the paper &lt;a href=&quot;http://www.nature.com/nature/journal/v427/n6976/abs/nature02298.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, I'm confused about the production of figure 4d. The method of production is detailed in the &lt;a href=&quot;http://www.nature.com/nature/journal/v427/n6976/suppinfo/nature02298.html&quot; rel=&quot;nofollow&quot;&gt;supplementary information&lt;/a&gt; under the heading &quot;Theoretical phase diagram&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically, I'm confused about the use of theta and what it means. I have tried reproducing the figure using MATLAB and the parameters in the paper to see whether I can understand it better, but nothing quite works out. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be clear, the paper obtains a steady state result for a series of ODEs: &#xA;$$&#xA;    y = \frac{\alpha  (1+(βy)^2)}{ρ+(βy)^2}&#xA;$$&#xA;Then rearranges as a cubic: &#xA;$$&#xA;    y^3 −αy^2 + \frac{ρ}{ β^2} y − \frac{α }{ β^2 } = 0 &#xA;$$&#xA;Apparently, a general cubic with two identical roots has the&#xA;form:&#xA;$$&#xA;    (y-a)(y-a)(y-aθ) = y^3 - (2 + θ)ay^2 + (1+2θ)a^2 y - θa^3&#xA;$$&#xA;The paper then equates coefficients:&#xA;\begin{align}&#xA;    ρ &amp;amp;= (1 + 2θ)(1 + 2/θ)\\&#xA;    aβ &amp;amp;= \frac{(2 + θ)^{3/2}}{θ^{1/2}}\tag{did you mean?}&#xA;\end{align}&#xA;And claims that these are the parametric equations that describe the graph in question. When plotting these equations, I get nothing like the graph. I can't really see where it comes from.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The graph in question and some equations are reproduced here on the last page:&#xA;http:// web.mit.edu/biophysics/sbio/PDFs/L7_notes.pdf&lt;/p&gt;&#xA;" OwnerUserId="15626" LastEditorUserId="15626" LastEditDate="2015-05-04T17:11:19.507" LastActivityDate="2015-05-04T23:34:36.657" Title="Multistability in the lactose ultization network" Tags="&lt;bioinformatics&gt;&lt;computational-model&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="33000" PostTypeId="2" ParentId="32999" CreationDate="2015-05-04T16:07:15.763" Score="3" Body="&lt;p&gt;The equation in the OP has been updated to $(y-a)^2(y-a\theta)$ which yields the correct expansion. Therefore, by equating the coefficients, we obtain&#xA;\begin{align}&#xA;\alpha &amp;amp;= (2+\theta)a\tag{1}\\&#xA;\rho/\beta^2 &amp;amp;= a^2(1+2\theta)\tag{2}\\&#xA;\alpha/\beta^2 &amp;amp;= a^3\theta\tag{3}&#xA;\end{align}&#xA;Using equations (1) to (3), we get the desired $\rho$ and $\alpha\beta$. Now the authors plotted $\frac{\alpha\beta}{\rho}$ and $\frac{1}{\rho}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By plotting $\frac{\alpha\beta}{\rho}$ and $\frac{1}{\rho}$, we can re-create the plot in Mathematica with&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ParametricPlot[{1/((1 + 2 x) (1 + 2/x)), (2 + x)^(3/2)/(&#xA;  Sqrt[x] (1 + 2 x) (1 + 2/x))}, {x, 0.01, 50 \[Pi]}, &#xA; PlotRange -&amp;gt; {{0, .15}, {0, 0.6}}, AspectRatio -&amp;gt; 3/4]&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/b54qm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you dont have Mathematica, here is some Python code that will plot it as well.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;import numpy as np&#xA;import matplotlib.pyplot as plt&#xA;&#xA;fig = plt.figure()&#xA;t = np.linspace(0.01, 25*np.pi, 5000)&#xA;x = 1/((1+2*t)*(1+2/t))&#xA;y = (2+t)**1.5/(np.sqrt(t)*(1+2*t)*(1+2/t))&#xA;plt.plot(x,y)&#xA;&#xA;plt.show()&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Here is the Python plot which has smoother lines compared to Mathematica's plot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jkHVg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="12909" LastEditorUserId="12909" LastEditDate="2015-05-04T23:34:36.657" LastActivityDate="2015-05-04T23:34:36.657" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="33001" PostTypeId="1" AcceptedAnswerId="34070" CreationDate="2015-05-04T16:43:16.170" Score="5" ViewCount="329" Body="&lt;p&gt;Lentivectors are widely used in molecular biology, most commonly to transduce in a stable way a desired gene. These vector system takes advantage from the ability of viruses to introduce their own genome in the host cell. Thus the lentivectors are transfected to a producer cell line (typically HEK) and there viruses are produced with the desired insert. Eventually this viruses will be harvested and the desired cell lines transduced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For bio-safety reasons, this system is engineered in a way that that the risk posed by the &quot;virus system&quot; is reduced. Thus the viruses produced by this system are incapable of replication, meaning with this that, as far as I understood, the viruses that are formed are then unable to form more in the second host as the genes in charge are not recruited. Yet, apparently the plasmids used can recombine and pose a possibility to create a replicating capable virus. Yet as far as I found in the literature this has never been detected and stands as a theoretical possibility. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My first question, in actual numbers, &lt;strong&gt;what is the probability that such event would take place (the number of recombinations in the specific locations)&lt;/strong&gt;. In the case that this would happen, the lentivector system would be potentially dangerous, as this system is based in HIV most of the times. Additionally, this vectors use not the endogenous HIV envelope protein but rather VSV/G from vesicular stomatitis virus, in order to increase the tropism and stability. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, even though HIV derived, most of the HIV genes are taken away from the lentivectors, yet in my opinion the most important ones are there. Second question, taking into consideration all of this, &lt;strong&gt;this theoretical &quot;created&quot; virus would be able to eventually cause AIDS or other whatever adverse effect?&lt;/strong&gt; it is noteworthy that now is able to infect almost all human cells due to the VSV protein, then is it correct to think that the disease would be much worse, and much more contagious than the original HIV? note that even the stability is increased. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet, I can additionally think that this recombinant new virus may be indeed destroyed by the immune system, despite the increased tropism, due to the fact that vesicular stomatitis virus does not cause pathologies in humans, and possibly this protein works as an antigen and can induce an enough immune response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Last, &lt;strong&gt;would theoretical recombinant virus be detected by a standard HIV test?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To simplify things, I am referring to third generation lentivectors &lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="3657" LastEditDate="2015-05-07T19:21:57.490" LastActivityDate="2015-05-08T06:01:24.767" Title="Lentivector biosafety" Tags="&lt;virology&gt;&lt;lentivirus&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="33003" PostTypeId="2" ParentId="32997" CreationDate="2015-05-04T18:30:45.767" Score="0" Body="&lt;p&gt;You are looking for light-emitting proteins. They gather energy from either absorption of photon (fluorescence) or via random thermal fluctuations. Problem is that fluorescence might be considered forced emission, whereas what you looking for is results of spontaneous transitions. That means that number of photons per second you can expect from latter proteins is $10^4$ times less (I don't have reference for that statement). You need very sensitive detectors and microscopy (sub- or just cellular) is almost impossible at that rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should look into phosphorescence. Also, such thing as GFP-aeqorin might be of interest. That is a calcium-sensistive construct, might give you starting point in searching for reviews.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another keyword is bioluminescence. See here for more: &lt;a href=&quot;http://www.olympusconfocal.com/applications/fluorescentproteins.html&quot; rel=&quot;nofollow&quot;&gt;http://www.olympusconfocal.com/applications/fluorescentproteins.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-05-04T18:30:45.767" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="33004" PostTypeId="1" CreationDate="2015-05-04T19:40:22.613" Score="0" ViewCount="690" Body="&lt;p&gt;Every chart of palindromic restriction enzymes I've seen lists their restriction sites from 5' to 3', something like this:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Eco&lt;/em&gt;R1 cuts GAATTC between the G and A:  &lt;br&gt; &#xA;          5' NNNGAATTCNNN 3' --&gt; 5' NNNG____ AATTCNNN 3'&lt;br&gt;&#xA;          3' NNNCTTAAGNNN 5' --&gt; 3' NNNCTTAA____ GNNN 5'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Will restriction enzymes match and cut a site if it's running antiparallel? For example, will &lt;em&gt;Eco&lt;/em&gt;R1 cut this sequence? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;5' NNNCTTAAGNNN 3'&lt;br&gt;&#xA;3' NNNGAATTCNNN 5'&lt;/p&gt;&#xA;" OwnerUserId="15628" LastActivityDate="2015-05-04T20:53:54.313" Title="Do restriction enzymes on read 3' to 5'?" Tags="&lt;molecular-genetics&gt;&lt;restriction-enzymes&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="33005" PostTypeId="2" ParentId="33004" CreationDate="2015-05-04T19:59:52.250" Score="2" Body="&lt;p&gt;Whatever sequence (plus direction) is target, so enzyme will cut. In your example &quot;correct&quot; and &quot;antiparallel&quot; sequences are two different sites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Actually, your example of 5'-CTTAAG-3' is cut by &lt;a href=&quot;https://www.neb.com/products/r0520-aflii&quot; rel=&quot;nofollow&quot;&gt;AflII&lt;/a&gt; enzyme.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="10456" LastEditDate="2015-05-04T20:53:54.313" LastActivityDate="2015-05-04T20:53:54.313" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="33006" PostTypeId="1" CreationDate="2015-05-04T21:36:10.193" Score="8" ViewCount="850" Body="&lt;p&gt;Why is it that only humans commit suicide?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many animals do 'brave' things to protect their children or family, and some male spiders sacrifice themselves so that they can impregnate the females. However, humans commit suicide without necessarily any intention to help their offspring. Why?&lt;/p&gt;&#xA;" OwnerUserId="15630" LastActivityDate="2015-05-06T20:14:37.667" Title="Why do only humans commit suicide?" Tags="&lt;death&gt;" AnswerCount="1" CommentCount="13" FavoriteCount="3" ClosedDate="2015-05-28T05:40:13.073" ContentLicense="CC BY-SA 3.0" />
  <row Id="33008" PostTypeId="1" CreationDate="2015-05-04T21:42:19.017" Score="3" ViewCount="100" Body="&lt;p&gt;Do macrophages in the dermis consume any foreign invader to the body, or simply pathogens and cellular debris?  For example, would macrophages consume vitamins or medications injected into the dermal layer of the skin?  Thank you&lt;/p&gt;&#xA;" OwnerUserId="15632" LastActivityDate="2015-05-06T19:09:32.170" Title="Macrophages and what they consume" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="33009" PostTypeId="1" AcceptedAnswerId="33018" CreationDate="2015-05-04T22:26:07.097" Score="0" ViewCount="212" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Hypoxia_(medical)%23Signs_and_symptoms&quot; rel=&quot;nofollow&quot;&gt;On this Wikipedia page&lt;/a&gt; it says that lower oxygen levels can cause light-headedness. Is there evidence that higher partial pressure of oxygen can &lt;em&gt;improve&lt;/em&gt; mental focus? &lt;/p&gt;&#xA;" OwnerUserId="15633" LastEditorUserId="9268" LastEditDate="2015-05-05T08:06:53.233" LastActivityDate="2020-02-03T14:14:13.207" Title="How does the partial pressure of oxygen affect mental focus?" Tags="&lt;respiration&gt;&lt;cognition&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="33010" PostTypeId="2" ParentId="32964" CreationDate="2015-05-04T23:30:13.823" Score="1" Body="&lt;p&gt;Would you consider the New York Times a suitable level of detail (while admittedly not a book)? If so then you may want to peruse this collection:&#xA;&lt;a href=&quot;http://topics.nytimes.com/top/news/science/topics/biology_and_biochemistry/index.html&quot; rel=&quot;nofollow&quot;&gt;http://topics.nytimes.com/top/news/science/topics/biology_and_biochemistry/index.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will have to be selective.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This was my first hit in Google searching for 'lay articles on biochemistry.' I would recommend my own textbook but it is aimed at 3rd year undergraduates, and would probably contravene the Biology SE rules.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-05-04T23:30:13.823" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="33011" PostTypeId="1" AcceptedAnswerId="33034" CreationDate="2015-05-04T23:52:54.977" Score="2" ViewCount="429" Body="&lt;p&gt;Apologies if this question it too open-ended; evolutionary biology is not my primary field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been reading a lot about the use of statistical mechanics in analyzing evolutionary dynamics. As an example, consider this paper: &lt;a href=&quot;http://www.pnas.org/content/102/27/9541.short&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/102/27/9541.short&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ideas are pretty straightforward. There is some genotype-fitness landscape and selection drives populations towards maximal fitness. However, genetic drift can pull these populations away from maximal fitness. These two concepts are analogous to minimization of internal energy and maximization of entropy in thermodynamics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, most of the papers that develop these models never properly explain how to apply them to observable phenomena. Is it because there is some disconnect between the parameters in the models and nature? For example, many of these models use the effective population size, which is unknown for most species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess my main question is this: are there any demonstrations on how to use these toy models to predict something in nature, or are they simply for theoretical purposes. &lt;/p&gt;&#xA;" OwnerUserId="15634" LastEditorUserId="14629" LastEditDate="2015-05-05T15:31:42.260" LastActivityDate="2015-05-06T14:42:37.990" Title="Are there any examples of how to apply evolutionary models?" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;fitness&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="33012" PostTypeId="2" ParentId="33008" CreationDate="2015-05-05T00:13:53.033" Score="1" Body="&lt;p&gt;Macrophages and dendritic cells generally recognize large foreign complexes. They often do this through the recognition of pathogen or damage-associated molecular patterns (PAMPs or DAMPs). Otherwise, cell-mediated pathways involve cyto/chemokines which direct macrophages and the like in the region. We also have to consider, does the compound in question belong in the region, or is it insoluble amongst the tissue? In these cases, the compounds are also degraded/engulfed. So how does the body go about recognizing small, soluble foreign molecules? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are called &lt;strong&gt;haptens&lt;/strong&gt;. If these small molecules can bind to a larger carrier complex in your body, so that it now &lt;em&gt;looks&lt;/em&gt; like there's something foreign, regardless if the initial carrier complex was foreign or not, this may present cause for immunologic reponse (as in the mechanism of urushiol, the toxin in poison ivy). There are certain T-cells, like NKT and γδ T cells, which can &quot;see&quot; these antigens despite their lacking a type I or II MHC presentation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The short answer is it depends on what the injected drug does once it begins interacting with your physiology. Vitamins, on the other hand, are regularly uptaken by cells for metabolism, and I wouldn't imagine macrophages engulfing exogenous vitamins outside of it's needs on their own.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source: Cellular and Molecular Immunology, 8th ED.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-05-05T00:13:53.033" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="33013" PostTypeId="2" ParentId="7492" CreationDate="2015-05-05T00:41:16.087" Score="-1" Body="&lt;p&gt;I see one possible advantage to round pupils. A slit pupil gives higher visual acuity vertically than horizontally because of diffraction and when a slit pupil is very nearly shut, there's high diffraction in the horizontal direction giving poor horizontal visual acuity. A round pupil on the other hand gives a creature the highest visual acuity in all directions for a given area of pupil. A smaller pupil is better for reducing chromatic aberration but chromatic aberration can be pretty much neglected because for any creature with evolutionary pressure for sharp vision in all directions, good accomodation will ensure at least one wavelength of light focuses onto the retina forming a sharp image because the sun emits a continuous range of wavelengths.&lt;/p&gt;&#xA;" OwnerUserId="15635" LastActivityDate="2015-05-05T00:41:16.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="33014" PostTypeId="1" CreationDate="2015-05-05T04:50:50.977" Score="2" ViewCount="738" Body="&lt;p&gt;My textbook states that repetitive self-pollination in the plants cause inbreeding depression which causes infertility thus plants develop techniques called outbreeding devices to encourage outcrossing. My question is how does inbreeding depression cause infertility?&lt;/p&gt;&#xA;" OwnerUserId="3881" LastActivityDate="2015-05-05T15:16:21.777" Title="How does inbreeding depression cause infertility?" Tags="&lt;agriculture&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="33015" PostTypeId="2" ParentId="32997" CreationDate="2015-05-05T06:23:55.613" Score="6" Body="&lt;p&gt;Have a look at &lt;a href=&quot;http://www.jbc.org/content/275/34/25879.long&quot;&gt;this&lt;/a&gt; paper. They have isolated a chromoprotein similar to GFP, and like the latter it does not have any prosthetic group.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This protein — asFP595 (because it was isolated from the anemone  &lt;em&gt;Anemonia sulcata.&lt;/em&gt;), is purple coloured under white light and also exhibits a little fluorescent emission in the red region  (λ&lt;sub&gt;max&lt;/sub&gt; = 595 nm).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also have a look at these two papers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0014579301029301&quot;&gt;GFP-like chromoproteins as a source of far-red fluorescent proteins&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007%2FPL00006956&quot;&gt;Major colour patterns of reef-building corals are due to a family of GFP-like proteins&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-05-05T06:23:55.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="33016" PostTypeId="5" CreationDate="2015-05-05T08:48:36.640" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2015-05-05T08:48:36.640" LastActivityDate="2015-05-05T08:48:36.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="33017" PostTypeId="4" CreationDate="2015-05-05T08:48:36.640" Score="0" Body="Questions about the biological function and structure of the human eye." OwnerDisplayName="user15629" LastEditorDisplayName="user15629" LastEditDate="2015-05-05T10:12:08.890" LastActivityDate="2015-05-05T10:12:08.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="33018" PostTypeId="2" ParentId="33009" CreationDate="2015-05-05T09:10:54.507" Score="2" Body="&lt;p&gt;Long term exposure to hyperoxia actually does more harm than good. Though short term hyperoxia is recommended after brain injuries (&lt;a href=&quot;http://www.medscape.com/viewarticle/741751_3&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.medscape.com/viewarticle/741751_3&lt;/a&gt;) as a valid clinical strategy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For lower concentrations of oxygen, there seems to be evidence that cognitive function is improved:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Y4DkI.png&quot; alt=&quot;External oxygen administration has been shown to have positive effects on memory formation (Moss &amp;amp; Scholey, 1996; Scholey, Moss, Neave, &amp;amp; Wesnes, 1999). Reaction time is faster with external oxygen administration when responding to previously presented words (Scholey et al., 1999). Oxygen administration has been found to improve aspects of everyday memory, including remembering shopping list items and matching names to faces (Winder &amp;amp; Borrill, 1998). Positive effects on the visuospatial cognitive performance of administration of highly concentrated oxygen resulted from an increase in cerebral activation and a decrease in cerebral lateralization (Chung, Tack, Kim, Lee, &amp;amp; Sohn, 2004). | Not all cognitive measures are improved by oxygen administration. For example, the level of working memory on a computerized test was unaffected by oxygen administration (Moss, Scholey, &amp;amp; Wesnes, 1998; Scholey, Moss, &amp;amp; Wesnes, 1998). Induced hyperoxia had no effect on forward or backward digit span performance (Scholey et al., 1998). Andersson, Berggren, Gronkvist, Magnusson, and Svensson (2002) observed that working memory, long-term memory, and prospective memory were not affected by oxygen inhalation.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read more about that here: &lt;em&gt;Chung, Soon-Cheol, et al. &quot;Effect of 30% oxygen administration on verbal cognitive performance, blood oxygen saturation and heart rate.&quot; Applied psychophysiology and biofeedback 31.4 (2006): 281-293.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And also this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;This study aimed to investigate whether inhalation&#xA;  of the air with 30% oxygen compared with normal air&#xA;  enhances cognitive functioning through increased activation in&#xA;  the brain. The verbal and visuospatial tasks were performed&#xA;  while brain images were scanned. The results showed that&#xA;  there were improvements in performance and also increased&#xA;  activation in several brain areas under the condition of 30%&#xA;  oxygen. These results suggest that a higher concentration of&#xA;  the inhaled oxygen increases the saturation of the blood&#xA;  oxygen in the brain, and facilitates cognitive performance. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Taken from: &lt;em&gt;Sohn, Jin-Hun, Soon-Cheol Chung, and Eun-Hye Jang. &quot;30% oxygen inhalation enhances cognitive performance through robust activation in the brain.&quot; Journal of physiological anthropology and applied human science 24.1 (2005): 51-53.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though you have to be a bit careful about oxygen poisoning.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;While oxygen is an essential component for living organisms, the&#xA;  formation of reactive O&lt;sub&gt;2&lt;/sub&gt; intermediates is commonplace in aerobically&#xA;  metabolizing cells. The stability of a variety of reactive O&lt;sub&gt;2&lt;/sub&gt;&#xA;  intermediates varies, but in some instances their interaction with the&#xA;  intracellular environment sets the basis for the pathophysiology of&#xA;  several disease states.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Adapted from: &lt;em&gt;Cadenas, Enrique. &quot;Biochemistry of oxygen toxicity.&quot; Annual review of biochemistry 58.1 (1989): 79-110.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/A80B4.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pathophysiological processes are associated with increased levels of&#xA;  hyperoxia-induced reactive O&lt;sub&gt;2&lt;/sub&gt; species (ROS) which may readily react&#xA;  with surrounding biological tissues, damaging lipids, proteins, and&#xA;  nucleic acids. Protective antioxidant defenses can become overwhelmed&#xA;  with ROS leading to oxidative stress.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The continuous exposure of newborn rats to 70–80 per cent oxygen at atmospheric pressure throughout the first 9 days of life significantly inhibited the growth of the brain which normally occurs during this period of life. The accumulations of DNA, RNA, total protein, and proteolipid protein which accompany brain growth during this period were all approximately proportionately depressed by the oxygen-enriched atmosphere. RNA/DNA and protein/DNA ratios were unaffected. The increase in brain mass in the first week of life reflects mainly cell proliferation, and since the decreased DNA accumulation occurred with no changes in RNA/DNA and protein/DNA ratios, we conclude that the effect of oxygen was to inhibit cellular division. We estimate that the oxygen exposure caused an approximately 7 per cent deficit in the cell population of the brain. These results indicate that the use of elevated concentrations of oxygen may have serious deleterious effects on the growth and development of the brain.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Taken from:* Grave, G. D., C. Kennedy, and L. Sokoloff. &quot;Impairment of growth and development of the rat brain by hyperoxia at atmospheric pressure.&quot; Journal of neurochemistry 19.1 (1972): 187-194.*&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also hydrogen peroxide is  produced:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Thus the H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; concentration in brains of rats exposed to room air is calculated to be about 7.7 pM, rises 60% when O&lt;sub&gt;2&lt;/sub&gt; tension is increased to 100% O&lt;sub&gt;2&lt;/sub&gt;, and increases 300% at 3 ATA 100% O&lt;sub&gt;2&lt;/sub&gt;, where symptoms of central nervous system toxicity first become apparent. These studies support the concept that H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; is an important mediator of O&lt;sub&gt;2&lt;/sub&gt;-induced injury to the central nervous system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Taken from: &lt;em&gt;Yusa, T. O. S. H. I. K. O., et al. &quot;Hyperoxia increases H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; production by brain in vivo.&quot; Journal of Applied Physiology 63.1 (1987): 353-358.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also always read the wiki page for oxygen poisoning: &lt;a href=&quot;http://en.wikipedia.org/wiki/Oxygen_toxicity&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Oxygen_toxicity&lt;/a&gt; and also hyperoxia itself: &lt;a href=&quot;http://en.wikipedia.org/wiki/Hyperoxia&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Hyperoxia&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="28834" LastEditDate="2020-02-03T14:14:13.207" LastActivityDate="2020-02-03T14:14:13.207" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="33019" PostTypeId="1" AcceptedAnswerId="41801" CreationDate="2015-05-05T11:08:39.017" Score="2" ViewCount="886" Body="&lt;p&gt;I understand that the majority of doctors consider the TSH test &quot;the gold standard&quot; for measuring thyroid function (examples stating that literally are &lt;a href=&quot;http://csinternalmed.com/?go=lab&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://www.thyroid.ca/Abbott/AB_810-10_Thyroid%20Disorders_E04.pdf&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reference range for what is a healthy TSH is under debate, but no matter what range is considered there tends to be a proportionately large difference between the top and bottom (eg &lt;a href=&quot;http://en.wikipedia.org/wiki/Thyroid-stimulating_hormone#Monitoring&quot; rel=&quot;nofollow&quot;&gt;0.3 to 3.0 μIU/mL&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However I've never seen anything indicating over what range TSH varies over the course of a day, or a few days. It's also unclear as to how much error there tends to be with a test result, even if tested from the same sample.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How much fluctuation in a TSH result is normal over the course of a day?&lt;/p&gt;&#xA;" OwnerUserId="6140" LastActivityDate="2015-12-27T09:34:50.510" Title="Over what range do Thyroid Stimulating Hormone (TSH) levels tend to fluctuate over the course of a day?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="33020" PostTypeId="1" CreationDate="2015-05-05T11:25:00.060" Score="0" ViewCount="323" Body="&lt;p&gt;Given this BLAST output, how can I determine the percentage of the query sequence in the alignment? I know that it's also referred to as 'query cover' but I can't seem to find anything online that tells me how to calculate this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rcSk6.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have given it a go and valued it as 145/147, but I'm not too sure on this. Can anybody clarify whether or not this is correct? Any help is highly appreciated &lt;/p&gt;&#xA;" OwnerUserId="15639" LastActivityDate="2015-05-05T11:25:00.060" Title="Determining the percentage of the query of an alignment from a BLAST output" Tags="&lt;bioinformatics&gt;&lt;sequence-alignment&gt;&lt;blast&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="33021" PostTypeId="1" CreationDate="2015-05-05T11:46:41.860" Score="3" ViewCount="342" Body="&lt;p&gt;We are studing in class the reproduction of plants.&#xA;We start the lesson by observing some components of flowers, it was the &lt;strong&gt;Géranium&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all we start counting the number of &lt;strong&gt;sepals&lt;/strong&gt; , &lt;strong&gt;petals&lt;/strong&gt; and &lt;strong&gt;stamens&lt;/strong&gt;.&#xA;The problem is that I found:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5 sepals &lt;/p&gt;&#xA;&#xA;&lt;p&gt;5 petals &lt;/p&gt;&#xA;&#xA;&lt;p&gt;9 stamens &lt;/p&gt;&#xA;&#xA;&lt;p&gt;and every other student found that the number of stamens was 9 or 8 or 10.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I asked my teacher and he says that he counted the number of stamens many times and he found 9.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it really 9? Do the number of stamens is depending of the number of sepals or petals? Is there any relation ?&lt;/p&gt;&#xA;" OwnerUserId="15640" LastEditorUserId="460" LastEditDate="2015-05-05T17:14:31.560" LastActivityDate="2015-05-05T17:14:31.560" Title="Is the number of stamens always 9 for geranium?" Tags="&lt;botany&gt;&lt;reproduction&gt;&lt;structural-biology&gt;&lt;flowers&gt;" AnswerCount="0" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="33022" PostTypeId="1" AcceptedAnswerId="33026" CreationDate="2015-05-05T13:27:46.200" Score="1" ViewCount="194" Body="&lt;p&gt;I am writing an English paper wherein I have to appeal for change in the way humans treat wildlife. I was initially given a situation wherein I took a ferry in a certain area and saw a dead baby dolphin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Along the way, I (it is written in second person) apparently notice how little water is now available for the dolphins (due to some bridge being constructed).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What exactly is bad for dolphins (or animals in general) when they have limited space to roam around?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far I thought of dolphins hitting boats due to the crowded state of the area in question.&lt;/p&gt;&#xA;" OwnerUserId="15642" LastActivityDate="2015-05-05T15:37:08.163" Title="Limited space for animals - how is that bad?" Tags="&lt;zoology&gt;&lt;environment&gt;&lt;habitat&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="33023" PostTypeId="1" CreationDate="2015-05-05T13:50:39.917" Score="3" ViewCount="183" Body="&lt;p&gt;I have read two papers related to modeling neurons. The first one is the paper by &lt;a href=&quot;http://www.caam.rice.edu/~cox/neuro/pinskyrinzel.pdf&quot; rel=&quot;nofollow&quot;&gt;Pinsky and Rinzel&lt;/a&gt; and the second one by &lt;a href=&quot;http://www.cns.nyu.edu/wanglab/publications/pdf/wang_buzaski1996.pdf&quot; rel=&quot;nofollow&quot;&gt;Wang and Buzsaki&lt;/a&gt;. The first mentioned neuron model is a excitatory neuron based on NMDA and AMPA neurotransmitters. The second one is inhibitory neuron model based on GABA. So I modeled them individually. Now trying to couple such that pre synaptic PR neuron will connect to post synaptic WB neuron which also connects to PR neuron. That is in effect an excitatory-inhibitory coupling with feedback. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Now how would the action potentials of both neuron look like?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Will both oscillate, or only WB neuron alone oscillate? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is there any specific conditions for the oscillations to occur? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Any speculations, ideas, references (like books, related papers) would be helpful.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;NOTE : By action potentials, I mean the neuronal membrane voltage signal which varies with time.&lt;/p&gt;&#xA;" OwnerUserId="5669" LastEditorUserId="5669" LastEditDate="2015-05-06T03:45:50.850" LastActivityDate="2017-01-21T20:15:18.750" Title="Neural coupling between Pinsky-Rinzel (reduced Traub) neuron with a Wang-Buzsaki neuron?" Tags="&lt;neuroscience&gt;&lt;computational-model&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="33025" PostTypeId="2" ParentId="33014" CreationDate="2015-05-05T15:16:21.777" Score="1" Body="&lt;p&gt;One of the main contributors to inbreeding depression are &lt;a href=&quot;http://en.wikipedia.org/wiki/Lethal_allele&quot; rel=&quot;nofollow&quot;&gt;recessive lethal&lt;/a&gt; alleles. Suppose you have an individual who has the genotype Aa, where A is the dominant, non-lethal allele and a is the recessive lethal allele. This recessive lethal allele is likely very rare in the population (selection would decrease the frequency of a recessive lethal allele), so our Aa individual can breed with almost any individual without consequence because most other individuals are AA, so the offspring of this individual will be either Aa or AA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if the Aa individual breeds with itself or with a close relative who has the Aa genotype, its offspring will have a chance of inheriting the two aa alleles, which is lethal, decreasing the fitness of the Aa individual that bred with itself (or a close relative). This decrease of fitness resulting from self-breeding will cause selective pressure to outcross instead of self.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important to note that the recessive allele doesn't need to be strictly lethal for this effect to happen - if the recessive allele causes infertility (for isntance, failure to produce gametes or something similar) the same effect will happen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, inbreeding can cause detrimental recessive alleles to become paired, causing lethality or infertility.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-05-05T15:16:21.777" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="33026" PostTypeId="2" ParentId="33022" CreationDate="2015-05-05T15:37:08.163" Score="2" Body="&lt;p&gt;The building of a bridge on a river seems like an example of &lt;a href=&quot;http://en.wikipedia.org/wiki/Habitat_fragmentation&quot; rel=&quot;nofollow&quot;&gt;habitat fragmentation&lt;/a&gt;. There are a number of reasons why this may be detrimental to the animals.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Reduced resources available. I'm not too familiar with dolphins, but all animals need food, shelter and a place to raise their young. A smaller habitat can't support as many animals due to limited resources.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Isolation from other habitats. The bridge may cut off the dolphins on one side of the bridge from the other side, meaning they can't mate with dolphins on the other side or migrate. The fact that dolphins on one side of the bridge can only mate with the other dolphins that share that size causes a decrease in the &lt;a href=&quot;http://en.wikipedia.org/wiki/Genetic_variability&quot; rel=&quot;nofollow&quot;&gt;genetic variability&lt;/a&gt; on both sides of the bridge. Decreased genetic variability means an increase in inbreeding depression and reduced ability to adapt to disease and environmental changes.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Edge_effects&quot; rel=&quot;nofollow&quot;&gt;edge effect&lt;/a&gt;. This means that areas next to the edge of the habitat (i.e. next to the bridge) will be even less suitable than they were before&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-05-05T15:37:08.163" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="33027" PostTypeId="1" CreationDate="2015-05-05T17:10:20.993" Score="1" ViewCount="153" Body="&lt;p&gt;I just got out of a lecture on mitosis and this part was incredibly confusing. After searching my textbook it doesn't cover it that well either. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The professor mentioned a NUMA protein that is released after NEBD, and that it helps form more Microtubules. I don't really understand how it does this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it just a protein that sits in the pericentriolar matrix and encourages microtubule nucleation? Or is it a a kinase that deactivates some GAPs that destabilize microtubules? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, if you would like, there's also this study question I feel is sort of related: What are two proteins located in the pericentriolar matrix that encourage microtubule nucleation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I feel like one of them is the y-tubulin ring complex. Would the other be NUMA?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for reading. &lt;/p&gt;&#xA;" OwnerUserId="15646" LastActivityDate="2015-05-05T17:10:20.993" Title="What is a &quot;NuMA protein&quot;?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="33028" PostTypeId="1" CreationDate="2015-05-05T17:24:49.207" Score="0" ViewCount="780" Body="&lt;p&gt;What I learned in class:&#xA;Normally chocolate agar is needed to grow &lt;em&gt;Haemophilus&lt;/em&gt; and &lt;em&gt;Neisseria&lt;/em&gt;. The Staph streak technique can be used for culturing &lt;em&gt;Haemophilus&lt;/em&gt; on blood agar by allowing the Staph to hemolyze the blood so &lt;em&gt;Haemophilus&lt;/em&gt; can grow around it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question:&#xA;Is there a reason this method couldn't be used for &lt;em&gt;Neisseria&lt;/em&gt; as well?&lt;/p&gt;&#xA;" OwnerUserId="15647" LastActivityDate="2015-05-06T07:39:24.947" Title="Can the Staph streak method be used for culturing Neisseria on blood agar?" Tags="&lt;microbiology&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="33029" PostTypeId="1" CreationDate="2015-05-05T17:32:14.827" Score="1" ViewCount="708" Body="&lt;p&gt;Is silencer the same as gene silencing?&#xA;I know that gene silencing refers to those heterochromatin concentrated at the telomeres or centromere. It is also related to methylation. But what about a silencer. Are they the same? Or is silencer an opposite of enhancer (repressor)?&lt;/p&gt;&#xA;" OwnerUserId="15648" LastActivityDate="2015-05-06T09:17:28.673" Title="(Genetics) Is a silencer the same as gene silencing (heterochromatin)?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;genomics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="33030" PostTypeId="2" ParentId="33028" CreationDate="2015-05-05T17:41:10.177" Score="1" Body="&lt;p&gt;It depends on your species of Neisseria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;N. meningitidis&lt;/em&gt; grows on BAP (Blood Agar Plate), with colonies being grey and unpigmented on  appearing round, smooth, moist, glistening, and convex, with a clearly defined edge&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read more about that &lt;a href=&quot;http://www.cdc.gov/meningitis/lab-manual/chpt07-id-characterization-nm.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/a63eu.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;N. gonorrhoeae&lt;/em&gt; is known not to grow on BAP.&#xA;More on that &lt;a href=&quot;http://www.microbiologyinpictures.com/neisseria%20gonorrhoeae.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-06T07:39:24.947" LastActivityDate="2015-05-06T07:39:24.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="33031" PostTypeId="2" ParentId="33029" CreationDate="2015-05-05T17:57:47.413" Score="2" Body="&lt;p&gt;You are a bit confused with your terms here. Remember, when you are talking about natural regulation of a transcriptome, you can control it at the level of the genome, transcriptome and the epigenome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The Repressor protein&lt;/strong&gt; is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator or associated silencers. Depending on where it binds, it regulates at the level of the genome or transcriptome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The Gene Silencer Region&lt;/strong&gt;, is a DNA sequence in the geneome that  that allows repressor proteins to bind to it. It is usually very near the promoter of the gene that it wants to control. This controls the expression of the gene at the level of the genome to repress the transcription of the gene. There exists a few types (Classc silencers, negative regulators and polycomb response) but lets not get into that). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example is the regulatory element in the classical Lac operon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1qSNL.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Gene Silencing&lt;/strong&gt; as you call it is epigenetic in nature. I'll point you towards the wiki as it is quite big and diverse to explain it here:&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Gene_silencing&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Gene_silencing&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;you can read more about it here:&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK26872/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK26872/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-06T09:17:28.673" LastActivityDate="2015-05-06T09:17:28.673" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="33032" PostTypeId="1" AcceptedAnswerId="41133" CreationDate="2015-05-05T18:12:38.300" Score="12" ViewCount="454" Body="&lt;p&gt;I experience big discrepancies when calculating &lt;strong&gt;&lt;em&gt;melting temperature&lt;/em&gt;&lt;/strong&gt; of &lt;strong&gt;RNA 7-mers&lt;/strong&gt; with Biopython over values generated by a popular algorithm. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried the nearest neighbour algorithm with RNA and salt concentrations as described in a respective paper (thermodynamic table used as in paper below from: &lt;em&gt;Freier et al 1986&lt;/em&gt;). Yet, the values largely differ (execute code below to see).&#xA;I tried all seven salt correction methods provided by Biopython, still I never get close to the values generated by siRNA design algorithm for the same 7-mers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone tell me how accurate Biopython's melting temperature nearest neighbour algorithm is? Especially for short oligomers like my 7-mers? Is there maybe something I am implementing wrong? Any suggestions?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Values derived from executing &lt;strong&gt;sample input&lt;/strong&gt;:&#xA;&lt;a href=&quot;http://sidirect2.rnai.jp/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://sidirect2.rnai.jp/&lt;/a&gt;&#xA;Tm is given for the seed duplex of the &lt;em&gt;guide strand&lt;/em&gt;: &lt;strong&gt;bases 2-7&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Literature:&lt;/strong&gt;&#xA;&quot;&lt;em&gt;Thermodynamic  stability  and  Watson–Crick&#xA;base  pairing  in  the  seed  duplex  are  major&#xA;determinants  of  the  efficiency  of  the&#xA;siRNA-based  off-target  effect&lt;/em&gt;&quot;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602766/pdf/gkn902.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602766/pdf/gkn902.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;from Bio.Seq import Seq  &#xA;from Bio.SeqUtils import MeltingTemp&#xA;&#xA;test_list = [&#xA;('GGAUUUG', 21.5),&#xA;('CUCAUUG', 18.1),&#xA;('CAUAUUC', 8.7),&#xA;('UUUGAGU', 19.2),&#xA;('UUUUGAG', 12.2),&#xA;('GUUUCAA', 14.9),&#xA;('AGUUUCG', 19.7),&#xA;('GAAGUUU', 13.3)&#xA;]&#xA;&#xA;&#xA;for t in test_list:&#xA;    myseq = Seq(t[0])&#xA;    tm = MeltingTemp.Tm_NN(myseq, dnac1=100, Na=100,   nn_table=MeltingTemp.RNA_NN1, saltcorr=7)  # NN1 = Freier et al (1986)&#xA;    tm = round(tm, 1)  # round to one decimal&#xA;    print 'BioPython Tm: ' + str(tm) + '  siDirect Tm: ' + str(t[1])&#xA;&#xA;&#xA;# Output:&#xA;&amp;gt;&amp;gt;&amp;gt; BioPython Tm: 10.1  siDirect Tm: 21.5  # GGAUUUG&#xA;&amp;gt;&amp;gt;&amp;gt; BioPython Tm: 8.2  siDirect Tm: 18.1   # CUCAUUG&#xA;&amp;gt;&amp;gt;&amp;gt; BioPython Tm: -2.0  siDirect Tm: 8.7   # CAUAUUC&#xA;&amp;gt;&amp;gt;&amp;gt; BioPython Tm: 8.2  siDirect Tm: 19.2   # UUUGAGU&#xA;&amp;gt;&amp;gt;&amp;gt; BioPython Tm: 1.3  siDirect Tm: 12.2   # UUUUGAG&#xA;&amp;gt;&amp;gt;&amp;gt; BioPython Tm: 4.4  siDirect Tm: 14.9   # GUUUCAA&#xA;&amp;gt;&amp;gt;&amp;gt; BioPython Tm: 9.0  siDirect Tm: 19.7   # AGUUUCG&#xA;&amp;gt;&amp;gt;&amp;gt; BioPython Tm: 2.1  siDirect Tm: 13.3   # GAAGUUU&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Question first asked at stack-exchange: &lt;a href=&quot;https://stackoverflow.com/questions/30037939/biopython-big-discrepancy-calculating-rna-melting-temperature-over-literature&quot;&gt;https://stackoverflow.com/questions/30037939/biopython-big-discrepancy-calculating-rna-melting-temperature-over-literature&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15650" LastEditorUserId="-1" LastEditDate="2017-05-23T12:35:01.883" LastActivityDate="2015-12-01T02:07:14.407" Title="Biopython - Big Discrepancy Calculating RNA melting Temperature over Literature" Tags="&lt;bioinformatics&gt;&lt;rna&gt;&lt;temperature&gt;&lt;biopython&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="33034" PostTypeId="2" ParentId="33011" CreationDate="2015-05-05T18:25:54.190" Score="1" Body="&lt;p&gt;&lt;strong&gt;Hypothesis testing in evolutionary biology&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pretty much any paper of empirical evolutionary biology tests hypothesis. If you go on google scholar and look for any empirical paper in the field of evolutionary biology such as &quot;does sexual selection has antagonist effect to natural selection&quot;, &quot;evolution of range limits&quot;, &quot;evolution of mutational robustness&quot; or &quot;sensory drive speciation&quot; you will find tons of papers that test hypotheses. Many of these hypotheses have been developed either in pure theory papers on in papers that mix some level of theory (no necessary need of complicated modelling) and empirical work. There is nothing in evolutionary biology that is different from the other field of biology or the other fields of science in our ability to test hypotheses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;A tiny bit of history&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the first half of the century most work in evolutionary biology was theoretic. Many hypotheses were left untested. Today, we perform lots of tests and the technics of molecular genetics (sequencing and stuff) help a lot to test hypotheses. Some papers, indeed uses metrics that are very hard to estimate, eventually too hard (too expensive) to be estimated today, it is true and it is an issue, an issue that all sciences know of. We sometimes have to wait for technical advancements before being able to test a hypothesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Concerning the paper you mention&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From your description of the work they performed in the paper you linked (I haven't read this paper) it sounds like they are describing the concept of &lt;a href=&quot;http://en.wikipedia.org/wiki/Shifting_balance_theory&quot; rel=&quot;nofollow&quot;&gt;shifting balance theory&lt;/a&gt;, a process that has been first hypothesize by S. Wrigth in 1932. As said on the wiki article, there is little empirical evidence for shifting balance theory (but you may want to read &lt;a href=&quot;http://www.sciencemag.org/content/253/5023/1015.short&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; and &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.0014-3820.2000.tb00033.x/abstract&quot; rel=&quot;nofollow&quot;&gt;that&lt;/a&gt;). The reason is that shifting balance theory is link to the concept of &lt;a href=&quot;http://en.wikipedia.org/wiki/Fitness_landscape&quot; rel=&quot;nofollow&quot;&gt;adaptive landscape&lt;/a&gt;. Adaptive landscape is what we call the relationship between fitness and phenotype or fitness and genotype. We have descriptions of fitness-phenotype relationship but we are only starting to offer good and complete descriptions fitness-phenotype-genotype relationship. Understanding the link between genotype and fitness is essential for testing shifting balance theory. Shifting balance theory is a logical consequence of the process of drift and selection, both of which are very well known (and well tested). Most of the issue is in the description of how rough is the fitness landscape to know whether shifting balance theory is indeed a thing that occurs in nature or whether it is very unlikely of such process to ever occur.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-05-06T14:42:37.990" LastActivityDate="2015-05-06T14:42:37.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="33036" PostTypeId="2" ParentId="7596" CreationDate="2015-05-05T19:20:05.900" Score="-1" Body="&lt;p&gt;I have used both Gibson assembly (what you mean by assembly?) and LCR as replacements for blunt or sticky ended cloning. LCR has, for me, worked better in that a higher proportion of constructs that come out have been assembled correctly and I have noticed no mutations after LCR while I have seen them somewhat often with Gibson.&lt;/p&gt;&#xA;" OwnerUserId="15651" LastActivityDate="2015-05-05T19:20:05.900" CommentCount="2" CommunityOwnedDate="2015-08-05T12:13:58.883" ContentLicense="CC BY-SA 3.0" />
  <row Id="33037" PostTypeId="1" AcceptedAnswerId="34630" CreationDate="2015-05-05T20:38:36.160" Score="1" ViewCount="170" Body="&lt;p&gt;In &amp;quot;&lt;a href=&quot;https://biology.stackexchange.com/questions/7703/least-painful-way-to-die&quot;&gt;Least painful way to die&lt;/a&gt;&amp;quot; we get an answer ...&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Companion animals (e.g., dogs and cats): injected barbiturates are recommended&lt;/p&gt;&#xA;&lt;p&gt;Laboratory animals (e.g., mice and rats): injected barbiturates are acceptable as are inhaled agents (isoflurane, carbon dioxide).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;And assume the butcher guy as soon as he comes to know the animal is gone, he will do the following....&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;A very sharp knife is used in this process: the point of the knife cuts into the animal's throat and cuts through the dewlap, trachea, esophagus and jugular vein immediately below the jaw-line to allow the blood to flow out.........Animals are bled out before being dressed because it prevents blood from coagulating in the tissues and thus making the meat go rancid. (Source &lt;a href=&quot;http://www.wikihow.com/Slaughter-Cattle&quot; rel=&quot;nofollow noreferrer&quot;&gt;Slaughter Cattle&lt;/a&gt; commercial method - Step 6)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Here's my question... What if the animal was killed using 'barbiturates', then is that animal safe for eating by humans or the high levels of 'barbiturates' in that body cause unwanted results in humans too (if they consume it)?&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;I'm new to biology. :)&lt;/p&gt;&#xA;" OwnerUserId="16367" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-05-28T08:03:38.370" Title="Consuming animals by slaughtering vs injecting barbiturates?" Tags="&lt;zoology&gt;&lt;pharmacology&gt;&lt;hematology&gt;" AnswerCount="1" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="34037" PostTypeId="2" ParentId="30551" CreationDate="2015-05-05T23:13:52.137" Score="0" Body="&lt;p&gt;Higher predators usually have the eyes in front of their head to see stereoscopically and judge distance visually. Prey usually has eyes on the side of the head to visually analyze the most possible area, giving up stereoscopic distance information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This puts human in the predator, carnivorous category. That being said, I am not sure that it is used by animals to judge unknown species.&lt;/p&gt;&#xA;" OwnerUserId="10118" LastActivityDate="2015-05-05T23:13:52.137" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34038" PostTypeId="2" ParentId="17327" CreationDate="2015-05-05T23:20:47.520" Score="2" Body="&lt;p&gt;Tetrahymena thermophila is an organism with 7 different &quot;fuzzy&quot; genders, not only male and female. Its seven sexes are rather prosaically named I, II, III, IV, V, VI and VII. An individual of a given sex can mate with individuals of any except its own, so there are 21 possible orientations. Here is the link: &lt;a href=&quot;http://www.newscientist.com/article/dn20191-zoologger-the-hairy-beast-with-seven-fuzzy-sexes.html&quot; rel=&quot;nofollow&quot;&gt;Zoologger: The hairy beast with seven fuzzy sexes&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10118" LastActivityDate="2015-05-05T23:20:47.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34039" PostTypeId="2" ParentId="2348" CreationDate="2015-05-05T23:25:27.863" Score="0" Body="&lt;p&gt;Often, they do fuse together but the chromosome pairing is not precise enough to guarantee faithful cell division without loss of genetic material. Consider for example a simple inversion of one large part of a chromosome. In a closely related species that does not have this inversion, either the inverted part pairs or the non-inverted ends pair, but never the whole chromosome. That leads to strand-breaks and loss of large amounts of genetic material. That's an easy event for speciation, since it does not disrupt much. Only the ends where the inverted piece joins has two disruption. So, maximally two genes might be broken, but the chromosomes modified in this way won't pair.&lt;/p&gt;&#xA;" OwnerUserId="10118" LastActivityDate="2015-05-05T23:25:27.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34042" PostTypeId="1" CreationDate="2015-05-06T01:55:59.270" Score="0" ViewCount="55" Body="&lt;p&gt;I remember reading about artificial or man-made, oxygen-transport protein that is somehow an improvement on hemoglobin, and that it is possibly immune to sickle-cell anemia, or something... But I forgot where I found it and what exactly it is...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you guys help me find it?&lt;/p&gt;&#xA;" OwnerUserId="15225" LastActivityDate="2015-05-06T01:55:59.270" Title="Some kind of better oxygen-transport protein or something... Can you help me find it?" Tags="&lt;hematology&gt;&lt;synthetic-biology&gt;&lt;red-blood-cell&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34043" PostTypeId="1" CreationDate="2015-05-06T06:36:19.967" Score="5" ViewCount="217" Body="&lt;p&gt;I see a lot of studies on GWAS not filter out for linkage disequilibrium or even make the slightest mention of it. Why is this the case? I would imagine that you want to keep SNPs that are only in linkage equilibrium to promote independence (and besides, without it an additive model makes no sense)&lt;/p&gt;&#xA;" OwnerUserId="15655" LastActivityDate="2019-03-19T15:53:23.803" Title="Linkage Disequilibrium in GWAS" Tags="&lt;gwas&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34044" PostTypeId="1" AcceptedAnswerId="34050" CreationDate="2015-05-06T09:30:43.333" Score="2" ViewCount="3828" Body="&lt;p&gt;I'm a bit curious as to how frame-shift mutation works. If you shift one amino acid towards another. How does this not affect the entire chromosome? Wouldn't this mean that the organism would be absolutely &quot;scrambled&quot; as it would essentially be &quot;missing&quot; a whole chromosome...Or having a chromosome that did all kinds of wrong things at least?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="6576" LastEditDate="2015-05-06T09:40:34.257" LastActivityDate="2015-05-06T22:36:58.473" Title="How does frame-shift mutation not absolutely ruin the organism?" Tags="&lt;human-biology&gt;&lt;genetics&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34045" PostTypeId="1" AcceptedAnswerId="34052" CreationDate="2015-05-06T10:25:55.227" Score="4" ViewCount="2510" Body="&lt;p&gt;Someone from my lab put the box of antibodies in the freezer instead the fridge.  Can I hope that they will still work?&lt;/p&gt;&#xA;" OwnerUserId="15123" LastEditorUserId="3624" LastEditDate="2015-05-11T11:18:00.590" LastActivityDate="2015-05-11T11:18:00.590" Title="Antibodies stored in freezer instead of fridge" Tags="&lt;antibody&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34047" PostTypeId="2" ParentId="33006" CreationDate="2015-05-06T10:35:41.217" Score="-2" Body="&lt;p&gt;Animals can hurt themselves to save their life for example foxes and tigers falling in traps are known to chew their paws to escape from the trap. Thus one can argue that all living creatures want to live and to escape death as well as losing freedom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;looking at how animals live, an animal can always use its capabilities to escape danger or problems as well as to look for food for survival. In humans who commit suicide sometimes it is because  there is no &quot;exit&quot;. for example some people commit suicide due to being unable to pay their loans it is the feeling of distress losing all hope and the fact that it is hard to escape from problems in a human society that lead to this thinking.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;so a person doing so is trying to escape the problems instead of facing them. further, the fact that humans have the concept of &quot;responsibility&quot; and being held accountable by members of the society all these lead to this thinking as the only escape&lt;/p&gt;&#xA;" OwnerUserId="14624" LastActivityDate="2015-05-06T10:35:41.217" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34048" PostTypeId="1" CreationDate="2015-05-06T10:47:05.977" Score="1" ViewCount="66" Body="&lt;p&gt;If HATs are destroyed in a eukaryotic cell, how will gene expression level be affected? Will all gene expression be affected or just be slowed down and most gene will still be expressed?&lt;/p&gt;&#xA;" OwnerUserId="15648" LastActivityDate="2015-05-06T10:47:05.977" Title="What will happen to transcription if histone acetyltransferases are removed from a eukaryotic cell?" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34049" PostTypeId="2" ParentId="34044" CreationDate="2015-05-06T11:46:27.100" Score="4" Body="&lt;p&gt;First of all, for a frame shift mutation to occur nucleotides (not amino acids) are either deleted or inserted into the sequence.  Read about &lt;a href=&quot;http://en.wikipedia.org/wiki/Frameshift_mutation&quot; rel=&quot;nofollow noreferrer&quot;&gt;details&lt;/a&gt; on this wiki page. Here's an image about frame shifts. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On panel A a new stop codon is formed  (TAG is trasncribed to UAG that is serves as stop codon during translation) thus the result is an abnormally short protein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On panel B the codon 37 is swapped to a G thus the TA from the codon 38 is shifted left by two resulting in the new codon GTA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On panel C exactly 3 nuleotides are deleted thus codon boundaries do not change, but a codon and the amino acid encoded by it is completely deleted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On panel D 4 bases are deleted thus the T form codon 171 and the C from 172 are merged with the G from 170.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qgAX4.jpg&quot; alt=&quot;frameshift&quot;&gt;&#xA;source: the linked wiki page.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It does not affect the choromosome in the way you describe because genes are separated and are independently transcribed (with some simplification). Every gene has its own translation  start that determines the correct frame in that gene If you think of a chormosome as a chapter of a book and the genes are paragraphs, you can see that deleting letters or words may scrable one paragraph, but the others are not affected by this because they have their own boundaries.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&#xA;During translation the ribosome reads the mRNA in the form of triplets. When a single nucleotide is deleted then the whole sequence from that point shifts to the left by one thus the first letter of the subsequent triplet gets mixed into the frame where the mutation happened (the same goes for insertion but the sequence is shifted to the right). This causes the change in the meaning of the triplet, and can ruin stop codons that would affect the translation of the mRNA but not the transcription of the gene to mRNA.It is important to understand that transcription is a countinous process and the DNA is transcribed from base to base not in triplets, and that transcriptions stop is not encoded in the from of stop codon.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-05-06T20:05:06.817" LastActivityDate="2015-05-06T20:05:06.817" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34050" PostTypeId="2" ParentId="34044" CreationDate="2015-05-06T13:47:51.120" Score="4" Body="&lt;p&gt;For transcription, the cell uses different signals from start- or stop- codons to determine the start and end of a transcript (see this &lt;a href=&quot;http://en.wikipedia.org/wiki/Transcription_%28genetics%29#Major_steps&quot; rel=&quot;nofollow&quot;&gt;wiki page&lt;/a&gt;). Codons (and hence frameshifts) are only relevant at translation of the mRNA to protein. Frameshift mutations occur in coding sequence, so the promoter and termination signals for transcription are unaffected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genes which are further downstream will be transcribed normally from their own promoter and their coding sequence is still in-frame with their &lt;b&gt;own&lt;/b&gt; start-codon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When a frameshift occurs in coding sequence, the genetic code downstream can indeed be considered 'scrambled', much alike random nucleotide sequence. In random sequence, three nucleotides have a 3/64 chance of being a stop codon. So one would not expect translation to go on beyond about 20 amino acids from the mutation. Additionally, &lt;a href=&quot;http://en.wikipedia.org/wiki/Nonsense-mediated_decay&quot; rel=&quot;nofollow&quot;&gt;non-sense mediated mRNA decay&lt;/a&gt; will detect these premature stop codons and destroy the mRNA.&lt;/p&gt;&#xA;" OwnerUserId="14698" LastActivityDate="2015-05-06T13:47:51.120" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34051" PostTypeId="2" ParentId="34045" CreationDate="2015-05-06T14:55:11.230" Score="4" Body="&lt;p&gt;You don't specify which temperature of freezer you're talking about. Antibody can be stored at -80 for long time, but needs to avoid freeze and thaw process. Some people store aliquot of antibody in -80. Another way is to dilute antibody in Glycerol, make 50% dilution. You need to mix well, and then store at -20. &lt;/p&gt;&#xA;" OwnerUserId="1141" LastActivityDate="2015-05-06T14:55:11.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34052" PostTypeId="2" ParentId="34045" CreationDate="2015-05-06T16:35:10.263" Score="5" Body="&lt;p&gt;Most IgGs should be fine when stored in the freezer.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Freezing at -20 or -80 in small aliquots is the optimal storage&#xA;  condition. Ali-quoting minimizes damage due to freezing and thawing,&#xA;  as well as contamination introduced by pipetting from a single vial&#xA;  multiple times. Aliquots are to be frozen and thawed once, with any&#xA;  remainder kept at 4 degrees C.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Enzyme-conjugated antibodies, should not be frozen at all and should&#xA;  instead be kept at 4 degrees C. Freezing and thawing will reduce&#xA;  enzymatic activity in addition to affecting the antibody binding&#xA;  capacity. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Antibodies of the IgG3 isotype are unique in their tendency to form&#xA;  aggregates upon thawing and should always be stored at 4 degrees C&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Personally, I store antibodies I use at -20 (they are in PBS), and they work fine for the first freeze thaw cycle. I have never tried more than one freeze thaw, so cant comment on that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.abcam.com/ps/pdf/protocols/antibody_storage.pdf&quot;&gt;http://www.abcam.com/ps/pdf/protocols/antibody_storage.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastActivityDate="2015-05-06T16:35:10.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34053" PostTypeId="2" ParentId="34044" CreationDate="2015-05-06T18:28:14.963" Score="2" Body="&lt;p&gt;No, it wouldn't. In order to understand why, you must understand that&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Genes are translated independently of one another. The &lt;a href=&quot;https://en.wikipedia.org/wiki/Ribosome&quot; rel=&quot;nofollow&quot;&gt;ribosome&lt;/a&gt; starts translating at a start codon (ATG) and stops at one of the three stop codons (TAG,TAA and TGA). Whether another gene has a frameshift mutation or not, does not affect the current gene in any way. The ribosome will always&lt;sup&gt;1&lt;/sup&gt; start at the ATG and stop at the STOP codon.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Genes make up only a tiny portion of the total DNA, especially in eukaryotic organisms. In humans, for example, genes are ~5% of the total DNA. &#xA;The vast majority of DNA falls in intergenic regions that do not code for protein. For example:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;  gene1             INTERGENIC REGION               gene2&#xA;---------|----------------------------------------|---------&#xA;ATGCCGTAGgcgtatagcgatatcgcatcgctatcgatacgctdcggcgcgATGCACTGA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;While a frameshift might throw the first gene out of sync, the second will not be affected. The intergenic regions are not translated, so frameshifts are irrelevant to them. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So, a frameshift will only affect the gene it occurs in. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt; There are some exceptions to this, some alternative start codons but they are not really relevant to the discussion here.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2015-05-06T22:36:58.473" LastActivityDate="2015-05-06T22:36:58.473" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34054" PostTypeId="2" ParentId="33008" CreationDate="2015-05-06T19:09:32.170" Score="1" Body="&lt;p&gt;Macrophages take up pathogens to present them to other specific immune cells. The things they take up via phagocytosis have specific markers on them called PAMPs (Pathogen Associated Molecular Patterns). Hence they won't phagocytose locally injected substances (until and unless it has a PAMP like region).&lt;/p&gt;&#xA;" OwnerUserId="11716" LastActivityDate="2015-05-06T19:09:32.170" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34055" PostTypeId="5" CreationDate="2015-05-06T19:59:57.940" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2015-05-06T19:59:57.940" LastActivityDate="2015-05-06T19:59:57.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34056" PostTypeId="4" CreationDate="2015-05-06T19:59:57.940" Score="0" Body="Questions related to the study of the distributions and changes of allele frequency in a population." OwnerDisplayName="user15629" LastEditorDisplayName="user15629" LastEditDate="2015-05-06T21:13:51.070" LastActivityDate="2015-05-06T21:13:51.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34057" PostTypeId="1" AcceptedAnswerId="34060" CreationDate="2015-05-06T21:28:52.073" Score="0" ViewCount="950" Body="&lt;p&gt;Genetic testing revealed these two mutations (hypothetically):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;IVS11+6G&gt;A and IVS11-4G＞A &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could you please explain every part of this notation, especially &quot;+&quot; and &quot;-&quot; signs. &lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-05-06T23:25:01.930" Title="Genetic notations" Tags="&lt;genetics&gt;&lt;mutations&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34060" PostTypeId="2" ParentId="34057" CreationDate="2015-05-06T23:07:14.573" Score="1" Body="&lt;p&gt;These describe mutations (SNPs) in introns. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;IVS stands for intervening sequence (which is another term for intron).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The number following IVS specifies which intron the mutation occurs in (intron 1 follows exon 1, etc). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The +n or -n, where n is an integer, gives the location of the nucleotide. +n counts 3' from the preceding exon whereas -n counts 5' from the following exon. I &lt;em&gt;think&lt;/em&gt; that the first and last nucleotide of each exon is given position 0 such that, for example, +1 refers to the first nucleotide of the intron and -1 refers to the last.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;X&gt;Y, where X and Y are nucleotides, describe what mutation has occurred. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;IVS11+6G&gt;A means a G to A transition at position +6 of intron 11&lt;/p&gt;&#xA;&#xA;&lt;p&gt;IVS11-4G＞A means a G to A transition at position -4 of intron 11&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-05-06T23:25:01.930" LastActivityDate="2015-05-06T23:25:01.930" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34062" PostTypeId="1" AcceptedAnswerId="34199" CreationDate="2015-05-07T05:13:46.427" Score="9" ViewCount="3910" Body="&lt;p&gt;Why have the eye and CNS have &lt;a href=&quot;http://en.wikipedia.org/wiki/Immune_privilege&quot; rel=&quot;nofollow&quot;&gt;immune privilege&lt;/a&gt;? Why does the body not develop tolerance against their tissue and instead risk their damage in case an accidental immune cell infiltration?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wiki:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...in immune privileged sites, tissue grafts can survive for extended periods of time without rejection occurring&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="11716" LastEditorUserId="5144" LastEditDate="2015-05-13T06:36:32.677" LastActivityDate="2015-05-13T07:27:10.547" Title="Why some parts of the human body have immune privilege?" Tags="&lt;immunology&gt;&lt;human-physiology&gt;&lt;human-evolution&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34066" PostTypeId="1" AcceptedAnswerId="35078" CreationDate="2015-05-07T13:02:56.817" Score="3" ViewCount="2869" Body="&lt;p&gt;I have attempted a few searches for a list of origins of replication for plasmids in &lt;em&gt;E. coli&lt;/em&gt;, but I was only able to find a list of origins, but not their individual sequences. The available plasmid maps are often extremely vague on where exactly do the origins start or end, and in any case it would be extremely tedious to collate a list of origins in order to determine the exact origin of replication of a plasmid. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a database of origins of replication available anywhere that would allow one to perform BLAST searches on the plasmid sequence in order to obtain the compatability group of the plasmid, in cases where the plasmid's origin of replication is not specified? &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-06-10T04:23:14.937" LastActivityDate="2015-06-10T04:23:14.937" Title="Identifying the origin of replication of an unannotated *E. coli* plasmid" Tags="&lt;bioinformatics&gt;&lt;plasmids&gt;" AnswerCount="4" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34067" PostTypeId="1" CreationDate="2015-05-07T13:19:30.877" Score="2" ViewCount="968" Body="&lt;p&gt;Our courseware materials say there are such fishes, but my Internet searches suggests fishes only have a single circulatory system.&lt;/p&gt;&#xA;" OwnerUserId="9207" LastEditorUserId="6561" LastEditDate="2015-10-12T23:50:14.453" LastActivityDate="2015-10-12T23:50:14.453" Title="Are there fishes with a double circulatory system?" Tags="&lt;physiology&gt;&lt;zoology&gt;&lt;blood-circulation&gt;&lt;ichthyology&gt;&lt;circulatory-system&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34068" PostTypeId="1" AcceptedAnswerId="34072" CreationDate="2015-05-07T13:24:08.730" Score="4" ViewCount="476" Body="&lt;p&gt;I'm about to start a bioinformatics research project but I haven't any biological background.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know my project is in regards to a performance analysis of DNA sequencing and searching &quot;weapons&quot; like Hadoop, Apache Spark and Apache Flink - so I've spent the last couple of days trying to put together the &quot;DNA picture&quot; before I get started with the programming stuff.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding of the situation is that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Next-generation sequencing (NGS) techniques are used to efficiently provide reads of DNA (conversions from real, physical DNA to something that can be read and analysed), however today's most practical methods provide reads that are short and in disorder.&lt;/li&gt;&#xA;&lt;li&gt;Reads tell us which nucleotides, labeled one of ACGT, occur in sequence. Different nucleotides or values to take their place may exist, like N or X. Reads could range from 50 to 1000s of nucleotides in length depending on the method of sequencing.&lt;/li&gt;&#xA;&lt;li&gt;You can find historical raw read data in various places online, including the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?&quot; rel=&quot;nofollow&quot;&gt;Sequence Read Archive&lt;/a&gt; (SRA). The same website contains lots of other DNA/bio related information. Reads are commonly stored in .fasta files which follow a simple and practical standard. A single file could contain a very small or very large read or sequence.&lt;/li&gt;&#xA;&lt;li&gt;Reads are then provided to DNA alignment programs like bowtie which will place them back in the correct order. The algorithms could use a template sequence to align them, or run &quot;de novo&quot; (without a template). The result of these alignments have also been indexed online however for the purpose of my studies I'll probably be aligning them myself.&lt;/li&gt;&#xA;&lt;li&gt;Once aligned (or maybe during alignment), nucleotide differences from a template sequence can be programmatically found or searched for, with crossbow for instance. Note that many other tasks can too be performed - not only this search. If a particular substitution occurs in more than 1% of a what I think is called a &quot;genome's&quot; population, then it is called a Single-nucleotide Polymorphism (SNP or snip). Most SNPs have two alleles, or two different recorded nucleotides (like either G or C), but more than two is possible.&lt;/li&gt;&#xA;&lt;li&gt;SNPs can be studied and mapped to various conditions or characteristics. A particular nucleotide could be responsible for part of one's emotional tendencies, reaction to particular medicines, or maybe anything, so a particular SNP could make a big difference.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What am I missing/what did I get wrong?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="15664" LastActivityDate="2015-05-07T18:35:45.450" Title="Trying to understand the big picture behind DNA sequencing, alignment and searching" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;snp&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34070" PostTypeId="2" ParentId="33001" CreationDate="2015-05-07T13:41:26.060" Score="9" Body="&lt;h2&gt;How many recombinations are required to achieve an active virus?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.fda.gov/ohrms/dockets/ac/01/slides/3794s2_02_takefman.ppt&quot; rel=&quot;nofollow noreferrer&quot;&gt;FDA has recognised the likelihood&lt;/a&gt; that lentivectors can be converted into actively replicating lentivirus if they undergo recombination with wild type HIV in a HIV positive patient. In this case, two recombination events are required to transfer the lentivector sequence into the HIV sequence (the mechanism of transfer is identical to the case of first-generation lentivectors).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.vcu.edu/oehs/chemical/biosafe/lentiviralvectors.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;This article from VCU&lt;/a&gt; describes another mechanism through which this can occur in &lt;strong&gt;first generation&lt;/strong&gt; lentivector systems, which consists of two recombination events between the lentivector and the helper plasmid. Note that the 3 genes &lt;em&gt;gag, pol&lt;/em&gt; and &lt;em&gt;env&lt;/em&gt; are present on the same plasmid, and that plasmid is flanked by LTRs. Second generation lentivectors, such as the &lt;a href=&quot;https://www.addgene.org/tools/protocols/pLKO/&quot; rel=&quot;nofollow noreferrer&quot;&gt;pLKO system&lt;/a&gt;, do not suffer from this problem and require wild type HIV to produce actively replicating lentivirus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/d3QsW.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To reduce the likelihood of this happening, second and third-generation lentivector systems split the genes into multiple plasmids, which then requires more recombination events to produce replication competent viruses. Additionally, the polyA tail of the 3' LTR is replaced to reduce likelihood of recombination events occurring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2EJtH.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;https://www.addgene.org/lentiviral/packaging/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Addgene's article on lentivector biosafety&lt;/a&gt;, the gene of interest's transfer plasmid (both 2nd and 3rd generations) has a deletion in the 3' LTR region which prevents it from becoming replicatively active. Therefore, the only likelihood for the recombination to occur is for the cell line expressing the virus to undergo replication with an active, wild-type HIV strain. An example is this &lt;a href=&quot;https://www.addgene.org/10878/&quot; rel=&quot;nofollow noreferrer&quot;&gt;pLKO transfer plasmid&lt;/a&gt;, which contains a truncated 3' LTR, preventing the sequence from replicating outside of &lt;em&gt;E. coli&lt;/em&gt;, which replicates it not using the LTR but instead using the plasmid origin of replication. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Are the active viruses produced by recombinations more dangerous in the wild than wild type HIV?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;This is difficult to answer, since recombination only allows an active virus to form, but it does not guarantee that the virus will be dangerous. Dangerous viruses are theoretically possible, but require far more recombinations than the minimal 2 for replication competency in 2nd generation lentivector systems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, lentivector systems generally do not encode for the viral proteins &lt;em&gt;vpr, vif, nef&lt;/em&gt; and &lt;em&gt;vpu&lt;/em&gt;. These proteins are necessary for increasing the infectivity of HIV in different types of tissues (but not cultured cells such as HEK293). The lack of these proteins in a hypothetical replication competent lentivector would significantly hamper its spread in the wild. Incorporation of these proteins is plausible but extremely unlikely, since more crossover recombination events will be required. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To use your example, the &lt;em&gt;env&lt;/em&gt; protein coding for the VSV protein coat resides in the envelope plasmid. Since the replication competent lentivector formed by 2 recombination events will be a &lt;a href=&quot;http://en.wikipedia.org/wiki/Pseudotyping&quot; rel=&quot;nofollow noreferrer&quot;&gt;pseudotype&lt;/a&gt; containing only the HIV &lt;em&gt;env&lt;/em&gt; proteins, it will need to further acquire the VSV gene to replace its &lt;em&gt;env&lt;/em&gt; proteins, since these genes are not present on the same regions. There is no homology between the two DNA strands, which would significantly hamper the likelihood of the VSV gene somehow being incorporated into active HIV. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The addition of various chimeric proteins and LTR regions in 3rd generation lentivectors only complicates the matter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall, I was unable to find any sources comparing the infectivity of these theoretical transgenic HIV versus the wild type. However, even though it is theoretically possible that a transgenic replication competent lentivector can have better tropism than HIV by acquiring the VSV gene, the likelihood of that occurring is far lower than that of it being produced in the first place. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Can a lentivector be detected by a HIV test?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Regarding the final question of whether a lentivector can be detected by a standard HIV test, the answer is that the detection is possible if the person who was infected with lentivectors, has obtained an immune response to the lentivector gag proteins, and the lentivector loads are high enough. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;HIV tests are specific to different parts of the virus, but &lt;a href=&quot;http://i-base.info/guides/testing/appendix-1-different-types-of-hiv-test&quot; rel=&quot;nofollow noreferrer&quot;&gt;most of them target&lt;/a&gt; the &lt;a href=&quot;http://en.wikipedia.org/wiki/P24_capsid_protein&quot; rel=&quot;nofollow noreferrer&quot;&gt;viral protein p24&lt;/a&gt;, which is a component of the &lt;em&gt;gag&lt;/em&gt; polyprotein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;PCR based HIV tests also exist, but these tests would depend on the specific primers produced and whether the RT-PCR would produce an amplicon given the specific sequence of the plasmids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since gag genes &lt;a href=&quot;https://www.addgene.org/lentiviral/packaging/&quot; rel=&quot;nofollow noreferrer&quot;&gt;are encoded for in most lentivector systems&lt;/a&gt;, it is therefore very likely that anyone infected with a lentivector would therefore express antibodies towards p24, and therefore result in a positive for the ELISA as well as the Western blot tests assuming that the p24 and antibody quantities are high enough to reach the cutoff point. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was unable to find publicly available cutoff levels for the ELISA and Western blot levels, but if (hypothetically speaking) a person was injected with a load of lentivectors, they would likely test positive for HIV. However, since the lentivector is not actively reproducing, it would quickly be cleared out by the immune system. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-05-08T06:01:24.767" LastActivityDate="2015-05-08T06:01:24.767" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="34071" PostTypeId="2" ParentId="34067" CreationDate="2015-05-07T13:47:31.197" Score="2" Body="&lt;p&gt;It seems that lungfish display the beginnings of a double circulatory system:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Lwl8U.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9207" LastActivityDate="2015-05-07T13:47:31.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34072" PostTypeId="2" ParentId="34068" CreationDate="2015-05-07T13:48:53.877" Score="4" Body="&lt;p&gt;Here's a quick summary of a few mis-hits in your otherwise good analysis:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not many bioinformatics applications use Hadoop, Apache Spark or Apache Flink. In fact, I have never heard of the Apache Spark and Flink tools, and I've seen only 2 people use Hadoop to process alignment files.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Reads are not &quot;converted&quot; real, physical DNA. They are representations of the signals from the molecules making up the DNA, as read by sequencing machines.&lt;/li&gt;&#xA;&lt;li&gt;A,T,C,G are molecules making up DNA. N refers to &quot;any of A,T,C,G&quot;, which translates to either unknown or ambiguous.&lt;/li&gt;&#xA;&lt;li&gt;Reads are stored in FASTQ files. Sequences are stored in FASTA files. Reads include sequence as well as quality information, so, FASTA+QUAL=FASTQ&lt;/li&gt;&#xA;&lt;li&gt;Re-ordering is a crude but approximate way to think about it. Remember, this process involves overlaps while reordering seldom does. Overlaps are crucial to the process of assembly/alignment. You are correct about the alignment to reference sequence and de novo assembly parts.&lt;/li&gt;&#xA;&lt;li&gt;This is correct, though statistical models are applied to account for differences that are not necessarily significant variants (such as for sequencing errors)&lt;/li&gt;&#xA;&lt;li&gt;Yes, variants, which include SNPs, can be correlated to differences in phenotype (traits). Emotional tendencies is something a bit too advanced, think of something more basic like diabetes or eye color.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The picture you have here is of a regular NGS analysis pipeline. This involves alignment/assembly, variant calling and biological analysis with relevant hypotheses. The assembly/alignment is the most computationally expensive part, and we use either HPC clusters or scalable cloud services such as AWS to get this done.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should definitely talk to a biologist that has some computational experience to gain insight into the reason behind our analyses. Once you understand the motivations, your contribution will be more relevant and helpful to the community.&lt;/p&gt;&#xA;" OwnerUserId="9665" LastEditorUserId="3340" LastEditDate="2015-05-07T17:53:56.160" LastActivityDate="2015-05-07T17:53:56.160" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34075" PostTypeId="1" AcceptedAnswerId="34076" CreationDate="2015-05-07T16:54:13.040" Score="6" ViewCount="3806" Body="&lt;p&gt;In my AP Biology class, we were taught that action potentials are &lt;em&gt;not&lt;/em&gt; electrical impulses in the same way current travels through a wire. Rather, we were taught that action potentials are changing concentration gradients of sodium and potassium ions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, when I looked into modeling action potentials I saw capacitances, inductances, and currents--properties associated with electrical circuits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question: action potentials--are they electrical currents in the classical sense? If so, what is the charge that is flowing (is sodium and potassium ions?), and how is the overall charge neutrality of the body maintained?&lt;/p&gt;&#xA;" OwnerUserId="15536" LastEditorUserId="9943" LastEditDate="2015-05-08T06:00:32.560" LastActivityDate="2015-05-08T06:00:32.560" Title="How to conceptualize the action potential?" Tags="&lt;biophysics&gt;&lt;neurophysiology&gt;&lt;action-potential&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34076" PostTypeId="2" ParentId="34075" CreationDate="2015-05-07T17:27:49.167" Score="4" Body="&lt;p&gt;First of all, electric current is defined as movement of charges, $I=\frac{dQ}{dt}$. In electronics that you see around that is not very useful definition, because electrons move much slower than signals, that is changing &lt;em&gt;electric field&lt;/em&gt;. Speed of electric field propagation reaches speed of light, whereas &lt;a href=&quot;http://c2.com/cgi/wiki?SpeedOfElectrons&quot; rel=&quot;nofollow&quot;&gt;electrons move&lt;/a&gt; at 1%-30% or $c$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In biology, especially regarding action potential, only movement of charges is important, not propagation of electric field, probably because conductance is much smaller than in copper wires. that is signal propagates not through interaction between charges, but via intermediate agent/amplifier -- ion channels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Charge in body is more or less constant, because action potentials are cyclic: after depolarization membrane comes back to -70mV or something. There is no flow of charge &lt;em&gt;out&lt;/em&gt; of the body.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-05-07T17:27:49.167" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34077" PostTypeId="2" ParentId="34068" CreationDate="2015-05-07T18:35:45.450" Score="3" Body="&lt;p&gt;RAM's answer is very good, I'll just add on the computational side, short reads are error prone.  That's important to account for when aligning or assembling.  The reads themselves can just be inaccurate, which we detect by having multiple reads overlapping by a lot; we assume that stray discrepancies seen in only a single read at a position are errors.  Also, if a reference genome is not quite close enough to the sample, reads might be misaligned.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genomes of many organisms also have repetitive elements which can make it hard to correctly align reads, and hard to make an accurate reference genome.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And note that there can be many more discrepancies other than single nucleotide substitutions, though anything more involved can be challenging to detect with short read data alone.  And most traits that are actually interesting to study are polygenic, so it's not exactly easy to say that one difference in DNA causes a detectable difference in phenotype.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2015-05-07T18:35:45.450" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34079" PostTypeId="1" AcceptedAnswerId="34098" CreationDate="2015-05-07T21:28:38.293" Score="5" ViewCount="585" Body="&lt;p&gt;I have often heard the saying that one shouldn't eat a mountain of food because blood will go to the stomach and it'll be difficult to sleep well because the stomach can't rest at night.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see that the blood goes to the stomach when you eat something to digest the food. Have any studies been done on whether it does actually affect the quality of sleeping?&lt;/p&gt;&#xA;" OwnerUserId="13243" LastEditorUserId="9829" LastEditDate="2015-05-08T19:59:18.937" LastActivityDate="2017-11-23T04:56:04.630" Title="Influence of eating at late night on sleep" Tags="&lt;sleep&gt;&lt;digestive-system&gt;&lt;digestion&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34083" PostTypeId="1" AcceptedAnswerId="34093" CreationDate="2015-05-08T00:37:28.157" Score="0" ViewCount="1614" Body="&lt;p&gt;I received a report that had a mutation notated as: &quot;MAP2K41161fs*12&quot;. I'm used to seeing this sort of thing: BRAF(V600E) or BRAF(T1799TA). Can someone tell me how to interpret &quot;MAP2K41161fs*12&quot; ?? Is it a deletion? An insertion? A translocation? Or What?&lt;/p&gt;&#xA;" OwnerUserId="15671" LastEditorUserId="6307" LastEditDate="2015-05-08T01:05:35.177" LastActivityDate="2015-05-08T16:59:52.217" Title="What does this mutation notation mean: MAP2K41161fs*12" Tags="&lt;mutations&gt;&lt;gene&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34084" PostTypeId="2" ParentId="34075" CreationDate="2015-05-08T05:32:42.037" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Action potentials are mediated by electric currents and can be modeled by electronic circuits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;An electric current is the &lt;em&gt;flow of charge&lt;/em&gt;. Therefore, action potentials are mediated by current flow. However, action potentials are mediated by the flow of ions across the membrane (Fig. 1), whereas current flow in electric circuits is typically mediated by the flow of electrons (Fig. 2). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Axjk4.jpg&quot; alt=&quot;AP&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Action potential propagation. Source: &lt;a href=&quot;http://bio1152.nicerweb.com/Locked/media/ch48/axon.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chen, Carnegie Mellon&lt;/a&gt;.&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The action potential propagates in the direction of the dendrite. However, the underlying current flow is perpendicular to the axonal membrane and is mediated by ion channels. These ion channels are activated through the sensing of the &lt;em&gt;electrical field&lt;/em&gt;. For example, voltage-operated Na&lt;sup&gt;+&lt;/sup&gt; channels are activated by a small depolarizing potential, while voltage-gated potassium channels open during the later phase of the action potential by a large depolarization.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whatever the differences, an axon can be well modeled by a parallel resistor-capacitor circuit powered by the membrane potential. The electrochemical properties of the cell membrane makes it equivalent to a circuit with a set of resistors (which are voltage-dependent), batteries (whose voltage depends on ion concentration differences), and a capacitor all connected in parallel (see Fig. 2). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/88fMK.jpg&quot; alt=&quot;model&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 2. Electronic circuit representation of the axon. Source: &lt;a href=&quot;http://teachers.yale.edu/curriculum/viewer/initiative_09.06.07_u&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yale University&lt;/a&gt;&lt;/sup&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to your question on charge balance; neutrality is maintained, because Na&lt;sup&gt;+&lt;/sup&gt; and K&lt;sup&gt;+&lt;/sup&gt; flow are going in opposite directions and neutralize the net flux of charge. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-08T05:58:19.993" LastActivityDate="2015-05-08T05:58:19.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34085" PostTypeId="1" CreationDate="2015-05-08T07:51:16.607" Score="5" ViewCount="2169" Body="&lt;p&gt;I am struggling to understand negative conductance shown on I-V curves on ion channels. Mechanistically, negative conductance means that inward (or outward) current increases when voltage across membrane decreases. I-V curves of such a channel have both positive and negative slopes. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2226091/pdf/588.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;How it is achieved by ion-channels&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, this is in addition to the example posted in the answer by aandreev. &lt;img src=&quot;https://i.stack.imgur.com/qAa8w.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6228" LastEditorUserId="9943" LastEditDate="2015-06-01T01:10:46.517" LastActivityDate="2015-06-01T01:10:46.517" Title="Mechanism behind negative conductance of ion channels" Tags="&lt;neuroscience&gt;&lt;biophysics&gt;&lt;electrophysiology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34087" PostTypeId="2" ParentId="34085" CreationDate="2015-05-08T08:14:51.577" Score="2" Body="&lt;p&gt;This is the figure OP talks about:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3rBQD.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2226091/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Negative Conductance Caused by Entry of Sodium and Cesium Ions into the Potassium Channels of Squid Axons&lt;/a&gt;, Francisco Bezanill, Clay M. Armstrong (1972).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Short answer is that in non-linear mode of ion channel operation other ions start passing through it (channel loses specificity). Cumulative effect (because of different concentrations of different ions) is negative total conductance, if you don't measure currents of specific ions.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-05-08T08:14:51.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34088" PostTypeId="1" CreationDate="2015-05-08T09:53:24.583" Score="2" ViewCount="94" Body="&lt;p&gt;Consider a population structured in groups of two individuals. Individuals' interactions follow an additive prisoner's dilemma:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;\begin{array}{c |c |c|}&#xA;&amp;amp; C &amp;amp; D \\&#xA;\hline&#xA;\text{Cooperate (} C \text{)} &amp;amp; b -c &amp;amp; -c \\&#xA;\hline&#xA;\text{Defect (} D\text{)} &amp;amp; b &amp;amp; 0 \\&#xA;\hline&#xA;\end{array}&#xA;where $b$ is the benefit and $c$ is the cost. The payoffs are to the player on the left. I need to calculate  the regression of individual fitness on individual phenotype, $\beta (w_i, p_i)$, where $p_i = 0$ if $i$ defects and $p_i = 1$ if $i$ cooperates. Note that I need to calculate the regression within groups rather than between groups. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought that the right way of calculating $\beta(w_i,p_i)$ would be to vary the strategy of the focal individual while keeping the strategy of the other individual constant (my thought was that the other individual becomes the environment for the focal individual). Because switching to cooperation causes an individual to lose $-c$ in fitness (if we keep the strategy of the other individual constant), I thought that $\beta(w_i,p_i) = -c$. But, to my surprise, $\beta(w_i,p_i) = -b -c$. To show why, McElreath &amp;amp; Boyd (&quot;Mathematical Models of Social Evolution&quot;, p. 242) draw the following graph:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XwPCE.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let $V(X|Y)$ be the payoff of individual $X$ when it interacts with $Y$ (in other words, $X$ is the focal individual; $Y$ is the other individual). I understand that McElreath and Boyd calculated the regression coefficient by computing $V(C|D) - V(D|C)$ --- as opposed to $V(C|C) - V(D|C)$, where you keep the strategy of the other individual constant. My question is &lt;strong&gt;why&lt;/strong&gt; this is the right way of calculating $\beta(w_i,p_i)$.&lt;/p&gt;&#xA;" OwnerUserId="11829" LastEditorUserId="3340" LastEditDate="2015-05-09T07:57:27.110" LastActivityDate="2015-05-09T07:57:27.110" Title="How to compute the regression of individual fitness on individual phenotype" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;mathematical-models&gt;&lt;population-genetics&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34090" PostTypeId="2" ParentId="34088" CreationDate="2015-05-08T15:40:27.840" Score="1" Body="&lt;p&gt;I am not sure I understood the question. Let me know if this helps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Case: N=2, freq=0.5&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's assume that the frequency of those who cooperate is 0.5. The slope of the regression line (which R.squared is equal to 1 as we have as many data point than degrees of freedom) is by definition $\frac{\Delta w}{\Delta p}$. You defined $\Delta p = 1$. What is $\Delta w$ then?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well, given that one cooperate and the other defect (as indicated in the fact that the frequency of cooperators is 0.5), then one will have the payoff of a cooperator that is facing a defector and the other one will have the payoff of a defector facing a cooperator. The cooperator has a fitness of $w_0 + b$ and the defector has a fitness of $w_0 - c$. I think you may misread the payoff matrix. To know the fitness of someone with strategy $i$ when facing someone with strategy $j$, you look that payoff at row $i$ and column $j$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, $\Delta w = (w_0 - c) - (w_0 + b) = - (b+c) = -b - c$, and so the slope is  $\frac{\Delta w}{\Delta p}=\frac{-b-c}{1} = - b -c$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Case: N&gt;2, freq=0.5&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In such case the slope of the regression will necessarily be lower than $-b-c$ because some cooperators will meet other cooperators, increasing their fitness (=highering the points on the right hand side of your graph) and some defectors will meet other defectors, decreasing their fitness (=lowering the points on the left hand side of your graph)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;At equilibrium&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only stable equilibrium is when the frequency of cooperators is 0. In such case, there is no variance and we cannot even talk about regression. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Conclusion&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The slope is not necessarily $-b-c$. It is $-b-c$ for the very special case where we have two individuals, one cooperate, the other one defects. In any other scenario the slope $s$ of the regression is lower. More specifically, the slope $s$ of the regression for any $N$ and for any $freq$ is $0 =&amp;lt; s &amp;lt; -( b+c)$&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-05-08T17:04:27.750" LastActivityDate="2015-05-08T17:04:27.750" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34091" PostTypeId="2" ParentId="17327" CreationDate="2015-05-08T16:21:03.003" Score="3" Body="&lt;p&gt;The closest thing you will find to what you're looking for, I think, are animals with multiple different mating strategies where one sex (usually the male) can have multiple distinct phenotypes. Some examples include:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/BF02382664&quot; rel=&quot;nofollow&quot;&gt;Patas monkeys&lt;/a&gt;, where some males are large and have harems of females while others are dubbed &quot;sneak maters&quot; and instead of having their own harem they sneak in and mate with females in another male's harem&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10675268&quot; rel=&quot;nofollow&quot;&gt;Scarab beetles&lt;/a&gt;, where males either have a horn or lack one. Horned males defend their females at their tunnel entrances while hornless males sneak into tunnels to mate with females&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-05-08T16:21:03.003" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34092" PostTypeId="1" AcceptedAnswerId="34094" CreationDate="2015-05-08T16:59:28.553" Score="4" ViewCount="1103" Body="&lt;p&gt;I need to have a RNA-Seq dataset and therefore, I've visited the following site &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64672&quot; rel=&quot;nofollow&quot;&gt;NCBI-geo C. Elegans&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the Supplemantary file part, I clicked the &lt;em&gt;SRP/SRP051/SRP051702  ftp&lt;/em&gt; and downloaded &lt;strong&gt;&lt;em&gt;sra&lt;/em&gt;&lt;/strong&gt; file. Then I need to convert it to fastq file format. For this purpose I've heard that there is a sra-toolkit and within it there is  fastq-dump exacutable. However in order to use it, first of all I have to figure out whether my sra file contains paired-end or single-end read data. So my question is that how could I know the type of reads in the dataset (in the first link) ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Without any information, I used &lt;strong&gt;&lt;em&gt;--split_files&lt;/em&gt;&lt;/strong&gt; flag of &lt;strong&gt;&lt;em&gt;fastq-dump&lt;/em&gt;&lt;/strong&gt; exacutable and it generated two 14 Gb  &lt;strong&gt;(both of them  are exactly 14.346.367.840 bytes)&lt;/strong&gt; files and their name are  &lt;em&gt;SRR1741330_1.fastq&lt;/em&gt; and &lt;em&gt;SRR1741330_2.fastq&lt;/em&gt; Does it mean my dataset is paired end ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an another question (different but related with part 1). In the SRR1741330_1.fastq file, at some lines, sequences contains different characters such as &lt;em&gt;CCCFFFFFGFHHHGJJJJI#1?FEIGGI&lt;/em&gt;... Before looking into these files, I have thought that these sequence lines should only contain the letters of A,G,T and C . What are these F,H,J,I,#,? etc.. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions might be trivial and unmeaningful but since I'm a totally new person in this area, I could not understand them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;New question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder one more thing, since its related with previous part of my question I asked it here instead of creating new question. After I generate fastq file with dump_fastq executable, all the sequences are length of 50. Does it because of parameters of the dump_fastq executable or its related with original sra file? In other words, could I increase this length?&lt;/p&gt;&#xA;" OwnerUserId="14759" LastEditorUserId="14759" LastEditDate="2015-05-08T17:39:51.897" LastActivityDate="2015-05-08T18:29:19.143" Title="How could I identify whether given RNA-seq data is paired end or single end" Tags="&lt;bioinformatics&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34093" PostTypeId="2" ParentId="34083" CreationDate="2015-05-08T16:59:52.217" Score="0" Body="&lt;p&gt;fs means frame shift and *12 gives the length of the new reading frame (ie the number of codons up to and including new stop codon). Usually before fs they give the first mutated amino acid, so I'm not sure what the number 41161 means (but apparently the OP does). &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-05-08T16:59:52.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34094" PostTypeId="2" ParentId="34092" CreationDate="2015-05-08T17:14:18.643" Score="2" Body="&lt;p&gt;To find out whether a dataset was paired-end or single-end, go to SRA, click on a run, and look under &quot;Library&quot;. Paired-end datasets will typically have &quot;Layout: paired&quot;. Note that people don't always mark this correctly, which causes no end of headaches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding lines like &quot;CCCFFFFFGFHHHGJJJJI#1?FEIGGI&quot;, that's the quality score line. Look at the fastq article in wikipedia for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt; Regarding the updated portion of your question, no you can not increase this length. The sequences produced by Illumina machines are a fixed length and that length (or whatever length was submitted) is what you're getting. As a general rule, you'll get whatever sequence was updated (unless you forget the --split3 (or whatever it's called) option).&lt;/p&gt;&#xA;" OwnerUserId="9523" LastEditorUserId="9523" LastEditDate="2015-05-08T18:29:19.143" LastActivityDate="2015-05-08T18:29:19.143" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="34095" PostTypeId="1" AcceptedAnswerId="36680" CreationDate="2015-05-08T17:43:17.143" Score="6" ViewCount="391" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Phylogenetic_comparative_methods#Phylogenetically_independent_contrasts&quot; rel=&quot;nofollow&quot;&gt;PICs&lt;/a&gt; are a popular phylogenetic comparative method and I was wondering what units the actual contrasts are in. I want to say they are unitless but I am not entirely sure.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastEditorUserId="3624" LastEditDate="2015-08-07T10:23:15.010" LastActivityDate="2015-08-07T10:47:47.577" Title="What are the units of Phylogenetic Independent Contrasts (PICs)" Tags="&lt;evolution&gt;&lt;phylogenetics&gt;&lt;statistics&gt;&lt;methods&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34097" PostTypeId="2" ParentId="34088" CreationDate="2015-05-08T17:51:18.263" Score="0" Body="&lt;p&gt;Here is my mistake, I think.  $w_i$ can be written in terms of $p_i$ in the following way (note that $p_i$ can only assume two values, 0 and 1):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_i (0) = w_0 + kb$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_i (1) = w_0 -c + (k-1)b$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $w_0$ is the baseline fitness and $k$ is the number of altruists in the group (so, $k$ can be 0, 1, or 2). When we are calculating $\beta (w_i, p_i)$ the question we are trying to answer is &quot;&lt;strong&gt;for a given group&lt;/strong&gt; in the population, what is the regression coefficient $\beta (w_i, p_i)$?&quot;. This implies that $k$ must be constant because, otherwise, we would be considering individuals from different groups. Accordingly, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\beta(w_i, p_i) = w_i(1) - w_i(0)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\beta (w_i, p_i) = -b -c$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For $\beta(w_i, p_i)$ to be equal to $-c$ we would need to consider the payoff of cooperators from different groups.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Following up on the equation Remi.b suggested in a comment below, we can write the regression coefficient to a population structured in groups of $n$ individuals. More specifically, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_i(0) = w_0 + [k/(n-1)] b$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$w_i (1) = w_0 -c + [(k-1)/(n-1)] b$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With this definitions, we get &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\beta (w_i, p_i) = w_i(1) - w_1 (0)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\beta (w_i, p_i) = -c - b/(n-1)$&lt;/p&gt;&#xA;" OwnerUserId="11829" LastEditorUserId="11829" LastEditDate="2015-05-08T22:34:58.373" LastActivityDate="2015-05-08T22:34:58.373" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34098" PostTypeId="2" ParentId="34079" CreationDate="2015-05-08T17:52:18.553" Score="6" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22171206&quot; rel=&quot;noreferrer&quot;&gt;Crispim &lt;em&gt;et al&lt;/em&gt; 2011&lt;/a&gt;, caloric intake late at night is correlated negatively with sleep quality:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We conclude that food intake during the nocturnal period is correlated with negative effects on the sleep quality of healthy individuals. Indeed, food intake near the sleeping period (dinner and late night snack) was negatively associated with sleep quality variables.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The paper is an interesting read. Here's their figure 1 which shows the correlation between sleep latency (how long it takes to fall asleep) and nocturnal caloric intake:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nE4QB.jpg&quot; alt=&quot;Figure 1&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thick line: men &lt;br&gt;&#xA;Thin line: women&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, it shows that people who eat more at night take longer to fall asleep, and other results show that it's also correlated negatively with other sleep quality indicators.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-05-08T17:52:18.553" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34099" PostTypeId="1" AcceptedAnswerId="34100" CreationDate="2015-05-08T18:13:51.403" Score="1" ViewCount="98" Body="&lt;p&gt;Seems like many of the famous evolutionary biologists are somehow related to each others. For example (and I might be mistaken), Ronald A. Fisher was mentored by a descendent of Charles Darwin. Joe Felsenstein did undergraduate research with James Crow and wrote his doctoral thesis under Richard Lewontin. Muller was mentored by Huxley, friend of Darwin. Brian Charlesworth was mentored by John Maynard Smith who was himself mentored by J.B.S Haldane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there anyone who is crazy enough and interested in the history of evolutionary biology enough to draw a &lt;strong&gt;network of relationships between most famous evolutionary biologists since Charles Darwin&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An arrow between any two evolutionary biologist might represent a relationship of the kind &lt;code&gt;family&lt;/code&gt;, &lt;code&gt;PhD supervision&lt;/code&gt; or &lt;code&gt;friendship&lt;/code&gt;. Of course there is no limit to the number of famous people to include and there is no good distinction of who should be included. But a network of the 20 (or 50 if you feel courageous) most famous evolutionary biologist would be awesome!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="13072" LastEditDate="2015-05-08T21:37:23.400" LastActivityDate="2015-05-08T21:37:23.400" Title="History: Building a &quot;Phylogenetic network&quot; of famous evolutionary biologists" Tags="&lt;evolution&gt;&lt;history&gt;" AnswerCount="1" CommentCount="6" ClosedDate="2015-05-09T03:55:18.253" ContentLicense="CC BY-SA 3.0" />
  <row Id="34100" PostTypeId="2" ParentId="34099" CreationDate="2015-05-08T20:53:51.747" Score="3" Body="&lt;p&gt;Maybe not exactly what you are searching for, but you should look at the evolutionary biology version of &lt;a href=&quot;http://academictree.org/evolution/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Academic tree&lt;/a&gt;. This provides family-tree type relationships between researchers, but mostly (only?) of supervisor-student relationships.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an example, &lt;a href=&quot;http://academictree.org/evolution/tree.php?pid=14954&quot; rel=&quot;nofollow noreferrer&quot;&gt;the tree for Joe Felsenstein&lt;/a&gt; includes links to e.g. Dobzhansky, Lewontin and Sewell Wright. You should be able to find much of the information you are looking for at this site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a small cutout of Joe Felsenstein's tree, just as an example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3peKK.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-05-08T21:06:07.017" LastActivityDate="2015-05-08T21:06:07.017" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34105" PostTypeId="2" ParentId="20310" CreationDate="2015-05-08T23:45:19.410" Score="2" Body="&lt;p&gt;There are two common ways to generate a scale bar:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Measure it&lt;/strong&gt;.  You can take a picture of an object with known spacing such as a &lt;a href=&quot;https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=7501&quot; rel=&quot;nofollow&quot;&gt;grid target&lt;/a&gt; and then measure the size of each pixel.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Compute it&lt;/strong&gt;.  If you know the magnification of your objective, and the magnification of any relay optics after the object but before your camera, you can compute the total optical magnification.  Then using the pixel size on your camera, you can get the actual pixel size.  For example, suppose you have a camera with 7.4 micron pixels, a 20x objective, and a 0.5x adapter lens before your camera, then you would have a pixel size in your image of 7.4/20/0.5 = 0.74 microns.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9561" LastActivityDate="2015-05-08T23:45:19.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34106" PostTypeId="2" ParentId="30216" CreationDate="2015-05-08T23:57:02.097" Score="1" Body="&lt;p&gt;Its probably not from heat.  Filters are basically a glass substrate with some ionic compound deposited in thin layers.  These won't oxidize at reasonable temperatures, and furthermore since you have it on the emission filter as well, its even less likely to be from the source.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More likely its just accumulated organic material from the environment.  7 years is a long time, and microscopes are exposed to a lot of chemicals and other substances which can gradually build up on optical surfaces.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most vendors have a recommended way of cleaning their optics, but usually it involves lens paper or lint free swabs and methanol (or sometimes acetone for more durable stains).  You must be very careful though, as you do not want to scratch the filter.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Semrock for instance has a detailed guide here:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.semrock.com/cleaning-optical-filters.aspx&quot; rel=&quot;nofollow&quot;&gt;http://www.semrock.com/cleaning-optical-filters.aspx&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9561" LastActivityDate="2015-05-08T23:57:02.097" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34107" PostTypeId="2" ParentId="15589" CreationDate="2015-05-09T00:00:32.090" Score="2" Body="&lt;p&gt;You may also want to look at acridine orange.  It binds both single stranded and double stranded DNA, but fluoresces green when bound to double sided DNA, and orange when bound to single stranded DNA/RNA, making it very easy to see both in the same image.  &lt;/p&gt;&#xA;" OwnerUserId="9561" LastActivityDate="2015-05-09T00:00:32.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34112" PostTypeId="1" CreationDate="2015-05-09T04:19:14.193" Score="3" ViewCount="275" Body="&lt;p&gt;Okazaki fragments are formed during replication of the lagging DNA strand. What determines the length of these fragments?&lt;/p&gt;&#xA;" OwnerUserId="15685" LastEditorUserId="6307" LastEditDate="2015-08-08T05:51:32.100" LastActivityDate="2015-08-08T05:51:32.100" Title="Specific numbers of nucleotides in Okazaki fragments" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;dna-replication&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34116" PostTypeId="2" ParentId="28588" CreationDate="2015-05-09T08:21:27.163" Score="1" Body="&lt;p&gt;Some background:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The new work involved misexpression of the Drosophila Ubx protein in the presumptive thorax of transgenic fruitfly embryos. Limb development was suppressed because of repression of Dll. By contrast, the misexpression of onychophoran and crustacean Ubx proteins did not interfere with Dll expression and the formation of thoracic limbs. These results raised the possibility that the Drosophila Ubx protein is functionally distinct from Ubx in onychophorans and crustaceans. One study suggests that Drosophila Ubx has acquired an alanine-rich peptide that mediates the repression of gene transcription; this peptide is lacking in onychophorans. The other study provides evidence that the crustacean Ubx contains an additional peptide that modulates the activity of the alanine-rich peptide, and possibly other repression domains, in crustacean Ubx.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MxsdA.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Insect-restricted sequences include four regions N-terminal to the&#xA;  homeodomain (I1–I4), a peptide motif (QAQAQK), and an extended run of&#xA;  alanine residues C-terminal to the homeodomain&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;The onychophoran Ubx protein might function as an activator of appendage development. When the onychophorans and arthropods diverged,&#xA;  Ubx acquired an alanine-rich repression domain near its carboxy&#xA;  terminus.&lt;/strong&gt; This domain mediates constitutive repression in insects.&#xA;  But in crustaceans the addition of the regulatory peptide causes it to&#xA;  function in a conditional fashion. As a result, Ubx does not suppress&#xA;  limb development in crustaceans. But it eliminates abdominal limbs in&#xA;  insects, greatly reducing the overall number of appendages compared&#xA;  with crustaceans.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can read about it here: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Levine, Mike. &quot;Evolutionary biology: how insects lose their limbs.&quot; Nature 415.6874 (2002): 848-849.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Galant, Ron, and Sean B. Carroll. &quot;Evolution of a transcriptional repression domain in an insect Hox protein.&quot; Nature 415.6874 (2002): 910-913.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-09T15:26:44.570" LastActivityDate="2015-05-09T15:26:44.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34120" PostTypeId="2" ParentId="19856" CreationDate="2015-05-09T10:59:47.893" Score="3" Body="&lt;p&gt;As far as I can see this paper is being a little misleading, by saying &quot;VPA mimics Nogo-66 receptor deletion&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The action of VPA doesn't seem to be related to this receptor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that blocking this receptor and applying VPA both increase plasticity, but it is like taking a car or taking a train -- entirely different modes of transport that achieve the same effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;VPA seems to facilitate LTP through increased availability of relevant proteins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is unconnected with growing new neural structure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The principal problem with growing new structure is, as hinted at the end of the question, that the adolescent/adult brain secretes a chemical that gets picked up by Nogo 66 receptor, which signals to collapse the axon growth cone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's why adult humans can't recover from spinal injuries. The axons won't reconnect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It so happens that a small molecule Nogo Antagonist has recently been developed by Professor Strittmatter.  He was kind to reply to my query, and I learned that this molecule is currently in the early stages of FDA approval. It's a very exciting discovery!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would caution anyone against taking VPA -- I have been encountering chest pains since experimenting with it (even though I dropped the experiment after a week due to pain). It looks as though this pain is inflammation of the stomach lining and a common reaction to VPA (VPA is an acid!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If someone is determined to take VPA, they should at least investigate taking it together with Omeprazole, which discourages the stomach from producing excess acid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am disappointed that I now need to take omeprazole quazi-regularly, it appears that my brief VPA experiment has caused some long-term upset in my chemical balance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also of note is that (again discovered by Strittmatter) Ibuprofen has been found to also interrupt the signalling pathway that leads to axon growth collapse. But it requires a high dosage, and ibuprofen also causes a similar imbalance.&lt;/p&gt;&#xA;" OwnerUserId="8435" LastEditorUserId="8435" LastEditDate="2015-05-27T17:17:03.417" LastActivityDate="2015-05-27T17:17:03.417" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34122" PostTypeId="1" AcceptedAnswerId="34125" CreationDate="2015-05-09T11:47:26.480" Score="1" ViewCount="4205" Body="&lt;p&gt;I'm trying to understand N50 on the wikipedia. But I was unable to get a sense of the definition:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Given a set of contigs, each with its own length, the N50 length is&#xA;  defined as the length for which the collection of all contigs of that&#xA;  length or longer contains at least half of the sum of the lengths of&#xA;  all contigs, and for which the collection of all contigs of that&#xA;  length or shorter also contains at least half of the sum of the&#xA;  lengths of all contigs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is there a simple example that illustrates this definition? Furthermore, why do we need this statistic? What does it really tell me? Do we want a higher or less value?&lt;/p&gt;&#xA;" OwnerUserId="14905" LastEditorUserId="14905" LastEditDate="2015-05-09T11:52:52.203" LastActivityDate="2015-05-09T12:14:01.630" Title="An example for N50? Why do we need it?" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34123" PostTypeId="2" ParentId="31323" CreationDate="2015-05-09T11:58:33.830" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;ATP prepares myosin for binding with actin by moving it to a&#xA;  higher-energy state and a &quot;cocked&quot; position.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Once the myosin forms a cross-bridge with actin, the Pi disassociates&#xA;  and the myosin undergoes the power stroke, reaching a lower energy&#xA;  state when the sarcomere shortens.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;ATP must bind to myosin to break the cross-bridge and enable the&#xA;  myosin to rebind to actin at the next muscle contraction.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DKp2c.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The muscle contraction cycle is triggered by calcium ions binding to&#xA;  the protein complex troponin, exposing the active-binding sites on the&#xA;  actin. As soon as the actin-binding sites are uncovered, the&#xA;  high-energy myosin head bridges the gap, forming a cross-bridge. Once&#xA;  myosin binds to the actin, the Pi is released, and the myosin&#xA;  undergoes a conformational change to a lower energy state. As myosin&#xA;  expends the energy, it moves through the &quot;power stroke,&quot; pulling the&#xA;  actin filament toward the M-line. When the actin is pulled&#xA;  approximately 10 nm toward the M-line, the sarcomere shortens and the&#xA;  muscle contracts. At the end of the power stroke, the myosin is in a&#xA;  low-energy position.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;After the power stroke, ADP is released, but the cross-bridge formed&#xA;  is still in place. ATP then binds to myosin, moving the myosin to its&#xA;  high-energy state, releasing the myosin head from the actin active&#xA;  site. ATP can then attach to myosin, which allows the cross-bridge&#xA;  cycle to start again; further muscle contraction can occur. Therefore,&#xA;  without ATP, muscles would remain in their contracted state, rather&#xA;  than their relaxed state.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Summary from: &lt;a href=&quot;https://www.boundless.com/biology/textbooks/boundless-biology-textbook/the-musculoskeletal-system-38/muscle-contraction-and-locomotion-218/atp-and-muscle-contraction-826-12069/&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.boundless.com/biology/textbooks/boundless-biology-textbook/the-musculoskeletal-system-38/muscle-contraction-and-locomotion-218/atp-and-muscle-contraction-826-12069/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially look up the cross bridge cycle (&lt;a href=&quot;http://muscle.ucsd.edu/musintro/bridge.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://muscle.ucsd.edu/musintro/bridge.shtml&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would also suggest reading it from the master himself here:&#xA;&lt;em&gt;Huxley, A. F. &quot;Muscular contraction.&quot; The Journal of physiology 243.1 (1974): 1-43.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-09T12:08:28.917" LastActivityDate="2015-05-09T12:08:28.917" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34124" PostTypeId="2" ParentId="7269" CreationDate="2015-05-09T12:13:01.887" Score="0" Body="&lt;p&gt;Are you sure that the RSA formula is right?&#xA;I have found a different description：Relative solvent accessibility classes are usually derived from the DSSP program by normalizing it at the maximum value of exposed surface area obtainable for each residue.Different arbitrary threshold values of solvent accessibility are chosen to define binary categories (buried and exposed) or ternary categories (buried, partially exposed, or exposed).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pollastri, G., Baldi, P., Fariselli, P., &amp;amp; Casadio, R. (2002). Prediction of coordination number and relative solvent accessibility in proteins. Proteins: Structure, Function, and Bioinformatics, 47(2), 142-153.&lt;/p&gt;&#xA;" OwnerUserId="15690" LastActivityDate="2015-05-09T12:13:01.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34125" PostTypeId="2" ParentId="34122" CreationDate="2015-05-09T12:14:01.630" Score="2" Body="&lt;p&gt;Contig or scaffold N50 is a weighted median statistic such that 50% of the entire assembly is contained in contigs or scaffolds equal to or larger than this value.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mathematically:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Given a set of sequences of varying lengths, the N50 length is defined&#xA;  as the length N for which 50% of all bases in the sequences are in a&#xA;  sequence of length L &amp;lt; N. This can be found mathematically as follows:&#xA;  Take a list L of positive integers. Create another list L' , which is&#xA;  identical to L, except that every element n in L has been replaced&#xA;  with n copies of itself. Then the median of L' is the N50 of L. For&#xA;  example: If L = {2, 2, 2, 3, 3, 4, 8, 8}, then L' consists of six 2's,&#xA;  six 3's, four 4's, and sixteen 8's; the N50 of L is the median of L' ,&#xA;  which is 6.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In simple words:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;scaffold N50 is the median contig size of your genomic assembly. It's&#xA;  a metric that you can use to evaluate the quality of your assembly,&#xA;  since an overly small N50 suggests that you were unable to generate&#xA;  many contigs of biologically meaningful size (i.e. you probably have a&#xA;  lot of bogus little contigs in your assembly). You can increase your&#xA;  N50 by eliminating sequences which are bound to cause you problems,&#xA;  e.g. short repetitive stretches.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;note that this metric only applies when doing de novo assembly. If you&#xA;  are aligning to a reference (i.e. for variant discovery applications)&#xA;  this metric doesn't apply&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For a sample workout on an arbitrary small dataset:&#xA;&lt;a href=&quot;http://www.r-bloggers.com/calculating-an-n50-from-velvet-output/&quot; rel=&quot;nofollow&quot;&gt;http://www.r-bloggers.com/calculating-an-n50-from-velvet-output/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This answer was compiled from multiple sources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.researchgate.net/post/What_is_N50_Scaffold_in_Genome_sequencing_Technique&quot; rel=&quot;nofollow&quot;&gt;http://www.researchgate.net/post/What_is_N50_Scaffold_in_Genome_sequencing_Technique&lt;/a&gt;&#xA;&lt;a href=&quot;http://seqanswers.com/forums/showthread.php?t=2332&quot; rel=&quot;nofollow&quot;&gt;http://seqanswers.com/forums/showthread.php?t=2332&lt;/a&gt;&#xA;&lt;a href=&quot;https://www.broad.harvard.edu/crd/wiki/index.php/N50&quot; rel=&quot;nofollow&quot;&gt;https://www.broad.harvard.edu/crd/wiki/index.php/N50&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastActivityDate="2015-05-09T12:14:01.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34126" PostTypeId="2" ParentId="34112" CreationDate="2015-05-09T16:49:50.483" Score="3" Body="&lt;p&gt;The length of Okazaki fragments is not necessarily a tight distribution. The lengths are determined by the spacing between adjacent sites where DNA primase has synthesized a short RNA primer on the lagging strand at an active DNA replication fork. In E. coli, as I recall, this occurs on an average of once per 1000 nt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA polymerase holoenzyme then uses that 3'-OH on the RNA primer as a substrate and synthesizes the DNA strand complementary to the Template strand UNTIL it bumps into the next RNA primer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is those nicks in the newly synthesized lagging strand, that have a deoxy-3'-OH, and a ribo-5'-phosphate, (that need to be removed and ligated) that mark the boundaries of individual Okazaki fragments.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-05-09T16:49:50.483" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34127" PostTypeId="1" CreationDate="2015-05-09T18:23:26.300" Score="2" ViewCount="2742" Body="&lt;p&gt;I'm going to be running some Taqman assays on cDNA generated from RNA collected from various samples, and will end up running a bunch of plates (right now the setup is 1/2 a plate per sample, including controls etc.). Since our thermocycler can only handle one 96-well plate at a time, it has been suggested that I make up the mixes all together, aliquot them into the plates, then store the plates at 4°C (well wrapped in plastic or Parafilm) until ready to run. I would imagine that the plates would be in the fridge for just one day, at max overnight. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is about the polymerase - can I add it ahead of time, and just take the plate out of the fridge and pop it in the thermocycler, or should I add it just before use? I've been kind of out of the DNA/RNA field for over 10 years, and I seem to remember from before that polymerases could have residual activity even at 4°C. Is this still the case, or have they improved to only be active at 60+°C or whatever your temperature is?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, is there another ingredient I should leave out until just before amplification? cDNA? Probes? Something else? Also, does the storage time make sense? Is overnight okay, or should I run them all the same day? Is over the weekend okay? I don't want this question to extend into a too-broad &quot;&lt;em&gt;How do I do qPCR?&lt;/em&gt;&quot; question, but any tips you have would be very helpful. As far as I'm aware, all the reagents are from Life Technologies/Applied Biosystems.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason I ask is because it seems to me that it would be much more accurate and reproducible to prepare the master mix with polymerase already included, instead of adding 1 μL of polymerase to each well just before running the assay.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2015-05-09T18:28:44.297" LastActivityDate="2018-05-08T14:53:25.407" Title="Storing Taqman plates with polymerase in fridge before running" Tags="&lt;molecular-biology&gt;&lt;experimental-design&gt;&lt;polymerase&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34128" PostTypeId="2" ParentId="26376" CreationDate="2015-05-09T22:55:15.363" Score="2" Body="&lt;p&gt;The term I was looking for was anautogeny, or an anautogenous insect. I had slightly confused the definition, with the actual definition being; '&lt;a href=&quot;http://en.wikipedia.org/wiki/Anautogeny&quot; rel=&quot;nofollow&quot;&gt;a gravid female insect that requires a blood meal before oviposition&lt;/a&gt;'. &lt;/p&gt;&#xA;" OwnerUserId="3382" LastActivityDate="2015-05-09T22:55:15.363" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34130" PostTypeId="1" AcceptedAnswerId="34137" CreationDate="2015-05-10T09:20:24.623" Score="3" ViewCount="696" Body="&lt;p&gt;Whenever a PCR is done, we have to use housekeeping genes like GAPDH, to self normalise the values to account for different starting cDNA/DNA. Now there are many different genes like GAPDH, ubiquitin, actin etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now when dealing with cells, I can understand that due to their immortal nature and frankly shocking number of generations undergone by them, the expression of the housekeeping gene may change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that I am not dealing with cells and instead with animal tissues, does it matter which house keeping gene I select? Or in other words is GAPDH going to give me the same consistency between samples as something like 18s Ribsomal RNA or am I missing something specific?&lt;/p&gt;&#xA;" OwnerUserId="15697" LastEditorUserId="5144" LastEditDate="2015-05-10T14:38:54.180" LastActivityDate="2015-05-10T20:44:33.427" Title="Why are some housekeeping genes considered better?" Tags="&lt;pcr&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34133" PostTypeId="2" ParentId="10456" CreationDate="2015-05-10T09:42:11.553" Score="2" Body="&lt;p&gt;You are correct that cats consume a lot of protein, and it's safe to assume a large share of this is broken down to amino acids, which are then oxidized to produce energy. But amino acids in general are &lt;em&gt;not&lt;/em&gt; catabolized via glucose; instead, they are converted into compounds that feed into the TCA cycle via other biochemical routes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Almost every of the 20 proteinogenic amino acids have their own specialized catabolism pathway, so this is a large topic. The general theme is that the amine nitrogen is first removed by a transaminase to yield a keto-acid, which is when converted into a carbohydrate that can enter the TCA cycle. To give but one example, leucine is converted in the mitochondrion by a series of CoA-coupled intermediates into acetyl-CoA and acetoacetate (a ketone body; see below). The acetoacetate in turn yields two more acetyl-CoA. A description of this pathway is found at &lt;a href=&quot;http://humancyc.org/HUMAN/NEW-IMAGE?type=PATHWAY&amp;amp;object=LEU-DEG2-PWY&amp;amp;detail-level=3&quot; rel=&quot;nofollow&quot;&gt;the HumanCyc database&lt;/a&gt;. This is a great resource for learning amino acid (and other) biochemical pathways, and provides literature references.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some amino acids are indeed used for gluconeogenesis, mainly by the liver, but this is not a requirement for their catabolism by most tissues. (It would be energetically inefficient to first generate glucose and then break it down again!) An exception is the central nervous system, which does require glucose and cannot subsist on fat or amino acids (for reasons that, to my knowledge, are still not well understood). So in order to support the CNS on amino acids, the route your describe via gluconeogenesis does occur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ketone bodies (acetone, acetoacetate and beta-hydroxybutyrate) are the main alternatives to glucose accepted by the CNS. Gluconeogenesis is energetically expensive in the long run, and if deprived of dietary sugar for a long time, the body will increase its usage of ketone bodies instead of glucose. However, ketone bodies can never fully replace glucose: even during prolonged starvation in humans, blood glucose is kept &gt; 2mM. The CNS would not function otherwise. I'm not an expert in cat physiology but I would bet the situation is similar.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-05-10T09:42:11.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34134" PostTypeId="1" AcceptedAnswerId="34145" CreationDate="2015-05-10T10:11:57.540" Score="6" ViewCount="303" Body="&lt;p&gt;The book &quot;Kuby Immunology&quot; states that normal infected cells might present antigenic peptides on their surface via MHC class I, but these can't activate naive CD8 cells. Only infected professional antigen presenting cells have the necessary co=stimulatory signals to do so. This is why cross presentation happens.&#xA;&lt;strong&gt;But then why does the process of antigen presentation on normal infected cells happen then, if it is of no use?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="11716" LastActivityDate="2015-05-11T18:45:42.640" Title="Why MHC class I antigen presentation exist in normal cells?" Tags="&lt;cell-biology&gt;&lt;immunology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34135" PostTypeId="1" CreationDate="2015-05-10T10:27:17.187" Score="0" ViewCount="65" Body="&lt;p&gt;Sugars is a common component in diet of mammals. Why then their teeth did not develop resistence to sugar decay?&lt;/p&gt;&#xA;" OwnerUserId="408" LastActivityDate="2015-05-10T12:47:01.663" Title="Why do teeth decay of sugar?" Tags="&lt;human-biology&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34136" PostTypeId="2" ParentId="6814" CreationDate="2015-05-10T10:30:44.283" Score="3" Body="&lt;p&gt;I am not so familiar with enzymatic kits for quantifying glutamine, but most enzyme-based analysis kits come with a number of fairly strong assumptions on the enzymology involved, and in my experience they are difficult to use reliably. Commercial kits are hopeless to troubleshoot since their components are not disclosed --- you don't know what you're working with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are you at a clinical chemistry facility? If so you may have access to analyzers used to measure blood biochemistry parameters, and some models measure glutamine, for example &lt;a href=&quot;http://www.ysilifesciences.com/index.php?page=ysi-2900-nutrient-biochemistry-analyzer&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt;. These instruments are also based on enzymatic assays, but they are carefully tested since they are used in human medicine, and so I would consider them more reliable than the average Sigma kit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best alternative I think is mass spectrometry, or NMR. Glutamine is easy to measure on any LC-MS or GC-MS setup (an old triple-quadrupole will do nicely), it ionizes well in positive mode electrospray, is well retained on a typical HILIC column, and isotope-labeled standards are readily available. I'm no expert in NMR but I know glutamine is measured routinely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another caveat with analyzing glutamine is that it decomposes spontaneously in water to form pyroglutamate, with a half life of about two weeks at room temperature, as shown in &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0014482762902902&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;. But I'm sure you're aware of that.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-05-10T10:30:44.283" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34137" PostTypeId="2" ParentId="34130" CreationDate="2015-05-10T11:18:09.813" Score="3" Body="&lt;p&gt;Yes, it does matter. Gene expression varies a lot thoughout tissues and living conditions, so you need to test a variety of genes and choose the ones with the smallest variation in the expression between sample and control. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you don't find any, you have to test other genes for this purpose. This &lt;em&gt;is&lt;/em&gt; important, as this can severly affect the outcome of your experiment, since you normalize to the housekeeping genes. If these are not constant, it will cause problems. Have a look into the references, this helped me a lot.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12184808&quot; rel=&quot;nofollow&quot;&gt;Accurate normalization of real-time quantitative RT-PCR data by&#xA;geometric averaging of multiple internal control genes.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18554498&quot; rel=&quot;nofollow&quot;&gt;The normalization of gene expression data in melanoma: investigating&#xA;the use of glyceraldehyde 3-phosphate dehydrogenase and 18S&#xA;ribosomal RNA as internal reference genes for quantitative real-time&#xA;PCR.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19264760&quot; rel=&quot;nofollow&quot;&gt;Normalization of qRT-PCR data: the necessity of adopting a&#xA;systematic, experimental conditions-specific, validation of&#xA;references.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-05-10T11:18:09.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34138" PostTypeId="2" ParentId="31542" CreationDate="2015-05-10T11:55:38.307" Score="2" Body="&lt;p&gt;Creatine itself is never &lt;em&gt;converted&lt;/em&gt; into ATP. Creatine-phosphate on the other hand can donate its phosphate group to ADP, phosphorylating to form ATP and creatine. This is a buffer system for high-energy phosphates, and is very important in organs with rapid ATP turnover, notably muscle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanism of the findings described in the papers is not fully understood yet I think. But it is not via ATP, because the supplementation is not creatine-phosphate, but creatine itself, which does not yield ATP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding NADH: ATP is very different from NAD/NADH in terms of molecular structure, and the two are not interconverted by any pathway that I know of. (Probably this is not what you meant, but just to be clear.) But it is certainly true that reducing power in the form of NADH can be used to phosphorylate ADP into ATP; this is the task of the mitochondrial respiratory chain, where NADH is oxidized to NAD by complex I. On the other hand, I am not aware of a physiologically relevant process that uses ATP to reduce NAD into NADH.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The liver is a main site of &lt;a href=&quot;http://humancyc.org/HUMAN/NEW-IMAGE?type=PATHWAY&amp;amp;object=GLYCGREAT-PWY&quot; rel=&quot;nofollow&quot;&gt;synthesis of creatine&lt;/a&gt; itself, and this syntesis consumes methyl groups donated by the S-adenosylmethionine system. The authors of your ref1 seem to suggest that reduced synthesis of creatine following supplementation is a possible mechanism. Similar effects have been observed with choline supplementation, but again this effect is not well understood and a current research topic. A recent review is &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22134222&quot; rel=&quot;nofollow&quot;&gt;found here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-05-10T11:55:38.307" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34139" PostTypeId="2" ParentId="34135" CreationDate="2015-05-10T12:47:01.663" Score="1" Body="&lt;p&gt;The reason for the decay are ever evolving bacteria, which happen to be very hard to overcome, even nowdays. There is a lot of research centered towards protein interactions, even mapping whole interactomes, which would help us get rid of decay, yet naturally our system wasn't able to evolve as fast as technological advances, but bacteria did.&lt;/p&gt;&#xA;" OwnerUserId="15699" LastActivityDate="2015-05-10T12:47:01.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34140" PostTypeId="1" CreationDate="2015-05-10T12:58:50.583" Score="0" ViewCount="74" Body="&lt;p&gt;In one book I read that pteranodons lived in huge colonies. But pteranodon's family in &quot;Dinosaur Train&quot; ( &lt;a href=&quot;https://en.wikipedia.org/wiki/Dinosaur_Train&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Dinosaur_Train&lt;/a&gt; ) does not seem to be a part of any colony. So, who is right? Did pteranodons live in colonies?&lt;/p&gt;&#xA;" OwnerUserId="15365" LastActivityDate="2015-05-10T12:58:50.583" Title="did pteranodons live in colonies?" Tags="&lt;palaeontology&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34141" PostTypeId="1" CreationDate="2015-05-10T14:20:01.787" Score="4" ViewCount="2067" Body="&lt;p&gt;We are regularly doing bacterial transformation and subculture from plate to liquid media to extract DNA. This usually goes very well and is straightforward, but occasionally, the colonies that grew well on a plate, will not grow in liquid culture (with the same antibiotics that were in the plate). This has happened now to three persons on multiple plasmids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, I was trying to ligate an ampicillin resistance gene (with its promoter) inside pENTR4 plasmid (already with Kanamycin resistance). My plate and LB both contained the two antibiotics, but the colonies only manage to get slightly turbid at a 16h timepoint. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phage contamination is very unlikely, and the effect cannot be due to a toxicity of the inserted fragment, as both insert and vector have been grown in these same bacteria multiple times without problem. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Help?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT1 - We use Carbenicillin in place of ampicillin in the plate, but not in the liquid media. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT2 - After managing to grow some colonies in liquid, I managed to get a small amount of the plasmid (profile was good; concentration = 70ng/ul). The weird thing is that when I retransformed this DNA in Stbl3 bacteria, I had absolutely no trouble. Do you think the bacteria stock could be responsible?&lt;/p&gt;&#xA;" OwnerUserId="12924" LastEditorUserId="12924" LastEditDate="2015-05-29T15:35:08.900" LastActivityDate="2018-03-12T17:57:53.817" Title="E. coli not growing in liquid medium" Tags="&lt;molecular-biology&gt;&lt;microbiology&gt;&lt;plasmids&gt;" AnswerCount="1" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="34142" PostTypeId="2" ParentId="34066" CreationDate="2015-05-10T14:31:05.253" Score="0" Body="&lt;p&gt;There must be some such information, because at the lab we are using the SnapGene software, and it is able to recognize the Ori sequences (and all other sequences). Since it is proprietary software, I doubt they would disclose their list, but others might have the same information. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you really need to find your origin for your plasmid, you could try the &lt;a href=&quot;http://www.snapgene.com/products/snapgene/free_trial/&quot; rel=&quot;nofollow&quot;&gt;demo&lt;/a&gt;. Good luck!&lt;/p&gt;&#xA;" OwnerUserId="12924" LastActivityDate="2015-05-10T14:31:05.253" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34143" PostTypeId="1" CreationDate="2015-05-10T15:48:31.047" Score="3" ViewCount="56" Body="&lt;p&gt;I'm thinking of creating my own laser tag system and am a bit concerned about the eye safety aspect. Most of the homebrew system I've seen use the TSAL 6100 diode(&lt;a href=&quot;http://www.vishay.com/docs/81009/tsal6100.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.vishay.com/docs/81009/tsal6100.pdf&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I've gathered from hobbyist forums it should be totally eye safe. However the math doesn't add up, my math could be wrong, read probably is, but I couldn't find any conclusive data that would disprove it. Also I cannot manage to factor in what effects lenses would have, which are a must to keep the beam from having to large a spread. Here are my calculations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First off using the inverse suqare law and a TSAL running at 1Amps (from what I've read most players run it at 1.5 Amps) at the minimum distance of 200mm we get the following result:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ee = 1.5W/sr / (0.2)^2m = 37.5W/m^2 (the 1.5 W/sr is from the TSALs datasheet at 1A)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The irriadiance of 37.5 is a bit high, but it's still under the 100W/m^2 safety limit for the cornea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same equation done at a distance of 100mm however yields an Ee of 150 W/m^2 which is above safety levels. Assuming you don't point a tagger in your face and start firing of shoots you'll be safe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I'm curious about is how a lens affects the safety characteristics. Assuming a lens with a focal length of 100mm. Won't the irradiance be the same with the irradiance at a distance of 100mm from the IRLED.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My math and understanding of the principals could be wrong, but I was curious if anyone could put my mind at ease. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've also made a rough calculation of the retinal hazzard. &#xA;R(lamb) = 0.33 rad&#xA;(angular subtense) alpha= 5mm/200mm = 0.025 rad&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We'll use an alphaeffective = 0.011rad and that gives us an emission limit for the radiance of 545mw/mm^2/sr&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and our iriadiance is Lir = 1500mw/sr * 0.33 / (5mm)^2 = 99mw/mm2/sr&lt;/p&gt;&#xA;&#xA;&lt;p&gt;that's way below the limit, but if we modify that active light source to 1mm it becomes 495, which is skirting the line. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(the tec doc doesn't define an active light source size, at least I couldn't find it so I used 5mm )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again the above calculations are for a source without a concentrating lens. What would happen if we added a lens in the mix? Would it stay in the safe zone? How does pulsing the diode effect intensity? I'm guessing it lowers it, but if anyone could manage it, I'd like a numerical demonstration that it brings it closer to safer bounds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above calculations are based on the folowing OSRAM paper (&lt;a href=&quot;http://www.osram-os.com/Graphics/XPic2/00052113_0.pdf/Application%20Note%20Eye%20Safety.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.osram-os.com/Graphics/XPic2/00052113_0.pdf/Application%20Note%20Eye%20Safety.pdf&lt;/a&gt;), which explains the principles involving &lt;/p&gt;&#xA;" OwnerUserId="15700" LastEditorUserId="5144" LastEditDate="2015-05-10T15:53:07.293" LastActivityDate="2015-05-10T15:53:07.293" Title="Infrared emitting diode eye safety" Tags="&lt;biophysics&gt;&lt;human-eye&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34144" PostTypeId="2" ParentId="34130" CreationDate="2015-05-10T16:06:33.733" Score="2" Body="&lt;p&gt;You need to watch out though. Some very used genes could be very uninformative as housekeeping genes in qPCR. ACTB and GAPDH have tons of pseudogenes (analogous genes not yielding proteins) that can interfere with the PCR. You can read more in this article (1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To make it even worse, the PCR amplification fragments can be of the exact same length as the ACTB amplicon, making it impossible to differentiate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, you have to consider the specific cell type/application/treatment, because some mRNAs could be very constant through treatment A on cell type 1, but vary with treatment B or on cell type 2. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the best would be to use multiple housekeeping (3-5) and see how they behave relative to one another. You could also use the mean of these housekeeping.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;(1) Sun, Yuan, et al. &quot;Pseudogenes as weaknesses of ACTB (Actb) and GAPDH (Gapdh) used as reference genes in reverse transcription and polymerase chain reactions.&quot; PloS one 7.8 (2012): e41659.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="12924" LastEditorUserId="12924" LastEditDate="2015-05-10T20:44:33.427" LastActivityDate="2015-05-10T20:44:33.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34145" PostTypeId="2" ParentId="34134" CreationDate="2015-05-10T16:42:22.100" Score="4" Body="&lt;p&gt;It is of use. They're saying that naive T cells cannot be activated by normal cells because the latter lack the appropriate co-stimulus, namely B7. However, activated CD8+ T cells can recognize antigens presented by normal cells and form a response. This is how cytotoxic T cells are able to eliminate transformed or infected cells. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="12924" LastEditDate="2015-05-11T18:45:42.640" LastActivityDate="2015-05-11T18:45:42.640" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34148" PostTypeId="1" CreationDate="2015-05-10T20:09:51.460" Score="1" ViewCount="334" Body="&lt;p&gt;I know that the D-loop is  a DNA complex in which the strands of double helix DNA molecule are separated for a stretch and held apart by a third strand of DNA. Usually, this third strand has a base sequence, which is complementary to one of the main strands and pairs in accordance with it. The third strand then sub sequentially displaces the complementary main strand in the region. Im also aware that D-loops occur in many DNA systems, such as in DNA repair, telomere activity, and in mitochondrial circular DNA molecules.  &lt;strong&gt;&lt;em&gt;However, my question is why does the D loop only provide information about maternal DNA ancestry?&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="8059" LastActivityDate="2015-05-10T21:14:22.103" Title="Mitochondrial D-Loop" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;genetic-linkage&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34149" PostTypeId="2" ParentId="34148" CreationDate="2015-05-10T21:14:22.103" Score="1" Body="&lt;p&gt;All the mitochondria of an individual are originating from the mother. This means that if the mother is afflicted by a mitochondrial disease, the offspring will also be affected. This is why the three parent model is being considered in some cases (1). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;(1) Pritchard, C. (2014, September 1). The girl with three biological parents. BBC News. From &lt;a href=&quot;http://www.bbc.com/news/magazine-28986843&quot; rel=&quot;nofollow&quot;&gt;http://www.bbc.com/news/magazine-28986843&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="12924" LastActivityDate="2015-05-10T21:14:22.103" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34150" PostTypeId="1" AcceptedAnswerId="34838" CreationDate="2015-05-10T22:32:19.997" Score="21" ViewCount="19354" Body="&lt;p&gt;Developmentally male rats don't have nipples because (&lt;a href=&quot;http://www.reddit.com/r/askscience/comments/1on00d/do_males_of_all_mammalian_species_have_nipples/&quot; rel=&quot;noreferrer&quot;&gt;reddit&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Testosterone release in the fetal male rat happens before the stage of mammogenesis where the teat is formed whereas other species halt that same process after the teat is formed.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;According to the same page, male rats and horses (and mice) are unique among non-monotreme mammals in not having nipples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Male humans have nipples because there's no evolutionary pressure for them not to. (&lt;a href=&quot;https://biology.stackexchange.com/questions/2073/why-do-men-have-nipples&quot;&gt;Why do men have nipples?&lt;/a&gt;) Then, why was there selection for males to lack nipples in the case of mice, rats, and horses?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Apparently, male horses lack nipples because &quot;female horses have their nipples between their hind legs, and in males, that real estate is used for other purposes&quot;. (&lt;a href=&quot;http://boards.straightdope.com/sdmb/archive/index.php/t-278243.html&quot; rel=&quot;noreferrer&quot;&gt;Straight Dope&lt;/a&gt;))&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolutionarily, why do male rats and horses lack nipples?&lt;/p&gt;&#xA;" OwnerUserId="15521" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2019-09-07T22:58:02.160" Title="Evolutionarily, why do male rats and horses lack nipples?" Tags="&lt;evolution&gt;&lt;mammals&gt;&lt;anatomy&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34151" PostTypeId="1" CreationDate="2015-05-10T23:01:11.380" Score="3" ViewCount="719" Body="&lt;p&gt;Humans (homo sapiens) have been on the earth for thousands of generations, and we have kept evolving throughout that time. Why don't we just keep evolving so that, let's say, we live for an average of 300 years? Or why don't we evolve so that we don't need to sleep?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This could also apply to many other species.&lt;/p&gt;&#xA;" OwnerUserId="15704" LastActivityDate="2015-09-22T22:10:29.800" Title="Why don't we keep evolving until we are super-human?" Tags="&lt;evolution&gt;&lt;human-evolution&gt;" AnswerCount="2" CommentCount="1" ClosedDate="2015-05-11T08:42:59.180" ContentLicense="CC BY-SA 3.0" />
  <row Id="34152" PostTypeId="2" ParentId="34151" CreationDate="2015-05-10T23:17:57.430" Score="0" Body="&lt;p&gt;Natural selection selects for individuals who can leave the most progeny in the next generation. Traits such as longer lifespan do not typically affect fecundity/fertility. So males and females who have the largest families as quickly as possible are providing the raw material for natural selection.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-05-10T23:17:57.430" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34153" PostTypeId="2" ParentId="34151" CreationDate="2015-05-11T00:51:49.637" Score="6" Body="&lt;p&gt;Welcome to Biology.SE!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a many misunderstanding of what evolutionary processes are in your post and it is therefore quite hard to answer (hence the current two close votes I guess). You might want to read some introductory textbook on evolutionary biology or other online resources such as the &lt;a href=&quot;https://www.khanacademy.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;understanding evolution&quot; project&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most obvious misunderstanding is that evolution is NOT some kind of forever &quot;improvement&quot; process in a static environment. Evolution is something else! But I can't make a good overview of evolutionary processes in just one post.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[why don't we live on] average of 300 years?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You may want to read about &lt;a href=&quot;https://biology.stackexchange.com/questions/17077/why-does-evolution-not-make-our-life-longer&quot;&gt;this post concerning the evolution of aging&lt;/a&gt; but it would probably be slightly too advanced but you would probably still get something out of the answers. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why don't we just keep evolving [..]?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Humans, definitely keep evolving. Nothing have stopped. We evolved as we have always and it won't stop until we get extinct! &lt;a href=&quot;https://biology.stackexchange.com/questions/20291/human-evolution-in-modern-times&quot;&gt;This post&lt;/a&gt; may for example help you to understand that evolution keep occurring today in humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you say &lt;code&gt;Humans (homo sapiens) have been on the earth for thousands of generations&lt;/code&gt; it sounds a bit like human have came to existence some time ago and have evolved since. It is a terribly misleading point of view, one of the reason is that one cannot date the existence of the first humans without making a very arbitrary decision about what a human is. A more correct way of looking at life on earth is that everything have come to existence about 3.5 billions years ago and everything have kept evolving since. Any single living thing on earth have been evolving for the exact same amount of time. Humans have evolved for 3.5 billions (even if we don't call earlier forms as humans) and unicellular algea have evolved for 3.5 billions years (even if we don't call earlier forms as algea). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helped!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-09-22T22:10:29.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34154" PostTypeId="1" AcceptedAnswerId="34155" CreationDate="2015-05-11T00:59:21.697" Score="3" ViewCount="129" Body="&lt;p&gt;We receive quite a lot of questions from layman in evolutionary biology in this site that are sometimes difficult to answer just because there is way too much to say. &lt;a href=&quot;https://biology.stackexchange.com/questions/34151/why-dont-we-keep-evolving-until-we-are-super-human&quot;&gt;Why don't human keep evolving?&lt;/a&gt; is a perfect example. I often want to give some pieces of information and link to a good source of information for them to get introductory knowledge in evolutionary biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously nobody that ask a question on a Stack website want to read an answer of the kind &lt;code&gt;You should read that book!&lt;/code&gt;. It is often not really pleasant to read a book, it takes time and the OP that get this answer will likely just forget about their question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What are the best online resources that offer a very introductory understanding in evolutionary biology?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Either a written course of videos such as &lt;a href=&quot;https://www.khanacademy.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;Khan Academy&lt;/a&gt; videos would do (I haven't watched the evolutionary biology section of &lt;a href=&quot;https://www.khanacademy.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;Khan Academy&lt;/a&gt; though and can't really judge of how good it is).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2018-06-29T22:58:10.347" LastActivityDate="2018-06-29T22:58:10.347" Title="Very introductory online source of information in evolutionary biology" Tags="&lt;evolution&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="34155" PostTypeId="2" ParentId="34154" CreationDate="2015-05-11T04:08:35.127" Score="5" Body="&lt;p&gt;At least online, I think the single best introductory evolution resource is the &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evo_01&quot; rel=&quot;noreferrer&quot;&gt;Evolution 101 tutorial&lt;/a&gt; at UC Berkeley's &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/home.php&quot; rel=&quot;noreferrer&quot;&gt;Understanding Evolution&lt;/a&gt; project. The site has been designed by some of the top evolutionary biologists and evolution educators in the country, and does a very good job presenting a basic overview of how evolution works. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-05-11T04:08:35.127" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34156" PostTypeId="1" CreationDate="2015-05-11T04:23:07.887" Score="0" ViewCount="76" Body="&lt;p&gt;If, for example, humans had an average lifespan of, say, 30 years, and we reached sexual maturity at age 10, then we could &quot;evolve&quot; more quickly and theoretically &quot;weed-out&quot; more genetic diseases because we would live for shorter times, hence more natural selection. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why don't we continually evolve for &lt;em&gt;shorter&lt;/em&gt; lifespans (or do we)?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="15704" LastEditorUserId="15704" LastEditDate="2015-05-11T15:09:02.540" LastActivityDate="2015-05-11T15:09:02.540" Title="Would it be more genetically efficient to have shorter lifespans?" Tags="&lt;evolution&gt;&lt;lifespan&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34157" PostTypeId="2" ParentId="34156" CreationDate="2015-05-11T04:43:24.910" Score="3" Body="&lt;p&gt;Extremely briefly, we do not evolve shorter lifespans because &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/misconceptions_faq.php#b4&quot; rel=&quot;nofollow&quot;&gt;natural selection does not act for the good of the species.&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an interesting historical aside, August Weismann proposed essentially the idea you are suggesting in 1889, in his &lt;em&gt;Essays upon heredity and kindred biological problems.&lt;/em&gt; Within a few years, however, he backed away from this hypothesis.&lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-05-11T04:43:24.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34158" PostTypeId="1" CreationDate="2015-05-11T04:44:18.617" Score="1" ViewCount="71" Body="&lt;p&gt;During ribosome pre-40S and pre-60S synthesis, many sources state the importance of UAF or UBF in initiation complex of ribosome DNA transcription. None of the sources I've seen mentions the other when mentioning UAF or UBF, so I want to know if they are actually the same thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another source of confusion is that Wikipedia has article for both:&#xA;&lt;a href=&quot;https://en.wikipedia.org/wiki/Upstream_activating_factor&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Upstream_activating_factor&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/UBTF&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/UBTF&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance.&lt;/p&gt;&#xA;" OwnerUserId="15558" LastActivityDate="2015-05-11T04:44:18.617" Title="Are upstream activating factor (UAF) and upstream binding factor (UBF) the same thing?" Tags="&lt;terminology&gt;&lt;transcription&gt;&lt;ribosome&gt;&lt;transcription-factor&gt;&lt;rrna&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34159" PostTypeId="1" CreationDate="2015-05-11T06:26:24.350" Score="18" ViewCount="20934" Body="&lt;p&gt;The strict dependence of the (human) brain on glucose has always been puzzling to me. While ketones can substitute for a portion of the brain's energy needs, it cannot substitute completely: blood glucose levels below 2--3mM somewhere causes serious neurological problems and can lead to unconsciousness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other body tissues are not strictly dependent on glucose, but can oxidize amino acids as well, which is a good backup solution since there is always lots of protein around. But not the brain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of evolution, this strict glucose dependence must be a major drawback --- falling unconscious just because you don't get enough sugar is probably a bad thing out in the wilderness, when the lions are after you ... So there must be a very important reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So why is the brain so dependent on glucose?&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2021-01-01T22:14:29.833" Title="Why is the brain dependent on glucose?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;physiology&gt;&lt;metabolism&gt;" AnswerCount="4" CommentCount="9" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34160" PostTypeId="1" CreationDate="2015-05-11T11:42:20.050" Score="0" ViewCount="99" Body="&lt;p&gt;I'm interested in modelling host-pathogen interactions using mathematics. I know there are good resources in Pubmed but seems I'm looking for a book or introductory reviews.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My background in maths is limited, knowing the basics about calculus and algebra, and more recently some machine learning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper inspiring this question is this one:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Front Microbiol. 2015; 6: 235.&#xA;A review on computational systems biology of pathogen–host interactionsA review on computational systems biology of pathogen–host interactions&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="4717" LastEditDate="2015-05-12T07:07:48.803" LastActivityDate="2015-05-12T07:07:48.803" Title="Mathematical modelling of omics data" Tags="&lt;genomics&gt;&lt;mathematical-models&gt;&lt;metabolomics&gt;" AnswerCount="2" CommentCount="1" ClosedDate="2015-05-13T00:04:45.953" ContentLicense="CC BY-SA 3.0" />
  <row Id="34161" PostTypeId="1" CreationDate="2015-05-11T11:47:58.140" Score="0" ViewCount="59" Body="&lt;p&gt;We performed RNA-Seq of in vivo bacterial samples and identified some key up- and down-regulated pathways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We compared bacteria during infection with conventional agar plate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which could be the next steps to validate our findings? We are interested in antibiotic and vaccine developemnt.&lt;/p&gt;&#xA;" OwnerUserId="4717" LastEditorUserId="4717" LastEditDate="2015-05-11T15:07:27.443" LastActivityDate="2015-05-11T15:51:14.487" Title="Downstream analysis after in vivo pathogen RNAseq" Tags="&lt;rna-sequencing&gt;&lt;antibiotics&gt;&lt;vaccination&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34162" PostTypeId="2" ParentId="31246" CreationDate="2015-05-11T14:19:06.673" Score="2" Body="&lt;p&gt;If you have access to a laboratory (or at the very least a centrifuge and pipettes) and some laboratory experience you can extract the DNA from the cells which would be much easier to store. There are a number of commercial DNA extraction kits available that are easy to find on google and order online. I don't want to promote any particular brand but I've mostly used DNEasy made by Qiagen (really just because that's what I'm used to). All the step-by-step instructions are in the kit and all the reagents are also in the kit with the exception of 100% ethanol which should be easy to obtain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have significant molecular biology experience and access to a full lab with a fumehood and appropriate safety installations you can try a manual extraction using trizol or phenol-chloroform. This would be slightly cheaper however given the toxicity of these agents I wouldn't recommend this for you. It really doesn't sound like you have these resources available to you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once you have the DNA extracted you can dilute it in Tris-EDTA or the elution buffer that comes in the kit. You can store extracted DNA in a regular fridge (4C) for several years. If you're looking to store for decades you may want to rent space in a -80C freezer but this would be more expensive. A fridge may be just right to suit your needs. You should be careful that this fridge has a backup power supply.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I should be clear that although extracting DNA is the easiest way to do this for somebody with experience, you should not try if you don't know what you're doing. Some of these reagents are dangerous and you are likely to ruin the samples you've taken from your family members and end up with no DNA at all. Good luck!&lt;/p&gt;&#xA;" OwnerUserId="15594" LastActivityDate="2015-05-11T14:19:06.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34163" PostTypeId="2" ParentId="31246" CreationDate="2015-05-11T14:27:37.490" Score="0" Body="&lt;p&gt;You could store DNA diluted in water at -20C for a very long time. The only problem with at home storage would be the type of freezer most households have. These come standard with defrosting feature, which thaws up the freezer to remove the ice accumulation... This would affect the stability of the DNA at long term scale. Having a styrofoam box to protect the samples could however dampen the elevation of temperature around your DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the DIY extraction, most extraction methods use either chloroform or chaotropic salts... those are very toxic and dangerous. A &quot;dirty&quot; extraction would be the best approach. You would still need a centrifuge, NaOH, EDTA, and Tris Base for a very simple approach (1). The referenced protocol is prescribed for rodent tissue, but could be applied to small skin snips or buccal frottis (not that I recommend ripping skin from your relatives...). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the various reagents, &lt;a href=&quot;http://www.sigmaaldrich.com/&quot; rel=&quot;nofollow&quot;&gt;Sigma-Aldrich&lt;/a&gt; sells pure chemicals, but I have no idea if particulars can buy on their website. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;(1) &lt;a href=&quot;http://jaxmice.jax.org/support/genotyping/dna-isolation-protocols.html&quot; rel=&quot;nofollow&quot;&gt;http://jaxmice.jax.org/support/genotyping/dna-isolation-protocols.html&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="12924" LastActivityDate="2015-05-11T14:27:37.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34164" PostTypeId="2" ParentId="34160" CreationDate="2015-05-11T15:26:05.807" Score="1" Body="&lt;p&gt;I'm a bit confused because your title and your question description don't seem to align perfectly (-omics data versus host-pathogen interactions). If you are interested in host-pathogen dynamics, in my opinion, the best general introductory text in this area is Keeling and Rohani &lt;a href=&quot;http://www.modelinginfectiousdiseases.org/&quot; rel=&quot;nofollow&quot;&gt;Modeling infectious diseases and humans and animals&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-05-11T15:26:05.807" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34165" PostTypeId="2" ParentId="34160" CreationDate="2015-05-11T15:50:14.813" Score="1" Body="&lt;p&gt;As @Corvus said before me, the core of your post talks about mathematical modelling of host-pathogen interactions. The title talks about analyzing omics data. What are you really interested in? I will assume you are interested in modelling of host-pathogen interactions (as @Corvus did).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I agree with @Corvus (+1) that &lt;a href=&quot;http://www.modelinginfectiousdiseases.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Modeling infectious diseases and humans and animals&lt;/a&gt; is a good book to understand host-pathogen dynamics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you feel a bit uneasy about mathematical modelling, I strongly recommend &lt;a href=&quot;http://www.amazon.ca/Biologists-Mathematical-Modeling-Ecology-Evolution/dp/0691123446&quot; rel=&quot;nofollow noreferrer&quot;&gt;A guide to mathematical modelling in ecology and evolution&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aside those recommendations, &lt;a href=&quot;http://www.amazon.ca/Evolutionary-Dynamics-Exploring-Equations-Life/dp/0674023382&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evolutionary dynamics&lt;/a&gt; might interest you to understand evolution of viruses including evolution of virulence. Finally you might appreciate &lt;a href=&quot;http://www.amazon.ca/Why-We-Get-Sick-Darwinian-ebook/dp/B006XWYJSI/ref=sr_1_1?s=books&amp;amp;ie=UTF8&amp;amp;qid=1431359358&amp;amp;sr=1-1&amp;amp;keywords=why%20we%20get%20sick&quot; rel=&quot;nofollow noreferrer&quot;&gt;why we get sick&lt;/a&gt; although it is not heavy on math and a bit outdated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case you are interested, you will find on &lt;a href=&quot;https://biology.stackexchange.com/questions/16470/book-recommendation-on-population-evolutionary-genetics/16474#16474&quot;&gt;this post&lt;/a&gt; book recommendations for theoretical population genetics.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-05-11T16:51:12.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34166" PostTypeId="2" ParentId="34161" CreationDate="2015-05-11T15:51:14.487" Score="1" Body="&lt;p&gt;Okay, first, I would say to everyone planning a high-throughput experiment: Hypothesis first, &lt;em&gt;then&lt;/em&gt; experiment. Otherwise you're setting up an expensive and time-consuming test that's not going to answer the questions you want answered. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case, the question your experiment is designed to answer is &quot;What genes are crucial to growth in vivo that are not crucial to growth on a plate?&quot;, which is probably not the clearest model for vaccine/antibiotic design.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess you could say that a difference between the plate sample and the in vivo sample is the presence of a host, and therefore it's possible that upregulated pathways represent the bacteria's host adaptation, and maybe you can attack the bacteria by attacking its ability to colonize the host. A gene involved in immune evasion could make a good target.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(That's a very messy model, as there are tons of other differences going on, but since you've already run the experiment it's probably the best you've got.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So then, use your data for a new round of hypothesis generation. Take your pathways and come up with a way that they might be allowing the bacteria to adapt to the host-- maybe a secretory pathway that could be interfering with the target immune system, or some membrane signalling molecules that get upregulated, or whatever.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now you have a hypothesis, so design an experiment. For instance, take a key upregulated member of a pathway. The hypothesis is that it's crucial to growth in a host but not to growth in general. So, knock it down, either with chemical inhibitors or with genomic editing, and see if it's less effective at host colonization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Although host colonization effectiveness is pretty difficult to measure ethically if your target organism is humans. But you have some sort of proxy or model system to measure that, right?)&lt;/p&gt;&#xA;" OwnerUserId="819" LastActivityDate="2015-05-11T15:51:14.487" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="34167" PostTypeId="2" ParentId="34159" CreationDate="2015-05-11T16:24:09.237" Score="2" Body="&lt;p&gt;Glucose is the only fuel normally used by brain cells. Because neurons cannot store glucose, they depend on the bloodstream to deliver a constant supply of this fuel.&#xA;Fatty acids do not serve as fuel for the brain, because they are bound to albumin in plasma and so do not traverse the blood-brain barrier. In starvation, ketone bodies generated by the liver partly replace glucose as fuel for the brain. (Biochemistry. 5th edition.Berg JM, Tymoczko JL, Stryer L.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, amino acid catabolism is the process of using amino acids as an energy source. Turning amino acids into molecules that can be used in the Krebs cycle takes energy, which means that burning protein for fuel is not as efficient as burning carbohydrates. In addition, your body needs amino acids to make new proteins. When amino acids are used as an energy source, it reduces the reserves of amino acids that are available for protein synthesis.&lt;/p&gt;&#xA;" OwnerUserId="15706" LastEditorUserId="15706" LastEditDate="2015-05-11T16:31:45.000" LastActivityDate="2015-05-11T16:31:45.000" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34168" PostTypeId="1" AcceptedAnswerId="34170" CreationDate="2015-05-11T17:03:26.393" Score="2" ViewCount="979" Body="&lt;p&gt;Six restriction enzymes discussed in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001074/&quot; rel=&quot;nofollow&quot;&gt;Sequence-specific cleavage of RNA by Type II restriction enzymes&lt;/a&gt; (Murray et al.) have the ability to detect and cut RNA strands with that enzyme's recognition sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you know, restriction enzymes come from a system carried by some bacteria referred to as a &lt;a href=&quot;http://en.wikipedia.org/wiki/Restriction_modification_system&quot; rel=&quot;nofollow&quot;&gt;restriction-modification system&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With this fact in mind while reading the paper above, I wondered how the bacteria carrying one of these six systems protects it's own RNA from restriction. Do the corresponding methyltranferase in each system methylate DNA as well as RNA? Would this not greatly sacrifice gene expression rates seeing as the methyltranferase surely cannot methylate &lt;em&gt;all&lt;/em&gt; the RNA sequences being produced?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps I misunderstood the paper somehow. Could it be only in some circumstances outside the cell that these restriction enzymes have this unique ability?&lt;/p&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="9829" LastEditDate="2015-06-10T19:47:13.483" LastActivityDate="2015-06-10T20:50:29.750" Title="Cleavage of RNA by restriction enzymes?" Tags="&lt;bacteriology&gt;&lt;rna&gt;&lt;restriction-enzymes&gt;&lt;nucleic-acids&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34170" PostTypeId="2" ParentId="34168" CreationDate="2015-05-11T17:19:36.453" Score="2" Body="&lt;p&gt;This paper found that these enzymes recognize RNA:DNA heteroduplexes. Such duplexes are unlikely to be encountered &lt;em&gt;in vivo&lt;/em&gt;. They are present when DNA is primed for replication, but these duplexes are relatively short and thus are less likely to randomly contain a recognition sequence. Furthermore, if the recognition sequence is found in the primer, the gDNA will be methylated specifically to protect it from degradation. RNA:DNA duplexes are also found during transcription, but they are also short and the gDNA would be methylated. Additionally, the transcription bubble where the heteroduplex forms is protected by RNA polymerase, which subsequently displaces the transcript from the gDNA as it leaves the elongating complex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's also important to note that this paper found that these enzymes don't cleave RNA:DNA as well as they do DNA:DNA duplexes and these results occurred under experimental conditions with relatively high concentrations of enzyme and substrate. The lower catalytic efficiency is likely due to lower binding affinity, which could be caused by:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;presence of uracil in RNA (this was explicitly mentioned in the paper)&lt;/li&gt;&#xA;&lt;li&gt;2'-OH presenting a steric barrier&lt;/li&gt;&#xA;&lt;li&gt;helix shape (RNA tends to adopt an A-form helix)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-06-10T20:50:29.750" LastActivityDate="2015-06-10T20:50:29.750" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="34171" PostTypeId="2" ParentId="32993" CreationDate="2015-05-11T17:20:55.030" Score="4" Body="&lt;p&gt;What you have observed is called shuttle streaming. This is how Physarum polycephalum (I assume this is the species of slime mold in the video) and many other slime molds move.&lt;/p&gt;&#xA;&lt;p&gt;I found this &lt;a href=&quot;http://en.wikipedia.org/wiki/Physarum_polycephalum&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The movement of P. polycephalum is termed shuttle streaming. Shuttle streaming is characterized by the rhythmic back-and-forth flow of the protoplasm; the time interval is approximately two minutes. The forces of the streaming vary for each type of microplasmodium.&lt;/p&gt;&#xA;&lt;p&gt;The force in amoeboid microplasmodia is generated by contraction and relaxation of a membranous layer probably consisting of actin (type of filament associated with contraction). The filament layer creates a pressure gradient, over which the protoplasm flows within limits of the cell periphery.&lt;/p&gt;&#xA;&lt;p&gt;The force behind streaming in the dumbbell-shaped microplasmodia is generated by volume changes in both the periphery of the cell and in the invagination system of the cell membrane.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-05-11T17:20:55.030" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34172" PostTypeId="1" CreationDate="2015-05-11T13:55:07.970" Score="0" ViewCount="169" Body="&lt;p&gt;I know, or at least I think I do, that the contents of the stomach are called chyme and that it is acidic.  What are the contents of the small bowel called and is it acidic? &lt;/p&gt;&#xA;" OwnerDisplayName="Justin" LastEditorUserId="5144" LastEditDate="2015-05-11T18:19:59.510" LastActivityDate="2015-05-11T19:01:48.370" Title="Question about contents of small bowel" Tags="&lt;diet&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34173" PostTypeId="2" ParentId="34172" CreationDate="2015-05-11T19:01:48.370" Score="1" Body="&lt;p&gt;I think its still called Chyme:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After hours of mechanical and chemical digestion, food has been&#xA;  reduced into chyme. As particles of food become small enough, they are&#xA;  passed out of the stomach at regular intervals into the small&#xA;  intestine, which stimulates the pancreas to release fluid containing a&#xA;  high concentration of bicarbonate. This fluid neutralizes the gastric&#xA;  juices, which can damage the lining of the intestine, resulting in&#xA;  duodenal ulcer. Other secretions from the pancreas, gallbladder,&#xA;  liver, and glands in the intestinal wall help in digestion.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;When food particles are sufficiently reduced in size and composition,&#xA;  they are absorbed by the intestinal wall and transported to the&#xA;  bloodstream. Some food material is passed from the small intestine to&#xA;  the large intestine. In the large intestine, bacteria break down&#xA;  proteins and starches in chyme that were not digested fully in the&#xA;  small intestine.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Chyme&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Chyme&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastActivityDate="2015-05-11T19:01:48.370" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34174" PostTypeId="1" CreationDate="2015-05-10T22:06:53.873" Score="2" ViewCount="140" Body="&lt;p&gt;This is potentially more or less a question about optics, but I've never been truly satisfied with any explanation that I've been given about Myopia. In fact, I almost can't even believe it. There are a million different versions of this diagram:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oe0Ba.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that images of things could appear blurry when those things are focused in front of the retina, but then what discriminates between near and far things? Shouldn't everything be blurry? What exactly is different about this image when the thing being viewed is in close proximity to the eye?&lt;/p&gt;&#xA;" OwnerUserId="15743" OwnerDisplayName="Abe Fehr" LastEditorUserId="10456" LastEditDate="2015-05-11T20:16:49.653" LastActivityDate="2015-05-11T20:16:49.653" Title="How does myopia actually work?" Tags="&lt;vision&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34175" PostTypeId="2" ParentId="32993" CreationDate="2015-05-11T19:57:51.147" Score="2" Body="&lt;p&gt;Adding to @CDB's answer:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...Saigusa speculates that it instead depends on an internal mechanism&#xA;  of some kind, perhaps involving the perpetually pulsating gelatinous&#xA;  contents of its one cell, known as cytoplasm. The slime mold's&#xA;  membrane rhythmically constricts and relaxes, keeping the cytoplasm&#xA;  within flowing. When the amoeba's membrane encounters food, it&#xA;  pulsates more quickly and expands, allowing more cytoplasm to flow&#xA;  into that region; when it stumbles onto something aversive—such as&#xA;  bright light—its palpitations slow down and cytoplasm moves elsewhere.&#xA;  Somehow, the slime mold may be keeping track of its own rhythmic&#xA;  pulsing, creating a kind of simple clock that would allow it to&#xA;  anticipate future events.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;from: &lt;a href=&quot;http://www.scientificamerican.com/article/brainless-slime-molds/&quot; rel=&quot;nofollow&quot;&gt;http://www.scientificamerican.com/article/brainless-slime-molds/&lt;/a&gt;&#xA;In the paper itself he says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The model is based on physiological observations. We assume that&#xA;  multiple chemical oscillators of a series of periods underlie the&#xA;  multirhythmicity of locomotion, as multiple rhythms were observed in&#xA;  cellular activities in a &lt;em&gt;Physarum plasmodium&lt;/em&gt;. This means that there&#xA;  are continuous frequencies of oscillation....&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;...Oscillators with the same biochemical identity can interact over a&#xA;  distance by chemical diffusion and active advection of protoplasmic&#xA;  streaming. These direct interactions will tend to synchronize phase,&#xA;  but it may not be enough to make a strong synchrony. In fact,&#xA;  macroscopic cellular behaviors often show fluctuating oscillatory&#xA;  variations rather than clear oscillations with a large amplitude, and&#xA;  the fluctuating oscillatory variations of different chemical&#xA;  identities display frequent switching between in-phase and&#xA;  out-of-phase relationships, although each biochemical component still&#xA;  shows the slightly oscillatory behavior. This consideration implies&#xA;  that the noise ξ should be small so that desynchronization effects are&#xA;  relatively weak.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From: &lt;em&gt;Saigusa, Tetsu, et al. &quot;Amoebae anticipate periodic events.&quot; Physical Review Letters 100.1 (2008): 018101.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastActivityDate="2015-05-11T19:57:51.147" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34176" PostTypeId="2" ParentId="34174" CreationDate="2015-05-11T20:11:31.727" Score="1" Body="&lt;p&gt;The image you gave is not clear because it does not show the fact that the divergence pattern of light from a close object is different from the divergence pattern of light from a distant object. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kErkY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Light rays from a close object (first image) diverge, and therefore they are in focus for the myopic eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Light rays from a distant object (second image) is approximately parallel, and therefore they are not in focus for the myopic eye. The lens corrects for this inability to focus and allows the distant object to become in focus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also note that the myopic person is still capable of focusing on close objects despite the lens because the lenses are still capable of dynamic adjustment, but less so than a person with perfect eyesight. You can test this by focusing on a near object, then putting on your glasses. The object should be initially out of focus, and then become in focus as the eye lenses adjust to the distance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Myopia/presbyopia is fundamentally an issue of the focal range of the eye becoming limited to a specific range. If the ability of the eye lenses to dynamically adjust is further weakened, it may require &lt;a href=&quot;http://en.wikipedia.org/wiki/Progressive_lens&quot; rel=&quot;nofollow noreferrer&quot;&gt;progressive lenses&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/Bifocals&quot; rel=&quot;nofollow noreferrer&quot;&gt;bifocals&lt;/a&gt; to correct the issue. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-05-11T20:11:31.727" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34179" PostTypeId="1" AcceptedAnswerId="34210" CreationDate="2015-05-11T21:26:19.203" Score="4" ViewCount="311" Body="&lt;p&gt;I need a mammalian promoter that will maintain stable expression through differentiation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was originally planning to employ UbC for this specific project, however new information from a different experiment has come to light and now I need a promoter that has both extreme stability and high strength (as you know, UbC is renowned for it's very low expression rates). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do any of you have suggestions? Perhaps I should look into a hybrid promoter of sorts...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CDB&lt;/p&gt;&#xA;" OwnerUserId="13496" LastActivityDate="2015-05-13T08:41:41.743" Title="Stable and strong promoter?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="34183" PostTypeId="1" AcceptedAnswerId="34196" CreationDate="2015-05-12T10:22:21.207" Score="2" ViewCount="310" Body="&lt;p&gt;Anyone knows of a table with average concentration that can be found in  white blood?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something like:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Neutrophils - 80%&lt;/li&gt;&#xA;&lt;li&gt;Mast cells - ?%&lt;/li&gt;&#xA;&lt;li&gt;Dendritic cells - ?%&lt;/li&gt;&#xA;&lt;li&gt;B cells - ?%&lt;/li&gt;&#xA;&lt;li&gt;Helper T cells - ?%&lt;/li&gt;&#xA;&lt;li&gt;Killer T cells - ?%&lt;/li&gt;&#xA;&lt;li&gt;Natural killers - ?%&lt;/li&gt;&#xA;&lt;li&gt;Others - (whatever is left)&#xA;(the sum should be 100%, of course :))&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Also: are helper T cells and killer T cells visually different? I can only find pictures of T cells, but not of each. I am also unable to find pictures of natural killers. - Thank you!&lt;/p&gt;&#xA;" OwnerUserId="15713" LastActivityDate="2015-05-12T19:03:11.483" Title="White blood: cells concentration" Tags="&lt;immunology&gt;&lt;hematology&gt;&lt;lymphatic-system&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34186" PostTypeId="1" AcceptedAnswerId="34187" CreationDate="2015-05-12T11:59:25.273" Score="4" ViewCount="426" Body="&lt;p&gt;It is interesting, why are &lt;em&gt;Oxyuranus&lt;/em&gt; species called &lt;em&gt;Taipan&lt;/em&gt;. The snakes are Australian but &lt;em&gt;taipan&lt;/em&gt; looks like of Chinese origin word (it means &lt;em&gt;big shot&lt;/em&gt; - important person).&lt;/p&gt;&#xA;" OwnerUserId="4123" LastEditorUserId="16866" LastEditDate="2017-04-26T19:35:58.820" LastActivityDate="2017-04-26T19:35:58.820" Title="Why are Oxyuranus snake species named Taipan?" Tags="&lt;zoology&gt;&lt;taxonomy&gt;&lt;nomenclature&gt;&lt;herpetology&gt;&lt;etymology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34187" PostTypeId="2" ParentId="34186" CreationDate="2015-05-12T13:16:57.703" Score="7" Body="&lt;p&gt;An answer is found at the Wikipedia page for &lt;a href=&quot;http://en.wikipedia.org/wiki/Taipan&quot; rel=&quot;noreferrer&quot;&gt;Taipan&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The common name, taipan, was coined by anthropologist Donald Thomson after the word used by the Wik-Mungkan Aboriginal people of central Cape York Peninsula, Queensland, Australia.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This passage is citing &lt;em&gt;Sutton. 1995. Wik Ngathan Dictionary&lt;/em&gt; as support. I cannot evaluate the truth in this statement though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For another reference see &lt;a href=&quot;http://www.jstor.org/discover/10.2307/27863347?uid=47232&amp;amp;uid=3738984&amp;amp;uid=2129&amp;amp;uid=2&amp;amp;uid=70&amp;amp;uid=47230&amp;amp;uid=3&amp;amp;uid=67&amp;amp;uid=62&amp;amp;sid=21106376592071&quot; rel=&quot;noreferrer&quot;&gt;McKnight. 1981. &lt;em&gt;The Wik-mungkan concept Nganwi: a study of mystical power and sickness in an Australian tribe&lt;/em&gt;. Bijdragen tot de Taal-, Land- en Volkenkunde 137&lt;/a&gt;, which refers to &lt;em&gt;Taipan&lt;/em&gt; as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Rainbow_Serpent&quot; rel=&quot;noreferrer&quot;&gt;Rainbow serpent&lt;/a&gt; (an Aboriginal mythical creature) of the Wik-Mungkan tribe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even more folklore is found in &lt;a href=&quot;https://books.google.se/books?id=oHJxueGDR2YC&amp;amp;pg=PA39&amp;amp;#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;noreferrer&quot;&gt;McNamee. 2000. &lt;em&gt;The Serpent's Tale: Snakes in Folklore and Literature&lt;/em&gt;&lt;/a&gt; in &quot;&lt;em&gt;Taipan the snake and the blue-tongued lizard&lt;/em&gt;&quot;.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-05-12T13:40:46.980" LastActivityDate="2015-05-12T13:40:46.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34188" PostTypeId="1" CreationDate="2015-05-12T13:50:32.537" Score="1" ViewCount="331" Body="&lt;p&gt;By reversed I mean their body is a complete mirror image of a normal human's.&lt;/p&gt;&#xA;" OwnerUserId="15715" LastActivityDate="2015-05-12T19:01:44.823" Title="Would somebody born 'reversed' (e.g. heart on their right side, etc.) be completely healthy?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34189" PostTypeId="2" ParentId="34188" CreationDate="2015-05-12T13:57:13.703" Score="5" Body="&lt;p&gt;Yes, such a conditions exists. It is called &quot;situs inversus&quot; (literally &quot;inverted sites&quot;). All major organs are placed on the opposite site, the condition is relatively rare with an incidence rate of 1:10.000. There are some even rarer forms occuring, when the organs are flipped, but the heart is still on the left side (levocardia) as opposed to the case when it is also on the other side (dextrocardia). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While some  of the patients are phenotypically normal (besides having their organs on the &quot;wrong&quot; side), congenital heart disease and ciliary disorders (also known as Kartagener syndrome) can occur. See the linked paper below for an overview.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Pyonz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more information see &lt;a href=&quot;http://en.wikipedia.org/wiki/Situs_inversus&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and &lt;a href=&quot;http://emedicine.medscape.com/article/413679-overview&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and the article:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ciliajournal.com/content/pdf/s13630-014-0010-9.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Situs inversus and ciliary abnormalities: 20 years later, what is the&#xA;connection?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-05-12T19:01:44.823" LastActivityDate="2015-05-12T19:01:44.823" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34191" PostTypeId="1" CreationDate="2015-05-12T15:14:27.937" Score="1" ViewCount="221" Body="&lt;p&gt;We used some universal primers to amplify rDNA in a certain isolated bacterial specie. The problem is that rDNA PCR is not amplifying. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Primers were working well in other strains of same bacterial specie.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do you know what could be happening? Maybe strain-specific PCR inhibitors? This strain was successfully amplified using ERIC PCR.&lt;/p&gt;&#xA;" OwnerUserId="4717" LastActivityDate="2015-05-12T15:14:27.937" Title="rRNA colony PCR amplification not working" Tags="&lt;pcr&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34192" PostTypeId="1" CreationDate="2015-05-12T16:15:33.893" Score="3" ViewCount="6074" Body="&lt;p&gt;This causes more transpiration to occur from lower leaf surface. What's the exact reason for why are there more stomatal openings on the lower surface of a dicot leaf?&lt;/p&gt;&#xA;" OwnerUserId="8257" LastActivityDate="2015-05-29T18:31:48.270" Title="Why are there more stomatal openings on the lower surface of a dicot leaf?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34193" PostTypeId="2" ParentId="32964" CreationDate="2015-05-12T16:51:12.037" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://books.google.com/books/about/Endless_Forms_Most_Beautiful_The_New_Sci.html?id=-SqwP8CLdIsC&quot; rel=&quot;nofollow&quot;&gt;Endless Form Most Beautiful: The New Science of Evo Devo&lt;/a&gt; introduces the reader to several classic embryology experiments and some key principles too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'll edit this answer when I find more books or reading material of this nature.&lt;/p&gt;&#xA;" OwnerUserId="15610" LastActivityDate="2015-05-12T16:51:12.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34195" PostTypeId="1" CreationDate="2015-05-12T18:38:05.560" Score="1" ViewCount="99" Body="&lt;p&gt;This is pretty specific question maybe. Anybody have an estimate? For Toll Like Receptors there are something like 10... &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jbc.org/content/276/4/2551.long&quot; rel=&quot;nofollow&quot;&gt;http://www.jbc.org/content/276/4/2551.long&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm only finding NOD1 and NOD2 =&gt; only 2?&lt;/p&gt;&#xA;" OwnerUserId="13334" LastEditorUserId="13334" LastEditDate="2015-05-12T22:10:22.260" LastActivityDate="2015-05-13T02:26:13.733" Title="How many NOD like receptors in Human?" Tags="&lt;cell-biology&gt;&lt;receptor&gt;&lt;inflammation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34196" PostTypeId="2" ParentId="34183" CreationDate="2015-05-12T19:03:11.483" Score="4" Body="&lt;p&gt;Here are some figures from &lt;em&gt;Cellular and Molecular Immunology&lt;/em&gt;, 8th Edition:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hGP9g.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JOIVP.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hopefully they're helpful in some way.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-05-12T19:03:11.483" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34197" PostTypeId="2" ParentId="94" CreationDate="2015-05-12T19:34:43.983" Score="1" Body="&lt;p&gt;Circulation of cerebrospinal fluid (CSF) through the ventricular system is driven by motile cilia on ependymal cells of the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hagenlocher C1, Walentek P, M Ller C, Thumberger T, Feistel K.Ciliogenesis and cerebrospinal fluid flow in the developing Xenopus brain are regulated by foxj1.Cilia. 2013 Sep 24;2(1):12. doi: 10.1186/2046-2530-2-12.&lt;/p&gt;&#xA;" OwnerUserId="15719" LastActivityDate="2015-05-12T19:34:43.983" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34199" PostTypeId="2" ParentId="34062" CreationDate="2015-05-12T20:49:20.167" Score="6" Body="&lt;p&gt;The immune privilege is happening for brain, CNS, eye, testis and the uterus. All these tissues (or structures) share that they cannot be regenerated once they get damaged by an overshooting immune reaction. Infections in the eye followed by a strong immune response often lead to the loss of the eye, in rodents loss if immune tolerance against the fetus leads to abortion. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So basically this is a protective mode for these tissues to protect them from a stong immune reaction. See the references for some more details (especially on how this works).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://classes.biology.ucsd.edu/bisp194-1.FA09/Niederkorn_2006.pdf&quot;&gt;See no evil, hear no evil, do no evil: the  lessons of immune&#xA;privilege&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3985/gzm7up87_pdf.htm&quot;&gt;What is immune privilege (not)?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3985/ur38ucsm_pdf.htm&quot;&gt;Immune privilege or privileged immunity?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3959614/&quot;&gt;Immune Privilege and the Philosophy of Immunology&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Each immune privileged tissue has a unique function. The eye must protect the light path and signals that stimulate the retina, and photoreceptors to preserve vision. The testis has to protect the sperm as they proceed to the epididymis where they mature. The maternal reproductive tract has to protect its eggs both before and after fertilization and thus has developed specialized mechanisms to modify the body’s response to foreign antigens. These unique challenges require different solutions and lead to unique immune privilege mechanisms. However, although microenvironment and the stromal cells that carry out the particular function may vary between tissues, and consequently the mechanisms that promote regulation may be unique to that cell or tissue, the goal is the same: limit collateral damage to preserve tissue integrity and maintain homeostasis to the extent possible, without compromising host defense.&lt;/li&gt;&#xA;  &lt;/ol&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="3703" LastEditDate="2015-05-13T07:27:10.547" LastActivityDate="2015-05-13T07:27:10.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34200" PostTypeId="2" ParentId="30630" CreationDate="2015-05-12T22:01:22.180" Score="0" Body="&lt;p&gt;To answer your question: No, there are no restrictions to what amino acid is next (&quot;a nearest neighbor&quot;) to its N-terminal or C-terminal neighbor.&lt;/p&gt;&#xA;" OwnerUserId="10118" LastActivityDate="2015-05-12T22:01:22.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34202" PostTypeId="2" ParentId="23189" CreationDate="2015-05-12T22:06:17.657" Score="1" Body="&lt;p&gt;The problem is the glucosepane bond is very strong, hence the molecules which would break this bond need be necessarily toxic and damaging to other molecules in the body.  Glucosepane breakers already exist, but they are too toxic, and perhaps all will necessarily be that way.  All hope is not lost however.  Other very effective medical drugs (like clot breaking agents) are extremely toxic although life saving if applied in a local fashion via angiography under controlled conditions.  My hunch is that the same will need to be done for the known glucosepane breakers.  Glucosepane is extracellular, so the problem is really to avoid liver and renal toxicity.  Animal studies should concentrate on delivering known glucosepane breakers under special conditions of renal, liver, and cardiovascular and respiratory support and though hyper-hydration, hypothermia, ECMO, dialysis, metabolic blocking agents, etc, to limit systemic toxicities.  It won't be easy, but it could be well worth the effort if such single shot therapies could be developed which might then have long lasting effects as glucosepane would take many years to decades to build up again.&lt;/p&gt;&#xA;" OwnerUserId="15721" LastEditorUserId="15721" LastEditDate="2015-05-12T22:15:31.137" LastActivityDate="2015-05-12T22:15:31.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34203" PostTypeId="2" ParentId="34195" CreationDate="2015-05-13T02:26:13.733" Score="1" Body="&lt;p&gt;This &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3797414/&quot; rel=&quot;nofollow noreferrer&quot;&gt;review&lt;/a&gt; 22 proteins in the NOD like human repetoire. It was published in 2013...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The families are broken down into 9 general groups according to their domain composition in Figure 1 from that review.  Most of them are not named &quot;NOD&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qnQ7x.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2015-05-13T02:26:13.733" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34204" PostTypeId="1" AcceptedAnswerId="34207" CreationDate="2015-05-13T03:41:00.963" Score="0" ViewCount="912" Body="&lt;p&gt;With respect to this website:&lt;br&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://horfdb.dfci.harvard.edu/&quot; rel=&quot;nofollow&quot;&gt;http://horfdb.dfci.harvard.edu/&lt;/a&gt; &lt;br&gt;&lt;br&gt;&#xA;what does the term clonal isolates mean?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="6307" LastEditDate="2015-05-13T04:36:45.123" LastActivityDate="2015-05-13T05:24:25.417" Title="What is meant by clonal isolates?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34205" PostTypeId="2" ParentId="30630" CreationDate="2015-05-13T04:21:37.947" Score="4" Body="&lt;p&gt;Short answer: there are no restrictions &lt;em&gt;in principle&lt;/em&gt; on which amino acids can follow which. That means that &lt;em&gt;in principle&lt;/em&gt; you can have polypeptide in any configuration: AAAA, WQWQWQ &lt;em&gt;etc&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Problem is that polypeptides must be functional and, because they are in aqueous solution, it puts restrictions on how polypeptide form secondary and tertiary structure. It means that having very rigid hydrophobic surface is energetically unfavorable. If cell where to produce such polypeptide, it might be either degraded or cause problems for cell, such as aggregates or other form of toxicity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That means that polypeptides has more restrictions than just linkage (C-N bonding) order. And of course it has been studied: &lt;a href=&quot;http://kaib.people.cofc.edu/research/PhysicaA.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Probabilistic analysis of the frequencies of amino acid pairs within characterized protein sequences.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Authors analyzed protein databases to find out which doublets of amino acids are more and less common. First of all, not all amino acids (of which there are 20 considered) have same occurrence, e.g. P(L, leucine)=0.096, P(W, tryptophan)=0.0118.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And, of course, not doublets are equally distributed (16 pairs out of 400 were picked as statistically significant):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hdoHR.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-05-13T04:21:37.947" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34207" PostTypeId="2" ParentId="34204" CreationDate="2015-05-13T05:24:25.417" Score="2" Body="&lt;p&gt;Often genes or other DNA fragments are inserted into an expression vector and used to transform bacteria or other cells. When a mixture of vectors is used containing various DNA fragments (e.g. a chopped-up genome), then individual (bacterial) &lt;em&gt;colonies&lt;/em&gt; need to be &lt;em&gt;isolated&lt;/em&gt; to make sure they carry only one insert. This can be done, e.g., by plating the transformed cell culture such that individual colonies are obtained. Theoretically, one colony represents the offspring of one cell, hence the colony as a whole has one DNA insert and is a &lt;em&gt;clonal isolate&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-05-13T05:24:25.417" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34208" PostTypeId="2" ParentId="3166" CreationDate="2015-05-13T06:23:01.790" Score="1" Body="&lt;p&gt;This is an old question by now, but thought I'd give it a shot anyway. I am guessing the &quot;insides in and outsides out&quot; refers to maintaining intracellular concentrations of nutrients and other important molecules.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cell does spend a lot of energy to maintain high concentrations of amino acids and other key metabolites in the cytoplasm. The cell membrane is permeable to these molecules to allow uptake from the surroundings, but this also creates the problem that molecules are as likely to diffuse out as diffuse in. To maintain a concentration of any molecule higher than that of its surrondings, the cell must actively &quot;pump&quot; molecules inwards, which obviously costs energy. This goes on all the time; it's a constant fight against thermodynamics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A number of active pumps exist in cells, and it's experimentally difficult to measure the energy consumption of all of them. One very important pump though is the Na/K-ATPase, which uses ATP (energy) to maintain sodium and potassium gradients across the cell membrane, which are in turn used to drive transport of other molecules. The energy requirement of the Na/K-ATPase is readily measurable; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9234964&quot; rel=&quot;nofollow&quot;&gt;this review article&lt;/a&gt; estimates 19--28% of total energy consumption. This should be viewed as a lower bound.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-05-13T06:23:01.790" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34210" PostTypeId="2" ParentId="34179" CreationDate="2015-05-13T08:41:41.743" Score="2" Body="&lt;p&gt;There seems to be quite an amount of resources to help OP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Addgene has a page on topic with list and description of common promoters usable in variety of organisms: &lt;a href=&quot;http://blog.addgene.org/plasmids-101-the-promoter-region&quot; rel=&quot;nofollow&quot;&gt;Plasmids 101: The Promoter Region&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://books.google.com/books?id=mB_SBQAAQBAJ&amp;amp;pg=PA140&amp;amp;lpg=PA140&amp;amp;dq=common%20mammalian%20promoters&amp;amp;source=bl&amp;amp;ots=NcX30vYRuq&amp;amp;sig=xmiRA2d3OVpt9nUr6XOjECox-uA&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=zgpTVfTSB8ProATphYC4Dg&amp;amp;ved=0CGsQ6AEwCA#v=onepage&amp;amp;q=common%20mammalian%20promoters&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;Experimental biophysics&lt;/a&gt; textbook mentions some useful promoters as well, or this &lt;a href=&quot;http://www.ohsu.edu/nod/documents/week1/genether.promot.pdf&quot; rel=&quot;nofollow&quot;&gt;review&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Surprisingly, there has been some quantitative analysis of promoter strength: &lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010611&quot; rel=&quot;nofollow&quot;&gt;Systematic Comparison of Constitutive Promoters and the Doxycycline-Inducible Promoter&lt;/a&gt;, as well as effort toward stronger synthetic (version of CMV) &lt;a href=&quot;http://www.pnas.org/content/107/6/2538.full&quot; rel=&quot;nofollow&quot;&gt;Synthetic design of strong promoters&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My conclusion is that either viral, or CAG (based on chicken actin) promoters might be useful candidates. But one cannot expect ubiquitous and even expression in various tissues/cells types without fine-tuning expression cassette.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-05-13T08:41:41.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34211" PostTypeId="1" CreationDate="2015-05-13T09:48:07.883" Score="3" ViewCount="90" Body="&lt;p&gt;I am wondering is there some proper terminology which is used to say that deleterious recessive alleles might be able to hide, reducing the the efficacy of selection, in diploid organisms/chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was thinking about Y chromosome linked mutation and their inability to hide from purging by selection behind other alleles by being recessive... perhaps something like &lt;em&gt;recessive sheltering&lt;/em&gt;? e.g. &quot;In the Y chromosome mutations are more easily purged because &lt;em&gt;recessive sheltering&lt;/em&gt; does not occur&quot; ?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2015-05-24T21:22:32.047" Title="Terminology for inefficacy of selection on recessive alleles" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;terminology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34213" PostTypeId="1" AcceptedAnswerId="34216" CreationDate="2015-05-13T13:37:49.000" Score="-1" ViewCount="597" Body="&lt;p&gt;Can anyone clarify my confusion about that the epistasis seen in &quot;Labradors , an example of recessive or dominant epistasis? ?&#xA; I am not getting definite results . It's dominant somewhere and recessive in some.:(&#xA;May anyone provide me with some definite sources??&#xA;Thank you! !:)&lt;/p&gt;&#xA;" OwnerUserId="11647" LastActivityDate="2015-05-13T15:07:49.030" Title="Dominant and recessive epistasis" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-05-13T16:35:18.450" ContentLicense="CC BY-SA 3.0" />
  <row Id="34214" PostTypeId="1" CreationDate="2015-05-13T13:56:48.447" Score="0" ViewCount="165" Body="&lt;p&gt;I'm working on some bioinformatic analysis of a non-model woody plant within the family with least information. So, I'm looking for a closest species to my plant. Any suggestion would be highly appreciated. Also, It will be great if I have know about the divergence time (? million year) between two species. Is there any documents or website to address this issue? Thanks&lt;/p&gt;&#xA;" OwnerUserId="10205" LastEditorUserId="10205" LastEditDate="2015-05-13T14:11:11.060" LastActivityDate="2015-05-18T15:30:02.660" Title="how to find accurately the closest species to my plant species?" Tags="&lt;evolution&gt;&lt;bioinformatics&gt;&lt;botany&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34215" PostTypeId="1" AcceptedAnswerId="34222" CreationDate="2015-05-13T14:13:05.113" Score="8" ViewCount="756" Body="&lt;p&gt;I have been taught that a $\ce{Na+/~K+}$  pump helps to recover normal polarisation after-hyperpolarisation in neurones. I could not find out how it does that, since I've also been taught that such a pump moves $\ce{3Na+}$  out of the cell and $\ce{2K+}$  into the cell. That implies that the potential can only get more negative. How does this work?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My hypothesis was that the potential 'leaks' out and recovers the 70 mV that way. I couldn't verify that, however.&lt;/p&gt;&#xA;" OwnerUserId="15726" LastEditorUserId="3553" LastEditDate="2017-03-23T05:38:23.700" LastActivityDate="2020-07-31T17:24:33.233" Title="What recovers normal polarisation after hyperpolarisation?" Tags="&lt;neuroscience&gt;&lt;cell-membrane&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34216" PostTypeId="2" ParentId="34213" CreationDate="2015-05-13T15:07:49.030" Score="2" Body="&lt;p&gt;I agree that the question is unclear. I personally don't know the example of the labrador and would need a reference (or a description from you) to talk about this specific case study.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following tables are displaying all possible kind of interactions (in a haploid and in a diploid) of two bi-allelic loci. Hope that helps! &lt;a href=&quot;http://en.wikipedia.org/wiki/Epistasis&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt; (wiki)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;For Haploids (the concept of dominant epistasis does not apply)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AAmwj.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;For Diploids&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BXl8G.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2015-05-13T15:07:49.030" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34217" PostTypeId="2" ParentId="34214" CreationDate="2015-05-13T16:13:40.467" Score="1" Body="&lt;p&gt;If you know the species name, you can search &lt;a href=&quot;http://treebase.org/treebase-web/search/treeSearch.html&quot; rel=&quot;nofollow&quot;&gt;TreeBase&lt;/a&gt; to find previously published phylogenetic trees which will point you towards close relatives to your species. Depending on how obscure your taxon is, though, you might not find much.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-05-13T16:13:40.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34218" PostTypeId="1" CreationDate="2015-05-13T19:41:53.217" Score="4" ViewCount="971" Body="&lt;p&gt;I kind of know where the hypoglossal nerve is located when I look at the diagram, but I'd like to know how far is the nerve from the skin and where is the closest area to the skin before and right after it's branching?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any video or schema showing the location of the Hypoglossal nerve relative to skin and not the skeleton? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this pic. I can't really tell the closest location of being able to detect the nerve near the skin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/i2Iic.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="15729" LastEditorUserId="3553" LastEditDate="2017-04-01T04:43:25.570" LastActivityDate="2019-09-19T17:25:40.550" Title="What is the location of the Hypoglossal nerve?" Tags="&lt;neuroscience&gt;&lt;human-anatomy&gt;&lt;neuroanatomy&gt;&lt;literature&gt;&lt;cranial-nerves&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34219" PostTypeId="2" ParentId="27580" CreationDate="2015-05-13T19:54:14.827" Score="1" Body="&lt;p&gt;I'm interpreting &quot;durability&quot; as the DNA's resistance to physical stress, such as shearing. The &lt;a href=&quot;http://research.physics.berkeley.edu/bustamante/&quot; rel=&quot;nofollow&quot;&gt;Bustamante&lt;/a&gt; lab at UC Berkeley does a lot of very cool single-molecule biophysics looking at forces involved in protein-protein interactions and protein-DNA interactions. This Bustamante &lt;em&gt;et al.&lt;/em&gt; review paper, &lt;a href=&quot;http://liphardtlab.stanford.edu/pdfs/MechanicsofDNA.pdf&quot; rel=&quot;nofollow&quot;&gt;Single-molecule studies of DNA mechanics&lt;/a&gt; includes a look at the force required to break ssDNA and dsDNA:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Single molecules of dsDNA were broken&#xA;  with a receding water meniscus [26] at forces estimated&#xA;  to be 960 pN (correcting Young’s modulus doubles the&#xA;  published scission force of 480 pN). Short dsDNA molecules  pulled  with  an  AFM  tip  [27]  sustained  forces&#xA;  over 1700 pN.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;pN = picoNewton &lt;br&gt;&#xA;AFM = &lt;a href=&quot;http://en.wikipedia.org/wiki/Atomic_force_microscopy&quot; rel=&quot;nofollow&quot;&gt;atomic force microscopy&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;dsDNA is more resistant to stretching/shearing forces because the double helix arrangement is &quot;springy&quot;. I recommend giving the paper a read for more info. Very cool stuff.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-05-13T19:54:14.827" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34220" PostTypeId="2" ParentId="31368" CreationDate="2015-05-13T20:15:20.207" Score="4" Body="&lt;p&gt;I couldn't find any information about ants starving in times of plenty, most likely since it's difficult to determine whether an ant colony is &quot;letting&quot; certain members starve or whether the ants have just died for whatever reason. To your second question, though, yes! This paper, &lt;a href=&quot;http://bio.fsu.edu/~tschink/publications/1980-3.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Effect of Colony Size and Starvation on Food Flow in the Fire Ant&lt;/a&gt; by Howard and Tschinkel, shows the effects of different lengths of starvation on the passing of radioactive food through different sized ant colonies. First, the queen:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Generally, queens received radioactive food earlier in starved colonies than in well-fed ones&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Starved foraging ants distributed food more quickly than forager ants who had not been starved:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5Yuy6.png&quot; alt=&quot;figure 7&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And interestingly, in large colonies, larger worker ants were more likely to receive food (radioactivity) than smaller ants. Very cool paper.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-05-13T20:15:20.207" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34221" PostTypeId="1" CreationDate="2015-05-13T22:14:53.907" Score="1" ViewCount="418" Body="&lt;p&gt;I have observed an interesting phenomena with my vision lately. I just think I have never reflected over this before but it might always have been this way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am nearsighted and have no problem with double vision as long as an object is in focus, either with or without glasses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However when I take my glasses off and look at, e.g. my phone screen, and push it slowly just out of focus, there is a phase where multiple distorted weak ghost images appear before everything just becomes a more Gaussian like blur. It is especially clear with bright lines on a dark surface.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not believe that there is anything else wrong with my eyes, since as soon as an object is in a range where I can focus on it, all ghosting disappears.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am interested in knowing if anyone else observes this.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But more interesting is what are the possible optical properties of the eye that contributes to this, or is it a property of how our brain processes the input from the eyes.&lt;/p&gt;&#xA;" OwnerUserId="15733" LastEditorUserId="15733" LastEditDate="2015-05-14T11:12:52.233" LastActivityDate="2018-10-13T16:54:57.437" Title="Why are there ghost images of objects just out of focus" Tags="&lt;vision&gt;&lt;human-eye&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34222" PostTypeId="2" ParentId="34215" CreationDate="2015-05-13T22:23:09.023" Score="7" Body="&lt;p&gt;Remember that the action potential gets more positive in the first place, so increasing positivity is achievable. Net Na+ movement into the cell makes the potential more positive. This occurs as the Na+ gate (right on the image below) are open. The key message is that the membrane can move charge to cause an increase in either positive and negative potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tdd2O.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine one side becomes more negative. The Na+ diffusion will correct this to reach an equilibrium around 3 to 4 milliseconds (ms) after the stimulus to reach the resting potential&#xA; (as alluded to my @MCM in the comments).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are some great animations demonstrating this principle on the &lt;a href=&quot;http://www.bris.ac.uk/synaptic/basics/basics-2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;University of Bristol's website&lt;/a&gt;. They clearly show how positive charge can be conferred over the membrane.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A (&lt;em&gt;now deleted&lt;/em&gt;) comment linked to the below image that shows the potential and when the gates are opened and closed. I would still go to the bristol website too to see it in action, but this figure is a quick go to once you get your head around the timing of ion flux.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Y0C3i.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As with most biology, it is a little more complicated than that overly simple model. There are entire books on how neurones control their charges.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Note&lt;/em&gt;:&lt;/strong&gt; The key terminology is somewhat muddled and there doesn't seem to be a standard term. I have seen this &quot;recovery&quot; phase called &lt;strong&gt;undershoot&lt;/strong&gt;, &lt;strong&gt;overshoot&lt;/strong&gt; (and overshoot rather unhelpfully also refers to another part of the action potential), &lt;strong&gt;the refractory period&lt;/strong&gt;, and discussed as &lt;strong&gt;part of hyperpolarization&lt;/strong&gt;. The go to term is &lt;a href=&quot;http://en.wikipedia.org/wiki/Afterhyperpolarization&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;afterpolarisation&lt;/strong&gt;&lt;/a&gt; if you want to research this more thoroughly.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2017-03-23T04:50:44.700" LastActivityDate="2017-03-23T04:50:44.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34224" PostTypeId="1" AcceptedAnswerId="34226" CreationDate="2015-05-14T00:25:49.693" Score="1" ViewCount="360" Body="&lt;p&gt;By stimuli that we can perceive, I mean what our five senses can perceive. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there an absolute minimum for humans, or can we &quot;train&quot; ourselves to perceive stimuli at lower intensity? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if there is an absolute minimum intensity, do we know what its value is?&lt;/p&gt;&#xA;" OwnerUserId="9795" LastEditorUserId="9943" LastEditDate="2015-05-14T02:02:05.320" LastActivityDate="2015-05-14T05:19:09.263" Title="Is there an absolute minimum intensity level to the stimuli we can perceive?" Tags="&lt;perception&gt;&lt;psychophysics&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="34226" PostTypeId="2" ParentId="34224" CreationDate="2015-05-14T00:45:25.307" Score="4" Body="&lt;p&gt;There are limits to what a sensory system can detect, which is called the &lt;strong&gt;detection threshold&lt;/strong&gt;. To determine the detection threshold &lt;em&gt;psychophysical&lt;/em&gt; methods can be used. A straightforward way to determine the detection threshold is with a &lt;em&gt;yes/no task&lt;/em&gt;, where the subject receives stimuli with various intensities. An arbitrary point, mostly the 50% correct-rate, is then defined as the detection threshold. At this point, the subject correctly detects the stimulus 50% of the times. The response curve in a psychophysical task typically takes the shape of a cumulative function such as the one shown in Fig. 1. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, the detection threshold is an arbitrary point, because people are not machines and show variability in their decisions. The detection limit of, e.g., electronic devices is much more precisely defined. The exact values of the detection limits depend on the exact stimulus (visual, tactile etc.) and depend highly on the exact stimulus. For example, in the visual domain the detection limit of light depends on the color, the location in the retina tested, dark adaptation etc etc, and in the tactile domain static pressure stimuli have a different threshold than vibratory, different body parts have different thresholds etc. etc.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mtzGV.jpg&quot; alt=&quot;psychometric curve&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Psychometric curve showing 50% threshold of a visual stimulus. source: &lt;a href=&quot;http://webvision.med.utah.edu/book/part-viii-gabac-receptors/psychophysics-of-vision/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Webvision&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Training to lower the detection threshold (i.e. improve detection limits) is indeed possible (&lt;a href=&quot;http://www.jneurosci.org/content/18/11/4417.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sterr et al., 1998&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.jneurosci.org/content/18/11/4417.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sterr et al., &lt;em&gt;J Neurosci&lt;/em&gt; (1998), &lt;strong&gt;18&lt;/strong&gt;: 4417-23&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-14T05:19:09.263" LastActivityDate="2015-05-14T05:19:09.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34227" PostTypeId="1" AcceptedAnswerId="34233" CreationDate="2015-05-14T01:22:45.570" Score="2" ViewCount="1067" Body="&lt;p&gt;In &lt;a href=&quot;http://en.wikipedia.org/wiki/Ribonuclease&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; link, it states:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It is worth noting that all intracellular RNAs are protected from RNase activity by a number of strategies including 5' end capping, 3' end polyadenylation, and folding within an RNA protein complex (ribonucleoprotein particle or RNP).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I do not understand how polyadenylation protects the intracellular RNA from ribonuclease. I always thought that polyadenylation was a way to mark RNA &lt;em&gt;for&lt;/em&gt; degradation, not protect it from degradation. Perhaps it is speaking of protection from exoribonuclease only and not endoribonuclease?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone explain this?&lt;/p&gt;&#xA;" OwnerUserId="13496" LastEditorUserId="9829" LastEditDate="2015-05-14T12:28:57.777" LastActivityDate="2015-05-14T19:43:27.687" Title="How can 3' end polyadenylation protect cellular RNA from ribonuclease degridation?" Tags="&lt;molecular-biology&gt;&lt;rna&gt;&lt;mrna&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34231" PostTypeId="1" CreationDate="2015-05-14T10:28:40.987" Score="14" ViewCount="17293" Body="&lt;p&gt;The simplest description of the difference between these two approaches that I have found are on &lt;a href=&quot;https://theartofmodelling.wordpress.com/2012/02/19/mechanistic-models-what-is-the-value-of-understanding/&quot; rel=&quot;noreferrer&quot;&gt;this site&lt;/a&gt; who summarise the difference as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Mechanistic model&lt;/strong&gt;: a hypothesized relationship between the variables in the data set where the nature of the relationship is specified in terms of the biological processes that are thought to have given rise to the data. The parameters in the mechanistic model all have biological definitions and so they can be measured independently of the data set referenced above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Phenomenological/Statistical model&lt;/strong&gt;: a hypothesized relationship between the variables in the data set, where the relationship seeks only to best describe the data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could someone exemplify this difference with a short example. I have used and understand the principals of a statistical model (multiple regression etc) but haven't come across any simplistic examples of a mechanistic model and I don't understand what the difference would be in practice. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: I am leaving the question open for a week to see if anyone wants to create a very small 'MWE' of the two types to illustrate what the difference would look like in practice, if not I will accept Memmings answer&lt;/p&gt;&#xA;" OwnerUserId="15736" LastEditorUserId="15736" LastEditDate="2015-05-16T07:48:22.273" LastActivityDate="2017-01-04T00:09:12.623" Title="What is the difference between a mechanistic and a statistical predictive model?" Tags="&lt;mathematical-models&gt;&lt;statistics&gt;&lt;computational-model&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="34233" PostTypeId="2" ParentId="34227" CreationDate="2015-05-14T12:26:28.290" Score="2" Body="&lt;p&gt;Actually, whether polyadenylation protects an mRNA or makes it susceptible to degradation depends on the organism. From &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867402011376&quot; rel=&quot;nofollow&quot;&gt;Dreyfus and Régnier 2002&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In eukaryotes, poly(A) tails usually act as stabilizers of intact mRNAs, whereas in E. coli they serve to accelerate the destruction of fragments.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is due to different protection mechanisms in prokaryotes and eukaryotes:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Poly(A) Binding Protein (PABP) inhibits deadenylation in mammalian cell-free assays. Although poly(A) binding proteins exist in E. coli as well and although they can protect poly(A) tails against PNPase in vitro (Feng et al., 2001), they may be unable to exert a significant protection in vivo because poly(A) tails never grow long enough to enable them to bind.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Important to note is that bacterial mRNA degradation usually starts &lt;em&gt;internally&lt;/em&gt;, in contrast to eukaryotic mRNA degradation which happens (exonucleotically?):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As noted above, another distinctive feature of bacteria is the fact that polyadenylation usually affects the degradation of fragments only, because the initial attack on most intact mRNAs is endonucleolytic.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;All of these quotes come from the review I referenced at the top of my answer, I recommend reading it as it's very comprehensive (and interesting).&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="9829" LastEditDate="2015-05-14T19:43:27.687" LastActivityDate="2015-05-14T19:43:27.687" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34234" PostTypeId="2" ParentId="34227" CreationDate="2015-05-14T12:48:57.857" Score="4" Body="&lt;p&gt;According to my book &lt;em&gt;Molecular Biology Principles of Genome Function&lt;/em&gt; by Craig et al, eukaryotic RNA degradation does not have an initiation, as in bacteria where pyrophoasphate hydrolase hydrolyses the 5'-triphosphate to 5'-monophosphate, and is therefore the initiatior. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In eukaryotes the polyA-tail is shortened by a deadenylase enzyme complex which contains a 3'to 5' exonuclease called CCR4. But deadenylation of polyA-tail doesn't necessesarily need to lead to degradation since it is reversible by post-translational readenylation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Poly A tail protects the mRNA by not letting the nucleases reach the mRNA itself. As long as poly A tail is degraded, its just fine, since it can readenylate back again. The figure below shows the degradation of mRNA in eukaryotes, which can be either in 5' to 3' direction or 3' to 5' direction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/M2hOb.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you are thinking of is ubiquitination of proteins, which is a post-translational process which can mark the proteins for degradation. &lt;/p&gt;&#xA;" OwnerUserId="15566" LastActivityDate="2015-05-14T12:48:57.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34235" PostTypeId="2" ParentId="34231" CreationDate="2015-05-14T14:58:13.833" Score="9" Body="&lt;p&gt;Mechanistic model answers the &lt;strong&gt;how&lt;/strong&gt; question. These models are usually biophysically detailed, and designed to be causal. Say you discovered a linear relation between blood pressure drug and heart rate. This would be a statistical model. It doesn't tell you how the two are related biophysically. One could build a detailed model that describes intermediate processes from the drug entering the system, to binding to receptors, and modulating levels of hormones, and acting as a signal to the heart rate modulation system. This model would have more parameters, and if it predicts the phenomena and generalizes well, then it might be a good approximation of the system. Moreover, it generates hypotheses and is more interpretable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That being said, I do not think the two concepts are mutually exclusive. Some mechanistic/biophysical models can also be statistical at the same time. It's a matter of having enough data and constraints to be able to fit the model or not.&lt;/p&gt;&#xA;" OwnerUserId="460" LastActivityDate="2015-05-14T14:58:13.833" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="34236" PostTypeId="1" AcceptedAnswerId="34237" CreationDate="2015-05-14T16:58:25.697" Score="0" ViewCount="172" Body="&lt;p&gt;Throughout the decades we heard that the heart is the only muscle whose nervous system is not acting. So who is he responsible for organising the heartbeat and its roles?&lt;/p&gt;&#xA;" OwnerUserId="15640" LastEditorUserId="15741" LastEditDate="2015-05-14T22:25:05.763" LastActivityDate="2015-05-14T22:25:05.763" Title="Who is organizing the heartbeat and its roles in the body?" Tags="&lt;central-nervous-system&gt;&lt;circulatory-system&gt;&lt;peripheral-nervous-system&gt;&lt;heart-output&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34237" PostTypeId="2" ParentId="34236" CreationDate="2015-05-14T17:27:37.743" Score="2" Body="&lt;p&gt;The Sinoatrial Node is a ganglion (clump of nerves) attached to the heart, which regulates heartbeat independently from the brain (&lt;a href=&quot;http://en.wikipedia.org/wiki/Sinoatrial_node&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Sinoatrial_node&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Heart rate can also be influenced by hormonal responses produced by the autonomic nervous system. To quote Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;While heart rhythm is regulated entirely by the sinoatrial node under&#xA;  normal conditions, heart rate is regulated by sympathetic and&#xA;  parasympathetic input to the sinoatrial node. The accelerans nerve&#xA;  provides sympathetic input to the heart by releasing norepinephrine&#xA;  onto the cells of the sinoatrial node, and the vagus nerve provides&#xA;  parasympathetic input to the heart by releasing acetylcholine onto&#xA;  sinoatrial node cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source: en.wikipedia.org/wiki/Heart_rate#Physiology&lt;/p&gt;&#xA;" OwnerUserId="368" LastEditorUserId="368" LastEditDate="2015-05-14T17:52:08.490" LastActivityDate="2015-05-14T17:52:08.490" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34238" PostTypeId="1" AcceptedAnswerId="34240" CreationDate="2015-05-14T17:46:23.760" Score="6" ViewCount="1483" Body="&lt;p&gt;If iI were to have access to funds for research, would learning this technique be a boon for me? Or are next-gen sequencing methods all the range now? My knowledge of both are limited. &lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="9943" LastEditDate="2015-05-15T12:21:10.587" LastActivityDate="2015-05-15T12:21:10.587" Title="Is Sanger sequencing still used in labs, and therefore worth learning?" Tags="&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34239" PostTypeId="2" ParentId="34238" CreationDate="2015-05-14T18:02:17.383" Score="0" Body="&lt;p&gt;No its not Depends on the scale you are workin on&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The dideoxy termination method of DNA sequencing (often called Sanger&#xA;sequencing after the technique’s inventor, Fred Sanger) has been the&#xA;workhorse of pretty much every molecular biology lab for the last 30&#xA;years. However, over the last few years the method has been&#xA;increasingly supplanted by so-called next-generation sequencing&#xA;technologies, which allow incredibly rapid generation of large amounts&#xA;of sequence data.&lt;/p&gt;&#xA;&lt;p&gt;Sanger sequencing is still widely used for&#xA;small-scale experiments and for “finishing” regions that can’t be&#xA;easily sequenced by next-gen platforms (e.g. highly repetitive DNA),&#xA;but most people see next-gen as the future of genomics.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The article also addresses issues on read length and cost between NGS and Sanger.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;For Sanger sequencing these reads are routinely 800-1000 base pairs long; next-gen methods produce much larger quantities of sequence, but in the form of much smaller reads (the two best-performing platforms generate 35-75 base pair reads, while a third, lower-throughput platform can manage 400 base pairs).&#xA;Read length is absolutely crucial when it comes to assembling accurate sequence, especially for genomes as complex and repetitive as the human genome. If a repetitive region is much longer than a platform’s read length, it can’t really be accurately assembled – so human genomes sequenced with current next-gen platforms actually consist of hundreds of thousands of accurately sequenced fragments interspersed by gaps....&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Taken from: &lt;a href=&quot;http://www.wired.com/2009/01/sanger-sequencing-is-not-dead/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.wired.com/2009/01/sanger-sequencing-is-not-dead/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-05-14T18:16:51.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34240" PostTypeId="2" ParentId="34238" CreationDate="2015-05-14T18:02:33.707" Score="6" Body="&lt;p&gt;Sanger sequencing is still used in the labs today - and not only on the side. Next-generation sequencing has its strength when it comes to sequencing very large amounts of DNA (basically whole genomes or exomes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sanger sequencing is used when you want to sequence smaller regions or portions of a genome/plasmid. Typical read length is (depeding on the machine and the skills of the operator) 600-900bp. This is enough to verify site directed mutagenesis, the presence of inserts you cloned as well that they are correct (if the insert is longer you will typically nest the single sequence reactions to cover the whole sequence) or look for a polymorphism. There are endless possibilities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally it is relatively cheap to sequence single samples (which is not really working on the next-gen machines), one sample comes between 8 and 10$ (at least the last time I sent this out). And you don't even have to do it yourself as there are a lot of service providers available. The technique itself is not hard to learn either.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-05-14T18:02:33.707" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34241" PostTypeId="2" ParentId="2056" CreationDate="2015-05-14T19:04:21.890" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Ultrasound emitting devices are used to repel mosquitoes. We tested&#xA;  the repelling properties of a commercially available ultrasound device&#xA;  in a domestic setting in Gabon. Devices emitting three different block&#xA;  frequencies ranging from 3 to 11 kHz were tested in a paired,&#xA;  cross-over blinded and placebo controlled trial during eighteen nights&#xA;  in nine pairs of houses. A total of 7485 mosquitoes (10% Anopheles,&#xA;  62% Culex, 27% Mansonia and 1% Aedes) were caught, 23 per house per&#xA;  night. There was no significant difference in landing rate between the&#xA;  houses with ultrasound device and the houses with placebo for any&#xA;  species of mosquito. Thus the ultrasound device used was not effective&#xA;  against mosquitoes in this strictly controlled trial.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10890136&quot; rel=&quot;nofollow&quot;&gt;Sylla el-H K, Lell B, Kremsner PG. A blinded, controlled trial of an ultrasound device as mosquito repellent. &lt;em&gt;Wiener Klinische Wochenschrift&lt;/em&gt;. 2000 May;112(10) 448-450. PubMed PMID: 10890136.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A bibliographic review about the use of electroacoustic devices with a&#xA;  supposed repellent action on the females of different species of&#xA;  hematophagous mosquitoes  is presented. 15 direct references and 2&#xA;  indirect ones are given, in which it is  concluded that these devices&#xA;  do not protect those who have them from the stings of mosquitoes. The&#xA;  names of 9 of the tested devices as well as of 16 of the main  species&#xA;  of mosquitoes present in the field tests are mentioned. These tests&#xA;  have  been carried out in very different ecological conditions from&#xA;  Alaska to Equatorial Africa. It is also stressed that the high&#xA;  intensity ultrasonic frequencies emitted by these devices produces a&#xA;  potentially harmful effect on man.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Rev Cubana Med Trop. 1998;50(2):89-92.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10349423&quot; rel=&quot;nofollow&quot;&gt;[Electronic repellents against mosquitoes: the propaganda and the reality].&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[Article in Spanish]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coro F(1), Suárez S.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Author information: &#xA;(1)Facultad de Biología, Universidad de La Habana, Ciudad de La Habana, Cuba.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PMID: 10349423  [PubMed - indexed for MEDLINE]&lt;/p&gt;&#xA;" OwnerUserId="9643" LastEditorUserId="9643" LastEditDate="2015-05-14T19:11:48.957" LastActivityDate="2015-05-14T19:11:48.957" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34242" PostTypeId="1" CreationDate="2015-05-14T19:07:42.423" Score="9" ViewCount="722" Body="&lt;p&gt;I'm reading through some oldish (1980s) papers on length-weight relationships in fish and crustaceans. Many report log-log relationships without specifying whether this is natural log, base 10, etc. In mathematics log is typically assumed to mean natural log, but the results reported in these papers make more sense if you assume &quot;log&quot; means &quot;log base 10&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a convention in biology that I should be aware of?&lt;/p&gt;&#xA;" OwnerUserId="15740" LastActivityDate="2015-05-18T04:32:31.097" Title="What is the convention for log notation in biology?" Tags="&lt;physiology&gt;&lt;zoology&gt;&lt;marine-biology&gt;&lt;allometry&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34243" PostTypeId="2" ParentId="31280" CreationDate="2015-05-14T19:43:21.853" Score="2" Body="&lt;p&gt;I am quoting this web page &lt;a href=&quot;http://spectrum.ieee.org/consumer-electronics/gadgets/backyard-star-wars&quot; rel=&quot;nofollow&quot;&gt;http://spectrum.ieee.org/consumer-electronics/gadgets/backyard-star-wars&lt;/a&gt; which describe a prototype of a system to kill mosquitoes by means of a LASER, for what regard the speed:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mosquitoes fly up to a meter per second.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This speed is compatible with 1.2 meter per second quoted in the paper&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6108094&quot; rel=&quot;nofollow&quot;&gt;SNOW, W. F. Field estimates of the flight speed of some West African mosquitoes. &lt;em&gt;Annals of tropical medicine and parasitology&lt;/em&gt;, 1980, 74.2: 239-242.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;There was a relationship between wind speed and catches of Anopheles&#xA;  melas and Culex thalassius which attempted to bite man at ground level&#xA;  and at 4 and 8 m on  an open scaffolding tower, in cleared bush in The&#xA;  Gambia. It was expected that in winds which exceeded their flight&#xA;  speed, no mosquitoes would be able to approach  and attack men on the&#xA;  tower. Catches of mosquitoes fell off sharply in winds of 120 cm/s,&#xA;  which may approximate to their flight speed, although some insects&#xA;  were still captured at the highest wind speeds encountered.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;For what regard the flying altitude:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The average flying altitude varies among mosquito species but is&#xA;  usually only about 2 meters. They will fly over obstacles when&#xA;  necessary—even into an upper-story window—but if your virtual fence is&#xA;  3 to 5 meters high, it can catch almost all mosquitoes that fly by.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The system is patented and the patent is specific about &lt;em&gt;Anopheles&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For example, more than 99% of &lt;em&gt;Anopheles&lt;/em&gt; mosquitoes (which may carry&#xA;  strains of malaria that can infect humans) fly at less than 3-5 meters&#xA;  of altitude&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.google.com/patents/US20140226860&quot; rel=&quot;nofollow&quot;&gt;HYDE, Roderick A., et al. &lt;em&gt;Photonic fence&lt;/em&gt;. U.S. Patent Application 14/255,119, 2014.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9643" LastEditorUserId="9643" LastEditDate="2015-05-14T20:07:53.107" LastActivityDate="2015-05-14T20:07:53.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34245" PostTypeId="1" AcceptedAnswerId="34253" CreationDate="2015-05-14T20:35:23.820" Score="0" ViewCount="140" Body="&lt;p&gt;This is the first time that I use NCBI-GEO and I've faced with 3 different categories inside it. They are &lt;code&gt;platform&lt;/code&gt;, &lt;code&gt;sample&lt;/code&gt; and &lt;code&gt;series&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NCBI-GEO have GEO-Overview section to explain these terms to ones who are new to this website, however; although I read it a couple of times, I could not understand it totally.&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/info/overview.html#org&quot; rel=&quot;nofollow&quot;&gt;GEO-Overview page&lt;/a&gt; The terms are a bit complex for the ones who are not familiar with the concepts. Therefore, is there anyone who could explain them with simpler words ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my situation, I use NCBI-GEO to get RNA-seq data for the &lt;code&gt;C. Elegans&lt;/code&gt; organism. I've downloaded the following SRA file : &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1576706&quot; rel=&quot;nofollow&quot;&gt;NCBI-geo C. Elegans sample&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I understood, a sample contains an individual organism's information.(In my case its a single C.elegans organism) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Series are somehow the collection of multiple samples I guess. I wonder what is the criteria to put different samples into same series?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And lastly, what is the differences between platforms and series ? I thought that each organism have a single platform, in other words, I thought I could find all the things about lets say C.elegans in its platform but I saw that a single organism type may have a lot of different platforms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, I'm seeking to learn these concepts and I think this website is the correct place to ask it. If my question is off topic, sorry about that I was not aware of it.&lt;/p&gt;&#xA;" OwnerUserId="14759" LastEditorUserId="14759" LastEditDate="2015-05-14T20:51:12.573" LastActivityDate="2015-05-15T03:55:54.160" Title="NCBI-geo differences between platforms,series and samples" Tags="&lt;rna&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34246" PostTypeId="2" ParentId="21396" CreationDate="2015-05-14T20:38:34.587" Score="1" Body="&lt;p&gt;Gillett studied the feeding behavior of Aedes africanus and Aedes aegypti, the abstract says that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;They showed that while the period between salivary injection and the&#xA;  onset of irritation was the same in both species (ca. 3 min)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It seems to me that the abstract does not say whether the hosts were humans or not. Unfortunately I am not able to get the full paper.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/167/1008/316&quot; rel=&quot;nofollow&quot;&gt;GILLETT, J. D. Natural selection and feeding speed in a blood-sucking insect. &lt;em&gt;Proceedings of the Royal Society of London B: Biological Sciences&lt;/em&gt;, 1967, 167.1008: 316-329.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9643" LastActivityDate="2015-05-14T20:38:34.587" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34249" PostTypeId="2" ParentId="28378" CreationDate="2015-05-14T21:38:26.973" Score="2" Body="&lt;p&gt;At typical physiological pHs glutamate does exist as glutamate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Broadly the acidity in the digestive track is enough to reduce glutamate to glutamic acid. The stomach for example has a healthy pH of between &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/003883.htm&quot; rel=&quot;nofollow&quot;&gt;1.5 to 3.5&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Canadianer points out in the comments that the active site during catalysis are protonated. There are obviously a lot of examples of this and sensitive evaluation by looking at the isocontours and surface potential of the protein structure are needed to draw conclusions if this might be important. &lt;/p&gt;&#xA;" OwnerUserId="15741" LastActivityDate="2015-05-14T21:38:26.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34250" PostTypeId="1" AcceptedAnswerId="34252" CreationDate="2015-05-14T21:50:43.323" Score="1" ViewCount="10056" Body="&lt;p&gt;Chemically polar amino acids have an uneven (AKA  &lt;em&gt;polar&lt;/em&gt;) distribution of electrons over their surface.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Charged amino acids have a charged ion in their structure. This is probably where my knowledge is a little shaky!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess I am confused at this point. Does this just mean that charged amino acids are &lt;strong&gt;&lt;em&gt;really&lt;/em&gt;&lt;/strong&gt; polar amino acids? If that is correct that would explain why I have seen histidine categorised as a charged amino acid, but has no clear ions.&lt;/p&gt;&#xA;" OwnerUserId="15741" LastEditorUserId="15741" LastEditDate="2015-10-06T09:54:55.407" LastActivityDate="2015-10-06T09:54:55.407" Title="What is the difference between polar and charged amino acids?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34251" PostTypeId="1" CreationDate="2015-05-14T22:02:00.103" Score="3" ViewCount="49" Body="&lt;p&gt;&lt;strong&gt;Modern techniques.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In recent years, DNA sequencing has become extremely cheap. This, compounded by the ability to PCR miniscule samples to viable samples for analysis, means that aDNA can be extracted and analysed from ancient tissue samples that 20 years ago would have been impossible to sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Pre sequencing techniques.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However ancient biochemical analysis was around before the human genome project revolutionised sequencing technology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although blood typing was fiddly, grossly time consuming, and expensive, people were able to define historical lineages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does the &quot;old-school&quot; approach of blood-typing compare in terms of cost, accuracy, sample required, and speed against the modern aDNA analysis? Do those sort of experiments still have a place in a modern ancient tissue lab?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2016-08-05T01:13:33.837" LastActivityDate="2016-08-05T01:13:33.837" Title="Does blood typing still provide a use for ancient tissue analysis?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;dna-sequencing&gt;&lt;hematology&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34252" PostTypeId="2" ParentId="34250" CreationDate="2015-05-15T01:24:15.717" Score="9" Body="&lt;p&gt;All amino acids with side chains that are charged at physiological pH are, by definition, also amino acids with polar side chains (e.g., lysine or glutamic acid). The converse is not true; in other words not all amino acids with polar side chains are necessarily amino acids with side chains that are charged at physiological pH (e.g., threonine or asparagine). The pKa of the nitrogen in histidine's imidazole ring is quite close to physiological pH, and in some situations would be charged and in other environments would be uncharged. In either case it would be considered polar (or largely hydrophilic in nature).&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-05-15T01:24:15.717" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34253" PostTypeId="2" ParentId="34245" CreationDate="2015-05-15T03:55:54.160" Score="1" Body="&lt;p&gt;The platform at NCBI-GEO means the particular microarray that was used (because originally most of GEO was just microarrays), OR, more recently, it could mean the type of NGS machine that was used.  For example, every microarray manufacturer creates an ADF (array data file) that maps the DNA sequence at every position on the Chip to an accession ID. And this ADF mapping file gets registered at GEO as a GPLxxxxxx. This was presumably to facilitate direct comparisons between different experiments from various labs using identical Chips (e.g. Affymetrix, or Nimblegen).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With the advent of NGS the Platform has to be a name from an approved list of companies and devices: ILLUMINA, HiSeq, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A series is constructed by the data providers and allows them to cluster the results from related samples. So, for example, in the modENCODE consortium, I believe all of the &lt;em&gt;C. elegans&lt;/em&gt; RNA-Seq from Bob Waterston's lab/Project are clustered together under one overarching GSExxxxxxx. More details at www.modencode.org and links therein.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-05-15T03:55:54.160" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34258" PostTypeId="2" ParentId="34242" CreationDate="2015-05-15T07:03:31.653" Score="8" Body="&lt;p&gt;There is a reason for prevalent usage of log&lt;sub&gt;2&lt;/sub&gt; and log&lt;sub&gt;10&lt;/sub&gt; compared to log&lt;sub&gt;e&lt;/sub&gt; in biology and other experimental sciences. Usually while doing measurements we are generally interested in fold changes and we generally talk in the sense of two-fold (or multiples of two) or ten-fold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Doubling is a common phenomenon at least in case of growth and so a two-fold change would represent an event of doubling. log&lt;sub&gt;2&lt;/sub&gt; gives you the extent of &quot;doubling&quot;. Even in computer systems memory is always in the exponents of two (because of binary); so even there log&lt;sub&gt;2&lt;/sub&gt; would make sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In biology you would generally not see a ten-fold change but in physics it is relatively common. Most values are represented in scientific notation which basically uses an exponent of 10. Also the metric units are in multiples of 10. Here log&lt;sub&gt;10&lt;/sub&gt; would be more suitable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;log&lt;sub&gt;e&lt;/sub&gt; has a special mathematical importance i.e. it can be denoted as a series. The euler's number has other important properties too. Therefore in most theoretical studies, both in biology and physics, log&lt;sub&gt;e&lt;/sub&gt; is preferred because it makes more mathematical sense.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To sum up, experimentalists prefer log&lt;sub&gt;2&lt;/sub&gt; or log&lt;sub&gt;10&lt;/sub&gt; because they are better for representing measurements whereas theoreticians prefer log&lt;sub&gt;e&lt;/sub&gt; because of its mathematical importance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;W.r.t the old paper that reports log-log relationships, the base of the logarithm wouldn't make any difference to the slope. But most likely it must be log&lt;sub&gt;10&lt;/sub&gt; (I think back then log&lt;sub&gt;10&lt;/sub&gt; was the default log; log&lt;sub&gt;2&lt;/sub&gt; would be much more suitable for lengths and weights of organisms compared to log&lt;sub&gt;10&lt;/sub&gt; because these measures would not vary in multiples of 10).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-05-18T04:32:31.097" LastActivityDate="2015-05-18T04:32:31.097" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34259" PostTypeId="1" AcceptedAnswerId="34262" CreationDate="2015-05-15T07:42:50.033" Score="1" ViewCount="259" Body="&lt;p&gt;Does cancer by any chance fall under host pathogen interaction domain? What I mean to ask is that, is there pathogen interaction involved in cancer? I went through this article:&lt;br&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_human_diseases_associated_with_infectious_pathogens&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/List_of_human_diseases_associated_with_infectious_pathogens&lt;/a&gt; &lt;br&gt;&lt;br&gt;&#xA;In the cancer category they have used the phrase &quot;can be cause&quot; by this and this pathogen.. Isn't cancer a disease that occurs due to abnormal growth of cells due to genetic change? &lt;/p&gt;&#xA;" OwnerUserId="8835" LastActivityDate="2015-05-15T08:43:18.653" Title="How is cancer associated with host pathogen interaction?" Tags="&lt;human-biology&gt;&lt;molecular-biology&gt;&lt;immunology&gt;&lt;cancer&gt;&lt;host-pathogen-interaction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34260" PostTypeId="2" ParentId="34214" CreationDate="2015-05-15T07:53:27.507" Score="1" Body="&lt;p&gt;Maybe you could get some information from the Angiosperm Phylogeny Group:&#xA;&lt;a href=&quot;http://www.mobot.org/MOBOT/research/APweb/&quot; rel=&quot;nofollow&quot;&gt;http://www.mobot.org/MOBOT/research/APweb/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They even have a tree where model organisms are highlighted:&#xA;&lt;a href=&quot;http://www.mobot.org/MOBOT/research/APweb/trees/modeltreemap.html&quot; rel=&quot;nofollow&quot;&gt;http://www.mobot.org/MOBOT/research/APweb/trees/modeltreemap.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1486" LastActivityDate="2015-05-15T07:53:27.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34261" PostTypeId="1" CreationDate="2015-05-15T08:42:17.110" Score="12" ViewCount="5271" Body="&lt;p&gt;My question is: Does voluntarily holding your breath &lt;strong&gt;at atmospheric pressure&lt;/strong&gt; for a few minutes can cause brain damage? I'm talking about periods of time around 3 minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've read there are some studies showing brain damage in deep-water divers. However, it seems to me as insufficient evidence for breath-holding in general: it could be that frequent changes in pressure are the cause for damage, for example. Or the fact that the person cannot resurface immediately after feeling the need to breathe, which might cause them to hold their breath for a longer period of time than their body allows.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So are there any studies showing results for the effect on the brain in (healthy) humans holding their breath?&lt;/p&gt;&#xA;" OwnerUserId="4592" LastEditorUserId="57" LastEditDate="2015-05-16T00:47:17.913" LastActivityDate="2017-01-19T11:56:45.083" Title="Does breath-holding cause permanent brain damage?" Tags="&lt;brain&gt;&lt;neurodegenerative-disorders&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34262" PostTypeId="2" ParentId="34259" CreationDate="2015-05-15T08:43:18.653" Score="1" Body="&lt;p&gt;No not necessarily. Cancer can also be caused by bacteria and viruses in your body&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The regulation of cancerous tumor development is converged upon by multiple pathways and factors. Besides environmental factors, gastrointestinal (GI) tract cancer can be caused by chronic inflammation, which is generally induced by bacteria, viruses, and parasites. The role of these inducers in cancer development, cell differentiation and transformation, cell cycle deregulation, and in the expression of tumor-associated genes cannot be ignored.&lt;/p&gt;&#xA;&lt;p&gt;Although Helicobacter pylori activates many oncogenic pathways, particularly those in gastric and colorectal cancers, the role of viruses in tumor development is also significant. Viruses possess significant oncogenic potential to interfere with normal cell cycle control and genome stability, stimulating the growth of deregulated cells. An increasing amount of recent data also implies the association of GI cancers with bacterial colonization and viruses.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;You can read more here: &lt;em&gt;Aituov, Bauyrzhan, et al. &amp;quot;Pathogen-driven gastrointestinal cancers: Time for a change in treatment paradigm.&amp;quot; Infectious agents and cancer 7.1 (2012): 18.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-05-15T08:43:18.653" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34264" PostTypeId="1" AcceptedAnswerId="34283" CreationDate="2015-05-15T10:57:09.320" Score="4" ViewCount="104" Body="&lt;p&gt;With respect to the following paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biomedcentral.com/1471-2105/13/162&quot; rel=&quot;nofollow&quot;&gt;Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a few questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;in page 2, in the table, what does 501 mean in GLC-501(I searched for GLC-501 in PDB,couldnt find anything)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;in page 3, in the table, the cavity center column has got two entries, what does that mean? does one entry belong to the protein and another entry to the ligand(left for protein and right for ligand)??&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="3340" LastEditDate="2015-05-18T05:18:28.563" LastActivityDate="2015-05-18T05:18:28.563" Title="Questions regarding a particular paper" Tags="&lt;biochemistry&gt;&lt;bioinformatics&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34266" PostTypeId="1" AcceptedAnswerId="34271" CreationDate="2015-05-15T11:31:07.547" Score="2" ViewCount="120" Body="&lt;p&gt;I'm concerned about the safety and mechanism of RF cautery. The frequency of the radio waves used is 4Mhz so normally there should not be any DNA damage BUT the thing you read everywhere is that only UV, X-rays and Gamma rays have enough energy to pop an electron from the orbit. Can't the same energy be reached with radio waves (higher amplitude instead of higher frequency). After all the RF cautery evaporates the cells why wouldn't it damage the DNA of the remaining cells? &lt;/p&gt;&#xA;" OwnerUserId="15747" LastEditorUserId="4109" LastEditDate="2015-05-15T21:32:49.037" LastActivityDate="2016-02-29T17:52:24.093" Title="RF Cautery DNA damage?" Tags="&lt;dna-damage&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34269" PostTypeId="1" AcceptedAnswerId="34282" CreationDate="2015-05-15T16:25:07.557" Score="4" ViewCount="1007" Body="&lt;p&gt;I have read the following sentence:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because this oxygenated hemoglobin is unaffected by magnetic fields,&#xA;  the response RF signal returned to the fMRI scanner is stronger when&#xA;  there is more brain activity and therefore more oxygenated hemoglobin&#xA;  in that brain tissue.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Oxygenated hemoglobin does not react to magnetic fields, while deoxygenated hemoglobin does. So in my view, if there is more brain activity and therefore more oxygenated hemoglobin, the signal should be weaker because the oxygenated hemoglobin does not react to the magnetic field? Why is it the other way around?&lt;/p&gt;&#xA;" OwnerUserId="15702" LastEditorUserId="9943" LastEditDate="2015-05-16T11:18:21.740" LastActivityDate="2015-05-16T11:18:21.740" Title="Oxygenated hemoglobin in MRI" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;blood-circulation&gt;&lt;mri&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34270" PostTypeId="2" ParentId="30810" CreationDate="2015-05-15T19:47:07.173" Score="0" Body="&lt;p&gt;IMO, &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0716732688&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; is by far the best introduction to enzyme mechanisms and protein folding, by a leading researcher in the field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding&lt;/p&gt;&#xA;&#xA;&lt;p&gt;by Alan Fersht &lt;/p&gt;&#xA;" OwnerUserId="1136" LastActivityDate="2015-05-15T19:47:07.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34271" PostTypeId="2" ParentId="34266" CreationDate="2015-05-15T21:50:38.923" Score="2" Body="&lt;p&gt;The thing about DNA is that it's very durable, compared to the rest of the cell. It's &lt;a href=&quot;http://www.promega.com/resources/pubhub/tpub_130-analyzing-dna-in-food-samples/&quot; rel=&quot;nofollow&quot;&gt;not too difficult&lt;/a&gt; to extract DNA from cooked and processed food, even though the definition of &quot;cooked&quot; is &quot;denatured and broken many of the proteins in the cell&quot;. The long DNA strands may be broken into long pieces, but overall the DNA holds up very well to heat. There's no risk of DNA damage to neighboring regions with RF radiation because the primary way RF energy destroys DNA is through heating, and at the temperatures where DNA starts to accumulate damage the cell around it is cooked/destroyed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The quantum explanation for why ionizing radiation &lt;em&gt;can&lt;/em&gt; destroy DNA is that high-frequency radiation is powerful enough to zip through the surrounding tissue and break/damage individual DNA molecules. Individual radio photons can't &quot;gang up&quot; on a DNA strand to do the same thing because of how quantum mechanics works, so you won't be able to break the strand or damage the bases without high-energy ionizing radiation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Metaphorically speaking it's like trying to get at a peach pit. Ionizing radiation is like a knife, it zips through the flesh and can get at a peach pit without damaging the peach much. RF radiation is like a belt sander. You can definitely get at the peach pit, but you'll cause a lot of collateral damage doing it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations or DNA damage that might cause cancer can only happen to cells that are alive that receive DNA damage. If the DNA is damaged by heat, the cell around it is dead, and that DNA damage doesn't really matter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I encourage you to read about &lt;a href=&quot;http://en.wikipedia.org/wiki/Ionizing_radiation&quot; rel=&quot;nofollow&quot;&gt;ionizing radiation&lt;/a&gt; and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Photoelectric_effect&quot; rel=&quot;nofollow&quot;&gt;photoelectric effect&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-05-15T21:50:38.923" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34272" PostTypeId="1" CreationDate="2015-05-15T23:35:12.053" Score="2" ViewCount="60" Body="&lt;p&gt;The probability of fixation $P$ of an allele is an very important measure and there exists several solutions to estimate this probability. Each method has its own assumptions and it is often hard to remember the methods that exists and what are their assumptions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example some use $P=2s$, this obviously cannot be right for be values of s, neither for deleterious mutations, and therefore, this approximation seems to make sens only for big population size. Haldane developed a method to calculate the probability of fixation based on the assumption that the fecundity follows a binomial distribution. Kimura used diffusion equation to approximate the probability to fixation. There might exist other solutions. I don't think I ever seen an equation that allows for varying dominance effect $h$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you make a summary of the methods you know for calculating the probability of fixation? Don't forget to highlight the assumptions. A comparison between the accuracy of the different methods would be great as well.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-05-16T00:07:24.570" LastActivityDate="2015-05-16T00:07:24.570" Title="Analytical Methods for Estimating Probability of Fixation" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;population-dynamics&gt;&lt;population-biology&gt;&lt;population-genetics&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34273" PostTypeId="1" AcceptedAnswerId="34276" CreationDate="2015-05-16T00:18:39.893" Score="1" ViewCount="166" Body="&lt;p&gt;Look, let's get something straight.  I am not the worlds biggest sissy when it comes to bugs, but I'm not David Attenborough either.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now that that's out of the way, down to business.  Living in Michigan as I do, I was quite surprised to find what looked like the spawn of Predator and a cicada living in my back yard.   Suffice to say it made me nervous.  In one of the pictures below, I have included a cigarette with about 3 drags smoked off of it for sizing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please offer insight into the true nature of this animal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fTPcp.jpg&quot; alt=&quot;img1&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/qcG5V.jpg&quot; alt=&quot;img2&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/JOBAv.jpg&quot; alt=&quot;img3&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4261" LastActivityDate="2015-05-16T08:12:34.043" Title="Insect (I hope) identification" Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="34276" PostTypeId="2" ParentId="34273" CreationDate="2015-05-16T03:27:49.717" Score="3" Body="&lt;p&gt;In the absence of someone more qualified, I believe this to be a prairie crayfish, based on where it was found (land) and what it is (decapod of some kind that looks like a crayfish). Therefore it is unfortunately not an insect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's in the right range and roughly the right terrain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I welcome entomologically qualified advice!&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="4109" LastEditDate="2015-05-16T08:12:34.043" LastActivityDate="2015-05-16T08:12:34.043" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34278" PostTypeId="1" CreationDate="2015-05-16T07:58:28.093" Score="8" ViewCount="172" Body="&lt;p&gt;It is known that some viruses embed themselves in the human genome. Is there a mechanism by which human genes can be transferred to other animals or plants by means of viruses shuttling them from humans to other organisms?&lt;/p&gt;&#xA;" OwnerUserId="408" LastEditorUserId="3624" LastEditDate="2015-05-19T08:39:49.170" LastActivityDate="2015-10-27T05:30:56.900" Title="Horizontal gene transfer from humans" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;human-genetics&gt;&lt;horizontal-gene-transfer&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34281" PostTypeId="2" ParentId="30219" CreationDate="2015-05-16T09:37:58.427" Score="1" Body="&lt;p&gt;Folate, or rather its active form tetrahydrofolate (THF), is a coenzyme that carries a 1-carbon group. The carbon group can occur in various redox states: CH3-THF (methyl-THF), CH2-THF (methylene-THF), CH-THF (methenyl-THF) or CHO-THF (formyl-THF). These can be interconverted by a variety of enzymes, and are used by cells to synthesize a number of products, including nucleotides and methionine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;MTHFR&lt;/em&gt; (methylene-THF reductase) converts CH2-THF into CH3-THF. The CH3-THF form is the most abundant folate in blood, and is therefore considered the &quot;transport&quot; form of folate. CH3-THF is also the form used to synthesize methionine, in the reaction&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CH3-THF + Homocysteine $\rightarrow$ THF + Methionine&lt;/p&gt;&#xA;&#xA;&lt;p&gt;catalyzed by methione synthase (gene symbol: &lt;em&gt;MTR&lt;/em&gt;). This enzyme requires cobalamin (B12) as a cofactor. Actually, the reaction occurs in two steps,&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;CH3-THF + Cobalamin --&gt; THF + CH3-Cobalamin&lt;/li&gt;&#xA;&lt;li&gt;CH3-Cobalamin + Homocysteine --&gt; Cobalamin + Methionine&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Loss of MTHFR leads to deficiency of CH3-THF, causing methionine synthase to run out of substrate, and homocysteine to accumulate. Lack of the B12 cofactor also blocks methionine synthase, and it should be clear from the reactions above why supplementing with either CH3-THF or CH3-cobalamin can alleviate the problem (at least in theory). I would guess the phenotypes seen in this condition is mainly due to lack of methionine though, rather than excess homocystine, since methionine is required for a variety of methylation reactions in cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a simplified view. There are many other interactions between B12 and folate; for example, the methinine synthase reaction is needed for cells to take up and store folates, and therefore B12 deficiency can create a folate deficiency as well. See for example &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6115113&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/6115113&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10466189&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/10466189&lt;/a&gt; for further reading.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-05-16T09:37:58.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34282" PostTypeId="2" ParentId="34269" CreationDate="2015-05-16T10:25:22.483" Score="3" Body="&lt;p&gt;I think that the type of fMRI you are referring to is blood-oxygenation-level-dependent fMRI or  &lt;a href=&quot;http://www.nature.com/milestones/milespin/full/milespin19.html&quot; rel=&quot;nofollow&quot;&gt;BOLD fMRI&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The principle behind MRI in general is the detection of proton signals from water molecules. The proton signal is generated by magnetizing the protons in tissue, which causes their spin to change. A subsequent powerful radio wave disrupts this spin and the following relaxation phase of the protons to the original state can be detected by MRI. Water, and hence protons are everywhere in the body, including the brain and the blood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Deoxygenated hemoglobin (hemoglobin without oxygen) in blood changes the proton signal in its immediate surroundings due to the magnetic properties of deoxyhemoglobin. This is caused by the fact that deoxygenated hemoglobin is paramagnetic and &lt;strong&gt;decreases the proton signal&lt;/strong&gt;. In fact, the &lt;em&gt;paramagnetic influence of deoxyhemoglobin has been regarded as noise in structural MRI scans&lt;/em&gt;, before its use in BOLD-fMRI became clear. Oxygenated hemoglobin does not have this property. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://radiopaedia.org/articles/bold-imaging&quot; rel=&quot;nofollow&quot;&gt;Radiopaedia&lt;/a&gt; has a nice explanation as to exactly how the BOLD signal is used in BOLD fMRI, and I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When a specific region of the cortex increases its activity in response to a task, the extraction fraction of oxygen from the local capillaries leads to an initial drop in oxygenated haemoglobin [...]. Following a lag of 2-6 seconds, cerebral blood flow (CBF) increases, delivering a surplus of oxygenated haemoglobin, &lt;strong&gt;washing away deoxyhemoglobin&lt;/strong&gt; and with it the attenuating effect on the MRI signal. It is this large rebound in local tissue oxygenation which is imaged, as it is accompanied by an &lt;strong&gt;increase in the MRI signal&lt;/strong&gt;. The difference is used to generate the BOLD fMRI response.  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So brain activity increases the BOLD signal by picking up oxygen-changes after an increased blood flow to that specific part of the brain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So your statement &lt;code&gt;[...] If there is more brain activity and therefore more oxygenated hemoglobin the signal should be less strong because the oxygenated hemoglobin does not react to the magnetic field&lt;/code&gt; is incorrect, because oxyhemoglobin attenuates the proton signal. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-05-16T10:25:22.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34283" PostTypeId="2" ParentId="34264" CreationDate="2015-05-16T10:25:27.653" Score="3" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;501 denotes 501&lt;sup&gt;st&lt;/sup&gt; residue in the corresponding PDB entry — 1BDG. See &lt;a href=&quot;http://marid.bioc.cam.ac.uk/credo/structures/1BDG&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A single protein can have multiple cavities (see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811767/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) and the multiple entries denote centres of different cavities. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-05-16T10:25:27.653" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="34284" PostTypeId="1" AcceptedAnswerId="34307" CreationDate="2015-05-16T11:19:54.307" Score="6" ViewCount="408" Body="&lt;p&gt;I have heard the theory that with the increase of CO&lt;sub&gt;2&lt;/sub&gt; in the air, the speed of the photosynthesis would increase, thereby limiting the increase of CO&lt;sub&gt;2&lt;/sub&gt; levels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is currently the rate limiting factor of photosynthetic reactions in plants? Is it really CO&lt;sub&gt;2&lt;/sub&gt;, or rather the limited energy that a plant can absorb from sunlight?&lt;/p&gt;&#xA;" OwnerUserId="15757" LastEditorUserId="3340" LastEditDate="2015-05-18T04:21:45.687" LastActivityDate="2015-05-18T04:23:25.147" Title="How does CO₂ concentration affect photosynthesis?" Tags="&lt;biochemistry&gt;&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34285" PostTypeId="1" AcceptedAnswerId="34294" CreationDate="2015-05-16T12:07:15.643" Score="4" ViewCount="98" Body="&lt;p&gt;First of all I have to say that I have no biology background since I'm a undergraduate computer science student. Nowadays, for my research I need to use some of the databases related with bioinformatics (&lt;code&gt;modENCODE&lt;/code&gt; and &lt;code&gt;NCBI-GEO&lt;/code&gt;). Currently, I'm searching RNA-Seq data and I have found the following one in modENCODE website which is stored in NCBI-GEO database.&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&amp;amp;m=data&amp;amp;s=viewer&amp;amp;run=SRR360120&quot; rel=&quot;nofollow&quot;&gt;RNA-Seq data&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the description part of it, it is written that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Synchronized L1 worms cultured at 25degC for about 91 hrs to a point&#xA;  at which ~100% worms are resistant to 1% SDS treatment. Illumina&#xA;  sequencing of C. elegans dauer daf-2(el370) sample 2-1 DauerDAF2-2-1&#xA;  polyA+ RNAseq random fragment library This sample is available through&#xA;  the modENCODE DCC (www.modencode.org) as: DauerDAF2-2-1 Local library&#xA;  name: DauerDAF2-2-1 Quality values are ASCII encoded Phred + 33.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Regarding with this paragraph, I want to ask that, what is &lt;code&gt;C. elegans dauer daf-2(el370)&lt;/code&gt; . I've searched on the internet and I have found that &lt;code&gt;dauer&lt;/code&gt; is kind of development stage of &lt;em&gt;C. elegans&lt;/em&gt;. However, I could not find any information about the &lt;code&gt;daf-2(el370)&lt;/code&gt; part (Actually all I found was that daf-2 is name of a gene of &lt;em&gt;C. elegans&lt;/em&gt;). Actually, my primarily concern is whether this RNA-Seq data contains the &lt;em&gt;C. elegans&lt;/em&gt;' whole transcriptome or it contains only mRNAs related with daf-2 gene. &lt;/p&gt;&#xA;" OwnerUserId="14759" LastEditorUserId="3340" LastEditDate="2015-05-16T19:46:23.057" LastActivityDate="2015-05-18T04:21:00.490" Title="determining meaning of basic biological keywords about C. elegans" Tags="&lt;bioinformatics&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34286" PostTypeId="1" CreationDate="2015-05-16T12:40:00.350" Score="1" ViewCount="1134" Body="&lt;p&gt;I.e., is exposure of sunlight onto the peripheral vision less damaging than exposure onto the fovea?&lt;/p&gt;&#xA;" OwnerUserId="15760" LastActivityDate="2015-05-16T13:49:39.197" Title="Is it safe to look indirectly at the Sun?" Tags="&lt;eyes&gt;&lt;human-eye&gt;&lt;light&gt;&lt;uv&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34287" PostTypeId="2" ParentId="14330" CreationDate="2015-05-16T13:11:55.077" Score="1" Body="&lt;p&gt;In a liquid chromatography coupled to mass spectrometry (LC-MS) analysis, as analytes elute from the chromatographic column they are sprayed through a hypodermic needle maintained at a high potential difference relative to the mass spectrometer. Combination of this potential difference and the pH of the LC buffers causes the analyte molecules to pick charge. Analyte ions are then pulled into the MS and guided using lenses. Then these ions are separated based on their m/z (mass-to-charge) ratios inside an analyser and then detected using a detector. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;At any given time, detected signals are typically represented on a 2-D map/graph between m/z on the x-axis and ion intensity/relative abundance on the y-axis. This is called as MS1 scan or precursor ion scan. Now, depending on the mode in which LC-MS analysis is being carried out, precursors are selected for fragmentation and further MS measurements, which is called as MS/MS or MS2 or product ion scan. Several of these MS1 or MS2 snap-shots can be used to construct a elution time profile for every ion. For an ion having a specific m/z ratio, this can be represented as a 2-D map between retention time on the x-axis and ion intensity on the y-axis. Area under this profile can be used to estimate the ion current of an analyte and under the given conditions it is proportional to the abundance of the analyte in the sample.&lt;/p&gt;&#xA;" OwnerUserId="15615" LastActivityDate="2015-05-16T13:11:55.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34288" PostTypeId="2" ParentId="34286" CreationDate="2015-05-16T13:49:39.197" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872277/&quot; rel=&quot;nofollow&quot;&gt;Behar-Cohen et al.&lt;/a&gt; notes the periphery of the cornea has a focusing effect:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;UVR incident from the periphery is refracted into the eye, and due to the focusing effect of the cornea, UV radiation is on average 22-fold stronger at the nasal limbus, which is the typical site for pterygium and pinguecula. Moreover, UV radiation is on average eight times stronger at the nasal lens cortex, the typical site for cortical cataract.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Authors note this in further papers as &lt;em&gt;peripheral light focusing&lt;/em&gt;. Essentially, the light is refracted from the periphery of the cornea into the anterior segment of the eye. By this notion, I'd say indirectly looking at the sun is no less damaging than directly looking at it (given there are no other restrictions, such as special lenses, etc.).&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-05-16T13:49:39.197" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34290" PostTypeId="1" CreationDate="2015-05-16T17:21:21.493" Score="4" ViewCount="7586" Body="&lt;p&gt;Note: I had asked &lt;a href=&quot;https://physics.stackexchange.com/questions/184360/wearing-sunglasses-during-a-solar-eclipse?noredirect=1#comment389179_184360&quot;&gt;this on Physics&lt;/a&gt;, but it is off-topic there due to being about safety.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the BBC's &lt;a href=&quot;http://www.bbc.co.uk/guides/zcytpv4&quot; rel=&quot;nofollow noreferrer&quot;&gt;guide to eclipse-watching&lt;/a&gt;, Dr Lucie Green says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Watching an eclipse with normal sunglasses provides virtually no protection. In fact, they trick your eyes to let in more light, so they can cause even more damage.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This doesn't seem right, because proper sunglasses should block UV to a safer level. Surely wearing proper sunglasses at any time is safer than not? Whilst I can understand staring at the sun with sunglasses on still allows too much UV in, why couldn't someone just glance at the eclipse from time to time?&lt;/p&gt;&#xA;" OwnerUserId="15760" LastEditorUserId="-1" LastEditDate="2017-04-13T12:40:13.457" LastActivityDate="2015-05-16T18:54:46.847" Title="Wearing sunglasses during a solar eclipse" Tags="&lt;eyes&gt;&lt;biophysics&gt;&lt;human-eye&gt;&lt;safety&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2015-05-17T07:21:11.303" ContentLicense="CC BY-SA 3.0" />
  <row Id="34292" PostTypeId="1" CreationDate="2015-05-16T18:32:37.057" Score="1" ViewCount="870" Body="&lt;p&gt;All herbivores produce vitamin B12 &lt;em&gt;de novo&lt;/em&gt;. Gorillas, for example, are &quot;vegans&quot; so I suppose some human ancestor was also herbivore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have we ever been B12 self-producers? If so, why have we lost that ability and do we have to obtain B12 from our diet? Have we just gotten &quot;used to&quot; being omnivores (i.e., we don't need self-production anymore)?&lt;/p&gt;&#xA;" OwnerUserId="6124" LastEditorUserId="9943" LastEditDate="2015-05-17T10:43:47.297" LastActivityDate="2015-07-05T09:06:34.680" Title="Were we able to create vitamin B12 in past?" Tags="&lt;evolution&gt;&lt;bacteriology&gt;&lt;vitamins&gt;&lt;vegetarianism&gt;" AnswerCount="0" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="34293" PostTypeId="2" ParentId="34290" CreationDate="2015-05-16T18:54:46.847" Score="1" Body="&lt;p&gt;Your eyes can dilate behind sunglasses, especially when the main source of light (the sun) is blocked, and ambient light decreases. Regular sunglasses offer &lt;em&gt;some&lt;/em&gt; protection against certain &lt;a href=&quot;http://en.wikipedia.org/wiki/Ultraviolet&quot; rel=&quot;nofollow&quot;&gt;UV&lt;/a&gt; wavelengths, but not enough to protect your eyes when looking directly at the sun (or, during an eclipse, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Corona&quot; rel=&quot;nofollow&quot;&gt;corona&lt;/a&gt;). Most sunglasses are mainly designed to, first and foremost, look good. After that, there is some protection against UVA (400-315 nm) and UVB (280-315 nm) light. Some sunglasses also offer &quot;UV400&quot; protection, which is short-wavelength blue light longer than 400 nm. &lt;a href=&quot;http://en.wikipedia.org/wiki/Polarizer&quot; rel=&quot;nofollow&quot;&gt;Polarized&lt;/a&gt; sunglasses do not protect against UV at all, only reflected light (such as shining off the water or from an automobile's body or glass) and glare. Different sunglasses tints (or colors) also do not protect against UV, but they can affect color perception.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Surely wearing proper sunglasses at any time is safer than not?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That is true, it is safer, the question is to what degree? Sunglasses offer some protection from indirect UV and visible light that has been scattered by the atmosphere and reflected off of things around us. However, the number and energy of &lt;a href=&quot;http://en.wikipedia.org/wiki/Photon&quot; rel=&quot;nofollow&quot;&gt;photons&lt;/a&gt; (the &quot;particles&quot; of light) reaching your eyes when looking directly at the sun is dramatically greater, and so &lt;em&gt;much&lt;/em&gt; more dangerous. Eyes can be damaged quite quickly by high-energy light of many wavelengths, including UV and visible, with the magnitude of the damage correlating to the energy of the light. Damage is also cumulative, accruing over a lifetime. Even small peeks directly at the sun will contribute to your overall lifetime risk of eye damage, and may cause permanent, irreversible harm &lt;strong&gt;very&lt;/strong&gt; quickly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a number of much &lt;a href=&quot;http://www.mreclipse.com/Totality2/TotalityCh11.html&quot; rel=&quot;nofollow&quot;&gt;safer alternatives&lt;/a&gt; for watching solar eclipses, including &lt;a href=&quot;http://www.timeanddate.com/eclipse/make-pinhole-projector.html&quot; rel=&quot;nofollow&quot;&gt;pinhole projectors&lt;/a&gt;, welding goggles rated higher than 14, various solar filters for cameras, telescopes, and binoculars, and fully exposed and developed black-and-white film (good luck finding that nowadays), among others. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Above all, make sure you're safe, and if you have any doubts consult with an expert, such as a science/natural history museum or local university's astronomy department.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-05-16T18:54:46.847" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34294" PostTypeId="2" ParentId="34285" CreationDate="2015-05-16T19:51:30.667" Score="4" Body="&lt;p&gt;Have you discovered &lt;a href=&quot;http://www.wormbase.org&quot; rel=&quot;nofollow&quot;&gt;wormbase&lt;/a&gt; yet? It will become your new best friend. In worms gene names reflect the loss-of-function (lf) phenotype. Daf means &quot;abnormal DAuer Formation,&quot; so &lt;em&gt;daf-2&lt;/em&gt; was the second daf gene identified (&lt;a href=&quot;http://www.wormbase.org/species/c_elegans/gene/WBGene00000898#0-9f-3&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;). The mutations are called alleles and each worm lab has their own allele designation. &lt;em&gt;e&lt;/em&gt; was for England and in that lab's strain list the &lt;em&gt;daf-2&lt;/em&gt; allele was the 1,370th on their list. So &lt;em&gt;daf-2(e1370)&lt;/em&gt; designation means that the strain carries a lf mutation in the &lt;em&gt;daf-2&lt;/em&gt; gene, and the specific allele is one that was isolated in Cambridge, UK. I believe that allele is temperature-sensitive (&lt;em&gt;ts&lt;/em&gt;) dauer-constitutive.&#xA;So at 25⁰C 100% of the animals were dauers. That is when they harvested RNA. It is the entire transcriptome. It sounds like you may be familiar with &lt;a href=&quot;http://intermine.modencode.org&quot; rel=&quot;nofollow&quot;&gt;modENCODE Data Warehouse&lt;/a&gt;. You can still ask questions about modENCODE datasets at &lt;a href=&quot;http://mailto:help@modencode.org&quot; rel=&quot;nofollow&quot; title=&quot;help@modencode.org&quot;&gt;help@modencode.org&lt;/a&gt;. While the modENCODE Data Coordination Center was mothballed at the end of the NIH funding period, there are a few people who still field queries like yours, to the Helpdesk. Also, moving forward the new ENCODE DCC has taken over curation of archival modENCODE metadata.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="3340" LastEditDate="2015-05-18T04:21:00.490" LastActivityDate="2015-05-18T04:21:00.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34295" PostTypeId="1" CreationDate="2015-05-16T20:40:17.513" Score="9" ViewCount="459" Body="&lt;p&gt;Not a biology student so forgive me if this is a very basic question. Are flowering plants (angiosperms) vital to all (or most) life on Earth?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, if flowering plants disappeared, would all (or most) life on this planet be gone as a result?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To give a bit more context, I'm arguing with a friend who claims (from a biblical perspective) that without flowering plants life couldn't exist.&lt;/p&gt;&#xA;" OwnerUserId="15764" LastActivityDate="2015-05-17T10:30:46.557" Title="Are flowers / flowering plants vital to all life on Earth?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34296" PostTypeId="2" ParentId="34295" CreationDate="2015-05-16T21:07:17.460" Score="19" Body="&lt;p&gt;Angiosperms -- that is, flowering plants -- only evolved relatively recently on an evolutionary timescale, about 125 millions years ago. So for most of the history of life on earth there have been no flowering plants. Thus it seems highly likely that if angiosperms were to suddenly disappear, life on earth would continue. There might be a massive disruption of current terrestrial communities, but it's hard to imagine this resulting in total global extinction. In particular it seems unlikely that ocean communities would be undermined by the loss of flowering plants. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="13072" LastEditDate="2015-05-17T05:08:01.363" LastActivityDate="2015-05-17T05:08:01.363" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34297" PostTypeId="1" CreationDate="2015-05-17T02:54:20.400" Score="3" ViewCount="149" Body="&lt;p&gt;Clearly numerous animals have a hierarchy - &lt;em&gt;hereditary&lt;/em&gt; one.  For example, I understand zebras have a pecking order, and must map this hierarchy from highest to first in line and lowest to last in line when traveling, and they can be brutalized for breaking this hierarchy.  (Interestingly, they allow looser rules for their young.)  (&lt;a href=&quot;http://www.slate.com/blogs/quora/2013/09/04/can_zebras_be_domesticated_and_trained.html&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cows apparently spend inordinate amounts of time with certain other animals, and avoid others still. (&lt;a href=&quot;http://www.veganpeace.com/animal_facts/Cows.htm&quot; rel=&quot;nofollow&quot;&gt;Reference&lt;/a&gt;.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: why do animals need the hierarchies and alliances?  Because human adults tend to make friends with people based on the kind of people they are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would imagine that they may have signals that indicate competing survival strategies (for example, a man with thick, tattoo covered arms vs a man in a tie) and that these likenesses try to propagate at the expense of others by forming alliances using organisms that possess these attributes (very vaguely akin to &quot;the selfish gene.&quot;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or does it have something to do with advertised fitness?  I just have to wonder how grazing animals manage to compete over food.  Does it control access to reproduction?&lt;/p&gt;&#xA;" OwnerUserId="8866" LastEditorUserId="948" LastEditDate="2015-05-17T03:10:06.677" LastActivityDate="2015-05-19T03:23:53.037" Title="Why do cows (and other hooved animals) need a hierarchy?" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34298" PostTypeId="1" AcceptedAnswerId="34834" CreationDate="2015-05-17T03:29:00.343" Score="7" ViewCount="1028" Body="&lt;p&gt;Are roe (fish eggs, caviar, etc.) single cells?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried looking this up on google (sadly, to no avail), and I am guessing they might be multicellular (like bird eggs) or consist of one cell plus corona cells, or indeed unicellular.&lt;/p&gt;&#xA;" OwnerUserId="4795" LastActivityDate="2015-06-02T08:36:23.227" Title="Are fish roe unicellular?" Tags="&lt;cell-biology&gt;&lt;ichthyology&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34299" PostTypeId="1" CreationDate="2015-05-17T03:57:05.567" Score="1" ViewCount="1879" Body="&lt;p&gt;I was recently reading about the wonderful chondrophores, and came across the terms &quot;neuston&quot; and &quot;pleuston&quot;.  According to Wikipedia, &quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/Neuston&quot; rel=&quot;nofollow&quot;&gt;neuston&lt;/a&gt;&quot; are &quot;the organisms that float on the top of water ... or live right under the surface&quot;, while &quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/Pleuston&quot; rel=&quot;nofollow&quot;&gt;pleuston&lt;/a&gt;&quot; are &quot;the organisms that live in the thin surface layer existing at the air-water interface of a body of water&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How are these terms used in the scientific literature?  Are pleuston considered a subset of neuston?  Some examples of organisms in one category but not the other would be helpful.&lt;/p&gt;&#xA;" OwnerUserId="11657" LastActivityDate="2017-10-15T09:27:40.100" Title="Neuston vs pleuston" Tags="&lt;terminology&gt;&lt;marine-biology&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34303" PostTypeId="2" ParentId="34297" CreationDate="2015-05-17T05:38:01.753" Score="1" Body="&lt;p&gt;Could not fit in a comment...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several issues with your question. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The correct question is not why such species need something but rather why it occurs in this species. In other words, why did a hierarchy evolved in a given species?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It is unclear to me why your are interest in cows (or other grazing animals) rather than any other species that has some kind of hierarchy and therefore your question is a bit unclear.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There are several questions in your post. A post should always be limited to one question.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I personally have never heard of the concept of &quot;advertised fitness&quot;. How do you define it?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I am not sure how much you are interested in the evolution of social traits and especially about &lt;code&gt;reputation&lt;/code&gt; and how much you are interested in &lt;code&gt;Machiavellian intelligence&lt;/code&gt;. In any case, you may probably want to read about the evolution of social traits (kin selection, it may take you some time) and about the social selection pressures for the evolution of cognition, such as Machiavelian intelligence.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;For all those reasons I vote to close. But I hoped that those comments can help you to clarify your post and to seek for more information.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastActivityDate="2015-05-17T05:38:01.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34304" PostTypeId="1" AcceptedAnswerId="34305" CreationDate="2015-05-17T07:09:40.013" Score="6" ViewCount="694" Body="&lt;p&gt;This insect was captured in Australia near Canberra. It has a very hard exoskeleton and is over an inch long. It seems to have 6 wings - 2 large pairs and one very small pair. I did not see a stinger - however I have no idea. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZuQmW.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/yKWP8.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14972" LastEditorUserId="3624" LastEditDate="2015-05-17T22:45:15.467" LastActivityDate="2015-05-17T22:45:15.467" Title="What is this flying insect?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34305" PostTypeId="2" ParentId="34304" CreationDate="2015-05-17T07:26:53.010" Score="4" Body="&lt;p&gt;I believe this is the Hairy Flower Wasp, &lt;em&gt;&lt;a href=&quot;http://gvcocks.homeip.net/Hymenoptera/Scoliidae/scolia_soror.htm&quot; rel=&quot;nofollow&quot;&gt;Scolia soror&lt;/a&gt;&lt;/em&gt;. I don't know what you mean when you refer to six wings, however. Like all other wasps, this species has four wings.&lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-05-17T07:26:53.010" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34306" PostTypeId="1" AcceptedAnswerId="34310" CreationDate="2015-05-17T10:03:52.293" Score="10" ViewCount="59067" Body="&lt;p&gt;Is there any actual difference between inoculation and vaccination or are these terms interchangeable? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In case the difference exists, would it be correct to say that inoculation is purposefully infecting a person with a pathogen in a controlled way, even when the person is already infected, to induce immunity while vaccination is administering dead or weakened pathogens to a healthy person as a preventive measure to check future infections?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, would it be correct to say that vaccination is an advanced form of inoculation? &lt;/p&gt;&#xA;" OwnerUserId="6129" LastEditorUserId="3340" LastEditDate="2017-08-23T16:00:26.143" LastActivityDate="2019-05-28T16:28:36.157" Title="Inoculation vs. vaccination" Tags="&lt;microbiology&gt;&lt;terminology&gt;&lt;vaccination&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34307" PostTypeId="2" ParentId="34284" CreationDate="2015-05-17T10:28:51.707" Score="6" Body="&lt;p&gt;The &lt;strong&gt;rate-limiting step of photosynthesis&lt;/strong&gt; is the CO&lt;sub&gt;2&lt;/sub&gt; assimilating enzyme &lt;strong&gt;&lt;em&gt;Rubisco&lt;/em&gt;&lt;/strong&gt; (short for ribulose-1,5-bisphosphate carboxylase/oxygenase) (&lt;a href=&quot;http://www.pnas.org/content/97/24/12937.long&quot; rel=&quot;nofollow&quot;&gt;Jensen, 2000&lt;/a&gt;). It uses ribulose-1,5-bisphosphate and CO&lt;sub&gt;2&lt;/sub&gt; as substrates to generate glucose. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that Rubisco is the rate limiting step in photosynthesis, an increase in its substrate CO&lt;sub&gt;2&lt;/sub&gt; would expectedly lead to an increase in photosynthesis. However, the regulation of Rubisco is complex and is influenced not only by &lt;strong&gt;CO&lt;sub&gt;2&lt;/sub&gt;&lt;/strong&gt;, but also by &lt;strong&gt;O&lt;sub&gt;2&lt;/sub&gt;&lt;/strong&gt; (which competes with CO&lt;sub&gt;2&lt;/sub&gt; for the active site), &lt;strong&gt;Mg&lt;sup&gt;2+&lt;/sup&gt;&lt;/strong&gt; and a regulating enzyme called &lt;strong&gt;&lt;em&gt;Rubisco activase&lt;/em&gt;&lt;/strong&gt; (&lt;a href=&quot;http://www.pnas.org/content/97/24/12937.long&quot; rel=&quot;nofollow&quot;&gt;Jensen, 2000&lt;/a&gt;). Hence, the effects of an increase in atmospheric CO&lt;sub&gt;2&lt;/sub&gt; may be more complex than simply enhancing photosynthesis by increasing Rubisco activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed, a review by &lt;a href=&quot;http://www.science.poorter.eu/1993_poorter_vegetatio.pdf&quot; rel=&quot;nofollow&quot;&gt;Poorter (1993)&lt;/a&gt; showed that a doubling of CO&lt;sub&gt;2&lt;/sub&gt; lead to an average increase in photosynthesis of only 37% across more than 150 plant species. He describes various factors that determine photosynthesis rates other than CO&lt;sub&gt;2&lt;/sub&gt;:  &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;One factor that limited photosynthesis under high CO&lt;sub&gt;2&lt;/sub&gt; was &lt;strong&gt;nitrogen (N)&lt;/strong&gt;. Since Rubisco is an enzyme, it has to be synthesized from amino acids. As &lt;strong&gt;Rubisco constitutes about 30% of the total protein&lt;/strong&gt; in a plant leaf, Rubisco is probably the most abundant protein on earth and a major sink for plant nitrogen (&lt;a href=&quot;http://www.pnas.org/content/97/24/12937.long&quot; rel=&quot;nofollow&quot;&gt;Jensen, 2000&lt;/a&gt;). For example, C&lt;sub&gt;3&lt;/sub&gt; species capable of symbiosis with N&lt;sub&gt;2&lt;/sub&gt;-fixing organisms had higher growth increases compared to other C&lt;sub&gt;3&lt;/sub&gt; species under high CO&lt;sub&gt;2&lt;/sub&gt;; &lt;/li&gt;&#xA;&lt;li&gt;Certain plants utilize CO&lt;sub&gt;2&lt;/sub&gt; better than others. &lt;strong&gt;&lt;a href=&quot;http://www.cropsreview.com/c3-plants.html&quot; rel=&quot;nofollow&quot;&gt;CAM species&lt;/a&gt;&lt;/strong&gt; were the least responsive, followed by &lt;strong&gt;&lt;a href=&quot;http://www.cropsreview.com/c3-plants.html&quot; rel=&quot;nofollow&quot;&gt;C&lt;sub&gt;4&lt;/sub&gt; plants&lt;/a&gt;&lt;/strong&gt;, while &lt;strong&gt;&lt;a href=&quot;http://www.cropsreview.com/c3-plants.html&quot; rel=&quot;nofollow&quot;&gt;C&lt;sub&gt;3&lt;/sub&gt; plants&lt;/a&gt; increased their photosynthesis rates the most&lt;/strong&gt; under high CO&lt;sub&gt;2&lt;/sub&gt;. Examples of C&lt;sub&gt;3&lt;/sub&gt; plants are herbaceous crop plants (&lt;a href=&quot;http://www.science.poorter.eu/1993_poorter_vegetatio.pdf&quot; rel=&quot;nofollow&quot;&gt;Poorter, 1993&lt;/a&gt;);&lt;/li&gt;&#xA;&lt;li&gt;Plants with a &lt;strong&gt;large intrinsic growth rate&lt;/strong&gt; may benefit more from high CO&lt;sub&gt;2&lt;/sub&gt;. These plants are said to have a high &lt;a href=&quot;http://plantsinaction.science.uq.edu.au/edition1/?q=content/13-3-2-sink-strength&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;sink strength&lt;/em&gt;&lt;/a&gt;, as they rapidly convert additional photosynthesis products into outgrowth. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.pnas.org/content/97/24/12937.long&quot; rel=&quot;nofollow&quot;&gt;Jensen, &lt;em&gt;PNAS&lt;/em&gt; (2000); &lt;strong&gt;97&lt;/strong&gt;(24): 12937–38&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.science.poorter.eu/1993_poorter_vegetatio.pdf&quot; rel=&quot;nofollow&quot;&gt;Poorter, &lt;em&gt;Veg&lt;/em&gt; (1993);&lt;strong&gt;104/105&lt;/strong&gt;: 77-97&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="3340" LastEditDate="2015-05-18T04:23:25.147" LastActivityDate="2015-05-18T04:23:25.147" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34309" PostTypeId="1" AcceptedAnswerId="34313" CreationDate="2015-05-17T11:00:29.250" Score="4" ViewCount="298" Body="&lt;p&gt;As far as I understand, uncoupling of the flow of protons and ATP-synthase  provides a bypass for protons between the outer and the inner membrane of mitochondria so that the protons don't have to go through the ATP-synthase on their way to the matrix. I see how it results in loss of electrochemical gradient. But why is heat produced?&lt;/p&gt;&#xA;" OwnerUserId="15773" LastEditorUserId="9943" LastEditDate="2015-05-17T11:18:09.433" LastActivityDate="2015-05-17T22:00:29.067" Title="How does loss of the electrochemical gradient result in heat production?" Tags="&lt;biochemistry&gt;&lt;biophysics&gt;&lt;mitochondria&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34310" PostTypeId="2" ParentId="34306" CreationDate="2015-05-17T11:23:44.110" Score="9" Body="&lt;p&gt;Both are forms of immunisation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Inoculation is exactly that. A live organism is introduced in a controlled way, so as to minimise the risk of infection, and is essentially the same process followed by many people in history.  It is inherently risky.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vaccination is introducing a weakened version of the pathogen, so that the immune response is triggered and the body is prepared to fight the actual pathogen if necessary. This was pioneered by Edward Jenner, wherein he noticed that cowpox (related to smallpox) immunised the milkmaids against smallpox.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-17T14:20:46.867" LastActivityDate="2015-05-17T14:20:46.867" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34311" PostTypeId="2" ParentId="31659" CreationDate="2015-05-17T13:41:06.263" Score="3" Body="&lt;h1&gt;3D structure.&lt;/h1&gt;&#xA;&lt;p&gt;Use the &lt;strong&gt;PDB&lt;/strong&gt; to identify structures that are similar to the one you have found (you can use &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi&quot; rel=&quot;nofollow noreferrer&quot;&gt;BLAST&lt;/a&gt; to search the PDB). A 30% match or above is &lt;em&gt;usually&lt;/em&gt; acceptable, and multiple alignments are of course useful at lower match scores. If structures exist that are similar enough, you can use homology modelling to generate a 3D structure (this is what the SWISS-MODEL server does, and I think it automates the BLAST alignments from PDB). If there are no similar structures, you can resort to &lt;em&gt;ab initio&lt;/em&gt; modelling if you have a reasonably straight forward globular domain, otherwise you might need to draw in additional expertise.&lt;/p&gt;&#xA;&lt;p&gt;There are so many specific factors that need to be taken into account for a project like this. Depending on what the model will be used for, different questions are relevant.&lt;/p&gt;&#xA;&lt;h1&gt;Secondary structure.&lt;/h1&gt;&#xA;&lt;p&gt;You will need a few different secondary structure predictors to make it convincing and then you will need to check that your secondary consensus matches your 3D structure. If they don't match you need to think about &amp;quot;why not?&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;If there is a difference it usually indicates that some 3D interaction is involved in the folding, so your 3D model usually &lt;em&gt;trumps&lt;/em&gt; the sequence structure predictions, but do check your 3D structure against the secondary structure predictions.&lt;/p&gt;&#xA;&lt;p&gt;Secondary structure prediction is more useful when a 3D structure is not available and modelling one is not an option.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-12-02T08:01:39.933" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34312" PostTypeId="1" CreationDate="2015-05-17T16:17:08.237" Score="4" ViewCount="503" Body="&lt;p&gt;I found a &lt;a href=&quot;http://umdberg.pbworks.com/f/Hobbie-EKG-1.pdf&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; presenting an &lt;em&gt;electrostatic model&lt;/em&gt; to explain the ECG recorded in various leads. This model essentially calls for considering the &lt;em&gt;depolarization wavefront&lt;/em&gt; to be the major contributing factor to the potential difference measured at the leads, especially the limb leads, by means of an aggregation of momentary dipoles with dipole moments organised according to the direction of propagation. It is also used in &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0071793119&quot; rel=&quot;nofollow&quot;&gt;this book here&lt;/a&gt;, under the ECG section under &lt;em&gt;Measurements of cardiac function&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper does not explain the observed ECG deformities in case of MI in detail. &lt;a href=&quot;http://en.wikipedia.org/wiki/ST_elevation&quot; rel=&quot;nofollow&quot;&gt;ST elevation&lt;/a&gt;, is a common finding in most MI cases. &lt;strong&gt;How do we explain this in light of the aforementioned model?&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My thoughts&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the normal case, ST segment is &lt;em&gt;isoelectric&lt;/em&gt;, as there is no depolarisation/repolarisation wavefront propagating. &lt;strong&gt;How is this isoelectric nature compromised in MI?&lt;/strong&gt; Assuming most infarcts include muscle death or damage due to focal insufficiency of coronary circulation, even if a region of heart was dead, during the ST segment, the graph should show an isoelectric line (no deflection) as the living tissue will either be depolarised or polarised, (but not switching states) and the dead tissue will have either a completely obliterated membrane polarity or an altered polarity throughout the cardiac cycle. In any case, no part of the heart will be switching its polarity then. &lt;strong&gt;Why is then, some resultant dipole (which indicates a propagating wavefront of altering polarities)obsereved during the ST segment?&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;alternative model&lt;/em&gt;&lt;br&gt;&#xA;   To explain the elevation, &lt;a href=&quot;https://www.elsevier.com/books/medical-physiology-2e-updated-edition/boron/978-1-4377-1753-2&quot; rel=&quot;nofollow&quot;&gt;this book&lt;/a&gt; (pg 522) provides a two cell model, and explains that the anoxic damage somehow&#xA;  causes the basal depolarised state of the cell to have a lower&#xA;  membrane potential difference, which causes all the segments of the&#xA;  ECG except the ST segment to be lowered, making the ST segment appear&#xA;  raised. I don't understand three things regarding this explanation.&#xA;  &lt;strong&gt;How will anoxic damage cause such a specific alteration in the polarity and the subsequent action potential? How can this two cell&#xA;  model be extrapolated to the whole heart with a focal infarct? How&#xA;  does this explanation be reconciled with the model presented at the&#xA;  head of the question?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Let me know if the question appears too broad and needs to be split, or if my assumptions are wrong in any way.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;MI-Myocardial Infarction&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;PS:-  I seem to have lost the touch with the formatting on this site, and hence don't know which tags to use. Will take some time to get back :)&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2015-05-27T12:21:26.730" LastActivityDate="2015-07-07T20:36:47.647" Title="Explanation of ECG in MI using an electrostatic model" Tags="&lt;human-biology&gt;&lt;cardiology&gt;&lt;biophysics&gt;&lt;electrophysiology&gt;&lt;electrocardiography&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34313" PostTypeId="2" ParentId="34309" CreationDate="2015-05-17T16:39:55.850" Score="4" Body="&lt;p&gt;ALiceD's comment is perfectly true. (Though in real cases, the short circuiting is seldom absolute as there is usually some finite resistance in the short circuiting wire.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can understand this in two ways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Intuitively&lt;/em&gt;&lt;/strong&gt;, the uncoupling provides a channel for the hydrogen ions to move across the membrane in the direction of their electrochemical gradient without having to do any work. Therefore, the energy it gains by traversing a potential difference, can be thought of as being converted to kinetic energy, i.e. the hydrogen ions are accelerated by the potential difference which causes them to gain speed and hence move at a higher speed than the average in the final compartment. This will cause increased collisions (and more energetic) with the surrounding molecules, slightly increasing their kinetic energy too, which will ultimately increase the average kinetic energy, the measure of which is called temperature. If it was coupled, the hydrogen ions would not have gained the kinetic energy, as the energy they gain by traversing the potential difference would have been used to do work in the ATP synthase machinery.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Rigorously&lt;/em&gt;&lt;/strong&gt;, you can show this using some chemical thermodynamics which includes using $\Delta G$ functions, $\mu$ functions and some related thermodynamic variables. Let me know if you want that explanation.(though I stand the risk of having lost the touch to the mathematical aspect of thermodynamics)  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;PS:-&lt;/strong&gt; &lt;em&gt;While the thermodynamic explanation also accounts for the increase in temperature due to obliterated concentration gradient, it is difficult to explain with the former model. You can think of this, as the neutralising of the concentration gradient changes the number of collisions per unit volume (and time), and hence also contributes to the observed temperature change.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3776" LastEditorUserId="3776" LastEditDate="2015-05-17T22:00:29.067" LastActivityDate="2015-05-17T22:00:29.067" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34316" PostTypeId="1" CreationDate="2015-05-17T22:07:52.383" Score="4" ViewCount="1345" Body="&lt;p&gt;What purpose is served by the pits and pores in xylem and phloem cells? I cant find what purpose that these components serve in the vascular tissues in plants&lt;/p&gt;&#xA;" OwnerUserId="15778" LastEditorUserId="25568" LastEditDate="2016-09-09T12:35:34.820" LastActivityDate="2016-09-09T12:35:34.820" Title="Pits and Pores in Vascular Tissue" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34317" PostTypeId="1" AcceptedAnswerId="34320" CreationDate="2015-05-17T22:18:27.747" Score="16" ViewCount="9835" Body="&lt;p&gt;I have seen numerous articles and various information about how cats and dogs see into the ultraviolet spectrum with interesting artistic renderings such as this:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/UdqGU.jpg&quot; alt=&quot;Cat UV Spectrum Example&quot;&gt;&#xA;&lt;a href=&quot;http://www.livescience.com/40459-what-do-cats-see.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.livescience.com/40459-what-do-cats-see.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I have been unable to find any specific parameters of what wavelength boundaries actually exist for cats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We know that humans see from around &lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/ems3.html&quot; rel=&quot;noreferrer&quot;&gt;750 to 400 nm&lt;/a&gt;, but what would a cat's range be?&lt;/p&gt;&#xA;" OwnerUserId="14667" LastEditorUserId="9943" LastEditDate="2015-05-18T02:02:03.997" LastActivityDate="2016-07-02T04:56:48.753" Title="What portion of the electromagnetic spectrum do cats see?" Tags="&lt;eyes&gt;&lt;vision&gt;&lt;feline&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34320" PostTypeId="2" ParentId="34317" CreationDate="2015-05-18T01:48:46.600" Score="15" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Spectral sensitivity of cats indeed ventures into the UV, but not beyond ~320 nm. Their maximum is likely similar to ours, i.e., ~750 nm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The spectral sensitivity of &lt;strong&gt;blue cones&lt;/strong&gt; (photoreceptors detecting low wavelengths) of many species, including humans and cats, &lt;strong&gt;extends into the UV&lt;/strong&gt; range (Fig. 1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WuqvP.png&quot; alt=&quot;cone spectra&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Human cone absorption spectra. Source: &lt;a href=&quot;https://www.unm.edu/~toolson/human_cone_response.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;University of Kentucky&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, the various structures in the eye, most notably the &lt;strong&gt;lens, filter out UV&lt;/strong&gt; in humans (Fig. 2). Indeed, &lt;strong&gt;surgical removal of the lens&lt;/strong&gt; in humans results in &lt;strong&gt;enhanced sensitivity to UV light&lt;/strong&gt; below 420 nm (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1455745&quot; rel=&quot;nofollow noreferrer&quot;&gt;Griswold &amp;amp; Stark, 1992&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/p6Gbl.gif&quot; alt=&quot;transmission spectra&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 2. Human transmission spectra. Source: &lt;a href=&quot;http://www.ciesin.org/docs/001-569/001-569.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Columbia University&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the &lt;strong&gt;cat&lt;/strong&gt;, however, the &lt;strong&gt;lens transmits a large portion of the UV light&lt;/strong&gt; in the range of &lt;strong&gt;320 - 400 nm&lt;/strong&gt;, while primates transmit virtually no light of these wavelengths. Figure 3 shows the lens transmission spectra of various species. At 50% transmission the second (dotted) line from the left is the cat (50% transmission at ~340 nm), while a primate (squirrel monkey, species representative for humans and other primates) in this graph is line number 7 from the left with (50% transmission at ~410 nm). Hence, &lt;strong&gt;cat lenses absorb less light in the UV region&lt;/strong&gt;, but transmission is virtually &lt;strong&gt;nil at 320 nm&lt;/strong&gt; (Fig. 3). Given that their cones, just like humans, are sensitive to UV, we can reasonably expect that cats can see in the UV region including wavelengths of 320 nm and up. Cats also have the 560 nm (red) cones, like we do, so their maximum wavelength is expectedly similar to ours (~750 nm).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kOX5Z.gif&quot; alt=&quot;Lens transmission&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 3. Lens transmission spectra of various species. Source: &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/281/1780/20132995&quot; rel=&quot;nofollow noreferrer&quot;&gt;Douglas &amp;amp; Jeffery, 2014&lt;/a&gt;&lt;/sup&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/281/1780/20132995&quot; rel=&quot;nofollow noreferrer&quot;&gt;Douglas &amp;amp; Jeffery, &lt;em&gt;Proc R Soc B&lt;/em&gt; (2014); &lt;strong&gt;281&lt;/strong&gt;: 20132995&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1455745&quot; rel=&quot;nofollow noreferrer&quot;&gt;Griswold &amp;amp; Stark, &lt;em&gt;Vis Res&lt;/em&gt; (1992); &lt;strong&gt;32&lt;/strong&gt;(9): 1739-43&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-07-02T04:56:48.753" LastActivityDate="2016-07-02T04:56:48.753" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34321" PostTypeId="2" ParentId="3755" CreationDate="2015-05-18T04:25:56.530" Score="2" Body="&lt;p&gt;Another example of multinucleated cells is osteoclasts, which are specialized derivatives of macrophages that degrade bone matrix.  They form by fusion of mononucleated progenitors and can accumulate many nuclei in a single large cell.  In cell culture with mouse macrophages, it's common to obtain individual osteoclasts with 50-100 or more nuclei each. &lt;/p&gt;&#xA;" OwnerUserId="15785" LastActivityDate="2015-05-18T04:25:56.530" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34322" PostTypeId="1" AcceptedAnswerId="34324" CreationDate="2015-05-18T04:56:37.827" Score="3" ViewCount="298" Body="&lt;p&gt;What is the meaning of the Gini index, as specificed in this link, which describes the &lt;a href=&quot;http://marid.bioc.cam.ac.uk/credo/ligands/1BDG/0/A/GLC%60501&quot; rel=&quot;nofollow&quot;&gt;Gini index of beta-glucopyranose bound to hexokinase&lt;/a&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this true that if Gini index has a very low value that means it doesn't interact much? If Gini index is high for a compound, it will interact?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="3624" LastEditDate="2015-05-18T08:43:38.900" LastActivityDate="2015-05-18T08:43:38.900" Title="What does the Gini index mean in a biochemical context?" Tags="&lt;biochemistry&gt;&lt;biostatistics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34323" PostTypeId="1" AcceptedAnswerId="34332" CreationDate="2015-05-18T05:53:04.090" Score="3" ViewCount="95" Body="&lt;p&gt;With respect to the &lt;a href=&quot;http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&amp;amp;object=ARGSYN-PWY&quot; rel=&quot;nofollow&quot;&gt;L-arginine Biosynthesis pathway&lt;/a&gt;, the very first reaction converts &lt;a href=&quot;http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION-IN-PATHWAY&amp;amp;object=N-ACETYLTRANSFER-RXN&quot; rel=&quot;nofollow&quot;&gt;L-glutamate to N-acetyl L-glutamate&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the linked reaction scheme, why are only L-glutamate and N-acetyl glutamate considered, and not acetyl-CoA or the coenzyme? Is this because L-glutamate and N-acetyl L-glutamate are the main compounds to be considered? Why are they the main compounds being considered? Are these two compounds (L-glutamate and N-acetyle L-glutamate) the ligands?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="9943" LastEditDate="2015-05-18T11:26:51.877" LastActivityDate="2015-05-18T11:26:51.877" Title="Question related to L-arginine biosynthesis" Tags="&lt;organic-chemistry&gt;&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34324" PostTypeId="2" ParentId="34322" CreationDate="2015-05-18T08:12:23.790" Score="3" Body="&lt;p&gt;The paper by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17948979&quot; rel=&quot;nofollow&quot; title=&quot;Graczyk. 2007. Gini coefficient: a new way to express selectivity of kinase inhibitors against a family of kinases. *J Med Chem.* 50(23)&quot;&gt;Graczyk (2007)&lt;/a&gt; is probably relevant for you. It says that the Gini index is a measure of reactive selectivity of kinases, with values close to zero indicating no selectivity and values close to one indicating high selectivity, and it is created in direct parallel to the Gini index in economics, which is used to describe economic inequality. In its basic form, the Gini coefficient is a &lt;a href=&quot;http://en.wikipedia.org/wiki/Gini_coefficient&quot; rel=&quot;nofollow&quot;&gt;measure of statistical disperson&lt;/a&gt;. Also see &lt;a href=&quot;http://www.nature.com/nbt/journal/v29/n11/full/nbt.2017.html?WT.ec_id=NBT-201111&quot; rel=&quot;nofollow&quot; title=&quot;Anastassiadis et al. 2011. Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity. Nature Biotechnology 29: 1039–1045&quot;&gt;Anastassiadis et al. (2011)&lt;/a&gt; for a more recent example where the index is used.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Abstract&lt;/strong&gt;&lt;br&gt;&#xA;  A novel application of the Gini coefficient for expressing selectivity of kinase inhibitors against a panel of kinases is proposed. This has been illustrated using single-point inhibition data for 40 commercially available kinase inhibitors screened against 85 kinases. Nonselective inhibitors are characterized by Gini values close to zero (Staurosporine, Gini 0.150). Highly selective compounds exhibit Gini values close to 1 (PD184352 Gini 0.905). The relative selectivity of inhibitors does not depend on the ATP concentration.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17948979&quot; rel=&quot;nofollow&quot; title=&quot;Graczyk. 2007. Gini coefficient: a new way to express selectivity of kinase inhibitors against a family of kinases. *J Med Chem.* 50(23)&quot;&gt;Graczyk. 2007. Gini coefficient: a new way to express selectivity of kinase inhibitors against a family of kinases. &lt;em&gt;J Med Chem.&lt;/em&gt; 50(23)&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nbt/journal/v29/n11/full/nbt.2017.html?WT.ec_id=NBT-201111&quot; rel=&quot;nofollow&quot; title=&quot;Anastassiadis et al. 2011. Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity. Nature Biotechnology 29: 1039–1045&quot;&gt;Anastassiadis et al. 2011. Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity. Nature Biotechnology 29: 1039–1045&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-05-18T08:37:01.517" LastActivityDate="2015-05-18T08:37:01.517" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34328" PostTypeId="1" CreationDate="2015-05-18T10:17:16.787" Score="7" ViewCount="130" Body="&lt;p&gt;In the evolution of wheat, there are two instances of chromosomal doubling, when Emmer wheat &lt;em&gt;Triticum turgidum&lt;/em&gt; was formed from Einkorn wheat, and when &lt;em&gt;Triticum aestivum&lt;/em&gt; was formed from Emmer wheat. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When allopolyploids are artificially made, chromosome doubling is done by chemicals. Here, it occurred by natural endoreplication. But for the entire plant to turn out with allotetraploidy and allohexaploidy respectively, wouldn't it be necessary for endoreplication to occur just after zygote formed--quickly, so all, or most, cells of the plant would have this genotype? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Isn't the probability of that happening twice in the process of evolution, both times in those incidences when the wheat crossed with the goatgrass species, very low? Is it just coincidence that it happened this way, at the right time, to allow for the allohexaploid species to develop naturally? &lt;/p&gt;&#xA;" OwnerUserId="15109" LastEditorUserId="1306" LastEditDate="2015-05-18T14:00:49.833" LastActivityDate="2019-03-18T22:05:31.720" Title="Evolution of Wheat" Tags="&lt;evolution&gt;&lt;genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34331" PostTypeId="1" AcceptedAnswerId="34334" CreationDate="2015-05-18T11:21:48.043" Score="14" ViewCount="1967" Body="&lt;p&gt;How can everyone have unique iris and fingerprints? After a certain amount of human beings have lived on earth, wouldn't it be possible to exhaust all possible combinations? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same principle applies to DNA. Lets say counting all the nucleotides on a strand of DNA we find that there are a total of $N$. We know there are 4 types of nucleotides, thus the total number of possible DNA sequences equals $4^N$. This is exponential, and since $N$ is immensely huge, $4^N$ will be unthinkably huge as well. However, since $4^N$ is a finite number, how can DNA be guaranteed to be unique? Doesn't that contradict the pigeon hole principle?&lt;/p&gt;&#xA;" OwnerUserId="15789" LastEditorUserId="16651" LastEditDate="2015-12-17T17:29:34.307" LastActivityDate="2015-12-17T17:29:34.307" Title="The Uniqueness of DNA Paradox" Tags="&lt;dna&gt;&lt;human-anatomy&gt;&lt;human-genetics&gt;&lt;iris&gt;&lt;forensics&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34332" PostTypeId="2" ParentId="34323" CreationDate="2015-05-18T11:23:43.940" Score="1" Body="&lt;p&gt;The synthesis of N-acetylglutamate is mediated by the enzyme &lt;em&gt;N-acetylglutamate synthase&lt;/em&gt;. This enzyme has &lt;strong&gt;L-glutamate as its substrate&lt;/strong&gt; and uses &lt;strong&gt;acetyl-coenzyme A&lt;/strong&gt; as a co-enzyme &lt;strong&gt;acetyl donor&lt;/strong&gt;. Acetylcoenzyme A (Acetyl-CoA) is generally abbreviated in structural formulas, because it is a relatively complex molecule. The only thing of relevance is the acetyl group which is transferred from a thiol group to L-glutamate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that &lt;em&gt;ligands&lt;/em&gt; is a term reserved for molecules binding to receptors; &lt;em&gt;substrates&lt;/em&gt; is the proper term for intermediates in enzymatic reactions.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/m3WtN.jpg&quot; alt=&quot;N-acetylglutamate&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;N-acetylglutamate synthesis. Source: &lt;a href=&quot;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Medical Biochemistry page&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-05-18T11:23:43.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34334" PostTypeId="2" ParentId="34331" CreationDate="2015-05-18T12:16:47.647" Score="24" Body="&lt;p&gt;The uniqueness of irises and fingerprints are, as you said, limited to the number of possible permutations of irises and fingerprints. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A similar problem exists in computer science, and is known as a &lt;a href=&quot;http://en.wikipedia.org/wiki/Collision_%28computer_science%29&quot;&gt;hash collision&lt;/a&gt;. Given sufficient samples, there will always be a collision for a hash of finite size. However, the sample space is sufficiently large for iris and fingerprint analysis for this to not be a problem. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cl.cam.ac.uk/~jgd1000/patrec.pdf&quot;&gt;A typical iris analysis system&lt;/a&gt; produces 2048 bits of entropy, while a typical &lt;a href=&quot;http://www.cedar.buffalo.edu/~govind/CSE717/papers/CancelableBiometrics.pdf&quot;&gt;fingerprint analysis system&lt;/a&gt; produces about 82 bits. Even accounting for the &lt;a href=&quot;http://en.wikipedia.org/wiki/Birthday_problem&quot;&gt;birthday problem&lt;/a&gt;, the information space is large enough that the chance of a given false positive is sufficiently low to prevent a random person from passing fingerprint/iris authentication. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For comparison, the current world human population is 7.2 billion, or slightly under 33 bits. The risk of a hash collision occurring is small enough to be negligible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, &lt;a href=&quot;http://www.contravex.com/2014/09/27/on-the-stupidity-of-biometric-security-for-smartphones-and-smartwatches/&quot;&gt;side-channel attacks&lt;/a&gt; against such biometric systems are relatively simple, but that's another issue altogether. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-05-18T12:28:07.863" LastActivityDate="2015-05-18T12:28:07.863" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34336" PostTypeId="1" CreationDate="2015-05-18T14:55:22.313" Score="4" ViewCount="102" Body="&lt;p&gt;The sterile insect technique (SIT) is used to control insect pests through overwhelming the population in sterile males. The increase in sterile males released into an environment causes the increase in infertile matings. This, in theory, would reduce the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, how would you calculate the number of sterile flies needed to be released in order to be effective? It would be dependent on the reproduction rate of the insect, initial density, and sex ratio in the young, but is there an equation to express this? Or is there simply a generic ratio of the target population that is used?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm looking at the example of the New World Screwworm fly, and the eradication in Central America. &lt;/p&gt;&#xA;" OwnerUserId="3382" LastActivityDate="2015-05-18T14:55:22.313" Title="How to calculate the number of sterile insects that must be released in SIT?" Tags="&lt;entomology&gt;&lt;population-dynamics&gt;&lt;parasitology&gt;&lt;parasitism&gt;&lt;pest-control&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34337" PostTypeId="2" ParentId="34214" CreationDate="2015-05-18T15:30:02.660" Score="1" Body="&lt;p&gt;You can try &lt;a href=&quot;http://timetree.org/&quot; rel=&quot;nofollow&quot;&gt;http://timetree.org/&lt;/a&gt; to get the divergence time if you already have the names of the taxa.&lt;/p&gt;&#xA;" OwnerUserId="15791" LastActivityDate="2015-05-18T15:30:02.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34338" PostTypeId="1" CreationDate="2015-05-18T15:47:19.933" Score="3" ViewCount="144" Body="&lt;p&gt;After experiencing things like stress, intense exercise, or using drugs such as caffeine and amphetamine, subjects often assume a depressive and lethargic state afterwards, known as a &quot;crash.&quot; What is the neuroscience behind it? Could it have to do with the depletion of neurotransmitters such as the catecholamines, or a downregulation of certain receptors in response to the overproduction of such neurotransmitters?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(This question is a remix of a previous question I posted, which was not focused enough)&lt;/p&gt;&#xA;" OwnerUserId="14975" LastActivityDate="2015-08-24T05:54:48.067" Title="Neuroscience behind the crash" Tags="&lt;neuroscience&gt;&lt;neurotransmitter&gt;&lt;receptor&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34339" PostTypeId="1" AcceptedAnswerId="34340" CreationDate="2015-05-18T16:10:10.330" Score="6" ViewCount="6361" Body="&lt;p&gt;Organelles are sub-cellular compartments in cells. However prokaryotes don't use organelles to organise their intracellular space. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolutionarily, there is evidence that mitochondria and chloroplasts are ancestors of symbiotic prokaryotes. This theory is called the &lt;a href=&quot;http://en.wikipedia.org/wiki/Symbiogenesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;endosymbiotic theory&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've tried to find an evolutionary story that explains other organelles, specifically the endoplasmic reticulum. There is plenty of literature about biogenesis of these organelles, but nothing about the history of their evolution. I don't think I have found the right area of literature. What did organelles originate from? I'm happy just to know a few keywords or a citation to look it up myself.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2017-01-12T08:31:33.113" LastActivityDate="2017-04-24T18:40:14.560" Title="How did the endoplasmic reticulum come to be?" Tags="&lt;evolution&gt;&lt;cell-biology&gt;&lt;cell-membrane&gt;&lt;literature&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34340" PostTypeId="2" ParentId="34339" CreationDate="2015-05-18T17:40:49.733" Score="5" Body="&lt;p&gt;Found the following on &lt;a href=&quot;http://en.wikipedia.org/wiki/Endomembrane_system#Evolution&quot; rel=&quot;noreferrer&quot;&gt;wikipedia&lt;/a&gt;. Seems pretty self explanatory:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The &lt;strong&gt;Golgi&lt;/strong&gt;, &lt;strong&gt;ER&lt;/strong&gt;, and &lt;strong&gt;lysosomes&lt;/strong&gt; are likely to have evolved as a result of&#xA;  the plasma membrane going through invagination. An increase in the&#xA;  overall volume of a cell would require the &lt;strong&gt;plasma membrane to fold in&#xA;  order to maintain a constant surface area to volume ratio&lt;/strong&gt;. These folds&#xA;  may have led to the &lt;strong&gt;specialization of internal membranes&lt;/strong&gt; to maintain&#xA;  communication with the environment. In the first stages of eukaryotic&#xA;  cell life, the membranes may have been interconnected and attached to&#xA;  the plasma membrane. Later on, as their functions diverged, the&#xA;  membranes may have become separate structures&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="11716" LastEditorUserId="3553" LastEditDate="2015-05-18T19:30:41.363" LastActivityDate="2015-05-18T19:30:41.363" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34341" PostTypeId="2" ParentId="20915" CreationDate="2015-05-18T18:23:15.917" Score="-2" Body="&lt;p&gt;Ive found that the study of this feature, the nose is far from complete.Although we see the evolution of other mammals and their faces has a great deal to do with there ability to survive different enviornments I believe it , our snozz is a genetic mutation in which allows us the ability to go from nonaquatic to aquatic with out needing a snorkel. ?.by defying why we have this thing on our face......some so large some so small I dont believe to have much to do with ancestial deviation of the jaw but the defying feature of the human race.....thank you&lt;/p&gt;&#xA;" OwnerUserId="15792" LastActivityDate="2015-05-18T18:23:15.917" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34344" PostTypeId="1" AcceptedAnswerId="34355" CreationDate="2015-05-18T22:02:33.490" Score="16" ViewCount="450" Body="&lt;p&gt;Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, &lt;a href=&quot;https://fold.it/portal/&quot;&gt;https://fold.it/portal/&lt;/a&gt;, etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question that I have is: How do you know when you get it right?  Is there some way of verifying, &lt;em&gt;in silico&lt;/em&gt;, that you have found a legitimate/correct structure for a protein?&lt;/p&gt;&#xA;" OwnerUserId="15796" LastEditorUserId="22057" LastEditDate="2017-02-25T20:21:27.727" LastActivityDate="2017-02-28T02:50:00.137" Title="How can computer predictions of protein folding be verified computationally?" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;proteins&gt;&lt;protein-folding&gt;&lt;computational-model&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34346" PostTypeId="2" ParentId="23620" CreationDate="2015-05-18T22:15:15.270" Score="1" Body="&lt;p&gt;One possibility is PTB Diagnostic ECG database &lt;a href=&quot;http://www.physionet.org/physiobank/database/ptbdb/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;. &#xA;However, its AAMI verification is still under process &lt;a href=&quot;https://biology.stackexchange.com/q/34345/86&quot;&gt;here&lt;/a&gt;. &#xA;Some ECHO findings also there. &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-05-18T22:15:15.270" CommentCount="0" CommunityOwnedDate="2015-05-18T22:15:15.270" ContentLicense="CC BY-SA 3.0" />
  <row Id="34347" PostTypeId="2" ParentId="21868" CreationDate="2015-05-18T22:17:30.330" Score="0" Body="&lt;p&gt;PTB Diagnostic ECG database &lt;a href=&quot;http://www.physionet.org/physiobank/database/ptbdb/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. &#xA;Review &lt;a href=&quot;http://www.beecardia.com/physiobank/database/ptbdb/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2015-05-18T22:17:30.330" CommentCount="0" CommunityOwnedDate="2015-05-18T22:17:30.330" ContentLicense="CC BY-SA 3.0" />
  <row Id="34348" PostTypeId="2" ParentId="24786" CreationDate="2015-05-18T22:24:05.843" Score="-4" Body="&lt;p&gt;Basically, it is because DNA is so hydrophobic that it does not substantially catalyse reactions in aqueous solutions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RNA is less hydrophobic and therefore more able to catalyse aqueous reactions, but the same reactivity means that it is more susceptible to degradation and so less suited than DNA to the storage of genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RNA is more polar and therefore less hydrophobic than DNA because of the increased polarity of the extra hydroxyl group in ribose compared to deoxyribose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means that DNA is more stable than RNA, because the strands are harder to separate because they are more attracted to each other than the surrounding water. Because it is more stable it is more suited to storing genetic sequences with less degradation than RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But because DNA is so stable it requires a substantial amount of machinery just to separate and keep separated the strands when they are needed. It is therefore unlikely DNA was the original genetic material that came about via much simpler prebiotic chemistry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RNA being more polar is easier to separate. It also unlike DNA can actually catalyse a wide variety of reactions requiring only the RNA and some prebiotic chemistry such as metallic ions or simple fatty acids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance the group I intron can catalyse single electron transfer in the presence of Iron (II) ions. And it can catalyse its excision from a section of RNA with Iron (II) or more commonly magnesium ions.&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365117/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365117/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact in almost every highly conserved biological process you will find remanent RNA chemistry if not small pieces of RNA held by proteins doing the heavy lifting. This leads to the RNA world hypothesis, which posits that RNA emerged before DNA and before proteins.&#xA;&lt;a href=&quot;https://www.youtube.com/watch?v=U6QYDdgP9eg&quot; rel=&quot;nofollow&quot;&gt;https://www.youtube.com/watch?v=U6QYDdgP9eg&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But being easier to separate RNA is more susceptible to degradation by aqueous reagents, and being less stable is less suited to the storage of genes without degradation. So if an organism found a way to turn its RNA to DNA for storage and back again it would have a significant selective advantage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such a mechanism might be as simple as protein or ribozyme that could preferentially hold DNA in contact with RNA. Then the normal mechanisms of strand ligation could work both to produce DNA from RNA templates and RNA from DNA templates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Over time there would tend to arise specialised versions to do each task, but each building on the original holding mechanism, which itself could have built on the ligase mechanism. Today there are a number of highly related small DNA and RNA binding RNAs involved in many analogous processes. Search for RNA Structure, Function and Recognition by Anna Marie Pyle on iBioseminars.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would link some more, but I don't have the reputation. But see also &quot;The Origin of the Genetic Code&quot; by cdk007 in the same series. Also there is an excellent 3 videos on abiogenesis, RNA and fatty acid vesicle &quot;protocells&quot; by Jack Szostak on ibiology. Just search for them.&lt;/p&gt;&#xA;" OwnerUserId="15795" LastActivityDate="2015-05-18T22:24:05.843" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="34349" PostTypeId="1" CreationDate="2015-05-18T23:05:56.320" Score="14" ViewCount="8850" Body="&lt;p&gt;This would seem to be an easy to answer question, but I was unable to find an answer (in g/L) for generic double-stranded DNA or plasmid neither on Google nor on BioNumbers. I would expect the solubility to vary slightly based on the sequence or length, but it probably wouldn't affect it very much due to the relative hydrophobicity of the bases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know I have made solutions of plasmid maxipreps of at least 1µg/µl, and the &lt;a href=&quot;http://www.nanodrop.com/Productnd2000specs.aspx&quot; rel=&quot;nofollow&quot;&gt;Nanodrop DNA quantifier datasheet&lt;/a&gt; has a maximum DNA detectable limit of 15µg/µl, but can anyone find a source for the maximum solubility level of generic DNA? For example, the solubility of a specific plasmid of approx. 5kb in length would be a good ballpark answer for this question. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-08-30T02:12:28.320" LastActivityDate="2015-08-30T02:12:28.320" Title="Solubility of DNA in water" Tags="&lt;biochemistry&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="34351" PostTypeId="1" CreationDate="2015-05-19T00:37:34.457" Score="7" ViewCount="301" Body="&lt;p&gt;What I understand about cross-immunoreactivity is that the antibody induced by one specific antigen is also fairly effective against another antigen. How would this be used for vaccine development? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, cross-immunoreactivity is related to epitopes. And how is how is cross-immunoreactivity defined among epitopes? Are variants of a specific virus hypervariable region some kinds of epitopes? What does antigenic convergence have to do with cross-immunoreactivity? Any comments or directions to further references are greatly appreciated.&lt;/p&gt;&#xA;" OwnerUserId="15799" LastEditorUserId="9943" LastEditDate="2015-05-19T01:15:00.477" LastActivityDate="2015-08-21T21:41:34.457" Title="What is cross-immunoreactivity, and how does it impact vaccine development?" Tags="&lt;immunology&gt;&lt;vaccination&gt;&lt;antigen&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34352" PostTypeId="2" ParentId="34344" CreationDate="2015-05-19T01:30:08.103" Score="1" Body="&lt;p&gt;At this point, it must be verified experimentally. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this foldit research paper, they use software and user input to design essentially an enhanced version of a naturally occurring protein, but they then physically make their new protein and determine its structure experimentally, using x-ray crystallography. Overall, they use a lot of trial and error &#xA;&lt;a href=&quot;http://homes.cs.washington.edu/~zoran/foldit-nbt-2012.pdf&quot; rel=&quot;nofollow&quot;&gt;http://homes.cs.washington.edu/~zoran/foldit-nbt-2012.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Projects like this are kind of geared towards towards the goal of being able to determine a protein's structure from its amino acid sequence &lt;em&gt;in silico&lt;/em&gt;. Once we achieve this ability, it will be revolutionary. However it is very difficult, because making such predictions accurately would require the use of quantum mechanics in a way that is extremely difficult to computationally model. These projects use shortcuts to get around this problem, so their results aren't very accurate, but they can be accurate enough to be useful, as shown in that paper.&lt;/p&gt;&#xA;" OwnerUserId="15798" LastActivityDate="2015-05-19T01:30:08.103" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34354" PostTypeId="2" ParentId="34349" CreationDate="2015-05-19T02:06:15.203" Score="10" Body="&lt;p&gt;DNA is a bit more complicated than some molecules due to it's length and composition variability.&lt;/p&gt;&#xA;&lt;h1&gt;In water.&lt;/h1&gt;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www3.idtdna.com/pages/support/technical-vault/faq-old/application-support/storage/faqs/2011/07/01/what-is-the-maximum-solubility-of-dna-in-water-(weight-unit-volume-unit)-&quot; rel=&quot;noreferrer&quot;&gt;Integrated DNA technologies&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;DNA oligos can be resuspended to a near maximum concentration of &lt;strong&gt;10mMolar&lt;/strong&gt;; to achieve such a high concentration will require a lot of vortexing and it may take up to a day for the oligo to go into the solution.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;DNA is a polar molecule and as far as I have experienced dissolves in water very readily. However there doesn't seem to be an &lt;em&gt;exact&lt;/em&gt; quantifiable number for DNA solubility in water. If I correctly understand it, &lt;a href=&quot;https://www.jku.at/JKU_Site/JKU/ipc/content/e166717/e166905/e172547/e172554/2010-002.pdf&quot; rel=&quot;noreferrer&quot;&gt;this paper&lt;/a&gt; claims that a 200,000Da-8,000,000Da oligonucleotide &lt;em&gt;&lt;strong&gt;is&lt;/strong&gt;&lt;/em&gt; soluble in water, however they never quantify this. &lt;a href=&quot;https://biology.stackexchange.com/a/35615/3553&quot;&gt;An answer&lt;/a&gt; on a related question pointed out that high molecular weight DNA oligomers, like genomic DNA, is enhanced in solutions with dilute monovalent cations.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://ac.els-cdn.com/0005278772902249/1-s2.0-0005278772902249-main.pdf?_tid=810fffe8-fdca-11e4-a22e-00000aab0f27&amp;amp;acdnat=1432000871_01906e936c60e304cbed98102bd2d553&quot; rel=&quot;noreferrer&quot;&gt;Cleaver &amp;amp; Boyer (1971)&lt;/a&gt; have some data on this, however it is somewhat outdated, and they were only using this solubility to demonstrate dialysis in water was capable of desalting the oligonucleotides.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Oligonucleotides larger than 5 bases in length remained within the dialysis&#xA;bag (Fig. 2) and losses of 10% and 40% occurred for tetra- and trinucleotides,&#xA;respectively.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;There is a lot of work done on optimal temperature and pH for solubility of DNA so perhaps a more specific query might throw up some results.&lt;/p&gt;&#xA;&lt;h1&gt;In ethanol.&lt;/h1&gt;&#xA;&lt;p&gt;Ethanol precipitates at least 10–20 % of all classes of oligonucleotides. Oligonucleotides longer than 15–16 nucleotides are precipitated to about 65%.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-29T13:06:38.983" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="34355" PostTypeId="2" ParentId="34344" CreationDate="2015-05-19T02:33:23.133" Score="13" Body="&lt;h2&gt;Overview&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Modelling has come on leaps and bounds over the last decade or so and in many cases has acted as a sometimes viable, and inexpensive substitute for experimental structures.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;How do you know when you get it right? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Ultimately, one still &lt;strong&gt;needs experimental evidence&lt;/strong&gt; to &lt;em&gt;know&lt;/em&gt; when a model generated &lt;em&gt;in silico&lt;/em&gt; is right. But there are ways of scoring a model for how &lt;em&gt;likely&lt;/em&gt; it is to be right.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is there some way of verifying, in silico, that you have found a legitimate/correct structure for a protein?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There are lots of ways to score and verify your models. Each method tells you something slightly different about the merits, or lack thereof, of your structural model. Some are designed to weed out the obviously awful models and some allow you to detect exactly where your model looks to be accurate or inaccurate.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;MODELLER Homology modelling output verification on the fly.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I am most familiar with modeller for homology modelling. Other softwares are available and they are each evaluated by &lt;a href=&quot;https://en.wikipedia.org/wiki/CASP&quot; rel=&quot;nofollow noreferrer&quot;&gt;CASP&lt;/a&gt; every two years since 1994.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In homology modelling there are 3 common scoring systems that can be used to assess the biochemical viability of a model. &lt;a href=&quot;https://salilab.org/archives/modeller_usage/2013/msg00016.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;This email&lt;/a&gt; covers when to use each one. My answer expands and explains a bit more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://salilab.org/modeller/9.11/manual/node468.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;molpdf&lt;/strong&gt;&lt;/a&gt; is the Modeller objective function.&#xA;&lt;strong&gt;GA341&lt;/strong&gt;, discussed &lt;a href=&quot;http://salilab.org/pdf/John_NucleicAcidsRes_2003.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; is derived from  Z-score (calculated with a statistical potential&#xA;function), which is a target-template sequence identity, and a&#xA;measure of structural compactness. &#xA;&lt;strong&gt;DOPE&lt;/strong&gt; is a more up to date method, first published in 2006, and is more true to &quot;biological viability&quot;. From &lt;a href=&quot;http://salilab.org/pdf/Shen_ProteinSci_2006.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;the publication&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;DOPE is based on an improved reference&#xA;  state that corresponds to noninteracting atoms in a homogeneous sphere with the radius dependent on&#xA;  a sample native structure; it thus accounts for the finite and spherical shape of the native structures.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Which to use depends on what you want to do with the model, but of those three scores, DOPE is the most reliable at separating native-like models from &quot;decoys&quot;.  DOPE is usually the starting place for figuring out which models might be right and which models are just plain rubbish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note:&lt;/strong&gt;  If you use Rosetta then there will be equivalents to these, or you can run your generated models through these techniques. If you are using &lt;a href=&quot;http://swissmodel.expasy.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;SWISS MODEL&lt;/a&gt; that comes with it's own somewhat black box verification techniques but you can still export the model for further verification.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;General model check against experimental data.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;A further validation of homology modelling methods or other structural models is &lt;a href=&quot;https://prosa.services.came.sbg.ac.at/prosa.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;ProSA&lt;/strong&gt;&lt;/a&gt;. ProSA provides a great visual representation of where the z-score lies amongst actual crystal and NMR structures. There are probably others that do similar functions, but this is my personal go-to to get an idea of where my structure lies among experimentally gathered structures.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Sensitive residue by residue verification.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Although the aforementioned methods examine each residue, they usually output an overall score. Residue by residue scores are also available and require a lot of careful interpretation. For example, if you are analysing catalytic activity, a surface looping region that scores poorly might not be an issue, but a core catalytic residue that scores poorly renders the model useless. This means that just because your model has a good (lower) overall DOPE score than another model, doesn't mean it is necessarily a more accurate model for what you are interested in. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are plenty of sensitive modelling scoring systems. Some of which are &lt;strong&gt;XdVal, MTZdump&lt;/strong&gt;, the famous albeit old-school &lt;strong&gt;Ramachandran Plotting&lt;/strong&gt; method, &lt;strong&gt;pdbU&lt;/strong&gt;, &lt;strong&gt;pdbSNAFU&lt;/strong&gt;, &lt;strong&gt;PROCHECK&lt;/strong&gt;, &lt;strong&gt;Verify3D&lt;/strong&gt;, and &lt;strong&gt;ERRAT&lt;/strong&gt; to name a few. Each has a place when checking how &lt;em&gt;correct&lt;/em&gt; your model is.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2017-02-28T02:50:00.137" LastActivityDate="2017-02-28T02:50:00.137" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34356" PostTypeId="1" AcceptedAnswerId="34358" CreationDate="2015-05-19T03:26:08.727" Score="10" ViewCount="13582" Body="&lt;p&gt;Can someone explain the differences between sequence, reads, and contigs of genetic material such as DNA, if possible with an example?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am new to bioinformatics, and I have not found any conclusive answers for all these concepts on the web.&lt;/p&gt;&#xA;" OwnerUserId="15804" LastEditorUserId="10456" LastEditDate="2015-05-19T05:39:14.607" LastActivityDate="2015-05-20T22:17:41.553" Title="What is the difference between sequence, reads, and contigs of genetic material?" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;dna&gt;&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34358" PostTypeId="2" ParentId="34356" CreationDate="2015-05-19T04:16:24.723" Score="10" Body="&lt;p&gt;My understanding of those three words as follows:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;sequence&lt;/strong&gt; is a generic name describing order of biological letters (DNA/RNA or amino acids). Both contigs and reads are DNA/RNA or aa sequences &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;reads&lt;/strong&gt; are just a short hand for sequenced reads. Usually sequenced reads refer to somewhat digital information obtained from the sequencing machine (for example Illumina MySeq) and stored in the &lt;code&gt;fastq&lt;/code&gt; file with quality scores per base. Reads are usually short. However &quot;short&quot; changes rapidly. Right now MySeq produces reads anywhere between 50-150 base pairs long (bp). From a single run (it will really depends on the run) you can get millions of reads, where each read will be set bp size e.g 100bp long. All reads are stored in a single &lt;code&gt;fastq&lt;/code&gt; file per replicate, where all reads in that file are usually of uniform size e.g all 5 million reads are 100bp long.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;As a bioinformatician your first job is to identify where about those &lt;strong&gt;reads&lt;/strong&gt; come from. Depending on the experimental goal and on what sort of sequencing you were doing e.g DNA-seq or RNA-seq you may or may not encounter &lt;strong&gt;contigs&lt;/strong&gt;.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;contigs&lt;/strong&gt; are simply reads that have been assembled together. For example if you are doing &lt;em&gt;de novo&lt;/em&gt; transcriptomics. Then you would:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;purify your transcript from a tissue and send it off for sequencing&lt;/li&gt;&#xA;&lt;li&gt;get your fastq files with sequenced reads, that are all short reads &#xA;(e.g 100 bp)&lt;/li&gt;&#xA;&lt;li&gt;assemble those 100bp reads into a longer &lt;strong&gt;contig&lt;/strong&gt; that hopefully will resemble your individual transcript&lt;/li&gt;&#xA;&lt;/ol&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="15435" LastEditorUserId="10456" LastEditDate="2015-05-19T05:38:37.107" LastActivityDate="2015-05-19T05:38:37.107" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34359" PostTypeId="2" ParentId="34356" CreationDate="2015-05-19T05:38:02.757" Score="3" Body="&lt;p&gt;I'm going to say the same thing as @Serine but in a slightly different context. Let's take an example where you want to compare smoking persons against non-smokers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this context, you'd want to take a DNA sequence of smoking persons.  However, due to technology limitation you won't get a single DNA sequence from the sequencing machine. You'll get millions of short overlapping DNA sequences known as reads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We need an &lt;a href=&quot;https://en.wikipedia.org/wiki/Sequence_assembly&quot; rel=&quot;nofollow&quot;&gt;assembler&lt;/a&gt; to &quot;map&quot; the reads and compare them with a reference genome. In this example, the reference genome could have been the human HG38.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The assembler would need to merge the overlapping-reads into a set of non-overalapping regions, known as contigs.&lt;/p&gt;&#xA;" OwnerUserId="14905" LastEditorUserId="1306" LastEditDate="2015-05-20T22:17:41.553" LastActivityDate="2015-05-20T22:17:41.553" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34361" PostTypeId="1" CreationDate="2015-05-19T07:46:14.347" Score="3" ViewCount="651" Body="&lt;p&gt;There is a lot of research on &lt;strong&gt;why nettle extracts causes skin irritation and a stinging sensation&lt;/strong&gt;. However, I cannot find information on &lt;strong&gt;how the extract is injected&lt;/strong&gt; in human skin. Similarly, I haven't been able to find information on  how the pressure is built up in the trichome, nor how the silica tip is inserted in the skin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suggestions for articles or books on this topic are welcomed. &lt;/p&gt;&#xA;" OwnerUserId="10045" LastEditorUserId="9943" LastEditDate="2015-05-19T13:22:08.377" LastActivityDate="2015-05-19T13:39:17.210" Title="What are the mechanistics of stinging nettles?" Tags="&lt;botany&gt;&lt;toxicology&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34363" PostTypeId="1" CreationDate="2015-05-19T08:37:49.117" Score="6" ViewCount="96" Body="&lt;p&gt;Sorry, the page I linked to is huge and you'll need to do a text search for &quot;CG&quot; to find the part I'm talking about.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found a graph on this page (&lt;a href=&quot;http://www.oftenpaper.net/sierpinski.htm&quot;&gt;http://www.oftenpaper.net/sierpinski.htm&lt;/a&gt;) showing that the eight DNA sequences including CG, i.e. four *CG and four CG* sequences are much rarer than the others in a human X chromosome. I realise that this is only for one sample of a human X chromosome (not even all human chromosomes) but I was wondering why this is? Obviously, if *CG is rare CG* will be too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From my limited understanding the equivalent RNA sequences would be *GC (redundant codes for four amino acids) and GC* (the only codes that produce Alanine). According to the &lt;a href=&quot;https://en.wikipedia.org/wiki/Alanine&quot;&gt;Wikipedia page on Alanine&lt;/a&gt; it accounts for 7.8% of genetic amino acids, well over the average.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this representative across all DNA? Across all human DNA? What does DNA have against coding CG sequences, even if only in the X chromosome? Do other chromosomes have an abundance of CG sequences but are rare in others?&lt;/p&gt;&#xA;" OwnerUserId="10204" LastActivityDate="2015-05-21T17:05:50.333" Title="Why aren't genetic triplets roughly evenly found in DNA?" Tags="&lt;dna&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34364" PostTypeId="2" ParentId="34361" CreationDate="2015-05-19T13:19:37.350" Score="8" Body="&lt;p&gt;The stinging hairs (&lt;em&gt;trichomes&lt;/em&gt;) of the common North American nettle (&lt;em&gt;Urtica dioica&lt;/em&gt;) are sharp, pointed cells. These nucleated cells are embedded in a base of smaller epidermal cells. The &lt;strong&gt;shaft of the trichome is composed of silica&lt;/strong&gt;. Upon touch, the &lt;strong&gt;tip breaks off, leaving a sharp tip similar to a hypodermic needle&lt;/strong&gt;. The hollow trichome &lt;strong&gt;penetrates the skin&lt;/strong&gt;, and toxin from the base is injected into the skin tissue. The stinging toxin includes a mixture of histamine, acetylcholine and 5-hydroxytryptamine (&lt;a href=&quot;http://waynesword.palomar.edu/wigandia.htm&quot; rel=&quot;noreferrer&quot;&gt;Online Textbook of Natural History&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Dp5lR.jpg&quot; alt=&quot;trichome&quot;&gt;  &lt;img src=&quot;https://i.stack.imgur.com/TMZSd.jpg&quot; alt=&quot;trichomes&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;&lt;strong&gt;Left&lt;/strong&gt;: schematic of a stinging cell, or trichome of a nettle. &lt;strong&gt;Right&lt;/strong&gt;: trichomes on the stem of &lt;em&gt;Hesperocnide tenella&lt;/em&gt;. Source: &lt;a href=&quot;http://waynesword.palomar.edu/wigandia.htm&quot; rel=&quot;noreferrer&quot;&gt;Online Textbook of Natural History&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I couldn't find any info on trichome pressure. It may be that the toxins are released passively. Otherwise, high concentrations of dissolved matter may attract water in the base, increasing the pressure (much like turgor present in many plant cells).  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-19T13:39:17.210" LastActivityDate="2015-05-19T13:39:17.210" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34366" PostTypeId="1" CreationDate="2015-05-19T14:07:17.393" Score="0" ViewCount="137" Body="&lt;p&gt;For &lt;code&gt;pdb&lt;/code&gt; files is there a simple programmatic way to determine if the file is made up of homodimers or heterodimers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have many files so an online tool or some psuedocode/scripts would help more than manually assessing each one.&lt;/p&gt;&#xA;" OwnerUserId="15811" LastEditorUserId="3553" LastEditDate="2015-05-19T19:19:55.547" LastActivityDate="2015-06-29T16:59:43.830" Title="Programmatic way to differentiate homodimers from heterodimers?" Tags="&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34370" PostTypeId="2" ParentId="34331" CreationDate="2015-05-19T16:35:13.470" Score="6" Body="&lt;p&gt;@March Ho's answer is an excellent answer based on the assumption that all of the observed phenotypic variance is due to genetic variance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Environmental variance&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genetic variance is not the only underlying variance that can explain variance in phenotypic traits. There is probably quite a lot of phenotypic variance that is caused by the underlying environmental variance between individuals. To have a better understanding of what are the different kind of variance you may want to have a look at &lt;a href=&quot;https://biology.stackexchange.com/questions/13669/do-genes-play-a-role-in-the-athleticism-and-shape-of-a-person&quot;&gt;this post&lt;/a&gt; for example. The heritability is typically equal to 0.3 (in fact most studies to report measures of heritability that are not significantly different from 0.3). If this was to be the case for the trait of interest, it would mean that 70% of the observed variance in fingerprints would be due to environmental variance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Developmental Noise&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, when talking about minor differences in phenotypes (such as fingerprints), developmental noise (inherent stochasticity of biological processes such as the decay rate of proteins or the production rate of mRNA) might be of real importance. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1360161/&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Raser and O'Shea, 2013)&lt;/a&gt; uses fingerprints as example of phenotypic trait which variance is in part determined by developmental noise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Relevance of an answer that cares only about genetic variance&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While @March Ho's answer is pleasant and interesting, I think that it is not of great relevance to the problem given the important amount of non-genetic variance that is underlying the phenotypic variance of interest.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-05-19T16:41:22.150" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34372" PostTypeId="2" ParentId="34366" CreationDate="2015-05-19T20:04:18.703" Score="1" Body="&lt;p&gt;I'd just compare the amino acid sequences of the individual protein chains. With some leeway for residues not observed in the density, ie only require 90 or 95% sequence identity, or ignore gaps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This will not tell you anything about whether the dimer (if you observe several molecules in the asymmetric unit) is actually real. For that, you'd need to do an experiment, literature research or see whether software like the PISA-server could give you a clue.&lt;/p&gt;&#xA;" OwnerUserId="14970" LastActivityDate="2015-05-19T20:04:18.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34373" PostTypeId="1" CreationDate="2015-05-19T20:18:42.923" Score="15" ViewCount="225" Body="&lt;p&gt;What research guidelines is a person legally mandated to follow if they want to do medical experimentation on themselves?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a large amount of variation in the types of medical experiments so I wanted to ask people focusing on the change in practice as a function of the type of medical experimentation you do in the biological sciences (e.g., drugs, blood samples, tissue regeneration, testing medical equipment), including invasive and non-invasive studies. This question seemed almost equally suited to academia and biology SE, but given the focus on different types of biological experiments I felt this might be the more suitable site. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am most interested on research practices in the United States, and anything touching FDA regulations would be great.&lt;/p&gt;&#xA;" OwnerUserId="15819" LastEditorUserId="948" LastEditDate="2016-02-02T14:49:25.170" LastActivityDate="2016-02-02T14:49:25.170" Title="Doing a medical study on yourself?" Tags="&lt;medicine&gt;&lt;experimental-design&gt;&lt;methods&gt;&lt;research-process&gt;" AnswerCount="1" CommentCount="9" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34374" PostTypeId="1" CreationDate="2015-05-19T22:38:16.197" Score="1" ViewCount="64" Body="&lt;p&gt;I have tried to use &lt;code&gt;flux simulation&lt;/code&gt; tool to generate simulated RNA-seq data. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I gave the following parameter file to flux-simulation shell script&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;## File locations&#xA;&#xA;REF_FILE_NAME   cElegansAnnotation.gtf&#xA;GEN_DIR         chromFa&#xA;&#xA;## Library preparation&#xA;# Expression&#xA;NB_MOLECULES    5000000&#xA;TSS_MEAN    50&#xA;POLYA_SCALE     100&#xA;POLYA_SHAPE     1.5&#xA;&#xA;# Fragmentation&#xA;FRAG_SUBSTRATE  RNA&#xA;FRAG_METHOD UR&#xA;FRAG_UR_ETA     350&#xA;&#xA;# Reverse Transcription&#xA;RTRANSCRIPTION  YES&#xA;RT_MOTIF    default&#xA;&#xA;# Amplification &#xA;PCR_DISTRIBUTION default&#xA;GC_MEAN      NaN&#xA;PCR_PROBABILITY  0.05&#xA;&#xA;# Size Filtering&#xA;FILTERING   NO&#xA;&#xA;&#xA;## Sequencing&#xA;READ_NUMBER 1000000&#xA;READ_LENGTH 100&#xA;PAIRED_END  YES&#xA;&#xA;# create a fastq file&#xA;FASTA           YES&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;According to this parameter, flux-simulation should have given reads with length 100. However when I look at the output, I have seen that reads with less then length of 100 are also included in my  fasta file:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt;chrI:47472-49416W:Y48G1C.12:3:651:351:594:A/1&#xA;CGTCGAAATTAGTGATATTTTTATCGGGAATCGGTCCGTGTGGTTCTCCGGTGAATATTCGATTCGTTGTGGAGACACGAGATCGCTGGGGTCCAAGGAC&#xA;&amp;gt;chrI:47472-49416W:Y48G1C.12:4:651:394:467:S/1&#xA;TACGCGACAAAAATGGGAAACCGAATCGCGTTTTTTGGCTTCAAGTACAAGTTATTCAGAATCATCAAAATGGG&#xA;&amp;gt;chrI:47472-49416W:Y48G1C.12:4:651:394:467:A/2&#xA;CCCATTTTGATGATTCTGAATAACTTGTACTTGAAGCCAAAAAACGCGATTCGGTTTCCCATTTTTGTCGCGTA&#xA;&amp;gt;chrI:47472-49416W:Y48G1C.12:5:651:126:142:S/2&#xA;AGTTGTAAAAGCGGATT&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So, is there anyone how could I fix it? &lt;/p&gt;&#xA;" OwnerUserId="14759" LastActivityDate="2015-05-19T22:38:16.197" Title="Getting read size less then specified in parameter file Flux Simulation" Tags="&lt;bioinformatics&gt;&lt;rna-sequencing&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34377" PostTypeId="1" AcceptedAnswerId="34448" CreationDate="2015-05-19T23:33:29.873" Score="4" ViewCount="145" Body="&lt;p&gt;I was reading the book &quot;Genetics and Analysis of Quantitative Traits&quot;, by Lynch and Walsh. I how the covariance between two individuals with IBD $\Theta$ gets divided into just the additive variance and dominance variance component, even in the simple $1$ locus case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here my understanding of the modelling (for the simple one allele case): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given a genotypic value $G_{i,j}$ of mean $0$, $i,j \in \{0,1\}$ we find numbers $\alpha_0$ and $\alpha_1$ minimising the least squares of the following form $\mathbb{E}(G_{i,j}-\alpha_i-\alpha_j)^2$, where the expectation is over the population. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We next define the error terms in each case as $\delta_{i,j}=G_{i,j}-\alpha_i-\alpha_j$. From the properties, viewed as functions of the population $\alpha_i$ is independent of $\delta_{i,j}$, and both have&#xA;mean $0$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The claim made in the book is that given two individuals, with IBD $\Theta$ and probability that the genotype is equal $\Delta$, the covariance of the genotypes $G_{i,j}$ and $G_{k,l}$ is given by,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\text{cov}(G_{i,j},G_{k,l}) = 2\Theta \sigma_A^2 +\Delta \sigma_D^2,$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $\sigma_A^2= \text{Var}(\alpha_i)$, and $\sigma_D^2 = \text{Var}(\delta_{i,j})$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Expanding the LHS of the expression, showing that $\mathbb{E}[(\alpha_i +\alpha_j)(\alpha_k+\alpha_l)] =\Theta \sigma_A^2$ is quite easy. It also seems to follow from the  that the the terms $\mathbb{E}[(\alpha_i +\alpha_j)\delta_{k,l}]=0$ from independence of errors from the $\alpha$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On analysing $\mathbb{E}[\delta_{i,j}\delta_{k,l}]$, we see that if both genotypes are equal, which occurs with probability $\Delta$, then this reduces to $\sigma_D^2$. This gives us a term $\Theta \sigma_D^2$. Further, if both $i,j$ and $k,l$ are not IBD then the covariance is $0$. However when one of the two alleles are IBD, then it is not clear to me that this the covariance will still be $0$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The book seems to claim that unless both alleles are IBD,  $\delta_{i,j}$ and $\delta_{k,l}$ are independent. I do not see why this is the case. Am I missing anything here? I'd appreciate any help wrt this.&lt;/p&gt;&#xA;" OwnerUserId="6353" LastEditorUserId="6353" LastEditDate="2015-05-21T21:43:39.533" LastActivityDate="2015-05-22T03:00:13.880" Title="The dominance variance on a single locus" Tags="&lt;genetics&gt;&lt;population-genetics&gt;&lt;biostatistics&gt;&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34378" PostTypeId="1" CreationDate="2015-05-20T00:20:25.770" Score="7" ViewCount="968" Body="&lt;p&gt;From what I understand in the alternation of generations in ferns, mature spores germinate into a haploid prothallium. But how does this gametophyte produce recombinant gametes if it itself develops mitotically from a haploid spore? And if the gametophyte produces its own (haploid?) eggs and sperm, how does it ultimately produce a diploid sporophyte with the same number of chromosomes as its parent? If the haploid prothallium fertilizes itself, that means it possesses two identical copies of its parent's chromosomes, which themselves are identical - there is no outcrossing between plants. So are all ferns genetic clones? Why even bother with meiosis if you don't have a recombinant mixing of alleles? Or do I have this totally confused?&lt;/p&gt;&#xA;" OwnerUserId="9914" LastEditorUserId="3624" LastEditDate="2015-05-21T11:26:34.127" LastActivityDate="2021-01-24T12:17:33.067" Title="If the haploid prothallium of a fern fertilizes itself into a diploid sporophyte, does this make all ferns clones?" Tags="&lt;botany&gt;&lt;reproduction&gt;&lt;sex&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34379" PostTypeId="2" ParentId="34378" CreationDate="2015-05-20T01:28:29.060" Score="1" Body="&lt;p&gt;In ferns (and seed plants) the dominant, largest stage of life is the diploid sporophyte. Within the sporophyte, meiosis occurs producing haploid spores. These spores are dispersed and grow into the small haploid gametophyte, AKA the prothallium. The gametophyte produces haploid gametes - both egg and sperm coming from the same individual, usually. The sperm fertilizes the egg forming a diploid zygote, which grows into an adult sporophyte.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This image should help. Let me know if anything is unclear&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/X0pNK.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-05-20T01:28:29.060" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34380" PostTypeId="1" CreationDate="2015-05-20T02:29:48.200" Score="2" ViewCount="49" Body="&lt;p&gt;Ultraviolet damage from sun exposure is related to the creation of free radicals. Iron is often involved in exacerbating damage by free radicals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having lower iron stores is associated with reduced risk of diabetes. Could having lower iron stores reduce UV-related damage from sun exposure?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;=========================================================================&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I add some references after being asked in the comments:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On iron and free radicals: &lt;a href=&quot;http://jn.nutrition.org/content/134/11/3171S.full&quot; rel=&quot;nofollow&quot;&gt;Iron, Free Radicals, and Oxidative Injury&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UV-light and free radicals: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8127935&quot; rel=&quot;nofollow&quot;&gt;Ultraviolet light-induced free radical formation in skin&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About high ferritin making diabetes worse:&#xA;&quot;Compared with those in the lowest quartile, subjects with diabetes in the highest ferritin quartile were 55% (P = 0.029) more likely to have microalbuminuria.&quot;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23756251&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17333112&quot; rel=&quot;nofollow&quot;&gt;Elevated serum ferritin levels predict new-onset type 2 diabetes&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15821" LastEditorUserId="15821" LastEditDate="2015-05-20T12:48:36.010" LastActivityDate="2015-05-20T12:48:36.010" Title="Do High Iron Stores (but within the healthy range) Make Sun Exposure Damage Worse?" Tags="&lt;hematology&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34382" PostTypeId="1" AcceptedAnswerId="34383" CreationDate="2015-05-20T04:54:35.850" Score="7" ViewCount="179" Body="&lt;p&gt;I was reading the article of &lt;a href=&quot;http://www.math.umn.edu/~othmer/papers/Dallon:1997:DCM.pdf&quot; rel=&quot;nofollow&quot;&gt;Dallon &amp;amp; Othmer (2010)&lt;/a&gt; which deals with cell aggregation in &lt;em&gt;Dictyostelium discoideum&lt;/em&gt;. In the introduction of the paper it is said that cells becomes &quot;&lt;strong&gt;relay competent&lt;/strong&gt;&quot;. I googled for the term but could not find a good explanation for it.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After a period of starvation they become chemotactically sensitive to cyclic adenosine 3 , 5- monophosphate (cAMP), as well as relay competent.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Can someone help me understand this term?&lt;/p&gt;&#xA;" OwnerUserId="5669" LastEditorUserId="5669" LastEditDate="2015-05-22T06:11:04.867" LastActivityDate="2015-05-22T06:11:04.867" Title="What does the term &quot;relay competent&quot; mean?" Tags="&lt;microbiology&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34383" PostTypeId="2" ParentId="34382" CreationDate="2015-05-20T05:00:23.690" Score="6" Body="&lt;p&gt;If you read the lines immediately following your quoted line (on p.391, left column, last paragraph in the linked article) it becomes clear what &lt;strong&gt;relay competent&lt;/strong&gt; means (and I quote):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As a result, the cells sense and move toward a source of cAMP, and they &lt;strong&gt;relay the signal as well by secreting cAMP&lt;/strong&gt;. [..] After about 8 h of starvation randomly located cells, called pacemakers, begin to emit cAMP periodically (Raman et al. 1976), the chemotactically competent cells move toward these pacemakers, and eventually the entire population forms a mound-shaped aggregate of up to 105 cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In other words, starvation makes cells move toward cAMP by chemotaxis, and  makes them &lt;strong&gt;secrete cAMP&lt;/strong&gt; as well, which factually &lt;strong&gt;relays&lt;/strong&gt; the cAMP signal back to other cells that are also attracted to cAMP due to starvation.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-20T10:58:20.517" LastActivityDate="2015-05-20T10:58:20.517" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34386" PostTypeId="1" CreationDate="2015-05-20T06:56:47.890" Score="1" ViewCount="792" Body="&lt;p&gt;Everyone knows that some animals, at least cats and dogs, keep their noses wet and cool. But why did they evolve it? What evolutionary advantages does it provide? Smell-sensing cells need cooling for precision, may be? Or the liquid dissolves smellful gases into itself, simplifying analysis this way? Or may be it just simplifies cleaning the nose from the previous sniffing act?&lt;/p&gt;&#xA;" OwnerUserId="15823" LastActivityDate="2015-05-20T12:21:43.737" Title="Evolutionary advantages of wet nose of cats and dogs?" Tags="&lt;dogs&gt;&lt;nose&gt;&lt;feline&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34387" PostTypeId="2" ParentId="34378" CreationDate="2015-05-20T08:17:39.813" Score="3" Body="&lt;p&gt;No, it would not be accurate to label them clones, and the organism still goes through sexual reproduction even if they are selfed. Selfed offspring would get two copies of the &quot;same&quot; chromosome (when selfed within the same prothallus), when the parent might have two chromosomes of different origins, and there will also be recombination during meiosis (during spore production in the sporangia), which will alter the chromosomes. And even if all selfed offspring from the same prothallus will carry that same chromosomes, different prothalli from the same parent will carry different chromosomes, which means that all offspring will not be identical. So to label selfed ferns as clones wouldn't be accurate, since the offspring wouldn't be genetically identical to their parents and offspring from different prothalli would also not be genetically identical. The situation is similar to e.g. monoecious plants that lack self-incompatibility (especially those pollinated by wind), where selfing will be common. The difference in ferns is that all gametes on the same prothallus will carry the same chromosomes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also note that some ferns have mechanisms to avoid self-fertilization, and that many species have a mixed mating strategy that allow both selfing and outcrossing, usually with higher fitness in outcrossed individuals.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-05-20T10:33:39.650" LastActivityDate="2015-05-20T10:33:39.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34388" PostTypeId="1" AcceptedAnswerId="71505" CreationDate="2015-05-20T09:22:16.213" Score="4" ViewCount="163" Body="&lt;p&gt;I'm thinking about doing that DNA test on all my grandparents to know where their genes come from. They are getting very old and I don't want to let the opportunity pass to gather more knowledge about my heritage, something I find very interesting.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of my grandparents died long ago, but he still has a brother and I was wondering if DNA testing him would reveal relevant information about my heritage from that branch of my family tree. Obviously all of his genes come from family of mine(his parents) but not all of his genes are the same as my grandparent's. Just how should I look at his tests to find information about my heritage?   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way can I really trust these sort of tests?&lt;/p&gt;&#xA;" OwnerUserId="15806" LastEditorUserId="15806" LastEditDate="2015-05-20T09:34:05.863" LastActivityDate="2018-06-16T21:02:53.550" Title="Can DNA test of my grandparent's brother reveal my heritage from that branch of the family?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34389" PostTypeId="2" ParentId="34386" CreationDate="2015-05-20T11:17:00.827" Score="3" Body="&lt;p&gt;&lt;strong&gt;Why did it evolve ?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mammals with rhinaria tend to have more acute olfaction, and the loss of the rhinarium in the haplorrhine primates is related to their decreased reliance on olfaction, being associated with other derived characteristics such as a reduced number of turbinates. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The rhinarium is very useful to animals with good sense of smell because it acts as a wind direction detector. The cold receptors in the skin respond to the place where evaporation is the highest. Thus the detection of a particular smell is associated with the direction it came from.&#xA;  The rhinarium is adapted for different purposes in different mammals according to ecological niche. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;In aquatic mammals, development of lobes next to the nostrils allow them to be closed for diving. In mammals that root, the rhinarium often develops into a hard pad, with the nostrils off to the side. In the elephants it has become a tactile organ. In the walrus, it is covered with stiff bristles to protect it during foraging for shellfish. In many animals the form and purpose of the rhinarium remains to be elucidated.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Essentially it is the case of having a better sense of smell provided by the extended surface area, which has evolved to fit whatever the organism in question needs. I'll update this when I find this in a few more papers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I took this from the wiki: &#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Rhinarium&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Rhinarium&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How does it work ?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A model of the canine nasal airway, developed from a 3-D&#xA;  reconstruction of high-resolution magnetic resonance imaging (MRI)&#xA;  scans, was used to study the aerodynamics of canine olfaction.&#xA;  Simulation results reveal that a unique olfactory airflow pattern&#xA;  exists within the canine nasal cavity during sniffing that is critical&#xA;  for efficient olfaction. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Calculations show that this novel olfactory airflow pattern provides a&#xA;  crucial residence time for odorant absorption in the sensory region&#xA;  and promotes spatiotemporal fractionation of odorant mixtures along&#xA;  the olfactory epithelium. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The canine nose functions similar to a chromatograph that imposes&#xA;  odorant-specific deposition patterns upon the thin mucus layer&#xA;  covering the nasal cavity....The results show that deposition patterns&#xA;  are primarily influenced by the intricate olfactory flowfield and the&#xA;  odorant solubility in the mucus layer.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Highly-soluble odorants are quickly absorbed near the entrance to the&#xA;  olfactory region, and thus do not reach the periphery with significant&#xA;  concentrations. In contrast, insoluble odorants are deposited more&#xA;  evenly and may even exit the olfactory region without being completely&#xA;  absorbed. Predicted odorant deposition patterns correspond with the&#xA;  anatomical organization of olfactory receptors known to occur in&#xA;  keen-scented (macrosmatic) mammals, providing a mechanism that helps&#xA;  explain the excellent olfactory acuity of the dog.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In short the mucus on a dog's nose 'pre-sorts' smells by trapping the passage of some odour particles more than others along the nose, with different types of molecules being picked up at different &quot;depths&quot; in the nasal cavity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read about it here: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Craven, Brent, Gary Settles, and Eric Paterson. &quot;The Aerodynamics and Transport Phenomena of Canine Olfaction.&quot; APS Division of Fluid Dynamics Meeting Abstracts. Vol. 1. 2008.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Lawson, Michael, et al. &quot;Odorant Transport and Deposition in the Canine Nasal Airways.&quot; APS Division of Fluid Dynamics Meeting Abstracts. Vol. 1. 2009.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Craven, Brent A. A fundamental study of the anatomy, aerodynamics, and transport phenomena of canine olfaction. ProQuest, 2008.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-20T12:21:43.737" LastActivityDate="2015-05-20T12:21:43.737" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34390" PostTypeId="2" ParentId="34373" CreationDate="2015-05-20T11:45:29.013" Score="14" Body="&lt;p&gt;One of the cornerstones of research ethics worldwide is the &lt;a href=&quot;http://www.cirp.org/library/ethics/nuremberg/&quot;&gt;&lt;strong&gt;Nuremberg code&lt;/strong&gt;&lt;/a&gt;, which was formulated shortly after the Second World War and set off by the cruelties performed by the Nazi Doctors. The &lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=7&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CEIQFjAG&amp;amp;url=http%3A%2F%2Fwww.wma.net%2Fen%2F30publications%2F10policies%2Fb3%2F17c.pdf&amp;amp;ei=BnRcVfy2Kojf8AWP_ILIAw&amp;amp;usg=AFQjCNE-wJOEVFcmGah2YY5uQzsixyaDPQ&amp;amp;sig2=YiZfLNIU9I7ZpUxMpl0yEw&amp;amp;bvm=bv.93756505,d.dGc&quot;&gt;&lt;strong&gt;Declaration of Helsinki&lt;/strong&gt;&lt;/a&gt;, which is currently widely used as the guiding principle of research ethics, was directly inspired by the Nuremberg code. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, article 5 in the Nuremberg code reads, and I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;No experiment should be conducted where there is an &lt;em&gt;a priori&lt;/em&gt; reason to believe that death or disabling injury will occur; &lt;strong&gt;except, perhaps, in those experiments where the experimental physicians also serve as subjects&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Basically what this tells you is that when you are a physician, you are not only ethically allowed to experiment on yourself, even when you can reasonably expect death may follow, you are even allowed to put others at that risk(!) Admittedly, it does not specifically talk about non-physicians. Nonetheless, with regard to your question, this Nuremberg article implies that self-experimentation is allowed, regardless the risks. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bmj.com/content/341/bmj.c7103&quot;&gt;Annas (2010)&lt;/a&gt;, rightfully argues that, even where risks are minimal, prior ethics committee review of research &lt;strong&gt;should always be sought&lt;/strong&gt;, if only to confirm the reasonableness of the risk assessment and regardless whether investigators are subjects. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem then becomes whether self-experimentation (an experiment done by the investigator on himself or herself only) must be reviewed and approved by an ethics committee before it is conducted. Here &lt;a href=&quot;http://www.bmj.com/content/341/bmj.c7103&quot;&gt;Annas (2010)&lt;/a&gt; concludes that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[...] When an investigator proposes to &lt;strong&gt;experiment only on him or herself, that activity is not properly categorized as research&lt;/strong&gt; at all, but as self indulgence (or, some may say, self abuse). Trivial interventions masquerading as research studies are primarily a source of amusement. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Although I do not necessarily share the concluding accusations against self-experimentation, I do share her view that self-experimentation should not be regarded as proper scientific research, and therefore should not be subject to ethical review.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.bmj.com/content/341/bmj.c7103&quot;&gt;Annas, &lt;em&gt;BMJ&lt;/em&gt; (2010); &lt;strong&gt;341&lt;/strong&gt;: c7103&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-20T14:57:41.367" LastActivityDate="2015-05-20T14:57:41.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34391" PostTypeId="1" AcceptedAnswerId="34395" CreationDate="2015-05-20T12:24:05.667" Score="0" ViewCount="142" Body="&lt;p&gt;Is the minimum criterion for life a single cell?  It seems that self-replicating RNA is not enough, but I don't know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would be the most basic cell that could fit this criterion and what cells today would be most similar?&lt;/p&gt;&#xA;" OwnerUserId="13238" LastEditorUserId="1306" LastEditDate="2015-05-20T13:43:00.220" LastActivityDate="2015-05-20T15:19:13.130" Title="What is the point at which abiogenesis is complete and evolution begins?" Tags="&lt;evolution&gt;&lt;molecular-evolution&gt;&lt;abiogenesis&gt;" AnswerCount="1" CommentCount="9" ClosedDate="2015-05-20T22:14:39.123" ContentLicense="CC BY-SA 3.0" />
  <row Id="34392" PostTypeId="5" CreationDate="2015-05-20T12:43:53.820" Score="0" Body="" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-20T12:43:53.820" LastActivityDate="2015-05-20T12:43:53.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34393" PostTypeId="4" CreationDate="2015-05-20T12:43:53.820" Score="0" Body="Ethics questions are off-topic, see the help center for more info.&#xD;&#xA;&#xD;&#xA;Methods, procedures and perspectives for the appropriate conduct of research. Cornerstones in medical research are the Nuremberg code and the Declaration of Helsinki.  &#xD;&#xA;&#xD;&#xA;" OwnerUserId="9943" LastEditorUserId="1590" LastEditDate="2016-02-02T15:06:03.840" LastActivityDate="2016-02-02T15:06:03.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34394" PostTypeId="1" CreationDate="2015-05-20T14:30:45.113" Score="4" ViewCount="99" Body="&lt;p&gt;A while ago I saw &lt;a href=&quot;http://blog.ted.com/why-your-brain-doesnt-want-you-to-lose-weight-sandra-aamodt-at-tedglobal-2013/&quot; rel=&quot;nofollow&quot;&gt;this TED talk about the futility of dieting&lt;/a&gt;. The speaker suggests that a body maintains a homeostatic weight point and returns to that weight after dieting has stopped:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Turns out the brain is an incredibly efficient regulator of body&#xA;  weight. Isn’t weight loss about how much you eat versus how much&#xA;  energy you burn? Nope, it’s not that simple an equation: it turns out&#xA;  that hunger and energy use are controlled by the brain, mostly behind&#xA;  the scenes, and this unconscious force is stronger than mere&#xA;  willpower. &lt;strong&gt;The brain has its own sense of what your body should weigh&#xA;  — no matter what you believe — called the set point, which has a range&#xA;  of about 15 pounds.&lt;/strong&gt; While lifestyle changes can shift your weight&#xA;  within this range, it’s much harder to move outside of it.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The speaker suggests that once she gave up dieting, she actually lost weight. Since then I've seen a number of other anecdotal reports of people losing weight once they let go of the need to diet and started to &quot;eat anything they wanted&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This makes me ask - &lt;strong&gt;does anxiety about weight and attempts to control one's eating cause people to put on weight?&lt;/strong&gt; In other words, if there's some unresolved anxiety issue in one's life, does it cause the human body to start preparing for hard times by storing extra fat?&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2017-02-27T20:19:35.750" Title="Does anxiety about weight or eating cause people to become overweight?" Tags="&lt;human-biology&gt;&lt;psychology&gt;&lt;diet&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34395" PostTypeId="2" ParentId="34391" CreationDate="2015-05-20T15:19:13.130" Score="2" Body="&lt;p&gt;I think it's a mistake to assume that there is such a point. All plausible seeming models of abiogenesis currently under consideration involve evolutionary processes long before they reach the stage we'd consider alive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution will occur whenever there is (a) replication-with-error and (b) selection (simplifying slightly). This is the case with a self-replicating RNA. It is replicating, but those replicates can be imperfect. Imperfections in replication that improve its ability to replicate will be favoured. That's evolution.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2015-05-20T15:19:13.130" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34396" PostTypeId="1" CreationDate="2015-05-20T15:57:59.593" Score="-1" ViewCount="685" Body="&lt;p&gt;Recently, I learned that pandas have a carnivore's digestive system but that it exists almost exclusively as a herbivore. If pandas hunted would they be able to find meat in their environment? Can't think of any reason why they would 'evolve' to eat only bamboo if this was true. It's like 2 million years ago some bears decided they wouldn't hunt, hibernate or even roar and are slowly committing suicide.&lt;/p&gt;&#xA;" OwnerUserId="14949" LastActivityDate="2017-07-03T15:46:21.943" Title="Can pandas hunt for meat?" Tags="&lt;evolution&gt;&lt;food&gt;&lt;diet&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34397" PostTypeId="1" AcceptedAnswerId="34398" CreationDate="2015-05-20T16:06:18.550" Score="10" ViewCount="24875" Body="&lt;p&gt;Are blood vessels classified as organs? Organs compose of 2 or more tissues and perform a certain function. Blood vessels have 3 different tissues and perform a function (transport blood), yet I do not see them being identified as an organ. Why is this? Are they organs? Or do they hold their own classification?&lt;/p&gt;&#xA;" OwnerUserId="6950" LastEditorUserId="9943" LastEditDate="2015-05-21T12:18:19.263" LastActivityDate="2019-03-05T21:27:38.460" Title="Are blood vessels organs?" Tags="&lt;terminology&gt;&lt;blood-circulation&gt;" AnswerCount="3" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34398" PostTypeId="2" ParentId="34397" CreationDate="2015-05-20T16:22:47.980" Score="11" Body="&lt;p&gt;The cardiovascular system is usually lumped together as an organ. So blood vessels would be included here but you are right in that this is a bit strange being that it includes the heart and the vasculature.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-05-20T16:22:47.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34399" PostTypeId="1" CreationDate="2015-05-20T18:12:57.253" Score="3" ViewCount="131" Body="&lt;p&gt;I have been reading about Pavlovian brain conditioning and it seems that documented cases are mostly limited to motor reflexes (like conditioning an eyelid to close when hearing a tone) or &lt;a href=&quot;http://en.wikipedia.org/wiki/Taste_aversion&quot; rel=&quot;nofollow&quot;&gt;taste aversion&lt;/a&gt; . Basically information flowing through Cerebellum and Hippocampus. Are there proofs or scientific studies about the limitations of such conditioning? Or studies about what can be associated and what not?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's imagine for example that a subject looks at a black neutral screen and whenever some tone is played, the screen turns bright red. After an intense conditioning would it be possible that this subject, when blindfolded would see some red when hearing that same tone?&lt;/p&gt;&#xA;" OwnerUserId="6213" LastEditorUserId="5144" LastEditDate="2018-03-09T11:30:55.317" LastActivityDate="2018-03-09T11:30:55.317" Title="Pavlovian Conditioning And Synesthesia" Tags="&lt;synesthesia&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34401" PostTypeId="2" ParentId="1191" CreationDate="2015-05-20T19:40:50.307" Score="2" Body="&lt;p&gt;You may create a new database with the new sequences and create an alias linking the old and new databases with &lt;code&gt;blastdb_aliastool&lt;/code&gt;&lt;/p&gt;&#xA;" OwnerUserId="1494" LastActivityDate="2015-05-20T19:40:50.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34402" PostTypeId="2" ParentId="34397" CreationDate="2015-05-20T20:19:55.180" Score="12" Body="&lt;p&gt;I don't know if they are classified as organs, but basically, blood vessels match the criteria for being organs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quoting &lt;a href=&quot;http://www.siumed.edu/~dking2/crr/cvguide.htm#vessels&quot;&gt;SIU School of Medicine&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Blood vessels are basically tubular organs found within other organs. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.biologyreference.com/Oc-Ph/Organ.html&quot;&gt;Biology Reference&lt;/a&gt; states the same:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Even the glands within the integument can be considered organs; any gland is primarily secretory epithelium surrounded by connective tissue for support and protection. Likewise, the &lt;strong&gt;blood vessels&lt;/strong&gt; and nerves in these organs &lt;strong&gt;are organs&lt;/strong&gt; unto themselves.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2015-05-20T20:19:55.180" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34403" PostTypeId="2" ParentId="34399" CreationDate="2015-05-20T21:31:10.273" Score="7" Body="&lt;p&gt;This has been attempted, with some success, though on grapheme-color synesthesia, rather than sound-color synesthesia. Beyond conditioning, there have also been somewhat successful attempts to induce synesthesia through various psychoactive drugs. In both of these cases, however, the effects are temporary and generally weaker than genuine synesthetic perceptions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There have been no studies (to my knowledge) about which associations can be induced and which cannot. I would say that sound-color might be a difficult association to generate, simply because no one would like to site and stare at a flashing screen while listening to various sounds, and it also predicates on the patients' ability to distinguish sounds, which can vary wildly from person to person. The grapheme-color experiment had the treatment group read materials with certain letters colored, which was much easier to implement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This raises the question of whether synesthesia can be classified as a low-level interaction between typically non-interacting parts of the brain, or if it operates on a higher cognitive level (i.e. ideathesia). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See the article for details about the grapheme-color study: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;&lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0039799&quot;&gt;Pseudo-Synesthesia through Reading Books with Colored Letters&lt;/a&gt;&quot;&lt;/p&gt;&#xA;" OwnerDisplayName="user15836" LastEditorUserId="5144" LastEditDate="2015-05-20T21:38:16.173" LastActivityDate="2015-05-20T21:38:16.173" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34404" PostTypeId="1" CreationDate="2015-05-20T22:00:57.947" Score="8" ViewCount="216" Body="&lt;p&gt;I'm about to present an exam about ecological interactions in biological control. Although the position of some groups is clear, in the case of parasitoids they are included sometimes as predators, some others as parasites, while sometimes they are included like an own group. For example, in this paper they&#xA; are included as parasites, but I wanted to know if there is a more recent reference or classification for these groups (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0169534702026150&quot; rel=&quot;nofollow noreferrer&quot;&gt;Trophic strategies,&#xA;animal diversity and body size Kevin D. Lafferty and Armand M. Kuris&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="15839" LastEditorUserId="3553" LastEditDate="2017-03-28T04:06:56.677" LastActivityDate="2017-03-28T04:06:56.677" Title="Recent classification for parasitoid (ecological relationships)" Tags="&lt;zoology&gt;&lt;community-ecology&gt;&lt;parasitism&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34406" PostTypeId="1" AcceptedAnswerId="34407" CreationDate="2015-05-21T02:32:44.160" Score="4" ViewCount="61" Body="&lt;p&gt;After reading an article, I saw expressions like &quot;cross-immunoreactivity among epitopes&quot;, &quot;cross-immunoreactivity among variants of virus&quot;, &quot;immunological reactions among pairs of peptides&quot; and so on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wish to verify my following understandings: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An epitope is also called antigenic determinant, and it is part of the antigen that is recognized by the antibody. An epitope, then, is a part of a virus variant. Peptides are short chains of amino acids. Thus, we can talk about the immunological reactions among peptide-pairs, because the virus variant itself is a protein, which is composed of peptides? Did I understand it correctly? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, I saw a sentence like &quot;this antibody is against a few variants while reacting with all tested peptides&quot;, so I guess reacting here includes against? Reacting may include other situations, right?&lt;/p&gt;&#xA;" OwnerUserId="15799" LastEditorUserId="9943" LastEditDate="2015-05-21T02:50:22.083" LastActivityDate="2015-05-21T12:03:38.243" Title="Terminology regarding cross-immunoreactivity" Tags="&lt;immunology&gt;&lt;terminology&gt;&lt;immunity&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34407" PostTypeId="2" ParentId="34406" CreationDate="2015-05-21T02:46:36.917" Score="2" Body="&lt;p&gt;Everything you state is correct, except that I disagree with your statement that a &lt;code&gt;&quot;[...] virus variant itself is a protein, which is composed of peptides&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A virus is typically composed of a protein capsule with genetic material on the inside. So technically, a virus &lt;em&gt;is&lt;/em&gt; not a protein, but &lt;strong&gt;its outer shell is composed of proteins&lt;/strong&gt;. Further, a protein does not necessarily have to be composed of (multiple) peptides - it can be a single amino acid chain.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-21T12:03:38.243" LastActivityDate="2015-05-21T12:03:38.243" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34408" PostTypeId="1" AcceptedAnswerId="34411" CreationDate="2015-05-21T08:25:02.097" Score="3" ViewCount="293" Body="&lt;p&gt;In a test I was asked why bacteria are insensitive to snake toxins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it their membrane that provides a barrier to the toxins? Or do snake poisons have specific targets and thus cannot bind to bacteria?&lt;/p&gt;&#xA;" OwnerUserId="15699" LastEditorUserId="9943" LastEditDate="2015-05-21T11:05:15.707" LastActivityDate="2019-06-19T12:44:44.837" Title="Why are bacteria immune to snake poisons?" Tags="&lt;toxicology&gt;&lt;poison&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34409" PostTypeId="1" AcceptedAnswerId="34412" CreationDate="2015-05-21T10:47:11.427" Score="7" ViewCount="31525" Body="&lt;p&gt;I've read a lot about cockroaches but was unable to find how they contribute to the ecological environment. Does anyone know?&lt;/p&gt;&#xA;" OwnerUserId="15847" LastActivityDate="2019-05-19T18:33:48.613" Title="What is the contribution of the cockroach to the ecological environment?" Tags="&lt;ecosystem&gt;&lt;pest-control&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34410" PostTypeId="2" ParentId="34409" CreationDate="2015-05-21T10:56:39.667" Score="15" Body="&lt;p&gt;They don't have to &quot;contribute&quot; as such. All they have to do is survive and pass on their genes to their offspring. Any benefits that they have (in terms of detritus cleaned up, etc.) or harms that they cause is purely coincidental.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's no &quot;desire&quot; on the behalf of species to make things &quot;better&quot;. All they &quot;do&quot; is try to survive in their existing environment but not make it &quot;worse&quot; for themselves. A species wouldn't survive very long if it ate &lt;strong&gt;all&lt;/strong&gt; of the food in an area or if its waste products polluted the area to such an extent that they couldn't survive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, that doesn't mean you can simply remove a species from an environment and not cause actual harm to that environment. The environment includes all the other species that co-exist and they have all evolved in the presence of each other. This means that other animals have evolved to cope with the fact that cockroaches prey on them, others have evolved to eat cockroaches. Remove the cockroaches and the population of the first species will explode and that of the second will collapse. This will have knock on effects to other species in that environment and so on.&lt;/p&gt;&#xA;" OwnerUserId="15848" LastEditorUserId="15848" LastEditDate="2017-04-13T20:40:17.217" LastActivityDate="2017-04-13T20:40:17.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34411" PostTypeId="2" ParentId="34408" CreationDate="2015-05-21T10:59:35.590" Score="16" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Many snake poisons target specific proteins not present in unicellular organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The question is admittedly broad but the idea behind this question is pretty much what you indicate in your post - many venoms target specific proteins and do not simply destroy their target by, e.g., disrupting gross cellular structure (like alcohol does for example). Instead, they target specific molecules that are essential for the survival of their prey.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Snake toxins can be categorized according to the organ systems they target, namely :&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;the central nervous system&lt;/li&gt;&#xA;&lt;li&gt;the cardiovascular system&lt;/li&gt;&#xA;&lt;li&gt;the muscular system&lt;/li&gt;&#xA;&lt;li&gt;the vascular system&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Central nervous system toxins are carried by elapid snakes like cobras, kraits and the taipan. Typical targets are the &lt;strong&gt;nicotinic acetylcholine receptor&lt;/strong&gt; and the &lt;strong&gt;muscarinic acetylcholine receptor&lt;/strong&gt;. Blockade of these receptors at the neuromuscular junctions resulting in death by asphyxiation. Acetylcholine receptors are not present in bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cardiovascular toxins are pretty &lt;strong&gt;diverse&lt;/strong&gt; and include things like angiotensin-converting &lt;strong&gt;enzyme inhibitors&lt;/strong&gt; (leading to a drop in blood pressure) and &lt;strong&gt;glycosaminoglycans&lt;/strong&gt; (the sulphated carbohydrate moieties that occur abundantly in cells of cardiovascular tissues) binding proteins that lead to cardiotoxicity. Again, the targets are &lt;strong&gt;specific&lt;/strong&gt; molecules involved in heart function and hormones, stuff not present in bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Muscular toxins include those that bind specifically to the sarcoplasmic reticulum of &lt;strong&gt;muscles&lt;/strong&gt; or interfere with specific &lt;strong&gt;second messenger systems&lt;/strong&gt; messing up muscular function. Again, quite specific targets not present in bacteria.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, typical vascular system toxins include &lt;strong&gt;anti-coagulants&lt;/strong&gt; such as protein C activators and inhibitors of prothrombin complex formation. Again, &lt;strong&gt;specific targets&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://link.springer.com/article/10.1007/s00018-006-6315-0#page-1&quot;&gt;Koh et al., &lt;em&gt;Cell. Mol. Life Sci&lt;/em&gt; (2006); &lt;strong&gt;63&lt;/strong&gt;: 3030–3041&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="3340" LastEditDate="2015-05-21T16:41:06.327" LastActivityDate="2015-05-21T16:41:06.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34412" PostTypeId="2" ParentId="34409" CreationDate="2015-05-21T11:14:12.187" Score="26" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Cockroaches are an integral part of the food chain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Cockroaches are an important &lt;strong&gt;source of food&lt;/strong&gt; for a number of organisms, such as arthropods, birds, and mammals. As such, they are an important part of the food chain. Cockroaches also play an important role in &lt;strong&gt;nutrient recycling&lt;/strong&gt;. Most species of cockroach are &lt;strong&gt;detritus feeders&lt;/strong&gt; and with the help of endogenous cellulases play an important role in degrading plant material. Some species, such as &lt;em&gt;Cryptocercus&lt;/em&gt;, feed directly on wood and play a major role in lignocellulose digestion in temperate forests.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA; - &lt;a href=&quot;http://icb.oxfordjournals.org/content/48/4/541.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bell et al., &lt;em&gt;Integr Comp Biol&lt;/em&gt;, 2008; &lt;strong&gt;48&lt;/strong&gt;(4): 541-3&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2019-05-19T18:33:48.613" LastActivityDate="2019-05-19T18:33:48.613" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="34413" PostTypeId="1" CreationDate="2015-05-21T11:23:47.407" Score="-1" ViewCount="1356" Body="&lt;p&gt;I'm studying microbiology right now and I have come across something confusing to me. I thought electrons provided energy to the cell by being incorporated into reducing powers and eventually driving the synthesis of ATP. However in classification of microbes energy sources (photo, chemo) and electron sources (litho, organo) are separate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a scenario in which the source of electrons and energy are different (besides phototrophy)?&lt;/p&gt;&#xA;" OwnerUserId="15850" LastEditorUserId="26120" LastEditDate="2016-09-03T08:44:39.833" LastActivityDate="2016-09-05T16:38:46.467" Title="What is the difference between electrons and energy?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;microbiology&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="2" ClosedDate="2015-05-21T12:50:09.340" ContentLicense="CC BY-SA 3.0" />
  <row Id="34415" PostTypeId="1" CreationDate="2015-05-21T12:27:46.497" Score="8" ViewCount="617" Body="&lt;p&gt;After searching online for &lt;strong&gt;peptide mapping&lt;/strong&gt; to my understanding it can be treated as the fingerprint of the protein. It is obtained at the end of several chemical processes and it helps to understand the protein being analyzed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does this method operate in &quot;sequence space&quot; then? If so, what exactly is the relation of the two? &lt;/p&gt;&#xA;" OwnerUserId="15799" LastEditorUserId="9943" LastEditDate="2015-05-21T15:08:52.450" LastActivityDate="2015-05-21T15:20:03.697" Title="What is peptide mapping?" Tags="&lt;proteins&gt;&lt;protein-structure&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34416" PostTypeId="2" ParentId="34413" CreationDate="2015-05-21T13:02:05.567" Score="9" Body="&lt;p&gt;You're basically confusing the fuel source with the energy it produces. For example, a car burns gasoline. That doesn't mean that gasoline is energy, only that gasoline can be &lt;em&gt;used&lt;/em&gt; to produce energy. Similarly, a cell uses electrons in the production of ATP (&lt;a href=&quot;http://www.cliffsnotes.com/sciences/biology/biochemistry-i/oxidative-phosphorylation/atp-synthesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Uf0H5.jpg&quot; alt=&quot;ATP synthesis&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the image above, electrons (symbolized by the flat arrow going from $\mathit{NADH}$ + $H^+$ to $\frac{1}{2}O_2$ + $2H^+$) flow from NADH-Q reductase (I) to cytochrome reductase (III), to cytochrome oxidase (IV). The electron flow across these complexes causes the pumping of hydrogen cations (protons) through the membrane to the extracellular space. This, in turn, produces a pH gradient and membrane potential which are used to drive the synthesis of ATP (by the $F_1F_0$ ATPase), which can be broken down to release energy (&lt;a href=&quot;http://greatneck.k12.ny.us/GNPS/SHS/dept/science/krauz/bio_h/images/08_09ATPHydrolysis_L.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zCx21.jpg&quot; alt=&quot;ATP hydrolysis&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, electrons are needed&lt;sup&gt;1&lt;/sup&gt; to produce ATP and ATP can be thought of as energy storage. When ATP is broken down to produce AMP and Phosphate, energy is released in the form of heat. This is why ATP is considered as &quot;energy currency&quot;. Neither ATP nor electrons, however, are &quot;energy&quot; themselves&lt;sup&gt;2&lt;/sup&gt;. No more than gasoline is. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;1&lt;/sup&gt; Are &lt;em&gt;used&lt;/em&gt;, anyway. There are other choices. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;2&lt;/sup&gt; No more than any other form of matter, at least. You can, actually, think of matter as condensed energy but that is really squarely in the realm of physics and not biology. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2016-09-05T16:38:46.467" LastActivityDate="2016-09-05T16:38:46.467" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34417" PostTypeId="1" CreationDate="2015-05-21T13:05:24.447" Score="1" ViewCount="424" Body="&lt;p&gt;We are looking to develop or customize a LIMS for our molecular lab. Do you know of a LIMS that you've used in a molecular lab before, or one that could be used.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for the help&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Edit)&#xA;Some of the attributes we'd like to store include:&#xA;    Patient information (Name, demographics, test ordered)&#xA;    Sample information (Accession #, Case ID, sample type (blood,bone, etc.) )&#xA;    Test information (Kit used, Kit lot #, associated expiration date)&#xA;Ideally this is Software as a Service so its usable on multiple operating systems.&lt;/p&gt;&#xA;" OwnerUserId="15855" LastEditorUserId="15855" LastEditDate="2015-05-21T17:22:08.803" LastActivityDate="2020-04-14T09:52:32.523" Title="Recommend any Molecular lab LIMS (Laboratory Information Management System)" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;lab-techniques&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="0" ClosedDate="2020-04-15T11:26:20.027" ContentLicense="CC BY-SA 3.0" />
  <row Id="34420" PostTypeId="1" CreationDate="2015-05-20T18:58:49.893" Score="2" ViewCount="5884" Body="&lt;p&gt;Is it possible that a full colon impinges on the sciatic nerve? Is there anything that physically separates the sciatic nerve from the colon?&lt;/p&gt;&#xA;" OwnerUserId="15872" OwnerDisplayName="Johannes Ernst" LastEditorUserId="9943" LastEditDate="2015-05-21T14:43:53.933" LastActivityDate="2015-11-26T16:36:52.507" Title="What is the distance between the sciatic nerve and the colon at the closest point?" Tags="&lt;human-anatomy&gt;&lt;neuroanatomy&gt;&lt;pain&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34421" PostTypeId="2" ParentId="34420" CreationDate="2015-05-21T14:38:02.373" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Sciatic nerve pain cannot be caused by a full colon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;background&lt;/strong&gt;&lt;br&gt;&#xA;The sciatic nerve runs at the back of the pelvis down the the leg. The sciatic nerve exits the spine from the lumbar spine to S3 in the sacrum (Fig. 1).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SCof5.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/YFmQW.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig.1. Left: sciatic nerve overview. Right: Sacral plexus. Source: &lt;a href=&quot;http://www.mbmyoskeletal.com/learning/sciatica/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Manchester Bedford Clinic&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence the sciatic nerve does not come into contact with the bowel and intestines located ventrally in the abdominal cavity (Fig. 2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TFhkv.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/wAtzt.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig.2. Left: sciatic nerve in detail showing dorsal location. Right: Intestines ventrally situated in abdominal cavity. Source: &lt;a href=&quot;http://www.mbmyoskeletal.com/learning/sciatica/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Manchester Bedford Clinic&lt;/a&gt; and &lt;a href=&quot;http://health.bwmc.umms.org/patiented/articles/colon_cancer_normal_anatomy_000126.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;University of Maryland&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pain in the sciatic nerve (sciatica) is often caused by compression or entrapment by muscles, tendons, and other soft tissues along the nerve path &lt;a href=&quot;http://www.mbmyoskeletal.com/learning/sciatica/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Manchester Bedford Clinic&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-21T21:42:23.400" LastActivityDate="2015-05-21T21:42:23.400" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34422" PostTypeId="2" ParentId="34415" CreationDate="2015-05-21T15:06:31.350" Score="6" Body="&lt;p&gt;&lt;a href=&quot;http://www.shimadzu.com/an/industry/pharmaceuticallifescience/peptide_mapping.htm&quot; rel=&quot;nofollow&quot;&gt;Shimadzu&lt;/a&gt; explains peptide mapping as follows:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Peptide mapping involves selectively cleaving the individual target [proteins] using an appropriate enzyme or chemical and analyzing the peptide fragments obtained using HPLC [high-performance liquid chromatography] or another suitable method. [... I]dentification of the peptide fragments separated by LC [...] [can be done] using amino acid composition analysis, N-terminal amino acid sequence analysis, or mass spectrometry.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As such, it does &lt;strong&gt;not provide a sequence of amino acids&lt;/strong&gt;. Instead, you get a specific set of peptides of different sizes, dependent on the method used, that in turn can be used for &lt;a href=&quot;http://www.ionsource.com/tutorial/protID/fingerprint.htm&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;protein fingerprinting&lt;/strong&gt;&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-21T15:20:03.697" LastActivityDate="2015-05-21T15:20:03.697" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34423" PostTypeId="2" ParentId="34363" CreationDate="2015-05-21T17:05:50.333" Score="3" Body="&lt;p&gt;No, it's not specific to the X chromosome. It's a general trend. CG sequences are underrepresented in mammalian genomes. In fact, the very nucleotides C and G are underrepresented. Instead of the ~25% you'd expect by chance, the real numbers for the human genome are (calculated on the hg19 version of the UCSC human genome):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;N: 234350281 = 7.5702%   &amp;lt;-- N means unknown&#xA;A: 844868045 = 27.2917%&#xA;C: 585017944 = 18.8978%&#xA;T: 846097277 = 27.3314%&#xA;G: 585360436 = 18.9089%&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;If we break this down by chromosome (chrM is the mitochondrial genome which should probably be ignored here), we get:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;chrM    A:5113 (30.9%)  C:5192 (31.3%)  T:4086 (24.7%)  G:2180 (13.2%)  N:0 (0%)    &#xA;chr1    A:65570891 (29.1%)  C:47024412 (20.9%)  T:65668756 (29.1%)  G:47016562 (20.9%)  N:0 (0%)    &#xA;chr2    A:71102632 (29.2%)  C:47915465 (19.7%)  T:71239379 (29.3%)  G:47947042 (19.7%)  N:4994855 (2.1%)    &#xA;chr3    A:58713343 (29.6%)  C:38653197 (19.5%)  T:58760485 (29.7%)  G:38670110 (19.5%)  N:3225295 (1.6%)    &#xA;chr4    A:57932980 (30.9%)  C:35885806 (19.1%)  T:57952068 (30.9%)  G:35890822 (19.1%)  N:0 (0%)    &#xA;chr5    A:53672554 (30.2%)  C:35089383 (19.7%)  T:53804137 (30.3%)  G:35129186 (19.8%)  N:0 (0%)    &#xA;chr6    A:50554433 (29.5%)  C:33143287 (19.4%)  T:50533923 (29.5%)  G:33163423 (19.4%)  N:3720001 (2.2%)    &#xA;chr7    A:45997757 (29.6%)  C:31671670 (20.4%)  T:46047257 (29.6%)  G:31636979 (20.4%)  N:0 (0%)    &#xA;chr8    A:42767293 (29.9%)  C:28703983 (20.1%)  T:42715025 (29.9%)  G:28702621 (20.1%)  N:0 (0%)    &#xA;chr9    A:35260078 (29.3%)  C:24826212 (20.7%)  T:35243882 (29.3%)  G:24813259 (20.7%)  N:0 (0%)    &#xA;chr10   A:38330752 (28.3%)  C:27308648 (20.1%)  T:38376915 (28.3%)  G:27298423 (20.1%)  N:4220009 (3.1%)    &#xA;chr11   A:38307244 (29.2%)  C:27236798 (20.8%)  T:38317436 (29.2%)  G:27268038 (20.8%)  N:0 (0%)    &#xA;chr12   A:38604831 (28.8%)  C:26634995 (19.9%)  T:38624517 (28.9%)  G:26617050 (19.9%)  N:3370502 (2.5%)    &#xA;chr13   A:29336945 (30.7%)  C:18412698 (19.3%)  T:29425459 (30.8%)  G:18414776 (19.3%)  N:0 (0%)    &#xA;chr14   A:25992966 (29.4%)  C:18027132 (20.4%)  T:26197495 (29.7%)  G:18071947 (20.5%)  N:0 (0%)    &#xA;chr15   A:23620876 (23%)    C:17247582 (16.8%)  T:23597921 (23%)    G:17228387 (16.8%)  N:20836626 (20.3%)  &#xA;chr16   A:21724083 (27.5%)  C:17630040 (22.3%)  T:21828642 (27.7%)  G:17701988 (22.4%)  N:0 (0%)    &#xA;chr17   A:21159933 (27.2%)  C:17727956 (22.8%)  T:21206981 (27.3%)  G:17700340 (22.8%)  N:0 (0%)    &#xA;chr18   A:22465380 (28.8%)  C:14838685 (19%)    T:22489493 (28.8%)  G:14863671 (19%)    N:3420019 (4.4%)    &#xA;chr19   A:14390632 (25.8%)  C:13478255 (24.2%)  T:14428951 (25.9%)  G:13511145 (24.2%)  N:0 (0%)    &#xA;chr20   A:16523053 (27.8%)  C:13107828 (22%)    T:16725227 (28.1%)  G:13149412 (22.1%)  N:0 (0%)    &#xA;chr21   A:10422924 (21.7%)  C:7160212 (14.9%)   T:10348785 (21.5%)  G:7174721 (14.9%)   N:13023253 (27.1%)  &#xA;chr22   A:9094775 (17.7%)   C:8375984 (16.3%)   T:9054551 (17.6%)   G:8369235 (16.3%)   N:16410021 (32%)    &#xA;chrX    A:45648952 (30.2%)  C:29813353 (19.7%)  T:45772424 (30.3%)  G:29865831 (19.8%)  N:0 (0%)    &#xA;chrY    A:7667625 (29.9%)   C:5099171 (19.9%)   T:7733482 (30.1%)   G:5153288 (20.1%)   N:0 (0%)    &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;As you can see, C and G are consistently less frequent than A and T across all chromosomes. The exception is the mitochondrial genome but that &lt;a href=&quot;https://en.wikipedia.org/wiki/Symbiogenesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;is not the genome of a vertebrate&lt;/a&gt;. So, overall, A and T occur almost 10% more often than C and G. But why does this happen?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as I know, the reasons are not entirely clear. Some factors that affect this, however, are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The C of the CG dinucleotides can be &lt;a href=&quot;http://en.wikipedia.org/wiki/DNA_methylation&quot; rel=&quot;nofollow noreferrer&quot;&gt;methytlated&lt;/a&gt;. Methylation is a chemical modification of the nucleotide and plays an important role in the regulation of gene expression. The regulatory sequences that control the way that genes are expressed (&lt;a href=&quot;https://en.wikipedia.org/wiki/Promoter_%28genetics%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;promoters&lt;/a&gt;), are often rich in CG sequences (these localized overrepresentations of CG are called &lt;a href=&quot;http://en.wikipedia.org/wiki/CpG_site#CpG_islands&quot; rel=&quot;nofollow noreferrer&quot;&gt;CpG islands&lt;/a&gt;) which enable the control of the associated gene's expression by the mechanism of methylation (which can &quot;turn off&quot; a gene). Not the kind of thing you want to have occurring randomly in your genes. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Methylated Cytosine (C) is often converted to Thymine (T): &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8g6SAm.png&quot; alt=&quot;Cytosine becomes Thymine&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This would result in a gradual loss of C in favor of T. This theory had long been considered to be the main reason why CpG is so rare in mammalian genomes, but see the next point.  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I found a study from 2004 &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0378111904000836&quot; rel=&quot;nofollow noreferrer&quot;&gt;[1]&lt;/a&gt; that shows that, among other things, there is no correlation between CpG and TpA shortages, suggesting that the deamination of Cytosine to Thymine is not enough to explain the phenomenon. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I should also point out that the fact that Alanine represents  7.8% of all aminoacids in proteins does not say anything at all about the frequency with which its codons appear in the genome at large. Only ~2% of the human genome (genes are ~5% and exons, those parts of genes that are translated into proteins, only ~2%) actually codes for proteins so it is only in that 2% where you will see this overrepresentation (if one exists) of Alanine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In conclusion, yes, the CpG shortage is a general feature of the human genome and not of chromosome X, but the precise reasons for this are not yet entirely clear (as far as I know, anyway). &lt;/p&gt;&#xA;&#xA;&lt;h3&gt;References&lt;/h3&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0378111904000836&quot; rel=&quot;nofollow noreferrer&quot;&gt;Jabbari K., and Bernardi G., &lt;em&gt;Gene&lt;/em&gt; &lt;strong&gt;333&lt;/strong&gt;:143-149, 2004&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2015-05-21T17:05:50.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34424" PostTypeId="2" ParentId="34408" CreationDate="2015-05-21T17:13:53.413" Score="6" Body="&lt;p&gt;Venoms from vipers contain high amount of proteolytic enzymes (serine proteases). Many of them act by cleaving fibrinogen and thereby causing blood clot (&lt;a href=&quot;http://cdn.intechopen.com/pdfs-wm/44718.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref&lt;/a&gt;). There is a likelihood that some of these proteases may affect other proteins also. In a study conducted by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3086185/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bottrall et al. (2010)&lt;/a&gt;, it was shown that snake venoms do have a general proteolytic activity. The best among tested was the venom of the viper &lt;em&gt;Bitis arietans&lt;/em&gt;. However, its activity was significantly lower than the positive control which consisted mainly of trypsin and proteinase-K.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the venom may have a little effect on the membrane proteins of bacteria.&#xA;But it might require extended treatment by venom to digest these proteins compared to that by stronger proteases like proteinase-K.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are indeed reports on antibacterial activity of snake venoms (&lt;a href=&quot;https://doi.org/10.1016/0041-0101(91)90210-I&quot; rel=&quot;nofollow noreferrer&quot;&gt;Stiles et al., 1991&lt;/a&gt;; &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/17309613&quot; rel=&quot;nofollow noreferrer&quot;&gt;Perumal Samy et al., 2007&lt;/a&gt;; &lt;a href=&quot;https://doi.org/10.1016/j.toxicon.2018.05.016&quot; rel=&quot;nofollow noreferrer&quot;&gt;Charvat et al., 2018&lt;/a&gt;). But the enzymes responsible for the antibacterial activity are phospholipase A2 and L-amino acid oxidase, and not the proteases. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2019-06-19T12:44:44.837" LastActivityDate="2019-06-19T12:44:44.837" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="34425" PostTypeId="1" CreationDate="2015-05-21T17:34:01.977" Score="4" ViewCount="156" Body="&lt;p&gt;The recent work by &lt;a href=&quot;http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.1816.html&quot; rel=&quot;nofollow&quot;&gt;DeLoache, et al.&lt;/a&gt; on a synthetic opiate-precursor production pathway in yeast has generated a lot of scare stories in the media about people homebrewing heroin as easily as they would beer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In connection with DeLoache and coworkers' research, the &lt;a href=&quot;http://www.nytimes.com/2015/05/19/health/a-way-to-brew-morphine-raises-concerns-over-regulation.html&quot; rel=&quot;nofollow&quot;&gt;New York Times has claimed&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Their DNA could be put on a watch list, as sequences for anthrax and smallpox are, so any attempt to buy them from DNA supply houses would raise flags.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I have never heard of such a watch list, and a thorough googling turned up nothing relevant save for the NYT article itself. Does this watch list exist?&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="948" LastEditDate="2016-02-02T14:49:08.323" LastActivityDate="2016-02-02T14:49:08.323" Title="Do DNA supply houses maintain a watch list for dangerous oligos (Anthrax, Smallpox, etc.)?" Tags="&lt;dna&gt;&lt;synthetic-biology&gt;&lt;safety&gt;&lt;gene-synthesis&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34426" PostTypeId="1" AcceptedAnswerId="34437" CreationDate="2015-05-21T17:59:11.973" Score="2" ViewCount="139" Body="&lt;p&gt;If I understand the basic &lt;a href=&quot;http://en.wikipedia.org/wiki/Hebbian_theory&quot; rel=&quot;nofollow&quot;&gt;Hebbian theory&lt;/a&gt;, when a neuron fires a pulse to another neuron and this pulse causes the target neuron to fire then the delta energy sent from the initial neuron to the target is increased. (Making it easier to trigger the target cell)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With this in mind is there a way for an inhibitory neuron to increase the delta energy it applies to a target neuron (reducing the excitation level of a target neuron). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the inhibitory neuron never triggers the target then I would assume it would never increase the decrease in energy it sends to the target. &lt;/p&gt;&#xA;" OwnerUserId="11661" LastEditorUserId="3340" LastEditDate="2015-05-21T18:22:31.407" LastActivityDate="2015-05-21T21:43:13.023" Title="Can the Hebbian theory apply to Inhibitory Neurons" Tags="&lt;neuroscience&gt;&lt;neurology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34427" PostTypeId="1" CreationDate="2015-05-21T18:16:57.027" Score="6" ViewCount="258" Body="&lt;p&gt;Yesterday, I bought a banana tree (&lt;strong&gt;Musa Basjoo&lt;/strong&gt;) from a local supermarket.&#xA;Today, I noticed a hive of small spiders on the tree.&#xA;I do not know where they came from, so I am curious to identify these small creatures.&#xA;I am living in Flossenbürg, Bavaria, Germany.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can someone help me identify the kind of spiders that are depicted on the photos?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A picture of the tree, it is still in front of my house door, planted in a pot:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/AxR58.jpg&quot; alt=&quot;a picture of the tree, it is still in front of my house door, planted in a pot.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A near shot of the spiders that are &quot;dwelling&quot; on the tree:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/EGzqY.jpg&quot; alt=&quot;a near zoom shot of the spiders that are &amp;quot;dwelling&amp;quot; on the tree&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user15861" LastEditorDisplayName="user15861" LastEditDate="2015-05-21T18:25:14.193" LastActivityDate="2015-05-28T06:23:33.843" Title="Zoology - Help identify the kind of spider" Tags="&lt;zoology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34428" PostTypeId="1" AcceptedAnswerId="34432" CreationDate="2015-05-21T18:28:36.323" Score="2" ViewCount="62" Body="&lt;p&gt;From the articles I read, expressions like &quot;broad cross-immunoreactivity&quot; pops up a lot. So, I was wondering, why &quot;broad&quot; is used here instead of large? Is there a specific reason?&lt;/p&gt;&#xA;" OwnerUserId="15799" LastEditorUserId="9943" LastEditDate="2015-05-22T10:10:12.023" LastActivityDate="2015-05-23T01:13:32.783" Title="Why &quot;broad&quot; instead of &quot;large&quot; cross-immunoreactivity?" Tags="&lt;immunology&gt;&lt;terminology&gt;&lt;nomenclature&gt;" AnswerCount="2" CommentCount="4" ClosedDate="2015-05-22T07:21:36.797" ContentLicense="CC BY-SA 3.0" />
  <row Id="34432" PostTypeId="2" ParentId="34428" CreationDate="2015-05-21T20:17:51.947" Score="3" Body="&lt;p&gt;In this context, &amp;quot;broad&amp;quot; is a buzzword, a piece of scientific jargon. It's a callback to Broadly Neutralizing Antibodies[1], bNAbs. The basic idea with bNAbs is that they target parts of viral proteins that tend not to mutate or change very much between individual strains of some particular virus.&lt;/p&gt;&#xA;&lt;h1&gt;Edit:&lt;/h1&gt;&#xA;&lt;p&gt;To clarify, I am not suggesting that an antibody with &amp;quot;broad cross-immunoreactivity&amp;quot; is the same thing as a bNAb. Immunoreactivity and neutralization are not the same thing (although there is some overlap).&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;1: Zwick, M. B., Labrijn, A. F., Wang, M., Spenlehauer, C., Saphire, E. O., Binley, J. M., et al. (2001). Broadly Neutralizing Antibodies Targeted to the Membrane-Proximal External Region of Human Immunodeficiency Virus Type 1 Glycoprotein gp41. Journal of Virology, 75(22), 10892–10905. &lt;a href=&quot;http://doi.org/10.1128/JVI.75.22.10892-10905.2001&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://doi.org/10.1128/JVI.75.22.10892-10905.2001&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="784" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-05-23T01:13:32.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34433" PostTypeId="1" AcceptedAnswerId="34434" CreationDate="2015-05-21T20:18:41.753" Score="2" ViewCount="86" Body="&lt;p&gt;I read something like &quot;some tested variants show self-immunoreactivity&quot;. So, what exacly is self-immunoreactivity? Is it something like antibodies induced by a specific variant showing immunoreactivity to this specific variant?&lt;/p&gt;&#xA;" OwnerUserId="15799" LastEditorUserId="9943" LastEditDate="2015-05-21T21:55:36.450" LastActivityDate="2015-05-21T21:58:37.013" Title="What is self-immunoreactivity?" Tags="&lt;immunology&gt;&lt;immunity&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34434" PostTypeId="2" ParentId="34433" CreationDate="2015-05-21T20:42:36.457" Score="5" Body="&lt;p&gt;The basic concept of the immune system is that it has to discriminate between self and foreign and that is only allowed to launch an immune reaction against something foreign. This is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Immune_tolerance&quot; rel=&quot;nofollow&quot;&gt;immune tolerance&lt;/a&gt; which basically makes sure that all immune cells which are directed against the own organism are destroyed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If these antibodies survive, they can attack the own body (and are hence called self immunoreactive) and cause damage. Self-immunoreativity is a reaction of the body against itself. Problems with the immune tolerance are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Autoimmune_disease&quot; rel=&quot;nofollow&quot;&gt;autoimmune diseases&lt;/a&gt;, examples would be  systemic lupus erythematosus, rheumatoid arthritis or type 1 diabetes. &lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="9943" LastEditDate="2015-05-21T21:58:37.013" LastActivityDate="2015-05-21T21:58:37.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34435" PostTypeId="1" AcceptedAnswerId="34436" CreationDate="2015-05-21T21:15:36.103" Score="2" ViewCount="190" Body="&lt;p&gt;I'd like to optimize the expression of a F&lt;sub&gt;ab&lt;/sub&gt; fragment in &lt;em&gt;Escherichia coli&lt;/em&gt;.&#xA;For induction of the &lt;em&gt;lac&lt;/em&gt; promoter on the pAK400 vector I use IPTG and sucrose. Do I optimize the expression in case I would just add IPTG?&lt;/p&gt;&#xA;" OwnerUserId="15865" LastEditorUserId="9099" LastEditDate="2015-05-26T13:38:50.637" LastActivityDate="2015-05-26T13:38:50.637" Title="Do I have to use sucrose to induce a lac promoter?" Tags="&lt;bacteriology&gt;&lt;lab-techniques&gt;&lt;protein-expression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34436" PostTypeId="2" ParentId="34435" CreationDate="2015-05-21T21:28:28.217" Score="3" Body="&lt;p&gt;You can induce the lac operon by two things: Lactose (or more precisely Allolactose a metabolite of it) and lactose analogons which are not metabolized by the bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lactose induces the expression and is metabolized while &lt;a href=&quot;https://en.wikipedia.org/wiki/Isopropyl_%CE%B2-D-1-thiogalactopyranoside&quot; rel=&quot;nofollow&quot;&gt;IPTG&lt;/a&gt; is not a target of the $\beta$-Galactosidase and will give you a strong and permanent induction. Sucrose will not have any effect on the promoter.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-05-21T21:28:28.217" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34437" PostTypeId="2" ParentId="34426" CreationDate="2015-05-21T21:43:13.023" Score="2" Body="&lt;p&gt;≈Yes, it's easy to conceptualize at a simple ganglionic circuit. A really good example is (I believe from Kandel's lab)demonstrated by Aplysia's gill withdrawal reflex. Repeated stimulation causes reduced EPSPs in motor neurons that innervate muscles that cause the withdrawal reflex. However when you apply a electric shock to the tail, the snail will immediately regain withdrawal reflex sensitivity. The tail sensory neuron response activates the serotonergic facilatory interneurons which have multiple IO with sensory and motor neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And don't forget, interneurons can inhibit other interneurons leading to disinhibition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For most LTP work you're probably ok using Hebbian models. Make sure to keep in mind that in more complex systems like cortical circuits.  there are some modes of communication that don't always play well with Hebb's Laws: gliotransmission, retrograde transmission, neuropeptides/GPCRs, and activation of perisynaptic receptors/receptors on adjacent cells.&lt;/p&gt;&#xA;" OwnerUserId="15866" LastActivityDate="2015-05-21T21:43:13.023" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34438" PostTypeId="1" CreationDate="2015-05-21T21:57:47.663" Score="5" ViewCount="2911" Body="&lt;p&gt;What is the mechanism of pollen tube formation when the pollen is close to the stigma ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it because of chemotaxis? In other words, is the growth triggered by some chemical substance that is released by the stigma? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We have learnt that on a stigma of a flower, you can sometimes find pollen of other plant species. Would these pollen grains also form tubes in response to a possible signal from the stigma of a different species? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;EDIT :&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JOcxd.jpg&quot; alt=&quot;the experience&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in this experiment we put pollen grains in 2 bottles which contained all chemical substance required for the formation of pollen tube. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In bottle 2 we observe that all pollen tubes are oriented to the stigma! If it really is some kind of chemotaxis then what is the chemical substance that causes this?&lt;/p&gt;&#xA;" OwnerUserId="15640" LastEditorUserId="3340" LastEditDate="2015-06-24T08:55:06.623" LastActivityDate="2015-06-24T08:55:06.623" Title="What is the trigger of pollen tube formation when the pollen is on the stigma?" Tags="&lt;botany&gt;&lt;reproductive-biology&gt;&lt;flowers&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34439" PostTypeId="1" CreationDate="2015-05-21T22:01:33.957" Score="3" ViewCount="70" Body="&lt;p&gt;Pretend a human had their body &quot;reflected&quot;: heart on the wrong side, etc.; but also at the biochemical level: proteins, sugars, cells, DNA, everything.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What would the effects be of that human's exposure to other Earth life?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume that quick death from malnutrition would be inevitable, but would there be more immediate life-threatening consequences?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would anyone who comes into contact with the mirrored person be at risk?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would reflected bacteria pose an immediate threat to the ecosystem?&lt;/p&gt;&#xA;" OwnerUserId="15867" LastEditorUserId="15867" LastEditDate="2015-05-22T19:38:27.763" LastActivityDate="2015-05-22T19:38:27.763" Title="What effects would be caused by exposure to common life forms with opposite enantiomer biology?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;food&gt;&lt;protein-binding&gt;&lt;protein-folding&gt;" AnswerCount="0" CommentCount="7" ClosedDate="2015-05-23T10:22:00.213" ContentLicense="CC BY-SA 3.0" />
  <row Id="34440" PostTypeId="1" CreationDate="2015-05-22T00:19:24.893" Score="5" ViewCount="2585" Body="&lt;p&gt;For years, I've noticed that the day after a night of poor sleep (4 hours or less), my balance noticeably degrades. For instance, while walking 20 feet to the coffee maker, I might stumble into the fridge. Is this a shared experience among humans, and is there a physiological explanation for it? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have noticed that other functions of my body degrade as well (e.g., my ability to focus), but I am particularly interested in the change in my ability to balance.&lt;/p&gt;&#xA;" OwnerUserId="15870" LastEditorUserId="9943" LastEditDate="2015-09-30T11:21:06.103" LastActivityDate="2020-01-30T14:29:25.763" Title="Can a lack of sleep degrade balance?" Tags="&lt;neuroscience&gt;&lt;sleep&gt;&lt;balance&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34441" PostTypeId="2" ParentId="19781" CreationDate="2015-05-22T00:19:34.830" Score="1" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;SSVEP frequency corresponds to stimulus frequency and SSVEP amplitude decreases with stimulus frequency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The simplest form of steady state visual-evoked potentials (SSVEPs) are those to flash stimuli. &lt;a href=&quot;http://cognitrn.psych.indiana.edu/busey/N611Q700/Week1103/Herrman1-100Hz.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Herrmann (2001)&lt;/a&gt; studied the SSVEP by recording the EEG from the visual cortex at various flash frequencies. He found that SSVEPs occurred at a &lt;strong&gt;frequency corresponding to the flicker stimulus&lt;/strong&gt;. &lt;strong&gt;Amplitudes decreased&lt;/strong&gt; steadily with frequency and SSVEPs could be recorded up to ~90 Hz flicker frequencies. The shape and frequency following of SSVEPs are shown in Fig. 1.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9owgm.png&quot; alt=&quot;SSVEPs&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. SSVEPs and FFT spectra at various frequencies. Source: &lt;a href=&quot;http://cognitrn.psych.indiana.edu/busey/N611Q700/Week1103/Herrman1-100Hz.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Herrmann (2001)&lt;/a&gt;&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, SSVEPs in response to some frequencies showed &lt;strong&gt;resonance phenomena&lt;/strong&gt;, indicating a selective frequency preference of the neural oscillators. Specifically, SSVEPs at around 10, 20, 40 and 80 Hz resulted in &lt;strong&gt;higher amplitudes&lt;/strong&gt; than stimuli flickering at adjacent frequencies (Fig. 2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AVG6o.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 2. SSVEPs showing resonance at 80 Hz. Source: &lt;a href=&quot;https://i.stack.imgur.com/AVG6o.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;Herrmann (2001)&lt;/a&gt;&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://cognitrn.psych.indiana.edu/busey/N611Q700/Week1103/Herrman1-100Hz.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Herrmann, &lt;em&gt;Exp Brain Res&lt;/em&gt; (2001); &lt;strong&gt;137&lt;/strong&gt;: 346–353&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-22T11:36:00.710" LastActivityDate="2015-05-22T11:36:00.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34442" PostTypeId="2" ParentId="34428" CreationDate="2015-05-22T00:40:39.070" Score="6" Body="&lt;p&gt;&lt;strong&gt;Broad&lt;/strong&gt; means &lt;strong&gt;wide&lt;/strong&gt; as in a wide range. Normally, antibodies have one epitope they recognize, i.e., one specific target; they are said to have a &lt;strong&gt;narrow range&lt;/strong&gt; of targets.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some antibodies, however, recognize multiple targets, i.e. the &lt;em&gt;number of targets&lt;/em&gt; they recognize is &lt;em&gt;larger&lt;/em&gt; and their &lt;strong&gt;target range&lt;/strong&gt; is &lt;strong&gt;widened&lt;/strong&gt;. They are said to have a &lt;strong&gt;broad&lt;/strong&gt; cross-immunoreactivity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A '&lt;em&gt;large&lt;/em&gt;' cross-immunoreactivity, however, is ambiguous, as &lt;em&gt;'large'&lt;/em&gt; can also imply &lt;em&gt;'large reactivity'&lt;/em&gt;, and then &lt;em&gt;'large'&lt;/em&gt; becomes synonymous to &lt;em&gt;'strong'&lt;/em&gt;. &lt;strong&gt;Wide&lt;/strong&gt; is unambiguous as it always implies a &lt;strong&gt;large range&lt;/strong&gt;.      &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-22T06:33:24.960" LastActivityDate="2015-05-22T06:33:24.960" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34443" PostTypeId="1" AcceptedAnswerId="34445" CreationDate="2015-05-22T00:41:14.433" Score="6" ViewCount="11608" Body="&lt;p&gt;In biology, why do we have terminologies in terms of female relatoinships such as daughter cells and sister chromatids and not in terms of male relationships. When did this custom started and is there a reason for it ?&lt;/p&gt;&#xA;" OwnerUserId="15871" LastEditorUserId="15871" LastEditDate="2018-06-25T02:10:20.547" LastActivityDate="2018-08-03T10:40:10.327" Title="Why sister chromatids and daughter cells but not brother chromatids and son cells?" Tags="&lt;terminology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="34444" PostTypeId="2" ParentId="34440" CreationDate="2015-05-22T01:02:39.867" Score="10" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Sleep negatively impacts attention, which in turn impairs balance control in cognitively challenging situations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://journals.lww.com/neuroreport/Abstract/1998/01050/Postural_control,_attention_and_sleep_deprivation.10.aspx&quot; rel=&quot;nofollow&quot;&gt;Schlesinger &lt;em&gt;et al.&lt;/em&gt; (1998)&lt;/a&gt; argue that under normal conditions, postural control appears to be automatic, and to require little or no attention in young, healthy adults during quiet standing with full sensory input. However, postural control appears to &lt;strong&gt;require increased attention&lt;/strong&gt; when &lt;strong&gt;sensory integration&lt;/strong&gt; or &lt;strong&gt;motor coordination&lt;/strong&gt; are required. Examples of such challenging conditions where increased attention is required are situations during reduced or conflicting sensory input conditions, or when one is subjected to balance perturbations. The &lt;strong&gt;regulation of attention&lt;/strong&gt;, in turn, is &lt;strong&gt;dependent on sleep&lt;/strong&gt;, because &lt;strong&gt;sleep deprivation&lt;/strong&gt; causes &lt;strong&gt;deficits in attention&lt;/strong&gt;. Hence, although sleep deprivation &lt;em&gt;per se&lt;/em&gt; has little or no effect on standing postural control, it can impair postural balance when one has to perform a cognitive challenging task. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://journals.lww.com/neuroreport/Abstract/1998/01050/Postural_control,_attention_and_sleep_deprivation.10.aspx&quot; rel=&quot;nofollow&quot;&gt;Schlesinger et al., &lt;em&gt;NeuroReport&lt;/em&gt; (1998); &lt;strong&gt;9&lt;/strong&gt;(1): 49-52&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-09-30T11:37:17.220" LastActivityDate="2015-09-30T11:37:17.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34445" PostTypeId="2" ParentId="34443" CreationDate="2015-05-22T01:27:26.240" Score="8" Body="&lt;p&gt;During the days when philosophers used to debate, they tended to regard  reproduction as a feminine trait. So naturally organisms/cells capable of producing offspring are also given a feminine trait. The parent cell is often called the mother cell, and the daughter cells are so named because they eventually become mother cell themselves. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I presume there exists a similar argument for sister chromatids, in that they are identical. When they separate, they are usually termed as undivided chromosomes.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastActivityDate="2015-05-22T01:27:26.240" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34446" PostTypeId="5" CreationDate="2015-05-22T01:50:14.257" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2015-05-22T01:50:14.257" LastActivityDate="2015-05-22T01:50:14.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34447" PostTypeId="4" CreationDate="2015-05-22T01:50:14.257" Score="0" Body="Balance refers to postural control, which is defined as the act of maintaining, achieving or restoring a state of balance during any posture or activity." OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-22T05:44:58.540" LastActivityDate="2015-05-22T05:44:58.540" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34448" PostTypeId="2" ParentId="34377" CreationDate="2015-05-22T03:00:13.880" Score="0" Body="&lt;p&gt;It looks like I could solve the question. My understanding is as follows.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let $(X_1,Y_1)$, $(X_2,Y_2)$ (corresponds to $i,j$ and $k,l$ in the question) be the genotypes of two individuals &#xA; at some location. We assume that neither individual&#xA; is in-bred. In this case define,&#xA; \begin{align*}&#xA;  \Delta_7&amp;amp;= \text{Pr}(\text{Both alleles $\{X_1,Y_1\}$ and $\{X_2, Y_2\}$ are IBD}),\\&#xA;  \Delta_8&amp;amp;= \text{Pr}(\text{Exactly one allele pair of the four pairs is  IBD}),\\&#xA;  \Delta_9&amp;amp;= \text{Pr}(\text{ No IBD between the two individuals}).&#xA; \end{align*}&#xA; $\Delta_7$, $\Delta_8$ and $\Delta_9$ are calculated from the pedigrees. &#xA; For example, for non-twin siblings, $\Delta_7 = \frac{1}{4}$, $\Delta_8=\frac{1}{2}$,&#xA; $\Delta_9 =\frac{1}{4}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We note that the IBD coefficient (also called kinship coefficient) $\Theta$ is &#xA; \begin{align*}&#xA;  \Theta = \frac{1}{2} \Delta_7 + \frac{1}{4} \Delta_8.&#xA; \end{align*}&#xA; Also the fraternity coefficient, $\Delta =\Delta_7$.&#xA;Thus we have that the covariance between the genotypic &#xA; value of two individuals is given by&#xA; \begin{align*}&#xA;  \mathbb{E}[G(X_1,Y_1)G(X_2,Y_2)] =&amp;amp; \Delta_7 \mathbb{E}[G(X_1,Y_1)G(X_2,Y_2)| \text{both IBD}] + \\&#xA;  &amp;amp;\Delta_8 \mathbb{E}[G(X_1,Y_1)G(X_2,Y_2)| \text{one IBD}] + \Delta_9  \mathbb{E}[G(X_1,Y_1)G(X_2,Y_2)| \text{no IBD}].&#xA; \end{align*}&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further note that,&#xA; \begin{align*}&#xA;  \mathbb{E}[G(X_1,Y_1)G(X_2,Y_2)| \text{both IBD}] &amp;amp;= \mathbb{E}[G^2(X_1,Y_1)],\\&#xA;  &amp;amp;= \sigma_A^2 +\sigma_D^2.&#xA; \end{align*}&lt;/p&gt;&#xA;&#xA;&lt;p&gt;\begin{align*}&#xA;  \mathbb{E}[G(X_1,Y_1)G(X_2,Y_2)| \text{no IBD}] &amp;amp;= \mathbb{E}[G(X_1,Y_1)] \mathbb{E}[G(X_2,Y_2)],\\&#xA;  &amp;amp;=0.&#xA; \end{align*}&lt;/p&gt;&#xA;&#xA;&lt;p&gt;\begin{align*}&#xA;  \mathbb{E}[G(X_1,Y_1)G(X_2,Y_2)| \text{one IBD}] &amp;amp;= \mathbb{E}[(\alpha(X)+\alpha(Y_1)+\delta(X,Y_1))(\alpha(X)+\alpha(Y_2)+\delta(X,Y_2))],\\&#xA;  &amp;amp;=\mathbb{E}[\alpha^2(X)] + 2 \mathbb{E}(\alpha(X) \delta(X,Y_1)) + \mathbb{E} [\delta(X,Y_1)\delta(X,Y_2)],\\&#xA;  &amp;amp;= \frac{1}{2} \sigma_A^2 + 2 \mathbb{E} [ \alpha(X) \mathbb{E}[\delta(X,Y_1) | X] ] +  \mathbb{E} [\mathbb{E}[\delta(X,Y_1)|X]\mathbb{E}[\delta(X,Y_2)|X]],\\&#xA;  &amp;amp;= \frac{1}{2} \sigma_A^2.&#xA; \end{align*}&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus we have that,&#xA; \begin{align*}&#xA;  \mathbb{E}[G(X_1,Y_1)G(X_2,Y_2)] =&amp;amp; \left(\frac{1}{2}\Delta_7 + \frac{1}{4}\Delta_8\right) 2 \sigma_A^2 + \Delta_7 \sigma_D^2,\\&#xA;  &amp;amp;= 2\Theta \sigma_A^2 + \Delta \sigma_D^2,&#xA; \end{align*}&#xA; which is as claimed.&lt;/p&gt;&#xA;" OwnerUserId="6353" LastActivityDate="2015-05-22T03:00:13.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34450" PostTypeId="1" AcceptedAnswerId="34452" CreationDate="2015-05-22T04:48:40.823" Score="6" ViewCount="101" Body="&lt;p&gt;After the fertilization when the zygote  is in the growing state to a foetus, the main canal is introduced first, from mouth to anus. But my question is when the canal is created first how does it determine which side is for mouth and which side is for anus? &lt;/p&gt;&#xA;" OwnerUserId="15874" LastEditorUserId="3340" LastEditDate="2015-05-22T04:54:28.780" LastActivityDate="2015-05-22T06:17:38.890" Title="How is it determined in a zygote state of foetus, that which side is mouth and which side is for anus?" Tags="&lt;development&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34452" PostTypeId="2" ParentId="34450" CreationDate="2015-05-22T06:17:38.890" Score="3" Body="&lt;p&gt;The gut tube is formed from endoderm that migrates through the primitive streak. Before this, however, the anterior-posterior axis of the embryo is defined by the formation of the streak at the beginning of gastrulation. In mice, which are phylotypic with humans at this stage, the streak forms posteriorly and then extends to the anterior. I'm not sure if you'll be able to find much research on humans, but mice and chicks are quite well studied. That said, I don't know the molecular and cellular mechanisms which define where the primitive streak forms. I don't even know if it is known. How much detail are you looking for? If I find the time, I can try and elaborate on this further. In the mean time, this review looks promising:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://m.dev.biologists.org/content/136/5/701.long&quot; rel=&quot;nofollow&quot;&gt;http://m.dev.biologists.org/content/136/5/701.long&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-05-22T06:17:38.890" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34453" PostTypeId="1" CreationDate="2015-05-22T07:05:29.457" Score="4" ViewCount="101" Body="&lt;p&gt;I was reading a paper by &lt;a href=&quot;http://www.math.umn.edu/~othmer/papers/Tang:1995:EOW.pdf&quot; rel=&quot;nofollow&quot;&gt;Tang &amp;amp; Othmer&lt;/a&gt; about oscillations and waves in &lt;em&gt;Dictyostelium discoideum&lt;/em&gt;. Under certain condition like starvation period in the life cycle of a &lt;em&gt;Dictyostelium discoideum&lt;/em&gt; community, they evolve itself into a multicellular organism in a process of cellular aggregation. I have read about &lt;em&gt;Pacemaker&lt;/em&gt; cells among these individuals which transmits periodic &lt;em&gt;cAMP&lt;/em&gt; and attracts other cells towards them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So I was wondering: When and How do these Pacemaker cells develop from a &quot;normal&quot; cell into a pacemaker cell excreting cAMP?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References, links or answers would be very helpful for me.&lt;/p&gt;&#xA;" OwnerUserId="5669" LastEditorUserId="5669" LastEditDate="2015-05-25T10:44:45.367" LastActivityDate="2015-05-25T10:48:31.157" Title="When and How do pacemaker cells develop during the cell aggregation process of Dictyostelium discoideum?" Tags="&lt;microbiology&gt;&lt;cell-signaling&gt;&lt;communication&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34454" PostTypeId="2" ParentId="31533" CreationDate="2015-05-22T07:33:22.853" Score="1" Body="&lt;p&gt;&lt;em&gt;You should really study the basics before asking specifics about a particular protein. I am not voting to close the question, however.&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA catalyses the formation mRNA (transcription) which in turn catalyses the formation of a polypeptide (translation); RNA polymerase and ribosome are co-catalysts respectively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A functional protein may have many polypeptide chains as in the case of Sodium channel (or even haemoglobin). The function of the protein complex may be compromised if:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The polypeptides chains are not formed&lt;/li&gt;&#xA;&lt;li&gt;The polypeptide chains are not associating properly&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The former can result either because of a block in translation or a block in the transcription. These blocks can also arise because of active regulation in response to a certain condition; this is a temporary change. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutations can lead to loss of function by either causing transcription/translation blocks or abolishing interaction between different polypeptides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a cell all biomolecules are continuously formed and degraded. The rate at which they are degraded is called the turnover. If a steady level has to be maintained then turnover rate should be balanced by the formation rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When formation is abolished then different biomolecules will disappear at a speed proportional to their degradation rates.&lt;br&gt;&#xA;If the mutation causes a loss of association of polypeptides then non-functional proteins will replace the functional ones with rate proportional to the degradation rate. (NOTE: Formation rate of a protein is proportional to the available mRNA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most intracellular and membrane proteins have high turnover. Extracellular structural proteins such as collagen have a relatively low turnover. So if sodium channel gene stops transcribing the effects would be felt very soon. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-05-22T08:19:04.357" LastActivityDate="2015-05-22T08:19:04.357" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34455" PostTypeId="2" ParentId="15814" CreationDate="2015-05-22T08:05:59.573" Score="4" Body="&lt;p&gt;No, a thrombus would be much too large to pass through the highly selective blood brain barrier.  However, there are some cases where intra-vascular thrombosis can cause stroke.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One example would be non anti-coagulated atrial fibrillation, where the inefficient beating of the heart causes blood to remain stagnant in the left atrium.  This can cause a thrombus to form within the atrium which can then throw off emboli, some of which may enter the cerebral circulation. These may then partially or fully occlude one of the arteries in the Circle of Willis (the brain's circulation system), however the blockage is &lt;strong&gt;proximal&lt;/strong&gt; to the blood brain barrier.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0140673607613002&quot; rel=&quot;nofollow&quot;&gt;Management of atrial fibrillation&lt;/a&gt; (GY Lip,2007) or for those hitting a pay-wall the &lt;a href=&quot;http://www.patient.co.uk/doctor/atrial-fibrillation-pro&quot; rel=&quot;nofollow&quot;&gt;professional reference section on AF&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2015-05-24T16:05:53.207" LastActivityDate="2015-05-24T16:05:53.207" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34456" PostTypeId="2" ParentId="30968" CreationDate="2015-05-22T08:43:41.170" Score="2" Body="&lt;p&gt;Assuming each gene symbol represents a unique gene or protein (this may not be true; see for gene name aliases in e.g. NCBI Entrez gene) you can get a lot of information programmatically. Below is an example using &lt;a href=&quot;http://www.r-project.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;R&lt;/a&gt; and &lt;a href=&quot;http://www.bioconductor.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bioconductor&lt;/a&gt; resources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Define your list of genes:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;# list of gene symbols, here we focus on one.&#xA;&amp;gt; genes &amp;lt;- &quot;KRAS&quot;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Load the annotation package &lt;a href=&quot;http://www.bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;org.Hs.eg.db&lt;/a&gt; and retrieve basic information including Gene Ontology ids:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;# annotation package for human genes.&#xA;&amp;gt; library(org.Hs.eg.db)&#xA;&#xA;# query Entrez gene id, description (GENENAME) and Gene Ontology id (GO)&#xA;&amp;gt; info &amp;lt;- select(org.Hs.eg.db, keys = genes, keytype = &quot;SYMBOL&quot;, columns = c(&quot;ENTREZID&quot;, &quot;GENENAME&quot;, &quot;GO&quot;))&#xA;&amp;gt; head(info)&#xA;  SYMBOL ENTREZID                                   GENENAME         GO EVIDENCE&#xA;1   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0000165      TAS&#xA;2   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0000186      TAS&#xA;3   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0001934      IMP&#xA;4   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0005515      IPI&#xA;5   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0005525      IEA&#xA;6   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0005737      IDA&#xA;  ONTOLOGY&#xA;1       BP&#xA;2       BP&#xA;3       BP&#xA;4       MF&#xA;5       MF&#xA;6       CC&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Load the &lt;a href=&quot;http://www.bioconductor.org/packages/release/data/annotation/html/GO.db.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;GO.db&lt;/a&gt; package and retrieve the term associated with the GO ids (this gives info about putative function):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt; library(GO.db)&#xA;&amp;gt; info$Term &amp;lt;- Term(GOTERM[info$GO])&#xA;&amp;gt; head(info)&#xA;  SYMBOL ENTREZID                                   GENENAME         GO EVIDENCE&#xA;1   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0000165      TAS&#xA;2   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0000186      TAS&#xA;3   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0001934      IMP&#xA;4   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0005515      IPI&#xA;5   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0005525      IEA&#xA;6   KRAS     3845 Kirsten rat sarcoma viral oncogene homolog GO:0005737      IDA&#xA;  ONTOLOGY                                           Term&#xA;1       BP                                   MAPK cascade&#xA;2       BP                   activation of MAPKK activity&#xA;3       BP positive regulation of protein phosphorylation&#xA;4       MF                                protein binding&#xA;5       MF                                    GTP binding&#xA;6       CC&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Load the &lt;a href=&quot;http://www.bioconductor.org/packages/release/bioc/html/RefNet.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;RefNet&lt;/a&gt; package and get information about interacting proteins:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt; library(RefNet)&#xA;&amp;gt; refnet &amp;lt;- RefNet() # this step downloads from AnnotationHub and may take some time.&#xA;&amp;gt; int &amp;lt;- interactions(refnet, species = &quot;9606&quot;, id = genes, provider = &quot;BioGrid&quot;)&#xA;# create data.frame with Entrez id of proteins.&#xA;&amp;gt; d &amp;lt;- int[,1:2]&#xA;&amp;gt; d$A &amp;lt;- sub(&quot;.*locuslink:(.*)\\|.*&quot;, &quot;\\1&quot;, d$A)&#xA;&amp;gt; d$B &amp;lt;- sub(&quot;.*locuslink:(.*)\\|.*&quot;, &quot;\\1&quot;, d$B)&#xA;&amp;gt; head(d)&#xA;      A    B&#xA;1  3065 3845&#xA;2  8841 3845&#xA;3 23411 3845&#xA;4  1994 3845&#xA;5  3845 9770&#xA;6  9770 3845&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Use the &lt;a href=&quot;http://igraph.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;igraph&lt;/a&gt; package to visualize the interacting proteins.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt; library(igraph)&#xA;&amp;gt; g &amp;lt;- igraph::simplify(graph.data.frame(d, directed = FALSE))&#xA;&#xA;# annotate the nodes with the symbol.&#xA;&amp;gt; V(g)$label &amp;lt;- select(org.Hs.eg.db, keys = V(g)$name, columns = c(&quot;SYMBOL&quot;), )$SYMBOL&#xA;&amp;gt; plot(g)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QBHc9.png&quot; alt=&quot;Interaction network of human KRAS&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then you could repeat the cycle with the interacting partners. There are many other things you can do, starting from a list of symbols; this is just a brief example. More detailed examples and workflows can be found &lt;a href=&quot;http://www.bioconductor.org/help/workflows/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastEditorUserId="9099" LastEditDate="2015-05-25T05:49:34.800" LastActivityDate="2015-05-25T05:49:34.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34458" PostTypeId="2" ParentId="8163" CreationDate="2015-05-22T11:29:10.000" Score="6" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Image blur on the retina is the most important monocular cue for lens accommodation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Focussing of an image on the retina is mediated by the lens. Re-shaping of the lens to focus the image on the retina is called &lt;strong&gt;accommodation&lt;/strong&gt;. In general , the main cues for focussing are retinal disparity and blur, and to a lesser extent proximal cues such as looming, motion parallax and overlay of contours.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When looking with two eyes (binocularly) at an object, &lt;strong&gt;retinal disparity&lt;/strong&gt; is by far the most important depth cue for accommodation. The two eyes look at an object from slightly different angles, so they get slightly different views of it. This difference is the disparity (imperfect match) between the two views. The visual system normally fuses these two images into a single perception and converts the disparity between the two images into perception of depth (Source: &lt;a href=&quot;http://www.indiana.edu/~p1013447/dictionary/binocdis.htm&quot;&gt;Indiana university&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When only one eye is available (monocular focussing), use of retinal disparity isn't possible, and &lt;strong&gt;retinal blur&lt;/strong&gt; becomes the most important factor for lens accommodation. When an image is out of focus, its representation on the retina is blurry. By adjusting the shape of the lens the visual system adjusts the image projection to bring it into focus such that blur is minimized (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0042698908002307&quot;&gt;Horwood &amp;amp; Riddell, 2008&lt;/a&gt;). &lt;strong&gt;Looming&lt;/strong&gt; (incoming object becomes apparently bigger), &lt;strong&gt;motion parallax&lt;/strong&gt; (objects further away move slower across the field of view) and &lt;strong&gt;overlay of contours&lt;/strong&gt; (objects closer by obscure things further away) also provide monocular cues for accommodation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0042698908002307&quot;&gt;Horwood &amp;amp; Riddell, &lt;em&gt;Vis Res&lt;/em&gt; (2008); &lt;strong&gt;48&lt;/strong&gt;:1613–24&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-05-22T11:29:10.000" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34460" PostTypeId="2" ParentId="15814" CreationDate="2015-05-22T14:14:19.027" Score="3" Body="&lt;p&gt;No, thrombi are far too bulky to cross the blood brain barrier. Now regarding the risk of stroke in case of systemic thrombi Yes, there are 2 situations where this can arise:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;floating thrombus of the great circulation proximal to the aortic arch (i.e. Most of the time, chronic atrial fibrillation)&lt;/li&gt;&#xA;&lt;li&gt;venous thrombus with an associated patent foramen ovale, allowing the thrombi to pass through the atrial septum and get to the great circulation.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="8804" LastEditorUserId="8804" LastEditDate="2015-06-09T11:27:06.717" LastActivityDate="2015-06-09T11:27:06.717" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34461" PostTypeId="2" ParentId="34438" CreationDate="2015-05-22T15:47:57.657" Score="6" Body="&lt;p&gt;Germination of the pollen tube begins when the pollen grain becomes hydrated on the tip of the stigma. The pollen grain absorbs water and also exchanges signals with the stigma. Microchannels form between the pollen grain and the tip of the stigma papillae and water is transferred from the stigma to the pollen grain (&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.arplant.48.1.461&quot;&gt;Taylor 1997&lt;/a&gt;). cAMP, which is produced by the protein PSiP, and cytosolic free calcium can be used as signals to orient the pollen tube to grow in the proper direction (&lt;a href=&quot;http://www.pnas.org/content/98/18/10481.short&quot;&gt;Moutinho et al 2001&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pollen tubes can also germinate in vitro even without contacting a stigma. If you place a pollen grain in germination medium, which contains calcium and boron, among other things, the tube will germinate but it will not grow to its full length.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Often when pollen of a different species lands on the stigma, the pollen will germinate but the pollen tube growth will stop before it reaches the ovary (&lt;a href=&quot;http://www.jstor.org/stable/2440745?seq=1#page_scan_tab_contents&quot;&gt;Ascher and Peloquin 1968&lt;/a&gt;). Mating barriers are very complicated, however, and there are many different mechanisms for species recognition and arrest of pollen tube growth. In some cases, the tube is halted in the style while in other cases the tube grows, but slowly and inefficiently (&lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.genet.38.072902.092356&quot;&gt;Swanson et al. 2004&lt;/a&gt;). Species recognition in some species (for example, tobacco) is related to self-incompatibility and the S-locus. Species recognition can also be unilateral: that is, the pollen of species A can fertilize the ovule of species B, but the pollen of species B cannot fertilize the ovule of species A.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would recommend that Swanson paper if you want to read more.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-05-22T15:47:57.657" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34462" PostTypeId="1" CreationDate="2015-05-22T15:54:33.330" Score="6" ViewCount="81" Body="&lt;p&gt;Sedimentation values of thyroglobulin and ferritin containing iron are 19S &#xA;&lt;sup&gt;[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2138561/pdf/1129.pdf&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]&lt;/sup&gt; and 51S &lt;sup&gt;[&lt;a href=&quot;http://jcb.rupress.org/content/48/1/15.full.pdf&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]&lt;/sup&gt;, respectively. But, by density gradient centrifuge, it seems thyroglobulin (19S) migrates faster than ferritin (51S). Could anyone explain this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 3 in &lt;a href=&quot;http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1000859&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article shows a migration pattern of GE High molecular weight marker containing ferritin and thyroglobulin. Thyroglobulin comes almost at the bottom but ferritin, in the middle, which I did not expect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS&#xA;I asked GE and confirmed ferritin in the marker contains Fe ions. &lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-05-31T06:43:10.863" LastActivityDate="2015-06-07T05:53:30.000" Title="THYROGLOBULIN (19S) comes to a heavier position than ferritin (51S). Why?" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34464" PostTypeId="1" AcceptedAnswerId="34465" CreationDate="2015-05-22T18:11:29.717" Score="7" ViewCount="1222" Body="&lt;p&gt;I remember reading about a concept—in evolutionary biology or natural selection, I think—whereby a particular trait is advantageous to the population or species but only so long as that trait is only exhibited by a minority of the population. That is, the population is more likely to survive if the trait's existence and expression is maintained, but only if that expression is limited to a small percentage of the population. If the trait becomes too common, the selection advantage of having it will decrease, and the fact that most of the population has it may even negatively impact the survivability of that population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't recall where I encountered it. It may have been in the context of reading about ADD, Aspberger's/Autism, neurotypicality, introversion, or mania/OCD. I want to revisit the topic and learn some more about it, but Google is failing me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone tell me the name of or term for the concept I'm thinking of?&lt;/p&gt;&#xA;" OwnerUserId="15880" LastActivityDate="2015-05-22T18:15:32.670" Title="Term for trait that is advantageous to a population only as long as it is rare" Tags="&lt;evolution&gt;&lt;population-genetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34465" PostTypeId="2" ParentId="34464" CreationDate="2015-05-22T18:15:32.670" Score="14" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Frequency-dependent_selection&quot;&gt;Frequency-dependent selection&lt;/a&gt; is the term you are looking for, I believe. Positive frequency-dependent selection encompasses traits that become more advantageous as they become more common. Negative frequency-dependent selection encompasses traits that become more advantageous as they become rarer. &lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-05-22T18:15:32.670" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34466" PostTypeId="1" AcceptedAnswerId="34471" CreationDate="2015-05-22T20:19:04.250" Score="12" ViewCount="1358" Body="&lt;p&gt;Consider a biological structure which no longer benefits an organism, such as the eyes of an organism whose population now lives in total darkness.  I can think of three reasons why such a structure might disappear:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;0) Random changes to the structure over time wouldn't be corrected by selection favoring the functional version of the structure, leading to a wider variation where most versions of the structure no longer effectively function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) The resources the structure demands could be better spent on structures which are actually being used; e.g. human eyes require a lot of blood that could be used elsewhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) Perhaps the existence of a very complex structure leads to biological problems which would no longer be an issue if the structure were not present; e.g. human breasts plus breast hormones frequently leads to cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these three examples reasonable means by which a feature would disappear?  Are there any other possible reasons?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a general name for the phenomenon of evolutionary removal of vestigial features due to those features no longer being useful to a population?&lt;/p&gt;&#xA;" OwnerUserId="15867" LastEditorUserId="14629" LastEditDate="2015-05-22T20:37:37.423" LastActivityDate="2017-11-30T21:19:52.873" Title="Is there a name for the evolutionary loss of vestigial structures?" Tags="&lt;evolution&gt;&lt;terminology&gt;&lt;vestigial&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34467" PostTypeId="2" ParentId="34211" CreationDate="2015-05-22T20:39:37.013" Score="2" Body="&lt;p&gt;I think &lt;strong&gt;recessive refuge&lt;/strong&gt; is the term you are looking for (this is the best link I could find, sorry: &lt;a href=&quot;https://quizlet.com/4176029/bio-experiment-1-and-2-flash-cards/&quot; rel=&quot;nofollow&quot;&gt;https://quizlet.com/4176029/bio-experiment-1-and-2-flash-cards/&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-05-22T20:39:37.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34468" PostTypeId="2" ParentId="34466" CreationDate="2015-05-22T21:02:26.720" Score="2" Body="&lt;p&gt;So-called &quot;vestigial&quot; features are defined in a post-hoc fashion as features which do not have a positive correlation with a population's fitness under its current living conditions. There are no special names for the evolutionary processes that lead to their loss, since they are exactly the same evolutionary processes that act upon any feature that has a neutral/negative effect on fitness.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2015-05-22T21:19:20.173" LastActivityDate="2015-05-22T21:19:20.173" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34469" PostTypeId="1" AcceptedAnswerId="34478" CreationDate="2015-05-22T20:51:11.873" Score="4" ViewCount="173" Body="&lt;p&gt;Are psychoactive drugs with lower lethal doses more neurotoxic (more damaging to the brain)? For example, tetrahydrocannabinol (one of the active components of cannabis) has a much higher lethal dose than benzoylmethylecgonine (cocaine), so could we deduce that cocaine is more damaging to the brain?&#xA;Moreover, is a mathematical relationship between neurotoxicity and lethal doses known?&lt;/p&gt;&#xA;" OwnerUserId="15882" OwnerDisplayName="St Vincent" LastEditorUserId="948" LastEditDate="2015-05-23T18:26:15.900" LastActivityDate="2016-01-22T23:43:48.247" Title="Relationship between toxicity of drugs and negative effects on brain" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34471" PostTypeId="2" ParentId="34466" CreationDate="2015-05-22T23:25:42.333" Score="14" Body="&lt;p&gt;This phenomenon can be (and has been) described as regressive evolution (the loss of a phenotypic trait). There are several reasons why this occurs:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Neutral_mutation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Neutral mutations&lt;/a&gt; which become fixed through &lt;a href=&quot;https://en.wikipedia.org/wiki/Genetic_drift&quot; rel=&quot;nofollow noreferrer&quot;&gt;genetic drift&lt;/a&gt;. &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Directional_selection&quot; rel=&quot;nofollow noreferrer&quot;&gt;Positive selection&lt;/a&gt; of regressive mutations that are beneficial. &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Antagonistic_pleiotropy_hypothesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pleiotropic antagonism&lt;/a&gt;: positive selection for one trait may have the consequence of disrupting another trait which isn't strongly selected for. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The eye degeneration example you chose is a good one because it is well studied in cavefish (which evolved from sighted surface fish and have degenerate eyes). Normal eye development is under the control of the &lt;a href=&quot;https://en.wikipedia.org/wiki/PAX6&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pax6&lt;/a&gt; transcription factor. Expression of another transcription factor, &lt;a href=&quot;https://en.wikipedia.org/wiki/Sonic_hedgehog&quot; rel=&quot;nofollow noreferrer&quot;&gt;Shh&lt;/a&gt;, reduces Pax6 expression. Shh expression along the embryonic midline is responsible for splitting the eye field bilaterally. &lt;a href=&quot;http://www.nature.com/nature/journal/v431/n7010/abs/nature02864.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Overexpression of Shh in surface fish leads to eye degeneration and, indeed, it was found that cavefish have an expanded Shh expression pattern.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cavefish have also undergone a behavioural shift to bottom feeding and have become less aggressive to focus more on finding food. As it happens, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/m/pubmed/19285488/&quot; rel=&quot;nofollow noreferrer&quot;&gt;the expanded Shh expression also causes a widening of the jaw and amplification of taste buds, both of which aid in scooping and sampling the river bottom.&lt;/a&gt; Furthermore, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0960982212012651&quot; rel=&quot;nofollow noreferrer&quot;&gt;increased Shh expression during brain development influences a decrease in aggressiveness and a shift to foraging behaviour&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is an example of pleiotropic antagonism: positive selection for jaw enhancements and behavioural changes via expanded Shh expression, which increase fitness in cave environments, can explain why the eye degenerated.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2017-11-30T21:19:52.873" LastActivityDate="2017-11-30T21:19:52.873" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34473" PostTypeId="1" AcceptedAnswerId="34475" CreationDate="2015-05-23T05:05:41.713" Score="2" ViewCount="49" Body="&lt;p&gt;Considering the Path-A based metabolic pathway prediction (&lt;a href=&quot;http://nar.oxfordjournals.org/content/34/suppl_2/W714.short&quot; rel=&quot;nofollow&quot;&gt;http://nar.oxfordjournals.org/content/34/suppl_2/W714.short&lt;/a&gt;). It uses machine learning for pathway prediction. Suppose that the input was a protein sequence of a query organism. I do not understand what these protein sequences are? Are these the enzymes for the reactions?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The basic algorithm has two inputs: a set of protein sequences from the query organism and a set of model pathways, one for each target pathway.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="9943" LastEditDate="2015-05-23T13:13:42.450" LastActivityDate="2015-05-23T13:13:42.450" Title="What is the protein sequence taken as input in the Path-A prediction system" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34475" PostTypeId="2" ParentId="34473" CreationDate="2015-05-23T09:02:38.080" Score="2" Body="&lt;p&gt;Not necessarily, they can be enzymes, but they include a lot more (the whole proteome).&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;It takes a FASTA format file containing a set of query protein sequences from a single organism (&lt;strong&gt;a partial or complete proteome&lt;/strong&gt;) and identifies those sequences that are likely to participate in any of its supported metabolic pathways&lt;/p&gt;&#xA;&lt;p&gt;Path-A predicts the pathways supported by arbitrary sets of proteins, using validated prediction techniques based on sequence alignment and machine learning.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-05-23T09:02:38.080" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34476" PostTypeId="1" CreationDate="2015-05-23T11:20:20.573" Score="4" ViewCount="147" Body="&lt;p&gt;Searching for an up-to-date book on regenerative brain medicine with a focus on stem cell therapy. &#xA;Also interesting in genetic engineering of neuronal stem cells for this purpose. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, a comprehensive review article is welcomed too. &lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="10104" LastEditDate="2015-06-05T20:03:04.867" LastActivityDate="2015-06-08T20:10:10.800" Title="Brain regeneration - book recommendation" Tags="&lt;brain&gt;&lt;book-recommendation&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34477" PostTypeId="2" ParentId="15447" CreationDate="2015-05-23T11:39:44.730" Score="1" Body="&lt;p&gt;I am not an ENT doctor, but I think the following diagnoses would suffice to determine each of the conditions:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Blocked Eustachian tube&lt;/strong&gt;: Complaints would be of sudden onset and likely associated with a common cold, or ear infection. Providing the patient with standard decongestant should provide quick relief.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Ruptured eardrum&lt;/strong&gt;: Patient should have subtle hearing loss apparent on audiogram and it would be relatively easily identified by routine otoscopic examination.  &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Perilymph fistula&lt;/strong&gt;: This condition is hard to diagnose and I quote from &lt;a href=&quot;http://vestibular.org/perilymph-fistula&quot; rel=&quot;nofollow&quot;&gt;Vestibular Disorders Association&lt;/a&gt;: &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A physician can arrive at a presumptive diagnosis [of a perilymph fistula] through a thorough probing for events close in time to the onset of symptoms, along with a variety of tests. These tests can include hearing tests (audiogram, ECOG), balance tests (VNG, VEMP) and some form of a “fistula test.”  &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The periplymph fistula is by far the most severe condition and the one with the most prominent effects on the vestibular system (balance). Multiple tests and rigorous medical exam is necessary.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regard to your presented case study: Again, I am not an ENT doctor but a ruptured ear drum can result in dizziness due to the fact that one inner ear is exposed to cold air due to a rupture and the other ear is not. Unilateral inner ear cooling can result in dizziness. However, blowing your nose is unlikely to cause a ruptured eardrum as it is generally caused by more serious barotrauma (diving accidents and in-air plane cabin pressure malfunctions) (&lt;a href=&quot;http://www.webmd.com/pain-management/ruptured-eardrum-symptoms-and-treatments?page=2&quot; rel=&quot;nofollow&quot;&gt;Web MD&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, the fistula is most often caused by more serious traumatic injuries (&lt;a href=&quot;http://vestibular.org/perilymph-fistula&quot; rel=&quot;nofollow&quot;&gt;Vestibular Disorders Association&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A blocked Eustachian tube sounds the most plausible, as it is associated with the common cold (&lt;a href=&quot;http://www.webmd.com/pain-management/ruptured-eardrum-symptoms-and-treatments?page=2&quot; rel=&quot;nofollow&quot;&gt;Web MD&lt;/a&gt;). Violently blowing your nose can cause fluid to travel up the middle ear, and possibly cause subsequent infections.  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-23T13:22:24.327" LastActivityDate="2015-05-23T13:22:24.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34478" PostTypeId="2" ParentId="34469" CreationDate="2015-05-23T12:55:34.570" Score="8" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;The causes of death after heroin, cocain or cannabis overdose are mainly due to &lt;em&gt;cardiac and respiratory arrest&lt;/em&gt;, and &lt;em&gt;not&lt;/em&gt; to neurotoxic effects. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The cause of death after a lethal overdose of your mentioned drugs are the following :&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Cocaine (lethal dose: 30 mg - 5 g via mucus membrane (&lt;a href=&quot;http://www.emcdda.europa.eu/publications/drug-profiles/cocaine&quot; rel=&quot;nofollow&quot;&gt;EMCDDA&lt;/a&gt;)): Cocaine-related deaths are often a result of &lt;strong&gt;cardiac arrest&lt;/strong&gt; followed by an &lt;strong&gt;arrest of breathing&lt;/strong&gt; (&lt;a href=&quot;http://www.drugabuse.gov/publications/drugfacts/cocaine&quot; rel=&quot;nofollow&quot;&gt;NIH&lt;/a&gt;). Cardiac effects are mediated via &lt;strong&gt;increased sympathetic output and a local anesthetic effect&lt;/strong&gt; &lt;a href=&quot;http://circ.ahajournals.org/content/122/24/2558.full&quot; rel=&quot;nofollow&quot;&gt;(Schwartz et al., 2010)&lt;/a&gt;; &lt;/li&gt;&#xA;&lt;li&gt;THC: (lethal dose: ~1000mg/kg i.v. in primates (&lt;a href=&quot;http://druglibrary.org/schaffer/library/studies/nc/nc1e.htm&quot; rel=&quot;nofollow&quot;&gt;Drug library&lt;/a&gt;)): No known cases of human fatalities. Toxicity appears as &lt;strong&gt;achypnea&lt;/strong&gt; (rapid breathing), &lt;strong&gt;tachycardia&lt;/strong&gt; (fast heart rate), &lt;strong&gt;ataxia&lt;/strong&gt;, &lt;strong&gt;hyperexcitability&lt;/strong&gt;, and &lt;strong&gt;seizures&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23796481&quot; rel=&quot;nofollow&quot;&gt;(Fitzgerald et al., 2013)&lt;/a&gt;, but death seems mostly associated with respiratory arrest and cardiac failure (&lt;a href=&quot;http://druglibrary.org/schaffer/library/studies/nc/nc1e.htm&quot; rel=&quot;nofollow&quot;&gt;Drug library&lt;/a&gt;); &lt;/li&gt;&#xA;&lt;li&gt;Heroin: (lethal dose 200 - 2000 mg i.v.(&lt;a href=&quot;http://www.emcdda.europa.eu/publications/drug-profiles/cocaine&quot; rel=&quot;nofollow&quot;&gt;EMCDDA&lt;/a&gt;)): overdose often due to &lt;strong&gt;respiratory arrest&lt;/strong&gt; &lt;a href=&quot;http://circ.ahajournals.org/content/122/24/2558.full&quot; rel=&quot;nofollow&quot;&gt;(Anoro et al. 2004)&lt;/a&gt; caused by mu-opiate receptor activation in the brainstem &lt;a href=&quot;https://www.crcpress.com/product/isbn/9780849316906&quot; rel=&quot;nofollow&quot;&gt;(Karch, 2006)&lt;/a&gt;. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Hence, &lt;strong&gt;heroin, THC and cocain&lt;/strong&gt; are lethal mainly due to &lt;strong&gt;peripheral causes&lt;/strong&gt; (i.e., cardiac and respiratory arrest). Although these effects are mediated, at least partly, through &lt;strong&gt;central mechanisms&lt;/strong&gt; (i.e., occurring in the central nervous system and specifically the brain), the drugs themselves do &lt;em&gt;not&lt;/em&gt; cause death because of neurotoxicity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And a closing comment, with credits to @MarchHo - In general, neurotoxins do not cause death due to neural toxicity &lt;em&gt;per se&lt;/em&gt;. Most notably even botulotoxin, being one of the most potent neurotoxins known, causes death due to respiratory failure (&lt;a href=&quot;http://www.cdc.gov/nczved/divisions/dfbmd/diseases/botulism/&quot; rel=&quot;nofollow&quot;&gt;CDC&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://circ.ahajournals.org/content/122/24/2558.full&quot; rel=&quot;nofollow&quot;&gt;Anorro et al., &lt;em&gt;Rev Esp Salud Publica&lt;/em&gt; (2004); &lt;strong&gt;78&lt;/strong&gt;(5): 601-8&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23796481&quot; rel=&quot;nofollow&quot;&gt;Fitzgerald et al., &lt;em&gt;Top Companion Anim Med&lt;/em&gt; (2013); &lt;strong&gt;28&lt;/strong&gt;(1):8-12&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;https://www.crcpress.com/product/isbn/9780849316906&quot; rel=&quot;nofollow&quot;&gt;Karch, Drug Abuse Handbook (2006)&lt;/a&gt; &#xA;- &lt;a href=&quot;http://circ.ahajournals.org/content/122/24/2558.full&quot; rel=&quot;nofollow&quot;&gt;Schwartz et al., &lt;em&gt;Circulation&lt;/em&gt; (2010); &lt;strong&gt;122&lt;/strong&gt;:2558-69&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-01-22T23:43:48.247" LastActivityDate="2016-01-22T23:43:48.247" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="34479" PostTypeId="1" CreationDate="2015-05-23T14:42:30.533" Score="3" ViewCount="95" Body="&lt;p&gt;I wanted to know what a suitable classical conditioning experiment would be to analyze learning and memory capabilities in rodent models with respect to hippocampal long-term potentiation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, I want to subject the animal to conditioning and test the behavioral readout at a certain time point after conditioning. Many , like fear conditioning experiments, are mostly attributed to amygdala processes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wish to know some classical conditioning task where I can understand primarily hippocampal processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also is there a way to monitor hippocampal CA1-CA3 firing pattern after the training period or during the training ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is, I want to check if LTP will sustain after the training period or is there is any increased sustenance of LTP post training. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if I am to do this electrophysiological experiment in hippocampal brain slices, how will I incorporate the conditioned and unconditioned aspect to this ?&lt;/p&gt;&#xA;" OwnerUserId="6497" LastEditorUserId="6497" LastEditDate="2015-05-23T16:18:56.150" LastActivityDate="2015-11-06T03:05:49.773" Title="classical conditioning paradigm for hippocampal learning" Tags="&lt;physiology&gt;&lt;neuroscience&gt;&lt;neurophysiology&gt;&lt;electrophysiology&gt;&lt;memory&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34481" PostTypeId="1" AcceptedAnswerId="34502" CreationDate="2015-05-23T16:33:44.983" Score="9" ViewCount="12398" Body="&lt;p&gt;Why are action potentials not initiated at dendrites, although dendrites are the first to receive input from the presynaptic cell?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, excitatory postsynaptic potentials (EPSPs) at the dendrites are smaller than in the cell body and axon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Considering the fact that dendrites have enough voltage gated ion channels, why is it that cation influx through these channels is not able to depolarize the dendrite above threshold and generate an action potential?&lt;/p&gt;&#xA;" OwnerUserId="6497" LastEditorUserId="36209" LastEditDate="2017-11-07T15:36:44.153" LastActivityDate="2017-11-07T15:36:44.153" Title="Why can action potentials not be initiated at dendrites?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;&lt;dendrites&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34482" PostTypeId="2" ParentId="7854" CreationDate="2015-05-23T16:50:05.040" Score="3" Body="&lt;p&gt;I'll have to disagree with Alan. If the plasmid is integrated into a chromosome it doesn't lose its episomal status. Actually the integration of the plasmid is a characteristic of an episome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a quote from this article: &lt;a href=&quot;http://www.qub.ac.uk/mlpage/courses/level3/plasmidhistoryreview.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.qub.ac.uk/mlpage/courses/level3/plasmidhistoryreview.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;... For a decade or more it was confused with ‘‘episome,’’ although that was carefully&#xA;  crafted (F. Jacob and E. L. Wollman, 1958, C. R. Acad. Sci. 247, 154–156) to mean agents with&#xA;  traffic in and out of chromosomes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also this book (&lt;a href=&quot;https://books.google.pt/books?id=YnXB54RtrR8C&amp;amp;pg=PA132&amp;amp;dq=episome&amp;amp;hl=pt-PT&amp;amp;sa=X&amp;amp;ei=oKZgVd3HEZOu7AaeoYPABQ&amp;amp;ved=0CCoQ6AEwAg#v=snippet&amp;amp;q=episome&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;https://books.google.pt/books?id=YnXB54RtrR8C&amp;amp;pg=PA132&amp;amp;dq=episome&amp;amp;hl=pt-PT&amp;amp;sa=X&amp;amp;ei=oKZgVd3HEZOu7AaeoYPABQ&amp;amp;ved=0CCoQ6AEwAg#v=snippet&amp;amp;q=episome&amp;amp;f=false&lt;/a&gt;) clearly mentions that an episome is a genetic element able to exist in an integrated form (associated with the chromosome) but also with it's  own origin of replication (autonomous form). So in fact &lt;strong&gt;an episome can be a plasmid or a viral genome&lt;/strong&gt;, but not all genetic elements have this ability.&lt;/p&gt;&#xA;" OwnerUserId="6753" LastEditorUserId="6753" LastEditDate="2015-05-23T17:05:05.067" LastActivityDate="2015-05-23T17:05:05.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34483" PostTypeId="1" CreationDate="2015-05-23T16:53:28.740" Score="3" ViewCount="847" Body="&lt;p&gt;A coeloblastula is that type of blastula which has a fluid-filled cavity. Since the blastocyst of mammals has a fluid-filled cavity too, can it be called a coeloblastula? My book however mentions the two as different, and it gives the frog as an example of animals having the coeloblastula and mammals as an example of having the blastocyst.&lt;/p&gt;&#xA;" OwnerUserId="15109" LastEditorUserId="16866" LastEditDate="2018-01-19T02:34:48.993" LastActivityDate="2018-07-18T04:41:50.007" Title="Is the blastocyst a coeloblastula?" Tags="&lt;development&gt;&lt;embryology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34484" PostTypeId="1" AcceptedAnswerId="34490" CreationDate="2015-05-23T19:16:35.647" Score="0" ViewCount="95" Body="&lt;p&gt;Biologically,  Brain controls our thinking,  ideas,  decisions everything along with controlling each body parts. My question is,  is there anything real as &quot;mind &quot;?  If it's controlled by brain then how does brain controls the mind? &lt;/p&gt;&#xA;" OwnerUserId="15874" LastEditorUserId="15874" LastEditDate="2015-05-23T21:24:37.967" LastActivityDate="2015-05-24T00:05:25.640" Title="Does &quot;mind&quot; has any physical reality in biology? Or is it just an assumptive concept?" Tags="&lt;brain&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34485" PostTypeId="1" CreationDate="2015-05-23T19:35:17.843" Score="7" ViewCount="959" Body="&lt;p&gt;When an action potential is induced on a neuron, the local transmembrane potential jumps from $E_{\mbox{rest}}$, the resting potential of the neuron, to $E_{\mbox{eq}}$, the equilibrium potential of an ion or group of ions in the vicinty. Current thus travels in and out of a part of the neuron's cell membrane as ions are exchanged during an action potential. This effect repeats itself as the neighboring regions of the membrane are depolarized, causing the action potential to propagate along the neuron's axon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take $\Delta Q$ to be the total charge exchanged locally during an action potential, $C$ to be the membrane capacitance, and $\Delta t$ to be the duration of the action potential. While we can approximate the local average current through an neuron's membrane by taking $$I = \frac{\Delta Q}{\Delta t} = C\frac{\Delta V}{\Delta t} = C\frac{E_{\mbox{eq}} - E_{\mbox{rest}}}{\Delta t}$$ Is there a way to approximate current traveling &lt;em&gt;along&lt;/em&gt; the axon of the neuron? Is there even such a thing?&lt;/p&gt;&#xA;" OwnerUserId="15893" LastEditorUserId="9943" LastEditDate="2015-05-24T09:43:14.583" LastActivityDate="2015-05-24T10:17:49.057" Title="Current along an axon" Tags="&lt;mathematical-models&gt;&lt;neurophysiology&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34486" PostTypeId="1" AcceptedAnswerId="34487" CreationDate="2015-05-23T20:30:58.927" Score="12" ViewCount="4514" Body="&lt;p&gt;I am reading up on preparatory work on working with nucleic acids and a lot of the instructions speak on excessive procedures on cleaning environments with high %ethanol and making sure the equipment is nuclease free, and autoclaved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these sterilization steps really necessary when doing research /running gels? Buying all of this equipment seems very excessive, and given that just one nuclease could compromise my results why bother?&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="9943" LastEditDate="2015-05-24T10:30:26.823" LastActivityDate="2015-05-26T13:31:26.963" Title="How sterile is sterile when working with nucleic acids to prevent contamination?" Tags="&lt;lab-techniques&gt;&lt;nucleic-acids&gt;&lt;sterilisation&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34487" PostTypeId="2" ParentId="34486" CreationDate="2015-05-23T20:43:13.730" Score="13" Body="&lt;p&gt;&lt;strong&gt;Short answer:&lt;/strong&gt; Yes&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long answer:&lt;/strong&gt; Depends what you are working with. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;DNA&lt;/strong&gt;: If you are working with DNA, its pretty stable and you can usually get away with a 70% ethanol wash/autoclave (mainly to prevent contamination and obtain consistent results). EDIT: Read Chris's answer also below&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;RNA:&lt;/strong&gt; If you are working with RNA well.. whatever you did for DNA doesnt apply anymore. You have to take it to the next level.  You will need to replace everything, you'll need nuclease free water, tubes, reagents and whatnots. Throw out ethanol and bring in RNAZap, DEPC water or something like that.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;An RNase free environment is essential when working with RNA samples. There are two main reasons for RNA degradation during RNA analysis. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;First, RNA by its very structure is inherently weaker than DNA. RNA is made up of ribose units, which have a highly reactive hydroxyl group on C2 that takes part in RNA-mediated enzymatic events. This makes RNA more chemically labile than DNA. RNA is also more prone to heat degradation than DNA. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Secondly, enzymes that degrade RNA, ribonucleases (RNases) are so ubiquitous and hardy; removing them often proves to be nearly impossible. For example, autoclaving a solution containing bacteria will destroy the bacterial cells but not the RNases released from the cells. Furthermore, even trace amounts of RNases are able to degrade RNA. Note that RNAses are present everywhere (skin, reagents, normal plastic etc).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Therefore, it is essential to avoid inadvertently introducing RNases into the RNA sample during or after the isolation procedure.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Remember that following microbiological aseptical techniques is usually good practice (and a requirement) when working in a molecular biology lab.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are excellent guides available online for working with RNA:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I took the above paragraph from here: &#xA;&lt;a href=&quot;http://www.bioline.com/us/rna-hints-and-tips&quot;&gt;http://www.bioline.com/us/rna-hints-and-tips&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Life tech has a few more tips for you: &lt;a href=&quot;https://www.lifetechnologies.com/uk/en/home/references/ambion-tech-support/nuclease-enzymes/general-articles/working-with-rna.html&quot;&gt;https://www.lifetechnologies.com/uk/en/home/references/ambion-tech-support/nuclease-enzymes/general-articles/working-with-rna.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a good pdf to have in your labbook as a reference sheet:&lt;a href=&quot;http://genomics.no/oslo/uploads/PDFs/workingwithrna.pdf&quot;&gt;http://genomics.no/oslo/uploads/PDFs/workingwithrna.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this scares you , that's good because when working with RNA there are a million things that can go wrong the first few times you try it. You have to be very careful, and adapting a cavalier attitude such as not bothering is going to come back and haunt you at night...&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-23T23:43:30.627" LastActivityDate="2015-05-23T23:43:30.627" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34488" PostTypeId="2" ParentId="34211" CreationDate="2015-05-23T20:52:40.020" Score="0" Body="&lt;p&gt;&lt;strong&gt;Masked allele&lt;/strong&gt; is a term that is sometimes used for recessive alleles, and it should be suitable to the situation you describe. A common phrasing could be; &quot;&lt;em&gt;The wild type allele is masking the expression of the deleterious allele X.&lt;/em&gt;&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For your particular example you could use:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Deleterious mutations on the Y chromosome are more easily purged since they cannot be masked by alleles on a homologous chromosome. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;An example can also be found in the abstract to &lt;a href=&quot;http://m.genetics.org/content/131/3/745.short&quot; rel=&quot;nofollow&quot;&gt;Otto &amp;amp; Goldstein (1992)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;With two copies of every gene, a diploid organism is able to mask recessive deleterious mutations. In this paper we present the analysis of a two-locus model designed to determine when the masking of deleterious alleles favors the evolution of a dominant diploid phase in organisms that alternate between haploid and diploid phases (&quot;alternation of generations&quot;). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-05-24T21:22:32.047" LastActivityDate="2015-05-24T21:22:32.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34489" PostTypeId="2" ParentId="34486" CreationDate="2015-05-23T23:30:04.917" Score="9" Body="&lt;p&gt;First of all, sterility is not necessary. It takes much more effort to reach this than just to wipe down everything with ethanol. What you need is a clean and controlled work environment (but this is something you need anyway to get reproducible results) and good and clean equipment. You will need more precautions for RNA work as RNA is more sensitive and RNAses are ubiquituous, but the general rules are the same. Some remarks from me about it:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;There is no need to wipe down everything in your environment before working. Will you DNA touch the desk or the outside of you pipette? Simply wear gloves, use fresh plasticware, do not touch the plasticware with your bare finger and you will be fine.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There is no general need to autoclave everything what you use (unless you explicitly need it sterile). Do not touch the stuff with your bare fingers. Autoclaves can also be a souce for contamination when they are badly maintained or used to also autoclave trash. Plasticware is generally nuclease free, thanks to the production process (melted plastic is not a good place to live on).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If you work with RNA try to set up a separated working space to avoid contaminations by your normal work. If you use glassware, wash it with DEPC treated water and autoclave it to get it RNAse free. Use gloves! Also use a different set of chemicals for this work to avoid cross-contamination. Filter-tips can be a good idea here. Besides being careful, RNA work is no magic but solid handcraft.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If you do PCR try to set up a different work place seperated from your normal work. PCR is very sensitive to contaminations sitting in you pipettes from your normal work. I have seen a number of cases of false positive amplifications from normal work.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="9099" LastEditDate="2015-05-26T13:31:26.963" LastActivityDate="2015-05-26T13:31:26.963" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34490" PostTypeId="2" ParentId="34484" CreationDate="2015-05-24T00:05:25.640" Score="3" Body="&lt;p&gt;The mind is an abstraction which arises from physical and chemical processes within the brain.  For a crude analogy, think of the brain as an incredibly complex, self-modifying, multithreaded program.  The mind would then be the abstraction arising from the &lt;em&gt;behavior&lt;/em&gt; of the program as it runs.  Consciousness would be the abstraction arising from the behavior of one particular thread in the program: a thread which has access to a limited buffer of its own (that thread's) behavior, and control over limited input and output from the body.  All of the other (unconscious) threads may affect the conscious thread, but the conscious thread has very limited access to information about the behavior of the other threads.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the conscious part of the mind has access to information about its own behavior, there is actually some recursive looping going on when it comes to thinking and feeling.  The feeling that this goes in circles somehow (which you seem to be expressing) is a common intuition, and it's almost certainly a correct one.  But the manner in which this occurs is not well-understood, and it's definitely not well-understood within biology at the macro level because the brain is unbelievably complex and plastic.  We really don't have a clue how to begin modeling the brain's processes.  This is one reason artificial intelligence is still extremely crude today (despite what Elon Musk and Bill Gates may try to say).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to read a scientifically-inspired theory of from whence consciousness comes, and of how it arises from the brain, I would recommend the book &lt;strong&gt;Godel, Escher, Bach&lt;/strong&gt; by Douglas Hofstadter.  Douglas does a good job of combining computational theory with biology, music, and art to illustrate a theory of consciousness the reader can grasp even if you don't have a strong background in any of those subjects.&lt;/p&gt;&#xA;" OwnerUserId="15867" LastActivityDate="2015-05-24T00:05:25.640" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34491" PostTypeId="2" ParentId="34485" CreationDate="2015-05-24T00:18:35.290" Score="-1" Body="&lt;p&gt;The electrical impulse through the axon is a transverse wave of ions moving in and out. There is no net change in charge to the axon itself.  It isn't an electric current at all; it is a transverse chemical wave powered by electric charges.&lt;/p&gt;&#xA;" OwnerUserId="15867" LastEditorUserId="9943" LastEditDate="2015-05-24T10:09:19.517" LastActivityDate="2015-05-24T10:09:19.517" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34494" PostTypeId="1" AcceptedAnswerId="34500" CreationDate="2015-05-24T01:37:25.710" Score="4" ViewCount="670" Body="&lt;p&gt;Around 6 molecules of G3P is produced at the end of the Calvin Cycle (light independent reactions of photosynthesis), and 5 of which are reverted back to RuBp.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The general equation that I read is 5 G3P -----&gt; 3 RuBp using 3 ATP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It however doesn't seem to add up (regarding balancing of the atoms) as 5 phosphates would be converted to 6.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would appreciate a link to any resource explaining this process in detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you and have a nice day ^^&lt;/p&gt;&#xA;" OwnerUserId="15002" LastActivityDate="2015-05-24T10:10:59.317" Title="How exactly is glyceraldehyde 3-Phosphate reverted to ribulose 1,5-bisphosphate for the continuation of the calvin cycle?" Tags="&lt;biochemistry&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34496" PostTypeId="1" AcceptedAnswerId="34509" CreationDate="2015-05-24T05:21:34.937" Score="3" ViewCount="181" Body="&lt;p&gt;Could any animal subject to the right conditions evolve human-level intelligence? Suppose that an artificial intelligence (AI) decided to artificially evolve a population of octopus (don't ask why, its for science) by restricting them to calculated environmental pressures, and over millions of years, the AI manages to produce a relative of the octopus that has a similar level of cognition to humans. Is this possible? If it is possible, what are some steps (in general) that might be required to evolve a complex animal brain (to human-level cognition or beyond)? &lt;/p&gt;&#xA;" OwnerUserId="15882" LastEditorUserId="9943" LastEditDate="2015-05-24T10:31:13.847" LastActivityDate="2015-05-26T01:15:23.803" Title="What would be required to evolve an animal (non-human) brain to obtain human-level cognition?" Tags="&lt;evolution&gt;&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ClosedDate="2015-05-27T19:52:53.193" ContentLicense="CC BY-SA 3.0" />
  <row Id="34497" PostTypeId="1" AcceptedAnswerId="34519" CreationDate="2015-05-24T09:24:54.823" Score="5" ViewCount="122" Body="&lt;p&gt;I just learned that all hornets and bumblebees except for the queen die at the end of the year and the queen starts a new nest in spring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But that means the next generation of queens have only brothers to breed with.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Should this lead to severe inbreeding, which over a couple of years would cause serious problems for survival?&lt;/p&gt;&#xA;" OwnerUserId="15898" LastEditorUserId="3952" LastEditDate="2015-05-24T16:15:22.357" LastActivityDate="2015-05-25T11:22:40.270" Title="How do bumblebees and hornets avoid the negative effects of inbreeding?" Tags="&lt;evolution&gt;&lt;entomology&gt;&lt;population-genetics&gt;&lt;sociality&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34498" PostTypeId="2" ParentId="34485" CreationDate="2015-05-24T09:57:31.360" Score="1" Body="&lt;p&gt;As far as I was able to find there exists two models of the action potential by using RC circuits. Do note that there is no flow of electrons per se across a tube, but rather a migration of potential. See &lt;a href=&quot;http://www.quora.com/I-thought-that-current-implied-a-flow-of-electrons-but-I-read-that-in-neurons-there-is-only-ionic-flow-across-the-membrane-Is-there-really-a-current-flowing-through-a-neuron/answer/Yohan-John?share=1&quot; rel=&quot;nofollow&quot; title=&quot;this&quot;&gt;this&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Hodgkins Huxley model :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Hodgkin–Huxley model, or conductance-based model, is a mathematical model that describes how action potentials in neurons are initiated and propagated. It is a set of nonlinear differential equations that approximates the electrical characteristics of excitable cells such as neurons and cardiac myocytes, and hence it is a continuous time model&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Fitzhugh-Nagumo model:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The FitzHugh–Nagumo model is a simplified version of the Hodgkin–Huxley model which models in a detailed manner activation and deactivation dynamics of a spiking neuron. In the original papers of FitzHugh, this model was called Bonhoeffer–van der Pol oscillator...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/FitzHugh%E2%80%93Nagumo_model&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/FitzHugh%E2%80%93Nagumo_model&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Quantitative_models_of_the_action_potential&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Quantitative_models_of_the_action_potential&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Hodgkin, Allan L., and Andrew F. Huxley. &quot;Currents carried by sodium and potassium ions through the membrane of the giant axon of Loligo.&quot; The Journal of physiology 116.4 (1952): 449-472.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I have not dealt with differential equations in quite a while, and hence may not be the best source for explaining the model itself, but I'll try and update the post with what (if anything) I understand.&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-24T10:17:49.057" LastActivityDate="2015-05-24T10:17:49.057" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34499" PostTypeId="2" ParentId="34485" CreationDate="2015-05-24T10:05:49.473" Score="0" Body="&lt;p&gt;Although it is not a flow of electrons like in an electronic circuit, it &lt;em&gt;is nonetheless current flow&lt;/em&gt; which drives action potential propagation. It could be seen as a positive current flow (outward Na&lt;sup&gt;+&lt;/sup&gt;), followed by a negative one (inward K&lt;sup&gt;+&lt;/sup&gt;) going from dendrite to synapse. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, a neuron can be modeled by a a basic electronic circuit with &lt;strong&gt;resistors&lt;/strong&gt; (representing &lt;em&gt;ion channels&lt;/em&gt;), &lt;strong&gt;capacitors&lt;/strong&gt; (representing the &lt;em&gt;membrane capacitance&lt;/em&gt;) and &lt;strong&gt;batteries&lt;/strong&gt; (representing the various &lt;em&gt;ion charge/concentration gradients&lt;/em&gt; that power the action potential), see Fig. 1. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UkheR.jpg&quot; alt=&quot;neuron circuit&quot;&gt;&lt;br&gt;&#xA;Fig. 1. Model of a neuron. Source: &lt;a href=&quot;http://teachers.yale.edu/curriculum/viewer/initiative_09.06.07_u&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yale university&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-24T10:12:19.573" LastActivityDate="2015-05-24T10:12:19.573" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34500" PostTypeId="2" ParentId="34494" CreationDate="2015-05-24T10:10:59.317" Score="4" Body="&lt;p&gt;You need to account for free phosphates (Pi) that derive from ATP and are released in phosphatase reactions. The regeneration of 3 ribulose-1,5-2P has the overall reaction&lt;/p&gt;&#xA;&#xA;&lt;p&gt;5 glyceraldehyde-3P + 3 ATP $\rightarrow$ 3 ribulose-1,5-2P + 3 ADP + 2 Pi&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in total eight phosphates (here counting ATP as 1) are redistributed, 6 of which end up in ribulose-1,5-2P, and two are released as free phosphates. (These Pi are then recaptured during ATP synthesis in the light-dependent reactions.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above is a summary reaction of course; the complete scheme involves 10 enzymatic reactions that rearrange carbons in various ways to form 5-carbon sugars from 3-carbon ones (which takes a bit of juggling of atoms). Release of free Pi occurs in the fructose biphosphatase and seduheptulose biphosphatase steps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A detailed account can be found in any major biochemistry textbook, like &lt;a href=&quot;http://www.amazon.co.uk/Biochemistry-International-Jeremy-M-Berg/dp/071676766X/ref=dp_ob_image_bk&quot; rel=&quot;nofollow&quot;&gt;Stryer's Biochemistry&lt;/a&gt;. Online resources like &lt;a href=&quot;http://metacyc.org/META/NEW-IMAGE?type=PATHWAY&amp;amp;object=CALVIN-PWY&quot; rel=&quot;nofollow&quot;&gt;MetaCyc&lt;/a&gt; can also be helpful.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-05-24T10:10:59.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34501" PostTypeId="1" CreationDate="2015-05-24T10:32:49.893" Score="2" ViewCount="407" Body="&lt;p&gt;An external sound or touch can awaken someone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can a light? It would have to be very strong, but part of the reason might be that it would have to penetrate the eyelids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And can a smell or taste?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When we are awake, the impact of sensory stimuli and of changes in them depend on which sense is stimulated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question concerns the kind and strength of impact the stimulation of each sense has when we are asleep, in relation to what is needed to wake us up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Note&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks to @Mithoron for linking to &lt;a href=&quot;https://biology.stackexchange.com/questions/28289/what-senses-are-active-while-sleeping&quot;&gt;another question&lt;/a&gt;, asked on this website by @Taladris. That question is certainly quite similar to this one and its answer contains some relevant material, even if the answer is not of high quality because of course our senses are &quot;dimmed&quot; when we are asleep and of course it is not true that &quot;that we respond to our own names in a similar fashion in sleep and in wakefulness&quot;. The present question asks specifically about awakening because of sensory input. I believe I am sometimes awakened by smells, although it is hard for me to tell whether or not I am right. Part of my question asks for views or facts concerning whether people can be woken by smells at all. This is different from asking whether we can smell when we are asleep.&lt;/p&gt;&#xA;" OwnerUserId="13394" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-05-24T16:49:40.717" Title="External sensory stimuli that awaken a person from sleep" Tags="&lt;sleep&gt;&lt;senses&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34502" PostTypeId="2" ParentId="34481" CreationDate="2015-05-24T12:38:41.693" Score="9" Body="&lt;p&gt;The exact site of action potential generation is debated, as is the underlying physiological mechanism &lt;a href=&quot;http://www.jneurosci.org/cgi/pmidlookup?view=long&amp;amp;pmid=8824308&quot; rel=&quot;nofollow&quot;&gt;(Colbert &amp;amp; Johnsten, 1996)&lt;/a&gt;. It is generally agreed upon that the initiation site is beyond the soma, at the axon hillock, or even further in the initial segment of the axon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for the distal axonal initiation site of action potentials is, according to the classical view, that the &lt;strong&gt;density of Na&lt;sup&gt;+&lt;/sup&gt; channels is not high enough in the soma&lt;/strong&gt;, while the density in the axon initial segment is substantially higher and sufficient. However, it has also been proposed that the &lt;strong&gt;threshold of action potential generation&lt;/strong&gt; is lower at the initial segment &lt;a href=&quot;http://www.nature.com/neuro/journal/v11/n2/abs/nn2040.html&quot; rel=&quot;nofollow&quot;&gt;(Kole et al., 2008)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding your questions in the comments:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;code&gt;So can't action potentials be initiated at dendrites and soma with the help of VGCCs?&lt;/code&gt; &#xA;&lt;strong&gt;Answer&lt;/strong&gt;: No. Channel density is too low; &lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;What are the channels required for AP?&lt;/code&gt;&lt;br&gt;&#xA;&lt;strong&gt;Answer&lt;/strong&gt;: Basically Na&lt;sup&gt;+&lt;/sup&gt; and K&lt;sup&gt;+&lt;/sup&gt; channels;&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;How is it that action potentials are initiated at axon hillock, although the input is at dendrites? Why can't enough depolarization happen at dendrites and soma?&lt;/code&gt;&lt;br&gt;&#xA;&lt;strong&gt;Answer&lt;/strong&gt;: Either due to a low density of Na&lt;sup&gt;+&lt;/sup&gt; channels, and/or a higher action potential threshold (e.g., due to the presence of K&lt;sup&gt;+&lt;/sup&gt; channels in the soma counteraction depolarization);&lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;As a corollary,if enough depolarization cannot occur at dendrites and soma,how then is it propagated to the axon, which is further down anatomically , in the neuron?&lt;/code&gt;&lt;br&gt;&#xA;&lt;strong&gt;Answer&lt;/strong&gt;: If the EPSP reaches a region with sufficient Na&lt;sup&gt;+&lt;/sup&gt; channels, depolarization becomes sufficient to activate a critical amount of Na&lt;sup&gt;+&lt;/sup&gt; channels that causes a sufficient increase in the membrane potential to sustain a full-blown action potential. Along the way, leaky K&lt;sup&gt;+&lt;/sup&gt; channels decrease the depolarization so a critical amount of channels is necessary, otherwise the EPSP dies out. &lt;/li&gt;&#xA;&lt;li&gt;&lt;code&gt;What about backpropagating APs from axon hillock to dendrites ? How is that possible?&lt;/code&gt;&lt;br&gt;&#xA;&lt;strong&gt;Answer&lt;/strong&gt;: the soma and dendritic region are believed to represent too big an &lt;a href=&quot;http://en.wikipedia.org/wiki/Electrical_load&quot; rel=&quot;nofollow&quot;&gt;electrical load&lt;/a&gt; to ensure action potential propagation in both the orthodromic and the antidromic direction. This &lt;a href=&quot;http://en.wikipedia.org/wiki/Impedance_matching&quot; rel=&quot;nofollow&quot;&gt;impedance mismatch&lt;/a&gt; can be overcome for an action potential propagating from the axon back into the somato-dendritic region when the initial segment and axon hillock provide additional current. This can be achieved with a high density of sodium channels in that region (&lt;a href=&quot;http://jn.physiology.org/content/80/2/715.full-text.pdf+html&quot; rel=&quot;nofollow&quot;&gt;Lüscher &amp;amp; Larkum, 1998&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.jneurosci.org/cgi/pmidlookup?view=long&amp;amp;pmid=8824308&quot; rel=&quot;nofollow&quot;&gt;Colbert &amp;amp; Johnsten, &lt;em&gt;J Neurosci&lt;/em&gt; (1996), &lt;strong&gt;16&lt;/strong&gt;(21): 6676–86&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.nature.com/neuro/journal/v11/n2/abs/nn2040.html&quot; rel=&quot;nofollow&quot;&gt;Kole et al., Nature Neurosci (2008); &lt;strong&gt;11&lt;/strong&gt;: 178-86&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://jn.physiology.org/content/80/2/715.full-text.pdf+html&quot; rel=&quot;nofollow&quot;&gt;Lüscher &amp;amp; Larkum, &lt;em&gt;J Neurophysiol&lt;/em&gt; (1998); &lt;strong&gt;80&lt;/strong&gt;(2): 715-29&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-04-22T09:00:05.493" LastActivityDate="2016-04-22T09:00:05.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34506" PostTypeId="1" AcceptedAnswerId="34508" CreationDate="2015-05-24T21:45:09.050" Score="6" ViewCount="312" Body="&lt;p&gt;When a discussion about evolution comes across abiogenesis - the typical reaction is that they are unrelated (see the headline at &lt;a href=&quot;http://www.factsnotfantasy.com/abiogenesis.php&quot;&gt;http://www.factsnotfantasy.com/abiogenesis.php&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to be that both are stochastic processes in which less ordered structures become ordered.  It seems that, in general, abiogenesis is the process of forming of life (whatever that is) whereas evolution is the process in which life would develop into more complex forms.  In other words, it seems that it's really just two phases of the same type of process and I'm wondering why they are considered as such isolated fields.&lt;/p&gt;&#xA;" OwnerUserId="13238" LastActivityDate="2015-05-25T05:22:29.940" Title="Why are abiogenesis and evolution considered unrelated?" Tags="&lt;evolution&gt;&lt;abiogenesis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34507" PostTypeId="1" AcceptedAnswerId="34517" CreationDate="2015-05-24T22:21:13.070" Score="4" ViewCount="10647" Body="&lt;p&gt;I saw a description of the &quot;minimum requirements&quot; for a cell at &lt;a href=&quot;http://creation.com/origin-of-life&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://creation.com/origin-of-life&lt;/a&gt; in the section called &quot;What are the minimum requirements for a cell to live?&quot; and I'm wondering if this is scientifically accurate - and if not - what are the real requirements?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[note/warning - the link above is to a creationist site - I'm only quoting this source because I'm trying find the science involved and I didn't find other sources talking about all the necessary pieces. I'm not trying to promote creationism with this question so please don't attack the source or me for bringing it.  If you can find a non-creationist source which outlines these requirements, I'll be happy to update the question and remove this source.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary it lists the requirements as follows:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;cell membrane&lt;/li&gt;&#xA;&lt;li&gt;way of storing information (DNA)&lt;/li&gt;&#xA;&lt;li&gt;way of reading 2. to make components needed&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;RNA polymerase&lt;/li&gt;&#xA;&lt;li&gt;gyrases to untwist DNA&lt;/li&gt;&#xA;&lt;li&gt;ribosomes to make proteins&lt;/li&gt;&#xA;&lt;li&gt;(a few others I omitted b/c I don't know if they're really important)&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;means of creating fuel (ATP synthase)&lt;/li&gt;&#xA;&lt;li&gt;a means of copying the information for reproduction&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The context of the question is similar to &lt;a href=&quot;https://biology.stackexchange.com/questions/406/can-scientists-create-totally-synthetic-life&quot;&gt;Can scientists create totally synthetic life?&lt;/a&gt; and a question I wrote &lt;a href=&quot;https://biology.stackexchange.com/questions/28100/what-is-the-most-complex-biological-organism-or-precursors-that-we-have-been-a&quot;&gt;What is the most complex biological organism (or precursors) that we have been able to synthesize from raw materials?&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm trying to understand what would be involved in making a cell from scratch. Somehow I found this source but I don't know if it's accurate.  &lt;/p&gt;&#xA;" OwnerUserId="13238" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-10-21T01:59:01.567" Title="What are the &quot;minimum requirements&quot; for a single cell?" Tags="&lt;molecular-biology&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34508" PostTypeId="2" ParentId="34506" CreationDate="2015-05-24T23:36:56.680" Score="8" Body="&lt;p&gt;I wouldn't go so far as to say that they are entirely unrelated -- our understanding of selective processes can certainly inform our study of the origin of life -- but I would say that they are quite different projects. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One important reason is that evolutionary biologists can use phylogenetic information to reconstruct much of the history of life. For example, genetic sequencing techniques allowed us to definitively work out the evolutionary relationships among humans, chimps, and gorillas. But this approach can only allow us to back as far as the last universal common ancestor (LUCA). LUCA was presumably a DNA-based (uni-)cellular lifeform, given that these characteristcs are shared across the entire tree of life. So we have no phylogenetic information that we can leverage to reconstruct what happened to get us from a soup of organic molecules to LUCA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another reason is that evolutionary biology focuses on what happens to a population in which we have variation, heritability, and selection. Early in the origin of life, a structured system of heredity would not yet have arisen and so we would not see natural selection occurring in the form that we usually study it -- though there could be interesting selective dynamics in such a system.&lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="13072" LastEditDate="2015-05-25T05:22:29.940" LastActivityDate="2015-05-25T05:22:29.940" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34509" PostTypeId="2" ParentId="34496" CreationDate="2015-05-25T02:16:38.480" Score="4" Body="&lt;p&gt;Answering the question what is needed for a human brain to evolve starting from a cephalopod brain is hard. However, I can expand on what is thought to have been the driving forces behind the evolution of the humanoid brain &lt;a href=&quot;https://www.scientificamerican.com/article/how-has-human-brain-evolved/&quot; rel=&quot;nofollow&quot;&gt;(Hawks, 2013)&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The species of the famous Lucy fossil, &lt;em&gt;Australopithecus afarensis&lt;/em&gt; (~3-4 mln yrs ago), had skulls with internal volumes of between 400 and 550 milliliters, which is comparable to chimpanzees and gorillas. Australopithecine brains started to show subtle changes in structure and shape as compared with apes. however. For instance, the neocortex was expanding, which is an indication that the evolutionary pressure on &lt;strong&gt;higher functions of the brain&lt;/strong&gt; was important. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Homo habilis&lt;/em&gt;, the first of our genus &lt;em&gt;Homo&lt;/em&gt;, who appeared 1.9 million years ago, saw a modest hop in brain size, including an expansion of a language-connected part of the frontal lobe called Broca's area. The first fossil skulls of Homo erectus, 1.8 million years ago, had brains averaging a bit larger than 600 ml. This shows that &lt;strong&gt;language development&lt;/strong&gt; is a likely factor that has driven evolution of the human brain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By 500,000 years ago, the humanoid brain reached a volume of about 1,000 ml. Early &lt;em&gt;Homo sapiens&lt;/em&gt; had brains within the range of people today, averaging 1,200 ml or more. It is thought that &lt;strong&gt;cultural&lt;/strong&gt; and &lt;strong&gt;linguistic complexity&lt;/strong&gt;, &lt;strong&gt;dietary needs&lt;/strong&gt; and &lt;strong&gt;technological prowess&lt;/strong&gt; took a significant leap forward at this stage, and that our brains grew to accommodate the changes. The shape changes we see accentuate the regions related to &lt;strong&gt;depth of planning&lt;/strong&gt;, &lt;strong&gt;communication&lt;/strong&gt;, &lt;strong&gt;problem solving&lt;/strong&gt; and other more &lt;strong&gt;advanced cognitive functions&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, in the past 10,000 years of human existence the brain actually shrank. Limited nutrition in agricultural populations may have been an important driver of this trend. Industrial societies in the past 100 years, however, have seen brain size rebound as &lt;strong&gt;nutrition&lt;/strong&gt; increased and &lt;strong&gt;disease&lt;/strong&gt; declined &lt;a href=&quot;https://www.scientificamerican.com/article/how-has-human-brain-evolved/&quot; rel=&quot;nofollow&quot;&gt;(Hawks, 2013)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed, one of the driving components behind the expansion of the human brain is increased availability of fatty fish to sustain the large amounts of fat needed in a brain - &lt;em&gt;survival of the fattest&lt;/em&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16828044&quot; rel=&quot;nofollow&quot;&gt;(Cunnane, 2006)&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although the past does not predict future evolution, a greater integration with technology may lead to further expansion of the human brain &lt;a href=&quot;https://www.scientificamerican.com/article/how-has-human-brain-evolved/&quot; rel=&quot;nofollow&quot;&gt;(Hawks, 2013)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16828044&quot; rel=&quot;nofollow&quot;&gt;Cunnane, &lt;em&gt;Med Sci (Paris)&lt;/em&gt; (2006); &lt;strong&gt;22&lt;/strong&gt;(6-7):659-63&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;https://www.scientificamerican.com/article/how-has-human-brain-evolved/&quot; rel=&quot;nofollow&quot;&gt;Hawks, &lt;em&gt;Sci Am&lt;/em&gt; (2013)&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-26T01:15:23.803" LastActivityDate="2015-05-26T01:15:23.803" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34510" PostTypeId="1" AcceptedAnswerId="34511" CreationDate="2015-05-25T03:41:23.087" Score="2" ViewCount="936" Body="&lt;p&gt;I am doing a Biology project involving the measurements of the density of algae (&lt;em&gt;Nannochloropsis&lt;/em&gt;) using absorbance colorimetry. What wavelength should I set my colorimeter to?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The issue is that there are two types of chlorophyll, each with a different absorbance optimum, there is spectral scatter to consider, as well as UV absorption when going to low wavelengths. What to do? &lt;/p&gt;&#xA;" OwnerUserId="10132" LastEditorUserId="9943" LastEditDate="2015-05-25T04:55:05.463" LastActivityDate="2015-05-25T05:21:33.330" Title="Which wavelength to use to determine algae using a colorimeter?" Tags="&lt;experiment&gt;&lt;measurement&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34511" PostTypeId="2" ParentId="34510" CreationDate="2015-05-25T04:07:39.797" Score="3" Body="&lt;p&gt;From &lt;strong&gt;&lt;a href=&quot;http://www.biotek.com/resources/articles/monitoring-of-algal-growth-using-intrinsic-properties.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Biotek&lt;/a&gt;&lt;/strong&gt; I learned the following:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Spectral scans of algae cultures demonstrate significant absorbance below 400 nm as well as two distinct absorbance peaks at 440 nm and 675 nm (Figure 1). Cell number determination is most consistent when light scatter is used rather than absorbance by cellular constituents. In order to avoid influence from absorbing material &lt;strong&gt;600 nm&lt;/strong&gt; [is best] to monitor growth.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iJ5pV.jpg&quot; alt=&quot;spectral scan&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Figure 1. Absorbance spectral curve of Microcystis aeruginosa suspension cultures.Source: &lt;a href=&quot;http://www.biotek.com/resources/articles/monitoring-of-algal-growth-using-intrinsic-properties.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Biotek&lt;/a&gt;&lt;/sup&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-25T05:21:33.330" LastActivityDate="2015-05-25T05:21:33.330" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34512" PostTypeId="1" AcceptedAnswerId="34559" CreationDate="2015-05-25T07:07:30.297" Score="2" ViewCount="361" Body="&lt;p&gt;After sperm meets ovum,the inactive nucleus starts following a particular path inside the zygote rather chase a path.This path is biologically known as fertilization path (as mentioned in an article of a local magazine named &quot;science reporter&quot;). But my question is how the pattern of the path is determined?  I came to know from the article that for every individual this particular path is very specific. Is it true?  If so then what does that specific path determine and why is it specific for every individual? &lt;/p&gt;&#xA;" OwnerUserId="15874" LastEditorUserId="15874" LastEditDate="2015-05-26T16:50:55.837" LastActivityDate="2015-05-26T18:31:52.747" Title="How the pattern of fertilization path is determined before the cell division to form the blastocyst? Is it individually specific?" Tags="&lt;reproduction&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34513" PostTypeId="2" ParentId="34507" CreationDate="2015-05-25T07:49:28.880" Score="-1" Body="&lt;p&gt;&lt;em&gt;Cell is the structural and functional unit of life, made up of a small mass of protoplasm delimited by a semi permeable membrane and capable of self reproduction without any living medium.&lt;/em&gt; This is a proper definition of cell and the minimal requirements would be all these mentioned here.&#xA;You can also see cell theory by M.J. Schleiden and Theodor Schwann. &#xA;But most importantly not only genetic information and membrane are required, most required part will be &lt;strong&gt;Cell should be capable of self reproduction without any living medium&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like for example RBC is not called cell cause they can't reproduce themselves. But nerve cell is called cell cause though they are not divisible but in embryonic condition the cell division occurred. Also in case of virus, as they can't reproduce without a host,they can't be called cell. &#xA;Red blood corpuscles aren't cells have a good proof in this article (check blood trivia part)&#xA;&lt;a href=&quot;http://www.redbloodcellbooks.com/rbc7.html&quot; rel=&quot;nofollow&quot;&gt;red blood corpuscle&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15874" LastEditorUserId="15874" LastEditDate="2015-05-25T20:43:13.333" LastActivityDate="2015-05-25T20:43:13.333" CommentCount="21" ContentLicense="CC BY-SA 3.0" />
  <row Id="34517" PostTypeId="2" ParentId="34507" CreationDate="2015-05-25T11:00:54.663" Score="1" Body="&lt;p&gt;So, to make cells from scratch you would need: amphiphilic molecules to form a membrane, a decent mix of simple molecules (sugars, nucleic acids, peptides) that serve as reactant and building blocks for more complex things, some simple catalyzer (metals, minerals, pepetides, aptamers, etc..) to run the reactions, enough energy to maintain lots of reactions running and keep them far from the equilibrium. Of course, lots of time...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An even more minimalistic approach would use a single molecule to do the enzymatic job while storing evolvable informations. In this case RNA alone has been proposed as substitute for proteins and DNA in a very minimal cell. In theory also DNA alone could do the same. However the minimal tasks needed to be done: maintain the self (to be compartimentalized), to grow (to have a flux of molecule not in equilibrium), to divide, to maintain the information stably enough to be useful for the next generation and at the same time prone too mutability to evolve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One more point. Life itself doesn't strictly require to be compartmentalized.&#xA;You can think of a network of chemical reactions that have the ability to grow, to replicate its components etc but without a cell membrane. However I think that a cell-like form of life is somewhat more likely to happen. &lt;/p&gt;&#xA;" OwnerUserId="12923" LastEditorUserId="12923" LastEditDate="2015-05-27T14:55:50.223" LastActivityDate="2015-05-27T14:55:50.223" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34518" PostTypeId="1" AcceptedAnswerId="34526" CreationDate="2015-05-25T11:05:00.717" Score="2" ViewCount="518" Body="&lt;p&gt;As I have read in (1), inhibition of translation initiation will increase the number of 80S ribosomes while decreasing the fraction of polysomes due to the polysome-runoff. The net effect is to decrease the polysome/monosome (P/M) ratio and we observe it for example by inducing ER stress by tunicamycin in (2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand the reduction in polysomes - since we don't interefere with elongation, polysomes work as normal, fallling of eventually, but new monosomes cannot proceed to polysomal stage due to inhibited initation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, why do the 80S ribosomes accumulate? I have always thought that 80S ribosome is always bound to mRNA, otherwise it dissociates as separate 40S and 60S subunits. Does this effect therefore mean that the accumulated 80S fraction is mRNA-free and therefore &quot;vacant 80S ribosomes&quot;, as decribed in (1), can exist?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks a lot!&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://books.google.co.uk/books?id=6sEq1xLu_hcC&amp;amp;pg=PA130&amp;amp;lpg=PA130&amp;amp;dq=polysome+translation+initiation&amp;amp;source=bl&amp;amp;ots=Un6JjImBJX&amp;amp;sig=ln9mn0KoJDJaVOGK8LbrEmMz9XE&amp;amp;hl=cs&amp;amp;sa=X&amp;amp;ei=x2JiVci8N4jX7Ab02YLgBQ&amp;amp;ved=0CGQQ6AEwCw#v=onepage&amp;amp;q=polysome%20translation%20initiation&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;https://books.google.co.uk/books?id=6sEq1xLu_hcC&amp;amp;pg=PA130&amp;amp;lpg=PA130&amp;amp;dq=polysome+translation+initiation&amp;amp;source=bl&amp;amp;ots=Un6JjImBJX&amp;amp;sig=ln9mn0KoJDJaVOGK8LbrEmMz9XE&amp;amp;hl=cs&amp;amp;sa=X&amp;amp;ei=x2JiVci8N4jX7Ab02YLgBQ&amp;amp;ved=0CGQQ6AEwCw#v=onepage&amp;amp;q=polysome%20translation%20initiation&amp;amp;f=false&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://jcs.biologists.org/content/115/11/2443/F4.large.jpg&quot; rel=&quot;nofollow&quot;&gt;http://jcs.biologists.org/content/115/11/2443/F4.large.jpg&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1721" LastActivityDate="2015-05-25T16:44:11.120" Title="Why does the inhibition of translation initiation cause the accumulation of 80S ribosomal monosomes?" Tags="&lt;molecular-biology&gt;&lt;proteins&gt;&lt;translation&gt;&lt;ribosome&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34519" PostTypeId="2" ParentId="34497" CreationDate="2015-05-25T11:06:28.870" Score="9" Body="&lt;p&gt;Queens do not generally breed with their brothers, but with males from other nests. In the life cycle of bees (and other social Hymenoptera), new queens are born late in the season along with haploid male drones. These all leave the nest and disperse in the landscape to find mates to reproduce with. After mating, all males die and the queens overwinter to start new colonies next spring. The situation is therefore not all that different compared to other annual, semelparous (single reproductive event) species, since you have population mixing before mating and reproduction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are a couple of mechanisms that bees avoid inbreeding:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Population mixing before reproduction&lt;/em&gt; (see above).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Inbreeding avoidance&lt;/em&gt;&lt;br&gt;&#xA;That queens prefer not to mate with close relatives has been shown in several species, see e.g. &lt;a href=&quot;http://www.jstor.org/stable/25085362?seq=1#page_scan_tab_contents&quot;&gt;Foster (1992)&lt;/a&gt; and &lt;a href=&quot;http://dx.doi.org/10.1051/apido/2009050&quot;&gt;Whitehorn et al (2009)&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Polyandry&lt;/em&gt;&lt;br&gt;&#xA;Each queen generally mates with several males (regulary more than 10 in honey bees, see &lt;a href=&quot;http://dx.doi.org/10.1051/apido:2000119&quot;&gt;Palmer &amp;amp; Oldroyd, 2000&lt;/a&gt;) and stores their sperm to fertilize eggs during the next year, which means that workers and the queens of next year will have different fathers (increasing genetic variability).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jstor.org/stable/25085362?seq=1#page_scan_tab_contents&quot;&gt;Foster. 1992. Nestmate Recognition as an Inbreeding Avoidance Mechanism in Bumble Bees (Hymenoptera: Apidae). Journal of the Kansas Entomological Society 65(3)&lt;/a&gt;  &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1051/apido/2009050&quot;&gt;Whitehorn et al. 2009. Kin recognition and inbreeding reluctance in bumblebees. Apidologie, 40(6)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1051/apido:2000119&quot;&gt;Palmer &amp;amp; Oldroyd. 2000. Evolution of multiple mating in the genus Apis. Apidologie 31(2)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-05-25T11:22:40.270" LastActivityDate="2015-05-25T11:22:40.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34520" PostTypeId="2" ParentId="31817" CreationDate="2015-05-25T11:52:25.480" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;A single pacemaker neuron can generate oscillatory behavior. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Given our exchange in the comments, I will focus on &lt;em&gt;single neurons with intrinsic oscillatory behavior&lt;/em&gt;. For example, thalamocortical relay neurons and inferior olive neurons have intrinsic oscillatory properties, mainly through the interaction of a hyperpolarization-activated cation current (I&lt;sub&gt;h&lt;/sub&gt;) and a low-threshold activated Ca&lt;sup&gt;2+&lt;/sup&gt; current (I&lt;sub&gt;T&lt;/sub&gt;) (&lt;a href=&quot;http://jn.physiology.org/content/68/4/1384.full-text.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;McCormick &amp;amp; Huguenard, 1992&lt;/a&gt;, and Fig. 1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jjB5b.png&quot; alt=&quot;Model for an oscillatory inferior olive neuron&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1 Model for an oscillatory inferior olive neuron. Source: &lt;a href=&quot;http://jn.physiology.org/content/77/6/3145&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bal &amp;amp; McCormick (1997)&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rhythmic burst firing is created through generation of a low-threshold Ca&lt;sup&gt;2+&lt;/sup&gt; current (I&lt;sub&gt;T&lt;/sub&gt;), which activates fast action potentials mediated by Na&lt;sup&gt;+&lt;/sup&gt;, K&lt;sup&gt;+&lt;/sup&gt;, and Ca&lt;sup&gt;2+&lt;/sup&gt; currents (I&lt;sub&gt;Na&lt;/sub&gt;, I&lt;sub&gt;K&lt;/sub&gt;, and I&lt;sub&gt;Ca&lt;/sub&gt;, respectively). Entry of Ca&lt;sup&gt;2+&lt;/sup&gt; in the cell during fast action-potential firing and low-threshold Ca&lt;sup&gt;2+&lt;/sup&gt; spiking result in after-hyperpolarization through activation of a Ca&lt;sup&gt;2+&lt;/sup&gt;-activated K&lt;sup&gt;+&lt;/sup&gt; current. This afterhyperpolarization activates I&lt;sub&gt;h&lt;/sub&gt;. Combined activation of I&lt;sub&gt;h&lt;/sub&gt; and decrease of a Ca&lt;sup&gt;2+&lt;/sup&gt; activated K&lt;sup&gt;+&lt;/sup&gt; current (I&lt;sub&gt;K,Ca&lt;/sub&gt;) results in depolarization of neuron, which activates another low-threshold Ca&lt;sup&gt;2+&lt;/sup&gt; spike. In this manner, I&lt;sub&gt;h&lt;/sub&gt; modulates frequency of oscillation. In addition, tonic activation of I&lt;sub&gt;h&lt;/sub&gt; also contributes to average membrane potential, and therefore to presence, strength, and frequency of oscillation&#xA;in these neurons.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the series of sub-questions - these are quite varied. Perhaps it is better to generate another one or two focused, well-formulated questions on this. For now, I will answer them curtly below. Further, the papers I linked contain a wealth of information, and the &lt;a href=&quot;http://jn.physiology.org/content/68/4/1384.full-text.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;McCormick &amp;amp; Huguenard (1992)&lt;/a&gt; paper is a detailed modeling study. Both papers are awesome and the authors are three of my all-time favorites so far.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;I want to know if these kind of oscillations are unique to some special kinds of neuron?&lt;/code&gt;&lt;br&gt;&#xA;&lt;strong&gt;Answer&lt;/strong&gt;: Yes quite unique, because I&lt;sub&gt;h&lt;/sub&gt; channels are quite unique (they have been called &quot;funny currents&quot;) and they are not present in every cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Is the control of oscillation parameter possible in every neurons and isolated neurons?&lt;/code&gt;&lt;br&gt;&#xA;&lt;strong&gt;Answer&lt;/strong&gt;: No, as the molecular machinery such as I&lt;sub&gt;h&lt;/sub&gt; channels may be lacking in most other cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Can a neuron or any other cell exhibit change in action potential independently?&lt;/code&gt;&lt;br&gt;&#xA;&lt;strong&gt;Answer&lt;/strong&gt;: That depends whether the cells are coupled through synapses or other means.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Do other cells except neuron and pacemaker cells exhibit oscillation?&lt;/code&gt;&lt;br&gt;&#xA;&lt;strong&gt;Answer&lt;/strong&gt;: Yes, some cells start to oscillate, for example in the degenerated retina (modeling work only) and there are non-neural cells that when cultured spontaneously start to oscillate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;Can a single neuron exhibit memory?&lt;/code&gt;&lt;br&gt;&#xA;&lt;strong&gt;Answer&lt;/strong&gt;: Yes, through long-term potentiation or depression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://jn.physiology.org/content/77/6/3145&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bal &amp;amp; McCormick, &lt;em&gt;J Neurophysiol&lt;/em&gt; (1997); &lt;strong&gt;77&lt;/strong&gt;:3145-56&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://jn.physiology.org/content/68/4/1384.full-text.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;McCormick &amp;amp; Huguenard, &lt;em&gt;J Neurophysiol&lt;/em&gt; (1992), &lt;strong&gt;68&lt;/strong&gt;(4): 1384-1400&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-25T12:42:12.073" LastActivityDate="2015-05-25T12:42:12.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34521" PostTypeId="1" AcceptedAnswerId="34523" CreationDate="2015-05-25T12:50:26.000" Score="7" ViewCount="249" Body="&lt;p&gt;&lt;em&gt;Myrmarachne plataleoides&lt;/em&gt;  is a jumping spider that mimics the Kerengga or weaver ant (&lt;em&gt;Oecophylla smaragdina&lt;/em&gt;) in both morphology and behaviour. However, the two sexes appear different:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oqfK4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;&lt;em&gt;Myrmarachne plataleoides&lt;/em&gt; (Female)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/beEds.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;&lt;em&gt;Myrmarachne plataleoides&lt;/em&gt; (Male)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some links suggest that in dimorphic arthropods the females more exactly mimic the model. Is this true? If so, why would this sex difference exist?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Phylogenetics_of_mimicry&quot; rel=&quot;nofollow noreferrer&quot;&gt;Phyologenetics of mimicry&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10294" LastEditorUserId="9943" LastEditDate="2015-05-26T03:46:28.950" LastActivityDate="2015-05-26T03:46:28.950" Title="Is Batesian mimicry more important for females?" Tags="&lt;entomology&gt;&lt;adaptation&gt;&lt;arachnology&gt;&lt;sexual-dimorphism&gt;&lt;antipredator-adaptation&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34522" PostTypeId="2" ParentId="15252" CreationDate="2015-05-25T13:12:13.017" Score="4" Body="&lt;p&gt;There are spontaneously firing neurons known as &lt;em&gt;intrinsically oscillatory neurons&lt;/em&gt;, or simply &lt;strong&gt;pacemaker neurons&lt;/strong&gt;. Under the right conditions these can fire action potentials in a rhythmic pattern without neuronal input. Examples are the thalamocortical relay neurons in the thalamus and inferior olive neurons. The basic mechanism is that a low-threshold Ca&lt;sup&gt;2+&lt;/sup&gt; current generates a small depolarization that in turn activates full-blown action potentials. In the recovery phase after the burst of action potentials, a &lt;em&gt;hyperpolarization-activated cation current&lt;/em&gt; is activated (I&lt;sub&gt;h&lt;/sub&gt;), which in turn depolarizes the neuron. This depolarization then initiates another Ca&lt;sup&gt;2+&lt;/sup&gt; current and the oscillation continues.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OHGtE.png&quot; alt=&quot;TC cell&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Thalamocortical cell with oscillatory behavior &lt;em&gt;in vivo&lt;/em&gt;. Source: &lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCUQFjAB&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fprofile%2FTerrence_Sejnowski%2Fpublication%2F14962878_Thalamocortical_oscillations_in_the_sleeping_and_aroused_brain%2Flinks%2F54a4aff80cf257a6360726ee.pdf&amp;amp;ei=Dh9jVZi_E9XV8gXagYLQDA&amp;amp;usg=AFQjCNFsYrKZbYtBMrsv-ouVw5vOFbuxQw&amp;amp;sig2=YlTbqiev3aIQ4xkRz7vWFQ&quot; rel=&quot;nofollow noreferrer&quot;&gt;Steriade et al. (1993)&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thalamocortical oscillations are thought to be imprtant in the generation of the slow-wave EEG seen in the early phases of sleep, as well as during &lt;em&gt;absence-epileptic&lt;/em&gt; seizures (&lt;em&gt;petite mal&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;https://www.google.com.au/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=2&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCUQFjAB&amp;amp;url=http%3A%2F%2Fwww.researchgate.net%2Fprofile%2FTerrence_Sejnowski%2Fpublication%2F14962878_Thalamocortical_oscillations_in_the_sleeping_and_aroused_brain%2Flinks%2F54a4aff80cf257a6360726ee.pdf&amp;amp;ei=Dh9jVZi_E9XV8gXagYLQDA&amp;amp;usg=AFQjCNFsYrKZbYtBMrsv-ouVw5vOFbuxQw&amp;amp;sig2=YlTbqiev3aIQ4xkRz7vWFQ&quot; rel=&quot;nofollow noreferrer&quot;&gt;Steriade et al., &lt;em&gt;Science&lt;/em&gt; (1993); &lt;strong&gt;162&lt;/strong&gt;: 679-85&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2019-07-27T20:33:37.310" LastActivityDate="2019-07-27T20:33:37.310" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="34523" PostTypeId="2" ParentId="34521" CreationDate="2015-05-25T14:05:17.057" Score="5" Body="&lt;p&gt;In sexually dimorphic ant-mimicking spiders, it depends on the specific species which sex resembles the ant most &lt;a href=&quot;http://www.hindawi.com/journals/psyche/2012/151989/&quot; rel=&quot;nofollow&quot;&gt;(Cushing, 2012)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In many cases of sexually dimorphic spider myrmecomorphs, the male is more mimetic than the female, such as in &lt;em&gt;Corinnidae&lt;/em&gt; species and the genus &lt;em&gt;Castianeira&lt;/em&gt;, &lt;em&gt;Oonopidae&lt;/em&gt; and &lt;em&gt;Antoonops&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such sexual dimorphism may be adaptive if the sexes are exposed to different predation pressures. The spider's mimicry of noxious ant species yields protective benefit from predators who would avoid the ants. However, the mimicry often results in being more conspicuous in their color markings than related spider species that are more camouflaged. Hence, conspicuousness can be considered a cost of Batesian mimicry. A palatable species may be evolutionary maximizing its level of protection for the smallest cost (in terms of conspicuousness). Sexual dimorphism, in which the more &lt;strong&gt;active sex&lt;/strong&gt; (which, in spiders, is &lt;strong&gt;typically the males&lt;/strong&gt;) evolves mimetic resemblance to noxious ants, whereas the other sex remains relatively more concealed and camouflaged behaviorally and morphologically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.hindawi.com/journals/psyche/2012/151989/&quot; rel=&quot;nofollow&quot;&gt;Cushing, &lt;em&gt;psyche&lt;/em&gt; (2012); &lt;strong&gt;151989&lt;/strong&gt;: 1-24&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-26T00:28:12.803" LastActivityDate="2015-05-26T00:28:12.803" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="34526" PostTypeId="2" ParentId="34518" CreationDate="2015-05-25T16:44:11.120" Score="1" Body="&lt;p&gt;It will depend on the drug you are using. There is a pathway that forms the translational initiation complex that starts with binding the mRNA's cap, the small subunit scans to find the AUG, then the large subunit binds, and so on. The 80 S peaks on the density gradients are not vacant, they are poised on mRNAs waiting to initiate (if you removed the inhibitor).&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-05-25T16:44:11.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34527" PostTypeId="1" AcceptedAnswerId="34530" CreationDate="2015-05-25T17:45:56.987" Score="2" ViewCount="61" Body="&lt;p&gt;This may be better suited for the English language SE, but When discussing evolutionary changes in species is it proper to refer to their phenotypes? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this context:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Imagine if a cow did not have to cart around however many gallons of&#xA;  culture nor expend personal time and effort into chewing its cud. It&#xA;  could lose all that anatomy and energy expenditure from its phenotype.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;it could just be me, but it sounds strange using it in that context.&lt;/p&gt;&#xA;" OwnerUserId="15910" LastActivityDate="2015-05-25T18:57:08.573" Title="Evolution and Phenotypes." Tags="&lt;evolution&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34529" PostTypeId="1" CreationDate="2015-05-25T18:33:39.647" Score="0" ViewCount="1328" Body="&lt;p&gt;No my study books says about that no Q waves in WPW syndrome.&#xA;They are about wide QRS complex often however. &#xA;I heard today that the characteristic property of WPW is often a missing Q wave, like here&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZEc2X.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is caused by the presence of an abnormal accessory electrical conduction pathway between the atria and the ventricles. &#xA;However, some books are about delta waves which is characteristic in the above picture. &#xA;However, it is many times very difficult to see. &#xA;These missing Q waves are however much easier when PRS complexes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How much false positives do you get if you categorize all missing Q waves and PRS complexes as WPW syndrome?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How characteristic is the missing Q wave for WPW syndrome?&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2015-05-25T20:01:06.070" Title="Is missing Q wave characteristic for Wolff-Parkinson-White Syndrome?" Tags="&lt;cardiology&gt;&lt;electrophysiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34530" PostTypeId="2" ParentId="34527" CreationDate="2015-05-25T18:57:08.573" Score="4" Body="&lt;p&gt;Yes, absolutely. That's what a phenotype is (definition from the &lt;a href=&quot;http://www.biology-online.org/dictionary/Phenotype&quot; rel=&quot;nofollow&quot;&gt;biology online dictionary&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;noun, plural: phenotypes&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(1) The physical appearance or biochemical characteristic of an&#xA;  organism as a result of the interaction of its genotype and the&#xA;  environment.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;(2) The expression of a particular trait, for example, skin color,&#xA;  height, behavior, etc., according to the individual’s genetic makeup&#xA;  and environment.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I don't see anything strange in the sentence you quoted. It is phenotypes that are selected for. Genotype differences that don't affect phenotype will have no selective advantage (or disadvantage) and cannot be acted upon by evolutionary forces. What else would you use when discussing evolutionary changes? That's what the word &lt;em&gt;phenotype&lt;/em&gt; is for. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2015-05-25T18:57:08.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34532" PostTypeId="2" ParentId="34529" CreationDate="2015-05-25T20:01:06.070" Score="3" Body="&lt;p&gt;In Wolff-Parkinson-White syndrome, the normal Q wave is usually masked by the preexcitation action potential which produces the delta wave. Despite this, missing Q wave is not a diagnosis criteria of the syndrome, and up to 70 percent of the patients show a negative delta wave which causes differential diagnosis problems because it is confused with Q, according to &lt;a href=&quot;http://www.emedu.org/ecg/wpw.htm&quot; rel=&quot;nofollow&quot;&gt;Emergency Electrocardiography&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When the delta wave is negative, this simulates a Q-wave. This is known as a pseudo-infarction pattern, and is seen in up to 70% of patients with WPW.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And this negative delta wave also helps in determining action potential origin, according to &lt;a href=&quot;http://emedicine.medscape.com/article/159222-workup#4&quot; rel=&quot;nofollow&quot;&gt;Medscape&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A general rule is that Q waves (negative delta waves) point away from the earliest site of ventricular activation, which is typically the insertion point of the bypass tract.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;No, you can't categorize PRS complexes as WPW syndrome. In fact there is no PRS complex. A classic ECG of WPW will show a shortened PR segment and a widened QRS (or RS or RSr' or however it looks) complex.&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2015-05-25T20:01:06.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34533" PostTypeId="1" CreationDate="2015-05-25T20:46:14.320" Score="2" ViewCount="2389" Body="&lt;p&gt;Whenever I feel a little light headed or tired, it helps to eat something sweet.&#xA;Specifically, simply chewing or sucking on a sweet seems to aleviate the symptoms within a matter of seconds and then the sugar seems to kick in. So I was wondering whether it is just a psychological effect, or whether sugars are absorbed in our mouth and reach the brain (or wherever the sugars exert their effects?) within seconds. Or is perhaps the &lt;em&gt;taste of sugar&lt;/em&gt; sufficient to signal the body that it can safely release some extra energy as resupply is imminent? &lt;/p&gt;&#xA;" OwnerUserId="15914" LastEditorUserId="9943" LastEditDate="2015-05-26T03:20:45.203" LastActivityDate="2015-05-26T03:20:45.203" Title="Can sugar be absorbed orally within seconds?" Tags="&lt;digestive-system&gt;&lt;blood-sugar&gt;" AnswerCount="1" CommentCount="6" ClosedDate="2015-05-25T22:15:33.327" ContentLicense="CC BY-SA 3.0" />
  <row Id="34534" PostTypeId="2" ParentId="34533" CreationDate="2015-05-25T20:56:35.577" Score="1" Body="&lt;p&gt;Yes we do. The first part of digestion starts in mouth. Digestion begins in the mouth, where chemical and mechanical digestion occurs. Saliva  produced by the salivary glands (located under the tongue and near the lower jaw), is released into the mouth. Saliva begins to break down the food, moistening it and making it easier to swallow. A digestive enzyme (amylase) in the saliva begins to break down the carbohydrates (starches and sugars). &lt;/p&gt;&#xA;" OwnerUserId="15874" LastActivityDate="2015-05-25T20:56:35.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34535" PostTypeId="1" CreationDate="2015-05-25T21:30:30.490" Score="6" ViewCount="17566" Body="&lt;p&gt;The word cosmid is derived from cos sites of lambda phages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why are cos sites called cos sites? What does this &quot;cos&quot; refer to?&lt;/p&gt;&#xA;" OwnerUserId="15915" LastEditorUserId="57" LastEditDate="2015-05-25T23:35:36.300" LastActivityDate="2021-01-27T12:51:40.983" Title="Where does the term &quot;cos site&quot; come from?" Tags="&lt;genetics&gt;&lt;terminology&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34536" PostTypeId="2" ParentId="34535" CreationDate="2015-05-25T21:50:24.350" Score="2" Body="&lt;p&gt;The 12 bp overlapping sticky ends at the termini of pure lambda DNA are generated during DNA packaging. Another term for this complementary base-pairing is &quot;cohesive&quot; and so cos is an abbreviation of that term. I believe it was italicized because it could also be mapped genetically. Scott Emmons is credited with coining this term (and using it first) when he was a grad student at Stanford.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-05-25T21:50:24.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34537" PostTypeId="2" ParentId="34535" CreationDate="2015-05-25T21:50:44.837" Score="1" Body="&lt;p&gt;Cos is for &quot;cohesive,&quot; as in these sites rather easily recircularize the linear phage DNA through complementary base-pairing (they're &lt;strong&gt;sticky ends&lt;/strong&gt;, generally G-C rich). See &lt;a href=&quot;http://en.wikipedia.org/wiki/Lambda_phage#Infection&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-05-25T21:50:44.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34538" PostTypeId="2" ParentId="34535" CreationDate="2015-05-25T21:53:08.947" Score="5" Body="&lt;p&gt;&amp;quot;Cos&amp;quot; is the abbreviation of &amp;quot;&lt;strong&gt;co&lt;/strong&gt;hesive end &lt;strong&gt;s&lt;/strong&gt;ite&amp;quot;. This is a speciality of the lambda phage which has to be linearized to fit into the phages head, but circularizes in the host cell. To achieve this, it has the cohesive (or sticky) sites at each end.&lt;/p&gt;&#xA;&lt;p&gt;See &lt;a href=&quot;http://ecoliwiki.net/colipedia/index.php/Phage_lambda&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and also the publication by Allan Campbell on &amp;quot;&lt;a href=&quot;http://web.archive.org/web/20190713121529/http://www.microinmuno.qb.fcen.uba.ar/03-Bacteriophage.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bacteriophages&lt;/a&gt;&amp;quot;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2021-01-27T12:51:40.983" LastActivityDate="2021-01-27T12:51:40.983" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="34539" PostTypeId="1" AcceptedAnswerId="34677" CreationDate="2015-05-26T00:04:57.340" Score="6" ViewCount="74" Body="&lt;p&gt;I had a quick look online. There seems to exist many different website of database archiving. Some data might be free of charge while some others might not be. I found things such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Dryad_(repository)&quot; rel=&quot;nofollow&quot;&gt;Dryad&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/TreeBASE&quot; rel=&quot;nofollow&quot;&gt;TreeBase&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/DataONE&quot; rel=&quot;nofollow&quot;&gt;DataOne&lt;/a&gt; or &lt;a href=&quot;http://en.wikipedia.org/wiki/GenBank&quot; rel=&quot;nofollow&quot;&gt;GeneBank&lt;/a&gt;. I think that several journals (American Naturalist, Molecular Ecology, Science and Nature for examples) force their authors to make their data available&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;General Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you make a short review of what different database exist, what are their properties (what kind of data, what license and fees) and how to seek for data (are datasets associated to keywords or do we have to look for a paper and then look for their data).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Case study&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine for example, you are looking for SNP data of a spatially explicit population that recently underwent a range expansion (might be too accurate, you may want to drop down some specifications). How would you go about to look for this kind of data? (No need to pull out data but only to describe a procedure).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-05-27T04:07:01.473" LastActivityDate="2015-05-29T06:20:30.797" Title="How to seek for available genetic data relevant to ecology and evolution?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;ecology&gt;&lt;population-genetics&gt;&lt;database&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34540" PostTypeId="1" AcceptedAnswerId="34541" CreationDate="2015-05-26T02:16:59.900" Score="1" ViewCount="46" Body="&lt;p&gt;I have this phenomenon that the human 18S rRNA reverse transcribed with polydT oligos serve as faithful RTPCR normalizers, tested with better known house keepers. I want to know what I'm amplifying exactly, so where can I find the reference sequence for mammalian rRNAs?&lt;/p&gt;&#xA;" OwnerUserId="15321" LastActivityDate="2015-05-26T04:21:14.920" Title="18S rRNA sequence" Tags="&lt;pcr&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34541" PostTypeId="2" ParentId="34540" CreationDate="2015-05-26T04:21:14.920" Score="1" Body="&lt;p&gt;If you're looking for reference sequences, RefSeq is a good bet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/?term=18S+ribosomal+RNA+AND+srcdb_refseq%5BPROP%5D&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/nuccore/?term=18S+ribosomal+RNA+AND+srcdb_refseq%5BPROP%5D&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-05-26T04:21:14.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34542" PostTypeId="1" AcceptedAnswerId="34557" CreationDate="2015-05-26T04:47:56.460" Score="18" ViewCount="991" Body="&lt;p&gt;&lt;strong&gt;Argument favouring learning:&lt;/strong&gt;&lt;br&gt;&#xA;A newborn sleeps for 20-22 hours. But overtime (s)he learns to focus sleeping time to night time, according to his or her needs and family needs. Some sleep from 1 am to 7 am, some from 11pm to 5 am. So it is learnt.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Argument favouring a genetic origin:&lt;/strong&gt;&lt;br&gt;&#xA;Somewhere I read (I don't exactly remember the article) where it was told that the biological clock is not of 24, but of 25 hours. This means that the synchronisation is not maintained with the earth. If it would be learnt, then why is it not in synchrony with the world? &lt;/p&gt;&#xA;" OwnerUserId="15919" LastEditorUserId="9943" LastEditDate="2015-05-26T12:57:43.610" LastActivityDate="2016-03-22T08:48:36.257" Title="Is the human biological clock genetically programmed or learnt?" Tags="&lt;genetics&gt;&lt;circadian-rhythms&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34544" PostTypeId="1" AcceptedAnswerId="34556" CreationDate="2015-05-26T06:03:31.550" Score="7" ViewCount="1066" Body="&lt;p&gt;We often associate Africa as the geographical location of the origin of humans. Why cannot there exist multiple geographic locations of origin (given same environmental conditions)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The same argument exists for other species as well. So what is the basis of the common ancestor (from single geographical location) theory?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please give me references so that I can read more on this subject. &lt;/p&gt;&#xA;" OwnerUserId="5669" LastEditorUserId="3624" LastEditDate="2015-05-26T12:18:15.030" LastActivityDate="2017-03-23T04:50:11.673" Title="Why cannot there be multiple sources for same species origins?" Tags="&lt;evolution&gt;&lt;phylogenetics&gt;&lt;speciation&gt;&lt;human-evolution&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34545" PostTypeId="1" AcceptedAnswerId="34555" CreationDate="2015-05-26T07:53:52.663" Score="0" ViewCount="65" Body="&lt;p&gt;Considering the Metabolic Pathway:&lt;br&gt;&#xA;&lt;a href=&quot;http://www.genome.jp/kegg-bin/show_module?M00166&quot; rel=&quot;nofollow&quot;&gt;http://www.genome.jp/kegg-bin/show_module?M00166&lt;/a&gt; &lt;br&gt;&lt;br&gt;&#xA;Consider the reaction R01523(the very first reaction). How is it possible to know that the compound  C00199(D-Ribulose 5-phosphate) will get transformed to C01182(D-Ribulose 1,5-bisphosphate)? &lt;br&gt;&lt;br&gt;What are the factors on which this transformation depends?One factor I know is structure but how does structure effect this transformation? Does two similar structured compound means that one of the compound can get transformed to the other one?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="8835" LastEditDate="2015-05-26T08:10:56.990" LastActivityDate="2015-05-26T11:35:54.153" Title="Factors on which one compound transforming to another compound depend" Tags="&lt;organic-chemistry&gt;&lt;biochemistry&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2015-05-28T05:41:28.253" ContentLicense="CC BY-SA 3.0" />
  <row Id="34546" PostTypeId="1" AcceptedAnswerId="34552" CreationDate="2015-05-26T08:40:18.893" Score="28" ViewCount="21304" Body="&lt;p&gt;Why is it when someone comes into contact with an electrical supply that their body freezes up and is unable to move away from the electrical source?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone explain this through a physiological perspective?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="3971" LastEditDate="2015-05-26T21:15:01.450" LastActivityDate="2017-01-24T15:08:37.587" Title="Why does an electrical shock freeze up muscles?" Tags="&lt;physiology&gt;&lt;muscles&gt;&lt;electrical-stimulation&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34547" PostTypeId="1" AcceptedAnswerId="34551" CreationDate="2015-05-26T08:45:42.367" Score="2" ViewCount="954" Body="&lt;p&gt;Heterozygous organisms profit from pairs of gene alleles. Harmful alleles when being recessive can be carried without any harm for the organism. Only when two harmful recessive alleles form a gene the negative effect is produced. As described in wiki article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Allele#Allelic_dominance_in_genetic_disorders&quot; rel=&quot;nofollow&quot;&gt;allele&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A number of genetic disorders are caused when an individual inherits two &lt;strong&gt;recessive&lt;/strong&gt; alleles for a single-gene trait. Recessive genetic disorders include Albinism, Cystic Fibrosis, Galactosemia, Phenylketonuria (PKU), and Tay-Sachs Disease. Other disorders are also due to recessive alleles, but because the gene locus is located on the X chromosome, so that males have only one copy (that is, they are hemizygous), they are more frequent in males than in females. Examples include red-green color blindness and Fragile X syndrome.    &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But some illnesses are carried by dominant alleles (from the same article):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Other disorders, such as Huntington disease, occur when an individual inherits only one &lt;strong&gt;dominant&lt;/strong&gt; allele.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My questions are: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;How does harm from alleles correlate with their recessiveness? Generally speaking, do harmful alleles tend to be more recessive?&lt;/li&gt;&#xA;&lt;li&gt;How does benefits from alleles correlate with their dominance? Generally speaking, do &quot;beneficial&quot; alleles tend to be more dominant?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="15922" LastActivityDate="2015-05-26T17:26:42.080" Title="Recessiveness of allele for protection of organism" Tags="&lt;genetics&gt;&lt;human-genetics&gt;&lt;allele&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34549" PostTypeId="2" ParentId="34546" CreationDate="2015-05-26T09:11:39.997" Score="12" Body="&lt;p&gt;When the body comes in contact with an electrical power supply, two things can happen. If the current flow is high enough, the body heats up just like a heating resistor, and opposed to the resistor, the body can't handle the heat, thus severe burns occur after electric shock.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if the current is low enough not to burn &quot;the conductor&quot; other effects are visible. The nervous system tissue has the best conductor properties from the body. More than that, it works with action potentials, which are small chemical generated currents. When an external current gets to a nervous fiber, the fiber will conduct electricity further to the efector tissue (muscle in this case).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If electric current of sufficient magnitude is conducted through a living creature (human or otherwise), its effect will be to override the tiny electrical impulses normally generated by the neurons, overloading the nervous system and preventing both reflex and volitional signals from being able to actuate muscles. Muscles triggered by an external (shock) current will involuntarily contract, and there's nothing the victim can do about it.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The result is a powerful contraction of the muscle. But the question is what muscular groups contract? Well, all that are under the influence of a nerve under electric shock. And from here comes the freeze effect, because antagonist muscular groups contract simultaneously (for example flexor and extensor, adductor and abductor muscles in the same time). The result of this forced contraction tends to move parts of the body as dictated by the muscles that are more powerful.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The forearm muscles responsible for bending fingers tend to be better developed than those muscles responsible for extending fingers, and so if both sets of muscles try to contract because of an electric current conducted through the person's arm, the &quot;bending&quot; muscles will win, clenching the fingers into a fist.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can read more on &lt;a href=&quot;http://www.allaboutcircuits.com/vol_1/chpt_3/2.html&quot;&gt;All About Circuits&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6422" LastActivityDate="2015-05-26T09:11:39.997" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34550" PostTypeId="2" ParentId="34547" CreationDate="2015-05-26T10:42:15.630" Score="0" Body="&lt;p&gt;Harmful alleles can be both recessive or dominant. They do not tend to be more recessive or more dominant. But, you must look at it from a population genetics point of view. When a allele is dominant, it tends to be a highly selected for trait, an analogy of this would be black eyes are a dominant trait compared to blue eyes or green eyes, which is why you see so many people with black eyes in the world than blue. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So therefore dominant alleles are highly selected than recessive ones and when a dominant trait is harmful, the subject tends to get killed off or the line is destroyed in the process by the natural course of reproduction. What remains are recessive alleles which do not get a chance to attain recessiveness and are therefore carried forward by evolution as passenger, never expressing themselves until they get the chance to attain homozygous recessive state.&lt;/p&gt;&#xA;" OwnerUserId="15807" LastActivityDate="2015-05-26T10:42:15.630" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34551" PostTypeId="2" ParentId="34547" CreationDate="2015-05-26T10:51:59.123" Score="2" Body="&lt;p&gt;Instead of dividing mutations into two classes, dominant vs. recessive, consider categorizing them into classes based on how the mutation affects the gene--or the gene product.  This yields loss-of-function (&lt;em&gt;lf&lt;/em&gt;) alleles, that reduce the activity of the gene, or its product, and gain-of-function (&lt;em&gt;gf&lt;/em&gt;) alleles that act as if they somehow increase the activity of the gene, or its product. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The logic underlying this classification was described in this classic reference: Muller, H. J. 1932. Further studies on the nature and causes of gene mutations. Proceedings of the 6th International Congress of Genetics, pp. 213–255.  Since this was before DNA had been shown to be the genetic material his arguments are based solely on the phenotype of animals carrying various combinations of chromosomes.  In particular he relies on genetic duplications and deficiencies (or deletions).  In this nomenclature &lt;em&gt;+&lt;/em&gt; indicates a chromosome carrying a wild-type (&lt;em&gt;wt&lt;/em&gt;) allele of the gene, and &lt;em&gt;m&lt;/em&gt; indicates a chromosome carrying a mutant allele of the gene.  So if an &lt;em&gt;+&lt;/em&gt;/&lt;em&gt;m&lt;/em&gt; animal appears Wild-Type then that allele is recessive.  Similarly, if an &lt;em&gt;+&lt;/em&gt;/&lt;em&gt;m&lt;/em&gt; animal has a Mutant phenotype then the allele is dominant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two types of &lt;em&gt;lf&lt;/em&gt; alleles: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;a hypomorph is a partial reduction in function and retains some residual gene function (e.g., a weak missense mutation, or a temperature-sensitive (&lt;em&gt;ts&lt;/em&gt;) mutation. A hypomorph is recessive to a &lt;em&gt;wt&lt;/em&gt; allele.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;an amorph is what we would call a true genetic and molecular null allele, a complete knockout of the gene, where there is no measurable function left (e.g., a nonsense mutation early in the protein coding region, or a small deletion that only removes a single gene).  Amorphs are normally recessive to a &lt;em&gt;wt&lt;/em&gt; allele (but see below for an exception)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;There are three types of &lt;em&gt;gf&lt;/em&gt; alleles:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;a hypermorph that elevates the level of the &lt;em&gt;wt&lt;/em&gt; gene function (e.g., a promoter mutation that removes a negative regulatory site, leading to increased expression). Hypermorphs are dominant.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;an antimorph, or so-called dominant-negative (&lt;em&gt;dn&lt;/em&gt;) allele that produces a mutant gene product that somehow interferes with the &lt;em&gt;wt&lt;/em&gt; gene product (think poison product as one model). Antimorphs are always dominant over &lt;em&gt;wt&lt;/em&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;a neomorph, an allele the results in a completely new gene function (e.g., if a glycolytic enzyme acquired sequence-specific DNA-binding activity, perhaps from a gene fusion event(?)). Neomorphic alleles are extremely rare and almost always dominant over wt.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So we have a straightforward mapping of &lt;em&gt;lf&lt;/em&gt; alleles to recessive phenotypes, and &lt;em&gt;gf&lt;/em&gt; alleles to dominant phenotypes.  However there is an important exception to this simple scheme for genes that are dose-sensitive, or haploinsufficient. These are dominant &lt;em&gt;lf&lt;/em&gt; alleles. For example, when halving the level of the gene product causes a mutant phenotype: &lt;em&gt;+&lt;/em&gt;/&lt;em&gt;null&lt;/em&gt;. Some well-known examples from the developmental genetics of model organisms are the &lt;em&gt;Ubx&lt;/em&gt; gene, and the &lt;em&gt;Notch&lt;/em&gt; gene from &lt;em&gt;D. melanogaster&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further discussion of these terms can also be found in &lt;a href=&quot;http://en.wikipedia.org/wiki/Muller%27s_morphs&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="14946" LastEditDate="2015-05-26T17:26:42.080" LastActivityDate="2015-05-26T17:26:42.080" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34552" PostTypeId="2" ParentId="34546" CreationDate="2015-05-26T11:07:19.537" Score="35" Body="&lt;p&gt;Interesting question!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An important factor here is the &lt;strong&gt;let-go phenomenon&lt;/strong&gt;, which is defined as the current level in the arm that will cause the hand to involuntarily grip the current source. When the fingers are wrapped around a large cable, most adults will be able to let go with a current of less than 6 mA. At 22 mA, however, more than 99% of adults will not be able to let go. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nearly all cases of inability to let go involve alternating current. Alternating current repetitively stimulates nerves and muscles, resulting in a &lt;strong&gt;tetanic (sustained) contraction&lt;/strong&gt; that lasts as long as the contact is continued. If this leads to the subject tightening his or her grip on a conductor, the result is continued electric current flow through the person and lowered contact resistance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that the &lt;strong&gt;current flow&lt;/strong&gt; in the forearm &lt;strong&gt;stimulates both the muscles of flexion and extension&lt;/strong&gt;, it seems surprising that one cannot let go. However, the &lt;strong&gt;muscles of flexion are stronger&lt;/strong&gt;, making the person unable to voluntarily let go (similar to the fact that a crocodile's jaws can be kept shut with your bare hands, but one should better not attempt to keep them open like that...). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Direct currents below 300 mA have no let-go phenomenon, because the hand is not involuntarily clamped.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several different outcomes may occur when a person grasps a conductor giving &lt;strong&gt;10 kV AC&lt;/strong&gt; hand-to-hand voltage. Within 10 to 100 milliseconds, muscles in the current path will strongly contract. The person may grasp the conductor more tightly. However, mostly subjects are propelled away from the contact, likely due to generalized muscle contractions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763825/&quot; rel=&quot;nofollow&quot;&gt;Fish &amp;amp; Geddes, &lt;em&gt;J Plastic Surg&lt;/em&gt; (2009); &lt;strong&gt;9&lt;/strong&gt;: 407-21&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-02-23T23:20:59.273" LastActivityDate="2016-02-23T23:20:59.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34553" PostTypeId="5" CreationDate="2015-05-26T11:15:39.157" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2015-05-26T11:15:39.157" LastActivityDate="2015-05-26T11:15:39.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34554" PostTypeId="4" CreationDate="2015-05-26T11:15:39.157" Score="0" Body="Electrical stimulation of the human body can be applied to restore bodily functions. Notable examples are auditory and visual prostheses to make the deaf hear and the blind see, and functional electrical stimulation to make the limp walk. It can be used for diagnosis (e.g., electromyography). Also, electrical stimulation can be used to treat (mental) illnesses (electrotherapy). Lastly, it can be the cause of injuries (e.g., due to a lightning strike).  " OwnerUserId="9943" LastEditorUserId="3340" LastEditDate="2015-06-04T10:17:04.973" LastActivityDate="2015-06-04T10:17:04.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34555" PostTypeId="2" ParentId="34545" CreationDate="2015-05-26T11:35:54.153" Score="0" Body="&lt;p&gt;From my answer on &lt;a href=&quot;https://chemistry.stackexchange.com/questions/32012/factors-on-which-one-compound-transforming-to-another-compound-depend/32016#32016&quot;&gt;chemistry&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After looking at the website I found the reaction is based off of an enzyme called: &lt;a href=&quot;http://www.genome.jp/dbget-bin/www_bget?ec:2.7.1.19&quot; rel=&quot;nofollow noreferrer&quot;&gt;phosphoribulokinase&lt;/a&gt;. In biological systems many reactions occur under the auspice of enzymes or proteins. These are incredibly large molecules made of an extremely long chain of amino acids which are a set of 26 or so small molecules that can 'hook' into the chain structure of a protein. Each amino acid has different properties and thus experiences different forces pulling it towards and away from other amino acids on the chain. What this means is the whole chain folds up into an extremely complex structure. For a protein to allow a reaction to occur it has a small region that the reacting molecule can hook into. There are then sets of atoms and molecules that act as scaffolds that allow atoms in the reacting molecule to be moved without the need for nearly as much energy as would be required without the scaffold. Now this is how it changes structure. Now whilst the protein can just as easily allow the molecule produced to be converted back to the original, this may be less energetically favourable which brings us to equilibrium chemistry involving dynamic forward and backward reactions. What makes this more complicated is that proteins often have separate 'hooks' for molecules to disable them. That is if a lot of substance A is around then the protein will be disabled and no longer convert B into A until more A is consumed and thus stops inhibiting the protein.&lt;/p&gt;&#xA;" OwnerUserId="9276" LastEditorUserId="-1" LastEditDate="2017-04-13T12:57:01.693" LastActivityDate="2015-05-26T11:35:54.153" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34556" PostTypeId="2" ParentId="34544" CreationDate="2015-05-26T11:39:04.677" Score="7" Body="&lt;p&gt;This is a very fundamental, and in my opinion, interesting question. You might not find many sources that directly cover this question because it is hard to test. If speciation did happen in two separate locations and the resulting species were so similar that they could breed with one another and not the original species, how would we be able to tell if the species originated in separate locations and that the new species didn't just travel to the new location? Below I'll try and explain why it's safe to assume they probably didn't have different locations for speciation.&lt;/p&gt;&#xA;&lt;h1&gt;Thought Experiment&lt;/h1&gt;&#xA;&lt;p&gt;Here is what happened in hypothetical land. Species X exists in &lt;em&gt;happy land&lt;/em&gt;. Individuals of X then move to &lt;em&gt;water land&lt;/em&gt;. Some more individuals from X move from &lt;em&gt;happy land&lt;/em&gt; to &lt;em&gt;H2O land&lt;/em&gt; (very similar to &lt;em&gt;water land&lt;/em&gt;). Species X undergoes speciation in &lt;em&gt;water land&lt;/em&gt; to species Y and speciation of X also occur in the &lt;em&gt;H2O land&lt;/em&gt; to species Z.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Can Z and Y be the same species with different origins where the niche conditions are the same?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;As you can imagine, the longer after geographical isolation the more mutations occur and the less likely it is that the new species will be able to breed successfully with similar species.&lt;/p&gt;&#xA;&lt;p&gt;Although the two environments may seem identical, ecology is notoriously complex and chaotic, and so in reality as far as ecology is concerned, they are very different environments. Even the &lt;em&gt;&lt;strong&gt;slightest difference between niches will naturally select different traits&lt;/strong&gt;&lt;/em&gt; that could make Z and Y sexually incompatible.&lt;/p&gt;&#xA;&lt;p&gt;Furthermore, when dealing with the geographical origin, you must assume that there was geographical isolation between the two speciation event locations. Since there is typically no contact between Z and Y species, there is &lt;em&gt;&lt;strong&gt;no selective pressure to remain genetically compatible&lt;/strong&gt;&lt;/em&gt; and given enough time, they will become unable to breed.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;h1&gt;Humans&lt;/h1&gt;&#xA;&lt;p&gt;There is a &lt;a href=&quot;http://www.nature.com/news/2009/090828/full/news.2009.870.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;contentious claim&lt;/a&gt; that ancient humans bred with chimpanzees after both speciation events from our common ancestor to humans and chimpanzees. Broadly I think this has now been dismissed. However, it is reasonably well accepted that in a more recent &amp;quot;Tolkien-esque&amp;quot; world &lt;a href=&quot;http://www.newscientist.com/article/dn26435-thoroughly-modern-humans-interbred-with-neanderthals.html#.VWRmRS_v32Y&quot; rel=&quot;nofollow noreferrer&quot;&gt;humans bred with Neanderthals&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;But ultimately I don't think there is a single example &lt;em&gt;(I am thoroughly open to being proven wrong!)&lt;/em&gt; in the natural world of two similar geographical isolation events driving exactly the same species to evolve and both versions of the new species are more genetically similar to one another than they are to the origin species. The odds are just too slim even if to us the conditions seem identical.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2017-03-23T04:50:11.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34557" PostTypeId="2" ParentId="34542" CreationDate="2015-05-26T11:53:34.520" Score="15" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;The biological master clock is neurologically and genetically hardwired. The biological clock is not affected by learning. Instead, it is constantly entrained mainly by daylight.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The biological clock is hardwired in the human body and can be traced back to the master clock in the &lt;strong&gt;suprachiasmatic nuclei&lt;/strong&gt; (SCN) of the hypothalamus (Fig. 1). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/22uDJ.png&quot; alt=&quot;SCN&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. The SCN is entrained by environmental light captured by the retina in the eyes. Source: &lt;a href=&quot;http://neurosciencenews.com/genetics-circadian-rhythm-rna-1229/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Neuroscience News&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The SCN is an &lt;strong&gt;intrinsic oscillator&lt;/strong&gt; that governs sleep and wake timing, rhythms of temperature, hormones, mood and cognitive acuity etc. etc. These rhythms are &lt;strong&gt;entrained to 24 hours&lt;/strong&gt; by the environmental &lt;strong&gt;light-dark cycle&lt;/strong&gt; primarily via a subset of photosensitive retinal ganglion cells that project directly to the SCN (Fig. 1). Using hormones and neuronal signals, the SCN entrains peripheral clocks of similar molecular mechanism present in many tissues &lt;a href=&quot;http://www.plosone.org/article/related/info%3Adoi%2F10.1371%2Fjournal.pone.0013376&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Pagani et al., 2010)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In humans and other organisms, the timing of 24-hour behavior is governed by the period length of the circadian oscillator. This period is &lt;strong&gt;approximately&lt;/strong&gt;, but not exactly, &lt;strong&gt;24 hours&lt;/strong&gt; long (&lt;strong&gt;&lt;em&gt;circa diem&lt;/em&gt;&lt;/strong&gt;), and ranges from 23.47–24.64 across people (23 hours 28 min to 24 hours 38 minutes) in laboratory conditions &lt;a href=&quot;http://www.plosone.org/article/related/info%3Adoi%2F10.1371%2Fjournal.pone.0013376&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Pagani et al., 2010)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why is it &lt;em&gt;circa diem&lt;/em&gt; and not exactly 24 hours?&lt;/strong&gt; Note that the absolute length of a day depends on the definition used. For example, one complete rotation of the earth around its axis (&lt;a href=&quot;http://www.physics.unlv.edu/~lepp/classes/ast103/s1small.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;the &lt;em&gt;sidereal day&lt;/em&gt;&lt;/a&gt;) actually takes &lt;a href=&quot;http://www.universetoday.com/14700/how-long-is-a-day-on-earth/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;23 hours, 56 minutes and 4.1 seconds&lt;/strong&gt;&lt;/a&gt;. The &lt;a href=&quot;http://www.universetoday.com/14700/how-long-is-a-day-on-earth/&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;solar day&lt;/em&gt;&lt;/a&gt; is 24 hours and is defined by the time it takes the sun to make an apparent circuit across the skies. More importantly, there is &lt;strong&gt;apparent solar time&lt;/strong&gt;, sometimes called &lt;strong&gt;true solar time&lt;/strong&gt;, which is determined by the daily apparent motion of the observed sun. It is based on the interval between two successive returns of the sun to the local meridian. The length of a solar day varies throughout the year, and the accumulated effect of these variations (equation of time) produces seasonal deviations of up to &lt;strong&gt;16 minutes&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.atmo.arizona.edu/students/courselinks/fall12/atmo336/lectures/sec4/seasons.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;length of a day&lt;/a&gt; can also be defined in the &lt;strong&gt;number or hours from sunrise to sunset&lt;/strong&gt;, which varies where you are on earth. At the equator every day of the year is exactly 12 hours long. At 50° latitude (e.g., &lt;a href=&quot;http://en.wikipedia.org/wiki/50th_parallel_north&quot; rel=&quot;nofollow noreferrer&quot;&gt;England &amp;amp; Canada&lt;/a&gt;) the longest day is 16.5 hours and the shortest day 7.5 hours. At 35° latitude (e.g. many US states and Greece) the longest day is 14.5 hours and the shortest day 9.5 hours. Given that light is the most effective way to entrain the circadian rhythm, it is obvious why the &lt;em&gt;absolute length of the intrinsic circadian rhythm&lt;/em&gt; is not important. As long as it is &lt;em&gt;circa diem&lt;/em&gt;, it will do.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.plosone.org/article/related/info%3Adoi%2F10.1371%2Fjournal.pone.0013376&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pagani et al., PloSONE (2010); &lt;strong&gt;5&lt;/strong&gt;(10): e13376&lt;/a&gt;&lt;/sub&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-03-22T08:48:36.257" LastActivityDate="2016-03-22T08:48:36.257" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34558" PostTypeId="2" ParentId="34404" CreationDate="2015-05-26T15:02:10.017" Score="3" Body="&lt;p&gt;I think the &lt;a href=&quot;http://en.wikipedia.org/wiki/Parasitoid#Definitions_and_distinctions&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia article defining parasitoids&lt;/a&gt; has it right on this one. The term is, and &lt;em&gt;should&lt;/em&gt; be flexible and it's definition defined by context. &lt;em&gt;i.e&lt;/em&gt; Case by case definitions are made obvious in the literature.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Patently there is no point to trying to draw arbitrary lines of distinction between such vague, and often variable, life histories. In each ecological or ethological study, the terms applied should reflect the facts in the contexts relevant to the matter in question. Such studies need not in all cases use the identical terminology, and there is no reason they should.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This means that you should always describe the life cycle even if you call the organism a parasitoid. There is too much variation between seemingly similar organism life histories to use a strict and specific term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For those struggling to see the &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0169534702026150&quot; rel=&quot;nofollow noreferrer&quot;&gt;link&lt;/a&gt; from the question, they suggest a parasitoid can be measured as a parasite that reduces host fitness to zero:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;... they are also quite different from these other parasites,&#xA;  in that, similar to a predator, they must kill their host.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A recent (2015) &lt;a href=&quot;http://www.annualreviews.org/doi/pdf/10.1146/annurev-ento-010814-021101&quot; rel=&quot;nofollow noreferrer&quot;&gt;review on Whiteflies&lt;/a&gt; refers to Hymenoptera as parasitoids of Whiteflies because the Hymenoptera are parasitoids as larvae as they kill the Whiteflies and then become free-living adults. &lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2017-03-27T03:54:31.130" LastActivityDate="2017-03-27T03:54:31.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34559" PostTypeId="2" ParentId="34512" CreationDate="2015-05-26T15:42:58.653" Score="5" Body="&lt;p&gt;First of all, the more commonly used term is &quot;copulation path,&quot; and I don't ether is used as a formal biological term, but rather in models for the public.  The term that is used in literature is &quot;pronuclear fusion&quot; for the process as a whole, and I don't know of a more technical term for the path itself.  Your inability to find information may have been linked to terms used.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, the copulation path doesn't have as much variability as the penetration path, which is what determines the copulation path.  The copulation path tends to be a relatively straight line between the two pronucleoli, dictated by and pushed along the cytoskeleton (&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/25061094&quot; rel=&quot;nofollow&quot;&gt;Lian et al, 2014&lt;/a&gt;).  It is worth noting that it is often not the shortest straight line (think of the number of lines between a smaller sphere and a larger one), but still a relatively straight line.  People tend to care about this, because what ever the copulation path, it sets the axis of division, which can effect in vitro fertilization techniques, particularly in plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Getting at what I think you are trying to ask, the penetration path is variable because it is an oscillatory phenomenon.  You actually have to move back in the fertilization process to the sperm impact angle (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25659799&quot; rel=&quot;nofollow&quot;&gt;Hedrih et al, 2015&lt;/a&gt; is the coolest model I've seen of this) to see how this can change.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To understand oscillatory phenomenon in general, you need to understand that a lot of the processes in biology are driven by the chaotic (used in the formal since) vibrating or shaking of molecules and fluid microcurrents.  This means that we can not know (regardless of how sensitive we measure) the conditions specific enough to create the specific path.  These things are not tied to genes or to the person in general (perhaps exuding of mutations/disorders that effect the morphology of sperm or egg).  Rather it is specific to any single fertilization reaction simple because of chance/chaos.&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2015-05-26T18:31:52.747" LastActivityDate="2015-05-26T18:31:52.747" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34561" PostTypeId="1" AcceptedAnswerId="34564" CreationDate="2015-05-26T16:15:07.267" Score="3" ViewCount="2312" Body="&lt;p&gt;I'm from a maths background and I'm doing some research on mathematical models of cancer. I've come across alot of literature mentioning &quot;multicell spheroids&quot; in the context of avascular tumours. I know that avascular means a lack of blood vessels but I am having trouble finding an explanation for multicell spheroids. Are these some kind of model/approximation of a certain types of tumours, or are they actually a real-phenomenon in and of themselves? It would be great if someone could fill me in on what they multicell spheroids actually are!&lt;/p&gt;&#xA;" OwnerUserId="15925" LastActivityDate="2015-05-26T17:12:51.257" Title="What are multicell spheroids?" Tags="&lt;cell-biology&gt;&lt;mathematical-models&gt;&lt;cell-membrane&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34563" PostTypeId="2" ParentId="34561" CreationDate="2015-05-26T16:27:11.860" Score="4" Body="&lt;p&gt;They are tridimensional cell cultures according to &lt;a href=&quot;http://www.researchgate.net/profile/Guozhang_Zou/publication/232529314_Multicellular_Tumor_Spheroids_as_an_In_Vivo-like_Tumor_Model_for_Three-dimensional_Imaging_of_Chemotherapeutic_And_Nano_Material_Cellular_Penetration/links/0c96051b0229db34cc000000.pdf&quot; rel=&quot;nofollow&quot;&gt;H Ma et al. 2012&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Multicellular tumor spheroids are one of the classic 3D culture models that can be applied to the development of anticancer drugs and treatments. By mimicking the 3D network of the cellular–matrix and cell–cell interactions, tumor spheroids resemble many aspects of the pathophysiologic environment within human tumor tissue.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Classical cell cultures are usually monolayer. Many of the differene between these cultures and real life tissues has been overcome by 3D cultures according to &lt;a href=&quot;http://www.nature.com/mtna/journal/v3/n3/full/mtna20145a.html&quot; rel=&quot;nofollow&quot;&gt;Carver et al. 2014&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The multicellular tumor spheroid (MCTS), a three-dimensional model that closely resembles small avascular tumors and micrometastases, has been utilized as an intermediate between monolayer culture and in vivo studies for the screening of small-molecule drugs. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;So is it a 'real life' entity or is it something that is computer generated?&lt;/em&gt;&lt;/strong&gt; It is real life. Let's think of an organ. It's made up of a specific tissue(s) and a stroma that contains vascular, nervous and other components that supply nutrients and limit the organ's specific tissue. This structure develops in vivo in 3D. The blood vessels will follow tissue development in a tree-like 3D structure in order to reach to all cells. But what you do with lab cell cultures? There are no blood vessels there. How do you supply nutrients to all cells? That is why most in vitro cell cultures are developed in monolayer structure. Yet cells are 3D structures. They are joined together in a tissue by intercellular junctions. Monolayer limits this joining to a single plane. Moreover, when it comes to cancer cells which have specific properties (they lose junctions and start to move) the monolayer model becomes limited. This is how spheroids have become a better model for studying in vivo processes using in vitro cell cultures.&lt;/p&gt;&#xA;" OwnerUserId="6422" LastEditorUserId="6422" LastEditDate="2015-05-26T17:12:51.257" LastActivityDate="2015-05-26T17:12:51.257" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34564" PostTypeId="2" ParentId="34561" CreationDate="2015-05-26T16:54:30.500" Score="3" Body="&lt;p&gt;Classical cell culture is a monolayer of cells on the surface of a cell culture dish. These cultures differ strongly from the microenvironment which cells have in tumors, as the cells only interact with their direct neighbours, but have otherwise a relatively optimal supply of nutrients and oxygen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a real-lige tumor a cell mass is growing uncontrolled in all three dimensions of the space producing these typical &quot;knots&quot; of tumors. As long as these are not getting supplied by own blood vessels (meaning they arevascularized) supply of oxygen, nutrients and growth factors and hormones differ very much between the cells in the outer layers of the tumor and cell in the inside. This causes different levels of stress and also physiological reactions of the cells. This looks like in the figure below (from &lt;a href=&quot;http://www.jcancer.org/v02p0507.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/c2WD2.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To resemble these micro-environments for research (and 2D and 3D cell culture differ quite a bit in the results) people are trying to simulate these. Technically this is achieved by embedding small amounts of cells (typically a few hundred) into a gel matrix (for example matrigel or collagen) which is getting hard and let the cells grow in small drops. If the conditions are right, the cells will develop into these multicellular spheroids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can even mix different cells types (for example turmor cells and cells which are usually present in the tissue where the tumor grows) to get an even better simulation. See the references for some more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9357753&quot; rel=&quot;nofollow noreferrer&quot;&gt;Three-dimensional cell cultures: from molecular mechanisms to&#xA;clinical applications.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18566957&quot; rel=&quot;nofollow noreferrer&quot;&gt;Recent advances in three-dimensional multicellular spheroid culture&#xA;for biomedical research.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25622895&quot; rel=&quot;nofollow noreferrer&quot;&gt;Spherical cancer models in tumor biology.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25299693&quot; rel=&quot;nofollow noreferrer&quot;&gt;Development of 3D in vitro technology for medical applications.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-05-26T17:05:10.147" LastActivityDate="2015-05-26T17:05:10.147" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34565" PostTypeId="1" AcceptedAnswerId="34570" CreationDate="2015-05-26T18:02:57.383" Score="4" ViewCount="1535" Body="&lt;p&gt;I do not understand how skin color in humans work, even after taking a basic genetics course and reading some on wikipedia. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From what I understand, skin is color based on multiple genes that control melanin and other products that affect appearance of skin. So then their are multiple alleles for &quot;skin color&quot; and also some of these alleles can be varying in their expression/inheritance? based on the other alleles presence?(epistasis) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So then a black person and a white person could have various skin colors (phenotypes?) And the offspring of these children could then have varying offspring as well?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diagrams would help me maybe in explaining the concept.&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="3971" LastEditDate="2015-05-26T18:23:19.317" LastActivityDate="2015-05-26T19:35:38.693" Title="Skin color explanation?" Tags="&lt;human-genetics&gt;&lt;skin&gt;&lt;pigmentation&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34566" PostTypeId="1" AcceptedAnswerId="34581" CreationDate="2015-05-26T19:01:18.037" Score="2" ViewCount="181" Body="&lt;p&gt;I have in my notes that:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Carbamazepinum increases threshold for glutamate&lt;/li&gt;&#xA;&lt;li&gt;Lamotriginum delays release of glutamic acid&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I would like to simplify these sentences into a single line. I would like to know if it would be correct to say the following:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;both Carbamazepinum and Lamotriginum increase glutamate threshold?&lt;/li&gt;&#xA;&lt;li&gt;&quot;both affect glutamate function&quot; should at least be correct&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Do both Carbamazepinum and Lamotriginum increase glutamate threshold?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Characterizing those drugs.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;A = group, B = mechanism of action and C = indications. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Carbamazepinum &#xA;A. Anticonvulsant, antiepileptic.&lt;br&gt;&#xA;B. Block Na+ ion channels and inhibit glutamatergic neurotransmission. Inhibit sustained repetitive neuronal firing. &#xA;C. 1st line of Epilepsy grand mall seizures, bipolar disorder, trigeminal neuralgia. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Lamotriginum &#xA;A. Unique antiepileptic. &#xA;B. Block Na+ ion channels and inhibit glutamatergic neurotransmission. Inhibit sustained repetitive neuronal firing. &#xA;C. 1st line Epilepsy - generalized, partial and absence - all types. Bipolar disorder - depression stage. Neuropathy. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2015-06-07T08:12:35.767" LastActivityDate="2015-06-07T08:12:35.767" Title="Do both Carbamazepinum and Lamotriginum increase glutamate threshold?" Tags="&lt;neuroscience&gt;&lt;pharmacology&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34567" PostTypeId="1" AcceptedAnswerId="34579" CreationDate="2015-05-26T19:23:43.377" Score="4" ViewCount="259" Body="&lt;p&gt;Even though we have a very high tech society, cancer is still a serious issue. We humans still are not entirely capable of fighting cancer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Radiation and chemotherapy are still considered the best methods for treating it and frequently, even these don't work. And, as for this disease, it is a phenomenon of uncontrolled cell growth that has lead to the death of many people. Within these main two treatments, there is plenty of controversy surrounding applying radiation and chemo in a proper sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are also some different methods known and available on the market to treat cancer. Among them, homeopathic and herbal treatments are the most common. So, my question is, do they really work and is there any scientific evidence of that?  If yes then what is it?  &lt;/p&gt;&#xA;" OwnerUserId="15874" LastEditorUserId="6289" LastEditDate="2015-05-27T03:33:45.863" LastActivityDate="2017-06-15T20:58:49.800" Title="Does homeopathic or herbal treatment of cancer have any scientific recognition?" Tags="&lt;human-biology&gt;&lt;pharmacology&gt;&lt;cancer&gt;&lt;medicine&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34568" PostTypeId="1" CreationDate="2015-05-26T19:27:15.433" Score="2" ViewCount="1466" Body="&lt;p&gt;What is a T7 tag and can if be used to purify synthesized proteins? Is it charge based like a His tag?&lt;/p&gt;&#xA;" OwnerUserId="15931" LastActivityDate="2015-06-25T19:56:05.620" Title="T7 Tagging in Synthetic Biology" Tags="&lt;cell-biology&gt;&lt;synthetic-biology&gt;&lt;purification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34569" PostTypeId="1" CreationDate="2015-05-26T19:29:55.883" Score="-4" ViewCount="2877" Body="&lt;p&gt;When many people look at sexual images, they often can become sexually aroused, including full genital arousal, and feel urges, known more often used as &quot;horny&quot; as slang/urban usage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does this process work in males and females? Is it different in males than in females, or is the network the same between the eyes and the brain, down to the genitals as a precursor to masturbation, sex, etc.? Also, what exactly happens in the brain before it tells the genitals to get horny or such? Examples would be in viewing porn, naughty images/pics, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Men and women and girls and boys alike can get full arousal from this. How does the process work?&lt;/p&gt;&#xA;" OwnerDisplayName="user15932" LastEditorUserId="8105" LastEditDate="2015-05-26T20:16:28.247" LastActivityDate="2015-05-27T10:30:59.753" Title="How does visual sexual arousal work between the eyes, brain, and genitals/gonads?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;&lt;sexuality&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2015-05-30T16:00:45.160" ContentLicense="CC BY-SA 3.0" />
  <row Id="34570" PostTypeId="2" ParentId="34565" CreationDate="2015-05-26T19:35:38.693" Score="7" Body="&lt;p&gt;The genetics of pigmentation is relatively complicated, as the pathway for the pigmentation (regulation of the pigment production, ratio between the melanins, maturation, trafficking and distribution of the melanins from the melanocytes to other cells) is quite long and also subject to different regulations. All the mutations found to date (at least to my knowledge) affect single parts of this long process (so for example MC1R mutations are affecting whether eumelanin is made, while Rab7 and Rab27a is most likely involved in the distribution of the melanosomes). Not all gene functions in this network have been understood so far.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Population studies have shown that the three main ethnic subgroups (west-africans, asians and europeans) have developed independently from a common ancestor with different (and independent) mutations in each arm. See the figure from reference 1 as an illustration, it also shows the genes involved in each arm:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HQrkA.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pigmentation is a protection against UV light, so there is a strong selection against mutations in areas with high UV light (west africa for example). The general theory is that in areas with less UV light the skin got lighter to allow the production of vitamin D (for which you need UV light). If you want to go through the single genes and their influence on pigmentation, please have a look at this &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_skin_color#Genetics_of_skin_color_variation&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt; page, which gives a good explanation. Also have a look at the references.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/milestones/skinbio4/full/skinbio20113a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Unpacking Human Evolution to Find the Genetic Determinants of Human&#xA;Skin Pigmentation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3999/xhe28qx5_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;The genetics of pigmentation: from fancy genes to complex traits.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://hmg.oxfordjournals.org/content/18/R1/R9.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Molecular genetics of human pigmentation diversity&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.imb.uq.edu.au/download/large/Bioessay.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Human pigmentation genetics: the difference is only skin deep&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/3999/o5apyij5_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;The etiology and molecular genetics of human pigmentation disorders&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-05-26T19:35:38.693" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34571" PostTypeId="2" ParentId="34568" CreationDate="2015-05-26T19:42:45.223" Score="2" Body="&lt;p&gt;The T7 tag is the first 11 amino acids of the T7 gene 10 protein. Basically, if you engineer a protein with the T7 tag, you've engineered a small, known epitope to the protein of interest which may be detected immunologically. The small size of the epitope reduces the chance it will disrupt the protein's normal function (to which it's tagged). If we look at the affinity purification kit on the &lt;a href=&quot;http://wolfson.huji.ac.il/expression/local/T7tag_affinity.pdf&quot; rel=&quot;nofollow&quot;&gt;following product page&lt;/a&gt; we can see that specific vectors can be used to express T7-tagged proteins, and an immunoaffinity column can be used to purify the protein of interest. The T7 tag chemical structure is denoted &lt;a href=&quot;http://www.apexbt.com/t7-tag.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-05-26T19:47:52.127" LastActivityDate="2015-05-26T19:47:52.127" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34572" PostTypeId="1" CreationDate="2015-05-26T19:54:36.930" Score="1" ViewCount="49" Body="&lt;p&gt;Will a T7 tag still work if it is placed next to a start codon? Meaning, will it still work with a Met attached to it in the amino acid sequence?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="15931" LastActivityDate="2015-05-28T04:58:32.170" Title="T7 Tagging Next to Met" Tags="&lt;cell-biology&gt;&lt;proteins&gt;&lt;synthetic-biology&gt;&lt;purification&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34573" PostTypeId="1" AcceptedAnswerId="34574" CreationDate="2015-05-26T19:59:14.960" Score="2" ViewCount="3283" Body="&lt;p&gt;When searching for a plasmid on Addgene what does it mean if it is said to be an &quot;empty backbone&quot;? Why would one want an empty backbone? &lt;/p&gt;&#xA;" OwnerUserId="15933" LastActivityDate="2016-12-19T01:16:53.860" Title="Plasmid: Empty Backbone?" Tags="&lt;plasmids&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34574" PostTypeId="2" ParentId="34573" CreationDate="2015-05-26T20:27:19.627" Score="1" Body="&lt;p&gt;If you look on a very basic plasmid map, you usually see three different features: An origin of replication (often abbreviated ori or origin) which is necessary for the replication of the plasmid, a resistance gene (not necessary but useful to select for) and and multi cloning site (abbreviated MCS) which contains a number of unique restriction enzyme recognition sites, see the figure (from here):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fNx9v.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In molecular biology plasmids are used to overexpress proteins in bacteria (or other cells) which are of any interest. To do this, you bring in the coding information for this gene into the plasmid using the MCS. Here you can cut the plasmid controlled (only open the ring on one site) and insert DNA of interest. An empty plasmid in this context means that it can readily used for cloning purposes as it does not contain any foreign DNA.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-05-26T20:27:19.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34576" PostTypeId="2" ParentId="34569" CreationDate="2015-05-26T20:36:55.307" Score="7" Body="&lt;p&gt;Sexual arousal is a very complex response, that includes a whole range of physiological changes, firing of lots of neural pathways, increased muscle tension, elevated heart rate  with increased blood flow to the skin, primary and secondary sexual organs and a whole lot of hormonal spikes.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Sexual desire is defined as the behavioural drive that motivates individuals to fantasize about or seek out sexual activity. In contrast, sexual arousal is defined as the autonomic physiological processes that prepare the body for sexual activity (Toledano, Pfaus., 2006).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The brain is rightfully regarded as the largest sexual organ, with most of the pleasure arising from the limbic system of the brain (which interestingly enough, is common to all mammals  regulating emotion and encouraging the avoidance of painful of aversive stimuli and the repetition of pleasurable experiences).&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;From a physiological perspective sexual arousal is controlled by the parasympathetic portion of the autonomic nervous system and manifests itself as vasodilation in sexual organs along with several other physiological phenomena including an increase in heart rate. An orgasm and in particular male ejaculation is controlled by the sympathetic portion, this is also accompanied by deactivation of many areas in the brain relating to external stimuli in particular fear, allowing the mind to focus on the task at hand.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Now it is a bit long to go into the details of the sexual response cycle, and hence here is a brief summary:&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Neural pathways:&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Prior to the physical stimulation, comes sexual desire. Largely mediated by emotion through the limbic system, activation of the amygdala can trigger penile erection, sexual feelings,(Georgiadis and Holstege, 2005) sensations of extreme pleasure (Olds and Milner, 1954), memories of sexual intercourse (Gloor, 1986), as well as ovulation, uterine contractions, and orgasm.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The amygdala is sexually differentiated part of the brain that is known to produce sex specific responses. In short the amygdala has a pathway (amygdalofugal pathway) that connects with the major regions of the brain that regulates sexual feelings. An increased density of enkephalins and opiate receptors can be also found in amydala, which induces extreme feelings of pleasure.&lt;/p&gt;&#xA;&lt;p&gt;interestingly...&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Males more then females, were found to have greater amygdala activation when presented with a sexually pleasing, visual stimuli (Hamann et al., 2004).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Moving on, other areas of the brain implicated in sexual arousal are...&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Input travels from the basolateral nuclei of the amygdala along the amygdalofugal pathway to the ventral striatum, made up of the nucleus accumbens, putamen and parts of the caudate nucleus. The nucleus accumbens plays a role in pleasure and reward due to a large large of dopaminergic neurons from the VTA (ventral tegmental area).&lt;/p&gt;&#xA;&lt;p&gt;The Vagus nerve is known to lead to the Nucleus Tractus Solitarii (NTS) in the Medulla Oblongata.  Following this stimulation of the brain via the vagus nerve during orgasm there was a difference in activity between preorgasm and orgasm. Areas of activation during and after orgasm include the hypothalamic paraventricular nucleus (PVN), midbrain central gray, amygdala, hippocampus, anterior cingulate, frontal, parietal, temporal and insular cortices, anterior basal ganglia, and cerebellum (Whipple, 2008). Although this may be the explanation for female orgasms, there is no evidence to suggest that this is the case for males.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Hormonal changes:&lt;/strong&gt;&#xA;I am not going to write too much about this as this information is readily accessible in the net. Sexual arousal causes the cerebral cortex to signal the hypothalamus to stimulate the production of testosterone, the production is regulated by a complex chain of events known as the hypothalamic-pituitary-gonadal axis, which ultimately causes the pitutary gland to release luteinizing hormone which signals the testes to produce testosterone and ovaries to produce oestrogen.&lt;/p&gt;&#xA;&lt;p&gt;You can read more here: &lt;a href=&quot;http://neurosciencefundamentals.unsw.wikispaces.net/Sex+and+the+Brain.+What+parts+are+involved%3F&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://neurosciencefundamentals.unsw.wikispaces.net/Sex+and+the+Brain.+What+parts+are+involved%3F&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;For an in-depth analysis I recommend this book:&#xA;&lt;em&gt;Greenberg, Jerrold S., Clint E. Bruess, and Sara B. Oswalt. Exploring the dimensions of human sexuality. Jones &amp;amp; Bartlett Publishers, 2014.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;This is a good review for endocrinology in sexual arousal:&#xA;&lt;em&gt;Bancroft, J. &amp;quot;The endocrinology of sexual arousal.&amp;quot; Journal of Endocrinology 186.3 (2005): 411-427.&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;As usual, wikipedia also covers a few models of sexual arousal (Singer, Basson's etc..) that I have not mentioned here: &lt;a href=&quot;http://en.wikipedia.org/wiki/Sexual_arousal&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Sexual_arousal&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-05-27T10:30:59.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34577" PostTypeId="1" CreationDate="2015-05-26T20:51:38.537" Score="1" ViewCount="75" Body="&lt;p&gt;I began working with panTro3 assembly of the UCSC. This assembly corresponds to CGSC Build 2.1.3. See here: &lt;a href=&quot;https://genome.ucsc.edu/FAQ/FAQreleases.html&quot; rel=&quot;nofollow&quot;&gt;https://genome.ucsc.edu/FAQ/FAQreleases.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, I have to cross annotations with ENSEMBL (Indeed, I need to use Biomart tool: &lt;a href=&quot;http://www.ensembl.org/biomart/martview/2e4aac505f5cf5e0ac255b4a215a056c&quot; rel=&quot;nofollow&quot;&gt;http://www.ensembl.org/biomart/martview/2e4aac505f5cf5e0ac255b4a215a056c&lt;/a&gt;). But It seems that between Release 64 and 65 they passed directly from Chimp 2.1 to Chimp 2.1.4. I researched some information and found that Chimp 2.1.3 renamed as a Pre! See here: &lt;a href=&quot;http://pre.ensembl.org/Pan_troglodytes/Info/Index&quot; rel=&quot;nofollow&quot;&gt;http://pre.ensembl.org/Pan_troglodytes/Info/Index&lt;/a&gt; and here &lt;a href=&quot;http://www.ensembl.info/blog/2011/06/10/new-pre-site-for-chimpanzee/&quot; rel=&quot;nofollow&quot;&gt;http://www.ensembl.info/blog/2011/06/10/new-pre-site-for-chimpanzee/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it a way to solve this problem? How may I use Chimp 2.1.3 assembly in Biomart with GrCh37 as reference genome (I was using an archived versions of the Ensembl: &lt;a href=&quot;http://grch37.ensembl.org/biomart/martview/cbe191dccbe8e5a314cfebeaa8862ca0&quot; rel=&quot;nofollow&quot;&gt;http://grch37.ensembl.org/biomart/martview/cbe191dccbe8e5a314cfebeaa8862ca0&lt;/a&gt;), but seems not possible to cross between different releases of the ENSEMBL.&lt;/p&gt;&#xA;" OwnerUserId="13373" LastEditorUserId="1306" LastEditDate="2015-05-26T21:53:49.030" LastActivityDate="2015-05-26T21:53:49.030" Title="Why Pan_troglodytes-2.1.3 Assembly renamed as a Pre in ENSEMBL?" Tags="&lt;bioinformatics&gt;" AnswerCount="0" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34578" PostTypeId="1" CreationDate="2015-05-26T21:10:58.447" Score="2" ViewCount="4574" Body="&lt;p&gt;Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Nested polymerase chain reaction (Nested PCR) is a modification of&#xA;  polymerase chain reaction intended to reduce non-specific binding in&#xA;  products due to the amplification of unexpected primer binding sites.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I understand that there are two steps and one of those steps involves a non-specific primer followed by a specific primer...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But this does not seem to have sense. What is the purpose of running a non-specific PCR just to hit it with a specific primer afterwards?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What do we gain when doing a nested PCR? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Practical example:&#xA;We are planning on sequencing human skin microbiome. Would the ratios of different bacterial species differ if we would use the nested PCR products for sequencing, as compared to standard PCR?&lt;/p&gt;&#xA;" OwnerUserId="15256" LastActivityDate="2015-06-02T08:10:22.400" Title="Why do we do nested PCR?" Tags="&lt;pcr&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34579" PostTypeId="2" ParentId="34567" CreationDate="2015-05-26T21:35:04.900" Score="14" Body="&lt;p&gt;The methodology behind homeopathy is scientific nonsense.  If you dilute anything a billion times, it will have no chemical effect, not even if you shake it all the while.  So no, homeopathy does nothing for cancer, or any medical condition at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course plants can have active compounds in them, once scientists have identified those compounds, they can be tweaked to make them act better in the human body, and then manufactured under strict guidelines to ensure purity, and tested to determine the optimum dosage; then it's just medicine.  Taxol comes from yew trees, it doesn't mean that native herbalists were successfully treating cancer with it for hundreds of years.  Native herbalists were using willow bark, which contains salicylic acid, which has anti-inflammatory properties, but chemists improved on it, reducing some of its negative side effects, by modifying it to acetylsalicylic acid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Millions of people get cancer.  Doctors get cancer.  Herbalists get cancer.  If curing cancer was as easy as mixing some leaves in a poultice, people would do that.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastEditorUserId="5148" LastEditDate="2015-05-26T23:24:03.333" LastActivityDate="2015-05-26T23:24:03.333" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34581" PostTypeId="2" ParentId="34566" CreationDate="2015-05-27T01:56:43.000" Score="2" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Both carbamazepine and lamotrigine are listed as &lt;strong&gt;Na&lt;sup&gt;+&lt;/sup&gt; channel blockers&lt;/strong&gt;. Carbamezipine's action is mainly associated with inhibition of postsynaptic neural activity, while lamotrigine is thought to inhibit glutamate release. Given that glutamate is the principal excitatory neurotransmitter in the brain, and if you insist of using a one-liner I would go for: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Both lamotrigin and carbamazepine can be said to &lt;strong&gt;inhibit glutatamatergic neurotransmission&lt;/strong&gt;, albeit carbamezipine does so in a non-specific way. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;My two most beloved drugs in one question! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First off, this answer is formulated from the perspective of both drugs being used as &lt;em&gt;anticonvulsants&lt;/em&gt; in generalized tonic-clonic epilepsies. As anti-epileptics, Both &lt;a href=&quot;http://www.drugbank.ca/drugs/DB00555&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;lamotrigine&lt;/strong&gt;&lt;/a&gt; (Lamictal) and &lt;a href=&quot;http://www.drugbank.ca/drugs/DB00564&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;carbamezipine&lt;/strong&gt;&lt;/a&gt; (Tegretol) are listed as &lt;strong&gt;Na&lt;sup&gt;+&lt;/sup&gt;-channel blockers&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carbamezipine does so quite specifically, and it inhibits sustained repetitive firing by blocking sodium channels. It does so in a very clever way, as it &lt;em&gt;only binds to Na&lt;sup&gt;+&lt;/sup&gt;-channels of rapidly firing neurons&lt;/em&gt;, which is exactly what makes it a good anti-convulsant (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6303804&quot; rel=&quot;nofollow&quot;&gt;Courtney &amp;amp; Etter, 1983&lt;/a&gt;). It also is believed to have anticholinergic, central antidiuretic, antiarrhythmic, muscle relaxant, antidepressant (possibly through blockade of norepinephrine release), sedative, and neuromuscular-blocking properties (&lt;a href=&quot;http://www.drugbank.ca/&quot; rel=&quot;nofollow&quot;&gt;Drug bank&lt;/a&gt;). Hence, your note that it increases the threshold for glutamate is true in the sense that it is likely to &lt;em&gt;increase the firing threshold of glutamate-activated neurons&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, note that carbamezipine (nor lamotrigine) &lt;strong&gt;does &lt;em&gt;not&lt;/em&gt; increase the threshold &lt;em&gt;for&lt;/em&gt; glutamate&lt;/strong&gt; - glutamate &lt;strong&gt;has no threshold&lt;/strong&gt; and hence it cannot be raised. It is incorrect word use.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lamotrigine is also listed as a Na&lt;sup&gt;+&lt;/sup&gt;-channel blocker, but the exact mechanism(s) behind its anti-convulsive and mood-stabilizing effects are unknown. &lt;em&gt;In vitro&lt;/em&gt; pharmacological studies suggest that lamotrigine's inhibiting effects on voltage-sensitive Na&lt;sup&gt;+&lt;/sup&gt; and/or Ca&lt;sup&gt;2+&lt;/sup&gt; channels stabilizes neuronal membranes and consequently modulates presynaptic transmitter release of excitatory amino acids (e.g., glutamate and aspartate). It has also been shown to enhance K&lt;sup&gt;+&lt;/sup&gt; currents and GABA-ergic inhibition (Coulter, 1997). Hence, your note that it decreases glutamate release is correct. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://jcn.sagepub.com/content/12/1_suppl/S2.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Coulter, &lt;em&gt;J Child Neurol&lt;/em&gt; (1997); &lt;strong&gt;12&lt;/strong&gt;: S2-9&lt;/a&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6303804&quot; rel=&quot;nofollow&quot;&gt;Courtney &amp;amp; Etter, &lt;em&gt;Eur J Pharmac&lt;/em&gt; (1983); &lt;strong&gt;88&lt;/strong&gt;: 1-9&lt;/a&gt;.  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-27T10:00:45.957" LastActivityDate="2015-05-27T10:00:45.957" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="34582" PostTypeId="1" AcceptedAnswerId="50806" CreationDate="2015-05-27T04:30:07.707" Score="9" ViewCount="5584" Body="&lt;p&gt;At first, the coconut is filled with liquid endosperm. Later when it ripens, the outer layers form brown fibrous covering, and the inner solid layer turns brown and hardens. Within that, a white layer forms (which is soft and thin at first and then gradually hardens and thickens). After ripening, there is a white layer with very little fluid. So, it's gotta be the liquid endosperm which has hardened over the course of time to form the white layer. So, how does it harden?&lt;/p&gt;&#xA;" OwnerUserId="14500" LastEditorUserId="20449" LastEditDate="2016-08-17T19:02:27.500" LastActivityDate="2019-08-20T17:15:59.230" Title="How does coconut water solidify into hardened coconut meat?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;fruit&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34583" PostTypeId="1" AcceptedAnswerId="34610" CreationDate="2015-05-27T05:03:23.037" Score="3" ViewCount="1094" Body="&lt;p&gt;I'm using the Q5 system and I'm PCRing a product that will have a final length of around 9500 bases. I have noticed that the product is there but very faint. The primer seems to be used up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is, can the dNTPs be rate limiting in a long reaction? That is, can all the dNTPs be used up in the first PCR cycles and maybe not be available for the later exponential rounds?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems you have about 1000 times the amount of dNTPs to the amount of primer (200 µM compared to 0.2 µM). So maybe...or is my basic chemistry off. Any precedence?&lt;/p&gt;&#xA;" OwnerUserId="3887" LastEditorUserId="3340" LastEditDate="2015-05-27T10:07:06.050" LastActivityDate="2015-05-27T23:31:51.923" Title="Is the amount of dNTPs rate limiting for very long PCR products?" Tags="&lt;molecular-biology&gt;&lt;pcr&gt;&lt;cloning&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34584" PostTypeId="1" CreationDate="2015-05-27T07:54:27.587" Score="10" ViewCount="1204" Body="&lt;p&gt;I photographed this flower in Central Europe. I looked in online databases but can't really identify the actual flower, since there are so many that look quite similar. Can you help me? What's the name of this flower?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vkw8D.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="608" LastEditorUserId="3624" LastEditDate="2015-05-27T08:47:02.937" LastActivityDate="2015-05-27T12:02:58.150" Title="What's the name of this flower?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34585" PostTypeId="2" ParentId="34584" CreationDate="2015-05-27T08:12:48.743" Score="13" Body="&lt;p&gt;It looks like the common &lt;a href=&quot;http://en.wikipedia.org/wiki/Geranium_sylvaticum&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Geranium sylvaticum&lt;/em&gt;&lt;/a&gt; (also called wood cranesbill or Mayflower), and it is at least a close relative (member of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Geranium&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Geranium&lt;/em&gt;&lt;/a&gt; genus). This plant is commonly found across Europe and in parts of Asia (see map below), and it is sometimes planted in gardens. It is a perennial herb that grows in many types of habitats (woods, meadows, road sides, mountain areas), and the flowers are most commonly violet to blue, but can also be white. &lt;a href=&quot;http://www.luontoportti.com/suomi/en/kukkakasvit/meadow-cranesbill&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Geranium pratense&lt;/em&gt;&lt;/a&gt; is very similar, but usually has more narrow leaf lobes and bent flower stalks. However, it might not be possible to separate these two species based on your picture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are also similar relatives found in North America (e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Geranium_maculatum&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Geranium maculatum&lt;/em&gt;&lt;/a&gt;) and Asia (e.g. &lt;a href=&quot;http://en.wikipedia.org/wiki/Geranium_himalayense&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Geranium himalayense&lt;/em&gt;&lt;/a&gt;) and many hybrids of plants from within this genus are cultivated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ohLpz.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;(picture from Swedish Wikipedia)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JgnJb.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;(distribution map from the Swedish Museum of Natural History: &lt;a href=&quot;http://linnaeus.nrm.se/flora/welcome.html&quot; rel=&quot;noreferrer&quot;&gt;Den virtuella floran&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="10456" LastEditDate="2015-05-27T12:02:58.150" LastActivityDate="2015-05-27T12:02:58.150" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34586" PostTypeId="2" ParentId="34584" CreationDate="2015-05-27T08:19:42.020" Score="7" Body="&lt;p&gt;My guess would be the meadow cranesbill (Geranium pratense), see this image (from &lt;a href=&quot;http://www.gartendatenbank.de/wiki/geranium-pratense&quot;&gt;here&lt;/a&gt;, more images are available there):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vQCdP.jpg&quot; alt=&quot;enter link description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The flower is quite common on meadows in europe, see &lt;a href=&quot;http://en.wikipedia.org/wiki/Geranium_pratense&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-05-27T08:19:42.020" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34588" PostTypeId="1" AcceptedAnswerId="34589" CreationDate="2015-05-27T10:39:30.790" Score="4" ViewCount="2193" Body="&lt;p&gt;Suppose the energy at the second trophic level as given in an energy pyramid is 100 kcal per square metre. It could mean either of the two following things:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;100 kcal is the energy this primary consumer has stored in its flesh - that is, the energy left over from the amount consumed, after assimilation and respiration. This would be the net productivity of that consumer, or the energy available to the secondary consumer which feeds on this. &lt;/li&gt;&#xA;&lt;li&gt;100 kcal is the energy this primary consumer consumes. It will utilise a part of this in respiration, lose some amount in assimilation, so that a small amount is left over which is then stored in it as mass, or flesh - which would be its net productivity. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Similarly, the first trophic level, the autotrophs' energy could represent either the total amount of food they make (the GPP), that is, the energy akin to the second case above, or the energy stored in them and available to the next trophic level (the NPP), like in the case 1 above. So which of these is correct - what do we represent as the energy of a trophic level in an energy pyramid? I think it should be the first case, the stored energies, since after all these are what you will measure as the energy of any trophic level - the &lt;em&gt;stored&lt;/em&gt; energy at that level.    &lt;/p&gt;&#xA;" OwnerUserId="15109" LastEditorUserId="9943" LastEditDate="2015-05-27T13:42:31.383" LastActivityDate="2015-05-27T13:43:48.483" Title="What does the energy in an energy pyramid represent?" Tags="&lt;ecology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34589" PostTypeId="2" ParentId="34588" CreationDate="2015-05-27T11:01:59.267" Score="4" Body="&lt;p&gt;Each layer in the energy pyramid represents the &lt;strong&gt;stored energy&lt;/strong&gt; in biomass in that layer. This energy is obtained from the previous layer. Because &lt;strong&gt;every layer&lt;/strong&gt; uses a certain amount of &lt;strong&gt;energy&lt;/strong&gt; needed for survival (combustion of sugars and fats through &lt;strong&gt;respiratory processes&lt;/strong&gt;) obtained from the previous layer, each &lt;strong&gt;subsequent level is smaller&lt;/strong&gt; than the previous one. Also, the autotrophs in the photosynthetic layer use up (solar) energy for living. The higher up you get, the more energy is cumulatively taken away to sustain life and growth of the previous layers. Therefore, it's a pyramid shape. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/s3ZYj.jpg&quot; alt=&quot;pyramid&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Energy pyramid. Source: &lt;a href=&quot;http://www.biocab.org/Energy_Pyramid.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Biocab&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-27T13:43:48.483" LastActivityDate="2015-05-27T13:43:48.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34590" PostTypeId="1" CreationDate="2015-05-27T11:26:36.880" Score="5" ViewCount="87" Body="&lt;p&gt;I want to look at genera as a whole, across the animal kingdom to determine the range of sizes of genera. I have examined species richness and genetic diversity (pairwise distance from sequence data sets), but I am looking to find more ways to look at 'how big is a genus?' in terms of biodiversity. Any ideas or comments are greatly appreciated! &lt;/p&gt;&#xA;" OwnerUserId="15942" LastActivityDate="2015-05-29T09:12:50.440" Title="What ways are there to determine how big genera are?" Tags="&lt;evolution&gt;&lt;bioinformatics&gt;&lt;taxonomy&gt;&lt;phylogenetics&gt;&lt;biodiversity&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34591" PostTypeId="1" AcceptedAnswerId="34599" CreationDate="2015-05-27T12:18:46.290" Score="0" ViewCount="98" Body="&lt;p&gt;Considering the &lt;a href=&quot;http://en.wikipedia.org/wiki/Pentose_phosphate_pathway&quot; rel=&quot;nofollow&quot;&gt;pentose phosphate pathway&lt;/a&gt; and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Dissimilatory_sulfate_reduction&quot; rel=&quot;nofollow&quot;&gt;sulfate reduction pathway&lt;/a&gt; in bacteria;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are these types of reactions called in biology? Bio degradation reactions or bio transformation reactions or something else? I wish to know whether there is a generalized names for these types of pathways.&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="9943" LastEditDate="2015-05-27T15:09:14.277" LastActivityDate="2015-05-27T15:09:14.277" Title="What are these pathways called in Biology?" Tags="&lt;organic-chemistry&gt;&lt;biochemistry&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34592" PostTypeId="1" AcceptedAnswerId="34593" CreationDate="2015-05-27T12:27:43.180" Score="18" ViewCount="1427" Body="&lt;p&gt;&lt;strong&gt;Previous research&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;A friend of mine shared a link of some beautiful fungi: &lt;a href=&quot;https://imgur.com/a/Dii3H&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://imgur.com/a/Dii3H&lt;/a&gt;. I was intrigued by the curious critter below -- it seems to have honed the power of buckyball geometry, presumably much before we Humans ever did (search: &lt;em&gt;Buckminsterfullerene&lt;/em&gt; to learn about a feat of chemical engineering).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Google reverse-image search almost got me the answer I needed, but no species name.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I've asked friends on Facebook with no answers yet. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the name of this species of fungus?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/c2daQ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Related Questions on Stack Biology&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Here's a related Species Identification question of a fungus: &lt;a href=&quot;https://biology.stackexchange.com/questions/10738/puffball-mushroom-species-id&quot;&gt;Puffball mushroom species ID?&lt;/a&gt; (by &lt;a href=&quot;https://biology.stackexchange.com/users/1590/rg255&quot;&gt;@rg255&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;: I'm an idiot... the Imgur had species names, thus answering my question, &lt;em&gt;post-mortem&lt;/em&gt;. Thanks &lt;a href=&quot;https://biology.stackexchange.com/users/3827/skymningen&quot;&gt;@skymningen&lt;/a&gt; for pointing that out.&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2017-08-08T07:20:47.110" Title="Species ID: Buckyball-like fungus" Tags="&lt;species-identification&gt;&lt;mycology&gt;&lt;mushroom&gt;" AnswerCount="1" CommentCount="10" FavoriteCount="3" ClosedDate="2017-03-21T23:01:00.600" ContentLicense="CC BY-SA 3.0" />
  <row Id="34593" PostTypeId="2" ParentId="34592" CreationDate="2015-05-27T12:32:47.643" Score="17" Body="&lt;p&gt;Looks very similar to &lt;a href=&quot;http://en.wikipedia.org/wiki/Clathrus_ruber&quot; rel=&quot;nofollow noreferrer&quot;&gt;Clathrus ruber&lt;/a&gt; fungus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Be careful, it is poisonous. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://upload.wikimedia.org/wikipedia/commons/thumb/b/ba/Clathrus_ruber_by_Micheli_1729.jpg/340px-Clathrus_ruber_by_Micheli_1729.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2017-08-08T07:20:47.110" LastActivityDate="2017-08-08T07:20:47.110" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34594" PostTypeId="1" CreationDate="2015-05-27T10:41:43.523" Score="8" ViewCount="285" Body="&lt;p&gt;What determines speciation at a molecular level?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At what point does a scientist determine two lineages are different enough to be considered separate species?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does it have a margin of error?&lt;/p&gt;&#xA;" OwnerDisplayName="sophie silec" LastEditorUserId="3624" LastEditDate="2015-06-01T13:17:21.933" LastActivityDate="2015-08-24T14:08:21.160" Title="How is genetic speciation defined?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;population-genetics&gt;&lt;speciation&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34595" PostTypeId="2" ParentId="34312" CreationDate="2015-05-27T13:42:28.840" Score="3" Body="&lt;p&gt;The concentration of K+ inside the cell is 30 time more than outside. Hypoxia causes loss of this intracellular Kalium and consequent/premature repolarization when measuring the potential of action.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the all the ECG theory is &lt;em&gt;Vector&lt;/em&gt; based, any abnormality in the electric pathways and myocytes will result in changes of ECG.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This picture depicts the ST changes due to different extension of injury. In addition, the explanation on &lt;a href=&quot;http://www.cvphysiology.com/CAD/CAD012.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;this site&lt;/a&gt; will probably resolve the issue of understanding. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wTpow.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;ADD&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article explains the ECG phenomena as a result of electric propagation of dipoles. If the dipoles propagate towards the lead we get upward wave etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the electrostatic model takes the whole heart as one dipole (as a sum of multiple dipoles) the minor infarcts can be missed on ECG. It is an actual fact, this is why other tests are important (for example, the troponin test). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The confusion point in your understanding is a &quot;dead&quot; tissue. In a case of infarct there is an hypoxic damage which leads to elevated permeability of the cell membrane with resulting K leak (as I explained above there are 30 times more Kalium inside the cell than outside). This means that &quot;dead&quot; area will have abnormal depolarization/repolarization pattern just because there are multiple &quot;non grouped&quot; dipoles in that area (look at the picts). There are diastolic and systolic theories of ST elevation, but none of them has won the battle yet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With time the scarring tissue replaces the infarcted myocardium and in that case the ST-segment will not be affected and will look nearly normal. This is the case you meant as &quot;dead&quot; tissue - scar tissue does not leak any electrolytes and consequently the ST segment is not affected in a chronic stage.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-07-07T20:36:47.647" LastActivityDate="2015-07-07T20:36:47.647" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34596" PostTypeId="2" ParentId="34594" CreationDate="2015-05-27T13:48:12.860" Score="6" Body="&lt;p&gt;Speciation in sexually-reproducing organisms can be identified as the &lt;strong&gt;&lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evo_42&quot; rel=&quot;nofollow&quot;&gt;inability to produce viable offspring&lt;/a&gt;&lt;/strong&gt;. In other words, when two suspected sub-species are not able to produce viable offspring, they can be considered to be two species. In this case it is not so much determined at the molecular level, but at the organismal level. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This mating procedure does not work in asexually reproducing species. In this case molecular techniques are needed. &lt;a href=&quot;http://www.sciencemag.org/content/300/5617/321&quot; rel=&quot;nofollow&quot;&gt;Navarro &amp;amp; Barton (2003)&lt;/a&gt; investigated what the molecular differences were induced by evolution by comparing the genomes of humans and chimpansees. These two species diverged relatively late in evolution and their DNA differs by about 2.1%. It turned out that the main differences between the two genomes were clustered around regions where chromosomes were rearranged. Although indicative of the &lt;em&gt;cause of speciation&lt;/em&gt;, it can nonetheless also be the &lt;em&gt;result&lt;/em&gt; of it. We can never be sure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.sciencemag.org/content/300/5617/321&quot; rel=&quot;nofollow&quot;&gt;Navarro &amp;amp; Barton, &lt;em&gt;Science&lt;/em&gt; (2003); &lt;strong&gt;300&lt;/strong&gt;: 321-4&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-08-24T14:08:21.160" LastActivityDate="2015-08-24T14:08:21.160" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34597" PostTypeId="1" AcceptedAnswerId="34598" CreationDate="2015-05-27T13:51:48.187" Score="2" ViewCount="65" Body="&lt;p&gt;Oogonia are the precursors of oocytes in females present during embryonic development. I was wondering whether these stem cells are still present in the ovaria at puberty?&lt;/p&gt;&#xA;" OwnerUserId="15945" LastEditorUserId="9943" LastEditDate="2015-05-27T14:01:56.603" LastActivityDate="2015-05-27T14:01:56.603" Title="Do females retain oogonia after puberty?" Tags="&lt;reproductive-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34598" PostTypeId="2" ParentId="34597" CreationDate="2015-05-27T14:01:26.373" Score="2" Body="&lt;p&gt;From &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10008/&quot; rel=&quot;nofollow&quot;&gt;Developmental Biology, 6&lt;sup&gt;th&lt;/sup&gt; edition&lt;/a&gt; I learned the following: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In humans, the oogonia divide to form a limited number of egg precursor cells. In the human embryo, the thousand or so &lt;strong&gt;oogonia&lt;/strong&gt; divide rapidly from the second to the seventh month of gestation to form roughly 7 million &lt;strong&gt;germ cells&lt;/strong&gt;. After the seventh month of embryonic development the number of germ cells drops and most oogonia die during this period, while the remaining oogonia enter the first meiotic division. These latter cells, called the &lt;strong&gt;primary oocytes&lt;/strong&gt;, progress through the first meiotic prophase until the diplotene stage, at which point they are maintained until puberty.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, at puberty the cells from the lineage of oogonia are called primary oocytes. So from a terminological perspective, you are correct that &lt;strong&gt;no oogonia are thought to be left at puberty&lt;/strong&gt;. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-05-27T14:01:26.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34599" PostTypeId="2" ParentId="34591" CreationDate="2015-05-27T14:20:13.443" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Assuming you wish to have a common name for both of these (widely differing!) pathways I basically agree with @Chris, and I would go for general terminology, namely &lt;strong&gt;metabolic pathways&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Pentose_phosphate_pathway&quot; rel=&quot;nofollow&quot;&gt;pentose-phosphate pathway&lt;/a&gt; is neither anabolic nor catabolic so those terms won't do. The pentose-phosphate pathway is, however, closely linked to general metabolism to supply the body with C&lt;sub&gt;5&lt;/sub&gt; sugars. So metabolic pathway sounds right to me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other pathway is a sulfate reduction pathway, which is an &lt;a href=&quot;http://en.wikipedia.org/wiki/Dissimilatory_sulfate_reduction&quot; rel=&quot;nofollow&quot;&gt;anaerobic respiration&lt;/a&gt; pathway that uses sulfate as the terminal electron acceptor instead of oxygen. It is an &lt;em&gt;entirely different pathway&lt;/em&gt;. However, it too is neither catabolic or anabolic, but still closely linked to metabolism. Hence, metabolic pathway is applicable here too.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-27T15:06:21.033" LastActivityDate="2015-05-27T15:06:21.033" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34600" PostTypeId="1" AcceptedAnswerId="34603" CreationDate="2015-05-27T14:32:43.133" Score="4" ViewCount="715" Body="&lt;p&gt;What is this plant? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Location: Bangalore, India&#xA;&lt;img src=&quot;https://i.stack.imgur.com/JAPB6.jpg&quot; alt=&quot;Fruit&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/oqkuE.jpg&quot; alt=&quot;Fruit&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/LjU6J.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="8186" LastActivityDate="2015-05-27T15:03:59.400" Title="What is this Tree?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34601" PostTypeId="1" AcceptedAnswerId="35314" CreationDate="2015-05-27T14:34:57.327" Score="3" ViewCount="599" Body="&lt;p&gt;I would like to know: how many restriction sites does a restriction enzyme use on a DNA molecule? In other words: If a sequence on a plasmid contains the following bases:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;ATT&lt;strong&gt;GCAGT&lt;/strong&gt;CTG&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and I want to have only the bases in bold as a new, separate molecule, will I need two restriction enzymes (One to cut the molecule between the T and G and another one to cut it between the T and C)? Or one restriction enzyme (that will cut them both)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It wasn't clear enough in Wikipedia and in my biology book.&lt;/p&gt;&#xA;" OwnerUserId="15946" LastEditorUserId="3340" LastEditDate="2015-06-18T10:29:36.030" LastActivityDate="2015-10-03T18:08:46.437" Title="Restriction sites" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;restriction-enzymes&gt;" AnswerCount="2" CommentCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="34602" PostTypeId="1" AcceptedAnswerId="39016" CreationDate="2015-05-27T14:50:54.977" Score="19" ViewCount="552" Body="&lt;p&gt;CNN &lt;a href=&quot;http://www.cnn.com/2015/05/19/africa/namibia-rhino-hunt/&quot;&gt;recently covered&lt;/a&gt; a sanctioned black rhino hunt in Namibia by Texan Corey Knowlton, who bid US$350,000 for the license. In the story, he claims that the hunt was actually supporting conservation of the &lt;a href=&quot;http://www.worldwildlife.org/species/black-rhino&quot;&gt;critically endangered&lt;/a&gt; species, as they were looking to kill an older, non-reproducing male that was consuming resources and potentially threatening younger, breeding males. The Namibian government has a list of 18 rhinos in the country (out of a total population of about 2,000) that meet the criteria.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Knowlton is targeting one of four black rhinos at the top of the government list, the ones considered &quot;high priority threats to the herd.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Knowlton eventually caught up to and killed the animal he was targeting, and &lt;a href=&quot;http://www.cnn.com/2015/05/20/africa/namibia-rhino-hunt-meat/&quot;&gt;donated the meat&lt;/a&gt; to a local village.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CNN.com later published two opinion pieces, one &lt;a href=&quot;http://www.cnn.com/2015/05/21/opinions/rhino-hunt-is-conservation/index.html&quot;&gt;in support of the hunt&lt;/a&gt; by Dr. Mike Knight, the Chairman of the International Union for Conservation of Nature (IUCN) Species Survival Commission's African Rhino Specialist Group (AfRSG) and the South African Development Community Rhino Management Group (SADC RMG), and one &lt;a href=&quot;http://www.cnn.com/2015/05/19/opinions/trophy-hunting-not-conservation-flocken/&quot;&gt;opposed to it&lt;/a&gt; by Jeffrey Flocken, the North America Regional Director of the International Fund for Animal Welfare (IFAW). Knight cites black rhino-specific data in his piece, arguing that in the case of this particular species, limited hunting is actually beneficial. Flocken instead uses a wider argument, citing hunting of polar bears, elephants, and lions, among other species, and claiming that the idea of &quot;conservation hunting&quot; as a whole is flawed. He does not, however, directly address the situation of black rhinos.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have evaluated each side's argument, but have not yet formed a solid opinion, which is why I'm asking here. In the specific case of the black rhino, does the science support the notion of limited elimination of older males? Are there studies that show this has led to an increase in other types of conservation efforts? Does the money spent for licenses actually go towards conservation and assistance for locals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a second, optional question: Are the arguments posed by Flocken against &quot;conservation hunting&quot; in general supported by independent research? Just thinking logically I can imagine they are, as a lot of what he says makes sense in a broader context, if not necessarily in the case of the black rhino. Is there a scientific case for limited, situation-specific hunting, or should all forms of it be discouraged?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;em&gt;Note: I'm asking this here instead of Skeptics because I'm looking for a scientifically-supported answer. If you think it's better suited there, let me know and I'll move it.&lt;/em&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="3624" LastEditDate="2015-05-27T21:50:11.450" LastActivityDate="2016-10-05T04:49:41.273" Title="Was the recent &quot;conservation hunt&quot; of a black rhino supported by science?" Tags="&lt;zoology&gt;&lt;ecology&gt;&lt;population-biology&gt;&lt;conservation-biology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34603" PostTypeId="2" ParentId="34600" CreationDate="2015-05-27T14:58:53.890" Score="11" Body="&lt;p&gt;It looks very very suggestive for Artocarpus altilis or &lt;a href=&quot;http://en.wikipedia.org/wiki/Breadfruit&quot; rel=&quot;nofollow noreferrer&quot;&gt;Breadfruit tree&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another variants -  &lt;a href=&quot;http://en.wikipedia.org/wiki/Artocarpus_camansi&quot; rel=&quot;nofollow noreferrer&quot;&gt;Artocarpus camansi&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/c02P4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-05-27T15:03:59.400" LastActivityDate="2015-05-27T15:03:59.400" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34604" PostTypeId="1" AcceptedAnswerId="34607" CreationDate="2015-05-27T16:28:25.747" Score="-1" ViewCount="203" Body="&lt;p&gt;If I wanted to examine human tissue samples, such as hair, blood, fingernails, etc, for their DNA, what primers would I use for the amplification of the DNA when extracted(PCR)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;edit: To look at the STR in the human genome based off of the FBI's CODIS system &lt;a href=&quot;http://en.wikipedia.org/wiki/Combined_DNA_Index_System&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Combined_DNA_Index_System&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;from wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;CODIS identifies genetic markers at 13 STR loci, plus Amelogenin (AMEL) to determine sex.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;CSF1PO&#xA;D3S1358&#xA;D5S818&#xA;D7S820&#xA;D8S1179&#xA;D13S317&#xA;D16S539&#xA;D18S51&#xA;D21S11&#xA;FGA&#xA;THO1&#xA;TPOX&#xA;vWA&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read something about CODIS, but I don't know too much about it, if any one could give me some specifics that would be helpful.&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="14815" LastEditDate="2015-05-27T17:52:13.740" LastActivityDate="2015-05-27T20:08:01.483" Title="Primers for human tissue?" Tags="&lt;human-genetics&gt;&lt;pcr&gt;&lt;primer&gt;" AnswerCount="2" CommentCount="4" ClosedDate="2015-05-28T04:30:21.410" ContentLicense="CC BY-SA 3.0" />
  <row Id="34606" PostTypeId="2" ParentId="34590" CreationDate="2015-05-27T18:30:24.857" Score="6" Body="&lt;p&gt;Bearing in mind that the information is bound to be incomplete (as is the list of existing species), you could use the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/taxonomy&quot;&gt;NCBI taxonomy&lt;/a&gt; database. For example, checking the page for the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&amp;amp;id=7215&amp;amp;lvl=3&amp;amp;keep=1&amp;amp;srchmode=1&amp;amp;unlock&quot;&gt;Drosophila genus&lt;/a&gt; will give you an idea of its size. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more precise numbers, you can download the &lt;code&gt;taxdump.tar.gz&lt;/code&gt; file from NCBI's FTP server (&lt;a href=&quot;ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz&quot;&gt;link&lt;/a&gt;), extract it and run the script below on the file &lt;code&gt;nodes.dmp&lt;/code&gt; (a dump of the database info). &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;#!/usr/bin/perl&#xA;use strict;&#xA;use warnings;&#xA;use Getopt::Std;&#xA;my (%opts,%children,%ranks);&#xA;getopts('t:',\%opts) || do { print STDERR &quot;Invalid option&quot;; exit(1); };&#xA;&#xA;my $taxid=$opts{t}||die &quot;Need a taxid: -t\n&quot;;&#xA;&#xA;sub getchildren{&#xA;    my $p=shift; ## The taxid of interest&#xA;        my $found=0; ## will be 0 unless we find a new kid&#xA;    ## For each child of this taxid&#xA;    foreach my $kid (keys%{$children{$p}}){&#xA;    	## Get the kid's kids&#xA;    	foreach my $gkid (keys%{$children{$kid}}){&#xA;    	    ## If this one hasn't been seen before&#xA;    	    unless (defined($children{$p}{$gkid})) {&#xA;    		## Add it to the list of this taxid's children&#xA;    		$children{$p}{$gkid}++;&#xA;    		## We found a new one, we need to test again. &#xA;    		$found=1;&#xA;    	    }&#xA;    	}&#xA;        }&#xA;        ## If we found a new one, run again&#xA;        getchildren($p) if $found==1;&#xA;    }&#xA;    while (&amp;lt;&amp;gt;) {&#xA;        ## Remove trailing newlines&#xA;        chomp;&#xA;        ## Parse the current line&#xA;        my ($name,$parent,$rank,$rest)=split(/\s*\|\s*/);&#xA;        ## Save the current taxid as a child of its parent&#xA;        $children{$parent}{$name}++;&#xA;        ## Save its rank (species, genus, order etc)&#xA;        $ranks{$name}=$rank;&#xA;}&#xA;&#xA;## Recursively get all children of this taxid&#xA;getchildren($taxid);&#xA;&#xA;# Count only species as children&#xA;my @kids=grep($ranks{$_} eq &quot;species&quot;, keys(%{$children{$taxid}}));&#xA;&#xA;# Print out the results&#xA;printf &quot;Genus %s has %s members\n&quot;, $taxid, scalar(@kids);&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Assuming you are on or have access to a *nix environment, save that file as &lt;code&gt;genus.pl&lt;/code&gt; and run it on the &lt;code&gt;nodes.dmp&lt;/code&gt;, giving the taxid of your genus of interest:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;perl genus.pl -t 9257 nodes.dmp&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The output of the above example (Ornithorhynchus) is:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;$ perl genus.pl -t 9257 nodes.dmp &#xA;Genus 9257 has 1 members&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;If we try on Drosophila, we get:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;$ perl genus.pl -t 7215 nodes.dmp &#xA;Genus 7215 has 738 members&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;This is realy not the most efficient way to do it (far better to do this in the script itself but I don't have the time to implement that now), but if you don't mind waiting, this will give you the numbers for &lt;em&gt;all&lt;/em&gt; genera:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;for i in $(grep -w genus nodes.dmp | awk '{print $1}'); do &#xA;        perl genus.pl -t $i nodes.dmp; &#xA;done&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2015-05-27T18:42:40.970" LastActivityDate="2015-05-27T18:42:40.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34607" PostTypeId="2" ParentId="34604" CreationDate="2015-05-27T18:52:39.963" Score="3" Body="&lt;p&gt;The &lt;a href=&quot;http://en.wikipedia.org/wiki/Combined_DNA_Index_System#References&quot; rel=&quot;nofollow&quot;&gt;References&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Combined_DNA_Index_System#External_links&quot; rel=&quot;nofollow&quot;&gt;External Links&lt;/a&gt; sections of the Wikipedia article in your question contain a great deal of relevant information to get you started. There is a link to the FBI's CODIS and NDIS (National DNA Index System) Fact Sheet, which contains a lot of relevant information, including part numbers for validated kits from several manufacturers. DOI numbers for some journal articles are given in the Wikipedia article as well, wherein you may be able to find specific primer sequences or references for them. Finally, there is a link to the main CODIS page on FBI.gov, which contains an abundance of useful information, including the NDIS operational procedures manual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You just need to look to find what you seek.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-05-27T18:52:39.963" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34608" PostTypeId="2" ParentId="34604" CreationDate="2015-05-27T20:08:01.483" Score="1" Body="&lt;p&gt;Extracting genomic DNA and PCR are different processes. Extracting genomic DNA means that you get all the DNA sequences from human genome. Using extracted DNA, you can amplify a specific region from the whole genomic sequence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A primer set is usually set at the both ends of a sequence you want to amplify the sequence. In your case, you the region highlighted in yellow in the figure &quot;CODIS markers&quot; of the wiki would be amplified.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Different people may set primers differently even if they want to amplify the same region; however, in this case, primer sequences are already determined to get consistent results. If you would like to know the actual sequences that FBI is using, you (or someone or I) have to search to find them.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-05-27T20:08:01.483" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34610" PostTypeId="2" ParentId="34583" CreationDate="2015-05-27T21:31:05.977" Score="3" Body="&lt;p&gt;200uM dNTPs in 50ul reaction mix could produce more than 10ug DNA if all dNTPs were consumed whatever the length of PCR products is. You could detect as low as 5ng DNA fragments by conventional electrophoresis using EtBr. You probably could see a clear band when you load more than 100ng of a DNA fragment. Therefore I am not worried much about the dNTP concentration. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The longer PCR products you amplify, the more difficult it is to amplify. Then you may not get enough efficiency to detect your PCR products. You might want to try lower annealing temp if you do not get any none-specific bands with/without some additives such as DMSO, betain, etc., or use more stronger enzymes. Also touch down PCR may be useful to get specific bands efficiently. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you increase dNTP concentration, Mg++ effects may be muted because dNTP could chelate Mg++ as Chris mentioned in the comment column.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-05-27T23:31:51.923" LastActivityDate="2015-05-27T23:31:51.923" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34611" PostTypeId="1" AcceptedAnswerId="34640" CreationDate="2015-05-27T22:39:27.803" Score="5" ViewCount="86" Body="&lt;p&gt;In martial art people hit their body (e.g., with small bean bags) to become more insensitive to pain. Can the sensory neurons die during this procedure? I think this is just an urban legend. Instead, I think the skin receptors desensitize, but they don't degenerate by the constant mechanical stress. However, I cannot find any research in the topic.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="9943" LastEditDate="2015-05-28T13:07:10.133" LastActivityDate="2015-05-28T22:04:05.353" Title="Can nociceptors die because of too much mechanical stress?" Tags="&lt;neuroscience&gt;&lt;sensation&gt;&lt;pain&gt;&lt;adaptation&gt;&lt;human-physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34613" PostTypeId="2" ParentId="34578" CreationDate="2015-05-27T23:17:24.457" Score="1" Body="&lt;p&gt;It may depend on which protocol you looking at, but you can use a specific primer set for the first PCR and another specific primer set for the second PCR. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if you use a none specific primer set for the first PCR, it could be easier to amplify your target sequence because your target sequence would be more abundant than the original solution before the first PCR is performed.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-05-27T23:17:24.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34614" PostTypeId="1" CreationDate="2015-05-27T23:22:51.607" Score="4" ViewCount="76" Body="&lt;p&gt;I found a very interesting branch last week, and have been trying to identify it but cannot seem to find the answer. If anyone has any suggestion, I would be grateful. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found it near the forest, around WA area.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's some picture:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ahQMj.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/WHGCn.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/VweT4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/1KnzF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="15954" LastEditorUserId="9686" LastEditDate="2018-06-25T05:36:21.317" LastActivityDate="2018-06-25T05:36:21.317" Title="Tree identification from dried branch" Tags="&lt;species-identification&gt;&lt;trees&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34615" PostTypeId="2" ParentId="34572" CreationDate="2015-05-27T23:23:18.587" Score="-1" Body="&lt;p&gt;You need a ribosomal binding site before the initial codon.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-05-27T23:23:18.587" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34616" PostTypeId="1" CreationDate="2015-05-28T00:07:52.060" Score="5" ViewCount="1125" Body="&lt;p&gt;There is a book that says to store Bacillus spores in 50% glycerol at -70 degrees Celsius (doesn't mention if the 50% is final concentration or not). But from what I know, the cells themselves can be stored in any % glycerol as long as the final glycerol concentration is 15% (v/v) at -80 degrees Celsius. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a difference between preserving spores and cells? Because the book said to preserve the cells at a certain glycerol concentration and the spores at a different glycerol concentration. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, say I scrape some B. subtilis out from the cryovial for reuse, and they are frozen. Do I wait for the scraped cells to thaw and then plate them, or plate them while they are still frozen? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if I want to sporulate these cells, should I recover these frozen cells by plating and incubating overnight, or can I just drop them directly into the sporulation medium? I want to get the details down properly.&lt;/p&gt;&#xA;" OwnerUserId="15955" LastEditorUserId="9943" LastEditDate="2015-05-28T02:34:52.547" LastActivityDate="2015-05-28T05:55:03.963" Title="Is there a protocol for freezing and thawing Bacillus subtilis cells?" Tags="&lt;biochemistry&gt;&lt;lab-techniques&gt;&lt;biotechnology&gt;&lt;lab-reagents&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34617" PostTypeId="1" CreationDate="2015-05-28T00:31:29.913" Score="6" ViewCount="87" Body="&lt;p&gt;I was jogging when I asked myself this question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In running contests the standard running direction is counterclockwise; I also believe to remember that the regulation is very old (right back to the Greeks and Romans). I suppose the reason is that most people have a stronger dominant right leg and running counterclockwise feels more natural.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now there are people who are &quot;left-legged&quot;: They have a stronger and dominant left leg. What I ask is: How would the times change overall if we revert the direction and let the runners run clockwise ? Has someone experimented with it ? Is the effect discernible or even decisive ? Would left-legged people get an advantage ?&lt;/p&gt;&#xA;" OwnerDisplayName="user10094" LastEditorUserId="9943" LastEditDate="2015-05-29T14:02:14.233" LastActivityDate="2015-11-17T08:28:29.603" Title="How pronounced is the difference if we would change the running direction for runners?" Tags="&lt;human-biology&gt;&lt;movement&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34618" PostTypeId="1" CreationDate="2015-05-28T01:02:54.747" Score="3" ViewCount="680" Body="&lt;p&gt;It's easy to keep your legs straight when you're standing up or laying flat on your back, but as soon as you try to sit up or bend down, you need to bend your knees as well as your waist.  (Try it.  Lay down flat on the floor, then try to sit up straight while keeping the backs of your knees pressed against the ground.  You'll have trouble long before you reach 90 degrees.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is this?&lt;/p&gt;&#xA;" OwnerUserId="6683" LastActivityDate="2015-05-28T05:41:34.120" Title="Why is it difficult to bend the waist while keeping the knees straight?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34620" PostTypeId="1" AcceptedAnswerId="34621" CreationDate="2015-05-28T01:42:41.070" Score="3" ViewCount="1238" Body="&lt;h2&gt;Disclaimer: This question is NOT about challenging the safety or efficacy of vaccines. It is only asking for tips on providing credible references that may show harmful effects of vaccination, if any.&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;In my French class, we were asked to debate an issue in current events. My topic is vaccines in children or adults. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The challenging part is that I was assigned to argue &lt;strong&gt;against&lt;/strong&gt; vaccination, and I have to back up my arguments with credible sources (not blogs) that are in French. Hopefully some of you could point me towards some links to articles or research papers in French.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Please avoid discussion on safety and efficacy of vaccines, including local and global policies on their use. I just need help with this topic for my French class&lt;/h2&gt;&#xA;" OwnerUserId="15957" LastEditorUserId="9943" LastEditDate="2015-05-29T00:51:34.287" LastActivityDate="2015-05-29T00:51:34.287" Title="Are there any papers arguing against vaccination in French?" Tags="&lt;vaccination&gt;" AnswerCount="4" CommentCount="15" FavoriteCount="1" ClosedDate="2015-05-28T20:04:54.777" ContentLicense="CC BY-SA 3.0" />
  <row Id="34621" PostTypeId="2" ParentId="34620" CreationDate="2015-05-28T01:56:12.747" Score="10" Body="&lt;p&gt;I wish you good luck, as 99.99% of the anecdotal claims out there that conclude vaccination is bad are based on unfounded rumors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that much of the negative public opinion is based on a fraudulent (and retracted) paper by &lt;a href=&quot;http://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2897%2911096-0/abstract&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Wakefield in The Lancet (1998)&lt;/em&gt;&lt;/a&gt;. Unfortunately for you, however, it is in English. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My French is a bit rusty, but if you go to &lt;a href=&quot;https://scholar.google.com.au/schhp&quot; rel=&quot;nofollow&quot;&gt;Google Scholar&lt;/a&gt; and type in a search term like &lt;strong&gt;vaccination results in autism&lt;/strong&gt; (&lt;em&gt;les résultats de la vaccination dans l'autisme&lt;/em&gt;) or &lt;em&gt;Wakefield vaccination autisme&lt;/em&gt; something might pop up in French that advocates against vaccination.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-28T11:18:32.467" LastActivityDate="2015-05-28T11:18:32.467" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34622" PostTypeId="2" ParentId="34620" CreationDate="2015-05-28T01:56:17.140" Score="4" Body="&lt;p&gt;The Wakefield study has &lt;a href=&quot;http://www.nytimes.com/2015/02/02/us/a-discredited-vaccine-studys-continuing-impact-on-public-health.html&quot; rel=&quot;nofollow&quot;&gt;collapsed as fraud&lt;/a&gt;, and there are no credible sources that make persuasive scientific arguments against being vaccinated in today's world -- not even in French. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="13072" LastEditDate="2015-05-28T01:57:20.060" LastActivityDate="2015-05-28T01:57:20.060" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34623" PostTypeId="2" ParentId="34618" CreationDate="2015-05-28T04:04:54.080" Score="4" Body="&lt;p&gt;First off, I would be careful generalizing people's experiences with this exercise (...&lt;em&gt;&quot;Try it...You'll have trouble long before you reach 90 degrees&quot;&lt;/em&gt;...):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HuTLm.jpg&quot; alt=&quot;ham strings&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: &lt;a href=&quot;http://www.yogatuneup.com/blog/2011/03/16/overstretching/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yoga Tune Up&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The muscles you are feeling at 90&lt;sup&gt;o&lt;/sup&gt;, and the lady pictured above perhaps not even at 180&lt;sup&gt;o&lt;/sup&gt; are the &lt;a href=&quot;http://www.precisionnutrition.com/quad-hamstring-ratio&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;hamstrings&lt;/strong&gt;&lt;/a&gt;. They run along the back of your thigh, attaching at both the hip and the knee. They flex the knee and extend (straighten) the hips. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SIvrj.jpg&quot; alt=&quot;hamstrings&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Source: &lt;a href=&quot;http://www.precisionnutrition.com/quad-hamstring-ratio&quot; rel=&quot;nofollow noreferrer&quot;&gt;Precision Nutrition&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you do the exercise you are describing, the pelvis starts pulling on the hamstrings from the top because your knees are staying in place. Bending the knees releases the stretch.  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-28T05:41:34.120" LastActivityDate="2015-05-28T05:41:34.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34624" PostTypeId="2" ParentId="34572" CreationDate="2015-05-28T04:58:32.170" Score="1" Body="&lt;p&gt;By &quot;still work&quot; I assume you are asking if it will still be recognized by an antibody? It might. Internal T7 tag fusions are done, though they may require different antibodies than terminally tagged fusions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, do you have a reason for inserting the the tag after methionine? The T7 tag already starts with methionine and naturally functions to initiate translation of T7 gene10. pET based vectors also contain it for this purpose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FYZlX.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;[&lt;a href=&quot;http://www.chem.agilent.com/library/usermanuals/Public/211521.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this vector, your gene of interest is typically inserted after the tag to create a fusion protein (using BamHI) or immediately after the start codon (using NheI). In either case, the T7 tag start codon is used. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-05-28T04:58:32.170" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34625" PostTypeId="2" ParentId="15897" CreationDate="2015-05-28T05:32:24.533" Score="3" Body="&lt;p&gt;As pointed out by others a reference gene should not change its expression between the control and test samples. Reference gene need not be a housekeeping gene; housekeeping genes are generally used because they are present in all cells are are not subject to any specific regulation. However, global changes in the cell, such as stress or development, can affect housekeeping genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you are not sure about which gene to choose as a reference then you can use a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17373485&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;spike in&lt;/strong&gt;&lt;/a&gt; control. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The change in your experiment could be a result of human error. You should replicate the experiment to see if the trend remains the same. If your gene shows consistent trend in all replicates then the change is not likely because of human error. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general you should choose the reference gene based on your prior knowledge about the condition that you are testing. For example if I am studying cell migration then I would not use Actin as a control. If you are studying processes that may affect metabolic rate then you should perhaps not use GAPDH as a control.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another good reference gene(s) that is also constitutive would be that for a ribosomal protein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also have a look at &lt;a href=&quot;https://biology.stackexchange.com/questions/31433/correct-complete-representation-of-rtpcr-statistics/31446#31446&quot;&gt;this&lt;/a&gt; post for statistical analysis of RTPCR data.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-05-28T05:32:24.533" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34626" PostTypeId="2" ParentId="34616" CreationDate="2015-05-28T05:55:03.963" Score="2" Body="&lt;p&gt;While I have never done bacterial stock cultures from spores, I don't think it is necessary, as the standard procedure for making bacterial stocks should work without problems. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For that you grow your bacteria in liquid culture until you reach the late log phase (so you have a lot of bacteria in your media), take 1 ml of the culture, mix it with 100% glycerol to reach a final glycerol concentration of 50% and then freeze it a -80°C. At this you can store it for long times (probably not indefinitely but for years is possible). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you want bring your cultures back to life, take the tube and either use an inocculation loop or a pipette tip to scrape a bit of the frozen culture and plate it on an appropriate agar plate. If you want to scale up, pick one colony from the plate into liquid media.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since glycerol is a pain to pipette (and can also have sterility problems), I have switched over to DMSO as a cryo-protective agent for bacterial cultures as well. Simply add 15% (end concentration) DMSO into the cryo vials (so 150ul DMSO to 850 of culture), mix and then freeze the cells. In my experience this works as good as glycerol.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-05-28T05:55:03.963" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34627" PostTypeId="2" ParentId="34427" CreationDate="2015-05-28T06:23:33.843" Score="2" Body="&lt;p&gt;Not too sure but it seems like the european garden spider- &lt;a href=&quot;http://en.wikipedia.org/wiki/Araneus_diadematus&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Araenus diadematus&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hqbnS.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[ &lt;a href=&quot;http://www.gettyimages.in/detail/photo/european-garden-or-cross-spider-spiderlings-high-res-stock-photography/106455259&quot; rel=&quot;nofollow noreferrer&quot;&gt;Image source&lt;/a&gt; ]&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-05-28T06:23:33.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34628" PostTypeId="2" ParentId="15897" CreationDate="2015-05-28T07:05:23.713" Score="2" Body="&lt;p&gt;I'm gonna throw a curve ball here. :) I think the &quot;housekeeping&quot; or &quot;reference gene&quot; concept is fundamentally flawed, because it rests on circular logic. In order to verify that a &quot;housekeeping&quot; gene X is constant across your samples, you must assume that the $C_t$ values themselves are actually a valid measure, so that you can assess the expression level of X directly. But if $C_t$ values are assumed valid, then you don't need a housekeeping gene in the first place! This procedure &lt;em&gt;assumes&lt;/em&gt; what it intends to prove; therefore it is circular.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The normalization problem is just not solvable without additional assumptions. A spike-in control works if you are worried about technical variation, but it does not address biological variation. A reasonable assumption I think is that the total mRNA pool is constant; this underlies most normalization methods used in microarray or RNA-seq analysis. For RT-PCR, this assumption can be tested using cDNA dyes, as &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16925017&quot; rel=&quot;nofollow&quot;&gt;in this paper&lt;/a&gt;. (cDNA is advantagous rather than isolated RNA, because the reverse transcription step is notoriously noisy and should be controlled for.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my mind, housekeeping genes are only useful it you really know &lt;em&gt;in advance&lt;/em&gt; that they &lt;em&gt;must&lt;/em&gt; be constant, and do not need to check this assumption; then the logic is not circular. In this case, if you observe changing $C_t$ values for the housekeeping gene, then you must conclude that the experiment went wrong somehow, and the data should be discarded. But I think this is rarely the case in practise.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not the most common opinion on this often-debated matter, but I think it is the right one. :)&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-05-28T07:05:23.713" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34629" PostTypeId="2" ParentId="21197" CreationDate="2015-05-28T07:21:34.073" Score="7" Body="&lt;p&gt;They do! It's called &lt;a href=&quot;https://en.wikipedia.org/wiki/Necrophoresis&quot;&gt;necrophoresis&lt;/a&gt;, and it's a way of keeping infections from spreading. A paper published in 2009 suggest that &lt;a href=&quot;http://www.newscientist.com/article/dn17075-stench-of-life-prevents-ants-from-being-buried-alive.html&quot;&gt;ants constantly produce &quot;I'm alive&quot; chemicals while they're alive&lt;/a&gt;; once they die, the chemical is no longer produced and the ants are carted off.&lt;/p&gt;&#xA;" OwnerUserId="87" LastActivityDate="2015-05-28T07:21:34.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34630" PostTypeId="2" ParentId="33037" CreationDate="2015-05-28T08:03:38.370" Score="4" Body="&lt;p&gt;For many drugs, the animal cannot be slaughtered for consumption within a certain time. Here are the slaughter withdrawal periods for some common drugs when used on cattle. There are also withdrawal periods for lactating dairy cattle, but I won't list them for brevity. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;flunixin (NSAID) - 6 days&lt;/li&gt;&#xA;&lt;li&gt;florfenicol (antibiotic) - 36 days intramuscular, 55 days subcutaneous&lt;/li&gt;&#xA;&lt;li&gt;penicillin G procaine (antibiotic) - 10-14 days&lt;/li&gt;&#xA;&lt;li&gt;tilmicosin (antibiotic) - 28 days&lt;/li&gt;&#xA;&lt;li&gt;oxytetracycline (antibiotic) - 28 days intramuscular, 48 days subcutaneous&lt;/li&gt;&#xA;&lt;li&gt;enrofloxacin (antibiotic) - 36 days, do not use in veal calves&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;More importantly for your question, I have found this &lt;a href=&quot;http://www.vmd.defra.gov.uk/productinformationdatabase/SPC_Documents/SPC_339773.DOC&quot; rel=&quot;nofollow&quot;&gt;report on pentobarbital used for euthanizing cattle.&lt;/a&gt; It says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Adequate measures should be taken to ensure that carcasses of animals treated with this product and the by-products of these animals do not enter the food chain and are not used for human or animal consumption.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Barbiturates are more dangerous than many other drugs and, furthermore, dead animals cannot metabolize them and they can be quite heat stable (ie won't readily decompose during cooking). &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-05-28T08:03:38.370" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34631" PostTypeId="2" ParentId="27988" CreationDate="2015-05-28T08:21:10.793" Score="2" Body="&lt;p&gt;I think there's a difference between a vernacular or common name (&quot;tiger&quot;, &quot;cat&quot;, &quot;pigeon&quot;, &quot;elm&quot;, &quot;pine&quot;) and a &lt;em&gt;pet&lt;/em&gt; name or nickname as you use it here. The former are names in human languages for a particular kind of animal or plant, while the latter are a colloquial name used by professionals to refer to a particular species, often based on its scientific name.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't think of many micro-organisms that have a true vernacular name -- most micro-organisms were given fancy scientific names, and those were used consistently thereafter. The only proper microscopic common name I can think of is &quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/Paramecium&quot; rel=&quot;nofollow&quot;&gt;slipper animalcules&lt;/a&gt;&quot; -- but I'd be happy to be proved wrong! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lots of micro-organisms have pet-names -- &lt;em&gt;E. coli&lt;/em&gt;, &lt;em&gt;C. diff.&lt;/em&gt;, &quot;smallpox&quot;, &quot;Ebola&quot;, &quot;white nose&quot;, even &lt;em&gt;Pelagibacter ubique&lt;/em&gt; -- but they're either based on the scientific name or on the disease the organisms cause. AFAIK (and based on the comments), &lt;em&gt;Pseudomonas aeruginosa&lt;/em&gt; doesn't have one. However, of the list of species you list, only &lt;em&gt;H. sapiens&lt;/em&gt; has a vernacular name, while the others only have nicknames based on their scientific name, so I'm not sure it's that surprising! IMO it's mostly macro-organisms that get vernacular names.&lt;/p&gt;&#xA;" OwnerUserId="87" LastActivityDate="2015-05-28T08:21:10.793" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34632" PostTypeId="2" ParentId="34614" CreationDate="2015-05-28T08:39:55.323" Score="5" Body="&lt;p&gt;This looks like dried &lt;a href=&quot;http://www.desertusa.com/mag99/may/papr/chollas.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;cholla cactus&lt;/a&gt;, although it will be hard to determine the species. It is sold commonly for fishtanks, so might even be found in places where it does not grow naturally if someone cleaned out their fish tank.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ctgQt.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT by Ilan: on this image you can clearly see that the tree identified right:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/womZX.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3827" LastEditorUserId="5755" LastEditDate="2015-05-28T09:37:48.720" LastActivityDate="2015-05-28T09:37:48.720" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34635" PostTypeId="2" ParentId="23115" CreationDate="2015-05-28T10:54:37.723" Score="0" Body="&lt;p&gt;False.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Theoretically, a vaccine could be constructed for any pathogen, but the value of doing so if different. In business, this is called 'Return on Investment'. So, vaccines against serious common diseases are more valuable than ones against minor rare ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Polio, smallpox, whooping cough, rubella and typhoid are not rare. They are rare &lt;strong&gt;now&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="15962" LastActivityDate="2015-05-28T10:54:37.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34636" PostTypeId="1" CreationDate="2015-05-28T11:14:56.663" Score="2" ViewCount="734" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;In the first step of glycolysis, the glucose ring is phosphorylated.&#xA;  &lt;strong&gt;Phosphorylation is the process of adding a phosphate group to a molecule derived from ATP.&lt;/strong&gt; As a result, at this point in glycolysis,&#xA;  1 molecule of ATP has been consumed.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Is it the phosphate group, or the molecule, that is derived from ATP ? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sparknotes.com/biology/cellrespiration/glycolysis/section1.rhtml&quot; rel=&quot;nofollow&quot;&gt;http://www.sparknotes.com/biology/cellrespiration/glycolysis/section1.rhtml&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="11760" LastEditorUserId="9943" LastEditDate="2015-05-28T12:21:52.703" LastActivityDate="2015-05-28T21:19:38.587" Title="A question on glycolysis" Tags="&lt;cell-biology&gt;&lt;glucose&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34637" PostTypeId="2" ParentId="23115" CreationDate="2015-05-28T11:44:48.953" Score="0" Body="&lt;p&gt;A vaccine is not made because a pathogen is rare. It's made because a pathogen is so vicious that you're body does not have enough time to counteract it. Your body is always attacked by invaders, even now. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But usually the &lt;a href=&quot;http://en.wikipedia.org/wiki/Innate_immune_system&quot; rel=&quot;nofollow&quot;&gt;Innate immune responses&lt;/a&gt; are enough to rid you of the threat. And, when it isn't, it acts as a barrier until the &lt;a href=&quot;http://en.wikipedia.org/wiki/Adaptive_immune_system&quot; rel=&quot;nofollow&quot;&gt;adaptive responses&lt;/a&gt; fire up. This time gap is crucial, because the adaptive system needs antigenic presentation from the dendritic cells to differentiate B-cells into plasma and memory cells, then create antibodies and finally these antibodies will opsonize the pathogenic agent and then let the complement system or the CTLs take over.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is where vaccines come in, Vaccines generally but not always stimulate the Adaptive responses, allowing the creation of Plasma B cells and memory cells. So next time when an invader arrives, the Adaptive response responds as soon as an antigen is encountered. Which is why, the diseases mentioned above have become such a rarity, but rest assured that if individuals choose not vaccinate then these diseases will re-emerge once again as they are doing now in the US.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I cannot post more than 2 links, so if you're interested read up. and If you're even more interested, pick up a copy of Kuby's Immunology, it helped me when I was in college and I'm sure it will help you out too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;http:// en.wikipedia.org/wiki/Antigen_presentation&#xA;  http:// en.wikipedia.org/wiki/Dendritic_cell&#xA;  http:// en.wikipedia.org/wiki/B_cell&#xA;  http:// en.wikipedia.org/wiki/Opsonin&lt;/p&gt;&#xA;" OwnerUserId="15807" LastActivityDate="2015-05-28T11:44:48.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34638" PostTypeId="2" ParentId="34636" CreationDate="2015-05-28T12:00:05.277" Score="7" Body="&lt;p&gt;The question is a bit unclear, it should be reframed as suggested by AliceD. To simply answer the question, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glucose is the substrate, and in the first step it is converted to Glucose-6-phosphate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Only the Phosphate group is added which originates from ATP, your notes also are a bit misleading because it tends to suggest that Hydrogen is released, which is not the case, the phostphate group in ATP loses an OH and Glucose loses an H in an &lt;a href=&quot;http://en.wikipedia.org/wiki/SN2_reaction&quot; rel=&quot;nofollow noreferrer&quot;&gt;SN2 reaction&lt;/a&gt; giving rise to Water in the process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Always remember that ATP is categorized as an energy donor which drives chemical reactions in your body by breaking chemical bonds. ATP or Adenosine Triphosphate has three phosphate groups. The last Phosphate in ATP produces the highest amount of energy in any given chemical reaction where ATP is involved.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is an ATP molecule.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9kZft.jpg&quot; alt=&quot;Adenosine Triphosphate&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first P that you see is the Phosphate which gets released, and the ring that you see is a five member ring called a ribose sugar, while glucose is a six member ring.&lt;/p&gt;&#xA;" OwnerUserId="15807" LastActivityDate="2015-05-28T12:00:05.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34639" PostTypeId="1" AcceptedAnswerId="34653" CreationDate="2015-05-28T12:31:53.487" Score="7" ViewCount="143" Body="&lt;p&gt;I have to analyse two datasets consisting of time-series measurements of gene expression. One set are &lt;em&gt;in vivo&lt;/em&gt; data from the expression profiles obtained between a few days before birth to several days post-partum. The second data set was obtained in a C2C12 cell line, where t = 0 was defined as the day in which 100% confluence was reached.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there an optimal way to align the two time series?&lt;/strong&gt; Simply aligning the two series using the two t= 0 samples as starting point seems arbitrary. &lt;/p&gt;&#xA;" OwnerUserId="15965" LastEditorUserId="9943" LastEditDate="2015-05-28T12:58:47.390" LastActivityDate="2015-05-28T17:32:51.903" Title="Comparison of gene expression time series in vitro and in vivo" Tags="&lt;bioinformatics&gt;&lt;gene-expression&gt;&lt;microarray&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34640" PostTypeId="2" ParentId="34611" CreationDate="2015-05-28T12:49:14.043" Score="4" Body="&lt;p&gt;As far as I know, adaptation of peripheral receptors, including pain receptors, is &lt;em&gt;transient&lt;/em&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3854565/&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Giniatullin &amp;amp; Nistri, 2013)&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead, my educated guess is that the increase in &lt;em&gt;subjective pain threshold&lt;/em&gt; plays an important role. Pain thresholds differ between the sexes &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0304395902003305&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Chesterton et al., 2003)&lt;/a&gt;, and depend on disease and physical status &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0304395902003305&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Kosak et al., 1996)&lt;/a&gt;. Repeated exposure to painful stimuli hardens one mentally (I have practiced martial arts for two decades ). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Morever, there is an interesting answer on &lt;a href=&quot;https://martialarts.stackexchange.com/&quot;&gt;Martial Arts SE&lt;/a&gt; on the question &lt;a href=&quot;https://martialarts.stackexchange.com/questions/375/how-should-i-expect-my-fist-to-change-over-time-from-punching&quot;&gt;How should I expect my fist to change over time from punching?&lt;/a&gt; Here it is shown that extensive training stimulates the growth of additional skin and bone. Extra skin (&lt;em&gt;calluses&lt;/em&gt;) may dampen the impact of painful pressure stimuli.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0304395902003305&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chesterton et al., &lt;em&gt;pain&lt;/em&gt; (2003); &lt;strong&gt;101&lt;/strong&gt;(3): 259–66&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3854565/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Giniatullin &amp;amp; Nistri, &lt;em&gt;Front Cell Neurosci&lt;/em&gt; (2013); &lt;strong&gt;7&lt;/strong&gt;(245): 1-9&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0304395902003305&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kosak et al., &lt;em&gt;pain&lt;/em&gt; (1996); &lt;strong&gt;64&lt;/strong&gt;(3): 415–23&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:49:44.180" LastActivityDate="2015-05-28T22:04:05.353" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34641" PostTypeId="2" ParentId="34620" CreationDate="2015-05-28T13:53:34.147" Score="4" Body="&lt;p&gt;You will not find good, credible sources arguing against vaccination. However, spewing nonsense is not necessary for winning your debate. You can collect good, credible sources arguing against specific vaccinations and use them to paint the opposing side as pro-vaccination zealots who unquestioningly want to stuff vaccines down everybody's veins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vaccines, like other treatments, have to be approved by health authorities, and therefore, the possible side effects are being studied in clinical trials. All you have to do is find a few cases where there side effects were a bit more severe than anticipated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A good start for your research could therefore be publications about the risks of vaccination. On Google Scholar, &quot;risques vaccination&quot; brings up hits like &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0248866305002742&quot; rel=&quot;nofollow&quot;&gt;Risk-Benefit assessment of hepatitis B vaccination in France (in French)&lt;/a&gt; that can give you a good basis for gathering material against vaccination. &lt;/p&gt;&#xA;" OwnerUserId="34" LastEditorUserId="34" LastEditDate="2015-05-28T15:38:49.407" LastActivityDate="2015-05-28T15:38:49.407" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34642" PostTypeId="2" ParentId="31522" CreationDate="2015-05-28T14:13:42.633" Score="1" Body="&lt;p&gt;The first resource I would look at would be the TCGA publication on NSCLC which can be found at &lt;a href=&quot;https://www.nature.com/articles/nature13385&quot; rel=&quot;nofollow noreferrer&quot;&gt;this location&lt;/a&gt;. The first figure shows the most frequently mutated genes. TP53 rises to the top as most frequently mutated gene in the cohort studied, however, one also sees on the list KEAP1, NF1, ARID1A, SMARCA4, RB1, and CDKN2 as commonly altered tumor suppressors TSGs. You will want to take into account copy number data and mutation data in the frequency count in cohort also. Another issue to check in the data set is stage of the tumors in TCGA. You mentioned 'early stage' in your query, but if all the samples in TCGA are recurrent then it may not be appropriate for your question. The cBioPortal resource allows you to look and manipulate the data and I encourage you to look at that resource. It is very well done and shouldn't have too much of a learning curve. You will be able to put in TSGs and get back the freq of mutations. They may also have information on stage so might be possible to filter for only those samples. There are also a couple of text-mining resources that you can ask queries through pubmed to get back gene lists or to link gene lists. One tool is Glad4U (search this name in google) which allows you to type a query such as: &quot;tumor suppressor AND early stage NSCLC&quot; and it will return a ranked list of genes. Ranking is based on co-citation. However, one must check the returned list to make sure the genes returned are TSGs. A listing of putative TSGs can be found &lt;a href=&quot;https://docs.google.com/spreadsheets/d/1JFUFg10UX8vxZ0hMbYIKHoceJJ7dzeDW8xbus9q-kyk/edit#gid=1679505956&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;. The second resource is CoCiter v2.0. On the Gene-Term search you can rank the lists of TSGs against search terms and it will return a ranking of the TSGs most associated with your search term. Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="15967" LastEditorUserId="15950" LastEditDate="2018-07-15T19:26:14.057" LastActivityDate="2018-07-15T19:26:14.057" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="34643" PostTypeId="1" AcceptedAnswerId="34648" CreationDate="2015-05-28T14:15:46.770" Score="5" ViewCount="699" Body="&lt;p&gt;I have the following assignment where I am to look at the &quot;tree&quot; (not sure the english word) and assign whether or not they can be autosomal dominant or recessive as well whether they can be X-linked recessive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/l5tP4.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My way to try and complete this assignment is by drawing a punnet's square but I quickly run into some confusion. When I draw my square, I know that is I'm checking for autosomal dominant, then I would draw the mother as A'a, the A' denoting the sick dominant allele. What I'm not sure is this: Can't I also draw her as A'A'? That would also mean she would be autosomal dominant but with 2 sick alleles. What about the father? Do I draw him as Aa, aa or AA? I'm a bit confused here!&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="3624" LastEditDate="2015-05-28T18:01:27.207" LastActivityDate="2015-05-28T18:01:27.207" Title="How do I know which alleles the parents have?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;homework&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34644" PostTypeId="2" ParentId="19575" CreationDate="2015-05-28T14:23:32.237" Score="1" Body="&lt;p&gt;Resonating provided a good general classification scheme that could be implemented for categorizing chemotherapeutic agents. Another resource that could be used is the following: &lt;a href=&quot;http://www.genome.jp/kegg/drug/&quot; rel=&quot;nofollow&quot;&gt;http://www.genome.jp/kegg/drug/&lt;/a&gt;. This is a pretty good classification of drugs based on ATC resource (&lt;a href=&quot;http://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Anatomical_Therapeutic_Chemical_Classification_System&lt;/a&gt;). These two resources are good starting points.&lt;/p&gt;&#xA;" OwnerUserId="15967" LastActivityDate="2015-05-28T14:23:32.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34645" PostTypeId="1" AcceptedAnswerId="34649" CreationDate="2015-05-28T14:25:34.143" Score="2" ViewCount="118" Body="&lt;p&gt;I see binding site and interface used almost interchangeably in the literature, but I'm not sure if it is exactly the same thing or not - what is the difference?&lt;/p&gt;&#xA;" OwnerUserId="13495" LastEditorUserId="948" LastEditDate="2015-05-28T16:31:14.520" LastActivityDate="2015-05-28T16:31:14.520" Title="In protein-protein interactions what is the difference between a binding site and an interface?" Tags="&lt;proteins&gt;&lt;protein-binding&gt;&lt;protein-interaction&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34646" PostTypeId="2" ParentId="34620" CreationDate="2015-05-28T14:27:23.297" Score="-1" Body="&lt;p&gt;The only angle I can think of that isn't &quot;Haha, I can't believe these people are allowed to vote&quot; is that the enemy we know is better than the enemy we do not know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see no reason why the classic argument of selection pressure doesn't apply. (See Warfrin(spelling?) resistance in rats, the resistant rats required more vitamin-k, thus more time out in the sun, so in a warfrin free environment are at a disadvantage, but thrive in an environment with warfrin)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately (fortunately) evidence doesn't really support that, in fact we have &lt;em&gt;eradicated&lt;/em&gt; several diseases already entirely and nothing replaced them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Long comment sorry)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way! Do tell us some of the arguments that come up! &lt;/p&gt;&#xA;" OwnerUserId="15968" LastActivityDate="2015-05-28T14:27:23.297" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34647" PostTypeId="2" ParentId="793" CreationDate="2015-05-28T14:41:59.510" Score="1" Body="&lt;p&gt;There are no perfect resources for this information in the public domain quite yet. However, there are three that are making really good progress. The first is mycancergenome at Vanderbilt. They were one of the first resources to put this type of information on the web. They tend to be pretty stringent in the level of evidence and type of aberrations that go on the Web site. However, I am not sure if you can programmatically access there information. The second resource, is the &lt;a href=&quot;https://pct.mdanderson.org&quot; rel=&quot;nofollow&quot;&gt;https://pct.mdanderson.org&lt;/a&gt; developed at MD Anderson. This is really good resources however, it is only for a handful of genes, but albeit some of the most frequently mutated. I don't see a programmatic access to the information. The third resource and most promising for the community is the CIVIC database: &lt;a href=&quot;https://civic.genome.wustl.edu/#/home&quot; rel=&quot;nofollow&quot;&gt;https://civic.genome.wustl.edu/#/home&lt;/a&gt;. This is crowdsourcing resource that is set up to aggregate cancer associated mutation to drugs, phenotypes, and outcomes. I highly recommend this site and encourage not only consumption of data but also to engage in comments. &#xA;   As someone that has been doing drug to genome matching a couple pieces of advice. DNA based alterations are the best evidence to use for matching. If you do RNA be a little bit more cautious of matching based on 'is a target' mechanism. So rank DNA based changes above RNA. Additionally, just start with drug targets as place holders but try to acquire information on alteration as it relates to drug response. So alterations in a drug target could be (and often) are passengers and not drivers and in this case will not respond to drug. Frequency in other tumors and mutations in important domains are good guides for triaging variants like this. Also, the information on the disease and the mutations is important. If a drug variant mutation is observed in one disease there maybe mechanisms intrinsic to another tumor type that would preclude acting on drug to variant association in the different tumor type. Lastly, drug mechanism is something to take into account. Certain drugs that hit the same target do so but in different mechanisms that may preclude them being given in the context of particular mutations. &#xA;Good luck in your endeavors.&lt;/p&gt;&#xA;" OwnerUserId="15967" LastActivityDate="2015-05-28T14:41:59.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34648" PostTypeId="2" ParentId="34643" CreationDate="2015-05-28T14:51:12.190" Score="2" Body="&lt;p&gt;Let's go step my step here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Going by your notation I'll call the square as Male and Circle as female.&#xA;So from this information I can confidently say that you disease is not X linked dominant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because Females carry XX, that would mean to be X linked dominant she had to be X'X' for the disease allele to manifest it's phenotype. But if it were X'X, it would lead to a loss in fitness. And since the Male is normal and XY he does not carry the disease which tells us that the disease is definitely not X linked dominant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore in a cross of X'X' and XY you get individuals X'X and X'Y in the ratio 1:1&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coming to AD Autosomal Dominant may mean A'A' as the disease allele is present in homozygous condition. A heterozygous condition would lead to loss in fitness, not necessarily a disease.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A Father may be AA or AA' &lt;/p&gt;&#xA;&#xA;&lt;p&gt;so this cross would give you individuals &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;AA' for A'A' x AA&lt;/li&gt;&#xA;&lt;li&gt;A'A A'A' for AA' x A'A'&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;so in this case you always get the disease in autosomal dominant, what remains is recessive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AA or AA' Father x A'A' Mother&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Products AA' for AA x A'A'&#xA;or AA' and A'A' for AA' x A'A'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;which tells us that the disease is actually Autosomal recessive on the mother.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The father's genotype for the allele is AA or homozygous dominant&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and the disease is autosomal recessive for the disease in the mother.&lt;/p&gt;&#xA;" OwnerUserId="15807" LastActivityDate="2015-05-28T14:51:12.190" CommentCount="3" CommunityOwnedDate="2015-05-28T14:51:12.190" ContentLicense="CC BY-SA 3.0" />
  <row Id="34649" PostTypeId="2" ParentId="34645" CreationDate="2015-05-28T15:29:06.860" Score="4" Body="&lt;p&gt;A protein-protein interaction (PPI) binding site is a &lt;em&gt;type&lt;/em&gt; of interface. If it has been established that the interface is a PPI binding site, then the terms can from that point forward be used interchangeably. But the word &quot;interface&quot; is very generic and does not have any specific scientific meaning so the nature of the interface must be defined or else the term is fairly meaningless.&lt;/p&gt;&#xA;" OwnerUserId="15966" LastActivityDate="2015-05-28T15:29:06.860" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34650" PostTypeId="1" AcceptedAnswerId="34651" CreationDate="2015-05-28T15:53:33.167" Score="4" ViewCount="429" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PkdTf.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;I came across a black cicada in northwest Missouri last week (May 2015). I am only familiar with brown cicadas. What makes this black one different? Is it a different species, or do the brown cicadas change color at some point in adulthood?&lt;/p&gt;&#xA;" OwnerUserId="4747" LastEditorUserId="16866" LastEditDate="2021-05-14T06:21:54.757" LastActivityDate="2021-05-18T05:20:15.140" Title="Insect Identification - Black Cicada" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="34651" PostTypeId="2" ParentId="34650" CreationDate="2015-05-28T17:23:56.587" Score="3" Body="&lt;p&gt;A little digging on wikipedia seems to have answered my question. This picture of a 17 year cicada, &lt;a href=&quot;http://en.wikipedia.org/wiki/Magicicada_septendecim&quot; rel=&quot;nofollow noreferrer&quot;&gt;Magicicada septendecim&lt;/a&gt; is pretty close to what I saw.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/k8tNy.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, this seems to match the time and place, as the &lt;a href=&quot;http://en.wikipedia.org/wiki/Periodical_cicadas#Broods&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kansas Brood of 17 year cicadas is scheduled to emerge this year&lt;/a&gt; and should appear in the Missouri-Kansas area. It also explains why I'm not familiar with these cicadas, 17 years ago I wasn't paying attention to them.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2015-05-28T17:23:56.587" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34653" PostTypeId="2" ParentId="34639" CreationDate="2015-05-28T17:32:51.903" Score="3" Body="&lt;p&gt;Direct comparison of the course would be difficult between tissues and cultured cells. In stead of time scale, you might want to use markers. &#xA;For example, Kislinger et al. show the expression peak of SIX1 is 2 days after differentiation; SMAD3, 4 days. I am not a right person who can tell which markers are good, but I believe you could find more information by literature search.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.mcponline.org/content/4/7/887.full&quot; rel=&quot;nofollow&quot;&gt;http://www.mcponline.org/content/4/7/887.full&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-05-28T17:32:51.903" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34654" PostTypeId="1" AcceptedAnswerId="34658" CreationDate="2015-05-28T18:06:06.140" Score="5" ViewCount="989" Body="&lt;p&gt;We know that viruses are non motile and cannot metabolise, and that it enters the host cells via binding to the receptors. But how exactly it reaches the host&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(that is, how it go from the transmission medium (e.g. the aerosols) to actually make contact with the cells in the host) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it rely on simply diffusion to bump into the host cells' receptors, what makes the odds high enough so that such proliferation strategy is efficient enough to ensure the virus to multiply and proliferate?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, once it has released its DNA into the cell, what helps the DNA to reach the nucleus and not drifting randomly within the cell for a long time, that is, is there exist mechanisms or transportation pathways that actually guide the DNA from the perimeter of the cell through the cytoplasm in the middle and towards the area where the nucleus lie?&lt;/p&gt;&#xA;" OwnerUserId="15973" LastEditorUserId="15973" LastEditDate="2015-05-29T01:25:01.097" LastActivityDate="2015-05-29T01:25:01.097" Title="How does a virus reach its host, it is always passive?" Tags="&lt;virology&gt;&lt;virus&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ClosedDate="2015-05-29T04:23:59.883" ContentLicense="CC BY-SA 3.0" />
  <row Id="34655" PostTypeId="1" CreationDate="2015-05-28T18:19:31.610" Score="4" ViewCount="2621" Body="&lt;p&gt;I am starting to work in molecular biology/ molecular genetic and I am looking for a really good book containing the main concepts and mostly the more recent techniques.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be interested in a book that has also protocol examples and examples on how to apply the different techniques.&#xA;My focus is on bacteria and fungi.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any suggestion?&lt;/p&gt;&#xA;" OwnerUserId="12942" LastEditorUserId="12942" LastEditDate="2015-05-29T07:54:32.107" LastActivityDate="2015-05-29T07:54:32.107" Title="Looking for good reference book in molecular biology" Tags="&lt;molecular-biology&gt;&lt;molecular-genetics&gt;&lt;book-recommendation&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="3" ClosedDate="2015-05-29T04:23:01.397" ContentLicense="CC BY-SA 3.0" />
  <row Id="34656" PostTypeId="2" ParentId="34655" CreationDate="2015-05-28T18:26:40.983" Score="4" Body="&lt;p&gt;These always have a place at my library&lt;/p&gt;&#xA;&#xA;&lt;p&gt;HF Lodish, Berk, Arnold, and S. Lawrence Zipursky. Molecular cell biology. Vol. 4. New York: WH Freeman, 2000.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alberts, Bruce, et al. &quot;Molecular biology of the cell.&quot; Garland Science, New York 4 (2002)(the first few editions had James Watson himself as the editor)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brown, Terence A. Genomes. Garland science, 2006.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For basics. I would recommend staring with Brown, and going on to Bruce Alberts and then Lodish. That's the way I learnt it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a really nice book with pictures (yes, we all like those) you might want to look into Lippincotts illustrated reviews (biochemistry, cell and molecular biology and the like). They are also quite good.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a specific emphasis on techniques, I'd  recommend this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sambrook, Joseph, Edward F. Fritsch, and Tom Maniatis. Molecular cloning. Vol. 1. No. 7.58. New York: Cold spring harbor laboratory press, 1989.&#xA;(You can read the contents here &lt;a href=&quot;http://www.molecularcloning.com/&quot; rel=&quot;nofollow&quot;&gt;http://www.molecularcloning.com/&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-05-28T20:49:53.793" LastActivityDate="2015-05-28T20:49:53.793" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34657" PostTypeId="1" CreationDate="2015-05-28T18:54:45.927" Score="2" ViewCount="1720" Body="&lt;p&gt;I wanted to buy black tea at a pharmacy and the pharmacist told me that russian tea is actually black tea so I bought it instead.It's made out of theae folium leaves and for some reason I can't find anything about that plant on the internet and I know that black tea is made out of camelia sinensis leaves, not theae folium.Can anyone tell me what is this plant and is it really russian tea (i found somewhere that russian tea is made from a different plant) and what is this &quot;Russian&quot; tea good for?&lt;/p&gt;&#xA;" OwnerUserId="15975" LastEditorUserId="3952" LastEditDate="2015-05-31T14:33:48.557" LastActivityDate="2015-05-31T14:33:48.557" Title="What is &quot;theae folium&quot;?" Tags="&lt;botany&gt;&lt;pharmacology&gt;&lt;food&gt;&lt;ethnobiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34658" PostTypeId="2" ParentId="34654" CreationDate="2015-05-28T18:56:12.990" Score="6" Body="&lt;p&gt;There are a number of different ways to spread a viral infection. Some viruses sit on surfaces (or infected persons) &quot;waiting&quot; for someone to touch and take them up, this is called smear infection. Other viruses are airborn inside of small droplets distributed by coughing or sneezing. These are inhaled and can then cause a new infection. Other viruses are transmitted through our body fluids (blood, semen) and either need a wound or can be transmitted sexually (for example Herpes or HIV). Other viruses are transmitted by animals which bite humans (Dengue and rabies would be examples here). Have a look into the &lt;a href=&quot;http://en.wikipedia.org/wiki/Transmission_%28medicine%29&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt; for more details and examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally viruses are produced in vast numbers by their hosts with most viral particles never reaching a new host. This strategy helps a lot to transmit further.s&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For entering the nucleus (which is an obstacle) the viruses use the &lt;a href=&quot;http://en.wikipedia.org/wiki/Nuclear_pore&quot; rel=&quot;noreferrer&quot;&gt;nuclear pore complex&lt;/a&gt; (NPC). Depending on what virus tries to enter the nucleus, different strategies are used. Some viruses are too big and release their DNA through the NPC into the nucleus, while others can pass through and some get stuck inside and release their DNA/RNA at this point. A last group uses the time during mitosis when there is no nucleus. See this figure (from &lt;a href=&quot;http://viralzone.expasy.org/all_by_protein/989.html&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;)&#xA;and also the references below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ek071.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22929056&quot; rel=&quot;noreferrer&quot;&gt;Virus strategies for passing the nuclear envelope barrier.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21167871&quot; rel=&quot;noreferrer&quot;&gt;How viruses access the nucleus.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24084236&quot; rel=&quot;noreferrer&quot;&gt;Viruses challenge selectivity barrier of nuclear pores.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-05-28T18:56:12.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34659" PostTypeId="2" ParentId="34636" CreationDate="2015-05-28T19:00:02.380" Score="2" Body="&lt;p&gt;&quot;Is it the phosphate group, or the molecule, that is derived from ATP ?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;Phosphate group&lt;/strong&gt; is derived from the ATP molecule (thus why Adenosine triphosphate) NOT from the molecule it would be attaching the phosphate group to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Phosphorylation&lt;/strong&gt; - The process of taking this phosphate group and adding it to another molecule in the energy chain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I hope this clears things up. &lt;/p&gt;&#xA;" OwnerUserId="15976" LastEditorUserId="15976" LastEditDate="2015-05-28T21:19:38.587" LastActivityDate="2015-05-28T21:19:38.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34660" PostTypeId="1" AcceptedAnswerId="34938" CreationDate="2015-05-28T19:26:13.117" Score="1" ViewCount="648" Body="&lt;p&gt;I just finished reading J. Craig Venter's book &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0143125907&quot; rel=&quot;nofollow&quot;&gt;Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life&lt;/a&gt;. The book is a little over a year old now, and Venter has an optimistic outlook that bacteriophage therapy will become an effective alternative to gene therapy and viral immunotherapy. He mentioned that the JCVI (J. Craig Venter Institute) is working on such projects. Are other companies also researching, and has progress been made? What are the expected risks? How can rogue, harmful phage mutations be controlled? Can this type of therapy be applied to cancers?&lt;/p&gt;&#xA;" OwnerUserId="9906" LastEditorUserId="948" LastEditDate="2015-05-28T23:26:42.890" LastActivityDate="2016-07-09T19:38:24.970" Title="Risks in bacterial phage therapy" Tags="&lt;bacteriology&gt;&lt;virus&gt;&lt;gene-therapy&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34661" PostTypeId="2" ParentId="34657" CreationDate="2015-05-28T19:38:26.060" Score="3" Body="&lt;p&gt;Judging by this image in wikipedia, I would say Theae folium is another name (probably a name in another language) for &lt;em&gt;Camellia sinensis&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hQEKk.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-05-28T19:38:26.060" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34663" PostTypeId="2" ParentId="31560" CreationDate="2015-05-28T21:21:10.987" Score="2" Body="&lt;p&gt;It is yet to be discovered by scientists. But there is a new study that finds that brain cells called &lt;strong&gt;astrocytes&lt;/strong&gt; supply the urge to sleep by releasing &lt;strong&gt;adenosine&lt;/strong&gt; a chemical known to have sleep-inducing effects. The chemical accumulates in the brain during waking hours, eventually helping to stimulate the unique patterns of brain activity that occur during sleep. &lt;br&gt;&#xA;You can find more about it in this link bellow &lt;br&gt; &lt;a href=&quot;http://healthysleep.med.harvard.edu/healthy/matters/benefits-of-sleep/why-do-we-sleep&quot; rel=&quot;nofollow&quot;&gt;http://healthysleep.med.harvard.edu/healthy/matters/benefits-of-sleep/why-do-we-sleep&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15978" LastActivityDate="2015-05-28T21:21:10.987" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34664" PostTypeId="2" ParentId="34654" CreationDate="2015-05-28T21:21:34.707" Score="3" Body="&lt;p&gt;Some virus DNA or RNA might wait cell division to get into nuclei. For example retrovirus genome is not integrated to the genome of the host cell until cells are divided. However, lentivirus does not need to wait for cell division, because one of proteins in lentivirus binding to virus RNA genome has a nuclear transport signal.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-05-28T22:01:04.347" LastActivityDate="2015-05-28T22:01:04.347" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34666" PostTypeId="2" ParentId="34655" CreationDate="2015-05-28T22:04:04.543" Score="2" Body="&lt;p&gt;If it's techniques you are interested in, &lt;a href=&quot;http://highered.mheducation.com/sites/0073525324/information_center_view0/index.html&quot; rel=&quot;nofollow&quot;&gt;Weaver&lt;/a&gt;, now in its 5th edition, has (had) a strong emphasis on recent experiments from the literature, and he is constantly updating the book. We used  to use it for a variety of courses.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-05-28T22:04:04.543" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34668" PostTypeId="2" ParentId="27508" CreationDate="2015-05-29T00:12:52.433" Score="5" Body="&lt;p&gt;&lt;strong&gt;Explaining phenotypic variance&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may want to make sure you have a good understanding of the concepts of the underlying variance of phenotypic variance (discussion linked to the concept of heritability) before reading this answer. In &lt;a href=&quot;https://biology.stackexchange.com/questions/16858/are-people-genetically-predisposed-to-being-interested-in-specific-fields-ideas/16862#16862&quot;&gt;this post&lt;/a&gt;, I linked several sources of information on the subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Culture (environmental variance)&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Variance in food preference is in part (in majority eventually) explained by cultural differences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Genetic variance&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess that very few people like the smell of rotten eggs. There is selection on taste and smell preferences. Those who don't like the smell of rotten food increase their chance to suffer from bacterial intoxication and mycotoxins. I remember from my Bachelor degree (can't find the study right now) Nestlé (among others probably) performed a genome-wide association study that showed genetic variance for food preferences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Adaptation&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are probably many loci that are now fixed (not polymorphic anymore) that were at some point under selection as explaining variance for food preference. In other words, at a given locus there might have no more genetic variance as the current allele is well adapted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;By-products&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also I suppose that a part of the underlying genetic and environmental variance for the variance for food preference might be qualified as by-products. For example, it might be beneficial to appreciate a given smell because the smell when present in the sweat of a partner is associated with greater health. If this odour (or similar odour) happen to be present in food, then we may be indirectly selected to appreciate this food item as a by-product of the selection for recognizing healthy partners.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-05-29T00:12:52.433" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34669" PostTypeId="2" ParentId="34655" CreationDate="2015-05-29T00:32:23.703" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://www.pearsonhighered.com/educator/product/Brock-Biology-of-Microorganisms-14E/9780321897398.page&quot; rel=&quot;nofollow&quot;&gt;Brock's Microbiology&lt;/a&gt; is a great book when you are interested in unicellular organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the publishers's website (&lt;a href=&quot;http://www.pearsonhighered.com/educator/product/Brock-Biology-of-Microorganisms-14E/9780321897398.page&quot; rel=&quot;nofollow&quot;&gt;Pearson&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The authoritative #1 textbook for introductory majors &lt;strong&gt;microbiology&lt;/strong&gt;, Brock Biology of Microorganisms continues to set the standard [...]. This book for biology, microbiology, and other science majors balances cutting edge research with the concepts essential for understanding the field of microbiology, including strong coverage of ecology, evolution, and metabolism. The Fourteenth Edition [...] pay[s] particular attention to &lt;strong&gt;molecular biology&lt;/strong&gt; and how the genomic revolution has changed and is changing the field.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-29T01:01:41.827" LastActivityDate="2015-05-29T01:01:41.827" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34670" PostTypeId="2" ParentId="34396" CreationDate="2015-05-29T01:25:37.700" Score="4" Body="&lt;p&gt;&lt;strong&gt;First: My opinion on why the question has received that many down votes&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There were many down votes to this question, not because the question is no of interest. The question actually makes sense and is interesting. The post attracted those down votes because the post and the comments of the OP shows little understanding of evolutionary processes. Here are some issues:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;code&gt;some bears decided&lt;/code&gt;. Evolution is not directed. There is no conscious decision from any species (except humans, see &lt;a href=&quot;http://en.wikipedia.org/wiki/Eugenics&quot; rel=&quot;nofollow&quot;&gt;eugenics&lt;/a&gt;) on how to evolve.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;code&gt;as far as I know humans are the only animals that don't live instinctively&lt;/code&gt;. I am not sure there is a common definition of the word &quot;instinctive&quot;. But I very much think that the vast majority of people would suggest definitions that forces us to accept that humans behave instinctively. And if the definition would accept that human can sometimes not behave instinctively, then the definition will very likely accept that some animals behave instinctively.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;code&gt;why they would 'evolve' to eat only bamboo&lt;/code&gt;. Why did you use quotes?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Eventually the question may show lack of effort as showed in the fact that the OP is stating the 2MYA the panda and the other bears diverged, while it was rather about 36 MYA (according to &lt;a href=&quot;http://www.onezoom.org/embed.htm#view=1&amp;amp;signs=1&amp;amp;common=1&amp;amp;polytomy=3&amp;amp;ltype=2&amp;amp;hltype=2&amp;amp;font=helvetica&amp;amp;colour=3&amp;amp;init=1&quot; rel=&quot;nofollow&quot;&gt;onezoom&lt;/a&gt; and even a bit older according to &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1055790304000788&quot; rel=&quot;nofollow&quot;&gt;this reference&lt;/a&gt;). &lt;a href=&quot;http://www.pnas.org/content/104/26/10932&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; however shows that pandas had an omnivorous acenstor 7 MYA only suggesting that pandas modern day diet has evolved less than 7 MYA. More information below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think that those evident misunderstandings deserves receiving down votes (not sure though).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Can't think of any reason why they would 'evolve' to eat only bamboo&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I had a quick look and I didn't find any good answer to your question. It seems that:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;In nature pandas has diet consisting almost uniquely of bamboo (&lt;a href=&quot;http://en.wikipedia.org/wiki/Giant_panda#cite_note-Britannica_Earth-27&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;). They can eat any of the 25 species of bamboo &lt;a href=&quot;http://en.wikipedia.org/wiki/Giant_panda&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Pandas have a digestive track that is very short (like most carnivorans and unlike most herbivorous). Because of their short digestive track they eat a lot (between 9kg and 14kg of bamboo per day!) and they poop a lot (40 times a day) &lt;a href=&quot;http://en.wikipedia.org/wiki/Giant_panda&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;!&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;As a consequence of its diet, the panda spend little energy and avoid any effort &lt;a href=&quot;http://en.wikipedia.org/wiki/Giant_panda&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Pandas seem to have evolved so that it is able to digest cellulose with the help of bacteria (&lt;a href=&quot;http://www.pnas.org/content/108/43/17714.short&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951497/&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;). According to wiki and &lt;a href=&quot;http://www.bbc.co.uk/nature/adaptations/Coprophagia&quot; rel=&quot;nofollow&quot;&gt;BBC&lt;/a&gt; this microbiome is not herited from the mother but is acquired later in life (it is quite common to see that). &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/zoo.20340/abstract&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; suggests that having such a fast transit prevent the ability to absorb other nutrients and therefore limits the benefit of having a more diverse source of food.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;pandas size and mouth are adapted to their diet. They have a large size and a round face with powerful jaw &lt;a href=&quot;http://en.wikipedia.org/wiki/Giant_panda&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;We actually know what genes are responsible for food preference in pandas (&lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022602&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;). The mutation for the &quot;I prefer bamboo&quot; allele is estimated to be 4.7 MY old (consistent with skull observation &lt;a href=&quot;http://www.pnas.org/content/104/26/10932&quot; rel=&quot;nofollow&quot;&gt;ref&lt;/a&gt;).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;According to many comments online and according to &lt;a href=&quot;http://en.wikipedia.org/wiki/Giant_panda&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; (but I couldn't find a trustful reference), as observed in zoo, pandas can eat other stuff when available. Citing from wikipedia &lt;code&gt;While primarily herbivorous, the giant panda still retains decidedly ursine teeth, and will eat meat, fish, and eggs when available.&lt;/code&gt;  &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Given the amount of information we're having there may be tons of possible scenarios. It is possible for example that there is inter-species competition in the wild for access to prey. It is possible that there was for some point a very low density of preys and pandas has shifted their diets. Once, pandas had evolved some features of herbivorous species, they would get stuck there and not be able to get back to a meant based diet (stuck onto a local optima on the fitness landscape). There might be many different explanations involving patterns of competition, parasites, sexual selection, etc... And it seems that we haven't been able to disentangle between all of these.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-05-29T03:07:59.647" LastActivityDate="2015-05-29T03:07:59.647" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="34671" PostTypeId="2" ParentId="34542" CreationDate="2015-05-29T02:31:59.920" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Is the human biological clock genetically programmed or learnt?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is genetically programmed.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A newborn sleeps for 20-22 hours. But overtime (s)he learns to focus&#xA;  sleeping time to night time, according to his or her needs and family&#xA;  needs. Some sleep from 1 am to 7 am, some from 11pm to 5 am. So it is&#xA;  learnt.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nih.gov/researchmatters/october2013/10282013clear.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sleep clears the brain&lt;/a&gt; of toxic metabolic byproducts. A newborn have different sleep requirement than an adult (it would be an interesting question why). The connection with the age is something like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LdogE.jpg&quot; alt=&quot;sleep requirements by age&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;- Figure 1. - Sleep requirements by age&lt;/em&gt; - &lt;a href=&quot;http://www.howsleepworks.com/need_age.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;ref&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it is not learnt, if they wouldn't sleep enough, they &lt;a href=&quot;http://en.wikipedia.org/wiki/Sleep_deprivation&quot; rel=&quot;nofollow noreferrer&quot;&gt;could have health problems or they could even die because of brain damage&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Somewhere I read (I don't exactly remember the article) where it was&#xA;  told that the biological clock is not of 24, but of 25 hours. This&#xA;  means that the synchronisation is not maintained with the earth. If it&#xA;  would be learnt, then why is it not in synchrony with the world?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is in sync with the world, every morning the &lt;a href=&quot;http://www.health.harvard.edu/staying-healthy/blue-light-has-a-dark-side&quot; rel=&quot;nofollow noreferrer&quot;&gt;blue light resets the clock&lt;/a&gt;, that's why we tend to use red light at night.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a clock in the hypothalamus (brain), which is entrained directly by the daily light/dark cycle. There are peripheral clocks in the liver, heart and in other tissues (probably in every single cell), which are weakly affected by the light/dark cycle, and strongly affected by the food intake (probably by other factors as well). The sleep/awake rhythm depends on all of these clocks. So it depends on the actual light/dark pattern and the metabolic (feeding) pattern of the individual.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When food is plentiful, circadian rhythms of animals are powerfully&#xA;  entrained by the light-dark cycle. However, if animals have access to&#xA;  food only during their normal sleep cycle, they will shift most of&#xA;  their circadian rhythms to match the food availability.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://www.sciencemag.org/content/320/5879/1074.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Differential Rescue of Light- and Food-Entrainable Circadian Rhythms&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://www.livescience.com/2562-beat-jet-lag-eat.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;How to Beat Jet Lag: Don't Eat&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2006 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867406009780&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nuclear Receptor Expression Links the Circadian Clock to Metabolism&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2008 - &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0378111908001704&quot; rel=&quot;nofollow noreferrer&quot;&gt;Effects of light cues on re-entrainment of the food-dominated peripheral clocks in mammals&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2011 - &lt;a href=&quot;http://www.clinsci.org/cs/120/cs1200065.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;The circadian clock and metabolism&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1460-9568.2009.06965.x/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Food-anticipatory circadian rhythms: concepts and methods&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;2009 - &lt;a href=&quot;http://jap.physiology.org/content/107/6/1972&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rev-erb-α: an integrator of circadian rhythms and metabolism&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2015-05-29T04:26:11.617" LastActivityDate="2015-05-29T04:26:11.617" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34672" PostTypeId="1" AcceptedAnswerId="34673" CreationDate="2015-05-29T03:09:46.247" Score="11" ViewCount="1307" Body="&lt;p&gt;I work in IT and I have observed many people who cannot remember their iPhone passwords or computer passwords off the top of their head. However, if presented with a keyboard or a phone with a functioning keypad, they can instantly remember exactly what their password or passcode is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm curious to know what this kind of memory is called. Since it's somewhat related to visuals, but not necessarily (you don't need to look at your keyboard to type out your password.)&lt;/p&gt;&#xA;" OwnerUserId="9111" LastEditorUserId="9943" LastEditDate="2015-05-29T03:29:54.867" LastActivityDate="2015-05-29T11:20:24.917" Title="What kind of memory is &quot;keyboard/keypad memory&quot;?" Tags="&lt;neuroscience&gt;&lt;memory&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34673" PostTypeId="2" ParentId="34672" CreationDate="2015-05-29T03:20:32.797" Score="16" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Motor memory&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;A striking personal example of your account pictured in the question was my experience where I had to type in my PIN at the bank counter on a keypad. It turned out I entered it incorrectly several times in a row, despite the fact that I had used that PIN a zillion times on ATM machines. Luckily, the bank employee had seen this phenomenon many times before, and she explained to me that the standard computer keypads have a different numerical layout than ATM machines. So to type in my PIN correctly I had to do it under visual guidance - an awkward experience. It showed quite strikingly that I had been entering my bank PIN using motor memory.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Much of our motor behavior is learned - think of learning to walk, cycle or ice skate. To achieve motor learning, the central nervous system is believed to use internal models that predict the mechanical dynamics necessary to execute a task. In theory, the internal model is an association from a desired trajectory for the hand to a pattern of muscle movements. This map is basically unique for the objects that we have learned to interact with. Because we routinely use our hands to interact with a remarkably diverse variety of mechanical systems, the ability to learn and recall internal memories is thought to be a fundamental property of the motor system (&lt;a href=&quot;http://www.jneurosci.org/content/17/1/409.full&quot;&gt;Shadmehr &amp;amp; Brashers-Krug, 1997)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.jneurosci.org/content/17/1/409.full&quot;&gt;Shadmehr &amp;amp; Brashers-Krug, &lt;em&gt;J Neurosci&lt;/em&gt; (1997); &lt;strong&gt;17&lt;/strong&gt;(1): 409-19&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-29T11:20:24.917" LastActivityDate="2015-05-29T11:20:24.917" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34674" PostTypeId="2" ParentId="15446" CreationDate="2015-05-29T03:38:49.797" Score="1" Body="&lt;p&gt;In vitro translation is not as efficient as other chemical polymer reactions. For example, when proteins are synthesized using in vitro translation systems, many researchers have been using radio-labeling to see the products because the yield is too low to detect them by other methods, although few small proteins have been successfully produced at a microgram level. It should be noted that it is also difficult to produce exogenous long peptides at sizes more than 100kDa in E coli in vivo expression system.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-05-29T03:38:49.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34675" PostTypeId="1" AcceptedAnswerId="34692" CreationDate="2015-05-29T03:40:20.463" Score="1" ViewCount="680" Body="&lt;p&gt;What can cause an erythematous, fluctuant, nontender mass in the middle of the neck?&lt;img src=&quot;https://i.stack.imgur.com/pFzIS.png&quot; alt=&quot;case&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Full Case Study: (Its the last of 6 cases and I just can't figure this one out,  because of all the possibilities, there is always something that doesn't line up.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The 26-year-old man presented for evaluation of a neck mass and a right axillary mass. The patient, who came to the United States from Vietnam 6 1/2 years ago, noted  midline neck mass. The mass gradually increased in size. Approximately 3 weeks prior to admission, he noted a midline neck mass. These masses were incised and drained twice. Samples of purulent material were sent for routine bacterial culture at an outside hospital. The patient had lost 3 kg (ca. 7 lbs) in the 2 months prior to admission but denied fever. Travel history was notable for his having lived in Arizona for 6 years prior to moving to Boston.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On examination, he was afebrile. An erythematous , fluctuant, nontender mass (8cm x 6cm) was present in the midline of the neck. (Fig. 5.1)  (computed tomogram[CT] scan in fig. 5.2).The right axilla demonstrated incision sites that were draining and were tender to palpation. He had no adenopathy elsewhere. His (PPD) purified protein derivative skin test was reactive, and his chest x-ray was notable for apical scarring in the right lung.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because of the positive PPD and apical scarring seen on the patient's chest x-ray, the clinical suspicion of cervical ________ was high, and the patient was begun on a four drug anti- _________________ regimen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several days after the neck mass was drained of several milliliters of purulent material for culture, a mold was found to grow on the blood agar plates in the routine bacteriology section of the microbiology laboratory. The mold was white (Fig. 5.3) and initially did not have any identifying characteristics when a lactophenol cotton blue preparation was examined under a phase-contrast microscope. It was subcultured at both room temperature and body temperature, and after subculture began to demonstrate the presence of  spores microscopically (Fig. 5.4) The identification was confirmed by using a commercially available genetic probe.&lt;/p&gt;&#xA;" OwnerUserId="15980" LastEditorUserId="9943" LastEditDate="2015-05-29T14:10:02.050" LastActivityDate="2015-05-30T21:22:14.467" Title="What can cause a lump in the middle of the neck? (homework case study)" Tags="&lt;microbiology&gt;&lt;homework&gt;&lt;pathology&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2015-05-30T04:37:47.623" ContentLicense="CC BY-SA 3.0" />
  <row Id="34677" PostTypeId="2" ParentId="34539" CreationDate="2015-05-29T06:20:30.797" Score="4" Body="&lt;p&gt;As a bioinformatician, one of my tasks is quite often to get information from databases or find the correct database to compare to. There are several big databases around, but even those are way too many for any single person to know.&#xA;There are databases specialising on genetic data, some specialising on taxonomic information, some on ecological information and then there are species specific databases which collect all kinds of data from a given species, genus or clade.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For me the biggest source of generalised information would be the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov&quot; rel=&quot;nofollow&quot;&gt;NCBI&lt;/a&gt; databases, including &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genbank&quot; rel=&quot;nofollow&quot;&gt;GenBank&lt;/a&gt; for nucleotide sequence, their &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/protein/&quot; rel=&quot;nofollow&quot;&gt;Protein&lt;/a&gt; database and maybe &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/snp/&quot; rel=&quot;nofollow&quot;&gt;dbSNP&lt;/a&gt; for, well, SNPs. Then there are multiple 16S databases I have used, there is &lt;a href=&quot;https://genome.ucsc.edu&quot; rel=&quot;nofollow&quot;&gt;UCSC&lt;/a&gt; for the basic data about the human genome, &lt;a href=&quot;http://flybase.org&quot; rel=&quot;nofollow&quot;&gt;flyBase&lt;/a&gt; for Drosophila,... I think the point should be clear. And those are only the ones that just sprang to my mind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you don't have a very exact question to answer like &quot;Is there a gene similar to gene x from Drosophila present in any Bacteria?&quot; it can be very hard to both choose the correct database and also find the important information in it efficiently. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there is the problem of metadata. I might be able to find sequencing data from the gut microbiome of a human treated with antibiotics quite easily. If I am looking for a specific antibiotic given over a minimal time of seven days to a different healthy humans, preferably including at least one breastfed child and it's mother (which was the one taking the antibiotics, not the child), then it's getting complicated. Here it is generally way easier to scan &lt;a href=&quot;http://flybase.org&quot; rel=&quot;nofollow&quot;&gt;PubMed&lt;/a&gt; for some relevant publications on the matter and find out if they used published datasets or published their own.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2015-05-29T06:20:30.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34678" PostTypeId="1" CreationDate="2015-05-29T06:33:41.957" Score="5" ViewCount="185" Body="&lt;p&gt;When papers refer to traits as being &lt;strong&gt;&lt;em&gt;sexually homologous&lt;/em&gt;&lt;/strong&gt; do they refer to traits which are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) present in both sexes but &lt;em&gt;can&lt;/em&gt; be dimorphic (e.g. body size is sexually homologous because both sexes have a measurable trait which has the same criteria in either sex, but this is frequently dimorphic)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or&lt;/p&gt;&#xA;&#xA;&lt;p&gt;b) present in both sexes &lt;em&gt;and&lt;/em&gt; not different between the sexes&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have always thought it is a, but I'm now using the term in a paper and want to check. I would have thought the latter would be &quot;homologous homomorphic traits&quot; or something like that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If an answer could have an example of the use(s) which make it obvious from published work that would be great!&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2015-05-29T11:36:43.133" LastActivityDate="2017-04-28T22:31:00.903" Title="Sexually homologous traits" Tags="&lt;terminology&gt;&lt;sexual-dimorphism&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34679" PostTypeId="1" CreationDate="2015-05-29T07:29:05.283" Score="9" ViewCount="12924" Body="&lt;p&gt;I just started learning about the structure and composition of cell's membrane and there is something that I fail to understand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The membrane is composed of a phospholipid bilayer. The phospholipid has a polar, hydrophilic head and a nonpolar, hydrophobic tail. My question: &lt;strong&gt;Why doesn't the hydrophilic head dissolve in the extracellular fluid outside the cell?&lt;/strong&gt; I suppose that the extracellular fluid is watery, so how come that the water-loving head doesn't interact with the water from the extracellular fluid?&lt;/p&gt;&#xA;" OwnerDisplayName="user15135" LastEditorUserId="3553" LastEditDate="2015-07-26T16:26:03.513" LastActivityDate="2017-09-20T08:21:33.133" Title="Why don't phospholipid bilayers dissolve?" Tags="&lt;biochemistry&gt;&lt;biophysics&gt;&lt;cell-membrane&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34680" PostTypeId="2" ParentId="34679" CreationDate="2015-05-29T07:52:15.680" Score="6" Body="&lt;p&gt;The answer to your question is basically:&#xA;It is a &lt;strong&gt;bi&lt;/strong&gt;layer. There are two layers of phospholipids, thus tucking the hydrophilic ends safely away from any extracellular and intracellular fluids. The whole surface of the bilayer is hydrophilic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4JjWh.gif&quot; alt=&quot;phospholipid bilayer&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Picture from &lt;a href=&quot;http://ndla.no/nb/node/126896&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;.)&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2015-05-29T07:52:15.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34681" PostTypeId="1" CreationDate="2015-05-29T07:55:53.717" Score="2" ViewCount="767" Body="&lt;p&gt;We have an algal enhancer element and a transcription factor that probably binds it. Basal expression of the enhancer element or full promoter driving luciferase in tobacco protoplast was extremely low. I heard this could be overcome by fusing it to a minimal 35S promoter fragment but I can't seem to find a clear sequence for this minimal promoter.The best I could find was on the cambia website where they say it is -90 &lt;a href=&quot;http://www.cambia.org/daisy/promoters/242/g1/250/264.html&quot; rel=&quot;nofollow&quot;&gt;http://www.cambia.org/daisy/promoters/242/g1/250/264.html&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Does anybody have experience with increasing the expression of enhancer elements like this? &#xA;2) And what sequence did you use for this?&lt;/p&gt;&#xA;" OwnerUserId="15138" LastEditorUserId="15138" LastEditDate="2015-05-29T14:24:51.667" LastActivityDate="2015-10-27T15:18:48.650" Title="Is there a consensus on the CaMV 35S minimal promoter sequence?" Tags="&lt;gene-expression&gt;&lt;transcription-factor&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34683" PostTypeId="1" AcceptedAnswerId="34688" CreationDate="2015-05-29T08:12:44.547" Score="60" ViewCount="9404" Body="&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/0RwtN.png&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/0RwtN.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was watching a nice &lt;a href=&quot;https://www.youtube.com/watch?v=iES23rXuMr4&quot; rel=&quot;noreferrer&quot;&gt;little video&lt;/a&gt; on youtube but couldn't help but notice how snappy smaller animals such as rats and chipmunks move. By snappy I mean how the animal moves in almost discrete states pausing between each movement. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this a trivial observation or something inherent in the neuro-synapse or muscular make-up of these animals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/p9aPR.png&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/p9aPR.png&quot; alt=&quot;Bikke the Chipmunk Yawning and Stretching&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="9020" LastEditDate="2016-07-02T02:29:29.073" LastActivityDate="2019-03-28T12:42:45.150" Title="Why do smaller mammals move intermittently?" Tags="&lt;neuroscience&gt;&lt;zoology&gt;&lt;muscles&gt;&lt;movement&gt;" AnswerCount="4" CommentCount="4" FavoriteCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="34685" PostTypeId="2" ParentId="34679" CreationDate="2015-05-29T09:00:42.133" Score="11" Body="&lt;p&gt;We should first understand what happens when a substance dissolves. During dissolution water interacts with the solute molecule; if the strength of interaction between the molecule and water is higher than the strength of interaction among the solute molecules then the solute dissolves. &#xA;&lt;br&gt;(Also have a look at &lt;a href=&quot;https://biology.stackexchange.com/questions/23763/is-there-a-difference-between-polarity-and-hydrophobicity/23917#23917&quot;&gt;this&lt;/a&gt; post).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phospholipid is an amphipathic molecule — it has both hydrophobic and hydrophilic parts (this you understand very well). The hydrophobic part is a long chain of hydrocarbon (hence tail) whereas the hydrophilic part is a small but highly polar region (hence head). You should note that these parts are not disjoint but are covalently bonded. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HZVnT.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even though the hydrophilic part interacts with water (which helps the cell survive in an aqueous environment), the strength of covalent bond (between hydrophilic and hydrophobic regions) is very strong and cannot be broken by physical interaction with water. &#xA;The lipid bilayer (even a monolayer) stays together because the water cannot interact with hydrophobic parts but they interact with each other via a pseudo-interaction called &lt;a href=&quot;http://chemwiki.ucdavis.edu/Physical_Chemistry/Physical_Properties_of_Matter/Atomic_and_Molecular_Properties/Intermolecular_Forces/Hydrophobic_interactions&quot; rel=&quot;nofollow noreferrer&quot;&gt;hydrophobic interaction&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;I call it a pseudo-interaction (not a standard usage) because there is not actual molecular interaction that stabilizes the system. Hydrophobic interaction happens via increase in entropy of the system. Read the wikipedia page for details.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-07-27T09:51:53.807" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34686" PostTypeId="2" ParentId="31733" CreationDate="2015-05-29T09:03:55.007" Score="0" Body="&lt;p&gt;How about &lt;a href=&quot;https://en.wikipedia.org/wiki/Italian_wall_lizard&quot; rel=&quot;nofollow&quot;&gt;the Italian wall lizards&lt;/a&gt; that &lt;a href=&quot;http://news.nationalgeographic.com/news/2008/04/080421-lizard-evolution_2.html&quot; rel=&quot;nofollow&quot;&gt;evolved new muscles around their intestines&lt;/a&gt; after being introduced to an island? (&lt;a href=&quot;http://scienceblogs.com/pharyngula/2008/04/23/still-just-a-lizard/&quot; rel=&quot;nofollow&quot;&gt;other article&lt;/a&gt;, &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2290806/&quot; rel=&quot;nofollow&quot;&gt;actual paper&lt;/a&gt;). The paper reports that these cecal valves are &quot;a structure previously unreported for this species and rare in this family and scleroglossan lizards in general&quot;; indeed, &quot;The fact that &amp;lt;1% of all currently known species of squamates have cecal valves ... illustrates the unusual nature of these structures in this population.&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is possible that these values are an ancestral structure that was reactivated by natural selection; however, we know that natural selection can act very quickly &lt;a href=&quot;http://news.nationalgeographic.com/news/2006/07/060714-evolution_2.html&quot; rel=&quot;nofollow&quot;&gt;to change the size of morphological structures&lt;/a&gt;, so it's also possible that existing muscles quickly changed size in response to selective pressure. Figuring out the developmental mechanism of cecal valves would sort that out.&lt;/p&gt;&#xA;" OwnerUserId="87" LastEditorUserId="87" LastEditDate="2015-05-29T20:45:04.630" LastActivityDate="2015-05-29T20:45:04.630" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="34687" PostTypeId="2" ParentId="34590" CreationDate="2015-05-29T09:12:50.440" Score="1" Body="&lt;p&gt;Genus sizes are usually measured in number of species, since a particular species under a single taxonomic authority shouldn't be found in more than one genus. Check out &lt;a href=&quot;http://onlinelibrary.wiley.com/enhanced/doi/10.1111/zsc.12087/&quot; rel=&quot;nofollow&quot;&gt;Strand and Panova, 2014&lt;/a&gt; for some numbers on number of species found in each genus on average across several thousand genera from eight major taxonomic groups.&lt;/p&gt;&#xA;" OwnerUserId="87" LastActivityDate="2015-05-29T09:12:50.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34688" PostTypeId="2" ParentId="34683" CreationDate="2015-05-29T11:04:13.700" Score="51" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Intermittent locomotion can &lt;em&gt;increase the detection of prey&lt;/em&gt; by predators (e.g.  rats), while it may lead to &lt;em&gt;reduced attack rates&lt;/em&gt; in prey animals (e.g., rats and chipmunks). It may also &lt;em&gt;increase physical endurance&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Rather than moving continuously through the environment, many animals interrupt their locomotion with frequent brief pauses. Pauses increase the time required to travel a given distance and add costs of acceleration and deceleration to the&#xA;energetic cost of locomotion. From an adaptation perspective, pausing should provide benefits that outweigh these costs &lt;a href=&quot;http://www.uoguelph.ca/~amclab/amclab/Publications_files/McAdam%26Kramer.98.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Adam &amp;amp; kramer, 1998)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One potential benefit of pausing is &lt;strong&gt;increased detection of prey&lt;/strong&gt; by predators. Slower movement speeds likely improve prey detection by providing more time to&#xA;scan a given visual field. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A second plausible benefit is &lt;strong&gt;reduced attack rate&lt;/strong&gt; by predators. Many predators are more likely to attack moving prey, perhaps because such prey is more easily detected or recognized. Indeed, motionlessness (‘freezing’) is a widespread&#xA;response by prey that detect a predator.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A third benefit may be &lt;strong&gt;increased endurance&lt;/strong&gt;. For animals moving faster than their aerobically sustainable speeds, the maximum distance run can be increased by taking pauses. These pauses allow the clearance of lactate from the muscles through aerobic mechanisms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS: If you mean with 'snappy' not only that small animals move intermittently, but also 'fast', then Remi.b's answers nicely covers the story why small critters are quick. Basically, it comes down to &lt;a href=&quot;http://physics.info/newton-second/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Newton's second law&lt;/a&gt;, namely acceleration is inversely proportional to mass (&lt;a href=&quot;http://zonalandeducation.com/mstm/physics/mechanics/forces/newton/newtonLaw2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;a = F/m&lt;/a&gt;), &lt;a href=&quot;https://biology.stackexchange.com/questions/1116/why-is-it-that-cats-can-jump-so-high-for-their-size-compared-with-humans&quot;&gt;but the size of muscle power is not&lt;/a&gt;. Hence, bigger animals have more mass and need a lot more force to build up to accelerate at the same speed. That build up of force needs time (ever witnessed the vertical lift-off of a space shuttle?) Hence, small critters accelerate quicker and allow them to move 'snappy'.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.uoguelph.ca/~amclab/amclab/Publications_files/McAdam%26Kramer.98.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Adam &amp;amp; kramer, &lt;em&gt;Anim Behav&lt;/em&gt; (1998); &lt;strong&gt;55&lt;/strong&gt;: 109–117&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2016-02-10T10:11:44.497" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34689" PostTypeId="1" AcceptedAnswerId="34693" CreationDate="2015-05-29T12:08:21.787" Score="1" ViewCount="643" Body="&lt;p&gt;I have a male colleague which has a son that does not resemble its father in any degree (apart of being male). The &quot;father&quot; is thin, tan-skinned, brown-eyed and the &quot;son&quot; has blue eyes, blond and already slightly overweight boy. Their faces have no any signs of similarity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since, the son gets Y-chromosome from a father, it is interesting to know if the Y-chromosome possesses any phenotypical feature apart of testicular development? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did not find any Y-gene that influences the phenotype. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the second part of the question: Can other 22 parental chromosomes be so &quot;recessive&quot; that a child will have no &quot;any&quot; external signs resembling its biologic father.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-05-29T13:42:00.320" Title="Y-chromosome and phenotype" Tags="&lt;human-genetics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34690" PostTypeId="1" AcceptedAnswerId="34697" CreationDate="2015-05-29T12:31:13.147" Score="2" ViewCount="812" Body="&lt;p&gt;I want to calculate the Jaccard index between two compounds. What is the algorithm? I have searched for it, it just gives the formula but how to apply it on compounds is not known to me. Can you help?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="9099" LastEditDate="2015-05-29T15:44:59.590" LastActivityDate="2015-05-29T15:44:59.590" Title="How to calculate the Jaccard index" Tags="&lt;statistics&gt;&lt;organic-chemistry&gt;&lt;biochemistry&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="1" ClosedDate="2015-06-02T06:16:55.347" ContentLicense="CC BY-SA 3.0" />
  <row Id="34691" PostTypeId="1" AcceptedAnswerId="34837" CreationDate="2015-05-29T12:46:36.143" Score="17" ViewCount="9478" Body="&lt;p&gt;An often heard theory is that newborns and babies resemble the father more than the mother, a theory apparently ignited by a Nature paper by &lt;a href=&quot;http://www.nature.com/nature/journal/v378/n6558/abs/378669a0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Christenfeld and Hill (1995)&lt;/a&gt;. Figure 1 shows one of the tests images. His subjects had to guess which picture was the real dad and which was the real mom. It turned out that tested subjects were indeed significantly better at guessing dads than moms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/cnYr5.png&quot; alt=&quot;son vs 3 dads&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Test stimulus of &lt;a href=&quot;http://www.nature.com/nature/journal/v378/n6558/abs/378669a0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Christenfeld and Hill (1995)&lt;/a&gt;. Which one is dad: a, b, or c?&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is suggested that paternal matching of a baby promotes identification of the father with his offspring. In turn, self-identification in his kin would prevent the father from doing harm and stimulate protective paternal behavior. This then is hypothesized to increase survival rates of his offspring and &lt;em&gt;et voila&lt;/em&gt;, a trait is born (pardon the pun) that makes baby paternal look-alikes fitter than those that don't. This hypothesis seems to have become part of parenting folklore.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, a &lt;a href=&quot;http://www.scientificamerican.com/article/babies-paternal-resemblance/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Scientific American paper by Matson (2011)&lt;/a&gt; contests this view and puts forward several primary research studies showing no preferred resemblance between mother or father, or even predominantly maternal features in babies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is the resemblance between father and baby fact or fiction?&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://psy2.ucsd.edu/~nchristenfeld/Publications_files/Baby.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Christenfeld &amp;amp; Hill. &lt;em&gt;Nature&lt;/em&gt; (1995); &lt;strong&gt;378&lt;/strong&gt;: 669&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.scientificamerican.com/article/babies-paternal-resemblance/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Matson, &lt;em&gt;Sci Am&lt;/em&gt; (2011) online article&lt;/a&gt;&lt;/sub&gt; &#xA;&lt;br&gt; &#xA;&lt;br&gt;&lt;br&gt;&#xA;&lt;sup&gt;Credits for this question go to @KoustavPal for his comment in &lt;a href=&quot;https://biology.stackexchange.com/questions/34689/y-chromosome-and-phenotype&quot;&gt;Y-chromosome and phenotype&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2016-02-20T20:03:38.393" Title="Do babies resemble their father?" Tags="&lt;evolution&gt;&lt;development&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34692" PostTypeId="2" ParentId="34675" CreationDate="2015-05-29T13:22:18.730" Score="0" Body="&lt;p&gt;You ask for the fungus causing &lt;code&gt;An erythematous , fluctuant, nontender mass (8cm x 6cm) was present in the midline of the neck.&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the brink of question closure I decided to do a quick search. Based on your descriptions, I found a &lt;em&gt;possible&lt;/em&gt; culprit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the referenced paper they talk about a fungal &lt;strong&gt;&lt;em&gt;&lt;a href=&quot;http://www.medicinenet.com/cryptococcosis/article.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cryptococcosis&lt;/em&gt; infection&lt;/a&gt;&lt;/strong&gt; causing, and I quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[A] fluctuant, non-tender mass, five by five cm. in the right costal vertebral angle which was not red or warm. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So this mass was found on the costal vertebral angle, but the remaining symptoms seem reminiscent of your case study. Fungi generally appear white when plated, as far as I know.&#xA;&lt;em&gt;However, more information is likely necessary to confirm this genus and identify the species&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EtfLc.jpg&quot; alt=&quot;CVA&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;costal vertebral angle (CVA). Source: &lt;a href=&quot;https://www.google.com.au/url?sa=i&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=images&amp;amp;cd=&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CAUQjhw&amp;amp;url=https%3A%2F%2Fwww.pinterest.com%2Fpin%2F521925044289869524%2F&amp;amp;ei=vWdoVcqHK-G7mQX14IGIBQ&amp;amp;bvm=bv.93990622,d.dGY&amp;amp;psig=AFQjCNFJJJdWUqbyhvVCxayloWgBbfPEew&amp;amp;ust=1432991848777672&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pinterest&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.nature.com/jid/journal/v28/n2/full/jid195717a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Moore, &lt;em&gt;J Invest Dermatol&lt;/em&gt; (1957); &lt;strong&gt;28&lt;/strong&gt;: 159–82&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-30T21:22:14.467" LastActivityDate="2015-05-30T21:22:14.467" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34693" PostTypeId="2" ParentId="34689" CreationDate="2015-05-29T13:42:00.320" Score="3" Body="&lt;p&gt;The Y-chromosome only really contains genes relevant to sex determination[&lt;a href=&quot;http://ghr.nlm.nih.gov/chromosome/Y&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;], with estimates of protein-coding genes ranging from 50-450. For instance the &lt;em&gt;SRY&lt;/em&gt; gene, also known as the &lt;em&gt;testis-determining factor&lt;/em&gt; [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/6736&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;], is only found on the Y-chromosome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phenotypes such as eye colour are coded on the &lt;em&gt;autosomes&lt;/em&gt; (i.e. not the sex chromosomes), and as such are determined by alleles inherited from both parents. As Koustav Pal mentions in his comment, many such traits are multi-allelic (i.e. determined by multiple regions of the genome), and are therefore more complex than first appear; eye-colour can change over time, and there are many more complexities that do not fit into the simple &quot;blue&quot;, &quot;brown&quot;, &quot;green/hazel&quot; categories [&lt;a href=&quot;http://udel.edu/~mcdonald/mytheyecolor.html&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;]. This also applies to hair, so the child you mention could become more like their father as they grow older (or not!).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because each individual posesses &lt;em&gt;two&lt;/em&gt; alleles for each possible trait (one from their mother, one from their father - we each have two whole copies of the human genome in our cells*) a person can be a carrier for traits, such as blue eyes, whilst themselves having brown eyes. In fact the situation is so complex (&gt;15 genes affect eye colour) that two blue-eyed parents could have a child with brown eyes [&lt;a href=&quot;https://www.uq.edu.au/news/article/2007/02/eyes-have-it-multiple-gene-question&quot; rel=&quot;nofollow&quot;&gt;4&lt;/a&gt;] - the historical perspective was the brown eyes were dominant over blue eyes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have focussed on eye colour because it is a good case-in-point: there are clear genetic determinants and heritability, and it is more complex than the popular perception. Regarding hair (or skin) colour, single-gene mutations can cause pale skin and red hair [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3095693/&quot; rel=&quot;nofollow&quot;&gt;5&lt;/a&gt;], but beyond these cases the same rules seem to apply; that there are multiple genetic determinants (which means the Mendelian single-allele dominant/recessive model does not really apply) that affect the amount of eumelanin (which is dark brown) and pheomelanin (which is reddish) produced, with together combine to make the spectrum of colours we see in the population - it is not true to say that there are only blond OR brown haired people, as many people lie somewhere between [&lt;a href=&quot;http://udel.edu/~mcdonald/mythredhair.html&quot; rel=&quot;nofollow&quot;&gt;6&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This has not been an exhaustive review of these topics by any means, and there may be further evidence either way, but it seems quite clear that it is not unusual for offspring to not actually take the appearance of one or both parents. There are many traits you mention (such as build) that I don't go into detail, but there is emerging evidence that these are incredibly polygenic (caused by many small-effect genetic variants - e.g. height [&lt;a href=&quot;http://www.nature.com/ng/journal/v46/n11/full/ng.3097.html&quot; rel=&quot;nofollow&quot;&gt;7&lt;/a&gt;]) and as such could lead to the same phenomenon.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://ghr.nlm.nih.gov/chromosome/Y&quot; rel=&quot;nofollow&quot;&gt;http://ghr.nlm.nih.gov/chromosome/Y&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene/6736&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/gene/6736&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://udel.edu/~mcdonald/mytheyecolor.html&quot; rel=&quot;nofollow&quot;&gt;http://udel.edu/~mcdonald/mytheyecolor.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.uq.edu.au/news/article/2007/02/eyes-have-it-multiple-gene-question&quot; rel=&quot;nofollow&quot;&gt;https://www.uq.edu.au/news/article/2007/02/eyes-have-it-multiple-gene-question&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3095693/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3095693/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://udel.edu/~mcdonald/mythredhair.html&quot; rel=&quot;nofollow&quot;&gt;http://udel.edu/~mcdonald/mythredhair.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/ng/journal/v46/n11/full/ng.3097.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/ng/journal/v46/n11/full/ng.3097.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;* well, most cells - red blood cells and gametes do not. &lt;/p&gt;&#xA;" OwnerUserId="740" LastActivityDate="2015-05-29T13:42:00.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34694" PostTypeId="1" CreationDate="2015-05-29T14:04:25.003" Score="1" ViewCount="253" Body="&lt;p&gt;Wikipedia states on &lt;a href=&quot;http://www.wikiwand.com/en/Oral_allergy_syndrome&quot; rel=&quot;nofollow&quot;&gt;its page&lt;/a&gt; that &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In addition, patients are advised to avoid the triggering foods, particularly nuts.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And same thing goes for &lt;a href=&quot;http://www.webmd.com/allergies/features/oral-allergy-syndrome-foods?page=2&quot; rel=&quot;nofollow&quot;&gt;webmd.com&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The basic rule: If a food makes you uncomfortable, don’t eat it.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So two very related questions flow from this:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Does continuous consumption cause such an allergic reaction to become stronger?&lt;/li&gt;&#xA;&lt;li&gt;And if that is the case, by what mechanisms does that happen?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8039" LastActivityDate="2015-05-29T16:55:17.147" Title="Oral allergy syndrom, continuation of continuous consumption of allergen" Tags="&lt;allergies&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34695" PostTypeId="5" CreationDate="2015-05-29T14:05:29.273" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2015-05-29T14:05:29.273" LastActivityDate="2015-05-29T14:05:29.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34696" PostTypeId="4" CreationDate="2015-05-29T14:05:29.273" Score="0" Body="Pertains anything concerning the act of moving, motion and locomotion as well as the change of place or posture." OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-29T18:31:50.870" LastActivityDate="2015-05-29T18:31:50.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34697" PostTypeId="2" ParentId="34690" CreationDate="2015-05-29T14:13:59.223" Score="3" Body="&lt;p&gt;The Jaccard index is a measure of similarity between two sets. Take a look at the Wikipedia article &lt;a href=&quot;http://en.wikipedia.org/wiki/Jaccard_index&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. It is very easy to compute:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Jaccard similarity coefficient for sets X and Y is defined as:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;J(X,Y) = |intersection(X,Y)| / |union(X,Y)|&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Where &lt;code&gt;| |&lt;/code&gt; indicates the size (number of elements) of the set. Imagine you have two sets X and Y defined as follows:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;X = {A, B, C, D}&#xA;Y = {C, D, E, F, G}&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Then:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;intersection(X,Y) = {C, D} =&amp;gt; |intersection(X,Y)| = 2&#xA;union(X,Y) = {A,B,C,D,E,F} =&amp;gt; |union(X,Y)| = 5&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Therefore: &lt;code&gt;J(X,Y) = 2/5&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatively, the Jaccard distance would be &lt;code&gt;D(X,Y) = 1 - J(X,Y) = 1 - 2/5 = 3/5&lt;/code&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Biology the Jaccard index has been used to compute the similarity between networks, by comparing the number of edges in common (e.g. &lt;a href=&quot;http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2728.html&quot; rel=&quot;nofollow&quot;&gt;Bass, Nature methods 2013&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Regarding applying it to compounds, if you have two sets with different compounds, you can find how similar the two sets are using this index. The elements on the sets, in this case the compounds, correspond to A, B, C, etc. in my example.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastEditorUserId="9099" LastEditDate="2015-05-29T14:20:47.217" LastActivityDate="2015-05-29T14:20:47.217" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34698" PostTypeId="2" ParentId="13645" CreationDate="2015-05-29T14:18:08.123" Score="1" Body="&lt;p&gt;Italians do have much less IBD sharing with other European populations and are more easy to distinguish based on aDNA from other European population, so this enforces the model of the ''genetic island''&lt;/p&gt;&#xA;&#xA;&lt;p&gt;''The map also identifies the existence of two genetic barriers within Europe. One is between the Finns (light blue, upper right) and other Europeans. It arose because the Finnish population was at one time very small and then expanded, bearing the atypical genetics of its few founders.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The other is between Italians (yellow, bottom center) and the rest. This may reflect the role of the Alps in impeding free flow of people between Italy and the rest of Europe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Data for the map were generated by gene chips programmed to test and analyze 500,000 sites of common variation on the human genome, although only the 300,000 most reliable sites were used for the map. Dr. Kayser's team tested almost 2,500 people and analyzed the data by correlating the genetic variations in all the subjects. The genetic map is based on the two strongest of these sets of correlations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The gene chips require large amounts of DNA, more than is available in most forensic samples. Dr. Kayser hopes to identify the sites on the human genome which are most diagnostic for European origin. These sites, if reasonably few in number, could be tested for in hair and blood samples, Dr. Kayser said.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Genomic sites that carry the strongest signal of variation among populations may be those influenced by evolutionary change, Dr. Kayser said. Of the 100 strongest sites, 17 are found in the region of the genome that confers lactose tolerance, an adaptation that arose among a cattle herding culture in northern Europe some 5,000 years ago. Most people switch off the lactose digesting gene after weaning, but the cattle herders evidently gained a great survival advantage by keeping the gene switched on through adulthood.''&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://nytimes.com/2008/08/13/science/13visual.html&quot; rel=&quot;nofollow&quot;&gt;http://nytimes.com/2008/08/13/science/13visual.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15988" LastEditorUserId="4101" LastEditDate="2015-05-29T15:44:05.120" LastActivityDate="2015-05-29T15:44:05.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34699" PostTypeId="2" ParentId="34657" CreationDate="2015-05-29T14:25:34.310" Score="3" Body="&lt;p&gt;If the labelling is correct, this should be &lt;em&gt;Camellia sinensis&lt;/em&gt;, the plant that produces black tea, green tea, etc. (although not many things that are commonly referred to or marketed as herbal teas).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Thea&lt;/em&gt; is the &lt;a href=&quot;http://www.tropicos.org/Name/31600166&quot; rel=&quot;nofollow noreferrer&quot;&gt;original genus name&lt;/a&gt; given by Linnaeus to the species we now call &lt;em&gt;Camellia sinensis&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's an old pharmacy tradition of specialized latin terminology for plant medicines. These will indicate the plant and also often the &lt;a href=&quot;http://abc.herbalgram.org/site/PageServer?pagename=Terminology#Plant%20Parts&quot; rel=&quot;nofollow noreferrer&quot;&gt;plant part&lt;/a&gt;. In this tradition, plants are often indicated with different terminology than modern scientific names. Here's a 19th century pharmacy textbook (Parrish and Weigand) explaining why:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/z0hSm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And here's the same source discussing the naming of plants parts (as CactusWoman mentions, in this case &lt;em&gt;folium&lt;/em&gt; = leaf):&#xA;&lt;img src=&quot;https://i.stack.imgur.com/s1JL2.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You still see this terminology around in some places (some European texts and occasionally translations of Traditional Chinese Medicine preparations), but it definitely has an 'old-fashioned' feel from the perspective of a botanist.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://books.google.com/books?id=3_BCAQAAMAAJ&amp;amp;lpg=PA61&amp;amp;ots=JbXCcClswV&amp;amp;dq=latin%20pharmacy%20names%20radix&amp;amp;pg=PA61#v=onepage&amp;amp;q&amp;amp;f=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;Parrish and Weigand 1884 &lt;em&gt;A Treatise on Pharmacy&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2015-05-29T15:12:07.957" LastActivityDate="2015-05-29T15:12:07.957" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34700" PostTypeId="1" AcceptedAnswerId="34703" CreationDate="2015-05-29T14:47:35.750" Score="8" ViewCount="2235" Body="&lt;p&gt;After the recent floods in central Texas this past weekend I noticed my that bedroom has suddenly been infested with these small insects that have climbed in through the window. Previously, the hole in the window was used by ladybugs who hatched larvae in the room (they didn't survive long).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, these insects have been here for 3 days now. They seem to disappear at odd times during the day (haven't nailed down a pattern yet) and return a bit later. There are roughly 20-30 of them in my room at a given time. They don't do much and seem very uninterested and passive, mostly just flying around or meandering across the walls on and off. Some of them have wings and others do not (that or the wings are hidden and they just aren't using them).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to identify what this insect is so I can find a way to get rid of them. A picture is linked below. Note in the picture that the white-ish segments on the leg are actually closer to yellow in color.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZkW7M.jpg&quot; alt=&quot;Insect on my wall&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="11630" LastEditorUserId="16866" LastEditDate="2019-11-30T22:44:51.317" LastActivityDate="2019-11-30T22:44:51.317" Title="What is this insect that has invaded my home in Texas?" Tags="&lt;species-identification&gt;&lt;entomology&gt;&lt;hemiptera&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34701" PostTypeId="1" CreationDate="2015-05-29T14:55:15.787" Score="11" ViewCount="296" Body="&lt;p&gt;By this question: &lt;a href=&quot;https://biology.stackexchange.com/questions/34542/is-the-human-biological-clock-genetically-programmed-or-learnt&quot;&gt;Is the human biological clock genetically programmed or learnt?&lt;/a&gt; we discussed that the sleep requirement depends on the age of the individual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LdogE.jpg&quot; alt=&quot;sleep requirements by age&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;- Figure 1. - Sleep requirements by age&lt;/em&gt; - &lt;a href=&quot;http://www.howsleepworks.com/need_age.html&quot; rel=&quot;noreferrer&quot;&gt;ref&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought I ask the question, why? &lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2019-01-03T21:01:55.420" Title="What is the connection between sleep requirement and age?" Tags="&lt;circadian-rhythms&gt;&lt;human-physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34702" PostTypeId="1" CreationDate="2015-05-29T15:16:35.920" Score="0" ViewCount="69" Body="&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0306987710001222&quot; rel=&quot;nofollow&quot;&gt;Impaired circadian rhythm is associated with cancer.&lt;/a&gt; Light pollution affects the circadian rhythm and the circadian rhythm affects the metabolism. But what is the (molecular) connection between impaired circadian rhythm altered metabolism and cancer?&lt;/p&gt;&#xA;" OwnerUserId="3703" LastEditorUserId="3703" LastEditDate="2015-05-29T15:23:55.090" LastActivityDate="2015-05-29T15:23:55.090" Title="Can light pollution cause cancer?" Tags="&lt;pathophysiology&gt;&lt;human-physiology&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34703" PostTypeId="2" ParentId="34700" CreationDate="2015-05-29T15:22:50.423" Score="13" Body="&lt;p&gt;&lt;em&gt;Myodocha serripes&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.americaninsects.net/ht/myodocha-serripes.html&quot;&gt;http://www.americaninsects.net/ht/myodocha-serripes.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nice picture! Generally, the body plan of this guy indicates Hemiptera (the 'true' bugs), but the long neck is a bit strange, so a google image search for &quot;Hemiptera + long neck' brought up this strong candidate. It looks like it's distributed in Texas, and is in fact, named for that distinctive neck: &quot;The Long-Necked Seed Bug&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also &lt;a href=&quot;http://bugguide.net/node/view/7632&quot;&gt;the BugGuide.net page for Myodocha&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3624" LastEditDate="2015-06-10T13:08:56.483" LastActivityDate="2015-06-10T13:08:56.483" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34704" PostTypeId="1" AcceptedAnswerId="35545" CreationDate="2015-05-29T16:19:17.250" Score="1" ViewCount="2797" Body="&lt;p&gt;I am having trouble trying to understand how GISTIC discretize copy number variation to values -2, -1, 0, 1, 2. I am using TCGA copy number variation for &lt;a href=&quot;http://firebrowse.org/?cohort=COADREAD#&quot; rel=&quot;nofollow noreferrer&quot;&gt;ColoRectal Adenocarcinoma&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;p&gt;In &lt;a href=&quot;http://www.cbioportal.org/faq.jsp#what-is-gistic-what-is-rae&quot; rel=&quot;nofollow noreferrer&quot;&gt;cBioPortal FAQ&lt;/a&gt; it is written that:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;For TCGA studies, the table in all_thresholded.by_genes.txt (which is the part of the GISTIC output that is used to determine the copy-number status of each gene in each sample in cBioPortal) is obtained by applying both low- and high-level thresholds to to the gene copy levels of all the samples. The entries with value +/- 2 exceed the high-level thresholds for amps/dels, and those with +/- 1 exceed the low-level thresholds but not the high-level thresholds. The low-level thresholds are just the 'amp_thresh' and 'del_thresh' noise threshold input values to GISTIC (typically 0.1 or 0.3) and are the same for every thresholds.&lt;/p&gt;&#xA;&lt;p&gt;By contrast, the high-level thresholds are calculated on a sample-by-sample basis and are based on the maximum (or minimum) median arm-level amplification (or deletion) copy number found in the sample. The idea, for deletions anyway, is that this level is a good approximation for hemizygous given the purity and ploidy of the sample.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;The low-level thresholds are quite clear, while the high-level threshold not (the ones used to label +/-2 values).&lt;/p&gt;&#xA;&lt;p&gt;I tried to reverse engineer the discretization function (the cutoffs are not available on firebrowse). The best solution I found is, for each sample, to:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;split the copy number values in two groups (amplified - positive values, deleted - negative values)&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;for each group (amplified - deleted)&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;compute the median copy number value inside each chromosome arm&lt;/li&gt;&#xA;&lt;li&gt;take the maximum (minimum for deleted group) median value across arms and use it as higher (lower) threshold&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;I tested it using the files:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;all_data_by_genes.txt&lt;/li&gt;&#xA;&lt;li&gt;all_thresholded.by_genes.txt&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;trying to get the correct discretized value (-2, -1, 0, 1, 2) of the second file from the first. However, a small part of the values are not correctly mapped. Am I missing something?&lt;/p&gt;&#xA;" OwnerUserId="3466" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-26T15:58:21.847" Title="How copy number variation thresholds are defined in GISTIC" Tags="&lt;tcga&gt;&lt;copy-number-variation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34705" PostTypeId="2" ParentId="34694" CreationDate="2015-05-29T16:55:17.147" Score="1" Body="&lt;p&gt;When you ingest an allergen for the first time, your body produces many of an antibody called IgE with specificity toward that allergen. These IgE antibodies bind to mast cells, and basophils. When you encounter more allergen, they bind to these IgE on the surface of the mast cells and basophils, causing them to release a host of chemicals like histamine. Massive amount of histamine are the cause of anaphylaxis, so when more allergen interacts with more and more IgE, the situation worsens. The following figure is a detailed mechanism,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/HWWhc.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://what-when-how.com/acp-medicine/allergic-response-part-1/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can also see, though, that histamine released is a function of total allergen, and eventually reaches a maximum regardless of allergen present,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zXiJR.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://openi.nlm.nih.gov/detailedresult.php?img=3199832_CTO-07-04-g-004&amp;amp;req=4&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;&#xA;Here they're showing histamine release vs allergen concentration while investigating allergic rhinitis.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-05-29T16:55:17.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34706" PostTypeId="2" ParentId="21875" CreationDate="2015-05-29T18:21:48.327" Score="0" Body="&lt;p&gt;There is a CBOL working group that categorizes protists based on genomic sequencing and barcoding. Here is a link to their publication: &lt;a href=&quot;http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001419&quot; rel=&quot;nofollow&quot;&gt;CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10118" LastActivityDate="2015-05-29T18:21:48.327" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34708" PostTypeId="2" ParentId="34192" CreationDate="2015-05-29T18:31:48.270" Score="3" Body="&lt;p&gt;Firstly, it is not necessary that all dicots have stomata on their lower surface of their leaves. The lotus &lt;em&gt;Nelumbo nucifera&lt;/em&gt; &lt;a href=&quot;http://www.researchgate.net/publication/249996139_Stomata_actively_regulate_internal_aeration_of_the_sacred_lotus_Nelumbo_nucifera&quot; rel=&quot;nofollow noreferrer&quot;&gt;has its stomata on its upper surface&lt;/a&gt;, due to the lower surface of its leaves being in contact with water, and therefore unable to transpire effectively. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason that stomata are usually on the lower surface has been analysed in &lt;a href=&quot;http://www.jstor.org/stable/2259142?seq=1#page_scan_tab_contents&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper&lt;/a&gt;, which rejects the commonly held hypothesis that stomata appear on the lower surface of leaves (hypostomatous) as a response to dryness, by citing that hypostomatous leaves are relatively less common in dry environments. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Xiev0.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper then analyses the correlation observed between parameters of leaves and their stomatal locations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LMHuM.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By using a number of computational models (which conclude that given the set of assumptions in the paper, leaves should not generally be hypostomatous), the paper addresses the faults of the model and concludes that there is no one single reason why leaves are usually hypostomatous, and then brings up a couple other possibilities that may help in explaining the majority of plants being hypostomatous. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oUUSU.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hyN0R.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EYf0h.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-05-29T18:31:48.270" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34710" PostTypeId="1" AcceptedAnswerId="94736" CreationDate="2015-05-29T20:10:24.830" Score="6" ViewCount="174" Body="&lt;p&gt;I was reading a couple of papers which talk about IBD (Identity by descent) among unrelated individuals (for eg. &lt;a href=&quot;http://www.pnas.org/content/109/4/1193.long&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/109/4/1193.long&lt;/a&gt;). However they do not seem to clearly define what they mean there. I was wondering how IBD is defined in such a context. I'd appreciate any help (especially suggested references to look this up).&lt;/p&gt;&#xA;" OwnerUserId="6353" LastEditorUserId="6353" LastEditDate="2015-05-30T00:56:10.570" LastActivityDate="2020-07-18T16:14:13.960" Title="Identity by descent among unrelated individuals" Tags="&lt;population-genetics&gt;&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34711" PostTypeId="1" AcceptedAnswerId="34712" CreationDate="2015-05-29T19:30:03.517" Score="2" ViewCount="46" Body="&lt;p&gt;When looking at Wikipedia, I read that the interosseus muscle is actually composed of 3 muscles, but on the French Wikipedia, they talk about a 4th muscle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how many interosseus muscle components are there, 3 or 4? &lt;/p&gt;&#xA;" OwnerUserId="16059" OwnerDisplayName="LiohAu" LastEditorUserId="57" LastEditDate="2015-05-29T23:33:47.877" LastActivityDate="2015-05-29T23:33:47.877" Title="How many smaller muscles compose the interosseus muscle in the human hand?" Tags="&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34712" PostTypeId="2" ParentId="34711" CreationDate="2015-05-29T20:57:46.430" Score="1" Body="&lt;p&gt;The number of interosseous muscles is not constant, because of the evolutional process continuing in modern generations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some individuals have &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22009503&quot; rel=&quot;nofollow noreferrer&quot;&gt;4 interosseous muscles, other have three&lt;/a&gt;, however there are still debates about the subject:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/n3Bl1.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;+&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GsRro.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-05-29T20:57:46.430" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34713" PostTypeId="1" AcceptedAnswerId="34718" CreationDate="2015-05-29T23:30:33.287" Score="5" ViewCount="120" Body="&lt;p&gt;Queller 1985 (&quot;Kinship, reciprocity and synergism in the evolution of social behavior&quot;) provides a generalization of Hamilton's rule that allows for non-additivity. To accomplish that, Queller writes the fitness of an individual as&#xA;\begin{align}&#xA;  W = W_{0} - CP + BP' + DPP'&#xA;\end{align}&#xA;where $W_0$ is the baseline fitness; $P$ is the phenotypic value (1 for altruist or 0 for nonaltruist); $P'$ is the phenotypic value of the interacting individual; $C$ is fitness cost if $P=1$; $B$ is the fitness&#xA;benefit if $P'=1$; $D$ is the deviation from additivity of $C$ and $B$ if&#xA;both were altruistic (i.e., $PP' = 1$). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Queller then substitutes this equation into Price's equation $\Delta G = Cov (G, W)$, where $G$ is the frequency of altruism allele in the focal individual($0$, $1/2$ or $1$). The resulting equation is:&#xA;\begin{equation}&#xA;  - \bar c + \bar b \frac{Cov(G,P')}{Cov(G,P)} + \bar d \frac{ Cov(G,PP') }{Cov(G,P)} &amp;gt; 0&#xA;\end{equation}&#xA;where $\bar c$, $\bar b$, and $\bar d$ are the sample means of $C$, $B$, and $D$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My question is:&lt;/strong&gt; how did Queller arrive at the sample means $\bar c$, $\bar b$, and $\bar d$? I understand that $Cov(aX,Y) = a\, Cov(X,Y)$, provided that $a$ is a constant. But what Queller is doing here is different; he seems to be saying that $Cov(AX,Y) = E(A)\, Cov(X,Y)$.&lt;/p&gt;&#xA;" OwnerUserId="11829" LastEditorUserId="57" LastEditDate="2015-05-31T00:36:45.117" LastActivityDate="2015-05-31T00:36:45.117" Title="Queller's 1985 version of Hamilton's rule" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;mathematical-models&gt;&lt;sociality&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34714" PostTypeId="2" ParentId="34701" CreationDate="2015-05-30T00:42:55.063" Score="1" Body="&lt;p&gt;I believe the current theory is that it is related to cell loss in the intermediate nucleus of the human hypothalamus. They have shown sleep disruptions due to lesions of the hypothalamic ventrolateral preoptic nucleus in rodents, and found that the intermediate nucleus in humans is homologous and shows a reduction in size in older adults that is correlated with sleep disruptions. &lt;a href=&quot;http://brain.oxfordjournals.org/content/137/10/2847&quot; rel=&quot;nofollow&quot;&gt;http://brain.oxfordjournals.org/content/137/10/2847&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15966" LastActivityDate="2015-05-30T00:42:55.063" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34716" PostTypeId="2" ParentId="34683" CreationDate="2015-05-30T05:54:54.687" Score="-4" Body="&lt;p&gt;From the systems theory point of view it is because they have a lot less inertia, so their feedback systems operate much more rapidly, with a 'snap' action.&lt;/p&gt;&#xA;" OwnerUserId="16003" LastActivityDate="2015-05-30T05:54:54.687" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="34717" PostTypeId="2" ParentId="34683" CreationDate="2015-05-30T06:35:00.047" Score="16" Body="&lt;p&gt;In addition to @AliceD's excellent answer, I would like to add that a simple mechanistic relationship between body size and &quot;snappiness&quot; may explain the observed pattern.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Basics of biophysics&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Difference in snappiness may result from a difference in the ability to accelerate your movement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An increase in body size over one dimension (=body length) &lt;span class=&quot;math-container&quot;&gt;$x$&lt;/span&gt; scales with an increase in volume and mass of the order of &lt;span class=&quot;math-container&quot;&gt;$x^3$&lt;/span&gt;. Muscle strength is dependent on the cross-sectional area of the muscle and therefore by a linear increase of &lt;span class=&quot;math-container&quot;&gt;$x$&lt;/span&gt;, strength increases by &lt;span class=&quot;math-container&quot;&gt;$x^2$&lt;/span&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Digging back to high school physics lectures, &lt;span class=&quot;math-container&quot;&gt;$F=Ma \left(\text{or } a=\frac{F}{M}\right)$&lt;/span&gt; , where &lt;span class=&quot;math-container&quot;&gt;$F$&lt;/span&gt; is a force, &lt;span class=&quot;math-container&quot;&gt;$M$&lt;/span&gt; a mass and &lt;span class=&quot;math-container&quot;&gt;$a$&lt;/span&gt; an acceleration. With an increase &lt;span class=&quot;math-container&quot;&gt;$x$&lt;/span&gt; of the individual size (over one dimension, the length of the individual if you prefer), the force increases by &lt;span class=&quot;math-container&quot;&gt;$x^2$&lt;/span&gt; and the mass increases by &lt;span class=&quot;math-container&quot;&gt;$x^3$&lt;/span&gt;, therefore the acceleration gets multiplied by &lt;span class=&quot;math-container&quot;&gt;$\frac{x^2}{x^3} = \frac{1}{x}$&lt;/span&gt;. Of course, nature is not all that easy, but if we assume it is, then the relation between the acceleration of movements and body size (=body length) should look like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4XiFW.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An animal that is 4 times as big should make accelerate its arms and legs 4 times less.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Contrasting to @AliceD's answer&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;@AliceD listed plausible hypotheses for why there might have a selection for snappy movement in small animals but simpler explanation based on the physical properties of bodies might be enough to explain the observed pattern. It would be interesting to know exactly what the relationship between body size (=body length) and &quot;snappiness&quot; look like in nature to further this discussion.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fun Facts&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;mantis shrimp&lt;/strong&gt; (see below picture) is able to accelerate its claws up to 10,400g (&lt;a href=&quot;http://www.nature.com/nature/journal/v428/n6985/full/428819a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;). More information about g (unit of acceleration) &lt;a href=&quot;http://en.wikipedia.org/wiki/G-force&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;. In short, a typical human can support up to 5g. 10,400g is absolutely insane! To offer some comparison: a baseball gets an acceleration that is only about a third of that of the mantis shrimp's claws. Mantis shrimps use their claws to break open clams. Here is a &lt;a href=&quot;https://www.youtube.com/watch?v=i-ahuZEvWH8&quot; rel=&quot;nofollow noreferrer&quot;&gt;video&lt;/a&gt;. According to &lt;a href=&quot;http://en.wikipedia.org/wiki/Mantis_shrimp&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;, due to the friction of the claws against the water, small bubbles are formed and the temperature at the edge of those bubbles can go up to several thousands of °C.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/q95gwm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently, a &lt;strong&gt;jellyfish stinger&lt;/strong&gt; can go up to 5,400,000g (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3773479/&quot; rel=&quot;nofollow noreferrer&quot;&gt;reference&lt;/a&gt;) which appears to be about 30 times more than a bullet. You will find a list of examples of things that undergo various levels of acceleration on this &lt;a href=&quot;http://en.wikipedia.org/wiki/Orders_of_magnitude_(acceleration)&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia list&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="3340" LastEditDate="2019-03-28T12:42:45.150" LastActivityDate="2019-03-28T12:42:45.150" CommentCount="6" ContentLicense="CC BY-SA 4.0" />
  <row Id="34718" PostTypeId="2" ParentId="34713" CreationDate="2015-05-30T10:45:41.633" Score="3" Body="&lt;p&gt;It is just worded a little wierdly in my opinion. The key line in the paper is: 'Fitness components are also defined for all individuals, for example, $C$ is defined, even for a non-altruist, as the cost it would incur if were altruistic.'&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially, if it doesn't matter what individual you are you always pay the same cost, then $C$ is a constant. This is pretty much the definition of a constant! The expectation of a constant is just the constant, $E(C) = C$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason it works is that to find whether or not the cost is realised, Queller simply multiplies by the focal individual's phenotype value $P$, which is either 0 or 1. So either the individual pays the cost or it doesn't. &lt;/p&gt;&#xA;" OwnerUserId="14849" LastActivityDate="2015-05-30T10:45:41.633" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34720" PostTypeId="2" ParentId="34085" CreationDate="2015-05-30T11:24:37.083" Score="0" Body="&lt;p&gt;The experiment described in the linked article &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2226091/&quot; rel=&quot;nofollow&quot;&gt;Bazanilla &amp;amp; Armstrong (1972)&lt;/a&gt; is about a voltage clamp experiment in squid axon. &lt;strong&gt;Voltage clamping&lt;/strong&gt; basically means that the &lt;strong&gt;potential difference&lt;/strong&gt; across the axonal membrane can be set at will by an external artificial electronic power source. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;NMDA receptors are channels that conduct positively charged ions (mainly Na&lt;sup&gt;+&lt;/sup&gt;). If the voltage is clamped at negative potentials under physiological conditions, &lt;strong&gt;positive current will be drawn inward&lt;/strong&gt;. This is generally plotted as a &lt;strong&gt;negative current&lt;/strong&gt;, as shown in your picture in your post. If, however, the &lt;strong&gt;voltage is made more positive&lt;/strong&gt;, current will &lt;strong&gt;reverse&lt;/strong&gt; at a certain point, and &lt;strong&gt;positive currents&lt;/strong&gt; will be measured by the electrodes. This positive current is characterized by an outward flow of positive ions through the NMDA receptor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The sign of the current is arbitrary, but the most important point to make is that &lt;em&gt;most channels allow current to pass both ways&lt;/em&gt;. There are &lt;em&gt;rectifier channels&lt;/em&gt;, however, that will only allow one-way traffic. Rectifiers are more exceptions than the rule. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Linked reference&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2226091/&quot; rel=&quot;nofollow&quot;&gt;Bazanilla &amp;amp; Armstrong, &lt;em&gt;J Gen Physiol&lt;/em&gt; (1972); &lt;strong&gt;60&lt;/strong&gt;: 588-608&lt;/a&gt;   &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-01T01:10:09.443" LastActivityDate="2015-06-01T01:10:09.443" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34721" PostTypeId="2" ParentId="34462" CreationDate="2015-05-30T11:53:49.780" Score="1" Body="&lt;ol&gt;&#xA;&lt;li&gt;Ferritin and iron-containing ferritin are different and the latter&#xA;would of course be heavier; it will therefore sediment faster.&lt;/li&gt;&#xA;&lt;li&gt;Figure 3 of the third article uses thyroglobulin and ferritin as molecular weight markers. For your information thyroglobulin is 650kDa whereas ferritin is 440kDa. Also note that apoferritin i.e. ferritin that is not bound with iron has a sedimentation rate of 18S (from the same article that measures the sedimentation rate of iron bound ferritin - ref#2).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;There seems to be some confusion regarding the sedimentation rate of ferritin. From &lt;a href=&quot;http://www.iopan.gda.pl/oceanologia/514potry.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One molecule of ferritin can bind up to 4500 Fe&lt;sup&gt;2+&lt;/sup&gt; ions.&#xA;  When fully loaded with iron, the ferritin can increase in mass up to&#xA;  ca 900 kDa; it then has a sedimentation coefficient of 24S (Chasteen &amp;amp;&#xA;  Harrison 1999).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;55S for ferritin seems dubious. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-07T05:53:30.000" LastActivityDate="2015-06-07T05:53:30.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34722" PostTypeId="1" AcceptedAnswerId="34728" CreationDate="2015-05-30T12:30:41.643" Score="1" ViewCount="791" Body="&lt;p&gt;My understanding:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In Hardy-Weinberg problems the frequency of a homozygous recessive genetic occurrence in a population is $q^2$. So if 1 in 100 people in a population have albinism (homozygous recessive disorder) then we say the frequency is $q^2=1/100$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We then say, to find the frequency of the allele count $q$ that $q=\sqrt{1/100}= 1/10$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't understand why we say this. Why would the allele count be the square root of the population frequency? There's 2 alleles per person. Why isn't it x2 or /2 instead?&#xA;I suppose my problem is understand &lt;strong&gt;what exactly is p and q&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="1590" LastEditDate="2015-06-01T09:10:01.533" LastActivityDate="2015-06-03T05:23:39.813" Title="Why is it $q^2$ for the individual count in hardy weinberg?" Tags="&lt;genetics&gt;&lt;population-genetics&gt;&lt;hardy-weinberg&gt;" AnswerCount="3" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="34723" PostTypeId="2" ParentId="34681" CreationDate="2015-05-30T13:05:52.940" Score="1" Body="&lt;p&gt;In case anybody ever has the same question: I found the answer in this paper by Ow et al. 1987 (fig1)&#xA;&lt;a href=&quot;http://www.pnas.org/content/84/14/4870.full.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.pnas.org/content/84/14/4870.full.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just to clarify, I did not want to boost expression of the enhancer element in my algae, it needed boosting in tobacco protoplasts/leaves.&lt;/p&gt;&#xA;" OwnerUserId="15138" LastActivityDate="2015-05-30T13:05:52.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34724" PostTypeId="2" ParentId="32988" CreationDate="2015-05-30T14:03:19.873" Score="1" Body="&lt;p&gt;Trait &lt;strong&gt;&lt;em&gt;z&lt;/em&gt;&lt;/strong&gt; is represented by &lt;strong&gt;&lt;em&gt;k&lt;/em&gt;&lt;/strong&gt; genes: &lt;strong&gt;&lt;em&gt;z&lt;sub&gt;1&lt;/sub&gt;....z&lt;sub&gt;k&lt;/sub&gt;&lt;/em&gt;&lt;/strong&gt; (I am using &lt;strong&gt;&lt;em&gt;k&lt;/em&gt;&lt;/strong&gt; instead of &lt;strong&gt;&lt;em&gt;l&lt;/em&gt;&lt;/strong&gt; because the former is visually differentiable from &lt;strong&gt;&lt;em&gt;1&lt;/em&gt;&lt;/strong&gt; ).&#xA;For simplicity let's assume that there is only one mutable site in a gene. So a mutation can impart a change of $\pm \Delta z$. Starting from initial state of &lt;strong&gt;&lt;em&gt;z&lt;/em&gt;&lt;/strong&gt; at zero, the system will proceed to equilibrium where the rate of forward mutation would be same as that of backward mutation; since the rates are same the deterministic steady state of &lt;strong&gt;&lt;em&gt;z&lt;/em&gt;&lt;/strong&gt; should be zero. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A mutation event can also be considered a binomially distributed RV. After &lt;strong&gt;&lt;em&gt;n&lt;/em&gt;&lt;/strong&gt; events, the mean number of forward mutations would be 0.5×&lt;strong&gt;&lt;em&gt;n&lt;/em&gt;&lt;/strong&gt;. &lt;br&gt; &lt;pre&gt;&lt;b&gt; Mean fitness = mean forward mutation — mean backward mutations = 0 &lt;/b&gt;&lt;/pre&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also model the mutation events as a &lt;a href=&quot;http://mathworld.wolfram.com/RandomWalk1-Dimensional.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;simple random walk&lt;/a&gt;. The mean of that is 0 and the variance is &lt;strong&gt;&lt;em&gt;n&lt;/em&gt;&lt;/strong&gt;. But what about large &lt;strong&gt;&lt;em&gt;n&lt;/em&gt;&lt;/strong&gt;; I am not sure. You should read about random walks or ask in &lt;a href=&quot;https://stats.stackexchange.com/&quot;&gt;CrossValidated&lt;/a&gt;. With $t\to \infty$, you would get a lot of variants but variants would be filtered out by selection (as the optimum is at 0). I think selection can be incorporated in the random walk with death rate being proportional to the distance from 0. But again I do not have much experience with such hybrid models. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried a simulation with n=10000000 (using Monte Carlo); different colours denote different runs (or in another words different loci). Y-axis denotes the value of z.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rjVpz.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:44:17.897" LastActivityDate="2015-05-30T15:37:20.403" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34725" PostTypeId="2" ParentId="31054" CreationDate="2015-05-30T14:06:02.217" Score="2" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Myopes may have some benefit in terms of identifying small objects due to their ability to focus objects nearer to their retina than emmetropes, but only marginally so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The more myopic you are, the more blurred your distance vision, but the closer up you can see clearly. Hence, &lt;strong&gt;myopes have a range of clear vision that is closer to their eyes&lt;/strong&gt; than emmetropes (normally sighted people) (&lt;a href=&quot;http://www.triadpublishing.com/eyecarereports/myopia-book.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;Triad Publishing&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A young emmetropic adult can focus at an object &lt;a href=&quot;http://www.tedmontgomery.com/the_eye/lens.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;some &lt;strong&gt;10 cm&lt;/strong&gt; away&lt;/a&gt;, which is defined as an amplitude of accommodation (lens adjustment) of &lt;a href=&quot;http://www.tedmontgomery.com/the_eye/lens.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;10 diopters&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;strong&gt;&lt;em&gt;severely&lt;/em&gt; myopic eye&lt;/strong&gt; can be up to &lt;a href=&quot;https://www.eyecaretyler.com/resources/how-the-eye-works/the-nearsighted-eye-myopia/&quot; rel=&quot;nofollow noreferrer&quot;&gt;minus 6 diopters&lt;/a&gt;, bringing the tally from 10 to 16 diopters, meaning you can view something up to &lt;a href=&quot;http://www.tedmontgomery.com/the_eye/lens.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;6 cm&lt;/a&gt; instead of 10 cm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bringing objects closer increases retinal image size and hence increases spatial detail. Going from 10 to 6 cm increases the &lt;a href=&quot;http://www.psypress.co.uk/mather/resources/swf/Demo6_3.swf&quot; rel=&quot;nofollow noreferrer&quot;&gt;retinal angle&lt;/a&gt; by 10/6 = &lt;strong&gt;~1.7 x&lt;/strong&gt;, so not even a doubling of the angle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A random search for a magnifying glass for the visually impaired that aids in reading small print (newspapers etc.) yielded one that magnified 4x (16 diopters):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fBzPS.jpg&quot; alt=&quot;reading aid&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Clip on reading aid. Source: &lt;a href=&quot;http://www.eschenbach.com/17470333-0726-4483-91d5-e8445b621c1b/products-spectacle-magnifiers-clip-on-systems-detail.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eschenbach&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Microscopes typically have lenses with magnification factors from &lt;a href=&quot;http://www.olympusmicro.com/primer/anatomy/magnification.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;4x to 100x&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in all, myopes do not have microscopic superpowers. A standard magnifying glass for the visually impaired magnifies several times more than a severely myopic eye.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-30T14:35:38.423" LastActivityDate="2015-05-30T14:35:38.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34726" PostTypeId="1" CreationDate="2015-05-30T14:58:01.857" Score="1" ViewCount="25" Body="&lt;p&gt;Are any natural (human or otherwise) antiviral mechanisms similar to the antiviral mechanisms of amantadine and rimantadine, or are these mechanisms undiscovered by evolution? Are drug researchers discovering completely new mechanisms to attack viruses?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.rapidreferenceinfluenza.com/chapter/B978-0-7234-3433-7.50014-1/aim/mechanisms-of-action-of-antivirals&quot; rel=&quot;nofollow&quot;&gt;http://www.rapidreferenceinfluenza.com/chapter/B978-0-7234-3433-7.50014-1/aim/mechanisms-of-action-of-antivirals&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanism by which antiviral drugs (amantadine and rimantadine) interrupt the replicative cycle of influenza is illustrated. M2 inhibitors prevent the M2-mediated acidification of the interior of the virus while it resides in endosomes and the subsequent uncoating of the viral genome, thus inhibiting viral replication. Neuraminidase inhibitors (NAIs) prevent cleavage of sialic acid residues and thus newly formed virus cannot be released from the cell surface to infect adjacent cells; also, virus particles remain associated to one another.&lt;/p&gt;&#xA;" OwnerUserId="15998" LastActivityDate="2015-05-30T14:58:01.857" Title="Are amantadine and rimantadine MOAs unknown to evolution?" Tags="&lt;evolution&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34727" PostTypeId="2" ParentId="34722" CreationDate="2015-05-30T15:48:33.903" Score="1" Body="&lt;p&gt;To understand population genetics and the Hardy-Weinberg equilibrium you first need to clearly separate &lt;strong&gt;genotype frequencies&lt;/strong&gt; (the frequency of individuals in a population having a genotype) and &lt;strong&gt;allele frequencies&lt;/strong&gt; (the frequency of an allele in the population gene pool). In your question &lt;strong&gt;p&lt;/strong&gt; and &lt;strong&gt;q&lt;/strong&gt; represents allele frequencies, while &lt;strong&gt;p&lt;sup&gt;2&lt;/sup&gt;&lt;/strong&gt;, &lt;strong&gt;q&lt;sup&gt;2&lt;/sup&gt;&lt;/strong&gt; and &lt;strong&gt;2pq&lt;/strong&gt; represents genotype frequencies (if $p=P(A)$, $p^2$ is $P(AA)$). Genotype frequencies can be thought of as the probability that two particular alleles are located in the same individual, and the calculation of these probabilities is a simple application of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Independence_%28probability_theory%29#Two_events&quot; rel=&quot;nofollow&quot;&gt;multiplication rule of probabilites&lt;/a&gt; for independent events.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, if the allele frequency &lt;strong&gt;p&lt;/strong&gt; is 0.2 the probability of having two copies of this allele is $p \times p = p^2 = 0.2^2 = 0.04$. If there are only two alleles in the population, q has to be 0.8, which means that the other two genotype frequencies are $ 2pq = 2\times0.2\times0.8 = 0.32$ and $ q^2 = 0.8^2 = 0.64$. As you can see, these genotype frequencies also sum to 1, since they represent the genotypes of all individuals in the population,&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-06-01T11:33:41.820" LastActivityDate="2015-06-01T11:33:41.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34728" PostTypeId="2" ParentId="34722" CreationDate="2015-05-30T15:52:27.297" Score="3" Body="&lt;p&gt;First of, let me correct your equation: $q = \sqrt{\frac{1}{100}} = \frac{1}{10} = 0.1 ≠ 10 $.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;From allele frequency to genotype frequency&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine you were to randomly sample an allele from a population of allele where the allele &lt;code&gt;A&lt;/code&gt; is present at frequency $q$. What is the probability that you draw allele &lt;code&gt;A&lt;/code&gt;? Answer: $P(A) = q$. Now, put this allele back in the pool and imagine you have to draw two alleles. What is the probability that the two alleles are &lt;code&gt;A&lt;/code&gt;. Well it is the probability that the first allele is &lt;code&gt;A&lt;/code&gt; times the probability that the second allele is &lt;code&gt;A&lt;/code&gt;, it is $P(A) \cdot P(A) = q \cdot q = q^2$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;From genotype frequency to allele frequency&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, under Hardy-Weinberg conditions, if the allele &lt;code&gt;A&lt;/code&gt; is at frequency $q$, then the homozygote genotype &lt;code&gt;AA&lt;/code&gt; is at frequency $q \cdot q = q^2$. Now let's denote the frequency of the genotype &lt;code&gt;AA&lt;/code&gt; by $f_{AA}$. You know that $f_{AA} = q^2$ from the above though experiment. If you take the square root of both sides, you get $\sqrt{f_{AA}} = \sqrt{q^2} = q$. In words, the frequency of the allele &lt;code&gt;A&lt;/code&gt; is the square root of the frequency of the genotype &lt;code&gt;AA&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Recessivity and dominance&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Btw, you'll note that those calculations tell nothing about the patterns of dominance/recessivity of alleles (Hardy-Weinberg principle assumes no selection anyway).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-06-01T16:43:24.393" LastActivityDate="2015-06-01T16:43:24.393" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34729" PostTypeId="1" CreationDate="2015-05-30T16:01:03.080" Score="0" ViewCount="955" Body="&lt;p&gt;What is Meriva Phytosome Curcumin other than being a food supplement?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it a plant? A type of plant extract?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I googled it but still couldn't figure out exactly what it is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason I'm asking is because I came across the following list in a site selling vitamins and other food supplements:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Meriva Phytosome Curcumin&#xA;Turmeric (Curcumin)&#xA;Turmeric Formulas&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;It wasn't clear to me if &lt;code&gt;Meriva Phytosome Curcumin&lt;/code&gt; is a specific kind of curcumin since it seems to be sold under a few different brands.&lt;/p&gt;&#xA;" OwnerUserId="16009" LastEditorUserId="16009" LastEditDate="2015-06-02T13:23:31.693" LastActivityDate="2016-07-20T07:22:05.277" Title="What is Meriva Phytosome Curcumin?" Tags="&lt;botany&gt;&lt;food&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34730" PostTypeId="2" ParentId="34366" CreationDate="2015-05-30T16:05:05.963" Score="1" Body="&lt;p&gt;In case you want to write your own subroutine,&lt;br&gt;&#xA;1. Scan the whole &lt;code&gt;.pdb&lt;/code&gt; file for number of chains present, if multiple then proceed.&lt;br&gt;&#xA;2. Create &lt;code&gt;index_counter&lt;/code&gt; for each amino acids of a single chain.&lt;br&gt;&#xA;3. Now, For SINGLE chain. While you scan for each amino acid perform a &lt;code&gt;i=i+1&lt;/code&gt; operation for that specific &lt;code&gt;amino-acid_counter&lt;/code&gt;.&lt;br&gt;&#xA;4. Compare the &lt;code&gt;amino-acid_counter&lt;/code&gt; between/among the chains.&lt;br&gt;&#xA;5. Exact match = homomer or non-exact match = heteromer.&lt;br&gt;&#xA;Hope you get the logic.   &lt;/p&gt;&#xA;" OwnerUserId="8607" LastEditorUserId="8607" LastEditDate="2015-05-30T16:26:49.687" LastActivityDate="2015-05-30T16:26:49.687" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34731" PostTypeId="2" ParentId="34729" CreationDate="2015-05-30T17:14:57.320" Score="2" Body="&lt;p&gt;Well, &lt;a href=&quot;http://meriva.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://meriva.org&lt;/a&gt; states that&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Meriva® is a patented formulation of curcumin, a dietary phenolic, with soy lecithin (non-GMO)(1). The two compounds form a non-covalent adduct in a 1:2 weight ratio, and two parts of microcrystalline cellulose are then added to improve formulation, with an overall contents of curcumin of 20%&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;A &lt;a href=&quot;https://en.wikipedia.org/wiki/Phytosome&quot; rel=&quot;nofollow noreferrer&quot;&gt;phytosome&lt;/a&gt; is&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;[...]  a complex of a natural active ingredient and a phospholipid.&lt;/p&gt;&#xA;&lt;p&gt;It is claimed that phytosome increases absorption of &amp;quot;conventional herbal extracts&amp;quot; or isolated active principles both topically as well as orally.&lt;/p&gt;&#xA;&lt;p&gt;The complexation with phospholipid has been applied to many popular herbal extract or active molecules including [...] curcumin isolated from turmeric [...].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;And &lt;a href=&quot;https://en.wikipedia.org/wiki/Curcumin&quot; rel=&quot;nofollow noreferrer&quot;&gt;Curcumin&lt;/a&gt; is&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;[...] is a diarylheptanoid. It is the principal curcuminoid of turmeric, which is a member of the ginger family (Zingiberaceae). Turmeric's other two curcuminoids are desmethoxycurcumin and bis-desmethoxycurcumin. The curcuminoids are natural phenols that are responsible for the yellow color of turmeric. Curcumin can exist in several tautomeric forms, including a 1,3-diketo form and two equivalent enol forms. The enol form is more energetically stable in the solid phase and in solution.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So, Meriva Phytosome Curcumin is a phytosome of curcumin developed by Meriva.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-05-31T12:13:58.573" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34732" PostTypeId="1" CreationDate="2015-05-30T17:24:36.457" Score="7" ViewCount="491" Body="&lt;p&gt;&lt;a href=&quot;http://www.chron.com/news/strange-weird/article/Earthworm-herds-brought-out-by-Texas-floods-6295345.php#photo-8068776&quot; rel=&quot;nofollow noreferrer&quot;&gt;This article&lt;/a&gt; shows pictures of earthworms during floods in Texas. The worms ball up, supposedly in order to survive the floods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/5XxiQ.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/5XxiQ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;Photo Credit: Texas Parks And Wildlife Department &lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone explain the phenomenon a little? I can't seem to find anything about this online. I know that earthworms surface when it rains for oxygen, but it seems weird that they meet in the middle of the street.&lt;/p&gt;&#xA;" OwnerUserId="1224" LastEditorUserId="16866" LastEditDate="2018-11-20T15:44:04.683" LastActivityDate="2019-05-13T14:39:02.733" Title="Why do these earthworms stay between the road lines?" Tags="&lt;zoology&gt;&lt;ethology&gt;&lt;annelida&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="34733" PostTypeId="1" AcceptedAnswerId="35650" CreationDate="2015-05-30T18:26:18.317" Score="5" ViewCount="1430" Body="&lt;p&gt;The senses of &lt;em&gt;taste&lt;/em&gt; and &lt;em&gt;smell&lt;/em&gt; in different fish classes are described as two distinct senses; smell is mediated by the nasal openings, and taste by epithelial taste buds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are both forms of chemoreception and therefore it is not clear to me what intrinsically defines them as two distinct senses. The more so because reception of chemical substances is mediated by water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What defines them as different senses? Is it only the difference of receptors that defines them as two distinct senses, or are there other reasons to differentiate them?&lt;/p&gt;&#xA;" OwnerUserId="8124" LastEditorUserId="9943" LastEditDate="2015-06-30T05:15:15.997" LastActivityDate="2015-06-30T09:13:17.907" Title="How are smell and taste in fish differentiated?" Tags="&lt;physiology&gt;&lt;zoology&gt;&lt;sensation&gt;&lt;olfaction&gt;&lt;gustation&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34734" PostTypeId="1" AcceptedAnswerId="34735" CreationDate="2015-05-30T20:24:00.410" Score="3" ViewCount="9008" Body="&lt;p&gt;What precisely is ecology? How does it differ from biology? Because I never studied biology after high school, please explain as if I were 10 years old. I only know that ecology is a subset of biology&lt;/p&gt;&#xA;&lt;p&gt;I tried some dictionaries but they  didn't  adequately discriminate. I tried to find an explanation from a scientist: the following appears to claim that only ecology concerns some organism's external interactions with other entities? But how? Biology must also? For example, suppose that someone studies prions' interactions with humans, and not just prions. Then this is biology, not ecology?&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;https://marineecologist.wordpress.com/2013/01/22/marine-ecology-or-marine-biology-whats-the-difference/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Source&lt;/a&gt;: by  &lt;a href=&quot;http://www.plants.uwa.edu.au/research/postgrads?profile/1/id/3895&quot; rel=&quot;nofollow noreferrer&quot;&gt;Matthew Fraser&lt;/a&gt;, &lt;a href=&quot;http://au.linkedin.com/pub/matthew-w-fraser/61/b0a/838&quot; rel=&quot;nofollow noreferrer&quot;&gt;PhD Candidate (Marine Ecology) at University of Western Australia&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;So what makes us fully fledged marine ecologist different from our biologist counterparts?  Well, I think that marine ecology is even cooler than marine biology because as marine ecologists we link what we know about the biology of a given species with other plants/animals and the environment as well. [...]&lt;/p&gt;&#xA;&lt;p&gt;If we were splitting hairs, ecology is technically a form of biology, but I felt the need to write this post given how passionately I see some researchers stating that they are in one camp or another. [...]  But as an ecologist (albeit a biased one!) what gets me excited isn’t just finding out how the amazing plants and animals we find in the ocean work, but how they interact with each other and their environment, explaining why we see certain species in some places and not others!&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="4466" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2018-12-18T13:18:32.223" Title="How does ecology differ from biology?" Tags="&lt;ecology&gt;&lt;terminology&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34735" PostTypeId="2" ParentId="34734" CreationDate="2015-05-30T21:05:26.353" Score="5" Body="&lt;p&gt;Ecology has two meanings. The &lt;strong&gt;popular&lt;/strong&gt; and the &lt;strong&gt;scientific&lt;/strong&gt; meaning.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Ecology: the popular definition&lt;/strong&gt;: Here the term ecology is probably quite poorly defined. To my gut feeling, the concept relates to the concept of global change. It encompass many fields such as biology (ecology (in the scientific sense), evolutionary biology and conservation biology especially), ethics and moral, politics, meteorology, public policy, ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Ecology: the scientific definition&lt;/strong&gt;: Ecology is a subfield of biology and earth sciences that studies &lt;em&gt;interactions&lt;/em&gt; among organisms and their environment. &lt;em&gt;interaction&lt;/em&gt; is an important word here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Biology&lt;/strong&gt; has a much broader meaning. Biology is the science that studies life. Biology studies the structure, the ecology (impact on their surrounding), the evolution, development biochemical processes, etc.. of living things. Biology is a very big field of science. A researcher in biology will probably not really consider him/herself as a biologist but rather as a molecular geneticist, a neurologist, a epidemiologist, a plant physiologist, a biochemist, a bioinformatician, a system biologist, etc.. For example, I would appreciate to consider myself as a population geneticist rather than as a biologist as there are many fields of biology I know nothing about. For example, I am a pretty bad naturalist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In short&lt;/strong&gt;, ecology is to biology what optics is to mechanics is to physics. Some people may not like this comparison as mechanics might take a larger part of physics that what ecology does to biology. Earth scientists may not like this comparison as well, as they are part of ecology without necessarily feeling like being part of biology. But anyway.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;From the text you cite&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[..] as an ecologist [..] what gets me excited isn’t just finding out how the amazing plants and animals we find in the ocean work, but how they interact with each other and their environment [..]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It shows that indeed ecologist are interested in the &lt;em&gt;interaction&lt;/em&gt; between organisms and between organisms and their abiotic environment. Matthew Fraser says &quot;he's not only interested in how they work&quot;. 'How they work' is obviously an extremely inaccurate sentence. A less misleading reformulation would be: I am not interested in everything about the biology of marine animals, &quot;I am especially interested in how animals interact with each other and how they interact with the environment&quot;, but obviously that is less exciting for the reader. The goal of Matthew I guess was to create the interest and the excitation of the reader (or audience) on ecology and for this purpose he kinda implied as ecology being more than biology, while ecology is only a subfield of biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;For more information, wikipedia is your friend!&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-10-09T14:23:42.130" LastActivityDate="2015-10-09T14:23:42.130" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34736" PostTypeId="1" CreationDate="2015-05-30T21:09:39.027" Score="3" ViewCount="1263" Body="&lt;p&gt;I'm not sure all heavy metals are toxic, but most are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some may be present as insoluble compounds, or otherwhise hard to get into an organism, but that's a side aspect.&#xA;For example, I would count copper as toxic, even if some salts are triggering to vomit just too quickly to swallow poisonous doses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in this sense, are they all toxic?&lt;br&gt;&#xA;Is the toxicity based on the same mechanism?&lt;/p&gt;&#xA;" OwnerUserId="6194" LastEditorUserId="5144" LastEditDate="2015-05-30T22:26:23.083" LastActivityDate="2015-06-02T09:13:22.217" Title="What makes heavy metals toxic?" Tags="&lt;toxicology&gt;&lt;dose&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34738" PostTypeId="1" AcceptedAnswerId="34739" CreationDate="2015-05-30T22:28:33.727" Score="1" ViewCount="766" Body="&lt;p&gt;&lt;strong&gt;TLDR: Can anyone state a extraction and isolation method(s) for genomic DNA for hair that will be used for PCR, in detail is preferable since I am a novice.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried googling for DNA extraction methods for hair(follicles and/or root) and found various sources, the one that had the most detail involved the use or organic compounds we do not have access to. Is their preferred method of extracting DNA from hair, given that the genomic DNA would be in low amounts, I figure that might have something to do with the extraction process.&lt;/p&gt;&#xA;" OwnerUserId="14815" LastActivityDate="2015-06-02T09:58:24.017" Title="DNA extraction methods for hair?" Tags="&lt;dna&gt;&lt;pcr&gt;&lt;hair&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="34739" PostTypeId="2" ParentId="34738" CreationDate="2015-05-31T00:08:38.973" Score="4" Body="&lt;p&gt;I've been trying to figure out something that works for some time.  I have recently tried 3 cheap protocols using commonly available lab reagents.  I was using buccal samples (0.2 ml of spit). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Boil the sample in Tris EDTA Buffer&#xA;2) NaOH Extraction&#xA;3) Direct N Lyse &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I compared them to a genomic DNA extraction kit (FAST DNA Prep - MP Biomedicals).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have heard lots of people use &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23121735&quot; rel=&quot;nofollow&quot;&gt;NaOH extraction&lt;/a&gt; to get DNA from tissue and cell preps, but none of the first three worked for me after 2-3 tries.  One of the people in my lab said that I could replace the bead beater with vortexing with glass beads.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried vortexing with beads with all four methods, including the kit and only the kit worked.  I got a PCR result from control primers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you look at the costs of getting all the ingredients for the buffers kits are not so expensive - $1-$2 per sample.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A lot of these kits can handle solid animal tissues, though the one I have doesn't specifically cite hair.  I would try it out.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I guess the point of my post was that there are lots of simple sounding published methods, but they don't always produce results without a bunch of debugging.  I know &lt;a href=&quot;http://faculty.plattsburgh.edu/donald.slish/Extraction.html&quot; rel=&quot;nofollow&quot;&gt;alkaline lysis&lt;/a&gt; has worked for several people I know and is the basis of the kits.  Its pretty simple. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's my experience anyway.&lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2015-06-02T06:05:30.070" LastActivityDate="2015-06-02T06:05:30.070" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34740" PostTypeId="1" AcceptedAnswerId="34754" CreationDate="2015-05-31T00:38:32.723" Score="2" ViewCount="387" Body="&lt;p&gt;Is there any resource that contains motor and sensory innervations, or pathways of all the twelve cranial nerves (i.e., cranial nerve I to XII)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have found &lt;a href=&quot;http://www.blackwellpublishing.com/patestas/chapters/15.pdf&quot; rel=&quot;nofollow&quot;&gt;this book chapter on the cranial nerves&lt;/a&gt;, but it is too broad for me -  I'm still at high school.&lt;/p&gt;&#xA;" OwnerUserId="16015" LastEditorUserId="9943" LastEditDate="2015-05-31T11:40:32.533" LastActivityDate="2015-05-31T12:08:50.633" Title="A request for an overview of the cranial nerves" Tags="&lt;neuroanatomy&gt;&lt;literature&gt;&lt;cranial-nerves&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34741" PostTypeId="2" ParentId="31616" CreationDate="2015-05-31T01:35:36.847" Score="3" Body="&lt;p&gt;I commented above that it will depend &lt;em&gt;heavily&lt;/em&gt; on at what pace you drink your rum, but in short, no, no you cannot.  If you do it quickly, you'll die of &lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/alcohol-poisoning/basics/definition/con-20029020&quot; rel=&quot;nofollow&quot;&gt;alcohol poisoning&lt;/a&gt;, and if you drink it slowly, you'll probably die of dehydration[1].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://io9.com/could-you-drink-beer-instead-of-water-and-still-survive-457081579&quot; rel=&quot;nofollow&quot;&gt;io9 summed up some research&lt;/a&gt; a few years ago, the majority of which is largely bunk.  One study (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9338423&quot; rel=&quot;nofollow&quot;&gt;ncbi&lt;/a&gt;, &lt;a href=&quot;http://jap.physiology.org/content/83/4/1152&quot; rel=&quot;nofollow&quot;&gt;free pdf&lt;/a&gt;) however, from 1996, claimed to find that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These results suggest that alcohol has a negligible diuretic effect&#xA;  when consumed in dilute solution after a moderate level of&#xA;  hypohydration induced by exercise in the heat. There appears to be no&#xA;  difference in recovery from dehydration whether the rehydration&#xA;  beverage is alcohol free or contains up to 2% alcohol, but drinks&#xA;  containing 4% alcohol tend to delay the recovery process.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So stick to (American) beer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sidenote: In Belgium, they divide their (truly excellent) beer into two categories: special, which are stronger and often bottled, and thirst-quenching, which have a lower alcohol content and are often had with lunch.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[1]: Citation: Personal experience and &lt;a href=&quot;https://www.youtube.com/watch?v=PlqdqNGhJaA&quot; rel=&quot;nofollow&quot;&gt;the story of Johnny Tarr&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="3340" LastEditDate="2015-09-13T11:32:47.410" LastActivityDate="2015-09-13T11:32:47.410" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34742" PostTypeId="1" CreationDate="2015-05-31T02:37:06.030" Score="4" ViewCount="378" Body="&lt;p&gt;I have noticed a lot of athletes hit their prime when they are in their 20s and that by the time they reach their 30s they are past it and start to decline. Great athletes tend to prolong their careers by adjusting their game strategy, but even so they can't do the things they used to do when they were younger. Examples of this are abundant in the NBA, NFL, MLB, NHL, football, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do athletes suddenly have such a drop off in performance? What happens to their bodies,  muscles, etc that prevents them from doing what they once did? Can someone explain the biological/physiological reason for this?&lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="11652" LastEditDate="2015-05-31T08:30:11.233" LastActivityDate="2015-05-31T08:30:11.233" Title="Why do athletes see a dip in performance in their thirties?" Tags="&lt;muscles&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34743" PostTypeId="2" ParentId="31293" CreationDate="2015-05-31T02:45:28.790" Score="2" Body="&lt;p&gt;Most of it isn't but a little bit is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When your body has very little glucose and a lot of fat(Which can be the case if an overweight or obese person goes on a low carb diet) the ketones and fatty acids and glucose produced by the liver are used almost exclusively to keep the body alive although a little is synthesized into glycogen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically when you don't eat anything gluconeogenesis alone supplies enough for 1 day. Then the fat metabolism accelerates because gluconeogenesis is not enough. This is when you get into a state of ketosis(this can also happen in bodybuilders since increased muscle = increased fat metabolism). This ketosis causes fast weight loss from not just water like a lot of other diets but also from fat. This fat then eventually depletes and it metabolizes protein exclusively(during all this time it does metabolise some protein). However that can't continue forever even if the amino acids get reused over and over again because some are used to produce ATP. Thus you eventually would die from starvation with obese people surviving longer than underweight people.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway as far as exercise assuming that you start off obese, getting your body into a state of ketosis makes your performance even better than on just glucose alone after a while of adjusting to fat metabolism since 1 molecule of palmatic acid(16 carbon fatty acid) produces 106 ATP compared to 32 ATP for 1 glucose molecule so your muscles can go longer without being exhausted. Theoretically someone who is 50 pounds overweight could exercise 24/7 for several days if he/she is in a state of ketosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a reference to the low glycogen and increased muscle performance:&#xA;&lt;a href=&quot;http://www.bodybuilding.com/fun/glen12.htm&quot; rel=&quot;nofollow&quot;&gt;http://www.bodybuilding.com/fun/glen12.htm&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to why it is 106 ATP it is because each NADH produces 2.5 ATP and each FADH2 produces 1.5 ATP and because of the activation step using 2 ATP just like how NADH transport from cytoplasm to mitochondria takes 2 ATP, 1 per NADH in glycolysis.&lt;/p&gt;&#xA;" OwnerUserId="5851" LastEditorUserId="5851" LastEditDate="2015-05-31T20:44:31.943" LastActivityDate="2015-05-31T20:44:31.943" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34744" PostTypeId="1" AcceptedAnswerId="34753" CreationDate="2015-05-31T03:24:44.423" Score="10" ViewCount="45118" Body="&lt;p&gt;I have read that red blood cells (RBCs) metabolize glucose. However they don't have any mitochondria because there is just so much hemoglobin that there is no room for mitochondria without expanding the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how is it possible for them to metabolize glucose if it is mainly O&lt;sub&gt;2&lt;/sub&gt;, CO&lt;sub&gt;2&lt;/sub&gt;, H&lt;sub&gt;2&lt;/sub&gt;O, fatty acids (in cell membrane), and hemoglobin? &lt;/p&gt;&#xA;" OwnerUserId="5851" LastEditorUserId="1320" LastEditDate="2017-05-21T18:55:32.690" LastActivityDate="2018-10-01T19:40:47.260" Title="If red blood cells have no mitochondria how are they able to metabolize glucose?" Tags="&lt;red-blood-cell&gt;&lt;carbohydrates&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34745" PostTypeId="2" ParentId="34744" CreationDate="2015-05-31T04:35:03.273" Score="4" Body="&lt;p&gt;While hemoglobin makes up about 90% of the protein in an RBC, there are many other proteins present as well, including enzymes in the anaerobic &lt;a href=&quot;http://en.wikipedia.org/wiki/Pentose_phosphate_pathway&quot; rel=&quot;nofollow&quot;&gt;pentose phosphate pathway&lt;/a&gt;, which is responsible for metabolizing about 90% of the glucose entering the cell (the &lt;a href=&quot;http://en.wikipedia.org/wiki/Glycolysis&quot; rel=&quot;nofollow&quot;&gt;aerobic pathway&lt;/a&gt; takes care of the other 10%). There are also proteins responsible for maintaining the oxidation state of the hemoglobin-bound iron atoms. The iron in oxidized hemoglobin, or &lt;a href=&quot;http://en.wikipedia.org/wiki/Methemoglobin&quot; rel=&quot;nofollow&quot;&gt;methemoglobin&lt;/a&gt; is in the $Fe^{3+}$ (ferric) state, which is unable to bind oxygen. The NADH-dependent enzyme methemoglobin reductase converts the iron to the $Fe^{2+}$ ferrous state, which binds $O_2$. NADH just happens to be one of the most important products of the pentose phosphate pathway, along with ATP and &lt;a href=&quot;http://en.wikipedia.org/wiki/2,3-Bisphosphoglyceric_acid&quot; rel=&quot;nofollow&quot;&gt;2,3&amp;ndash;BPG&lt;/a&gt;, which helps regulate $O_2$ release from hemoglobin. NADPH is also produced by the anaerobic pathway, and is a cofactor in the reduction of oxidized &lt;a href=&quot;http://en.wikipedia.org/wiki/Glutathione&quot; rel=&quot;nofollow&quot;&gt;glutathione&lt;/a&gt;, acting as one of the major reducing agents in the cell to protect against oxidative stress. Other enzymes such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Superoxide_dismutase&quot; rel=&quot;nofollow&quot;&gt;superoxide dismutase&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Glutathione_peroxidase&quot; rel=&quot;nofollow&quot;&gt;glutathione peroxidase&lt;/a&gt;, and &lt;a href=&quot;http://en.wikipedia.org/wiki/Catalase&quot; rel=&quot;nofollow&quot;&gt;catalase&lt;/a&gt; also help prevent or reverse oxidation. All of the oxygen moving to and fro results in the formation of &lt;a href=&quot;http://en.wikipedia.org/wiki/Reactive_oxygen_species&quot; rel=&quot;nofollow&quot;&gt;reactive oxygen species&lt;/a&gt; such as superoxide and hydroperoxyl radicals ($\cdot{O_2^-}$ and $HO_2\unicode{x22c5}$) and peroxides like hydrogen peroxide ($H_2O_2$), necessitating the presence of these defensive proteins. &lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-05-31T04:35:03.273" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34746" PostTypeId="2" ParentId="34742" CreationDate="2015-05-31T04:37:21.320" Score="1" Body="&lt;p&gt;The decline in athletic performance is a result of &lt;a href=&quot;http://en.wikipedia.org/wiki/Senescence&quot; rel=&quot;nofollow noreferrer&quot;&gt;senescence&lt;/a&gt;; the question then becomes &quot;why do we senescence?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A number of questions on this site have addressed this. These include &lt;a href=&quot;https://biology.stackexchange.com/questions/17077/why-does-evolution-not-make-our-life-longer&quot;&gt;Why does evolution not make our life longer?&lt;/a&gt;, &lt;a href=&quot;https://biology.stackexchange.com/questions/344/why-do-we-age-or-do-we-have-a-theory-of-senescence&quot;&gt;Why do we age?&lt;/a&gt;, and any number of others that one can pull up &lt;a href=&quot;https://biology.stackexchange.com/search?q=senescence&quot;&gt;with a search for senescence&lt;/a&gt;. It is key to distinguish between proximate (how, physiologically ) and ultimate (why, evolutionarily) explanations. It's not entirely clear to me from your question which of the two you are asking. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-05-31T04:37:21.320" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34747" PostTypeId="1" CreationDate="2015-05-31T05:37:05.283" Score="3" ViewCount="2307" Body="&lt;p&gt;For example, humans. It would seem like, to me, if our brains and eyes, ears, etc. were situated in our stomach area they would be more protected from harm and more central than up at the top in and on a fragile skull. The same goes for other organisms. For example, horses have eyes on the sides of their heads; why wouldn't the eyes be near their stomach area? To me, it would seem like it would make it more safe and the horse could still see alot. I looked at &lt;a href=&quot;https://biology.stackexchange.com/questions/28582/why-did-the-brain-develop-in-the-front-in-most-organisms&quot;&gt;this question&lt;/a&gt;, but it didn't fully answer my question.&lt;/p&gt;&#xA;" OwnerUserId="15704" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-06-01T05:56:27.647" Title="Why don't most animals have &quot;heads&quot; in the middle of their bodies?" Tags="&lt;evolution&gt;" AnswerCount="4" CommentCount="0" ClosedDate="2015-06-01T05:58:17.340" ContentLicense="CC BY-SA 3.0" />
  <row Id="34748" PostTypeId="2" ParentId="30858" CreationDate="2015-05-31T05:55:44.783" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Capillary_refill&quot; rel=&quot;nofollow&quot;&gt;Capillary refill time&lt;/a&gt; is defined as the time taken for the capillaries to refill after the blood in them has been squeezed out by pressure. It is widely used as a quick way to determine the effectiveness of the circulatory system in humans by doctors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a normal living organism, the capillaries will take time to refill after they have been emptied. Muscle volume consists of the cell volume (which is fixed in the absence of lysis), the blood, as well as lymph and other intracellular fluids (which will be displaced elsewhere when it is deformed by pressure). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the organism is dead, there is no more circulation in both the blood and lymphatic systems, and therefore any fluids squeezed out by pressure will remain elsewhere, and the deformation is permanent without any regulatory effect by the circulatory system. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-05-31T06:03:46.070" LastActivityDate="2015-05-31T06:03:46.070" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34749" PostTypeId="2" ParentId="34683" CreationDate="2015-05-31T07:11:10.110" Score="3" Body="&lt;p&gt;Layman's hypothesis, but... It seems an animal using intermittent movement alternates between a hard-to-see state and a hard-to-catch state, with some degree of safety in both. Operating at a slower, sustained pace offers neither of these benefits and significantly less safety.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wondering if &quot;small mammals&quot; is the right descriptor. The obvious examples seem to be rodents. Also vague: cats are small relative to horses, but they're not intermittent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe another way to look at this is &quot;When/why does an animal uses their maximum speed?&quot; Rodents seem to do it as a matter of routine locomotion, most mammals do it only when actively fleeing or pursuing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Small lizards seem more akin to rodents in this regard than not-quite-as-small mammals.&lt;/p&gt;&#xA;" OwnerUserId="16017" LastActivityDate="2015-05-31T07:11:10.110" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34751" PostTypeId="2" ParentId="31909" CreationDate="2015-05-31T08:24:18.943" Score="8" Body="&lt;p&gt;Barnard's wonderful text &lt;em&gt;&lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0130899364&quot;&gt;&quot;Animal Behavior: Mechanism, Development, Function and Evolution&quot;&lt;/a&gt;&lt;/em&gt; offers some enlightening summary to the discussion of homosexuality in a biological context!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brief Summary to ch 12, page 606:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;What we know so far:&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;homosexual behavior is recorded all throughout animal kingdom&lt;/li&gt;&#xA;  &lt;li&gt;there are evidence for genetic basis to homosexuality in various species including humans&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Three interrelated schools of thoughts:&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;ol&gt;&#xA;  &lt;li&gt;&lt;p&gt;Homosexuality is maladaptive - external stress creates homosexuality&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;&lt;p&gt;reduce resource stress on family unit, youngest child tend to be gay (E.M. Miller 2000)&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;*** mitochondrial DNA carries male killing genes, with male being a dead-end (Hurst 1991)&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ul&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Homosexuality as an adaptive early phase of development - homosexual acts are just target practice&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;homosexuality is just males practicing sex on each other, most homosexual acts are performed by bisexuals with just as high fertility&#xA;  as straight males (Baker &amp;amp; Bellis 1995)&lt;/li&gt;&#xA;  &lt;/ul&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;Homosexuality advantages in other aspects of reproduction - homosexuality may imply better parenting&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;homosexual genes induces feminine attributes in males such as sensitivity, empathy and kindness hereby increasing likelihood of long&#xA;  term pair bonding and paternal care (E.M. Miller 2000)&lt;/li&gt;&#xA;  &lt;/ul&gt;&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;*** original text: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A completely different suggestion is that homosexuality may reflect&#xA;  the interests of selfish genetic elements (see 2.4.3.2) inherited&#xA;  maternally on mitochondrial DNA for which males are effectively a dead&#xA;  end. Some insects have been shown to carry 'male-killing' genes on&#xA;  their mitochondrial DNA, so perhaps homosexuality is a similar, if&#xA;  more benign, rout to sidelining males (Hurst 1991)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9020" LastEditorUserId="9020" LastEditDate="2015-05-31T09:16:40.620" LastActivityDate="2015-05-31T09:16:40.620" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34752" PostTypeId="2" ParentId="34734" CreationDate="2015-05-31T10:34:12.273" Score="3" Body="&lt;p&gt;Yes, there is overlap and the line is rather fuzzy.  As a distinct discipline within biology, ecology is a fairly young science.  The word itself did not exist until &lt;a href=&quot;http://en.wikipedia.org/wiki/Ernst_Haeckel&quot; rel=&quot;nofollow&quot;&gt;1866&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biology is focused on living things usually at the organismal level or smaller (organs, cells, proteins, biochemistry, etc.)   Generally when biologists consider &lt;a href=&quot;http://en.wikipedia.org/wiki/Abiotic_component&quot; rel=&quot;nofollow&quot;&gt;abiotic factors&lt;/a&gt;, it is how those factors affect an organism (water, light, air needed to live).&#xA;Ecology usually looks at the organismal level and higher (species, population, community, etc.).  Ecologists also study the two-way &lt;a href=&quot;http://en.wikipedia.org/wiki/Systems_ecology&quot; rel=&quot;nofollow&quot;&gt;interaction&lt;/a&gt; between biotic and abiotic factors, how organisms change their habitat, and how the habitat changes the population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Modern biology is such a &lt;a href=&quot;http://en.wikipedia.org/wiki/Biology#Branches&quot; rel=&quot;nofollow&quot;&gt;large subject&lt;/a&gt; that most scientists will &lt;a href=&quot;http://en.wikipedia.org/wiki/Biologist#Specialists&quot; rel=&quot;nofollow&quot;&gt;specialize&lt;/a&gt; in a sub-field such as botany, zoology, genetics, etc.  One of those sub-fields is ecology, but ecology is also &lt;a href=&quot;http://en.wikipedia.org/wiki/Systems_ecology&quot; rel=&quot;nofollow&quot;&gt;interdisciplinary&lt;/a&gt; and draws from fields beyond biology  like chemistry, geology, climatology, etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;http://en.wikipedia.org/wiki/Biologist&quot; rel=&quot;nofollow&quot;&gt;biologist&lt;/a&gt; might study one or two species of fish in a lake and the plants they feed on.  An ecologist might study the lake itself, how the water got there, how an invasive species is changing the lake's &lt;a href=&quot;http://en.wikipedia.org/wiki/Biodiversity&quot; rel=&quot;nofollow&quot;&gt;biodiversity&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4228" LastActivityDate="2015-05-31T10:34:12.273" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34753" PostTypeId="2" ParentId="34744" CreationDate="2015-05-31T10:47:48.660" Score="12" Body="&lt;p&gt;In humans (and all mammals), red blood cells lack mitochondria and therefore has no functional TCA cycle. They metabolize glucose mainly via &lt;a href=&quot;http://humancyc.org/HUMAN/NEW-IMAGE?type=PATHWAY&amp;amp;object=PWY66-400&quot; rel=&quot;noreferrer&quot;&gt;glycolysis&lt;/a&gt;, forming lactate which is released from the cells; this yields 2 ATP for each glucose molecule, much less than complete oxidation (ca 30 ATP), but enough to support the red blood cells' energy needs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is &lt;em&gt;some&lt;/em&gt; oxidation of glucose to CO2 in red blood cells though. This occurs mainly in the &lt;a href=&quot;http://humancyc.org/HUMAN/NEW-IMAGE?type=PATHWAY&amp;amp;object=PENTOSE-P-PWY&quot; rel=&quot;noreferrer&quot;&gt;pentose phosphate pathway&lt;/a&gt; or &quot;shunt&quot;, where 1 carbon of glucose is released as CO2, and the energy extracted is used to reduce NADP to NADPH, which functions as an antioxidant. The resulting 5-carbon sugars (pentoses) are then rearranged to a 3-carbon sugar (glyceraldehyde phosphate) which enter glycolysis again. Hence the term &quot;shunt&quot;: 5/6 of the glucose carbon that enter actually comes back to glycolysis again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By varying flux through the PPP, cells can balance the use of glucose for ATP (energy) or NADPH (antioxidant). Studies estimate that in human red blood cells, 10--30% of hexokinase flux is diverted through the PPP, and the remainder through upper glycolysis (see &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1753-4887.1960.tb01772.x/abstract&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; and &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0165022X99000056&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; article). This corresponds to 2--5% of glucose carbon released as CO2, and the remainder metabolized to lactate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the above apply to mammalian red blood cells. Red cells of other vertebrates, including birds and fish, retain both their nucleus and mitochondria, and their metabolism is different.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-05-31T10:47:48.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34754" PostTypeId="2" ParentId="34740" CreationDate="2015-05-31T11:13:27.243" Score="3" Body="&lt;p&gt;I am not entirely sure what you are after, but I (as have others that commented on this question) interpret your question as &quot;&lt;em&gt;The linked chapter contains too much technical information&lt;/em&gt;&quot;. Quite frankly, after scanning the book chapter, I have to agree with you. Therefore I have sought for a quick overview image of all the cranial nerves including their sensory and motor targets.&#xA;&lt;br&gt;&#xA;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.britannica.com/EBchecked/topic/621522/vagus-nerve&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Encyclopedia Britannica&lt;/strong&gt;&lt;/a&gt; has published all the cranial nerves and their sensory and motor innervations in a single comprehensive figure:&#xA;&lt;br&gt;&#xA;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IS2d1.jpg&quot; alt=&quot;Cranial Nerves&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Cranial Nerves and their targets. Source: &lt;a href=&quot;http://www.britannica.com/EBchecked/topic/621522/vagus-nerve&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Encyclopedia Britannica&lt;/strong&gt;&lt;/a&gt;&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can highly recommend this online encyclopedia. Their articles are more concise and better accessible than similar topics on wikipedia. Moreover, this encyclopedia is not freely editable by everyone on the planet, and everything I have seen so far on their website is credible. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-31T12:08:50.633" LastActivityDate="2015-05-31T12:08:50.633" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34755" PostTypeId="2" ParentId="34740" CreationDate="2015-05-31T11:26:59.280" Score="0" Body="&lt;p&gt;If you're still learning the names and functions of all 12 cranial nerves, something like this page may help you get ready for more in depth material like the chapter you found.&#xA;&lt;a href=&quot;https://faculty.washington.edu/chudler/cranial.html&quot; rel=&quot;nofollow&quot;&gt;https://faculty.washington.edu/chudler/cranial.html&lt;/a&gt;&#xA;&lt;br/&gt;I like the fact that they include activities for each nerve to help give you one more way to remember their functions.&lt;/p&gt;&#xA;" OwnerUserId="4228" LastActivityDate="2015-05-31T11:26:59.280" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34756" PostTypeId="2" ParentId="29893" CreationDate="2015-05-31T13:03:08.667" Score="3" Body="&lt;p&gt;I have been contemplating about this question for months and although I cannot provide you with a concise &lt;em&gt;short answer&lt;/em&gt;, I do wish to share what I have so far. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First off, the acoustic beam that is &lt;strong&gt;&lt;em&gt;sent&lt;/em&gt;&lt;/strong&gt; is not really part of the echolocation resolution (the bat's echo-locating acuity). Consider the human field of view, which is &lt;a href=&quot;http://en.wikipedia.org/wiki/Human_eye&quot; rel=&quot;nofollow&quot;&gt;nearly 180&lt;sup&gt;o&lt;/sup&gt; wide&lt;/a&gt; in the horizontal plane. Covering your eyes and obscuring, say, half of the field will not substantially improve visual acuity, because it simply blocks half of the retinal surface from receiving light - it &lt;em&gt;does not double the retinal surface devoted to the field of view&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, I think it is not so much the bat's projected beam that matters, it is the incoming echo that matters. Note that objects such as a tree may scatter the sound that is reflected back, so the projected beam of 40&lt;sup&gt;o&lt;/sup&gt; may be a dramatic underestimation of the chaotic signals bouncing back to the bat. What can they do to improve spatial detail in the received acoustic field of view?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bats may &lt;strong&gt;increase the pulse repetition rate&lt;/strong&gt; when they are approaching a target. Hence, they basically build a map by sampling the environment multiple times. Sampling frequencies may exceed 50 Hz (&lt;a href=&quot;http://www.biolbull.org/content/114/1/10.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Grinnell and Griffin, 1985&lt;/a&gt;). For example, imagine you are blindfolded and allowed to scan an object with your fingers. Scanning it multiple times will definitely help you to mentally reconstruct the image. Indeed, bats can &lt;strong&gt;assemble information about echo delay changes over time&lt;/strong&gt;, enabling them to &lt;strong&gt;temporally integrate information of the auditory scene&lt;/strong&gt;. Moreover, they can &lt;strong&gt;change the spectral content of their calls&lt;/strong&gt; that may help in echolocation &lt;a href=&quot;http://www.batlab.dk/pubs/01Moss.pdf&quot; rel=&quot;nofollow&quot;&gt;(Moss &amp;amp; Surlykke, 2001)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, to conclude with a personal thought - &lt;em&gt;I think&lt;/em&gt; that &lt;strong&gt;bats must &lt;em&gt;learn&lt;/em&gt; to decode complex echo profiles&lt;/strong&gt;. For example, a chaotic huge blob of echo with low-echo efficiency (lots of sound is absorbed) that only changes when &lt;em&gt;the bat moves&lt;/em&gt; is probably a tree. A big blob with a large echo-efficiency (a lot of sound comes back) with well-defined edges that only changes when the bat moves is likely a human structure or a rock. A pinpoint-echo that moves &lt;em&gt;with respect to the bat&lt;/em&gt; is likely something tasty.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.biolbull.org/content/114/1/10.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Grinnell &amp;amp; Griffin, &lt;em&gt;Biol Bull&lt;/em&gt; (1958): 10-22&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.batlab.dk/pubs/01Moss.pdf&quot; rel=&quot;nofollow&quot;&gt;Moss &amp;amp; Surlykke, &lt;em&gt;JASA&lt;/em&gt;; &lt;strong&gt;110&lt;/strong&gt;(4): 2207-26&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-05-31T14:09:25.710" LastActivityDate="2015-05-31T14:09:25.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34757" PostTypeId="2" ParentId="30858" CreationDate="2015-05-31T13:10:12.693" Score="4" Body="&lt;p&gt;One difference between living and dead tissue, but specific to muscles is &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Muscle_tone&quot; rel=&quot;nofollow noreferrer&quot;&gt;tonus&lt;/a&gt;&lt;/em&gt;.  In living skeletal muscle, random nerve impulses fire to keep muscles in a partially contracted, &lt;a href=&quot;http://www.bristol.ac.uk/phys-pharm/media/plangton/ugteach/ugindex/m1_index/nm_tension/page2.htm#section4&quot; rel=&quot;nofollow noreferrer&quot;&gt;ready-to-use state&lt;/a&gt;.  Without this low-level tension sarcomeres, the basic units of skeletal muscle, would not recover from being poked and could more easily be pulled out of optimal position and &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1440-1681.2004.04029.x/abstract?deniedAccessCustomisedMessage=&amp;amp;userIsAuthenticated=false&quot; rel=&quot;nofollow noreferrer&quot;&gt;damaged&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vOOqF.png&quot; alt=&quot;sarcomere&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And yes, there are also structural changes unique to dead meat.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Rigor_mortis#Physiology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rigor mortis&lt;/a&gt; happens when the sarcomeres exhaust all ATP after death and become trapped in a bound state.  Eventually putrefaction sets in and enzymes break off the mechanism and the muscle becomes permanently flaccid.&lt;/p&gt;&#xA;" OwnerUserId="4228" LastActivityDate="2015-05-31T13:10:12.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34758" PostTypeId="2" ParentId="34747" CreationDate="2015-05-31T14:02:45.187" Score="1" Body="&lt;p&gt;Here too is a speculative answer, but evolutionary &lt;em&gt;why&lt;/em&gt; questions are many times speculation, as it cannot be directly scientifically tested (there &lt;em&gt;are no animals with a head in their tummies&lt;/em&gt;), only &lt;em&gt;inferred&lt;/em&gt; in retrospect. I will sum up a few reasons to build the eyes and ears into a solid, rotational structure and &lt;em&gt;not&lt;/em&gt; in the torso:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The eyes are hardwired to see &lt;em&gt;depth&lt;/em&gt;. The most important depth cue is &lt;a href=&quot;https://biology.stackexchange.com/questions/24589/how-does-the-eye-know-whether-to-focus-further-out-or-nearer-in-order-to-bring-a&quot;&gt;&lt;strong&gt;retinal disparity&lt;/strong&gt;&lt;/a&gt;, which is defined by a slight difference in the positioning of the field of view on both the retinas. This retinal disparity varies between people because it is dependent on the &lt;em&gt;exact distance&lt;/em&gt; between the eyes. Hence, babies must &lt;em&gt;learn&lt;/em&gt; to judge depth, as it is subjective perception deducted from a &lt;em&gt;flat retinal surface&lt;/em&gt;. Hence, you want the two eyes to be contained in a solid, unmoldable structure and not in a bodily structure that is subject to change due to adipose tissue (belly) or breathing (rib cage).&lt;/li&gt;&#xA;&lt;li&gt;The ears are hardwired to sense &lt;em&gt;direction&lt;/em&gt;. The auditory nervous system does this by &lt;strong&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/30571/are-unilaterally-deaf-people-able-to-determine-where-sound-comes-from/30587#30587&quot;&gt;measuring microsecond-delays&lt;/a&gt;&lt;/strong&gt; between the sound arriving in both ears to sense the azimuth. Again, along the same reasoning as for the eyes,  the ears must be contained in a solid structure.&lt;/li&gt;&#xA;&lt;li&gt;Directional hearing is less well-developed in the vertical plane, and when a sound comes from behind it may be hard to figure out exactly where it comes from. Also, pure-tone sounds are hard to distinguish in terms of elevation. Simply turning your head helps to re-locate the source to the side, or simply being able to &lt;em&gt;see&lt;/em&gt; it. If you have to move the whole body, you lose time and effort. In case of a &lt;em&gt;T. rex&lt;/em&gt; running in attack modus from behind, it means the difference of life and death.   &lt;/li&gt;&#xA;&lt;li&gt;Eating needs a mouth. Consider a bat using &lt;a href=&quot;https://biology.stackexchange.com/questions/29893/how-can-bats-achieve-good-resolution-with-wide-beams&quot;&gt;&lt;strong&gt;echolocation&lt;/strong&gt;&lt;/a&gt;. If the bat targets a fly using echolocation, it wants to devour it. If the ears are in the belly, it still couldn't catch its prey. The same goes for vision (birds of prey) etc.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-05-31T14:16:07.147" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="34759" PostTypeId="2" ParentId="1116" CreationDate="2015-05-31T14:10:12.977" Score="3" Body="&lt;p&gt;Both the mass of an animal and the amount of energy their muscle can release rapidly are proportional to their volume. The height to which they can jump is proportional to the ratio of the two, so most animals can jump as high as any other to within a small factor. The remaining difference between those who can who can jump about 6' such as your cat or Javier Sotomayor, and yourself, is practice.&lt;/p&gt;&#xA;" OwnerUserId="8224" LastActivityDate="2015-05-31T14:10:12.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34760" PostTypeId="2" ParentId="34747" CreationDate="2015-05-31T15:22:10.023" Score="4" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;We generally define a &quot;head&quot; as something that comes at the top/front of the body. I think that, we're likely to ignore examples of animals with nervous systems / sensory systems not at the top/front of their body as &quot;animals without heads&quot; rather than &quot;animals whose heads are not at the top/front&quot;. For example, sponges and jellyfish.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Some animals who do, arguably, have heads, have their heads in the center of their bodies:&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/3Wz8W.jpg&quot; alt=&quot;CC BY-NC-ND 2.0 james_michael_hill&quot;&gt;&#xA;&lt;a href=&quot;https://www.flickr.com/photos/james_michael_hill/12974976464/in/photolist-kLy9sL-dd9JGH-4JwBsp-4T4yoU-4Fou9i-8pCXJu-9SdMNY-8ABerJ-jKa7mc-Pp1n7-2GcZCy-ffwo9z-7qDGts-acjsie-oZ99Ne-6L1Ns3-4F85jJ-4nL5Rp-7BuZTM-7UkBad-bS4NWx-ahEa4b-23sXdm-civ4bW-31k5Ts-9q5fAU-2ETRAr-9aGVmS-nEjDby-7ByPoQ-5DVXeP-cjTjD9-8dkXs5-47FJHZ-3H9m5C-8GGCeH-dzcdX5-c5oTzL-8MPQbL-bB7iyh-344Hi7-7JdbZk-bUcjB7-9z94fQ-9rkVnN-bUci6s-5oSnwc-83XZwp-6nKkbb-qjdzax&quot; rel=&quot;nofollow noreferrer&quot;&gt;Image by james_michael_hill (CC BY-NC-ND 2.0)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;The evolutionary - developmental roots of head position (or having a &quot;head&quot; at all) &lt;a href=&quot;http://en.wikipedia.org/wiki/Bilateria&quot; rel=&quot;nofollow noreferrer&quot;&gt;go very deep&lt;/a&gt; (although despite this, some organisms, like the starfish above, shifted evolutionarily and shift developmentally from bilateral to radial symmetry).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2015-05-31T16:04:36.330" LastActivityDate="2015-05-31T16:04:36.330" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34761" PostTypeId="1" AcceptedAnswerId="34763" CreationDate="2015-05-31T15:55:13.420" Score="38" ViewCount="15979" Body="&lt;p&gt;There is place in my house where I cut my nails. Here, there is an ant hole where an ant colony is seen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whenever I cut my nails from here, they take my nails inside their hole. I was wondering what they do with them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do they protect their houses with them or feed them to their young ones?&lt;/p&gt;&#xA;" OwnerUserId="16020" LastEditorUserId="22057" LastEditDate="2017-03-07T20:14:25.493" LastActivityDate="2017-03-07T20:14:25.493" Title="What do ants do with human finger nails?" Tags="&lt;human-biology&gt;&lt;entomology&gt;&lt;food&gt;&lt;ant&gt;" AnswerCount="2" CommentCount="10" FavoriteCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="34762" PostTypeId="2" ParentId="34729" CreationDate="2015-05-31T16:02:45.023" Score="0" Body="&lt;p&gt;To summarize terdon's excellent answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;curcumin is a chemical found in the plant turmeric (&lt;em&gt;Curcuma longa&lt;/em&gt;)&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2015-05-31T16:02:45.023" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34763" PostTypeId="2" ParentId="34761" CreationDate="2015-05-31T16:14:14.937" Score="22" Body="&lt;p&gt;There are &lt;a href=&quot;https://scholar.google.com/scholar?hl=en&amp;amp;q=keratin+metabolism+fungi&quot;&gt;a number of papers&lt;/a&gt; studying the ability of fungi to metabolize &lt;a href=&quot;http://en.wikipedia.org/wiki/Keratin&quot;&gt;keratin&lt;/a&gt;, the primary structural component of nails (as well as skin and hair). Ants are also known to &lt;a href=&quot;http://en.wikipedia.org/wiki/Ant%E2%80%93fungus_mutualism&quot;&gt;cultivate fungi&lt;/a&gt; for nutrients, so this may simply be a case where the ants are bringing food for their &quot;farm animals.&quot;&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-05-31T16:14:14.937" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34764" PostTypeId="2" ParentId="34732" CreationDate="2015-05-31T16:53:08.063" Score="4" Body="&lt;p&gt;The first question: what the worms do on the ground during the flood? One of the answers to this question is -&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;It gives them an opportunity to move greater distances across the soil surface than they could do through soil,&quot; &lt;a href=&quot;http://www.accuweather.com/en/weather-news/why-do-earthworms-surface-afte/28916&quot; rel=&quot;nofollow&quot;&gt;said Dr. Lowe&lt;/a&gt;. &quot;They cannot do this when it is dry because of their moisture requirements.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second question: why they form ball after moving to the ground. There are two answers to this question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, as a part of surviving mechanism to prevent drying. As you can see, they cannot come back to the soil across the asphalt, thus they form balls and wait the weather to improve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second reason to form the balls - &lt;a href=&quot;http://news.bbc.co.uk/earth/hi/earth_news/newsid_8604000/8604584.stm&quot; rel=&quot;nofollow&quot;&gt;communication&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;The earthworms use touch to communicate and influence each other's behaviour, according to research published in the journal Ethology.&#xA;By doing so the worms collectively decide to travel in the same direction as part of a single herd.&quot;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-05-31T16:53:08.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34765" PostTypeId="1" AcceptedAnswerId="34766" CreationDate="2015-05-31T17:21:11.000" Score="2" ViewCount="199" Body="&lt;p&gt;I found him in a kitchen located in Toronto, Ontario, Canada.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0eL5Z.jpg&quot; alt=&quot;Mysterious bug on a piece of paper.&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/m4mOT.jpg&quot; alt=&quot;Mysterious bug on a piece of wood.&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/r1Ylp.jpg&quot; alt=&quot;Mysterious bug scurrying away.&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9855" LastEditorUserId="9855" LastEditDate="2015-05-31T23:06:07.880" LastActivityDate="2015-05-31T23:06:07.880" Title="What's the name of this beetle?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34766" PostTypeId="2" ParentId="34765" CreationDate="2015-05-31T17:27:35.957" Score="3" Body="&lt;p&gt;This looks very similar to a &lt;a href=&quot;https://en.wikipedia.org/wiki/Click_beetle&quot; rel=&quot;nofollow&quot;&gt;click beetle&lt;/a&gt;. Some of them are pretty popular in south Canada.&lt;/p&gt;&#xA;" OwnerDisplayName="user1629" LastActivityDate="2015-05-31T17:27:35.957" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34767" PostTypeId="1" AcceptedAnswerId="34776" CreationDate="2015-05-31T17:34:47.320" Score="3" ViewCount="371" Body="&lt;p&gt;It was found in the state of Virginia, on the east coast of the United States.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8EcDQ.jpg&quot; alt=&quot;Mystery caterpillar on a leaf.&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9855" LastActivityDate="2015-06-01T00:21:49.277" Title="What's the name of this caterpillar?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34768" PostTypeId="2" ParentId="34767" CreationDate="2015-05-31T17:52:56.040" Score="0" Body="&lt;p&gt;It's Woolly Bear Caterpillar: &lt;a href=&quot;http://en.wikipedia.org/wiki/Pyrrharctia_isabella&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Pyrrharctia_isabella&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16020" LastActivityDate="2015-05-31T17:52:56.040" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34769" PostTypeId="2" ParentId="34679" CreationDate="2015-05-31T18:37:37.040" Score="3" Body="&lt;p&gt;The hydrophilic region of phospholipids is actually interacting with water or other hydrophilic molecules. At the same time hydrophobic region of phospholipids would be repelled from water because water is forming hydrogen-bond networks, which is a more stable state. You could imagine hydrophobic molecules in water would disturb the network. As a result the hydrophobic parts of phospholipids aggregate together and phospholidis would not come out into water not to expose the hydrophobic parts.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-05-31T18:37:37.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34770" PostTypeId="1" CreationDate="2015-05-31T18:47:41.323" Score="3" ViewCount="3761" Body="&lt;p&gt;I have seen corn described as a seed, a grain and a fruit. &#xA;What are the kernels or a corncob considered to be? A grain, a seed or a fruit?&lt;/p&gt;&#xA;" OwnerUserId="16023" LastEditorUserId="10456" LastEditDate="2015-05-31T19:21:18.783" LastActivityDate="2015-05-31T19:25:21.327" Title="Are corn kernels considered a grain" Tags="&lt;botany&gt;&lt;nomenclature&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34771" PostTypeId="2" ParentId="34770" CreationDate="2015-05-31T19:25:21.327" Score="2" Body="&lt;p&gt;The grain of corn is known as a &lt;a href=&quot;http://www.merriam-webster.com/dictionary/caryopsis&quot; rel=&quot;nofollow noreferrer&quot;&gt;caryopsis&lt;/a&gt;, which Merriam-Webster defines as:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;a small one-seeded dry &lt;a href=&quot;http://en.wikipedia.org/wiki/Dehiscence_%28botany%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;indehiscent&lt;/a&gt; fruit (as of corn or wheat) in&#xA;  which the fruit and seed fuse in a single grain&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QSAyF.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This image by Encyclopedia Britannica shows that the corn seed, enclosed by the seed coat (testa) is then further surrounded by the &lt;a href=&quot;http://en.wikipedia.org/wiki/Fruit_anatomy#Pericarp_layers&quot; rel=&quot;nofollow noreferrer&quot;&gt;pericarp&lt;/a&gt;, which consists of the layers of tissue around the fruit. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, the corn kernel can be described as any of the terms that you have mentioned. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-05-31T19:25:21.327" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34772" PostTypeId="2" ParentId="31909" CreationDate="2015-05-31T22:09:23.887" Score="3" Body="&lt;p&gt;There is a study that found that female maternal relatives of homosexuals have higher fecundity than those of heterosexuals [&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15539346&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]. This suggests that an allele predisposing to homosexuality may propagate because it increases reproductive success in some situations, not necessarily in the homosexual individual.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, many factors can influence a persons sexuality, such as birth order (in males each additional older brother increases the odds of homosexuality by approximately 33%) [&lt;a href=&quot;http://link.springer.com/article/10.1023/A:1014031201935&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;], so genetics only tells part of the story, and I found no comparable explanation for female homosexuality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's an interesting article if you want further reading [&lt;a href=&quot;http://www.iflscience.com/health-and-medicine/born-way-evolutionary-view-%E2%80%98gay-genes%E2%80%99&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Camperio-Ciani &lt;em&gt;et al&lt;/em&gt;, 2004. &lt;em&gt;Proc Biol Sci.&lt;/em&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15539346&quot; rel=&quot;nofollow&quot;&gt;Evidence for maternally inherited factors favouring male homosexuality and promoting female fecundity&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;Cantor &lt;em&gt;et al&lt;/em&gt;, 2002. &lt;em&gt;Archives of Sexual Behaviour.&lt;/em&gt; &lt;a href=&quot;http://link.springer.com/article/10.1023/A:1014031201935&quot; rel=&quot;nofollow&quot;&gt;How Many Gay Men Owe Their Sexual Orientation to Fraternal Birth Order?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;IFL Science. &lt;a href=&quot;http://www.iflscience.com/health-and-medicine/born-way-evolutionary-view-%E2%80%98gay-genes%E2%80%99&quot; rel=&quot;nofollow&quot;&gt;Born this way? An evolutionary view of ‘gay genes’&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastActivityDate="2015-05-31T22:09:23.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34773" PostTypeId="1" CreationDate="2015-05-31T22:51:41.017" Score="1" ViewCount="224" Body="&lt;p&gt;I have been interested in Colloidal Coomassie Staining to detect proteins in PAGE gel.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found 2 different recipes: one of them uses aluminium sulfate, the other, (NH4)2SO4. I am wondering about sensitivities of these recipes, and other advantages/disadvantages compering these two.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149902/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149902/&lt;/a&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This article describes a recipe using aluminum sulfate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/elps.200305844/epdf&quot; rel=&quot;nofollow&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1002/elps.200305844/epdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(NH4)2SO4 is used in this article.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-05-31T22:51:41.017" Title="aluminum sulfate vs (NH4)2SO4 in Colloidal Coomassie Staining Sol" Tags="&lt;biochemistry&gt;&lt;proteins&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34774" PostTypeId="1" CreationDate="2015-05-31T22:57:34.400" Score="2" ViewCount="145" Body="&lt;p&gt;I'm a physicist by training am looking to learn more about the biophysics of plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you give me your recommendation of good resources on plant biophysics? Books are preferred.&lt;/p&gt;&#xA;" OwnerUserId="16026" LastEditorUserId="4108" LastEditDate="2015-05-31T23:13:59.650" LastActivityDate="2015-05-31T23:13:59.650" Title="Book-recommendation: plant biophysics" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;biophysics&gt;&lt;book-recommendation&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="1" ClosedDate="2015-06-02T02:26:26.483" ContentLicense="CC BY-SA 3.0" />
  <row Id="34775" PostTypeId="1" AcceptedAnswerId="34778" CreationDate="2015-05-31T23:05:42.420" Score="3" ViewCount="115" Body="&lt;p&gt;It was found a few days ago in the state of Virginia, on the east coast of the United States.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PoHBq.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9855" LastActivityDate="2015-05-31T23:41:17.327" Title="What species does this moth belong to?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34776" PostTypeId="2" ParentId="34767" CreationDate="2015-05-31T23:22:32.537" Score="3" Body="&lt;p&gt;I think it might be a species of Fritillary. Below is a picture of a Marsh Fritillary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4OdSP.jpg&quot; alt=&quot;Marsh fritillary&quot;&gt;&#xA;&lt;sup&gt;Marsh fritillary. Source: &lt;a href=&quot;http://butterfly-conservation.org/files/marsh-fritillary-larva1_peter_eeels_web.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Butterfly Conservation.org&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not think it is a woolly bear or giant leopard moth, just because the hairs seems too sparse for a woolly bear and it lacks the distinct red striping of the giant leopard moth caterpillar. It does not seem to be arctiinae to me. &lt;/p&gt;&#xA;" OwnerUserId="16028" LastEditorUserId="9943" LastEditDate="2015-06-01T00:21:49.277" LastActivityDate="2015-06-01T00:21:49.277" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34777" PostTypeId="1" AcceptedAnswerId="34800" CreationDate="2015-05-31T23:25:42.970" Score="2" ViewCount="132" Body="&lt;p&gt;I was wondering why the flu vaccination doesn't protect us from all different types of flu. I know there are 3 major groups A, B and C and they mutate really fast. For example Influenza A virus has 2 different proteins on the surface hemagglutinin (H) and the neuraminidase (N). There are 18 different hemagglutinin subtypes and 11 different neuraminidase subtypes. So if they produce a vaccination which covers 187 of the virus (from H1N1 to H18N11) wouldn't it mean that the Influenza Type A could be eradicated from the world ? And wouldn't it work the same way for Type B and C? &lt;/p&gt;&#xA;" OwnerUserId="16027" LastEditorUserId="4101" LastEditDate="2015-06-01T20:06:48.330" LastActivityDate="2015-06-01T20:06:48.330" Title="Why does flu vaccination only work against specific strains?" Tags="&lt;virus&gt;&lt;influenza&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34778" PostTypeId="2" ParentId="34775" CreationDate="2015-05-31T23:27:39.143" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Hemithea&quot; rel=&quot;nofollow&quot;&gt;Hemithea&lt;/a&gt; maybe, is as close as I can figure, although since there is so much variation between them it is very hard to tell.&lt;/p&gt;&#xA;" OwnerUserId="16028" LastEditorUserId="16028" LastEditDate="2015-05-31T23:41:17.327" LastActivityDate="2015-05-31T23:41:17.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34779" PostTypeId="1" CreationDate="2015-05-31T23:49:06.230" Score="1" ViewCount="73" Body="&lt;p&gt;1) What happens in the ovary and in the bloodstream that brings about this change in the uterus?&#xA;2) Why does the level of FSH decrease and remain at a relatively low level during the luteal phase of the cycle?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;For 1 I was thinking: So estrogen levels increase and the follicle matures which first cause menstruation and then the lining reforms?? &#xA;For 2 I was thinking: the follicle has already ruptured by the luteal phase &lt;/p&gt;&#xA;" OwnerUserId="16029" LastEditorUserId="3827" LastEditDate="2015-06-01T10:12:54.897" LastActivityDate="2015-06-01T10:12:54.897" Title="The Human Menstrual Cycle" Tags="&lt;homework&gt;&lt;reproduction&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2015-06-01T10:42:19.797" ContentLicense="CC BY-SA 3.0" />
  <row Id="34780" PostTypeId="1" AcceptedAnswerId="34781" CreationDate="2015-06-01T01:06:29.047" Score="1" ViewCount="2243" Body="&lt;p&gt;&lt;a href=&quot;http://www.science20.com/news_releases/electropositive_alloy_makes_a_great_shark_repellant_for_fishing_gear&quot; rel=&quot;nofollow&quot;&gt;Stroud&lt;/a&gt; claims that sharks are effectively repelled by the use of rare earth metals in the water. There has even been a &lt;a href=&quot;http://www.google.com/patents/US20120085018&quot; rel=&quot;nofollow&quot;&gt;patent issued by the same author&lt;/a&gt; for rare earth-wrapped fish hooks to reduce the shark by-catch. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently these metals work by generating an electric current that repels sharks via the shark's electric sensing organ. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is the repellent action of rare earth metals scientifically confirmed?&lt;/strong&gt; And if so would it be effective even on the largest and aggressive white sharks?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also if effective why haven't dive equipment manufacturers developed shark repellent devices for sport divers?&lt;/p&gt;&#xA;" OwnerUserId="9906" LastEditorUserId="9943" LastEditDate="2015-06-01T14:22:32.047" LastActivityDate="2015-06-02T01:43:57.827" Title="Do rare earth metals actually repel sharks?" Tags="&lt;neuroscience&gt;&lt;marine-biology&gt;&lt;ichthyology&gt;" AnswerCount="1" CommentCount="14" FavoriteCount="0" ClosedDate="2015-06-02T08:34:21.603" ContentLicense="CC BY-SA 3.0" />
  <row Id="34781" PostTypeId="2" ParentId="34780" CreationDate="2015-06-01T01:53:35.510" Score="2" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Electropositive metals such as the Lanthanides generate electrical currents when they come in contact with (sea) water. This electrical activity may repel sharks by over-stimulating their lateral line organ. However, the effectiveness of lanthanides as shark repellent depends on many factors. For example, hungry sharks, or sharks engaged in a feeding frenzy may simply ignore the stimulus altogether. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Rare earth metals are Lanthanides - metals with a &lt;a href=&quot;https://www.wou.edu/las/physci/ch412/activity.htm&quot; rel=&quot;nofollow&quot;&gt;low electronegativity&lt;/a&gt;. Metals with low electronegativity are called &lt;a href=&quot;http://en.wikipedia.org/wiki/Electropositive_shark_repellent&quot; rel=&quot;nofollow&quot;&gt;electropositive&lt;/a&gt;. Electropositive metals (EPMs) react vigorously with water when immersed and generate electrical potentials that are thought to overstimulate the sharks’ highly sensitive electroreceptors, the &lt;a href=&quot;https://antonyhall.wordpress.com/2007/07/23/electro-sensitivity-in-sharks/&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;ampullae of Lorenzini&lt;/em&gt;&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many electropositive metals fall in groups I and II of the &lt;a href=&quot;http://www.ptable.com/&quot; rel=&quot;nofollow&quot;&gt;periodic table&lt;/a&gt; and explosively react with water. Examples include sodium and lithium. The &lt;a href=&quot;http://chemwiki.ucdavis.edu/Inorganic_Chemistry/Descriptive_Chemistry/f-Block_Elements/The_Lanthanides&quot; rel=&quot;nofollow&quot;&gt;Lanthanides&lt;/a&gt;, on the other hand, contain some less reactive elements. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is in fact a considerable &lt;strong&gt;body of primary literature&lt;/strong&gt; on the &lt;strong&gt;use of EPMs to deter sharks&lt;/strong&gt;, because the by-catch of sharks is a recognized problem of modern fishery. However, much of this literature shows very mixed results of EPMs, and therefore I have based my (second :-) answer attempt on a recent review article by &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/1749-4877.12095/full&quot; rel=&quot;nofollow&quot;&gt;Hart and Collin (2015)&lt;/a&gt;, which is available on-line and cites some fifteen primary research articles on the topic: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EPMs are primarily intended as a mechanism to reduce shark bycatch and catch depredation in longline fisheries, without affecting the catch of non-electrosensitive target teleost fishes. As you indicate in the question, EPMs can be formed into shapes that are easily attached to a fishing line or hook. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Early tests in the laboratory with captive sharks showed that several EPMs (including magnesium and rare-earth lanthanide elements such as cerium, lanthanum, neodymium and praseodymium) were effective in repelling various shark species. However, more recently, several studies showed no such repellent effects other species of shark, and it was shown that &lt;strong&gt;aversive behavior was highly dependent on various factors&lt;/strong&gt; such as duration of &lt;strong&gt;food deprivation&lt;/strong&gt; prior to testing. Specifically, &lt;strong&gt;hungry sharks ignored the EPM&lt;/strong&gt;, especially when feeding in groups (feeding frenzies).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The results of field trials with EPMs were also mixed, with some studies showing a &lt;strong&gt;reduction in the catch rate&lt;/strong&gt; of various shark species, while other studies showed &lt;strong&gt;no such effect&lt;/strong&gt;. The authors of the review article summarize a range of factors that may influence the efficacy of EPMs in repelling sharks, including the &lt;strong&gt;type of EPM&lt;/strong&gt; used, the relative &lt;strong&gt;sensitivity of the electrosensory system&lt;/strong&gt;, &lt;strong&gt;shark density&lt;/strong&gt; and &lt;strong&gt;competition&lt;/strong&gt;, &lt;strong&gt;hunger level&lt;/strong&gt;, and differences in &lt;strong&gt;feeding ecology&lt;/strong&gt;. Other impediments to large-scale adoption of EPM technology by commercial fisheries include the relatively high cost of the rare-earth metals (although magnesium may represent a cheaper alternative), potential toxicity to other marine animals, and the fact that they dissolve rapidly in seawater and, therefore, must be replaced frequently. The use of EPMs for personal shark deterrent devices is also hampered by the limited effective range (&amp;lt;85 cm) of the electrical field they generate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead, for use in scuba dive gear a rechargeable battery-powered capacitor-discharge unit connected to two or four electrodes is sufficient as shark repellent. Also, electro-magnetic induction using permanent magnets may be a more suitable alternative &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/1749-4877.12095/full&quot; rel=&quot;nofollow&quot;&gt;(Hart and Collin, 2015)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding the great white: this shark has a lateral line featuring ampullae of Lorenzini, so EPMs may repel it, theoretically. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/1749-4877.12095/full&quot; rel=&quot;nofollow&quot;&gt;Hart &amp;amp; Collin. &lt;em&gt;Integrative Zoology&lt;/em&gt;; &lt;strong&gt;10&lt;/strong&gt;(1): 38–64&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-02T01:43:57.827" LastActivityDate="2015-06-02T01:43:57.827" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34782" PostTypeId="1" CreationDate="2015-06-01T02:58:17.533" Score="3" ViewCount="440" Body="&lt;p&gt;I am not a biologist, but recently while reading an article on Scholarpedia about &lt;a href=&quot;http://www.scholarpedia.org/article/Self-organization&quot; rel=&quot;nofollow&quot;&gt;self-organization&lt;/a&gt; I encountered a fascinating biological observation concerning immune response to infections.  To quote the article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Whether the resulting patterns are stable or oscillating depends on the relation of the time constants. If the antagonistic reaction has a longer time constant than the self-enhancing reaction, oscillations or burst-like activations will occur. An example is the time course of an infection: The infection with few viruses could be sufficient to trigger a sickness since the viruses replicate themselves (self-enhancement). The antagonistic reaction, mediated by the immune system, is much slower. It takes a day to become sick, but a week to become healthy again. (What appears on a first inspection as a disadvantage is in fact a good strategy. If the immune system would be much faster, an equilibrium between virus production and virus removal would be established. After a single infection we would fight for the rest of our life against the virus. However, due to the burst mode, we become sick for a short while but the virus is subsequently completely eliminated).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Since the quote may be hard to parse out of context, I'll recapitulate: The writer is asserting that the immune system's response to infections is slower than might be physically possible because such slowness actually makes the response more effective.  By waiting a few days, the patient is sick for longer than they might be happy about, but when the infection goes away, it's gone for good.  If the immune system responded immediately to an infection, it might result in a low-level infection that persists indefinitely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This makes me wonder: For chronic diseases, is the reason they are chronic related to the time scale of the infection vs. that of the immune system's response?  Could such diseases possibly be cured by &lt;em&gt;suppressing&lt;/em&gt; the immune system for a time so as to get the &quot;burst&quot; effect alluded to in the quote above?&lt;/p&gt;&#xA;" OwnerUserId="16030" LastActivityDate="2020-08-27T02:44:00.407" Title="Can suppression of the immune system help cure chronic diseases?" Tags="&lt;immunology&gt;&lt;infection&gt;" AnswerCount="2" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="34783" PostTypeId="1" CreationDate="2015-06-01T03:40:41.387" Score="3" ViewCount="5020" Body="&lt;p&gt;I haven't been able to find anything that tells me how much ATP is needed for DNA replication, transcription, and translation in humans, just papers that mention ATP used in those processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I need to know how much ATP is needed for these processes because once my cell from scratch is alive I feed each cell 50 nanograms of glucose which yields 5 trillion ATP. If I use these numbers plus the numbers for other metabolic processes I get roughly the amount of ATP needed per cell before mitosis. If I know this then I will know if I need to feed my cells more glucose or if 50 nanograms is enough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So how much ATP is needed for DNA replication, transcription, and translation? I want it in terms of per nucleotide and per amino acid so that I can multiply that by the amount of DNA total, amount of DNA in any given gene, and amount of amino acids in any given protein.&lt;/p&gt;&#xA;" OwnerUserId="5851" LastActivityDate="2015-11-25T05:14:04.237" Title="ATP required for cell processes" Tags="&lt;transcription&gt;&lt;translation&gt;&lt;dna-replication&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2015-06-02T06:16:46.697" ContentLicense="CC BY-SA 3.0" />
  <row Id="34784" PostTypeId="2" ParentId="34761" CreationDate="2015-06-01T04:14:14.020" Score="33" Body="&lt;p&gt;I believe that MattDMo's hypothesis is incorrect.  Only one group of ants, the Attini tribe, cultivates fungus as a food source.  This group is exclusively a New World group, thought to have originated in the Amazon rainforest and spread out from there.  I see from your profile that you are located in India, which is outside the range of the fungus-cultivating ants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So if the ants aren't using your fingernails for fungus cultivation, what are they doing with them?  Fingernails are primarily composed of keratin, a very tough protein which ants cannot digest.  However, it is likely that the clippings also contain materials like dead skin, nail fungus, or other organic substances that the ants can eat, making them worthwhile for the ants to collect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;U.G. Mueller, T.R. Schultz, C.R. Currie, R.M.M. Adams, &amp;amp; D. Malloch (2001). &quot;&lt;a href=&quot;http://www.jstor.org/stable/2664003&quot;&gt;The origin of the attine ant-fungus mutualism&lt;/a&gt;&quot;. &lt;em&gt;Quarterly Review of Biology&lt;/em&gt; &lt;strong&gt;76&lt;/strong&gt; (2): 169–197. doi:&lt;a href=&quot;http://dx.doi.org/10.1086/393867&quot;&gt;10.1086/393867&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11657" LastEditorUserId="11657" LastEditDate="2015-06-01T16:48:03.857" LastActivityDate="2015-06-01T16:48:03.857" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="34785" PostTypeId="2" ParentId="34783" CreationDate="2015-06-01T04:33:35.180" Score="4" Body="&lt;p&gt;For DNA replication and transcription you need NTPs. In a dsDNA purine content will be same as pyrimidine content. I am considering that all nucleotides are synthesized &lt;em&gt;de novo&lt;/em&gt; which would consume more ATP than getting nucleotides from the salvage pathway.&#xA;&lt;hr&gt;&#xA;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/JUC4E.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fig 1: Pyrimidine synthesis. Taken from &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleotide#Synthesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/tSIGZ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Fig 2: Purine synthesis. Taken from &lt;a href=&quot;http://en.wikipedia.org/wiki/Nucleotide#Synthesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;CTP synthesis requires one extra ATP:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;UTP + Glutamine + ATP + H&lt;sub&gt;2&lt;/sub&gt;O → CTP + ADP + P&lt;sub&gt;i&lt;/sub&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;UTP synthesis requires 2 (Step 1; Fig 1) + 1 (Step 5; Fig 1: PRPP requires 1 ATP to form) + &lt;br&gt; 2 (UMP → UTP) = 5 ATPs&lt;/p&gt;&#xA;&#xA;&lt;p&gt;CTP requires 6 ATPs&lt;/p&gt;&#xA;&#xA;&lt;p&gt;GTP requires 8 ATPs (Fig 2) (ATP synthesis would also require 8 ATPs but for simplicity let us assume that ATP is already present).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conversion of dNTP from NTP requires thioredoxin which in turn requires NADP but let us forget that.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming a 50% GC content one base pair of DNA would require in an average 10 ATPs (assume a stretch of 4nt — ACTG, this would require 1+6+5+8 ATPs; i.e. 5 ATPs per nt; 10 ATP per bp)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For RNA the ATP consumption would be 5 ATPs per nt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For protein synthesis, for every codon, the elongation factor requires &lt;a href=&quot;http://en.wikipedia.org/wiki/Translation_%28biology%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;one molecule of GTP&lt;/a&gt; and &lt;a href=&quot;http://en.wikipedia.org/wiki/Aminoacyl_tRNA_synthetase&quot; rel=&quot;nofollow noreferrer&quot;&gt;aminoacyl-tRNA synthetase&lt;/a&gt; requires 1 molecule of ATP. So the net consumption per amino acid would be 9 ATPs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am ignoring the initiation reaction that also requires ATP to phosphorylate the initiation factor. Also, I assume that amino acids are obtained from diet and are not synthesized by the organism. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-11-25T05:14:04.237" LastActivityDate="2015-11-25T05:14:04.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34786" PostTypeId="2" ParentId="34747" CreationDate="2015-06-01T05:06:22.933" Score="3" Body="&lt;p&gt;Animals with a &quot;front&quot; and a &quot;back&quot; are known as &lt;a href=&quot;https://en.wikipedia.org/wiki/Bilateria&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bilaterians&lt;/a&gt;.  There is ongoing scientific debate about what the most recent common ancestor of the bilaterians, or &quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/Urbilaterian&quot; rel=&quot;nofollow noreferrer&quot;&gt;urbilaterian&lt;/a&gt;&quot;, was like.  One proposed form is a simple wormlike animal with some form of eyelike structures, a segmented body with internal organs, and a centralized nervous system.  This is contrast to animals like jellyfish which have radial symmetry with a central mouth and a network of nervous system structures distributed throughout the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Bilateral animals often exhibit directional motion with a defined &quot;front&quot; and &quot;back&quot; end.  Eyes and other sensory structures are positioned at the front end so the animal can sense where it is going and what it encounters.  The brain is located near the eyes because these structures require fast, intensive information processing.  This process may also have been constrained by development, since evolution occurs by gradual modifications to the existing features of an organism.  The Wikipedia article on &lt;a href=&quot;https://en.wikipedia.org/wiki/Cephalization&quot; rel=&quot;nofollow noreferrer&quot;&gt;cephalization&lt;/a&gt; has some more discussion of this topic.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Here is an example of two possible urbilaterians, taken from (Hejnol &amp;amp; Martindale 2008):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/frOSd.jpg&quot; alt=&quot;urbilaterians&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image (a) shows a &quot;traditional&quot; model with segmentation, an anteriorly-located mouth (light blue), and a central nervous system (yellow).  Image (b) shows an alternate model proposed by the authors of the paper with a mouth in the middle of the body and a decentralized network of neural tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hejnol, Andreas; Martindale, Mark Q (27 April 2008). &quot;&lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/363/1496/1493&quot; rel=&quot;nofollow noreferrer&quot;&gt;Acoel development supports a simple planula-like urbilaterian&lt;/a&gt;&quot;. &lt;em&gt;Phil. Trans. R. Soc. B&lt;/em&gt; &lt;strong&gt;363&lt;/strong&gt;: 1493–1501. doi:&lt;a href=&quot;http://dx.doi.org/10.1098/rstb.2007.2239&quot; rel=&quot;nofollow noreferrer&quot;&gt;10.1098/rstb.2007.2239&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="11657" LastEditorUserId="11657" LastEditDate="2015-06-01T05:28:26.437" LastActivityDate="2015-06-01T05:28:26.437" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34787" PostTypeId="2" ParentId="34747" CreationDate="2015-06-01T05:56:27.647" Score="1" Body="&lt;p&gt;I think part of the reason is that our distant ancestors were aquatic - fish, for us vertebrates*.  Living in the water, fish need to be streamlined, so a long, narrow body plan works well.  Given this, and adding in the often limited visibility underwater, it makes sense to put the mouth towards the front, and sense organs near them, since they get to the food first.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This body plan got inherited by the descendants of that first fish to crawl out on land.  It would require a major re-organization of the genes to get a radically different plan, and there was no great evolutionary pressure towards some different one.  In many cases the mouth &amp;amp; eyes in the front works best - for predators, of course, but also think of a giraffe trying to browse on trees if its eyes were near its stomach.  For most land vertebrates, food goes directly to the mouth.  Only a few types - humans, elephants, and so on - have anything like hands to get food at a distance.  (And if you look at an elephant, they do seem partway to a mouth near the stomach plan.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you think about creatures like the starfish, that have a central mouth, &quot;brain&quot;, and sense organs, their food tends to be sessile.  The starfish commonly crawls on top of its prey, and everts its stomach to digest it, so their the radially symmetric body plan works well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*I don't know that much about arthropod evolution, but am guessing similar logic applies.&lt;/p&gt;&#xA;" OwnerUserId="11736" LastActivityDate="2015-06-01T05:56:27.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34789" PostTypeId="2" ParentId="34722" CreationDate="2015-06-01T08:09:46.027" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;In Hardy-Weinberg problems the frequency of a homozygous recessive&#xA;  genetic occurrence in a population is q2.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Sort of but not quite. If the locus has two possible alleles, $A$ and $a$, the frequency of each allele in the population is $p$ and $q$ respectively. If the population size ($N$) is 500 diploid individuals, there are 1000  loci ($2*N$, because of diploidy) which each could have either $A$ or $a$, and each of the 500 individuals could have the genotypes $AA$, $Aa$, or $aa$. If we know that the population of loci has 100 copies of $A$ then $p = 100/1000 = 0.1$, and $q$, the frequency of $a$, must then be $1-p = q = 0.9$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The value of $q^2$ tells us how many individuals in the population, under the assumptions of &lt;a href=&quot;http://www.nature.com/scitable/definition/hardy-weinberg-equation-299&quot; rel=&quot;nofollow&quot;&gt;HWE&lt;/a&gt;, will be of the genotype $aa$ - &lt;strong&gt;it says nothing about the recessivity (or dominance) of the allele, nor the phenotype.&lt;/strong&gt; In the example above, $q^2 = 0.9^2 = 0.81$ - under assumptions of HWE 81% of the population will be genotype $aa$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of math it is simple probability theory. If we have a bag of coloured marbles, 5 red and 5 blue, the frequency of red ($p$) is 0.5, and blue ($q$) is 0.5. If we draw one marble from the bag, the probability of the marble being blue, $P(blue)$, is equal to the frequency of blue, $q$, which is 0.5. If we then return the marble to the bag and make a second draw, the probability of drawing a blue marble is again $b$, 0.5. The probability of both of the drawn marbles being blue $P(blue) * P(blue) = 0.5 * 0.5$, or $q^2$. The probability of drawing one red and one blue is $2 * p * q$, and probability of two red marbles is $p^2$. &lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2015-06-03T05:23:39.813" LastActivityDate="2015-06-03T05:23:39.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34790" PostTypeId="1" AcceptedAnswerId="34796" CreationDate="2015-06-01T08:12:51.327" Score="3" ViewCount="1909" Body="&lt;p&gt;I was reading some old description of the protocols used for the transformation of bacterial cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the description I read that the transformation works best with low amount of DNA, and if we increase the amount of DNA used the amount of transformant cells does not increase proportionally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I just wonder why, since in my eyes the process of entering the cell is mainly related to the diffusion principles, and therefore concentration dependent.&lt;/p&gt;&#xA;" OwnerUserId="12942" LastActivityDate="2015-06-01T13:58:26.723" Title="Why increasing the vector concentration does not increase the effeciency of bacterial transformation?" Tags="&lt;molecular-biology&gt;&lt;microbiology&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34792" PostTypeId="1" CreationDate="2015-06-01T09:07:11.010" Score="1" ViewCount="667" Body="&lt;p&gt;That &quot;eukaryotic cells are more complex&quot; and &quot;compartmentalized&quot; are used to justify the need of more level of control of gene expression. I get the basic idea but can't convince myself why complexity or compartmentalization leads to more complex control (i.e. multiple levels) of gene regulation!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In control theory, we often use multiple level of control to minimize the variance (there are few other benefits as well from design perspective); probably that is what eukaryotic cell would also do. Moreover, simple combinatorics suggest that two level of control with $n_1$ and $n_2$ molecules involved at each level respectively would give me $n_1n_2$ possibilities of output which is higher than $n_1 + n_2$ distinct output I might get if I were to use these molecules with 1 level of control/regulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering if such simple reasoning are correct and can be used in the context of evolution? Are there other reasons as well?&lt;/p&gt;&#xA;" OwnerUserId="6228" LastEditorUserId="6228" LastEditDate="2015-06-01T09:20:18.387" LastActivityDate="2015-06-01T10:11:04.747" Title="Why is the gene regulation in eukaryotic cells needs multiple level of control than in prokaryotic cells?" Tags="&lt;evolution&gt;&lt;cell-biology&gt;&lt;gene-regulation&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34794" PostTypeId="2" ParentId="34792" CreationDate="2015-06-01T10:11:04.747" Score="1" Body="&lt;p&gt;I think you need to consider the overall amount of information that is needed to implement a proper control system in living organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In prokaryotic cells, in most of the cases, you will find that one gene code for one enzyme, so if a simple organisms need 500 enzymes to stay alive you can expect 500 genes that code for that enzymes.&#xA;A more complex organism may need 100 times more enzymes to stay alive and so theoretically 100 times more genes. Now, evolution wise, to have a linear increase of DNA vs complexity is not a good option for very complex organisms. To keep everything compartmentalised in one single membrane is also not a good idea if you need to run millions of chemical reactions using thousands of enzymes that can cross react and need different optimal conditions to work properly, so multi-compartimentalization is a must.&#xA;Linked with it arises the problem of sending the right enzyme in the right place and this has been solved by adding tags, transporter enzymes, etc... in the pot... So, lots of more information is needed to make everything run smoothly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It turned out that an efficient way to code for all that enzymes, tags, promoters and other regulators without increment the size of the DNA too much is by multi level control of the expression of a gene i.e. the same gene can be used to produce different enzymes (splicing etc...). The tradeoff to pay to have a more compact genome is to increase the complexity of its control system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, consider that differently from normal electronic controllers, the biological one do affect each other. A biological controller system may produce an output molecule that interact with the system under control but also with other reactions going on all over... that is another burden that require an increase of complexity in the control system to make it work.&lt;/p&gt;&#xA;" OwnerUserId="12923" LastActivityDate="2015-06-01T10:11:04.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34796" PostTypeId="2" ParentId="34790" CreationDate="2015-06-01T11:33:06.320" Score="3" Body="&lt;p&gt;According to the &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0022283683802848&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hanahan transformation protocol&lt;/a&gt; (one of the highest competencies published), a transformation of 200µl will contain $1×10^8 - 1.7×10^8$ cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming that the &lt;a href=&quot;http://www.genscript.com/conversion.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;pBR322 plasmid&lt;/a&gt; is used, 1ng of plasmid will convert to 0.36fmol of plasmid, or $6×10^8$ plasmid copies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As we can clearly see, even at very low quantities of DNA used, there are multiple plasmids per cell. Since transformation is thought to be mediated &lt;a href=&quot;http://en.wikipedia.org/wiki/Transformation_%28genetics%29#Artificial_competence&quot; rel=&quot;nofollow noreferrer&quot;&gt;by DNA channels&lt;/a&gt;, massively increasing the quantities of DNA would not equally increase transformation efficiency once all of these channels are saturated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The example from &lt;a href=&quot;https://www.neb.com/products/c2984-neb-turbo-competent-e-coli-high-efficiency&quot; rel=&quot;nofollow noreferrer&quot;&gt;NEB Turbo DH5α cells&lt;/a&gt; seems to show this quite well, that once DNA quantities exceed 1ng, the transformation efficiency drops precipitously. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ykSgt.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This being said, if the amount of plasmids available is very large, there is no reason to avoid adding more than 1ng of DNA, as they would not reduce the total number of transformation colonies, but only the efficiency. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-06-01T13:58:26.723" LastActivityDate="2015-06-01T13:58:26.723" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34797" PostTypeId="1" CreationDate="2015-06-01T12:42:53.307" Score="0" ViewCount="379" Body="&lt;p&gt;I am not sure if this is a duplicate of my previous question, it is somewhat related, so sorry if I misunderstood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is, can i use the above kit for samples like hair, fingernails, etc?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are the guides:&#xA;&lt;a href=&quot;https://www.promega.com/~/media/files/resources/protcards/wizard%20genomic%20dna%20purification%20kit%20quick%20protocol.pdf&quot; rel=&quot;nofollow&quot;&gt;https://www.promega.com/~/media/files/resources/protcards/wizard%20genomic%20dna%20purification%20kit%20quick%20protocol.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and the extended guide:&#xA;&lt;a href=&quot;https://www.promega.com/~/media/files/resources/protocols/technical%20manuals/0/wizard%20genomic%20dna%20purification%20kit%20protocol.pdf&quot; rel=&quot;nofollow&quot;&gt;https://www.promega.com/~/media/files/resources/protocols/technical%20manuals/0/wizard%20genomic%20dna%20purification%20kit%20protocol.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It says that for the animal tissue:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Animal Tissue (Mouse Liver and Brain), so I figure it wont apply given that these cells might have higher percentage of DNA that hair(roots/shaft) could have, or fingernails.&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="14815" LastEditDate="2015-06-01T13:50:57.353" LastActivityDate="2015-06-01T13:50:57.353" Title="Can these &quot;Promega Wizard genomic DNA Purification kit&quot; be used for samples not stated directly?" Tags="&lt;dna&gt;&lt;dna-isolation&gt;" AnswerCount="0" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="34798" PostTypeId="2" ParentId="34594" CreationDate="2015-06-01T13:11:25.147" Score="5" Body="&lt;p&gt;As you probably know, there exists many different &lt;strong&gt;species concepts&lt;/strong&gt; (or &lt;em&gt;definitions of species&lt;/em&gt;). Often, you see a separation into at least six different categories of species concepts, which are then often subcategorized futher (and they can also overlap to some extent), namely:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Biological species concept&lt;/li&gt;&#xA;&lt;li&gt;Phylogenetic/cladistic species concept&lt;/li&gt;&#xA;&lt;li&gt;Evolutionary species concept&lt;/li&gt;&#xA;&lt;li&gt;Ecological species concept&lt;/li&gt;&#xA;&lt;li&gt;Cohesion species concept&lt;/li&gt;&#xA;&lt;li&gt;Morphological/Phenetic species concept&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Broadly, these groupings show up in different forms in e.g. Futuyma (1998), DeQueiroz (2007) and Mallet (2007). The &lt;a href=&quot;http://en.wikipedia.org/wiki/Species#Definitions_of_species&quot;&gt;Wikipedia page on species concepts&lt;/a&gt; also provides a useful overview.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The biological species concept is probably the most well-known, but is very difficult to apply for many organisms, due to for example lack of knowledge (we know very little about the reproductive biology for most species of earth), their breeding system or maybe because we are dealing with extinct organisms. &lt;strong&gt;Your question&lt;/strong&gt; is most closely connected to the &lt;strong&gt;phylogenetic/cladistic group&lt;/strong&gt; of species concepts, which aims to delimit species based on lineages/clades/monophyletic groups, often using molecular phylogenetics for inferences.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know the literature of the phylogenetic/cladistic species concept well enought to answer your question fully, but I know that there exists multiple ways to delimit species within this group of species concepts. The most &quot;extreme&quot; forms/interpretations state that a species can be any monophyletic group with inhereted characteristics that you can diagnose, and this can lead to very narrow species definitions and &quot;splitting&quot; of one species into several. However, more conservative definitions look at e.g. monophyletic gene trees, where several geographic subspecies can be grouped withing the same species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All-in-all, I don't think it is possible to give a definite answer to your question &quot;&lt;em&gt;At what point does a scientist determine two lineages are different enough to be considered separate species?&lt;/em&gt;&quot;. It depends on the species concept that is used, and how this is interpreted by the taxonomists conducting a specific study. Also note that phylogenetic/cladistic species concepts are related to the idea of &lt;em&gt;Least-inclusive taxonomic units&lt;/em&gt; (LITUs, see Pleijel &amp;amp; Rouse, 2000), that aim to partially separate &quot;species&quot; from taxonomy and instead only consider taxonomic units, based on current knowledge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Futuyma. 1998. Evolutionary biology. Sinauer.  &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://sysbio.oxfordjournals.org/content/56/6/879.abstract&quot;&gt;DeQueiroz. 2007. Species Concepts and Species Delimitation. Syst.Biol. 56&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ucl.ac.uk/taxome/jim/Sp/species.pdf&quot;&gt;Mallet, J. (1998).  Species concepts.  In Calow, P. (ed.) Encyclopaedia of Ecology and Environmental Management. Blackwell Press&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1690571/&quot;&gt;Pleijel &amp;amp; Rouse. 2000. Least-inclusive taxonomic unit: a new taxonomic concept for biology. Proc Biol Sci. 267&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-06-01T13:23:44.697" LastActivityDate="2015-06-01T13:23:44.697" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34799" PostTypeId="2" ParentId="34777" CreationDate="2015-06-01T13:55:19.547" Score="0" Body="&lt;p&gt;There are 18 different hemagglutinin subtypes and 11 different neuraminidase subtypes that have been reported! The point is that many more are present in the overall viral population and some variant will escape the effect of the vaccination. In general however, to cover multiple variants with the same vaccination sounds a good idea.&lt;/p&gt;&#xA;" OwnerUserId="12923" LastActivityDate="2015-06-01T13:55:19.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34800" PostTypeId="2" ParentId="34777" CreationDate="2015-06-01T14:00:21.517" Score="5" Body="&lt;p&gt;I'm going to try and focus on the latter part of your question; if you want to know why the tri- or quadrivalent flu vaccine doesn't provide protection like many other vaccines, that's &lt;a href=&quot;https://biology.stackexchange.com/q/15637/4101&quot;&gt;already been answered&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, the main reason we can't is because there are simply too many.  You say 187 (not sure why, &lt;code&gt;18*11=198&lt;/code&gt;) but the truth is that not all H1s are the same.  The different subtypes constantly mutate, so one H1N1 may not be the same as another H1N1.  There are hundreds upon hundreds of flu types, constantly changing.  And that's not even accounting for type B viruses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you make a vaccine, you need a certain amount of protein.  The major &lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMoa1215817&quot; rel=&quot;nofollow noreferrer&quot;&gt;quadrivalent vaccine study&lt;/a&gt; used 15µg of protein of each strain.  The more protein you put in, the bigger the vaccine, the &lt;strong&gt;more it hurts&lt;/strong&gt;, and the more likely the body is to have a &lt;strong&gt;significant negative reaction&lt;/strong&gt;.  You'd have to test all of them as well - the FDA doesn't usually work on a &quot;three is safe, four is safe, so hundreds is safe&quot; principle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plus, you have to MAKE all that protein.  We're not very good at making enough for the tri- or quadrivalent vaccines now, much less hundreds or thousands of times more.  We simply don't have the capacity for that level of production.  Even if we could, it's not likely that immunity to all strains would take.  Besides, erradication is unlikely because there are large animal flu reservoirs (avian and swine, most famously) that can and will jump over to humans.  That's the piece everyone forgets about smallpox - with no animal reservoir, it was easy to eradicate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That's not to say the cause is lost.  Intense research &lt;a href=&quot;http://www.fda.gov/BiologicsBloodVaccines/ScienceResearch/ucm353397.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;has begun&lt;/a&gt; on universal flu antibodies, and it looks &lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0055435&quot; rel=&quot;nofollow noreferrer&quot;&gt;somewhat promising&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4101" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-06-01T20:03:44.367" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34801" PostTypeId="1" AcceptedAnswerId="34804" CreationDate="2015-06-01T14:01:12.853" Score="4" ViewCount="68" Body="&lt;p&gt;Since mockingbirds imitate songs of other birds, how do they find each other during mating season? How can they tell it's a mockingbird singing, instead of other birds? Is there something in their imitations that still identifies them as a Mockingbird?&lt;/p&gt;&#xA;" OwnerUserId="976" LastActivityDate="2015-06-01T15:47:22.400" Title="How do Mockingbirds find each other during mating season?" Tags="&lt;zoology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34802" PostTypeId="1" CreationDate="2015-06-01T14:37:15.090" Score="3" ViewCount="1535" Body="&lt;p&gt;I'm a pharmacy student working on my thesis. I just want to ask the probable sources of vegetable cellulose found in vegetable capsule? Note: I'm referring to the capsule itself not for its possible content. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="16038" LastActivityDate="2019-05-28T01:33:20.063" Title="Vegetable Cellulose" Tags="&lt;botany&gt;&lt;nutrition&gt;&lt;ethnobiology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34803" PostTypeId="1" AcceptedAnswerId="34806" CreationDate="2015-06-01T15:02:48.103" Score="7" ViewCount="238" Body="&lt;p&gt;From this video it is evident, that octopus can make tentacles push:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://youtu.be/zaE-LwDowcU&quot;&gt;https://youtu.be/zaE-LwDowcU&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is it possible, if it is said, that muscles can only contract?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What types of muscles can distract?&lt;/p&gt;&#xA;" OwnerUserId="5720" LastActivityDate="2015-06-02T06:58:16.497" Title="How can octopus walk if muscles can only contract?" Tags="&lt;muscles&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34804" PostTypeId="2" ParentId="34801" CreationDate="2015-06-01T15:47:22.400" Score="2" Body="&lt;p&gt;Wildlife biologist Daniel Edelstein implies as much &lt;a href=&quot;https://baynature.org/articles/do-mockingbirds-have-their-own-specific-song-or-are-they-mimicking-other-birds-songs/&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;: he says that there are in fact variations in tone and context that distinguish mockingbirds from other birds they imitate. (He was writing about the possibility of mockingbirds attracting the birds they are imitating, which doesn't happen. I can't find much about what specifically attracts female mockingbirds, except for the variety he alludes to.)&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2015-06-01T15:47:22.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34805" PostTypeId="1" AcceptedAnswerId="72830" CreationDate="2015-06-01T16:30:41.567" Score="6" ViewCount="975" Body="&lt;p&gt;Methyl-alcohol is the weakest alcohol in terms of bactericidal properties. However, I have read that it also works as sporicide. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the effectiveness of methyl-alcohol in killing the spores of fungi and bacteria compared to other substances and what is the best dilution?&lt;/p&gt;&#xA;" OwnerUserId="4826" LastEditorUserId="4826" LastEditDate="2015-06-02T07:15:56.733" LastActivityDate="2018-04-26T12:20:55.980" Title="What is effectiveness of methyl-alcohol as sporicide?" Tags="&lt;microbiology&gt;&lt;mycology&gt;&lt;medicinal-chemistry&gt;&lt;sterilisation&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34806" PostTypeId="2" ParentId="34803" CreationDate="2015-06-01T16:57:09.877" Score="9" Body="&lt;p&gt;&lt;a href=&quot;http://sites.biology.duke.edu/kksmithlab/papers/Kier_Smith_1985.pdf&quot;&gt;Kier and Smith&lt;/a&gt; wrote a paper on how tongues tentacles and trunks worked. It explains in detail exactly how their legs (and our tongues) elongate, shorten and move about without any bones for support. It's called muscular-hydrostat. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Movement of the limb actually depends on which muscle is being contracted. If it's contracting the muscles longitudinally it will make the limb short and wide, while if it contracts laterally it will cause the limb to extend and be short and thin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you watch the video carefully you can actually see the changes in thickness of the limbs as the lateral muscles release and the longitudinal muscles contract so the octopus can move its leg forward. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to see it work in person, go into the bathroom and move your tongue around and watch in the mirror. It uses the same mechanics to move your food around your mouth, lick your teeth, help you get that bit of food that is stuck up against your gum, and who can forget rolling the tongue into a cylinder or making tongue clovers. &lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="16041" LastEditDate="2015-06-02T06:58:16.497" LastActivityDate="2015-06-02T06:58:16.497" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34807" PostTypeId="2" ParentId="34298" CreationDate="2015-06-01T17:15:04.533" Score="3" Body="&lt;p&gt;If the fish eggs are unfertilised, then they are single celled (but in the haploid state - a state with half of a full set of DNA for an organism). However, if it is fertilised it will only remain in the single celled stage for approximately 45 minutes (depending on species (in this case I'm using the zebra fish). After that 45 minute period the cell begins to divide. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What actually makes caviar so expensive is that (according to most websites I've found) it actually is an unfertilised egg collected from a Sturgeon. There seem to be a few different ways that caviar is extracted. Extracting the ovaries after stunning the fish (which is explained on &lt;a href=&quot;http://science.howstuffworks.com/innovation/edible-innovations/caviar2.htm&quot; rel=&quot;nofollow&quot;&gt;Science: How Stuff Works&lt;/a&gt; - and gives more information on caviar), more or less giving the fish a Caesarian section, and the final way that I noticed was called &quot;stripping&quot; which is a non-sergical way using an ultrasound. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.latimes.com/food/dailydish/la-dd-sturgeon-massage-vivace-caviar-without-killing-fish-20140403-story.html&quot; rel=&quot;nofollow&quot;&gt;News Article&lt;/a&gt; on the ultrasound procedure of collecting the roe suggested that it wasn't yielding good results. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, caviar is actually a single haploid cell. &lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="16041" LastEditDate="2015-06-02T07:44:14.540" LastActivityDate="2015-06-02T07:44:14.540" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34808" PostTypeId="2" ParentId="31831" CreationDate="2015-06-01T18:41:01.067" Score="2" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.livescience.com/33087-how-oil-form-petroleum.html&quot; rel=&quot;nofollow&quot;&gt;Live Science&lt;/a&gt;, the temperatures are in the 120 to 300 degree-Fahrenheit range (48-148 degree-Celcius) when crude oil is forming. DNA in &quot;dry&quot; conditions completely degrades at temperatures above 190 degree-Celcius. Which means that there could be DNA in the oil itself if there are some surviving cells, however, outside the cells there are DNases which will chew up DNA. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the DNA they are talking about is like the DNA studied by &lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040842&quot; rel=&quot;nofollow&quot;&gt;Gong et. al&lt;/a&gt;, where they're looking at the live bacteria in the crude oil, which would be descendants of the bacteria that was around when the oil first began its degradation from organic material.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On both NCBI and PLOS ONE there appear to be a number of papers studying the bacterial growth in crude oil. Which would be why you may have seen articles about DNA in the oil. &lt;/p&gt;&#xA;" OwnerUserId="16041" LastActivityDate="2015-06-01T18:41:01.067" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34809" PostTypeId="1" AcceptedAnswerId="34818" CreationDate="2015-06-01T19:22:58.703" Score="4" ViewCount="138" Body="&lt;p&gt;We're an undergraduate independent research team and we are having trouble purchasing commercial proline iminopeptidase as it is unavailable on Sigma Aldrich and very expensive on other websites. We need to test that this peptidase will cut a series of tripeptides we are synthesizing in e coli.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could we purchase proline &lt;strong&gt;amino&lt;/strong&gt;peptidase instead of proline &lt;strong&gt;imino&lt;/strong&gt;peptidase; will the peptidase function the same way?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;https://books.google.com/books?id=LlW7i28psqsC&amp;amp;pg=PA700&amp;amp;lpg=PA700&amp;amp;dq=proline%20aminopeptidase%20vs%20proline%20iminopeptidase&amp;amp;source=bl&amp;amp;ots=-K1FuiIw0_&amp;amp;sig=CECDBxEfSGOgIjScqA0I8sZpKSE&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=ca1sVbnNErPIsAS52oKYAQ&amp;amp;ved=0CEMQ6AEwBQ#v=onepage&amp;amp;q=proline%20aminopeptidase%20vs%20proline%20iminopeptidase&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; says that they are the same, but this &lt;a href=&quot;http://femsre.oxfordjournals.org/content/femsre/18/4/319.full.pdf&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; says that they are different. Does anyone have any experience with this commercial peptidase?&lt;/p&gt;&#xA;" OwnerUserId="15931" LastActivityDate="2015-06-01T23:15:21.400" Title="Proline Iminopeptidase v Proline Aminopeptidase" Tags="&lt;cell-biology&gt;&lt;proteins&gt;&lt;enzymes&gt;&lt;synthetic-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34810" PostTypeId="2" ParentId="34802" CreationDate="2015-06-01T19:30:21.980" Score="5" Body="&lt;p&gt;Vegetarian capsules are made of hydroxypropylmethylcellulose (also called &lt;a href=&quot;https://en.wikipedia.org/wiki/Hypromellose&quot; rel=&quot;noreferrer&quot;&gt;hypromellose&lt;/a&gt;). The cellulose from which this material is prepared is usually from tree fiber, commonly from pine or poplar species (as noted &lt;a href=&quot;http://capsuleconnection.com/capsule-ingredients/&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;).&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2015-06-01T19:30:21.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34811" PostTypeId="1" CreationDate="2015-06-01T20:07:23.983" Score="4" ViewCount="219" Body="&lt;p&gt;In the context of the bacterial systems (not the gene editing tool), I was wondering what happens to the foreign DNA after the Cas proteins have created a new spacer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is really not clear to me, most of the documentation I have found focuses on the subsequent steps (expression and interference) and do not discuss the fate of said foreign DNA. For example, see this image from wikipedia &lt;a href=&quot;https://en.wikipedia.org/wiki/CRISPR#/media/File:Crispr.png&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/CRISPR#/media/File:Crispr.png&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16046" LastEditorUserId="20449" LastEditDate="2016-12-30T13:41:51.070" LastActivityDate="2016-12-30T13:41:51.070" Title="CRISPR-Cas Systems" Tags="&lt;dna&gt;&lt;microbiology&gt;&lt;crispr&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34812" PostTypeId="5" CreationDate="2015-06-01T20:10:16.473" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2015-06-01T20:10:16.473" LastActivityDate="2015-06-01T20:10:16.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34813" PostTypeId="4" CreationDate="2015-06-01T20:10:16.473" Score="0" Body="An infection, also known as the flu, caused by one of the many strains of influenzavirus, a segmented, single-stranded, negative-sense RNA virus in the family Orthomyxoviridae." OwnerUserId="4101" LastEditorUserId="4101" LastEditDate="2015-06-01T23:11:34.270" LastActivityDate="2015-06-01T23:11:34.270" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34814" PostTypeId="2" ParentId="31678" CreationDate="2015-06-01T20:45:36.127" Score="2" Body="&lt;p&gt;This patchy frog looks similar to one of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Gastrotheca&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gastrotheca&lt;/a&gt; species:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;for example - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Gastrotheca pseustes - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9xxTx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-06-01T20:45:36.127" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34815" PostTypeId="2" ParentId="34782" CreationDate="2015-06-01T20:55:09.923" Score="2" Body="&lt;p&gt;I think the person who wrote the quote does not really understand how an immune response is happening. There is no real &quot;waiting period&quot; until the immune system starts attacking the virus (or bacteria or whatever), this happens instantaneously when the virus is recognized.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To do so, we have two, independent systems, the &lt;a href=&quot;http://en.wikipedia.org/wiki/Innate_immune_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;innate immune system&lt;/a&gt; and the &lt;a href=&quot;http://en.wikipedia.org/wiki/Adaptive_immune_system&quot; rel=&quot;nofollow noreferrer&quot;&gt;adaptive immune system&lt;/a&gt;. The innate imune system reacts immediately and launches a unspecific, but still very effective answer to a virus. The adaptive immune system delivers a highly specific (via antibodies) immune response, which takes a while since the generation of specific antibodies takes some time (the body produces antibodies which are then matched against the virus). It works like shown in the figure (from &lt;a href=&quot;http://pulmotect.com/products/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wuD8v.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also the adaptive immune system which mediates the long-lived immunity against pathogens which have triggered a immune response. Once you get in contact with such a pathogen again, the adaptive immune system can react immediately and protect you. This is also how vaccinations work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both immune answers start immediately upon pathogen recognition, there is not benefit in delaying (or suppressing) this immune response. In contrary, this is highly dangerous for the individual, as you can see in persons, which have received a transplant. These need to suppress their immune system in order to prevent a transplant rejection, but at the price that they get sick a lot easier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are some diseases, where a partly modulation of the immune system is beneficial. These are autoimmune diseases where the immune system is directed against the own body. &lt;a href=&quot;http://en.wikipedia.org/wiki/Immunosuppression&quot; rel=&quot;nofollow noreferrer&quot;&gt;Examples&lt;/a&gt; would be rheumatoid and reactive athritis.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-06-02T05:31:40.013" LastActivityDate="2015-06-02T05:31:40.013" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34816" PostTypeId="1" CreationDate="2015-06-01T21:01:20.450" Score="5" ViewCount="1590" Body="&lt;p&gt;During Telophase, homologous chromosome pairs reach the poles of the cell with the help of microtubules. From there, nuclear membranes form around each new set of chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My confusion originates from a single question: How did these nuclear membranes form around the chromosomes?&lt;/p&gt;&#xA;" OwnerUserId="16047" LastActivityDate="2015-06-02T15:14:26.320" Title="How do nuclear membranes form during Telophase of Mitosis/Meiosis?" Tags="&lt;meiosis&gt;&lt;mitosis&gt;&lt;membrane&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34817" PostTypeId="1" CreationDate="2015-06-01T21:11:06.013" Score="4" ViewCount="39" Body="&lt;p&gt;I'm working on a project where I collect ECG signal from multiple volunteers, derive ECG derived respiration(EDR) from the timestamped ECG signal and calculate the cross correlation between EDR and Respiration signals collected from &lt;a href=&quot;https://neulog.com/respiration-monitor-belt/&quot; rel=&quot;nofollow&quot;&gt;NeuLog&lt;/a&gt; device which is treated as reference respiration signal. The problem is that the NeuLog moniter, although widely in use for monitoring respiration, is very cumbersome and uncomfortable for the volunteers to wear and restricts breathing. Is there any alternative respiration monitering devices which doesn't have to be strapped around the chest and less cumbersome to wear?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The following are the other requirements.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Respiration signal should be time stamped(to synchronize with ECG signal).&lt;/li&gt;&#xA;&lt;li&gt;Minimum Sampling rate of atleast 5sps.&lt;/li&gt;&#xA;&lt;li&gt;Should collect data offline for atleast 10 hours in single charge of the battery.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I found &lt;a href=&quot;http://www.masimo.com/rra/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; device which seems to be more comfortable than NeuLog but it is not clear whether it measures only respiration rate or can also log Respiration signals along with timestamps.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If anyone knows any alternative products meeting the above requirements, please do share the details.&lt;/p&gt;&#xA;" OwnerUserId="15376" LastActivityDate="2015-06-01T21:11:06.013" Title="Non-cumbersome respiration sensor for sleep study?" Tags="&lt;respiration&gt;&lt;electrocardiography&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34818" PostTypeId="2" ParentId="34809" CreationDate="2015-06-01T23:15:21.400" Score="2" Body="&lt;p&gt;There are two related enzymes that cleave an N-terminal residue. Enzyme &lt;a href=&quot;http://metacyc.org/META/NEW-IMAGE?type=EC-NUMBER&amp;amp;object=EC-3.4.11.9&quot; rel=&quot;nofollow&quot;&gt;3.4.11.9&lt;/a&gt; cleaves any residue from a peptide when the next residue is proline. Enzyme &lt;a href=&quot;http://metacyc.org/META/NEW-IMAGE?type=EC-NUMBER&amp;amp;object=EC-3.4.11.5&quot; rel=&quot;nofollow&quot;&gt;3.4.11.5&lt;/a&gt; cleaves an N-terminal proline from a peptide. Unfortunately, it appears that both are sometimes referred to as proline aminopeptidase. However, only 3.4.11.5 is referred to as proline iminopeptidase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The vendor should certainly specify which enzyme they are offering.&lt;/p&gt;&#xA;" OwnerUserId="10143" LastActivityDate="2015-06-01T23:15:21.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34819" PostTypeId="1" CreationDate="2015-06-02T01:32:15.840" Score="2" ViewCount="1743" Body="&lt;p&gt;I am expected to track cell growth by measuring the incubating culture's cell concentration every 30 minutes or so. So my questions are: Why do I need to do serial dilution (assuming that I do)? Why can't I just fill up a cuvette with the cuvette's volume's worth of incubating culture and measure that against the blank every 30 minutes? And if I do need to dilute, how far should I dilute (1:100, 1:1000, etc)? This is for a culture filled with E. coli.&lt;/p&gt;&#xA;" OwnerUserId="15955" LastEditorUserId="9943" LastEditDate="2015-06-02T13:29:16.270" LastActivityDate="2015-06-02T13:29:16.270" Title="Do I need to serially dilute E. coli cultures for optical density measures?" Tags="&lt;cell-biology&gt;&lt;bacteriology&gt;&lt;cell-culture&gt;&lt;ecoli&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34820" PostTypeId="1" AcceptedAnswerId="34821" CreationDate="2015-06-02T01:45:08.493" Score="9" ViewCount="1621" Body="&lt;p&gt;I suspect that the pork sold at a certain shop is infected with the parasite pork tapeworm (&lt;em&gt;Taenia solium&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a way I can prove this without special equipment? Would it work to leave the raw meat in the fridge (at 4 degrees Celcius, or higher?) for a week or so and the worms will come out of their eggs and grow big enough for the eye?&lt;/p&gt;&#xA;" OwnerUserId="16050" LastEditorUserId="9943" LastEditDate="2015-06-02T03:20:58.320" LastActivityDate="2015-06-02T23:53:49.953" Title="How to prove that pork meat has parasites" Tags="&lt;parasitology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34821" PostTypeId="2" ParentId="34820" CreationDate="2015-06-02T03:11:39.490" Score="12" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;&lt;em&gt;T. solium&lt;/em&gt; infection can be identified in pork meat by visual inspection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The stage of the life cycle of the tape worm &lt;em&gt;T. solium&lt;/em&gt; in pigs is characterized by &lt;em&gt;cysticerci&lt;/em&gt;, which is the larval stage consisting of a &lt;a href=&quot;http://ivs.ku.dk/english/research/about_parasitology_and_aquatic_diseases/parasitic_zoonoses/cwgesa/cysticercosis_in_short/&quot; rel=&quot;nofollow noreferrer&quot;&gt;protoscolex&lt;/a&gt; (head) of the tapeworm. &lt;strong&gt;Humans are the &lt;a href=&quot;http://smallfarms.oregonstate.edu/beef/meat-measles&quot; rel=&quot;nofollow noreferrer&quot;&gt;definitive host&lt;/a&gt;&lt;/strong&gt;, which means they are the species in which the parasite completes its life cycle, reaches adulthood and is able to produce eggs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The larvae are observable in pork meat, and &lt;a href=&quot;http://smallfarms.oregonstate.edu/beef/meat-measles&quot; rel=&quot;nofollow noreferrer&quot;&gt;cysticercosis is generally identified during slaughter&lt;/a&gt; when cysts can be seen in muscle or organs (Fig. 1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Qtt0d.jpg&quot; alt=&quot;cysticerci&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. &lt;em&gt;T. solium&lt;/em&gt; cysticerci. (A): as seen in infected pork. (B): excised into a Petri dish. The white dot in each cyst corresponds to the scolex. Source: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3103219/#!po=3.84615&quot; rel=&quot;nofollow noreferrer&quot;&gt;Garcia et al. (2011)&lt;/a&gt;&lt;/sup&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is not until these cysticerci are ingested by humans that the tape worm starts to develop fully into a &lt;a href=&quot;http://web.stanford.edu/group/parasites/ParaSites2001/taeniasis/solium2.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;meters-long tape worm&lt;/a&gt;, as it enters the next and final stage of its life cycle (Fig. 2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mNaoM.gif&quot; alt=&quot;Taenia life cycle&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 2. &lt;em&gt;Taenia&lt;/em&gt; life cycle. Source: &lt;a href=&quot;http://www.cdc.gov/parasites/taeniasis/biology.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;CDC&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, leaving the meat in the fridge will not induce growth, as a human is needed to induce outgrowth of the protoscolex into the mature tape worm. &#xA;&lt;br&gt;&#xA;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3103219/#!po=3.84615&quot; rel=&quot;nofollow noreferrer&quot;&gt;Garcia et al., &lt;em&gt;Lancet&lt;/em&gt; (2011): &lt;strong&gt;362&lt;/strong&gt; (9383): 547–56&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-02T23:53:49.953" LastActivityDate="2015-06-02T23:53:49.953" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34822" PostTypeId="2" ParentId="34819" CreationDate="2015-06-02T03:50:33.557" Score="1" Body="&lt;p&gt;Reading the optical density of a log phase microbial culture at a fixed wavelength approximates the Beer-Lambert law where A = ecl. This relationship is not linear as the Absorbance approaches 1.0 so at higher cell densities you will eventually underestimate the cell density of the culture. Likewise the law is not accurate below an Absorbance below ~ 0.05, so a 10-fold dilution should be fine.  Eventually the culture's growth will slow down.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-06-02T03:50:33.557" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34824" PostTypeId="1" CreationDate="2015-06-02T05:11:31.913" Score="1" ViewCount="26" Body="&lt;p&gt;In studying the correlation of folded versus unfolded proteins and their impact on neuro-degeneration, it looks like improper phosphorylation in the chaperones (at least, in part) causes the mis-folding of proteins? If so, would it be possible to regulate proper phosphorylation so the UPR wouldn't initiate a reactionary cell death in important cells?&lt;/p&gt;&#xA;" OwnerUserId="15325" LastActivityDate="2015-06-02T05:11:31.913" Title="Would it be possible to regulate proper phosphorylation so the UPR wouldn't initiate a reactionary cell death in important cells?" Tags="&lt;biochemistry&gt;&lt;phosphorylation&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34825" PostTypeId="2" ParentId="34819" CreationDate="2015-06-02T05:39:53.500" Score="5" Body="&lt;p&gt;One is not normally required to serially dilute &lt;em&gt;E. coli&lt;/em&gt; cultures for spectrophotometric measurements, at least in the experiments where the OD value is important. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For most protein expression work, the consensus is to start the induction at OD 0.6, and for most chemically competent cells, the optimal OD ranges from 0.3 to 0.8 depending on the competency protocol. At no point in time do you need to perform dilutions, as they are all within the linear range of cell count:OD ratio. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only time you need to dilute the culture is when you want to find the OD of a very concentrated culture (for example after 24 hours of vigorously shaken incubation). &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-06-02T05:39:53.500" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34826" PostTypeId="2" ParentId="34819" CreationDate="2015-06-02T05:48:47.837" Score="0" Body="&lt;p&gt;It depends on your purpose, but you could seed cells into multiwell plate and let microplate reader monitor the growth. Some microplate readers can incubate cells at a temperature you set, shake the plate, and monitor OD.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-06-02T05:48:47.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34827" PostTypeId="1" AcceptedAnswerId="34829" CreationDate="2015-06-02T05:55:20.657" Score="9" ViewCount="2486" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Triclosan&quot;&gt;Triclosan&lt;/a&gt; is a chemical often referred to as a &quot;biocide&quot; instead of an &quot;antibiotic&quot;. However, its &lt;a href=&quot;http://en.wikipedia.org/wiki/Triclosan#Mechanism_of_action&quot;&gt;mode of action&lt;/a&gt; seems to suggest that it is an antibiotic. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Triclosan binds to bacterial enoyl-acyl carrier protein reductase&#xA;  (ENR) enzyme, which is encoded by the gene FabI. This binding&#xA;  increases the enzyme's affinity for nicotinamide adenine dinucleotide&#xA;  (NAD+). This results in the formation of a stable, ternary complex of&#xA;  ENR-NAD+-triclosan, which is unable to participate in fatty acid&#xA;  synthesis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is nearly identical to the action of many other antibiotics, such as penicillins (inhibits cell wall synthesis enzymes), quinolones (inhibit DNA gyrase) or sulfonamides (inhibit folate synthesis). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11506900&quot;&gt;this paper&lt;/a&gt; describes the mechanism of resistance to triclosan and notes that it is identical to many antibiotics. Why then, is triclosan not classified as an antibiotic and is still prophylatically used in so many places (such as hospitals)?&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2016-08-29T09:03:44.743" Title="Why is triclosan not considered an antibiotic?" Tags="&lt;microbiology&gt;&lt;antibiotics&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34828" PostTypeId="2" ParentId="34827" CreationDate="2015-06-02T06:02:19.407" Score="4" Body="&lt;p&gt;I think this is mostly a semantic differentiation, when you look up definitions for antibiotics you can find very narrow which only include the classic and modern antibiotics, while others include almost everything which has an bacteriocidal (or also anti-fungal) effect, regardless of the mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Wikipedia article on &lt;a href=&quot;http://en.wikipedia.org/wiki/Antibiotics&quot; rel=&quot;nofollow&quot;&gt;antibiotics&lt;/a&gt; contains the following paragraph, which I find pretty good as a definition: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Sometimes the term antibiotic is used to refer to any substance used&#xA;  against microbes, synonymous to antimicrobial. Some sources&#xA;  distinguish between antibacterial and antibiotic; antibacterials used&#xA;  in soaps and cleaners etc., but not as medicine. This article treats&#xA;  the terms as synonymous and according to the most widespread&#xA;  definition of antibiotics being a substance used against bacteria.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-06-02T06:02:19.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34829" PostTypeId="2" ParentId="34827" CreationDate="2015-06-02T06:11:08.397" Score="6" Body="&lt;p&gt;I agree with @Chris that this is mostly a matter of definitions - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Greenfacts defines &lt;a href=&quot;http://www.greenfacts.org/glossary/abc/biocide.htm&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;biocides&lt;/strong&gt;&lt;/a&gt; as: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;According to the Biocides Directive (98/8/EC), biocidal products are those that are intended to destroy, render harmless, prevent the action of, or otherwise exert a controlling effect on any harmful organism by chemical or biological means. Examples include disinfectants, preservatives, antiseptics, pesticides, herbicides, fungicides and insecticides.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and &lt;strong&gt;&lt;a href=&quot;http://www.greenfacts.org/glossary/abc/antibiotics.htm&quot; rel=&quot;nofollow&quot;&gt;antibiotics&lt;/a&gt;&lt;/strong&gt; as: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Antibiotics are widely used as medication against disease-causing bacteria. However, bacteria can acquire resistance to particular antibiotics through mutation or gene transfer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So the key difference is that antibiotics act more specific and may induce resistance. &lt;strong&gt;Antiseptics such as alcohol&lt;/strong&gt; stay active, even after repeated use, because they &lt;strong&gt;act broadly&lt;/strong&gt;. Now that triclosan is argued to have a specific molecular target, it may have to be re-defined from a general biocide to antibiotic. This means that its widespread use may be alarming, and I quote from your linked article &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11506900&quot; rel=&quot;nofollow&quot;&gt;(Schweizer, 2001)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[Triclosan is used in a] multitude of health care and consumer products [and has] germicidal properties [and has] flooded the market in recent years in response to the public's fear of communicable bacteria. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11506900&quot; rel=&quot;nofollow&quot;&gt;Schweizer, &lt;em&gt;FEMS Microbiol Lett&lt;/em&gt; (2001); &lt;strong&gt;202&lt;/strong&gt;(1): 1-7&lt;/a&gt;&lt;/sub&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-11-09T09:14:22.573" LastActivityDate="2015-11-09T09:14:22.573" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34830" PostTypeId="1" AcceptedAnswerId="34860" CreationDate="2015-06-02T06:16:43.093" Score="6" ViewCount="195" Body="&lt;p&gt;Primary epithelial cells, for example human mammary epithelium, fail to proliferate (arrest) in serum-containing medium. Therefore, a common growth medium for epithelium contains pituitary extract instead of serum (&lt;a href=&quot;http://www.pnas.org/content/81/17/5435.short&quot;&gt;Hammond et al, 1984&lt;/a&gt;). This may be related to the fact that epithelium is normally not in contact with serum in the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, many epithelium-like cell lines grow well in serum, and most tumor-derived cell lines are cultured this way. But it can be difficult to establish such lines from epithelial cancers: often, only fibroblasts grow out of tumor explants in serum-containing medium, while the (epithelial) cancer cells do not. In contrast to epithelium, fibroblasts increase their proliferation when exposed to serum, and this process is well studied (&lt;a href=&quot;http://www.sciencemag.org/content/283/5398/83.short&quot;&gt;Iyer et al, 1999&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Why does epithelium arrest in response to serum? Are any mechanisms known? Is there any study of epithelium gene expression response to serum? Why is the behavior of epithelium so different from that of fibroblasts --- is there a physiological explanation, perhaps related to wound healing?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is this true for all types of (human) epithelium?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Should we consider epithelial-like cells growing in serum to be adapted / selected? Have such cell lines then lost some part of the epithelial phenotype? Is this a serious artefact?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Any pointers to literature would be appreciated!&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-07-13T16:22:41.003" Title="Why do epithelial cells arrest in response to serum?" Tags="&lt;cell-biology&gt;&lt;physiology&gt;&lt;cancer&gt;&lt;cell-culture&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34831" PostTypeId="2" ParentId="34827" CreationDate="2015-06-02T06:36:14.870" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Triclosan binds to bacterial enoyl-acyl carrier protein reductase&#xA;  (ENR) enzyme, which is encoded by the gene FabI. This binding&#xA;  increases the enzyme's affinity for nicotinamide adenine dinucleotide&#xA;  (NAD+). This results in the formation of a stable, ternary complex of&#xA;  ENR-NAD+-triclosan, which is unable to participate in fatty acid&#xA;  synthesis.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you notice, you would see that this mechanism is attributed to low concentrations of triclosan when it acts as a bacteriostatic. Disinfectants, IMO cause direct chemical damage to cell (denaturation of proteins/destruction of the membrane etc) unlike antibiotics which inhibit some vital metabolic processes. Triclosan is generally used in the form of a disinfectant (at high concentrations). Even though its enzyme inhibitory properties have been studied, it is not systemically administered in the form of an antibacterial drug.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The terms &lt;em&gt;antibiotics&lt;/em&gt; and &lt;em&gt;bactericidal&lt;/em&gt; were coined when mechanisms were not really known. Even then, antibiotic is traditionally known as a substance that is produced by one organism (a fungus in case of penicillin) to prevent the growth of the other. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to differ from Christiaan's opinion that antibiotics are substances against which resistance can be developed. It is possible to acquire resistance towards a conventional, broad spectrum, direct damage agent. For instance there are bacteria that can survive heat/UV/γ-rays (which are physical disinfectants). Microbes can also develop resistance to chemical agents and though I cannot cite an example at the moment, I can think about how the cell can achieve it. One way is to develop a stronger cell wall. &#xA;&lt;br&gt;Also note that alcohol is not considered a disinfectant at concentrations &amp;lt; 70%. At much lower concentrations alcohol can actually serve as an energy source. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I think this is the tacitly accepted definition:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Disinfectants are usually synthetic chemicals that inflict direct damage whereas antibiotics are primarily natural chemicals that inhibit some vital metabolic process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term bactericidal or biocidal denotes the consequence rather than the nature of the mechanism. Antibiotics can be bactericidal too. Many herbicides are inhibitors of chloroplastidial metabolism.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-08-29T09:03:44.743" LastActivityDate="2016-08-29T09:03:44.743" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34832" PostTypeId="2" ParentId="34736" CreationDate="2015-06-02T07:35:45.673" Score="6" Body="&lt;p&gt;Heavy metal toxicity is actually due to the inhibition of the body's natural enzymes as well as the denaturing of proteins that it causes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4144270/&quot; rel=&quot;nofollow&quot;&gt;Tchounwou et. al&lt;/a&gt; go into detail about the mechanics of different heavy metals and how they interact with the human body specifically. It even suggests ways that the heavy metals could be introduced. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A short summary on the damage caused by what was studied:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Arsenic&lt;/strong&gt; inhibits DNA repair. &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Cadmium&lt;/strong&gt; toxicity isn't well known, but they think it causes single&#xA;strand DNA damage.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Chromium&lt;/strong&gt; causes chromosomal abnormalities thought to be caused by&#xA;oxidative damage.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Lead&lt;/strong&gt; prevents the body from interacting with Calcium which is a key&#xA;element in many biological processes. It also competes with other&#xA;metals for the active sites in different enzymes.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Mercury&lt;/strong&gt; depletes the body's antioxidants.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;So to answer your question, no, the heavy metals are not all working on the same mechanism. It all depends on what dose, how it was introduced, and the particular metal. Also, anything can be toxic in the right amount (people have died from water toxicity in drinking contests). &lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="3340" LastEditDate="2015-06-02T09:13:22.217" LastActivityDate="2015-06-02T09:13:22.217" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34833" PostTypeId="2" ParentId="34578" CreationDate="2015-06-02T08:10:22.400" Score="2" Body="&lt;p&gt;In the paper by &lt;a href=&quot;http://www.icmr.nic.in/ijmr/2005/august/0910.pdf&quot; rel=&quot;nofollow&quot;&gt;K. Lily Therese, U. Jayanthi &amp;amp; H.N. Madhavan&lt;/a&gt; traditional PCR wasn't sensitive enough to allow for an accurate reading on what they were trying to study. By using nPCR they were able to amplify around the gene they were interested in and then amplify &lt;strong&gt;just&lt;/strong&gt; the gene they were interested in for a more accurate and sensitive study. The successive PCR allowed them to amplify their specific gene even if there was only one copy in the sample. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I recall using this procedure in Molecular Genetics Lab, it was used to make sure that our sample was purer. &lt;/p&gt;&#xA;" OwnerUserId="16041" LastActivityDate="2015-06-02T08:10:22.400" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34834" PostTypeId="2" ParentId="34298" CreationDate="2015-06-02T08:36:23.227" Score="4" Body="&lt;p&gt;Yes; the first division starts at around &lt;strong&gt;45min&lt;/strong&gt; post fertilization in zebrafish. This picture is stuck in every zebrafish lab.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/3v1qe.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-06-02T08:36:23.227" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34835" PostTypeId="2" ParentId="34819" CreationDate="2015-06-02T08:50:45.557" Score="1" Body="&lt;p&gt;You should dilute (not necessarily serially dilute) if:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;You are exceeding the concentration range detectable by the machine&lt;/li&gt;&#xA;&lt;li&gt;Scattering starts overwhelming absorption (at high cell densities scattering will overwhelm absorbance). In such cases you can use a turbidimeter. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;As such there is no issue of the law not holding true at certain limits of absorbance. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So a general thumb rule for dilution of cells is that the suspension should not look very turbid (You should be able to see your thumb from the other side of the test tube ;-) ).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-02T10:52:33.210" LastActivityDate="2015-06-02T10:52:33.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34837" PostTypeId="2" ParentId="34691" CreationDate="2015-06-02T10:35:02.897" Score="10" Body="&lt;p&gt;&lt;strong&gt;Resemblance between parent and offspring is certainly true&lt;/strong&gt;. Some traits are more obvious than others, for example skin colour would be very obvious. As babies mature they will gradually begin to look more and more like their parents, the features of babies often change rapidly, for example pretty much every baby has a little nose, but by the time they are a fully grown adult it probably resembles that of one the parents fairly well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More obvious example would be height - imagine being presented with a baby and two males who are identical in every way, except one is two metres tall, and the other is 1.5 metres tall. As a baby it would be very difficult to assign paternity on the criteria of height/size, &lt;strong&gt;but as the child develops it would likely become easier and easier&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The resemblance between parent and offspring relates to the &lt;a href=&quot;http://en.wikipedia.org/wiki/Heritability&quot; rel=&quot;nofollow noreferrer&quot;&gt;heritability&lt;/a&gt; of a trait but, because there can be &lt;a href=&quot;https://www.youtube.com/watch?v=UH1x5aRtjSQ&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;temporal variation within an individual&lt;/strong&gt;&lt;/a&gt;, heritability can only be properly determined by measuring the traits in parent and offspring at the same time point (e.g. father's height at 18 years old and son's height at 18 years old), otherwise it will introduce noise in to the estimation, likely reducing the estimate of heritability (and specific to your question, making it harder to assign paternity based on phenotypic characters).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In the context of your question:&lt;/strong&gt; Ability to assign paternity would depend on a) the resolution with which the traits available can be distinguished among all individuals in the test and b) the variance among all individuals in the test. E.g. If the only trait available was number of fingers per hand, and all potential fathers and the child had five then the lack of variance would make it impossible to use this as a criterion, while if both one of the potential fathers, and the focal baby, had six fingers on one hand then there would be pretty good clue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whether babies more resemble their fathers more than mothers (which I think is the true question you are asking here) there is &lt;a href=&quot;http://www.jstor.org/stable/info/10.1086/673296&quot; rel=&quot;nofollow noreferrer&quot;&gt;evidence from &lt;em&gt;Drosophila&lt;/em&gt; that within-sex heritability is much higher than cross-sex for lifespan and aging,&lt;/a&gt; i.e. the lifespan of males (females) far more resembles the lifespan of the father (mother) than the mother (father). This would suggest that there is a sex specific element. Meanwhile there is &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/279/1748/4836&quot; rel=&quot;nofollow noreferrer&quot;&gt;evidence of high cross-sex genetic correlations in humans preventing&lt;/a&gt; males and females from becoming more different (thus maintaining resemblance to opposite sex parents). I would think that resemblance to the father could offer some benefit in assigning paternity by care giving males (stopping males devoting resources to other males offspring) but some of the resemblance could be generated by genetic correlations to sex-specific genetic variance, for example, males (females) will look more like their father (mother) in many ways purely because they are of the same sex, so it will heavily depend on the traits you look at to judge resemblance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a related answer about heritability on biology SE see:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/23110/is-it-possible-for-a-child-to-grow-taller-than-their-tallest-parent/23142#23142&quot;&gt;Is it possible for a child to grow taller than their tallest parent?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-06-02T10:35:02.897" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34838" PostTypeId="2" ParentId="34150" CreationDate="2015-06-02T12:51:56.670" Score="16" Body="&lt;p&gt;Male mice lack nipples too. Mice are frequently used for embryonic research as they are small and reproduce quickly. It is thought that male mice do develop nipples, but that they regress during development &lt;a href=&quot;http://dev.biologists.org/content/125/7/1285.long&quot; rel=&quot;noreferrer&quot;&gt;(Wysolmerski, 1998)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, it is thought that &lt;strong&gt;mammalian organisms develop as females by default&lt;/strong&gt; when there is no male (Y) chromosome present &lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMp048185&quot; rel=&quot;noreferrer&quot;&gt;(Hughes, 2004)&lt;/a&gt;. Notably, X_ individuals and XY individuals with certain Y-chromosome deletions also develop as females. Basically, it is testosterone that &lt;em&gt;suppresses&lt;/em&gt; female features. Hence, also boys with testosterone production, but without the appropriate receptors also develop as females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, &lt;strong&gt;&lt;em&gt;men have nipples because females do&lt;/em&gt;&lt;/strong&gt; &lt;a href=&quot;http://www.nature.com/news/1999/990805/full/news990805-1.html&quot; rel=&quot;noreferrer&quot;&gt;(Simons, 2003)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The development of nipples is a pretty complex process &lt;a href=&quot;http://dev.biologists.org/content/125/7/1285.long&quot; rel=&quot;noreferrer&quot;&gt;(Wysolmerski, 1998)&lt;/a&gt;. Disruptions in the process cause regression. Indeed, in mice, the tissues typical for nipples &lt;strong&gt;&lt;em&gt;do develop in males&lt;/em&gt;&lt;/strong&gt; during embryogenesis, but degenerate within a few days, leaving no trace of nipples at birth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, given the mouse example, I &lt;em&gt;think&lt;/em&gt; that &lt;em&gt;every mammalian male species develops by default nipples&lt;/em&gt; somewhere in development like mice, but that development is halted at various stages across species. The later in development it halts, the more it resembles female nipples. When it is stopped very early after gestation, they regress completely, like in mice.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is there a difference between species as to &lt;em&gt;when the nipple development halts&lt;/em&gt;? Because the nipple developmental sequence is complex &lt;a href=&quot;http://dev.biologists.org/content/125/7/1285.long&quot; rel=&quot;noreferrer&quot;&gt;(Wysolmerski, 1998)&lt;/a&gt;, and because evolution typically prefers &lt;em&gt;losing things&lt;/em&gt; over gaining them, it is likely that by happenstance one of many crucial genes was lost in males, but selective pressure was simply too small to be of any significant advantage over males with slightly better-developed nipples. But from here on, it is guessing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.nejm.org/doi/full/10.1056/NEJMp048185&quot; rel=&quot;noreferrer&quot;&gt;Hughes, &lt;em&gt;N Engl J Med&lt;/em&gt; (2004); &lt;strong&gt;351&lt;/strong&gt;(8): 248-50&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.nature.com/news/1999/990805/full/news990805-1.html&quot; rel=&quot;noreferrer&quot;&gt;Lawrence, &lt;em&gt;Nature News&lt;/em&gt;, &lt;em&gt;August&lt;/em&gt; 1999&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.nature.com/news/1999/990805/full/news990805-1.html&quot; rel=&quot;noreferrer&quot;&gt;Simons, &lt;em&gt;Sci Am&lt;/em&gt;, &lt;em&gt;September&lt;/em&gt; 2003&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://dev.biologists.org/content/125/7/1285.long&quot; rel=&quot;noreferrer&quot;&gt;Wysolmerski et al., &lt;em&gt;Development&lt;/em&gt; (1998); &lt;strong&gt;125&lt;/strong&gt;: 1285-94&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-02-21T22:42:30.243" LastActivityDate="2016-02-21T22:42:30.243" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34839" PostTypeId="1" AcceptedAnswerId="34851" CreationDate="2015-06-02T13:30:22.053" Score="1" ViewCount="5178" Body="&lt;p&gt;I am thinking why electrical cardioversion is contraindicated in atrial fibrillation with digitalis toxicity/poisoning. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cardiac digitalis is also called digoxin and cardiac glycoside. &#xA;It is antiarrhythmic agent against supraventricular arrhythmias. &#xA;It is contraindicated in Atrial Fibrillation with digitalis toxicity. &#xA;The Pubmed's article about the topic is a &lt;a href=&quot;https://pubchem.ncbi.nlm.nih.gov/compound/56840973&quot; rel=&quot;nofollow&quot;&gt;stub&lt;/a&gt; without describing its Pharmacology. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Digitalis toxicity is a complication of digitalis therapy, here used for atrial fibrillation. &#xA;This may be due to kidney failure when the medication accumulates in the body. &#xA;Its treatment is activated charcoal and gastric lavage. &#xA;However, assume that these methods do not help in treatment or that we in acute digitalis toxicity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think the reason why we cannot recently do electrical cardioversion in digitalis poisoning is the high probability of repolarizing incidences so the likelihood to stimulate heart at the right moment is very small. &#xA;This is because digitalis poisoning is associated with cardiac disturbances: ventricular tachycardia, ventricular fibrillation, SA block and AV block. &#xA;Without knowing more precisely about the complication, I think the electrical cardioversion has high risk of failure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is electrical cardioversion contraindicated in Digitalis Poisoning of AF treatment?&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2015-06-02T20:15:44.667" Title="Why is Electrical Cardioversion contraindicated in AF and Digitalis Poisoning?" Tags="&lt;pharmacology&gt;&lt;cardiology&gt;&lt;toxicology&gt;&lt;electrophysiology&gt;&lt;electrocardiography&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34840" PostTypeId="1" CreationDate="2015-06-02T13:45:31.373" Score="8" ViewCount="12006" Body="&lt;p&gt;All of them feed on dead and decaying matter (detritus). Detrivores and decomposers are distinct, as it says on Wikipedia, in the fact detrivores consume macroscopic clumps of detritus while decomposers metabolise detritus on a microscopic scale. Are detrivores and decomposers both types of saprotrophs? Also, what exactly does the term &quot;saprozoic&quot; mean, and how is it distinct from &lt;em&gt;saprotroph&lt;/em&gt; and &lt;em&gt;decomposer&lt;/em&gt;?&lt;/p&gt;&#xA;" OwnerUserId="15109" LastEditorUserId="16460" LastEditDate="2017-03-20T09:53:47.560" LastActivityDate="2018-10-12T01:58:08.940" Title="What is the distinction between the terms detrivores, decomposers, saprotrophs and saprozoic organisms?" Tags="&lt;ecology&gt;&lt;terminology&gt;&lt;nutrition&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34841" PostTypeId="2" ParentId="34840" CreationDate="2015-06-02T14:10:13.257" Score="10" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Detritivore&quot; rel=&quot;nofollow noreferrer&quot;&gt;Detritivores&lt;/a&gt; consume (eat) &lt;a href=&quot;https://en.wikipedia.org/wiki/Detritus&quot; rel=&quot;nofollow noreferrer&quot;&gt;detritus&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Saprotrophic_nutrition&quot; rel=&quot;nofollow noreferrer&quot;&gt;Saprotrophs&lt;/a&gt; feed on dead organic matter by the means of extracellular digestion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Saprozoic organisms are protozoans that are saprotrophs. This actually comes from an obsolete classification of plants and animals where bacteria and fungi were grouped with plants and were therefore called sapro&lt;strong&gt;phytes&lt;/strong&gt; if they are saprotrophic. Protozoans were considered animals; so sapro&lt;strong&gt;zoic&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Decomposer is a broad class including both detritivores and saprotrophs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Scavenger&quot; rel=&quot;nofollow noreferrer&quot;&gt;Scavengers&lt;/a&gt; also consume dead organisms. They are distinct from detritivores because the former consumes a relatively larger amount of dead matter. Often, scavengers are the first to consume dead organisms; the leftovers are processed by decomposers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;I could not find any authoritative source for these definitions. A peer-reviewed article by &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032891/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Getz (2010)&lt;/a&gt; attempts to classify organisms based on their eating habits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/9qeyS.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/9qeyS.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2017-03-20T15:36:04.340" LastActivityDate="2017-03-20T15:36:04.340" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34842" PostTypeId="2" ParentId="24766" CreationDate="2015-06-02T14:56:50.997" Score="1" Body="&lt;p&gt;Contrarily to the main opinion expressed so far, I would say that, in theory, it is possible that an Influenza virus can be a vector for another virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22922205&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; is a paper about using influenza virus as vector for a variety of genes.&#xA;The same method can be leveraged to engineer an Influenza virus particle that contains, for example, genes coming from another virus. Upon infection, the Influenza virus will infect the host cells with both genomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this way you will end up with an Influenza virus that act as vector for another virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, such a hybrid looks very unlikely to occur in nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But it can be certainly made in lab.&lt;/p&gt;&#xA;" OwnerUserId="12923" LastEditorUserId="12923" LastEditDate="2015-06-14T18:52:43.000" LastActivityDate="2015-06-14T18:52:43.000" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34843" PostTypeId="2" ParentId="34816" CreationDate="2015-06-02T15:14:26.320" Score="2" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK9890/&quot; rel=&quot;nofollow&quot;&gt;this book&lt;/a&gt;, during disassembly of the nuclear envelope, the nuclear membranes are broken down into vesicles. The nuclear membranes reform at the end of mitosis as the vesicles bind to the surface of chromosomes and fuse with each other to form a double membrane around the chromosomes (how this happens is not clear, except that integral membrane proteins and lamins may be involved, but physical contact is supposedly the first step). &lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2015-06-02T15:14:26.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34844" PostTypeId="1" AcceptedAnswerId="34865" CreationDate="2015-06-02T16:10:07.390" Score="7" ViewCount="113" Body="&lt;p&gt;Are there eukaryotic organisms with fully working mitochondria that do not have genes in the mitochondria?  By fully working, I mean ones which can carry out oxidative phosphorylation, unlike reduced mitochondria like organelles such as mitosomes in &lt;em&gt;Giardia lamblia&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to transfer all mitochondrial genes to the nuclear DNA and still have fully-functioning mitochondria?&lt;/p&gt;&#xA;" OwnerUserId="16060" LastEditorUserId="3340" LastEditDate="2015-06-03T05:56:48.967" LastActivityDate="2015-06-03T12:43:04.913" Title="Are there eukaryotes with fully working mitochondria but without mitochondrial genes?" Tags="&lt;mitochondria&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34845" PostTypeId="2" ParentId="34782" CreationDate="2015-06-02T16:12:51.413" Score="3" Body="&lt;p&gt;No, this wouldn't happen. The logic of your proposition assumes that chronic diseases are caused by the strength of the immune response being insufficient to kill off the virus, resulting in a long-term equilibrium between the amount of virus particles produced and the amount of virus particles killed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In reality, this is not how chronic diseases work. Only a small amount of chronic diseases are caused by viruses. There are many which have other causes, not all of which can be defended against by the immune system - e.g. chronic depression is not curable by immune response. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But even if we focus on chronic virus infections such as herpes simplex, they are not sustained by the mechanism you describe. They happen due to the fact that our immune system simply does not know how to get them out of their new home within our body, they are just that good at hiding during latency. So even if you could cause a strong immune response all at once, it wouldn't kill all viruses at once. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if we have viruses whose serum presence depends on a constant growth vs. destruction dynamic (I don't know if these exist at all), an overly strong immune response won't be that good for the human host. Inflammation is a dangerous state, most of the unpleasant feeling you get when you are sick is not due to the virus itself but due to your own immune response, which causes the fever, muscle pains etc. associated with many acute infectious diseases. If we were to ramp this up, you'd probably get a fever high enough to cook you alive, or some other undesirable effects. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;On a side note, I also doubt the author's argument which suggests that long-ish convalescence times evolved because shorter ones would leave the system in an undesirable equilibrium. Sure, an alternative reality is thinkable where the innate and adaptive responses described by Chris occur much stronger at the beginning, leading to steeper curves and shorter healing times. But the simpler explanation for that is that 1) our immune system is not perfect, and it evolved to the highest healing speed it could achieve, and 2) an immune system with higher acceleration would have been way too costly in terms of resources available to the body. An evolutionary advantage in having a low-acceleration immune system is a strong assumption for which I see no support, especially considering that the residual immunity provided by the adaptive immune system would prevent the dynamic equilibrium suggested in your quote. &lt;/p&gt;&#xA;" OwnerUserId="1578" LastActivityDate="2015-06-02T16:12:51.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34846" PostTypeId="1" AcceptedAnswerId="34856" CreationDate="2015-06-02T19:19:49.543" Score="3" ViewCount="622" Body="&lt;p&gt;Sorry if this is too much of a soft question or if it is too broad for this site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a person who has much more experience with math than biology, I've always been really interested in the mathematical side of biology. As I study math in biology, however, I am left with the question of &quot;how is this actually useful?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What kind of unique insight can mathematical models give us about biological systems that we couldn't just find experimentally?&lt;/p&gt;&#xA;" OwnerUserId="15536" LastActivityDate="2015-06-12T15:48:46.580" Title="Value of mathematical models in biology" Tags="&lt;mathematical-models&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ClosedDate="2015-06-03T04:15:46.560" ContentLicense="CC BY-SA 3.0" />
  <row Id="34847" PostTypeId="2" ParentId="450" CreationDate="2015-06-02T19:40:40.390" Score="5" Body="&lt;p&gt;There are several parts to my answer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, evolution has selected the current system(s) over countless generations through natural selection.  Natural selection depends on differences (major or minor) in the efficiency of various solutions (fitness) in the light (ho ho!) of the current environment.  Here's where the solar energy spectrum is important as well as local environmental variables such as light absorption by water etc. as pointed out by another responder. After all that, what you have is what you have and that turns out to be (in the case of typical green plants), chlorophylls A and B and the &quot;light&quot; and &quot;dark&quot; reactions.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, how does this lead to green plants that appear green?  Absorption of light is something that occurs at the atomic and molecular level and usually involves the energy state of particular electrons.  The electrons in certain molecules are capable of moving from one energy level to another without leaving the atom or molecule.  When energy of a certain level strikes the molecule, that energy is absorbed and one or more electrons move to a higher energy level in the molecule (conservation of energy).  Those electrons with higher energy usually return to the &quot;ground state&quot; by emitting or transferring that energy.  One way the energy can be emitted is as light in a process called fluorescence.  The second law of thermodynamics (which makes it impossible to have perpetual motion machines) leads to the emission of light of lower energy and longer wavelength.  (n.b. wavelength (lambda) is inversely proportional to energy; long wavelength red light has less energy per photon than does short wavelength violet (ROYGBIV as seen in your ordinary rainbow)).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyway, chlorophylls A and B are complex organic molecules (C, H, O, N with a splash of Mg++) with a ring structure.  You will find that a lot of organic molecules that absorb light (and fluoresce as well) have a ring structure in which electrons &quot;resonate&quot; by moving around the ring with ease.  It is the resonance of the electrons that determine the absorption spectrum of a given molecule (among other things).  Consult Wikipedia article on chlorophyll for the absorption spectrum of the two chlorophylls.  You will note that they absorb best at short wavelengths (blue, indigo, violet) as well as at the long wavelengths (red, orange, yellow) but not in the green.  Since they don't absorb the green wavelengths, this is what is left over and this is what your eye perceives as the color of the leaf.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, what happens to the energy from the solar spectrum that has been temporarily absorbed by the electrons of chlorophyll?  Since its not part of the original question, I'll keep this short (apologies to plant physiologists out there).  In the &quot;light dependent reaction&quot;, the energetic electrons get transferred through a number of intermediate molecules to eventually &quot;split&quot; water into Oxygen and Hydrogen and generate energy-rich molecules of ATP and NADPH. The ATP and NADPH then are used to power the &quot;light independent reaction&quot; which takes CO2 and combines it with other molecules to create glucose.  Note that this is how you get glucose (at least eventually in some form, vegan or not) to eat and oxygen to breath.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take a look at what happens when you artificially uncouple the chlorophylls from the transfer system that leads to glucose synthesis.  &lt;a href=&quot;http://en.wikipedia.org/wiki/Chlorophyll_fluorescence&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://en.wikipedia.org/wiki/Chlorophyll_fluorescence&lt;/a&gt;  Notice the color of the fluorescence under UV light!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alternatives?  Look at photosynthetic bacteria.&lt;/p&gt;&#xA;" OwnerUserId="16064" LastEditorUserId="16866" LastEditDate="2019-03-15T01:41:23.943" LastActivityDate="2019-03-15T01:41:23.943" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="34848" PostTypeId="1" AcceptedAnswerId="34853" CreationDate="2015-06-02T19:43:57.223" Score="0" ViewCount="64" Body="&lt;p&gt;We are looking to secrete the protease proline iminopeptidase by attaching the secretion signal HlyA to the protease in a gene circuit. Since the natural HlyA secretion sequence in &lt;em&gt;Escherichia coli&lt;/em&gt; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0167488904001168#&quot; rel=&quot;nofollow&quot;&gt;isn't cleaved&lt;/a&gt; from the protein, it will remain attached to the protease in the extracellular matrix. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Will the &lt;a href=&quot;http://femsre.oxfordjournals.org/content/femsre/18/4/319.full.pdf&quot; rel=&quot;nofollow&quot;&gt;protease&lt;/a&gt; still function and cleave the peptide chain at the n-terminal proline residue with the HlyA signal still attached?&lt;/p&gt;&#xA;" OwnerUserId="15931" LastEditorUserId="6307" LastEditDate="2015-06-02T21:55:42.760" LastActivityDate="2015-06-02T22:11:52.063" Title="Will tagging a protease with HlyA for secretion inactivate the protease?" Tags="&lt;genetics&gt;&lt;proteins&gt;&lt;synthetic-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34851" PostTypeId="2" ParentId="34839" CreationDate="2015-06-02T20:02:42.230" Score="1" Body="&lt;p&gt;The mechanism of action of digitalis-like preparations based on inhibition of myocardial NA+/K+-ATPase as well as of cardiac conducting tissue. The inhibition of latter (conducting) is 2.5 greater than those of former (myocardial). This is why the main feature of digitalis intoxication are arrhythmias due to ectopic electric impulses and spontaneous depolarization (there is overloading of conducting system by Calcium as well as excess amounts of Noradrenaline released from sympathetic endings).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These metabolic changes in a case of digitalis intoxication could lead to irreversible ventricular arrhythmias after cardioversion - there are sporadic reports about this phenomenon. Based on these reports, it was thought that the use of digitalis during electrical cardioversion would provoke ventricular arrhythmias in patient even with clinically desirable concentration of digitalis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jccjournal.org/article/0883-9441(87)90160-2/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;In a study&lt;/a&gt; in patients with therapeutic nontoxic digitalis levels determined that these patients may safely undergo electrical cardioversion without reducing or withholding the dose of digitalis. Thus, the cardioversion is not contraindicated in a patient without signs of digitalis toxicity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although, the exact mechanism of the ventricular arrhythmias after cardioversion is not well understood, it is clear that mentioned above changes in electrolytes concentrations with electrical stimulation lead to premature beats overtaking restored sinoatrial pace. The rate of ventricular arrhythmias is in direct correlation with the level of the energy used for the cardioversion (this is why there is &quot;pre-cardioversion&quot; with low-energy pulses). Until these metabolic changes are not corrected, the resulting ventricular arrhythmias can be irreversible. This is why, digitalis intoxication is relative contraindication to electric cardioversion of atrial fibrillation/flatter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Excerpt from the article mentioned:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ZZbZP.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-06-02T20:15:44.667" LastActivityDate="2015-06-02T20:15:44.667" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34852" PostTypeId="1" CreationDate="2015-06-02T20:06:25.610" Score="9" ViewCount="257" Body="&lt;p&gt;I did a quick search (here and elsewhere) and couldn't find anything on this subject.&#xA;If all introns in a given primary transcript were spliced out in the same way, then this wouldn't matter.  But lots of eukaryotic transcripts have alternate splicing patterns so that one version of the mRNA will contain coding regions that are absent in other alternate forms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem relates to maintaining an open reading frame, avoiding a frame shift and the attendant (and unpredictable) consequences. If a splice donor site occurs within the 3-base codon, it might require that the two (or more) alternate acceptor sites would be in the same relative position in a related codon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The simplest solution to this problem in my view is to make sure that all splice donor and acceptor sites would be at a codon/word boundary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any evidence that this is true?&lt;/p&gt;&#xA;" OwnerUserId="16064" LastEditorUserId="3340" LastEditDate="2015-06-03T11:17:03.807" LastActivityDate="2015-06-08T05:29:54.420" Title="Are there constraints on where intron/exon boundaries occur with respect to the triplet codons of the reading frame?" Tags="&lt;bioinformatics&gt;&lt;molecular-genetics&gt;&lt;mrna&gt;&lt;splicing&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34853" PostTypeId="2" ParentId="34848" CreationDate="2015-06-02T20:42:41.540" Score="2" Body="&lt;p&gt;Unless someone has actually done this specific fusion and reported on the activity, this question won't have an answer. I can't find anything about proline aminopeptidase fusions, but enzyme-HlyA fusions have been done that retained activity similar to the wild-type protein (examples: &lt;a href=&quot;http://www.microbialcellfactories.com/content/pdf/1475-2859-11-8.pdf&quot; rel=&quot;nofollow&quot;&gt;cutinase&lt;/a&gt;, &lt;a href=&quot;http://download.springer.com/static/pdf/626/art%253A10.1007%252FBF00290371.pdf?originUrl=http%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2FBF00290371&amp;amp;token2=exp=1433278714~acl=%2Fstatic%2Fpdf%2F626%2Fart%25253A10.1007%25252FBF00290371.pdf%3ForiginUrl%3Dhttp%253A%252F%252Flink.springer.com%252Farticle%252F10.1007%252FBF00290371*~hmac=31b9fd78fb6342bbacc8919a24748f7932bd9ee7d58db39a3c7c100e275804db&quot; rel=&quot;nofollow&quot;&gt;β-lactamase&lt;/a&gt;). Your fusion might work fine or folding might be disrupted after secretion (either by the tag itself or by the absence of chaperones, if required). In other words, you need to try it yourself. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Bacillus subtilis&lt;/em&gt; is commonly used for secretory protein production and may present another/better option. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-06-02T22:11:52.063" LastActivityDate="2015-06-02T22:11:52.063" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34854" PostTypeId="2" ParentId="34852" CreationDate="2015-06-02T21:17:18.380" Score="1" Body="&lt;p&gt;I don't have time to find examples right now but no, it's not true. You often get cases like this (lower case letters represent the intron):&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ACCTGTaccttgcaacttgcatAGCTGAC&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Which would be spliced to:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;ACCTCTGAC&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Note that the second codon consists of one nucleotide from exon1 and two from exon2. I'll try and update this with real world examples, but I can assure you it is possible and I have seen it quite often. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2015-06-02T21:17:18.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34855" PostTypeId="1" CreationDate="2015-06-02T21:23:57.510" Score="3" ViewCount="305" Body="&lt;p&gt;I am very interested in privacy preserving technolgies, such as &lt;a href=&quot;http://research.microsoft.com/en-us/projects/PINQ/&quot; rel=&quot;nofollow&quot;&gt;Microsoft PINQ&lt;/a&gt; and would like to see if this is applicable to DNA comparison.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Given that I don't have a background in biology, I would appreciate it if someone could tell me how DNA is represented in a computer (in computer science terms), and how DNA is compared in a binary format (or logical equivalent).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The privacy preserving technology I'm using allows the patient to have granular control over what DNA data they share, and how it's used. The receiving agency (medical research, FBI, fertility clinics) will receive cryptographic proof of a DNA result, without exposing all DNA values.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect that each of the following use-cases focus on a certain subset of data, and if the same information was presented to all of them, it would be a breach of privacy:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Combined DNA Index System, or CODIS&lt;/li&gt;&#xA;&lt;li&gt;State DNA index system (SDIS)&lt;/li&gt;&#xA;&lt;li&gt;National DNA Index System (NDIS)&lt;/li&gt;&#xA;&lt;li&gt;FBI's 13-Loci &lt;/li&gt;&#xA;&lt;li&gt;Other government's DNA matching requirements for inclusion/exclusion&lt;/li&gt;&#xA;&lt;li&gt;Disease susceptibility via single nucleotide polymorphism (SNP), and related heredity &lt;/li&gt;&#xA;&lt;li&gt;Paternity tests&lt;/li&gt;&#xA;&lt;li&gt;Evolutionary patterns&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Furthermore, based on my independent research, I understand that there are many ways to determine the DNA of a given sample.  What I don't understand is if every test has the same output? (e.g. are all chromosomes are returned, vs only 23? (or less))&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The value-add I am trying to provide the patient privacy, while fulfilling all legal, moral, and ethical disclosures of data requested of them.  The recipient will have assurance the data is authentic, despite the inherent double blinding of the field data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cryptography allows for&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Redacting (or black out) certain values &lt;/li&gt;&#xA;&lt;li&gt;Anonymously compare a numerical value, (greater than, less than, equal to) without disclosing that value.&lt;/li&gt;&#xA;&lt;li&gt;Prove, or verifiably disprove, that a value is not in a certain list of arbitrary values.&lt;/li&gt;&#xA;&lt;li&gt;The agency to know which DNA testing firm generated the results&lt;/li&gt;&#xA;&lt;li&gt;The DNA testing firm to not know who the patient is, especially in cases of partial disclosure of DNA data.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Your response will help me contribute what I believe to be the moral, ethical, and socially responsible way to handling PII and DNA data.  (yes it will be open source) &lt;/p&gt;&#xA;" OwnerUserId="5399" LastEditorUserId="5399" LastEditDate="2015-06-03T17:41:50.753" LastActivityDate="2015-06-03T18:22:07.003" Title="From a computer science perspective, how is DNA compared for various purposes?" Tags="&lt;dna&gt;&lt;chromosome&gt;&lt;dna-isolation&gt;&lt;research-process&gt;&lt;sex-chromosome&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34856" PostTypeId="2" ParentId="34846" CreationDate="2015-06-02T21:34:15.517" Score="7" Body="&lt;p&gt;This question is broad.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are plenty of uses of mathematical modelling in biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Wikipedia&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may want to read the wikipedia article: &lt;a href=&quot;http://en.wikipedia.org/wiki/Mathematical_and_theoretical_biology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mathematical and Theoretical Biology&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Books&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are tons of books on theoretical biology. I am personally working in the field of population genetics, a field where much of the theory has been expressed mathematically. &lt;a href=&quot;https://biology.stackexchange.com/questions/16470/book-recommendation-on-population-evolutionary-genetics&quot;&gt;Here are book recommendations&lt;/a&gt; for this particular field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;On Biology.SE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We have a tag for mathematical-models (you used it in your post). You may want to see what kind of &lt;a href=&quot;https://biology.stackexchange.com/questions/tagged/mathematical-models&quot;&gt;posts are tagged for mathematical-models&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To repeat @fileunderwater's comment, &lt;a href=&quot;https://biology.stackexchange.com/questions/27450/what-physics-knowledge-can-be-applied-to-biology-of-organisms-and-ecosystems&quot;&gt;What physics knowledge can be applied to biology of organisms and ecosystems&lt;/a&gt; and &lt;a href=&quot;https://biology.stackexchange.com/questions/1310/when-are-population-dynamics-models-useful&quot;&gt;When are population dynamics models useful?&lt;/a&gt; are examples of posts you may want to read.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/15514/what-prevents-predator-overpopulation&quot;&gt;What prevents predator overpopulation?&lt;/a&gt; will give you an example of an easy and classical mathematical model to describe population dynamics of predators and preys.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Personal historical/philosophical note&lt;/em&gt;: At some point physicists have started to describe the laws of nature with mathematical expressions and at that time many physicists didn't quite like the idea that physics could be described by math. Biology has gone through the same phase but much later. Early mathematical biologists developed the modern science of statistics (Francis Galton, Karl Pearson, Ronald Fisher). Biologists used existing mathematical tools such as diffusion processes (Kimura). Note that part of the work in the field of diffusion equations have been done by physicist (Einstein solved the 2D equations for diffusion processes). Note also that the dynamic of diffusion processes called brownian motion have been named after a biologist. Today, biology produces massive amount of data that require good computational skills to treat. The time when biologists had only to know how to recognize species is over, now there are few biologists left that aren't able to code in at least one programming language.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-06-12T15:48:46.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34858" PostTypeId="2" ParentId="14793" CreationDate="2015-06-03T01:07:34.973" Score="1" Body="&lt;p&gt;The &lt;a href=&quot;https://en.wikipedia.org/wiki/Locus_%28genetics%29#Nomenclature&quot; rel=&quot;nofollow&quot;&gt;cytogenetic notation&lt;/a&gt; seems to refer to parts of the chromosome when they're being &lt;a href=&quot;https://en.wikipedia.org/wiki/Karyotype&quot; rel=&quot;nofollow&quot;&gt;karyotyped&lt;/a&gt; when the chromsomes are condensed in metaphase. If so, I think you might be able to use &lt;a href=&quot;https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization&quot; rel=&quot;nofollow&quot;&gt;FISH&lt;/a&gt; to look for pieces of maternal or paternal genetic content on the chromosome. It &lt;a href=&quot;https://en.wikipedia.org/wiki/Cytogenetic_notation&quot; rel=&quot;nofollow&quot;&gt;looks like&lt;/a&gt; you can use &lt;code&gt;mat&lt;/code&gt; and &lt;code&gt;pat&lt;/code&gt; to refer to a maternal or paternal chromosome.&lt;/p&gt;&#xA;" OwnerUserId="87" LastActivityDate="2015-06-03T01:07:34.973" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34860" PostTypeId="2" ParentId="34830" CreationDate="2015-06-03T02:23:53.430" Score="6" Body="&lt;p&gt;TGF-beta would be a good candidate. To cite:&#xA;&quot;TGF-β inhibits G1/S progression in a variety of eukaryotic cell types. Among these, untransformed epithelial cells are particularly sensitive to the growth inhibition by TGF-β.&quot;&#xA;&lt;a href=&quot;http://genesdev.cshlp.org/content/14/24/3093.full&quot;&gt;http://genesdev.cshlp.org/content/14/24/3093.full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fetal bovine serum (FBS) contains a high level of latent TGF-β. Human serum as well has high level of TGF-beta (20-50ng/ml)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is also possible that growth arrest is part of the induction of terminal differentiation by serum factor(s) such as TGFb. &#xA;&quot;Type beta transforming growth factor is the primary differentiation-inducing serum factor for normal human bronchial epithelial cells.&quot;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2871553&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/2871553&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: got more reputation, so now I can post more than two links. Here is a review on TGFb signalling: &lt;a href=&quot;http://genesdev.cshlp.org/content/14/6/627.full&quot;&gt;http://genesdev.cshlp.org/content/14/6/627.full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also a link to serum levels of TGFb:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16845225&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/16845225&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="16068" LastEditorUserId="16068" LastEditDate="2015-06-03T04:31:20.680" LastActivityDate="2015-06-03T04:31:20.680" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34861" PostTypeId="2" ParentId="34846" CreationDate="2015-06-03T02:51:27.583" Score="2" Body="&lt;p&gt;Models are often used to calculate the probability of certain biological outcomes. Such predictions are great help for prioritization of further studies or making other decisions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example: EPA uses an array of in vitro assays for fast and cheap analysis of thousands of potentially toxic environmental compounds (ToxCast and Tox21 projects).&#xA;Next, they use the obtained data to build mathematical models to prioritize chemicals for further more expensive and slow animal studies or to decide on administrative actions to restrict usage of high priority (most dangerous) chemicals. Their prioritization models integrate toxicity data and complex exposure models (including manufacturing and usage logistics, possibility of accidental exposure etc).       &lt;/p&gt;&#xA;" OwnerUserId="16068" LastActivityDate="2015-06-03T02:51:27.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34864" PostTypeId="2" ParentId="34852" CreationDate="2015-06-03T04:07:12.367" Score="2" Body="&lt;p&gt;Here is exon size data of some random gene (human ROR-gamma). &#xA;Link: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/NM_005060.3&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/nuccore/NM_005060.3&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It gets cut at all three possible positions of codon: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;exon 2  30&lt;/p&gt;&#xA;&#xA;&lt;p&gt;exon 3  86&lt;/p&gt;&#xA;&#xA;&lt;p&gt;exon 4  142&lt;/p&gt;&#xA;&#xA;&lt;p&gt;exon 5  513&lt;/p&gt;&#xA;&#xA;&lt;p&gt;exon 6  122&lt;/p&gt;&#xA;&#xA;&lt;p&gt;exon 7  133&lt;/p&gt;&#xA;&#xA;&lt;p&gt;exon 8  108&lt;/p&gt;&#xA;&#xA;&lt;p&gt;exon 9  111&lt;/p&gt;&#xA;&#xA;&lt;p&gt;exon 10 110&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alernatively spliced isoform B of this gene gets different first exon. At the junction codon ACA (isoform A) gets replaced with codon TCA (isoform B). &lt;/p&gt;&#xA;" OwnerUserId="16068" LastEditorUserId="16068" LastEditDate="2015-06-03T04:24:17.340" LastActivityDate="2015-06-03T04:24:17.340" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34865" PostTypeId="2" ParentId="34844" CreationDate="2015-06-03T05:14:37.720" Score="5" Body="&lt;p&gt;No there aren't any organisms with fully functional mitochondria which (the latter) do not retain the minigenome. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On whether it is theoretically possible to transfer all the mitochondrial genes to the nucleus: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps it is possible and mitochondria may work just like lysosomes and ER, but I think that the responses will be greatly delayed. At present there are no mathematical models that can provide a better understanding of that possibility. Nonetheless, some studies have shown that chloroplasts and mitochondria also have redox dependent gene regulation by which the expression of some components of the ETC is regulated by the redox state of the quinone. This helps in optimization of the ETC; if all genes were in the nucleus then this would not be possible. This pheonomenon is, however, better studied in chloroplasts. See &lt;a href=&quot;http://www.pnas.org/content/early/2015/05/15/1500012112.abstract&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; review. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-03T12:43:04.913" LastActivityDate="2015-06-03T12:43:04.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34870" PostTypeId="2" ParentId="31665" CreationDate="2015-06-03T06:43:25.223" Score="2" Body="&lt;p&gt;It is widely accepted that &lt;a href=&quot;http://en.wikipedia.org/wiki/Evolution_of_birds&quot; rel=&quot;nofollow noreferrer&quot;&gt;birds &lt;em&gt;are in fact&lt;/em&gt; dinosaurs&lt;/a&gt;. Cladistically speaking, no DNA technology is required to create a living dinosaur, as they already exist. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assuming you want to do the same to a &lt;em&gt;non-avian&lt;/em&gt; dinosaur (a paraphyletic group), however, a better idea would be to ask on &lt;a href=&quot;https://worldbuilding.stackexchange.com/&quot;&gt;World Building SE&lt;/a&gt;, as there have been little to no scientific research on the topic, and speculative answers are generally considered off topic here. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="-1" LastEditDate="2017-04-13T12:52:23.867" LastActivityDate="2015-06-03T06:43:25.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34871" PostTypeId="1" AcceptedAnswerId="34874" CreationDate="2015-06-03T09:09:57.713" Score="4" ViewCount="1156" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Mesothorax length (the distance from the tip of the scutellum to the&#xA;  most anterior part of the mesothorax)&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From &lt;a href=&quot;http://www.genetics.org/content/180/1/567.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bergland et al 2008.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would that be this distance (green line)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0n9wx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If not, how would you describe that distance?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="3624" LastEditDate="2015-06-03T10:05:47.160" LastActivityDate="2015-06-03T17:56:09.983" Title="Measuring body size in flies/insects" Tags="&lt;entomology&gt;&lt;drosophila&gt;&lt;morphology&gt;&lt;methods&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34872" PostTypeId="2" ParentId="14793" CreationDate="2015-06-03T09:43:32.100" Score="1" Body="&lt;p&gt;It is not possible to know in most cases whether a chromosome is maternal or paternal without knowing the genome sequence of both mother and father (with some additional effort; see below). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are certain exceptions and these include chromosomes that bear &lt;a href=&quot;http://en.wikipedia.org/wiki/Genomic_imprinting&quot; rel=&quot;nofollow noreferrer&quot;&gt;imprinted genes&lt;/a&gt;. For example &lt;a href=&quot;http://en.wikipedia.org/wiki/H19_%28gene%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;H19 gene&lt;/a&gt; on chromosome-1 is maternally imprinted i.e. the paternal copy is silenced by DNA methylation. Likewise there are many imprinted genes; a list of imprinted genes could be found &lt;a href=&quot;http://www.geneimprint.com/site/genes-by-species&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A technique called &lt;a href=&quot;http://en.wikipedia.org/wiki/Bisulfite_sequencing&quot; rel=&quot;nofollow noreferrer&quot;&gt;bisulphite sequencing&lt;/a&gt; (also &lt;a href=&quot;http://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation&quot; rel=&quot;nofollow noreferrer&quot;&gt;MeDIP-seq&lt;/a&gt;) can be used to find methylated regions in the genome but to map chromosomes using this methylation information is not straightforward. You have to do either of these two:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Segregate chromosomes before checking for methylation&lt;/li&gt;&#xA;&lt;li&gt;Identify a variable region, proximal to the methylation site, that can be detected by &lt;a href=&quot;http://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization&quot; rel=&quot;nofollow noreferrer&quot;&gt;FISH&lt;/a&gt;. (It is difficult to find such regions in homologous chromosomes because the differences are small that FISH cannot resolve.)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;With X-chromosome it is possible to find out which one is paternal in relatively easy way but this check has to be done at neonatal stage (when placenta is still present). See &lt;a href=&quot;https://biology.stackexchange.com/questions/14621/determining-whether-x-chromosome-from-sperm-or-egg&quot;&gt;this&lt;/a&gt; post.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-06-03T09:59:09.237" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34873" PostTypeId="1" CreationDate="2015-06-03T09:44:40.193" Score="3" ViewCount="73" Body="&lt;p&gt;I'm not a biology expert, but I have often wondered about the following facts of life:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All mammals have precisely 5 fingers on each of our 4 extremities. Granted, some may not be seen, but the bone structure of 5 fingers is there in all mammals, from whales to bats to humans. This, I guess, tells me that changing the number of finger bones is, genetically speaking, fairly difficult (as it never happened during the evolution of mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, pigs have 12 nipples, dogs have 6, and humans have 2. Pigs have 44 teeth, dogs have 42, and humans (the lucky ones) have 32. This, I guess, means that it is easy to change the number of teeth in a species, as this happened often during the evolution of mammals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is this: What is the reason behind this discrepancy? Why is it that much easier to change one thing and not the other? And a subquestion: why do we still have 32 teeth when the 4 wisdom teeth cause nothing but trouble? Wouldn't having only 28 teeth be an evolutionary advantage?&lt;/p&gt;&#xA;" OwnerUserId="16073" LastActivityDate="2015-06-03T09:44:40.193" Title="Differing number of &quot;things&quot; in mammals" Tags="&lt;evolution&gt;&lt;anatomy&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2015-06-03T18:12:29.710" ContentLicense="CC BY-SA 3.0" />
  <row Id="34874" PostTypeId="2" ParentId="34871" CreationDate="2015-06-03T10:05:02.310" Score="3" Body="&lt;p&gt;I think you are correct, but I'm not an expert in Diptera/Drosophila morphology. Since the prothorax (pronotum) and metathorax are greatly reduced in flies, you mostly see the mesonotum in dorsal view, and this includes the scutellum. Personally, I think it would have been more accurate of them to label this structure &lt;strong&gt;mesonotum&lt;/strong&gt;, or at least &lt;em&gt;dorsal mesothorax length&lt;/em&gt;, since &lt;em&gt;mesothorax&lt;/em&gt; could just as well imply a ventral view (mesosternum).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More information can be found at this webpage: &lt;a href=&quot;http://www.giand.it/diptera/morph/?id=5&amp;amp;lang=en&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Flies - Morphology and anatomy: Thorax&lt;/em&gt;&lt;/a&gt;, which state that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The mesonotum occupies most of dorsal view of the thorax. In order anteroposterior we can identify four parts, called as follow (McAlpine, 1981): prescutum, scutum, scutellum, and postnotum. The scutum is the most large, condition considered apomorphic for the entire order of Diptera.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Also see this picture of the mesonotum from &lt;a href=&quot;http://www.diptera.info/infusions/terms/terms.php?op=view&amp;amp;id=5&quot; rel=&quot;nofollow noreferrer&quot;&gt;diptera.net&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Qg93b.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-06-03T17:56:09.983" LastActivityDate="2015-06-03T17:56:09.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34875" PostTypeId="2" ParentId="34852" CreationDate="2015-06-03T11:16:34.497" Score="3" Body="&lt;p&gt;As pointed out by others this is not true. I just verified this for humans (annotations from &lt;a href=&quot;http://www.gencodegenes.org/releases/21.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;gencode21&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;p&gt;Methodology:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Obtained the start points of the CDS for all genes&lt;/li&gt;&#xA;&lt;li&gt;For each exon of each gene, calculated the distance between the CDS start and exon end&lt;/li&gt;&#xA;&lt;li&gt;Obtained the remainder after dividing this value  by 3 (modulo)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Commands:&lt;/p&gt;&#xA;&lt;pre&gt;&#xA;&lt;b&gt;Command-1:&lt;/b&gt;&#xA;    awk 'BEGIN{FS=&quot;\t|;&quot;;OFS=&quot;\t&quot;} &lt;span class=&quot;math-container&quot;&gt;$3==&quot;CDS&quot;{print $4,$&lt;/span&gt;9}' gencode.v21.annotation.gtf &gt; cdsstart.txt &#xA;&#xA;&lt;b&gt;Command-2:&lt;/b&gt;&#xA;    awk 'BEGIN{FS=&quot;\t|;&quot;;OFS=&quot;\t&quot;} NR==FNR{a[&lt;span class=&quot;math-container&quot;&gt;$2]=$&lt;/span&gt;1;next} (&lt;span class=&quot;math-container&quot;&gt;$3==&quot;exon&quot; &amp;amp;&amp;amp; $&lt;/span&gt;9 in a){if(&lt;span class=&quot;math-container&quot;&gt;$4&amp;gt;a[$&lt;/span&gt;9]) q[(&lt;span class=&quot;math-container&quot;&gt;$5-a[$&lt;/span&gt;9])%3]++} END{for(i in q) print i,q[i]}' cdsstart.txt gencode.v21.annotation.gtf&#xA;&#xA;&lt;/pre&gt;&#xA;&lt;p&gt;Result:&lt;/p&gt;&#xA;&lt;pre&gt;&#xA;position | # cases&#xA;&lt;sup&gt;_______________________&lt;/sup&gt;&#xA;   -2    | 101191&#xA;   -1    | 100954&#xA;    0    | 99499&#xA;&lt;/pre&gt;&#xA;&lt;p&gt;As you can see the exons do not necessarily terminate at the third position of the codon.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-03T12:39:14.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34877" PostTypeId="1" AcceptedAnswerId="34879" CreationDate="2015-06-03T13:45:53.480" Score="6" ViewCount="1422" Body="&lt;p&gt;In DNA sequencing and analysis, what is a genetic marker? I've heard that microsatellites are genetic markers? Those are repetitive strands of bases such as GCAGCAGCAGCA etc. Why are they markers and what defines a genetic marker?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many different KINDS of genetic markers as defined by wikipedia, RFLP, SNP and many more. But when you click these, you get a &lt;strong&gt;technique&lt;/strong&gt; not a sequence. So I'm confused as to whether markers are techniques to find DNA sequences or if they are literally DNA sequences?&#xA;If they are literally DNA sequences, are they sequences that &lt;strong&gt;everyone&lt;/strong&gt; has?&#xA;Example of RFLP: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In molecular biology, restriction fragment length polymorphism, or&#xA;  RFLP (commonly pronounced “rif-lip”), is a technique that exploits&#xA;  variations in homologous DNA sequences.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="6576" LastEditDate="2015-06-03T14:25:39.550" LastActivityDate="2018-05-03T09:01:43.857" Title="What is a genetic marker?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;&lt;dna-sequencing&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="34878" PostTypeId="2" ParentId="21730" CreationDate="2015-06-03T14:06:33.053" Score="12" Body="&lt;p&gt;Long story short, use sequence information if you can.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The long story long:&#xA;Sequence information and the trees generated from them are strictly more reliable than morphological characters. For instance: sharks are pretty much the same shape they were millions of years ago, but they've been accumulating genetic differences 'invisibly' that allows us to group the different kinds of shark accurately. Where genetic data is unavailable (paleontology as a rule, certain kinds of field taxonomy where it's cheaper to code the morphological features of each new beetle than sequence them all) morphological trees are still used. So in terms of which tree type is more common: It depends.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of which tree type is more accepted, it's genetic data by a landslide. Genetic data by and large is much less affected by homologous structures and convergent evolution. In addition, it works on species that all look pretty much identical (imagine trying to code hundreds of bacterial species that are all closely related). Using highly conserved cellular machinery, trees for very distant species can be constructed. Using unconserved noncoding sequences trees for very closely related individuals trees can be constructed with a reasonable degree of accuracy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some examples: &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitochondrial_Eve&quot;&gt;Mitochondrial Eve&lt;/a&gt; would be impossible to date with morphological characters. There's just not enough morphological variation between humans.&#xA;&lt;a href=&quot;http://en.wikipedia.org/wiki/Opabinia#Classification&quot;&gt;Opabinia&lt;/a&gt; is a really good example of how hard it is to classify things based on shape, especially when they're a weird shape.&#xA;Something you can do yourself: &lt;a href=&quot;http://www.ezbiocloud.net/eztaxon/hierarchy?m=browse&amp;amp;k=AC068881&amp;amp;d=2&quot;&gt;Human &lt;/a&gt; and &lt;a href=&quot;https://microbewiki.kenyon.edu/index.php/Thermodesulfatator_atlanticus&quot;&gt;Thermodesulfator&lt;/a&gt;&lt;a href=&quot;http://www.ezbiocloud.net/eztaxon/hierarchy?m=browse&amp;amp;k=AJ969460&amp;amp;d=2&quot;&gt;(seq)&lt;/a&gt; are about as morphologically distinct as two living things can be. One is you, and one eats carbon dioxide and breathes sulfate and hydrogen. It lives at the bottom of the sea and would be more at home in a cup of hot coffee than outside it. Nevertheless, the two species show ~50% sequence similarity using 16S, twice as much as would be expected by chance and easily enough to classify a third thing as more closely related to one or the other. &lt;a href=&quot;http://www.ch.embnet.org/software/LALIGN_form.html&quot;&gt;Try it yourself if you like.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="4109" LastEditDate="2015-07-08T19:58:41.137" LastActivityDate="2015-07-08T19:58:41.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34879" PostTypeId="2" ParentId="34877" CreationDate="2015-06-03T14:31:33.643" Score="0" Body="&lt;p&gt;Genetic markers are sequences of DNA that tend to co-occur with some biological property, in a population.&lt;/p&gt;&#xA;&lt;h3&gt;Examples&lt;/h3&gt;&#xA;&lt;p&gt;E.g. Imagine you have 200 individuals in a population. 100 individuals have some sequence GGGCCCGGGCCC at some locus (position on the genome), and those 100 individuals have blue eyes. The remaining 100 individuals have AAATTTAAATTT, at the same locus and happen to have other eye colors (green, brown, etc). Then GGGCCCGGGCCC is a marker for the biological property that is &amp;quot;blue eyes&amp;quot;.&lt;/p&gt;&#xA;&lt;p&gt;Other biological properties with associated markers can include the following: (i) predisposition to having a certain disease, e.g. Alzeimers, (ii) high intelligence, (iii) and even the presence of another gene, that is you can have markers for the biological property that is &amp;quot;presence of gene X&amp;quot;.&lt;/p&gt;&#xA;&lt;h3&gt;Markers of genes vs. the genes themselves&lt;/h3&gt;&#xA;&lt;p&gt;One often finds that markers for certain biological properties are the genes themselves. But this is not obvious unless one sequences the entire genomes of several individuals of a population, and doing so is expensive. It is cheaper to rely on screening for markers.&lt;/p&gt;&#xA;&lt;h3&gt;One marker to many properties, many markers to one property&lt;/h3&gt;&#xA;&lt;p&gt;You do not always have to have one marker per biological property, there may be several markers scattered across the genome that are all associated with some biological property. You can also have a marker associated with &lt;em&gt;several&lt;/em&gt; biological properties.&lt;/p&gt;&#xA;" OwnerUserId="5005" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-04T10:10:53.030" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34880" PostTypeId="1" CreationDate="2015-06-03T14:32:04.567" Score="0" ViewCount="5619" Body="&lt;p&gt;I'm doing some &lt;a href=&quot;http://en.wikipedia.org/wiki/ELISA&quot; rel=&quot;nofollow&quot;&gt;ELISA&lt;/a&gt; development, and I'd like some justification/best practices for background correction. I'm using a &lt;a href=&quot;http://en.wikipedia.org/wiki/Horseradish_peroxidase&quot; rel=&quot;nofollow&quot;&gt;horseradish-peroxidase&lt;/a&gt; (HRP) detection system along with a &lt;a href=&quot;http://en.wikipedia.org/wiki/3,3%27,5,5%27-Tetramethylbenzidine&quot; rel=&quot;nofollow&quot;&gt;TMB&lt;/a&gt; substrate and an acid-based stop solution, which is quite common. When TMB is cleaved by HRP, it produces a blue (maximum absorbance (A&lt;sub&gt;max&lt;/sub&gt;) of 650 nm) product. The addition of the acid not only stops the reaction for endpoint detection, but it amplifies the signal two- to three-fold, and turns the solution yellow, so that it should be read at its A&lt;sub&gt;max&lt;/sub&gt; of 450 nm. The acid itself &lt;a href=&quot;http://www.interchim.fr/ft/6/664780.pdf&quot; rel=&quot;nofollow&quot;&gt;supposedly&lt;/a&gt; has an A&lt;sub&gt;max&lt;/sub&gt; of 540 nm, which is why you should use that wavelength for background correction, subtracting it from the A&lt;sub&gt;450&lt;/sub&gt;. &lt;a href=&quot;http://www.rndsystems.com/resources/images/5670.pdf&quot; rel=&quot;nofollow&quot;&gt;Other sources&lt;/a&gt; claim the A&lt;sub&gt;540&lt;/sub&gt; reading is supposed to correct for &quot;optical imperfections&quot; in the plate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using either of these explanations, one would assume that the A&lt;sub&gt;540&lt;/sub&gt; would be relatively uniform across the plate, independent of the A&lt;sub&gt;450&lt;/sub&gt; of the same well. However, in my experience, that is not the case at all. My blanks and negative controls are averaging about 0.041 absorbance units (AU) at 540 nm, with an average A&lt;sub&gt;450&lt;/sub&gt; of about 0.065. However, an A&lt;sub&gt;450&lt;/sub&gt; of 0.9 gives an A&lt;sub&gt;540&lt;/sub&gt; of 0.051, 1.4 gives 0.6, 2.0 gives 0.73, and 3.5 gives about 0.14. The &lt;a href=&quot;http://edoc.hu-berlin.de/oa/degruyter/cclm.1989.27.10.791.pdf&quot; rel=&quot;nofollow&quot;&gt;absorbance spectrum&lt;/a&gt; (Fig. 2) of the substrate appears to be quite minimal at 540 nm, so why am I seeing this dose-dependent increase as the A&lt;sub&gt;450&lt;/sub&gt; increases?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More practically, how should I do background correction? Currently, I'm subtracting each individual well's A&lt;sub&gt;540&lt;/sub&gt; from its A&lt;sub&gt;450&lt;/sub&gt;. Should I continue this practice, or should I determine an average plate background at 540 nm using my blanks and negative controls, and subtract that value from each individual A&lt;sub&gt;450&lt;/sub&gt;?&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-08-06T19:26:43.040" Title="Background correction when reading ELISA with TMB substrate" Tags="&lt;biochemistry&gt;&lt;assay-development&gt;&lt;elisa&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34881" PostTypeId="1" AcceptedAnswerId="34939" CreationDate="2015-06-03T14:44:15.363" Score="2" ViewCount="712" Body="&lt;p&gt;I am studying copy-number variation. I am reading &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;C. H. Mermel, S. E. Schumacher, B. Hill, M. L. Meyerson, R. Beroukhim, and G. Getz, “GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers,” Genome Biol., vol. 12, no. 4, p. R41, 2011.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here, it is written that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Segmented copy number profiles represent the summed outcome of all the SCNAs [somatic copy number alterations] that occurred during cancer development. Accurate modeling of the background rate of copy-number alteration requires analysis of the individual SCNAs. However, because SCNAs may overlap, it is impossible to directly infer the underlying events from the final segmented copy-number profile alone.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is not clear to me how a segmented copy number profile represents the summed outcome of all the SCNAs. Is it because different alterations can be present in the same sample, or can alter the copy-number in different moments, or both?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And, do they overlap spatially, temporally, or both?&lt;/p&gt;&#xA;" OwnerUserId="3466" LastActivityDate="2016-07-06T22:17:35.073" Title="What's a segmented copy number profile" Tags="&lt;cancer&gt;&lt;copy-number-variation&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34882" PostTypeId="1" AcceptedAnswerId="34900" CreationDate="2015-06-03T15:51:56.497" Score="5" ViewCount="213" Body="&lt;p&gt;In &lt;a href=&quot;http://www.technologyreview.com/news/408374/electric-fields-kill-tumors/&quot; rel=&quot;nofollow&quot;&gt;MIT's Technology review&lt;/a&gt; it is explained that electric fields can cause dividing cancer cells to explode, while these fields have no significant impact on non-dividing tissues. The original research was done by Palti &lt;em&gt;et al.&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the mechanism behind this? It does not seem to be related to thermal effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;: The treatment in question seems controversial. A clinical trial showed improvement but it is not rock-solid data. &lt;/p&gt;&#xA;" OwnerUserId="4321" LastEditorUserId="9943" LastEditDate="2015-08-05T14:19:55.713" LastActivityDate="2015-08-05T14:19:55.713" Title="How can electric fields inhibit tumor growth?" Tags="&lt;cancer&gt;&lt;electrical-stimulation&gt;&lt;biomedical-engineering&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34883" PostTypeId="2" ParentId="31301" CreationDate="2015-06-03T17:08:01.710" Score="3" Body="&lt;p&gt;The mushroom suggestive for one of the inki ones of Coprinus family, especially Coprinus comatus. The black color can be very intensive in some stage of their development, since it is a part of the spread mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;Members of the &lt;a href=&quot;http://botit.botany.wisc.edu/toms_fungi/may2004.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;genus Coprinus&lt;/a&gt; have been collectively known as the &quot;inky caps&quot; because of the curious character of autodeliquescence of their gills-- in other words self-digestion to release their basidiospores. Most of these species have gills that are very thin and very close to one another, which does not allow for easy release of the spores. Moreover the elongated shape of mushroom does not allow for the spores to be shot off the basidia and get caught in air currents as in most other mushrooms. Coprinus species &quot;compensate&quot; for this by a sequential maturation of the spores from the bottom of the gill towards the top. After the spores have matured and been released, the gill tissue digests itself and begins to curl up, allowing easy release of the basidiospores above. In other words, the digestion opens up the fruiting body so that spores from further up the gills become exposed to the air and a clear path of spore release. The self-digestion continues until the entire fruiting body has turned to black ink. In the olden days this ink was actually used for writing. The self-digestion is also a way of releasing the spores over a longer period of time, and allowing the release of spores from very closely spaced narrow gills borne inside a longitudinally tall pileus. If any Coprinus species are collected for eating or for scientific study, they must be cooked or dried right away, since the self-digesting enzymes seem to kick into high gear after the mushroom is removed from its substrate. They're pretty easy to find too-- the genus name Coprinus gives you a pretty good idea where to look for these mushrooms-- in dung or very rich organic soil.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;examples:&#xA;&lt;a href=&quot;https://blog.mycology.cornell.edu/2008/07/01/the-dish-on-deliquescence-in-coprinus-species/&quot; rel=&quot;nofollow noreferrer&quot;&gt;1.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ghsp1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.shutterstock.com/pic-4692496/stock-photo-coprinus-comatus-ink-mushrooms-on-a-green-forest-background.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;2.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/McTyI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Coprinus_comatus-2_hg.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;3.&lt;/a&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/eXd5g.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-06-03T17:08:01.710" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34885" PostTypeId="2" ParentId="31302" CreationDate="2015-06-03T17:41:55.497" Score="1" Body="&lt;p&gt;&lt;em&gt;This is more of a comment&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Mutation in tumour suppressor is a recessive trait and there is no active &quot;silencing&quot; of the mutation. If a tumour suppressor is a TF then a mutation in the DNA binding domain can have no effect if there is a complementary mutation in its binding site. This is just a theoretical possibility and I have not heard of any examples as such. I don't think any other mechanisms exist for &quot;silencing&quot; any loss of function mutation.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-06-03T17:41:55.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34886" PostTypeId="2" ParentId="34852" CreationDate="2015-06-03T18:09:54.960" Score="1" Body="&lt;p&gt;As Alex M shows, many lengths of exons are 3n+1 or +2. It seems cells do not care about in-frame.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In some cases, exon insertion by alternative splicing shift the frame and produce a short version of gene product or introduce premature stop codon (PTC). When PCT is recognized in cells, the spliced transcript is quickly degraded. This is called nonsense mediated decay (NMD). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Splicing machinery does not care about frame of CDS, and this makes various gene regulations possible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://genesdev.cshlp.org/content/24/21/2343.full&quot; rel=&quot;nofollow&quot;&gt;http://genesdev.cshlp.org/content/24/21/2343.full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This review shows an example of NMD by alternative splicing. See the description about caspase-2.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-06-08T05:29:54.420" LastActivityDate="2015-06-08T05:29:54.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34887" PostTypeId="2" ParentId="34855" CreationDate="2015-06-03T18:22:07.003" Score="4" Body="&lt;p&gt;From a computer science perspective, there's nothing at all special about DNA. It's stored as a simple ASCII text file consisting of repetitions of 4-15 different letters. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;DNA, the molecule, is a long chain of nearly identical smaller molecules (nucleotides) joined together. The nucleotides differ only in which of four possible &lt;a href=&quot;https://en.wikipedia.org/wiki/Nucleobase&quot; rel=&quot;nofollow&quot;&gt;bases&lt;/a&gt; (A,C,T/U or G) they have attached. Therefore, when representing a DNA sequence, we only need to represent the bases.&#xA;There are also the so-called &lt;a href=&quot;http://droog.gs.washington.edu/parc/images/iupac.html&quot; rel=&quot;nofollow&quot;&gt;&quot;ambiguity codes&quot;&lt;/a&gt; which represent different possibilities:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;IUPAC Code   Meaning             &#xA;  A            A                   &#xA;  C            C                   &#xA;  G            G                   &#xA;  T/U          T                   &#xA;  M            A or C              &#xA;  R            A or G              &#xA;  W            A or T              &#xA;  S            C or G              &#xA;  Y            C or T              &#xA;  K            G or T              &#xA;  V            A or C or G         &#xA;  H            A or C or T         &#xA;  D            A or G or T         &#xA;  B            C or G or T         &#xA;  N            G or A or T or C    &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The vast majority of sequences, however, won't use the ambiguity codes and will only have A,C,T,G and the occasional N. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most common DNA sequence format is &lt;a href=&quot;https://en.wikipedia.org/wiki/FASTA_format&quot; rel=&quot;nofollow&quot;&gt;FASTA&lt;/a&gt;, which consists of one or more sequences each of which has a header (lines beginning with a &lt;code&gt;&amp;gt;&lt;/code&gt;) and 60-character long sequences. This, for example, is an excerpt of human chromosome 17:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt;chr17&#xA;AAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGT&#xA;CCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTC&#xA;CCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCT&#xA;GCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTT&#xA;AACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCC&#xA;AGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACA&#xA;GTGcctgcgacaaagctgaatgctatcatttaaaaactccttgctggttt&#xA;gagaggcagaaaatgatatctcatagttgctttactttgcatattttAAA&#xA;ATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAG&#xA;AAAATGCATGTGGACAAAAGTTGGGATTAGGAGagagaaatgaagacata&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So, in conclusion, there's nothing special about DNA. If you're writing software that compares DNA sequences, you are writing software that compares ASCII text. You can hash it, salt it and anything else you might want to do. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The only thing you should be aware of is that minor variations are very rarely meaningful. The level of identity you will need will depend on the precise biological question being asked but as a general rule, a single nucleotide difference is as likely to be a sequencing error as a real difference. You will need to collaborate with biologists in order to set up the right threshold for whatever your project is looking at. &lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2015-06-03T18:22:07.003" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34889" PostTypeId="1" AcceptedAnswerId="34898" CreationDate="2015-06-03T19:28:53.100" Score="7" ViewCount="17764" Body="&lt;p&gt;Last year I read a course in biology. During that course I learnt that Protozoa like Lamblia intestinalis or Entamoeba hystolitica form &lt;em&gt;cysts&lt;/em&gt; in unfavourable conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This year I read a course in microbiology. I learnt that bacteria like Clostridium perfringens or Bacillus anthracis form &lt;em&gt;spores&lt;/em&gt; in unfavourable conditions. So far so good. But then I learnt that prokaryotic Borrelia burgdorferi can form a &lt;em&gt;cyst&lt;/em&gt;, not a spore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Firstly, I would highly appreciate any comments that would cast some light on these terms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, I would also like to know if the spore inside, say, B.anthracis is the same organism as B.anthracis that produced the spore. Does a spore and the bacteria that produced it have the same DNA sequence? In other words, &lt;strong&gt;if I were a sporeforming bacteria, would my spore be myself, my bodypart or my child?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="15773" LastEditorUserId="15773" LastEditDate="2015-06-04T03:25:16.317" LastActivityDate="2018-01-21T06:22:27.720" Title="What is the difference between a spore and a cyst?" Tags="&lt;microbiology&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34890" PostTypeId="1" AcceptedAnswerId="34893" CreationDate="2015-06-03T20:15:01.080" Score="5" ViewCount="493" Body="&lt;p&gt;I was reading an article by Montgomery on the therapeutic effect of pets (&lt;a href=&quot;https://www.bostonglobe.com/lifestyle/2015/01/12/your-brain-pets/geoJHAfFHxrwNS4OgWb7sO/story.html&quot; rel=&quot;nofollow&quot;&gt;Boston Globe, January 12, 2015&lt;/a&gt;), and I found this quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;All animals appear to have cells directly under the skin that activate oxytocin in the brain. So gentle touch&lt;/strong&gt; — from grooming your&#xA;  horse’s coat to making love with your spouse — is a powerful trigger.&#xA;  But so is simply thinking about someone you love, whether it’s a&#xA;  person or a pet. And in fact, a small study published this fall at&#xA;  Massachusetts General Hospital found that MRI scans of women’s brains&#xA;  lit up in the same areas when shown pictures of their pets as when&#xA;  shown pictures of their children.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do humans have oxytocin triggering skin cells or formations under the skin?&lt;/strong&gt; If so, are there higher concentrations of these cells in certain areas of the body? In the human erogenous zones, like neck, lips, etc?&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="9943" LastEditDate="2016-03-10T21:12:20.703" LastActivityDate="2016-03-11T12:32:48.050" Title="Do humans have skin cells that trigger oxytocin release in the brain?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;endocrinology&gt;&lt;neurophysiology&gt;&lt;touch&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34891" PostTypeId="2" ParentId="31724" CreationDate="2015-06-03T20:16:46.967" Score="4" Body="&lt;p&gt;According to this &lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/370/1667/20140131&quot; rel=&quot;nofollow&quot;&gt;study&lt;/a&gt;, artificial lighting similar to that provided by streetlights in the UK can &lt;em&gt;reduce&lt;/em&gt; flowering in at least one plant, which also affects the aphids that feed on it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;https://www.extension.purdue.edu/extmedia/fnr/fnr-faq-17.pdf&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; discusses it in more general terms - night lighting doesn't affect photosynthesis, but can affect the length of day/night perceived by plants and alter growth accordingly. There are two examples given of how it is harmful:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Young trees grow longer and don't enter dormancy, making them increasingly susceptible to cold temperatures.&lt;/li&gt;&#xA;&lt;li&gt;The stomatal pores of leaves remain open longer, making some trees more susceptible to pollution and water stress.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2015-06-03T20:16:46.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34893" PostTypeId="2" ParentId="34890" CreationDate="2015-06-04T00:43:43.270" Score="7" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Oxytocin release has been associated with the cutaneous low-threshold (CT) afferent fibers in hairy skin.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Oxytocin is released from the paraventricular nucleus in the brain in response to low intensity stimulation of the skin, such as touch, stroking and warm temperatures. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a recent review &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290532/&quot; rel=&quot;nofollow&quot;&gt;Uvnäs-Moberg et al. (2015)&lt;/a&gt; report that the specific sensory nerve type mediating oxytocin release in the brain is unknown. Although myelinated somatosensory fibers mediating the &lt;strong&gt;discriminative sense of touch&lt;/strong&gt; may be involved, a more likely candidate mediating &lt;strong&gt;affective touch&lt;/strong&gt; are the unmyelinated low-threshold mechanosensory nerves, called &lt;strong&gt;C low-threshold mechanoreceptors&lt;/strong&gt; (CLTMs) in animals or &lt;strong&gt;C-tactile afferents&lt;/strong&gt; (CTs) in humans. Their terminal morphology (i.e., the skin receptor they connect to) is currently unknown. The fibers have been characterized mainly through  electrophysiological and electron microscopy research &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0896627314003870&quot; rel=&quot;nofollow&quot;&gt;(McGlone at al., 2014)&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The association of CT fibers with &lt;strong&gt;affective&lt;/strong&gt; touch stems mainly from the finding that their activation patterns with various stroking velocities correlates with subjective pleasantness ratings. Specifically, the relationship between brush-stroking velocity and firing rate was distinctly different between CT and myelinated afferents. CTs showed an inverted U-shaped relationship,&#xA;whereas mean firing rates increased monotonically with brushing velocity in all myelinated afferents &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0896627314003870&quot; rel=&quot;nofollow&quot;&gt;(McGlone at al., 2014)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, CT fibers have only been identified in hairy skin in mammals, and the fibers mediating affective touch through glabrous skin (including the fingertips, palms and lips) are unknown &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0896627314003870&quot; rel=&quot;nofollow&quot;&gt;(McGlone at al., 2014)&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0896627314003870&quot; rel=&quot;nofollow&quot;&gt;McGlone &lt;em&gt;et al.&lt;/em&gt;, &lt;em&gt;Neuron&lt;/em&gt; (2014); &lt;strong&gt;82&lt;/strong&gt;: 737-55&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290532/&quot; rel=&quot;nofollow&quot;&gt;Uvnäs-Moberg &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Front Neurosci&lt;/em&gt; (2015); &lt;strong&gt;5&lt;/strong&gt;(1529): 1-16&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-03-11T12:32:48.050" LastActivityDate="2016-03-11T12:32:48.050" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34894" PostTypeId="1" AcceptedAnswerId="34896" CreationDate="2015-06-04T00:47:54.823" Score="0" ViewCount="633" Body="&lt;p&gt;Do humans have a huge impact on the ecosystem ? is it possible for other animals to live without us ? &lt;/p&gt;&#xA;" OwnerUserId="16022" LastEditorUserId="9943" LastEditDate="2015-06-04T01:34:15.423" LastActivityDate="2015-06-04T03:27:10.223" Title="Are Humans Considered Keystone species?" Tags="&lt;ecology&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-06-04T05:24:56.637" ContentLicense="CC BY-SA 3.0" />
  <row Id="34895" PostTypeId="1" CreationDate="2015-06-04T00:57:35.653" Score="6" ViewCount="577" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Vrrag.jpg&quot; alt=&quot;Mystery plant&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone identify this plant? It was growing under my 2 year old's climbing wall / play house thing. I live in &lt;a href=&quot;https://en.wikipedia.org/wiki/West_Virginia#Geography&quot; rel=&quot;nofollow noreferrer&quot;&gt;West Virginia, USA&lt;/a&gt; and it's currently June 3rd (if that helps from a climate standpoint).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know there are some potentially dangerous invasive plants like the giant hogweed. I hope someone here can help me identify this and give me any tips on what to do about it if it is in fact hogweed.&lt;/p&gt;&#xA;" OwnerUserId="16083" LastEditorUserId="3535" LastEditDate="2015-06-05T07:10:45.720" LastActivityDate="2015-06-05T07:10:45.720" Title="Can someone identify this plant?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34896" PostTypeId="2" ParentId="34894" CreationDate="2015-06-04T02:41:43.160" Score="3" Body="&lt;p&gt;I am voting to close as homework question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I felt like I would give you a few hints though.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;is it possible for other animals to live without us?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Life on earth have existed for almost 4 billions years. Animals have existed for about 600 millions years. Modern human (&lt;a href=&quot;http://en.wikipedia.org/wiki/Anatomically_modern_humans&quot; rel=&quot;nofollow noreferrer&quot;&gt;AMHS&lt;/a&gt;) have existed for 0.2 million years.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Do humans have a huge impact on the ecosystem?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Here are just a few pictures taken by airplane of agricultural lands&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0OBQw.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/iuPqKm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Zx6NJm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and a koala searching its home after a rapid man-made deforestation&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Z3C2I.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-06-04T03:27:10.223" LastActivityDate="2015-06-04T03:27:10.223" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34897" PostTypeId="2" ParentId="19836" CreationDate="2015-06-04T03:18:08.423" Score="0" Body="&lt;p&gt;In babel: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;babel my.mol2 my.pdbqt -xh&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;-x states options for writing .pdbqt files&#xA;-h says keep hydrogens&lt;/p&gt;&#xA;" OwnerUserId="16085" LastActivityDate="2015-06-04T03:18:08.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34898" PostTypeId="2" ParentId="34889" CreationDate="2015-06-04T03:28:12.770" Score="3" Body="&lt;p&gt;The bacterial spores you are referring to are called endospores. The spore is formed during unfavorable conditions, by duplication of the bacterial chromosomes, and consequent envelopment by various membranes and protective coatings (while still within the original cell). The spore is dormant and remains so as the outer cell degrades during harsh conditions, releasing the spore. I guess I'd call the spore a clone of the original?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may enjoy reading the relevant sections in this &lt;a href=&quot;http://www.microbiologytext.com/index.php?module=book&amp;amp;func=displayarticle&amp;amp;art_id=68&quot; rel=&quot;nofollow&quot;&gt;book&lt;/a&gt;, which go into greater detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;edit: as Souvik has pointed out, this is only one type of &quot;protective&quot; spore. Actinomycetes also form spores, via differentiation of the cells, and cyanobacteria form akinetes also via differentiation (but this structure is not as durable as endospores).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Information about cyst formation is difficult to find, but in bacteria it appears to develop via changes in cell wall composition.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2015-06-04T16:51:20.387" LastActivityDate="2015-06-04T16:51:20.387" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34899" PostTypeId="2" ParentId="34877" CreationDate="2015-06-04T03:47:29.150" Score="3" Body="&lt;p&gt;As hello_there_andy (and also the Wikipedia page) has indicated, genetic markers are DNA sequences that can be used to distinguish individuals (can also be tissues, cells, etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Linkage_analysis&quot; rel=&quot;nofollow&quot;&gt;Linkage&lt;/a&gt; of a phenotype with genetic markers is used to identify regions of the genome that are likely causative for that phenotype, as hello_there_andy says, but there is nothing inherent to how a marker is chosen that says it has to be linked to any phenotype. Markers are typically chosen for an analysis because they are easy to measure and track, individuals differ at the locus (so you know that if your phenotype of interest segregates perfectly with the marker, it's unlikely to be chance), and they cover the genome (or the region of the genome you already know is linked) appropriately, among other things.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastEditorUserId="3059" LastEditDate="2015-06-04T16:38:10.663" LastActivityDate="2015-06-04T16:38:10.663" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34900" PostTypeId="2" ParentId="34882" CreationDate="2015-06-04T04:13:01.913" Score="5" Body="&lt;p&gt;In a PNAS paper by Palti's group (&lt;a href=&quot;http://www.pnas.org/content/104/24/10152.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;2007&lt;/a&gt;) they explain the hypothesis behind the technique:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They reason alternating currents of 100 kHz to 1 MHz specifically affects dividing cells and thereby targets cancer cells. Note that this is the same basic idea as chemotherapy and radiotherapy, which also target dividing cells mostly. The mechanism of action of alternating electric fields on dividing cells is though to be the result of a specific effect on the  bridge separating the daughter (cancer) cells during cell division (Fig. 1). They think it &lt;strong&gt;interferes with spindle tubulin orientation and induces electrophoretic effects&lt;/strong&gt; (&lt;a href=&quot;http://www.pnas.org/content/104/24/10152.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kirson et al., 2007&lt;/a&gt;), resulting in a &lt;strong&gt;pile-up of cytoplasmatic organelles at the cleavage furrow&lt;/strong&gt;. This is thought to interfere with cytokinesis, and to lead to cell destruction** (&lt;a href=&quot;http://cancerres.aacrjournals.org/content/64/9/3288.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kirson et al., 2004&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note it is the frequency that differentiates between the various effects of current stimuli. At very low frequencies (1 KHz) electric fields stimulate excitable tissues through membrane depolarization. At higher frequencies this excitatory effect is lost. At very high frequencies (&gt;1 MHz) tissue heating results (e.g., microwave ovens).  Hence, alternating electric fields of intermediate frequencies (10 kHz to 1 MHz) were considered not to have any meaningful thermal effects (&lt;a href=&quot;http://cancerres.aacrjournals.org/content/64/9/3288.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kirson et al., 2004&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/km7YO.png&quot; alt=&quot;Palti&amp;#39;s electrophoresis&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Palti's electric field hypothesis. Source: &lt;a href=&quot;http://www.pnas.org/content/104/24/10152.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kirson &lt;em&gt;et al&lt;/em&gt;. (2007)&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://cancerres.aacrjournals.org/content/64/9/3288.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kirson &lt;em&gt;et al., Cancer Res&lt;/em&gt; (2004); &lt;strong&gt;64&lt;/strong&gt;: 3288-95&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.pnas.org/content/104/24/10152.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kirson &lt;em&gt;et al., PNAS&lt;/em&gt; (2007); &lt;strong&gt;104&lt;/strong&gt;(24): 10152–57&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-04T10:59:14.127" LastActivityDate="2015-06-04T10:59:14.127" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34901" PostTypeId="2" ParentId="34895" CreationDate="2015-06-04T04:30:46.793" Score="8" Body="&lt;p&gt;As @dd3 stated, it's a &lt;a href=&quot;http://www.eattheweeds.com/newsletter-30-april-2013/&quot; rel=&quot;noreferrer&quot;&gt;spiny (or prickly) sow thistle&lt;/a&gt;. It's an annual common in most of the US.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The leaf itself does not have a stem, and if you break the central stalk, it should be hollow and there should be a milky exudate. The plant spreads by fluffy seeds produced from a small dandelion-like flower.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you pick it while young, it won't hurt (as much); if you prevent it from flowering, it should not spread, although unsprouted seeds can sprout still for a few years (it can come in on the wind as well.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eEVje.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.illinoiswildflowers.info/weeds/plants/prk_sowthistle.htm&quot; rel=&quot;noreferrer&quot;&gt;Prickly Sowthistle&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-06-04T04:30:46.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34903" PostTypeId="1" AcceptedAnswerId="34905" CreationDate="2015-06-04T05:23:22.373" Score="2" ViewCount="424" Body="&lt;p&gt;This little flower was growing on dry ranchland in Kelowna, it flowered in April:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0bbeJ.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16087" LastEditorUserId="5563" LastEditDate="2015-06-04T10:17:21.443" LastActivityDate="2015-06-04T10:17:21.443" Title="What is the name of this flower? The photo was taken in the Okanagan Valley, British Columbia" Tags="&lt;species-identification&gt;&lt;flowers&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34904" PostTypeId="1" CreationDate="2015-06-04T05:45:15.073" Score="1" ViewCount="199" Body="&lt;p&gt;I design my primers in Primer3PLUS and analyze them in Oligoanalyzer3.1, A big problem that I have this is that I got very nice output in NCBI-Primer BLAST for their specificity but a very negative ΔG for self or hetrodimer even under -7 or-13. is it possible use them for PCR by adding DMSO or Formamide? what other way may be helpful?&lt;/p&gt;&#xA;" OwnerUserId="9101" LastEditorUserId="3340" LastEditDate="2015-06-04T07:23:55.247" LastActivityDate="2015-06-04T07:23:55.247" Title="Primer heterodimer problem" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;pcr&gt;&lt;primer&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34905" PostTypeId="2" ParentId="34903" CreationDate="2015-06-04T05:45:35.777" Score="4" Body="&lt;p&gt;Looks a lot like &lt;a href=&quot;http://www.pnwflowers.com/flower/claytonia-lanceolata&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Claytonia lanceolata&lt;/em&gt;&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="16041" LastEditDate="2015-06-04T05:56:04.930" LastActivityDate="2015-06-04T05:56:04.930" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34907" PostTypeId="1" AcceptedAnswerId="34909" CreationDate="2015-06-04T07:46:38.267" Score="3" ViewCount="81" Body="&lt;p&gt;I took this photo near Stratford upon Avon by the side of a road. Can anyone identify this flower?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/TGa61.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-06-04T07:57:54.787" Title="Flower identification (England, late May)" Tags="&lt;species-identification&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34908" PostTypeId="2" ParentId="34907" CreationDate="2015-06-04T07:57:52.417" Score="0" Body="&lt;p&gt;Could be &lt;a href=&quot;http://www.bhg.com/gardening/plant-dictionary/bulb/allium/&quot; rel=&quot;nofollow&quot;&gt;pink allium&lt;/a&gt;, considering the thickness of the stem?&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2015-06-04T07:57:52.417" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34909" PostTypeId="2" ParentId="34907" CreationDate="2015-06-04T07:57:54.787" Score="3" Body="&lt;p&gt;MY guess would be &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Centranthus_ruber&quot; rel=&quot;nofollow noreferrer&quot;&gt;Centranthus ruber coccineus&lt;/a&gt;&lt;/em&gt;, also known as red valerian. See this picture (from &lt;a href=&quot;http://imgkid.com/centranthus-ruber-coccineus.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/B9y6E.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-06-04T07:57:54.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34910" PostTypeId="1" CreationDate="2015-06-04T09:49:20.210" Score="6" ViewCount="216" Body="&lt;p&gt;I am curious as to how complex behavior is passed down genetically? For example, how is the building of a web genetically coded in a spider? And how is the complex behavior of constricting prey coded into a boa? As these critters do not get raised by their parents, and hence cannot learn to copy these behaviors, it has to be genetically imprinted. &lt;strong&gt;How&lt;/strong&gt;? &lt;/p&gt;&#xA;" OwnerUserId="14949" LastEditorUserId="14949" LastEditDate="2015-06-04T12:45:25.353" LastActivityDate="2015-06-04T13:11:40.833" Title="How are behaviors genetically coded in animals?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34911" PostTypeId="5" CreationDate="2015-06-04T10:56:29.657" Score="0" Body="&lt;h2&gt;General Introduction&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;According to the &lt;a href=&quot;http://goldbook.iupac.org/L03571.html&quot; rel=&quot;nofollow&quot;&gt;IUPAC Gold book&lt;/a&gt;, &lt;em&gt;&quot;&lt;strong&gt;lipids&lt;/strong&gt;&quot;&lt;/em&gt; is a:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A loosely defined term for substances of biological origin that are&#xA;  soluble in nonpolar solvents. They consist of saponifiable lipids,&#xA;  such as glycerides (fats and oils) and phospholipids, as well as&#xA;  nonsaponifiable lipids, principally steroids.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Lipids are essential biomolecules required for both maintenance of cellular structure and for signalling. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glyceride-&lt;a href=&quot;http://en.wikipedia.org/wiki/Phospholipid&quot; rel=&quot;nofollow&quot;&gt;phospholipids&lt;/a&gt; make up the plasma membrane of eukaryotes and most prokaryotes with an exception of archaea which use &lt;a href=&quot;http://en.wikipedia.org/wiki/Terpenoid&quot; rel=&quot;nofollow&quot;&gt;isoprenoid&lt;/a&gt; lipids. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Steroids have functional roles as &lt;a href=&quot;http://en.wikipedia.org/wiki/Steroid_hormone&quot; rel=&quot;nofollow&quot;&gt;hormones&lt;/a&gt; as in the case of cortisone, testosterone etc as well as structural roles as in the case of cholesterol, that provides rigidity to plasma membranes and also forms an essential component of &lt;a href=&quot;http://en.wikipedia.org/wiki/Lipid_raft&quot; rel=&quot;nofollow&quot;&gt;lipid rafts&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fatty acid derivatives such as prostaglandins and leukotrienes play crucial role in the process of inflammation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several secondary metabolites of plant origin (mostly of isoprenoid type), that may be of commercial/therapeutic importance. Vitamins such as vitamin-A (retinol) and vitamin-E (tocopherol) are also isoprenoid lipids.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h2&gt;Questions that should have this tag&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Questions that should have this tag include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Questions on biochemistry of lipids&lt;/li&gt;&#xA;&lt;li&gt;Questions on laboratory analysis of lipids&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-04T11:39:36.743" LastActivityDate="2015-06-04T11:39:36.743" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34912" PostTypeId="4" CreationDate="2015-06-04T10:56:29.657" Score="0" Body="A broad group of consisting of biomolecules that are soluble in non-polar solvents. Most of these molecules have huge hydrocarbon chains (linear or cyclic). Examples include glycerides (glyceryl esters), isoprenoids and steroids." OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-04T11:39:25.583" LastActivityDate="2015-06-04T11:39:25.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34913" PostTypeId="5" CreationDate="2015-06-04T11:01:52.357" Score="0" Body="&lt;p&gt;Nucleic acids and proteins are heteropolymers and therefore have a sequence which is read from 5' to 3' in case of nucleotides and N-terminal to C-terminal in case of proteins. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First step of comparing two nucleic acids or proteins is to compare their sequences; this process is technically a string comparison and is called sequence alignment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a local alignment, subsequences (substrings) of the query are compared to the reference. This method is used to find shorter stretches of high homology. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Global alignment involves and end-to-end alignment of the query to the reference. This method is used to overall compare the two genes or proteins (finding homologs). &lt;a href=&quot;http://biology.stackexchange.com/a/11280/3340&quot;&gt;This&lt;/a&gt; post summarizes these methods. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alignment process generates a score which is in very simple terms total number of matches. In case of nucleic acid there can be either a match or a mismatch but for proteins, amino acids with similar chemical properties can be considered a partial match. These scoring rules are obtained from &lt;a href=&quot;https://en.wikipedia.org/wiki/Point_accepted_mutation&quot; rel=&quot;nofollow&quot;&gt;PAM&lt;/a&gt; or &lt;a href=&quot;https://en.wikipedia.org/wiki/BLOSUM&quot; rel=&quot;nofollow&quot;&gt;BLOSUM&lt;/a&gt; matrices.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some sequence alignment tools include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;BLAST and its variants&lt;/li&gt;&#xA;&lt;li&gt;CLUSTALW&lt;/li&gt;&#xA;&lt;li&gt;TCOFFEE&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;More tools can be found here:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ebi.ac.uk/Tools/psa/&quot; rel=&quot;nofollow&quot;&gt;http://www.ebi.ac.uk/Tools/psa/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ebi.ac.uk/Tools/msa/&quot; rel=&quot;nofollow&quot;&gt;http://www.ebi.ac.uk/Tools/msa/&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What questions can have this tag?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Questions regarding basics of sequence alignment algorithm but not going deep into the computational aspects such as dynamic programming&lt;/li&gt;&#xA;&lt;li&gt;Questions related to technical aspects of running these tools (parameter suggestion, scoring etc)&lt;/li&gt;&#xA;&lt;li&gt;Questions related to interpretation of alignment data&lt;/li&gt;&#xA;&lt;li&gt;Questions related to application of sequence alignment&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-18T13:26:22.900" LastActivityDate="2015-06-18T13:26:22.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34914" PostTypeId="4" CreationDate="2015-06-04T11:01:52.357" Score="0" Body="A computational technique to compare two nucleotide or protein sequences. There are two basic types of sequence alignment i.e. local alignment (local comparison of subsequences) or global alignment (end to end comparison of the entire sequences)." OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-04T11:39:39.750" LastActivityDate="2015-06-04T11:39:39.750" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34915" PostTypeId="5" CreationDate="2015-06-04T11:13:25.527" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2015-06-04T11:13:25.527" LastActivityDate="2015-06-04T11:13:25.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34916" PostTypeId="4" CreationDate="2015-06-04T11:13:25.527" Score="0" Body="A rapid change in the membrane potential of excitable cells such as neurons and muscles; this usually involves a steep rise  (depolarization) followed by a steep fall in membrane potential (repolarization). The cell subsequently enters a short refractory period (hyperpolarized state) during which it cannot generate another action potential." OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-04T11:39:33.700" LastActivityDate="2015-06-04T11:39:33.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34917" PostTypeId="5" CreationDate="2015-06-04T11:19:57.337" Score="0" Body="" OwnerUserId="-1" LastEditorUserId="-1" LastEditDate="2015-06-04T11:19:57.337" LastActivityDate="2015-06-04T11:19:57.337" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34918" PostTypeId="4" CreationDate="2015-06-04T11:19:57.337" Score="0" Body="Health and medicine questions are off-topic unless dealing with the biology underlying health and medicine. Please carefully explore the tour, help centre, and meta before posting health and medicine questions. &#xD;&#xA;&#xD;&#xA;Health is a physiological state of well-being referring to the (ab)normality of the cellular or organismal physiology." OwnerUserId="3340" LastEditorUserId="1590" LastEditDate="2016-03-15T12:15:02.600" LastActivityDate="2016-03-15T12:15:02.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34919" PostTypeId="2" ParentId="31258" CreationDate="2015-06-04T11:31:09.407" Score="1" Body="&lt;p&gt;The latin name for this animal is &lt;a href=&quot;http://en.wikipedia.org/wiki/Leiobunum_rotundum&quot; rel=&quot;nofollow noreferrer&quot;&gt;Leiobunum rotundum&lt;/a&gt; and Nelima fuscifrons, order Opiliones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;examples:&#xA;&lt;a href=&quot;http://fauneflore06.voila.net/pages/arachnid/pisaure.htm#Faucheux&quot; rel=&quot;nofollow noreferrer&quot;&gt;link&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wnjeY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EFFqa.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-06-04T11:31:09.407" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34921" PostTypeId="2" ParentId="34910" CreationDate="2015-06-04T12:54:11.757" Score="3" Body="&lt;p&gt;I will focus my answer on the evolution of orb web spiders (Fig. 1), because &lt;em&gt;arachnids&lt;/em&gt;, like insects, are relatively non-complex creatures with an obvious systematic behavior (the weaving of highly symmetric, repeating structures). Hence I reasoned this would be a good approach of investigating the answer to this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The orb-weavers (&lt;em&gt;Orbiculariae&lt;/em&gt;, an informal name for the taxon containing the superfamilies &lt;em&gt;Deinopoidea&lt;/em&gt; and &lt;em&gt;Araneoidea&lt;/em&gt;) are among the most diverse lineages of spiders &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24160416&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Hormiga &amp;amp; Griswold, 2014)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RMWml.jpg&quot; alt=&quot;Orb&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Orb web. Source: &lt;a href=&quot;http://www.britannica.com/EBchecked/topic/431089/orb-web&quot; rel=&quot;nofollow noreferrer&quot;&gt;Encyclopedia Britannica&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822(14)00750-7?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982214007507%3Fshowall%3Dtrue&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bond &lt;em&gt;et al.&lt;/em&gt; (2014)&lt;/a&gt; report that according to various estimations the date of the origin of the orb web was somewhere around the Lower Jurassic 201 million years ago and 52 million years ago, and the authors support the view of a monophyletic origin of the orb web.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite this excellent opportunity to elucidate the (monophyletic) genetic underpinnings of the evolution, and hence the passing down of orb weaving, are largely unknown. Not only is the evolution of orb weaving unknown, even the evolution of the intricate physical properties of the silk are largely unknown. For example, how the sticky glue &lt;em&gt;araneoid&lt;/em&gt; orb web evolved is a mystery. This complex multicharacter trait is hypothesized as a key innovation to explain the increase in diversity of &lt;em&gt;araneoidea&lt;/em&gt;. For example, &lt;em&gt;araneoid&lt;/em&gt; orbs contain viscous adhesives and they have low UV-reflectance and are hence less visible to insects. There exists one proposed evolutionary pathway from the dry, cribellate orb web of &lt;em&gt;deinopoids&lt;/em&gt; to the sticky glue orb web of &lt;em&gt;araneoids&lt;/em&gt;, but that's about it &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24160416&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Hormiga &amp;amp; Griswold, 2014)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In all, physical properties of silks contained in webs are hardly explained in evolutionary terms, let alone the behavioral profiles necessary to make a web out of it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822(14)00750-7?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982214007507%3Fshowall%3Dtrue&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bond &lt;em&gt;et al., Curr Biol&lt;/em&gt; (2014); &lt;strong&gt;24&lt;/strong&gt;(15): 1765–71&lt;/a&gt;&lt;br&gt;&#xA;- &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24160416&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hormiga &amp;amp; Griswold, &lt;em&gt;Annu Rev Entomol&lt;/em&gt; (2014); &lt;strong&gt;59&lt;/strong&gt;:487–512&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-04T13:11:40.833" LastActivityDate="2015-06-04T13:11:40.833" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34922" PostTypeId="1" CreationDate="2015-06-04T13:15:38.333" Score="1" ViewCount="244" Body="&lt;p&gt;I read that Huntington's is a disorder caused by dynamic mutations in the DNA, which means that a triplet sequence of DNA changes from generation to generation. Say we have the sequence ATGATGATGATG. The child of this person with have ATTATGATGATG and the grandchild will have ATTATTATGATG etc.&#xA;This means that Huntington's will be worse (debut earlier) the longer the generation lasts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions are: Is my understanding of dynamic mutation correct? Is there no MINIMUM age where Huntington's will debut? In other words, if a generation is very long and has Huntington's, can a baby have symptoms at birth?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-06-08T10:34:20.083" Title="Dynamic mutation and huntington's" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;&lt;pathology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34923" PostTypeId="2" ParentId="34889" CreationDate="2015-06-04T13:45:43.713" Score="1" Body="&lt;p&gt;dd3 summed up the 1st part of your q nicely.....now 'bout the second part...&lt;a href=&quot;http://en.wikipedia.org/wiki/Bacterial_spore&quot; rel=&quot;nofollow&quot;&gt;bacterial spore-s&lt;/a&gt; (&lt;strong&gt;not necessarily endospores only...but akinets &amp;amp; spores produced by actinomycets&lt;/strong&gt;) are produced by simple &lt;a href=&quot;http://en.wikipedia.org/wiki/Mitosis&quot; rel=&quot;nofollow&quot;&gt;mitosis&lt;/a&gt;...so the genetic make-up stays the same as the parent cell.....so if  you were a spore-forming bacteria, the spore would be essentially you..in scientific jargon...your &quot;&lt;a href=&quot;http://en.wikipedia.org/wiki/Cloning&quot; rel=&quot;nofollow&quot;&gt;clone&lt;/a&gt;&quot;...&lt;/p&gt;&#xA;" OwnerUserId="10045" LastActivityDate="2015-06-04T13:45:43.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34924" PostTypeId="1" CreationDate="2015-06-04T14:36:15.423" Score="3" ViewCount="648" Body="&lt;p&gt;I'm doing old exam assignments to prepare for my finals on Monday and I've stumbled on one assignment that I'm not sure how to tackle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A family with 2 children is examined for cataracts using PCR with 4 markers, A, B, C and D. The results are seperated on a gel and the genotypes are as follow:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PNrAf.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where Far = father, Mor = mother, Barn = child.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notice that there was an error with the analysis so child 2's alleles are undetermined.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question states: Draw a pedigree with each of their haplotypes. What is the most likely haplotype of child 2?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't understand exactly what it's asking. I'm not sure what a HAPLOtype is. I know what a genotype is and that is what the answer seems to indicate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer for the father is: 4 3, 1 2, 11 5, 7 4. Now the only difference between these numbers and the given numbers are the re-arrangement of 5 and 11 in marker C?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="1590" LastEditDate="2016-01-02T09:37:32.213" LastActivityDate="2016-01-02T09:37:32.213" Title="Write the haplotypes of the family" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34925" PostTypeId="1" CreationDate="2015-06-04T16:32:03.733" Score="2" ViewCount="229" Body="&lt;p&gt;It is often claimed, in popular media, that the golden ratio (Fibonacci series) in for example some face measurements is aesthetically (and hence reproductively) attractive with respect to the humans. I wonder if this is particular for today's (maybe since 10,000's of years or so) human anatomy and aesthetics. As in an after-the-fact acquired taste which was culturally psychologically emerged from the actual human ratios of anatomy as it has happened to evolve for whatever practical reasons, way out of intuitive comprehension for human consciousness. Or if it is deeply biological and evolutionary across all lifeforms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the golden ratio as verifiable (if at all) also for the primates who came before us? Some examples are easy to find, but how statistically significant is the golden ratio as an advantage for sexual evolution for non-humans?&lt;/p&gt;&#xA;" OwnerUserId="8025" LastEditorUserId="8025" LastEditDate="2015-06-04T17:14:38.907" LastActivityDate="2015-06-04T20:51:03.470" Title="Is the golden ratio of anatomic measurements universally beneficial for sexual reproduction?" Tags="&lt;human-anatomy&gt;&lt;psychology&gt;&lt;sexual-selection&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2015-06-05T20:00:05.830" ContentLicense="CC BY-SA 3.0" />
  <row Id="34926" PostTypeId="2" ParentId="31222" CreationDate="2015-06-04T19:06:04.103" Score="-4" Body="&lt;p&gt;It is possible to insert a new gene in another organism. &lt;br&gt; &#xA;The technique is very new. I know I have done it at school where we had a colony of bacteria, and we did some things to them that some of those bacteria would 'adopt' a gene that would make them able to live on a different pertium dish. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are intrested in these subjects you should try to google on &quot;Genetically modified bacteria&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also here is a site that shows with a few images what technigue is actualy used: &lt;a href=&quot;http://www.abpischools.org.uk/page/modules/diabetes/diabetes6.cfm?coSiteNavigation_allTopic=1&quot; rel=&quot;nofollow&quot;&gt;Link&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit:&#xA;As for the cutting of the DNA, for some bacteria (like E-coli) there whole genetic structure is known. So there are markers available that cut the DNA of the bacteria right at a certain place. &lt;/p&gt;&#xA;" OwnerUserId="16093" LastActivityDate="2015-06-04T19:06:04.103" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34927" PostTypeId="1" AcceptedAnswerId="34928" CreationDate="2015-06-04T19:13:06.843" Score="5" ViewCount="1149" Body="&lt;p&gt;As a team of undergraduate researchers we are looking to transform two genes of interest into our competent E.coli cells. Both of these genes are in separate plasmids and we would like to put them into one E.coli cell. Is it possible for a cell to uptake two plasmids in one transformation process? If the last question is impossible, is it possible to transform a cell and then transform the colonies produced by that transformation? Thank you very much.&lt;/p&gt;&#xA;" OwnerUserId="15933" LastActivityDate="2015-06-05T12:44:15.353" Title="Transformation of E.coli cells" Tags="&lt;plasmids&gt;&lt;transformation&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34928" PostTypeId="2" ParentId="34927" CreationDate="2015-06-04T19:47:12.423" Score="5" Body="&lt;p&gt;Double transformation (you may want to try searches using that term) has been &lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00276222&quot;&gt;doable&lt;/a&gt; for a very long time, but the efficiency will of course be less than either single transformation below the saturation point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for your second question, if the cells are made competent, I think a sequential transformation should work.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2015-06-04T19:47:12.423" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34929" PostTypeId="2" ParentId="34925" CreationDate="2015-06-04T20:51:03.470" Score="4" Body="&lt;p&gt;I have some insight into this from an engineering perspective. Years ago, I worked on some computational and search algorithms which used a growth factor to determine how far to widen a search space, or how much more memory to allocate. For some of these algorithms, I ran a series of random trials to search for an optimal growth factor and found that for some, that optimal factor approached 1.618. Completely outside the realm of biology, this golden mean popped up as the most efficient growth factor for some of my algorithms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Over the years since then, I have recognized that this is an optimal factor for various engineering problems (although in practice I often find it more trouble than it's worth to explain to colleagues why they want to use it). So, I have gradually come to believe that this is why we see this ratio all over nature, in the way seashells grow, the proportions of various body parts, the arrangement of seed structures, etc. It appears that natural processes have ultimately led various lifeforms all over our world to tend toward this ratio to optimize their own functions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fact that we find this ratio &quot;beautiful&quot; is a far more fascinating study of what appears to be a meta-adaptation. Consider all of the various ways that the recognition of this ratio is important beyond just sexual reproduction. When we select our food, choosing vegetable or meat specimens which exhibit this ratio most perfectly is more likely to lead us to the healthiest food. Choosing to take shelter under the more &quot;beautiful&quot; tree may also be a good bet that it is the more stable, healthy tree. Making tools, clothing, or structures with this ratio may serendipitously lead us to better formed products. We don't have to find this ratio more beautiful to look at, but because we do, it leads us to better choices in a variety of odd ways. So, those of us whose brains appreciate these things thrive a little more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question was not about underlying causes, but about statistical prevalence. I don't know the answer to that. And I think it would be very difficult to obtain those numbers accurately for another loosely related reason. The human brain is very attuned to finding patterns, &lt;em&gt;and&lt;/em&gt; the human brain likes to find this ratio. Taken together, this presents a huge bias for any researcher trying to objectively measure the frequency of this ratio in nature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, once we understand that this ratio is the solution to a variety of engineering problems, it becomes clear that it is an indicator of optimization, or proximity to perfection. And even if we cannot say how many species are able to recognize, appreciate, and seek after this ratio, we can say that those who do will most likely find it a beneficial adaptation.&lt;/p&gt;&#xA;" OwnerUserId="5018" LastActivityDate="2015-06-04T20:51:03.470" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34930" PostTypeId="2" ParentId="34927" CreationDate="2015-06-04T21:57:24.407" Score="6" Body="&lt;p&gt;The two plasmids have to have &lt;em&gt;different&lt;/em&gt; origins of replication. Two plasmids from the same incompatibility group cannot survive together in the same cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This quote is from the &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Plasmid&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; entry on plasmids:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Plasmids can also be classified into incompatibility group. A microbe can harbour different types of plasmids, however, different plasmids can only exist in a single bacterial cell if they are compatible. If two plasmids are not compatible, one or the other will be rapidly lost from the cell. Different plasmids may therefore be assigned to different incompatibility group depending on whether they can coexist together. Incompatible plasmids normally share the same replication or partition mechanisms.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is a nice definition/explanation from an OpenAccess &lt;a href=&quot;http://www.researchgate.net/profile/Katie_Hopkins/publication/7805787_Identification_of_plasmids_by_PCR-based_replicon_typing/links/0deec51cbe6ee97be6000000.pdf&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A formal scheme of plasmid classification is based on incompatibility (Inc) groups (Novick, 1987). The procedure for incompatibility grouping is based on the introduction, by conjugation or transformation, of a plasmid of an &quot;unknown&quot; Inc group into a strain carrying a plasmid of a known Inc group. If the resident plasmid is eliminated in the progeny, the incoming plasmid is assigned to its same Inc group (Datta and Hedges, 1971). Plasmids with the same replication control are &quot;incompatible&quot;, whereas plasmids with different replication controls are &quot;compatible&quot;. On this basis two plasmids belonging to the same Inc group cannot be propagated in the same cell line (Datta and Hughes, 1983; Couturier et al., 1988). Inc group identification has been frequently used to classify plasmids. The method has been an important tool to trace the diffusion of plasmids conferring antimicrobial resistance and also to follow the evolution and spread of emerging plasmids (Anderson et al., 1977).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;http://www.einsten.net/pdf/3120251550.pdf&quot; rel=&quot;nofollow&quot;&gt;synopsis&lt;/a&gt; of the Datta &amp;amp; Hedges article sited above:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Classification&lt;/strong&gt;&#xA;  In 1971, Hedges and Datta proposed a plasmid classification scheme based on the stability of plasmids during conjugation (incompatibility). The first incompatibility (Inc) groups were IncI, IncN, IncF, and IncP. Currently, 26 Inc groups are recognized in Enterobacteriaceae including six IncF (FII to VII) and three IncI (I1, Iγ, I2) variants. Major plasmid families occurring in Enterobacteriaceae are HI2, HI1, I1-γ, X, L/M, N, FIA, FIB, FIC, W, Y, P, A/C, T, K, B/O, FII, FIII, FIV. IncF plasmids are low- copy-number plasmids, often carrying more than one replicon with at least one replicon strongly conserved.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;One way to think about it is: if one prepares a plasmid cloning vector to accept foreign inserts, and ligates in a &quot;shotgun&quot; collection of fragments from some DNA of interest. After transformation, selection and growth on plates, none of the colonies whose plasmids carry inserts &lt;strong&gt;&lt;em&gt;ever&lt;/em&gt;&lt;/strong&gt; contain more than one unique plasmid.  In other words, it may be possible for two different inserts to be inserted during ligation into the same vector backbone, but it is not possible to find a single pure colony that contains cells harbouring two different plasmids, each carrying a different insert. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a cell gets transformed by two different plasmids from the same &lt;em&gt;inc&lt;/em&gt; group only one plasmid will &quot;win.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples of compatible &lt;em&gt;ori&lt;/em&gt;'s commonly encountered:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;pMB9 (pBR322, pUC, etc., etc.,)&lt;/li&gt;&#xA;&lt;li&gt;F (fosmids)&lt;/li&gt;&#xA;&lt;li&gt;bacteriophage lambda (some cosmids)&lt;/li&gt;&#xA;&lt;li&gt;bacteriophage M13 and relatives (also yields ssDNA phage useful for Sanger sequencing)&lt;/li&gt;&#xA;&lt;li&gt;bacteriophage P1&lt;/li&gt;&#xA;&lt;li&gt;pSC101&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Here is a nice &lt;a href=&quot;http://blog.addgene.org/plasmid-101-origin-of-replication&quot; rel=&quot;nofollow&quot;&gt;table&lt;/a&gt;, but I cannot vouch for its accuracy.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="14946" LastEditDate="2015-06-05T12:44:15.353" LastActivityDate="2015-06-05T12:44:15.353" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34931" PostTypeId="1" AcceptedAnswerId="34960" CreationDate="2015-06-04T22:40:03.740" Score="7" ViewCount="1219" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;One of the problems that occur during (artificial) neural network training is called overfitting. The error on the training set is driven to a very small value, but when new data is presented to the network the error is large. The network has memorized the training examples, but it has not learned to generalize to new situations.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The human brain does not overfit when training at some task, but becomes better and better instead. Why? Or conversely, why do artificial neural networks overfit when are trained too much, in contrast with the human brain?&lt;/p&gt;&#xA;" OwnerUserId="1061" LastEditorUserId="16099" LastEditDate="2015-06-05T12:39:33.250" LastActivityDate="2016-03-24T13:04:43.640" Title="Why does the human brain not overfit when training at some task?" Tags="&lt;neuroscience&gt;" AnswerCount="3" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34932" PostTypeId="1" AcceptedAnswerId="34933" CreationDate="2015-06-05T00:27:44.980" Score="2" ViewCount="132" Body="&lt;p&gt;The context for this question can be found in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412442/&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; by Lara-Astiaso et al. Here, to study H3K4 trimethylation in various cell types, they &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;sort cells&lt;/li&gt;&#xA;&lt;li&gt;sonicate chromatin&lt;/li&gt;&#xA;&lt;li&gt;immobilize chromatin on Dynabeads with anti-H3 antibody&lt;/li&gt;&#xA;&lt;li&gt;index chromatin (barcode)&lt;/li&gt;&#xA;&lt;li&gt;pool samples&lt;/li&gt;&#xA;&lt;li&gt;perform H3K4me3 ChIP&lt;/li&gt;&#xA;&lt;li&gt;sequence&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I am interested in the purpose of step 3 and how that contributes to step 4. What could be the purpose of essentially adding another IP step?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Supplementary Materials (where all the methodology is described) mentions that &quot;magnet based bead capture was used to efficiently add, wash and remove the different master mixes used in the indexing process.&quot; I'm somewhat confused as to how this adds efficiency, as I thought barcoding prior to sequencing is typically performed as a ligation step without selection (they perform the H3K4me3 ChIP after the indexing step anyway, so why select for histone H3 chromatin first?).&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2017-01-25T06:54:36.840" Title="How is magnet based bead capture used for indexing-first ChIP-seq?" Tags="&lt;methods&gt;&lt;chip-seq&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34933" PostTypeId="2" ParentId="34932" CreationDate="2015-06-05T02:14:03.893" Score="1" Body="&lt;p&gt;The anti-H3 antibody will precipitate all chromatin. They could have used an antibody against any histone monomer; that they initially used anti-H3 and then later used anti-H3K4me3 is coincidental. The idea behind the first immunoprecipitation is to immobilize the chromatin on the beads to allow easy recovery of pure chromatin after each step of the indexing process. These steps are seen in the supplementary material (4. Chromatin Indexing). For example, after immobilization, they perform end repair using specific buffers and T4 polymerase and polynucleotide kinase. These enzymes must be removed and the buffer exchanged before the subsequent indexing. The beads facilitate this process. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-06-05T02:14:03.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34934" PostTypeId="1" CreationDate="2015-06-05T06:11:11.337" Score="6" ViewCount="102" Body="&lt;p&gt;I have morphometric measurements for a trait across various animal taxa, and would like to study the relationship between the size of this trait, and the animals' body size. In theory, I can account for the non-independence of the data with phylogenetic methods, such as independent contrasts. However, I have very different groups in my tree (for example insects and lizards), and even within more closely related groups, the structures are often not homologous. Does this present a problem for independent contrasts/phylogenetic least squares? For example, the structure is not homologous between ants and flies, yet every (sensible?) tree would treat a fly as more similar to an ant than to any lizard. Is this justified if structures are analogous? If not, are there any ways to deal with this problem?&lt;/p&gt;&#xA;" OwnerUserId="15247" LastActivityDate="2015-06-05T14:52:24.693" Title="Independent contrasts with non-homologous traits" Tags="&lt;evolution&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34935" PostTypeId="1" AcceptedAnswerId="34936" CreationDate="2015-06-05T06:28:48.503" Score="3" ViewCount="817" Body="&lt;p&gt;In a recent TV documentary it was said that a particular tree root could grow miles long. However, I forgot the name of the tree and I don't remember the name of the TV program as well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I searched on the internet but I could not get it. Does any one know about this tree and how tall its roots can grow? &lt;/p&gt;&#xA;" OwnerUserId="16098" LastEditorUserId="9943" LastEditDate="2015-06-05T11:29:26.693" LastActivityDate="2015-06-05T11:29:26.693" Title="Which tree's root can grow the longest?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34936" PostTypeId="2" ParentId="34935" CreationDate="2015-06-05T08:14:16.610" Score="6" Body="&lt;p&gt;Was it &lt;a href=&quot;http://en.wikipedia.org/wiki/Pando_%28tree%29&quot;&gt;Pando&lt;/a&gt;? Pando is a single, massive 80,000 year old &lt;a href=&quot;http://en.wikipedia.org/wiki/Populus_tremuloides&quot;&gt;&lt;em&gt;Populus tremuloides&lt;/em&gt;&lt;/a&gt; (quaking aspen) individual, that is assumed to have a single, massive root system covering 106 acres.&lt;/p&gt;&#xA;" OwnerUserId="87" LastActivityDate="2015-06-05T08:14:16.610" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34937" PostTypeId="2" ParentId="30274" CreationDate="2015-06-05T08:35:12.980" Score="0" Body="&lt;p&gt;I'd guess that this varies quite a lot among different insects; in some, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1691077/&quot; rel=&quot;nofollow&quot;&gt;lying on their backs was a sign of their impending death&lt;/a&gt;, while others &lt;a href=&quot;https://www.butterflies.org/blue-death-feigning-beetle&quot; rel=&quot;nofollow&quot;&gt;will flip over onto their backs to play dead&lt;/a&gt;. This isn't really surprising --- there's over a million described insect species, so some amount of variety is to be expected! Here's a &lt;a href=&quot;https://www.youtube.com/watch?v=nPa-lWvU19g&quot; rel=&quot;nofollow&quot;&gt;video of a bunch of insects exhibiting different strategies for turning themselves over&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="87" LastActivityDate="2015-06-05T08:35:12.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34938" PostTypeId="2" ParentId="34660" CreationDate="2015-06-05T08:56:52.933" Score="1" Body="&lt;p&gt;The Eliava Institute in Tiflis (Georgia (a country)) has been at it since the 1930`s. A US company sells a phageproduct for desinfection of meat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The risk of Phagetherapy is there, if the phage is ill choosen or contaminated with other phage it could introduce pathogenic genes to the target or other bacteria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If those risks are eliminated there is very little risk in phage therapy aside from the fact that it may not work at all. Phagetherapy is most useful in regions where bacteria are normally found, in other places the immunesystem will make short work of it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The faster and cheaper sequencing gets the more effective phagetherapy will become. Since a &quot;bad&quot; bacteria can quickly be isolated and a proper &quot;phage cocktail&quot; can be prepared. If we get to the point that we can sequence the whole microbiom of a person then i bet that Phagetherapy will be a very normal thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To your cancer question, i think its rather hard to apply it to cancer therapy except if u are looking to combat the cancer with a Intracellular bacteria...but then again. How u get the phage to it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A excellent read on this topic is the Book &quot;the bacteriophages&quot;.&lt;/p&gt;&#xA;" OwnerUserId="6054" LastActivityDate="2015-06-05T08:56:52.933" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34939" PostTypeId="2" ParentId="34881" CreationDate="2015-06-05T11:53:45.853" Score="2" Body="&lt;p&gt;Yes, one sample can contain different alterations. For each patient there is typically one tumour specimen that is removed. That specimen may be divided up into several samples (e.g. one for DNA sequencing, one for RNA sequencing, one for methylation microarray, and one for copy-number variation microarray), however each sample contains thousands of individual cells and two adjacent cells may have different CNVs (depending on their clonal ancestry, etc.). In other words, a tumour is a heterogeneous collection of cells. For some tumour types there can even be healthy cells mixed in.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The term in the literature is &lt;em&gt;clonal evolution&lt;/em&gt;, there is a nice image in this article: &lt;a href=&quot;http://en.m.wikipedia.org/wiki/Tumour_heterogeneity&quot; rel=&quot;nofollow&quot;&gt;Tumor Heterogeneity&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-06-05T11:53:45.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34940" PostTypeId="1" AcceptedAnswerId="34947" CreationDate="2015-06-05T12:41:40.543" Score="4" ViewCount="3335" Body="&lt;p&gt;I have a city garden (see picture below) and yesterday I was nurturing it and I pulled up a small plant. I saw its root system and laid it in the sun to dry a bit and then scraped of the rest of the earth from it. That gave me a better look at the roots. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then the question appeared to me. How do roots obtain water and nutrition from their environment. I mean what structures are we dealing with and how does the uptake take place? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/godoC.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user14636" LastEditorUserId="4101" LastEditDate="2015-06-05T13:10:49.200" LastActivityDate="2016-05-09T17:00:07.903" Title="How do roots obtain nutrition?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;nutrition&gt;&lt;plant-anatomy&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34941" PostTypeId="1" AcceptedAnswerId="34944" CreationDate="2015-06-05T13:48:13.797" Score="3" ViewCount="81" Body="&lt;p&gt;1/330 of white people in south Africa have a disease called Porphyri.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the frequency of the gene if it is inherited autosomal recessive?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This one I understand. The genotype frequency is $q^2 = 1/300$ so the gene frequency has to be $\sqrt{1/300}$ as it is inherited aa.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the frequency of the gene if it is inherited autosomal dominant?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's where I run into trouble. So if $p$ is the dominant allele and $q$ is the recessive allele the allele frequency has to be $2pq+p^2$ right? As we can either see them as $Aa$ or $AA$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But my book says it is $2pq+q^2$ and then solves it algebraically by pretending $q^2$ is so close to 0 that it's not in the calculations. I strongly disagree that $p^2$ is very small if I am right with my assumption. Which one is right and why?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="1590" LastEditDate="2015-06-06T13:33:21.853" LastActivityDate="2015-06-06T13:33:21.853" Title="Gene frequency problem" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34942" PostTypeId="2" ParentId="7074" CreationDate="2015-06-05T14:48:30.257" Score="2" Body="&lt;p&gt;It could be &lt;a href=&quot;http://www.vision-and-eye-health.com/vitreous-detachment.html&quot; rel=&quot;nofollow&quot;&gt;posterior detachment of the vitreous humor&lt;/a&gt;. Stress on the optic nerve caused by motion of the vitreous humor inside the eye can lead to the sensation of lights. And since the nerve is circular, you see a pattern of circular light. Normally its not serious, and many people experience it as age progresses. If you are not hydrating well during your climbing that might also be aggravating it. To be safe you should have an eye doc check you out though since there is slight risk it could lead to retinal detachment.&lt;/p&gt;&#xA;" OwnerUserId="9906" LastActivityDate="2015-06-05T14:48:30.257" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34943" PostTypeId="2" ParentId="34934" CreationDate="2015-06-05T14:52:24.693" Score="2" Body="&lt;p&gt;When you calculate the PICs of a trait, you are making a statement about how that trait evolved. The purpose of PICs is to account for phylogenetic non-independence. However, when you are comparing two analogous traits, those two traits are in fact phylogenetically independent of each other; they do not share a common origin. Thus, I think it would be an error to perform PICs on analogous traits because those traits do not share an evolutionary origin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How to deal with this problem would depend on the specific question you are asking. One thing to do would be to perform PICs on each trait independently on just the portion of the tree that that trait occurs so you are not comparing analogous traits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You've probably already read this, but I recommend that anyone who hasn't check out &lt;a href=&quot;http://www.jstor.org/stable/2461605&quot; rel=&quot;nofollow&quot;&gt;Felsenstein's 1985&lt;/a&gt; paper describing the PIC method.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-06-05T14:52:24.693" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34944" PostTypeId="2" ParentId="34941" CreationDate="2015-06-05T14:53:03.613" Score="2" Body="&lt;p&gt;I think you pretty much nailed the problem. If I understand correctly, you are just confused about the approximation that your textbook does, an approximation that is correct but not needed. Let me restate the solution to the problem first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Resolution of the problem&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you said the frequency of sick people $\frac{1}{300} = 2pq + q^2$ in this case, where $q = 1-p$ is the frequency of the (dominant) allele causing the disease. It is a simple quadratic equation with one unknown so one doesn't even need to make any approximation to solve for $q$ (or for $p$). Rearranging the equation and expressing $p$ in terms of $q$ (p=1-q), you'll find that $q ≈ 0.00167$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are the results intuitive?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the frequency needed to create a frequency of $\frac{1}{300}$ sick individuals is $\sqrt{\frac{1}{300}} ≈ 0.05$ if the allele causing the disease is recessive while it is only about $0.0016$ (31 times less frequent) if the allele causing the disease is dominant. It shows that indeed a lower frequency of a more dominant allele is enough to create more sick people.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is the $q^2$ term negligible?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that $q ≈ 0.00167$, the term $q^2 ≈ 10^{-6}$, while the term $2pq ≈ 10^{-3}$. So, indeed the term $q^2$ is rather negligible compared to $2pq$. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-06-05T21:40:56.333" LastActivityDate="2015-06-05T21:40:56.333" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34945" PostTypeId="1" AcceptedAnswerId="34949" CreationDate="2015-06-05T14:53:48.767" Score="3" ViewCount="129" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Three polymorph microsatellite markers are used to try and narrow down the location of a disease locus, with the use of PCR with 2&#xA;  flanks on each side of the actual polymorphic area. The PCR product is&#xA;  then put on gel.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I need help understanding exactly what is going on here. I understand polymorph as &quot;two or more phenotypes in the same population&quot; as by wikipedia. I don't understand what they mean here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is the PCR different with 2 flanks from a normal PCR?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do understand how the gel works.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="24354" LastEditDate="2020-07-16T19:35:53.637" LastActivityDate="2020-07-16T19:35:53.637" Title="Walk me through microsatellite markers and PCR" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;molecular-biology&gt;&lt;dna&gt;&lt;pcr&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34946" PostTypeId="1" CreationDate="2015-06-05T15:38:51.363" Score="5" ViewCount="20454" Body="&lt;p&gt;I am confused with this element or nutrient classification in the plants, since some authors set elements like $\ce{S}$ and $\ce{Ni}$ as mobile and other as immobile elements (&lt;a href=&quot;http://www.gettextbooks.com/isbn/9780824759049&quot; rel=&quot;nofollow&quot;&gt;Citation 1&lt;/a&gt;, &lt;a href=&quot;http://msue.anr.msu.edu/news/knowing_nutrient_mobility_is_helpful_in_diagnosing_plant_nutrient_deficienc&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;, &lt;a href=&quot;http://broome.soil.ncsu.edu/ssc012/Lecture/topic17.html&quot; rel=&quot;nofollow&quot;&gt;3&lt;/a&gt;, &lt;a href=&quot;http://lee.ifas.ufl.edu/Hort/Videos_and_Powerpoints/Presentation2013.pdf&quot; rel=&quot;nofollow&quot;&gt;4&lt;/a&gt;, &lt;a href=&quot;http://nrcca.cals.cornell.edu/soilFertilityCA/CA1/CA1_print.html&quot; rel=&quot;nofollow&quot;&gt;5&lt;/a&gt;). Then, I would like to know if there is a fixed and official classification.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found a classification only for those elements:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mobile: $\ce{N}$, $\ce{Mg}$, $\ce{P}$, $\ce{S}$, $\ce{K}$, $\ce{Ni}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Immobile: $\ce{B}$, $\ce{Ca}$, $\ce{Mn}$, $\ce{Fe}$, $\ce{Co}$, $\ce{Cu}$, $\ce{Zn}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And what about the rest of elements like $\ce{Sr}$, $\ce{Mo}$, $\ce{Ba}$, $\ce{Pb}$, etc?&lt;/p&gt;&#xA;" OwnerUserId="16101" LastEditorUserId="9829" LastEditDate="2015-06-05T21:56:46.170" LastActivityDate="2019-08-05T04:06:33.930" Title="Which are mobile and immobile elements in plants?" Tags="&lt;biochemistry&gt;&lt;plant-physiology&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34947" PostTypeId="2" ParentId="34940" CreationDate="2015-06-05T16:32:14.057" Score="7" Body="&lt;p&gt;One thing to remember when you uproot a plant is that some of the smallest structures break off most readily. What you will usually see after uprooting the plant are the largest parts of the root structure, but there are often smaller parts which have broken off.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Root structure is highly variable, but the general idea is that one or more primary trunk-like roots strike out toward the most important water sources, and from those primary roots, smaller roots branch out to more broadly extend the reach of the root system. Depending on the size of the plant, there may be several levels of branching, just like you might find in the top of the plant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally, the nutrients that the roots need to absorb come to the plant with the water. They become dissolved in the water and the roots receive them along with the water. Dirt is chunky, not usually homogenous. So there may be more of the nutrients a plant needs in one area than another, or water may flow more easily through one area than another. The roots are able to grow in the direction of what they need, which is why you will occasionally find strong roots actually breaking into plumbing to get at your water. Mostly, it is water that they seek out, because the nutrients are dissolved in the water, but the plant may also show preference for a more nutrient rich stream over a larger, cleaner water source. The roots seek out what the plants need over the long term as they grow in one direction or another. For many plants, by the way, this means a simple strategy of simply growing straight down (a tap root), because that's almost always where they find more water with more of the right stuff dissolved into it. This is similar to the fact that many plants grow as tall as they can because that's where they will find the most sunlight, though the general idea is to grow leaves wherever that light might be captured.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wherever the primary roots land themselves, the smaller root branches extend into the space to absorb as much as they can. They have to be greedy, because there may be days or even weeks when the ground gets very dry, so they have to get while the getting is good. If one of these smaller branches finds itself in a particularly sweet spot, the plant grows that branch more than its neighbors, which is part of how it places its largest root branches in the best spots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another very interesting part of the story of how the plant covers the maximum area of soil is symbiosis. I recommend further research into &lt;a href=&quot;http://en.wikipedia.org/wiki/Mycorrhiza&quot;&gt;mycorrhizae&lt;/a&gt;, especially if you are a gardener. It's absolutely fascinating, and an important part of the story of how plants absorb nutrients and water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know less about the microscopic porous cellular structure of the roots. They essentially serve the same purpose as our stomachs and there are some loose similarities to be drawn, but of course, plant tissues, made of plant cells, which have a &lt;a href=&quot;http://en.wikipedia.org/wiki/Cell_wall&quot;&gt;cell wall&lt;/a&gt; are very different from animal tissues.&lt;/p&gt;&#xA;" OwnerUserId="5018" LastEditorUserId="5018" LastEditDate="2015-06-05T16:39:18.600" LastActivityDate="2015-06-05T16:39:18.600" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34948" PostTypeId="2" ParentId="28539" CreationDate="2015-06-05T16:34:53.697" Score="5" Body="&lt;p&gt;The radius of tree is not a good measure of the tree age, the most efficient technique to know the age of a tree is with dendrochronological methods, this is the less invasive technique. However, knowing very well the dynamics of growth of each species you can infer the age, check out this study: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.google.com/url?sa=t&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=web&amp;amp;cd=3&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CCYQFjAC&amp;amp;url=http%3A%2F%2Fauf.isa-arbor.com%2Frequest.asp%3FJournalID%3D1%26ArticleID%3D3041%26Type%3D2&amp;amp;ei=IM5xVe6xB6_isAT134GYBg&amp;amp;usg=AFQjCNGwj4FfRxQodFMHBzKbfTRYE_qsrg&amp;amp;sig2=-dkAUsfwILy-92ywHgVIEQ&amp;amp;bvm=bv.95039771,d.cWc&quot; rel=&quot;noreferrer&quot;&gt;Jan Lukaszkiewicz and Marek Kosmala. 2008. Determining the Age of Streetside Trees with Diameter at Breast Height-based Multifactorial Model&lt;/a&gt; (note this is a direct link to a pdf)&lt;/p&gt;&#xA;" OwnerUserId="16101" LastEditorUserId="3059" LastEditDate="2015-06-05T17:36:28.220" LastActivityDate="2015-06-05T17:36:28.220" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34949" PostTypeId="2" ParentId="34945" CreationDate="2015-06-05T17:22:03.743" Score="5" Body="&lt;p&gt;It's actually very simple. You misunderstood the term polymorph in this situation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A &lt;a href=&quot;http://en.wikipedia.org/wiki/Microsatellite&quot; rel=&quot;nofollow&quot;&gt;microsatellite&lt;/a&gt; is a sequence composed of a short &lt;strong&gt;repeated&lt;/strong&gt; DNA motif. A polymorph satellite is then simply a microsatellite varying in length between individuals, i.e. composed of more or less repeats of the motif.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The flanks of the microsatellite are the DNA sequences targeted by the primers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In essence, using two primers flanking the microsatellite you will amplify this specific DNA region and because it varies in length between individuals you can detect that by simple gel electrophoresis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: Microsatellites can also change in sequence (also called polymorphic regions) as they are prone to a high-mutation rate but in this case you would need to sequence it to know how the sequence differs between individuals.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-06-05T17:35:37.663" LastActivityDate="2015-06-05T17:35:37.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34950" PostTypeId="2" ParentId="34476" CreationDate="2015-06-05T23:54:03.610" Score="1" Body="&lt;p&gt;Neural regeneration is addressed broadly in this chapter from a book published in 2013 (though I would say for a topic such as this, you're probably going to want to read primary literature or recent, less comprehensive reviews in addition to any book chapters published in the few years):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/chapter/10.1007%2F82_2012_302&quot; rel=&quot;nofollow&quot;&gt;Neural Regeneration&lt;/a&gt; by Melissa M. Steward, Akshayalakshmi Sridhar, Jason S. Meyer, published in New Perspectives in Regeneration.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The chapter includes two sections on stem cell therapy and one section on reprogramming of somatic cells to neural lineages.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2015-06-05T23:54:03.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34951" PostTypeId="1" AcceptedAnswerId="34955" CreationDate="2015-06-06T08:47:17.117" Score="0" ViewCount="40" Body="&lt;p&gt;I do not understand this sentence&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Angina can be treated ambulatory (in out-patient) in stable angina. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think ambulatory refers to ambulatory ECG monitoring. &#xA;So I understand this that you can treat stable angina based on ambulatory ECG. &#xA;How do you understand this sentence about &quot;ambulatory&quot; angina? &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="5755" LastEditDate="2015-06-06T12:41:20.367" LastActivityDate="2015-06-06T12:41:20.367" Title="What does this sentence about angina mean?" Tags="&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34952" PostTypeId="2" ParentId="31094" CreationDate="2015-06-06T09:22:48.113" Score="0" Body="&lt;p&gt;In short, electrostatic forces and mechanical forces. Electrostatic forces are responsible for the classic Watson and Crick base pairing that is de facto  what brings together codons and anticodons. Mechanical forces are involved in the displacement of the pairing and the shift of the RNAs. The ribosome's subunits literally grab and move both messenger and tRNAs.&lt;/p&gt;&#xA;" OwnerUserId="12923" LastActivityDate="2015-06-06T09:22:48.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34953" PostTypeId="1" AcceptedAnswerId="34956" CreationDate="2015-06-06T09:33:35.143" Score="4" ViewCount="431" Body="&lt;p&gt;I'm not a biology person so please forgive me if this question is formulated badly :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm curious. Are there any species that has an ancestor species that is still alive today?&lt;/p&gt;&#xA;" OwnerUserId="16104" LastActivityDate="2017-10-24T00:04:56.667" Title="Are there examples of now-living species where one is descended from the other?" Tags="&lt;evolution&gt;&lt;species&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34954" PostTypeId="2" ParentId="7596" CreationDate="2015-06-06T10:29:41.383" Score="-1" Body="&lt;p&gt;In any PCR reaction ( including  the assembly PCR ) the substrate of the reaction is a mix of mono nucleotides. Specific oligos serve as primer by annealing on the template and that are extended by a DNA polymerase. It is a polymerization reaction.&#xA;In the LCR there are no mono nucleotides instead you have many different oligos that anneal one after the other on the template and a DNA ligase is used to join them together to form a longer DNA molecule. It is a ligation reaction.&#xA;This two reactions have much in common. Firstly, they rely on the annealing of oligos on a template. Secondly, both the polymerase and the ligase need to be thermostable. In fact, both reactions leverage the thermostability of the enzymes to carry on cycles of annealing, reaction (polymerization or ligation) and melting. After each cycle the template DNA is copied so you end up with an exponential amplification of your template with both techniques.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.slideshare.net/SHBZaidi/ligase-chain-reactionlcr&quot; rel=&quot;nofollow&quot;&gt;Here&lt;/a&gt; a nice presentation that showing these concepts with some graphics.&lt;/p&gt;&#xA;" OwnerUserId="12923" LastActivityDate="2015-06-06T10:29:41.383" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34955" PostTypeId="2" ParentId="34951" CreationDate="2015-06-06T11:59:33.300" Score="1" Body="&lt;p&gt;Ambulatory means there is no emergency and refers to where the patient is and not to the disease itself (here the patient is out of hospital): for example there is no need to perform urgent PTCA or other procedures related to unstable CAD (coronary artery disease).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another option is - to hospitalize the patient to perform urgent or planned procedures if the patient is unstable and there is deterioration in his/her status which may worsen and threaten the life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key word in this sentence &quot;&lt;strong&gt;stable&lt;/strong&gt;&quot;.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-06-06T12:36:32.437" LastActivityDate="2015-06-06T12:36:32.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34956" PostTypeId="2" ParentId="34953" CreationDate="2015-06-06T13:42:30.780" Score="4" Body="&lt;p&gt;First, you probably want to have a look at &lt;a href=&quot;https://biology.stackexchange.com/questions/52700/why-do-the-ancestors-of-birds-still-exist/52729#52729&quot;&gt;this answer who offers an introduction to phylogeny&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are few subjects that yield to as many semantic issues than the definition of species and the definition of life. Your question is at the border of the species definition. Therefore the question is not so much about Biology than about Philosophy, so let me advertise: The following answer is nothing else than a semantic discussion (philosophy) and has no relevance of our understanding of evolutionary processes. Note however that semantic discussions might be very helpful to evolutionary biologists as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sexual organisms&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Dogs and wolves&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Commonly, in sexual organisms, species are defined by the concept of reproductive isolation. To address @WYSIWYG's comment, wolves can breed with dog. The offspring is called a &lt;a href=&quot;http://en.wikipedia.org/wiki/Wolfdog&quot; rel=&quot;nofollow noreferrer&quot;&gt;wolfdog&lt;/a&gt; and it suffers from little inbreeding depression.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Is the MRCA contained in the species of one descendent&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I'll use the wolf example anyway and make some fake assumptions. There are probably better examples I could pick though. Let's assume that wolves and dogs can't interbreed, that they are therefore separate species. Let's assume as well that somehow we manage to recreate the Most Recent Common Ancestor (MRCA) of wolves and dogs (which has some issue due to parental effect incl. culture and epigenetic) and this MRCA can breed with wolves and but not with dogs, then we could eventually say that the MRCA and the current wolf (there are actually 3 species of wolves that are probably not real species) are the same species. One could then say that dogs descend from the wolf.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Feeling that we talk about improvement over another species&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that much of the issue in saying that the dog descend from the wolf is that some people would understand things like &quot;dog is more evolved than the wolf&quot;, which makes no sense. Both the current wolf and the current dog has evolved for exactly the same amount of time. Any living species on earth has evolved for exactly the same amount of time (&lt;a href=&quot;http://en.wikipedia.org/wiki/Abiogenesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;almost 4 billion years&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Temporal constraint in the definition of species&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, it is eventually possible to say that one node on a phylogenetic tree is of the same species that the previous and the next node. I think that in reaction to the misleading feeling that early evolutionary biologists and current non-biologists people have in hearing that one species descent from another one, we tend to make a temporal constraint to the species. A species is what it is only at the exact moment we talk about it. This prevents us to consider a MRCA as being of the same species of any descendent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the definition of species yield to various issues such as the case of &lt;a href=&quot;https://biology.stackexchange.com/questions/11240/transitivity-of-species-definitions/11243#11243&quot;&gt;ring species&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Asexual organisms&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Same issue as above&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, if we talk about asexual species. There is no clear definition of what is a species there. Of course if we were to use the definition based on reproductive isolation, then any asexual individual would be a new species. We therefore define a species when we see a group of phylogenetically related individuals that all share some feature that we find &quot;interesting enough&quot; (very arbitrary) to describe this group as a different species from the some other group of individuals. In asexuals, you may see one lineage that accumulate 10 mutations, while the other lineage accumulates 1000 mutations (this other lineage may eventually live in a different environment than the MRCA of the two lineages). Therefore, you get to the same issue when thinking about asexuals than about sexual organisms. If one lineage ressemble more their MRCA than the other lineage, then is their MRCA part of the species of one lineage?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is a species a thing?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well... the concept of species is useful in the sense that it is often not ambiguous to classify one individual into one species or into another. The concept of species allows us to better communicate.. so yes I guess it is useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concept of species existed way before we had any understanding of natural selection, mutations, genetic drift and other basic concepts in evolutionary biology. Aristotle used the concept of species (he also thought without having any good evidence that life evolves). This concept of species has been very well conserved because of the static view we had on what a species is before Darwin. Now that we have a better understanding of evolutionary biology, ecology and reproductive biology we discover that the concept of species is not a &lt;a href=&quot;http://en.wikipedia.org/wiki/Prototype_theory&quot; rel=&quot;nofollow noreferrer&quot;&gt;natural category&lt;/a&gt; but is a man-made unclear category.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other discussion on the subject&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/11240/transitivity-of-species-definitions/11243#11243&quot;&gt;In this post&lt;/a&gt; I made an overview of the issue related to the concept of species. I did not go into the details but tried to list important concepts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will find many websites that address the concept of species in philosophy. I particularly like discussion in the concern of how current bad semantic may yield to bias in the way we think nature and may yield to bad decision in applied science. &lt;a href=&quot;http://www.unil.ch/gse/fr/home/menuinst/la-faculte/seminaire-interfacultaire/archives/la-biodiversite/programme-2013/pierre-henri-gouyon.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here is a podcast&lt;/a&gt; (in french) on the origin and consequences of the concept of species.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2017-10-24T00:04:56.667" LastActivityDate="2017-10-24T00:04:56.667" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="34958" PostTypeId="1" CreationDate="2015-06-06T14:36:42.443" Score="1" ViewCount="314" Body="&lt;p&gt;How do delete a single gene encoded in an operon on a plasmid using E. coli? Could you use the same principle as when knocking out a gene from the bacterial chromosome which is e.g. suicide vector-derived allelic replacement through homologous recombination? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your response.&lt;/p&gt;&#xA;" OwnerUserId="16106" LastActivityDate="2015-07-06T16:56:46.340" Title="Plasmid gene knockout" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34959" PostTypeId="1" AcceptedAnswerId="34961" CreationDate="2015-06-06T14:44:15.143" Score="-1" ViewCount="841" Body="&lt;p&gt;Please observe the following pedigree and come up with a conclusion as to which type of inheritance is most likely&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/e6zDD.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now it should be obvious that it's either autosomal dominant or autosomal recessive. BUT it could also be X-recessive if the women I2 and II5 are carriers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyways, if it's autosomal dominant than about 50% of children should be sick according to a punnet square.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If autosomal recessive about 25% should be sick according to the same logic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;33% of children are sick so what do you answer? My book states a very clear and only answer without explaining how it could be other forms too, autosomal dominant. Why not autosomal recessive just as likely?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="6576" LastEditDate="2015-06-06T17:38:17.467" LastActivityDate="2015-06-06T17:38:17.467" Title="Pedigree problem and type of inheritance" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2015-06-07T13:56:20.780" ContentLicense="CC BY-SA 3.0" />
  <row Id="34960" PostTypeId="2" ParentId="34931" CreationDate="2015-06-06T14:49:09.590" Score="13" Body="&lt;p&gt;I would say the human brain overfits all the time! Gambling addiction,  superstition and anxiety disorders are all examples of overfitting. We are optimized for seeking patterns and avoiding threats. Our brains mess this up all the time! But having said that, one of the major differences between the human brain and a neural network is the amount of information that's being supplied. Neural networks overfit in part because of limited data sets. Our brains have nearly unlimited data sets available, and this provides us at least the opportunity for some self correction.&lt;/p&gt;&#xA;" OwnerUserId="15966" LastActivityDate="2015-06-06T14:49:09.590" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="34961" PostTypeId="2" ParentId="34959" CreationDate="2015-06-06T15:35:16.077" Score="3" Body="&lt;p&gt;Let's consider all the options.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;X-linked recessive:&#xA;I:2 is a carrier and II:5 is also a carrier, and I:1 is affected. Everyone who marries into this family(except for II:2, lucky guy. He better not have any sons though.) is a carrier for the same genetic disorder. While it does work, it's vastly less &lt;em&gt;likely&lt;/em&gt; than the other options. Observe: II:4 is affected, but only because I:2 is a carrier. I:1 is entirely irrelevant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Autosomal recessive:&#xA;I:2 and II:5 are still required to carry the same genetic disorder, but at least I:1 contributes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Autosomal dominant: The only individual required to have the disease genotype is the affected I:1 individual, and everyone else inherits from him.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem asks which inheritance pattern is most likely and not which inheritance pattern is possible because of cases like this. Most genetic disorders are rare, and it's far more likely that random chance had 25% instead of 50% of four children affected than this small family inherited two sources of this genetic illness.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-06-06T15:35:16.077" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34962" PostTypeId="1" CreationDate="2015-06-06T15:57:06.207" Score="1" ViewCount="230" Body="&lt;p&gt;I want to conduct some research on red and white muscle fibers, why do some people tire during certain movements while others do not. Obviously I can't get a biopsy on the subjects so I wanted to hear if anyone here maybe had a suggestion to a reliable method to test for amount of red vs. white muscle fibers?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Maybe some strength measurements, endurance tests etc. I'm looking for something that is documented to work.&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-06-06T16:35:56.657" Title="Is there a way to examine amount of red/white muscle fibers without biopsy?" Tags="&lt;human-biology&gt;&lt;muscles&gt;&lt;measurement&gt;&lt;research-tools&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34963" PostTypeId="2" ParentId="34962" CreationDate="2015-06-06T16:23:40.617" Score="2" Body="&lt;p&gt;Indeed, a paper was published in 2011 regarding the same for humans by using a magnetic resonance spectroscopy to measure carnosine content.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;A significant positive correlation was found between muscle carnosine, measured by 1H-MRS, and percentage area occupied by type II fibers. Explosive athletes had ∼30% higher carnosine levels compared to a reference population, whereas it was ∼20% lower than normal in typical endurance athletes.&lt;/p&gt;&#xA;&lt;p&gt;Muscle carnosine content shows a good reflection of the disciplines of elite track-and-field athletes and is able to distinguish between individual track running distances. The differences between endurance and sprint muscle types is also observed in young talents and former athletes, suggesting this characteristic is genetically determined and can be applied in early talent identification. This quick method provides a valid alternative for the muscle biopsy method. In addition, this technique may also contribute to the diagnosis and monitoring of many conditions and diseases that are characterized by an altered muscle fiber type composition.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021956&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Baguet, Audrey, et al. &amp;quot;A new method for non-invasive estimation of human muscle fiber type composition.&amp;quot; PLoS One 6.7 (2011): e21956.&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-06T16:35:56.657" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="34964" PostTypeId="1" AcceptedAnswerId="34967" CreationDate="2015-06-06T16:53:40.983" Score="7" ViewCount="341" Body="&lt;p&gt;I had a conversation with a family member who is a bio-computer-scientist and he talked to me about what his colleagues (biologist) are doing and I feel confused about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They work in Chile and are studying plants that live in the desert.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I understand correctly his team is trying to explore the idea that some viruses might actually be good for the plants they are infecting and might have been &quot;selected&quot; and are now &quot;part&quot; of the species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The way I understand it is that they collect samples of plants and somehow by analyzing their DNA notice that these plants are all infected by some kind of virus and they tell themselves that maybe if all the plants have the virus it's because it's good for the plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My questions are: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Does any of this make sense?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) If it does how would the selection process happen ? Combining my (old) high-school knowledge and Wikipedia I see a virus as a piece of DNA that goes into a cell and then uses the cell's tools for it's own purpose, but it is not part of DNA. So how can it be treated as part of the plant ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) Do you know any good references (preferably for an enthusiast layman) about this subject (i.e. the potential good of some viruses and maybe potential applications in bio-engineering) ? I find especially fascinating the idea that maybe evolution isn't just the result of mutations but also of &quot;contamination&quot;.&lt;/p&gt;&#xA;" OwnerUserId="16109" LastEditorUserId="6194" LastEditDate="2019-10-03T12:59:54.863" LastActivityDate="2019-10-03T12:59:54.863" Title="Viruses selected by evolution" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;ecology&gt;&lt;virology&gt;&lt;host-pathogen-interaction&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="34965" PostTypeId="2" ParentId="34958" CreationDate="2015-06-06T16:55:55.123" Score="1" Body="&lt;p&gt;Well the simplest way is to cut the gene at the both ends from operon by means of proper restriction enzymes but in case that you get more than one recognition site then you can use microRNA or proper oligo to make a hairpin loop and break that part &#xA;If you only want to silence the operon then you just need to cut it nearly at middle of the gene and ligate it with a nonsense sequence, then it will loose it's functionality.&lt;/p&gt;&#xA;" OwnerUserId="16108" LastActivityDate="2015-06-06T16:55:55.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34966" PostTypeId="1" AcceptedAnswerId="34971" CreationDate="2015-06-06T17:37:14.133" Score="0" ViewCount="115" Body="&lt;p&gt;Please observe the following pedigree of a family with a x-recessive disease (bleeder disease).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mPNLR.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The A's are genetic markers so close to the disease gene that recombination is negligible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand it like this: They place markers that cut the DNA at the locus of the diseased gene. If you have the disease, your gene snip will be different in size than someone who does NOT have the disease and this will be visible on a gel.&#xA;So if A1 is the disease marker, how come II:1 is not affected? He only has 1 X-chromosome and has the A1 marker?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: Another problem:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5zY1u.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the coming child affected? Here I don't understand how the mother A1,A1 is NOT affected when the child A1 is?! Obviously A1 is the diseased marker and the mother has two of them...So she should be sick? Unless it's spontaneous?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Am I misunderstanding something fundamentally?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="6576" LastEditDate="2015-06-06T17:46:24.900" LastActivityDate="2015-06-06T19:17:26.480" Title="X-recessive disorders and genetic markers" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;&lt;dna-sequencing&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34967" PostTypeId="2" ParentId="34964" CreationDate="2015-06-06T18:10:07.790" Score="8" Body="&lt;p&gt;Welcome to Biology.SE!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;About your title&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me first react to your title: &lt;code&gt;Viruses selected by evolution&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution is any process of genetic (and eventually phenotypic) change in a population through time. Selection (Natural Selection for example) is one of such process. Genetic drift is another such process. So, evolution doesn't select viruses unlike your title suggests. Viruses are selected and therefore evolution occurs. When saying &quot;viruses are selected&quot;, it means some viruses have a higher fitness (fitness is a function of both survival and reproductive success) than others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Species interactions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Generalities&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Species interact. Species actually interact a lot. One can classify species interactions into categories. Here is a table of possible biological interactions (comes from &lt;a href=&quot;http://en.wikipedia.org/wiki/Biological_interaction&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki&lt;/a&gt;), where a &lt;code&gt;+&lt;/code&gt; indicates &quot;beneficial&quot;, a &lt;code&gt;-&lt;/code&gt; indicates &quot;detrimental&quot; and a &lt;code&gt;0&lt;/code&gt; indicates it has no effect on fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PG9hr.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Note about symbiosis&lt;/em&gt; - comes in reaction to @Gerhard's comment&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Different authors use the word &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Symbiosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;symbiosis&lt;/a&gt;&lt;/em&gt; differently. From wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The definition of symbiosis is controversial among scientists. Some believe symbiosis should only refer to persistent mutualisms, while others believe it should apply to any type of persistent biological interaction (i.e. mutualistic, commensalistic, or parasitic).&lt;a href=&quot;http://en.wikipedia.org/wiki/Polymerase_chain_reaction&quot; rel=&quot;nofollow noreferrer&quot;&gt;4&lt;/a&gt; After 130+ years of debate,&lt;a href=&quot;https://biology.stackexchange.com/questions/34953/are-there-examples-of-now-living-species-where-one-is-descended-from-the-other/34956#34956&quot;&gt;5&lt;/a&gt; current biology and ecology textbooks now use the latter &quot;de Bary&quot; definition or an even broader definition (i.e. symbiosis = all species interactions), with the restrictive definition no longer used (i.e. symbiosis = mutualism)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Blurry limits&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Generalities&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It may seem pretty obvious that two species should have either one type or another type of interaction. However, the reality is often more complicated than that. An interaction might fall under one set of environmental conditions and fall under another category under another set of environmental conditions. In addition to that, it is not uncommon that due to selection on the host genes due to the presence of a parasite, the host evolve so to tolerate the presence of the parasite up to the point of actually having a lower fitness in the absence of the parasite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Example&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Parasites often have different life cycle of alternance of generation. That is a parasite sometimes need several hosts such as the parasite causing malaria for example that need both mosquitoes and a primate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider for example a snail which is infected by a parasite. Let's assume (I think it is a real world example but I am too lazy to find out a reference) that the parasite need the snail to be eaten in order to reproduce in the body of the predator. In order to improve the chance of its host to be eaten the parasite is selected so to diminish the thickness of the snail's shell. In response to that, there is selection (which intensity depend also on the proportion of infected snails in the population) for having thicker shells. But now, snails that are not infected have shells that are so thick that the can't move as fast as they'd need to forage. So, by the end infected snails may have a higher fitness than non-infected snails. And therefore the interaction between the snail and its parasite is not a parasitic interaction anymore but a mutualistic interaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can viruses have non-parasitic relationship with their host?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well... why not? There is nothing so fundamental about viruses that would prevent them to have mutualistic relationship with their host. Actually I am aware of a few relationships. For example, female &lt;a href=&quot;http://en.wikipedia.org/wiki/Parasitoid_wasp&quot; rel=&quot;nofollow noreferrer&quot;&gt;parasitoid wasps&lt;/a&gt; (&lt;a href=&quot;http://en.wikipedia.org/wiki/Parasitoid&quot; rel=&quot;nofollow noreferrer&quot;&gt;parasitoids&lt;/a&gt;: parasite that kill their host). parasitoid wasps lay their egg in other insects larvea (host), the egg (and later the larvea I think) develop in the larvea (host), eat the larvea (host) and once the host is dead, the individual metamorphose to its adult form and fly away to find a mate a parasite the next larvea. Some lineage of those wasps have viruses in their ovary that infect the host to reduce the immune defence of the host to protect the growth of their egg (&lt;a href=&quot;http://www.pnas.org/content/88/21/9770.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Flemming and Summers 1991&lt;/a&gt;). This is an example of mutualistic relationship between the wasp and the virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sequencing to know if the plants are infected&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You said&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;they collect samples of plants and somehow by analyzing their DNA notice that these plants are all infected by some kind of virus&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Most likely, they make a &lt;a href=&quot;http://en.wikipedia.org/wiki/Polymerase_chain_reaction&quot; rel=&quot;nofollow noreferrer&quot;&gt;PCR&lt;/a&gt; (amplification of DNA, that is increasing the number of copies of a given DNA sequence) on viral DNA and look for a signal. In other words they are not sequencing (=reading) the plant DNA but only seeking for viral DNA. If they find viral DNA, then the plant is infected if not, the plant is not infected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is unclear to me from your text&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From your post, it is unclear to me yet how your &quot;family member&quot; plans to decide the type of interaction there are between viruses and plants. Knowing the frequency of infected plants won't tell you much about the interaction between the plant and the virus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They will likely have to make growth experiment and try to measure the fitness of infected and non-infected plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt; - Following the first comment&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Knowing that every plant individual is infected doesn't tell much of the virulence of the virus. The frequency of infected is not an information that can help understand the &quot;type of biological interaction&quot; (paratism, mutualism, etc..). One will need to actually make growth experiment and measure fitness (or measure phenotypic traits that are known to be good proxy for fitness).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One question about your answer is : can we really speak of a virus as a species and especially does your table really apply in this situation ?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The concept of species is not a natural category. It is a man-made, unclear, sometimes useful, category. Typically, it is hard to even talk of species for organisms that don't have sexual reproduction (which is the case of viruses). I wrote &lt;a href=&quot;https://biology.stackexchange.com/questions/34953/are-there-examples-of-now-living-species-where-one-is-descended-from-the-other/34956#34956&quot;&gt;this other answer&lt;/a&gt; today about the concept of species, you may want to read it. &lt;a href=&quot;https://biology.stackexchange.com/questions/11240/transitivity-of-species-definitions&quot;&gt;Here&lt;/a&gt; is another post on the subject. Btw, talking about semantic issue, &lt;a href=&quot;https://biology.stackexchange.com/questions/9438/why-isnt-a-virus-alive&quot;&gt;viruses are often not considered as alive&lt;/a&gt;. All those semantic issues don't have any impact on our understanding of biological processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But yes, the table applies to viruses as well. This table is indifferent to the concept of species. Consider just two genotypes (two individuals), one plant and one virus, the existence of the virus has (or has not) an impact on the fitness of the plant (and vice-verse) and therefore, you can classify the relationship between those two genotypes (individuals) into one category of the table. As a reminder, the nature of those relationship may depend on the environment. Typically, a photosynthetic endosymbiote might be very beneficial to the &quot;host&quot; if there is some sunlight but might be quite detrimental in the absence of sun light.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2017-07-27T18:44:18.013" LastActivityDate="2017-07-27T18:44:18.013" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="34968" PostTypeId="1" AcceptedAnswerId="34969" CreationDate="2015-06-06T18:21:26.907" Score="0" ViewCount="680" Body="&lt;p&gt;A reciprocal translocation is denoted for example: t(4;12)(q32;q24) indicating that q32 on chromosome 4 being swapped with q24 on chromosome 12 if I understand this correctly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: How do I know whether this is a balanced or an unbalanced translocation?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-06-07T02:37:39.140" Title="Chromosomal translocation notation" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34969" PostTypeId="2" ParentId="34968" CreationDate="2015-06-06T18:28:30.800" Score="1" Body="&lt;p&gt;This translocation is balanced: if it was not there was a specific sign for specific unbalanced event, for example &quot;del&quot; for deletion or &quot;+&quot; and &quot;-&quot; signs etc.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-06-06T18:28:30.800" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34970" PostTypeId="2" ParentId="34880" CreationDate="2015-06-06T18:47:16.810" Score="1" Body="&lt;p&gt;Using different wavelength for reference give some advantages. You can measure a baseline of each well. All well might not have the same baseline because each well might not be the exactly same as others. In addition, you could make scratches on it, you might touch the bottom, or you get some dirt from your bench. And this can be corrected by A540 in your case. So, variations at a lower range are not much concerned. Sometimes, even if you choose a wavelength where the absorbance seems not to change after reaction, there might be a small change. This is not concerned ether, because both absorbances are concentration dependent unless states in solution do not change (froming complexes or something like that).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But still, you get high background from samples showing 1.4 or more at A450. I do not have experiences for this substrate, but you might want to think several possibility:&#xA;1)You might get bubbles on the top of your solution in the wells,&#xA;2)You might not get accurate values because OD is too high,&#xA;3)The solution might get precipitates&#xA;4)This may be a very less possibility, but some secondary reaction occurs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For 2), 3), and 4). You might want to check linearity by drawing a standard curve, and avoid to use the range deviating from the liner relation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS&#xA;I should've mention that you would check the specification of your plate reader. OD=3 could be way to high to measure it. Because light intensity decreases to one thousandth though 1 cm light path at OD=3. It is very hard to measure such weak lights exactly. Probably many specifications of plate readers say you could measure ODs up to around 2, but some people think it is ideal to measure ODs up to around 1.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-06-07T19:08:08.530" LastActivityDate="2015-06-07T19:08:08.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34971" PostTypeId="2" ParentId="34966" CreationDate="2015-06-06T19:17:26.480" Score="1" Body="&lt;p&gt;Genetic markers don't cut the DNA. They're simply regions of DNA sequence that happen to be variable between individuals (see my answer to your previous question). They might be &lt;em&gt;measured&lt;/em&gt; using restriction enzymes (i.e. RFLP) to identify the exact difference, but it's not the marker that's cutting DNA. Furthermore, they don't necessarily cause disease. They're used in pedigree analysis to find regions that are linked with various phenotypes, among which is disease. However, linkage does not imply causation, especially with so few individuals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer your first question II:1 isn't in the affected family - he married into it. In the affected family, A1 has become linked with the disease mutation. &lt;strong&gt;It is not necessarily linked with the disease in other families.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is also the answer to your second question. I:2 has A1 marker on one chromosome associated with the disease allele, and one that's not. II:3 presumably inherited an X chromosome with the disease allele.&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2015-06-06T19:17:26.480" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34972" PostTypeId="1" CreationDate="2015-06-06T21:09:45.677" Score="5" ViewCount="1791" Body="&lt;p&gt;I'm learning about the ecosystem and its relation to organisms, So organisms in a food chain can be put from producers to tertiary organisms. I just don't get the part where an organism can be labeled into 2 trophic levels ? how is it placed in the pyramid if so ?  &lt;/p&gt;&#xA;" OwnerUserId="16022" LastEditorUserId="3624" LastEditDate="2015-12-17T14:40:08.623" LastActivityDate="2015-12-17T14:40:08.623" Title="How can omnivores be in more than one trophic level?" Tags="&lt;ecology&gt;&lt;ecosystem&gt;&lt;food-web&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34973" PostTypeId="1" AcceptedAnswerId="34975" CreationDate="2015-06-06T21:38:32.430" Score="23" ViewCount="1803" Body="&lt;p&gt;&lt;strong&gt;My Background:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm a mathematics graduate student with a physics background.  I have a very little biology knowledge and a little knowledge of machine learning and statistics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Topic:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I recently found out about the following computational biology breakthrough: A computer managed to independently develop an explanatory theory for a 120 year old problem in biology. It is detailed in the popular media &lt;a href=&quot;http://www.wired.co.uk/news/archive/2015-06/05/computer-develops-scientific-theory-independently&quot;&gt;&lt;strong&gt;here&lt;/strong&gt;&lt;/a&gt; and &lt;a href=&quot;http://www.popularmechanics.com/science/a15886/computer-scientific-theory/&quot;&gt;&lt;strong&gt;here&lt;/strong&gt;&lt;/a&gt; and in great detail in this &lt;a href=&quot;http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004295&quot;&gt;&lt;strong&gt;paper&lt;/strong&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Questions:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I lack domain expertise but I'm very curious as to how this was possible and why it happened now. For example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Were these methods novel (from a machine learning perspective), or does the novelty lie in using old tools/techniques and adapting them to a&#xA;workable problem?&lt;/li&gt;&#xA;&lt;li&gt;Mathematically speaking, what kind of models were produced by the computer? Are these standard in this field of genetics/biology? Is this area particularly mathematically tractable?&lt;/li&gt;&#xA;&lt;li&gt;What about this particular biological problem made it amenable to this machine learning approach?&lt;/li&gt;&#xA;&lt;li&gt;What other kinds of low hanging fruit (in biology or science in general) could we expect to see tackled with these techniques?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="16110" LastEditorUserId="3340" LastEditDate="2015-06-07T19:22:42.630" LastActivityDate="2015-09-27T21:37:20.933" Title="120-year-old gene regulation problem independently solved by a computer. How?" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;gene-regulation&gt;&lt;computational-model&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="34974" PostTypeId="2" ParentId="34940" CreationDate="2015-06-07T00:01:35.827" Score="2" Body="&lt;p&gt;The uptake system in plants is much more complicated, as Mr.Baily opened the anatomy and structure of root I will only explain the uptaking system.&#xA;When plant absorbs water it absorbs some elements too, but there is a broblem which is soil particles as the clay is a cloidical substance of soil wich does contain negative charge and most of essential elements are cathionic forms sothey won't solve in water. When a plant want to absorb nutrients it releas protons in soil ,these protons will be replaced by cathions and that's when plant can absorb them .&#xA;For negative charged elements it is much more easier cause they don't need proton exchange.&#xA;Plants also need some sugar, bigg ionic compounds,and organic matters ( mostly acids ) to uptake these paticles it's even more complicated, as there is some protein channels wich use energy to insert these materials inside the roots ( last system works based on aqua-porous) &#xA;Then plant never uptake cathions more than it needs,elemental and metal poisoning is based on flaccid and turgor pressure and parallel exchange or protein channel damages&lt;/p&gt;&#xA;" OwnerUserId="16108" LastActivityDate="2015-06-07T00:01:35.827" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34975" PostTypeId="2" ParentId="34973" CreationDate="2015-06-07T01:08:47.257" Score="20" Body="&lt;p&gt;The fruit, sadly, does not hang so low.&lt;/p&gt;&#xA;&lt;h1&gt;Short version&lt;/h1&gt;&#xA;&lt;p&gt;Lobo et al (the work you refer to) is a nice and not especially novel application of basic Systems Biology modeling approaches to the wound healing system in flat worms. The main barrier to the wider application of such work is the lack of the necessary experimental data. Lobo et al themselves don't really have enough data to justify their models.&lt;/p&gt;&#xA;&lt;h1&gt;Long version&lt;/h1&gt;&#xA;&lt;p&gt;Lobo et al  can be thought of as consisting of two separate parts: the models themselves, and their genetic algorithm based search of modelspace.&lt;/p&gt;&#xA;&lt;h2&gt;The Models&lt;/h2&gt;&#xA;&lt;p&gt;The models aren't novel. Their basic form is extremely common in Systems Biology work. Take a look at the equations in the methods section of their paper and in their &lt;a href=&quot;http://journals.plos.org/ploscompbiol/article/asset?unique&amp;amp;id=info:doi/10.1371/journal.pcbi.1004295.s010&quot; rel=&quot;noreferrer&quot;&gt;Supporting Information&lt;/a&gt;. For example:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ehpNO.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;This is a very standard way of representing a set of coupled biological &amp;quot;species&amp;quot;. Some of those species correspond directly to the concentration of some specific protein (ie βcat), whereas other species are more vaguely constructed (ie head) and presumably correspond to some generalized set of biological elements (eg proteins, DNA, lipids, etc).&lt;/p&gt;&#xA;&lt;p&gt;The first term in each of the equations is a production term. It represents how the given species is increasing with time. Each of the fractions takes the form of something called a Hill Function. These come up all over the place in biological modeling. The important thing to know about Hill Functions is that they vary either from 0-&amp;gt;1 (for activators) or from 1-&amp;gt;0 (for inhibitors) as the concentration of the relevant species varies from 0-&amp;gt;infinity, with a smooth transition region in between.&lt;br /&gt;&#xA;The min and max operators are meant to stand in for the Boolean operators AND and OR, respectively. In other words, if two of the Hill Functions are related by a min operator, they both have to be in an ON state in order for the overall term to be in an ON state. If the two Hill Functions were instead related by a max operator, only one of them would need to be in the ON state for the term to be in the ON state overall.&lt;/p&gt;&#xA;&lt;p&gt;The second term is a degradation term. It represents how the given species is decreasing with time. The particular form of the degradation term (directly proportional to species concentration) derives from the fact that the main sink for generic biomolecules is dilution via cellular growth and division.&lt;/p&gt;&#xA;&lt;p&gt;The third term (the thing with ∇² in it) is a diffusion term. This describes how the species moves around the in the worm, assuming that it is free to do so (not all proteins/species can exit the cell). Not all of the species have this diffusion term.&lt;/p&gt;&#xA;&lt;h2&gt;The Search of Modelspace&lt;/h2&gt;&#xA;&lt;p&gt;Their modelspace search isn't novel either, although some very specific aspects of it may be.&lt;/p&gt;&#xA;&lt;h3&gt;the basics of modelspace search&lt;/h3&gt;&#xA;&lt;p&gt;The basic problem of modelspace search works like this: imagine a generalized form of your model in which every species interacts with every other species in every possible way. Each of the equations will have a (large) set of free parameters associated with it. You then take a set of experimental observations and-using any one of a number of methods-find a set of parameter values such that your model will reproduce those observations. This is called parameter fitting. In order to find the unique set of parameters that describes the &amp;quot;real&amp;quot; system that you're trying to model, in general you need at least as many independent experimental observations as you have independent parameters in your model. If you have more parameters than you have data, then you will be able to find infinitely many different parameter sets that reproduce your experimental data.&lt;/p&gt;&#xA;&lt;p&gt;Here's where things start to get complicated, and a bit fuzzy. What separates modelspace search from standard parameter fitting is that you usually employ some version of the Principle of Parsimony in modelspace search. The Principle of Parsimony can be thought of as equivalent to Occam's Razor: the simplest model is usually best. In practice, what this means is that when you don't have enough experimental data to uniquely parameterize your model, you should favor versions of your model with as few species-species interactions as possible.&lt;/p&gt;&#xA;&lt;p&gt;The Principle of Parsimony is one specific example of a broad category of modelspace constraints known as &amp;quot;prior knowledge&amp;quot;. This refers to everything you know in advance about what your final model &amp;quot;should&amp;quot; look like. Prior knowledge tends to be specific to the particular modelsearch at hand, and it can be incorporated into the search algorithms in many different ways.&lt;/p&gt;&#xA;&lt;p&gt;With enough prior knowledge the modelsearch can be constrained to an extent such that, in theory, it should become possible to identify the one true parameter set, even when you only have a relatively small set of experimental observations. Good luck constructing a formal proof for that, though. In fact, for a complex system it's usually impossible to quantify the extent to which a given piece of prior knowledge reduces the number of experimental observations required to uniquely fit the parameter set.&lt;/p&gt;&#xA;&lt;h3&gt;the modelspace search in Lobo&lt;/h3&gt;&#xA;&lt;p&gt;For the type of model used in Lobo, a rough calculation says there's going to be&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$3n^2 + 4n$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;independent parameters (where n is the number of species). Further, there's going to be a set of parameters that describes whether each species-species interaction is activating or inhibiting, and another set of parameters that describes the Boolean logic of those interactions.&lt;/p&gt;&#xA;&lt;p&gt;The &amp;quot;comprehensive&amp;quot; model in Lobo has 14 species, so there are at least&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$3\cdot14^2 + 4\cdot14 = 644$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;644 free parameters to fit during the modelspace search. Against those 644 parameters they have exactly 16 independent experimental observations.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-09-27T21:37:20.933" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34976" PostTypeId="2" ParentId="34968" CreationDate="2015-06-07T02:37:39.140" Score="1" Body="&lt;p&gt;Chromosomal aberrations have defined notations you can find &lt;a href=&quot;http://www.informatics.jax.org/mgihome/nomen/anomalies.shtml&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The notation rule for multiple genetic abnormalities is to concatenate them. In the presence of an unbalanced translocation two abnormalities will be indicated as you have both a translocation and another event (e.g. deletion, duplication, ...).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your example, as no other abnormalities/events are indicated, this is a balanced translocation.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastActivityDate="2015-06-07T02:37:39.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34979" PostTypeId="2" ParentId="34877" CreationDate="2015-06-07T05:49:58.127" Score="0" Body="&lt;p&gt;A genetic marker is, by empirical definition, something that you can unequivocally place on a genetic map.  A genetic marker &lt;em&gt;may&lt;/em&gt; be an allele of a known gene that confers either a dominant, or a recessive phenotype. Alternatively, a genetic marker could be either a restriction fragment length polymorphism--whose segregation can be detected by either a Southern blot or a PCR experiment, or a single nucleotide polymorphism--whose segregation could be detected by a PCR experiment, or by DNA sequencing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If two genetic markers segregate independently after a genetic cross the we say that they are unlinked--by which we mean they map to separate chromosomes. If two genetic markers do not segregate independently after a genetic cross (i.e., a mating) then we say they are linked--by which we mean the map to the same chromosome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Knowing nothing about chromosomes, or DNA, it is still possible, given enough genetic markers, to construct a genetic map for an organism. All of the markers that map as if they are linked to each other are said to form a &quot;linkage group&quot;.  When there are enough genetic markers to identify all of the linkage groups then the number of different linkage groups will equal the number of chromosomes (this assumes one crossover per chromosome during meiosis).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is important to remember that chromosomes can only be seen with a microscope, cytologically, typically after fixation, and staining, whereas linkage groups, and genetic maps, do not require, or rely on, chromosomes. A genetic map, made up of different genetic markers, is an abstraction.  In some cases a genetic marker can actually be placed on the physical map of a chromosome--for example, in a species with a sequenced genome--this allows us to coordinate the genetic map with the physical map (for that locus).&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-06-07T05:49:58.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34980" PostTypeId="1" CreationDate="2015-06-07T08:34:42.477" Score="1" ViewCount="74" Body="&lt;p&gt;I am thinking which pathway is more important in hypertension, ADHD and withdrawal of clonidine:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;alpha-2 agonist&lt;/li&gt;&#xA;&lt;li&gt;imidazoline receptor agonist (maybe) &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Alpha-2 is the classical one. Pubchem starts to have more more info about imidazoline receptors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does clonidine work in hypertension, ADHD and withdrawal? &lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2015-06-07T08:34:42.477" Title="Imidazoline receptor agonist in clonidine?" Tags="&lt;pharmacology&gt;&lt;central-nervous-system&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34981" PostTypeId="1" CreationDate="2015-06-07T08:42:50.443" Score="3" ViewCount="106" Body="&lt;p&gt;I am thinking the role of doxorubicin's pathways in cancers such as leukemia and lymphoma:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;topoisomerase inhibitor and inhibit DNA activity&lt;/li&gt;&#xA;&lt;li&gt;intercalant - intercalant DNA bases and inhibit DNA activity&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am interested in which of these mechanisms are most relevant in leukemia and lymphoma. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How does doxorubicin work in leukemia and lymphoma?&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2015-06-08T05:54:13.613" Title="Doxorubicin's intercalant and topoisomerase inhibition in leukemia?" Tags="&lt;pharmacology&gt;&lt;cancer&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34982" PostTypeId="2" ParentId="34973" CreationDate="2015-06-07T09:33:48.410" Score="21" Body="&lt;p&gt;The paper by Lobo and Levin is an attempt to learn a model that represents the inner workings of a biological system by fitting parameters to data. This is a common topic in &quot;systems biology&quot;, a model-based approach to studying biology that is popular in some fields. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even for small systems, this is a phenomenally hard problem. Unlike most machine learning problems, achieving good accuracy (on independent test sets) is not enough; the model structure itself must be correct, meaning that it should reflect the actual mechanisms operating in the cell or organism. It's like trying to identify the actual structure of an integrated circuit by only observing inputs and outputs --- not only identifying the logical rule that the system exhibits, but the actual wiring diagram that implements that rule. It is of course quite possible that alternative models exist that perfectly captures the behavior, and yet is completely different &quot;on the inside&quot;. In other words, the system may not be identifiable from the data --- two different models may produce exactly the same behavior. So there's no way to know beforehand if these problems are even theoretically solvable (let alone practically feasible).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lobo and Lewin claim to have accomplished this task for a small system of gene products. As far as I can tell, the central piece of evidence is that the model they come up with does capture some mechanisms previously known to exist. Whether this is just plain luck, overfitting, or a special case where (parts of) the system is actually identifiable from data is hard to tell. But it's notable that Lobo and Levin fall back on demonstrating predictive accuracy in the end, which is not enough to support their thesis. The critical test is to take a &lt;em&gt;new&lt;/em&gt; prediction from their model and actually test it experimentally, to prove their (strong!) claim that their method can actually infer new mechanisms. Doing so is expensive and time-consuming, and much more difficult to get right than tweaking models to fit mechanisms you already knew beforehand --- which is exactly why I want to see that evidence. If the authors really believe that their method is a breaktrough, those experiments should have been done.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, these type of algorithms are applied to models containing only a handful of components, and typically to systems that have been studied for decades and are very well-characterized to begin with. In most of biology, the problems are orders of magnitude more complex, and often we don't even know what the components are. So I thik there are a limited number of cases where this approach is feasible.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastEditorUserId="15695" LastEditDate="2015-06-07T12:37:47.437" LastActivityDate="2015-06-07T12:37:47.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34983" PostTypeId="2" ParentId="31000" CreationDate="2015-06-07T11:30:51.450" Score="0" Body="&lt;p&gt;Meristems in plant's kingdom are functionally similar to stem cells in animal kingdom, even you can see it in their names, meri&lt;strong&gt;STEM&lt;/strong&gt;s &amp;amp; &lt;strong&gt;STEM&lt;/strong&gt; cells ,stem cells are more flexible,okay going back to meristems ,buds are complex of apical or lateral meristems which are covered by special kind of leafs according to enzymatic change,photoperiod and climate conditions buds can produce new leafs,branches or reproductive parts such as flowers, so we can say that buds are some kind of meristems themselves,but there are some other kind of meristems which act more particular and they are referred as cambium which usually cause the production of cork and cause the lateral growth and vascular elements reproduction.&lt;/p&gt;&#xA;" OwnerUserId="16108" LastActivityDate="2015-06-07T11:30:51.450" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34984" PostTypeId="1" AcceptedAnswerId="34991" CreationDate="2015-06-07T12:11:44.063" Score="2" ViewCount="999" Body="&lt;p&gt;Many culinary vegetables are botanically fruits. For example, the tomato, bittergourd and the cucumber are generally considered culinary vegetables, but they are botanically considered fruits. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the reverse also hold true, in that are there any plant parts that are considered fruits culinarily, but are botanically not considered fruits or &lt;a href=&quot;http://en.wikipedia.org/wiki/Accessory_fruit&quot; rel=&quot;nofollow&quot;&gt;accessory fruits&lt;/a&gt;?&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-06-07T18:08:01.813" Title="Are there any culinary fruits that are not botanically fruits or accessory fruits?" Tags="&lt;botany&gt;&lt;terminology&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-06-07T22:18:03.863" ContentLicense="CC BY-SA 3.0" />
  <row Id="34985" PostTypeId="1" AcceptedAnswerId="34987" CreationDate="2015-06-07T14:01:54.403" Score="1" ViewCount="336" Body="&lt;p&gt;In many places it says PGF2-alpha. &#xA;Now, I am thinking PGE2 is a substype of PGF2-alpha. &#xA;However, I am not sure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is dinoprost PGE2?&lt;/p&gt;&#xA;" OwnerUserId="86" LastActivityDate="2015-06-07T15:02:07.473" Title="Is dinoprost PGF2-alpha or PGE2?" Tags="&lt;pharmacology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34986" PostTypeId="1" CreationDate="2015-06-07T14:40:55.520" Score="2" ViewCount="1013" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/57XRV.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The child has gotten 2 &amp;quot;sick&amp;quot; chromosomes from his dad and 1 healthy from his mom, leaving it with trisomy 13.&lt;/p&gt;&#xA;&lt;p&gt;I can see how this can happen in the second meiotic division of the father but I can ALSO see how this can happen in the FIRST meiotic division by non-disjunction.&lt;/p&gt;&#xA;&lt;p&gt;Let me illustrate both ways which I see it and you can tell me where I go wrong as my book only illustrates that is the second division:&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EUWOz.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The black is the healthy chromosome and the red is the &amp;quot;sick&amp;quot; one. As you can see, we should end up with a double sick chromosome in both cases??&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-04-01T10:18:58.603" Title="Why can't this be 1st meiotic division non-disjunction as well?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;&lt;gene&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="34987" PostTypeId="2" ParentId="34985" CreationDate="2015-06-07T15:02:07.473" Score="1" Body="&lt;p&gt;Prostaglandins A,B,C,D,E,F represent different &lt;strong&gt;non-inclusive&lt;/strong&gt; classes of prostaglandins and all have different chemical structure. Hence (by classification), PgE cannot be subtype of PgF:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PgE have an &lt;strong&gt;oxo&lt;/strong&gt; group at C9, while PgF have &lt;strong&gt;hydroxyl&lt;/strong&gt; group at C9.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Back to Dinoprost, it is PgF2alpha and not PgE2 which &lt;strong&gt;is&lt;/strong&gt; Dinoprostone.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-06-07T15:02:07.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34988" PostTypeId="1" AcceptedAnswerId="35010" CreationDate="2015-06-07T16:16:31.640" Score="1" ViewCount="3940" Body="&lt;p&gt;I was thinking like whenever when we feel emotional or whenever we got hurt we got tears from our eyes but why is that happen ? Why our eyes got wet ? &lt;/p&gt;&#xA;" OwnerUserId="15862" LastActivityDate="2016-08-09T02:41:50.397" Title="Why does our eyes got wet when we feel emotional or whenever we are hurt?" Tags="&lt;human-biology&gt;&lt;eyes&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-06-08T02:45:56.743" ContentLicense="CC BY-SA 3.0" />
  <row Id="34989" PostTypeId="2" ParentId="9722" CreationDate="2015-06-07T17:31:02.890" Score="2" Body="&lt;p&gt;Seeing in animals is at some level using Gabor wavelets (&lt;a href=&quot;https://www.osapublishing.org/josa/abstract.cfm?uri=josa-70-11-1297&quot; rel=&quot;nofollow&quot;&gt;Marčelja 1980&lt;/a&gt; and later authors). Your images reminds of a combination of two low frequency Gabor basis vectors. Apparently the nervous system does not have time to model the incoming image into Gabor components of other frequencies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a picture of two low frequency Gabor basis vectors added. (In this image rotated 45 degrees compared to your image.)&#xA;&lt;a href=&quot;http://medicalxpress.com/news/2013-01-feature-combination-perceptual-identification.html&quot; rel=&quot;nofollow&quot;&gt;http://medicalxpress.com/news/2013-01-feature-combination-perceptual-identification.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a signal processing or a linear algebra question as much as a biology question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One could argue that even lower frequency Gabor vectors would model the original images even better. &lt;/p&gt;&#xA;" OwnerUserId="11654" LastEditorUserId="11654" LastEditDate="2015-06-09T20:46:36.713" LastActivityDate="2015-06-09T20:46:36.713" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34991" PostTypeId="2" ParentId="34984" CreationDate="2015-06-07T17:41:08.877" Score="3" Body="&lt;p&gt;I think there aren't any, with two tentative positive results. Of course, it is hard to prove a negative. But here are my arguments: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Logic. there is little reason for this to happen. A culinary fruit is supposed to be sweet, and plants tend to store sugars in their botanical fruits, not in other parts (although by this logic, there should be tuber-fruits too). &lt;/li&gt;&#xA;&lt;li&gt;Source checking. I went through two books intended as comprehensive reference works in the kitchen, &lt;em&gt;The professional chef&lt;/em&gt; and &lt;em&gt;McGee On Food and Cooking&lt;/em&gt;. They don't list a (culinary) fruit which I could identify as a botanical non-fruit, with one contentious case. Note that &lt;em&gt;On Food and cooking&lt;/em&gt;'s chapter on vegetables is structured according to plant part, and it has a subchapter called &quot;fruits used as vegetables&quot; - but it does not have a chapter of &quot;vegetables used as fruit&quot; or similar. &lt;/li&gt;&#xA;&lt;li&gt;Language. People tend to mix up the two categories of &quot;culinary fruit&quot; and &quot;botanical fruit&quot; until the difference is pointed out to them. While they don't follow the correct botanical definition of fruit, a plant part seems to have to check the &quot;used by the plant for reproduction&quot; check box to be called a fruit, to the point where many words related to &quot;fruit&quot; evoke a harvest-like image such as &quot;to come to fruition&quot;, or also words for &quot;barren&quot; in many languages which literally translate to &quot;without fruit&quot;, e.g. the German &lt;em&gt;unfruchtbar&lt;/em&gt;. So even when a food fulfills the &quot;plant part&quot; and &quot;sweet snack&quot; criteria, it is not called a fruit if it's not (commonly perceived as) a seed container. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The contentious case coming from the books is rhubarb. &lt;em&gt;The professional chef&lt;/em&gt; lists it as a fruit, while McGee calls it &quot;a tart stand-in for fruit&quot; in the vegetable chapter, and mentions it again in the fruit chapter, as &quot;a vegetable that often masquerades as a fruit&quot;. Kitchen terminology is by no means standardized, so if you were to question random cooks about rhubarb categorization, I guess you'd get a mixture of &quot;a fruit&quot; , &quot;a vegetable&quot; and &quot;I don't know&quot; answers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An idea I had while writing the answer: maybe you can count ginger. Ginger has many uses in the kitchen, but it is available as a candied snack, which is else only common for fruit. McGee lists it as a spice, although he explicitly speaks of &quot;the dried spice&quot; without giving a category for the fresh rhizome. I think most cooks won't dub ginger &quot;a fruit&quot; but would be willing to include candied ginger in a bowl of mixed candied fruit. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some petals and leaves are also made into jams, which would support a fruit categorization. Nevertheless, I've never heard of them being referred to as fruits. Prominent examples are rose petals, violet petals and verbena leaves (although one could argue that preserving verbena produces a herb jelly, not a jam). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This answer encompasses Western cooking traditions. It is possible that other cuisines have a different view of what a &quot;fruit&quot; is - for example aloe is frequently used in sweet preparations, maybe the leaf flesh is eaten as fruit somewhere. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in the end, it comes mostly to your willingness to stretch the definition of a culinary fruit. It is certainly not the case for the most commonly eaten fruits.&lt;/p&gt;&#xA;" OwnerUserId="1578" LastEditorUserId="1578" LastEditDate="2015-06-07T18:08:01.813" LastActivityDate="2015-06-07T18:08:01.813" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34992" PostTypeId="2" ParentId="34986" CreationDate="2015-06-07T18:11:25.367" Score="0" Body="&lt;p&gt;Your illustration is wrong. During second meiosis the sister chromosomes go to each their cell, not the same cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This would correspond to switching the colors up in your illustration like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EVfK7.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-06-07T18:11:25.367" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34993" PostTypeId="1" AcceptedAnswerId="34999" CreationDate="2015-06-07T19:02:15.330" Score="2" ViewCount="1007" Body="&lt;p&gt;A man has the genotype AaBbCc, in other words he is heterozygous in three uncoupled loci on three different chromosomes. A, B and C are the dominant alleles while a, b and c are the recessive alleles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1. How many gametes can he form?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer is 8 and I can see how you derive that by just manually writing each and every one down but what is the mathematical method to derive this? I tried permutations but none I came up with worked.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. He has a child with a woman of the same genotype (AaBbCc) how many different genotypes can the offspring have?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here the answer is 27. I'm not sure how they came to this conclusion either?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;3. What is the probability that the offspring has the genotype AaBbCc?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is about the time I start flipping tables because it seems to me that it's 1 out of 27. There are 27 different genotypes and this is ONE of them?!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the answer is 1/8 as there's a 50% chance of Aa, Bb and Cc when mixing apparently so it becomes 1/2*1/2*1/2. Why isn't it just 1 of the possible genotypes?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-06-07T23:17:03.907" Title="Confused with gamete sorting problem" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;homework&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="34997" PostTypeId="2" ParentId="34981" CreationDate="2015-06-07T20:31:53.453" Score="2" Body="&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Doxorubicin&quot; rel=&quot;nofollow&quot;&gt;Doxorubicin&lt;/a&gt; is part of chemotherapy drugs. Most of them are targeting proliferation of cells, e.g. by blocking cell division or DNA replication.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intercalants and topoisomerase inhibitors are powerful in interfering with DNA replication (not &lt;em&gt;DNA activity&lt;/em&gt;). Other chemo drugs might inhibit proper operation of cell division machinery, such as through interfering with cytoskeleton functions.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-06-07T20:31:53.453" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="34999" PostTypeId="2" ParentId="34993" CreationDate="2015-06-07T21:51:58.043" Score="1" Body="&lt;ol&gt;&#xA;&lt;li&gt;Since there are 2 alleles of each gene and 3 different genes, 2EE3 = 8? Let's test this by making a table, for 1 gene there are two different kinds of gametes, so 2EE1 = 2, for 2 genes there are 4 different kinds of gametes (AB, Ab, aB, ab) so 2EE2 = 4, and you already did the calculation yourself for 3 genes, and 2EE3 =  8. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Why don't you try working it out yourself for 4 genes and see if you come up with 16 different kinds of gametes?&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;Two words: Punnett Square. In this case for a trihybrid cross:&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JBBIK.jpg&quot; alt=&quot;triple-het x triple-het cross found on Google Image&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;3&quot;&gt;&#xA;&lt;li&gt;That is a Bernoulli coin-flipping probability. If you are flipping a true coin three times in a row, how often will you get three heads in a row? 1/8? All the events are independent, right? what about the Punnett square? Does it give the same result somehow?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Here is the &lt;a href=&quot;http://www.saylor.org/site/wp-content/uploads/2011/07/A-Trihybrid-Cross-Example-Using-Mendel%E2%80%99s-Sweet-Peas.pdf&quot; rel=&quot;nofollow noreferrer&quot; title=&quot;answer&quot;&gt;answer&lt;/a&gt; worked out for you.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="14946" LastEditDate="2015-06-07T23:17:03.907" LastActivityDate="2015-06-07T23:17:03.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35000" PostTypeId="1" CreationDate="2015-06-07T23:24:10.780" Score="0" ViewCount="226" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oClrk.png&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;This is a pedigree of a family in which bleeder disease, an x-recessive disease, is present. I am asked which marker, A or B, the disease is linked to.&lt;/p&gt;&#xA;&lt;p&gt;I've asked about this type of problem before: &lt;a href=&quot;https://biology.stackexchange.com/questions/34966/x-recessive-disorders-and-genetic-markers&quot;&gt;X-recessive disorders and genetic markers&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;The solution there was the fact that the families were unrelated so the disease being linked with a marker in one family did not correspond to the disease being linked to the same marker in another family.&lt;/p&gt;&#xA;&lt;p&gt;The answer to this problem is &amp;quot;A&amp;quot;. However this is ONE family and there are males in this family with the A marker on their only X-chromosomes who are &lt;strong&gt;unaffected&lt;/strong&gt; and women with two A markers who are also unaffected. How would you explain that? They have the marker for the disease on both alleles but not the disease?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-09T00:36:15.277" Title="X-recessive disorder pedigree confusing me" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;dna&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35001" PostTypeId="1" CreationDate="2015-06-07T21:39:29.607" Score="3" ViewCount="313" Body="&lt;p&gt;I have electric fencing enclosing five acres, and moles always seem to tunnel in a straight line just under the electric fence - are they following a force field? Can that be?&lt;/p&gt;&#xA;" OwnerDisplayName="woolfarm" LastEditorUserId="284" LastEditDate="2015-06-09T13:11:48.530" LastActivityDate="2015-06-09T21:50:02.033" Title="Why do surface mole tunnels follow directly below the electric fenceline" Tags="&lt;behaviour&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35002" PostTypeId="2" ParentId="35001" CreationDate="2015-06-07T23:53:15.723" Score="5" Body="&lt;p&gt;Rumor has it that some moles, such as the star nosed mole, &lt;a href=&quot;http://en.wikipedia.org/wiki/Star-nosed_mole&quot;&gt;have electroreceptors in their nose&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In 1993, Gould and colleagues proposed that the star-like proboscis had electroreceptors and that the mole was therefore able to sense the electrical field of its prey[24] prior to mechanical inspection by its appendages. Through behavioral experiments, they demonstrated that moles preferred an artificial worm with the simulated electrical field of a live earthworm to an identical arrangement without the electrical field. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They may thus be sensing the electrical field of the fence, and interpreting it as a nearby tasty worm.&lt;/p&gt;&#xA;" OwnerUserId="16119" LastActivityDate="2015-06-07T23:53:15.723" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35004" PostTypeId="2" ParentId="31027" CreationDate="2015-06-08T00:28:24.413" Score="2" Body="&lt;p&gt;Interesting question, but the answer is simpler than you might think.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antibiotics put selective pressure on bacteria. Bacteria resistant to that antibiotic evolve as only the resistant ones survive. But this is the key, there has to be at least some already resistant bacteria from which the new (resistant) population will emerge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With contraception, this is not the case. There are no spermatozoids capable of penetrating condoms, for example, and you should also bear in mind that in most cases mild hormonal disbalance is enough to prevent conception. It's a very delicate process, and contraception is basically an overkill.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if some spermatozoids could penetrate condoms, that trait would have to be hereditary in order for evolution to occur.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you'd want to prove that contraception constitutes selective pressure on humans you'd first have to prove that there are spermatozoids and egg cells that can beat contraception, and that it's hereditary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution doesn't work the way you think it does. If you kill a random person, even if you kill a million people, it's not necessarily selective pressure. There are rules to evolution, and one of them is that it has to be hereditary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It wouldn't even come close to being artificial selection, let alone natural selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides, there's 7.3 billion of us. More than ever. We can hardly say contraception is reducing the world's population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You also fail to see one thing, that a person who uses contraception in teenage years still has kids as a young adult. Contraception just &lt;em&gt;delays&lt;/em&gt; pregnancy until you're ready. In evolution, there's a concept of &quot;surviving long enough to reproduce&quot;. You can both use contraception and be an organism with 10 kids - though not at the same time.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2015-06-08T00:28:24.413" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35005" PostTypeId="2" ParentId="30260" CreationDate="2015-06-08T00:42:40.150" Score="1" Body="&lt;p&gt;Because it's favorable for the process of aerobic respiration which requires O2 to produce ATP, which is the little power storage unit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With a bigger concentration of O2, it was possible to produce more ATP, should you evolve in that direction and you needed that constraint to be removed.&lt;/p&gt;&#xA;" OwnerUserId="6003" LastActivityDate="2015-06-08T00:42:40.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35006" PostTypeId="1" CreationDate="2015-06-08T00:47:38.017" Score="2" ViewCount="553" Body="&lt;p&gt;I would like to know how carrier RNAs increase yield in RNA/DNA sequencing experiments. Is their main function in the precipitation steps of each protocol (i.e. small quantities are difficult to precipitate and the carrier RNAs add material), or do they have a role at other stages in the process as well?&lt;/p&gt;&#xA;" OwnerUserId="3059" LastActivityDate="2015-07-08T03:15:56.453" Title="How do carrier RNAs increase yield in sequencing experiments?" Tags="&lt;dna-sequencing&gt;&lt;rna-sequencing&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35007" PostTypeId="1" AcceptedAnswerId="35009" CreationDate="2015-06-08T01:08:04.263" Score="10" ViewCount="2357" Body="&lt;p&gt;I took an undergrad class in genetics. I felt it was not too intensive and I do not feel prepared for grad school (if I can manage to get in.) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone know of a preferably free resource for learning genetics? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know the field is very large, but I would like to be competent in the field, considering I also want to learn more about genomics as well. And I figure one must first have a fundamental understanding of either computer science or biology to be successful in genomics, both of which I lack. &lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="-1" LastEditDate="2015-06-08T09:01:30.823" LastActivityDate="2018-04-19T03:41:55.363" Title="A free book/resource for learning genetics?" Tags="&lt;genetics&gt;&lt;book-recommendation&gt;" AnswerCount="3" CommentCount="6" FavoriteCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="35008" PostTypeId="2" ParentId="35006" CreationDate="2015-06-08T01:19:20.737" Score="1" Body="&lt;p&gt;If you are adding phenol-chloroform extracted tRNA then that is a carrier for the precipitation steps. Some people use linear acrylamide for the same purpose.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-06-08T01:19:20.737" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35009" PostTypeId="2" ParentId="35007" CreationDate="2015-06-08T01:29:55.003" Score="9" Body="&lt;p&gt;As you said, the question is pretty broad. Genetics is a big gigantic field and it is quite hard to know what you are exactly looking for. If you could refine into one of the subfields (molecular genetics, population genetics, phylogenetics, etc..) it would be much easier to give you better advice. As you talk about both biology and bioinformatics, it might be worth to specify whether you are looking for learning more in fundamental genetics or learning more in the methodologies to analyse genetic data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Principles of Genetics&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may want in an introductory class in genetics. &lt;a href=&quot;http://ocw.mit.edu/courses/biology/7-03-genetics-fall-2004/&quot;&gt;Here&lt;/a&gt; is a course on MIT Open CourseWare, but it may be too easy for you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Bioinformatics&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may want to take a bioinformatics course. There are so many bioinformatics course online that there is a wikipedia page to list them (&lt;a href=&quot;http://en.wikipedia.org/wiki/List_of_free_online_bioinformatics_courses&quot;&gt;there&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Side skills&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Programming&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may just want to learn to code in R, Python, Perl or Shell script (to cite few examples). You'll find tons of beginner tutorial online.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Statistics&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or you might want to learn more about statistics. &lt;a href=&quot;https://www.khanacademy.org/math/probability&quot;&gt;KhanAcademy&lt;/a&gt; has a very good (but very introductory) statistics class.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-06-08T04:36:46.250" LastActivityDate="2015-06-08T04:36:46.250" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35010" PostTypeId="2" ParentId="34988" CreationDate="2015-06-08T01:49:48.317" Score="1" Body="&lt;p&gt;The lacrimal gland, the major source for tear production, is situated just above the eye. It sends it's secretions to the eye via the lacrimal duct. Tears secreted collect in the conjunctiva of the upper lid. There is also a nasolacrimal duct which drains the tears from the eye into the nasal cavity. Hence the sniffles when we cry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is it controlled? The lacrimal nucleus in the brain is the major source for innervating the lacrimal gland, is a subnucleus of the superior salivary nucleus in the tegmentum of the pons (part of the brain stem). The lacrimal nucleus is connected to the lacrimal gland by the facial nerve (more specifically the greater petrosal nerve). This is parasympathetic (meaning it is part of the autonomic nervous sytem) and the neurotransmitter transmitting the signal from nerve to gland is acetylcholine (the receptor is muscarinic subtype of the cholinergic... though strangely wikipedia says nicotinic subtype is involved as well, but maybe this is simply poorly worded and is just refering to the ganglia stopover between pre/post ganglionic parasympathetic neurons), this information helps explain how some drugs affect lacrimation (tearing up).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taken from source (1) [I do not know how reliable this website is]: How is the lacrimal nucleus told to start lacrimation? The lacrimal nucleus receives projections from the autonomic nervous system as well as from various brain structures, including the frontal lobe, globus pallidus, thalamus, and hypothalamus. The projections from the frontal lobe are thought to be important in human psychic lacrimation (crying because of emotions). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I know: Another brain area called the limbic system is involved in production of basic emotional drives, such as anger, fear, etc. The limbic system [in the case of sympathetic nervous system it would be the hypothalamus specifically, but this is irrelevant here since parasympathetic nerves cause lacrimation] also has a degree of control over the autonomic system. As I under stand it, the frontal lobe usually inhibits the limbic system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again from source (1): While humans across the world produce psychic tears in response to both positive and negative emotions, and while similar emotions have been identified in other animal species, no reports exist of other animals showing psychic lacrimation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;according to wiki (3): Compared to tearing for physical reasons,  tears for emotional reasons have s different chemical composition. They are composed of more protein-based hormones, such as prolactin, adrenocorticotropic, and leucine enkephalin (a natural pain killer), which is suggested to be the mechanism behind the experience of crying from emotion making an individual feel better.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;sources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) &lt;a href=&quot;http://carta.anthropogeny.org/moca/topics/lacrimation-tearing&quot; rel=&quot;nofollow&quot;&gt;http://carta.anthropogeny.org/moca/topics/lacrimation-tearing&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) &lt;a href=&quot;http://en.wikipedia.org/wiki/Lacrimal_gland#Innervation&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Lacrimal_gland#Innervation&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3) &lt;a href=&quot;http://en.wikipedia.org/wiki/Tears&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Tears&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4433" LastEditorUserId="4433" LastEditDate="2016-08-09T02:41:50.397" LastActivityDate="2016-08-09T02:41:50.397" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35011" PostTypeId="2" ParentId="34972" CreationDate="2015-06-08T01:50:09.050" Score="2" Body="&lt;p&gt;I am not sure I fully understand where is your misunderstanding. I think your whole misunderstanding boils down to the representation of food chain. Actually, let's talk about food web as the name gives an intuition of what is happening that is more correct than the term food chain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The conceptual view of the food web in a pyramid is super misleading. This is not how ecosystem work. But anyway, if one might want to make some ugly approximations and represent food web into a pyramid, then this person is totally free to represent one species twice, at two different levels. It makes sense that a species can eat things at several level in the same time. Just like you. You probably eat vegetables, salads, fruits, rice, corn, bread, etc... but also eventually fish and meat. Note also as indicated by @fileunderwater in the comments, that some species have different relationship with their ecosystem (typically eat different things) at different life stages.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are few examples of more or less realistic food webs. As you can see, one can roughly make category of trophic level but it is not all that clear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/669K3.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/qhon9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/V9bSJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-06-10T12:47:59.233" LastActivityDate="2015-06-10T12:47:59.233" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35012" PostTypeId="1" AcceptedAnswerId="35029" CreationDate="2015-06-08T01:55:17.890" Score="5" ViewCount="1021" Body="&lt;p&gt;I know that some plants die for old age like a &#xA;lettuce. But there are trees like Baobabs or larger Ficus in the tropics of whom we don't know their age. And trees like &lt;a href=&quot;http://www.sciencedaily.com/releases/2008/04/080416104320.htm&quot;&gt;spruce reaching 9950 years old&lt;/a&gt;, which die for environmental factors and not by age. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, E.g. when we multiply vegetatively an olive or cacao tree, we use a fragment or clone from a unique individual passing the same genetic information, again and again. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, can these plants live forever? &lt;/p&gt;&#xA;" OwnerUserId="16101" LastActivityDate="2015-06-08T17:54:47.183" Title="Can plants live forever?" Tags="&lt;genetics&gt;&lt;plant-physiology&gt;&lt;senescence&gt;" AnswerCount="2" CommentCount="1" ClosedDate="2015-06-09T05:06:03.317" ContentLicense="CC BY-SA 3.0" />
  <row Id="35013" PostTypeId="2" ParentId="34981" CreationDate="2015-06-08T03:16:15.393" Score="2" Body="&lt;p&gt;I do not have the complete answer, but the links below could be useful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748742/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748742/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article above says etoposide, which is top II inhibitor and effective against cancer, is not a intercalator.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ingentaconnect.com/content/ben/cpd/2001/00000007/00000017/art00004?crawler=true&quot; rel=&quot;nofollow&quot;&gt;http://www.ingentaconnect.com/content/ben/cpd/2001/00000007/00000017/art00004?crawler=true&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You would find the description below in the article. I just quote their description here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;As with many other DNA intercalating drugs,&#xA;topoisomerase II-dependent DNA cleavage is&#xA;thought to be the critical event responsible for the&#xA;anticancer activity, [101] whereas free radicalmediated&#xA;DNA cleavage is probably more closely&#xA;related to the cardiotoxic side effects [118].&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.degruyter.com/view/j/aiht.2013.64.issue-4/10004-1254-64-2013-2371/10004-1254-64-2013-2371.xml&quot; rel=&quot;nofollow&quot;&gt;http://www.degruyter.com/view/j/aiht.2013.64.issue-4/10004-1254-64-2013-2371/10004-1254-64-2013-2371.xml&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The chemical, MLN944 (XR5944) described in the link above was designed as Topo inhibitor, but the topo inhibitory effects were less regardless of anti-tumor activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is another type of anti-cancer drugs intercalating into DNA: cisplatin. Interaction of DNA with cisplatin result in formation of DNA adducts. Therefore, it may be difficult to explain anti-cancer effects by only intercalation. For the reference of cisplatin: &lt;a href=&quot;http://en.wikipedia.org/wiki/Cisplatin&quot; rel=&quot;nofollow&quot;&gt;http://en.wikipedia.org/wiki/Cisplatin&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-06-08T03:16:15.393" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35014" PostTypeId="2" ParentId="31229" CreationDate="2015-06-08T04:27:29.967" Score="3" Body="&lt;p&gt;From the comment section:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We don't have to see the actual changes. It's like chemists who will mix compounds together and obtain a new molecule. They dont see the chemical reaction per se but can test the new molecule to make sure what they predicted would happen had happened. Finally we often use fluorescent proteins to track some of the modification performed (which could involve a microscope). For the how, well that's a bit broad and involves too many notions to make a summary here.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastActivityDate="2015-06-08T04:27:29.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35015" PostTypeId="2" ParentId="31250" CreationDate="2015-06-08T04:30:18.723" Score="1" Body="&lt;p&gt;From the comment section:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mostly segregation of PCR-amplified DNA from non-amplified DNA. Typically no DNA or sample should ever enter a specific room designed to prepare the MasterMix for PCR (this is true for diagnostic labs, in the research one I never saw that). For the rest, following good laboratory practices (google that) should be enough.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastActivityDate="2015-06-08T04:30:18.723" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35016" PostTypeId="2" ParentId="31249" CreationDate="2015-06-08T04:33:18.637" Score="2" Body="&lt;p&gt;From the comment section:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cells divide and when they do the two daughter cells will not only have copies of the DNA but also of the organelles, the cellular machineries and the cell membrane which implies that yes the daughter cells receive also ribosomes. The replication happens during the interphase.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastActivityDate="2015-06-08T04:33:18.637" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35017" PostTypeId="2" ParentId="35007" CreationDate="2015-06-08T05:32:32.287" Score="5" Body="&lt;p&gt;I work at the Wellcome Trust Sanger Institute, one of the world's largest genomics centres. We do maintain a website for the public wanting to learn about genomics, but it might be a bit basic for you: &lt;a href=&quot;http://www.yourgenome.org&quot; rel=&quot;noreferrer&quot;&gt;YourGenome.org&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can get into this field without going through grad school:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;learn at least one programming language (Python is probably the key one today; perl was everything 10 years ago but not much new is starting in that language now)&lt;/li&gt;&#xA;&lt;li&gt;try getting involved in open source bioinformatics projects, such as the &lt;a href=&quot;http://genomicsandhealth.org&quot; rel=&quot;noreferrer&quot; title=&quot;Global Alliance for Genomics and Health&quot;&gt;Global Alliance&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;apply for a support role in a genomics centre, such as working as a programmer within a research group, or in their IT support groups.  Genomics is a field you can learn on the job.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="16124" LastActivityDate="2015-06-08T05:32:32.287" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35018" PostTypeId="2" ParentId="31249" CreationDate="2015-06-08T05:38:36.900" Score="2" Body="&lt;p&gt;Each daughter cell, following mitosis, will contain some ribosomes and DNA transcription machinery already, so it can already synthesise more ribosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of the fertilised ovum, when the organism is only a single cell, the first ribosomes will be those already present in the unfertilised ovum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So cells never have to start from scratch with no ribosomes.&lt;/p&gt;&#xA;" OwnerUserId="16124" LastActivityDate="2015-06-08T05:38:36.900" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35019" PostTypeId="2" ParentId="34981" CreationDate="2015-06-08T05:54:13.613" Score="2" Body="&lt;p&gt;Doxorubicin and etoposide are both inhibitors of DNA topoisomerase II.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When chromosomes replicate as a cell divides, the helical nature of DNA results in the daughter molecules being tangled up (catenated).  Topo II is an amazing enzyme; it binds to DNA, cuts a gap in both strands, and then passes another DNA molecule through the gap.  Thus it untangles DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you inhibit Topo II, two things happen.  Firstly, the inhibition usually takes place after the first DNA molecule has been cut.  Thus inhibiting Topo II causes severe double stranded DNA damage, which is hard for the cancer cell to repair, and it dies.  Secondly, the physical entanglement which remains stops the clean separation of the chromosomes during mitosis.  Depending on the Topo II inhibitor in use, this can trigger a cell cycle checkpoint which stops the cell dividing &lt;a href=&quot;http://www.nature.com/nature/journal/v372/n6505/abs/372467a0.html&quot; rel=&quot;nofollow&quot;&gt;Downes &lt;em&gt;et al&lt;/em&gt;, 1994&lt;/a&gt;, or can cause the cell to rip the chromosomes to pieces as it tries to separate them anyway.  I worked in the same lab as Downes &lt;em&gt;et al&lt;/em&gt;, above, and have done this experiment with several Topo II inhibitors, including etoposide and doxorubicin.  It's quite spectacular. &lt;/p&gt;&#xA;" OwnerUserId="16124" LastActivityDate="2015-06-08T05:54:13.613" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35020" PostTypeId="2" ParentId="34946" CreationDate="2015-06-08T08:24:41.190" Score="4" Body="&lt;h3&gt;What does it mean for an element to be mobile or immobile in plants?&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Generally speaking, mobile elements are those that can be moved from older to newer tissue in the plant, while immobile ones cannot be.  For example, calcium is incorporated into the cell wall, so it is immobile; it cannot be relocated later.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants with a deficiency of mobile elements (&lt;em&gt;e.g.&lt;/em&gt; nitrogen) will exhibit damage to older tissues as the nutrients are moved to new growth.  Conversely, plants lacking immobile elements (&lt;em&gt;e.g.&lt;/em&gt; calcium) will exhibit stunted new growth while the older tissues stay healthy.  Some elements (&lt;em&gt;e.g.&lt;/em&gt; sulphur) fall somewhere between these two extremes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To illustrate this concept, here is a plant with nitrogen deficiency (&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Spitskool_stikstofgebrek_(nitrogen_deficiency)_Brassica_oleracea_convar._capitata_var._alba.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;).  Notice how the older leaves are dying while the newer leaves are relatively normal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dhc3m.jpg&quot; alt=&quot;Brassica oleracea with nitrogen deficiency&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Is there an official list of mobile and immobile elements?&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;No.  You will probably have to survey the literature yourself to come up with such a list.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Why are some elements not mentioned in the sources?&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;Elements like Pb or Sr do not appear in either list because plants generally do not use these elements at all.  Only a few elements are present in any appreciable quantity in plants.  The main elements used are C, H, O, P, K, N, S, Ca, Fe, and Mg. Additionally, some other elements such as Cu, Mo, Al, and Cl are used in trace amounts as enzymatic cofactors.  Si is used for structural purposes in some plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, even for &quot;useless&quot; elements, it is possible to study how these elements are absorbed transported through a given plant.  For instance, Rediske and Selders (1953) studied the absorption of strontium by bean plants using radioactive labeling, and concluded that the element was not relocated once absorbed by the plant.  This would make it an immobile element.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;References&lt;/h3&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Feldman, Lewis J. (23 February 2015). &lt;em&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=rdancUsQb20&amp;amp;t=32m20s&quot; rel=&quot;nofollow noreferrer&quot;&gt;Water Relations, Mineral Nutrition, Fruit Development&lt;/a&gt;&lt;/em&gt; (YouTube). Biology 1B. UC Berkeley. At 32:20.&lt;/li&gt;&#xA;&lt;li&gt;Lewis, Helen (9 January 2012). &lt;a href=&quot;http://masteringhorticulture.blogspot.com/2012/01/mobile-vs-immobile-nutrients.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&quot;Mobile vs Immobile Nutrients&quot;&lt;/a&gt;. &lt;em&gt;Mastering Horticulture&lt;/em&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Rediske, J. H. and Selders, A. A. (October 1953). &quot;The Absorption and Translocation of Strontium by Plants&quot;. &lt;em&gt;Plant Physiology&lt;/em&gt; 28 (4): 594–605. PMC &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540423&quot; rel=&quot;nofollow noreferrer&quot;&gt;540423&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="11657" LastActivityDate="2015-06-08T08:24:41.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35021" PostTypeId="2" ParentId="34973" CreationDate="2015-06-08T10:30:43.703" Score="3" Body="&lt;p&gt;Christian, great idea to ask this question here before taking important decisions.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Are those media articles a hype?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Yes. Over the last 10 years I constantly see those hype stories in media about &quot;revolutionary&quot; large-scale-study/big data projects with mind-blowing numbers (gigabases, teraflops, terabytes, thousands of papers and hundreds of genes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Journalists are competing for readers with pompous titles as well as scientists need to promote their results. I recall that ~7 years ago Russian national TV came up with nothing less than &lt;em&gt;&quot;Scientists unravel the mystery of Russian soul&quot;&lt;/em&gt;, when one of our scientific institutions, close to government, finally managed to actually launch (not buy and put on hold as usual) a next-generation sequencing machine and sequence a full genome. Curiously &quot;Russian soul&quot; belongs to half-jewish, half-armenian guy. :)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though it's nice that in media papers journalists and scientists managed to explicitly articulate the problem we can't solve: how to predict morphology using molecular biology data. This work is not even close to doing that. It essentially predicts a binary trait, &quot;heads or tails&quot;.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Is this a new breakthrough approach in science, connecting areas that noone could imagine to connect?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;No. This approach is called &lt;a href=&quot;http://en.wikipedia.org/wiki/Systems_biology&quot; rel=&quot;nofollow&quot;&gt;Systems Biology&lt;/a&gt;. It's been getting popular, I'd say, since late 90s-2000s. This paper is not like &quot;look, I've invented a DNA computer/quantum computer&quot; etc. It's an ordinary systems biology study, its quality is a matter of discussion.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Is this a good systems biology paper?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I don't claim that it's bad. But some things sound strange to me:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;I don't think that &lt;em&gt;de-novo&lt;/em&gt; &lt;strong&gt;predicting&lt;/strong&gt; the network of interactions should be done by systems biology, when some facts are known from literature and could be enriched by &lt;a href=&quot;http://en.wikipedia.org/wiki/Omics&quot; rel=&quot;nofollow&quot;&gt;Omics&lt;/a&gt;. If you're modelling a molbiol/biochem network, too much freedom might render your network totally different from reality.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Robustness test is unconvincing to me. Ok, &quot;We dropped 3 crucial papers&quot; and still network holds. Ok, network predicted some results from papers, not taken into account upon its construction. But this is not a systematic test. Split the data into two parts, optimize the network on one part and test it on another one.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Small number of genes involved in the described process and binary trait in consideration make the authors do overambitious claims, IMHO.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;h2&gt;Can a smart and diligent person as yourself make a better career, doing systems biology than something else? Will your higher IQ and/or mathematical background give you an edge?&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I think, no. I think, this area downplays the difference in intellect between people, while you might prefer a more discriminating area, even if you allow the assumption that you're not the single brightest person to ever live on Earth. :) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should have worked out (or have from birth) some mental habits (e.g. habit to consider simple examples with small numbers of elements; use modular thinking; not to get stuck with a single approach - switch tricks; etc. etc.) that less smart people lack. Systems biology often works with too complex objects to imagine, thus your edge might be lost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Complexity:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In reality cascades of biological pathways include huge numbers of players involved. Moreover often a single protein has several seemingly unrelated functions. I was a bit shocked at first, when &lt;a href=&quot;http://en.wikipedia.org/wiki/Aconitase&quot; rel=&quot;nofollow&quot;&gt;aconitase&lt;/a&gt;, a Crebbs-cycle protein turned out to be at the same time an iron-responsive element and regulator of mRNA turnover. What a mad engineer could've created this?! Later I heard that many Crebbs-cycle proteins have seemingly unrelated &quot;part-time jobs&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Stability of solution:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Look at any pathway in &lt;a href=&quot;http://www.genome.jp/kegg/&quot; rel=&quot;nofollow&quot;&gt;KEGG&lt;/a&gt;. Or &lt;a href=&quot;http://en.wikipedia.org/wiki/Signal_transduction&quot; rel=&quot;nofollow&quot;&gt;this one: a famous cascade of cell signal transfer&lt;/a&gt;: . Although, it's not that complex, when you know all those proteins by heart, it might be hard to work with it quantitatively. Solutions might be unstable. Lack of experimental data may lead your simulation in a wrong direction. For instance, famous p53 protein (in this cascade it has 3 arrows or so) in reality has more than a hundred counter-agents, loss of interaction with one of them might lead your simulation to a state, critically different from reality.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Publish-ability:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another problem for  systems biology papers is lack of comprehensible results. People are usually interested in a paper, when they can build something on top of it or at least when it's an interesting special case to know about. To be honest, I can't make myself read them.&#xA;What's the scientific takeaway of this paper for instance? It doesn't exist. I can't use it as a scientist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Systems biology guys often speak of &lt;a href=&quot;http://en.wikipedia.org/wiki/Holism&quot; rel=&quot;nofollow&quot;&gt;holism&lt;/a&gt; approach as opposed to reductionism. To me it's an empty word - the only comprehensible (and thus publishable) way to approach complex entities for human being is modular thinking - you just replace a complex cascade with a black box with a set of inputs/outputs and rates and treat it as a single object, reducing the complexity that way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I feel that systems biology approach is better suited for commercial use in industry than for small-lab science. You need tools to mine data, to visualize results etc. Companies can afford building them for themselves.&#xA;As for the results, in industry you don't need them to be publishable. In agricultural industry you can optimize producing organism's metabolism with systems biology means to make it output more product of interest e.g. in cows or chemicals-producing organisms (though same goal can often be attained with pure genetic engineering easier). May be pharmacology can be interested in this to optimize their drugs to find best way to modify particular coefficients in particular reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Practical achievements based on fundamental biological science still make use of reductionist works. They stem from little facts that cervical carcinoma is caused by a specific virus and vaccination against it seems (silver bullet warning) to prevent it. Or the fact that &lt;a href=&quot;http://en.wikipedia.org/wiki/CCR5&quot; rel=&quot;nofollow&quot;&gt;CCR5&lt;/a&gt; mutants are seemingly immune to AIDS or similar results for causative agents for stomach cancer or hepatitis. Or useful discoveries of tools, such as siRNAs, Crispr/CAS9 or Tal effectors.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;If you still decide to give biology a try, it won't take you too long to grasp the molecular biology. You can mostly work with it without knowledge of biology or chemistry. In a month you'll grasp the basic concepts such as replication-transcription-translation, in a year will be familiar with most key processes, in ~3 years will be a good specialist in some area.&lt;/p&gt;&#xA;" OwnerUserId="16123" LastEditorUserId="16123" LastEditDate="2015-06-08T10:55:16.593" LastActivityDate="2015-06-08T10:55:16.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35022" PostTypeId="2" ParentId="34922" CreationDate="2015-06-08T10:34:20.083" Score="2" Body="&lt;p&gt;At the moment, the youngest diagnosed Huntington's case was 2 years of age. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12886981&quot; rel=&quot;nofollow noreferrer&quot;&gt;This&lt;/a&gt; paper appears to discuss not only this boy's onset, but also the diagnosis of symptoms in the early-onset disease. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.researchgate.net/profile/Ryan_Brinkman/publication/8674868_A_new_model_for_prediction_of_the_age_of_onset_and_penetrance_for_Huntington&amp;#39;s_disease_based_on_CAG_length/links/0912f50c7b5514d383000000.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; they research a link between age-of-onset and the length at which the repeats are. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thing is that these repeats won't just constantly get longer. There is &quot;slippage&quot; during replication which causes the repeats to get longer, but it also causes the repeats to get shorter. It's possible that mom's bad chromosome may have been inherited but because of the slippage, it no longer produces Huntington's symptoms. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This image doesn't show actual mechanics of it happening, but it shows how the repeats can be added and subtracted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bGOgw.jpg&quot; alt=&quot;From Cell&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As it turns out &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1569685/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kayser et. al&lt;/a&gt; decided to look at chimps and humans to discover which of two proposed mechanisms are more likely. Their findings suggest the slippage is closest to the &quot;heterozygote instability model&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The model suggests:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;heterozygous loci might have a higher mutation rate due to mismatch repair events that occur during synapsis&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;To answer your question in short: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It appears that the &quot;minimum age&quot; so far is 2, however, that does not mean that it hasn't occurred earlier. Huntington's is characterised by a change in motor skills, and if the change occurs before birth it might not be noticed. In theory, it is possible that Huntington's symptoms can start pre-birth.&lt;/p&gt;&#xA;" OwnerUserId="16041" LastActivityDate="2015-06-08T10:34:20.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35023" PostTypeId="2" ParentId="34476" CreationDate="2015-06-08T11:08:13.193" Score="-1" Body="&lt;p&gt;Regeneration... What a lovely word since 2010&#xA;You could start with &lt;a href=&quot;http://www.pnas.org/content/107/13/5845.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;This&lt;/a&gt; text published on 2010 which shows how P21 and it's controller(P53 gene) could regulate regeneration of mammalians' body parts and within them is neurons too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/exM5O.jpg&quot; alt=&quot;Regeneration of a hole on ear of MRL mouse or p21 knockout one&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regeneration of a hole on ear of MRL mouse or p21 knockout one&#xA;This event was accidentally observed ten years before the text get published.&#xA;They just couldn't find the ear tagged mice, because there was no hole on their ear anymore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And you could continue with &lt;a href=&quot;http://www.jneurosci.org/content/16/19/5961.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; text which explains:&#xA;p53-Independent Cyclin G Expression in a Group of Mature Neurons and Its Enhanced Expression during Nerve Regeneration&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Google Scholar is full of texts, experiments and their results which you need to gadder your information about pathways just by studying and comparing them.&#xA;But the most interesting one of them for me was p21 knocked out mice.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As physics helps computation world(Quantum Computers) to do biophysical calculations faster and faster, watching how these proteins and genes play with each other in a 3D simulated human cell like software, will not be a dream anymore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;hope it helps&lt;/p&gt;&#xA;" OwnerUserId="8540" LastEditorUserId="8540" LastEditDate="2015-06-08T20:10:10.800" LastActivityDate="2015-06-08T20:10:10.800" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35024" PostTypeId="1" AcceptedAnswerId="40100" CreationDate="2015-06-08T11:43:07.827" Score="8" ViewCount="234" Body="&lt;p&gt;On a recent fossil hunting trip, I found a small fossil that an expert identified for me as an ammonite beak. He told me such fossils are not uncommon, but are not normally found with their parent shell due to the decay of the soft tissues holding the beak in place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that under some unusual conditions, (i.e. the Burgess Shale) the soft tissues of animals can be preserved. And a quick google search reveals that there are rare belemnite fossils with their tentacles in place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However I can find no reference to any ammonite fossils, nor any of the orthocone clades, with soft part preservation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Shells of similar shape and structure are not unknown in other groups of mollusic (i.e gastropods). So: what characteristics of the shell make taxonomists sure that ammonites and orthocones are cephalopods rather than some other kind of mollusc?&lt;/p&gt;&#xA;" OwnerUserId="5083" LastEditorUserId="9906" LastEditDate="2016-07-11T13:30:14.763" LastActivityDate="2019-05-08T20:27:46.657" Title="How do we know that ammonites are a kind of cephalopod rather than another type of mollusc?" Tags="&lt;taxonomy&gt;&lt;palaeontology&gt;&lt;molluscs&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35025" PostTypeId="2" ParentId="35007" CreationDate="2015-06-08T11:59:06.990" Score="3" Body="&lt;p&gt;The Coursera &lt;a href=&quot;https://www.coursera.org/course/geneticsevolution&quot; rel=&quot;nofollow&quot;&gt;Introduction to Genetics and Evolution&lt;/a&gt; is an excellent MOOC. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I remember correctly it contains links chapters in the online version of Griffiths et al (i.e. deep links to this: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21766/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK21766/&lt;/a&gt; ) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also &lt;a href=&quot;https://www.edx.org/course/introduction-biology-secret-life-mitx-7-00x-2&quot; rel=&quot;nofollow&quot;&gt;Introduction to Biology - The Secret of Life&lt;/a&gt; from EdX, it is not just genetics, it covers a lot of molecular biology and biochem too, but it is by far the best course of it's type I've ever taken, and I'd say you could jump in on the genetics and skip the biochem if that is your preference. The simulation &quot;experiments&quot; (e.g. breeding fruit flies) are superb.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to get in to bioinformatics and you don't have strong programming skills then take a look at &lt;a href=&quot;https://www.coursera.org/course/algobioprogramming&quot; rel=&quot;nofollow&quot;&gt;Algorithms, Biology, and Programming for Beginners&lt;/a&gt;. The same people also offer more advanced courses on Coursera too, if you have more programming experience. The course is language agnostic, but Python is really the main language in the field so I'd strongly suggest you do any dev work in that.&lt;/p&gt;&#xA;" OwnerUserId="1566" LastActivityDate="2015-06-08T11:59:06.990" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35026" PostTypeId="1" AcceptedAnswerId="35046" CreationDate="2015-06-08T13:34:03.303" Score="0" ViewCount="1781" Body="&lt;p&gt;Both are beta lactams. &#xA;However, benzylpenicillin, which is also called penicillin G i.e. narrow group antibiotic. &#xA;I have now in both the following as a mechanism of action&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Binds to PBP in bacterial cell wall, causing deficit in the cell wall and causing cell death. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;where I would like to differentiate clearly benzylpenicillin from amocillin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is benzylpenicillin better in bacterial meningitis than amoxicillin? &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="86" LastEditDate="2015-06-08T15:00:11.310" LastActivityDate="2018-09-20T16:41:44.813" Title="Why is Benzylpenicillin better in Bacterial Meningitis than Amoxicillin?" Tags="&lt;pharmacology&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35028" PostTypeId="1" AcceptedAnswerId="35054" CreationDate="2015-06-08T14:21:12.313" Score="0" ViewCount="1537" Body="&lt;p&gt;Amiodarone is potassium channel blocker but also voltage-gated Na&lt;sup&gt;+&lt;/sup&gt; channel blocker according to &lt;a href=&quot;https://pubchem.ncbi.nlm.nih.gov/compound/2157#section=2D-Structure&quot; rel=&quot;nofollow&quot;&gt;Pubchem&lt;/a&gt;. However, upon reading my notes I discovered &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Amiodarone blocks potassium channels and block alpha and beta channels. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I think it must be alpha and beta &lt;strong&gt;&lt;em&gt;receptors&lt;/em&gt;&lt;/strong&gt; here, instead of &lt;em&gt;channel&lt;/em&gt;. Pubchem proposes that there may beta-blocker-like properties in amiodarone. &#xA;However, its alpha-like properties are obscure to me as I cannot find any sources. How is amiodarone working as alpha and beta blocker? &lt;/p&gt;&#xA;" OwnerUserId="86" LastEditorUserId="9943" LastEditDate="2015-06-09T04:17:20.460" LastActivityDate="2015-06-09T11:51:27.817" Title="How does amiodarone act as an alpha and beta blocker?" Tags="&lt;pharmacology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35029" PostTypeId="2" ParentId="35012" CreationDate="2015-06-08T15:05:03.230" Score="5" Body="&lt;p&gt;The answers to these questions often boil down to &quot;what do you mean by live forever?&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You've included vegetative cloning, so I infer that counts as one living organism for your purposes. In that case, the answer is absolutely.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Pando_%28tree%29&quot;&gt;Pando&lt;/a&gt; is at least 10 thousand years old and only getting larger. The Cavendish banana is about 150 years old, but produces at least 70 million tons of bananas yearly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Clonal_colony&quot;&gt;See here&lt;/a&gt; for other giant clones. Of particular interest is &lt;a href=&quot;http://en.wikipedia.org/wiki/Lomatia_tasmanica&quot;&gt;King's Lomatia&lt;/a&gt;, represented as a species by a single, sterile, individual. Fossilized triploid leaves are too old for carbon dating(at least 45 thousand years old), so it's essentially unknown how old it is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be comfortable declaring Pando immortal, since it's way too big to be eaten, too resilient to burn down, and has already survived the middle and end(at least!) of an ice age. That just leaves (ha) disease and basically nothing else as possible threats. &lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-06-08T15:05:03.230" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35030" PostTypeId="2" ParentId="31186" CreationDate="2015-06-08T16:22:35.683" Score="0" Body="&lt;p&gt;Probably, there are narrow and wide definitions for imprinting. I am guessing the history of researches about imprinting would be like the followings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Initially, maternal or paternal phenotype transmissions were recognized and some of such phenotype seemed because the maternal or paternal responsible gene does not work. As you know this is clearly imprinting. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, DNA methylation was discovered and turned out to be responsible for inactivation of imprinting genes defined above. However DNA methylation and repression of the expression by methylation occur to other genes, too. ES cells have distinct a DNA methylation pattern, which can probably explain the distinct gene expression pattern at least partially, I think. In addition, suppression of some tumor suppressor genes by methylation occurs during the course of carcinogenesis. It looks like DNA methylation regulates gene expressions as well as imprinting defined above. I know people call all gene regulations by DNA methylation imprinting. This is the wide definition.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-06-08T16:22:35.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35032" PostTypeId="1" AcceptedAnswerId="35037" CreationDate="2015-06-08T17:20:11.293" Score="7" ViewCount="1114" Body="&lt;p&gt;There are many differences in for example the digestive system between carnivores, herbivores and omnivores.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems that in certain kinds of species adaptability with respect to diet is possible. What I have heard is that it is impossible for carnivores to survive on a non-meat diet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore I wanted to ask: Is it really impossible for a carnivore to survive on a vegetarian diet, even when the fruits/vegetables/plants are processed? I could see how their digestive tract would not allow for them to survive on grass, but what about certain kinds of nuts, mushrooms, or even processed plant based foods?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If it is impossible to survive on these diets, why?(With respect to either causes in their digestive system or substantial differences between meats and any type of vegetarian food. &lt;/p&gt;&#xA;" OwnerUserId="16132" LastActivityDate="2015-06-09T19:29:29.333" Title="Can carnivores survive on a (processed) vegetarian diet? Why or why not?" Tags="&lt;physiology&gt;&lt;zoology&gt;&lt;plant-physiology&gt;&lt;nutrition&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35033" PostTypeId="2" ParentId="35032" CreationDate="2015-06-08T17:50:27.807" Score="-1" Body="&lt;p&gt;Of course it is possible for a carnivore to live with a vegetarian diet. Technically you could come up with a complete meal out of vegetables and make a carnivore pup live with it. Dogs and cats are good example of it. They can learn to eat vegi-processed food and as far the nutrients needed are present they will grow and live well. To make them eat raw vegetables is more difficult.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As correctly asked by the commenters, here some links where you can find some info about:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://ncbi.nlm.nih.gov/pmc/articles/PMC3651966&quot; rel=&quot;nofollow&quot;&gt;Vitamin D3 in plants&lt;/a&gt; (many thinks that only meat/fish contains it) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Carnosine also can be synthesise by the body, &lt;a href=&quot;http://genome.jp/dbget-bin/www_bget?enzyme%206.3.2.11&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; the main references&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://livestrong.com/article/291208-vegetarian-sources-of-dha-epa&quot; rel=&quot;nofollow&quot;&gt;DHA that is contained in several veg food&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20108213&quot; rel=&quot;nofollow&quot;&gt;Vitamin B12 from cyanobacteria&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12923" LastEditorUserId="12923" LastEditDate="2015-06-09T07:46:38.510" LastActivityDate="2015-06-09T07:46:38.510" CommentCount="15" ContentLicense="CC BY-SA 3.0" />
  <row Id="35034" PostTypeId="2" ParentId="35012" CreationDate="2015-06-08T17:54:47.183" Score="-2" Body="&lt;p&gt;Forever no. For thousands of years yes. And not only plants, other organisms have what is called biological immortality. Look here for some examples &lt;a href=&quot;https://en.m.wikipedia.org/wiki/List_of_long-living_organisms&quot; rel=&quot;nofollow&quot;&gt;https://en.m.wikipedia.org/wiki/List_of_long-living_organisms&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12923" LastActivityDate="2015-06-08T17:54:47.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35035" PostTypeId="7" CreationDate="2015-06-08T18:07:41.170" Score="0" Body="&lt;p&gt;&#xA;    On Stack Exchange, we believe the core moderators should come &lt;i&gt;from&lt;/i&gt; the community, and be elected by the community itself through popular vote. We hold regular elections to determine who these community moderators will be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&#xA;    Community moderators are &lt;a href=&quot;http://blog.stackoverflow.com/2009/05/a-theory-of-moderation/&quot;&gt;accorded the highest level of privilege on our community&lt;/a&gt;, and should themselves be exemplars of positive behavior and leaders within the community.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&#xA;    Our general criteria for moderators is as follows:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;    &lt;li&gt;patient and fair&lt;/li&gt;&#xA;    &lt;li&gt;leads by example&lt;/li&gt;&#xA;    &lt;li&gt;shows respect for their fellow community members in their actions and words&lt;/li&gt;&#xA;    &lt;li&gt;open to some light but firm moderation to keep the community on track and resolve (hopefully) uncommon disputes and exceptions&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&#xA;    Every election has three phases:&#xA;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;    &lt;li&gt;Nomination&lt;/li&gt;&#xA;    &lt;li&gt;Primary&lt;/li&gt;&#xA;    &lt;li&gt;Election&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&#xA;    Please participate in the moderator elections by voting, and perhaps even by nominating yourself to be a community moderator!&#xA;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://chat.stackexchange.com/rooms/89900/2019-biology-moderator-election-chat&quot;&gt;Election chat room&lt;/a&gt; - discuss the election, candidates, etc.&lt;/li&gt;&#xA;&lt;li&gt;For questions about the election process itself, visit &lt;a href=&quot;https://biology.meta.stackexchange.com/tags/election&quot;&gt;Meta&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;&lt;a href=&quot;https://biology.meta.stackexchange.com/questions/3908/2019-moderator-election-qa-questionnaire&quot;&gt;The candidates answer your questions&lt;/a&gt;&lt;/strong&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="-1" LastEditorUserId="1" LastEditDate="2019-02-18T20:00:37.253" LastActivityDate="2019-02-18T20:00:37.253" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="35036" PostTypeId="1" AcceptedAnswerId="35047" CreationDate="2015-06-08T18:43:49.047" Score="6" ViewCount="48193" Body="&lt;p&gt;Is it even possible that plants with non-green leaves have chlorophyll, and do such non-green leaved plants carry out photosynthesis? &lt;/p&gt;&#xA;" OwnerUserId="15862" LastEditorUserId="9943" LastEditDate="2015-06-09T02:08:01.853" LastActivityDate="2016-02-03T16:39:53.693" Title="Do plants with non-green leaves have chlorophyll and photosynthesis?" Tags="&lt;botany&gt;&lt;photosynthesis&gt;&lt;chloroplasts&gt;" AnswerCount="4" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35037" PostTypeId="2" ParentId="35032" CreationDate="2015-06-08T18:50:52.420" Score="6" Body="&lt;p&gt;With arbitrarily broad meaning of &quot;processed&quot;, yes. If absolutely nothing else, elemental purification and inorganic synthesis of something chemically resembling meat in nutrition is possible. Prohibitively expensive and stupid, yes, but possible. So then the question becomes exactly how much processing you need to do. Without clear bounds on that question and inadequate research on the metabolism of obligate carnivores, nothing closer than a broad stab at an answer makes sense. That said, here's a broad stab.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, you'd probably need to synthesize &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7843559&quot; rel=&quot;nofollow&quot;&gt;vitamin D3&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Carnosine&quot; rel=&quot;nofollow&quot;&gt;carnosine&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Docosahexaenoic_acid&quot; rel=&quot;nofollow&quot;&gt;DHA&lt;/a&gt;, and a handful of other things from plant extract, which is possible but difficult. Carnivores often have carnosine synthases, for instance. Cats have &lt;a href=&quot;http://www.uniprot.org/uniparc/UPI0005AD04F6&quot; rel=&quot;nofollow&quot;&gt;two&lt;/a&gt; &lt;a href=&quot;http://www.uniprot.org/uniparc/UPI0003F1979B&quot; rel=&quot;nofollow&quot;&gt;distinct&lt;/a&gt; carnosine synthases. In terms of dietary sufficiency, that may or may not be enough. To be sure, you'd have to break it down to amino acids and build it back up again, essentially. Obligate carnivores are likely to have a number of other metabolic needs that aren't met with, for instance, pulverized soybeans. You're going to need at least one vat for fermenting raw amino acids into carnosine, and probably another for vitamin D3. Seawater microalgae contain lots of DHA, so that is probably something to look into. You could oversupplement &lt;a href=&quot;http://en.wikipedia.org/wiki/Alpha-Linolenic_acid&quot; rel=&quot;nofollow&quot;&gt;alpha-linolenic acid&lt;/a&gt; instead of supplementing DHA, which might or might not work. There's not a lot of study into carnivore metabolism, so prepare to make some discoveries the hard way. Genetic studies can only take you so far, so don't try this on your favorite pet first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short: yes, you can raise carnivores on a diet made from plants and plant material. Rhetorical you, as in it is possible. It's probably not something you can do at home, even if you're wealthy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I'm assuming &quot;feeding the vegetable matter to chickens&quot; falls outside the domain of &quot;processed&quot; but it would be much easier than large-scale amino acid purification and fermentation.)&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="4109" LastEditDate="2015-06-09T19:29:29.333" LastActivityDate="2015-06-09T19:29:29.333" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35038" PostTypeId="2" ParentId="35036" CreationDate="2015-06-08T18:54:28.243" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.nytimes.com/2013/07/23/science/how-does-a-plant-with-red-leaves-support-itself-without-green-chlorophyll.html&quot; rel=&quot;nofollow&quot;&gt;They do have chlorophyll&lt;/a&gt;, at least in general. There are a couple very rare exceptions, but if it can stand up on its own, it contains chlorophyll. The green is just washed out by a very bright red pigment.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-06-08T18:54:28.243" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35039" PostTypeId="1" CreationDate="2015-06-08T19:10:30.350" Score="12" ViewCount="1703" Body="&lt;p&gt;I found this one on a hill here in Palestine. It's about 20 cm in height. Note that it does exist in this regions, but scantily. &lt;img src=&quot;https://i.stack.imgur.com/qNPwI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16133" LastEditorUserId="6307" LastEditDate="2015-06-08T19:17:46.873" LastActivityDate="2015-06-09T07:24:48.190" Title="What is the scientific name of this plant?" Tags="&lt;botany&gt;&lt;species-identification&gt;&lt;taxonomy&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35040" PostTypeId="2" ParentId="35036" CreationDate="2015-06-08T19:31:23.327" Score="1" Body="&lt;p&gt;Parasitic plants such as &lt;a href=&quot;http://en.wikipedia.org/wiki/Orobanche&quot; rel=&quot;nofollow&quot;&gt;Orobanche&lt;/a&gt; lack chlorophyll and cannot photosynthesize. They obtain all of their energy from paratising another organism.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-06-08T19:31:23.327" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35041" PostTypeId="2" ParentId="35039" CreationDate="2015-06-08T20:20:42.277" Score="14" Body="&lt;p&gt;The plant is of Lamiaceae family and its common name is Shell Flower or Bells of Ireland.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its &quot;scientific&quot; aka latin name is &lt;a href=&quot;http://en.wikipedia.org/wiki/Moluccella_laevis&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Moluccella laevis&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MVdRe.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="3340" LastEditDate="2015-06-09T07:24:48.190" LastActivityDate="2015-06-09T07:24:48.190" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35043" PostTypeId="1" AcceptedAnswerId="35049" CreationDate="2015-06-08T20:49:02.060" Score="7" ViewCount="1320" Body="&lt;p&gt;I live in Denmark, Europe and I found this insect wandering around in my garden the other day. It's some kind of beetle, but I don't know what kind it is or the species. The beetle could also fly and had red wings beneath its armor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Help would be much appreciated. Thank you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/glUAJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wQOly.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6DLl1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user14636" LastEditorDisplayName="user14636" LastEditDate="2017-06-24T15:36:14.353" LastActivityDate="2017-06-24T15:36:14.353" Title="What kind of beetle is this?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35044" PostTypeId="2" ParentId="35036" CreationDate="2015-06-08T21:07:52.407" Score="2" Body="&lt;p&gt;All photosynthesis reaction does need chlorophyll,even in cyanobacteria and algae the difference is the type of chlorophyll ( which depends on available wavelength of light and energy efficiency ) fully parasite plants on the other hand doesn't contain chlorophyll and this force them to live as parasites ( keep in mind that we do have half parasitic plants too,which their problem is lack of roots,they do photosynthesis just like other plants ) plants with non-green leafs does contain chlorophyll in some cases even more than green plants ( in my own experience berberis which is a red to alizarin crimson violet shade has more chlorophyll than a greek lettuce) the other pigments are working as helping energy harvesters in photosynthetic reactions, light/shade controllers or simply a survival strategic materials in answer to climate changes,habitat problems and environmental stresses &lt;/p&gt;&#xA;" OwnerUserId="16108" LastActivityDate="2015-06-08T21:07:52.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35045" PostTypeId="2" ParentId="35043" CreationDate="2015-06-08T21:15:22.053" Score="5" Body="&lt;p&gt;The beetle resembles &lt;a href=&quot;http://en.wikipedia.org/wiki/Soldier_beetle&quot; rel=&quot;noreferrer&quot;&gt;Soldier beetle&lt;/a&gt;, especially Cantharis lecontei&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Soldier Beetles (Cantharidae) » Cantharinae » Cantharini » &lt;a href=&quot;http://bugguide.net/node/view/1057958/bgimage&quot; rel=&quot;noreferrer&quot;&gt;Cantharis&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xw66U.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4TYcN.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-06-08T21:27:37.480" LastActivityDate="2015-06-08T21:27:37.480" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="35046" PostTypeId="2" ParentId="35026" CreationDate="2015-06-08T21:15:26.523" Score="1" Body="&lt;p&gt;Amoxicillin is just penicillin with a hydroxyl group off the ring and an extra amine group..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/WY6Wd.png&quot; alt=&quot;enter image description here&quot;&gt;  &lt;img src=&quot;https://i.stack.imgur.com/KrG8U.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Their mechanisms of action are the same. Their ability to cross the blood-brain barrier are the same. They can both cause seizures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both are used to treat to meningitis. The selection of one over the other would be based on the sensitivity of the infecting organism, and the ability to cross the blood-brain barrier in inflamed meninges.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are better drugs to treat meningitis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952976/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Penetration of Drugs through the Blood-Cerebrospinal Fluid/Blood-Brain Barrier for Treatment of Central Nervous System Infections&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="6307" LastEditDate="2015-07-12T02:01:54.133" LastActivityDate="2015-07-12T02:01:54.133" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35047" PostTypeId="2" ParentId="35036" CreationDate="2015-06-08T21:23:54.943" Score="9" Body="&lt;p&gt;Yes, it is possible, but not necessarily the case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Non-green leaves with chlorophyl&lt;/strong&gt;: There are leaves that don't appear green, but do have chlorophyl and therefore can conduct photosynthesis. (See, for instance, &lt;a href=&quot;https://biology.stackexchange.com/questions/1415/how-do-white-caladiums-perform-enough-photosynthesis-to-support-their-mass?rq=1&quot;&gt;refraction effects in white caladiums&lt;/a&gt; or the link in the answer by Resonating).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Non-green leaves without chlorophyl&lt;/strong&gt;: There are leaves that don't appear green because they have no chlorophyl, and so do not conduct photosynthesis. (See, for instance, parasitic plants like the Oronbanche linked by Cactuswoman or this Monotropa)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/i5zU2.jpg&quot; alt=&quot;Monotropa hypopitys, Yunnan China, by me&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-06-08T21:23:54.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35048" PostTypeId="1" CreationDate="2015-06-08T22:00:30.923" Score="2" ViewCount="14911" Body="&lt;p&gt;For how long can a human sustain a temperature of 180 degrees Fahrenheit (82&lt;sup&gt;o&lt;/sup&gt;C) without damage in a confined place?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, suppose a person is sitting in a steam-filled room, without external air flow (but with enough oxygen) - how long could one resist the heat before permanent physical damage would occur?  &lt;/p&gt;&#xA;" OwnerUserId="16135" LastEditorUserId="9943" LastEditDate="2015-06-09T04:35:45.960" LastActivityDate="2019-06-25T22:13:59.683" Title="How much heat can a human sustain?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;temperature&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35049" PostTypeId="2" ParentId="35043" CreationDate="2015-06-08T23:13:52.623" Score="8" Body="&lt;p&gt;As @Ilan wrote, this is a &lt;a href=&quot;https://en.wikipedia.org/wiki/Soldier_beetle&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cantharidae&lt;/a&gt; but most probably &lt;a href=&quot;https://en.wikipedia.org/wiki/Cantharis_fusca&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Cantharis fusca&lt;/em&gt;&lt;/a&gt;, which is very common species in northern Europe. &lt;em&gt;Cantharis rustica&lt;/em&gt; is similar but has reddish femurs and the black spot is more centered on the pronotum. It is not &lt;em&gt;C. lecontei&lt;/em&gt;, which is a North American species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you go looking at flowers of &lt;em&gt;Anthriscus sylvestris&lt;/em&gt; for an hour or two, you will most likely see at least &lt;em&gt;Cantharis fusca&lt;/em&gt;, &lt;em&gt;Cantharis rustica&lt;/em&gt; and &lt;em&gt;Cantharis obscura&lt;/em&gt; - they are all very common in Scandinavia during early spring/summer. The larvae of all these species live on the ground/in plant litter as predators.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Cantharis fusca&lt;/em&gt;&lt;/strong&gt;&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/hePZv.jpg&quot; alt=&quot;enter image description here&quot;&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Cantharis rustica&lt;/em&gt;         .................... &lt;em&gt;Cantharis obscura&lt;/em&gt;&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/3GoNzm.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/ARDzcm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-06-09T13:40:53.957" LastActivityDate="2015-06-09T13:40:53.957" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35050" PostTypeId="2" ParentId="35000" CreationDate="2015-06-09T00:12:17.593" Score="1" Body="&lt;p&gt;Remember: A and B are genetic markers that might be linked to the disease gene. Neither A nor B are actually the hemophilia disease mutation (or gene), A or B are proxies, or substitutes for the mutation in the disease gene. &#xA;Since it is an X-linked recessive, it is only the Mother's two X chromosomes that are candidates.  You can completely ignore the Father's copy of X that also happens to carry the A marker. &#xA;In the F1 generation every male who received the copy of the Mother's X marked with A died, and every male who received her X marked with B survived. Therefore her X marked with A is linked to the mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Those other AA females are either heterozygotes, or outsiders who married into the family. The outsiders do not carry the mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Perhaps your confusion is due in part to the fact that some key facts are not explicit in the pedigree diagram from your instructor's course materials? Try drawing the various genotypes out like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nvelJ.jpg&quot; alt=&quot;Parental Genotypes&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="14946" LastEditDate="2015-06-09T00:36:15.277" LastActivityDate="2015-06-09T00:36:15.277" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35051" PostTypeId="1" AcceptedAnswerId="35053" CreationDate="2015-06-09T01:08:19.740" Score="2" ViewCount="923" Body="&lt;p&gt;In the Materials and Methods section of &lt;strong&gt;&lt;a href=&quot;http://www.researchgate.net/profile/Paul_Cornwell2/publication/10848938_Analysis_of_DNA_in_hair_fibers/links/546b49560cf2f5eb18091791.pdf&quot; rel=&quot;nofollow&quot;&gt;this paper on DNA extraction and analysis from hair&lt;/a&gt;&lt;/strong&gt; I do not understand some parts of their protocol methods. In particular:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;The digested hair solution was then extracted twice with two volumes of phenol saturated by Tris-EDTA (TE) buffer (Sigma), and once with two volumes of chloroform. &quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;How do the volumes of phenol and chloroform come into play? I know they are used for an organic-solvent extraction, but what was the actual procedure used, i.e., the steps for adding each chemical? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another question I had was on the buffer they used:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;0.01 M Tris-HCL(ph8), 0.005 M EDTA, 0.1 M NaC1, 0.039 M DTT, 2% SDS&quot; &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That whole combination would be the &quot;Tris buffer&quot; then yes? And the proteinase K would then be added to some of this buffer to digest the hair?&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="9943" LastEditDate="2015-06-09T01:27:20.940" LastActivityDate="2015-06-09T01:47:02.363" Title="Explanation of protocol in DNA extraction experiment" Tags="&lt;protocol&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35053" PostTypeId="2" ParentId="35051" CreationDate="2015-06-09T01:42:29.653" Score="5" Body="&lt;p&gt;The DNA solution has a fixed volume (e.g., 0.1 mL). To a suitable test tube is added 0.2 mL of buffer-saturated phenol. After closing the test tube the mixture is mixed well, typically using a vortex mixer, but possibly by careful, repeated inversion. The aqueous phase and the organic phase are barely miscible. The tube is centrifuged to speed up the equilibration, and concentrate the denatured protein at the interface. After centrifugation the aqueous layer is carefully removed to a fresh test tube.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is one organic extraction. This is repeated with a fresh aliquot of buffer-saturated phenol (another 0.2 mL). Then the aqueous phase is decanted again and extracted with 0.2 mL of CHCl3.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the recipe you provided, the buffer-saturated phenol was purchased from a vendor (Sigma-Aldrich Chemicals, of St. Louis, Missouri, USA), so you can look up the ingredients and composition on their online catalogue (no doubt).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The buffer recipe you provided is the proteinase K digestion buffer. It is typically performed at an elevated temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This protocol is designed to isolate DNA from the nuclei of hair cells. Fully half of the contents of a eukaryotic nucleus are chromosomal proteins, by mass, so the proteinase K digestion step not only breaks open the hair cells, but also helps to remove all of the unwanted, contaminating cellular and nuclear proteins.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="14946" LastEditDate="2015-06-09T01:47:02.363" LastActivityDate="2015-06-09T01:47:02.363" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35054" PostTypeId="2" ParentId="35028" CreationDate="2015-06-09T04:01:38.130" Score="2" Body="&lt;p&gt;Amiodarone inhibits sodium, potassium and calcium currents. Its major antiarrhythmic properties are thought to be related to prolongation of the&#xA;action potential duration. Amiodarone also exerts an antiadrenergic&#xA;effect by non competitively inhibiting alpha- and beta-receptors &lt;a href=&quot;https://www.google.com.au/search?q=Amiodarone+blocks+potassium+channels+and+block+alpha+and+beta+channels.&amp;amp;oq=Amiodarone+blocks+potassium+channels+and+block+alpha+and+beta+channels.&amp;amp;aqs=chrome..69i57.283j0j4&amp;amp;sourceid=chrome&amp;amp;es_sm=93&amp;amp;ie=UTF-8#&quot; rel=&quot;nofollow&quot;&gt;(Ghuran &amp;amp; Camm, 2000)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Alpha blockers&lt;/strong&gt; relax certain muscles and help small blood vessels remain open by antagonizing norepinephrine's tightening effects on the muscles in the walls of smaller arteries and veins, which &lt;strong&gt;improves blood flow and lowers blood pressure&lt;/strong&gt; &lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/high-blood-pressure/in-depth/alpha-blockers/art-20044214&quot; rel=&quot;nofollow&quot;&gt;(Mayo Clinic)&lt;/a&gt;. &lt;strong&gt;Beta blockers&lt;/strong&gt; decrease the effects of epinephrine (adrenaline), reducing heart rate and reducing its force, thereby &lt;strong&gt;reducing blood pressure&lt;/strong&gt;. Beta blockers also help blood vessels open up to &lt;strong&gt;improve blood flow&lt;/strong&gt; &lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/high-blood-pressure/in-depth/beta-blockers/art-20044522&quot; rel=&quot;nofollow&quot;&gt;(Mayo Clinic)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.adrenoceptor.com/alphaintro.htm&quot; rel=&quot;nofollow&quot;&gt;Alpha-adrenergic receptors&lt;/a&gt; and Beta-adrenergic receptors are G-protein coupled receptors &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs00059-002-2434-z&quot; rel=&quot;nofollow&quot;&gt;(Wallukat, 2002)&lt;/a&gt;. Hence, they do not form channels and your notes are incorrect. The ion currents &lt;em&gt;are&lt;/em&gt; mediated by channels, though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;https://www.google.com.au/search?q=Amiodarone+blocks+potassium+channels+and+block+alpha+and+beta+channels.&amp;amp;oq=Amiodarone+blocks+potassium+channels+and+block+alpha+and+beta+channels.&amp;amp;aqs=chrome..69i57.283j0j4&amp;amp;sourceid=chrome&amp;amp;es_sm=93&amp;amp;ie=UTF-8#&quot; rel=&quot;nofollow&quot;&gt;Ghuran &amp;amp; Camm, &lt;em&gt;J Clin Basic Cardiol&lt;/em&gt; (2000); &lt;strong&gt;3&lt;/strong&gt;: 206&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs00059-002-2434-z&quot; rel=&quot;nofollow&quot;&gt;Wallukat, &lt;em&gt;Herz&lt;/em&gt; (2002); &lt;strong&gt;27&lt;/strong&gt;(7): 683-90&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-09T11:51:27.817" LastActivityDate="2015-06-09T11:51:27.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35056" PostTypeId="2" ParentId="35048" CreationDate="2015-06-09T05:32:59.153" Score="8" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Water of &lt;strong&gt;180 &lt;sup&gt;o&lt;/sup&gt;F&lt;/strong&gt; (82 &lt;sup&gt;o&lt;/sup&gt;C) causes &lt;em&gt;immediate&lt;/em&gt; &lt;a href=&quot;http://en.wikipedia.org/wiki/Scalding&quot; rel=&quot;noreferrer&quot;&gt;scalding&lt;/a&gt; (thermal burn wounds).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The severity of a scald injury depends on the temperature to which the skin is exposed, and for how long. Residential water heaters warm up tap water typically to 120 &lt;sup&gt;o&lt;/sup&gt;F (48 &lt;sup&gt;o&lt;/sup&gt;C). At this temperature, the skin of adults requires an average of five minutes of exposure for a full thickness burn to occur. When the temperature of a hot liquid is increased to 140 &lt;sup&gt;o&lt;/sup&gt;F (60 &lt;sup&gt;o&lt;/sup&gt;C)) it takes only five seconds or less for a serious burn to occur. Coffee, tea, hot chocolate and other hot beverages are usually served at &lt;strong&gt;160 to 180 &lt;sup&gt;o&lt;/sup&gt;F&lt;/strong&gt; (71 - 82 &lt;sup&gt;o&lt;/sup&gt;C), resulting in almost &lt;strong&gt;instantaneous burns that will require surgery&lt;/strong&gt; (&lt;a href=&quot;http://www.ameriburn.org/&quot; rel=&quot;noreferrer&quot;&gt;American Burn Association&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How these numbers apply to steam I am not sure, but I think they will be comparable, given that steam is essentially made up of a dense mass of water droplets. Further, the amount of steam obviously matters. Consider these numbers: The temperature in a &lt;a href=&quot;http://goaskalice.columbia.edu/steam-room-vs-sauna&quot; rel=&quot;noreferrer&quot;&gt;sauna&lt;/a&gt; typically ranges from 160-200 &lt;sup&gt;o&lt;/sup&gt;F (71 - 93 &lt;sup&gt;o&lt;/sup&gt;C) with a low level of humidity (ranging from 5 - 30%). &lt;a href=&quot;http://goaskalice.columbia.edu/steam-room-vs-sauna&quot; rel=&quot;noreferrer&quot;&gt;Steam rooms&lt;/a&gt; provide moist heat from a water-filled generator pumping steam into the enclosed room. The temperature in a steam room typically ranges from 110-114 degrees Fahrenheit (43 - 46 &lt;sup&gt;o&lt;/sup&gt;C) with a humidity level of 100%.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is anecdotal evidence of the Russia-born Ivan Ivanitz Chabert (&lt;em&gt;1792-1859&lt;/em&gt;), who supposedly entered an iron oven in Paris (&lt;a href=&quot;https://play.google.com/books/reader?id=y2QNAAAAYAAJ&amp;amp;printsec=frontcover&amp;amp;output=reader&amp;amp;hl=en&amp;amp;pg=GBS.PR3&quot; rel=&quot;noreferrer&quot;&gt;Times telescope, 1831&lt;/a&gt;) with a few trays of meat, and stayed there unscathed for 5 minutes at a temperature of 380 degrees F (193 &lt;sup&gt;o&lt;/sup&gt;C). When he re-emerged from the oven the meat was cooked, while the only noticeable effect on him were profuse sweating and a dramatic increase in heart rate (from 98 to 168 bpm). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This experiment shows the remarkable capacity of the human body to reduce overheating by means of evaporative cooling (&lt;a href=&quot;http://en.wikipedia.org/wiki/Perspiration&quot; rel=&quot;noreferrer&quot;&gt;sweating&lt;/a&gt;). However, the effects of steam are far more devastating to the human body than dry heat. Not only does it carry much &lt;a href=&quot;http://en.wikipedia.org/wiki/Energy_density&quot; rel=&quot;noreferrer&quot;&gt;more energy than hot air&lt;/a&gt;, it also prevents perspiration by saturating the air with water vapor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ameriburn.org/Preven/ScaldInjuryEducator%27sGuide.pdf&quot; rel=&quot;noreferrer&quot;&gt;American Burn Association Educator's Guide&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;https://play.google.com/books/reader?id=y2QNAAAAYAAJ&amp;amp;printsec=frontcover&amp;amp;output=reader&amp;amp;hl=en&amp;amp;pg=GBS.PR3&quot; rel=&quot;noreferrer&quot;&gt;Times Telescope, 1831&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-09T09:49:00.740" LastActivityDate="2015-06-09T09:49:00.740" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35057" PostTypeId="1" CreationDate="2015-06-09T06:00:57.483" Score="4" ViewCount="551" Body="&lt;p&gt;I would have some related questions about the mating types of fungi.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Does a single spore generate a mycelium possessing only one mating type? If it does not in general, do Ascomycota and Basidiomycota possess only one mating type per individual mycelium?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are homothallism and heterothallism properties of the individual mycelium or of the species? The definitions that I find in my book and on line confuse me. I understand that &lt;em&gt;homothallism&lt;/em&gt; is the property of a mycelium (possessing only one mating type or can it possess many mating types in a similar way to hermaphrodite animals? cfr. question 1) that can mate with itself (if it can possess many mating types and it can mate with itself only by using gametes of different mating types, is it still homothallic?) and &lt;em&gt;heterothallism&lt;/em&gt; is the property of a mycelium that is not homothallic, but I am not sure I understand, because I read of &lt;em&gt;homothallic&lt;/em&gt; and &lt;em&gt;heterothallic species&lt;/em&gt; too: is a homothallic species a species where at least some individual is homothallic, where all individuals are homothallic or something else?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I am sure that mating type is a property characterising at least gametes, but is it a property of indiviual cells too? As an example, I know that it is necessary, among many species of fungi, for two gametes to belong to two different mating types in order to produce a zygote. Some fungi, as it is the rule among Basidiomycota, reproduce by somatogamy, i.e. the nuclei generating the zygote are from somatic cells, other than gametes. In such cases, are there species where it is necessary for the somatic cells of a homothallic mycelium to belong to a different type than the type with which they are undergoing plasmogamy? Thank you very much for any answer!&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="8124" LastEditorUserId="8124" LastEditDate="2015-06-09T19:41:17.063" LastActivityDate="2021-05-13T01:06:30.677" Title="Mating types in fungi (and somatogamy)" Tags="&lt;botany&gt;&lt;reproduction&gt;&lt;reproductive-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35058" PostTypeId="1" AcceptedAnswerId="35453" CreationDate="2015-06-09T06:36:11.747" Score="7" ViewCount="3703" Body="&lt;p&gt;I have found the following definitions of different types of gametes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;isogametes&lt;/em&gt;: gametes looking and behaving the same;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;heterogametes&lt;/em&gt;: gametes different in size or in behaviour;&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;oogametes&lt;/em&gt;: gametes different in size and behaviour.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I have some doubts about the exact meaning of &lt;em&gt;behaviour&lt;/em&gt; in such definitions. I know that there exist species where gametes of the same mating type can originate a zygote, for ex. in some fungi.&#xA;Do differing heterogametes and oogametes always belong to different mating types?&#xA;Thank you very much for any clarification!&lt;/p&gt;&#xA;" OwnerUserId="8124" LastEditorUserId="8124" LastEditDate="2015-06-14T10:01:08.797" LastActivityDate="2019-03-22T01:59:57.943" Title="Isogametes and oogametes" Tags="&lt;reproduction&gt;&lt;reproductive-biology&gt;&lt;gamete&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35059" PostTypeId="1" AcceptedAnswerId="35060" CreationDate="2015-06-09T09:11:15.587" Score="2" ViewCount="1197" Body="&lt;p&gt;I need to establish a cell line starting from single cells seeded on a 96 wells plate by a FACS sorter. The cells I am using are human fibroblasts RPE-1 cultured in F12 medium supplemented with 10% FBS and antibiotics. After having seeded 5x96 cells (one cell per well in 5 plates) I have obtained only 4 colonies. Does anyone know any good (preferably personally tested) protocol to efficiently grow fibroblast colonies from single cells?&lt;/p&gt;&#xA;" OwnerUserId="12923" LastActivityDate="2015-06-23T17:03:38.117" Title="How to grow fibroblast colonies from single cells?" Tags="&lt;cell-culture&gt;&lt;eukaryotic-cells&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35060" PostTypeId="2" ParentId="35059" CreationDate="2015-06-09T10:40:00.720" Score="2" Body="&lt;p&gt;This should be relatively straight forward. Sort the cells into single wells so all descendants are clones of the sorted cell and let them grow until they are dense enough to be transferred into a bigger plate (probably 48 or 24 well). Continue this process until you can go into big cell culture flasks or plates and make sure that you freeze away a number of aliquots as a backup if something goes wrong. Expand the cells further until you have enough cells to do an analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Keratinocytes need some time to get highly proliferative (around a week or so) and if you don't grow them on a layer of feeder cells, usually also need a special conditioned medium. See the references below (if you have trouble accessing the papers, let me know).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What often also helps is the use of conditioned media. I know this from other cells in the skin which often don't like to grow (at least not as primary cells) unless you use conditioned media. For this, take of the media from the same sort of cells (here it would be keratinocytes) before it is completely used (typically yellow if the media contains pH indicators), centrifuge it to remove any cell debris and then mix it with fresh media to let your cells grow. You might need to experiment a bit with the mixing ratio between the &quot;used&quot; and the fresh media, but 50%:50% is usually a good starting point.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.salk.edu/labs/belmonte/pubs/2010/2010-184-np.aasen.pdf&quot; rel=&quot;nofollow&quot;&gt;Isolation and cultivation of human keratinocytes  from skin or&#xA;plucked hair for the generation of  induced pluripotent stem cells&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0305417992901043&quot; rel=&quot;nofollow&quot;&gt;Culture techniques for human keratinocytes&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0305417993900287&quot; rel=&quot;nofollow&quot;&gt;Improvement of human keratinocyte isolation and culture using&#xA;thermolysin&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-06-23T17:03:38.117" LastActivityDate="2015-06-23T17:03:38.117" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35061" PostTypeId="6" CreationDate="2015-06-09T11:19:02.873" Score="0" Body="&lt;p&gt;I am Chris, better known as &lt;strong&gt;AliceD&lt;/strong&gt;, and a postdoc with a passion for sensory systems and Neuroscience. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First off, the &lt;em&gt;current moderators&lt;/em&gt; are awesome and there are other &lt;em&gt;giants&lt;/em&gt; at Biology.SE who surpass me in experience. However, while I might be relatively new, I have actively participated in the efforts in the last 7 months leading to this site's graduation and I have identified many great things and also some bottle necks that need attention. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;A few of the many great things to keep:&lt;/strong&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Overall, the &lt;em&gt;current vigor&lt;/em&gt; on keeping this site's quality as set by the most active users is awesome and should be sustained;&lt;/li&gt;&#xA;&lt;li&gt;The &lt;em&gt;general tone&lt;/em&gt;, most notably towards new users has been great of late. &#xA;&lt;br&gt;&lt;br&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Things to change:&lt;/strong&gt;&lt;br&gt;  &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Closing questions is one thing; &lt;em&gt;editing questions and making them suitable for this site&lt;/em&gt; is where the challenge is; &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Personal and/or very specific questions&lt;/em&gt; are a worthy target, because questions should be interesting and understandable to the community at large; &lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Overlap between sites&lt;/em&gt;, most notably Cognitive Sciences (where I am also active), as well as Skeptics and Health could be more explicitly defined.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-13T11:28:11.227" LastActivityDate="2015-06-13T11:28:11.227" CommentCount="7" CommunityOwnedDate="2015-06-09T11:19:02.873" ContentLicense="CC BY-SA 3.0" />
  <row Id="35062" PostTypeId="6" CreationDate="2015-06-09T12:19:43.670" Score="0" Body="&lt;p&gt;Hello,&#xA;I am Chris, and a biochemist by training. I discovered this community about 1.5 years ago and have been hooked on to it since then. I have been actively participating during that time (and will in the future). For me Biology.SE is a very interesting way to get into contact with new topics in biology. Also it is a great platform to help other people with the knowledge I have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wasn't sure at first if I should participate in this election or not but eventually I decided it is a very good way to participate in this community (besides answering questions) and help to bring on and develop this community.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why I think I am a good candidate:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;I have been an active participant for quite a while now and know the community quite well.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I am a moderator for other forums as well, so I know how to handle problematic cases and spam and I am usually a calm person. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Why I think I'm not a good candidate:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Since I work actively in biomedical research, there are times when I cannot participate too much, due to time constraints. I don't think this is too much of a problem as I will be able to find time for moderation purposes.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-06-09T12:38:57.340" LastActivityDate="2015-06-09T12:38:57.340" CommentCount="2" CommunityOwnedDate="2015-06-09T12:19:43.670" ContentLicense="CC BY-SA 3.0" />
  <row Id="35063" PostTypeId="1" AcceptedAnswerId="35077" CreationDate="2015-06-09T12:43:37.597" Score="3" ViewCount="103" Body="&lt;p&gt;Body organs are kept cold in-between explanting them from the donor and implanting them in the new host. How do these cold conditions help organs to stay viable while they haven't fresh blood, energy and oxygen supply?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="9943" LastEditDate="2015-06-09T12:50:14.333" LastActivityDate="2015-06-09T19:56:44.857" Title="How do cold conditions help organ transplants?" Tags="&lt;physiology&gt;&lt;temperature&gt;&lt;decay&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35067" PostTypeId="6" CreationDate="2015-06-09T15:18:48.480" Score="0" Body="&lt;p&gt;Hello,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am known in this community as &lt;strong&gt;WYSIWYG&lt;/strong&gt;. I have worked in different aspects of biology which include molecular and cell biology, bioinformatics and computational biology (mathematical modeling). So, I just call myself a biologist. I joined this site by chance when I was looking for a forum for Q/A about biology. Since then, I have been an active user.&#xA;I am applying for the position of a moderator because I wish to play my part in maintaining as well as improving the quality of our forum. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why would I be a good moderator?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;I have been an active user for about two years now&lt;/li&gt;&#xA;&lt;li&gt;I have also been active in meta discussions about how to ensure quality&lt;/li&gt;&#xA;&lt;li&gt;My interdisciplinary background would let me judge diverse topics&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What do I wish to to implement as a moderator?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I wish to see this site grow to the level of StackOverflow, which in my opinion will happen only if we get good quality questions and answers. My primary focus therefore would be quality control. I also would want to decide a general policy, based on a meta discussion, about our community's stand on homework, personal and creationism related questions (and other issues which have remained unresolved).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-09T15:18:48.480" LastActivityDate="2015-06-09T15:18:48.480" CommentCount="0" CommunityOwnedDate="2015-06-09T15:18:48.480" ContentLicense="CC BY-SA 3.0" />
  <row Id="35068" PostTypeId="2" ParentId="35059" CreationDate="2015-06-09T15:27:57.960" Score="2" Body="&lt;p&gt;Although I have not yet done, in general, cells are happier in a conditioning medium. Grow the original cells in 10cm dishes and save the medium and use it to grow single colonies. You might want to mix used and fresh medium (1:1 ratio).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Growth factors are another option. Insulin is sometimes used, but it also depends on cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Coating the surface of well with extracellular matrix such as collagen could be effective. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your cells are normal human fibroblast, cells get senescent, stopping growing. You might want to use immortalized cells like &lt;a href=&quot;http://www.atcc.org/products/all/CRL-4000.aspx&quot; rel=&quot;nofollow&quot;&gt;hTERT RPE-1&lt;/a&gt;, although you should be careful because immortalization could cause characteristic changes.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-06-09T18:32:46.313" LastActivityDate="2015-06-09T18:32:46.313" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35069" PostTypeId="2" ParentId="15814" CreationDate="2015-06-09T15:41:03.690" Score="4" Body="&lt;p&gt;This question seems to stem from a misunderstanding of the nature of the Blood-Brain-Barrier, the circulatory system of the brain and of thrombi. The BBB is describes differences in the structure of the walls of the blood vessels of the brain, it is not a barrier to flow within the vessel, but a specialized barrier to flow out of the vessel. In many tissues the walls of capillaries (the smallest vessels) are not tightly adjoined, small molecules and even some proteins from the blood are able to pass through these minute gaps between the endothelial cells and into the tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in the brain, these endothelial cells are tightly linked in a specialized fashion that prevents the non-specific travel of solutes between cells. Instead, molecules that cannot diffuse through the membranes of the cells must be actively transported across them (cannot leak across).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An intravascular thrombus is much larger than these minute gaps, it is often considerably larger than these small vessels and becomes lodged in larger arteries, blocking flow. There is no passage through the BBB, but there is no passage of the thrombus through the walls of other capillaries in the body either. The damage caused by the infarct is due to the blockage of flow in the larger vessels.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The circle of Willis is no magical stopping point either. Many important sites of infarct (such as the MCA middle cerebral artery), micro-infarcts in even smaller vessels can also cause difficulties.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, thrombi and the Blood-Barrier-Brain exist on different scales, the presence or absence of the BBB is irrelevant when discussing the capacity of a thrombus to occlude arteries.&lt;/p&gt;&#xA;" OwnerUserId="16147" LastActivityDate="2015-06-09T15:41:03.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35071" PostTypeId="1" CreationDate="2015-06-09T17:11:09.417" Score="1" ViewCount="690" Body="&lt;p&gt;Acromegaly is a disorder in adults involving excess growth hormone production. Since epiphyseal fusion has already taken place in most bones of adults , this does not cause an increase in stature. Certain features of the face such as the jaw may be changed due the fact that the flat bones, such as the maxilla do not undergo epiphyseal fusion and may enlarge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several reports describe a prominent zygomatic arch due to arcomegaly, such as &lt;a href=&quot;http://journals.lww.com/annalsplasticsurgery/Abstract/1981/07000/Surgical_Treatment_of_Facial_Deformity_Secondary.11.aspx&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;. As I understand ,the zygomatic bone cannot enlarge due to its being fused in adults.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can acromegaly cause an actual enlargement of the underlying zygomatic bone ?&lt;/p&gt;&#xA;" OwnerUserId="15535" LastActivityDate="2015-11-04T15:00:30.630" Title="Does Acromegaly cause actual expansion of the zygomatic(cheek) bone" Tags="&lt;human-biology&gt;&lt;bone-biology&gt;&lt;growth&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35072" PostTypeId="1" AcceptedAnswerId="35076" CreationDate="2015-06-09T17:49:55.263" Score="3" ViewCount="192" Body="&lt;p&gt;For modelling the population of a single species in a region, the logistic equation is used&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ \frac{dN}{dt} =kN\Big(1-\frac{N}{K}\Big) $$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $N$ is the number of organisms, $K$ is the carrying capacity, and $k$ is a constant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, for most real primary consumers, in the absence of predation, the population usually deviates from the standard sigmoidal curve in two ways&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The population typically overshoots the carrying capacity before decaying again to the carrying capacity&lt;/li&gt;&#xA;&lt;li&gt;The population usually oscillates around the carrying capacity, rather then remaining constant&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Are there any better mathematical models for describing growth mediated by density dependent factors of primary consumers in the absence of predation?&lt;/p&gt;&#xA;" OwnerUserId="15536" LastEditorUserId="15536" LastEditDate="2015-06-10T16:05:09.730" LastActivityDate="2015-06-10T16:05:09.730" Title="Better population models than the logistic equation" Tags="&lt;mathematical-models&gt;&lt;population-dynamics&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ClosedDate="2015-06-10T11:47:16.423" ContentLicense="CC BY-SA 3.0" />
  <row Id="35074" PostTypeId="2" ParentId="34066" CreationDate="2015-06-09T19:00:54.163" Score="0" Body="&lt;p&gt;Try &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/nuccore/K00042.1&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;. I would suggest &lt;a href=&quot;http://pombe.oridb.org/&quot; rel=&quot;nofollow&quot;&gt;OriDB&lt;/a&gt; also, because it's precisely what you asked for. Getting the sequences out for easy blasting might be a chore, depending.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-06-09T19:00:54.163" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35075" PostTypeId="1" AcceptedAnswerId="35089" CreationDate="2015-06-09T19:15:03.320" Score="8" ViewCount="390" Body="&lt;p&gt;I read recently that we can &quot;work back&quot; to a dinosaur by selectively turning off certain genes in chickens, and we were able to create a chicken with a snout instead of a beak.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How many dinosaur genes are still hanging around in a chicken genome? I understand there is a lot of overlap for vertebrates, but shouldn't these genes have shuffled out over time?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Otherwise, couldn't we work back to worm or even earlier life forms? Is the whole history of a creature's evolution contained in its genome?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt; This was a news story about a month ago. Here's excerpts from the &lt;a href=&quot;http://www.bbc.com/earth/story/20150512-bird-grows-face-of-dinosaur&quot;&gt;BBC's write-up&lt;/a&gt;: &quot;Chicken grows face of dinosaur: A chicken embryo with a dinosaur-like snout instead of a beak has been developed by scientists&quot;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;To understand how one changed into another, a team has been tampering&#xA;  with the molecular processes that make up a beak in chickens.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;By doing so, they have managed to create a chicken embryo with a&#xA;  dinosaur-like snout and palate, similar to that of small feathered&#xA;  dinosaurs like Velociraptor. The results are published in &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/evo.12684/abstract;jsessionid=7481D58F08F749BE3470637A5DB18778.f02t02&quot;&gt;the journal&#xA;  Evolution&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Link to Evolution paper included. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also &lt;a href=&quot;http://www.washingtonpost.com/national/health-science/paleontologist-jack-horner-is-hard-at-work-trying-to-turn-a-chicken-into-a-dinosaur/2014/11/10/cb35e46e-4e59-11e4-babe-e91da079cb8a_story.html&quot;&gt;this piece&lt;/a&gt; from about a year ago: &quot;Paleontologist Jack Horner is hard at work trying to turn a chicken into a dinosaur&quot;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In 2009, the world’s most famous paleontologist made a bold claim. In&#xA;  “How to Build a Dinosaur,” Jack Horner proposed re-creating a small&#xA;  dinosaur by reactivating ancient DNA found in its descendants,&#xA;  chickens.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;The toothy snout is already here. At his lab at Harvard Medical&#xA;  School, Matthew Harris has made chicken embryos that express ancient&#xA;  genes for the growth of conical, crocodile-like teeth.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="976" LastEditorUserId="976" LastEditDate="2015-06-09T23:32:38.773" LastActivityDate="2017-05-17T21:24:40.877" Title="How many dinosaur genes are in a chicken genome?" Tags="&lt;genomics&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35076" PostTypeId="2" ParentId="35072" CreationDate="2015-06-09T19:44:50.203" Score="2" Body="&lt;p&gt;&lt;strong&gt;It is not complicated to make your own model of population growth&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can make a model with any kind of function, it is not super hard. It just happen that logistic growth offer quite a good match to observations. You can have exponential growth, linear growth, quadratic growth, ...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;However, there are more possible behaviours behind those models than what you think!&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The behaviour that you describe is totally possible with a discrete time logistic model. In short, consider the recursion equation $n_{t+1} = f(n_t)$. Consider also $\hat n$ as being an equilibrium of your system (typically n=0 or n=k, where k is the carrying capacity). In other words, $\hat n$ satisfies the equation $\hat n = f(\hat n)$. And finally consider the statistics $\lambda$ which is equal to the derivative of $f(n)$ over $n$ evaluated at the equilibrium $\hat n$. If $\lambda &amp;lt; 0$, then you have oscillatory behaviour (and therefore overshoot) at the vicinity of the equilibrium $\hat n$. Using the correct parameters, the logistics equation gives you a lambda smaller than 0 (typically between $-1 &amp;gt; \lambda &amp;gt; 0$), and therefore you can have the oscillatory behaviour you describe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have any trouble to make these basic analyses of those models, I strongly recommend &lt;a href=&quot;http://www.amazon.ca/Biologists-Mathematical-Modeling-Ecology-Evolution/dp/0691123446/ref=sr_1_1?ie=UTF8&amp;amp;qid=1433907448&amp;amp;sr=8-1&amp;amp;keywords=sarah%20otto%20guide&quot; rel=&quot;nofollow&quot;&gt;that book&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-06-10T03:39:19.240" LastActivityDate="2015-06-10T03:39:19.240" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35077" PostTypeId="2" ParentId="35063" CreationDate="2015-06-09T19:56:44.857" Score="4" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088735/&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; actually goes into the whole history of organ transplants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short it seems to have the following effects:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;preservation - usually with a specific solution to help.&lt;/li&gt;&#xA;&lt;li&gt;slows down extracorporeal ischaemic damage&lt;/li&gt;&#xA;&lt;li&gt;slows down hypoxic damage &lt;/li&gt;&#xA;&lt;li&gt;slows down the metabolism (energy consumption) and thus the need for oxygen that blood provides.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Remember that the cooling doesn't allow the organ to live indefinitely, and may only work for a few short hours depending on the organ. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I highly recommend reading the paper if you'd like to know more about organ transplant. They went into great detail about the past and present and the abstract also says they discuss new techniques about to be don't in clinical trials.&lt;/p&gt;&#xA;" OwnerUserId="16041" LastActivityDate="2015-06-09T19:56:44.857" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35078" PostTypeId="2" ParentId="34066" CreationDate="2015-06-09T20:56:07.537" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://wishart.biology.ualberta.ca/PlasMapper/&quot; rel=&quot;nofollow&quot;&gt;Plasmapper&lt;/a&gt; Is quite good a recognizing common origins of replication. You will have to look up compatibility yourself. It is what I usually use when confronted with unnannotated plasmids.&lt;/p&gt;&#xA;" OwnerUserId="15138" LastActivityDate="2015-06-09T20:56:07.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35079" PostTypeId="2" ParentId="31285" CreationDate="2015-06-09T21:44:01.127" Score="4" Body="&lt;p&gt;Born and raised in Texas here. I think people have a hard time comprehending the size of Texas. It has every climate (except extreme cold) and terrain. The coast is tropical and humid. The west is hot and dry desert. The central part is lush hills. The east side is forest, thick forest (see piney woods and Big Thicket)&lt;/p&gt;&#xA;" OwnerUserId="16150" LastActivityDate="2015-06-09T21:44:01.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35081" PostTypeId="2" ParentId="34066" CreationDate="2015-06-09T22:04:39.363" Score="0" Body="&lt;p&gt;Go this &lt;a href=&quot;https://www.addgene.org/browse/sequence/79022/&quot; rel=&quot;nofollow&quot;&gt;URL&lt;/a&gt;&#xA;And click pBR322 origin in the map. Then, the corresponding sequence will be highlighted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;2248-2867: pBR322_origin&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2201    cccttaacgt  gagttttcgt  tccactgagc  gtcagacccc  gtagaaa&lt;strong&gt;aga&lt;/strong&gt;  2250&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2251    &lt;strong&gt;tcaaaggatc    ttcttgagat  cctttttttc  tgcgcgtaat  ctgctgcttg&lt;/strong&gt;    2300&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2301    &lt;strong&gt;caaacaaaaa    aaccaccgct  accagcggtg  gtttgtttgc  cggatcaaga&lt;/strong&gt;    2350&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2351    &lt;strong&gt;gctaccaact    ctttttccga  aggtaactgg  cttcagcaga  gcgcagatac&lt;/strong&gt;    2400&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2401    &lt;strong&gt;caaatactgt    ccttctagtg  tagccgtagt  taggccacca  cttcaagaac&lt;/strong&gt;    2450&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2451    &lt;strong&gt;tctgtagcac    cgcctacata  cctcgctctg  ctaatcctgt  taccagtggc&lt;/strong&gt;    2500&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2501    &lt;strong&gt;tgctgccagt    ggcgataagt  cgtgtcttac  cgggttggac  tcaagacgat&lt;/strong&gt;    2550&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2551    &lt;strong&gt;agttaccgga    taaggcgcag  cggtcgggct  gaacgggggg  ttcgtgcaca&lt;/strong&gt;    2600&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2601    &lt;strong&gt;cagcccagct    tggagcgaac  gacctacacc  gaactgagat  acctacagcg&lt;/strong&gt;    2650&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2651    &lt;strong&gt;tgagctatga    gaaagcgcca  cgcttcccga  agggagaaag  gcggacaggt&lt;/strong&gt;    2700&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2701    &lt;strong&gt;atccggtaag    cggcagggtc  ggaacaggag  agcgcacgag  ggagcttcca&lt;/strong&gt;    2750&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2751    &lt;strong&gt;gggggaaacg    cctggtatct  ttatagtcct  gtcgggtttc  gccacctctg&lt;/strong&gt;    2800&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2801    &lt;strong&gt;acttgagcgt    cgatttttgt  gatgctcgtc  aggggggcgg  agcctatgga  2850&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2851    &lt;strong&gt;aaaacgccag    caac&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find various ori sequences from this site.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-06-09T22:04:39.363" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35082" PostTypeId="1" CreationDate="2015-06-09T22:12:34.507" Score="10" ViewCount="1071" Body="&lt;p&gt;So, I have an XX, &amp;amp; I got an X from my mom, &amp;amp; an X from my dad. My dad would have gotten his only X from his mother, &amp;amp; my mother could have gotten the X I got from her father or mother. That would mean I did not get either X gene from either my mom's mom or dad, or my dad's dad - does that mean that I have &quot;less&quot; of their genetics in me? Say I got my mom's dad's X, would that mean I have less of my mom's mom's genetic traits? &lt;/p&gt;&#xA;" OwnerUserId="16152" LastActivityDate="2020-06-27T18:53:20.507" Title="Do I not have any alleles from my mom's mom &amp; my dad's dad?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;gene-synthesis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35083" PostTypeId="1" AcceptedAnswerId="35115" CreationDate="2015-06-09T22:46:59.490" Score="5" ViewCount="712" Body="&lt;p&gt;Ermines turn white during the winter, with only the tip of the tail remaining black. However, in the southern regions of the ermine's range it clearly doesn't get so white. &lt;a href=&quot;http://eol.org/pages/328587/details&quot; rel=&quot;nofollow noreferrer&quot;&gt;Encyclopedia of Life&lt;/a&gt; says that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;However, in the Netherlands, the animals are often only partially white.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Ermine's range is clearly much more southern than the Netherlands:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yyRpi.png&quot; alt=&quot;image of the range of the ermine&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://commons.wikimedia.org/wiki/File:Stoat_area.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikimedia, stoat range&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I was wondering where does the border go, north of which the ermines are completely white and south of which they remain more brown? I understand it necessarily is not a clear cut line, mountains have impact and subspecies may differ, but I would assume someone must have mapped this. Or is it just weather related, will a southern ermine turn white if the winter is really cold?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm just asking this out of curiosity, but the question is rather relevant. Ermine pelt has a long history as an important trade item, and the most valued pelts must have originated on the white side of this line.&lt;/p&gt;&#xA;" OwnerUserId="11817" LastEditorUserId="9829" LastEditDate="2015-06-10T18:53:20.080" LastActivityDate="2015-06-10T18:53:20.080" Title="The ermine's colour and geographical range" Tags="&lt;mammals&gt;&lt;adaptation&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35084" PostTypeId="1" AcceptedAnswerId="35092" CreationDate="2015-06-09T22:56:17.027" Score="8" ViewCount="10684" Body="&lt;p&gt;So after bacteria have been transformed to perhaps grow up a plasmid of interest, why pick only a single bacterial colony from a selective plate for further expansion?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that this is to ensure that you are only working with a single genetic makeup because each separate colony is derived from only a single bacterium. What I can't rationalize is that if I am trying to expand and isolate a plasmid of interest, all colony expansions on a selective antibiotic plate should contain my plasmid. So is it really necessary to take only a single colony, because all colonies I pick should  be useful to me.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-06-10T04:31:15.940" Title="Why pick just a single bacterial transformed colony" Tags="&lt;genetics&gt;&lt;bacteriology&gt;&lt;transformation&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35085" PostTypeId="2" ParentId="35084" CreationDate="2015-06-09T23:00:35.160" Score="4" Body="&lt;p&gt;While all colonies on a selective media SHOULD contain a resistance gene, that's a long way from them containing the plasmid you want. A typical cloning experiment will insert a gene of interest into a empty vector backbone to make an intact plasmid. The backbone usually contains some antibiotic resistance gene. If your gene of interest is not correctly inserted, but the empty vector religates on itself, it will make a viable colony without your gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, I have seen mutations happen even when an insert is correctly inserted, and if you're doing blunt end ligation, there is always a risk of getting your insert in backwards or ligating two vectors together.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2015-06-09T23:00:35.160" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35086" PostTypeId="1" AcceptedAnswerId="35088" CreationDate="2015-06-09T15:30:40.223" Score="4" ViewCount="596" Body="&lt;p&gt;In my spare time I have been reading an introductory Psychology textbook and this question came to my mind after reading about action potentials.  I have no previous knowledge in chemistry so if I do need some sort of other knowledge I would appreciate if I could be told what I need to learn in order to understand the physiology of the nervous system better. So &lt;strong&gt;Why do negative ions come into a cell during an inhibitory synapse even though a neuron has a negative charged resting potential?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand this question might be extremely vague and impossible to answer without previous knowledge of the physiology of the nervous system. Any help would be greatly appreciated.&lt;/p&gt;&#xA;" OwnerUserId="16154" OwnerDisplayName="user16831" LastEditorUserId="3553" LastEditDate="2015-07-10T01:03:34.130" LastActivityDate="2015-07-10T01:12:25.540" Title="Why do negative ions flow into a cell in an inhibitory synapse, even though a neuron has a negative resting potential?" Tags="&lt;biochemistry&gt;&lt;neuroscience&gt;&lt;biophysics&gt;&lt;neurophysiology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35087" PostTypeId="2" ParentId="35082" CreationDate="2015-06-10T00:07:10.590" Score="20" Body="&lt;p&gt;Speaking of your DNA in general, you have alleles from all four of your grandparents.  The 22 pairs of autosomes (non-sex chromosomes) can receive DNA from all four with random mixing.  On a few chromosome pairs you may be missing alleles from one of your grandparents due to the randomness, but on average you will have about a quarter of your autosomes from each of them.&lt;/p&gt;&#xA;&lt;p&gt;The X (and Y, for males) chromosomes are special, though.  The X you inherit from your mother will have alleles from both your maternal grandparents.  The X that you, as a female, get from your father has no alleles from his father, so that grandfather's X alleles are always missing from your genome.&lt;/p&gt;&#xA;&lt;p&gt;Because of the random mixing, you will have slightly varying amounts of DNA from each of your grandparents: it won't be exactly 25% for each of them.  Because of the special X inheritance, your paternal grandfather will on average contribute slightly less than the other three grandparents.  (Because of another quirk, mitochondrial inheritance, your maternal grandmother will contribute on average a very small amount more than the other three grandparents.)&lt;/p&gt;&#xA;" OwnerUserId="231" LastEditorUserId="231" LastEditDate="2020-06-27T18:53:20.507" LastActivityDate="2020-06-27T18:53:20.507" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="35088" PostTypeId="2" ParentId="35086" CreationDate="2015-06-10T00:08:05.650" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Negative ions can flow against the &lt;em&gt;electrical gradient&lt;/em&gt; into the cell, provided their &lt;em&gt;concentration gradient&lt;/em&gt; across the cell membrane is large enough.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;When an ion channel opens, the resultant ion flow is dependent on two things; the membrane potential (which is indeed negative at rest) and the concentration gradient of the ion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider the activation of a GABA&lt;sub&gt;A&lt;/sub&gt; receptor. GABA is the principial inhibitory neurotransmitter in the nervous system. GABA opens the associated Cl&lt;sup&gt;-&lt;/sup&gt; channel on GABA&lt;sub&gt;A&lt;/sub&gt; receptors. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using the &lt;a href=&quot;http://www.physiologyweb.com/lecture_notes/resting_membrane_potential/resting_membrane_potential_nernst_equilibrium_potential.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Nernst equation&lt;/strong&gt;&lt;/a&gt; one can approximate the membrane potential (V&lt;sub&gt;eq&lt;/sub&gt;) at which an ion is in equilibrium. It mainly depends on the concentration of the ion X outside and inside the cell ([X]&lt;sub&gt;o&lt;/sub&gt; and [X]&lt;sub&gt;i&lt;/sub&gt;, respectively).[Cl]&lt;sub&gt;o&lt;/sub&gt; is approximately 103 mM, and [Cl]&lt;sub&gt;i&lt;/sub&gt; 4 mM. Hence, there exists a large concentration gradient with lots of it outside the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gsizH.jpg&quot; alt=&quot;Nernst&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Nernst equation. Source: &lt;a href=&quot;http://www.physiologyweb.com/lecture_notes/resting_membrane_potential/resting_membrane_potential_nernst_equilibrium_potential.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Physiology Web&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a neuron, the &lt;a href=&quot;http://courses.washington.edu/conj/membpot/equilpot.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Nernst potential of Cl&lt;sup&gt;-&lt;/sup&gt; is around -71 mV&lt;/strong&gt;&lt;/a&gt;. Hence, given that the resting membrane potential is approximately &lt;strong&gt;&lt;a href=&quot;http://www.ucl.ac.uk/~sjjgsca/NerveRestingPot.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;-70 mV&lt;/a&gt;&lt;/strong&gt; for a typical neuron, no Cl&lt;sup&gt;-&lt;/sup&gt; flux will occur when Cl&lt;sup&gt;-&lt;/sup&gt; channels open, because the resting membrane potential is equal to the equilibrium potential of Cl&lt;sup&gt;-&lt;/sup&gt;. However, when a neuron is depolarized by stimulatory neurotransmitters (e.g., glutamate), the membrane potential may be reduced to, say, -60 mV. This is still more negative than the &lt;a href=&quot;https://en.wikipedia.org/wiki/Action_potential&quot; rel=&quot;nofollow noreferrer&quot;&gt;action potential threshold&lt;/a&gt; (about -55 mV), but very close to it. So without any inhibition the neuron would be close to firing a spike. However, when GABA is released presynaptically, opening of the Cl&lt;sup&gt;-&lt;/sup&gt; channels coupled to GABA&lt;sub&gt;A&lt;/sub&gt; receptors will result in Cl&lt;sup&gt;-&lt;/sup&gt; influx, because the membrane potential is higher (more positive) than the equilibrium potential of Cl&lt;sup&gt;-&lt;/sup&gt;. In effect, Cl&lt;sup&gt;-&lt;/sup&gt; will enter the cell until its equilibrium potential is reached, re-polarizing the neuron back to -70 mV and hence inhibiting it. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-10T01:06:51.523" LastActivityDate="2015-07-10T01:06:51.523" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35089" PostTypeId="2" ParentId="35075" CreationDate="2015-06-10T00:52:11.507" Score="8" Body="&lt;p&gt;Be careful when reading media as they tend to exaggerate. That Abzhanov paper is interesting; it will be better when it's published and the figures released. He does a lot of &lt;a href=&quot;https://en.wikipedia.org/wiki/Evolutionary_developmental_biology&quot; rel=&quot;nofollow noreferrer&quot;&gt;evo-devo&lt;/a&gt; work surrounding beak development. What they did in this paper was to inhibit in chick embryos two signalling pathways (which are actually conserved amongst all animals, not just birds and reptiles) so that their expression domain more closely matched that of extant reptiles (which lack medial activation, as opposed birds). They found that doing so results in premaxillary and palatine bones which resemble ancestral archosaurs. While incredibly interesting, this is a far cry from creating living chickens with dinosaur snouts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To somewhat answer your question, chickens do not contain all of the genes that dinosaurs once had. They will have both gained and lost information. There will be much conservation in the same way that there is conservation between all organisms. For example, the Wnt pathway studied in this paper is conserved across all animals, from chickens to humans to placazoans to, presumably, dinosaurs. It's impossible to say how much has changed since we do not have any whole dinosaur genomes, but it's also important to note that it's not only which genes an organism has but also when and where they are expressed and how they interact. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2017-05-17T21:24:40.877" LastActivityDate="2017-05-17T21:24:40.877" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35091" PostTypeId="1" AcceptedAnswerId="35095" CreationDate="2015-06-10T04:03:01.217" Score="8" ViewCount="88" Body="&lt;p&gt;I'm thinking of things like antibiotics for meningitis or tuberculosis, or thiamine for Wernicke-Korsakoff syndrome. In those cases the magnitude of the treatment effect might have been so great that it would have been unethical to assign subjects to a placebo group. However, I couldn't find any sources to attest that randomized control trials were never done in relation to those treatments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm referring to treatments trialled in a time and place in which randomized control trials were an option.&lt;/p&gt;&#xA;" OwnerUserId="10184" LastEditorUserId="10184" LastEditDate="2015-06-10T04:47:09.250" LastActivityDate="2015-06-10T06:12:21.477" Title="Are there medical treatments that were so effective they were never subjected to a randomized control trial?" Tags="&lt;medicine&gt;&lt;clinical-trial&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35092" PostTypeId="2" ParentId="35084" CreationDate="2015-06-10T04:31:15.940" Score="10" Body="&lt;p&gt;This is a matter of pragmatism in the culture process. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Taking 100 colonies instead of 1 increases the inoculation volume by a factor of 100, which then saves you perhaps 2 hours of bacterial growth time before your culture reaches the OD you want. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, mutations and loss of plasmid in culture, while unlikely, are possible, especially if the bacteria were not cloning strains with their recombinases knocked out. In such a case, you would risk the downstream experiments being contaminated with mutants, be that protein expression, retroviral plasmid production, or something else. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Worse still, the mixture of bacteria containing mutants is less likely to be detected, since had you picked a single mutant colony, there would be absolutely no result, but a contaminated culture would produce a low but still positive result. Therefore, you may end up wasting many days or weeks troubleshooting your downstream experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, picking single colonies is simply a matter of &quot;better safe than sorry&quot;. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-06-10T04:31:15.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35093" PostTypeId="1" AcceptedAnswerId="35094" CreationDate="2015-06-10T04:52:35.627" Score="6" ViewCount="1619" Body="&lt;p&gt;I have heard from many homeless people that they &lt;strong&gt;sniff glue&lt;/strong&gt; just to reduce appetite, as it comes cheap and is more affordable than actual food.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this true, and if yes, why? This is totally opposite to the effects of marijuana where people feel hungry.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;GLUE SNIFFING&lt;/strong&gt; : Involves inhaling the fumes from domestic and&#xA;  industrial products (glue etc.). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6802" LastEditorUserId="6" LastEditDate="2015-06-10T06:19:50.150" LastActivityDate="2015-06-10T13:06:10.190" Title="Does inhaling glue (glue sniffing) reduce appetite?" Tags="&lt;human-biology&gt;&lt;pharmacology&gt;&lt;digestive-system&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35094" PostTypeId="2" ParentId="35093" CreationDate="2015-06-10T05:43:12.467" Score="9" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Various inhalants, most notably organic solvents including those used in paint and glue suppress appetite.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;From the &lt;a href=&quot;http://www.well.com/user/woa/fsinhale.htm&quot; rel=&quot;nofollow&quot;&gt;Division of Alcohol and Drug Abuse&lt;/a&gt; I learned the following: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Initial effects [of various inhalants] include nausea [...], and a &lt;strong&gt;loss of appetite&lt;/strong&gt;. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And the &lt;a href=&quot;http://www.irinnews.org/report/74899/nepal-street-children-sniff-glue-to-beat-hunger-pangs&quot; rel=&quot;nofollow&quot;&gt;Humanitarian Irin News&lt;/a&gt; reports the following on Nepali street youths: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The adhesive glue contains toluene, [an] intoxicating hydrocarbon [...]. The solvent [...] causes hallucinations as well as &lt;strong&gt;dampening hunger pangs&lt;/strong&gt; [...].&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Indeed, &lt;em&gt;acute exposure&lt;/em&gt; to &lt;strong&gt;organic solvents&lt;/strong&gt; has been associated with a &lt;strong&gt;loss of appetite&lt;/strong&gt; &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/ajim.4700140608/abstract&quot; rel=&quot;nofollow&quot;&gt;(Gregerson, 1998)&lt;/a&gt;, and &lt;em&gt;chronic exposure&lt;/em&gt; to toluene in the industrial workforce has also been linked to appetite suppression &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0013935183711151&quot; rel=&quot;nofollow&quot;&gt;(Kishi &lt;em&gt;et al&lt;/em&gt;., 1993)&lt;/a&gt;.         &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/ajim.4700140608/abstract&quot; rel=&quot;nofollow&quot;&gt;Gregerson, &lt;em&gt;Am J Industr Med&lt;/em&gt; (1998); &lt;strong&gt;14&lt;/strong&gt;(6): 681–701&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0013935183711151&quot; rel=&quot;nofollow&quot;&gt;Kishi &lt;em&gt;et al., Environmental Res&lt;/em&gt; (1993); &lt;strong&gt;62&lt;/strong&gt;(2): 303–13&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-10T13:06:10.190" LastActivityDate="2015-06-10T13:06:10.190" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35095" PostTypeId="2" ParentId="35091" CreationDate="2015-06-10T06:12:21.477" Score="7" Body="&lt;p&gt;In recent years, clinical trials are all necessary. You have to have the randomised control To make sure it isn't a placebo effect. If and only if the drug seems to be super effective will they cut the randomised control short and give the real drug to everyone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sadly, while it may seem unethical, there was a cancer treatment that two cousins got into. The normal treatment guaranteed death, while the new drug actually had people practically bouncing off their death beds. One got the placebo - in this case normal treatment since it's unethical to not at least give standard care - and the other got the drug. The drug worked so well, the doctors tried to push to cut the trial short but they wouldn't and the one on the normal treatment died.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This drug was PLX4032.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://acriclinicalresearchinstitute.blogspot.ie/2013/12/role-play-tale-of-two-cousins-this.html&quot;&gt;blogspot uproar&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://clinicaltrials.gov/ct2/show/NCT00405587&quot;&gt;clinical trial information&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nytimes.com/2010/09/19/health/research/19trial.html?_r=0&quot;&gt;NYTimes article &lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So to my knowledge about clinical trials, no trial has been able to skip that stage. It's actually Called Phase III testing of the drug, followed by Phase IV which is administration to the public. It can, however, be shortened if it is promising enough.&lt;/p&gt;&#xA;" OwnerUserId="16041" LastActivityDate="2015-06-10T06:12:21.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35096" PostTypeId="2" ParentId="31747" CreationDate="2015-06-10T06:29:00.527" Score="3" Body="&lt;p&gt;ATP synthase is basically a pump operating in reverse: while transporters such as the Na/K ATPase uses ATP to push ions against a chemical gradient (resulting in potential energy), ATP synthase uses the H+ gradient across the mitochondrial membrane to make new ATP.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A pump uses ATP (chemical energy) to achieve one-way transport by inducing conformation changes in the protein (mechanical energy), which either opens the channel only when ions come in contact with the low-concentration side, or closes the channel when ions come in contact with the high-concentraton side. In either case, the result is that ions can pass only in one direction, and a concentration gradient will build up (potenial energy).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of ATP synthase, the process is simply reversed: an H+ ion entering the channel from the high-concentration side (the intermembrane space) causes a conformation change that opens the channel, and is coupled to the synthesis of ATP. Precisely how the ATP synthase accomplishes this on the molecular level is a complicated topic, and still an active area of research. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581510/&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; for an overview.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that ATP synthase is clearly reversible: if the mitochondrial H+ gradient collapses, for example if respiration is blocked, then ATP synthase can run in reverse, consuming ATP to pump H+ out of the matrix. There is even an &lt;a href=&quot;http://en.wikipedia.org/wiki/ATPIF1&quot; rel=&quot;nofollow&quot;&gt;ATPase inhibiting protein&lt;/a&gt; dedicated to blocking the ATP synthase in this situation, to prevent the depletion of ATP. Also, the &lt;a href=&quot;http://en.wikipedia.org/wiki/V-ATPase&quot; rel=&quot;nofollow&quot;&gt;lysosomal ATPase&lt;/a&gt; is structurally similar, but operates in the reverse direction to create low pH in lysosomes.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-06-10T06:29:00.527" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35097" PostTypeId="2" ParentId="7317" CreationDate="2015-06-10T07:25:12.463" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8957219&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; was looking at inhibition of dynorphin converting enzymes and their importance. Although they don't seem to know if it is a single enzyme, or if it is multiple enzymes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17087727&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; looked at bikunin as an endogenous inhibitor of dynorphin convertase in human cerebrospinal fluid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://informahealthcare.com/doi/abs/10.3109/14756369109030394&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; looked at several inhibitors (some of which are known to irreversibly inhibit other enzymes), like &lt;em&gt;N&lt;/em&gt;-peptidyl-&lt;em&gt;O&lt;/em&gt;-acyl hydroxylamines and their effects on hCSF-DCE, the enzyme that cleaves dynorphin A, dynorphin B and alpha-neoendorphin to release Leu-enkephalin-Arg&lt;sup&gt;6&lt;/sup&gt;. However, it is known to inhibit serine and cysteine proteinases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I don't see any actual medications that are meant to inhibit Dynorphin enzymes. Instead I found &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15359581&quot; rel=&quot;nofollow&quot;&gt;Al-Fayoumi et. al&lt;/a&gt; were actually looking to identify stabilized dynorphin A derivatives instead of just inhibition of enzymes. &lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="9943" LastEditDate="2015-06-10T13:10:27.360" LastActivityDate="2015-06-10T13:10:27.360" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35098" PostTypeId="1" CreationDate="2015-06-10T07:33:47.253" Score="3" ViewCount="902" Body="&lt;p&gt;I am preparing competent cells, and I finished inoculating a single colony in SOB. It has been incubating at 37 degrees Celsius for almost 16 hours since, and it's getting very late where I live. I wanted to do the large-scale inoculation a few (at least 7) hours from now instead of right away, but I do not want the cells to start dying. Can I take the cells out of the incubator and leave the cells in room temperature? I'm hesitant about this because even at room temperature, wouldn't cells still be growing, making it possible for cells to die as well? What extra steps, if any, should I take before using the cells?&lt;/p&gt;&#xA;" OwnerUserId="15955" LastEditorUserId="15955" LastEditDate="2015-06-10T07:39:32.577" LastActivityDate="2015-06-10T07:39:32.577" Title="Can I leave BL21(DE3) cells in room temperature?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;ecoli&gt;" AnswerCount="0" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="35099" PostTypeId="1" AcceptedAnswerId="35102" CreationDate="2015-06-10T07:45:35.883" Score="7" ViewCount="869" Body="&lt;p&gt;I photographed a dragonfly but can't really identify the species using &lt;a href=&quot;http://www.libellen.tv/&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.libellen.tv/&lt;/a&gt;. Are there any other resources I could use?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pictures were taken in early June, around 11:00 next to a lake at 1700 meters above sea level. The pictures were taken in the Alps in Austria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pOrdY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4FUQ1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="608" LastEditorUserId="608" LastEditDate="2015-06-10T07:50:03.710" LastActivityDate="2016-03-10T13:48:05.277" Title="What dragonfly is this?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35102" PostTypeId="2" ParentId="35099" CreationDate="2015-06-10T08:17:55.703" Score="10" Body="&lt;p&gt;This is &lt;a href=&quot;https://en.wikipedia.org/wiki/Four-spotted_chaser&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Libellula quadrimaculata&lt;/em&gt;&lt;/a&gt;, which is a common and very widespread species (North America, Europe, Asia at least). This is based on the relatively wide and flat abdomen (hard to judge due to the angle though), which suggests &lt;em&gt;Libellula&lt;/em&gt;, brown/golden colour and a brownish wingbase. The main problem I have with the pictures (which makes my suggestion more uncertain) is that it is really hard to see the wingspots in your pictures, due to sun glare. &lt;em&gt;Libellula quadrimaculata&lt;/em&gt; is one of the few European species that has four wing-spots (hence the english name &lt;em&gt;Four-spotted chaser&lt;/em&gt;), which is why the wing-spots are important to see. However, I think I see hints of wing-spots at the middle of the wing (greyish patches on the top picture), which suggests four spots on each wing pair.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;&#xA;The distinctive four spots vary greatly in size among individuals and though small they are clearly present. The yellowish tint in the wings and the hairy thorax are also distinctive. The shining wings suggest this individual just emerged (from its larval stadium).  Colors may be less distinctive in these young individuals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are no similair species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/u0NL8.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;(picture from wikipedia)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More pictures of the species can be found &lt;a href=&quot;http://www.artportalen.se/Media/Taxon/208311&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="19468" LastEditDate="2016-03-10T13:48:05.277" LastActivityDate="2016-03-10T13:48:05.277" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35103" PostTypeId="1" CreationDate="2015-06-10T10:00:25.163" Score="5" ViewCount="376" Body="&lt;p&gt;We have a lot of those questions here that base on personal anecdotes and I try to avoid asking any of those. Still, after skipping breakfast and an extremely effective work day so far I started wondering.&#xA;I have always felt, that for most cognitive tasks I perform best before breakfast. Of course some of it is sure related to being very awake and supposedly having a biorhythm that favours working in the morning, but I have always related this to not having eaten and also surprisingly not feeling hungry at all until basically deciding to eat &quot;because I really should eat something&quot; around noon.&#xA;So today I decided to find out, if this phenomenon is more widely known or just anecdotal for me. Of course there is a lot of information on how digestion makes you feel tired and you should not expect to be very productive directly after eating. That was not what I am looking for.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally I found this 2006 NY Times article about &quot;&lt;a href=&quot;http://www.nytimes.com/2006/12/10/magazine/10section1C.t-1.html?_r=0&quot;&gt;Empty-Stomach Intelligence&lt;/a&gt;&quot;, where it is stated that at least for mice being &quot;mildly starving&quot; seems to increase cognitive ability based on the hormone ghrelin targeting not only the hippothalamus, but also the hippocampus. &#xA;I then tried finding a relevant publication and was only lead to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618869/&quot;&gt;this one&lt;/a&gt;, describing the original study about ghrelin influencing food intake, but seemingly not the &quot;sidetrack&quot; of it influencing cognitive abilities during starving.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now I am lost. Is there any newer publication about this phenomenon that I completely missed, possibly even in relation to how humans can perform cognitive tasks while being mildly starved?&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2015-06-10T10:00:25.163" Title="Is hunger pushing cognitive ability in humans?" Tags="&lt;endocrinology&gt;&lt;intelligence&gt;&lt;cognition&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="1" ClosedDate="2015-06-10T17:50:54.123" ContentLicense="CC BY-SA 3.0" />
  <row Id="35104" PostTypeId="1" CreationDate="2015-06-10T10:34:02.803" Score="1" ViewCount="3032" Body="&lt;p&gt;Wikipedia suggests 'mE/l' is the dutch or german translation (using 'eenheid'/'einheit' for 'unit') for '&lt;a href=&quot;https://en.wikipedia.org/wiki/International_unit&quot; rel=&quot;nofollow&quot;&gt;mU/l&lt;/a&gt;', which can also be written as 'mIU/l'. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article mentions &lt;code&gt;The IU should not be confused with the enzyme unit, also known as the International unit of enzyme activity and abbreviated as U.&lt;/code&gt;. Is it safe to assume that in case of the unit 'mU/l' one never means the enzyme unit? I figure this is because the enzyme unit specifies a rate of conversion, which is not a blood value and would be meaningless to specify 'per liter'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have also encountered '&lt;a href=&quot;https://en.wikipedia.org/wiki/Equivalent_%28chemistry%29&quot; rel=&quot;nofollow&quot;&gt;mEq/l&lt;/a&gt;', of which I am pretty sure it is different from 'mU/l', going by the wikipedia article.&lt;/p&gt;&#xA;" OwnerUserId="16160" LastEditorUserId="16160" LastEditDate="2015-06-10T14:22:43.463" LastActivityDate="2015-06-10T14:22:43.463" Title="What's the difference between blood value units 'mE/l', 'mU/l', 'mIU/l' and 'mEq/l'?" Tags="&lt;hematology&gt;&lt;measurement&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35105" PostTypeId="1" AcceptedAnswerId="35110" CreationDate="2015-06-10T10:35:04.313" Score="1" ViewCount="379" Body="&lt;p&gt;I previously read &lt;a href=&quot;https://biology.stackexchange.com/questions/31401/why-is-it-harder-to-sequence-plant-genomes-than-animal-genomes&quot;&gt;this question&lt;/a&gt; and &lt;a href=&quot;http://www.genomebiology.com/2012/13/4/243&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper&lt;/a&gt; and learned good things about this topic. my current question is that scientists use which tools, algorithms, soft wares... to sequence, assemble and annotate plant genomes?&#xA;For each genome project do they develop new tools and algorithms or there are some tools that are useful for (almost) all genome projects?&#xA;Are there any comprehensive site, book or paper that have plant genome sequencing and annotation protocols?  &lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-06-11T01:58:46.310" Title="How Scientists sequence, assemble and annotate plant genomes?" Tags="&lt;genomes&gt;&lt;gene-annotation&gt;&lt;sequence-assembly&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ClosedDate="2015-06-11T05:43:58.847" ContentLicense="CC BY-SA 3.0" />
  <row Id="35106" PostTypeId="6" CreationDate="2015-06-10T11:43:35.237" Score="0" Body="&lt;p&gt;Hello, I am Rob (aka: GriffinEvo and rg255), currently in the last few weeks of a PhD in Evolutionary Genetics at Uppsala University. I also have a BSc in Conservation Biology and Ecology, and MSc in Evolutionary and Behavioural Ecology, both from the University of Exeter, along with 7 years experience in active research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been involved with Biology SE for over 2 and a half years, visiting several times on most days, and use a few other stack exchange sites. While I have not been active in posting questions and answers of late, I have been devoting a lot of effort to other quality control type duties (e.g. flagging, commenting, voting, editing etc.) - being so close to the end of a PhD I haven't had much time to give but still wanted to contribute. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As of next month it's all over and it will be great to get back to Biology SE - and I would love for that to be in the role of a moderator! Given the experiences I have had in my time here and the lessons I've learned along the way, I think I can make a useful contribution as a moderator. I am so impressed by the work we do as a community here and want to help push Biology SE to be the best it can!&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2015-06-11T08:38:06.377" LastActivityDate="2015-06-11T08:38:06.377" CommentCount="2" CommunityOwnedDate="2015-06-10T11:43:35.237" ContentLicense="CC BY-SA 3.0" />
  <row Id="35108" PostTypeId="1" AcceptedAnswerId="35109" CreationDate="2015-06-10T12:45:11.483" Score="11" ViewCount="766" Body="&lt;p&gt;I'm looking for a tool to simulate sequence evolution given a specific mutation model and birth-death model. I'm aware of tools and packages like INDELible, Seq-Gen and PhyloSim, but they simulate evolution along phylogenetic trees. What I want is to give a sequence and ask the tool to simulate the evolution of this sequence through N generations. The output should be a big bunch of descendant sequences. I've been thinking about writing such a tool myself, but it's always better to look for something already coded.&lt;/p&gt;&#xA;" OwnerUserId="13338" LastActivityDate="2018-07-26T22:26:23.667" Title="Sequence evolution simulation tool" Tags="&lt;evolution&gt;&lt;bioinformatics&gt;&lt;phylogenetics&gt;&lt;sequence-analysis&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35109" PostTypeId="2" ParentId="35108" CreationDate="2015-06-10T12:59:23.777" Score="11" Body="&lt;p&gt;There exists a bunch of population genetics forward and backward (coalescence) simulation platforms. Here is a non-exhaustive list. They all differ and you'll have to go through their manual to see what is more adapted to your needs.&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;List of softwares&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://popmodels.cancercontrol.cancer.gov/gsr/packages/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here is a long list of such platforms&lt;/a&gt;. The list might arguably be a little bit outdated today though and many of these softwares might be slow or abandoned by their authors.&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Most common softwares to my experience&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;Some are more known than others. Personally, I already saw uses of the following platforms in publication: SimCoal, Nemo, Slim and SFS_Code.&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;SimBit&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;Of course, I must indicate my own simulation platform &lt;a href=&quot;https://github.com/RemiMattheyDoret/SimBit&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;SimBit&lt;/strong&gt;&lt;/a&gt;. To my experience, SimBit is typically faster than Nemo. It is slower than SFS_Code and SLim for very small simulations but become much much faster than SFS_Code and SLim when you need simulations with a descent amount of genetic diversity. &lt;/p&gt;&#xA;&#xA;&lt;h1&gt;Most important point about these softwares&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;You should compare softwares based on&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Availability&lt;/strong&gt; of the author to advice and bring new features&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I won't talk about my personal experience here by respect for the authors!&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Speed / RAM usage&lt;/strong&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I think SimBit is typically faster (and use less RAM) than Nemo. SFS_code and SLim are very fast for simulations with low genetic diversity but very slow for simulations with high genetic diversity.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Flexibility&lt;/strong&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Nemo, SLim and SimBit are very flexible (but they do different things) but SFS_code is not really.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;User interface&lt;/strong&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;I find Nemo error report pretty poor. I like SimBit error report. SLim interface is very nice (using eidos) and it even comes with a GUI (I have never used the GUI myself).&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Free of Bugs&lt;/strong&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Several people have found important bugs in SFS_code (personal communication and experience). &lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;h1&gt;Slightly more detailed comparison between Nemo, SLim, SFS_code and SimBit&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;I have personally used NEMO, SFS_CODE and SLim in the past (I now use SimBit only). So I can only talk about these 4 below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All four models are well updated and maintained by their authors and of course everyone has a access to the source code.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;SFS_code and SLim are very fast for small simulations. The issue of SFS_code and SLim is that the RAM usage and run time are exponential function of the genetic diversity. This means that some simulations can quickly become totally unmanageable. But it is a great tool if you expect little genetic diversity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;SimBit is typically faster than Nemo, at least for large genomes. This difference becomes particularly obvious for large genomes. One might think &quot;Oh I am fine to wait a few extra days to get my results&quot; but the difference in speed between two softwares can also be a difference in whether you have to wait a week or 20 years to get your results, so &lt;em&gt;do not neglect the importance of running time and RAM usage&lt;/em&gt; without estimating your needs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nemo is very flexible when it comes to the order of life-cycle events (is migration before or after selection for example) and the newest version allows for simulating age structured population. SimBit is very flexible, very fast and allow for simulating multi-species and their ecological interactions. SFS_code is less flexible. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;My only concerns about NEMO are that each individual dies after reproduction and that there can't be more than 256 alleles at the same time.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;SFS_code limits the number of alleles to 4. Nemo limits the number of alleles to 256 (but you can also use phenotype and have a float number at each locus). SimBit uses either bi-allelic loci, a block in which the number of mutations are counted (max: 256 mutations; this is different than 256 alleles per say) or continuous float number at each locus for the phenotype. Do you really need more alleles? Why can't you just use several loci to represent a sequence with multiple alleles? Real biology can only have 4 alleles in its smallest locus! SimBit uses a bit-per-bit system. If you need, say 50,000 alleles, then you just need to ask for a sequence of 16 bits (2 bytes) and you can get $2^{16} = 65,536$ alleles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you need more alleles in a single block (which is a little surprising to me a priori), you can probably just ask the author and he might accept to helping you if you convince him it is of interest to add this feature (he might also be more willing to help in exchange of authorship if you need more support).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope that helps. Good luck!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2018-07-26T22:26:23.667" LastActivityDate="2018-07-26T22:26:23.667" CommentCount="6" ContentLicense="CC BY-SA 4.0" />
  <row Id="35110" PostTypeId="2" ParentId="35105" CreationDate="2015-06-10T15:01:14.797" Score="5" Body="&lt;p&gt;Let's try and answer all three parts of your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Sequencing&lt;/strong&gt;&#xA;The general method is the same. Sequencing is just sequencing. But as for every single sequencing, there are factors to consider and protocols to be selected. &#xA;One important thing is, that you might want comparably long reads to cope with the repeats and the general large size of plant genomes. To get long reads, you need long input DNA sequences. Therefor you would want to follow a suitable protocol for &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC324241/&quot;&gt;high molecular weight plant DNA&lt;/a&gt;. That might be hard, because plant DNA can be difficult to extract based on the plant and tissue you have, as most easily put you have to &quot;crack open&quot; the cell wall in the very beginning.&#xA;After that, it is general sequencing. Although, as I already said you might opt for long reads (PacBio) and/or good coverage. If that is not at all feasible, you might choose to do targeted sequencing and only capture the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4241023/&quot;&gt;whole exome&lt;/a&gt; (or only the genes you are interested in) to reduce both cost and analysis complexity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Assembly&lt;/strong&gt;&#xA;Now you have probably accumulated a lot of sequence and also potentially long sequence. There are multiple tools you could use for assembly and generally you can use the same for plants that you might want to use for example for a human genome assembly. One example that works well on large plant genomes is &lt;a href=&quot;http://www.genome.umd.edu/masurca.html&quot;&gt;MaSuRCA&lt;/a&gt;, another is &lt;a href=&quot;http://www.pnas.org/content/108/4/1513.abstract&quot;&gt;Allpaths-LG&lt;/a&gt;. There are some assemblers designed to cope with long repeats, but quite often you just assemble and then try figuring out the repeat regions later, for example by improving a shotgun read assembly with long reads from another technique.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Annotation&lt;/strong&gt;&#xA;This one definitely has specific tools for plant genomes. Well, large genomes. The main thing in annotation is finding potential genes and comparing them to databases to annotate them with function. Plants do splice and plants can have long introns, even ones including long repeats. &#xA;One gene prediction software example that works on plants is &lt;a href=&quot;http://bioinf.uni-greifswald.de/augustus/&quot;&gt;Augustus&lt;/a&gt;, but for some model organisms there are even organism-specific pipelines and tools for this task. And of course, on the database part you would choose to rely on a plant specific database (if you do not use NCBI-NR anyway). Those can also be species or genus specific like the ones you find on the &lt;a href=&quot;https://www.arabidopsis.org&quot;&gt;TAIR&lt;/a&gt; (Arapidopsis) project.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TLDR:&#xA;It's in fact complicated. On one hand, there is a need of specific tools and databases, on the other you might go well with standard tools, but would have to adapt parameters, do additional pre- or post-processing steps and so on.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2015-06-10T15:01:14.797" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35111" PostTypeId="1" AcceptedAnswerId="35117" CreationDate="2015-06-10T16:04:43.520" Score="5" ViewCount="99" Body="&lt;p&gt;Found in Kustaankartano, Helsinki, Finland in June 2015.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(for closeup view, copy image URL and open in new window and then zoom in)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qJCia.jpg&quot; alt=&quot;&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/J2ejg.jpg&quot; alt=&quot;&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/HaQYq.jpg&quot; alt=&quot;&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Xndly.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3280" LastEditorUserId="3280" LastEditDate="2015-06-10T17:28:39.393" LastActivityDate="2015-06-10T19:02:43.900" Title="What is this plant on the photos?" Tags="&lt;botany&gt;&lt;species-identification&gt;&lt;flowers&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35115" PostTypeId="2" ParentId="35083" CreationDate="2015-06-10T18:26:45.223" Score="3" Body="&lt;p&gt;The color change of &lt;em&gt;Mustela erminea&lt;/em&gt; (more commonly known as &lt;a href=&quot;http://www.britannica.com/EBchecked/topic/191701/ermine&quot; rel=&quot;nofollow&quot;&gt;ermine/stoat/short-tailed weasel&lt;/a&gt;) is both temperature-dependent and photoperiodic (depending on the length of the day). &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.2164-0947.1943.tb00865.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Bissonette 1943&lt;/a&gt; and &lt;a href=&quot;http://www.tandfonline.com/doi/pdf/10.1080/03014223.1982.10423841&quot; rel=&quot;nofollow&quot;&gt;King and Moody 2012&lt;/a&gt; show that the molting of the ermine happens as a result of the change in daylight lengths.  The King and Moody paper addresses the temperature dependence, using stoats (ermines) in New Zealand as an example:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In temperate countries such as New Zealand, stoats frequently fail to complete the full change to white. Such animals are not necessarily all caught in the process of moulting. If ambient temperature fell below the threshold for whitening of the lower part of the body but not the rest, new hair would grow white on the tail and flanks and brown on the head and back.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This is a chemical effect of lower temperature (King and Moody):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Experimental work has established that production of brown hair depends on melanocyte-stimulating hormone (MSH); in cold climates in autumn the synthesis of MSH by the pituitary is inhibited. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They don't provide a specific temperature at which the white color change does or doesn't occur, but I suspect that in nature it'd be very difficult to create a map since temperature is not constant year-to-year. There would most likely be an intermediate zone of partially white animals (both in terms of a mixture of brown and white animals, and a single animal that is not fully white).&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-06-10T18:26:45.223" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35116" PostTypeId="2" ParentId="34168" CreationDate="2015-06-10T19:02:11.650" Score="2" Body="&lt;p&gt;As to why they don't recognize RNA-DNA heteroduplexes (which are present during transcription, for example), I suspect that the methylation which protects bacterial genomic dsDNA (see the DNA modifying enzyme section of this &lt;a href=&quot;http://www.columbia.edu/cu/biology/courses/c2005/lectures/lec17_10.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Columbia University lecture&lt;/a&gt; for more info) also protects RNA-DNA hybrids, as the genomic DNA would still be methylated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that most of the enzymes featured in the paper are listed by New England Biolabs as methylation sensitive (for example: &lt;a href=&quot;https://www.neb.com/products/r0153-avaii&quot; rel=&quot;nofollow noreferrer&quot;&gt;AvaII&lt;/a&gt;, &lt;a href=&quot;https://www.neb.com/products/r0118-bani&quot; rel=&quot;nofollow noreferrer&quot;&gt;BanI&lt;/a&gt;, &lt;a href=&quot;https://www.neb.com/products/r0155-hinfi&quot; rel=&quot;nofollow noreferrer&quot;&gt;HinfI&lt;/a&gt;, &lt;a href=&quot;https://www.neb.com/products/r0149-taqi&quot; rel=&quot;nofollow noreferrer&quot;&gt;TaqI&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;@canadianer and @user137 provide a host of reasons that these restriction enzymes cannot cleave ds/ssRNA in the comments on &lt;a href=&quot;https://biology.stackexchange.com/a/34170/9829&quot;&gt;canadianer's answer&lt;/a&gt; (different helix form, different interaction strengths between strands).&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-06-10T19:02:11.650" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35117" PostTypeId="2" ParentId="35111" CreationDate="2015-06-10T19:02:43.900" Score="6" Body="&lt;p&gt;It is one of the many species and hybrids of &lt;a href=&quot;https://en.m.wikipedia.org/wiki/Clematis&quot; rel=&quot;nofollow noreferrer&quot;&gt;Clematis&lt;/a&gt; that is grown in gardens. It looks similar to the common &lt;a href=&quot;https://en.m.wikipedia.org/wiki/Clematis_alpina&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Clematis alpina&lt;/em&gt;&lt;/a&gt; but might be a closely related species or à hybrid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Goyd4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;(Picture of C. alpina fr.o.m. Wikipedia)&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2015-06-10T19:02:43.900" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35119" PostTypeId="1" AcceptedAnswerId="35121" CreationDate="2015-06-10T20:50:17.800" Score="9" ViewCount="12893" Body="&lt;p&gt;Lets imagine 5 plots of different size are sampled for a target species:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;plot#  count  area(m^2)  plot_density&#xA;  1      1       5         0.2&#xA;  2      3       2         1.5&#xA;  3      0      10         0.0&#xA;  4      5       1         5.0&#xA;  5      2       6         0.33&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;What is this species' density?  I see two ways to calculate the density that give completely different values.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The first way averages the density at each plot:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;\frac{\Sigma(\frac{count_i}{area_i})}{5} = 1.41/m^2&#xA;$$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This seems &lt;em&gt;OK&lt;/em&gt; but it doesn't do much to control for changing plot sizes.  For example if plot 3 above was 10 times larger the density would still be the same.  In a situation where plot sizes are determined by the environment (say, under natural cover objects) this seems less than ideal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second way totals the counts and the search area and divides them:&lt;br&gt;&#xA;$$&#xA;\frac{\Sigma(count_i)}{\Sigma(area_i)}=0.46/m^2&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I prefer the second method because it seems to describe the animals' density more accurately. And I would be happy to use the second method, but my issue is that I am unsure how to calculate a summary statistic for method two since a mean was never calculated.  Method one gives a standard deviation of 2.1. What is the standard deviation for method two??   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One possible solution I've come up with involves breaking the larger plots into 1m^2 plots and dividing the number of animals across those smaller plots.  So now I have 24 1m^2 plots with the following &quot;counts&quot;:  &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;plot#  count  area(m^2)  plot_density&#xA;1-5      0.2       1         0.2&#xA;6-7      1.5       1         1.5&#xA;8-17     0.0       1         0.0&#xA;18       5.0       1         5.0&#xA;19-24    0.33      1         0.33 &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Now, using the first equation above I get:&#xA;$$&#xA;\frac{\Sigma(\frac{count_i}{area_i})}{24} = 0.73/m^2&#xA;$$ &#xA;With a standard deviation of 1.26.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this a reasonable approach?  Is there an established solution to this problem?&lt;/p&gt;&#xA;" OwnerUserId="16166" LastEditorUserId="3624" LastEditDate="2015-06-10T22:53:07.890" LastActivityDate="2015-12-09T09:32:21.890" Title="How should species density be calculated for a clumped distribution?" Tags="&lt;ecology&gt;&lt;population-biology&gt;&lt;statistics&gt;&lt;landscape-ecology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35120" PostTypeId="2" ParentId="31879" CreationDate="2015-06-10T21:58:14.620" Score="6" Body="&lt;p&gt;If you're willing to accept many orders of magnitude and define life as the Last Universal Common Ancestor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the rest of this answer, life begins 3.5 Gya with cyanobacterial mats and stromatolites and so on. Genetically the &lt;a href=&quot;http://en.wikipedia.org/wiki/Last_universal_ancestor&quot;&gt;LUCA&lt;/a&gt; is dated to around this time, which matches the fossil record and everything's great. The LUCA can't have sprung from nothingness, so there may(will) have been (many)generations before the LUCA of things we would recognize as life, but I'm ignoring them. If they wanted to be considered they should have left descendants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fastest doubling times for modern bacteria are about &lt;a href=&quot;http://genomea.asm.org/content/1/4/e00648-13.full&quot;&gt;7-9 minutes&lt;/a&gt; but most are longer. E. coli takes about 20 minutes, and yeast takes hours. Given the 3.5 billion year clock, that gives an upper bound of about 1x10^14 generations. (Green sea turtles take 20-30 years to reach sexual maturity, or 1.1x10^9 generations). Something a bit representative is probably &lt;a href=&quot;http://en.wikipedia.org/wiki/Pelagibacter_ubique&quot;&gt;Pelagobacter ubique&lt;/a&gt;, which is vastly successful and takes about 29 hours to divide. Averaging out ice ages and so on and skipping the slowing of generations multicellularity probably implies(the Cambrian explosion is 82% of the way to the present day, being only 543 million years ago. We could account for it, but our guesses on generation time are way more inaccurate than any possible effect that could have) would estimate about 1x10^12 generations.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-06-10T21:58:14.620" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35121" PostTypeId="2" ParentId="35119" CreationDate="2015-06-10T22:44:12.623" Score="6" Body="&lt;p&gt;To me, there are two issues that are mixed up here (if I understand you correctly). First, do you want to estimate the mean and variance for a statistical population (i.e. to characterize a larger population by independent samples), or do you want to calculate the actual density for a particular area, where you have counted all occurences in that entire area (but maybe divided the area into subareas out of convenience when counting)? This is not clear from your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the second case, your second option of pooling counts and areas is suitable. However, then you have only calculated the actual density in that particular area (ignoring issues of detectability of the organism when counting), and you cannot draw any inferences about a larger statistical population.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your aim is to draw inferences for a larger statistical population, a start is to calculate the mean and standard deviation (sd) of your sample. In that case, I assume that your samples are chosen randomly and independently from a larger statistical population. Your first option is then the right approach. However, since your samples have different sizes, you might want to attach more weight to larger samples, since they can be assumed to better describe the population average than smaller samples. This is called a &lt;a href=&quot;https://en.wikipedia.org/wiki/Weighted_arithmetic_mean&quot; rel=&quot;nofollow&quot;&gt;weighted mean&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally, the weighted arithmetic mean is defined as: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\bar{x}_w = \dfrac{\sum_{i=1}^nw_ix_i}{\sum_{i=1}^nw_i}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $w_i$ are the weights for each sample ($x_i$) and $n$ are the number of samples. Using this formula, you will arrive at exactly the same value for the weighted mean as you calculated in your second attempt (0.458), if you use the areas as weights. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The weighted standard deviation is a bit more problematic, in the sense that there doesn't exist one single standard way of calculating this. However, a commonly used formula is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ \sigma_{w_1} = \sqrt{ \frac{ \sum_{i=1}^n w_i (x_i - \bar{x}_w)^2 }{ \frac{(M-1)}{M} \sum_{i=1}^n w_i } },$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $M$ are the number of nonzero weights. Other definitions of the weighted standard deviation can be found at &lt;a href=&quot;https://en.wikipedia.org/wiki/Weighted_arithmetic_mean#Weighted_sample_variance&quot; rel=&quot;nofollow&quot;&gt;Wikipedia: weighted sample variance&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another version is defined as (called &quot;reliability weights&quot; on the wiki page):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ \sigma_{w_2} = \sqrt{ \frac{ \sum_{i=1}^n w_i (x_i - \bar{x}_w)^2 }{  \sum_{i=1}^n w_i - \frac{\sum_{i=1}^n w_i^2}{\sum_{i=1}^n w_i}}},$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I haven't made a mistake, these will give the standard deviations 1.15 and 1.22, using your data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the &lt;strong&gt;biological interpretation&lt;/strong&gt;, all calculations of average densities indicate a clumped distribution, since the coefficient of variation (CV) is larger than 1 (CV = sd/mean), but more so if you use a weighted mean. The CV using the arithmetric mean is 1.5, while it is 2.5-2.65 for the weighted mean, which is reasonable since you are giving more weight to the large area sample with a zero count. However, I should also note that you should be cautious about using a weighted mean when you have a strongly clumped distribution, since your run the risk that e.g. a large sample plot land on an area with no occurences, which might bias your density estimate. Generally, when you have a clumped distribution, you need to sample more intensively to get a good estimate of average density, and many small samples is often better than a few large ones.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-12-09T09:32:21.890" LastActivityDate="2015-12-09T09:32:21.890" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35122" PostTypeId="1" CreationDate="2015-06-10T22:47:09.713" Score="4" ViewCount="1538" Body="&lt;p&gt;My professor claims that the autonomic nervous system is only activated by stimuli from organs but I really feel like I've read that it can be activated by outside stimuli, although I'm not sure what receptors that would be.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is my professor right?&lt;/p&gt;&#xA;" OwnerUserId="6576" LastActivityDate="2015-06-12T04:15:03.557" Title="Is the autonomic nervous system only activated by internal stimuli?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;brain&gt;&lt;central-nervous-system&gt;&lt;autonomic-nervous-system&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35123" PostTypeId="2" ParentId="35122" CreationDate="2015-06-11T00:25:26.260" Score="3" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;External stimuli can drive autonomic responses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The autonomic nervous system is a &lt;em&gt;visceral&lt;/em&gt; sensory and motor system. The viscera are the internal organs. Virtually all visceral reflexes are mediated by local circuits in the brain stem or spinal cord (Fig. 1). It is one of two major subdivisions of the nervous system; the other being the somatic (or voluntary) nervous system. The main distinction between the two is that the latter is involved in voluntary and conscious actions (e.g., movement, perception and cognition), while the autonomic nervous system is engaged in &lt;em&gt;involuntary&lt;/em&gt; processes, such as regulating heart rate, breathing and bowel function (Fig. 1). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/m5Pth.jpg&quot; alt=&quot;Autonomic nervous system&quot;&gt;&#xA;&lt;sup&gt;Fig. 1. Autonomic nervous system. Source: &lt;a href=&quot;http://www.austincc.edu/apreview/PhysText/PNSefferent.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Austin Community College&lt;/a&gt;&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although by far most stimuli driving autonomous responses come from within (think muscle movements driving bowel movements, increased heart rates during physical exercise), outside stimuli do directly impinge on the autonomous system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, the cilliary muscle in the iris is under the control of light coming into the retina. The &lt;a href=&quot;http://www.neuroexam.com/neuroexam/content.php?p=19&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;pupillary light reflex&lt;/strong&gt;&lt;/a&gt; test is based on this principle, and is routinely used to diagnose damage to the visual system. Also, &lt;strong&gt;production of saliva&lt;/strong&gt; is controlled by external stimuli (smell and taste of food and see the striking example below from @anongoodnurse). And technically, the entire digestive tract can be considered to be &lt;em&gt;outside&lt;/em&gt; the body, as it is continuous with the skin and lining of the mouth. Hence, the mechanical stimuli impinging on the intestines by a moving bolus of food that drives the waves of &lt;strong&gt;peristaltic movements&lt;/strong&gt; can, arguably, be considered to be caused by external stimuli too. Lastly, the fight-flight-fright response involving the hypothalamic-pituitary-adrenal gland &lt;a href=&quot;http://www.health.harvard.edu/staying-healthy/understanding-the-stress-response&quot; rel=&quot;nofollow noreferrer&quot;&gt;(&lt;strong&gt;HPA) axis&lt;/strong&gt;&lt;/a&gt; is often initiated by external stimuli (loud sudden noises etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The most important characteristic of the autonomic nervous system, as said, is that the autonomous responses are &lt;strong&gt;not voluntarily controlled&lt;/strong&gt;. While you can decide to look or track a visual stimulus, you cannot decide to move the bolus of food back up to your stomach, or voluntarily constrict your pupil. The way the input is received may not be the best way to distinguish it from the voluntary nervous system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Didactic answer&lt;/strong&gt;&lt;br&gt;&#xA;If you are left with questions, the first place to go to is your professor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://neurology.mhmedical.com/book.aspx?bookID=1049&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kandel et al. Principles of Neural Science 4&lt;sup&gt;th&lt;/sup&gt; ed. (2000). Ch.49 The autonomic nervous system and hypothalamus. p.960-81&lt;/a&gt;     &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-12T04:15:03.557" LastActivityDate="2015-06-12T04:15:03.557" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35126" PostTypeId="1" AcceptedAnswerId="35131" CreationDate="2015-06-11T06:39:04.203" Score="3" ViewCount="898" Body="&lt;p&gt;My textbook says that the yellow appearance of a jaundiced person is due to the accumulation of bile pigments in the skin. I am unable to understand why these pigments are not deposited in a healthy person? Please help.&lt;/p&gt;&#xA;" OwnerUserId="16142" LastActivityDate="2015-06-12T01:02:37.110" Title="Pigmentation in Jaundice" Tags="&lt;human-biology&gt;&lt;pigmentation&gt;&lt;health&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35127" PostTypeId="1" AcceptedAnswerId="35129" CreationDate="2015-06-11T07:00:42.247" Score="3" ViewCount="543" Body="&lt;p&gt;In the section describing the Calvin Cycle, under the subheading &quot;Reduction&quot;,  my textbook states that:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The steps involve utilisation of 2 molecules of ATP for Phosphorylation...&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I could not get where is ATP used in Phosphorylation (ATP synthesis by cells)? Please help me to understand.  &lt;/p&gt;&#xA;" OwnerUserId="3881" LastEditorUserId="5563" LastEditDate="2015-06-11T07:16:00.463" LastActivityDate="2015-07-16T17:10:21.943" Title="Where is ATP used in Phosphorylation?" Tags="&lt;plant-physiology&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35128" PostTypeId="1" AcceptedAnswerId="35134" CreationDate="2015-06-11T07:11:33.863" Score="7" ViewCount="773" Body="&lt;p&gt;According to the linked report, people with &lt;a href=&quot;http://www.dailymail.co.uk/news/article-3043767/I-exist-gray-29-year-old-looks-like-woman-male-genitalia-speaks-rare-intersex-condition.html&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;androgen insensitivity syndrome&lt;/strong&gt;&lt;/a&gt; appear as male, but have both feminine and masculine outer genitalia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I was not able to find out whether their internal reproductive system is functional, i.e., if these people have a functional uterus.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is it possible for such a person to get pregnant?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5563" LastEditorUserId="9943" LastEditDate="2015-06-12T05:10:11.243" LastActivityDate="2016-08-05T00:01:28.033" Title="Can androgen-insensitive genetic-males get pregnant?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;&lt;pathology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35129" PostTypeId="2" ParentId="35127" CreationDate="2015-06-11T07:12:51.813" Score="4" Body="&lt;p&gt;In biology &lt;a href=&quot;http://en.wikipedia.org/wiki/Phosphorylation&quot; rel=&quot;nofollow noreferrer&quot;&gt;phosphorylation&lt;/a&gt; marks the addition of inorganic phosphate groups to proteins or other organic molecules. The phospho-group usually comes from ATP which is converted into ADP in this process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the context of the &lt;a href=&quot;http://en.wikipedia.org/wiki/Light-independent_reactions#Calvin_Cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;Calvin Cycle&lt;/a&gt; there are two positions where molecules get phosphorylated. The first is the phosphorylation of 3-phosphogylcerate to 1,3-bisphosphoglyerate, the other is the phosphorylation of Ribulose 5-phosphate to Ribulose 1,5-bisphosphate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See the image (from &lt;a href=&quot;http://en.wikipedia.org/wiki/Light-independent_reactions#Calvin_Cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zoe77.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-06-11T07:12:51.813" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35131" PostTypeId="2" ParentId="35126" CreationDate="2015-06-11T07:57:14.587" Score="7" Body="&lt;p&gt;The yellow color comes from the accumulation of &lt;a href=&quot;http://en.wikipedia.org/wiki/Bilirubin&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bilirubin&lt;/a&gt; in the body. Bilirubin is a breakdown product of hemoglobin (contained in erythrocytes, also known as red blood cells, and responsible for the oxygen transport in the body). (This is also the reason why bruises get colored, as the blood which was released into the skin gets removed.) As erythrocytes live only for around 120 days, the hemoglobin needs to be recycled at the end of the life cycle, as free hemoglobin is a pretty problematic substance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The recycling of the erythrocytes happens in the liver, the iron is recycled, and the hemoglobin is split in the globin (which is further broken down into the amino acids) and the heme which is oxidized by the heme oxidase to biliverdin and further by the biliverdin reductase to bilirubin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As bilirubin is not water soluble it is bound to albumin and released into the bloodstream for the transport to the liver. In the liver this process goes on further until the bilirubin is water soluble and can be released with the bile into the intestine where it is finally excreted. See the image (from &lt;a href=&quot;http://www.zuniv.net/physiology/book/chapter23.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;) for an illustration:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GgLC3.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If your liver is not working properly (for example due to an infection) the break-down process of the albumin-bound bilirubin is reduced or doesn't work and the yellow bilirubin accumulates in the body until the skin gets yellow. So this indicates a liver malfunction and is usually nothing to take easy.&lt;/p&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="948" LastEditDate="2015-06-11T23:49:25.293" LastActivityDate="2015-06-11T23:49:25.293" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35133" PostTypeId="6" CreationDate="2015-06-11T09:40:13.003" Score="0" Body="&lt;p&gt;I am very eager to see this site succeed and I would therefore be willing to be involved in moderating this site.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I subscribe to the philosophy of minimal moderator intervention allowing the community to shape the site's development, but at the same time I believe in maintaining the strict quality standards for questions and answers characteristic of the stack exchange network.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While the volume of my questions and answers is not as great as many of the other candidates, I try to ensure that my questions and answers are of the highest quality.  I have found this site to be extremely useful in helping me understand biology and therefore I am very eager to ensure the site continues to be successful, allowing the site to continue to help many others too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://stackexchange.com/users/1823107/mew?tab=accounts&quot;&gt;http://stackexchange.com/users/1823107/mew?tab=accounts&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="1472" LastEditorUserId="1472" LastEditDate="2015-06-11T09:46:31.997" LastActivityDate="2015-06-11T09:46:31.997" CommentCount="3" CommunityOwnedDate="2015-06-11T09:40:13.003" ContentLicense="CC BY-SA 3.0" />
  <row Id="35134" PostTypeId="2" ParentId="35128" CreationDate="2015-06-11T12:13:23.997" Score="12" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;People with androgen insensitivity syndrome do not have a functional uterus and cannot bear a child.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Androgen-insensitive genetic males may develop female genitalia and internal female reproductive organs. However, in both partial androgen insensitivity syndrome (PAIS) and complete androgen insensitivity syndrome (CAIS) the uterus is absent, or is present only in a rudimentary form. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for the absence, or rudimentary form of the uterus is the fact that Mullerian inhibiting substance (MIS), produced by the Sertoli cells of the fetal testes is present. MIS controls the regression of the mullerian ducts, and in its absence in XX females, the mullerian system develops into the uterus, oviducts, and upper vagina. However, in XY individuals with CAIS (and likely also with PAIS), MIS is produced normally by the testes resulting in inhibition of the growth of the uterus and fallopian tubes &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19064222&quot; rel=&quot;nofollow&quot;&gt;(Oakes &lt;em&gt;et al&lt;/em&gt;., 2008)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19064222&quot; rel=&quot;nofollow&quot;&gt;Oakes &lt;em&gt;et al., J Pediatr Adolesc Gynecol&lt;/em&gt; (2008); &lt;strong&gt;21&lt;/strong&gt;: 305-10&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-12-22T20:31:37.080" LastActivityDate="2015-12-22T20:31:37.080" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35135" PostTypeId="1" CreationDate="2015-06-11T14:22:34.317" Score="2" ViewCount="205" Body="&lt;p&gt;I am reading chapter 7 of &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0582243025&quot; rel=&quot;nofollow&quot;&gt;Falconer and Mackay&lt;/a&gt; where they give a formula to calculate the population mean as a deviation from the heterozygote genotypic value.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As an example, imagine a one locus two allele trait, with alleles $A_1$ and $A_2$, with respective frequencies $p$ and $q$, and genotypic values ($\theta$) of $A_1A_1 = \theta_{1,1} = 0.5$, $A_1A_2 = \theta_{1,2} = 0.4$, and $A_2A_2 = \theta_{2,2} = 0.3$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mean is given by &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$ M = a_1(p-q) + 2pqd$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $a_1$ is the deviation between the genotypic value of $A_1$ homozygotes and genotypic value heterozygotes, and, because $d=0$ (the dominance deviation), this equation reduces to &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$ M = a_1(p-q)$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For my above example, if $p = 0.7$ then $M = 0.04$ and the population mean should be &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\frac{1}{2} \theta_{1,1} + \frac{1}{2} \theta_{2,2} + M = 0.44$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\frac{1}{2} \theta_{1,2} + M = 0.44$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this correct?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What is the correct term and notation for the genotypic values (which I termed $\theta$)&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2015-06-11T14:56:25.240" LastActivityDate="2015-06-11T14:56:25.240" Title="Falconer &amp; Mackay population mean calculation &amp; genotypic values" Tags="&lt;population-genetics&gt;&lt;quantitative-genetics&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35136" PostTypeId="1" AcceptedAnswerId="35138" CreationDate="2015-06-11T14:36:24.013" Score="-3" ViewCount="100" Body="&lt;p&gt;I am working on an independent research project for which I require access to the MORF database created by Hsu et al. From where can I download the database of MORFs of IDPs and their binding partners that was created by Hsu et al.?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would appreciate a link to that page. I have searched a lot of keywords on Google but I could not come up with it. I might have, but I'm not too certain of it. I have already wasted 3 days searching for it.&lt;/p&gt;&#xA;" OwnerUserId="15415" LastActivityDate="2015-06-11T15:56:04.397" Title="From where can I download the database created by Hsu et al for MORFs?" Tags="&lt;database&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-06-12T17:18:45.043" ContentLicense="CC BY-SA 3.0" />
  <row Id="35137" PostTypeId="1" AcceptedAnswerId="35145" CreationDate="2015-06-11T15:47:03.877" Score="2" ViewCount="702" Body="&lt;p&gt;Reading &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0582243025&quot; rel=&quot;nofollow&quot;&gt;Falconer and Mackay&lt;/a&gt; looking at equation $V_A = 2pqa^2$ (equation 8.5, page 126).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am trying to write a clear explanation of how additive genetic variance is defined and calculated, but I keep getting twisted up in the books I am working from.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just what is the term $a$ and how is it calculated?&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2015-06-11T17:23:24.947" LastActivityDate="2015-06-11T19:24:46.620" Title="Additive genetic variance $V_A= 2pqa^2$ ... what is $a$?" Tags="&lt;quantitative-genetics&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35138" PostTypeId="2" ParentId="35136" CreationDate="2015-06-11T15:56:04.397" Score="1" Body="&lt;p&gt;I'm assuming you're looking for the dataset that was used to train MorfPred from this paper? &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22689782&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/22689782&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's a link to it on this page: &lt;a href=&quot;http://biomine-ws.ece.ualberta.ca/MoRFpred/index.html&quot; rel=&quot;nofollow&quot;&gt;http://biomine-ws.ece.ualberta.ca/MoRFpred/index.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're referring to another paper, it is likely they used the same data set. The best way to find the supplementary data, is to read the paper thoroughly - this is a better approach than a Google search! Keep in mind though, that sometimes the data set is not publicly available and you must e-mail the researcher in question to request it. &lt;/p&gt;&#xA;" OwnerUserId="15966" LastActivityDate="2015-06-11T15:56:04.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35140" PostTypeId="1" CreationDate="2015-06-11T16:31:56.613" Score="10" ViewCount="972" Body="&lt;p&gt;I recently heard of &lt;a href=&quot;http://plant-e.com/technology.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;a successful effort&lt;/a&gt; that harvests energy from soil at plants' bases due to apparently bacterial breakdown of wastes from the plants:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Via photosynthesis a plant produces organic matter. Part of this&#xA;  organic matter is used for plant-growth, but a large part can’t be&#xA;  used by the plant and is excreted into the soil via the roots. Around&#xA;  the roots naturally occurring micro-organisms break down the organic&#xA;  compounds to gain energy from. In this process, electrons are released&#xA;  as a waste product. By providing an electrode for the micro-organisms&#xA;  to donate their electrons to, the electrons can be harvested as&#xA;  electricity. Research has shown that plant-growth isn’t compromised by&#xA;  harvesting electricity, so plants keep on growing while electricity is&#xA;  concurrently produced.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/aKUfU.png&quot; alt=&quot;Root energy&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently there is &lt;a href=&quot;http://www.plantpower.eu&quot; rel=&quot;nofollow noreferrer&quot;&gt;more research here&lt;/a&gt;, and this was particularly interesting (&lt;a href=&quot;http://plantpower.eu/onewebmedia/Abstractboek%20Symposium%20Gent.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;a PDF&lt;/a&gt;) as it states more clearly that we are indeed talking about bacteria:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The PlantPower concept is based on the cooperation of plants and&#xA;  microorganisms to produce in-situ electricity. Plants take up carbon&#xA;  dioxide and water and capture light energy. This energy is stored in&#xA;  the chemical bonds of sugars produced, using carbon dioxide and water.&#xA;  Part of this chemically stored energy is transferred to the roots of&#xA;  the plants. This energy present in the root zone can then be captured&#xA;  by the so-called electro-chemical active bacteria. These organisms are&#xA;  capable to oxidize the organic matter present in the root zone and&#xA;  transfer the energy rich electrons to an electrode. The energy carried&#xA;  by the electrons can be used as electrical energy, after which the&#xA;  electrons react at another electrode with oxygen to form water.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would like to understand this process as far as what bacteria or &quot;micro organism(s)&quot; are being leveraged here.  It seems that they are supplementing the soil with some kind of bacteria that acts in this specific way of releasing additional electrons that can then be harvested.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any idea as to what kind of micro organisms or bacteria have this kind of reaction wherein they release or excrete harvestable energy (and apparently CO&lt;sub&gt;2&lt;/sub&gt; + H+) upon consumption of plant &quot;excretions&quot; (C&lt;sub&gt;6&lt;/sub&gt;H&lt;sub&gt;12&lt;/sub&gt;O&lt;sub&gt;6&lt;/sub&gt;)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After doing a bit more digging, I have found some, perhaps, interesting information &lt;a href=&quot;https://en.wikipedia.org/wiki/Microbial_fuel_cell#Mediator-free_microbial_fuel_cell&quot; rel=&quot;nofollow noreferrer&quot;&gt;from Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://cl.ly/image/0z3c3h00400s/more%20info%20from%20wikipedia-1.png&quot; alt=&quot;Wikipedia extract&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What ultimately confuses me here is that the other method noted earlier does not really emphasize any particular &lt;em&gt;kind&lt;/em&gt; of plant and therefore I can't help but think that perhaps there are some other more useful bacteria for this scenario...&lt;/p&gt;&#xA;" OwnerUserId="14667" LastEditorUserId="-1" LastEditDate="2017-03-10T09:42:48.943" LastActivityDate="2018-10-17T03:12:19.960" Title="What bacteria shed harvestable energy from root zone organic matter?" Tags="&lt;botany&gt;&lt;bacteriology&gt;&lt;ecology&gt;&lt;energy&gt;&lt;soil&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35141" PostTypeId="1" CreationDate="2015-06-11T16:32:06.237" Score="7" ViewCount="178" Body="&lt;p&gt;To my (limited) understanding, there are 2 main ways that mutations can occur in DNA: Environmental (UV, etc) and mistakes during cell division.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering if there is a mechanism that can give priority to certain genes to be accurately duplicated. Some sort of trigger that says &quot;&lt;em&gt;double-check this specific gene&lt;/em&gt; before continuing with the duplication&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And if there &lt;em&gt;is&lt;/em&gt; such a mechanism, then I wonder if there is some sort of dependency system for genes that control groups of other genes. So that if a certain gene &quot;activates&quot; the double-check trigger, it would automatically add that trigger to the group of genes which are affected by it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="16172" LastEditorUserId="6307" LastEditDate="2015-06-11T18:59:39.373" LastActivityDate="2016-05-29T02:13:23.663" Title="Following DNA replication during S-phase of the cell-cycle, are all genomic regions subjected to the same stringent level of DNA-Repair?" Tags="&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;mutations&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35143" PostTypeId="1" AcceptedAnswerId="35171" CreationDate="2015-06-11T18:15:49.040" Score="5" ViewCount="61" Body="&lt;p&gt;I'm hoping that somebody here can explain this unusual result that I'm getting with some pyrosequencing data. I have bisulphite converted a few samples a couple of times over the years for different projects. Recently I was collecting some of this disparate data together and I noticed that when the same pyrosequencing assay was used on these samples, those that were converted later had decreased methylation at the CpG sites of interest compared to the initial bisulphite converted samples. The original conversion was in 2010 and the repeat conversions were in 2014/2015. The assays are the same and it's difficult to blame this on PCR amplifying one clone over another since I've done technical replicates on each aliquot. Even the 2010 converted sample has the same result in 2015 that it did in 2010 but this is different from the 2015 converted sample. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We are using the same kit (Qiagen) for bisulphite conversion and haven't made a major change to our procedure (we follow the Qiagen protocol without modification). Has anybody noticed this phenomenon before? Is it possible that stored DNA would experience methylation changes? It seems more likely that the issue is technical but I'm having trouble figuring out exactly what that technical issue is.&lt;/p&gt;&#xA;" OwnerUserId="15594" LastEditorUserId="15594" LastEditDate="2015-06-12T15:04:08.640" LastActivityDate="2015-06-12T15:50:17.630" Title="One Sample, Different Methylation Values" Tags="&lt;lab-techniques&gt;&lt;dna-methylation&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35144" PostTypeId="1" AcceptedAnswerId="35150" CreationDate="2015-06-11T19:19:19.550" Score="13" ViewCount="572" Body="&lt;p&gt;What are the upper and lower limits for chromosome length? Are these limits different in different species or kingdoms? If there is any limit, which cellular or molecular factors are reasons? &lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="10456" LastEditDate="2015-06-11T20:43:48.847" LastActivityDate="2015-06-11T22:39:56.593" Title="What limits chromosomal length?" Tags="&lt;chromosome&gt;&lt;genomes&gt;&lt;dna-helix&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35145" PostTypeId="2" ParentId="35137" CreationDate="2015-06-11T19:21:53.050" Score="3" Body="&lt;p&gt;This information is given in p.118.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;In essence $a$ represents the deviation from the population mean due additive genetic effects.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Say a trait is controlled solely by locus X with the effect alleles &lt;em&gt;X&lt;/em&gt; impacting the phenotype Y in an additive manner (no dominance and epistasis effect), then we can calculate the effect size of carrying the &lt;em&gt;X&lt;/em&gt; allele, called $a$, and representing the distance from the population phenotypic mean of homozygote &lt;em&gt;XX&lt;/em&gt;. Based on this definition, the distance from the mean for individual with the following genotype is given by:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;XX&lt;/em&gt;: $a$&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Xx&lt;/em&gt; : 0&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;xx&lt;/em&gt;: $-a$&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;This makes more sense using the genetic model:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$P=G+E=BV+I+E=A+D+I+E$ (parameters listed at the bottom)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the example, the locus has only an additive effect then D=0 and assuming there is no epistasis then I=0 as well which gives $P=BV+E=A+E$ therefore $BV=A$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this case $a$ can be computed directly from the BV, with p=f(X) and q=f(x), as:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;$BV(XX)=2qa$&lt;/li&gt;&#xA;&lt;li&gt;$BV(Xx)=(q-p)a$&lt;/li&gt;&#xA;&lt;li&gt;$BV(xx)=-2pa$&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Now for the complete case of both additive and dominant effects, i.e. $BV=A+D$, you can refer to table 7.3 in p.118 which describe that XX individuals are given the value $a$, Xx -&gt; $d$ and xx -&gt; $-a$ with the corresponding relationship to the BV given by (care here it's not $a$ but alpha $\alpha$):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;$BV(XX)=2q\alpha$&lt;/li&gt;&#xA;&lt;li&gt;$BV(Xx)=(q-p)\alpha$&lt;/li&gt;&#xA;&lt;li&gt;$BV(xx)=-2p\alpha$&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;with $\alpha=a+d(q-p)$&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;P=phenotype&lt;/li&gt;&#xA;&lt;li&gt;BV=A+D=Breeding value&lt;/li&gt;&#xA;&lt;li&gt;G=Genotypic effect&lt;/li&gt;&#xA;&lt;li&gt;E=Environmental effect&lt;/li&gt;&#xA;&lt;li&gt;A=Additive genetic effect quantified by $a$&lt;/li&gt;&#xA;&lt;li&gt;D=Dominant genetic effect quantified by $d$&lt;/li&gt;&#xA;&lt;li&gt;I=Epistasis effect&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="14826" LastActivityDate="2015-06-11T19:21:53.050" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35150" PostTypeId="2" ParentId="35144" CreationDate="2015-06-11T22:25:25.593" Score="11" Body="&lt;p&gt;There is both an upper and lower limit which are species specific. The upper limit is caused by incomplete segregation of sister chromatids and subsequent trimming of the long arm(s). The reason for the lower limit is, as far as I can tell, unknown.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;strong&gt;Upper Limit&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://ac.els-cdn.com/S0092867400818917/1-s2.0-S0092867400818917-main.pdf?_tid=7e0f35c2-1079-11e5-b9e4-00000aacb35e&amp;amp;acdnat=1434055149_76ddb8d6af25e65f500d1c79c9744aa5&quot; rel=&quot;noreferrer&quot;&gt;Schubert I, Oud JL. 1997. There is an Upper Limit of Chromosome Size for Normal Development of an Organism. Cell 88:515-520.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/m/pubmed/12584450/&quot; rel=&quot;noreferrer&quot;&gt;Hudakova S, Künzel G, Endo TR, Schubert I. 2002. Barley chromosome arms longer than half of the spindle axis interfere with nuclear divisions. Cytogenet Genome Res 98:101-107.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/m/pubmed/17021850/?i=3&amp;amp;from=/12584450/related&quot; rel=&quot;noreferrer&quot;&gt;Rens W, Torosantucci L, Degrassi F, Ferguson-Smith MA. 2006. Incomplete sister chromatid separation of long chromosome arms. Chromosoma 115(6):481-490.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;In these papers they found that in mono- and dicotic plants and one animal, the chromosome arm length is limited to half of the average length of the spindle arm axis (the length between the centromeres). Due to the mechanism and its presence in both plants and animals, it might be reasonable to expect that other domains of life are subject to similar constraints. Schubert and Oud (1997) speculate that the spindle axis length is fixed species specifically.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/LUCLp.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;These are confocal microscope images of dividing &lt;em&gt;Vicia faba&lt;/em&gt; (bean) cells (Schubert and Oud, 1997). &lt;strong&gt;(a)&lt;/strong&gt; Wild-type cell at anaphase. &lt;strong&gt;(b-d)&lt;/strong&gt; When the chromosome arms are longer, the chromatids cannot be completely separated at anaphase. &lt;strong&gt;(e)&lt;/strong&gt; Wild-type cell at telophase. &lt;strong&gt;(f, g)&lt;/strong&gt; Longer chromatids cannot be separated sufficiently and a bridge forms between the two daughter nuclei. &lt;strong&gt;(h-j)&lt;/strong&gt; The bridge is broken when the cell plate forms. &lt;strong&gt;(k)&lt;/strong&gt; Wild-type cell at interphase. &lt;strong&gt;(l)&lt;/strong&gt; Breaking of the bridge between cells with lengthened chromosomes creates irregularly shaped nuclei and micronuclei - these micronuclei represent loss of DNA from the genome and are eventually lost outright through further cell divisions.&lt;/p&gt;&#xA;&lt;hr /&gt;&#xA;&lt;p&gt;&lt;strong&gt;Lower Limit&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;There is a lower limit, but it doesn't seem that anyone knows why, which makes it impossible to accurately define.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;Schubert and Oud (1997):&lt;/strong&gt; Data from various eukaryotic kingdoms indicate the existence of a lower limit of chromosome size for stable mitotic and meiotic segregation. Yeast artificial chromosomes do not exhibit normal meiotic stability until they are of a size between 120 to 500 kb which comes close to the order of size of native yeast chromosomes, in addition to functional telomere and centromere sequences (Niwa et al., 1989). For a Drosophila minichromosome, an island of complex DNA of 220 kb was shown to be necessary for proper centromere function (Murphy and Karpen, 1995). However, for stable mitotic and meiotic segregation an additional 200 kb of a flanking satellite sequence was required. For stable achiasmate disjunction of minichromosomes during meiosis in female Drosophila, 1000 kb of overlapping centric heterochromatin sequences are necessary (Karpen et al., 1996). Schriever-Schwemmer and Adler (1993) have shown that a minichromosome representing the small centric product of a translocation between chromosomes 7 and 15 of the mouse and comprising about 1% of the haploid genome got lost during meiosis in the female carrier organism while the corresponding product of a translocation involving chromosomes 4 and 8 did not. The latter was somewhat larger. Either this different behavior was due to the presence of essential genetic information on the small translocation product 4⁸, or the minichromosome 7¹⁵ was just too small for stable segregation, although it contained a complete centromere as well as telomeres. Finally, we have observed that the frequency of meiotic missegregation, but not of transmission to the next generations, is inversely correlated with the size of translocation chromosomes in &lt;em&gt;Vicia faba&lt;/em&gt; (Schubert et al., 1986). Thus, the existence of a proper length range for eukaryotic chromosomes is obvious.&lt;/p&gt;&#xA;&lt;p&gt;The physical reasons for the lower limit that still enables stable mitotic and meitotic segregation are less clear at present than the constraints for an upper limit of chromosome length&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Of course, &amp;quot;present&amp;quot; in that paper refers to the late 90's but, in my admittedly brief search, I have been unable to find too much in the way of more recent results. The following paper seems somewhat promising, but I don't have access to it and can only quote from the abstract. It's not much more recent, either.&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/m/pubmed/11528109/&quot; rel=&quot;noreferrer&quot;&gt;Schubert I. 2001. Alteration of chromosome numbers by generation of minichromosomes -- is there a lower limit of chromosome size for stable segregation? Cytogenet Cell Genet 93:175-181.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;[A] lower size limit for a stable chromosome transmission … might be based, for instance, on insufficient lateral support of centromeres or on insufficient bivalent stability due to the incapability of chiasma formation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-11T22:39:56.593" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35151" PostTypeId="1" CreationDate="2015-06-11T22:28:36.053" Score="4" ViewCount="1853" Body="&lt;p&gt;For example, in this protocol for E. coli competent cell preparation, it says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Plate 10 uL E. coli BL21(DE3) cells on a LB-agar plate; incubate overnight (12 hours).&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Prepare 500 mL SOB medium so it can be pre-warmed in the 37 degrees Celsius incubator the day before.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Pick a single selected colony and inoculate in 5 mL of SOB medium and grow for 16 hours at 37 degrees Celsius and 250 rpm in a shaker.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Inoculate 500 mL of prewarmed SOB medium with 5 mL of the fresh overnight culture.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and then in the protocol for overexpressing proteins after transformation of these cells, I basically follow similar steps as above but this time, without prewarming the large-scale inoculation lqiuid medium. Why is that?&lt;/p&gt;&#xA;" OwnerUserId="15955" LastActivityDate="2015-06-12T00:46:58.010" Title="Why do some protocols require prewarming a liquid medium before inoculating?" Tags="&lt;molecular-biology&gt;&lt;proteins&gt;&lt;bacteriology&gt;&lt;gene-expression&gt;&lt;cell-culture&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35152" PostTypeId="1" AcceptedAnswerId="35154" CreationDate="2015-06-11T22:50:15.207" Score="1" ViewCount="1381" Body="&lt;p&gt;I will be first year undergraduate at Physics department next year and last year I was at the Medicine faculty. I want do double major in the second year of faculty with Molecular Biology and Genetics. The intersection of biology and physics is my interest. I have two books about biology, first one is &lt;strong&gt;What is Life?-Mind and Matter by Erwin Schrödinger&lt;/strong&gt; and the second one is &lt;strong&gt;This is Biology by Ernst Mayr&lt;/strong&gt;. Which one should I read to acquire general knowledge about Biology?&lt;/p&gt;&#xA;" OwnerUserId="16179" LastActivityDate="2015-06-12T15:33:15.737" Title="Choosing a book to gain general knowledge about biology" Tags="&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="0" ClosedDate="2015-06-12T11:34:45.743" ContentLicense="CC BY-SA 3.0" />
  <row Id="35153" PostTypeId="2" ParentId="17207" CreationDate="2015-06-11T22:56:12.957" Score="1" Body="&lt;p&gt;For me it looks like an &lt;a href=&quot;http://en.wikipedia.org/wiki/Geometer_moth&quot; rel=&quot;nofollow noreferrer&quot;&gt;inchworms&lt;/a&gt; which are the larvae of geometer moth or Geometridae.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By your picture it is almost impossible to see of which type it is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I took picture of one in Switzerland (but likely not the same as yours).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/h7hZz.jpg&quot; alt=&quot;caterpillar-geometer&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Full resolution here: &lt;a href=&quot;https://flic.kr/p/utFsiU&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://flic.kr/p/utFsiU&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6561" LastActivityDate="2015-06-11T22:56:12.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35154" PostTypeId="2" ParentId="35152" CreationDate="2015-06-11T23:32:20.870" Score="6" Body="&lt;p&gt;&lt;strong&gt;The books you have&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The books you cited won't help you to get a solid and general basic knowledge in biology. I haven't read those books but I think that &lt;code&gt;This is Biology&lt;/code&gt; is a book of philosophy of biology written by a biologist and philosopher. &lt;code&gt;What is life&lt;/code&gt; is a very influential book written by a physicist who more or less predicted the structure of DNA that was later discovered by Watson and Crick. You won't learn much of biology through these books.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Book Suggestions&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/10376/introductory-biology-text-for-an-outsider&quot;&gt;This post&lt;/a&gt; offers book suggestions for general introductory biology. &lt;a href=&quot;https://biology.stackexchange.com/questions/21475/books-for-beginners/21477#21477&quot;&gt;Here&lt;/a&gt; is another post that may also interest you&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are interested in a specific field of biology, then you may want to ask for book suggestions for this particular field. I think that most biologists that come from a background in physics are in the fields of theoretical evolutionary biology, bioinformatics and biophysics (incl. molecular biophysics).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are a bunch of other posts asking for book recommendations that I imagine you may like reading about.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/27450/what-physics-knowledge-can-be-applied-to-biology-of-organisms-and-ecosystems&quot;&gt;What physics knowledge can be applied to biology of organisms and ecosystems?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/14168/book-recommendations-for-algorithms-used-in-evolutionary-biology&quot;&gt;Book recommendations for algorithms used in evolutionary biology&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/16577/book-recommendations-for-evolutionary-models&quot;&gt;Book recommendations for evolutionary models&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/9243/how-to-learn-biomathematics/9245#9245&quot;&gt;How to learn biomathematics?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/16470/book-recommendation-on-population-evolutionary-genetics&quot;&gt;Book recommendation on population/evolutionary genetics?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/2580/introductory-literature-for-synthetic-systems-biology&quot;&gt;Introductory literature for synthetic / systems biology?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And eventually you may want to read &lt;a href=&quot;https://biology.stackexchange.com/questions/34846/value-of-mathematical-models-in-biology&quot;&gt;Value of mathematical models in biology&lt;/a&gt; although the post has been closed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, you might want to read a bunch of wikipedia pages such as &lt;a href=&quot;https://en.wikipedia.org/wiki/Biophysics&quot; rel=&quot;nofollow noreferrer&quot;&gt;Biophysics&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Molecular_biophysics&quot; rel=&quot;nofollow noreferrer&quot;&gt;Molecular Biophysics&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Mathematical_and_theoretical_biology#Mathematical_biophysics&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mathematical and Theoretical Biology&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Biostatistics&quot; rel=&quot;nofollow noreferrer&quot;&gt;Biostatistics&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Computational_biology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Computational Biology&lt;/a&gt;, &lt;a href=&quot;http://en.wikipedia.org/wiki/Bioinformatics&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bioinformatics&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-06-12T15:33:15.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35155" PostTypeId="2" ParentId="35151" CreationDate="2015-06-12T00:39:36.063" Score="4" Body="&lt;p&gt;It's because &lt;em&gt;E.coli&lt;/em&gt; BL21(DE3) are competent cells. The competent is the key here as the cells were chemically treated so the transfection can be performed by heat-shock with high efficiency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This means these bacteria are quite fragile, due to the chemical treatment, and therefore are very sensitive to both mechanical and thermal shocks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pre-heating the media simply avoids damaging the cells and maximizes the growth rate.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-06-12T00:46:58.010" LastActivityDate="2015-06-12T00:46:58.010" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35157" PostTypeId="1" AcceptedAnswerId="35160" CreationDate="2015-06-12T01:22:38.217" Score="3" ViewCount="1179" Body="&lt;p&gt;We use a lentivirus packaging vector called &lt;a href=&quot;https://www.addgene.org/17293/&quot; rel=&quot;nofollow&quot;&gt;pLenti_puro_DEST&lt;/a&gt;. We use puromycin to select for the cloned gene in 293T cells. However, the pLenti_Neo_Dest has been discontinued, so I'm cloning a Neomycin resistance gene into the pLenti_Puro_Dest thus replacing Puromycin with Neomycin. I usually just grow up this gene in &lt;a href=&quot;https://www.lifetechnologies.com/order/catalog/product/11635018&quot; rel=&quot;nofollow&quot;&gt;Stb3 or Stb4&lt;/a&gt; cells from invitrogen. I'm wondering if I can select for cloned pDEST vectors in these cells using Neomycin or G418. According to the &lt;a href=&quot;http://www.invivogen.com/g418&quot; rel=&quot;nofollow&quot;&gt;G418 manual,&lt;/a&gt; you can theoretically use it for bacterial selection, but I think that may be for libraries and not actually growing up the plasmid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So is it possible to select for my plasmid in these cells by adding a little G418 to the ampicillin plate? Is this common? I can't find anyone selecting bacteria by Neomycin anywhere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT - The main reason I ask, is that the resistance gene is under a PGK promoter that I have no idea if it works in bacterial cells.&lt;/p&gt;&#xA;" OwnerUserId="3887" LastEditorUserId="9943" LastEditDate="2015-06-12T02:52:40.533" LastActivityDate="2015-06-12T08:21:57.457" Title="Neomycin resistance gene in E. coli stb3 cells" Tags="&lt;molecular-biology&gt;&lt;cloning&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35158" PostTypeId="2" ParentId="31879" CreationDate="2015-06-12T02:18:15.797" Score="4" Body="&lt;p&gt;This question has actually been covered (although not to the complete extent of evolutionary history) by Richard Dawkins in his book &lt;a href=&quot;http://en.wikipedia.org/wiki/The_Ancestor%27s_Tale&quot; rel=&quot;nofollow&quot;&gt;The Ancestor's Tale.&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;He gives the following estimates of LUCA time and generations:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Monkeys and apes: 40MY(3M)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mammals: 180MY(120M)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reptiles: 310MY(170M)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ray finned fish: 440MY(195M)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sharks, hagfish and lampreys: 530MY(240M)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lancelets and all chordates: 560MY(270M)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, he ceases to provide any generation estimates from here onwards, due to the error and general uncertainties being too large for a meaningful answer. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-06-12T02:18:15.797" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35159" PostTypeId="2" ParentId="1205" CreationDate="2015-06-12T05:14:37.760" Score="0" Body="&lt;p&gt;Three follicular stages are recognised,&#xA;1) Primary/Preantral Follicles (with primary oocyte inside)&#xA;2) Secondary/Antral Follicles (with primary oocyte inside)&#xA;3) Pre Ovulatory Follicles (with secondary oocyte inside)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pre ovulatory Follicles are formed ~36 hrs before ovulation at time of LH surge. This coincides with completion of Meiosis I and formation of the secondary oocyte. The secondary oocyte immediately enters Meosis II. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Appx. 3 hrs before ovulation, the Pre ovulatory Follicle (with the secondary oocyte inside) is arrested in the metaphase of Meiosis II and is extruded out of the ovary - a process called as Ovulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It comes to rest in the ampulla of the fallopian tube and here it is fertilised. As the sperm pronucleus is released into the cytoplasm, the Secondary Oocyte (now called the ovum) completes Meiosis II and releases the second polar body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="16183" LastActivityDate="2015-06-12T05:14:37.760" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35160" PostTypeId="2" ParentId="35157" CreationDate="2015-06-12T05:26:10.493" Score="1" Body="&lt;p&gt;PGK is mammalian (murine) phosphoglycerate kinase promoter. It will therefore not work in bacterial systems. Why don't you select using ampicillin only? You can increase the ampicillin concentration if you want. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I can't find anyone selecting bacteria by Neomycin anywhere.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Kanamycin is generally used for bacterial selection. The Neomycin resistance gene works on Neomycin, Kanamycin and G418 (a gentamycin variant). The gene basically codes for an aminoglycoside phosphotransferase and different variants of the gene have different affinities for different aminoglycoside substrates. For a basic reference see &lt;a href=&quot;http://openwetware.org/wiki/Kanamycin&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-12T08:21:57.457" LastActivityDate="2015-06-12T08:21:57.457" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35161" PostTypeId="1" AcceptedAnswerId="55345" CreationDate="2015-06-12T06:10:27.487" Score="4" ViewCount="51" Body="&lt;p&gt;CpG content varies a lot across the human genome. What does determine a promoter to be silenced through DNA methylation: the fraction of CpG sites that are methylated or the total number of methylated CpG sites? Any reference?&lt;/p&gt;&#xA;" OwnerUserId="16184" LastActivityDate="2017-01-17T23:25:25.780" Title="Gene silencing: relative or absolute number of methylated CpG sites?" Tags="&lt;transcription&gt;&lt;dna-methylation&gt;&lt;cpg&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35162" PostTypeId="2" ParentId="35157" CreationDate="2015-06-12T07:37:09.087" Score="1" Body="&lt;p&gt;In this paper &lt;a href=&quot;http://www.nature.com/ng/journal/v37/n3/pdf/ng1505.pdf&quot; rel=&quot;nofollow&quot;&gt;(Li and Elledge, Nature Genetics, 2005)&lt;/a&gt; it is shown that the PGK promoter works in E.coli but it has very little activity. So, I don't think it is suited to properly express resistance enzyme.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About Neomycin, many aminoglycosides resistance enzymes (not all) that work on Kanamycin works well also with Neomycin. I have personally selected E.coli expressing Kan resistance (from a pET vector) using Neomycin without problems.&lt;/p&gt;&#xA;" OwnerUserId="12923" LastActivityDate="2015-06-12T07:37:09.087" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35163" PostTypeId="1" CreationDate="2015-06-12T07:45:48.287" Score="9" ViewCount="2913" Body="&lt;p&gt;This is an extension of this question about &lt;a href=&quot;https://biology.stackexchange.com/questions/35144/what-limits-chromosomal-length&quot;&gt;What limits chromosomal length?&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am wondering what could be the specific reasons behind the number of chromosomes an organism carries. In other words, what drives the number of chromosomes and is there anything &quot;stabilizing&quot; the number of chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course I am not talking about multiple copies of the same chromosome, i.e. trisomy, but rather the reasons behind the partition of the genetic information into a defined number of chromosomes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the question I referred to, chromosomes have an upper length limit which is based on their physical size, i.e basically they must be shorter than half of the spindle arm axis and they probably also have a lower limit. Yet it is unclear to me if any non-random equilibrium exists between chromosome number and length other than just being bound by an upper and lower limit in size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also let's restrict this question to diploid organisms to avoid organisms such as the &lt;em&gt;&lt;a href=&quot;http://en.wikipedia.org/wiki/Oxytricha_trifallax&quot; rel=&quot;nofollow noreferrer&quot;&gt;Oxytricha trifallax&lt;/a&gt;&lt;/em&gt; which has 16,000 chromosomes but is also ampliploid or plants such as wheat which can be tetraploid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried to search in the literature and couldn't find a satisfying answer. Also I had in mind the example of the Hela cells which have completely shuffled chromosomes yet still exactly 46.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2017-12-03T20:12:56.400" Title="What determines the number of chromosomes an organism carries?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;molecular-genetics&gt;&lt;chromosome&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35164" PostTypeId="2" ParentId="30764" CreationDate="2015-06-12T12:07:14.647" Score="1" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Skewed X-inactivation may lead to phenotypic manifestation of X-linked color blindness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;What an interesting question!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a study by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1682669/pdf/ajhg00066-0066.pdf&quot; rel=&quot;nofollow&quot;&gt;Jorgensen et al. (1992)&lt;/a&gt; two female identical twins that were heterozygotes for X-linked &lt;strong&gt;deuteranomaly&lt;/strong&gt; were investigated. &lt;a href=&quot;http://www.color-blindness.com/deuteranopia-red-green-color-blindness/&quot; rel=&quot;nofollow&quot;&gt;Phenotypically, deuteranomaly&lt;/a&gt; refers to anomalous trichromacy, i.e., reduced perception of a color. Note that deuteranopes are totally color &lt;em&gt;blind&lt;/em&gt;. Deuteronomaly in the twins was associated with a defective gene derived from their father. Interestingly, while monozygotic twins are genetically identical, one of the twins was phenotypically deuteranomalous, while the other had normal color vision.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Analysis of skin cells of the color vision-defective twin revealed that almost all skin cells had the paternal abnormal X chromosome active, explaining her color-vision defect. In contrast, skin cells from her sister with normal color vision had predominantly the maternal X chromosome active. Hence, deuteranomaly in one of the twins could be explained by &lt;strong&gt;an extremely skewed X inactivation&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As pointed out by @mdperry, extreme skewed X-inactivation is rare, and most heterzygous females for color blindness (&lt;em&gt;carriers&lt;/em&gt;) are indeed asymptomatic &lt;a href=&quot;http://vision.psychol.cam.ac.uk/jdmollon/papers/JordanMollon_Carriers.pdf&quot; rel=&quot;nofollow&quot;&gt;(Jordan &amp;amp; Mollon, 1993)&lt;/a&gt;. Regarding your second question, all gene mutations leading to color blindness are recessive (&lt;a href=&quot;http://ghr.nlm.nih.gov/condition/color-vision-deficiency&quot; rel=&quot;nofollow&quot;&gt;NIH&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://vision.psychol.cam.ac.uk/jdmollon/papers/JordanMollon_Carriers.pdf&quot; rel=&quot;nofollow&quot;&gt;Jordan &amp;amp; Mollon, &lt;em&gt;Vis Res&lt;/em&gt; (1993); &lt;strong&gt;33&lt;/strong&gt;(1): 1495-1508&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1682669/pdf/ajhg00066-0066.pdf&quot; rel=&quot;nofollow&quot;&gt;Jorgensen &lt;em&gt;et al. Am J Hum Genet&lt;/em&gt; (1992); &lt;strong&gt;51&lt;/strong&gt;: 291-8&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-12T14:22:39.663" LastActivityDate="2015-06-12T14:22:39.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35166" PostTypeId="2" ParentId="452" CreationDate="2015-06-12T12:49:10.890" Score="9" Body="&lt;p&gt;&lt;strong&gt;Another small addition&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;There is class of oxidoreductases called &lt;strong&gt;oxygenases&lt;/strong&gt; which incorporate molecular oxygen into the substrates and not just use it as an electron acceptor like in oxidases (note that the terminal enzyme in ETC is an oxidase and there are other such oxidases). In other words, oxygen is not a cofactor but a co-substrate. Oxygenases are further classified into dioxygenases and monooxygenases which incorporate two oxygen atoms and one oxygen atom respectively. Examples:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Cytochrome P450 family (monooxygenease): involved in detoxification of xenobiotics&lt;/li&gt;&#xA;&lt;li&gt;Cyclooxygenase (dioxygenase): involved in production of prostaglandins which are involved in pain and inflammation. Many NSAID painkillers like aspirin, paracetamol and ibuprofen target cyclooxygenase-2 (COX2)&lt;/li&gt;&#xA;&lt;li&gt;Lipoxygenase (dioxygenase): Involved in production of leukotrienes which are involved in inflammation.&lt;/li&gt;&#xA;&lt;li&gt;Monoamine oxidase (monooxygenase): Involved in catabolism of neurotransmitters such as epinephrine, norepinephrine and dopamine. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Does oxygen deprivation result in death just due to the halting of ATP&#xA;  production, or is there some other reason as well?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Death predominantly occurs because of halt in ATP production. Some cells such as neurons (and also perhaps cardiac muscles) are highly sensitive to loss of oxygen (for energy requirements) and clinical death because of hypoxia usually occurs because of loss basic brain function. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What percentage of the oxygen we take in through respiration is&#xA;  expelled later through the breath as carbon dioxide?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As already mentioned, it is said that there is a rough 1:1 ratio of CO&lt;sub&gt;2&lt;/sub&gt; production and O&lt;sub&gt;2&lt;/sub&gt; consumption. However, as indicated in a comment by CurtF, O&lt;sub&gt;2&lt;/sub&gt; does not form CO&lt;sub&gt;2&lt;/sub&gt;; it forms water in the last reaction of ETC. CO&lt;sub&gt;2&lt;/sub&gt; is produced in other reactions of Krebs cycle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glycolysis produces 32 molecules of ATP for 1 molecule of glucose via ETC (see &lt;a href=&quot;http://www.uic.edu/classes/bios/bios100/lecturesf04am/lect12.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;). There are three complexes in ETC and the third is dependent on oxygen; so you can assume that 1/2 a molecule of O&lt;sub&gt;2&lt;/sub&gt; consumed for production of 3 ATP molecules. Therefore 32 molecules of ATP would consume 4 molecules of O&lt;sub&gt;2&lt;/sub&gt;. Seems like there is a 1:1 ratio of CO&lt;sub&gt;2&lt;/sub&gt; production and O&lt;sub&gt;2&lt;/sub&gt; consumption.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can see it like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;FADH&lt;sub&gt;2&lt;/sub&gt; enters ETC at the second complex whereas NADH enters at the first. We can say that as long as NADH is present FADH&lt;sub&gt;2&lt;/sub&gt; would not require an extra oxygen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An NADH or a FADH&lt;sub&gt;2&lt;/sub&gt; molecule would require 1/2 molecule of O&lt;sub&gt;2&lt;/sub&gt;. There are 8 molecules of NADH and 2 molecules of FADH&lt;sub&gt;2&lt;/sub&gt; produced during glycolysis+krebs cycle which would require 10/2 = &lt;strong&gt;5&lt;/strong&gt; molecules of O&lt;sub&gt;2&lt;/sub&gt;. Glycolysis produces 4 molecules of CO&lt;sub&gt;2&lt;/sub&gt; during krebs cycle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, 2 cytosolic NADH molecules require 2 ATPs (in other words another NADH molecule) to be transported to mitochondria. So the net effect may be actually close to 1:1 O&lt;sub&gt;2&lt;/sub&gt;:CO&lt;sub&gt;2&lt;/sub&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another factor to keep in consideration is that the three complexes do not actually produce ATP; they just pump proton to create a chemical potential. The F&lt;sub&gt;0&lt;/sub&gt;F&lt;sub&gt;1&lt;/sub&gt;-ATP synthase would probably work only after a threshold of H&lt;sup&gt;+&lt;/sup&gt; potential is established. The 1 ATP molecule per complex is most likely the mean value and not exactly what really happens per reaction.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2020-02-16T11:58:43.107" LastActivityDate="2020-02-16T11:58:43.107" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="35168" PostTypeId="2" ParentId="23865" CreationDate="2015-06-12T14:46:38.797" Score="2" Body="&lt;p&gt;Action potentials of single neurons (APs) are the building blocks of compound action potentials (CAPs). While each of the individual APs is a yes-or-no response with a clear-cut defined threshold, CAPs are not. CAPs are build up of hundreds or thousands of neuronal contributions in, e.g., the auditory nerve. Decreased responsiveness as well as desynchronization of the neuronal responses can decrease the amplitude of the CAP. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It all depends on the amount of background noise and stimulus artifacts versus the amplification factor (the gain) whether a CAP can be recorded and identified yes or no. Typically, gross-potential recordings do not allow for single APs to be measured. CAPs are therefore stochastic phenomena and hence the CAP threshold should either be defined by visual examination (subjective), or through noise-dependent threshold criteria (objective). Therefore, unlike AP thresholds, CAP thresholds are arbitrary and heavily dependent on the noise level.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-13T12:05:05.837" LastActivityDate="2015-06-13T12:05:05.837" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35170" PostTypeId="1" CreationDate="2015-06-12T15:33:50.600" Score="1" ViewCount="40" Body="&lt;p&gt;I hope the question is not silly, but I wonder if a sort of genetically modified plant &quot;cancer&quot; could be used for carbon sequestration. For example, cancer cells like &lt;a href=&quot;https://en.wikipedia.org/wiki/HeLa&quot; rel=&quot;nofollow&quot;&gt;HeLa&lt;/a&gt; have been reproduced in tons, and as far as I know their growth rate is very high.   &lt;/p&gt;&#xA;" OwnerUserId="16187" LastActivityDate="2015-06-12T15:33:50.600" Title="Can photosyntetic cells be genetically modified to grow at a faster rate?" Tags="&lt;botany&gt;&lt;cancer&gt;&lt;photosynthesis&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35171" PostTypeId="2" ParentId="35143" CreationDate="2015-06-12T15:50:17.630" Score="3" Body="&lt;p&gt;I looked into this and if the effect is real, which it sounds like it is, it may be 5-formylcytosine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Methylcytosine oxidizes into hydroxymethylcytosine, which reacts with bisulphite exactly like you expect (identically). Hydroxymethylcytosine further oxidizes to 5-formylcytosine, which behaves like unmodified cytosine (i,e. deaminates to form U). TET enzymes mediate this behavior in vivo but I can't find any data on spontaneous methyl group oxidation or what the kinetics might be like. &lt;a href=&quot;http://www.sciencemag.org/content/336/6083/934&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; relies on the properties of 5-formylcytosine outlined above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could use &lt;a href=&quot;http://www.nature.com/nchem/journal/v6/n5/full/nchem.1893.html&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; to test if that's true. Reduction with sodium borohydride converts 5-formylcytosine back to hydroxymethylcytosine, which reads as methylated under bisulfite sequencing.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-06-12T15:50:17.630" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35175" PostTypeId="1" AcceptedAnswerId="35176" CreationDate="2015-06-12T17:02:43.713" Score="5" ViewCount="178" Body="&lt;p&gt;Can anyone tell me which plant or flower is this. I have found it in Darjeeling,  West Bengal, India. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/61QQ0.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16142" LastEditorUserId="3952" LastEditDate="2015-06-13T15:57:03.607" LastActivityDate="2015-06-13T15:57:03.607" Title="Identify the plant" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35176" PostTypeId="2" ParentId="35175" CreationDate="2015-06-12T18:33:04.073" Score="6" Body="&lt;p&gt;Those are known as Rhododendrons, and I'd ID that one as &lt;em&gt;R. hodgsonii&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-06-12T18:33:04.073" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35177" PostTypeId="1" CreationDate="2015-06-12T18:48:29.947" Score="7" ViewCount="14483" Body="&lt;p&gt;From my understanding, humid weather means that the air has a lot of water in it. Therefore, someone who lives in this kind of weather would be hydrating himself just by breathing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does that mean that, to stay hydrated, one needs to drink less water in humid weather than in dry weather?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Of couse, I know that humid weathers are usually hotter, which accelerates dehydration. But in this case, let's assume the temperature is independent of the humidity of the air.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="16192" LastActivityDate="2018-01-27T15:39:39.097" Title="Do we need to drink less water in humid weather than in dry weather?" Tags="&lt;human-biology&gt;&lt;hydration&gt;&lt;dehydration&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35178" PostTypeId="1" CreationDate="2015-06-12T19:22:09.943" Score="4" ViewCount="116" Body="&lt;p&gt;I am working a basic mathematical/computer simulation of an ecosystem, and I need to know the birth rate of each organism in my simulation. However, I could not find any data for how often a small, asexually-reproducing plant, like a fern or dandelion, reproduces. Does anybody know either a) the time to reach sexual maturity and the expected offspring of one dandelion or fern OR b) when starting with one plant, the expected living dandelion or fern plants after a year?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, if I plant one dandelion or fern in a closed system (providing it with requisite water, food, sunlight, etc), how many can I expect to find at the end of the year?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These values don't have to be exact, I can adjust them later, but I need something to use as a baseline.&lt;/p&gt;&#xA;" OwnerUserId="16193" LastActivityDate="2018-11-15T09:19:40.730" Title="Expected reproduction rate of a dandelion and/or fern" Tags="&lt;botany&gt;&lt;reproduction&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35179" PostTypeId="1" AcceptedAnswerId="35199" CreationDate="2015-06-12T19:40:43.947" Score="2" ViewCount="977" Body="&lt;p&gt;I've a Begonia species. Somehow it started to grow new leaves on top and right in the center of an existing leaf which you can see in the center of the image. Why is it doing this? Apparently it is not a disease because the Begonia itself is growing fast. Will the new leaves eventually become a new Begonia which can survive on its own?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oxUem.jpg&quot; alt=&quot;A Begonia growing leaves on top of a leaf&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16013" LastEditorUserId="16013" LastEditDate="2015-06-13T00:27:37.093" LastActivityDate="2019-07-16T03:25:05.907" Title="Leaves growing on a leaf of a Begonia" Tags="&lt;botany&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35180" PostTypeId="1" AcceptedAnswerId="35182" CreationDate="2015-06-12T19:58:10.720" Score="14" ViewCount="43234" Body="&lt;p&gt;The heart is a vital organ in our body, as it drives blood circulation. I was wondering if a heart keeps beating if it is separated from the body? If yes, then why?&lt;/p&gt;&#xA;" OwnerUserId="15862" LastEditorUserId="16866" LastEditDate="2017-04-13T03:52:22.540" LastActivityDate="2017-04-13T03:52:22.540" Title="Will the heart keep beating if it's separated from the body?" Tags="&lt;human-biology&gt;&lt;cardiology&gt;&lt;human-physiology&gt;&lt;circulatory-system&gt;" AnswerCount="4" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35181" PostTypeId="2" ParentId="35180" CreationDate="2015-06-12T20:00:45.030" Score="10" Body="&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/store/10.1113/jphysiol.2004.060731/asset/jphysiol.2004.060731.pdf?v=1&amp;amp;t=iauo2601&amp;amp;s=4ebc14d9a457dfba30a37e922efbb5b577b0e188&quot; rel=&quot;noreferrer&quot;&gt;Sydney Ringer showed in 1882&lt;/a&gt; that when the heart, when separated from the body and immersed in lactated Ringer's solution, or even isotonic saline solution, will beat because it has its own pacemaker systems at the level of the Sinoatrial node and Atrioventricular node. This activity will continue until there is insufficient ATP to support it energetically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Ringer sources &lt;a href=&quot;http://www.blackwellpublishing.com/products/journals/suppmat/tjp/tjp161/tjp161appendixA1.pdf&quot; rel=&quot;noreferrer&quot;&gt;link&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Miller, David J. &quot;Sydney Ringer; physiological saline, calcium and the contraction of the heart.&quot; The Journal of physiology 555.3 (2004): 585-587.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-06-14T12:02:10.503" LastActivityDate="2015-06-14T12:02:10.503" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="35182" PostTypeId="2" ParentId="35180" CreationDate="2015-06-12T20:02:22.993" Score="22" Body="&lt;p&gt;&lt;strong&gt;Short version&lt;/strong&gt;&#xA;The heart  has the ability to beat independently of the brain as long as it has oxygen. The heart will eventually stop beating as all bodily systems begin to stop working shortly after brain death. Remember the heart can beat, but your diaphragm and lungs wont. hence the cardiac muscles undergo asphyxiation and die off. However, immediately after death, there is enough oxygenated blood in the body to keep thing moving for a while&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Long version&lt;/strong&gt;&#xA;There is a simple explanation why.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you know every muscle in the body has to receive stimuli from the neuromuscular junctions (and subsequently the nervous system) in order to contract. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heart is a bit different in that it is not regulated by the brain, but the regulatory mechanisms lie within the heart itself. The heart conductive system contains a special group of cells called the pace maker cells (SA node) that fire at regular intervals and cause the heart to beat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KIWFf.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Each heart beat is triggered by an electrical pacemaker - a group of cells in the heart that have the ability to generate electrical activity. They cause electrical impulses to spread over the heart and make it contract.&#xA;  The largest natural pacemaker of the heart is called the sinoatrial or SA node and is found in the right atrium. From it, specialised groups of cells that carry the electrical charge lead off to the rest of the heart.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(Taken from &lt;a href=&quot;http://www.netdoctor.co.uk/hearthealth/howtheheartworks.htm&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The brain regulates the rate of the heart beat sure, but it does not send the signals that cause the heart to beat in itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In short, even after disconnection, the SA node still sends the impulse down the AV node and purkinje fibres that spread out across the cardiac musculature and cause them to contract, causing the heart to beat. This will continue for a while till they run out of energy and stop.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can read more about it here:&lt;a href=&quot;https://en.wikipedia.org/wiki/Cardiac_pacemaker&quot; rel=&quot;noreferrer&quot;&gt;Wiki&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-06-13T17:54:57.357" LastActivityDate="2015-06-13T17:54:57.357" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="35183" PostTypeId="1" AcceptedAnswerId="41154" CreationDate="2015-06-12T23:15:04.780" Score="2" ViewCount="1303" Body="&lt;p&gt;I am just starting to learn to use bioinformatics tools.  My university has a limited and expensive bioinformatics team, so I'm mostly on my own except for big questions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am planning to use GATK to run 58 cancer control/normal pairs of Exome sequencing data (Illumina) from FASTQ or BAM file format, through the pipeline, with an output of a VCF &amp;amp; MAF format for analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The current GATK pipeline is used for disease but not cancer, so I was wondering if anyone knew if there should be changes made for cancer.  Here's the current pipeline starting with BAM files:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;(Non-GATK) Picard Mark Duplicates or Samtools roundup&lt;/li&gt;&#xA;&lt;li&gt;Indel Realignment (Realigner TargetCreator + Indel Realigner)&lt;/li&gt;&#xA;&lt;li&gt;Base Quality Score Reacalibration (Base Recalibrator + PrintReads)&lt;/li&gt;&#xA;&lt;li&gt;HaplotypeCaller&lt;/li&gt;&#xA;&lt;li&gt;VQSR (VariantRecalibrator and ApplyRecalibrator in SNP and INDEL mode)&lt;/li&gt;&#xA;&lt;li&gt;Annotation using Oncotator (?)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I'd like some verification that this pipeline will output what I need to run my samples on MuTect, MutSig, or some other analysis program.  I appreciate any advice.&lt;/p&gt;&#xA;" OwnerUserId="16196" LastActivityDate="2015-12-02T01:18:56.597" Title="GATK workflow for Cancer" Tags="&lt;bioinformatics&gt;&lt;cancer&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35184" PostTypeId="2" ParentId="30710" CreationDate="2015-06-12T23:24:12.207" Score="6" Body="&lt;p&gt;Genes that were once functional but no longer are are called pseudogenes (as Corvus pointed out in the comments).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many genes that are similar today (homologs) are hypothesized to have come from duplication events in the past.  In most cases, these duplicates diverge.  The divergence can happen in several ways:&#xA;1) one retains the original function while the other obtains a novel function&#xA;2) a dosage response occurs where both (keeping the original function) become necessary for that function&#xA;3) one retains its function while the other loses all functionality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This third group are the pseudogenes.  This isn't the only way pseudogenes come to be, but it is probably the most well-characterized.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several resources for lists of these.  I'll just point you in that direction.  I assume you are interested in a particular group (i.e. genes important in development or patterning), so that you can dig more deeply into:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://seqanswers.com/forums/showthread.php?t=32054&quot;&gt;http://seqanswers.com/forums/showthread.php?t=32054&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.genomebiology.com/2012/13/9/r51&quot;&gt;http://www.genomebiology.com/2012/13/9/r51&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="16196" LastActivityDate="2015-06-12T23:24:12.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35185" PostTypeId="1" AcceptedAnswerId="35189" CreationDate="2015-06-13T02:25:43.550" Score="2" ViewCount="705" Body="&lt;p&gt;Some years ago, in a 1000~ level biology course we learned that the DNA essentially encodes formulas for creating proteins from amino acids. While the human body can synthesize many many amino acids, some we are unable to synthesize and we dub these as &lt;em&gt;essential amino acids&lt;/em&gt; because we must obtain them from our diet. However, surely something must be capable of synthesizing the amino acids, otherwise they would not make it up the food chain to us, which opens the door to the possibility that animals may have varying capabilities in regards to amino acid synthesis. Presumably, this is why cats have to obtain a high protein diet, as they have high need for protein but a poor ability to synthesize them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, in doing basic research into nutrition to plan a regular workout schedule there is some need to distinguish protein sources as not all protein sources are considered to be &lt;em&gt;complete proteins&lt;/em&gt; because they do not provide all amino acids, or otherwise do not provide them in the right balance.  Particularly, many fruits and vegetables tend to be poor sources of protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For plants which are incomplete protein sources, they would seem to lack the ability to synthesize some amino acids. They also would not be able to obtain these through diet, as they're plants. Consequently, does this mean that some plants may not encode for a specific amino acid throughout their entire DNA?&lt;/p&gt;&#xA;" OwnerUserId="16199" LastActivityDate="2015-06-14T12:58:15.933" Title="Consequence of Plants as Incomplete Protein Source" Tags="&lt;dna&gt;&lt;proteins&gt;&lt;nutrition&gt;&lt;amino-acids&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35186" PostTypeId="2" ParentId="35180" CreationDate="2015-06-13T02:53:13.123" Score="4" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I was wondering if a heart keeps beating if it is separated from the body?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes, it does. Here's a video showing it (&lt;strong&gt;don't click if you're squeamish!&lt;/strong&gt;): &lt;a href=&quot;https://www.youtube.com/watch?v=NEuSCPifKhA&quot; rel=&quot;nofollow&quot;&gt;https://www.youtube.com/watch?v=NEuSCPifKhA&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's a classical physiology experiment to remove a heart and keep it beating for some time in a jar with liquid solution. In fact, acetylcholine, the first neurotransmitter to be discovered, was detected via &lt;a href=&quot;https://faculty.washington.edu/chudler/chnt1.html&quot; rel=&quot;nofollow&quot;&gt;an experiment involving disembodied, still-beating frog hearts&lt;/a&gt;. As a result, Otto Loewi (who conducted the experiment) &lt;a href=&quot;https://en.wikipedia.org/wiki/Acetylcholine#History&quot; rel=&quot;nofollow&quot;&gt;received the Nobel prize&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course it won't go on forever, as the heart eventually runs out of nutrients and air (without access to lungs). There are also other problems. Taking steps such as supplying oxygenated blood, putting the heart in an isotonic solution, ensuring stable temperature, adding adrenaline (which stimulates the heart) can extend the duration of beating.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If yes, then why?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why not? Tissue doesn't die the moment it's removed from the body (it's not like individual cells can telepathically tell they've been cut off, they have no way of knowing). It lives for some time before nutrients are exhausted, blood in capillaries drains off, oxygen is depleted, temperature falls, desiccation occurs, and cells finally die. Note how when an accident severs body parts, they can often be surgically reattached and function normally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most tissues don't seem to be doing much when you sever them. For instance, a severed hand won't make any movements (actually severed animal limbs can often keep on twitching) but that is because no signal is coming from the brain. If you could emulate the signal, you could get it to move before necrosis occurs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The heart has a central cluster of neurons, who's function is to generated a regular signal which causes the heart to beat. Because of this, the heart muscle continues to receive a signal even if cut out. The pacemaker cells don't keep perfect rhythm (and more over heart rate is a complicated matter), so in a normal human the brain fine-tunes the rate of beating through hormones and the vagus nerve. If you cut off the vagus connection, the beating won't be as ragular or as rapid as inside the body.&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2015-06-13T02:53:13.123" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35188" PostTypeId="1" AcceptedAnswerId="35195" CreationDate="2015-06-13T09:52:06.737" Score="2" ViewCount="411" Body="&lt;p&gt;I am trying to figure out how to find the number of child terms associated with a specific Gene Ontology (GO) term using &lt;a href=&quot;http://www.ebi.ac.uk/QuickGO/&quot; rel=&quot;nofollow noreferrer&quot;&gt;QuickGO&lt;/a&gt;, without just counting the amount of terms in a list. For example when I want to find the number of child terms associated with the GO term '&lt;a href=&quot;http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0007507#term=info&amp;amp;info=4&quot; rel=&quot;nofollow noreferrer&quot;&gt;heart development&lt;/a&gt;'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could just click on the tab 'Child Terms' and count, but what if it would be a very long list, how can I find the correct amount? &lt;img src=&quot;https://i.stack.imgur.com/4voIs.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume there is some way to do this by going to Protein Annotation and applying a filter, but I do not know how to do this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PzQPZ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help?&lt;/p&gt;&#xA;" OwnerUserId="15136" LastEditorUserId="1306" LastEditDate="2015-06-13T15:41:02.857" LastActivityDate="2015-06-13T15:53:47.193" Title="How do I find the number of child terms associated with a specific GO term?" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35189" PostTypeId="2" ParentId="35185" CreationDate="2015-06-13T11:19:52.713" Score="4" Body="&lt;p&gt;With a few exceptions among some bacteria, all species on the planet make protein from the same 21 amino acids, and the relative abundances of amino acids is very similar in proteins from plants, animals, fungi and even prokaryotes. See for example &lt;a href=&quot;http://www.worldscientific.com/doi/abs/10.1142/s0219720006002016&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt; (available as &lt;a href=&quot;http://www.researchgate.net/profile/Alexei_Finkelstein/publication/6964785_Trend_of_amino_acid_composition_of_proteins_of_different_taxa/links/02bfe5113d405e8704000000.pdf&quot; rel=&quot;nofollow&quot;&gt;PDF here&lt;/a&gt;). So protein from pretty much any food provides the same amino acids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea that plant proteins are &quot;incomplete&quot; and lack some amino acids seems to be a myth: see for example &lt;a href=&quot;http://circ.ahajournals.org/content/105/25/e197.full&quot; rel=&quot;nofollow&quot;&gt;this correspondence&lt;/a&gt; in the American Heart Association's journal Circulation. Plants generally contain less protein than meats per weight, but there is nothing wrong with the protein they contain. Most people in the world obtain the majority of their protein from plants. There are probably some specific parts of some plants that are not nutritionally optimal --- if you for example lived &lt;em&gt;exclusively&lt;/em&gt; on peanuts for a year, you might experience some problems ... But any commonsense, varied plant diet will provide all amino acids. A detailed report (and some mythbusting) is &lt;a href=&quot;http://ajcn.nutrition.org/content/59/5/1203S.short&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding essential amino acids, as mentioned in comments this is a species-specific concept. Humans and most animals can synthesize about half of the 21 amino acids, while the remaining are essential. There are some species differences --- arginine is essential for cats, for example, but not for adult humans. In contrast, plants can synthesize all amino acids. But their protein composition is similar in the end.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastEditorUserId="1306" LastEditDate="2015-06-14T12:58:15.933" LastActivityDate="2015-06-14T12:58:15.933" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35190" PostTypeId="6" CreationDate="2015-06-13T12:12:42.030" Score="0" Body="&lt;p&gt;I've been a moderator for more than three years on this site, and for more than four years on Skeptics. I know the SE network and software pretty well, and I'm very active on the main Stack Exchange Meta. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My moderation style focuses on catching problems early, and on avoiding escalating minor issues. Resolving issues quietly, if possible, without drawing attention is important, as is stopping discussions in comments that are getting a bit too heated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I often let the community deal with issues like closing questions, especially if the issue is a bit more fuzzy and not clear-cut. But we moderators have binding votes for a reason and I don't hesitate to use them in clear cases. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The site is working well in my opinion, but there's still a lot to do, especially with regards to defining the borders of our scope. But this is something moderators don't do alone, but discuss together with the community on meta.&lt;/p&gt;&#xA;" OwnerUserId="6" LastEditorUserId="6" LastEditDate="2015-06-13T12:12:42.030" LastActivityDate="2015-06-13T12:12:42.030" CommentCount="1" CommunityOwnedDate="2015-06-13T12:12:42.030" ContentLicense="CC BY-SA 3.0" />
  <row Id="35191" PostTypeId="1" AcceptedAnswerId="35192" CreationDate="2015-06-13T14:11:54.633" Score="18" ViewCount="29862" Body="&lt;p&gt;Trees use carbon dioxide and produce oxygen in the presence of sunlight. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But is there any other source? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If yes, are trees the most important source of oxygen, or is there any other source which produce more than trees do?&lt;/p&gt;&#xA;" OwnerUserId="15862" LastEditorUserId="6440" LastEditDate="2015-06-14T04:20:59.523" LastActivityDate="2016-07-15T19:39:16.007" Title="Are trees the only source of large amounts of oxygen?" Tags="&lt;photosynthesis&gt;&lt;environment&gt;" AnswerCount="4" CommentCount="6" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35192" PostTypeId="2" ParentId="35191" CreationDate="2015-06-13T14:35:17.813" Score="39" Body="&lt;p&gt;&lt;a href=&quot;http://(**71%25**)&quot;&gt;71% of the earth's surface is taken up by water&lt;/a&gt;. Not surprisingly therefore, the seas are an important source of oxygen. &lt;a href=&quot;http://news.nationalgeographic.com/news/2004/06/0607_040607_phytoplankton.html&quot;&gt;National Geographic&lt;/a&gt; claims that photosynthesis by &lt;strong&gt;&lt;a href=&quot;http://earthobservatory.nasa.gov/Features/Phytoplankton/&quot;&gt;phytoplankton&lt;/a&gt;&lt;/strong&gt; (mostly single-celled &lt;a href=&quot;http://en.wikipedia.org/wiki/Phototroph&quot;&gt;phototrophs&lt;/a&gt;, such as cyanobacteria, green algae and diatoms) account for &lt;strong&gt;half of the earth's oxygen production&lt;/strong&gt;. The other half, they claim, is produced on land by trees, shrubs, grasses, and other plants.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.ecology.com/about-us/&quot;&gt;Ecology Global Network&lt;/a&gt; takes it a step further and claims that &lt;em&gt;all marine plants&lt;/em&gt; (including phytoplankton) together produce &lt;a href=&quot;http://www.ecology.com/2011/09/12/important-organism/&quot;&gt;70 to 80 percent of the oxygen in the atmosphere&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Based on these reports, hence, marine phototrophs account for 50 - 80% of the earth's oxygen production. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;With regard to terrestrial oxygen production, &lt;a href=&quot;http://earthobservatory.nasa.gov/Features/ForestCarbon/&quot;&gt;NASA&lt;/a&gt; reports that 30% of the land is covered by trees, and as much as 45 percent of the carbon stored on land is tied up in forests. So on land, trees are definitely large contributors to oxygen production.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-14T11:24:47.087" LastActivityDate="2015-06-14T11:24:47.087" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35193" PostTypeId="2" ParentId="35191" CreationDate="2015-06-13T14:38:32.587" Score="9" Body="&lt;p&gt;I am not sure which class of organisms have the &lt;strong&gt;highest&lt;/strong&gt; contribution in oxygen production but &lt;a href=&quot;https://en.wikipedia.org/wiki/Diatom&quot;&gt;diatoms&lt;/a&gt; do have a significant contribution. The introduction in &lt;a href=&quot;http://www.pnas.org/content/108/10/3830.full.pdf&quot;&gt;this&lt;/a&gt; paper says that diatoms account for 40% of marine photosynthesis which according to &lt;a href=&quot;http://www.genoscope.cns.fr/spip/Phaeodactylum-tricornutum,463.html&quot;&gt;this&lt;/a&gt; site is &quot;1/4 of the oxygen we breathe.&quot;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-13T18:42:19.943" LastActivityDate="2015-06-13T18:42:19.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35194" PostTypeId="2" ParentId="35191" CreationDate="2015-06-13T14:45:07.007" Score="7" Body="&lt;p&gt;Trees are definitely not the only source of oxygen. First, all green plants do photosynthesis, not only trees. Moreover, about half of all photosynthesis on earth is done by microorganisms in the oceans known as &lt;a href=&quot;https://en.wikipedia.org/wiki/Phytoplankton&quot;&gt;phytoplankton&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-06-13T14:45:07.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35195" PostTypeId="2" ParentId="35188" CreationDate="2015-06-13T15:24:19.150" Score="5" Body="&lt;p&gt;I don't think it's possible to do this via QuickGO. You can, however, do it from &lt;a href=&quot;http://geneontology.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;GO's website&lt;/a&gt;, using their &lt;a href=&quot;http://amigo.geneontology.org/goose&quot; rel=&quot;nofollow noreferrer&quot;&gt;GOOSE tool&lt;/a&gt;. This offers an interface to the GO SQL database and lets you run queries. It also offers example searches, one of which (&quot;Find descendants of the node 'nucleus'&quot;) can easily be modified to return what you are asking for:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;SELECT COUNT(*)&#xA;FROM&#xA; term&#xA; INNER JOIN graph_path ON (term.id=graph_path.term1_id)&#xA; INNER JOIN term AS descendant ON (descendant.id=graph_path.term2_id)&#xA;WHERE term.name='heart development' AND distance = 1 ;&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;In the query above, I modified the example and changed 'nucleus' to 'heart development' (GO:0007507) and changed &lt;code&gt;distance &amp;lt;&amp;gt; 0&lt;/code&gt; to &lt;code&gt;distance = 1&lt;/code&gt; to make it list only direct descendants. Finally, I also changed &lt;code&gt;SELECT DISTINCT descendant.acc, descendant.name, descendant.term_type&lt;/code&gt; to simply &lt;code&gt;SELECT COUNT(*)&lt;/code&gt; since all we are interested in is the number of descendants. If you also want their names, leave the &lt;code&gt;SELECT&lt;/code&gt; line as is. That will show both the list of names &lt;em&gt;and&lt;/em&gt; the total in the output. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The modified query shows us that this term has 30 descendants:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rtgxM.png&quot; alt=&quot;GO SQL query output&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1306" LastEditorUserId="1306" LastEditDate="2015-06-13T15:53:47.193" LastActivityDate="2015-06-13T15:53:47.193" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35196" PostTypeId="2" ParentId="35177" CreationDate="2015-06-13T15:56:02.540" Score="5" Body="&lt;p&gt;You don't get hydrated by breathing moist air. That may at best hydrate your respiratory tract. You should drink more water in dry weather because the body gets dehydrated more. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humid weather is not hotter, it just feels more uncomfortable. But dry heat is actually more harmful, because it dehydrates you (not in the sense of extreme heat).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="9943" LastEditDate="2015-10-29T01:42:57.910" LastActivityDate="2015-10-29T01:42:57.910" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="35197" PostTypeId="2" ParentId="35180" CreationDate="2015-06-13T16:50:09.160" Score="2" Body="&lt;p&gt;In order to clear some issues with the question and answers I add this one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question itself was &quot;will a heart keeps beating if it is separated from the body?&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer to this question as it was asked: &lt;strong&gt;No, the heart removed from the body &quot;as is&quot; will stop beating almost immediately&lt;/strong&gt;. Denervation and stopping oxygen and electrolytes supply will cause short fibrillation and eventual asystole.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if we convert the question to &quot;What are the conditions that will allow the denervated heart to keep beating?&quot;, the answer will be different:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you supply it with solution of electrolytes it will continue beating for some time. If one want extend that time - other chemical compounds should be added as well as the temperature of the organ should be artificially lowered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.madsci.org/posts/archives/2001-03/986058306.Gb.r.html&quot; rel=&quot;nofollow&quot;&gt;nice link&lt;/a&gt; that says exactly the same as my answer (provided by @RoverEye )&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-06-13T17:58:40.250" LastActivityDate="2015-06-13T17:58:40.250" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="35198" PostTypeId="2" ParentId="20224" CreationDate="2015-06-13T17:59:17.913" Score="-2" Body="&lt;p&gt;Hydrogen carbonate is an indicator commonly used for testing photosynthesis. It shows changes in carbon dioxide concentration in the air. You would set up the plant in a sealed system next to a tray of hydrogen carbonate indicator solution and observe the colour change.&lt;/p&gt;&#xA;" OwnerUserId="16205" LastActivityDate="2015-06-13T17:59:17.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35199" PostTypeId="2" ParentId="35179" CreationDate="2015-06-13T21:04:58.840" Score="3" Body="&lt;p&gt;The phenomenon you are observing is probably Adventitious buds. The plantlets can develop on intact leaves or on injured one. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Back to Begonia, this phenomenon usually occurs on injured leaves, so, probably, the plant was injured during movement/by insect or by other means and because of this started to create plantlets. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Wi7iH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-06-13T21:04:58.840" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35200" PostTypeId="2" ParentId="35191" CreationDate="2015-06-13T22:52:09.070" Score="2" Body="&lt;p&gt;I thought it was fairly well understood that trees make NO net contribution to the oxygen supply.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a tree (or any plant) grows, it locks carbon within itself and releases the O from the CO2 into the atmosphere. When that tree dies, it decays by being consumed. All of the C gets recombined with O2 during the decay. Therefore, a quantity of oxygen is lost from the atmosphere and this loss is, by definition, exactly equal the the oxygen produced when it grew.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The best we can say is that trees are constantly &lt;em&gt;locking up&lt;/em&gt; a huge quantity of carbon (and therefore allowing an equally huge amount of free oxygen to exist in the atmosphere) but no net gain/loss ever takes place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, this still doesn't excuse destroying rain forests because that definitely &lt;em&gt;does&lt;/em&gt; release CO2 and absorb oxygen in the process.&lt;/p&gt;&#xA;" OwnerUserId="14750" LastActivityDate="2015-06-13T22:52:09.070" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35201" PostTypeId="1" AcceptedAnswerId="35413" CreationDate="2015-06-14T06:35:02.277" Score="9" ViewCount="483" Body="&lt;p&gt;So in theory, insulin hormone is the one that tells the body &quot;eat more. don't burn body fat&quot;. Alongside with glucose blood level regulation and turning excessive glucose into liver (which later goes into muscles as glycogen or into fat cells). Fats are the only thing that do not provoke insulin secretion. 0 glycemic index.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in theory, if I eat 2 or 3 times more worth the energy I spend during the day, I'll never store body fat because of 0 glycemic index?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or will I still gain because such huge fat intake will make liver into making glucose from fats &amp;amp; proteins?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Surely u'll never find a sustainable product to eat that is 100% fat, but just a few examples are butter, lard, heavy cream. This is just a theoretical question, where the proteins/carbs intake is so low that it is not count.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could you please clarify it since I got lost.&lt;/p&gt;&#xA;" OwnerUserId="14503" LastEditorUserId="15051" LastEditDate="2015-06-14T11:27:17.330" LastActivityDate="2015-06-21T19:05:26.090" Title="If eating 100% fat 2 times more worth the energy I spend during the day, will I store body fat?" Tags="&lt;liver&gt;&lt;fat-metabolism&gt;&lt;insulin&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35202" PostTypeId="1" AcceptedAnswerId="35206" CreationDate="2015-06-14T06:37:47.920" Score="3" ViewCount="119" Body="&lt;p&gt;I was wondering why is it that &quot;AAUAAA&quot; is a strong Polyadenylation signal whereas the rest of the polyadenylation signals show reduced cleavage and polyadenylation efficiency?&lt;/p&gt;&#xA;" OwnerUserId="15756" LastEditorUserId="8105" LastEditDate="2015-06-14T14:01:42.797" LastActivityDate="2015-06-14T14:39:25.473" Title="What makes a strong polyadenylation signal a strong signal?" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35205" PostTypeId="1" CreationDate="2015-06-14T14:03:25.740" Score="6" ViewCount="184" Body="&lt;p&gt;Micronuclei are cellular structures that are formed as a by-product of, usually, defective mitosis. The piece of chromosome in a micronucleus may, or may not contain a centromere and the DNA is wrapped in a double lipid membrane. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried to find information, but I failed to find out what the fate of these structures is within the cell once formed? And is the DNA within it lost for the cell?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="9943" LastEditDate="2015-06-15T00:00:43.027" LastActivityDate="2015-09-05T16:53:29.687" Title="What is the fate of micronucleus DNA?" Tags="&lt;cell-biology&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35206" PostTypeId="2" ParentId="35202" CreationDate="2015-06-14T14:33:08.010" Score="3" Body="&lt;p&gt;&lt;em&gt;Just expanding on aandreev's comment.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Polyadenylation is initiated by binding of CPSF (Cleavage and Polyadenylation specificity factor) after its binding to the &lt;code&gt;AAUAAA&lt;/code&gt; motif.&lt;br&gt;&#xA;From the introduction of &lt;a href=&quot;http://rnajournal.cshlp.org/content/7/6/920.full.pdf&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;CPSF (cleavage and polyadenylation specificityfactor) binds to the&#xA;  AAUAAA hexamer via its 160-kDa subunit and possibly its 30-kDa subunit&#xA;  (Keller et al., 1991; Murthy &amp;amp; Manley,1992; Jenny et al.,1994;&#xA;  Barabino et al.,1997). CstF (cleavage  stimulation  factor) binds to&#xA;  the U- or G/U-rich element downstream of the cleavage site, and&#xA;  stabilizes the binding of CPSF to the AAUAAA sequence of the pre-mRNA&#xA;  (reviewed in Colgan &amp;amp; Manley,1997; Wahle &amp;amp; Kuhn,1997).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Any alteration in the CPSF binding site will lead to reduced polyadenylation efficiency. Polyadenylation efficiency also depends on other factors such as &lt;a href=&quot;http://nar.oxfordjournals.org/content/27/2/446.long&quot; rel=&quot;nofollow&quot;&gt;secondary structure&lt;/a&gt; and presence of proximal &lt;a href=&quot;http://www.frontiersin.org/Journal/DownloadFile/1/3450/44311/1/21/fendo-04-00053_pdf&quot; rel=&quot;nofollow&quot;&gt;CstF sites&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-14T14:39:25.473" LastActivityDate="2015-06-14T14:39:25.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35207" PostTypeId="1" CreationDate="2015-06-14T15:08:31.430" Score="3" ViewCount="83" Body="&lt;p&gt;I know that the cristae of the inner membrane can be tubular or vesicular but I would like to know what are the functions of each .&lt;/p&gt;&#xA;" OwnerUserId="10317" LastEditorUserId="10317" LastEditDate="2015-06-14T15:15:11.460" LastActivityDate="2017-01-16T16:43:09.377" Title="Mitochondrial inner membrane" Tags="&lt;cell-biology&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35209" PostTypeId="1" AcceptedAnswerId="35222" CreationDate="2015-06-14T18:27:42.103" Score="3" ViewCount="356" Body="&lt;p&gt;I understand so far that most of the air surrounding us contains mold spores so that given the right environment and a food source they start to grow. I assume this is true for air close to the earth. But how high mold spores are still common?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To clarify: I don't want to grow mold, I want to know how high into the air on earth mold spores are usually common.&lt;/p&gt;&#xA;" OwnerUserId="16082" LastEditorUserId="16082" LastEditDate="2015-06-14T18:44:11.263" LastActivityDate="2015-06-15T01:33:33.937" Title="How high into the air are spores of molds commonly occurring?" Tags="&lt;mycology&gt;&lt;species-distribution&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35210" PostTypeId="2" ParentId="35207" CreationDate="2015-06-14T19:45:28.793" Score="1" Body="&lt;p&gt;There is a reasonable speculation. That is to get more areas where ATP synthases are localized in order to produce ATP. But this doesn't tell why the structure has to be the exactly that shape.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the review Ilan show, the shape seems to be determined by ATP synthase dimerizetion. The shap may be just a consequence of ATP synthase dimerizetion, although it successfully enlarges the area where ATP synthase is localized.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-06-15T06:26:19.020" LastActivityDate="2015-06-15T06:26:19.020" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35211" PostTypeId="1" CreationDate="2015-06-14T20:01:56.763" Score="5" ViewCount="597" Body="&lt;p&gt;Cisplatin (structure below) is a platinum-based chemotherapeutic agent which is very effective in the treatment of some cancers. Its introduction was responsible for improving the cure rate for testicular cancer from 10% to 85% according to the &lt;a href=&quot;https://en.wikipedia.org/wiki/Cisplatin&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia page on cisplatin&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it is not very effective for other types of cancers; interestingly, ovarian cancer does not respond well to it &lt;a href=&quot;http://www.nature.com/onc/journal/v22/n47/full/1206933a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Siddick, 2003)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does someone know why cisplatin is so specific to testicular cancer? I haven't found any sources explaining this. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/44CYx.png&quot; alt=&quot;Cisplatin chemical structure&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14630" LastEditorUserId="9943" LastEditDate="2015-06-15T13:05:13.043" LastActivityDate="2015-06-20T19:13:19.563" Title="Why is cisplatin a very potent antineoplastic for testicular cancer, but not necessarily for other cancers?" Tags="&lt;pharmacology&gt;&lt;cancer&gt;&lt;pharmacodynamics&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35213" PostTypeId="1" CreationDate="2015-06-14T20:39:48.183" Score="1" ViewCount="1967" Body="&lt;p&gt;I am doing an experiment where I have treat the cells with a drug and calculate their counts. I would like to know if is bad to trypsinize the cells in consecutive days i.e. twice within 48 hours. How much time do the cells need to attach again on the surface of the flask? I want to know if I can treat them with drug the same day I add trypsin for counting. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks.&lt;/p&gt;&#xA;" OwnerUserId="16214" LastEditorUserId="3340" LastEditDate="2015-06-15T07:28:45.973" LastActivityDate="2015-06-16T10:14:26.460" Title="Trypsin and cell culture" Tags="&lt;cell-biology&gt;&lt;lab-techniques&gt;&lt;cell-culture&gt;&lt;lab-reagents&gt;" AnswerCount="3" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35214" PostTypeId="1" AcceptedAnswerId="35224" CreationDate="2015-06-14T21:42:36.237" Score="6" ViewCount="922" Body="&lt;p&gt;Given the existence of coastal deserts such as in the picture below, I was wondering whether terrestrial plants can survive on sea water alone? If yes, why then do coastal deserts exist, instead of being grown over with belts of such plants along the shores? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If terrestrial plants thriving on sea water do not exist, then why? Especially given that there are marine plants like kelp and sea grass?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Jfdeg.jpg&quot; alt=&quot;coastal desert&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4038" LastEditorUserId="9943" LastEditDate="2015-06-15T05:25:56.473" LastActivityDate="2015-06-15T06:11:31.183" Title="Are there terrestrial plants that thrive on sea water?" Tags="&lt;botany&gt;&lt;salt&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35215" PostTypeId="6" CreationDate="2015-06-14T21:49:11.450" Score="0" Body="&lt;p&gt;Hi All!  If anyone hasn't encountered me yet I'm Rory, a third year medical student from the UK and one of the three pro tempore moderators throughout the beta period of Biology Stack Exchange.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;During this time I have become well versed in using the moderation tools provided by Stack Exchange to help resolve any of the unusual situations that are not taken care of by our excellent group of higher reputation users. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of my main focusses is to try and assist new users who may not be used to how Stack Exchange sites work (rather than wielding the mod-hammer in the first instance).  I very often leave comments when taking moderator-specific actions with the aim of educating new users as I'm sure it can be very disheartening when a well-intentioned post is rapidly downvoted and closed without much explanation.  I feel this is something we could work to improve as a community.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be delighted to continue as a permanent community moderator after this election in order to help Biology keep growing past its graduation.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2015-06-14T21:49:11.450" LastActivityDate="2015-06-14T21:49:11.450" CommentCount="0" CommunityOwnedDate="2015-06-14T21:49:11.450" ContentLicense="CC BY-SA 3.0" />
  <row Id="35218" PostTypeId="2" ParentId="35211" CreationDate="2015-06-15T00:35:13.613" Score="4" Body="&lt;p&gt;From the dedicated &lt;a href=&quot;http://www.cisplatin.org/&quot; rel=&quot;nofollow&quot;&gt;cisplatin website&lt;/a&gt; and &lt;a href=&quot;http://chemwiki.ucdavis.edu/Development_Details/Approaches/ChemCases/Cisplatin%3A_The_Invention_of_an_Anticancer_Drug/Cisplatin_x12._Modes_of_Action_of_Cisplatin&quot; rel=&quot;nofollow&quot;&gt;Drugbank&lt;/a&gt; it appears its use is quite diverse and not confined to testicular cancers. Further, your linked &lt;a href=&quot;http://www.nature.com/onc/journal/v22/n47/full/1206933a.html&quot; rel=&quot;nofollow&quot;&gt;(Siddick, 2003)&lt;/a&gt; paper mentions on the first line of its abstract that cisplatin has &lt;code&gt;clinical activity against a wide variety of solid tumors&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.cisplatin.org/&quot; rel=&quot;nofollow&quot;&gt;Cisplatin.org&lt;/a&gt; mentions that cisplatin finds use as chemotherapy against a range of cancers:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cisplatin is a chemotherapy drug which is used to treat cancers including: &lt;strong&gt;sarcoma, small cell lung cancer, germ cell tumors, lymphoma, and ovarian cancer&lt;/strong&gt;. [I]t can be a valuable part of a combination chemotherapy regimen. Look at the regimens given to patients and you will often see cisplatin as one of the drugs. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Moreover, cisplatin is &lt;em&gt;explicitly used to treat &lt;strong&gt;ovarian cancer&lt;/em&gt;&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Treatment of ovarian cancer&lt;/strong&gt; involves putting the cisplatin into the peritoneal cavity rather than a blood vessel. The type and extent of a cancer determines the exact dose and schedule of administering the drug. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As to your comment that cisplatin has &quot;magical powers&quot; I can say that it does not. The article that your &lt;a href=&quot;https://en.wikipedia.org/wiki/Cisplatin&quot; rel=&quot;nofollow&quot;&gt;linked cisplatin wikipedia&lt;/a&gt; page refers to &lt;a href=&quot;http://jco.ascopubs.org/content/8/11/1777.abstract&quot; rel=&quot;nofollow&quot;&gt;(Einhorn, 1990)&lt;/a&gt; is a review paper that describes the efficacy of  &lt;em&gt;combination therapies&lt;/em&gt; with cisplatin. The high cure rate of 75% was reached when &lt;em&gt;cisplatin&lt;/em&gt; was used in combination with &lt;em&gt;etoposide&lt;/em&gt; plus &lt;em&gt;bleomycin&lt;/em&gt;. The last 10% was theorized to be achievable with 'salvage chemotherapy'. Hence, it is &lt;em&gt;not cisplatin on its own&lt;/em&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, it is common practice to use various chemotherapeutic agents in consort, preferably with differing modes of action to reduce the dose of each and hence lessening the side effects. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://jco.ascopubs.org/content/8/11/1777.abstract&quot; rel=&quot;nofollow&quot;&gt;Einhorn, &lt;em&gt;JCO&lt;/em&gt; (1990); &lt;strong&gt;8&lt;/strong&gt;(11): 1777-81&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.nature.com/onc/journal/v22/n47/full/1206933a.html&quot; rel=&quot;nofollow&quot;&gt;Siddick, &lt;em&gt;Oncogene&lt;/em&gt; (2003); &lt;strong&gt;22&lt;/strong&gt;: 7265–79&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-17T14:00:46.083" LastActivityDate="2015-06-17T14:00:46.083" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35219" PostTypeId="1" AcceptedAnswerId="35221" CreationDate="2015-06-15T00:53:34.643" Score="3" ViewCount="399" Body="&lt;p&gt;I've searched the position and SNP ID of &lt;strong&gt;HLA-B*1502&lt;/strong&gt; variation. However, I couldn't find that where this variant exactly located on genome or HLA-B gene.&lt;/p&gt;&#xA;" OwnerUserId="13292" LastEditorUserId="4101" LastEditDate="2015-06-15T16:59:48.860" LastActivityDate="2015-06-15T16:59:48.860" Title="What is the genomic position of HLA-B*1502 variation?" Tags="&lt;genomics&gt;&lt;hla&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35221" PostTypeId="2" ParentId="35219" CreationDate="2015-06-15T01:25:16.740" Score="7" Body="&lt;p&gt;HLA-B*1502 is not a SNP ID but rather, a name of &lt;a href=&quot;https://en.wikipedia.org/wiki/HLA-B75&quot;&gt;an allele of HLA-B&lt;/a&gt;. This allele is made up of multiple mutations which can be found &lt;a href=&quot;http://www.ebi.ac.uk/cgi-bin/ipd/imgt/hla/get_allele.cgi?B*1502&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="766" LastActivityDate="2015-06-15T01:25:16.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35222" PostTypeId="2" ParentId="35209" CreationDate="2015-06-15T01:33:33.937" Score="4" Body="&lt;p&gt;Air currents can carry bacteria and mold spores into stratospheric altitudes.  Early balloon collections found bacteria and mold in air samples at a &lt;a href=&quot;http://www.citizensinspace.org/2013/11/spores-in-the-stratosphere/&quot; rel=&quot;nofollow&quot;&gt;little above 71 thousand feet altitude&lt;/a&gt;.  There were only a few colonies, but we also know that our bacterial media often do not allow many microorganisms to grow. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;More &lt;a href=&quot;http://gbe.oxfordjournals.org/content/7/5/1216.long&quot; rel=&quot;nofollow&quot;&gt;recent studies&lt;/a&gt; of the atmospheric microbiome have indicated that a wide variety of bacteria and fungi can routinely be found &lt;a href=&quot;http://aem.asm.org/content/75/15/5121.abstract?ijkey=bb308469a8ac45c7b867dbdb3ef6b4c4dd5e58e8&amp;amp;keytype2=tf_ipsecsha&quot; rel=&quot;nofollow&quot;&gt;in the atmosphere thousands of feet up&lt;/a&gt;.  Modern measurements find about 10 million living microbes per cubic meter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sandstorms or jet streams are known to be able to move living bacteria long distances.  Spores are often of about the same size and I see no reason why we will not find that they do the same. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2015-06-15T01:33:33.937" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35223" PostTypeId="2" ParentId="35183" CreationDate="2015-06-15T01:38:27.090" Score="3" Body="&lt;p&gt;This post goes over what &lt;a href=&quot;http://gatkforums.broadinstitute.org/discussion/4462/what-input-files-does-mutect-accept-require&quot; rel=&quot;nofollow&quot;&gt;MuTec requires as input&lt;/a&gt;. mark duplicates and indel realignment will probably have to be done on bam file to use it as input. BQSR is optional and does not change the quality too much. HaplotypeCaller is used for germline not somatic variant calling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have followup bioinformatics questions, you might be able to find answers more quickly on &lt;a href=&quot;https://www.biostars.org/&quot; rel=&quot;nofollow&quot;&gt;biostars&lt;/a&gt; or &lt;a href=&quot;http://gatkforums.broadinstitute.org/&quot; rel=&quot;nofollow&quot;&gt;GATK forums&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="766" LastActivityDate="2015-06-15T01:38:27.090" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35224" PostTypeId="2" ParentId="35214" CreationDate="2015-06-15T05:16:52.143" Score="7" Body="&lt;p&gt;The &lt;a href=&quot;http://www.botgard.ucla.edu/&quot; rel=&quot;nofollow noreferrer&quot;&gt;University of California, LA&lt;/a&gt; mentions some genera and species of salt-loving plants (&lt;strong&gt;&lt;em&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Halophyte&quot; rel=&quot;nofollow noreferrer&quot;&gt;halophytes&lt;/a&gt;&lt;/em&gt;&lt;/strong&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genus Atriplex (Family Chenopodiaceae), saltbush, is found worldwide along saline shorelines. On the surfaces of the leaf are vesiculated &lt;a href=&quot;https://en.wikipedia.org/wiki/Trichome&quot; rel=&quot;nofollow noreferrer&quot;&gt;trichomes&lt;/a&gt; (hairs). Each trichome has a stalk and a balloon-like tip, the bladder cell. The leaves use the bladder cells to excrete salt. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/r17Fn.jpg&quot; alt=&quot;coastal saltbush&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Coastal saltbush. Source: &lt;a href=&quot;http://www.enviroactive.com.au/node/528&quot; rel=&quot;nofollow noreferrer&quot;&gt;Enviro Active Australia&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Excreting &lt;a href=&quot;https://en.wikipedia.org/wiki/Salt_gland&quot; rel=&quot;nofollow noreferrer&quot;&gt;salt glands&lt;/a&gt; occur in numerous unrelated plant groups, including grasses that live in alkali sink and salt pans and in warm temperate to tropical salt marshes (&lt;em&gt;Sporoboleae, Chlorideae, and Aeluroideae&lt;/em&gt; (Family &lt;em&gt;Poaceae&lt;/em&gt;)). These include such well-known tidal saltmarsh plants as the cordgrasses (&lt;em&gt;Spartina alterniflora, S. patens&lt;/em&gt;), alkali grass (&lt;em&gt;Puccinellia phryganodes&lt;/em&gt;), saltgrass (&lt;em&gt;Distichlis spicata&lt;/em&gt;), and shoregrass (&lt;em&gt;Monanthochloe littoralis&lt;/em&gt;). Short, two-celled trichomes have evolved as collecting chambers for salts, from which salts are excreted through tiny pores.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xONLd.jpg&quot; alt=&quot;cordgrass&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Cordgrass in the Chesapeake Bay. Source: &lt;a href=&quot;http://www.chesapeakebay.net/fieldguide/critter/smooth_cordgrass&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chesapeake Bay Program&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Frankenia&lt;/em&gt; (Family &lt;em&gt;Frankeniaceae&lt;/em&gt;) is a genus found both in coastal salt marsh and inland saline habitats. &lt;em&gt;Saltcedar&lt;/em&gt; (Tamarix, Family Tamaricaceae) grows around the world in arid and semiarid regions. All of these taxa have salt glands, i.e., trichomes, in which salts are accumulated and excreted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several common mangroves secrete salts from leaves. So much crystalline salt can occur on the leaf of black mangrove, &lt;em&gt;Avicennia germinans&lt;/em&gt;, that it appears whitish. &lt;em&gt;Aegialitis annulata&lt;/em&gt; is a salt-excreting mangrove of Family &lt;em&gt;Plumbaginaceae&lt;/em&gt;, a group in which other species are salt excreters in salt marsh and oceanside (Limonium and Armeria) or have chalk glands and live in dry, alkaline habitats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hwVkv.jpg&quot; alt=&quot;Black mangrove&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Black Mangrove. Source: &lt;a href=&quot;http://www.plantdex.com/index.php/species-growing-guides/trees-and-shrubs/228-black-mangrove&quot; rel=&quot;nofollow noreferrer&quot;&gt;PlantDex&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Halophytic succulence is demonstrated in many genera of plants that inhabit saline environments, such as the mud flats of coastal salt marsh, but also is commonly observed on the leading edge of vegetation on coastal beaches, i.e., in strand vegetation. Common examples of succulence can be found in Family &lt;em&gt;Chenopodiaceae&lt;/em&gt;: &lt;em&gt;Allenrolfea, Arthrocnemum, Halimione, Nitrophila, Salicornia&#xA;Suaeda&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Succulence (fleshiness) also occurs in other famous and widespread species, such as &lt;em&gt;Batis maritima, Sesuvium portulacastrum, Trianthema portulacastrum&lt;/em&gt;, and many Old World species of &lt;em&gt;Zygophyllum&lt;/em&gt;. True succulents in the ice plant family, &lt;em&gt;Aizoaceae&lt;/em&gt;, are also commonly found in saline habitats: &lt;em&gt;Aizoon and Mesembryanthemum&lt;/em&gt;. By depositing salts in vacuoles, the toxicity is partitioned from the cytoplasm and organelles of the cells. As in &lt;em&gt;Atriplex&lt;/em&gt;, salts are removed from the plant when the leaf of stem segment is shed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PP8iI.jpg&quot; alt=&quot;Trianthema portulacastrum&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Halophytic succulent &lt;em&gt;Trianthema portulacastrum&lt;/em&gt;. Source: &lt;a href=&quot;http://luirig.altervista.org/pics/index4.php?search=Sesuvium+portulacastrum&amp;amp;page=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Altervista&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Among the halophytes, the seagrasses, which are submerged plants of shallow marine meadow, have salt tolerance, because the osmolality of cytoplasm is adjusted to match the osmolality of the seawater, so that desiccation of the plant does not occur. This contrasts the strategies of excluders and succulents, which are primarily salt avoiding mechanisms, attempts to reduce salt concentrations within the cytoplasm of photosynthetic cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to &lt;em&gt;why&lt;/em&gt; some shores may be devoid of plants, it may have to do with extreme temperatures, lack of nutrients, phytotoxic material etc.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-15T06:11:31.183" LastActivityDate="2015-06-15T06:11:31.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35225" PostTypeId="1" CreationDate="2015-06-15T05:41:26.593" Score="3" ViewCount="713" Body="&lt;p&gt;What motivates this question is the apparent discrepancy between the concept of &lt;strong&gt;Work&lt;/strong&gt; in physics and in physiology.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Work&lt;/strong&gt; in physics is defined as the dot product of the force applied to move a certain object by its displacement:&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$W = \vec{F} \cdot \vec{d}$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$\text{ Work  =  (Force) $\cdot$ (Displacement)}$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;Where &lt;span class=&quot;math-container&quot;&gt;$\vec{F}$&lt;/span&gt; is the force vector, and &lt;span class=&quot;math-container&quot;&gt;$\vec{d}$&lt;/span&gt; is the displacement vector.&lt;/p&gt;&#xA;&lt;p&gt;Now if there is some weight lying on a table, it takes no &lt;strong&gt;Work&lt;/strong&gt; at all to maintain its present configuration, since both &lt;span class=&quot;math-container&quot;&gt;$\vec{F}$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$\vec{d}=0$&lt;/span&gt;, As a result &lt;span class=&quot;math-container&quot;&gt;$W=0$&lt;/span&gt;. In other words, this weight-table system does not need to be provided with energy at all, for the table to be able to support the weight, because it takes no energy to support it.&lt;/p&gt;&#xA;&lt;p&gt;What about an identical case but with a human hand supporting a weight(at a constant height) at this time? Although according to the above reasoning one should expect that it does not need any energy to support the weight, this is not what we observe in everyday life, because when I hold the weight, it takes a tremendous amount of effort to support and maintain its position.&lt;/p&gt;&#xA;&lt;p&gt;When I looked up the reason behind this, I found out that it has to do with the fact that the muscles of the arm are &lt;strong&gt;skeletal&lt;/strong&gt; muscles not a &lt;strong&gt;smooth&lt;/strong&gt; one.&lt;/p&gt;&#xA;&lt;p&gt;If the arm were made out of &lt;strong&gt;smooth&lt;/strong&gt; muscles, then it would take no effort or energy at all to support any weight at a fixed height.On the other hand, the muscle fibers that contract to support the weight in &lt;strong&gt;Skeletal&lt;/strong&gt; muscles has to be continuously provided with energy to be able to support it, and hence although no mechanical work is applied on the weight so &lt;span class=&quot;math-container&quot;&gt;$W=0$&lt;/span&gt;, nevertheless energy is wasted in the form of heat in this process, and hence we get tired after holding an object for some time.&lt;/p&gt;&#xA;&lt;p&gt;So what is the mechanism by which &lt;strong&gt;Skeletal&lt;/strong&gt; muscles support certain weight? Why it needs continuous supply of energy while holding an object? How is this energy supplied( my guess is:some component of a cell breaking down molecules so as to transfer chemical energy to mechanical contraction of muscle fibers)?And how it differs from &lt;strong&gt;smooth&lt;/strong&gt; muscles?&lt;/p&gt;&#xA;" OwnerUserId="16220" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-17T13:41:33.810" Title="Why a continuous supply of energy is needed to support a weight?" Tags="&lt;muscles&gt;&lt;energy&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35226" PostTypeId="2" ParentId="35225" CreationDate="2015-06-15T07:15:34.780" Score="1" Body="&lt;p&gt;You should note that even in pure mechanical examples, the energy consumed may not be equal to work done because some energy is also used up in countering the frictional force. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your example you consider an object kept on a wooden table and in this case the weight is balanced by the reaction force by the table. You have not considered the material properties of the table. The reaction force would be equal to weight only if the weight does not cause any distortion to the object that it is resting on. When distortion happens; for e.g. the if wooden plank bends, the resting object comes closer to ground with a reduction in its potential energy. Now the weight is balanced by the reaction force which is basically the force exerted on the plank to get back to its original position (analogous to the spring; $F=-kx$). Even in this case the material property of the wood is, more or less, invariant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Getting back to biology. Muscles consume energy in order to maintain their material properties, even if they do not perform work. Muscles can be thought of as dynamic materials because their material properties can change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you are holding a dumbbell in your hand with your arm poised at an angle then your biceps need energy to keep maintaining that tension (a temporary material property). The energy is supplied in the form of &lt;a href=&quot;https://en.wikipedia.org/?title=Adenosine_triphosphate&quot; rel=&quot;nofollow&quot;&gt;ATP&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I won't discuss the case of smooth muscles. You should read more about what they exactly do.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-15T08:16:46.647" LastActivityDate="2015-06-15T08:16:46.647" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35227" PostTypeId="2" ParentId="35213" CreationDate="2015-06-15T07:41:54.427" Score="1" Body="&lt;p&gt;It is not advisable to trypsinize the cells too often when you have to maintain them. However, in your case the situation is different. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Time required to attach depends on cell type. In any case while performing an experiment, your cells should not be already under stress. Therefore you should seed the flasks/culture plates with a smaller concentration of cells such that they reach around 60% confluence in 24 hours. 24 hours is generally considered to be enough for cells to recover from stress due to trypsinization. (You can have a look at &lt;a href=&quot;https://biology.stackexchange.com/a/13724/3340&quot;&gt;this&lt;/a&gt; post for doubling times of some cell lines). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After doing the treatment you can count cells whenever you think it is fine; this actually depends on your experiment and you can treat the cells for the time that suits the drug's pharmacokinetcs. Trypsinizing is fine now because you won't be using these cells again. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there are methods to calculate cell numbers without trypsinizing. Assuming that your flask is homogeneous, you can choose a section of it and calculate cell numbers manually using microscope. You may also use software like ImageJ to make the task easier. GFP expressing cells will also make the task easier. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-06-15T20:47:10.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35228" PostTypeId="2" ParentId="35213" CreationDate="2015-06-15T07:50:31.240" Score="2" Body="&lt;p&gt;It would be stressful for cells to be trypsinized 24 hours after seeding. After cells are plated, there is a lag time to start growing. Perhaps, during the lag time, physiological state of cells is stabilized. They have to express proteins digested by trypsin and display on the surface etc. Then you could disturb the state again by trypsinizing cells again if you replate cells after 24 hours. &#xA;I would not deny some cells are not affected by trypsin much, but you should be carful. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;if I can treat them with drug the same day I add trypsin for counting.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It is not preferable, but in some cases, such a way is taken actually. If you could, you might want to give us more information about which cells and drugs you are going to use.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you trypsinize cells to count and do not replate them, you do not need to worry about the cell condition, as WYSIWYG says.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-06-15T21:04:09.503" LastActivityDate="2015-06-15T21:04:09.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35230" PostTypeId="1" AcceptedAnswerId="35231" CreationDate="2015-06-15T09:32:26.990" Score="0" ViewCount="4053" Body="&lt;p&gt;I would like to calculate the half-life of a biological drug.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This biological drug is said to have a biological half-life of:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;3.33 days when a patient is receiving a dose of 0.04 mg/kg of body weight,&#xA;13.4 days when the dose is 0.2 mg/kg&#xA;and 14.9 when the dose is 1 mg/kg&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;How could I extrapolate this information to get biological half-life estimate for 2 mg/kg of body weight?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could I also graph this? for example in R?&lt;/p&gt;&#xA;" OwnerUserId="15256" LastActivityDate="2015-06-15T12:58:23.153" Title="How to calculate biological half life of a drug that is dose dependent?" Tags="&lt;pharmacokinetics&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35231" PostTypeId="2" ParentId="35230" CreationDate="2015-06-15T09:50:07.827" Score="3" Body="&lt;p&gt;I plotted your data using MATLAB and it looks like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/PIxYJ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most degradation or clearance processes happen via first order kinetics. However when the clearance/degradation machinery gets saturated then degradation proceeds via a zeroth order kinetics i.e. it becomes independent of the concentration of the drug. The half life in first order reactions is independent of the initial state. Only in the case of the zeroth order reactions, the half life is directly proportional to initial state (See &lt;a href=&quot;http://chemwiki.ucdavis.edu/Physical_Chemistry/Kinetics/Reaction_Rates/Zero-Order_Reactions&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;). In this graph there is a huge gap in half life, between the first and the second points. We need more data points to say anything conclusively about this observation. However, I am assuming that the clearance reaction is already in the zeroth order kinetics as half life increases with concentration (though at different rates). For a rough calculation let us consider second point onwards. By calculating the slope between second and third points you can obtain the half life corresponding to dosage of 2mg/kg.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$Slope=\frac{t_3 -t_2}{x_3-x_2}\\ t_4=x_2+slope\times2=17.15\ days$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There can be other complicated explanations too, such as the drug inhibiting its own clearance etc. But for assuming such models we would require more information.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-15T12:58:23.153" LastActivityDate="2015-06-15T12:58:23.153" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35232" PostTypeId="1" CreationDate="2015-06-15T11:27:57.013" Score="14" ViewCount="3057" Body="&lt;p&gt;We eat food for getting energy to our body parts, and we excrete the wastes through urine, feces, and perspiration. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why has nature combined the urinary tract with the genital system (urogenital system) in humans?&lt;/strong&gt; &lt;/p&gt;&#xA;" OwnerUserId="16224" LastEditorUserId="5144" LastEditDate="2018-12-11T16:57:56.407" LastActivityDate="2018-12-11T16:57:56.407" Title="Why are the organs for reproduction and urinary excretion combined?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="3" CommentCount="11" FavoriteCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="35233" PostTypeId="2" ParentId="35232" CreationDate="2015-06-15T15:28:14.593" Score="13" Body="&lt;p&gt;Developmentally, the urinary and genital systems (typically you will hear them referred to as &quot;urogenital system&quot;) are derived from the same embryonic tissue, the intermediate mesoderm. The embryonic kidneys are drained by the mesonephric duct in both females and males. This embryonic tissue also gives rise to the ovaries and testes. The mesonephric duct degenerates in females, and becomes the ductus deferens in males. A second tube, the paramesonephric duct develops in both, but degenerates in males. The female paramesonephric duct becomes the uterine (Fallopian) tube.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Embryonically, the ureter, which drains the adult kidney is connected to the mesonephric duct. This connection is maintained in males, so that both urine and semen share a tube (urethra) for some of their exit pathway. In females, the paramesonephric duct and urethra are separate, so there are two openings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In males, sphincter muscles and autonomic control prevent the simultaneous expulsion of urine and semen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nSAo7.gif&quot; alt=&quot;Urogenital development&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This system has worked acceptably well in mammals for at least about 200 million years (and in humans for the last 4 million or so), so I think it's not correct to call it a mistake. It's not how you would consciously design such a system, but evolution doesn't have a conscious designer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.slideshare.net/ananthatiger/embryology-urogenital-system&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here are some slides&lt;/a&gt; that cover the embryology of the human urogenital system.&lt;/p&gt;&#xA;" OwnerUserId="107" LastEditorUserId="107" LastEditDate="2015-06-15T18:00:29.683" LastActivityDate="2015-06-15T18:00:29.683" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35235" PostTypeId="1" AcceptedAnswerId="35237" CreationDate="2015-06-15T16:32:59.410" Score="11" ViewCount="2192" Body="&lt;p&gt;There is question at Space.SE &lt;a href=&quot;https://space.stackexchange.com/questions/9527&quot;&gt;If I drop a feather from orbit, would it burn up or “hit” the ground?&lt;/a&gt; there is an attempt to answer the question, but the mass of pigeon tail feather and possibly the drag coefficient is required to complete the answer.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have looked around on the web and if there is an answer it is not jumping out at me. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the mass &amp;amp; drag coefficient of a pigeon tail feather?&lt;/p&gt;&#xA;" OwnerUserId="4240" LastEditorUserId="-1" LastEditDate="2017-04-13T12:58:55.703" LastActivityDate="2015-06-15T17:33:33.930" Title="What is the mass of a pigeon tail feather?" Tags="&lt;biophysics&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35236" PostTypeId="2" ParentId="31347" CreationDate="2015-06-15T16:49:40.100" Score="4" Body="&lt;p&gt;The short answer is that it is likely a bad experiment; being that it would be expensive and is not likely to provide useful new information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The long answer (i.e. why) is identifying an interesting target gene (e.g. caspase-9 in breast cancer) is only the first step, and considerable study of what is already known is required before planning an experiment (especially an expensive one that requires numerous mice).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Caspase-9 is a critical effector of apoptosis through the mitochondrial pathway. Many different signals such as DNA damage, Endoplasmic reticulum stress, etc induce cells to die through this pathway. This is important both in normal development and in preventing cancer. Homozygous deletion of caspase-9 is lethal, the mice will not live to adulthood. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK6153/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/books/NBK6153/&lt;/a&gt;) A conditional knock-out of caspase-9 in breast cancer cells would be needed, not a global deletion.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, the given the known functions of caspase-9 this experiment is not likely to provide interesting new information. This pathway is well characterized and known to play an important role in cancer (Resisting cell death; a hallmark of cancer: &lt;a href=&quot;http://www.cell.com/abstract/S0092-8674(11)00127-9&quot; rel=&quot;nofollow&quot;&gt;http://www.cell.com/abstract/S0092-8674(11)00127-9&lt;/a&gt; ) Loss of caspase-9 activity makes cells resistant to apoptotic signals through the mitochondrial pathway(they won't die when they receive these &quot;suicide&quot; signals). This allows mutant cells to survive when they should otherwise die. Cancer cells can also become resistant to this pathway through other means (such as the up regulation of anti-apoptotic Bcl-2 family members. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many scientists are already studying how to restore normal function of this pathways in various cancers; what do you hope to learn by breaking it that isn't already known (I'm not saying that there couldn't be a good reason, but if you don't have one, you shouldn't do it.)&lt;/p&gt;&#xA;" OwnerUserId="16147" LastEditorUserId="16147" LastEditDate="2015-06-15T16:57:08.497" LastActivityDate="2015-06-15T16:57:08.497" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35237" PostTypeId="2" ParentId="35235" CreationDate="2015-06-15T17:18:35.027" Score="18" Body="&lt;p&gt;I just weighed a pigeon tail feather (~10 cm) long. The mass was 0.05 g. Although all tail feathers are not equal in length (and all pigeons are not equal in size), this is probably a good approximation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Measuring the drag coefficient is going to be very challenging, because it will vary with the orientation of the oncoming airflow. A feather falling with its broad surface (in this feather ~1.2 cm in chord width) perpendicular to the flow will have a much high drag coefficient than a feather falling with the broad surface parallel to flow.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2015-06-15T17:18:35.027" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35238" PostTypeId="6" CreationDate="2015-06-15T17:40:17.320" Score="0" Body="&lt;p&gt;Hi, I'm fileunderwater, a researcher in ecology from Sweden. I've been visiting Biology SE for about two years, during a time when the community and the site has grown quite a bit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have been an active user of the site by answering questions, commenting, voting and flagging, but also by being relatively active at our Meta site under the discussion and support tags. I think moderation should be rather light and non-confrontational, and that issues such as closing should be resolved by the community if possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the future, I would like for Biology-SE to grow and become more established, with a much wider professional user base. At the moment, a quite small number of users answer most of the questions, and we lack expertise in many areas. Therefore, I think it is important that we clarify out scope further (e.g. on homework and poorly researched content) and closely monitor the quality of questions. Otherwise, we run the risk of alienating new expert users, which are essential for the long-term success of the site. Questions are of course essential as well, since they lead to new answers and content, but without a knowledgeable user-base they cannot be answered.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-06-15T18:11:14.617" LastActivityDate="2015-06-15T18:11:14.617" CommentCount="0" CommunityOwnedDate="2015-06-15T17:40:17.320" ContentLicense="CC BY-SA 3.0" />
  <row Id="35239" PostTypeId="2" ParentId="31347" CreationDate="2015-06-15T18:36:52.527" Score="0" Body="&lt;p&gt;It seems you are confused with some other gene instead of caspase 9, but if KO of some gene causes development of breast cancer, and you want to compare something between none-cancerous and cancerous states, you could take several ways:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;See if you could have littermates carrying and not carrying cancer. You could compare them. Sometimes, phenotype do not express 100% among mice through the life spam or at younger age. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Breast cancer is rare in human males, probably in murine males, too; think you could compare what you want to see between males and females.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When you cross KO mice with other strains, occurrence of phenotype could vary. Then you could compare what you want to see between less and more susceptible mice strains.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-06-15T21:08:14.037" LastActivityDate="2015-06-15T21:08:14.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35241" PostTypeId="1" AcceptedAnswerId="35259" CreationDate="2015-06-15T20:48:51.073" Score="8" ViewCount="34786" Body="&lt;p&gt;There have been papers discussing this, and whether the abstinence period should be 1 week, 2 weeks or other [1, 2]. Some think the time to maximum ejaculation volume is even longer than this.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;doi: &lt;a href=&quot;http://dx.doi.org/10.1530/jrf.0.0570391&quot; rel=&quot;noreferrer&quot;&gt;10.1530/jrf.0.0570391&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;PMID: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7114956&quot; rel=&quot;noreferrer&quot;&gt;7114956&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="16234" LastEditorUserId="740" LastEditDate="2015-06-16T14:27:27.657" LastActivityDate="2015-06-16T14:46:23.247" Title="What is the optimum length of abstinence for maximum ejaculation volume in humans?" Tags="&lt;human-biology&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35242" PostTypeId="1" AcceptedAnswerId="35244" CreationDate="2015-06-15T20:51:52.533" Score="5" ViewCount="736" Body="&lt;p&gt;My background is in mathematics, and not biology, so please bear with me. I am currently working on a project involving the effects of Epidermal growth factor treatment (EGF) on cell migration. I am reading a review of EGF signaling (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23953842&quot; rel=&quot;nofollow&quot;&gt;Epidermal growth factor receptor targeting in cancer: A review of trends and strategies&lt;/a&gt; by Chetan Yewale, et. al.), and it states that &quot;Various ligands can activate EGFR ... These ligands are expressed as integral membrane proteins.&quot; This statement makes absolutely no sense to me, and makes me question my understanding of signal transduction. I think of ligands as freely floating molecules that may eventually come into contact with the cell membrane and attach to some receptor. But a ligand expressed as an integral membrane protein? This seems contradictory to my understanding of ligands, which (I thought) are released from the cell in order to signal with cells (be it the same, neighbor, or distant cells). Integral membrane protein ligands would only be useful for autocrine signaling, which I don't think is true of EGF.&lt;/p&gt;&#xA;" OwnerUserId="16235" LastEditorUserId="948" LastEditDate="2015-06-16T02:28:02.823" LastActivityDate="2015-06-16T19:36:18.010" Title="How can a ligand be an integral membrane protein?" Tags="&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;cell-signaling&gt;" AnswerCount="3" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35244" PostTypeId="2" ParentId="35242" CreationDate="2015-06-15T21:22:12.903" Score="5" Body="&lt;p&gt;In biology ligand is a very broad term. Everything is called a ligand that has a receptor for it, regardless whether it is free or membrane-bound. There is very much sense in membrane bound ligands, because many cells in our body are capable of actively moving around (for example T-cells). Cells can use signal transduction by direct cell-to-cell contact - like in activation of T-cells, or cytotoxic T-cell killing. &lt;a href=&quot;https://en.wikipedia.org/wiki/Cell_signaling&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; wiki page covers the basics quite well. &#xA;Also, a quite thorough &lt;a href=&quot;https://en.wikipedia.org/wiki/Ligand&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt; page on ligands.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the comments under the question by @WYSIWYG:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These kind of ligands act via juxtacrine signalling because they&#xA;  cannot diffuse. Ephrin is another example.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-06-16T09:44:24.610" LastActivityDate="2015-06-16T09:44:24.610" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35245" PostTypeId="1" CreationDate="2015-06-15T21:36:05.257" Score="1" ViewCount="563" Body="&lt;p&gt;I am aligning paired end sequence reads using &lt;code&gt;bwa mem&lt;/code&gt; and I get an error saying that &lt;code&gt;paired reads have different names: &quot;M01814:86:000000000-A6MU9:1:1101:15545:1335&quot;, &quot;M01814:86:000000000-A6MU9:1:1101:16059:1338&quot;&lt;/code&gt; So it looks like the locations for some of the reads don't quite match up. Is there a way to ignore these reads? Or to use them but not treat them as pairs?&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-06-15T21:36:05.257" Title="Different names in paired-end sequence files" Tags="&lt;dna-sequencing&gt;" AnswerCount="0" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="35246" PostTypeId="2" ParentId="35242" CreationDate="2015-06-15T22:16:01.843" Score="6" Body="&lt;p&gt;A perfectly reasonable definition of a ligand from &lt;a href=&quot;https://en.wikipedia.org/wiki/Ligand_(biochemistry)&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;A ligand can be anything, so long as it binds to a biomolecule. Often, the ligand is a small molecule or peptide, and the thing that it binds to is a protein. On the other hand, both ligand and binding partner can certainly be proteins (or one could be a Mg&lt;span class=&quot;math-container&quot;&gt;$^{2+}$&lt;/span&gt; ion and the other an RNA molecule, etc.). Ligand is a very broad term, and is often used in other biochemical areas aside from signaling. For example, the things that an enzyme binds to (substrates, allosteric regulators, etc) can be called its ligands.&lt;/p&gt;&#xA;&lt;p&gt;Also, the things you describe in your post:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;This seems contradictory to my understanding of ligands, which (I thought) are released from the cell in order to signal with cells (be it the same, neighbor, or distant cells).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;are hormones, which is a much more specific category of thing than is ligand.&lt;/p&gt;&#xA;&lt;h1&gt;Edit&lt;/h1&gt;&#xA;&lt;p&gt;There seem to be some 'ahem'... doubters as to the broadness of the definition of ligand, so, time for some examples from the literature:&lt;/p&gt;&#xA;&lt;p&gt;From the biochemistry textbook &lt;a href=&quot;http://bcs.whfreeman.com/berg7e/#t_644431____&quot; rel=&quot;nofollow noreferrer&quot;&gt;Berg, 7e&lt;/a&gt; (emphasis added):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The final step is affinity chromatography with the use of a &lt;strong&gt;ligand&lt;/strong&gt; specific for the target enzyme.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;From the paper &lt;a href=&quot;http://www.pnas.org/content/95/11/5942.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Electrostatic steering and ionic tethering in enzyme–ligand binding: Insights from simulations, Wade et al&lt;/a&gt; (emphasis added):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;To bind at an enzyme’s active site, a &lt;strong&gt;ligand&lt;/strong&gt; must diffuse or be transported to the enzyme’s surface, and, if the binding site is buried, the ligand must diffuse through the protein to reach it.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;From the paper &lt;a href=&quot;http://link.springer.com/article/10.1007/BF01590996#page-1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Geometries of functional group interactions in enzyme-ligand&#xA;complexes: Guides for receptor modelling, Tintelnot et al&lt;/a&gt; (emphasis added):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;There are many more examples of arginine-carboxyl interactions that appear to have key functional&#xA;roles in enzymes, including some in which an arginine-like structure in the &lt;strong&gt;ligand&lt;/strong&gt; interacts&#xA;with a carboxyl group from the binding site (i.e., the reverse of that described above).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;It is true that the one particular compound that natively binds to an enzyme's active site is often called a substrate, in part to differentiate it from allosteric regulators and other ligands that can also bind to the enzyme. Thus, the set of all of an enzyme's substrates can be thought of as a subset of the enzyme's ligands. Again, ligand is an extremely broad concept that simply refers to something which binds.&lt;/p&gt;&#xA;&lt;h1&gt;Edit 2&lt;/h1&gt;&#xA;&lt;p&gt;Fun fact! The modern word ligand comes from the latin verb ligāre, meaning &amp;quot;to bind&amp;quot;. More specifically, ligand derives from the gerundive form of ligāre, ligandus, which translates to something like &amp;quot;(that which is) to be bound&amp;quot;.&#xA;Not that this has much bearing on how it's used in the modern scientific literature. I just thought it was cool.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-16T19:36:18.010" CommentCount="15" ContentLicense="CC BY-SA 3.0" />
  <row Id="35247" PostTypeId="2" ParentId="35242" CreationDate="2015-06-15T22:23:57.740" Score="0" Body="&lt;p&gt;Most ligands are synthesized as the same way as receptors integrated in membrane: synthesized on rough-ER, pulled into the lumen of ER. If proteins synthesized on rough-ER have a hydrophobic amino acid sequence, the hydrophobic region could stay in membrane because inside of membrane is hydrophobic and has affinity to hydrophobic amino acid sequences. Soluble ligands do not have such a region in the sequences, but membrane integrated ligands have it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I mentioned above there are ligands integrated on membrane: Fas, TNF, Notch ligand family, etc. As you mention in the question, they are not soluble so that ligand-receptor signaling occurs by cell to cell contact.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see various types of membrane integrated ligands from the URLs below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/onc/journal/v27/n38/full/onc2008229a.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/onc/journal/v27/n38/full/onc2008229a.html&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.sanfordburnham.org/talent/Pages/CarlWare.aspx&quot; rel=&quot;nofollow&quot;&gt;http://www.sanfordburnham.org/talent/Pages/CarlWare.aspx&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.sci-online.org/article/view/3946/4855&quot; rel=&quot;nofollow&quot;&gt;http://www.sci-online.org/article/view/3946/4855&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.bio.davidson.edu/courses/immunology/students/spring2003/swails/fas.html&quot; rel=&quot;nofollow&quot;&gt;http://www.bio.davidson.edu/courses/immunology/students/spring2003/swails/fas.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-06-16T00:15:16.143" LastActivityDate="2015-06-16T00:15:16.143" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35249" PostTypeId="1" CreationDate="2015-06-16T01:57:58.813" Score="2" ViewCount="47" Body="&lt;p&gt;I have read that chimpanizees have distinct personalities. Do we have evidence of heritable personality traits in them? &lt;/p&gt;&#xA;" OwnerUserId="16102" LastActivityDate="2015-06-16T19:25:50.993" Title="Do we have evidence of heritable personality traits in chimpanzees?" Tags="&lt;genetics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35250" PostTypeId="1" AcceptedAnswerId="35257" CreationDate="2015-06-16T03:45:10.253" Score="1" ViewCount="8336" Body="&lt;p&gt;I've read that the bacterial capsule protects the bacterium from phagocytes and prevents water (and nutrients, possibly?) leakage from the bacterium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A less organized and less dense version is called a slime layer. It seems that the slime layer has similar functions, according to &lt;a href=&quot;https://en.wikipedia.org/wiki/Slime_layer&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the differences between the effects a capsule and a slime layer bring to a bacterium?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought about the followings:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The capsule covers most part of the bacterium, so adhesion proteins and transport proteins on the plasma membrane do not work effectively, whereäs with a slime layer, more proteins on the plasma membrane are exposed to the exterior, making them work more effectively.&lt;/li&gt;&#xA;&lt;li&gt;Maintenance of the capsule takes more energy than that of the slime layer simply because there are more glycoproteins in the capsule.&lt;/li&gt;&#xA;&lt;li&gt;Bacteria with capsules are less likely to lyse than those with slime layers.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Is there anything else significant that goes on this list? Or are there any points I made that are not true?&lt;/p&gt;&#xA;" OwnerUserId="4254" LastActivityDate="2015-06-16T13:33:16.467" Title="Bacterial capsule vs. slime wall" Tags="&lt;microbiology&gt;&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35252" PostTypeId="2" ParentId="24766" CreationDate="2015-06-16T07:48:41.817" Score="1" Body="&lt;p&gt;In bacteriophage, the viral capsules serve as vectors for other DNA so frequently that there is a common name for this: &lt;a href=&quot;https://en.wikipedia.org/wiki/Transduction_%28genetics%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;transduction&lt;/a&gt;. The image below, from the Wikipedia, illustrates the basic process. Here a phage, with pink DNA, accidentally packages up other DNA -- in this case, from the bacterium -- in one of the capsules and thereby serves as a vector for this DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CTIlk.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Something a bit like this happens any time we have recombinational assortment in the influenza virus. The influenza virus genome segmented, with 8 &quot;chromosomes&quot;. When an individual is multiply infected with different strains, new combinations of the 8 chromosomes can be packaged up within an given viral particle. This process is often responsible for new epizootic strains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In principle, genetic material from another virus could be packaged up accidentally into an influenza virus particle. If it happened to enter the right kind of cell, the influenza capsule could in that way act as a vector for the other virus's DNA. In practice, I would imagine that this would require remarkable coincidence and thus would be extremely uncommon in nature. &lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-06-16T07:48:41.817" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35253" PostTypeId="2" ParentId="35213" CreationDate="2015-06-16T10:14:26.460" Score="1" Body="&lt;p&gt;Might be considered &quot;not answering the question&quot; but:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Option 1:&lt;/strong&gt;&#xA;Depending on the type of cells you are using, you can use milder methods to detach cells.  Example include Versene which is essentially PBS + EDTA.  Milder still is to just use PBS that has no Mg or Ca (no chelation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Option 2:&lt;/strong&gt;&#xA;Duplicate your setup - instead of two dishes - one with drug, one without, you make 4 dishes (dispensed from a common source - i.e. if your dish is a 6cm dish with 3ml media, you make 4.5x3mls of cells at the final dilution you want) each plate gets 3mls from the same source so you know they have the same number of cells.  Two dishes you add drugs, two you don't.  On the day you want to count, you take the replicate plates and count them.  This way, you get the count without touching the final dishes at all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side experiment, if you put those trypsinized cells back on two dish (and replace the drug media in the drug treated replicate), and you count all plates on the last day of your experiment, provided cells are not at 100% confluency, any difference you see from your trypsinized vs untrypsinized can be viewed as potential error that you would have introduced if you went through your original methodology.&lt;/p&gt;&#xA;" OwnerUserId="16242" LastActivityDate="2015-06-16T10:14:26.460" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35254" PostTypeId="2" ParentId="9419" CreationDate="2015-06-16T11:29:27.823" Score="12" Body="&lt;p&gt;Looks like some parasitoid wasps have zinc coated barbs on their ovipositors which may function to help them bore through wood and lay their eggs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's the blog entry about it on &lt;a href=&quot;http://www.iflscience.com/plants-and-animals/these-wasps-have-zinc-tipped-drill-bits&quot;&gt;IFL Science&lt;/a&gt;, and the original article:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;parasitoid ovipositor specimens had a weight percentage of zinc of 7.19±3.8% (N=42) in the tip regions, which was significantly higher (P&amp;lt;0.05) than that in pollinator and parasitoid remote regions (&amp;lt;1%; N=10).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://jeb.biologists.org/content/217/11/1946.full&quot;&gt;Kundanati and Gundiah (2014) Biomechanics of substrate boring by fig wasps. &lt;em&gt;J Exp Bio&lt;/em&gt; 217: 1946-1954&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16243" LastEditorUserId="3952" LastEditDate="2015-06-16T19:01:14.150" LastActivityDate="2015-06-16T19:01:14.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35257" PostTypeId="2" ParentId="35250" CreationDate="2015-06-16T13:33:16.467" Score="1" Body="&lt;p&gt;According to the Wikipedia section on &lt;a href=&quot;https://en.wikipedia.org/wiki/Bacterial_capsule&quot; rel=&quot;nofollow&quot;&gt;bacterial capsules&lt;/a&gt;, they're made of the same thing:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When the amorphous viscid secretion (that makes up the capsule) diffuses into the surrounding medium and remains as a loose undemarcated secretion, it is known as slime layer.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.textbookofbacteriology.net/structure_4.html&quot; rel=&quot;nofollow&quot;&gt;Todar's Online Textbook of Bacteriology&lt;/a&gt; synonymizes &quot;slime layer&quot; and &quot;biofilm&quot;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A true capsule is a discrete detectable layer of polysaccharides deposited outside the cell wall. A less discrete structure or matrix which embeds the cells is a called a slime layer or a biofilm.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This makes sense with what I remember learning about slime walls--the main difference I saw was that the capsule was directly associated with/only protects a single bacterial cell, whereas the slime layer is associated with/protects multiple bacteria. I'm not sure that I'd call it a biofilm though, as those are notoriously difficult to remove; their removal in hospital and food processing sysyems is a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20198521&quot; rel=&quot;nofollow&quot;&gt;current research topic&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regarding your three points above, I might instead argue that the slime layer provides another layer of protection in addition to the bacterial capsule.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-06-16T13:33:16.467" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35259" PostTypeId="2" ParentId="35241" CreationDate="2015-06-16T14:46:23.247" Score="7" Body="&lt;p&gt;There don't appear to be many robust studies on this, but this study by De Longe &lt;em&gt;et al&lt;/em&gt; in 2004 suggests that, whilst the volume of the ejaculate is increased after 5-days of abstinence (in most participants), for many this did not increase further after 8-days [&lt;a href=&quot;https://i.stack.imgur.com/JtB77.png&quot; rel=&quot;noreferrer&quot;&gt;1&lt;/a&gt;].&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are the 11 participant included (along the x-axis), and for each participant there are four coloured boxes:  dark blue, day 1 (corresponds to 24 hours' abstinence); red, day 3 (corresponds to 3 days' abstinence); yellow, day 5 (corresponds to 5 days' abstinence); light blue, day 8 (corresponds to 8 days' abstinence).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JtB77.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This study has a very small sample size, and really shows how the variability between people is massive. There could be &lt;em&gt;many&lt;/em&gt; other factors affecting individuals, from smoking and drinking behaviours, to exercise and stress.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What seems much clearer is that sperm &lt;em&gt;concentration&lt;/em&gt; increases with abstinence [&lt;a href=&quot;https://i.stack.imgur.com/tw80N.gif&quot; rel=&quot;noreferrer&quot;&gt;2&lt;/a&gt;]. This study included 27 men and did not specifically ask them to remain abstinent for periods of time, but asked them how long. The average abstinence is about 2-days.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tw80N.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could not find any study which investigated abstinence for longer periods - but there are undoubtedly more that I did not see.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;De Longe, &lt;em&gt;at al&lt;/em&gt;. 2004. &lt;strong&gt;Influence of the abstinence period on human sperm quality&lt;/strong&gt;. &lt;em&gt;Fertility and Sterility&lt;/em&gt; (&lt;a href=&quot;http://dx.doi.org/10.1016/j.fertnstert.2004.03.014&quot; rel=&quot;noreferrer&quot;&gt;http://dx.doi.org/10.1016/j.fertnstert.2004.03.014&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;li&gt;Carlsen, &lt;em&gt;et al&lt;/em&gt;, 2004. &lt;strong&gt;Effects of ejaculatory frequency and season on variations in semen quality&lt;/strong&gt;. &lt;em&gt;Fertility and Sterility&lt;/em&gt; (&lt;a href=&quot;http://dx.doi.org/10.1016/j.fertnstert.2004.01.039&quot; rel=&quot;noreferrer&quot;&gt;http://dx.doi.org/10.1016/j.fertnstert.2004.01.039&lt;/a&gt;)&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastActivityDate="2015-06-16T14:46:23.247" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35260" PostTypeId="1" AcceptedAnswerId="35261" CreationDate="2015-06-16T14:54:05.370" Score="5" ViewCount="5587" Body="&lt;p&gt;This is a question which plagues many people and today I was wondering it myself while writing a grant. Indeed, I've seen many people use the terms interchangeably, but they are all very different from each other. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So What is the difference between SNPs, Mutations and Structural Variations?&lt;/p&gt;&#xA;" OwnerUserId="15807" LastEditorUserId="14852" LastEditDate="2016-06-06T03:01:33.830" LastActivityDate="2016-06-06T03:01:33.830" Title="What is the difference between Single Nucleotide Polymorphism (SNP), Mutation and Structural Variation(SV)?" Tags="&lt;genomics&gt;&lt;mutations&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35261" PostTypeId="2" ParentId="35260" CreationDate="2015-06-16T14:54:05.370" Score="10" Body="&lt;p&gt;Lets state what a Mutation is first.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mutation: A mutation is any change in an organism's genetic sequence which varies from that of the wild-type reference sequence (hg19/GrCH37 from 2009 or hg38/GrCH38 from 2013, which are the most current genome assembly). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Single Nucleotide Polymorphisms (SNPs): These are any single nucleotide base mutations which have been validated to be present in more than 1% of the population with the help of Genome-wide Association Studies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Structural Variations: These are any mutations which cause a change in the organism's chromosome structure, such as Insertions, deletions, copy number variations, duplications, inversions and translocation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more please read &lt;a href=&quot;https://en.wikipedia.org/wiki/Human_genetic_variation&quot;&gt;Wiki Link&lt;/a&gt; here.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Thanks to WYSIWYG for his interesting question regarding SNPs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This piqued my interest a bit, and to my surprise I found that the same actually applies to all other species for example chickens; This &lt;a href=&quot;http://www.gsejournal.org/content/pdf/1297-9686-34-3-275.pdf&quot;&gt;paper&lt;/a&gt; from way back in 2002 describes how EST mining was sometimes used to generate potential SNPs but also notes the possible false positives due to the possibility of RNA-Editing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.ucm.es/data/cont/docs/345-2013-11-08-SNP_trazeability_cattle.pdf&quot;&gt;paper&lt;/a&gt; describes the usage of SNPs to allocate bovine individuals to their source population. As does this &lt;a href=&quot;http://rd.springer.com/article/10.1007%2Fs00335-001-2146-3&quot;&gt;paper&lt;/a&gt; which highlights the economic importance that SNPs may hold for identifying pure breeds and crossbreeds.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apparently there are also SNP chips available for other animals as highlighted by this particular &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.2011.02243.x/abstract&quot;&gt;paper&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="15807" LastEditorUserId="15807" LastEditDate="2015-06-16T15:31:23.693" LastActivityDate="2015-06-16T15:31:23.693" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35262" PostTypeId="1" CreationDate="2015-06-16T15:11:29.527" Score="2" ViewCount="817" Body="&lt;p&gt;I am working in the field of neuroscience with a background in computer science. I try to find new ways of analyzing brain imaging data (mostly MRI, EEG, MEG, fMRI) with modern machine learning methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to take a step up by adding genetics to the data arsenal. My work this far has found connections between some X and Y but not really shed insight to &lt;em&gt;why&lt;/em&gt; things should be like that. I hope I could get a partial answer from biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To get started, I would need some good material to read. It does not matter if the content would be difficult in mathematical/statistical/technical aspects, but it should be approachable with limited knowledge in biology and/or chemistry and physics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suggestions?&lt;/p&gt;&#xA;" OwnerUserId="16250" LastActivityDate="2015-06-16T19:31:13.927" Title="Introductory book in genetics?" Tags="&lt;genetics&gt;&lt;neuroscience&gt;&lt;bioinformatics&gt;&lt;book-recommendation&gt;" AnswerCount="2" CommentCount="2" ClosedDate="2015-06-17T05:21:07.220" ContentLicense="CC BY-SA 3.0" />
  <row Id="35264" PostTypeId="1" AcceptedAnswerId="35271" CreationDate="2015-06-16T17:02:19.760" Score="4" ViewCount="9840" Body="&lt;p&gt;What causes the crease through the pericarp of a drupe fruit (peach, nectarine, olive)?  It may just be in exocarp as @Ilan pointed out, but I assumed (perhaps wrongly), that the division continued through the pericarp.  I'm also not sure if this true generically for drupe fruit, so I'm not sure which phylogenetic step down to take.  Olives for example have a divot that seems to extend from the stem down, but it stops well before the midline of the fruit in most cases.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume the crease has something to the initial genesis of the fruit tissue, but I haven't found any arguments on it's formation.  A more technical term might be &quot;cleavage,&quot; but that was after some searching and not coming up with more certain term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Botany is not my strong suite, but I recently entered into a collaboration where we will be making some recombinant alpha viruses (which is within my strong suite) that will infect drupe tissue.  Finding good &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3059.2008.01842.x/citedby&quot; rel=&quot;nofollow noreferrer&quot;&gt;pathology&lt;/a&gt; papers has been difficult, and they tend to be &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0304423808000058&quot; rel=&quot;nofollow noreferrer&quot;&gt;specific&lt;/a&gt; (not trying to imply that's bad).  Can anyone point towards a reference text/article on the genius of drupe fruit if the cause of the &quot;crease&quot; is not clear?  Disruption of the crease seems to be a particular phenotype of infection for some strains, and I'm searching for the correct terminology and mechanisms that might be effected.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I can get permission I will include photos of an infected vs control peach.  In the mean time to clarify what I mean, the line that seems to transverse from one poll to the other of the fruit:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Peach:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Nqx6J.png&quot; alt=&quot;image of peach&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nectarine:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ipSjz.jpg&quot; alt=&quot;image of nectarines on tree&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the sea mango it is pronounced, but on most other mango it seems like just a slight marking along the exocarp:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/g8zoD.jpg&quot; alt=&quot;sea mango image&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even the coconut seems to have at least one:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/a2tcQ.jpg&quot; alt=&quot;coconut&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3971" LastEditorUserId="3971" LastEditDate="2015-06-16T19:23:11.610" LastActivityDate="2015-06-16T19:39:49.873" Title="Cause of Crease in Drupe Fruit" Tags="&lt;botany&gt;&lt;development&gt;&lt;fruit&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35268" PostTypeId="2" ParentId="35262" CreationDate="2015-06-16T19:06:46.320" Score="2" Body="&lt;p&gt;GENETICS: Analysis and Principles, 4th edition, Robert J. Booker&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This book is used in my school's ( NYU Poly) undergraduate genetics class. &lt;/p&gt;&#xA;" OwnerUserId="16256" LastActivityDate="2015-06-16T19:06:46.320" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35269" PostTypeId="2" ParentId="35249" CreationDate="2015-06-16T19:25:50.993" Score="1" Body="&lt;p&gt;There has been some research in order to explore this direction, for instance, see this reference:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.researchgate.net/profile/Aurelio_Figueredo/publication/12223447_The_heritability_of_personality_factors_in_chimpanzees_(Pan_troglodytes)/links/00b7d5319d00f58589000000.pdf&quot; rel=&quot;nofollow&quot;&gt;A. Weiss et al. - &quot;&lt;em&gt;The Heritability of Personality Factors in Chimpanzees&lt;/em&gt;&quot;, Behavior Genetics, Vol. 30, No. 3, 2000.&lt;/a&gt;, &lt;/p&gt;&#xA;&#xA;&lt;p&gt;in which the authors study five human-like factors - Surgency,&#xA;Dependability, Emotional Stability, Agreeableness, and Openness. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Quoting verbatim their findings:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Only Dominance ... was significantly heritable. Dependability showed evidence that it might be heritable, but the parameter estimates were not statistically significant ... Two other personality traits, Agreeableness and Emotional Stability, showed positive heritability estimates but the parameter&#xA;  estimates were nonsignificant and small. Openness and Surgency showed no evidence of heritability. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In fact, the statistical correlation between dominance and heritability makes a strong sense.  Here's what I make out of this - this was a correlation based study, or kind of an experiment, hence the stress on statistical significance. But the question it raises is - is there a causal relationship between the two, i.e. does there exist any proper &lt;em&gt;mechanism&lt;/em&gt; for the inheritance of &quot;dominance&quot;. Finding such a mechanism was clearly beyond the scope of this study, but I believe the requisite answer for your question is if one stumbles on to such mechanisms, and not statistical correlations, which are mere pointers. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But on the basis of the study at least, all that one can safely conclude is - &lt;em&gt;statistical correlations suggest that inheritance of &quot;dominance&quot; appears plausible, but the exact mechanism of how this implements out in practice, is beyond the scope of this study&lt;/em&gt;.   &lt;/p&gt;&#xA;" OwnerUserId="15494" LastActivityDate="2015-06-16T19:25:50.993" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35270" PostTypeId="2" ParentId="35262" CreationDate="2015-06-16T19:31:13.927" Score="2" Body="&lt;p&gt;MIT Open Course Ware has &lt;a href=&quot;http://ocw.mit.edu/courses/biology/7-03-genetics-fall-2004/&quot; rel=&quot;nofollow&quot;&gt;a course on genetics&lt;/a&gt;, which uses the following text:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;&lt;em&gt;An Introduction to Genetic Analysis&lt;/em&gt;&quot;, Griffiths, Anthony J. F., Jeffrey H. Miller, David T. Suzuki, Richard C. Lewontin, and William M. Gelbart, 7th ed. New York: W. H. Freeman, 2000.   &lt;/p&gt;&#xA;" OwnerUserId="15494" LastActivityDate="2015-06-16T19:31:13.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35271" PostTypeId="2" ParentId="35264" CreationDate="2015-06-16T19:39:49.873" Score="2" Body="&lt;p&gt;The structure you are relating to is a seam (suture). This seam is formed during development of a carpel. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The indentation of the seam varies and depends on the climate and environment: for example, &lt;a href=&quot;http://ucanr.edu/sites/fruitreport/Irrigation/Deficit_Irrigation_Strategies/?repository=40865&quot; rel=&quot;nofollow noreferrer&quot;&gt;water stress&lt;/a&gt; will give a very deep suture - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IxugU.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-06-16T19:39:49.873" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35272" PostTypeId="1" AcceptedAnswerId="35301" CreationDate="2015-06-16T20:50:50.310" Score="0" ViewCount="289" Body="&lt;p&gt;I am reading the paper &quot;Neutral evolution of mutational robustness&quot;. Because I am new to neutral evolution, I have a few questions. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Firstly, from my understanding, genotypic neutrality means the genotype is not responsible for an increase in fitness. What else can we say about genotypic neutrality? Does it have something to do with the population being randomly selected? &lt;/li&gt;&#xA;&lt;li&gt;Secondly, how to understand a neutral network exactly? Another article says &quot;by linking every pair of genotypes that are mutually accessible through mutations, genotypes organize themselves into neutral networks&quot;, so what means &quot;mutually accessible through mutations&quot;? &lt;/li&gt;&#xA;&lt;li&gt;Thirdly, the neutral network is like an assumed black box we know nothing about, is it right? That is why in the original article with title &quot;neutral evolution of mutational robustness&quot;, the authors mentioned that &quot;one can infer important structural information about neutral networks from data on evolving populations.&quot; &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="15799" LastEditorUserId="9943" LastEditDate="2015-06-17T04:20:07.483" LastActivityDate="2015-06-17T21:54:20.167" Title="What is a selectively neutral genotypic change?" Tags="&lt;evolution&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35273" PostTypeId="1" CreationDate="2015-06-16T22:03:04.427" Score="1" ViewCount="6860" Body="&lt;p&gt;This may sound like a strange question. But could a &lt;strong&gt;Cancerous cell&lt;/strong&gt; be transferred from one person to another from Oral contact e.g. Through &lt;strong&gt;Saliva&lt;/strong&gt;, or other exchange of bodily fluids?&#xA;I know that other diseases from &lt;strong&gt;Bacteria / Viral&lt;/strong&gt; can be transferred in this way, but does the same apply to Cancerous cells? - or would the recipient's body just breakdown and destroy the cancerous cells?&lt;/p&gt;&#xA;" OwnerUserId="10453" LastActivityDate="2016-04-04T13:47:16.877" Title="Can you Transfer Cancer Between People via Saliva or other Bodily Fluids?" Tags="&lt;cell-biology&gt;&lt;cancer&gt;&lt;pathology&gt;&lt;antibody&gt;&lt;antigen&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35274" PostTypeId="2" ParentId="35273" CreationDate="2015-06-16T23:25:50.050" Score="6" Body="&lt;p&gt;Although transmissible cancer has been found in some species, such as &lt;a href=&quot;https://en.wikipedia.org/wiki/Devil_facial_tumour_disease&quot;&gt;Tasmanian Devils&lt;/a&gt; and &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867415002433&quot;&gt;clams&lt;/a&gt;, it is &lt;a href=&quot;https://en.wikipedia.org/wiki/Clonally_transmissible_cancer#Instances_of_transmission_of_human_cancer&quot;&gt;quite rare&lt;/a&gt; in most species. Certain viral and bacterial agents that &lt;em&gt;cause&lt;/em&gt; cancer, however, can be transmitted. One example is &lt;a href=&quot;http://www.cancer.gov/about-cancer/causes-prevention/risk/infectious-agents/hpv-fact-sheet&quot;&gt;HPV&lt;/a&gt;, which can cause cervical cancer&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-06-16T23:25:50.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35275" PostTypeId="1" AcceptedAnswerId="35276" CreationDate="2015-06-16T23:42:29.347" Score="2" ViewCount="1169" Body="&lt;p&gt;For example, take &lt;em&gt;Canis lupus&lt;/em&gt;, the species of dog and wolf. Within their species, can all dog and wolf types crossbreed? We can forget the logistics and assume this is all done through artificial insemination or in vitro methods (let's assume that the in vitro methods would be feasible).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If yes to the main question, does cross-breeding stop at the species class, or does cross-breeding extend across other taxonomic classes? From what I gathered, the taxonomic classes seem somewhat loose in their definitions. Perhaps I should ask, is there a rule &quot;in general&quot; to cross-breeding?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me know if this question ought to be refined in any way.&lt;/p&gt;&#xA;" OwnerUserId="16259" LastEditorUserId="3340" LastEditDate="2015-06-17T05:04:55.050" LastActivityDate="2018-03-27T16:15:24.017" Title="Can all animals of the same species crossbreed?" Tags="&lt;genetics&gt;&lt;taxonomy&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35276" PostTypeId="2" ParentId="35275" CreationDate="2015-06-16T23:51:38.857" Score="2" Body="&lt;p&gt;Species definitions are a somewhat contentious part of biology. There are no hard boundaries in nature that mean &quot;this group here is one species, this group here is another species&quot;. Some people don't even believe that species truly exist and there are only gradations of relatedness. That being said, the &lt;a href=&quot;http://evolution.berkeley.edu/evosite/evo101/VA1BioSpeciesConcept.shtml&quot; rel=&quot;nofollow&quot;&gt;Biological Species Concept&lt;/a&gt; is one of the more popular species definitions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the linked website: &quot;The biological species concept defines a species as members of populations that actually or potentially interbreed in nature&quot;. Thus, by definition, all animals of the same species can and do interbreed in nature. If two individuals breed in nature, they are considered the same species (under this definition). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, you can already see some problems with this definition. Under the BSC, are a dog and a wolf the same species? Do dogs and wolves breed &quot;in nature&quot;? Of course, fertile half-dog half-wolf animals exist, but does it even make sense to ask whether a domestic species breeds &quot;in nature&quot;. I suppose you can say they can &quot;potentially&quot; breed in nature. But how do you define &quot;potentially&quot; breeding? Asking questions about species can lead to many exciting debates.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-06-16T23:51:38.857" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35278" PostTypeId="1" AcceptedAnswerId="35383" CreationDate="2015-06-17T04:34:16.190" Score="8" ViewCount="1503" Body="&lt;p&gt;Quite certainly, muted mosquitoes would be much more effective as far as their blood-sucking pursuits are concerned, since mosquito sound is predominantly responsible for sealing their fate (between the two palms of the hand). Muting themselves would certainly reduce the chances of being caught in the act. For instance, unless you notice by looking, leeches go undetected for long periods because there isn't any obvious sound emanating from them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, reasoning says - this should be favorable from the point of view of evolution, unless there is a some indispensable purpose served by this sound, which can not be otherwise served. This &lt;a href=&quot;http://www.mosquitoreviews.com/mosquitoes-buzz-ears.html&quot; rel=&quot;noreferrer&quot;&gt;page&lt;/a&gt; seems to suggest that this is so from the point of view of mating. In fact, quoting verbatim:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Since female mosquitoes are larger, they flap their wings slower, and males know it. They use the distinctive pitch of the females' buzz to recognize them. Louis M. Roth, who studied yellow fever mosquitoes for the U.S. Army during World War II, noticed that males ignored females whenever the females were quietly resting, but whenever the females were flying, and therefore buzzing, the males wanted to mate with them. The males even wanted to mate with recordings of female mosquitoes or tuning forks that vibrated at the same pitch.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But mating signals could also be of other forms, like some chemicals secreted (I envisage something like pheremones). Why is making sound so important? Why can't this noise be either less intense, or lie outside the audio range for humans (their targets)?&lt;/p&gt;&#xA;" OwnerUserId="15494" LastEditorUserId="15494" LastEditDate="2015-06-17T05:06:53.147" LastActivityDate="2019-03-07T04:23:12.860" Title="Why don't mosquitoes evolve towards muting themselves?" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35279" PostTypeId="2" ParentId="35278" CreationDate="2015-06-17T05:13:49.217" Score="9" Body="&lt;p&gt;Gliders do not actively fly and there is no work done by them in producing motion. Other flying machines do make a sound. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a trait exists then it means that there is not enough pressure against it. You can hear a mosquito only if it flies close to your ears; otherwise, they seem to be undetectable by hearing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To produce ultrasonic sounds the mosquito has to flap its wings too fast- which is energy intensive. Conversely, to produce just infrasonics, it has to flap the wings too slowly which may not provide it with enough thrust.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A recent study by &lt;a href=&quot;http://dx.doi.org/10.1038/nature21727&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bomphrey et al. (2017)&lt;/a&gt; suggests that mosquito flight is different from other insects and the aerodynamics are rather complex. Mosquitoes are known to use low amplitude, high-frequency flapping that generates the buzz.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the abstract:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Mosquitoes exhibit unusual wing kinematics; their long, slender wings&#xA;  flap at remarkably high frequencies for their size (&gt;800 Hz)and with&#xA;  lower stroke amplitudes than any other insect group&lt;sup&gt;1&lt;/sup&gt;. This shifts&#xA;  weight support away from the translation-dominated, aerodynamic&#xA;  mechanisms used by most insects&lt;sup&gt;2&lt;/sup&gt;, as well as by helicopters and&#xA;  aeroplanes, towards poorly understood rotational mechanisms that occur&#xA;  when pitching at the end of each half-stroke. Here we report&#xA;  free-flight mosquito wing kinematics, solve the full Navier–Stokes&#xA;  equations using computational fluid dynamics with overset grids, and&#xA;  validate our results with in vivo flow measurements. We show that,&#xA;  although mosquitoes use familiar separated flow patterns, much of the&#xA;  aerodynamic force that supports their weight is generated in a manner&#xA;  unlike any previously described for a flying animal. There are three&#xA;  key features: leading-edge vortices (a well-known mechanism that&#xA;  appears to be almost ubiquitous in insect flight), trailing-edge&#xA;  vortices caused by a form of wake capture at stroke reversal, and&#xA;  rotational drag. The two new elements are largely independent of the&#xA;  wing velocity, instead relying on rapid changes in the pitch angle&#xA;  (wing rotation) at the end of each half-stroke, and they are therefore&#xA;  relatively immune to the shallow flapping amplitude. Moreover, these&#xA;  mechanisms are particularly well suited to high aspect ratio mosquito&#xA;  wings.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Bottomline is that evolution does not know where the best optimum is and it does not really try to proceed to a global optimum. If a trait is disadvantageous, it is selected against. Neutral mutations stay but do not get amplified unless they have some kind of advantage.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3553" LastEditDate="2017-04-10T09:32:02.763" LastActivityDate="2017-04-10T09:32:02.763" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35281" PostTypeId="1" AcceptedAnswerId="57754" CreationDate="2015-06-17T06:13:16.390" Score="20" ViewCount="457" Body="&lt;p&gt;I have heard that the Human Botfly &lt;a href=&quot;https://books.google.ca/books?id=eqegRf2UstIC&amp;amp;pg=PA192&amp;amp;hl=en#v=onepage&amp;amp;q&amp;amp;f=false&quot;&gt;transfers its eggs through other invertebrates&lt;/a&gt;, and it strikes my curiosity that if an insect could simply land on its host directly to deposit its eggs, then why have intermediate hosts?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have speculated that the vectors may be better specialized for penetrating hosts, and that penetrating hosts may be difficult, or that approaching hosts is risky. Another speculation on my part is that the Human Botfly may be filling a niche where it does not need to compete.&lt;/p&gt;&#xA;" OwnerUserId="11538" LastEditorUserId="3624" LastEditDate="2016-11-04T09:04:43.367" LastActivityDate="2017-03-28T15:10:22.123" Title="Selection for less efficient egg transfer in Human Botfly life cycle" Tags="&lt;entomology&gt;&lt;invertebrates&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35283" PostTypeId="2" ParentId="26074" CreationDate="2015-06-17T07:13:58.920" Score="5" Body="&lt;p&gt;Dolphins and orcas do have dialects. Of course there are species specific dialects and it has been &lt;a href=&quot;http://scitation.aip.org/content/asa/journal/jasa/136/4/10.1121/1.4893906&quot; rel=&quot;noreferrer&quot;&gt;shown&lt;/a&gt; that orcas reared with bottlenose dolphins tend to learn the latter's dialect. Dolphins of the same species also seem to have regional dialects, as mentioned in this &lt;a href=&quot;http://news.bbc.co.uk/2/hi/uk_news/wales/mid_/6669469.stm&quot; rel=&quot;noreferrer&quot;&gt;BBC post&lt;/a&gt; (I personally do not trust in non-research articles much, but nonetheless in this case the article indicates a certain possibility of a phenomenon). However, &lt;a href=&quot;http://www.shannondolphins.ie/article.asp?id=43&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt; page also reports the same finding and this source seems to be much more reliable. There are citations too that are at present inaccessible to me. Both the sources say that bottlenose dolphins from Shannon estuary in Ireland, &quot;speak&quot; different dialect compared to those from Cardigan Bay in Wales.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The actual research work is this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;&lt;em&gt;Hickey, R.&lt;/strong&gt; (2005) Comparison of whistle repertoire and characteristics between Cardigan Bay and the Shannon estuary&#xA;  populations of Bottlenose dolphins (Tursiops truncatus) with&#xA;  implications for passive and active survey techniques. School of&#xA;  Biological Sciences, University of Wales, Bangor&lt;/em&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apart from having regional dialects, the cetacean communication also seems to have other features of a &quot;language&quot;. I am pasting excerpts from this &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0003347210005233&quot; rel=&quot;noreferrer&quot;&gt;article&lt;/a&gt; which basically reports a study on the acoustic communication or &lt;strong&gt;codas&lt;/strong&gt; in sperm whales. This may apply to dolphins as well.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Individuals within social units have preferred associates among&#xA;  members (Gero et al. 2008), indicating differences in the way an&#xA;  individual interacts with other members of its unit. These preferred&#xA;  associations among unit members suggest the possibility of an&#xA;  individual discrimination system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;br&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;.... most adult animals within a social unit shared the most common coda&#xA;  types, with the exception of the mother-calf pair whose repertoires&#xA;  were different from those of other unit members and each other. Apart&#xA;  from the mother-calf differences, the repertoire similarities of other&#xA;  members did not support the hypothesis of individually distinctive&#xA;  coda type repertoires. This sharing of coda repertoires suggests that&#xA;  they allow group membership recognition, at either the unit or clan&#xA;  levels. This hypothesis is further supported by the fact that social&#xA;  units seem to form groups preferentially with other units of their own&#xA;  clan (Rendell &amp;amp; Whitehead 2003b).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-17T09:31:28.570" LastActivityDate="2015-06-17T09:31:28.570" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35284" PostTypeId="1" CreationDate="2015-06-17T08:45:33.897" Score="4" ViewCount="105" Body="&lt;p&gt;I am currently doing some work on modelling the effects of treated nets usage on mosquito populations. Nets do not retain their maximum efficacy forever. They lose their chemical efficacy after about three years and all that is left is the physical protection offered by the net which I estimate to be 20% of the original efficacy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am trying to model this behaviour. I need continuous function over the interval $[0,1095]$ which decreases slowly  from 1 when $x=0$ and asymptotically approaches 0.2 when $x \rightarrow 1095 $.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tried an ellipse of the form $y=\sqrt{1-\dfrac{x^2}{(1095)^2}}$, but i realized the function is equal to zero when $x=1095$ which is not what i want.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help will be appreciated. Thank you.&lt;/p&gt;&#xA;" OwnerUserId="16265" LastEditorUserId="3340" LastEditDate="2015-06-17T09:13:09.600" LastActivityDate="2015-06-17T22:12:02.707" Title="Modelling insecticide net efficacy loss" Tags="&lt;mathematical-models&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2015-06-18T14:44:14.790" ContentLicense="CC BY-SA 3.0" />
  <row Id="35286" PostTypeId="2" ParentId="35284" CreationDate="2015-06-17T11:28:25.197" Score="3" Body="&lt;p&gt;As @WYSIWYG suggested, this is probably more suitable for Math-SE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From you question, it is unclear exactly what shape you are looking for, and there are many functions that could describe the behaviour you're after, i.e. a continuous, smooth decrease towards an asymptote. However, two possible options could be the negative exponential and a negative &lt;a href=&quot;https://en.wikipedia.org/wiki/Gompertz_function&quot; rel=&quot;nofollow noreferrer&quot;&gt;gompertz function&lt;/a&gt;. Possible forms of these could be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Negative exponential&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$y(x)=e^{−ax+ln(1-b)}+b,$  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $b=0.2$ and a is a rate parameter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Negative Gompertz&lt;/strong&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$y(x) = 1-\alpha e^{-\beta e^{-\gamma x}},$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $\alpha=0.8$ (describing the asymptote), $\beta$ in an inflection parameter (given a displacement along the x-axis), and $\gamma$ is a rate parameter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These functions can give results such as:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/QltOG.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In these examples, $a = 0.005$ for the negative exponential and $\beta = 150$, $\gamma = 0.008$ for the &lt;em&gt;gompertz v1&lt;/em&gt; and $\beta = 5$, $\gamma = 0.005$ for the &lt;em&gt;gompertz v2&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An alternative parametrization of the Gompertz, which might be easier to understand, is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$y(x) = 1-\alpha e^{-e^{-\gamma (x-\beta)}},$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where the inflection point ($\beta$) is directly related to the scale of the x-axis (so $\beta = 400$ would give an inflection at x = 400).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are these examples interesting for your application? Hopefully they can provide a starting point for you.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-06-17T22:12:02.707" LastActivityDate="2015-06-17T22:12:02.707" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="35287" PostTypeId="1" AcceptedAnswerId="35288" CreationDate="2015-06-17T13:04:19.373" Score="7" ViewCount="665" Body="&lt;p&gt;Found this little guy crawling around the back garden - South Coast of the UK.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ql6DQ.jpg&quot; alt=&quot;First shot&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mZ528.jpg&quot; alt=&quot;Second shot&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The closest things I could find online (with an admittedly weak knowledge of where to look up these things, aside a google search for &lt;code&gt;red beetle&lt;/code&gt;) were the &lt;a href=&quot;https://en.wikipedia.org/wiki/Red_flour_beetle&quot; rel=&quot;noreferrer&quot;&gt;red flour beetles&lt;/a&gt;. However, it doesn't look quite like what we had, this being more stockier, with a dark head, and more splayed feelers.&lt;/p&gt;&#xA;" OwnerUserId="16268" LastEditorUserId="16268" LastEditDate="2015-06-17T13:25:11.540" LastActivityDate="2020-05-15T22:26:24.333" Title="Is this species a variant of a red flour beetle?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35288" PostTypeId="2" ParentId="35287" CreationDate="2015-06-17T13:17:37.693" Score="8" Body="&lt;p&gt;This does not look like a red flour beetle, but more like some species of &lt;a href=&quot;https://en.wikipedia.org/wiki/Melolontha&quot;&gt;&lt;em&gt;Melolontha&lt;/em&gt;&lt;/a&gt;, possibly a &lt;a href=&quot;https://en.wikipedia.org/wiki/Cockchafer&quot;&gt;cockchafer&lt;/a&gt;. For more specific information, we would need to know, where your back garden is and maybe something to scale the bug. I would go for &lt;em&gt;Melolontha melolontha&lt;/em&gt;, the common cockchafer.&#xA;Of the two other european species of &lt;em&gt;Melolontha&lt;/em&gt;, &lt;em&gt;M. hippocastani&lt;/em&gt; usually has a black edge of the elytra (see &lt;a href=&quot;https://artportalen.se/Image/656473&quot;&gt;this&lt;/a&gt; picture), which this one doesn't seem to have, and &lt;em&gt;M. pectoralis&lt;/em&gt; is very rare and mostly (only?) found in Germany.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastEditorUserId="3624" LastEditDate="2015-06-17T14:33:31.260" LastActivityDate="2015-06-17T14:33:31.260" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35289" PostTypeId="2" ParentId="35287" CreationDate="2015-06-17T13:20:10.530" Score="4" Body="&lt;p&gt;I totally agree with skymningen, definitely a &lt;a href=&quot;http://www.uksafari.com/cockchafer.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;cockchafer&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iPjgO.jpg&quot; alt=&quot;cockchafer&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-06-17T13:20:10.530" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35290" PostTypeId="2" ParentId="35225" CreationDate="2015-06-17T13:41:33.810" Score="3" Body="&lt;p&gt;For skeletal muscles, you'll find a discussion in the Physics SE: &lt;a href=&quot;https://physics.stackexchange.com/questions/1984/why-does-holding-something-up-cost-energy-while-no-work-is-being-done&quot;&gt;https://physics.stackexchange.com/questions/1984/why-does-holding-something-up-cost-energy-while-no-work-is-being-done&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To make things short: while holding a position, muscles need to maintain a given length. However, internally, the muscle looks like a collapsible array of filaments, with myosin heads acting as crossbridges between them. Even when the muscle is not contracting, myosin heads unbind and rebind at some rate and would let the muscle relax -- unless you input more energy to compensate this with a further contraction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For smooth muscle, according to &lt;a href=&quot;http://humupd.oxfordjournals.org/content/16/6/725&quot; rel=&quot;nofollow noreferrer&quot;&gt;this article&lt;/a&gt;, the rate of unbinding can be very slow:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Once the contraction has occurred, the cross bridge attachments need&#xA;  to be released in order that the muscle can relax. Although less is&#xA;  known about this phenomenon, it appears to be related to&#xA;  dephosphorylation of MLC20. In some situations, the dephosphory- lated&#xA;  MLC20 is very slow to allow detachment of the actin from the myosin&#xA;  cross bridge, resulting in a prolonged contraction. This has been&#xA;  referred to as a ‘latch-bridge’ (Hai and Murphy, 1988). This&#xA;  phenomenon may be of great value especially for tonically active SM&#xA;  beds as it would allow them to maintain basal tone through holding in&#xA;  an isometric state without a great energy cost.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So as the muscle is not relaxing, no input of energy is needed to adjust its length to the desired one. I assume a disadvantage of that is that the reaction time of the muscle is slower.&lt;/p&gt;&#xA;" OwnerUserId="6224" LastEditorUserId="-1" LastEditDate="2017-04-13T12:40:13.457" LastActivityDate="2015-06-17T13:41:33.810" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35291" PostTypeId="2" ParentId="35273" CreationDate="2015-06-17T14:53:00.843" Score="0" Body="&lt;p&gt;Cancer is successful at killing it's victims because it is genetically still very similar to the host.  The immune system does not respond to it sufficiently to eradicate the mutated cells and this allows it to grow out of control.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When dealing with any kind of transmittal this would be close to an organ donation.  Without a very close match, and Immunosuppressants the body will &quot;reject&quot; any cancer cells, and wipe them out.  Saying this here have been freak incidents where in an organ transplant scenario, cancer was transmitted.&lt;/p&gt;&#xA;" OwnerUserId="1625" LastActivityDate="2015-06-17T14:53:00.843" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35293" PostTypeId="2" ParentId="15685" CreationDate="2015-06-17T15:34:51.293" Score="1" Body="&lt;p&gt;Check out the sources of &lt;a href=&quot;https://en.wikipedia.org/wiki/Stab_wound&quot; rel=&quot;nofollow&quot;&gt;Wikipedia article&lt;/a&gt;: the mortality rate is up to 4%.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main causes of &quot;immediate&quot; death in penetrating trauma are shock (low blood pressure due to external/internal hemorrhage, especially arterial hemorrhage), pneumothorax, penetrating heart injury (with resultant hemopericardium) and other less frequent causes. &#xA;The same causes account for &quot;later&quot; lethal case plus some specific causes like infections, emboly etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The overall mortality rate of stab wounds is far from 100%, and according to different studies is between 1% to 4%, but rarely more. The morbidity depends on depth of wound, place of injury, overall health status etc, thus multifactorial analysis is required to get an overall image of the penetrating wounds of the body. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some sources:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2627025/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2627025/&lt;/a&gt; - &#xA; (4.3% mortality in stab wounds to the anterior abdomen, back, and flank). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3798182&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/3798182&lt;/a&gt; - the mortality in back/flank stab wounds was 1.3%.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-06-17T15:44:41.433" LastActivityDate="2015-06-17T15:44:41.433" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35295" PostTypeId="1" CreationDate="2015-06-17T15:58:30.793" Score="7" ViewCount="999" Body="&lt;p&gt;I'm looking for the karyotype of a specific cell line. Some karyotypes are well known, such as HeLa or some carcinomas, but some are very hard to find, such as LG2 (B cells). Is there a database dedicated to karyotypes of human cell lines?&lt;/p&gt;&#xA;" OwnerUserId="15927" LastEditorUserId="22956" LastEditDate="2017-05-23T11:03:11.647" LastActivityDate="2020-04-08T17:28:19.173" Title="Is there a karyotype database for human cell lines?" Tags="&lt;cell-biology&gt;&lt;cell-culture&gt;&lt;database&gt;&lt;karyotype&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35296" PostTypeId="1" CreationDate="2015-06-17T17:35:26.880" Score="3" ViewCount="2956" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1065158/&quot; rel=&quot;nofollow&quot;&gt;I noticed that the native molecular weight for an enzyme is different from its subunit molecular weight.&lt;/a&gt; Why are they different? Aren't the genes needed to express the enzyme the same in the native organism and in the heterologous expression system? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does the heterologous expression system happen to affect the molecular weight of the final enzyme product? If so, how?&lt;/p&gt;&#xA;" OwnerUserId="15955" LastEditorUserId="1590" LastEditDate="2015-06-18T14:46:52.563" LastActivityDate="2015-06-18T14:46:52.563" Title="How is the subunit molecular weight different from the native molecular weight?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;enzymes&gt;&lt;protein-expression&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35297" PostTypeId="2" ParentId="35232" CreationDate="2015-06-17T18:26:58.047" Score="2" Body="&lt;p&gt;I would just modify the excellent previous by pointing out that the embryology describes a local maxima of fitness whose barrier to change is higher than any selective pressure.  The re-use of the &quot;logic&quot; of the intermediate mesoderm was either initially a bifurcation from one or the other, or, was of enough selective advantage to have the two developmental processes and the resultant physical systems folded together.&lt;/p&gt;&#xA;" OwnerUserId="16274" LastActivityDate="2015-06-17T18:26:58.047" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35299" PostTypeId="2" ParentId="35296" CreationDate="2015-06-17T20:10:08.257" Score="1" Body="&lt;p&gt;Your question is answered in the paper, the protein likely exists as a homodimer in vivo and denaturation (such as performed with SDS PAGE -&gt; Western Blot) separates the dimers into monomers:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;To determine the quaternary structure, size exclusion high-performance liquid chromatography was performed using an Agilent 1100 series high-performance liquid chromatography system with a Bio-Sil SEC-250 column (300 by 7.8 mm) and a mobile phase of 0.1 M Na2PO4, 0.15 M NaCl, and 0.01 M NaN3, pH 6.8. A Bio-Rad standard was used to standardize the column's retention time with respect to molecular mass (supplemental data). All experiments were repeated twice with &amp;lt;0.05 min of deviation in the retention times. The molecular mass of XR was calculated from its retention time to be ∼53 kDa. Monomerization could be induced in the presence of 15% SDS, causing XR to elute as a single peak, with a retention time corresponding to a molecular mass of ∼34 kDa. The data suggest that the native XR is a noncovalently linked dimer. &lt;strong&gt;The significant difference between the calculated molecular weight of the dimer and its apparent molecular weight is not uncommon for XRs from other species (7, 21, 33), which also typically exist as dimers.&lt;/strong&gt; However, to be certain of the protein size, N. crassa XR was subjected to mass analysis by electrospray ionization-quadrupole time of flight mass spectrometry. The highest abundance peak had a value of 38,381 m/z, corresponding exactly with the predicted molecular mass for the His6-tagged XR with the N-terminal fMet removed (supplemental data). Additionally, a 2M+ peak of about 20% abundance at 76,759 m/z corresponds well with the predicted mass of the dimeric form of the enzyme (76,762 Da).&quot;&lt;/p&gt;&#xA;" OwnerUserId="16147" LastActivityDate="2015-06-17T20:10:08.257" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35300" PostTypeId="2" ParentId="35232" CreationDate="2015-06-17T20:28:56.330" Score="2" Body="&lt;p&gt;kmm gives what is likely the best possible answer, as it is argued from causality rather than teleology. As my ninth grade biology teacher used to say, &quot;there is no 'why' in biology, only 'how'&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, it is fun to speculate! Here's my two cents in the form of a &lt;a href=&quot;http://bahfest.com/&quot; rel=&quot;nofollow&quot;&gt;Bad ad hoc Hypothesis&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Holes going into the body are an expensive and risky prospect at best for any animal. In order to maintain homeostasis they need to keep any holes constantly supplied with fresh mucus and a ton of antibodies. Total orifice count tends to be kept to a highly conserved minimum along evolutionary lineages. Thus, the reason why urinary and genital systems are merged along a single urogential tract is so that they can both efficiently share the same hole. As evidence for this view, consider the reptile: they manage to use their holes even more efficiently than we do, mating and excreting both liquid and solid waste out of their single cloaca.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="784" LastActivityDate="2015-06-17T20:28:56.330" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35301" PostTypeId="2" ParentId="35272" CreationDate="2015-06-17T21:13:18.167" Score="2" Body="&lt;p&gt;Mutations in DNA or RNA sequences do not necessarily result in significant changes in the functions of the proteins they encode (or in the case of RNA ribozymes, ribozyme function ). This is because, for a variety of reasons, the change in DNA/RNA sequence may not significantly alter the structure and function of the ribozyme/protein (the function that contributes to the fitness of the organism). If two alleles of a gene with different sequence have equivalent function (again with regard to the function of the gene that provides fitness) the differences between them are selectively neutral.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The neutral network consists of every variation in the sequence of the gene that can be reached from another sequence (of equivalent fitness) by a single base pair mutation (these aren't the only type of mutation, possible, but they are common and more likely to be neutral than more drastic changes). So for example (using an unrealistically short sequence), if I had a gene with the sequence  0 AACAATGCTGACTGA, and alleles 1 AACAATGCTGACTAA, 2 AACAATGCTGACAGA, 3 AACAATGCTGACTGG with equivalent function, 1, 2, and 3 would be directly linked to 0 in the neutral network as they all differ from 0 by a single base pair. The sequence 4 GACAATGCTGACTAA if of equivalent function would also be in the network as it differs by one base pair from sequence 1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each gene in the network being mutually accessible through mutations means that I could start out with any of the above sequences and reach any of the others through a series of single base pair mutations that traverse the network (i.e. I could mutate 0 into 4 by first mutating to 1, another network member, then to 4). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genotypic space includes the sequences of all extant alleles of the gene. &lt;a href=&quot;http://www.pnas.org/content/96/17/9716.full.pdf&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; suggests that there is a tendency for these sequences to form these networks and especially to evolve towards highly interconnected networks. This is the structural information the author refers to. It should be easy to imagine how this might confer robustness to deleterious mutation. Let's think about our sequences from above, imagine if every sequence was only linked to two other selectively neutral sequences forming a long chain. The sequence AACAATGCTGACTGA is 15 base pairs long with 45 possible single mutations, if only two of those are selectively neutral, the chance of mutating to a neutral network member is low, and even if you do hit on a neutral mutation, your chance of hitting another neutral mutation next time (reverting back or moving on down the chain) is still only 2/45. Now imagine that the neutral network is highly interconnected, with sequence 0 linked to sequences 1, 2, 3 and several other neutral 1 base pair changes, imagine those sequences are linked through each other by other neutral intermediates (being 2 base pair mutations away from 0). Not only is the chance of a single mutation being neutral higher, but subsequent mutations (remember that these include reversions from prior mutations) are more likely to stay within the network (you're more likely to come back around to 0. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would you have more long-term success walking around a fitness plateau or walking across a fitness rope suspended over the abyss?&lt;/p&gt;&#xA;" OwnerUserId="16147" LastEditorUserId="4108" LastEditDate="2015-06-17T21:54:20.167" LastActivityDate="2015-06-17T21:54:20.167" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35307" PostTypeId="1" AcceptedAnswerId="35308" CreationDate="2015-06-18T01:35:44.680" Score="7" ViewCount="3742" Body="&lt;p&gt;&lt;a href=&quot;http://rt.com/news/267310-white-blood-cells-death/&quot; rel=&quot;nofollow&quot;&gt;This simplified video and RT.com article&lt;/a&gt; discusses how the mechanics of the death of a white blood cell can be useful as an &quot;alert mechanism&quot; to other white blood cells of an incoming infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also in the article it describes how this same notification mechanism might enable the transmission of certain types of pathogens and it has the following quote:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;We found that a commonly used antidepressant can block this whole process and an antibiotic can promote this event,” said Ms Atkin-Smith.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://www.nature.com/ncomms/2015/150615/ncomms8439/full/ncomms8439.html&quot; rel=&quot;nofollow&quot;&gt;full report is available here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone explain, (with a summary in layman terms) the impact of Sertraline on white blood cells? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does taking Sertraline increase the risk of susceptibility to illness, or decrease it? &lt;/p&gt;&#xA;" OwnerUserId="5399" LastEditorUserId="9943" LastEditDate="2015-06-18T02:44:55.053" LastActivityDate="2017-01-09T11:39:26.037" Title="What is the impact of sertraline on white blood cells?" Tags="&lt;immunology&gt;&lt;antibiotics&gt;&lt;immunosuppression&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35308" PostTypeId="2" ParentId="35307" CreationDate="2015-06-18T02:07:01.657" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;While sertraline may theoretically affect the immune system, there is no evidence, as far as I know, that it negatively impacts immune status.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;In the article (&lt;a href=&quot;http://www.nature.com/ncomms/2015/150615/ncomms8439/full/ncomms8439.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Atkin-Smith et al., 2015&lt;/a&gt;) sertraline (a.k.a. Zoloft, an antidepressant) is shown to block the formation of ‘beads-on-a-string’ protrusions and apoptotic bodies after from dying white blood cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Generally, when cells die physiologically, they do not just disintegrate, they undergo programmed cell death called &lt;a href=&quot;https://en.wikipedia.org/wiki/Apoptosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;apoptosis&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AVVNk.jpg&quot; alt=&quot;beads-on-a-string&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Beads-on-a-string from a apoptotic monocyte. Source: (&lt;a href=&quot;http://www.nature.com/ncomms/2015/150615/ncomms8439/full/ncomms8439.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Atkin-Smith et al., 2015&lt;/a&gt;).&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The authors hypothesize that these beads-on-a-string and apoptotic bodies may boost &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000821.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;immune responses&lt;/a&gt; by containing &lt;a href=&quot;https://en.wikipedia.org/wiki/Antigen&quot; rel=&quot;nofollow noreferrer&quot;&gt;antigenic&lt;/a&gt; material, or that they may contain a warning signal for other immune cells that a &lt;a href=&quot;http://www.iaff.org/hs/resi/infdis/what_is_a_pathogen.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;pathogen&lt;/a&gt; is on the loose.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These claims, however, are hypotheses. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are many reported &lt;a href=&quot;http://www.drugs.com/sfx/sertraline-side-effects.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;side effects of sertaline&lt;/a&gt;, but &lt;a href=&quot;https://en.wikipedia.org/wiki/Immunosuppression&quot; rel=&quot;nofollow noreferrer&quot;&gt;immune suppressant&lt;/a&gt; effects are not evident. The only side effects reported touching on it are, e.g., a fever and a sore throat. However, such general symptoms can be caused by a variety of causes and were not reported frequently. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Indeed, in a small study in &lt;a href=&quot;https://en.wikipedia.org/?title=HIV&quot; rel=&quot;nofollow noreferrer&quot;&gt;HIV patients&lt;/a&gt;, sertraline showed no adverse effects on the immune system &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7961520&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Rabkin &lt;em&gt;et al&lt;/em&gt;., 1994)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.nature.com/ncomms/2015/150615/ncomms8439/full/ncomms8439.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Atkin-Smith &lt;em&gt;et a. Nat Comm&lt;/em&gt; (2015); &lt;strong&gt;6&lt;/strong&gt;: 7439&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7961520&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rabkin &lt;em&gt;et al. J Clin Psychiatry&lt;/em&gt; (1994); &lt;strong&gt;55&lt;/strong&gt;(10):433-9&lt;/a&gt;  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-18T13:41:58.837" LastActivityDate="2015-06-18T13:41:58.837" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35309" PostTypeId="1" AcceptedAnswerId="35310" CreationDate="2015-06-18T03:40:30.040" Score="4" ViewCount="617" Body="&lt;p&gt;I'm no biologist, but I'm curious what the rough phylogenetic tree looks like for Hominin.  Could you create a rough sketch that includes:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Homo rudolfensis&lt;/li&gt;&#xA;&lt;li&gt;Homo ergaster&lt;/li&gt;&#xA;&lt;li&gt;H. georgicus&lt;/li&gt;&#xA;&lt;li&gt;H. antecessor&lt;/li&gt;&#xA;&lt;li&gt;H. cepranensis&lt;/li&gt;&#xA;&lt;li&gt;H. rhodesiensis&lt;/li&gt;&#xA;&lt;li&gt;Homo neanderthalensis&lt;/li&gt;&#xA;&lt;li&gt;Denisova hominin&lt;/li&gt;&#xA;&lt;li&gt;Homo floresiensis&lt;/li&gt;&#xA;&lt;li&gt;H. heidelbergensis&lt;/li&gt;&#xA;&lt;li&gt;H. neanderthalensis&lt;/li&gt;&#xA;&lt;li&gt;H. sapiens&lt;/li&gt;&#xA;&lt;li&gt;H. erectus&lt;/li&gt;&#xA;&lt;li&gt;H. habilus&lt;/li&gt;&#xA;&lt;li&gt;any others I may have missed&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Feel free to correct any incorrect assumptions I may have made here, or clarify anything that could be instructive.&lt;/p&gt;&#xA;" OwnerUserId="16277" LastEditorUserId="9943" LastEditDate="2015-06-18T04:08:20.263" LastActivityDate="2015-06-18T04:08:20.263" Title="What does the hominin phylogenetic tree look like?" Tags="&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35310" PostTypeId="2" ParentId="35309" CreationDate="2015-06-18T04:01:05.537" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://www.mef.org.ar/~muspal/images/stories/investigacion/iescapa_docs/gonzales_et_al_2008.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gonzalez-Jose &lt;em&gt;et al.&lt;/em&gt; (2008)&lt;/a&gt; published the following cladograms, based on two analyses (parsimony versus maximum likelihood). The table shows the legend. The interesting case of &lt;em&gt;Homo floriensis&lt;/em&gt;, among others are not included, likely because of their recent discoveries and limitations of the study cited.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/N3hdS.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/h3Wye.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.mef.org.ar/~muspal/images/stories/investigacion/iescapa_docs/gonzales_et_al_2008.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gonzalez-Jose &lt;em&gt;et al. Nature&lt;/em&gt; (2008); &lt;strong&gt;453&lt;/strong&gt; 775-79&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-06-18T04:01:05.537" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35311" PostTypeId="1" AcceptedAnswerId="35327" CreationDate="2015-06-18T04:11:27.027" Score="1" ViewCount="275" Body="&lt;p&gt;I'm a computational physicist by trade, and today I was working with a student that is coding a simulation that requires the interactions of different genotypes to determine which phenotype will be expressed. This student drew a Punnent Square like so:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$&#xA;\begin{equation}&#xA;\begin{matrix}&#xA;&amp;amp; O &amp;amp; Y \\ &#xA;\_ &amp;amp;\_ &amp;amp; \_ \\ &#xA;Y&amp;amp; |YO&amp;amp; YY \\B &amp;amp;|BO &amp;amp; BY &#xA;\end{matrix}&#xA;\end{equation}&#xA;$  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;and then stated that each genotype should have a 25% probability of being expressed. I remember learning this as well in highschool bio, but since finishing my Bachelor's in Physics (with some focus on complex adaptive systems/chaos theory) I am a bit skeptical that biology &lt;em&gt;really&lt;/em&gt; obeys the probabilities of the Punnet Square. Are there examples in biology where the probabilities of the Punnet Square are clearly broken?&lt;/p&gt;&#xA;" OwnerUserId="16278" LastEditorUserId="16278" LastEditDate="2015-06-18T14:45:49.523" LastActivityDate="2015-06-18T16:11:11.437" Title="Punnet Square for Genotype Probabilities" Tags="&lt;genomics&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35314" PostTypeId="2" ParentId="34601" CreationDate="2015-06-18T07:09:55.250" Score="2" Body="&lt;p&gt;Most restriction enzymes have a 6bp restriction site (some have 8bp site also). So two restriction sites generally have to span 12bp. However some restriction sites can overlap. For example BamHI and SmaI:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&#xA;BamHI&#xA;|&lt;sup&gt;______&lt;/sup&gt;|&#xA;GGATCCCGGG&#xA;    |&lt;sup&gt;______&lt;/sup&gt;|&#xA;     SmaI&#xA;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;In this case the total length has reduced to 10bp. However such combinations are not that common and at max you will achieve a 2-3bp overlap. A restriction endonuclease only makes a single cut. To make double cuts you need two restriction sites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if the sites are non-overlapping there has to be a minimum length of separation otherwise the binding of one enzyme will hinder the binding of the other enzyme in a double digest. A 6 nucleotide gap between the restriction sites should be fine. If there is no gap then double digest may not be very efficient. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also have two restriction sites of the same enzyme so that you need not use two separate enzymes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW the sequence in your question does not have any restriction site. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this answers your question.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-06-18T07:09:55.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35316" PostTypeId="1" CreationDate="2015-06-18T07:42:09.397" Score="4" ViewCount="1008" Body="&lt;p&gt;As far as I know there is no absolute time measurement (one that would measure time in a non-environment-dependent fashion) in any life form. Only such time measurements exist, which are dependent upon cyclic changes like the strength of the sunlight, heat, amount of water, etc. (In case this assumption of mine is false, than please answer it in mind of life forms which in deed have only relative)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Theoretically, if we could change everything a given life form is dependent upon, could we increase it's entire lifespan?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example if we were to put a plant inside a manually controllable environment and slow down the day/night cycle to it's third, maybe even decrease air pressure and the strength of gravity(thus eliminating any problem that might arise from the actual transport of water and the solution of organic matters produced in photosynthesizing cells), change (even though I'm not sure if this could be physically possible at all, but my whole question is theoretical, thus it should not cause a problem) the adhesion/cohesion as well (so the speed of transports in the cells would change accordingly) and change other, (for me) unthinkable aspects that, for example, regulates the time between cell divisions, would it live for longer?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if we could not change every aspect that regulates a given life form's working, changing many could we (although this time not linearly) increase it's actual lifespan?&lt;/p&gt;&#xA;" OwnerUserId="15051" LastEditorUserId="3624" LastEditDate="2015-06-18T09:11:36.050" LastActivityDate="2015-06-18T14:37:20.407" Title="Could we slow down life?" Tags="&lt;ecology&gt;&lt;development&gt;&lt;life-history&gt;&lt;lifespan&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="4" ClosedDate="2015-06-18T14:47:59.430" ContentLicense="CC BY-SA 3.0" />
  <row Id="35317" PostTypeId="2" ParentId="35316" CreationDate="2015-06-18T08:11:46.243" Score="8" Body="&lt;p&gt;&lt;strong&gt;Short answer:&lt;/strong&gt; Changing something (instead of everything) yes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several studies on the impact of environmental factors on life span.&#xA;Of course &lt;strong&gt;it depends from organism to organism&lt;/strong&gt;. Diet restriction for example has been shown to extend life span of worms and mice. Temperature is also working well, at least with microorganisms, the metabolism of E.coli for example (that usually grows at 37 Celsius) can be greatly slowed down at lower temperatures. Also, there are enzymes involved in the &quot;ageing pathway&quot; some of these enzymes can be promoted or repressed by small molecules, like resveratrol does, and as result you get some increment in life span. The opposite is also true, you can accelerate ageing with external factors. For plants works as well, changing the environment you can definitely have an effect on the life span and the overall metabolism rate, indeed tricking the light cycle is a very well known method to induce flowering for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here some interesting links if you wanna dig more into this topic.&#xA;&lt;a href=&quot;http://web.mit.edu/biology/guarente/&quot; rel=&quot;nofollow&quot;&gt;http://web.mit.edu/biology/guarente/&lt;/a&gt;&#xA;&lt;a href=&quot;http://genetics.med.harvard.edu/sinclair/&quot; rel=&quot;nofollow&quot;&gt;http://genetics.med.harvard.edu/sinclair/&lt;/a&gt;&#xA;&lt;a href=&quot;http://www.ted.com/talks/cynthia_kenyon_experiments_that_hint_of_longer_lives?language=en&quot; rel=&quot;nofollow&quot;&gt;http://www.ted.com/talks/cynthia_kenyon_experiments_that_hint_of_longer_lives?language=en&lt;/a&gt;&#xA;&lt;a href=&quot;http://jxb.oxfordjournals.org/content/58/12/3099.full&quot; rel=&quot;nofollow&quot;&gt;http://jxb.oxfordjournals.org/content/58/12/3099.full&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12923" LastEditorUserId="12923" LastEditDate="2015-06-18T12:24:05.507" LastActivityDate="2015-06-18T12:24:05.507" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35318" PostTypeId="2" ParentId="35316" CreationDate="2015-06-18T08:12:33.940" Score="0" Body="&lt;p&gt;First, I find this too broad, speculative and opinion-based to be suitable for the SE format. You mention a huge number of processes, which will also interact with eachother.&lt;/p&gt;&#xA;&lt;p&gt;However, taking a general view, life span and generation time can definitely be increased. Changes in temperature and nutrition will often change the metabolic rates and growth rate of organisms, but the actual effect will depend on which organism you are looking at. For instance, the length of the larval stage of many longhorn beetles can increase by several years in colder climates or site conditions, under shorter growing seasons and/or poor wood substrates, compared to ideal conditions or warmer microclimates. The mechanism here is often lower activity levels or lower nutrient contents, leading to lower growth rates, which means that it will take more time before the larvae reaches maturity. This means that individuals of the same species (also the same genotype) may have a life span of 6 years in one location and 2 ys in another location. This is just a single example, and lots of similar processes can also be found in other organism groups, especially considering the large number of factors that you mention in your question.&lt;/p&gt;&#xA;&lt;h3&gt;References:&lt;/h3&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Bilý, S. &amp;amp; Mehl, O. 1989. Longhorn Beetles (Coleoptera, Cerambycidae) of Fennoscandia and Denmark. Fauna Ent. Scand. Vol. 22: 47–48.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Cherepanov, A.I. 1990. Cerambycidae of Northern Asia. Leiden, The Netherlands: E.J. Brill Publishing Company.&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-18T12:10:40.853" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35319" PostTypeId="1" CreationDate="2015-06-18T08:20:25.763" Score="4" ViewCount="917" Body="&lt;p&gt;I would like to know, with references from the literature, what is the half life of a linear dsDNA transfected in a mammalian cells.&#xA;For example, if I transfect human cells with a PCR product (500-2000 bp), that does not contain any replication or transcription signal, how fast will it be degraded by the cell (hours, days, weeks...)? Is there any difference in the half life if the DNA is in the cytosol or in the nucleus?&lt;/p&gt;&#xA;" OwnerUserId="12923" LastActivityDate="2019-02-08T00:10:33.217" Title="How stable is linear DNA transfected in eukaryotic cells?" Tags="&lt;dna&gt;&lt;eukaryotic-cells&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35320" PostTypeId="1" CreationDate="2015-06-18T10:20:13.573" Score="3" ViewCount="182" Body="&lt;p&gt;What is the longest observed lifespan of a mosquito, especially of the species &lt;em&gt;Anopheles arabiensis&lt;/em&gt;? How long does it take for &lt;em&gt;Plasmodium&lt;/em&gt; parasites to develop and move into the salivary glands of these mosquitoes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I need this information to calibrate my model on malaria transmission.&lt;/p&gt;&#xA;" OwnerUserId="16265" LastEditorUserId="9829" LastEditDate="2015-06-18T21:02:16.000" LastActivityDate="2018-04-24T22:30:37.820" Title="Anopheles arabiensis lifespan and sporogony duration" Tags="&lt;entomology&gt;&lt;mathematical-models&gt;&lt;epidemiology&gt;&lt;death&gt;&lt;malaria&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35321" PostTypeId="1" AcceptedAnswerId="35324" CreationDate="2015-06-18T11:13:36.327" Score="-3" ViewCount="216" Body="&lt;p&gt;Consider a natural cause of death (no car accidents etc) -&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it true that death is generally preceded by suffering? In other words, are we destined to experience the most severe suffering we could not ever imagine, that will ultimately end with death?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is true, is it true for all living things?&lt;/p&gt;&#xA;" OwnerUserId="10490" LastEditorUserId="9943" LastEditDate="2015-06-18T12:09:03.893" LastActivityDate="2015-06-18T12:19:44.463" Title="Normal death experience" Tags="&lt;pain&gt;&lt;death&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2015-06-18T12:26:06.557" ContentLicense="CC BY-SA 3.0" />
  <row Id="35322" PostTypeId="1" CreationDate="2015-06-18T11:50:09.193" Score="1" ViewCount="55" Body="&lt;p&gt;Is it possible that the DNA of an individual changes significantly over a period ?&lt;/p&gt;&#xA;" OwnerUserId="16285" LastActivityDate="2015-06-18T11:50:09.193" Title="Is it possible that the DNA of an individual changes significantly over a period?" Tags="&lt;dna&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2015-06-18T13:45:37.843" ContentLicense="CC BY-SA 3.0" />
  <row Id="35324" PostTypeId="2" ParentId="35321" CreationDate="2015-06-18T12:19:44.463" Score="1" Body="&lt;p&gt;No and no.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure what is a &quot;natural cause&quot; in this context, but if it's cardiac arrest caused by age-related dystrophy of the cardiac muscles, then no, there is no suffering, at least not universally: Since age-related dystrophy hits all parts of the body, it's likely preceded by increasing amounts of bed rest, leading to quietly drifting off into the great sleep.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, if you add on other natural causes like age-related diseases or being eaten by predators, the suffering can be great indeed, or not: A tiger will sneak up on you and crush your skull without you ever knowing what happened.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adding on further causes still, like dehydration or hunger, and the suffering is back.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But is suffering a universal fixture of death? Emphatically no.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for the &quot;all living things&quot; part of the question, the answer isn't just &quot;no&quot;; it's &quot;that's nonsensical&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By individual count, practically no life is complex enough for suffering to be a relevant concept.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't have an exact number for you, because how would I get one, but at a rough estimate, bacteria, algae and archea constitute 100% of all individual life forms by count, and suffering is not a concept that makes sense for them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we ignore simple life, even among complex life there is so much variety of capabilities that basically &lt;em&gt;nothing&lt;/em&gt; universal exists.&lt;/p&gt;&#xA;" OwnerUserId="1095" LastActivityDate="2015-06-18T12:19:44.463" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35325" PostTypeId="1" CreationDate="2015-06-18T13:21:38.877" Score="3" ViewCount="1420" Body="&lt;p&gt;The genome size of human is 3.000.000.000 bp and for Arabidopsis it is 255.000.000 bp. I know these numbers because their genomes have been published. Which methods are used by scientists to estimate the genome size before they sequence that genome?&lt;/p&gt;&#xA;" OwnerUserId="1916" LastEditorUserId="9099" LastEditDate="2015-06-18T14:41:29.660" LastActivityDate="2015-06-19T07:02:25.930" Title="How to estimate a genome's size?" Tags="&lt;genomes&gt;" AnswerCount="3" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35326" PostTypeId="2" ParentId="35311" CreationDate="2015-06-18T13:28:27.187" Score="0" Body="&lt;p&gt;The clearest example of a Mendelian exception (in my opinion) are &lt;a href=&quot;http://www.biotecharticles.com/Genetics-Article/Lethal-Alleles-Its-Instances-in-Humans-Plants-and-Animals-2144.html&quot; rel=&quot;nofollow&quot;&gt;lethal alleles&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your example, let's say that the $YY$ phenotype causes a fatal phenotype &lt;em&gt;in utero&lt;/em&gt; (in humans, &lt;a href=&quot;https://en.wikipedia.org/wiki/Achondroplasia&quot; rel=&quot;nofollow&quot;&gt;Achondroplasia&lt;/a&gt; is fatal for homozygotes). Your Punnett square might instead look something like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$&#xA;\begin{equation}&#xA;\begin{matrix}&#xA;&amp;amp; O &amp;amp; Y \\ &#xA;\ &amp;amp;\_ &amp;amp; \_ \\ &#xA;Y&amp;amp; |YO&amp;amp; ☹ \\B &amp;amp;|BO &amp;amp; BY &#xA;\end{matrix}&#xA;\end{equation}&#xA;$  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This would also change your observed population proportions, rather than seeing the typical ~25% (1:3 ratio) you'll start to see a ~33% (1:2 ratio) population segmentation, which is a good indication that something fishy is going on. This can happen with both dominant (Achondroplasia) and negative alleles (&lt;a href=&quot;https://en.wikipedia.org/wiki/Hypophosphatasia&quot; rel=&quot;nofollow&quot;&gt;Hypophosphatasia&lt;/a&gt;). In the case of a dominant allele like Achondroplasia, heterozygotes show a phenotype (dwarfism) but only the homozygous genotype is immediately fatal.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-06-18T13:28:27.187" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35327" PostTypeId="2" ParentId="35311" CreationDate="2015-06-18T13:48:56.387" Score="1" Body="&lt;p&gt;Our germ cells are haploid, while our somatic cells are diploid. The diploid cells of a child result from the fusion of a paternal haploid germ cell and a maternal haploid germ cell. When these germ cells are generated during meiosis, the paired diploid chromosomes of each parent (which they in turn received one of from each parent) are randomly segregated such that for a given chromosomal pair there is an approximately equal chance of a given germ cell containing either member of the pair independent of the what other chromosomes it receives.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of a single gene with a single copy on both the maternal and paternal chromosomes, the Punnet Square accurately estimates the probably of inheriting each possible &lt;strong&gt;genotype.&lt;/strong&gt; (50% chance of getting one of two alleles from dad * 50% chance of getting one of two alleles from mom). In the case of multiple genes on different chromosomes, the 50% chance of any given allele still holds, as all the genes segregate independently. &lt;em&gt;The accuracy of the Punnet Square fails when genes are sufficiently close to each other on the same chromosome. Genes distant from each other on the same chromosome still segregrate independently due to a high level of recombination events between chromosomes in meiosis I, but genes in close physical proximity no longer segregate independently. The closer two genes are physically the more they tend to co-segregate. This tendency is reported empirically as a &quot;distance&quot; in centiMorgans and is related to physical distance in base pairs (kB or mB) but is not completely proportional to physical distance due to the existence of recombination &quot;hot spots.&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's important to note that is accurately predicts genotypic ratios, but not necessarily phenotype. Phenotypes can be less than 100% penetrant, can cause embryonic lethal, epistasis, etc. Such that the observed phenotypic ratio does not match the predicted ratio. (For example, if YY was known to be 100% embryonic lethality, live births -&gt; observed phenotypes instead be expected at 1/3 of each of the remaining genotypes. If Y was instead phenotypically dominant (one copy of Y determines phenotype), then 75% of children would be expected to be phenotypically Y (genotypically, the Y phenotypic children would be expected to distribute evenly between YO, YY, BY).&lt;/p&gt;&#xA;" OwnerUserId="16147" LastEditorUserId="16147" LastEditDate="2015-06-18T16:11:11.437" LastActivityDate="2015-06-18T16:11:11.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35328" PostTypeId="2" ParentId="35325" CreationDate="2015-06-18T13:54:46.423" Score="-1" Body="&lt;p&gt;I guess you could estimate the length various ways. Pulse field electrophoresis could show DNA length, but you need a standard. &#xA;When you combine Karyogram and FISH, you would could make a map. By genetical approaches, you could estimate distance on the map by centimorgan. Then you could know how many centimorgan chromosomes are. One centimorgan would be 1 million base pairs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oh, I forgot the simplest way. For example, take 1 million cells and estimate how many grams of DNA there. &lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-06-18T14:12:31.270" LastActivityDate="2015-06-18T14:12:31.270" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35329" PostTypeId="2" ParentId="35325" CreationDate="2015-06-18T13:56:02.130" Score="3" Body="&lt;p&gt;Gel electrophoresis is a basic lab method to get size info about nucleotide fragments, although one might need to chop up larger DNA to be able to apply this method. The &lt;a href=&quot;https://en.wikipedia.org/?title=Gel_electrophoresis&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; page covers the topic well, thus I'd suggest reading it. I'll just give a short outline:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Nucleotide fragments are loaded into a gel (agarose or acrylamide). &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The gel is put into a static electric field &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;Nucleotide fragment move to the positive end, because they have negative charge&lt;/li&gt;&#xA;&lt;li&gt;larger fragments migrate slower than smaller fragments&lt;/li&gt;&#xA;&lt;li&gt;standardized DNA ladder can be used to get approx size.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;UV fluorescent dye is used to stain the fragments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way, is to check closely related species. Among closely related species it is a fair assumption that they have similar genome size. You can also hybridize the unknown DNA to a DNA of such close relative to see how much of them are similar and you can also make estimates based on the size of the hybridized regions.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-06-19T07:02:25.930" LastActivityDate="2015-06-19T07:02:25.930" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35330" PostTypeId="1" CreationDate="2015-06-18T14:16:37.973" Score="8" ViewCount="3475" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/su6bT.png&quot; alt=&quot;Genetic Relationship Matrix&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genetic relationship matrix (GRM) can estimate the genetic relationship between two individuals ($j$ and $k$) over $m$ SNPs and $i$ representing a specific SNP. What I don't understand from their equation is why we divide our summation by $m$ (the number of SNPs). $x_{ij}$ is the number of copies of the minor allele for the $j$-th individual in SNP $i$. $p_i$ is the frequency of the minor allele for SNP $i$.&lt;/p&gt;&#xA;" OwnerUserId="16289" LastEditorUserId="15950" LastEditDate="2017-06-24T16:34:24.853" LastActivityDate="2020-12-15T16:57:35.917" Title="Math behind the Genetic Relationship Matrix" Tags="&lt;genetics&gt;" AnswerCount="4" CommentCount="4" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35333" PostTypeId="2" ParentId="35330" CreationDate="2015-06-18T15:07:45.887" Score="9" Body="&lt;p&gt;This expression is a mean&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$\frac{1}{m}\sum_{i=1}^m ...$$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;(&lt;span class=&quot;math-container&quot;&gt;$m$&lt;/span&gt; is the number of SNPs) of the ratio&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$\frac{numerator}{denominator}$$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;where the numerator is a covariance&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$(a_i-C)(b_i-C)$$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;and the denominator is the expected heterozygosity (it is also the variance of binomial distribution with &lt;code&gt;n=2&lt;/code&gt;)&lt;/p&gt;&#xA;&lt;p&gt;&lt;span class=&quot;math-container&quot;&gt;$$2p_i(1-p_i)$$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;p&gt;Therefore, it represents how much do two individuals covary &lt;span class=&quot;math-container&quot;&gt;$(x_{ij})(x_{ik}-p_i)$&lt;/span&gt; respectively to what is expected on average &lt;span class=&quot;math-container&quot;&gt;$2p_i(1-p_i)$&lt;/span&gt; averaged over all SNPs &lt;span class=&quot;math-container&quot;&gt;$\frac{1}{m}\sum_{i=1}^m...$&lt;/span&gt;, where &lt;span class=&quot;math-container&quot;&gt;$m$&lt;/span&gt; is the number of SNPs.&lt;/p&gt;&#xA;&lt;p&gt;It is a relative measure (relative to the expected heterozygosity) of covariance between each individual (averaged over all SNPs).&lt;/p&gt;&#xA;&lt;p&gt;Does it help?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2020-12-07T08:05:30.037" LastActivityDate="2020-12-07T08:05:30.037" CommentCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="35334" PostTypeId="2" ParentId="24458" CreationDate="2015-06-18T15:53:46.863" Score="2" Body="&lt;p&gt;&quot;The flicker fusion frequencies of six laboratory insects, and the response of the compound eye to mains fluorescent ‘ripple’&quot; (&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1365-3032.1978.tb00139.x/abstract&quot; rel=&quot;nofollow&quot;&gt;Miall, 1978&lt;/a&gt;) touches on flicker fusion thresholds for six different insect species commonly used in laboratory settings:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Locusta migratoria&lt;/em&gt;, &lt;em&gt;Periplaneta americana&lt;/em&gt;, &lt;em&gt;Saturnia pavonia&lt;/em&gt;, &lt;em&gt;Antheraea pernyi&lt;/em&gt;, &lt;em&gt;Glossina morsitans&lt;/em&gt; and &lt;em&gt;Drosophila hydei&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I also found this paper: Potential Biological and Ecological Effects of Flickering Artificial Light (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4038456/&quot; rel=&quot;nofollow&quot;&gt;Boyles, 2014&lt;/a&gt;) that includes an exhaustive literature search of flicker-fusion thresholds and other related data for many species (including insects). If you're looking for an authoritative source, I'd say that this is it (as there doesn't seem to be a database with this information).&lt;/p&gt;&#xA;" OwnerUserId="9829" LastEditorUserId="9829" LastEditDate="2015-06-20T20:27:35.583" LastActivityDate="2015-06-20T20:27:35.583" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35337" PostTypeId="1" AcceptedAnswerId="35353" CreationDate="2015-06-18T17:04:04.157" Score="18" ViewCount="20920" Body="&lt;p&gt;Across the electromagnetic spectrum, 400-700 nm is a narrow spectrum of frequencies and focused in the region of short wavelengths. For example, radio waves cover a large range of frequencies unexploited by the visual system. So what biological reason is there that evolved us to use such a small frequency bandwidth for vision?&lt;/p&gt;&#xA;" OwnerUserId="16294" LastEditorUserId="9943" LastEditDate="2015-06-19T02:18:52.063" LastActivityDate="2020-08-15T04:31:48.727" Title="Why is human vision restricted to 400-700 nm?" Tags="&lt;vision&gt;&lt;human-eye&gt;&lt;light&gt;" AnswerCount="6" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35339" PostTypeId="2" ParentId="35320" CreationDate="2015-06-18T17:22:39.143" Score="2" Body="&lt;p&gt;&lt;strong&gt;What is the longest observed lifespan of a mosquito, especially of the species &lt;em&gt;Anopheles arabiensis&lt;/em&gt;?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mean lifespan calculations for &lt;em&gt;Anopheles arabiensis&lt;/em&gt; range from 14 days (&lt;a href=&quot;http://ir.jkuat.ac.ke/bitstream/handle/123456789/1337/Karoki,%20SM-%20Msc%20Epidemeiology%20and%20Lab.pdf&quot; rel=&quot;nofollow&quot;&gt;Karoki, 2013&lt;/a&gt;)* to 21 days (&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0001706X14003829&quot; rel=&quot;nofollow&quot;&gt;Yamada &lt;em&gt;et al&lt;/em&gt;. 2014&lt;/a&gt;)**&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*This Masters thesis tests efficacy of different drugs against &lt;em&gt;An. arabiensis&lt;/em&gt;, 14 days is the mean control lifespan.&lt;br&gt;&#xA;**These &lt;em&gt;An. arabiensis&lt;/em&gt; are of a specific strain but no indication is given that the life span is different than normal &lt;em&gt;An. arabiensis&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The CDC &lt;a href=&quot;http://www.cdc.gov/malaria/about/biology/mosquitoes/index.html&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Anopheles&lt;/em&gt; mosquito page&lt;/a&gt; is another good source for information on &lt;em&gt;Anopheles&lt;/em&gt; life spans:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The adult females can live up to a month (or more in captivity) but most probably do not live more than 1-2 weeks in nature.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How long does it take for &lt;em&gt;Plasmodium&lt;/em&gt; parasites to develop and move into the salivary glands of these mosquitoes?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;US &lt;a href=&quot;http://www.niaid.nih.gov/topics/malaria/pages/lifecycle.aspx&quot; rel=&quot;nofollow&quot;&gt;National Institutes of Health&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Growth and division of each oocyst produces thousands of active haploid forms called sporozoites. After 8-15 days, the oocyst bursts, releasing sporozoites into the body cavity of the mosquito, from which they travel to and invade the mosquito salivary glands.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.phsource.us/PH/PARA/Chapter_9.htm&quot; rel=&quot;nofollow&quot;&gt;United States Air Force&lt;/a&gt; (USAF):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The length of the developmental stage in the mosquito not only depends on the &lt;em&gt;Plasmodium&lt;/em&gt; species but also the mosquito host and the ambient temperature.  This may range from eight days in &lt;em&gt;Plasmodium vivax&lt;/em&gt; to as long as 30 days in &lt;em&gt;Plasmodium malariae&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Wikipedia (&lt;a href=&quot;https://en.wikipedia.org/wiki/Plasmodium_falciparum_biology#Mosquito_stage&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Plasmodium falciparum&lt;/em&gt;&lt;/a&gt;) :&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Over the period of a 1–3 weeks, the oocyst grows to a size of tens to hundreds of micrometres... The sporozoites then migrate to the salivary glands and complete their differentiation. Once mature, the sporozoites can proceed to infect a human host during a subsequent mosquito bite.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;US &lt;a href=&quot;http://www.cdc.gov/malaria/about/biology/&quot; rel=&quot;nofollow&quot;&gt;Center for Disease Control&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After 10-18 days, the parasites are found (as &quot;sporozoites&quot;) in the mosquito's salivary glands. When the &lt;em&gt;Anopheles&lt;/em&gt; mosquito takes a blood meal on another human, the sporozoites are injected with the mosquito's saliva and start another human infection when they parasitize the liver cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Overall&lt;/strong&gt;, it depends who you ask, but especially on the species of &lt;em&gt;Plasmodium&lt;/em&gt; you're working with. I'd look for specific papers on the development cycle you're modeling and run with it.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-06-18T17:22:39.143" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35340" PostTypeId="1" AcceptedAnswerId="35341" CreationDate="2015-06-18T17:23:54.010" Score="1" ViewCount="640" Body="&lt;p&gt;I've had an Araucaria tree in my garden for more than 30 years.&#xA;Today a fruit fell off the tree. It looks just like this one:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/n5UGq.jpg&quot; alt=&quot;Araucaria fruit&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to know if it is toxic?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can I eat it? If so, how?&lt;/p&gt;&#xA;" OwnerUserId="16295" LastEditorUserId="9829" LastEditDate="2015-06-18T21:01:36.687" LastActivityDate="2015-06-18T21:01:36.687" Title="Is Araucaria fruit toxic?" Tags="&lt;botany&gt;&lt;toxicology&gt;&lt;fruit&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2015-06-19T12:59:19.400" ContentLicense="CC BY-SA 3.0" />
  <row Id="35341" PostTypeId="2" ParentId="35340" CreationDate="2015-06-18T17:33:30.927" Score="4" Body="&lt;p&gt;&lt;em&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Araucaria_araucana&quot; rel=&quot;nofollow noreferrer&quot;&gt;Araucaria araucana&lt;/a&gt;&lt;/em&gt; is an evergreen. The pictured &quot;fruit&quot; is actually more of a cone (which I don't think you'd want to eat). However, the seeds are edible, and look like this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FaMPv.jpg&quot; alt=&quot;Araucaria seeds&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let the cone dry and it should open up.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-06-18T17:33:30.927" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35342" PostTypeId="2" ParentId="35337" CreationDate="2015-06-18T21:06:19.013" Score="-3" Body="&lt;p&gt;These wavelengths happen to satisfy two conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, shorter wavelength photons (EM radiation) tend to be dangerous for biology. Even UV light (&amp;lt;350nm) is already can damage DNA. That is due to the fact that bond energies in biological molecules tend to have values close to energy of short-wavelength EM radiation. These is why high-energy particles called ionizing radiation. For reference, see &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/jp049270k&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper&lt;/a&gt;. ionization energy for DNA estimated in 4-5eV range, which is 300-250nm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, on low-energy hand of spectrum, water absorbs a lot of IR radiation:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/KgufS.jpg&quot; alt=&quot;Water absorption spectrum&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, as you can see, what we see &lt;em&gt;aka&lt;/em&gt; visible spectrum is sitting nicely in valley of water absorption but does not extend to area of harsh UV light that will damage chemicals of your body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, why is that so? Because atoms have these masses and electrons around them have these energies. So bonds and molecular interactions have these values.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(In radio range of frequencies you, opposite to UV, have not enough energy to elicit any significant molecular changes, which is why you can't perceive WiFi)&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-06-18T22:56:08.810" LastActivityDate="2015-06-18T22:56:08.810" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35343" PostTypeId="2" ParentId="35337" CreationDate="2015-06-18T22:04:45.267" Score="-2" Body="&lt;p&gt;&quot;Visible light&quot; is the wavelength of the light that we can see, if human beings could see UV or IR, those wavelengths had been included in the &quot;visible light&quot; definition.&#xA;Now, our Sun is brightest in yellow-green light, which (you guess?) is right in the midle of the &quot;visible light&quot; spectrum. So the only remaining question is: &quot;Why can we only see that short spectrum?&quot; The answer is EVOLUTION.&#xA;The same reason that made us to have only 5 fingers in our hands, only 2 eyes and only two kidneys.&#xA;The bandwith of the &quot;visible spectrum&quot; is enough to make the human beings (as specie) survive.&lt;/p&gt;&#xA;" OwnerUserId="16296" LastEditorUserId="16296" LastEditDate="2015-06-18T23:08:28.370" LastActivityDate="2015-06-18T23:08:28.370" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35345" PostTypeId="1" AcceptedAnswerId="35346" CreationDate="2015-06-18T22:26:23.427" Score="5" ViewCount="431" Body="&lt;p&gt;Building on &lt;a href=&quot;https://biology.stackexchange.com/questions/13600/where-does-all-the-carbon-go&quot;&gt;this question&lt;/a&gt;, &#xA;I understand pretty clearly why forests are carbon sinks (trees grow, and there is carbon stored in soil and biomass). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about the oceans, though? Are underwater plants the real actors here?&lt;/p&gt;&#xA;" OwnerUserId="16187" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2016-12-15T00:25:00.973" Title="Why are oceans carbon sinks?" Tags="&lt;photosynthesis&gt;&lt;marine-biology&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35346" PostTypeId="2" ParentId="35345" CreationDate="2015-06-18T22:59:43.287" Score="7" Body="&lt;p&gt;Check out the excellent Wikimedia picture of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Carbon_cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;carbon cycle&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Y5mkM.jpg&quot; alt=&quot;carbon cycle&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All the numbers are in billions of tons of carbon: white = stored, yellow = natural flux, red = human contribution. Notice that the deep ocean stores much more accessible carbon than &lt;em&gt;any&lt;/em&gt; other carbon cycle source, and is only surpassed by the &lt;a href=&quot;https://en.wikipedia.org/wiki/Lithosphere&quot; rel=&quot;nofollow noreferrer&quot;&gt;lithosphere&lt;/a&gt;* in overall quantity of carbon stored on the planet. Some is stored by algae/sea plants, but the vast majority is &lt;a href=&quot;https://en.wikipedia.org/wiki/Carbon_cycle#Oceans&quot; rel=&quot;nofollow noreferrer&quot;&gt;stored as dissolved CO2&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*The lithosphere (crust and upper mantle) is not involved in the carbon cycle, and is therefore not shown in the above image.&lt;/p&gt;&#xA;" OwnerUserId="9829" LastActivityDate="2015-06-18T22:59:43.287" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35348" PostTypeId="2" ParentId="8295" CreationDate="2015-06-19T00:21:28.373" Score="4" Body="&lt;p&gt;Gallstones 'block' the plumbing system (i.e. the biliary tree) that drains bile produced in the liver from flowing into the duodenum through the ampulla of Vater. Since bile is a dietary detergent for fats (cholesterol, triglycerides, free fatty acids), the blockage of bile impairs fat absorption in the small intestine and the fat passes into the large intestine and then into the stool. There is always a small amount of fat that passes into the feces (typically very low though), but if bile is not present to aid fat absorption then you get &quot;fatty stool&quot; aka &lt;a href=&quot;https://en.wikipedia.org/wiki/Steatorrhea&quot; rel=&quot;nofollow&quot;&gt;steatorrhea&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="16299" LastEditorUserId="9943" LastEditDate="2015-06-19T01:22:23.163" LastActivityDate="2015-06-19T01:22:23.163" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35349" PostTypeId="2" ParentId="30883" CreationDate="2015-06-19T00:34:34.480" Score="1" Body="&lt;p&gt;Triglycerides are &quot;huge&quot; molecules relatively speaking compared to carbohydrates like glucose or amino acids like alanine. Within the intestinal lumen they are broken down by lipases and solubilized by bile for absorption, which also enhances the activity of pancreatic lipase. So, to get into the enterocytes of the small intestine they need to be broken down. However, once they are reformed you can't just excrete them into the venous circulation because there are exceedingly hydrophobic and can't circulate in their native form. In fact, they first pass into the intestinal lymphatics before entering the arterial circulation. Before this happens, though, triglyceride particles and other lipids like cholesterol are packaged onto lipoprotein molecules for their transport. These lipoprotein molecules are still large, but they have proteins (i.e. Apo-B48) that act as signals to the peripheral tissues for particle uptake into the muscle, adipocytes, etc.&lt;/p&gt;&#xA;" OwnerUserId="16299" LastActivityDate="2015-06-19T00:34:34.480" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35350" PostTypeId="2" ParentId="35337" CreationDate="2015-06-19T00:36:45.930" Score="-1" Body="&lt;p&gt;This is my speculation, but there are no or few organic chemicals which can absorb radio waves having longer wave lengths. Eyes sense lights by absorbing light with organic chemicals, but to sense longer wave length, eyes might need more sophisticated devices like tuners. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, less than 100nm radio waves from the outer space are absorbed by the atmosphere, so even if eyes could sense such radio waves, you don't see any signals on the earth.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-06-19T00:36:45.930" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35351" PostTypeId="2" ParentId="1835" CreationDate="2015-06-19T00:41:31.217" Score="1" Body="&lt;p&gt;Blood volume is not a dimensionless number - it's a volume. Historically we used to measure this in patients or volunteers by giving a large carbohydrate molecule like a starch that is not digestible or harmful to the body. Just like every other body fluid compartment volume (i.e. plasma, interstitial fluid, intracellular and extracellular) that we have, blood volume is estimated by intravenously injecting a known concentration of a particular compound. Once that compound equilibrates you take a blood sample and measure the compound's concentration again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Initial Concentration * Initial Volume = Final Concentration * Final Volume&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you inject a known volume of a known concentration that only fills the &quot;blood&quot; component, and then you measure a final concentration - you can then solve for the &quot;Final Volume&quot; for &quot;blood volume&quot;.&lt;/p&gt;&#xA;" OwnerUserId="16299" LastEditorUserId="16299" LastEditDate="2015-06-19T01:43:31.933" LastActivityDate="2015-06-19T01:43:31.933" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="35352" PostTypeId="2" ParentId="35337" CreationDate="2015-06-19T00:45:18.210" Score="10" Body="&lt;p&gt;Most of the light from the sun doesn't actually reach the earth's surface due to the atmosphere.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CxDPY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[&lt;a href=&quot;http://imagine.gsfc.nasa.gov/science/toolbox/emspectrum1.html&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the light reaching earth includes near-UV, visible, near-IR and a band of radio waves. Seeing any other part of the spectrum would be impossible since it doesn't reach earth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You asked why we only see in the visible light range; this is due to evolution. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/004269899490149X&quot; rel=&quot;noreferrer&quot;&gt;Birds, among other animals, can see UV light&lt;/a&gt;. In fact, &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1034/j.1600-0706.2002.980315.x/abstract&quot; rel=&quot;noreferrer&quot;&gt;all vertebrates have the potential for near-UV vision&lt;/a&gt;. &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0042698994901473?via%3Dihub&quot; rel=&quot;noreferrer&quot;&gt;Humans, as vertebrates, also have UV-sensitive photoreceptors&lt;/a&gt;. However, our lens is opaque to UV light: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fXN1C.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[from &lt;em&gt;Clinical Ocular Anatomy and Physiology&lt;/em&gt; via &lt;a href=&quot;http://www.clspectrum.com/articleviewer.aspx?articleID=103351&quot; rel=&quot;noreferrer&quot;&gt;this website&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just speculating, it would seem that the ability to see near-UV is an ancestral condition which we lost at some point; either it provided no significant advantage (neutral regression) or there was some advantage provided by a UV-opaque lens, either directly (such as protection from UVB light) or indirectly (through pleiotropic antagonism). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, human photoreceptors cannot detect IR light. Again, this is a product of evolution.  &lt;a href=&quot;http://m.hopkinsmedicine.org/news/media/releases/why_animals_dont_have_infrared_vision&quot; rel=&quot;noreferrer&quot;&gt;These researchers hypothesize that the longer the wavelength of light detected, the more noise is produced.&lt;/a&gt; This noise is due to activation of the pigment molecule by heat. Or, it could just be that never happened. An IR-sensitive photoreceptor might be possible, but evolution doesn't lead to perfect adaptation. In other words, there isn't necessarily a reason why.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for radio waves, they are too low energy to interact appreciably with matter, at least as far as vision is concerned. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-06-22T07:04:22.673" LastActivityDate="2015-06-22T07:04:22.673" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35353" PostTypeId="2" ParentId="35337" CreationDate="2015-06-19T00:46:54.610" Score="21" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;The visible spectrum has the highest energy in sunlight at the earth's surface, explaining the gross location of the visible spectrum in life on earth. The specific frequency range varies across species and can be explained by species-specific survival strategies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;When you look at the solar light spectrum at the earth's surface the &lt;strong&gt;visible spectrum has the highest intensity&lt;/strong&gt; (fig. 1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4BIlO.jpg&quot; alt=&quot;solar irradiation&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Solar irradiation. Source: &lt;a href=&quot;http://solarwiki.ucdavis.edu/The_Science_of_Solar/Solar_Basics/B._Basics_of_the_Sun/III._Solar_Radiation_Outside_the_Earth&amp;#39;s_Atmosphere&quot; rel=&quot;noreferrer&quot;&gt;University of California&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it makes sense to use the range of frequencies that is represented most in sunlight as a starting point.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then the question becomes, why do &lt;strong&gt;humans utilize approximately 400 to 700 nm&lt;/strong&gt;, and not infrared or UV? That can be explained because we do not need it. Our range has been hypothesized to be related to &lt;strong&gt;foraging behaviors&lt;/strong&gt; and our visual system is particularly sensitive in the frequency range of the &lt;strong&gt;coloring of (ripe) fruits&lt;/strong&gt;, which is thought to have been of great benefit to our hominid ancestors &lt;a href=&quot;https://physics.stackexchange.com/questions/144936/is-there-a-physical-reason-for-colors-to-be-located-in-a-very-narrow-band-of-the&quot;&gt;(Osorio &amp;amp; Vorobyev, 1996)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why then do animals extend their vision into &lt;strong&gt;UV&lt;/strong&gt;? Many fish, amphibian, reptilian, avian, and some mammalian species use UV vision. Many birds can identify UV-reflected &lt;strong&gt;nectar and berries&lt;/strong&gt;, and UV-reflecting plumages in birds, and scales in fishes are used for &lt;strong&gt;recognition&lt;/strong&gt; &lt;a href=&quot;http://www.pnas.org/content/100/14/8308.full&quot; rel=&quot;noreferrer&quot;&gt;(Shi &amp;amp; Yokoyama, 2003)&lt;/a&gt;. Moreover, some arthropod species are know to use UV vision to &lt;strong&gt;reduce light-reflection distortions&lt;/strong&gt; under water, such as in the mantis shrimp that features 12 photoreceptor types (as opposed to four in humans) &lt;a href=&quot;http://www.sciencemag.org/content/343/6169/411.short&quot; rel=&quot;noreferrer&quot;&gt;(Thoen &lt;em&gt;et al&lt;/em&gt;., 2014)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why then do animals extend their dynamic range into the &lt;strong&gt;infrared&lt;/strong&gt;? A notable beneficial effect of perceiving infrared is the detection of &lt;strong&gt;body heat&lt;/strong&gt;. The generation of heat is accompanied by the generation of infrared light. The detection of this emitted light is highly useful for nocturnal predators, like the rattle snake &lt;a href=&quot;http://www.scientificamerican.com/article/the-infrared-vision-of-snakes/&quot; rel=&quot;noreferrer&quot;&gt;(Hartline &amp;amp; Newman, 1982)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.scientificamerican.com/article/the-infrared-vision-of-snakes/&quot; rel=&quot;noreferrer&quot;&gt;Hartline &amp;amp; Newman, &lt;em&gt;Sci Am&lt;/em&gt; (1982); &lt;strong&gt;246&lt;/strong&gt;(3): 116-27&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;https://physics.stackexchange.com/questions/144936/is-there-a-physical-reason-for-colors-to-be-located-in-a-very-narrow-band-of-the&quot;&gt;Osorio &amp;amp; Vorobyev, &lt;em&gt;Proc Roc Soc B&lt;/em&gt; (1996); &lt;strong&gt;263&lt;/strong&gt;(1370)&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.pnas.org/content/100/14/8308.full&quot; rel=&quot;noreferrer&quot;&gt;Shi &amp;amp; Yokoyama, &lt;em&gt;PNAS&lt;/em&gt; (2003); &lt;strong&gt;100&lt;/strong&gt;(142003): 8308-13&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.sciencemag.org/content/343/6169/411.short&quot; rel=&quot;noreferrer&quot;&gt;Thoen &lt;em&gt;et al., Science&lt;/em&gt; (2014); &lt;strong&gt;343&lt;/strong&gt;(6169): 411-3&lt;/a&gt; &lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Further Reading&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;1.&lt;/strong&gt; &lt;a href=&quot;https://biology.stackexchange.com/questions/24481/is-our-color-vision-calibrated-to-sky-vegetation-and-blood/24544#24544&quot;&gt;Is our color vision calibrated to sky, vegetation, and blood?&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;2.&lt;/strong&gt; &lt;a href=&quot;https://physics.stackexchange.com/questions/144936/is-there-a-physical-reason-for-colors-to-be-located-in-a-very-narrow-band-of-the&quot;&gt;Is there a physical reason for colors to be located in a very narrow band of the EM spectrum?&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2016-09-19T17:41:12.983" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35355" PostTypeId="2" ParentId="23324" CreationDate="2015-06-19T03:05:30.743" Score="1" Body="&lt;p&gt;You are correct - we suction out subcutaneous fat (fat in-between the skin and muscle layers) which is commonly referred to as &quot;liposuction&quot;. Then we make a &quot;slurry&quot; type of solution with the fat and saline-like solution. Then using long needles we inject this 'transplanted' fat into another area. Many times if a woman has a breast reconstructive procedure and needs some contouring done around an implant (i.e. to smooth the surface under the skin where the breast implant and surrounding tissue meet) this can be done. Not all the transplanted fat will grow enough blood vessels in this new area and some of the fat tissue will die. This dying process is called &quot;necrosis&quot; and the body will reabsorb the dead cells and their contents. It works very well overall.&lt;/p&gt;&#xA;" OwnerUserId="16299" LastActivityDate="2015-06-19T03:05:30.743" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35359" PostTypeId="2" ParentId="35325" CreationDate="2015-06-19T03:56:08.163" Score="3" Body="&lt;p&gt;In the absence of molecular sequencing data the most accurate estimates are based on reassociation kinetics, more commonly known as Cot curves. Here is a classic &lt;a href=&quot;http://www.genetics.org/content/77/1/95.long&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt; from 1974 that describes the basic approach. While pulsed field electrophoresis &lt;em&gt;can&lt;/em&gt; be used to resolve the chromosomes of species with relatively short chromosomes (like baker's yeast), there are really no suitable size markers that you could use to construct a standard curve for size estimation. &lt;em&gt;C. elegans&lt;/em&gt; has six chromosomes, but they are all fairly close to each other in length, and the genome size of 100 Mb is the same as a single long human chromosome.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-06-19T03:56:08.163" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35361" PostTypeId="1" CreationDate="2015-06-19T10:51:41.403" Score="1" ViewCount="50" Body="&lt;p&gt;Bacterial species like &lt;em&gt;E. coli&lt;/em&gt; are easy to transform using a variety of methods, including both chemical transformation and electroporation. Chemical transformation is especially nice to use as it can be done in high throughput. I'd like to start working with &lt;em&gt;Mycobacterium smegmatis&lt;/em&gt;, though, and have only been able to find electroporation-based transformation methods like the one described &lt;a href=&quot;http://www.jove.com/video/761/electroporation-of-mycobacteria&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. Can chemically-competent mycobacteria be prepared? If so, are they just very inefficient? Is it worth testing some &lt;em&gt;E. coli&lt;/em&gt;-specific methods with mycobacteria? &lt;/p&gt;&#xA;" OwnerUserId="16303" LastEditorUserId="3340" LastEditDate="2015-06-19T11:34:25.827" LastActivityDate="2015-06-19T11:34:25.827" Title="Has anyone tried to prepare chemically competent Mycobacteria?" Tags="&lt;transformation&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35362" PostTypeId="1" AcceptedAnswerId="35372" CreationDate="2015-06-19T12:26:56.837" Score="1" ViewCount="290" Body="&lt;p&gt;In his &lt;strong&gt;&lt;em&gt;Origin of species&lt;/em&gt;&lt;/strong&gt;, in the chapter entitled '&lt;strong&gt;&lt;em&gt;Mutual Affinities of Organic Beings: Morphology: Embryology: Rudimentary Organs&lt;/em&gt;&lt;/strong&gt;', Darwin, speaking of the nature of classification systems of living organisms, writes:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Such expressions as that famous one of Linnaeus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent, the only known cause of the similarity of organic beings, is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What does he mean by  &quot;&lt;em&gt;that the characters do not make the genus, but that the genus gives the characters&lt;/em&gt;&quot;?&lt;/p&gt;&#xA;" OwnerUserId="16220" LastEditorUserId="16220" LastEditDate="2015-06-20T00:19:43.757" LastActivityDate="2015-06-20T19:35:58.023" Title="Characters do not make the genus, but the genus gives the characters?" Tags="&lt;evolution&gt;&lt;taxonomy&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35364" PostTypeId="1" AcceptedAnswerId="35365" CreationDate="2015-06-19T13:10:02.730" Score="27" ViewCount="4939" Body="&lt;p&gt;I have been looking at pictures of different species of mosquito and several times I came across pictures where the mosquito seems to be secreting some kind of fluid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the pictures one can clearly see that the mosquito both secretes transparent fluid and blood.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What kind of fluid is the transparent stuff? Could it be plasma from the host's blood?&lt;/li&gt;&#xA;&lt;li&gt;Why does the mosquito do it?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SoOuv.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/vsjr7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/6mw86.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user14636" LastEditorDisplayName="user14636" LastEditDate="2015-06-21T20:24:09.657" LastActivityDate="2019-02-03T04:42:16.043" Title="What is this droplet of liquid that comes out of a mosquito?" Tags="&lt;zoology&gt;&lt;entomology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35365" PostTypeId="2" ParentId="35364" CreationDate="2015-06-19T13:39:31.153" Score="20" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Excretion of blood and urine may prevent overheating by reducing body temperature through evaporative coolong (akin to perspiration). Excretion of blood and urine also concentrates the ingested blood. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Female &lt;em&gt;Anopheles&lt;/em&gt; mosquitoes seek blood for nutrients necessary to egg production. The cold-blooded insects may excrete some freshly ingested blood as a way to &lt;strong&gt;avoid overheating&lt;/strong&gt; when consuming blood as warm as 104 degrees Fahrenheit (40°C). It is thought that excretion of a droplet of fluid aids in evaporative cooling, similar to perspiration in humans, to reduce the animal's temperature. The excretion of urine may serve a similar purpose, namely avoiding overheating during blood ingestion. By keeping the urine or blood droplet attached to the abdomen, excessive heat can be eliminated &lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822%2811%2901311-X&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Lahonde &amp;amp; Lazarri, 2012)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the malaria mosquito (&lt;em&gt;Anopheles stephens&lt;/em&gt;) the excretion of fluids has been investigated in detail. Females ingest blood meals that are equivalent to more than twice their unfed body mass. Engorged animals can fly only with great difficulty, making them more prone to predation. The blood meal serves primarily as a source of protein for egg development, but it also contains considerable amounts of unwanted salts and water that threaten haemolymph homeostasis. To counter this, a rapid natriuresis and diuresis commences even before the blood meal is completed, and ∼40% of the imbibed plasma volume and salt are voided within 1–2 h of feeding &lt;a href=&quot;http://jeb.biologists.org/content/208/17/3281.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Coast et al., 2005)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://jeb.biologists.org/content/208/17/3281.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;Coast &lt;em&gt;et al. Exp Biol&lt;/em&gt; (2005); &lt;strong&gt;208&lt;/strong&gt;: 3281-91&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.cell.com/current-biology/abstract/S0960-9822%2811%2901311-X&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lahonde &amp;amp; Lazarri, &lt;em&gt;Curr Biol&lt;/em&gt; (2012); &lt;strong&gt;22&lt;/strong&gt;: 40–5&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Further readings&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;https://skeptics.stackexchange.com/questions/23072/do-mosquitoes-urinate-on-you-when-they-bite-you&quot;&gt;Do mosquitoes urinate on you when they bite you?&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2016-06-09T10:43:13.550" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35367" PostTypeId="1" AcceptedAnswerId="35371" CreationDate="2015-06-19T14:38:45.223" Score="4" ViewCount="217" Body="&lt;p&gt;I live in Denmark, Europe and I have in my garden this gigantic vegetable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has a big bump on the top and i was wondering about what comes out of it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XUYE0.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user14636" LastEditorDisplayName="user14636" LastEditDate="2015-06-19T14:56:28.550" LastActivityDate="2015-06-19T17:02:41.733" Title="What comes out of this bump in this vegetable?" Tags="&lt;botany&gt;&lt;plant-anatomy&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35368" PostTypeId="1" CreationDate="2015-06-19T15:54:12.123" Score="2" ViewCount="17" Body="&lt;p&gt;Say we measure bats activity as number of passes through given area. Can it differ significantly depending from day to day or it stays on average roughly the same? I am wondering whether the following might have an effect:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Weather conditions (wind or rain). I do not mean here heavy conditions (strong wind or rain), those understandably will affect bats eagerness to fly&lt;/li&gt;&#xA;&lt;li&gt;Moon cycle&lt;/li&gt;&#xA;&lt;li&gt;Mating&lt;/li&gt;&#xA;&lt;li&gt;For insect-easting bats: the prey not being active every night&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I would welcome some good reading on the subject.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question stems from the following problem. Say I have one detector and want to measure activity in three locations. If I rotate it between them, will I get unbiased result?&lt;/p&gt;&#xA;" OwnerUserId="16308" LastEditorUserId="3340" LastEditDate="2015-06-19T16:00:47.433" LastActivityDate="2015-06-19T16:00:47.433" Title="Does level of bats activity differs from day to day?" Tags="&lt;ethology&gt;&lt;mammals&gt;&lt;experimental-design&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35369" PostTypeId="1" CreationDate="2015-06-19T16:18:24.690" Score="4" ViewCount="847" Body="&lt;p&gt;I've been preparing wet slides for my kids to look at from pond water. I have a mason jar of pond water. What can I do to keep the microbes in the jar alive going forward so that we can look at it any time we want without having to go back to get more pond water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I remember we did something like this in 7th grade biology, it seems like we put in sugar, or oatmeal, or something. I can't quite remember that though, it's been over 30 years. Thanks!&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Thanks for the comments. The pond water I get keeps for a couple of days easily. I can always get more at the pond.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I want amoebas, I go near dark and get them at the bottom of the pond. If I just want paramecia and other critters, I grab some scum and fill the rest of the jar up with water.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paramecia water I give moderate sunlight. The amoeba sample I keep in the dark. And I just pitch it after a few days. No Legionella for my family, please and thank you.&lt;/p&gt;&#xA;" OwnerUserId="16309" LastEditorUserId="69" LastEditDate="2015-06-23T16:11:31.033" LastActivityDate="2016-03-29T07:45:24.507" Title="How can I keep pond water &quot;alive&quot;?" Tags="&lt;microbiology&gt;&lt;microscopy&gt;" AnswerCount="0" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="35370" PostTypeId="1" AcceptedAnswerId="35374" CreationDate="2015-06-19T16:58:30.633" Score="22" ViewCount="2959" Body="&lt;p&gt;I just finished watching &lt;a href=&quot;https://youtu.be/L4AJmvzImbM?t=388&quot;&gt;a video&lt;/a&gt; where it was mentioned that nowadays birds are dinosaurs and non-avians dinosaurs could have feathers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I confirmed this from wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Bird#Dinosaurs_and_the_origin_of_birds&quot;&gt;&lt;strong&gt;Birds are highly advanced theropod dinosaurs&lt;/strong&gt;&lt;/a&gt;, characterised&#xA;  by feathers, a beak with no teeth, the laying of hard-shelled eggs, a&#xA;  high metabolic rate, a four-chambered heart, and a lightweight but&#xA;  strong skeleton.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Direct &lt;strong&gt;fossil evidence of feathers&lt;/strong&gt; or feather-like structures has&#xA;  been discovered in a diverse array of species &lt;a href=&quot;https://en.wikipedia.org/wiki/Dinosaur#Feathers&quot;&gt;&lt;strong&gt;in many non-avian&#xA;  dinosaur groups&lt;/strong&gt;&lt;/a&gt;, both among saurischians and ornithischians.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And this &lt;a href=&quot;https://en.wikipedia.org/wiki/Reptile#Phylogeny&quot;&gt;&lt;strong&gt;family tree of reptiles&lt;/strong&gt;&lt;/a&gt; mentions: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Archosauriformes&quot;&gt;Archosauriformes&lt;/a&gt; (crocodiles, birds, dinosaurs and extinct relatives)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;And later in the &lt;a href=&quot;https://en.wikipedia.org/wiki/Reptile#The_Mesozoic_era&quot;&gt;Mesozoic era&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The dinosaurs also developed smaller forms, including the feather-bearing smaller &lt;a href=&quot;https://en.wikipedia.org/wiki/Theropoda&quot;&gt;theropods&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So, were these non-avian dinosaurs with feathers actually reptiles?&lt;/p&gt;&#xA;" OwnerUserId="16310" LastActivityDate="2019-03-26T20:49:13.563" Title="If dinosaurs could have feathers, would they still be reptiles?" Tags="&lt;ornithology&gt;&lt;reptile&gt;&lt;cladistics&gt;" AnswerCount="2" CommentCount="13" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35371" PostTypeId="2" ParentId="35367" CreationDate="2015-06-19T17:02:41.733" Score="4" Body="&lt;p&gt;I think your vegetable is a leek, or a closely related allium. If this is the case, you are seeing its flowerbud. Congratulations, it will become quite pretty in some days, I know people who use leeks as decoration plants instead of vegetables. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Hxqfx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="1578" LastActivityDate="2015-06-19T17:02:41.733" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35372" PostTypeId="2" ParentId="35362" CreationDate="2015-06-19T17:04:54.683" Score="5" Body="&lt;p&gt;It has been a long time since, I've read The Origin of Species, but it sounds like the intent of the phrase is to suggest that the presence of similar characteristics in two species do not imply that they are related, but that related species would be expected to share characteristics. I.e. that similar characteristics do not imply relatedness, but relatedness implies similar characteristics. Genus -&gt; Characteristics, rather than Characteristics -&gt; Genus. These two possibilities are logically distinct.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The assumption that Genus -&gt; Characteristics segues into the key concept of his theory of evolution, that related species (a genus) arise from the descent with modification of an shared ancestral population. Remember that Darwin wrote long before we understand the role of DNA as the carrier of genetic information. He knew nothing about the physical substance or the mechanism of transmission that passed characteristics to offspring, but through his observations built a strong case that such a substance exists and that gradual changes in this substance occur over time in a population. He later posits that natural selection leads to the accumulation subsets of descendants with modifications that are advantageous in their environment. Thus the species within a genus could arise, their similarities the result of their shared ancestry, their differences that result of descent with modification and selection.&lt;/p&gt;&#xA;" OwnerUserId="16147" LastActivityDate="2015-06-19T17:04:54.683" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35374" PostTypeId="2" ParentId="35370" CreationDate="2015-06-19T18:30:38.647" Score="36" Body="&lt;p&gt;&lt;strong&gt;Source of information on Biology.SE&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/52700/why-do-the-ancestors-of-birds-still-exist/52729#52729&quot;&gt;This answer&lt;/a&gt; offers an introduction to phylogeny on the case study of dinosaurs and birds. If you are not at ease with the concept of monophyletic group, you should definitely have started with this introduction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/14877/birds-and-dinosaurs&quot;&gt;This post&lt;/a&gt; is somewhat related.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Origin of your misunderstanding&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is all about nomenclature (and a little bit of semantics). One can call reptiles whatever (s)he wants. The question is what do we define as being a reptile? And the answer is that there are two possible definitions, a common &quot;bad&quot; definition (&lt;code&gt;Definition 1&lt;/code&gt;) and a phylogenetic-based &quot;good&quot; definition (&lt;code&gt;definition 2&lt;/code&gt;). I think your confusion comes from the use of the same term to mean two different (but related) things.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Definition 1: reptiles&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, when people talk about reptiles, they talk about &lt;a href=&quot;https://en.wikipedia.org/wiki/Turtle&quot; rel=&quot;nofollow noreferrer&quot;&gt;turtles&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Rhynchocephalia&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rhynchocephalia&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Squamata&quot; rel=&quot;nofollow noreferrer&quot;&gt;Squamata&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Crocodilia&quot; rel=&quot;nofollow noreferrer&quot;&gt;Crocodilia&lt;/a&gt;. In this sense, the term reptile is NOT a &lt;a href=&quot;https://en.wikipedia.org/wiki/Monophyly&quot; rel=&quot;nofollow noreferrer&quot;&gt;monophyletic&lt;/a&gt; group. In other words, all species being called reptiles (according to this definition) do not share a common ancestor who has no other descendants that the species being called reptiles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Definition 2: &lt;em&gt;Reptilia&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there is a defined monophyletic group called &lt;em&gt;Reptilia&lt;/em&gt;. &lt;em&gt;Reptilia&lt;/em&gt; is a group that contains all &lt;a href=&quot;https://en.wikipedia.org/?title=Amniote&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Amniota&lt;/em&gt;&lt;/a&gt; except the &lt;em&gt;Synapsida&lt;/em&gt; (&lt;a href=&quot;https://en.wikipedia.org/?title=Mammal&quot; rel=&quot;nofollow noreferrer&quot;&gt;mammals&lt;/a&gt; and their extinct close relatives). In other words, &lt;em&gt;Reptilia&lt;/em&gt; contains all generally called reptiles (as defined above) and all birds as well as all extinct species that are descendent from this same common ancestor.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Exploring the tree of life by yourself&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You will find the tree of life on &lt;a href=&quot;http://tolweb.org/tree/&quot; rel=&quot;nofollow noreferrer&quot;&gt;tolweb.org&lt;/a&gt; or on &lt;a href=&quot;http://www.onezoom.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;onezoom.org&lt;/a&gt; (see &lt;a href=&quot;https://biology.stackexchange.com/questions/52142/the-best-free-and-most-up-to-date-phylogenetic-tree-on-the-internet&quot;&gt;The best free and most up to date phylogenetic tree on the internet?&lt;/a&gt; for more info).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using tolweb.org: here are the roots of the tree of the &lt;a href=&quot;http://tolweb.org/Amniota/14990&quot; rel=&quot;nofollow noreferrer&quot;&gt;Amniota&lt;/a&gt;. And you will probably want to search for the &lt;em&gt;Dinosauria&lt;/em&gt; (&lt;a href=&quot;http://tolweb.org/Dinosauria/14883&quot; rel=&quot;nofollow noreferrer&quot;&gt;there&lt;/a&gt;) and see how closely related they are to the birds but not so much to the turtles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Addressing your question directly&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If dinosaurs could have feathers, would they still be reptiles?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If by reptiles you mean &lt;em&gt;Reptilia&lt;/em&gt;, then whether a given dinosaur has feathers, endothermy, or an exoskeleton (!) doesn't change anything to the fact that this dinosaur is a reptile.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If by reptiles you mean &lt;a href=&quot;https://en.wikipedia.org/wiki/Turtle&quot; rel=&quot;nofollow noreferrer&quot;&gt;turtles&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Rhynchocephalia&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rhynchocephalia&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Squamata&quot; rel=&quot;nofollow noreferrer&quot;&gt;Squamata&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Crocodilia&quot; rel=&quot;nofollow noreferrer&quot;&gt;Crocodilia&lt;/a&gt;, then whether a given dinosaur has feathers or not doesn't change anything to the fact that this dinosaur is NOT a reptile!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Known Dinosaurs with feathers?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that birds are the only animals that have feathers and that birds are dinosaurs, we don't know of any species that has a feather that is not a dinosaur! However, when we think of dinosaurs, we usually don't think about a pigeon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, the &lt;a href=&quot;https://en.wikipedia.org/wiki/Archaeopteryx&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Archaeopteryx&lt;/em&gt;&lt;/a&gt; had feathers too. &lt;em&gt;Archaeopteryx&lt;/em&gt; is an avian (bird-like) dinosaur. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/s4fNnm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But even non-avian dinosaurs such as &lt;em&gt;Velociraptor&lt;/em&gt; probably had feathers as well. More info about how closely related is Velociraptor to the birds (Aves) &lt;a href=&quot;http://tolweb.org/Coelurosauria/15769&quot; rel=&quot;nofollow noreferrer&quot;&gt;there on tolweb.org&lt;/a&gt;. You probably remember the so-called &lt;em&gt;Velociraptor&lt;/em&gt; from Jurassic Park movie (on the left) but here is what a &lt;em&gt;Velociraptor&lt;/em&gt; probably really looked like (on the right). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/5MIf8m.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/X5WuIm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;velociraptors&quot; from Jurassic park actually look more like a large &lt;a href=&quot;https://en.wikipedia.org/wiki/Deinonychus&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Deinonychus&lt;/em&gt;&lt;/a&gt; without feathers than a &lt;em&gt;Velociraptor&lt;/em&gt; (Thank you @Gaurav in the comments). However as &lt;em&gt;Deinonychus&lt;/em&gt; is much harder to pronounce and way less sexy than &lt;em&gt;Velociraptor&lt;/em&gt;, they chose to use &lt;em&gt;Velociraptor&lt;/em&gt; in the movie Jurassic Park and deceived an entire generation about what a &lt;em&gt;Velociraptor&lt;/em&gt; is! More information about what the species of Dinosaurs the Jurassic Park movie features in the youtube video (in French): &lt;a href=&quot;https://www.youtube.com/watch?v=xWhcv6vZ97A&quot; rel=&quot;nofollow noreferrer&quot;&gt;Le Vélociraptor&lt;/a&gt; from Max Bird.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might want to have a look at the post &lt;a href=&quot;https://biology.stackexchange.com/questions/17546/were-there-any-flying-dinosaurs&quot;&gt;Were there any flying dinosaurs?&lt;/a&gt; that is very related.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;At least, all these big and extinct things with scales are dinosaurs, right?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Well.... not exactly. There are species that you would probably call dinosaurs that we typically don't consider as dinosaurs. Have a look at &lt;a href=&quot;https://www.youtube.com/watch?v=HIbG-dUFnf4&quot; rel=&quot;nofollow noreferrer&quot;&gt;the MinuteEarth video called &quot;What makes a dinosaur?&quot;&lt;/a&gt; for more information in this regard.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fun and instructive videos&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=qcejX_11UUk&quot; rel=&quot;nofollow noreferrer&quot;&gt;Les dinosaures ont disparu ?&lt;/a&gt; from Max Bird and Jamy (in french)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=xWhcv6vZ97A&quot; rel=&quot;nofollow noreferrer&quot;&gt;Le Vélociraptor&lt;/a&gt; from Max Bird (in French)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=HIbG-dUFnf4&quot; rel=&quot;nofollow noreferrer&quot;&gt;What makes a dinosaur?&lt;/a&gt; from MinuteEarth&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-26T19:25:56.460" LastActivityDate="2019-03-26T19:25:56.460" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="35377" PostTypeId="1" CreationDate="2015-06-19T21:06:16.757" Score="1" ViewCount="167" Body="&lt;p&gt;I am looking for a cell line (preferably hematopoietic) that has an inactivating DNMT3a mutation. I have checked the &lt;a href=&quot;http://www.broadinstitute.org/ccle/home&quot; rel=&quot;nofollow&quot; title=&quot;Cancer Cell Line Encyclopedia&quot;&gt;Cancer Cell Line Encyclopedia&lt;/a&gt; but of all the hematopoietic cell lines I know I can't find any with a DNMT3a mutation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It would be great if somebody knows of a cell line with a DNMT3a mutation, but it would also be helpful if somebody knows of a database that I could use to find this information in the future. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-06-19T21:06:16.757" Title="Cell Line With DNMT3a Mutation" Tags="&lt;cell-biology&gt;&lt;cancer&gt;" AnswerCount="0" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35378" PostTypeId="2" ParentId="35362" CreationDate="2015-06-19T23:59:55.497" Score="1" Body="&lt;p&gt;I'm not sure when the concept first arose but I would assume it was after Darwin had come up with the Theory of Evolution.  The concept I am talking about is &quot;Convergent Evolution&quot; which in essence explains &quot;characteristics do not make the genus&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Convergent Evolution is the concept that two completely different organisms, given the same selection pressures, may, independent evolve to exhibit similar characteristics.  If one was to assume &quot;characteristics makes the genus&quot; one would think these two must be genetically similar when they are not.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One example I found illustrated from &lt;a href=&quot;http://bio-ditrl.sunsite.ualberta.ca/detail/?P_MNO=1800&quot; rel=&quot;nofollow noreferrer&quot;&gt;link&lt;/a&gt; is:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/uJdxJ.jpg&quot; alt=&quot;Example of convergent Evolution&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you look at the external characteristics, we would say the 3 must be closely related - tail fin, dorsal fin, pectoral fins all pretty much the same.  But looking at the bones and others we know that they each evolved from very different species.  Not only are they from different &lt;code&gt;genus&lt;/code&gt;, their divergence goes all the way up to the &lt;code&gt;class&lt;/code&gt; level (Kingdom, Phylum, &lt;strong&gt;Class&lt;/strong&gt;, Order, Genus Species).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why then do they all look similar?  The reason is they all have to deal with the common selection pressure of &lt;strong&gt;water&lt;/strong&gt;.  Living in water, moving efficiently in water to be able to catch prey and evade predators.  Separately, they all gradually evolved fins because the ones that did not, were out competed by there &quot;better finned&quot; peers.  The better finned shark ancestor out bred the poorer finned sharks, the better finned porpoise ancestor out bred the poorer finned porpoise.  The ichthyosaur too except it finally did not evolve sufficiently and became extinct.&lt;/p&gt;&#xA;" OwnerUserId="16242" LastActivityDate="2015-06-19T23:59:55.497" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35379" PostTypeId="1" AcceptedAnswerId="35380" CreationDate="2015-06-20T01:15:36.593" Score="9" ViewCount="276" Body="&lt;p&gt;I am interested in the relationship between blood leptin concentration and fat mass.  It is well known that as fat mass increases, leptin increases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have there been studies that look into whether the relationship is linear, or perhaps as fat mass increases, the level of leptin increases at a decreasing rate (e.g. logarithmic relationship) or an increasing rate (exponential) etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, for two individuals with identical fat mass, is there a high variance of leptin concentration?&lt;/p&gt;&#xA;" OwnerUserId="16316" LastEditorUserId="9943" LastEditDate="2015-06-20T05:28:48.577" LastActivityDate="2015-06-20T16:14:00.313" Title="Leptin and fat mass?" Tags="&lt;endocrinology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35380" PostTypeId="2" ParentId="35379" CreationDate="2015-06-20T06:34:01.673" Score="3" Body="&lt;p&gt;The obese gene (OB gene) secretes a protein that functions in the signaling pathway of adipose tissue and adipocytes (fat cells) produce the hormone leptin (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8717050&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When the amount of fat in the body increases, the amount of leptin&#xA;  released into the blood also increases and signals to the brain that&#xA;  the body has enough to eat (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK22251/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Inversely, studies in rodents suggest &#xA;  that a reduction in leptin level during weight loss signals to the brain &#xA;  to increase feeding and decrease energy expenditure (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430504/&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Other molecules have a role to play in the ratio of BMI to leptin like the ghrelin hormone (&lt;a href=&quot;https://en.wikipedia.org/wiki/Ghrelin&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). The genetic and environmental factors other than overall adiposity may also regulate leptin concentrations (&lt;a href=&quot;http://europepmc.org/abstract/med/8910093&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;) which is why individuals with the same weight may have different leptin concentrations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A study has reported finding a strong exponential relationship for leptin levels with body mass index (BMI) (&lt;a href=&quot;http://press.endocrine.org/doi/abs/10.1210/jcem.82.9.4251&quot; rel=&quot;nofollow&quot;&gt;reference&lt;/a&gt;). Hope that answers both your questions. &lt;/p&gt;&#xA;" OwnerUserId="5762" LastEditorUserId="5762" LastEditDate="2015-06-20T06:58:30.230" LastActivityDate="2015-06-20T06:58:30.230" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35381" PostTypeId="1" AcceptedAnswerId="39347" CreationDate="2015-06-20T07:40:59.567" Score="4" ViewCount="2563" Body="&lt;p&gt;In &lt;em&gt;Guyton and Hall Textbook of Medical Physiology (12e)&lt;/em&gt; the retinal ganglion cells (RGCs) are classified into W, X, and Y types. However, in &lt;em&gt;&lt;a href=&quot;http://www.us.elsevierhealth.com/gray-anatomy/gray-anatomy-expert-consult/9780443066849/&quot; rel=&quot;nofollow&quot;&gt;Gray's Anatomy (40&lt;sup&gt;th&lt;/sup&gt; ed.)&lt;/a&gt;&lt;/em&gt;, RGS are subdivided into midget and parasol cells. What is the relationship between the W-X-Y versus midget-parasol classifications?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Summary of the WXY classification as in &lt;em&gt;Medical Physiology&lt;/em&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About 40% ganglion cells are W cells. They are the smallest (&amp;lt;10 μm), and the slowest (8 m/s) to transmit signals, but they have the broadest receptive field. They receive signals from rods and detect directional movement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About 55% are X cells. They have medium size (10~15 μm) and transmission speed (14 m/s). Their fields are small. They transmit color vision.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;About 5% are Y cells. They are the largest (&amp;lt;35 μm) and the fastest (35 m/s) to transmit signals. They have broad fields. They respond to rapid changes in the vision.&lt;/p&gt;&#xA;" OwnerUserId="16317" LastEditorUserId="9943" LastEditDate="2015-10-07T10:03:27.287" LastActivityDate="2015-10-08T01:54:43.207" Title="What is the relationship between W, X, Y and P, M retinal ganglion cells?" Tags="&lt;physiology&gt;&lt;vision&gt;&lt;neurophysiology&gt;&lt;neuroanatomy&gt;&lt;histology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35382" PostTypeId="1" AcceptedAnswerId="35384" CreationDate="2015-06-20T12:05:39.583" Score="3" ViewCount="2006" Body="&lt;p&gt;I have a postgraduate degree in computer science, and I wish to undertake research in bioinformatics. I had chemistry but no biology in high school. I have read bioinformatics books like &quot;biological sequence analysis&quot; by durbin and &quot;fundamental concepts of bioinformatics&quot; by krane, etc. But I wish to read a comprehensive book on biology (genetics) that will help me undertake research in bioinformatics properly. I have been considering 2 books: &quot;molecular biology of the cell&quot; and &quot;molecular biology of the gene&quot;. Are these books comprehensive enough? Please suggest some good books as I have almost no knowledge of biology at highschool or graduate levels.&lt;/p&gt;&#xA;" OwnerUserId="16322" LastActivityDate="2015-06-20T23:25:50.270" Title="best book for a comprehensive introduction to biology for a computer science graduate interested in undertaking research in bioinformatics" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ClosedDate="2015-06-21T05:33:49.867" ContentLicense="CC BY-SA 3.0" />
  <row Id="35383" PostTypeId="2" ParentId="35278" CreationDate="2015-06-20T12:57:57.910" Score="10" Body="&lt;p&gt;Your question is really good, but in actuality, they do evolve towards muting themselves, actually, they have pretty much done &quot;most of the work&quot;:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;It is assumed that microscopic scales along veins and wind margin&#xA;play an important role as a silencer as downs on the flight feather of owl.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;From this we can assume that the effectiveness of these scales are high, as they had plenty of time to evolve; thus the other factor they should alter to make them quieter is the frequency of their flapping $f$, which can be calculated from the following equation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$f=K m^{-1/6}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $m$ is the mass of the animal and $K$ is the proportionality constant. The resulting number is around several hundred hertz (Remi.b observed a value around 440 Hz)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two options for them, either increasing the frequency up until our ear is incapable of hearing it which would be impossible as even the highest flapping frequency can hardly exceed 1000 Hz, which is nowhere near the required 20,000 Hz. By increasing their body mass they could decrease the frequency but the needed 15-20 Hz is pretty low compared to the actual several hundred, thus it would likely need a complete body structure change which is not something to happen in the near-future.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An another solution might be a different strategy in flying. Gliding attacks might pay off really well (that's why owls on the other hand can't be heard during flight), but even though there are some insects capable of such&lt;a href=&quot;https://en.wikipedia.org/wiki/Insect_wing#Gliding&quot; rel=&quot;noreferrer&quot;&gt;&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt;, it would need an immerse amount of time, not talking about the problems that might arise from the bumping into of our body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't think that the mating signaling would be indispensable from an evolutionary perspective, but this statement of mine can't be proved.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;These are the physical/biological difficulties of the problem, here is one from an evolutionary aspect: They are not likely to have experienced a strong selection against this feature, as most of the possible victims are incapable of doing much against a mosquito due to the absent of hands (and tails are seldom enough to stop them). The first possibly blood-sucking mosquito was found to be living 79 million years ago, while animals that might be able to &quot;seal their fate&quot; are much more recent, while not even having success most of the time.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.jstage.jst.go.jp/article/jsmec1997/43/4/43_4_895/_pdf&quot; rel=&quot;noreferrer&quot;&gt;https://www.jstage.jst.go.jp/article/jsmec1997/43/4/43_4_895/_pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.geologica-acta.com/pdf/aghv3501a12.pdf&quot; rel=&quot;noreferrer&quot;&gt;http://www.geologica-acta.com/pdf/aghv3501a12.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.physics.emory.edu/faculty/weeks//lab/papers/jwang-arf05.pdf&quot; rel=&quot;noreferrer&quot;&gt;http://www.physics.emory.edu/faculty/weeks//lab/papers/jwang-arf05.pdf&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="15051" LastEditorUserId="15494" LastEditDate="2015-06-20T16:40:22.223" LastActivityDate="2015-06-20T16:40:22.223" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35384" PostTypeId="2" ParentId="35382" CreationDate="2015-06-20T13:51:22.837" Score="1" Body="&lt;p&gt;Welcome to Biology and welcome to Biology.SE!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is hard to answer such a question as the domains you describe are very vast.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want a book in an introductory book to biology, then you want to read &lt;a href=&quot;https://biology.stackexchange.com/questions/10376/introductory-biology-text-for-an-outsider&quot;&gt;this post&lt;/a&gt; and &lt;a href=&quot;https://biology.stackexchange.com/questions/35152/choosing-a-book-to-gain-general-knowledge-about-biology&quot;&gt;this post&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are more interested in population genetics and molecular evolution then &lt;a href=&quot;https://biology.stackexchange.com/questions/16470/book-recommendation-on-population-evolutionary-genetics&quot;&gt;this post&lt;/a&gt; will interest you. Still talking about evolution I'd like to attract your attention to &lt;a href=&quot;https://biology.stackexchange.com/questions/16577/book-recommendations-for-evolutionary-models/16579#16579&quot;&gt;this post&lt;/a&gt; for the second suggestion in the first answer:  &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0198567022&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yang, Computational molecular evolution&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You'll probably want to have a look at the post &lt;a href=&quot;https://biology.stackexchange.com/questions/35007/a-free-book-resource-for-learning-genetics&quot;&gt;A free book/resource for learning genetics?&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/14168/book-recommendations-for-algorithms-used-in-evolutionary-biology&quot;&gt;Book recommendations for algorithms used in evolutionary biology&lt;/a&gt; and &lt;a href=&quot;https://biology.stackexchange.com/questions/35262/introductory-book-in-genetics&quot;&gt;Introductory book in genetics&lt;/a&gt; might be a post of interest as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately I don't know any of the two books you cite so I can't quite give you advice for them. &lt;code&gt;molecular biology of the cell&lt;/code&gt; is a very common book among first year biology. It sounds like a potential good reading for you. I know nothing about &lt;code&gt;molecular biology of the gene&lt;/code&gt; except what I just read about it on Amazon.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am hoping one will give you a better criticisms about very general books about molecular biology.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-06-20T23:25:50.270" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35385" PostTypeId="1" AcceptedAnswerId="35387" CreationDate="2015-06-20T14:02:58.300" Score="0" ViewCount="52" Body="&lt;p&gt;I've been doing a lot of research on Alu repeats and how they mediate the gene expression. I read the following article &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs00018-007-7084-0&quot; rel=&quot;nofollow&quot;&gt;&quot;Useful junk: Alu RNAs in the human transcriptome&quot;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And it says that alu repeats embedded in 5'UTR makes stable secondary structure that prevents the assembly of ribosomal subunits, thus blocking the process of translation. I've been reading various articles to find out why Alu repeats form this secondary structure and why only in the 5'UTR and not in the 3'UTR. But haven't been able to find an answer.&lt;/p&gt;&#xA;" OwnerUserId="15756" LastEditorUserId="6" LastEditDate="2015-06-20T14:46:45.183" LastActivityDate="2015-06-20T14:53:15.117" Title="Why do Alu repeats form secondary structures?" Tags="&lt;gene-expression&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35386" PostTypeId="1" CreationDate="2015-06-20T14:23:57.190" Score="1" ViewCount="25" Body="&lt;p&gt;I'm looking for a list of non-native terrestrial molluscs in California. Ideally, I also need the date each taxon was introduced into California. Can anyone help?&lt;/p&gt;&#xA;" OwnerUserId="1216" LastEditorUserId="1216" LastEditDate="2015-06-20T14:29:31.513" LastActivityDate="2015-06-20T14:29:31.513" Title="List of non-native terrestrial molluscs in California?" Tags="&lt;zoology&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35387" PostTypeId="2" ParentId="35385" CreationDate="2015-06-20T14:53:15.117" Score="1" Body="&lt;p&gt;Single-stranded RNA can easily form secondary structures, a very important example of this are tRNAs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a quick look at the article you read it seems that these Alu repeats work similar to riboswitches in the 5'-UTR. They can form secondary structures that block translation initiation, riboswitches commonly do this by hiding the Shine-Dalgarno sequence in a stable helix.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This kind of regulation of translation can obviously only work in the 5'-UTR as that is the place where the translation starts. The 3'-UTR can't affect translation in this way as the translation starts at the other end of the mRNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Alu repeats still can form secondary structures in the 3'-UTR, and the article suggests that those might have an effect on mRNA stability.&lt;/p&gt;&#xA;" OwnerUserId="6" LastActivityDate="2015-06-20T14:53:15.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35388" PostTypeId="2" ParentId="35379" CreationDate="2015-06-20T16:14:00.313" Score="2" Body="&lt;p&gt;The over-simplified answer to the question: &quot;Have studies examined the linearity or non-linearity of leptin concentrations in the blood and body fat?&quot; - is &quot;yes&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/?title=Leptin&quot; rel=&quot;nofollow&quot;&gt;Leptin&lt;/a&gt; (the product of the &lt;em&gt;ob&lt;/em&gt; gene - that is, the &lt;em&gt;obese&lt;/em&gt; gene) is typically thought of as being secreted in proportion to the amount of adipose (fat) tissue that an organism (mice, rats, primates, humans) has overall. Like most things in biology, though, it's likely not a perfect linear relationship across species or across a wide range of individual body weights within a particular species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even the plasma concentrations across individuals within a particular species with the exact (or very close) body weight is still different. In my own experience, when trying to &quot;normalize&quot; or &quot;adjust&quot; the estimated fat mass based on the leptin concentration there's still a good amount of variability between individuals. The leptin concentrations for a number of individuals at one specific body fat percentage are not identical - which could be due to some error in the measurement, but also due to biologic variability from other sources (for a example of this variability in animals matched for body weight &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/16493121&quot; rel=&quot;nofollow&quot;&gt;see here&lt;/a&gt;). This is probably because there are a lot of other modifying factors or variables within the body that can affect leptin concentrations in the plasma (like other hormones or nutrients from the gastrointestinal tract). So yes, these other hormonal and/or nutrient signals probably contribute to the high variance of plasma leptin concentration for individuals with the same fat mass for all of the reasons listed above (I don't have any references that examine this specific question, though).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To my knowledge there are no studies that have examined leptin concentrations across multiple species or even within a large cohort of one species. Even though this might be interesting from a scientific perspective, it's not really necessary to be able to predict fat mass from leptin concentrations (or vice versa) for medical purposes, because we have 'good enough' methods for accurately determining fat mass in patients or animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall leptin is an adipose tissue hormone thought to be involved in control of body weight over long-term (weeks to months) time courses. For a good review of the long-term actions of leptin and other hormones controlling body weight see &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10766253&quot; rel=&quot;nofollow&quot;&gt;a great review on CNS control of body weight that discusses leptin&lt;/a&gt; and other factors that modify leptin and body weight regulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, Dr. Jeffrey Flier in Boston is a senior physician-scientist at Harvard Univeristy and has studied leptin biology and has some very nice articles on leptin including &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17498506&quot; rel=&quot;nofollow&quot;&gt;this review on leptin in energy balance and long term control of fat mass&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="16299" LastActivityDate="2015-06-20T16:14:00.313" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35390" PostTypeId="2" ParentId="35211" CreationDate="2015-06-20T19:13:19.563" Score="2" Body="&lt;p&gt;Any apparently &quot;magical&quot; powers of cisplatin in testicular cancer have more to do with the disease than the drug.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unlike the similarly male-specific prostate cancer, testicular cancer is generally seen in young men &lt;a href=&quot;http://seer.cancer.gov/statfacts/html/testis.html&quot; rel=&quot;nofollow&quot;&gt;in their 20s or 30s&lt;/a&gt; (click on &quot;number of new cases and deaths&quot;). &lt;a href=&quot;http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0025978&quot; rel=&quot;nofollow&quot;&gt;This paper&lt;/a&gt; suggests, as is generally thought to be the case for earlier-onset types of cancer, that the affected individuals thus had some predisposing mutation or change in gene regulation prior to 10 years of age. As a result, it takes fewer sporadic acquired mutations to lead to this early-onset cancer versus a late-onset type like prostate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This difference in incidence pattern is important because a late-onset tumor has had more opportunity to develop a broad range of cancer cells having different mutations within the tumor. Such intra-tumor heterogeneity has been recognized for &lt;a href=&quot;http://cancerres.aacrjournals.org/content/44/6/2259.long&quot; rel=&quot;nofollow&quot;&gt;over 30 years&lt;/a&gt; as a reason for resistance of tumors to cell-killing therapy like chemotherapy. For example, a heterogeneous tumor might be more likely to have cells that have mutated in a way that happens to make them resistant to cisplatin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, testicular cancers develop in an accessible part of the anatomy that typically receives a lot of attention from men of the ages of peak incidence, so they are much more likely to be caught at an early stage than are prostate, ovarian, or colon cancers within the abdomen.&lt;/p&gt;&#xA;" OwnerUserId="16326" LastActivityDate="2015-06-20T19:13:19.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35397" PostTypeId="1" AcceptedAnswerId="35405" CreationDate="2015-06-20T22:52:58.643" Score="2" ViewCount="15594" Body="&lt;p&gt;I've seen flies leave dark spots on lacquered wood, mirrors, glass and monitors. Why do they do that? Is it some food stash or are they dumping waste in a single spot? Why pick a smooth surface?&lt;/p&gt;&#xA;" OwnerUserId="1373" LastActivityDate="2015-06-21T07:35:03.707" Title="Why do flies leave dirty spots on shiny/glossy surfaces?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35399" PostTypeId="2" ParentId="30557" CreationDate="2015-06-21T01:40:33.363" Score="-2" Body="&lt;p&gt;The morbidity is high because autosomal trisomies affect somatic / autosomal chromosomes, which are essential to the process of life. In fact, the majority of fetuses affected by autosomal trysomy are miscarried, with a few exceptions (Down syndrome is one). The sex cells have only half the number of chromosomes,23, of which the affected ones are usually the XX or XY. Their functions are different and although tremendously important, they are not vital, people can survive and live normal lives with these disorders: X, XXX, XXY, XYY. Mader, chapter 24.&lt;/p&gt;&#xA;" OwnerUserId="16332" LastEditorUserId="16332" LastEditDate="2015-06-21T03:06:28.333" LastActivityDate="2015-06-21T03:06:28.333" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35400" PostTypeId="2" ParentId="30557" CreationDate="2015-06-21T02:59:38.607" Score="6" Body="&lt;p&gt;It has to do with &lt;a href=&quot;https://en.wikipedia.org/wiki/Dosage_compensation&quot; rel=&quot;nofollow noreferrer&quot;&gt;dosage compensation&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;The Y chromosome contains relatively few genes. Interestingly, chromosome 21 and 18, which are over represented in the most common viable trisomies, are also relatively small. &lt;/li&gt;&#xA;&lt;li&gt;Humans already possess a mechanism to compensate for additional X chromosomes: &lt;a href=&quot;https://en.wikipedia.org/wiki/X-inactivation&quot; rel=&quot;nofollow noreferrer&quot;&gt;X-inactivation&lt;/a&gt;. Normally this inactivates one of the two X chromosomes in females but can also inactivate two in cases of X trisomy. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Humans are much more able to tolerate extra sex chromosomes than extra autosomes. … Compared to autosomal trisomies, … sex chromosome trisomies are fairly benign. Affected individuals generally show reduced sexual development and fertility, but they often have normal life spans, and many of their symptoms can be treated by hormone supplementation. The ability of humans to tolerate supernumerary sex chromosomes is quite remarkable, as individuals can survive with as many as four sex chromosomes. &lt;strong&gt;This tolerance most likely relates to both X inactivation and to the small number of genes on the Y chromosome.&lt;/strong&gt; In fact, when cells from individuals with more than one copy of the X chromosome are analyzed under a microscope, all but one of the X chromosomes appear as condensed Barr bodies, the cytological manifestations of X-chromosome inactivation. Supernumerary copies of the Y chromosome may be tolerated because the few gene products of the Y chromosome are not required for survival.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From: &lt;a href=&quot;http://www.nature.com/scitable/topicpage/chromosomal-abnormalities-aneuploidies-290&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chromosomal Abnormalities: Aneuploidies by Clare O'Connor&lt;/a&gt; (emphasis added)&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;An added bonus (and I feel as though I should actually write something myself), I recently read a paper studying trisomy 21: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848249/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Jiang J, Jing Y, Cost GJ, Chiang JC, Kolpa HJ, Cotton AM, Carone DM, Carone BR, Shivak DA, Guschin DY, Pearl JR, Rebar EJ, Byron M, Gregory PD, Brown CJ, Urnov FD, Hall LL, Lawrence JB. 2013. Translating dosage compensation to trisomy 21. Nature 500(7462):296-300.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using zinc finger nucleases, they inserted a &lt;a href=&quot;https://en.wikipedia.org/wiki/XIST&quot; rel=&quot;nofollow noreferrer&quot;&gt;XIST&lt;/a&gt; transgene into chromosome 21 of cells derived from Down syndrome patients. XIST is a gene centrally involved in X-inactivation. They found that, by inserting it into chromosome 21, they were able to silence one and revert the trisomic cells to a more normal phenotype.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2018-06-26T05:29:32.047" LastActivityDate="2018-06-26T05:29:32.047" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="35402" PostTypeId="1" AcceptedAnswerId="35403" CreationDate="2015-06-21T06:21:54.417" Score="3" ViewCount="175" Body="&lt;p&gt;What plant species is this? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Its stalk looks like a grapevine, but the leaves &amp;amp; flowers not. It bloomed this week (Mid-June). I have found it in Turkey, Amasya.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/gme80.jpg&quot; alt=&quot;flower&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want, I can add more shots of plant.&lt;/p&gt;&#xA;" OwnerUserId="15398" LastEditorUserId="9943" LastEditDate="2015-06-21T10:09:28.427" LastActivityDate="2015-06-21T10:09:28.427" Title="Plant identification" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35403" PostTypeId="2" ParentId="35402" CreationDate="2015-06-21T06:30:47.470" Score="6" Body="&lt;p&gt;That is a kind of honeysuckle. The picture below is for Japanese honeysuckle (Lonicera japonica), but your specimen is different in the way the flowers are arranged and that the distal-most paired leaves are clasping the stem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rn3sm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It might be Lionicera periclymenum, or Lonicera etrusca (there are about 150 species of honeysuckle); &lt;a href=&quot;https://en.wikipedia.org/wiki/Lonicera_etrusca&quot; rel=&quot;nofollow noreferrer&quot;&gt;L. etrusca&lt;/a&gt; is pictured below (the color is irrelevant) which is native to Europe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UXDj1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-06-21T07:08:35.667" LastActivityDate="2015-06-21T07:08:35.667" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35404" PostTypeId="1" AcceptedAnswerId="35411" CreationDate="2015-06-21T07:16:09.690" Score="0" ViewCount="175" Body="&lt;p&gt;I am new to this area. I am a researcher working on fast pattern searching in general scenarios (e.g., regex in string matching). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am curious about the &quot;regular expression (regex)&quot; (pattern/motif) in bioinformatics. Can anyone help point out some repository where I can see some &quot;regex&quot; instances (used by people in real cases)? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So that I can get a sense how complex they are and the possibility to apply our techniques. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!&lt;/p&gt;&#xA;" OwnerUserId="16334" LastActivityDate="2015-06-21T20:45:35.457" Title="Patterns/Motifs Repository" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;dna-sequencing&gt;" AnswerCount="3" CommentCount="1" ClosedDate="2015-06-22T07:54:13.440" ContentLicense="CC BY-SA 3.0" />
  <row Id="35405" PostTypeId="2" ParentId="35397" CreationDate="2015-06-21T07:35:03.707" Score="3" Body="&lt;p&gt;House flies (Musca domestica) prefer to rest on light colored surfaces, and what is lighter than windows, windowframes, glossy surfaces that reflect light, etc.? Where they rest (not eat) is where they defecate (or regurgitate), leaving marks politely called &quot;fly specks&quot;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;House flies also leave &lt;a href=&quot;http://www.ipm.ucdavis.edu/PMG/PESTNOTES/pn7457.html&quot; rel=&quot;nofollow&quot;&gt;dark fecal and regurgitation spots&lt;/a&gt; on wall surfaces where they rest, and with a preference for resting on light colored surfaces, these spots can be quite noticeable when fly numbers are high.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you ever visit an &quot;open&quot; barn, you'll notice the phenomenon is quite remarkable. If the number of flies is high, there will be specks everywhere, but the windows and other shiny surfaces will be more densely covered.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-06-21T07:35:03.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35406" PostTypeId="2" ParentId="35404" CreationDate="2015-06-21T09:35:19.600" Score="3" Body="&lt;p&gt;Regular expressions are not commonly used for DNA or Protein analysis, but many people use Hidden-Markov-Models (HMMs).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are looking at protein domains, you can find many HMMs here:&#xA;&lt;a href=&quot;http://pfam.xfam.org/&quot; rel=&quot;nofollow&quot;&gt;http://pfam.xfam.org/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15791" LastActivityDate="2015-06-21T09:35:19.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35407" PostTypeId="1" AcceptedAnswerId="35409" CreationDate="2015-06-21T09:39:48.460" Score="2" ViewCount="843" Body="&lt;p&gt;Most &lt;a href=&quot;https://en.wikipedia.org/wiki/Biological_life_cycle&quot; rel=&quot;nofollow noreferrer&quot;&gt;life cycles&lt;/a&gt; we knew of consist of a juvenile stage (e.g. larval for insects, sporozoite for some intracellular parasites), a reproductive stage and an adult stage. Usually the reproductive stage occur when the organism reached the adult stage.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But are their examples of organisms where its natural life cycle involve reproduction at an early stage, and then the parent then went through more distinctive stages after the reproductive stage and then dies off? For example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qP3RZ.png&quot; alt=&quot;hand-drawn illustration of what OP means&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The closest thing I can think of is the life cycle of mayflies, which dies a short period after the mating stage. But &lt;strong&gt;mayflies has only one adult stage&lt;/strong&gt; thus it is does not really answer the question&lt;/p&gt;&#xA;" OwnerUserId="15973" LastEditorUserId="9829" LastEditDate="2015-06-21T15:01:31.377" LastActivityDate="2015-06-21T17:43:08.333" Title="Any examples of an organism's life cycle where the reproductive stage occur before the 'adult' stage?" Tags="&lt;development&gt;&lt;life-history&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35409" PostTypeId="2" ParentId="35407" CreationDate="2015-06-21T15:33:35.207" Score="4" Body="&lt;p&gt;There are two important points here:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The adult phase is defined as the phase during which reproduction occurs. It is therefore impossible for reproduction not to occur during the adult phase as you would immediately call this phase the adult phase. Because of this purely semantic issue (nothing to do with biology) the answer to your question is necessarily &quot;no&quot;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Only kin selection/group selection/lineage selection makes life after the reproductive age possible. It is therefore a pretty rare phenomenon. If this is unclear, you may want to read things about the evolution of ageing such as &lt;a href=&quot;https://biology.stackexchange.com/questions/17077/why-does-evolution-not-make-our-life-longer&quot;&gt;this post&lt;/a&gt; for example.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Maybe a question that would be of higher interest would be something along the lines of: &quot;Can you list species that have non/reproductive phases in between a reproductive phase and death?&quot; or &quot;Are there any species that undergo different reproductive phases during their lives such as being first a sneaker and then territorial (yes) or such reproducing asexually at first and then sexually (probably but can't think of any examples)?&quot;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-06-21T17:43:08.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35410" PostTypeId="1" AcceptedAnswerId="35412" CreationDate="2015-06-21T18:27:13.140" Score="5" ViewCount="541" Body="&lt;p&gt;I have a &lt;em&gt;Chamaerops humilis&lt;/em&gt; in my apartment and in there is these small plants growing. I live in Denmark, Europe and my palm tree has only been inside my apartment since i got it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone identify this plant?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&lt;sub&gt;Click on photos for full size&lt;/sub&gt;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oz9YDm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/GeEQCm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Qhv09m.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user14636" LastEditorDisplayName="user14636" LastEditDate="2015-06-21T20:26:44.310" LastActivityDate="2015-06-21T20:26:44.310" Title="Can anyone help me identify this plant?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35411" PostTypeId="2" ParentId="35404" CreationDate="2015-06-21T18:53:28.713" Score="1" Body="&lt;p&gt;Prosite (&lt;a href=&quot;http://prosite.expasy.org/&quot; rel=&quot;nofollow&quot;&gt;http://prosite.expasy.org/&lt;/a&gt;) uses regular expressions to search for protein domains, in contrast with Pfam. If you look at an entry, such as &lt;a href=&quot;http://prosite.expasy.org/cgi-bin/prosite/prosite-search-ac?PDOC00022&quot; rel=&quot;nofollow&quot;&gt;http://prosite.expasy.org/cgi-bin/prosite/prosite-search-ac?PDOC00022&lt;/a&gt;, you can see the consensus pattern under the PATTERN section towards the bottom. Prosite does not have the same coverage as Pfam, but the ease of searching means it is updated much more frequently and has tighter integration with UniProt.&lt;/p&gt;&#xA;" OwnerUserId="15966" LastActivityDate="2015-06-21T18:53:28.713" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35412" PostTypeId="2" ParentId="35410" CreationDate="2015-06-21T19:02:03.167" Score="7" Body="&lt;p&gt;It's a bit early yet, but it looks very much like a weed known in my area as &quot;cleavers&quot; or &quot;clingweed&quot; (&lt;a href=&quot;https://en.wikipedia.org/wiki/Galium_aparine&quot; rel=&quot;nofollow noreferrer&quot;&gt;Galium aparine&lt;/a&gt;) because of it's tiny stiff hairs which make it catch and cling to clothing. The picture below is for a fully mature plant, which is stiffer and stickier than when they first sprout. Note the whorl arrangement of (usually six) leaves, with each leaf having a &quot;point&quot; protruding from the tip, the distrubution of hooked hairs along stem and leaf, and the initially prostrate habit (they grow along the ground initially). The mature stem will be squarish and easily crushed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/t1gR6.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though your plant's leaves are broader, there are ~650 species of Galium, and I believe yours will be either Galium aparine or &lt;a href=&quot;http://www.torrens.org.uk/FFF/plants/G/Galium/Mollugo6.jpeg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Galium mollugo&lt;/a&gt;. But you'll be able to tell what it truly is when it flowers.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-06-21T19:02:03.167" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="35413" PostTypeId="2" ParentId="35201" CreationDate="2015-06-21T19:05:26.090" Score="6" Body="&lt;p&gt;There are a couple of reasons why this approach doesn't work quite as well as you might hope.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, insulin doesn't go away after a high-fat meal. &lt;a href=&quot;http://www.jissn.com/content/8/1/19&quot;&gt;This paper&lt;/a&gt; reports changes in serum insulin following pure-sugar and pure-fat meals. Although there is much less of an increase in insulin following the pure-fat versus the pure-sugar meal, you will notice in Figure 1 that the insulin levels following the pure-fat meals (panel A) are higher than the levels during a fast (panel B). So even if high insulin were the only signal for fat storage, your dream of eliminating insulin with a high-fat meal is not realistic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, when a high-fat diet is designed for &lt;a href=&quot;https://en.wikipedia.org/wiki/Ketogenic_diet&quot;&gt;medical purposes&lt;/a&gt;, a good deal of care is required to avoid significant potential adverse effects. Adequate protein intake is still required, and amino acids from the protein can be converted to glucose. Furthermore, ketoacids are produced when fatty acids from ingested fat are in excess. (As noted in comments, humans do not convert fatty acids to glucose.) Although ketoacids can be excreted in the urine (admittedly, heading toward your goal of not storing all the calories you consume), the net metabolic effect on the body when you excrete ketoacids is increased acidification, which in turn can lead to difficulties with potassium regulation and thus, in severe cases, with heart function. In the extreme if this were continued for a long time, you may face a problem of life-threatening &lt;a href=&quot;https://en.wikipedia.org/wiki/Ketoacidosis&quot;&gt;ketoacidosis&lt;/a&gt; as occurs in type-1 diabetics (low/no insulin) whose disease is not being managed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That said, your basic idea is similar to the arguments for &lt;a href=&quot;https://en.wikipedia.org/wiki/Low-carbohydrate_diet&quot;&gt;low-carbohydrate diets&lt;/a&gt;. How well they work and, if they do, through what mechanisms are still somewhat controversial, as I understand. Insofar as they work through excreting some of the ingested fat through urinary loss of ketoacids, however, the associated risks need to be considered.&lt;/p&gt;&#xA;" OwnerUserId="16326" LastActivityDate="2015-06-21T19:05:26.090" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35414" PostTypeId="1" AcceptedAnswerId="57957" CreationDate="2015-06-21T19:10:48.057" Score="6" ViewCount="169" Body="&lt;p&gt;I understand that the vertical tails of fish and the horizontal flukes of cetaceans evolved due to the spinal movements of their ancestors but I was just wondering if there has been any investigation into which was the most efficient for swimming (speed, required effort etc...)?&lt;/p&gt;&#xA;" OwnerDisplayName="user16263" LastEditorUserId="3553" LastEditDate="2017-04-03T05:06:38.317" LastActivityDate="2017-04-03T05:06:38.317" Title="Best tail for swimming?" Tags="&lt;zoology&gt;&lt;marine-biology&gt;&lt;ichthyology&gt;&lt;locomotion&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35415" PostTypeId="1" AcceptedAnswerId="35422" CreationDate="2015-06-21T19:23:27.610" Score="15" ViewCount="2382" Body="&lt;p&gt;Chromosome number differs across species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the amount of DNA comparable between organisms, just being split into smaller chunks in those species with more chromosomes, or do species have different genome sizes? If so, does the genome size correlate roughly with the complexity of the species?&lt;/p&gt;&#xA;" OwnerUserId="9910" LastEditorUserId="6307" LastEditDate="2017-10-18T00:23:41.383" LastActivityDate="2018-06-01T05:24:53.623" Title="Is the size of the genome across species roughly the same?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;chromosome&gt;&lt;species&gt;&lt;genomes&gt;" AnswerCount="3" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="35417" PostTypeId="2" ParentId="35404" CreationDate="2015-06-21T20:45:35.457" Score="0" Body="&lt;p&gt;You will probably want to read up on Position Frequency Matrices (PFMs) and Position Weight Matrices (PWMs).  These tend to be much more sensitive and useful for pattern recognition in nuclei acid sequences. Two examples of databases with these patterns are TRANSFAC and JASPAR. Regex patterns can be useful in protein sequences sometimes, although PWM have application there as well.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-06-21T20:45:35.457" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35418" PostTypeId="2" ParentId="35415" CreationDate="2015-06-21T23:54:22.663" Score="2" Body="&lt;p&gt;I can show the facts here. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Human:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;total length: about 3,000,000,000&lt;/p&gt;&#xA;&#xA;&lt;p&gt;coding genes: about 50,000 (included predicted ones)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3,000,000,000/50,000=60,000&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chromosome number: 23&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Zebrafish:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;total length: about 1,400,000,000&lt;/p&gt;&#xA;&#xA;&lt;p&gt;coding genes: about 36,000 (included predicted ones)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1,400,000,000/36,000=38,889&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chromosome number: 25&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fruitfly:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;total length: about 1,400,000,000&lt;/p&gt;&#xA;&#xA;&lt;p&gt;coding genes: about 19,000 (included predicted ones)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1,400,000,000/19,000=73,684&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chromosome number: 4&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Saccharomyces cerevisiae:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;total length: about 12,000,000&lt;/p&gt;&#xA;&#xA;&lt;p&gt;coding genes: about 7,000 (included predicted ones)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;12,000,000/7,000=1,714&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chromosome number: 16&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://useast.ensembl.org/Homo_sapiens/Info/Annotation&quot; rel=&quot;nofollow&quot;&gt;http://useast.ensembl.org/Homo_sapiens/Info/Annotation&lt;/a&gt;&#xA;&lt;a href=&quot;http://useast.ensembl.org/Danio_rerio/Info/Annotation&quot; rel=&quot;nofollow&quot;&gt;http://useast.ensembl.org/Danio_rerio/Info/Annotation&lt;/a&gt;&#xA;&lt;a href=&quot;http://useast.ensembl.org/Drosophila_melanogaster/Info/Annotation&quot; rel=&quot;nofollow&quot;&gt;http://useast.ensembl.org/Drosophila_melanogaster/Info/Annotation&lt;/a&gt;&#xA;&lt;a href=&quot;http://useast.ensembl.org/Saccharomyces_cerevisiae/Info/Annotation&quot; rel=&quot;nofollow&quot;&gt;http://useast.ensembl.org/Saccharomyces_cerevisiae/Info/Annotation&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-06-21T23:54:22.663" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35422" PostTypeId="2" ParentId="35415" CreationDate="2015-06-22T05:09:12.810" Score="28" Body="&lt;p&gt;Chart of C-values (the mass of DNA in a single haploid cell); there is no logical order to the groups:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nxOdG.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[&lt;a href=&quot;https://www.genomesize.com/statistics.php&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Base pairs in haploid genome (some examples):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;em&gt;Escherichia coli&lt;/em&gt; (bacterium): ~4.5 million&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Caenorhabditis elegans&lt;/em&gt; (nematode worm): ~100 million&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Homo sapiens&lt;/em&gt; (we all know what these are): ~3 billion&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Pinus taeda&lt;/em&gt; (coniferous tree): ~22 billion&lt;/li&gt;&#xA;&lt;li&gt;&lt;em&gt;Prorocentrum micans&lt;/em&gt; (single-celled algae): ~245 billion&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;From these data we can conclude:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Different species do not have the same genome size. &lt;/li&gt;&#xA;&lt;li&gt;Genome size is not correlated with complexity. Organismal complexity can be hard to define but, qualitatively, I think we can all agree that a human is more complex than a single-celled alga. And yet, humans have a genome that is 80 times smaller. This is known as the C-value paradox. Note, however, that this paradox has been resolved after it was found that the genomes of most eukaryotes contain a large proportion of non-coding and repetitive DNA.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Further reading:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.cell.com/current-biology/fulltext/S0960-9822(12)01154-2&quot; rel=&quot;nofollow noreferrer&quot;&gt;The C-value paradox, junk DNA and ENCODE by Eddy SR&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity-437&quot; rel=&quot;nofollow noreferrer&quot;&gt;Eukaryotic Genome Complexity by Pray L&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2018-06-01T05:24:53.623" LastActivityDate="2018-06-01T05:24:53.623" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="35423" PostTypeId="2" ParentId="35415" CreationDate="2015-06-22T05:26:00.430" Score="7" Body="&lt;p&gt;It is already mentioned by canadianer that genome size differs between organisms. But what about complexity?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First we should define what complexity is: complexity can be defined as number of different cell types that a multicellular organism can produce, with the same genome. Yes complexity does not correlate with genome size. However, it seems to correlate with number of genes. According to Kauffman, the number of cell types i.e. complexity is linearly correlated (direct correlation) with the square root of number of genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Wy0ZF.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Though Kauffman says that complexity increases with DNA content, which is not actually true, it is certainly possible that that complexity is correlated with number of genes. The book is a little old and certainly molecular and cell biology has seen a lot of progress in this time. However, theoretically higher number of distinct genes should produce more complex phenotypes which Kauffman justifies using his NK-model. This assumption has again been &lt;a href=&quot;http://www.genomebiology.com/2010/11/5/206&quot; rel=&quot;nofollow noreferrer&quot;&gt;disproved&lt;/a&gt;. The catch would be that exact duplicates/polyploid genes should not be counted as different genes. Moreover metabolic genes should also not be counted (plants/bacteria have a higher number of functional metabolic pathways). Organismal complexity arises because of the complexity of gene regulatory network which in-turn is dependent on the number of regulatory genes. NK model also in a way assumes regulatory genes (i.e. genes that can interact with each other). Surely complexity cannot arise out of nothing. I can't find the data for this at the moment but the theory is quite strongly plausible. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another point I would like to add is that complexity need not only mean spatial complexity. Complexity can also be temporal. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt; Reference:&#xA;&lt;br&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;Stuart A Kauffman (1993) The Origins of Order, Chapter 12 &lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-22T10:35:38.053" LastActivityDate="2015-06-22T10:35:38.053" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35425" PostTypeId="1" CreationDate="2015-06-22T08:14:28.077" Score="3" ViewCount="1321" Body="&lt;p&gt;I have a general question regarding which method would you recommend me to use if I would like to investigate the difference in the level of several proteins in tissue samples and compare different treatment groups. I could either do an LCMS/MS or a Western blot. Which one would you recommend and would you do both for validation? I am looking for time- and cost-effective techniques. &#xA;I'll appreciate any suggestions.&#xA;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="16347" LastEditorUserId="3340" LastEditDate="2015-06-22T13:34:17.407" LastActivityDate="2015-06-23T11:37:52.773" Title="LCMS/MS versus Western Blot" Tags="&lt;proteins&gt;&lt;lab-techniques&gt;&lt;western-blot&gt;&lt;methods&gt;" AnswerCount="3" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35426" PostTypeId="2" ParentId="35425" CreationDate="2015-06-22T09:22:57.620" Score="3" Body="&lt;p&gt;Western blot, though is a commonly used technique and is relatively simple to do, has some issues:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Low throughput: it is difficult to analyse multiple proteins simultaneously&lt;/li&gt;&#xA;&lt;li&gt;Limited cross comparability: since antibodies to different proteins can have different affinities, they cannot be compared with each other.&lt;/li&gt;&#xA;&lt;li&gt;Low sensitivity&lt;/li&gt;&#xA;&lt;li&gt;Not very quantitative&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;LCMS addresses all the above limitations of western blot. It is also possible to do &lt;a href=&quot;http://www.nature.com/nmeth/journal/v10/n1/full/nmeth.2285.html&quot; rel=&quot;nofollow&quot;&gt;targeted proteomics&lt;/a&gt; i.e. study just some few proteins instead of the entire proteome.&#xA;An LCMS system has a high initial setting up cost but a relatively lower run cost. However, the mass spectrometer has to be maintained and it is not an easy job; you basically need a facility and a dedicated technical staff.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Which one would you recommend and would you do both for validation?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Which technique to use depends on what you really want to see and what resources you have at hand. It is a commonly practised approach to do a western blot for re-validating a few selected genes identified from LCMS experiment, which is just to prove that the result can be obtained using another technique too. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-22T13:31:23.147" LastActivityDate="2015-06-22T13:31:23.147" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35427" PostTypeId="1" AcceptedAnswerId="35428" CreationDate="2015-06-22T11:03:44.310" Score="3" ViewCount="674" Body="&lt;p&gt;Is it &lt;a href=&quot;http://www.uamshealth.com/heartmyth&quot; rel=&quot;nofollow&quot;&gt;fact&lt;/a&gt; or &lt;a href=&quot;http://www.webmd.com/allergies/features/11-surprising-sneezing-facts?page=2&quot; rel=&quot;nofollow&quot;&gt;myth&lt;/a&gt; that our heart stops beating for moments when we sneeze? If it is fact, what drives the heart to start beating again?&lt;/p&gt;&#xA;" OwnerUserId="16350" LastEditorUserId="9943" LastEditDate="2015-06-22T11:54:54.333" LastActivityDate="2015-06-23T12:43:19.323" Title="Does our heart stop when we sneeze?" Tags="&lt;human-biology&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35428" PostTypeId="2" ParentId="35427" CreationDate="2015-06-22T11:43:45.117" Score="6" Body="&lt;p&gt;Both your linked &lt;a href=&quot;http://www.uamshealth.com/heartmyth&quot; rel=&quot;nofollow&quot;&gt;fact from the University of Arkansas&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When you sneeze, the intrathoracic pressure in your body momentarily increases. This will decrease the blood flow back to the heart. The &lt;em&gt;heart compensates&lt;/em&gt; for this by changing its regular heart beat momentarily to adjust. However, the &lt;strong&gt;electrical activity of the heart does not stop&lt;/strong&gt; during the sneeze. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;...as well as your &lt;a href=&quot;http://www.webmd.com/allergies/features/11-surprising-sneezing-facts?page=2&quot; rel=&quot;nofollow&quot;&gt;'myth' from webMD&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;For instance, it's &lt;strong&gt;&lt;em&gt;not true that your heart stops&lt;/em&gt;&lt;/strong&gt; when you sneeze. When your chest contracts because of a sneeze, your blood flow is momentarily constricted as well. As a result, the rhythm of your heart may change, but it definitely doesn't stop.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;...come to the &lt;strong&gt;same conclusion&lt;/strong&gt;, namely the heart does not stop during a sneeze.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-23T12:43:19.323" LastActivityDate="2015-06-23T12:43:19.323" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35429" PostTypeId="2" ParentId="31716" CreationDate="2015-06-22T11:57:52.890" Score="1" Body="&lt;p&gt;&lt;em&gt;This is more of a hypothesis&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I am not sure if suffocation per se would cause pain. Asphyxia, as RoryM indicated in their comments, can lead to anxiety and panic but not really pain. However, forceful breathing may lead to muscular fatigue which may result in pain. Pain induced by muscle fatigue is called myalgia. Myalgia is possibly triggered by low pH generated by lactic acid, via ASIC3 (Acid Sensing Ion Channel) receptor. Carbon dioxide has no role in this process either directly or as a synergist. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;&lt;strong&gt;Reference&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alan R. Light, Charles J. Vierck, and Kathleen C. Light. (2010) &lt;em&gt;Translation from Mouse Sensory Neurons to Fibromyalgia and Chronic Fatigue Syndromes&lt;/em&gt;. Boca Raton, FL: CRC Press; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK57253/&quot; rel=&quot;nofollow&quot;&gt;Chapter 11 (Myalgia and Fatigue)&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-22T13:04:11.937" LastActivityDate="2015-06-22T13:04:11.937" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35430" PostTypeId="2" ParentId="35425" CreationDate="2015-06-22T12:35:41.307" Score="1" Body="&lt;p&gt;Although quantitative methods using MS have been developed, MS is not inherently quantitative. Quantification with MS could be quite tricky. Therefore, it is not the first choice. But, if you do not know which protein levels change and want to find proteins the expression levels of which are different between your samples you are going to compare, MS is not bad idea. In this case, validation is necessary. In other words, MS is not used to validate WB results in general.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In your case, you know which proteins you want to see. Therefore, I would suggest WB. This is a more direct way. Validation of WB may not be necessary, but it is better to get some supportive data: the protein activities in lysates, mRNA levels, etc.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-06-22T12:35:41.307" CommentCount="18" ContentLicense="CC BY-SA 3.0" />
  <row Id="35431" PostTypeId="1" AcceptedAnswerId="35433" CreationDate="2015-06-22T13:05:31.353" Score="5" ViewCount="376" Body="&lt;p&gt;Falling asleep or states of subconsciousness does not stop the mind from making its own fictional images. These seem like sensations just like those received from human eyes. But, how do we define these visual sensations biologically? &lt;/p&gt;&#xA;" OwnerUserId="16350" LastEditorUserId="9943" LastEditDate="2015-06-22T14:21:32.137" LastActivityDate="2016-02-21T23:12:50.873" Title="What are dreams, biologically?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;vision&gt;&lt;sensation&gt;&lt;dreaming&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35432" PostTypeId="2" ParentId="17565" CreationDate="2015-06-22T13:52:35.773" Score="4" Body="&lt;p&gt;Well it depends what you mean by helping digestion. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;https://skeptics.stackexchange.com/posts/11169/edit&quot;&gt;answer&lt;/a&gt; in skeptics may shade some light:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;b&gt;a walk after my lunch [is] a healthy habit that helps with digestion.&lt;/b&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Walking may be a healthy habit but it does not specifically assist digestion. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Digestion is a process which takes place in resting conditions. Exercise is characterised by a shift in blood flow away from the gastrointestinal (GI) tract towards the active muscle and the lungs.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;From: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8460288&quot; rel=&quot;nofollow noreferrer&quot;&gt;Is the gut an athletic organ? Digestion, absorption, and exercise. [Sports Med. 1993] - PubMed - NCBI&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So it's seems walking help sugar level (but this is independent to having eaten just before) but seems to not be beneficial to the digestion (in particular stomach contractions ― nutrient absorption will only start in general two hours after your meal, once the food leave the stomac)   &lt;/p&gt;&#xA;" OwnerUserId="5908" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2015-06-22T13:58:47.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35433" PostTypeId="2" ParentId="35431" CreationDate="2015-06-22T13:54:47.327" Score="12" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;In terms of visual function, the low-tier primary visual cortex and high-tier frontal cortex are inactivated. The activity of the intermediate ventral stream and limbic regions are increased, apparently uncoupling low- and high-level vision processing from the system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The sleep stage where visualizations (dreaming) occur is called the rapid-eye movement &lt;a href=&quot;http://sleepfoundation.org/sleep-disorders-problems/rem-behavior-disorder&quot; rel=&quot;nofollow&quot;&gt;(REM) sleep&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Brain imaging studies have shown pronounced effects of REM sleep on the functioning of the visual system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the awake state, the primary visual cortex &lt;a href=&quot;http://thebrain.mcgill.ca/flash/d/d_02/d_02_cr/d_02_cr_vis/d_02_cr_vis.html&quot; rel=&quot;nofollow&quot;&gt;(V1, or &lt;em&gt;striate cortex&lt;/em&gt;)&lt;/a&gt; is activated, which is mainly concerned with low-level visual processing such as contrast perception. This cortical region in turn projects to higher-level (&lt;em&gt;extrastriate&lt;/em&gt;) regions for more complex processing of visual information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During REM sleep, however, a selective activation of extrastriate visual cortices is observed. Particularly the ventral processing stream is activated, which is associated with perception and recognition in the awake state &lt;a href=&quot;http://www.universitaet-bielefeld.de/psychologie/ae/Ae01/People/Werner%20Schneider/Deubel_Schneider_Paprotta1998.pdf&quot; rel=&quot;nofollow&quot;&gt;(Deubel &lt;em&gt;et al&lt;/em&gt;., 1998)&lt;/a&gt;. Also the &lt;a href=&quot;https://en.wikipedia.org/wiki/Limbic_system&quot; rel=&quot;nofollow&quot;&gt;limbic&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Paralimbic_cortex&quot; rel=&quot;nofollow&quot;&gt;paralimbic&lt;/a&gt; regions are active (the emotional brain centers).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, activity in the primary visual cortex (V1) is attenuated, as well as the frontal association areas of the brain. V1 is the primary, most 'primitive' visual cortex, while the frontal association areas are the highest-tier cortex that integrates complex perceptual information across perceptual modalities &lt;a href=&quot;http://www.researchgate.net/profile/Gregory_Belenky/publication/235234796_Dissociated_Pattern_of_Activity_in_Visual_Cortices_and_Their_Projections_During_Human_Rapid_Eye_Movement_Sleep/links/0fcfd5112e21157cd0000000.pdf&quot; rel=&quot;nofollow&quot;&gt;(Braun &lt;em&gt;et al&lt;/em&gt;., 1998)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall, this pattern suggests a model of REM sleep where visual association cortices and their paralimbic projections may operate as a closed system dissociated from the regions at either end of the visual hierarchy that mediate interactions with the external world &lt;a href=&quot;http://www.researchgate.net/profile/Gregory_Belenky/publication/235234796_Dissociated_Pattern_of_Activity_in_Visual_Cortices_and_Their_Projections_During_Human_Rapid_Eye_Movement_Sleep/links/0fcfd5112e21157cd0000000.pdf&quot; rel=&quot;nofollow&quot;&gt;(Braun &lt;em&gt;et al&lt;/em&gt;., 1998)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.researchgate.net/profile/Gregory_Belenky/publication/235234796_Dissociated_Pattern_of_Activity_in_Visual_Cortices_and_Their_Projections_During_Human_Rapid_Eye_Movement_Sleep/links/0fcfd5112e21157cd0000000.pdf&quot; rel=&quot;nofollow&quot;&gt;Braun &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Science&lt;/em&gt; (1998); &lt;strong&gt;279&lt;/strong&gt;: 91-5&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.universitaet-bielefeld.de/psychologie/ae/Ae01/People/Werner%20Schneider/Deubel_Schneider_Paprotta1998.pdf&quot; rel=&quot;nofollow&quot;&gt;Deubel &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Vis Cognition&lt;/em&gt; (1998); &lt;strong&gt;5&lt;/strong&gt;(1/2), 81–107&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-02-21T23:12:50.873" LastActivityDate="2016-02-21T23:12:50.873" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35434" PostTypeId="1" AcceptedAnswerId="35435" CreationDate="2015-06-22T14:13:50.797" Score="5" ViewCount="1599" Body="&lt;p&gt;I know some elementary chemistry and biology. I also think I know what a gene is (it's a sequence of DNA which encodes a particular protein). I also know that on a chromosome there are sections of DNA which are kind of junk and do nothing. But being armed with this information, doesn't seem enough for me to understand what it means to &quot;map the human genome&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some possibilities:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;a. It tells me the entire sequences of nucleotides that make up a particular human's chromosomes (it could not possibly do this for humans in general because of course the sequence is different from one human to another).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;b. It tells me the entire sequences of nucleotides that make up a human's chromosomes... with some annotations along the lines of &quot;at this point in the molecule, we could optionally have nucleotides A, B or C&quot;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It tells me the start and stop points for each of the genes along the chromosome.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;It tells me the function of every gene.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Something completely different!&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="16353" LastEditorUserId="16353" LastEditDate="2015-06-23T07:07:31.850" LastActivityDate="2015-06-23T08:36:28.987" Title="What does it mean to &quot;map the human genome&quot;" Tags="&lt;dna&gt;&lt;chromosome&gt;&lt;gene&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35435" PostTypeId="2" ParentId="35434" CreationDate="2015-06-22T14:51:16.747" Score="4" Body="&lt;p&gt;So, the very first map of the human genome was of a few pooled samples with a single nucleotide called at each position.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is basically okay, though, because humans are 99.9 (with possibly a few more 9s) % similar to one another. So you can get a lot of broadly-applicable information out of a single individual's DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Further genome-mapping efforts brought data from new individuals and started to give us information about variants, like in your option 1b. At this point, there are projects like &lt;a href=&quot;http://www.1000genomes.org/&quot; rel=&quot;nofollow&quot;&gt;the 1000 Genomes Project&lt;/a&gt; that are trying to get 1000 full human genomes from a variety of ethnic groups sequenced and to characterize all the common variations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your point 2 was a different project, but was also part of mapping the genome. It's mostly complete now-- in that we know almost all of the RNA sequences that are produced by most cell types and mostly where they come from on the genome, with a few mysteries left around the edges. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Point 3-- no. Lots about the genome we still don't know. We're pretty good about where genes are encoded, but how they're regulated, how they interact... and remember that the part of the genome that codes for genes is a very small percentage of the overall sequence. Something like the &lt;a href=&quot;https://en.wikipedia.org/wiki/ENCODE&quot; rel=&quot;nofollow&quot;&gt;the ENCODE Project&lt;/a&gt; is trying to figure out the various biochemical interactions present at every position of DNA, but even if that data were complete and reliable, which it's not, it still wouldn't tell us the &quot;purpose&quot; of all DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, when we say we've &quot;mapped&quot; a genome, we generally mean (A) we have (something pretty close to) full sequence of at least one individual's DNA (or a consensus sequence from a pool) and (B) we know where genes are on it. That's a huge step but only the beginning of understanding genetics. In the case of humans, we're adding on to that understanding by learning where variants are and how common they are.&lt;/p&gt;&#xA;" OwnerUserId="819" LastEditorUserId="3340" LastEditDate="2015-06-23T08:36:28.987" LastActivityDate="2015-06-23T08:36:28.987" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35437" PostTypeId="1" CreationDate="2015-06-22T15:54:13.760" Score="0" ViewCount="671" Body="&lt;p&gt;First of all,I am very bad at biology. So please bear if it sounds elementary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I heard about lasik operation for reshaping cornea.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Assume the patient is suffering from myopia implying lens is thicker than expected.So if i think logically ,to correct the lens thickness ,lens must be reduced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In lasik, do they cut the lens's tissue.If yes what happens to the part that is cut and if no then how exactly lens thickness is reduced?&lt;/p&gt;&#xA;" OwnerUserId="16355" LastActivityDate="2015-06-22T17:45:35.833" Title="What happens in lasik operation?" Tags="&lt;eyes&gt;&lt;human-eye&gt;&lt;surgery&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35438" PostTypeId="1" CreationDate="2015-06-22T17:21:32.353" Score="4" ViewCount="643" Body="&lt;p&gt;Assuming two trees have similar shape and leaf coverage, could differences in the biological processes among them lead to differences in the temperature of the shadow they cast?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What biological processes occurring in plants could affect this?&lt;/strong&gt; I was thinking that transpiration will cause heat loss, and photosynthesis also absorbs energy, so these would contribute. What other processes that occur in a tree could affect the dissipation of heat causing cooler shade? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Has there been any studies specific to rates of transpiration and photosynthesis, and the effect on shade temperature?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="16866" LastEditDate="2018-11-01T01:04:09.317" LastActivityDate="2018-11-01T01:04:09.317" Title="What biological processes can affect the temperature of the shadow a tree casts?" Tags="&lt;biochemistry&gt;&lt;botany&gt;&lt;biophysics&gt;&lt;trees&gt;" AnswerCount="1" CommentCount="10" ContentLicense="CC BY-SA 4.0" />
  <row Id="35439" PostTypeId="2" ParentId="35437" CreationDate="2015-06-22T17:45:35.833" Score="1" Body="&lt;p&gt;There are two possible ways to perform refractive operation: first,  to perform the procedure on the cornea, the second - to exchange the crystalline lens with the artificial one. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The second approach is extremely rare, because the lens (1) is inside the eye and (2) it allows us to accommodate (=change the focus of vision). Thus, this method is relevant only to extremely high myops and people who have some degree of cataract (the clouding of the lens).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In &quot;classic&quot; myopia the eye is larger than &quot;normal&quot; one, and the lens thickness is less relevant in the terms of treatment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Back to LASIK - the operation is performed on the cornea: for myopic eye the corneal thickness should be reduced, for hyperopic eye there are other protocols (special thickness reduction). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XoOB1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-06-22T17:45:35.833" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35441" PostTypeId="1" AcceptedAnswerId="35454" CreationDate="2015-06-22T18:21:38.900" Score="3" ViewCount="86" Body="&lt;p&gt;The viscosity of a population is the tendency of offspring to remain&#xA;near their place of birth. Taylor 1992 (&quot;Altruism in viscous populations&quot;) provides a model to study how viscosity affects the evolution of altruism in a patch-structured population. In Taylor's model, the marginal inclusive fitness is given by&#xA;\begin{equation}&#xA;  W = bR -c - s^{2}(b-c)R&#xA;\end{equation}&#xA;where $R$ is the relatedness of a mother to random offspring born on her breeding patch and $s$ is the probability the offspring will remain on the natal patch. The altruistic act creates $b$ offspring with average relatedness $R$ and $-c$ offspring with relatedness 1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is about the term $s^{2}(b-c)R$. Taylor explains this term as follows:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;these b - c extra offspring remain on the natal patch with probability&#xA;  s and will therefore displace s(b - c) random individuals competing&#xA;  for the next generation breeding spots on that patch, and these will&#xA;  be native to that patch with probability s and in this case will have&#xA;  average relatedness R to the actor. Thus these displaced individuals&#xA;  will have average relatedness sR (p. 353)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My question is:&lt;/strong&gt; Why is the average relatedness $sR$ (as opposed to $R$)? In other words, why is the term that accounts for competition among relatives $s^2(b-c)R$---as opposed to $s(b-c)R$?&lt;/p&gt;&#xA;" OwnerUserId="11829" LastActivityDate="2015-06-22T22:29:15.500" Title="Altruism in viscous (asexual) populations" Tags="&lt;evolution&gt;&lt;mathematical-models&gt;&lt;population-genetics&gt;&lt;sociality&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35442" PostTypeId="1" AcceptedAnswerId="35455" CreationDate="2015-06-22T18:49:37.827" Score="4" ViewCount="320" Body="&lt;p&gt;The figures below are from Felsenstein's paper &quot;Phylogenies and the Comparative Method&quot;. I was wondering if there was a specific name for this effect where there is an apparant correlation that is actually the result of the data being structured into two separate groups, where there is no correlation within groups but an apparent correlation between groups. &quot;Phylogenetic non-independence&quot; doesn't seem specific enough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DuDSs.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14629" LastEditorUserId="9943" LastEditDate="2015-06-23T00:37:37.647" LastActivityDate="2015-06-23T01:09:10.153" Title="Is there a name for this phenomenon described in &quot;Phylogenies and the Comparative Method&quot;?" Tags="&lt;evolution&gt;&lt;terminology&gt;&lt;phylogenetics&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35443" PostTypeId="2" ParentId="30875" CreationDate="2015-06-22T18:50:42.747" Score="1" Body="&lt;p&gt;Yes there are many such mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One of the simplest, but perhaps most easily overlooked, is metabolism.  Conjugation requires ATP.  In environments with low levels of nutrients, heterotrophs might not have enough &quot;extra&quot; ATP to fuel the conjugation process.  Note that both donor and recipient need to expend ATP in conjugation.  The donor needs to make the nicking enzyme, the pilus, and extrude the DNA into the recipient, and the recipient needs to synthesize DNA from the single-strand DNA that it has received.&lt;/p&gt;&#xA;" OwnerUserId="15679" LastActivityDate="2015-06-22T18:50:42.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35445" PostTypeId="2" ParentId="35442" CreationDate="2015-06-22T19:14:13.297" Score="0" Body="&lt;p&gt;The fact that species are not independent observations because of their specific phylogenetic relationship is sometimes called &lt;strong&gt;phylogenetic dependence&lt;/strong&gt; (see its use in &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1055790307004289&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; for example).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most often though, we talk about the existence of such phylogenetic dependence for a particular trait and we talk about &lt;a href=&quot;https://en.wikipedia.org/wiki/Phylogenetics#Phylogenetic_signal&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;phylogenetic signal&lt;/strong&gt;&lt;/a&gt; for this trait.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think (correct me if I am wrong) you're searching for a name to describe a situation where two quantitative traits correlate along a phylogeny (when you have one data point per species) but not within any of the species of this phylogeny. If this is the case, I don't think you will actually find a name for this pattern as it it is already quite specific. You could eventually say that there is an inter-species correlation between the two traits but not an intra-species correlation. &lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-06-23T01:09:10.153" LastActivityDate="2015-06-23T01:09:10.153" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35446" PostTypeId="1" AcceptedAnswerId="35451" CreationDate="2015-06-22T19:36:52.893" Score="35" ViewCount="4827" Body="&lt;p&gt;There are plenty of different hand soaps out there, as well as hand sanitizers. Is there an advantage to soaps that claim that they're antibacterial vs soaps that just say soap?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular I'm looking at Softsoap who offers normal soap and antibacterial soap. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Examples:&lt;/em&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Normal:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/KICCXm.jpg&quot; alt=&quot;Regular Softsoap&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Antibacterial: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jYnyam.jpg&quot; alt=&quot;Antibacterial Softsoap&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="3624" LastEditDate="2015-06-25T08:00:20.600" LastActivityDate="2015-06-27T21:03:22.540" Title="Is there an advantage to antibacterial soap?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;epidemiology&gt;" AnswerCount="5" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35447" PostTypeId="1" CreationDate="2015-06-22T19:52:52.653" Score="12" ViewCount="4233" Body="&lt;h2&gt;First definition.&lt;/h2&gt;&#xA;&lt;p&gt;Two publications by von Heijne in &lt;a href=&quot;http://europepmc.org/abstract/med/2677744&quot; rel=&quot;nofollow noreferrer&quot;&gt;1989&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1593632&quot; rel=&quot;nofollow noreferrer&quot;&gt;1992&lt;/a&gt; coined the 'Positive-Inside rule' and showed it's practical value in topology prediction of transmembrane helices. It was clearly defined and evidenced that in bacteria the positively charged residues more commonly were found on the &amp;quot;inside&amp;quot; of a membrane (the cytoplasm rather than the periplasm).&lt;/p&gt;&#xA;&lt;h2&gt;Recent Literature.&lt;/h2&gt;&#xA;&lt;p&gt;However it seems the field has moved away from the idea of &amp;quot;inside the compartment&amp;quot; to &amp;quot;inside the cytoplasm&amp;quot; as more data became available. In a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17139331&quot; rel=&quot;nofollow noreferrer&quot;&gt;2006 review&lt;/a&gt; even von Heijne describes some transmembrane helices as abiding to the positive inside rule because their positively charged residues were inside the cytoplasm, although never explicitly backtracks on the original definition. A similar review in &lt;a href=&quot;http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.458.7756&amp;amp;rep=rep1&amp;amp;type=pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;2007 by von Heijne&lt;/a&gt; offers a more definitive refinement of the rule, however removes the concept from being applicable to subcellular membranes.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;...the loops connecting the helices differ in amino acid composition, depending on whether they face the inside or outside of the cell (the “positive-inside” rule).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;We are now faced with an awkward rule that doesn't account for proteins elsewhere in the secretory pathway or in the other organelles. All those proteins are inside the cell.&lt;/p&gt;&#xA;&lt;p&gt;More recently still large-scale analysis of transmembrane helices from different biological membrane surfaces, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20603021&quot; rel=&quot;nofollow noreferrer&quot;&gt;Sharpe &lt;em&gt;et al.,&lt;/em&gt; 2010&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22588483&quot; rel=&quot;nofollow noreferrer&quot;&gt;Baeza-Delgado &lt;em&gt;et al.,&lt;/em&gt; 2013&lt;/a&gt;, show the clustering of positive charge being cytosolic rather than discussing it in terms of the inside of the compartment. Both of these papers still say that they corroborate with the positive inside rule.&lt;/p&gt;&#xA;&lt;h2&gt;Question.&lt;/h2&gt;&#xA;&lt;p&gt;To me it seems that the definition is somewhat sloppy and can broadly be used to say &amp;quot;inside the cytoplasm&amp;quot;, despite publications being reluctant to define the rule clearly. &lt;strong&gt;Has the definition ever explicitly been changed, or has the field silently changed what &amp;quot;inside&amp;quot; means?&lt;/strong&gt; ... Or have I completely misinterpreted something? How do the organelles fit into any of these definitions?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2016-05-04T06:32:44.730" Title="What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;biophysics&gt;&lt;cell-membrane&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35448" PostTypeId="2" ParentId="2263" CreationDate="2015-06-22T19:57:50.650" Score="0" Body="&lt;p&gt;Bobthejoe's comment is the best answer so far.  Despite many other types of bacterial colonies being &quot;more&quot; yellow than E. coli, E. coli is definitely not white.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Flavins, especially riboflavins, are the predominant compound responsible for this coloration.&lt;/p&gt;&#xA;" OwnerUserId="15679" LastActivityDate="2015-06-22T19:57:50.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35450" PostTypeId="2" ParentId="35446" CreationDate="2015-06-22T20:13:10.220" Score="14" Body="&lt;p&gt;Chris has correctly identified the antibacterial agent in the hand soap depicted in the image in the question, and therefore his answer is superior as a direct answer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nevertheless, other members of the Softsoap series of hand soap uses &lt;a href=&quot;https://en.wikipedia.org/wiki/Triclosan&quot; rel=&quot;nofollow noreferrer&quot;&gt;triclosan, 0.15%&lt;/a&gt; as their antibacterial agent, as seen in an image of their ingredient list on the reverse of the bottle. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(click for enlarged image)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/sx2SZ.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/sx2SZs.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Triclosan has been shown to be effective by &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/019567019290033I&quot; rel=&quot;nofollow noreferrer&quot;&gt;Webster et al (1992)&lt;/a&gt; in reducing the incidence of MRSA infection as well as being milder to the skin as compared to chlorhexidine gluconate in a neonatal ward. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The average number of new cases of MRSA per week was reduced from 3·4 to 0·14 (P &amp;lt; 0·0001) in the experimental ward whilst no significant changes occurred in the control ward. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Triclosan has also been shown by &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0196655300900270&quot; rel=&quot;nofollow noreferrer&quot;&gt;Jones et al (2000)&lt;/a&gt; to be effective on a large variety of different bacterial, viral and fungal strains. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DAOgE.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SzS9Q.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/p1KuO.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, the usage of triclosan is effective as an antibacterial agent, and would likely result in less bacteria on the hands after washing. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-06-22T20:19:15.173" LastActivityDate="2015-06-22T20:19:15.173" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="35451" PostTypeId="2" ParentId="35446" CreationDate="2015-06-22T20:14:55.627" Score="50" Body="&lt;p&gt;Short answer: There is no benefit for their use in households. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Long answer: These soaps (see &lt;a href=&quot;http://www.colgate.com/app/Softsoap/US/EN/Ingredients.cvsp&quot;&gt;here&lt;/a&gt; for the complete list) contain the so called quaternary ammonium compounds &lt;a href=&quot;https://en.wikipedia.org/wiki/Benzalkonium_chloride&quot;&gt;Benzalkonium chloride&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Cetrimonium_chloride&quot;&gt;Cetrimonium chloride&lt;/a&gt; which indeed have antimicrobial properties.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While they do not promote resistance to these compounds (see reference 1), their use is still not recommended, as their permanent use might dry out the skin, can cause contact allergies and the products released into the environment are also problematic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are two studies, which compared the use of normal soap (which has some antibacterial properties on its own) to antibacterial soaps in household environments and found no differences. See article linked in reference 2 for a summary and references 3 and 4 for details on the studies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This doesn't mean that antibacterial soaps are useless at all, they simply make no sense in households. For hospitals or doctors they are an important tool to protect their patients before operations. But here detailed instructions for how long and how the hands have to be washed are provided. Hand washing is also followed by another disinfection step, which helps with efficiency. But this is very much different from the way people wash their hands at home. See reference 5 for some opinions here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/17006819&quot;&gt;Use of germicides in the home and the healthcare setting: is there a&#xA;relationship between germicide use and antibiotic resistance?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://phys.org/news/2007-08-plain-soap-effective-antibacterial.html&quot;&gt;Plain soap as effective as antibacterial but without the risk&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17683018&quot;&gt;Consumer antibacterial soaps: effective or just risky?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14996673&quot;&gt;Effect of antibacterial home cleaning and handwashing products on&#xA;infectious disease symptoms: a randomized, double-blind trial.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.health.com/health/article/0,,20433634,00.html&quot;&gt;The Burning Question: Is It Safe to Use Antibacterial Soap?&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5144" LastEditDate="2015-06-24T18:11:15.037" LastActivityDate="2015-06-24T18:11:15.037" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35453" PostTypeId="2" ParentId="35058" CreationDate="2015-06-22T21:00:44.960" Score="3" Body="&lt;p&gt;Allow me to start off with a nice picture showing the differences - note female gametes are on the left while male gametes are on the right in my examples:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/miiCB.jpg&quot; alt=&quot;Picture differences&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Isogametes&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a gamete to be considered an isogamete the other gamete that it meets up with to produce is exactly the same in both size, structure and movement. [&lt;a href=&quot;http://dictionary.reference.com/browse/isogamete&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;] It is literally trying to find itself. The &quot;male&quot; and &quot;female&quot; are literally no different and it is impossible to tell which is which. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you look at the picture the two gametes are exactly the same in every way except that they are facing each other in this picture. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The next two are forms of anisogamy:&#xA;&lt;a href=&quot;https://i.stack.imgur.com/OihLA.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/OihLA.jpg&quot; alt=&quot;Picture&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sub&gt;(source: &lt;a href=&quot;http://ulsfmovie.org/images/anisogamy_different_types.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;ulsfmovie.org&lt;/a&gt;)&lt;/sub&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Heterogametes&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;These gametes differ in at least one of the following:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;size&lt;/li&gt;&#xA;&lt;li&gt;structure&lt;/li&gt;&#xA;&lt;li&gt;sex&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Although it can also be a combination of these three things. [&lt;a href=&quot;http://dictionary.reference.com/browse/heterogamete?s=t&quot; rel=&quot;nofollow noreferrer&quot;&gt;3&lt;/a&gt;] As you can see here the female can be structurally the same as the male. (Bottom and top examples of the second picture). From my understanding (although someone can come and prove me wrong) Oogametes are a specific from of heterogamous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Oogametes&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oogametes differ in size, sex AND function. Females are stationary while males move. [&lt;a href=&quot;http://dictionary.reference.com/browse/oogamete?s=t&quot; rel=&quot;nofollow noreferrer&quot;&gt;4&lt;/a&gt;] Females are also much larger than males. (For instance in humans the cell that divides to make sperm divides equally while the cell that divides in the female divides to make one egg and three polar bodies.)&lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="15950" LastEditDate="2019-03-22T01:59:57.943" LastActivityDate="2019-03-22T01:59:57.943" CommentCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="35454" PostTypeId="2" ParentId="35441" CreationDate="2015-06-22T22:29:15.500" Score="4" Body="&lt;p&gt;The $sR$ that your looking at is the average relatedness of the &lt;em&gt;next generation&lt;/em&gt;.  This assumes that the new immigrants into the the population are completely unrelated. So if the population is completely viscous ($s=1$) the average relatedness of the next generation equals that of the current generation.  On the other hand, if the population is not viscous ($s=0$) the next generation would be entirely unrelated because it would only be made up of unrelated immigrants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The $s(b-c)$ is the number if individuals that are displaced by new offspring.  Again if all of the new generation sticks around ($s=1$) then the number of displaced individuals equals the number of new individuals.  And if all new progeny leave ($s=0$), there are no displaced individuals.&lt;/p&gt;&#xA;" OwnerUserId="16166" LastActivityDate="2015-06-22T22:29:15.500" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35455" PostTypeId="2" ParentId="35442" CreationDate="2015-06-23T01:06:43.080" Score="3" Body="&lt;p&gt;I've seen this termed &quot;phylogenetic pseudoreplication&quot;, but I can't remember offhand where. I'll see if I can find it. Without a tree, the boxes and Xs essentially represent 2 data points. As Remi.b suggests, this is really just high phylogenetic signal.&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2015-06-23T01:06:43.080" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35461" PostTypeId="1" AcceptedAnswerId="35464" CreationDate="2015-06-23T05:25:57.133" Score="7" ViewCount="197" Body="&lt;p&gt;What species is this ? It is a stinky, hairy plant. I have found it nearby a river. It had reached a height of 1 meter. Bloomed three weeks ago. Found in Turkey.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GJeW0.jpg&quot; alt=&quot;rotated image&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="15398" LastEditorUserId="9943" LastEditDate="2015-06-23T11:43:38.660" LastActivityDate="2015-06-23T11:43:38.660" Title="Plant identification in Turkey" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35464" PostTypeId="2" ParentId="35461" CreationDate="2015-06-23T07:29:42.920" Score="7" Body="&lt;p&gt;Looks like a &lt;a href=&quot;https://en.wikipedia.org/wiki/Hyoscyamus_niger&quot;&gt;&lt;em&gt;Hyoscyamus niger&lt;/em&gt;&lt;/a&gt; also called &lt;em&gt;stinking nightshade&lt;/em&gt;. &lt;/p&gt;&#xA;" OwnerUserId="15257" LastEditorUserId="3624" LastEditDate="2015-06-23T07:52:27.113" LastActivityDate="2015-06-23T07:52:27.113" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35465" PostTypeId="1" AcceptedAnswerId="35483" CreationDate="2015-06-23T08:40:44.033" Score="8" ViewCount="294" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FJ6E4.jpg&quot; alt=&quot;unknown caterpillar&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could anyone try to help identify this caterpillar, there are loads of them all over my garden and I've got three of them in a makeshift caterpillar house. I've had them for about a week and they've grown to about 3 or 4 centimetres in length and I am yet to see any of them form pupae. I am from London by the way. &#xA;EDIT: they don't seem to be too fussy about what they eat, I have found them on honeysuckle, rose bushes and even some nibbling on the bind weed I've pulled recently.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/abjWp.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/CDkEY.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Ku0Qw.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16370" LastEditorUserId="16370" LastEditDate="2015-06-23T18:48:36.743" LastActivityDate="2019-09-14T19:13:49.677" Title="Identify this caterpillar" Tags="&lt;zoology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35466" PostTypeId="2" ParentId="35425" CreationDate="2015-06-23T11:37:52.773" Score="0" Body="&lt;p&gt;The best way is to use FPLC if you know what kind of protein you're looking for.in case you don't know what are you looking for,then you can run a 2D-PAGE and after analyzing spots then use LC MS/MS to identify your proteins and then continue with FPLC ( for record FPLC is a method of HPLC or LC which is protein friendly and even you can use it to isolate and purify your chosen protein )&lt;/p&gt;&#xA;" OwnerUserId="16108" LastActivityDate="2015-06-23T11:37:52.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35467" PostTypeId="2" ParentId="35446" CreationDate="2015-06-23T13:32:19.450" Score="-1" Body="&lt;p&gt;Human immune defense response is primed by cell damage products as it does not have prior knowledge about bacterial or viral &quot;malware&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The whole purpose of disinfectant substances is damaging cells and potential organic disease carriers.  As those substances are not discriminating, frequent use of them will prime your immune defense against benign organic matter as well.  In combination with solvents that remove protective layers of fat and thus increase the permeation of this kind of cell waste into top skin layers, this sounds like a recipe for allergies and neurodermitic reactions in the long run.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a high correlation of countries (and eras) with high standards of living including household hygiene and autoimmune response problems.  Finding actual causations is work in progress.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While that is still the case, it is my gut feeling that contact with disinfectants should be reserved to cases of tangible risk.&lt;/p&gt;&#xA;" OwnerUserId="16380" LastActivityDate="2015-06-23T13:32:19.450" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35468" PostTypeId="2" ParentId="35163" CreationDate="2015-06-23T15:31:24.040" Score="2" Body="&lt;p&gt;Practically, there is an obvious barrier to changes in chromosome number: haploid cells produced by diploids must contain exactly one copy of each chromosome (or chromosome section, or locus). Otherwise over- or under- expression of genes can lead to dosage problems. Across all of diploids some large groups show strong conservation of number of chromosomes but others seem fairly free to change the number. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example of conservation are the Drosophilids (fruit flies) where for approximately 100 million years they have maintained five or six chromosomes (search for Muller elements). Incidentally, with a huge amount of intra-chromosomal shuffling of genes &lt;a href=&quot;http://dx.doi.org/10.1038/nature06341&quot; rel=&quot;nofollow&quot;&gt;&quot;Drosophila 12 Genomes Consortium&quot;, 2007, Nature&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An extreme example of changes in chromosome number can be seen between similar species of &lt;a href=&quot;https://en.wikipedia.org/wiki/Indian_muntjac#Genetics&quot; rel=&quot;nofollow&quot;&gt;Muntjac deer&lt;/a&gt; . Where in a relatively short time period (of the order of a million years or less (?) - my guess), the number of chromosomes has reduced from 46 to six (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/5444269&quot; rel=&quot;nofollow&quot;&gt;Wurster, D. H., Benirschke, K., Jun. 1970&lt;/a&gt;). Someone may correct me but I think amongst vertebrates, mammals show particularly fast evolution of chromosome number relative to, say, birds (though more birds also have micro-chromosomes...).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above changes (or lack of change in Drosophilids) appear to be independent of genome size - so that was a long way round to saying &quot;It's not genome size&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It could be repetitive DNA. The centrosomes (where mitotic spindles attach) of mammals are full of repetitive DNA and for this reason have been hard to sequence accurately (&lt;a href=&quot;http://dx.doi.org/10.1186/1755-8166-4-22&quot; rel=&quot;nofollow&quot;&gt;Graphodatsky, A. S., Trifonov, V. A., Stanyon, R., 2011. &lt;/a&gt;). These repeats evolve (in sequence and copy number) and may promote more or fewer spindle attachments. Drosophilids (in general) have fewer repeats but I don't know if this is a diploid-wide pattern [Research anyone?].&lt;/p&gt;&#xA;" OwnerUserId="1128" LastEditorUserId="1128" LastEditDate="2015-06-29T09:15:45.560" LastActivityDate="2015-06-29T09:15:45.560" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35471" PostTypeId="2" ParentId="8806" CreationDate="2015-06-23T17:06:49.277" Score="3" Body="&lt;p&gt;Excess nitrogen must be excreted by the body and can come from nitrogen in the diet (e.g. amino groups from excess amino acids) or nitrogen-containing compounds produced by bacteria in the gastrointestinal tract (GI tract).&lt;/p&gt;&#xA;&lt;p&gt;Normally the liver and kidneys are involved in excreting ammonia (&lt;span class=&quot;math-container&quot;&gt;$NH_3$&lt;/span&gt;) and ammonium (&lt;span class=&quot;math-container&quot;&gt;$NH_4^+$&lt;/span&gt;) from the body. Ammonia can be toxic in high concentrations, but the body can detoxify it through conversion to other nitrogen-containing substances (i.e. &lt;a href=&quot;https://en.wikipedia.org/wiki/Urea&quot; rel=&quot;nofollow noreferrer&quot;&gt;urea&lt;/a&gt;) or excrete the ammonia itself.&lt;/p&gt;&#xA;&lt;p&gt;Ammonia in the blood is freely filtered at the kidney glomerulus and can be &amp;quot;trapped&amp;quot; in the urine flow by accepting a proton to become ammonium (i.e. &lt;span class=&quot;math-container&quot;&gt;$H^+ + NH_3 = NH_4^+$&lt;/span&gt;) . Because of the positive charge the ammonium ion is unable to passively diffuse back across the tubules into the blood. This is one mechanism that ammonia is excreted. In the liver, the Urea Cycle (see any basic or clinical biochemistry text for more information) is a set of enzymes that converts most of the excess nitrogen in the form of ammonia to urea, which is a non-toxic, water soluble organic compound that can also be excreted in the urine. The body uses these processes to dispose of excess nitrogen from amino acids as well as ammonia that is produced as a by-product of bacterial metabolism in the GI tract.&lt;/p&gt;&#xA;&lt;p&gt;Some patients with significant liver disease (e.g. &lt;a href=&quot;https://en.wikipedia.org/wiki/Cirrhosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;cirrhosis&lt;/a&gt; from either &lt;a href=&quot;https://en.wikipedia.org/wiki/Non-alcoholic_fatty_liver_disease&quot; rel=&quot;nofollow noreferrer&quot;&gt;NAFLD&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Hepatitis&quot; rel=&quot;nofollow noreferrer&quot;&gt;hepatitis&lt;/a&gt; or any other liver-damaging disease) have lost the ability to convert all the excess ammonia to urea. In these patients, an easy way to prevent excessive nitrogen uptake in the gastrointestinal tract is by treating them with lactulose. Lactulose is a carbohydrate that that is not digestible or absorbable by the body, but is osmotically active (pulls water into the intestinal lumen) and acts to speed up intestinal transit. Since lactulose works by speeding up GI transit it makes you stool more frequently (which is why it is very useful for constipation). For liver disease patients, however, the lactulose acidifies (i.e. decreases pH) the lumen of the intestines and ammonia is protonated to form ammonium, which effectively traps it in the intestinal lumen. A lot of the excess ammonium can then pass into the feces and decrease the amount of ammonia that the liver needs to process. This is similar to the mechanism of ammonium in the urine as mentioned above. Additionally, lactulose also decreases the amount of GI bugs that produce ammonia containing compounds as well, which also lessens the amount of ammonia for detoxification by the liver. (Lactulose can also be used for a treatment for small intestinal overgrowth). These GI bacteria metabolize dietary amino acids and other compounds in the gut for energy metabolism, which liberates nitrogen-containing compounds that can be absorbed by the intestines.&lt;/p&gt;&#xA;&lt;p&gt;Edit: Here is a &lt;a href=&quot;https://www.ncbi.nlm.nih.gov/books/NBK536930/&quot; rel=&quot;nofollow noreferrer&quot;&gt;link&lt;/a&gt; for a great reference on NCBI that explains the mechanism of action of lactulose.&lt;/p&gt;&#xA;" OwnerUserId="16299" LastEditorUserId="16299" LastEditDate="2020-07-27T20:12:53.217" LastActivityDate="2020-07-27T20:12:53.217" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="35472" PostTypeId="1" CreationDate="2015-06-23T17:36:13.023" Score="3" ViewCount="665" Body="&lt;p&gt;I'm a college sophomore, and I was just accepted into a research lab that works with retroviruses. Since I haven't taken any classes on the topic yet, does anyone have recommendations for good, intro-level virology textbooks I could work through to learn some background information?&lt;/p&gt;&#xA;" OwnerUserId="16384" LastEditorUserId="3340" LastEditDate="2015-06-24T05:54:06.050" LastActivityDate="2015-09-23T09:37:17.530" Title="Recommendations for an intro level virology textbook?" Tags="&lt;virology&gt;&lt;virus&gt;&lt;book-recommendation&gt;&lt;retrovirus&gt;" AnswerCount="0" CommentCount="5" FavoriteCount="2" ClosedDate="2015-09-24T05:48:27.077" ContentLicense="CC BY-SA 3.0" />
  <row Id="35473" PostTypeId="1" CreationDate="2015-06-23T20:35:59.383" Score="4" ViewCount="342" Body="&lt;p&gt;Can somebody explain how is the following differential equation found? It is about the blood alcohol content. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this &lt;a href=&quot;http://s3.amazonaws.com/zanran_storage/www.uwec.edu/ContentPages/18159357.pdf&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt; (pages 3 and 4). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They say the concentration of blood alcohol satisfies (in the drinking phase): $$\dfrac{dC}{dt}=u-\dfrac{\alpha C}{C+\beta}\quad; \quad C(0)=0,$$ where $\alpha, \beta$ are the liver and the kidney parameters. For the Recovery Phase we have: $$\dfrac{dC}{dt}=-\dfrac{\alpha C}{C+\beta}\quad; \quad C=C_{max}.$$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't see how they came to these equations. The only thing they say about the origin of this model is that it comes from a continuity argument: the amount of alcohol that is introduced in the body, equals the amount of the alcohol that leave the body.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wonder if there is a model which takes into account all parameters in the above article plus the amount of food in the stomach. &lt;/p&gt;&#xA;" OwnerUserId="16387" LastEditorUserId="3340" LastEditDate="2015-06-25T08:03:31.393" LastActivityDate="2015-06-25T08:03:31.393" Title="Michaelis-Menten equation type - how it is derived?" Tags="&lt;biochemistry&gt;&lt;theoretical-biology&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="35478" PostTypeId="1" AcceptedAnswerId="35577" CreationDate="2015-06-24T02:26:01.687" Score="2" ViewCount="3101" Body="&lt;p&gt;There is an attribute defined as DP (Total Depth) in VCF file format. For example, &lt;a href=&quot;http://www.1000genomes.org/node/101&quot; rel=&quot;nofollow&quot;&gt;http://www.1000genomes.org/node/101&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does this attribute mean? If I get a value of like DP=128. How can be that be interpreted?&lt;/p&gt;&#xA;" OwnerUserId="14905" LastActivityDate="2017-12-16T17:49:02.910" Title="What's read depth in VCF?" Tags="&lt;bioinformatics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35479" PostTypeId="1" CreationDate="2015-06-24T03:24:52.743" Score="8" ViewCount="1462" Body="&lt;p&gt;Let's suppose a healthy fit barefoot young adult standing comfortably on a flat solid surface.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A reasonable guess is somewhere around the foot.&#xA;But is it the ankle, the heel, or the Metatarsus?&lt;/p&gt;&#xA;" OwnerUserId="16393" LastEditorUserId="3340" LastEditDate="2015-06-24T08:56:58.547" LastActivityDate="2015-06-25T09:42:53.943" Title="Which part of human body sustains most pressure when standing up straight?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;biophysics&gt;&lt;bio-mechanics&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35480" PostTypeId="2" ParentId="35478" CreationDate="2015-06-24T04:02:51.117" Score="0" Body="&lt;p&gt;That number refers to the number of reads that overlap that base pair that has the variant. Sequencing reads in this case almost always refer to &lt;a href=&quot;http://www.illumina.com/content/dam/illumina-marketing/documents/products/illumina_sequencing_introduction.pdf&quot; rel=&quot;nofollow&quot;&gt;next generation sequencing&lt;/a&gt;. These metrics and other VCF fields are used to give some indicator of confidence for variant.&lt;/p&gt;&#xA;" OwnerUserId="766" LastEditorUserId="766" LastEditDate="2015-06-25T23:57:31.483" LastActivityDate="2015-06-25T23:57:31.483" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35481" PostTypeId="2" ParentId="35473" CreationDate="2015-06-24T06:36:47.293" Score="5" Body="&lt;p&gt;These kind of equations (the Michaelis-Menten [MM] like term) denote  saturation kinetics. The basic mechanistic assumption behind saturation kinetics is this:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A rate (of lets say product formation) is dependent on the concentration of a molecule such that the rate increases linearly with increase in the concentration of the molecule.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Example 1: Substrate in an enzyme catalysed reaction&lt;/li&gt;&#xA;&lt;li&gt;Example 2: Transcription factor in a transcriptional activation&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;However at a certain point increasing the concentration of the molecule will have no effect on the rate of reaction. For the above examples this point will arrive when (respectively):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Active sites in all the enzyme molecules are bound and there is no more space to accommodate a new substrate molecule.&lt;/li&gt;&#xA;&lt;li&gt;All the binding sites in the DNA are occupied by the existing TF molecules and no more can bind.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In other words, the reaction kinetics changes from first order to zeroth order.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can provide mechanistic explanations for some cases but in many we do not know how exactly the saturation happens. In modelling we just use a function that will &lt;strong&gt;mimic&lt;/strong&gt; this kind of behaviour.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why functions of the form $\dfrac{X}{K+X}$ ? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;In deterministic modelling using differential equations, it would be preferred to use a continuous function (instead of using a piecewise linear function) because:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Numerical integration is better in case of continuous functions&lt;/li&gt;&#xA;&lt;li&gt;In biochemical systems, operations are always continuous. There is no digital logic.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The MM function can actually be derived using an equilibrium or a quasi-steady state approximation (See the &lt;a href=&quot;https://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_kinetics&quot; rel=&quot;nofollow&quot;&gt;wikipedia page&lt;/a&gt; for the explanation).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the MM function, when $X \gg K$ then the function is almost 1. This multiplied by the maximum rate constant will give you the max catalytic rate. At $X=0$ the rate will also be equal to zero. Note that in this model the catalytic rate will not indefinitely increase with $X$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several functions that have values between 0 and 1 for increasing concentration of the substrate. &lt;a href=&quot;https://en.wikipedia.org/wiki/Hill_equation_%28biochemistry%29&quot; rel=&quot;nofollow&quot;&gt;Hill function&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Logistic_function&quot; rel=&quot;nofollow&quot;&gt;logistic function&lt;/a&gt; are common examples. However MM is a simpler model. You can always revise your modelling approach when you have better information of the biological system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Now back to your question:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this model $C$ denotes alcohol concentration $\alpha$ denotes maximum clearance rate and $\beta$ denotes half saturation concentration (concentration of alcohol at which the rate of clearance is half the maximum rate). Intuitively you can think about the mechanism like this: rate of clearance of alcohol depends on the level of alcohol i.e. if you have a lot of alcohol the amount of it removed per unit time will be higher. Think of it as water that is pumped through a pipe; more water in the tank will result in higher flow rate. However when the kidney (or pipe) is overloaded or &quot;clogged&quot; with an already excess of alcohol then clearance rate would remain the same (the maximum that the kidneys can excrete). &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;the amount of alcohol that is introduced in the body, equals the amount of the alcohol that leave the body&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;That is called mass balance which can be summarized as follows:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Accumulation = Input + Production - (Output + Degradation)&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-24T13:18:04.150" LastActivityDate="2015-06-24T13:18:04.150" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35483" PostTypeId="2" ParentId="35465" CreationDate="2015-06-24T10:39:09.453" Score="7" Body="&lt;p&gt;Actually, the animal is not a caterpillar but larva.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The species is &lt;a href=&quot;https://nl.wikipedia.org/wiki/Abia_lonicerae&quot; rel=&quot;nofollow noreferrer&quot;&gt;Abia lonicerae&lt;/a&gt; Sawfly, discovered by Linnaeus 1758.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(&lt;a href=&quot;http://mywildlifefriendlygarden.zenfolio.com/p415675779/h6276BECE#h6276bece&quot; rel=&quot;nofollow noreferrer&quot;&gt;Another picture&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GtAt1.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/f2PDm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-06-24T10:39:09.453" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35484" PostTypeId="1" CreationDate="2015-06-24T11:43:16.220" Score="5" ViewCount="77" Body="&lt;p&gt;this is my first question on BiologySE. I am a Physics and Mathematics student currently doing a project on cell growth simulation. I am doing literature survey and I have a question about cellular biology experimental methods.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that the membrane potential is a measure of mitochondrial functionality (higher potential means more efficient electron transport chain). Additionally, the mitochondrial volume is also an indicator of mitochondrial efficiency (higher volume, higher area, more places to do electron transport).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to have some points elucidated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, can these mitochondrial membrane potential and volume...&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;be measured for a single cell, or only in a population?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;be measured non-destructively, leaving the cell alive?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;be measured simultaneously, or experiments measuring one necessarily make the other unavailable?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I am thinking mostly of &lt;em&gt;in vitro&lt;/em&gt; experiments of course.&lt;/p&gt;&#xA;" OwnerUserId="16398" LastEditorUserId="16398" LastEditDate="2015-06-25T10:26:33.300" LastActivityDate="2015-06-25T10:26:33.300" Title="How are the physiological properties of mitochondria measured?" Tags="&lt;cell-biology&gt;&lt;mitochondria&gt;&lt;experimental&gt;&lt;methods&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35485" PostTypeId="1" AcceptedAnswerId="35486" CreationDate="2015-06-24T12:02:03.940" Score="4" ViewCount="2367" Body="&lt;p&gt;Here's the problem:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One red blood cell is placed in a hypertonic solution of NaCl, another is&#xA;placed in a solution of CaCl&lt;sub&gt;2&lt;/sub&gt; equimolar with the NaCl solution. What&#xA;would you expect to happen and why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My reasoning is that the red blood cell will shrink due to water loss by osmosis when placed in hypertonic NaCl. It will shrink even further due to the larger osmosis gradient due to there being such low concentration of Ca&lt;sup&gt;2+&lt;/sup&gt; normally in the cell. However, I'm not sure if this is right so could someone please explain the correct answer?&lt;/p&gt;&#xA;" OwnerUserId="10520" LastEditorUserId="3340" LastEditDate="2015-06-24T12:42:00.767" LastActivityDate="2015-06-25T13:57:04.777" Title="What happens to the red blood cell in CaCl₂ solution?" Tags="&lt;cell-biology&gt;&lt;homework&gt;&lt;red-blood-cell&gt;&lt;osmosis&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35486" PostTypeId="2" ParentId="35485" CreationDate="2015-06-24T12:34:46.657" Score="8" Body="&lt;p&gt;The reason why the cell would shrink more in CaCl&lt;sub&gt;2&lt;/sub&gt; solution is because it has a higher &lt;a href=&quot;https://en.wikipedia.org/wiki/Van_%27t_Hoff_factor&quot;&gt;van't Hoff factor&lt;/a&gt; i.e. total number of dissociated ionic species per solute molecule (it is 2 for NaCl whereas it is 3 for CaCl&lt;sub&gt;2&lt;/sub&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(&lt;em&gt;Nonionic solutes do not dissociate and will therefore have a van't Hoff factor of 1&lt;/em&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Osmotic pressure (and other &lt;a href=&quot;https://en.wikipedia.org/wiki/Colligative_properties&quot;&gt;colligative properties&lt;/a&gt;) are proportional to van't Hoff factor. Therefore osmotic pressure in CaCl&lt;sub&gt;2&lt;/sub&gt; solution will be 3/2 times of that in an equimolar NaCl solution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the ionic chemical potential is not what drives osmosis; it is the differential concentration of water (or any other solvent) that drives it. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-24T12:40:30.453" LastActivityDate="2015-06-24T12:40:30.453" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35487" PostTypeId="2" ParentId="35484" CreationDate="2015-06-24T12:50:02.757" Score="5" Body="&lt;p&gt;A simple method would me to express a fluorescent protein in the cell that specifically localizes to mitochondria. &lt;a href=&quot;http://www.clontech.com/US/Support/Applications/Fluorescent_Proteins_by_Color/ibcGetAttachment.jsp?cItemId=27575&amp;amp;fileId=6509872&amp;amp;sitex=10020:22372:US&quot;&gt;mito-dsRed&lt;/a&gt; is a Red Fluorescent Protein which has that property; it can be expressed from a plasmid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Using fluorescent microscopy and image analysis, you would be able to measure the geometric properties of the mitochondria. This can be done at a single cell level too (using confocal microscope) and non-destructively. Volume can be measured by what is known as &lt;a href=&quot;https://en.wikipedia.org/wiki/Focus_stacking&quot;&gt;Z-stacking&lt;/a&gt;— an automated technique by which the microscope takes several 2D snaps at different planes and stacks them to construct a 3D image. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can implement this in live cells too; this method is called &lt;a href=&quot;https://en.wikipedia.org/wiki/Live_cell_imaging&quot;&gt;live cell imaging&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-24T12:55:27.040" LastActivityDate="2015-06-24T12:55:27.040" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35488" PostTypeId="1" CreationDate="2015-06-24T14:58:31.577" Score="3" ViewCount="182" Body="&lt;p&gt;My understanding is that the relatedness coefficient in kin selection models measures &lt;em&gt;positive assortment&lt;/em&gt;. That is, altruism is more likely to evolve if altruists tend to interact with other altruists. As an example, consider a general model of kin selection due to Queller (Queller 1992 &quot;A general model of kin selection&quot;). According to this model, relatedness is viewed as the regression coefficient $\beta_{G'G}$, where $G$ is the individual's frequency of the altruism allele and $G'$ is the average value of $G$ of an individual's neighbors. Queller's definition of relatedness is a measure of positive assortment because, by definition, &#xA;$$\beta_{G'G} = \frac{E(G'\mid G) - E(G')}{G - E(G)}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If relatedness is positive, if the focal individual is more altruist than average ($G-E(G)&amp;gt;0$), then this individual will tend to interact with individuals that are more altruist than average ($E(G'\mid G) - E(G')&amp;gt;0$).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, in Taylor's 1992 kin selection model in patch-structured populations with asexual reproduction (&quot;Altruism in viscous populations&quot;), relatedness $R$ is defined as the recursion (p. 354):&#xA;$$ R' = \frac{1}{N} + \frac{N-1}{N}s^2R$$&#xA;where $N$ is the number of individuals in each patch and $s$ is the probability the offspring will remain on the natal patch (&lt;a href=&quot;https://biology.stackexchange.com/questions/35441/altruism-in-viscous-asexual-populations&quot;&gt;link to a question about $s$&lt;/a&gt;). Here $R$ doesn't seem to be a measure of positive assortment, but simply the chance that two alleles picked &lt;em&gt;at random&lt;/em&gt; within the patch will be of the same type.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On one hand, $R$ in standard models of kin selection (e.g., Queller's) measures positive assortment. On the other hand, Taylor's kin selection model for patch-structured populations $R$ does not seem to measure positive assortment within a group but the chance that two random individuals share the same allele. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I tended to think of Queller's model as a general formulation of kin selection (accordingly, Taylor's model would be a particular instance of Queller's model). But, as I tried to explain above, my impression is that Taylor's model is an entirely different way of modeling kin selection ($R$ does not measure positive assortment). Am I missing some connection between Queller's and Taylor's models of kin selection? Or is there any way of connecting the two definitions of relatedness mentioned above?&lt;/p&gt;&#xA;" OwnerUserId="11829" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-06-24T15:32:24.013" Title="How to understand relatedness in an infinite island model?" Tags="&lt;evolution&gt;&lt;theoretical-biology&gt;&lt;population-genetics&gt;&lt;sociality&gt;&lt;evolutionary-game-theory&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35489" PostTypeId="1" CreationDate="2015-06-24T15:14:29.603" Score="1" ViewCount="70" Body="&lt;p&gt;I am part of an undergraduate research group and we are trying to produce a protease in an E.coli gene circuit. We are not sure where to place the His tag in our circuit. The sequence is&#xA;...OmpA(gene)-&gt;linker-&gt;his tag-&gt;protease-&gt;Terminator-&gt;res site &#xA;Should the His tag be in this position, before the linker, or after the protease? OmpA is a outer membrane protein that will allow a protein to be taken to, and linked to, the outer membrane of the E.coli. Our fear is that the protease will not fold correctly and will be nonfunctional. &lt;/p&gt;&#xA;" OwnerUserId="15933" LastEditorUserId="15933" LastEditDate="2015-06-24T16:58:57.367" LastActivityDate="2015-06-24T16:58:57.367" Title="His Tag location in gene circuit" Tags="&lt;synthetic-biology&gt;&lt;protein-folding&gt;&lt;gene&gt;" AnswerCount="0" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="35491" PostTypeId="2" ParentId="35479" CreationDate="2015-06-24T19:15:06.383" Score="7" Body="&lt;p&gt;It is logically clear that the ankle could only partly be analyzed in the group of joints that are below its height. There is no direct way to measure the pressure on ankle joint (on talus bone), but from the logic it is clear that it should be the point of highest pressure in the group of points lister in the question, however the pressure is distributed through the other joints of the foot. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below are the graphs of pressure distribution according to surfaces (not joints). From the graph we can conclude that part of the pressure experienced by ankle joint distributed tangentially to metatarsal region and other surfaces.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Indeed the highest pressure in standing person in on feets. The term you are asking about is foot pressure distribution (FPD).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In we assess the FPD dynamically, in younger persons the FPD is nearly equivalent between calcaneus region and metatarsal region, while in older persons the FDT in calcaneus region is higher than metatarsal pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During stance:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/EmZnb.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Foot pressure distribution. A. Maximum pressure distribution on all sensors during stance for one subject. B. The nine anatomical masks superimposed on the insole (MC = medial calcaneus, LC = lateral calcaneus, MA = medial arch, LA = lateral arch, MT1 = first metatarse, 3 = second and third metatarse, 4 = fourth and fifth metatarse, H = hallux, and T = toes).&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Pressure distribution by anatomical region. Normalized maximum pressure distribution for the young (white bar) and elderly (black bar) group for each anatomical region (medial calcalneus mask p = 0.0001, lateral calcaneus mask p = 0.03):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2Cemg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1173105/&quot; rel=&quot;nofollow noreferrer&quot;&gt;source article&lt;/a&gt;, you can find much more using FPD as a keyword. &lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-06-25T05:03:55.903" LastActivityDate="2015-06-25T05:03:55.903" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35492" PostTypeId="1" CreationDate="2015-06-24T21:26:12.230" Score="2" ViewCount="173" Body="&lt;p&gt;I have recently found articles and various claims that turtles (Blanding's turtles as an exact example) could possibly live indefinitely. &lt;a href=&quot;http://discovermagazine.com/2002/jun/featturtle&quot; rel=&quot;nofollow&quot;&gt;http://discovermagazine.com/2002/jun/featturtle&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is said to be due to the fact that they &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;don't senesce— deteriorate physically— as they grow old&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am highly skeptical of that claim, and on the other side are links such as this &lt;a href=&quot;http://www.nature.org/ourinitiatives/regions/northamerica/unitedstates/indiana/journeywithnature/blandings-turtles.xml&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.org/ourinitiatives/regions/northamerica/unitedstates/indiana/journeywithnature/blandings-turtles.xml&lt;/a&gt; which say they can live up to 70 years (though in the actual article it says 70+)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize in the wild that predation, disease, and other causes other than old age could kill turtles, but my question is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can blandings turtles die of old age? If so, around what age would this be?&lt;/p&gt;&#xA;" OwnerUserId="9700" LastEditorUserId="9700" LastEditDate="2015-06-24T21:38:20.060" LastActivityDate="2015-06-25T02:56:54.550" Title="Do Blanding's Turtles die of old age?" Tags="&lt;senescence&gt;&lt;life-history&gt;&lt;reptile&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35493" PostTypeId="2" ParentId="35446" CreationDate="2015-06-24T21:50:42.087" Score="6" Body="&lt;p&gt;You may be interested to look into the &lt;em&gt;Old friends hypothesis&lt;/em&gt;, since this is related to how the human immune system may respond to reduced biodiversity in the microbiota. The basic idea is that the human immune system is developed by exposture to the microbiota, and without exposture to organisms from our evolutionary past, immune system regulation might fail. This can then lead to poorly regulated inflammatory responses and &#xA;maybe allergies or other chronic inflammatory diseases. Since the exposture to our evolutionary &lt;em&gt;Old friends&lt;/em&gt; is lower in developed countries and urban areas, this hypothesis might potentially (partially) explain the increased prevalence of allergies in developed countries. Even though it is somewhat tangential to your question, and does not directly answer the question of the pros and cons of antibacterial soap, it should still be relevant for a more general case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Two good starting points are &lt;a href=&quot;http://www.pnas.org/content/110/46/18360&quot; rel=&quot;nofollow&quot;&gt;Rook (2013)&lt;/a&gt; and &lt;a href=&quot;http://www.pnas.org/content/109/21/8334&quot; rel=&quot;nofollow&quot;&gt;Hanski et al (2012)&lt;/a&gt;. Rook (2013) is a general overview of the theory with many good references to empirical studies that relate to the hypothesis, by one of the main proponents of the theory. Hanski et al (2012) is an interesting epidemiological paper, where they relate the allergic disposition of individuals to both the general biodiversity in their larger living environment as well as the generic diversity of their skin microbiota. In the paper, they find a positive relationship in healthy individuals between immune responses and the abundance of the gammaproteobacterial genus Acinetobacter on the skin, but they do not find the same pattern in atopic individuals. The study also finds a negative relationship between the environmental biodiversity close to the homes of study subjects and the frequency of atopy (so high biodiversity -&gt; lower levels of atopy).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To be clear, this is still a hypothesis that needs further testing and support. However, there are many interesting case studies that can lend support to it, and indicate plausible mechanisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pnas.org/content/110/46/18360&quot; rel=&quot;nofollow&quot;&gt;Rook. 2013. &lt;em&gt;Regulation of the immune system by biodiversity from the natural environment: An ecosystem service essential to health&lt;/em&gt;. PNAS 110(46)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.pnas.org/content/109/21/8334&quot; rel=&quot;nofollow&quot;&gt;Hanski et al. 2012. &lt;em&gt;Environmental biodiversity, human microbiota, and allergy are interrelated&lt;/em&gt;. PNAS 109(21)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://emph.oxfordjournals.org/content/2013/1/46&quot; rel=&quot;nofollow&quot;&gt;Rook. 2013. &lt;em&gt;Microbial ‘Old Friends’, immunoregulation and stress resilience&lt;/em&gt;. Evolution, Medicine, and Public Health&#xA;2013(1)&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-06-25T07:51:40.143" LastActivityDate="2015-06-25T07:51:40.143" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35494" PostTypeId="1" AcceptedAnswerId="35495" CreationDate="2015-06-24T23:46:31.027" Score="3" ViewCount="206" Body="&lt;p&gt;Food is cooked/baked at temperatures that are significantly higher than what's considered normal for proteins/amino acids (40&amp;deg;C). Why is it, then, that such food is still considered nutritious after cooking? (meat, cheesecake, lentils, quinoa, mushrooms, etc.)&lt;/p&gt;&#xA;" OwnerUserId="13437" LastEditorUserId="16866" LastEditDate="2017-04-03T17:52:25.533" LastActivityDate="2017-04-03T21:53:00.380" Title="Why cooked food considered nutritious if proteins decompose at much lower temperatures?" Tags="&lt;proteins&gt;&lt;food&gt;&lt;nutrition&gt;&lt;temperature&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35495" PostTypeId="2" ParentId="35494" CreationDate="2015-06-25T00:14:59.610" Score="9" Body="&lt;p&gt;Cooking is just a form of digestion.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What is digestion?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Digestion is the process of breaking down big molecules into smaller molecules. When you cook food you break down big molecules into its small components.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why do we digest food?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Think about a long sequence of DNA for example. You eat corn and you have in your body a long sequence of corn DNA. What can you do with that long molecule....well, nothing. You need to break this long molecule down in order to be able to &lt;em&gt;assimilate&lt;/em&gt; the constitutive &lt;em&gt;nutrients&lt;/em&gt;. With those nutrients, you can now make up your own DNA. In other words, we need to break the big Lego castle that is food to get the building blocks in order to rebuild a spaceship. Digestion refer to the first process (breaking up the Lego castle). We refer to the part of the metabolism who breaks things down as catabolism and we refer to the part of metabolism that build things up as anabolism. Note that catabolism + anabolism = metabolism.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why do we cook then instead of digesting by ourself&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Digestion takes much energy and require the organism to have the right organs and to have the right matter (enzymes and stuff). We can save up energy (and the other stuff) by digesting the food outside our body. One could say that humans, (just like spiders for example) are performing external digestion.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Why cooked food considered nutritious&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Cooked food don't have more nutrients than raw food. It is actually likely that in the process of cooking you would lose some nutrients going in the water that you throw away typically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The big difference is that nutrients in cooked food are easy to assimilate which might end up being more healthy depending on the specific food source. Cooking may also destroy potentially toxic products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that in response to the cooking behaviour, human gut has evolved to be shorter than it was in our ancestor.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2017-04-03T21:53:00.380" LastActivityDate="2017-04-03T21:53:00.380" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35496" PostTypeId="2" ParentId="35492" CreationDate="2015-06-25T02:19:53.880" Score="3" Body="&lt;p&gt;It looks like &lt;a href=&quot;https://biology.stackexchange.com/questions/20465/in-practice-do-fishes-die-from-old-age?rq=1&quot;&gt;as in fishes&lt;/a&gt;, the lack of an intrinsic cause of death in turtles in general is seen:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Like in fishes, the reptiles appear to show three types of senescence. The African skink, Mabuya buettneri, shows rapid senescence similar to death at mating observed in Salmon and marsupial mouse. Most of the lizards and snakes undergo gradual senescence comparable to the pattern exhibited by a majority of vertebrates. On the other hand, turtles, tortoises and crocodiles continue to grow throughout life and are thus credited with slow or negligible senescence.&#xA;  &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7926857&quot; rel=&quot;nofollow noreferrer&quot;&gt;Patnaik 1994 &lt;em&gt;Gerontology&lt;/em&gt; 40(2–4):200–20.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The main article by Congdon, the researcher who the Discover article profiles, also seems to be fairly definitive about this lack of senescence (or negative senescence?) in Blanding's Turtles specifically:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Survivorship, reproductive frequency and size-adjusted mean clutch size were all higher in the Oldest age group compared to the younger age groups.&#xA;  &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0531556500002424&quot; rel=&quot;nofollow noreferrer&quot;&gt;Congdon et al 2001 &lt;em&gt;Experimental Gerontology&lt;/em&gt; 36(4–6): 813–827&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-06-25T02:56:54.550" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35497" PostTypeId="2" ParentId="35479" CreationDate="2015-06-25T04:12:19.290" Score="2" Body="&lt;p&gt;Note that estimations in this answer are very very crude. I can speak with confidence that the &lt;em&gt;mean&lt;/em&gt; pressure of ankel joint is greater than the heel and the metatarsus. However I do not trust that it can pin down &lt;em&gt;the point with most pressure&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;@Ilan gave a very good synopsis on foot pressure distribution. &lt;del&gt;However, pressure in ankles was not analyzed in his answer.&lt;/del&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/BF01246141#page-1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kimizuka et. al.&lt;/a&gt; measured contact area of human ankle joints under various load-force configurations. The main results were shown in the graph below.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.imgur.com/CvT2Mw4.png&quot; alt=&quot;Fig. Load-contact area&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a $70kg$ human, the contact area of each ankle is about $3cm^2$, whereas of each foot with ground surface is approximately $37 cm^2$. Please note that we include only the heel ($4cm\times4cm$) and the metatarsus ($7cm\times 3cm$) in above calculation, which sustain most pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can safely ignore the mass of both feet compared to the whole body. So it seems that ankle pressure is the clear winner here.&lt;/p&gt;&#xA;" OwnerUserId="16393" LastEditorUserId="16393" LastEditDate="2015-06-25T09:42:53.943" LastActivityDate="2015-06-25T09:42:53.943" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35498" PostTypeId="1" AcceptedAnswerId="35499" CreationDate="2015-06-25T06:47:49.273" Score="10" ViewCount="8549" Body="&lt;p&gt;On most female-hormone supplements you get a warning that is something like this:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The use of a combination hormonal contraceptives (CHC), like NuvaRing, is associated with increased risks of several serious side effects, including blood clots, stroke, or heart attack. (&lt;a href=&quot;http://www.nuvaring.com/consumer/&quot;&gt;Nuvaring&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The use of a CHC, like NuvaRing, is associated with increased risks of several serious side effects, including blood clots, stroke, or heart attack.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It also goes onto state that smoking can increase these risks. &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What makes these hormones so dangerous (prone to clotting)?&lt;/li&gt;&#xA;&lt;li&gt;If a person is naturally high in these hormones are they at a higher risk of blood clots?&lt;/li&gt;&#xA;&lt;li&gt;Why/How does smoking affect the hormones - or is the increase risk just due to the natural risk of smoking?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="5144" LastEditDate="2015-06-25T06:53:31.353" LastActivityDate="2015-07-14T19:29:26.337" Title="How do female hormones cause blood to clot?" Tags="&lt;human-biology&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35499" PostTypeId="2" ParentId="35498" CreationDate="2015-06-25T07:37:10.057" Score="6" Body="&lt;p&gt;These combination contraceptives contain two substances: Estrogen and progestin (a synthetic progesterone). Both are used together to overcome the negative effects of single substance drugs as acne or sickness. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The risk for blood clots has been known for quite a while (see reference 1 and 2) and is generally caused by raised levels of clotting factors (especially VII and X), increased plasma fibrinogen, increased platelet aggregation in the blood and reduced activity of antithrombin III (which inhibits coagulation). This can happen as well in pregnancy when the factors are naturally elevated (that's the way these contraceptives simulate pregnancy to the body). The paper shows this nicely for two of the factors of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Coagulation&quot; rel=&quot;nofollow noreferrer&quot;&gt;blood coagulation cascade&lt;/a&gt; (factor VII and X):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yxbZG.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This risk is relatively rare, it affects only about 1-5 in 10.000 women, but is still not negligible. The risk is much higher in persons with defects in the blood coagulation cascade. Compared to this, pregnant women have a risk for blood clots of 5-20 per 10.000 women (for details see &lt;a href=&quot;http://www.straighthealthcare.com/oral-contraceptives.html#blood-clots&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Blood coagulation is really fine tuned to ensure proper function when necessary but no blood clotting when not. Basically activating and deactivating hold a balance, as depicted in figure 1 from reference 3:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9VRZ1.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Smoking now disturbs this balance by inhibiting fibrinolysis and promoting the accumulation of fibrin and pushes it more to the site of coagulation. What causes the problem here is the elevation of clotting factors in combination with the disturbance of the balance between activation and inhibition of clotting. See reference 3 for the details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This effect seems to be limited to high concentration single estrogen and estrogen/progestin combination preparations, while there seems to be no such effect in progestin single preparations (although data is limited here). There is also a significant difference in the type of estrogen used. See references 4 and 5 for more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mechanism of how this works is relatively straightforward. The estrogen binds to the estrogen receptor on the cell surface and forms a receptor-ligand complex. This leads to signalling inside the cells which finally results in changed gene expression. Additionally the complex can be internalized by the cell. Inside the cell this complex can bind to the so-called &quot;hormone response element&quot; and also regulate the expression of genes. This is explained in detail for Factor XII in reference 6 (and works like this for other parts as well). See the image for illustration (from reference 7):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/dVKDk.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1436047/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Relation between oral contraceptive hormones and blood clotting&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.bmj.com/content/350/bmj.h2135&quot; rel=&quot;nofollow noreferrer&quot;&gt;Use of combined oral contraceptives and risk of venous&#xA;thromboembolism: nested case-control studies using the QResearch and&#xA;CPRD databases&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10368523&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hemostatic effects of smoking and oral contraceptive use&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/2960241&quot; rel=&quot;nofollow noreferrer&quot;&gt;Coagulation effects of oral contraception.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://archinte.jamanetwork.com/article.aspx?articleid=1741892&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lower Risk of Cardiovascular Events in Postmenopausal Women Taking&#xA;Oral Estradiol Compared With Oral Conjugated Equine Estrogens&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://press.endocrine.org/doi/abs/10.1210/endo.136.11.7588244&quot; rel=&quot;nofollow noreferrer&quot;&gt;Molecular basis of estrogen regulation of Hageman factor XII gene&#xA;expression.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23348042&quot; rel=&quot;nofollow noreferrer&quot;&gt;Estrogen synthesis and signaling pathways during aging: from&#xA;periphery to brain&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="5009" LastEditDate="2015-07-14T19:29:26.337" LastActivityDate="2015-07-14T19:29:26.337" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35500" PostTypeId="1" CreationDate="2015-06-25T07:38:12.560" Score="0" ViewCount="33" Body="&lt;p&gt;Why polysomes are not able to load properly onto a transcript if a transcript has a double-stranded structure in it?&lt;/p&gt;&#xA;" OwnerUserId="15756" LastActivityDate="2015-06-25T07:38:12.560" Title="Why is polysome loading affected by double stranded structure?" Tags="&lt;gene-expression&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35505" PostTypeId="1" CreationDate="2015-06-25T12:20:11.803" Score="4" ViewCount="3517" Body="&lt;p&gt;I am attempting to understand neurogenesis related to learning. Does learning increase the number of neurons in the human brain? What would be some good scientific publications to read?&lt;/p&gt;&#xA;" OwnerUserId="16406" LastEditorUserId="9943" LastEditDate="2015-07-13T11:16:23.587" LastActivityDate="2017-04-11T14:53:40.893" Title="Does learning increase the number of neurons in the brain?" Tags="&lt;neuroscience&gt;&lt;neuroanatomy&gt;&lt;neurophysiology&gt;&lt;learning&gt;" AnswerCount="2" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35506" PostTypeId="1" AcceptedAnswerId="35516" CreationDate="2015-06-25T13:09:50.233" Score="2" ViewCount="839" Body="&lt;p&gt;I have a dataset containing IC50 data for each of my cell lines and up to 80 drugs. Basically for each drug I want to be able to define an IC50 threshold where if a cell line has an IC50 above that threshold it is resistant, and if it is below that threshold it is sensitive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm trying to think of the best way of doing this: I was thinking of taking the median for each drug as the threshold but I realize that's quite crude. Are there any more robust statistical techniques I could use to define such a threshold for each drug?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="16407" LastActivityDate="2015-06-26T01:21:45.047" Title="Defining Resistance and Sensitivity Thresholds for IC50" Tags="&lt;pharmacology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35507" PostTypeId="2" ParentId="35506" CreationDate="2015-06-25T13:36:22.860" Score="3" Body="&lt;p&gt;IC50 has an exact definition, that is half-maximal inhibitory concentration. To get this you need to make a series of dilutions of each of your drugs and test your cell lines in each concentration and assess how they grow (eg measure Optical density, colony size, cell count or whatever applies to your cells and setup). Then you can set up a inhibition curve that is a function of the concentration. This most likely looks like a sigmoid curve and the inflection point gives you the IC50 value.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example image form the &lt;a href=&quot;https://en.wikipedia.org/wiki/IC50&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt; page of IC50 (recommended to read):&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ctZgl.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in your case, you already have IC50 values (for wild types I assume), and you need to assess your (probably mutant ?) cell lines to see if they are sensitive or resistant. Standard lab practice recommends using wild-type controls and at least 3 parallel controls. You can compare the average growth of WTs to your cell line at the IC50 concentration you already got in your dataset, and calculate standard deviation, and 95% confidence interval. With some simplification if the 95%CI of your cell line is greater than the wt 95%CI it is most likely that your cell line is resistant to that drug, on the other hand if its lower then that cell line is sensitive to the drug in question.&lt;/p&gt;&#xA;" OwnerUserId="14735" LastEditorUserId="14735" LastEditDate="2015-06-25T13:49:26.373" LastActivityDate="2015-06-25T13:49:26.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35509" PostTypeId="1" AcceptedAnswerId="35510" CreationDate="2015-06-25T14:24:28.797" Score="7" ViewCount="5374" Body="&lt;p&gt;Someone asked this in my class and my instructor wasn't sure in her answer, doesn't anyone know what happens in protein synthesis if a mutation causes mRNA to not possess a stop codon? Would the protein eventually stop? Would it keep coding into the poly-A chain and insert a bunch of phenylalanine?&lt;/p&gt;&#xA;" OwnerUserId="16411" LastEditorUserId="3340" LastEditDate="2015-06-26T05:44:39.257" LastActivityDate="2015-06-26T06:17:27.763" Title="Mutation That Loses Stop Codon" Tags="&lt;molecular-biology&gt;&lt;rna&gt;&lt;transcription&gt;&lt;translation&gt;&lt;mrna&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35510" PostTypeId="2" ParentId="35509" CreationDate="2015-06-25T14:42:25.573" Score="7" Body="&lt;p&gt;No, this will not happen. mRNAs are inspected in the nucleus before they are exported into the cytoplasm (at least in eukaryotes), where transcription and translation don't happen at the same place. This ensures that no mRNAs without stop codons or premature stop codons are exported. This phenomenon is called&#xA;&quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/MRNA_surveillance&quot;&gt;mRNA surveillance&lt;/a&gt;&quot;. mRNAs that do not pass this quality check, are degraded. See the Wiki reference for some basic information and the references below for more.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/4029/hyr2twfb_pdf.htm&quot;&gt;Process or perish: quality control in mRNA biogenesis.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbr.muni.cz/~stefl/Publications_files/VanacovaStefl_EMBORep2007.pdf&quot;&gt;The exosome and RNA quality control in the nucleus&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/4029/7k5ldqd8_pdf.htm&quot;&gt;A faux 3′-UTR promotes aberrant termination and triggers&#xA;nonsense-mediated mRNA decay&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-06-25T14:42:25.573" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35511" PostTypeId="1" AcceptedAnswerId="35512" CreationDate="2015-06-25T15:04:20.190" Score="9" ViewCount="940" Body="&lt;p&gt;I always see these Lumosity ads on TV, and I personally feel they are just trying to &quot;sell me something&quot;. I did some layman's research (&lt;a href=&quot;https://en.wikipedia.org/wiki/Lumosity&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;) and read that &quot;Studies of Lumosity's effectiveness have shown mixed results&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone with knowledge on the topic of learning know if the &quot;brain games&quot; they post are simply games? I guess the proper question would be:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can games like the ones Lumosity offers increase cognitive ability?&lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="36209" LastEditDate="2018-10-04T22:12:47.243" LastActivityDate="2018-10-04T22:12:47.243" Title="Is lumosity.com based on science?" Tags="&lt;neuroscience&gt;&lt;learning&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 4.0" />
  <row Id="35512" PostTypeId="2" ParentId="35511" CreationDate="2015-06-25T16:45:15.753" Score="13" Body="&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23672446&quot; rel=&quot;nofollow noreferrer&quot;&gt;Zickefoose et al.&lt;/a&gt; did a study, and showed that while you might improve while playing the game, it called into question if you actually improved outside of just getting better at the game.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22708717&quot; rel=&quot;nofollow noreferrer&quot;&gt;Redick et al.&lt;/a&gt; also reported that when they did a double blind study in brain games like Luminosity that you improved in the games, but they didn't see any transfer from game to every-day life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also see my previous answer on the topic: &lt;a href=&quot;https://cogsci.stackexchange.com/questions/10302/what-benefit-is-there-to-playing-highly-repetitive-games/10338#10338&quot;&gt;Cognitive Science Forum&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="-1" LastEditDate="2017-04-13T12:56:15.910" LastActivityDate="2015-06-25T17:16:11.373" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35513" PostTypeId="1" AcceptedAnswerId="35522" CreationDate="2015-06-25T18:37:05.910" Score="4" ViewCount="571" Body="&lt;p&gt;I have relatively good knowledge in evolutionary biology and in population genetics. I am getting more and more interested in the &lt;em&gt;evolution of ...&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;genetic developmental processes&lt;/li&gt;&#xA;&lt;li&gt;gene interactions&lt;/li&gt;&#xA;&lt;li&gt;gene expression&lt;/li&gt;&#xA;&lt;li&gt;plasticity&lt;/li&gt;&#xA;&lt;li&gt;intrinsic or cellular noise&lt;/li&gt;&#xA;&lt;li&gt;mutational robustness&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It seems that i am getting increasingly interested in a field that is in &lt;em&gt;between population genetics and system biology&lt;/em&gt;. I know very little about system biology.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you please give me some recommendations for books (and other readings such as reviews) that talk about the evolution of those processes that are usually studied by system biologists? I am much more interested in a book that presents &lt;em&gt;concepts and methods&lt;/em&gt; than a book listing empirical observations. Also, I am not interested in medicine but in biology.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-06-25T19:50:44.973" LastActivityDate="2015-06-26T02:51:30.883" Title="System biology and evolution: Book-recommendations" Tags="&lt;evolution&gt;&lt;theoretical-biology&gt;&lt;book-recommendation&gt;&lt;systems-biology&gt;&lt;evo-devo&gt;" AnswerCount="1" CommentCount="5" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35514" PostTypeId="1" AcceptedAnswerId="35520" CreationDate="2015-06-25T18:37:55.857" Score="4" ViewCount="385" Body="&lt;p&gt;Metaphorically thinking, if one endured the pain of constant burning for decades, would the pain slowly lose its strength?&lt;/p&gt;&#xA;" OwnerUserId="16413" LastActivityDate="2015-07-15T13:34:07.553" Title="If one endures the same form pain over a long period of time, would the pain begin to lose intensity?" Tags="&lt;pain&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35515" PostTypeId="1" CreationDate="2015-06-25T18:59:52.950" Score="8" ViewCount="4703" Body="&lt;p&gt;I have observed that parents having brown eyes had three female offspring with blue eyes, one son with green eyes, while only the youngest daughter had brown eyes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can they produce so many blue-eyed offspring?&lt;/p&gt;&#xA;" OwnerUserId="16414" LastEditorUserId="3553" LastEditDate="2015-06-27T13:20:19.387" LastActivityDate="2015-06-27T15:14:11.340" Title="How is it possible for only one in five children to have brown eyes when their parents both have brown eyes?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35516" PostTypeId="2" ParentId="35506" CreationDate="2015-06-25T19:03:45.917" Score="0" Body="&lt;p&gt;You might want to see the distribution of IC50s. If the majority do not obtain resistance, the histogram may show a normal distribution. Then you would know where less than 5% or 1% of population distribute. &#xA;If you have a few cell lines know as resistant against the chemical, you could use them to decide threshold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each drug has different effective dosage. You can not draw the same threshold for different drugs. If you have lots of cell lines, you could apply the strategy I mentioned above for a single drug.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-06-26T01:21:45.047" LastActivityDate="2015-06-26T01:21:45.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35517" PostTypeId="2" ParentId="35515" CreationDate="2015-06-25T19:31:47.250" Score="5" Body="&lt;p&gt;Possible...yes of course! The answer could stop there but I guess you want to ask how likely it is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a chart of probability of a given kid to have eyes of a certain color given the parents eyes color. (Note that the second column contain probabilites and not odds contrary to what the figure is stating).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/bj4ZT.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The probability that $k$ kids out of $n$ have eyes of a color which appears with probability $p$ is given by the probability mass function of the binomial distribution $\binom{n}{k} p^k (1-p)^{n-k}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Knowing that both parents have brown eyes (even for your oldest sister):&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The probability that exactly one out of 5 offsprings have brown eyes (and the others have eyes of another color) is about 0.015 (3 out of 200).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The probability that exactly 3 offsprings have blue eyes (and the others have eyes of another color) is about 0.0021 (2 out of 1000)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You might want to calculate the probability of having $k$ or more kids that have eyes of a given color (a p.value) is obtained by summing probabilities. For example, the probability that 3 or more kids (out of 5) have blue eyes is  $\binom{5}{3} 0.0625^3 (1-0.0625)^{5-3} + \binom{5}{4} 0.0625^4 (1-0.0625)^{5-4} + \binom{5}{5}  0.0625^5  (1-0.0625)^{5-5} ≈ 0.0022$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Learn more about Stats&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You'll probably want to learn a bit about statistics if some things are unclear. You might want to make sure you understand the concept of p.value and its interest and make sure you understand what a binomial distribution is. You may also want to understand the concept of multiple testing to avoid falling in simple pitfalls.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-06-27T15:14:11.340" LastActivityDate="2015-06-27T15:14:11.340" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="35518" PostTypeId="1" AcceptedAnswerId="45234" CreationDate="2015-06-25T19:54:14.680" Score="3" ViewCount="787" Body="&lt;p&gt;Can a kit fox (&lt;em&gt;Vulpes macrotis&lt;/em&gt;) and a red fox (&lt;em&gt;Vulpes vulpes&lt;/em&gt;) together produce offspring?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would such a hybrid be fertile?&lt;/p&gt;&#xA;" OwnerUserId="16415" LastEditorUserId="17400" LastEditDate="2016-04-15T01:15:12.597" LastActivityDate="2016-04-15T01:15:12.597" Title="Can kit foxes and red foxes produce offspring?" Tags="&lt;zoology&gt;&lt;mammals&gt;&lt;hybridization&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35519" PostTypeId="1" CreationDate="2015-06-26T00:04:33.050" Score="-1" ViewCount="340" Body="&lt;p&gt;I read somewhere in the internet and wondered if human genes have deactivated immortality genes locked somewhere in the DNA strand. Is this statement true? What does it mean for human lifespan?&lt;/p&gt;&#xA;" OwnerUserId="10403" LastActivityDate="2015-06-28T20:18:07.300" Title="Immortality Gene? Really?" Tags="&lt;dna&gt;&lt;gene&gt;" AnswerCount="3" CommentCount="6" ClosedDate="2015-06-27T06:41:11.697" ContentLicense="CC BY-SA 3.0" />
  <row Id="35520" PostTypeId="2" ParentId="35514" CreationDate="2015-06-26T00:27:38.443" Score="3" Body="&lt;p&gt;Under the assumption that the temperature experienced is not high enough to simply burn the nerves responsible for the pain (which would lead to insensible regions), yes and it would due to what is called &lt;a href=&quot;https://en.wikipedia.org/wiki/Homologous_desensitization&quot; rel=&quot;nofollow noreferrer&quot;&gt;receptor desensitization&lt;/a&gt;. In the case of burning pain the receptor involved is called the transient-receptor potential channel V1 (TRPV1). It is the same receptor involve in the oral burning sensation of spiciness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now two scenarios are possible given your question, namely a constant stimulus over a long period and &quot;oscillating&quot; stimuli (i.e. a repetition of stimuli followed by non-stimulated periods).&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Constant stimulus&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I provided a similar answer to this question: &lt;a href=&quot;https://biology.stackexchange.com/questions/14238/what-features-cause-mechano-sensory-adaptation/30914#30914&quot;&gt;What features cause mechano sensory adaptation?&lt;/a&gt;. This is the scenario where you keep the painful stimulus constant over a period of time. Here desensitization, i.e. reduction in pain feeling, is due to a direct receptor desensitization. This happens because the receptor is internalized (also called &lt;a href=&quot;https://en.wikipedia.org/wiki/Receptor-mediated_endocytosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;receptor-mediated endocytosis&lt;/a&gt;) into the cell after being activated and it takes some times for the receptor to reach the cell membrane again meaning if the stimulus remains constant, pretty much no receptors will be left on the cell membrane.  After decades long term desensitization will occur and is slightly different in it's mechanism compared to standard desensitization as described hereafter.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;&quot;Oscillating&quot; stimuli&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;In the case you are talking about a chronic pain interrupted by periods of non stimulation then long term desensitization will occur. In this scenario, the concentration of receptors will be reduced semi-permanently (i.e. reduced expression of the receptor) in the receptor cells reducing the pain signal. This is what happens with spiciness sensation. People eating regularly very spicy will physiologically be less sensitive to spices as they have less receptors sensing the spices provoking a reduced burning sensation.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Just as a footnote, very long chronic pain will also change the brain wiring of the pain signal but as I don't know enough about neurobiology I will leave that appart.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-06-26T01:42:10.363" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35522" PostTypeId="2" ParentId="35513" CreationDate="2015-06-26T02:34:20.160" Score="3" Body="&lt;p&gt;Here there are a couple that I own:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;classic&quot; from Uri Alon touches many of the topics you mention. It is easy to read and goes relatively deep into the methods. There seems to be a new edition (if you search it in Amazon it will pop up), but it was planned for last year's April and then delayed so no so clear when will be actually published. For the original one: &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/1584886420&quot; rel=&quot;nofollow&quot;&gt;Amazon link&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Title: An Introduction to Systems Biology: Design Principles of Biological Circuits&#xA;Year: 2006&#xA;Author: Uri Alon&#xA;Publisher: Chapman &amp;amp; Hall/CRC Mathematical and Computational Biology&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The other book is this textbook &quot;Systems biology&quot; by  Edda Klipp and others. I attended a talk by Edda Klipp two years ago and she seems to be doing interesting things. This book is more general, covering, somewhat superficially, many topics. It can be good to get a general idea on the field. &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/3527318747&quot; rel=&quot;nofollow&quot;&gt;Amazon link.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Title: Systems Biology Paperback&#xA;Year: 2009&#xA;Author: Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig&#xA;Publisher: Wiley-Blackwell&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;There are many others (see Amazon results &lt;a href=&quot;http://www.amazon.com/s/ref=nb_sb_ss_c_0_15?url=search-alias%3Dstripbooks&amp;amp;field-keywords=systems+biology&amp;amp;sprefix=systems+biology%2Caps%2C321&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;). Maybe other members can comment on some of the other titles.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastEditorUserId="9099" LastEditDate="2015-06-26T02:51:30.883" LastActivityDate="2015-06-26T02:51:30.883" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35523" PostTypeId="2" ParentId="35519" CreationDate="2015-06-26T03:18:43.153" Score="2" Body="&lt;p&gt;In tissue culture and cell engineering fields, the word &quot;immortal&quot; is often used to express something else instead of human or animal life spun. When you take cells from human tissues and grow them in test tubes--although flasks or dishes are used in reality--, cells stop growing after long term culture. They say it is cellular senescence. Several genes actually regulate this cellular senescence, and inactivation of these genes causes infinite cell proliferation. This is immortalization of cells. Then, cells in a human bodies are immortalized, do they get immortal? Probably, not. Cellular senescence partially explains senescence of bodies, but these two are different things. In human bodies, cellular immortalizaion occasionally occur. It is tumor pathologically.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-06-26T06:19:56.520" LastActivityDate="2015-06-26T06:19:56.520" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35524" PostTypeId="2" ParentId="35509" CreationDate="2015-06-26T04:38:21.767" Score="4" Body="&lt;p&gt;Yes you are correct. These mRNAs, that lack stop codon will cause translation to continue into the poly-A tail (it will result in addition of lysines not phenylalanine). Since no stop codon is present, the ribosome remains attached to the mRNA. Under these circumstances, a pathway known as non-stop decay is activated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;An important protein in this pathway — &lt;em&gt;Ski7&lt;/em&gt; detects a stalled ribosome and initiates the decay process for both the peptide and the mRNA. The poly-lysine tail of the peptide has been shown to fasten the peptide decay process. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/CYK20.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;In prokaryotes too, the non-stop mutations cause the ribosome to run through the stop codon and to eventually stall. However, there are no poly-A tails and ribsosome recovery pathway is different from that of eukaryotes. An RNA called tmRNA (a hybrid of tRNA and mRNA) binds to the the A-site using its tRNA-like domain. Then the translation proceeds through the mRNA domain of tmRNA (this is called trans-translation) which causes an addition of a peptide tag (that acts like a degradation signal) to the stalled polypeptide and finally leads to ribosome release when the stop codon is reached. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/UyPqq.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;h1&gt;References:&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Non-stop decay&lt;/strong&gt;: &#xA;&lt;br&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;Klauer and van Hoof. &lt;a href=&quot;http://dx.doi.org/10.1002%2Fwrna.1124&quot; rel=&quot;nofollow noreferrer&quot;&gt;Degradation of mRNAs that lack a stop codon: A decade of nonstop progress&lt;/a&gt;. &lt;em&gt;Wiley Interdiscip Rev RNA&lt;/em&gt;. 2012 Sep-Oct; 3(5): 649–660. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;tmRNA&lt;/strong&gt;: &lt;br&gt; &amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;Jannsen and Hayes. &lt;a href=&quot;http://dx.doi.org/10.1016%2FB978-0-12-386497-0.00005-0&quot; rel=&quot;nofollow noreferrer&quot;&gt;The tmRNA ribosome rescue system&lt;/a&gt;. &lt;em&gt;Adv Protein Chem Struct Biol.&lt;/em&gt; 2012; 86: 151–191.  &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-06-26T05:59:56.767" LastActivityDate="2015-06-26T05:59:56.767" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35525" PostTypeId="2" ParentId="35509" CreationDate="2015-06-26T06:17:27.763" Score="0" Body="&lt;p&gt;In fact, it is rare that stop codon mutation causes translation of polyA sequence in mammalian cells because you will find another in-frame stop codon downstream. And some stop codon mutations still producing the protein stably(&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0925443998000520&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, as WYSIWYG mentions, in the absence of alternative in-frame stop codon, mRNAs would be degraded. It is also called none-stop decay(&lt;a href=&quot;https://en.wikipedia.org/wiki/Non-stop_decay&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;). I am not sure that this phrase gets popularity though.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-06-26T06:17:27.763" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35526" PostTypeId="1" AcceptedAnswerId="35530" CreationDate="2015-06-26T07:31:40.240" Score="1" ViewCount="818" Body="&lt;p&gt;So the pancreatic acinar cell synthesizes, stores and secretes digestive enzyme precursors called zymogens e.g. pepsinogen. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The structure of the acinar cell shows that there is an apical and basal side. The basal half of the cell is almost entirely filled with rough endoplasmic reticulum which can be shown with pyronin stain showing up pink due to the rRNA of ribosomes. The nucleus is also on the basal side which explains why rER is there too, since the nuclear envelop is connected with the ER membrane. Zymogen granules are on the apical region. Any thoughts as to why there is this polarity in cell?&lt;/p&gt;&#xA;" OwnerUserId="10520" LastEditorUserId="9943" LastEditDate="2015-07-26T12:09:05.350" LastActivityDate="2015-08-25T12:17:57.693" Title="How does the structure of the pancreatic acinar cell relates to its function?" Tags="&lt;cell-biology&gt;&lt;proteins&gt;&lt;homework&gt;&lt;staining&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35529" PostTypeId="2" ParentId="35519" CreationDate="2015-06-26T10:48:58.643" Score="1" Body="&lt;p&gt;I think you read about the telomerase: &lt;a href=&quot;https://en.wikipedia.org/wiki/Telomerase&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Telomerase&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The chromosomes while duplicating, they loose some of the DNA segments from their ends, from the telomer. This is believed to have a direct effect on senescence. &#xA;The telomerase reproduces the end DNA strip of the chromosomes. This enzyme is found in active form in stem cells and in white blood cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The DNA sequence coding this enzyme is found in every cell, but in an inactivated form. Probably the article you are referring to, was talking about the telomerase, because it can be activated in almost every cell in our body. But this can lead to uncontrolled growth of the cells, and when this happens we talk about cancer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More information at: &lt;a href=&quot;https://en.wikipedia.org/wiki/Telomere#Structure.2C_function_and_evolutionary_biology&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Telomere#Structure.2C_function_and_evolutionary_biology&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16410" LastActivityDate="2015-06-26T10:48:58.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35530" PostTypeId="2" ParentId="35526" CreationDate="2015-06-26T11:07:05.457" Score="2" Body="&lt;p&gt;The secretion pushes the cell organelles to the basal part.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(although the fat cells have no polarity, their organelles have been pushed to one side of the cell: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ANh59.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Comparing to adipose cells, the acinar cells secrete their specific proteins on one specific end of the cell, this is why in contrast with fat cells they have well defined polarity.  &lt;/p&gt;&#xA;" OwnerUserId="16410" LastEditorUserId="5144" LastEditDate="2015-06-26T11:41:19.850" LastActivityDate="2015-06-26T11:41:19.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35531" PostTypeId="1" AcceptedAnswerId="35994" CreationDate="2015-06-26T11:47:35.343" Score="4" ViewCount="1176" Body="&lt;p&gt;Haemolytic disease of the newborn can result from Rhesus incompatibility in utero.  In this disease an Rh- mother becomes exposed to the antigens of an Rh+ foetus by fetomaternal haemorrhage causing her to mount an immune response against the D antigen.  In her second pregnancy, repeat exposure to the D antigen activates memory cells causing a large production of IgG Anti-D antibodies that cross the placenta adhering to foetal red blood cells, which are then destroyed.&lt;/p&gt;&#xA;&lt;p&gt;To prevent this, Rh- mothers are normally given exogenous Anti-D at 28 and 34 weeks gestation or after any sensitising event.  The aim of this treatment as I understand it is to 'mop up' any D antigen in the maternal bloodstream, covering it in exogenous antigen so the mother's immune system does not mount its own response.&lt;/p&gt;&#xA;&lt;p&gt;I had previously assumed that these exogenous antibodies would be IgM to avoid them crossing the placenta, however looking at the &lt;a href=&quot;https://web.archive.org/web/20200809084419/https://www.medicines.org.uk/emc/product/9724/smpc&quot; rel=&quot;nofollow noreferrer&quot;&gt;summaries of&lt;/a&gt; &lt;a href=&quot;https://www.medicines.org.uk/emc/product/6791/smpc&quot; rel=&quot;nofollow noreferrer&quot;&gt;product characteristics&lt;/a&gt; for some of the common preparations I see that &amp;quot;at least 95%&amp;quot; of protein content other than albumin is IgG.  I then wondered if the exogenous antibodies had a much reduced half life, however the half life is &amp;quot;about 3-4 weeks.&amp;quot;&lt;/p&gt;&#xA;&lt;p&gt;Why does the exogenous IgG not cause haemolytic disease of the newborn in the exact same way that endogenous IgG would in a previously exposed woman who had not had prophylaxis?  Is it dose-dependent or am I missing something entirely?&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="948" LastEditDate="2020-11-20T03:02:43.323" LastActivityDate="2020-11-20T03:02:43.323" Title="Why is the administration of exogenous Anti-D not harmful to the foetus?" Tags="&lt;pathology&gt;&lt;hematology&gt;&lt;antibody&gt;&lt;pregnancy&gt;&lt;treatment&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="35532" PostTypeId="1" CreationDate="2015-06-26T11:53:22.683" Score="83" ViewCount="19244" Body="&lt;p&gt;If a trait would be advantageous to an organism then why hasn't it evolved yet?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conversely, if a trait is not advantageous or mildly disadvantageous, why does it exist?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words why does evolution not make the organism more &quot;perfect&quot;?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;This is a general question that would be applicable for any kind of trait. Please keep the answers precise and scientific.&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Read this meta post for more information: &lt;a href=&quot;https://biology.meta.stackexchange.com/q/3116/6786&quot;&gt;Questions asking for evolutionary reasons&lt;/a&gt;&lt;/em&gt; &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-03-16T15:49:46.677" LastActivityDate="2019-03-28T20:44:49.100" Title="Why do some bad traits evolve, and good ones don't?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;&lt;adaptation&gt;" AnswerCount="8" CommentCount="4" FavoriteCount="28" CommunityOwnedDate="2015-06-26T11:53:29.283" ContentLicense="CC BY-SA 3.0" />
  <row Id="35533" PostTypeId="2" ParentId="35532" CreationDate="2015-06-26T12:07:38.557" Score="74" Body="&lt;p&gt;During the process of selection, individuals having disadvantageous traits are weeded out. If the selection pressure isn't strong enough then mildly disadvantageous traits will continue to persist in the population. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the reasons for why a trait is not evolved even though it may be advantageous to the organism, are:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;There is no strong pressure against the individuals not having that trait. In other words lack of the trait is not strongly disadvantageous.&lt;/li&gt;&#xA;&lt;li&gt;The trait might have a tradeoff which essentially makes no change to the overall fitness. &lt;/li&gt;&#xA;&lt;li&gt;Not enough time has elapsed for an advantageous mutation to get fixed. This doesn't mean that the mutation had not happened yet. It means that the situation that rendered the mutation advantageous had arisen quite recently. Consider the example of a mutation that confers resistance against a disease. The mutation wouldn't be advantageous if there was no disease. When a population encounters the disease for the first time, then the mutation would gain advantage but it will take some time to establish itself in the population.&lt;/li&gt;&#xA;&lt;li&gt;The rate for that specific mutation is low and therefore it has not yet happened. Mutation rates are not uniform across the genome and certain regions acquire mutations faster than the others. Irrespective of that, if the overall mutation rate is low then it would take a lot of time for a mutation to arise and until then its effects cannot be seen.&lt;/li&gt;&#xA;&lt;li&gt;The specific trait is too genetically distant: it &lt;em&gt;cannot&lt;/em&gt; be the result of a mutation in a single generation. It might, conceivably, develop after successive generations, each mutating farther, but if the intervening mutations are at too much of a disadvantage, they will not survive to reproduce and allow a new generation to mutate further away from the original population.&lt;/li&gt;&#xA;&lt;li&gt;The disadvantage from not having the trait normally arises only after the reproductive stage of the individual's lifecycle is mostly over.  This is a special case of &quot;no strong pressure&quot;, because evolution selects genes, not the organism. In other words the beneficial mutation does not alter the reproductive fitness.&lt;/li&gt;&#xA;&lt;li&gt;Koinophillia resulted in the trait being unattractive to females. Since most mutations are detrimental females don't want to mate with anyone with an obvious mutation, since there is a high chance it will be harmful to their child.  Thus females instinctually find any obvious physical difference unattractive, even if it would have been beneficial.  This tends to limit the rate or ability for physical differences to appear in a large &amp;amp; stable mating community.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Evolution is not a directed process and it does not actively try to look for an optimum. The fitness of an individual does not have any meaning in the absence of the selection pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;&lt;em&gt;If you have a relevant addition then please feel free to edit this answer.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="5925" LastEditDate="2018-02-03T12:18:05.537" LastActivityDate="2018-02-03T12:18:05.537" CommentCount="5" CommunityOwnedDate="2015-06-26T12:07:38.557" ContentLicense="CC BY-SA 3.0" />
  <row Id="35535" PostTypeId="1" CreationDate="2015-06-26T12:33:13.443" Score="3" ViewCount="372" Body="&lt;p&gt;Is there a methodology to select a reasonable threshold for copy number variation in a CNV (SNP array) TCGA dataset, to define when there is a significative alteration?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can I download CNV data for normal samples and take the 95th percentile of distribution? Are there better methods?&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Update&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;This is the percentiles plot of the two distribution (Tumor vs Normal) of values, for the same technology (SNP array) and the same genome (hg19). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The tumor distribution has slightly more extreme values, though it is not enough in my opinion. For this reason I think I should not use a percentile score (the 5th and the 95th percentile of the normal samples distribution, for instance) to define the thresholds to call CNV alterations in the tumor samples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/H1TF5.png&quot; alt=&quot;distributions&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3466" LastEditorUserId="3466" LastEditDate="2015-06-26T15:09:55.090" LastActivityDate="2015-06-26T15:09:55.090" Title="Deciding a reasonable threshold for copy number variation in a CNV (SNP array) TCGA dataset" Tags="&lt;bioinformatics&gt;&lt;cancer&gt;&lt;tcga&gt;&lt;copy-number-variation&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35537" PostTypeId="2" ParentId="35532" CreationDate="2015-06-26T13:28:24.453" Score="15" Body="&lt;p&gt;Below are the reasons I can think of. The list is not exhaustive and there are some conceptual overlaps.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The trait seems advantageous but it is not, maybe due to its effect on another component of fitness (trade-off). It sounds to me to be the most likely explanation whenever you are wondering why a given species does not carry a given trait. In other words, the fitness landscape matter.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The trait is not that easy to build it requires a series of mutations that are either neutral, quasi-neutral or deleterious.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The mutation just hasn't happened yet (lag load).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the mutant variant had appeared several times but got extinct because of genetic drift even though it was beneficial (assuming no fitness valley to cross).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Putting the two previous points together, if only one mutation (one SNP) is needed to build this trait and if the trait is beneficial but quasi-neutral, then the expected time before fixation to occur is around &lt;span class=&quot;math-container&quot;&gt;$10^9$&lt;/span&gt; generations. Here is why. Let &lt;span class=&quot;math-container&quot;&gt;$N$&lt;/span&gt; be the population size and &lt;span class=&quot;math-container&quot;&gt;$\mu$&lt;/span&gt; be the mutation rate. In a diploid population (but the end result is the same for the haploids), there are &lt;span class=&quot;math-container&quot;&gt;$2n\mu$&lt;/span&gt; appearing at this locus each generation. As the mutation is quasi-neutral, its probability of fixation (calculated from Wright-Fisher equations or Moran birth-death process, or from Kimura's diffusion equation) is &lt;span class=&quot;math-container&quot;&gt;$\frac{1}{2}N$&lt;/span&gt;. Therefore the rate at which fixation occur is &lt;span class=&quot;math-container&quot;&gt;$2N\mu \frac{1}{2N} = \mu$&lt;/span&gt;. &lt;span class=&quot;math-container&quot;&gt;$\mu$&lt;/span&gt; for an SNP in a species that has a large genome is around  &lt;span class=&quot;math-container&quot;&gt;$10^{-9}$&lt;/span&gt;. The probability that fixation occurs in &lt;span class=&quot;math-container&quot;&gt;$t$&lt;/span&gt; generations is given by the exponential distribution with parameter &lt;span class=&quot;math-container&quot;&gt;$\mu$&lt;/span&gt; ad the expected value of this exponential distribution is &lt;span class=&quot;math-container&quot;&gt;$\frac{1}{10^{-9}} = 10^9$&lt;/span&gt; generations. If there is one generation per year, that takes a lot of time! Of course, those calculations are a good approximation when the trait of interest is quasi-neutral. If the positive selection is very very strong on this trait to the point that we can completely neglect drift, then the expected time for the mutant to occur is &lt;span class=&quot;math-container&quot;&gt;$\frac{1}{2N\mu}$&lt;/span&gt;, which is &lt;span class=&quot;math-container&quot;&gt;$10^5$&lt;/span&gt; for a population size of &lt;span class=&quot;math-container&quot;&gt;$N = 10000$&lt;/span&gt; which is still quite a lot. In the meantime, the environment or the genetic background may change so that the trait is not advantageous anymore. The above calculations assumed that the trait appeared with only one mutation and that only one SNP can cause the trait to exist. One can be more general by summing exponential distribution (for multiple mutation scenarios) and increasing the mutation rate (for mutations at different loci can make the trait exist).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the mutant variant had appeared several times but got extinct because of drift because the Ne in the genomic region is very low due to the act that there are many loci under selection in the surroundings (background selection).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;the trait is beneficial and occur sometime but either stay at low frequency or even regularly disappear due to a migration of individuals coming from an environment where this trait is strongly deleterious (dispersal load).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Be careful to understand what evolution does and therefore to understand what advantageous mean. Taking kin selection/group selection/lineage selection apart to make things easier, an advantageous allele is the one who increases the fitness of its carrier. The effect of a given allele depends on the environment and on the genetic background in which it exists. A beneficial allele does not necessarily increase survival or increase the probability of the population to not get extinct. Think about sexual selection typically.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="49230" LastEditDate="2019-03-28T20:35:38.267" LastActivityDate="2019-03-28T20:35:38.267" CommentCount="0" CommunityOwnedDate="2015-06-26T13:28:24.453" ContentLicense="CC BY-SA 4.0" />
  <row Id="35538" PostTypeId="2" ParentId="35535" CreationDate="2015-06-26T13:44:03.767" Score="1" Body="&lt;p&gt;Your suggested approach of comparing to the baseline distribution on a point-by-point basis isn't bad, although it's going to be susceptible to small false positives from noise. You'd probably want to only use events that span a certain minimum number of consecutive observations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You might also want to look into circular binary segmentation, as described here: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15475419&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/15475419&lt;/a&gt;. &lt;/p&gt;&#xA;" OwnerUserId="819" LastActivityDate="2015-06-26T13:44:03.767" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35539" PostTypeId="2" ParentId="35535" CreationDate="2015-06-26T13:46:50.563" Score="1" Body="&lt;p&gt;There are many methods for the analysis of CNV. If you are an &lt;a href=&quot;http://www.r-project.org&quot; rel=&quot;nofollow&quot;&gt;R&lt;/a&gt; user I would recommend you to take a look at the &lt;a href=&quot;http://www.bioconductor.org&quot; rel=&quot;nofollow&quot;&gt;Bioconductor&lt;/a&gt; package list, in particular the section for &lt;a href=&quot;http://www.bioconductor.org/packages/release/BiocViews.html#___CopyNumberVariation&quot; rel=&quot;nofollow&quot;&gt;copy number variation&lt;/a&gt;. Currently it contains 50 packages!&lt;/p&gt;&#xA;" OwnerUserId="9099" LastActivityDate="2015-06-26T13:46:50.563" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35540" PostTypeId="2" ParentId="35532" CreationDate="2015-06-26T14:05:52.427" Score="34" Body="&lt;p&gt;There's always the most obvious: Evolution is chance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some traits allow an individual to have a higher chance to produce offspring. That doesn't mean individuals with that trait have more offspring, not even on average unless &lt;a href=&quot;https://en.wikipedia.org/wiki/Law_of_large_numbers&quot; rel=&quot;nofollow noreferrer&quot;&gt;the law of large numbers&lt;/a&gt; applies. A randomly mutated perfect squirrel could appear, and since it's only one, it gets run over by a car before it can reproduce and all perfect traits are lost.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there is a chance that a trait is beneficial for the individual, but doesn't have a significant effect on its chance of having offspring. For example, take human eyesight. People with really poor eyesight have a disadvantage. But most people have good enough eyesight until they are too old to have kids, so it doesn't matter to evolution if they fall off a cliff afterwards. It may even be advantageous if kids don't have to spend resources to care for their parents.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And a very nice effect is a swarm effect where you look at entire swarms, for example of fish. Take a swarm or community that reproduces primarily within itself, where for some reason only traits that are beneficial for the individual can get inherited. As soon as the swarm gets into competition with a superior swarm - where traits that benefited the swarm got inherited - the entirety of the former swarm may die. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's also the effect of society. If during one decade a society thinks people with green hair are not attractive partners - even though it's better for camouflage - it sucks to have green hair during that decade. This doesn't only apply to humans. I remember reading that among some bird species the singing evolves and which songs are &quot;hip&quot;/attractive depends on social factors as well as genes. Just imagine what would have happened if a small number of humans would have started to grow bat wings that made them fully capable of flight, during the time of the Spanish Inquisition - rather than spreading the new gene they would have burned on a stake.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's not forget about the really cool effect of &lt;a href=&quot;https://en.wikipedia.org/wiki/Frequency-dependent_selection&quot; rel=&quot;nofollow noreferrer&quot;&gt;frequency dependent selection&lt;/a&gt; where a trait is only beneficial if not too many other individuals have it. These traits can be beneficial for an individual, or a species, or both, but only if not too many individuals carry the trait. A community of humans can benefit from super smart people who have limited control of their bodies and emotions, but if all humans in the community are like that the community has a problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Last but not least, there's the change in external conditions. If conditions change, many species will simply go extinct (e.g. Ice Age). Imagine all viruses disappear. If there are no viruses, a trait that makes the immune system more efficient against bacteria and cancer at the expense of having no defense against viruses, is clearly a beneficial trade. Then viruses come back and every species that adapted the &quot;no defense against viruses&quot; trait goes extinct from a viral infection. This can make it beneficial to not adapt new traits too quickly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In summary: By accepting that evolution is a random process where individuals with more advantageous traits are simply somewhat more likely to have more offspring, and where entire communities or subspecies are slightly more likely to go extinct if the traits are less beneficial for the community, you get all of the above effects and many more. Keep in mind that individuals with advantageous traits are in no way guaranteed to have more offspring, and communities can be wiped out or flourish due to all kinds of incidents that completely ignore how advantageous or disadvantageous their traits are.&lt;/p&gt;&#xA;" OwnerUserId="16424" LastEditorUserId="43480" LastEditDate="2019-03-15T03:21:37.083" LastActivityDate="2019-03-15T03:21:37.083" CommentCount="4" CommunityOwnedDate="2015-06-26T14:05:52.427" ContentLicense="CC BY-SA 4.0" />
  <row Id="35541" PostTypeId="1" CreationDate="2015-06-26T14:30:28.327" Score="0" ViewCount="295" Body="&lt;p&gt;I am reading about ligamentum arteriosum which connects the left pulmonary artery and descending aorta. But I am seeing that if any figure shows left brachiochephalic vein it does not show left pulmonary artery (and vice versa). Are they both the same?&lt;/p&gt;&#xA;" OwnerUserId="16425" LastEditorUserId="3340" LastEditDate="2015-06-26T14:49:13.233" LastActivityDate="2015-06-26T15:15:30.693" Title="is left brachiochephalic vein and left pulmonary artery is same?" Tags="&lt;anatomy&gt;&lt;lungs&gt;&lt;veins&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35542" PostTypeId="2" ParentId="35541" CreationDate="2015-06-26T15:15:30.693" Score="1" Body="&lt;p&gt;No, they are not the same.  The left brachiocephalic vein receives de-oxygenated blood from the left subclavian vein (draining the left arm) and the left internal jugular vein (draining the brain and parts of the face).  The brachiocephalic vein then joins with the superior vena cava which flows into the right atrium.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The left pulmonary artery carries the deoxygenated blood that has just passed through the right atrium and ventricle, through the pulmonary trunk to the left lung for oxygenation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the foetal circulation, the ductus arteroisus (before it closes into the ligamentum arteriosum) allows blood to bypass the lungs, which are not oxygenated in the uterus!  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please see this diagram (which shows the foetal circulation including PDA for you).  The left brachiocephalic vein is circled in yellow, whilst the left pulmonary artery is circled in green.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fMm4x.png&quot; alt=&quot;Diagram showing left pulmonary artery and left brachiocephalic vein&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:Gray502.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;Image&lt;/a&gt; from public domain edition of Gray's.&lt;/p&gt;&#xA;" OwnerUserId="69" LastActivityDate="2015-06-26T15:15:30.693" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35543" PostTypeId="2" ParentId="35381" CreationDate="2015-06-26T15:19:13.957" Score="0" Body="&lt;p&gt;According to &lt;em&gt;Comparative Vertebrate Neuroanatomy&lt;/em&gt;, the XYW classfication is used for cat retina. They roughly correspond to the M, P, K cells in primates, respectively.&lt;/p&gt;&#xA;" OwnerUserId="16317" LastActivityDate="2015-06-26T15:19:13.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35544" PostTypeId="1" AcceptedAnswerId="35555" CreationDate="2015-06-26T15:54:51.347" Score="3" ViewCount="1954" Body="&lt;p&gt;Coming out of the pool the other day, I felt very cold because I was wet and the wind picked up. My idea is that a &quot;cold&quot; feeling should be associated with low temperatures, but it's indeed wrong. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why do we perceive wind at a farely normal temperature as cold?&lt;/p&gt;&#xA;" OwnerUserId="16428" LastActivityDate="2015-06-26T19:13:11.150" Title="Why is wind cold for humans?" Tags="&lt;human-biology&gt;&lt;perception&gt;" AnswerCount="3" CommentCount="11" FavoriteCount="0" ClosedDate="2015-06-27T07:21:06.950" ContentLicense="CC BY-SA 3.0" />
  <row Id="35545" PostTypeId="2" ParentId="34704" CreationDate="2015-06-26T15:58:21.847" Score="0" Body="&lt;p&gt;The best solution is to use only the broad alterations, using the file &lt;code&gt;broad_values_by_arm.txt&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, for each sample, the highest threshold is computed as the sum of the noise (low-level) threshold (e.g. 0.1) plus the maximum value of copy number variation for the sample over all the arms. Similarly, the lowest threshold is the minimum value for the sample over all the arms plus the negative noise (low-level) threshold (e.g. -0.1).&lt;/p&gt;&#xA;" OwnerUserId="3466" LastActivityDate="2015-06-26T15:58:21.847" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35546" PostTypeId="2" ParentId="35505" CreationDate="2015-06-26T16:05:48.317" Score="0" Body="&lt;p&gt;The no. of neurons only increase during development.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As, a person grows, the no. of neurons is constant or decreases (degradation due to injury or other brain diseases). The no. never increases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kLdcP.jpg&quot; alt=&quot;Effect of usage of neurons on conduction&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Learning anything (say, a phone no.) requires repeated thinking. The thinking can be continuous in the brain or re-induced by revision. Therefore, learning anything STRENGTHENS the connections; not increase in neuron no.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't help you with any Scientific Paper. The image was taken from a Textbook.&lt;/p&gt;&#xA;" OwnerUserId="4503" LastActivityDate="2015-06-26T16:05:48.317" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35547" PostTypeId="1" CreationDate="2015-06-26T16:17:18.950" Score="2" ViewCount="922" Body="&lt;p&gt;I'm studying V(D)J recombination. I think I have two incompatible books about explantaion of the process. Which is right?&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;In Molecular Biology of the Cell 5th Ed., firstly RAG (-1?) combines to RSSs of V and J genes independently. After that, a hairpin loop is formated by paring random(?) RAGs.&lt;/li&gt;&#xA;&lt;li&gt;In Janeway's Immunobiology 8th Ed., RAG complex (RAG-1 and RAG-2) has two sites for RSSs from the beginning. And in the figure, V gene is firstly recruited for a site. J gene combines to the RAG complex after V gene.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="16417" LastActivityDate="2015-10-24T20:18:20.167" Title="Which process is right to describe V(D)J recombination? RAG-1 and RSS recurring process" Tags="&lt;immunology&gt;&lt;recombination&gt;&lt;immunity&gt;&lt;immunoglobin&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35548" PostTypeId="2" ParentId="35544" CreationDate="2015-06-26T16:25:09.150" Score="7" Body="&lt;p&gt;This phenomena has nothing to do with any different kinds of receptors.&#xA;When we are wet, we have lots of water on our surface. The evaporation of water causes cooling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Blowing wind tends to make evaporation faster. So, even if wind blows at normal temperature, we feel cold. If we are not wet, there is some water on our body surface. This water is low in quantity as compared  to when we are wet. So, we feel less cooling this time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, water has high specific heat i.e. it doesen't change temperature very easily. So,even on a warm day, we don't feel the heat if we are soaked.&lt;/p&gt;&#xA;" OwnerUserId="4503" LastActivityDate="2015-06-26T16:25:09.150" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35549" PostTypeId="2" ParentId="35544" CreationDate="2015-06-26T16:41:34.533" Score="5" Body="&lt;p&gt;As other answers and comments have stated the reason that you feel cooler when the wind is blowing (wind chill factor often gets talked about on the news) is because evaporation is speed up by the wind. The reason that this evaporation causes cooling (explained in more detail &lt;a href=&quot;http://www.planetseed.com/relatedarticle/evaporative-cooling&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;) is because when water evaporates, that water takes its energy with it. That energy loss to you is in the form of heat, thus making you feel colder.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, there is a little bit more to it than that. If you look on &lt;a href=&quot;http://science.howstuffworks.com/nature/climate-weather/atmospheric/question70.htm&quot; rel=&quot;nofollow&quot;&gt;How stuff works - windchill factor&lt;/a&gt; they go onto to talk about how the process of &lt;a href=&quot;http://home.howstuffworks.com/thermos1.htm&quot; rel=&quot;nofollow&quot;&gt;convection&lt;/a&gt; is what makes you feel cooler. What's happening is you're actually warming the air around your body up, and as the wind blows it's wisking that nice warm air away from your body replacing it with much colder air. The faster the wind blows, the faster your warm air is taken away from your body. When the wind blows fast the molecules around you move away from you faster so you have less time to heat them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How Stuff Works says this about convection:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Convection - Convection is a property of liquids and gases. It occurs&#xA;  because when a liquid or gas gets hot, it tends to rise above the rest&#xA;  of the body of liquid or gas. So, if you have a hot bowl of soup on&#xA;  the table, it heats a layer of air surrounding the bowl. That layer&#xA;  then rises because it is hotter than the surrounding air. Cold air&#xA;  fills in the space left by the rising hot air. This new cold air then&#xA;  heats up and rises, and the cycle repeats. It is possible to speed up&#xA;  convection -- that is why you blow on hot soup to cool it down. If it&#xA;  weren't for convection your soup would stay hot a lot longer, because&#xA;  it turns out that air is a pretty poor heat conductor.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So while evaporation plays a minor roll, it's most likely because you're no longer able to heat up the air around you as efficiently when the wind blows all that nice warm air away.&lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="16041" LastEditDate="2015-06-26T17:52:08.150" LastActivityDate="2015-06-26T17:52:08.150" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35550" PostTypeId="1" CreationDate="2015-06-26T17:12:49.940" Score="2" ViewCount="2037" Body="&lt;p&gt;If you feel your head hair, it typically feels a lot softer and is easier to manage (comb, brush, fix) than a lot of other hair on your body - specifically I'm thinking about beard hair and pubic hair, which typically are a lot coarser than the hair on your head. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why are these hairs thicker?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What causes them to grow differently than the hair on our head?&lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="16041" LastEditDate="2015-06-26T17:21:26.957" LastActivityDate="2015-06-28T01:09:45.537" Title="What causes head hair to be different than body and face hair?" Tags="&lt;human-biology&gt;" AnswerCount="0" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35551" PostTypeId="1" CreationDate="2015-06-26T17:20:19.027" Score="1" ViewCount="99" Body="&lt;p&gt;Why do hair continuously grow on human heads, while the same doesn't happen on other parts of the human body? Where there &lt;em&gt;are&lt;/em&gt; hair, they only usually grow to a fixed length; but they seem to have no limit (or at least a much higher limit) as long as the head is concerned (and the face, in men).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why does this only happen on humans? When did it start happening? What kind of evolutionary advantage could there be in overly-long head hair, so that humans have them while other primates and mammals don't?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I know there are various questions around about why humans have much less body hair than other mammals; mine is related but different: why are we the only species with so much hair on our head, to the point that they might even become inconvenient if we don't cut them?&lt;/p&gt;&#xA;" OwnerUserId="805" LastEditorUserId="805" LastEditDate="2015-06-26T17:34:24.250" LastActivityDate="2015-06-26T18:11:17.383" Title="Why do human have continuously-growing hair on their head?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;hair&gt;&lt;human-evolution&gt;" AnswerCount="0" CommentCount="11" ClosedDate="2015-06-26T18:11:35.543" ContentLicense="CC BY-SA 3.0" />
  <row Id="35553" PostTypeId="2" ParentId="35532" CreationDate="2015-06-26T17:36:46.080" Score="19" Body="&lt;p&gt;Because evolution is an effect, not a cause.  That is, there's no &quot;&lt;a href=&quot;http://wiki.lspace.org/mediawiki/God_of_Evolution&quot;&gt;God of Evolution&lt;/a&gt;&quot; out there deciding that this or that trait would be beneficial to a species, and deciding to add it.  Evolution just works* on whatever random variations happen to come along.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*And as others have pointed out, it works statistically, not deterministically.&lt;/p&gt;&#xA;" OwnerUserId="11736" LastEditorUserId="11607" LastEditDate="2015-10-29T19:28:56.883" LastActivityDate="2015-10-29T19:28:56.883" CommentCount="2" CommunityOwnedDate="2015-06-26T17:36:46.080" ContentLicense="CC BY-SA 3.0" />
  <row Id="35554" PostTypeId="2" ParentId="35547" CreationDate="2015-06-26T18:08:22.483" Score="1" Body="&lt;p&gt;Excerpt from &lt;em&gt;Cellular and Molecular Immunology&lt;/em&gt;, 8th ED, p.181-182. Don't up-vote me, i just thought this text offers a good, up-to-date explanation.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;The Mechanism of V(D)J Recombination&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Rearrangement of Ig and TCR genes represents a special kind of non-homologous DNA recombination &#xA;  event, mediated by the coordinated activities of several &#xA;  enzymes, some of which are found only in developing &#xA;  lymphocytes, whereas others are ubiquitous DNA double-stranded break repair (DSBR) enzymes&lt;/strong&gt;.Although &#xA;  the mechanism of V(D)J recombination is fairly well &#xA;  understood and will be described here, how exactly &#xA;  specific loci are made accessible to the machinery &#xA;  involved in recombination remains to be determined. &#xA;  It is likely that the accessibility of the Ig and TCR loci to &#xA;  the enzymes that mediate recombination is regulated &#xA;  in developing B and T cells by several mechanisms, &#xA;  including epigenetic alterations in chromatin structure &#xA;  and DNA as discussed earlier, and basal transcriptional &#xA;  activity in the gene loci.&#xA;  The process of V(D)J recombination can be divided &#xA;  into four distinct events that flow sequentially from one &#xA;  to the next (Fig. 8-10):&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;1. Synapsis&lt;/strong&gt;: Portions of the chromosome on which the &#xA;  antigen receptor gene is located are made accessible &#xA;  to the recombination machinery. Two selected coding segments and their adjacent RSSs are brought &#xA;  together by a chromosomal looping event and held &#xA;  in position for subsequent cleavage, processing, and &#xA;  joining.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;2. Cleavage&lt;/strong&gt;: Double-stranded breaks are enzymatically generated at RSS-coding sequence junctions &#xA;  by machinery that is lymphoid specific. Two proteins encoded by lymphoid-specific genes, called &#xA;  recombination-activating gene 1and recombination-activating gene 2(RAG1and RAG2), form &#xA;  a  complex, containing two molecules of each protein, &#xA;  that plays an essential role in V(D)J recombination. &#xA;  The Rag-1/Rag-2complex is also known as the V(D)J &#xA;  recombinase.The Rag-1 protein, in a manner similar to a restriction endonuclease, recognizes the DNA &#xA;  sequence at the junction between a heptamer and a &#xA;  coding segment and cleaves it, but it is enzymatically &#xA;  active only when complexed with the Rag-2 protein. &#xA;  The Rag-2 protein may help link the Rag-1/Rag-2 tetramer to other proteins, including accessibility factors that bring these proteins to specific open receptor &#xA;  gene loci at specific times and at defined stages of lymphocyte development. Rag-1 and Rag-2 contribute to &#xA;  holding together gene segments during the process of &#xA;  chromosomal folding or synapsis. Rag-1 then makes &#xA;  a nick (on one DNA strand) between the coding end &#xA;  and the heptamer. The released 3′OH of the coding &#xA;  end then attacks a phosphodiester bond on the other &#xA;  DNA strand, forming a covalent hairpin. The signal &#xA;  end (including the heptamer and the rest of the RSS) &#xA;  does not form a hairpin and is generated as a blunt &#xA;  double-stranded DNA terminus that undergoes no &#xA;  further processing. This double-stranded break results &#xA;  in a closed hairpin of one coding segment being held &#xA;  in apposition to the closed hairpin of the other coding end and two blunt recombination signal ends being placed next to each other. Rag-1 and Rag-2, apart &#xA;  from generating the double-stranded breaks, also hold &#xA;  the hairpin ends and the blunt ends together before &#xA;  the modification of the coding ends and the process of &#xA;  ligation.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;RAGgenes are lymphoid specific and are expressed &#xA;  only in developing B and T cells. Rag proteins are &#xA;  expressed mainly in the G0and G1&#xA;  stages of the cell &#xA;  cycle and are inactivated in proliferating cells. It is &#xA;  thought that limiting DNA cleavage and recombination &#xA;  to the G&#xA;  0 and G1&#xA;  stages minimizes the risk of generating inappropriate DNA breaks during DNA replication or during mitosis. Mice without functional Rag1&#xA;  or Rag2genes (Ragknockout mice) fail to develop B or &#xA;  T lymphocytes, and Rag-1 or Rag-2 deficiency is also &#xA;  a rare cause of SCID, in which patients also lack all &#xA;  lymphocytes.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;3. Hairpin opening and end-processing&lt;/strong&gt;: The broken &#xA;  coding ends are modified by the addition or removal &#xA;  of bases, and thus greater diversity is generated. After the formation of double-stranded breaks, hairpins must be resolved (opened up) at the coding &#xA;  junctions, and bases may be added to or removed &#xA;  from the coding ends to ensure even greater diversification. Artemisis an endonuclease that opens &#xA;  up the hairpins at the coding ends. In the absence &#xA;  of Artemis, hairpins cannot be opened, and mature &#xA;  T and B cells cannot be generated. Mutations in &#xA;  ARTEMIS are a rare cause of SCID, similar to patients with RAG1or RAG2mutations. (see Chapter &#xA;  21). A lymphoid-specific enzyme, called terminal &#xA;  deoxynucleotidyl transferase (TdT), adds bases to &#xA;  broken DNA ends and will be discussed later in the &#xA;  chapter in the context of junctional diversity.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;4. Joining&lt;/strong&gt;: The broken coding ends as well as the signal ends are brought together and ligated by a double-stranded break repair process found in all cells &#xA;  that is called nonhomologous end joining. A number &#xA;  of ubiquitous factors participate in nonhomologous &#xA;  end joining. Ku70 and Ku80 are DNA end-binding &#xA;  proteins that bind to the breaks and recruit the catalytic subunit of DNA-dependent protein kinase &#xA;  (DNA-PK), a double-stranded DNA repair enzyme. &#xA;  This enzyme is defective in mice carrying the severe &#xA;  combined immunodeficiency (scid)mutation, and mutations in the gene encoding this enzyme have also &#xA;  been discovered in human SCID patients (see Chapter &#xA;  21). Like Rag-deficient mice, scidmice fail to produce &#xA;  mature lymphocytes. DNA-PK also phosphorylates &#xA;  and activates Artemis, which, as mentioned before, is &#xA;  involved in end processing. Ligation of the processed &#xA;  broken ends is mediated by DNA ligase IV and XRCC4, &#xA;  the latter being a non-catalytic but essential subunit of &#xA;  the ligase.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Rb3mm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Figure 8-10, Cellular and Molecular Immunology, 8e, p182.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-08-25T19:41:02.697" LastActivityDate="2015-08-25T19:41:02.697" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35555" PostTypeId="2" ParentId="35544" CreationDate="2015-06-26T19:13:11.150" Score="14" Body="&lt;p&gt;One important point that you might not be considering is the heat of vaporization.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may be aware that while it normally takes 4.18 J (1 calorie) of heat to raise 1 gram of water 1 °C, it takes around 2250 J of heat to raise 1 g of water from liquid at 99.5 °C to gas at 100.5 °C, due to the energy needed to go from a liquid to a gas. - What you may not know is that the enthalpy of vaporization isn't limited to vaporization at the boiling point. &lt;em&gt;Any&lt;/em&gt; conversion of water to water vapor requires heat of vaporization, though exactly how much is &lt;a href=&quot;https://en.wikipedia.org/wiki/Enthalpy_of_vaporization&quot;&gt;temperature dependant&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So when water evaporates, it cools things much more than one might expect from the &quot;average&quot; energy (or even statistically above average energy) a water molecule may have in the liquid state - several hundred times more. All this is driven by the entropic benefits of having water molecules in the gaseous state rather than the liquid state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Wind makes the process more efficient because it removes the water-vapor laden air, unbalancing the equilibrium of the process in favor of further evaporation. More water makes it more efficient (to a point), because there's more water to evaporate and the rate of evaporation increases, increasing the removal of heat.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not just a physiological perception effect - one can actually measure the temperature drop when water evaporates. &lt;a href=&quot;https://en.wikipedia.org/wiki/Evaporative_cooler&quot;&gt;Evaporative coolers&lt;/a&gt; make use of this effect, and traditional wet-bulb hygrometers (psychrometers) use exactly this effect to measure the humidity -- in some cases you can get a temperature differential of 20 °C or more between a dry bulb thermometer and a wet bulb thermometer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a small perceptual effect in that the evaporative cooling is happening on your skin, where a large number of temperature receptors are located. Therefore, your skin (and temperature receptors) feel a cooling effect even if your core temperature doesn't change detectably. Local cooling produces a larger temperature change than might be expected if you calculated for a whole-body heat change. &lt;/p&gt;&#xA;" OwnerUserId="16433" LastActivityDate="2015-06-26T19:13:11.150" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35556" PostTypeId="1" CreationDate="2015-06-26T19:15:53.703" Score="5" ViewCount="772" Body="&lt;p&gt;If you inhale to your maximum capacity and hold your breath for an extended period of time, it begins to feel uncomfortable; slowly releasing your breath at this point seems to provide relief from this discomfort.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a biological reason why this is so, or is this something psychological?&lt;/p&gt;&#xA;" OwnerUserId="16434" LastActivityDate="2015-07-06T13:10:34.080" Title="Exhalation while holding breath" Tags="&lt;breathing&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35557" PostTypeId="2" ParentId="35556" CreationDate="2015-06-26T20:17:18.827" Score="-2" Body="&lt;p&gt;This occurs because the feelings of needing more air to breath result from changes in the concentration of carbon dioxide in the bloodstream. This happens because the carbon dioxide gets dissolved in blood, turning into carbonic acid (H2CO3). This, since it is an acid, dissociates into ions, and your body can detect that change in acidity. These changed PH levels are not desirable because they reduce the efficiency of proteins and can cause negative effects. Therefore, the body detects these changes and creates the discomfort from the desire to breath out. This also holds true for too little carbon dioxide, because it will result in the reverse effect on the acidity in the blood stream (it will raise the PH/make it more basic). Passing out occurs when the acid levels are too high and nothing is making them return to normal (breathing out) so the brain says &quot;this idiot cannot breath correctly&quot; and shuts off the control center to do it itself (unconsciousness).&lt;/p&gt;&#xA;" OwnerUserId="16436" LastEditorUserId="16436" LastEditDate="2015-07-06T13:10:34.080" LastActivityDate="2015-07-06T13:10:34.080" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35558" PostTypeId="2" ParentId="35556" CreationDate="2015-06-26T21:04:50.363" Score="7" Body="&lt;p&gt;The exact causes of the discomfort relief  after the breath-hold breakpoint  is unknown yet.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It has been stated that breath &quot;pacemaker&quot; continue to work independently of voluntary breath holding. Thus, while breath holding, the breath center is trying to activate the diaphragm and the afferent feedback from the diaphragm normally causes the feeling of discomfort. Thus, upon starting breathing again, i.e. actual diaphragm movements, the discomfort will diminish and the subject will feel relief.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Breath-holding and its breakpoint. Experimental Physiology Volume 91, Issue 1, January 2006.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1113/expphysiol.2005.031625/full&quot;&gt;full text of cited article&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-06-26T21:04:50.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35559" PostTypeId="2" ParentId="35519" CreationDate="2015-06-26T22:10:09.200" Score="1" Body="&lt;p&gt;The article probably had a scrap of truth to it. Ageing is not plastic and longevity can be altered in a variety of ways. Although &lt;a href=&quot;http://www.sciencemag.org/content/285/5432/1390.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;caloric restriction&lt;/a&gt; seems to affect longevity the most, there are also &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11051192&quot; rel=&quot;nofollow noreferrer&quot;&gt;longevity genes&lt;/a&gt; from a range of cellular processes that have been identified in yeast and mice, indicating that ageing is a whole system process. But &lt;strong&gt;none of those genes are &quot;immortality genes&quot;&lt;/strong&gt;. Finding and testing their effects in humans is difficult. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a &lt;a href=&quot;https://www.youtube.com/watch?v=jc4yK0zZ-cQ&quot; rel=&quot;nofollow noreferrer&quot;&gt;video&lt;/a&gt; on the background on ageing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Related &lt;a href=&quot;https://biology.stackexchange.com/a/28033/3553&quot;&gt;answer&lt;/a&gt; that you might find interesting.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-06-28T20:18:07.300" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35560" PostTypeId="1" CreationDate="2015-06-26T22:27:10.027" Score="1" ViewCount="4377" Body="&lt;p&gt;I was hoping to get some clarification on how drug response data (i.e. IC50) are presented. On publicly available datasets like Genomics of Drug Sensitivity in Cancer, area under the curve (AUC) values are also presented alongside IC50 values. How are these AUC values for a particular drug/cell line calculated and are they correlated with the IC50 values?  If I want to compare the potency and efficacy of many drugs for a cell line (i.e. rank the drugs from highest potentcy/efficacy to lowest) should I use the AUC or IC50 values?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help would be greatly appreciated!&lt;/p&gt;&#xA;" OwnerUserId="16407" LastActivityDate="2015-06-26T22:43:09.173" Title="IC50 and area under the curve" Tags="&lt;pharmacology&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35561" PostTypeId="1" CreationDate="2015-06-26T22:34:42.513" Score="4" ViewCount="171" Body="&lt;p&gt;I am not biologist and just work in Bioinformatics field.&#xA;Does anyone know what is the meaning of conservation in the context of miRNAs and their pairings to mRNAs?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Each of these duplexes has a region called the “seed”, a site located at 5’ part of miRNA (positions 2-7) which is characterized by a strict or almost strict Watson-Crick pairing between miRNA and its target site and shows the best conservation among the miRNA sequence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3182075/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3182075/&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="16438" LastActivityDate="2015-06-26T22:34:42.513" Title="What is the meaning of conservation site in miRNA-mRNA pairing context?" Tags="&lt;mrna&gt;&lt;microrna&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35564" PostTypeId="1" CreationDate="2015-06-27T02:50:33.233" Score="2" ViewCount="137" Body="&lt;p&gt;Why do organisms have some traits that do not appear to have any evolutionary advantage?&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-06-27T02:50:33.233" Title="If a trait does not appear to be advantageous to organism, why does the organism have it?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-06-27T06:27:49.097" ContentLicense="CC BY-SA 3.0" />
  <row Id="35565" PostTypeId="2" ParentId="35564" CreationDate="2015-06-27T02:50:33.233" Score="1" Body="&lt;p&gt;There are many reasons why an organism might have a trait that does not appear to be beneficial.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The trait is actually advantageous even if it does not appear to be.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The trait is a byproduct of another trait, which is beneficial. Not all traits are the product of direct selection; traits that are byproducts of other traits are known as &quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/Spandrel_(biology)&quot; rel=&quot;nofollow&quot;&gt;spandrels&lt;/a&gt;&quot;, a trait coined by &lt;a href=&quot;http://faculty.washington.edu/lynnhank/GouldLewontin.pdf&quot; rel=&quot;nofollow&quot;&gt;Stephen J. Gould and Richard Lewontin&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The trait was fixed by some process other than natural selection, such as genetic drift. Genetic drift can fix traits that are neutral or even evolutionarily disadvantageous.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-06-27T02:50:33.233" CommentCount="1" CommunityOwnedDate="2015-06-27T02:50:33.233" ContentLicense="CC BY-SA 3.0" />
  <row Id="35568" PostTypeId="1" AcceptedAnswerId="35571" CreationDate="2015-06-27T07:41:56.587" Score="0" ViewCount="1487" Body="&lt;p&gt;So I want to choose the correct set of pair of primers to amplify the ORF of the gene that corresponds to amino acids in a protein. The start and stop codons are underlined. (I know that these need to be synthesised by the primer also for correct PCR technique)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RDdzg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The boxed sets of nucleotides are the primer options I have at hand. I know that the DNA synthesis can only carry out from 5' to 3' and there is a forward and reverse primer. The forward primer should be easy enough but non of the options seem acceptable? Could someone please explain to me how to go about this problem?&lt;/p&gt;&#xA;" OwnerUserId="10520" LastActivityDate="2015-06-27T10:39:03.947" Title="Which pair of primers should be used to amplify the ORF in PCR?" Tags="&lt;dna&gt;&lt;homework&gt;&lt;dna-sequencing&gt;&lt;pcr&gt;&lt;primer&gt;" AnswerCount="1" CommentCount="1" ClosedDate="2015-07-02T21:25:31.517" ContentLicense="CC BY-SA 3.0" />
  <row Id="35569" PostTypeId="1" AcceptedAnswerId="35574" CreationDate="2015-06-27T10:17:06.857" Score="22" ViewCount="29770" Body="&lt;p&gt;I know what the effects are of a dangerous situation on the brain, &lt;em&gt;i.e.&lt;/em&gt;, an activation of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Hypothalamic%E2%80%93pituitary%E2%80%93adrenal_axis&quot; rel=&quot;nofollow noreferrer&quot;&gt;hypothalamic-pituitary-adrenal (HPA) axis&lt;/a&gt; which eventually results in an increased heart rate and elevated blood pressure. However, I do not understand why enhanced blood circulation would result in a paling of the skin? Do red blood cells actively change direction? &lt;/p&gt;&#xA;" OwnerUserId="6124" LastEditorUserId="16866" LastEditDate="2017-04-16T11:42:12.200" LastActivityDate="2017-04-16T11:42:12.200" Title="Why does the face turn pale in dangerous situations?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;&lt;endocrinology&gt;&lt;blood-circulation&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35570" PostTypeId="2" ParentId="35569" CreationDate="2015-06-27T10:29:50.183" Score="4" Body="&lt;p&gt;It has nothing to do with blood cells &lt;em&gt;per se&lt;/em&gt;. Blood vessels constrict in areas not necessary for flight-and-fight response (sympathetic nervous system response).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By constricting blood vessels around face, blood is redirected to organs more important in resolving dangerous situations: muscles of legs, spinal cord, and brain. Same way pupils get dilated to capture more light..&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-06-27T10:29:50.183" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35571" PostTypeId="2" ParentId="35568" CreationDate="2015-06-27T10:39:03.947" Score="2" Body="&lt;p&gt;First of all, if this is a homework question, add that tag to it. And show what work you have done so far.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, primers for amplifications should lie on opposite strands. Primers are typed in 5'-to-3' direction (aka left-to-right on leading strand).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Appropriate primers will be: primer 4=GTG... and primer 5=GAA.... Note how those primers are always in 5'-3' orientation. That is how you order those.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Again, if this is homework (looks like it) it is very bad taste to just ask question without any work shown. It displays laziness and usually not respected behavior when asking for help.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-06-27T10:39:03.947" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35572" PostTypeId="2" ParentId="35515" CreationDate="2015-06-27T10:47:38.883" Score="3" Body="&lt;p&gt;After thinking about it for a while I have arrived to a slightly but important different view on this problem. I will try to explain the statistics behind it to the best of my knowledge. I will use the eyes’ color probabilities in @Remi.b’s response, but of course those may not be accurate and the results can change accordingly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The problem is to determine how likely is to have 3 children with blue eyes, 1 with green eyes and 1 with brown eyes when the parents both have brown eyes. I will assume each child is independently born (e.g. there are not identical twins). We can use the analogy of a bag with balls from which we draw 5 balls independently.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Imagine you have several bags with $n=100$ balls each. The balls can be brown (M), blue (B) and green (G). Depending on the bag, you will have different proportion of balls. For example, in the bag labelled MM (for brown:brown), there are 75 M balls, 19 G balls and 6 B balls (rounding the probabilities in @Remi.b's answer). The bag labelled GB does not have any M balls (0), and has 50 G and 50 B balls. And so on. This gives us for each bag the probabilities defined in @Remi.b’s response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although there are many bags in our particular case we only care about the MM bag, so we should only consider those probabilities. Imagine now you pick five balls at random from this (the MM) bag. What is the probability that you will get $m=1$, $g=3$ and $b=1$ (with &lt;em&gt;m&lt;/em&gt;, &lt;em&gt;g&lt;/em&gt; and &lt;em&gt;b&lt;/em&gt; representing the number of M, G and B balls respectively)? Because there are three types of balls (or categories) this is described by the &lt;a href=&quot;https://en.wikipedia.org/wiki/Multinomial_distribution&quot; rel=&quot;nofollow&quot;&gt;multinomial distribution&lt;/a&gt; (and not the &lt;a href=&quot;https://en.wikipedia.org/wiki/Binomial_distribution&quot; rel=&quot;nofollow&quot;&gt;binomial&lt;/a&gt;, which describes events involving two categories, like the flip of a coin). The &lt;a href=&quot;https://en.wikipedia.org/wiki/Multinomial_distribution#Probability_mass_function&quot; rel=&quot;nofollow&quot;&gt;multinomial probability mass function&lt;/a&gt; is defined in this problem as:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$ Pr(M=m,G=g,B=b) = \frac{n!}{m!g!b!} p_M^{m} p_G^{g} p_B^b&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Where $P_i$ are the probabilities described above, n is the total number of childs, and m, g, and b are the number of childs with M, G and B eye color respectively. Therefore, for our family we have the following computation:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$&#xA;Pr(M=1,G=1,B=3) = \frac{5!}{1!1!3!}(0.75)^1(0.1875)^1(0.0625)^3 = 0.000686643&#xA;$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The probability (~0.07%) looks very low, but it is basically about 7 out of 10,000 families with parents having both brown eyes and 5 children. Given the large human population it is difficult but not impossible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally, I knew a family where the parents had both brown eyes and the two children had blue eyes. Always wondered about it but this is the first time I actually tried to think about the probabilities! In this case the probability would be 0.00390625 (~0.4%).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW, you can easily compute the same in &lt;a href=&quot;http://www.r-project.org&quot; rel=&quot;nofollow&quot;&gt;R&lt;/a&gt; with the following code:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt; dmultinom(c(1,1,3), 5, c(.75, .1875, .0625))&#xA;[1] 0.0006866455&#xA;&amp;gt; dmultinom(c(0,0,2), 2, c(.75, .1875, .0625))&#xA;[1] 0.00390625&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="9099" LastActivityDate="2015-06-27T10:47:38.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35573" PostTypeId="1" AcceptedAnswerId="35575" CreationDate="2015-06-27T11:01:25.887" Score="2" ViewCount="81" Body="&lt;p&gt;I'm looking for all possible sources of clinically tested human SNPs. There is a handful of databases that store SNPs (like dbSNP), but I only need those that have validated presence/absence of phenotypic effects with some additional metadata. Thank you in advance. &lt;/p&gt;&#xA;" OwnerUserId="13338" LastEditorUserId="3340" LastEditDate="2015-06-27T12:28:13.587" LastActivityDate="2015-08-12T18:07:32.237" Title="Database of medically validated SNPs" Tags="&lt;human-biology&gt;&lt;genomics&gt;&lt;database&gt;&lt;snp&gt;" AnswerCount="2" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="35574" PostTypeId="2" ParentId="35569" CreationDate="2015-06-27T11:12:54.167" Score="25" Body="&lt;p&gt;Red blood cells are not equipped with a motor system to propel them through the blood stream. Instead, they are passively transported through the vasculature by the the pumping action of the heart. The effects of dangerous situations on the skin have to do with hormonal effects on the blood vasculature, and not with direct effects on red blood cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dangerous situations trigger the fight-fright-flight response, and is a direct result of adrenaline being released into the bloodstream. Adrenaline prepares the body to fight for its life. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adrenaline has a variety of effects including enhancing &lt;strong&gt;perspiration&lt;/strong&gt; (or &lt;em&gt;diaphoresis&lt;/em&gt;, which prepares the body for the increase in temperature associated with fleeing/fighting), &lt;strong&gt;dilation of the pupils&lt;/strong&gt; (which increases light sensitivity, but reduces acuity), &lt;strong&gt;dry mouth&lt;/strong&gt; (gastric juices and saliva production decreases because blood flow to the digestive system is decreased), &lt;strong&gt;enhanced smell&lt;/strong&gt; and &lt;strong&gt;hearing&lt;/strong&gt;, and a &lt;strong&gt;cool, pale skin&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cool and pale skin is caused by a reduced blood flow to the surface of the body, while blood flow to the arms, legs, shoulders, brain, eyes, ears and nose can be increased. Besides getting ready to run and fight, the body is preparing to think quickly and be aware of threats by hearing, seeing and smelling things better. Pulling blood away from the skin also helps decrease bleeding from cuts and scrapes (Source: &lt;a href=&quot;http://www.youngdiggers.com.au/fight-or-flight&quot; rel=&quot;nofollow noreferrer&quot;&gt;Army, Navy &amp;amp; Air Force Australia&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Adrenaline stimulates alpha-adrenoreceptors in blood vessels, which causes the smooth muscles around the vessels to constrict &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6100732&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Bolli &lt;em&gt;et al&lt;/em&gt;., 1984)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xWr1W.jpg&quot; alt=&quot;adrenaline&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Adrenaline (epinephrine) released from the bloodstream dilates vessels in the skeletal muscle via beta-receptors, and constricts them in the digestive system and the skin through alpha-adrenergic receptors. Source: &lt;a href=&quot;http://www.cvpharmacology.com/vasoconstrictor/alpha-agonist&quot; rel=&quot;nofollow noreferrer&quot;&gt;Marian University College, Indiana&lt;/a&gt;.&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/6100732&quot; rel=&quot;nofollow noreferrer&quot;&gt;Bolli &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;J Hypertens&lt;/em&gt; (1984); &lt;strong&gt;2&lt;/strong&gt;(3): S115-8&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2016-01-27T09:57:35.503" LastActivityDate="2016-01-27T09:57:35.503" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35575" PostTypeId="2" ParentId="35573" CreationDate="2015-06-27T12:27:17.937" Score="2" Body="&lt;p&gt;You can search by traits (mostly diseases) for genome wide association, in these databases:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://jjwanglab.org/gwasdb&quot; rel=&quot;nofollow&quot;&gt;Gwasdb2&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://gwas.biosciencedbc.jp/&quot; rel=&quot;nofollow&quot;&gt;Human genome variation Database&lt;/a&gt;: it also links to a Copy number Variation (CNV) database. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-06-27T12:27:17.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35576" PostTypeId="1" CreationDate="2015-06-27T14:41:00.387" Score="1" ViewCount="4740" Body="&lt;p&gt;Can both heterotrophic and autotrophic organism survive in anaerobic conditions? If an autotrophic organism does not produce carbon dioxide but requires oxygen, it should not be present in anaerobic conditions, instead the heterotrophic organism can develop. Is this correct?&lt;/p&gt;&#xA;" OwnerUserId="16447" LastEditorUserId="1590" LastEditDate="2015-06-30T07:40:36.643" LastActivityDate="2018-02-19T08:58:40.597" Title="Autotrophic and heterotrophic organisms in anaerobic condition" Tags="&lt;microbiology&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35577" PostTypeId="2" ParentId="35478" CreationDate="2015-06-27T16:08:44.997" Score="3" Body="&lt;p&gt;So the general sequencing analysis pipeline is to generate a bunch of read sequences, figure out how they match to a reference genome and align them, then call any differences between the reference genome and the sequencing reads. The following image, from the Broad Institute's Interactive Genome Viewer, may help you visualize what is happening here. As you can see in the image, the human reference DNA is found at the top of the window, and the sequence of bases for the current selection, at the very bottom of the window. Then each of the gray bars that you see below that is an individual sequencing read that matches to that particular location along the human DNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/WD8EJ.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/WD8EJ.png&quot; alt=&quot;Interactive Genome Viewer from the Broad Institute&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you use a variant caller like &lt;a href=&quot;https://github.com/ekg/freebayes&quot; rel=&quot;nofollow noreferrer&quot;&gt;Freebayes&lt;/a&gt;, it will list out information about locations along the reference genome that had differences in your actual sequences. For instance, as you bring up, DP or read depth. Looking back at the IGV image, you can see a location that had a lot of 'G' showing in the sequence reads, where the reference DNA has 'A'. Variant callers will pick up on this and list it as a possible variant. They will also tell you the read depth at that location which is the total number of sequence reads overlapping that position. In this case there are 21 gray bars (sequence reads) overlapping at that position, meaning that DP=21.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even though it is not listed in the VCF example to which you refer, variant callers can also give other data like AO, which is times that a variant was observed, and RO which is the number of times the reference base was observed. This information allows you to decide whether or not an identified variant was a sequencing error, or a real variant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance if DP=1, AO=1, RO=0, that means there was only a single read at that location and it was not what is listed in the reference genome. Because the depth is so low, and the error rate of a next-gen sequencer is somewhere between 0.5-5%, you cannot say that this is a mutation or just a sequencing error. However, as DP increases, you gain more confidence in whatever was called. So if DP=10, AO=10, RO=0 you can be quite confident that the reason you read an alternate base at a given location, it is not just a sequencing error because you read this location 10 times and every time you saw the same variant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me know if I can clarify further.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastEditorUserId="38942" LastEditDate="2017-12-16T17:49:02.910" LastActivityDate="2017-12-16T17:49:02.910" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35578" PostTypeId="2" ParentId="35576" CreationDate="2015-06-27T16:42:27.137" Score="1" Body="&lt;p&gt;It is not necessary that all heterotrophs are aerobic. Many are anaerobes (yeast etc.)&#xA;&lt;a href=&quot;http://www.sparknotes.com/testprep/books/sat2/biology/chapter8section1.rhtml&quot; rel=&quot;nofollow&quot;&gt;Anaerobic Heterotrophs&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These anaerobes live on glycolysis and fermentation (as far as I know). These two processes don't require Oxygen for release of energy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bio.miami.edu/~cmallery/255/255atp/glycolysis_pathway.jpg&quot; rel=&quot;nofollow&quot;&gt;Glycolysis&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://classconnection.s3.amazonaws.com/583/flashcards/751135/jpg/alcohol-fermentation.jpg&quot; rel=&quot;nofollow&quot;&gt;Alcohol Fermentation&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://classconnection.s3.amazonaws.com/583/flashcards/751135/jpg/lactic-acid-fermentation.jpg&quot; rel=&quot;nofollow&quot;&gt;Lactic Acid Fermentation&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Alcohol Fermentation takes place in yeast (just an example) and Lactic Acid Fermentation in Muscle Cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The autotrophs will take care of themselves as photosynthesis require no Oxygen. If place in correct conditions (light and water are available), then they will thrive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the answer to your question would be that both can survive. It varies from species to species. If you select the correct one then, both would survive or only one of them.&lt;/p&gt;&#xA;" OwnerUserId="4503" LastEditorUserId="4503" LastEditDate="2015-06-29T16:07:13.847" LastActivityDate="2015-06-29T16:07:13.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35579" PostTypeId="1" AcceptedAnswerId="35580" CreationDate="2015-06-27T17:04:44.397" Score="4" ViewCount="489" Body="&lt;p&gt;What species is this? It was found in Turkey. It was dead, I did not kill it.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YTRKs.jpg&quot; alt=&quot;image1&quot; /&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/9lpjC.jpg&quot; alt=&quot;image2&quot; /&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/SnmYz.jpg&quot; alt=&quot;image3&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="15398" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2019-02-15T16:21:18.670" Title="What is this small black bug found in Turkey?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="35580" PostTypeId="2" ParentId="35579" CreationDate="2015-06-27T17:52:03.100" Score="5" Body="&lt;p&gt;Looks like a scarab beetle (Coleoptera, Scarabaeidae). Species is difficult to tell without better pictures, but perhaps &lt;em&gt;Scarabaeus typhon&lt;/em&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit&lt;/strong&gt;: OP has IDed in comment as &lt;em&gt;Scarabaeus jalof&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2015-06-28T15:56:19.877" LastActivityDate="2015-06-28T15:56:19.877" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35581" PostTypeId="2" ParentId="35569" CreationDate="2015-06-27T20:44:26.007" Score="1" Body="&lt;p&gt;Totally agree with the answers already provided: It is directly caused by constriction of blood vessels in the face.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, from a behavioral perspective, I feel there is an additional function for 'turning pale', that is not yet mentioned:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For social animals (such as humans), the face has great expressive value.&#xA;The face turning pale might fulfill the function of warning our fellow species that there is a certain threat. This form of communication might be preferable over, for example, yelling. Yelling might attract to much unwanted attention from predators (if predator was reason why individual is afraid). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is true, then we should expect turning pale of the face would more often occur in groups than alone and would also happen more often to the 'weaker' individuals of the group, because stronger individuals that seek help from their weaker friends would not be so advantageous.&lt;/p&gt;&#xA;" OwnerUserId="16451" LastActivityDate="2015-06-27T20:44:26.007" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35582" PostTypeId="2" ParentId="35446" CreationDate="2015-06-27T21:03:22.540" Score="2" Body="&lt;p&gt;Probably, it is worth to add some historic (and ironic) &quot;perspective&quot; to this question. It will probably explain that even without scientific research the answer to this question is probably &quot;no&quot; and that real use of bacterial soap should probably be reduced to hospital settings and not expanded to households as suggest promotions and commercials.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The historic perspective I wanted to add relates to the book &quot;The Hermit in the Garden&quot; by Gordon Campbell. Here live hermits are described (there were non-alive as well, this is why I call these &quot;live&quot;). Campbell cites another book -  &quot;Sir William Gell's A Tour in the Lakes Made in 1797&quot;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;the hermit is never to leave the place, or hold conversation with anyone for &lt;strong&gt;seven years&lt;/strong&gt; during which he is &lt;strong&gt;neither to wash himself or cleanse himself in any way whatever&lt;/strong&gt;, but is to let his hair and nails both on hands and feet, grow as long as nature will permit them.&quot; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this &quot;work&quot; description we can &lt;em&gt;speculate&lt;/em&gt; that &quot;dangerous&quot; infections were not expected during such a long period of soapless live. This is why we could assume that any soap is probably of limited &quot;antibacterial&quot; value for otherwise healthy person. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Remark: This &quot;exclamation&quot; not trying to answer the question in a scientific way, but just to add some &quot;color&quot; to the question and the answers posted. I hope, it is worth to place it here instead of a comment). &lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-06-27T21:03:22.540" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35583" PostTypeId="1" CreationDate="2015-06-27T21:45:28.753" Score="6" ViewCount="12698" Body="&lt;p&gt;Are humans more attracted to people from their own ethnic groups? I ask this because most of the time people have relationships with people of their own ethnicity, and I wonder if it's purely social, or if there's more behind it.&lt;/p&gt;&#xA;" OwnerUserId="16452" LastEditorUserId="10456" LastEditDate="2015-06-28T18:03:18.163" LastActivityDate="2015-06-29T10:33:07.623" Title="Are we more attracted to people of the same ethnicity?" Tags="&lt;evolution&gt;&lt;ethology&gt;&lt;sexual-selection&gt;&lt;behaviour&gt;" AnswerCount="2" CommentCount="16" FavoriteCount="3" ClosedDate="2015-07-01T08:39:52.163" ContentLicense="CC BY-SA 3.0" />
  <row Id="35584" PostTypeId="2" ParentId="35583" CreationDate="2015-06-27T22:24:09.363" Score="5" Body="&lt;p&gt;The answer in extreme brief is &lt;a href=&quot;http://web.stanford.edu/~neilm/Political%20Ideology%20and%20Racial%20Preferences%20in%20Online%20Dating.pdf&quot; rel=&quot;nofollow&quot;&gt;yes&lt;/a&gt;.  Only about 9% of whites and 16% of blacks engage in interracial marriage in the U.S.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But really this deserves a fuller discussion.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The predominant pattern of mate selection in human beings is to &lt;a href=&quot;http://web.stanford.edu/~neilm/Political%20Ideology%20and%20Racial%20Preferences%20in%20Online%20Dating.pdf&quot; rel=&quot;nofollow&quot;&gt;marry within their ethnic group&lt;/a&gt;.  I say 'ethnic group' rather than 'race' because 'race' has no strong scientific definition. Racial groups as usually understood have about the same &lt;a href=&quot;http://www.nature.com/ng/journal/v36/n11s/full/ng1435.html&quot; rel=&quot;nofollow&quot;&gt;genetic variance as the overall species&lt;/a&gt;.  I need to point out here that races can have a strong geographical point of origin and thus races can in some cases be genetically identified, but these correlate poorly often with, say health risks or other clinical data. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because its clear that interracial marriages are on the rise in the US, mating choices are often argued to be socially defined preferences.  Social attitudes affect men and women differently and different cultures too, as tracked by regional differences. Not the least is a limit of opportunities.  Being comfortable with people from other cultures or who simply look different. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, Women at least in American studies are much more likely to &lt;a href=&quot;http://web.stanford.edu/~neilm/Political%20Ideology%20and%20Racial%20Preferences%20in%20Online%20Dating.pdf&quot; rel=&quot;nofollow&quot;&gt;state a same-race preference&lt;/a&gt; (see p17), while men are likely to demur from stating a preference, but act out a bias unconsciously, making both genders equally biased. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As mentioned in the comments by @AliceD, Mating preferences as described in traditional population biology are adapted from availability.  That's to say people don't meet because of ethnic boundaries such as geography, socioeconomic or social strata. Then there are socialized preferences.  I.e. growing up we are imprinted by the sorts of people we see, which can create preferences later in life.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly there may be genetically conveyed preferences. The human race has been spreading out over the past 200,000 years or so.  That's a pretty small amount of time.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are cases where such mating preferences have evolved.  There are 17 species of arctic penguins, species caused by migration around the globe.  Each species can actually mate with others nearby, but where the penguins met at the far end of the globe, the species do not mate because they have been separated for so long they have diverged.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But speciation events can take millions of years.  Its clear that human beings from the far corners of the globe can produce offspring - we are one species.  It seems as if we are only a fraction of the way towards two neighboring penguin species in the example above.  There doesn't seem to be any evidence that we are genetically predisposed to ethinic self mating.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Only by way of example (not to offend anyone!) you can choose an ethnic group which has divergent behavior and try to get an estimate of how big a role the social context plays.  Looking at the jewish community we see that &lt;a href=&quot;http://www.interfaithfamily.com/news_and_opinion/synagogues_and_the_jewish_community/Jewish_Intermarriage_Statistics.shtml&quot; rel=&quot;nofollow&quot;&gt;47% of jewish people have married out of group&lt;/a&gt; in recent statistics.  They are thinly distributed over a wide geographical region and availability is high for out-group marriage.  All this while orthodox jews have a &lt;a href=&quot;http://www.pewresearch.org/fact-tank/2013/10/17/eight-facts-about-orthodox-jews-from-the-pew-research-survey/&quot; rel=&quot;nofollow&quot;&gt;practically non-existent out-group marriage rate&lt;/a&gt;. Not judging here, but only for illustrative purposes we can guess that social attitudes and behaviors are playing a large role here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As and endnote, I'd also like to point out that since whites are about 50% of the US population and african americans are about 10%, the percentages not so disparate as they seem - all things being equal the average person one meets in the US is white.  For caucasians, approximately 50% of the population the average interracial marriage rate with no racial biases is is 50%.  For blacks its 90%.  Again, just using random shuffling for statistical point of view. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastEditorUserId="3632" LastEditDate="2015-06-28T17:22:05.010" LastActivityDate="2015-06-28T17:22:05.010" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="35585" PostTypeId="2" ParentId="13580" CreationDate="2015-06-27T23:14:11.350" Score="1" Body="&lt;p&gt;It's possible that they do, depending on the intensity of the dream and the amount of brain activity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, if the dreamer is thinking too much or is having a dream that's way too intense, the brain activity goes up and they're not as rested.  However, lucid dreaming can be good for sleep if the dreamer creates a more relaxed dream.  This can possibly be better for the sleeper, especially if they're someone who experiences nightmares every night.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, it just depends on what you're dreaming about.  The calmer and more relaxing the dream is, the better.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&#xA;-www.world-of-lucid-dreaming.com&lt;/p&gt;&#xA;" OwnerUserId="16454" LastEditorUserId="16454" LastEditDate="2015-06-27T23:50:44.350" LastActivityDate="2015-06-27T23:50:44.350" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35586" PostTypeId="2" ParentId="14897" CreationDate="2015-06-27T23:33:03.930" Score="3" Body="&lt;p&gt;It's commonly believed that it's muscle cells that have the largest amount of mitochondria, and for good reason.  Muscle cells are continually used to move the body, so they have the most mitochondria because of the large energy requirement.  If you want to be more specific, the muscle cells of a marathon runner have even more since the muscle cells involved in running need to be able to do a lot of aerobic respiration.  Another example is the cells in the heart; the amount of mitochondria makes up 40% of the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The truth is, retinal cells with photoreceptors most likely have the most (80% of the cell volume) since they need to reset the potassium/sodium pump to keep the action potential in the nerves the same.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're curious, the cells with the least amount of mitochondria are skin cells and erythrocytes (red blood cells) since skin is just a protective barrier and red blood cells don't need to exert any effort or energy to move.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://hyperphysics.phy-astr.gsu.edu/hbase/biology/mitochondria.html&quot; rel=&quot;nofollow&quot;&gt;http://hyperphysics.phy-astr.gsu.edu/hbase/biology/mitochondria.html&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12511073&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/12511073&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="16454" LastEditorUserId="16454" LastEditDate="2015-06-28T15:21:33.037" LastActivityDate="2015-06-28T15:21:33.037" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35589" PostTypeId="1" AcceptedAnswerId="35602" CreationDate="2015-06-28T07:32:08.530" Score="6" ViewCount="118" Body="&lt;p&gt;I saw a &lt;a href=&quot;https://biology.stackexchange.com/questions/35532/if-a-trait-would-be-advantageous-to-an-organism-why-hasnt-it-evolved#comment57988_35533&quot;&gt;comment on an answer to another question&lt;/a&gt; that touched on an interesting topic:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;keeping diversity is useful for parameter exploration or to adapt to future environmental change&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;My initial thought was that evolution doesn't &quot;know&quot; about the future, so natural selection might decrease genetic diversity even if it meant dooming the species in the long term.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, species that have low genetic diversity may be more likely to go extinct eventually.  So perhaps over time the surviving taxa are those that have evolved mechanims to &quot;hedge their bets&quot; against future environmental changes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's clear that some of the parameters that affect genetic diversity within a species (e.g. mate selection, mutation rate) are heritable, but it's unclear to me how the short-term processes of natural selection relate to the extremely long-term processes of speciation and extinction.  This gets into some of the same issues as group selection — how can natural selection, acting on individuals, lead to traits that benefit entire populations or clades?  (Perhaps this simply cannot happen.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Has any work been done on the topic of extinction resistance or the evolution of mechanisms to create and preserve diversity within populations or taxa?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a big question so I don't expect a full answer here.  I'm just looking for some references as a starting point to learn more about this topic.&lt;/p&gt;&#xA;" OwnerUserId="11657" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-06-28T16:38:40.427" Title="Evolution of diversity and extinction resistance" Tags="&lt;population-genetics&gt;&lt;literature&gt;&lt;extinction&gt;&lt;macroevolution&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35590" PostTypeId="2" ParentId="35576" CreationDate="2015-06-28T09:04:05.310" Score="1" Body="&lt;p&gt;Autotrophs: Organisms that can synthesize organic carbon from inorganic carbon (carbon fixation). Nitrogen fixation is not considered an essential condition to qualify as autotrophs. &lt;em&gt;True&lt;/em&gt; autotrophs can fix both carbon and nitrogen (Some algae. This &lt;em&gt;true&lt;/em&gt; autotrophs is not an actual terminology).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Aerobes are organism that require oxygen for metabolism; it is not really dependent on whether the organism is autotrophic or heterotrophic. Anaerobes do not use oxygen for metabolism. Some anaerobes are aerotolerant i.e. they can tolerate oxygen (oxygen is highly reactive and can damage tissues) while others are not. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;You can have a look at &lt;a href=&quot;https://biology.stackexchange.com/a/31775/3340&quot;&gt;this&lt;/a&gt; post for some basics on aerobic and anaerobic respiration.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Examples of anaerobic autotroph include &lt;em&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0003986166810470&quot; rel=&quot;nofollow noreferrer&quot;&gt;Ferrobacillus sulfooxidans&lt;/a&gt;&lt;/em&gt; and &lt;a href=&quot;http://jb.asm.org/content/109/2/707.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Methanobacterium thermoautotrophicus&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some organisms are called &lt;a href=&quot;https://en.wikipedia.org/wiki/Microaerophile&quot; rel=&quot;nofollow noreferrer&quot;&gt;microaerophilic&lt;/a&gt; i.e. they need oxygen but not in high concentrations. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-06-28T09:21:25.133" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35593" PostTypeId="1" AcceptedAnswerId="35612" CreationDate="2015-06-28T10:37:55.627" Score="6" ViewCount="1265" Body="&lt;p&gt;Suppose the two parents of a child have blood groups A+ve and O+ve, and the child has O-ve type. For blood group, there are two alleles. Since the child has O, the father must have one 'A' allele and one 'O' allele.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does such a reasoning hold for the Rhesus factor too? Should I interpret that both the parents have one + allele and one - allele?&lt;/p&gt;&#xA;" OwnerUserId="629" LastEditorUserId="9943" LastEditDate="2015-06-28T13:04:15.213" LastActivityDate="2015-06-29T14:58:52.163" Title="Parents are Rh +ve and child Rh -ve" Tags="&lt;hematology&gt;&lt;blood-group&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35594" PostTypeId="1" AcceptedAnswerId="36020" CreationDate="2015-06-28T11:40:36.010" Score="12" ViewCount="213" Body="&lt;p&gt;Some lizards are famous for their ability to voluntarily shed their tail to elude predators (&lt;a href=&quot;https://en.wikipedia.org/wiki/Autotomy&quot; rel=&quot;noreferrer&quot;&gt;Autotomy&lt;/a&gt;). After a while, the tail will be regenerated, though with slightly different qualities, as visible in this photograph:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6AegH.jpg&quot; alt=&quot;&quot;&gt;&#xA;(&lt;a href=&quot;https://commons.wikimedia.org/wiki/File:White-headed_dwarf_gecko.jpg&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question: Can this regrown tail be discarded again voluntarily, or is it a one-time feat?&lt;/p&gt;&#xA;" OwnerDisplayName="user6890" LastEditorUserId="5144" LastEditDate="2015-06-28T11:45:37.987" LastActivityDate="2015-07-13T07:52:34.543" Title="Can a lizard shed a regrown tail again?" Tags="&lt;zoology&gt;&lt;reptile&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35597" PostTypeId="1" AcceptedAnswerId="35606" CreationDate="2015-06-28T15:52:53.437" Score="3" ViewCount="1015" Body="&lt;p&gt;I found a tiny, white animal in my mouth on the morning of June 28, 2015, in Toronto, Ontario. Luckily I don't seem to have hurt it. I was eating some sunflower and pumpkin seeds at the time. I believe that's how it got there. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pictures include a toothpick and a Canadian cent to give an idea of its size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also took a video of it crawling around. I will post it if the pictures are not sufficient for identification. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/wx3Xl.jpg&quot; alt=&quot;Unidentified animal.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vckhq.jpg&quot; alt=&quot;Unidentified animal.&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9855" LastEditorUserId="5755" LastEditDate="2015-06-28T19:13:23.013" LastActivityDate="2015-06-28T19:13:23.013" Title="Animal identification (larva)" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35598" PostTypeId="1" AcceptedAnswerId="35599" CreationDate="2015-06-28T16:04:21.000" Score="7" ViewCount="573" Body="&lt;p&gt;I found it in Toronto, Ontario, during early June, 2015.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When prodded it seemed to jump around, or at least to move very fast.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can also post a short video of it if needed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kkQgM.jpg&quot; alt=&quot;Unidentified spider.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lIynB.jpg&quot; alt=&quot;Unidentified spider.&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XpRdX.jpg&quot; alt=&quot;Unidentified spider.&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9855" LastEditorUserId="5755" LastEditDate="2015-06-28T18:32:13.540" LastActivityDate="2015-06-28T18:32:13.540" Title="Toronto spider identification" Tags="&lt;zoology&gt;&lt;species-identification&gt;&lt;arachnology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35599" PostTypeId="2" ParentId="35598" CreationDate="2015-06-28T16:15:34.970" Score="10" Body="&lt;p&gt;That jumping spider is a Jumping Spider! (That is, family Salticidae, commonly called Jumping Spiders).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's a lot of diversity in the family, but your pictures look similar to the &lt;a href=&quot;http://bugguide.net/node/view/14618&quot;&gt;Zebra Jumping Spider&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2015-06-28T16:59:27.857" LastActivityDate="2015-06-28T16:59:27.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35600" PostTypeId="1" CreationDate="2015-06-28T16:21:21.203" Score="4" ViewCount="40" Body="&lt;p&gt;Given a plant $P$, predict its height $H$ at time $t$ since planting given some environmental variables $E_1, \dots, E_n$. How accurate are the state-of-the-art models for such thing? What data is used to make the prediction?&lt;/p&gt;&#xA;" OwnerUserId="16465" LastActivityDate="2015-06-28T23:53:57.870" Title="Accuracy of best plant growth models?" Tags="&lt;plant-physiology&gt;&lt;theoretical-biology&gt;&lt;plant-anatomy&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35601" PostTypeId="1" AcceptedAnswerId="35615" CreationDate="2015-06-28T16:23:39.227" Score="2" ViewCount="557" Body="&lt;h1&gt;DNA solubility data in only water is scarce.&lt;/h1&gt;&#xA;&lt;p&gt;A &lt;a href=&quot;https://biology.stackexchange.com/questions/34349/solubility-of-dna-in-water/34354#34354&quot;&gt;previous question&lt;/a&gt; asked for a quantification of DNA solubility in water. It seemed like it would be easily answerable, however isn't quite that simple since no data seems to exist for DNA solubility in &lt;strong&gt;exclusively water&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;p&gt;Even the small amount of data about water was in the context of washing away organic compounds from the solution. This got me thinking. DNA is in an aqueous solution in biological situations, and is usually handled in aqueous solutions in labs. So why is solubility data so scarce for &lt;em&gt;pure&lt;/em&gt; water? What is important about organic compounds for DNA solutions?&lt;/p&gt;&#xA;&lt;h1&gt;Why are other additives important for laboratory DNA solutions?&lt;/h1&gt;&#xA;&lt;p&gt;So my question is &lt;em&gt;&lt;strong&gt;why&lt;/strong&gt;&lt;/em&gt; is DNA dissolved in &lt;strong&gt;exclusively water&lt;/strong&gt; seemingly &amp;quot;uncommon&amp;quot; in laboratories? Is there something about pure water that is bad for DNA storage? Is it that functionally DNA never needs to be in water because it is inaccessible to proteins? Or have I misinterpreted the lack of solubility data; water is common-place and no data exists because there is no need?&lt;/p&gt;&#xA;&lt;p&gt;I imagine PCR is where most of the data on DNA solutions exists. What about the polar organic solvents/compounds makes them important for DNA solutions?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-29T13:28:25.290" Title="Why do many DNA solutions contain additional compounds?" Tags="&lt;biochemistry&gt;&lt;dna&gt;&lt;lab-techniques&gt;&lt;dna-sequencing&gt;&lt;lab-reagents&gt;" AnswerCount="2" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="35602" PostTypeId="2" ParentId="35589" CreationDate="2015-06-28T16:38:40.427" Score="6" Body="&lt;p&gt;The topic you describe is very interesting and known as &quot;species selection.&quot; Some traits exist that not only affect the reproductive success of individuals, but also affect the diversification rate of the entire species, either through affecting the extinction rate, the speciation rate, or both. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To give you an example, I'll summarize this paper by &lt;a href=&quot;http://www.uic.edu/labs/igic/papers/Goldberg_et_al_2010.pdf&quot;&gt;Goldberg et al 2010&lt;/a&gt;. Self-incompatibility (SI) in plants is the ability of a plant to reject its own pollen to prevent inbreeding. This mechanism is expected to increase the genetic diversity of the plant's offspring. Self-incompatibility has been lost many times in the history of flowering plants, yielding self-compatibility (SC), which allows a plant to breed with itself. A plant that can breed with itself has an advantage in that even if the population size is low and it can't 'find' another individual to breed with, it can still breed with itself to produce offspring. However, this trait is expected to result in decreased genetic diversity in the offspring due to inbreeding.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The transition from SI to SC is a common transition that cannot easily be reversed. One might expect, then, that SI would be very uncommon as lineages would lose it to SC. However, it turns out that SC lineages have a lower diversification rate than SI plants in the Solanaceae due to the fact that SC lineages have a higher extinction rate than speciation rate. This difference in diversification allows SI to persist. This is an example of trait-dependent net diversification rate. It is not known exactly why SI lineages have a higher net diversification rate, but it could be related to the higher effective population size which results in &quot;increased polymorphism,&#xA;lower linkage disequilibrium, more&#xA;efficient response to purifying selection, more&#xA;extensive geographic distribution of genetic diversity,&#xA;and lower rates of extinction&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you want to read more, I can suggest a few more papers:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jstor.org/stable/2096764&quot;&gt;The Units of Selection&lt;/a&gt; by R.C. Lewontin&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencemag.org/content/216/4544/380.short&quot;&gt;Darwainism and the Expansion of Evolutionary Theory&lt;/a&gt; by S.J. Gould&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jstor.org/stable/30245174&quot;&gt;Species Selection: Theory and Data&lt;/a&gt; by D. Jablonski&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-06-28T16:38:40.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35603" PostTypeId="1" CreationDate="2015-06-28T17:20:23.443" Score="2" ViewCount="51" Body="&lt;p&gt;The G zipper motif is found in transmembrane proteins at an above &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/10677292&quot; rel=&quot;nofollow&quot;&gt;random frequency&lt;/a&gt; and there are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1242278/&quot; rel=&quot;nofollow&quot;&gt;models explaining how it might help with multiple transmembrane intra-membrane helix bundle assembly&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However there are a bunch of different &quot;flavours&quot; of these G zipper motifs. Here are the ones I have come across so far:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;GXXXG &lt;/li&gt;&#xA;&lt;li&gt;GVXXGV&lt;/li&gt;&#xA;&lt;li&gt;GXXXGXXXG&lt;/li&gt;&#xA;&lt;li&gt;AXXXGXXXG&lt;/li&gt;&#xA;&lt;li&gt;SXXXGXXXG&lt;/li&gt;&#xA;&lt;li&gt;GXXXGXXXS&lt;/li&gt;&#xA;&lt;li&gt;GXXXGXXXT&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I don't think I am completely up to date so that is a non-exhaustive list. Have I missed any? Broadly speaking what accounts for their variation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;note: &lt;a href=&quot;https://en.wikipedia.org/wiki/FASTA_format#Sequence_representation&quot; rel=&quot;nofollow&quot;&gt;X refers to a non specific amino acid in FASTA protein sequences.&lt;/a&gt;&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2015-06-28T18:49:39.087" LastActivityDate="2015-06-28T18:49:39.087" Title="What are all of the currently known variations of the G zipper motif?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;cell-membrane&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35604" PostTypeId="1" AcceptedAnswerId="35611" CreationDate="2015-06-28T17:31:08.243" Score="4" ViewCount="1604" Body="&lt;p&gt;Is protein &lt;strong&gt;dephosphorylation&lt;/strong&gt; most commonly spontaneous (without need of ATP)? I came across some &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22730321&quot; rel=&quot;nofollow&quot;&gt;papers&lt;/a&gt; that mention it, as well as the opposite case (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21401736&quot; rel=&quot;nofollow&quot;&gt;ATP-driven&lt;/a&gt;), but I can't figure out which is common or which is rare.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the case of protein &lt;strong&gt;phosphorylation&lt;/strong&gt;, I would say ATP is always needed since it provides the phosphate? Or could you have a spontaneous phosphorylation using free phosphates that float around?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am aware that in the end, pretty much everything is possible, so I am more looking for likelihood. What is commonly accepted, wide spread, and what may happen but is rare.&lt;/p&gt;&#xA;" OwnerUserId="9662" LastEditorUserId="9662" LastEditDate="2015-06-28T19:26:07.493" LastActivityDate="2015-06-28T22:54:54.040" Title="Phosphorylation-Dephosphorylation : ATP-driven VS spontaneous" Tags="&lt;phosphorylation&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35605" PostTypeId="1" AcceptedAnswerId="35608" CreationDate="2015-06-28T17:34:17.073" Score="8" ViewCount="5311" Body="&lt;p&gt;I was walking through a small park when two crows started cawing at me, and followed me, flying from tree-to-tree as I walked. I speculate that this is a territorial or protective behaviour, but what I found different was the crows were violently pecking the branches nearby them. I have no memories coming to mind of seeing this behaviour beforehand. I speculate that this behaviour could be threat displays, but a quick search on Google did not reveal to me any authoritative studies on this phenomenon. I'd appreciate more information and sources. &lt;/p&gt;&#xA;" OwnerUserId="11538" LastEditorUserId="16866" LastEditDate="2018-12-03T01:11:37.280" LastActivityDate="2019-05-29T03:27:40.283" Title="Crow branch pecking behaviour" Tags="&lt;zoology&gt;&lt;ornithology&gt;&lt;ethology&gt;&lt;behaviour&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="35606" PostTypeId="2" ParentId="35597" CreationDate="2015-06-28T18:59:24.693" Score="2" Body="&lt;p&gt;This animal is moth &lt;a href=&quot;https://en.wikipedia.org/wiki/Larva&quot; rel=&quot;nofollow noreferrer&quot;&gt;larva&lt;/a&gt;. The images presented are blurry, but if there are no any dots on the larva my first suggestion is:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Indian_mealmoth&quot; rel=&quot;nofollow noreferrer&quot;&gt;pantry/Indian meal moth&lt;/a&gt; larvae - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UGwuA.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&quot;They are a common grain-feeding pest found around the world, feeding on cereals and similar products.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(&lt;a href=&quot;http://pixshark.com/indian-meal-moth-larvae-webbing.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;picture source&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-06-28T19:11:03.373" LastActivityDate="2015-06-28T19:11:03.373" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35607" PostTypeId="2" ParentId="35583" CreationDate="2015-06-28T20:00:18.307" Score="0" Body="&lt;p&gt;To keep it simple: The term here is &lt;a href=&quot;https://en.wikipedia.org/wiki/Assortative_mating&quot; rel=&quot;nofollow&quot;&gt;assortative mating&lt;/a&gt; which describes the tendency of individuals to select reproductive partners based on some arbitrary measure of &quot;likeness&quot; considering the available within-species variation. The &quot;likeness&quot; could be anything from a general evaluation to being based on one specific trait.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a evolutionary significant phenomenon, and when it comes to humans there are a lot of factors that seems to be related to human assortative mating, including both race (whatever the term's biological significance) and ethnicity, among other things like height, religion, politics and even altruism. &lt;sup&gt;&lt;sub&gt;See wiki for ref.&lt;/sup&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As seen in the article Shigeta liked to, racial belongingness is generally very significant in human assortative mating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the concept of choosing &quot;similar&quot; partners as we see in humans is a common biological phenomenon with evolutionary significance, although by what exact mechanisms this selection works in humans and how culturally dependent it is (maybe some assortative selection traits are more or less biologically/culturally founded than others) is probably in need of more research.&lt;/p&gt;&#xA;" OwnerUserId="9124" LastEditorUserId="9124" LastEditDate="2015-06-29T10:33:07.623" LastActivityDate="2015-06-29T10:33:07.623" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="35608" PostTypeId="2" ParentId="35605" CreationDate="2015-06-28T20:32:14.130" Score="11" Body="&lt;p&gt;This is a good question. This type of behavior -- pecking at a branch, wiping the side of the beak on a branch, pulling off twigs and dropping them, or knocking off pieces of bark -- is quite common among many corvid species, particularly when they are interrupted by something or someone that they might consider a threat. This includes not only potential predators but also potentially hostile conspecifics.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is typically considered to be a form of &lt;a href=&quot;http://www.animalbehavioronline.com/displacementbehavior.html&quot;&gt;displacement behavior&lt;/a&gt;. The concept of displacement behavior, from classical ethology, posits that when an animal experiences two conflicting drives to do two different things, it doesn't know which to do and does a third thing instead to dissipate the drive or anxiety. For branch-pecking in crows, see E.g Kilham and Waltermire 1990 Ch. 12. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Referece:&lt;/strong&gt; Kilham, L., &amp;amp; Waltermire, J. (1990). &lt;em&gt;The American crow and the common raven&lt;/em&gt;. Texas A&amp;amp;M University Press.&lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-06-28T20:32:14.130" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35609" PostTypeId="1" CreationDate="2015-06-28T20:57:41.553" Score="3" ViewCount="142" Body="&lt;p&gt;I found &lt;a href=&quot;https://biology.stackexchange.com/questions/2378/mechanism-of-tear-gas-chloropicrin-trichloro-methane&quot;&gt;the question about tear gas&lt;/a&gt; very interesting. Shigeta says there that crying helps the cells of the eye to wash themselves clear of the toxic components in the tear gas.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Does non-emotional tearing always work this way? Is tearing not caused by cells in the tear duct working as receptors? If not, why we have tear duct (the first in-eye part of it)?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;What is the cause of tear-production associated with crying during strong emotions? Is it due to hormones or nerve activation?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6124" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-06-29T16:15:54.903" Title="How does tearing work?" Tags="&lt;eyes&gt;&lt;reflexes&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35610" PostTypeId="2" ParentId="11152" CreationDate="2015-06-28T21:34:48.233" Score="1" Body="&lt;p&gt;Looking over your code I see that you are using the Fisher exact test (FET). Several assumptions of the FET are not meet when testing gene sets by GO annotation (&lt;a href=&quot;http://www.nature.com/srep/2014/140226/srep04191/full/srep04191.html&quot; rel=&quot;nofollow&quot;&gt;cite&lt;/a&gt;). If this is for a school project FET is good enough. However, if this data set is for publication I would recommend using a different analysis. I don't know what your data looks like and the questions your trying to answer, but I would start by looking at these: &lt;a href=&quot;http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375&quot; rel=&quot;nofollow&quot;&gt;Review&lt;/a&gt;, Camera (Wu 2012), ROAST (Wu 2010), and the first article I linked to.     &lt;/p&gt;&#xA;" OwnerUserId="14701" LastActivityDate="2015-06-28T21:34:48.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35611" PostTypeId="2" ParentId="35604" CreationDate="2015-06-28T22:54:54.040" Score="2" Body="&lt;p&gt;First, I would like to clarify what is meant by &quot;spontaneous&quot;. In chemistry, thermodynamically favorable reactions ($\Delta G &amp;lt; 0$) are indeed termed spontaneous because they will &lt;em&gt;eventually&lt;/em&gt; occur, regardless of how slowly. But if transition states are unfavorable (high energy barrier), the reaction rate can be extremely slow --- millions of years in some cases. For example, combustion of wood is highly favorable and, chemically speaking, it is spontaneous. But that doesn't mean trees are unstable and likely to catch fire any minute.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most biologists would probably call a reaction &quot;spontaneous&quot; only if it actually happens on a reasonable time scale, perhaps on the order of hours, depending on the context. So the terminology is a bit messy. But neither chemists nor biologists would call a molecule &quot;unstable&quot; if it has a reasonable half-life, I think. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now for the actual questions. Dephosphorylations are typically not ATP-driven, because breaking the P-O bonds is usually favorable already (although I'm sure there exceptions). However, the reaction is typically too slow to be useful to cells, so it is not &quot;spontaneous&quot; in this sense, and therefore needs to be catalyzed by phosphatases. A typical example is &lt;a href=&quot;https://en.wikipedia.org/wiki/Alkaline_phosphatase&quot; rel=&quot;nofollow&quot;&gt;alkaline phosphatase&lt;/a&gt; which dephosphorylates a wide range of proteins and other substrates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phosphorylation requires a phosphate source of course, but also an energy source, because forming P-O bonds is not a favorable reaction on its own (the reverse of the above). So adding a lone phosphate would not be favorable, but transfering one from ATP is much better, because this simultaneously involves breaking a P-O bond in ATP, &quot;freeing up&quot; energy to drive the reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, an interesting point is that ATP itself is actually a quite stable molecule, with a &lt;a href=&quot;http://pubs.acs.org/doi/abs/10.1021/bi00902a030&quot; rel=&quot;nofollow&quot;&gt;half-life of about two weeks&lt;/a&gt;. So ATP hydrolysis is not &quot;spontaneous&quot; in the biologist's sense, and enzyme catalysis is required (kinases). In fact, the combination of a high &quot;energy content&quot; and good stability is probably key to the role of ATP as an energy currency in cells: if ATP was indeed unstable, it would randomly phosphorylate everything. Stability means enzyme catalysis can be used to control phosphorylation events. Truly unstable compounds are never used by cells, because their reactivity causes damage and toxicity.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-06-28T22:54:54.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35612" PostTypeId="2" ParentId="35593" CreationDate="2015-06-28T22:58:21.447" Score="6" Body="&lt;p&gt;Rhesus antigen (Rh-D) is inherited in an &lt;strong&gt;autosomal dominant&lt;/strong&gt; pattern.  Therefore you are correct in your reasoning.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Simple problems like this are often best worked out using Punnet Squares, shown below for the scenarios you have considered.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Because the inheritance pattern is dominant, if &lt;em&gt;either&lt;/em&gt; parent was homozygous (DD) for Rh-D then 100% of their offspring will be Rh+ve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/pqbMo.png&quot; alt=&quot;Punnet square for Rhesus disease with homozygous positive and negative parents&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to have a rhesus negative child, &lt;em&gt;neither&lt;/em&gt; parent must be homozygous for the D allele.  You are correct that one possible scenario is a matching pair of heterozygotes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0i5Oj.png&quot; alt=&quot;Rhesus inheritance punnet square for matching heterozygote parents&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this situation 3/4 of the children are rhesus positive and 1/4 rhesus negative.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is an alternative where one parent is Rhesus negative and the other positive.  In this case there is one heterozygous parent and one homozygous negative parent:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PXv5v.png&quot; alt=&quot;Punnet square for rhesus inheritance with one homozygote negative and one heterozygote&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this scenario, half of the children are rhesus positive and half rhesus negative.&lt;/p&gt;&#xA;" OwnerUserId="69" LastEditorUserId="69" LastEditDate="2015-06-29T14:58:52.163" LastActivityDate="2015-06-29T14:58:52.163" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35613" PostTypeId="2" ParentId="31733" CreationDate="2015-06-28T23:37:37.837" Score="3" Body="&lt;p&gt;It seems like you are attempting to frame this as a question about current evolutionary theory. However, current evolutionary theory doesn't expect anything as complex as an organ to arise spontaneously without any precursors. You suggest a new claw in an insect would be something &quot;spontaneous&quot; enough for you. This again shows that your question and the answer you are looking for are not related to evolutionary theory. The insect organs you are talking about are all modified appendages. This includes claws, mandibles, antennae, legs, fangs. These appendages all share a common genetic and developmental framework that has been slightly modified over long periods of time to give raise to the variety of insect appendages that we see today. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea that evolutionary theory supports the spontaneous creation of organs is a willful ignorance of evolutionary theory. The molecular mechanisms that generate novelty (e.g. genome duplication, gene duplication, de novo genes, mutation, gene regulation) for natural selection to work on are relatively well understood. Since we have an understanding of how novelty is created it is known that spontaneous organ generation has never happened or is expected to happen under evolutionary theory. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_toc_01&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt; to the University of California, Berkeley's webpage designed to teach the public about evolution. &lt;/p&gt;&#xA;" OwnerUserId="14701" LastEditorUserId="14701" LastEditDate="2015-06-29T03:44:58.873" LastActivityDate="2015-06-29T03:44:58.873" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35614" PostTypeId="2" ParentId="35600" CreationDate="2015-06-28T23:53:57.870" Score="2" Body="&lt;p&gt;I've worked on a couple of these for biofuel production. The answer varies widely according to plant P and how well studied plant P is. In terms of what data is used, it includes but is not limited to: temperature, insolation, length of the day, cloud cover, rain, soil composition, soil type, soil density, other local effects like wind or pests, altitude, humidity, and pH. For corn(food) and miscanthus(experimental biofuel crop) the models are quite good if the year is pretty normal and you're in a well-studied parameter space, mostly because corn and grass grows straight up. For trees, non-crops, non-corn crops, etc the models are almost completely useless. It's a question of testing nearly every possible combination of parameters for each plant P, and how much people care about how tall it gets.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given how much data goes in, it surprises me that even under ideal conditions(well-studied) some of the parameters the model spits out are impossible/wrong. There's a measure of leaf overlap(just as an example) that's especially poorly defined but a rough proxy might be &quot;number of leaves that shade a specific point, on average&quot; and it's regularly measured at &amp;lt;10 and regularly predicted at well north of 50. &lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-06-28T23:53:57.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35615" PostTypeId="2" ParentId="35601" CreationDate="2015-06-29T00:33:36.250" Score="5" Body="&lt;h1&gt;DNA in pure water.&lt;/h1&gt;&#xA;&lt;p&gt;The only time that nucleic acids would encounter pure water would be in a laboratory setting--for example after an oligonucleotide is synthesized in vitro, the protecting groups are removed from the reactive atoms in the finished sequence and the final product is cleaved from the supporting matrix.  At that point you can lyophilize (freeze dry) the ammonium hydroxide solution, and resuspend the single-stranded oligo in pure water.&lt;/p&gt;&#xA;&lt;h1&gt;Additional compounds enhance heavy oligomer solubility.&lt;/h1&gt;&#xA;&lt;p&gt;However, as noted in the comments, nucleic acid solubility, particularly high molecular weight DNA, like genomic DNA,  is enhanced in solutions with dilute monovalent cations. 10 mM TrisHCl, pH 8.0, 1 mM EDTA suffices for almost every application. The EDTA inhibits any errant DNAses, and also slightly inhibits microbial growth.&lt;/p&gt;&#xA;&lt;h1&gt;Compounds act as pH buffers.&lt;/h1&gt;&#xA;&lt;p&gt;Tris is not the best biological buffer but has high solubility and is relatively cheap and stable. If the solution becomes too basic the DNA strands will melt, and if the solution becomes too acidic the purines will start to deaminate.&lt;/p&gt;&#xA;&lt;h1&gt;DNA never experiences pure water in biology.&lt;/h1&gt;&#xA;&lt;p&gt;From the moment that DNA is synthesized in a cell until that cell dies and its DNA is ultimately degraded, it does not encounter a pure water environment.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-06-29T13:28:25.290" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35616" PostTypeId="2" ParentId="35609" CreationDate="2015-06-29T01:03:00.620" Score="3" Body="&lt;p&gt;The regulation of tear production (&lt;em&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Tears&quot; rel=&quot;nofollow noreferrer&quot;&gt;lacrimation&lt;/a&gt;&lt;/em&gt;) involves reflexes initiated by sensory neurons in the &lt;a href=&quot;https://nei.nih.gov/health/cornealdisease&quot; rel=&quot;nofollow noreferrer&quot;&gt;cornea&lt;/a&gt;. &lt;strong&gt;Corneal pain receptors&lt;/strong&gt; (nociceptors) and mechanoreceptors detect &lt;strong&gt;damaging stimuli&lt;/strong&gt; and induce tearing to cleanse the ocular surface (and, hence, Shigeta is right as tear gas stimulates pain receptors). Corneal neurons sensitive to drying of the ocular surface also appear to increase tearing. These neurons also respond to cooling and hyperosmotic stimuli &lt;a href=&quot;http://jn.physiology.org/content/109/10/2517.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Kurose &amp;amp; Meng, 2013)&lt;/a&gt;. The tear duct is necessary to drain the tears away from the eye into the nasal cavity (Fig. 1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gLKm8.jpg&quot; alt=&quot;Tear glands and tear ducts&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Tear glands and tear ducts. Source: &lt;a href=&quot;http://www.mayoclinic.org/tear-glands-and-tear-ducts/img-20008059&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mayo Foundation for Medical Education and Research.&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Strong emotional responses like crying can result in an overflow of tears (&lt;em&gt;epiphora&lt;/em&gt;). Epiphora is mediated by the &lt;strong&gt;&lt;a href=&quot;https://www.dartmouth.edu/~rswenson/NeuroSci/chapter_9.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;limbic system&lt;/a&gt;&lt;/strong&gt; (the emotional center of the brain), especially the &lt;strong&gt;&lt;a href=&quot;http://www.endocrineweb.com/endocrinology/overview-hypothalamus&quot; rel=&quot;nofollow noreferrer&quot;&gt;hypothalamus&lt;/a&gt;&lt;/strong&gt;. Such strong &lt;em&gt;parasympathetic&lt;/em&gt; stimulation is accompanied by other symptoms, like reddening of the face and convulsive breathing (&lt;a href=&quot;http://www.d.umn.edu/~jfitzake/Lectures/DMED/Vision/Optics/Crying.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;University of Minnesota, Duluth)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://jn.physiology.org/content/109/10/2517.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kurose &amp;amp; Meng, &lt;em&gt;J Neurophysiol&lt;/em&gt; (2013); &lt;strong&gt;109&lt;/strong&gt;(10): 2517-22&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-29T03:34:45.673" LastActivityDate="2015-06-29T03:34:45.673" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35617" PostTypeId="1" AcceptedAnswerId="35619" CreationDate="2015-06-29T01:14:06.607" Score="2" ViewCount="205" Body="&lt;p&gt;I have been trying to model calcium oscillations using MatLab, but I cannot obtain the oscillation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I created a function where I put all the equations and used ode15s to call the function.  I have listed the equations and the code.     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone tell me why I am not obtaining the oscillations?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;These are the equations along with the codes:&lt;/strong&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Sn9hg.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;r(:,3) = ( (((.029*0.13*1.049 + .21.*.5.*.144).*initi(:,1)) ./  (.144.*1.049.*(.5+ .13)) ) .*( 1- initi(:,3)) ) - (( (.21 *.5 + .029 *.9434) ./ (.5 +.9434) ).*initi(:,3)); &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The values of the upper case Ks are obtained as follows:&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Dc5Is.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;and the value of p is 0.5&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zro0h.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;a(:,1) = power (( (.5 .* initi(:,1) .*(1 - initi(:,3))) ./ ((.5 + .13 ).*(initi(:,1) + .0823)) ),3); % p_o&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qWNRA.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Jserca is directly substituted in the equation shown below&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/89UAz.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;r(:,1) = (( 1.11.*  a(:,1) + .02 ) .* (  initi(:,2) - initi(:,1) ) ) -( .9 .*  power(initi(:,1),2)) ./ ( power(.1,2) + power(initi(:,1),2) );&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1rf3X.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt; r(:,2) = - r(:,1) .*5.5; % Ce&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;The constants are shown here:&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Xp5UQ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/b4DUc.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;And this is the desired result:&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/eCp7L.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;But I obtain this!&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rC4Z2.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;And this is my code:&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;function[t, initi, r,a]= deyoung()&#xA;clear all;&#xA;clc; &#xA;close all;&#xA;&#xA;&#xA;%--------------------------------------------------------------------------&#xA;% Initial conditions&#xA;%--------------------------------------------------------------------------&#xA;initi(:,1) = 0;  %  C  &#xA;initi(:,2) = .9; %  y&#xA;initi(:,3) = .5; %  Ce&#xA;&#xA;&#xA;%--------------------------------------------------------------------------&#xA;% ODEs&#xA;%--------------------------------------------------------------------------&#xA;icon=initi; &#xA;&#xA;tspan=[0 100];&#xA;&#xA;options = odeset('RelTol', 1e-08, 'AbsTol', 1e-08);&#xA;&#xA;[t,initi] = ode15s(@(t,initi) oper(t,initi),tspan,icon, options );&#xA;&#xA;[r,a] = oper(t,initi);&#xA;&#xA;figure();&#xA;plot(t,initi(:,1),t,initi(:,3));&#xA;&#xA;end&#xA;&#xA;function [r,a]=oper(t,initi)&#xA;&#xA;    initiSize = size(initi);&#xA;&#xA;    initiColumnCount = initiSize(2);&#xA;&#xA;    if ( initiColumnCount == 1)&#xA;        initi = initi';&#xA;        a = zeros(1,1); &#xA;    else&#xA;        initiRowCount = initiSize(1);&#xA;        a = zeros(initiRowCount, 1);&#xA;        r = zeros(initiRowCount, initiColumnCount);&#xA;    end&#xA;&#xA;&#xA;    % y&#xA;    r(:,3) = ( (((.029*0.13*1.049 + .21.*.5.*.144).*initi(:,1)) ./  (.144.*1.049.*(.5+ .13)) ) .*( 1- initi(:,3)) ) - (( (.21 *.5 + .029 *.9434) ./ (.5 +.9434) ).*initi(:,3));      &#xA;&#xA;    %Po       &#xA;    a(:,1) = power (( (.5 .* initi(:,1) .*(1 - initi(:,3))) ./ ((.5 + .13 ).*(initi(:,1) + .0823)) ),3); % p_o&#xA;&#xA;    %C&#xA;    r(:,1) = (( 1.11.*  a(:,1) + .02 ) .* (  initi(:,2) - initi(:,1) ) ) - ( .9 .*  power(initi(:,1),2)) ./ ( power(.1,2) + power(initi(:,1),2) );&#xA;&#xA;    %Ce&#xA;    r(:,2) = - r(:,1) .*5.5; % Ce&#xA;&#xA;    r = r';&#xA;&#xA;end&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="16468" LastEditorUserId="9943" LastEditDate="2015-06-29T03:01:36.400" LastActivityDate="2015-06-29T05:34:46.550" Title="Has anyone modelled calcium oscillations using Matlab software?" Tags="&lt;biophysics&gt;&lt;computational-model&gt;&lt;calcium&gt;" AnswerCount="1" CommentCount="15" ClosedDate="2015-06-29T04:22:26.110" ContentLicense="CC BY-SA 3.0" />
  <row Id="35618" PostTypeId="1" CreationDate="2015-06-29T01:22:08.570" Score="2" ViewCount="3454" Body="&lt;p&gt;Sometimes it's difficult falling asleep for almost an entire night. You might feel like getting up and being productive instead, or 'pull an all-nighter'.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or you can try to simply lay in bed to relax and rest, even though sleep does not kick in. In this situation, you may eventually fall asleep, only to be woken by your alarm just an hour or two later. Upon waking from such short sleep you can feel completely wrecked.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It leaves me wondering if you would feel more rested if you didn't sleep for just one hour. Maybe if you could relax throughout the night without really sleeping, you'd feel more rested by the time your alarm goes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But is it physically possible to recharge as if you were sleeping without actually sleeping?&lt;/p&gt;&#xA;" OwnerUserId="15433" LastEditorUserId="15433" LastEditDate="2015-06-29T15:23:12.160" LastActivityDate="2015-06-29T15:23:12.160" Title="Can you recharge without sleeping?" Tags="&lt;sleep&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2015-06-29T15:18:44.647" ContentLicense="CC BY-SA 3.0" />
  <row Id="35619" PostTypeId="2" ParentId="35617" CreationDate="2015-06-29T02:54:07.383" Score="2" Body="&lt;p&gt;I wish to share an open-source modelling study on Ca&lt;sup&gt;2+&lt;/sup&gt; oscillations in astrocytes which contains a detailed description of the underlying math and even better, it has supplementary Matlab code published alongside &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770604/&quot; rel=&quot;nofollow&quot;&gt;(Zeng et al., 2009)&lt;/a&gt;. This may be of help to check your formulae and script.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unfortunately I do not feel inclined to start troubleshooting and bug-fixing your formulae and Matlab code, because, as mentioned in the comments, the issue can be &lt;em&gt;anywhere&lt;/em&gt; in the chain of events.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770604/&quot; rel=&quot;nofollow&quot;&gt;Zeng &lt;em&gt;et al., Biophys J&lt;/em&gt; (2009); &lt;strong&gt;97&lt;/strong&gt;(9): 2429–37&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-29T05:34:46.550" LastActivityDate="2015-06-29T05:34:46.550" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35620" PostTypeId="1" AcceptedAnswerId="35631" CreationDate="2015-06-29T03:04:53.207" Score="5" ViewCount="642" Body="&lt;p&gt;First off, I apologize if this isn't the right stackexchange sub-site for asking thsi question.  I was torn as to where I should post this question: it could plausibly belong in Biology, User Experience or even Arqade.  However, given the root of my question has to do with the &quot;wiring&quot; of the human hand, I elected to post it here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My hypothesis/question:&lt;/strong&gt;&lt;br&gt;&#xA;Let's assume that wrist adduction/abduction is responsible for horizontal movement of the mouse cursor and that finger extension/flexion is responsible for vertical movement of the mouse cursor.  (I am, of course, willing to revisit this assumption, if necessary.)  Would it be accurate to say that we are &quot;hard-wired&quot; to be capable of higher precision in vertical movement of the mouse cursor than in horizontal movement?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Description of mouse grip:&lt;/strong&gt;&lt;br&gt;&#xA;In making the above assumptions, I assume a fingertip-grip style of the mouse (as opposed to the claw and palm grips). The (corner of the) wrist rests on the table and acts as a pivot for allowing side-to-side motion (i.e., horizontal motion of the mouse cursor).  Meanwhile, flexing/extending the fingers allows for pulling/pushing the mouse away from us, (i.e., vertical motion of the cursor).  The main (admittedly unscientific) reason behind my hypothesis is that vertical movement of the mouse cursor uses similar finger motions as those used for hand-writing (which is, after all, a highly precise activity).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;(I understand that my question makes the assumption that we are capable of more precise movement with certain muscles of our body than we are with others - please let me know if that's a flawed assumption.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why do I care about this?:&lt;/strong&gt;&lt;br&gt;&#xA;If my hypothesis is correct, there would be implications on mouse settings (namely, horizontal and vertical DPI*) that are conducive to both high accuracy and speed.  The key issue is that if we keep our wrist in place (i.e., no sliding/lifting of our pivot point) - then we're able to move the mouse a greater distance side-to-side (i.e., horizontal motion of cursor) than we're able to move it toward/away from us (i.e., vertical motion of cursor).  However, if there is evidence to support my hypothesis, than an appropriate adjustment (which wouldn't result in a loss of accuracy) would be to have a slightly higher vertical DPI than horizontal DPI.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*DPI = dots (i.e., pixels per inch).  For example, I have a resolution of 1366x768 (which is in units of dots or pixels) and a 600 dpi mouse, which means that my (physical) mouse needs to be moved ~2.3 inches (1366 divided by 600) in order for the mouse cursor to move the full horizontal distance of my monitor.  To put it simply, lower DPI results in higher accuracy but it is preferable for our wrist to remain in-place in the interest of speed.&lt;/p&gt;&#xA;" OwnerUserId="16471" LastActivityDate="2015-06-30T00:09:06.243" Title="Does the anatomy of our hand result in (computer) mouse-accuracy that varies by direction of movement?" Tags="&lt;human-anatomy&gt;&lt;movement&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35621" PostTypeId="1" AcceptedAnswerId="35623" CreationDate="2015-06-29T04:00:04.187" Score="4" ViewCount="9118" Body="&lt;p&gt;Could someone help me understand this equation please? I found it in a paper which said that it was DNA replication, but why?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\ce{dNTP + dNMP_{n} -&amp;gt; dNMP_{n +1} + PPi}$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found that &lt;strong&gt;dNTP&lt;/strong&gt; means &lt;em&gt;deoxy nucleotide triphosphate&lt;/em&gt; and &lt;strong&gt;dNTP&lt;/strong&gt; means &lt;em&gt;deoxy nucleotide monophosphate&lt;/em&gt;. Deoxy nucleotide monophosphate is a monomer in DNA, but dNTP isn't.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I also would like to know if there is an equation like this in other processes in the central dogma (such as transcription and translation)?&lt;/p&gt;&#xA;" OwnerUserId="15623" LastEditorUserId="9943" LastEditDate="2015-06-29T10:51:43.003" LastActivityDate="2015-06-29T10:58:32.447" Title="What does this equation about DNA replication mean?" Tags="&lt;biochemistry&gt;&lt;molecular-genetics&gt;&lt;replication&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35622" PostTypeId="1" AcceptedAnswerId="35627" CreationDate="2015-06-29T04:27:16.570" Score="65" ViewCount="6120" Body="&lt;p&gt;While hiking on the northern Idaho-Montana border, I encountered a large area where virtually every tree is bent at the base in the downhill direction.  Only the very largest and very smallest trees are straight.  What could cause this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/d93pJ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Eymn9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5862" LastActivityDate="2015-06-29T08:50:34.207" Title="What could cause a forest of bent trees?" Tags="&lt;botany&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="13" ContentLicense="CC BY-SA 3.0" />
  <row Id="35623" PostTypeId="2" ParentId="35621" CreationDate="2015-06-29T04:39:56.403" Score="5" Body="&lt;p&gt;The notation you are referring to is &lt;em&gt;a&lt;/em&gt; way to express the elongation of a nucleotide strand (Fig. 1).&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;dNTP + dNMP&lt;sub&gt;(n)&lt;/sub&gt; → dNMP&lt;sub&gt;(n+1)&lt;/sub&gt; + PP&lt;sub&gt;i&lt;/sub&gt; &lt;/pre&gt;  &#xA;&#xA;&lt;p&gt;means&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Existing strand  +  deoxynucleotidetriphosphate  →  elongated-strand  +  pyrophospate.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/X7K0M.jpg&quot; alt=&quot;elongation&quot;&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;Fig. 1. Elongation of DNA. Source: &lt;a href=&quot;http://bio3400.nicerweb.com/Locked/media/ch11/chain_elongation.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Concepts in Genetics&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;This reaction holds for DNA replication as well as transcription. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Translation is all about protein synthesis from amino acid precursors. Each subsequent amino acid is coupled to the growing peptide by a peptide bond between the carboxyl of the growing peptide and the amino group of the new amino acid. A water molecule is eliminated during the reaction (Fig. 2).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/008sP.png&quot; alt=&quot;peptide synthesis&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 2. Peptide bond formation. Source: &lt;a href=&quot;https://en.wikibooks.org/wiki/An_Introduction_to_Molecular_Biology/Function_and_structure_of_Proteins&quot; rel=&quot;nofollow noreferrer&quot;&gt;An Introduction to Molecular Biology&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence translation can be written analogously to replication as:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&#xA;amino acid + peptide&lt;sub&gt;(n)&lt;/sub&gt; → peptide&lt;sub&gt;(n+1)&lt;/sub&gt; &lt;/pre&gt; &#xA;&#xA;&lt;p&gt;However, also in this polymerization reaction energy is needed and amino acids are &lt;a href=&quot;http://www.nobelprize.org/educational/medicine/dna/a/translation/trna_aminoact.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;activated&lt;/a&gt; while they are bound to the messenger RNA (mRNA) through the action of ATP. Moreover, during translation the &lt;a href=&quot;http://bscb.org/learning-resources/softcell-e-learning/ribosome/&quot; rel=&quot;nofollow noreferrer&quot;&gt;ribosome (i.e., the protein synthesizing machinery)&lt;/a&gt; uses another source of energy to move across the RNA template, namely GTP. Hence, the &lt;em&gt;net&lt;/em&gt; reaction can be written as:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&#xA;amino acid + peptide&lt;sub&gt;(n)&lt;/sub&gt; + ATP + GTP → peptide&lt;sub&gt;(n+1)&lt;/sub&gt; + AMP + GDP + PP&lt;sub&gt;i&lt;/sub&gt; + P&lt;sub&gt;i&lt;/sub&gt; &lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Note that this notation in itself is &lt;em&gt;not&lt;/em&gt; a dogma as other ways are in use to denote DNA and RNA synthesis. According to &lt;a href=&quot;http://www.merriam-webster.com/dictionary/dogma&quot; rel=&quot;nofollow noreferrer&quot;&gt;Merriam-Webster&lt;/a&gt; a dogma is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A belief or set of beliefs that is accepted by the members of a group without being questioned or doubted.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="3340" LastEditDate="2015-06-29T10:58:32.447" LastActivityDate="2015-06-29T10:58:32.447" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35625" PostTypeId="2" ParentId="35621" CreationDate="2015-06-29T06:09:27.923" Score="0" Body="&lt;p&gt;DNA is a polymer of dNMPs (dAMP, dTMP, dCMP, and dGMP). That's why you could describe DNA by dNMPn (n base length). When another dNTP is added to DNA (dNMPn), one pyrophosphate (PPi) is released. It is obvious that the length of the DNA results in n+1 bases.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-06-29T06:09:27.923" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35626" PostTypeId="2" ParentId="35601" CreationDate="2015-06-29T07:38:58.353" Score="0" Body="&lt;p&gt;While physiological experiments could be conducted without organic solvents, chemical syntheses of DNA or analogs, chemical modification of DNA, and purification after chemical reaction could be performed in the presence of organic solvents. Such experiments are not directly relevant to physiology, but we use chemically synthesized DNA and DNA analogs. In addition, chemical properties of DNA in the presence of organic solvents may tell how DNA behave in physiological conditions. &#xA;People doing PCR and/or molecular biology may not be interested in the solubility of DNA, because under the condition they are using, the concentrations are far less than the saturated condition.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-06-29T07:38:58.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35627" PostTypeId="2" ParentId="35622" CreationDate="2015-06-29T08:50:34.207" Score="65" Body="&lt;p&gt;The phenomenon in question is probably related to &lt;a href=&quot;https://en.wikipedia.org/wiki/Gravitropism&quot; rel=&quot;noreferrer&quot;&gt;geotropism&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the hill soil is &quot;on the move&quot; it will cause the bend on the trees - &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If the soil in a slope is moving downward, the trees on this slope&#xA;  will tip downward.  As the tree continues to try to grow upward, the&#xA;  trunk will show a curve. The degree of bending could indicate the rate&#xA;  or amount of movement of the soil.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OiDpq.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.geocaching.com/geocache/GC3T6RQ_beware-of-bent-trees&quot; rel=&quot;noreferrer&quot;&gt;source&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-06-29T08:50:34.207" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35628" PostTypeId="2" ParentId="35618" CreationDate="2015-06-29T10:02:21.273" Score="4" Body="&lt;p&gt;No, you cannot. Although we don't know how sleep works, we know that lack of sleep is very devastating to the body, and nothing (including laying in bed relaxed but awake) can replace it. If a rat experiences 100% lack of sleep (somebody keeps it awake all the time), this will kill it sooner than 100% lack of food would. There are no wake-until-you-die studies in humans, but even reduced sleep has very bad effects, both cognitive (it impairs you similarly as if you were drunk) and physiological (metabolic changes: you need more energy for the same actions, and food intake increases disproportionally). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you have insomnia (and yours sounds severe), you need to get it treated. There are different options depending on whether an underlying cause is found, and whether behavioral therapies turn out to work for you. There are no alternatives which replace sleep. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The above is just a summary. For a dry but very reliable source on sleep, see Principles of neural science (ed. Kandel et al), Chapter 51 written by David McCormick and Gary Westbrook. For a very good popular science book on the subject, see &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0684831848&quot; rel=&quot;nofollow&quot;&gt;Sleep thieves&lt;/a&gt; by Stanley Coren, I can recommend it for anybody with insomnia. &lt;/p&gt;&#xA;" OwnerUserId="1578" LastEditorUserId="1578" LastEditDate="2015-06-29T14:58:43.587" LastActivityDate="2015-06-29T14:58:43.587" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35629" PostTypeId="2" ParentId="13580" CreationDate="2015-06-29T10:02:33.820" Score="1" Body="&lt;p&gt;Yes, when you are dreaming, brain activity increases ( called the REM phase because of the effect of the increased neural activity: rapid eye movements ). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can tell this by looking at the EEG, from witch we can state that our brain is more active and therefore is consuming more energy, making the regenerative effect of the sleeping less efficient. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Rapid_eye_movement_sleep#Electrical_activity_in_brain&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Rapid_eye_movement_sleep#Electrical_activity_in_brain&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16410" LastActivityDate="2015-06-29T10:02:33.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35630" PostTypeId="1" CreationDate="2015-06-29T12:40:08.513" Score="1" ViewCount="52" Body="&lt;p&gt;Assuming that one knows the maximum area of the canopy and the age of the tree when it achieves this. And given an initial canopy size from the nursery. How would I calculate the canopy size at a future date. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whilst certain aspects of the growth are obviously variable... how would I model the growth over the year(s)? I'm looking for a simple formula that I could give to a user in a planning department to develop adaptive lighting solutions for trees in streets. &lt;/p&gt;&#xA;" OwnerUserId="476" LastActivityDate="2015-06-29T12:40:08.513" Title="Calculating the canopy size (crown) of a newly planted tree at a future date" Tags="&lt;botany&gt;&lt;growth&gt;&lt;trees&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35631" PostTypeId="2" ParentId="35620" CreationDate="2015-06-29T12:59:29.363" Score="1" Body="&lt;p&gt;Assuming the case where you move a mouse left and right with the wrist and up and down with the fingers, then yes, &lt;strong&gt;finger movements are more precise&lt;/strong&gt;. The fingers and facial musculature are body parts with the most exquisite fine motor-control. The wrist, on the other hand, probably less so. The wrist is definitely involved in fine motor skills such as writing, but the fingers even more so. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wasn't able to find a good reference about the level of precision for different body parts at the behavioral level. I can, however, approach the question from a &lt;em&gt;neurophysiological&lt;/em&gt; point of view. The amount of motor control available for different body parts can be visualized by means of a &lt;strong&gt;motor &lt;em&gt;homunculus&lt;/em&gt;&lt;/strong&gt;. The motor homunculus shows &lt;em&gt;how many neurons are available&lt;/em&gt; in the cortex for a given body part. The larger the cortical surface dedicated to a body part, the larger the corresponding body part is presented in the homunculus (Fig. 1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UmRxU.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/Xhd4K.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Homunculus drawn on the motor cortex (left) and the homunculus presented as a figurine (right). Sources: &lt;a href=&quot;http://www.sigchi.org/chi97/proceedings/paper/rb2.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Conference on Human factors (1997)&lt;/a&gt; and &lt;a href=&quot;http://www.autismindex.com/Therapies/Therapy_Key_Word_Site_Map/sensory/motor_sensory_homunculus.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Autism Index&lt;/a&gt;, respectively.&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;fingers have a huge amount of motor cortex&lt;/strong&gt; dedicated to them compared to the wrist. There are a lot of 'buts' to add, most notably the larger number of muscles in the fingers versus the wrist, which explains part of the difference. Nonetheless, the homunculus does show the relative &lt;strong&gt;&lt;em&gt;functional&lt;/em&gt;&lt;/strong&gt; importance of the fingers in motor processing power of the brain, while the wrist is virtually invisible on the homunculus (Fig. 1, left panel).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lastly, you seem to be mixing up 'distance' and 'precision' in your question. While the wrist may cover a greater distance, it is not because of this that the precision is smaller. The &lt;strong&gt;fingers have more neuronal processing power&lt;/strong&gt; behind them and can be exquisitely fine tuned. In other words, the &lt;em&gt;precision is not determined by the &lt;strong&gt;dynamic range&lt;/strong&gt; (distance), but by the &lt;strong&gt;processing power&lt;/strong&gt; dedicated to the motor function&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note, because of &lt;a href=&quot;http://physioworks.com.au/injuries-conditions-1/rsi-repetitive-strain-injury&quot; rel=&quot;nofollow noreferrer&quot;&gt;RSI&lt;/a&gt;, it is recommendable to use gross &lt;em&gt;arm movements&lt;/em&gt; instead of fine wrist and finger movements. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-30T00:09:06.243" LastActivityDate="2015-06-30T00:09:06.243" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35632" PostTypeId="1" CreationDate="2015-06-29T13:18:37.140" Score="3" ViewCount="4184" Body="&lt;p&gt;In the light-dependent reactions of photosynthesis, H&lt;sup&gt;+&lt;/sup&gt; ions pass to the thylakoid space. Where do these protons come from?&lt;/p&gt;&#xA;" OwnerUserId="15946" LastEditorUserId="9943" LastEditDate="2015-06-29T13:56:28.367" LastActivityDate="2016-04-19T21:19:27.100" Title="Where do the H+ ions come from in light reactions?" Tags="&lt;molecular-biology&gt;&lt;metabolism&gt;&lt;photosynthesis&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35633" PostTypeId="1" AcceptedAnswerId="35642" CreationDate="2015-06-29T13:28:56.803" Score="4" ViewCount="140" Body="&lt;p&gt;A friend took this photo of a bee in his back yard in central Utah (&amp;copy; Jon Mott, CC-BY 3.0). I have no formal training in systematics or entomology, so to me everything looks like the bees' poster child &lt;em&gt;Apis mellifera&lt;/em&gt;. Can someone with a bit more experience confirm or refute this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/91DXZ.jpg&quot; alt=&quot;honey drinker&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="43" LastEditorUserId="1590" LastEditDate="2015-06-30T07:41:46.830" LastActivityDate="2019-01-16T04:26:56.700" Title="Identify bee in photo (found in Utah, USA)" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35636" PostTypeId="1" CreationDate="2015-06-29T15:17:40.923" Score="15" ViewCount="613" Body="&lt;p&gt;From Wikipedia:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;An L-system or Lindenmayer system is a parallel rewriting system and a type of formal grammar.&lt;/p&gt;&#xA;&lt;p&gt;L-systems were introduced and developed in 1968 by Aristid Lindenmayer, a Hungarian theoretical biologist and botanist at the University of Utrecht. Lindenmayer used L-systems to describe the behaviour of plant cells and to model the growth processes of plant development.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I tried to find biological research that has actually used this system but I could not find any. Perhaps this is because I do not know biology that well.&lt;/p&gt;&#xA;&lt;p&gt;Are these models important? Still taught?&lt;/p&gt;&#xA;&lt;p&gt;They do produce pretty pictures (again from Wikipedia)&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8NBg5.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;" OwnerUserId="16478" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2017-08-04T22:23:41.257" Title="What have the L-systems (Lindenmayer systems) been actually used for in biology?" Tags="&lt;theoretical-biology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35637" PostTypeId="1" CreationDate="2015-06-29T15:29:05.377" Score="6" ViewCount="126" Body="&lt;p&gt;I have seen lot of people sleep or say that they are feeling sleepy after taking some medicines. Why? I mean, if a medicine acts on some cell of the body because that cell has got its receptors and other cells have receptor for another part of that molecule, then too why do a large range of medicine induce sleep?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This also points to a doubt that there are only one kind of receptors for sleep inducing medicines (the real ones not the ones which have sleep as side effect) or many? If many are there, then it can be possible that a large range of medicines induce sleep.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it due to induction of sleep gives relaxation and thus give time for action of other medicines? Or is it just a natural process? If latter, why only some?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't want metabolism, just a reason.&lt;/p&gt;&#xA;" OwnerUserId="4503" LastEditorUserId="4503" LastEditDate="2015-07-03T16:07:59.907" LastActivityDate="2015-07-03T16:07:59.907" Title="Why do some medicines induce sleep?" Tags="&lt;molecular-biology&gt;&lt;sleep&gt;&lt;medicine&gt;" AnswerCount="0" CommentCount="20" FavoriteCount="0" ClosedDate="2015-06-30T16:07:15.187" ContentLicense="CC BY-SA 3.0" />
  <row Id="35640" PostTypeId="1" AcceptedAnswerId="35651" CreationDate="2015-06-29T16:38:36.313" Score="4" ViewCount="478" Body="&lt;p&gt;My question is closely related to &lt;a href=&quot;https://biology.stackexchange.com/questions/35108/sequence-evolution-simulation-tool&quot;&gt;this post&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a number of existing platforms to perform numerical individual-based simulation in populations genetics. An almost exhaustive list of such platforms can be found &lt;a href=&quot;https://popmodels.cancercontrol.cancer.gov/gsr/packages/&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some program (like NEMO or SFS_CODE for example) perform forward simulations while some others (like SIMCOAL2 for example) perform backward (coalescence) simulations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I am asking for a general comparison between those two methods.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Is one faster than the other? Why? (Intuitively I'd expect backward simulations to be faster).&lt;/li&gt;&#xA;&lt;li&gt;Does backward simulation allow for simulating selection, recombination, gender-specific mutation rate, complex demography, etc..&lt;/li&gt;&#xA;&lt;li&gt;Why/when would one use a backward/forward simulation model rather than the other type of model?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-06-30T13:26:55.360" Title="Forward versus backward numerical simulations in population genetics" Tags="&lt;evolution&gt;&lt;theoretical-biology&gt;&lt;population-dynamics&gt;&lt;population-genetics&gt;&lt;computational-model&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35641" PostTypeId="1" AcceptedAnswerId="35643" CreationDate="2015-06-29T17:47:49.313" Score="7" ViewCount="1677" Body="&lt;p&gt;Cholesterol, which is hydrophobic, cannot simply travel in the bloodstream, and instead is enclosed in lipoprotein (LDL, HDL). Steroids, which are derived from cholesterol, are also hydrophobic (right?). So how do they travel in the bloodstream? If they are enclosed by anything, what is the molecular mechanism of their entering the target cell?&lt;/p&gt;&#xA;" OwnerUserId="9207" LastActivityDate="2015-06-29T18:16:27.207" Title="How do steroids travel in the bloodstream?" Tags="&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35642" PostTypeId="2" ParentId="35633" CreationDate="2015-06-29T17:50:58.127" Score="6" Body="&lt;p&gt;Yes, this looks like &lt;em&gt;Apis mellifera&lt;/em&gt;, which is also one of the most common bees you'll run into. If you have other pictures, you could check the identification tips at &lt;a href=&quot;http://bugguide.net/node/view/3080#id&quot;&gt;the bugguide page for the species&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a side note, in general to really &lt;strong&gt;confirm&lt;/strong&gt; an identification a specialist would need to see a collected specimen (that is, a live or pinned bee) as the distinctive characters (things like size, wing veins, or in this case, long hairs on the eye) may not be visible in photographs.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2015-06-29T17:50:58.127" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35643" PostTypeId="2" ParentId="35641" CreationDate="2015-06-29T18:16:27.207" Score="10" Body="&lt;p&gt;Steroid hormones are transported in an inactive form bound to proteins in the bloodstream. Androgens and estrogen are bound to &lt;a href=&quot;https://en.wikipedia.org/wiki/Sex_hormone-binding_globulin&quot;&gt;Sex hormone-binding globulin&lt;/a&gt; (SHBG), while glucocorticoids and progestins are bound to &lt;a href=&quot;https://en.wikipedia.org/wiki/Transcortin&quot;&gt;transcortin&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7195404&quot;&gt;Transport of steroid hormones: binding of 21 endogenous steroids to&#xA;both testosterone-binding globulin and corticosteroid-binding&#xA;globulin in human plasma.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3548415&quot;&gt;Plasma protein-mediated transport of steroid and thyroid hormones.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://press.endocrine.org/doi/abs/10.1210/edrv-11-1-80&quot;&gt;The Functions of Corticosteroid-Binding Globulin and Sex&#xA;Hormone-Binding Globulin: Recent Advances&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-06-29T18:16:27.207" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35646" PostTypeId="1" CreationDate="2015-06-29T22:29:05.117" Score="1" ViewCount="150" Body="&lt;p&gt;Specifically, I'm trying to find the sequence of BxB1 and its att sites.  I have success finding the att site sequences, but I'm having a bit more of an issue with finding the sequence of the actual recombinase.  I've looked through Genebank, but I can't find a definitive sequence of the BxB1 recombinase.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How should I go about looking for this sequence?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: One more thing I'm concerned about is the validity of the sequences that I do find.  For example, I have seen that Addgene has this &lt;a href=&quot;https://www.addgene.org/browse/sequence/77884/&quot; rel=&quot;nofollow&quot;&gt;pCAG-NLS-HA-Bxb1&lt;/a&gt; sequence.  However, I'm not sure how to verify that this sequence is correct.&lt;/p&gt;&#xA;" OwnerUserId="14741" LastEditorUserId="3340" LastEditDate="2015-06-30T05:38:50.097" LastActivityDate="2015-06-30T06:16:25.857" Title="How do I find the sequence of the phage BxB1 gene?" Tags="&lt;genetics&gt;&lt;sequence-analysis&gt;&lt;recombination&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35647" PostTypeId="2" ParentId="35646" CreationDate="2015-06-29T23:16:41.577" Score="1" Body="&lt;p&gt;&lt;a href=&quot;http://phagesdb.org/phages/Bxb1/&quot; rel=&quot;nofollow&quot;&gt;http://phagesdb.org/phages/Bxb1/&lt;/a&gt; here you can click &quot;Locally BLAST this genome&quot; it will give you the sequence in FASTA format and then you can click BLAST if you want additional information about the sequence, alignment, etc&lt;/p&gt;&#xA;" OwnerUserId="16489" LastActivityDate="2015-06-29T23:16:41.577" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35648" PostTypeId="1" CreationDate="2015-06-30T01:39:26.233" Score="3" ViewCount="227" Body="&lt;p&gt;The current taxonomy has family names like Canidae and Felidae. But Felidae has sub families like Felinae and Pantherinae. Roaring cats and non-roaring cats. My question is based on the fact that we can have common words for these families based in Latin: Felines, Canines, Pantherines. Can every family in the taxonomy be represented by this latter form? Is Pantherine a valid name? Is was created by dropping the a from the subfamily but caninine was created by dropping the da from the main family and replacing with in.&lt;/p&gt;&#xA;" OwnerUserId="14949" LastEditorUserId="14949" LastEditDate="2015-06-30T01:45:00.937" LastActivityDate="2015-07-02T23:23:15.230" Title="Application of Latin names for Taxonomy" Tags="&lt;taxonomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35650" PostTypeId="2" ParentId="34733" CreationDate="2015-06-30T05:09:51.980" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;One way to distinguish between the olfactory and gustatory system in fish is by their  anatomical differences. For example, olfactory receptors are clustered in the nasal region, while gustatory receptors are scattered in the head region and beyond. In turn, olfactory information is sent via a single cranial nerve to the brain, while the gustatory system includes three cranial nerves.&lt;br&gt;&#xA;&lt;br&gt;&lt;br&gt;&#xA;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10982/&quot; rel=&quot;nofollow noreferrer&quot;&gt;olfactory&lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/nature/journal/v486/n7403_supp/full/486S2a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;gustatory system&lt;/a&gt; both receive their inputs through chemoreceptor cells. The chemoreceptor proteins in both systems are G-protein coupled receptor systems. However, the olfactory and gustatory systems are anatomically separated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;olfactory end organ&lt;/strong&gt; is in fish comparable to that in humans, namely sensory epithelia situated in nostrils. The olfactory receptor cells form axons that are grouped into the &lt;strong&gt;&lt;em&gt;olfactory nerve&lt;/em&gt;&lt;/strong&gt; (cranial nerve I). The nerve innervates the olfactory bulb, where its axons synapse onto mitral cells. Mitral cell axons group into the olfactory tract that projects to the telencephalon in the brain.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Nmadl.jpg&quot; alt=&quot;fish&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Schematic of olfactory system of a fish (not all structures shown). Source: &lt;a href=&quot;http://globalwarmingtropicalfishes.blogspot.com.au/p/solutions.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Global Warming Australia&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;gustatory end organs&lt;/strong&gt; are less well anatomically localized. The taste buds can be found in various structures including gills, barbels, fins, oral cavity and pharynx, dependent on the species. Unlike the olfactory system, gustatory information is transmitted to the brain via three separate cranial nerves: &lt;strong&gt;&lt;em&gt;facial&lt;/em&gt;&lt;/strong&gt; (cranial nerve VII), &lt;strong&gt;&lt;em&gt;glossopharyngeal&lt;/em&gt;&lt;/strong&gt; (cranial nerve IX) and &lt;strong&gt;&lt;em&gt;vagal nerve&lt;/em&gt;&lt;/strong&gt; (cranial nerve x). Normally, the facial nerve innervates taste buds on the extraoral surface, the glossopharyngeal on the anterior part of the oral cavity, and the vagal nerve on the pharynx. The facial and vagal nerves respectively terminate in the facial and vagal lobes in the medulla. The glossopharyngeal nerve terminates in a dorsal medullary region between the facial and vagal lobes.&#xA;&lt;br&gt;&lt;br&gt;&lt;br&gt; &#xA;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF00043259&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hara, &lt;em&gt;Rev Fish Biol Fisheries&lt;/em&gt; (1994); &lt;strong&gt;4&lt;/strong&gt;: 1-35&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-06-30T09:13:17.907" LastActivityDate="2015-06-30T09:13:17.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35651" PostTypeId="2" ParentId="35640" CreationDate="2015-06-30T05:36:43.660" Score="2" Body="&lt;p&gt;Your intuitions all seem correct. Coalescent simulation should be faster, because you don't track the entire population history over all t generations as you do in the forward simulation. Rather, as you work backwards in time you are tracking a smaller and small population. And with coalescent simulations it is probably very hard to incorporate the full range of evolutionary processes whereas doing so is more or less trivial with forward simulations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A 2008 paper by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679650/&quot; rel=&quot;nofollow&quot;&gt;Carvajal-Rodriguez&lt;/a&gt; reviews some of the issues in more detail that I have here.&lt;/p&gt;&#xA;" OwnerUserId="13072" LastActivityDate="2015-06-30T05:36:43.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35653" PostTypeId="1" CreationDate="2015-06-30T07:02:18.923" Score="8" ViewCount="3016" Body="&lt;p&gt;This plant is found in India. It is an evergreen plant. Would love to know the scientific name.&lt;img src=&quot;https://i.stack.imgur.com/Jl4eX.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/uKgDl.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/kGKVw.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16497" LastEditorUserId="6561" LastEditDate="2015-07-01T22:20:18.727" LastActivityDate="2015-07-01T22:20:18.727" Title="What is the scientific name of this evergreen plant?" Tags="&lt;botany&gt;&lt;species-identification&gt;&lt;taxonomy&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35654" PostTypeId="1" AcceptedAnswerId="35656" CreationDate="2015-06-30T07:16:34.280" Score="46" ViewCount="3549" Body="&lt;p&gt;I've heard that the wonderful smell of a fresh rain is actually chemicals  released from the trees and grass and other plants.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What is the process that allows these chemicals to be released?&lt;/li&gt;&#xA;&lt;li&gt;What are the chemicals that create that smell?&lt;/li&gt;&#xA;&lt;li&gt;How is it advantageous for the plant to release the chemicals rather than hold onto them?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="9943" LastEditDate="2015-07-01T04:26:26.483" LastActivityDate="2016-01-18T05:50:54.180" Title="What is it that creates that wonderful smell after a fresh rain?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="15" ContentLicense="CC BY-SA 3.0" />
  <row Id="35656" PostTypeId="2" ParentId="35654" CreationDate="2015-06-30T07:30:48.490" Score="43" Body="&lt;p&gt;That molecule is called &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1058374/&quot;&gt;Geosmin&lt;/a&gt;. It is mainly produced &lt;sup&gt;1&lt;/sup&gt; by &lt;em&gt;Actinomycetes&lt;/em&gt; such as &lt;em&gt;Streptomyces&lt;/em&gt; which are filamentous bacteria that live in soil. Other organisms also produce geosmin:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24289950&quot;&gt;Cyanobacteria&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.2307/3761199&quot;&gt;Certain fungi&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;An amoeba called &lt;a href=&quot;http://dx.doi.org/10.1111/j.1550-7408.1991.tb04798.x&quot;&gt;&lt;em&gt;Vanella&lt;/em&gt;&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;A &lt;a href=&quot;http://ci.nii.ac.jp/naid/40005331488/en/&quot;&gt;liverwort&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;It is an intracellular metabolite and cell damage is the primary reason attributed to its release. However &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24289950&quot;&gt;oxidant exposure&lt;/a&gt; and &lt;a href=&quot;http://dx.doi.org/10.2166/wpt.2010.049&quot;&gt;transmembrane pressure&lt;/a&gt; also causes geosmin release in cyanobacteria. It seems that the release is triggered by some kind of stress. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am not quite sure about their advantage to the host species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;&lt;sup&gt;1&lt;/sup&gt; &lt;em&gt;or perhaps the most well-studied in&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-01-18T05:50:54.180" LastActivityDate="2016-01-18T05:50:54.180" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35658" PostTypeId="2" ParentId="35532" CreationDate="2015-06-30T08:35:07.610" Score="11" Body="&lt;p&gt;&lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_02&quot; rel=&quot;nofollow noreferrer&quot;&gt;Evolution&lt;/a&gt; occurs by a change in gene frequencies, with gene frequencies potentially affected by &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evo_14&quot; rel=&quot;nofollow noreferrer&quot;&gt;four mechanisms&lt;/a&gt; (mutation, migration, drift, and selection). &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;The answer to the question &lt;strong&gt;Why does the seemingly advantageous trait X &lt;em&gt;not&lt;/em&gt; evolve?&lt;/strong&gt; could be:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;The &lt;a href=&quot;https://en.wikipedia.org/wiki/Mutation&quot; rel=&quot;nofollow noreferrer&quot;&gt;mutations&lt;/a&gt; for a trait have never occurred within a population, or such genes have never migrated into the population&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The mutation(s) to cause such a trait may have once been present in a population but migration and/or drift and/or selection has since removed them from the population&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Selection has removed the mutations causing the seemingly advantageous trait because the same (or tightly linked) genes have other deleterious effects by &lt;a href=&quot;https://en.wikipedia.org/wiki/pleiotropy&quot; rel=&quot;nofollow noreferrer&quot;&gt;pleiotropy&lt;/a&gt; &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Similarly, the answer to the question &lt;strong&gt;Why does the seemingly disadvantageous trait X evolve?&lt;/strong&gt; could be any of the following:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Alternative genes have never been introduced to the population by mutation or migration&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Mutation, drift, and migration have allowed the gene to fix over other more advantageous genes&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Selection has spread the mutations causing the seemingly disadvantageous trait because the same (or tightly linked) genes have other beneficial effects by pleiotropy&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Note also that the trait may seem (dis)advantageous in the &lt;em&gt;current&lt;/em&gt; adaptive landscape, but selection exhibits temporal variation&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/2944/genetic-diversity-and-adaptation/44286#44286&quot;&gt;Read here&lt;/a&gt; on why and how genetic variation is required for evolution/adaptation to occur&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/42050/if-evolution-is-not-about-increased-complexity-why-does-so-much-complexity-evol/42063#42063&quot;&gt;Read here&lt;/a&gt; for more about the process of adaptation&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/15958/what-is-the-standing-genetic-variation/15962#15962&quot;&gt;Read here&lt;/a&gt; for more on genetic variation&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/5529/evolution-in-37-years-is-it-possible/5534#5534&quot;&gt;Read here&lt;/a&gt; for more on rapid evolution&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;https://biology.stackexchange.com/questions/41813/why-even-if-all-requirements-for-natural-selection-are-met-it-may-not-happen/41843#41843&quot;&gt;Read here&lt;/a&gt; for more on the relationship between multivariate selection and adaptation&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A detrimental phenotypic character may have no genetic variance, so it may be impossible for selection to stop such occurring; many diseases have considerable environmental inducers (e.g. selection can't work against emphysema developed as a result of smoking, but it can work against genes that increase the tendency of developing emphysema).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="49230" LastEditDate="2019-03-28T20:36:15.953" LastActivityDate="2019-03-28T20:36:15.953" CommentCount="0" CommunityOwnedDate="2015-06-30T08:35:07.610" ContentLicense="CC BY-SA 4.0" />
  <row Id="35659" PostTypeId="2" ParentId="20173" CreationDate="2015-06-30T09:00:05.107" Score="1" Body="&lt;p&gt;First I'd like to point out that there are over 500 species of leeches. Most of them live in fresh water (nearly 90%), and so most tree-living animals would not come into contact with these leeches. Because of this a leech's biggest predator would be fish.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://www.newworldencyclopedia.org/entry/Leech&quot; rel=&quot;nofollow&quot;&gt;The New World Encyclopaedia&lt;/a&gt; the predators of leeches are fish, crayfish, turtles, birds, frogs, dragonflies, and damselflies. It states that many of their predators have also been their prey. &lt;a href=&quot;http://www.ecospark.ca/changingcurrents/leech&quot; rel=&quot;nofollow&quot;&gt;Ecospark&lt;/a&gt; also adds snails and other insects to the list. &lt;a href=&quot;http://www.ecospark.ca/changingcurrents/leech&quot; rel=&quot;nofollow&quot;&gt;Biokids&lt;/a&gt; also points out that leeches will eat other leeches. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.britannica.com/animal/leech&quot; rel=&quot;nofollow&quot;&gt;Britannica&lt;/a&gt; cautions humans about swimming and drinking water with leeches in it. They can attach to internal cavities - such as the nose and throat and then the leeches can drop into the lungs and cause suffocation. In Asia, it is common for a domesticated animal to die in this fashion. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://animals.mom.me/predators-eat-leeches-7191.html&quot; rel=&quot;nofollow&quot;&gt;Animals.mom.me&lt;/a&gt; monkeys and other omnivorous animals will eat leeches that live on land, but land leeches aren't very common. After over an hour of searching various websites and information about leeches, there is no other source stating that mammals eat leeches. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it is possible to eat leeches. They did it on a television show called &lt;a href=&quot;https://www.youtube.com/watch?v=nG9QrEvgw8c&quot; rel=&quot;nofollow&quot;&gt;Fear Factor&lt;/a&gt; (video of the leeches being eaten linked). Before you go eating leeches though, remember these people were monitored both during and after ingestion of the leeches.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Short answer:&lt;/strong&gt; There are no &lt;em&gt;recorded&lt;/em&gt; mammals as predators to leeches, but it is known that pets have eaten leeches (as well as breathed them in). And humans are also able to eat leeches. It's all about if the leech is within grabbing distance when the mammal is hungry.&lt;/p&gt;&#xA;" OwnerUserId="16041" LastActivityDate="2015-06-30T09:00:05.107" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35661" PostTypeId="1" CreationDate="2015-06-30T11:48:58.657" Score="1" ViewCount="1259" Body="&lt;p&gt;Someone asked me:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If a striped cat is the result of a white and a black cat, why the result of a white woman and a black man is not a striped child?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I know the answer. I also know that the result of a black cat and a white one is not a striped cat. But I'm looking for a simple answer. I'm looking for an explanation without a genetics background required. I'm looking for a metaphor or something similar. &lt;/p&gt;&#xA;" OwnerUserId="16502" LastEditorUserId="1590" LastEditDate="2015-06-30T13:51:54.820" LastActivityDate="2016-02-28T07:32:54.293" Title="Why a striped baby is not the result of a white and a black parent?" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35664" PostTypeId="1" CreationDate="2015-06-30T12:44:44.147" Score="0" ViewCount="254" Body="&lt;p&gt;A exmaple of a contig name generated by velvet assembler:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;NODE_127_length_39203_cov_244.873016&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;What does &lt;code&gt;cov_244.873016&lt;/code&gt; mean? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It sounds like &lt;code&gt;coverage&lt;/code&gt;. Does it mean &lt;code&gt;reads coverage&lt;/code&gt; or other statistical description of the contig?&lt;/p&gt;&#xA;" OwnerUserId="5035" LastEditorUserId="3340" LastEditDate="2015-06-30T12:57:39.840" LastActivityDate="2015-06-30T12:57:39.840" Title="What does the &quot;cov&quot; mean in a velvet assembler generated contig name?" Tags="&lt;dna-sequencing&gt;&lt;sequence-analysis&gt;&lt;sequence-assembly&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35665" PostTypeId="2" ParentId="35661" CreationDate="2015-06-30T12:53:12.287" Score="4" Body="&lt;p&gt;Skin colour is determined by additive effects. That is, the amount of pigment is determined additively by the genes. For the basic genetics of it I will give a simple example, which is just illustrative and a gross oversimplification, it's probably much more complex (many loci all acting at once).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Imaginary example:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suppose skin colour is affected by a single locus (at one position) within the DNA, which determines the amount of pigment produced. At this locus there are two alleles within a population, that is two versions of the DNA (e.g. ACGTCCATT and GACTTAACT are different DNA sequences). Allele one ($A_1$) produces a small amount of pigment, and allele 2 ($A_2$) produces a large amount. Thus people with $A_1 A_1$ genotype (people are diploid, i.e. they get a version from each parent) have light skin, $A_2 A_2$ genotypes have dark skin, and $A_1 A_2$ have an intermediate skin colour. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Analogy&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is analogous to mixing fruit juice with water - if you mix &lt;a href=&quot;https://en.wikipedia.org/wiki/Ribena&quot; rel=&quot;nofollow&quot;&gt;blackcurrant cordial&lt;/a&gt; with water the colour is determined by the proportions. If you put out two bottles, one with cordial and one with water, allow two people to randomly choose a bottle, and use their choices to mix a glass of drink, 50% of the time you will end up with 1/2 water mixed with 1/2 cordial, while 25% of the time just a glass full of water, and the remaining 25% of the time just a glass full of cordial.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why stripes don't occur&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Note: although stripes occur in animals including humans (see chris' answer), it's not I'm the way your question insinuates&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For stripes to occur you would have to have structure in the skin with two different types of skin cell, where bands/stripes of type occur - alternating between expressing the allele inherited from the mother, and that inherited from the father. That would require structure in the skin and something called genomic imprinting so parent of origin could be a factor. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The analogy with the glass of cordial is what going on in each cell, for stripes you would have to have organised and alternating clusters of glasses (cells) which get their contents determined by one individuals choice of cordial, with the selector alternating with the cluster of glasses.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2015-07-04T07:12:06.267" LastActivityDate="2015-07-04T07:12:06.267" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35667" PostTypeId="2" ParentId="35664" CreationDate="2015-06-30T12:55:51.203" Score="2" Body="&lt;p&gt;It means &lt;strong&gt;k-mer coverage&lt;/strong&gt;. From the &lt;a href=&quot;http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf&quot; rel=&quot;nofollow&quot;&gt;velvet manual&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;4.2.1 The contigs.fa file&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;This fasta file contains the sequences of the contigs longer than 2 k&#xA;  , where k is the word-length used in velveth.  If you have specified a&#xA;  &lt;em&gt;min_contig_length&lt;/em&gt; threshold, then the contigs shorter than that value are omitted. Note  that  the  length  and  coverage  information&#xA;  provided  in  the  header  of each contig should therefore be&#xA;  understood in k-mers and in k-mer coverage (cf. 5.2 ) respectively. &#xA;  E.g.  for a 500bp contig and a k-mer length of 21, the length in the&#xA;  header will be 480.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-06-30T12:55:51.203" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35668" PostTypeId="2" ParentId="35661" CreationDate="2015-06-30T13:31:50.997" Score="8" Body="&lt;p&gt;The reason that there are no stripes when black and white people get babies is the fact that the number of pigment cells is the same for black and white people. What is different is the amount of pigment produced, and it will be different in the kids as well (lighter than the dark parent, darker than the light parent) See references 1 and 2 for details on the melanocyte density. Skin color is a multigenic trait, so the genetic background of both parents and their effects on pigmentation come into full play here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides this effect, humans do have stripes, although they are mostly not visible. They are called &lt;a href=&quot;https://en.wikipedia.org/wiki/Blaschko%27s_lines&quot; rel=&quot;noreferrer&quot;&gt;Blaschko's lines&lt;/a&gt; and look like below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QN3OQ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These develop from the migration pattern of the melanocytes (and their precursor cells) in the developing embryo. They can get visible in some rare genetic conditions or by diseases. See reference 3 for a more popular explanation and reference 4 for a review on this field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://rstb.royalsocietypublishing.org/content/252/779/447&quot; rel=&quot;noreferrer&quot;&gt;The Regional Anatomy of the Human Integument with Special Reference&#xA;to the Distribution of Hair Follicles, Sweat Glands and Melanocytes&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/9780470987100.ch3/summary&quot; rel=&quot;noreferrer&quot;&gt;General Biology of Mammalian Pigmentation&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://scienceblogs.com/pharyngula/2010/08/12/blaschkos-lines/&quot; rel=&quot;noreferrer&quot;&gt;Blaschko’s Lines&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.filedropper.com/bolognia1994&quot; rel=&quot;noreferrer&quot;&gt;Lines of Blaschko.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="9943" LastEditDate="2015-06-30T13:56:44.240" LastActivityDate="2015-06-30T13:56:44.240" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35669" PostTypeId="1" AcceptedAnswerId="35675" CreationDate="2015-06-30T05:28:20.487" Score="4" ViewCount="907" Body="&lt;p&gt;For example, here is a picture of the root systems for some prairie grasses:&#xA;&lt;a href=&quot;http://www.conservationresearchinstitute.org/assets/rootsposter.enlarge.pdf&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/yyyzl.gif&quot; alt=&quot;prairie root network&quot;&gt;&lt;/a&gt;&#xA;&lt;sup&gt;(Click image for higher-resolution PDF) from: &lt;a href=&quot;http://www.conservationresearchinstitute.org/educational-offerings.html&quot; rel=&quot;noreferrer&quot;&gt;http://www.conservationresearchinstitute.org/educational-offerings.html&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is it possible to follow one root thread 15 feet down? Especially when they are so densely packed in the top foot of soil that you couldn't dig at all without destroying roots.&lt;/p&gt;&#xA;" OwnerUserId="6575" OwnerDisplayName="Philip" LastEditorUserId="13254" LastEditDate="2015-06-30T14:14:33.177" LastActivityDate="2015-07-03T12:59:46.847" Title="How do researchers map root systems of plants?" Tags="&lt;botany&gt;&lt;plant-anatomy&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35670" PostTypeId="2" ParentId="35669" CreationDate="2015-06-30T13:48:38.880" Score="2" Body="&lt;p&gt;...why do you assume that it's non-destructive? It's effectively performing an &quot;archeological dig style&quot; excavation, and the particular plant is not likely to survive it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's a couple links to descriptions of &quot;an improved method&quot; along with a description of the &quot;usual method&quot; it's &quot;improved&quot; over, circa 1938 and 1940. jstor previews as these things do mostly get discussed in academic journals. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jstor.org/stable/1930591?seq=1#page_scan_tab_contents&quot; rel=&quot;nofollow&quot;&gt;http://www.jstor.org/stable/1930591?seq=1#page_scan_tab_contents&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="Ecnerwal" LastEditorUserId="3340" LastEditDate="2015-06-30T14:14:13.653" LastActivityDate="2015-06-30T14:14:13.653" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35671" PostTypeId="1" CreationDate="2015-06-30T14:10:25.433" Score="1" ViewCount="211" Body="&lt;p&gt;I've a question about ORF and translation into protein. Say I have an RNA transcript that contains two ORFs, one in phase 1 ; one in phase2 ; as:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;ORF number 1 in reading frame 1 on the direct strand extends from base 529 to base 759.&lt;/p&gt;&#xA;&lt;p&gt;ORF number 2 in reading frame 3 on the direct strand extends from base 849 to base 1223.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So ORF number 1 comes earlier in the transcript, but ORF number 3 is longer ..&lt;/p&gt;&#xA;&lt;p&gt;Is it always the first ORF that is translated ?&lt;/p&gt;&#xA;&lt;p&gt;Edit &amp;gt;&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;It's in an eukaryoytic organism and same gene (it's the same transcript)&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I use ORF finder (&lt;a href=&quot;http://www.bioinformatics.org/sms2/orf_find.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.bioinformatics.org/sms2/orf_find.html&lt;/a&gt;) on my transcript sequence and it gives me two potential ORFs (ORF 1 and ORF 2 within two different frames)&lt;/p&gt;&#xA;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="359" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-07-02T19:25:58.607" Title="Which ORF will be translated" Tags="&lt;translation&gt;&lt;orf&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35672" PostTypeId="1" CreationDate="2015-06-30T16:09:26.040" Score="2" ViewCount="1356" Body="&lt;p&gt;Does the human digestive system processes petroleum jelly? In other words, does it pass through the digestive system without any interaction, or is it absorbed and/or metabolized?&lt;/p&gt;&#xA;" OwnerUserId="16508" LastEditorUserId="9943" LastEditDate="2015-07-01T04:08:08.807" LastActivityDate="2015-07-01T13:47:47.067" Title="(How) Does the human digestive system process petroleum jelly, aka petrolatum?" Tags="&lt;human-biology&gt;&lt;digestion&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35673" PostTypeId="1" CreationDate="2015-06-30T16:15:08.883" Score="1" ViewCount="183" Body="&lt;p&gt;I would like to know whether there are substances that are safe for humans to consume, are not absorbed and do not interact with any digestive process. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, food is disqualified because although it may be safe, it is processed by the digestive system and is metabolized. I'm looking for things that go entirely unprocessed (other than passage).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One such material, or a discrete class of materials is sufficient.&lt;/p&gt;&#xA;" OwnerUserId="16508" LastEditorUserId="9943" LastEditDate="2015-07-01T22:55:45.593" LastActivityDate="2015-07-01T22:55:45.593" Title="What is a substance that is safe to eat, not absorbed and not metabolized?" Tags="&lt;human-biology&gt;&lt;digestion&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35674" PostTypeId="2" ParentId="35673" CreationDate="2015-06-30T17:06:33.297" Score="3" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Simethicone&quot; rel=&quot;nofollow&quot;&gt;Simethicone&lt;/a&gt; is one example. It is a mixture of &lt;a href=&quot;https://en.wikipedia.org/wiki/Silica_gel&quot; rel=&quot;nofollow&quot;&gt;silica gel&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Polydimethylsiloxane&quot; rel=&quot;nofollow&quot;&gt;dimethicone&lt;/a&gt; (polydimethyl siloxane); they are individually inert too. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Simethicone/dimethicone is used as antigas (they help the gas bubbles coalesce). It does have a laxative effect, though. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-07-01T06:05:45.900" LastActivityDate="2015-07-01T06:05:45.900" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35675" PostTypeId="2" ParentId="35669" CreationDate="2015-06-30T17:28:31.410" Score="5" Body="&lt;p&gt;You originally posted this question on the Garden and Landscaping Section - that's where I'm from, and though it was moved here instead, I'll answer it anyway:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That image you've shown isn't like a photograph, its an impression of what the roots are like. Usual method of working out root patterns on plants is to remove what's known as a monolith, or a block of soil where the plant is - the soil is then either carefully removed by hand, in the manner that archaeologists use, or air blasted, or soaked off in water to reveal as much of the roots as possible. For trees or plants with very large roots, newer methods include geophysical surveying by machine, or electric resistance surveying. Even this doesn't reveal everything - many roots may penetrate too far down, or run along cracks in rocks beneath the soil. The root length and distribution pattern vary according to local conditions, so its hard to be definite about where the roots of any particular plant are in a particular position in the landscape. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference and further reading:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.springer.com/us/book/9780412232305&quot; rel=&quot;nofollow&quot;&gt;Plant Physiological Ecology&lt;/a&gt; (ISBN 978-94-009-2221-1; Google books &lt;a href=&quot;https://books.google.co.uk/books?id=8rD1CAAAQBAJ&amp;amp;pg=PA367&amp;amp;dq=mapping%20of%20root%20systems%20of%20plants&amp;amp;hl=en&amp;amp;sa=X&amp;amp;ei=RNSSVbObG9C2uQTa9YPABA&amp;amp;ved=0CCwQ6AEwAg#v=onepage&amp;amp;q=mapping%20of%20root%20systems%20of%20plants&amp;amp;f=false&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;em&gt;Especially, check the Introduction on page No.367&lt;/em&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="16511" LastEditorUserId="16511" LastEditDate="2015-07-03T12:59:46.847" LastActivityDate="2015-07-03T12:59:46.847" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35676" PostTypeId="2" ParentId="35653" CreationDate="2015-06-30T19:34:51.150" Score="9" Body="&lt;p&gt;The tree in question belongs to the &lt;strong&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Araucariaceae&quot; rel=&quot;noreferrer&quot;&gt;Araucariaceae&lt;/a&gt;&lt;/strong&gt; family,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are multiple species of Genus &lt;strong&gt;Araucaria&lt;/strong&gt;,&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd place &lt;a href=&quot;https://en.wikipedia.org/wiki/Araucaria_araucana&quot; rel=&quot;noreferrer&quot;&gt;Araucaria araucana&lt;/a&gt; on the first place, but there are multiple others:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Araucaria araucana&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/hgHXt.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Araucaria luxurians&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Eek9O.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Araucaria columnaris&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Cl3FU.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Araucaria subulata&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/kCNKD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-06-30T19:34:51.150" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35677" PostTypeId="2" ParentId="19396" CreationDate="2015-06-30T22:00:03.350" Score="1" Body="&lt;p&gt;Not all animals are equally predisposed for &lt;a href=&quot;https://en.wikipedia.org/wiki/Domestication&quot; rel=&quot;nofollow&quot;&gt;domestication&lt;/a&gt;. To be easily domesticated, animal should have:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Flexible diet - and not compete with humans for food&lt;/li&gt;&#xA;&lt;li&gt;Reasonably fast growth rate&lt;/li&gt;&#xA;&lt;li&gt;Ability to be bred in captivity&lt;/li&gt;&#xA;&lt;li&gt;Pleasant disposition&lt;/li&gt;&#xA;&lt;li&gt;Temperament which makes it unlikely to panic &lt;/li&gt;&#xA;&lt;li&gt;Modifiable social hierarchy&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Wikipedia link above has plenty of details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So sharks, tigers and alligators are (according to above) are NOT good candidates, because of 4 and 6 at least. Alligators are bred in captivity in &lt;a href=&quot;https://en.wikipedia.org/wiki/Crocodile_farm&quot; rel=&quot;nofollow&quot;&gt;farms&lt;/a&gt; but are not really domesticated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also &lt;a href=&quot;https://en.wikipedia.org/wiki/Domestication#Approximate_dates_and_locations_of_original_domestication&quot; rel=&quot;nofollow&quot;&gt;dates and places of domestication&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9679" LastEditorUserId="9679" LastEditDate="2015-07-01T13:19:51.327" LastActivityDate="2015-07-01T13:19:51.327" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35678" PostTypeId="2" ParentId="35673" CreationDate="2015-06-30T22:23:50.813" Score="0" Body="&lt;p&gt;How about gold. You can find it on foods, but it is inert and also not absorbed.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-06-30T22:23:50.813" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35679" PostTypeId="1" AcceptedAnswerId="35681" CreationDate="2015-06-30T23:04:10.347" Score="6" ViewCount="5067" Body="&lt;p&gt;I'm suspicious that it might be crayfish, which I'd think was insane (I still kind of do), if I hadn't found a dead one around  my house earlier this summer.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is that definitely what it is, or do I have to worry it might be wasps?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm located in Michigan.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sOQwt.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4261" LastEditorUserId="1590" LastEditDate="2015-07-01T08:32:38.093" LastActivityDate="2015-07-02T15:07:21.607" Title="Is this a crayfish hole? or wasp nest?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35680" PostTypeId="2" ParentId="35679" CreationDate="2015-07-01T00:51:36.210" Score="8" Body="&lt;p&gt;This is the nest of a cicada killer wasp, &lt;a href=&quot;https://en.wikipedia.org/wiki/Sphecius_speciosus&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Sphecius speciosus&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/P25Ll.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Harmless, solitary and  &lt;strong&gt;Cicada-killer&lt;/strong&gt; wasp holes are ½ half to 1-inch around with thinly scattered loose soil, usually where there is no grass. Cicada-killer burrows have a U-shaped mound of soil at the entrance. Adults emerge June/July.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Source: &lt;a href=&quot;http://allthedirtongardening.blogspot.com/2013/01/holes-in-yard-gophers-moles-voles.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;All the Dirt on Gardening blog&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the Wikipedia article linked above:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;this species occurs in the eastern and midwest U.S. and southwards into Mexico and Central America. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;so being in Michigan, you are certainly within the region in which the insect is found.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Parenthetically, also according to the blog from above: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Crayfish holes are 1-inch wide, 2-inches high and made of mud balls.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and the texture of that hole looks more even.&#xA;&lt;hr&gt;&#xA;Related Bio.SE question:  &lt;a href=&quot;https://biology.stackexchange.com/questions/20136/cicada-killer-behavior&quot;&gt;Cicada Killer Behavior&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="57" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-07-01T00:58:02.083" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35681" PostTypeId="2" ParentId="35679" CreationDate="2015-07-01T01:50:42.510" Score="8" Body="&lt;p&gt;It is indeed a crayfish hole (sometimes referred to as a &quot;snakehole&quot; in Michigan, even though it is not from a snake), albeit it has eroded from weather. If you have one in your yard, you likely have dozens, and they will range in their appearance due to soil and weather conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://kkyr.com/pattersons-pixels-9-results/&quot;&gt;Example 1&lt;/a&gt; and &lt;a href=&quot;http://wonderofcreation.org/ambling/on-crayfish-and-%E2%80%9Csnakeholes%E2%80%9D/&quot;&gt;Example 2&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerDisplayName="user16391" LastActivityDate="2015-07-01T01:50:42.510" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35682" PostTypeId="1" CreationDate="2015-07-01T03:23:41.150" Score="1" ViewCount="11798" Body="&lt;p&gt;My gym clothes retain an unpleasant musk even after washing them with warm water and detergent. I've experimented with soaking my gym clothes in salty water before washing them. My hypothesis is that the high salt concentration will cause plasmolysis in the cells of the bacteria. It has worked with mixed results; I'm never sure how much salt I should add or how long to soak the clothes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've looked for answers but I can only find papers with highly technical results.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(1) Can the odor-causing bacteria be killed with a salt treatment?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(2) If so, what concentration of table salt is needed?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(3) How long does the treatment need to last for plasmolysis to occur?&lt;/p&gt;&#xA;" OwnerUserId="16519" LastEditorUserId="9943" LastEditDate="2015-07-01T12:48:41.723" LastActivityDate="2017-02-22T19:03:08.837" Title="What concentration of table salt is needed to kill bacteria in sweaty gym clothes?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35683" PostTypeId="1" CreationDate="2015-07-01T05:30:09.847" Score="6" ViewCount="558" Body="&lt;p&gt;I want to transfect Adipose Derived stem cells using a clone of my own. My problem is that I get a lot of contamination (not only genomic, but due to the nature of the technique, I get undesired products I haven't been able to get rid of). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I was thinking about running a gel with my plasmid DNA samples and gel purify my desired bands. I don't know, however, if Ethidium Bromide contamination in my sample would be a problem or if a regular gel extraction kit gets rid of it.&lt;/p&gt;&#xA;" OwnerUserId="16521" LastEditorUserId="1306" LastEditDate="2015-07-01T11:10:12.790" LastActivityDate="2015-07-01T11:10:12.790" Title="How bad is ethidium bromide in your plasmid for downstream applications?" Tags="&lt;molecular-biology&gt;&lt;gel-electrophoresis&gt;&lt;cloning&gt;&lt;plasmids&gt;&lt;dna-isolation&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35684" PostTypeId="2" ParentId="35683" CreationDate="2015-07-01T05:46:42.283" Score="4" Body="&lt;p&gt;Purification and isolation of DNA bands by cutting them from agarose gel is commonplace &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22546956&quot; rel=&quot;nofollow&quot;&gt;(Lee &lt;em&gt;et al&lt;/em&gt;., 2012)&lt;/a&gt;. The purification step after excision of the band gets rid of most of the EtBr and other impurities. E.g., see the websites from &lt;a href=&quot;http://www.isogen-lifescience.com/pcr-clean-up&quot; rel=&quot;nofollow&quot;&gt;Isogen&lt;/a&gt; and &lt;a href=&quot;http://www.sigmaaldrich.com/life-science/molecular-biology/dna-and-rna-purification/minus-etbr-spin-columns.html&quot; rel=&quot;nofollow&quot;&gt;Sigma-Aldrich&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22546956&quot; rel=&quot;nofollow&quot;&gt;Lee &lt;em&gt;et al. J Vis Exp&lt;/em&gt; (2012); &lt;strong&gt;62&lt;/strong&gt;: e3923&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-01T06:03:24.690" LastActivityDate="2015-07-01T06:03:24.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35688" PostTypeId="2" ParentId="35671" CreationDate="2015-07-01T10:43:29.970" Score="1" Body="&lt;p&gt;The most common case like this is a prokaryotic mRNA, where polycistronic genes show up regularly.  &lt;a href=&quot;http://mol-biol4masters.masters.grkraj.org/html/Protein_Synthesis2-Prokaryotic_Mechanism_of_Synthesis.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;In that case the ribosomes are free to attach to the RNA and both genes are usually co-translated&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ejnp4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The proportion of translation between the two genes does vary depending on the affinity of the ribosome to the mRNA, which is partially determined by the ribosome binding site sequence.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If there is a lot of transcription activity on the mRNA, many ribosomes at once can translate any single ORF, as you can see in the micrograph above. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2015-07-01T10:43:29.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35689" PostTypeId="1" AcceptedAnswerId="35690" CreationDate="2015-07-01T11:37:44.777" Score="14" ViewCount="39006" Body="&lt;p&gt;So school has taught us that eukaryotes have DNA that is linear and inside of a membrane - called the nucleus. And that prokaryotes have circular DNA that is free floating inside of the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;We also know the pros and cons of both linear and circular DNA.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Are there organisms with circular DNA that also have a cell nucleus?&lt;/li&gt;&#xA;&lt;li&gt;Are there organisms with linear DNA that is also free-floating within the cell?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="1590" LastEditDate="2015-07-01T11:52:45.427" LastActivityDate="2018-11-27T14:18:49.943" Title="Linear and Circular DNA" Tags="&lt;dna&gt;&lt;eukaryotic-cells&gt;&lt;prokaryotic-cells&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35690" PostTypeId="2" ParentId="35689" CreationDate="2015-07-01T11:50:30.910" Score="13" Body="&lt;p&gt;Yes there are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1974809/&quot; rel=&quot;noreferrer&quot;&gt;prokaryotes with linear chromosomes&lt;/a&gt; (especially archaea). Eukayotic chromosomes are almost always linear but &lt;a href=&quot;http://www.nature.com/ng/journal/v20/n2/full/ng1098_203.html&quot; rel=&quot;noreferrer&quot;&gt;this&lt;/a&gt;, study reports that yeasts with a loss of function mutation in the &lt;em&gt;ATM&lt;/em&gt; homolog genes &lt;em&gt;TEL1&lt;/em&gt; and &lt;em&gt;rad3&lt;/em&gt;, form circular chromosomes as a consequence of lack of telomeres. Upon prolonged culture these yeasts were found to undergo mitosis but not meiosis. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-07-01T18:35:08.897" LastActivityDate="2015-07-01T18:35:08.897" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35692" PostTypeId="2" ParentId="35682" CreationDate="2015-07-01T12:14:16.100" Score="7" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Toxicity of salt depends on contact time. 50 g NaCl per liter kills nearly all bacteria in 2 days. 100 g NaCl/L may do a quite thorough job in 30 minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Body odor is caused by bacteria that feed on the fluids produced by the &lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/sweating-and-body-odor/basics/causes/con-20014438&quot; rel=&quot;nofollow noreferrer&quot;&gt;apocrine glands&lt;/a&gt;, mainly present under the arm pits and other areas with abundant hair follicles. Bacteria in the skin feed on the products of the apocrine glands and convert it into odorous compounds. &lt;a href=&quot;http://www.dermnetnz.org/bacterial/microorganisms.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Skin microfauna&lt;/a&gt; includes &lt;em&gt;Staphylococcus, Micrococcus, Corynebacterium, Dermabacter&lt;/em&gt; and others. As pointed out by others in the comments, treating your cloths against bacterial growth may not be the most efficient approach, as the bacteria are residents of the skin. Nonetheless, the following studies addressed the antimicrobial effects of salt.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A study using the gut bacterium &lt;em&gt;E.coli&lt;/em&gt; showed that survival in &lt;strong&gt;5% NaCl&lt;/strong&gt; (50 g NaCl per liter H&lt;sub&gt;2&lt;/sub&gt;O) was &lt;strong&gt;&amp;lt;0.01%&lt;/strong&gt;. In &lt;strong&gt;2% NaCl&lt;/strong&gt; survival survival was &lt;strong&gt;8%&lt;/strong&gt;. The contact time was &lt;em&gt;48 hours&lt;/em&gt; &lt;a href=&quot;http://aem.asm.org/content/8/4/247.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Carlucci and Pramer, 1958)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another study examined the effects of &lt;a href=&quot;https://en.wikipedia.org/wiki/Salinity#Definitions&quot; rel=&quot;nofollow noreferrer&quot;&gt;salinity&lt;/a&gt; on &lt;em&gt;E. coli&lt;/em&gt; using a shorter contact time of &lt;em&gt;30 minutes&lt;/em&gt;, and concluded that &lt;strong&gt;10% salinity killed 80%&lt;/strong&gt; of organisms &lt;a href=&quot;http://www.technicaljournalsonline.com/jers/VOL%20II/JERS%20VOL%20II%20ISSUE%20IV%20OCTOBER%20DECEMBER%202011/ARTICLE%209%20JERS%20VOLII%20ISSUE%20IV%20OCT%20DEC%202011.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Somani &lt;em&gt;et al&lt;/em&gt;., 2011)&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sea water, which has a &lt;a href=&quot;http://water.usgs.gov/edu/whyoceansalty.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;salinity of about 3.5%&lt;/a&gt; contains low numbers of bacteria &lt;a href=&quot;http://aem.asm.org/content/8/4/247.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Carlucci and Pramer, 1958)&lt;/a&gt;, suggestive of toxic concentrations of NaCl, the major salty constituent in sea water. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Although &lt;em&gt;E. coli&lt;/em&gt; has been associated with skin fauna and body odor, I must note that Gram negative gut bacteria as used in the two studies above may not be representative of the mainly Gram positive microfauna found on the skin &lt;a href=&quot;http://www.nature.com/jid/journal/v27/n2/full/jid195679a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Strauss &amp;amp; Kligman, 1956)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://aem.asm.org/content/8/4/247.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Carlucci and Pramer, &lt;em&gt;Am Soc Microbiol&lt;/em&gt; (1958)&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.technicaljournalsonline.com/jers/VOL%20II/JERS%20VOL%20II%20ISSUE%20IV%20OCTOBER%20DECEMBER%202011/ARTICLE%209%20JERS%20VOLII%20ISSUE%20IV%20OCT%20DEC%202011.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Somani &lt;em&gt;et al., J Eng Res Studies&lt;/em&gt; (2011): 40-43&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.nature.com/jid/journal/v27/n2/full/jid195679a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Strauss &amp;amp; Kligman, &lt;em&gt;J Invest Dermatol&lt;/em&gt; (1956); &lt;strong&gt;27&lt;/strong&gt;: 67–71&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2017-02-22T19:03:08.837" LastActivityDate="2017-02-22T19:03:08.837" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35693" PostTypeId="1" CreationDate="2015-07-01T12:47:40.333" Score="2" ViewCount="137" Body="&lt;p&gt;I am using 2D gel electrophoresis to visualize polyubiquitinated proteins. However, while I can see actin and heat shock protein using when appropriate antibodies, I cannot visualize them using anti-ubiquitin antibody. Could it be degradation problem? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I run isoelectric focusing at 200 V overnight (at least 18 hours) and 700 V the last 30 minutes. I am worried that I am applying more volts than needed, because the standard protocol is 200 V for 20 minutes, 450 V for 15 minutes, 750 V for 15 minutes, 2000 V for 30 minutes, but due to problems with the power unit I cannot do this.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am sure I have polyubiquitination because I use a drug that triggers polyubiquitinated protein accumulation inside the cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to add also that cells are collected by scraping in cold PBS and then they are placed in ice and the pellet is also collected at 4 degrees to prevent protein degradation. &lt;/p&gt;&#xA;" OwnerUserId="16214" LastEditorUserId="948" LastEditDate="2015-07-01T13:28:33.297" LastActivityDate="2015-07-02T02:26:21.370" Title="Why does my anti-ubiquitin antibody visualization not work on my PAGE gel?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;lab-techniques&gt;&lt;gel-electrophoresis&gt;&lt;western-blot&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35694" PostTypeId="2" ParentId="35689" CreationDate="2015-07-01T13:27:21.540" Score="17" Body="&lt;p&gt;Strictly speaking, all nucleated (eukaryotic) cells contain linear DNA. In addition to the nucleus, the mitochondria (which break down food molecules and create chemical energy) and chloroplasts (which facilitate photosynthesis) also have small stores of their own DNA and this DNA is circular. This adds weight to the hypothesis that these organelles were once prokaryotic cells that came to exist in symbiosis with early eukaryotes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is also cytoplasmic DNA free-floating in eukaryotic cells. These are also circular and normally contain short copies of chromosomal DNA sequences. Their function is not well understood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In prokaryotes, some species of spirochaetes and bacteria have been found with linear chromosomes. In addition, prokayrotes contain extra-chromosomal DNA called plasmids. Bacteria are able to pass plasmids from one to another and express the genes on them: this is an important source of the spread of antibiotic resistance genes through bacterial populations. Plasmids are also normally circular, but linear structures also exist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Cohen, Sarit; Andreas Houben; Daniel Segal (2008). &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18088310&quot; rel=&quot;nofollow noreferrer&quot;&gt;Extrachromosomal circular DNA derived from tandemly repeated genomic sequences in plants&lt;/a&gt;&quot;. The Plant Journal 53 (6): 1027–1034.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Hinnebusch J; Tilly K (1993). &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7934868&quot; rel=&quot;nofollow noreferrer&quot;&gt;Linear plasmids and chromosomes in bacteria&lt;/a&gt;&quot;. Molecular Microbiology. 10(5):917-22&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Finbarr Hayes (2003). &quot;Chapter 1 - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12904641&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Function and Organization of Plasmids&lt;/a&gt;&quot;. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5083" LastEditorUserId="47716" LastEditDate="2018-11-27T14:18:49.943" LastActivityDate="2018-11-27T14:18:49.943" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="35695" PostTypeId="2" ParentId="35672" CreationDate="2015-07-01T13:38:57.603" Score="1" Body="&lt;p&gt;There are controversial case reports about systemic absorption of paraffin used for constipation. These reports mention systemic effects of paraffin absorption and one of them report liquid paraffin accumulations in&#xA;abdominal visceral organs. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1718886/pdf/v085p00121.pdf&quot; rel=&quot;nofollow&quot;&gt;full text&lt;/a&gt; article about paraffin) &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;https://www.medicines.org.uk/emc/medicine/25338&quot; rel=&quot;nofollow&quot;&gt;Liquid paraffin&lt;/a&gt; is indigestible and is absorbed only to a limited&#xA;  extent following ingestion.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;+&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As inert substances the ingested mineral oils mostly are excreted&#xA;  intact in feces and to some degree in urine. However, some absorption&#xA;  form the small intestine has been observed (Stryker 1941). Using&#xA;  radiolabeled mineral oil, it was established that the amount absorbed&#xA;  in rat was appr. 1.5 % (Ebert  et al. 1966).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;  (&lt;a href=&quot;http://www.cepi.org/system/files/public/documents/positionpapers/recycling/2011/summary-20111125-00001-01-E.pdf&quot; rel=&quot;nofollow&quot;&gt;full text article&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-07-01T13:47:47.067" LastActivityDate="2015-07-01T13:47:47.067" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35696" PostTypeId="1" CreationDate="2015-07-01T13:56:53.190" Score="1" ViewCount="446" Body="&lt;p&gt;I would like to design a number of arbitrary degenerate primers (primers with variable bases, e.g. &lt;code&gt;NGATWGCTSATNGC&lt;/code&gt;) for a &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14501069&quot; rel=&quot;nofollow&quot;&gt;TAIL-PCR&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to be able to specify the following parameters for the design function:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Annealing temperature (ideally 44°C)&lt;/li&gt;&#xA;&lt;li&gt;Degeneracy (how many variations of the AD primer there are (ideally 128 or 256)&lt;/li&gt;&#xA;&lt;li&gt;Binding frequency on (mouse) genome (ideally 1/3000) - though this may be contingent on the degeneracy, and vice-versa.&lt;/li&gt;&#xA;&lt;li&gt;Non-binding area (of course I would not like any variation of the primer to bind to the known-sequence area in between my specific primers and the unknown area which I want to sequence)&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Any ideas of any tools that can help me with the above steps? For Primer design I have used &lt;a href=&quot;http://emboss.bioinformatics.nl/cgi-bin/emboss/eprimer3&quot; rel=&quot;nofollow&quot;&gt;eprimer3&lt;/a&gt; thus far (with invariably satisfactory results) - but it seems to not support the concept of arbitrary degenerate primers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ideally, if I had a function which could sort out the first of the above criteria, I could use Biopython and BLAST to script the rest myself. Though the binding frequency would take hours if not a day or two, for BLAST to determine it. It would greatly help if anybody already wrote something more elaborate for this. &lt;/p&gt;&#xA;" OwnerUserId="4795" LastEditorUserId="3340" LastEditDate="2015-07-02T08:47:12.660" LastActivityDate="2015-07-03T06:27:56.643" Title="Design arbitrary degenerate primers (with non-binding criteria)" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;pcr&gt;&lt;sequence-analysis&gt;&lt;primer&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35698" PostTypeId="1" CreationDate="2015-07-01T16:24:24.747" Score="2" ViewCount="106" Body="&lt;p&gt;I often dream long extended dreams.  Sometimes I wonder if the timeline of the story of my dream occurs compressed, in a moment, or other times extended slowly over a long duration.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Is there any way to scientifically detect this, and how would it be accomplished?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Are there any prior examples of this study being performed?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="5399" LastActivityDate="2015-07-01T16:24:24.747" Title="Is perceived time compressed or expanded while dreaming? (or does it match reality)" Tags="&lt;brain&gt;&lt;perception&gt;&lt;dreaming&gt;" AnswerCount="0" CommentCount="5" ClosedDate="2015-07-01T18:45:24.117" ContentLicense="CC BY-SA 3.0" />
  <row Id="35699" PostTypeId="1" CreationDate="2015-07-01T16:26:59.767" Score="4" ViewCount="384" Body="&lt;p&gt;Does anyone know the name of the bird in the pictures? It was found in the south of Spain in the month of June. (it is certainly neither a house sparrow nor a swallow nor a robin). Thanks for the help!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/k7q10.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gFyze.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16534" LastEditorUserId="6561" LastEditDate="2015-07-01T18:25:43.597" LastActivityDate="2017-11-17T12:47:47.890" Title="What is the name of this bird?" Tags="&lt;species-identification&gt;&lt;ornithology&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35703" PostTypeId="2" ParentId="19396" CreationDate="2015-07-01T22:00:43.510" Score="-1" Body="&lt;p&gt;No and yes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you perceive as domestication has a lot to do with intelligence or even social intelligence of animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Common fish is too stupid (from our point of view), to have any social bond with humans. Mammals are usually much closer and have similar structure of intelligence and patterns of behaviour.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That only if you consider domestication as something more and not just human utilization as with breeding fish for food, spiders and snakes for fun (or even snakes for rat-catching, as some African tribes did according to wiki).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So not all animals could be domesticated, they need certain qualities, mostly connected (or we are connecting them) with intelligence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, once you look at mammals, which usually have enough social intelligence, you could breed them into domestic animals. It would be hard, there would usually be no other purpose than &quot;We can, so we do&quot;, but you could. There were various experiments. One is famous Russian experiment with foxes, another is infamous Hitler's experiment with cows (experiment with bringing back Aurochs, Heck cattle, cows were &quot;undomesticated&quot;). There, in controlled environment, true genetic plasticity of behaviour were showed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that as other posters wrote, this is theoretical. In nature and by natural means, domestication was always hindered by immediate usefulness (not even potential future usefulness). Most of domesticated animals are highly social in their natural form and not very aggressive. Even big cats are quite close. Tigers not as much as cheetahs, which were traditionally bred (or kept as pet) from ancient times.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;In short, can you theoretically get any animal to have heritable traits?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;All animals have heritable traits. That's genetics.&lt;/p&gt;&#xA;" OwnerUserId="16539" LastActivityDate="2015-07-01T22:00:43.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35704" PostTypeId="1" CreationDate="2015-07-01T22:19:02.947" Score="1" ViewCount="494" Body="&lt;p&gt;Which of the following assays can be used to determine whether cell death specifically due to apoptosis has occurred in a given cell sample? Choose all that apply. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;WST-1 Assay &lt;/li&gt;&#xA;&lt;li&gt;Caspase Colorimetric Assay &lt;/li&gt;&#xA;&lt;li&gt;Trypan Blue Staining &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Which of the following assays can provide direct information about the plasma membrane integrity and/or morphological features of apoptotic cells? Choose all that apply &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Annexin V-FITC / Propidium Iodide staining. &lt;/li&gt;&#xA;&lt;li&gt;WST-1 Assay &lt;/li&gt;&#xA;&lt;li&gt;Caspase Colorimetric Assay &lt;/li&gt;&#xA;&lt;li&gt;Trypan Blue Staining &lt;/li&gt;&#xA;&lt;li&gt;Wright Staining&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;My knowledge is very limited with these assays. I know Trypan Blue is used to measure a cell's viability, with dead cells stained blue. Wright Staining is used to study the cell's morphology and makes fragmentation visible. Caspase color and the WST assay seem very similar to me. Both measure cell viability with spectrophotometry.&lt;/p&gt;&#xA;" OwnerUserId="16542" LastEditorUserId="948" LastEditDate="2015-07-03T15:19:48.090" LastActivityDate="2015-07-03T15:19:48.090" Title="Choosing the best assay for my experiment?" Tags="&lt;cell-biology&gt;&lt;experimental-design&gt;&lt;apoptosis&gt;&lt;staining&gt;&lt;assay-development&gt;" AnswerCount="1" CommentCount="6" ClosedDate="2015-07-07T01:40:38.327" ContentLicense="CC BY-SA 3.0" />
  <row Id="35705" PostTypeId="1" CreationDate="2015-07-01T22:54:48.877" Score="2" ViewCount="2843" Body="&lt;p&gt;I sometimes think about just how huge humans are in comparison to most animals. Even compared to a squirrel, which is really a pretty large organism in the grand scheme of things, humans are hulking giants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know humans are classified as &lt;a href=&quot;https://en.wikipedia.org/wiki/Megafauna&quot; rel=&quot;nofollow&quot;&gt;megafauna&lt;/a&gt;, but we're neither the smallest nor the largest animals in that group. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How many animal species currently exist where the average adult individual is more massive than the average adult human?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources that cite other measures of size, like height or length, might be useful, but I would expect the focus to be on mass.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously, new species are being discovered all the time, and we don't have exhaustive measurements for every species, but considering how few megafauna there are, I would expect a fairly accurate estimate to be possible.&lt;/p&gt;&#xA;" OwnerUserId="16543" LastEditorUserId="16543" LastEditDate="2015-07-02T16:30:23.167" LastActivityDate="2015-07-02T16:30:23.167" Title="How many animal species are larger than humans?" Tags="&lt;zoology&gt;" AnswerCount="0" CommentCount="12" ClosedDate="2015-07-02T06:37:48.910" ContentLicense="CC BY-SA 3.0" />
  <row Id="35706" PostTypeId="1" AcceptedAnswerId="35707" CreationDate="2015-07-01T22:59:19.097" Score="3" ViewCount="4764" Body="&lt;p&gt;I recently saw this beetle while on a trip in central Texas, USA (in a rural area just before sundown). The body was about 2-3 inches long (compare to nearby chair leg and floorboards) and had a long body. It was very vivid green, and its upper legs were very bright orange (which made me wonder if this is aposematism). Its antennae had very uniform half-circle arcs (instead of the uneven parabolic shape often seen in cockroaches and similar common insects) and didn't seem to bend besides being rotated ~5 degrees up and down. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It carried itself pretty high off the ground, perhaps half an inch between the belly and ground-level. It seemed to move fairly fast, but not as fast as a cockroach. It didn't fly in the few minutes I observed, and didn't seem like it could fly since the shell appeared solid, but I might have mistaken well-fitting sheaths for fused ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xTvgx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the most likely species? Is it poisonous?&lt;/p&gt;&#xA;" OwnerUserId="540" LastActivityDate="2015-07-01T23:08:33.407" Title="Beetle with long, slender iridescent green body and orange legs" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35707" PostTypeId="2" ParentId="35706" CreationDate="2015-07-01T23:08:33.407" Score="7" Body="&lt;p&gt;I'm going to guess it's an Plinthocoelium suaveolens, based on the image found &lt;a href=&quot;http://bugguide.net/node/view/307334/bgimage&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;, which I show below:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/iYEiS.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found this link through a Texas beetle page &lt;a href=&quot;http://texasento.net/TXBycidPix.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; and is the best I can do from the image provided.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2015-07-01T23:08:33.407" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35708" PostTypeId="2" ParentId="35693" CreationDate="2015-07-01T23:50:16.267" Score="2" Body="&lt;p&gt;There are stable ubiquitinated proteins in mammalian cell lysates even if active proteosomes exist in cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, you might want to make sure that the antibody is applicable to WB. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then, you would ask if your WB system using the antibody works. You could optimize the condition using just 1D SDS-PAGE followed by WB. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the condition for isoelectric focusing, when focusing is completed, you get very high electric resistance, so you might want to monitor current after you change the voltage to 700 V. Current decreases gradually, and get stable at some level. But I do not know you can see stabilization by 700 V.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You also might want to check if major proteins such as actin form spots nicely at the expected pI. That could tell if forcusing is completed roughly.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-07-02T02:26:21.370" LastActivityDate="2015-07-02T02:26:21.370" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35710" PostTypeId="2" ParentId="35704" CreationDate="2015-07-02T02:41:36.573" Score="0" Body="&lt;p&gt;Necrotic cells could be trypan blue positive. &lt;a href=&quot;http://www.biocompare.com/Product-Reviews/40930-Cell-Proliferation-Reagent-WST-1-From-Roche-Applied-Science/&quot; rel=&quot;nofollow&quot;&gt;WST-1 Assay could reflect cell number by measuring mitochondrial dehydrogenase&lt;/a&gt;, therefore, you could not know how many cells die in dishes. When you define apoptosis in your experiment as caspase dependent cell death, measuring caspase activity is the best.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PS&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trypan Blue Staining actually is a method to see membrane integrity.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-07-02T05:44:48.893" LastActivityDate="2015-07-02T05:44:48.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35712" PostTypeId="1" CreationDate="2015-07-02T06:06:18.507" Score="0" ViewCount="1397" Body="&lt;p&gt;Well we all learned at school the classic evolutionarily theory   &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;From:          To: &#xA;fish           amphibian&#xA;amphibian      reptile&#xA;reptile        mammal&#xA;reptile        bird&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;But what always interested me:&lt;br&gt;&#xA;What about invertebrates?&lt;br&gt;&#xA;Do they also have some evolutionary table like vertebrates or was there evolution never that interesting to begin with?&lt;br&gt;&#xA;I can roughly imagine that there are giant evolutionary gaps between an insect and a jellifish but is there any common ancestor of all of them? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question has essentially two parts:&lt;br&gt;&#xA;1. What is the common ancester between vertebrates, arthropods and molluscs&lt;br&gt;&#xA;2. Is there an evolutionary Tree for the last two like for the vertebrates&lt;/p&gt;&#xA;" OwnerUserId="16546" LastEditorUserId="1590" LastEditDate="2015-07-02T07:36:40.367" LastActivityDate="2015-07-03T15:13:59.807" Title="Evolution of insects, spiders and jellyfish" Tags="&lt;evolution&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35713" PostTypeId="1" AcceptedAnswerId="35716" CreationDate="2015-07-02T06:47:45.617" Score="11" ViewCount="9341" Body="&lt;p&gt;Almost everyone nowadays wants that nice summer tan, but what exactly is going on beneath the skin? I've heard a few different theories about tanning - such as a tan is nothing but the pigmentation in your cells burning, but is this true?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My questions:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;What exactly is happening to our skin as we tan?&lt;/li&gt;&#xA;&lt;li&gt;Are pigments being burned (like I was told in school), or is pigment being produced by the cells. ?&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Bonus related question:&lt;/strong&gt; &#xA; &lt;a href=&quot;https://biology.stackexchange.com/questions/35718/why-do-some-people-burn-and-others-tan&quot;&gt;Why do some people burn and others tan?&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Bonus related question:&lt;/strong&gt; &lt;a href=&quot;https://biology.stackexchange.com/questions/35719/how-does-our-tan-disappear&quot;&gt;https://biology.stackexchange.com/questions/35719/how-does-our-tan-disappear&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-07-02T15:34:58.653" Title="What is happening when we get a tan?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;tissue&gt;&lt;tissue-repair&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35714" PostTypeId="1" CreationDate="2015-07-02T07:34:55.227" Score="0" ViewCount="564" Body="&lt;p&gt;I created an algorithm to generate SNPs for random people of different descents - based on HapMap data. While this works good, there is something else I want to take into consideration. So if a SNP has a MAF of 0.01, with an LD of 1, the generated results will, in most cases be sufficient. This is not the case for a MAF of 0.4 and LD of 0.8.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The HapMap LD files have, besides the LD data, also LOD and D-prime. The question is, is there a set of parameters so that as much of the relevant LDs are filtered out of the total set?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I want to filter this out, since, for example, there are LDs described with a value of 0, or an LOD &amp;lt; 1, and problematic D-primes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Trying to rephrase the question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given a huge set of LD information (250GB), which are not filtered on statistical power, I want to make a subselection of LD information that are 'relatively' descriptive of the link with respect to another SNP. So I need to have a set of parameters to filter the LD information from HapMap. Of which possible values are LD, LOD, and D-prime.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Eyeballing the LD dataset, it doesn't gives a good instinctive boundary. A problem with using the data as is, is that both the D' as LOD can be both high and low. I know the parameters have an interdependence, but not a one-to-one mapping. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anybody have experience in filtering non-descriptive LD values from (for instance) the HapMap LD dataset? &lt;/p&gt;&#xA;" OwnerUserId="16548" LastEditorUserId="16548" LastEditDate="2015-07-03T06:19:01.587" LastActivityDate="2015-07-03T06:19:01.587" Title="Cut-off values for LD, LOD and D-prime as algorithmic input" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;snp&gt;&lt;genetic-linkage&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35715" PostTypeId="2" ParentId="35713" CreationDate="2015-07-02T07:50:54.623" Score="4" Body="&lt;p&gt;First, one should mention types of skin: skin type defines how the person will tan - &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xrKTh.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/oMfmg.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, the solar radiation (UV) absorbed by sun defines the amount of melanin produced by melanocytes of the skin to protect the skin = melanogenesis (which in turn depends on skin type).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When the solar exposure diminish, the natural repair processes causes melanocytes to remove excessive amounts of melanin. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As mention by WYSIWYG, the question too broad, you can continue your education via &lt;a href=&quot;https://en.wikipedia.org/wiki/Sun_tanning&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-07-02T07:55:19.017" LastActivityDate="2015-07-02T07:55:19.017" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35716" PostTypeId="2" ParentId="35713" CreationDate="2015-07-02T08:04:43.853" Score="13" Body="&lt;p&gt;When our skin is exposed to the sun, this can cause some damage in the upper layers of skin. This activates DNA damage repair and also induces signalling towards the melanocytes (which produce the pigment). Signalling means the excretion of signalling molecules (mostly alpha-Melanocyte stimulating hormone, aMSH) which binds to the MC1R receptor (melanocortin 1 receptor) on the surface of the melanocyte (the cell which produces the pigment) and induces (or increases) the production of melanin. The melanin is then transferred in the melanosomes to the adjacent keratinocytes, which are then better protected from the sun. This figure (from this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25414302&quot; rel=&quot;nofollow noreferrer&quot;&gt;article&lt;/a&gt;) illustrates this process nicely:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JFkDo.jpg&quot; alt=&quot;diagram of UV effects on the cellular level&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Short term tans (the fast reaction) are based on the changed distribution of melanosomes (granules containing pigment) from the melanocytes to keratinocytes. Longer term suntans are caused by increased pigmentation in the skin as a reaction to the UV exposure by the accumulation of melanin and by the burning of cells. So it is no wonder that it looks like increased pigmentation, it really is. People tan differently because of their genetic background. This influences their ability to react to sun exposure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is relatively little known about the degradation of the melanosomes (the granules containing the melanin). What is known is that they are degraded in the lysosome, and that the melanin is most likely degraded through oxidation. There happens to be a permanent turnover of the melanosomes, and when the body is producing fewer new melanosomes than are degraded, your skin will get lighter again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22404235&quot; rel=&quot;nofollow noreferrer&quot;&gt;Shining light on skin pigmentation: the darker and the brighter side&#xA;of effects of UV radiation.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/4036/fgm9a2k9_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Melanocyte biology and skin pigmentation.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.directupload.net/file/d/4036/agomik2j_pdf.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Melanosome Degradation: Fact or Fiction&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastEditorUserId="9829" LastEditDate="2015-07-02T15:34:58.653" LastActivityDate="2015-07-02T15:34:58.653" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35717" PostTypeId="2" ParentId="35696" CreationDate="2015-07-02T08:35:47.887" Score="1" Body="&lt;p&gt;If you already know the basic sequence i.e. the fixed regions in the primer; for e.g. the known nucleotides in the sequence -  &lt;code&gt;NGATWGCTSATNGC&lt;/code&gt;, then you can implement your algorithm like this:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Fix the max length of the primers. Lets say 20nt.&lt;/li&gt;&#xA;&lt;li&gt;Generate all combinations of primers (20nt): that is pretty straightforward. You will have &lt;br&gt; &lt;strong&gt;4&lt;sup&gt;N&lt;/sup&gt; × 2&lt;sup&gt;(R+Y+S+W+K+M)&lt;/sup&gt; × 3&lt;sup&gt;(B+D+V+H)&lt;/sup&gt;&lt;/strong&gt; number of combinations, where each alphabet denotes number of such instances. Chek &lt;a href=&quot;http://www.bioinformatics.org/sms/iupac.html&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; site for the nucleotide codes. &lt;/li&gt;&#xA;&lt;li&gt;Calculate the Tm of the primer-template pairs. UNAfold has a nucleotide hybridization Tm calculator. You can specify parameters like salt concentration etc. There are other such tools too. These can be run on the commandline. &lt;/li&gt;&#xA;&lt;li&gt;Discard all primers have Tm below the acceptable limit.&lt;/li&gt;&#xA;&lt;li&gt;For those that exceed the acceptable Tm, keep dropping a base from the 3' until the Tm reaches within the range.&lt;/li&gt;&#xA;&lt;li&gt;If primer length goes below 14nt then discard the primer.&lt;/li&gt;&#xA;&lt;li&gt;Now with all these selected primers check for parameters like self hybridization, GC clamp etc (OPTIONAL). You can use &lt;a href=&quot;http://primer3.ut.ee/primer3web_help.htm&quot; rel=&quot;nofollow&quot;&gt;primer3&lt;/a&gt; for these purposes by running it on the &lt;code&gt;primer_check&lt;/code&gt; mode.&lt;/li&gt;&#xA;&lt;li&gt;Download the &lt;code&gt;nr/nt&lt;/code&gt; BLAST database.&lt;/li&gt;&#xA;&lt;li&gt;Adjust BLAST parameters for short nucleotide search: Decrease the word length, increase e-value cutoff etc (See &lt;a href=&quot;https://www.biostars.org/p/47203/&quot; rel=&quot;nofollow&quot;&gt;this biostar post&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/blast/html/BLASThomehelp.html&quot; rel=&quot;nofollow&quot;&gt;BLAST help&lt;/a&gt;).&lt;/li&gt;&#xA;&lt;li&gt;BLAST your primers against the database in &lt;code&gt;plus-minus&lt;/code&gt; mode. &lt;/li&gt;&#xA;&lt;li&gt;Worry only about cases where there is significant alignment at the 3' of the primer as only these can cause extension. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;These instructions can be automated using any language or shell script. &#xA;&lt;hr&gt;&#xA;&lt;em&gt;Questions on script writing would be off-topic in this site. You can ask specific doubts about coding in stackoverflow.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-07-03T06:27:56.643" LastActivityDate="2015-07-03T06:27:56.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35718" PostTypeId="1" AcceptedAnswerId="35722" CreationDate="2015-07-02T08:56:38.847" Score="2" ViewCount="1315" Body="&lt;p&gt;Connected to &lt;a href=&quot;https://biology.stackexchange.com/questions/35713/what-is-the-biology-of-tanning&quot;&gt;What is happening when we get a tan?&lt;/a&gt; - Why do some people burn while other people tan?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Very pale people tend to just burn while other people tan very nicely, what causes this difference? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I assume it has something to do with pigmentation - so what is the pigmentation in our skin actually doing in order to protect us from getting a sunburn?&lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-07-02T09:48:49.470" Title="Why do some people burn and others tan?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;&lt;tissue&gt;&lt;tissue-repair&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35721" PostTypeId="2" ParentId="35713" CreationDate="2015-07-02T09:21:44.977" Score="5" Body="&lt;p&gt;Some additional details on the same lines as Chris' answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799903/&quot; rel=&quot;nofollow&quot;&gt;Coelho et al.&lt;/a&gt; have studied the short and long term effects of UV on human skin and they report that there are different stages of tanning:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Immediate pigment darkening: happens in a few minutes and persists for some hours. It is most probably due to melanosome redistribution and melanin oxidation by UV. &lt;/li&gt;&#xA;&lt;li&gt;Persistent pigment darkening: happens in a few hours and can persist for days. It happens because of new melanin synthesis in the epidermis.&lt;/li&gt;&#xA;&lt;li&gt;Delayed pigmentation: happens in a few days and persists for weeks. It results from &quot;prolonged increases in melanin content&quot;.&lt;/li&gt;&#xA;&lt;li&gt;Long-lasting pigmentation:  persists fore more than 9 months after the first UV exposure. The mechanisms underlying this response are not very clear.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;IFN$\gamma$ signalling is involved in inhibition of melanogenesis and apoptosis of melanocytes &lt;sup&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3926048/&quot; rel=&quot;nofollow&quot;&gt;[1&lt;/a&gt;,&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25721262&quot; rel=&quot;nofollow&quot;&gt;2]&lt;/a&gt;&lt;/sup&gt;. This is one possible pathway of detanning. This happens in the order of days.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-07-02T09:26:57.537" LastActivityDate="2015-07-02T09:26:57.537" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35722" PostTypeId="2" ParentId="35718" CreationDate="2015-07-02T09:37:44.250" Score="3" Body="&lt;p&gt;There are two things happening: First melanin absorbs the energy from the UV radiation and releases it as infrared energy and thus protects the cells in the skin. This happens in all people, the deeper the skin color is, the better is the protection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is different between people is the amount of pigment they produce, the number of melanocytes is approximately the same. This depends on their genetic backgroud and is influenced by mutations in the pigment production pathway. As this is relatively complex, there are numerous positions which can influence the ability to tan, so I will only name a few.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The rate limiting enzyme for the pigmentation is &lt;a href=&quot;https://en.wikipedia.org/wiki/Tyrosinase&quot; rel=&quot;nofollow&quot;&gt;Tyrosinase&lt;/a&gt; which catalyzes the first step of the melanin biosynthesis and oxidizes the amino acid tyrosine into DOPA. Without tyrosinase humans are not able to make any pigment at all which causes albinism. This is pretty drastic and doesn't happen too often. See reference 1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other possibilities are mutation in the signalling towards pigmentation, more specifically mutations in the MC1R gene which encodes on of the receptors. These mutations affect the ability to tan and are associated with red hair color, pale skin and freckles (most of the red-haired people carry at least one mutation in their MC1R gene). See reference 2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then there are mutations in the tyrosinase gene, which results in an enzyme with a lower processing rate. Because of this, less pigment can be made as the amount of materials is limited. See references 3 and 4.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The diversity of the human pigmentation is influenced by all these (and much more) genes. Have a look at references 5 and 6 for details.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;References:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7886000&quot; rel=&quot;nofollow&quot;&gt;Analysis of tyrosinase mutations associated with tyrosinase-related&#xA;oculocutaneous albinism (OCA1).&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18484624&quot; rel=&quot;nofollow&quot;&gt;Red hair is the null phenotype of MC1R.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jbc.org/content/275/11/8169.full.html&quot; rel=&quot;nofollow&quot;&gt;Mutations at Critical N-Glycosylation Sites Reduce Tyrosinase&#xA;Activity by Altering Folding and Quality Control&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.jbc.org/content/267/33/23707.short&quot; rel=&quot;nofollow&quot;&gt;Mutational mapping of the catalytic activities of human tyrosinase.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://hmg.oxfordjournals.org/content/18/R1/R9&quot; rel=&quot;nofollow&quot;&gt;Molecular genetics of human pigmentation diversity&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://hmg.oxfordjournals.org/content/15/suppl_2/R176&quot; rel=&quot;nofollow&quot;&gt;The genetic architecture of normal variation in human pigmentation:&#xA;an evolutionary perspective and model&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-07-02T09:37:44.250" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35724" PostTypeId="1" AcceptedAnswerId="35804" CreationDate="2015-07-02T11:52:45.450" Score="3" ViewCount="116" Body="&lt;p&gt;There are many &lt;a href=&quot;http://web.expasy.org/protscale/&quot; rel=&quot;nofollow&quot;&gt;hydrophobicity scales&lt;/a&gt; for protein analysis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Broadly, I gather the differences between them are from the experimental method to acquire the data and the normalisation (or lack thereof) of the data.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To detect/predict transmembrane segments one method is to use a window of 19-20 of these residue scales to detect a region of hydrophobicity above a threshold. The Eisenberg &lt;em&gt;et al.&lt;/em&gt; scale is used by &lt;a href=&quot;http://www.uniprot.org/help/transmem&quot; rel=&quot;nofollow&quot;&gt;uniprot&lt;/a&gt; for example.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Uniprot don't seem to explain their choice of using the Eisenberg &lt;em&gt;et al.&lt;/em&gt; scale.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why might one use a certain scale over another when predicting transmembrane segments?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2015-07-02T11:59:15.777" LastActivityDate="2015-07-06T03:26:28.670" Title="Which hydrophobicity scales are best for detecting transmembrane regions, and why?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;biophysics&gt;&lt;cell-membrane&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35726" PostTypeId="2" ParentId="35712" CreationDate="2015-07-02T13:24:52.397" Score="1" Body="&lt;p&gt;You have to be very careful when saying what evolved into what.&#xA;In fact you can only say that e.g. ancestors of modern amphibians evolved from the ancestors of modern fish.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ad. 1 Have a look at this simplified picture of &lt;a href=&quot;https://muttslikeme.files.wordpress.com/2009/07/treeolife3.jpg%3Fw%3D500%26h%3D600&quot; rel=&quot;nofollow&quot;&gt;the evolutionary tree of life&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ad. 2 Yes all living organism including plants, bacteria, fungi, and animals can be placed on one evolutionary tree goverened by the same principles of evolution&lt;/p&gt;&#xA;" OwnerUserId="733" LastActivityDate="2015-07-02T13:24:52.397" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35727" PostTypeId="1" CreationDate="2015-07-02T13:48:39.237" Score="0" ViewCount="123" Body="&lt;p&gt;If water has a low salt content, it hydrates us. When water has too high salt concentration, like sea water, it drains water out of us instead when we drink it. At what salt concentration would water leave us completely unaffected?&lt;/p&gt;&#xA;" OwnerUserId="6433" LastActivityDate="2015-07-02T22:28:25.350" Title="At what saltiness will water simply pass through us?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35729" PostTypeId="1" AcceptedAnswerId="35736" CreationDate="2015-07-02T14:36:59.363" Score="6" ViewCount="3695" Body="&lt;p&gt;Consumption of mustard (spicy English Mustard), wasabi and horseradish based food dressings usually result in a burning, tingling or freezing sensation in the brain/scalp and nostrils as the vapour goes through the nasal cavity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read somewhere, the checmical which gives the burning sensation is &lt;strong&gt;isothyocyanates&lt;/strong&gt;. And some of the posts roughly mention about sinuses being agitated due to this chemical vapour.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How to explain this from biochemical and biology aspect? e.g. What sort of a cell reaction, if any receptors involved etc. (Appreciate an answer that is &lt;a href=&quot;https://youtu.be/R8JMfbYW2p4&quot;&gt;similar to &lt;strong&gt;the type of explanation&lt;/strong&gt; here.&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="8709" LastEditorUserId="8709" LastEditDate="2015-07-04T04:31:38.667" LastActivityDate="2015-07-04T04:31:38.667" Title="What is the biochemical explanation for tingling and burning sensation in brain due to certain food?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;sensation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35730" PostTypeId="2" ParentId="35712" CreationDate="2015-07-02T14:46:39.327" Score="4" Body="&lt;p&gt;Welcome to Biology.SE&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Answering your question fully will require to write a whole book. Evolutionary Biology is a big field and I would recommend that your take some time to get an introduction (slightly more advanced than what you received in school). I am suggesting you take advantage of &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/evo_01&quot; rel=&quot;nofollow noreferrer&quot;&gt;this free online resource&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am briefly making comments and answering your question(s) below. They may be hard (or easy, I don't know) to understand but for more info you should really get to the above free online resource.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Species A evolved from species B&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution did not make mammals out of reptiles, mammals are reptiles. Evolution did not make birds out of reptiles, birds are reptiles as well (I am using here the phylogenetic definition of reptiles (&lt;em&gt;Reptilia&lt;/em&gt;), more info &lt;a href=&quot;https://biology.stackexchange.com/questions/35370/if-dinosaurs-could-have-feathers-would-they-still-be-reptiles&quot;&gt;there&lt;/a&gt;). It is wrong to think of any two extant species as one having evolved from the other one. But it is correct to understand how closely related are two extant species. It is also correct to make predictions about how the most recent common ancestor (MRCA) look like and it is true the the MRCA might look more like one of its descendents than like another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We talk about clade as a lineage including many species. In these terms both any lizard species and any given bird species belong to the same clade, the &lt;em&gt;Reptilia&lt;/em&gt;, they are both reptiles. They are also both vertebrates (&lt;em&gt;Vertebrata&lt;/em&gt;) and animals (&lt;em&gt;Metazoa&lt;/em&gt;) and eukaryotes (&lt;em&gt;Eukaryota&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the statements of the kind &quot;mammals evolved from reptiles&quot; are very misleading the statement &quot;amphibians evolved from reptiles&quot; is simply wrong. The MRCA of reptiles and amphibians was not a reptile (neither an amphibian), it was a tetrapoda (vertebrate).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;I can roughly imagine that there are giant evolutionary gaps between an insect and a jellyfish but is there any common ancestor of all of them?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any two species on earth have a common ancestor. The universal common ancestor, that is the common ancestor that any living thing (bacteria, plants, lizard, human, fungi, jellyfish, Archea, etc...) is called LUCA (Last Universal Common Ancestor). So yes, jellyfish and insects have a common ancestor. LUCA is one of them. Their MRCA is the same guy as the MRCA between jellyfish and you, as insects and primates are more closely related than are insects and jellyfish. This MRCA is an animal (a &lt;em&gt;metazoa&lt;/em&gt;) and therefore is also a eukaryote (&lt;em&gt;Eukaryota&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do they also have some evolutionary table like vertebrates or was there evolution never that interesting to begin with?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Evolution occurs in every single living population. So yes, evolution occurs in jellyfish as it occurs in insects. The clade of jellyfish contains several thousands of species (most of them belong to the clade &lt;em&gt;Hydrozoa&lt;/em&gt;). There are almost a million species of insects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are just a few fun facts that come to my mind when I think about jellyfish:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Some species have tentacles, some don't.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Some species have &lt;em&gt;alternance of generation&lt;/em&gt; (a given individual is either a sticking thing on the ground while its descendent is swimming).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Size of jellyfish vary wildly&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And a few fun facts about insects:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Some have evolved 3 pairs of wings to fly (we think it evolved from gills but it might have evolved from the exoskeleton as well).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Some live in water, some not, some live in water in the larvea stage and not in their adult stage.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;They have all sorts of diet&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;When flight evolved at first, they had 3 pairs of wings. All extant species (who are descendents of this species that evolved flight) have now lost at least one pair of wings, the one closest to the head.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Some species have lost flight.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Some species have lost a second pair of wings (&lt;em&gt;diptera&lt;/em&gt;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Some have evolved crazy mimetism and defense mechanism from the developmental pathway of the third pair of wings.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Eusociality (which is arguably one of the most mind boggling things in evolutionary biology) has evolved several times in insects.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Some species have sex that is determined the ploidy (number of sets of chromosomes) level (it is the case in many eusocial species).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;1. What is the common ancestor between vertebrates, arthropods and molluscs?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can explore the tree of life by yourself on &lt;a href=&quot;http://tolweb.org/tree/&quot; rel=&quot;nofollow noreferrer&quot;&gt;tolweb.org&lt;/a&gt;. Arthropods and molluscs are more closely related than any of them are to vertebrates. The MRCA of vertebrates, arthropods and molluscs was a &lt;em&gt;Bilateria&lt;/em&gt; (animal, eukaryote). You can see this bifurcation &lt;a href=&quot;http://tolweb.org/Animals/2374&quot; rel=&quot;nofollow noreferrer&quot;&gt;here on tolweb.org&lt;/a&gt;. I'd recommend to explore a bit this tree of life, it is pretty fun to do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;2. Is there an evolutionary tree for the last two like for the vertebrates?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, see above.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;BTW, I noticed that you talk about spiders in your title but not in your post. You'll find the spiders &lt;a href=&quot;http://tolweb.org/Arachnida/2536&quot; rel=&quot;nofollow noreferrer&quot;&gt;here on tolweb.org&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.130" LastActivityDate="2015-07-03T15:13:59.807" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35734" PostTypeId="1" AcceptedAnswerId="35741" CreationDate="2015-07-02T16:35:07.810" Score="9" ViewCount="312" Body="&lt;p&gt;Like snakes or lizards, did any dinosaur molt ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;if yes, have we any proof of it ?&lt;/p&gt;&#xA;" OwnerUserId="16557" LastEditorUserId="16557" LastEditDate="2015-07-02T18:57:52.503" LastActivityDate="2016-07-16T18:16:08.817" Title="Did any dinosaur molt?" Tags="&lt;palaeontology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35735" PostTypeId="1" CreationDate="2015-07-02T17:11:12.533" Score="3" ViewCount="291" Body="&lt;p&gt;I'm doing an experiment with 4 kale plants, each in their own small deep water culture (DWC) system. Each plant was transplanted in rockwool with netpots and clay pebbles. But I need to periodically and accurately measure the biomass of each plant. The roots have grown through the rockwool and netpots and I don't want to rip out the roots. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there an easy way to do this?&lt;/p&gt;&#xA;" OwnerUserId="16949" OwnerDisplayName="skootsa" LastEditorUserId="948" LastEditDate="2015-07-03T14:55:13.330" LastActivityDate="2021-04-14T22:00:31.660" Title="How to measure the biomass of hydroponic plants in netpot/rockwool DWC system?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;experimental-design&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35736" PostTypeId="2" ParentId="35729" CreationDate="2015-07-02T18:55:07.947" Score="5" Body="&lt;p&gt;You are right the compounds provoking this burning/tingling sensation is called allyl isothiocyanate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We (human) perceive these compounds in two different ways when ingested, namely via the gustatory and olfactory systems. The molecular receptor sensing isothiocyanates is called the &lt;a href=&quot;https://en.wikipedia.org/wiki/Transient_receptor_potential_cation_channel,_member_A1&quot; rel=&quot;nofollow noreferrer&quot;&gt;transient receptor channel A1&lt;/a&gt; (TRPA1) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK5237/&quot; rel=&quot;nofollow noreferrer&quot;&gt;[ref]&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here a simplistic view of how ingredients are perceived:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/i83wb.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Gustatory sensation&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;First we get a burning sensation in the buccal cavity due to TRPA1 receptors present on the surface of the sensory neurons of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Trigeminal_nerve#Sensory_branches&quot; rel=&quot;nofollow noreferrer&quot;&gt;trigeminal nerve&lt;/a&gt;. In essence isothiocyanates dissolved in the saliva will activate those neurons via TRPA1 provoking electrical impulses in the trigeminal nerve which leads to a burning sensation.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Retronasal olfactory sensation&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;For several food ingredients we also perceived an &lt;a href=&quot;https://en.wikipedia.org/wiki/Odor&quot; rel=&quot;nofollow noreferrer&quot;&gt;aroma&lt;/a&gt; (taste = gustation, aroma = olfaction, taste + aroma = flavor). The aroma of an ingredient is perceived by &lt;a href=&quot;https://en.wikipedia.org/wiki/Olfactory_receptor_neuron&quot; rel=&quot;nofollow noreferrer&quot;&gt;olfactory sensory neurons&lt;/a&gt; in the nasal cavity and because some of the ingested ingredient will be vaporized inside the buccal cavity and travel through the nasal cavity where they are perceived (retronasal perception).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not so surprisingly, isothiocyanates will again be perceived by sensory cells of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Olfaction&quot; rel=&quot;nofollow noreferrer&quot;&gt;olfaction system&lt;/a&gt; via TRPA1 hence a burning sensation in the nostrils.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;How receptor activation leads to a neuronal stimuli&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;This is a very broad subject and I will only give an overview of what is happening. We first start with the activation of a receptor by an agonist (in your question, isothiocyanates binding and activating TRPA1). Upon binding of the agonist the conformation of the receptor will change from an inactive to an active state. The way the signal is transduced varies according to the type of receptor but for the TRPA1 channel what happens is that the channel opens leading to an influx of calcium ions ($Ca^{2+}$) in the cells which changes its electrical state (as calcium ions are positively charged), a phenomena called &lt;a href=&quot;https://en.wikipedia.org/wiki/Depolarization&quot; rel=&quot;nofollow noreferrer&quot;&gt;depolarization&lt;/a&gt;. Depolarization of specific sensory cells (here the one expressing TRPA1) start an electrical signal in the nerve which travels to the brain where it is then decoded. The exact way the brain decodes sensory signals is still under debate but a likely explanation is that only some neurons within the nerve are activated which allows the brain to decode the sensory signal based on the nerve activation pattern. As an analogy, it would be the same as having only specific wires (neurons) turned on within a bundle of wires (nerve).&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Further reading&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;If you want to further extend your knowledge on taste perception at the molecular level read this excellent review &lt;a href=&quot;http://www.nature.com/nature/journal/v444/n7117/full/nature05401.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Chandrashekar, 2006&lt;/a&gt;. For a in-depth review on olfaction refer to this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK11032/&quot; rel=&quot;nofollow noreferrer&quot;&gt;book&lt;/a&gt;. For a book on signal transduction refer to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK21661/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; while for TRP channels activation &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK92819/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt; is a good reading.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The field is quite broad and there are many good references. Sensory perception includes two distinct and broad fields namely neurosciences and cell signalling.&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="948" LastEditDate="2015-07-03T14:59:29.990" LastActivityDate="2015-07-03T14:59:29.990" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35737" PostTypeId="2" ParentId="35671" CreationDate="2015-07-02T19:25:58.607" Score="3" Body="&lt;p&gt;If both of the ORFs that the web tool predicted start with an AUG initiation codon, then the textbook answer is that the 5' cap on eukaryotic mRNAs is the first feature that is recognized by the translational apparatus, and the ribosome scans along until it finds the first AUG (it is a simplified description). However, if there are several AUGs near each other then the one that matches the best to the Kozak PWM (position weight matrix) will be preferred. The Kozak sequence can be approximated by: CCATGG which is also recognized by the restriction enzyme NcoI. Highly expressed genes tend to match most closely to the Kozak consensus.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-07-02T19:25:58.607" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35738" PostTypeId="1" AcceptedAnswerId="36182" CreationDate="2015-07-02T20:17:30.310" Score="6" ViewCount="156" Body="&lt;p&gt;Has there ever been an experiment performed that demonstrated a form of 'spatial memory' in a unicellular organism?  I'm imagining something analogous to the classic 'rat in maze' experiments, but obviously on a much smaller scale.  Possibly even something as simple as following a concentration gradient, but choosing to go either upstream or downstream based on some sort of prior reward in a similar circumstance.&lt;/p&gt;&#xA;" OwnerUserId="9155" LastActivityDate="2015-07-18T05:05:21.747" Title="Spatial learning in microorganisms" Tags="&lt;cell-biology&gt;&lt;microbiology&gt;&lt;learning&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35739" PostTypeId="1" CreationDate="2015-07-02T20:21:56.077" Score="2" ViewCount="122" Body="&lt;p&gt;&lt;strong&gt;Intro and description of the data&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am simulating the evolution of very long DNA sequences. The model works well, is performant and will output data in the following kind of fasta format&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;&amp;gt;it0pop0ind0locus0&#xA;ATGTTG...&#xA;&amp;gt;it0pop0ind1locus0&#xA;ATGTTG...&#xA;&amp;gt;it0pop0ind2locus0&#xA;ATGTTG...&#xA;&amp;gt;it0pop0ind3locus0&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;, where &lt;code&gt;it&lt;/code&gt; stands for iteration (replicate of the same simulation), &lt;code&gt;pop&lt;/code&gt; stands for population (or subpopulation of the metapopulation if you prefer), &lt;code&gt;ind&lt;/code&gt; stands for the individual chromosome that was sampled, &lt;code&gt;locus&lt;/code&gt; stands for locus which is defined as a very big sequence (0.1GB or 1 GB maybe).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Issues&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I never had to analyze genetic data (or only during my Bachelor degree). As I know nothing about the available algorithms that exist to make this kind of analysis, I first thought I would just make my own code (in Python). It turns out that I might have a lot of data to analyse and my Python code will be way too slow. I may also experience RAM-related issues&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Moreover, I want to measure a whole series of different statistics of population divergence (Fst for each site, Fst averaged over many sites following Cochramm and Weir, Gsd, absolute number of fixed sites that differ, etc..), so the algorithm would need to be quite flexible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are a bunch of existing efficient algorithms that would eventually fit my needs. Can you please give me some recommendations and make a few comparisons of what's available out there?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An efficient algorithm that takes in input:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;a description of the naming convention in the fasta file, or a list of positions for each locus and each population in the fasta file.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;A description of how I want the statistics to be calculated&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;and that outputs those statistics. That'd be great!&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-07-03T01:37:38.397" LastActivityDate="2015-07-03T01:37:38.397" Title="Efficient algorithm to calculate various population divergence statistics" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;population-genetics&gt;&lt;statistics&gt;&lt;sequence-analysis&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35740" PostTypeId="1" CreationDate="2015-07-02T20:40:33.043" Score="7" ViewCount="127" Body="&lt;p&gt;It's well known that one of human chromosomes is the result of fusion between two chromosomes in a primate ancestor. If we put anthropocentrism aside, it becomes clear that fusion events happened a lot of times, since chromosome count varies in different species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yet some people claim that while fusion event is probable, getting it fixed in the population is not, because it would require simultaneous mutation in two animals of opposite sex.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could anyone explain in layman terms the scenario of this trait's propagation? I may only suppose that even if one parent has two distinct chromosomes and another a single fused chromosome, then two chromosomes may attach to the fused one, and then (probably) get fused themselves, thus leaving fewer and fewer specimens with distinct chromosomes in each generation. Is this a viable and likely scenario, or is some other way of propagation more likely?&lt;/p&gt;&#xA;" OwnerUserId="16560" LastActivityDate="2015-07-14T01:42:32.247" Title="How does chromosome fusion get fixed in the population?" Tags="&lt;evolution&gt;&lt;chromosome&gt;&lt;human-evolution&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35741" PostTypeId="2" ParentId="35734" CreationDate="2015-07-02T21:40:13.817" Score="8" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Richard_Prum&quot;&gt;Richard Prum&lt;/a&gt; (the author of &lt;a href=&quot;http://prumlab.yale.edu/sites/default/files/prum_1999_mde_development.pdf&quot;&gt;Evolution of feathers&lt;/a&gt;) says that ornithology is mostly a science about dinosaurs. He insists that dinosaurs were very close to birds, part of them had feathers and these feathered dinosaurs &quot;shed (molt) them as birds of our days do&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, we can conclude that dinosaurs probably possessed at least one molting-like mechanism, while others are the subjects for consecutive investigations. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;sources&#xA;&lt;a href=&quot;http://www.nature.com/nature/journal/v468/n7320/full/nature09480.html&quot;&gt;Moulting tail feathers in a juvenile oviraptorisaur&lt;/a&gt;. Nature, 2010.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-02T21:40:13.817" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35742" PostTypeId="2" ParentId="35727" CreationDate="2015-07-02T22:28:25.350" Score="3" Body="&lt;p&gt;&quot;Unaffected&quot; is impossible. If you meant homeostasis, where fluid ingested = fluid excreted, well that happens all the time, and all &quot;output&quot; is not through urine. Sweat, respiration, fluid in feces, etc. are fluid loss. The body constantly needs water. Fluid regulation is a highly complex system managed by the body through a variety of osmotic gradients in the body and hormones which is not driven solely on the osmolarity of the fluid ingested. Under no circumstances would fluid ingested pass through the stomach, small and large intestine, and colon without absorption. Once absorbed from the GI tract to the bloodstream, our kidneys regulate fluid balance. For more reading, reference the renin–angiotensin–aldosterone system.&lt;/p&gt;&#xA;" OwnerUserId="16563" LastActivityDate="2015-07-02T22:28:25.350" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35743" PostTypeId="2" ParentId="35648" CreationDate="2015-07-02T23:23:15.230" Score="4" Body="&lt;p&gt;Is &quot;Pantherine&quot; a valid vernacular name for this group in English? Sure, although &quot;panther&quot; is much clearer (&quot;Pantherine&quot; in English would mean &quot;&lt;a href=&quot;https://en.wiktionary.org/wiki/pantherine&quot; rel=&quot;nofollow&quot;&gt;like a panther&lt;/a&gt;&quot;, not &quot;a panther&quot;). Also, many family names are fairly obscure: even a pretty well-known group, like &lt;a href=&quot;http://en.wikipedia.org/wiki/Apidae&quot; rel=&quot;nofollow&quot;&gt;Apidae&lt;/a&gt;, would become &quot;Apinine&quot; in your scheme, which is less clear to me than &quot;a family of bees&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it a valid family name? No. The International Code of Zoological Nomenclature (ICZN Code), which governs all scientific names for animals, says:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp?nfv=&amp;amp;article=29#2&quot; rel=&quot;nofollow&quot;&gt;Article 29.2&lt;/a&gt;. &lt;strong&gt;Suffixes for family-group names.&lt;/strong&gt; The suffix -OIDEA is used for a superfamily name, &lt;strong&gt;-IDAE for a family name, -INAE for a subfamily name&lt;/strong&gt;, -INI for the name of a tribe, and -INA for the name of a subtribe. These suffixes must not be used at other family-group ranks. The suffixes of names for taxa at other ranks in the family-group are not regulated. [emphasis mine]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Family names that don't have an &quot;-idae&quot; suffix need to be corrected (ICZN Code &lt;a href=&quot;http://www.nhm.ac.uk/hosted-sites/iczn/code/index.jsp?nfv=&amp;amp;article=32#5.3.1&quot; rel=&quot;nofollow&quot;&gt;Article 32.5.3.1&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the ICZN Code doesn't cover other ranks in the family-group or above.&lt;/p&gt;&#xA;" OwnerUserId="87" LastActivityDate="2015-07-02T23:23:15.230" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35744" PostTypeId="1" CreationDate="2015-07-03T01:55:02.437" Score="9" ViewCount="1929" Body="&lt;p&gt;So, earlier, I read online (&lt;a href=&quot;http://io9.com/butterflies-remember-a-mountain-that-hasnt-existed-for-509321799&quot;&gt;http://io9.com/butterflies-remember-a-mountain-that-hasnt-existed-for-509321799&lt;/a&gt;) that Monarch butterflies veer east during their southward migration to avoid a mountain that no longer exists. If this is true, how do butterflies know to continue avoiding the &quot;mountain&quot; after countless generations, and does it have to do with evolution? Do other animals have similar abnormalities in their migration routes?&lt;/p&gt;&#xA;" OwnerUserId="16568" LastEditorUserId="9943" LastEditDate="2015-07-03T12:15:34.473" LastActivityDate="2015-07-03T14:08:31.323" Title="Do butterflies pass over migration patterns to their offspring?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;entomology&gt;&lt;memory&gt;&lt;migration&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35745" PostTypeId="1" CreationDate="2015-07-03T08:28:34.327" Score="11" ViewCount="249" Body="&lt;p&gt;I have just started reading about the endocrine system and I am having some difficulty understanding the basis of distribution of glands and associated hormones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am using multifuntionality to describe the amount of relatively independent input and output that are shared through a same organ or proximal space. Many of these organs have a heterogenous mixture of endocrine cells sharing the same glandular space.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There appear to be some glands that are considered &quot;master glands&quot; such that they take a variety of relatively independent input, apply some control logic via a diverse set of endocrine cells and tissue and secrete a diverse hormonal output. The pituitary and hypothalamus are the best examples, however the adrenal cortex and the pancreas also fit this definition to a certain extent. Many times the diversity of hormones and cells within an organ have no obvious connection (eg thyroid). Some glands appear more specialized with a relatively straightforward endocrine axis of input and output (eg testes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of this multifunctionality seems unnecessary, in that insulin secretion could occur anywhere and be effective in the manner of an insulin pump, or contain risks due to excessive centralization as in a pituitary tumor or renal artery stenosis, so there must be some advantages I do not understand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My textbook (Headley, Levine, 6th) seems to minimally cover multiplexing, signal cross-talk and competition between diverse endocrine cells sharing an organ. Its focus on discrete pathways and axes suggests these are evolutionarily unfavorable.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there synergistic advantages in shared endocrine infrastructure such as vascularity or metabolic pathways?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there some overlying logic that can be used to explain this distribution of glands and hormones regarding multifuntionality-specialization, or is it necessary to view the distribution of vertebrate endocrine system as the outcome of evolutionary contingencies?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="16572" LastEditorUserId="16572" LastEditDate="2015-07-05T10:50:20.677" LastActivityDate="2016-12-12T15:59:53.837" Title="What is basis of multifunctionality of &quot;master glands&quot; in the endocrine system?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;endocrinology&gt;" AnswerCount="1" CommentCount="12" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35747" PostTypeId="1" CreationDate="2015-07-03T13:27:14.707" Score="1" ViewCount="89" Body="&lt;p&gt;Question is asked above, simply put.&lt;/p&gt;&#xA;" OwnerDisplayName="user16574" LastActivityDate="2015-07-03T13:47:36.153" Title="What is the term for all of the RNA in a cell at any given time?" Tags="&lt;genetics&gt;&lt;cell-biology&gt;&lt;rna&gt;" AnswerCount="1" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="35748" PostTypeId="2" ParentId="35747" CreationDate="2015-07-03T13:47:36.153" Score="4" Body="&lt;p&gt;&lt;a href=&quot;https://www.qiagen.com/us/resources/faq?id=06a192c2-e72d-42e8-9b40-3171e1eb4cb8&amp;amp;lang=en&quot; rel=&quot;nofollow&quot;&gt;Qiagen&lt;/a&gt; and &lt;a href=&quot;https://www.lifetechnologies.com/au/en/home/references/ambion-tech-support/rna-isolation/general-articles/rna-yields-from-tissues-and-cells.html&quot; rel=&quot;nofollow&quot;&gt;Life Technologies&lt;/a&gt; call it  &lt;strong&gt;&lt;em&gt;RNA content&lt;/em&gt;&lt;/strong&gt;, &lt;strong&gt;&lt;em&gt;total RNA&lt;/em&gt;&lt;/strong&gt;, or &lt;strong&gt;&lt;em&gt;total cellular RNA&lt;/em&gt;&lt;/strong&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-07-03T13:47:36.153" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35749" PostTypeId="1" CreationDate="2015-07-03T14:05:29.090" Score="3" ViewCount="1352" Body="&lt;p&gt;I just got my finger burnt (first degree burn $\Rightarrow$ I didn't even bother to bear the wound). It didn't hurt much, even when I pressed the wound.&#xA;However, when exposed to heat (hot water, but not so hot to hurt undamaged skin), the pain became &lt;em&gt;at least&lt;/em&gt; nasty.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it an evolutionary adaptation to avoid hot objects not to get burnt again? &lt;/p&gt;&#xA;" OwnerUserId="14597" LastEditorUserId="948" LastEditDate="2015-07-03T14:32:49.420" LastActivityDate="2015-07-03T14:32:49.420" Title="Skin extra sensitive to heat after burn" Tags="&lt;physiology&gt;&lt;human-anatomy&gt;&lt;pain&gt;&lt;perception&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35750" PostTypeId="2" ParentId="35744" CreationDate="2015-07-03T14:08:31.323" Score="3" Body="&lt;p&gt;If you think about it, monarchs must have a pretty strong genetic component to migration since often &lt;a href=&quot;http://www.monarchbutterflyfund.org/node/148&quot; rel=&quot;nofollow&quot;&gt;they only make one round trip at most in a lifetime&lt;/a&gt;. But its not as simple as passing a map in the DNA.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If a mountain springs up on the route, the 'common sense' of the butterflies are still operational and they will tend to find their way around it.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The paper discussed here is older.  More recent Monarch butterfly migration  of some genetics &lt;a href=&quot;http://www.nature.com/nature/journal/v514/n7522/full/nature13812.html&quot; rel=&quot;nofollow&quot;&gt;that have been done&lt;/a&gt; shows some traits that are related to migration patterns by sampling over many butterflies whose patterns vary tremendously.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glancing over the paper, I'd say that there may be some 'muscle' memory in migration, but probably the mechanisms encoding the route of migration are not yet discernable.  This is far from something we understand well. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The insect is following patterns of behavior but doesn't turn into a robot just because its migrating.  Migration patterns are probably linked to a series of environmental cues.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Changes in climate or shifts in magnetic fields can change migration patterns. Butterflies would be very different than say migratory birds in terms of the social and environmental markers for migration. &lt;/p&gt;&#xA;" OwnerUserId="3632" LastActivityDate="2015-07-03T14:08:31.323" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35757" PostTypeId="1" AcceptedAnswerId="35765" CreationDate="2015-07-04T05:43:42.330" Score="6" ViewCount="1047" Body="&lt;p&gt;I'm taking a course on biochemistry at &lt;a href=&quot;https://www.edx.org/course/principles-biochemistry-harvardx-mcb63x-0&quot; rel=&quot;nofollow&quot;&gt;edx&lt;/a&gt;.&#xA;Since I'm a computer science student, I'm having some trouble in understanding many biochemical concepts. While the first module was just fine, I found the second module really hard to understand. I have problems to learn and understand about amino acids and proteins, so I would like to study apart from some good resources.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which is a good resource to learn about amino acids and macromolecules?&#xA;Also, please let me know if &lt;a href=&quot;http://rads.stackoverflow.com/amzn/click/0198504748&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; book is up to date?&lt;/p&gt;&#xA;" OwnerUserId="16494" LastEditorUserId="948" LastEditDate="2015-07-04T15:08:12.280" LastActivityDate="2015-07-06T04:21:51.787" Title="Need some good resources to learn about Protein function and structure" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;book-recommendation&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35758" PostTypeId="1" CreationDate="2015-07-04T07:56:44.787" Score="5" ViewCount="132" Body="&lt;p&gt;I'm looking for bird studies that have found either a negative correlation or no correlation between habitat quality and reproductive success. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or in other words, bird studies that have found that reproductive success was lower in lower quality habitats. Or, that have found there was no difference in reproductive success between habitat classified as high quality and low quality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone help?&lt;/p&gt;&#xA;" OwnerUserId="1216" LastEditorUserId="1216" LastEditDate="2015-07-04T08:17:52.197" LastActivityDate="2015-07-04T08:17:52.197" Title="Negative association between habitat quality and reproductive success in birds" Tags="&lt;ecology&gt;&lt;ornithology&gt;&lt;reproductive-biology&gt;&lt;fitness&gt;&lt;habitat&gt;" AnswerCount="0" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35759" PostTypeId="1" CreationDate="2015-07-04T09:06:42.303" Score="0" ViewCount="55" Body="&lt;p&gt;I would like to learn more about the exact mechanism behind our movements, especially about what happens during intense training when anaerobic state arises.&lt;/p&gt;&#xA;" OwnerUserId="15051" LastActivityDate="2015-07-04T09:06:42.303" Title="Book recommendation on the human muscle system" Tags="&lt;muscles&gt;&lt;book-recommendation&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35760" PostTypeId="1" AcceptedAnswerId="35763" CreationDate="2015-07-04T10:38:36.013" Score="4" ViewCount="2645" Body="&lt;p&gt;According to my chemistry book, water has higher surface tension than lipids. But in my biology book it is written that &quot;the gall forms an emulsion of water and lipids by lowering the lipid's surface tension&quot;. This will increase the difference between the two substances even more. How can this be beneficial?&lt;/p&gt;&#xA;" OwnerUserId="16552" LastEditorUserId="3340" LastEditDate="2015-07-04T14:08:43.443" LastActivityDate="2015-07-04T16:40:06.437" Title="How does decreasing surface tension of lipids help to emulsify them?" Tags="&lt;biochemistry&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35763" PostTypeId="2" ParentId="35760" CreationDate="2015-07-04T12:38:48.657" Score="3" Body="&lt;p&gt;There appears to be either a typo or transcription error in your textbook. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to this &lt;a href=&quot;http://www.nuffieldfoundation.org/practical-chemistry/detergents-soaps-and-surface-tension&quot; rel=&quot;nofollow&quot;&gt;Nuffield Foundation and Royal Society of Chemistry article&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Molecules of most detergents and soaps are long chain hydrocarbon&#xA;  molecules with an ionic group at one end, usually carrying a negative&#xA;  charge, thus making it an anion. This charge is balanced by the&#xA;  opposite charge of a soluble cation, for example Na+. The long&#xA;  hydrocarbon chains do not interact well with water molecules, and many&#xA;  of them are effectively ‘squeezed out’ to the interfaces between the&#xA;  water and the air or the glass sides of the beaker. The effect of&#xA;  these molecules on the water surface is to considerably weaken the&#xA;  forces between water molecules there, thus lowering the surface&#xA;  tension.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Soaps, detergents, and bile (all examples of amphiphilic compounds) act to reduce the surface tension of water, not the lipids. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-07-04T12:38:48.657" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35764" PostTypeId="1" CreationDate="2015-07-04T15:51:04.603" Score="2" ViewCount="231" Body="&lt;p&gt;The tricuspid and bicuspid valves are atrioventricular valves. Both are valves that prevent backflow of blood pumped from the atria to the ventricles. However, the former has 3 &quot;flaps&quot; while the latter has 2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Despite searching the internet, I could not find a biological explanation for this difference.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Might this be just a relic of evolution or some sort?&lt;/p&gt;&#xA;" OwnerUserId="15002" LastActivityDate="2015-07-04T18:07:06.447" Title="Physiology of tricuspid and bicuspid(mitral) valves" Tags="&lt;physiology&gt;&lt;human-anatomy&gt;&lt;cardiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35765" PostTypeId="2" ParentId="35757" CreationDate="2015-07-04T16:15:00.197" Score="4" Body="&lt;p&gt;Given your background (not a biologist or chemist) you would probably find the introductory material in a biochemistry &quot;lite&quot; textbook more accessible/useful than a hardcore text for specialists.  As a co-author of a biochemistry textbook, I can tell you that there are essentially three different classes, or types of texts. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Comprehensive textbooks, of which I think Voet &amp;amp; Voet is an outstanding example, are designed for biochemistry majors who will be taking a full year, in-depth course, typically in the 3rd year of their undergraduate studies.  &lt;/li&gt;&#xA;&lt;li&gt;The general introductory texts are usually thinner, and are designed to whip through the same material in half a year--aimed at life-science students in other majors. Some of these books that I described as &quot;lite&quot; are further targeted to, for example, nursing, medical, or dental school students.  &lt;/li&gt;&#xA;&lt;li&gt;The third category of text tries to be multi-purpose, and appeal to both markets. The current versions of Stryer and Lehninger fall into this class (they are both excellent in my opinion); the instructors can cherrypick the readings if they want to use the book for a half-year course. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Voet, Voet, and Pratt (mentioned in the comments above) is a very good diluted version of Voet &amp;amp; Voet. As you can also tell from the comments, different texts have different flavors, and so which one is best depends on the reader.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It sounds like a more general &quot;concept&quot; based book might be useful for you (to provide background and context). The very thick &quot;Molecular Biology of the Cell&quot; by Alberts &lt;em&gt;et al.,&lt;/em&gt; has a lighter cousin named Essential Cell Biology which would be well worth looking into.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Keep in mind that when tackling a university-level biochemistry course the instructor has to assume that you have passed university level introductory courses in general chemistry and in organic chemistry. Biochemistry majors typically complete full year courses in both these subjects, as well as a watered-down version of physical chemistry.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-07-04T16:15:00.197" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35767" PostTypeId="2" ParentId="35760" CreationDate="2015-07-04T16:40:06.437" Score="1" Body="&lt;p&gt;Surface tension is about how much energy you need to create new surface between not mixing materials e.g. water and lipids. Surfactants like &lt;a href=&quot;https://en.wikipedia.org/wiki/Bile&quot; rel=&quot;nofollow&quot;&gt;bile&lt;/a&gt; makes this easier (lowers the energy required). So they can form small bubbles of lipids: &lt;a href=&quot;https://en.wikipedia.org/wiki/Micelle&quot; rel=&quot;nofollow&quot;&gt;micelles&lt;/a&gt;, which can be handled much easier by the digestive system. Another usage of surfactants to make foams, creams, etc... &lt;a href=&quot;https://en.wikipedia.org/wiki/Physical_chemistry&quot; rel=&quot;nofollow&quot;&gt;physical-chemistry&lt;/a&gt; / &lt;a href=&quot;https://en.wikipedia.org/wiki/Surface_rheology&quot; rel=&quot;nofollow&quot;&gt;surface rheology&lt;/a&gt; is all about them.&lt;/p&gt;&#xA;" OwnerUserId="3703" LastActivityDate="2015-07-04T16:40:06.437" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35768" PostTypeId="1" CreationDate="2015-07-04T17:18:13.247" Score="0" ViewCount="67" Body="&lt;p&gt;I would like to obtain a complete genome of a canine (with mitochondrial DNA too) at 100% accuracy. Is it even possible with the current technology? The source I have is potential degraded, i.e. dried saliva, dried blood, whisker root, fur roots, etc...&lt;/p&gt;&#xA;" OwnerUserId="16582" LastActivityDate="2015-07-04T18:59:45.753" Title="Is 100% accuracy in DNA sequencing possible?" Tags="&lt;dna-sequencing&gt;&lt;mitochondria&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35770" PostTypeId="2" ParentId="35764" CreationDate="2015-07-04T18:07:06.447" Score="1" Body="&lt;p&gt;During embryogenesis at the level of an atrioventricular canal there is so called endocardial &quot;cushion&quot; tissue. This tissue bulges to the left side more than it does to the right and &lt;a href=&quot;http://www.madsci.org/posts/archives/1997-03/855255174.An.r.html#conclusion&quot; rel=&quot;nofollow noreferrer&quot;&gt;contribute to the fusion of the valvular ring&lt;/a&gt; to a one leaflet, while from the remaining part of the ring develops the second leaflet:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/62Sh4.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AVEC = atrioventricular endocardial cushions&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As has been stated, the cushion tissue bulges more to the left, thus on the right side where the tricuspid valve is forming the leaflets does not &quot;merge&quot; and develop into three-leaflet valve.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, this left side &quot;suture&quot; might sometimes fail to develop with resulting &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21269417&quot; rel=&quot;nofollow noreferrer&quot;&gt;three-leaflet mitral valve&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-04T18:07:06.447" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35771" PostTypeId="2" ParentId="7778" CreationDate="2015-07-04T18:18:40.613" Score="2" Body="&lt;p&gt;I work with membrane proteins and in my experience some proteins can be frozen and thawed without any problems, other proteins just don't like that. It's linked to the stability of the protein. If you really need to freeze the protein you may think about playing around with different detergents to see if you can improve the stability of the protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;General rules:&#xA;- freezing membrane proteins at -80°C without glycerol&#xA;- avoiding protein freeze-thaw cycles, making aliquots before freezing&#xA;- keeping them at 4°C only for short term use&#xA;- after concentration always spinning the protein (10 min at 100k for example) to precipitate aggregated material. Aggregation causes aggregation, so you want to get rid of it.&lt;/p&gt;&#xA;" OwnerUserId="16581" LastActivityDate="2015-07-04T18:18:40.613" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35772" PostTypeId="2" ParentId="35768" CreationDate="2015-07-04T18:59:45.753" Score="2" Body="&lt;p&gt;Current DNA sequencing techniques are based on &lt;a href=&quot;https://en.wikipedia.org/wiki/Shotgun_sequencing&quot; rel=&quot;nofollow&quot;&gt;shotgun sequencing&lt;/a&gt;, randomly breaking the chromosomes into small pieces, sequencing the pieces (by various techniques), and then computationally reassembling the pieces by looking for overlapping patterns. This depends on sequencing each piece of DNA multiple times; the more &lt;a href=&quot;https://en.wikipedia.org/wiki/Shotgun_sequencing#Coverage&quot; rel=&quot;nofollow&quot;&gt;coverage or depth&lt;/a&gt;, the more reliable the results. However, especially with long repeating base sequences, 100% coverage is uncommon with small genomes, and almost impossible with large genomes.&lt;/p&gt;&#xA;" OwnerUserId="11620" LastActivityDate="2015-07-04T18:59:45.753" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35773" PostTypeId="1" AcceptedAnswerId="35914" CreationDate="2015-07-04T19:54:09.537" Score="1" ViewCount="397" Body="&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Consider a very long (eventually infinite) DNA sequence of neutral sites. Consider a panmictic population of constant size $N$ with a per site mutation rate of $\mu$ where all individuals have the exact same fitness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;What is the fraction of sites that we'd expect to be polymorphic in the population (SNPs)?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Motivation behind this question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am asking this question to verify the results of simulations I run. For example, I run a simulation with $x$ ($x$ will be varying below) neutral sites, with a per-site mutation rate $\mu = 10^{-9}$ and a population size of $N=100$. I run the simulations for 10,000 generations. There is no recombination. When the number of sites:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;$x=10^3$ I get 0 SNP&lt;/li&gt;&#xA;&lt;li&gt;$x=10^4$ I get 1 SNP&lt;/li&gt;&#xA;&lt;li&gt;$x=10^5$ I get 3 SNPs&lt;/li&gt;&#xA;&lt;li&gt;$x=10^6$ I get 25 SNPs&lt;/li&gt;&#xA;&lt;li&gt;$x=10^7$ I get 238 SNPs&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Is there a bug in my model or is it what we'd expect given the parameters?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the human genome, 1 out of 300 sites are polymorphic (SNPs) (&lt;a href=&quot;http://ghr.nlm.nih.gov/handbook/genomicresearch/snp&quot; rel=&quot;nofollow&quot;&gt;ref.&lt;/a&gt;). This is a frequency of SNPs that is 100 times greater than what I observe in my simulations. Note however, that the assumption of neutrality and out demographic assumptions would not perfectly hold and this result could pretty far off neutral expectation. My goal is not to reproduce something that look like the human genome but only to reproduce the neutral expectations for the moment.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-07-04T22:52:55.120" LastActivityDate="2015-07-15T08:47:32.450" Title="What fraction of sites are expected to be polymorphic?" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;theoretical-biology&gt;&lt;population-genetics&gt;&lt;snp&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35774" PostTypeId="1" CreationDate="2015-07-04T19:59:27.207" Score="3" ViewCount="295" Body="&lt;p&gt;My question is about the neurological signals. In our body when a signal, for example a hearing signal from hair cells, is built, it goes through a lot of neurons and it passes a lot of synapses. I am wondering how it doesn't lose it's correct path and chooses the right way to auditory cortex? I mean what are the features of a neurological signal that shows it the correct way?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In other words, how can a neurological signal be created and sent through a chain of neurons to the brain, how can it 'know' when entering a synapse contacting multiple neurons which is the correct one for going through it?&lt;/p&gt;&#xA;" OwnerUserId="16584" LastEditorUserId="9943" LastEditDate="2015-07-05T14:43:50.497" LastActivityDate="2015-07-05T17:37:27.060" Title="What determines the pathway of a neurological signal?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35775" PostTypeId="2" ParentId="31222" CreationDate="2015-07-04T20:44:40.367" Score="0" Body="&lt;p&gt;When you ask:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is it possible to take out a gene from an organism and put in a totally different one?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The answer is yes. &lt;a href=&quot;https://en.wikipedia.org/wiki/Knockout_mouse&quot; rel=&quot;nofollow&quot;&gt;Gene knockout technologies&lt;/a&gt; are available in experimental scientific fields. You can destroy your target gene by swapping the gene with a drug resistant gene. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can swapping genes using culturing cells, however it would be almost impossible to swap genes in cells of an animal body. But there is still hope. iPS cells can be generated from human and other animals. Then the technology can be applied to culturing iPS cells. Transplantation of differentiated iPS cells may be possible to replace tissues having a problems if anatomical structures allow you to do so. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do not know details of pain perception, but it may be not that simple. You can classified genes by sensitivities of pain, but at biochemical level, the mechanisms to gain sensitivities may be different. I might check on this, although I might not able to draw the conclusion.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-07-04T20:44:40.367" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35776" PostTypeId="1" CreationDate="2015-07-04T20:59:53.240" Score="5" ViewCount="112" Body="&lt;p&gt;From &lt;a href=&quot;https://youtu.be/NGuIezLFidY?t=16m45s&quot;&gt;this fascinating documentary on monotremes&lt;/a&gt; it is mentioned that the Platypus is born less than 1 cm in length, but has doubled its size by day three when it begins to nurse. &lt;strong&gt;How does the animal grow before feeding?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Surely by &lt;a href=&quot;https://en.wikipedia.org/wiki/Conservation_of_mass&quot;&gt;conservation of mass&lt;/a&gt; there must be some alternate process by which materials are being processed and absorbed by the young animal. Does it absorb nutrients from the air or surrounding environment? Sucking on dirt? Osmosis?&lt;/p&gt;&#xA;" OwnerUserId="6967" LastActivityDate="2018-10-27T03:17:25.503" Title="How does the Platypus grow before it eats?" Tags="&lt;reproduction&gt;&lt;mammals&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35777" PostTypeId="2" ParentId="35773" CreationDate="2015-07-04T21:12:03.093" Score="2" Body="&lt;p&gt;The fraction of polymorphic sites that exist in a population is dependent on the biology of the organism. For instance, you would expect to find different rates of polymorphism in related plants that have different breeding systems, e.g. in Silene [&lt;a href=&quot;http://www.genetics.org/content/181/2/631.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;1&lt;/a&gt;]. Past bottlenecks are also expected to decrease polymorphisms [&lt;a href=&quot;http://www.genetics.org/content/123/3/597.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;2&lt;/a&gt;]. So, the answer to your question would depend on the exact species and population that you are looking at. &lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-07-04T21:12:03.093" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35778" PostTypeId="1" AcceptedAnswerId="36393" CreationDate="2015-07-04T21:32:02.887" Score="9" ViewCount="393" Body="&lt;p&gt;&lt;strong&gt;In short&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at the genetic code, it appears that most redundancy is on the third letter rather than on the first or the second letter of the codon. &lt;em&gt;Why has it evolved this way?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Longer version&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to compare the relative redundancy accounted by each letter of the codon, let's assume that that every codon occurs at equal frequency. It is probably wrong but useful for the sake of the calculations. Using observed frequencies of codon usage in a given population would change the following probabilities but the question of why some positions in the codon has more redundancy than some others still hold.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A substitution of the first letter of the codon has a probability of $\frac{1}{2048}≈0.00005$ (Stop codon) to be synonymous. A substitution of the second letter of the codon has a probability $\frac{3}{256}≈0.012$ (nucleobases U and G) to be synonymous. A substitution of the third letter has a probability of exactly $\frac{2}{3}$ to be synonymous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Probability of a substitution to be synonymous given that it occurred on the...&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;First letter: $\frac{1}{2048}≈0.00005$&lt;/li&gt;&#xA;&lt;li&gt;Second letter: $\frac{3}{256}≈0.012$&lt;/li&gt;&#xA;&lt;li&gt;Third letter: $\frac{2}{3}$&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why are there more redundancy on the third position than on the second (which has more redundancy than the first position) in the codon?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/baapb.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-07-04T23:12:40.517" LastActivityDate="2015-07-25T13:50:01.573" Title="Evolution of the Redundancy of the Genetic Code" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;dna&gt;&lt;molecular-evolution&gt;&lt;genetic-code&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35780" PostTypeId="1" CreationDate="2015-07-05T06:35:37.220" Score="2" ViewCount="3233" Body="&lt;p&gt;Why the nails are of white colour from bottom? then why they are pink and again white in the end?&lt;/p&gt;&#xA;" OwnerUserId="16587" LastActivityDate="2015-07-07T03:57:21.103" Title="What is the cause of colours of nail" Tags="&lt;pigmentation&gt;" AnswerCount="2" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35781" PostTypeId="1" AcceptedAnswerId="35789" CreationDate="2015-07-05T08:05:43.807" Score="7" ViewCount="1474" Body="&lt;p&gt;I attended a talk that glossed over some biology as it was talking about a certain protein. The speaker mentioned humans can hear up to, often less than 20kHz frequencies, whereas bats can hear up to 100kHz. Presumably this is to do with differences in cochlear anatomy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What about the inner ear of bats is different form ours, and how does this allow them to hear such high frequencies?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="9943" LastEditDate="2015-07-05T12:49:27.437" LastActivityDate="2015-07-06T00:53:54.313" Title="How can bats hear such high frequencies?" Tags="&lt;zoology&gt;&lt;anatomy&gt;&lt;sensation&gt;&lt;hearing&gt;&lt;senses&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35782" PostTypeId="1" CreationDate="2015-07-05T08:53:57.633" Score="1" ViewCount="116" Body="&lt;p&gt;I have come across the term &quot;internal symmetry&quot; in the context of membrane proteins, but have never found a satisfactory definition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm struggling to figure out exactly what this term means... &lt;strong&gt;What plane is this symmetry&lt;/strong&gt; seen on? Is it dimers that are symmetrical or &lt;strong&gt;can a monomer also be internally symmetrical&lt;/strong&gt;?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastActivityDate="2016-02-10T23:54:05.827" Title="What is internal symmetry in membrane proteins?" Tags="&lt;proteins&gt;&lt;cell-membrane&gt;&lt;structural-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35784" PostTypeId="1" AcceptedAnswerId="42806" CreationDate="2015-07-05T04:18:34.757" Score="1" ViewCount="168" Body="&lt;p&gt;While doing morning-walk in Keweenaw Penisula, Michigan; I found this juvenile bird wandering around looking for her mother ! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone spot which bird is it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/INadI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6963" OwnerDisplayName="kaka" LastActivityDate="2016-01-29T20:47:30.467" Title="Which bird of Upper Michigan is it?" Tags="&lt;ornithology&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35786" PostTypeId="1" AcceptedAnswerId="35793" CreationDate="2015-07-05T10:47:00.963" Score="17" ViewCount="3881" Body="&lt;p&gt;This question came about from reading the comments of &lt;a href=&quot;https://biology.stackexchange.com/questions/34292/were-we-able-to-create-vitamin-b12-in-past&quot;&gt;this (very unclear) question&lt;/a&gt;, which the author did not properly clarify. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vegans are often &lt;a href=&quot;https://www.vegansociety.com/resources/nutrition-health/vitamins-minerals-and-more/vitamin-b12-your-key-facts/what-every-vegan-should-know-about-vitamin-b12&quot; rel=&quot;noreferrer&quot;&gt;recommended to take vitamin B12 supplements&lt;/a&gt;, as the vitamin is not present in sufficient quantities within vegan food. This implies that plants do not produce (or need) vitamin B12 in their metabolic processes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, herbivorous animals do not require any vitamin B12 supplementation, yet &lt;a href=&quot;http://ods.od.nih.gov/factsheets/vitaminb12&quot; rel=&quot;noreferrer&quot;&gt;contain significant amounts of vitamin B12&lt;/a&gt; in their food products.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What, then, is so different about the digestive tracts of humans and other herbivores that prevent humans from obtaining sufficient vitamin B12 from bacterial sources? Can humans be supplemented with gut bacteria from herbivores, allowing them to obtain sufficient vitamin B12 while on a vegan diet without requiring supplementation?&lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2017-06-01T12:47:06.553" Title="Why do humans require vitamin B12 supplementation while herbivores do not?" Tags="&lt;biochemistry&gt;&lt;nutrition&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35787" PostTypeId="2" ParentId="35774" CreationDate="2015-07-05T10:59:33.580" Score="2" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Neuronal signals neither choose where to go, nor do they carry routing flags of some sort to guide them. Instead, neuronal signals are guided by the &lt;em&gt;hard wiring&lt;/em&gt; of the nervous system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Neuronal signals (&lt;a href=&quot;https://en.wikipedia.org/wiki/Action_potential&quot; rel=&quot;nofollow noreferrer&quot;&gt;action potentials&lt;/a&gt;) basically follow a one-way path. When they encounter a cross roads, action potentials are simply propagated to all of those alternatives. External effects of neurons, hormones or drugs may alter these signals, for example by inhibiting action potential formation or propagation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To take the example of the auditory system (Fig. 1):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zQhNq.jpg&quot; alt=&quot;auditory system&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Auditory system. Source: &lt;a href=&quot;http://www.cns.nyu.edu/~david/courses/perception/lecturenotes/localization/localization.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;New York University&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One can readily see that the signal from the hair cells are routed into the auditory nerve to the cochlear nucleus, from there to the &lt;em&gt;colliculi&lt;/em&gt; in the brain stem and further up to the auditory cortex via the &lt;em&gt;medial geniculate&lt;/em&gt;. Basically this is a one-way, straightforward route.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is complexity in the system, however. For example, the fibers of the auditory nerve bifurcate on entering the cochlear nucleus and make synapses on a number of morphologically different types of neuron. Each of the latter sends its axon out of the &lt;em&gt;cochlear nucleus&lt;/em&gt; with a distinctive projection pattern that gives rise to further divergence. Specifically, some cochlear nucleus neurons project directly to the &lt;em&gt;inferior colliculus&lt;/em&gt;, whereas others project to various divisions of the &lt;em&gt;superior olivary complex&lt;/em&gt; and nuclei of the &lt;em&gt;lateral lemniscus&lt;/em&gt;, which in turn project to the &lt;em&gt;inferior colliculus&lt;/em&gt; &lt;a href=&quot;http://link.springer.com/chapter/10.1007/978-1-4612-2838-7_4&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Irvine, 1992)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But even in this complexity the divergence is basically generated by simple bifurcations. An action potential reaching such a junction by default simply gives rise to two parallel signals; &lt;em&gt;there is no choice involved&lt;/em&gt;. Regulation is due to other neurons targeting these pathways. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://link.springer.com/chapter/10.1007/978-1-4612-2838-7_4&quot; rel=&quot;nofollow noreferrer&quot;&gt;Irvine, The Mammalian Auditory Pathway: Neurophysiology Springer Handbook of Auditory Research (1992).&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-05T11:38:38.960" LastActivityDate="2015-07-05T11:38:38.960" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35789" PostTypeId="2" ParentId="35781" CreationDate="2015-07-05T12:31:32.657" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Echolocating bats have relatively large sensory epithelia in their inner ear, that &lt;em&gt;may&lt;/em&gt; correlate with their high upper frequency limit of up to 200 kHz. The basilar membrane is thinner and stiffer, possibly allowing it to decode higher frequencies. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;In terms of the place theory of hearing, the cochlea acts as a frequency transformer, where high frequencies are encoded basally, and low frequencies apically. The cells responsive to sound, the hair cells, are located along the &lt;em&gt;basilar membrane&lt;/em&gt; (BM). Going from base (high frequency) to apex (low frequency), the BM becomes wider and less stiff, making it more susceptible to encode low frequencies apically. Note that sound is encoded as a travelling wave, where the point of resonance of a particular frequency corresponds with the characteristic frequency of the hair cells (Fig. 2). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/mlVCm.jpg&quot; alt=&quot;cochlea&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Rolled out cochlea. Source: &lt;a href=&quot;http://www.cns.nyu.edu/~david/courses/perception/lecturenotes/pitch/pitch.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;New York University&lt;/a&gt;.&lt;/sup&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/7M1sp.png&quot; alt=&quot;Travelling wave&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 2. Travelling wave and resonance frequencies along the basilar membrane. Source: &lt;a href=&quot;http://www.d.umn.edu/~jfitzake/Lectures/DMED/InnerEar/CochlearPhysiology/PlacePrinciple.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;University of Minnesota&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A study in &lt;em&gt;Microchiroptera&lt;/em&gt; species revealed that the basal part of the basilar membrane was relatively &lt;strong&gt;narrow and stiff&lt;/strong&gt;, which increases the resonance frequency of the basal part of the BM and hence may allow it to &lt;strong&gt;encode higher frequencies&lt;/strong&gt; in these bats &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/5956244&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Pye, 1966)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the high frequencies are encoded basally, it would be tempting to speculate the basal region would be enlarged in echo locating bats. Although this is true in some species, it may have more to do with frequency sensitivity than the upper limit of hearing, simply because a larger surface of the BM allows for more exquisite resolution of the BM. Although &lt;strong&gt;there is a tendency for larger BM lengths in echolocating bats&lt;/strong&gt;, it is not consistent &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598973/#B29&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Davies &lt;em&gt;et al&lt;/em&gt;., 2013)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The human BM is 33.5 mm, while the BM of the bat with the highest frequency limit known (200 kHz, &lt;em&gt;Hipposideros bicolor&lt;/em&gt;) is only 9.13 mm. However, compared to that of acoustically unspecialized mammals of a similar body size, e.g. &lt;em&gt;Sorex araneus&lt;/em&gt; (BM length 4.4 mm) and &lt;em&gt;Mus musculus&lt;/em&gt; (BM 7.0 mm) it is &lt;em&gt;relatively&lt;/em&gt; long. However, as said, other bats with lower upper-frequency limits have longer BM lengths, e.g., &lt;em&gt;Pteronotus parnellii&lt;/em&gt; (13.2 mm) and &lt;em&gt;Rhinolophus ferrumequinum&lt;/em&gt; (16.1 mm). Indeed, the BM length has been correlated both with an extension in frequency range as well as enhanced frequency resolution &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1880079&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Dannhof &amp;amp; Bruns, 1991)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1880079&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dannhof &amp;amp; Bruns, &lt;em&gt;Hear Res&lt;/em&gt; (1991); &lt;strong&gt;53&lt;/strong&gt;: 253-68&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598973/#B29&quot; rel=&quot;nofollow noreferrer&quot;&gt;Davies &lt;em&gt;et al., Front Zool&lt;/em&gt; (2013); &lt;strong&gt;10&lt;/strong&gt;: 2&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/5956244&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pye, &lt;em&gt;J Morph&lt;/em&gt; (1966), &lt;strong&gt;118&lt;/strong&gt;: 495-510&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-06T00:53:54.313" LastActivityDate="2015-07-06T00:53:54.313" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35790" PostTypeId="2" ParentId="35780" CreationDate="2015-07-05T12:56:58.893" Score="3" Body="&lt;p&gt;The Nail itself consists of dead keratinous cells that shrink upon dying and become translucent. This gives the nail itself its white coloration. The reason it appears pink when it overlaps the finger is because of underlying blood vessels that color the live tissue pink just like your skin, and this shows through the nail itself. The lunula is the most proximal region of the fingernail that is crescent shaped and appears more white than the rest of the nail bed. The reason for the whiter color is that the underlying blood vessels are obscured by a denser stratum basale (one of the lower layers of the skin).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See: &lt;a href=&quot;https://books.google.com/books?id=OCUwcAAACAAJ&amp;amp;dq=human%20anatomy%20martini&amp;amp;source=gbs_book_other_versions&quot; rel=&quot;nofollow&quot;&gt;Human Anatomy by Martini&lt;/a&gt;&#xA;If you don't have this book, you could at least start at wikipedia which does describe the anatomy of the fingernail with more or less accuracy: &lt;a href=&quot;https://en.wikipedia.org/wiki/Nail_(anatomy)&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14587" LastEditorUserId="14587" LastEditDate="2015-07-05T13:15:36.833" LastActivityDate="2015-07-05T13:15:36.833" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35791" PostTypeId="2" ParentId="35780" CreationDate="2015-07-05T14:17:53.127" Score="4" Body="&lt;p&gt;The Nightman is giving you a headstart to understand and read about nail colour. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to add a different view to this question from &quot;Colour and Pathology&quot; point of view. Finger nails have been an excellent source of evidence for the initial physical diagnosis process. Nail colour and texture can be an indiator for a wide range of medical conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may take a look at this &lt;a href=&quot;http://stanfordmedicine25.stanford.edu/the25/hand.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;link : The hand in Diagnosis Process and discusses about nail pathology.&lt;/a&gt;. However this diagnosis gets a little tedious if the patient has &lt;em&gt;colourfully&lt;/em&gt; painted their nails with nail polish...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see many of the answers do include an image - well at the end it's anatomy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DUffl.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://biologicalexceptions.blogspot.sg/2013/07/tough-as-nails.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here's a relative simple and fun to read article to clarify any doubts you have about Keratin in nails being dead or not, for its colour and why it's tough.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;The cuticle and matrix are white because the melanocytes there are inactive, so there is no pigment produced.&lt;/strong&gt; The matrix cells divide and the new cells produce a lot of keratin protein. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;The older cells fill with keratin and die, and the new cells push them out of the way – this means toward the end of your finger. This is how your nails grow.&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;But our fingernail doesn’t look like individual cells. You are&#xA;   sloughing millions of skin cells each day, but for a nail the dead&#xA;   cells all mass together. Nails only wear away or must be trimmed.&#xA;   Individual cells are not lost. &lt;strong&gt;The solidity of the nail comes from the&#xA;   connecting of the dead cells together by junctions between the cells&#xA;   called desmosomes&lt;/strong&gt;, and by the interlocking of the cells like jigsaw&#xA;   puzzle pieces. But there’s more.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Individual keratin protein filaments also become connected so that the entire mass of keratin becomes one solid structure. This is called cornification, like the stratum corneum (the outer, dead layers) of your skin.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;One of the two main forms of keratin in your nails is crystalline keratin, which is rigid, stronger, and has an ordered structure - like a tinker toy cube. &lt;strong&gt;Transmitted light is less likely to strike an atom and bounce back when the atoms are all lined up, so this is why many crystalline lattices appear translucent.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8709" LastEditorUserId="8709" LastEditDate="2015-07-07T03:57:21.103" LastActivityDate="2015-07-07T03:57:21.103" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35792" PostTypeId="1" AcceptedAnswerId="35796" CreationDate="2015-07-05T16:56:53.940" Score="6" ViewCount="270" Body="&lt;p&gt;Most gastropods exhibit sinistral  (right hand) winding of their shells. But very few species are anti sinistral. Have there been any theories as to why such a great difference?&lt;/p&gt;&#xA;" OwnerUserId="9906" LastActivityDate="2015-07-05T19:00:25.340" Title="Are there any theories why such an imbalance in chirality of molluscs?" Tags="&lt;evolution&gt;&lt;invertebrates&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35793" PostTypeId="2" ParentId="35786" CreationDate="2015-07-05T17:18:28.940" Score="15" Body="&lt;p&gt;The bacteria in the foregut of cud chewing animals (e.g. cows) provide enough B12 and other B vitamins. Uptake of B12 happens mainly in the small intestine. There are lots of bacteria in the human intestine but most fermentation of plant matter happens in the hindgut. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hindgut fermentation also produces B12 but since this happens past the small intestine it is not sufficient to provide enough B12. Therefore non foregut fermenting herbivores (e.g. rabbits) get their B12 when they consume their own feces, which they do anyway to obtain higher digestion efficiency of plant matter. I would not recommend this process to any vegan human though. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As mentioned by bonCodigo, these animals need to take up enough cobalt, and their requirements for this element are higher than our own. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Source:&#xA;&lt;a href=&quot;http://physrev.physiology.org/content/78/2/393.short&quot;&gt;Contributions of Microbes in Vertebrate Gastrointestinal Tract to Production and Conservation of Nutrients&lt;/a&gt;&#xA;C. EDWARD STEVENS , IAN D. HUME&#xA;Physiological Reviews Published 1 April 1998 Vol. 78 no. 2, 393-427&lt;/p&gt;&#xA;" OwnerUserId="15138" LastEditorUserId="10456" LastEditDate="2015-07-05T23:22:54.827" LastActivityDate="2015-07-05T23:22:54.827" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35794" PostTypeId="1" AcceptedAnswerId="35798" CreationDate="2015-07-05T17:37:10.923" Score="11" ViewCount="7889" Body="&lt;p&gt;I've seen a few videos about chickens being laid on their backs for a few seconds after which the chickens stay in that position until they are turned over. Comments around the video suggested that lying on their backs is a very unnatural position for most birds and so they don't have any reflexes or instincts that would help them get back up. But this is only speculation. Why is that really happening? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here's one video demonstrating the effect:&#xA;&lt;a href=&quot;https://youtu.be/R9mzz9jxNsM&quot;&gt;https://youtu.be/R9mzz9jxNsM&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've been told &lt;a href=&quot;https://en.wikipedia.org/wiki/Chicken_hypnotism&quot;&gt;Chicken hypnotism&lt;/a&gt; is related to this.&lt;/p&gt;&#xA;" OwnerUserId="1373" LastEditorUserId="1373" LastEditDate="2015-07-05T17:53:06.643" LastActivityDate="2015-07-05T19:28:59.550" Title="Why do chickens not try to get up if laid on their backs?" Tags="&lt;ornithology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35796" PostTypeId="2" ParentId="35792" CreationDate="2015-07-05T17:41:40.433" Score="3" Body="&lt;p&gt;&lt;strong&gt;Why so many molluscs exhibit sinistral winding?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The estimates of the number of &lt;a href=&quot;https://en.wikipedia.org/wiki/Mollusca&quot; rel=&quot;nofollow&quot;&gt;molluscs&lt;/a&gt; vary quite greatly between 50,000 and 200,000 species. Of those molluscs species, about 70'000 are &lt;a href=&quot;https://en.wikipedia.org/wiki/Gastropoda&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Gasteropoda&lt;/em&gt;&lt;/a&gt;. &lt;em&gt;Gasteropa&lt;/em&gt; is most diverse &lt;em&gt;Mollusca&lt;/em&gt; phylum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The winding you describe is present in all &lt;em&gt;Gasteropoda&lt;/em&gt; and is often called &lt;a href=&quot;https://en.wikipedia.org/wiki/Torsion_(gastropod)&quot; rel=&quot;nofollow&quot;&gt;the torsion&lt;/a&gt;. So the answer to why there are so many molluscs that make a torsion is simply, because of phylogenetic independence. The torsion evolved only once in the gastropods. The answer to the more specific question, why is the torsion right handed rather than left handed in all gastropods is 1) phylogenetic independence again. The torsion evolved only once and was therefore either sinistral or anti-sinistral. There is no need for an explanation of why they are all sinistral because the observations are not independent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why has the torsion evolved at first place?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One may ask &lt;code&gt;but why did the torsion evolved at first place?&lt;/code&gt;. I think the reasons are still to be discovered. The following is a summary of what I read on wikipedia (&lt;a href=&quot;https://en.wikipedia.org/wiki/Torsion_(gastropod)#Evolutionary_roles&quot; rel=&quot;nofollow&quot;&gt;torsion#evolution&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&quot;Why torsion is bad&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a result of this torsion, the anus is found next to the mouth which is an obvious hygiene issue and therefore seems rather deleterious. Moreover, there are a whole bunch of issues about organs spinning around and entwining. Also, ventilation seems to be reduced by the torsion which is pretty deleterious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;&quot;Why torsion is good&quot;&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, because there's no &quot;hole&quot; left in the posterior position, the torsion may help preventing sediments. Some have suggested that the torsion may allow to move sensory organs closer to the head. The most likely explanation is that the torsion might have evolved as a defense mechanisms against predation as torsion allow an organism to hide its head behind its shell. Finally, citing from wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The evolution of an asymmetrical conispiral shell allowed gastropods to grow larger but resulted in an unbalanced shell. Torsion allows repositioning of the shell, bringing the centre of gravity back to the middle of the gastropod’s body, and thus helps prevent the animal or the shell from falling over.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Note also that&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Whatever original advantage resulted in the initial evolutionary success of torsion, subsequent adaptations linked to torsion have provided modern gastropods with further advantages.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why sinistral rather than anti-sinistral&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To repeat myself, we only have one single observation of torsion (as it evolved only once) and this observation is either sinistral or anti-sinistral. It sounds therefore quite likely that stochastic processes have driven the evolution of sinistral (rather than anti-sinistral) torsion. In other words, the first mutation allowing for some degree of torsion was probably causing a sinistral torsion and this is it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But there might eventually be a more functional reason for why torsion evolved to be sinistral. The reasons would then be related to the already existing asymmetry of organs. For example, anti-sinistral torsion may yield to more entwining between the gut and the respiratory system, or to not squeeze too much the one lung, who'd be smaller than the other one due to the presence of circulatory organs. I don't have enough knowledge in the anatomy of the molluscs ancestors to have a good intuition of whether I'd expect sinistral or anti-sinistral torsion to be more beneficial.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-07-05T19:00:25.340" LastActivityDate="2015-07-05T19:00:25.340" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35797" PostTypeId="1" AcceptedAnswerId="35834" CreationDate="2015-07-05T17:46:34.417" Score="3" ViewCount="141" Body="&lt;p&gt;I am viewing (through &lt;a href=&quot;https://www.edx.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;edX&lt;/a&gt; ) an introduction course to computational neuroscience. In the second lecture, the Hodgin-Huxley model is considered. I am going over some of the questions and have encountered a problem with one of them (a picture of the exercise is attached below). I have a strong background in mathematics, but my background in biology is yet very poor. I am having a hard time connecting the biology to the math. Can anyone help with this question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/rYgfs.png&quot; alt=&quot;enter image description here&quot;&gt; &#xA;&lt;img src=&quot;https://i.stack.imgur.com/bjfvC.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you!!&lt;/p&gt;&#xA;" OwnerUserId="16594" LastEditorUserId="16594" LastEditDate="2015-07-06T01:06:35.727" LastActivityDate="2015-07-06T22:47:37.853" Title="Hodgin-Huxley model for a single neuron" Tags="&lt;neuroscience&gt;&lt;homework&gt;&lt;neurophysiology&gt;&lt;computational-model&gt;" AnswerCount="1" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="35798" PostTypeId="2" ParentId="35794" CreationDate="2015-07-05T19:19:43.757" Score="11" Body="&lt;p&gt;This phenomenon is called tonic immobility. And those speculations you've mentioned are wrong: they do get back on their feet, only remain in that state for a prolonged time, which depends on the distance and eye contact with whoever laid the chicken on its back, as stated &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0003347272801878&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From this experiment, it can be concluded, that this behavior in which the animal is immobile is a defense against predation, because most attackers sense motion primary.&lt;/p&gt;&#xA;" OwnerUserId="15051" LastEditorUserId="15051" LastEditDate="2015-07-05T19:28:59.550" LastActivityDate="2015-07-05T19:28:59.550" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35799" PostTypeId="1" CreationDate="2015-07-05T20:59:55.913" Score="6" ViewCount="745" Body="&lt;p&gt;From some basic googling, I found that nobody has ever proven that people are born gay and that environment plays a great part in homosexuality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wish to know if there is a genetic component to homosexual behaviour. If so, how significant is that component (in some measure such as percentage contribution to the behaviour). What are other factors that play a role in homosexuality i.e. what constitutes environmental factors?&lt;/p&gt;&#xA;" OwnerUserId="16596" LastEditorUserId="3340" LastEditDate="2015-07-06T05:08:52.580" LastActivityDate="2017-03-24T11:37:27.767" Title="How significant is the genetic component of homosexual behaviour?" Tags="&lt;human-biology&gt;&lt;genetics&gt;&lt;behaviour&gt;&lt;homosexuality&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35800" PostTypeId="1" CreationDate="2015-07-05T22:54:55.097" Score="1" ViewCount="36" Body="&lt;p&gt;Do we have documented cases of animals purposely and consciously trying to end their own life? What leads to animal suicide, and is it preventable?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've heard mixed answers from various biologists. Is anyone here capable of providing an answer?&lt;/p&gt;&#xA;" OwnerUserId="16599" LastActivityDate="2015-07-05T22:54:55.097" Title="Do animals commit suicide?" Tags="&lt;zoology&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2015-07-06T04:19:14.483" ContentLicense="CC BY-SA 3.0" />
  <row Id="35803" PostTypeId="1" CreationDate="2015-07-06T03:18:47.510" Score="17" ViewCount="13973" Body="&lt;p&gt;Classically, the linkage between two loci can be measured in centimorgans (cM), which represents the percent chance that these two loci will recombine an odd number of times (generating a recombinant genotype).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Due to independent assortment, markers on different chromosomes are expected to recombine 50% of the time. As I understand, if one conducts a classic experiment and counts various progeny, then deduces the apparent linkage, values of 50 cM or more are interpreted as &quot;&lt;em&gt;impossible to determine whether on separate chromosomes or just recombines very often&lt;/em&gt;&quot;. See (&lt;a href=&quot;https://www.ndsu.edu/pubweb/~mcclean/plsc431/linkage/linkage2.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;source&lt;/a&gt;), with grammar corrected:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The final point that we need to make regards the maximum distance that we can measure. Because of the way in which the calculations are performed, we can never have more (than) 50% recombinant gametes. Therefore the (maximum) distance that two genes can be apart and still measure that distance is just less (than) 50 cM. If two genes are greater than 50 cM apart, then we can not determine if they reside on the same chromosome or are on different chromosomes.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Wikipedia gives an &lt;a href=&quot;https://en.wikipedia.org/wiki/Centimorgan&quot; rel=&quot;nofollow noreferrer&quot;&gt;analytical solution&lt;/a&gt; and also remarks that (d is physical distance):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The probability of recombination is approximately d/100 for small values of d and approaches 50% as d goes to infinity.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, what happens if the linkage &lt;em&gt;is&lt;/em&gt; greater than 50 cM? It seems like classical experiments aside, such a situation is possible in reality.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For instance, &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/projects/mapview/maps.cgi?taxid=4932&amp;amp;chr=IV&quot; rel=&quot;nofollow noreferrer&quot;&gt;yeast chromosome IV is 1530 kb long&lt;/a&gt;, and &lt;a href=&quot;http://www.yeastgenome.org/pgMaps/pgMap.shtml&quot; rel=&quot;nofollow noreferrer&quot;&gt;averages 0.31 cM/kbp&lt;/a&gt;. Let's take two genes on Chr.IV:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene?cmd=retrieve&amp;amp;dopt=full_report&amp;amp;list_uids=851667&quot; rel=&quot;nofollow noreferrer&quot;&gt;DNF2&lt;/a&gt; is at about +631 kb.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene?cmd=retrieve&amp;amp;dopt=full_report&amp;amp;list_uids=852068&quot; rel=&quot;nofollow noreferrer&quot;&gt;TOM1&lt;/a&gt; is at about +1370 kb.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The physical distance between these is about 734 kb. According to the cM/kbp value, the centimorgan distance is &lt;span class=&quot;math-container&quot;&gt;$734\text{ kb} \cdot 0.31\text{ cM}/\text{kb} = 228 \text{ cM}$&lt;/span&gt; . How to interpret this 228?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If I mate a haploid yeast which is &lt;em&gt;DNF2 TOM1&lt;/em&gt; with another which is &lt;em&gt;dnf2 tom1&lt;/em&gt; (lowercase indicating minor allele rather than deletion), then sporulate them, what is the chance of getting spores with &lt;em&gt;DNF2 tom1&lt;/em&gt; or &lt;em&gt;dnf2 TOM1&lt;/em&gt; genotypes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I realize that the cM/kbp value is only a simplification and that in practice linkage is a more complex phenomenon. Nevertheless, it seems plausible that several crossover events can happen on Chr.IV since it is so big. This includes the possibility of 1, 3, 5 and more crossovers which would create a hybrid (assuming they all happen between these two loci), as well as the possibility of 2, 4, etc crossovers which would create a non-hybrid spore (at least as far as our chosen markers are concerned).&lt;/p&gt;&#xA;" OwnerUserId="540" LastEditorUserId="43480" LastEditDate="2019-03-29T22:58:11.573" LastActivityDate="2020-09-17T14:07:20.190" Title="Genetic linkage greater than 50 centimorgans" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;recombination&gt;&lt;genetic-linkage&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="5" ContentLicense="CC BY-SA 4.0" />
  <row Id="35804" PostTypeId="2" ParentId="35724" CreationDate="2015-07-06T03:26:28.670" Score="3" Body="&lt;p&gt;This has been studied by some of my labmates in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24753217&quot; rel=&quot;nofollow&quot;&gt;Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales?&lt;/a&gt; I am not involved in their research, but here is the gist of the paper:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Different scales are, as you say, developed based on different criteria. In particular, Eisenberg scale is one of the consensus scales, that is hopefully at least as good as all of its components. It was believed that there were no big performance differences between scales. This could be why Uniprot doesn't specify their choice of scale: at the time, it didn't matter too much. A study in 2009 showed that the new UHS scale was actually better than others.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The results of the benchmark are that the differences are indeed not so big: roughly $\pm2\%$ in difference in prediction accuracy. The overall winner? &lt;a href=&quot;http://www.nature.com/nature/journal/v433/n7024/abs/nature03216.html&quot; rel=&quot;nofollow&quot;&gt;Hessa&lt;/a&gt;, scoring $1.29\ \sigma$ over the average of the scales, but closely followed by UHS, PM1D and PM3D. Eisenberg performance, by the way, is average.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Final note: they found that a near optimal window size for all the scales was 21 with double the weight in the central third.&lt;/p&gt;&#xA;" OwnerUserId="13086" LastActivityDate="2015-07-06T03:26:28.670" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35805" PostTypeId="2" ParentId="35757" CreationDate="2015-07-06T04:21:51.787" Score="2" Body="&lt;p&gt;I want to add a book to the list that may be easier for you since it takes it from the perspective of Physics:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finkelstein &amp;amp; Ptitsyn, &lt;em&gt;Protein Physics&lt;/em&gt;, Academic Press (2002). ISBN 0-12-256781-1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It covers structure, thermodynamical processes in proteins, mechanism of folding, function, a bit of bioinformatics. It is designed as a master level course in Biophysics, but it takes most things from the beginning: it even explains what the partition function is (but it helps if you know it already). No prior knowledge in biochemistry is required.&lt;/p&gt;&#xA;" OwnerUserId="13086" LastActivityDate="2015-07-06T04:21:51.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35806" PostTypeId="1" AcceptedAnswerId="35809" CreationDate="2015-07-06T04:41:20.580" Score="18" ViewCount="5086" Body="&lt;p&gt;Many instances of this worm-like creature were found in a water system for a mountain cabin in the Sierra Nevada mountains of the US, in late June / early July.  The water system collects water from an enclosed spring.  Can you help identify this creature?  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Clues:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The worms have two &quot;points&quot; on their heads. &lt;/li&gt;&#xA;&lt;li&gt;They can stretch out and be long and thin, or when poked (or are resting) they contract into a small blob.  &lt;/li&gt;&#xA;&lt;li&gt;Here is a picture of a single worm with markings shown.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/hIiWZ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/li&gt;&#xA;&lt;li&gt;Here is a picture of a few worms, somewhat contracted.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Ux4HJ.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=xCBjzdkL7lA&amp;amp;authuser=0&quot;&gt;Here&lt;/a&gt; is a movie of them moving, in natural light.  &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.youtube.com/watch?v=XgaZMEjlLK0&amp;amp;authuser=0&quot;&gt;Here&lt;/a&gt; is a movie of them moving, with backlight.&lt;/li&gt;&#xA;&lt;li&gt;Here are pictures of their undersides and their internal structures.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/KDGUr.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ZRxBe.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/nh1ne.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/TIYig.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/li&gt;&#xA;&lt;li&gt;Whenever I pull some out of the water and put them into a tupperware with the same water, they only survive for around 24 hours, after which they seem to disintegrate.  Here is a picture of about 20 of the worms after about 24 hours, the bulk of them have halfway-decomposed and form a heap in the upper right.  After another day it'll just look like debris in the water, you wouldn't even recognize that there were worms in it.  There is a piece of bacon in there because some suggested putting it there to test if they were leeches, but this disintegration happens repeatably and regardless of the bacon; please ignore the bacon.&lt;br&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/V5xvH.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/li&gt;&#xA;&lt;li&gt;Someone suggested that they are trematodes, but there are no snails, frogs, or other creatures in the storage and collection sections of the water system;  we have looked very closely.  There may be something within a 30-foot section of pipe, but we doubt it.  &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Can you help us identify this creature?  Even just possible families of creatures or general categories would be helpful for us.  &lt;/p&gt;&#xA;" OwnerUserId="16604" LastEditorUserId="3340" LastEditDate="2015-07-06T08:59:35.180" LastActivityDate="2016-09-07T07:06:39.830" Title="Help identify this worm-like thing" Tags="&lt;zoology&gt;&lt;species-identification&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35807" PostTypeId="2" ParentId="35806" CreationDate="2015-07-06T07:36:59.410" Score="5" Body="&lt;p&gt;Their capacity to elongate / contract and their two head lobes make me think they are &lt;a href=&quot;https://en.wikipedia.org/wiki/Planarian&quot; rel=&quot;noreferrer&quot;&gt;Planarians&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The two points  on their heads must be their eyes: &lt;a href=&quot;https://en.wikipedia.org/wiki/Simple_eye_in_invertebrates#Ocelli_or_eye_spots&quot; rel=&quot;noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Simple_eye_in_invertebrates#Ocelli_or_eye_spots&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="1486" LastEditorUserId="1486" LastEditDate="2015-07-06T07:45:30.353" LastActivityDate="2015-07-06T07:45:30.353" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35809" PostTypeId="2" ParentId="35806" CreationDate="2015-07-06T08:55:19.470" Score="16" Body="&lt;p&gt;I am not too sure but this looks like &lt;em&gt;Polycelis sierrensis&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Though it is apparent that the worm in your pictures is a tricladid planarian, I was not too sure about the species and the geographical distribution. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, from the &lt;a href=&quot;http://www.sil.si.edu/smithsoniancontributions/Zoology/pdf_hi/SCTZ-0476.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Smithsonian list of freshwater planarians in North America&lt;/a&gt;, I deduced that this should be &lt;em&gt;Polycelis sierrensis&lt;/em&gt; which is found in California and Nevada (&lt;a href=&quot;http://www.sil.si.edu/smithsoniancontributions/zoology/pdf_hi/SCTZ-0135.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kenk ,1973&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://eol.org/pages/4976580/overview&quot; rel=&quot;nofollow noreferrer&quot;&gt;EOL page&lt;/a&gt; on this species also concurs with the geographical distribution. Moreover, the shape and dimensions of the worm, as described in EOL, matches with that of the ones you have got. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could not find a picture of &lt;em&gt;P. sierrensis&lt;/em&gt; but this is how a general &lt;em&gt;Polycelis&lt;/em&gt; looks like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xwfNt.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-09-07T07:06:39.830" LastActivityDate="2016-09-07T07:06:39.830" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35810" PostTypeId="1" CreationDate="2015-07-06T09:50:40.200" Score="0" ViewCount="83" Body="&lt;p&gt;I'm having a bit of trouble tackling this question. Any help on what I should write about or the points I should mention would be much appreciated. I keep seeing articles about eQTL and QTL are these relevant as well? &lt;/p&gt;&#xA;" OwnerUserId="16609" LastEditorUserId="9943" LastEditDate="2015-07-06T10:12:46.683" LastActivityDate="2015-07-06T10:25:28.507" Title="Critical discussion: Gene expression and systems biology allows us to understand the control of complex traits" Tags="&lt;gene-expression&gt;&lt;systems-biology&gt;&lt;gene&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35811" PostTypeId="2" ParentId="35810" CreationDate="2015-07-06T10:25:28.507" Score="-3" Body="&lt;p&gt;Turns to be too long for a comment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are looking for explanation of the title/question, than it is following (roughly).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we get information about gene expression from all different cell types, and extract also interactions between those genes (if &lt;em&gt;a&lt;/em&gt; gets higher then &lt;em&gt;b&lt;/em&gt; gets lower), this will allow studying multigene traits. E.g., life quality, height, mental disabilities, cardiovascular risks etc. Thing is that for most health problems that stem from single gene variation we already know named gene, or can easily find it out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More complex issues are often hidden in statistics, links are not so clear. So, for example, autism is described by genetic variations (so far) only in less than 30% of cases or so. In other cases there is no genetic predisposition or strong evidence. Mainly that is so because many genes interact to produce final trait or illness. Looking with microscope one gene at a time will not provide information about it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You should look into multi-gene traits, maybe pick your favourite illness (e.g. autism) and see how it is hereditary (tip: not fully). Whole-genome sequencing is important tool in tracing such issues because it gives wide overview and &lt;em&gt;a lot&lt;/em&gt; of genetic information about patient.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-07-06T10:25:28.507" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35814" PostTypeId="1" AcceptedAnswerId="35821" CreationDate="2015-07-06T12:19:07.583" Score="5" ViewCount="2217" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Pulse&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pulse rate&lt;/a&gt; is easily felt when gently pressing the arteries in the wrist or neck region (Fig. 1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XUeVZ.jpg&quot; alt=&quot;assessing pulse rate&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Feeling the pulse at the radial artery. Source: &lt;a href=&quot;https://en.wikipedia.org/wiki/Pulse&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Arteries supply the thin vasculature in the capillary bed where the blood flow encounters a large increase in resistance due to the narrow vasculature and blood flow is reduced, albeit the pressure may still be relatively high. The capillary bed, in turn, feeds the venous system (Fig. 2), characterized by a low blood pressure and relatively slow and &lt;strong&gt;&lt;em&gt;continuous&lt;/em&gt;&lt;/strong&gt; blood flow. This steady, slow blood flow is apparent during blood sampling procedures from the veins in the arm, where I have never noticed any pulsatile flow by visual observation (anecdotal evidence, but quite representative I'm sure).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JPLXF.jpg&quot; alt=&quot;vasculature&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 2. Blood vessels. Source: &lt;a href=&quot;http://www.arubastudy.org/images/normalVessel.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Aruba trial&lt;/a&gt;.&lt;/sup&gt;   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there an observable/measurable pulse in the capillaries and veins, or is blood flow continuous in these vessels?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;PS. This question was re-formulated based on a deleted question posted by @laggingreflex and credits go to OP.&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-07T05:31:55.020" LastActivityDate="2015-07-07T05:31:55.020" Title="Is pulse rate measurable in the capillary bed and venous vasculature?" Tags="&lt;blood-circulation&gt;&lt;circulatory-system&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35816" PostTypeId="1" CreationDate="2015-07-06T12:35:39.843" Score="2" ViewCount="932" Body="&lt;p&gt;In &lt;a href=&quot;http://www.nature.com/nsmb/journal/v21/n7/pdf/nsmb.2845.pdf&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; the authors depleted core histone heterodimers H3-H4 at 90 % from the cytoplasm of &lt;em&gt;Xenopus&lt;/em&gt; oocytes. They state that their concentration is in the order of 6 uM. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is, are histones found in cytoplasm besides the nucleus location? (ignoring the newly sythesized ones), and if so, is there any known function? &lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="9943" LastEditDate="2015-07-06T13:48:39.300" LastActivityDate="2015-07-06T23:34:30.317" Title="Are there histones present in the cytoplasm?" Tags="&lt;cell-biology&gt;&lt;histone&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35817" PostTypeId="1" AcceptedAnswerId="35822" CreationDate="2015-07-06T12:40:13.217" Score="6" ViewCount="4134" Body="&lt;p&gt;As per my understanding a &lt;a href=&quot;https://en.wikipedia.org/wiki/Sphygmomanometer&quot; rel=&quot;nofollow noreferrer&quot;&gt;sphygmomanometer&lt;/a&gt; when wrapped around the arm and inflated only measures the &lt;strong&gt;pressure of the air inside the cuff&lt;/strong&gt;, doesn't it? How does that translate directly to the pressure value of blood flowing across the artery?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/y6Xs7.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3141" LastEditorUserId="8709" LastEditDate="2015-07-07T08:38:43.480" LastActivityDate="2015-07-07T15:16:42.057" Title="How does pressure measured by sphygmomanometer translate directly to blood pressure?" Tags="&lt;blood-pressure&gt;&lt;measurement&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35818" PostTypeId="1" AcceptedAnswerId="35876" CreationDate="2015-07-06T12:52:05.480" Score="2" ViewCount="242" Body="&lt;p&gt;Nanodiscs have changed they way we can study the structures, insertion, and functions of transmembrane proteins. Below is an image of a nanodisc bilayer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/G4Mjd.png&quot;&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The key difference, as far as I can tell, over traditional liposome studies are that one can alter the lipid composition more easily.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Have any studies been achieved on quantifying energetics in these nanodiscs &lt;em&gt;ie&lt;/em&gt; energy transfer upon insertion, or stability of the protein in the nanodisc &lt;em&gt;etc&lt;/em&gt;?&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2015-07-06T17:02:30.630" LastActivityDate="2015-07-07T23:39:52.693" Title="Can Nanodiscs be used to study membrane energetics?" Tags="&lt;biochemistry&gt;&lt;proteins&gt;&lt;biophysics&gt;&lt;cell-membrane&gt;&lt;lipids&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35821" PostTypeId="2" ParentId="35814" CreationDate="2015-07-06T14:24:40.667" Score="2" Body="&lt;p&gt;In the capillary bed? Absolutely! In the venous return? Depends!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I had to build one of &lt;a href=&quot;https://en.wikipedia.org/wiki/Pulse_oximetry#Indicationm&quot; rel=&quot;nofollow&quot;&gt;these&lt;/a&gt; for class. In short: you can tell how oxygenated the blood is by its color, but you have to correct for how much blood there is: The dilation of the arterioles and capillaries with the heartbeat increases the size of the area being measured, and changes all sorts of properties including conductance. There's a neat heartbeat monitoring method method that involves putting two electrodes on your arm, one at the wrist and one at the elbow, and measuring the increase in conductivity every time your heart beats and your arm swells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Depending on heart rate and all sorts of other things, there's not usually a detectable heartbeat in the veins right outside the heart (see the &lt;a href=&quot;https://en.wikipedia.org/wiki/Central_venous_pressure&quot; rel=&quot;nofollow&quot;&gt;CVP&lt;/a&gt;, which is pretty much flat). However, the jugular venous pressure is the pressure of the internal jugular vein that drains the head, and that has heartbeat oscillations (not one-to-one, there are &quot;echoes&quot; and other weirdnesses because it's almost connected to the heart. See &lt;a href=&quot;https://en.wikipedia.org/wiki/Jugular_venous_pressure&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; for more). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In sum: The capillary bed absolutely swells and contracts with each heartbeat, but in the veins blood usually just oozes along. There are a couple exceptions but mostly they're silent.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(The Korotkoff sounds you're talking about are a fluid dynamics thing. When the veins are regular-sized they're wide enough to permit laminar flow(where all the blood moves in a straight line), which is smooth but still pulsatile. Like &lt;a href=&quot;https://www.youtube.com/watch?v=8PQNIESnz58&quot; rel=&quot;nofollow&quot;&gt;these guys&lt;/a&gt; the blood flow starts and stops but is in sync with itself. When you compress them you increase the &lt;a href=&quot;https://en.wikipedia.org/wiki/Reynolds_number#Transition_and_turbulent_flow&quot; rel=&quot;nofollow&quot;&gt;Reynolds number&lt;/a&gt; and you get turbulent flow, which you can hear because it's making noise.)&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-07-06T14:24:40.667" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35822" PostTypeId="2" ParentId="35817" CreationDate="2015-07-06T14:39:19.610" Score="5" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Korotkoff_sounds&quot; rel=&quot;nofollow&quot;&gt;Korotkoff sounds&lt;/a&gt;!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The blood pressure measurement process is fairly cool, and goes like this.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Inflate the cuff to well over plausible blood pressures (250mmHg or so).&lt;/li&gt;&#xA;&lt;li&gt;Slowly deflate the cuff while listening to the artery.&lt;/li&gt;&#xA;&lt;li&gt;When you start to hear sounds, that's when the systolic blood pressure is higher than the cuff pressure and the heart can squeeze a little blood through the cuff, which makes a little squirty noise.&lt;/li&gt;&#xA;&lt;li&gt;As cuff pressure continues to drop it stays between the systolic and diastolic blood pressures and therefore bloodflow stops and starts and creates audible turbulence.&lt;/li&gt;&#xA;&lt;li&gt;When the artery stops making noise, the cuff pressure is below the diastolic blood pressure and the cuff has no effect on the artery, so it goes back to laminar flow that doesn't make noise.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Measuring the pressure of the cuff is just part of controlling the pressure of the cuff. You could conceivably measure blood pressure by submerging their arm in water(mercury would not require a conversion, but vats of mercury are unpopular in doctor's offices) and listening for Korotkoff sounds and measuring the depths where they start and stop.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: The &lt;em&gt;actual question&lt;/em&gt; here is how does cuff pressure physically change the arterial surroundings, not how do we link the two clinically.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The body is mostly water, and water is incompressible. For small strains(amount of deformation) flesh isn't that springy and mostly &quot;flows&quot; like water. When you pressurize the cuff around the arm, the flesh of the arm equilibrates to the cuff pressure the way balloons equilibrate to the air pressure, only less dramatically because water is mostly incompressible. For small pressures and large cuffs, therefore, the cuff pressure &lt;em&gt;is&lt;/em&gt; the pressure on the artery wall, and by listening for Korotkoff sounds while varying the cuff pressure the blood pressure can be roughly established.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason why you don't lose all blood flow to your extremities while diving underwater is because the systemic pressure on all of your body raises your internal blood pressure, making the net external pressure on any part of your body zero. (The cuff works by exerting a relative pressure difference on part of your body.) At high altitude the sphygmanometer is still accurate-ish because the cuff pressure relative to the atmosphere is still the same as the blood pressure, relative to the atmosphere. If you had air for blood(or any compressible fluid) your veins would collapse underwater. This is why your ears hurt while diving deeply if you don't equalize them: your ear is full of compressible air, and at depth the air attempts to shrink more than the flesh around it, pulling things out of place painfully.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="4109" LastEditDate="2015-07-07T15:16:42.057" LastActivityDate="2015-07-07T15:16:42.057" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="35823" PostTypeId="1" CreationDate="2015-07-06T15:09:36.237" Score="3" ViewCount="67" Body="&lt;p&gt;GM tomatoes seem less tasty. Has there been any research on GMOs with regard to taste?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can scientists introduce a gene to, let's say, tomatoes, which would enhance the flavour? If not, why?&lt;/p&gt;&#xA;" OwnerUserId="16612" LastEditorUserId="9943" LastEditDate="2015-07-06T23:03:37.313" LastActivityDate="2015-07-06T23:03:37.313" Title="Do genetic modifications exist to enhance the taste of tomatoes?" Tags="&lt;genetics&gt;&lt;sensation&gt;" AnswerCount="0" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="35824" PostTypeId="1" CreationDate="2015-07-06T15:38:11.380" Score="7" ViewCount="768" Body="&lt;p&gt;I am reading the classic &lt;a href=&quot;http://www.jstor.org/stable/2408641&quot; rel=&quot;nofollow&quot;&gt;Weir and Cockerham 1984&lt;/a&gt; paper about $F_{ST}$ estimation. At the beginning (first page, right column), they define 3 statistics.&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;$F$ is the correlation of genes within individuals (&quot;inbreeding&quot;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;$\theta$ is the correlation of genes of different individuals in the same population (&quot;coancestry&quot;)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;$f$ is the correlation of genes within individuals within populations.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;They also state that the 3 statistics are related by&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$f = (F-\theta)(1-\theta)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't quite understand those 3 statistics and especially I don't understand why this relationship holds true. Can you help me with that?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2016-08-06T17:19:23.260" LastActivityDate="2016-10-25T15:50:57.120" Title="Understanding F-statistics in population genetics" Tags="&lt;evolution&gt;&lt;theoretical-biology&gt;&lt;population-genetics&gt;&lt;population-biology&gt;&lt;statistics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35825" PostTypeId="2" ParentId="35806" CreationDate="2015-07-06T15:45:04.207" Score="6" Body="&lt;p&gt;The overall shape appears to match that of a &lt;a href=&quot;https://en.wikipedia.org/wiki/Flatworm&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;flatworm&lt;/strong&gt;&lt;/a&gt; or &lt;a href=&quot;https://en.wikipedia.org/wiki/Planarian&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;planarian&lt;/strong&gt;&lt;/a&gt;, but those don't have eyestalks. Also, in the images you posted, none of the worms appear to have the characteristic eyespots of a flatworm, although they DO look planarian-like in some photos:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/gNjY4.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If they didn't look so thin, I'd say they were common &lt;a href=&quot;https://en.wikipedia.org/wiki/Slug&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;garden slugs&lt;/strong&gt;&lt;/a&gt;. We get them all the time down in Southeast Texas, and they're attracted to humid areas, especially wetness. They usually have thicker bodies, though:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nOoEx.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've never put salt on a planarian before, but the behavior you describe is exactly what happens when a common slug hits salt. They curl up into what looks like a wad of gum, then shrivel up into a blackened husk. On the other hand, slugs are definitely NOT mountainous creatures. And they're definitely NOT leeches, which we also get down in Southeast Texas.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Based on your location and the images, you're probably looking at some sort of freshwater planarian. They're most likely in the source spring itself.&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="16613" LastActivityDate="2015-07-06T15:45:04.207" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35827" PostTypeId="1" CreationDate="2015-07-06T17:34:54.253" Score="3" ViewCount="315" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;At equivalent pore sizes and pressures, which exhibits faster flow rates, cellulose acetate membranes or glass microfiber filters? &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;I know cellulose acetate exhibits low protein binding, but what about glass microfibers? Would they be suitable when protein recovery is essential?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="16615" LastActivityDate="2015-07-07T05:15:49.847" Title="Cellulose acetate membrane filters vs. glass microfiber filters" Tags="&lt;microbiology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35828" PostTypeId="2" ParentId="35803" CreationDate="2015-07-06T19:37:18.677" Score="7" Body="&lt;p&gt;Just to be clear, markers on different linkage groups (chromosomes) do not recombine 50% of the time. It is just that unlinked mutations co-segregate 50% of the time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a direct quote from Strickberger's textbook &quot;Genetics&quot; 3rd ed. 1985 p 397:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&gt;&#xA;  After many tests involving numerous sex-linked genes, the entire X chromosome of &lt;em&gt;D. melanogaster&lt;/em&gt; was mapped and found to have a length of 68 map units. This, however, does not mean that there is a recombination frequency of 68 percent in a linkage experiment between &lt;em&gt;yellow&lt;/em&gt; and &lt;em&gt;bobbed&lt;/em&gt; which are at the extreme ends of the X chromosome.  As explained previously, no more than 50 percent recombination is expected between any two loci, since only two of four chromatids in a meiotic tetrad are involved in any particular crossover point.  In fact, the actual recombination value observed between &lt;em&gt;yellow&lt;/em&gt; and &lt;em&gt;bobbed&lt;/em&gt; may be even less than 50 percent in a linkage experiment for the simple reason that not every X chromosome bivalent may have a crossover in that particular interval.&#xA;  &amp;lt;&amp;lt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;1 percent recombination = 1 map unit&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-07-06T19:37:18.677" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35829" PostTypeId="2" ParentId="14593" CreationDate="2015-07-06T19:48:41.547" Score="2" Body="&lt;p&gt;The corneal thickness is genetically programmed. There are multiple genes that induce the final corneal thickness:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;USP37, Chromosome 2; &#xA;GPR15, 3;&#xA;TIPARP, 3;&#xA;CWC27-ADAMTS6, 5;&#xA;RXRACOL5A1, 9;&#xA;LCN12-PTGDS, 9;&#xA;FGF9-SGCG, 13;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and at least 6 other genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/ng/journal/v45/n2/full/ng.2506.html&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;other questions had to be asked as separate ones&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-06T19:48:41.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35830" PostTypeId="2" ParentId="20992" CreationDate="2015-07-06T20:16:04.740" Score="1" Body="&lt;p&gt;&lt;strong&gt;TL;DR : Food gives the human body much more than simply vitamins &amp;amp; minerals. A healthy diet is essential to overall healthiness, not just this one aspect of it.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Micronutrients&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The component you're asking about - vitamins &amp;amp; minerals - are referred to as &quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/Micronutrient&quot; rel=&quot;nofollow&quot;&gt;micronutrients&lt;/a&gt;&quot;, and is only a quarter or so of what the body &lt;a href=&quot;https://en.wikipedia.org/wiki/Healthy_diet&quot; rel=&quot;nofollow&quot;&gt;needs&lt;/a&gt;. Micronutrients are the vitamins like &lt;a href=&quot;https://en.wikipedia.org/wiki/Vitamin_A&quot; rel=&quot;nofollow&quot;&gt;Vitamin A&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/B_vitamins&quot; rel=&quot;nofollow&quot;&gt;Vitamin B&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Vitamin_C&quot; rel=&quot;nofollow&quot;&gt;Vitamin C&lt;/a&gt;, etc. but it's also trace elements like zinc, iron, iodine, and many other metals that the body requires in very small quantities.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is the part of the diet that most people actually overlook, and is what pills like the &quot;once-a-day&quot; vitamin are intended to supplement.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Macronutrients&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Much of what we get from food falls in the category of &quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/Nutrient&quot; rel=&quot;nofollow&quot;&gt;macronutrients&lt;/a&gt;&quot;. These nutrients are the actual building blocks of the body - things like fats, proteins, calcium, carbon, hydrogen, etc. A lot of macronutrients are required on a daily basis, and it would be difficult to condense these into a pill form. An average-sized pill would have to be taken 5-6 times a day in order to provide even a less-than-average amount of macronutrients for the average person.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Digestion&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;The human body is designed to be an engine. The act of eating is hard-coded into human physiology, and the act of digesting food kick-starts a great many processes throughout the body. Digestion is a rather efficient process, and it's one that only works properly when it has enough food to break down. A handful of pills could never fuel this process correctly, since they would simply dissolve in the stomach and never require any kind of breaking down.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Psychological&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Lastly, food &amp;amp; drink have a psychological component to them as well. The human brain is wired so that it desires food on a psychological level. The physical act of eating something soothes that desire in a way that a pill never could. One of the greatest obstacles to someone trying to lose weight is this very component - even when their body technically has what it needs from vitamins, supplements, or shakes, this psychological aspect of hunger makes them want food anyway.&lt;/p&gt;&#xA;" OwnerUserId="16613" LastActivityDate="2015-07-06T20:16:04.740" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35831" PostTypeId="2" ParentId="11157" CreationDate="2015-07-06T20:33:33.147" Score="1" Body="&lt;p&gt;&lt;strong&gt;This is speculation on my part, but it could be a sort of hard-wired biodiversity conservation.&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And as others have noted, it's not restricted to humans. In fact, this &quot;weakness&quot; to cuteness seems to extend throughout the animal kingdom, especially in mammals. There are numerous examples in nature of one species - even a predator - caring for the young of another species. Of course, there are certainly examples of the opposite as well, with predators killing &amp;amp; consuming young prey on a fairly regular basis. It seems most prevalent in mammals &amp;amp; birds, although fish also have examples.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &quot;cuteness&quot; factor may be a way of nature ensuring that not ALL young for a particular species are killed off. The reaction to young may be a way of increasing the survival odds for the otherwise defenseless babies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;With humans in particular, there is a very strong psychological reaction when faced with an infant. Even those adults who normally don't want anything to do with an infant will react when they hear (or see) an infant in distress. As a result, a baby who might otherwise die gets cared for.&lt;/p&gt;&#xA;" OwnerUserId="16613" LastActivityDate="2015-07-06T20:33:33.147" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35833" PostTypeId="1" CreationDate="2015-07-06T21:08:12.120" Score="7" ViewCount="785" Body="&lt;p&gt;I am looking for a data base of life history traits for bird species. Is there such data base? If not, what are your advice on how to collect those data? Is there a handy website that list characteristics of birds around the world? I started to gather those data using wikipedia (and the references anytime wikipedia actually have reference) but it is very cumbersome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The kind of data I am looking for are: &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Reproductive age&lt;/li&gt;&#xA;&lt;li&gt;Average lifespan&lt;/li&gt;&#xA;&lt;li&gt;Average gestation time&lt;/li&gt;&#xA;&lt;li&gt;Number of eggs per reproduction event&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="16618" LastEditorUserId="4108" LastEditDate="2015-07-07T16:25:52.423" LastActivityDate="2016-09-14T02:13:47.887" Title="How to gather life-history traits data on bird species?" Tags="&lt;ecology&gt;&lt;database&gt;&lt;life-history&gt;&lt;data&gt;" AnswerCount="2" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35834" PostTypeId="2" ParentId="35797" CreationDate="2015-07-06T22:47:37.853" Score="2" Body="&lt;p&gt;Since you didn't get the right answer to #6, let's review the basis for this model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The basis of the model is precisely the statement in #6: an individual channel has a defined conductance when it is &lt;em&gt;conducting&lt;/em&gt;, and if all of them are &lt;em&gt;conducting&lt;/em&gt; then the total conductance is the single-channel conductance times the number of channels (conductances in parallel add).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Confusion comes from the fact that, in the terminology used here, an &quot;open&quot; channel is not necessarily &lt;em&gt;conducting&lt;/em&gt;. The probability that a single channel is &lt;em&gt;conducting&lt;/em&gt; is the product $r^{n_1}s^{n_2}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$r^{n_1}$ describes the &quot;activation&quot; process, while $s^{n_2}$ describes the &quot;inactivation&quot; process. These are two separate processes, with the activation process now known to be driven by voltage-dependent changes in the configuration of transmembrane domains of the channel protein, while the inactivation process is a charged part of the protein inside the cell that more slowly moves to block the channel when the cell is depolarized. See &lt;a href=&quot;http://www.scholarpedia.org/article/Gating_currents&quot; rel=&quot;nofollow&quot;&gt;this summary&lt;/a&gt; by Clay Armstrong, who contributed much to our understanding of these processes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in the terminology here, a channel can be &quot;open&quot; (in terms of the $r$ process) but still &quot;inactivated&quot; (through the $s$ process) and thus be &lt;em&gt;non-conducting&lt;/em&gt;. It can also be &quot;closed&quot; (in terms of the $r$ process) and &quot;inactivated&quot;, in which case it is also &lt;em&gt;non-conducting&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The way this is modeled is that $s=1$ means &lt;em&gt;no&lt;/em&gt; inactivation, while $s=0$ means &lt;em&gt;fully inactivated&lt;/em&gt;. So that covers question 3. This is in contrast to the activation process, in which $r=1$ is full activation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Question 4 might be a bit misleading as there may be a hidden assumption that you are starting from being at potential $u_0$ for a long-enough time and then increasing $u$ suddenly (which is how action potentials normally are generated). In that case your understanding of differential equations should make it clear that $\tau_r$ and $\tau_s$ are the time constants for the responses of the $r$ and $s$ processes to a change in $u$. The process with a shorter time constant responds more quickly, so activation precedes inactivation (on the average). The different powers associated with the $r$ and $s$ processes ($n_1,n_2$) might confuse things a bit, but try running this model and you should be convinced.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This might seem convoluted at first, but Hodgkin and Huxley worked out this model based solely on their electophysiological studies (with help from Bernard Katz). It's amazing how this model's postulates of multiple single channels and separate activation and inactivation processes have been so well verified at the molecular level over the past decades.&lt;/p&gt;&#xA;" OwnerUserId="16326" LastActivityDate="2015-07-06T22:47:37.853" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35836" PostTypeId="2" ParentId="35816" CreationDate="2015-07-06T23:34:30.317" Score="2" Body="&lt;p&gt;In early embryogenesis, cell division called cleavage occurs &lt;a href=&quot;http://worms.zoology.wisc.edu/frogs/cleavage/clea_modcell.html&quot; rel=&quot;nofollow&quot;&gt;every 30 min&lt;/a&gt; and there is no transcriptional activity. Oocytes have accumulated important gene transcripts and synthesize the proteins at right times. However, histone is one of the most abundant proteins and it would be difficult to supply enough histone proteins during early embryogenesis while oocytes translate other gene transcripts regulating differentiation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is my speculation, but the article calls cytosolic histones &quot;stockpile&quot;. Just in case, I don't mean that I deny some other roles of histones in cytosol if there are any.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-07-06T23:34:30.317" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35837" PostTypeId="1" AcceptedAnswerId="35846" CreationDate="2015-07-06T23:38:10.510" Score="3" ViewCount="208" Body="&lt;p&gt;Of course we have heard that during stress our immune system is suppressed. This leads me to wonder, does the immune system get suppressed when we are sleeping and why? During both these conditions the body might need to save energy for other biochemical processes, so I wouldn't be surprised that the immune system is suppressed while a person is asleep. &lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="9943" LastEditDate="2015-07-07T00:36:33.790" LastActivityDate="2015-07-07T08:49:03.237" Title="Is the immune system suppressed during sleep?" Tags="&lt;immunology&gt;&lt;sleep&gt;&lt;immunosuppression&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35838" PostTypeId="1" CreationDate="2015-07-07T00:45:35.100" Score="1" ViewCount="290" Body="&lt;p&gt;When measuring your blood pressure in your arm, when you hear the sound to measure the systolic, is that sound NOT the heartbeat?  &lt;/p&gt;&#xA;" OwnerUserId="16622" LastActivityDate="2016-09-19T09:52:28.450" Title="Blood pressure measurement" Tags="&lt;blood-pressure&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35839" PostTypeId="1" CreationDate="2015-07-07T02:03:23.373" Score="7" ViewCount="268" Body="&lt;p&gt;The current global Tiger population is roughly 5100 according to Wikipedia. With habitat destruction and poaching continuing and no effective improvement in conservation, most likely the Tiger population will continue to decrease. I'm wondering what is the theoretical maximum population to which the Tiger species could be restored. Suppose poaching and habitat destruction stopped today and conservation efforts were increased drastically, so the only factors limiting population growth are the natural dynamics between the species and its prey. Could we then restore the global population of tigers to its pre-20th century level of 100,000?&lt;/p&gt;&#xA;" OwnerUserId="13409" LastEditorUserId="3624" LastEditDate="2015-07-21T09:32:44.480" LastActivityDate="2016-01-17T12:07:08.110" Title="Is it theoretically possible to restore the Tiger population to 100,000?" Tags="&lt;zoology&gt;&lt;ecology&gt;&lt;population-dynamics&gt;&lt;mammals&gt;&lt;conservation-biology&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="35840" PostTypeId="1" CreationDate="2015-07-07T02:52:20.923" Score="3" ViewCount="87" Body="&lt;p&gt;Blood donation websites tell you to avoid eating fats a few days before the donation, because when there is a lot of fat in the blood, they can't test for infectious diseases and must discard the blood.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does that mean that if you have, say, high triglycerides, the result of an infection disease blood test will be invalid? Say you test syphilis, HIV, etc. If at the same time you get a result of high triglycerides, does that mean the results of infectious diseases can't be trusted?&lt;/p&gt;&#xA;" OwnerUserId="16623" LastActivityDate="2015-07-07T02:52:20.923" Title="Do High Triglycerides Invalidate Tests for Infections?" Tags="&lt;hematology&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35842" PostTypeId="2" ParentId="35838" CreationDate="2015-07-07T03:40:28.330" Score="3" Body="&lt;p&gt;The sound in question is called the &lt;a href=&quot;https://en.wikipedia.org/wiki/Korotkoff_sounds&quot; rel=&quot;nofollow&quot;&gt;Korotkoff sound&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If the pressure is dropped to a level equal to that of the patient's&#xA;  systolic blood pressure, the first Korotkoff sound will be heard. As&#xA;  the pressure in the cuff is the same as the pressure produced by the&#xA;  heart, some blood will be able to pass through the upper arm when the&#xA;  pressure in the artery rises during systole. This blood flows in&#xA;  spurts as the pressure in the artery rises above the pressure in the&#xA;  cuff and then drops back down beyond the cuffed region, resulting in&#xA;  turbulence that produces an audible sound.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-07T03:40:28.330" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35845" PostTypeId="2" ParentId="35827" CreationDate="2015-07-07T05:15:49.847" Score="1" Body="&lt;ol&gt;&#xA;&lt;li&gt;It would also depend on the pore densities and pressure resistance. &lt;/li&gt;&#xA;&lt;li&gt;Silica is used for gel filtration chromatography to separate proteins. This can be achieved when proteins do not have affinity to silica, and most of proteins could be analyzed with silica gel. Silica and grass are similar materials. However, glass and silica have negative charges on the surface. Under low ionic strength condition, positive charged proteins or positive charged surface of proteins may bind to glass. Cellulose acetate does not have charge but it is hydrophilic.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-07-07T05:15:49.847" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35846" PostTypeId="2" ParentId="35837" CreationDate="2015-07-07T05:46:09.690" Score="1" Body="&lt;p&gt;During stress glucocorticoids, which are steroid hormones produced by adrenal glands (such as cortisol and corticosterone), are released into the blood-stream. These hormones have anti-inflammatory effects. You may say that they suppress the immune system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The circadian rhythm, which controls the sleep-wake cycle, also controls glucocorticoid secretion, thereby reinforcing the sleep-wake responses &lt;a href=&quot;http://dx.doi.org/10.1016/j.bbadis.2011.02.003&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[1]&lt;/sup&gt;&lt;/a&gt;. Sleep deprivation is a form of stress and it causes an elevation in the levels of glucocorticoids. The effect of sleep deprivation could be replicated by adrenectomy (surgical removal of adrenal glands); there is a transcriptional downregulation of several neuroprotective genes &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/20857860&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[2]&lt;/sup&gt;&lt;/a&gt;. Via glucocorticoid mediated signalling, sleep deprivation also results in inhibition of adult neurogenesis in the hippocampus &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/17135354&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[3]&lt;/sup&gt;&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another study says that cytokine (TNFα and IL6) secretion by immune-system cells, are inherently affected by circadian rhythm via a glucocorticoid independent mechanism &lt;a href=&quot;http://dx.doi.org/10.1073/pnas.0906361106&quot; rel=&quot;nofollow&quot;&gt;&lt;sup&gt;[4]&lt;/sup&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Overall, sleep is inversely correlated with reduced inflammation because both the processes are under the control of the circadian clock. Sleep deprivation, as a form of stress, is also correlated with glucocorticoid secretion. It should be understood that sleep doesn't necessarily inhibit glucocorticoid secretion and it would be incorrect to say that reduced inflammatory effects are because of sleep.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-07-07T08:49:03.237" LastActivityDate="2015-07-07T08:49:03.237" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35848" PostTypeId="1" AcceptedAnswerId="35849" CreationDate="2015-07-07T08:15:39.153" Score="0" ViewCount="45" Body="&lt;p&gt;After checking the NCBI &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/hiv-1/interactions/help/&quot; rel=&quot;nofollow&quot;&gt;help page&lt;/a&gt;, I am still unclear about the difference between &lt;strong&gt;protein&lt;/strong&gt; and &lt;strong&gt;replication&lt;/strong&gt; interactions for HIV.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/hiv-1/interactions/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/hiv-1/interactions/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="1590" LastEditDate="2015-07-07T09:14:03.180" LastActivityDate="2015-07-07T09:14:03.180" Title="What is the difference between options protein and replication in the NCBI database?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;virology&gt;&lt;protein-interaction&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35849" PostTypeId="2" ParentId="35848" CreationDate="2015-07-07T08:54:41.357" Score="2" Body="&lt;p&gt;Interactions denote protein-protein interactions, which means physical association between proteins. By nature, these networks/graphs are undirected. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Replication interactions (actually a not very good term) denote gene regulatory interactions that affect HIV replication. These sets also include the regulatory effects of HIV genes on host genes (and hence the terminology is unsuitable). These networks are directed as well as signed (positive or negative interactions i.e. activation or inhibition respectively).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see for yourself, from the dropdown boxes and the interaction lists in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/hiv-1/interactions/browse/&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; page.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-07-07T09:01:33.823" LastActivityDate="2015-07-07T09:01:33.823" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35851" PostTypeId="1" AcceptedAnswerId="35853" CreationDate="2015-07-07T09:26:46.747" Score="18" ViewCount="2859" Body="&lt;p&gt;Ten years ago, I emailed a prominent lung specialist with my suggestion for a treatment for Tuberculosis. His lack of response led me to believe that the idea had no merit whatsoever – but I had no idea what the failings might be. I still don’t and I’m hoping someone will enlighten me as to why this is not worth exploring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The idea is based upon the fact that Mycobacterium Tuberculosis is aerobic – in fact Wikipedia states it “requires high levels of oxygen”. I’d heard that the TB “Sanatoriums” used to practice the treatment of breaking ribs on one side to collapse that lung and “rest” it. It seemed to me that this resting was actually starving the bacterium of Oxygen and killing the infestation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My suggestion is that we take advantage of having two lungs by inserting a pair of breathing tubes into the respiratory tract and into the head of the two bronchi: it may be necessary to use ultrasound or other imaging to accurately position the tubes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We feed pure Nitrogen into one tube, and 40/60 Oxygen/Nitrogen into the other – double Oxygen concentration. The patient therefore receives all their Oxygen requirements through one lung. After some period of time, when we judge that the bacteria in the “starved” lung are all dead, we switch the supplies to the 2 tubes and treat the other lung.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can anyone see why this idea is so flawed?&lt;/p&gt;&#xA;" OwnerUserId="14750" LastEditorUserId="3340" LastEditDate="2015-07-07T17:09:41.027" LastActivityDate="2016-10-07T08:39:30.580" Title="Where’s the flaw in my proposed TB Treatment?" Tags="&lt;human-biology&gt;&lt;medicine&gt;&lt;tuberculosis&gt;" AnswerCount="4" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35852" PostTypeId="1" AcceptedAnswerId="37126" CreationDate="2015-07-07T09:37:28.903" Score="2" ViewCount="1474" Body="&lt;p&gt;I would like to view the chromatogram traces from a few ABI (.ab1) files. I would prefer to use python for this, or a function with python bindings, or at least some open source package such as EMBOSS.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If after viewing a plot I could also extract the plotted data in the form of an array, that would be a huge plus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have tried &lt;a href=&quot;https://www.biostars.org/p/2464/&quot; rel=&quot;nofollow noreferrer&quot;&gt;the relevant Biopython parser&lt;/a&gt;, but it only returns a list of nucleotides (not th actual chromatogram). I have also tried abiview, but I get plots such as this, which makes absolutely no sense:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/xtGOO.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Could you help me out?&lt;/p&gt;&#xA;" OwnerUserId="4795" LastActivityDate="2016-11-29T12:19:06.900" Title="View ABI chromatogram plots with python" Tags="&lt;dna-sequencing&gt;&lt;chromatography&gt;&lt;biopython&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35853" PostTypeId="2" ParentId="35851" CreationDate="2015-07-07T09:45:18.683" Score="23" Body="&lt;ul&gt;&#xA;&lt;li&gt;High oxygen concentration can be deleterious; it can induce oxidative&#xA;damage.&lt;/li&gt;&#xA;&lt;li&gt;The systemic blood circulation would supply oxygen to the&#xA;&quot;oxygen-deprived&quot; lung.&lt;/li&gt;&#xA;&lt;li&gt;Moreover, &lt;em&gt;Mycobacteria&lt;/em&gt; &lt;a href=&quot;http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1002287&quot; rel=&quot;nofollow&quot;&gt;can survive&lt;/a&gt; in anaerobic conditions.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And what if both lungs are infected? There are many flaws in the proposed therapy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Adding this point from one of the comments below:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are several cases of extrapulmonary tuberculosis and in these cases treating just the lung would not make sense.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-07-08T13:32:18.560" LastActivityDate="2015-07-08T13:32:18.560" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="35854" PostTypeId="1" AcceptedAnswerId="35856" CreationDate="2015-07-07T09:48:59.640" Score="2" ViewCount="195" Body="&lt;p&gt;Question migrated from World Building SE.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(For fictional use only, of course :) )&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking for an anasthetic which fulfills the following criteria:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;very strong effect, induces a comatose state in a very short period of time&lt;/li&gt;&#xA;&lt;li&gt;quickly wears off (30 minutes~) with only minor impediments to the recipent upon awakening.&lt;/li&gt;&#xA;&lt;li&gt;Can be 'partially blocked' or delayed by the intake of some medicine or other substance (which needs to be not too uncommon). Maybe some receptors for the anasthetic are blocked by the substance or something similar. Ideally this would result in the recipent falling into a dream-like state for some minutes before the real effect kicks in.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Does the anasthetic have to be made up, or does something like this actually exist?&lt;/p&gt;&#xA;" OwnerDisplayName="user16628" LastActivityDate="2015-07-07T14:22:57.853" Title="Is there a short-term, very strong anesthetic, which can be blocked/delayed by other substances?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;medicinal-chemistry&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35855" PostTypeId="1" AcceptedAnswerId="35863" CreationDate="2015-07-07T09:50:04.953" Score="2" ViewCount="275" Body="&lt;p&gt;In all of the sites I've looked on, one of the symptoms of Celiac's Disease is the failure to grow in children. Why would an immune attack against gluten cause stunted growth?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://celiac.org/celiac-disease/what-is-celiac-disease/&quot; rel=&quot;nofollow&quot;&gt;Celiac.org states:&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;When people with celiac disease eat gluten (a protein found in wheat,&#xA;  rye and barley), their body mounts an immune response that attacks the&#xA;  small intestine. These attacks lead to damage on the villi, small&#xA;  fingerlike projections that line the small intestine, that promote&#xA;  nutrient absorption. When the villi get damaged, nutrients cannot be&#xA;  absorbed properly into the body&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://journals.lww.com/jpgn/Abstract/1994/11000/Catch_up_Growth_in_60_Children_with_Celiac.5.aspx&quot; rel=&quot;nofollow&quot;&gt;Journal of Pediatric Gastroenterology &amp;amp; Nutrition&lt;/a&gt; published a study on catch-up growth in children diagnosed with Celiac's before the age of nine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the lack of nutrients what causes the impaired growth, or is there more to it than that?&lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="16041" LastEditDate="2015-07-07T11:24:49.993" LastActivityDate="2015-07-07T16:34:12.047" Title="How does Celiac's Disease cause people to stop growing?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;immunology&gt;&lt;autoimmune&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35856" PostTypeId="2" ParentId="35854" CreationDate="2015-07-07T09:54:25.393" Score="1" Body="&lt;p&gt;Xenon. It is like an ideal anaesthetic. See &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15181400&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Xenon is an interesting anesthetic as it appears to lack negative&#xA;  inotropicy and vasodilatation, giving great advantages to both&#xA;  patients with limited cardiovascular reserve or those who require&#xA;  hemodynamic stability. It has low toxicity and is not teratogenic.&#xA;  Xenon gives rapid induction and recovery, due to its low blood/gas&#xA;  partition coefficient (0.15), and has a MAC of 63%. Several vitro&#xA;  studies showed that Xenon may protect neural cells against ischaemic&#xA;  injury. Its low blood solubility can take to diffusion hypoxia if&#xA;  Xenon is not substituted by 100% oxygen at the end of anesthesia. It&#xA;  has been shown that, compared to other anesthetic regimens, Xenon&#xA;  anesthesia produces the highest regional blood flow in the brain,&#xA;  liver, kidney and intestine. In conclusion, the most important&#xA;  positive effects of Xenon are cardiovascular stability, cerebral&#xA;  protection and favourable pharmacokinetics. Negative points are high&#xA;  cost and the limited number of ventilators supplying Xenon.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-07-07T09:54:25.393" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="35857" PostTypeId="1" CreationDate="2015-07-07T12:57:55.203" Score="3" ViewCount="824" Body="&lt;p&gt;How to extract protein sequences from a GBK(GenBank) file without scripting?&#xA;I know that writting a script using BioPerl or Biopython can do this, but it is not elegant and daunting to beginners and biology persons. Any thing like&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;$ SOME_PKG_MANAGER install PKG&#xA;$ CMD ab.1234.gbk &amp;gt; ab.1234.faa&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="5035" LastEditorUserId="5035" LastEditDate="2015-07-08T02:28:43.303" LastActivityDate="2015-07-08T02:28:43.303" Title="Extract protein sequences from a GBK(GenBank) file without scripting" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="8" FavoriteCount="1" ClosedDate="2015-07-08T06:09:00.283" ContentLicense="CC BY-SA 3.0" />
  <row Id="35858" PostTypeId="2" ParentId="35854" CreationDate="2015-07-07T13:44:58.837" Score="0" Body="&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Propofol#Pharmacokinetics&quot; rel=&quot;nofollow&quot;&gt;Propofol&lt;/a&gt;&lt;/strong&gt;: a widely used i.v. anesthetic with &lt;a href=&quot;https://en.wikipedia.org/wiki/GABA_receptor&quot; rel=&quot;nofollow&quot;&gt;GABA&lt;/a&gt; agonistic properties. It has to be given continuously &lt;em&gt;i.v.&lt;/em&gt; When stopped, effects wear off in minutes, and recovery is without serious side effects and little nausea. Induction is quick (minutes or less) since it is administered &lt;em&gt;i.v.&lt;/em&gt; &lt;a href=&quot;https://en.wikipedia.org/wiki/Aminophylline&quot; rel=&quot;nofollow&quot;&gt;Aminophylline&lt;/a&gt; (theophylline ethylenediamine), an adenosine receptor antagonist, antagonizes its effects &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs00540-007-0587-x&quot; rel=&quot;nofollow&quot;&gt;(Sakurai &lt;em&gt;et al&lt;/em&gt;., 2008)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Sufentanil&quot; rel=&quot;nofollow&quot;&gt;&lt;strong&gt;Sufentanil&lt;/strong&gt;&lt;/a&gt;: an &lt;a href=&quot;https://en.wikipedia.org/wiki/Opioid&quot; rel=&quot;nofollow&quot;&gt;opioid&lt;/a&gt;. Like propofol, when administered i.v. it is fast acting (onset after 6 minutes) and its effects wear off in ~30 min. Because of its short half life, recovery is fast with few side effects &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24485553&quot; rel=&quot;nofollow&quot;&gt;(Mendel, 2014)&lt;/a&gt;. Full opiate antagonists like &lt;a href=&quot;https://en.wikipedia.org/wiki/Naloxone&quot; rel=&quot;nofollow&quot;&gt;naloxone&lt;/a&gt;, or partial antagonists like &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/druginfo/meds/a605002.html&quot; rel=&quot;nofollow&quot;&gt;buprenorphine&lt;/a&gt; can be used to counteract opioid anesthesia. Note that more common opioids, including heroin, morphine and fentanyl are longer-acting (say hours after injection) and probably not what you are after.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Ketamine&quot; rel=&quot;nofollow&quot;&gt;Ketamine&lt;/a&gt;&lt;/strong&gt;: an NMDA receptor antagonist. It is only used in animal surgeries nowadays, and it is not used for human anesthesia anymore. I mention ketamine only because its effects last for about 30 min after oral ingestion, and it's onset is very rapid (within a minute i.v.). Its side effects include delirium and hallucinations up to 24 hours after use. These side effects are pretty serious and reason for its ban in human anesthesia. I am not aware of antagonists of ketamine action. Theoretically spoken, &lt;a href=&quot;https://en.wikipedia.org/wiki/NMDA_receptor&quot; rel=&quot;nofollow&quot;&gt;NMDA receptor agonists&lt;/a&gt; would do the job, but that is a pretty dangerous class of drugs and mostly applied experimentally as far as I know. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24485553&quot; rel=&quot;nofollow&quot;&gt;Mendel &lt;em&gt;J Clin Anesth&lt;/em&gt; (2014); &lt;strong&gt;26&lt;/strong&gt;: S1–S7&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://link.springer.com/article/10.1007%2Fs00540-007-0587-x&quot; rel=&quot;nofollow&quot;&gt;Sakurai &lt;em&gt;et al., J Anesth&lt;/em&gt; (2008); &lt;strong&gt;22&lt;/strong&gt;:86–8&lt;/a&gt;    &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-07T14:22:57.853" LastActivityDate="2015-07-07T14:22:57.853" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35859" PostTypeId="1" AcceptedAnswerId="35877" CreationDate="2015-07-07T14:43:23.317" Score="2" ViewCount="71" Body="&lt;p&gt;As  continuation to &lt;a href=&quot;https://biology.stackexchange.com/questions/35797/hodgin-huxley-model-for-a-single-neuron&quot;&gt;This&lt;/a&gt; question I have posted. Another set of questions is given for the same model :&#xA;&lt;img src=&quot;https://i.stack.imgur.com/juSJm.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;This time it is also given that for $t&amp;lt;0$ the membrane potential is $u_0$, and at $t=0$ it is instantaneusly jumps to $u'$, and that $u_0,u',u_2,u_{ion}$ are maintained for $t \geq 0$.&#xA;So, with this additional data I could actually compute $r(t)$ and $s(t)$ for $t \geq 0$ in the following way:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For $t \geq 0$, $u(t)=u'$ &#xA;so $r_0(0)=r_0(u') \approx 1$ and $s_0(0)=s_0(u') \approx 0$.&#xA;Also, $\tau_r(0)=\tau_r(u') = 1$ and $\tau_s(0)=\tau_2(u') = 15$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, we get: &#xA;$r' = -\frac{r-1}{1}$ and $s'=-\frac{s-0}{15}$ $\Rightarrow$ &#xA;$r' + r = 1$ and $s' + \frac{s}{15} = 0$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These are a first order linear diff. equation of the form: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;$y'(x)+p(x)y=q(x)$ &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So their solution is of the form:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;$e^{-\int{p(x)dx}}(\int{q(x)^{\int{p(x)d(x)}}}+C)$ ($C$ is a constant)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So I get:&#xA;$r(t)=C_1e^{-t}+1$ and $s(t)=C_2e^{-t/15}$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that we have no way of knowing our initial conditions $r(t=0)$ and $s(t=0)$ (&lt;strong&gt;am I right?&lt;/strong&gt;)&#xA;So for simplisity let's assume that $C_1=C_2=1$ and we get:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;$r(t)=e^{-t}+1$ and $s(t)=e^{-t/15}$.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So for example: $r(t=100) = e^{-100}+1 \approx 1$ and $s(t=100) = e^{-100/15} = 0.0013$ and $r(t=3) = e^{-3}+1 = 1.0498$ and $s(t=3) = e^{-3/15} = 0.8187$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So my question is:&lt;/strong&gt;&#xA;How come answers 4 and 7 below denoted as true?&#xA;&lt;img src=&quot;https://i.stack.imgur.com/ebn43.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16594" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-07-08T00:13:53.967" Title="Hodgin-Huxley model for a single neuron - continuation" Tags="&lt;bioinformatics&gt;&lt;neuroscience&gt;&lt;homework&gt;&lt;neurophysiology&gt;&lt;computational-model&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35861" PostTypeId="1" CreationDate="2015-07-07T15:23:12.977" Score="2" ViewCount="1640" Body="&lt;p&gt;I have been reading some books and am getting slightly confused. Here is roughly what I have read. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The greater the blood urea nitrogen the greater the usage of proteins (since blood urea nitrogen is created via the metabolism of proteins). &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A positive nitrogen balance (where nitrogen balance $=$ N intake $-$ N loss) indicates a greater usage of proteins. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;To me these two seem to be contradictory, if you have greater blood urea nitrogen then surly you will have more nitrogen lost meaning the nitrogen balance would be more negative. So do these two statements contradict and either way please can you explain. &lt;/p&gt;&#xA;" OwnerUserId="16635" LastActivityDate="2015-07-16T06:45:16.490" Title="Blood urea nitrogen and usage of proteins?" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35863" PostTypeId="2" ParentId="35855" CreationDate="2015-07-07T16:34:12.047" Score="1" Body="&lt;p&gt;The &quot;proper&quot; term to use in a case of growth retardation in children is &quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/Failure_to_thrive&quot; rel=&quot;nofollow&quot;&gt;failure to thrive&lt;/a&gt;&quot;, abbreviated as FTT.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Celiac disease is one of the most common Organic endogenous (genetically based) FTT syndromes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main cause of FTT in pediatric celiac patients is malabsorption. In a case of &lt;a href=&quot;http://emedicine.medscape.com/article/931041-clinical&quot; rel=&quot;nofollow&quot;&gt;insufficient vitamins and nutrients&lt;/a&gt; absorption the &lt;a href=&quot;http://patient.info/doctor/coeliac-disease-pro&quot; rel=&quot;nofollow&quot;&gt;child will&lt;/a&gt; (have) FTT.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-07T16:34:12.047" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35868" PostTypeId="2" ParentId="35857" CreationDate="2015-07-07T19:26:44.010" Score="3" Body="&lt;p&gt;My colleagues and I have recently published a toolbox of command-line utilities that are modeled after GNU Textutils (e.g. grep, cut, tr, uniq) called FAST: Fast Analysis of Sequences  (&lt;a href=&quot;http://journal.frontiersin.org/article/10.3389/fgene.2015.00172/full&quot; rel=&quot;nofollow&quot;&gt;cite&lt;/a&gt;).   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To install FAST you can use:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;perl -MCPAN -e 'install FAST'&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Or install the current development version from &lt;a href=&quot;https://github.com/tlawrence3/FAST&quot; rel=&quot;nofollow&quot;&gt;github&lt;/a&gt;. The FAST install comes with a cookbook, sample dataset and all utilities have &lt;code&gt;man&lt;/code&gt; pages. The cookbook is also available on the github wiki. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;To convert the features annotated in a genbank file to fastA sequences you can use &lt;code&gt;gbfcut&lt;/code&gt;. Below are examples of using &lt;code&gt;gbfcut&lt;/code&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To convert all annotated features of a genbank file to fastA format:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;gbfcut genbank-file&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Output only tRNA features:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;gbfcut -k tRNA genbank-file&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Output all feature sequences with a &quot;note&quot; qualifier containing &quot;telomere&quot;:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;gbfcut -q note=telomere genebank-file&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="14701" LastEditorUserId="14701" LastEditDate="2015-07-07T21:10:59.957" LastActivityDate="2015-07-07T21:10:59.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35871" PostTypeId="1" CreationDate="2015-07-07T20:03:28.447" Score="1" ViewCount="40" Body="&lt;p&gt;I remember there being a significant difference in the pathogen-associated molecular patterns (PAMPs) used for detection of lipopolysaccharide (LPS) by mammalian cells and the Limulus amoebocyte lysate (LAL) assay. However, I cannot seem to find a paper that indicated what structure on the LPS lipid A moiety is used for detection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In humans, structure-and-function relationships exist between the phosphate groups of bisphosphorylated glucosamine disaccharide backbone as well as the six fatty acyl tails and the MD-2/TLR-4 co-receptor system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have a paper, or a general lead, as to where I can find what area LAL uses for detection? I haven't had much luck with Google Scholar. &lt;/p&gt;&#xA;" OwnerUserId="16637" LastEditorUserId="948" LastEditDate="2015-07-07T20:08:23.430" LastActivityDate="2015-07-07T20:08:23.430" Title="Differences in structural target for LPS detection by LAL and MD-2/TLR4" Tags="&lt;biochemistry&gt;&lt;immunology&gt;&lt;structural-biology&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35872" PostTypeId="1" AcceptedAnswerId="35884" CreationDate="2015-07-07T21:30:09.457" Score="6" ViewCount="774" Body="&lt;p&gt;I found these creatures stuck to a leaf on my tomato plant in the greenhouse/glasshouse, in early June, in south Oxfordshire in the United Kingdom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They are each about 1-2mm in size. They didn't move much, even when gently nudged, although some did crawl tentatively.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would be very interested to know what these are, especially if they are a beneficial species or a pest!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NIRRa.jpg&quot; alt=&quot;Tiny dark red insects&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16642" LastActivityDate="2019-08-05T08:32:00.800" Title="What are these tiny dark red insects?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35873" PostTypeId="2" ParentId="35851" CreationDate="2015-07-07T22:42:23.270" Score="3" Body="&lt;p&gt;The most evident problem I can see for this TB treatment is that mycobacteria can survive without oxygen. Latent TB (a person is infected but doesn't have active TB) is one of the major problem in the treatment of TB and one-third of the world's population has latent TB! (&lt;a href=&quot;http://www.who.int/mediacentre/factsheets/fs104/en/&quot; rel=&quot;nofollow&quot;&gt;http://www.who.int/mediacentre/factsheets/fs104/en/&lt;/a&gt;). A new TB treatment can only be effective if it targets both active and dormant bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course other aspects need to take into account. Over 95% of TB deaths occur in low- and middle-income countries with reduced access to medications and hospitals. A new treatment needs to have an affordable price, be simple and fast (&lt;a href=&quot;http://aac.asm.org/content/53/3/849.full&quot; rel=&quot;nofollow&quot;&gt;http://aac.asm.org/content/53/3/849.full&lt;/a&gt;). These are other limitations of to the suggested treatment.&lt;/p&gt;&#xA;" OwnerUserId="16581" LastActivityDate="2015-07-07T22:42:23.270" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35874" PostTypeId="2" ParentId="35851" CreationDate="2015-07-07T22:54:27.787" Score="9" Body="&lt;p&gt;The accepted answer is correct but I would like to point out a misunderstanding that has to underly the idea that this would work:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In reality lungs aren't a magical one-way gate for the various gases.  Lungs do not extract oxygen from the air, they permit oxygen exchange between the air and the blood.  Since the air normally has a higher oxygen level than the blood the result is a net transfer of oxygen to the blood--something we see as extracting the oxygen from the air.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, in an anoxic environment you'll get the reverse--oxygen will move from the blood (admittedly, not too much of it as this is blood that has already passed through the body) into the air.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is also why too much carbon dioxide is lethal--the lungs likewise have no magic ability to expel it.  It just normally moves from the higher concentration (the blood) to the lower concentration (the air in the lungs.)  Too much and you can't get rid of it, or in extreme cases even get more of it.&lt;/p&gt;&#xA;" OwnerUserId="8412" LastActivityDate="2015-07-07T22:54:27.787" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35875" PostTypeId="1" AcceptedAnswerId="35879" CreationDate="2015-07-07T23:25:33.080" Score="0" ViewCount="3497" Body="&lt;p&gt;I am interested in learning more about both genomics and bioinformatics, with emphasis on genomics. I was told after taking an introductory course of genomics that the programming language &quot;R&quot; and &quot;python&quot; are widely used. However having asked about learning genomics before on this fourm, I was suggested alot of books for learning genomics with &quot;Perl&quot;. I was also told anecdotally that &quot;perl&quot; is falling &quot;out of favor&quot; and &quot;Python&quot; and &quot;R&quot; are desired.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To give background on my coding skills, I flunked out of computer science due to poor coding skills and poor math skills. I still had an interest in the field and therefore started studying genomics and biology instead.&#xA;I would categorize my self as a beginner in java and python in terms of skills.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was also told anecdotally that the best way to learn coding is by having a project. But I feel incompetent in my coding skills to even attempt anything.&#xA;I tried to learn Python via &quot;Codecademy&quot; and their 13 hour course for python. Having completed it I felt lost enough to make this post, looking for further guidance. I tried to read a bioinformatics book based in Python, but I missed the handholding and directed exercises that Codecademy gave me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Should one interested in genomics learn the coding language, R or Perl? Also what would be the best ways to learn these for one who does &quot;not excel&quot; in coding?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this post seems opinion based mods feel free to delete it or move it, I just was not sure how to phrase my concerns adequately. &lt;/p&gt;&#xA;" OwnerUserId="14815" LastEditorUserId="14826" LastEditDate="2015-07-08T05:15:50.153" LastActivityDate="2015-07-08T09:42:31.537" Title="What are the programming languages important to learn for a geneticist or bioinformatician?" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;" AnswerCount="2" CommentCount="10" ClosedDate="2015-07-08T05:15:53.633" ContentLicense="CC BY-SA 3.0" />
  <row Id="35876" PostTypeId="2" ParentId="35818" CreationDate="2015-07-07T23:39:52.693" Score="1" Body="&lt;p&gt;Nanodiscs are very powerful technology for membrane protein invented in Stephen Sligar's lab at the University of Illinois.&#xA;A nanodisc is composed of a membrane protein, lipids and two monomers of a &quot;scaffold protein&quot;. The most used scaffold protein is an N-terminal truncation of apolipoprotein A-1 (apoA-1), which is the primary protein component of high-density lipoprotein (HDL) particles. But because the size of the scaffold protein defines the size of the nanodisc, membrane proteins with different size could require different type of scaffold protein.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reconstitution of a membrane protein into a lipid disc is a self assembled process. The reaction consists in mixing the membrane protein solubilised in detergent with lipids (that can be chosen according to the protein) and the scaffold protein. Removal of the detergent (using for example Bio-Beads™ SM-2 Resin) starts the self assembled process and the nanodiscs are created. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nanodiscs provide an environment where membrane proteins are stable and compatible with aqueous environments in a native-like phospholipid bilayer. The aquesous environment makes membrane proteins compatible with analytical methods that have primarily been limited to investigating soluble proteins. The lipidic environment, that can be chosen and optimised, keeps the membrane protein stable, monodisperse and active. The stoichiometry of the protein can also be controlled. &#xA;Compared to nanodiscs, liposome are large, unstable and difficult to prepare with precisely controlled size and stoichiometry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Several membrane proteins have now been reconstitued into nanodiscs and used for different type of studies, for example for studying ligand affinities  and kinetics, for NMR, for studying protein association state, signalling properties, and ion channels (&lt;a href=&quot;http://molsense.com/applications/trubind-at-work/ion-channel-inhibitors/&quot; rel=&quot;nofollow&quot;&gt;http://molsense.com/applications/trubind-at-work/ion-channel-inhibitors/&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0014579309007960&quot; rel=&quot;nofollow&quot;&gt;http://www.sciencedirect.com/science/article/pii/S0014579309007960&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16581" LastActivityDate="2015-07-07T23:39:52.693" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35877" PostTypeId="2" ParentId="35859" CreationDate="2015-07-08T00:13:53.967" Score="2" Body="&lt;p&gt;Actually there is a way to determine the initial conditions for this problem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We assume that the gating variables $r$ and $s$ are at a steady state before the membrane potential jump from$u_0$ to $u'$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we look at the first graph(the steady state relation versus membrane potential) we can see that at the membrane potential $u_0$ that $r(t=0)\approx 0$ and $s(t=0)\approx 1$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Then we make our jump in voltage from$u_0$ to $u'$ and now our $r(t)$ and $s(t)$ will change towards their new steady values $r'=1$ $s'=0$ with time constants given by the second graph.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your equations $r(t) =C_1 e^{-t}+1$ and $s(t)=0+C_2 e^{-t/15}$ are correct, but using the information from the graphs we can se that $C_1= -1$ and $C_2= 1$. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From these equations we can see that $r(3)=1-e^{-3}\approx .9502$ and $s(3)= e^{\frac{-1}{5}}\approx .81$ (note that .81 is close enough to 1 for this particular problem). This means that the channel is mostly open as statement 4 asserts.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now for statement 7 we have $t= 100$ and while $r(100)= 1-e^{-100}\approx1$, and $s(100)=e^{\frac{-100}{15}}\approx 0$. This means the product $r(100)^2* s(100)\approx 1^2 * 0 \approx 0$ thus the channel is mostly closed. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps. &lt;/p&gt;&#xA;" OwnerUserId="13388" LastActivityDate="2015-07-08T00:13:53.967" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35878" PostTypeId="2" ParentId="35851" CreationDate="2015-07-08T00:37:05.903" Score="6" Body="&lt;p&gt;What a great question! I'm sorry to add another blow to your theory... but... Even if oxygen depletion would be effective, &lt;strong&gt;treating the lungs alone is not good enough&lt;/strong&gt;. True enough, &lt;em&gt;Mycobacterium tuberculosis&lt;/em&gt; bacteria usually attack the lungs, but TB bacteria can also attack other parts of the body such as the kidney, spine, and brain (Fig. 1). If not treated properly, TB disease can be fatal. Because the TB bacterium has the potential to infect various parts of the body, a systemic treatment is necessary and long-term antibiotics are therefore the first-line treatment (Source: &lt;a href=&quot;http://www.cdc.gov/tb/topic/treatment/&quot; rel=&quot;noreferrer&quot;&gt;Center for Disease Control and Prevention&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, there is tuberculosis of the &lt;strong&gt;lungs&lt;/strong&gt;, tuberculous meningitis (infection of the &lt;strong&gt;brain&lt;/strong&gt; membranes), &lt;strong&gt;skeletal&lt;/strong&gt; TB, &lt;strong&gt;genitourinary&lt;/strong&gt; TB and &lt;strong&gt;gastrointestinal&lt;/strong&gt; TB (Source: &lt;a href=&quot;http://emedicine.medscape.com/article/230802-overview&quot; rel=&quot;noreferrer&quot;&gt;Medscape&lt;/a&gt;).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/sNJhW.png&quot; alt=&quot;TB&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Signs and symptoms of TB infection in various parts of the body. Source: &lt;a href=&quot;http://www.infectionlandscapes.org/2013/04/tuberculosis.html&quot; rel=&quot;noreferrer&quot;&gt;Infection Landscapes&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-08T01:15:57.677" LastActivityDate="2015-07-08T01:15:57.677" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35879" PostTypeId="2" ParentId="35875" CreationDate="2015-07-08T01:33:12.667" Score="3" Body="&lt;p&gt;I have found that this chapter by Lincoln Stein is a very easy, accessible, and useful introduction to writing a Perl script: &lt;a href=&quot;https://www.dropbox.com/s/lmurjde0bgy3smb/using_perl_to_faciliate_biological_analysis_scanned_book_ch_lincoln_stein_2005.pdf?dl=0&quot; rel=&quot;nofollow&quot;&gt;Using Perl to facilitate biological analysis&lt;/a&gt;. It is Chapter 18 in &quot;Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins&quot; 3rd edition, by Baxevanis and Ouellette.  I use Perl and bash for almost everything, but most of my co-workers prefer Python.  I only use R when I need to.  One software engineer I know swears by Ruby.  As long as your scripting language has lots of useful libraries I don't know if it makes a big difference which one you select.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="14946" LastEditDate="2015-07-08T01:42:17.567" LastActivityDate="2015-07-08T01:42:17.567" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35880" PostTypeId="1" CreationDate="2015-07-08T01:46:50.330" Score="5" ViewCount="1726" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1210391/pdf/1097.pdf&quot; rel=&quot;nofollow&quot;&gt;this (old) paper&lt;/a&gt; there are 10 times more mutations during meiosis than during mitosis. One reason for that is that recombination often causes replication error and therefore mutations. However, in many multicellular organisms, germ cells undergo many cell divisions (mitosis during development) before finally undergoing meiosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that intuitively many people (me at least) think of new mutations* that are transmitted to the offspring as mutations occurring during meiosis. I would like to have a notion of how important are the two processes (mitosis and meiosis) in generating heritable new germ-line mutations in multicellular animals.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Let's consider humans for example. Out of 100 new germ-line mutations transmitted to the babies, how many of those mutations occurred during mitosis (during the development)?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;*I call &quot;new mutations&quot;, any mutation that is transmitted to a baby but that was not present in any of the two eggs of the parents (even before the parents started the gastrulation).&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="9943" LastEditDate="2015-07-09T13:49:57.577" LastActivityDate="2015-07-09T13:49:57.577" Title="Where do most mutations come from, mitosis or meiosis?" Tags="&lt;evolution&gt;&lt;physiology&gt;&lt;mutations&gt;&lt;development&gt;&lt;mitosis&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35881" PostTypeId="2" ParentId="35875" CreationDate="2015-07-08T02:03:06.877" Score="5" Body="&lt;p&gt;&lt;strong&gt;Comparing some commonly used languages in bioinformatics&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that indeed Perl is losing users but there are still quite a lot of people using it. Bash (or other shell) is essential. While one can replace Python with C or Java and eventually replace R by Python or Julia, I find Bash to be really necessary. To compare Python to R, Python is much faster. If you are a purist, you'll like Python much more than R. R is a weird language, I use it a lot but you always have to deal with very special kind of objects. The big advantage of R is its community; There are tons and tons of functions. Typically, for any task you you want to do and related to statistics or to phylogenetics, you'll find an already existing package that will do the job for you. C is nice and very popular. It is super fast but it is not super handy for most tasks. Moreover, C doesn't have an interpreter which is always kinda annoying when you're use to high level languages such as R typically. I know nobody who uses Ruby and I don't code in Ruby but it is an important language. Some may use it for bioinformatics and it is very much used in many other disciplines (unlike R, which only statisticians know).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What I personally use&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally, I use mostly R, Python, C/C++ and Bash. Bash to organize stuff, modify files and manage processes on my machine and on remote machines. R for data analysis. Python when R is too slow (to analyze more data such as sequence data for example) and C/C++ to run individual based simulation. I happen to use some other languages for my work but not as often.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How to learn&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nobody excels at coding to start with. Actually, after my first class of programming I had in mind that programming was not meant for me. Now, I don't excel, I am just a biologist who codes a bit and not a computer scientist but I spend the majority of time coding and I love that. I learn a lot everyday but ever since I started to feel a bit confident, I found that I could do much with this knowledge. You'll probably realize after some time that few people are really good at coding and you can already do much with only a few days of training. Don't be afraid. I think that indeed one of the best way to learn a language is to use it for a project. Here are a bunch of things you could do:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Go on Dryad.com, get some data and analyze them. You can redo the analysis they did on the original paper for example. Or, better you could try to discover something by yourself by combining some existing data.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;individual-based (OOP) simulations in population genetics&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;simulate genetic drift in populations. Try to estimate the probability of a new mutation to fix and the time it takes to get fixed.&lt;/li&gt;&#xA;&lt;li&gt;Simulate the process of selective sweep with defining chromosomes.&lt;/li&gt;&#xA;&lt;li&gt;You'd basically have to have a function that creates a list of objects of type individuals. Each individual has two objects called chromosomes. You have a function that simulate reproduction (without selection, recombination nor mutations to start with). And you need a function to print the statistics you need on a file. I think you could do a simple individual-based simulation in a few days only and then you'd feel more comfortable with the language and you would also have a better grasp on how one can numerically simulate a population through time.&lt;/li&gt;&#xA;&lt;/ul&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="1486" LastEditDate="2015-07-08T09:42:31.537" LastActivityDate="2015-07-08T09:42:31.537" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35884" PostTypeId="2" ParentId="35872" CreationDate="2015-07-08T06:25:04.420" Score="7" Body="&lt;p&gt;These little creatures look a lot like White-margined Burrowing Bug or &lt;em&gt;Sehirus cinctus&lt;/em&gt; nymphs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/XgygO.jpg&quot; alt=&quot;Sehirus cintus nymphs&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Very interesting thing about the &lt;em&gt;Sehirus cinctus&lt;/em&gt; is their brooding behavior. The female watches the eggs and even feeds the young for a few days. Have a look around. You might see it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/1C4q0.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;AFAIK they don't harm your plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More info:&lt;br&gt;&#xA;&lt;a href=&quot;http://polyploid.net/bugs/bugs.html&quot; rel=&quot;noreferrer&quot;&gt;http://polyploid.net/bugs/bugs.html&lt;/a&gt; &lt;br&gt;&#xA;&lt;a href=&quot;https://en.wikipedia.org/wiki/Sehirus_cinctus&quot; rel=&quot;noreferrer&quot;&gt;https://en.wikipedia.org/wiki/Sehirus_cinctus&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15257" LastEditorUserId="1590" LastEditDate="2015-07-08T07:01:32.427" LastActivityDate="2015-07-08T07:01:32.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35887" PostTypeId="1" AcceptedAnswerId="35890" CreationDate="2015-07-08T09:38:35.927" Score="5" ViewCount="1326" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;You are your bacteria! The probiotics and the antibiotics...&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;There has been on going discussions about how our gut bacteria is important for a healthy lifestyle. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Figure 1:&lt;/strong&gt; Schematic diagram illustrating potential or known mechanisms&#xA;  whereby probiotic bacteria might impact on the microbiota. These&#xA;  mechanisms include (1) competition for dietary ingredients as growth&#xA;  substrates, (2) bioconversion of, for example, sugars into&#xA;  fermentation products with inhibitory properties, (3) production of&#xA;  growth substrates, for example, EPS or vitamins, for other bacteria,&#xA;  (4) direct antagonism by bacteriocins, (5) competitive exclusion for&#xA;  binding sites, (6) improved barrier function, (7) reduction of&#xA;  inflammation, thus altering intestinal properties for colonization and&#xA;  persistence within, and (8) stimulation of innate immune response (by&#xA;  unknown mechanisms). IEC: epithelial cells, DC: dendritic cells,&#xA;  T:T-cells. For further details, see main text.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/DGl2X.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, an online search provides numerous articles about diet aspect that alters our gut bacteria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;e.g.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;1.&lt;/code&gt;&lt;a href=&quot;http://www.livescience.com/41869-gut-bacteria-change-diet.html&quot; rel=&quot;noreferrer&quot;&gt;A New Diet Quickly Alters Gut Bacteria-&lt;em&gt;(not sure about the credibility and relevance to humans as the study is on mice)&lt;/em&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;2.&lt;/code&gt;&lt;a href=&quot;http://www.medicaldaily.com/artificial-sweeteners-change-how-our-gut-bacteria-work-paving-way-diabetes-and-obesity-303562&quot; rel=&quot;noreferrer&quot;&gt;Artificial Sweeteners Change How Our Gut Bacteria Work, Paving The Way To Diabetes And Obesity&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;code&gt;3.&lt;/code&gt;&lt;a href=&quot;http://newsroom.ucla.edu/releases/changing-gut-bacteria-through-245617&quot; rel=&quot;noreferrer&quot;&gt;Changing gut bacteria through diet affects brain function&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As far as the GIT is concerned, health, lifestyle, eating habits and the environment a person is living may be at large influence and affect one's gut microbes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there day to day encounters, in-depth examples and references that can prove the &lt;strong&gt;factors&lt;/strong&gt; which influence our gut microbes the most?&lt;/p&gt;&#xA;" OwnerUserId="8709" LastActivityDate="2015-07-09T12:32:16.860" Title="What are the most important factors influencing a person’s gut microbes?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;bacteriology&gt;&lt;health&gt;&lt;diet&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35888" PostTypeId="1" AcceptedAnswerId="35889" CreationDate="2015-07-08T10:13:50.870" Score="15" ViewCount="2016" Body="&lt;p&gt;My question is about making fake auditory signals. The ear collects sounds from the environment, which are transformed into a neural signal by the hair cells in the inner ear. This signal is sent through the auditory nerve to the to brain, where it is decoded into a hearing sensation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now can we make fake signals and feed them into the auditory nerve to bring it to the brain? E.g., instead of the ear collecting sound, could we use an electrical instrument for collecting sound and convert this signal into a neural signal in the auditory nerve?&lt;/p&gt;&#xA;" OwnerUserId="16593" LastEditorUserId="9943" LastEditDate="2015-08-05T14:16:22.563" LastActivityDate="2015-09-26T13:34:17.393" Title="How to make a fake auditory signal?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;&lt;hearing&gt;&lt;electrical-stimulation&gt;&lt;biomedical-engineering&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35889" PostTypeId="2" ParentId="35888" CreationDate="2015-07-08T10:37:59.420" Score="20" Body="&lt;p&gt;Devices that bypass the hair cells in the inner ear and directly stimulate the auditory nerve are called &lt;strong&gt;&lt;a href=&quot;http://www.nidcd.nih.gov/health/hearing/pages/coch.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;cochlear implants&lt;/a&gt;&lt;/strong&gt;. Cochlear implants are used to treat deafness caused by the loss of hair cells in the &lt;a href=&quot;https://en.wikipedia.org/wiki/Cochlea&quot; rel=&quot;nofollow noreferrer&quot;&gt;cochlea&lt;/a&gt;. The &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK11122/&quot; rel=&quot;nofollow noreferrer&quot;&gt;hair cells&lt;/a&gt; are the sensory cells that convert sound vibrations into electric neural signals (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK11122/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Purves &lt;em&gt;et al&lt;/em&gt;., 2001&lt;/a&gt;). With state-of-the-art devices, the better performing implant wearers are able to talk over the phone(!) An exclamation mark is in place, because it means they can understand the spoken word &lt;em&gt;without the need for lip reading or sign language&lt;/em&gt;. Hence, cochlear implants are the answer to your question, but they definitely are not designed to generate fake signals. Instead, they are used as an effective treatment for deafness and are capable of transmitting meaningful speech information.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cochlear prosthetics consist of an array of typically 20-24 electrodes that are inserted in the &lt;a href=&quot;http://www.britannica.com/science/scala-tympani&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;scala tympani&lt;/em&gt;&lt;/a&gt; of the cochlea. The inner ear is &lt;a href=&quot;https://en.wikipedia.org/wiki/Tonotopy&quot; rel=&quot;nofollow noreferrer&quot;&gt;tonotopically organized&lt;/a&gt;, which means that high frequencies are coded in the base of the cochlea, while low frequencies are encoded in the tip. Hence, each electrode stimulates a separate frequency band (Fig. 1). By using a microphone and sending the acoustic signal through a filter bank, a number of auditory frequency bands can be obtained equal to the number of electrodes in the implant. After this &lt;a href=&quot;http://biomed.brown.edu/Courses/BI108/2006-108websites/group10cochlearimplant/pages/speechprocessor.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;speech processing&lt;/a&gt; step, the acoustic frequency bands are converted into trains of biphasic pulses. These pulse trains are sent to the electrodes in the cochlea, which then activate the auditory nerve directly, effectively replacing the degenerated hair cells in the inner ear &lt;a href=&quot;http://dspace.library.uu.nl/handle/1874/44671&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Stronks, 2010)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FFAQh.jpg&quot; alt=&quot;CI&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Cochlear implant. Source: &lt;a href=&quot;http://www.mayoclinic.org/tests-procedures/cochlear-implants/care-at-mayo-clinic/treatment/prc-20021470&quot; rel=&quot;nofollow noreferrer&quot;&gt;Mayo Clinic&lt;/a&gt;.&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK11122/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Purves &lt;em&gt;et al&lt;/em&gt;., Neuroscience (2001) 2&lt;sup&gt;nd&lt;/sup&gt; ed.&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://dspace.library.uu.nl/handle/1874/44671&quot; rel=&quot;nofollow noreferrer&quot;&gt;Stronks (2010). PhD thesis, Utrecht University&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-09-26T13:34:17.393" LastActivityDate="2015-09-26T13:34:17.393" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="35890" PostTypeId="2" ParentId="35887" CreationDate="2015-07-08T11:16:42.237" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://doi.org/10.1186/s13059-015-0664-7&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Our Unique Microbial Identity&lt;/em&gt;&lt;/a&gt; (Gilbert 2015) suggests that the gut microbiome is shaped and stablized during infancy and tends to restore equilibrium if it is disturbed later in life. Antibiotics temporarily change the composition of the gut microbiome (by suppressing the growth of certain groups of bacteria more than others), but it tends to drift back to resemble its original (stable) community after treatment is stopped, likely due to the interdependency of individual strains as producers/consumers of particular compounds (i.e., some bacteria will eventually arrive to serve a particular role in the microbial community). A &lt;a href=&quot;http://www.the-scientist.com/?articles.view/articleNo/43422/title/Antibiotics-and-the-Gut-Microbiome/&quot; rel=&quot;nofollow&quot;&gt;recent study&lt;/a&gt; in antibiotic treatment provides some empirical evidence of the long term effects of antibiotic treatment on the human gut microbiome.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://humanfoodproject.com/americangut/&quot; rel=&quot;nofollow&quot;&gt;American Gut Project&lt;/a&gt; is currently open to the public for participation, and it has the goal of identifying exactly the factors you describe. They are accepting samples from individuals across the country, along with lifestyle information, including dietary habits. A &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0092867412001043&quot; rel=&quot;nofollow&quot;&gt;related publication&lt;/a&gt; by the group provides a summary of the common gut bacteria implicated in a variety of diseases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Timeline_of_peptic_ulcer_disease_and_Helicobacter_pylori&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;H. pylori&lt;/em&gt;&lt;/a&gt; infections are a common gut microbiome health issue. This bacteria is present in about half of gut microbiomes and are not generally harmful unless the stomach lining is already compromised (e.g., due to medication or diet). In those cases, they can become opportunistic pathogens that can persist for decades and cause peptic ulcers which can lead to a variety of difficult to diagnose ailments such as arthritis.&lt;/p&gt;&#xA;" OwnerDisplayName="user16391" LastEditorDisplayName="user16391" LastEditDate="2015-07-09T12:32:16.860" LastActivityDate="2015-07-09T12:32:16.860" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35892" PostTypeId="2" ParentId="35888" CreationDate="2015-07-08T13:47:26.547" Score="8" Body="&lt;p&gt;As @AliceD mentioned, cochlear implant is one of the earliest achievements of neural engineering. However, there are orders of magnitude more inner hair cells (IHC) and even more auditory nerve fibers (AN) in human cochlear than the current cochlear implants offer electrodes. If you are interested in a more detailed model of IHC to AN signal transmission, there are tons of research, for example:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Meddis, R. (1986). Simulation of mechanical to neural transduction in the auditory receptor. The Journal of the Acoustical Society of America, 79(3):702-711.&lt;/li&gt;&#xA;&lt;li&gt;Walsh, E. J. and McGee, J. (1987). Postnatal development of auditory nerve and cochlear nucleus neuronal responses in kittens. Hearing Research, 28(1):97-116.&lt;/li&gt;&#xA;&lt;li&gt;Sumner, C. J., Lopez Poveda, E. A., O'Mard, L. P., and Meddis, R. (2002). A revised model of the inner-hair cell and auditory-nerve complex. The Journal of the Acoustical Society of America, 111(5):2178-2188.&lt;/li&gt;&#xA;&lt;li&gt;Heinz, M. G., Colburn, H. S., and Carney, L. H. (2001). Evaluating auditory performance limits: I. One-Parameter discrimination using a computational model for the auditory nerve. Neural Computation, 13(10):2273-2316.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="460" LastEditorUserId="460" LastEditDate="2015-07-08T15:24:47.990" LastActivityDate="2015-07-08T15:24:47.990" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35894" PostTypeId="1" CreationDate="2015-07-08T16:07:41.530" Score="3" ViewCount="88" Body="&lt;p&gt;I noticed this plant growing on the Azores islands. It has a surprisingly perfect distribution of branches, which gives it the appearance of a fake decorative plant. Does anybody know what type of tree this is?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/33WPp.jpg&quot; alt=&quot;the tree&quot;&gt;&lt;br&gt;&#xA;I apologise for the image, I could not find any better ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Edit:&lt;/strong&gt; here is another image I found:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.imgur.com/DvCxk1o.jpg&quot; alt=&quot;a better image&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16482" LastActivityDate="2015-07-08T16:07:41.530" Title="What is the name of this tree?" Tags="&lt;species-identification&gt;&lt;trees&gt;" AnswerCount="0" CommentCount="8" FavoriteCount="1" ClosedDate="2015-07-10T13:54:10.603" ContentLicense="CC BY-SA 3.0" />
  <row Id="35895" PostTypeId="1" CreationDate="2015-07-08T18:10:03.943" Score="1" ViewCount="524" Body="&lt;p&gt;How does C-DNA have 9.33 base pairs per turn? The number of base pairs should be quantised. How can it be a decimal?&lt;/p&gt;&#xA;" OwnerUserId="16657" LastEditorUserId="6307" LastEditDate="2015-07-08T19:03:31.943" LastActivityDate="2015-07-08T19:17:42.870" Title="C Form DNA Base Pairs Per Turn" Tags="&lt;dna&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35898" PostTypeId="2" ParentId="35895" CreationDate="2015-07-08T19:17:42.870" Score="5" Body="&lt;p&gt;There is no requirement that DNA should have a whole number of base pairs per turn. As a thought experiment, say you have a helix of dsDNA with 10 base pairs that completes one helical turn (ie it has 10 bp/turn). Now, twist that DNA along its axis so that it completes 1.5 turns. There is still only 10 bp and thus 6.67 bp/turn (which you should notice is a decimal). &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-07-08T19:17:42.870" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35901" PostTypeId="1" CreationDate="2015-07-08T19:48:52.450" Score="1" ViewCount="30" Body="&lt;p&gt;When learning about &quot;families of animals&quot; in mid-primary school, my son asked me if there is not a better way to classify animals than by looking at them (they were taught that animals are grouped into families based on what covers the skin (hair, feathers, nothing), number of legs, the way they breathe, etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;He was wondering if there would be a more quantifiable way of grouping them (this is my wording). I told him that since all animals share the same genetic coding principles, we could try to calculate how different their genetic material is, and derive a &quot;distance&quot;. This would allow grouping animals in possibly novel ways, and maybe have some of them cluster in &quot;families&quot; (possibly different from the existing ones).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After having played my role of super-hero-dad, I now wonder if this makes sense? (and if so - is it used? and if so - why still using some classifications from centuries ago?)&lt;/p&gt;&#xA;" OwnerUserId="4016" LastActivityDate="2015-07-08T19:48:52.450" Title="why not classify organisms based on genetic distance?" Tags="&lt;genetics&gt;&lt;classification&gt;" AnswerCount="0" CommentCount="2" ClosedDate="2015-07-08T19:55:59.387" ContentLicense="CC BY-SA 3.0" />
  <row Id="35903" PostTypeId="1" CreationDate="2015-07-08T20:40:58.070" Score="7" ViewCount="587" Body="&lt;p&gt;I am working with a few novel transcripts of genes- before I confirm their existence experimentally, I would like to perform some bioinformatic analysis. I have already considered coding potential, protein domain prediction, transcription factor binding sites, sequence homology, and RNA secondary structure (still a little unsure how to use this one). These transcripts were discovered using RNA-Seq. Are there any other elements of genes/confirmed transcripts that I should look for in the sequence of my transcripts and corresponding softwares? (I can find the software myself if necessary, but I have run out of characteristics to search for). I would like to characterize these transcripts structurally and functionally as completely as possible, including potential protein function, mRNA degradation, etc - some new features for what to look into would be appreciated. &lt;/p&gt;&#xA;" OwnerUserId="8704" LastEditorUserId="8704" LastEditDate="2015-07-08T23:02:47.370" LastActivityDate="2015-07-17T17:30:41.057" Title="What are some (bioinformatic) methods to characterize potentially novel gene transcripts?" Tags="&lt;genetics&gt;&lt;bioinformatics&gt;&lt;proteins&gt;&lt;rna&gt;" AnswerCount="2" CommentCount="7" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35905" PostTypeId="1" CreationDate="2015-07-08T21:32:18.937" Score="1" ViewCount="48" Body="&lt;p&gt;Can I explain the kinetics of a ligand binding to a target protein (association and dissociation rates) by looking at the protein-ligand co-structure?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Editing my question after a few comments: &#xA;I have a set of ligands targeting the same protein. These ligands show different kinetics properties, i.e. different association and dissociation rates. Would it be possible to explain why they have a different kinetics if I had the x-ray structure of the different protein-ligand complexes? Would I be able to say that ligand A has a slower dissociation time compared to ligand B because it makes for example 3 H-bonds instead of 2? How accurate would this conclusion be? Would I need in any case MD simulations? &lt;/p&gt;&#xA;" OwnerUserId="16581" LastEditorUserId="16581" LastEditDate="2015-07-10T23:32:06.467" LastActivityDate="2015-07-10T23:32:06.467" Title="Can I explain the kinetics of a ligand looking at the ligand-protein co-structure?" Tags="&lt;biochemistry&gt;&lt;pharmacology&gt;&lt;structural-biology&gt;" AnswerCount="0" CommentCount="5" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35906" PostTypeId="2" ParentId="35880" CreationDate="2015-07-09T01:20:03.447" Score="1" Body="&lt;p&gt;@Remi.b I think we can do better than 1962. Let's fast-forward here to 2014, in the post-genomic era.  I think this paper provides some data relevant to your query: &lt;a href=&quot;http://genome.cshlp.org/content/early/2014/07/16/gr.175547.114&quot; rel=&quot;nofollow&quot; title=&quot;Possible mechanisms for Chromothripsis&quot;&gt;Possible mechanisms for Chromothripsis &lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-07-09T01:20:03.447" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35908" PostTypeId="1" CreationDate="2015-07-09T04:50:40.467" Score="2" ViewCount="114" Body="&lt;p&gt;How does a RNAP locate a specific gene? For instance, growth hormone has to be produced and the RNAP has to locate the gene. But the promoter (TATA box) will also be present infront of all cistrons. So how does the RNAP choose the specific gene? Are the promoters specific for specific gene?&lt;/p&gt;&#xA;" OwnerUserId="16657" LastActivityDate="2015-07-09T07:48:10.007" Title="DNA dependent RNA polymerase" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;human-genetics&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35909" PostTypeId="1" AcceptedAnswerId="35913" CreationDate="2015-07-09T07:37:00.923" Score="4" ViewCount="257" Body="&lt;p&gt;IP&lt;sub&gt;3&lt;/sub&gt; molecules bind to IP&lt;sub&gt;3&lt;/sub&gt; receptors and open up the calcium channels on the endoplasmic reticulum. I am wondering what happens to IP&lt;sub&gt;3&lt;/sub&gt; molecules after they have been released from the IP&lt;sub&gt;3&lt;/sub&gt; receptor? Do they remain as IP&lt;sub&gt;3&lt;/sub&gt; molecules, or do they break down? Do they have any purpose after they have been released, and perhaps after been broken down?&lt;/p&gt;&#xA;" OwnerUserId="16468" LastEditorUserId="9943" LastEditDate="2015-07-09T13:47:42.750" LastActivityDate="2015-07-09T13:47:42.750" Title="What happens to IP3 molecules after release from IP3 receptors?" Tags="&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;cell-signaling&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35910" PostTypeId="2" ParentId="35908" CreationDate="2015-07-09T07:48:10.007" Score="2" Body="&lt;p&gt;It could be difficult for RNApol to access genes inactivated because inactivated genes are often tightly packed by chromatin. Many genes have enhancer elements(specific DNA sequences) as well as TATA, and transcriptional enhancers, which are proteins, would recognize enhancer elements in a sequence dependent manner and loosen chromatin structure to make RNApol access TATA sequences easily. Transcriptional enhancers also bind to the General Transcriptional Factor complex (GTF), which contains RNApol, therefore enhancers could bring RNApol to TATA sequences.&#xA;Many tissue specific and/or developmentally-regulated transcriptional enhancers are identified. You could say transcriptional enhancers regulate RNApol which to bind.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/General_transcription_factor&quot; rel=&quot;nofollow&quot;&gt;You can check this link&lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/scitable/topicpage/gene-expression-14121669&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-07-09T07:48:10.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35911" PostTypeId="1" AcceptedAnswerId="36108" CreationDate="2015-07-09T08:17:17.273" Score="1" ViewCount="145" Body="&lt;p&gt;Noticed two grasshoppers jumping together on the porch, and started wondering if they are monogamous? I am aware they have males and females.&lt;/p&gt;&#xA;" OwnerUserId="16673" LastActivityDate="2015-07-16T01:14:19.077" Title="Are grasshoppers monogamous?" Tags="&lt;zoology&gt;&lt;ethology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35913" PostTypeId="2" ParentId="35909" CreationDate="2015-07-09T08:52:42.640" Score="5" Body="&lt;p&gt;All biomolecules are eventually broken down. This process is called turnover. Since inositol is a signalling molecule it is necessary to remove in order to terminate the signal, despite adaptive mechanism in the ER calcium channels. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;IP3 is generally dephosphorylated by a family of phosphatase enzymes called inositol polyphosphate phosphatases. After dephosphorylation, the inositol can be recycled into the membrane by phosphatidyl-inositol synthase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Reference:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=245&quot; rel=&quot;noreferrer&quot;&gt;The IUPHAR/BPS Guide to PHARMACOLOGY&lt;/a&gt; &lt;sup&gt;1&lt;/sup&gt;&#xA;&lt;hr&gt;&#xA;&lt;sup&gt;1&lt;/sup&gt; &lt;em&gt;I'm citing this website instead of a research article because apart from citing the original research articles, it also has other informative links about the enzymes and the substrate molecules. It is also from a very reliable source.&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-07-09T08:52:42.640" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35914" PostTypeId="2" ParentId="35773" CreationDate="2015-07-09T13:31:40.707" Score="2" Body="&lt;p&gt;Reiterating the above comments. Have a look at Tajima's D. It provides an estimate for the number of segregation sites for a population under a neutral mutation model.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The general form of the estimation for a diploid population is $E[S]=4N\mu\sum_{i=0}^{n-1} \frac{1}{i}$.  Here the mutation rate of is per-genome not per-site, so $\mu=L * 10^{-9}$ where $L$ is the genome size. Estimating the segregation sites of an entire population of $n=N=100$ with genome size of $L=10^{7}$ where each site has a per genome mutation rate of $\mu=10^{-2}$ one would expect that $E[S] \approx 20.75$. So, your numbers seem higher than expected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've written some example simulation software that is capable of performing such evolutionary scenarios (&lt;a href=&quot;http://www.biomedcentral.com/1471-2105/16/191&quot; rel=&quot;nofollow&quot;&gt;Clotho manuscript&lt;/a&gt;). Similarly, you can check your numbers against a population generated using &lt;a href=&quot;http://home.uchicago.edu/rhudson1/&quot; rel=&quot;nofollow&quot;&gt;MS&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="16659" LastActivityDate="2015-07-09T13:31:40.707" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35915" PostTypeId="1" CreationDate="2015-07-09T14:26:47.657" Score="3" ViewCount="196" Body="&lt;p&gt;A few days ago I read about MHC1 knockout pigs for organ transplantation research. &#xA;I was just wondering, is it enough to knock out MHC1 in the donor (lets say from same species, pig to pig) for successful transplantation? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that someone without MHC1 is more sensitive to  viruses, cancer, to NK and more. But the study pigs lived fine, so in theory it is possible to have knockout MHC1 and survive. &#xA;But is it enough for successful  transplantation from one pig (donor with knockout) to another (fully healthy, normal pig) ?&lt;/p&gt;&#xA;" OwnerUserId="10104" LastEditorUserId="10104" LastEditDate="2015-08-02T09:11:21.290" LastActivityDate="2015-08-02T09:11:21.290" Title="Is MHC1 knockout sufficient to prevent transplant rejection?" Tags="&lt;immunology&gt;&lt;organs&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35916" PostTypeId="1" CreationDate="2015-07-09T14:29:03.967" Score="3" ViewCount="165" Body="&lt;p&gt;It has been shown that the X chromosome is frequently enriched for female biased genes, and has a deficit of male biased genes. For example in &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12511656&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;, and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24084777&quot; rel=&quot;nofollow&quot;&gt;this one&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I'm struggling to find papers which test the general distribution sex-biased genes. I am trying to find out if the X is enriched for sex biased genes, e.g. if the X hosts 20% of all protein coding genes, it would be enriched if it carried 30% of all sex-biased genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any such studies?&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;I think I found an answer tucked in the methods section at the back of the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24084777&quot; rel=&quot;nofollow&quot;&gt;Allen paper&lt;/a&gt; where 15% of sex-biased genes were X-linked, I'd suggest this means that 15.55% ($100 \times (\frac{1075}{1075 + 4938 + 4323})$) of sex-biased genes are X-linked - &lt;strong&gt;other examples are still sought&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&quot;Genes associated with chromosomes 2 (4,323 genes, 37%), 3 (4,938&#xA;  genes, 43%), and X (1,705 genes, 15%) were used in the analysis; these&#xA;  chromosomes accounted for 10,967 (95%) of the genes... a further 547&#xA;  (4.7%) of the genes ... were omitted&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2015-07-09T14:50:10.203" LastActivityDate="2015-07-10T21:02:48.150" Title="Sex biased gene expression in the X chromosome" Tags="&lt;gene-expression&gt;&lt;genomics&gt;&lt;sex-chromosome&gt;&lt;sexual-dimorphism&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35917" PostTypeId="2" ParentId="30112" CreationDate="2015-07-09T14:33:04.383" Score="3" Body="&lt;p&gt;In XY sex determination systems the females carry two copies of the X chromosomes, thus can be homo- and heterozygous. Males however, carry one X chromosome, meaning that all loci are hemizygous (excluding those with homologs on the X). Under conditions of complete dosage compensation, often through up-regulation of X linked loci, they are effectively homozygous, as demonstrated &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24084777&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt; where expression levels of X-linked genes are at a ratio of near 1:1 with autosomally linked genes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An interesting potential consequence is that males will exhibit more &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/evo.12224/abstract&quot; rel=&quot;nofollow&quot;&gt;additive genetic variance in X-linked loci&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="1590" LastEditorUserId="1590" LastEditDate="2015-07-10T08:15:18.040" LastActivityDate="2015-07-10T08:15:18.040" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35918" PostTypeId="2" ParentId="35916" CreationDate="2015-07-09T15:14:45.173" Score="2" Body="&lt;p&gt;You can answer this question for yourself using the modMine data warehouse for modENCODE datasets.  All you need is a list of female-specific genes (using your identifier of choice, although FlyBase FBGxxxxxxxx are the simplest). You can use their list tools to upload your own list of identifiers, and then there are a bunch of widgets that will tell you things like GO Term enrichment, PubMed references, and one is a histogram plot showing the chromosomal distribution of your genes, and a second histogram showing the &quot;expected&quot; distribution. Access to many modENCODE sites can be found at &lt;a href=&quot;http://www.modencode.org&quot; rel=&quot;nofollow noreferrer&quot;&gt;www.modencode.org&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Okay, I went and did this myself.  modMine was quite slow, but fortunately the intermine server at FlyMine is working fine.  I downloaded Supplemental table 25 from Graveley et al., Nature, 2011 and cut and pasted all of the &quot;Female Biased&quot; IDs for those rows that had FlyBase Gene Identifiers.  This figure shows the chromosomal distribution of the 928 genes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/YRcVU.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Labels on the X-axis do not line up properly (for some reason), so here is a table with the Chromosome names and the counts:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chrom     Actual    Expected&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2L:     157      169&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2R:     176      186&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3L:     143      173&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3R:     174      217&lt;/p&gt;&#xA;&#xA;&lt;p&gt;4:       0       10&lt;/p&gt;&#xA;&#xA;&lt;p&gt;X:     264      150&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="14946" LastEditDate="2015-07-10T21:02:48.150" LastActivityDate="2015-07-10T21:02:48.150" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35919" PostTypeId="2" ParentId="30112" CreationDate="2015-07-09T15:21:04.163" Score="3" Body="&lt;p&gt;All of the other answers are basically correct, I just wanted to add that there are some genes which are present in both the X and Y chromosomes, in the pseudoautosomal regions. These genes are inherited in an autosomal manner (hence the name). A male has two copies of each, just as a female would, and can thus be homo- or heterozygous. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-07-09T15:33:57.420" LastActivityDate="2015-07-09T15:33:57.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35921" PostTypeId="1" AcceptedAnswerId="35928" CreationDate="2015-07-09T18:02:42.753" Score="32" ViewCount="5772" Body="&lt;p&gt;We humans can easily control the direction a tree falls by making a number of strategic cuts, essentially creating a hinge:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/CoF1Q.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This prevents trees from falling on equipment and people and sets them up in a good location for the subsequent processing steps. I'm curious if beavers also perform directional felling and, if they do, how do they choose the direction (eg to fell the tree towards the damn, in a river, away from thick brush, etc)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/UOrGR.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this picture (and others), it appears as though the beaver has created a hinge. Is their any method to their technique or do they just start chewing and hope for the best?&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2017-05-16T18:25:37.280" LastActivityDate="2019-10-19T14:49:19.153" Title="Can beavers control the direction a tree falls?" Tags="&lt;ecology&gt;&lt;ethology&gt;&lt;behaviour&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35922" PostTypeId="2" ParentId="31766" CreationDate="2015-07-09T18:13:04.070" Score="1" Body="&lt;p&gt;If a portion of sequence ends up in the mature RNA, it is by definition not an intron (save for abnormal splicing events and rare intron retention).&lt;/p&gt;&#xA;&lt;p&gt;Specific to your question, it seems each form is under the control of its own promoter. This means that A8 will have to splice out the first exons of all other forms (this would be exon skipping). On the other hand, the A1 pre-mRNA doesn't contain any other first exons to begin with. These would be classified as gene isoforms&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/m/pubmed/16399340/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Owens IS, Basu NK, Banerjee R. 2005. UDP-glucuronosyltransferases: gene structures of UGT1 and UGT2 families. Methods Enzymol 400:1-22.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene?Db=gene&amp;amp;Cmd=ShowDetailView&amp;amp;TermToSearch=54658&quot; rel=&quot;nofollow noreferrer&quot;&gt;NCBI Gene: UGT1&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-07-09T18:27:19.100" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35923" PostTypeId="1" CreationDate="2015-07-09T18:28:41.937" Score="0" ViewCount="819" Body="&lt;p&gt;Why the sense strand is only involved in transcription though the antisense strand just has the compliment strand of the sense strand?&lt;/p&gt;&#xA;" OwnerUserId="16657" LastActivityDate="2015-07-10T15:00:10.587" Title="Sense and anti sense strand" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;&lt;human-genetics&gt;" AnswerCount="3" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35924" PostTypeId="1" CreationDate="2015-07-09T18:34:50.713" Score="2" ViewCount="28" Body="&lt;p&gt;We can easily recall our visual stimulus and auditory stimulus but why can't we recall chemical stimulus like smell and pain?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can recall a song or picture but we can't exactly recall smell and pain. Why is that so?&lt;/p&gt;&#xA;" OwnerUserId="16657" LastActivityDate="2015-07-09T18:34:50.713" Title="Peculiarity of chemo senses" Tags="&lt;physiology&gt;&lt;neurophysiology&gt;&lt;human-physiology&gt;&lt;senses&gt;" AnswerCount="0" CommentCount="3" FavoriteCount="0" ClosedDate="2015-07-10T04:24:41.570" ContentLicense="CC BY-SA 3.0" />
  <row Id="35926" PostTypeId="2" ParentId="31766" CreationDate="2015-07-09T19:22:45.340" Score="2" Body="&lt;p&gt;Most of the transcripts you show have different transcription start sites. In other words, this happens because of alternative transcription start sites. So this is not typical alternative slicing. Some genes have different transcriptional start sites, but the case you show has exceptionally many start sites.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-07-09T19:32:07.890" LastActivityDate="2015-07-09T19:32:07.890" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35927" PostTypeId="2" ParentId="35923" CreationDate="2015-07-09T19:24:06.403" Score="2" Body="&lt;p&gt;The short answer is the transcription machinery will only bind on the correct orientation.  The binding of proteins and such to the promoter DNA strand is determined by the sequence of the DNA, the sequence is not correct on the anti-sense strand for a given gene.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2015-07-09T19:24:06.403" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35928" PostTypeId="2" ParentId="35921" CreationDate="2015-07-09T19:45:53.327" Score="28" Body="&lt;p&gt;It is difficult to find a scientific answer to this question, but let me insert this citation from a &lt;a href=&quot;http://www.furmanagers.com/#!beaver/c1pvp&quot; rel=&quot;noreferrer&quot;&gt;specialist site&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Contrary to popular belief, beaver cannot plan the direction in which trees will fall. Many trees become hung up in the branches of surrounding trees and are lost to the colony. In heavily forested areas, this loss may amount to one-half of the trees felled.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.scienceworld.ca/sites/default/files/Beavers_TG.pdf&quot; rel=&quot;noreferrer&quot;&gt;Another source&lt;/a&gt; says the same.&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;But &lt;a href=&quot;http://www.uregina.ca/science/biology/people/faculty-research/brigham-mark/files/Samways_etal_2004_NW_Nat.pdf&quot; rel=&quot;noreferrer&quot;&gt;scientists think&lt;/a&gt; beavers may actually plan the direction of falling:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;By measuring the falling angle of 888 trees of a variety of sizes cut&#xA;  near 8 different dams in southwestern Saskatchewan, we tested the&#xA;  hypothesis that beavers (Castor canadensis) fell trees in a non-random&#xA;  direction. We predicted that trees would be preferentially felled&#xA;  towards the dam to minimize the costs of transporting materials to the&#xA;  dam and to minimize the amount of time beavers spend on land. We&#xA;  established a 150 m wide × 250 m long transect at each dam and&#xA;  determined the felling angle of at least 100 aspen trees cut in each&#xA;  transect. We found that trees were felled by beavers with a mean&#xA;  felling angle of 357.9°, a direction not significantly different from&#xA;  that of the dam. In all, 62% of trees were felled within 45° of the&#xA;  direction of the dam. While our data are consistent with the&#xA;  hypothesis, an experimental test is required to establish the&#xA;  reason(s) for the pattern we found.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Their picture is better than thousands of words:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RQ5LT.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And &lt;a href=&quot;https://kb.osu.edu/dspace/bitstream/handle/1811/23987/V103N5_143.pdf?sequence=1&quot; rel=&quot;noreferrer&quot;&gt;another paper&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We studied patterns in the orientation of cutting when beavers (Castor canadensis) cut trees around Alum Creek Lake in central Ohio. For 462 trees, we measured the slope at the base of the tree, the orientation of the cut relative to this slope, the distance of the tree from the water, the radius of the tree, and the symmetry of the cut. The land around Alum Creek Lake generally slopes toward the water, so to direct the fall of a tree towards the water a beaver should cut a symmetrical tree from the downhill side. Cutting from the downhill side occurred for trees &gt;9.0 m from the water. Near the shore, trees tended to lean toward the water and would fall toward the water regardless of the side from which the beaver cut. At distances &amp;lt;9-0 m from shore, beavers cut predominantly from the uphill side where it should be easy to sit and there is little danger of the tree falling on them. At all distances, beavers showed random orientation when cutting trees on shallow slopes (&amp;lt;20°), whereas on steep slopes (especially slopes &gt;30°) they cut predominantly from the uphill side. Beavers cut small trees (&amp;lt;5.0 cm diameter) mostly from the downhill side, but tended to cut trees &gt;5.0 cm in diameter from the uphill side. Overall, enough factors interacted that no single pattern of cutting existed for all trees.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="6307" LastEditDate="2015-07-10T18:47:54.257" LastActivityDate="2015-07-10T18:47:54.257" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="35930" PostTypeId="2" ParentId="35923" CreationDate="2015-07-09T20:37:16.093" Score="1" Body="&lt;p&gt;One of the reasons why DNA is double stranded--this means DNA has sense and antisense strands--is to make a copy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;During transcription, RNAs are transcribed referring to anti-sense strand sequences--making base pairs with anti-sense strand. In other words, the sense strand does not do anything during transcription.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-07-09T20:37:16.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35931" PostTypeId="1" CreationDate="2015-07-09T20:38:48.973" Score="0" ViewCount="276" Body="&lt;p&gt;I am considering starting a treatment with Accutane(Isotretinoin), however I am not sure about what the effects on the brain are. Here are two studies that contradict each other:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/11696672&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/11696672&lt;/a&gt;&#xA;The first one states that using an antagonist, they increased the rats' working memory. So logically, using the agonist (isotretinoin), it would cause a loss of working memory?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3360864/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3360864/&lt;/a&gt;&#xA;Here they state that not only did isotretinoin not have negative effects, but it actually had positive effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am more inclined to believe that it has negative effects, because most anecdotal evidence says that it makes patients feel &quot;foggy&quot; and &quot;forgetful&quot;. Can anyone please enlighten me? What exacly does this stuff do to the brain and is it irreversible?&lt;/p&gt;&#xA;" OwnerUserId="10474" LastActivityDate="2021-04-02T10:07:25.770" Title="Isotretinoin and retinoid receptors in brain confusion?" Tags="&lt;brain&gt;&lt;receptor&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35932" PostTypeId="1" CreationDate="2015-07-09T21:49:35.757" Score="2" ViewCount="508" Body="&lt;p&gt;Small pink flower, started out as tiny buds, leaves look almost like Maple leaves..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/EGoAbm.jpg&quot; alt=&quot;&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16687" LastEditorUserId="1590" LastEditDate="2015-07-10T06:59:54.553" LastActivityDate="2015-07-10T06:59:54.553" Title="Can anyone Id this flower?" Tags="&lt;species-identification&gt;&lt;flowers&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35936" PostTypeId="2" ParentId="35086" CreationDate="2015-07-10T00:17:07.563" Score="0" Body="&lt;p&gt;I can't add any detail to AliceD's answer, but I can put it in different terms, and perhaps that could be helpful to you. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, Cl&lt;sup&gt;-&lt;/sup&gt; ions are negatively charged, and the neuron is very often negatively charged. Given &lt;em&gt;only those two facts&lt;/em&gt;, yes, you would think Cl&lt;sup&gt;-&lt;/sup&gt; would not enter the neuron. But there is another key fact: &lt;strong&gt;diffusion.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Cl&lt;sup&gt;-&lt;/sup&gt; ions feel the force of electrical repulsion, but since they are at body temperature they also feel the force of slamming into each other at very high speeds and bouncing every which way. This &quot;slamming force&quot; tends to spread them out, and that is otherwise known as diffusion. Since there are many more of them outside the neuron than inside (due to active pumping them to that imbalanced state), the force of diffusion tends to drive them &lt;em&gt;inside&lt;/em&gt; the neuron--at least as long as it's not &lt;em&gt;too&lt;/em&gt; negative in there! If it is too negative, then no, the force of diffusion is not enough to push the Cl&lt;sup&gt;-&lt;/sup&gt; ions into the neuron, and in fact they may leave the neuron.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I've written here is, I think, (essentially) equivalent to AliceD's fine answer. &lt;/p&gt;&#xA;" OwnerUserId="587" LastEditorUserId="9943" LastEditDate="2015-07-10T01:12:25.540" LastActivityDate="2015-07-10T01:12:25.540" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35937" PostTypeId="2" ParentId="35932" CreationDate="2015-07-10T00:42:09.593" Score="5" Body="&lt;p&gt;It's a mallow.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/275gV.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The leaves - they look like maple leaves - and the flower are identical.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mallows are from the family Malvaceae, which includes food plants (okra, cocoa beans, kola nut), economic plants (cotton), and ornamentals (e.g. hibiscus) One species of this family (Althaea officinalis) is actually the original ingredient to make marshmallows.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure which &lt;a href=&quot;https://en.wikipedia.org/wiki/Malvaceae&quot; rel=&quot;nofollow noreferrer&quot;&gt;mallow&lt;/a&gt; it is (there are 243 genera with 4225+ species), but it's a common &lt;s&gt;weed&lt;/s&gt; wildflower all over the world.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-07-10T01:10:13.970" LastActivityDate="2015-07-10T01:10:13.970" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35939" PostTypeId="1" AcceptedAnswerId="36004" CreationDate="2015-07-10T01:53:42.037" Score="3" ViewCount="188" Body="&lt;p&gt;Is it true that color vision is sex-linked for all species with binary sexes? Is there an evolutionary significance to the fact that color vision is X-linked in humans? E.g., only female humans can be tetrachromats.&lt;/p&gt;&#xA;" OwnerUserId="16691" LastEditorUserId="9943" LastEditDate="2015-07-10T04:00:10.930" LastActivityDate="2015-07-12T12:26:57.700" Title="Color vision across species" Tags="&lt;genetics&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35943" PostTypeId="1" CreationDate="2015-07-10T06:32:11.563" Score="3" ViewCount="152" Body="&lt;p&gt;Why do bug bites and cuts itch when scratching them clearly doesn't help us survive? Did our early ancestors need to rely on this itching sensation, or is it just that the receptors for itches just happen to be stimulated by histamine?&lt;/p&gt;&#xA;" OwnerUserId="16696" LastActivityDate="2017-03-24T10:43:27.543" Title="Why are our bodies created to itch when histamine is released by our immune systems?" Tags="&lt;human-biology&gt;&lt;sensation&gt;&lt;senses&gt;" AnswerCount="3" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35944" PostTypeId="1" CreationDate="2015-07-10T08:41:08.073" Score="3" ViewCount="183" Body="&lt;p&gt;Background : &lt;em&gt;B.thuringiensis&lt;/em&gt; produces an inactive crystalline toxin during sporulation which when ingested by an insect, gets activated and causes pore formation in gut , subsequently leading to death of the insect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Question : What is the  role of the toxin in bacteria's own metabolism ? Does it &quot;unintentionally&quot; kill the insects or is there an evolutionary advantage gained by the bacteria ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3340" LastEditDate="2015-07-10T09:10:04.490" LastActivityDate="2015-07-10T09:10:04.490" Title="Why does bacillus thuringiensis produce bt toxin?" Tags="&lt;evolution&gt;&lt;microbiology&gt;&lt;biotechnology&gt;&lt;bacterial-toxins&gt;" AnswerCount="0" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35945" PostTypeId="2" ParentId="31747" CreationDate="2015-07-10T09:21:41.507" Score="0" Body="&lt;p&gt;ATP synthase is a wonderful protein. I'll try to answer to your question without going into too much detail.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The protein complexes of the respiratory chain actively pump H+ to form a proton gradient between the two side of the membrane. ATP synthase uses the movement of the protons down their electrochemical gradient to synthesizes ATP molecules. &#xA;The transmembrane domain of the ATP synthase (FO) is a passive proton channel. Flow of protons causes the rotation of FO. Rotation of FO causes the rotation of the gamma subunit that connects FO with the catalytic domain of the ATP synthase (F1). Rotation of the gamma subunit causes the rotation of F1 that causes the synthesize of ATP. So the mechanical energy is transferred from FO to F1 via the gamma subunit. In F1 the mechanical energy is transformed into chemical energy via the synthesize of ATP.&lt;/p&gt;&#xA;" OwnerUserId="16581" LastActivityDate="2015-07-10T09:21:41.507" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35946" PostTypeId="1" AcceptedAnswerId="35947" CreationDate="2015-07-10T11:28:05.827" Score="0" ViewCount="105" Body="&lt;p&gt;My question is what does the word 'factor' mean in words like transcription-factor or nerve growth-factor? What is similar between these different compounds such that they deserve the word 'factor' in their name?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Edit: My confusion comes perhaps from the use of the word 'factor' in statistics, where it refers to a variable that can take on discrete values (e.g., the factor Gender takes on values 'male' and 'female'). Here a different meaning of the word seems to be used.&lt;/p&gt;&#xA;" OwnerUserId="16532" LastEditorUserId="16532" LastEditDate="2015-07-11T10:18:25.770" LastActivityDate="2015-07-11T10:18:25.770" Title="What are 'factors' in biology?" Tags="&lt;terminology&gt;" AnswerCount="1" CommentCount="9" ClosedDate="2015-07-11T04:37:05.187" ContentLicense="CC BY-SA 3.0" />
  <row Id="35947" PostTypeId="2" ParentId="35946" CreationDate="2015-07-10T11:42:04.680" Score="3" Body="&lt;p&gt;There are many meanings of &quot;factor&quot; in Biology. In the context where you place it, namely &lt;strong&gt;bio-active substances, such as hormones and enzymes&lt;/strong&gt; I would go for the definition given by the &lt;a href=&quot;http://medical-dictionary.thefreedictionary.com/Biological+factors&quot; rel=&quot;nofollow&quot;&gt;Medical Dictionary&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;&lt;em&gt;factor&lt;/em&gt;&lt;/strong&gt; [fak´ter] :&#xA;  an agent or element that contributes to the production of a result.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Within this definition, a transcription factor contributes to the transcription of DNA into mRNA, and nerve growth factor contributes to the growth and survival of neurons.   &lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-07-10T11:42:04.680" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35949" PostTypeId="2" ParentId="35923" CreationDate="2015-07-10T15:00:10.587" Score="1" Body="&lt;p&gt;Either strand of DNA can be sense or antisense.  SWBarnes2 posts that the &quot;transcription machinery will only bind on the correct orientation&quot; and that is indeed what determines which strand is sense.  But note his important statement &quot;the sequence is not correct on the anti-sense strand FOR A GIVEN GENE&quot; (my emphasis).  As you move from gene to gene, the sense strand can swap strands.  Coding sequences can overlap running in opposite directions, making both strands sense; this is more commonly a viral trick.  Sense and antisense are defined by what sequence is found in RNA and so the map of sense and antisense strands on DNA is complicated. As you move along a strand of DNA one strand might be sense, then the other, then both, then neither.&lt;/p&gt;&#xA;" OwnerUserId="10430" LastActivityDate="2015-07-10T15:00:10.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35950" PostTypeId="1" CreationDate="2015-07-10T15:45:04.420" Score="1" ViewCount="162" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/h6JJn.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am really concerned with this since I've never seen a cocoon this color before and can't find it anywhere on the internet. I found it just laying on the ground not attached to anything, but it seems to be alive because when you touch it, it will wiggle abit. Any answers are appreciated.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BdsYj.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16701" LastEditorUserId="19679" LastEditDate="2015-10-29T19:32:30.600" LastActivityDate="2015-10-29T21:46:29.580" Title="Does anyone know what type of Cocoon this is?" Tags="&lt;entomology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35951" PostTypeId="1" CreationDate="2015-07-10T15:51:08.920" Score="2" ViewCount="1025" Body="&lt;p&gt;The development of t-lymphocytes are done by thymus and we also know that the thymus degenerates before puberty and we also know the maximum lifespan of WBC's is 15 days. So, how do t-lymphocytes become mature if thymus has lost his function?  &lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="16041" LastEditDate="2015-07-10T18:42:51.400" LastActivityDate="2015-07-11T08:06:25.380" Title="How do t-lymphocytes become mature if thymus has lost its function?" Tags="&lt;physiology&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35952" PostTypeId="2" ParentId="35861" CreationDate="2015-07-10T16:39:19.127" Score="0" Body="&lt;p&gt;The thing to remember is that no living system is 100% efficient. Firstly lets deal with your statement here:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;A positive nitrogen balance (where nitrogen balance = N intake − N loss) indicates a greater usage of proteins.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Basically means what it says on the tin. If your body is utilising more nitrogen then it is giving out:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Positive nitrogen balance is associated with periods of growth, hypothyroidism, tissue repair, and pregnancy. This means that the intake of nitrogen into the body is greater than the loss of nitrogen from the body, so there is an increase in the total body pool of protein.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Now we really cant measure notrogen on a weighing scale. So the blood urea level is used as an estimator for nitrogen metabolism.&lt;/p&gt;&#xA;&lt;p&gt;Now, as mentioned below, no system is 100% efficient, and the purpose of urea is infact to be as a vehicle to excrete toxic ammonia. Sure the body looses a few nitrogens in the form of urea, but as a whole, it gains a lot more from the metabolism.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;An analogy:&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;In other words, think of it like this: When you make something out of wood (proteins), you get wood shavings (ammonia). Now you cant reconstitute the wood shavings back to a full wood (proteins), nor can you use wood shavings (ammonia) as they are toxic for you. So you group up the wood shavings (urea) and get rid of it.&lt;/p&gt;&#xA;&lt;p&gt;The formula is essentially:&lt;/p&gt;&#xA;&lt;p&gt;The number of furniture made = Function of (Weight of wood delivered - weight of saw dust taken out)&lt;/p&gt;&#xA;&lt;p&gt;If you use a lot of wood (proteins), and are a good craftsman (healthy human)  you'll ultimately have a bit more shavings (blood urea nitrogen), but a lot more furniture to move around. Now since you cant see the furniture (proteins in tissues), but you can see the shavings coming out (blood urea nitrogen) there will be a rise in the BUN.&lt;/p&gt;&#xA;&lt;p&gt;Now if you are a poor carpenter (disease or something), you mess up and you end up wasting a lot more wood as shavings than getting the furniture right. So for say 10 kilos of wood, you can only make one couch and 9 kilos of saw dust..  you are really not doing it right, and this is where the BUN gets in the negative territory (I know 10-9 is not negative, but remember the body has a baseline need of say 6 couches and you are only giving it 1, the body will get that from somewhere to the detriment if your health)&lt;/p&gt;&#xA;&lt;p&gt;Apologies for the long winded analogy. I hope you understood what I was trying to imply. I am pretty sure someone out there will give a more scientifically accurate answer, so you might want to wait on that also.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Further reading from the &lt;a href=&quot;https://en.wikipedia.org/wiki/Urea&quot; rel=&quot;nofollow noreferrer&quot;&gt;wiki:&lt;/a&gt;&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Amino acids from ingested food that are not used for the synthesis of proteins and other biological substances — or produced from catabolism of muscle protein — are oxidized by the body, yielding urea and carbon dioxide, as an alternative source of energy.&lt;/p&gt;&#xA;&lt;p&gt;The &lt;strong&gt;oxidation pathway starts with the removal of the amino group by a transaminase;&lt;/strong&gt; the amino group is then fed into the urea cycle. The &lt;strong&gt;first step in the conversion of amino acids from protein into metabolic waste in the liver is removal of the alpha-amino nitrogen, which results in ammonia. Because ammonia is toxic, it is excreted immediately by fish, converted into uric acid by birds, and converted into urea by mammals.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;Ammonia (NH3) is a common byproduct of the metabolism of nitrogenous compounds. Ammonia is smaller, more volatile and more mobile than urea. If allowed to accumulate, ammonia would raise the pH in cells to toxic levels. Therefore many organisms convert ammonia to urea, even though this synthesis has a net energy cost. Being practically neutral and highly soluble in water, urea is a safe vehicle for the body to transport and excrete excess nitrogen.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-07-10T16:46:09.233" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35953" PostTypeId="1" AcceptedAnswerId="35964" CreationDate="2015-07-10T19:05:27.690" Score="3" ViewCount="127" Body="&lt;p&gt;Are there respectable scientific journals for publishing models of protein-protein interactions obtained by docking simulations? I would also discuss the biological significance of the particular mode of docking that I found through the simulations, and how it is consistent with available experimental evidence. The point is that my paper wouldn't have any new experimental evidence. Rather, I analyze existing experimental evidence in the literature and demonstrate that the model of interaction I propose explains this data. Are there respectable journals accepting this type of research? Can you post some example journals like this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, can you post some references to good papers like these, hopefully highly cited, if there are any?&lt;/p&gt;&#xA;" OwnerUserId="561" LastEditorUserId="561" LastEditDate="2015-07-10T21:07:25.043" LastActivityDate="2016-05-07T07:31:49.023" Title="Are there journals for theoretical models of protein-protein interactions?" Tags="&lt;bioinformatics&gt;&lt;peer-review-journal&gt;&lt;publishing&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="35954" PostTypeId="2" ParentId="2375" CreationDate="2015-07-10T19:53:48.243" Score="3" Body="&lt;p&gt;I highly recommend you to visit &lt;strong&gt;&lt;a href=&quot;http://pathguide.org/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pathguide&lt;/a&gt;&lt;/strong&gt; to get a sense of how vast is the catalog of Pathway Databases. Looking into the category &lt;strong&gt;&lt;a href=&quot;http://pathguide.org/#4&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pathway Diagrams&lt;/a&gt;&lt;/strong&gt; or in &lt;strong&gt;Transcription Factors / Gene Regulatory Networks&lt;/strong&gt; should help in your task.&lt;/p&gt;&#xA;&lt;p&gt;I would start by looking at these DataBases:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;GeneMania&lt;/li&gt;&#xA;&lt;li&gt;BioCarta&lt;/li&gt;&#xA;&lt;li&gt;WikiPathways&lt;/li&gt;&#xA;&lt;li&gt;Reactome&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;If you are working with a species other than human, perhaps you'll find a more suitable database in PathGuide.&lt;/p&gt;&#xA;&lt;p&gt;Good luck!&lt;/p&gt;&#xA;&lt;p&gt;PS: Sorry New user limitations impede me to post more than two links :/&lt;/p&gt;&#xA;" OwnerUserId="16663" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-07-10T19:53:48.243" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35955" PostTypeId="2" ParentId="35951" CreationDate="2015-07-10T20:03:10.417" Score="2" Body="&lt;p&gt;A few points, I'll expand on this later and add references if I have time:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The thymus starts degenerating at puberty but continues to function in thymocyte maturation for decades, albeit at a lower level&lt;/li&gt;&#xA;&lt;li&gt;Many mature T cells can live for years&lt;/li&gt;&#xA;&lt;li&gt;Through homeostatic proliferation, peripheral T cells maintain their population size&lt;/li&gt;&#xA;&lt;li&gt;Immune surveillance generally decreases with age&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Note that extended lifespans and homeostatic proliferation (points 2 and 3) don't contribute to TCR diversity but only maintain the existing repertoire. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-07-10T22:59:00.783" LastActivityDate="2015-07-10T22:59:00.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35956" PostTypeId="2" ParentId="3177" CreationDate="2015-07-10T20:44:05.650" Score="4" Body="&lt;p&gt;I just found a research about possibility of organism with loop DNA (Mostly bacteria) could use there DNA as antenna to transmit and receive radio wave around 1kHz&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.wired.com/2011/04/bacterial-radio/&quot; rel=&quot;nofollow&quot;&gt;http://www.wired.com/2011/04/bacterial-radio/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But as other said. Communication mostly evolve from sensory organ. So the radio wave has too much noise and could not give useful information about situation. They don't selectively evolve to the point that they could be used to communicate&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But the bacteria has inherently possibility from start. So they may actually do some communication&lt;/p&gt;&#xA;" OwnerUserId="9910" LastActivityDate="2015-07-10T20:44:05.650" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35957" PostTypeId="1" AcceptedAnswerId="35958" CreationDate="2015-07-10T20:49:39.170" Score="2" ViewCount="121" Body="&lt;p&gt;These are outside a window in Phoenix, Arizona. I looked on the internet for pictures and these guys looked very similar to winged termites.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/SvRRm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ffrCg.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zz6Sf.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16703" LastEditorUserId="15051" LastEditDate="2015-07-10T21:17:04.330" LastActivityDate="2015-07-11T13:33:31.160" Title="Are these termites?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35958" PostTypeId="2" ParentId="35957" CreationDate="2015-07-10T21:21:42.623" Score="1" Body="&lt;p&gt;They could be halictid bees, possibly &lt;em&gt;Agapostemon splendens&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yours looks very similar to this picture&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8rUw1.jpg&quot; alt=&quot;CC by 2.0 by Bob Peterson&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.flickr.com/photos/pondapple/9962435963/in/photolist-gbm68i-4UTbZp-ozM511-6XPoeR-9DJ4HH-okaBM1-fb4yAr-aobyMZ-o6YfJb-vzDkuE-r36DPi-fb4yRk-fbiPoS-fbiPhU-5rU9Pd-6zDB7g-tksqre-sSKDsj-tam6ya-6Rbojh-t3PMzq-vss6nJ-tksygn-avN3hU-4YiWbe-enJ5DK-6VQqMs-6VDyzJ-tk8n1A-8ytLy4-taoy7c-drSYgg-afSau7-obHu8C-acJa4C-gSGrGL-eXRH35-nEupa-soo5JQ-smkWjs-mDvwnD-vPngwm-gkSfp2-gkSrX3-gkS5Rd-33UefA-obDmbL-rGi7uC-7eDps6-pxEvuh&quot; rel=&quot;nofollow noreferrer&quot;&gt;(by Bob Peterson)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Compare also with this one &lt;a href=&quot;http://bugguide.net/node/view/155774&quot; rel=&quot;nofollow noreferrer&quot;&gt;on bugguide&lt;/a&gt; and to the pictures of &lt;em&gt;Agapostemon&lt;/em&gt; species in &lt;a href=&quot;http://voices.nationalgeographic.com/2014/10/24/hair-bands-and-giant-trousers-a-lesson-in-how-little-i-know-about-bees/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this National Geographic article&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Compare the metallic head and thorax (that's the middle segment), the striped abdomen (the last segment), the apparent large size of eyes and place of antennae attachment, and the 'buff' hindlegs.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastEditorUserId="3952" LastEditDate="2015-07-11T13:33:31.160" LastActivityDate="2015-07-11T13:33:31.160" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35959" PostTypeId="1" CreationDate="2015-07-10T21:34:20.333" Score="2" ViewCount="69" Body="&lt;p&gt;My question is can we change the direction of a neurological signal? When a neurological signal is generated it goes to the brain. Along the way it passes synapses. Can we make it change it's pathway to go through another neurone instead of the neurone it was going to ?&lt;/p&gt;&#xA;" OwnerUserId="16584" LastEditorUserId="9943" LastEditDate="2015-07-11T14:04:27.857" LastActivityDate="2015-07-11T14:04:27.857" Title="Can we change the direction of a neurological signal?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2015-07-11T06:16:44.730" ContentLicense="CC BY-SA 3.0" />
  <row Id="35960" PostTypeId="1" CreationDate="2015-07-10T21:54:06.143" Score="3" ViewCount="178" Body="&lt;p&gt;I was wondering: some companies plan to colonize Mars, many of us know.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But if one were to live on Mars, would this person live longer?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems to me that a lower gravity would mean less overall damage to the body cells, so they could last longer: resulting in a longer lifespan.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Or maybe lack of gravity = lack of exercise = lesser lifespan?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd like the opinion of some expert in the matter. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="16705" LastActivityDate="2015-07-15T17:32:40.970" Title="Would a person live longer, if such a person lived in a planet with lower gravity? (say, Mars)" Tags="&lt;senescence&gt;&lt;life&gt;&lt;lifespan&gt;" AnswerCount="2" CommentCount="1" ClosedDate="2015-07-15T18:10:54.713" ContentLicense="CC BY-SA 3.0" />
  <row Id="35961" PostTypeId="2" ParentId="35861" CreationDate="2015-07-10T22:22:17.593" Score="1" Body="&lt;p&gt;The quotes in the question provide incomplete information at best.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's focus on the nitrogen (N) that comes from protein, ignoring for now how metabolism differs among amino acids. We'll assume for simplicity that liver function is OK so that the urea N production &lt;em&gt;rate&lt;/em&gt; is a reasonable measure of protein N degradation &lt;em&gt;rate&lt;/em&gt; (say in units like moles of N per hour).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, consider simple conservation of mass:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Intake = Loss + Net Storage&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you think about this in terms of protein N from the perspective of the &lt;em&gt;whole body&lt;/em&gt;, you start to see the limitations in those quotes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, loss &lt;em&gt;from the whole body&lt;/em&gt; of metabolized protein N in the form of urea N mostly occurs via the urine. Impaired kidney function may lead to less urea being excreted than is being formed. You will then have &quot;Net Storage&quot; of urea N in the blood and body fluids, so BUN can rise even if metabolism of protein is unchanged. In fact, &lt;a href=&quot;http://www.mayoclinic.org/tests-procedures/blood-urea-nitrogen/basics/definition/prc-20020239&quot; rel=&quot;nofollow&quot;&gt;BUN tests&lt;/a&gt; can be used with other tests to provide information about kidney function. Thus BUN &lt;em&gt;levels&lt;/em&gt; don't necessarily tell you much about the urea N production &lt;em&gt;rate&lt;/em&gt; or protein degradation &lt;em&gt;rate&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, you have to consider that one &quot;use&quot; of proteins can be &quot;Net Storage&quot; to build muscle mass. That type of &quot;use&quot; won't show up in increased urea N production. Alternatively, body protein in muscle can be broken down to be &quot;used&quot; for metabolism/catabolism during an overnight fast, possibly leading to increased urea N production &lt;em&gt;rate&lt;/em&gt; depending on how the mix of protein, fat, and carbohydrate catabolism has changed. Furthermore, the effects on BUN &lt;em&gt;levels&lt;/em&gt; will depend on kidney function. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both storage and degradation/catabolism are important &quot;uses&quot; of protein N, but they have different implications for production of urea N, and BUN &lt;em&gt;levels&lt;/em&gt; don't necessarily represent the urea production &lt;em&gt;rate&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="16326" LastActivityDate="2015-07-10T22:22:17.593" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35962" PostTypeId="2" ParentId="35960" CreationDate="2015-07-11T00:27:25.437" Score="1" Body="&lt;p&gt;It sounds reasonable that reducing the physical stress on a body would reduce the wear and tear, and thus increase the owner's lifetime.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it's just as reasonable that human bodies are designed to be under stress, and drastically changing the environment will harm the body in subtle and even obvious ways. For instance, &lt;a href=&quot;http://www.nature.com/pr/journal/v50/n1/full/pr2001138a.html&quot; rel=&quot;nofollow&quot;&gt;some research shows&lt;/a&gt; that lung and heart cells won't grow properly if not cyclically stretched.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Until we get some serious long-term research, in space or on a smaller planet, we won't really know.&lt;/p&gt;&#xA;" OwnerUserId="11620" LastActivityDate="2015-07-11T00:27:25.437" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35963" PostTypeId="1" CreationDate="2015-07-11T01:20:26.110" Score="2" ViewCount="1198" Body="&lt;p&gt;We have all had those moments of intense concentration on some tough exam, perhaps a college test or whatever...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is it that when we squint, it feels like we can focus and concentrate better on the test, and get answers more easily? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do we actually get a better mental performance when we are squinting?  If so, why?&lt;/p&gt;&#xA;" OwnerUserId="16705" LastEditorUserId="-1" LastEditDate="2015-07-11T06:18:02.320" LastActivityDate="2015-07-12T10:57:02.940" Title="Does &quot;squinting&quot; make you concentrate better on a logic test?" Tags="&lt;brain&gt;&lt;vision&gt;&lt;eyes&gt;&lt;anatomy&gt;&lt;perception&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35964" PostTypeId="2" ParentId="35953" CreationDate="2015-07-11T02:21:47.177" Score="4" Body="&lt;p&gt;Protein-protein interactions is an area of biophysics, so certainly &lt;a href=&quot;http://www.cell.com/biophysj/home&quot; rel=&quot;nofollow&quot;&gt;Biophysical Journal&lt;/a&gt; (published by Cell) is a nice place to look.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org&quot; rel=&quot;nofollow&quot;&gt;PNAS&lt;/a&gt; has a broad range of areas and they pay a lot of attention to nice biophysics and modeling. But also they require (seems to me) experimental evidence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;a href=&quot;http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1096-987X&quot; rel=&quot;nofollow&quot;&gt;Journal of computational chemistry&lt;/a&gt; certainly about a lot of simulations and modeling, so see for yourself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for publications, the fact that you are asking for references makes me think you haven't done your homework on literature review, as it is always first and foremost job in a research project.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="9099" LastEditDate="2015-07-11T04:09:38.337" LastActivityDate="2015-07-11T04:09:38.337" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35965" PostTypeId="2" ParentId="35959" CreationDate="2015-07-11T02:32:41.483" Score="-1" Body="&lt;p&gt;&quot;Neurological signal&quot;, or as I would put it, action potential, or activity propagation can be modeled as current in an electrical circuit. Trick is that such a circuit contains a bunch of highly regulated and non-linear and non-static elements. Imaging bunch of potentiometers (variable resistances) in your circuit. And all of them behave depending on something else in the system. So certainly currents will go somewhere, but level of control and complexity is phenomenal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An example that should let you appreciate possibility of rerouting is simple Pavlovian conditioning. Neutral stimulus (bell) that has no evident connection to stomach, after conditioning elicits response there. Even though circuitry is very complicated and signal propagation is hard to investigate, this is an evidence that changing path of signals is very possible in some way. (Of course, conditioning require changes in higher-than-stomach systems, some intermediate levels).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On more practical note, we can readout neuronal activity in region A (of brain, muscle or else) and rely it via electrical stimulation somewhere in brain or muscle or gland. Both parts of this are available technology. As of drugs, some people report &lt;a href=&quot;https://en.wikipedia.org/wiki/Synesthesia&quot; rel=&quot;nofollow&quot;&gt;&quot;seeing&quot; sounds&lt;/a&gt; while intoxicated, this might be an example of such temporary effects.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="9943" LastEditDate="2015-07-11T04:54:10.573" LastActivityDate="2015-07-11T04:54:10.573" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35966" PostTypeId="2" ParentId="35915" CreationDate="2015-07-11T02:35:50.880" Score="2" Body="&lt;p&gt;No, MHCII mismatch can also lead to transplant rejection, though through different mechanisms. CD8+ Tcells (that recognize class I) may become activated and directly kill donor cells*, and some NK subtypes can see the lack of self MHCI and also induce cell death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;MHCII mismatch on antigen presenting cells (APCs) brought along in the tissue may activate CD4+ (helper) Tcells, which do not kill directly. However, they can secrete a lot of pro-inflammatory cytokines which will make a generally hostile environment, and can also activate b-cells to produce antibodies against minor histocompatibility loci. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to your other question, lacking MHCI entirely would be really rough on an animal in the wild, but under laboratory conditions where pathogens can be managed a bit more, it doesn't matter so much. It's the same reason we can keep mice that have gross immunological deficiencies alive, where humans with the same defects would be screwed.&lt;/p&gt;&#xA;" OwnerUserId="12905" LastEditorUserId="12905" LastEditDate="2015-07-11T14:53:18.337" LastActivityDate="2015-07-11T14:53:18.337" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="35967" PostTypeId="2" ParentId="35963" CreationDate="2015-07-11T04:14:58.573" Score="3" Body="&lt;p&gt;The phenomenon in question is probably related to people with uncorrected/undercorrected &lt;a href=&quot;https://en.wikipedia.org/wiki/Myopia&quot; rel=&quot;nofollow noreferrer&quot;&gt;myopia&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &quot;ancient&quot; phenomenon is called &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1444-0938.1932.tb01100.x/abstract?&quot; rel=&quot;nofollow noreferrer&quot;&gt;stenopeic slit effect&lt;/a&gt; (a case of pinhole effect): when the person squints the visual acuity becomes better because of smaller blur circles: the &quot;slit&quot; between the eyelids is the key point improving blurring. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One can check if it works by creating slit in paper or plastic:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RUi6H.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some &quot;charlatans/witch-doctors/quacksalver/etc&quot; can &quot;treat&quot; refractive error with &lt;a href=&quot;https://en.wikipedia.org/wiki/Pinhole_glasses&quot; rel=&quot;nofollow noreferrer&quot;&gt;pinhole/stenopeic glasses&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/yIttf.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is known that children with refractive errors have attention issues because they cannot see the objects sharply (this is why they can be mistakenly diagnosed with ADHD), thus your concentration improvement related mostly to your vision improve and not a better &quot;understanding&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you mean by squint using mimic muscles and &lt;a href=&quot;https://en.wikipedia.org/wiki/Corrugator_supercilii_muscle&quot; rel=&quot;nofollow noreferrer&quot;&gt;corrugator muscle&lt;/a&gt; the answer should point out that not a &quot;squint&quot; improves your concentration, but your attempt to improve your concentration causes this type of &quot;squint&quot;.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-07-11T04:21:19.227" LastActivityDate="2015-07-11T04:21:19.227" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35968" PostTypeId="1" CreationDate="2015-07-11T04:41:10.640" Score="2" ViewCount="85" Body="&lt;p&gt;I've read from &lt;a href=&quot;https://doi.org/10.1111/j.1365-2222.1993.tb00287.x&quot; rel=&quot;nofollow noreferrer&quot;&gt;an academic article&lt;/a&gt; that diamine oxidase cannot be supplemented  but it had no explanation as for why. I am curious as to why this?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Food rich in histamine or red wine may cause allergy‐like symptoms&#xA;  such as sneezing, flush, skin itching, diarrhoea and even shortness of&#xA;  breath. The suspected reason is a diminished histamine degradation&#xA;  based on a deficiency of diamine oxidase. &lt;strong&gt;As diamine oxidase cannot be&#xA;  supplemented, a histamine‐free diet was implemented to reduce&#xA;  histamine intake.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="16709" LastEditorUserId="3340" LastEditDate="2019-02-21T16:21:45.710" LastActivityDate="2019-03-23T18:01:00.277" Title="Why can't diamine oxidase be supplemented?" Tags="&lt;biochemistry&gt;&lt;medicine&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="35970" PostTypeId="1" AcceptedAnswerId="35972" CreationDate="2015-07-11T06:09:08.183" Score="0" ViewCount="538" Body="&lt;p&gt;After reading an admittedly foolish question about 1 googol ants vs. 1000 humans, I had a question. Could a human survive solely on eating ants (common ants, not the stinging kind, or leafcutters etc.)&lt;/p&gt;&#xA;" OwnerUserId="16672" LastActivityDate="2015-07-11T06:17:35.980" Title="Would a human survive eating only living ants?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;human-anatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35972" PostTypeId="2" ParentId="35970" CreationDate="2015-07-11T06:17:35.980" Score="0" Body="&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1469-7998.1984.tb02339.x/abstract&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; study in 1984 suggests it's a bad idea and other sites have said eating ants is for weight loss.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The abstract says that it goes into detail about the problems associated with eating ants as well as their low nutritional value.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I believe the answer is no. You could not survive long term on a diet of only ants.&lt;/p&gt;&#xA;" OwnerUserId="16041" LastActivityDate="2015-07-11T06:17:35.980" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35973" PostTypeId="1" CreationDate="2015-07-11T06:20:15.477" Score="-3" ViewCount="4003" Body="&lt;p&gt;Are there any reliable indicators?&lt;/p&gt;&#xA;" OwnerUserId="16696" LastActivityDate="2015-07-11T21:42:48.880" Title="How do you identify a mosquito's sex without letting it bite you?" Tags="&lt;entomology&gt;&lt;sex&gt;" AnswerCount="1" CommentCount="2" ClosedDate="2015-07-11T20:46:44.173" ContentLicense="CC BY-SA 3.0" />
  <row Id="35974" PostTypeId="2" ParentId="35951" CreationDate="2015-07-11T07:21:49.750" Score="0" Body="&lt;p&gt;The key thing is this: yes, the thymus involutes at puberty but that doesn't halt  thymopoiesis. The thymus continues to produce naive T lymphocytes throughout our lives (even up to 70 years of age-see references) albeit at a very reduced rate. This mechanism is very important for example in HIV-infected individuals who are still able to repopulate their immune cells through a combination of peripheral T cell division and thymic production of naive T cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;References: &lt;a href=&quot;http://www.nature.com/nature/journal/v396/n6712/full/396690a0.html&quot; rel=&quot;nofollow&quot;&gt;Reference_1&lt;/a&gt;, &lt;a href=&quot;http://www.impactaging.com/papers/v2/n2/full/100122.html#bibl_1&quot; rel=&quot;nofollow&quot;&gt;Reference_2&lt;/a&gt;, &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0531556514000060&quot; rel=&quot;nofollow&quot;&gt;Reference_3&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3773" LastEditorUserId="3773" LastEditDate="2015-07-11T08:06:25.380" LastActivityDate="2015-07-11T08:06:25.380" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35975" PostTypeId="1" AcceptedAnswerId="35983" CreationDate="2015-07-11T08:43:33.343" Score="-1" ViewCount="6264" Body="&lt;p&gt;Why does a gene have two alleles?&#xA;When there is a gene for producing the color pigment for a flower, why are there there two alleles, producing either same color or different color (homozygous and heterozygous)?&lt;/p&gt;&#xA;" OwnerUserId="16657" LastEditorUserId="231" LastEditDate="2015-07-11T16:13:43.357" LastActivityDate="2015-07-11T16:27:06.553" Title="Why does a gene have two alleles?" Tags="&lt;genetics&gt;&lt;molecular-genetics&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="0" ClosedDate="2015-07-11T19:09:44.200" ContentLicense="CC BY-SA 3.0" />
  <row Id="35976" PostTypeId="1" AcceptedAnswerId="35985" CreationDate="2015-07-11T09:11:11.643" Score="3" ViewCount="169" Body="&lt;p&gt;I need to find out the name of a nineteenth century biologist who compared developmental biology to crystallography. His idea was that crystals are formed from 'cells' (defined molecular units) that bond together to form arrays. In living organisms cells are bound together but the rules that form the structures change as the organism grows, especially in animals, which is why we have different organs. In both cases you have units that coalesce undirected but according to rules to form structures. I remember finding out about this biologist from a documentary which also showed illustrations from the book he wrote on the subject. I can't find his name or that of his book using a web search because it's too obscure and that would only work with the correct terms. Does anyone know anything about this?&lt;/p&gt;&#xA;" OwnerUserId="16713" LastActivityDate="2015-07-11T19:25:03.867" Title="Who compared developmental biology to crystallography?" Tags="&lt;cell-biology&gt;&lt;development&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35977" PostTypeId="1" AcceptedAnswerId="85567" CreationDate="2015-07-11T11:11:34.970" Score="4" ViewCount="404" Body="&lt;p&gt;There is now a paper wasp nest hanging from the eaves of my bedroom. Not very big, I supposed about a hundred chambers and about 7 to 10 adults in total. I observe it every now and then.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It just occurred to me that when the larvae first hatch, they are so small compared to the chamber diameter. So here are two questions:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;How do they not fall off, being suspended and all?&lt;/li&gt;&#xA;&lt;li&gt;Is there any known statistics of how often larvae fall off (for a particular species, let's say)?&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="1114" LastEditorUserId="1114" LastEditDate="2015-07-12T03:20:32.007" LastActivityDate="2020-08-23T22:45:20.043" Title="How do paper wasp larvae not fall from their nest?" Tags="&lt;entomology&gt;&lt;wasps&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35978" PostTypeId="1" CreationDate="2015-07-11T13:27:44.313" Score="5" ViewCount="738" Body="&lt;p&gt;I recently read about a fossil called &lt;a href=&quot;https://en.wikipedia.org/wiki/Opabinia&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Opabinia&lt;/em&gt;&lt;/a&gt;. What intrigues me is that it had five eyes. I was under the impression that most features, such as eyes, ears and legs are always even-numbered, i.e., 2, 4, 6 etc. Why did Opabinia have 5 eyes?&lt;/p&gt;&#xA;" OwnerUserId="16082" LastEditorUserId="9943" LastEditDate="2015-07-12T03:40:31.243" LastActivityDate="2015-07-12T03:40:31.243" Title="Why did Opabinia have 5 eyes?" Tags="&lt;eyes&gt;&lt;anatomy&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35979" PostTypeId="2" ParentId="35973" CreationDate="2015-07-11T14:27:08.103" Score="8" Body="&lt;p&gt;&lt;strong&gt;Males and females mosquitoes are morphologically quite different.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The majority of individuals you see are females. The males are not attracted to humans and so we see them less often.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main obvious difference is the size of the antenna. When you see the large feather-like antennas of a male, you'll have no doubt; it is a male. The male also tend to be smaller than the female but given the inter-species variation in size I wouldn't use this criterion to tell the gender especially the antenna criterion is so obvious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/lfxB6.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find many more pictures if you just google &lt;code&gt;mosquito male female&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why do males have these large antennas?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The male's large antennas are for sensing the females. There is a very important sexual selection among male mosquitos for accessing a mate. Female beat their wing at another frequency than males and they therefore produce different sounds when flying. So males compete on their ability to hear and recognize female. Females are attracted to CO&lt;sub&gt;2&lt;/sub&gt; and warm bodies but males are incredibly attracted to the sound of the female. During my Bachelor degree I once played a 440Hz harmonic to male &lt;em&gt;Anopheles gambiae&lt;/em&gt;. It is surprising how quickly they respond to this sound and fly toward the speaker.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-07-11T21:42:48.880" LastActivityDate="2015-07-11T21:42:48.880" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35980" PostTypeId="2" ParentId="35978" CreationDate="2015-07-11T14:32:21.390" Score="6" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;The number of eyes are not always even-numbered. In fact, many present-day lower vertebrates feature an uneven number of eyes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Eyes can be generally defined as photosensitive organs. Besides the regular paired eyes, lower vertebrates such as fish, amphibians and reptiles feature an unpaired (single) brain structure called the &lt;strong&gt;pineal gland&lt;/strong&gt;, or &lt;em&gt;parietal eye&lt;/em&gt;. It is primarily a photoreceptor organ, and its electrical activity changes in response to environmental lighting (Fig. 1). The pineal does not mediate vision, and it is mainly involved in regulation of circadian rhythms &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7219554&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Deguchi, 1981)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, many &lt;strong&gt;lower vertebrates can be considered to have 3 eyes&lt;/strong&gt;. In fact, the blind cavefish &lt;em&gt;Astyanax mexicanus&lt;/em&gt; undergoes bilateral eye degeneration during embryonic development. Despite the absence of light in the cave environment, cavefish have retained a structurally intact pineal eye. Hence, cavefish can be said to have a single eye (&lt;a href=&quot;http://jeb.biologists.org/content/211/3/292.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yoshizawa &amp;amp; Jeffery, 2008&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vTVw7.jpg&quot; alt=&quot;Third eye&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Reptilian parietal eye. Source: &lt;a href=&quot;https://universe-review.ca/&quot; rel=&quot;nofollow noreferrer&quot;&gt;review of the Universe&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The mammalian pineal gland is a secretory organ only, and no longer responds to direct illumination. In mammals it is situated deep in the brain and the mammalian skull does not admit light into the brain. Instead, the mammalian pineal needs input from the eyes to regulate the circadian rhythm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/7219554&quot; rel=&quot;nofollow noreferrer&quot;&gt;Deguchi, &lt;em&gt;Nature&lt;/em&gt; (1981); &lt;strong&gt;290&lt;/strong&gt;(5808):706-7&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://jeb.biologists.org/content/211/3/292.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yoshizawa &amp;amp; Jeffery, &lt;em&gt;J Exp Biol&lt;/em&gt;; &lt;strong&gt;211&lt;/strong&gt;:292-9&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-11T21:11:59.660" LastActivityDate="2015-07-11T21:11:59.660" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35982" PostTypeId="2" ParentId="35975" CreationDate="2015-07-11T16:07:36.600" Score="2" Body="&lt;p&gt;A flower (or a person) has two alleles for a gene because it inherits one set of chromosomes from one parent and another, comparable, set of chromosomes from the other parent.  Hence there are two copies of each gene, and so there are two alleles for each gene.&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2015-07-11T16:07:36.600" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35983" PostTypeId="2" ParentId="35975" CreationDate="2015-07-11T16:27:06.553" Score="1" Body="&lt;p&gt;Allele is a variant form of a gene. How many alleles there are depends on number of copies of the gene and number of variants. In theory you can have 5 identical copies or single copy and single allele (Y-linked genes come to mind).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Regulation is very complicated, I'll refer you to reading on recessiveness, dominance. Barr bodies also have to do with various expression profiles in same thing.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-07-11T16:27:06.553" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35985" PostTypeId="2" ParentId="35976" CreationDate="2015-07-11T19:25:03.867" Score="1" Body="&lt;p&gt;The idea to compare biologic cells and crystal is mostly related to a German physiologist &lt;a href=&quot;https://en.wikipedia.org/wiki/Theodor_Schwann&quot; rel=&quot;nofollow noreferrer&quot;&gt;Theodor Schwann&lt;/a&gt; (1810-1882):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/U72yr.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;His work &quot;Microscopic researches on the Conformity in Structure and Growth Between Animals and Plants, 1839 relates to this idea. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;He &lt;a href=&quot;http://scienceworld.wolfram.com/biography/Schwann.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;believed&lt;/a&gt; that new cells form principally outside pre-existing&#xA;  cells, and wanted to draw an &lt;strong&gt;analogy to crystal formation&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://bitesizebio.com/166/history-of-cell-biology/&quot; rel=&quot;nofollow noreferrer&quot;&gt;another source&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The cell is the unit of structure, physiology, and organization in&#xA;  living things. The cell retains a dual existence as a distinct entity&#xA;  and a building block in the construction of organisms. Cells form by&#xA;  free-cell formation, similar to the &lt;strong&gt;formation of crystals&lt;/strong&gt; (spontaneous&#xA;  generation).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;(other related scientists are Schleiden, Virchow, Muller).&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-11T19:25:03.867" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35986" PostTypeId="1" AcceptedAnswerId="35999" CreationDate="2015-07-11T19:46:10.033" Score="3" ViewCount="2683" Body="&lt;p&gt;I downloaded a PDB file of a dimer, but it only contains the monomer, and it says that the dimer can be obtained from C2 symmetry. For an example see here: &lt;a href=&quot;http://www.rcsb.org/pdb/explore/explore.do?structureId=2PJY&quot; rel=&quot;nofollow&quot;&gt;http://www.rcsb.org/pdb/explore/explore.do?structureId=2PJY&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can I generate the PDB for the full dimer?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am comfortable with PyMol, so an answer using PyMol is preferred.&lt;/p&gt;&#xA;" OwnerUserId="561" LastActivityDate="2018-11-15T16:40:53.260" Title="Generate full dimer from monomer with C2 symmetry?" Tags="&lt;protein-structure&gt;&lt;pymol&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35987" PostTypeId="2" ParentId="35903" CreationDate="2015-07-11T20:05:29.757" Score="5" Body="&lt;p&gt;It sounds like you have considered most of the obvious alternatives (and thank you for clarifying the question).  I suppose the first question in an alternatively spliced transcript with a retained intron is whether the open reading frame of the protein is maintained.  If there is a termination codon that now becomes in-frame due to the intron then the protein would ordinarily be truncated.  The mRNA could also get targeted for degradation due to the nonsense-mediated decay pathway (i.e., from introducing an early stop-codon).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the alternatively-spliced transcript lacks any significant ORFs, or if there is an ORF but no suitable translation initiation codon then you have entered the realm of non-coding RNAs, of which there are two loose categories, microRNAs (there are several classes) or long non-coding RNAs.  most miRNAs have recognizable sequence motifs, may be contained in mir-Base, and may be complementary (in part) to a regulatory target elsewhere in the genome. lncRNAs are less well-defined. Perhaps the best criteria are transcripts that are stable enough to be detected, but lack noticeable protein coding features.  I don't even think there is a consensus on the minimum length of a transcript to be considered an lncRNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What sort of databases have you searched? For example the ancient dbEST contains all kinds of short cDNA reads from all over the planet, dating back to 1992 (or so).  Evolutionary conservation of exons and splice-sites, or reading frames can all be used to support the hypothesis that a transcribed region has a biological function.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a really deep fishing expedition you can use tblastn, etc. to take a potential translated ORF and search all 6 conceptually translated reading frames of all the sequences in a database--it takes longer, and there can be many spurious matches that you have to search through, but if you are studying something that has never been annotated it might be worth considering.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RE: folding RNA (secondary structure) every sequence can be folded into some kind of structure (try it and see), but structurally conserved compact loops typically fall into one of a small class of selected families (like GNRY). Stems are easy to find, but if the single-stranded loop is huge, how likely is that structure to fold up in real time?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;RE: TFBS not clear to me at all what you mean by this. Transcription factors bind dsDNA not ssRNA. There are families of protein domains that bind RNA but not typically with such sequence-specificity.  So unless this alternatively spliced transcript is being transcribed from some type of alternative promoter, I am not sure where you would even be looking for TFBS.  It's true that some large introns can indeed contain regulatory regions for the gene as a whole (cf. immunoglobulin heavy chain enhancer is conveniently stored in an intron), but it is not clear to me if that would have an affect when transcribed into RNA.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I do like your idea that a retained intron could now contain a binding site for a regulatory miRNA, but if I understand the theory this would lead to the transcript being degraded--so it would be more difficult to detect.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="14946" LastEditDate="2015-07-11T20:19:22.367" LastActivityDate="2015-07-11T20:19:22.367" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="35988" PostTypeId="1" AcceptedAnswerId="35992" CreationDate="2015-07-11T21:39:28.423" Score="3" ViewCount="522" Body="&lt;p&gt;I can create a new Genbank record in Biopython with the following code:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;from Bio import SeqIO, SeqFeature&#xA;from Bio.SeqRecord import SeqRecord&#xA;from Bio.Seq import Seq&#xA;from Bio.Alphabet import generic_dna&#xA;from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA&#xA;&#xA;my_sequence = &quot;ATAGGGACUCATAGATA&quot;&#xA;my_record = SeqRecord(Seq(my_sequence, IUPACAmbiguousDNA()))&#xA;my_feature_location = SeqFeature.FeatureLocation(2,5, strand=1)&#xA;my_feature = SeqFeature.SeqFeature(my_feature_location, type=&quot;CDS&quot;, id=&quot;Cre&quot;)&#xA;my_feature.qualifiers[&quot;foo&quot;] = &quot;bar&quot;&#xA;my_record.features.append(my_feature)&#xA;&#xA;print my_record.format(&quot;gb&quot;)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;The corresponding genbank file then looks like:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;LOCUS       .                         17 bp    DNA              UNK 01-JAN-1980&#xA;DEFINITION  .&#xA;ACCESSION   &amp;lt;unknown id&amp;gt;&#xA;VERSION     &amp;lt;unknown id&amp;gt;&#xA;KEYWORDS    .&#xA;SOURCE      .&#xA;  ORGANISM  .&#xA;            .&#xA;FEATURES             Location/Qualifiers&#xA;     CDS             3..5&#xA;                     /foo=&quot;bar&quot;&#xA;ORIGIN&#xA;        1 atagggacuc atagata&#xA;//&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;How can I change this bit &lt;code&gt;UNK 01-JAN-1980&lt;/code&gt;?&lt;/p&gt;&#xA;" OwnerUserId="4795" LastActivityDate="2015-08-24T09:06:10.503" Title="Change Genbank entry date with Biopython" Tags="&lt;sequence-analysis&gt;&lt;biopython&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35990" PostTypeId="1" CreationDate="2015-07-11T22:14:02.987" Score="5" ViewCount="1067" Body="&lt;p&gt;Since deaf people can't hear, is relaxing and falling asleep easier for them? In general, do they sleep better than hearing people?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course some hearing people have no trouble getting to sleep, but others awaken whenever they hear a sound.&lt;/p&gt;&#xA;" OwnerUserId="10463" LastActivityDate="2015-07-15T17:12:53.233" Title="Do deaf people sleep better?" Tags="&lt;sleep&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="35992" PostTypeId="2" ParentId="35988" CreationDate="2015-07-12T00:25:46.043" Score="5" Body="&lt;p&gt;So, the problem is that you are probably using wrong class for your record. Compare &lt;a href=&quot;http://biopython.org/DIST/docs/api/Bio.SeqRecord.SeqRecord-class.html&quot; rel=&quot;nofollow&quot;&gt;Bio.SeqRecord class&lt;/a&gt; with &lt;a href=&quot;http://biopython.org/DIST/docs/api/Bio.GenBank.Record.Record-class.html&quot; rel=&quot;nofollow&quot;&gt;Bio.GenBank.Record class&lt;/a&gt;. Reason why in your GenBank format you have this reference date (01-JAN-1980) is because your record has intrinsically no date attribute, so &lt;code&gt;SeqRecord.format&lt;/code&gt; set undefined fields to default (look through the source code to see where this happens).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What you want to do for creating GenBank record is following:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;$ python&#xA;Python 2.7.10 |Anaconda 2.3.0 (x86_64)| (default, May 28 2015, 17:04:42) &#xA;[GCC 4.2.1 (Apple Inc. build 5577)] on darwin&#xA;Type &quot;help&quot;, &quot;copyright&quot;, &quot;credits&quot; or &quot;license&quot; for more information.&#xA;Anaconda is brought to you by Continuum Analytics.&#xA;&amp;gt;&amp;gt;&amp;gt; from Bio import GenBank&#xA;&amp;gt;&amp;gt;&amp;gt; from Bio.GenBank import Record&#xA;&amp;gt;&amp;gt;&amp;gt; my_rec = Record.Record()&#xA;&amp;gt;&amp;gt;&amp;gt; my_rec&#xA;&amp;lt;Bio.GenBank.Record.Record object at 0x1030b1890&amp;gt;&#xA;&amp;gt;&amp;gt;&amp;gt; my_rec.sequence = Seq(my_sequence)&#xA;&amp;gt;&amp;gt;&amp;gt; my_rec.sequence&#xA;Seq('ATAGGGACUCATAGATA', Alphabet())&#xA;&amp;gt;&amp;gt;&amp;gt; print(my_rec)&#xA;LOCUS                         bp                                         &#xA;DEFINITION  .&#xA;KEYWORDS    .&#xA;SOURCE      .&#xA;  ORGANISM  .&#xA;            .&#xA;ORIGIN      &#xA;        1 atagggacuc atagata&#xA;//&#xA;&amp;gt;&amp;gt;&amp;gt; my_rec.date = '13-JUL-2015'&#xA;&amp;gt;&amp;gt;&amp;gt; my_rec.features.append(my_feature)&#xA;&amp;gt;&amp;gt;&amp;gt; my_rec.data_file_division = &quot;ROD&quot;&#xA;&amp;gt;&amp;gt;&amp;gt; print(my_rec)&#xA;LOCUS                         bp                    ROD       13-JUL-2015&#xA;DEFINITION  .&#xA;KEYWORDS    .&#xA;SOURCE      .&#xA;  ORGANISM  .&#xA;            .&#xA;FEATURES             Location/Qualifiers&#xA;type: CDS&#xA;location: [2:5](+)&#xA;id: Cre&#xA;qualifiers:&#xA;    Key: foo, Value: bar&#xA;ORIGIN      &#xA;        1 atagggacuc atagata&#xA;//&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Notice, how &lt;code&gt;print(my_seq)&lt;/code&gt; outputs data in GenBank format by default (since that is a GenBank record after all). I am sorry I cannot really talk on differences between &lt;code&gt;GenBank.Record&lt;/code&gt; and &lt;code&gt;Bio.SeqRecord&lt;/code&gt; and why/when use one object or another.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Anyways, looking up reference documentation is always a good habit: &lt;a href=&quot;http://biopython.org/DIST/docs/api/Bio.GenBank.Record.Record-class.html&quot; rel=&quot;nofollow&quot;&gt;http://biopython.org/DIST/docs/api/Bio.GenBank.Record.Record-class.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-07-13T13:28:46.537" LastActivityDate="2015-07-13T13:28:46.537" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="35994" PostTypeId="2" ParentId="35531" CreationDate="2015-07-12T03:37:43.267" Score="2" Body="&lt;p&gt;I've had a difficult time getting anything definitive to support my answer to your &lt;strong&gt;&lt;em&gt;specific&lt;/em&gt;&lt;/strong&gt; question of safety, however, I thought I'd go out on a limb and give you my understanding. A recent review of what is known about this can be found at: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2809506/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2809506/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think you are on the right track with your 'dose-dependence' hypothesis. This is exactly what the makers of RhoGAM suggest, saying that the amount of antibody administered at 28 weeks into the pregnancy is sufficient to block any Rh antigen on Red Blood Cells that escape into the mother's blood, but insufficient to cross the placenta and be a problem. At this time the child will be large enough that any RhoGAM that does cross the placenta will not kill enough Red Blood Cells to harm the child.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Mom gets another dose of antibody after the delivery in order to ensure thorough coverage of antigen that results from mixing of blood at that time, however this dose is not a problem as the baby has already left the mother.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;By the way, the rationale for the antenatal dose is that post-partum administration alone failed to prevent sero-conversion in almost 2% of Rh- women, putatively due to transplacental hemorrhaging. &lt;/p&gt;&#xA;" OwnerUserId="4139" LastActivityDate="2015-07-12T03:37:43.267" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="35995" PostTypeId="1" AcceptedAnswerId="36013" CreationDate="2015-07-12T04:43:51.780" Score="3" ViewCount="674" Body="&lt;p&gt;Cell lines are &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23723166&quot; rel=&quot;nofollow&quot;&gt;often immortalised&lt;/a&gt; by artificial expression of proteins which specifically cause the knockout of important cancer suppression genes or the activation of proto-oncogenes. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cellular immortality happens upon impairment of cell-cycle checkpoint&#xA;  pathways (p53/p16/pRb), reactivation or up-regulation of telomerase&#xA;  enzyme, or upregulation of some oncogenes or oncoproteins leading to a&#xA;  higher rate of cell division.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, this would appear to fall under the purview of &lt;a href=&quot;https://en.wikipedia.org/wiki/Biosafety_level#Biosafety_level_3&quot; rel=&quot;nofollow&quot;&gt;Biosafety Level 3&lt;/a&gt; since the protein expression vectors are capable of causing cancer in the researcher when they infect the researcher. Cancer can certainly be considered a serious or lethal disease, and aerosolisation of the vectors, while rare, is not impossible (for example during a spill). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the &lt;a href=&quot;http://ehs.columbia.edu/Policy2.2.html#two.3&quot; rel=&quot;nofollow&quot;&gt;biosafety definitions of Columbia University&lt;/a&gt;, &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Agents: serious or lethal diseases transmissible via aerosols, e.g.,&#xA;  M. tuberculosis, SARS.  Recombinant DNA activities using genetic&#xA;  material from BSL-3 organisms or such organisms as host cells.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why then, does the CDC &lt;a href=&quot;http://www.cdc.gov/biosafety/publications/bmbl5/BMBL5_appendixH.pdf&quot; rel=&quot;nofollow&quot;&gt;classify cell line work, including work with viral production cells, as a BSL-2 activity&lt;/a&gt; requiring only BSL-2 containment levels, when the act of immortalising the cells would involve working with viral agents that can cause cancer?&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Cells immortalized with  viral agents such as SV-40, EBV adenovirus or&#xA;  HPV, as  well as cells carrying viral genomic material also present&#xA;  potential hazards to  laboratory workers. Tumorigenic human cells also&#xA;  are potential hazards as a  result of self-inoculation.[...]&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Human and other primate cells should be handled using  BSL-2 &#xA;  practices and containment. All work should be performed in a BSC,  and&#xA;  all  material decontaminated by autoclaving or  disinfection before&#xA;  discarding. BSL-2  recommendations for personnel protective equipment&#xA;  such as  laboratory  coats, gloves  and eye protection should be&#xA;  rigorously followed.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Are the transformation cells (eg the 293T viral cells containing the transformant viruses) considered Level 3 biosafety risk, and if not, why not? &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-07-12T13:05:45.853" LastActivityDate="2015-07-12T16:26:42.067" Title="Cell line immortalisation biosafety" Tags="&lt;cell-culture&gt;&lt;safety&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35996" PostTypeId="1" AcceptedAnswerId="35998" CreationDate="2015-07-12T05:43:03.887" Score="1" ViewCount="439" Body="&lt;p&gt;The KEGG module &lt;a href=&quot;http://www.genome.jp/kegg-bin/show_module?M00115&quot; rel=&quot;nofollow&quot;&gt;M00115&lt;/a&gt; includes a set of reactions while &lt;a href=&quot;http://www.genome.jp/kegg-bin/show_module?M00542&quot; rel=&quot;nofollow&quot;&gt;M00542&lt;/a&gt; does not have any; it just shows the list of enzymes. Is the reaction set for M00542 still unknown?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="9099" LastEditDate="2015-07-12T11:03:52.837" LastActivityDate="2015-07-12T11:03:52.837" Title="Difference between modules in KEGG Module" Tags="&lt;database&gt;&lt;pathogenesis&gt;&lt;data&gt;&lt;host-pathogen-interaction&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35997" PostTypeId="2" ParentId="35996" CreationDate="2015-07-12T05:51:39.773" Score="3" Body="&lt;p&gt;M00115 is a pathway module (NAD biosynthesis) whereas M00542 is a signature module (EHEC/EPEC pathogenicity signature).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the &lt;a href=&quot;http://www.genome.jp/kegg/module.html&quot; rel=&quot;nofollow&quot;&gt;KEGG page on modules&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;&lt;p&gt;&lt;strong&gt;pathway modules&lt;/strong&gt; – representing tight functional units in KEGG&#xA;  metabolic pathway maps, such as M00002 (Glycolysis, core module&#xA;  involving three-carbon compounds)&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;li&gt;&lt;p&gt;&lt;strong&gt;signature modules&lt;/strong&gt; – as markers of phenotypes, such as M00363 (EHEC&#xA;  pathogenicity signature, Shiga toxin)&lt;/p&gt;&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-07-12T05:51:39.773" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="35998" PostTypeId="2" ParentId="35996" CreationDate="2015-07-12T08:07:21.977" Score="2" Body="&lt;p&gt;&lt;em&gt;Module&lt;/em&gt; means, as defined in the &lt;a href=&quot;http://www.genome.jp/kegg/module.html&quot; rel=&quot;nofollow&quot;&gt;KEGG Module page&lt;/a&gt;, a functional unit. So it can be anything, from groups of enzymes to genes to metabolites. About the two that concerns you:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Pathway modules&lt;/strong&gt; represent groups of functionally related enzymes part of the metabolic network. I think this one is easy to understand because it represents the classical understanding of &quot;module&quot;. The modules involve metabolites (compounds with id starting with &quot;C&quot;), enzymes (represented by KEGG ortholog ids starting with &quot;K&quot;) and reactions (represented by ids starting with &quot;R&quot;). The reactions integrate compounds and enzymes in a particular step in the chain of reactions included in that module.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Signature modules&lt;/strong&gt; represent molecules associated with a particular phenotype. In particular, the example listed in the KEGG page points to EHEC pathogenicity signature, Shiga toxin. The two molecules in module &lt;a href=&quot;http://www.genome.jp/kegg-bin/show_module?M00363&quot; rel=&quot;nofollow&quot;&gt;M00363&lt;/a&gt; are associated with the phenotype, which is in this case &lt;em&gt;EHEC pathogenicity&lt;/em&gt;. But in principle they do not necessarily need to be related to each other (in this case they are, but not in the same meaning as the metabolic module).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;In your particular examples, &lt;a href=&quot;http://www.genome.jp/kegg-bin/show_module?M00115&quot; rel=&quot;nofollow&quot;&gt;M00115&lt;/a&gt; is again a pathway module including enzymes, compounds and reactions, all connected in an integrated manner. Module &lt;a href=&quot;http://www.genome.jp/kegg-bin/show_module?M00542&quot; rel=&quot;nofollow&quot;&gt;M00542&lt;/a&gt; on the other hand shows the proteins part of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Type_three_secretion_system&quot; rel=&quot;nofollow&quot;&gt;T3SS&lt;/a&gt; (Type three secretion system) used by Gram-negative bacteria for infection. These are not enzymatic reactions, just proteins associated with the EHEC/EPEC pathogenicity phenotype. They are however related in that they form a protein interaction complex that mediates infection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other &lt;em&gt;Module&lt;/em&gt; categories include:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;strong&gt;Structure complexes&lt;/strong&gt; related to molecular machineries.&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Functional sets&lt;/strong&gt; seems like a miscellaneous category.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;You could argue that the T3SS is a molecular machine and should be classified in the &lt;em&gt;Structural complexes&lt;/em&gt; category. Indeed, something important to remember is, as stated in the KEGG module's page:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;KEGG MODULE is a collection of manually defined functional units [...]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As anything manually defined, there is some degree of arbitrariness. Use the information in KEGG modules as far as it serves your needs, but it would be better not take it as written in stone.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastActivityDate="2015-07-12T08:07:21.977" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="35999" PostTypeId="2" ParentId="35986" CreationDate="2015-07-12T08:55:16.337" Score="5" Body="&lt;p&gt;This article will probably be informative for you:&#xA;&lt;a href=&quot;http://www.rcsb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Looking at Structures: Introduction to Biological Assemblies and the PDB Archive&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The PDB file contains the asymmetric unit found in a particular crystallographic study. The biological assembly is the quaternary structure known or predicted to be found in living systems. For many proteins (but not 2PJY), the biological assembly can be downloaded directly from RCSB. For other proteins, the PDB file may contain the transformation matrix used to create the biological assembly from the asymmetric unit. &lt;a href=&quot;http://www.rcsb.org/pdb/files/2PJY.pdb&quot; rel=&quot;nofollow noreferrer&quot;&gt;If you look at the file in a text editor&lt;/a&gt;, this information is found under remark 350: &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;REMARK 350 BIOMOLECULE: 1                                                       &#xA;REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC                         &#xA;REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC                  &#xA;REMARK 350 SOFTWARE USED: PISA                                                  &#xA;REMARK 350 TOTAL BURIED SURFACE AREA: 8880 ANGSTROM**2                          &#xA;REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C                               &#xA;REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            &#xA;REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            &#xA;REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            &#xA;REMARK 350   BIOMT1   2  1.000000  0.000000  0.000000        0.00000            &#xA;REMARK 350   BIOMT2   2  0.000000 -1.000000  0.000000        0.00000            &#xA;REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000        0.00000    &#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Note that the actual biological assembly of 2PJY is a hexamer and the asymmetric unit in the PDB file is a trimer. You can see that the first matrix is identity (ie keeps the original asymmetric unit). The second matrix transforms the assymmetric unit to create the full hexamer. This matrix is both author and &lt;a href=&quot;http://www.ebi.ac.uk/pdbe/pisa/&quot; rel=&quot;nofollow noreferrer&quot;&gt;PISA&lt;/a&gt; predicted. You can actually go to the PISA website and have it predict the biological assembly of a particular PDB file, and it will spit out the coordinates of the hexamer (and other predicted assemblies) which you can then load into PyMOL.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;PDB files may also contain a &lt;a href=&quot;http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#CRYST1&quot; rel=&quot;nofollow noreferrer&quot;&gt;CRYST1 record&lt;/a&gt;, which gives information about the unit cell and space group of the crystal. Via the &lt;a href=&quot;http://www.pymolwiki.org/index.php/Symexp&quot; rel=&quot;nofollow noreferrer&quot;&gt;symexp&lt;/a&gt; command, PyMOL can use this information to recreate neighboring asymmetric units. By limiting the cut-off distance (and this requires trial-and-error), the biological assembly can be recreated. This script, for example, will generate the hexamer:&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;fetch 2PJY&#xA;symexp 2PJY, 2PJY, 2PJY, 2.5&#xA;hide everything&#xA;show cartoon&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0QfG8.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2018-02-11T18:05:07.470" LastActivityDate="2018-02-11T18:05:07.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36001" PostTypeId="1" AcceptedAnswerId="36018" CreationDate="2015-07-12T10:01:20.197" Score="1" ViewCount="2509" Body="&lt;p&gt;In my school biology book, it is written that cuticle covers the epidermal cells in aerial parts of plants and root epidermis doesn't have cuticle. My question is that whether aerial roots, in plants like kalanchoe, also not have cuticle? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do all kinds of roots not have cuticle?&lt;/p&gt;&#xA;" OwnerUserId="16723" LastEditorUserId="3340" LastEditDate="2015-07-12T10:08:14.330" LastActivityDate="2019-03-02T06:06:31.440" Title="Can roots have cuticle, especially aerial roots?" Tags="&lt;botany&gt;&lt;plant-physiology&gt;&lt;plant-anatomy&gt;&lt;plant-perception&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36002" PostTypeId="1" AcceptedAnswerId="36005" CreationDate="2015-07-12T10:47:18.200" Score="1" ViewCount="30" Body="&lt;p&gt;While browsing through the home page of &lt;a href=&quot;http://www.genome.jp/kegg/module.html&quot; rel=&quot;nofollow&quot;&gt;KEGG Module&lt;/a&gt;, I clicked the button named &lt;a href=&quot;http://www.genome.jp/kegg/docs/module_statistics.html&quot; rel=&quot;nofollow&quot;&gt;Module statistics&lt;/a&gt;.&#xA;Can someone tell me what does these numbers signify? What are they the statistics of?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="3340" LastEditDate="2015-07-12T11:26:22.353" LastActivityDate="2015-07-12T11:27:49.420" Title="What information does the KEGG Module statistics page show?" Tags="&lt;human-biology&gt;&lt;molecular-biology&gt;&lt;database&gt;&lt;data&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36004" PostTypeId="2" ParentId="35939" CreationDate="2015-07-12T11:10:15.720" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Human females do not benefit much from an extra cone class, as color discrimination is hardly affected in most tetrachromats. In fact, tetrachromats often show increased error rates in their color discrimination. In dichromatic New World monkeys the heterozygous females do functionally benefit from their extra cone as they gain trichromatic vision.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;&lt;a href=&quot;http://www.colourblindawareness.org/colour-blindness/types-of-colour-blindness/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Anomalous trichromats&lt;/a&gt;&lt;/strong&gt; have all of their three cone types to perceive colors, but one type of cone perceives light slightly out of alignment. There are three different types of effect produced depending upon which cone type is affected.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The different anomalous conditions are &lt;em&gt;protanomaly&lt;/em&gt; (reduced sensitivity to red light), &lt;em&gt;deuteranomaly&lt;/em&gt; (reduced green sensitivity - the most common type) and &lt;em&gt;tritanomaly&lt;/em&gt; (reduced blue sensitivity - extremely rare). People with deuteranomaly and protanomaly are collectively known as &lt;strong&gt;red-green colour blind&lt;/strong&gt; and they generally have difficulty distinguishing between reds, greens, browns and oranges. They also commonly confuse different types of blue and purple hues. Red and green cones are indeed coded on the &lt;strong&gt;X-chromosome&lt;/strong&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One source of variation is the very common Ser180Ala polymorphism that accounts for two spectrally different red pigments and that plays an important role in variation in normal color vision as well as defective color vision. The most common source of variation is the existence of several types of red/green pigment chimeras. The red and green-pigment genes are arranged in an array on the X-chromosome with one red-pigment gene followed by one or more green-pigment genes. Recombination events have given rise to red/green hybrid genes and deletion of the green-pigment genes. Only the first two genes in the tandem are expressed. The severity of red-green color vision defects is inversely proportional to the difference between the wavelengths of maximal absorption of the photopigments encoded by these two genes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Females who are heterozygous for red and green pigment genes that encode three&#xA;spectrally distinct photopigments have the potential for &lt;strong&gt;enhanced color vision&lt;/strong&gt;, as they are effectively tetrachromats (&lt;a href=&quot;http://www.mbfys.ru.nl/staff/j.vangisbergen/endnote/endnotepdfs/colleges/NEUROBIOFYSICA/HC%20colleges/plaatjes%20en%20files/vision/kleurenzien/DEEB_hybride-genen-kleur.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Deeb, 2005&lt;/a&gt;, &lt;a href=&quot;http://www.sciencemag.org/content/252/5008/971.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Neitz &lt;em&gt;et al&lt;/em&gt;., 1991&lt;/a&gt;). However, sensitive color-contrast testing on 43 tetrachromats has revealed that most of these females have no deviating color-discrimination whatsoever. 8 subjects showed relatively small effects, while only one showed a clear increased sensitivity in a narrow range of frequencies. It is believed that the &lt;strong&gt;human visual system is not plastic enough to cope with the extra spectral input&lt;/strong&gt;. In fact, in the group there was an overall increase in error rates on some color tests (pseudoisochromatic plates, and Nagel anomaloscope color matching) &lt;a href=&quot;http://www.imbs.uci.edu/~kjameson/JordanMollon1993.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Jordan &amp;amp; Mollon, 1993)&lt;/a&gt;.       &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In New World Monkeys, however, the situation is different. &lt;strong&gt;Squirrel monkeys are basically a dichromatic species&lt;/strong&gt;, but two-thirds of the females are heterozygous, and &lt;strong&gt;gain trichromatic vision&lt;/strong&gt; by expressing two of three possible alleles coding for pigments in the middle- to long-wave range of the spectrum. X-chromosome inactivation serves to segregate the alternative allelic products in different subsets of cones. The &lt;strong&gt;visual system&lt;/strong&gt; of the heterozygous female is apparently &lt;strong&gt;plastic enough to take advantage of the presence of three classes of cone&lt;/strong&gt;, because heterozygous monkeys have enhanced &lt;strong&gt;color selectivity in the red-green range&lt;/strong&gt; that are impossible for all males and for homozygous females. This advantage perhaps enables the heterozygote to judge better the ripeness of fruit, or to find fruit or conspecifics &lt;a href=&quot;http://www.imbs.uci.edu/~kjameson/JordanMollon1993.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Jordan &amp;amp; Mollon, 1993)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that the emergence of trichromacy in humans and some other primates was the result of the red/green gene duplication. Trichromacy in primates was evolutionary selected for likely because of the enhanced capability to discern (ripe) fruits &lt;a href=&quot;http://www.mbfys.ru.nl/staff/j.vangisbergen/endnote/endnotepdfs/colleges/NEUROBIOFYSICA/HC%20colleges/plaatjes%20en%20files/vision/kleurenzien/DEEB_hybride-genen-kleur.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Lucas &lt;em&gt;et al&lt;/em&gt;., 2003)&lt;/a&gt;. It has nothing to do with sex-differences, because not many human females benefit from tetrachromacy in terms of enhanced color vision. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.mbfys.ru.nl/staff/j.vangisbergen/endnote/endnotepdfs/colleges/NEUROBIOFYSICA/HC%20colleges/plaatjes%20en%20files/vision/kleurenzien/DEEB_hybride-genen-kleur.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Deeb, &lt;em&gt;Clin Genet&lt;/em&gt; (2005); &lt;strong&gt;67&lt;/strong&gt;: 369–377&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.imbs.uci.edu/~kjameson/JordanMollon1993.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Jordan &amp;amp; Mollon, &lt;em&gt;Vis Res&lt;/em&gt; (1993); &lt;strong&gt;33&lt;/strong&gt;(11): 1495-1508&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.mbfys.ru.nl/staff/j.vangisbergen/endnote/endnotepdfs/colleges/NEUROBIOFYSICA/HC%20colleges/plaatjes%20en%20files/vision/kleurenzien/DEEB_hybride-genen-kleur.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lucas &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Evolution&lt;/em&gt; (2003); &lt;strong&gt;57&lt;/strong&gt;(11): 2636–43&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.sciencemag.org/content/252/5008/971.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Neitz &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Science&lt;/em&gt; (1991); &lt;strong&gt;252&lt;/strong&gt;(5008): 971-4&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Further reading&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;https://biology.stackexchange.com/questions/24481/is-our-color-vision-calibrated-to-sky-vegetation-and-blood/24544#24544&quot;&gt;Is our color vision calibrated to sky, vegetation, and blood?&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.013" LastActivityDate="2015-07-12T12:26:57.700" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36005" PostTypeId="2" ParentId="36002" CreationDate="2015-07-12T11:21:01.413" Score="1" Body="&lt;p&gt;My understanding is that these statistics show the coverage for each KEGG Module in the particular phylogenetic group. For example, M00001, is found in 275 of the eukaryotic organisms in KEGG (which represents 90.5% of the eukaryotes in KEGG). The same logic applies for other groups.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An quick example demonstrating this hypothesis, done with the Protists group found in &lt;a href=&quot;http://www.kegg.jp/kegg/catalog/org_list.html&quot; rel=&quot;nofollow&quot;&gt;KEGG Organisms&lt;/a&gt; (since it is easier to count by eye). There are 43 protists, and in the statistics it says (as of 2015/7/9) that module M00001 is found in 33 of them, hence: $33/43=0.7674419$ which agrees with the 76.7% shown.&lt;/p&gt;&#xA;" OwnerUserId="9099" LastEditorUserId="9099" LastEditDate="2015-07-12T11:27:49.420" LastActivityDate="2015-07-12T11:27:49.420" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36006" PostTypeId="2" ParentId="35995" CreationDate="2015-07-12T13:03:23.323" Score="2" Body="&lt;p&gt;Maybe, cells should be contained under BSL-2 and agents (viral particles etc) under stricter BSL-3? That is, after immortalization you can keep cells under lower security.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;em&gt;Biosafety Level 2&lt;/em&gt; builds upon BSL-1. BSL-2 is suitable for work involving agents that pose &lt;strong&gt;moderate hazards&lt;/strong&gt; to personnel and the environment.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;em&gt;Biosafety Level 3&lt;/em&gt; is applicable to clinical, diagnostic, teaching, research, or production facilities where work is performed with indigenous or exotic agents&#xA;  that may cause serious or potentially lethal disease &lt;strong&gt;through the inhalation route of exposure&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;http://www.cdc.gov/biosafety/publications/bmbl5/BMBL5_sect_IV.pdf&quot; rel=&quot;nofollow&quot;&gt;CDC Biosafety in Microbiological and Biomedical Laboratories, Laboratory Biosafety Level Criteria&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;As of HEK 293 cells, check this out:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Biosafety level 2 practices and containment facilities for all activities involving HEK-293 cell lines. &lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;a href=&quot;http://www.bio-safety.wsu.edu/biosafety/Documents/.../HEK_Cell_Line.docx&quot; rel=&quot;nofollow&quot;&gt;HEK 293 Cell Line Risk Assessment - IBC&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-07-12T13:20:59.973" LastActivityDate="2015-07-12T13:20:59.973" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36007" PostTypeId="1" AcceptedAnswerId="36014" CreationDate="2015-07-12T15:33:07.727" Score="21" ViewCount="1949" Body="&lt;p&gt;Could we use viruses that only affect bacteria to act as antibiotics?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The more bacteria, the more times the virus divides, so the stronger it gets. Is this practical?&lt;/p&gt;&#xA;" OwnerUserId="16638" LastActivityDate="2015-07-16T20:21:46.673" Title="Could viruses be used as antibiotics?" Tags="&lt;virus&gt;&lt;antibiotics&gt;&lt;eukaryotic-cells&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36013" PostTypeId="2" ParentId="35995" CreationDate="2015-07-12T16:26:42.067" Score="2" Body="&lt;p&gt;Work with vectors expressing oncogenes or knocking down tumor suppressor genes (particularly if vectors are based on lentivirus) is often done under &quot;BSL-2+&quot; conditions. This essentially means that personal protective measures required for BSL-3 are used, but the specialized ventilation systems and so forth of BSL-3 physical laboratory space are not required. That would seem to address the investigator-safety issues raised in this question. See the complete &lt;a href=&quot;http://ehs.columbia.edu/BiosafetyLevelsAndRiskAssessmentPolicy.pdf&quot; rel=&quot;nofollow&quot;&gt;Columbia policy&lt;/a&gt; as an example of the details and the risk-assessment process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As noted already, once cultured cells have been infected with these vectors the risks to personnel are substantially diminished if not eliminated, so less stringent protections are then required.&lt;/p&gt;&#xA;" OwnerUserId="16326" LastActivityDate="2015-07-12T16:26:42.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36014" PostTypeId="2" ParentId="36007" CreationDate="2015-07-12T17:06:01.830" Score="21" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;Could we use viruses that only affect bacteria to act as antibiotics?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Yes. The specific class you're referring to is called a &quot;bacteriophage&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There's quite a bit of research going on surrounding phage therapy as a stand-in or replacement for traditional antibiotics. Here's a &lt;a href=&quot;http://www.nature.com/nbt/journal/v22/n1/full/nbt0104-31.html&quot;&gt;Nature Biotechnology article from 2004&lt;/a&gt; that discusses your very topic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is practical, carries some risks (mutations being a known and accepted risk), and I wouldn't be surprised to see phages in practice now or sometime soon.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2015-07-12T17:06:01.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36017" PostTypeId="1" CreationDate="2015-07-12T18:33:02.403" Score="1" ViewCount="687" Body="&lt;p&gt;I've recently been performing shRNA transfections and was hoping to get some advice on why I'm not seeing any knockdown via western blot&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I transfected by MDAMB468 breast cancer cell lines with shRNA against PTEN from the pLKO.1 lentiviral vector. I selected for the transfected cells using 1ug/ml  puromycin for approximately 6 days. During this time there was very few cell death amongst the cells compared to my control plate (untransfected cells with 1ug/ml puromycin), suggesting that the transfection was successful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After the 6 days I harvested my cells for protein and RNA extraction. I performed a western yesterday to assess knockdown, but noticed that there was hardly any differences (if any!) compared to my shGFP control. I haven't done a qpcr yet but I plan to this week.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering if anyone has experienced something similar, especially when working with PTEN? could it be that the cells need to be selected for a longer period (i.e. more than a week) before assessing protein knockdown?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="16407" LastActivityDate="2015-07-12T21:34:08.700" Title="shRNA knockdown not showing with Western" Tags="&lt;molecular-biology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36018" PostTypeId="2" ParentId="36001" CreationDate="2015-07-12T19:17:23.023" Score="0" Body="&lt;p&gt;According to &lt;a href=&quot;http://www.jstor.org/stable/2474789&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;, &lt;em&gt;Selaginella&lt;/em&gt; aerial roots have a thick root cap that possesses a cuticle. Roots that have breached the soil do not have cuticles.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-07-12T19:17:23.023" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36019" PostTypeId="2" ParentId="35990" CreationDate="2015-07-12T19:43:35.427" Score="2" Body="&lt;p&gt;Let's firstly differentiate deafness - profoundly impaired ability to hear, and other states where the subjects can still hear at different degrees.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, differentiate the congenital deafness &amp;amp; infantile hearing loss and hearing loss in adults who previously had normal hearing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The subjects with congenital and very early infantile hearing loss would have better sleep characteristics (this state will affect psychological state in a lesser degree than one acquired in more mature &amp;amp; &quot;conscious&quot; state), while persons who have lost their normal hearing &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4158149/&quot; rel=&quot;nofollow&quot;&gt;would have&lt;/a&gt; abnormal sleep patterns at least in the period when they have just realized that they are going to lose their hearing. After this &quot;preliminary&quot; period, the sleep pattern should be dependent on the person's psychological status and other similar factors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many persons will mention that while using ear plugs they feel that their sleep is better comparing with &quot;un-plugged&quot; sleep. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;sources&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9658468&quot; rel=&quot;nofollow&quot;&gt;Characteristics of sleep in deafness&lt;/a&gt;. Rev Neurol. 1998 Jun;26(154).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Non-scientific &lt;a href=&quot;http://limpingchicken.com/2014/05/08/the-question-do-deaf-people-sleep-better-at-night-than-hearing-people/&quot; rel=&quot;nofollow&quot;&gt;source&lt;/a&gt;. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Please pay attention that scientific sources are scarce, thus take the answer as one of limited evidence. &lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-12T19:43:35.427" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36020" PostTypeId="2" ParentId="35594" CreationDate="2015-07-12T21:10:28.760" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer:&lt;/strong&gt; many species can drop a regrown tail again and again again, however a few can only drop it once, while some lizards cannot drop their tails at all. It all depends on the species.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background information:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to &lt;a href=&quot;http://ladywildlife.com/animals/howlizardslosetheirtails.html&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt; the tail will only be able to be shed above the site it originally broke off. Although according to &lt;a href=&quot;http://scienceline.ucsb.edu/getkey.php?key=1103&quot; rel=&quot;nofollow&quot;&gt;UCSB&lt;/a&gt; there are a few species of lizard that only have their tail grow back once.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Every site I've visited has said that the tail is nearly a completely different structure than the one it originally had. The original tail has &quot;score marks&quot; (fracture planes) which were studied by &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526639/&quot; rel=&quot;nofollow&quot;&gt;Sanggaard et al.&lt;/a&gt; (there are a few figures that you can see in their paper).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, according to &lt;a href=&quot;http://jcs.biologists.org/content/s2-65/257/63.full.pdf&quot; rel=&quot;nofollow&quot;&gt;W. N. F. Woodland, D.Sc. (Lond.)&lt;/a&gt;, there is no apparent limit to the amount of times a Gecko can drop its tail, &quot;save the longevity of the animal&quot;. His paper goes into great detail, and has a lot of information about autotomy (limb dropping) of the gecko. I highly recommend going through it if you're interested. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So tail re-dropping looks like it primarily depends on the lizard that you're studying.&lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="16041" LastEditDate="2015-07-13T07:52:34.543" LastActivityDate="2015-07-13T07:52:34.543" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="36021" PostTypeId="2" ParentId="36017" CreationDate="2015-07-12T21:34:08.700" Score="1" Body="&lt;p&gt;I assume that you transfected the plasmid directly not producing viruses. If you want stable transformants, you might want to subculture them and maintain a bit longer. It is because efficiency of integration of plasmids into genome could not be that high--less than 0.1% of population obtain stable resistance by integration into genome. After 6 days, cells were still healthy in your case. This means you might get good transfection efficiency and after several times of cell division, your plasmids were diluted and the effects might be low even if cells maintain resistance against puromycin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If transient expression (KD) works in your experiment, you might want to check expression level of your target at day 2 or 3. If you prefer stable cell lines, you can increase puromycin concentration, and if you agree, you pick up single colonies after cells not having plasmids in genome are dead. Among these colonies, some have more plasmid copies other have less. You can choose cells least expressing your targets as well as moderately expressing cells if you want. Because you might want to see expression level dependency.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For some cells, 5ug/ml puromycine is used according to this &lt;a href=&quot;https://www.lifetechnologies.com/us/en/home/life-science/cell-culture/transfection/selection/puromycin.html&quot; rel=&quot;nofollow&quot;&gt;link&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-07-12T21:34:08.700" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36024" PostTypeId="1" AcceptedAnswerId="36036" CreationDate="2015-07-12T22:39:22.953" Score="9" ViewCount="2234" Body="&lt;p&gt;If I understand correctly, calorie restriction may extend life expectancy slightly (not proven exactly how much for human). But according to the statistics, skinny healthy people have even shorter life expectancy than healthy, slightly obese people. Could you explain why this is not considered as contradictory?   &lt;/p&gt;&#xA;" OwnerUserId="4858" LastActivityDate="2015-11-03T10:52:14.887" Title="Why do skinny people live for shorter than the norm even though calorie restriction extends life expectancy?" Tags="&lt;lifespan&gt;" AnswerCount="1" CommentCount="7" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36026" PostTypeId="1" AcceptedAnswerId="36061" CreationDate="2015-07-12T23:46:56.113" Score="5" ViewCount="115" Body="&lt;p&gt;Can brain tissue from one species be implanted into the brain of another species? Because the brain is tolerant to the introduction of antigens (it is said to be &lt;a href=&quot;https://en.wikipedia.org/wiki/Immune_privilege&quot; rel=&quot;nofollow&quot;&gt;immuno-privileged&lt;/a&gt;), I was wondering whether neurons would be subject to graft rejection? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If neurons from another species survive in their new host, would they create functional connections?&lt;/p&gt;&#xA;" OwnerUserId="16730" LastEditorUserId="9943" LastEditDate="2015-07-14T00:39:26.433" LastActivityDate="2015-07-14T10:47:23.363" Title="Is transplantation of neurons between species possible?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;&lt;species&gt;&lt;transplantation&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36027" PostTypeId="2" ParentId="36007" CreationDate="2015-07-13T00:40:33.103" Score="14" Body="&lt;p&gt;Yes you could.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It used to be a big deal before antibiotics were discovered, and continued for a bit in the Soviet Union.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, due to the success of antibiotics, it fell out of grace. Due to the lower level of applied research in the Soviet Union (not research itself, although equipment might have been often outdated a bit and the Soviets did isolate themselves quite a bit, but a great deal of research originally discovered behind the Iron Curtain was actually commercialized in the US, such as contact lenses; many Soviet research projects are actually getting rediscovered, such as the great experiment about the domestication of foxes), it never became the thing, and after the fall of the SU, it was nearly forgotten.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, now it is becoming trendy again. There are several reasons:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;resistance against antibiotics have grown out of proportions&lt;/li&gt;&#xA;&lt;li&gt;it is quite trendy to use &quot;natural predators&quot; against pests&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Phage_therapy&quot;&gt;https://en.wikipedia.org/wiki/Phage_therapy&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="16539" LastEditorUserId="-1" LastEditDate="2015-07-13T14:54:41.777" LastActivityDate="2015-07-13T14:54:41.777" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36028" PostTypeId="1" CreationDate="2015-07-13T01:48:30.433" Score="1" ViewCount="146" Body="&lt;p&gt;Which method is it the most effective, but also the most reliable for elongating muscle and tendons for clinical trial; using modern growth factor technology or using modern stem cell technology?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Being able to stimulate muscle elongation is a key step towards improving the standard of living for people afflicted with severe Poliomyelitis or people with limb Malformations. There are already techniques to culture living bone implants in the lab from stem cells for human beings. I am looking for an analog for muscle tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please provide references with your answers.&lt;/p&gt;&#xA;" OwnerUserId="5479" LastEditorUserId="16651" LastEditDate="2015-07-18T15:44:09.900" LastActivityDate="2015-07-27T09:27:12.090" Title="Which of these methods is both effective and reliable in elongate muscle and tendon for use in humans: growth factors or stem cell technology" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;literature&gt;&lt;stem-cells&gt;&lt;growth&gt;" AnswerCount="0" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36029" PostTypeId="1" CreationDate="2015-07-13T03:16:45.807" Score="-1" ViewCount="8221" Body="&lt;p&gt;I watched this horrifying video on &lt;a href=&quot;https://www.youtube.com/watch?v=d54PyNN1EdU&quot; rel=&quot;nofollow&quot;&gt;Youtube&lt;/a&gt;. It shows movement beneath the skin of a banana and then a spider pushes it's way out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Suffice to say I'm too scared to eat bananas anymore!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would like to know what is the probability that an insect is hiding inside a banana that I buy at the market? Even if there was just one chance in a million that an insect is hiding inside I would stop eating bananas forever.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I postulate that an insect could lay it's eggs in a banana and then the offsprings would be born inside the banana. Or perhaps an insect tries to eat a small chunk of the banana, it cuts his way out inside the banana, it gets trapped inside, and then someone buys the banana. Both of these ideas are troublesome since I'm not sure if there is air to breathe inside the banana.&lt;/p&gt;&#xA;" OwnerUserId="9757" LastEditorUserId="3553" LastEditDate="2015-07-13T13:02:21.390" LastActivityDate="2017-02-07T10:22:07.247" Title="If I buy a banana at the market, is there any chance that an insect is hiding inside it?" Tags="&lt;entomology&gt;&lt;food&gt;&lt;fruit&gt;&lt;arachnology&gt;" AnswerCount="1" CommentCount="5" ClosedDate="2015-07-14T04:37:52.857" ContentLicense="CC BY-SA 3.0" />
  <row Id="36030" PostTypeId="1" AcceptedAnswerId="36032" CreationDate="2015-07-13T03:54:59.067" Score="2" ViewCount="39" Body="&lt;p&gt;Considering the following module: &lt;br&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.kegg.jp/kegg-bin/show_module?M00115+C00003&quot; rel=&quot;nofollow&quot;&gt;http://www.kegg.jp/kegg-bin/show_module?M00115+C00003&lt;/a&gt; &lt;br&gt;&lt;br&gt;&#xA;why is the compound C00003 marked in red?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="9099" LastEditDate="2015-07-13T05:55:35.880" LastActivityDate="2015-07-13T05:55:35.880" Title="Why is there a compound highlighted in red in a KEGG Module search?" Tags="&lt;human-biology&gt;&lt;biochemistry&gt;&lt;cell-biology&gt;&lt;database&gt;&lt;data&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36031" PostTypeId="1" AcceptedAnswerId="36033" CreationDate="2015-07-13T04:22:48.903" Score="0" ViewCount="47" Body="&lt;p&gt;From the &lt;a href=&quot;http://www.genome.jp/kegg/docs/module_statistics.html&quot; rel=&quot;nofollow&quot;&gt;statistics&lt;/a&gt; page, I found that the &lt;a href=&quot;http://www.genome.jp/kegg-bin/show_module?M00008&quot; rel=&quot;nofollow&quot;&gt;Module-M00008&lt;/a&gt; is present only in bacteria and not Eukaryotes. Why so? I noticed that all the compounds necessary or the reaction are present in human body and also all the enzymes required for the reactions are present in human body too. Then why does that reaction not happen in humans?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastActivityDate="2015-07-13T04:30:45.123" Title="Presence of reaction module in bacteria but not in Eukaryotas (human)" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;database&gt;&lt;data&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36032" PostTypeId="2" ParentId="36030" CreationDate="2015-07-13T04:26:40.997" Score="4" Body="&lt;p&gt;It is just a way of highlighting your search term. If you search &lt;a href=&quot;http://www.kegg.jp/kegg-bin/show_module?M00115+C03722&quot; rel=&quot;nofollow&quot;&gt;M00115+C03722&lt;/a&gt;, you will see C03722 in red.  &lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-07-13T04:26:40.997" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36033" PostTypeId="2" ParentId="36031" CreationDate="2015-07-13T04:30:45.123" Score="2" Body="&lt;p&gt;That module represents &lt;a href=&quot;https://en.wikipedia.org/wiki/Entner%E2%80%93Doudoroff_pathway&quot; rel=&quot;nofollow&quot;&gt;Entner-Duodoroff&lt;/a&gt; pathway, which is an alternative pathway to the Embden-Mayerhof-Parnas pathway of glycolysis. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Entner-Duordoff pathway exists only in prokaryotes.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-07-13T04:30:45.123" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="36034" PostTypeId="1" AcceptedAnswerId="36035" CreationDate="2015-07-13T04:33:17.680" Score="4" ViewCount="568" Body="&lt;p&gt;In microbiology we have two types of microbial diagnosis. The direct method is where we detect the invader's DNA, Antigens or culture to see the exact pathogen while the second, indirect, method is the reacting the antibodies of patient's serum with different reagents. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we use the indirect method (antibody reaction) and find that they are producing antibodies against a specific disease (let's say streptococcus A) what is the benefit of having found that they are fighting Strep A since the body is already clearly fighting it and putting up the best defence to fight the disease?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would a doctor really prescribe antibiotics even though here is already an immune reaction against the infection?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If diagnosis and treatment are useless then why do we waste the time to do it?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="16041" LastEditDate="2015-07-13T09:14:49.597" LastActivityDate="2015-08-17T13:57:05.360" Title="Why lab technicians use indirect (antibody reaction) method for diagnosing?" Tags="&lt;microbiology&gt;&lt;lab-techniques&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36035" PostTypeId="2" ParentId="36034" CreationDate="2015-07-13T08:47:03.567" Score="3" Body="&lt;p&gt;&lt;strong&gt;Short answer:&lt;/strong&gt; Antibiotic treatment is important because the body can't always keep up with the infection even if it has launched a response.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, let's look at what the antibody reaction method is actually doing.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Taking a sample of blood or body fluid&lt;/li&gt;&#xA;&lt;li&gt;Testing the sample with known pathogens - viruses, bacteria, fungi, etc.&lt;/li&gt;&#xA;&lt;li&gt;Identifying which infection causes a reaction.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This allows us to determine which infection we are dealing with. This can be especially useful when the infection is hidden in a place we are unable to easily swab - the stomach, heart, a small wound that has already healed. Sometimes this test is just used to monitor how well you are fighting the infection, but it also allows them to evaluate what the best course of treatment is for you. (&lt;a href=&quot;http://www.healthcommunities.com/infectious-diseases/antigen-antibody-tests.shtml&quot; rel=&quot;nofollow&quot;&gt;Reference 1&lt;/a&gt;) &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just because the body has an immune reaction doesn't mean that the body's immune system can actually finish the battle against a disease. In the example case of &lt;a href=&quot;http://www.nhs.uk/conditions/Streptococcal-infections/Pages/Introduction.aspx&quot; rel=&quot;nofollow&quot;&gt;Strep A&lt;/a&gt;, you may be able to get over the infection yourself but it will take longer than if you are prescribed antibiotics against it. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;See this question on the &lt;a href=&quot;http://www.cdc.gov/groupastrep/about/faqs.html&quot; rel=&quot;nofollow&quot;&gt;CDC&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Q: How common is invasive group A streptococcal disease?&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;A: Approximately 9,000-11,500 cases of invasive GAS (Group A Streptococcus) disease occur each&#xA;  year in the United States, resulting in 1,000-1,800 deaths annually.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Note that invasive Strep A usually infects children, elderly, and  immunocompromised people (anyone with a weaker immune system typically). &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Unless you have absolutely no immune system at all, there will be an antibody response put out by your body. &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000821.htm&quot; rel=&quot;nofollow&quot;&gt;The NHS&lt;/a&gt; goes into detail about different parts of your immune system. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Recall also that Strep A (our example) could divide faster than the body can keep up with. So we would need antibiotic help to fight the disease. Using the &quot;indirect&quot; method we can find a hidden infection. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;According to the &lt;a href=&quot;http://www.nhs.uk/conditions/Antibiotics-penicillins/Pages/Introduction.aspx&quot; rel=&quot;nofollow&quot;&gt;NHS&lt;/a&gt; the antibiotics put a stop to growth and spread which allows the body to come in and finally finish them all off, or they disrupt a process the bacteria needs to survive and kill the infection for the body. Thereby helping the immune system (the body's best line of defence) finish off the infection when it couldn't do it on its own.&lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="16041" LastEditDate="2015-07-13T12:44:50.893" LastActivityDate="2015-07-13T12:44:50.893" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36036" PostTypeId="2" ParentId="36024" CreationDate="2015-07-13T09:38:06.630" Score="9" Body="&lt;p&gt;This is an interesting point you raise, and as the study you linked to states, &quot;the link between physique and life expectancy is not clearly understood,&quot; which is certainly true at the moment. The relationship between BMI and lifespan in humans is a very different story to controlled dietary restriction in model organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dietary restriction is defined as &quot;undernutrition without malnutrition&quot; [1], and by definition model organisms live in controlled environments. In contrast, humans have confounding factors that may reduce weight &lt;em&gt;and&lt;/em&gt; health (for instance smoking status, early-life diseases, malnutrition, etc) that are not modelled in these experiments.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, the relationship between BMI and mortality is complicated in older humans, known as the 'obesity paradox'; overweight and obese elderly hospital patients have a lower mortality risk than low-normal weight patients [2]. There are a number of hypotheses regarding this, but the favoured one appears to be that the association is not actually paradoxial, but that higher BMI only &lt;em&gt;appears&lt;/em&gt; protective because losing weight is associated with many diseases of ageing, so after accounting for many of these confounding factors (e.g. dementia, cancer, etc) high BMI no longer appears protective.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore the study you found only appears to be contradictory to the dietary restriction experiments; in human populations the situation is much more complicated. Additionally, there is conflicting evidence as to whether dietary restriction even works in primates [3], let alone in humans (the largest effects are observed in worms and drosophila). &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Weindruch &lt;em&gt;et al&lt;/em&gt;. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3958810&quot;&gt;The retardation of aging in mice by dietary restriction: longevity, cancer, immunity and lifetime energy intake.&lt;/a&gt; (1986) &lt;em&gt;J Nutrition&lt;/em&gt;; &lt;strong&gt;116&lt;/strong&gt;(4):641-54&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Yamauchi &lt;em&gt;et al&lt;/em&gt;. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/25525351&quot;&gt;Paradoxical association between body mass index and in-hospital mortality in elderly patients with chronic obstructive pulmonary disease in Japan.&lt;/a&gt; (2014) &lt;em&gt;Int J Chron Obstruct Pulmon Dis&lt;/em&gt;; &lt;strong&gt;9&lt;/strong&gt;:1337-46&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Maxmen. &lt;a href=&quot;http://www.nature.com/news/calorie-restriction-falters-in-the-long-run-1.11297&quot;&gt;Calorie restriction falters in the long run.&lt;/a&gt; (2012) &lt;em&gt;Nature&lt;/em&gt;; &lt;strong&gt;488&lt;/strong&gt;, 569&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="740" LastActivityDate="2015-07-13T09:38:06.630" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36038" PostTypeId="2" ParentId="35505" CreationDate="2015-07-13T11:11:01.430" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Training increases white and gray matter densities in the brain. This may reflect increases in neuronal cell counts especially in the hippocampus. In the cortex, however, such observed changes are probably more reflective of other processes, such as synaptogenesis.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;&lt;a href=&quot;http://www.indiana.edu/~p1013447/dictionary/greywhit.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Gray matter&lt;/strong&gt;&lt;/a&gt; is generally viewed as being the neuronal cell bodies, while &lt;a href=&quot;http://www.indiana.edu/~p1013447/dictionary/greywhit.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;white matter&lt;/strong&gt;&lt;/a&gt; corresponds to myelinated fiber tracts. Changes in both can be reflective of changes in cellular content, but changes in gray matter are generally more directly related to changes in &lt;em&gt;cell numbers&lt;/em&gt;, which you are after.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A striking example of the effects of learning on the brain is observed in subjects that start to learn to &lt;strong&gt;juggle&lt;/strong&gt;. These people have been shown to have &lt;strong&gt;increased gray matter density&lt;/strong&gt; in the occipito-parietal regions (the visual motion areas). These changes are apparent after as little as 7 days of training. Such experience-dependent changes are &lt;strong&gt;also observed in white matter&lt;/strong&gt;. Occipito-parietal regions are involved in visuo-motor coordination, reaching and grasping. There have been a host of other studies that showed similar changes in the brain. For example, &lt;strong&gt;taxi drivers&lt;/strong&gt; were shown to have increased &lt;strong&gt;hippocampal volumes&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is good evidence for &lt;strong&gt;adult neurogenesis&lt;/strong&gt; occurring with learning in the &lt;strong&gt;hippocampus&lt;/strong&gt;. Adult neuro­genesis also produces thousands of new granule cells in the dentate gyrus every month, but this is a relatively small increase in total number of hippocampal neurons. Furthermore, although there have been reports of neurogenesis in the mammalian adult neocortex, this is controversial.&#xA;Thus, &lt;strong&gt;&lt;em&gt;neurogenesis is likely a minor factor in MRI changes&lt;/em&gt;&lt;/strong&gt;, particularly those found outside the hippocampus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead, other factors such as increase in glial cell numbers, synaptogenesis, changes in dendritic structures, axonal sprouting and re-routing and even vascular changes may underly the observed changes in imaging studies.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;Note: there is a host of imaging studies available on effects of learning on structural changes in the brain. The referenced review article cites many.&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.nature.com/neuro/journal/v15/n4/abs/nn.3045.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Zatorre &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Nature Neurosci&lt;/em&gt; (2012); &lt;strong&gt;15&lt;/strong&gt;: 528–36&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2017-04-11T14:53:40.893" LastActivityDate="2017-04-11T14:53:40.893" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36039" PostTypeId="1" AcceptedAnswerId="36042" CreationDate="2015-07-13T12:07:57.150" Score="5" ViewCount="2228" Body="&lt;p&gt;I've encountered the following question and am quite stumped by it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A female with genotype AABBCC has been hybridized with a male that has the genotype aabbcc. The first generation (F1) has been hybridized again (backcross) with offsprings that have the genotype aabbcc. Given the following genetic map, what would be the percentage of F2 offsprings that are heterozygous to all three genes:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A------- 20 MU ------- B -- 10 MU --- C&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;How should I approach the following question&lt;/strong&gt;, the brute force approach is too difficult, I keep getting things wrong.&lt;/p&gt;&#xA;" OwnerUserId="16736" LastEditorUserId="9943" LastEditDate="2015-07-13T12:41:43.727" LastActivityDate="2015-07-14T04:55:43.390" Title="How to calculate the percentage of heterozygous cells based on a gene map" Tags="&lt;genetics&gt;&lt;homework&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="36040" PostTypeId="2" ParentId="36029" CreationDate="2015-07-13T12:42:01.990" Score="7" Body="&lt;p&gt;&lt;a href=&quot;http://kaleblechowski.tumblr.com&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kaleb Lechowski&lt;/a&gt;, creator of that video, is a digital creator and animator of critters. I would propose that he did a very good job of rendering a CGI spider to burst from a banana. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Spiders (which are not insects remember) won't eat bananas. In fact, only one species is known to be mostly herbivorous: &lt;a href=&quot;https://en.wikipedia.org/wiki/Bagheera_kiplingi&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Bagheera kiplingi&lt;/em&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, don't eat that banana just yet! The internet is littered with tales of horror about spiders in fruit. Like this &lt;a href=&quot;http://www.telegraph.co.uk/news/earth/wildlife/11650715/Black-widow-spider-found-in-grapes-from-Asda-in-Leamington-Spa.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Black Widow&lt;/a&gt; in a bunch of grapes. There is no bursting out of the fruit like Alien, but what has happened is the spider has unwittingly found itself being picked from its natural environment and transported with the fruit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Fruit is good.&lt;/strong&gt; Stay sceptical of internet rumours that are trying to get clicks with fear, and stay measured enough to remember that the benefits of eating (washed, clean) fruit far outweigh the extraordinarily low chance of finding a nasty bug hiding away.&lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="3553" LastEditDate="2017-02-07T10:22:07.247" LastActivityDate="2017-02-07T10:22:07.247" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36041" PostTypeId="1" CreationDate="2015-07-13T13:16:48.850" Score="2" ViewCount="178" Body="&lt;p&gt;An article I read about Neuroblastoma states that the fact that Neuroblstoma has a small mutanome means that it is not viable to apply the classic T-cell immunotherapy. Why is this so?&#xA;The article can be found here: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386662/&quot; rel=&quot;nofollow&quot;&gt;Neuroblastoma: Developmental Biology, Cancer Genomics, and Immunotherapy&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8644" LastEditorUserId="5144" LastEditDate="2015-07-24T13:04:12.600" LastActivityDate="2015-07-24T21:01:46.703" Title="Why does T-cell Cancer Therapy require a large tumor mutanome?" Tags="&lt;immunology&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36042" PostTypeId="2" ParentId="36039" CreationDate="2015-07-13T14:40:58.783" Score="2" Body="&lt;p&gt;&lt;strong&gt;Units of genetic distance&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It took me a little while to understand what &lt;code&gt;MU&lt;/code&gt; means. I have never seen &lt;code&gt;MU&lt;/code&gt; but rather &lt;code&gt;m.u.&lt;/code&gt; for &lt;code&gt;map unit&lt;/code&gt;, or &lt;code&gt;cM&lt;/code&gt; for &lt;code&gt;centiMorgane&lt;/code&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Solving the problem&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This problem got me thinking a little bit. My logic is the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Probability of being heterozygous at the first locus&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You cross two individuals (we'll call them individual &lt;code&gt;1&lt;/code&gt; and &lt;code&gt;2&lt;/code&gt;)that are both heterozygote at each locus &lt;code&gt;A&lt;/code&gt;, &lt;code&gt;B&lt;/code&gt; and &lt;code&gt;C&lt;/code&gt; (not to be confused with the alleles &lt;code&gt;A&lt;/code&gt; and &lt;code&gt;a&lt;/code&gt;, &lt;code&gt;B&lt;/code&gt; and &lt;code&gt;b&lt;/code&gt; and &lt;code&gt;C&lt;/code&gt; and &lt;code&gt;c&lt;/code&gt;). We'll start with locus &lt;code&gt;A&lt;/code&gt;. The probability of being heterozygous at locus &lt;code&gt;A&lt;/code&gt; is the probability that individual &lt;code&gt;2&lt;/code&gt; gives another allele than individual &lt;code&gt;1&lt;/code&gt;. This occurs with probability 0.5. If the three loci were perfectly independent, then the probability of being heterozygous for a given offspring at all 3 loci would just be $0.5^3 = 0.125$... but that would be too easy so let's keep going with the second locus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Probability of being heterozygote at the two first loci&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So let's assume our offspring of interest, got two different alleles for the locus &lt;code&gt;A&lt;/code&gt;. The probability to receive two different alleles at the locus &lt;code&gt;B&lt;/code&gt; is the probability that either no individual recombine between &lt;code&gt;A&lt;/code&gt; and &lt;code&gt;B&lt;/code&gt; or both individuals recombine between &lt;code&gt;A&lt;/code&gt; and &lt;code&gt;B&lt;/code&gt;. It is therefore: $0.2^2 + 0.8^2$. Put together this probability with the probability that the first locus was heterozygote it gives $0.5 \cdot (0.2^2 + 0.8^2)$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Probability of being heterozygous for all 3 loci&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Finally, we can just keep going with he next locus. Let's assume that the offspring have received two different alleles for both loci &lt;code&gt;A&lt;/code&gt; and &lt;code&gt;B&lt;/code&gt;. The probability to receive different alleles at locus &lt;code&gt;C&lt;/code&gt; is the probability that either both parents recombine (between &lt;code&gt;B&lt;/code&gt; and &lt;code&gt;C&lt;/code&gt;) or none recombine. This occurs with probability $0.1^2 + 0.9^2$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Put the whole thing together, the probability of a given offspring to be heterozygote (or the frequency of heterozygotes offsprings if you prefer) is $0.5 \cdot (0.2^2 + 0.8^2) \cdot (0.1^2 + 0.9^2) = 0.2788$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that calculating the probability that exactly 2 loci are heterozygous would have been a bit trickier.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Good luck for your exam tomorrow!&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-07-14T04:55:43.390" LastActivityDate="2015-07-14T04:55:43.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36043" PostTypeId="2" ParentId="34830" CreationDate="2015-07-13T16:22:41.003" Score="0" Body="&lt;p&gt;I don't think that there is a one-size-fits-all answer to this question. There are different types of arrest and there might be different triggers depending on the epithelial cell type.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even in the cited &lt;a href=&quot;http://www.pnas.org/content/81/17/5435.full.pdf&quot; rel=&quot;nofollow&quot;&gt;Hammond et al paper&lt;/a&gt;, note that the effect of serum is not an immediate arrest. Human mammary epithelial cells (HMEC) could already go through 3 to 4 passages in serum (at 1:10 splits), according to the Introduction to the paper; the improvement with the serum-free medium was to allow 10-20 passages. And even in that paper, near the end of the Results you will see a difference between HMEC and human keratinocytes in terms of response to calcium; calcium makes keratinocytes differentiate and lose proliferative capacity, while HMEC do best at high calcium.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3349876/&quot; rel=&quot;nofollow&quot;&gt;Recent work&lt;/a&gt; has developed ways that can allow many types of epithelial cells (both normal and tumor cells) to proliferate indefinitely in culture, in the presence of 5% serum. Inhibition of the Rho-associated kinase ROCK is critical, as is the production of some yet-undefined factor by feeder fibroblasts. So even if some component of serum tends to lead to differentiation or senescence and growth arrest, that effect can be avoided.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note, however, that the authors of this newer work do call the cells treated this way &quot;reprogrammed,&quot; recognizing that they are not the same as the original epithelial cells in some important ways. What that &quot;reprogramming&quot; entails is under active investigation, and your concerns about selection, adaptation, and potential artifacts of culture are very important. But even if this is considered an artifact, understanding the mechanisms at work should produce some important advances in understanding epithelial biology.&lt;/p&gt;&#xA;" OwnerUserId="16326" LastActivityDate="2015-07-13T16:22:41.003" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36044" PostTypeId="1" CreationDate="2015-07-12T15:15:27.227" Score="8" ViewCount="1260" Body="&lt;p&gt;About two weeks ago I noticed a new wasp nest in my back yard. I generally leave them as long as they aren't interfering with anything, but this nest has suddenly grown quite large and they are swarming when I mow the lawn. From the nest appearance, I was afraid these were &lt;a href=&quot;https://en.wikipedia.org/wiki/Bald-faced_hornet&quot; rel=&quot;nofollow noreferrer&quot;&gt;bald-faced hornets&lt;/a&gt;, but up close they look more like &lt;a href=&quot;https://en.wikipedia.org/wiki/Yellow_jacket&quot; rel=&quot;nofollow noreferrer&quot;&gt;yellowjackets&lt;/a&gt;, I'm uncertain of the species. This is as close as I dared to get with the camera.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/NBnU1.jpg&quot; alt=&quot;wasp nest&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/P8omj.jpg&quot; alt=&quot;close up&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am willing to live and let live until October (when the nest is vacated), but I have two concerns that may change my mind:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;How large might this nest become?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;If I leave them this summer, are they likely to return to the same place next year?&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerDisplayName="user16391" LastEditorUserId="16866" LastEditDate="2017-03-31T22:12:52.070" LastActivityDate="2017-04-01T15:43:19.540" Title="How large might a paper wasp nest become?" Tags="&lt;zoology&gt;&lt;entomology&gt;&lt;wasps&gt;" AnswerCount="2" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36045" PostTypeId="2" ParentId="35943" CreationDate="2015-07-13T17:37:57.340" Score="2" Body="&lt;p&gt;Scratching is getting potentially poisonous or at least irritant substances out and removes lodged insects like ticks.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Removing subcutane parasites like scapies mites is not feasible without scratching yourself bloody.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't see how &quot;scratching them clearly doesn't help us survive&quot;.  Behaviors and skin reactions evolved way before our modern hygiene and parasite cures.&lt;/p&gt;&#xA;" OwnerUserId="16744" LastActivityDate="2015-07-13T17:37:57.340" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36048" PostTypeId="1" AcceptedAnswerId="36850" CreationDate="2015-07-13T19:34:18.833" Score="2" ViewCount="680" Body="&lt;p&gt;Say you have the flu and a normal immune system. Now you're all better but your antibody level is still elevated. How long does it take for those antibody levels to go back to a base value?&lt;/p&gt;&#xA;" OwnerUserId="16041" LastActivityDate="2015-08-14T19:05:37.640" Title="How long does it take unused antibodies to clear the system?" Tags="&lt;immunology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="36049" PostTypeId="2" ParentId="20610" CreationDate="2015-07-13T19:34:49.227" Score="2" Body="&lt;p&gt;The substances that bees consume do end up in honey. There was a high-profile case in Brooklyn in 2010 (&lt;a href=&quot;http://www.nytimes.com/2010/11/30/nyregion/30bigcity.html?_r=0&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;The Mystery of the Red Bees of Red Hook&lt;/em&gt;&lt;/a&gt;) where bees from several hives began producing red honey after feeding on dyed maraschino cherry juice from a local factory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A follow-up article from 2015 (&lt;a href=&quot;http://www.thedailybeast.com/articles/2015/03/03/how-bees-revealed-a-pot-farm-beneath-the-maraschino-cherries.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;How Bees Revealed a Pot Farm Beneath the Maraschino Cherries&lt;/em&gt;&lt;/a&gt;) claims that the substance they began producing was not honey but “red gunk”; however, that may have been editorial license.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JBQ9X.jpg&quot; alt=&quot;A “honeycomb” from Mr. Selig’s hives. Credit Ozier Muhammad/The New York Times&quot;&gt;&lt;/p&gt;&#xA;" OwnerDisplayName="user16391" LastActivityDate="2015-07-13T19:34:49.227" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36050" PostTypeId="1" AcceptedAnswerId="36054" CreationDate="2015-07-13T19:35:03.047" Score="4" ViewCount="315" Body="&lt;p&gt;To my understanding, large polypeptides such as botulinum toxin cannot pass the intestinal lining intact. How, then, can it enter the bloodstream and cause botulism poisoning?&lt;/p&gt;&#xA;" OwnerUserId="16748" LastActivityDate="2015-07-13T21:44:28.840" Title="How does botulinum toxin enter the blood stream from the digestive tract?" Tags="&lt;biochemistry&gt;&lt;microbiology&gt;&lt;pathology&gt;&lt;digestive-system&gt;&lt;poison&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36051" PostTypeId="1" AcceptedAnswerId="36052" CreationDate="2015-07-13T19:45:44.373" Score="17" ViewCount="1862" Body="&lt;p&gt;Bread gets mouldy pretty quickly. My parents (both of whom are nurses) throw out a loaf of bread after a spot of mould is seen (because &quot;if you can see one spot, it means the whole thing is covered in mould spores&quot;) because they say you'll get sick if you eat it. The USDA also has a handy chart on it's mould page telling you &lt;a href=&quot;http://www.fsis.usda.gov/wps/portal/fsis/topics/food-safety-education/get-answers/food-safety-fact-sheets/safe-food-handling/molds-on-food-are-they-dangerous_/!ut/p/a1/jZFfT4MwFMU_iw88lhaZy-YbITGCDrIQtevLUkb_EFlL2iLBT2-3Pblsutune-7vpL2nkEAMiaJfraCu1Yp2h57Mt2iN5tEyRXm5jJ5QVryvy5c0RYvqwQObP4AivtF_pRL0nz-_4YJ7s0pXApKeOglaxTXEgjlAlR2ZsRBzrRtgKWduApzuHLCSMecHBw0cp5KqpmuVgHivu8YCrU46NQw4ySbQUCWY0YPdwg9Ifj8KRf5kRVzNnvMiRuXsHLiQ2gm4HovfW3S6Pn7RJlF1vPALGsaZYSYcjJelc719DFCAxnEMhdaiY-FOh8NngC6ZpLYO4nMW9vs3_P2a8CoDpJ7Gux-wDK4F/#16&quot; rel=&quot;nofollow noreferrer&quot;&gt;when you should discard food with mould on it.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it the mould itself that makes us sick or is it something that the mould is releasing? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What are the mechanisms that cause us to feel sick after eating mouldy food?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.fsis.usda.gov/wps/portal/fsis/topics/food-safety-education/get-answers/food-safety-fact-sheets/safe-food-handling/molds-on-food-are-they-dangerous_/&quot; rel=&quot;nofollow noreferrer&quot;&gt;The USDA&lt;/a&gt; says that there can also be bacteria along with the mould on the the food - is this what is really making us feel ill? &lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="16866" LastEditDate="2017-04-03T17:22:16.823" LastActivityDate="2018-12-14T11:04:35.067" Title="Why does mouldy food make you sick?" Tags="&lt;human-biology&gt;&lt;microbiology&gt;&lt;food&gt;&lt;digestive-system&gt;&lt;mycology&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36052" PostTypeId="2" ParentId="36051" CreationDate="2015-07-13T20:10:51.857" Score="16" Body="&lt;p&gt;One of the most common toxins in mouldy food/bread is &lt;a href=&quot;https://en.wikipedia.org/wiki/Aflatoxin&quot; rel=&quot;nofollow&quot;&gt;aflatoxin&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The exposure to high amount of aflatoxin can lead to &lt;a href=&quot;http://www.fda.gov/Food/FoodborneIllnessContaminants/CausesOfIllnessBadBugBook/ucm071020.htm&quot; rel=&quot;nofollow&quot;&gt;acute aflatoxicosis&lt;/a&gt; with fulminant hepatic failure and even death.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While mild exposure to aflatoxin could be asymptomatic, it is better not to take a chance considering possible complications (citation from the link above): &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Aflatoxins produce acute necrosis, cirrhosis, and carcinoma of the&#xA;  liver in a number of animal species; no animal species is resistant to&#xA;  the acute toxic effects of aflatoxins; hence it is logical to assume&#xA;  that humans may be similarly affected. A wide variation in LD50 values&#xA;  has been obtained in animal species tested with single doses of&#xA;  aflatoxins. For most species, the LD50 value ranges from 0.5 to 10&#xA;  mg/kg body weight. Animal species respond differently in their&#xA;  susceptibility to the chronic and acute toxicity of aflatoxins. The&#xA;  toxicity can be influenced by environmental factors, exposure level,&#xA;  and duration of exposure, age, health, and nutritional status of diet.&#xA;  Aflatoxin B1 is a very potent carcinogen in many species, including&#xA;  nonhuman primates, birds, fish, and rodents. In each species, the&#xA;  liver is the primary target organ of acute injury. Metabolism plays a&#xA;  major role in determining the toxicity of aflatoxin B1; studies show&#xA;  that this aflatoxion requires metabolic activation to exert its&#xA;  carcinogenic effect, and these effects can be modified by induction or&#xA;  inhibition of the mixed function oxidase system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="9943" LastEditDate="2015-10-08T13:42:13.117" LastActivityDate="2015-10-08T13:42:13.117" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36054" PostTypeId="2" ParentId="36050" CreationDate="2015-07-13T20:36:50.783" Score="4" Body="&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Transcytosis&quot; rel=&quot;nofollow&quot;&gt;Transcytosis&lt;/a&gt; is a process by which large macromolecules are transported across a cell, such as those in the intestinal epithelium. It is used by many toxins and even whole organisms to enter the body. &lt;a href=&quot;http://www.hindawi.com/journals/bmri/2010/974943/&quot; rel=&quot;nofollow&quot;&gt;Botulinum toxin also apparently uses this mechanism.&lt;/a&gt; I'm not sure how detailed of an answer you want, but the linked to-review is pretty in-depth.&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-07-13T21:44:28.840" LastActivityDate="2015-07-13T21:44:28.840" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36055" PostTypeId="1" AcceptedAnswerId="36058" CreationDate="2015-07-13T20:40:46.980" Score="2" ViewCount="1007" Body="&lt;p&gt;Is it true that in an enzyme-catalyzed reaction, the rate of reaction does not vary with varying osmotic pressure?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead of just a true or false answer, why does it, or why does it not vary with osmotic pressure?&lt;/p&gt;&#xA;" OwnerUserId="16749" LastActivityDate="2015-07-14T02:19:11.857" Title="Osmotic Pressure and Enzyme Activity" Tags="&lt;osmosis&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36056" PostTypeId="1" CreationDate="2015-07-13T21:08:02.717" Score="1" ViewCount="167" Body="&lt;p&gt;I am doing research on inherited risk of Autism Spectrum Disorders(ASD) due to common Copy Number Variants(CNVs) One of the mutations is the 'CC' variant of Rs1858830 in the promoter region of the MET gene. (&lt;a href=&quot;http://www.snpedia.com/index.php/Rs1858830&quot; rel=&quot;nofollow&quot;&gt;http://www.snpedia.com/index.php/Rs1858830&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After digging a bit deeper I found that hepatocyte growth factor is a pretty ubiquitous compound in the body and it's necessary for growth/repair of many tissues, namely the liver and digestive tract. I am trying to separate the direct causal effect of the mutation itself from the effects it has on other tissue which may themselves have an effect on ASD risk.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question comes from a study which measured reduced serum HGF levels in autistic children with this mutation. (&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694825/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694825/&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am confused about the implied causal effect of the 'CC' variant on HGF levels even though it is merely the ligand for the MET gene? Please help me understand where in the gene signalling process does HGF come in, what does it do, what proteins are transcribed by the MET gene, and how this mutation effects the transcription of these proteins.&lt;/p&gt;&#xA;" OwnerUserId="16750" LastActivityDate="2015-08-13T00:35:33.660" Title="How does the MET gene work and what happens when the promoter region gets mutated?" Tags="&lt;genetics&gt;&lt;proteins&gt;&lt;transcription&gt;&lt;snp&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36057" PostTypeId="2" ParentId="36056" CreationDate="2015-07-13T22:00:12.610" Score="1" Body="&lt;p&gt;HGF is the ligand for Met, which is a membrane receptor involved in multiple transduction pathways. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/gene?Db=gene&amp;amp;Cmd=ShowDetailView&amp;amp;TermToSearch=4233&amp;amp;ordinalpos=1&amp;amp;itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum&quot; rel=&quot;nofollow&quot;&gt;Gene ID 4233&lt;/a&gt; we're looking at a single gene product for MET. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we're just reading through the wikipedia page for c-Met, when HGF binds to Met, it activates the tyrosine kinase activity of Met. Met recruits Gab1, and this complex mediates interactions with Ras, P13K, ß-catenin.. not just pathways associated w/ Autism, but also associated with invasive growth cancers. An interesting note about the C allele, it's associated with decreased Met transcription. Quoting a recent article,&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The present morphological and functional studies have revealed a highly novel mechanism conferred by MET receptor signaling, which we show serves a pleiotrophic role in controlling both neuronal and spine morphology, and the time course of glutamatergic synapse maturation on CA1 hippocampal neurons. Such findings are consistent with the possibility that mistimed maturation of glutamatergic synapses underlie aberrant function of neural circuits that are enriched in MET during development.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jneurosci.org/content/34/49/16166.full&quot; rel=&quot;nofollow&quot;&gt;Source&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the critical results from the same study showed that when Met got knocked down or deleted, we saw maturation of neural tissue. So now, if i'm thinking about Met and HGF, your article notes that HGF is decreased in autism brains. If we (1) need HGF for Met function, and (2) ASD may be attributed to decreased Met function, and (3) the C allele decreases Met levels, we're basically looking at a system that's modulating for ASD.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-07-13T22:00:12.610" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="36058" PostTypeId="2" ParentId="36055" CreationDate="2015-07-13T23:07:54.560" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/92/8/3444.full.pdf&quot;&gt;This paper&lt;/a&gt; is a compelling example of an effect of osmotic pressure on enzyme function. Restriction enzymes are normally very selective in the base sequences of sites at which they cut DNA, but in some conditions they show cutting at off-target sites, called &quot;star activity.&quot; &quot;Star activity&quot; increased for some restriction enzymes almost linearly with osmotic pressure generated by a range of non-ionic solutes. Supporting the idea that the higher osmotic pressure was directly responsible, increased hydrostatic pressure reversed the effect of increased osmotic pressure.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Increasing the osmotic pressure is essentially decreasing the &lt;a href=&quot;https://en.wikipedia.org/wiki/Thermodynamic_activity&quot;&gt;chemical activity&lt;/a&gt; of the water in the system. So it's not surprising that any enzyme reaction might be affected, particularly if the structures of active sites of enzymes are altered as suggested by the authors of the paper cited above.&lt;/p&gt;&#xA;" OwnerUserId="16326" LastActivityDate="2015-07-13T23:07:54.560" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36059" PostTypeId="1" CreationDate="2015-07-13T23:08:25.520" Score="0" ViewCount="1314" Body="&lt;p&gt;A popular &quot;well-known fact&quot; is that all creatures on Earth consist mostly of water (i.e. H2O). Indeed, a liquid called &quot;normal saline solution&quot; is just a solution of 0.9% sodium chloride in distilled water. It is generally considered the &quot;safe&quot; liquid to be injected into human body in relatively high volumes without any bad effects.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that the same 0.9% solution &lt;a href=&quot;http://www.peteducation.com/article.cfm?c=26+1303&amp;amp;aid=3223&quot; rel=&quot;nofollow&quot;&gt;is also used in vet practice&lt;/a&gt; for at least cats and dogs. As far as I understand, that's because blood circulation structure and basic blood regeneration specs are more or less the same for cats and dogs as for humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But what about other animals? My wild guess is that same 0.9% solution would be ok for all mammals (probably because their blood tract is similar), but what about others? Birds? Fish? Vertebrae? Invertebrae? Animals? Plants?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If 0.9% solution is not universal, what are the other possible variants? (i.e. could you provide examples of other compositions for some other species?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If 0.9% is indeed universal, I'd be glad to hear any pointers on why does it happen (i.e. is it related to evolution of life in Earth history, is it related to chemical composition of bodies, related to some specific cells, etc).&lt;/p&gt;&#xA;" OwnerUserId="16751" LastActivityDate="2015-07-13T23:08:25.520" Title="Saline solution for animals" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;hematology&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36060" PostTypeId="1" CreationDate="2015-07-14T00:24:28.483" Score="10" ViewCount="5112" Body="&lt;p&gt;I've found a website (Pearson's BioCoach) that claims centrioles duplicate in Prophase II. Is this accurate? Does it depend on the species in question?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at three textbook illustrations of meiosis, none of their illustrations are consistent. All depict the movement and number of centrioles through Telophase I the same way: centrioles replicate in S of Interphase, then do their thing through Meiosis I. We end up at Telophase I with 2 centrosomes, each with 2 centrioles. There is one centrosome at either pole of the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;After that, the diagrams are unclear:  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One text (general biology) seems to indicate either centrioles or entire centrosomes replicate after Telophase I, because Prophase II is shows both cells with 2 centrosomes, each with 2 centrioles.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another (basic genetics) illustrates 2 daughter cells of Meiosis I inherit one centrosome each following Telophase I. In Prophase I, the centrioles in this centrosome splits, with one centriole going to either pole. Cytokinesis after Meiosis II results in 4 daughter cells, each with one centriole.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A third (more thorough genetics) stops depicting centrioles after Telophase I, instead showing the spindles growing in an aster formation from an empty space, the space where there were 2 centrioles up until Telophase I. &lt;/p&gt;&#xA;" OwnerUserId="16754" LastActivityDate="2020-06-09T16:07:06.933" Title="How is centriole number maintained during meiosis?" Tags="&lt;cell-biology&gt;&lt;reproduction&gt;&lt;meiosis&gt;&lt;cytoskeleton&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36061" PostTypeId="2" ParentId="36026" CreationDate="2015-07-14T00:31:12.607" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Neural xenografts can survive and form functional connections in the host.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Across-species (&lt;a href=&quot;http://medical-dictionary.thefreedictionary.com/xenogeneic+graft&quot; rel=&quot;nofollow&quot;&gt;xenogeneic grafting&lt;/a&gt;) grafting of cerebral cortex from a fetal rat to an adult mouse brain and &lt;em&gt;vice versa&lt;/em&gt;, have shown that &lt;a href=&quot;https://en.wikipedia.org/wiki/Immunocompetence&quot; rel=&quot;nofollow&quot;&gt;immunocompetent&lt;/a&gt; hosts can reject a graft in less than 30 days. Rejection results in destruction of  the graft tissue presumably by &lt;a href=&quot;http://www.nature.com/nri/focus/macrophages/index.html&quot; rel=&quot;nofollow&quot;&gt;macrophages&lt;/a&gt;. &lt;a href=&quot;http://www.medicinenet.com/script/main/art.asp?articlekey=3942&quot; rel=&quot;nofollow&quot;&gt;Immunosuppression&lt;/a&gt; can be used to prevent graft rejection &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3796814&quot; rel=&quot;nofollow&quot;&gt;(Mason &lt;em&gt;et al&lt;/em&gt;., 1986)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A review article on this topic shows that in the absence of immunosuppression, neural &lt;a href=&quot;https://en.wikipedia.org/wiki/Xenotransplantation&quot; rel=&quot;nofollow&quot;&gt;xenografts&lt;/a&gt; (donors were fetal to adult-aged) in a rat host brain survive in 37% of the cases in case of a mouse donor, 16% in case of a hamster donor, 9% in case of a rabbit rabbit, 7% from a pig donor, and 0% when human donor tissue was used. Hence, &lt;strong&gt;species-separation&lt;/strong&gt; seems to be a determining factor in xenograft rejection. Induction of &lt;strong&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK27156/&quot; rel=&quot;nofollow&quot;&gt;MHC-I and MHC-II expression&lt;/a&gt;&lt;/strong&gt; in the xenograft mediates graft rejection in the brain. Hence, despite the fact that the brain is immunopriviliged because of the relative low expression levels of MHC class proteins, it is still sufficient to reject grafts &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0306452294903387&quot; rel=&quot;nofollow&quot;&gt;(Pakzaban &amp;amp; Isacson, 1994)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Xenografts have been shown to generate functional afferent and efferent axonal connections with the host brain&lt;/strong&gt; when grafts of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Striatum&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;striatum&lt;/em&gt;&lt;/a&gt;, &lt;a href=&quot;https://en.wikipedia.org/wiki/Substantia_nigra&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;substantia nigra&lt;/em&gt;&lt;/a&gt;, &lt;a href=&quot;http://psycheducation.org/brain-tours/memory-learning-and-emotion-the-hippocampus/&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;hippocampus&lt;/em&gt;&lt;/a&gt; and &lt;a href=&quot;http://webvision.med.utah.edu/&quot; rel=&quot;nofollow&quot;&gt;retina&lt;/a&gt; were &lt;a href=&quot;https://en.wikipedia.org/wiki/Homotopy&quot; rel=&quot;nofollow&quot;&gt;homotopically&lt;/a&gt; transplanted. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Functional (behavioral) studies have confirmed these physiological studies&lt;/strong&gt;. Rats with &lt;a href=&quot;http://www.parkinsons.org.au/what-is-parkinsons&quot; rel=&quot;nofollow&quot;&gt;Parkinson's disease&lt;/a&gt; could be successfully treated with &lt;em&gt;substantia nigra&lt;/em&gt; grafting from mouse, hamster, rabbit, pig and even humans. Similarly, retinal xenografts have resulted in functional pupil responses, &lt;em&gt;hippocampal&lt;/em&gt; xenografts have restored learning deficits, and &lt;a href=&quot;http://healthysleep.med.harvard.edu/image/200&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;suprachiasmatic nucleus&lt;/em&gt;&lt;/a&gt; xenografts have been shown to restore &lt;a href=&quot;http://www.nigms.nih.gov/Education/Pages/Factsheet_CircadianRhythms.aspx&quot; rel=&quot;nofollow&quot;&gt;circadian rhythms&lt;/a&gt; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0306452294903387&quot; rel=&quot;nofollow&quot;&gt;(Pakzaban &amp;amp; Isacson, 1994)&lt;/a&gt;.     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3796814&quot; rel=&quot;nofollow&quot;&gt;Mason &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Neurosci&lt;/em&gt; (1986); &lt;strong&gt;19&lt;/strong&gt;(3): 685-94&lt;/a&gt;.&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0306452294903387&quot; rel=&quot;nofollow&quot;&gt;Pakzaban &amp;amp; Isacson, &lt;em&gt;Neurosci&lt;/em&gt; (1994); &lt;strong&gt;62&lt;/strong&gt;(4): 989-1001&lt;/a&gt;.   &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-14T10:47:23.363" LastActivityDate="2015-07-14T10:47:23.363" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36062" PostTypeId="1" AcceptedAnswerId="36064" CreationDate="2015-07-14T01:02:46.623" Score="1" ViewCount="127" Body="&lt;p&gt;I notice many wikipedia articles, courses, pathway sites use a different abbreviation for the same enzyme. Eg: Wikipedia lists the abbreviation of phosphoglycerate mutase as PGM, whilst wikipaths lists it as PGAM in the glycolysis pathway. Then there's enzymes like glyceraldehyde 3 phosphate abbreviated either as GAPDH or G3PDH. This has led to many confusions, particularly when the enzyme abbreviation is completely different to the gene abbreviation, eg: protein kinase A (PKA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the official names of genes, I'm using genenames.org. I thought it might be common practice to abbreviate an enzyme with its gene abbreviation, but I see this is problematic due to many enzymes being encoded by multiple subunits and genes from different locations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a site, or a way, to unambiguously know the correct, and most widely recognized, official name/abbreviation for an enzyme, like there is for genes?&lt;/p&gt;&#xA;" OwnerUserId="15295" LastActivityDate="2015-07-14T01:48:59.513" Title="Correct enzyme nomenclature" Tags="&lt;nomenclature&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36063" PostTypeId="2" ParentId="35740" CreationDate="2015-07-14T01:42:32.247" Score="1" Body="&lt;p&gt;Looking at this 2001 review paper by Rieseberg: &lt;a href=&quot;http://evolution.powernet.ru/library/Scienc9.pdf&quot; rel=&quot;nofollow&quot;&gt;http://evolution.powernet.ru/library/Scienc9.pdf&lt;/a&gt; (especially Box 2), drift and inbreeding are suggested ways that chromosomal rearrangements can become fixed. These forces are strongest small, isolated populations, such as populations experiencing the founder effect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another model discussed in that paper is the suggestion that some centric fusions (Robertsonian translocations) lead to little or no loss of fertility in the heterozygotes.&lt;/p&gt;&#xA;" OwnerUserId="16754" LastActivityDate="2015-07-14T01:42:32.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36064" PostTypeId="2" ParentId="36062" CreationDate="2015-07-14T01:48:59.513" Score="2" Body="&lt;p&gt;No, not that I have ever seen. Classically, the Enzyme Commission (E.C.) identifiers are the only way to be certain that two (or more) abbreviations or acronyms are all referring to the same enzyme activity. Sometimes, when the situation becomes very complicated interested parties will co-author a proposed new naming convention within their subfield. Some journals may require specific abbreviations, but otherwise authors are free to use whatever nomenclature they like.&lt;/p&gt;&#xA;" OwnerUserId="16667" LastActivityDate="2015-07-14T01:48:59.513" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36066" PostTypeId="2" ParentId="36055" CreationDate="2015-07-14T02:19:11.857" Score="1" Body="&lt;p&gt;In order to achieve initiation of DNA replication &lt;em&gt;in vitro&lt;/em&gt; at the &lt;em&gt;E. coli&lt;/em&gt; chromosomal origin of replication, Arthur Kornberg's lab had to include polyethylene glycol (PEG) in their reactions. &#xA;The proposed mechanism for this enhancement was termed &quot;molecular crowding&quot; which was thought to increase the local concentration of the substrates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A similar effect has been seen in reactions with T4 DNA ligase. Blunt-ended ligations are more efficient in buffers containing PEG.&lt;/p&gt;&#xA;" OwnerUserId="16667" LastActivityDate="2015-07-14T02:19:11.857" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36067" PostTypeId="2" ParentId="3696" CreationDate="2015-07-14T03:42:53.430" Score="0" Body="&lt;p&gt;Mixing of alcohol and energy drinks can be detrimental to ones health as both alcohol and the caffeine in energy drinks are both stimulants which can cause adverse effects on the heart especially if one has a natural sensitivity to caffeine.  One also has to be careful as both caffeine and alcohol are diuretics which when combined can cause even greater risk of dehydration.  And some studies suggest that taurine, which while naturally occurring (and even quite necessary in the developmental stages of humans) may cause adverse affects on kidneys and combine that with two diuretics all tied together...it could cause serious potential for health risks.  At least in some individuals. [ 1 ] [ 2 ]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I conducted a non-scientific experiment one night when friends were discussing the merits of 'alcohol before liquor' and vice versa where I decided to mix a pint of beer and three shots of Bacardi 151 in stein and consumed it as I would a straight beer.  Personally I felt no ill effects but I also had a hell of a tolerance for alcohol.  I agree that mixing alcohols can 'confuse' someone regarding just how much alcohol they have consumed and should be watched carefully.  Although vigilance is often not one of the virtues displayed by people who consume such drinks.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Kristen Kirkpatrick M.S., R.D., L.D. - &lt;a href=&quot;http://www.doctoroz.com/blog/kristin-kirkpatrick-ms-rd-ld/energy-drinks-demystified&quot; rel=&quot;nofollow&quot;&gt;http://www.doctoroz.com/blog/kristin-kirkpatrick-ms-rd-ld/energy-drinks-demystified&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Time Magazine Online - &lt;a href=&quot;http://time.com/3677044/alcohol-energy-drinks/&quot; rel=&quot;nofollow&quot;&gt;http://time.com/3677044/alcohol-energy-drinks/&lt;/a&gt;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="16756" LastEditorUserId="16756" LastEditDate="2015-07-14T16:37:18.507" LastActivityDate="2015-07-14T16:37:18.507" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36068" PostTypeId="1" CreationDate="2015-07-14T07:19:18.933" Score="3" ViewCount="909" Body="&lt;p&gt;Generally domesticated animals do not need to worry about their food and other predators, and they have a lower probability of getting sick. &lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it seems there is no sharp difference between the life expectancy of wild pigs and domesticated pigs. Both can survive more than ten years if they are not killed.&lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is it normal for domesticated animals to have a longer life span?&lt;/strong&gt; Is it necessarily so? &lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Is there an example of a wild animal that statistically lives longer than its domesticated counterpart?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5688" LastEditorUserId="16866" LastEditDate="2017-02-14T16:57:37.023" LastActivityDate="2017-02-14T16:57:37.023" Title="Do domesticated animals necessarily live longer than wild animals? counterexample wanted!" Tags="&lt;zoology&gt;&lt;senescence&gt;" AnswerCount="0" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="36070" PostTypeId="1" CreationDate="2015-07-14T13:42:03.007" Score="1" ViewCount="41" Body="&lt;p&gt;I had an idea of making electric current from bacteria. There are some bacteria that can photosynthesize, and some others are capable of transmitting electrons through each other. Is it possible that through genetic engineering, we could insert the genome that allows bacteria to perform photosynthesis, with other capable of transmitting electricity, and therefor making a bacterial culture, big enough to make a free energy source? &lt;/p&gt;&#xA;" OwnerUserId="16759" LastEditorUserId="9943" LastEditDate="2015-07-14T14:04:00.857" LastActivityDate="2015-08-14T19:26:22.910" Title="Is it possible to merge the genomes of photosynthesizing and electron-transporting bacteria to make an electric cell?" Tags="&lt;genetics&gt;&lt;bacteriology&gt;&lt;energy&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36071" PostTypeId="2" ParentId="9026" CreationDate="2015-07-14T14:02:00.170" Score="1" Body="&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://www.columbia.edu/cu/psychology/courses/1010/mangels/neuro/neurocells/neurocells.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dendrites&lt;/a&gt;&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Means &lt;strong&gt;&lt;em&gt;Trees&lt;/em&gt;&lt;/strong&gt; in Greek;&lt;/li&gt;&#xA;&lt;li&gt;Are the &lt;strong&gt;input&lt;/strong&gt; of the neuron; &lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Receive information&lt;/strong&gt; from other neurons or the external environment;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Transfer information&lt;/strong&gt; to the cell body and axons;&lt;/li&gt;&#xA;&lt;li&gt;Are &lt;strong&gt;numerous&lt;/strong&gt;, relatively &lt;strong&gt;short&lt;/strong&gt;, and &lt;strong&gt;branch&lt;/strong&gt; extensively in a tree-like fashion&lt;/li&gt;&#xA;&lt;li&gt;May have numerous &lt;strong&gt;spines&lt;/strong&gt; on them to provide a greater surface area for other neurons to synapse on;&lt;/li&gt;&#xA;&lt;li&gt;&lt;strong&gt;Receive information&lt;/strong&gt; from other cells at these synapses. This makes dendrites &lt;strong&gt;postsynaptic&lt;/strong&gt;.&lt;/li&gt;&#xA;&lt;li&gt;The connection between axons that synapse on dendrites is called &lt;strong&gt;axodendritic&lt;/strong&gt;;&lt;/li&gt;&#xA;&lt;li&gt;The connection between dendrites that synapse on other dendrites is called &lt;strong&gt;dendrodendritic&lt;/strong&gt;.&#xA;&lt;br&gt;&lt;br&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://www.columbia.edu/cu/psychology/courses/1010/mangels/neuro/neurocells/neurocells.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Axon&lt;/a&gt;&lt;/strong&gt; &#xA; - Means &lt;strong&gt;&lt;em&gt;axis&lt;/em&gt;&lt;/strong&gt; in Greek&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The &lt;strong&gt;output&lt;/strong&gt; of the neuron;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Transfers information&lt;/strong&gt; to other neurons;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Begins at the &lt;strong&gt;axon hillock&lt;/strong&gt;, which is a swelling at the junction of the axon and soma where there are many Na&lt;sup&gt;+&lt;/sup&gt; channels and the action potential starts;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Is relatively &lt;strong&gt;long&lt;/strong&gt; (some reaching several feet);&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Has terminal &lt;strong&gt;boutons&lt;/strong&gt; at the end where the synapse is located. This makes axons &lt;strong&gt;presynaptic&lt;/strong&gt;. These swellings at the terminal bouton is where the neuron synapses with another neuron;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Contains numerous &lt;strong&gt;vesicles&lt;/strong&gt; which hold &lt;strong&gt;neurotransmitter&lt;/strong&gt;;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Has many &lt;strong&gt;Ca&lt;sup&gt;2+&lt;/sup&gt; channels&lt;/strong&gt; in the membrane;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The space between the terminal boutons and the next cell is known as the &lt;strong&gt;synaptic cleft&lt;/strong&gt;, and is approximately 20 nm thick;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Most are &lt;strong&gt;myelinated&lt;/strong&gt;, i.e., have myelin sheaths that are made by Schwann cells or oligodendrocytes. Myelin acts as insulator to help conduction of action potential. There are openings between the Schwann cells called &lt;strong&gt;Nodes of Ranvier&lt;/strong&gt;. These help with the conduction of action potentials.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Synapse&lt;/strong&gt; on other cells in various forms;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Axoaxonal&lt;/strong&gt;: Axon is connected to another neuron’s axon;&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Axodendritic&lt;/strong&gt;: Axon is connected to another neuron’s dendrites&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;strong&gt;Axosomatic&lt;/strong&gt;: Axon is connected directly to another neuron’s soma&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;In &lt;strong&gt;neuromuscular junctions&lt;/strong&gt;, axons synapse directly on muscles.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/6H9A6.jpg&quot; alt=&quot;synapse&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Presynaptic and postsynaptic neuron. The synapse is shown enlarged in the inset. Source: &lt;a href=&quot;http://www.rhsmpsychology.com/Handouts/synapse.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Rowland Hall&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-07-14T14:02:00.170" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36073" PostTypeId="1" AcceptedAnswerId="36074" CreationDate="2015-07-14T17:28:01.303" Score="4" ViewCount="164" Body="&lt;p&gt;I'm attempting to model the chemical concentration between several compartments of the eye, including the retina. Does anyone have any idea what the rate of fluid removal is in the retina, or could direct me to a study of this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: It appears that Müller cells play a crucial role in this, dehydrating the retinal tissue. I am attempting to find the rate at which they achieve this. (see link)&#xA;&lt;a href=&quot;http://retinatoday.com/2008/11/1108_07.php/&quot; rel=&quot;nofollow&quot;&gt;http://retinatoday.com/2008/11/1108_07.php/&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9834" LastEditorUserId="9834" LastEditDate="2015-07-14T17:35:06.777" LastActivityDate="2015-07-14T17:50:30.913" Title="What is the fluid clearance rate inside the retina?" Tags="&lt;human-eye&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36074" PostTypeId="2" ParentId="36073" CreationDate="2015-07-14T17:50:30.913" Score="4" Body="&lt;p&gt;As I mentioned in a comment, the RPE (retinal pigment epithelium) is in charge of absorbing the &quot;water&quot; from the retina and beneath it. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Water &lt;a href=&quot;http://webvision.med.utah.edu/book/part-ii-anatomy-and-physiology-of-the-retina/the-retinal-pigment-epithelium/&quot; rel=&quot;nofollow&quot;&gt;is eliminated from subretinal space&lt;/a&gt; by active transport by the&#xA;  RPE. The transportation rate was estimated to range from 1.4 to 11 µl&#xA;  x cm-2 x h-1.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-14T17:50:30.913" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36075" PostTypeId="1" AcceptedAnswerId="36099" CreationDate="2015-07-14T19:43:03.767" Score="0" ViewCount="354" Body="&lt;p&gt;What specific mutations can cause the apoptosis mechanisms in a cell to malfunction? Are any such mutations 'reversible' , somehow or are they generally permanent? what kind of mutations can happen without disrupting the apoptosis mechanisms?&lt;/p&gt;&#xA;" OwnerUserId="11605" LastActivityDate="2015-07-15T13:55:49.863" Title="What specific mutations can cause an apoptosis mechanism to malfunction?" Tags="&lt;cancer&gt;&lt;mutations&gt;&lt;apoptosis&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="36078" PostTypeId="1" AcceptedAnswerId="36080" CreationDate="2015-07-14T21:39:49.517" Score="8" ViewCount="516" Body="&lt;p&gt;I got this green plant as a gift many years ago, but I have never seen it flower before. It has a strong, pleasant scent and cool flowers so I'd really would like to know what it is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/goHlb.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/n6aml.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9124" LastEditorUserId="3624" LastEditDate="2015-07-14T22:42:51.767" LastActivityDate="2015-07-14T22:42:51.767" Title="What flowering green plant is this?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36079" PostTypeId="1" AcceptedAnswerId="36082" CreationDate="2015-07-14T22:26:57.957" Score="9" ViewCount="1860" Body="&lt;p&gt;Often the names of herbal ingredients in certain cosmetics products are given by their scientific names like &lt;em&gt;Anthemis nobilis&lt;/em&gt; instead of chamomile or &lt;em&gt;Lavandula angustifolia&lt;/em&gt; instead of lavender. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any reason why this practice is followed? Wouldn't those who have allergies to certain plant materials be better off reading &quot;coriander leaf extract&quot; instead of scratching their heads over what &quot;&lt;em&gt;Coriandrum sativum&lt;/em&gt; leaf extract&quot; is? Why put something more complex when something simpler would be more beneficial to the consumer?&lt;/p&gt;&#xA;" OwnerUserId="16765" LastEditorUserId="3340" LastEditDate="2015-07-15T04:29:26.547" LastActivityDate="2015-07-16T01:17:23.450" Title="Why are plants referred to by their Latin species names, and not by their popular names?" Tags="&lt;botany&gt;&lt;nomenclature&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36080" PostTypeId="2" ParentId="36078" CreationDate="2015-07-14T22:33:14.510" Score="13" Body="&lt;p&gt;It looks like a &quot;Spider lily&quot; from the &lt;a href=&quot;https://en.wikipedia.org/wiki/Hymenocallis&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Hymenocallis&lt;/em&gt;&lt;/a&gt; genus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is a picture of &lt;em&gt;Hymenocallis caribaea&lt;/em&gt; from wikipedia for comparison:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/Eeo6r.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are however ~65 species in the genus (according to wikipedia), and I cannot say exactly what species you have.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2015-07-14T22:33:14.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36081" PostTypeId="2" ParentId="36070" CreationDate="2015-07-15T00:09:48.490" Score="1" Body="&lt;p&gt;What you're describing is a &lt;a href=&quot;https://en.wikipedia.org/wiki/Microbial_fuel_cell#Phototrophic_biofilm_microbial_fuel_cell&quot; rel=&quot;nofollow&quot;&gt;phototrophic biofilm microbial fuel cell&lt;/a&gt;! They're pretty neat. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Essentially the sun powers the bacteria and the bacteria in the anaerobic side passes electrons through the graphite electrode to use oxygen at the cathode. There's another explanation &lt;a href=&quot;http://www.bioelectrogenesis.com/en/if-you-are-not-an-expert.html&quot; rel=&quot;nofollow&quot;&gt;here.&lt;/a&gt; You could also &quot;unfold&quot; cyanobacteria and layer them and you'd probably get an efficiency increase but the system would be pretty fragile. Compared to other MFCs, though, everything is fragile. Dirt even works(not very well, but it's dirt).&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-07-15T00:09:48.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36082" PostTypeId="2" ParentId="36079" CreationDate="2015-07-15T00:27:13.433" Score="25" Body="&lt;p&gt;The use of a &lt;em&gt;genus-species&lt;/em&gt; notation gives &lt;strong&gt;more exact information&lt;/strong&gt;. For example there are &lt;a href=&quot;http://www.encyclopedia.com/topic/chamomile.aspx&quot;&gt;multiple species of chamomile&lt;/a&gt;: There is Roman chamomile (&lt;em&gt;Chamaemelum nobile&lt;/em&gt;), German chamomile (&lt;em&gt;Matricaria recutita&lt;/em&gt;, or &lt;em&gt;Chamomilla recutita&lt;/em&gt;) and Dyer's chamomile (&lt;em&gt;Anthemis tinctora&lt;/em&gt;). The first two species are appraised for their medicinal properties and help to calm upset tummies and to aid sleep, among other things. The latter species, however, does not have these properties and is used for dyeing. This illustrates the fact why 'chamomile' alone is insufficient.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Popularly, &lt;a href=&quot;http://www.britannica.com/science/taxonomy&quot;&gt;classifications&lt;/a&gt; of living organisms arise according to need and are often superficial. Anglo-Saxon terms such as 'worm' have been used to refer to any creeping thing including snakes, earthworms and intestinal parasites. The term 'fish' is used in shellfish, crayfish, and starfish. However, there are more anatomical differences between a shellfish and a starfish than there are between a bony fish and man. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In science it has been the convention to use the genus-species notation since &lt;a href=&quot;http://www.britannica.com/science/taxonomy&quot;&gt;Carl Linnaeus&lt;/a&gt; &lt;a href=&quot;https://en.wikipedia.org/wiki/Linnaean_taxonomy&quot;&gt;introduced it in the 1700's&lt;/a&gt;. This formal classification serves as a basis for a relatively uniform and internationally understood nomenclature. A uniform classification system simplifies cross-referencing and retrieval of information. The &lt;a href=&quot;https://en.wikipedia.org/wiki/Linnaean_taxonomy&quot;&gt;Linnaean taxonomical system&lt;/a&gt; aids in this purpose and is widely used. The genus-species system can be extended by including subspecies and varieties. Many (plant) species don't even have an (English) trivial name. Taking your lavender example: there are some &lt;a href=&quot;http://everything-lavender.com/lavender.html&quot;&gt;39 &lt;em&gt;Lavendula&lt;/em&gt; species known&lt;/a&gt; and obviously, many of them don't have a trivial name. Here one has to fall back to the Latin names to be sure what it is.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-16T01:17:23.450" LastActivityDate="2015-07-16T01:17:23.450" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="36084" PostTypeId="1" CreationDate="2015-07-15T02:16:02.397" Score="3" ViewCount="339" Body="&lt;p&gt;I have no idea where this plant came from, or what it is. What I do know is its leaves are covered in little hairs, there's little thorns growing all over it, and just by rubbing its leaf it burns you and leaves a red mark as well as blisters. It stung my mother and I would like to know what it is so I can find a remedy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ou5r7.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;larger image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://i1094.photobucket.com/albums/i449/cupcaketurtle1/20150714_225505_zpskr24gklq.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://i1094.photobucket.com/albums/i449/cupcaketurtle1/20150714_225505_zpskr24gklq.jpg&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16768" LastEditorUserId="9943" LastEditDate="2015-07-15T06:19:18.317" LastActivityDate="2015-07-15T11:32:21.247" Title="Can someone identify this stinging plant?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36085" PostTypeId="2" ParentId="36084" CreationDate="2015-07-15T02:21:01.450" Score="6" Body="&lt;p&gt;I think it is a common stinging nettle, &lt;a href=&quot;https://en.wikipedia.org/wiki/Urtica_dioica&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Urtica dioica&lt;/em&gt;&lt;/a&gt;. It is a native to Europe, Asia, northern Africa, and western North America and is the best-known member of the nettle genus &lt;em&gt;Urtica&lt;/em&gt;. As commented by others, your geographical location would be helpful to obtain a more accurate identification. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like other stinging nettles, it is unpleasant to the touch, but harmless. Just be patient. &lt;a href=&quot;http://www.healthdirect.gov.au/stinging-plants&quot; rel=&quot;nofollow noreferrer&quot;&gt;The redness and burning/itching will disappear&lt;/a&gt;. If the pain gets serious or other complaints arise, go to your GP. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/zhQyc.jpg&quot; alt=&quot;stinging nettle&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Stinging nettle. Source: &lt;a href=&quot;http://www.healthdirect.gov.au/stinging-plants&quot; rel=&quot;nofollow noreferrer&quot;&gt;Health Direct&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-15T11:32:21.247" LastActivityDate="2015-07-15T11:32:21.247" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36086" PostTypeId="1" AcceptedAnswerId="36087" CreationDate="2015-07-15T03:45:59.757" Score="3" ViewCount="406" Body="&lt;p&gt;While playing with a blue/violet laser (5 mW, 405 nm) tonight, I noticed that on dark, non-fluorescing surfaces, the beam reflection was trailed by what looked like a dimmer reflection of the beam. The effect was most easily observed when I moved the laser in a circular motion. The apparent 2&lt;sup&gt;nd&lt;/sup&gt; reflection was not produced by a side lobe of the laser diode, as it always trailed the main reflection, regardless of clockwise or counterclockwise rotation. Also when I stop moving the beam, the second 'reflection' quickly merged with the main beam reflection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I doubt it is caused by phosphorescence of the material (cloth) I was lasering, as it also showed up when I pointed the laser at the floor, other sorts of cloth and painted walls.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, do rods, cones, visual purple or other eye components phosphoresce when hit with deep blue light?&lt;/p&gt;&#xA;" OwnerUserId="16119" LastEditorUserId="16119" LastEditDate="2015-07-16T23:57:14.843" LastActivityDate="2015-07-16T23:57:14.843" Title="Does 405 nm light set off phosphorescence in the eye?" Tags="&lt;vision&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36087" PostTypeId="2" ParentId="36086" CreationDate="2015-07-15T04:00:52.317" Score="4" Body="&lt;p&gt;Instead of &lt;a href=&quot;https://en.wikipedia.org/wiki/Phosphorescence&quot; rel=&quot;nofollow&quot;&gt;phosphorescence&lt;/a&gt;, a more parsimonious explanation is the perception of &lt;strong&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Afterimage&quot; rel=&quot;nofollow&quot;&gt;afterimages&lt;/a&gt;&lt;/strong&gt;. Afterimages regularly appear after viewing a &lt;strong&gt;bright stimulus&lt;/strong&gt;. They occur in the same location in the visual field as the original stimulus, but lack clarity. Afterimages depend on the intensity and &lt;em&gt;contrast&lt;/em&gt; of the original stimulus (i.e., they are more pronounced with bright stimuli in a dark environment), the time of &lt;em&gt;fixation&lt;/em&gt; (i.e., longer fixation generate more persistent afterimages), and &lt;em&gt;retinal adaptation&lt;/em&gt; (i.e., dark environments enhance afterimages).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;After images are almost always the &lt;a href=&quot;https://faculty.washington.edu/chudler/after.html&quot; rel=&quot;nofollow&quot;&gt;complementary color (negative afterimage)&lt;/a&gt; to the original stimulus, but can very briefly be the same color (positive afterimage) when viewing an exceptionally bright stimulus. A stimulus consistently produces the same afterimage, which varies in size based on the distance between the person and the background. After images are often revived by blinking. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Afterimages are thought to derive mainly from &lt;a href=&quot;https://en.wikipedia.org/wiki/Cone_cell&quot; rel=&quot;nofollow&quot;&gt;photobleaching&lt;/a&gt; of the retina, although cerebral processes may contribute too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Phosphorescence in the retina has to be induced by injecting phosphorescent markers &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690278/&quot; rel=&quot;nofollow&quot;&gt;(Wanek &lt;em&gt;et al&lt;/em&gt;., 2013)&lt;/a&gt;. As far as I know, the retina is not autophosphorescent. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.surveyophthalmol.com/article/S0039-6257(14)00128-3/pdf&quot; rel=&quot;nofollow&quot;&gt;Gersztenkorn &amp;amp; Lee, &lt;em&gt;Survey Ophthalmol&lt;/em&gt;, (2015): 1-35&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690278/&quot; rel=&quot;nofollow&quot;&gt;Wanek &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Curr Eye Res&lt;/em&gt; (2012); &lt;strong&gt;37&lt;/strong&gt;(2): 132–137&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-15T11:47:24.133" LastActivityDate="2015-07-15T11:47:24.133" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="36089" PostTypeId="2" ParentId="36079" CreationDate="2015-07-15T07:42:30.140" Score="9" Body="&lt;p&gt;The Latin names are known in all countries. The &quot;popular&quot; names are only popular in one or maybe two languages/countries. So, learning the Latin names, enables you to communicate international more easily.&lt;/p&gt;&#xA;" OwnerUserId="16730" LastActivityDate="2015-07-15T07:42:30.140" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36090" PostTypeId="2" ParentId="36084" CreationDate="2015-07-15T07:53:26.993" Score="3" Body="&lt;p&gt;It's a nettle (genus &lt;a href=&quot;https://en.wikipedia.org/wiki/Urtica&quot; rel=&quot;nofollow&quot;&gt;Urtica&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The one on your photo really looks like the one I'm used to see in France:&#xA;&lt;a href=&quot;https://en.wikipedia.org/wiki/Urtica_dioica&quot; rel=&quot;nofollow&quot;&gt;Urtica dioica&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I read in herbal lore books that the sting of the nettle could be appeased by rubbing it with &lt;a href=&quot;https://en.wikipedia.org/wiki/Plantago&quot; rel=&quot;nofollow&quot;&gt;Plantago&lt;/a&gt; leafs. But that might just be placebo effect.&#xA;See also &lt;a href=&quot;https://en.wikipedia.org/wiki/Urtica_dioica#Nettle_sting_treatment&quot; rel=&quot;nofollow&quot;&gt;this section&lt;/a&gt; of the wikipedia page.&lt;/p&gt;&#xA;" OwnerUserId="1486" LastActivityDate="2015-07-15T07:53:26.993" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36091" PostTypeId="1" AcceptedAnswerId="36096" CreationDate="2015-07-15T08:39:11.543" Score="5" ViewCount="223" Body="&lt;p&gt;I usually would search for myself, but I need to be &lt;strong&gt;super&lt;/strong&gt; sure about the identification because I need to know if I need to get an exterminator in here or not. (I think it might be a giant house spider, but don't let me influence your analysis.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I live in the northern part of Ireland (About 40 minutes from Derry Northern Ireland over in County Donegal) and I went to my bathroom to a VERY fun surprise this morning. It was this wonderful spider in my bathroom. For reference, the lip of the glasses it is depicted in are 8 - 8.5 cm in diameter. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The missing leg was not my fault either, I was very gentle with the spider and released it outside post photo-shoot. (&lt;strong&gt;Warning:&lt;/strong&gt; these are macro shots of the said spider)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;hr&gt;&#xA;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/2R4bR.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;hr&gt;&#xA;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/EodGj.jpg&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;hr&gt;&#xA;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;img src=&quot;https://i.stack.imgur.com/9RPnX.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;More high resolution photos available on my Flickr (&lt;a href=&quot;https://www.flickr.com/photos/125596053@N08&quot; rel=&quot;noreferrer&quot;&gt;SolarLunix&lt;/a&gt;). &lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="16041" LastEditDate="2015-07-15T09:25:01.050" LastActivityDate="2021-04-10T23:55:26.493" Title="Species Identification: Spider" Tags="&lt;species-identification&gt;&lt;arachnology&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36092" PostTypeId="2" ParentId="35773" CreationDate="2015-07-15T08:47:32.450" Score="0" Body="&lt;p&gt;we included a script to calculate this in supplemental material &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/mec.13034/full&quot; rel=&quot;nofollow&quot;&gt;http://onlinelibrary.wiley.com/doi/10.1111/mec.13034/full&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;....single segregating site per locus or up to a maximum of four SNPs, as is expected for short-read genomic data (see attached R script for estimation).&lt;/p&gt;&#xA;" OwnerUserId="16773" LastActivityDate="2015-07-15T08:47:32.450" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36094" PostTypeId="2" ParentId="36079" CreationDate="2015-07-15T12:13:06.443" Score="8" Body="&lt;p&gt;It generally won't be more helpful.  Not only will the names be different in different countries, there may be different types of the same species with different properties, or even different species with the same common name.  If you have an allergy to something like coriander, being able to read the label and see what contains actual coriander and what contains curry leaf is essential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Lavender is a great example.  Any gardener could tell you that English lavender (angustifolia) is a very different plant from French lavender (dentata), even though they're the same family.  I've no idea what the essential oils will smell like, but I'm pretty sure they won't be identical.  And more importantly, if you're talking allergies then I'm pretty sure they won't have the same chemical composition.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even worse, consider bergamot.  Bergamot oil should come from the skin of the bergamot orange, but there's also a species of flower (monarda) which is commonly called bergamot because its scent is similar to bergamot orange.  If your contents just said &quot;bergamot&quot;, which one? And even worse, there are two types of monarda which are completely different plants.&lt;/p&gt;&#xA;" OwnerUserId="16776" LastEditorUserId="16765" LastEditDate="2015-07-15T12:46:42.247" LastActivityDate="2015-07-15T12:46:42.247" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36095" PostTypeId="2" ParentId="35514" CreationDate="2015-07-15T12:26:16.567" Score="3" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Chronic pain may be very persistent and even worsen over time, but it will depend on the underlying pathology. If the pathology disappears over time, so may the pain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;There are roughly &lt;a href=&quot;http://www.painaustralia.org.au/consumers/what-is-pain.html&quot; rel=&quot;nofollow&quot;&gt;two kinds of pain&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Acute pain&lt;/em&gt; is pain that lasts for a short time and occurs following surgery or trauma or other condition. It acts as a warning to the body to seek help. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;&lt;em&gt;Chronic pain&lt;/em&gt; is pain that lasts beyond the time expected for healing healing following surgery or trauma or other condition. It can also exist without a clear reason at all.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;A large body of basic research indicates that chronic pain is associated with neuroplastic changes in the nervous system at peripheral, spinal cord and brain levels. Thus chronic pain is shown to have a distinct pathology that often &lt;strong&gt;worsens over time&lt;/strong&gt;, and constitutes a serious separate disease entity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, if the underlying pathology disappears, the pain may lessen. However, based on the cited paper, I do not think chronic pain gets less severe over time due to neural adaptation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Excerpt from the linked article upon request: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These and other changes may contribute to the development of alterations in central [spinal] neuronal responsiveness, which share features of wind-up and long-term potentiation and are collectively known as “&lt;strong&gt;central sensitization&lt;/strong&gt;.” [...] These alterations in cell responsiveness may be evidenced by a number of symptoms and signs, including spontaneous pain [...]. This [...] has been demonstrated in patients who have chronic pain associated with whiplash injury and fibromyalgia and suggests that the presence of pain [...] is associated with &lt;strong&gt;&lt;em&gt;increased sensitivity of spinal neurons&lt;/em&gt;&lt;/strong&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.123.4971&amp;amp;rep=rep1&amp;amp;type=pdf&quot; rel=&quot;nofollow&quot;&gt;Siddall &amp;amp; Cousins, &lt;em&gt;Anesth Analg&lt;/em&gt; (2004); &lt;strong&gt;99&lt;/strong&gt;: 510-520&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-15T13:34:07.553" LastActivityDate="2015-07-15T13:34:07.553" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36096" PostTypeId="2" ParentId="36091" CreationDate="2015-07-15T13:04:06.647" Score="6" Body="&lt;p&gt;Looks like a &lt;a href=&quot;https://en.wikipedia.org/wiki/Tegenaria_domestica&quot; rel=&quot;noreferrer&quot;&gt;house spider (&lt;em&gt;Tegenaria domestica&lt;/em&gt;)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QgMfw.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-07-15T13:04:06.647" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36097" PostTypeId="1" AcceptedAnswerId="36098" CreationDate="2015-07-15T13:08:03.180" Score="5" ViewCount="1519" Body="&lt;p&gt;I have encountered this black-colored growth on onion skins a lot. It seems to develop over the course of weeks and I have rarely, if ever, encountered the material on fresh ones. If I peel the onion and it streaks the onion flesh, it appears, dark blue-ish. It looks like a fungus, perhaps a bacterium, but I am unsure. It is often found 'hiding' under the outer layer of skin on the deeper skin layers. In the photo the outer layer of skin was peeled off. It never seems to invade the edible parts below, though.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The pictures below are standard white onions from the local supermarket in Canberra, Australia (Canberra [Australia's capitol yes!] lies between Sydney and Melbourne). I must admit, I don't know if they are imported. The pictures below were taken mid-winter. Temperatures in our kitchen plummet during the day because of bad insulation. In the evenings and weekends it's room temp with heating. The onions are stored in the dark, in a kitchen cabinet. Humidity is low and mostly the days are dry and sunny. However, we cook in the kitchen so at times there is plenty of moist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, I wonder, would it be harmful? No self-help medical issues here, I always wash and fry/cook my stuff and no issues whatsoever, just curious.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/fNHUf.jpg&quot; alt=&quot;onion2&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;I understand there is little to go with. However, a general &lt;em&gt;genus&lt;/em&gt; or group of fungi would already be cool. I googled and sought for images to no avail.&lt;/sup&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2020-04-11T23:12:02.107" LastActivityDate="2020-04-11T23:12:02.107" Title="Identification of black growth on onion skin" Tags="&lt;microbiology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="36098" PostTypeId="2" ParentId="36097" CreationDate="2015-07-15T13:22:18.770" Score="8" Body="&lt;p&gt;I think it is &lt;a href=&quot;https://en.wikipedia.org/wiki/Aspergillus_niger&quot; rel=&quot;noreferrer&quot;&gt;Aspergillus niger&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4esl8.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the second place I'd suggest  Black Mold disease caused by &lt;a href=&quot;https://en.wikipedia.org/wiki/Alternaria&quot; rel=&quot;noreferrer&quot;&gt;Alternaria&lt;/a&gt; species. &lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-07-15T13:28:41.213" LastActivityDate="2015-07-15T13:28:41.213" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36099" PostTypeId="2" ParentId="36075" CreationDate="2015-07-15T13:55:49.863" Score="1" Body="&lt;p&gt;There are lots and lots of specific single mutations that cause problems with apoptosis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the most common are in P53, PTEN, MYC, APC, and KRAS. If you want a specific amino acid change, KRAS G12D is particularly potent. It works by disabling a regulatory domain and causing KRAS to be constitutively active.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These aren't &quot;reversible&quot; in a strict sense (except, I guess, for the struck-by-lightning-while-holding-a-winning-lottery-ticket level improbability of a second replication error in the same place back to the original base) but in many cases the cells will upregulate compensatory pathways or activate senescence pathways instead, rather than instantaneously becoming full-blown malignant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for mutations that &lt;em&gt;don't&lt;/em&gt; cause disruptions to apoptosis,there are almost an infinite number, in that silent mutations or mutations to genes that aren't involved in apoptosis would count. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you mean what kind of non-silent mutations can happen to genes that are important to apoptosis without causing problems, there are still a lot: swapping similar amino acids in non-active parts of proteins are unlikely to have huge effects.&lt;/p&gt;&#xA;" OwnerUserId="819" LastActivityDate="2015-07-15T13:55:49.863" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="36100" PostTypeId="1" CreationDate="2015-07-15T14:34:41.670" Score="3" ViewCount="411" Body="&lt;p&gt;From my own reading, there are three ways used by the body to produce energy:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;Alactic anaerobic (direct degradation of ATP and creatine phosphate for regeneration of ATP)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Lactic anaerobic (breakdown of muscle glycogen with lactic acid production)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Aerobic (breakdown of carbohydrates and fats primarily and secondarily of proteins)&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;My questions are:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) Knowing that the anaerobic mechanisms (alactic and lactic) are triggered when the effort is intense and / or greater than body oxygenation capacity, it seems logical, at rest, the body uses mainly aerobic way for producing energy. Am I right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) If 1) is true, what are the conditions (trigger elements, trigger events) which lead to muscle catabolism (so protein degradation) in order to produce energy? ? Is it well the last resort used by the body to produce energy that is to say after degradation of total carbohydrates and lipids?&lt;/p&gt;&#xA;" OwnerUserId="16777" LastEditorUserId="15225" LastEditDate="2017-06-25T07:44:47.710" LastActivityDate="2017-06-25T14:51:23.320" Title="At what levels of muscle energy intake does catabolism start?" Tags="&lt;metabolism&gt;&lt;muscles&gt;&lt;anaerobic-respiration&gt;&lt;energy&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36101" PostTypeId="2" ParentId="3545" CreationDate="2015-07-15T15:12:56.947" Score="3" Body="&lt;p&gt;Zabner &lt;em&gt;et al&lt;/em&gt; (J. Biol. Chem., 1995, &lt;strong&gt;270&lt;/strong&gt;, 18997-19007) monitored the lipid-DNA complex formation and uptake which was found to be predominantly by endocytosis. Dot blot experiment shows that cells (50% population) took up 60% of the DNA. The DNA-protein complex was observed to be deposited in the perinuclear cytoplasm and formed a series of regularly packed tubules. They also verified that the endosomes carrying the complex did not fuse with lysosome.&lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some of the DNA escapes the endosome (which is a known mechanism of increasing the efficiency of endocytosis based transfections) and might be taken up by the nucleus. When they compared expression of a reporter gene upon direct injection into the nucleus and upon direct injection into the cytoplasm, no expression was observed in the latter (acc. to Capecchi (Cell, 1980) the ratio of expression is around 1000:1. PDF available on Utah Uni Website). This means that the DNA uptake by the nucleus from cytoplasm is very inefficient.&lt;br/&gt; &#xA;Lower amount of lipids in protein-DNA complex increases the efficiency.&lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your question has been partly answered. How does all that DNA cell takes up gets inside the nucleus? It mostly doesn't. It accumulates around the nucleus. But some of the free DNA does get taken up by the nucleus. This, probably, was the starting point for Dean's group.&lt;br/&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vaughan &amp;amp; Dean (Mol.Ther., 2006, &lt;strong&gt;13(2)&lt;/strong&gt; 422-428) have proposed that the plasmids get transported into the nucleus with the help of microtubule associated motor protein Dynein. They observed that disrupting the microtubule network functionality inhibited expression. When the plasmids were injected directly into the nuclei of cells, this did not have an effect. Now, microtubules transport stuff with the help of motor proteins out of which Dynein transports stuff towards the nucleus. It was observed that inhibiting Dynein action reduced the expression. The mechanism of how dynein binds to plasmid is unknown. (I've worked with dynein; it's complicated when it comes to binding mechanisms. The whole negatively charged N-terminal is disordered.)&#xA;&lt;br/&gt;&#xA;If you read the discussion of the paper, It'd become apparent that the process is chaotic. The more the dispersion of DNA in cytoplasm around the nucleus, the more is it's uptake by the nucleus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no Nuclear localization signal involved here. Mesika &lt;em&gt;et al&lt;/em&gt; (Human Gene Ther., 2005) have increased the efficiency of plasmid expression by binding the plasmids to a protein with NLS. This is not the natural process. Vaughan and Dean have speculated that the DNA targeting sequence (&lt;em&gt;e.g.&lt;/em&gt; SV40, CMV etc.) binds to proteins that have NLS or have adapters to bind dynein(like, Transcription factors) which might help the plasmid uptake by the nucleus. This can also explain the sequence based differential uptake of plasmids. None of these mechanisms have been experimentally verified.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[I have also been wondering about this. I bugged a lot of seniors and scoured the net for the answers. And then I found this question. Thank you for asking]&lt;/p&gt;&#xA;" OwnerUserId="8606" LastEditorUserId="8606" LastEditDate="2015-07-16T14:23:24.550" LastActivityDate="2015-07-16T14:23:24.550" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36102" PostTypeId="2" ParentId="6900" CreationDate="2015-07-15T15:52:54.767" Score="-1" Body="&lt;p&gt;People can satisfy their sexual urges on their own (that is, without a sexual partner) through masturbating. They cannot satisfy their hunger on their own (that, without food).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suppose people could eat one food while looking at another kind of food pretending that the food they are eating is the one that they are watching, but where's the fun in that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Having sex with an attractive person is an indicator of biological desirability ----- namely that another human being wants you in the way you want to be wanted due to your accomplishments or social status. Thus, people watch or read porn to satisfy their need to be accepted or to make them feel as if they are such a person with accomplishments or social status or to compensate for things not going their way in life and subsequently masturbate to such porn.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As for hunger, a better analogy for porn would be taking those kind of drugs that make you feel less hungry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So yeah, for sex, people watch porn. For hunger, people do not compensate for their inability to eat by looking at food that they cannot have. They would probably take drugs or something. I'm not quite sure if such a thing exists, but I swear one of my grade school teachers said that there was some kind of drug that makes people stop feeling hungry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think a better analogy for looking at food they cannot have is looking through pictures of a lustful or romantic interest with his/her romantic partner.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This may sound like a stupid answer that is more philosophical than biological from some loser with 1 reputation. I request commentary along with any downvotes.&lt;/p&gt;&#xA;" OwnerUserId="16654" LastActivityDate="2015-07-15T15:52:54.767" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36104" PostTypeId="1" CreationDate="2015-07-15T16:36:11.797" Score="2" ViewCount="69" Body="&lt;p&gt;I am working on an enzyme activity assay using NADPH as a cofactor. The &lt;a href=&quot;https://www.interprise.com.br/produtos/download/90289.pdf&quot; rel=&quot;nofollow&quot;&gt;MSDS&lt;/a&gt; for NADPH Tetrasodium Salt, tells to store it in a place away from heat and light. Does this include UV light or just visible light? I was told that a pure NADPH stock solution (with pH 7 phosphate buffer as solvent) could be re-used after absorbing UV light at 340 nm, but based on my understanding of the MSDS it seems that shouldn't be the case. So my question is: could I reuse a sample of pure NADPH stock solution that was exposed to UV for my enzyme activity assay?&lt;/p&gt;&#xA;" OwnerUserId="16779" LastEditorUserId="3340" LastEditDate="2015-07-15T18:14:13.437" LastActivityDate="2015-07-15T18:39:24.473" Title="Is NADPH unstable in UV light?" Tags="&lt;enzymes&gt;&lt;protocol&gt;&lt;enzyme-kinetics&gt;&lt;assay-development&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36107" PostTypeId="2" ParentId="35960" CreationDate="2015-07-15T17:32:40.970" Score="2" Body="&lt;p&gt;Probably not. There's a thing called Hayflick limit, which is basically a limit of life expectancy caused by a shortening of telomeres with every cell division. And since most of our cells complete cycles more based on time (life cycle of RBC 100 days), and not due to damages to a cell, our telomeres would still shorten at the same rate. Of course the gravity could play a small part once organs have started failing, but there are many other factors that affect how long it takes for everything to completely deteriorate, and wouldn't have a big role. In fact, it could even shorten life expectancy, seeing as how our bodies are currently built to live in our current gravitational field. Without gravity, our muscles could become weak, causing other problems, which is why people at the space stations have frequent dedicated times to workout, to keep their muscles fit.&lt;/p&gt;&#xA;" OwnerUserId="16781" LastActivityDate="2015-07-15T17:32:40.970" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36108" PostTypeId="2" ParentId="35911" CreationDate="2015-07-15T17:47:48.240" Score="3" Body="&lt;p&gt;Male grasshoppers often mate several times with multiple female, and some females will mate again after, and perhaps even before they lay their eggs. So no, they are not monogamous. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Rufous grasshoppers for example have a very special mating cycle, the male will attract other females, possibly more than one with &quot;pursuit sounds&quot;. After copulation, he keeps her close to prevent other males from mating with her, and the females enter a defensive mode where they refuse intercourse from other males. After laying eggs however, she enters a &quot;relaxed&quot; mode where she is open to others for mating.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sources:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://science.jrank.org/pages/3123/Grasshoppers-Courtship-mating.html&quot; rel=&quot;nofollow&quot;&gt;jrank&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.inaturalist.org/taxa/rufous_grasshopper&quot; rel=&quot;nofollow&quot;&gt;Rufous grasshopper: inaturalist&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16781" LastEditorUserId="16781" LastEditDate="2015-07-16T01:14:19.077" LastActivityDate="2015-07-16T01:14:19.077" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36110" PostTypeId="2" ParentId="36104" CreationDate="2015-07-15T18:39:24.473" Score="1" Body="&lt;p&gt;In my experience, reuse of NADPH stock solutions maintained at pH 7.0 or above is perfectly acceptable. Taking an absorbance spectrum every half-hour or so will probably show that definitively.  However, NADPH is VERY unstable in acid, leading to a 'bleaching' of the absorbance at 340nm.  Try measuring a rate at pH  6 or below, 340nm,  with 100 micromolar NADPH and no enzyme or cosubstrate. There will be a very significant decrease in absorbance with time (ie a 'blank' rate) which will make estimation of enzymic reactions at low pH virtually impossible. &lt;/p&gt;&#xA;" OwnerUserId="1136" LastActivityDate="2015-07-15T18:39:24.473" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36111" PostTypeId="2" ParentId="36070" CreationDate="2015-07-15T18:49:07.040" Score="0" Body="&lt;p&gt;You do not need to merge anything. Photosynthesis already includes the electron transport across the inner membrane of the chloroplast (in case of plants) or across the bacterial membrane (in case of bacteria), creating voltage difference between inner and outer side. The only problem, this voltage is relatively difficult to take away. &lt;/p&gt;&#xA;" OwnerUserId="5924" LastActivityDate="2015-07-15T18:49:07.040" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36112" PostTypeId="1" CreationDate="2015-07-15T18:59:17.333" Score="4" ViewCount="1204" Body="&lt;p&gt;I am aware that dopamine cannot cross the blood-brain barrier, but can't it be pumped inside the cerebrospinal fluid via some permanent tube implant? Wouldn't Parkinson patients chose that over succumbing to the disease? Why hasn't it even been ever tried?&lt;/p&gt;&#xA;" OwnerUserId="10474" LastEditorUserId="9943" LastEditDate="2015-07-16T02:14:57.990" LastActivityDate="2016-08-05T00:14:28.863" Title="Why is dopamine or a dopamine-receptor agonist not pumped into the brain of Parkinson patients?" Tags="&lt;pharmacology&gt;&lt;brain&gt;&lt;dopamine&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36113" PostTypeId="1" AcceptedAnswerId="36208" CreationDate="2015-07-15T19:07:16.553" Score="2" ViewCount="91" Body="&lt;p&gt;I'm thinking of crosslinking two proteins. The crystallographic nature of the interaction and the binding motif for each molecule is know. The paper says the intermolecular contacts (over 50; van der Waals radius 5 angstrom) are made between the motifs in these two proteins. I also know that one of the motifs on one protein has a sulfhyryl (Methionine) and for the other motif on the other molecule I (think) can use a primary amide reactive moieties. Now this is where my question is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would I be correct in thinking that the best cross linker to use is a heterobifunctional cross linker, with a spacer of 10 (or 5?) angstrom in order to pick this interaction up specifically and stabilise it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I desperately need a guidance on this. I have used the life technologies &lt;a href=&quot;https://www.lifetechnologies.com/uk/en/home/life-science/protein-biology/protein-labeling-crosslinking/protein-crosslinking/crosslinker-selection-tool.html&quot; rel=&quot;nofollow&quot;&gt;crosslinker selection tool&lt;/a&gt; and the &lt;a href=&quot;https://tools.lifetechnologies.com/content/sfs/brochures/1602163-Crosslinking-Reagents-Handbook.pdf&quot; rel=&quot;nofollow&quot;&gt;crosslinking technologies hand book&lt;/a&gt; but I can't quite figure out based on the information I have, what cross linker length I need to use. I'm not worried about the cleavability, solubility and membrane permeability parameters.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that the binding motif on the first protein it has Tyrosine, Proline and Methionine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Looking at the groove contacts, the second protein is interacting with this motif, using Tyrosine and Glutamine BUT the second protein also has Tryptophan, Lysine, Glutamic acid and Methionine.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE 2:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I found specially close Glutamic acid (E) and leucine (L) on my first protein, specially close to Lysine (L) on my second protein although its not in the consensus sequence for the second protein. They are less than 10 angstrom apart. is that any better? So presumably I can use the homobifunctional linker?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many thanks in advance&lt;/p&gt;&#xA;" OwnerUserId="6511" LastEditorUserId="6511" LastEditDate="2015-07-17T09:28:21.957" LastActivityDate="2015-07-19T07:04:43.113" Title="Determining the appropriate bioconjugate" Tags="&lt;amino-acids&gt;&lt;protein-interaction&gt;&lt;xray-crystallography&gt;" AnswerCount="2" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="36115" PostTypeId="1" CreationDate="2015-07-15T20:54:08.733" Score="-1" ViewCount="126" Body="&lt;p&gt;Do herbaceous plants, especially perennial plants have woody parts, like woody stem?&lt;/p&gt;&#xA;" OwnerUserId="16723" LastActivityDate="2015-07-15T23:49:06.493" Title="Do herbaceous plants have woody parts?" Tags="&lt;plant-physiology&gt;&lt;plant-anatomy&gt;&lt;plant-perception&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ClosedDate="2015-07-16T05:40:05.570" ContentLicense="CC BY-SA 3.0" />
  <row Id="36119" PostTypeId="2" ParentId="36115" CreationDate="2015-07-15T23:49:06.493" Score="1" Body="&lt;p&gt;By definition, no. An herbaceous plant is defined as a plant that has &lt;a href=&quot;https://en.wikipedia.org/wiki/Herbaceous_plant&quot; rel=&quot;nofollow&quot;&gt;no woody parts&lt;/a&gt;. Herbaceous perennials die down to the roots at the end of the year and then sprout up again at the start of the next growing season, but they do not have woody parts. A plant that is small and herblike but has woody parts may be called a &lt;a href=&quot;https://en.wikipedia.org/wiki/Subshrub&quot; rel=&quot;nofollow&quot;&gt;subshrub&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="14629" LastActivityDate="2015-07-15T23:49:06.493" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36120" PostTypeId="1" AcceptedAnswerId="36122" CreationDate="2015-07-15T23:56:42.867" Score="12" ViewCount="1135" Body="&lt;p&gt;We've known that offspring inherit various traits from their parents since (at least) Aristotle. In The Elements of Plant Hybridization, &lt;a href=&quot;https://en.wikipedia.org/wiki/Gregor_Mendel&quot; rel=&quot;nofollow&quot;&gt;Gregor Mendel&lt;/a&gt; treats that fact as common knowledge. Clearly, we don't credit Mendel with discovering it. Accordingly, it seems to me that Mendel's only notable discovery was the discovery of the existence of dominant and recessive genes. However, that discovery doesn't seem to justify the title 'founder of modern genetics', which Wikipedia, and other sources, use to refer to him. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why is Mendel the big deal that he is?&lt;/p&gt;&#xA;" OwnerUserId="16788" LastEditorUserId="948" LastEditDate="2015-07-18T04:40:47.350" LastActivityDate="2015-07-20T01:37:03.193" Title="Is the discovery of dominant and recessive genes the only reason Mendel matters?" Tags="&lt;genetics&gt;&lt;hybridization&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36121" PostTypeId="2" ParentId="36112" CreationDate="2015-07-16T00:56:17.693" Score="5" Body="&lt;p&gt;&lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/parkinsons-disease/basics/treatment/con-20028488&quot; rel=&quot;nofollow noreferrer&quot;&gt;Levo-Dopa&lt;/a&gt; is used as a first-line treatment of Parkinson's disease. Unlike dopamine, L-Dopa is able to cross the blood-brain barrier. There it is converted into dopamine. To prevent premature breakdown in the gastro-intestinal and circulatory system after oral intake, &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/druginfo/meds/a601068.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;carbidopa&lt;/a&gt; can be co-administered. Also &lt;a href=&quot;http://www.parkinson.org/Parkinson-s-Disease/Treatment/Medications-for-Motor-Symptoms-of-PD/MAO-B-inhibitors&quot; rel=&quot;nofollow noreferrer&quot;&gt;MAO-B inhibitors&lt;/a&gt; and &lt;a href=&quot;http://www.webmd.com/parkinsons-disease/comt-inhibitors-for-parkinsons-disease&quot; rel=&quot;nofollow noreferrer&quot;&gt;COMT inhibitors&lt;/a&gt; can be applied to prevent breakdown of L-Dopa in the brain. Oral medication is preferable over invasive intracranial infusion of medication. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Pm2z2.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Conversion of L-Dopa into dopamine. Source: &lt;a href=&quot;http://adhd-treatment-options.blogspot.com.au/2010/02/does-tyrosine-for-adhd-actually-work-a.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;ADHD treatments&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.webmd.com/parkinsons-disease/dopamine-agonists-for-parkinsons-disease&quot; rel=&quot;nofollow noreferrer&quot;&gt;Dopamine agonists&lt;/a&gt; are also in use. Unlike L-Dopa, dopamine agonists are not converted into dopamine. Instead, they mimic dopamine effects in your brain. They aren't as effective as L-Dopa, but they last longer and may be used alongside L-Dopa to smooth the sometimes off-and-on effect. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;a href=&quot;http://umm.edu/health/medical/reports/articles/parkinsons-disease&quot; rel=&quot;nofollow noreferrer&quot;&gt;Parkinson's disease is not fatal&lt;/a&gt;&lt;/strong&gt;, but it can reduce longevity. The disease progresses more quickly in older patients, and may lead to severe incapacity within 10 - 20 years. Older patients also tend to have muscle freezing and greater declines in mental function and daily functioning than younger people. L-Dopa treatment in the long run causes adverse effects, such as dyskinesias, toxicity, or loss of efficacy &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9358193&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Marsden, 1994)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9358193&quot; rel=&quot;nofollow noreferrer&quot;&gt;Marsden, &lt;em&gt;Clin Neuropharmacol&lt;/em&gt; (1994); &lt;strong&gt;17&lt;/strong&gt;: S2:S32-44&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-16T05:59:20.993" LastActivityDate="2015-07-16T05:59:20.993" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="36122" PostTypeId="2" ParentId="36120" CreationDate="2015-07-16T01:48:40.217" Score="21" Body="&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Independent assortment. Mendel showed that his genetic markers for different traits, or phenotypes are transmitted randomly to the F1 generation. This was before the concept of linkage was discovered, so fortunately he selected unlinked genes.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Segregation of alleles. The dominant and recessive alleles segregate away from each other when the germ cells are created, therefore each parent has two copies of every Gene.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Distinguishing phenotype from genotype in a predictable and testable framework.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The test cross. It was only careful record keeping and back crosses that revealed the recessive copies of mutant alleles in heterozygotes.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;One description of his contributions is available on &lt;a href=&quot;https://en.m.wikipedia.org/wiki/Mendelian_inheritance&quot;&gt;Wikipedia&lt;/a&gt;.  Other sites include &lt;a href=&quot;http://www.mendelweb.org&quot;&gt;MendelWeb&lt;/a&gt;, &lt;a href=&quot;http://learn.genetics.utah.edu/content/basics/&quot;&gt;Learn Genetics&lt;/a&gt;, &lt;/p&gt;&#xA;" OwnerUserId="16667" LastEditorUserId="16667" LastEditDate="2015-07-20T01:37:03.193" LastActivityDate="2015-07-20T01:37:03.193" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36123" PostTypeId="1" AcceptedAnswerId="36127" CreationDate="2015-07-16T02:37:29.410" Score="5" ViewCount="1256" Body="&lt;p&gt;My bio teacher was discussing the ratios of different ions inside versus outside the cell. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\text{OUT:IN}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\text{K}^+ (1:20)$$&#xA;$$\text{Cl}^- (11.5:1)$$&#xA;$$\text{Ca}^{2+} (10000:1)$$&#xA;$$\text{Na}^+ (10:1)$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone provide specific details as to the relative quantities of these different ions relative to each other? &lt;strong&gt;In other words, given these ion ratios, provide me with how much of each type of ion there are and show why this adds to to -70 mV.&lt;/strong&gt; I just want to make sure I have a realistic picture of the concentrations.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think I am mixing up concentration with the ratio between inside and out. Although for every potassium ion outside there are 20 inside, the charge from the total number of potassium ions must be less than that of chloride or it would not be negative inside, right? &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="9943" LastEditDate="2015-07-16T06:15:28.383" LastActivityDate="2015-07-20T06:00:07.857" Title="If the average resting potential of a neuron is -70 mV, why is there such a high ratio of potassium ions inside relative to out?" Tags="&lt;biophysics&gt;&lt;electrophysiology&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36124" PostTypeId="1" AcceptedAnswerId="36142" CreationDate="2015-07-16T02:48:05.677" Score="5" ViewCount="184" Body="&lt;p&gt;Although it seems impossible with current technology to connect organ's capillaries to the recipient's capillaries and its motor neuron to the CNS, transplanted organ works for years. But why? &lt;/p&gt;&#xA;" OwnerUserId="4858" LastEditorUserId="4858" LastEditDate="2015-07-16T02:57:30.930" LastActivityDate="2019-01-31T22:19:21.670" Title="Why does organ transplant work although it seems organ's motor neuron isn't connected to recipient's CNS" Tags="&lt;organs&gt;&lt;transplantation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36125" PostTypeId="1" CreationDate="2015-07-16T04:29:07.167" Score="1" ViewCount="72" Body="&lt;p&gt;I need to collected soil sample from agricultural area far away from my lab. It would required about a week for the sample to arrive to lab. I need the soil sample for genomic DNA isolation (metagenomics) as well for isolation of certain species and culture them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, the cells in the soil sample needs to be viable. What are the possible ways to long distance transportation of soils sample with intact viable cells?&lt;/p&gt;&#xA;" OwnerUserId="15125" LastActivityDate="2019-02-21T10:43:07.227" Title="Requirements for soil sample transportation over long distance" Tags="&lt;bacteriology&gt;&lt;mycology&gt;&lt;soil&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36126" PostTypeId="1" AcceptedAnswerId="36129" CreationDate="2015-07-16T05:16:16.140" Score="2" ViewCount="551" Body="&lt;p&gt;Can someone please explain me what extreme pathways are? I found this definition in &lt;a href=&quot;http://www.biomedcentral.com/1471-2105/8/363&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Extreme pathways are a unique and minimal set of vectors that&#xA;  completely characterize the steady-state capabilities of genome-scale&#xA;  metabolic networks.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now, frankly speaking, I did not understand the head or tail of this definition? What is steady state? What does it mean by steady state capabilities? Can someone please explain me in a simpler way?&#xA;PS: I am a computer Science student&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="8835" LastEditDate="2015-07-16T06:24:09.283" LastActivityDate="2015-07-16T06:24:09.283" Title="What is the meaning and significance of extreme pathways" Tags="&lt;metabolism&gt;&lt;pathway&gt;&lt;metabolomics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36127" PostTypeId="2" ParentId="36123" CreationDate="2015-07-16T05:19:08.353" Score="5" Body="&lt;p&gt;Representative &lt;a href=&quot;http://www.ucl.ac.uk/~sjjgsca/NerveRestingPot.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;ion concentrations&lt;/strong&gt;&lt;/a&gt; are shown in Fig. 1:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jaDhr.gif&quot; alt=&quot;K+&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The membrane is mainly permeable to K&lt;sup&gt;+&lt;/sup&gt;. Because the Na&lt;sup&gt;+&lt;/sup&gt;,K&lt;sup&gt;+&lt;/sup&gt;-ATPase pumps K&lt;sup&gt;+&lt;/sup&gt; inside of the cell, it tends to diffuse outward again, thereby taking positive charge outside the cell and making it negative inside (extracellular space is pretty much devoid of charge due to its vastness). Because the membrane is mainly permeable to K&lt;sup&gt;+&lt;/sup&gt;, the membrane potential can be estimated using the &lt;a href=&quot;http://www.physiologyweb.com/calculators/nernst_potential_calculator.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Nernst equation&lt;/strong&gt;&lt;/a&gt; by taking into account only [K&lt;sup&gt;+&lt;/sup&gt;]:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/a8HZJ.gif&quot; alt=&quot;Nernst&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This delivers about &lt;a href=&quot;http://www.physiologyweb.com/calculators/nernst_potential_calculator.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;-90 mV&lt;/a&gt;, using the values in Fig. 1, which is quite close to the cell membrane resting potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, other ions have some limited permeability too and especially Cl&lt;sup&gt;-&lt;/sup&gt; also has quite a large leak current. To add the &lt;a href=&quot;http://www.st-andrews.ac.uk/~wjh/neurotut/mempot.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;permeability &lt;em&gt;p&lt;/em&gt;&lt;/a&gt; of the various ions (for K&lt;sup&gt;+&lt;/sup&gt; &lt;em&gt;p&lt;/em&gt;=1, for Na&lt;sup&gt;+&lt;/sup&gt; &lt;em&gt;p&lt;/em&gt;=0.04 and Cl&lt;sup&gt;-&lt;/sup&gt; &lt;em&gt;p&lt;/em&gt;=0.45) into the equation and take multiple ions into account, the &lt;strong&gt;&lt;a href=&quot;http://www.physiologyweb.com/calculators/ghk_equation_calculator.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Goldman equation&lt;/a&gt;&lt;/strong&gt; is needed:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/tJNSP.gif&quot; alt=&quot;GK&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This equation yields closer estimates of the membrane potential than the Nernst equation taking only K&lt;sup&gt;+&lt;/sup&gt; into consideration. However, other factors such as buffer effects (Cl&lt;sup&gt;-&lt;/sup&gt; is often buffered) as well as active transport mechanisms may alter the outcome of the Goldman equation slightly.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-20T06:00:07.857" LastActivityDate="2015-07-20T06:00:07.857" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36129" PostTypeId="2" ParentId="36126" CreationDate="2015-07-16T06:23:11.403" Score="1" Body="&lt;p&gt;For any dynamic system defined by different components, the steady state is the state of the system in which the components remain constant over time. If you consider the example of growth (by cell division) the point at which the total number of cells remain constant would be the steady state. This is a point at which &lt;strong&gt;birth rate = death rate&lt;/strong&gt;. Similarly for a multi-component system such as a gene and its activator, the steady state would be the point where the mRNAs and the proteins of the gene and its activator are constant. If only few components are constant then the system is said to be in a quasi-steady state. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A point to be noted that in chemical (or biochemical) systems steady state, as a term, is different from equilibrium (in physics these terms are used interchangeably). Equilibrium is a condition when, for a single reversible reaction, the forward rate = backward rate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In mathematical terms steady state is a point where the rate of change of components = 0. In an ordinary differential equations based model:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{d\bar{X}}{dt}=0 \\$$ &#xA;where $\bar{X}$ is a vector in which each element is a component of the system. In case of the transcription example, $X(1),X(2)..$ would be mRNA, protein, activator mRNA and so on. In other words $\dfrac{dX(i)}{dt}=0$ for all $i$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Steady state capabilities should mean the properties of the system at its steady state.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The kind of study described in the question is called &lt;a href=&quot;https://en.wikipedia.org/wiki/Flux_balance_analysis&quot; rel=&quot;nofollow noreferrer&quot;&gt;metabolic flux balance analysis&lt;/a&gt; in which different metabolic reactions are described in the form of linear equations represented by $Sv=0$ where $v$ is the vector of all fluxes (metabolic reaction rates) $S$ is the stoichiometry matrix (which has the stoichiometry of all components in different metabolic reactions). The RHS is zero because we are evaluating the system at its steady state i.e. we are interested in finding out the condition in which the net metabolic reaction flux is 0. In other words all metabolic reactions, balance each other. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;You need to read more about this. There are a lot of books on this topic. You can start with this &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108565/&quot; rel=&quot;nofollow noreferrer&quot;&gt;review&lt;/a&gt;.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In flux balance analysis, the linear equations are overdetermined i.e. there are many solutions. People generally use linear programming (simplex algorithm) to find optimal solutions. In the space of the optimal solutions, the vertices represent extreme reactions. The entire optimal solution space can be described as a linear combination of these extreme reactions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/GO0I5.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Schematic representation of a convex cone characterized by five&#xA;  extreme pathways. Extreme Pathways 1–5 (EP&lt;sub&gt;1&lt;/sub&gt;, EP&lt;sub&gt;2&lt;/sub&gt;, EP&lt;sub&gt;3&lt;/sub&gt;, EP&lt;sub&gt;4&lt;/sub&gt;, and EP&lt;sub&gt;5&lt;/sub&gt;)&#xA;  circumscribe the solution space for the three fluxes indicated (v&lt;sub&gt;A&lt;/sub&gt;,&#xA;  v&lt;sub&gt;B&lt;/sub&gt;, v&lt;sub&gt;C&lt;/sub&gt;). EP&lt;sub&gt;4&lt;/sub&gt; lies in the plane formed by fluxes v&lt;sub&gt;A&lt;/sub&gt; and v&lt;sub&gt;B&lt;/sub&gt;.&#xA;  Consequently, flux v&lt;sub&gt;C&lt;/sub&gt; does not participate in that extreme pathway.&#xA;  EP&lt;sub&gt;3&lt;/sub&gt;, EP&lt;sub&gt;4&lt;/sub&gt;, and EP&lt;sub&gt;5&lt;/sub&gt; are all close and represent different uses of a&#xA;  network to achieve a similar overall result. All points within the&#xA;  convex cone can be described as a non-negative linear combination of&#xA;  the extreme pathways &lt;a href=&quot;http://genome.cshlp.org/content/12/12/1889.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;sup&gt;[&lt;strong&gt;1&lt;/strong&gt;]&lt;/sup&gt;&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-07-16T06:23:11.403" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36130" PostTypeId="2" ParentId="35861" CreationDate="2015-07-16T06:45:16.490" Score="0" Body="&lt;p&gt;Urea is the major nitrogenous end product of protein metabolism, and its production reflects both the dietary intake of protein as well as the protein catabolic rate. The magnitude of these processes have a similar influence on urea concentration in the blood stream. Please note, that BUN, aka blood urea nitrogen is a misnomer, here plasma or serum urea nitrogen is meant and not the urea concentration in the red blood cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Urea biosynthesis from ammonia is carried out exclusively by liver via urea cycle. As explained above, dietary protein intake as well as the protein catabolism end up with a certain amount of ammonia which converted to urea in the liver. This is why, the higher the protein intake, the higher the urea concentration; the more protein disintegrated via catabolism, the higher the urea concentration. The excretion of urea is carried out mostly by kidneys in a certain (almost constant) rate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the positive nitrogen balance means that in the system there is an increase of “net storage” of nitrogen (and we deal with azotemia). The important point is - the urea metabolism is a continuous event where two processes are going in almost (but not absolute) parallel: the urea production (liver) and urea excretion (kidneys). There is a constant “delay” between the urea production and urea excretion and if the organism is in high protein intake and/or high protein catabolism rate this delay will bigger. On the other hand, the bigger the excessive amount of urea, the more urea is excreted until its concentration is normalized. If the urea production will decrease (normal protein intake, normal metabolism), the system will eventually excrete the excessive amount of urea and nitrogen balance will be around zero value (never will be absolute zero though).  So,  if the blood sample from an otherwise healthy individual is taken in the middle of the explained cycle (higher protein intake/catabolism), there will be a positive nitrogen balance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As can be seen from the explanation (I hope that it can), there is no contradictions between the clauses in the question. &lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-16T06:45:16.490" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36133" PostTypeId="1" AcceptedAnswerId="36135" CreationDate="2015-07-16T11:25:38.577" Score="3" ViewCount="2368" Body="&lt;p&gt;My question is regarding the biological nature of the separation between the vitreous humour and aqueous humour of the human (or mammal) eye. What connects the two in terms of the passive transport of proteins between the two? Is there a single membrane?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If so what is the name of this membrane and is it the only thing separating the aqueous from the vitreous? What is the anatomical difference between the aqueous and the vitreous?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apologies, I am far from a biologist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Specifically what sort of transport is arrow 9 in the figure below representing? And is backward transport (from the aqueous to the vitreous) possible?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any links to papers detailing this mechanism would be highly appreciated, I can only find references to experimental readings of concentrations, but nothing about the transport process itself.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/T7diT.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="9834" LastEditorUserId="9834" LastEditDate="2015-07-16T17:29:51.487" LastActivityDate="2018-08-27T13:35:24.747" Title="How are the vitreous humour and aqueous humour of the eye, connected?" Tags="&lt;eyes&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="36135" PostTypeId="2" ParentId="36133" CreationDate="2015-07-16T11:54:49.407" Score="4" Body="&lt;p&gt;Don't be confused by the word &quot;humour&quot;: the vitreous body is presented in birth and has very low &quot;exchange&quot; rate of its components, while aqueous is in constant turnover. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Secondly, the vitreous is an organ-like structure and is &lt;em&gt;separated&lt;/em&gt; from other eye structures by &lt;a href=&quot;https://en.wikipedia.org/wiki/Vitreous_membrane&quot; rel=&quot;nofollow noreferrer&quot;&gt;its membrane&lt;/a&gt;, while aqueous is fluid produced by ciliary body processes into the posterior chamber and moves  anteriorly throughout the pupil. Aqueous can move posteriorly in a case of trauma, operations and other non-physiologic states.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;ADD (after attachment of the image)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd correct some things in the scheme - call Vitreous as Vitreous, not Vitreous humour, change arrow pointing at the ciliary body as on the following image, depict the vitreous body membrane as I did. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/erwx4.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition learn two terms: Cloquet canal and Berger's space.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Number 9 shows a vitreo-aqueous route which will follow blood, drugs injected to the vitreous (not an only route), etc. &lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-07-16T17:59:09.933" LastActivityDate="2015-07-16T17:59:09.933" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36137" PostTypeId="1" CreationDate="2015-07-16T15:20:25.000" Score="3" ViewCount="84" Body="&lt;p&gt;I've been trying to research this question, but most if not all the on-line journals require costly subscription, and the studies that are posted look at tremor frequency with regards to other factors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question has to do with the tremor frequency, starting at early onset to later stages of Parkinson's disease - over the course of the disease, and without drug treatment (such as L-dopa), does the tremor frequency generally increase?&lt;/p&gt;&#xA;" OwnerUserId="9906" LastEditorUserId="9906" LastEditDate="2015-07-24T14:29:28.603" LastActivityDate="2015-08-15T21:08:19.000" Title="Does tremor frequency generally increase as Parkinson's disease progresses?" Tags="&lt;neuroscience&gt;&lt;pathology&gt;&lt;muscles&gt;&lt;neurophysiology&gt;&lt;synapses&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36138" PostTypeId="1" CreationDate="2015-07-16T15:49:46.330" Score="3" ViewCount="84" Body="&lt;p&gt;I am wondering how do genes become sex-biased? that is, how does a gene evolve expression which is regulated in a sex-specific manner (assuming no effect from sex-limited Y/W chromosomes).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand that gene duplication can lead to two sex-limited genes, the derived being expressed in one sex and the ancestral being expressed in the other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can the sex determining cascade cause sex-biased expression of a single locus?&lt;/strong&gt; My thinking is that upstream differences between males and females might bring about regulatory opportunity to loci under sexually antagonistic selection over expression level. For example, if males favour upregulation in a locus, males who evolve some kind of transcription factor affecting that locus which responds to male-specific isoforms of DSX (in &lt;em&gt;Drosophila&lt;/em&gt;), which could then cause the antagonistically selected locus to be more highly expressed in males without producing a negatively selected correlated response in females.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this correct? Are there other ways?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Note: I'm looking for a clear explanation of the mechanics behind sex biased gene expression. &lt;em&gt;Drosophila&lt;/em&gt; examples would be of particular worth)&lt;/p&gt;&#xA;" OwnerUserId="1590" LastActivityDate="2015-07-16T15:49:46.330" Title="How do sex biased genes evolve?" Tags="&lt;genetics&gt;&lt;gene-expression&gt;&lt;drosophila&gt;&lt;sex-determination&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36139" PostTypeId="2" ParentId="36112" CreationDate="2015-07-16T16:35:15.987" Score="3" Body="&lt;p&gt;The &lt;a href=&quot;https://en.wikipedia.org/wiki/Blood%E2%80%93brain_barrier&quot; rel=&quot;nofollow&quot;&gt;blood-brain barrier&lt;/a&gt; isn't a bag that surrounds the brain that you could puncture and then inject dopamine. It is a thin layer of cells around every blood vessel and capillary in the brain that mediate transfer of substances between the blood and the brain cells. As such, it is incredibly complex and branched (as complex and branched as the myriad blood vessels in the brain).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In theory, you could inject dopamine directly into the cells of the brain, inside the barrier. But, the dopamine wouldn't diffuse far, and so wouldn't affect anything except for a very small area (millimeters?) around the injection point. So, to get an even distribution of dopamine, you'd need to inject at thousands (millions? more?) of points throughout the brain, and do it repeatedly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And even with that, there's no guarantee that directly applying dopamine to the brain cells would actually help. In fact, bathing nerve cells in a neurotransmitter seems like a great way to mess up their signal transmission system.&lt;/p&gt;&#xA;" OwnerUserId="11620" LastEditorUserId="11620" LastEditDate="2015-07-16T22:18:57.440" LastActivityDate="2015-07-16T22:18:57.440" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36142" PostTypeId="2" ParentId="36124" CreationDate="2015-07-16T18:00:44.870" Score="4" Body="&lt;p&gt;Capillaries only transport blood for short distances, and within an organ. The blood supply to/from a major organ is generally carried over a few major blood vessels (usually one artery, one vein). Splicing such larger blood vessels are what surgeons earn their pay to do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of nerves, &lt;a href=&quot;http://www.quora.com/Surgery/How-do-transplanted-organs-function-without-nerve-connections&quot; rel=&quot;nofollow noreferrer&quot;&gt;most transplanted organs function fairly well without being connected to the CNS&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="11620" LastEditorUserId="11620" LastEditDate="2019-01-31T22:19:21.670" LastActivityDate="2019-01-31T22:19:21.670" CommentCount="2" ContentLicense="CC BY-SA 4.0" />
  <row Id="36145" PostTypeId="1" CreationDate="2015-07-16T23:03:25.883" Score="0" ViewCount="26" Body="&lt;p&gt;Have there been carbon fixation pathways of, in particular, oxygen-producing bacteria, that have been replicated in the lab or at least the enzymes for the pathways have been successfully produced in the lab?&lt;/p&gt;&#xA;" OwnerUserId="10401" LastActivityDate="2015-07-16T23:03:25.883" Title="Synthetic carbon fixation pathways" Tags="&lt;photosynthesis&gt;&lt;carbohydrates&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36146" PostTypeId="2" ParentId="36113" CreationDate="2015-07-16T23:13:05.230" Score="3" Body="&lt;p&gt;There are general guidelines for cross-linking protein-protein interactions, but specific parameters (i.e. cross-linker sub-types,  spacer length, linker concentration, reaction pH and temperature) are often determined experimentally. Common protein cross-linkers target reactive functional groups that are more likely found on the surface of the protein than in its &quot;active site&quot; or &quot;interface&quot; that is often buried.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given your relatively hydrophobic, non-reactive binging motif (Tyr/Pro/Met), if you do not need a large amount of cross-linked protein sample, then you could label it with photoactivatable amino acid such as &lt;a href=&quot;http://www.nature.com/nmeth/journal/v2/n4/full/nmeth752.html&quot; rel=&quot;nofollow&quot;&gt;L-photo-Met&lt;/a&gt;. Since Met is not often found on the surface, internal cross-linking would stabilize your protein and its binding partner.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you need a large amount of cross-linked protein (e.g. in mg) for further structural studies, labeling can be costly. You could possibly &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19622871&quot; rel=&quot;nofollow&quot;&gt;cross-link the protein (complex) crystal itself&lt;/a&gt; (since there were crystals as you mentioned), often just by glutaraldehyde. If the complex is there in the crystal, it would now be as solid as rock.&lt;/p&gt;&#xA;" OwnerUserId="9731" LastActivityDate="2015-07-16T23:13:05.230" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36149" PostTypeId="1" CreationDate="2015-07-17T01:57:24.893" Score="1" ViewCount="89" Body="&lt;p&gt;I'm not a biologist but I have an idea for a cure for cancer and it is very simple and probably has flaws (if it worked it probrably wouldn't be a cure for all) or is not possible but ... I'm still going to ask why because I want to learn why it doesn't work and I want to learn more in general, so you can use all the biology terms you like. The idea is essentially to use a virus and manipulate/change it (this would be mechanized if it were to be mass produced and the type of virus is unknown to me because you want one that is fast growing and goes across only specific parts of the body depending on the cancer). This virus would not have any bad parts (parts that make you sick) to it because when the virus &quot;injects&quot; it's DNA or manipulates the existing for copying it would instead manipulate the DNA in the cell it is going into to have growth limits and other cancer genes that are set to being back to normal and then copy itself. Eventually it would be fought off by the immune system and most of the virus would be gone (along with the cancer) because this virus would last for a long period of time (week(s)).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I appreciate anyone who answers this question because I'm sure it sounds stupid from your perspective but this is the place to learn.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks,&#xA;Jackson&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note: This is not an idea I'm trying to make, obviously, I just couldn't get it off my mind and wanted to see what is wrong and if it is fixable.&lt;/p&gt;&#xA;" OwnerUserId="16809" LastActivityDate="2015-07-17T15:10:31.327" Title="Why doesn't Manipulated Virus for Cancer Cure Work" Tags="&lt;pharmacology&gt;&lt;cancer&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2015-07-18T01:33:16.697" ContentLicense="CC BY-SA 3.0" />
  <row Id="36150" PostTypeId="1" AcceptedAnswerId="36163" CreationDate="2015-07-17T03:08:29.947" Score="1" ViewCount="2344" Body="&lt;p&gt;I have a time-dependent system of varying number of particles (~100k particles). In fact, each particle represents an interaction in a 3D space with a particular strength. Thus, each particle has (X,Y,Z;w) which is the coordinate plus a weight factor between 0 and 1, showing the strength of interaction in that coordinate. Here &lt;a href=&quot;http://pho.to/9Ztti&quot; rel=&quot;nofollow&quot;&gt;http://pho.to/9Ztti&lt;/a&gt; I have uploaded 10 real-time snapshots of the system, with particles are represented as reddish small dots; the redder the dot, the stronger the interaction is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The question is: how one can produce a 3D (spatial) density map of these particles, preferably in Matlab or Origin Pro 9 or ImageJ? Is there a way to, say, take the average of these images based on the red-color intensity in ImageJ?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since I have the numerical data for particles (X,Y,Z;w) I can analyze those data in other software as well. So, you are welcome to suggest any other analytical approach/software&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any ideas/comments are welcome!&lt;/p&gt;&#xA;" OwnerUserId="16810" LastActivityDate="2015-07-17T13:32:14.637" Title="How to create a 3D density map of a system of varying number of particles?" Tags="&lt;imaging&gt;" AnswerCount="3" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36151" PostTypeId="2" ParentId="36150" CreationDate="2015-07-17T03:26:09.937" Score="0" Body="&lt;p&gt;Trying to analyze that much data in ImageJ seems likely to end in frustration. Matlab is probably a more productive angle. Personally, I would use Python. Specifically, the numpy module. Try looking into the &lt;a href=&quot;http://docs.scipy.org/doc/numpy/reference/generated/numpy.histogramdd.html&quot; rel=&quot;nofollow&quot;&gt;histogramdd&lt;/a&gt; function in numpy. It might be able to accomplish what you're after.&lt;/p&gt;&#xA;" OwnerUserId="784" LastActivityDate="2015-07-17T03:26:09.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36152" PostTypeId="2" ParentId="28047" CreationDate="2015-07-17T03:26:16.047" Score="-1" Body="&lt;p&gt;Terminology involved makes everything lie a bit.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All the &quot;immortality&quot; and so complicate things a bit. We perceive life as life of our individual bodies. Thus if our body is immortal, that means that it is persistent, without us bothering about our individual cells.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But, there isn't any distinction like that in single cell organisms where cells themselves are taken as &quot;individuals&quot;. When cell divide, there isn't usually any distinction of which one is &quot;mother&quot; and which one is &quot;daughter&quot;. Both new cells are usually the same. So either it may seem that cells are immortal because they are not dying by old age, or that we define new cells as new individuals and thus the old one died to give birth of two new ones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But we could take certain aspect of this viewpoint on multicellular organisms as well. Our bodies are defacto created by very old cell-line (or in sexually engaged organism, two cell lines) and then this cell-line created vehicle for itself. From this viewpoint, which is not very different from viewpoint taken when speaking about these laboratory cell-lines, whole life is single cell-line. And from this point of view, life itself is immortal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the whole problem is that our point of view, on which we define immortality and individuals, is made only for special types of organism, as has no sense when speaking about single cell organisms. Immortality of cancer cells is thus only buzzword.&lt;/p&gt;&#xA;" OwnerUserId="16539" LastActivityDate="2015-07-17T03:26:16.047" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36153" PostTypeId="1" AcceptedAnswerId="36155" CreationDate="2015-07-17T04:31:51.307" Score="0" ViewCount="133" Body="&lt;p&gt;In a section of &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bit.260310611/abstract;jsessionid=859164671D3BA23A8D51FDEA4E7639E6.f01t04&quot; rel=&quot;nofollow&quot;&gt;this&lt;/a&gt; paper.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;However, if the question of independency is posed in the&#xA;  form: “Does each pathway shown define an independent&#xA;  genotype?,” then each of these three pathways is indeed&#xA;  independent. This is the way that MPS defines the independence&#xA;  of pathways.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What does “Does each pathway shown define an independent&#xA;genotype?,” mean?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="6307" LastEditDate="2015-07-17T05:07:01.487" LastActivityDate="2015-07-17T05:07:01.487" Title="What does &quot;each pathway define an independent genotype&quot; mean?" Tags="&lt;biochemistry&gt;&lt;bioinformatics&gt;&lt;metabolism&gt;&lt;pathway&gt;&lt;metabolomics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36154" PostTypeId="1" AcceptedAnswerId="36302" CreationDate="2015-07-17T04:44:45.600" Score="4" ViewCount="50438" Body="&lt;p&gt;I was under the impression the only signals neurons send using changes in membrane potential are action potentials. But my biology professor showed us diagrams of graded potentials and action potentials and to me they looked very similar.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the difference between a graded potential and an action potential?  &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="9943" LastEditDate="2015-07-22T13:19:49.273" LastActivityDate="2015-07-28T00:03:33.210" Title="What is the difference between a graded potential and an action potential?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;&lt;action-potential&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36155" PostTypeId="2" ParentId="36153" CreationDate="2015-07-17T05:01:56.967" Score="2" Body="&lt;p&gt;This is somewhat outside my field, but basically it seems they're defining the independence of the three hypothetical metabolic pathways in two different ways:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Mathematically the pathways are not independent since P₃ is a combination of P₁ and P₂. &lt;/li&gt;&#xA;&lt;li&gt;Biologically the pathways are independent since each requires a different combination of enzymes and therefore genes (the genotype). This is the method used in MPS. &lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Does that answer your question?&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-07-17T05:01:56.967" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36156" PostTypeId="2" ParentId="35903" CreationDate="2015-07-17T07:25:19.980" Score="3" Body="&lt;p&gt;Some suggestions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For identifying function do a homology search. There is little functional annotation of lncRNAs. So homology based information can be obtained only for protein sequences. So you can try these:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Check the coding potential. Find ORFs (perhaps set a minimum length cutoff). To be stringent you can also check for &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2241899/&quot; rel=&quot;nofollow&quot;&gt;Kozak consensus sequences&lt;/a&gt; (for eukaryotes) in these novel transcripts. &lt;a href=&quot;http://atgpr.dbcls.jp/&quot; rel=&quot;nofollow&quot;&gt;This&lt;/a&gt; program apparently includes the Kozak rule in start codon prediction.&lt;/li&gt;&#xA;&lt;li&gt;Translate the RNA and run &lt;a href=&quot;http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;amp;PAGE=Proteins&amp;amp;PROGRAM=blastp&amp;amp;RUN_PSIBLAST=on&quot; rel=&quot;nofollow&quot;&gt;psi-BLAST&lt;/a&gt;. Psi-BLAST is better than normal BLASTp in identifying distant homologs. &lt;/li&gt;&#xA;&lt;li&gt;You can obtain the GO (functional annotation) data for these homologs and relate them to your novel transcript.&lt;/li&gt;&#xA;&lt;li&gt;For lncRNAs, you can find if they overlap with any other known transcript. Many lncRNAs seem to have overlapping loci with their target genes (both sense/antisense).&lt;/li&gt;&#xA;&lt;li&gt;Search for RNA motifs. &lt;a href=&quot;http://www.nature.com/nature/journal/v499/n7457/full/nature12311.html&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; reports an extensive study towards identification of different RNA motifs (RBP binding sites) in humans and Drosophila. Other interesting motifs include &lt;a href=&quot;http://nar.oxfordjournals.org/content/early/2015/05/09/nar.gkv355.full&quot; rel=&quot;nofollow&quot;&gt;quadruplex forming motifs&lt;/a&gt; and &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013810/&quot; rel=&quot;nofollow&quot;&gt;ARE&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;If you have the genome sequence then you can map your transcripts to the genome and identify the introns. Actually your RNAseq assembly, if reference guided, would produce a GTF file. You can extract introns using the GTF. You may check for potential miRNAs in these introns, based on stem loop predictions. However it is better to have a small-RNAseq data for predicting miRNAs reliably.&lt;/li&gt;&#xA;&lt;li&gt;As you had already considered, you can check for miRNA binding sites. For this purpose &lt;a href=&quot;http://www.microrna.org/microrna/getDownloads.do&quot; rel=&quot;nofollow&quot;&gt;miRanda&lt;/a&gt; is the best for novel transcripts (TargetScan is a pain). You can use &lt;a href=&quot;http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/&quot; rel=&quot;nofollow&quot;&gt;RNAhybrid&lt;/a&gt; too and take a consensus of miRanda and RNAhybrid results.&lt;/li&gt;&#xA;&lt;li&gt;You can do other kinds of analysis based on just the sequence of the transcripts. These include checking for codon usage (for potential protein coding RNAs), GC richness (comparison with the known transcripts) etc.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-07-17T17:30:41.057" LastActivityDate="2015-07-17T17:30:41.057" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36157" PostTypeId="1" AcceptedAnswerId="36159" CreationDate="2015-07-17T08:24:21.410" Score="1" ViewCount="115" Body="&lt;p&gt;Background : Certain plants have been genetically engineered to have sense-antisense gene of a parasitic nematode. The dsRNA produced by the plant then inactivates the mRNA produced in the nematode, who, then isn't able to synthesize the corresponding protein and dies as a result. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Question : How is the dsRNA from the plant transfered to the nematode's cell ? By transformation ?&lt;/p&gt;&#xA;" OwnerUserId="3615" LastEditorUserId="3615" LastEditDate="2015-07-17T08:37:39.863" LastActivityDate="2015-07-17T08:51:40.900" Title="RNAi in nematode resistant plants" Tags="&lt;plant-physiology&gt;&lt;pathology&gt;&lt;biotechnology&gt;&lt;mrna&gt;&lt;rna-interference&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36159" PostTypeId="2" ParentId="36157" CreationDate="2015-07-17T08:39:35.790" Score="1" Body="&lt;p&gt;The question is little bit unclear: is in vitro or in vivo introduction in question?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In vivo:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;As the nematode feeds on the plant during its parasitic phase, it&#xA;  consequently assures the introduction of dsRNA and/or siRNA molecules&#xA;  into the nematode’s digestive system.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;in vitro introduction etc  -&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://journal.frontiersin.org/article/10.3389/fmicb.2014.00760/abstract&quot; rel=&quot;nofollow&quot;&gt;The status of RNAi-based transgenic research in plant nematology&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-07-17T08:51:40.900" LastActivityDate="2015-07-17T08:51:40.900" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="36161" PostTypeId="1" AcceptedAnswerId="36171" CreationDate="2015-07-17T09:49:40.813" Score="1" ViewCount="3524" Body="&lt;p&gt;Recently when my PCR reaction was running there was power fluctuation and the entire lab was blacked out for a few minutes and unfortunately PCR that I was running got switched off. So, would it be okay to restart the PCR? What would happen if the same PCR program was run again? &lt;/p&gt;&#xA;" OwnerUserId="16813" LastEditorUserId="948" LastEditDate="2015-07-18T04:18:14.613" LastActivityDate="2015-07-18T04:18:14.613" Title="What happens when we re-start a PCR reaction?" Tags="&lt;molecular-biology&gt;&lt;pcr&gt;&lt;polymerase&gt;" AnswerCount="2" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="36162" PostTypeId="2" ParentId="36161" CreationDate="2015-07-17T10:19:29.883" Score="1" Body="&lt;p&gt;In this case you can run your PCR for another 18 cycles (if your total number of cycles was 30). However, do the initial denaturation for 1-2min. You may run the same program again (full 30 cycles) but you'll just end up wasting time because after a point all the dNTPs and primers would be exhausted and further cycles will have no effect on the concentration of the amplicon.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-07-17T10:19:29.883" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36163" PostTypeId="2" ParentId="36150" CreationDate="2015-07-17T11:15:58.557" Score="1" Body="&lt;p&gt;R packages &lt;a href=&quot;https://cran.r-project.org/web/packages/misc3d/misc3d.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;code&gt;misc3d&lt;/code&gt;&lt;/a&gt; and &lt;a href=&quot;https://cran.r-project.org/web/packages/rgl/rgl.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;code&gt;rgl&lt;/code&gt;&lt;/a&gt;. The function &lt;code&gt;image3d&lt;/code&gt; in &lt;code&gt;misc3d&lt;/code&gt; does what you need and is very parametrizable via &lt;code&gt;rgl&lt;/code&gt; (change the transparency, the view angle, axes, etc...). I used it with fairly big arrays (~10000000 data points/plots) and it produced great 3D density plots.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both R (e.g. package &lt;code&gt;biOps&lt;/code&gt;) and Matlab (image processing toolbox) have very powerful tools for image analysis if you need to get for example RBG levels in your plots but as far as I understood, you have the 3D arrays containing the interaction values, right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Matlab proposes similar tools if you prefer Matlab (don't remember the exact functions) over R and both will require a fair amount of RAM as the data must be loaded in the environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As your system is time dependent you can also create movies fairly easily if you wish so (e.g. rgl's &lt;code&gt;movie3d&lt;/code&gt; function).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here a quick example of a 3D density plot:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/FqbW3.png&quot; alt=&quot;enter image description here&quot;&gt;&#xA;&lt;img src=&quot;https://i.stack.imgur.com/nXjZq.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="14826" LastEditorUserId="14826" LastEditDate="2015-07-17T11:52:48.047" LastActivityDate="2015-07-17T11:52:48.047" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="36164" PostTypeId="2" ParentId="36150" CreationDate="2015-07-17T13:32:14.637" Score="1" Body="&lt;p&gt;One approach: fit a &lt;a href=&quot;https://en.wikipedia.org/wiki/Kernel_density_estimation&quot; rel=&quot;nofollow noreferrer&quot;&gt;kernel density estimator&lt;/a&gt; to the observed coordinates $\{ (X_i,Y_i,Z_i) \}$ and color by density: &lt;a href=&quot;https://stackoverflow.com/questions/25286811/how-to-plot-a-3d-density-map-in-python-with-matplotlib/25354417#25354417&quot;&gt;https://stackoverflow.com/questions/25286811/how-to-plot-a-3d-density-map-in-python-with-matplotlib/25354417#25354417&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Incorporating the weights $w$ of each observation is a bit trickier, but there's code to do this: &lt;a href=&quot;https://stackoverflow.com/questions/27623919/weighted-gaussian-kernel-density-estimation-in-python/27623920#27623920&quot;&gt;https://stackoverflow.com/questions/27623919/weighted-gaussian-kernel-density-estimation-in-python/27623920#27623920&lt;/a&gt; , which you can swap in instead of &lt;code&gt;stats.gaussian_kde&lt;/code&gt;.&lt;/p&gt;&#xA;" OwnerUserId="16808" LastEditorUserId="-1" LastEditDate="2017-05-23T12:35:01.883" LastActivityDate="2015-07-17T13:32:14.637" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36165" PostTypeId="1" CreationDate="2015-07-17T14:04:02.353" Score="-2" ViewCount="56" Body="&lt;p&gt;Let's think ProteinA can phosphorylate proteinB, proteinC and proteinD.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Condition1: All proteins are expressed and proteinA phosphorylates proteinB, proteinC and proteinD. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Condition2: Only proteinA and proteinB are expressed for that reason protein A phosphorylates only proteinB.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which is more realistic?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) In condition1; proteinB, proteinC and proteinD will be 3 times less phosphorylated in comparison to proteinB in condition2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The proteins of both conditions will be phosphorylated same.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cheers&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cankut&lt;/p&gt;&#xA;" OwnerUserId="16814" LastActivityDate="2015-07-17T21:04:51.143" Title="Phosphorylation capacity of an enzyme" Tags="&lt;proteins&gt;&lt;phosphorylation&gt;" AnswerCount="1" CommentCount="7" ClosedDate="2015-07-19T15:20:30.817" ContentLicense="CC BY-SA 3.0" />
  <row Id="36167" PostTypeId="2" ParentId="36149" CreationDate="2015-07-17T15:10:31.327" Score="1" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;This is not an idea I'm trying to make, obviously, I just couldn't get it off my mind and wanted to see what is wrong and if it is fixable.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Since everybody else is giving you a bad attitude in the comments...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;While it &lt;em&gt;might&lt;/em&gt; work for some cancers, it is completely impractical for the majority of cancers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;SOME&lt;/strong&gt; cancers do occur because of a specific mutation or specific set of mutations. Some genes predispose people to greater risk for certain cancers. These have a much greater chance of being treatable via viral therapy, but there are still barriers:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The length of coding material (DNA or RNA) a retrovirus can hold and propagate is limited. The mutated gene or stretch of DNA may be much larger than the length a retrovirus could potentially replace.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The retroviral material is not guaranteed to &quot;rewrite&quot; or &quot;overwrite&quot; any bad DNA. Retroviral DNA is inserted fairly randomly into the host genome with little regard for where since it is generally an entire gene meant to be read in its entirety to eventually produce proteins. You'd expect &lt;strong&gt;BOTH&lt;/strong&gt; gene versions to exist simultaneously. This wouldn't end in a cure, but some middleground between cured and affected. &lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There are tissues where cancers develop that wouldn't be infected. Any sort of brain tumor would remain completely untouched by retroviral therapy, for example.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Targeting specific cancerous tissues while leaving surrounding or other tissues alone is a big problem, even for non-retroviral therapies. Replacing bad genes in a cancerous cell is good, but replacing good genes in a healthy cell could lead to that cell's death or -- ironically -- possibly turn it into a cancerous cell as well.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The majority of cancers are not specific mutations and do not have known genes that predispose their bearers. The majority are an accumulation of mutations across sections of the genome. As MattDMo said in the comments (paraphrased): For these cancers, viral therapy is nearly impossible. Every mutated gene would required its own retrovirus. At that point, the time and financial investments start to rise exponentially. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;While I'm not one to say it's impossible (&lt;em&gt;I'm not involved in the research, so if anybody who is can correct me on anything in this post, I'd appreciate it&lt;/em&gt;) -- it is certainly very improbable with current knowledge and methods. Every bullet point above (which isn't an exhaustive list) represents a mountain to climb on hands and knees before an &quot;inject-and-forget&quot; end product could be developed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kudos for the critical thinking and forming a working theory from the knowledge you had, but unfortunately it does break down with some more specialized information.&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2015-07-17T15:10:31.327" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36168" PostTypeId="1" CreationDate="2015-07-17T15:50:00.893" Score="2" ViewCount="56" Body="&lt;p&gt;Algae are a source of taurine and mushrooms are a source of vitamin D3. Both also contain high protein. So, it seems possible to feed a cat or other felines without any meat. Are there any concerns to have them live with this kind of diet?&lt;/p&gt;&#xA;" OwnerUserId="9910" LastEditorUserId="6307" LastEditDate="2015-07-17T16:39:53.093" LastActivityDate="2015-07-17T16:39:53.093" Title="Could felines live without meat?" Tags="&lt;nutrition&gt;&lt;diet&gt;&lt;feline&gt;&lt;vegetarianism&gt;" AnswerCount="0" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36171" PostTypeId="2" ParentId="36161" CreationDate="2015-07-17T17:47:16.083" Score="2" Body="&lt;p&gt;The polymerase used in PCR is extremely stable at room temperature. I would expect you to be able to continue your PCR reaction from the cycle it was stopped at without too much trouble. However, it is important to not over cycle your product. This will produce non-specific products. If a clean result is imperative, take a 1-5ul sample from your original reaction to use as a template in a new reaction.&lt;/p&gt;&#xA;" OwnerUserId="16816" LastActivityDate="2015-07-17T17:47:16.083" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36173" PostTypeId="1" AcceptedAnswerId="36304" CreationDate="2015-07-17T19:46:02.117" Score="5" ViewCount="261" Body="&lt;p&gt;I sometimes wonder how many different individual musical scales could be perceived by human ears. I define a musical scale as a collection of notes that relate to some fundamental frequency by specific ratios. For instance&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;do $2^{0}f$&lt;/li&gt;&#xA;&lt;li&gt;re $2^{\frac{1}{6}}f$&lt;/li&gt;&#xA;&lt;li&gt;mi $2^{\frac{1}{3}}f$&lt;/li&gt;&#xA;&lt;li&gt;fa $2^{\frac{5}{12}}f$&lt;/li&gt;&#xA;&lt;li&gt;sol $2^{\frac{7}{12}}f$&lt;/li&gt;&#xA;&lt;li&gt;la $2^{\frac{9}{12}}f$&lt;/li&gt;&#xA;&lt;li&gt;ti $2^{\frac{11}{12}}f$&lt;/li&gt;&#xA;&lt;li&gt;do $2^{1}f$&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;I once did an experiment where I took various sine waves at different frequencies and multiplied them by the appropriate ratios. I found for the ones I tried that I did indeed heard the major scale. But a mathematician will look at the positive real numbers $\Bbb{R}^+$ and say there are an infinite, uncountable number of possible frequencies. However, Biologically I cannot imagine the human ear is capable of distinguishing between an infinite number of frequencies.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the biological limit on hearing resolution? Is there a way to estimate how many different major scales one can hear? In other words, how many different frequencies can be heard? &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="9943" LastEditDate="2015-07-22T14:02:02.220" LastActivityDate="2015-07-23T00:31:34.607" Title="What is the biological limit on hearing resolution?" Tags="&lt;neurophysiology&gt;&lt;sensation&gt;&lt;hearing&gt;&lt;psychophysics&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36174" PostTypeId="2" ParentId="36165" CreationDate="2015-07-17T21:04:51.143" Score="2" Body="&lt;p&gt;Don't be discouraged. At least &lt;em&gt;in vitro&lt;/em&gt;, if there is ample chemical substrates (e.g. ATP) and protein A (i.e. kinase) remains active, the kinase will just keep phosphorylating its protein substrates (B alone or a mixture of B, C, D) until the substrates are depleted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, all substrates will be phosphorylated eventually. The contrived Condition 1 may occur only if you only supply enough ATP for A to phosphorylate one mol equivalent of its protein substrate AND A has exactly the same catalytic efficiency toward B, C, and D that are present in equal amount. Of course, any or all of B/C/D may have more than one phosphorylation sites, each of which has its own phosphorylation rate.&lt;/p&gt;&#xA;" OwnerUserId="9731" LastActivityDate="2015-07-17T21:04:51.143" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36176" PostTypeId="1" CreationDate="2015-07-17T22:37:16.580" Score="1" ViewCount="755" Body="&lt;p&gt;I am attempting to validate existence of a transcript using 40 cycle qPCR. I designed primers for a unique feature of this transcript, and also designed primers for a sequence in the transcript that is common to several transcripts of this gene, and finally I used GAPDH as a control. I already knew beforehand that this transcript has very low expression. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the unique region, my ct values for primer 1 were between 31-34.8, and my ct values for primer2 and primer 3 were all consistently 35, and primers 4-6 gave no result at all. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For the region that is common to several transcripts of this gene, the ct values were between 30-34 for one primer, and consistently 35 for another primer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For GAPDH, ct values were around 22. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can I use these results to indicate that my transcript exists (or even may exist?) in the samples I tested? Is the fact that the ct values for the region unique to the transcript I am targeting and the region in common between several transcripts are quite close indicative of anything? On the graph from the qPCR, there are distinct rises respectively around 33 and 35 for the unique region amplicon. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT: I was doing a bit more research, and it appeared that this study: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296690/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296690/&lt;/a&gt;&lt;br&gt;&#xA;also had results that came up &quot;late cp call last five cycles has higher uncertainty&quot; and considered these results positive if they could be replicated in a duplicate - if I were to show this as well, can I use this data in a paper?&lt;/p&gt;&#xA;" OwnerUserId="8704" LastEditorUserId="8704" LastEditDate="2015-07-17T22:45:39.017" LastActivityDate="2015-07-17T22:45:39.017" Title="Interpretation of qPCR results for low expression genes" Tags="&lt;bioinformatics&gt;&lt;gene-expression&gt;&lt;lab-techniques&gt;&lt;pcr&gt;" AnswerCount="0" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="36177" PostTypeId="1" CreationDate="2015-07-17T19:24:52.023" Score="16" ViewCount="2106" Body="&lt;p&gt;Membranes of our cells consist of lipid bilayer (with some other components mixed in).  Why wouldn't those lipid bilayers glue to each other and make the cells merge? If you suppose that it's due to additional components in the membrane that prevent them from gluing together, consider the case of liposomes, which don't contain additional components, but seemingly don't glue as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm primarily interested in quantitative physical chemistry aspect of the matter.&lt;/p&gt;&#xA;" OwnerUserId="16123" OwnerDisplayName="Bob" LastEditorUserId="16123" LastEditDate="2015-07-18T06:49:50.090" LastActivityDate="2015-07-18T12:03:39.267" Title="Why don't our cells merge when their phospholipid membranes touch each other?" Tags="&lt;biophysics&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36178" PostTypeId="2" ParentId="36177" CreationDate="2015-07-17T21:33:47.907" Score="0" Body="&lt;p&gt;I think lipid membranes in mutual contact do in some cases merge, search liposomes. However, this does not always happen, because the membranes have some degree of cohesiveness and quasi-rigidity. This is said to be due to hydrophobic effect - in aqueous environment, the lipid molecules are repelled from water molecules as the latter attract each other much more strongly than lipid molecules do (water molecules are polar + they experience hydrogen bonding).&lt;/p&gt;&#xA;" OwnerDisplayName="Ján Lalinský" LastActivityDate="2015-07-17T21:33:47.907" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36179" PostTypeId="2" ParentId="36177" CreationDate="2015-07-17T23:41:07.003" Score="22" Body="&lt;p&gt;Phospholipid bilayers found in cells are usually negatively charged. The phosphate groups repel each other by like charges and prevent two membranes from coming too close to each other. Membranes are also full of proteins and often coated with carbohydrates, which serve to keep membranes from interacting too strongly. See this diagram of a membrane bilayer:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/2dIqg.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even this diagram is probably cleaned up.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From a more physical chemistry perspective, the energy barrier for flipping a lipid in a bilayer is pretty high, since the polar head group doesn't like passing through the hydrophobic layer. Bringing two membranes together would require overcoming the charge-charge repulsion and flipping around the inner two layers of lipids, so you go from 4 layers to 2.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, there are mechanisms for fusing membranes, such as using &lt;a href=&quot;http://www.lifetechnologies.com/us/en/home/references/gibco-cell-culture-basics/transfection-basics/gene-delivery-technologies/cationic-lipid-mediated-delivery/how-cationic-lipid-mediated-transfection-works.html&quot;&gt;cationic lipids&lt;/a&gt;. These would turn charge repulsion into charge attraction. The lipid ion pairs tend to have shapes that don't support bilayer formation, and tend to prefer micelle or inverted micelle shapes. These have been utilized to break down vesicle membranes and allow large molecules to pass through, like DNA or proteins, and are used in genetic modification of cells.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2015-07-17T23:41:07.003" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36181" PostTypeId="1" AcceptedAnswerId="94271" CreationDate="2015-07-18T02:44:27.057" Score="5" ViewCount="2508" Body="&lt;p&gt;I'm curious what plant this is! I found it at &lt;a href=&quot;https://www.google.com/maps/place/37%C2%B052&amp;#39;23.2%22N+122%C2%B016&amp;#39;55.3%22W/@37.873124,-122.282019,190m&quot; rel=&quot;noreferrer&quot;&gt;37°52'23.2&quot;N 122°16'55.3&quot;W&lt;/a&gt; (north of Oakland, California, USA).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/0IqZr.jpg&quot; alt=&quot;mystery plant&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16822" LastEditorUserId="6307" LastEditDate="2015-07-18T02:53:25.740" LastActivityDate="2020-06-20T17:18:17.253" Title="Which plant is this?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36182" PostTypeId="2" ParentId="35738" CreationDate="2015-07-18T05:05:21.747" Score="3" Body="&lt;p&gt;To build on busukxuan's answer, there are a lot of single-celled organism responses that kind of resemble memory:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.pnas.org/content/109/43/17490.short&quot; rel=&quot;nofollow&quot; title=&quot;Slime mold uses an externalized spatial &amp;#39;memory&amp;#39; to navigate in complex environments&quot;&gt;Slime mold uses an externalized spatial 'memory' to navigate in complex environments&lt;/a&gt; - essentially, a slime mold leaves behind a trail, which it then avoids, allowing it to avoid where it has traveled in the past.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you apply a periodic stimulus to Physarum, it will anticipate the next stimulus: &lt;a href=&quot;http://www.nature.com/news/2008/080123/full/451385a.html&quot; rel=&quot;nofollow&quot;&gt;Popular, openly accessible summary&lt;/a&gt; &lt;a href=&quot;http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.100.018101&quot; rel=&quot;nofollow&quot;&gt;Paywalled journal article&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the amoeba Dictyostelium sees an increasing cAMP gradient, it will follow that gradient - and then be less sensitive to a reversal in the gradient: &lt;a href=&quot;http://www.pnas.org/content/111/40/14448.short&quot; rel=&quot;nofollow&quot;&gt;Cellular memory in eukaryotic chemotaxis&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, even bacteria have some memory - they can figure out whether or not they are going up a chemoattractant gradient by making a comparison with the signal they observed a few seconds ago: &lt;a href=&quot;http://www.pnas.org/content/83/23/8987.short&quot; rel=&quot;nofollow&quot;&gt;Temporal comparisons in bacterial chemotaxis&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8780" LastActivityDate="2015-07-18T05:05:21.747" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36183" PostTypeId="2" ParentId="36181" CreationDate="2015-07-18T05:27:52.570" Score="9" Body="&lt;p&gt;It looks a lot like Queen Anne's Lace, but yellow and with more slender leaves. I believe it's Sweet Fennel (Foeniculum vulgare). It's in the &lt;a href=&quot;https://en.wikipedia.org/wiki/Apiaceae&quot; rel=&quot;noreferrer&quot;&gt;Apiaceae family&lt;/a&gt;, which has a &lt;em&gt;lot&lt;/em&gt; of edibles: carrots, parsley, fennel, anise, caraway, celery, chervil, cicely, cilantro, cumin, dill, parsnips and more. Black swallowtail butterflies lay their eggs on this, so often you can find a really fine caterpillar on them; bees like the flowers as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Apiaceae has 3,700 species spread across 434 genera; it is the 16th-largest family of flowering plants. It has a few poisonous plants, like water hemlock (white flower) and poison hemlock (also white). Wild parsnip has a very similar yellow flower but it's sap is wildly irritating in the medical sense (it will cause pain and blisters); its leaves are very different. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qAVMI.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you crush some of the slender leaves between your fingers, it should smell like fennel (a common spice, e.g. in Italian sausage), or if you aren't familiar with that, a bit licorice-like.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/PP6gZm.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/H1hXjm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sweet fennel (left, up to 6 feet tall)        &lt;a href=&quot;http://www.nyis.info/user_uploads/files/Wild%20Parsnip%20-%20PA%20DNR.pdf&quot; rel=&quot;noreferrer&quot;&gt;Wild Parsnip&lt;/a&gt; (right, 3-5 feet tall)&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-07-18T05:34:36.040" LastActivityDate="2015-07-18T05:34:36.040" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="36184" PostTypeId="2" ParentId="36051" CreationDate="2015-07-18T05:31:26.417" Score="6" Body="&lt;p&gt;Here's a bit of additional information (Although there's an answer from Ilan that satisfied you.)&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Is it the mould itself that makes us sick or is it something that the&#xA;mould is releasing?&lt;/p&gt;&#xA;&lt;p&gt;What are the mechanisms that cause us to feel sick after eating mouldy&#xA;food?&lt;/p&gt;&#xA;&lt;p&gt;The USDA says that there can also be bacteria along with the mould on&#xA;the the food - is this what is really making us feel ill?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;There are two things to consider.&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Food infection : bacteria or other microbes that infect the body after consumption&lt;/li&gt;&#xA;&lt;li&gt;Food intoxication : ingestion of toxins contained within the food (includes modls), including bacterial produced exotoxins&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;Majority of food poisoning is caused by bacteria, viruses, and parasites rather than toxic substances in the food. e.g. Staphylococcus aureas, salmonella, Bacillus cereus, three common types of &lt;strong&gt;bacteria&lt;/strong&gt; that can lead to food poisoning.&lt;/p&gt;&#xA;&lt;p&gt;Molds are neither plant or an animal. They are microscopic fungi. Some food molds produce toxins that cause allergic reactions and respiratory problems. And a few molds in the right conditions, around the Mycelleum,  &lt;strong&gt;Mycotoxins&lt;/strong&gt; are produced; poisonous substances that can make you ill. Mycotoxins also tend to affect more biological systems in our body than do pesticides or heavy metals, partly because fungi have the ability to dodge our immune system by rapidly mutating, while at the same time producing chemicals that suppress our immune system. (&lt;em&gt;You will find more information &lt;a href=&quot;http://cmr.asm.org/content/16/3/497.full&quot; rel=&quot;noreferrer&quot;&gt;Mycotoxins here.&lt;/a&gt;&lt;/em&gt;)&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Mycotoxins&lt;/strong&gt; as a group cannot be classified according to their mode of action, toxicology or metabolism. These vary according to the different chemical structures, sensitivity of the species to the toxin and also factors such as sex, age, health and diet. There are a large number of mycotoxins with a great diversity in their mode of action. Additionally, additive and synergistic effects can occur in the presence of two or more mycotoxins. Following there are the most important mycotoxins and their mode of actions, toxicology and metabolism as well as main symptoms and target organs. (&lt;a href=&quot;http://www.mycotoxins.info/myco_info/science_moa.html&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;This link explains in great detail&lt;/em&gt;.&lt;/a&gt;)&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;» Aflatoxins (discussed above by Ilan)&lt;/li&gt;&#xA;&lt;li&gt;» Trichothecenes&lt;/li&gt;&#xA;&lt;li&gt;» Ochratoxins&lt;/li&gt;&#xA;&lt;li&gt;» Fumonisins&lt;/li&gt;&#xA;&lt;li&gt;» Zearalenone&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Ochratoxin A (OTA) is a carcinogenic compound produced by several species of molds, such as Aspergillus and Penicillium, found in a wide range of foods, including cereals, dried fruits, coffee, cocoa products, wine, grape juice, beer, liquorice, blood products, baby foods and spices.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://nutritionreview.org/2015/03/mold-toxin-in-cereals-coffee-and-wine-inhibits-cell-regeneration-in-adult-mammalian-brains/&quot; rel=&quot;noreferrer&quot;&gt;New studies confirm Ochratoxin A inhibits Neurogenesis(the formation of new neurons in the brain).&lt;/a&gt; Other than that, its toxicological effects include nephro-&#xA;toxicity, nephrocarcinogenicity and immunotoxicity as well.&lt;/p&gt;&#xA;&lt;p&gt;Aspergillus on Bread - Mold.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/f3ifh.jpg&quot; alt=&quot;Aspergillus on Bread - Mold&quot; /&gt;&lt;/p&gt;&#xA;&lt;p&gt;The molds that we see on the surface of the food is just a &lt;em&gt;tip of the ice berg&lt;/em&gt;. It is an &lt;em&gt;invader&lt;/em&gt;, whose roots like threads may have gone deep down entire food (&lt;a href=&quot;https://en.wikipedia.org/wiki/Penicillium_roqueforti&quot; rel=&quot;noreferrer&quot;&gt;although some says bleu cheese with mold is edible&lt;/a&gt;). Growing right along with mold are what are called &lt;a href=&quot;http://www.niaid.nih.gov/topics/antimicrobialresistance/examples/gramnegative/Pages/default.aspx&quot; rel=&quot;noreferrer&quot;&gt;&amp;quot;gram negative&amp;quot; &lt;em&gt;(e.g. Escherichia coli)&lt;/em&gt; and &amp;quot;gram positive&amp;quot; bacteria.&lt;/a&gt; Just like mold, they require moisture and organic material to thrive and are often found growing in the same places as mold, and the synergistic action between mold and bacteria further worsen inflammatory health conditions. Oftentimes, those bacterial infections occuring alongside fungal infections make treatment more complicated.&lt;/p&gt;&#xA;" OwnerUserId="8709" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-07-18T16:24:38.037" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36185" PostTypeId="1" CreationDate="2015-07-18T05:46:29.350" Score="2" ViewCount="160" Body="&lt;p&gt;In the biochemistry book I'm reading (Box 10-1, Lehninger Principles of Biochemistry), an example is given in whales of how spermaceti (a wax located in the whale head), when at sea level is a liquid, and allows the whale to float due to its buoyancy. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the whale dives deeper, the wax turns into a solid (due to the colder temperatures), and hence this more dense wax is less buoyant and prevents the whale from floating back up due to the greater density of the seawater at these depths.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My limited understanding is that density effects buoyancy in so far as that the weight of the object displaces an equivalent weight of water. If the quantity of the water displaced is small enough that the surface area of the object isn't completely submerged, it can float.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now with the whale example, considering the wax is fully enclosed by the head, how would this change in local density effect the buoyancy of the whale as a whole? The weight of the wax still remains the same (in so far as the example used in the book), the only thing that changes is its density inside the whale.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So with a constant weight, and only a variable local density enclosed by an object (the head) and limited to these conditions only (as this is all the example in the book uses), how is this possible?&lt;/p&gt;&#xA;" OwnerUserId="15295" LastActivityDate="2015-07-18T05:46:29.350" Title="How spermaceti makes a whale float" Tags="&lt;biophysics&gt;" AnswerCount="0" CommentCount="14" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36188" PostTypeId="2" ParentId="36177" CreationDate="2015-07-18T12:03:39.267" Score="1" Body="&lt;p&gt;well it's based on the tissue type for example take loose connective tissue which lies under epithelium they don't merge because of the profound matrix separating them while in the epithelium in cuboidal and columnar epithelium at side corner and upper portion of their membranes the two neighboring cells fused completely preventing any flow of material whatever may be the size it's called tight junction and is due to the physical change in lipid layer of both cell causing this adherence.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;or if by merging you mean that the cells should remove their barriers (side membranes) to make their self one cell it is also depending on tissue like macro phages becoming giant cells by merging and forming one cell.   &lt;/p&gt;&#xA;" OwnerUserId="5700" LastActivityDate="2015-07-18T12:03:39.267" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36189" PostTypeId="1" AcceptedAnswerId="36193" CreationDate="2015-07-18T12:32:42.230" Score="4" ViewCount="2985" Body="&lt;p&gt;Why can't plasma proteins shift from capillaries to connective tissue but WBCs can be very rich in connective tissue even though obviously the WBCs had to go through capillaries.  Another example: in alveolar sacs neutrophils are there in the lumen  despite the presence of epithelia of alveolar sacs,  and it can only reach there via capillaries. So, how can they get into lumen despite the epithelia lining? Histology textbooks say that no plasma proteins can enter or leave capillaries, but WBCs (which are much larger than proteins) can move to connective tissue via capillaries?&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="231" LastEditDate="2015-07-18T16:03:53.347" LastActivityDate="2016-10-19T18:00:01.867" Title="Why can't plasma proteins migrate from capillaries?" Tags="&lt;histology&gt;" AnswerCount="3" CommentCount="3" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36190" PostTypeId="2" ParentId="36154" CreationDate="2015-07-18T12:50:03.337" Score="5" Body="&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/QCvy3.jpg&quot; alt=&quot;Graded potential&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Graded potentials are initiated by a stimulus that vary in magnitude depending on the strength of the stimulus. (The stronger the stimulus the more gated channels open causing larger depolarisation). Graded potentials occur in dendrites, cell bodies and sensory receptors. Graded potentials dissipate with distance from stimulus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/jtv0v.jpg&quot; alt=&quot;Action Potential&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the other hand, action potentials occur when graded potentials reach the axon hillock at a certain level of depolarisation (around -55mV). This opens the activation gate letting sodium flood into the membrane. This is an &quot;all or nothing&quot; event, once the threshold triggers the membrane depolarises quickly to around +30mV.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could just save you time and show you this table:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/8fnAS.jpg&quot; alt=&quot;Comparison of Graded Potentials and Action Potentials (2011 Pearson Education)&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16731" LastActivityDate="2015-07-18T12:50:03.337" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36191" PostTypeId="2" ParentId="36189" CreationDate="2015-07-18T16:54:16.587" Score="1" Body="&lt;p&gt;Generally, for plasma proteins to enter the tissue space, they must be able to passively diffuse out of the vessel into the tissue. This requires sufficiently large gaps between the endothelial cells of the vessel wall (and if passing into the lumen, space between the epithelial cells forming the barrier of entry into the lumen.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, under the proper circumstances, white blood cells can actively invade the tissue across the endothelial barrier, migrate through the tissue, and may even cross over into the tissue lumen. This is a active, highly coordinated process  allowing the white blood cell to bind the endothelium and push its way through a gap and allowing it to bind extracellular matrix proteins to migrate through the tissue to its destination.&lt;/p&gt;&#xA;" OwnerUserId="16147" LastActivityDate="2015-07-18T16:54:16.587" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36192" PostTypeId="1" AcceptedAnswerId="36196" CreationDate="2015-07-18T17:03:34.537" Score="3" ViewCount="95" Body="&lt;p&gt;According to the &lt;a href=&quot;http://apps.who.int/iris/bitstream/10665/42716/1/9241546123.pdf?ua=1&quot; rel=&quot;nofollow&quot;&gt;WHO publications&lt;/a&gt; biotin is a thing we need. Although its non toxic, so you can't get too much.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, excluding a few (small) lists that deal exclusively with biotin content there doesn't generally seem to be any information on how much of it given foods contain. For instance this page gives a very impressive &lt;a href=&quot;http://nutritiondata.self.com/facts/fruits-and-fruit-juices/1934/2&quot; rel=&quot;nofollow&quot;&gt;summary of a kiwi&lt;/a&gt;, but there is no mention of biotin.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If this is something we need, why is it not normally listed? &lt;/p&gt;&#xA;" OwnerUserId="16829" LastActivityDate="2015-07-18T19:31:21.650" Title="Why is it so hard to find the amount of biotin in food?" Tags="&lt;nutrition&gt;&lt;health&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-07-20T05:07:50.020" ContentLicense="CC BY-SA 3.0" />
  <row Id="36193" PostTypeId="2" ParentId="36189" CreationDate="2015-07-18T17:34:28.700" Score="6" Body="&lt;p&gt;Cells of the endothelium are joined by tight cell junctions which are impermeable or selectively permeable. Generally, proteins can only migrate through the endothelium via active transcytosis.&lt;/p&gt;&#xA;&lt;p&gt;Leukocytes (specifically neutrophils, lymphocytes and monocytes) express various adhesion molecules and cytokine receptors which allow them to interact with endothelial cells and facilitate their movement (diapedesis) either between (paracellular) or through (transcellular) the cells. The process of leukocytes leaving the endothelial lumen is known as extravasation.&lt;/p&gt;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/g1J94.jpg&quot; alt=&quot;enter image description here&quot; /&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://jcs.biologists.org/content/122/17/3025.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Carman CV. 2009. Mechanisms for transcellular diapedesis: probing and pathfinding by `invadosome-like protrusions'. J Cell Sci 122:3025-3035.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;(C,D) The process of diapedesis, whether during intravasation or extravasation, can occur by two distinct pathways: paracellular or transcellular. (C) Paracellular diapedesis. Leukocytes and endothelial cells coordinately disassemble endothelial cell-cell junctions and open up a gap between two or more endothelial cells (Muller, 2003). (D) Transcellular diapedesis. Leukocytes migrate directly through individual endothelial cells via a transient transcellular pore that leaves endothelial cell-cell junctions intact. Note that the two individual endothelial cells in C and D are distinguished by different shades of pink.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-07-20T05:53:57.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36194" PostTypeId="1" AcceptedAnswerId="36205" CreationDate="2015-07-18T18:09:40.107" Score="1" ViewCount="6728" Body="&lt;p&gt;I am reading about scorpion venoms and toxins for my bio class and they appear to have a variety of potassium channel blockers. My professor asked &quot;What effect would this have on a neuron?&quot; and naturally two things came to mind &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Potassium channels are necessary for repolarization &lt;/li&gt;&#xA;&lt;li&gt;Potassium channels participate in controlling the concentration gradient of the cell. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;I have found evidence in articles supporting the first claim, but I don't know much about the second. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Do potassium channel blockers affect the resting membrane potential?  Would they significantly alter the concentration gradient? &lt;/p&gt;&#xA;" OwnerUserId="11652" LastActivityDate="2015-07-23T02:02:20.823" Title="Do potassium channel blockers affect the resting membrane potential?" Tags="&lt;toxicology&gt;&lt;action-potential&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36195" PostTypeId="1" AcceptedAnswerId="36308" CreationDate="2015-07-18T18:14:05.320" Score="4" ViewCount="865" Body="&lt;p&gt;Potassium channels help to repolarize the cell after depolarization. But if the potassium channels are blocked, potassium ions cannot flow out of the cell to increase the membrane potential. Thus, one would expect that, at least for some period of time, the cell would be &quot;stuck&quot; in a depolarized state. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How long can this state last? Can a neuron go on indefinitely in a depolarized state if potassium ion channels are blocked? Will it find some other way to depolarize the cell? Will the cell die? &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="9943" LastEditDate="2015-07-22T20:42:47.557" LastActivityDate="2015-07-22T20:42:47.557" Title="If a blocker prevents repolarization, will the neuron be stuck in a depolarized state forever?" Tags="&lt;pharmacology&gt;&lt;action-potential&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36196" PostTypeId="2" ParentId="36192" CreationDate="2015-07-18T19:31:21.650" Score="1" Body="&lt;p&gt;Apparently, it's really hard to measure biotin levels in food accurately.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From &quot;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1450323/pdf/nihms-9393.pdf&quot; rel=&quot;nofollow&quot;&gt;Determination of the biotin content of select foods using accurate&#xA;and sensitive HPLC/avidin binding&lt;/a&gt;&quot; (2004, emphasis added):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Total biotin content of 87 foods was determined using acid&#xA;  hydrolysis and the HPLC/avidin-binding assay. These values are consistent with published values&#xA;  in that meat, fish, poultry, egg, dairy, and some vegetables are relatively rich sources of biotin.&#xA;  However, these biotin values disagreed substantially with published values for many foods. Assay&#xA;  values varied between 247 times greater than published values for a given food to as much as 36%&#xA;  less than the published biotin value. Among 51 foods assayed for which published values were&#xA;  available, only seven agreed within analytical variability (720%). &lt;strong&gt;We conclude that published values&#xA;  for biotin content of foods are likely to be inaccurate.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="784" LastActivityDate="2015-07-18T19:31:21.650" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36199" PostTypeId="1" AcceptedAnswerId="36202" CreationDate="2015-07-19T00:51:53.853" Score="3" ViewCount="3463" Body="&lt;p&gt;I was recently studying about ATP and how it functions as an energy carrier to all biological processes; however, I came across a confusing and paradoxical statement from two sources:&#xA;&lt;a href=&quot;https://www.youtube.com/watch?v=AcNDiCzz3do&quot; rel=&quot;nofollow&quot;&gt;(at 7:36)&lt;/a&gt;&#xA;and&#xA;&lt;a href=&quot;http://cnx.org/contents/ba32d63f-d9a0-49fd-b06e-ed8a91ba3bf8@1.1:12/AP-Biology---Part-1:-The-Cell&quot; rel=&quot;nofollow&quot;&gt;(the free response question in the bottom of the page)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Basically, in the video, it says that ATP hydrolysis has a high activation energy which is why all of the ATP isn't randomly used by the cell processes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;And in the free response question, the answer is that ATP hydrolysis has a low activation energy and low free energy making it a spontaneous reaction.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A follow up question is: How then does the ATP of the cell used in a selective way to certain processes only?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your help.&lt;/p&gt;&#xA;" OwnerUserId="16834" LastActivityDate="2015-07-20T16:26:36.493" Title="Does ATP hydrolysis reaction have a high or low activation energy?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;bioenergetics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36201" PostTypeId="1" CreationDate="2015-07-19T02:18:05.380" Score="0" ViewCount="234" Body="&lt;p&gt;I'm looking for a textbook in neuroscience for a rigorous introduction to the topic as an autodidact. I have no prior exposure to the field.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular, I'm interested in the chemical mechanisms of enzyme modulation, ideally something similar to Lehninger's Principles of Biochemistry where specific Protein Databank ID's are given, so I can load an enzyme in PyMOL and view where the inhibitors/activators bind, in conjunction with an explanation of the actual pathways involved from a molecular level. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've read Wade: Organic Chemistry, and a good part of Clayden's Organic Chemistry, before self-studying biochemistry for 6 months, to give a little background of my knowledge.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm leaning towards Kandel's Principles of Neuroscience after reading some other suggestions here, but this seems like a gigantic text, and I'm unsure how detailed the biochemistry side of things is (which is my main interest)? Could anyone share some thoughts regarding that, or recommend an alternative smaller text with a specific focus on biochemistry?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm also concerned that a large amount of data and publications in the field of neuroscience fail replication (something as high as 60% I believe), so the book would need to contain only factual, widely accepted information and not cutting-edge speculative studies that haven't been replicated and widely accepted. Also, as little pharmaceutical-industry influenced as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultimately, my interest lies in understanding how different medications and drugs cause different mental states, their exact pathways and mechanisms, and how they form tolerance. I'd like to one day conduct research in how to minimize said tolerance, eg: reverse receptor desensitization. Which book should I begin with to head towards this goal?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks!&lt;/p&gt;&#xA;" OwnerUserId="15295" LastEditorUserId="27323" LastEditDate="2017-01-30T08:44:55.453" LastActivityDate="2019-03-22T05:44:30.027" Title="Neuroscience book recommendations" Tags="&lt;neuroscience&gt;&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36202" PostTypeId="2" ParentId="36199" CreationDate="2015-07-19T02:33:53.813" Score="2" Body="&lt;p&gt;High and low are not very descriptive since they are relative. ATP hydrolysis may have a high activation energy compared to some reactions and low when compared to others.  The important point is that the activation energy is sufficiently high enough such that ATP is not rapidly hydrolysed under physiological conditions before it can do useful work. In other words ATP hydrolysis is kinetically unfavourable but thermodynamically favourable. The reaction rate is increased by enzymes (by lowering the activation energy), which couple ATP hydrolysis to other processes to do useful work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, a note on reaction spontaneity: it has nothing to do with activation energy but rather depends on the change in free energy; ATP hydrolysis is spontaneous because it is exergonic. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-07-19T04:59:09.177" LastActivityDate="2015-07-19T04:59:09.177" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36203" PostTypeId="1" AcceptedAnswerId="36221" CreationDate="2015-07-19T04:04:46.587" Score="8" ViewCount="23855" Body="&lt;p&gt;Do all primates have to trim their fingernails in some way, or do some primates' fingernails wear off through natural use? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, is constant nail growth common to all primates?&lt;/p&gt;&#xA;" OwnerUserId="16835" LastEditorUserId="16866" LastEditDate="2017-04-26T17:45:00.493" LastActivityDate="2018-06-24T15:01:20.623" Title="How do other primates treat their fingernails?" Tags="&lt;zoology&gt;&lt;anatomy&gt;&lt;ethology&gt;&lt;mammals&gt;&lt;homology&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36205" PostTypeId="2" ParentId="36194" CreationDate="2015-07-19T05:18:06.643" Score="2" Body="&lt;blockquote&gt;&#xA;  &lt;ol start=&quot;2&quot;&gt;&#xA;  &lt;li&gt;Potassium channels participate in controlling the concentration gradient of the cell.&lt;/li&gt;&#xA;  &lt;/ol&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I would rephrase this to &quot;Sodium/potassium &lt;em&gt;pumps&lt;/em&gt; establish the concentration gradients of sodium and potassium across the cell membrane.&quot; Potassium &lt;em&gt;channels&lt;/em&gt; do not.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;I have found evidence in articles supporting the first claim, but I&#xA;  don't know much about the second.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Right; because the channels don't set up concentration gradients.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Do potassium channel blockers affect the resting membrane potential? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If they block the resting state &quot;leak&quot; potassium channels, you bet. The resting membrane potential is largely set by the electrical conductance through those channels. Blocking them would greatly depolarize the cell compared to typical resting membrane potential values. But there are many different potassium channels. You may be thinking of blocking the delayed rectifier potassium channel, which shouldn't do much at all to change the resting membrane potential.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Would they significantly alter the concentration gradient? &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Probably not, since though the cell would be losing less potassium through this conductance, what matters more to the concentration gradient of potassium are the sodium/potassium pumps.&lt;/p&gt;&#xA;" OwnerUserId="587" LastEditorUserId="587" LastEditDate="2015-07-19T17:56:10.757" LastActivityDate="2015-07-19T17:56:10.757" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36206" PostTypeId="2" ParentId="28047" CreationDate="2015-07-19T06:06:17.470" Score="0" Body="&lt;p&gt;I think, a story about &lt;a href=&quot;https://en.wikipedia.org/wiki/Alexis_Carrel&quot; rel=&quot;nofollow&quot;&gt;Alexis Carrel&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Leonard_Hayflick&quot; rel=&quot;nofollow&quot;&gt;Leonard Hayflick&lt;/a&gt; is appropriate here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the beginning of 20th century a Nobel prize-winning medicist/biologist Alexis Carrel published a series of papers, claiming that growth of a culture of cells of normal somatic differentiated tissue can be maintained indefinitely without undergoing cellular senescence. This wrong result was held for a fact for many years, before being disproved by Leonard Hayflick, who's shown that normal somatic cells undergo a limited number of divisions before dying and immoratlization happens in cancer cells. It's worth mentioning that the cause of Dr.Carrel's error might be attributed to his personality. For instance (quote from Wikipedia): &lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;Carrel claimed the existence of a &quot;hereditary biological aristocracy&quot; and argued that &quot;deviant&quot; human types should be suppressed using techniques similar to those later employed by the Nazis.&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;So, the results of his finding might be attributed to a version that he's just scared his laboratory members so much, that they started to secretly replace a deteriorating culture with a new one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I may be rough on the corners and attribute sins to the man, he's innocent of. For a &quot;fair trial&quot; with evidence etc., you'd better address this paper: &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1082700/&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1082700/&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also this popular paper: &lt;a href=&quot;http://www.theguardian.com/science/2015/feb/18/haruko-obokata-stap-cells-controversy-scientists-lie&quot; rel=&quot;nofollow&quot;&gt;http://www.theguardian.com/science/2015/feb/18/haruko-obokata-stap-cells-controversy-scientists-lie&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16123" LastActivityDate="2015-07-19T06:06:17.470" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36207" PostTypeId="1" CreationDate="2015-07-19T06:11:43.080" Score="2" ViewCount="836" Body="&lt;p&gt;While going through the feedback regulation, the control of blood glucose level by insulin and glucagon is quite discussed in multiple materials including the textbook. I also understand the basic fever and cold feedback regulation with regards to hypothalumus given in the below picture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4bFCZ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I am not able to find either a digram or a material that explains the &lt;strong&gt;relationship between hypothalamus, pituitary gland and thyroid gland in controling temperature&lt;/strong&gt;&lt;sup&gt;1&lt;/sup&gt;, specially for those who are suffering from thyroid diseases. e.g. &lt;em&gt;some people with thyroid issues feel too cold or too hot (fingers, hands, legs, skin is quickly cold or hot depending on the external change). Their body seem to fail in maintaining the set point of temperature.&lt;/em&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What's the endocrine and feedback regulation behind this&lt;sup&gt;1&lt;/sup&gt; scenario? What's the hormone pathway? Also in terms of energy, heat and metabolism.&lt;/p&gt;&#xA;" OwnerUserId="8709" LastActivityDate="2015-07-19T06:11:43.080" Title="What's the feedback regulation of Thyroid diseases and body temperature?" Tags="&lt;endocrinology&gt;&lt;temperature&gt;&lt;homeostasis&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36208" PostTypeId="2" ParentId="36113" CreationDate="2015-07-19T07:04:43.113" Score="2" Body="&lt;p&gt;If protein 1 contains a glutamate near the binding site with protein 2 and is close enough to the lysine on protein 2, it &lt;strong&gt;may&lt;/strong&gt; be possible to link the glutamate to the lysine through &lt;a href=&quot;https://en.wikipedia.org/wiki/1-Ethyl-3-%283-dimethylaminopropyl%29carbodiimide&quot; rel=&quot;nofollow noreferrer&quot;&gt;EDC&lt;/a&gt; coupling.&#xA;&lt;img src=&quot;https://i.stack.imgur.com/kFV8C.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDC is 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide, which reacts with carboxyl groups to form an &quot;active ester&quot;. This ester is highly reactive with primary amines, but can also react with water or hydroxyl ions. The general reactions are outlined below:&#xA;&lt;img src=&quot;https://i.stack.imgur.com/BpvO6.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The active ester is compound 2, which you probably want to react with the lysine on protein 2 to produce the amide in compound 3, with the isourea 4 as a byproduct. This shows that other products are possible, depending on what hits the active ester first. This reaction is most effective at pH of 4 - 5, and produces a 0 length linkage, so if you have to reach 10 angstroms across, this might not work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDC coupling is often followed by NHS ester formation, which is more stable than the EDC active ester, but is usually done when you intend on storing the active ester as a dry product for some time.&lt;/p&gt;&#xA;" OwnerUserId="4747" LastActivityDate="2015-07-19T07:04:43.113" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36209" PostTypeId="2" ParentId="36100" CreationDate="2015-07-19T08:22:29.257" Score="1" Body="&lt;p&gt;1) Yes, most cells in the body derive energy from oxidative metabolism, unless oxygen is not available for some reason. There are some exceptions, for example red blood cells lack mitochondria and so have no respiration, and various types of rapidly proliferating cells such as activated immune cells have high glycolysis and lactate production (for reasons that are still not well understood).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The main fuel of exercising muscle is glycogen, which can account for 60-80% of energy requirements (&lt;a href=&quot;http://journals.cambridge.org/action/displayAbstract?fromPage=online&amp;amp;aid=789424&amp;amp;fileId=S0029665195000140&quot; rel=&quot;nofollow&quot;&gt;article&lt;/a&gt;). Triacyglycerols (fat) stored in muscle tissue may account for most of the remainder (&lt;a href=&quot;http://jap.physiology.org/content/93/4/1185&quot; rel=&quot;nofollow&quot;&gt;artice&lt;/a&gt;). Normally, muscle protein is not a major energy source during exercise. Some muscle protein breakdown has been observed after 2-3 hours of intense exercise (think marathon runners), when glycogen stores are depleted. See this &lt;a href=&quot;http://www.annualreviews.org/doi/abs/10.1146/annurev.nutr.20.1.457&quot; rel=&quot;nofollow&quot;&gt;review article&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If glycogen is not synthesized and stored normally while resting, then muscle may be more likely to catabolize protein during intense exercise. This can happen to some extent in diabetes, see for example &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/12453829&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt;. There are also severe genetic disorders that disrupt glycogen synthesis, but those are very rare. I would guess fasting also makes it difficult to replenish muscle glycogen stores (and muscle triglycerides as well), so strenuous exercise combined with fasting might result in muscle protein breakdown, but I don't know of a study on this.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-07-19T08:22:29.257" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36210" PostTypeId="1" CreationDate="2015-07-19T14:44:55.227" Score="3" ViewCount="75" Body="&lt;p&gt;When we have a sex with partner, we feel so tired that we don't have any power to do anything. Then it would be disadvantage to the animals, of course humans too, for they are exposed to danger. For example, the predator's atack. But you know, we cannot help having a sex. Then what is the advantage of being tired after having a sex?    &lt;/p&gt;&#xA;" OwnerUserId="16838" LastActivityDate="2015-07-19T14:44:55.227" Title="What is the advantage of being tired after having a sex?" Tags="&lt;sex&gt;" AnswerCount="0" CommentCount="2" FavoriteCount="1" ClosedDate="2015-07-19T14:56:19.177" ContentLicense="CC BY-SA 3.0" />
  <row Id="36211" PostTypeId="1" CreationDate="2015-07-19T18:05:53.873" Score="1" ViewCount="98" Body="&lt;p&gt;I'm a graduate student in cognitive science doing work on people's explanations and learning, particularly having to do with natural selection.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Often, students misunderstand natural selection as a &quot;goal-directed&quot; process, one in which organisms are directed to adapt towards beneficial traits. This kind of thinking can be tempting, since most evolved traits are beneficial in obvious and straightforward ways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I'm very curious about traits whose benefits are NOT at all obvious, and can only be understood under careful consideration of the evolutionary process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An prototypical example would be the evolution of altruism, or of homosexuality. But I'm looking for more examples like these, and preferably ones that are more specific/concrete (e.g., the existence of a specific trait/behavior, rather than someone general like altruism). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Any help would be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="16840" LastActivityDate="2015-07-19T18:05:53.873" Title="Name/Examples of Traits whose benefit is non-obvious and/or which evolve despite apparent mal-adaptivness?" Tags="&lt;evolution&gt;&lt;natural-selection&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36213" PostTypeId="1" AcceptedAnswerId="36518" CreationDate="2015-07-19T18:12:32.363" Score="3" ViewCount="273" Body="&lt;p&gt;I am studying the effects of tetrodotoxin and its symptoms when consumed. Numbness is one of the first sensations reported. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But I googled numbness and I couldn't find information about whether this means all touch sensations (e.g. thermal, mechano, etc) have to be absent for numbness or just one specific kind. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;My Question:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Define numbness&lt;/li&gt;&#xA;&lt;li&gt;Explain whether numbness is the absence of one or more than one or all touch sensations. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="9943" LastEditDate="2016-03-10T20:54:46.807" LastActivityDate="2016-03-10T20:54:46.807" Title="Is numbness the absence of one or all touch sensations?" Tags="&lt;neuroscience&gt;&lt;homework&gt;&lt;neurophysiology&gt;&lt;touch&gt;" AnswerCount="2" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36215" PostTypeId="1" AcceptedAnswerId="36219" CreationDate="2015-07-19T18:53:05.967" Score="4" ViewCount="144" Body="&lt;p&gt;why do marine organisms orient with their bellies facing downwards (like most creatures) given that they have relatively fewer constraints on their orientations than land or air organisms?&lt;/p&gt;&#xA;" OwnerUserId="16557" LastActivityDate="2015-07-19T23:27:06.840" Title="why do marine organisms orient with their bellies facing downwards?" Tags="&lt;evolution&gt;&lt;ichthyology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36216" PostTypeId="2" ParentId="36203" CreationDate="2015-07-19T20:01:58.420" Score="1" Body="&lt;p&gt;Why some human beings bite their nails? Because, they are primates - it is inherited way to treat our nails, called &lt;strong&gt;onychophagia&lt;/strong&gt;. While normal in some primates (and this is the way they treat their nails), it is considered &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19479125&quot; rel=&quot;nofollow noreferrer&quot;&gt;abnormal in human&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BBnH3.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-07-19T20:09:34.890" LastActivityDate="2015-07-19T20:09:34.890" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36218" PostTypeId="1" CreationDate="2015-07-19T22:12:23.440" Score="2" ViewCount="110" Body="&lt;p&gt;I am learning about calcium ion channel blockers (CCBs) and am confused whether there are neurotoxins that are CCBs. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;If they exist, what is an example of a CCB neurotoxin? &lt;/li&gt;&#xA;&lt;li&gt;What animals use CCB neurotoxins as a weapon / defense tool?  &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="11652" LastActivityDate="2015-07-19T22:12:23.440" Title="Are there calcium channel blocking neurotoxins?" Tags="&lt;neurophysiology&gt;" AnswerCount="0" CommentCount="8" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36219" PostTypeId="2" ParentId="36215" CreationDate="2015-07-19T23:27:06.840" Score="2" Body="&lt;p&gt;I'll address fish here. It's hard to tell which way is up with many sea-dwelling invertebrates, e.g. sea cucumbers. Sea urchins often are oriented &quot;sideways&quot; if you count their mouths as &quot;down&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;All animals normally orient themselves in the most advantageous manner dependent on their situation. Probably the most important determiners are field of vision and the inner ears, which work much like those of humans (who walk upright even if blind.) Unlike land vertebrates, the ear of fish is thought to have evolved as a vestibular organ for balance and orientation in space rather than as an auditory organ. Fish (and other sea creatures) also have other sensory apparatus which orient them, such as lateral lines. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pipe fish swim in a horizontal manner like other fish, but rest vertically, swaying with the sea grass around it. Flatfish start &quot;normal&quot; but as the eye shifts position to the other side of the head, it will assume a bottom dwelling &quot;sideways&quot; position, with a contorted mouth and a fin squashed against the sand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/X2chbm.jpg&quot; alt=&quot;enter image description here&quot;&gt; &lt;img src=&quot;https://i.stack.imgur.com/ccN7hm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;“&lt;a href=&quot;http://www.pbs.org/wgbh/nova/next/evolution/flatfish-evolution/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Flatfish are the most asymmetrically-shaped vertebrate to ever live on earth&lt;/a&gt;,” says Alexander Schreiber, a flatfish expert at St. Lawrence University. “It sounds likes a really dramatic thing to say, but as far as vertebrates go, it’s true.”&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Apparently flatfish brains start to receive stronger signals from one inner ear than the other.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Two organs — the eyes and inner ears — work together to keep typical fish in an upright swimming posture... If the eyes are not receiving the same amount of light on each retina... retinal neurons trigger the brain to tilt the entire animal and set it straight. ...As a fish’s vertical orientation in water changes, the brain combines information from the eyes and ears to figure out which way is up. ...[f]latfish larvae that are deliberately blinded adopt a sideways swimming posture.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;When snorkeling, it is not at all uncommon to see any of a number of fish flip to their sides side to get a good look at you (floating above) with one eye, as opposed to maneuvering itself to face you. I imaging they assess the threat; since I wasn't a threat, they would just reorient themselves normally and go about their business.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Whatever aids survival within the parameters they are confined to (were born with) in that niche will be what you see.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.pbs.org/wgbh/nova/next/evolution/flatfish-evolution/&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Improbable—but True—Evolutionary Tale of Flatfishes&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.researchgate.net/publication/264976968_Vestibular_system_and_sense_of_equilibrium_in_fish&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Vestibular System and Sense of Equilibrium in Fish&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-07-19T23:27:06.840" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36221" PostTypeId="2" ParentId="36203" CreationDate="2015-07-20T00:02:37.607" Score="8" Body="&lt;p&gt;Both. Many primates bite their nails. Some do not. It's not species specific.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Chimpanzees, for example, usually bite their nails; some prefer to leave them alone. They do grow continuously, and nails not kept trimmed probably break off (looking at the thickness of those nails, I get the impression that this might be rather painful if they break too short.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The caption for the picture below (taken from a chimpanzee sanctuary) states&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Annie likes to pick Missy’s nose. Missy tolerates it but doesn’t seem to enjoy it. I don’t blame her – Annie doesn’t &lt;a href=&quot;http://www.chimpsanctuarynw.org/blog/tag/grooming/&quot; rel=&quot;noreferrer&quot;&gt;bite her nails down&lt;/a&gt; like the other chimps do.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/vPVVE.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They bite their toenails as well.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-07-20T00:11:16.630" LastActivityDate="2015-07-20T00:11:16.630" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36222" PostTypeId="1" AcceptedAnswerId="36687" CreationDate="2015-07-20T00:10:11.173" Score="5" ViewCount="642" Body="&lt;p&gt;I have heard from a (usually very knowledgeable) friend before, that a human can only tap his fingers 7 times per second.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I generalized this to &quot;our muscles are limited to 7 hertz&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When my wife heard this she was like &quot;no way, I'm faster&quot; and we recorded a video of her blinking as fast as she could (her eyes hurt afterwards) and over 5 seconds she averaged &lt;strong&gt;exactly&lt;/strong&gt; 7 blinks per second.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't find any articles on the subject, but I did find this &lt;a href=&quot;http://www.telegraph.co.uk/news/newsvideo/weirdnewsvideo/10187844/Worlds-fastest-drummer-sets-record-with-over-20-beats-per-second.html&quot; rel=&quot;noreferrer&quot;&gt;video&lt;/a&gt; of a drummer doing 1208 beats in 60 sec, setting him up at 20.13hz, meaning 10hz each hand. However if you look at his hand, his muscles are not even really tapping, they are just in a vibration (like a spasm), while holding the drumsticks, which than do all the tapping...&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ussain Bolt sprinted 100m in 9.6 seconds, with 41 steps, that's a little over 4 steps per second.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Both these are very impressive. The drummer sticks out for coordinating his 10 taps per second on each hand, alternating with the other hand, while the motion is certainly faster then our eyes can see.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what's up with the 7 Hz speed limit? Is it a thing, or did the drummer disprove it? Could the 100m world record be beaten by another 25% when we can find a tall guy capable of doing 7 or even 10 steps per second?&lt;/p&gt;&#xA;" OwnerUserId="16843" LastActivityDate="2017-01-30T08:45:04.287" Title="Why are our muscles limited to 7 Hertz?" Tags="&lt;muscles&gt;&lt;central-nervous-system&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36223" PostTypeId="1" CreationDate="2015-07-20T00:35:41.707" Score="4" ViewCount="1559" Body="&lt;p&gt;I am currently conducting an experiment which involves FACS-sorting a specific population of cells using an antibody of interest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order to validate the type of cells I have collected using this marker, I want to perform qPCR on their extracted RNA, using certain known cell-type marker primers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My problem is that in each sorting session, I am only able to collect anywhere from 5,000 - 10,000 cells. Do you know if it is possible to perform RT-qPCR on such a small sample size?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have collected the cells in 1mL of Trizol.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Would I maybe have to amplify the cDNA after reverse transcription in a general manner ( using random primers)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks for your help. &lt;/p&gt;&#xA;" OwnerUserId="12971" LastEditorUserId="3340" LastEditDate="2015-07-20T13:03:44.393" LastActivityDate="2015-07-21T17:36:05.477" Title="How to Extract RNA and perform RT-qPCR from very few cells ( ~5,000)?" Tags="&lt;molecular-biology&gt;&lt;rna&gt;&lt;lab-techniques&gt;&lt;pcr&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36225" PostTypeId="2" ParentId="35839" CreationDate="2015-07-20T08:19:07.910" Score="1" Body="&lt;p&gt;I don't think your core question can be answered exactly, namely &quot;&lt;em&gt;...the theoretical maximum population to which the Tiger species could be restored&lt;/em&gt;&quot;, since there are too many variables to consider. However, the comment from @Remi.b is apt, in the sense that it shows that population growth rate per se (or reproductive rate) should not be the limiting factor. The bottleneck will probably be some concept of carrying capacity (the number of tigers that the current tiger habitats can sustain). This number will naturally depend on many factors, for instance whether all hunting of tigers and their prey is removed from the remaining habitats.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could arrive at a ballpark estimate of the current &quot;theoretical&quot; maximum population size by finding the area of suitable tiger habitat and dividing this by the average size of tiger territories. However, the size of tiger territories differ quite a bit between males and females and between areas with different prey densities, and probably also between different tiger subspecies (which will covary with average prey density to some extent - Siberian tigers generally live in habitats with lower prey densities). Looking at estimates from &lt;a href=&quot;http://nationalzoo.si.edu/Animals/GreatCats/tigerfacts.cfm&quot; rel=&quot;nofollow&quot;&gt;the Smithsonian&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Tiger#Social_activity&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt;, territory sizes seems to range between 20 to 510 km&lt;sup&gt;2&lt;/sup&gt;, with maybe even larger male territories in Siberia (so quite a big range). The &lt;a href=&quot;http://www.iucnredlist.org/details/15955/0&quot; rel=&quot;nofollow&quot;&gt;IUCN Red list assessment of tigers&lt;/a&gt; state that the current tiger range is to 1.185 million km&lt;sup&gt;2&lt;/sup&gt; (from &lt;a href=&quot;http://www.panthera.org/sites/default/files/WCS_WWF_et_al_2006_TechAssesment_Wild_Tigers_2005-2015.pdf&quot; rel=&quot;nofollow&quot;&gt;Sanderson et al. 2006&lt;/a&gt; as &quot;&lt;em&gt;Tiger Conservation Landscapes&lt;/em&gt;&quot;). It is however unclear whether this number corresponds to the total range extent or to the actual amount of suitable habitat (probably the former though). Nevertheless, lets say that the average territory size is 265km&lt;sup&gt;2&lt;/sup&gt; (probably way to high on average), that the estimated area from IUCN is correct, and lets assume that territories never overlap (which they do; male territories overlap with several female territories and female territories can also overlap to some extent). In that case, we will arrive at an estimated theoretical popultion size of ~4500 tigers. If we instead use a more modest territory size of 40km&lt;sup&gt;2&lt;/sup&gt; we will arrive at a population size of ~30000 tigers. Since territories can overlap, these estimates should be biased low, given their other assumptions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.panthera.org/sites/default/files/WCS_WWF_et_al_2006_TechAssesment_Wild_Tigers_2005-2015.pdf&quot; rel=&quot;nofollow&quot;&gt;Sanderson et al. (2006)&lt;/a&gt; however also includes a summary of &quot;&lt;em&gt;Effective Potential Habitat&lt;/em&gt;&quot; of tigers, which sum to 5.65 million km&lt;sup&gt;2&lt;/sup&gt;. If this number is used to calculate the estimated theoretical popultion size you will arrive at ~21300 or 141000 tigers, using the same territory sizes as above. However, this completely ignores issues such as landscape connectivity, and that tigers are completely missing from large parts of their former distribution (these factors, and others, were used to define the &quot;&lt;em&gt;Tiger Conservation Landscapes&lt;/em&gt;&quot;). Also note that much of the potential habitat lies in low-productivity areas (Russia and parts of China), where territory sizes are relatively large.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another perspective would be to use the historical population size pre-20th century and the amount of decrease in tiger habitat to estimate a theoretical population size. I don't know anything about the historical population size, but let's say that your 100000 is accurate (source?). &lt;a href=&quot;http://bioscience.oxfordjournals.org/content/57/6/508.full#F1&quot; rel=&quot;nofollow&quot; title=&quot;Dinerstein et al. 2007. The Fate of Wild Tigers. Bioscience 57 (6): 508-514. doi: 10.1641/B570608&quot;&gt;Dinerstein et al (2007)&lt;/a&gt; state that current tiger ranges correspond to 7% of historical ranges. Using only these numbers, you could arrive at a current theoretical population size of 7000 tigers (100000*0.07), assuming that the tiger population should directly mirror the amount of available habitat. However, the current 7% of historical ranges include range contractions due to hunting, so this estimate should be biased low (maybe strongly so) with respect to the possible population size that could be obtained if all hunting stopped.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;These calculations should show that the current Tiger populations could probably be increased quite a bit with strong and effective conservation efforts (in your words: if &quot;&lt;em&gt;poaching and habitat destruction stopped today and conservation efforts were increased drastically&lt;/em&gt;&quot;), but that 100000 will probably be extremely hard to obtain, given that so much of the historical range has been lost. With reintroduction programmes and a long timeframe it doesn't appear to be impossible though, but this is ignoring potential future problems such as increased tiger-human conflicts. Also note that I don't know much about Tiger biology, that these are merely rough back-of-an-envelope calculations, and an expert could certainly give you a more detailed and accurate answer.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;References:&lt;/h2&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://bioscience.oxfordjournals.org/content/57/6/508.full#F1&quot; rel=&quot;nofollow&quot; title=&quot;Dinerstein et al. 2007. The Fate of Wild Tigers. Bioscience 57 (6): 508-514. doi: 10.1641/B570608&quot;&gt;Dinerstein et al. 2007. The Fate of Wild Tigers. Bioscience 57 (6): 508-514. doi: 10.1641/B570608&lt;/a&gt;  &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.panthera.org/sites/default/files/WCS_WWF_et_al_2006_TechAssesment_Wild_Tigers_2005-2015.pdf&quot; rel=&quot;nofollow&quot;&gt;Sanderson et al. 2006. Setting Priorities for the Conservation and Recovery of Wild Tigers: 2005-2015. The Technical Assessment. WCS, WWF, Smithsonian, and NFWF-STF, New York – Washington, D.C.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://nationalzoo.si.edu/Animals/GreatCats/tigerfacts.cfm&quot; rel=&quot;nofollow&quot;&gt;The Smithsonian: Tigers&lt;/a&gt;  &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Tiger&quot; rel=&quot;nofollow&quot;&gt;Wikipedia: Tiger&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.iucnredlist.org/details/15955/0&quot; rel=&quot;nofollow&quot;&gt;IUCN Red List: Panthera tigris&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-07-20T09:52:06.473" LastActivityDate="2015-07-20T09:52:06.473" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36228" PostTypeId="1" AcceptedAnswerId="36250" CreationDate="2015-07-20T09:00:12.353" Score="8" ViewCount="229" Body="&lt;p&gt;I found this plant near the MSU, Moscow, Russia. Could someone help me to identify it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/RDqdW.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ixamv.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="13338" LastEditorUserId="13338" LastEditDate="2015-08-01T21:15:15.313" LastActivityDate="2015-08-01T21:15:15.313" Title="Flower identification: Moscow, Russia" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36229" PostTypeId="1" CreationDate="2015-07-20T09:08:18.150" Score="3" ViewCount="391" Body="&lt;p&gt;Can a gene continue on from one chromosome to another separate chromosome? For example, can part of an eye colour gene be on one chromosome and the rest of it be on the next chromosome? &lt;/p&gt;&#xA;" OwnerUserId="16848" LastActivityDate="2015-07-20T13:00:17.777" Title="Can a same gene stretch from one chromosome to another separate chromosome?" Tags="&lt;genetics&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36230" PostTypeId="2" ParentId="36229" CreationDate="2015-07-20T09:17:49.937" Score="1" Body="&lt;p&gt;No, a gene is confined to a single chromosome. A gene is characterized by a start sequence in the DNA (among many other things), which indicates that the nucleotides are to be read and transcribed to RNA. This stretch of DNA in the gene is contiguous, although some parts may be skipped in transcription. Because different chromosomes are physically distinct, the cellular machinery would require two start sequences, which really means there are just two separate genes. Instead of finding one eye color gene on multiple chromosomes, you instead find multiple eye color genes on multiple chromosomes.&lt;/p&gt;&#xA;" OwnerUserId="16849" LastActivityDate="2015-07-20T09:17:49.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36231" PostTypeId="2" ParentId="36229" CreationDate="2015-07-20T09:33:48.070" Score="6" Body="&lt;p&gt;Usually not (as described in the other answer, non-contiguous pieces of DNA are not considered as a part of a single gene). However there are some cases of &lt;a href=&quot;http://dx.doi.org/10.1002/wrna.71&quot; rel=&quot;noreferrer&quot;&gt;trans-splicing&lt;/a&gt; in which the spliceosome can splice together RNAs arising from different genomic locations. But these are rare and do not have a direct effect on distinct phenotypes such as eye colour, to be classified as genes. Not much progress has happened in this aspect of transcriptomics, actually.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-07-20T13:00:17.777" LastActivityDate="2015-07-20T13:00:17.777" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36232" PostTypeId="2" ParentId="36229" CreationDate="2015-07-20T09:34:19.493" Score="1" Body="&lt;p&gt;Gene is usually defined as piece of DNA that produces certain product, be it RNA or polypeptide molecule. In both cases RNA is produced as intermediate or final product. Nature of RNA production from DNA (aka transcription) is such that it requires double-stranded DNA as substrate, that is a continuous polymer of nucleotides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, only parts of chromosomes (which are really long linear polymers) can be used as substrate or template for RNA production.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, regulatory elements, which are extremely important, can be anywhere, as long as they are able to function. Since those elements are just special sequences of DNA that interact with transcription factors and other elements of DNA-&gt;RNA machinery, they can be on different chromosome than gene of interest.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-07-20T09:34:19.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36233" PostTypeId="2" ParentId="36213" CreationDate="2015-07-20T09:53:57.247" Score="1" Body="&lt;p&gt;An Initial clarification of what &amp;quot;loss of sensation&amp;quot; means:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The history in the patient with “numbness” is extremely important. First of all, as with most neurologic complaints, you must determine what the patient means by “numbness.” Some patients are describing loss of sensitivity (anesthesia or hypesthesia) or distorted sensations (paresthesia), which is often described as tingling. Actual loss of sensitivity is more likely to represent true damage to sensory pathways in the nervous system, while paresthesia has a much broader differential. Dysesthesia, that is the perception of an unpleasant (often burning) sensation or allodynia (the perception of innocuous stimuli as being painful) may result from damage to the nervous system or, more commonly, be the manifestation of an underlying painful condition.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Some properties of numbness&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The pattern of numbness may help define its origin. Numbness confined to a specific nerve or nerve root distribution (see the maps of dermatomes and peripheral nerve sensory innervation) lead to consideration of peripheral nerve or nerve root damage. Loss of sensation on one side of the body is more likely to result from central nervous system damage and if the sensory loss also involves the same side of the face, you can be sure that the cause is located above the level of the pons.&lt;/p&gt;&#xA;&lt;p&gt;When there is a clear sensory level (a line on the body, below which sensations are lost), a spinal cord lesion must be suspected. Loss of sensation over the upper limbs or upper part of the trunk bilaterally, with preservation over the lower limbs and buttocks, suggests an expanding intraspinal mass. This so-called “sacral sparing” is seen with intraspinal tumors or syrinxes. Numbness over one side of the face, while being a relatively common presentation of psychiatric disease, can also be caused by damage to the lateral part of the brain stem, or upper spinal cord (spinal tract of the trigeminal). Lateral brain stem damage can also produce a picture of sensory decrease on one side of the head and on the opposite side of the body.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;But the article concludes&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;In summary, the evaluation of numbness can be quite frustrating due to its subjective nature.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;So it is in essence a term that &lt;em&gt;can&lt;/em&gt; have specific meanings uncertain contexts, but one must be careful to clarify exactly how the term is being used since there isn't one single meaning.&lt;/p&gt;&#xA;&lt;p&gt;This is all from this link here&#xA;&lt;a href=&quot;https://www.dartmouth.edu/%7Edons/part_2/chapter_13.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.dartmouth.edu/~dons/part_2/chapter_13.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-07-20T09:53:57.247" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="36234" PostTypeId="1" CreationDate="2015-07-20T09:59:37.660" Score="3" ViewCount="41" Body="&lt;p&gt;I read that cytoplasmic incompatibility in Wolbachia occurs when wolbachia-infected male insects mate with wolbachia-free female insects and produce non-viable offspring. By contrast, wolbachia-infected female hosts produce successful offspring irrespective of the infection status of their mate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was wondering - what are the long-term effects of this on the size/structure of a insect population? How will this be different from a non-infected population?&lt;/p&gt;&#xA;" OwnerUserId="16851" LastEditorUserId="3624" LastEditDate="2015-07-20T12:53:12.807" LastActivityDate="2015-07-20T12:53:12.807" Title="Wolbachia - cytoplasmic incompatibility" Tags="&lt;evolution&gt;&lt;entomology&gt;&lt;pathology&gt;&lt;infection&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36235" PostTypeId="1" CreationDate="2015-07-20T10:39:19.660" Score="3" ViewCount="175" Body="&lt;p&gt;So we know that our sperm and egg cells get set aside relatively early so that they aren't going through unnecessary cell divisions and causing DNA damage or telomere shortening, but since each new generation starts from one cell each generation has germ cells that have divided more than the previous generation's germ cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, does this have an effect on age? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is a second generation baby technically older than a first generation baby due to these extra cell divisions, or is telomerase and DNA repair able to keep each generation at the same relative life span?&lt;/p&gt;&#xA;" OwnerUserId="16041" LastActivityDate="2015-07-22T08:59:58.150" Title="Is each generation getting older?" Tags="&lt;human-biology&gt;&lt;dna&gt;&lt;human-genetics&gt;&lt;telomere&gt;&lt;dna-damage&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ClosedDate="2015-07-23T00:10:07.337" ContentLicense="CC BY-SA 3.0" />
  <row Id="36236" PostTypeId="2" ParentId="36235" CreationDate="2015-07-20T11:28:05.163" Score="5" Body="&lt;p&gt;In germ cells &lt;a href=&quot;https://en.wikipedia.org/wiki/Telomerase&quot; rel=&quot;nofollow&quot;&gt;telomerase&lt;/a&gt; enzyme &lt;a href=&quot;http://www4.utsouthwestern.edu/cellbio/shay-wright/intro/facts/sw_facts.html&quot; rel=&quot;nofollow&quot;&gt;is active and elongates telomeres&lt;/a&gt;, so youngsters are not born older than their parents due to telomeres.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Still, they do receive mutations, accumulated by their parents' germ-line cells, i.e. eggs and sperm. Most of the mutations occur upon division of the cell. Egg cells don't undergo many divisions - they are created in the course of embryonic development of a woman and then are spent one-by-one. At the same time, precursors of sperm cells divide constantly, thus accumulating mutations at a constant rate.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Got no time to look for a hyperlink, but I read that no matter what is the age of the mother, she gives 15 new single-nucleotide mutations on average to her offspring. Father gives about 10 mutations for each year of his life after reaching puberty, historically 70 on average. Out of those mutations most are neutral or silent (due to genetic code degeneracy), but on average ~1/70 leads to a change in aminoacid sequence of some protein, usually harmful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, although babies don't get older, but alas, they get uglier as generations pass :( Natural selection is what saves us from deterioration, so that the weakest are sentenced to childlessness.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Added a couple of hyperlinks as requested: decay of cognitive indicators of children with parent's age:&#xA;&lt;a href=&quot;http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1000040&quot; rel=&quot;nofollow&quot;&gt;http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1000040&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another link: drosophila simulation of middle-class neighborhood (MCN) population, where each family has exactly 2 children, son and daughter, and no natural selection pressure is applied: such population rapidly deteriorates with fitness in wilderness decreasing by 2% per generation:&#xA;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/9371795&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/9371795&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16123" LastEditorUserId="16123" LastEditDate="2015-07-22T08:59:58.150" LastActivityDate="2015-07-22T08:59:58.150" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36237" PostTypeId="2" ParentId="36223" CreationDate="2015-07-20T13:49:50.007" Score="1" Body="&lt;p&gt;You can consider use of single-cell RT-qPCR kits &lt;a href=&quot;https://www.lifetechnologies.com/order/catalog/product/4458237&quot; rel=&quot;nofollow&quot;&gt;such as this one&lt;/a&gt; if you have the budget for them. (Note: I have not personally used this kit, just putting out an idea)&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Ambion® Single Cell-to-CT™ Kit contains a complete validated&#xA;  workflow for gene expression analysis for samples containing 1–10&#xA;  cells. Each kit contains reagents for sample preparation, reverse&#xA;  transcription, pre-amplification, and qPCR that have been optimized&#xA;  together in a simple workflow that can be completed in only 5 steps&#xA;  (see figure).&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-07-20T13:49:50.007" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36238" PostTypeId="1" CreationDate="2015-07-20T15:27:52.807" Score="2" ViewCount="184" Body="&lt;p&gt;I'm looking for a great textbook on biochemistry that covers core topics: relevant aspects of thermodynamics, reaction kinetics, metabolism (e.g. krebs cycle, respiration, etc.). Ideally it would also be quantitative in its approach and use mathematical models where relevant. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The classic textbook is Voet &amp;amp; Voet &amp;amp; Pratt (Fundamentals of Biochemistry) and I think that's a horribly written textbook. It uses concepts before actually defining them (and when it does define them the definitions are obtuse and have no conceptual motivation). Is there an alternative to this? Any recommendations?&lt;/p&gt;&#xA;" OwnerUserId="16854" LastEditorUserId="3624" LastEditDate="2015-07-21T07:40:43.967" LastActivityDate="2015-07-21T07:40:43.967" Title="Textbook for quantitative biochemistry with thermodynamics, as an alternative to Voet, Voet &amp; Pratt (Fundamentals of Biochemistry)?" Tags="&lt;biochemistry&gt;&lt;theoretical-biology&gt;&lt;book-recommendation&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36239" PostTypeId="1" AcceptedAnswerId="42648" CreationDate="2015-07-20T15:44:08.427" Score="2" ViewCount="3286" Body="&lt;p&gt;Everybody seems to agree that endocytosis is an energy-using process, and as such requires ATP hydrolysis. However, which particular step requires it? More precisely, which 'molecular machine' involved in endocytosis requires ATP? I cannot seem to find a good answer in the literature.&lt;/p&gt;&#xA;" OwnerUserId="16855" LastActivityDate="2016-01-25T16:52:46.163" Title="Which step in endocytosis requires ATP?" Tags="&lt;cell-biology&gt;&lt;cell-membrane&gt;&lt;bioenergetics&gt;&lt;energy&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36241" PostTypeId="1" AcceptedAnswerId="36248" CreationDate="2015-07-20T16:18:33.970" Score="33" ViewCount="4913" Body="&lt;p&gt;I have heard (from multiple sources) that the current scientific opinion is that the human species arose in Africa. What are the reasons for this opinion? If possible, simple and non-technical explanations (as far as possible) would be appreciated.&lt;/p&gt;&#xA;" OwnerUserId="284" LastEditorUserId="-1" LastEditDate="2015-07-20T20:47:59.487" LastActivityDate="2015-07-21T18:46:39.050" Title="How do we know the human species arose in Africa?" Tags="&lt;human-evolution&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="36242" PostTypeId="2" ParentId="36199" CreationDate="2015-07-20T16:26:36.493" Score="0" Body="&lt;p&gt;The video response is more accurate. In particular, saying that the activation barrier is high enough for the reaction not to occur spontaneously in water means that the activation energy is much higher than the thermal energy, $k_B T$, where $k_B$ is Boltzmann's constant and $T$ is the temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You ask, &quot;How do cells control how ATP is used?&quot;. As mentioned in the other answer, this energy barrier is lowered by enzymes, in particular ATPases. These are 'machines', such as for example molecular motors or ion pumps, which have a binding pocket for an ATP. When the ATP comes inside this pocket, the activation barrier is lowered and hydrolysis can happen. And, crucially, these 'machines' then use the released energy to perform some useful task. If hydrolysis happened by itself in water, the released energy would be 'lost' in the form of heat.&lt;/p&gt;&#xA;" OwnerUserId="16855" LastActivityDate="2015-07-20T16:26:36.493" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36243" PostTypeId="2" ParentId="36241" CreationDate="2015-07-20T16:42:43.177" Score="3" Body="&lt;p&gt;People previously argued for a multiregional theory in which humans arose from many different places on the globe, but have come to the conclusion that humans came originally from Africa. I believe that their reasoning is that the oldest skulls found have been found solely in Africa. This article expands on my answer if you are interested:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://news.nationalgeographic.com/news/2007/07/070718-african-origin.html&quot; rel=&quot;nofollow&quot;&gt;http://news.nationalgeographic.com/news/2007/07/070718-african-origin.html&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16537" LastActivityDate="2015-07-20T16:42:43.177" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36247" PostTypeId="1" CreationDate="2015-07-20T17:27:39.530" Score="1" ViewCount="599" Body="&lt;p&gt;I've learned that there are &lt;a href=&quot;https://skeptics.stackexchange.com/questions/1964/has-increased-computer-use-led-to-increased-myopia&quot;&gt;two primary hypotheses to explain myopia: not enough use of distance vision &lt;em&gt;or&lt;/em&gt; not enough sunlight&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the distance between an eye and what it's focusing on is the primary cause, then having a VR screen inches away would seem like a recipe for exacerbating myopia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, since people with 20/20 vision can use VR headsets, while others need the maximum correction and still see everything out of focus, clearly there is something more than at play than simply focal distance between the eye and the screen.  Could this be used to help minimize, prevent, or possible reduce myopia?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Likewise, if the cause is primarily lack of sunlight, could sunny simulations be used to help minimize, prevent, or possible reduce myopia?  Or is the light produced too artificial?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Knowing that myopia is on the rise, and VR is going to be more prevalent in the near future, these seem like important relationships to understand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, it could be they are simply two factors of many; but they are extremely relevant to this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More recently, my ophthalmologist was adamant that I needed to follow the 20/20/20 rule, i.e. every 20 minutes focus on things more than 20 feet away for at least 20 seconds, which leads me to believe he at least subscribes to the distance hypothesis.&lt;/p&gt;&#xA;" OwnerUserId="16860" LastEditorUserId="15950" LastEditDate="2019-07-28T23:59:35.700" LastActivityDate="2019-07-28T23:59:35.700" Title="Would a VR headset exacerbate myopia or could it be used to retrain the eyes?" Tags="&lt;vision&gt;&lt;eyes&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 4.0" />
  <row Id="36248" PostTypeId="2" ParentId="36241" CreationDate="2015-07-20T19:16:08.673" Score="51" Body="&lt;p&gt;There are two big prongs of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Recent_African_origin_of_modern_humans&quot; rel=&quot;nofollow noreferrer&quot;&gt;out of Africa theory&lt;/a&gt; or whichever name you wish to call it.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prong the first: fossil evidence. There are lots of different kinds of protohuman fossils. &lt;em&gt;Homo erectus/ergaster&lt;/em&gt; are found all across Europe, Asia, and into Indonesia from about 1.5 million years or so until about 70 thousand years ago, where they stop showing up. Up until 125 thousand years ago anatomically modern humans were only found in Africa. About 70 thousand years ago they start showing up in the Middle East, and then they spread out roughly following &lt;a href=&quot;https://en.wikipedia.org/wiki/Early_human_migrations#/media/File:Spreading_homo_sapiens_la.svg&quot; rel=&quot;nofollow noreferrer&quot;&gt;these paths&lt;/a&gt;. The fossil record shows not-humans or almost-humans (&lt;em&gt;Homo erectus&lt;/em&gt; mostly) for millions of years, then humans show up at a certain point and then there's loads of human fossils. This point gets more recent as you get further from East Africa.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Prong the second: genetic diversity. Starting with &lt;a href=&quot;http://www.nature.com/nature/journal/v325/n6099/abs/325031a0.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;this paper&lt;/a&gt; (not sure if this is behind a paywall but the details are not important anyway) human mitochondrial DNA was compared using restriction enzyme mapping. This kind of mapping is super crude (roughly analogous to grinding pottery into a fine dust and grouping the dusts by color) and the original study was pretty limited by the computers available at the time. Nonetheless, they showed that the most genetically diverse geographical group was Africa, and furthermore that any two people from outside Africa are likely more closely related to each other than any two people inside Africa. Genetic diversity goes down the further away from East Africa you get, matching what you'd expect if humans hadn't been living there long. There have only been (very roughly) 60 generations since humans colonized New Zealand. All Maori people, therefore, are at most 58th cousins. All indigenous Australians are at most 1998th cousins. All Africans are at most 8000th cousins.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More recently we've done proper sequencing on the mitochondrial DNA (actually knowing whats written there) and that's allowed much more precise estimation of this sort of thing, and estimation of the timeframes involved. The genetic evidence backs up the fossil record, by and large. (There are a few interesting examples where interbreeding with Neanderthals and maybe &lt;a href=&quot;https://en.wikipedia.org/wiki/Denisovan&quot; rel=&quot;nofollow noreferrer&quot;&gt;Denisovans&lt;/a&gt; can be detected, and that the settlement of the middle east by modern humans about 125 thousand years ago failed. They left no descendants.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Fun side consideration (warning, extra science, proceed with caution): all humans inherit their mitochondria from their mother, and all males inherit their Y-chromosomes from their father. This lets us trace matrilineal lines with a relatively high degree of accuracy, since mitochondria reproduce asexually. To clarify: your matrilineal line is your mother, and her mother, and so on. Your paternal grandmother is not part of your matrilineal line, nor are your aunts or sisters. These lines are statistically guaranteed to eventually converge on a single woman whose mitochondrial descendants now live in all of us. The &lt;a href=&quot;https://en.wikipedia.org/wiki/Genetic_drift&quot; rel=&quot;nofollow noreferrer&quot;&gt;reasons&lt;/a&gt; for this are &lt;a href=&quot;https://en.wikipedia.org/wiki/Fixation_(population_genetics)&quot; rel=&quot;nofollow noreferrer&quot;&gt;complicated&lt;/a&gt;. There are actually lots of these women, since she inherited her mitochondria from her mother, ad infinitum (well, not infinitum. Ad failed-endocytosis-of-an-alpha-proteobacterium-leading-to-mitochondria doesn't roll off the tongue though). Science has tight estimates on the &lt;em&gt;most recent&lt;/em&gt; mitochondrial ancestor, or &quot;Mitochondrial Eve&quot;. To be clear: there were loads of other women alive at the time, and we inherit a lot of their non-mitochondrial DNA. Over millennia all those other women had fewer daughters, and their matrilineal lines died out. She lived about 200 thousand years ago, plus minus 20 thousand years. As a mathematical guarantee we'll never find her body or have a really tight estimate on how long ago she lived, but she's genetically guaranteed to exist. The same principle applies to patrilineal inheritance, but the estimates for the most recent ancestor of all Y-chromosomes are a little looser (200-300 thousand years ago). &lt;a href=&quot;https://biology.stackexchange.com/questions/7184/what-is-a-mitochondrial-eve-and-y-chromosomal-adam&quot;&gt;See here&lt;/a&gt; for a more detailed handling of Eve and what's going on there.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In sum: old fossils only in Africa, everyone outside Africa is only 2800th cousins with each other or less, but intra-African relatedness is less than half that (more than twice as far away genetically).&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-07-21T18:46:39.050" CommentCount="21" ContentLicense="CC BY-SA 3.0" />
  <row Id="36249" PostTypeId="1" CreationDate="2015-07-20T19:31:41.527" Score="4" ViewCount="276" Body="&lt;p&gt;I'm looking for a dichotomous key to identify primates by physical and possibly geographical traits.  Any format is fine (print, web, mobile app, etc.).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other than classroom activities and genetic classification references the best I have found is on WikiBooks: &lt;a href=&quot;https://en.wikibooks.org/wiki/Dichotomous_Key/Primates&quot; rel=&quot;nofollow&quot;&gt;https://en.wikibooks.org/wiki/Dichotomous_Key/Primates&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16862" LastActivityDate="2015-07-20T19:31:41.527" Title="Looking for a dichotomous key to identify primates" Tags="&lt;literature&gt;&lt;species-identification&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36250" PostTypeId="2" ParentId="36228" CreationDate="2015-07-20T20:25:11.663" Score="8" Body="&lt;p&gt;It looks very similar to &lt;a href=&quot;https://commons.wikimedia.org/wiki/Category:Cephalaria_gigantea&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cephalaria gigantea&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/siN7r.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-20T20:25:11.663" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36252" PostTypeId="1" CreationDate="2015-07-20T21:16:10.973" Score="1" ViewCount="139" Body="&lt;p&gt;I am trying to design primers using Primer-BLAST such that the forward primer spans a specific base pair site. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am looking at KRAS for which I believe the &lt;strong&gt;RefSeq ID&lt;/strong&gt; is &lt;strong&gt;NG_007524.1&lt;/strong&gt; and the forward primer should span &lt;strong&gt;chr12:25398285&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I'm not sure how to restrict the design to accomplish this. Thanks.&lt;/p&gt;&#xA;" OwnerUserId="14587" LastEditorUserId="16651" LastEditDate="2015-11-19T13:21:19.490" LastActivityDate="2016-02-17T15:35:06.507" Title="Primer Design with Primer-BLAST over specific site" Tags="&lt;molecular-biology&gt;&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;blast&gt;&lt;primer&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36253" PostTypeId="1" CreationDate="2015-07-20T23:24:13.107" Score="2" ViewCount="44" Body="&lt;p&gt;Most sources I've seen say that about 90% of humans are right handed, and 10% are left handed. Why is this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My only guess would be that it has something to do with different parts of the brain developing differently and causing right or left &quot;handedness&quot;, but this is coming from my very little knowledge of the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Furthermore, about 2/3 of people are right eye dominant, and more people are right ear dominant than left ear dominant.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;Why the right side?!?&lt;/em&gt;&lt;/p&gt;&#xA;" OwnerUserId="15704" LastActivityDate="2015-07-20T23:24:13.107" Title="Why are humans mostly right-handed?" Tags="&lt;human-biology&gt;&lt;brain&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ClosedDate="2015-07-21T04:59:24.273" ContentLicense="CC BY-SA 3.0" />
  <row Id="36255" PostTypeId="1" AcceptedAnswerId="36256" CreationDate="2015-07-21T03:47:38.840" Score="1" ViewCount="499" Body="&lt;p&gt;For general techniques involving molecular biology, I know of &lt;a href=&quot;http://www.molecularcloning.com/&quot; rel=&quot;nofollow&quot;&gt;Sambrook and Maniatis Molecular Cloning&lt;/a&gt; which covers many of the standard cloning techniques. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, mammalian cell culture has many significant differences from bacterial cell culture, some of which include the &lt;a href=&quot;http://www.protocol-online.org/biology-forums/posts/26803.html&quot; rel=&quot;nofollow&quot;&gt;many different variants&lt;/a&gt; of cell culture media as well as the relatively complex systems which cannot be provided using standardised media such as LB or TB in E. coli culture. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any similar textbooks/lab manuals for cell culture? Alternatively, good review papers covering the different kinds of media used in mammalian cell culture and their relative benefits would also be a good answer to this question. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-07-21T04:53:32.097" Title="Textbook/lab manual for mammalian cell culture" Tags="&lt;book-recommendation&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36256" PostTypeId="2" ParentId="36255" CreationDate="2015-07-21T04:53:32.097" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://as.wiley.com/WileyCDA/WileyTitle/productCd-0470528125.html&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;Culture of Animal Cells: A Manual of Basic Technique and Specialized Applications&lt;/em&gt;&lt;/a&gt; by Ian Freshney is the most popular book on the topic of animal cell culture.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also refer to &lt;a href=&quot;http://www.atcc.org/~/media/PDFs/Culture%20Guides/AnimCellCulture_Guide.ashx&quot; rel=&quot;nofollow&quot;&gt;ATCC animal cell culture guide&lt;/a&gt; which also has information about media formulations.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastActivityDate="2015-07-21T04:53:32.097" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36257" PostTypeId="1" AcceptedAnswerId="36293" CreationDate="2015-07-21T07:41:49.063" Score="5" ViewCount="312" Body="&lt;p&gt;There's a relatively big scare in local news about the &lt;em&gt;Heracleum sosnowskyi&lt;/em&gt; plant, considering &lt;a href=&quot;http://www.dailymail.co.uk/health/article-3137347/Gardener-left-horrific-burns-brushing-against-poisonous-giant-hogweed-fishing-t-expose-leg-sun-seven-YEARS.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;how dangerous it can be.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I was strolling through the park when I noticed these plants - the ones I photographed were rather small, but there have been a lot bigger examples in the park as well. For reference, I live in Poznań, Poland.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a feeling this isn't &lt;em&gt;Heracleum sosnowskyi&lt;/em&gt;, but the only reason I'm thinking this is because it was in a local park where there are a lot of people / kids, and if there were any dangerous plants there there would be an uproar... but I'd rather be sure, thus I'm posting this question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/BjA9p.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/BjA9pm.jpg&quot; alt=&quot;Photo 1&quot;&gt;&lt;/a&gt;&#xA;&lt;a href=&quot;https://i.stack.imgur.com/gvQBN.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/gvQBNm.jpg&quot; alt=&quot;Photo 2&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is this &lt;em&gt;Heracleum sosnowskyi&lt;/em&gt;?&lt;/p&gt;&#xA;" OwnerUserId="16872" LastEditorUserId="16872" LastEditDate="2015-07-22T07:03:05.840" LastActivityDate="2015-07-22T12:40:36.920" Title="Is this Heracleum sosnowskyi?" Tags="&lt;botany&gt;&lt;species-identification&gt;" AnswerCount="2" CommentCount="5" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36258" PostTypeId="1" AcceptedAnswerId="36263" CreationDate="2015-07-21T08:48:34.757" Score="4" ViewCount="2071" Body="&lt;p&gt;Why can't we (human, or even unicellular organisms) withstand low (body) temperatures (5 - 25°C). I have a limited background in chemistry and biology, so this might be obvious, but not to me.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I know that low temperature reduce the speed of chemical reactions, so any creature cold enough should just perform slower? Or are there any other cold-induced effects that prevent certain reactions? (a reaction requiring more energy to happen, would still happen, but at a lesser rate, right?)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And, supposing a bacteria/virus/small&amp;amp;simple organism was subjected to low temperature (above freezing, but low enough to stop working), what would prevent this organism from booting up again when subjecting to &quot;normal&quot; temperature?&lt;/p&gt;&#xA;" OwnerUserId="16873" LastEditorUserId="39703" LastEditDate="2018-01-24T16:45:07.667" LastActivityDate="2018-01-26T09:10:39.270" Title="Why are low temperatures lethal?" Tags="&lt;temperature&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36259" PostTypeId="1" CreationDate="2015-07-21T10:12:41.267" Score="5" ViewCount="625" Body="&lt;p&gt;How do people digest fat after gallbladder removal surgery? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How can they tolerate a high fat diet?&lt;/p&gt;&#xA;" OwnerUserId="16875" LastEditorUserId="16299" LastEditDate="2015-11-25T21:27:07.187" LastActivityDate="2015-11-25T21:27:07.187" Title="How do people digest fat after gall bladder removal surgery?" Tags="&lt;digestion&gt;&lt;bile&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36260" PostTypeId="2" ParentId="36259" CreationDate="2015-07-21T10:42:25.913" Score="5" Body="&lt;p&gt;This is not a problem, since the gall bladder &quot;only&quot; stores bile, but the production itself happens in the liver. There are some cases described which can get problems digesting very fatty food, but for most people this is not a problem. Additionally eating low-fat food in the first few weeks after the removal is recommended. See &lt;a href=&quot;http://www.everydayhealth.com/gallbladder/living-without-a-gallbladder.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; for some more details.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The picture below shows the location of the gall bladder and also the bile ducts (picture from &lt;a href=&quot;http://www.webmd.com/digestive-disorders/picture-of-the-gallbladder&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt;)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/2jlNr.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="5144" LastActivityDate="2015-07-21T10:42:25.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36262" PostTypeId="1" AcceptedAnswerId="36272" CreationDate="2015-07-21T12:55:02.450" Score="1" ViewCount="2270" Body="&lt;p&gt;Is there an epidimiological way to define &lt;strong&gt;rare&lt;/strong&gt; and &lt;strong&gt;common&lt;/strong&gt; diseases ?&lt;/p&gt;&#xA;" OwnerUserId="16284" LastActivityDate="2015-07-21T17:47:54.170" Title="Definitions of common and rare disease" Tags="&lt;epidemiology&gt;&lt;definitions&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="36263" PostTypeId="2" ParentId="36258" CreationDate="2015-07-21T14:00:29.033" Score="4" Body="&lt;p&gt;Low temperatures change the speed of different chemical reactions, throwing delicately balanced systems out of balance. How resilient a creature is to temperature changes is largely a function of how complex it is, and how buffered it is against this kind of change. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Tardigrade&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tardigrades&lt;/a&gt; as kmm mentioned essentially can't be killed by cold, surviving down to almost absolute zero (absolute zero ≈ minus 273.15°C). Most unicellular organisms can be frozen (especially if frozen quickly or &lt;a href=&quot;https://en.wikipedia.org/wiki/Cryoprotectant&quot; rel=&quot;nofollow noreferrer&quot;&gt;cryoprotected&lt;/a&gt; with something like DMSO) and revived later without any change. Most strain libraries of bacteria are kept frozen for cost reasons. Even human cell cultures can be &lt;a href=&quot;http://www.lifetechnologies.com/us/en/home/references/gibco-cell-culture-basics/cell-culture-protocols/freezing-cells.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;frozen&lt;/a&gt; and &lt;a href=&quot;http://www.lifetechnologies.com/us/en/home/references/gibco-cell-culture-basics/cell-culture-protocols/thawing-cells.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;thawed&lt;/a&gt;, even though some of the cells will die. (If even 10% of your cells died you as a person would probably die, so freezing is off the table unless you are very clever indeed.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Humans and most mammals are pretty sensitive to temperature changes, even though reptiles are not. Most fish are cold-blooded and are adapted to cope with the relatively cold temperatures, but the human heart is not well adapted to even relatively warm temperatures. The atria and the ventricles of the heart stop communicating below 27°C (80.6°F)or so, and &lt;a href=&quot;https://en.wikipedia.org/wiki/Hypothermia#Diagnosis&quot; rel=&quot;nofollow noreferrer&quot;&gt;below 20°C (68°F) the heart can stop beating entirely&lt;/a&gt;. Nerves are complex systems, and absent regulation systems in the nerves themselves to compensate for the changes in temperature, they can stop firing completely. A simple heart can run with less sophisticated orchestration, and is, therefore, more resistant to temperature change. A complicated heart involving the coordination of the atria and the ventricles to produce effective pumping action is affected much more strongly by the drop in temperature. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in general, more complicated implies more vulnerable to temperature changes. There are exceptions, however. Bears can hibernate and drop their core body temperatures without any ill-effects, so it's possible to adapt to. Fish deal very well with cold temperatures if exposed gradually, and &lt;a href=&quot;https://en.wikipedia.org/wiki/Notothenioidei&quot; rel=&quot;nofollow noreferrer&quot;&gt;some fish&lt;/a&gt; could live quite happily in a slushie, salinity notwithstanding.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastEditorUserId="12923" LastEditDate="2018-01-26T09:10:39.270" LastActivityDate="2018-01-26T09:10:39.270" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36264" PostTypeId="1" CreationDate="2015-07-21T14:08:21.733" Score="7" ViewCount="108" Body="&lt;p&gt;Can you please identify this butterfly. It was seen in Dorset England 9th July. I think it is a female Silver Studded Blue.&lt;img src=&quot;https://i.stack.imgur.com/HnkjH.jpg&quot; alt=&quot;Unknown Butterfly&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="16881" LastEditorUserId="5755" LastEditDate="2015-07-21T15:19:59.763" LastActivityDate="2015-08-01T18:19:13.160" Title="Butterfly identification: Dorset England, July." Tags="&lt;species-identification&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36265" PostTypeId="1" AcceptedAnswerId="36290" CreationDate="2015-07-21T14:57:03.593" Score="5" ViewCount="435" Body="&lt;p&gt;Very simple cells, such as &lt;code&gt;Nanoarchaeum equitans&lt;/code&gt;, require a host to provide certain essential ingredients for life. Complex life-forms (like humans) require a whole ecosystem of other life-forms to survive (either externally, to provide food, or internally, in a symbiotic relationship).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the simplest cell that has been discovered so far that can live in an environment where there are no other life-forms, not even in a decomposed state? Does such an organism exist, or is all life inextricably dependent on other life?&lt;/p&gt;&#xA;" OwnerUserId="16882" LastEditorUserId="3340" LastEditDate="2015-07-21T15:19:52.117" LastActivityDate="2017-05-03T00:42:42.327" Title="What is the simplest autotrophic cell?" Tags="&lt;microbiology&gt;&lt;reproduction&gt;" AnswerCount="2" CommentCount="6" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36266" PostTypeId="1" CreationDate="2015-07-21T15:57:19.817" Score="2" ViewCount="2770" Body="&lt;p&gt;Yesterday I had my wisdom teeth removed. This morning, when I heard our phone ringing, it sounded a little lower-pitched than usual (I have perfect pitch). Sure enough, when I opened FL Studio (music-making software) and loaded up one of my projects, I had to adjust the master pitch up by about 20 cents for it to sound &quot;in-tune&quot;. What could cause this shift in pitch perception?&lt;/p&gt;&#xA;" OwnerUserId="16884" LastActivityDate="2015-10-02T23:35:29.330" Title="Pitch shift in hearing after wisdom teeth removal" Tags="&lt;sensation&gt;&lt;hearing&gt;&lt;senses&gt;" AnswerCount="0" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="36267" PostTypeId="1" CreationDate="2015-07-21T16:17:30.800" Score="0" ViewCount="87" Body="&lt;p&gt;Do different values of the smoothing parameter lambda for estimating the divergence times (in situ Sanderson 2002) will affect trait conservatism (e.g., Blomberg's K)?&lt;/p&gt;&#xA;" OwnerUserId="8856" LastActivityDate="2015-11-18T21:22:36.430" Title="Blomberg's K and branch length" Tags="&lt;community-ecology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36268" PostTypeId="2" ParentId="36257" CreationDate="2015-07-21T16:31:29.797" Score="2" Body="&lt;p&gt;I'd say it's an imposter, but depending on the stage of it's life cycle, characteristics may differ. The following webpage lists &lt;a href=&quot;http://www.dec.ny.gov/animals/72766.html&quot; rel=&quot;nofollow&quot;&gt;identifying factors&lt;/a&gt; for giant hogweed, as well as some plants that may be mistaken for it (but of course, they aren't). The lack of purple splotches and white hairs around the stalk bases, and leaves are signaling to me that this &lt;strong&gt;is not&lt;/strong&gt; giant hogweed. It looks like it may just be wild parsnip. Take a look at that webpage, giant hogweed is quite... giant.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-07-21T16:31:29.797" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36270" PostTypeId="2" ParentId="36223" CreationDate="2015-07-21T17:36:05.477" Score="1" Body="&lt;p&gt;With good technique, you can reliably perform RT-PCR or RT-qPCR on a sample size of about 100 cells. Some of the comments are correct that you will need to compensate for the reduction of the initial cell input with additional PCR cycles. However, each magnitude in reduction of cells corresponds to about 3 extra PCR cycles (2^3 = 8 ~= 10), so your overall qPCR cycle number will not change significantly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since you are dealing with a small amount of cells, and isolating by TRIzol, the pellet could be difficult to see. I would suggest you use something like Glycogen (&lt;a href=&quot;https://www.lifetechnologies.com/order/catalog/product/AM9516&quot; rel=&quot;nofollow&quot;&gt;Glycoblue from Ambion&lt;/a&gt;) to co-precipitate the pellet into something more visible. You would add this prior to the Isopropanol to precipitate your nucleic acids.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your use of extra TRIzol is not a problem unless you're lab is short of money. It will dilute your concentration of nucleic acid, which will make precipitation harder, but using glycogen will compensate for this. Using an amount less than the manual directed ratios can be problematic as it could result in incomplete lysis and denaturation of your cellular components.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As user137 recommends, Pre-amplification of the products is not a good idea as it will likely distort your final results. I'm not sure what gene expressions you're looking at, but it is always a good idea to include multiple housekeeping genes as baselines to calculate your relative expression numbers, provided you have enough RNA isolate to use as input.&lt;/p&gt;&#xA;" OwnerUserId="16816" LastActivityDate="2015-07-21T17:36:05.477" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36272" PostTypeId="2" ParentId="36262" CreationDate="2015-07-21T17:47:54.170" Score="2" Body="&lt;p&gt;While &quot;common disease&quot; has obscure incidence and prevalence definitions, &quot;Rare&quot; or &quot;&lt;a href=&quot;https://en.wikipedia.org/wiki/Rare_disease&quot; rel=&quot;nofollow&quot;&gt;orphan disease&lt;/a&gt;&quot; is more defined. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Rare_Diseases_Act_of_2002&quot; rel=&quot;nofollow&quot;&gt;In the US&lt;/a&gt;, the rare disease defined as a condition which affect one (or less) of 200,000 people in population. However, this definition can be different in other countries, p.e. in Japan 1:50,000 or less.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can assume that &quot;common&quot; disease is much frequent than &quot;rare&quot; one, thus the incidence and prevalence are much greater than per &quot;rare disease&quot; definition. However, again, there is no agreement of clear cut of &quot;common disease&quot; incidence and prevalence. &lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-21T17:47:54.170" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36274" PostTypeId="1" CreationDate="2015-07-21T18:44:12.083" Score="8" ViewCount="281" Body="&lt;p&gt;I'm reading the book called &quot;&lt;a href=&quot;http://www.reuniting.info/download/pdf/Cupid_PR_author.pdf&quot;&gt;Cupid's poison arrow&lt;/a&gt;&quot;, which revolves around a rather simple assumption: most mammals, including humans have a genetic program that is responsible for ever increasing dissatisfaction with a mate after intercourse with orgasm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The book proceeds to give a number of examples, here's what I remember:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Coolidge_effect&quot;&gt;Coolidge effect&lt;/a&gt;, where libido is revived upon exposure to a novel, receptive partner.&lt;/li&gt;&#xA;&lt;li&gt;Male rate copulating on average 8 times with a receptive female before losing interest&lt;/li&gt;&#xA;&lt;li&gt;Sexual &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319191/&quot;&gt;satiety setting off a 14-15 day hormonal cycle&lt;/a&gt; where [a male rat] would lose all interest in a partner&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;The book contains a &lt;strong&gt;large amount of anecdotal evidence&lt;/strong&gt; of humans experiencing negative outlook on their partner after orgasmic intercourse, with more intense intercourse producing more intense dissatisfaction. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The author proceeds to formulate a hypothesis that humans and other mammals have a genetic program that fosters sepratation between mates and seeking of a novel mate as a mechanism to promote more genetic diversity in offspring (as opposed to monogamy)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there a scientific basis for such claims -  &lt;strong&gt;do mammals have a mechanism that draws them apart after intercourse or sexual satiety is achieved?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastActivityDate="2017-01-17T17:18:35.733" Title="Is there a mechanism by which mammals lose interest in a partner after mating?" Tags="&lt;human-biology&gt;&lt;zoology&gt;&lt;sexual-selection&gt;&lt;reproductive-biology&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36275" PostTypeId="2" ParentId="36267" CreationDate="2015-07-21T18:46:21.737" Score="2" Body="&lt;p&gt;I don't know if lambda for estimating divergence times works in the same way as it does for scaling internal tree nodes, but I'm going to assume it does given the context of your question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My gut reaction was: of course it must because K is the ratio of observed to expected variance and tip variance is moderated in part by branch lengths. So if you change the node positions, the expected tip variance should also change.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A quick simulation shows that this appears to be true.&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;library(&quot;ape&quot;)&#xA;library(&quot;picante&quot;)&#xA;library(&quot;geiger&quot;)&#xA;&#xA;set.seed(5)&#xA;&#xA;tree &amp;lt;- rtree(30)&#xA;y &amp;lt;- rTraitCont(tree)&#xA;&#xA;lambdas &amp;lt;- seq(1.0, 0.05, by = -0.05)&#xA;M &amp;lt;- data.frame(lambda = lambdas, k = numeric(length(lambdas)))&#xA;&#xA;for (lambda in lambdas){&#xA;  tree_trans &amp;lt;- rescale(x = tree,&#xA;                        model = &quot;lambda&quot;, lambda = lambda)&#xA;  M$k[M$lambda == lambda] &amp;lt;- phylosignal(y, tree_trans)$K&#xA;}&#xA;&#xA;plot(k ~ lambda, data = M)&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;Generate a tree with 30 tips and generate random data along the branches. Then rescale the tree for a series of lambda values and calculate k for each lambda scaling.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/4o7iG.png&quot; alt=&quot;K vs lambda&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="107" LastActivityDate="2015-07-21T18:46:21.737" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36278" PostTypeId="1" CreationDate="2015-07-21T20:41:28.447" Score="2" ViewCount="2990" Body="&lt;p&gt;I cannot find a reliable way to kill fleas after removing them from my cats with a flea comb.  Soap and water does not do the job and they climb back out of the drain.&#xA;Will cooking oil  suffocate fleas?  If so how long of time until the flea expires?&lt;/p&gt;&#xA;" OwnerUserId="16891" LastEditorUserId="3340" LastEditDate="2015-07-22T06:19:43.777" LastActivityDate="2015-08-21T06:53:16.323" Title="Can cooking oil kill fleas?" Tags="&lt;parasitology&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36279" PostTypeId="2" ParentId="36278" CreationDate="2015-07-21T21:09:50.830" Score="2" Body="&lt;p&gt;Short answer: Mire them in a viscous liquid then leave them in there long enough for them to die, instead of immediate disposal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Cooking oil is viscous, so yes you can viably use it to mire the fleas. You'll need to wait until they die though to dispose of them or else they'll come crawling back as you've stated. The DIY option is generally a water/dish soap mixture in a container: you'll put the fleas in and they sink to the bottom almost immediately. Just leave them in there and they'll eventually die in about 5 minutes. Some individuals suggest Dawn dish soap, much like &lt;a href=&quot;http://www.vetinfo.com/homemade-dog-flea-shampoo.html#b&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;, where the claim is that the Dawn contains compounds which suffocate the fleas.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can also make a flea trap for around the house, with a bowl of dish soap and water near a night light. They'll jump for the light and end up falling into the flea trap.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-07-21T21:09:50.830" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36281" PostTypeId="1" CreationDate="2015-07-21T23:18:29.057" Score="2" ViewCount="112" Body="&lt;p&gt;I've received freeze-dried bacteria that I intend to use for a study I'm doing on slime mold; however, I've never dealt with freeze-dried, only frozen, bacterial cells. After reconstituting these cells in 6mL media, is it alright to split this in to halves and place one aliquot into DMSO or glycerol to make a permanent stock right away? Or is it best to plate, isolate, suspend, grow, and then make a permanent stock?&lt;/p&gt;&#xA;" OwnerUserId="16637" LastActivityDate="2015-07-21T23:18:29.057" Title="What is the standard protocol for creating permanent stocks from freeze-dried bacteria?" Tags="&lt;cell-culture&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36282" PostTypeId="1" AcceptedAnswerId="36315" CreationDate="2015-07-22T00:08:35.163" Score="3" ViewCount="3335" Body="&lt;p&gt;I read an interesting post on Facebook the other day saying that we all have a visible scar since birth - our belly button. This got me thinking (and research for me only found results regarding belly button piercing) is the belly button made up of scar tissue?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I seem to recall that there are some stem cells still within the umbilical cord (which is why doctors tell you to spend the money to have it saved (I think)) so I was wondering if scar tissue closed the hole left by our cut umbilical cord, or if the stem cells divided to produce normal skin tissue. &lt;/p&gt;&#xA;" OwnerUserId="16041" LastActivityDate="2015-08-31T14:51:57.993" Title="Do our belly buttons consist of scar tissue?" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;&lt;human-physiology&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36283" PostTypeId="1" AcceptedAnswerId="36284" CreationDate="2015-07-22T01:18:17.647" Score="4" ViewCount="9570" Body="&lt;p&gt;What determines whether an action potential is inhibitory or excitatory? Is it determined by the receptors, the neurotransmitters, or some other mechanism? &lt;/p&gt;&#xA;" OwnerUserId="11652" LastEditorUserId="9943" LastEditDate="2015-07-22T02:02:23.873" LastActivityDate="2019-07-27T20:34:02.380" Title="What determines whether an action potential is inhibitory or excitatory?" Tags="&lt;neuroscience&gt;&lt;biophysics&gt;&lt;neurophysiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36284" PostTypeId="2" ParentId="36283" CreationDate="2015-07-22T01:50:32.493" Score="7" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;The physiological state of the postsynaptic cell ultimately determines the effect of an incoming action potential.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;An action potential occurring in a chemical synapse is neither inhibitory or excitatory. An action potential is a binary '1', an-all-or-nothing signal without any information, i.e., there is not a -1 or +1 action potential. Similarly, there are no excitatory or inhibitory neurotransmitters. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Notably, the principal excitatory neurotransmitter in the nervous system, glutamate, can have inhibitory effects dependent on the receptor activated. While most metabotropic glutamate receptors (mGluRs) and ionotropic AMPA and NMDA receptors are indeed all excitatory, the inhibitory glutamate receptors (iGluRs) are not &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8938647&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Cleland, 1996)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Conversely, GABA, the principal inhibitory neurotransmitter in the nervous system, can have excitatory postsynaptic effects. For example, hyperpolarized neurons may actually depolarize upon GABA&lt;sub&gt;A&lt;/sub&gt; receptor activation, simply because the resting membrane potential is more negative than the reversal potential of Cl&lt;sup&gt;-&lt;/sup&gt; (i.e., Cl&lt;sup&gt;-&lt;/sup&gt; flows &lt;em&gt;out&lt;/em&gt; of the cell due to the negative membrane potential) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15927683&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Marty &amp;amp; Liano, 2005)&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The existence of both excitatory and inhibitory glutamate receptors shows that it is the &lt;strong&gt;postsynaptic receptor&lt;/strong&gt; that determines whether an action potential will inhibit or excite the postsynaptic neuron. The excitatory effect of GABA&lt;sub&gt;A&lt;/sub&gt; activation shows that on top of that, even principal inhibitory neurotransmitters (GABA) with principal inhibitory receptors (GABA&lt;sub&gt;A&lt;/sub&gt;) can excite a neuron dependent on its &lt;strong&gt;physiological state&lt;/strong&gt;.    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Besides chemical synapses there are electrical synapses. In these synapses action potentials are transmitted directly electrically through gap junctions. In this case, &lt;em&gt;any action potential&lt;/em&gt; is excitatory as the signal will be carried forward if it is strong enough &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK11164/&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Purves e&lt;em&gt;t al&lt;/em&gt;., 2001)&lt;/a&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8938647&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cleland, &lt;em&gt;Mol Neurobiol&lt;/em&gt; (1996); &lt;strong&gt;13&lt;/strong&gt;(2): 97-136&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/15927683&quot; rel=&quot;nofollow noreferrer&quot;&gt;Marty &amp;amp; Liano, &lt;em&gt;Trends Neurosci&lt;/em&gt; (2005); &lt;strong&gt;28&lt;/strong&gt;(6): 284-9&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK11164/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Purves &lt;em&gt;et al&lt;/em&gt;., Neuroscience, 2&lt;sup&gt;nd&lt;/sup&gt; ed. Sunderland (MA): Sinauer Associates; 2001.&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2019-07-27T20:34:02.380" LastActivityDate="2019-07-27T20:34:02.380" CommentCount="9" ContentLicense="CC BY-SA 4.0" />
  <row Id="36285" PostTypeId="1" AcceptedAnswerId="37046" CreationDate="2015-07-22T02:21:19.937" Score="1" ViewCount="691" Body="&lt;p&gt;While researching the F12 cell culture medium &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC219509/pdf/pnas00154-0064.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Ham, 1965)&lt;/a&gt;, I came across the term &quot;&lt;strong&gt;essentially diploid&lt;/strong&gt; Chinese hamster ovary cells&quot;. The terms &quot;subdiploid&quot; and &quot;near diploid&quot; were also used to refer to the same cells. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/MCQAk.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Attempts at searching Google Scholar and regular Google failed to turn up a definition of the phrase. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What exactly is meant by &quot;essentially diploid&quot;, and how is it different from regular diploid cells?&lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-08-21T17:08:11.807" Title="Definition of &quot;essentially diploid&quot;" Tags="&lt;genetics&gt;&lt;terminology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36288" PostTypeId="2" ParentId="36252" CreationDate="2015-07-22T05:28:15.730" Score="2" Body="&lt;p&gt;I think various ways can be apply, but the easiest way could be to indicate the range to set a forward primer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Decide the length of primer you are going to get. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say you would like 25 mer. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can set the range from &lt;strong&gt;chr12:25398261&lt;/strong&gt; to &lt;strong&gt;chr12:25398309&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you identify where &lt;strong&gt;chr12:25398285&lt;/strong&gt; is in &lt;strong&gt;NG_007524.1&lt;/strong&gt;, you are ready to design your primers.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="16651" LastEditDate="2015-11-19T13:24:14.647" LastActivityDate="2015-11-19T13:24:14.647" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36289" PostTypeId="1" AcceptedAnswerId="36300" CreationDate="2015-07-22T06:21:35.997" Score="1" ViewCount="75" Body="&lt;p&gt;Among the 6 secretion systems in bacteria, can these 6 ways be sorted out in the order of how harmful it is to the human host? Like say type 3 is highly virulent so that comes first, but I don't know about the rest of the systems. Being a computer science student, I have failed to understand the Wikipedia article to derive this order. Does a discrete order even exist? Can anyone answer this question?&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="3340" LastEditDate="2015-07-22T08:58:50.113" LastActivityDate="2015-07-22T15:08:19.137" Title="Secretion in Gram negative bacteria" Tags="&lt;bacteriology&gt;&lt;virology&gt;&lt;pathogenesis&gt;&lt;bacterial-toxins&gt;&lt;host-pathogen-interaction&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36290" PostTypeId="2" ParentId="36265" CreationDate="2015-07-22T06:50:46.390" Score="4" Body="&lt;p&gt;If by &quot;simplest&quot; you mean smallest genome, then according to Brock's Biology of Microrganisms (13th ed, p 319) the smallest autotroph is &lt;em&gt;Aquifex aeolicus&lt;/em&gt;, a chemolithotroph bacterium. It's genome is 1.5M bases, about 1/3 of that of E.Coli, and was sequenced in 1998 (&lt;a href=&quot;https://www.ncbi.nlm.nih.gov/pubmed/9537320&quot; rel=&quot;nofollow&quot;&gt;https://www.ncbi.nlm.nih.gov/pubmed/9537320&lt;/a&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The genome is densely packed though and still carries some 1,500 open reading frames. The authors of the genome sequencing paper states that &quot;metabolic flexibility seems to be reduced as a result of the limited genome size&quot;, which I guess is some evidence of &quot;simplicity&quot;.&lt;/p&gt;&#xA;" OwnerUserId="15695" LastActivityDate="2015-07-22T06:50:46.390" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36291" PostTypeId="1" AcceptedAnswerId="36383" CreationDate="2015-07-22T07:24:51.917" Score="6" ViewCount="734" Body="&lt;p&gt;From Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Lotka–Volterra equations, also known as the predator–prey equations, are a pair of first-order, non-linear, differential equations frequently used to describe the dynamics of biological systems in which two species interact, one as a predator and the other as prey. The populations change through time according to the pair of equations:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;\begin{align}&#xA;\frac{dx}{dt} = \alpha x - \beta x y \\&#xA;\frac{dy}{dt} = \delta x y  - \gamma y&#xA;\end{align}&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Ocuoy.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This looks very similar to how Insulin and Glucose interact with each other in the body. &#xA;&lt;img src=&quot;https://i.stack.imgur.com/V3jq2.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Glucose uptake release insulin and glucagon offsets the effect of insulin through glycogenesis.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can the Glucose-Insulin dynamic be described as Lotka Volterra?&lt;/p&gt;&#xA;" OwnerUserId="9020" LastActivityDate="2015-08-10T07:00:53.273" Title="Is Insulin-Glucose dynamic Lotka-Volterra?" Tags="&lt;theoretical-biology&gt;&lt;literature&gt;&lt;glucose&gt;&lt;insulin&gt;" AnswerCount="4" CommentCount="1" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36292" PostTypeId="1" CreationDate="2015-07-22T07:44:46.623" Score="7" ViewCount="14192" Body="&lt;p&gt;So apparently we produce roughly 300 million sperm daily. Is there a reason why this is necessary? Wouldn't a much smaller (but still large) number be sufficient? Like, one million?&lt;/p&gt;&#xA;" OwnerUserId="16897" LastActivityDate="2016-04-09T23:16:34.910" Title="Why do we produce so many sperm?" Tags="&lt;reproduction&gt;" AnswerCount="2" CommentCount="12" ContentLicense="CC BY-SA 3.0" />
  <row Id="36293" PostTypeId="2" ParentId="36257" CreationDate="2015-07-22T07:50:59.087" Score="5" Body="&lt;p&gt;No, I don't think it looks like &lt;em&gt;Heracleum sosnowskyi&lt;/em&gt;. To me, the plant in your pictures looks similar to &lt;a href=&quot;https://en.wikipedia.org/wiki/Angelica_sylvestris&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Angelica sylvestris&lt;/em&gt;&lt;/a&gt; (which is common in Poland), but there are many species in &lt;a href=&quot;https://en.wikipedia.org/wiki/Apiaceae&quot; rel=&quot;nofollow noreferrer&quot;&gt;Apiaceae&lt;/a&gt; with a similar apparence and I'm not familiar with all of them. Species in the &lt;em&gt;Heracleum&lt;/em&gt; genus has leafs that are &quot;lobed&quot; and all leaflets aren't as separated as the plant in your pictures (overall, the leafs of &lt;em&gt;Heracleum&lt;/em&gt; look quite different), and the stem is usually &quot;swollen&quot; where the leafs connect (i.e. the leaf stems are swollen). Plants of &lt;em&gt;Heracleum sosnowskyi&lt;/em&gt; (and &lt;em&gt;H. mantegazzianum&lt;/em&gt;) are also much larger, and they often have a fussy apparence because of the bristle hairs. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Angelica sylvestris&lt;/em&gt;&lt;/strong&gt; (picture from from wikimedia commons)&#xA;&lt;img src=&quot;https://i.stack.imgur.com/N7Dwh.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-07-22T12:40:36.920" LastActivityDate="2015-07-22T12:40:36.920" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36294" PostTypeId="2" ParentId="36289" CreationDate="2015-07-22T07:58:30.817" Score="1" Body="&lt;p&gt;I think you cannot find a better answer then the following review:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.nature.com/nrmicro/journal/v13/n6/full/nrmicro3456.html&quot; rel=&quot;nofollow&quot;&gt;http://www.nature.com/nrmicro/journal/v13/n6/full/nrmicro3456.html&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was published in 2015, and it gives a good overview about the secretion systems. Anyway, T6SS can also be virulent. &lt;em&gt;Vibrio cholerae&lt;/em&gt; can use an effector of this SS to cross-link actin in the host cell and modify its morphology and its cytoskeleton behaviour. &#xA;In general I think that there is not a general order of virulence, also because the T3SS was discovered long ago. Whereas, the T6SS just recently, so the amount of information about its function is still somehow limited. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hope this helps.&lt;/p&gt;&#xA;" OwnerUserId="12942" LastEditorUserId="12942" LastEditDate="2015-07-22T15:08:19.137" LastActivityDate="2015-07-22T15:08:19.137" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36296" PostTypeId="1" AcceptedAnswerId="36297" CreationDate="2015-07-22T08:47:08.373" Score="1" ViewCount="256" Body="&lt;p&gt;In this &lt;a href=&quot;http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html&quot; rel=&quot;nofollow&quot;&gt;paper&lt;/a&gt;, the cuffcompare RNA package is reported:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Because of the stochastic nature of sequencing, assembly of the same&#xA;  transcript in two different samples may result in transfrags of&#xA;  slightly different lengths. A Cufflinks transfrag was considered a&#xA;  complete match when there was a transcript with an identical chain of&#xA;  introns in the combined annotation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;What does this mean in terms of comparing two transcripts to see if they are the same? Does that mean two transcripts are considered equal if they have the same introns, even some exons are missing in one of the transcript? What do they mean by transfrag? Is there an example?&lt;/p&gt;&#xA;" OwnerUserId="14905" LastEditorUserId="5144" LastEditDate="2015-07-22T09:29:52.627" LastActivityDate="2015-07-22T09:29:52.627" Title="How to compare two RNA transcripts?" Tags="&lt;bioinformatics&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36297" PostTypeId="2" ParentId="36296" CreationDate="2015-07-22T08:53:38.000" Score="1" Body="&lt;p&gt;If some exons are missing in one of the samples then the introns will, by definition, be different. What this allows is for the bounds of the outermost exons to vary a bit. This is particularly useful for exon 1, which often has lower coverage.&lt;/p&gt;&#xA;" OwnerUserId="9523" LastActivityDate="2015-07-22T08:53:38.000" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36298" PostTypeId="2" ParentId="36292" CreationDate="2015-07-22T09:30:34.810" Score="2" Body="&lt;p&gt;The answer, if you search &lt;a href=&quot;http://goaskalice.columbia.edu/why-does-it-take-millions-sperm-fertilize-egg&quot; rel=&quot;nofollow&quot;&gt;for&lt;/a&gt; a &lt;a href=&quot;http://scienceline.org/2008/06/ask-olson-sperm/&quot; rel=&quot;nofollow&quot;&gt;bit&lt;/a&gt;, boils down to geometry. It takes X amount of sperm cells to successfully fertilize an egg. If you optimize delivery system (e.g. vagina geometry), you'll need less. In species where one male fertilize number of eggs (aka polygamy) and are able to have progeny from number of females, you need less cells in ejaculate to produce single child, because chances are higher with higher number of matings.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In humans it is quite often one male-one female relationship, so you have to bump number of cells in ejaculate so that mating season is fruitful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Final point of real-life statistics:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;http://www.pennmedicine.org/encyclopedia/em_DisplayAnimation.aspx?gcid=000120&amp;amp;ptid=17&quot; rel=&quot;nofollow&quot;&gt;Of the 300 million sperm ejaculated, only about 200 or so will survive to reach the egg cell and only one will succeed in fertilizing it.&lt;/a&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You need to beat these odds ($10^{-6}$) in order to reproduce. Why female reproductive organs are so restrictive? Probably because there is some link between male's overall fitness and number of sperm cells. Fit males (those that hunt better than others) are able to spend more energy for generating sperm, rather than &quot;feeding&quot; their own body. If they able to &quot;feed&quot; 300 million sperm cells, they probably will be able to feed a child.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastEditorUserId="14552" LastEditDate="2015-07-22T14:55:04.580" LastActivityDate="2015-07-22T14:55:04.580" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36300" PostTypeId="2" ParentId="36289" CreationDate="2015-07-22T12:09:08.877" Score="1" Body="&lt;p&gt;Theoretically there are two very basic things to consider in judging virulence for the secretion systems: &#xA;a) Can it secrete into any human cell? (If not, chances of being virulent are smaller, but not zero as whatever is secreted in the environment of a cell could also be harmful for the cell.) &#xA;b) Does it secrete some agent (protein, RNA, molecule), which is potentially harmful for a human cell? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;a) alone is not sufficient for it to be virulent if b) is not also given.&#xA;(As it could inject something in a cell that the cell can handle without a problem.)&#xA;b) alone is not sufficient, as it has to get inside the cell somehow. Although, b) alone can work, if the agent has another way to get inside a cell or to harm the cell from outside.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, generally, without knowing ALL the bacterial secretion systems and secreted agents, it is impossible to decide if one secretion system (alone) is always, sometimes or never harmful.&lt;/p&gt;&#xA;" OwnerUserId="3827" LastActivityDate="2015-07-22T12:09:08.877" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="36301" PostTypeId="1" CreationDate="2015-07-22T13:12:41.973" Score="1" ViewCount="1193" Body="&lt;p&gt;I am a computer science student and I'm in an internship at a genomics and biotechnologies research institute. My current task is to calculate the IC50 and the EC50 given a set of data as a table.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/WWINM.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/WWINM.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The thing is, I am required to find a way to automate these calculations, currently working in excel. Which proves to be really difficult for me having no biology background. I have asked around and the people there kindly explained to me what the IC50 is and why it is needed, how the data is gathered, what tools they use to gather it and so on. &#xA;My problem though, is that what I need is a way to calculating it. A mathematical way, something I could use to write a formula in excel, or preferably a software I could write.(Once I know how to calculate it)&#xA;During my research I found this video on how to calculate the IC50 using an excel macro function, but I do not know if it actually works, having been provided a limited ammount of test data. (I am not sure on how reliable that algorithm is either)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=ynMcHziZhvs&quot; rel=&quot;nofollow noreferrer&quot;&gt;https://www.youtube.com/watch?v=ynMcHziZhvs&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can someone please help me with an actual mathematical way to calculate the IC50/EC50? &#xA;My reading seems to not be of very much help no matter how much I try to use the internet's free resources to gather theoretical information about the topic.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ok the question seems to have been marked as off-topic homework because I didn't present my way of solving it. First of all, it's not homework, it's a work problem I've encountered and need help with. Second, here is my attempt at solving it using an excel Macro&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;&lt;pre&gt;&lt;code&gt;Function HalfWay(Ys As Range) As Double&#xA;    Dim pMin As Double, pMax As Double&#xA;    pMin = WorksheetFunction.Min(Ys)&#xA;    pMax = WorksheetFunction.Max(Ys)&#xA;    HalfWay = pMax - (pMax - pMin) / 2 &#xA;    End Function  &#xA;Function ECIC(X As Range, Y As Range) As Variant &#xA;    Y50=HalfWay(Y)&#xA;    Dim iRow1 As Integer, iRow2 As Integer, Asc As Integer, X1 As String, Y1 As String&#xA;    If Y.Cells(1, 1) &amp;lt; Y.Cells(2, 1) Then Asc = 1 Else Asc = -1&#xA;    iRow1 = WorksheetFunction.Match(Y50, Y, Asc)&#xA;    iRow2 = WorksheetFunction.Match(Y50, Y, Asc) + 1&#xA;    X1 = X.Cells(iRow1, 1).Address &amp;amp; &quot;:&quot; &amp;amp; X.Cells(iRow2, 1).Address&#xA;    Y1 = Y.Cells(iRow1, 1).Address &amp;amp; &quot;:&quot; &amp;amp; Y.Cells(iRow2, 1).Address&#xA;    ECIC = WorksheetFunction.Trend(Range(X1), Range(Y1), Y50) &#xA;    End Function&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This code basically draws a line in memory between the points that are before and after the IC50/EC50 point on the graph and calculates the EC/IC's corresponding concentration based on its actual effectiveness. I am not sure how reliable this method is though.&lt;/p&gt;&#xA;" OwnerUserId="16903" LastEditorUserId="16903" LastEditDate="2015-07-23T07:24:03.347" LastActivityDate="2015-07-23T07:24:03.347" Title="IC50 calculation" Tags="&lt;bioinformatics&gt;&lt;genomics&gt;&lt;toxicology&gt;" AnswerCount="1" CommentCount="10" ClosedDate="2015-07-23T04:43:04.043" ContentLicense="CC BY-SA 3.0" />
  <row Id="36302" PostTypeId="2" ParentId="36154" CreationDate="2015-07-22T13:19:27.540" Score="7" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;An action potential is a binary all-or-nothing event, while a graded potential is an analog signal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Action potentials, once initiated, are basically all-or-nothing events. Amplitudes may admittedly be variable, but basically it is the spike rate that is relevant to the neural code &lt;a href=&quot;http://www.pnas.org/content/94/24/12740.full&quot; rel=&quot;noreferrer&quot;&gt;(Gerstner &lt;em&gt;et al&lt;/em&gt;., 1997)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In contrast, graded potentials code information mainly by &lt;em&gt;amplitude&lt;/em&gt;. A notable example of the significance of graded potentials is the function of the inner hair cells in the cochlea (the inner ear). The mechanoreceptors on the hair cells open when deflected in one direction, while they close in the other. This is important, as that property depolarizes the cell on one phase of an input sinusoid, while it hyperpolarizes the cell in the subsequent phase. Also, stronger (louder) input increases the response, while softer stimulu generate less response (Fig. 1). In the auditory nerve this graded potential is translated into spike rates (Fig. 2). Basically the hair-cell and auditory nerve system is an analogue-to-digital converter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/ccEp3.jpg&quot; alt=&quot;CM&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Cochlear microphonic: a graded potential that increases amplitude with increasing loudness. Source: &lt;a href=&quot;http://www.elsevier.es/en-revista-acta-otorrinolaringologica-espanola-402-articulo-cochlear-microphonic-latency-90341040&quot; rel=&quot;noreferrer&quot;&gt;Juaristi &amp;amp; Martínez-Conde, 2014&lt;/a&gt;&lt;/sup&gt;    &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/JZSPL.jpg&quot; alt=&quot;CM versus spike rate&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 2. In the auditory nerve amplitude is coded as action potential (spike) rates, low frequencies as burst-repetition rate. Source: &lt;a href=&quot;http://www.cns.nyu.edu/~david/courses/perception/lecturenotes/loudness/loudness.html&quot; rel=&quot;noreferrer&quot;&gt;NY University&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.pnas.org/content/94/24/12740.full&quot; rel=&quot;noreferrer&quot;&gt;Gerstner &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;PNAS&lt;/em&gt; (1997); &lt;strong&gt;94&lt;/strong&gt;(24): 12740–1&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.elsevier.es/en-revista-acta-otorrinolaringologica-espanola-402-articulo-cochlear-microphonic-latency-90341040&quot; rel=&quot;noreferrer&quot;&gt;Juaristi &amp;amp; Martínez-Conde, &lt;em&gt;Acta Otorrinolaringol Española&lt;/em&gt; (2014); &lt;strong&gt;65&lt;/strong&gt;(04)&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-28T00:03:33.210" LastActivityDate="2015-07-28T00:03:33.210" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36304" PostTypeId="2" ParentId="36173" CreationDate="2015-07-22T13:59:47.983" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;The main limitation to frequency discrimination is &lt;em&gt;loudness&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;The cochlea is tonotopically organized - it basically acts as a Fourier transformer, where different frequencies are analyzed on a place map  (Fig. 1). Frequency tuning of cochlear hair cells is mainly limited by sound intensity. The louder a pure-tone sound stimulus gets, the larger the area on the basilar membrane that is activated and hence the wider the range of cochlear hair cells that is activated, and hence the worse the frequency resolution becomes (Fig. 2).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/AhBih.png&quot; alt=&quot;Cochlear tonotopy&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Cochlear tonotopy. Source: &lt;a href=&quot;http://cochlearimplanthelp.com/journey/choosing-a-cochlear-implant/electrodes-and-channels/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cochlear Implant Help&lt;/a&gt;&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/BNEOv.png&quot; alt=&quot;ANF tuning&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Auditory nerve fiber tuning. The louder the stimulus, the worse the tuning to frequency. Source: &lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.nature.com/nrn/journal/v7/n1/full/nrn1828.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fettiplace &amp;amp; Hackney, 2006&lt;/a&gt;&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to the quantitative aspect of this question, namely what the frequency difference limen is, and an indication &lt;em&gt;how many&lt;/em&gt; frequency bands can be distinguished I refer you to below linked question. Both depend highly on the method used to determine the just-noticeable-difference, and as said also on the sound intensity applied. Moreover, it is dependent on the frequency under consideration. The higher the frequency, the larger the frequency band becomes expressed in Hz. This is an example of Weber-Fechner's law &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2140693/pdf/235.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Hecht, 1924)&lt;/a&gt;. The cochlea is organized in octaves, meaning that higher frequencies have less cochlear space devoted to them and hence less hair cells to code a particular frequency range.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Further Readings&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;https://biology.stackexchange.com/questions/31059/whats-the-frequency-resolution-of-the-human-ear&quot;&gt;What's the frequency resolution of the human ear?&lt;/a&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2140693/pdf/235.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Hecht, &lt;em&gt;J General Physiol&lt;/em&gt; (1924): 235-67&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.nature.com/nrn/journal/v7/n1/full/nrn1828.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Fettiplace &amp;amp; Hackney, &lt;em&gt;Nature Rev Neurosci&lt;/em&gt; (2006); &lt;strong&gt;7&lt;/strong&gt;: 19-29&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:10.773" LastActivityDate="2015-07-23T00:31:34.607" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36305" PostTypeId="1" AcceptedAnswerId="36307" CreationDate="2015-07-22T14:00:09.107" Score="14" ViewCount="1161" Body="&lt;p&gt;Using &lt;code&gt;organism:&quot;Homo sapiens (Human) [9606]&quot;&lt;/code&gt; as a &lt;a href=&quot;http://www.uniprot.org/uniprot/?query=organism%3A&amp;quot;Homo+sapiens+%28Human%29+%5B9606%5D&amp;quot;&amp;amp;sort=score&quot; rel=&quot;nofollow&quot;&gt;query in uniprot&lt;/a&gt; returns about 146,000 proteins. I was under the impression that there were only &lt;a href=&quot;https://www.google.co.uk/search?q=how+many+proteins+in+the+human+genome&amp;amp;gws_rd=cr&amp;amp;ei=_qCvVb2HLcSv7Aaf1YLoBg&quot; rel=&quot;nofollow&quot;&gt;20-25,000 protein coding genes in the human genome&lt;/a&gt;. Is this something to do with splice isoforms, like those from &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/24273012&quot; rel=&quot;nofollow&quot;&gt;SpliceProt&lt;/a&gt;, or another splice isoform database or tool? &lt;/p&gt;&#xA;" OwnerUserId="3553" LastEditorUserId="16905" LastEditDate="2018-01-26T10:36:01.723" LastActivityDate="2018-01-26T10:36:01.723" Title="Why and how does uniprot list around 150,000 proteins in the human genome?" Tags="&lt;bioinformatics&gt;&lt;proteins&gt;&lt;database&gt;&lt;isoforms&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36306" PostTypeId="2" ParentId="36305" CreationDate="2015-07-22T14:11:13.863" Score="4" Body="&lt;p&gt;There are 20+ thousand genes in the genome, but each of these can produce multiple proteins. In addition to this, you have protein fragments and cleavage products further increasing the number of entries.&lt;/p&gt;&#xA;" OwnerUserId="9523" LastActivityDate="2015-07-22T14:11:13.863" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36307" PostTypeId="2" ParentId="36305" CreationDate="2015-07-22T14:24:41.993" Score="20" Body="&lt;p&gt;Well you are assuming one sequenced genome/proteome per NCBI tax id. That is no longer true. So if you click on the proteome filter it decreases by half.&#xA;Which gets you into the 60,000 range. Now not all of these are &quot;different&quot; conceptual proteins, many are artifacts from the way GenBank/EMBL/DDBJ interact with the TrEMBL section of UniProtKB i.e. they are not normalized in db speak. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So for the human case you also want to add the Swiss-Prot filter to get a decent proteome that gives you about 20,000 proteins. Corresponding to the predicted/confirmed human gene count.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In all bioinformatics databases you need to pay attention to difference between database records and biological concepts. They rarely map cleanly one to one. In this case an UniProt record is not a protein, but information about a protein and a different record could have information about the same &quot;protein&quot;. Or at least the same under some definitions of &quot;same&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See &lt;a href=&quot;http://www.uniprot.org/help/2008/09/02/release&quot;&gt;the announcement of the draft human proteome in UniProtKB&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The known isoforms are most often stored in the alternative products section of an UniProt entry. In some rare cases when the splice variant has a completly different biological function they are described in separate UniProt entries. For UniProtKB/Swiss-Prot Human there is a near 1 to 1 relation between genes and proteins. Cases as above and fusion proteins are the exceptions to this rule.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;TrEMBL tries to automatically reduce redundancy in INSDC by auto merging entries in the same taxid and now proteome that have an identical reported sequence. However, variations of single gene products due to mutations and or limit what auto merging can do. For example there are &lt;a href=&quot;http://www.uniprot.org/uniprot/?query=organism%3A9606%20gene%3Ap53%20reviewed%3Ano&amp;amp;sort=score&quot;&gt;8&lt;/a&gt; records for the P53 gene in TrEMBL today. Many of them from mutants, i.e. cancer genomes etc... &lt;/p&gt;&#xA;" OwnerUserId="16905" LastEditorUserId="16905" LastEditDate="2015-07-22T14:43:47.460" LastActivityDate="2015-07-22T14:43:47.460" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36308" PostTypeId="2" ParentId="36195" CreationDate="2015-07-22T14:34:31.847" Score="5" Body="&lt;p&gt;The &lt;strong&gt;voltage-gated&lt;/strong&gt; potassium channels are there only to &lt;em&gt;swiftly&lt;/em&gt; repolarize the membrane potential. Ultimately it is the Na,K-ATPase that has to pump the various ions back where they belong (Na out, K in), also when potassium channels are active. So when the potassium channels are blocked, the Na,K-ATPase will restore the membrane potential, albeit in the order of seconds instead of milliseconds.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastActivityDate="2015-07-22T14:34:31.847" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36309" PostTypeId="2" ParentId="36301" CreationDate="2015-07-22T14:50:46.013" Score="3" Body="&lt;p&gt;As I understand, what you really asking is:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;What is the mathematical model one can use to fit drug lethality/efficiency data?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;With answer to that you can go to stackexchange and bug them for fitting solution in language of your choice.&#xA;However, answer to that is quite complicated, it depends on your system and experiment. And also, how well you want to model your observation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'd suggest start with something like 4-parameter sigmoid, which in your case will degrade to two-parameter sigmoid: LD50 (shift along X) and steepness (how fast you transition from life to death) with edge cases that are either 0 or 1.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, &lt;a href=&quot;http://ajpheart.physiology.org/content/291/4/H2003&quot; rel=&quot;nofollow&quot;&gt;this paper&lt;/a&gt; discusses one model (4-parameter sigmoid). It looks roughly like $y=\frac{x}{1+e^{\alpha(x-LD50)}}$, where $\alpha$ is steepness parameter&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another way to do such fit is to use &lt;a href=&quot;http://mathworld.wolfram.com/Erf.html&quot; rel=&quot;nofollow&quot;&gt;error function&lt;/a&gt;. That is an integral of gaussian distribution. I do like that approach (theoretically) because normal distribution is important in data analysis of independent observations, and many random values in biology behave normally.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let me reiterate. You have to have a model for your data in the first place. Maybe lethality drops down a little after LD50. Maybe you have some other weird stuff. What you can do is to pick a model and then see how well it describes your data.&lt;/p&gt;&#xA;" OwnerUserId="14552" LastActivityDate="2015-07-22T14:50:46.013" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36310" PostTypeId="1" AcceptedAnswerId="36316" CreationDate="2015-07-22T15:12:49.827" Score="1" ViewCount="3051" Body="&lt;p&gt;Wikipedia has two images, of a &lt;a href=&quot;https://en.m.wikipedia.org/wiki/File:Gene_structure_eukaryote_2_annotated.svg&quot; rel=&quot;nofollow&quot;&gt;eukaryotic gene&lt;/a&gt; and of a &lt;a href=&quot;https://en.m.wikipedia.org/wiki/File:Gene_structure_prokaryote_2_annotated.svg&quot; rel=&quot;nofollow&quot;&gt;prokaryotic gene&lt;/a&gt;. &#xA;They show the difference that the prokaryotic gene also has an operator while the eukaryotic gene does not. Both also have enhancers and silencers separately. I thought enhancers and silencers were types of operators. Is this wrong?&lt;/p&gt;&#xA;" OwnerUserId="15109" LastEditorUserId="15109" LastEditDate="2015-12-26T14:36:05.340" LastActivityDate="2015-12-26T14:36:05.340" Title="Operators and Enhancers/Silencers" Tags="&lt;genetics&gt;&lt;molecular-biology&gt;&lt;molecular-genetics&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36311" PostTypeId="1" CreationDate="2015-07-22T15:39:14.843" Score="6" ViewCount="170" Body="&lt;p&gt;At least among more complex organisms, I cannot think of any examples of highly mobile species (like animals) that also incorporate photosynthesis. Perhaps there are examples that I'm unaware of, but even so it seems to be exceedingly rare.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there some good reason for this, or is it a mere chance of evolution?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I could speculate, perhaps, in that photosynthesis just doesn't provide enough energy for the relatively high metabolism of mobile species; but even then, there seems there should be a &quot;sweet spot&quot; where some level of mobility would still be &quot;worth it&quot; for a photosynthesizing species, rather than the strict dichotomy that seems to be observable, so I naïvely find that explanation somewhat dissatisfactory. There just seems to be little reason for animals to &lt;em&gt;not&lt;/em&gt; practice photosynthesis, if only to be able to eat &lt;em&gt;less&lt;/em&gt; than they need to without it.&lt;/p&gt;&#xA;" OwnerUserId="16906" LastEditorUserId="16906" LastEditDate="2015-07-22T16:12:43.920" LastActivityDate="2020-05-24T12:47:10.170" Title="Why is there a seeming dichotomy between mobility and photosynthesis?" Tags="&lt;evolution&gt;&lt;photosynthesis&gt;" AnswerCount="4" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36312" PostTypeId="2" ParentId="36285" CreationDate="2015-07-22T15:43:23.843" Score="0" Body="&lt;p&gt;&quot;Essentially diploid&quot; means that a normal (most common normal) state is diploid, while any other state will be considered rare (can be normal yet) or abnormal or unusual. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &quot;essentially diploid&quot; is in some way a tautologic, since we can say &quot;human somatic cell is essentially diploid&quot; as well as &quot;human somatic cell is diploid&quot; omitting &quot;essentially&quot;. But the goal of &quot;essentially&quot; is to clarify other states:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If some essentially diploic organism has one chromosome set it will be called &quot;monoploid&quot;, while cell/organism etc which normally has one set will be called &quot;haploid&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sub-Diploid and Near diploid means there are incomplete (aka less than normal) sets of genetic material.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-22T15:43:23.843" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36315" PostTypeId="2" ParentId="36282" CreationDate="2015-07-22T18:47:14.350" Score="4" Body="&lt;p&gt;The place where the cord was cut do not stay with us - &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/imagepages/9055.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;it falls in a week&lt;/a&gt; +- after the birth, while the umbilicus is the only visible natural scar formed by natural processes, not by gynecologists:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/E1Tcd.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/E1Tcd.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Multiple sources say the umbilicus has a scar tissue in it.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;After birth the umbilicus is the only naturally formed visible scar on&#xA;  the body.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Br J Plast Surg. 1998 Oct;51(7):538-41. Umbilicosculpture: a concept revisited.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Umbilicus &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/21404518&quot; rel=&quot;nofollow noreferrer&quot;&gt;is a scar&lt;/a&gt;, which is the place of the previous merger of the&#xA;  fetus with the umbilical cord.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-22T18:47:14.350" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36316" PostTypeId="2" ParentId="36310" CreationDate="2015-07-22T19:00:43.603" Score="1" Body="&lt;p&gt;Enhancers and silencers are binding sequences for transcriptional activators or repressors, in which case the sequence is often located some distance upstream or downstream of the gene it regulates. See regulation of transcription for information about how these interact with their target genes (through DNA bending, mediator, etc.). A note about enhancers and silencers, though, they're not necessarily &lt;em&gt;required&lt;/em&gt; for transcription: they help the gene attain robust up- or down-regulation of transcription.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The operator, on the other hand, influences whether the promoter will do something, or nothing. If we're talking about inducible systems, the repressor is bound to the operator, blocking action to/from the promoter (an inducer will bind the repressor and keep the operator from blocking the promoter). If we're talking about a repressible system, the repressor will need a corepressor to bind the operator to abrogate transcription by blocking action to/from the promoter.&lt;/p&gt;&#xA;" OwnerUserId="12877" LastActivityDate="2015-07-22T19:00:43.603" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36317" PostTypeId="1" CreationDate="2015-07-22T19:49:00.247" Score="0" ViewCount="411" Body="&lt;p&gt;I'm a junior Biology Student and I came across this Human Anatomy Question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In respect to the bone characteristics, mark the correct answer:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A) Even bones: Palatine, Inferior jaw, Parietal.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;B) Examples of Long Bones: Sternum and Radius-clavicle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C) Some Mixed Bones are (I couldn't find a better translation for &quot;ossos mistos&quot; in portuguese): vertebrae, ribs, hip bones.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;D)Plane Bones protect organs and form cavities, for instance we have: Ribs and Sternum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;E)Odd and Plane Bones: Occipital, Frontal and Sternum.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I am almost sure that options A through C are incorrect. I'm between options D and E, but in option E I am really sure only that the Sternum Bone is correct. I couldn't find a reliable source that said explicitly that the Occipital and Frontal Bone are Plane and Odd.&#xA;And I think option D has a flaw mainly because the Sternum Bone does not form any cavities.&lt;/p&gt;&#xA;" OwnerUserId="16912" LastEditorUserId="16866" LastEditDate="2017-02-27T13:34:09.983" LastActivityDate="2017-02-27T13:34:09.983" Title="Human Bones classification and anatomy quiz" Tags="&lt;human-biology&gt;&lt;human-anatomy&gt;" AnswerCount="2" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="36319" PostTypeId="2" ParentId="36292" CreationDate="2015-07-22T22:35:54.600" Score="5" Body="&lt;p&gt;The term you should look up is &lt;strong&gt;sperm competition&lt;/strong&gt;, there is an introductory wikipedia article about it &lt;a href=&quot;https://en.wikipedia.org/wiki/Sperm_competition&quot;&gt;here&lt;/a&gt;, where you can get the basic picture and get some references to explore.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Simply said, males often compete with other males in the reproductive tract of the female, thus a higher number of sperm will lead to a higher chance of fertilizing the female in competition with other males - leading to an arms-race of the number of sperms a male eject into the female.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is a lot more to it, of course, but I believe this well explains the most fundamental driver of why males generally produce and eject so many sperms.&lt;/p&gt;&#xA;" OwnerUserId="9124" LastActivityDate="2015-07-22T22:35:54.600" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36321" PostTypeId="1" CreationDate="2015-07-23T01:53:30.170" Score="11" ViewCount="1592" Body="&lt;p&gt;Can we change our dopamine baseline levels? High dopamine levels improve alertness, problem solving, but may also cause anxiety and aggression. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I've read that smiling and laughing, eating certain foods, or having unexpected rewards can elevate dopamine levels in the brain. I also read that expecting a reward in the future (such as an upcoming vacation) elevates dopamine levels. Can these actions, if repeated over a prolonged period, increase baseline dopamine levels? Or will dopamine return to original levels once these actions are stopped?&lt;/p&gt;&#xA;" OwnerUserId="16917" LastEditorUserId="9943" LastEditDate="2015-07-23T05:52:24.533" LastActivityDate="2015-07-27T10:30:28.257" Title="Can we change our dopamine baseline levels?" Tags="&lt;neuroscience&gt;&lt;brain&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36322" PostTypeId="2" ParentId="36194" CreationDate="2015-07-23T01:53:58.663" Score="1" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Scorpion venom mostly affects neuronal firing activity by inhibiting recovery.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;There are some 100 subtypes of K&lt;sup&gt;+&lt;/sup&gt; channels and some 120 different scorpion toxins known. Of this host of toxins, the majority were tested on&#xA;Shaker-related channels (subfamily KV1.x). Some peptides were shown to act on the Ca&lt;sup&gt;2+&lt;/sup&gt;-activated K&lt;sup&gt;+&lt;/sup&gt; channels (KCa1.1, KCa3.1, KCa2.x. The family of so-called g-KTx toxins is specific for the ether-a-go-go family of K&lt;sup&gt;+&lt;/sup&gt; channels (KV11.x) &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0041010104001345&quot; rel=&quot;nofollow&quot;&gt;(Rodriguez de la Vega &amp;amp; Possani, 2004)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Shaker subfamily and the ether-a-go-go family are all voltage-gated channels and hence closely involved in action potential generation &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1471-4159.1999.0730849.x/pdf&quot; rel=&quot;nofollow&quot;&gt;(Coleman &lt;em&gt;et al&lt;/em&gt;., 1999&lt;/a&gt;; &lt;a href=&quot;http://schizophreniabulletin.oxfordjournals.org/content/33/6/1263.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;Shepard &lt;em&gt;et al&lt;/em&gt;., 2007&lt;/a&gt;)]; the Ca&lt;sup&gt;2+&lt;/sup&gt;-activated K&lt;sup&gt;+&lt;/sup&gt; channels are activated when Ca&lt;sup&gt;2+&lt;/sup&gt; enters the cell, which is an event typically associated with action potentials too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, based on this information I conclude that scorpion venom mainly blocks the repolarization phase of neurons, meaning the maximum firing rate will be drastically reduced because recovery is blocked. Neurons can fire, but they will not be able to recover from continuous firing. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scorpion venom is not strongly associated with potassium leak channels (KCNK family). Although other families may also affect the resting membrane potential, it is the KNCK family that is mostly associated with generating the cell resting membrane potential &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19404634&quot; rel=&quot;nofollow&quot;&gt;(Cohen &lt;em&gt;et al&lt;/em&gt;., 2009)&lt;/a&gt;. hence, scorpion venom will not affect the resting membrane potential too much.     &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1046/j.1471-4159.1999.0730849.x/pdf&quot; rel=&quot;nofollow&quot;&gt;Coleman &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;J Neurochem&lt;/em&gt; (1999); &lt;strong&gt;73&lt;/strong&gt;: 849–58&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0041010104001345&quot; rel=&quot;nofollow&quot;&gt;Rodriguez de la Vega &amp;amp; Possani, &lt;em&gt;Toxicon&lt;/em&gt; (2004); &lt;strong&gt;43&lt;/strong&gt;: 865–875&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://schizophreniabulletin.oxfordjournals.org/content/33/6/1263.full.pdf+html&quot; rel=&quot;nofollow&quot;&gt;Shepard &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Schizophrenia Bulletin&lt;/em&gt;; &lt;strong&gt;33&lt;/strong&gt;(6): 1263–9&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19404634&quot; rel=&quot;nofollow&quot;&gt;Cohen &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Eur Biophys J&lt;/em&gt; (2009); &lt;strong&gt;39&lt;/strong&gt;(1): 61-73&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-23T02:02:20.823" LastActivityDate="2015-07-23T02:02:20.823" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36324" PostTypeId="2" ParentId="36321" CreationDate="2015-07-23T05:51:31.960" Score="6" Body="&lt;p&gt;&lt;strong&gt;Feelings of pleasure and reward are transient&lt;/strong&gt; in nature. Similarly, the dopamine release in the reward centers (the &lt;a href=&quot;https://www.dartmouth.edu/~rswenson/NeuroSci/chapter_9.html&quot; rel=&quot;nofollow&quot;&gt;limbic structures&lt;/a&gt;) is transient, namely in the order of seconds &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006899397010044&quot; rel=&quot;nofollow&quot;&gt;(Rebec &lt;em&gt;et al&lt;/em&gt;., 1997)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One way to &lt;strong&gt;chronically elevate dopamine&lt;/strong&gt; levels is by administering certain drugs. A notable/notorious example is &lt;a href=&quot;http://www.pbs.org/wgbh/pages/frontline/meth/body/&quot; rel=&quot;nofollow&quot;&gt;methamphetamine&lt;/a&gt;, which elevates mood and generates euphoria for &lt;a href=&quot;http://www.macalester.edu/academics/psychology/whathap/ubnrp/meth08/biochemistry/dopamine.htm&quot; rel=&quot;nofollow&quot;&gt;8-12 hours&lt;/a&gt;. However, after chronic use, people may report a &lt;a href=&quot;http://www.ehd.org/health_meth_2.php&quot; rel=&quot;nofollow&quot;&gt;lack of motivation and anhedonia&lt;/a&gt; when they stop taking the drug. Anhedonia is an absence of pleasure in response to acts that had previously been pleasurable. Anhedonia may be reported as long as 2 years after the last use of methamphetamine in addicts. Chronic use of the drug overstimulates the dopamine neurons in the limbic system (and elsewhere), and destroys the dopamine receptors, explaining the anhedonia. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hence, even with hard drugs like meth, the effects on dopamine levels are &lt;strong&gt;transient&lt;/strong&gt;, just less transient as with physiological reward responses.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S0006899397010044&quot; rel=&quot;nofollow&quot;&gt;Rebec &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;Brain Res&lt;/em&gt; (1997); &lt;strong&gt;776&lt;/strong&gt;(1–2): 61–7&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-27T10:30:28.257" LastActivityDate="2015-07-27T10:30:28.257" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36326" PostTypeId="1" AcceptedAnswerId="36328" CreationDate="2015-07-23T06:34:45.790" Score="1" ViewCount="176" Body="&lt;p&gt;I understand that Circle of Willis is a circulatory anastomotic system that provided blood to the brain.  I want to understand if this system is unique to humans or does it exist in other species or mammals to be more specific? &lt;/p&gt;&#xA;" OwnerUserId="16898" LastActivityDate="2015-07-23T09:05:12.957" Title="Is Circle of Willis unique to humans?" Tags="&lt;brain&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-07-24T20:37:55.760" ContentLicense="CC BY-SA 3.0" />
  <row Id="36327" PostTypeId="2" ParentId="36317" CreationDate="2015-07-23T08:17:15.547" Score="0" Body="&lt;p&gt;If I had 90 seconds to answer this question I'd mark answer &quot;&lt;strong&gt;C&lt;/strong&gt;&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Vertebrae &amp;amp; Ribs &amp;amp; Hip bones all are mixed bones. &lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-23T08:17:15.547" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36328" PostTypeId="2" ParentId="36326" CreationDate="2015-07-23T09:05:12.957" Score="2" Body="&lt;p&gt;I found two references that talk about the circle of Willis in different kind of mammals so i think it's right to say that this particular anastomotic system of arteries is not exclusive to humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are the two references:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.neuroanatomy.org/2008/054_065.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.neuroanatomy.org/2008/054_065.pdf&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/14651482&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/pubmed/14651482&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="16284" LastActivityDate="2015-07-23T09:05:12.957" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36329" PostTypeId="1" CreationDate="2015-07-23T09:16:00.680" Score="0" ViewCount="92" Body="&lt;p&gt;&lt;a href=&quot;http://www.symmetrymagazine.org/breaking/2008/07/18/fangs-claws-and-jaws-pack-metal&quot; rel=&quot;nofollow&quot;&gt;This article&lt;/a&gt; states that some shelled animals - spiders, scorpions, crabs, worms and other creatures - have metal atoms in their claws, jaws and fangs.&#xA;I believe through anabolism, since they eat sand, soil and insects that are full of a mix of those.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For most human beings, it would seem silly to eat soil or sand, or even insects - and yet, I wonder if our bodies would be able to digest and create anabolic processes around, for example, metals, in such way that we would end up having stronger bones / teeth / hair / nails (or other things).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To a certain extent, I also wonder how anabolism isn't use to regenerate cells that become old or faulty in the body as we age or get sick (a special diet would help &quot;regenerate&quot; blood balance, feeble skin, brain cells, etc, if we knew what foods would turn into these cells the best by anabolic process).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This question is becoming a bit confused, so I'll end up rephrasing it: is there a document / research / map / experiences of all the foods &amp;amp; materials that the human body can not only digest (and in what quantities) but also &lt;strong&gt;&lt;em&gt;how&lt;/em&gt;&lt;/strong&gt; they transform into our cells (and a list of foods / materials that are NOT taken into account by anabolic processes). I.e., at what speeds they can become part of us, and how they can/could change and alter the body cells in a strengthening kind of way (not in a way that makes us sick or dead).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;NOTE: I am not a scientist, just a writer, but I am fondly interested in the subject.&lt;/p&gt;&#xA;" OwnerUserId="16926" LastActivityDate="2015-08-16T19:54:26.230" Title="How to mimic / approach some animals/insects' anabolism?" Tags="&lt;human-biology&gt;&lt;cell-biology&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36335" PostTypeId="2" ParentId="36311" CreationDate="2015-07-23T13:57:41.690" Score="2" Body="&lt;p&gt;Why be mobile? To follow the sun?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Plants are mobile. Their seeds are. We have plants living on other plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once they have a spot on the sun though moving does not necessarily improve your situation, being stationary and defending your territory though does. (Growing taller, deeper roots, wider crowns)&lt;/p&gt;&#xA;" OwnerUserId="6137" LastActivityDate="2015-07-23T13:57:41.690" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36336" PostTypeId="1" AcceptedAnswerId="36423" CreationDate="2015-07-23T14:42:56.263" Score="4" ViewCount="717" Body="&lt;p&gt;From my understanding, neurons decrease their sensitivity to neurotransmitters by reducing the amount of receptors on the cell membrane in response to sustained neurotransmitter activity. One explanation I heard is that cells do that to protect themselves from damage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This makes me ask - what kind of damage could be caused by sustained neurotransmitter activity in the brain, if cells did not reduce their sensitivity? &lt;strong&gt;Can a brain survive/thrive if neurons always had the same number of neurotransmitter receptors?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="577" LastEditorUserId="9943" LastEditDate="2015-07-23T22:48:46.047" LastActivityDate="2018-12-19T08:19:05.687" Title="What would happen if brain neurons did not reduce their sensitivity to neurotransmitters after prolonged exposure?" Tags="&lt;human-biology&gt;&lt;neuroscience&gt;&lt;brain&gt;&lt;neurophysiology&gt;&lt;neurotransmitter&gt;" AnswerCount="2" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36337" PostTypeId="1" CreationDate="2015-07-23T15:00:53.973" Score="-1" ViewCount="430" Body="&lt;p&gt;The pomegranate fruit has been cultivated since ancient times, particularly in the Middle East and the Mediterranean.  It has a hard outer rind, and inside are several chambers, each of which contains a multitude of seed pods, consisting of a single hard seed wrapped in a protective cushion of liquid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take every detail of that description, make it a bit smaller, a bit softer, and a whole lot more edible, and what you've got is the exact description of the &lt;em&gt;tomato&lt;/em&gt; fruit.  One could certainly be forgiven for assuming that they were genetically related, but if you look at the phylogeny of the two plants, you see that that hypothesis could hardly be more wrong--not to mention the minor little detail of tomatoes being native to the Americas, literally on the other side of the world from the pomegranate's home!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So what's going on here?&lt;/p&gt;&#xA;" OwnerUserId="6683" LastEditorUserId="3952" LastEditDate="2015-07-23T18:21:39.763" LastActivityDate="2015-07-23T18:21:39.763" Title="Why do tomatoes look so much like pomegranates?" Tags="&lt;botany&gt;&lt;phylogenetics&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-07-23T20:02:50.587" ContentLicense="CC BY-SA 3.0" />
  <row Id="36338" PostTypeId="2" ParentId="36337" CreationDate="2015-07-23T17:36:36.913" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;So what's going on here?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Personally speaking, I don't think the tomato is anything like the pomegranate. However, generally speaking the appearance of similar traits despite widely divergent ancestry is called &lt;a href=&quot;https://en.wikipedia.org/wiki/Convergent_evolution&quot;&gt;Convergent Evolution&lt;/a&gt;. Some traits -- let's say round fruit and red coloring -- may be so advantageous that they evolved multiple different times throughout history.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take wings, for another example. Wings have evolved in insects, avians (obviously), and mammals. The last common ancestor (often shortened to &quot;LCA&quot;) is billions of years back, but wings persist.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, the real answer is not quite &quot;by chance,&quot; but closer to &quot;because they're very good traits to have.&quot;&lt;/p&gt;&#xA;" OwnerUserId="1231" LastActivityDate="2015-07-23T17:36:36.913" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36339" PostTypeId="2" ParentId="36336" CreationDate="2015-07-23T17:38:55.557" Score="1" Body="&lt;p&gt;In principle, many neurotransmitter receptors work as ion channels and the actual mechanism of signalling involves allowing the influx/efflux of calcium, potassium, magnesium, etc. A good example of this is the acetylcholine receptor. Presumably, if the cell retained the same number of receptors even in the presence of abundant ligands, the cell would flood with ions. Not only would this render the signalling pathway insensitive it may lead to survival issues for the cell/inappropriate cross-talk with other pathways.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is at least how it should work in the models of neurotransmitter signalling I'm familiar with, it seems quite likely that a neuro lab somewhere has a cell, or animal model that can provide a real world answer.&lt;/p&gt;&#xA;" OwnerUserId="10257" LastEditorUserId="9943" LastEditDate="2015-07-27T10:31:58.627" LastActivityDate="2015-07-27T10:31:58.627" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36340" PostTypeId="1" CreationDate="2015-07-23T17:55:10.927" Score="2" ViewCount="2092" Body="&lt;p&gt;we were told that agglutination occurs when the matching antibody react with its antigen on the RBC surface (as antibody B with antigen B)....&#xA;Also when blood transfusion, Donors plasma with antibodies is diluted , so when o-donor gives blood to  B-recipient , B antibodies ( of the donor) is diluted&lt;br&gt;&#xA;........&#xA;My question is in lab cross-matching test  when we put recipient's plasma(o with b antibodies for example) on the donor's RBCs (B with b antigens)..... is there agglutination, If so, how would we know the right group then?....if not ,Why not?&#xA;if the whole thing is misunderstood ,i wish to be told how it's done.&lt;/p&gt;&#xA;" OwnerUserId="16875" LastActivityDate="2015-07-23T19:43:31.067" Title="agglutination test using blood of the donor and the recipient" Tags="&lt;blood-group&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36341" PostTypeId="1" AcceptedAnswerId="36342" CreationDate="2015-07-23T18:02:55.783" Score="4" ViewCount="372" Body="&lt;p&gt;I was out hiking, and was walking along the side of a road, and saw this little guy on some gravel. Hes a light blue/grey color, hairy, spotted with red,and looks like he has horns and a tail. I've been trying to search for what species it is. If anyone knows, please share! &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/xb5zX.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/xb5zX.jpg&quot; alt=&quot;Caterpillar&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sup&gt;(Click to view full image)&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="16938" LastEditorUserId="6703" LastEditDate="2015-07-23T19:13:54.150" LastActivityDate="2015-07-23T19:13:54.150" Title="Does anyone know what kind of caterpillar this is?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36342" PostTypeId="2" ParentId="36341" CreationDate="2015-07-23T18:20:14.510" Score="6" Body="&lt;p&gt;Looks similar to a Rusty Tussock Moth (&lt;em&gt;Orgyia antiqua&lt;/em&gt;) caterpillar, but you might want to check &lt;a href=&quot;http://bugguide.net/node/view/28152&quot;&gt;the bugguide page for the species&lt;/a&gt;, or submit your photo there for a second opinion.&lt;/p&gt;&#xA;" OwnerUserId="3952" LastActivityDate="2015-07-23T18:20:14.510" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36343" PostTypeId="2" ParentId="36340" CreationDate="2015-07-23T19:35:57.447" Score="1" Body="&lt;p&gt;&lt;strong&gt;Disregarding Rh factor&lt;/strong&gt; for a moment: when you add A-antibodies to a blood sample and agglutination occurs, this means the blood contained A-antigens (A-type). The same can be said for a sample of blood to which B-antibodies are added (B-type). If agglutination for &lt;em&gt;both&lt;/em&gt; antibodies occurs in separate assays on the same sample of blood, it means the sample contains both A and B antigens (AB-type). If the sample is said to be O-type, this means neither A or B antigen would be present in these cells. It's safe to transfuse O-type blood into any recipient due to this fact. What you also want to watch out for, is attack on the recipients RBC's by antibodies in the donor's plasma. This can result in a hemolytic transfusion reaction (HTR), but it's noted in the &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK2265/&quot; rel=&quot;nofollow&quot;&gt;following text&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Red blood cell incompatibility may also occur when the patient's RBC antigens are attacked by antibodies from the donor's plasma. This tends to be a minor problem because of the small amount of antibody present in the donated plasma, which is further diluted on transfusion into the recipient's circulation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you're in the lab doing a Coombs test, for example, you're checking to see if there are any extraneous antigens present that might results in a HTR. In a normal result, ergo there aren't any antibodies to RBC's in the sample mixture, you wont see any agglutination. This is for considerations outside of ABO antibodies, generally. If you're adding to B-type RBC's a plasma with known antibodies to B antigen, like O-type plasma, you can probably expect an event. To my knowledge, O-type plasma wouldn't be safe to give to anyone but an O-type recipient.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://mytransfusion.com.au/node/blood-groups-and-compatibility&quot; rel=&quot;nofollow&quot;&gt;additional source&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12877" LastEditorUserId="12877" LastEditDate="2015-07-23T19:43:31.067" LastActivityDate="2015-07-23T19:43:31.067" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="36344" PostTypeId="1" AcceptedAnswerId="36364" CreationDate="2015-07-23T20:24:39.297" Score="15" ViewCount="885" Body="&lt;p&gt;I'm curious about what happens when you insert organelles from a cell into another. In particular, mitochondria.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Take two cells from your own body. Somehow extract a mitochondria from one cell and somehow insert it in the other cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Will the cell with the foreign mitochondria make use of it (respiration), or will it dispose it?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What if the foreign mitochondria comes from someone else's body?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What if the foreign mitochondria comes from another species' cell?&lt;/p&gt;&#xA;" OwnerUserId="16897" LastEditorUserId="9943" LastEditDate="2015-07-23T23:05:33.597" LastActivityDate="2016-09-16T06:52:48.050" Title="Are mitochondria transferable between cell types, individuals and species?" Tags="&lt;cell-biology&gt;&lt;mitochondria&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36345" PostTypeId="1" CreationDate="2015-07-23T20:27:43.787" Score="3" ViewCount="189" Body="&lt;p&gt;What form of reproduction did the first animals on land use*? Were they hermaphrodites, or did they have male and female sexes? [Is there a proper term for sexual separation in a species?]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Were any land species believed to have evolved from hermaphrodite ocean species (that crossed to land on roughly the same geological time periods that land creatures first evolved)?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;*I know that 'first on land' is a complicated concept itself, since it could mean first creatures be able to survive on land at all, first to freely travel between land and water, or first to only live on land, or anywhere in between.  I assume all three categories were sexual though?  &lt;/p&gt;&#xA;" OwnerUserId="9788" LastEditorUserId="9943" LastEditDate="2015-07-23T23:51:29.733" LastActivityDate="2015-07-23T23:51:29.733" Title="What form of reproduction did the first land animals use?" Tags="&lt;evolution&gt;&lt;sex&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36346" PostTypeId="2" ParentId="36344" CreationDate="2015-07-23T20:39:02.097" Score="4" Body="&lt;p&gt;I'm not entirely sure about cross species organelle transfer (lets focus on mitochondria), but some people have already made three parent babies, therefore mitochondria are at least transferable between individuals of the same species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason for the operation was to cure a disease that was inherent to the mitochondria of the mother (mitochondria always come from the mother, never the father). They used the genetic material from the nuclei of the mother and father, and used the mitochondria of a &quot;foster&quot; mother. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bbc.com/news/health-31594856&quot; rel=&quot;nofollow&quot;&gt;http://www.bbc.com/news/health-31594856&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="12924" LastEditorUserId="10456" LastEditDate="2015-07-24T03:52:49.500" LastActivityDate="2015-07-24T03:52:49.500" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36347" PostTypeId="1" CreationDate="2015-07-23T20:49:34.190" Score="3" ViewCount="495" Body="&lt;p&gt;The title says it all.  I know that 'complex' is a pretty ambiguous term to use, but I can't think of a more scientific term/definition for my meaning.  I can't think of any large (larger then a small rodent) hermaphrodite species, or any that we tend to think of as having complex structures; hermaphrodite species all seem pretty boring really.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I get why sex is a huge advantage, but by that regard hermaphrodites seem quite powerful.  The ability to both produce your own young and impregnate others allow for more young.  Plus, it provides the opportunity for a species to choose to self fertilize if no mate is available.  I realize sexual reproduction is preferable, by it's nice to have Autogamy as a backup option just in case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I understand why there &lt;em&gt;are&lt;/em&gt; advantages to two sexes, particularly in terms of sexual dimorphism which allows male to be better at potentially reproducing with many females by specializing in it.  I completely understand how two genders would evolve and be successful.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What I find odd is that nearly all larger or complex species seem to have genders.  I would have thought that, like many other mating strategies, there would be variance across species; with some choosing to be hermaphrodites to increase the maximum children they can produce as a species, by having twice the child bearers, and others choosing to go the sexual dimorphism route by having roles that they are best at.   I mean even Obligate parthenogenesis has evolved separately many larger specie like lizards, despite it arguably being an evolutionary dead end in the long term due to the lose of the advantages of sexual reproduction.  If adaptations that completely toss away the power of sex evolve all over the place why do new hermaphrodite species never seem to evolve, and existing hermaphrodite species never seem to grow bigger or more diverse?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular sequential hermaphrodite, like many aquatic fish use, seems a pretty effective strategy.  When your young, and small, play a female role to have guaranteed offspring, only once your big and at your most fit bother competing as a male for access to multiple mates. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A related question, associated with my own attempt to explain why existing hermaphrodite species don't seem to take as many varied forms; but which I'm not really sure I buy.  Is it possible that the lack of sexual conflict (primarily, but not limited to, competition between males for mates, driven from the fact that males would have more drive to compete then hermaphrodites since it's their &lt;em&gt;only&lt;/em&gt; reproductive strategy), would mean there was less of a drive towards adaptation in hermphrodite species?  A sort of red-queen scenario, where your own species is the red queen?&lt;/p&gt;&#xA;" OwnerUserId="9788" LastEditorUserId="9943" LastEditDate="2015-07-23T23:12:22.617" LastActivityDate="2015-07-23T23:12:22.617" Title="Why are there no complex hermaphrodite land animals?" Tags="&lt;evolution&gt;&lt;sex&gt;" AnswerCount="0" CommentCount="7" FavoriteCount="2" ClosedDate="2015-07-24T06:51:28.197" ContentLicense="CC BY-SA 3.0" />
  <row Id="36348" PostTypeId="1" CreationDate="2015-07-23T21:01:57.933" Score="5" ViewCount="453" Body="&lt;p&gt;From what I understand, pain is an useful mechanism that signals us that something is not quite right with our body (in particular, we're under attack). It's good - it alert us and tells us that we got to do something (stop the threat, or run away, etc). From Wikipedia:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Pain motivates the individual to withdraw from damaging situations, to&#xA;  protect a damaged body part while it heals, and to avoid similar&#xA;  experiences in the future.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, there are damages that cause &lt;em&gt;too much pain&lt;/em&gt;. If you are stabbed in a particular place, you will most likely have so much pain that you simply can't fight back or run away. The shock makes it incredibly hard to &lt;em&gt;do something&lt;/em&gt; or even &lt;em&gt;think properly&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So my question is: is there a reason why pain can elevate to such high levels? I'm just assuming that if we had some sort of hard limit on the amount of pain we receive, we could perform better in several dangerous situations. In other words: instead of hurting so much that we can't even think properly, it hurts &lt;em&gt;enough&lt;/em&gt; to let us know we are in grave danger but still capable of assess the situation and perhaps even act accordingly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Obviously some physical damages will render you unable to act anyway. Like, damages on the spine that may cause your limbs to malfunction. But I mean damages such as a large open wound on the abdomen: if that didn't hurt so much, I'd imagine you could probably stand up and run away (you'd probably bleed out but at least you'll have a chance to escape the threat).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My guess is that it &quot;cannot be helped&quot;. Pain are signals from different parts of the body to the brain, and once a signal is sent, the brain has no choice but to process it accordingly.&lt;/p&gt;&#xA;" OwnerUserId="16897" LastEditorUserId="5198" LastEditDate="2015-07-23T22:50:21.493" LastActivityDate="2015-07-23T22:50:21.493" Title="Why isn't the upper limit of pain lower in humans?" Tags="&lt;pain&gt;&lt;peripheral-nervous-system&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36350" PostTypeId="1" AcceptedAnswerId="36352" CreationDate="2015-07-23T22:24:59.243" Score="1" ViewCount="106" Body="&lt;p&gt;As I was studying for my GRE exam, I was reading on Mitochondria. I then remembered that they undergo replication similar to bacteria. So I googled for info and found on Wikipedia that there is a &quot; near-absence of genetic recombination in mitochondrial DNA&quot; &#xA;&lt;a href=&quot;https://en.wikipedia.org/wiki/Mitochondrion#Replication_and_inheritance&quot; rel=&quot;nofollow&quot;&gt;https://en.wikipedia.org/wiki/Mitochondrion#Replication_and_inheritance&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So then, &lt;strong&gt;if there is a lack of genetic diversity, how can these mitochondria still be functional&lt;/strong&gt;? If we assume they are affected by random mutations as DNA can be. Is it the case that they replicate infrequently enough to not suffer ill-effects of low diversity?&lt;/p&gt;&#xA;" OwnerUserId="14815" LastActivityDate="2015-08-03T08:31:13.647" Title="Genetic Diversity in Mitochondria" Tags="&lt;genetics&gt;&lt;mitochondria&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36351" PostTypeId="2" ParentId="36348" CreationDate="2015-07-23T22:47:23.983" Score="3" Body="&lt;p&gt;You are assuming that fighting back with a bad wound would be more useful than dropping to the ground. That is not always the case.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dropping to the ground and ceasing activity is very adaptive in almost any situation involving potentially significant blood loss. Becoming prone or supine prevents loss of consciousness, the most critical aspect of survival. Decreased movement is also likely to decrease the rate of blood loss (though not in as significant a manner as consciousness).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Certainly with a significant abdominal wound, running would increase cardiac output, which would increase bleeding. Is running from a traumatic event advantageous if you pass out before escaping? On the other hand, lying prone and holding the wound (instinctive) may reduce bleeding and prolong consciousness and life.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What &quot;cannot be helped&quot; (like withdrawing a hand from a flame) &lt;em&gt;is&lt;/em&gt; usually advantageous.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;An infant's cry changes during circumcision (an involuntary reaction to pain). The cry in turn naturally produces a visceral reaction in nearby adults that compels action (causes a state of strong sympathetic nervous system activation.) The adult either avoids the cry by trying to distance themself, or responds by coming to the infant's cry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The infant cannot help changing the intensity of the cry with intense pain. If a &quot;certain level of pain&quot; was as far as one could feel, the baby might not elicit the sense of urgency in adults which it does.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/3359867&quot; rel=&quot;nofollow&quot;&gt;Newborn pain cries and vagal tone: parallel changes in response to circumcision.&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://homepage.psy.utexas.edu/HomePage/Group/Neallab/pubs/assessment_cry.pdf&quot; rel=&quot;nofollow&quot;&gt;ASSESSMENT OF INFANT CRY: ACOUSTIC CRY ANALYSIS AND PARENTAL PERCEPTION&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-07-23T22:47:23.983" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36352" PostTypeId="2" ParentId="36350" CreationDate="2015-07-23T22:53:43.070" Score="4" Body="&lt;p&gt;Your claim that &quot;there is a lack of genetic diversity&quot; in mitochondria is not correct. There is no connection between recombination and mutation rates &lt;em&gt;per se&lt;/em&gt;. In fact, mitochondria &lt;a href=&quot;http://mbe.oxfordjournals.org/content/25/1/120.short&quot; rel=&quot;nofollow&quot;&gt;have much higher mutation rates&lt;/a&gt; than nucleus and different types of mitochondrial DNA can even co-exist in one organism, a phenomenon called &lt;a href=&quot;https://en.wikipedia.org/wiki/Heteroplasmy&quot; rel=&quot;nofollow&quot;&gt;heteroplasmy&lt;/a&gt; (which is found &lt;a href=&quot;http://www.pnas.org/content/111/29/10654&quot; rel=&quot;nofollow&quot;&gt;at a frequency of ~90%&lt;/a&gt; in human).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But: &lt;a href=&quot;https://books.google.com/books?id=pBq69Luwf7UC&quot; rel=&quot;nofollow&quot;&gt;there is a connection&lt;/a&gt; between mutation &lt;a href=&quot;https://en.wikipedia.org/wiki/Fixation_%28population_genetics%29&quot; rel=&quot;nofollow&quot;&gt;fixation&lt;/a&gt; rate and &lt;a href=&quot;https://en.wikipedia.org/wiki/Effective_population_size&quot; rel=&quot;nofollow&quot;&gt;effective population size&lt;/a&gt;. Because mitochondria are normally inherited through maternal line, effective population size for their genome is smaller than that of the nuclear genome, and thus any mutations in the mitochondrial DNA reach fixation faster, but again this is counteracted by high mutation rates.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is no problem with functionality: as always if something gets broken (and it is easy to break something in the mitochondrial genome, since genes are normally tightly packed in it) respective genotype is eliminated or reduced in frequency by &lt;a href=&quot;https://en.wikipedia.org/wiki/Natural_selection&quot; rel=&quot;nofollow&quot;&gt;natural selection&lt;/a&gt;. In the case of mitochondria this selection acts both upon the level of &lt;a href=&quot;http://www.pnas.org/content/112/8/2491.abstract&quot; rel=&quot;nofollow&quot;&gt;individual organisms&lt;/a&gt; (intra-individual somatic pool of mitochondria: positive and negative selection) and the level of populations (&lt;a href=&quot;http://www.ivypub.org/BF/download/12588.shtml&quot; rel=&quot;nofollow&quot;&gt;mostly purifying selection&lt;/a&gt; in humans). It is nevertheless true, that given the virtual lack of recombination, selection becomes the only force of purging deleterious mutations.&lt;/p&gt;&#xA;" OwnerUserId="4579" LastEditorUserId="4579" LastEditDate="2015-08-03T08:31:13.647" LastActivityDate="2015-08-03T08:31:13.647" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36360" PostTypeId="2" ParentId="36311" CreationDate="2015-07-24T04:01:18.967" Score="4" Body="&lt;p&gt;The difference in energy requirements of a motile species make photosynthesis an unsuitable form of primary energy generation for them. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since plants are sessile, their energy consumption rates are lower. Plants have approximate respiration:photosynthesis rates of 0.35-0.9, as can be seen in &lt;a href=&quot;http://tinyurl.com/cjxrym&quot; rel=&quot;nofollow noreferrer&quot;&gt;this table (click to enlarge)&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/ImUpI.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/ImUpIm.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Once the energy consumption rates exceed 1, the organisms will, by definition, no longer be full autotrophs, as they will need to obtain their energy from alternative sources. Therefore, the relative low energy content of sunlight makes it impossible for motile animals, which have a larger energy requirement, to survive fully via photosynthesis. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-07-24T04:01:18.967" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36363" PostTypeId="1" AcceptedAnswerId="36365" CreationDate="2015-07-24T07:23:54.300" Score="9" ViewCount="479" Body="&lt;p&gt;Is there a database of organisms which would contain their queriable geographic location? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would need to perform a rather simple query, such as &lt;code&gt;Animals of &amp;lt;Location&amp;gt;&lt;/code&gt;, where Location is some well defined geographic area such as Czech Republic or Europe.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So far I have found multiple lists on Wikipedia and other webpages, however they seem to be quite incomplete as their intersect is quite small. Moreover, I have found EOL (Encyclopedia of Life) collections but they appear to struggle the same way.&lt;/p&gt;&#xA;" OwnerUserId="16947" LastEditorUserId="3624" LastEditDate="2015-07-24T09:04:31.450" LastActivityDate="2016-07-31T20:51:21.413" Title="Database of Geographic Range of Species" Tags="&lt;ecology&gt;&lt;database&gt;&lt;biodiversity&gt;&lt;species-distribution&gt;" AnswerCount="2" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36364" PostTypeId="2" ParentId="36344" CreationDate="2015-07-24T08:52:21.080" Score="18" Body="&lt;p&gt;There is evidence that cells can exchange mitochondria. There are some donor cells that transfer mitochondria to recipient cells via cytoplasmic nanotubes (within the same species). This happens endogenously and triggering factors may include stress.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1186%2F1479-5876-11-94&quot; rel=&quot;noreferrer&quot;&gt;Pasquier &lt;em&gt;et al&lt;/em&gt;. 2013&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1002/embj.201386030&quot; rel=&quot;noreferrer&quot;&gt;Ahmad &lt;em&gt;et al.&lt;/em&gt; 2014&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/cdd.2014.211&quot; rel=&quot;noreferrer&quot;&gt;Wang and Gerdes. 2015&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://dx.doi.org/10.1038/nature18928&quot; rel=&quot;noreferrer&quot;&gt;Hayakawa &lt;em&gt;et al&lt;/em&gt;. 2016&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;On interspecies mitochondria transfer.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a study by &lt;a href=&quot;http://dx.doi.org/10.1093/nar/gks639&quot; rel=&quot;noreferrer&quot;&gt;Yang and Koob&lt;/a&gt;, the feasibility of mitochondrial transplants was studied. Mitochondria isolated from donor cells were initially injected into mouse oocytes/embryos. Then mitochondria, along with a chunk of cytoplasm and membrane was taken out; these cell-like structures were called  &lt;em&gt;mitocytoplasts&lt;/em&gt;. Then, these mitocytoplasts were fused with recipient cells (mouse rho0 cells - these lack mitochondria) with the help of a viral fusion protein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;They found that the recipient cells supported mitochondria from the same species (donor species include mouse, rat, Mongolian gerbils and Golden Syrian hamsters).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The success of the &quot;mitochondrial xenograft&quot; depends on how different the species are and as shown in the abovementioned experiment, a donor cell (mouse) would not support the mitochondria from even a closely related species (rat). This incompatibility would primarily be based on the dependency of mitochondria on the nuclear genome which may be different for different species. It is possible that &quot;mitochondrial xenografts&quot; may be accepted; the impossibility of it has not been exhaustively verified.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2016-09-16T06:52:48.050" LastActivityDate="2016-09-16T06:52:48.050" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36365" PostTypeId="2" ParentId="36363" CreationDate="2015-07-24T08:59:45.810" Score="6" Body="&lt;p&gt;This is to a large extent a question of how reliable the data in the database needs to be. Reliability (and spatial scale) will differ between datasets and between species groups within datasets, and it is difficult to give a general recommendation. I doubt that you will find a single database with good coverage over all taxonomic groups, even if it is in the form of country checklists. For the most reliable information, curated country checklists for specific taxonomic groups will probably be best, but these have to be searched for individually for each taxonomic group of interest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As a starting point, you might want to look at the occurence data that can be found in &lt;a href=&quot;http://www.gbif.org&quot;&gt;gbif.org&lt;/a&gt; (The Global Biodiversity Facility). The data found there is certainly not complete, and it will be misleading for many species. However, for the current distribution of relatively well-known groups of species it will give you a good idea of their distribution. This has to be evaluated on a case-by-case basis though. You can access the data in gbif using external tools, for instance using R through &lt;a href=&quot;https://github.com/ropensci/rgbif&quot;&gt;rgbif&lt;/a&gt; (there is also tools for python or other languages). At the blog recology.info you can find &lt;a href=&quot;http://recology.info/2012/10/rgbif-newfxns/&quot;&gt;a tutorial on how to get a species list&lt;/a&gt; for a particular country using rgbif (more specifically the function &lt;code&gt;density_spplist&lt;/code&gt;).&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-07-24T10:43:29.590" LastActivityDate="2015-07-24T10:43:29.590" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36366" PostTypeId="1" AcceptedAnswerId="36719" CreationDate="2015-07-24T09:16:59.370" Score="2" ViewCount="456" Body="&lt;p&gt;Previously, when I needed to find a genomic feature (promoter, CDS, repeat etc) that underwent mutation (SNP) I used my own scripts to load an annotation file, parse it, map the SNP's position and output the sequence of the feature. Now that I'm moving from microbes to mammals with huge annotations, introns/exons and huge genomes, my scripts don't work that well and I'm sort of lazy to optimize the code or rewrite it in a faster language, since I'm sure there should be some prominent tools for the task. That's it, could you recommend me some tools that do the following:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Given a reference genome, annotation and a VCF (or similar variant file) match the SNPs to genomic features in the annotation &lt;/li&gt;&#xA;&lt;li&gt;Output the entire feature that underwent mutation, e.g. if the SNP happened in a protein-coding gene, I need to have the entire protein-coding sequence not just an exon/intron. &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance. &lt;/p&gt;&#xA;" OwnerUserId="13338" LastActivityDate="2018-10-01T19:24:46.340" Title="A tool to get annotation features by position in the reference genome" Tags="&lt;bioinformatics&gt;&lt;research-tools&gt;" AnswerCount="1" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36369" PostTypeId="2" ParentId="36291" CreationDate="2015-07-24T12:38:58.427" Score="2" Body="&lt;p&gt;Interpreting your question as &quot;would the Lotka-Volterra predator-prey model be a good model for the glucose-insulin system?&quot; my answer is &quot;no&quot;. The predator-prey equations capture assumptions about how prey and predator interact with each other, and how they would fare on their own. These assumptions are not equivalent to any reasonable assumptions about the glucose-insulin system. The fact that both prey and predator population sizes as well as glucose and insulin concentrations oscillate is not enough to say the two systems may be modelled by the same equations. In fact, the oscillations in the figures you show are very different form each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let us go through some of the assumptions of the Lotka-Volterra predator-prey model to see why most of them do not resemble anything related to the glucose-insulin system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;1) In the absence of predators, the prey population grows exponentially without limits. This follows from self-reproduction. If glucose were likened to prey, glucose would increase exponentially in the absence of insulin. If prey were likened to insulin, insulin would increase exponentially in the absence of glucose. Is that reasonable?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;2) The population growth rate of the prey is reduced by a quantity proportional to the population sizes of both prey and predator. The underlying assumption is that prey and predator meet a rate proportional to their population densities and that a fraction of these encounters leads to the death of the prey. The assumption about the encounter rate is called the Law of Mass-Action, and applies well to chemical compounds in a liquid, like glucose and insulin. However, glucose and insulin do not interact directly, and it is not clear to me how realistic assumptions abut their interaction would work out.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;3) New predators are born at a rate proportional to the encounter rate in 2). In the glucose-insulin system this would mean that more insulin is produced if more insulin is present. Is that realistic?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The answer to these questions is, according to me, &quot;no&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(On a side note: the Lotka-Volterra model is structurally unstable, meaning that slightest change in the assumptions would fundamentally alter the outcome of the model. One of these outcomes are neutrally stable predator-prey cycles, that is, cycles of which the amplitude and period depend on the initial population sizes. Changing the assumption that the prey population grows exponentially by including a term - $m \times x^2$ to the first equation changes the oscillations into damped oscillations so that the populations settle at a stable equilibrium.)&lt;/p&gt;&#xA;" OwnerUserId="8552" LastEditorUserId="8552" LastEditDate="2015-07-27T13:20:22.307" LastActivityDate="2015-07-27T13:20:22.307" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36372" PostTypeId="2" ParentId="36291" CreationDate="2015-07-24T13:39:16.753" Score="0" Body="&lt;p&gt;There is an important difference in the dynamics of the 2 situations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Lotka-Volterra model undergoes repeated oscillations in predator and prey levels. Changes in one population affect the changes in the other population, &lt;em&gt;and vice versa&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the glucose-control model, what you have plotted are the changes in glucose and insulin levels following a meal or infusion of glucose. Note that there is no subsequent peak of glucose after the insulin levels have dropped, unlike the peaks in prey levels after predator levels have dropped in the Lotka-Volterra model. &lt;/p&gt;&#xA;" OwnerUserId="16326" LastActivityDate="2015-07-24T13:39:16.753" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36374" PostTypeId="1" CreationDate="2015-07-24T14:06:16.630" Score="12" ViewCount="2398" Body="&lt;p&gt;There aren't any eusocial animals (hives of wasps, ants, termites, etc) that hunt large prey, are there?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm thinking prey in the size range of, say, a rabbit, or even a deer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can't see a rabbit or a deer having any real effective way to defend against a swarm of hornets, especially if you supposed that the hornets' venom could easily be adapted to be particularly effective against such prey.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intuitively, this seems like it would be a lucrative little niche.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;A swarm could bring down a kill without risking losing too many members.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The return seems like it could be very high.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There shouldn't be too much of a risk of losing much of the kill to scavengers or whatever.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;And after starting down the evolutionary pathway into such a niche, they could easily develop methods of preserving meat (I'm imagining a horrifying hive full of natural ham, here).&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Protecting this ham-hive wouldn't be any more difficult than protecting a honey-hive from bears etc.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;And such a niche doesn't seem that evolutionarily distant from where hornets already are.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Like:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;They already do seriously hurt or even kill large animals that they perceive as threatening their hive.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;They already do scavenge large animals they find dead, and even steal the occasional chunk of flesh from living animals.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;But as far as I know, nothing like this exists, right?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why not?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(And, like... maybe the most important question: How can we make sure it &lt;em&gt;never&lt;/em&gt; comes into existence?)&lt;/p&gt;&#xA;" OwnerUserId="5767" LastActivityDate="2015-07-25T05:49:51.327" Title="There aren't any animals like hornets that hunt large prey (like a rabbit, or even up to a deer), right? Why not?" Tags="&lt;evolution&gt;&lt;predation&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36375" PostTypeId="2" ParentId="36374" CreationDate="2015-07-24T14:43:25.160" Score="3" Body="&lt;p&gt;Unfortunately for you, such animals do exist &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1744-7429.2005.00091.x/abstract&quot; rel=&quot;nofollow&quot;&gt;(O'Donnell &lt;em&gt;et al.&lt;/em&gt; 2005)&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a direct field observation of a swarm of army ants attacking and consuming a 60cm long earthworm, as well as consuming a 10cm long snake. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;em&gt;From the linked article:&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;We collected workers from two &lt;em&gt;Cheliomyrmex andicola&lt;/em&gt; foraging raids.&#xA;  During raid 1 on 26 September 2003 at 1030 h, we encountered a large&#xA;  &lt;em&gt;C. andicola&lt;/em&gt; raid column in primary terra firme forest, exiting from soil-covered foraging trails that the ants had constructed on a slope.&#xA;  The sky was clear, and ground surface temperature was 25.9°C. Beneath&#xA;  the raised tunnel of soil particles that the ants had constructed, we&#xA;  found the partially consumed carcass of a snake (1 cm in diameter and&#xA;  10 cm long). Most of the snake's scales and skin had been removed.&#xA;  &lt;em&gt;Cheliomyrmex andicola&lt;/em&gt; workers were observed chewing on the snake and carrying away bits of flesh in their mandibles. As we dug near the&#xA;  carcass, the ant workers responded by biting and stinging our hands.&#xA;  The workers clung to our skin, and we noted that their stings were&#xA;  more painful than those of other army ants from the site (e.g.,&#xA;  &lt;em&gt;Eciton burchellii&lt;/em&gt; and &lt;em&gt;Eciton hamatum&lt;/em&gt;). We collected ant workers and samples of snake flesh into 70 percent ethanol. During raid 2 on 1&#xA;  October 2003 at 1205 h, during a brief rain shower, our attention was&#xA;  drawn by rustling sounds in the leaf litter on a slope in a partially&#xA;  cleared area of terra firme forest adjacent to the station buildings.&#xA;  A subterranean column of &lt;em&gt;C. andicola&lt;/em&gt; workers erupted from the soil&#xA;  in pursuit of a fleeing giant earthworm (possibly a species in the&#xA;  genus Martiodrilus: Zicsi 1990). Several hundred ant workers emerged&#xA;  from the soil and ran over the leaf litter in the direction taken by&#xA;  the worm. Five &lt;em&gt;C. andicola&lt;/em&gt; workers mounted the worm and were biting&#xA;  and apparently stinging its body. After the worm crawled for a&#xA;  distance of 3 m down slope from where it exited the soil, its body&#xA;  contracted from over 40 cm in length to approximately 20 cm in length.&#xA;  The worm abruptly stopped moving and became rigid on the soil surface&#xA;  within 10 sec of exiting the soil, and was then unresponsive to human&#xA;  touch. We assumed that the worm was either paralyzed or dead. We&#xA;  lifted the worm to examine it, and we collected ant workers from its&#xA;  body and from the raid column as it arrived where the worm came to&#xA;  rest. Workers collected from both raids had no prey (other than snake&#xA;  flesh at raid 1) in their mandibles.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;However, most army ants are (fortunately) not predators of large animals. This appeared to be the only unambiguous literature reference of predation of large animals by eusocial insects that I could find in a brief literature search.&lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="3340" LastEditDate="2015-07-25T05:49:51.327" LastActivityDate="2015-07-25T05:49:51.327" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="36376" PostTypeId="1" CreationDate="2015-07-24T14:46:46.923" Score="5" ViewCount="218" Body="&lt;p&gt;Edward O. Wilson, in The Diversity of Life wrote (emphasis mine):&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Ninety-nine percent of the animals find their way by chemical trails.  […]&lt;/p&gt;&#xA;&lt;p&gt;Animals are masters of this chemical channel, where we are&#xA;idiots. But we are geniuses of the audiovisual channel, equaled in&#xA;this modality only by a few odd groups (whales, monkeys, birds). So we&#xA;wait for dawn, while they wait for the fall of darkness; &lt;strong&gt;and because&#xA;sight and sound are the evolutionary prerequisites of intelligence, we&#xA;alone have come to reflect on such matters&lt;/strong&gt; […]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;I'm getting this from an anthology (Dawkins' &amp;quot;Modern Science Writing&amp;quot;) so I don't see how Wilson supports this statement, and my google-fu is bringin up nothing relevant-seeming.&lt;/p&gt;&#xA;&lt;p&gt;My question is: why are sight and sound prerequisites for a species to evolve intelligence?&lt;/p&gt;&#xA;" OwnerUserId="16951" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-07-26T12:20:36.333" Title="Why are sight and sound prerequisites for intelligence?" Tags="&lt;evolution&gt;&lt;intelligence&gt;" AnswerCount="3" CommentCount="0" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36377" PostTypeId="2" ParentId="36374" CreationDate="2015-07-24T15:16:55.537" Score="8" Body="&lt;p&gt;They do exist. Many such examples can be found. Such as the most terrifying one, being social groups formed by Spiders, &lt;a href=&quot;http://www.nature.com/news/2008/080804/full/news.2008.1007.html&quot;&gt;&lt;em&gt;Anelosimus eximius&lt;/em&gt;&lt;/a&gt; documented here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Colonies of upto 9000 individuals have been documented by the scientists in their report.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also let's not forget Piranhas, another group of social animals, which take down much larger prey due to their larger colony size.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This particular phenomenon is concisely explained in this article in wikipedia under &lt;a href=&quot;https://en.wikipedia.org/wiki/Cooperative_hunting&quot;&gt;Cooperative Hunting&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As the models explain and I also think the same, that the only reason a social aggregation would seem necessary to any animal is because it provides increased fitness or survival. This particular phenomenon can be viewed from the perspective of Human society as well. I given an income source X, would always choose to rent a private space for myself. If my income does not allow me such an option my best option is to cooperate with another in a shared system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So the same can be said for Insects if availability of prey which can be candidates of solo hunting goes down, the only option left for the species to survive is to either compete if that is the only available source of food, or if larger prey is available for group hunting where individuals don't come into direct conflict, then to go for the option which provides the greatest fitness to the species as a whole. Obviously, in such a case you go for aggregation and not competition such as those seen in ant colonies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many more such systems exist I am sure, but I am no evolutionary biologist only a humble genomics guy. They will be able to provide much more comprehensive answers.&lt;/p&gt;&#xA;" OwnerUserId="15807" LastActivityDate="2015-07-24T15:16:55.537" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="36378" PostTypeId="2" ParentId="36374" CreationDate="2015-07-24T15:53:46.007" Score="10" Body="&lt;p&gt;&lt;strong&gt;They're not fast enough&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A hornet has a top speed of around 40 kph, while a rabbit is only a touch faster, a deer can hit 75 kph (all figures from Wikipedia). In order to act as hunting insects they need to match the speed of these large animals in large enough numbers to surround and overpower them but these animals could easily match their speed or outpace them. Let's suppose they can overcome that limitation somehow and bring the prey down. They've now bagged a big lump of protein but it's a long way from the hive because they've had to chase it down first. That means that a long round trip is required every time they visit the kill and thus reduces the energy yield as well as increasing the chance of losing it to scavengers.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Against this you have the simpler option of eating smaller, easier to catch, prey as they do now.&lt;/p&gt;&#xA;" OwnerUserId="2938" LastActivityDate="2015-07-24T15:53:46.007" CommentCount="10" ContentLicense="CC BY-SA 3.0" />
  <row Id="36379" PostTypeId="2" ParentId="36376" CreationDate="2015-07-24T16:00:28.650" Score="2" Body="&lt;p&gt;He may be referring to the fact that many nocturnal animals wait for the cover of darkness to be able to get their food safely or in order to cloak themselves to approach their prey better. However, this seems to be a matter of personal opinion. He wants you to think that we are smarter because we have to hide and hunt in broad daylight. I haven't been able to support his theory as &lt;a href=&quot;http://www.ethlife.ethz.ch/archive_articles/110214_fledermaus_soziologie_per/index_EN&quot; rel=&quot;nofollow&quot;&gt;bats can be considered very intelligent&lt;/a&gt; - and they primarily hunt at night. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact, we also consider dogs - and their wolf counterparts - to be intelligent as well, and you typically only see &lt;a href=&quot;http://www.wolfcountry.net/information/WolfHunting.html&quot; rel=&quot;nofollow&quot;&gt;wolves at night&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Also, studies are showing that humans who are &quot;Night Owls&quot; are smarter than people who are &quot;Morning Larks&quot; according to a study in &lt;a href=&quot;https://www.psychologytoday.com/blog/the-scientific-fundamentalist/201005/why-night-owls-are-more-intelligent-morning-larks&quot; rel=&quot;nofollow&quot;&gt;Psychology&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you're interested in different kinds of behaviours and how intelligent they are you can look at &lt;a href=&quot;http://www.bbc.co.uk/nature/adaptations&quot; rel=&quot;nofollow&quot;&gt;BBC Animal Adaptations&lt;/a&gt;, which has a really cool list of what abilities each animal has split into categories. Particularly, they have an &quot;Animal Intelligence&quot; section which goes into detail about particular behaviours humans consider to be signs of intelligence. Personally, I think their list is a little out of date - where it is missing a few animals - but by their standards, many of the nocturnal animals have not made it onto the list. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A reason that hearing could be a prerequisite for intelligence is that communication is considered to be a HUGE part of intelligent behaviour. Tool use could be a reason that sight is considered a prerequisite for being intelligent. Really, the five senses (sight, hearing, touch, taste and smell) allow us to really take in the world and adapt to it properly. Sight, hearing and smell typically allow us to be warned of dangers but the fact is that we have to be intelligent enough to know what to do with the information. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Summary:&lt;/strong&gt; Intelligence can be measured in many different ways. Edward O. Wilson could have been looking at a number of different things when he came to his conclusion (where sight and sound were required for intelligent beings). The truth is that it is all speculative.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If you judge a fish's intelligence by its ability to climb a tree, it will grow up thinking that it's stupid. &lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Subsequently if you judge my intelligence by my ability to spell, I will also go on thinking I'm stupid ;)&lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="1306" LastEditDate="2015-07-26T11:52:44.973" LastActivityDate="2015-07-26T11:52:44.973" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36380" PostTypeId="2" ParentId="36376" CreationDate="2015-07-24T16:11:20.120" Score="3" Body="&lt;p&gt;To answer your question, we must first ask the question What is defined as intelligence? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A googling will tell you that most people believe intelligence to be something related to apes or even more conservatively to humans. But, I find this to be a bit unpragmatic. The closest level of abstraction I find towards defining intelligence is this wiki on &lt;a href=&quot;https://en.wikipedia.org/wiki/Animal_cognition&quot; rel=&quot;nofollow&quot;&gt;Animal Cognition&lt;/a&gt;. Having said so, I personally would define intelligence on a much more abstract level. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Intelligence can be broadly defined as a learned response towards an external stimulus, providing the organism with an increased fitness/survival within it's ecosystem.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So Intelligence can be broken down into two parts &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Memory of a stimulus&lt;/li&gt;&#xA;&lt;li&gt;A programmed response towards that stimulus&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;This is a very famous video showcasing intelligence in the animal world; &lt;a href=&quot;https://www.youtube.com/watch?v=JY8-gP3Sw_8&quot; rel=&quot;nofollow&quot;&gt;Crow Intelligence test&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But My objective is to state that sight and sound are are not at all prerequisites of intelligence. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This paper from way back in 2014 is I think the best that I can state&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177670/&quot; rel=&quot;nofollow&quot;&gt;Memory and Fitness Optimization of Bacteria under Fluctuating Environments&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In this particular paper the authors test the capacity of E coli to produce a response within fluctuating environments, and they find that as the generations progress the later generations take lesser time to produce a response towards the stimulus. They also note that what happens if the prior external environmental state is restored. In such a case later generations become optimised for that particular state. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a very good example of memory which is stored at the level of DNA, and a level of intelligence is manifested in a microbial system. So therefore, can you really state that &quot;sight- and sound&quot; are pre-requisites of intelligence. I would say No They are not, that would be an over-simplistic way of what intelligence really is. &lt;/p&gt;&#xA;" OwnerUserId="15807" LastActivityDate="2015-07-24T16:11:20.120" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36381" PostTypeId="2" ParentId="36291" CreationDate="2015-07-24T18:34:03.767" Score="1" Body="&lt;p&gt;No, the Lotka-Volterra model is a description of predator-prey dynamics. Although in some respects over-simplifying it is well suited for educating population dynamics and basic research.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The physiology of carbohydrate homeostasis is different. Although, similar to population count in the Lotka-Volterra model, the elimination of both glucose and insulin depend on their respective concentrations (which represents a very basic form of autoregulation), their interdependence is different. Here, we have to consider distribution processes, receptor binding, enzyme kinetics etc.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Numerous mathematical and cybernetic models have attempted to describe glucose-insulin homeostasis. The following review articles provide a good overview of the topic:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Ajmera I, Swat M, Laibe C, Novère NL, Chelliah V. The impact of mathematical modeling on the understanding of diabetes and related complications. CPT Pharmacometrics Syst Pharmacol. 2013 Jul 10;2:e54. &lt;a href=&quot;http://dx.doi.org/10.1038/psp.2013.30&quot; rel=&quot;nofollow&quot;&gt;doi 10.1038/psp.2013.30&lt;/a&gt;. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23842097&quot; rel=&quot;nofollow&quot;&gt;PMID 23842097&lt;/a&gt;; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3731829/&quot; rel=&quot;nofollow&quot;&gt;PMCID PMC3731829&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Palumbo P, Ditlevsen S, Bertuzzi A, De Gaetano A. Mathematical    modeling of the glucose-insulin system: a review. Math Biosci. 2013    Aug;244(2):69-81. &lt;a href=&quot;http://dx.doi.org/10.1016/j.mbs.2013.05.006&quot; rel=&quot;nofollow&quot;&gt;doi 10.1016/j.mbs.2013.05.006&lt;/a&gt;. Epub 2013 Jun 1. Review. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/23733079&quot; rel=&quot;nofollow&quot;&gt;PMID 23733079&lt;/a&gt;.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="3865" LastActivityDate="2015-07-24T18:34:03.767" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36383" PostTypeId="2" ParentId="36291" CreationDate="2015-07-24T20:40:03.280" Score="7" Body="&lt;p&gt;Is the standard Lotka-Volterra (LV) model an &lt;em&gt;exact&lt;/em&gt; fit for insulin-glucose (IG) dynamics? No. Can a similar model built on the same principles capture most of the essential features of the IG dynamics? &lt;em&gt;Absolutely&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;How to capture most of the insulin-glucose dynamics using a slightly modified Lotka-Volterra model&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;We can figure out how to change the LV equations to fit the IG dynamics by figuring out how our assumptions have changed. Like Daan mentioned, neither insulin nor glucose undergo self-reproduction. So we'll drop those terms from the equation, and we'll represent an influx of glucose (as from, say, a meal) as a simple time-dependent linear spike. Your rate equations will now look like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\frac{dx}{dt} = \alpha[t_{gi} &amp;lt; t&amp;lt; t_{gf}]-\beta x y$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\frac{dy}{dt} = \delta x-\gamma x y$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $x$ is glucose concentration, $y$ is insulin concentration, and $[t_{gi} &amp;lt; t&amp;lt; t_{gf}]$ is equal to 1 if the current time $t$ is greater than the time when the glucose spike starts $t_{gi}$ and less than the time when the glucose spike ends $t_{gf}$, and is equal to zero if the time $t$ does not meet this condition. &lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Simulation of insulin-glucose dynamics using the above LV model&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;I ran a simulation of the above model in Matlab, and here's what it looks like:&#xA;&lt;a href=&quot;https://i.stack.imgur.com/FWpD2.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/FWpD2.png&quot; alt=&quot;simulation of basic LV model of IG dynamics&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The basic features of the insulin-glucose dynamics from the example graph the OP posted are present. Just like in the real system, first the glucose spikes, then the insulin spikes after a short lag, then they both return to baseline.&lt;/p&gt;&#xA;&#xA;&lt;h1&gt;With some small improvements, the LV model can capture the dynamics of the infamous &quot;sugar crash&quot; phenomenon&lt;/h1&gt;&#xA;&#xA;&lt;p&gt;Now for the really cool part.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As can be seen on the OP's graph, glucose levels tend to fall somewhat below their baseline following a large glucose spike. This is the physiological basis for the sugar crash that people sometimes get a little while after eating something really sugary like a candy bar. &lt;a href=&quot;http://www.theguardian.com/lifeandstyle/wordofmouth/2014/feb/25/do-children-really-get-sugar-rush-hyperactivity&quot; rel=&quot;nofollow noreferrer&quot;&gt;Regardless of whether the psychological symptoms actually occur&lt;/a&gt;, the dip in glucose levels is a real thing.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In order for a model to be considered &quot;good&quot;, it has to be able to capture these kinds of complex but important phenomena in their underlying systems. The glucose dip did not show up in my original LV model, so the question is, can the model be modified in a simple way so that it will capture the dip? Let's take another crack at it!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Part of the problem with trying to study phenomena related to baseline levels using the previous model is that the baseline levels of both insulin and glucose are effectively fixed at 0 in that model. We can set the baseline levels by adding what's called a zeroth-order production term (essentially a fixed constant that isn't multiplied by the concentration of anything) to each of our rate equations. The rate equations now look like:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\frac{dx}{dt} = \alpha[t_{gi} &amp;lt; t&amp;lt; t_{gf}]+\epsilon-\beta x y$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$\frac{dy}{dt} = \delta x+\eta-\gamma x y$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;where $\epsilon$ is the 0th order glucose production term, $\eta$ is the 0th order insulin production term, and everything else is exactly the same.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;Simulation of insulin-glucose dynamics using the &quot;dip-enabled&quot; LV model&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;Again using Matlab, I ran a simulation of the &quot;dip-enabled&quot; LV model:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/Z2Nkc.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/Z2Nkc.png&quot; alt=&quot;simulation of dip enabled LV model of IG dynamics&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;and this time the dip shows up.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Notes:&lt;/h3&gt;&#xA;&#xA;&lt;p&gt;-The term with the times in it is called an &lt;a href=&quot;https://en.wikipedia.org/wiki/Iverson_bracket&quot; rel=&quot;nofollow noreferrer&quot;&gt;Iverson Bracket&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;-You could make this model more physiologically relevant by using a more complex function for the glucose spike, but for simplicity's sake we'll stick with a linear function. A smoother function, like for example a Hill function, would probably help to reproduce your original graph of the IG dynamics.&lt;/p&gt;&#xA;&#xA;&lt;h3&gt;Matlab code&lt;/h3&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;function dxdt = insulin_glucose_birth_death_dxdt(t, x, kip, bip, kid, kgp, bgp, kgd)&#xA;dxdt = [kip*x(2) + bip - kid*x(1),&#xA;    kgp*(t&amp;gt;1 &amp;amp;&amp;amp; t&amp;lt;2) + bgp - kgd*x(1)*x(2)];&#xA;end&#xA;&#xA;function [t,x] = insulin_glucose_birth_death_odesol(tspan, x0, kip, bip, kid, kgp, bgp, kgd)&#xA;opts=odeset();&#xA;[t,x]=ode45(@(t,x)insulin_glucose_birth_death_dxdt(t, x, kip, bip, kid, kgp, bgp, kgd), tspan, x0, opts);&#xA;end&#xA;&#xA;function [t,x] = insulin_glucose_birth_death_plot(tspan, x0)&#xA;%run with:&#xA;%   tspan = [-10, 5];&#xA;%   x0 = [0,0];&#xA;%   [t,x] = insulin_glucose_birth_death_plot(tspan,x0);&#xA;&#xA;kip = 2;&#xA;bip = 0;  % set to .01 for the &quot;dip&quot; simulation&#xA;kid = 1;&#xA;kgp = .1;&#xA;bgp = 0;   % set to .1 for the &quot;dip&quot; simulation&#xA;kgd = 50;&#xA;&#xA;[t,x] = insulin_glucose_birth_death_odesol(tspan, x0, kip, bip, kid, kgp, bgp, kgd);&#xA;&#xA;figure(gcf)&#xA;hold on&#xA;plot(t, x(:,1), 'b', t, x(:,2), 'r')&#xA;legend('insulin','glucose')&#xA;xlabel('time')&#xA;ylabel('concentration')&#xA;axis([0 inf -inf inf])&#xA;hold off&#xA;end&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;" OwnerUserId="784" LastEditorUserId="784" LastEditDate="2015-08-10T07:00:53.273" LastActivityDate="2015-08-10T07:00:53.273" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36384" PostTypeId="2" ParentId="36041" CreationDate="2015-07-24T21:01:46.703" Score="3" Body="&lt;p&gt;Understanding the link between the size of the tumor mutanome and its immunogenicity requires a basic understanding of T-cell development and regulation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When normal human cells degrade proteins via the proteasome, some fragments of these proteins, called peptides, are bound to specialized cell-surface proteins called MHC. T-cells express a specialized receptor, called the TCR, which recognizes peptides bound by MHC proteins on other cells. The specificity of the TCR, what peptide/MHC combinations a T-cell can recognize, is randomly generated by targeted mutations and VDJ recombination in the TCR genes during a T-cells development. Each clonal population of T-cells (T-cells derived from the same precursor) have a unique TCR that recognizing different peptide/MHC pairs. When a T-cell's TCRs recognize a peptide/MHC combo on another cell, the T-cell is activated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Because the TCR is generated randomly, many TCRs in T-cell precursors can recognize peptides derived from normal human proteins. To prevent these precursors from becoming T-cells that can attack the body, they are regulated in several ways. Many self-peptide recognizing precursors are destroyed in development, others are converted into regulatory T-cells that instead produce anti-inflammatory cytokines that tune down immune responses. Those those that escape these regulatory processes are later inactivated by other means.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What does this have to do with cancer? Well, most of a tumor's proteins are normal human proteins, and the human body does its best to suppress immune responses against normal human proteins, making it hard to generate an attack against cancer cells with T-cells that recognize normal self-peptide/MHC. Worse, overcoming this protective response could lead to an auto-immune attack on normal, healthy cells. Therefore, we want to make or use T-cells that recognize mutant-peptide/MHC combos. Such cells would not attack or be effectively suppressed in normal tissues, but could attack tumors.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, to get these ideal, tumor-targeted T-cells, we need the tumor to produce mutant proteins whose peptide fragments ARE DISTINCT from the peptide fragments of normal proteins. Some tumors have far more of these kinds of mutations than others, and not every mutation is immunogenic (not every mutation can be differentially recognized by T-cells). For example, point mutations (single amino acid changes) that activate proto-oncogenes like BRAF don't necessarily lead to the production of structurally different peptide fragments. A larger mutanome offers a greater chance of immunogenic mutations.&lt;/p&gt;&#xA;" OwnerUserId="16147" LastActivityDate="2015-07-24T21:01:46.703" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36385" PostTypeId="1" CreationDate="2015-07-24T21:29:20.743" Score="4" ViewCount="414" Body="&lt;p&gt;I know that conception is a multi-step process. A sperm fuses with an egg. Its contents diffuse into the cytoplasm. &#xA;Dad's DNA is transported to the nucleus. Proteins are gradually made from Dad's DNA. Do we know how long that process takes?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm most curious about conception in humans, but information about other species is welcome too.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;EDIT:  The time I'm interested in is between the fusing of sperm and egg, and the first transcription of the newly incorporated paternal DNA within the zygote's nucleus. However, if conception is better defined by different events, feel free to correct me. I'm far from a specialist in the subject.&lt;/p&gt;&#xA;" OwnerUserId="15727" LastEditorUserId="15727" LastEditDate="2015-07-25T03:25:57.520" LastActivityDate="2015-07-25T03:25:57.520" Title="How long does conception take?" Tags="&lt;human-biology&gt;&lt;reproduction&gt;" AnswerCount="0" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36387" PostTypeId="2" ParentId="36311" CreationDate="2015-07-25T01:26:03.590" Score="1" Body="&lt;p&gt;There is at least one species of highly mobile animal that can photosynthesize, depending on your definition of &quot;highly mobile&quot;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.boredpanda.com/leaf-sheep-sea-slug-costasiella-kuroshimae/&quot; rel=&quot;nofollow&quot;&gt;Sea Sheep? This Adorable Sea Slug Eats So Much Algae It Can Photosynthesize&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The catch is that this animal does not produce its own chloroplast.&lt;/p&gt;&#xA;" OwnerUserId="1114" LastActivityDate="2015-07-25T01:26:03.590" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36388" PostTypeId="1" CreationDate="2015-07-25T06:04:24.450" Score="4" ViewCount="280" Body="&lt;p&gt;Let's assume we have two toxins - one of which is routinely metabolized by the liver, and the other is new to the organism (consider for example alcohol in a heavy drinker and any other drug that is taken for the first time) and they are administered at once. &#xA;Does the liver have any way to prioritize metabolizing either of these substances or does it happen simultaneously for both?&lt;/p&gt;&#xA;" OwnerUserId="16963" LastEditorUserId="16299" LastEditDate="2015-12-05T04:26:34.580" LastActivityDate="2015-12-05T04:26:34.580" Title="Can the liver prioritize it's metabolizing potential?" Tags="&lt;pharmacology&gt;&lt;toxicology&gt;&lt;liver&gt;&lt;alcohol&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36393" PostTypeId="2" ParentId="35778" CreationDate="2015-07-25T13:34:28.570" Score="5" Body="&lt;p&gt;To fully comprehend the concept of wobble base-pairing we need to consider the nucleotide sequences of the anti-codons in the tRNAs that have to &quot;read&quot; the genetic code when the mRNA is being translated on the ribosome.  The nucleotide in the anti-codon's wobble position is, for example, often inosine.  Under the rules for wobble base-pairing an Inosine can potentially base-pair with three other nucleotides.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In real terms that means a cell can use less than 63 unique tRNA genes to decode mRNAs carrying messages made of the 63 different &quot;words&quot; (codons).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In an active cell the Ribosome's A-site, where the charged tRNA binds, is occupied by the incorrect tRNA &lt;strong&gt;most of the time&lt;/strong&gt; (based on the law of mass action where any charged tRNA can randomly diffuse into the binding site).  With tRNAs that can recognize multiple codons (which is what the wobble hypothesis gets us), any given protein can be translated faster (assuming  that correct charged tRNAs are limiting for the polypeptide polymerization reaction).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So those are the practical ramifications of the table that you presented, but the explanation, as for most &lt;em&gt;why&lt;/em&gt; based questions about biological evolution, is a retrofit.  Natural selection can only work with the materials at hand, and so we can infer that during the period when this genetic code was finalized that the organisms who used it were more successful than the others.  And the current code is based on whatever the previous one looked like. &quot;Descent by modification&quot; is the original description.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;[whoops, sorry about the pedantic voice on the &quot;how selection works&quot; bit, I just looked at your profile and realized you can likely teach me on this subject]&lt;/p&gt;&#xA;" OwnerUserId="14946" LastEditorUserId="14946" LastEditDate="2015-07-25T13:50:01.573" LastActivityDate="2015-07-25T13:50:01.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36394" PostTypeId="1" AcceptedAnswerId="36531" CreationDate="2015-07-25T15:22:13.787" Score="7" ViewCount="433" Body="&lt;p&gt;A recent review article, &lt;a href=&quot;http://informahealthcare.com/doi/abs/10.3109/15368378.2015.1043557&quot;&gt;Oxidative mechanisms of biological activity of low-intensity radiofrequency radiation&lt;/a&gt; reached a surprising conclusion&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;our analysis demonstrates that low-intensity RFR [Radio Frequency Radiation] is an expressive oxidative agent for living cells with a high pathogenic potential and that the oxidative stress induced by RFR exposure should be recognized as one of the primary mechanisms of the biological activity of this kind of radiation.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;They suggest the oxidative stress can cause cancer and non-cancer pathologies.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This study has received next to no media coverage. With RFR impacting so many people it makes me wonder, is this study valid? I would expect this to be front page news given the large number of studies reviewed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are low-intensity radio-waves carcinogenic?&lt;/p&gt;&#xA;" OwnerUserId="16971" LastActivityDate="2015-08-01T01:02:16.483" Title="Are low-intensity radio-waves carcinogenic?" Tags="&lt;cancer&gt;&lt;radiation&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36395" PostTypeId="1" CreationDate="2015-07-25T19:10:18.333" Score="4" ViewCount="8628" Body="&lt;p&gt;Does spitting on stains help with removal?&#xA;Saliva is high in amylase that should help with the breakdown of protein rich stains like blood and semen. It also contains antimicrobial enzymes and antibacterial compounds. Does semen contain any kind of surfactant agents?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, my questions are: &#xA;Does spitting on a semen stain aid in or add to the cleanup?&#xA;On which stains are saliva beneficial and how long does it have to sit?&lt;/p&gt;&#xA;" OwnerUserId="16973" LastEditorUserId="3553" LastEditDate="2015-07-27T14:12:07.813" LastActivityDate="2018-07-22T21:52:52.993" Title="Do the enzymes and compounds in saliva help with stain removal?" Tags="&lt;human-biology&gt;&lt;proteins&gt;&lt;enzymes&gt;&lt;stomach&gt;" AnswerCount="3" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36396" PostTypeId="1" AcceptedAnswerId="36433" CreationDate="2015-07-25T20:48:59.830" Score="11" ViewCount="1746" Body="&lt;p&gt;I've always wondered if having different iris colors, (eye colors) may have any advantages or disadvantages on ones vision. Specifically regarding the effects of light.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Personally, I have troubles being out in the bright sun without sunglasses. My girlfriend on the other hand does not share this issue. Coincedentally my eyes are a light blue and hers are brown. After realizing this, I began to notice a trend when it comes to blue eyed people having this same issue. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, on a bright day, does a person with blue eyes have a higher sensitivity to the light than their darker counterparts?  Thank you.&lt;/p&gt;&#xA;" OwnerUserId="16976" LastEditorUserId="16976" LastEditDate="2015-07-27T20:33:33.753" LastActivityDate="2015-07-28T00:39:03.340" Title="Does your iris color have an effect on your vision?" Tags="&lt;eyes&gt;&lt;light&gt;&lt;iris&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36399" PostTypeId="1" AcceptedAnswerId="36400" CreationDate="2015-07-26T05:58:56.980" Score="1" ViewCount="707" Body="&lt;p&gt;I read a lot about speciation. To my knowledge, a species is often defined as a group of individuals that actually or potentially interbreed in nature and produce fertile offspring. Speciation is a lineage-splitting event that produces two or more separate species. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, some creationists claim that there is &lt;strong&gt;no&lt;/strong&gt; speciation, rather &lt;strong&gt;variation&lt;/strong&gt; in the same species. As in &quot;fruit fly experiment&quot;, I read that two groups of fruit flies don't interbreed after the evolution and speciation takes place. As per the definition of species (biological concept of species), they are supposed to be &lt;strong&gt;two separate species&lt;/strong&gt; (reproductive isolation). Nevertheless, creationist claim they are still fruit flies and there is no speciation. They say that's just a &lt;strong&gt;variation&lt;/strong&gt; in fruit flies, not speciation. I can't understand their claim. &lt;/p&gt;&#xA;" OwnerUserId="16984" LastEditorDisplayName="user13145" LastEditDate="2016-10-23T00:16:33.977" LastActivityDate="2016-10-23T00:16:33.977" Title="What is variation in Speciation" Tags="&lt;evolution&gt;&lt;speciation&gt;&lt;macroevolution&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36400" PostTypeId="2" ParentId="36399" CreationDate="2015-07-26T06:26:14.660" Score="2" Body="&lt;p&gt;You are asking explanations about a creationist argument. One could provide explanations about some hypothesis that you may found in a science paper but not explanations for a creationist argument just because, by definition, a creationist argument is not supported by any evidence and logical thoughts. However, you may want to link to a creationist website making a specific claim of interest and we may eventually talk about whether the claim is wrong/misleading. It would be very handy to have the claim in quotes rather than an explanation of what the claim is.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You say&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[..] after the evolution and speciation [..]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This piece of sentence sounds weird. You could say after the evolution of something (meaning the appearance of this something through evolutionary processes that are mutations, natural selection, drift and eventually others) but just &quot;after the evolution&quot; sounds as if evolution may not exist during some periods of time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Talking about speciation in fruit flies, you will likely be interested in reading &lt;a href=&quot;https://biology.stackexchange.com/questions/17799/have-we-ever-observed-two-drosophila-lineages-that-evolved-reproductive-isolatio&quot;&gt;this post&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPDATE&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, when talking about fruit flies we talk about the &lt;a href=&quot;https://en.wikipedia.org/wiki/Tephritidae&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tephriditae&lt;/a&gt;. Tephriditae is a family of flies which contain about 5000 described species (including the model organism &lt;em&gt;Drosophila melanogaster&lt;/em&gt;).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, there is definitely different species of fruit flies. Of course, within any population (to the exception of populations of exact clones by definition), you have variation. This variation is a key concept in evolutionary biology. If this is unclear to you you may want to learn a bit more about evolutionary biology, including the concept of heritability ($h_N=\frac{V_A}{V_P}$).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Speciation took place in Tephriditae (otherwise we wouldn't have the species we have today) and is still taking place. &lt;a href=&quot;https://biology.stackexchange.com/questions/17799/have-we-ever-observed-two-drosophila-lineages-that-evolved-reproductive-isolatio&quot;&gt;The post I linked above&lt;/a&gt; gives an example of speciation between lineages of &lt;em&gt;Drosophila melanogaster&lt;/em&gt; that has been directly observed in the labs.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Your issue seems to likely be a semantic one. As there is variation within a lineage and this variation is associated with groups that are in reproductive isolation, then the two lineages you consider do not belong to the same species anymore. Therefore, there was a speciation event.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-07-26T07:01:55.090" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="36401" PostTypeId="1" AcceptedAnswerId="36414" CreationDate="2015-07-26T06:43:03.513" Score="0" ViewCount="877" Body="&lt;p&gt;I was wondering whether plants could feel pain, for example, does grass feel pain when you mow the lawn? Or do the plants and trees that grow vegetables and fruits feel pain when you harvest them?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The internet is very vague about it. There are several articles on the internet, but they just say that plants do not feel pain, they only send out a chemical substance. Others say that almost all multicellular organisms feel pain, because pain is defined as any signal of having impaired tissue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think that plants can't feel pain because they have no nerves or central nervous system. However I'm not sure whether this means that plants can't feel pain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Since the question is clear when pain is defined as any signal of having impaired tissue, I think it would be more interesting in the case that pain is defined as actual discomfort, like humans and animals (maybe it should be restricted to &lt;em&gt;Eumetazoa&lt;/em&gt;) feel it. &lt;/p&gt;&#xA;" OwnerUserId="16985" LastEditorUserId="16985" LastEditDate="2015-07-26T20:02:12.053" LastActivityDate="2015-07-26T21:00:39.093" Title="Can plants feel pain?" Tags="&lt;neuroscience&gt;&lt;plant-physiology&gt;" AnswerCount="1" CommentCount="10" ClosedDate="2015-07-27T04:56:19.323" ContentLicense="CC BY-SA 3.0" />
  <row Id="36403" PostTypeId="1" CreationDate="2015-07-26T10:48:19.127" Score="3" ViewCount="122" Body="&lt;p&gt;It's known that when somebody is not relaxed (nervous,worried....) , they can't concentrate , what exactly in being nervous is the problem?&lt;/p&gt;&#xA;" OwnerUserId="16875" LastActivityDate="2017-12-27T18:30:33.023" Title="How does being afraid or nervous affect mental performance?" Tags="&lt;psychology&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36404" PostTypeId="1" AcceptedAnswerId="36415" CreationDate="2015-07-26T11:35:23.647" Score="3" ViewCount="122" Body="&lt;p&gt;It is well known that if DNA occurs in the cytoplasm of eukaryotic cells, an immune response may be triggered through a myriad of DNA receptors and pathways as part of the immuno response. Yet, apparently the nuclear DNA does not induce any type of such response. Is it known why this happens? Is it just due to the fact that the nuclear DNA is immuno-privileged?&lt;/p&gt;&#xA;" OwnerUserId="3657" LastEditorUserId="3657" LastEditDate="2015-07-26T12:20:33.890" LastActivityDate="2015-08-08T21:48:59.753" Title="Is nuclear DNA immuno-privileged?" Tags="&lt;molecular-biology&gt;&lt;dna&gt;&lt;immunity&gt;" AnswerCount="1" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="36405" PostTypeId="1" CreationDate="2015-07-26T11:58:44.417" Score="1" ViewCount="2391" Body="&lt;p&gt;When one tries to express a protein from a synthetic plasmid in E. coli, how many base pairs should there be between stop codon and the transcription terminator site?&lt;/p&gt;&#xA;" OwnerUserId="3317" LastActivityDate="2015-07-26T12:05:44.123" Title="What is the spacing between stop codon and transcription terminator?" Tags="&lt;transcription&gt;&lt;synthetic-biology&gt;&lt;ecoli&gt;&lt;translation&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36406" PostTypeId="2" ParentId="36405" CreationDate="2015-07-26T12:05:44.123" Score="1" Body="&lt;p&gt;In general, there is no need for a spacing between stop codon and terminator. They can be right next to each other.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When transcribed, transcription terminator forms a hairpin-like structure which interacts with the RNA polymerase to stop the transcription. Usually, the upstream sequence will not interact with the terminator and it will be transcribed normally. In a rare case the coding sequence might contain sequences that extend the hairpin and might result in interrupted translation. This can be avoided by doing a thermodynamical inspection of the secondary mRNA structure, but this is usually unnecessary.&lt;/p&gt;&#xA;" OwnerUserId="3317" LastActivityDate="2015-07-26T12:05:44.123" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36407" PostTypeId="1" CreationDate="2015-07-26T12:08:01.597" Score="12" ViewCount="657" Body="&lt;p&gt;&lt;a href=&quot;http://www.scientificamerican.com/article/strange-but-true-humans-carry-more-bacterial-cells-than-human-ones/&quot;&gt;This Scientific American article&lt;/a&gt; states that &quot;[human] infestation [by bacteria] begins at birth&quot;. This would suggest that unborn babies are free from any bacteria. However, if the mother catches a bacterial infection, her unborn baby risks catching it, too. This would seem to contradict the Scientific American article.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Presumably, when a human egg is fertilized by a sperm, the resulting cell may be free of any bacteria. At some point, bacteria begin to colonize the growing human body. Which bacteria are the earliest to colonize, and at what point in the development cycle does this occur?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In particular: does the health of the foetus depend on the presence of certain bacteria?&lt;/p&gt;&#xA;" OwnerUserId="16882" LastEditorUserId="3340" LastEditDate="2015-07-27T05:09:41.353" LastActivityDate="2015-07-27T05:09:41.353" Title="What bacteria do unborn babies contain?" Tags="&lt;human-biology&gt;&lt;bacteriology&gt;&lt;reproduction&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36409" PostTypeId="2" ParentId="36376" CreationDate="2015-07-26T12:20:36.333" Score="2" Body="&lt;p&gt;With all due respect to Dr. Wilson, this is just an anthropocentric, &lt;a href=&quot;https://en.wikipedia.org/wiki/Post_hoc_ergo_propter_hoc&quot; rel=&quot;nofollow&quot;&gt;post hoc ergo propter hoc&lt;/a&gt; logical fallacy. Dr. Wilson looked around the world we live in, saw that most intelligent creatures navigate by sight and/or sound and concluded that those sense are a prerequisite for intelligence. I see absolutely no evidence to support this theory. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all, that is a classic fallacy. It is the equivalent of a 17th century European going to Africa and concluding that having pinkish skin is a prerequisite for the development of technology. Or if I were to go to Japan and conclude that having an epicanthic fold is a prerequisite for making good sushi. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The fact that the paths chosen by the evolutionary process on this planet are skewed towards sight and sound for more intelligent species does not in any way imply that those senses are &lt;em&gt;needed&lt;/em&gt; for intelligence. What is needed are ways of detecting and reacting to the environment as quickly as possible. Light and sound are indeed particularly well suited for this since they travel several orders of magnitude faster than chemical diffusion. That's a good reason to conclude they might have given a selective advantage to the species relying on those two waves to detect their predators or prey. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are, however, other options. Radar (bats) and sonar (dolphins) can be thought of as sight (or hearing) but are quite different. They both involve the emission of a wave and analysis of what is reflected back. Sight involves the analysis of light emitted by the sun and reflected by the environment. Being able to use your own body to emit the energy needed for your perception would seem to be a huge advantage. Our wonderful sight only works half of the time. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You could also, conceivably, have very fast perception based on things like:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Quantum_entanglement&quot; rel=&quot;nofollow&quot;&gt;Quantum entanglement&lt;/a&gt;; actually faster than light. &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Magnetoception&quot; rel=&quot;nofollow&quot;&gt;Magnetoception&lt;/a&gt;; &lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Electroreception&quot; rel=&quot;nofollow&quot;&gt;Electrolocation&lt;/a&gt;;&lt;/li&gt;&#xA;&lt;li&gt;Gravity;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Some of the above already exist in species on this planet, others do not. Admittedly, using quantum entanglement would be kind of tricky. On the other hand, I see no reason why tiny disturbances in the gravitic field could not be detected just as tiny disturbances in the electromagnetic fields are by animals like sharks and cockroaches. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The main point of all this is that the fact that intelligent animals on this planet tend to do X does not in any way imply that X is a prerequisite for intelligence. Quite frankly, I expected better of someone like Dr. Wilson than such baseless speculation presented as fact.&lt;/p&gt;&#xA;" OwnerUserId="1306" LastActivityDate="2015-07-26T12:20:36.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36411" PostTypeId="1" AcceptedAnswerId="36437" CreationDate="2015-07-26T16:07:54.973" Score="2" ViewCount="105" Body="&lt;p&gt;It seem one can distinguish three different kinds of genetic determinism of common patterns of human behavior:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;behavior that is directly wired into our nervous system, e.g. face-related mirror neurons and chewing,&lt;/li&gt;&#xA;&lt;li&gt;behavior that is within reach of operand conditioning, i.e. that is predisposed by certain features of our bodies (and environment) and relatively easily discoverable by exploration, e.g. how to throw something,&lt;/li&gt;&#xA;&lt;li&gt;behavior that is passed on culturally, e.g. tool use.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Does there exist something like this in the literature?&lt;/p&gt;&#xA;" OwnerUserId="16914" LastEditorUserId="16914" LastEditDate="2015-07-26T22:07:16.523" LastActivityDate="2015-07-30T21:58:45.587" Title="Is there a schema for how human behavior is genetically determined?" Tags="&lt;human-biology&gt;&lt;evolution&gt;&lt;behaviour&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36412" PostTypeId="1" CreationDate="2015-07-26T18:19:38.273" Score="3" ViewCount="962" Body="&lt;p&gt;In computer science, 'convolutional neural networks' are used, that are meant to be inspired by biological network structures like found in the human brain visual cortex. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the computer implementation, the 'convolution' means that any neuron of a certain 'layer' is linked with several spatial adjacent neurons in the previous layer. When those networks are trained, the 'weights', which are analog to synaptic strength, of all neurons of one layer have an equivalent local topology, and thus can be mapped between the neurons, and finally unified. This way, only one 'weight' is trained for all equivalent synapses on all neurons of an layer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is there any biological mechanism found that may sport this feature? My guess would be that the vision cortex is partly organised by self structuring not depending on neural activation to achieve low level vision processing. Otherwise, all neurons in one 'layer' would need a way to exchange information to synchronize their synaptic structure. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I guess that the human brain would have some mechanism of this kind, as it would provide for example the ability to learn the detection of certain visual patterns or events independent of their retinal position, without learning the detection individually for every image location. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is any such mechanism known or how could it work?&lt;/p&gt;&#xA;" OwnerUserId="16989" LastActivityDate="2016-03-09T05:51:27.267" Title="Biological implementation of convolutional neural networks" Tags="&lt;neuroscience&gt;&lt;brain&gt;&lt;visual-system&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36413" PostTypeId="2" ParentId="36407" CreationDate="2015-07-26T18:41:22.847" Score="6" Body="&lt;p&gt;Babies are bacteria-free at birth. The meconium (the first stool) contains no bacteria if secured early enough.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Meconium is a sterile mucilaginous material that accumulates in the fetal intestine and is expelled soon after birth. It contains secretions of intestinal glands, gut constituents (proteins, bile acids, fatty acids, and steroids), and components of amniotic fluid and vernix caseosa.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Bacterial colonization of infants begins at birth - literally. They pick up bacteria from the mother's vaginal canal in passing, which they swallow. This is not seen in infants delivered by C-section. The importance of colonization picked up through normal birth is such, that some hospitals are swabbing the vagina of mothers delivering by CS and colonizing the oropharynx that way.  Breast-milk also contains lactobacilli and bifidobacteria that probably contribute to the initial establishment of the gut flora of newborns.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And, yes, an infection the mother has while delivering must be taken into account. Herpes and Group B strep are both dangerous for a neonate.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first microbes to colonize the intestines of newborn babies are the aerobic bacteria Escherichia coli and Streptococci. Later, the gut is colonized with anaerobic bacteria, e.g. Bacteroides, Bifidobacteria, and Clostridia. In 1–2 y, the gastrointestinal tract of infants has developed a natural microflora, which resembles the microflora of adults.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The infant continues to pick up bacteria from all people they come into regular contact with, including nurses.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The effect of the maternal flora on the initial gut colonization may be less than expected as the fecal flora of infants started to resemble both the fecal flora of the mother as well as that of the first nurse.&#xA;  Breast milk may contain bacteria which colonizes the gut as well&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Infants aren't overwhelmed by infection due to the presence of  antimicrobial peptides found on their skin, GI tract, and immunity is conferred via breast milk.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Several AMP have been characterized in vernix and skin of the newborn, indicating a well-developed innate immune system, which may play a pivotal role at the time of postnatal colonization.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;a href=&quot;http://www.nature.com/pr/journal/v61/n5-1/full/pr2007106a.html&quot; rel=&quot;nofollow&quot;&gt;Antimicrobial Components of the Neonatal Gut Affected Upon Colonization&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0463.2006.apm_488.x/abstract?userIsAuthenticated=false&amp;amp;deniedAccessCustomisedMessage=&quot; rel=&quot;nofollow&quot;&gt;Dynamics of gut colonization and source of intestinal flora in healthy newborn infants&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.nature.com/pr/journal/v61/n1/abs/pr20073a.html&quot; rel=&quot;nofollow&quot;&gt;Protection of the Neonate by the Innate Immune System of Developing Gut and of Human Milk&lt;/a&gt;&lt;/sub&gt;&lt;br&gt;&#xA;&lt;sub&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1075996410000235&quot; rel=&quot;nofollow&quot;&gt;Establishment and development of lactic acid bacteria and bifidobacteria microbiota in breast-milk and the infant gut&lt;/a&gt;&lt;/sub&gt;  &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="1306" LastEditDate="2015-07-26T20:21:53.097" LastActivityDate="2015-07-26T20:21:53.097" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="36414" PostTypeId="2" ParentId="36401" CreationDate="2015-07-26T21:00:39.093" Score="3" Body="&lt;p&gt;I think before discussing &quot;pain&quot;, we'd probably have to discuss whether plants actually can &quot;feel&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is also down to how one wants to define this (hence &quot;opinion based&quot;), but I assume most people (?) would equal the lack of a brain/neurons with the lack of the capability to feel. And I presume so do you, as you show by using the tag &quot;neuroscience&quot;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In which case the answer to your question &quot;Can plants feel pain?&quot; is &quot;no&quot;, regardless of whether plants react to damage through the release of chemicals or not, and whether one would like to classify this as &quot;pain&quot; or not. &lt;/p&gt;&#xA;" OwnerUserId="14970" LastActivityDate="2015-07-26T21:00:39.093" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36415" PostTypeId="2" ParentId="36404" CreationDate="2015-07-27T01:42:54.960" Score="4" Body="&lt;p&gt;Pattern recognition receptors (PRRs) can potentially discriminate between endogenous and exogenous DNA:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Microbial nucleic acids can be discriminated from self nucleic acids using various parameters, such as their sequence, their tertiary structure, their molecular modifications and their localization. In addition, mislocalized DNA and RNA can be an indicator of cellular damage and infection. [&lt;a href=&quot;http://www.nature.com/nri/journal/v13/n8/abs/nri3479.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt;]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Microbial nucleic acids are discriminated from self nucleic acids based on different parameters, such as their sequence, structure, molecular modifications and localization. On the other hand, mislocalized self nucleic acids — such as extranuclear DNA or extracellular RNA — can be recognized as DAMPs, probably because they are reliable indicators of cellular damage. [&lt;a href=&quot;http://www.nature.com/nri/journal/v12/n7/full/nri3247.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;2&lt;/a&gt;]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Somewhat suspect is the similarity of those quotes; I only link to both reviews so as to include both in the references for further reading. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Distinguishing by sequence and structure are self-explanatory. Molecular modifications could include unmethylated CpG sites which are more common in bacterial and viral genomes and are recognized by TLR9. [&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/rmv.633/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;3&lt;/a&gt;] Mislocalized DNA means any that is found outside the nucleus, which is a sign of damage or infection. Most of the well-studied nucleic-acid-recognizing PRRs are found outside the nucleus: TLRs are constrained to endosomes and the extracellular environment while RLRs are found in the cytoplasm. The as of yet identified DNA sensors like DAI also seem to localize to the cytoplasm. Extranuclear PRRs do not necessarily need to discriminate between endogenous and exogenous DNA: any that they sense is mislocalized. However, at least one dsDNA-recognizing PRR, IFI16, localizes to the nucleus as well as the cytoplasm, where it can recognize viral dsDNA. [&lt;a href=&quot;http://www.cell.com/cell-host-microbe/abstract/S1931-3128(11)00130-2?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1931312811001302%3Fshowall%3Dtrue&quot; rel=&quot;nofollow noreferrer&quot;&gt;4&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;It has been assumed that cells distinguish viral from cellular DNA due to the former's presence in the cytosol. However, … Kerur et al. (2011) propose that the DNA genome of Kaposi's sarcoma-associated herpesvirus (KSHV) is recognized inside the nucleus by the DNA sensor IFI16, leading [to] inflammasome activation. [&lt;a href=&quot;http://www.cell.com/cell-host-microbe/abstract/S1931-3128(11)00136-3?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1931312811001363%3Fshowall%3Dtrue&quot; rel=&quot;nofollow noreferrer&quot;&gt;5&lt;/a&gt;]&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;IFI16 apparently distinguishes exogenous from endogenous DNA by its length. [&lt;a href=&quot;http://m.pnas.org/content/111/1/E62.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;6&lt;/a&gt;] &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/R5y12.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Endogenous DNA is present &lt;em&gt;in vivo&lt;/em&gt; as chromatin and the amount of exposed linker DNA between histones is too short to promote the cooperative binding and oligomerization that IFI16 requires for signalling (B). An older model, where IFI16 binds independently, is also shown (A), but it suggests that IFI16 should bind self-DNA and doesn't fit with experimental results. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;That is just one specific example of how a PRR can distinguish self from non-self. DNA sensors actually seem to be on the cutting edge of research into the innate immune system and, as such, the complete picture has yet to be determined.  &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References:&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nri/journal/v12/n7/full/nri3247.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;Broz P, Monack DM. 2013. Newly described pattern recognition receptors team up against intracellular pathogens. Nat Rev Immunol 13(8):551-565.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/rmv.633/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Desmet CJ, Ishii KJ. 2012. Nucleic acid sensing at the interface between innate and adaptive immunity in vaccination. Nat Rev Immunol 12(7):479-491.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cell.com/cell-host-microbe/abstract/S1931-3128(11)00130-2?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1931312811001302%3Fshowall%3Dtrue&quot; rel=&quot;nofollow noreferrer&quot;&gt;Yoneyama M, Fujita T. 2010. Recognition of viral nucleic acids in innate immunity. Rev Med Virol 20(1):4-22.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.cell.com/cell-host-microbe/abstract/S1931-3128(11)00136-3?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1931312811001363%3Fshowall%3Dtrue&quot; rel=&quot;nofollow noreferrer&quot;&gt;Kerur N, Veettil MV, Sharma-Walia N, Bottero V, Sadagopan S, Otageri P, Chandran B. 2011. IFI16 Acts as a Nuclear Pathogen Sensor to Induce the Inflammasome in Response to Kaposi Sarcoma-Associated Herpesvirus Infection. Cell Host Microbe 9(5):363-375.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://m.pnas.org/content/111/1/E62.short&quot; rel=&quot;nofollow noreferrer&quot;&gt;Unterholzner L, Bowie AG. 2011. Innate DNA Sensing Moves to the Nucleus (comment on Kerur et al., 2011). Cell Host Microbe 9(5):351-353.&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://i.stack.imgur.com/R5y12.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;Morrone SR, Wang T, Constantoulakis LM, Hooy RM, Delannoy MJ, Sohn J. 2014. Cooperative assembly of IFI16 filaments on dsDNA provides insights into host defense strategy. PNAS 111(1):62-67. &lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-08-08T21:48:59.753" LastActivityDate="2015-08-08T21:48:59.753" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36417" PostTypeId="1" AcceptedAnswerId="36428" CreationDate="2015-07-27T03:19:16.167" Score="4" ViewCount="8298" Body="&lt;p&gt;Why are nitrogenous bases of DNA hydrophobic if they can hydrogen bond?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it that they are only relatively hydrophobic?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.physicsforums.com/threads/2-questions.222122/&quot; rel=&quot;nofollow&quot;&gt;This forum&lt;/a&gt; explains it but does not give an example of the structure.&lt;/p&gt;&#xA;" OwnerUserId="16992" LastEditorUserId="3340" LastEditDate="2015-07-28T05:18:28.787" LastActivityDate="2021-05-06T02:38:39.427" Title="Why are nitrogenous bases of DNA hydrophobic if they can hydrogen bond?" Tags="&lt;genetics&gt;&lt;biochemistry&gt;&lt;dna&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="36419" PostTypeId="1" AcceptedAnswerId="36420" CreationDate="2015-07-27T04:08:33.690" Score="8" ViewCount="685" Body="&lt;p&gt;It's a green lizard with a silver tail, and it has pretty, bluish eyes. I saw it today, July 26th, trying to get some shade on a hot, sunny day (32 degrees) at around 18:00 in Austin, TX USA. It's been hot and dry here the past few weeks, but it rained a lot a few months back.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Austin has a humid subtropical climate. The city is characterized by hot summers and mild winter days and usually cool to cold winter nights. The geo coordinates are 30.4 (lat), -97.7 (long).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oh, it was able to jump a good meter.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/VvhJa.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/VvhJa.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="16993" LastEditorUserId="6307" LastEditDate="2015-07-27T05:34:53.027" LastActivityDate="2017-07-25T01:43:00.070" Title="Can someone tell me the species of this lizard?" Tags="&lt;species&gt;&lt;species-identification&gt;&lt;classification&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36420" PostTypeId="2" ParentId="36419" CreationDate="2015-07-27T05:48:23.617" Score="8" Body="&lt;p&gt;I know nothing about lizards, but this looks like a &lt;a href=&quot;https://en.m.wikipedia.org/wiki/Green_anole&quot; rel=&quot;noreferrer&quot;&gt;Carolina anole (&lt;em&gt;Anolis carolinensis&lt;/em&gt;), also known as a green anole&lt;/a&gt;. Apparently they can change colour:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/OqQHE.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-07-27T05:48:23.617" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36423" PostTypeId="2" ParentId="36336" CreationDate="2015-07-27T11:16:05.190" Score="2" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;As far as I am aware, neurotoxic effects of chronic excitatory stimulation are &lt;em&gt;not&lt;/em&gt; prevented by receptor trafficking. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;I think the question assumes that 1) neural damage related to continuous activation (&lt;em&gt;excitotoxicity&lt;/em&gt;) is preventable by 2) the dynamic regulation of receptor numbers on the neuronal membrane. As far as I can see, these two processes are unrelated. &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;strong&gt;&lt;em&gt;Excitotoxicity&lt;/em&gt;&lt;/strong&gt; is &#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;...the ability of glutamate or related excitatory amino acids to mediate the death of central neurons [...] for example, after intense exposure. [...] Excitotoxicity has substantial cellular specificity and, in most cases, is mediated by glutamate receptors. On average, NMDA receptors activation may be able to trigger lethal injury more rapidly than AMPA or kainate receptor activation, perhaps reflecting a greater ability to induce calcium influx and subsequent cellular calcium overload &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1361523&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Choi, 1992)&lt;/a&gt;.      &lt;br&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;Hence, it is the influx of toxic amounts of Ca&lt;sup&gt;2+&lt;/sup&gt; that induce cell death. Not much Ca&lt;sup&gt;2+&lt;/sup&gt; is needed to accomplish this. For example, a &lt;em&gt;status epilepticus&lt;/em&gt; (a sustained epileptic seizure) can lead to hippocampal damage, due to persistent excitation and glutamate release &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1790773&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Meldrum, 1991)&lt;/a&gt;. Epileptic seizures lasting longer than 5 minutes are regarded as dangerous in this sense and after 30 minutes they are potentially fatal (often not directly related to excitotoxicity though) &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824929/&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Cherian &amp;amp; Thomas, 2009)&lt;/a&gt;. &lt;strong&gt;In this short time span regulation of cell-surface receptor densities are unlikely to play a substantial role&lt;/strong&gt;. For example, serotonin-specific reuptake inhibitors need 2 weeks to lower the amount of 5HT1A receptors &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1865459/&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Tylee &amp;amp; Wolters, 2009)&lt;/a&gt;.         &lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;&lt;strong&gt;Dynamic regulation of receptors&lt;/strong&gt;. The regulation of the number of receptors is linked via feedback loops. A great example is the way glutamatergic AMPA receptors are regulated through endocytosis (Fig. 1).&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/Z5j41.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. AMPA receptor trafficking. Source: &lt;a href=&quot;http://qbi.uq.edu.au/dr-victor-anggono-synaptic-neurobiology&quot; rel=&quot;nofollow noreferrer&quot;&gt;Anggono Lab&lt;/a&gt;.&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;AMPA receptors are the principal receptors that mediate most of the fast excitatory synaptic transmission in the mammalian brain &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10802/&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Purves &lt;em&gt;et al&lt;/em&gt;., 2001)&lt;/a&gt;. The dynamic trafficking and proper synaptic targeting of AMPA receptors are crucial in determining the &lt;strong&gt;strength and plasticity of excitatory synaptic transmission&lt;/strong&gt;. This dynamic regulation may also impact learning and memory processes. The process of receptor trafficking is, as far as I know, typically &lt;em&gt;not&lt;/em&gt; associated with emergency rescue operations to prevent excitotoxicity. Nonetheless, &lt;strong&gt;&lt;em&gt;these mechanisms, are essential to sustain an adaptable brain capable of learning, forgetting and restructuring itself&lt;/em&gt;&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sub&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824929/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Cherian &amp;amp; Thomas, &lt;em&gt;Ann Indian Acad Neurol&lt;/em&gt; (2009); &lt;strong&gt;12&lt;/strong&gt;(3): 140–53&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1361523&quot; rel=&quot;nofollow noreferrer&quot;&gt;Choi, &lt;em&gt;J Neurobiol&lt;/em&gt; (1992); &lt;strong&gt;23&lt;/strong&gt;(9):1261-76&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/1790773&quot; rel=&quot;nofollow noreferrer&quot;&gt;Meldrum, &lt;em&gt;Epilepsy Res&lt;/em&gt; (1991); &lt;strong&gt;10&lt;/strong&gt;(1): 55-61&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/books/NBK10802/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Purves &lt;em&gt;et al&lt;/em&gt;., Neuroscience. 2&lt;sup&gt;nd&lt;/sup&gt; ed. Sunderland (MA): Sinauer Associates; 2001&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1865459/&quot; rel=&quot;nofollow noreferrer&quot;&gt;Tyllee &amp;amp; Wolters, &lt;em&gt;BMJ&lt;/em&gt; (2007); &lt;strong&gt;334&lt;/strong&gt;(7600): 911–2&lt;/a&gt;&lt;/sub&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2018-12-19T08:19:05.687" LastActivityDate="2018-12-19T08:19:05.687" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="36426" PostTypeId="1" CreationDate="2015-07-27T12:40:44.083" Score="5" ViewCount="388" Body="&lt;p&gt;During healing of wound (almost in final stage) it begins to itch a lot around wound. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I wondering what the reason for this is? &lt;/p&gt;&#xA;" OwnerUserId="17002" LastEditorUserId="5144" LastEditDate="2015-07-27T13:01:15.083" LastActivityDate="2015-08-27T10:01:02.580" Title="Why does a wound itch while it's healing?" Tags="&lt;healing&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36427" PostTypeId="1" AcceptedAnswerId="36745" CreationDate="2015-07-27T12:59:06.997" Score="2" ViewCount="100" Body="&lt;p&gt;The Drosophila Histone Cluster is a gene cluster that contains more than a hundred copies of a sequence that encodes several histone proteins. These copies are very similar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is what mechanism are known that could have played a role in the genesis of this cluster?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm aware of the possibility of recombination, which might expand the cluster on one chromosome, shortening it on the other. Are there any other mechanisms to expand or change the cluster and are there telltale signs left by these mechanisms in the genome sequence?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given that in most species histone genes aren't clustered, it would be weird to assume that recombination is the only mechanism to duplicate these sequences. Also, at one end of the cluster bits and pieces of histone genes are mixed with other sequences, a bit like all the broken copies got pushed to one end. It would be interesting to have an explanation for this pattern.&lt;/p&gt;&#xA;" OwnerUserId="17001" LastEditorUserId="17001" LastEditDate="2015-08-03T10:50:49.867" LastActivityDate="2015-08-11T01:37:37.950" Title="Through which mechanisms did the Drosophila Histone Cluster evolve?" Tags="&lt;sequence-analysis&gt;&lt;drosophila&gt;&lt;histone&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36428" PostTypeId="2" ParentId="36417" CreationDate="2015-07-27T15:56:26.270" Score="5" Body="&lt;p&gt;These two concepts are not mutually exclusive. You have constructed a false dichotomy.  Both of these facts are true:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The electrons in the pi orbitals of the conjugated double bonds in the planar rings are hydrophobic and can &quot;stack&quot; on each other as shown in this drawing of a DNA helix where the bases are shown as planar rectangles:&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/aVqyr.jpg&quot; alt=&quot;A model of a kinked DNA helix&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;2&quot;&gt;&#xA;&lt;li&gt;The nitrogen and oxygen molecules (either in the rings, or as substituents on the rings) can participate in hydrogen bonds (H-bonds):&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/9AiHy.jpg&quot; alt=&quot;H-bonds in Watson Crick base pairs&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There are other examples of hydrophobicity and H-bonds co-existing.  For example on the interior of proteins.&lt;/p&gt;&#xA;" OwnerUserId="16667" LastEditorUserId="16667" LastEditDate="2015-08-07T22:44:58.227" LastActivityDate="2015-08-07T22:44:58.227" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="36429" PostTypeId="1" AcceptedAnswerId="36431" CreationDate="2015-07-27T16:36:15.963" Score="0" ViewCount="326" Body="&lt;p&gt;The title says it all. I'm just curious. I read that scientists mapped the genome for Malus Domestica, but I can't find a sequence anywhere.If this is a stupid question, I would appreciate if you tell me where I'm wrong in this!&lt;/p&gt;&#xA;" OwnerUserId="17005" LastActivityDate="2015-07-27T20:56:15.547" Title="What is the DNA Sequence for an apple?" Tags="&lt;dna&gt;&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36430" PostTypeId="1" AcceptedAnswerId="36447" CreationDate="2015-07-27T16:45:59.420" Score="15" ViewCount="483" Body="&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/dQCYJ.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/dQCYJ.jpg&quot; alt=&quot;Here is the creature&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the creature I found on the glass lid of my light bulb. I guess they are attracted to light as they all concentrate on the light source. I live in Hong Kong. The brown things aren't moving (those might be eggs). The green creatures are about 0.6-0.7 cm long in body length (excluding appendages and antennae). They are sluggish in movement.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Can you help me to identify these tiny creatures?&lt;/p&gt;&#xA;" OwnerUserId="17004" LastEditorUserId="17004" LastEditDate="2015-07-28T03:01:03.500" LastActivityDate="2015-07-29T04:51:29.040" Title="Identify ~6-7mm long green creature" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36431" PostTypeId="2" ParentId="36429" CreationDate="2015-07-27T16:58:46.147" Score="3" Body="&lt;p&gt;&lt;a href=&quot;https://www.rosaceae.org/species/malus/malus_x_domestica/genome_v1.0&quot; rel=&quot;nofollow&quot;&gt;https://www.rosaceae.org/species/malus/malus_x_domestica/genome_v1.0&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can see the data in the URL above. The details are described in &lt;a href=&quot;http://www.nature.com/ng/journal/v42/n10/full/ng.654.html&quot; rel=&quot;nofollow&quot;&gt;this article&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;As others said, NCBI seems useful.&#xA;Go to &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/assembly/GCA_000148765.1&quot; rel=&quot;nofollow&quot;&gt;this site&lt;/a&gt;.&#xA;Chose chromosome you want to see and click genebank or refsequence corresponding to the chromosome in the table (Assembly Unit: Primary Assembly). &#xA;You can see overview of the sequence.&#xA;Find FASTA in the page showing the overview and click FASTA. Then the sequence data will be downloaded.&lt;/p&gt;&#xA;" OwnerUserId="15878" LastEditorUserId="15878" LastEditDate="2015-07-27T20:56:15.547" LastActivityDate="2015-07-27T20:56:15.547" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36433" PostTypeId="2" ParentId="36396" CreationDate="2015-07-27T20:21:58.230" Score="10" Body="&lt;p&gt;Firstly, note that &quot;eye color&quot; is actually &lt;em&gt;iris&lt;/em&gt; color.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The person with a lighter iris will have more straylight compared to person with brown iris:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/sWhfd.png&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/sWhfd.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The graph represents Intraocular straylight of the age-matched groups. Participants with light-blue-colored iris showed significantly higher values for intraocular straylight than those of the other groups.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Persons with light-blue-colored eyes have significant higher IOSL&#xA;  (intraocular straylight)&#xA;  values than persons with darker-colored irises (blue-grey,&#xA;  green-hazel, and brown). Light-blue-colored eyes had 0.07 to 0.08 log&#xA;  units higher IOSL values, which is an increase by a factor of 1.2. In&#xA;  regard to CS (contrast sensitivity), subjects with light-blue iris color showed also lower CS&#xA;  values than subjects with other iris color.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Edit: The study concluded that in people with blue irises, IOSL was significantly higher. Although IOSL did not affect best-corrected visual acuity (e.g. visual function based on a standard letter chart test at the optometrist), it did affect &lt;em&gt;contrast acuity&lt;/em&gt;, meaning that folks with blue eyes had more difficulty assessing contrast differences (e.g., telling apart two grays with a slightly different brightness). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/22527312&quot; rel=&quot;noreferrer&quot;&gt;Christian Nischler &amp;amp; al. Iris color and visual functions. Graefes Arch Clin Exp Ophthalmol (2013) 251:195–202.&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="9943" LastEditDate="2015-07-28T00:39:03.340" LastActivityDate="2015-07-28T00:39:03.340" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36435" PostTypeId="2" ParentId="36429" CreationDate="2015-07-27T20:39:01.783" Score="1" Body="&lt;p&gt;Here is the apple genome on NCBI. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/genome/?term=Apple&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/genome/?term=Apple&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-07-27T20:39:01.783" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36437" PostTypeId="2" ParentId="36411" CreationDate="2015-07-28T04:33:04.357" Score="1" Body="&lt;p&gt;&lt;strong&gt;We can only observe correlations&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's just talk about statistics. You can see a correlation between two things only if there is variation for these two things. It therefore, make no sense to look at a single trait that has no variance and ask &quot;is it genetically coded?&quot;. The only thing that makes sense is to understand what variables explain the observed variance for the trait of interest. Here, in your question, you are interested in behavioural traits. This answer stands for behavioural traits as it stands for any other phenotypic traits.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;What variables could explain variance in a given trait?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To make it easy, let's consider only two variables, genetics and environment. In reality, one should consider other variables such as epigenetic for example. The total variance in phenotype that you observe is the result of the addition of the variance of this phenotype that is due to genetics variance ($V_G$) and the variance of this phenotype that is due to environmental variance ($V_E$) and their covariance ($COV_{GE}$). In other words:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$V_P≈V_E+V_G+COV_{GE}$$ &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It is very common to express the phenotypic variance as being the sum of the genetic and environmental variances (and some others such as epigenetic variance). However, you are free to make this partitioning as you feel it useful for you.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Let's investigate those variables a bit further&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, $V_E$ and $V_G$ can be further decoupled into a sum of variances (and covariances). And you are free to do the decoupling exactly as you want to. For example $V_E$ could be defined as the sum of the phenotypic variance that is due to variance in temperature ($V_T$), the phenotypic variance that is due to variance in water availability ($V_W$) and the phenotypic variance that is due to variance in the culture of the parents ($V_P$) (and all the covariance). $V_E = V_T + V_W + V_P + ... $&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Similarly, the genetic variance $V_G$ can be further decoupled. It is standard to decouple this variance in dominance vs additive effects (relating to the genetic architecture underlying the trait) but this won't be of great help to you. How about talking about variance in the genes affecting brain morphology $V_B$ and variance in the genes affecting hormones concentration $V_H$ and their covariance (epistasis and pleiotropy) $V_G = V_B + V_H + ...$.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Common schema&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To my knowledge there is no common schema in how to partition those variances for the specific study of the mechanistic of behaviour. I don't really understand what is the partitioning that you're suggesting in your post but I am hoping that this answer can help you to think further and eventually come up with a satisfying schema.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-07-30T21:58:45.587" LastActivityDate="2015-07-30T21:58:45.587" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36440" PostTypeId="2" ParentId="36395" CreationDate="2015-07-28T07:42:20.850" Score="1" Body="&lt;p&gt;It would depend on the stain - and more specifically the material and staining agent. Saliva contains blood clotting agents so I doubt it would help with removing blood stains. The enzymes in saliva are unlikely to help with the stain removal. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The water in saliva would be more likely to help, dissolving the stain. So your probably better off with water.&lt;/p&gt;&#xA;" OwnerUserId="476" LastActivityDate="2015-07-28T07:42:20.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36441" PostTypeId="1" AcceptedAnswerId="36446" CreationDate="2015-07-28T09:39:51.920" Score="0" ViewCount="492" Body="&lt;p&gt;This is a question regarding the anatomy of the human eye, however for my purposes medium sized mammals should do. I am interested in estimating the surface area of the hyaloid membrane of the vitreous humour which has contact with the aqueous humour circulating in the posterior and anterior chamber of a typical human eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The surface area in question is highlighted in red in this schematic of the cross section of the human eye.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/u9uGr.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/u9uGr.png&quot; alt=&quot;Anatomical schematic of the human eye.&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="9834" LastActivityDate="2015-07-28T20:02:45.707" Title="What is the surface area of the vitreous humour in contact with aqueous humour?" Tags="&lt;human-anatomy&gt;&lt;eyes&gt;&lt;human-eye&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36442" PostTypeId="2" ParentId="36426" CreationDate="2015-07-28T09:45:17.160" Score="2" Body="&lt;p&gt;While healing your wound the cells in and around it are enhancing their communication via messenger substances to quicken and coordinate the healing process. These messengers irritate the sore nerves which we feel as itching.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Skin tension is another factor to itching.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Scratching is bad for the healing process in any way.&lt;/p&gt;&#xA;" OwnerUserId="15257" LastActivityDate="2015-07-28T09:45:17.160" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36443" PostTypeId="1" CreationDate="2015-07-28T13:34:54.117" Score="6" ViewCount="17131" Body="&lt;p&gt;Below are graphs which illustrate the cross-sectional area, velocity, and fluid pressure through each vascular segment of the cardiovascular system.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/aGCSS.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/aGCSS.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It makes sense that velocity and cross-sectional area should be inversely related graphically (by the equation of continuity, (&lt;span class=&quot;math-container&quot;&gt;$v_1A_1=v_2A_2$&lt;/span&gt;). However, Bernoulli’s principle states that where velocity is high, pressure is low, and vice versa. However, in the graph above, clearly pressure is decreasing as you move away from the aorta, regardless of velocity.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I can understand how the pressure in capillaries will be higher than those in venules, since a higher pressure in capillaries would accelerate the blood as it moves into the venules with a lesser total cross-sectional area. This agrees graphically, since, past the purple stripe, the pressure curve decreases as the velocity curve rises. Yet the mean arterial pressure in the aorta and arteries seems to violate the relationship between velocity and pressure stated in Bernoulli’s principle. What is there to make of this?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Image taken from Campbell Biology, 10th edition)&lt;/p&gt;&#xA;" OwnerUserId="15272" LastEditorUserId="48636" LastEditDate="2019-01-28T12:53:20.017" LastActivityDate="2019-01-28T12:53:20.017" Title="How does Bernoulli’s Principle apply to the cardiovascular system?" Tags="&lt;human-biology&gt;&lt;physiology&gt;&lt;cardiology&gt;&lt;hematology&gt;&lt;biophysics&gt;" AnswerCount="2" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 4.0" />
  <row Id="36445" PostTypeId="1" CreationDate="2015-07-28T14:31:35.267" Score="1" ViewCount="44" Body="&lt;p&gt;I have assessed the specificity of a particular monoclonal antibody against a virus by immunofluorescence. I'd like to further validate it by testing it by IHC. Therefore I'd like to infect cells in culture, and then inject them in a piece of fresh organ, fix in formalin, embed in paraffin and then cut slides before performing IHC. Is there any protocol or references to do so ?&lt;/p&gt;&#xA;" OwnerUserId="17016" LastActivityDate="2015-10-26T21:59:27.593" Title="How to validate the use of an anti-virus monoclonal antibody in IHC by spiking a fresh organ with infected cultured cells?" Tags="&lt;virus&gt;&lt;cell-culture&gt;&lt;antibody&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36446" PostTypeId="2" ParentId="36441" CreationDate="2015-07-28T14:33:00.813" Score="1" Body="&lt;p&gt;Area=πr², d≈2cm (less than maximal d) -&gt; r≈1cm,  thus the area in question is roughly &lt;/p&gt;&#xA;&#xA;&lt;p&gt;3.14*1cm*1cm≈3.14cm²&lt;/p&gt;&#xA;&#xA;&lt;p&gt;UPD by request (ref):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The vitreous body base middle is at ora serrata (+-2mm), so we should calculate the area at this level. Here is the reference of the diameter:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/wSTrE.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/wSTrE.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;from: Basic and Clinical Science Course, Section 02&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="5755" LastEditDate="2015-07-28T20:02:45.707" LastActivityDate="2015-07-28T20:02:45.707" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36447" PostTypeId="2" ParentId="36430" CreationDate="2015-07-28T15:25:48.590" Score="9" Body="&lt;p&gt;Let's take a look at the magnified body of the insect (it is a nymphe btw) - we can see 2 brown dots one above the other along the body line. This pattern is very suggestive to Chelinidea species (the most common is &lt;strong&gt;&lt;em&gt;Chelinidea vittiger aequoris&lt;/em&gt;&lt;/strong&gt;):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/4XXVG.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/4XXVG.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I stop my search at &lt;strong&gt;Coreidae&lt;/strong&gt; family, because multiple species (a lot of bugs actually) of this family have similar appearance, for example:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;Gonocerus acuteangulatus&lt;/em&gt;&lt;/strong&gt;:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/5znG0.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/5znG0.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But other enthusiasts can start from here (Coreidae family) and trace it down more precisely - I am sure they will succeed. &lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="3340" LastEditDate="2015-07-29T04:51:29.040" LastActivityDate="2015-07-29T04:51:29.040" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36448" PostTypeId="1" CreationDate="2015-07-28T15:47:52.957" Score="5" ViewCount="2529" Body="&lt;p&gt;In all histology books, it is stated that all sensory nerve endings (receptors) consist of dendrites that translate physical stimuli from the environment into neural signals. However, several sensory neurons seem to include axons, such as the merkel and olfactory cells shown below. They act as receptors, but feature axons as well. So is it the pictures, or the texts that are incorrect? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/5brsj.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/5brsj.jpg&quot; alt=&quot;merkel cell innervation&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/qFSGZ.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/qFSGZ.jpg&quot; alt=&quot;olfactory cells&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="5700" LastEditorUserId="9943" LastEditDate="2015-07-31T13:48:52.613" LastActivityDate="2015-11-28T16:18:35.577" Title="Can axons act as receptors?" Tags="&lt;neuroscience&gt;&lt;neurophysiology&gt;&lt;histology&gt;" AnswerCount="2" CommentCount="8" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36449" PostTypeId="2" ParentId="36448" CreationDate="2015-07-28T19:04:22.580" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;In all histology books, it is stated that all sensory nerve endings&#xA;  (receptors) are made of dendrites which conduct sensation from&#xA;  environment to body but it doesn't seem to be true.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The phrase &quot;nerve endings&quot; (or &quot;free nerve endings&quot;. See &lt;a href=&quot;https://en.wikipedia.org/wiki/Free_nerve_ending&quot; rel=&quot;nofollow&quot;&gt;Wiki page&lt;/a&gt;) is typically associated with fine hairlike structures throughout the skin and organs that act as (one type of) touch, pain, or heat sensors. These are, yes, extensions of the dendrites of sensory neurons whose cell bodies live in the dorsal root ganglia of the spinal cord and who send the signal on via axons, either locally within the spinal cord or to brain structures.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But this is not the same as saying that all sensory structures of any sense modality are dendrites or extensions of them. Each sense has specialized cells to detect that sensory stimulus. The eye has photoreceptors (rods and cones), the ear has inner hair cells, the nose has olfactory receptor neurons, the tongue has taste cells, and the skin and organs have free nerve endings and specialized mechnoreceptors such as pacinian corpuscles. Most of these do the work of transducing the stimulus in a specialized receptor portion of the cell, such as the rod itself, or the cilia of a hair cell or ORN, etc., and then the signal is sent to the next cell in the sensory chain via a synapse, sometimes via a very short axon or just sort of axon &quot;nub&quot;.&lt;/p&gt;&#xA;" OwnerUserId="587" LastActivityDate="2015-07-28T19:04:22.580" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36450" PostTypeId="2" ParentId="36445" CreationDate="2015-07-28T20:36:51.360" Score="1" Body="&lt;p&gt;Injecting into a fresh organ seems like a needless complication if you're just validating your antibody and not interested in gathering data about the interaction between the cells and the organ. (In fact, if you're using anything more complex than a flatworm I'd hope your IRB would have problems with needlessly sacrificing animals to get those organs.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It seems like your purpose would be better fulfilled by making an FFPE cell plug and doing your IHC on that. Here's a protocol for making cell plugs:&#xA;&lt;a href=&quot;http://%20tmalab.jhmi.edu/docs/Cell_line_block_procedure_Jan2013.pdf&quot; rel=&quot;nofollow&quot;&gt;Johns Hopkins Tissue Microarray Lab Cell Plug Protocol&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="819" LastActivityDate="2015-07-28T20:36:51.360" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36451" PostTypeId="2" ParentId="36443" CreationDate="2015-07-28T21:01:46.157" Score="1" Body="&lt;p&gt;I think there are several things that keep Bernoulli's principle from being straightforwardly applied.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First, Bernoulli's principle would help us calculate the pressure exerted by the blood on the walls of the vessels, but that's not what blood pressure measures. Blood pressure measures the amount of force that has to be applied to stop the blood from flowing forward. There's some relationship between the two, but it's not clean.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Second, the branching makes the surface area calculations different from a single pipe. The arteries have more cross-sectional area than the aorta, but they have have much, much more surface area-- way more of a difference than a single pipe with those cross-sectional characteristics would have.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So Bernoulli's principle does mean that blood is exerting more pressure on the surface of the arteries and arterioles than it is in the aorta. However, pressure is force per unit area, and there's much more area in the smaller vessels, so the pressure in any single vessel is less.&lt;/p&gt;&#xA;" OwnerUserId="819" LastActivityDate="2015-07-28T21:01:46.157" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36452" PostTypeId="1" CreationDate="2015-07-28T22:00:40.603" Score="13" ViewCount="634" Body="&lt;p&gt;In the last three days, I have found two snails infected by some species of &lt;em&gt;Leucochloridium&lt;/em&gt;. I found them in my garden in the south-west of Sweden. Now I'm wondering if they are the same species or not. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;One has broodsacs with green stripes and looks like a typical &lt;em&gt;Leucochloridium paradoxum&lt;/em&gt;, and the other has brown stripes, which makes me think it's a &lt;em&gt;Leucochloridium variae&lt;/em&gt;, but I've seen it mentioned that their appearance can vary.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Update&lt;/strong&gt;: I have learned that there is only one (documented) species of Leucochloridium in Sweden, so maybe I should close this question, but I would still like to know if there is a way to tell the difference just by appearance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/l4k1a.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/l4k1a.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&#xA;&lt;a href=&quot;https://i.stack.imgur.com/CpyHC.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/CpyHC.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;And here they are in animated form in case that is helpful:&#xA;&lt;a href=&quot;https://i.stack.imgur.com/CrcT9.gif&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/CrcT9.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&#xA;&lt;a href=&quot;https://i.stack.imgur.com/Pydtn.gif&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/Pydtn.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8630" LastEditorUserId="8630" LastEditDate="2017-06-13T22:10:35.053" LastActivityDate="2018-09-06T13:02:46.427" Title="Two different Leucochloridium infected snails - different species?" Tags="&lt;species-identification&gt;&lt;parasitology&gt;" AnswerCount="1" CommentCount="6" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36453" PostTypeId="1" CreationDate="2015-07-28T23:30:07.327" Score="4" ViewCount="6029" Body="&lt;p&gt;Why is the pituitary gland located in the brain in humans, instead of elsewhere in the body? Why would this be an evolutionary beneficial adaptation?&lt;/p&gt;&#xA;" OwnerUserId="17017" LastEditorUserId="9943" LastEditDate="2015-07-29T07:14:37.757" LastActivityDate="2016-08-17T15:10:17.757" Title="Why is the pituitary gland located in the brain?" Tags="&lt;evolution&gt;&lt;neuroanatomy&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36454" PostTypeId="2" ParentId="36453" CreationDate="2015-07-29T00:10:48.477" Score="8" Body="&lt;p&gt;The evolutionary pressure on the location of the &lt;a href=&quot;http://www.britannica.com/science/pituitary-gland&quot; rel=&quot;nofollow noreferrer&quot;&gt;pituitary&lt;/a&gt; is likely not the reason why it resides at the basis of the brain. Instead, its (partly) neural origin makes it anatomically (and functionally) part of the brain. Why would it migrate out of the brain when it doesn't have to? What would the evolutionary pressure be on increasing the length of the axons connecting it to the other parts of the brain? It is part of the brain, hence it is located there. It &lt;strong&gt;clashes with the &lt;a href=&quot;http://evolution.berkeley.edu/evolibrary/article/phylogenetics_08&quot; rel=&quot;nofollow noreferrer&quot;&gt;principle of parsimony&lt;/a&gt;&lt;/strong&gt; to have the pituitary evolve to a structure located farther from the brain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The neuroanatomy of the pituitary is schematically as follows (Fig. 1):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/IeFkI.jpg&quot; alt=&quot;pituitary&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Pituitary gland. Source: &lt;a href=&quot;http://www.imagekb.com/pituitary-gland&quot; rel=&quot;nofollow noreferrer&quot;&gt;Imagekb&lt;/a&gt;.&lt;/sup&gt;  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The &lt;strong&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Posterior_pituitary&quot; rel=&quot;nofollow noreferrer&quot;&gt;posterior lobe&lt;/a&gt;&lt;/strong&gt; of the pituitary gland consists largely of extensions of processes (axons) from the hypothalamus and are part of the neurohypophyseal system. There are neural connections to the brain and other centres of the hypothalamus. Hence, the posterior lobe is &lt;strong&gt;neural tissue&lt;/strong&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The cells constituting the &lt;strong&gt;&lt;a href=&quot;http://www.britannica.com/science/pituitary-gland&quot; rel=&quot;nofollow noreferrer&quot;&gt;anterior lobe&lt;/a&gt;&lt;/strong&gt; of the pituitary gland are embryologically derived from an outpouching of the roof of the pharynx, known as Rathke’s pouch. &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-08-07T21:00:49.610" LastActivityDate="2015-08-07T21:00:49.610" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36455" PostTypeId="1" AcceptedAnswerId="38664" CreationDate="2015-07-29T00:13:38.490" Score="2" ViewCount="161" Body="&lt;p&gt;I was in Germany recently, and I saw again a flower that I'd only ever encountered before at Meijer Gardens. It's interesting to me because I'd never seen a flower with color variation in only the 'interior' petals. Try as I might, however, I can't seem to find it anywhere! Can anyone tell me what this is? I'd like to be able to learn more about it.&lt;img src=&quot;https://i.stack.imgur.com/zZUUT.jpg&quot; alt=&quot;, &quot;&gt;&lt;/p&gt;&#xA;" OwnerUserId="17019" LastEditorUserId="16866" LastEditDate="2020-04-15T13:24:50.517" LastActivityDate="2020-04-15T13:24:50.517" Title="What is this flower?" Tags="&lt;species-identification&gt;&lt;botany&gt;&lt;flowers&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36459" PostTypeId="1" CreationDate="2015-07-29T05:12:52.947" Score="1" ViewCount="37" Body="&lt;p&gt;I am working on an assay for phenol products created by a colony of bacteria. I have searched up a paper that involves gibbs reageant but the protocol is kind of unclear.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does any of you know where I can look for a detailed protocol for a gibbs reagent colormetric assay (preferably one that uses cell medium)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="8279" LastActivityDate="2015-12-12T00:36:44.740" Title="Colormetric assay for a phenol product?" Tags="&lt;biotechnology&gt;&lt;synthetic-biology&gt;&lt;assay-development&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36462" PostTypeId="1" CreationDate="2015-07-29T10:51:55.303" Score="1" ViewCount="147" Body="&lt;p&gt;I want to know what is the definition of the life biologically , on the other hand ,  what is the definition of the death biologically  ?? However, I think it is a very difficult question to answer . &lt;/p&gt;&#xA;" OwnerUserId="16931" LastEditorUserId="9943" LastEditDate="2015-07-29T11:23:58.143" LastActivityDate="2015-07-30T00:01:50.690" Title="What is the definition of the life biologically ?" Tags="&lt;terminology&gt;&lt;life&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-07-29T16:41:47.230" ContentLicense="CC BY-SA 3.0" />
  <row Id="36463" PostTypeId="1" CreationDate="2015-07-29T13:49:58.453" Score="3" ViewCount="753" Body="&lt;p&gt;We know geckos can climb vertically or even upside down a surface like glass. But can they do that on wet glass?&lt;/p&gt;&#xA;" OwnerUserId="17027" LastEditorUserId="9943" LastEditDate="2015-07-30T01:47:55.050" LastActivityDate="2015-07-30T01:47:55.050" Title="Can geckos climb a wet surface?" Tags="&lt;biophysics&gt;&lt;bio-mechanics&gt;&lt;locomotion&gt;" AnswerCount="1" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36464" PostTypeId="2" ParentId="9197" CreationDate="2015-07-29T14:01:21.050" Score="5" Body="&lt;p&gt;The phenomenon in question is &lt;strong&gt;anisochromatopsia&lt;/strong&gt;, however this term is rarely used. This phenomenon is always present, however it is rarely mentioned subjectively, while objective color testing will reveal it easily.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In pathologic state, the term &lt;strong&gt;Color Desaturation&lt;/strong&gt; is being used defining that the previous status of color vision has changed to &quot;abnormal&quot; one. The causes to this change could be multiple, for example the most common one &lt;a href=&quot;http://www.uptodate.com/contents/optic-neuritis-pathophysiology-clinical-features-and-diagnosis&quot; rel=&quot;noreferrer&quot;&gt;Optic neuritis&lt;/a&gt; in Multiple sclerosis.&lt;/p&gt;&#xA;" OwnerUserId="5755" LastActivityDate="2015-07-29T14:01:21.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36465" PostTypeId="2" ParentId="36463" CreationDate="2015-07-29T14:28:18.813" Score="4" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Yes they can, but with less efficiency. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Efficiency of sticking to a glass surface decreases about 20-fold when the gecko's feet are wet &lt;a href=&quot;http://jeb.biologists.org/content/215/17/3080.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Stark &lt;em&gt;et al&lt;/em&gt;., 2012)&lt;/a&gt;. On dry glass, &lt;em&gt;Gekko gecko&lt;/em&gt; holds on with about 18 N, which is about 18 times their own body weight. Hence, the gecko attachment system is over-designed &lt;a href=&quot;http://jeb.biologists.org/content/215/17/i.1.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Knight, 2012)&lt;/a&gt;. Wetted toe pads reduce the adhesive force significantly down to 0.9 N. A wetted glass surface does not significantly affect the grip of &lt;em&gt;Gekko gecko&lt;/em&gt;, except after the gecko takes multiple steps. Hence, geckos can cling to wet surfaces, but only when their feet are not getting too wet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that gecko attachment is not based on suction, such as the &lt;a href=&quot;https://en.wikipedia.org/wiki/Octopus&quot; rel=&quot;nofollow noreferrer&quot;&gt;suction cups&lt;/a&gt; seen in octopus. Instead, geckos cling to surfaces with &lt;a href=&quot;http://www.chemguide.co.uk/atoms/bonding/vdw.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;Van der Waals forces&lt;/strong&gt;&lt;/a&gt;. Van-der-Waals-based adhesive systems take advantage of weak intermolecular forces between two surfaces. Upside is that these forces are not surface specific, allowing geckos to climb trees, rocks, walls and even glass windows. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Geckos achieve their strong attractive force to the substrate by utilizing small hair-like structures on their toes called &lt;a href=&quot;https://en.wikipedia.org/wiki/Seta&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;strong&gt;&lt;em&gt;setae&lt;/em&gt;&lt;/strong&gt;&lt;/a&gt;, which are made primarily of keratin (Fig. 1). Setae contain flexible &lt;em&gt;&lt;a href=&quot;http://www.laboratory-journal.com/science/material-science/gecko-s-adhesive-system-secret-it&quot; rel=&quot;nofollow noreferrer&quot;&gt;spatulae&lt;/a&gt;&lt;/em&gt; which make intimate contact with rough and even dirty surfaces. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/srIue.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/srIue.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;  &lt;a href=&quot;https://en.wikipedia.org/wiki/Seta&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/M7vj5.gif&quot; alt=&quot;setae]&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Left panel: Close-up of the underside of a gecko's foot as it walks on vertical glass. Source: &lt;a href=&quot;https://en.wikipedia.org/wiki/Seta&quot; rel=&quot;nofollow noreferrer&quot;&gt;Wikipedia&lt;/a&gt;. Right panel: Images of (A) dry and (B) wet &lt;em&gt;setae&lt;/em&gt; using the same digit of an individual tokay gecko (&lt;em&gt;Gekko gecko&lt;/em&gt;). The image in A was taken prior to exposure to water and the image in B was taken after 30 min of soaking in water. Source: &lt;a href=&quot;http://jeb.biologists.org/content/215/17/3080.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Stark &lt;em&gt;et al&lt;/em&gt;., 2012)&lt;/a&gt;&lt;/sup&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The drawback of using Van-der-Waals forces for grip is that the Van-der-Waals forces only exist across surfaces very close together, and an intimate contact between the spatulae and the substrate is required for van der Waals forces to be effective in the gecko adhesive system &lt;a href=&quot;http://jeb.biologists.org/content/215/17/3080.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Stark &lt;em&gt;et al&lt;/em&gt;., 2012)&lt;/a&gt;. Wetting of the feet decreases the Van der Waals interaction with the surface.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://jeb.biologists.org/content/215/17/i.1.full&quot; rel=&quot;nofollow noreferrer&quot;&gt;Knight, &lt;em&gt;J Exp Biol&lt;/em&gt; &lt;strong&gt;215&lt;/strong&gt;, i&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://jeb.biologists.org/content/215/17/3080.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Stark &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;J Exp Biol&lt;/em&gt;; &lt;strong&gt;215&lt;/strong&gt;: 3080-6&lt;/a&gt;&lt;/sup&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-30T01:36:30.510" LastActivityDate="2015-07-30T01:36:30.510" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36466" PostTypeId="2" ParentId="36462" CreationDate="2015-07-29T14:34:59.117" Score="0" Body="&lt;p&gt;Could not fit in a comment..&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;The question is off-topic&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biology is the study of life. Without a good definition of life, Biology itself is poorly defined. It appears that there is no universally accepted definition of life and therefore Biology (just like Chemistry and Physics to cite other examples) is a poorly defined field of study. But it is not scientists job to decide whether their work should stand within one category or another, nor whether those categories are natural categories (see &lt;a href=&quot;https://en.wikipedia.org/wiki/Prototype_theory&quot; rel=&quot;nofollow&quot;&gt;prototype theory&lt;/a&gt;) or not. It is the job of philosophers and therefore this question is about philosophy and is off-topic here.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Few notes about the definition of life&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Most often, philosophers see a continuum from not living to living things and not a clear dichotomy (&lt;a href=&quot;http://www.amazon.fr/Comment-d%C3%A9finir-vie-Hugues-Bersini/dp/2711748650&quot; rel=&quot;nofollow&quot;&gt;ref.&lt;/a&gt;). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Biologists, most often just assume that bacteria, archea and eukaryotes are living things while viruses, viroids and prions are not living things. This arbitrary dichotomy is based on the concept of metabolism. However, this dichotomy can lead to some limit cases. Typically, considering viruses as not being living things yields to intuitive issues when thinking about macroviruses such as &lt;a href=&quot;https://en.wikipedia.org/wiki/Marseillevirus&quot; rel=&quot;nofollow&quot;&gt;Marseillovirus&lt;/a&gt; and Lausanevirus.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;There are two questions in your post&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Of course, the definition of what is dead is a total different question from the question of what is a living thing. A stone is not dead it is just not a living thing. Even then, the definition of death is of interest to philosophers, not to biologists. You should always try to limit your post to a single question.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-07-30T00:01:50.690" LastActivityDate="2015-07-30T00:01:50.690" CommentCount="11" ContentLicense="CC BY-SA 3.0" />
  <row Id="36468" PostTypeId="1" CreationDate="2015-07-29T16:16:16.270" Score="1" ViewCount="47" Body="&lt;p&gt;I understand how tracer kinetics can be used to determine binding potential but how it can be used to detect perfusion eludes me. &lt;/p&gt;&#xA;" OwnerUserId="17028" LastActivityDate="2015-07-29T16:16:16.270" Title="What is the general mechanism behind perfusion PET imaging" Tags="&lt;imaging&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36471" PostTypeId="1" CreationDate="2015-07-29T19:57:59.133" Score="5" ViewCount="16838" Body="&lt;p&gt;Is there a specific reason that the letter Y is used as the symbol for the male chromosome and X is used for the female chromosome?&lt;/p&gt;&#xA;" OwnerUserId="17035" LastEditorUserId="6307" LastEditDate="2015-07-30T03:49:44.737" LastActivityDate="2017-10-12T13:58:54.410" Title="Why are the sex chromosomes called X and Y?" Tags="&lt;terminology&gt;&lt;history&gt;&lt;sex-chromosome&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36474" PostTypeId="2" ParentId="36388" CreationDate="2015-07-29T23:07:25.643" Score="1" Body="&lt;p&gt;Aside from &quot;toxins&quot;, the liver metabolizes a host of endogenous and exogenous compounds. Endogenous compounds are compounds that are normally present and produced within the body like ammonia and estrogens for example. Exogenous compounds are those like ethanol/alcohol, acetaminophen, and other drugs/etc that are not normally in the body but rather we take a mediations or recreational drugs, etc. Most of the compounds that the liver metabolizes are through a set of enzymes called the &lt;a href=&quot;https://en.wikipedia.org/wiki/Cytochrome_P450&quot; rel=&quot;nofollow&quot;&gt;cytochrome P450 system&lt;/a&gt;, which includes numerous enzymes (too many to list here) that catalyze a number of reactions that help detoxify a substance and/or make it more likely to be excreted in the urine by the kidneys.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If the liver &quot;sees&quot; old and new compounds it doesn't differentiate between which it might metabolize first - that is based on concentrations within the liver. In fact, only if the compounds are metabolized by the same liver enzymes will they compete with one another. If they are metabolized by the same exact P450 enzymes, then the concentrations of each of these substances within the hepatocytes (liver cells) will determine which one gets metabolized more frequently. For example, if the concentration of substance A is much, much higher than substance B, then substance A is going to outcompete the other substance for the enzymes that metabolize it (similar to &lt;a href=&quot;https://en.wikipedia.org/wiki/Competitive_inhibition&quot; rel=&quot;nofollow&quot;&gt;competitive inhibition&lt;/a&gt; in biochemistry). Most of the time, endogenous and exogenous compounds do not necessarily compete at the same P450 enzymes because there are so many different P450 enzymes within the liver. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The liver does not have any way of prioritizing different compounds, however, if the liver is exposed to a particular substance over a long amount of time then it may express more of a particular cytochrome P450 enzyme that metabolizes that particular substance. This is similar to alcoholics being able to metabolize a lot more alcohol than someone who has never drank alcohol previously.&lt;/p&gt;&#xA;" OwnerUserId="16299" LastActivityDate="2015-07-29T23:07:25.643" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36476" PostTypeId="2" ParentId="36471" CreationDate="2015-07-30T00:08:30.333" Score="3" Body="&lt;p&gt;&lt;a href=&quot;http://www.nature.com/scitable/topicpage/sex-chromosomes-and-sex-determination-44565&quot; rel=&quot;nofollow&quot;&gt;Sex Chromosomes and Sex Determination by Ilona Miko&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The first inkling that sex chromosomes were unique from all other chromosomes came from experiments conducted by German biologist Hermann Henking in 1891… Henking saw that some wasp sperm cells had 12 chromosomes, while others had only 11. Moreover, while observing the stages of meiosis that formed these sperm cells, Henking noticed that the mysterious twelfth chromosome looked different from all the others. He thus named this chromosome the &quot;X element,&quot; to represent its unknown nature.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.m.wikipedia.org/wiki/Y_chromosome&quot; rel=&quot;nofollow&quot;&gt;Wikipedia - Y Chromosome&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The Y chromosome was identified as a sex-determining chromosome by Nettie Stevens … during a study of the mealworm &lt;em&gt;Tenebrio molitor&lt;/em&gt; … Stevens proposed that chromosomes always existed in pairs and that the Y chromosome was the pair of the X chromosome discovered in 1890 by Hermann Henking … Stevens named the chromosome &quot;Y&quot; simply to follow on from Henking's &quot;X&quot; alphabetically.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I know that this is not the most reputable source, but it does cite a couple of books. Take it as it is. Keep in mind that all human chromosomes, even the Y chromosome, appear as X shaped when replicated and condensed. The Y chromosome is quite acrocentric and so the short arms may appear to be one, but they're not. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastActivityDate="2015-07-30T00:08:30.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36477" PostTypeId="2" ParentId="36471" CreationDate="2015-07-30T00:09:29.870" Score="3" Body="&lt;p&gt;During metaphase, all chromosomes look like an &lt;code&gt;X&lt;/code&gt; with the exception of the chromosome &lt;code&gt;Y&lt;/code&gt;. See below&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/tJUeB.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/tJUeB.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why &lt;code&gt;Y&lt;/code&gt; then? Well, according to &lt;a href=&quot;https://en.m.wikipedia.org/wiki/Y_chromosome&quot; rel=&quot;nofollow noreferrer&quot;&gt;wikipedia&lt;/a&gt;, just because the letter &lt;code&gt;Y&lt;/code&gt; follows the letter &lt;code&gt;X&lt;/code&gt; in the alphabet. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that many species don't have sexual chromosomes and note that in many species, the &lt;code&gt;Y&lt;/code&gt;-looking chromosome is present in the female but not in the male. In such case we call this &lt;code&gt;Y&lt;/code&gt;-looking chromosome &lt;code&gt;W&lt;/code&gt; and we call the &lt;code&gt;X&lt;/code&gt;-looking chromosome &lt;code&gt;Z&lt;/code&gt;. Very likely &lt;a href=&quot;https://biology.stackexchange.com/questions/27511/do-males-of-all-sexual-species-have-y-chromosomes&quot;&gt;this post will interest you&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-07-30T04:32:17.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36478" PostTypeId="1" CreationDate="2015-07-30T00:56:17.237" Score="5" ViewCount="915" Body="&lt;p&gt;I accidentally left a delivery of NADPH Tetrasodium Salt (Santa Cruz Biotechnology) at room temperature for a little over half an hour.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In addition, when I opened up the package, I briefly held the bottle by the body instead of the cap (which would have prevented body heat from contacting it). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It was packed with airbags, but no ice packs, which is why I am asking this: is the powder still stable and usable?&lt;/p&gt;&#xA;" OwnerUserId="15955" LastEditorUserId="6307" LastEditDate="2015-07-30T04:07:32.330" LastActivityDate="2015-08-06T12:36:16.263" Title="Is NADPH salt still usable after an hour at room temperature?" Tags="&lt;biochemistry&gt;&lt;lab-reagents&gt;" AnswerCount="3" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="36479" PostTypeId="2" ParentId="36478" CreationDate="2015-07-30T02:21:32.527" Score="3" Body="&lt;p&gt;I think when they sent it to you without dry ice, it is probably OK to store it at room temperature.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sigma seems to advise on their &lt;a href=&quot;https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Product_Information_Sheet/2/n7505pis.pdf&quot; rel=&quot;nofollow&quot;&gt;NADPH&lt;/a&gt; to store &lt;a href=&quot;http://www.sigmaaldrich.com/catalog/product/sigma/n9910?lang=en&amp;amp;region=AU&quot; rel=&quot;nofollow&quot;&gt;dehydrated NADPH&lt;/a&gt; at room temperature, while they advise to store the &lt;a href=&quot;http://www.sigmaaldrich.com/catalog/product/sigma/n1630?lang=en&amp;amp;region=AU&quot; rel=&quot;nofollow&quot;&gt;hydrated&lt;/a&gt; &lt;a href=&quot;http://www.sigmaaldrich.com/catalog/product/sigma/n7505?lang=en&amp;amp;region=AU&quot; rel=&quot;nofollow&quot;&gt;forms&lt;/a&gt; at -20&lt;sup&gt;o&lt;/sup&gt;C. Likely the presence or absence of molecular water in the material is crucial for its storage.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;disclaimer: I am not an organic chemist and when you are doing crucial experiments with your material and you doubt its quality, I'd recommend to chuck this batch away and order new. Likely, a single day of futile experimentation in the lab due to bad reagents is more expensive than the purchase of another jar of NADPH.&lt;/sup&gt;  &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-30T02:40:08.800" LastActivityDate="2015-07-30T02:40:08.800" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36480" PostTypeId="1" AcceptedAnswerId="38992" CreationDate="2015-07-30T03:29:46.270" Score="2" ViewCount="104" Body="&lt;p&gt;I understand that one limiting factor in non-human animal populations is that increased pathogen populations decrease animal populations from killing them, which decreases the density of the animals, which makes it harder for pathogens to infect other animals. However, pathogens, at least in developed nations, don't seem to kill a large enough number of people for this to be the main limiting factor. So what else are the limiting factors?&lt;/p&gt;&#xA;" OwnerUserId="14904" LastActivityDate="2015-09-23T04:56:43.640" Title="What are the limiting factors of pathogen population size in human populations?" Tags="&lt;pathology&gt;&lt;population-dynamics&gt;&lt;host-pathogen-interaction&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36481" PostTypeId="1" CreationDate="2015-07-30T03:42:59.577" Score="1" ViewCount="793" Body="&lt;p&gt;My eyesight is pretty much perfect, but I noticed that whenever I try any of my friends glasses, from really thin to extremely thick, my eyes seem to adjust to them within seconds and let me see perfectly fine. Is this weird or abnormal, I was just really curious.&lt;/p&gt;&#xA;" OwnerUserId="17040" LastEditorUserId="9943" LastEditDate="2015-07-30T03:58:02.910" LastActivityDate="2015-08-05T09:30:24.787" Title="Can my eyes adjust instantly to my friend's glasses?" Tags="&lt;human-biology&gt;&lt;vision&gt;" AnswerCount="1" CommentCount="3" ClosedDate="2015-08-01T09:25:55.393" ContentLicense="CC BY-SA 3.0" />
  <row Id="36483" PostTypeId="2" ParentId="36478" CreationDate="2015-07-30T05:04:53.203" Score="4" Body="&lt;p&gt;You could measure OD at 340nm. If OD340 is much lower than expected, NADPH is oxidized and does not have much biochemical activity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.bmglabtech.com/media/35216/1043734.pdf&quot; rel=&quot;nofollow&quot;&gt;http://www.bmglabtech.com/media/35216/1043734.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15878" LastActivityDate="2015-07-30T05:04:53.203" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36485" PostTypeId="1" AcceptedAnswerId="36488" CreationDate="2015-07-30T07:47:42.963" Score="-3" ViewCount="486" Body="&lt;p&gt;I would like to know if speciation really occurs (trans-speciation). Have we had enough time for millions of species? A creationist argument is that the slow changes in traits in organisms, taking tens of thousands of years to yield a visible change in variation as evolution suggests, does eventually trap yourself in to a problem of &quot;Time Riddle&quot;. You just don't have enormous enough time at hand for all these species to come into being. A quick average time calculation suggests that you should have a new species come into being every 15-20 yrs [just rough average time estimation suggests that in about 1 billion yrs ~50 million distinct species evolved]. Though I believe in evolution, I cant understand this part.&lt;/p&gt;&#xA;" OwnerUserId="16984" LastEditorUserId="948" LastEditDate="2015-07-31T14:36:56.087" LastActivityDate="2015-07-31T14:36:56.087" Title="Driving force for speciation for millions of species today" Tags="&lt;evolution&gt;&lt;speciation&gt;&lt;macroevolution&gt;" AnswerCount="2" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="36487" PostTypeId="1" AcceptedAnswerId="36490" CreationDate="2015-07-30T12:11:34.507" Score="2" ViewCount="83" Body="&lt;p&gt;Forgive me if this question is too trivial.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have the gene IDs of the following type&lt;/p&gt;&#xA;&#xA;&lt;pre&gt;&lt;code&gt;EOG6STSR2&#xA;EOG60ZRJB&#xA;EOG6SBFJ2&#xA;EOG6P5KX3&#xA;EOG6B5PRW&#xA;&lt;/code&gt;&lt;/pre&gt;&#xA;&#xA;&lt;p&gt;from the first supplementary file in &lt;a href=&quot;http://genome.cshlp.org/content/suppl/2014/05/21/gr.159384.113.DC1.html&quot; rel=&quot;nofollow&quot;&gt;Comparative validation of the D. melanogaster modENCODE transcriptome annotation &lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not sure as to the type of the IDs. I learned that IDs beginning with &lt;em&gt;EOG&lt;/em&gt; are &lt;em&gt;Eukaryotic Orthologous Group&lt;/em&gt; IDs but I couldn't find these particular ones in any of the databases.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it possible to map them to &lt;em&gt;Ensembl&lt;/em&gt; IDs or any of the other commonly used ones?&lt;/p&gt;&#xA;" OwnerUserId="17046" LastActivityDate="2015-07-30T13:28:34.873" Title="Map gene IDs to Ensembl gene ID" Tags="&lt;gene&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36488" PostTypeId="2" ParentId="36485" CreationDate="2015-07-30T12:44:06.037" Score="3" Body="&lt;p&gt;This answer is towards the question, what forces primarily drive evolution such that we can observe a million species today? which is what the user wanted answered.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To answer this question, we can start off at many places. So I wanted to start off at Kimura's &lt;a href=&quot;https://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution&quot; rel=&quot;nofollow noreferrer&quot;&gt;neutral theory of evolution&lt;/a&gt; which encompasses both &lt;a href=&quot;https://en.wikipedia.org/wiki/Natural_selection&quot; rel=&quot;nofollow noreferrer&quot;&gt;Natural selection&lt;/a&gt; and &lt;a href=&quot;https://en.wikipedia.org/wiki/Genetic_drift&quot; rel=&quot;nofollow noreferrer&quot;&gt;genetic drift&lt;/a&gt;. I wanted to start here because although it is true, it also brings to light a fundamental trait of &lt;a href=&quot;https://en.wikipedia.org/wiki/Phenotype&quot; rel=&quot;nofollow noreferrer&quot;&gt;phenotype&lt;/a&gt; which has been highlighted in this paper which suggests that &lt;a href=&quot;http://www.umich.edu/~zhanglab/clubPaper/05_04_2012.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;mutation rate in a species as a whole is not very divergent, but the same rate varies by several magnitudes when comparing genes having lower rates in highly expressed genes and higher in lowly expressed ones&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This brings to light another feature of gene mutation. A very simplistic view is that gene products are perfect for their function, that is not the case (I need to find a proper reference for this, maybe someone can help me with that?). Gene products are never the most thermodynamically stable nor the best at performing their intended function, but rather they are positively selected for once a mutation produces a product that provides increased fitness to the organism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Till now this answers two things:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Mutation is the governing factor driving evolution.&lt;/li&gt;&#xA;&lt;li&gt;Unless a new mutation increases fitness of the organism it is considered as a neutral one.&lt;/li&gt;&#xA;&lt;li&gt;A species as a whole has nearly the same mutation rate.&lt;/li&gt;&#xA;&lt;li&gt;Depending on their contribution to survival genes have different mutation rates.&lt;/li&gt;&#xA;&lt;li&gt;A gene will choose to preserve function over improvement because it may result in a loss of function.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So now let us come to the part about millions of species. If you followed me till now, you understood that based on different mutations changes will arise. I would now like to bring in the theory of &lt;a href=&quot;https://en.wikipedia.org/wiki/Punctuated_equilibrium&quot; rel=&quot;nofollow noreferrer&quot;&gt;Punctuated equilibrium&lt;/a&gt; which basically states that a species once developed remains nearly the same for it's geological history. Below is an interesting image from the wiki page.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/SUh9G.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/SUh9G.png&quot; alt=&quot;Fossil records showing the appearance and disappearance of species within the hominid line&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So according to this theory once a species has appeared, until it disappears it will remain largely the same. It will disappear does not mean the entire line will die off. Rather, it means a substantial part of will die off, allowing niche populations to colonise the now empty ecosystem. Or a change in climate may now allow a certain niche species to migrate out of their ecosystem to provide competition to the already existing species in the ecosystem and then to oust them from their place (look at yourself for example), the migratory pattern exhibited by homo sapiens during the end of the last ice age led to the removal of neanderthals from their ecosystem (this is very traditional and overly simplistic but mostly correct so I will not provide the complicated parts here).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This theory worked on the theory of &lt;a href=&quot;https://en.wikipedia.org/wiki/Allopatric_speciation&quot; rel=&quot;nofollow noreferrer&quot;&gt;geographical speciation&lt;/a&gt; which goes on to state that geographical changes may lead to population separation, which leads to the different species. This is because, in their own ecosystems they will be privy to very different environmental stresses such as climatic conditions, competition, predation, food availability and disease. So after a million years these two populations which were the same will now be very different.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So I think, I have provided a suitable answer to this question, because your view evolution as something very linear. Which it hardly is. There are many factors which guide it, and this is how today you can see millions of species. Another thing to note is that of the millions and millions of species identified on earth today, multicellular organisms represents a handful of crumbs from the pie. Most of it is actually micro-organisms (Anyone know the source for some exact numbers?)&lt;/p&gt;&#xA;" OwnerUserId="15807" LastActivityDate="2015-07-30T12:44:06.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36489" PostTypeId="2" ParentId="36443" CreationDate="2015-07-30T12:44:35.407" Score="3" Body="&lt;p&gt;Bernoulli's principle can be a little tricky when applied to the cardiovascular system, but it still holds true across the entire system. You mention a good point that the relationship doesn't seem quite right at the aorta or arteries, because of the constant fluctuation of pressure between systolic and diastolic without a significant change in diameter of the vessel. Remember that this is due to the pulsatile flow of blood from the heart, and has nothing to do with Bernoulli's principle. If the flow was constant (i.e. not pulsatile) then the pressure would be constant as the diameter of the vessels is constant. As the diameter of the vessels begins to decrease the velocity would increase to maintain a constant value. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As you mention, Bernoulli's principle describes how the product of area and velocity of flow must be constant across a system. When the total surface area of the system increases, the pressure decreases as well as flow. It is important to remember that even though the capillaries are so small and individually high resistance (which you would think according to Bernoulli's principle should increase the velocity), you are effectively adding an innumerable number of these very small resistors in parallel (not in series) and the resistance overall (and subsequently pressure + flow) decreases greatly. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;When adding resistance in series the total resistance is additive and it adds up quickly! $$R_{Total} = R_1 + R_2 + R_3$$&#xA;While resistance in parallel adds the reciprocal of the resistor, meaning that as more resistors (or capillary pathways) are added the total resistance continues to decrease because of the following relationship: $$\frac{1}{R_{Total}} = \frac{1}{R_1}+\frac{1}{R_2}+\frac{1}{R_3}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The parallel resistance stuff was difficult for me to grasp when I was a student, because it never seemed to make sense in my mind that the resistance significantly decreased when you added all these small capillaries. One of my physiology professors described it well when he said, &quot;Think of adding resistance in parallel, in the way that capillary beds and other vessels are in the cardiovascular system, &lt;strong&gt;like giving the blood another place to go&lt;/strong&gt;.&quot; If the blood has more places that it can go, then it's easier to see why resistance falls so much when you add a bunch of extra places for the blood to flow.&lt;/p&gt;&#xA;" OwnerUserId="16299" LastEditorUserId="16299" LastEditDate="2016-02-16T16:42:13.027" LastActivityDate="2016-02-16T16:42:13.027" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36490" PostTypeId="2" ParentId="36487" CreationDate="2015-07-30T13:28:34.873" Score="2" Body="&lt;p&gt;These are not gene ids, but groups of orthologous genes -- try to search for the ids on Google, I can find this page &lt;a href=&quot;http://cegg.unige.ch/orthodb6/fasta.fasta?ogs=EOG6STSR2&amp;amp;swaptree=&quot; rel=&quot;nofollow&quot;&gt;http://cegg.unige.ch/orthodb6/fasta.fasta?ogs=EOG6STSR2&amp;amp;swaptree=&lt;/a&gt; and thus you should be able to download the sequences and ids from &lt;a href=&quot;http://cegg.unige.ch/orthodb6/&quot; rel=&quot;nofollow&quot;&gt;OrthoDB&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that, strictly speaking, the are no Ensembl ids for Drosophila, only FlyBase ids that are also used by Ensembl. &lt;/p&gt;&#xA;" OwnerUserId="112" LastActivityDate="2015-07-30T13:28:34.873" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36493" PostTypeId="1" AcceptedAnswerId="36495" CreationDate="2015-07-30T15:04:40.777" Score="3" ViewCount="23387" Body="&lt;p&gt;Tobacco use is the leading cause of preventable death around the world.&lt;a href=&quot;http://bmjopen.bmj.com/content/3/11/e003304.full?rss=1&quot; rel=&quot;nofollow noreferrer&quot;&gt;$\ce{^1}$&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/z77mX.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/z77mX.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The stain is considered as a &quot;tell-tale&quot; sign for identifying smokers. Multiple materials stated that it's due to tar (nicotine) disposition. The colouring fades away after the smoker quits. There are also number of search results that point to &quot;removing&quot; these smoking stains in the skin. If it can be removed using chemicals then I wonder what sort of a chemical it utilized there as well.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is it only nicotine that causes the yellow stains on the skin? What is the role of oxygen deprivation in this scenario? Can this be categorized under smoker's melanosis? What tissues/cells are being &quot;transformed&quot; in this case? What's the biochemical explanation behind the colouring of skin?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How is this staining differe from a ink stain in the skin which lasts for about about 3-4 days?&lt;/p&gt;&#xA;" OwnerUserId="8709" LastEditorUserId="8709" LastEditDate="2015-07-31T03:02:55.710" LastActivityDate="2015-08-05T10:31:40.263" Title="How does a smoker's finger or mustache get yellowish by nicotine?" Tags="&lt;biochemistry&gt;&lt;skin&gt;&lt;pigmentation&gt;" AnswerCount="2" CommentCount="4" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36495" PostTypeId="2" ParentId="36493" CreationDate="2015-07-30T15:42:59.727" Score="7" Body="&lt;p&gt;&lt;a href=&quot;http://www.sigmaaldrich.com/catalog/product/sigma/n3876?lang=en&amp;amp;region=US&quot; rel=&quot;nofollow&quot;&gt;Pure nicotine&lt;/a&gt; is a yellow colored liquid (although &lt;a href=&quot;https://en.wikipedia.org/wiki/Nicotine#Physical_and_chemical_properties&quot; rel=&quot;nofollow&quot;&gt;some sources&lt;/a&gt; say it's a clear liquid.) &quot;Tar&quot; is a complex sludge that is also yellow-brown. So it's difficult to distinguish 'nicotine stain' from a 'tar stain' based on visual inspection. Let's go to other considerations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The concept of a 'stain' implies that simple hand washing doesn't remove the coloration. Since nicotine is water miscible, one would expect it's easily removed with soap and water. &lt;strong&gt;That implies that either a) a smoker's stain is &lt;em&gt;not&lt;/em&gt; primarily nicotine, or b) the nicotine reacts with the skin to create the stain.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Nicotine is sufficiently functionalized that it could conceivably undergo some interesting chemical reactions with proteins, but I don't think that's what's happening. A simple observation is that transdermal nicotine patches do not contain a colored agent, and do not stain the skin. Score one point for the &quot;mostly tar&quot; explanation. Cigarette smoke contains far more tar than nicotine, and tar will deposit on most-any surface (at ambient temperatures), so &lt;strong&gt;it's parsimonious to proceed with the &quot;mostly tar&quot; explanation.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The picture shows that the stain occurs on both fingernails and skin. The most abundant protein that's common to those two tissues is keratin. Like other examples of &lt;a href=&quot;https://en.wikipedia.org/wiki/Coomassie_Brilliant_Blue&quot; rel=&quot;nofollow&quot;&gt;protein staining&lt;/a&gt;, the mechanism is complicated and poorly understood, but the basic outline is that parts of keratin are greasy (the non-polar amino acids) that associate with other greasy things.  (EDIT: AliceD's answer also depicts the well-known staining of teeth, which are not keratinized, showing that the staining mechanism is likely a nonspecific adsorption of greasy things onto surfaces.)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The stain can be fixed through the involvement of free radicals and other reactive species in cigarette smoke, like formaldehyde. In this sense, reactive oxygen species are active participants. I don't think oxygen deprivation plays a role here. I don't think this can be described as a melanosis, as the skin isn't producing melanin in response to smoking but is simply being coated in tar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Even if the stain was completely fixed, the coloring would fade away as the exterior skin cells are sloughed off, consistent with normal skin physiology.&lt;/strong&gt; This is the explanation for the fading of any stained epidermis. The persistence of tar stains on teeth (which do not exfoliate) further evinces that the stain is removed through the replacement of skin cells.&lt;/p&gt;&#xA;" OwnerUserId="3336" LastEditorUserId="3336" LastEditDate="2015-07-31T20:44:55.737" LastActivityDate="2015-07-31T20:44:55.737" CommentCount="14" ContentLicense="CC BY-SA 3.0" />
  <row Id="36496" PostTypeId="1" AcceptedAnswerId="36498" CreationDate="2015-07-30T15:49:16.950" Score="8" ViewCount="1107" Body="&lt;p&gt;Most amphibians - at least, all the ones I know of - start their lives in the water (at least, after they hatch). They then spend time maturing before venturing onto land, where they can breed. The cycle than begins again.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Are there any cases where the reverse is true, i.e. a young amphibian starts life on land before venturing into the water as an adult?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Amphibian&quot; rel=&quot;nofollow&quot;&gt;Wikipedia&lt;/a&gt; hints that this may be the case, but fails to provide examples:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Amphibians typically start out as larvae living in water, but some&#xA;  species have developed behavioural adaptations to bypass this.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="9458" LastEditorUserId="3553" LastEditDate="2016-04-20T04:35:20.070" LastActivityDate="2016-04-20T05:33:20.887" Title="Do any amphibians start their lives on land?" Tags="&lt;zoology&gt;&lt;life-history&gt;" AnswerCount="3" CommentCount="1" FavoriteCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36497" PostTypeId="1" AcceptedAnswerId="36499" CreationDate="2015-07-30T15:54:11.520" Score="3" ViewCount="1354" Body="&lt;p&gt;I was reading &lt;a href=&quot;http://www.genetics.org/content/190/1/5.short&quot; rel=&quot;nofollow&quot;&gt;this review&lt;/a&gt;. On page 11, left column, first paragraph, one can read:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;[..] there is a Poisson distribution of the equilibrium number of mutations per individual, if fitness effects are multiplicative.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;with no further explanations. In other words, let the variable $X$ be the number of (deleterious) mutations found in one individual (irrespectively to whether the mutation occurred in the parents gonads or is older back in the lineage). The variable $X$ is Poisson distributed.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Why is this statement true? I suppose that the statement also assumes that all mutations have the same effect on fitness, is that true?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-07-30T19:21:14.623" LastActivityDate="2015-07-31T06:17:33.023" Title="Why does the number of mutations per individuals follow a Poisson distribution?" Tags="&lt;evolution&gt;&lt;theoretical-biology&gt;&lt;population-dynamics&gt;&lt;population-genetics&gt;&lt;population-biology&gt;" AnswerCount="1" CommentCount="2" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36498" PostTypeId="2" ParentId="36496" CreationDate="2015-07-30T16:39:23.423" Score="8" Body="&lt;p&gt;From &lt;a href=&quot;https://en.wikipedia.org/wiki/Amphibian&quot; rel=&quot;nofollow&quot;&gt;wiki&lt;/a&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Most amphibians lay their eggs in water and have aquatic larvae that undergo metamorphosis to become terrestrial adults&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;This suggests clearly that not all of them do so.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here are a few interesting cases I could think of:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;p&gt;The &lt;strong&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Common_midwife_toad&quot; rel=&quot;nofollow&quot;&gt;common midwife toad&lt;/a&gt;&lt;/strong&gt; carry the eggs on their back. The eggs are not necessarily submerged by water then.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;To my knowledge, the &lt;strong&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Seepage_salamander&quot; rel=&quot;nofollow&quot;&gt;Seepage salamander&lt;/a&gt;&lt;/strong&gt; have terrestrial larvae but they don't feed before they reach the adult age.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The &lt;strong&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Lungless_salamander&quot; rel=&quot;nofollow&quot;&gt;lungless salamanders&lt;/a&gt;&lt;/strong&gt; has a larval stage that is within the egg. When the egg hatches, the individual that comes out is already an adult.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2016-04-20T05:33:20.887" LastActivityDate="2016-04-20T05:33:20.887" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36499" PostTypeId="2" ParentId="36497" CreationDate="2015-07-30T17:05:29.660" Score="5" Body="&lt;p&gt;A &lt;a href=&quot;https://en.wikipedia.org/wiki/Poisson_process&quot; rel=&quot;nofollow&quot;&gt;Poisson process&lt;/a&gt; follows these postulates:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;$\lim\limits_{h\to0+}\frac{P(N_h=1)}h=\lambda$ &lt;br&gt; &lt;br&gt;i.e. the probability of occurrence one event in a very small interval of time is equal to the macroscopic rate or intensity ($\lambda\,$).&lt;br&gt;&lt;br&gt;&lt;/li&gt;&#xA;&lt;li&gt;$P(N_h\geqslant2)=o(h)$ &lt;br&gt;&lt;br&gt;i.e. the probability of occurrence of more than one events in an infinitesimal interval is essentially zero. &lt;br&gt;&lt;br&gt;&lt;/li&gt;&#xA;&lt;li&gt;Events are independent.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;If you consider a single individual (for simplicity assume a single cell), then the DNA will undergo mutations at some fixed rate (which we assume to be uniform for all loci). Now each mutation event is independent of the previous event and in a very small interval of time the chance of two or more mutations is negligible. Considering all these facts and assumptions, it can be said that mutation in a single cell would behave like a Poisson process.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the Poisson postulates you can derive the expression for the Poisson distribution which describes the probability of $k$ number of events in a given time interval, $t$. Hence, the number of mutations in an individual for a fixed time window ($t\,$) follows a Poisson distribution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$P(N=k)=\frac{(\lambda t)^k e^{-\lambda t}}{k!}$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can find the derivation of Poisson distribution from the postulates from many sources. I referred to this book:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Hogg, Robert V., and Allen T. Craig. &lt;em&gt;Introduction to mathematical statistics&lt;/em&gt;. New York: Macmillan, 1978.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The effect of deleterious mutations, in the mentioned section of the linked paper talks about Muller's ratchet that describes the accumulation of deleterious mutations and its effect on the population (i.e. extinction). &lt;strong&gt;Like any mutation event, accumulation of deleterious mutations will also follow Poisson distribution.&lt;/strong&gt; Muller's ratchet just says that beyond a tolerance limit, deleterious mutations will cause extinction of asexually reproducing organisms. Perhaps if each deleterious mutation had a strong effect on the fitness, then sampling from the population may lead to non-Poissonian estimates. &lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-07-31T06:17:33.023" LastActivityDate="2015-07-31T06:17:33.023" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="36500" PostTypeId="2" ParentId="36485" CreationDate="2015-07-30T17:20:29.820" Score="1" Body="&lt;p&gt;Your math is wrong.  Assume for simplicity that speciation is binary: that is, a speciation event divides one species into two.  50 million species is between 2^25 and 2^26.  So producing that number of species in 3 billion years would require any lineage to speciate on the order of once per 120 million years.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Remember, as per comments above, that evolution works in parallel!&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Another point to remember is that most of the species existing today are insects or microorganisms.  Would we even notice the development of say a new species of beetle, if it happened in the Amazon Basin or New Guinea highlands?&lt;/p&gt;&#xA;" OwnerUserId="11736" LastEditorUserId="11736" LastEditDate="2015-07-30T19:18:49.850" LastActivityDate="2015-07-30T19:18:49.850" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36501" PostTypeId="1" AcceptedAnswerId="36920" CreationDate="2015-07-30T18:50:24.173" Score="7" ViewCount="170" Body="&lt;p&gt;I am reading &lt;a href=&quot;http://journals.cambridge.org/action/displayAbstract?fromPage=online&amp;amp;aid=3317&amp;amp;fileId=S0016672397002954&quot; rel=&quot;nofollow noreferrer&quot;&gt;Charlesworth et al. 1997&lt;/a&gt;. They talk about diversity within and between allelic classes.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Nucleotide diversities (&lt;span class=&quot;math-container&quot;&gt;$π$&lt;/span&gt;) at each neutral site were estimated from the mean of &lt;span class=&quot;math-container&quot;&gt;$2 \sum z_t (1-z_t)$&lt;/span&gt;, over replicated introductions at the site of single variants, where zt is the frequency of the neutral variant at time t, and summation is over all times until either fixation or loss occurs.&lt;/p&gt;&#xA;&lt;p&gt;The total genetic diversity at the neutral sites (&lt;span class=&quot;math-container&quot;&gt;$π_T$&lt;/span&gt;) was also decomposed into that within and between allelic classes at the polymorphic locus. Diversity within allelic classes, which will be written here as &lt;span class=&quot;math-container&quot;&gt;$π_A$&lt;/span&gt;, was estimated from the mean of &lt;span class=&quot;math-container&quot;&gt;$2 \sum \left( x_t(1-x_t)+y_t)(1-y_t) \right)$&lt;/span&gt; where &lt;span class=&quot;math-container&quot;&gt;$x_t$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$y_t$&lt;/span&gt; are the frequencies of the neutral variant within the first and second allelic classes, respectively. Diversity between allelic classes with respect to the polymorphic locus was calculated as the difference between the total diversity values and &lt;span class=&quot;math-container&quot;&gt;$π_A$&lt;/span&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;Note that the parentheses don't match up but this this is what is written in the paper!&lt;/em&gt;&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Why am I confused about this text?&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;I am confused about the term allelic class. I first think there is anything fancy in here and I think we can simply replace the term &amp;quot;allelic class&amp;quot; by &amp;quot;allele&amp;quot;. but then when I saw the equation for &lt;span class=&quot;math-container&quot;&gt;$\pi_A$&lt;/span&gt; I realize that the frequency of the two allelic classes does not necessarily adds to 1 (even though we consider only two allelic classes).&lt;/p&gt;&#xA;&lt;p&gt;I also got also a little confused about the difference between &lt;span class=&quot;math-container&quot;&gt;$\pi$&lt;/span&gt; and &lt;span class=&quot;math-container&quot;&gt;$\pi_T$&lt;/span&gt; but I think that they just used two notations for the same think (&lt;span class=&quot;math-container&quot;&gt;$\pi = \pi_T$&lt;/span&gt;)&lt;/p&gt;&#xA;&lt;p&gt;In population genetics's jargon, diversity just mean expected heterozygosity. &lt;span class=&quot;math-container&quot;&gt;$\pi_T$&lt;/span&gt; makes sense to me. It is just the average heterozygosity &lt;span class=&quot;math-container&quot;&gt;$\left(2 z(1-z)\right)$&lt;/span&gt; calculated over all time steps. Maybe a more intuitive to put it would to integrate rather than summing over time rather than time steps.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;Question&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;I can read the equation for &lt;span class=&quot;math-container&quot;&gt;$\pi_A$&lt;/span&gt; but I fail to get any intuition behind what it means. For example, I have no idea why it should be called within-allelic class diversity. Where does &lt;span class=&quot;math-container&quot;&gt;$2(x(1-x)+y)(1-y)$&lt;/span&gt; come from? My whole issue might boil down to the definition of &lt;em&gt;allelic class&lt;/em&gt;.&lt;/p&gt;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;p&gt;The term &lt;code&gt;allelic class&lt;/code&gt; is defined in &lt;a href=&quot;http://journals.cambridge.org/action/displayAbstract?fromPage=online&amp;amp;aid=3317&amp;amp;fileId=S0016672397002954&quot; rel=&quot;nofollow noreferrer&quot;&gt;Innan and Tajima (1997)&lt;/a&gt;&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Suppose that there are two nucleotides, say A and T, in a particular site. Then, we can divide DNA sequences into two classes: one class includes sequences with A and the other includes sequences with T in this site. We call such a class an allelic class&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;(&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/8722806&quot; rel=&quot;nofollow noreferrer&quot;&gt;Slatkin 1996&lt;/a&gt; might help as well).&lt;/p&gt;&#xA;&lt;p&gt;I am still not quite sure what the &lt;code&gt;within allelic class variance&lt;/code&gt;. Maybe it is: Take the most common sequence in the considered allelic class. For each, sequence, calculate the number of pairwise differences to the most common sequence and square this value. Sum over all sequence and divide by the number of sequences. In math form it would be: &lt;span class=&quot;math-container&quot;&gt;$\frac{1}{2N}\sum_i^{2N} (D_i)^2$&lt;/span&gt;, where &lt;span class=&quot;math-container&quot;&gt;$N$&lt;/span&gt; is the population size and &lt;span class=&quot;math-container&quot;&gt;$D_i$&lt;/span&gt; is the number of pairwise difference between the sequence &lt;span class=&quot;math-container&quot;&gt;$i$&lt;/span&gt; and the most common sequence in the considered allelic class. Does it sound right to you?&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-08-17T22:28:16.173" Title="Within and Between Allelic Class Diversity" Tags="&lt;evolution&gt;&lt;genetics&gt;&lt;theoretical-biology&gt;&lt;population-genetics&gt;&lt;population-biology&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36502" PostTypeId="2" ParentId="36478" CreationDate="2015-07-30T21:31:24.000" Score="5" Body="&lt;p&gt;In my experience, half an hour at room temperature will make absolutely no difference.  Boehringer Mannheim (now &lt;a href=&quot;http://www.nytimes.com/1997/05/27/business/roche-plans-an-11-billion-acquisition.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;part of Roche&lt;/a&gt;), who at one time supplied the best NADPH, used to recommend storage at 4&lt;sup&gt;o&lt;/sup&gt; C. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;By A&lt;sub&gt;340&lt;/sub&gt; callibration, NAD(P)H is typically about 85% 'pure' based on dry weight measurements, and Sigma will try to tell you that the remainder is mainly water.  That is, if you calculate a concentration based on the dry weight, the A&lt;sub&gt;340&lt;/sub&gt; will be about 85% what you expect.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Even if some water is absorbed from the atmosphere, this will make little difference as you are probably going to calculate the concentration based on&#xA;the A&lt;sub&gt;340&lt;/sub&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As &lt;a href=&quot;https://biology.stackexchange.com/users/15878/243&quot;&gt;User 243&lt;/a&gt; has &lt;a href=&quot;https://biology.stackexchange.com/a/36483/1136&quot;&gt;pointed out&lt;/a&gt;, if you are concerned that the NAD(P)H is degraded or oxidized, then an A&lt;sub&gt;340&lt;/sub&gt; &#xA;measurement will probably set things right.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If you are concerned that all the A&lt;sub&gt;340&lt;/sub&gt;  absorbing material is not NAD(P)H, or that a significant proportion is in the &amp;alpha;-form (Oppenheimer &amp;amp; Kaplan, 1975) or is otherwise enzymically inactive, the best thing is an enzymic calibration. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is done by adding limiting amounts of NAD(P)H to an assay system containing excess substrate and calibrating enzyme, and measuring the total decrease in absorbance (Racker, 1957).  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;A popular calibrating enzyme for NADH is aldehyde dehydrogenase (&lt;a href=&quot;http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/2/1/3.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;EC 1.2.1.3&lt;/a&gt;), as the reaction is practically irreversible, and it makes it easy to 'drive' the calibrating reaction to completing (and you don't have to worry about equilibria). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As I said in a previous post, NAD(P)H is UNSTABLE IN ACID (Oppenheimer and Kaplan, 1974). To put it crudely, 'the head (nicotinamide moiety) falls off', causing a bleaching of the absorbance at 340nm.  Making 100mM acetate, pH 5, 100 micromolar in NAD(P)H produces a very significant decrease in A&lt;sub&gt;340&lt;/sub&gt; absorbance with time (which may be very easily monitored in a spectrophotometer). &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Just because all the A&lt;sub&gt;340&lt;/sub&gt; material is due to NAD(P)H, this does not necessarily mean that the commercial preparation is pure.  In fact, far from it.  Dalziel (1963) showed that commercial preparations of NADH then available contained a competitive inhibitor of many dehydrogenases, most probably adenosine diphosphate ribose. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Accepting Dalziel's value of 17 600 M&lt;sup&gt;-1&lt;/sup&gt;cm&lt;sup&gt;-1&lt;/sup&gt; for the extinction coefficient for NADH at 260nm, and assuming that NADPH has an identical value, then highly purified samples of NAD(P)H should have an A&lt;sub&gt;260&lt;/sub&gt;/A&lt;sub&gt;340&lt;/sub&gt; ratio of about 2.83, and values &lt;strong&gt;higher&lt;/strong&gt; than this may indicate the presence of impurities that absorb at 260nm, but not at 340nm. ADP-ribose is a prime example, but NAD(P)&lt;sup&gt;+&lt;/sup&gt; is another possibility.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I notice that in one of the &lt;a href=&quot;https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Product_Information_Sheet/2/n7505pis.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;links&lt;/a&gt; given by &lt;a href=&quot;https://biology.stackexchange.com/users/9943/aliced&quot;&gt;AliceD&lt;/a&gt;, Sigma quote a A&lt;sub&gt;260&lt;/sub&gt;/A&lt;sub&gt;340&lt;/sub&gt; ratio of 2.32. So is the higher value due to the presence of residual NAD(P)&lt;sup&gt;+&lt;/sup&gt;, or something else (a breakdown product?), or both? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You may need to use chromatography, typically on an anion-exchange resin, to obtain NAD(P)H free of impurities. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Dalziel, K. (1963). The purification of nicotinamide adenine dinucleotide and the kinetic effects of nucleotide impurities.  J. Biol. Chem. 238, 1538 - 1543.  [&lt;a href=&quot;http://www.jbc.org/content/238/4/1538.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oppenheimer, N. J. &amp;amp; Kaplan, N. O. (1974). Structure of the primary acid rearrangement product of reduced nicotinamide adenine dinucleotide (NADH). Biochemistry 13, 4675 - 4685.[&lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/?term=Structure+of+the+primary+acid+rearrangement+product+of+reduced+nicotinamide+adenine+dinucleotide+%28NADH%29&quot; rel=&quot;nofollow noreferrer&quot;&gt;pubmed&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Oppenheimer, N. J. &amp;amp; Kaplan, N. O. (1975). The alpha, beta-epimerization of reduced nicotinamide adenine dinucleotide.  Arch. Biochem. Biophys.166,  526 - 535. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Racker, E. (1949). Aldehyde dehydrogenase, a diphosphopyridine nucleotide-linked enzyme.  J. Biol. Chem. 177, 883 - 892. [&lt;a href=&quot;http://www.jbc.org/content/177/2/883.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Racker, E. (1957). Spectrophotometric enzymatic methods for the determination of aldehydes and ketoaldehydes.  Methods Enzymol. III, 293 - 296. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Other References&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ciotti, M. M. &amp;amp; Kaplan, N. O. (1957). Procedures for determination of pyridine nucleotides.  Methods Enzymol. III, 890 - 899&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Horecker, B. L. &amp;amp; Kornberg, A. (1948). The extinction coefficients of the reduced band of pyridine nucleotides.  J. Biol. Chem. 175, 385 - 390. [The definitive determination of the extinction coefficient at 340nm] [&lt;a href=&quot;http://www.jbc.org/content/175/1/385.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Kornberg, A. &amp;amp; Pricer, W. E. (1950). On the structure of triphosphopyridine nucleotide.  J. Biol. Chem. 186, 557 - 567. &#xA;[This paper shows that the 'extra' phosphate in NADP(H) is attached to the  2' position of a ribose.  In Coenzyme A, of course, the phosphate attached to the ribose is on the 3' position. [&lt;a href=&quot;http://www.jbc.org/content/186/2/557.full.pdf+html&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Pullman, M. E., San Pietro, A. &amp;amp; Colowick, S. P. (1954). On the structure of reduced diphosphopyridine nucleotide.  J. Biol. Chem. 206, 129 - 141 [&lt;a href=&quot;http://www.jbc.org/content/206/1/129.long&quot; rel=&quot;nofollow noreferrer&quot;&gt;pdf&lt;/a&gt;]&lt;/p&gt;&#xA;" OwnerUserId="1136" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-08-06T12:36:16.263" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36503" PostTypeId="1" CreationDate="2015-07-30T22:26:39.363" Score="1" ViewCount="35" Body="&lt;p&gt;I'm trying to source a procedure for a transplanting tissue in regenerating polyps. Would anyone happen to know where I can find a method of adhering to donor to host tissue? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks&lt;/p&gt;&#xA;" OwnerUserId="17049" LastActivityDate="2015-07-30T22:26:39.363" Title="Tissue grafting in marine invertebrates" Tags="&lt;development&gt;&lt;transplantation&gt;" AnswerCount="0" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36504" PostTypeId="2" ParentId="36493" CreationDate="2015-07-31T00:24:00.210" Score="5" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;Tar deposition is the cause of the yellow cigarette stains.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Both &lt;a href=&quot;http://quitsmoking.about.com/od/chemicalsinsmoke/a/tar_in_cigs.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;tar&lt;/a&gt; and &lt;a href=&quot;http://www.nlm.nih.gov/medlineplus/ency/article/000953.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;nicotine&lt;/a&gt; cause yellow to brown staining. Although nicotine itself is colorless/white, it turns &lt;a href=&quot;http://bmjopen.bmj.com/content/3/11/e003304.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;yellow upon exposure to air&lt;/a&gt;.   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In a study on cigarette stains, the author speaks of tobacco-tar stains, implicitly acknowledging it is tar and not nicotine &lt;a href=&quot;http://bmjopen.bmj.com/content/3/11/e003304.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;(John et al., 2013)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Interestingly, &lt;a href=&quot;http://www.volcanoecigs.com/blog/entertainment/does-the-nicotine-in-ecigs-turn-your-teeth-yellow.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;e-cigarettes&lt;/a&gt; which contain nicotine, but no tar, are reported to &lt;a href=&quot;http://www.jeffersondentalclinics.com/blog/2014/05/15/e-cigarette-dental-health-risks/&quot; rel=&quot;nofollow noreferrer&quot;&gt;leave no stains&lt;/a&gt;, pointing to &lt;strong&gt;tar&lt;/strong&gt; as the culprit, and not nicotine. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;As to physiological causes of the stains I can say it is simply a tar stain and it has nothing to do with pigment or anoxic conditions, because the teeth and nails also stain yellow:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/qjRIv.gif&quot; alt=&quot;enter image description here&quot;&gt;&lt;br&gt;&#xA;&lt;sup&gt;Tar stains on skin and nails. Source: &lt;a href=&quot;http://bmjopen.bmj.com/content/3/11/e003304.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;John &lt;em&gt;et al&lt;/em&gt;., 2013&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/ej4p9.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/ej4p9.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sup&gt;Tar staining of the teeth. Source: &lt;a href=&quot;http://www.identalhub.com/article_stained-and-discoloured-teeth-4.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;Identalhub&lt;/a&gt;.&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://bmjopen.bmj.com/content/3/11/e003304.abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;John &lt;em&gt;et al&lt;/em&gt;., &lt;em&gt;BMJ Open&lt;/em&gt; (2013); &lt;strong&gt;3&lt;/strong&gt;:e003304&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-08-05T10:31:40.263" LastActivityDate="2015-08-05T10:31:40.263" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="36505" PostTypeId="1" CreationDate="2015-07-31T03:30:17.407" Score="2" ViewCount="159" Body="&lt;p&gt;I notice on dbSNP rs6352 has an ancestral allele of G - &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs6352&quot; rel=&quot;nofollow&quot;&gt;http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs6352&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The hapmap in humans for this allele is very rare, the homozygous version practically not existing at all &lt;a href=&quot;http://hapmap.ncbi.nlm.nih.gov/cgi-perl/snp_details_phase3?name=rs6352&amp;amp;source=hapmap3r3_B36&amp;amp;tmpl=snp_details_phase3&quot; rel=&quot;nofollow&quot;&gt;http://hapmap.ncbi.nlm.nih.gov/cgi-perl/snp_details_phase3?name=rs6352&amp;amp;source=hapmap3r3_B36&amp;amp;tmpl=snp_details_phase3&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My understanding has been that the ancestral allele refers to the common gene that an ancestor in all humans once shared. Now, I thought the ancestral allele was usually the most frequent in a population, but I can see this was most likely a wrong assumption.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Was it a wrong assumption, or was this example above just a rare exception? Is deviation from ancestral alleles nearly worthless as a metric to investigate possible mutated alleles that may be leading to disease? I realize the proper answer may be too long, but just a brief summary would be appreciated. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Many thanks.&lt;/p&gt;&#xA;" OwnerUserId="15295" LastActivityDate="2017-02-22T22:40:54.667" Title="Ancestral Allele and Hapmap" Tags="&lt;genetics&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36509" PostTypeId="1" CreationDate="2015-07-31T08:34:53.207" Score="0" ViewCount="30" Body="&lt;p&gt;When performing an experiment to report gain of body mass in an experiment, do any of you know of a paper whose authors have used a bootstrap to improve their confidence intervals?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I have a n = 10 per group for a total of 6 groups, measuring whole body mass on a weekly basis in small animal models of a disease. Experimental design is essentially treatment by the use of a drug, over a period of ten weeks, and analysis of the final gain of body weight&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(essentially think of a google search term as bootstrap, body mass, mouse)&lt;/p&gt;&#xA;" OwnerUserId="8105" LastEditorUserId="8105" LastEditDate="2015-07-31T09:38:50.993" LastActivityDate="2015-07-31T09:38:50.993" Title="Does anyone use bootstrapping to report mass gain during experiment?" Tags="&lt;statistics&gt;" AnswerCount="0" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="36514" PostTypeId="2" ParentId="36448" CreationDate="2015-07-31T13:44:55.487" Score="1" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;The textbooks are right; the receptor part of sensory neurons is always considered to be the dendrite. Axons are nonetheless an integral part of some receptor types to send the signal to the brain. Other, more specialized sensory cells do not have an axon and therefore rely on secondary neurons to send the signal to the brain. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;There are three types of sensory cells, namely those with &lt;em&gt;free nerve endings&lt;/em&gt;, those with &lt;em&gt;specialized dendritic structures&lt;/em&gt;, and &lt;em&gt;specialized receptor cells that synapse directly onto a secondary neuron&lt;/em&gt; (Fig. 1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/05mtG.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/05mtG.png&quot; alt=&quot;sensory neurons&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Types of sensory neurons. Source: &lt;a href=&quot;https://www.premedhq.com/sensory-receptors&quot; rel=&quot;nofollow noreferrer&quot;&gt;Premed HQ&lt;/a&gt;.&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Sensory neurons with free nerve endings have an exposed dendrite that functions as receptor. Examples are &lt;a href=&quot;http://www.pnas.org/content/108/Supplement_3/15596/F1.expansion.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;nociceptors&lt;/a&gt; (pain receptors) and &lt;a href=&quot;http://fog.ccsf.cc.ca.us/~mmalacho/anatomy/Skin/Sensors.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;hair follicle receptors&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;Other sensory neurons are complex cells that feature a dendritic region specialized for a particular receptor function. Examples are the &lt;a href=&quot;http://humanphysiology.tuars.com/program/section1/1ch5/s1ch5_4.htm&quot; rel=&quot;nofollow noreferrer&quot;&gt;Pacinian corpuscle&lt;/a&gt; and &lt;a href=&quot;http://www.nature.com/neuro/journal/v2/n2/fig_tab/nn0299_106_F1.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;olfactory neurons&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;The most common receptor type are specialized receptor neurons that have no axon and need a secondary sensory neuron to send the signal to the brain. Examples are the &lt;a href=&quot;https://www.google.com.au/search?q=photoreceptors&amp;amp;es_sm=93&amp;amp;source=lnms&amp;amp;tbm=isch&amp;amp;sa=X&amp;amp;ved=0CAcQ_AUoAWoVChMI1r_Iq76FxwIVxiWmCh1MLQuQ&amp;amp;biw=1129&amp;amp;bih=566#imgrc=hp3Vn3YyU8V39M%3A&quot; rel=&quot;nofollow noreferrer&quot;&gt;photoreceptor cells&lt;/a&gt; in the retina, the &lt;a href=&quot;http://what-when-how.com/neuroscience/auditory-and-vestibular-systems-sensory-system-part-1/&quot; rel=&quot;nofollow noreferrer&quot;&gt;hair cells&lt;/a&gt; in the cochlea and &lt;a href=&quot;https://biology.stackexchange.com/questions/24349/why-merkel-cells-are-innervated-by-axon-and-not-by-dendrite-end&quot;&gt;Merkel cells&lt;/a&gt;.  &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.080" LastActivityDate="2015-07-31T13:57:29.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36515" PostTypeId="2" ParentId="24349" CreationDate="2015-07-31T14:05:56.213" Score="2" Body="&lt;p&gt;There is nothing out of the ordinary with the Merkel cell, as it functions in the same way as photoreceptors and hair cells (see Further Reading #1).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/OKdJ0.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/OKdJ0.jpg&quot; alt=&quot;Merkel cell&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Merkel cell. Source: &lt;a href=&quot;https://www.google.com.au/url?sa=i&amp;amp;rct=j&amp;amp;q=&amp;amp;esrc=s&amp;amp;source=images&amp;amp;cd=&amp;amp;cad=rja&amp;amp;uact=8&amp;amp;ved=0CAUQjhxqFQoTCJ3JqrTEhccCFeUupgodFkcA1A&amp;amp;url=http%3A%2F%2Fgallery4share.com%2Fm%2Fmerkel-cell.html&amp;amp;ei=C4C7Vd2XC-XdmAWWjoGgDQ&amp;amp;bvm=bv.99261572,d.dGY&amp;amp;psig=AFQjCNGhvVkOupwpdg_7RoZCOiK5IvD10A&amp;amp;ust=1438437766767917&quot; rel=&quot;nofollow noreferrer&quot;&gt;Gallery for Share&lt;/a&gt;.&lt;/sup&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The Merkel cell depicted in Fig. 1 is a specialized receptor neuron. It has no axon. It relies on a &lt;em&gt;secondary sensory neuron&lt;/em&gt; (a somatosensory afferent) onto which it synapses to direct the touch signal to the brain.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that neural information flow goes from dendrite to axon. An axon terminates into a synapse. The Merkel cell, which does not have an axon, features a synapse directly onto the dendrite of the secondary neuron (See Further Reading #2).   &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;Further Readings&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;1.&lt;/strong&gt; &lt;a href=&quot;https://biology.stackexchange.com/questions/36448/can-axons-act-as-receptors&quot;&gt;Can axons act as receptors?&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;2.&lt;/strong&gt; &lt;a href=&quot;https://biology.stackexchange.com/questions/9026/what-are-the-functions-and-differences-between-axons-and-dendrites&quot;&gt;What are the functions and differences between axons and dendrites?&lt;/a&gt;&lt;/sup&gt;.&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-07-31T14:16:47.317" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36516" PostTypeId="1" CreationDate="2015-07-31T14:28:03.733" Score="4" ViewCount="58" Body="&lt;p&gt;What is the Methow Valley (esp. Winthrop, WA) area's susceptibility to bark beetles?  Did the 2014 Carlton Complex wildfires increase the vulnerability due to the large numbers of dead, dying, and stressed pine and fir species in the area.  Are there ways I can reduce the vulnerability of my property, which is already in open, park-like stands? &lt;/p&gt;&#xA;" OwnerUserId="17060" LastActivityDate="2019-08-24T00:03:40.487" Title="Will bark-beetles infest the Methow Valley?" Tags="&lt;ecology&gt;&lt;landscape-ecology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36517" PostTypeId="1" CreationDate="2015-07-31T14:40:18.497" Score="1" ViewCount="1878" Body="&lt;p&gt;I have several .ab1 files generated from Chromas. I want to merge all of them into a single FASTA sequence file. How can I do this in an automated way?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that I don't have Chromas installed (the files were generated by someone else). I am using linux, so open-source, command line tools are preferred.&lt;/p&gt;&#xA;" OwnerUserId="561" LastActivityDate="2019-03-09T11:06:10.677" Title="Merge several .ab1 sequence files into a single FASTA file?" Tags="&lt;bioinformatics&gt;" AnswerCount="3" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36518" PostTypeId="2" ParentId="36213" CreationDate="2015-07-31T14:44:09.037" Score="2" Body="&lt;p&gt;The definition of numbness has been answered by yourself, and I will focus on the second part of the question.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In terms of the underlying physiological mechanism behind numbness I think it's good to narrow the question down and focus on &lt;strong&gt;local anesthetics&lt;/strong&gt;, which numb a local area of the body for minor surgical procedures. Cocaine and related compounds have been shown to block not only pain, but also warmth, cold and touch perception, as well as blocking motor function. Cocain and related compounds are basically voltage-gated Na&lt;sup&gt;+&lt;/sup&gt; channel blockers, but also block K&lt;sup&gt;+&lt;/sup&gt; channels to some extent. Their affinity to various different channels differs, explaining the differential effects. E.g., pain is blocked more effectively than motor functions &lt;a href=&quot;http://bja.oxfordjournals.org/content/89/1/52.full&quot; rel=&quot;nofollow&quot;&gt;(Scholz, 2002)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We all know the feeling of numbness when our limbs are asleep due to restriction of blood flow. Likely all neural activity is blocked here too, as the cutting off of oxygen affects all neurons.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given the broad range of effects of local anesthetics and restriction of blood flow, I would tentatively conclude that numbness can be interpreted as a &lt;em&gt;reduction of sensitivity of all the senses&lt;/em&gt;.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;Reference&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://bja.oxfordjournals.org/content/89/1/52.full&quot; rel=&quot;nofollow&quot;&gt;Scholz, &lt;em&gt;Br J Anaesth&lt;/em&gt; (2002); &lt;strong&gt;89&lt;/strong&gt;; 52-61&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-07-31T14:54:04.360" LastActivityDate="2015-07-31T14:54:04.360" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36519" PostTypeId="2" ParentId="36517" CreationDate="2015-07-31T17:07:04.797" Score="1" Body="&lt;p&gt;DNA Baser has a batch abi to fasta converter &lt;a href=&quot;http://www.dnabaser.com/download/Abi-to-Fasta-converter/abi-to-fasta-converter.html&quot; rel=&quot;nofollow&quot;&gt;here&lt;/a&gt;. After files have been converted to .fa files, they can be concatenated together in UNIX/MAC using &lt;code&gt;cat *fa &amp;gt; output.fa&lt;/code&gt;&lt;/p&gt;&#xA;" OwnerUserId="14587" LastActivityDate="2015-07-31T17:07:04.797" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36522" PostTypeId="1" AcceptedAnswerId="36523" CreationDate="2015-07-31T19:28:47.400" Score="5" ViewCount="471" Body="&lt;p&gt;I would like to know how many days or years do the bacteria live approximately.    &lt;/p&gt;&#xA;" OwnerUserId="17053" LastEditorUserId="3340" LastEditDate="2015-08-01T09:06:33.437" LastActivityDate="2015-08-01T09:27:04.063" Title="Approximately how long do bacteria live for?" Tags="&lt;bacteriology&gt;" AnswerCount="1" CommentCount="8" ClosedDate="2015-08-01T09:07:07.743" ContentLicense="CC BY-SA 3.0" />
  <row Id="36523" PostTypeId="2" ParentId="36522" CreationDate="2015-07-31T19:53:30.957" Score="15" Body="&lt;p&gt;They're effectively immortal, albeit in a Phoenix-rising-from-the-ashes sort of way.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In general, a bacterial cell will divide as soon as it's biochemically able to do so, leaving behind two daughter cells. Neither daughter cell is actually the same as the mother cell, so in one sense the mother cell will have &quot;died&quot;. On the other hand, the daughter cells are genetically identical to the mother cell and all of the physical material present in each of the daughter cells at the moment right after they split came from the mother cell.&lt;/p&gt;&#xA;" OwnerUserId="784" LastEditorDisplayName="user1629" LastEditDate="2015-08-01T09:27:04.063" LastActivityDate="2015-08-01T09:27:04.063" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36524" PostTypeId="1" CreationDate="2015-07-31T19:53:55.797" Score="2" ViewCount="369" Body="&lt;p&gt;This infographic claims that the sugar content in a can of Coca Cola would cause vomiting if not for the phosphoric acid. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/rSMmfm.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/rSMmfm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;In The First 10 minutes: 10 teaspoons of sugar hit your system. (100% of your recommended daily intake.) You don’t immediately vomit from the overwhelming sweetness because phosphoric acid cuts the flavor allowing you to keep it down.&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Now this question came up on &lt;a href=&quot;https://skeptics.stackexchange.com/questions/28612/is-this-description-of-the-processes-which-take-place-in-the-body-for-an-hour-af&quot;&gt;skeptics.SE&lt;/a&gt; and the remaining question is whether (flavourless) water with sugar would cause vomiting. Very specifically we're talking about 200ml of final concentration and 39 grams of sugar. I would try it out myself, but per the rules of skeptics.SE I am not allowed to do this so I am posting it as a question here.&lt;/p&gt;&#xA;" OwnerUserId="8039" LastEditorUserId="-1" LastEditDate="2017-04-13T12:46:43.517" LastActivityDate="2017-07-03T04:05:23.637" Title="Will a 0.2g/mL sugar concentration cause vomiting in humans?" Tags="&lt;human-biology&gt;&lt;digestive-system&gt;&lt;human-physiology&gt;" AnswerCount="1" CommentCount="4" ClosedDate="2017-07-05T21:44:21.380" ContentLicense="CC BY-SA 3.0" />
  <row Id="36525" PostTypeId="1" CreationDate="2015-07-31T20:09:20.063" Score="1" ViewCount="63" Body="&lt;p&gt;In this documentary about a lioness and a leopard the leopard is in heat for months.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://www.youtube.com/watch?v=MGqmylkOuKw&quot; rel=&quot;nofollow&quot;&gt;https://www.youtube.com/watch?v=MGqmylkOuKw&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Usually a big cat would be in heat for 5 days and then not in heat for 27 more days. Doesn't matter if it is a lion, tiger, cheetah, jaguar, or leopard, they have a very similar estrus cycle.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why then is this leopard in heat for months until she finally becomes pregnant? The lioness is only in heat for 2 days because after 48 hours she becomes pregnant. In fact the lioness has 2 litters in the same period of time as the leopard has 1 litter.&lt;/p&gt;&#xA;" OwnerUserId="5851" LastActivityDate="2015-07-31T20:17:25.743" Title="Big cat in heat for months?" Tags="&lt;reproduction&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36528" PostTypeId="1" AcceptedAnswerId="36533" CreationDate="2015-07-31T21:45:23.837" Score="1" ViewCount="1775" Body="&lt;p&gt;I'm trying to empirically calculate the approx &lt;strong&gt;final&lt;/strong&gt; magnification (mag) of digital images rendered through our confocal microscope. Using a micrometer and the microscopy equipment I have, the following is known: &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Objective mag = 63x&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ocular mag =10x&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diameter of field of view when viewing specimen through &lt;strong&gt;occular&lt;/strong&gt; = 320µm&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Diameter of field of view when live viewing specimen on the &lt;strong&gt;screen&lt;/strong&gt; = 100µm&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the final mag of the rendered image on the &lt;strong&gt;screen&lt;/strong&gt;?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is not a homework question. The manufacturers specification for the degree of magnification that the camera and confocal  (and obviously there is some) provide is unknown.&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2015-08-01T13:56:34.130" LastActivityDate="2015-08-01T14:16:57.600" Title="Calculation of final magnification when using a CCD camera" Tags="&lt;microscopy&gt;&lt;fluorescent-microscopy&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="36530" PostTypeId="1" CreationDate="2015-07-31T23:13:46.567" Score="4" ViewCount="95" Body="&lt;p&gt;what is the reason people die naturally even though they have no known disease?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I see people become physically weak at times they get old and die eventually in case they are not attacked by any known disease. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is what reasons leads human to death? &lt;/p&gt;&#xA;" OwnerUserId="17063" OwnerDisplayName="mostafiz" LastEditorUserId="3952" LastEditDate="2015-08-01T01:25:40.590" LastActivityDate="2015-08-01T01:25:40.590" Title="Why do people die?" Tags="&lt;human-biology&gt;&lt;senescence&gt;&lt;life-history&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2015-08-01T08:45:57.093" ContentLicense="CC BY-SA 3.0" />
  <row Id="36531" PostTypeId="2" ParentId="36394" CreationDate="2015-08-01T01:02:16.483" Score="3" Body="&lt;blockquote&gt;&#xA;&lt;p&gt;This study has received next to no media coverage. With RFR impacting so many people it makes me wonder, is this study valid?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Well first of all, lets be clear: that is not a study.  Its a review article, basically a paper that summarizes a series of studies published.  The review itself isn't valid or invalid necessarily, it simply takes a series of papers (which may or may not be correct or relevant) and then summarizes them.&lt;/p&gt;&#xA;&lt;p&gt;As for validity, that is a summary of a lot of obscure papers on mechanisms by which RF fields could interact with cells, rats or in a few cases plants.  Its hard to say if the conclusions are valid, but selecting a few papers at random, they are mostly very obscure journals and many report very specialized measurements that are far removed from demonstrating carcinogenic effects in humans.  Its difficult to draw conclusions that are relevant to human health from that, although it does seem plausible that low frequency fields could have a measureable effect on cells or even rats.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Are low-intensity radio-waves carcinogenic?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Assuming you mean in people, that is a hard question to answer, and not the right question given a review article that does not address effects in people.  A better place to look may be this review article:&lt;/p&gt;&#xA;&lt;p&gt;&lt;a href=&quot;http://dx.doi.org/10.1016/S1470-2045(11)70147-4&quot; rel=&quot;nofollow noreferrer&quot;&gt;Carcinogenicity of radiofrequency electromagnetic fields&lt;/a&gt;&lt;/p&gt;&#xA;&lt;p&gt;published in The Lancet and addressing evidence of carcinogenicity in humans.  To summarize:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;The Working Group concluded that there is “limited evidence in humans” for the carcinogenicity of RF-EMF, based on positive associations between glioma and acoustic neuroma and exposure to RF-EMF from wireless phones. A few members of the Working Group considered the current evidence in humans “inadequate”. In their opinion there was inconsistency between the two case-control studies and a lack of an exposure-response relationship in the INTERPHONE study results; no increase in rates of glioma or acoustic neuroma was seen in the Danish cohort study,4 and up to now, reported time trends in incidence rates of glioma have not shown a parallel to temporal trends in mobile phone use.&lt;/p&gt;&#xA;&lt;p&gt;The Working Group reviewed more than 40 studies that assessed the carcinogenicity of RF-EMF in rodents, including seven 2-year cancer bioassays. Exposures included 2450 MHz RF-EMF and various RF-EMF that simulated emissions from mobile phones. None of the chronic bioassays showed an increased incidence of any tumour type in tissues or organs of animals exposed to RF-EMF for 2 years. An increased total number of malignant tumours was found in RF-EMF-exposed animals in one of the seven chronic bioassays. Increased cancer incidence in exposed animals was noted in two of 12 studies with tumour-prone animals12 and 13 and in one of 18 studies using initiation-promotion protocols.14 Four of six co-carcinogenesis studies showed increased cancer incidence after exposure to RF-EMF in combination with a known carcinogen; however, the predictive value of this type of study for human cancer is unknown. Overall, the Working Group concluded that there is “limited evidence” in experimental animals for the carcinogenicity of RF-EMF.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;Note that cancers that people theorize to be associated with exposure to nonionizing EM fields tend to be extremely rare, meaning that studying them is very difficult.  This leads to a lot of uncertainty, because one must try to correlate very rare events with environmental effects. Therefore &amp;quot;limited evidence&amp;quot; does not mean &amp;quot;no&amp;quot;, it just means that the effect is hard to measure and may or may not be significant given what we know.&lt;/p&gt;&#xA;" OwnerUserId="9561" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-08-01T01:02:16.483" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36532" PostTypeId="1" AcceptedAnswerId="36594" CreationDate="2015-08-01T01:28:59.907" Score="5" ViewCount="171" Body="&lt;p&gt;The following guys (about an inch long) were seen in the Willamette Valley of Oregon in summer.  When one would fly by a resting one, they'd get into a high-speed little &quot;dogfight&quot;.  What genus might they be (or species, if you know).  Are they in the &quot;skipper&quot; group of butterflies?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/dS3ut.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/dS3ut.jpg&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&#xA;&lt;a href=&quot;https://i.stack.imgur.com/EDJ8F.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/EDJ8F.jpg&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&#xA;&lt;a href=&quot;https://i.stack.imgur.com/H5wO8.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/H5wO8.jpg&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="231" LastActivityDate="2015-08-03T10:47:04.833" Title="What is this butterfly?" Tags="&lt;entomology&gt;&lt;species-identification&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36533" PostTypeId="2" ParentId="36528" CreationDate="2015-08-01T04:51:21.043" Score="1" Body="&lt;p&gt;Assuming that the FOV that is captured by the CCD on the screen is 100µm wide as determined by the micrometer, and you are viewing the 920 pixel wide image on a standard 96 ppi monitor, the zoom would be approximately 2434 times. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;$$\frac{920p}{96p/in}/100µm \approx 2434$$&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Additionally, you should ensure that the minimum resolution on the micrometer is at least twice as large as each pixel on your microscope CCD. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason that the pixel size must be at least 2 times smaller than the minimum resolution present in the image is due to the &lt;a href=&quot;https://en.wikipedia.org/wiki/Nyquist%E2%80%93Shannon_sampling_theorem&quot; rel=&quot;nofollow noreferrer&quot;&gt;Nyquist-Shannon sampling theorem&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This being said, all microscopes (and arguably all measurement devices) should be calibrated against a standard. &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/18638190&quot; rel=&quot;nofollow noreferrer&quot;&gt;This paper&lt;/a&gt; explains the usage of a standard to calibrate confocal microscopes. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/OlLuJ.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/OlLuJ.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A similar technique used to &lt;a href=&quot;https://www.microscopeworld.com/t-calibration.aspx&quot; rel=&quot;nofollow noreferrer&quot;&gt;calibrate normal optical microscopes&lt;/a&gt; using a stage micrometer standard can be used if you do not possess such a standard. First calibrate the normal microscope, then image an identical sample using both microscopes in order to obtain the size of the field of view. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/pXFHb.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/pXFHb.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-08-01T14:16:57.600" LastActivityDate="2015-08-01T14:16:57.600" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36534" PostTypeId="2" ParentId="36496" CreationDate="2015-08-01T05:01:44.573" Score="1" Body="&lt;p&gt;Arguably, since &lt;a href=&quot;http://io9.com/5621249/ultra-tiny-frogs-discovered-living-like-faeries-inside-pitcher-plants/&quot; rel=&quot;nofollow noreferrer&quot;&gt;this frog&lt;/a&gt; spends the entire larval stage inside a pitcher plant on land, it has started its life cycle on land.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/ThRii.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/ThRii.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;A group of zoologists with Conservation International say they found&#xA;  the frogs by the side of the road in Borneo, near a national park.&#xA;  They were very hard to locate because of their small size, but the&#xA;  scientists followed the frog's loud calls (you can listen to some&#xA;  here) and discovered them living among pitcher plants. They lay their&#xA;  eggs on the inside of the pitchers, and tadpoles grow up swimming in&#xA;  the tiny pools of rainwater that collect in the bottom of these&#xA;  plants. While most species of pitcher plant are carnivorous, the ones&#xA;  preferred by these tiny frogs only eat leaves - in fact, the frogs&#xA;  most likely help break down the leaf material and aid in the plant's&#xA;  digestion.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-08-01T05:01:44.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36535" PostTypeId="1" CreationDate="2015-08-01T05:07:40.997" Score="3" ViewCount="749" Body="&lt;p&gt;Say there were 2 creatures of the same species. Creature 1 has a longer genome than creature 2, it may be just a few base pairs, but what would happen when the genes were crossed to create creature 3 (via Sexual Reproduction)? Do the genes know where to match up or are there genes that end up being corrupted during this process?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thanks in advance&lt;/p&gt;&#xA;" OwnerUserId="17064" LastActivityDate="2015-08-01T05:07:40.997" Title="What happens when a genome is shorter than the other?" Tags="&lt;genetics&gt;&lt;dna&gt;&lt;mutations&gt;&lt;genomes&gt;" AnswerCount="0" CommentCount="3" ClosedDate="2015-08-06T02:45:53.953" ContentLicense="CC BY-SA 3.0" />
  <row Id="36536" PostTypeId="2" ParentId="36481" CreationDate="2015-08-01T05:16:50.807" Score="1" Body="&lt;p&gt;The phenomenon you described as &quot;my eyes seem to adjust&quot; is a particular case of accommodation - adjustment of the &lt;a href=&quot;https://en.wikipedia.org/wiki/Dioptric_correction&quot; rel=&quot;nofollow noreferrer&quot;&gt;dioptric power&lt;/a&gt; of the crystalline lens to the object's distance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When you place a lens before your eye, any object seen through this lens will initially appear at a different distance (and of different size of course) and will be blurred at different degrees (i.e out of focus). Thus, to overcome this discrepancy the eye must accommodate. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Now, the amplitude of accommodation is the maximal power which can be added to the current power of the crystalline lens. The younger the subject, the higher amplitude of accommodation he/she has:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/JQUlf.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/JQUlf.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, if one young &lt;a href=&quot;https://en.wikipedia.org/wiki/Emmetropia&quot; rel=&quot;nofollow noreferrer&quot;&gt;emmetropic&lt;/a&gt; person (person 1) wears some other person's &lt;a href=&quot;https://en.wikipedia.org/wiki/Myopia&quot; rel=&quot;nofollow noreferrer&quot;&gt;myopic&lt;/a&gt; glasses (person 2) with a concave lens with minus power to lessen the actual &quot;overpower&quot; of the optic system, and this power does not have the refractive error of person 1's has (less myopia if they have any &quot;hidden&quot; myopia), the eye must accommodate, i.e. by increasing the convexity of the crystalline lens. If the amplitude of accommodation is much higher than the glasses in question, person 1 will easily adjust to these glasses by elimination of dioptric discrepancy.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thus, Sherlock Holmes could deduce the following:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are a young person (under the age of 30) with a high amplitude of accommodation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You have a lot of &quot;four-eyed&quot; friends suffering from myopia. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;From these facts the fiction writer could assume even your nationality (developed country) and level of close work (reading books, using computers) your friends are doing but - let's leave those assumptions to writers! :)&lt;/p&gt;&#xA;" OwnerUserId="5755" LastEditorUserId="2999" LastEditDate="2015-08-05T09:30:24.787" LastActivityDate="2015-08-05T09:30:24.787" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36537" PostTypeId="1" CreationDate="2015-08-01T09:06:08.200" Score="3" ViewCount="914" Body="&lt;p&gt;I ask, because I have a different interpretation of the experiments performed on web-weaving spiders. The famous Robert Pirsig maintains that LSD is somehow helpful to web-weaving spiders, because it makes their web more straight. Pirsig seems to imply, as I remember, that the spider is somehow more attentive to its web while on LSD.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I maintain that it isn't the case and that it is actually the reverse.  The spider is much less attentive, for it needs chaos in its web to catch the fly!  &lt;/p&gt;&#xA;" OwnerUserId="17068" LastEditorUserId="9943" LastEditDate="2015-08-01T13:44:26.703" LastActivityDate="2015-08-02T09:05:34.020" Title="Have webs woven by LSD-intoxicated spiders ever been studied for their efficiency in fly catching?" Tags="&lt;neuroscience&gt;&lt;entomology&gt;&lt;pharmacology&gt;" AnswerCount="1" CommentCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="36538" PostTypeId="2" ParentId="36517" CreationDate="2015-08-01T09:21:49.900" Score="2" Body="&lt;p&gt;In general you should use a &lt;a href=&quot;https://en.wikipedia.org/wiki/Base_calling&quot; rel=&quot;nofollow noreferrer&quot;&gt;base calling&lt;/a&gt; algorithm to generate the sequences from the chromatogram and not directly convert it to fasta (&lt;a href=&quot;http://seqanswers.com/forums/showthread.php?t=3165&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;em&gt;Courtesy: Sven [SEQanswers]&lt;/em&gt; &lt;/a&gt;). As mentioned in the link, &lt;a href=&quot;http://www.phrap.org/consed/consed.html#howToGet&quot; rel=&quot;nofollow noreferrer&quot;&gt;phred&lt;/a&gt; and &lt;a href=&quot;https://sourceforge.net/projects/tracetuner/&quot; rel=&quot;nofollow noreferrer&quot;&gt;TraceTuner&lt;/a&gt; are popular base calling software that can generate a fasta output.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The software mentioned by &lt;em&gt;The Nightman&lt;/em&gt; can be used for converting &lt;code&gt;.ab1&lt;/code&gt; to fasta. You can also try this BioPython module called &lt;a href=&quot;https://github.com/bow/abifpy&quot; rel=&quot;nofollow noreferrer&quot;&gt;abifpy&lt;/a&gt;. You can easily read each &lt;code&gt;.ab1&lt;/code&gt; file, using a python script, and write the sequences in fasta format as a single file.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Combining multiple fasta is quite trivial. You can use &lt;code&gt;cat&lt;/code&gt; as mentioned by others.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2019-03-09T11:06:10.677" LastActivityDate="2019-03-09T11:06:10.677" CommentCount="0" ContentLicense="CC BY-SA 4.0" />
  <row Id="36539" PostTypeId="1" AcceptedAnswerId="36541" CreationDate="2015-08-01T10:25:53.870" Score="3" ViewCount="72" Body="&lt;p&gt;I am currently working on a project which involves growing some plants in a integrating sphere made of foam. I have added temperature, humidity and soil moisture sensors as well as a Spectrometer (350 - 800nm) and a webcam which takes images of the plant every 30 minutes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought of calculating the LAI (Leaf area index) from the webcam images. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have any other suggestions/ideas on what I could calculate with the given data from these sensors?&lt;/p&gt;&#xA;" OwnerUserId="17069" LastEditorUserId="9943" LastEditDate="2015-08-01T14:03:36.457" LastActivityDate="2016-02-28T01:46:33.080" Title="Possible calculations with temperature, humidity, images and VIS spectrum of a plant in an Integrating sphere" Tags="&lt;physiology&gt;&lt;botany&gt;&lt;measurement&gt;" AnswerCount="1" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36540" PostTypeId="2" ParentId="36537" CreationDate="2015-08-01T12:02:05.087" Score="2" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;A low dose of LSD has been shown to lead to larger, more regular webs. This obsessive perfection of the web comes with an increased effort and likely an increased required building time. Whether LSD-affected webs are more effective or not has not been assessed as far as I am aware. Personally I think that, if anything, larger webs are more efficient for their purpose, regardless of their enhanced regularity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;I traced down the experiments with &lt;em&gt;d&lt;/em&gt;-lysergic acid dietheylamide (LSD-25) and web-building spiders to the experiments of [Peter Witt]*&lt;a href=&quot;https://en.wikipedia.org/wiki/Effect_of_psychoactive_drugs_on_animals&quot; rel=&quot;nofollow noreferrer&quot;&gt;1&lt;/a&gt; performed in the 1950's and 60's.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The original article of &lt;a href=&quot;http://link.springer.com/article/10.1007/BF02150560&quot; rel=&quot;nofollow noreferrer&quot;&gt;Witt (1951)&lt;/a&gt;, dealing with the effects of &lt;a href=&quot;http://www.drugs.com/illicit/lsd.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;LSD&lt;/a&gt; on the web building behavior of spiders (&lt;em&gt;Zygiellax nohta&lt;/em&gt;) is not accessible to me. He reiterates on the data in a review &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bs.3830160109/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Witt, 1971)&lt;/a&gt;. In this review he discusses the effect of a low dose of LSD on web building (Fig. 1).&#xA;&lt;br&gt; &#xA;&lt;a href=&quot;https://i.stack.imgur.com/IP6q4.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/IP6q4.png&quot; alt=&quot;&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 1. Web of an untreated spider (&lt;em&gt;Araneus diadematus&lt;/em&gt;) (left) and a web of a spider (&lt;em&gt;Zygiellax nohta&lt;/em&gt;) treated with a low dose of LSD-25. Source: &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bs.3830160109/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Witt, 1971&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Witt concludes that &lt;em&gt;low dosages of LSD &lt;strong&gt;increase the regularity&lt;/strong&gt; of the webs&lt;/em&gt;. Spiders which had received less than 0.05 pg LSD-25 built &lt;strong&gt;larger&lt;/strong&gt; webs, with &lt;strong&gt;fewer oversized angles&lt;/strong&gt; and significantly &lt;strong&gt;more regular central angles&lt;/strong&gt;. The &lt;strong&gt;spiral was unusually regularly spaced&lt;/strong&gt;. He did not investigate the effectiveness of these webs &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bs.3830160109/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Witt, 1971)&lt;/a&gt;. However, I reckon that because of the larger size they may be more effective. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Witt notes that the normal web is far from a perfect geometric structure and that one can think of a web as &lt;em&gt;a compromise between regularity, which serves to cover a wide area with a trap of a certain mesh size, and a quick construction&lt;/em&gt;. For example, &lt;em&gt;Araneus diadematus&lt;/em&gt; makes a new web every morning before sunrise. It requires quite some labor producing and the webs are, arguably, structures of precision and beauty (Fig. 1). The webs take between 20 and 30 minutes to build. &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bs.3830160109/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Witt, 1971)&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;&lt;em&gt;The balance between regularity and quick construction of the web is what may be distorted&lt;/em&gt;&lt;/strong&gt; after relatively low doses of LSD &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bs.3830160109/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;(Witt, 1971)&lt;/a&gt;. The spider seems to put too much and almost compulsory effort in making the perfect web, and likely without too much benefit in efficiency &lt;a href=&quot;http://www.theguardian.com/science/2014/oct/04/spiders-lsd-drugs-experiment-1971&quot; rel=&quot;nofollow noreferrer&quot;&gt;(The Guardian, 1971)&lt;/a&gt;. But again, the author has not addressed this hypothesis directly.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that higher dosages of LSD (&gt;0.05 pg) result in smaller and more irregular webs. &lt;a href=&quot;http://www.theguardian.com/science/2014/oct/04/spiders-lsd-drugs-experiment-1971&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Guardian (1971)&lt;/a&gt; reproduced some figures on this (Fig. 2), showing an example of a grossly distorted and inefficient web.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/6xN7U.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/6xN7U.png&quot; alt=&quot;webs&quot;&gt;&lt;/a&gt;&lt;br&gt;&#xA;&lt;sup&gt;Fig. 2. Web before and after a high dose of LSD. Source: &lt;a href=&quot;http://www.theguardian.com/science/2014/oct/04/spiders-lsd-drugs-experiment-1971&quot; rel=&quot;nofollow noreferrer&quot;&gt;The Guardian (1971)&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://link.springer.com/article/10.1007/BF02150560&quot; rel=&quot;nofollow noreferrer&quot;&gt;Witt, &lt;em&gt;Experientia&lt;/em&gt; (1951); &lt;strong&gt;7&lt;/strong&gt;(8): 310-1&lt;/a&gt;&lt;br&gt;&#xA;&lt;strong&gt;-&lt;/strong&gt; &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1002/bs.3830160109/abstract&quot; rel=&quot;nofollow noreferrer&quot;&gt;Witt, &lt;em&gt;Behav Sci&lt;/em&gt; (1971); &lt;strong&gt;16&lt;/strong&gt;(1): 98-113&lt;/a&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;sup&gt;&lt;strong&gt;Note&lt;/strong&gt;&lt;br&gt;&#xA;*&lt;a href=&quot;https://en.wikipedia.org/wiki/Robert_M._Pirsig&quot; rel=&quot;nofollow noreferrer&quot;&gt;Robert Pirsig&lt;/a&gt; is an American writer and philosopher who has not devoted his time to spiders as far as I know.&lt;/sup&gt; &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="3340" LastEditDate="2015-08-02T09:05:34.020" LastActivityDate="2015-08-02T09:05:34.020" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36541" PostTypeId="2" ParentId="36539" CreationDate="2015-08-01T13:42:59.253" Score="1" Body="&lt;p&gt;With the images you could, perhaps, assess growth rate of the plant which can be plotted against spectral content of light to investigate effects of light quality on growth. Using moist and water and temperature the same can be done. Multivariate analysis can help to implement all the values, while ANCOVA may may help to correct for covariance.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A detailed experimental set up may help to answer this question. Not specifically the hardware, but how the effect of water stress is measured. E.g., are multiple plants tested under different watering conditions? In that case all the other measures (temperature, light) are probably used to check whether everything is constant across all specimens except water availability. This may limit the usefulness of analysis of these additional measures. I think the other parameters (light, water, temperature) may be not so interesting other than covariates for water stress as they are either not controlled or deliberately kept constant. Moreover, probably their effects on plants are pretty obvious too.    &lt;/p&gt;&#xA;" OwnerUserId="9943" LastEditorUserId="9943" LastEditDate="2015-08-01T21:29:44.600" LastActivityDate="2015-08-01T21:29:44.600" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36542" PostTypeId="1" AcceptedAnswerId="36548" CreationDate="2015-08-01T16:31:16.857" Score="6" ViewCount="396" Body="&lt;p&gt;A flower has grown on a &lt;strong&gt;leaf&lt;/strong&gt; in our garden. What is the name of this flower? Give some description.&lt;a href=&quot;https://i.stack.imgur.com/fU9gm.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/fU9gm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt; &lt;/p&gt;&#xA;" OwnerUserId="16927" LastEditorUserId="6703" LastEditDate="2015-08-02T19:29:20.920" LastActivityDate="2015-08-02T19:29:20.920" Title="What is the name of this flower?" Tags="&lt;botany&gt;&lt;species-identification&gt;&lt;flowers&gt;" AnswerCount="1" CommentCount="3" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36544" PostTypeId="2" ParentId="36264" CreationDate="2015-08-01T18:19:13.160" Score="3" Body="&lt;p&gt;The silver-studded blue is frequently found feeding on this plant, cross-leaved heath. There are good numbers of this species to be found on the heaths of Dorset in July and I would suggest that this is certainly silver-studded blue.&lt;/p&gt;&#xA;" OwnerUserId="17073" LastActivityDate="2015-08-01T18:19:13.160" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36546" PostTypeId="1" CreationDate="2015-08-01T22:02:57.390" Score="23" ViewCount="7501" Body="&lt;p&gt;In &lt;a href=&quot;https://www.youtube.com/watch?v=QOCaacO8wus&quot;&gt;the video &quot;What is Life? Is Death Real?&quot;&lt;/a&gt;, the subject of mitochondria is raised at 2:58. At 3:12, the narrator says &quot;[mitochondria] are not alive any more: they are dead.&quot;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What currents of thought lead to this affirmation?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When I search for &lt;a href=&quot;https://www.google.ca/webhp?#q=mitochondria%20are%20dead&quot;&gt;mitochondria are dead&lt;/a&gt; on Google, I get many links about the role of mitochondria in cell death, but I don't see anywhere that the assertion in this video is discussed.&lt;/p&gt;&#xA;" OwnerUserId="16882" LastEditorUserId="16882" LastEditDate="2015-08-01T22:17:54.887" LastActivityDate="2016-03-23T01:47:16.460" Title="Are mitochondria dead?" Tags="&lt;mitochondria&gt;&lt;life&gt;" AnswerCount="4" CommentCount="9" FavoriteCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="36547" PostTypeId="2" ParentId="36546" CreationDate="2015-08-01T22:39:11.003" Score="14" Body="&lt;p&gt;&lt;strong&gt;Short answer:&lt;/strong&gt; According to the &lt;a href=&quot;http://www.biology-online.org/dictionary/Life&quot; rel=&quot;nofollow&quot;&gt;definition of life&lt;/a&gt;, yes, &lt;a href=&quot;http://www.biologyreference.com/Ma-Mo/Mitochondrion.html&quot; rel=&quot;nofollow&quot;&gt;Mitochondria&lt;/a&gt; are &quot;dead&quot;. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;To be considered alive an organism must meet the following criteria:&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;ul&gt;&#xA;  &lt;li&gt;organized structure performing a specific function&lt;/li&gt;&#xA;  &lt;li&gt;an ability to sustain existence, e.g. by nourishment &lt;/li&gt;&#xA;  &lt;li&gt;an ability to respond to stimuli or to its environment &lt;/li&gt;&#xA;  &lt;li&gt;capable of adapting &lt;/li&gt;&#xA;  &lt;li&gt;an ability to germinate or reproduce&lt;/li&gt;&#xA;  &lt;/ul&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Are Mitochondria organised?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, they have a structure that allows them to metabolise energy brought to it by the cell.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can Mitochondria sustain their own existence?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No, many of the genes that mitochondria need to function are no longer in the mitochondria. They need the host cell to provide much of what they need for them.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Note that I am pointing to the Mitochondria's genetics. They used to be included in the Mitochondria itself and have been moved into the cell host DNA. This is why I consider them to be &quot;dead&quot; because they are no longer their own organism, they are an organelle that helps the cell stay alive.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We can stop here since this disqualifies Mitochondria from being considered alive. However, for completion, I will continue.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can Mitochondria respond to stimuli?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, in order for it to divide it receives signalling from the cell. I would consider this a response to its environment.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Can Mitochondria reproduce?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Yes, their reproduction is much like a bacteria reproduces - through a process called &lt;a href=&quot;http://youtu.be/hOyUcjqcGpQ&quot; rel=&quot;nofollow&quot;&gt;fission&lt;/a&gt;. &lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Conclusion:&lt;/strong&gt; Since Mitochondria cannot sustain existence, alone (thanks to no longer holding their full genome) they are dead.&lt;/p&gt;&#xA;" OwnerUserId="16041" LastEditorUserId="22057" LastEditDate="2016-03-23T01:47:16.460" LastActivityDate="2016-03-23T01:47:16.460" CommentCount="17" ContentLicense="CC BY-SA 3.0" />
  <row Id="36548" PostTypeId="2" ParentId="36542" CreationDate="2015-08-01T23:29:37.643" Score="7" Body="&lt;p&gt;It appears to me to be a Night Blooming Cereus:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/qIeKa.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/qIeKa.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We had one in our greenhouse in Botany. It rarely bloomed, and the bloom was wilted by mid-morning.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Night-blooming cereus is the common name referring to &lt;strong&gt;a large number of flowering ceroid cacti that bloom at night&lt;/strong&gt;. The flowers are short lived, and some of these species, such as Selenicereus grandiflorus, bloom only once a year, for a single night. &lt;sub&gt;&lt;sup&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Night-blooming_cereus&quot; rel=&quot;noreferrer&quot;&gt;Wikipedia&lt;/a&gt;&lt;/sub&gt;&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://davesgarden.com/guides/pf/go/2443/&quot; rel=&quot;noreferrer&quot;&gt;Dave's garden&lt;/a&gt; lists it as &quot;Dutchman's Pipe Cactus, Night blooming Cereus&quot;&#xA;&lt;em&gt;Epiphyllum oxypetalum&lt;/em&gt;.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastActivityDate="2015-08-01T23:29:37.643" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36549" PostTypeId="2" ParentId="36524" CreationDate="2015-08-02T00:06:31.440" Score="8" Body="&lt;p&gt;Sugar (be it sucrose, glucose, fructose or honey) does not have &lt;a href=&quot;http://chestofbooks.com/health/materia-medica-drugs/Pharmacology-Therapeutics/Emetics.html#.Vb1aPEXqmto&quot; rel=&quot;noreferrer&quot;&gt;emetic&lt;/a&gt; properties in any concentration, unless there is a personal (and highly individual) psychological adverse reaction to sweet substances.&#xA;&lt;a href=&quot;https://i.stack.imgur.com/i6qse.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/i6qse.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sugar is not a local gastric irritant (like dishwashing detergent, or syrup of ipecac, copper sulphate, zinc sulphate; yellow mercuric sulphate, ammonium carbonate, powdered mustard and other local gastric irritants.) Some non-irritating substances (e.g. cod liver oil) &lt;em&gt;may&lt;/em&gt; induce emesis because of a repugnant smell, taste, or texture. Few people find the taste of sugar repugnant. Gastric distension to the point of emesis does not occur with 12 or 16 oz. of fluid.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Psychological causes of vomiting include aversions (e.g. some people vomit when they see someone else vomit.) That would involve a cerebral cortex mechanism.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;No sugar of any concentration is listed here as an emetic. If it were true, we would have a much less significant incidence of obesity. &lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-08-02T17:39:16.783" LastActivityDate="2015-08-02T17:39:16.783" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36550" PostTypeId="2" ParentId="36546" CreationDate="2015-08-02T00:46:42.370" Score="12" Body="&lt;p&gt;I would like to expand a bit on SolarLunix's post, because the logic used in the conclusion would also mean that endosymbionts, such as &lt;a href=&quot;https://en.wikipedia.org/wiki/Buchnera_(bacterium)&quot;&gt;https://en.wikipedia.org/wiki/Buchnera_(bacterium)&lt;/a&gt;, who cannot survive outside their host are also &quot;dead&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I think many of us disagree with that notion, so instead I would say that it's the fact that so many of their genes have been relocated to the nucleus that makes them organelles and thus substructures of the eukaryotic cell and thus &quot;dead&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Ultimately though, I think it's more a matter of semantics, since you could argue that they represent an advanced stage of endosymbiosis.&lt;/p&gt;&#xA;" OwnerUserId="15385" LastEditorUserId="15385" LastEditDate="2015-08-02T18:02:39.587" LastActivityDate="2015-08-02T18:02:39.587" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36551" PostTypeId="2" ParentId="36546" CreationDate="2015-08-02T01:08:20.600" Score="38" Body="&lt;p&gt;SolarLunix posted &lt;a href=&quot;https://biology.stackexchange.com/a/36547/948&quot;&gt;an excellent answer&lt;/a&gt; detailing the criteria for being classified as &quot;alive&quot;, and showed that by those criteria, mitochondria could be considered as &quot;dead&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, I would argue that the narrator's statement in your video does not make any sense. The currently-accepted theory of the evolution of mitochondria (and possibly other organelles) from free-living &lt;a href=&quot;https://en.wikipedia.org/wiki/Prokaryote&quot; rel=&quot;nofollow noreferrer&quot;&gt;prokaryotes&lt;/a&gt; is called &lt;a href=&quot;https://en.wikipedia.org/wiki/Symbiogenesis&quot; rel=&quot;nofollow noreferrer&quot;&gt;symbiogenesis&lt;/a&gt; and postulates that the mitochondrial progenitors began living symbiotically with the precursors to &lt;a href=&quot;https://en.wikipedia.org/wiki/Eukaryote&quot; rel=&quot;nofollow noreferrer&quot;&gt;eukaryotes&lt;/a&gt; some 1.5 billion years ago. Life originated on Earth about 3.5 billion years ago, so eukaryotic cells (carrying mitochondria) have been around for a little less than half of that time.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In that incredibly large span of time (if you counted 1 number per second, you'd reach 1.5 billion in about 47.5 years), what used to be an independent organism (we assume) has become an organelle - an integral part of the eukaryotic cell. It absolutely could not survive outside the cell on its own, and relies on signals from the cell (mainly, the cell's energy needs as detected by &quot;sensor&quot; proteins to key molecules like glucose and ATP) to reproduce.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Therefore, it is most appropriate to think of mitochondria simply as another organelle, just like the endoplasmic reticulum, lysosomes, or the nucleus. It doesn't make sense to think of those other structures as &quot;alive&quot; or &quot;dead&quot;, just as it doesn't make sense to think of mitochondria in the same way. Yes, they &lt;em&gt;used&lt;/em&gt; to be independent, but are no longer; instead they are a well-integrated part of the whole cell.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.170" LastActivityDate="2015-08-02T18:18:15.440" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36554" PostTypeId="1" AcceptedAnswerId="45934" CreationDate="2015-08-02T05:19:19.610" Score="15" ViewCount="4792" Body="&lt;p&gt;Last year I photographed this juvenile Sally Lightfoot Crab (&lt;em&gt;Grapsus grapsus&lt;/em&gt;) 'spitting' &lt;sub&gt;&lt;sup&gt;(click for larger view)&lt;/sup&gt;&lt;/sub&gt;:&lt;br&gt;&#xA;&lt;a href=&quot;https://i.stack.imgur.com/2VHjg.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/2VHjg.jpg&quot; alt=&quot;Spitting Crab&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I thought I'd look up more information on this behavior, but couldn't find any explanation regarding its actual function. I can imagine a few potential functions this could serve:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Secreting excess salt&amp;mdash;just as Marine Iguanas &lt;a href=&quot;http://www.geo.cornell.edu/geology/GalapagosWWW/MarineIguanas.html&quot; rel=&quot;nofollow noreferrer&quot;&gt;sneeze&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;A means of evaporative cooling&amp;mdash;like the mosquito's behavior &lt;a href=&quot;https://biology.stackexchange.com/a/35365/6703&quot;&gt;described here&lt;/a&gt;.&lt;/li&gt;&#xA;&lt;li&gt;An attempt to eject irritants from the crab's mouthparts.&lt;/li&gt;&#xA;&lt;li&gt;Possibly a means of self-defense.&lt;/li&gt;&#xA;&lt;li&gt;Any combination of the above or something I hadn't even considered.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Has there been any research regarding the biological function of this behavior? On a side note, I'm curious about how widespread this behavior is&amp;mdash;is it only this species or is it nearly all land crabs?&lt;/p&gt;&#xA;" OwnerUserId="6703" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2016-06-09T03:13:57.727" Title="Why do crabs spit?" Tags="&lt;zoology&gt;&lt;behaviour&gt;&lt;invertebrates&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36559" PostTypeId="1" AcceptedAnswerId="36573" CreationDate="2015-08-02T09:01:29.693" Score="1" ViewCount="77" Body="&lt;p&gt;Searching for some protein, that I could use as extracellular marker for mammalian cells. I need to insert mRNA to cell, and to detect the protein outside the cell (not on membrane) if the mRNA successfully enter and been translated. (not GFP, I need protein that exit from the cell in big numbers)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Thank you.&lt;/p&gt;&#xA;" OwnerUserId="10104" LastActivityDate="2015-08-02T21:51:10.037" Title="Protein that exit from the cell - as marker" Tags="&lt;proteins&gt;" AnswerCount="2" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36560" PostTypeId="1" CreationDate="2015-08-02T09:01:56.167" Score="9" ViewCount="6352" Body="&lt;p&gt;We know that almost all cats are solitary. &#xA;How did the Lions (&lt;em&gt;Panthera leo&lt;/em&gt;) end up social animals? Do we have an explanatory evolutionary path describing how the Lions became social while the rest of the felines remained solitary?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm not asking what general rules apply to evolution, but, rather - what evolutionary path has led to &lt;strong&gt;this specific outcome&lt;/strong&gt;. &#xA;I know a bit of evolutionary game theory. No need to reiterate the obvious. I'm asking if we know the mechanism or the evolutionary pressure in this particular case.&lt;/p&gt;&#xA;" OwnerUserId="17085" LastEditorUserId="3624" LastEditDate="2015-08-04T09:27:03.747" LastActivityDate="2019-04-29T11:46:05.187" Title="Why are lions the only social cats?" Tags="&lt;evolution&gt;&lt;zoology&gt;&lt;sociality&gt;&lt;feline&gt;" AnswerCount="3" CommentCount="10" FavoriteCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36561" PostTypeId="1" AcceptedAnswerId="36617" CreationDate="2015-08-02T09:11:01.783" Score="8" ViewCount="209" Body="&lt;p&gt;I was thinking specifically about random marshy water holes on farmers fields. It seems that you can visit just about any one of these and you will find frogs if you look hard enough.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They usually don't seem to be connected to each other. If it were any other land animal I would figure they walk from one spot to another, but in the case of frogs, I don't imagine their range is very vast. But often these marshy spots can be separated by fairly large distances to a frog.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So this brings me to my question: &lt;strong&gt;how do each of these spots end up with frogs in them?&lt;/strong&gt;  I don't imagine a frog is going to go hopping over a hill to get to a marsh on the other side, is it?&lt;/p&gt;&#xA;" OwnerUserId="13100" LastEditorUserId="3624" LastEditDate="2015-08-03T14:09:22.490" LastActivityDate="2015-08-04T14:17:36.860" Title="How do animals end up in remote areas?" Tags="&lt;zoology&gt;&lt;ecology&gt;&lt;species-distribution&gt;&lt;migration&gt;" AnswerCount="2" CommentCount="9" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36562" PostTypeId="1" AcceptedAnswerId="36575" CreationDate="2015-08-02T10:25:41.227" Score="3" ViewCount="292" Body="&lt;p&gt;&lt;a href=&quot;https://earthscience.stackexchange.com/questions/5250/what-is-the-evidence-it-is-feasible-to-reverse-ocean-acidification-by-adding-lar&quot;&gt;This question&lt;/a&gt; asked: &lt;strong&gt;What is the evidence it is feasible to reverse ocean acidification by adding large quantities of a base (bicarb soda)?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://earthscience.stackexchange.com/a/5251/895&quot;&gt;The result&lt;/a&gt; was: &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Danny Harvey of the University of Toronto has already looked into &lt;a href=&quot;http://www.whoi.edu/cms/files/HARVEY_Scripps_Ocean_Acidification_28205.ppt&quot; rel=&quot;nofollow noreferrer&quot;&gt;this&lt;/a&gt;. His solution is to deposit 4 Gt/yr of limestone into the oceans. To put this in perspective, &lt;a href=&quot;http://www.worldcoal.org/resources/coal-statistics/&quot; rel=&quot;nofollow noreferrer&quot;&gt;global coal production in 2013&lt;/a&gt; was nearly double this at 7.823 Gt and it is more than &lt;a href=&quot;https://en.wikipedia.org/wiki/List_of_countries_by_iron_ore_production&quot; rel=&quot;nofollow noreferrer&quot;&gt;global iron ore production in 2014&lt;/a&gt; of 3.22 Gt.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The respondent then posed the question: &lt;em&gt;What impact would such a huge annual deposition of limestone have of ocean life forms and biodiversity?&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;My question is: &lt;strong&gt;What would be the impact of depositing limestone in the oceans (to reverse acidification) on ocean life forms and biodiversity?&lt;/strong&gt;&lt;/p&gt;&#xA;" OwnerUserId="5417" LastEditorUserId="-1" LastEditDate="2017-04-13T12:50:30.153" LastActivityDate="2015-08-03T05:20:49.937" Title="What would be the impact of depositing limestone in the oceans (to reverse acidification) on ocean life forms and biodiversity?" Tags="&lt;marine-biology&gt;&lt;biodiversity&gt;&lt;aquatic-biology&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36563" PostTypeId="2" ParentId="36505" CreationDate="2015-08-02T10:49:53.067" Score="0" Body="&lt;p&gt;Typically, the ancestral allele is inferred from the allele chimpanzees as our closest relative (and possibly some primates) have. While for most sites humans and chimps have the same allele, there are many cases where the ancestral allele is even completely absent from humans, and where all humans have a different allele from chimpanzees, which we call a substitution.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A substitution in a critical part of a protein can indeed indicate some biological significance, a classical example is the &lt;a href=&quot;https://en.wikipedia.org/wiki/FOXP2&quot; rel=&quot;nofollow&quot;&gt;FOXP2&lt;/a&gt; gene, that is related to speech development. In most cases however, substitutions are merely due to genetic drift occurring over millions of years.&lt;/p&gt;&#xA;" OwnerUserId="3193" LastActivityDate="2015-08-02T10:49:53.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36564" PostTypeId="1" AcceptedAnswerId="36631" CreationDate="2015-08-02T12:47:09.017" Score="7" ViewCount="1820" Body="&lt;p&gt;Currently I am looking into what muscles groups are most used during a football kick. I have a hypothesis that the quadriceps are not as used as most people think because the momentum the swing creates makes the knee extend to fast for the quadriceps to contract.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To prove this I need to know the speed the knee extends during a football kick and the time it takes for the quadriceps to contract. I know how fast the knee extends through my own research. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Does anyone have any information on the speed of muscle contraction?&#xA;Quadriceps contraction time would be optimal, but any information relevant would be very helpful&lt;/p&gt;&#xA;" OwnerUserId="17089" LastActivityDate="2015-08-05T04:52:52.863" Title="What is the top speed of muscle contraction?" Tags="&lt;physiology&gt;" AnswerCount="1" CommentCount="0" FavoriteCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36566" PostTypeId="2" ParentId="36546" CreationDate="2015-08-02T15:59:59.123" Score="5" Body="&lt;p&gt;What a brilliant question for promoting a discussion.  Mitochondria definitely reproduce, they maintain a better energy flow than any other part of the cell, and they maintain a very low entropy state by exploiting that energy flow.  It may not be a textbook answer but being alive really is about decreasing your local entropy by exploiting a flow of energy.  I suspect that mitochondria have ceased to change under the pressures of natural selection, but so what - they have been practically perfect for a billion years.  &lt;/p&gt;&#xA;" OwnerUserId="17093" LastActivityDate="2015-08-02T15:59:59.123" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36567" PostTypeId="1" CreationDate="2015-08-02T16:50:28.407" Score="3" ViewCount="6231" Body="&lt;p&gt;HIV has a very high mutation rate due to its inability to correct errors in DNA replication and it is very adaptable to its environment. Hence I wonder whether is it possible for it to mutate such that it becomes an airborne virus and what mutations was needed for it to occur. After all other viruses such as influenza have done so before. Furthermore from the virus point of view, doing so will allow it to be more successful evolutionary speaking since that would allow the virus to infect more people and hence reproduce itself more quickly. And what will be the consequence if it happens?   &lt;/p&gt;&#xA;" OwnerUserId="17096" LastEditorUserId="948" LastEditDate="2015-08-02T18:24:38.850" LastActivityDate="2017-11-30T15:02:35.627" Title="Can HIV mutate to become airborne?" Tags="&lt;hiv&gt;" AnswerCount="0" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36569" PostTypeId="1" CreationDate="2015-08-02T17:42:10.383" Score="1" ViewCount="2052" Body="&lt;p&gt;If I understand correctly, the concept of the &lt;a href=&quot;http://www.actionbioscience.org/evolution/poolepaper.html&quot; rel=&quot;nofollow&quot;&gt;LUCA&lt;/a&gt; (last universal common ancestor) is based on the hypothesis that archaea and bacteria share common ancestry.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the realm of mathematics, the same discoveries have often been made more than once, in different places. Sometimes (like with calculus) these independent discoveries were made almost simultaneously. Sometimes the discoveries appear to  be totally unrelated (Hipparchus affirmative compound propositions before 100 BC, and David Hough's work on inserting parentheses in 1944).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If &quot;life&quot; started on Earth in some kind of primordial soup, it is conceivable that it started not once but many times, in different places and at different times.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;How strong is the evidence that bacteria and archaea &lt;em&gt;do not&lt;/em&gt; represent quite separate discoveries of &quot;life&quot;, which (because of the nature of the chemical substances that they use) happen to share a number of features, such as DNA?&lt;/p&gt;&#xA;" OwnerUserId="16882" LastEditorUserId="3624" LastEditDate="2015-08-04T08:37:32.677" LastActivityDate="2015-09-04T09:24:02.180" Title="What are the evidence that all life today descended from a common ancestor (LUCA), and which organisms (if any) challenge the concept?" Tags="&lt;evolution&gt;&lt;bacteriology&gt;&lt;archaea&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36570" PostTypeId="2" ParentId="36569" CreationDate="2015-08-02T17:59:07.617" Score="1" Body="&lt;p&gt;It is quite likely (but impossible to study) that the first stages of life originated more than once. However, the evidence that all &lt;em&gt;currently existing&lt;/em&gt; life originated from the same population is very strong. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;On the most basic level, many of the basic building blocks of life, RNA, DNA, amino acids are chiral, which means they come in multiple forms, but for the basic processes in nature, always the same one is chosen. For example, the DNA double-helix is almost always right-handed in nature,&#xA;&lt;a href=&quot;http://www.michaeleisen.org/blog/?p=334&quot; rel=&quot;nofollow&quot;&gt;see also here&lt;/a&gt;. If there were multiple origins of archaea and bacteria, we would expect some to pick another form, if not other molecules. In addition, many crucial proteins such as DNA- and RNA- polymerases are very similar between all species, the probability that they would have originated independently is simply minuscule.&lt;/p&gt;&#xA;" OwnerUserId="3193" LastActivityDate="2015-08-02T17:59:07.617" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36571" PostTypeId="1" AcceptedAnswerId="36576" CreationDate="2015-08-02T01:06:47.820" Score="1" ViewCount="1262" Body="&lt;p&gt;Obviously, there are &quot;innies&quot; and &quot;outies&quot; in the human belly button world.  Both are the result of a knot tied in the umbilical cord just after birth.  &lt;/p&gt;&#xA;&#xA;&lt;p&gt;But why do some belly buttons become outies while others become innies?  Is it related to how the doctor ties the knot, or is it related to how the knot heals?  &lt;/p&gt;&#xA;" OwnerUserId="17099" OwnerDisplayName="Wad Cheber" LastActivityDate="2015-08-02T19:54:56.793" Title="What leads to the different types of navels?" Tags="&lt;pregnancy&gt;&lt;children&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36572" PostTypeId="2" ParentId="36561" CreationDate="2015-08-02T19:04:46.793" Score="5" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;I don't imagine a frog is going to go hopping over a hill to get to a marsh on the other side, is it?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why not? In wet weather, the conditions would be just fine for an enterprising amphibian to go exploring, perhaps driven by predators or lack of available resources, not to mention Ro Siv's &lt;a href=&quot;https://biology.stackexchange.com/questions/36561/how-do-animals-end-up-in-remote-areas#comment60872_36561&quot;&gt;comment&lt;/a&gt; about &lt;a href=&quot;https://en.wikipedia.org/wiki/Rain_of_animals&quot; rel=&quot;nofollow noreferrer&quot;&gt;wind-borne dispersal of animals&lt;/a&gt;. Birds of prey may also pick up small animals, fly away with them, then drop them for whatever reason.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are also neglecting the fact that these organisms have existed for millions of years, and the landscape has changed tremendously in that time, with &lt;a href=&quot;https://en.wikipedia.org/wiki/Glacial_period&quot; rel=&quot;nofollow noreferrer&quot;&gt;glacial periods&lt;/a&gt; interspersed with &lt;a href=&quot;https://en.wikipedia.org/wiki/Interglacial&quot; rel=&quot;nofollow noreferrer&quot;&gt;interglacials&lt;/a&gt; every 20-50,000 years or so. As glaciers melt, large lakes form, and as those dried the organisms were dispersed across the land into smaller bodies of water. Streams and rivers form, transporting aquatic life forms, and may dry out and form isolated ponds, or they may be blocked for any number of reasons (mudslides, earthquakes, volcanic eruptions, beaver dams, fallen trees, etc.). As erosion and landscape remodeling occur, all traces of the original body of water may be erased, except for the wide distribution of similar organisms.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="-1" LastEditDate="2017-04-13T12:48:11.513" LastActivityDate="2015-08-02T19:04:46.793" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36573" PostTypeId="2" ParentId="36559" CreationDate="2015-08-02T19:20:17.040" Score="1" Body="&lt;p&gt;You can always express GFP or your favorite protein in a secretory vector like &lt;a href=&quot;https://www.lifetechnologies.com/order/catalog/product/K602501&quot; rel=&quot;nofollow&quot;&gt;&lt;code&gt;pSecTag&lt;/code&gt;&lt;/a&gt; or &lt;a href=&quot;https://www.lifetechnologies.com/order/catalog/product/V90020&quot; rel=&quot;nofollow&quot;&gt;&lt;code&gt;pSecTag2&lt;/code&gt;&lt;/a&gt; from Invitrogen/Life/ThermoFisher/SuperUltraBioMegaMart. There are probably others, but those were the first ones I came across. They contain the mouse Ig&amp;kappa; signal sequence for efficient secretion (so the website says, I've never used it).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I don't know the details of your experiment, but are you sure you want to use a secreted protein as a transfection marker? Remember, it's possible that only a small fraction of your cell population will take up the vector (or mRNA, if that's what you're using, but there are &lt;a href=&quot;http://www.invivogen.com/review-tlr7-tlr8&quot; rel=&quot;nofollow&quot;&gt;issues&lt;/a&gt; with that), but you will see secreted protein regardless of the number of cells that take it up.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2015-08-02T19:26:40.480" LastActivityDate="2015-08-02T19:26:40.480" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36575" PostTypeId="2" ParentId="36562" CreationDate="2015-08-02T19:54:23.630" Score="1" Body="&lt;p&gt;To simplify, acidification of oceans is due to excess anthropogenic carbon dioxide CO&lt;sub&gt;2&lt;/sub&gt;:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;H&lt;sub&gt;2&lt;/sub&gt;O + &lt;strong&gt;CO&lt;sub&gt;2&lt;/sub&gt;&lt;/strong&gt; → H&lt;sub&gt;2&lt;/sub&gt;CO&lt;sub&gt;3&lt;/sub&gt; → &lt;strong&gt;H&lt;sup&gt;+&lt;/sup&gt;&lt;/strong&gt; + HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Seawater is naturally saturated with another base, &lt;em&gt;carbonate ion&lt;/em&gt; (CO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;2-&lt;/sup&gt;) that acts like an &quot;antacid&quot; to neutralize the H+, forming more bicarbonate. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;CO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;2-&lt;/sup&gt; + &lt;strong&gt;H&lt;sup&gt;+&lt;/sup&gt;&lt;/strong&gt; → HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You want to alkalinize the ocean by dumping CaCO&lt;sub&gt;3&lt;/sub&gt;. That sounds pretty good, and not only would it add more buffer (and decrease acidification) but it would also help the sea creatures which use dissolved Ca&lt;sup&gt;2+&lt;/sup&gt; and CO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;2-&lt;/sup&gt; to make shells of calcium carbonate CaCO&lt;sub&gt;3&lt;/sub&gt;. (The other effect of excess CO&lt;sub&gt;2&lt;/sub&gt; is the leaching of CaCO&lt;sub&gt;3&lt;/sub&gt; from shells and corals or other marine organisms:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;CaCO&lt;sub&gt;3&lt;/sub&gt; + &lt;strong&gt;H&lt;sup&gt;+&lt;/sup&gt;&lt;/strong&gt; → HCO&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;-&lt;/sup&gt; + Ca&lt;sup&gt;2+&lt;/sup&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;The limestone mined today is used for gravel, in concrete, road surfacing, foundation support beneath weight-bearing structures, the boulder faces of earthen dams, Portland cement (N.B. the burning of limestone in the cement-making process liberates &lt;strong&gt;CO&lt;sub&gt;2&lt;/sub&gt;&lt;/strong&gt; gas), Aglime (pulverized limestone) and quicklime (process liberates &lt;strong&gt;CO&lt;sub&gt;2&lt;/sub&gt;&lt;/strong&gt; gas) which are both soil stabilizers, hydrated lime used to filter potable water supplies and to treat solid and liquid waste and in processing petroleum. These are only the &lt;strong&gt;major&lt;/strong&gt; uses of limestone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The average annual limestone production in Missouri (the largest deposit of limestone in the world) is about 89 million short tons/year. The cement industry &lt;em&gt;alone&lt;/em&gt; is a MAJOR producer of CO&lt;sub&gt;2&lt;/sub&gt;. Producing a ton of cement requires 4.7 million BTU of energy (some of which will release CO&lt;sub&gt;2&lt;/sub&gt;), equivalent to about 400 pounds of coal, and &lt;em&gt;generates nearly a ton of CO&lt;sub&gt;2&lt;/sub&gt;.&lt;/em&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So, in addition to the CO&lt;sub&gt;2&lt;/sub&gt; &lt;em&gt;produced&lt;/em&gt; by the use of limestone in everyday life, you want to mine it and dump it into the sea. Unfortunately, even finely ground limestone (remember all that CO&lt;sub&gt;2&lt;/sub&gt; it takes to mine and crush it) is poorly soluble in water (pH 7.0). It does increase with acid, but still is very slow. Also, it sinks. The worst acidification of the ocean is in &lt;strong&gt;surface waters.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/E3WWZ.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/E3WWZ.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some estimates suggest that close to 100 million tons of limestone are mined globally each year. (It's probably much more than that; see Missouri alone.) You want to mine, crush (to between 40µm - 10µm!!), and deliver an additional 4 Gt/yr of limestone, even though in the paper you cite, that amount &lt;em&gt;per year&lt;/em&gt; would not help:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Extraordinary additional measures (adding 4 Gt limestone/yr to the ocean for &gt; 200 years) provides a &lt;em&gt;modest additional benefit&lt;/em&gt; (additional to cutting CO2 emissions.)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Why? What difference would knowing the effect on biodiversity be when just procuring, processing and delivering the stuff would generate more CO&lt;sub&gt;2&lt;/sub&gt; than it could possibly buffer, and would have a minimal effect anyway?&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="3340" LastEditDate="2015-08-03T05:20:49.937" LastActivityDate="2015-08-03T05:20:49.937" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36576" PostTypeId="2" ParentId="36571" CreationDate="2015-08-02T19:54:56.793" Score="3" Body="&lt;p&gt;After childbirth, the umbilical cord is either tied (similar to a tourniquet - the cord itself is not tied into a knot) or clamped to cut off the blood supply. It is then cut distal to the clamp/tie, separating the child from the rest of the cord and the attached placenta. The remaining cells die and dessicate, and the stump eventually falls off, forming the umbilicus or belly button. The default result, barring any issues, is an &quot;innie&quot;. However, an &quot;outie&quot; may form if the child was born with a tiny &lt;a href=&quot;http://www.mayoclinic.org/diseases-conditions/umbilical-hernia/basics/definition/con-20025630&quot; rel=&quot;nofollow&quot;&gt;umbilical hernia&lt;/a&gt;, or there was a small unnoticed infection at the base of the umbilical cord. Either of these could lead to the formation &lt;a href=&quot;https://en.wikipedia.org/wiki/Granulation_tissue&quot; rel=&quot;nofollow&quot;&gt;granulation tissue&lt;/a&gt;, described colloquially as an &quot;outie&quot;. People can also have combination navels, with the indentation of an &quot;innie&quot; but a small amount of protruding granulation tissue inside.&lt;/p&gt;&#xA;" OwnerUserId="948" LastActivityDate="2015-08-02T19:54:56.793" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36580" PostTypeId="2" ParentId="36559" CreationDate="2015-08-02T21:51:10.037" Score="1" Body="&lt;p&gt;SEAP, secreted alkaline phosphatase, and vectors engineered to express fusions to this reporter gene may be well-suited to solve your problem.&lt;/p&gt;&#xA;" OwnerUserId="14946" LastActivityDate="2015-08-02T21:51:10.037" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36581" PostTypeId="1" AcceptedAnswerId="36583" CreationDate="2015-08-02T21:57:09.307" Score="2" ViewCount="79" Body="&lt;p&gt;I came across a reference to dAT joining in my reading of &lt;em&gt;Genentech&lt;/em&gt; by Sally Hughes. The technique is described in passing as a technique for joining DNA fragments used around the late sixties to early seventies (likely prior and after, too, of course).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;A quick query into earlier visits of the topic on the exchange returned no relevant results, but the results may have been have been obscured by the copious references to the neurologic &quot;DAT&quot; term (dopamine transporter).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Please provide a quick explanation to this concept/technique if you're familiar. &lt;/p&gt;&#xA;" OwnerUserId="17106" LastActivityDate="2015-08-03T04:38:42.333" Title="dAT joining: please define" Tags="&lt;biochemistry&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36583" PostTypeId="2" ParentId="36581" CreationDate="2015-08-02T23:24:54.463" Score="3" Body="&lt;p&gt;In the context of this book, dAT joining is a method used in molecular cloning to join two DNA molecules. Basically, terminal transferase is used to add polyA or polyT to the 3' ends of each DNA molecule. This creates cohesive ends which can anneal and then be ligated together, giving a covalently closed circular DNA molecule.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;img src=&quot;https://i.stack.imgur.com/nSSVt.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Image from: &lt;a href=&quot;http://m.pnas.org/content/69/10/2904.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Jackson DA, Symons RH, Berg P. 1972. Biochemical Method for Inserting New Genetic Information into DNA of Simian Virus 40: Circular SV40 DNA Molecules Containing Lambda Phage Genes and the Galactose Operon of Escherichia coli. Proc Nat Acad Sci USA 69(10):2904-2909.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;See also: &lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/0022283673904683&quot; rel=&quot;nofollow noreferrer&quot;&gt;Lobban PE, Kaiser AD. 1973. Enzymatic end-to-end joining of DNA molecules. J Mol Bio 78(3):453-460.&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;dAT joining can also refer to an assay of DNA ligase activity. Linear dAT oligomers are incubated with the ligase, which can circularize them and make them resistant to exonuclease digestion. This resistance to digestion correlates with DNA ligase activity. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://www.jbc.org/content/245/14/3626.full.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;Modrich P, Lehman IR. 1970. Enzymatic Joining of Polynucleotides. J Biol Chem 245(14):3626-3631.&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-08-03T04:38:42.333" LastActivityDate="2015-08-03T04:38:42.333" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36586" PostTypeId="1" AcceptedAnswerId="36621" CreationDate="2015-08-03T05:28:55.217" Score="3" ViewCount="155" Body="&lt;p&gt;Suppose we have a bacterial protein that performs a function and let's say we can measure the efficiency of the protein. Let's say we have two species, species A and B, both of which have this protein. One of these species, species A, is close to the common ancestor of A and B, in terms of evolutionary distance, while B is farther although for both cases, it took two speciation events to end up with species A and species B. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Let's say for both for species A and species B, we measure the protein efficiency in different environments. The species A protein has the efficiency highest in an environment most similar to its own and the same is true for the species B protein. But let's say we have two situations:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;When species A protein has best efficency, it has a lower efficiency compared to species B best efficiency&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;Species B protein best efficiency is lower than the species A best efficiency&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;In these two cases, what conclusions can we make in particular about the evolution of the protein itself? Can we show that the protein evolved to a degree to suit the different environment of species B compared to species A?&lt;/p&gt;&#xA;" OwnerUserId="10401" LastEditorUserId="3340" LastEditDate="2015-08-03T05:51:08.213" LastActivityDate="2015-08-06T22:11:52.593" Title="Evolution of protein and protein efficiency" Tags="&lt;evolution&gt;&lt;protein-evolution&gt;" AnswerCount="2" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36587" PostTypeId="1" CreationDate="2015-08-03T05:33:11.097" Score="4" ViewCount="90" Body="&lt;p&gt;Is there some sort of measure of the light harvesting efficiency (possibly like transfer time) that is directly related to the photosynthetic efficiency in some sort of equation? Also, how important is light harvesting efficiency to photosynthetic efficiency?&lt;/p&gt;&#xA;" OwnerUserId="10401" LastActivityDate="2015-08-03T05:33:11.097" Title="Photosynthetic efficiency and light harvesting efficiency" Tags="&lt;biophysics&gt;&lt;photosynthesis&gt;" AnswerCount="0" CommentCount="0" FavoriteCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36588" PostTypeId="1" CreationDate="2015-08-03T05:55:07.293" Score="10" ViewCount="7320" Body="&lt;p&gt;Almost all modern lab protocols have an addendum prohibiting pipetting by mouth, instead mandating that a Gilson pipette, a rubber pipette ball, or a serological Pipet-Aid be used. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;However, it was clear that some time in the previous century, prior to the invention of the aforementioned tools, many labs did in fact use mouth pipetting to transfer liquids, some of which were highly hazardous. An example can be seen here (from this &lt;a href=&quot;http://io9.com/when-lab-scientists-used-to-pipette-with-their-mouths-1550674701&quot; rel=&quot;noreferrer&quot;&gt;IO9 article&lt;/a&gt;, which dates the photo to the year 1943):&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/zifQMm.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/zifQMm.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;When did pipetting by mouth stop being recommended in labs? &lt;/p&gt;&#xA;" OwnerUserId="10456" LastEditorUserId="10456" LastEditDate="2015-08-03T07:06:34.450" LastActivityDate="2021-03-07T11:34:43.803" Title="When did mouth pipetting stop becoming a way to handle liquids in a lab?" Tags="&lt;lab-techniques&gt;&lt;history&gt;&lt;safety&gt;" AnswerCount="1" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36589" PostTypeId="2" ParentId="36588" CreationDate="2015-08-03T06:14:58.820" Score="13" Body="&lt;p&gt;Mouth pipetting, while almost unheard of in modern laboratories in developed countries, is still very much a current protocol in many parts of the world. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;For example, &lt;a href=&quot;http://www.jidc.org/index.php/journal/article/view/2236&quot;&gt;this paper&lt;/a&gt; analyses the proportion of clinical labs in Pakistan and found evidence of poor biosafety practices (emphasis mine):&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Results: A total of 1,647 (92.4%) males and 135 (7.6%) females&#xA;  participated in the study, with over half (59.7%) having more than&#xA;  five years of work experience. Results showed that 28.4% of the&#xA;  laboratory technicians from Punjab, 35.7% from Sindh, 32% from&#xA;  Balochistan and 38.4% from Khyber Pakhtoon Khawa (KPK) did not use any&#xA;  personal protective equipment. Almost 46% of the respondents (34.2%&#xA;  from Punjab, 61.9% from Sindh, 25.2% from Balochistan and 85% from&#xA;  KPK) said they reused syringes either occasionally or regularly.&#xA;  Furthermore, 30.7% of the respondents said they discard used syringes&#xA;  directly into municipal dustbins. The majority (66.7%) claimed there&#xA;  are no separate bins for sharps, so they throw these in municipal&#xA;  dustbins. &lt;strong&gt;Mouth pipetting was reported by 28.3% technicians.&lt;/strong&gt;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Additionally, a &lt;a href=&quot;https://scholar.google.co.uk/scholar?q=%22mouth%20pipette%22&amp;amp;hl=en&amp;amp;as_sdt=0%2C5&amp;amp;as_ylo=2010&amp;amp;as_yhi=2015&quot;&gt;Google Scholar search for papers published in the past 5 years&lt;/a&gt; involving mouth pipetting turned up 670 hits out of 284000 total hits, a proportion of 0.23%. This is further evidence that this dangerous technique has not been fully eradicated from labs. &lt;/p&gt;&#xA;" OwnerUserId="10456" LastActivityDate="2015-08-03T06:14:58.820" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36590" PostTypeId="1" AcceptedAnswerId="36591" CreationDate="2015-08-03T06:59:44.450" Score="5" ViewCount="275" Body="&lt;p&gt;Rhesus disease occurs when an Rh- mother is exposed to Rh antigens (often due to blood contact with an Rh+ child during delivery) and mounts an immune response which eventually results in the production of IgG Rh antibodies. In subsequent pregnancies, these antibodies cross the placenta. When the foetus is Rh+, these antibodies can bind to the corresponding antigens on the foetal erythrocytes and cause haemolysis, which can result in anaemia or even, in serious cases, stillbirth.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Given all of this, &lt;strong&gt;why does the same principle not apply to A and B antibodies?&lt;/strong&gt; In other words, what is special about Rhesus antigens or antibodies that does not apply to other erythrocytic antigens or their corresponding antibodies?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm specifically wondering about Rhesus disease and its effects on the foetus, and why similar effects do not occur &lt;em&gt;on the foetus&lt;/em&gt; in the case of an ABO type mismatch between mother and foetus.&lt;/p&gt;&#xA;" OwnerUserId="13187" LastEditorUserId="13187" LastEditDate="2015-08-03T07:18:07.957" LastActivityDate="2015-08-03T07:36:58.093" Title="Lack of A/B-antigen equivalent to Rhesus disease" Tags="&lt;immunology&gt;&lt;hematology&gt;&lt;pregnancy&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36591" PostTypeId="2" ParentId="36590" CreationDate="2015-08-03T07:30:56.233" Score="5" Body="&lt;p&gt;So it turns out it can occur. It's called &lt;a href=&quot;https://en.wikipedia.org/wiki/Hemolytic_disease_of_the_newborn_%28ABO%29&quot; rel=&quot;nofollow&quot;&gt;Hemolytic Disease of the Newborn (ABO)&lt;/a&gt;, and according to the article (the relevant citations are a book and some journals to which I do not have access), it is very rare, and severe cases are even more rare. Apparently anti-A and anti-B antibodies are typically of the &lt;a href=&quot;https://en.wikipedia.org/wiki/IgM&quot; rel=&quot;nofollow&quot;&gt;IgM&lt;/a&gt; isotype, which cannot cross the placental barrier. However, occasionally &lt;a href=&quot;https://en.wikipedia.org/wiki/IgG&quot; rel=&quot;nofollow&quot;&gt;IgG&lt;/a&gt; is produced, which &lt;em&gt;can&lt;/em&gt; cross. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is what causes the hemolysis in the fetus - if the mother is type O, and the baby is either A or B, the mother is exposed to unknown antigen and produces antibodies. If they happen to &lt;a href=&quot;https://en.wikipedia.org/wiki/Immunoglobulin_class_switching&quot; rel=&quot;nofollow&quot;&gt;class-switch&lt;/a&gt; to IgG, they can cross the placenta and, if in large enough quantities, cause the &lt;a href=&quot;https://en.wikipedia.org/wiki/Opsonin&quot; rel=&quot;nofollow&quot;&gt;opsonization&lt;/a&gt; and lysis of red blood cells.&lt;/p&gt;&#xA;" OwnerUserId="948" LastEditorUserId="948" LastEditDate="2015-08-03T07:36:58.093" LastActivityDate="2015-08-03T07:36:58.093" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36593" PostTypeId="1" CreationDate="2015-08-03T09:31:08.213" Score="1" ViewCount="891" Body="&lt;p&gt;What is the relationship between term &quot;Gene isoform&quot; and &quot;Protein isoform&quot;? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Say a gene can make 3 isoforms, will it produce only (maximum) 3 isoform protein?&lt;/p&gt;&#xA;" OwnerUserId="755" LastActivityDate="2015-08-03T12:05:08.913" Title="Gene and Protein isoform" Tags="&lt;proteins&gt;&lt;molecular-genetics&gt;&lt;gene-expression&gt;&lt;isoforms&gt;" AnswerCount="1" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36594" PostTypeId="2" ParentId="36532" CreationDate="2015-08-03T09:55:07.570" Score="8" Body="&lt;p&gt;Yes, it is a skipper (family Hesperiidae) and very similar to European species in &lt;a href=&quot;https://en.wikipedia.org/wiki/Ochlodes&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Ochlodes&lt;/em&gt;&lt;/a&gt;, and my guess is that it belongs to one of the North American species in this genus. For instance, it is very similar to &lt;a href=&quot;https://en.wikipedia.org/wiki/Ochlodes_sylvanoides&quot; rel=&quot;noreferrer&quot;&gt;&lt;em&gt;Ochlodes sylvanoides&lt;/em&gt;&lt;/a&gt; (also called Woodland Skipper), which is common in the western parts of the US. However, I'm not familiar with North American butterflies, and there might be closely related similar species that I'm ignoring.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Images of &lt;em&gt;Ochlodes sylvanoides&lt;/em&gt; from &lt;a href=&quot;http://butterfliesofamerica.com/t/Ochlodes_sylvanoides_a.htm&quot; rel=&quot;noreferrer&quot;&gt;http://butterfliesofamerica.com/t/Ochlodes_sylvanoides_a.htm&lt;/a&gt;:&lt;br&gt;&#xA;&lt;a href=&quot;https://i.stack.imgur.com/LRoRD.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/LRoRD.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&#xA;&lt;a href=&quot;https://i.stack.imgur.com/HLN8w.jpg&quot; rel=&quot;noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/HLN8w.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;More pictures can also be seen at &lt;a href=&quot;http://bugguide.net/node/view/9577/bgimage&quot; rel=&quot;noreferrer&quot;&gt;Bugguide.net&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="3624" LastEditorUserId="3624" LastEditDate="2015-08-03T10:47:04.833" LastActivityDate="2015-08-03T10:47:04.833" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36595" PostTypeId="1" AcceptedAnswerId="36596" CreationDate="2015-08-03T11:37:19.540" Score="8" ViewCount="9595" Body="&lt;p&gt;It's a simple question but I've come across many people who have this question, is the reference genome Positive of Negative strand? Indeed, I've had heated arguments over the same issue. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So here's to putting all those questions to rest.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is the reference genome a positive or a negative strand? And why so.&lt;/p&gt;&#xA;" OwnerUserId="15807" LastEditorUserId="231" LastEditDate="2015-08-03T20:05:26.407" LastActivityDate="2018-09-13T08:30:44.843" Title="What is the strand specificity of a reference genome?" Tags="&lt;bioinformatics&gt;&lt;dna-sequencing&gt;&lt;genomes&gt;&lt;human-genome&gt;" AnswerCount="3" CommentCount="4" FavoriteCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="36596" PostTypeId="2" ParentId="36595" CreationDate="2015-08-03T11:37:19.540" Score="5" Body="&lt;p&gt;First of all, the reference genome strand specificity is referred to as sense (positive strand) or antisense (negative strand). Now let's consider to sequencing data or FASTQ files. When we align reads, a resulting SAM or BAM file has a column specifying strand information, we usually see a + or - strand.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For more background on the strand names here's a somewhat incorrect note from the wiki article under &lt;a href=&quot;https://en.wikipedia.org/wiki/Sense_(molecular_biology)&quot; rel=&quot;nofollow noreferrer&quot;&gt;sense (molecular biology)&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The strand names actually depend on which direction you are writing&#xA;  the sequence that contains the information for proteins (the &quot;sense&quot;&#xA;  information), not on which strand is on the top or bottom (that is&#xA;  arbitrary). The only real biological information that is important for&#xA;  labeling strands is the location of the 5' phosphate group and the 3'&#xA;  hydroxyl group because these ends determine the direction of&#xA;  transcription and translation. A sequence 5' CGCTAT 3' is equivalent&#xA;  to a sequence written 3' TATCGC 5' as long as the 5' and 3' ends are&#xA;  noted. If the ends are not labeled, convention is to assume that the&#xA;  sequence is written in the 5' to 3' direction. Watson strand refers to&#xA;  5' to 3' top strand (5' → 3'), whereas Crick strand refers to 5' to 3'&#xA;  bottom strand (3' ← 5').[4] Both Watson and Crick strands can be&#xA;  either sense or antisense strands depending on the gene whose&#xA;  sequences are displayed in the genome sequence database. For example,&#xA;  YEL021W, an alias of URA3 gene used in NCBI database, defines that&#xA;  this gene is located on the 21st open reading frame (ORF) from the&#xA;  centromere of the left arm (L) of Yeast (Y) chromosome number V (E),&#xA;  and that the expression coding strand is Watson strand (W). YKL074C&#xA;  defines the 74th ORF to the left of the centromere of chromosome XI&#xA;  and denotes coding strand from the Crick strand (C). Another confusing&#xA;  term referring to &quot;Plus&quot; and &quot;Minus&quot; strand is also widely used.&#xA;  Whatever the strand is a sense (positive) or antisense (negative), the&#xA;  default query sequence in NCBI BLAST alignment is &quot;Plus&quot; strand.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Although it is correct when it says &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Watson = Sense = Plus Strands&lt;/li&gt;&#xA;&lt;li&gt;Crick = Antisense = Negative Strands&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;A satisfactory answer/convention is provided/suggested in this PMC article covering &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055211/&quot; rel=&quot;nofollow noreferrer&quot;&gt;the terminology of the Watson and Crick strands&lt;/a&gt; &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Below are some interesting excerpts from the publication:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;The earliest reference that we could find to the &quot;Watson strand&quot; and&#xA;  the &quot;Crick strand&quot; is somewhat tongue-in-cheek and comes from a pair&#xA;  of papers in 1967 by Wacław Szybalski and colleagues. They&#xA;  bound the two DNA strands of phage λ to the synthetic polynucleotide,&#xA;  poly(IG), which has an affinity to cytosine-rich regions. They then&#xA;  separated the two strands by density, which turned out to be&#xA;  determined by the amount of bound poly(IG). In a cesium-chloride&#xA;  density gradient, the strand with more bound poly(IG) was denser and&#xA;  heavier than its complement. Because the &quot;dense&quot; strand was&#xA;  cytosine-rich, Szybalski and colleagues called it the &quot;C strand.&quot;&#xA;  Logically, thus, the complementary strand, which was guanine rich,&#xA;  should have been the &quot;G strand.&quot; Instead, it was christened the &quot;W&#xA;  strand.&quot;&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;So the authors note that the Strands started on their terminology journey with their roles reversed with the Crick strand specifying the heavy strand (with IG) and the Watson strand specifying the lighter one.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They also note that the present day terminology of the WC model is non-arbitratrily based on the current horizontal drawing convention where one strand is placed on top and the other at the bottom.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;They also suggested a typical convention which is followed today. If it was due to their suggestion is a different matter altogether, but beyond the scope of this question.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Given the amount of effort already spent on standardizing such&#xA;  databases, and their influence on other disciplines, we feel that the&#xA;  genomic definition of Watson and Crick strands has the most mass&#xA;  behind it. Specifically, we find that the unambiguous usage of the&#xA;  Saccharomyces Genome Database to be the most useful. Under the first&#xA;  part of our proposal, the centromere is a reference point that divides&#xA;  a chromosome into two arms of unequal length. The chromosome is&#xA;  oriented so that shorter arm is on the left and the longer arm on the&#xA;  right. Furthermore, the top strand has its 5'-end at the left&#xA;  (short-arm) telomere and its 3'-end at the right (long-arm) telomere.&#xA;  This strand is the Watson strand. Similarly, the bottom strand has its&#xA;  5'-end at the right telomere and its 3' at the left telomere and is&#xA;  the Crick strand. We further propose that &quot;top&quot;, &quot;forward&quot;, and &quot;plus&quot;&#xA;  be used as synonyms for the Watson strand and &quot;bottom&quot;, &quot;reverse&quot;, and&#xA;  &quot;minus&quot; for the Crick strand.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;and later on...&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;If it is ultimately impossible to distinguish Watson and Crick strands&#xA;  using biological properties, then we propose that Watson should refer&#xA;  to the stand arbitrarily used as a reference in a database (i.e. the&#xA;  &quot;plus&quot; stand) and the Crick strand should refer to its complement&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;But let's come back to sequencing data or FASTQ files. When we align reads, a resulting SAM or BAM file has a column specifying strand information, we usually see a + or - strand. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Which suggests that the product originated from either the Watson (positive) or the Crick (negative) strands. For example, a read is actually the reverse complement of the product, but since you do a PCR step during you library preparation, that particular bit of information is lost and therefore the downstream analysis protocols tend to consider the entire loci any single product aligns to.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The difference between strand specific sequencing and non-strand specific sequencing are covered &lt;a href=&quot;https://biology.stackexchange.com/questions/1958/difference-between-strand-specific-and-not-strand-specific-rna-seq-data&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="15807" LastEditorUserId="45177" LastEditDate="2018-09-09T02:12:43.580" LastActivityDate="2018-09-09T02:12:43.580" CommentCount="2" CommunityOwnedDate="2015-08-03T19:28:52.580" ContentLicense="CC BY-SA 4.0" />
  <row Id="36598" PostTypeId="2" ParentId="36593" CreationDate="2015-08-03T12:05:08.913" Score="3" Body="&lt;p&gt;The term isoform has become a little ambiguous over the years (see &lt;a href=&quot;http://blogs.cornell.edu/collinslab/2012/05/30/protein-isoform/&quot; rel=&quot;nofollow&quot;&gt;http://blogs.cornell.edu/collinslab/2012/05/30/protein-isoform/&lt;/a&gt;)... still some things are consistent:&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;In some genetics literature 'isoform' has been used in the place of &lt;a href=&quot;https://en.wikipedia.org/wiki/Allele&quot; rel=&quot;nofollow&quot;&gt;allele&lt;/a&gt; when talking about the allele states at a locus for a gene&lt;/li&gt;&#xA;&lt;li&gt;Typically a &lt;a href=&quot;https://en.wikipedia.org/wiki/Gene_isoform&quot; rel=&quot;nofollow&quot;&gt;gene isoform&lt;/a&gt; is equivalent an alternate transcript. The gene isoforms are the set of mRNAs that can be produced by a gene.&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;https://en.wikipedia.org/wiki/Protein_isoform&quot; rel=&quot;nofollow&quot;&gt;Protein isoform&lt;/a&gt; commonly refers to the set of proteins produced by a gene, this can include variations produced by alternative splicing and post-translational modification. Note that in some contexts the set of products from closely related gene duplications can also be included.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;Note that databases will typically have a specific definition in mind for their use of isoform in their annotation, check their documentation for details (e.g. in UniProt see &lt;a href=&quot;http://www.uniprot.org/help/canonical_and_isoforms&quot; rel=&quot;nofollow&quot;&gt;What is the canonical sequence? Are all isoforms described in one entry?&lt;/a&gt;)&lt;/p&gt;&#xA;" OwnerUserId="4117" LastActivityDate="2015-08-03T12:05:08.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36599" PostTypeId="2" ParentId="36517" CreationDate="2015-08-03T12:41:28.573" Score="1" Body="&lt;p&gt;Typical possibilities that come to mind are programs available in &lt;a href=&quot;http://emboss.open-bio.org/&quot; rel=&quot;nofollow&quot;&gt;EMBOSS&lt;/a&gt; and &lt;a href=&quot;http://staden.sourceforge.net/&quot; rel=&quot;nofollow&quot;&gt;Staden&lt;/a&gt;. However the question of how to access the sequence data stored in .ab1 files has been asked on Biostars a number of times, so I suggest having a look at the various answers there for options that are suitable for your environment and use case, see &lt;a href=&quot;https://www.biostars.org/local/search/page/?q=ab1&quot; rel=&quot;nofollow&quot;&gt;Biostars search &quot;ab1&quot;&lt;/a&gt;.&lt;/p&gt;&#xA;" OwnerUserId="4117" LastActivityDate="2015-08-03T12:41:28.573" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36600" PostTypeId="1" AcceptedAnswerId="36602" CreationDate="2015-08-01T05:39:09.360" Score="3" ViewCount="3964" Body="&lt;p&gt;My father-in-law claims that since plants need nitrogen to produce proteins, and since ammonia is NH3, that Ammonia should be fine for the plants, since it's just nitrogen and water and hydrogen, according to him. We were cleaning a rusty chain and a bunch of spilled into our garden. I'm talking about household ammonia.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is that true?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I'm thoroughly convinced he is an utter idiot but then again he could be right since he does say he minored in Chemistry in his college days.&lt;/p&gt;&#xA;" OwnerUserId="9111" OwnerDisplayName="thinly veiled question mark" LastActivityDate="2015-08-03T14:06:41.050" Title="Is household ammonia okay for plants?" Tags="&lt;organic-chemistry&gt;" AnswerCount="1" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36602" PostTypeId="2" ParentId="36600" CreationDate="2015-08-03T14:06:41.050" Score="4" Body="&lt;p&gt;Okay, he's not wrong, technically speaking. Practically speaking &lt;em&gt;never ever fertilize your plants with ammonia&lt;/em&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The ammonia you spilled will be &lt;a href=&quot;https://en.wikipedia.org/wiki/Nitrifying_bacteria&quot; rel=&quot;nofollow&quot;&gt;converted into nitrates&lt;/a&gt; eventually, so it's not like you spilled lead into your garden. On the other hand the populations of nitrifying bacteria take a fairly long time to adapt to a bounty like &quot;a bunch&quot; of household ammonia (their idea of a banquet beyond their wildest dreams is 2-4 ppm ammonia) but they will eventually eat it all.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;(Fishkeepers should know about the nitrogen cycle, because you have to set up a &lt;a href=&quot;http://www.fishlore.com/NitrogenCycle.htm&quot; rel=&quot;nofollow&quot;&gt;complete yet tiny&lt;/a&gt; version of the real thing, which takes at least a week to establish)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So your plants will be fine... next year. This year they might have a little bit of trouble considering ammonia is a base and can burn plants directly or &lt;a href=&quot;http://www.greenhouse.cornell.edu/crops/factsheets/AmmoniumToxicity.pdf&quot; rel=&quot;nofollow&quot;&gt;indirectly.&lt;/a&gt; &lt;a href=&quot;http://homeguides.sfgate.com/ammonia-kill-plants-outside-93873.html&quot; rel=&quot;nofollow&quot;&gt;Don't fertilize your plants with ammonia.&lt;/a&gt; They will probably die.&lt;/p&gt;&#xA;" OwnerUserId="4109" LastActivityDate="2015-08-03T14:06:41.050" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36603" PostTypeId="1" AcceptedAnswerId="36629" CreationDate="2015-08-03T16:34:18.553" Score="6" ViewCount="235" Body="&lt;p&gt;I am trying to understand the current work on abiogenesis in biology, e.g. primordial soup, the Miller-Urey experiment, etc. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;How has our understanding of abiogenesis been revised since the Miller-Urey 'primordial soup' hypothesis?&lt;/p&gt;&#xA;" OwnerUserId="17118" LastEditorUserId="948" LastEditDate="2015-08-04T16:26:17.987" LastActivityDate="2015-08-05T03:33:37.067" Title="Current understanding of abiogenesis" Tags="&lt;life&gt;&lt;abiogenesis&gt;&lt;literature&gt;" AnswerCount="1" CommentCount="9" ContentLicense="CC BY-SA 3.0" />
  <row Id="36604" PostTypeId="1" CreationDate="2015-08-03T19:01:16.103" Score="1" ViewCount="209" Body="&lt;p&gt;(Sorry that I'm on mobile, so I can't make a good formated question (no links). I will add them later. Just can't resist the urge to ask)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the recent hot question about whether mitochondrial is alive or dead (it's technically dead), the top answers don't only explain whether it is dead or not, but also further explain why it doesn't matter: they just do what they need to do. This provokes me a question:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Q&lt;/strong&gt;: Biologically, do life and death matter? Is the &lt;strong&gt;functionality&lt;/strong&gt; of something the only thing that life cares?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;We human are scare of death. Because of that, we tend to apply that idea into everything we can observe, even if it's meaningless. But why is death scary? Isn't it because when you die, you stop function anymore? So ultimately, isn't what we really mean when discussing whether something is dead or not the functionality of that?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Not only that, &quot;there is no consensus regarding the answer to the question as to when does life begin&quot;. If we approach this in a different way: the time when an individual function begins to work, will there be a consensus? I mean, just don't think if an organism is alive or not, just think that how much functions of it have started to work.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;If we are the combination of the numerous of selfish genes, would &quot;humanity&quot; be a collection of functions?&lt;/p&gt;&#xA;" OwnerUserId="6786" LastActivityDate="2015-08-04T05:13:42.340" Title="Biologically, does life and death matter?" Tags="&lt;life&gt;&lt;death&gt;&lt;philosophy-of-science&gt;" AnswerCount="1" CommentCount="9" ClosedDate="2015-08-04T00:50:36.917" ContentLicense="CC BY-SA 3.0" />
  <row Id="36607" PostTypeId="2" ParentId="36604" CreationDate="2015-08-03T21:18:06.220" Score="3" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;We human are scare of death. Because of that, we tend to apply that idea into everything we can observe, even if it's meaningless. But why is death scary? Isn't it because when you die, you stop function anymore?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Fear of death is hard-wired into our nervous systems. A thirsty wildebeest will approach crocodile-infested water very, very reluctantly. The wildebeest isn't thinking about the selfish gene or the loss of his function in the world; he's hardwired to be afraid of the situation. The same is true for any prey animal: fawn, rabbit, gazelle, mouse. The difference (maybe; simplifying for convenience) is that we are rational, and like all of our primitive fears (e.g., of the dark, when there really were sharp-toothed predators with better night vision than ourselves), we try to rationalize them. We also rationalize our existence. &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Is the functionality of something the only thing that life cares?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Nature is red in tooth and claw. If you want to anthropomorphize Nature, then sure, we matter (we're destroying the earth at unprecedented speeds). If you believe in a spirit, we matter. But if you believe in none of it, the only purpose we serve is to propagate ourselves, and when the last of our species is gone, Nature will not care a whit. Just as it doesn't care that dinosaurs, wooly mammoths, passenger pigeons, tasmanian tigers or baiji river dolphin are gone.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It can be argued that in the grand scheme of things (and here I'm speaking of the entire Universe), biological life doesn't matter at all.&lt;/p&gt;&#xA;" OwnerUserId="5198" LastEditorUserId="5198" LastEditDate="2015-08-04T05:13:42.340" LastActivityDate="2015-08-04T05:13:42.340" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36608" PostTypeId="2" ParentId="3905" CreationDate="2015-08-03T22:27:05.913" Score="0" Body="&lt;p&gt;Color of light matters. As the Answer with the graph shows, chlorophyll absorbs certain colors of light best. It is strange that it does not seem to absorb yellow light well, considering that the sun has the highest emission level there, but perhaps it was to keep the plants from roasting in excessive sun conditions. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I did an experiment in High School where I placed colored transparent gel material over otherwise identical plants. One was the control with no box over it, then there was Red, Yellow, Green and Blue. The Yellow and Green did very poorly and the plants appeared to be whitish, perhaps due to inadequate chlorophyll production? The plant under the Blue appeared normal, and the one under Red grew 'leggy' and very fast. This is a known result that plants growing under foliage tend to receive excess red relative to blue light, and it triggers rapid growth, presumably so that the part of the plant can get out from under other foliage. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;In my apartment and workplace, I have north-facing windows, sometimes the shades are closed during the day, both factors simulating red-light effect, and the Wandering Jew plants that I have grow like crazy.&lt;/p&gt;&#xA;" OwnerDisplayName="user17124" LastActivityDate="2015-08-03T22:27:05.913" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36609" PostTypeId="2" ParentId="31222" CreationDate="2015-08-03T22:54:08.223" Score="1" Body="&lt;p&gt;It's been possible for a long time now. Take a look at this article related to trials with &lt;a href=&quot;http://www.nature.com/nature/journal/v420/n6912/full/420116a.html&quot; rel=&quot;nofollow&quot;&gt;retroviral vectors used for gene therapy trials&lt;/a&gt;. A single child developed leukemia, and following that trials across the world were suspended. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;The article although notes that many countries decided to proceed with trials, since as they say &quot;for the greater good&quot;. But mainstream media articles tend to glorify the actual reasons behind such decisions, because such questions are governed by much more complex ethical considerations.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;But moving on this recognised the need for targeted gene therapies, so one of the most promising techniques right now is the &lt;a href=&quot;http://www.nature.com/nbt/journal/v32/n4/full/nbt.2842.html&quot; rel=&quot;nofollow&quot;&gt;Crispr/Cas9&lt;/a&gt; technique as noted by the comments above above. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;So do we have the technology? Yes we do.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Should we go forward with it? &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I would say no. But, I would also say yes.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Why such a division in opinion?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;There is much that we do not understand. Until a few years ago, the non-coding part of the genome was just junk. Now, it's an essential regulatory partner. Even more recently, the understanding of chromosome architecture was not understood, now we know that Chromosome architecture has a role to play in gene expression. In 2002 epigenomics was in it's infancy, we believed &quot;central dogma&quot; to be a dogma, non-coding RNAs were just some junk that you tended to pick up because the transcription machinery did not know what it was doing, and chromosome architecture? that hardly mattered in the grander scheme of the cell. All in all the cell was a much simpler place. Now we know more than we did yesterday and less than we will know tomorrow, so if I was a person whose entire life is a prolonged episode of suffering I would take my current options. If I was a person who could live with a mild discomfort I would work around it.  &lt;/p&gt;&#xA;" OwnerUserId="15807" LastActivityDate="2015-08-03T22:54:08.223" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36611" PostTypeId="1" AcceptedAnswerId="36615" CreationDate="2015-08-04T08:31:40.453" Score="2" ViewCount="57" Body="&lt;p&gt;I have come across a &lt;a href=&quot;http://www.kegg.jp/kegg-bin/show_pathway?map01200&quot; rel=&quot;nofollow noreferrer&quot;&gt;map&lt;/a&gt; and a part of it looks like this: &lt;br&gt;&lt;br&gt;&#xA;&lt;a href=&quot;https://i.stack.imgur.com/oj2T6.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/oj2T6.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt; &lt;br&gt;&lt;br&gt;&#xA;Now I have not been able to locate the reaction that converts alpha D-Glucose to Glucono-1,5-lactone but was successfully able to locate the &lt;a href=&quot;http://www.kegg.jp/dbget-bin/www_bget?R01786&quot; rel=&quot;nofollow noreferrer&quot;&gt;reaction&lt;/a&gt; that converts alpha D-glucose Glucose to Glucose-6P. Since an arrow exist from alpha D-Glucose to Glucono-1,5-lactone, i am assuming that such a reaction exist. But could not locate it. I clicked on the arrow marked in blue in the picture, but could not find the desired reaction.(alpha D glucose and beta D glucose are different compounds)  What is the reaction and how is it possible to find the reaction from the map?&#xA;NB: The arrows are clickable so are the circles that denote the compound.&lt;/p&gt;&#xA;" OwnerUserId="8835" LastEditorUserId="3340" LastEditDate="2015-08-04T14:05:06.413" LastActivityDate="2015-08-04T14:05:06.413" Title="Finding a reaction from a KEGG map" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;database&gt;&lt;pathway&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36612" PostTypeId="1" AcceptedAnswerId="36614" CreationDate="2015-08-04T09:09:25.593" Score="1" ViewCount="619" Body="&lt;p&gt;According to &lt;a href=&quot;https://en.wikipedia.org/wiki/Chimeric_gene&quot; rel=&quot;nofollow&quot;&gt;wikipedia&lt;/a&gt; on chimeric genes:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;These mutations are distinct from fusion genes which merge whole gene&#xA;  sequences into a single reading frame and often retain their original&#xA;  functions.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I am not totally sure I understand the statement. My interpretation is that a fusion gene is caused by a translocation of DNA in a single gene; therefore, it &quot;retains their original functions&quot;. This is different from a chimeric gene where DNA from two or more different genes are translocated to a new location to form a completely new gene.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Is my interpretation correct?&lt;/p&gt;&#xA;" OwnerUserId="14905" LastEditorUserId="6307" LastEditDate="2015-08-04T09:21:07.457" LastActivityDate="2015-08-04T09:40:57.200" Title="Chimeric Gene vs Fusion Gene?" Tags="&lt;terminology&gt;&lt;mutations&gt;&lt;gene&gt;" AnswerCount="1" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36613" PostTypeId="2" ParentId="36560" CreationDate="2015-08-04T09:25:58.643" Score="13" Body="&lt;p&gt;This is not a direct answer to your question, but I want to point out that your basic premise is partially incorrect. Other felines also form social groups. For instance, &lt;a href=&quot;https://en.wikipedia.org/wiki/Cheetah#Males&quot;&gt;male cheetahs form coalitions&lt;/a&gt; (also see &lt;em&gt;Cheetah outreach&lt;/em&gt; at &lt;a href=&quot;http://www.cheetah.co.za/c_info.html&quot;&gt;http://www.cheetah.co.za/c_info.html&lt;/a&gt;), often for life, which generally makes them more successful in defending territories. Female feral cats also form social groups in some environments (see e.g. &lt;a href=&quot;http://onlinelibrary.wiley.com/doi/10.1111/j.1439-0310.2006.01320.x/full#b21&quot;&gt;Natoli et al, 2007&lt;/a&gt;), where females sometimes co-rear kittens. There is even evidence that tigers share kills with related or unrelated individuals (see &lt;a href=&quot;https://en.wikipedia.org/wiki/Tiger#Social_activity&quot;&gt;Wikipedia: Tiger&lt;/a&gt; for examples), and tiger home ranges can overlap in complex ways. On the other hand, lions (both males and females) are sometimes solitary, and this partially interacts with their living environment. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;My point is mainly that sociality (in general or in felines in particular) is not either/or for a particular species, and other felines also show social behaviours and sometimes form groups (so sociality should be viewed as a sliding scale). Granted, lions are definitely the feline with the strongest social behaviors, and they form the largest social groups. It is therefore interesting to think about why that is the case, and what group dynamics and tradeoffs that determine the social behaviours of lions.&lt;/p&gt;&#xA;" OwnerUserId="3624" LastActivityDate="2015-08-04T09:25:58.643" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36614" PostTypeId="2" ParentId="36612" CreationDate="2015-08-04T09:33:21.407" Score="2" Body="&lt;p&gt;A chimeric gene is formed from fragments of other genes whereas a fusion gene is formed from the entirety of other genes. Often in the literature you'll see the term fusion gene used for both cases. &lt;/p&gt;&#xA;" OwnerUserId="6307" LastEditorUserId="6307" LastEditDate="2015-08-04T09:40:57.200" LastActivityDate="2015-08-04T09:40:57.200" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36615" PostTypeId="2" ParentId="36611" CreationDate="2015-08-04T09:44:53.727" Score="2" Body="&lt;p&gt;It was a simple search. You could have easily searched for glucose oxidase in KEGG, and you would have got &lt;a href=&quot;http://www.genome.jp/dbget-bin/www_bget?reaction+R01522&quot; rel=&quot;nofollow&quot;&gt;this reaction&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In fact if you had clicked the link for glucunolactone's &lt;a href=&quot;http://www.kegg.jp/dbget-bin/www_bget?C00198&quot; rel=&quot;nofollow&quot;&gt;&lt;em&gt;compound&lt;/em&gt; page&lt;/a&gt;, you would have got a list of many different reactions that convert glucose to glucunolactone. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can even click the arrow which opens the &lt;em&gt;KEGG-ORTHOLOGY&lt;/em&gt; page. You can find a field called &lt;em&gt;RN&lt;/em&gt; in the section called &quot;Other DBs&quot;. The links corresponding to this field would give you the exact reactions, that the pathway uses.&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="3340" LastEditDate="2015-08-04T13:58:45.773" LastActivityDate="2015-08-04T13:58:45.773" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36616" PostTypeId="2" ParentId="14164" CreationDate="2015-08-04T14:07:29.923" Score="5" Body="&lt;p&gt;The excellent answers from Chris and One Face have already written about why the claim is wrong, so I'm going to add a hypothesis for how this sort of nonsense could even originate in the first place.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The reason why lemons are acidic is because they contain a lot of citric acid, so in a solution part of this citric acid ionizes to citrate which increases the concentration of H3O+, thus increasing pH. Now imagine some quackjob with poor knowledge of chemistry reading about this, and only picking up the word &quot;citrate&quot;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Citrate is of course a weak base (since 3rd pka of citric acid is 6.40 then pkb of citrate must be 7.60) so if we pour some kind of citrate salt into water we would get a basic solution.&#xA;So basically, I think that the originators of this fad forgot about or didn't know about the H3O+ ions, which of course do not magically disappear when we ingest lemon juice.&lt;/p&gt;&#xA;" OwnerUserId="15385" LastEditorUserId="15385" LastEditDate="2015-08-04T15:06:10.300" LastActivityDate="2015-08-04T15:06:10.300" CommentCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36617" PostTypeId="2" ParentId="36561" CreationDate="2015-08-04T14:17:36.860" Score="5" Body="&lt;p&gt;This question pertains to organism dispersal, which is a very active field of study with relation to it's impact on conservation efforts. Much of what I will say below has been covered in this &lt;a href=&quot;https://en.wikipedia.org/wiki/Biological_dispersal&quot;&gt;wiki&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Definition: From the Wiki&lt;/strong&gt; &lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Technically, dispersal is defined as any movement that has the&#xA;  potential to lead to gene flow.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It can be broadly classified into two categories: &lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Density dependent dispersal&lt;/li&gt;&#xA;&lt;li&gt;Density independent dispersal &lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;The question of frogs and fishes both refer to Density independent dispersal, while an example of density independent dispersal can be the &lt;a href=&quot;http://goo.gl/UQNF76&quot;&gt;competition for habitat space between big cats and humans&lt;/a&gt; (this is a WWF pdf)&lt;/p&gt;&#xA;&#xA;&lt;p&gt;From the wiki:&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;&lt;strong&gt;Density-independent dispersal&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Organisms have evolved adaptations for dispersal that take advantage&#xA;  of various forms of kinetic energy occurring naturally in the&#xA;  environment. This is referred to as density independent or passive&#xA;  dispersal and operates on many groups of organisms (some&#xA;  invertebrates, fish, insects and sessile organisms such as plants)&#xA;  that depend on animal vectors, wind, gravity or current for dispersal.&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;&lt;strong&gt;Density-dependent dispersal&lt;/strong&gt;&lt;/p&gt;&#xA;  &#xA;  &lt;p&gt;Density dependent or active dispersal for many animals largely depends&#xA;  on factors such as local population size, resource competition,&#xA;  habitat quality, and habitat size.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Currently, some studies suggest the same.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;http://goo.gl/JL1vp3&quot;&gt;This study&lt;/a&gt; in particular studied the movement and habitat occupancy patterns within ephemeral and permanent water bodies in response to flooding. They found that during flooding these frogs moved out to flooded ephemeral water bodies and later on moved back again to the permanent ones. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Other suggested readings for those highly interested in the subject may include &lt;a href=&quot;http://goo.gl/agcr0d&quot;&gt;this&lt;/a&gt; (a phd thesis) and &lt;a href=&quot;http://goo.gl/6vb6yp&quot;&gt;this&lt;/a&gt; (a project report)&lt;/p&gt;&#xA;" OwnerUserId="15807" LastActivityDate="2015-08-04T14:17:36.860" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36618" PostTypeId="1" CreationDate="2015-08-04T14:19:54.897" Score="3" ViewCount="77" Body="&lt;p&gt;I want to know the trigger behind the change of asexual to sexual ectomycorrhiza when symbiosis with a tree root is formed. As ectomycorrhiza attaches itself to a root, it forms a relationship wherein phosphorous to the tree/plant is exchanged for glucose to the fungus. When this symbiosis occurs, the fungus, which is normally asexual, becomes sexual(male/female components) and buds form as a result. Thus I could hypothesize that if glucose is the catalyst, I could saturate the soil and cause this reaction. However, I am not sure what the actual chemical signal is, or if there is an unforeseen factor causing this change. Does anyone have any knowledge on the subject of what the aforementioned catalyst would be?&lt;/p&gt;&#xA;" OwnerUserId="17130" LastEditorUserId="19099" LastEditDate="2016-04-21T06:28:22.863" LastActivityDate="2016-04-21T06:28:22.863" Title="What Chemical Trigger Causes Ectomycorrhiza To Change From Asexual To Sexual?" Tags="&lt;biochemistry&gt;&lt;molecular-biology&gt;&lt;cell-biology&gt;&lt;botany&gt;&lt;mycology&gt;" AnswerCount="0" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36620" PostTypeId="1" AcceptedAnswerId="36624" CreationDate="2015-08-04T18:45:36.230" Score="41" ViewCount="10995" Body="&lt;p&gt;It seems kind of anti-productive in terms of survival for a plant to produce an addictive chemical as that plant will constantly be sought after by animals that ingest it. In this instance, I'm looking for a possible general &amp;amp; inclusive answer here that would describe most plants that make this. Not a specific instance (although if provided as an example would be a plus).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;To appreciate the scope of this is terms of number of plants producing potentially addictive compounds - see this compendium:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://en.m.wikipedia.org/wiki/List_of_psychoactive_plants&quot; rel=&quot;noreferrer&quot;&gt;compendium of botanicals reported to produce toxic, physchoactive or addictive compounds&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="6061" LastEditorUserId="6061" LastEditDate="2016-03-26T01:00:51.813" LastActivityDate="2016-03-26T01:00:51.813" Title="Why would a plant evolve to produce an addictive chemical?" Tags="&lt;evolution&gt;&lt;botany&gt;&lt;addiction&gt;" AnswerCount="4" CommentCount="16" FavoriteCount="5" ContentLicense="CC BY-SA 3.0" />
  <row Id="36621" PostTypeId="2" ParentId="36586" CreationDate="2015-08-04T19:40:57.597" Score="2" Body="&lt;p&gt;&lt;strong&gt;A few details&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;One of these species, species A, is close to the common ancestor of A and B, in terms of evolutionary distance, while B is farther although for both cases, it took two speciation events to end up with species A and species B.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;I have two issues here.&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;I don't understand why this information matter for your question.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;There are several metrics of evolutionary distance. In terms of time to common ancestor and therefore, in terms of number of neutral substitutions (it is ok if you don't understand why I talk about neutral substitutions) species A and species B are at exactly the same &quot;evolutionary distance&quot; to any of their common ancestor. However, you may want to talk about evolutionary distance in terms of &quot;By how many standard deviations of a quantitative trait did the mean trait value shifted since the common ancestor (in haldanes unit by definition)&quot;, then one species might be more closely related to the ancestor indeed. But in such case, you need to talk about the quantitative trait resulting from protein changes and not directly at the discrete, non-ordinal (nominal) nature of proteins.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;And a third general issue I have&lt;/p&gt;&#xA;&#xA;&lt;ol start=&quot;3&quot;&gt;&#xA;&lt;li&gt;As I understand the question, I don't think the question is specific to proteins at all. The question seem rather to relate to &quot;environment specific adaptation in comparative genomics and reaction norms&quot; and would be completely legitimate to look at that at the level of a protein or of a quantitative traits.&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;To answer your question&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You are interested in the measure of fitness as a function of both environment and the protein under consideration. The relationship between the fitness (and other quantitative traits) and the envrionment is referred to as the &lt;a href=&quot;https://en.wikipedia.org/wiki/Reaction_norm&quot; rel=&quot;nofollow noreferrer&quot;&gt;reaction norm&lt;/a&gt;.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/00JZq.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/00JZq.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here the graph display the quantitative trait (could be fitness) in the Y axis and environment in the X axis (as it is usually represented).There are two lines, for two different genotypes (the two different proteins in your case).&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;Can we show that the protein evolved to a degree to suit the different environment of species B compared to species A?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;Well, looking at the graphs it looks like indeed one protein has been under selection in one environment while the other has been under selection under the other environment. Testing this is just a matter of statistics. Basically, to test for this, you run a linear model with the quantiative trait (eventually fitness) as the response variable and the environment, the genotype and their interaction as explainatory variables. If the interaction term is significant (and if the directionality of the interaction is the one you would expect, that is genotypes are more fit in the environment where they live and if each genotype outcompete the other in at least one environment), then the genotypes are locally adapted.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;EDIT&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;what counts as significant?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;You can chose the level of significance that you wish (0.05 for example). If this is unclear, you'll probably want to learn more about stats before.&lt;/p&gt;&#xA;&#xA;&lt;blockquote&gt;&#xA;  &lt;p&gt;can you provide an example of when this method you have described was used the literature to show the evolution of a protein?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;If you want example from the literature you can just type &lt;code&gt;Genotype by Environment Interaction&lt;/code&gt; on google scholar and will get tons of hits. &lt;a href=&quot;http://link.springer.com/article/10.1007/BF00220855#page-1&quot; rel=&quot;nofollow noreferrer&quot;&gt;Here&lt;/a&gt; is a paper discussing this methodology specifically and &lt;a href=&quot;http://www.amazon.ca/Genotype---Environment-Interaction-Manjit-Kang/dp/0849340039/ref=sr_1_1?ie=UTF8&amp;amp;qid=1438886290&amp;amp;sr=8-1&amp;amp;keywords=Genotype+-by-+environment+interaction&quot; rel=&quot;nofollow noreferrer&quot;&gt;here&lt;/a&gt; is a (old) book on the subject. I am not sure why you're still talking about proteins. Most often those studies are done at the level of the gene (or directly on the phenotypic trait). But you can find the gene and get the protein sequence from it or even play around to visualize it with various biophysics softwares.&lt;/p&gt;&#xA;" OwnerUserId="4108" LastEditorUserId="4108" LastEditDate="2015-08-06T22:11:52.593" LastActivityDate="2015-08-06T22:11:52.593" CommentCount="4" ContentLicense="CC BY-SA 3.0" />
  <row Id="36623" PostTypeId="2" ParentId="36586" CreationDate="2015-08-04T20:26:39.770" Score="0" Body="&lt;blockquote&gt;&#xA;  &lt;p&gt;In these two cases, what conclusions can we make in particular about&#xA;  the evolution of the protein itself?&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&#xA;&lt;p&gt;It's not clear to me that it is right to make any evolutionary conclusions based on function alone.  DNA sequence would be a FAR better way to estimate evolutionary relatedness.&lt;/p&gt;&#xA;" OwnerUserId="5148" LastActivityDate="2015-08-04T20:26:39.770" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36624" PostTypeId="2" ParentId="36620" CreationDate="2015-08-04T21:17:17.300" Score="68" Body="&lt;p&gt;It's a matter of perspective. Most of the chemicals that are addictive to &lt;em&gt;us humans&lt;/em&gt; (particularly alkaloids), and may be addictive for some other animals as well, are also insecticides. Lots of plants that we consider poisonous are good food for other species, and lots of plants that insects would consider poisonous are treats for us.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This is a great example of the aimless nature of evolution. The plants that could successfully defend themselves against insects stabilize on a solution that happens to be bad for them in certain ways. Although, you would be hard pressed to find a better way to guarantee reproduction than being addictive to humans.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background reference&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007/BF01013489&quot;&gt;Plant-insect coevolution and inhibition of acetylcholinesterase&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://link.springer.com/article/10.1007%2FBF01920763?LI=true&quot;&gt;The defensive role of alkaloids in insects and plants&lt;/a&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.sciencedirect.com/science/article/pii/S1359644697011677&quot;&gt;Exploration of nature's chemodiversity: the role of secondary metabolites as leads in drug development&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Also of interest&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;&lt;a href=&quot;http://www.nature.com/nature/journal/v521/n7550/full/nature14414.html&quot;&gt;Bees prefer foods containing neonicotinoid pesticides&lt;/a&gt;&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;" OwnerUserId="2999" LastEditorUserId="2999" LastEditDate="2015-08-10T05:58:42.437" LastActivityDate="2015-08-10T05:58:42.437" CommentCount="6" ContentLicense="CC BY-SA 3.0" />
  <row Id="36625" PostTypeId="2" ParentId="36620" CreationDate="2015-08-04T21:36:32.320" Score="27" Body="&lt;p&gt;As someone commented earlier, chemicals such as nicotine and morphine were products of evolution meant to repel animals. It is explained in more details in this article &lt;a href=&quot;http://rspb.royalsocietypublishing.org/content/275/1640/1231&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Evolutionary biologists studying plant–herbivore interactions have convincingly argued that many plant secondary metabolites, including alkaloids such as nicotine, morphine and cocaine, are potent neurotoxins that evolved to deter consumption by herbivores.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;But it seems that those same chemicals produce adverse effects to what they were originally intended for:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;For example, one or more plant alkaloids have been identified that interfere with nearly every step in neural signalling. Targets include neurotransmitter synthesis, storage, release, binding, deactivation and reuptake, ion channel activation and function, and key enzymes involved in signal transduction.&lt;/p&gt;&#xA;&lt;p&gt;Paradoxically, the same properties invoked to explain why common drugs like caffeine, nicotine and cocaine are toxic are also those invoked to explain why these compounds are rewarding. It is therefore important to stress that these and other addictive drugs appear to have evolved only &lt;strong&gt;because they successfully deterred&lt;/strong&gt;, not rewarded or reinforced, plant consumption.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;For example, let's take a closer look at nicotine. This compound is not present at all times in the plant, instead it is produced as a reaction to a trigger.&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;&lt;em&gt;Nicotiana attenuata&lt;/em&gt; is an important model species for the analysis of plant–herbivore interactions involving nicotine. It is a domesticated North American tobacco plant that is attacked by over 20 different herbivores, ranging from mammalian browsers to intracellular-feeding insects. These attacks elicit a battery of defensive responses, including nicotine production.&lt;/p&gt;&#xA;&lt;p&gt;&lt;em&gt;Nicotiana&lt;/em&gt; has therefore evolved to allocate chemical defences strategically by concentrating them in the most valuable parts of the plant, such as young leaves, stems and reproductive organs, and by modulating its production according to the type of herbivore and extent of leaf damage.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;This last example concentrates on nicotine, but it makes it easier to grasp how plants might use the production of such a chemical as a mean of protection.&lt;/p&gt;&#xA;&lt;p&gt;Also, depending on the substance and the creature which consumes the plant, one might witness different outcomes. I found interesting information in this less detailed text &lt;a href=&quot;http://www.decodedscience.com/drugs-nature-chemistry-addictive-alkaloids/53057&quot; rel=&quot;noreferrer&quot;&gt;here&lt;/a&gt;:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Defensive compounds from plants, like nicotine and cocaine, usually target nervous system components in insects. These components include proteins that have important roles on the insect’s physiology, which may include specific receptors, ion channels, enzymes, etc. In most cases, the defensive chemical kills the insect by interfering with one or more of these proteins; in other cases, the chemicals just make the plant distasteful for the insect, and therefore, the bug will leave the plant alone.&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;" OwnerUserId="17126" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-08-05T00:54:37.210" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36626" PostTypeId="1" CreationDate="2015-08-05T00:29:51.763" Score="1" ViewCount="402" Body="&lt;p&gt;My first university biology classes begin in September. In preparation, but increasingly out of curiosity, I've been studying some basic biology. Saying that to say, I know as much about DNA replication as the Khan Academy videos teach. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Presently, I'm reading about the two efforts to sequence the genome. From what I've read, Collins' project used &quot;polymerase catalysis and nucleotide labeling&quot;; whereas, Venter's project used &quot;shotgun sequencing&quot;. I didn't know enough to understand the article I read on &quot;shotgun sequencing&quot; and couldn't find one that described the other technique. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;I suspect that, in order to comprehend a concise description of the two techniques, I'd need to learn more than I could learn from an answer to this question. That said, it'd still be nice to have a very rough idea of what each process involves and how they differ from each other. A crude analogy to something concrete would be great. &lt;/p&gt;&#xA;" OwnerUserId="16788" LastActivityDate="2020-12-01T12:25:37.693" Title="Is there a good analogy that illustrates the difference between early DNA sequencing techniques and shotgun sequencing?" Tags="&lt;dna-sequencing&gt;" AnswerCount="2" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36627" PostTypeId="2" ParentId="36626" CreationDate="2015-08-05T00:46:42.447" Score="2" Body="&lt;p&gt;The public effort, led by Collins, relied on a physical map of each chromosome.  Very large pieces of genomic DNA were sub cloned into cloning vectors and used to create genomic libraries in cosmids, BACs and YACs.  The sub clones are ordered using hybridization probes from either known genes, or RFLP genetic markers. In this way a physical map of each chromosome was built up, and then the project would march down the ordered clones, sequencing the sub clones.  If the physical map is good then you have a very good idea of where the sequence comes from.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Shotgun sequencing, in contrast, involves randomly fragmenting the entire genome into small fragments (using sonication, for example), sub cloning those pieces and sequencing everything.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;In the first method each base is sequenced a minimal number of times, whereas in the second approach each base ends up being sequenced many times (on average).&lt;/p&gt;&#xA;&#xA;&lt;p&gt;For a whole genome, shotgun sequencing requires an excellent computer algorithm to &quot;assemble&quot; the resulting data into overlapping contigs.&lt;/p&gt;&#xA;" OwnerUserId="16667" LastActivityDate="2015-08-05T00:46:42.447" CommentCount="3" ContentLicense="CC BY-SA 3.0" />
  <row Id="36628" PostTypeId="1" AcceptedAnswerId="36652" CreationDate="2015-08-05T01:35:42.753" Score="4" ViewCount="8099" Body="&lt;p&gt;This was taken in Ann Arbor, MI.  It looks a bit different from the wolf and grass spiders I'm used to seeing.  Anyone know  what this might be?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;edit:&lt;/strong&gt; Per request, I've uploaded a better picture.  Actually, it's the same picture, but I postprocessed the first image quite a bit to ease identification.  The second one is not post processed but (hopefully) clearer.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Processed image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/uqx9l.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/uqx9l.jpg&quot; alt=&quot;Processed image&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Unprocessed image:&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/KyPYr.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/KyPYr.jpg&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="4261" LastEditorUserId="2999" LastEditDate="2015-08-05T20:29:21.713" LastActivityDate="2018-08-09T08:15:40.300" Title="Spider Identification Michigan" Tags="&lt;species-identification&gt;&lt;arachnology&gt;" AnswerCount="1" CommentCount="7" ContentLicense="CC BY-SA 3.0" />
  <row Id="36629" PostTypeId="2" ParentId="36603" CreationDate="2015-08-05T02:14:43.307" Score="3" Body="&lt;p&gt;Our understanding of how life began on earth has indeed advanced substantially since Haldane, Oparin, Miller, and Urey. To learn about the latest ideas, I can't think of a better place to start than this &lt;a href=&quot;http://www.ibiology.org/ibioseminars/evolution-ecology/jack-szostak-part-1.html&quot; rel=&quot;nofollow&quot;&gt;excellent video series&lt;/a&gt; with Nobel Laureate Jack Szostack, who is currently doing some of the leading work on the subject.&lt;/p&gt;&#xA;" OwnerUserId="13072" LastEditorUserId="6307" LastEditDate="2015-08-05T03:33:37.067" LastActivityDate="2015-08-05T03:33:37.067" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36630" PostTypeId="1" CreationDate="2015-08-05T03:46:23.877" Score="1" ViewCount="119" Body="&lt;p&gt;We know that many animals entertain themselves by playing games. But sports actually increases risks of death,or at least accidents. So why did evolution choose it? And why did evolution decide to make us look for entertainment every now and then?&lt;/p&gt;&#xA;" OwnerUserId="17132" LastActivityDate="2015-08-05T05:37:25.557" Title="How did evolution support sports, fun, entertainment etc" Tags="&lt;evolution&gt;" AnswerCount="1" CommentCount="10" ClosedDate="2015-08-05T04:59:17.930" ContentLicense="CC BY-SA 3.0" />
  <row Id="36631" PostTypeId="2" ParentId="36564" CreationDate="2015-08-05T04:32:29.003" Score="3" Body="&lt;p&gt;Your question is a good one. The velocity of muscle contraction depends on the:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Initial length of the muscle&lt;/li&gt;&#xA;&lt;li&gt;The Load on the muscle&#xA;&lt;a href=&quot;https://i.stack.imgur.com/QpCeb.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/QpCeb.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&#xA;&lt;sub&gt;&lt;em&gt;Source&lt;/em&gt;: Medical Physiology : a cellular and molecular approach by Walter F. Boron, Emile L. Boulpaep - 2nd ed. Page 248&lt;/sub&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;From the above picture we can see that:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;The velocity of muscle contraction is not constant. Initially it is zero and then it accelerates to reach a peak&lt;/li&gt;&#xA;&lt;li&gt;The maximum velocity of muscle contraction is constant at any different initial muscle length&lt;/li&gt;&#xA;&lt;li&gt;The lower the load the steeper the rise of velocity&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;So the velocity of muscle contraction should be calculated on a case by case basis.&lt;/p&gt;&#xA;&#xA;&lt;h2&gt;What can be calculated&lt;/h2&gt;&#xA;&#xA;&lt;p&gt;What can be calculated is the displacement and frequency of actin myosin cross-bridging.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Under microscopically isotonic conditions, the quantal displacement of a single cross-bridge is ~11 nm.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;The frequency of actin-myosin cross-bridging depends on atleast:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;ATP concentration&lt;/li&gt;&#xA;&lt;li&gt;Temperature&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;At an ATP concentration of 1 µM the frequency is 3.8 ± 0.4 M&lt;sup&gt;-1&lt;/sup&gt;s&lt;sup&gt;-1&lt;/sup&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;At 17&lt;sup&gt;0&lt;/sup&gt;C the mean time for single displacement was 15±20 ms. While at 25&lt;sup&gt;0&lt;/sup&gt;C the mean was 6.4±3.6 ms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;a href=&quot;https://i.stack.imgur.com/3c03q.png&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/3c03q.png&quot; alt=&quot;enter image description here&quot;&gt;&lt;/a&gt;&#xA;&lt;sub&gt;&lt;strong&gt;Source&lt;/strong&gt;: Characterization of Single Actin-Myosin Interactions by Jeffrey T. Finer, Amit D. Mehta and James A. Spudich.&lt;/sub&gt; &#xA;&lt;sub&gt;Biophysical Journal, Volume 68, April 1995, p.291s-297s&lt;/sub&gt;&lt;/p&gt;&#xA;&#xA;&lt;hr&gt;&#xA;&#xA;&lt;p&gt;Concerning your actual question regarding the quadriceps velocity and the velocity of the swing, you should keep the following in mind while calculating:&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;&lt;p&gt;Quadriceps acts over a second order lever: The Knee is the fulcrum, the effort is put over the tibial tuberosity where the quadriceps is inserted and the load is the foot and whatever it hits/lifts...&lt;/p&gt;&lt;/li&gt;&#xA;&lt;li&gt;&lt;p&gt;The contraction of the quadriceps is calculated as linear velocity while the kicking action is circular - so what you actually observe is the angular velocity. So appropriate angular velocity to linear velocity conversion should be made.&lt;/p&gt;&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;All the best!&lt;/p&gt;&#xA;" OwnerUserId="11841" LastEditorUserId="11841" LastEditDate="2015-08-05T04:52:52.863" LastActivityDate="2015-08-05T04:52:52.863" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36632" PostTypeId="2" ParentId="36620" CreationDate="2015-08-05T04:40:43.363" Score="12" Body="&lt;p&gt;I am providing an example which somewhat contradicts the points mentioned in the other answers regarding toxicity of alkaloids to insects.&lt;/p&gt;&#xA;&lt;p&gt;Caffeine is a stimulant and is toxic at high doses (also for humans) but at low doses it has a stimulating pharmacological effect on the organism. The same principle applies to insects as well. A study by &lt;em&gt;&lt;a href=&quot;http://dx.doi.org/10.1126/science.1228806&quot; rel=&quot;noreferrer&quot;&gt;Wright et. al (2013)&lt;/a&gt;&lt;/em&gt; has revealed that caffeine in the nectar of some flowers, enhances the bee's memory of that flower (a reward, in general).&lt;/p&gt;&#xA;&lt;p&gt;They have also mentioned that:&lt;/p&gt;&#xA;&lt;blockquote&gt;&#xA;&lt;p&gt;Two caffeine-producing plant genera, &lt;em&gt;Citrus&lt;/em&gt; and &lt;em&gt;Coffea&lt;/em&gt;, have large&#xA;floral displays with strong scents and produce more fruits and seeds&#xA;when pollinated by bees (8, 9)&lt;/p&gt;&#xA;&lt;/blockquote&gt;&#xA;&lt;p&gt;However, caffeine tastes bitter and bees would reject nectar (sugar solutions) containing high levels of caffeine (&amp;gt;1mM).&lt;/p&gt;&#xA;" OwnerUserId="3340" LastEditorUserId="-1" LastEditDate="2020-06-16T11:19:53.573" LastActivityDate="2015-08-11T05:03:16.553" CommentCount="8" ContentLicense="CC BY-SA 3.0" />
  <row Id="36633" PostTypeId="2" ParentId="36630" CreationDate="2015-08-05T05:02:53.513" Score="2" Body="&lt;p&gt;This answer can be from many different perspectives! I'll try to blend them all together as much as possible.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;First of all evolution did not choose to make us love sports. Evolution made us social animals. And sports is just one of the tools we use for that purpose. Think about it, because if evolution gave us sports, then you will play sports, your kids will inherit that bit of experience from you and they would be that much better than you. But no, we all start from level 0 when we try to play any games or sports. This is because, sports is primarily a &lt;a href=&quot;https://en.wikipedia.org/wiki/Motor_learning&quot; rel=&quot;nofollow&quot;&gt;motor memory&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;So why are we social?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;This &lt;a href=&quot;http://www.nature.com/neuro/journal/v17/n1/abs/nn.3594.html&quot; rel=&quot;nofollow&quot;&gt;study&lt;/a&gt; back in 2014 was one of the first to suggest that memory can be heritable. It generated a lot of attention and the authors themselves suggested that their findings were standing on a very capricious footing and required further validation. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;This point is valid because evolutionary forces require mechanisms by which features/mechanism which bestow advantages towards the survival of the species are positively reinforced. In this case social behaviour is the function. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Do not go googling the word Social behaviour, for some reason the wiki article looks only at dogs and cats. That is unpragmatic, because we also have the same function.&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;I will broadly breakdown social behaviour into&lt;/p&gt;&#xA;&#xA;&lt;ol&gt;&#xA;&lt;li&gt;Accommodation of non-aggressive behaviour from individuals in neutral territory.&lt;/li&gt;&#xA;&lt;li&gt;A means to communicate&lt;/li&gt;&#xA;&lt;/ol&gt;&#xA;&#xA;&lt;p&gt;But, you may ask how does social behaviour benefit you? Well the answer is simple, increased survival capacity, and better chances of propagation.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Such studies exist in &lt;a href=&quot;https://www.st-andrews.ac.uk/news/archive/2012/title,91404,en.php&quot; rel=&quot;nofollow&quot;&gt;crows&lt;/a&gt;, which have studied social behaviour. Indeed, if you start to consider studies in behavioural biology, you would find that there are instances where &lt;a href=&quot;http://www.nature.com/news/2009/091231/full/news.2009.1167.html&quot; rel=&quot;nofollow&quot;&gt;female mosquitoes do not just mate with any male mosquitoes&lt;/a&gt;, even in this case you can call it a very rudimentary form of socialising.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;So in your case sports is a tool which allows us to accommodate and communicate with others in neutral territory.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;You can take a look at this which better explains the social aspects of &lt;a href=&quot;http://thescipub.com/html/10.3844/jssp.2012.33.38&quot; rel=&quot;nofollow&quot;&gt;sports&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="15807" LastEditorUserId="15807" LastEditDate="2015-08-05T05:37:25.557" LastActivityDate="2015-08-05T05:37:25.557" CommentCount="1" ContentLicense="CC BY-SA 3.0" />
  <row Id="36635" PostTypeId="2" ParentId="20912" CreationDate="2015-08-05T08:52:00.953" Score="0" Body="&lt;p&gt;There are indeed massive evolutionary control systems integrated into DNA. They constitute the major force for efficient change in living beings. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Random DNA mutations are not as beneficial as controlled ones, you can see random single gene mutations at work in medical books: Anemia, cancer, cheese smelling sweat, no sweat glands, skin conditions, scales, brittle bones, lactose tolerance, These are all examples of mutations of single proteins and single growth hormones and so on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Instead of random DNA mutations, life-forms control their rate of change and types of variations in very efficient ways, changes in color, longer and shorter bones/arms/legs which you can see in humans, physical maturation times, length and quantity of hair, all these things are safe for an animal to have lots of genetic variation with. Changes in bone length vary more than 10 percent in a single generation of humans, but changes like lactose tolerance occur only every 100ds of generations. Therefore there are hundreds of genes for controlling growth hormones as it's selection-important. If color changes become important to an animal, for example, birds, fish, and butterflies, then hundreds of genes are devoted to color. If color is not important, for example, northern and snow animals, then few gene changes are devoted to color, The many Color genes of a tropical animal would go dormant very fast if it were exposed to snowy conditions.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It makes sense for DNA to favor developments that encourage reproduction and survival in variable settings, and indeed DNA is supercharged to deliver mostly useful morphological and chemical changes in large numbers. Plants, conversely, need to change their chemicals alot to attract and repel animals, whereas animals do not need to attract other animals for food, only to defend themselves, that one reason why animals have a lot less chemical variety than plants. Only Chinese use animals for medicine, and there are few aspirins and sedatives derived from animals. Animals cannot produce powerful random chemicals because their nervous system hormones and cell walls are less robust than cellulose cells and plant hormones. Otherwise, animals would have more variable smell and taste, but all mammals taste similar.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's the same with computer evolution. If you tell a computer program to vary DNA randomly or to create life-forms randomly, it will have epileptic, disorganised animals that flop around, roll around, hit walls, and that is not what animals do to evolve. If you equip a computer evolution program with DNA tool kits copied from nature, you will much faster have meaningful animals... i.e. simple locomotive insects. If you tell the computer to use sinusoidal limb movements like fish fins, millipede legs, insect legs, using nerve impulses, and to create metameric life forms, you will have alot more success than just adding limbs onto random parts of the body, using random pattern nerve impulses and so on. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;It's not an easy thing to study, as it is very complex. I would love some statistics and journals regarding types of evolutionary changes that are prevalent in different life-forms.&lt;/p&gt;&#xA;" OwnerUserId="8952" LastEditorUserId="43480" LastEditDate="2019-03-29T17:05:51.283" LastActivityDate="2019-03-29T17:05:51.283" CommentCount="1" ContentLicense="CC BY-SA 4.0" />
  <row Id="36636" PostTypeId="2" ParentId="36569" CreationDate="2015-08-05T09:22:52.940" Score="1" Body="&lt;p&gt;The genetic code of the tree of life is actively studied. So far, all the living beings have conformed to LUCA model. They are all RNA and DNA dependent, and no other life forms are known. All the RNA and DNA life forms share a tree like inheritance pattern with more simple organisms.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes there is doubt about wether mushrooms are more closely related to animals or plants.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Sometimes it is debated wether Prions are life forms or not. They are proteins that can reproduce by tricking human cells to making them and then transmit themselves, but they have not developed into anything else than a protein. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Some Virii have a special relationship with DNA, in that they just hyjack and eat DNA using RNA tricks, but their code is basically a lego block of other DNA they have hyjacked, they have fascinating evolution mechanism. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;Here is the Tree Of Life, for the moment all genetic testing has found a tree structure shared by common acenstors, in all organsims, hence a LUCA:&#xA;&lt;a href=&quot;https://i.stack.imgur.com/vgae3.jpg&quot; rel=&quot;nofollow noreferrer&quot;&gt;&lt;img src=&quot;https://i.stack.imgur.com/vgae3.jpg&quot; alt=&quot;tree of life&quot;&gt;&lt;/a&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;here you can see it in detail, so far 50 000 species are on there, from the same philae and DNA -tested, and soon they will have more species, like 200k or something.&#xA;huge pdf poster: &#xA;&lt;a href=&quot;http://www.timetree.org/public/data/poster/timetree24x32.pdf&quot; rel=&quot;nofollow noreferrer&quot;&gt;http://www.timetree.org/public/data/poster/timetree24x32.pdf&lt;/a&gt;&lt;/p&gt;&#xA;" OwnerUserId="8952" LastActivityDate="2015-08-05T09:22:52.940" CommentCount="0" ContentLicense="CC BY-SA 3.0" />
  <row Id="36640" PostTypeId="1" CreationDate="2015-08-05T12:28:44.403" Score="8" ViewCount="5688" Body="&lt;p&gt;An Indian old man claims he is [180 years old] now.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;We are not able to tell he is 180 or 181 probably. But can we tell he is 90, 120, 100 or 150?&lt;/strong&gt;&lt;/p&gt;&#xA;&#xA;&lt;p&gt;Different people may age differently. &lt;br/&gt; &#xA;A 60-year old person may appear to be 80, while somebody else could appear younger than their mathematical age. Some other people may have progeria. &lt;/p&gt;&#xA;&#xA;&lt;p&gt;What is the most accurate way to identify a living person's age nowadays?&#xA;Are there reliable parameters to measure?&lt;/p&gt;&#xA;&#xA;&lt;p&gt;C-14 needs a long time base line. Hence, it is suitable for the bone of dead people.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;What kind of method can guarantee it can distinguish a 30y and a 80y old person?  What's the error bar of that method?&lt;/p&gt;&#xA;" OwnerUserId="5688" LastEditorUserId="5688" LastEditDate="2016-12-12T13:04:12.367" LastActivityDate="2016-12-12T13:04:12.367" Title="How to identify the age of a &quot;living&quot; person?" Tags="&lt;human-biology&gt;" AnswerCount="1" CommentCount="11" FavoriteCount="2" ContentLicense="CC BY-SA 3.0" />
  <row Id="36641" PostTypeId="2" ParentId="36620" CreationDate="2015-08-05T12:48:49.407" Score="8" Body="&lt;p&gt;&lt;strong&gt;Short answer&lt;/strong&gt;&lt;br&gt;&#xA;The appearance of psychoactive compounds in plants has nothing to do with their addictiveness in man.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;&lt;strong&gt;Background&lt;/strong&gt;&lt;br&gt;&#xA;Psychoactive plants were there long before humans. The question therefore should be: &quot;&lt;strong&gt;Why would humans evolve brains that exhibit addictive propensity to poisonous compounds abundantly available in nature&lt;/strong&gt;&quot;? The answer is: because our brain evolved in the absence of addictive substances.&lt;/p&gt;&#xA;&#xA;&lt;p&gt;One has to realize that addictive compounds are &lt;em&gt;grown&lt;/em&gt; and &lt;em&gt;processed&lt;/em&gt;. When humanoids evolved over millions of years, for the larger part there were no means to grow, harvest and process coffee beans, tobacco and coca leaves. Moreover, the most addictive drugs like injectable heroin and smokable cocaine (crack) are chemically &lt;strong&gt;&lt;em&gt;purified&lt;/em&gt;&lt;/strong&gt;. Methamphetamine and many addictive opiates are purely &lt;strong&gt;&lt;em&gt;synthetic&lt;/em&gt;&lt;/strong&gt;. In their native form, coca leaves and poppies are &lt;strong&gt;far less addictive&lt;/strong&gt;, because in the raw form they &lt;strong&gt;lack the dopamine rush&lt;/strong&gt;. Instead, the chewing of raw plant materials like coca leaves produces a mild high with a slow onset, and a mild offset. The sudden dopamine rush is what evokes the blissful euphoric state chased by heroin, crack and meth addicts, while the dreadful crash associated by these purified drugs is one of the strong motivators to seek for another hit. Also note that tobacco i